 
REBASE version 901                                              refmgra.901
 
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    REBASE, The Restriction Enzyme Database   http://rebase.neb.com
    Copyright (c)  Dr. Richard J. Roberts, 2018.   All rights reserved.
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Rich Roberts                                                    Dec 28 2018
 
TY  - Type of reference.
AU  - Authors, listed one per line.
TI  - Title.
JO  - Journal.
PY  - Year.
SP  - Starting page.
EP  - Ending page.
VL  - Volume number.
AB  - Abstract.
ER  - End of Record.

TY  - JOUR
AU  - Aagaard, C.
AU  - Awayez, M.J.
AU  - Garrett, R.A.
TI  - Profile of the DNA recognition site of the archaeal homing endonuclease I-DmoI.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 1523
EP  - 1530
VL  - 25
AB  - I-DmoI is a homing enzyme of the LAGLI-DADG type that recognizes up to 20 bp of DNA and is
AB  - encoded by an archaeal intron of the hyperthermophilic archaeon Desulfurococcus mobilis.  A
AB  - combined mutational and DNA footprinting approach was employed to investigate the specificity
AB  - of the I-DmoI-substrate interaction.  The results indicate that the enzyme binds primarily to
AB  - short base paired regions that border the sites of DNA cleavage and intron insertion.  The
AB  - minimal substrate spans no more than 15 bp and while sequence degeneracy is tolerated in the
AB  - DNA binding regions, the sequence and size of the cleavage region is highly conserved.  The
AB  - enzyme has a slow turnover rate and cuts the coding strand with a slight preference over the
AB  - non-coding strand.  Complex formation produces some distortion of the DNA double helix within
AB  - the cleavage region.  The data are compatible with the two DNA-binding domains of I-DmoI
AB  - bridging the minor groove, where cleavage occurs, and interacting within the major groove on
AB  - either side, thereby stabilizing a distorted DNA double helix.  This may provide a general
AB  - mode of DNA interaction at least for the LAGLIDADG-type homing enzymes.
ER  -

TY  - JOUR
AU  - Aagaard, C.
AU  - Dalgaard, J.Z.
AU  - Garrett, R.A.
TI  - Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1995
SP  - 12285
EP  - 12289
VL  - 92
AB  - Some intron-containing rRNA genes of archaea encode homing-type endonucleases, which
AB  - facilitate intron insertion at homologous sites in intron- alleles. These archaeal rRNA genes,
AB  - in contrast to their eukaryotic counterparts, are present in single copies per cell, which
AB  - precludes intron homing within one cell. However, given the highly conserved nature of the
AB  - sequences flanking the intron, homing may occur in intron- rRNA genes of other archaeal cells.
AB  - To test whether this occurs, the intron-containing 23S rRNA gene of the archaeal
AB  - hyperthermophile Desulfurococcus mobilis, carried on nonreplicating bacterial vectors, was
AB  - electroporated into an intron- culture of Sulfolobus acidocaldarius. PCR experiments
AB  - demonstrated that the intron underwent homing and spread through the culture. By using a
AB  - double drug-resistant mutant of S. acidocaldarius, it was shown that spreading resulted partly
AB  - from a selective advantage of intron+ cells and partly from intercellular mobility of the
AB  - intron and homing.
ER  -

TY  - JOUR
AU  - Aalbaek, B.
AU  - Jensen, L.K.
AU  - Jensen, H.E.
AU  - Olsen, J.E.
AU  - Christensen, H.
TI  - Whole-Genome Sequence of Staphylococcus aureus S54F9 Isolated from a Chronic Disseminated Porcine Lung Abscess and Used in Human Infection Models.
JO  - Genome Announcements
PY  - 2015
SP  - e01207
EP  - e01215
VL  - 3
AB  - We obtained a draft genome sequence of Staphylococcus aureus strain S54F9, which  was isolated
AB  - from a chronic disseminated porcine lung abscess and used in porcine infection models. Genes
AB  - coding for a number of toxins, including enterotoxins and superantigen, were demonstrated in
AB  - this strain.
ER  -

TY  - JOUR
AU  - Aapola, U.
AU  - Kawasaki, K.
AU  - Scott, H.S.
AU  - Ollila, J.
AU  - Vihinen, M.
AU  - Heino, M.
AU  - Shintani, A.
AU  - Kawasaki, K.
AU  - Minoshima, S.
AU  - Krohn, K.
AU  - Antonarakis, S.E.
AU  - Shimizu, N.
AU  - Kudoh, J.
AU  - Peterson, P.
TI  - Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family.
JO  - Genomics
PY  - 2000
SP  - 293
EP  - 298
VL  - 65
AB  - We have isolated the DNMT3L gene that is related to the cytosine-5-methyltransferase 3 (DNMT3)
AB  - family. The gene is located on chromosome 21q22.3 between the AIRE and the KIAA0653 genes and
AB  - spans approximately 16 kb of genomic sequence. The encoded protein of 387 amino acids has a
AB  - cysteine-rich region containing a novel-type zinc finger domain that is conserved in DNMT3A
AB  - and DNMT3B but also in ATRX, a member of the SNF2 protein family. The novel domain, called an
AB  - ADD (ATRX, DNMT3, DNMT3L)-type zinc finger, contains two subparts: a C2C2 and an imperfect PHD
AB  - zinc finger. Expression of the DNMT3L mRNA was not detectable by Northern blotting; however,
AB  - RT-PCR amplification revealed that it is expressed at low levels in several tissues including
AB  - testis, ovary, and thymus.
ER  -

TY  - JOUR
AU  - Aapola, U.
AU  - Liiv, I.
AU  - Peterson, P.
TI  - Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3602
EP  - 3608
VL  - 30
AB  - DNMT3L is a regulator of imprint establishment of normally methylated maternal genomic
AB  - sequences. DNMT3L shows high similarity to the de novo DNA methyltransferases, DNMT3A and
AB  - DNMT3B, however, the amino acid residues needed for DNA cytosine methyltransferase activity
AB  - have been lost from the DNMT3L protein sequence.  Apart from methyltransferase activity,
AB  - Dnmt3a and Dnmt3b serve as transcriptional repressors associating with histone deacetylase
AB  - (HDAC) activity. Here we show that DNMT3L can also repress transcription by binding directly
AB  - to HDAC1 protein. We have identified the PHD-like zinc finger of the ATRX domain as a main
AB  - repression motif of DNMT3L, through which DNMT3L recruits the HDAC activity needed for
AB  - transcriptional silencing.  Furthermore, we show that DNMT3L protein contains an active
AB  - nuclear localisation signal at amino acids 156-159.  These results describe DNMT3L as a
AB  - co-repressor protein and suggest that a transcriptionally repressed chromatin organisation
AB  - through HDAC activity is needed for establishment of genomic imprints.
ER  -

TY  - JOUR
AU  - Aapola, U.
AU  - Lyle, R.
AU  - Krohn, K.
AU  - Antonarakis, S.E.
AU  - Peterson, P.
TI  - Isolation and initial characterization of the mouse Dnmt3L gene.
JO  - Cytogenet. Cell Genet.
PY  - 2001
SP  - 122
EP  - 126
VL  - 92
AB  - We have isolated and sequenced the mouse zinc finger gene, Dnmt3l (DNA
AB  - cytosine-5-methyltransferase 3-like), on mouse chromosome 10, showing similarity to members of
AB  - the DNMT3/Dnmt3 family. The Dnmt3l protein contains an ADD zinc finger, which Dnmt3l shares
AB  - with other Dnmt3 family members and Atrx. RT-PCR analysis showed Dnmt3l expression in testis,
AB  - thymus, ovary, and heart, as well as in 7-day, 15-day, and 17-day mouse embryos.
ER  -

TY  - JOUR
AU  - Aapola, U.
AU  - Maenpaa, K.
AU  - Kaipia, A.
AU  - Peterson, P.
TI  - Epigenetic modifications affect the Dnmt3L expression.
JO  - Biochem. J.
PY  - 2004
SP  - 705
EP  - 713
VL  - 380
AB  - Imprinted genes are expressed from a single allele due to differential methylation of maternal
AB  - or paternal alleles during gametogenesis. Dnmt3L, a member of de novo methyltranferase Dnmt3
AB  - protein family, is a regulator of maternal imprinting. In the present study, we have
AB  - characterised the promoter region of the mouse Dnmt3L gene. Transient transfection assays
AB  - performed with 5'-deletion promoter constructs indicated a minimal promoter area within 440
AB  - bp upstream from the translational start. Longer promoter constructs showed decreased activity
AB  - suggesting the presence of repressor elements within the upstream sequences. According to
AB  - electrophoretic mobility shift assays and mutation analysis minimal promoter region contained
AB  - four functional binding sites for the Sp1 family of transcription factors, Sp1 and Sp3. In
AB  - vitro methylation of Dnmt3L promoter constructs decreased the transcriptional activity
AB  - dramatically demonstrating downregulation by cytosine methylation. This was supported by the
AB  - results from bisulfite sequencing and quantitative RT-PCR analysis of different mouse cell
AB  - lines and tissues. In testis and ES cells showing strong Dnmt3L expression, all studied CpG
AB  - sites were fully unmethylated whereas non-expressive cell-lines and tissues with lesser Dnmt3L
AB  - expression showed complete or diverse CpG methylation levels. Treatment of Dnmt3L
AB  - non-expressive cell lines with deacetylase inhibitor trichostatin A and methyltransferase
AB  - inhibitor 5-aza-2'-deoxycytidine induced the expression of Dnmt3L mRNA. Furthermore, we show
AB  - that repressional effect of longer promoter fragments was also relieved by these inhibitors,
AB  - altogether indicating an epigenetic control for Dnmt3L gene regulation.
ER  -

TY  - JOUR
AU  - Aarab, S.
AU  - Arakrak, A.
AU  - Ollero, F.J.
AU  - Megias, M.
AU  - Gomes, D.F.
AU  - Ribeiro, R.A.
AU  - Hungria, M.
TI  - Draft Genome Sequence of Pseudomonas fluorescens Strain ET76, Isolated from Rice  Rhizosphere in Northwestern Morocco.
JO  - Genome Announcements
PY  - 2016
SP  - e00356
EP  - e00316
VL  - 4
AB  - Pseudomonas fluorescens ET76 was isolated from rice rhizosphere in northwestern Morocco. Its
AB  - draft genome was estimated to be 6,681,652 bp with 5,789 coding
AB  - sequences (CDSs). Genes encoding for type I to VI secretion systems, PvdQ,
AB  - proteases, siderophores, hydrogen cyanide synthase, ACC-deaminase, among others,
AB  - highlight its potential use in biological control of plant pathogens.
ER  -

TY  - JOUR
AU  - Abadjieva, A.
AU  - Patel, J.
AU  - Webb, M.
AU  - Zinkevich, V.
AU  - Firman, K.
TI  - A deletion mutant of the type IC restriction endonuclease EcoR124I expressing a novel DNA specificity.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4435
EP  - 4443
VL  - 21
AB  - We have developed a complementation assay which allows us to distinguish between mutations
AB  - affecting subunit assembly and mutations affecting DNA binding in the DNA recognition subunit
AB  - (HsdS) of the multimeric restriction endonuclease EcoR124I. A number of random point mutations
AB  - were constructed to test the validity of this assay. Two of the mutants produced were found to
AB  - be truncated polypeptides that were still capable of complementation with the EcoR124I Hsd
AB  - subunits to give an active restriction enzyme of novel DNA specificity. The N-terminal
AB  - variable domain (responsible for recognition of GAA from the EcoR124I recognition sequence
AB  - GaannnnnnRTCG) and the spacer region (central conserved region) is intact in both of these
AB  - mutants. One of these mutant genes (hsdS(del50)) has been cloned as an active Mtase.
AB  - Purification of the Mtase proved to be difficult because the complex is weak. However, Mtase
AB  - activity was obtained from a soluble cell extract, and this allowed us to determine the DNA
AB  - recognition sequence of the Mtase to be GAAnnnnnnnTTC. This recognition sequence is an
AB  - inverted repeat of the 5'-end of the EcoR124I recognition sequence. This suggests that the
AB  - mutant Mtase is assembled from two inverted HsdS(D50) subunits, possibly held together by the
AB  - HsdM subunits.
ER  -

TY  - JOUR
AU  - Abadjieva, A.
AU  - Patel, J.
AU  - Zinkevich, V.
AU  - Weiserova, M.
AU  - Firman, K.
TI  - The domain structure of the DNA specificity subunit of type I restriction endonucleases.  II.  Mutations affecting subunit assembly.
JO  - DNA Transfer and Gene Expression in Microorganisms
PY  - 1993
SP  - 189
EP  - 196
VL  - 0
AB  - Type I restriction endonucleases are complex multimeric enzymes comprising three subunits.
AB  - HsdM and HsdS are sufficient to produce an active methylase and have the stoichiometry M2S.
AB  - To produce an active endonuclease the HsdR subunit is also required along with the cofactors
AB  - ATP, Mg2+ and S-adenosylmethionine.  The stoichiometry of the endonuclease is less well
AB  - defined and may be influenced by the level of production of the individual subunits.
AB  - Classically mutations within the hsdR gene of type I R-M systems produced an R- M+ phenotype,
AB  - while those in the hsdM or the hsdS produced an R-M- phenotype.  However, recently we have
AB  - described temperature-sensitive mutations within the hsdS and hsdM genes of EcoK that are
AB  - altered in their restriction phenotype.  These mutations appear to affect the ability of the
AB  - HsdS or HsdM subunits to interact with the HsdR subunit.  In this paper we describe a number
AB  - of observations that suggest the assembly of these multi-subunit enzymes may be controlled by
AB  - the concentration of the individual subunits.  This type of control is shown to be correct and
AB  - it represents a novel method for genetic control of enzyme function, beyond that of the
AB  - control of transcription and translation.  We also propose a testable model of how this
AB  - control may function within type I R-M systems.
ER  -

TY  - JOUR
AU  - Abadjieva, A.
AU  - Scarlett, G.
AU  - Janscak, P.
AU  - Dutta, C.F.
AU  - Firman, K.
TI  - Characterization of an EcoR1241 restriction-modification enzyme produced from a deleted form of the DNA-binding subunit, which results in a novel DNA specificity.
JO  - Folia Microbiol. (Praha)
PY  - 2003
SP  - 319
EP  - 328
VL  - 48
AB  - We purified and characterized both the methyltransferase and the endonuclease containing the
AB  - HsdS delta 50 subunit (type I restriction
AB  - endonucleases are composed of three subunits--HsdR required for
AB  - restriction, HsdM required for methylation and HsdS responsible for DNA
AB  - recognition) produced from the deletion mutation hsdS delta 50 of the type
AB  - IC R-M system EcoR 124I; this mutant subunit lacks the C-terminal 163
AB  - residues of HsdS and produces a novel DNA specificity. Analysis of the
AB  - purified HsDs delta 50 subunit indicated that during purification it is
AB  - subject to partial proteolysis resulting in removal of approximately 1 kDa
AB  - of the polypeptide at the C-terminus. This proteolysis prevented the
AB  - purification of further deletion mutants, which were determined as having
AB  - a novel DNA specificity in vivo. After biochemical characterization of the
AB  - mutant DNA methyltransferase (MTase) and restriction endonuclease we found
AB  - only one difference comparing with the wild-type enzyme--a significantly
AB  - higher binding affinity of the MTase for the two substrates of
AB  - hemimethylated and fully methylated DNA. This indicates that MTase delta
AB  - 50 is less able to discriminate the methylation status of the DNA during
AB  - its binding. However, the mutant MTase still preferred hemimethylated DNA
AB  - as the substrate for methylation. We fused the hsdM and hsdS delta 50
AB  - genes and showed that the HsdM-HsdS delta 50 fusion protein is capable of
AB  - dimerization confirming the model for assembly of this deletion mutant.
ER  -

TY  - JOUR
AU  - Abadjieva, A.
AU  - Webb, M.
AU  - Patel, J.
AU  - Zinkevich, V.
AU  - Firman, K.
TI  - Deletions within the DNA recognition subunit of M.EcoR124I that identify a region involved in protein-protein interactions between HsdS and HsdM.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 35
EP  - 43
VL  - 241
AB  - The DNA recognition subunit (HsdS) of type I restriction endonucleases can be divided into
AB  - domains by means of amino acid identity between subunits from the same family. It has been
AB  - proposed that DNA-protein interactions occur within the variable domains of the subunit and
AB  - that protein-protein interactions involve the conserved domains. We have constructed a number
AB  - of deletion mutants of HsdS that have allowed us to investigate protein-protein interactions.
AB  - Using a combination of a "competitive" complementation assay and the ability of HsdM to
AB  - "solubilize" HsdS, we have defined a region within the central conserved domain of HsdS that
AB  - is responsible for HsdS-HsdM interaction. Computer analysis of amino acid identity between the
AB  - N-terminal half and the C-terminal half of HsdS identifies a region (repeated in both
AB  - conserved domains), one copy of which overlaps the region we have identified as essential for
AB  - HsdS-HsdM interactions, which may be responsible for such protein-protein interactions.
ER  -

TY  - JOUR
AU  - Abaev, I.
AU  - Skryabin, Y.
AU  - Kislichkina, A.
AU  - Bogun, A.
AU  - Korobova, O.
AU  - Dyatlov, I.
TI  - Draft Genome Sequences of Eight Staphylococcus aureus Strains Isolated during Foodborne Outbreaks.
JO  - Genome Announcements
PY  - 2018
SP  - e01557
EP  - e01517
VL  - 6
AB  - We report here the draft genome sequences of eight Staphylococcus aureus strains  isolated
AB  - during three large food poisoning outbreaks in the Russian Federation.
AB  - The strains were collected from clinical specimens and various foodstuff samples.
ER  -

TY  - JOUR
AU  - Abaev, I.
AU  - Skryabin, Y.
AU  - Kislichkina, A.
AU  - Bogun, A.
AU  - Korobova, O.
AU  - Mayskaya, N.
AU  - Shemyakin, I.
AU  - Dyatlov, I.
TI  - Draft Genome Sequences of Exfoliative Toxin A-Producing Staphylococcus aureus Strains B-7772 and B-7777 (CC8/ST2993) and B-7774 (CC15/ST2126), Isolated in a  Maternity Hospital in the Central Federal District of Russia.
JO  - Genome Announcements
PY  - 2016
SP  - e00064
EP  - e00016
VL  - 4
AB  - Staphylococcus aureus clonal complex 8 (CC8) has not been associated with staphylococcal
AB  - scalded-skin syndrome (SSSS) in newborns and exfoliative toxin
AB  - genes. Here, we report the draft genome sequences of exfoliative toxin
AB  - A-producing B-7772, B-7777 (both CC8), and B-7774 (CC15) strains associated with
AB  - SSSS in newborns.
ER  -

TY  - JOUR
AU  - Abbasalizadeh, S.
AU  - Salehi, J.G.
AU  - Motamedi, J.M.
AU  - Azarbaijani, R.
AU  - Parsa, Y.L.
AU  - Ahmad, R.M.
AU  - Mardi, M.
AU  - Salekdeh, G.H.
TI  - Draft Genome Sequence of Ureibacillus thermosphaericus Strain Thermo-BF, Isolated from Ramsar Hot Springs in Iran.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4431
EP  - 4431
VL  - 194
AB  - Ureibacillus thermosphaericus strain Thermo-BF is an aerobic, thermophilic bacillus which has
AB  - been characterized to biosynthesize gold nanoparticles. Here
AB  - we present the draft genome sequence of Ureibacillus thermosphaericus strain
AB  - Thermo-BF which consists of a 2,864,162-bp chromosome. This is the first report
AB  - of a shotgun sequenced draft genome of a species in the Ureibacillus genus.
ER  -

TY  - JOUR
AU  - Abbasifar, R.
AU  - Kropinski, A.M.
AU  - Sabour, P.M.
AU  - Ackermann, H.W.
AU  - Lingohr, E.J.
AU  - Griffiths, M.W.
TI  - Complete Genome Sequence of Cronobacter sakazakii Bacteriophage vB_CsaM_GAP161.
JO  - J. Virol.
PY  - 2012
SP  - 13806
EP  - 13807
VL  - 86
AB  - Cronobacter sakazakii is an opportunistic pathogen that causes infant meningitis
AB  - and is often associated with milk-based infant formula. We have fully sequenced
AB  - the genome of a newly isolated lytic C. sakazakii myovirus, vB_CsaM_GAP161,
AB  - briefly named GAP161. It consists of 178,193 bp and has a G+C content of 44.5%. A
AB  - total of 277 genes, including 275 open reading frames and two tRNA-encoding
AB  - genes, were identified. This phage is closely related to coliphages RB16 and RB43
AB  - and Klebsiella pneumoniae phage KP15.
ER  -

TY  - JOUR
AU  - Abdallah, A.M.
AU  - Rashid, M.
AU  - Adroub, S.A.
AU  - Arnoux, M.
AU  - Ali, S.
AU  - van Soolingen, D.
AU  - Bitter, W.
AU  - Pain, A.
TI  - Complete Genome Sequence of Mycobacterium phlei Type Strain RIVM601174.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3284
EP  - 3285
VL  - 194
AB  - Mycobacterium phlei is a rapidly growing nontuberculous Mycobacterium species that is
AB  - typically nonpathogenic, with few reported cases of human disease. Here
AB  - we report the whole genome sequence of M. phlei type strain RIVM601174.
ER  -

TY  - JOUR
AU  - Abdallah, A.M.
AU  - Rashid, M.
AU  - Adroub, S.A.
AU  - Elabdalaoui, H.
AU  - Ali, S.
AU  - van Soolingen, D.
AU  - Bitter, W.
AU  - Pain, A.
TI  - Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3282
EP  - 3283
VL  - 194
AB  - Mycobacterium xenopi is a slow-growing, thermophilic, water-related Mycobacterium species.
AB  - Like other nontuberculous mycobacteria, M. xenopi more commonly infects
AB  - humans with altered immune function, such as chronic obstructive pulmonary
AB  - disease patients. It is considered clinically relevant in a significant
AB  - proportion of the patients from whom it is isolated. We report here the whole
AB  - genome sequence of M. xenopi type strain RIVM700367.
ER  -

TY  - JOUR
AU  - Abdel-Haleem, A.M.
AU  - Rchiad, Z.
AU  - Khan, B.K.
AU  - Abdallah, A.M.
AU  - Naeem, R.
AU  - Nikhat, S.S.
AU  - Solovyev, V.
AU  - Ahmed, A.
AU  - Pain, A.
TI  - Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.
JO  - Genome Announcements
PY  - 2015
SP  - e01166
EP  - e01115
VL  - 3
AB  - The emergence and spread of multidrug-resistant (MDR) bacteria have been regarded as major
AB  - challenges among health care-associated infections worldwide. Here, we report the draft genome
AB  - sequence of an MDR Stenotrophomonas maltophilia strain isolated in 2014 from King Abdulla
AB  - Medical City, Makkah, Saudi Arabia.
ER  -

TY  - JOUR
AU  - Abdelbary, M.M.H.
AU  - Prod'hom, G.
AU  - Greub, G.
AU  - Senn, L.
AU  - Blanc, D.S.
TI  - Draft Genome Sequences of Two Carbapenemase-Producing Acinetobacter baumannii Clinical Strains Isolated from Albanian and Togolese Patients.
JO  - Genome Announcements
PY  - 2017
SP  - e00115
EP  - e00117
VL  - 5
AB  - We report here the draft genome sequences of two multidrug-resistant Acinetobacter baumannii
AB  - clinical strains, H31499 and H31506, which were isolated
AB  - at the Lausanne University Hospital in 2015 from an Albanian and a Togolese
AB  - patient, respectively.
ER  -

TY  - JOUR
AU  - Abdelhamed, H.
AU  - Ozdemir, O.
AU  - Tekedar, H.C.
AU  - Arick, M.A.I.I.
AU  - Hsu, C.Y.
AU  - Karsi, A.
AU  - Lawrence, M.L.
TI  - Complete Genome Sequence of Multidrug-Resistant Plesiomonas shigelloides Strain MS-17-188.
JO  - Genome Announcements
PY  - 2018
SP  - e00387
EP  - e00318
VL  - 6
AB  - Plesiomonas shigelloides is a Gram-negative bacterium isolated from diverse environments.
AB  - Here, we describe the complete genome sequence of the
AB  - multidrug-resistant P. shigelloides strain MS-17-188, isolated from a diseased
AB  - catfish. Availability of this genome will be beneficial for characterizing the
AB  - molecular mechanisms of antibiotic resistance in this strain.
ER  -

TY  - JOUR
AU  - Abdelhamed, H.
AU  - Tekedar, H.C.
AU  - Ozdemir, O.
AU  - Hsu, C.Y.
AU  - Arick, M.A.I.I.
AU  - Karsi, A.
AU  - Lawrence, M.L.
TI  - Complete Genome Sequence of Multidrug-Resistant Edwardsiella ictaluri Strain MS-17-156.
JO  - Genome Announcements
PY  - 2018
SP  - e00477
EP  - e00418
VL  - 6
AB  - Edwardsiella ictaluri is a significant pathogen of cultured fish, particularly channel
AB  - catfish. Here, we present the complete genome sequence of a
AB  - multidrug-resistant E. ictaluri strain, MS-17-156, isolated from diseased channel
AB  - catfish. The genome sequence of this multidrug-resistant strain is expected to
AB  - help us understand the molecular mechanism of antibiotic resistance in this
AB  - important pathogen.
ER  -

TY  - JOUR
AU  - Abdul-Majid, S.
AU  - Graw, M.F.
AU  - Nguyen, H.
AU  - Hay, A.G.
TI  - Draft Whole-Genome Sequence of Urease-Producing Sporosarcina koreensis.
JO  - Genome Announcements
PY  - 2016
SP  - e00096
EP  - e00016
VL  - 4
AB  - Urease-producing microbes are of significance due to their potential application  in biocement
AB  - production. Sporosarcina koreensis Q1 is a urease-producing bacterium belonging to the phylum
AB  - Firmicutes. Here, we present the draft whole-genome sequence of S. koreensis Q1, isolated from
AB  - a barchan sand dune in Qatar.
ER  -

TY  - JOUR
AU  - Abdul-Momin, M.H.F.
AU  - Liakopoulos, A.
AU  - Wareham, D.W.
TI  - Draft Genome Sequence of a Multidrug-Resistant Sequence Type 231 Outbreak-Associated Clone of Klebsiella pneumoniae, KP41-2015, Producing OXA-232 Carbapenemase.
JO  - Genome Announcements
PY  - 2017
SP  - e00604
EP  - e00617
VL  - 5
AB  - Carbapenem-resistant Klebsiella pneumoniae infection is a rising public health threat due to
AB  - limited therapeutic options. Here, we report the genome sequence of a multidrug-resistant K.
AB  - pneumoniae sequence type 231 (ST231) strain associated with an outbreak of infections in an
AB  - intensive care unit that carries a unique complement of resistance determinants.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Belichenko, O.A.
AU  - Lebedeva, N.A.
AU  - Degtyarev, S.K.
TI  - PsiI, a novel restriction endonuclease recognizing the DNA sequence 5'-TTA^TAA-3'.
JO  - Biokhimiia
PY  - 1999
SP  - 574
EP  - 576
VL  - 64
AB  - PsiI, a novel restriction endonuclease produced by the bacterial strain Pseudomonas sp.
AB  - SE-G49, has been isolated and characterized. The enzyme cleaves DNA in the middle of its
AB  - palindromic recognition sequence 5'-TTA^TAA-3'.  Thus, PsiI belongs to a rare group of type
AB  - II restriction endonucleases whose recognition sites consist of AT base pairs only.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Belichenko, O.A.
AU  - Shevchenko, A.V.
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - BstAPI, an ApaBI isoschizomer, cleaves DNA at 5'-GCANNNN/NTGC-3'.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2301
EP  - 2302
VL  - 25
AB  - Cleavage positions of BstAPI, a new restriction endonuclease (Enase) that recognizes
AB  - palindromic interrupted DNA sequence, have been determined.  Recognition sequences and
AB  - cleavage sites comparison shows that BstAPI shares similarity with a number of type II
AB  - restriction enzymes.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Belichenko, O.A.
AU  - Shevchenko, A.V.
AU  - Degtyarev, S.K.
TI  - N.BstSE - site-specific nuclease from Bacillus stearothermophilus SE-589 - restriction endonuclease production.
JO  - Mol. Biol. (Mosk)
PY  - 1996
SP  - 1261
EP  - 1267
VL  - 30
AB  - A site-specific nickase recognizing and cleaving
AB  - the DNA site 5'-GAGTCNNNN^N-3' was isolated from Bacillus
AB  - stearothermophilus SE-589 and named N.BstSE. Its properties
AB  - indicate probable relation with type II restriction
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Belichenko, O.A.
AU  - Shevchenko, A.V.
AU  - Degtyarev, S.K.
TI  - SimI, a new restriction endonuclease that recognizes non-palindromic sequence 5'-GGGTC-3'(-3/0).
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 2571
EP  - 2572
VL  - 23
AB  - SimI, a type II restriction endonuclease, has been isolated from Staphylococcus intermedius 6H
AB  - using heparin and hydroxyapatite chromatographic steps. The crude extract contained
AB  - approximately 3000 U SimI per gram of cells. Three cleavage positions of SimI on pUC19 DNA
AB  - (approximately 999, 1480 and 1768) have been mapped by double digests with enzymes, BglI,
AB  - Acc1131I (isoschizomer of ScaI), SalI, PvuI, NruGI (isoschizomer of Eam11051) and Mly1131
AB  - (isoschizomer of NarI). A homology search has revealed that the pentanucleotide sequence
AB  - 5'-GGGTC-3' was located at these positions. The recognition sequence has been confirmed by
AB  - comparison of cleavage patterns generated with SimI on commonly used DNAS with computer
AB  - predicted ones. The number of SimI sites that occur in lambda, T7, adenovirus-2, pBR322 and
AB  - pUC19 DNA, are 40, 94, 73, 8 and 3, respectively. The cleavage points of the restriction
AB  - endonuclease SimI have been determined by sequencing of alpha-32P-labelled HindIII-XbaI and
AB  - XbaI-EcoRI fragments of the pMVPRL plasmid by the modified Maxam-Gilbert method. The results
AB  - indicate the SimI cleaves the DNA sequence shown below: 5'-GG/GTC-3' 3'-CCCAG/-5'.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Kileva, E.V.
AU  - Myakisheva, T.V.
AU  - Dedkov, V.S.
AU  - Shevchenko, A.V.
AU  - Degtyarev, S.K.
TI  - AccBSI: A new restriction endonuclease from Acinetobacter calcoaceticus BS.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1997
SP  - 556
EP  - 558
VL  - 33
AB  - The recognition site of a new restriction endonuclease from Acinetobacter calcoaceticus BS was
AB  - determined.  This is a nonpalindromic sequence 5'-GAGCGG-3' 3'-CTCGCC-5.  AccBSI
AB  - restrictase cleaves DNA chains in the middle of the recognition sequence; therefore, ligation
AB  - of its digestion fragments restored AccBSI recognition sites and generated palindromic
AB  - sequences recognized by SacI and SacII restrictases.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Kileva, E.V.
AU  - Shinkarenko, N.M.
AU  - Shevchenko, A.V.
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - BstF5I, an unusual isoschizomer of FokI.
JO  - Gene
PY  - 1996
SP  - 49
EP  - 51
VL  - 172
AB  - BstF5, a new restriction endonuclease (Enase) from Bacillus stearothermophilus
AB  - F5, has been discovered.  This enzyme recognizes 5'-GGATG-3' and cleaves DNA, generating a
AB  - 2-base 3' extension: 5'-GGATG NN/-3' / 3'-CCTAC/NN-5'.  BstF5I is an isoschizomer of FokI
AB  - and seems to be evolutionarily close to other nonpalindromic-recognizing ENases from
AB  - thermophilic bacilli.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Netesova, N.A.
AU  - Golikova, L.N.
AU  - Gutorov, V.V.
AU  - Belavin, P.A.
AU  - Degtyarev, S.K.
TI  - The second methyltransferase of the BstF5I restriction-modification system is homologous to the C-terminal domains of FokI and StsI methylases.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 87
EP  - 94
VL  - 34
AB  - Nucleotide sequence of DNA-methyltransferase gene M. BstF51-2 was determined. This
AB  - enzyme is a part of the restriction-modification system of Bacillus stearothermophilus strain
AB  - F. On bacterial chromosome, gene bstF51M2 is located behind methylase gene M.BStF51-1 and has
AB  - the same orientation. Protein encoded by gene bstF1M-2 contains conservative regions specific
AB  - for adenine DNA-methyltransferase of class D12. DNA-methylase M.BstF51-2 is homologous to
AB  - C-terminal domains of DNA methylases Fok1 enzymes M.Fok1 and M.Sts1 modifying the second DNA
AB  - strand in the recognition site and Sts1 possessing the same recognition sequence. It is shown
AB  - that the restriction-modification system BstF51 contains a unique enzyme M.BstF51-1 modifying
AB  - the upper strand of the recognized sequence and M.BstF51-2 homologous to C-terminal parts of
AB  - enzymes modifying the second DNA strand in the recognition site.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Okhapkina, S.S.
AU  - Netesova, N.A.
AU  - Golikova, L.N.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - The unique FauI restriction-modification system: Cloning and protein sequence comparisons.
JO  - Mol. Biol. (Mosk)
PY  - 2003
SP  - 619
EP  - 624
VL  - 37
AB  - The nucleotide sequence was established for the full-length Flavobacterium aquatile operon
AB  - coding for the FauI restriction-modification system. The
AB  - operon is unusual in structure and has the gene order control protein
AB  - gene-DNA methyltransferase A gene-restriction endonuclease gene-DNA
AB  - methyltransferase B gene, other than in the known analogs. The genes are
AB  - similarly oriented and overlap. On evidence of sequence analysis, both
AB  - methyltransferases are C5 enzymes, the control protein is similar to that
AB  - of other restriction-modification systems, and restriction endonuclease is
AB  - low-homologous to other enzymes cleaving the DNA upper strand in position
AB  - 4 or 5 relative to the recognition site.
ER  -

TY  - JOUR
AU  - Abdurashitov, M.A.
AU  - Tomilov, V.N.
AU  - Chernukhin, V.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Comparative analysis of human chromosomal DNA digestion with restriction endonucleases in vitro and in silico.
JO  - Medical Genetics
PY  - 2007
SP  - 29
EP  - 36
VL  - 6
AB  - Theoretical analysis of human chromosomal DNA cleavage at 15 nucleotide sequences, which are
AB  - the recognition sites of various restriction endonucleases, has been carried out.
AB  - Distribution diagrams of calculated DNA fragments have been constructed based on earlier
AB  - proposed method of mammalian genomes digestion in silico.  A similar study of human Alu- and
AB  - LINE1-repeats nucleotide sequences, which are present in informational databases, has been
AB  - performed and corresponding diagrams of DNA fragments distribution have been plotted.
AB  - Distribution diagrams of chromosomal DNA digestion, which results in formation of low
AB  - molecular weight DNA fragments, correspond to those for Alu-repeats; whereas the digestion,
AB  - which results in formation of large molecular weight DNA fragments - are similar to those for
AB  - LINE-repeats.  All theoretical data have been compared to experimental patterns of human
AB  - genomic DNA cleavages with respective restriction endonucleases and a good correspondence for
AB  - the most of DNA diagrams has been observed.
ER  -

TY  - JOUR
AU  - Abeijon, M.M.C.
AU  - Saavedra, L.
AU  - Gauffin, C.M.P.
AU  - Hebert, E.M.
AU  - Medina, R.B.
TI  - Draft Genome Sequence of the Feruloyl Esterase-Producing Strain Lactobacillus fermentum CRL1446, a Probiotic for Malnutrition.
JO  - Genome Announcements
PY  - 2018
SP  - e00225
EP  - e00218
VL  - 6
AB  - We report here the draft genome sequence of Lactobacillus fermentum CRL1446 (2,148,781 bp,
AB  - 51.4% G+C content). This strain exhibits feruloyl esterase
AB  - activity and important technological and probiotic properties. Because of its
AB  - proven beneficial effects in vivo, it represents an interesting candidate for the
AB  - development of functional foods or pharmabiotics for malnutrition.
ER  -

TY  - JOUR
AU  - Abendroth, C.
AU  - Hahnke, S.
AU  - Codoner, F.M.
AU  - Klocke, M.
AU  - Luschnig, O.
AU  - Porcar, M.
TI  - Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.
JO  - Genome Announcements
PY  - 2017
SP  - e00686
EP  - e00617
VL  - 5
AB  - A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a
AB  - mesophilic and anaerobic two-stage lab-scale leach-bed system for
AB  - biomethanation of fresh grass. It is assumed that the bacterial isolate
AB  - contributes to plant biomass degradation. Here, we report a draft annotated
AB  - genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Abicht, H.K.
AU  - Mancini, S.
AU  - Karnachuk, O.V.
AU  - Solioz, M.
TI  - Genome Sequence of Desulfosporosinus sp. OT, an Acidophilic Sulfate-Reducing Bacterium from Copper Mining Waste in Norilsk, Northern  Siberia.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6104
EP  - 6105
VL  - 193
AB  - We have sequenced the genome of Desulfosporosinus sp. OT, a Gram-positive, acidophilic
AB  - sulfate-reducing Firmicute isolated from copper tailing
AB  - sediment in the Norilsk mining-smelting area in Northern Siberia, Russia.
AB  - This represents the first sequenced genome of a Desulfosporosinus species.
AB  - The genome has a size of 5.7 Mb and encodes 6,222 putative proteins.
ER  -

TY  - JOUR
AU  - Abin, C.A.
AU  - Hollibaugh, J.T.
TI  - Draft Genome Sequence for the Type Strain Vulcanibacillus modesticaldus BR, a Strictly Anaerobic, Moderately Thermophilic, and Nitrate-Reducing Bacterium  Isolated from Deep-Sea Hydrothermal Vents of the Mid-Atlantic Ridge.
JO  - Genome Announcements
PY  - 2016
SP  - e01246
EP  - e01216
VL  - 4
AB  - Vulcanibacillus modesticaldus BRT was isolated from calcite-rich, metalliferous core samples
AB  - collected at the Rainbow deep-sea hydrothermal vent field on the
AB  - Mid-Atlantic Ridge. Here, we report the 2.2-Mb draft genome sequence for this
AB  - strain, consisting of 100 contigs with a G+C content of 33.6% and 2,227
AB  - protein-coding sequences.
ER  -

TY  - JOUR
AU  - Abin, C.A.
AU  - Hollibaugh, J.T.
TI  - Draft Genome Sequence of the Type Strain Desulfuribacillus alkaliarsenatis AHT28, an Obligately Anaerobic, Sulfidogenic Bacterium Isolated from Russian Soda Lake  Sediments.
JO  - Genome Announcements
PY  - 2016
SP  - e01244
EP  - e01216
VL  - 4
AB  - Desulfuribacillus alkaliarsenatis AHT28T is an obligately anaerobic, sulfur- and
AB  - arsenate-reducing haloalkaliphile that was isolated from Russian soda lake
AB  - sediments. Here, we present the 3.1-Mb draft genome sequence for this strain,
AB  - consisting of 36 contigs with a G+C content of 37.5% and 2,978 protein-coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Abo-Aba, S.E.
AU  - Sabir, J.S.
AU  - Baeshen, M.N.
AU  - Sabir, M.J.
AU  - Mutwakil, M.H.
AU  - Baeshen, N.A.
AU  - D'Amore, R.
AU  - Hall, N.
TI  - Draft Genome Sequence of Bacillus Species from the Rhizosphere of the Desert Plant Rhazya stricta.
JO  - Genome Announcements
PY  - 2015
SP  - e00957
EP  - e00915
VL  - 3
AB  - In order to better understand the ecology and diversity of microbes in the rhizosphere of
AB  - desert plants, we undertook a survey of Bacillus species isolated
AB  - from soil around Rhazya stricta plants from the area around Jeddah, in The
AB  - Kingdom, Saudi Arabia. We have sequenced the genomes of 8 Bacillus isolates
AB  - representing four different species.
ER  -

TY  - JOUR
AU  - Abolnik, C.
AU  - Beylefeld, A.
TI  - Complete Genome Sequence of Mycoplasma gallinaceum.
JO  - Genome Announcements
PY  - 2015
SP  - e00712
EP  - e00715
VL  - 3
AB  - Mycoplasma gallinaceum strain B2096 8B was isolated from domestic chickens in South Africa.
AB  - The 845,307-bp full genome was sequenced, assembled, and annotated.
ER  -

TY  - JOUR
AU  - Aboubaker, O.D.
AU  - Phelippeau, M.
AU  - Musso, D.
AU  - Robert, C.
AU  - Michelle, C.
AU  - Croce, O.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Strain MT43, a Representative of the Manu2 Genotype.
JO  - Genome Announcements
PY  - 2015
SP  - e00579
EP  - e00515
VL  - 3
AB  - We announce the draft genome sequence of Mycobacterium tuberculosis strain MT43,  isolated
AB  - from a pulmonary form of tuberculosis in French Polynesia. Analyzing its
AB  - 4,145,007-bp, 65.17% G+C chromosome confirmed a fully antibiotic-susceptible
AB  - Manu2 spoligotype.
ER  -

TY  - JOUR
AU  - Aboubaker, O.D.
AU  - Phelippeau, M.
AU  - Musso, D.
AU  - Robert, C.
AU  - Michelle, C.
AU  - Croce, O.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Strain MT11, Which Represents a New Lineage.
JO  - Genome Announcements
PY  - 2015
SP  - e00573
EP  - e00515
VL  - 3
AB  - We sequenced the genome of Mycobacterium tuberculosis strain MT11, which exhibits a specific
AB  - 16S rRNA gene mutation found in 6% of French Polynesian M.
AB  - tuberculosis isolates. It comprises a 4,110,293-bp chromosome with 65.15% G+C
AB  - content, and it encodes 3,949 proteins and contains 85 predicted RNA genes. The
AB  - TbD1 region is absent in strain MT11 as in modern M. tuberculosis strains.
ER  -

TY  - JOUR
AU  - Abouelkhair, M.A.
AU  - Riley, M.C.
AU  - Bemis, D.A.
AU  - Kania, S.A.
TI  - Complete Genome Sequence of Staphylococcus pseudintermedius Type Strain LMG 22219.
JO  - Genome Announcements
PY  - 2017
SP  - e01651
EP  - e01616
VL  - 5
AB  - We report the first complete genome sequence of LMG 22219 (=ON 86T = CCUG 49543T), the
AB  - Staphylococcus pseudintermedius type strain isolated from feline
AB  - lung tissue. This sequence information will facilitate phylogenetic comparisons
AB  - of staphylococcal species and other bacteria at the genome level.
ER  -

TY  - JOUR
AU  - Abouelkhair, M.A.
AU  - Thompson, R.
AU  - Riley, M.C.
AU  - Bemis, D.A.
AU  - Kania, S.A.
TI  - Complete Genome Sequences of Three Staphylococcus pseudintermedius Strains Isolated from Botswana.
JO  - Genome Announcements
PY  - 2018
SP  - e01599
EP  - e01517
VL  - 6
AB  - We report here the first whole-genome sequences for 3 strains of Staphylococcus
AB  - pseudintermedius (112N, 113N, and 114N) isolated in Africa. Samples of this
AB  - opportunistic pathogen were collected from nasal swabs obtained from healthy
AB  - carrier dogs in Botswana. The sequence information will facilitate spatial
AB  - phylogenetic comparisons of staphylococcal species and other bacteria at the
AB  - genome level.
ER  -

TY  - JOUR
AU  - Abraham, S.
AU  - O'Dea, M.
AU  - Trott, D.J.
AU  - Abraham, R.J.
AU  - Hughes, D.
AU  - Pang, S.
AU  - McKew, G.
AU  - Cheong, E.Y.
AU  - Merlino, J.
AU  - Saputra, S.
AU  - Malik, R.
AU  - Gottlieb, T.
TI  - Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats.
JO  - Sci. Rep.
PY  - 2016
SP  - 35527
EP  - 35527
VL  - 6
AB  - Carbapenem-resistant Enterobacteriaceae (CRE) are a pressing public health issue
AB  - due to limited therapeutic options to treat such infections. CREs have been
AB  - predominantly isolated from humans and environmental samples and they are rarely
AB  - reported among companion animals. In this study we report on the isolation and
AB  - plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica
AB  - Typhimurium from a companion animal. Carbapenemase-producing S. enterica
AB  - Typhimurium carrying blaIMP-4 was identified from a systemically unwell (index)
AB  - cat and three additional cats at an animal shelter. All isolates were identical
AB  - and belonged to ST19. Genome sequencing revealed the acquisition of a
AB  - multidrug-resistant IncHI2 plasmid (pIMP4-SEM1) that encoded resistance to nine
AB  - antimicrobial classes including carbapenems and carried the
AB  - blaIMP-4-qacG-aacA4-catB3 cassette array. The plasmid also encoded resistance to
AB  - arsenic (MIC-150 mM). Comparative analysis revealed that the plasmid pIMP4-SEM1
AB  - showed greatest similarity to two blaIMP-8 carrying IncHI2 plasmids from
AB  - Enterobacter spp. isolated from humans in China. This is the first report of CRE
AB  - carrying a blaIMP-4 gene causing a clinical infection in a companion animal, with
AB  - presumed nosocomial spread. This study illustrates the broader community risk
AB  - entailed in escalating CRE transmission within a zoonotic species such as
AB  - Salmonella, and in a cycle that encompasses humans, animals and the environment.
ER  -

TY  - JOUR
AU  - Abraham, W.P.
AU  - Thomas, S.
TI  - Draft Genome Sequence of Pseudomonas psychrophila MTCC 12324, Isolated from the Arctic at 79 degrees N.
JO  - Genome Announcements
PY  - 2015
SP  - e00578
EP  - e00515
VL  - 3
AB  - Pseudomonas psychrophila MTCC 12324 is a facultatively psychrophilic bacterium isolated from
AB  - the Arctic fjord Ny-alesund in the Svalbard Archipelago. Here, we
AB  - present a 5.2-Mb draft genome sequence of P. psychrophila MTCC 12324, reported
AB  - for the first time, from the Arctic. This enables a study of the cold adaptation
AB  - mechanisms to survive under the extreme cold conditions.
ER  -

TY  - JOUR
AU  - Abrahante, J.E.
AU  - Hunter, S.S.
AU  - Maheswaran, S.K.
AU  - Hauglund, M.J.
AU  - Tatum, F.M.
AU  - Briggs, R.E.
TI  - Draft Genome Sequence of Pasteurella multocida Isolate P1062, Isolated from Bovine Respiratory Disease.
JO  - Genome Announcements
PY  - 2015
SP  - e01254
EP  - e01215
VL  - 3
AB  - Here, we report the draft genome of Pasteurella multocida isolate P1062 recovered from
AB  - pneumonic bovine lung in the United States in 1959.
ER  -

TY  - JOUR
AU  - Abrahante, J.E.
AU  - Johnson, T.J.
AU  - Hunter, S.S.
AU  - Maheswaran, S.K.
AU  - Hauglund, M.J.
AU  - Bayles, D.O.
AU  - Tatum, F.M.
AU  - Briggs, R.E.
TI  - Draft Genome Sequences of Two Virulent Serotypes of Avian Pasteurella multocida.
JO  - Genome Announcements
PY  - 2013
SP  - e00058
EP  - e00012
VL  - 1
AB  - Here we report the draft genome sequences of two virulent avian strains of Pasteurella
AB  - multocida. Comparative analyses of these genomes were done with the
AB  - published genome sequence of avirulent P. multocida strain Pm70.
ER  -

TY  - JOUR
AU  - Abrahante, J.E.
AU  - Veeregowda, B.M.
AU  - Hogtapur, S.S.
AU  - Briggs, R.E.
AU  - Maheswaran, S.K.
AU  - Sreevatsan, S.
TI  - Draft Genome Sequences of Two Pasteurella multocida Strains Isolated from Buffaloes in India with Hemorrhagic Septicemia Disease.
JO  - Genome Announcements
PY  - 2014
SP  - e00798
EP  - e00714
VL  - 2
AB  - Pasteurella multocida serotype B:2 is the causative agent of hemorrhagic septicemia in cattle
AB  - and buffaloes in Asia. It is an acute fatal disease and is
AB  - considered one of the most economically important diseases in this region of the
AB  - world. We present here the draft genome sequences of strains 2213 and 3213 of P.
AB  - multocida.
ER  -

TY  - JOUR
AU  - Abrams, A.J.
AU  - Trees, D.L.
AU  - Nicholas, R.A.
TI  - Complete Genome Sequences of Three Neisseria gonorrhoeae Laboratory Reference Strains, Determined Using PacBio Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e01052
EP  - e01015
VL  - 3
AB  - Neisseria gonorrhoeae, the etiological agent that causes the sexually transmitted infection
AB  - gonorrhea, is a significant public health concern due to the emergence  of antimicrobial
AB  - resistance. We report the complete genome sequences of three reference isolates with varied
AB  - antimicrobial susceptibility that will aid in elucidating the genetic mechanisms that confer
AB  - resistance.
ER  -

TY  - JOUR
AU  - Abriouel, H.
AU  - Benomar, N.
AU  - Perez, P.R.
AU  - Canamero, M.M.
AU  - Galvez, A.
TI  - Annotated genome sequence of Lactobacillus pentosus MP-10, which has probiotic potential, from naturally fermented Alorena green table olives.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4559
EP  - 4560
VL  - 193
AB  - Lactobacillus pentosus MP-10 was isolated from brines of naturally-fermented Alorena green
AB  - table olives. MP-10 has potential probiotic traits: inhibition of human pathogenic bacteria,
AB  - survival at low pH (1.5) and bile slat tolerance (3%). Here, we report for the first time the
AB  - annotated genome sequence of Lb. pentosus.
ER  -

TY  - JOUR
AU  - Abriouel, H.
AU  - Perez, M.B.
AU  - Casado, M.M.C.
AU  - Lavilla, L.L.
AU  - Hidalgo, P.M.
AU  - Caballero, G.N.
AU  - Franz, C.M.
AU  - Galvez, A.
AU  - Benomar, N.
TI  - Complete Genome Sequence of a Potential Probiotic, Lactobacillus pentosus MP-10,  Isolated from Fermented Alorena Table Olives.
JO  - Genome Announcements
PY  - 2016
SP  - e00854
EP  - e00816
VL  - 4
AB  - We report here a 3,698,214-bp complete genome sequence of a potential probiotic Lactobacillus
AB  - pentosus strain, MP-10, isolated from brines of naturally fermented
AB  - Alorena green table olives; it is considered the largest sequenced genome among
AB  - lactobacilli to date. The annotated genome sequence revealed the presence of
AB  - 3,558 open reading frames (ORFs) and 87 structural RNAs.
ER  -

TY  - JOUR
AU  - Abrol, S.
AU  - Chaudhary, V.K.
TI  - Excess PCR primers inhibit DNA cleavage by some restriction endonucleases.
JO  - Biotechniques
PY  - 1993
SP  - 630
EP  - 632
VL  - 15
AB  - For cloning DNA segments into expression vectors, restriction endonuclease recognition sites
AB  - can be generated by polymerase chain reaction utilizing synthetic oligonucleotides as PCR
AB  - primers that contain the relevant sites.  Following PCR amplification, there usually remains a
AB  - 10-fold to 100-fold molar excess of unused primers over the desired amplified product in the
AB  - reaction mixture.  These excess oligonucleotides may inhibit the cleavage of amplified
AB  - products by the restriction enzyme and thus interfere in the generation of DNA fragments with
AB  - compatible termini for cloning into expression vectors.  We have investigated the effect of
AB  - single-stranded oligonucleotides containing a restriction endonuclease recognition site on the
AB  - digestion of linearized double-stranded DNA substrates (mimicking PCR product) by the
AB  - respective restriction enzymes.  This information will be useful in deciding if the removal of
AB  - excess oligonucleotide primers is necessary or not.
ER  -

TY  - JOUR
AU  - Abrosimova, L.
AU  - Monakhova, M.
AU  - Schierling, B.
AU  - Volkov, E.
AU  - Romanova, E.
AU  - Wende, W.
AU  - Pingoud, A.
AU  - Kubareva, E.
AU  - Oretskaya, T.
TI  - Light dependent activity of restriction endonucleases.
JO  - FEBS J.
PY  - 2013
SP  - 597
EP  - 597
VL  - 280
AB  - Sequence-specific endonucleases with extended recognition sites can cleave a unique site in
AB  - complex genomes. Since the nucleases can show off-target cleavage activity, spatio-temporal
AB  - control of their activity is necessary for the precise genome engineering.  It would be
AB  - desirable to control the enzymatic activity by an external signal, e.g. by light.  Such
AB  - photoregulation is based on the azobenzene 'photoswitch'.  Azobenzene isomerizes between the
AB  - extended trans- and the cis-configuration by illumination with UV (trans-cis) or blue light
AB  - (cis-trans) as well as by thermal relaxation (cis-trans).  We are developing the 'molecular
AB  - gate's strategy based on the fact that most type II restriction endonucleases are homodimers.
AB  - The DNA-binding center is located in the interface between the two subunits.  It is possible
AB  - to modify the protein at the entrance of the DNA-binding site and block its activity.  To
AB  - create the obstacle for DNA penetration to the active center we suggest to use the ability of
AB  - oligonucleotides containing azobenzene insertion to form a duplex.  Azobenzene in
AB  - trans-configuration stabilizes the duplex and cis-configuration causes destabilization.  Thus
AB  - formation and dissociation of the duplex can be reversibly photo-regulated.  The strategy is
AB  - illustrated for the type II RE SsoII.  To choose the optimal length of the duplex 10-mer and
AB  - 15-mer modified oligonucleotides were synthesized.  After attachment to the protein these
AB  - oligonucleoties are supposed to form 10-mer DNA duplexes.  The initial rates of DNA cleavage
AB  - at 37oC upon UV-illumination was two times higher than upon blue light illumination.  Our
AB  - results demonstrate the possibility of changing the enzymatic activity upon illumination. This
AB  - work was supported by the program 'International Research Training Groups' (grants RFBR-DFG
AB  - 11-04-91338 and GRK 1384).
ER  -

TY  - JOUR
AU  - Abrosimova, L.A.
AU  - Monakhova, M.V.
AU  - Migur, A.Y.
AU  - Wolfgang, W.
AU  - Pingoud, A.
AU  - Kubareva, E.A.
AU  - Oretskaya, T.S.
TI  - Thermo-switchable Activity of the Restriction Endonuclease SsoII Achieved by Site-Directed Enzyme Modification.
JO  - Life
PY  - 2013
SP  - 1012
EP  - 1016
VL  - 65
AB  - In this work, the possibility of constructing a thermo-switchable enzyme according to the
AB  - molecular gate strategy is demonstrated. The approach is based on the covalent attachment of
AB  - oligodeoxyribonucleotides to cysteine residues of an enzyme adjacent to its active center to
AB  - form a temporal barrier for enzyme-substrate complex formation. The activity of the modified
AB  - enzyme that had been studied herethe restriction endonuclease SsoII (R.SsoII)was diminished by
AB  - a factor of 180 at 25 degrees C that alm st abolished the enzymatic activity when compared
AB  - with the unmodified enzyme. However, heating of the modified enzyme to 45 degrees C resulted
AB  - in a 30-fold increase of activity. The activity of unmodified R.SsoII also increased on
AB  - heating from 25 to 45 degrees; however, the difference did not exceed a factor of 3-4. The
AB  - changes in enzymatic activity observed were shown to be reversible for both the unmodified and
AB  - the modified R.SsoII. Variation of the length and the sequence of the attached oligodeoxyribon
AB  - ucleotides might allow greater modulation of the activity of DNA-protein conjugates.
ER  -

TY  - JOUR
AU  - Abt, B. et al.
TI  - Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as  Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae   and the genus Sphaer.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 194
EP  - 209
VL  - 6
AB  - Spirochaeta coccoides Droge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835,
AB  - one of the oldest named genera within the Bacteria. S. coccoides
AB  - is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that
AB  - was isolated from the hindgut contents of the termite Neotermes castaneus. The
AB  - species is of interest because it may play an important role in the digestion of
AB  - breakdown products from cellulose and hemicellulose in the termite gut. Here we
AB  - provide a taxonomic re-evaluation for strain SPN1(T), and based on physiological
AB  - and genomic characteristics, we propose its reclassification as a novel species
AB  - in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta.
AB  - The 2,227,296 bp long genome of strain SPN1(T) with its 1,866 protein-coding and
AB  - 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Abt, B. et al.
TI  - Complete genome sequence of Cellulomonas flavigena type strain (134).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 15
EP  - 25
VL  - 3
AB  - Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of
AB  - the genus Cellulomonas of the actinobacterial family
AB  - Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for
AB  - their ability to degrade cellulose and hemicellulose, particularly with regard to
AB  - the use of biomass as an alternative energy source. Here we describe the features
AB  - of this organism, together with the complete genome sequence, and annotation.
AB  - This is the first complete genome sequence of a member of the genus Cellulomonas,
AB  - and next to the human pathogen Tropheryma whipplei the second complete genome
AB  - sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp
AB  - long single replicon genome with its 3,735 protein-coding and 53 RNA genes is
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Abt, B. et al.
TI  - Complete genome sequence of Leadbetterella byssophila type strain (4M15).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 2
EP  - 12
VL  - 4
AB  - Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of
AB  - the family Cytophagaceae in the phylum Bacteroidetes. Members
AB  - of the phylum Bacteroidetes are widely distributed in nature, especially in
AB  - aquatic environments. They are of special interest for their ability to degrade
AB  - complex biopolymers. L. byssophila occupies a rather isolated position in the
AB  - tree of life and is characterized by its ability to hydrolyze starch and
AB  - gelatine, but not agar, cellulose or chitin. Here we describe the features of
AB  - this organism, together with the complete genome sequence, and annotation. L.
AB  - byssophila is already the 16(th) member of the family Cytophagaceae whose genome
AB  - has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613
AB  - protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Abt, B. et al.
TI  - Complete genome sequence of Cellulophaga algicola type strain (IC166).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 72
EP  - 80
VL  - 4
AB  - Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within  the phylum
AB  - 'Bacteroidetes' and was isolated from Melosira collected from the
AB  - Eastern Antarctic coastal zone. The species is of interest because its members
AB  - produce a wide range of extracellular enzymes capable of degrading proteins and
AB  - polysaccharides with temperature optima of 20-30 degrees C. This is the first
AB  - completed genome sequence of a member of the genus Cellulophaga. The 4,888,353 bp
AB  - long genome with its 4,285 protein-coding and 62 RNA genes consists of one
AB  - circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and
AB  - Archaea project.
ER  -

TY  - JOUR
AU  - Abt, B. et al.
TI  - Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta  stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema  caldaria comb. nov., T.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 88
EP  - 105
VL  - 8
AB  - Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped
AB  - bacterium that is motile via periplasmic flagella. The type strain,
AB  - H1(T), was isolated in 1990 from cyanobacterial mat samples collected at a
AB  - freshwater hot spring in Oregon, USA, and is of interest because it enhances the
AB  - degradation of cellulose when grown in co-culture with Clostridium thermocellum.
AB  - Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic
AB  - analyses of 16S rRNA sequences and whole genomes, and propose the
AB  - reclassification of S. caldaria and two other Spirochaeta species as members of
AB  - the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta
AB  - possess well-distinguished genomic features related to their divergent
AB  - lifestyles, the physiological and functional genomic characteristics of
AB  - Spirochaeta and Treponema appear to be intermixed and are of little taxonomic
AB  - value. The 3,239,340 bp long genome of strain H1(T) with its 2,869 protein-coding
AB  - and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Abu, C.M.
AU  - Wailan, A.M.
AU  - Sidjabat, H.E.
AU  - Zhang, L.
AU  - Marsh, N.
AU  - Rickard, C.M.
AU  - Davies, M.R.
AU  - McMillan, D.J.
TI  - Draft Genome Sequence of Roseomonas mucosa Strain AU37, Isolated from a Peripheral Intravenous Catheter.
JO  - Genome Announcements
PY  - 2017
SP  - e00128
EP  - e00117
VL  - 5
AB  - Roseomonas mucosa is an opportunistic pathogen that causes infections in humans and is often
AB  - associated with vascular catheter-related bacteremia. Here, we
AB  - report the draft genome sequence of Roseomonas mucosa strain AU37, isolated from
AB  - a peripheral intravenous catheter tip.
ER  -

TY  - JOUR
AU  - AbuLaban, N.
AU  - Tan, B.
AU  - Dao, A.
AU  - Foght, J.
TI  - Draft Genome Sequence of Uncultivated Toluene-Degrading Desulfobulbaceae Bacterium Tol-SR, Obtained by Stable Isotope Probing Using [13C6]Toluene.
JO  - Genome Announcements
PY  - 2015
SP  - e01423
EP  - e01414
VL  - 3
AB  - The draft genome of a member of the bacterial family Desulfobulbaceae (phylum
AB  - Deltaproteobacteria) was assembled from the metagenome of a sulfidogenic
AB  - [(13)C6]toluene-degrading enrichment culture. The 'Desulfobulbaceae bacterium Tol-SR' genome
AB  - is distinguished from related, previously sequenced genomes by suites of genes associated with
AB  - anaerobic toluene metabolism, including bss, bbs, and bam.
ER  -

TY  - JOUR
AU  - AbuLaban, N.
AU  - Tan, B.
AU  - Dao, A.
AU  - Foght, J.
TI  - Draft Genome Sequence of Uncultivated Desulfosporosinus sp. Strain Tol-M, Obtained by Stable Isotope Probing Using [13C6]Toluene.
JO  - Genome Announcements
PY  - 2015
SP  - e01422
EP  - e01414
VL  - 3
AB  - A draft Desulfosporosinus genome was assembled from the metagenome of a methanogenic
AB  - [(13)C6]toluene-degrading community. The Desulfosporosinus sp. strain Tol-M genome is
AB  - distinguished from that of previously published Desulfosporosinus strain by containing bss,
AB  - bbs, and bam genes encoding enzymes for anaerobic biodegradation of monoaromatic hydrocarbons
AB  - and lacking dsrAB genes for dissimilatory sulfate reduction.
ER  -

TY  - JOUR
AU  - Abulencia, C.B.
AU  - Wyborski, D.L.
AU  - Garcia, J.A.
AU  - Podar, M.
AU  - Chen, W.
AU  - Chang, S.H.
AU  - Chang, H.W.
AU  - Watson, D.
AU  - Brodie, E.L.
AU  - Hazen, T.C.
AU  - Keller, M.
TI  - Environmental whole-genome amplification to access microbial populations in contaminated sediments.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 3291
EP  - 3301
VL  - 72
AB  - Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that
AB  - have limited use for direct, native analysis and
AB  - screening. Multiple displacement amplification (MDA) using phi29 DNA
AB  - polymerase was used to amplify whole genomes from environmental,
AB  - contaminated, subsurface sediments. By first amplifying the genomic DNA
AB  - (gDNA), biodiversity analysis and gDNA library construction of microbes
AB  - found in contaminated soils were made possible. The MDA method was
AB  - validated by analyzing amplified genome coverage from approximately five
AB  - Escherichia coli cells, resulting in 99.2% genome coverage. The method was
AB  - further validated by confirming overall representative species coverage
AB  - and also an amplification bias when amplifying from a mix of eight known
AB  - bacterial strains. We extracted DNA from samples with extremely low cell
AB  - densities from a U.S. Department of Energy contaminated site. After
AB  - amplification, small-subunit rRNA analysis revealed relatively even
AB  - distribution of species across several major phyla. Clone libraries were
AB  - constructed from the amplified gDNA, and a small subset of clones was used
AB  - for shotgun sequencing. BLAST analysis of the library clone sequences
AB  - showed that 64.9% of the sequences had significant similarities to known
AB  - proteins, and "clusters of orthologous groups" (COG) analysis revealed
AB  - that more than half of the sequences from each library contained sequence
AB  - similarity to known proteins. The libraries can be readily screened for
AB  - native genes or any target of interest. Whole-genome amplification of
AB  - metagenomic DNA from very minute microbial sources, while introducing an
AB  - amplification bias, will allow access to genomic information that was not
AB  - previously accessible. The reported SSU rRNA sequences and library clone
AB  - end sequences are listed with their respective GenBank accession numbers,
AB  - DQ 404590 to DQ 404652, DQ 404654 to DQ 404938, and DX 385314 to DX
AB  - 389173.
ER  -

TY  - JOUR
AU  - Accetto, T.
AU  - Peterka, M.
AU  - Avgustin, G.
TI  - Type II restriction modification systems of Prevotella bryantii TC1-1 and Prevotella ruminicola 23 strains and their effect on the efficiency  of DNA introduction via electroporation.
JO  - FEMS Microbiol. Lett.
PY  - 2005
SP  - 177
EP  - 183
VL  - 247
AB  - The restriction endonucleases PbrTI and Pru2I, isoschizomers of Sau3AI and HaeIII, were
AB  - partially purified and characterized from anaerobic
AB  - rumen bacteria Prevotella bryantii TCl-1 and Prevotella ruminicola 23,
AB  - respectively. These are the first type II restriction endonucleases
AB  - discovered in strains of the genus Prevotella, and they represent one
AB  - of the barriers hindering gene transfer in these microorganisms.
AB  - Heterologous DNA was protected against the action of PbrTI or Pru2I
AB  - by incubation in a cell-free extract of the respective strain which
AB  - contained 20 mM EDTA. This led to the development of a protocol
AB  - enabling successful electrotransformation of the P. bryantii TCl-1
AB  - strain with a pRH3 Bacteroides-Escherichia coli shuttle vector
AB  - containing up to 7-kb long DNA inserts. Plasmid DNA isolated from the
AB  - transformed strain facilitated the transfer with further increased
AB  - efficiency and made possible the introduction of ligation reaction
AB  - products directly to P. bryantii TCl-1 without passing them first
AB  - through E. coli.
ER  -

TY  - JOUR
AU  - Acedo, J.Z.
AU  - Ibarra, R.C.
AU  - Miyata, S.T.
AU  - Blaine, A.H.
AU  - McMullen, L.M.
AU  - Vederas, J.C.
AU  - van Belkum, M.J.
TI  - Draft Genome Sequence of Enterococcus canintestini 49, a Potential Probiotic That Produces Multiple Bacteriocins.
JO  - Genome Announcements
PY  - 2017
SP  - e01131
EP  - e01117
VL  - 5
AB  - Enterococcus canintestini 49, isolated from dog feces, is active against Clostridium
AB  - perfringens, vancomycin-resistant enterococci, and Listeria
AB  - monocytogenes Its draft genome sequence reported herein contains a gene cluster
AB  - encoding multiple bacteriocins and indicates the absence of genes for virulence
AB  - factors. These characteristics signify the strain's potential for use as a
AB  - probiotic.
ER  -

TY  - JOUR
AU  - Acharya, A.S.
AU  - Roy, K.B.
TI  - An alternative approach for screening active Bam HI variants: Overexpression in T-7 RNA polymerase based system.
JO  - Indian J. Biochem. Biophys.
PY  - 2001
SP  - 303
EP  - 308
VL  - 38
AB  - The type II restriction endonuclease, BamHI, has been overexpressed in E. coli by cloning the
AB  - BamHI gene in frame with an E. coli Ribosome
AB  - Binding Site (RBS) under the T7 promoter of an E. coli expression
AB  - vector pRSET A. The expression level of BamHI endonuclease using this
AB  - construct was found to be higher than that reported of the
AB  - overexpressing clone pAEK14. Our overexpressing clone, pAABRw in BL21
AB  - cells in presence of BamHI methylase in pMAP6 following induction with
AB  - IPTG yields about 9.2x10(6) units per gram wet cell paste. In vivo
AB  - activity of the recombinant endonuclease could be confirmed by the SOS
AB  - induction assay in JH139 cells even in the absence of T7 polymerase and
AB  - cognate BamHI methylase because of leaky expression in E.coli. This
AB  - provides an alternate way to screen the active endonuclease and its
AB  - variants.
ER  -

TY  - JOUR
AU  - Acharya, A.S.
AU  - Roy, K.B.
TI  - Reduced activity of BamHI variants C54I, C64W, and C54D/C64R is consistent with the substrate-assisted catalysis model.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2001
SP  - 153
EP  - 159
VL  - 287
AB  - Three specific mutants, C54I, C54W, and a double-mutant C54D:C64R of restriction endonuclease
AB  - BamHI, were generated and studied to investigate the role, if any, of the 54th and 64th
AB  - cysteine residues in the catalysis of BamHI. The mutation was achieved using the megaprimer
AB  - approach for PCR. The mutant genes were cloned and characterized by sequencing. The mutant and
AB  - the wild-type proteins were expressed and purified and their kinetic parameters were
AB  - determined using short synthetic oligonucleotides as substrates. All mutants had higher K(m)
AB  - values than that of the wild-type enzyme suggesting a decrease in the affinity of the enzyme
AB  - for its substrate. The mutant protein C54W showed significant changes in the CD spectra
AB  - vis-a-vis wild-type enzyme and had the lowest K(m)/K(cat) value among the mutants indicative
AB  - of changes in the secondary structure of the protein. The melting curves of the mutant
AB  - proteins overlapped that of the wild-type enzyme. Analysis of the K(cat) values in the context
AB  - of cocrystal structure suggests that the effect of Cys54 mutation is probably through the
AB  - perturbation of the local structure whereas reduced activity of the double mutant is
AB  - consistent with the substrate-assisted catalysis mechanism.
ER  -

TY  - JOUR
AU  - Acuna-Amador, L.
AU  - Primot, A.
AU  - Cadieu, E.
AU  - Roulet, A.
AU  - Barloy-Hubler, F.
TI  - Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
JO  - BMC Genomics
PY  - 2018
SP  - 54
EP  - 54
VL  - 19
AB  - BACKGROUND: Without knowledge of their genomic sequences, it is impossible to
AB  - make functional models of the bacteria that make up human and animal microbiota.
AB  - Unfortunately, the vast majority of publicly available genomes are only working
AB  - drafts, an incompleteness that causes numerous problems and constitutes a major
AB  - obstacle to genotypic and phenotypic interpretation. In this work, we began with
AB  - an example from the class Bacteroidia in the phylum Bacteroidetes, which is
AB  - preponderant among human orodigestive microbiota. We successfully identify the
AB  - genetic loci responsible for assembly breaks and misassemblies and demonstrate
AB  - the importance and usefulness of long-read sequencing and curated reannotation.
AB  - RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled
AB  - from massively parallel sequencing linearly correlates with genomic repeats of
AB  - the same or greater size than the reads. We also demonstrated that some of these
AB  - repeats, especially the long ones, correspond to misassembled loci in three
AB  - reference Porphyromonas gingivalis genomes marked as circularized (thus complete
AB  - or finished). We prove that even at modest coverage (30X), long-read resequencing
AB  - together with PCR contiguity verification (rrn operons and an integrative and
AB  - conjugative element or ICE) can be used to identify and correct the wrongly
AB  - combined or assembled regions. Finally, although time-consuming and
AB  - labor-intensive, consistent manual biocuration of three P. gingivalis strains
AB  - allowed us to compare and correct the existing genomic annotations, resulting in
AB  - a more accurate interpretation of the genomic differences among these strains.
AB  - CONCLUSIONS: In this study, we demonstrate the usefulness and importance of
AB  - long-read sequencing in verifying published genomes (even when complete) and
AB  - generating assemblies for new bacterial strains/species with high genomic
AB  - plasticity. We also show that when combined with biological validation processes
AB  - and diligent biocurated annotation, this strategy helps reduce the propagation of
AB  - errors in shared databases, thus limiting false conclusions based on incomplete
AB  - or misleading information.
ER  -

TY  - JOUR
AU  - Adaikpoh, B.I.
AU  - Dowd, S.E.
AU  - Stevens, D.C.
TI  - Draft Genome Sequence of Archangium sp. Strain Cb G35.
JO  - Genome Announcements
PY  - 2017
SP  - e01678
EP  - e01616
VL  - 5
AB  - In an effort to explore myxobacterial natural product biosynthetic pathways, the  draft genome
AB  - sequence of Archangium sp. strain Cb G35 has been obtained. Analysis
AB  - of the genome using antiSMASH predicts 49 natural product biosynthetic pathways.
AB  - This genome will contribute to the investigation of myxobacterial secondary
AB  - metabolite biosynthetic pathways.
ER  -

TY  - JOUR
AU  - Adam, E.
AU  - Muller, H.
AU  - Erlacher, A.
AU  - Berg, G.
TI  - Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens  and plant growth promoting abilities.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 61
EP  - 61
VL  - 11
AB  - The Serratia plymuthica strains 3Rp8 and 3Re4-18 are motile, Gram-negative, non-sporulating
AB  - bacteria. Strain 3Rp8 was isolated from the rhizosphere of
AB  - Brassica napus L. and strain 3Re4-18 from the endorhiza of Solanum tuberosum L.
AB  - Studies have shown in vitro activity against the soil-borne fungi Verticillium
AB  - dahliae Kleb., Rhizoctonia solani Kuhn, and Sclerotinia sclerotiorum. Here, we
AB  - announce and describe the complete genome sequence of S. plymuthica 3Rp8
AB  - consisting of a single circular chromosome of 5.5 Mb that encodes 4954
AB  - protein-coding and 108 RNA-only encoding genes and of S. plymuthica 3Re4-18
AB  - consisting of a single circular chromosome of 5.4 Mb that encodes 4845
AB  - protein-coding and 109 RNA-only encoding genes. The whole genome sequences and
AB  - annotations are available in NCBI under the locus numbers CP012096 and CP012097,
AB  - respectively. The genome analyses revealed genes putatively responsible for the
AB  - promising plant growth promoting and biocontrol properties including predicting
AB  - factors such as secretion systems, iron scavenging siderophores, chitinases,
AB  - secreted proteases, glucanases and non-ribosomal peptide synthetases, as well as
AB  - unique genomic islands.
ER  -

TY  - JOUR
AU  - Adam, Z.
AU  - Chen, Q.
AU  - Xu, R.
AU  - Diange, A.E.
AU  - Bromfield, E.S.
AU  - Tambong, J.T.
TI  - Draft Genome Sequence of Pseudomonas simiae Strain 2-36, an In Vitro Antagonist of Rhizoctonia solani and Gaeumannomyces graminis.
JO  - Genome Announcements
PY  - 2015
SP  - e01534
EP  - e01514
VL  - 3
AB  - Pseudomonas simiae 2-36, isolated from a field plot under long-term mineral fertilization,
AB  - exhibited strong in vitro antagonistic activities against
AB  - Rhizoctonia solani and Gaeumannomyces graminis. We report here the draft genome
AB  - sequence of Pseudomonas simiae 2-36, consisting of 6.4 Mbp with a 60.25% G+C
AB  - content and 5,790 predicted protein-coding sequences.
ER  -

TY  - JOUR
AU  - Adam, Z.
AU  - Tambong, J.T.
AU  - Chen, Q.
AU  - Lewis, C.T.
AU  - Levesque, C.A.
AU  - Xu, R.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain 2-92, a Biological Control Strain Isolated from a Field Plot Under Long-Term Mineral Fertilization.
JO  - Genome Announcements
PY  - 2014
SP  - e01121
EP  - e01113
VL  - 2
AB  - Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term  mineral
AB  - fertilization, strongly inhibits the growth of Fusarium graminearum,
AB  - Rhizoctonia solani, and Gaeumannomyces graminis. Here, we report the draft genome
AB  - sequence of Pseudomonas sp. strain 2-92.
ER  -

TY  - JOUR
AU  - Adam, Z.
AU  - Tambong, J.T.
AU  - Lewis, C.T.
AU  - Levesque, C.A.
AU  - Chen, W.
AU  - Bromfield, E.S.
AU  - Khan, I.U.
AU  - Xu, R.
TI  - Draft Genome Sequence of Pantoea ananatis Strain LMG 2665T, a Bacterial Pathogen  of Pineapple Fruitlets.
JO  - Genome Announcements
PY  - 2014
SP  - e00489
EP  - e00414
VL  - 2
AB  - We report the draft genome sequence of Pantoea ananatis LMG 2665(T), the bacterial causal
AB  - agent of pineapple fruitlet rot.
ER  -

TY  - JOUR
AU  - Adam, Z.
AU  - Whiteduck-Leveillee, K.
AU  - Cloutier, M.
AU  - Chen, W.
AU  - Lewis, C.T.
AU  - Levesque, C.A.
AU  - Topp, E.
AU  - Lapen, D.R.
AU  - Tambong, J.T.
AU  - Talbot, G.
AU  - Khan, I.U.
TI  - Draft Genome Sequence of Arcobacter cibarius Strain LMG21996T, Isolated from Broiler Carcasses.
JO  - Genome Announcements
PY  - 2014
SP  - e00034
EP  - e00014
VL  - 2
ER  -

TY  - JOUR
AU  - Adam, Z.
AU  - Whiteduck-Leveillee, K.
AU  - Cloutier, M.
AU  - Chen, W.
AU  - Lewis, C.T.
AU  - Levesque, C.A.
AU  - Topp, E.
AU  - Lapen, D.R.
AU  - Tambong, J.T.
AU  - Talbot, G.
AU  - Khan, I.U.
TI  - Draft genome sequences of two arcobacter strains isolated from human feces.
JO  - Genome Announcements
PY  - 2014
SP  - e00113
EP  - e00114
VL  - 2
AB  - Arcobacter species are members of the family Campylobacteraceae and are considered emerging
AB  - enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of
AB  - two Arcobacter strains isolated from human feces in an effort to provide further genetic
AB  - resources for understanding the pathogenic dynamics and diversity of this important genus.
ER  -

TY  - JOUR
AU  - Adam, Z.
AU  - Whiteduck-Leveillee, K.
AU  - Cloutier, M.
AU  - Tambong, J.T.
AU  - Chen, W.
AU  - Lewis, C.T.
AU  - Levesque, C.A.
AU  - Topp, E.
AU  - Lapen, D.R.
AU  - Talbot, G.
AU  - Khan, I.U.
TI  - Draft genome sequences of three arcobacter strains of pig and dairy cattle manure origin.
JO  - Genome Announcements
PY  - 2014
SP  - e00377
EP  - e00314
VL  - 2
AB  - The genus Arcobacter has been associated with human illness and fecal contamination by humans
AB  - and animals. Here, we announce the draft genome sequences
AB  - of three strains of Arcobacter species cultured from pig and dairy cattle manure
AB  - tanks. This information will assist in the characterization of features related
AB  - to host specificities and identify potential pathogenic health risks to humans
AB  - and animals.
ER  -

TY  - JOUR
AU  - Adamczyk-Poplawska, M.
AU  - Kondrzycka, A.
AU  - Urbanek, K.
AU  - Piekarowicz, A.
TI  - Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems.
JO  - Microbiology
PY  - 2003
SP  - 3311
EP  - 3319
VL  - 149
AB  - All known type I restriction and modification (R-M) systems of Escherichia coli and Salmonella
AB  - enterica belong to one of four discrete families: type
AB  - IA, IB, IC or ID. The classification of type I systems from a wide range
AB  - of other genera is mainly based on complementation and molecular evidence
AB  - derived from the comparison of the amino acid similarity of the
AB  - corresponding subunits. This affiliation was seldom based on the strictest
AB  - requirement for membership of a family, which depends on relatedness as
AB  - demonstrated by complementation tests. This paper presents data indicating
AB  - that the type I NgoAV R-M system from Neisseria gonorrhoeae, despite the
AB  - very high identity of HsdM and HsdR subunits with members of the type IC
AB  - family, does not show complementation with E. coli type IC R-M systems.
AB  - Sequence analysis of the HsdS subunit of several different potential type
AB  - IC R-M systems shows that the presence of different tetra-amino-acid
AB  - sequence repeats, e.g. TAEL, LEAT, SEAL, TSEL, is characteristic for type
AB  - IC R-M systems encoded by distantly related bacteria. The other regions of
AB  - the HsdS subunits potentially responsible for subunit interaction are also
AB  - different between a group of distantly related bacteria, but show high
AB  - similarity within these bacteria. Complementation between the NgoAV R-M
AB  - system and members of the EcoR124 R-M family can be restored by changing
AB  - the tetra-amino-acid repeat within the HsdS subunit. The authors propose
AB  - that the type IC family of R-M systems could consist of several
AB  - complementation subgroups whose specificity would depend on differences in
AB  - the conserved regions of the HsdS polypeptide.
ER  -

TY  - JOUR
AU  - Adamczyk-Poplawska, M.
AU  - Lower, M.
AU  - Piekarowicz, A.
TI  - Characterization of the NgoAXP: phase-variable type III restriction-modification system in Neisseria gonorrhoeae.
JO  - FEMS Microbiol. Lett.
PY  - 2009
SP  - 25
EP  - 35
VL  - 300
AB  - Methyltransferases associated with type III restriction-modification (RM) systems are
AB  - phase-variably expressed in a variety of pathogenic
AB  - bacteria. NgoAXP, the type III RM system encoded by Neisseria
AB  - gonorrhoeae, was characterized in this study. The cloned resngoAXP and
AB  - ngoAXPmod genes were expressed in Escherichia coli strains. The
AB  - restriction and modification activities of NgoAXP were confirmed in
AB  - vivo by the lambda phage restriction and modification test and in vitro
AB  - by the methylation of DNA substrates in the presence of
AB  - [methyl-3H]AdoMet. As in all known type III systems, the restriction
AB  - activity needed the presence of both genes, while the presence of the
AB  - ngoAXPmod gene was sufficient for DNA methylation. Following its
AB  - overexpression, the DNA methyltransferase M.NgoAXP was purified to
AB  - apparent homogeneity using metal affinity chromatography. The specific
AB  - sequence recognized by this enzyme was determined as a nonpalindromic
AB  - sequence: 5'-CCACC-3', in which the adenine residue is methylated. We
AB  - observed that in E. coli cells, the expression of the restriction
AB  - phenotype associated with NgoAXP switched randomly. This phase
AB  - variation was associated with the change in the number of
AB  - pentanucleotide repeats (5'-CCAAC/G-3') present at the 5'-end of the
AB  - coding region of the ngoAXPmod gene.
ER  -

TY  - JOUR
AU  - Adamczyk-Poplawska, M.
AU  - Lower, M.
AU  - Piekarowicz, A.
TI  - Deletion of One Nucleotide within the Homonucleotide Tract Present in the hsdS Gene Alters the DNA Sequence Specificity of Type I  Restriction-Modification System NgoAV.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6750
EP  - 6759
VL  - 193
AB  - As a result of a frameshift mutation, the hsdS locus of the NgoAV type IC restriction and
AB  - modification (RM) system comprises two genes, hsdS(NgoAV1)
AB  - and hsdS(NgoAV2). The specificity subunit, HsdS(NgoAV), the product of the
AB  - hsdS(NgoAV1) gene, is a naturally truncated form of an archetypal
AB  - specificity subunit (208 N-terminal amino acids instead of 410). The
AB  - presence of a homonucleotide tract of seven guanines (poly[G]) at the 3'
AB  - end of the hsdS(NgoAV1) gene makes the NgoAV system a strong candidate for
AB  - phase variation, i.e., stochastic addition or reduction in the guanine
AB  - number. We have constructed mutants with 6 guanines instead of 7 and
AB  - demonstrated that the deletion of a single nucleotide within the 3' end of
AB  - the hsdS(NgoAV1) gene restored the fusion between the hsdS(NgoAV1) and
AB  - hsdS(NgoAV2) genes. We have demonstrated that such a contraction of the
AB  - homonucleotide tract may occur in vivo: in a Neisseria gonorrhoeae
AB  - population, a minor subpopulation of cells appeared to have only 6
AB  - guanines at the 3' end of the hsdS(NgoAV1) gene. Escherichia coli cells
AB  - carrying the fused gene and expressing the NgoAVDelta RM system were able
AB  - to restrict lambda phage at a level comparable to that for the wild-type
AB  - NgoAV system. NgoAV recognizes the quasipalindromic interrupted sequence
AB  - 5'-GCA(N(8))TGC-3' and methylates both strands. NgoAVDelta recognizes DNA
AB  - sequences 5'-GCA(N(7))GTCA-3' and 5'-GCA(N(7))CTCA-3', although the latter
AB  - sequence is methylated only on the complementary strand within the
AB  - 5'-CTCA-3' region of the second recognition target sequence.
ER  -

TY  - JOUR
AU  - Adams, G.M.
TI  - Preventing autorestriction: A functional analysis of the pvuIIM and pvuIIW gene products.
JO  - Diss. Abstr.
PY  - 1996
SP  - 108
EP  - 108
VL  - 57
AB  - Restriction-modification systems must be regulated to prevent lethal
AB  - autorestriction of the bacterial DNA.  Little is known about this regulation.  This
AB  - dissertation examines several ways in which the restriction is controlled.  To date, the
AB  - PvuII restriction-modification system had been understood to contain three genes coding
AB  - for a DNA methyltransferase, a restriction endonuclease and a protein required for
AB  - endonuclease expression.  There is a fourth open reading frame (ORF) within and opposite
AB  - to the methyltransferase gene.  This ORF is transcribed  and has also been found in the
AB  - SmaI restriction-modification system.  The sequence of the PvuII ORF resembles that of
AB  - the PvuII endonuclease dimer interface.  Cells carrying clones of the ORF along with the
AB  - intact restriction modification systems had decreased ability to restrict.  The synthetic
AB  - peptide corresponding to this ORF inhibited renaturation of urea-denatured endonuclease in
AB  - a concentration-dependent manner.  The ORF, named pvuIIW may delay appearance of
AB  - endonuclease activity by increasing the concentration needed for dimerization, giving the
AB  - methyltransferase additional time to protect the bacterial DNA.  A kinetic anlaysis of PvuII
AB  - methyltransferase is the first reported for an N4-methylcytosine methyltransferase.  It
AB  - revealed an ordered Bi Bi mechanism, with the preferred order of substrate binding as
AB  - DNA first followed by S-adenosyl-L-methionine (AdoMet).  The enzyme was found to
AB  - have a kcat of 0.07s-1, KmAdoMet was 4.2 uM and the KmDNA was 0.58 uM.  When the
AB  - methyltransferase was preincubated with [3H-CH3]-AdoMet, the expected burst of product
AB  - formation resulted when DNA was added.  However, preincubation of the
AB  - methyltransferase with DNA gave a 3-5 second lag in product formation after the addition
AB  - of AdoMet.  This suggests that the enzyme forms a catalytically-incompetent, dead-end
AB  - complex with DNA in the absence of AdoMet.  The methyltransferase was also found to
AB  - bind two molecules of the substrate AdoMet, each with a distinct affinity.  A kinetic model
AB  - was proposed to explain formation of the dead-end complex with DNA in the absence of
AB  - AdoMet, as well as a role for the second bound molecule of AdoMet.
ER  -

TY  - JOUR
AU  - Adams, G.M.
AU  - Blumenthal, R.M.
TI  - The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine.
JO  - Biochemistry
PY  - 1997
SP  - 8284
EP  - 8292
VL  - 36
AB  - Earlier studies have shown that PvuII methyltransferase is monomeric and transfers a methyl
AB  - group from S-adenosyl-L-methionine to cytosine, generating N4-methylcytosine in duplex
AB  - 5'-CAGCTG-3' DNA.  This study examines the interactions between PvuII methyltransferase and
AB  - AdoMet.  Trypsin preferentially cleaved the protein into two large fragments, with initial
AB  - cleavages after Arg183 and Lys186.  UV-mediated photochemical labeling with [3H-CH3]AdoMet,
AB  - followed by trypsin digestion, revealed that both large fragments of the protein were labeled.
AB  - Rapid gel filtration confirmed that each molecule of the intact enzyme bound two molecules of
AB  - AdoMet (net Kd = 9.3 microM).  When PvuII methyltransferase was preincubated with a range of
AB  - [3H-CH3}AdoMet concentrations, bursts of product formation resulted upon DNA addition.  These
AB  - data indicate that PvuII methyltransferase is catalytically competent with one and with two
AB  - bound molecules of AdoMet.  These results, together with those from earlier studies, suggest
AB  - possible roles for the second molecule of AdoMet.
ER  -

TY  - JOUR
AU  - Adams, G.M.
AU  - Blumenthal, R.M.
TI  - Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association.
JO  - Gene
PY  - 1995
SP  - 193
EP  - 199
VL  - 157
AB  - The PvuII restriction-modification system has been found to contain three genes which code for
AB  - a DNA methyltransferase (MTase), a restriction endonuclease (ENase) and a small protein
AB  - required for expression of the ENase-encoding gene.  In addition, there is a small open
AB  - reading frame (ORF) within and opposite to the MTase-encoding gene.  The region containing
AB  - this ORF is transcribed, and the ORF has an excellent Shine-Dalgarno sequence with an ATA
AB  - start codon.  A closely related ORF is present in the SmaI system.  The 28-amino-acid (aa)
AB  - predicted peptide from the PvuII ORF resembles a region of the PvuII ENase at the dimer
AB  - interface.  We have cloned this ORF, giving it an ATG start codon and putting it under the
AB  - control of an inducible promoter: induction leads to a slight but significant decrease in
AB  - restriction of bacteriophage lambda.  We also have obtained the 28-aa synthetic peptide, and
AB  - are exploring the possibility that it modulates ENase subunit association.  While this peptide
AB  - has no detectible effect on dimeric PvuII ENase, it inhibits renaturation of urea-denatured
AB  - ENase in a concentration-dependent manner.  The ORF may represent an additional safeguard
AB  - during establishment of the PvuII restriction-modification system in a new host cell, helping
AB  - to delay the appearance of active ENase dimers, while the MTase accumulates and protects the
AB  - host chromosome.
ER  -

TY  - JOUR
AU  - Adams, G.M.
AU  - Blumenthal, R.M.
TI  - What is the significance of the internal duplication in the PvuII DNA methyltransferase?
JO  - FASEB J.
PY  - 1995
SP  - A1399
EP  - A1399
VL  - 9
AB  - The DNA methyltransferases (MTases) from type II restriction-modification systems are
AB  - suggested to have evolved via a gene duplication mechanism. The evidence for this varies in
AB  - quality and, in most MTases, any duplication which may have occurred has been obscured by
AB  - divergence. The MTase gene from the PvuII restriction-modification system was previously
AB  - cloned, sequenced and overexpressed in this laboratory. It contains an unusually clear
AB  - sequence duplication, consistent with earlier gene duplication. We have studied the
AB  - proteolytic susceptibility of PvuII MTase, and its interaction with the substrate methyl donor
AB  - S-adenosylmethionine (AdoMet), to investigate the possibility that this monomeric MTase is
AB  - functionally symmetrical. We have found that trypsin preferentially cleaves in the predicted
AB  - hinge region between the sequence repeats, and that both parts of the protein can be
AB  - crosslinked by UV irradiation to [3H-CH3]AdoMet.
ER  -

TY  - JOUR
AU  - Adams, K.L.
AU  - Clements, M.J.
AU  - Vaughn, J.C.
TI  - The Peperomia mitochondrial coxI group I intron: Timing of horizontal transfer and subsequent evolution of the intron.
JO  - J. Mol. Evol.
PY  - 1998
SP  - 689
EP  - 696
VL  - 46
AB  - The Peperomia polybotrya coxI gene intron is the only currently reported group I intron in a
AB  - vascular plant mitochondrial genome and it likely originated by horizontal transfer from a
AB  - fungal donor.  We provide a clearer picture of the horizontal transfer and a portrayal of the
AB  - evolution of the group I intron since it was gained by the Peperomia mitochondrial genome.
AB  - The intron was transferred recently in terms of plant evolution, being restricted to the
AB  - single genus Peperomia among the order Piperales.  Additional support is presented for the
AB  - suggestion that a recombination/repair mechanism was used by the intron for integration into
AB  - the Peperomia mitochondrial genome, as a perfect 1:1 correspondence exists between the
AB  - intron's presence in a species and the presence of divergent nucleotide markers flanking the
AB  - intron insertion site.  Sequencing of coxI introns from additional Peperomia species revealed
AB  - that several mutations have occurred in the intron since the horizontal transfer, but sequence
AB  - alterations have not caused frameshifts or created stop codons in the intronic open reading
AB  - frame.  In addition, two coxI pseudogenes in Peperomia cubensis were discovered that lack a
AB  - large region of coxI exon 2 and contain a truncated version of the group I intron that likely
AB  - cannot be spliced out.
ER  -

TY  - JOUR
AU  - Adams, M.D. et al.
TI  - The genome sequence of Drosophila melanogaster.
JO  - Science
PY  - 2000
SP  - 2185
EP  - 2195
VL  - 287
AB  - The fly Drosophila melanogaster is one of the most intensively studied organisms in biology
AB  - and serves as a model system for the investigation of many developmental and cellular
AB  - processes common to higher eukaryotes, including humans. We have determined the nucleotide
AB  - sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila
AB  - genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based
AB  - sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under
AB  - way to close the remaining gaps; however, the sequence is of sufficient accuracy and
AB  - contiguity to be declared substantially complete and to support an initial analysis of genome
AB  - structure and preliminary gene annotation and interpretation. The genome encodes approximately
AB  - 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with
AB  - comparable functional diversity.
ER  -

TY  - JOUR
AU  - Adams, M.D.
AU  - Chan, E.R.
AU  - Molyneaux, N.D.
AU  - Bonomo, R.A.
TI  - Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii.
JO  - Antimicrob. Agents Chemother.
PY  - 2010
SP  - 3569
EP  - 3577
VL  - 54
AB  - Multidrug resistance has emerged as a significant concern with infections
AB  - caused by Acinetobacter baumannii. Ample evidence supports the involvement
AB  - of mobile genetic elements in the transfer of antibiotic resistance genes,
AB  - but the extent of variability and the rate of genetic change associated
AB  - with the acquisition of antibiotic resistance have not been studied in
AB  - detail. Whole-genome sequence analysis of six closely related clinical
AB  - isolates of A. baumannii, including four from the same hospital, revealed
AB  - extensive divergence of the resistance genotype that correlated with
AB  - observed differences in antimicrobial susceptibility. Resistance genes
AB  - associated with insertion sequences, plasmids, and a chromosomal
AB  - resistance gene island all showed variability. The highly dynamic
AB  - resistance gene repertoire suggests rapid evolution of drug resistance.
ER  -

TY  - JOUR
AU  - Adams, M.D.
AU  - Goglin, K.
AU  - Molyneaux, N.
AU  - Hujer, K.M.
AU  - Lavender, H.
AU  - Jamison, J.J.
AU  - MacDonald, I.J.
AU  - Martin, K.M.
AU  - Russo, T.
AU  - Campagnari, A.A.
AU  - Hujer, A.M.
AU  - Bonomo, R.A.
AU  - Gill, S.R.
TI  - Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii.
JO  - J. Bacteriol.
PY  - 2008
SP  - 8053
EP  - 8064
VL  - 190
AB  - The recent emergence of multidrug resistance (MDR) in Acinetobacter
AB  - baumannii has raised concern in health care settings worldwide. In order
AB  - to understand the repertoire of resistance determinants and their
AB  - organization and origins, we compared the genome sequences of three MDR
AB  - and three drug-susceptible A. baumannii isolates. The entire MDR phenotype
AB  - can be explained by the acquisition of discrete resistance determinants
AB  - distributed throughout the genome. A comparison of closely related MDR and
AB  - drug-susceptible isolates suggests that drug efflux may be a less
AB  - significant contributor to resistance to certain classes of antibiotics
AB  - than inactivation enzymes are. A resistance island with a variable
AB  - composition of resistance determinants interspersed with transposons,
AB  - integrons, and other mobile genetic elements is a significant but not
AB  - universal contributor to the MDR phenotype. Four hundred seventy-five
AB  - genes are shared among all six clinical isolates but absent from the
AB  - related environmental species Acinetobacter baylyi ADP1. These genes are
AB  - enriched for transcription factors and transporters and suggest
AB  - physiological features of A. baumannii that are related to adaptation for
AB  - growth in association with humans.
ER  -

TY  - JOUR
AU  - Adams, R.L.P.
TI  - Eukaryotic DNA methyltransferases - structure and function.
JO  - Bioessays
PY  - 1995
SP  - 139
EP  - 145
VL  - 17
AB  - Methylation of DNA plays an important role in the control of gene expression in higher
AB  - eukaryotes. This is largely achieved by the packaging of methylated DNA into chromatin
AB  - structures that are inaccessible to transcription factors and other proteins. Methylation
AB  - involves the addition of a methyl group to the 5-position of the cytosine base in DNA, a
AB  - reaction catalysed by a DNA (cytosine-5) methyltransferase. This reaction occurs in nuclear
AB  - replication foci where the chromatin structure is loosened for replication, thereby allowing
AB  - access to methyltransferases. Partly as a result of their recognizing the presence of a
AB  - methylcytosine on the parental strand following replication, these large enzymes are able to
AB  - maintain the distribution of methyl groups along the DNA of somatic cells and, thereby,
AB  - maintain tissue-specific patterns of gene expression.
ER  -

TY  - JOUR
AU  - Adams, R.L.P.
AU  - Pradhan, S.
AU  - Johnson, C.A.
AU  - Lindsay, H.
AU  - Shek, E.W.L.
AU  - Jenkins, G.I.
AU  - Urwin, N.A.R.
TI  - Plant methyltransferases and their targets in the plant genome.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 95
EP  - 108
VL  - 0
AB  - In addition to the methylation of cytosine in some CG dinucleotides, plant genomes contain
AB  - 5-methylcytosine (a cytosine with a methyl group in place of the hydrogen at position 5) in
AB  - the trinucleotide sequence mCNG, where N is reportedly any of the four common DNA bases.
AB  - 5-Methylcytosine has also been found in nonsymmetrical sequences in transgenes, but there is
AB  - no evidence in plants for the N-4 methylcytosine that is found in some prokaryotes.  We have
AB  - shown that CG and CNG methylation are carried out by different methyltransferases, and one
AB  - possible consequence of this is that the two reactions could be independently regulated.  This
AB  - would allow the methylation of CG and CNG sequences to have unrelated functions in the plant
AB  - cell, although to date there are no data to support this suggestion.
ER  -

TY  - JOUR
AU  - Adegboye, M.F.
AU  - Lobb, B.
AU  - Babalola, O.O.
AU  - Doxey, A.C.
AU  - Ma, K.
TI  - Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e00632
EP  - e00618
VL  - 6
AB  - We report here the draft genome sequences of two novel strains of Streptomyces (NWU339 and
AB  - NWU49) isolated from South African rhizosphere soils. Both strains
AB  - were found to possess strong cellulolytic activity and contain numerous putative
AB  - cellulase genes. Both genomes possess benzoate degradation pathways, while NWU49
AB  - contains the genomic potential for enediyne biosynthesis.
ER  -

TY  - JOUR
AU  - Adelskov, J.
AU  - Patel, B.K.
TI  - Draft Genome Sequence of Bacillus subtilis Strain D7XPN1, Isolated from Commercial Bioreactor-Degrading Food Waste.
JO  - Genome Announcements
PY  - 2014
SP  - e00989
EP  - e00914
VL  - 2
AB  - The analysis of the 4.1-Mb draft genome sequence of a moderately thermophilic, heterotrophic,
AB  - and facultatively anaerobic bacterium, Bacillus subtilis strain
AB  - D7XPN1, identified genes for a range of enzymes with potential in the
AB  - biodegradation of food waste, a property consistent with the ecological habitat
AB  - of the isolate.
ER  -

TY  - JOUR
AU  - Adelskov, J.
AU  - Patel, B.K.
TI  - Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading,  Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial  Bioreactor Degrading Food Waste.
JO  - Genome Announcements
PY  - 2015
SP  - e01484
EP  - e01414
VL  - 3
AB  - The analysis of the ~5.8-Mb draft genome sequence of a moderately thermophilic, heterotrophic,
AB  - facultative anaerobic bacterium, Paenibacillus strain P1XP2,
AB  - identified genes for enzymes with the potential for degrading complex food
AB  - wastes, a property consistent with the ecological habitat of the isolate.
ER  -

TY  - JOUR
AU  - Adelskov, J.
AU  - Patel, B.K.
TI  - Draft Genome Sequence of Cellulosilyticum sp. I15G10I2, a Novel Bacterium Isolated from a Coal Seam Gas Water Treatment Pond.
JO  - Genome Announcements
PY  - 2017
SP  - e01616
EP  - e01616
VL  - 5
AB  - Cellulosilyticum sp. strain I15G10I2 was isolated from a coal seam gas water treatment pond at
AB  - the Spring Gully water treatment facility, Roma, Queensland,
AB  - Australia. Analysis of the genome of 4,489,861 bp and G+C content of 35.23%
AB  - revealed that strain I15G10I2 shared limited similarity to members of the genus
AB  - Cellulosilyticum, family Lachnospiraceae.
ER  -

TY  - JOUR
AU  - Adelskov, J.
AU  - Patel, B.K.C.
TI  - Draft Genome Sequence of the 1,2-Dichloroethane-Utilizing Micrococcus sp. Strain  NDB3Y10, Isolated from an Australian Bore Well Producing Coal Seam Gas.
JO  - Genome Announcements
PY  - 2017
SP  - e00255
EP  - e00217
VL  - 5
AB  - Micrococcus luteus strain NDB3Y10, which utilizes 1,2-dichloroethane as a carbon  source, was
AB  - isolated from a bore well that produces coal seam gas. The draft
AB  - genome size of the strain was 2.49 Mb with a G+C content of 72.97%. Genes
AB  - involved in the metabolism of halogenated substrates, including halogenated
AB  - hydrocarbons, were identified.
ER  -

TY  - JOUR
AU  - Adelskov, J.
AU  - Patel, B.K.C.
TI  - Draft Genome Sequence of Microbacterium sp. TNHR37B Isolated from a Heated Aquifer Bore Well of the Great Artesian Basin, Australia.
JO  - Genome Announcements
PY  - 2017
SP  - e00251
EP  - e00217
VL  - 5
AB  - Microbacterium sp. strain TNHR37B was isolated from a geothermal bore well sample (50 degrees
AB  - C) collected from a region of coal seam gas extraction activities.
AB  - The 3.5-Mb genome with a G+C content of 69.9% contained unique genes, and a low
AB  - similarity value for average nucleotide identity using BLAST was observed with
AB  - the available 73 Microbacterium sp. genomes.
ER  -

TY  - JOUR
AU  - Adeniji, J.A.
AU  - Faleye, T.O.C.
AU  - Adewumi, O.M.
AU  - Olayinka, O.A.
AU  - Donbraye, E.
AU  - Oluremi, B.
AU  - George, U.E.
AU  - Arowolo, O.A.
AU  - Omoruyi, E.C.
AU  - Ifeorah, M.I.
AU  - Akande, A.
TI  - Draft Genome Sequence of Mycoplasma arginini Strain NGR_2017.
JO  - Genome Announcements
PY  - 2018
SP  - e00577
EP  - e00518
VL  - 6
AB  - We present the draft genome of Mycoplasma arginini strain NGR_2017. This strain was recovered
AB  - in Nigeria from cell culture in 2017. The assembly contains 620,555
AB  - bp in 12 contigs. It contains 561 coding sequences, 34 RNAs (29 tRNAs, 4 rRNAs,
AB  - and 1 transfer-messenger RNA [tmRNA]), and a >26-kb integrative and conjugative
AB  - element.
ER  -

TY  - JOUR
AU  - Adessi, A.
AU  - Spini, G.
AU  - Presta, L.
AU  - Mengoni, A.
AU  - Viti, C.
AU  - Giovannetti, L.
AU  - Fani, R.
AU  - De Philippis, R.
TI  - Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 24
EP  - 24
VL  - 11
AB  - Rhodopseudomonas palustris strain 42OL was isolated in 1973 from a sugar refinery waste
AB  - treatment pond. The strain has been prevalently used for hydrogen
AB  - production processes using a wide variety of waste-derived substrates, and
AB  - cultured both indoors and outdoors, either freely suspended or immobilized. R.
AB  - palustris 42OL was suitable for many other applications and capable of growing in
AB  - very different culturing conditions, revealing a wide metabolic versatility. The
AB  - analysis of the genome sequence allowed to identify the metabolic pathways for
AB  - hydrogen and poly-beta-hydroxy-butyrate production, and confirmed the ability of
AB  - using a wide range of organic acids as substrates.
ER  -

TY  - JOUR
AU  - Adimpong, D.B.
AU  - Sorensen, K.I.
AU  - Nielsen, D.S.
AU  - Thorsen, L.
AU  - Rasmussen, T.B.
AU  - Derkx, P.M.
AU  - Jespersen, L.
TI  - Draft Whole-Genome Sequence of Bacillus sonorensis Strain L12, a Source of Nonribosomal Lipopeptides.
JO  - Genome Announcements
PY  - 2013
SP  - e0009713
EP  - e0009713
VL  - 1
AB  - The Bacillus sonorensis L12 draft genome sequence is approximately 4,647,754 bp in size with a
AB  - G+C content of 45.2%. Over 86% of the genome contains
AB  - protein-encoding genes, including several gene clusters for de novo biosynthesis
AB  - of the nonribosomal lipopeptides iturin, bacitracin, and fengycin, which could
AB  - mean that the strain exhibits antifungal effects.
ER  -

TY  - JOUR
AU  - Adlakha, N.
AU  - Ritturaj, K.H.
AU  - Rajagopal, R.
AU  - Yazdani, S.S.
TI  - Draft Genome Sequence of the Paenibacillus sp. Strain ICGEB2008 (MTCC 5639) Isolated from the Gut of Helicoverpa armigera.
JO  - Genome Announcements
PY  - 2013
SP  - e00026
EP  - e00012
VL  - 1
AB  - Paenibacillus sp. strain ICGEB2008 (MTCC 5639) is a Gram-positive cellulolytic bacterium,
AB  - isolated from the gut of Helicoverpa armigera. Here, we report the draft genome sequence of
AB  - Paenibacillus sp. ICGEB2008. The annotation of the ~5.7-Mb sequence indicated a cluster of
AB  - genes related to the glycosyl hydrolase family and the butanediol biosynthesis pathway.
ER  -

TY  - JOUR
AU  - Adler, S.P.
AU  - Nathans, D.
TI  - Studies of SV40 DNA: V. Conversion of circular to linear SV40 DNA by restriction endonuclease from Escherichia coli B.
JO  - Biochim. Biophys. Acta
PY  - 1973
SP  - 177
EP  - 188
VL  - 299
AB  - Restriction endonuclease preparations from Escherichia coli strains B, K(P1)
AB  - and B(RTF2) have been found to cleave SV40 DNA.  Purified E. coli B restriction
AB  - endonuclease converted covalently closed circular SV40 DNA to predominantly
AB  - full length linear molecules with intact single strands; open circular
AB  - molecules were intermediates in the reaction.  After denaturation and
AB  - renaturation, the linear products formed circular duplexes with high
AB  - efficiency, indicating that individual SV40 DNA molecules had been cleaved by
AB  - the B enzyme at different sites.  Consistent with this conclusion was the
AB  - finding that digestion of the linear product with restriction endonuclease from
AB  - Hemophilus influenzae yielded DNA fragments indistinguishable
AB  - electrophoretically from those found after digestion of circular SV40 DNA with
AB  - the same enzyme.
ER  -

TY  - JOUR
AU  - Adnani, N.
AU  - Braun, D.R.
AU  - McDonald, B.R.
AU  - Chevrette, M.G.
AU  - Currie, C.R.
AU  - Bugni, T.S.
TI  - Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01369
EP  - e01316
VL  - 5
AB  - Micromonospora sp. strain WMMB235 was isolated in 2011 off the coast of the Florida Keys, USA,
AB  - from a marine ascidian as part of an ongoing drug discovery
AB  - project. Analysis of the ~7.1-Mb genome provides insight into this strain's
AB  - biosynthetic potential, means of regulation, and response to coculturing
AB  - conditions.
ER  -

TY  - JOUR
AU  - Adnani, N.
AU  - Braun, D.R.
AU  - McDonald, B.R.
AU  - Chevrette, M.G.
AU  - Currie, C.R.
AU  - Bugni, T.S.
TI  - Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e01406
EP  - e01416
VL  - 4
AB  - The Rhodococcus strain WMMA185 was isolated from the marine sponge Chondrilla nucula as part
AB  - of ongoing drug discovery efforts. Analysis of the 4.44-Mb genome
AB  - provides information regarding interspecies interactions as pertains to
AB  - regulation of secondary metabolism and natural product biosynthetic potentials.
ER  -

TY  - JOUR
AU  - Adriaenssens, E.M.
AU  - Guerrero, L.D.
AU  - Makhalanyane, T.P.
AU  - Aislabie, J.M.
AU  - Cowan, D.A.
TI  - Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e00212
EP  - e00214
VL  - 2
AB  - Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic
AB  - hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An
AB  - analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation
AB  - processes at low temperatures and potentially aid in bioremediation applications.
ER  -

TY  - JOUR
AU  - Advani, S.
AU  - Mishra, P.
AU  - Dubey, S.
AU  - Thakur, S.
TI  - Categoric prediction of metal ion mechanisms in the active sites of 17 select type II restriction endonucleases.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2010
SP  - 177
EP  - 179
VL  - 402
AB  - Recently determined crystal structures of type II restriction endonucleases have produced a
AB  - plethora of information on the basis for
AB  - target site sequence selectivity. The positioning and role of metal
AB  - ions in DNA recognition sites might reflect important properties of
AB  - protein-DNA interaction. Although acidic and basic groups in the active
AB  - sites can be identified, and in some cases divalent-metal binding sites
AB  - delineated, a convincing picture clarifying the way in which the
AB  - attacking hydroxide ion is generated, and the leaving group stabilized,
AB  - has not been elucidated for any of the enzymes. We have examined the
AB  - interatomic distances between metal ions and proposed key catalytic
AB  - residues in the binding sites of seventeen type II restriction
AB  - endonucleases whose crystal structures are documented in literature.
AB  - The summary and critical evaluation of structural assignments and
AB  - predictions made earlier have been useful to group these enzymes. All
AB  - the enzymes used for this study have been categorized on the basis of
AB  - the number of metal ions identified in their crystal structures. Among
AB  - 17 experimentally characterized (not putative) type II REases, whose
AB  - apparently full-length sequences are available in REBASE, we predict 8
AB  - (47%) to follow the single metal ion mechanism, 5 to follow the two
AB  - metal ion mechanism, 2, the three metal ion mechanism, 1, the four
AB  - metal ion mechanism and 1 the six metal ion mechanism.
ER  -

TY  - JOUR
AU  - Advani, S.
AU  - Roy, K.B.
TI  - Properties and secondary structure analysis of BanI endonuclease: identification of putative active site.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2000
SP  - 11
EP  - 16
VL  - 279
AB  - Biochemical properties of Type II restriction enzyme BanI were characterized. Kinetic
AB  - parameters were evaluated and an enhancement of rate was observed when the recognition site
AB  - was located in a more central position in the substrate, suggesting that BanI locates its
AB  - recognition site by a sliding mechanism. As BanI has three cysteine residues in its primary
AB  - sequence, the effect of thiol inhibitors on BanI activity was also studied. Partial inhibition
AB  - was observed only at a very high concentration of the inhibitor indicating that cysteine
AB  - residues are not directly involved in catalysis. The gel electrophoretic mobility shift assay
AB  - demonstrated specific complex formation between BanI and the DNA substrate in the presence of
AB  - poly dI-dC and Mg(2+). A secondary structure analysis and comparison with EcoRI and BamHI
AB  - crystal structure revealed a putative active site similar to that seen in BamHI but different
AB  - in the order in which the catalytic domain (central beta-sheet) and recognition domain
AB  - (adjacent alpha-helix) were arranged in the protein.
ER  -

TY  - JOUR
AU  - Advani, S.
AU  - Roy, K.B.
TI  - BanI restriction endonuclease binds in the major groove of DNA: An inhibition kinetic study using substrates with mismatch basepairs.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2000
SP  - 35
EP  - 40
VL  - 269
AB  - Structural information on BanI-DNA interaction was obtained from simple inhibition kinetic
AB  - assays using altered substrates. Self-complementary 13-mer oligodeoxynucleotides with or
AB  - without mismatch basepairs in the BanI recognition sequence (GGPyPuCC) were synthesized. UV
AB  - melting curves and CD spectra indicated double-stranded B-DNA structure for all the oligomers.
AB  - Among the seven oligomers with recognition sequences, GGTACC, GGTGCC, GGTATC, GGCACC, GGAGCC,
AB  - GGTAAC, and GGATCC, only the first two were cleaved with BanI. Kinetics of BanI cleavage of
AB  - the native substrate was inhibited competitively by all of the other oligomers except the one
AB  - with sequence GGCACC. From inhibition kinetic analysis in presence of a fixed concentration of
AB  - the inhibitor, apparent K(m) and K(I) were determined. The data were analyzed in the context
AB  - of alterations made in the hydrogen bonding potential in the major and minor groove of DNA
AB  - within the recognition sequence due to basepair mismatches. Such analyses led to the
AB  - conclusion that BanI, like BamHI, binds in the major groove and the central thymines make
AB  - important contact with the protein.
ER  -

TY  - JOUR
AU  - Aeling, K.A.
AU  - Steffen, N.R.
AU  - Johnson, M.
AU  - Hatfield, G.W.
AU  - Lathrop, R.H.
AU  - Senear, D.F.
TI  - DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions.
JO  - IEEE/ACM Trans. Comput. Biol. Bioinform.
PY  - 2007
SP  - 117
EP  - 125
VL  - 4
AB  - Proteins that bind to specific locations in genomic DNA control many basic cellular functions.
AB  - Proteins detect their binding sites using
AB  - both direct and indirect recognition mechanisms. Deformation energy,
AB  - which models the energy required to bend DNA from its native shape to
AB  - its shape when bound to a protein, has been shown to be an indirect
AB  - recognition mechanism for one particular protein, Integration Host
AB  - Factor (IHF). This work extends the analysis of deformation to two
AB  - other DNA-binding proteins, CRP and SRF, and two enclonucleases, I-Crel
AB  - and I-Ppol. Known binding sites for all five proteins showed
AB  - statistically significant differences in mean deformation energy as
AB  - compared to random sequences. Binding sites for the three DNA-binding
AB  - proteins and one of the enclonucleases had mean deformation energies
AB  - lower than random sequences. Binding sites for I-Ppol had mean
AB  - deformation energy higher than random sequences. Classifiers that were
AB  - trained using the deformation energy at each base pair step showed good
AB  - cross-validated accuracy when classifying unseen sequences as binders
AB  - or nonbinders. These results support DNA deformation energy as an
AB  - indirect recognition mechanism across a wider range of DNA-binding
AB  - proteins. Deformation energy may also have a predictive capacity for
AB  - the underlying catalytic mechanism of DNA-binding enzymes.
ER  -

TY  - JOUR
AU  - Aertsen, A.
AU  - Mebrhatu, M.T.
AU  - Michiels, C.W.
TI  - Activation of the Salmonella Typhimurium Mrr protein.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2008
SP  - 435
EP  - 439
VL  - 367
AB  - The Mrr protein of Escherichia coli K12 is a cryptic type IV restriction endonuclease with
AB  - specificity for methylated DNA. Recently
AB  - it was discovered that endogenous activation of E. coli Mrr could be
AB  - triggered by high pressure stress, resulting in the generation of
AB  - double strand breaks in the host chromosome and concomitant induction
AB  - of the SOS response. In this report we focused on Mrr activity of
AB  - Salmonella Typhimurium LT2, and although we surprisingly found no
AB  - evidence of high pressure induced activation, a large number of
AB  - constitutively activated Mrr mutants could be isolated when the mrr
AB  - gene was routinely cloned in an expression vector. Analysis of several
AB  - spontaneous mutants revealed different single mutations that rendered
AB  - the Mrr protein constitutively active. Moreover, a spontaneous S.
AB  - Typhimurium mutant could be isolated that displayed an increased basal
AB  - SOS induction because of a point mutation in the chromosomal mrr gene.
AB  - Based on these findings the physiological role of Mrr in the cell is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Aertsen, A.
AU  - Michiels, C.W.
TI  - Mrr instigates the SOS response after high pressure stress in Escherichia coli.
JO  - Mol. Microbiol.
PY  - 2005
SP  - 1381
EP  - 1391
VL  - 58
AB  - The bacterial SOS response is not only a vital reply to DNA damage but also constitutes an
AB  - essential mechanism for the generation of genetic
AB  - variability that in turn fuels adaptation and resistance development in
AB  - bacterial populations. Despite the extensive depiction of the SOS regulon
AB  - itself, its activation by stresses different from typical DNA damaging
AB  - treatments remains poorly characterized. Recently, we reported the RecA-
AB  - and LexA-dependent induction of the SOS response in Escherichia coli
AB  - MG1655 after exposure to high hydrostatic pressure (HP, approximately 100
AB  - MPa), a physical stress of which the cellular effects are not well known.
AB  - We now found this HP mediated SOS response to depend on RecB and not on
AB  - RecF, which is a strong indication for the involvement of double strand
AB  - breaks. As the pressures used in this work are thermodynamically unable to
AB  - break covalent bonds in DNA, we hypothesized the involvement of a cellular
AB  - function or pathway in the formation of this lesion. A specialized
AB  - screening allowed us to identify the cryptic type IV restriction
AB  - endonuclease Mrr as the final effector of this pathway. The HP SOS
AB  - response and its corresponding phenotypes could be entirely attributed to
AB  - the HP triggered activation of Mrr restriction activity. Several
AB  - spontaneously occurring alleles of mrr, incapable of triggering the
AB  - HP-induced SOS response, were isolated and characterized. These results
AB  - provide evidence for a specific pathway that transmits the perception of
AB  - HP stress to induction of the SOS response and support a role for Mrr in
AB  - bacterial stress physiology.
ER  -

TY  - JOUR
AU  - Afouda, P.
AU  - Dubourg, G.
AU  - Labas, N.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Agrococcusbaldri Strain Marseille-P2731.
JO  - Genome Announcements
PY  - 2017
SP  - e00015
EP  - e00017
VL  - 5
AB  - Agrococcus baldri strain Marseille-P2731 was isolated from a Siberian permafrost  specimen
AB  - dated around 10 million years. The 3,021,022-bp genome of strain
AB  - Marseille-P2731, with a 71.82% G+C content, includes 2,844 protein-coding genes,
AB  - 72 toxin/antitoxin modules, nine bacteriocin-encoding genes, and 1,266 genes
AB  - associated with mobilome.
ER  -

TY  - JOUR
AU  - Agarkova, I.V.
AU  - Dunigan, D.D.
AU  - Van Etten, J.L.
TI  - Virion-associated restriction endonucleases of Chloroviruses.
JO  - J. Virol.
PY  - 2006
SP  - 8114
EP  - 8123
VL  - 80
AB  - Chloroviruses are large, double-stranded-DNA, plaque-forming viruses that infect certain
AB  - eukaryotic chlorella-like green algae. The
AB  - prototype of the genus is Paramecium bursaria chlorella virus 1
AB  - (PBCV-1). Chlorovirus genomes contain various amounts of methylated
AB  - nucleotides due to virus-encoded DNA methyltransferases (NITases);
AB  - about 25% of the MTases are associated with companion DNA site-specific
AB  - (restriction) endonucleases (REases). These enzymes constitute virally
AB  - encoded restriction-modification (R/M) systems. Although several of the
AB  - chlorovirus R/M systems are characterized, their biological functions
AB  - are unknown. The PBCV-1 proteome reveals that two virus-encoded REases,
AB  - but not their companion MTases, are virion associated, suggesting that
AB  - viral REases might help degrade the host DNA early in infection. To
AB  - test this hypothesis, host chromosomal DNA from PBCV-1-infected cells
AB  - was examined by pulsed-field gel electrophoresis. Initiation of host
AB  - chromosomal DNA degradation occurred within 5 min postinfection (p.i.).
AB  - The DNA degradation was insensitive to protein synthesis inhibitors or
AB  - UV inactivation of virus particles, consistent with the agent being a
AB  - small protein associated with the virion. Nuclease activities,
AB  - including those of the two predicted REases and an uncharacterized
AB  - general nuclease(s), were detected in disrupted PBCV-1 particles. The
AB  - general nuclease(s) degraded both host and viral DNAs in vitro,
AB  - although the viral DNA was not degraded in vivo, suggesting
AB  - differential intracellular trafficking of the virion-associated
AB  - nucleases. Infection with chloroviruses lacking an R/M system(s)
AB  - resulted in either delayed host chromosomal DNA degradation or no
AB  - detectable host chromatin changes. These immediate-early events
AB  - associated with chlorovirus infections may facilitate rapid switching
AB  - of the host transcriptional apparatus to viral transcription, which
AB  - begins within 5 to 10 min p.i.
ER  -

TY  - JOUR
AU  - Agarwal, B.
AU  - Agarwala, N.
AU  - Saikia, S.
AU  - Sarkar, S.
AU  - Ahmed, G.
TI  - Draft Genome Sequence of a Polymyxin B-Resistant Sequence Type 195 Clinical Isolate of Acinetobacter baumannii from India.
JO  - Genome Announcements
PY  - 2018
SP  - e00031
EP  - e00018
VL  - 6
AB  - Acinetobacter baumannii has emerged as a troublesome nosocomial pathogen worldwide. We report
AB  - here the draft genome sequence of polymyxin B-resistant
AB  - sequence type 195 (ST195) A. baumannii strain GU71, isolated from a tertiary care
AB  - hospital in the city of Guwahati, Assam, India.
ER  -

TY  - JOUR
AU  - Agarwal, L.
AU  - Purohit, H.J.
TI  - Genome Sequence of Rhizobium lupini HPC(L) Isolated from Saline Desert Soil, Kutch (Gujarat).
JO  - Genome Announcements
PY  - 2013
SP  - e00071
EP  - e00012
VL  - 1
AB  - The Rhizobium lupini strain HPC(L) was isolated from saline desert soil. It grows on minimal
AB  - media supplemented with CaCO(3) as a carbon source. It can also grow under both oligotrophic
AB  - and heteroptrophic conditions. We report the annotated genome sequence of this strain in a
AB  - 5.27-Mb scaffold.
ER  -

TY  - JOUR
AU  - Agarwal, P.K.
AU  - Bhattacharya, S.K.
TI  - Construction of a multi RE module: Exploitation of mechanochemistry of restriction endonucleases.
JO  - Biotechnol. Bioeng.
PY  - 1999
SP  - 233
EP  - 239
VL  - 65
AB  - We describe the construction of a multi-immobilized restriction endonuclease module (Multi RE
AB  - module). We demonstrate that the applied mechanical stress enables modulation of enzyme
AB  - activity and modulation of recognition site selectivity (in oligonucleotides of approximately
AB  - 200 bp) of immobilized restriction endonucleases. The central module which consists of
AB  - different strips of immobilized restriction endonucleases allows limited digestion of a large
AB  - DNA sample in a controlled manner as a function of applied mechanical stress on strips. The
AB  - stress-activity relationship and the effect of repeated cycles of stress and relaxation on the
AB  - immobilized strips are presented here.
ER  -

TY  - JOUR
AU  - Aggarwal, A.K.
TI  - Crystallization of DNA binding proteins with oligodeoxynucleotides.
JO  - Methods
PY  - 1990
SP  - 83
EP  - 90
VL  - 1
AB  - In contrast to oligodeoxynucleotides, protein:DNA complexes crystallize from a broad range of
AB  - precipitants and conditions, much as proteins by themselves.  There are, however, a number of
AB  - factors that should be considered, at least in the early stages of cocrystallization attempts.
AB  - These include the length and construction of the oligodeoxynucleotide itself, a pH near or
AB  - below neutrality, a stoichiometric excess of DNA, and di- and polyvalent cations.  By far the
AB  - more important of these factors are the length of the DNA fragment and the nature of the
AB  - terminal nucleotides.  Unfortunately, experience suggests that, in general, the length and
AB  - construction of the DNA fragment for optimal crystal growth cannot be predictd in advance.  A
AB  - systematic search of cocrystallization conditions with different DNA fragments will normally
AB  - be required.  It is important to avoid sequences that provide possible subsites within the
AB  - fragment or at junctions between fragments related by translations.  Sample purity, especially
AB  - that of the DNA, can also have important effects.  Detailed protocols for the purification of
AB  - chemically synthesized fragments are suggested.  Finally, a set of conditions for initial
AB  - cocrystallization trails with a new DNA binding protein is suggested.
ER  -

TY  - JOUR
AU  - Aggarwal, A.K.
TI  - Structure and function of restriction endonucleases.
JO  - Curr. Opin. Struct. Biol.
PY  - 1995
SP  - 11
EP  - 19
VL  - 5
AB  - Structures of two restriction endonucleases, BamHI and PvuII, were reported in the past year.
AB  - This doubles the number of restriction endonuclease structures now known from two to four, and
AB  - enables a comparative analysis of their structures and modes of DNA recognition. Despite a
AB  - lack of sequence homology between the enzymes, BamHI turns out to resemble EcoRI, and PvuII
AB  - turns out to resemble EcoRV. The active-site regions are structurally similar in all four
AB  - enzymes, but their mechanisms of cleavage may differ.
ER  -

TY  - JOUR
AU  - Aggarwal, A.K.
AU  - Wah, D.A.
TI  - Novel site-specific DNA endonucleases.
JO  - Curr. Opin. Struct. Biol.
PY  - 1998
SP  - 19
EP  - 25
VL  - 8
AB  - Site-specific hydrolysis of DNA is common to many biological processes.  Three new structures,
AB  - FokI, I-CreI and PI-SceI, were reported in the past year, providing the first view of type IIs
AB  - endonucleases and homing endonucleases.  Together, they reveal an extraordinary set of new
AB  - mechanisms by which endonucleases target the hydrolysis of specific DNA sequences.
ER  -

TY  - JOUR
AU  - Aggarwal, R.K.
AU  - Dawar, C.
AU  - Das, S.
AU  - Sharma, S.
TI  - Draft Genome Sequences of Two Drug-Resistant Isolates of Pseudomonas aeruginosa Obtained from Keratitis Patients in India.
JO  - Genome Announcements
PY  - 2015
SP  - e01404
EP  - e01414
VL  - 3
AB  - We report here the draft genomes of two drug (fluoroquinolone)-resistant clinical isolates of
AB  - Pseudomonas aeruginosa obtained from the corneal scrapings of
AB  - keratitis patients from India. The two annotated genomes are 6.31 Mb and 6.41 Mb
AB  - in size. These genomes are expected to facilitate the identification and
AB  - understanding of the genes associated with acquired multidrug resistance.
ER  -

TY  - JOUR
AU  - Aggarwal, R.K.
AU  - Dawar, C.
AU  - Phanindranath, R.
AU  - Mutnuri, L.
AU  - Dayal, A.M.
TI  - Draft Genome Sequence of a Versatile Hydrocarbon-Degrading Bacterium, Rhodococcus pyridinivorans Strain KG-16, Collected from Oil Fields in India.
JO  - Genome Announcements
PY  - 2016
SP  - e01704
EP  - e01715
VL  - 4
AB  - We describe here a 5.8-Mb draft genome sequence of Rhodococcus pyridinivorans strain KG-16,
AB  - which was obtained from the soil samples collected from the
AB  - oilfields of Krishna-Godavari basin in India. This genomic resource can provide
AB  - insights into the pathways and mechanisms of hydrocarbon degradation and
AB  - potentially aid in bioremediation applications.
ER  -

TY  - JOUR
AU  - Aghnatios, R.
AU  - Cayrou, C.
AU  - Garibal, M.
AU  - Robert, C.
AU  - Azza, S.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species  exhibiting two variants.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 120
EP  - 120
VL  - 10
AB  - Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in
AB  - France, using a new culture medium. It is an aerobic
AB  - microorganism with optimal growth at pH 8, at 30 degrees C and salinity </= 1.25
AB  - % NaCl. G. massiliana is resistant to beta-lactam antibiotics, due to lack of
AB  - peptidoglycan in its cell wall.G. massiliana shares a 97 % 16S rRNA gene sequence
AB  - similarity with the nearest species, Gemmata obscuriglobus; and 99 % similarity
AB  - with unnamed soil isolates. Its 9,249,437-bp genome consists in one chromosome
AB  - and no detectable plasmid and has a 64.07 % G + C content, 32.94 % of genes
AB  - encoding for hypothetical proteins. The genome contains an incomplete 19.6-kb
AB  - phage sequence, 26 CRISPRs, 3 CAS and 15 clusters of secondary metabolites. G.
AB  - massiliana genome increases knowledge of a poorly known world of bacteria.
ER  -

TY  - JOUR
AU  - Agren, J.
AU  - Finn, M.
AU  - Bengtsson, B.
AU  - Segerman, B.
TI  - Microevolution during an Anthrax Outbreak Leading to Clonal Heterogeneity and Penicillin Resistance.
JO  - PLoS ONE
PY  - 2014
SP  - E89112
EP  - E89112
VL  - 9
AB  - Anthrax is a bacterial disease primarily affecting grazing animals but it can
AB  - also cause severe disease in humans. We have used genomic epidemiology to study
AB  - microevolution of the bacterium in a confined outbreak in cattle which involved
AB  - emergence of an antibiotic-resistant phenotype. At the time of death, the animals
AB  - contained a heterogeneous population of Single Nucleotide Variants (SNVs), some
AB  - being clonal but most being subclonal. We found that independent isolates from
AB  - the same carcass had similar levels of SNV differences as isolates from different
AB  - animals. Furthermore the relative levels of subclonal populations were different
AB  - in different locations in the same carcass. The heterogeneity appeared to be
AB  - derived in part from heterogeneity in the infectious dose. The resistance
AB  - phenotype was linked to clonal mutations in an anti-sigma factor gene and in one
AB  - case was preceded by an acquisition of a hypermutator phenotype. In another
AB  - animal, small subclonal populations were observed with counteracting mutations
AB  - that had turned off the resistance genes. In summary, this study shows the
AB  - importance of accounting for both acquired and inherited heterogeneity when doing
AB  - high-resolution infection tracing and when estimating the risks associated with
AB  - penicillin treatment.
ER  -

TY  - JOUR
AU  - Agron, P.G.
AU  - Sobecky, P.
AU  - Andersen, G.L.
TI  - Establishment of uncharacterized plasmids in Escherichia coli by in vitro transposition.
JO  - FEMS Microbiol. Lett.
PY  - 2002
SP  - 249
EP  - 254
VL  - 217
AB  - We present a simple approach that permits any circular plasmid, such as uncharacterized
AB  - plasmids from diverse prokaryotes, to be established in
AB  - Escherichia coli, thereby facilitating subsequent structural and
AB  - functional studies. An in vitro transposition reaction is used to
AB  - introduce a well-characterized replicon and selectable marker into
AB  - purified plasmids, which are then used to transform E. coli. The
AB  - approach was demonstrated using a small 3.4-kb archaeal plasmid and a
AB  - large 60-kb uncharacterized plasmid from a Gram-negative bacterium.
AB  - Replicon function in E coli was tested for each plasmid, and direct
AB  - sequencing of the large plasmid revealed similarity to
AB  - restriction-modification systems.
ER  -

TY  - JOUR
AU  - Aguado-Urda, M.
AU  - Lopez-Campos, G.H.
AU  - Blanco, M.M.
AU  - Fernandez-Garayzabal, J.F.
AU  - Cutuli, M.T.
AU  - Aspiroz, C.
AU  - Lopez-Alonso, V.
AU  - Gibello, A.
TI  - Genome sequence of Lactococcus garvieae 21881, isolated in a case of human septicemia.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4033
EP  - 4034
VL  - 193
AB  - Lactococcus garvieae is a Gram-positive bacterium considered as an important opportunistic
AB  - emerging human pathogen and also a well recognized
AB  - fish pathogen. Here, we present the draft genome sequence of Lactococcus
AB  - garvieae strain 21881 (2,164,557 bp, with a G+C content of 37.9%), which
AB  - represents the first report of a genome sequence on Lactococcus garvieae.
ER  -

TY  - JOUR
AU  - Aguado-Urda, M.
AU  - Lopez-Campos, G.H.
AU  - Gibello, A.
AU  - Cutuli, M.T.
AU  - Lopez-Alonso, V.
AU  - Fernandez-Garayzabal, J.F.
AU  - Blanco, M.M.
TI  - Genome Sequence of Lactococcus garvieae 8831, Isolated from Rainbow Trout Lactococcosis Outbreaks in Spain.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4263
EP  - 4264
VL  - 193
AB  - Lactococcus garvieae is the etiological agent of lactococcosis, one of the most important
AB  - disease threats to the sustainability of the rainbow trout
AB  - farming industry. Here, we present the draft genome sequence of
AB  - Lactococcus garvieae strain 8831, isolated from diseased rainbow trout,
AB  - which is composed of 2,087,276 bp with a G+C content of 38%.
ER  -

TY  - JOUR
AU  - Aguilar-Bultet, L.
AU  - Calderon-Copete, S.P.
AU  - Frey, J.
AU  - Falquet, L.
TI  - Draft Genome Sequence of the Virulent Avibacterium paragallinarum Serotype A Strain JF4211 and Identification of Two Toxins.
JO  - Genome Announcements
PY  - 2013
SP  - e00592
EP  - e00513
VL  - 1
AB  - Avibacterium paragallinarum is an important pathogen of chicken livestock causing infectious
AB  - coryza. Here, we report the draft genome sequence of the virulent A.
AB  - paragallinarum serotype A strain JF4211 (2.8 Mbp and G+C content of 41%) and the
AB  - two toxin operons discovered from the annotation of the genome.
ER  -

TY  - JOUR
AU  - Aguirre-Arteta, A.M.
AU  - Grunewald, I.
AU  - Cardoso, M.C.
AU  - Leonhardt, H.
TI  - Expression of an alternative Dnmt1 isoform during muscle differentiation.
JO  - Cell Growth Differ.
PY  - 2000
SP  - 551
EP  - 559
VL  - 11
AB  - The methylation pattern of genomic DNA undergoes dramatic changes during
AB  - mammalian development, with extensive de novo methylation occurring during
AB  - gametogenesis and after implantation. We identified an alternative Dnmt1
AB  - transcript in skeletal muscle by Northern blot analysis and cloned the
AB  - corresponding cDNA by rapid amplification of cDNA ends and reverse
AB  - transcription-PCR. Using an in vitro skeletal muscle differentiation
AB  - system, we show that this alternative Dnmt1 isoform is specifically
AB  - expressed in differentiated myotubes, whereas the ubiquitously expressed
AB  - isoform is down-regulated during myogenesis. Sequence analysis showed that
AB  - this skeletal Dnmt1 isoform is identical to the one present in testis,
AB  - which had been described as untranslatable. Here we present evidence that
AB  - this alternative Dnmt1 transcript present in testis and skeletal muscle is
AB  - translated despite the presence of several out-of-frame upstream ATGs and
AB  - gives rise to a shorter Dnmt1 isoform, which could play an active role in
AB  - the change of DNA methylation patterns during gametogenesis and
AB  - myogenesis.
ER  -

TY  - JOUR
AU  - Ahad, R.
AU  - Zhou, T.
AU  - Lepp, D.
AU  - Pauls, K.P.
TI  - Draft Genome Sequence of Citrobacter freundii Strain A47, Resistant to the Mycotoxin Deoxynivalenol.
JO  - Genome Announcements
PY  - 2017
SP  - e00019
EP  - e00017
VL  - 5
AB  - Here, we present the draft genome sequence of Citrobacter freundii strain A47 with a length of
AB  - 4,878,242 bp, which contains 4,357 putative protein coding
AB  - genes, including 270 unique genes. This work is expected to assist in obtaining
AB  - novel gene(s) that code for deoxynivalenol (DON) de-epoxidation enzyme(s).
ER  -

TY  - JOUR
AU  - Aherfi, S.
AU  - Pagnier, I.
AU  - Fournous, G.
AU  - Raoult, D.
AU  - La Scola, B.
AU  - Colson, P.
TI  - Complete genome sequence of Cannes 8 virus, a new member of the proposed family 'Marseilleviridae'.
JO  - Virus Genes
PY  - 2013
SP  - 550
EP  - 555
VL  - 47
AB  - Marseillevirus is a giant virus that was isolated in 2007 by culturing water
AB  - collected from a cooling tower in Paris, France, on Acanthamoeba polyphaga. Since
AB  - then, five other marseilleviruses have been detected in environmental or human
AB  - samples. The genomes of two of the six marseilleviruses have been described in
AB  - detail. We describe herein the genome of Cannes 8 virus, a new member of the
AB  - proposed family "Marseilleviridae." Cannes 8 virus was isolated from water
AB  - collected from a cooling tower in Cannes in southeastern France. Its genome is a
AB  - circular double-stranded DNA molecule with 374,041 base pairs, larger than the
AB  - Marseillevirus and Lausannevirus genomes. This genome harbors 484 open reading
AB  - frames predicted to encode proteins with sizes ranging from 50 to 1,537 amino
AB  - acids, among which 380 (79 %) and 272 (56 %) are bona fide orthologs of
AB  - Marseillevirus and Lausannevirus proteins, respectively. In addition, 407 and 336
AB  - predicted proteins have significant hits against Marseillevirus and Lausannevirus
AB  - proteins, respectively, and 294 proteins are shared by all three
AB  - marseilleviruses. The Cannes 8 virus genome has a high level of collinearity (for
AB  - 96 % of orthologs) with the Marseillevirus genome. About two-thirds of the Cannes
AB  - 8 virus gene repertoire is composed of family ORFans. The description and
AB  - annotation of the genomes of new marseilleviruses that will undoubtedly be
AB  - recovered from environmental or clinical samples will be helpful to increase our
AB  - knowledge of the pan-genome of the family "Marseilleviridae."
ER  -

TY  - JOUR
AU  - Ahir, V.B.
AU  - Roy, A.
AU  - Jhala, M.K.
AU  - Bhanderi, B.B.
AU  - Mathakiya, R.A.
AU  - Bhatt, V.D.
AU  - Padiya, K.B.
AU  - Jakhesara, S.J.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
TI  - Genome Sequence of Pasteurella multocida subsp. gallicida Anand1_poultry.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5604
EP  - 5604
VL  - 193
AB  - We report the finished and annotated genome sequence of Pasteurella multocida gallicida strain
AB  - Anand1_poultry, which was isolated from the
AB  - liver of a diseased adult female chicken. The strain causes a disease
AB  - called 'fowl cholera,' which is a contagious disease in birds. We compared
AB  - it with the published genome sequence of Pasteurella multocida Pm70.
ER  -

TY  - JOUR
AU  - Ahlert, D.
AU  - Stegemann, S.
AU  - Kahlau, S.
AU  - Ruf, S.
AU  - Bock, R.
TI  - Insensitivity of chloroplast gene expression to DNA methylation.
JO  - Mol. Genet. Genomics
PY  - 2009
SP  - 17
EP  - 24
VL  - 282
AB  - Presence and possible functions of DNA methylation in plastid genomes of higher plants have
AB  - been highly controversial. While a number of
AB  - studies presented evidence for the occurrence of both cytosine and
AB  - adenine methylation in plastid genomes and proposed a role of cytosine
AB  - methylation in the transcriptional regulation of plastid genes, several
AB  - recent studies suggested that at least cytosine methylation may be
AB  - absent from higher plant plastid genomes. To test if either adenine or
AB  - cytosine methylation can play a regulatory role in plastid gene
AB  - expression, we have introduced cyanobacterial genes for adenine and
AB  - cytosine DNA methyltransferases (methylases) into the tobacco plastid
AB  - genome by chloroplast transformation. Using DNA cleavage with
AB  - methylation-sensitive and methylation-dependent restriction
AB  - endonucleases, we show that the plastid genomes in the transplastomic
AB  - plants are efficiently methylated. All transplastomic lines are
AB  - phenotypically indistinguishable from wild-type plants and, moreover,
AB  - show no alterations in plastid gene expression. Our data indicate that
AB  - the expression of plastid genes is not sensitive to DNA methylation
AB  - and, hence, suggest that DNA methylation is unlikely to be involved in
AB  - the transcriptional regulation of plastid gene expression.
ER  -

TY  - JOUR
AU  - Ahlgren, N.A.
AU  - Chen, Y.
AU  - Needham, D.M.
AU  - Parada, A.E.
AU  - Sachdeva, R.
AU  - Trinh, V.
AU  - Chen, T.
AU  - Fuhrman, J.A.
TI  - Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.
JO  - Environ. Microbiol.
PY  - 2017
SP  - 2434
EP  - 2452
VL  - 19
AB  - Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative
AB  - laboratory-cultured strains. We report the cultivation of Candidatus
AB  - Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature
AB  - tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment,
AB  - strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate
AB  - Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing
AB  - features: putative phosphorothioation (PT) DNA modification genes; a region
AB  - containing probable viral genes; and putative urea utilization genes. The PT
AB  - modification genes and an adjacent putative restriction enzyme (RE) operon likely
AB  - form a restriction modification (RM) system for defence from foreign DNA. PacBio
AB  - sequencing showed >98% methylation at two motifs, and inferred PT guanine
AB  - modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals
AB  - the putative virus region and PT modification and RE genes are present in 18-26%,
AB  - 9-14% and <1.5% of natural populations at 150 m with >/=85% identity to strain
AB  - SPOT01. The presence of multiple probable RM systems in a highly streamlined
AB  - genome suggests a surprising importance for defence from foreign DNA for dilute
AB  - populations that infrequently encounter viruses or other cells. This new strain
AB  - provides new insights into the ecology, including viral interactions, of this
AB  - important group of marine microbes.
ER  -

TY  - JOUR
AU  - Ahmad, F.
AU  - Huang, X.
AU  - Lan, H.X.
AU  - Huma, T.
AU  - Bao, Y.M.
AU  - Huang, J.
AU  - Zhang, H.S.
TI  - Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.).
JO  - Gen. Mol. Res.
PY  - 2014
SP  - 5159
EP  - 5172
VL  - 13
AB  - Cytosine DNA methylation is a conserved epigenetic regulatory mechanism in both plants and
AB  - animals. DNA methyltransferases (DNA MTases) not only initiate (de novo) but also maintain the
AB  - process of DNA methylation. Here, we characterized the genome-wide expression profiles of 10
AB  - cytosine DNA MTase genes belonging to 4 subfamilies, MET1, CMT, DNMT2, and DRM, in rice.
AB  - Tissue-specific gene expression analysis showed that all family members varied widely in their
AB  - expression and specificities and might be involved in some basic metabolic pathways.
AB  - Similarly, the expression of all rice cytosine DNA MTase genes was not regulated by plant
AB  - hormones except OsDRM1a and OsDRM1b, which were downregulated by jasmonic acid. The
AB  - transcription level of 10 genes in rice shoots and roots was also measured under salt and
AB  - osmotic stress. Meanwhile, quantitative polymerase chain reaction data of the japonica and
AB  - indica rice cultivars revealed that there is large variation in the expression activities of
AB  - all genes. The results provide a foundation to further explore the roles of DNA MTases and the
AB  - epigenetic regulation of abiotic stress responses in rice.
ER  -

TY  - JOUR
AU  - Ahmad, I.
AU  - Krishnamurthy, V.
AU  - Rao, D.N.
TI  - DNA recognition by the EcoP15I and EcoPI modification methyltransferases.
JO  - Gene
PY  - 1995
SP  - 143
EP  - 147
VL  - 157
AB  - The DNA-binding properties of the EcoP15I DNA methyltransferase (M.EcoP15I; MTase) were
AB  - studied using electrophoretic mobility shift assays.  We show by molecular size-exclusion
AB  - chromatography and dimethyl suberimidate crosslinking that M.EcoP15I is a dimer in solution.
AB  - While M.EcoP15I binds approximately three-fold more tightly to its recognition sequence,
AB  - 5'-CAGCAG-3', than to non-specific sequences in the presence of AdoMet or its analogs, the
AB  - discrimination between specific and non-specific sequences significantly increases in the
AB  - presence of ATP.  These results suggest for the first time a role for ATP in DNA recognition
AB  - by type-III restriction-modification enzymes.  Furthermore, we show that although c2 EcoPI
AB  - mutant MTases are defective in AdoMet binding, they are still able to bind DNA in a
AB  - sequence-specific manner.
ER  -

TY  - JOUR
AU  - Ahmad, I.
AU  - Kulkarni, M.
AU  - Gopinath, A.
AU  - Saikrishnan, K.
TI  - Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 6229
EP  - 6237
VL  - 46
AB  - Endonucleolytic cleavage of DNA by Type III restriction-modification (RM) enzymes requires
AB  - long-range communication between at least two recognition sites in
AB  - inverted orientation. This results in convergence of two nuclease domains, one
AB  - each from the enzymes loaded at the recognition sites with one still bound to the
AB  - site. The nucleases catalyze scission of the single-strands leading to
AB  - double-strand DNA break. An obscure feature of the Type III RM enzymes EcoP1I and
AB  - EcoP15I is their ability to cleave DNA having a single recognition site under
AB  - certain conditions. Here we demonstrate that single-site cleavage is the result
AB  - of cooperation between an enzyme bound to the recognition site in cis and one in
AB  - trans. DNA cleavage is catalyzed by converging nucleases that are activated by
AB  - hydrolysis-competent ATPase in presence of their respective DNA substrates.
AB  - Furthermore, a single activated nuclease cannot nick a strand on its own, and
AB  - requires the partner. Based on the commonalities in the features of single-site
AB  - and two-site cleavage derived from this study, we propose that their mechanism is
AB  - similar. Furthermore, the products of two-site cleavage can act as substrates and
AB  - activators of single-site cleavage. The difference in the two modes lies in how
AB  - the two cooperating enzymes converge, which in case of single-site cleavage
AB  - appears to be via 3D diffusion.
ER  -

TY  - JOUR
AU  - Ahmad, I.
AU  - Rao, D.N.
TI  - Photolabeling of the EcoP15 DNA methyltransferase with S-adenosyl-L-methionine.
JO  - Gene
PY  - 1994
SP  - 67
EP  - 71
VL  - 142
AB  - Radioactivity from S-adenosyl-L[methyl-3H]methionine ([methyl-3H]AdoMet) was bound to the
AB  - EcoP15 DNA methyltransferase (M.EcoP15) following short-wave ultraviolet (UV) irradiation. The
AB  - labeled protein was subjected to polyacrylamide-gel electrophoresis in the presence of sodium
AB  - dodecyl sulfate (SDS-PAGE), and detected by fluorography and autoradiography. Labeling was
AB  - found to be dependent on the concentration of AdoMet and time of UV irradiation. The
AB  - photolabeling by [methyl-3H]AdoMet was specific and blocked by S-adenosyl-L-homocysteine
AB  - (AdoHcy) and sinefungin which are known to function as competitive inhibitors. Limited
AB  - digestion of the M.EcoP15-AdoMet adduct by Staphylococcus aureus protease V8 generated three
AB  - peptides of approx. 50, 32 and 30 kDa. Interestingly, only the 30-kDa peptide fragment
AB  - contained radioactivity, as detected by SDS-PAGE, followed by fluorography and
AB  - autoradiography. Further, sequencing of a few amino acids at the N-terminus of these peptides
AB  - showed that the 30-kDa fragment was the N-terminal portion of M.EcoP15. These results suggest
AB  - that photolabeling is at the AdoMet-binding site and that the N-terminal half of M.EcoP15 may
AB  - be involved in substrate binding.
ER  -

TY  - JOUR
AU  - Ahmad, I.
AU  - Rao, D.N.
TI  - Chemistry and biology of DNA methyltransferases.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 1996
SP  - 361
EP  - 380
VL  - 31
AB  - Recognition of a specific DNA sequence by a protein is probably the best example of
AB  - macromolecular interactions leading to various events.  It is a prerequisite to understanding
AB  - the basis of protein-DNA interactions to obtain a better insight into fundamental processes
AB  - such as transcription, replication, repair, and recombination.  DNA methyltransferases with
AB  - varying sequence specificities provide an excellent model system for understanding the
AB  - molecular mechanism of specific DNA recognition.  Sequence comparison of cloned genes, along
AB  - with mutational analyses and recent crystallographic studies, have clearly defined the
AB  - functions of various conserved motifs.  These enzymes access their target base in an elegant
AB  - manner by flipping it out of the DNA double helix.  The drastic protein-induced DNA
AB  - distortion, first reported for HhaI DNA methyltransferase, appears to be a common mechanism
AB  - employed by vairous proteins that need to act on bases.  A remarkable feature of the catalytic
AB  - mechanism of DNA (cytosine-5) methyltransferases is the ability of these enzymes to induce
AB  - deamination of the target cytosine in the absence of S-adenosyl-L-methionine or its analogs.
AB  - The enzyme-catalyzed deamination reaction is postulated to be the major cause of mutational
AB  - hotspots at CpG islands responsible for various human genetic disorders.  Methylation of
AB  - adenine residues in Escherichia coli is known to regulate various processes such as
AB  - transcription, replication, repair, recombination, transposition, and phage packaging.
ER  -

TY  - JOUR
AU  - Ahmad, I.
AU  - Rao, D.N.
TI  - Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5'-CAGCAG-3'.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 378
EP  - 388
VL  - 242
AB  - EcoP15I DNA methyltransferase (Mtase) recognizes the asymmetric sequence CAGCAG and catalyzes
AB  - the transfer of a methyl group from S-adenosyl-L-methionine to the second adenine residue. We
AB  - have investigated the DNA binding properties of EcoP15I DNA Mtase using gel mobility shift
AB  - assays. EcoP15I DNA Mtase binds approximately threefold more tightly to DNA containing its
AB  - recognition sequence, CAGCAG, than to non-specific sequences in the absence or presence of
AB  - cofactors. Interestingly, in the presence of ATP the discrimination between specific and
AB  - non-specific sequences increases significantly. These results suggest for the first time a
AB  - role for ATP in DNA recognition by type III restriction-modification enzymes. In addition, we
AB  - have shown that bromodeoxyuridine-containing oligonucleotides form complexes with EcoP15I DNA
AB  - Mtase that are cross-linked upon irradiation. More importantly, we have shown that the
AB  - crosslink site is at the site of DNA binding, since it can be suppressed by an excess of
AB  - unmodified oligonucleotide. EcoP15I DNA Mtase exhibited Michaelis-Menten kinetics with both
AB  - unmodified and bromodeoxyuridine-substituted DNA, with a higher specificity constant for the
AB  - latter. Furthermore, gel mobility shift assays showed that proteolyzed EcoP15I DNA Mtase
AB  - formed a specific complex with DNA, which had similar mobility as the native protein-DNA
AB  - complex. Taken together these results form the basis for a detailed structure-function
AB  - analysis of EcoP15I DNA Mtase.
ER  -

TY  - JOUR
AU  - Ahmad, I.
AU  - Rao, D.N.
TI  - Functional analysis of conserved motifs in EcoP15I DNA methyltransferase.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 229
EP  - 240
VL  - 259
AB  - EcoP15I DNA methyltransferase recognizes the sequence 5'-CAGCAG-3' and transfers a methyl
AB  - group to N-6 of the second adenine residue in the recognition sequence.  All N-6 adenine
AB  - methyltransferases contain two highly conserved sequences, FxGxG (motif 1), postulated to form
AB  - part of the S-adenosyl-L-methionine binding site and (D/N/S)PP(Y/F) (motif IV) involved in
AB  - catalysis.  We have altered the second glycine residue in motif I to arginine and serine, and
AB  - substituted tyrosine in motif IV with tryptophan in EcoP15I DNA methyltransferase, using
AB  - site-directed mutagenesis.  The mutant enzymes were overexpressed, purified and characterized
AB  - by biochemical methods.  The mutations in motif I completely abolished AdoMet binding but left
AB  - target DNA recognition unaltered.  Although the mutation in motif IV resulted in loss of
AB  - enzyme activity, we observed enhanced crosslinking of S-adenosyl-L-methionine and DNA.  This
AB  - implies that DNA and AdoMet binding sites are close to motif IV.  Taken together, these
AB  - results reinforce the importance of motif I in AdoMet binding and motif IV in catalysis.
AB  - Additionally, limited proteolysis and UV crosslinking experiments with EcoP15I DNA
AB  - methyltransferase imply that DNA binds in a cleft formed by two domains in the protein.
AB  - Methylation protection analysis provides evidence for the fact that EcoP15I DNA Mtase makes
AB  - contacts in the major groove of its substrate DNA.  Interestingly, hypermethylation of the
AB  - guanine residue next to the target adenine residue indicates that the protein probably flips
AB  - out the target adenine residue.
ER  -

TY  - JOUR
AU  - Ahmad, N.
AU  - Hii, S.Y.
AU  - Hashim, R.
AU  - Issa, R.
TI  - Draft Genome Sequence of Salmonellaenterica Serovar Typhi IMR_TP298/15, a Strain  with Intermediate Susceptibility to Ciprofloxacin, Isolated from a Typhoid  Outbreak.
JO  - Genome Announcements
PY  - 2017
SP  - e01740
EP  - e01716
VL  - 5
AB  - Salmonella enterica serovar Typhi with reduced susceptibility to ciprofloxacin is increasingly
AB  - being reported globally. An outbreak caused by Salmonella Typhi with
AB  - decreased ciprofloxacin susceptibility has not been reported before in Malaysia.
AB  - We present here the annotated draft genome of a Salmonella Typhi strain involved
AB  - in a typhoid outbreak.
ER  -

TY  - JOUR
AU  - Ahmad, N.
AU  - Hii, S.Y.
AU  - Mohd, K.M.K.
AU  - Abd, W.M.A.
AU  - Hashim, R.
AU  - Tang, S.N.
AU  - Liow, Y.L.
AU  - Hamzah, H.
AU  - Dahalan, N.A.
AU  - Seradja, V.
TI  - First Draft Genome Sequences of Malaysian Clinical Isolates of Corynebacterium diphtheriae.
JO  - Genome Announcements
PY  - 2017
SP  - e01670
EP  - e01616
VL  - 5
AB  - Corynebacterium diphtheriae has caused multiple isolated diphtheria cases in Malaysia over the
AB  - years. Here, we report the first draft genome sequences of 15
AB  - Malaysia C. diphtheriae clinical isolates collected from the years 1981 to 2016.
ER  -

TY  - JOUR
AU  - Ahmed, A.
AU  - Earl, J.
AU  - Retchless, A.
AU  - Hillier, S.L.
AU  - Rabe, L.K.
AU  - Cherpes, T.L.
AU  - Powell, E.
AU  - Janto, B.
AU  - Eutsey, R.
AU  - Hiller, N.L.
AU  - Boissy, R.
AU  - Dahlgren, M.E.
AU  - Hall, B.G.
AU  - Costerton, J.W.
AU  - Post, J.C.
AU  - Hu, F.Z.
AU  - Ehrlich, G.D.
TI  - Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with  Subspeciation into Genovars.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3922
EP  - 3937
VL  - 194
AB  - Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high
AB  - degrees of genetic heterogeneity among stains. Seventeen G.
AB  - vaginalis isolates were subjected to a battery of comparative genomic analyses to
AB  - determine their level of relatedness. For each measure, the degree of difference
AB  - among the G. vaginalis strains was the highest observed among 23 pathogenic
AB  - bacterial species for which at least eight genomes are available. Genome sizes
AB  - ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the
AB  - core genome, consisting of only 746 genes, makes up only 51.6% of each strain's
AB  - genome on average and accounts for only 27% of the species supragenome.
AB  - Neighbor-grouping analyses, using both distributed gene possession data and core
AB  - gene allelic data, each identified two major sets of strains, each of which is
AB  - composed of two groups. Each of the four groups has its own characteristic genome
AB  - size, GC ratio, and greatly expanded core gene content, making the genomic
AB  - diversity of each group within the range for other bacterial species. To test
AB  - whether these 4 groups corresponded to genetically isolated clades, we inferred
AB  - the phylogeny of each distributed gene that was present in at least two strains
AB  - and absent in at least two strains; this analysis identified frequent homologous
AB  - recombination within groups but not between groups or sets. G. vaginalis appears
AB  - to include four nonrecombining groups/clades of organisms with distinct gene
AB  - pools and genomic properties, which may confer distinct ecological properties.
AB  - Consequently, it may be appropriate to treat these four groups as separate
AB  - species.
ER  -

TY  - JOUR
AU  - Ahmed, I.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Ohmori, Y.
AU  - Fujiwara, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T.
JO  - Genome Announcements
PY  - 2014
SP  - e00097
EP  - e00014
VL  - 2
AB  - Gracilibacillus boraciitolerans JCM 21714(T) has been characterized as a highly boron-tolerant
AB  - and moderately halotolerant bacterium. Here, we report the draft
AB  - genome sequence of this strain. The genome sequence facilitates an understanding
AB  - of the biochemical functions of boron and provides a base to identify the gene(s)
AB  - involved in the boron tolerance mechanism of the strain.
ER  -

TY  - JOUR
AU  - Ahmed, I.H.
AU  - Manning, G.
AU  - Wassenaar, T.M.
AU  - Cawthraw, S.
AU  - Newell, D.G.
TI  - Identification of genetic differences between two Campylobacter jejuni strains with different colonization potentials.
JO  - Microbiology
PY  - 2002
SP  - 1203
EP  - 1212
VL  - 148
AB  - The consumption of poultry meat contaminated with Campylobacter jejuni is considered to be a
AB  - risk factor for human campylobacteriosis. The
AB  - development of targeted strategies to control campylobacters in
AB  - broilers would benefit from knowledge of those bacterial factors
AB  - important in colonization of the avian gut. During preliminary studies
AB  - it was noted that C. jejuni NCTC 11168 was a poorer colonizer of
AB  - chickens than strain 81116. This poor colonization could not be fully
AB  - restored by in vivo passage, suggesting that it was a genetically
AB  - endowed property of strain 11168. As the genome sequence is available
AB  - for this strain, the technique of subtractive hybridization was used to
AB  - identify gene fragments of strain 81116 not present in strain 11168.
AB  - After two screening cycles, 24 out of 42 clones were identified as
AB  - having DNA inserts specific for strain 81116. Six of these 24 clones
AB  - contained gene fragment inserts with similarities to
AB  - restriction-modification enzymes found in other bacteria. Two inserts
AB  - had similarity to arsenic-resistance genes, whereas four others had
AB  - similarities to cytochrome c oxidase III, dTDP-glucose 4,6-dehydratase,
AB  - gamma-glutamyl transpeptidase and an abortive phage-resistance protein.
AB  - At least some of these genes may be involved with colonization. A
AB  - further six inserts had weak similarities to hypothetical proteins or
AB  - to proteins with assigned functions from strain 11168. The remaining
AB  - six clones had gene-fragment inserts with no database matches.
AB  - Southern-blot analysis confirmed that strain-dependent variation
AB  - existed for each of these DNA inserts. These results indicate that
AB  - subtractive hybridization can successfully identify genes that are
AB  - absent from the only C. jejuni strain for which the genome sequence is
AB  - currently available.
ER  -

TY  - JOUR
AU  - Ahmed, N.
AU  - Saini, V.
AU  - Raghuvanshi, S.
AU  - Khurana, J.P.
AU  - Tyagi, A.K.
AU  - Tyagi, A.K.
AU  - Hasnain, S.E.
TI  - Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.
JO  - PLoS ONE
PY  - 2007
SP  - E968
EP  - E968
VL  - 2
AB  - BACKGROUND: Evolutionary dynamics plays a central role in facilitating the
AB  - mechanisms of species divergence among pathogenic and saprophytic mycobacteria.
AB  - The ability of mycobacteria to colonize hosts, to proliferate and to cause
AB  - diseases has evolved due to its predisposition to various evolutionary forces
AB  - acting over a period of time. Mycobacterium indicus pranii (MIP), a taxonomically
AB  - unknown 'generalist' mycobacterium, acts as an immunotherapeutic against leprosy
AB  - and is approved for use as a vaccine against it. The large-scale field trials of
AB  - this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and
AB  - adjuvant property has led to human clinical evaluations of MIP in interventions
AB  - against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as
AB  - 'Immuvac', is currently the focus of advanced phase III clinical trials for its
AB  - antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-a-vis
AB  - evolutionary path, underpinning its immanent immunomodulating properties is of
AB  - the highest desiderata. PRINCIPAL FINDINGS: Genome wide comparisons together with
AB  - molecular phylogenetic analyses by fluorescent amplified fragment length
AB  - polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC)
AB  - based genotyping and candidate orthologues sequencing revealed that MIP has been
AB  - the predecessor of highly pathogenic Mycobacterium avium intracellulare complex
AB  - (MAIC) that did not resort to parasitic adaptation by reductional gene evolution
AB  - and therefore, preferred a free living life-style. Further analysis suggested a
AB  - shared aquatic phase of MAIC bacilli with the early pathogenic forms of
AB  - Mycobacterium, well before the latter diverged as 'specialists'.
AB  - CONCLUSIONS/SIGNIFICANCE: This evolutionary paradigm possibly affirms to marshall
AB  - our understanding about the acquisition and optimization of virulence in
AB  - mycobacteria and determinants of boundaries therein.
ER  -

TY  - JOUR
AU  - Ahmed, S.A. et al.
TI  - Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage  stx2.
JO  - PLoS ONE
PY  - 2012
SP  - e48228
EP  - e48228
VL  - 7
AB  - In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga
AB  - toxin 2-converting phage caused a large outbreak of bloody
AB  - diarrhea in Europe which was notable for its high prevalence of hemolytic uremic
AB  - syndrome cases. Several studies have described the genomic inventory and
AB  - phylogenies of strains associated with the outbreak and a collection of
AB  - historical E. coli O104:H4 isolates using draft genome assemblies. We present the
AB  - complete, closed genome sequences of an isolate from the 2011 outbreak
AB  - (2011C-3493) and two isolates from cases of bloody diarrhea that occurred in the
AB  - Republic of Georgia in 2009 (2009EL-2050 and 2009EL-2071). Comparative genome
AB  - analysis indicates that, while the Georgian strains are the nearest neighbors to
AB  - the 2011 outbreak isolates sequenced to date, structural and nucleotide-level
AB  - differences are evident in the Stx2 phage genomes, the mer/tet antibiotic
AB  - resistance island, and in the prophage and plasmid profiles of the strains,
AB  - including a previously undescribed plasmid with homology to the pMT virulence
AB  - plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that
AB  - 2009EL-2071 possessed higher resistance to polymyxin and membrane-disrupting
AB  - agents. Finally, we show evidence by electron microscopy of the presence of a
AB  - common phage morphotype among the European and Georgian strains and a second
AB  - phage morphotype among the Georgian strains. The presence of at least two stx2
AB  - phage genotypes in host genetic backgrounds that may derive from a recent common
AB  - ancestor of the 2011 outbreak isolates indicates that the emergence of stx2
AB  - phage-containing E. coli O104:H4 strains probably occurred more than once, or
AB  - that the current outbreak isolates may be the result of a recent transfer of a
AB  - new stx2 phage element into a pre-existing stx2-positive genetic background.
ER  -

TY  - JOUR
AU  - Ahn, Y.S.
AU  - Piamsomboon, P.
AU  - Tang, K.F.J.
AU  - Han, J.E.
AU  - Kim, J.H.
TI  - Complete Genome Sequence of Acute Hepatopancreatic Necrosis Disease-Causing Vibrio campbellii LA16-V1, Isolated from Penaeus vannamei Cultured in a Latin  American Country.
JO  - Genome Announcements
PY  - 2017
SP  - e01011
EP  - e01017
VL  - 5
AB  - We report here the complete genome sequence of Vibrio campbellii, isolated from Penaeus
AB  - vannamei cultured in a Latin American country. The Tn3-like transposon
AB  - and pirAB genes were encoded on the plasmid pLA16-2. These data support the
AB  - geographical variations in the virulence plasmid found among acute
AB  - hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates from Latin
AB  - America and Asia.
ER  -

TY  - JOUR
AU  - Ahrenfeldt, J.
AU  - Skaarup, C.
AU  - Hasman, H.
AU  - Pedersen, A.G.
AU  - Aarestrup, F.M.
AU  - Lund, O.
TI  - Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.
JO  - BMC Genomics
PY  - 2017
SP  - 19
EP  - 19
VL  - 18
AB  - BACKGROUND: Whole genome sequencing (WGS) is increasingly used in diagnostics and
AB  - surveillance of infectious diseases. A major application for WGS is to use the
AB  - data for identifying outbreak clusters, and there is therefore a need for methods
AB  - that can accurately and efficiently infer phylogenies from sequencing reads. In
AB  - the present study we describe a new dataset that we have created for the purpose
AB  - of benchmarking such WGS-based methods for epidemiological data, and also present
AB  - an analysis where we use the data to compare the performance of some current
AB  - methods. RESULTS: Our aim was to create a benchmark data set that mimics
AB  - sequencing data of the sort that might be collected during an outbreak of an
AB  - infectious disease. This was achieved by letting an E. coli hypermutator strain
AB  - grow in the lab for 8 consecutive days, each day splitting the culture in two
AB  - while also collecting samples for sequencing. The result is a data set consisting
AB  - of 101 whole genome sequences with known phylogenetic relationship. Among the
AB  - sequenced samples 51 correspond to internal nodes in the phylogeny because they
AB  - are ancestral, while the remaining 50 correspond to leaves. We also used the
AB  - newly created data set to compare three different online available methods that
AB  - infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and
AB  - REALPHY. One complication when comparing the output of these methods with the
AB  - known phylogeny is that phylogenetic methods typically build trees where all
AB  - observed sequences are placed as leafs, even though some of them are in fact
AB  - ancestral. We therefore devised a method for post processing the inferred trees
AB  - by collapsing short branches (thus relocating some leafs to internal nodes), and
AB  - also present two new measures of tree similarity that takes into account the
AB  - identity of both internal and leaf nodes. CONCLUSIONS: Based on this analysis we
AB  - find that, among the investigated methods, CSI Phylogeny had the best
AB  - performance, correctly identifying 73% of all branches in the tree and 71% of all
AB  - clades. We have made all data from this experiment (raw sequencing reads,
AB  - consensus whole-genome sequences, as well as descriptions of the known phylogeny
AB  - in a variety of formats) publicly available, with the hope that other groups may
AB  - find this data useful for benchmarking and exploring the performance of
AB  - epidemiological methods. All data is freely available at:
AB  - https://cge.cbs.dtu.dk/services/evolution_data.php .
ER  -

TY  - JOUR
AU  - Ahuja, Y.R.
TI  - Bacterial infection restriction endonucleases, genetic damage and cancer.
JO  - Biol. Zentralbl.
PY  - 1991
SP  - 179
EP  - 187
VL  - 110
AB  - Restriction endonucleases are known to cut naked DNA at specific sites by
AB  - recognizing their palindromes.  Similarly, in vitro in human and mammalian
AB  - cells, restriction endonucleases have been shown to cause nonrandom chromosome
AB  - damage, in addition to inducing gene amplification and mutations.  Bacteria,
AB  - which are the source of restriction endonucleases, have also been shown to be
AB  - clastogenic in vivo in human and mammalian cells.  Furthermore, it has been
AB  - demonstrated that the bacteria cause nonrandom chromosome damage.  Normally,
AB  - bacteria are phagocytized and their contents degraded by the cellular enzymes.
AB  - However, it is possible that for some reason (mutation or physiological) the
AB  - restriction endonucleases may cause specific chromosome damage, gene mutation
AB  - or gene amplification, which in turn may involve oncogene activation, leading
AB  - to cancer.
ER  -

TY  - JOUR
AU  - Ahuja, Y.R.
AU  - Obe, G.
TI  - Are rogue cells an indicator of cancer risk due to the action of bacterial restriction endonucleases?
JO  - Mutat. Res.
PY  - 1994
SP  - 103
EP  - 112
VL  - 310
AB  - Cytogenetic surveys in normal individuals have occasionally shown the occurrence of cells with
AB  - multiple chromosome-type aberrations in some of the subjects.  These cells, which are rare,
AB  - have been termed as rogue cells.  Rogue cells, which have been observed worldwide, have a
AB  - mysterious nature.  It has been suggested that they may give rise to cancer.  Various
AB  - mechanisms have been considered for the causation of the rogue-cell phenomenon in the past but
AB  - none of them appears to be fully justified.  In this paper we propose their occurrence due to
AB  - the action of bacterial restriction endonucleases.
ER  -

TY  - JOUR
AU  - Ai, C.
AU  - McCarthy, S.
AU  - Schackwitz, W.
AU  - Martin, J.
AU  - Lipzen, A.
AU  - Blum, P.
TI  - Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01142
EP  - e01115
VL  - 3
AB  - Metallosphaera sedula is a thermoacidophilic crenarchaeote with a 2.19-Mb genome. Here, we
AB  - report the genome sequences of several evolved derivatives of M. sedula  generated through
AB  - adaptive laboratory evolution for enhanced arsenate resistance.
ER  -

TY  - JOUR
AU  - Ai, H.
AU  - Zhang, J.
AU  - Yang, M.
AU  - Yu, P.
AU  - Li, S.
AU  - Zhu, M.
AU  - Dong, H.
AU  - Wang, S.
AU  - Wang, J.
TI  - Draft Genome Sequence of an Anaerobic, Thermophilic Bacterium, Thermoanaerobacterium aotearoense SCUT27, Isolated from a Hot Spring in China.
JO  - Genome Announcements
PY  - 2014
SP  - e00041
EP  - e00014
VL  - 2
AB  - Thermoanaerobacterium aotearoense SCUT27, isolated from a hot spring in China, is a strictly
AB  - anaerobic, thermophilic bacterium capable of degrading xylan and
AB  - converting both pentose and hexose to ethanol with high yields. Here, we report
AB  - the draft genome sequence of SCUT27, which reveals insights into the mechanisms
AB  - of carbon source coutilization and xylan degradation in this thermophilic
AB  - microorganism.
ER  -

TY  - JOUR
AU  - Ai, L.
AU  - Chen, C.
AU  - Zhou, F.
AU  - Wang, L.
AU  - Zhang, H.
AU  - Chen, W.
AU  - Guo, B.
TI  - Complete genome sequence of probiotic Lactobacillus casei BD-II.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3160
EP  - 3161
VL  - 193
AB  - Lactobacillus casei BD-II, a patented probiotic strain (U.S. patent 7,270,994 B2), was
AB  - isolated from homemade koumiss in China and has been
AB  - implemented in the industrial production as starter cultures. Here we
AB  - report the complete genome sequence of BD-II which shows high similarity
AB  - with the well studied probiotic BL23.
ER  -

TY  - JOUR
AU  - Aiba, Y.
AU  - Sumaoka, J.
AU  - Komiyama, M.
TI  - Artificial DNA cutters for DNA manipulation and genome engineering.
JO  - Chem. Soc. Rev.
PY  - 2011
SP  - 5657
EP  - 5668
VL  - 40
AB  - This tutorial review provides recent developments in artificial cutters for site-selective
AB  - scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for
AB  - molecular biology and biotechnology, since their site-selectivity of scission is much higher
AB  - than that of naturally occurring restriction enzymes and also their scission site is freely
AB  - chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a
AB  - sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in
AB  - single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of
AB  - nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an
AB  - artificial restriction DNA cutter, prepared from Ce(IV)/EDTA and pseudo-complementary peptide
AB  - nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and
AB  - scission specificity are determined simply in terms of the Watson-Crick rule so that even the
AB  - whole genome of human beings was selectively cut at one predetermined site. Consistently,
AB  - homologous recombination in human cells was successfully promoted by this tool. For the
AB  - purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also
AB  - briefly described. The potential applications of these cutters and their future aspects are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Aigle, A.
AU  - Michotey, V.
AU  - Bonin, P.
TI  - Draft-genome sequence of Shewanella algae strain C6G3.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 43
EP  - 43
VL  - 10
AB  - Shewanella algae strain C6G3, isolated from the 2 uppermost centimeters of muddy  sediment of
AB  - Arcachon Bay (SW Atlantic French coast, sampled in October 2007) has  the capability to use a
AB  - large panel of terminal electron acceptors under anaerobic condition, such as nitrate, nitrite
AB  - and metal-oxide, and presents a great metabolic versatility. Here, we present the
AB  - non-contiguous draft-genome sequence of Shewanella algae C6G3, which consists of a 4,879,425
AB  - bp. The chromosome contains 5792 predicted genes. In total, the genome consists of 24 rRNA
AB  - genes, 86 tRNA genes and 5660 genes assigned as protein-coding genes.
ER  -

TY  - JOUR
AU  - Aikawa, C.
AU  - Furukawa, N.
AU  - Watanabe, T.
AU  - Minegishi, K.
AU  - Furukawa, A.
AU  - Eishi, Y.
AU  - Oshima, K.
AU  - Kurokawa, K.
AU  - Hattori, M.
AU  - Nakano, K.
AU  - Maruyama, F.
AU  - Nakagawa, I.
AU  - Ooshima, T.
TI  - Complete Genome Sequence of the Serotype k Streptococcus mutans Strain LJ23.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2754
EP  - 2755
VL  - 194
AB  - Streptococcus mutans is the major pathogen of dental caries and occasionally causes infective
AB  - endocarditis. Here we report the complete genome sequence of
AB  - serotype k S. mutans strain LJ23, which was recently isolated from the oral
AB  - cavity of a Japanese patient.
ER  -

TY  - JOUR
AU  - Aiken, C.
AU  - Gumport, R.I.
TI  - Restriction endonuclease RsrI from Rhodobacter sphaeroides, an isoschizomer of EcoRI:  purification and properties.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 7901
EP  - 7916
VL  - 16
AB  - We have purified RsrI endonuclease (R.RsrI), an isoschizomer of EcoRI, from Rhodobacter
AB  - sphaeroides strain 630. The enzyme is homogeneous as judged by polyacrylamide gel
AB  - electrophoresis and size-exclusion high-performance liquid chromatography. RsrI endonuclease
AB  - is a dimer over the concentration range of 0.05 to 1.4 mg/ml. The reduced and denatured
AB  - molecular weight of the enzyme is 30,000 Da. R.RsrI, like R.EcoRI, catalyzes the cleavage of
AB  - duplex DNA and oligodeoxyribonucleotides between the first two residues of the sequence
AB  - GAATTC. R.RsrI exhibits a kM of 14 nM and a kcat of 6.5 min-1 when reacting with pBR322 DNA at
AB  - 25C. R.RsrI differs from R.EcoRI in its N-terminal amino acid sequence, susceptibility to
AB  - inhibition by antibodies, sensitivity to N-ethylmaleimide, isoelectric point, state of
AB  - aggregation at high concentrations, temperature lability, and conditions for optimal reaction.
AB  - R.RsrI displays a reduction of specificity (star activity) under conditions that also relax
AB  - the specificity of R.EcoRI.
ER  -

TY  - JOUR
AU  - Aiken, C.
AU  - Gumport, R.I.
TI  - Interaction of RsrI endonuclease, an isoschizomer of EcoRI, with oligodeoxyribonucleotides containing base analogues.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 79
EP  - 79
VL  - 13D
AB  - We have initiated a systematic kinetic study of the RsrI endonuclease, an
AB  - isoschizomer of EcoRI, using oligodeoxyribonucleotides containing base
AB  - analogues as substrates.  Several of these substrates were provided by Dr. L.
AB  - McLaughlin, Boston College, who tested them with EcoRI.  All of the base
AB  - substitutions tested affect the interaction of both enzymes with DNA.  In
AB  - general, the effects with RsrI are more pronounced than with EcoRI, as measured
AB  - by the greater reduction in the specificity constant (kcat/Km) for a given
AB  - substitution.  For two substrates, the RsrI-catalyzed reaction was very slow;
AB  - less than one-tenth the rate of the corresponding EcoRI reaction.  The lower
AB  - tolerance of RsrI for base analogues in its recognition sequence may reflect a
AB  - difference in the mechanisms by which these two enzymes recognize the same DNA
AB  - sequence and cut it at the same site.  We are presently determining whether
AB  - RsrI kinks and unwinds DNA to the same extent that EcoRI does.
ER  -

TY  - JOUR
AU  - Aiken, C.
AU  - Milarski-Brown, K.
AU  - Gumport, R.I.
TI  - RsrI and EcoRI are two different restriction endonucleases that recognize the same DNA sequence.
JO  - Fed. Proc.
PY  - 1986
SP  - 1914
EP  - 1914
VL  - 45
AB  - In order to study the recognition of specific DNA sequences by proteins, we
AB  - have isolated RsrI endonuclease from Rhodopseudomonas sphaeroides strain 630.
AB  - The preparation is approximately 80% pure, with one major band which comigrates
AB  - on SDS gels with EcoRI endonuclease (M=30,000+-2000).  RsrI cleaves the duplex
AB  - octanucleotide pGGAATTCC to form pGG.  Plasmid and phage DNA digests confirm
AB  - that RsrI and EcoRI cleave the same sequence.  However, the enzymes appear to
AB  - be different.  Antiserum to EcoRI required 1000-fold increased concentrations
AB  - to effectively inhibit RsrI activity.  In addition, amino acid sequence
AB  - analysis of the first 40 amino acids of RsrI revealed little homology with
AB  - EcoRI.  Furthermore, the R. sphaeroides genome shows little homology with the
AB  - EcoRI gene when tested by Southern blotting and hybridization with washing at
AB  - low stringency.  A corresponding RsrI methylase activity has been identified
AB  - and separated from the endonuclease by chromatography on phosphocellulose.
AB  - This activity catalyzes the transfer of methyl groups from AdoMet to DNA,
AB  - rendering the DNA resistant to cleavage by both RsrI and EcoRI endonucleases.
AB  - It will be of interest to compare the mechanisms by which these enzymes
AB  - recognize their common DNA sequence.
ER  -

TY  - JOUR
AU  - Aiken, C.R.
TI  - Sequence-specific recognition of DNA by RsrI endonuclease of Rhodobacter sphaeroides, an isoschizomer of EcoRI.
JO  - Diss. Abstr.
PY  - 1991
SP  - 1399
EP  - 1399
VL  - 52
AB  - In order to study the interaction of RsrI endonuclease with its DNA recognition sequence and
AB  - to determine whether RsrI recognizes DNA using a mechanism similar to that of EcoRI, I have
AB  - purified milligram amounts of the enzyme to near homogeneity from its natural source,
AB  - Rhodobacter sphaeroides strain 630. The enzyme comigrates with EcoRI during SDS-PAGE, with a
AB  - reduced and denatured molecular weight of 30,000+/- 2000 Da. RsrI endonuclease is a dimer at
AB  - concentrations of 0.05 to 1.4 mg/ml. In contrast to EcoRI, no tetrameric form was observed.
AB  - The isoelectric point of the endonuclease was determined to be 7.0-different than the value of
AB  - 6.3 reported for EcoRI. The temperature and salt-dependence of the catalytic activity of RsrI
AB  - also differ from those of EcoRI. The reaction exhibits Michaelis-Menten kinetics, and values
AB  - of 14 nM and 6.5 min-1 were determined for Km and kcat, respectively using plasmid pBR322 as a
AB  - substrate. RsrI endonuclease, unlike EcoRI, is inactivated by preincubating the enzyme with 10
AB  - mM N-ethylmaleimide. This suggests that RsrI but not EcoRI has an essential sulfhydryl. RsrI
AB  - endonuclease cleaves noncanonical sequences in reactions containing 12.5 mM Tris-HCl, 2.5 mM
AB  - MgCl2, and 26% ethylene glycol. RsrI binding bends DNA by approximately 50 degrees and unwinds
AB  - the DNA helix by 25 +/- 5 degree - values similar to those reported for EcoRI endonuclease.
AB  - RsrI binding protects 12 nucleotides from cleavage by hydroxyl radical and MPE-Fe(II)
AB  - footprinting reagents. I have tested the RsrI endonuclease with a series of
AB  - decadeoxyribonucleotides containing base analogues as substrates. The kinetics of RsrI
AB  - cleavage are affected by each substitution, and the effects are generally more pronounced than
AB  - with EcoRI, as shown by the greater reduction in the specificity constant kcat/Km for a given
AB  - substitution. For several substrates, cleavage by RsrI was very slow - less than one-tenth the
AB  - rate of the corresponding EcoRI reaction. This lower tolerance of the RsrI endonuclease for
AB  - functional group changes in its recognition site may reflect differences in the mechanisms by
AB  - which RsrI and EcoRI recognize and cleave DNA.
ER  -

TY  - JOUR
AU  - Aiken, C.R.
AU  - Fisher, E.W.
AU  - Gumport, R.I.
TI  - The specific binding, bending, and unwinding of DNA by RsrI endonuclease, an isoschizomer of EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 19063
EP  - 19069
VL  - 266
AB  - To determine whether RsrI endonuclease recognizes and cleaves the sequence
AB  - GAATTC in duplex DNA similarly to its isoschizomer EcoRI we initiated a
AB  - functional comparison of the two enzymes.  Equilibrium binding experiments
AB  - showed that at 20C RsrI endonuclease binds to specific and nonspecific
AB  - sequences in DNA with affinities similar to those of EcoRI.  At 0C the affinity
AB  - of RsrI for its specific recognition sequence is reduced 7-fold whereas the
AB  - affinity for noncanonical sequences remains relatively unchanged.  Unlike
AB  - EcoRI, incubation of RsrI endonuclease with N-ethylmaleimide inactivates the
AB  - enzyme; however, preincubation with DNA prevents the inactivation.  The
AB  - N-ethylmaleimide-treated enzyme fails to bind DNA as assayed by gel mobility
AB  - shift assays.  Comparison of the deduced amino acid sequences of RsrI and EcoRI
AB  - endonucleases suggests that modification of Cys245 is responsible for the
AB  - inactivation.  Fe(II).EDTA and methidiumpropyl-EDTA.Fe(II) footprinting results
AB  - indicate that RsrI, like EcoRI, protects 12 base pairs from cleavage when bound
AB  - to its specific recognition sequence in the absence of Mg2+.  RsrI bends DNA by
AB  - approximately 50 degrees, as determined by measuring the relative
AB  - electrophoretic mobilities of specific RsrI-DNA complexes with the binding site
AB  - in the center or near the end of the DNA fragment.  This value is similar to
AB  - that reported for EcoRI.  RsrI also unwinds the DNA helix by 25 degrees +/- 5
AB  - degrees, a value close to that reported for EcoRI endonuclease.  Collectively,
AB  - these results indicate that the overall structural changes induced in the DNA
AB  - by the binding of RsrI and EcoRI endonucleases to DNA in the absence of Mg2+
AB  - are similar.  In the accompanying paper (Aiken, C.R., McLaughlin, L.W., and
AB  - Gumport, R.I. (1991) J. Biol. Chem. 266, 19070-19078) we present results of
AB  - studies of RsrI endonuclease using oligonucleotide substrates containing base
AB  - analogues which suggest differences in the ways the two enzymes cleave DNA.
ER  -

TY  - JOUR
AU  - Aiken, C.R.
AU  - Gumport, R.I.
TI  - Base analogs in study of restriction enzyme-DNA interactions.
JO  - Methods Enzymol.
PY  - 1991
SP  - 433
EP  - 457
VL  - 208
AB  - Enzymologists have long sought to discern the topography of the active sites of enzymes by
AB  - examining substrate analogs for their ability to serve as reactants. Such investigations aim
AB  - to contribute to our understanding of the kinetic and chemical mechanisms as well as the
AB  - stereochemistry and stereoselectivity of a reaction.
ER  -

TY  - JOUR
AU  - Aiken, C.R.
AU  - McLaughlin, L.W.
AU  - Gumport, R.I.
TI  - The highly homologous isoschizomers RsrI endonuclease and EcoRI endonuclease do not recognize their target sequence identically.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 19070
EP  - 19078
VL  - 266
AB  - Using a series of decadeoxyribonucleotides containing base analogues as
AB  - substrates we measured the steady-state kinetic parameters for the reaction
AB  - catalyzed by RsrI endonuclease and compared the results to those with its
AB  - isoschizomer EcoRI.  The kinetics of RsrI cleavage are affected by each
AB  - substitution, with the effects being generally more deleterious than with
AB  - EcoRI, as shown by the greater reduction in the specificity constant kcat/Km.
AB  - The magnitudes of the effects of several substitutions are consistent with the
AB  - formation of direct enzyme-nucleobase contacts at the indicated positions.
AB  - With substrates containing 2-amino-purine or 2,6-diaminopurine at the central
AB  - adenine or uracil at the outermost thymine in the recognition sequence,
AB  - cleavage by RsrI was very slow, less than one-tenth the rate of the
AB  - corresponding EcoRI-catalyzed reaction.  The lower tolerance of RsrI
AB  - endonuclease for functional group changes in its recognition site may reflect
AB  - differences in the mechanisms of DNA recognition by the two enzymes.  Although
AB  - RsrI and EcoRI endonucleases bind with similar affinities to specific and
AB  - nonspecific DNA sequences and appear to introduce similar structural
AB  - distortions in DNA upon binding, the use of substrate analogues reveals
AB  - significant differences at the level of catalysis in the mechanisms by which
AB  - these two endonucleases recognize the duplex sequence GAATTC.
ER  -

TY  - JOUR
AU  - Ailloud, F.
AU  - Lowe, T.M.
AU  - Robene, I.
AU  - Cruveiller, S.
AU  - Allen, C.
AU  - Prior, P.
TI  - In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum.
JO  - PeerJ
PY  - 2016
SP  - e1549
EP  - e1549
VL  - 4
AB  - Background. Ralstonia solanacearum is an economically important plant pathogen
AB  - with an unusually large host range. The Moko (banana) and NPB (not pathogenic to
AB  - banana) strain groups are closely related but are adapted to distinct hosts.
AB  - Previous comparative genomics studies uncovered very few differences that could
AB  - account for the host range difference between these pathotypes. To better
AB  - understand the basis of this host specificity, we used RNAseq to profile the
AB  - transcriptomes of an R. solanacearum Moko strain and an NPB strain under in vitro
AB  - and in planta conditions. Results. RNAs were sequenced from bacteria grown in
AB  - rich and minimal media, and from bacteria extracted from mid-stage infected
AB  - tomato, banana and melon plants. We computed differential expression between each
AB  - pair of conditions to identify constitutive and host-specific gene expression
AB  - differences between Moko and NPB. We found that type III secreted effectors were
AB  - globally up-regulated upon plant cell contact in the NPB strain compared with the
AB  - Moko strain. Genes encoding siderophore biosynthesis and nitrogen assimilation
AB  - genes were highly up-regulated in the NPB strain during melon pathogenesis, while
AB  - denitrification genes were up-regulated in the Moko strain during banana
AB  - pathogenesis. The relatively lower expression of oxidases and the denitrification
AB  - pathway during banana pathogenesis suggests that R. solanacearum experiences
AB  - higher oxygen levels in banana pseudostems than in tomato or melon xylem.
AB  - Conclusions. This study provides the first report of differential gene expression
AB  - associated with host range variation. Despite minimal genomic divergence, the
AB  - pathogenesis of Moko and NPB strains is characterized by striking differences in
AB  - expression of virulence- and metabolism-related genes.
ER  -

TY  - JOUR
AU  - Ainala, S.K.
AU  - Ashok, S.
AU  - Ko, Y.
AU  - Park, S.
TI  - Glycerol assimilation and production of 1,3-propanediol by Citrobacter amalonaticus Y19.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2013
SP  - 5001
EP  - 5011
VL  - 97
AB  - Citrobacter amalonaticus Y19 (Y19) was isolated because of its ability for carbon
AB  - monoxide-dependent hydrogen production (water-gas shift reaction). This paper
AB  - reports the assimilation of glycerol and the production of 1,3-propanediol
AB  - (1,3-PDO) by Y19. Genome sequencing revealed that Y19 contained the genes for the
AB  - utilization of glycerol and 1,2-propanediol (pdu operon) along with those for the
AB  - synthesis of coenzyme B(12) (cob operon). On the other hand, it did not possess
AB  - the genes for the fermentative metabolism of glycerol of Klebsiella pneumoniae,
AB  - which consists of both the oxidative (dhaD and dhaK) and reductive (dhaB and
AB  - dhaT) pathways. In shake-flask cultivation under aerobic conditions, Y19 could
AB  - grow well with glycerol as the sole carbon source and produced 1,3-PDO. The level
AB  - of 1,3-PDO production was improved when vitamin B(12) was added to the culture
AB  - medium under aerobic conditions. Under anaerobic conditions, cell growth and
AB  - 1,3-PDO production on glycerol was also possible, but only when an exogenous
AB  - electron acceptor, such as nitrate or fumarate, was added. This is the first
AB  - report of the glycerol metabolism and 1,3-PDO production by C. amalonaticus Y19.
ER  -

TY  - JOUR
AU  - Ainala, S.K.
AU  - Somasundar, A.
AU  - Park, S.
TI  - Complete Genome Sequence of Pseudomonas denitrificans ATCC 13867.
JO  - Genome Announcements
PY  - 2013
SP  - e00257
EP  - e00213
VL  - 1
AB  - Pseudomonas denitrificans ATCC 13867, a Gram-negative facultative anaerobic bacterium, is
AB  - known to produce vitamin B12 under aerobic conditions. This paper
AB  - reports the annotated whole-genome sequence of the circular chromosome of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Ainsworth, S.
AU  - Mahony, J.
AU  - van Sinderen, D.
TI  - The Plasmid Complement of Lactococcus lactis UC509.9 Encodes Multiple Bacteriophage Resistance Systems.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 4341
EP  - 4349
VL  - 80
AB  - Lactococcus lactis subsp. cremoris strains are used globally for the production of fermented
AB  - dairy products, particularly hard cheeses. Believed to be of plant origin, L. lactis strains
AB  - that are used as starter cultures have undergone extensive adaptation to the dairy
AB  - environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids
AB  - that specify technologically important phenotypic traits. Here, we present a detailed analysis
AB  - of the eight plasmids of L. lactis UC509.9, an Irish dairy starter strain. Key industrial
AB  - phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were
AB  - identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified,
AB  - including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed
AB  - phage resistance of L. lactis UC509.9. AbiB escape mutants were generated for phage sk1, which
AB  - were found to carry mutations in orf6, which encodes the major capsid protein of this phage.
ER  -

TY  - JOUR
AU  - Ainsworth, S.
AU  - Zomer, A.
AU  - de Jager, V.
AU  - Bottacini, F.
AU  - van Hijum, S.A.
AU  - Mahony, J.
AU  - van Sinderen, D.
TI  - Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage.
JO  - Genome Announcements
PY  - 2013
SP  - e00119
EP  - e00112
VL  - 1
AB  - Here, we report the complete genome of Lactococcus lactis subsp. cremoris UC509.9, an Irish
AB  - dairy starter. The circular chromosome of L. lactis UC509.9
AB  - represents the smallest among those of the sequenced lactococcal strains, while
AB  - its large complement of eight plasmids appears to be a reflection of its
AB  - adaptation to the dairy environment.
ER  -

TY  - JOUR
AU  - Aizawa, Y.
AU  - Xiang, Q.
AU  - Pyle, A.M.
TI  - Kinetic dissection of the multistep process in L1.ltrB intron mobility.
JO  - Nucleic Acids Res. Suppl.
PY  - 2001
SP  - 249
EP  - 250
VL  - 1
AB  - A kinetic characterization is presented for intron insertion into a target duplex DNA site
AB  - during L1.ltrB intron mobility. This reaction is catalyzed by a ribonucleoprotein particle
AB  - (RNP), consisting of a lariat form of group II intron RNA and the intron-encoded LtrA protein.
AB  - In the first stage of intron mobility, the RNA component of the enzyme by itself inserts
AB  - directly into the target ds DNA site, and thus, the RNP enzyme does not carry out turnover.
AB  - Using single-turnover kinetics, we established an in vitro kinetic assay system and
AB  - investigated mechanism of the intron RNA insertion process.
ER  -

TY  - JOUR
AU  - Aizenberg-Gershtein, Y.
AU  - Izhaki, I.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Reddy, T.
AU  - Huntemann, M.
AU  - Pillay, M.
AU  - Markowitz, V.
AU  - Goker, M.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Halpern, M.
TI  - High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 4
EP  - 4
VL  - 11
AB  - Phaseolibacter flectens strain ATCC 12775(T) (Halpern et al., Int J Syst Evol Microbiol
AB  - 63:268-273, 2013) is a Gram-negative, rod shaped, motile, aerobic,
AB  - chemoorganotroph bacterium. Ph. flectens is as a plant-pathogenic bacterium on
AB  - pods of French bean and was first identified by Johnson (1956) as Pseudomonas
AB  - flectens. After its phylogenetic position was reexamined, Pseudomonas flectens
AB  - was transferred to the family Enterobacteriaceae as Phaseolibacter flectens gen.
AB  - nov., comb. nov. Here we describe the features of this organism, together with
AB  - the draft genome sequence and annotation. The DNA GC content is 44.34 mol%. The
AB  - chromosome length is 2,748,442 bp. It encodes 2,437 proteins and 89 RNA genes.
AB  - Ph. flectens genome is part of the Genomic Encyclopedia of Type Strains, Phase I:
AB  - the one thousand microbial genomes study.
ER  -

TY  - JOUR
AU  - Ajdic, D.
AU  - McShan, W.M.
AU  - McLaughlin, R.E.
AU  - Savic, G.
AU  - Chang, J.
AU  - Carson, M.B.
AU  - Primeaux, C.
AU  - Tian, R.
AU  - Kenton, S.
AU  - Jia, H.
AU  - Lin, S.
AU  - Qian, Y.
AU  - Li, S.
AU  - Zhu, H.
AU  - Najar, F.
AU  - Lai, H.
AU  - White, J.
AU  - Roe, B.A.
AU  - Jerretti, J.J.
TI  - Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 14434
EP  - 14439
VL  - 99
AB  - Streptococcus mutans is the leading cause of dental caries (tooth decay) worldwide and is
AB  - considered to be the most cariogenic of all of the oral streptococci. The genome of S. mutans
AB  - UA159, a serotype c strain, has been completely sequenced and is composed of 2,030,936 base
AB  - pairs. It contains 1,963 ORFs, 63% of which have been assigned putative functions. The genome
AB  - analysis provides further insight into how S. mutans has adapted to surviving the oral
AB  - environment through resource acquisition, defense against host factors, and use of gene
AB  - products that maintain its niche against microbial competitors. S. mutans metabolizes a wide
AB  - variety of carbohydrates via nonoxidative pathways, and all of these pathways have been
AB  - identified, along with the associated transport systems whose genes account for almost 15% of
AB  - the genome. Virulence genes associated with extracellular adherent glucan production,
AB  - adhesins, acid tolerance, proteases, and putative hemolysins have been identified. Strain
AB  - UA159 is naturally competent and contains all of the genes essential for competence and quorum
AB  - sensing. Mobile genetic elements in the form of IS elements and transposons are prominent in
AB  - the genome and include a previously uncharacterized conjugative transposon and a composite
AB  - transposon containing genes for the synthesis of antibiotics of the gramicidin/bacitracin
AB  - family; however, no bacteriophage genomes are present.
ER  -

TY  - JOUR
AU  - Akamatsu, M.A.
AU  - Nishiyama, M.Y. Jr.
AU  - Morone, M.
AU  - Oliveira, U.C.
AU  - Bezerra, M.F.
AU  - Sakauchi, M.A.
AU  - Raw, I.
AU  - Junqueira-de-Azevedo, I.L.
AU  - Kitajima, J.P.
AU  - Carvalho, E.
AU  - Ho, P.L.
TI  - Whole-Genome Sequence of a Bordetella pertussis Brazilian Vaccine Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01570
EP  - e01514
VL  - 3
AB  - Despite the reduction in incidence after vaccination, pertussis disease is still considered a
AB  - public health problem worldwide, mainly due to recent and potential  new outbreaks. We report
AB  - here the complete genome of the Bordetella pertussis Butantan strain used in the Brazilian
AB  - National Immunization Program as a whole-cell pertussis antigen to compose vaccines such as
AB  - DTwP (diphtheria, tetanus, and whole-cell pertussis).
ER  -

TY  - JOUR
AU  - Akasaka, T.
AU  - Matsuura, K.
AU  - Emi, N.
AU  - Kobayashi, K.
TI  - Conjugation of plasmid DNAs with lactose via diazocoupling enhances resistance to restriction enzymes and acquires binding affinity to galactose-specific lectin.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1999
SP  - 323
EP  - 328
VL  - 260
AB  - Oligosaccharide-plasmid DNA conjugates were synthesized simply and effectively via the
AB  - diazocoupling method.  Plasmids (pUC19, pTRI-beta-actin, and pEGFP-C1) were treated with an
AB  - N-beta-lactoside-substituted diazonium salt to yield diazocoupling products with degree of
AB  - substitutions of 2.5-3.1 mol% of overall nucleobases. The lactose-pUC19 conjugate was found to
AB  - resist restriction enzymes more strongly than the nonconjugated plasmid DNA and to acquire a
AB  - strong binding affinity to galactose-specific lectin RCA(120). The diazocoupling modification
AB  - of pTRI-beta-actin plasmid DNA little influenced in vitro transcription with T7 RNA
AB  - polymerase. When lactose-pEGFP-C1 conjugate was transfected to baby hamster kidney (BHK) cells
AB  - by means of cationic lipids, transduced gene was expressed in BHK cells similarly with the
AB  - nonconjugated pEGFP-C1. The modification of plasmid DNA with carbohydrate enhanced the
AB  - resistance to restriction enzymes and developed a strong binding affinity to
AB  - galactose-specific lectin.
ER  -

TY  - JOUR
AU  - Akatov, A.K.
AU  - Zueva, V.S.
AU  - Dmitrenko, O.A.
TI  - A new approach to establishing the set of phages for typing methicillin-resistant Staphylococcus aureus.
JO  - J. Chemother.
PY  - 1991
SP  - 275
EP  - 278
VL  - 3
AB  - A new approach to using experimental phages for typing methicillin-resistant S.
AB  - aureus (MRSA) non-sensitive to the phages of International Basic Set (IBS) is
AB  - described.  The collection includes phage 85, modified on a culture of MRSA,
AB  - and 5 phages induced from MRSA strains isolated in clinics of Moscow in
AB  - 1975-76.  Firstly, the modified phage selects cultures according to the
AB  - specific character of its restriction-modification system, then the induced
AB  - phages differentiate the selected strains into 5 groups (1,2,3,4,5) based on
AB  - the specificity of the prophages they contain.  Group 1 strains can further be
AB  - differentiated into 5 subgroups (A,B,C,D,E) by additional phages.  Forty-one
AB  - MRSA strains isolated in 1987-90 in various hospitals of Moscow showing no
AB  - sensitivity to IBS phages, were lysed by the modified phage, 15 of them
AB  - belonging to Group 2 and isolated in the traumatological hospital, 26 belonging
AB  - to Group 1 and were circulating in the burn center.  Twenty-three strains of
AB  - Group 1 appertain to subgroup 1B and were isolated over a 4-year period from
AB  - the burned surface of patients and from the throat of a medical staff carrier.
ER  -

TY  - JOUR
AU  - Akbar, S.
AU  - Dowd, S.E.
AU  - Stevens, D.C.
TI  - Draft Genome Sequence of Cystobacter ferrugineus Strain Cbfe23.
JO  - Genome Announcements
PY  - 2017
SP  - e01601
EP  - e01616
VL  - 5
AB  - In an effort to explore myxobacterial natural product biosynthetic pathways, the  draft genome
AB  - sequence of Cystobacter ferrugineus strain Cbfe23 has been obtained.
AB  - Analysis of the genome using antiSMASH suggests a multitude of unique natural
AB  - product biosynthetic pathways. This genome will contribute to the investigation
AB  - of secondary metabolism in other myxobacterial species.
ER  -

TY  - JOUR
AU  - Akbar, S.
AU  - Rout, S.P.
AU  - Humphreys, P.N.
TI  - Draft Genome Sequence of the Biofilm-Forming Stenotrophomonas maltophilia Strain  53.
JO  - Genome Announcements
PY  - 2015
SP  - e00312
EP  - e00315
VL  - 3
AB  - A clinical strain of Stenotrophomonas maltophilia (designated strain 53) was obtained, and a
AB  - whole-genome sequence was generated. The subsequent draft
AB  - whole-genome sequence demonstrated the presence of a number of genes encoding for
AB  - proteins involved in resistance to a number of antimicrobial therapies.
ER  -

TY  - JOUR
AU  - Akbar, S.
AU  - Rout, S.P.
AU  - Humphreys, P.N.
TI  - Draft Genome Sequences of Pseudomonas aeruginosa Strain PS3 and Citrobacter freundii Strain SA79 Obtained from a Wound Dressing-Associated Biofilm.
JO  - Genome Announcements
PY  - 2015
SP  - e00561
EP  - e00515
VL  - 3
AB  - Two isolates, one from the genus Pseudomonas and the second from Citrobacter, were isolated
AB  - from a wound dressing-associated biofilm. Following whole-genome
AB  - sequencing, the two isolates presented genes encoding for resistance to
AB  - antibiotics and those involved in exopolysaccharide production.
ER  -

TY  - JOUR
AU  - Akcelik, M.
TI  - The conjugal plasmid pLL10236 encodes lactose fermentation ability, restriction/modification activity, bacteriocin production and immunity in Lactococcus lactis subsp. Lactis LL102.
JO  - Food Microbiol.
PY  - 1999
SP  - 487
EP  - 494
VL  - 16
AB  - A 36 kb plasmid, designed as pLL 10236, was determined in Lactococcus lactis subsp. Lactis
AB  - LL102.  This plasmid mediates lactose fermentation ability (Lac+), bacteriocin production
AB  - (Bac+) and immunity (Imm+), and restriction/modification (R+M+) activity against bacteriophage
AB  - O1120 in strain LL102.  The conjugal ability of pLL 10236 and expression of pLL 10236 encoding
AB  - traits were determined by using a Lac-, Bac-, Imm- and (R-M-) recipient strain L. lactis
AB  - subsp. Lactis P81-1.
ER  -

TY  - JOUR
AU  - Akcelik, M.
AU  - Sanlibaba, P.
AU  - Tukel, C.
TI  - Phage resistance in Lactococcus lactis subsp lactis strains isolated from traditional fermented milk products in Turkey.
JO  - Int. J. Food Sci. Technol.
PY  - 2000
SP  - 473
EP  - 481
VL  - 35
AB  - Lactococcus lactis subsp. lactis strains isolated from traditional fermented milk products in
AB  - Turkey were used to determine their phage
AB  - resistance against three different lactic phages. The following modes
AB  - of action were examined: phage adsorption inhibition in five strains,
AB  - abortive infection (heat sensitive phage resistance) in three strains,
AB  - restriction/modification in four strains and blocking of phage DNA
AB  - injection in one strain. The genetic nature of the phage resistance
AB  - systems in these strains was determined by comparison of phage
AB  - proliferation parameters, e.g. adsorption (%), EOP, burst size, latent
AB  - period and production of major capsid protein, between wild-type
AB  - strains and their plasmid-cured derivatives.
ER  -

TY  - JOUR
AU  - Akhtar, M.
AU  - Perehinec, T.M.
AU  - Nazli, A.
AU  - Hill, P.J.
AU  - Rees, C.E.D.
TI  - Partial DNA methylation in Listeria monocytogenes creates variable populations of cells with altered virulence.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 411
EP  - 411
VL  - 101
AB  - We have recently identified variable patterns of DNA methylation sites in the major virulence
AB  - region of the food borne pathogen Listeria
AB  - monocytogenes. The degree of partial methylation is specific to the
AB  - particular isolate, but high level methylation was only found in
AB  - serotype 4b strains, which are associated with outbreaks of
AB  - listeriosis. The methylation is visualised as reproducible band
AB  - patterns when DNA from a culture of cells is subjected to restriction
AB  - digest and southern hybridisation using a prfA-hlyA gene probe.
AB  - Controls were carried out to ensure that this partial restriction was
AB  - due to specific methylation and not due to simple enzyme inhibition.
AB  - Use of isoschizomers with differing methylation sensitivities allowed
AB  - us to identify this as cytosine-specific methylation. The gene
AB  - responsible for this methylation was cloned and found to have homology
AB  - to other cytosine methyl-transferases. To create these reproducible
AB  - patterns of partial DNA methylation, the methylation event must be
AB  - controlled. To investigate this, single Listeria monocytogenes cells,
AB  - which can only be methylated at one of the susceptible sites, were used
AB  - to inoculate tubes of broth and allowed to grow to stationary phase.
AB  - When the DNA was recovered from each of these cultures, all samples
AB  - exhibited exactly the same mixed pattern of DNA methylation indicating
AB  - that these patterns are not inherited, but rather methylation at this
AB  - locus must occur in a controlled manner. Either activity of the
AB  - methylase is directly modulated or architecture of the chromosomal DNA
AB  - must control access of the methylase to susceptible sites. In invasion
AB  - assays using Caco-2 cell lines, a correlation could be found between
AB  - the degree of DNA methylation associated with an isolate and the
AB  - invasiveness of that strain. This suggests that the methylation may
AB  - have an influence on gene expression and that in these cultures with
AB  - highly variable methylation patterns, some cells may be pre-primed to
AB  - cause disease.
ER  -

TY  - JOUR
AU  - Akita, H.
AU  - Kimura, Z.
AU  - Yusoff, M.Z.
AU  - Nakashima, N.
AU  - Hoshino, T.
TI  - Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00630
EP  - e00616
VL  - 4
AB  - Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City
AB  - in Hiroshima Prefecture, Japan. Here, we present a draft
AB  - genome sequence of this strain, which consists of a total of 4 contigs containing
AB  - 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Akita, H.
AU  - Kimura, Z.I.
AU  - Hoshino, T.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain CCA1, Isolated from Leaf Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01371
EP  - e01316
VL  - 4
AB  - Pseudomonas sp. strain CCA1 was isolated from leaf soil collected in Higashi-Hiroshima City in
AB  - Hiroshima Prefecture, Japan. Here, we present a draft
AB  - genome sequence of this strain. The genome consists of 24 contigs for a total of
AB  - 6,993,992 bp, 8,917 predicted coding sequences, and a GC content of 67.2%.
ER  -

TY  - JOUR
AU  - Akita, H.
AU  - Kimura, Z.I.
AU  - Matsushika, A.
TI  - Complete Genome Sequence of Ureibacillus thermosphaericus A1, a Thermophilic Bacillus Isolated from Compost.
JO  - Genome Announcements
PY  - 2017
SP  - e00910
EP  - e00917
VL  - 5
AB  - Ureibacillus thermosphaericus A1 was isolated from compost collected in Munakata  City,
AB  - Fukuoka Prefecture, Japan. Here, we report the first complete genome
AB  - sequence of U. thermosphaericus The complete genome of this strain consists of
AB  - 3,488,104 bp with a GC content of 36.3% and comprises 3,362 predicted coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Akiyama, T.
AU  - Ishige, T.
AU  - Kanesaki, Y.
AU  - Ito, S.
AU  - Oinuma, K.
AU  - Takaya, N.
AU  - Sasaki, Y.
AU  - Yajima, S.
TI  - Draft Genome Sequence of Microbacterium sp. Strain HM58-2, Which Hydrolyzes Acylhydrazides.
JO  - Genome Announcements
PY  - 2016
SP  - e00554
EP  - e00516
VL  - 4
AB  - We report the draft genome sequence of Microbacterium sp. strain HM58-2, which produces
AB  - hydrazidase, an enzyme hydrolyzing acylhydrazides. The estimated genome
AB  - size is 3.9 Mb. Genome sequence information of this strain will help to identify
AB  - an assimilating mechanism of nonnatural compounds in this strain and to develop
AB  - ecological applications.
ER  -

TY  - JOUR
AU  - Aklujkar, M.
AU  - Young, N.D.
AU  - Holmes, D.
AU  - Chavan, M.
AU  - Risso, C.
AU  - Kiss, H.E.
AU  - Han, C.S.
AU  - Land, M.L.
AU  - Lovley, D.R.
TI  - The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.
JO  - BMC Genomics
PY  - 2010
SP  - 490
EP  - 490
VL  - 11
AB  - BACKGROUND: Geobacter species in a phylogenetic cluster known as
AB  - subsurface clade 1 are often the predominant microorganisms in subsurface
AB  - environments in which Fe(III) reduction is the primary electron-accepting
AB  - process. Geobacter bemidjiensis, a member of this clade, was isolated from
AB  - hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and
AB  - is closely related to Geobacter species found to be abundant at other
AB  - subsurface sites. This study examines whether there are significant
AB  - differences in the metabolism and physiology of G. bemidjiensis compared
AB  - to non-subsurface Geobacter species. RESULTS: Annotation of the genome
AB  - sequence of G. bemidjiensis indicates several differences in metabolism
AB  - compared to previously sequenced non-subsurface Geobacteraceae, which will
AB  - be useful for in silico metabolic modeling of subsurface bioremediation
AB  - processes involving Geobacter species. Pathways can now be predicted for
AB  - the use of various carbon sources such as propionate by G. bemidjiensis.
AB  - Additional metabolic capabilities such as carbon dioxide fixation and
AB  - growth on glucose were predicted from the genome annotation. The presence
AB  - of different dicarboxylic acid transporters and two oxaloacetate
AB  - decarboxylases in G. bemidjiensis may explain its ability to grow by
AB  - disproportionation of fumarate. Although benzoate is the only aromatic
AB  - compound that G. bemidjiensis is known or predicted to utilize as an
AB  - electron donor and carbon source, the genome suggests that this species
AB  - may be able to detoxify other aromatic pollutants without degrading them.
AB  - Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which
AB  - makes it the first Geobacter species identified as having a vitamin
AB  - requirement. Several features of the genome indicated that G. bemidjiensis
AB  - has enhanced abilities to respire, detoxify and avoid oxygen. CONCLUSION:
AB  - Overall, the genome sequence of G. bemidjiensis offers surprising insights
AB  - into the metabolism and physiology of Geobacteraceae in subsurface
AB  - environments, compared to non-subsurface Geobacter species, such as the
AB  - ability to disproportionate fumarate, more efficient oxidation of
AB  - propionate, enhanced responses to oxygen stress, and dependence on the
AB  - environment for a vitamin requirement. Therefore, an understanding of the
AB  - activity of Geobacter species in the subsurface is more likely to benefit
AB  - from studies of subsurface isolates such as G. bemidjiensis than from the
AB  - non-subsurface model species studied so far.
ER  -

TY  - JOUR
AU  - Akman, L.
AU  - Rio, R.V.M.
AU  - Beard, C.B.
AU  - Aksoy, S.
TI  - Genome size determination and coding capacity of Sodalis glossinidius, an enteric symbiont of Tsetse flies, as revealed by hybridization to Escherichia coli gene arrays.
JO  - J. Bacteriol.
PY  - 2001
SP  - 4517
EP  - 4525
VL  - 183
AB  - Recent molecular characterization of various microbial genomes has revealed differences in
AB  - genome size and coding capacity between obligate symbionts and intracellular pathogens versus
AB  - free-living organisms. Multiple symbiotic microorganisms have evolved with tsetse fly, the
AB  - vector of African trypanosomes, over long evolutionary times. Although these symbionts are
AB  - indispensable for tsetse fecundity, the biochemical and molecular basis of their functional
AB  - significance is unknown. Here, we report on the genomic aspects of the secondary symbiont
AB  - Sodalis glossinidius. The genome size of Sodalis is approximately 2 Mb. Its DNA is subject to
AB  - extensive methylation and based on some of its conserved gene sequences has an A+T content of
AB  - only 45%, compared to the typically AT-rich genomes of endosymbionts. Sodalis also harbors an
AB  - extrachromosomal plasmid about 134 kb in size. We used a novel approach to gain insight into
AB  - Sodalis genomic contents, i.e., hybridizing its DNA to macroarrays developed for Escherichia
AB  - coli, a closely related enteric bacterium. In this analysis we detected 1,800 orthologous
AB  - genes, corresponding to about 85% of the Sodalis genome. The Sodalis genome has apparently
AB  - retained its genes for DNA replication, transcription, translation, transport, and the
AB  - biosynthesis of amino acids, nucleic acids, vitamins, and cofactors. However, many genes
AB  - involved in energy metabolism and carbon compound assimilation are apparently missing, which
AB  - may indicate an adaptation to the energy sources available in the only nutrient of  the tsetse
AB  - host, blood. We present gene arrays as a rapid tool for comparative genomics in the absence of
AB  - whole genome sequence to advance our understanding of closely related bacteria.
ER  -

TY  - JOUR
AU  - Akman, L.
AU  - Yamashita, A.
AU  - Watanabe, H.
AU  - Oshima, K.
AU  - Shiba, T.
AU  - Hattori, M.
AU  - Aksoy, S.
TI  - Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia.
JO  - Nat. Genet.
PY  - 2002
SP  - 402
EP  - 407
VL  - 32
AB  - Many insects that rely on a single food source throughout their developmental cycle harbor
AB  - beneficial microbes that provide nutrients
AB  - absent from their restricted diet. Tsetse flies, the vectors of African
AB  - trypanosomes, feed exclusively on blood and rely on one such intracellular
AB  - microbe for nutritional provisioning and fecundity. As a result of
AB  - co-evolution with hosts over millions of years, these mutualists have lost
AB  - the ability to survive outside the sheltered environment of their host
AB  - insect cells. We present the complete annotated genome of Wigglesworthia
AB  - glossinidia brevipalpis, which is composed of one chromosome of 697,724
AB  - base pairs (bp) and one small plasmid, called pWig1, of 5,200 bp. Genes
AB  - involved in the biosynthesis of vitamin metabolites, apparently essential
AB  - for host nutrition and fecundity, have been retained. Unexpectedly, this
AB  - obligate's genome bears hallmarks of both parasitic and free-living
AB  - microbes, and the gene encoding the important regulatory protein DnaA is
AB  - absent.
ER  -

TY  - JOUR
AU  - Akopyants, N.S.
AU  - Clifton, S.W.
AU  - Kersulyte, D.
AU  - Crabtree, J.E.
AU  - Youree, B.E.
AU  - Reece, C.A.
AU  - Bukanov, N.O.
AU  - Drazek, E.S.
AU  - Roe, B.A.
AU  - Berg, D.E.
TI  - Analyses of the cag pathogenicity island of Helicobacter pylori.
JO  - Mol. Microbiol.
PY  - 1998
SP  - 37
EP  - 53
VL  - 28
AB  - Most strains of Helicobacter pylori from patients with peptic ulcer disease or intestinal-type
AB  - gastric cancer carry cagA, a gene that encodes
AB  - an immunodominant protein of unknown function, whereas many of the strains
AB  - from asymptomatically infected persons lack this gene. Recent studies
AB  - showed that the cagA gene lies near the right end of a approximately 37kb
AB  - DNA segment (a pathogenicity island, or PAI) that is unique to cagA+
AB  - strains and that the cag PAI was split in half by a transposable element
AB  - insertion in the reference strain NCTC11638. In complementary experiments
AB  - reported here, we also found the same cag PAI, and sequenced a 39 kb
AB  - cosmid clone containing the left 'cagII' half of this PAI. Encoded in
AB  - cagII were four proteins each with homology to four components of
AB  - multiprotein complexes of Bordetella pertussis ('Ptl'), Agrobacterium
AB  - tumefaciens ('Vir'), and conjugative plasmids ('Tra') that help deliver
AB  - pertussis toxin and T (tumour inducing) and plasmid DNA, respectively, to
AB  - target eukaryotic or prokaryotic cells, and also homologues of eukaryotic
AB  - proteins that are involved in cytoskeletal structure. To the left of cagII
AB  - in this cosmid were genes for homologues of HsIU (heat-shock protein) and
AB  - Era (essential GTPase); to the right of cagII were homologues of genes for
AB  - a type I restriction endonuclease and ion transport functions. Deletion of
AB  - the cag PAI had no effect on synthesis of the vacuolating cytotoxin, but
AB  - this deletion and several cag insertion mutations blocked induction of
AB  - synthesis of proinflammatory cytokine IL-8 in gastric epithelial cells.
AB  - Comparisons among H. pylori strains indicated that cag PAI gene content
AB  - and arrangement are rather well conserved. We also identified two genome
AB  - rearrangements with end-points in the cag PAI. One, in reference strain
AB  - NCTC11638, involved IS605, a recently described transposable element (as
AB  - also found by others). Another rearrangement, in 3 of 10 strains tested
AB  - (including type strain NCTC11637), separated the normally adjacent cagA
AB  - and picA genes and did not involve IS605. Our results are discussed in
AB  - terms of how cag-encoded proteins might help trigger the damaging
AB  - inflammatory responses in the gastric epithelium and possible
AB  - contributions of DNA rearrangements to genome evolution.
ER  -

TY  - JOUR
AU  - Akopyants, N.S.
AU  - Fradkov, A.
AU  - Diatchenko, L.
AU  - Hill, J.E.
AU  - Siebert, P.D.
AU  - Lukyanov, S.A.
AU  - Sverdlov, E.D.
AU  - Berg, D.E.
TI  - PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 13108
EP  - 13113
VL  - 95
AB  - Genes that are characteristic of only certain strains of a bacterial species can be of great
AB  - biologic interest.  Here we describe a PCR-based subtractive hybridization method for
AB  - efficiently detecting such DNAs and apply it to the gastric pathogen Helicobacter pylori.
AB  - Eighteen DNAs specific to a monkey-colonizing strain (J166) were obtained by subtractive
AB  - hybridization against an unrelated strain whose genome has been fully sequenced (26695).
AB  - Seven J166-specific clones had no DNA sequence match to the 26695 genome, and 11 other clones
AB  - were mixed, with adjacent patches that did and did not match any sequences in 26695.  At the
AB  - protein level, seven clones had homology to putative DNA restriction-modification enzymes, and
AB  - two had homology to putative metabolic enzymes.  Nine others had no database match with
AB  - proteins of assigned function.  PCR tests of 13 unrelated H. pylori strains by using primers
AB  - specific for 12 subtracted clones and complementary Southern bot hybridizations indicated that
AB  - these DNAs are highly polymorphic in the H. pylori population, with each strain yielding a
AB  - different pattern of gene-specific PCR amplification.  The search for polymorphic DNAs, as
AB  - described here, should help identify previously unknown virulence genes in pathogens and
AB  - provide new insights into microbial genetic diversity and evolution.
ER  -

TY  - JOUR
AU  - Akter, A. et al.
TI  - Extremely low genomic diversity of Rickettsia japonica distributed in Japan.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 124
EP  - 133
VL  - 9
AB  - Rickettsiae are obligate intracellular bacteria that have small genomes as a
AB  - result of reductive evolution. Many Rickettsia species of the spotted fever group
AB  - (SFG) cause tick-borne diseases known as "spotted fevers." The life cycle of SFG
AB  - rickettsiae is closely associated with that of the tick, which is generally
AB  - thought to act as a bacterial vector and reservoir that maintains the bacterium
AB  - through transstadial and transovarial transmission. Each SFG member is thought to
AB  - have adapted to a specific tick species, thus restricting the bacterial
AB  - distribution to a relatively limited geographic region. These unique features of
AB  - SFG rickettsiae allow investigation of how the genomes of such biologically and
AB  - ecologically specialized bacteria evolve after genome reduction and the types of
AB  - population structures that are generated. Here, we performed a nationwide,
AB  - high-resolution phylogenetic analysis of R. japonica, an etiological agent of
AB  - Japanese spotted fever that is distributed in Japan and Korea. The comparison of
AB  - complete or nearly complete sequences obtained from 31 R. japonica strains
AB  - isolated from various sources in Japan over the past 30 years demonstrated an
AB  - extremely low level of genomic diversity. In particular, only 34 single
AB  - nucleotide polymorphisms were identified among the 27 strains of the major
AB  - lineage containing all clinical isolates and tick isolates from the three tick
AB  - species. Our data provide novel insights into the biology and genome evolution of
AB  - R. japonica, including the possibilities of recent clonal expansion and a long
AB  - generation time in nature due to the long dormant phase associated with tick life
AB  - cycles.
ER  -

TY  - JOUR
AU  - Akulenko, N.V.
AU  - Ivashina, T.V.
AU  - Shaloiko, L.A.
AU  - Shlyapnikov, M.G.
AU  - Ksenzenko, V.N.
TI  - New site-specific endonucleases F-TflI, F-TflII, and F-TflIV encoded by bacteriophage T5.
JO  - Mol. Biol. (Mosk)
PY  - 2004
SP  - 530
EP  - 537
VL  - 38
AB  - Site-specific endonucleases F-TflI, F-TflII, and F-TflIV have been revealed, which belong to
AB  - the H-N-H family and are encoded by ORFs
AB  - located in the tRNA gene region of bacteriophage T5. It has been shown
AB  - that endonuclease F-TflIV introduces a double-strand break in a 17-bp
AB  - pseudopalindromic DNA sequence to yield 1-nt 3'-protruding ends. Unlike
AB  - F-TflIV, F-TflI, and F-TflII introduce single-strand breaks in
AB  - asymmetrical, highly degenerate sequences, each cleaving only one
AB  - (template or coding) strand. Amino acid sequence analysis has revealed
AB  - a high homology of the enzymes in the region of the H-N-H motif and in
AB  - the putative C-terminal catalytic domain. The N-terminal region of
AB  - F-TflIV proved to be homologous to the HTH domain of LuxR-related
AB  - transcriptional regulators, which is responsible for DNA recognition
AB  - and binding. The N-terminal regions of F-TflI and F-TflII contain a
AB  - composite motif NUMOD4, which is characteristic of a putative
AB  - recognition domain of some H-N-H endonucleases. A two-domain structure,
AB  - with the N-terminal recognition and C-terminal catalytic domains, and
AB  - evolutionary origin via recombination of the catalytic and recognition
AB  - domain-coding regions are proposed for F-TflI, F-TflII, and F-TflIV.
ER  -

TY  - JOUR
AU  - Akulinin, G.E.
AU  - Getko, G.A.
AU  - Repin, V.E.
AU  - Degtyarev, S.K.
TI  - New restriction endonuclease from the soil strain Bacillus megaterium 12.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1988
SP  - 105
EP  - 108
VL  - 14
AB  - The soil strain Bacillus megaterium 12 carrying a restriction-modification
AB  - system has been discovered.  A Type 2 restriction endonuclease has been
AB  - partially purified.  Bme12I has been shown to be an isoschizomer of Sau3AI.
ER  -

TY  - JOUR
AU  - Akuzawa, S.
AU  - Nagaoka, J.
AU  - Kanekatsu, M.
AU  - Kanesaki, Y.
AU  - Suzuki, T.
TI  - Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish.
JO  - Genome Announcements
PY  - 2016
SP  - e01621
EP  - e01615
VL  - 4
AB  - Oceanobacillus picturae strain Heshi-B3 was isolated from rice bran in a traditional fermented
AB  - seafood dish named Heshiko, which was produced in Fukui
AB  - Prefecture in Japan. Here, we report the draft genome sequence of O. picturae
AB  - strain Heshi B-3.
ER  -

TY  - JOUR
AU  - Akuzawa, S.
AU  - Nagaoka, J.
AU  - Kanekatsu, M.
AU  - Kubota, E.
AU  - Ohtake, R.
AU  - Suzuki, T.
AU  - Kanesaki, Y.
TI  - Draft Genome Sequence of Paenibacillus amylolyticus Heshi-A3, Isolated from Fermented Rice Bran in a Japanese Fermented Seafood Dish.
JO  - Genome Announcements
PY  - 2016
SP  - e00218
EP  - e00216
VL  - 4
AB  - Paenibacillus amylolyticusstrain Heshi-A3 was isolated in Fukui prefecture, Japan, from
AB  - fermented rice bran in Heshiko, a traditional dish that is produced
AB  - by aging salted mackerel with fresh rice bran at an ambient temperature for
AB  - around 7 months to over one year. Here, we report the draft genome sequence
AB  - ofPaenibacillus amylolyticusstrain Heshi-A3.
ER  -

TY  - JOUR
AU  - Al-Awadhi, S.
AU  - Welch, S.G.
AU  - Smith, K.E.
AU  - Williams, R.A.D.
TI  - BstB7SI (R/CCGGY), a thermostable isoschizomer of Cfr10I, from a strain of Bacillus stearothermophilus isolated from oil-contaminated soil in Kuwait.
JO  - FEMS Microbiol. Lett.
PY  - 1998
SP  - 205
EP  - 208
VL  - 160
AB  - Isolates of thermophilic bacteria from desert soil in Kuwait, heavily
AB  - contaminated with crude
AB  - oil, have been screened for the presence of restriction endonuclease activity. One of the
AB  - isolates (B7S),
AB  - identified as Bacillus stearothermophilus, showed a high level of restriction endonuclease
AB  - activity when a cell-
AB  - free extract was incubated with lambda bacteriophage DNA at 65oC.  A type II restriction
AB  - endonuclease
AB  - (BstB7SI) has been partially purified from this isolate.  BstB7SI recognizes the six-base
AB  - sequence RCCGGY
AB  - (R=A or G; Y=T or C) and hydrolyses the phosphodiester bond in both strands of the
AB  - DNA substrate
AB  - between the first and second bases of the recognition sequence 5'-R/CCGGY-3' producing
AB  - four-base 5'
AB  - overhangs.  BstB7SI is therefore an isoschizomer of the mesophilic prototype restriction
AB  - endonuclease
AB  - Cfr10I.  BstB7SI has a pH optimum of 9.7, requires 10 mM MgCl2 and 75 mM NaCl for
AB  - maximum activity,
AB  - and retains full enzyme activity when incubated for 5 min at temperatures up to 70oC.
ER  -

TY  - JOUR
AU  - Al-Rashdi, A.S.A.
AU  - Jadhav, B.L.
AU  - Deshpande, T.
AU  - Deshpande, U.
TI  - Whole-Genome Sequencing and Annotation of a Clinical Isolate of Mycobacterium tuberculosis from Mumbai, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00154
EP  - e00114
VL  - 2
AB  - We report here the annotated genome sequence of a clinical isolate of Mycobacterium
AB  - tuberculosis from Mumbai, India.
ER  -

TY  - JOUR
AU  - Al-Saari, N.
AU  - Meirelles, P.M.
AU  - Mino, S.
AU  - Suda, W.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Ohkuma, M.
AU  - Thompson, F.L.
AU  - Gomez-Gil, B.
AU  - Sawabe, T.
AU  - Sawabe, T.
TI  - Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota.
JO  - Genome Announcements
PY  - 2014
SP  - e01095
EP  - e01014
VL  - 2
AB  - Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium
AB  - aphoticum C119, which were isolated from the coral reef vicinity
AB  - in Okinawa, Japan, are reported. The genome provides further insight into the
AB  - genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and
AB  - evolution, of these genera.
ER  -

TY  - JOUR
AU  - Al-Sayegh, A.
AU  - Al-Wahaibi, Y.
AU  - Joshi, S.
AU  - Al-Bahry, S.
AU  - Elshafie, A.
AU  - Al-Bemani, A.
TI  - Draft Genome Sequence of Bacillus subtilis AS2, a Heavy Crude Oil-Degrading and Biosurfactant-Producing Bacterium Isolated from a Soil Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e00969
EP  - e00917
VL  - 5
AB  - Here, we report the draft genome sequence of Bacillus subtilis AS2 that was isolated from
AB  - heavy crude oil-contaminated soil samples from sludge pits of an
AB  - Omani heavy-oil field. B. subtilis AS2 was able to biodegrade heavy crude oil and
AB  - produce biosurfactant. In order to provide a better understanding of the
AB  - biodegradation mechanism and biosynthesis of metabolites, the B. subtilis AS2
AB  - genome was sequenced and compared to those of other B. subtilis strains.
ER  -

TY  - JOUR
AU  - Alam, M.
AU  - Roy, C.
AU  - Pyne, P.
AU  - Agarwal, A.
AU  - George, A.
AU  - Ghosh, W.
TI  - Whole-Genome Shotgun Sequence of the Sulfur-Oxidizing Chemoautotroph Pseudaminobacter salicylatoxidans KCT001.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4743
EP  - 4744
VL  - 194
AB  - The facultatively sulfur-oxidizing chemolithoautotrophic alphaproteobacterium Pseudaminobacter
AB  - salicylatoxidans KCT001 (MTCC 7265) belongs to the family
AB  - Phyllobacteriaceae of the order Rhizobiales. Analysis of its genome offers
AB  - valuable insight into the adaptive specializations and evolution of free-living
AB  - soil bacteria that are phylogenetically closely related to symbiotic and invasive
AB  - rhizobacteria.
ER  -

TY  - JOUR
AU  - Alam, N.
AU  - Sittman, D.B.
TI  - Characterization of the cytotoxic effect of a chimeric restriction enzyme, H1 degrees-FokI.
JO  - Gene Ther. Mol. Biol.
PY  - 2006
SP  - 147
EP  - 159
VL  - 10A
AB  - Our primary goal was to create an efficient cytotoxic agent. To do this, we created a gene
AB  - that expresses a chimeric hybrid of the linker
AB  - histone, H1(0) and the nuclease domain of the type IIs restriction
AB  - enzyme, FokI. The linkage of the FokI nuclease domain to a high
AB  - affinity but low DNA-sequence-specificity binding protein is unique. It
AB  - is highly cytotoxic. We demonstrate, by transiently transfecting 3T3
AB  - mouse fibroblasts, that 63% of the cells taking up the chimeric gene
AB  - are killed. The chimeric protein is localized to the nucleus. An
AB  - extract of the protein produced in E. coli degrades DNA, indicating
AB  - that it is nucleolytically active. The ultimate mechanism through which
AB  - the chimeric protein produces cell death is likely through the
AB  - induction of apoptosis.
ER  -

TY  - JOUR
AU  - Alatossava, T.
AU  - Klaenhammer, T.R.
TI  - Molecular characterization of three small isometric-headed bacteriophages which vary in their sensitivity to the lactococcal phage resistance plasmid pTR2030.
JO  - Appl. Environ. Microbiol.
PY  - 1991
SP  - 1346
EP  - 1353
VL  - 57
AB  - Lactococcus lactis LMA12-4 is a pTR2030 transconjugant that has been used as an
AB  - industrial starter culture because of its resistance to phages predominant in
AB  - cheese plants.  Plasmid pTR2030 interferes with susceptible phages in this host
AB  - strain via two mechanisms, restriction and modification (R/M) and abortive
AB  - infection (Hsp).  After prolonged use of LMA12-4 transconjugants in the
AB  - industry, two different bacteriophages, designated nck202.Phi 48 (Phi 48) and
AB  - nck202.Phi 50 (Phi 50), were isolated which could produce plaques on LMA12-4
AB  - containing pTR2030.  In this study, these two phages were characterized and
AB  - compared with a third phage, nck202.Phi 31 (Phi 31), which is susceptible to
AB  - both the R/M and Hsp activities encoded by pTR2030.  Phage Phi-48 was not
AB  - susceptible to inhibition by Hsp, whereas Phi 50 was unaffected by either the
AB  - R/M or Hsp mechanisms.  All three were small isometric-headed phages, but small
AB  - differences were noted between the phages in the structural details of the tail
AB  - base plate, susceptibility to chloroform treatment, and requirements for
AB  - calcium infectivity.  The phage genomes were all between 29.9 and 31.9 kb in
AB  - length.  Phages Phi 31 and Phi 48 harbored cohesive ends, whereas the phage Phi
AB  - 50 genome was circularly permuted, terminally redundant, and carried a putative
AB  - packaging initiation site.  DNA-DNA hybridization experiments conducted between
AB  - the phages revealed a common region in Phi 48 and Phi 50 that may correlate
AB  - with the resistance of the two phages to the Hsp-abortive infection induced by
AB  - pTR2030.  Phage Phi 50 also harbored DNA sequences that shared homology to
AB  - pTR2030 in the region where R/M activities have been localized on the plasmid.
AB  - Molecular characterization of the three phages localized regions within the
AB  - genomes of the pTR2030-resistant phages that may be responsible for
AB  - circumventing plasmid-encoded Hsp and R/M defense mechanisms in lactococci.
ER  -

TY  - JOUR
AU  - Alawi, M.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Horn, F.
AU  - Bakermans, C.
AU  - Wagner, D.
TI  - Genome Sequence of Methanosarcina soligelidi SMA-21, Isolated from Siberian Permafrost-Affected Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00270
EP  - e00215
VL  - 3
AB  - Here, we announce the genome sequence of Methanosarcina soligelidi SMA-21, an anaerobic
AB  - methanogenic archaeon that was previously isolated from Siberian
AB  - permafrost-affected soil. The sequencing of strain SMA-21 yielded a 4.06-Mb
AB  - genome with 41.5% G+C content, containing a total of 2,647 open reading frames.
ER  -

TY  - JOUR
AU  - Alba, J.
AU  - Marcaida, M.J.
AU  - Prieto, J.
AU  - Montoya, G.
AU  - Molina, R.
AU  - D'Abramo, M.
TI  - Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.
JO  - J. Comput. Aided Mol. Des.
PY  - 2017
SP  - 1063
EP  - 1072
VL  - 31
AB  - I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG
AB  - homing endonuclease protein family. Its members are highly specific
AB  - enzymes capable of recognizing long DNA target sequences, thus providing
AB  - potential tools for genome manipulation. Working towards this particular
AB  - application, many efforts have been made to generate mesophilic variants of
AB  - I-DmoI that function at lower temperatures than the wild-type. Here, we report a
AB  - structural and computational analysis of two I-DmoI mesophilic mutants. Despite
AB  - very limited structural variations between the crystal structures of these
AB  - variants and the wild-type, a different dynamical behaviour near the cleavage
AB  - sites is observed. In particular, both the dynamics of the water molecules and
AB  - the protein perturbation effect on the cleavage site correlate well with the
AB  - changes observed in the experimental enzymatic activity.
ER  -

TY  - JOUR
AU  - Albalat, R.
TI  - Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae.
JO  - Dev. Genes Evol.
PY  - 2008
SP  - 691
EP  - 701
VL  - 218
AB  - DNA methylation is an epigenetic mark associated with gene regulation and cell memory,
AB  - silencing of transposable elements, genomic
AB  - imprinting, and repression of spurious transcription of duplicated
AB  - sequences. These roles have varied widely during animal evolution and
AB  - current functions depend on the specific methylation pattern of the
AB  - species under consideration. The patterns of methylation are
AB  - established, maintained, and translated into appropriate functional
AB  - states by the DNA-methylation machinery, which includes three groups of
AB  - methyltransferase enzymes, Dnmt1, Dnmt2 and Dnmt3, and five methyl-DNA
AB  - binding proteins, Mbd1, Mbd2, Mbd3, Mbd4, and MeCP2. In this study, I
AB  - have identified the members of the Dnmt and the Mbd gene families in
AB  - the cephalochordate amphioxus (Branchiostoma floridae), the most basal
AB  - extant chordate and one of the closest sister groups of vertebrates.
AB  - Database searches, phylogenetic studies and protein domain analyses
AB  - revealed the presence of the three major groups of Dnmt enzymes in the
AB  - cephalochordate genome, whereas only two Mbd members, Mbd2/3 and Mbd4,
AB  - were found. Analysis of the amphioxus methylation machinery suggested
AB  - that the complexity and the structural organization of cephalochordate
AB  - methyltransferases do not differ substantially from those of current
AB  - vertebrate enzymes, while new Mbd proteins arose in vertebrates, which
AB  - perhaps minimized certain collateral effects associated with the major
AB  - genomic changes that occurred during the invertebrate-vertebrate
AB  - transition.
ER  -

TY  - JOUR
AU  - Albarracin, O.A.G.
AU  - Tobares, R.A.
AU  - Ducasse, D.A.
AU  - Smania, A.M.
TI  - Draft Genome Sequence of Bacillus subtilis ALBA01, a Strain with Antagonistic Activity against the Soilborne Fungal Pathogen of Onion Setophoma terrestris.
JO  - Genome Announcements
PY  - 2016
SP  - e00455
EP  - e00416
VL  - 4
AB  - Bacillus subtilis is a nonpathogenic bacterium that lives in soil and has long been used as
AB  - biological control agent in agriculture. Here, we report the genome
AB  - sequence of a B. subtilis strain isolated from rhizosphere of onion that shows
AB  - strong biological activity against the soilborne fungal pathogen Setophoma
AB  - terrestris.
ER  -

TY  - JOUR
AU  - Albersmeier, A.
AU  - Bomholt, C.
AU  - Glaub, A.
AU  - Ruckert, C.
AU  - Soriano, F.
AU  - Fernandez-Natal, I.
AU  - Tauch, A.
TI  - Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Dermabacter hominis 1368.
JO  - Genome Announcements
PY  - 2014
SP  - e00728
EP  - e00714
VL  - 2
AB  - Dermabacter hominis is a common colonizer of the healthy human skin and is rarely detected as
AB  - an opportunistic human pathogen. The genome sequence of the
AB  - multidrug-resistant D. hominis strain 1368, isolated from blood cultures of a
AB  - pyelonephritis patient, provides insights into the repertoire of antibiotic
AB  - resistance genes.
ER  -

TY  - JOUR
AU  - Albert, K.
AU  - Sela, D.A.
TI  - Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces.
JO  - Genome Announcements
PY  - 2018
SP  - e00559
EP  - e00518
VL  - 6
AB  - The draft genome sequence of an isolate identified as Bifidobacterium longum is communicated
AB  - herein. This strain was isolated from the feces of a 1-week-old
AB  - Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is
AB  - 2.39 Mb in length, with a G+C content of 60.1%.
ER  -

TY  - JOUR
AU  - Albert, K.
AU  - Sela, D.A.
TI  - Draft Genome Sequences of Alloscardovia macacae UMA81211 and UMA81212, Isolated from the Feces of a Rhesus Macaque (Macaca mulatta).
JO  - Genome Announcements
PY  - 2017
SP  - e00581
EP  - e00517
VL  - 5
AB  - Here, we provide the draft genome sequences of two isolates identified as Alloscardovia
AB  - macacae These bacteria originated from the feces of a rhesus
AB  - macaque. The draft genomes of both Alloscardovia macacae isolates are ~1.8 Mb in
AB  - length, with a G+C content of 56.1%.
ER  -

TY  - JOUR
AU  - Albert, P.
AU  - Varga, B.
AU  - Zsibrita, N.
AU  - Kiss, A.
TI  - Circularly permuted variants of two CG-specific prokaryotic DNA methyltransferases.
JO  - PLoS ONE
PY  - 2018
SP  - e0197232
EP  - e0197232
VL  - 13
AB  - The highly similar prokaryotic DNA (cytosine-5) methyltransferases (C5-MTases) M.MpeI and
AB  - M.SssI share the specificity of eukaryotic C5-MTases (5'-CG), and can
AB  - be useful research tools in the study of eukaryotic DNA methylation and
AB  - epigenetic regulation. In an effort to improve the stability and solubility of
AB  - complementing fragments of the two MTases, genes encoding circularly permuted
AB  - (CP) variants of M.MpeI and M.SssI were created, and cloned in a plasmid vector
AB  - downstream of an arabinose-inducible promoter. MTase activity of the CP variants
AB  - was tested by digestion of the plasmids with methylation-sensitive restriction
AB  - enzymes. Eleven of the fourteen M.MpeI permutants and six of the seven M.SssI
AB  - permutants had detectable MTase activity as indicated by the full or partial
AB  - protection of the plasmid carrying the cpMTase gene. Permutants cp62M.MpeI and
AB  - cp58M.SssI, in which the new N-termini are located between conserved motifs II
AB  - and III, had by far the highest activity. The activity of cp62M.MpeI was
AB  - comparable to the activity of wild-type M.MpeI. Based on the location of the
AB  - split sites, the permutants possessing MTase activity can be classified in ten
AB  - types. Although most permutation sites were designed to fall outside of conserved
AB  - motifs, and the MTase activity of the permutants measured in cell extracts was in
AB  - most cases substantially lower than that of the wild-type enzyme, the high
AB  - proportion of circular permutation topologies compatible with MTase activity is
AB  - remarkable, and is a new evidence for the structural plasticity of C5-MTases. A
AB  - computer search of the REBASE database identified putative C5-MTases with CP
AB  - arrangement. Interestingly, all natural circularly permuted C5-MTases appear to
AB  - represent only one of the ten types of permutation topology created in this work.
ER  -

TY  - JOUR
AU  - Albertsen, H.M.
AU  - Le Paslier, D.
AU  - Abderrahim, H.
AU  - Dausset, J.
AU  - Cann, H.
AU  - Cohen, D.
TI  - Improved control of partial DNA restriction enzyme digest in agarose using limiting concentrations of Mg++.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 808
EP  - 808
VL  - 17
AB  - Partial digests of DNA for cloning experiments are usually performed using
AB  - either the quantity of restriction enzyme or incubation time, or both, as
AB  - controlling factors.  However, we have found that more precise and reproducible
AB  - partial digests are obtained, when a limiting concentration of the required
AB  - cofactor Mg++ is used.  This method is especially useful for partial digests of
AB  - DNA contained in agarose.  In agarose, diffusion time of the much smaller Mg++
AB  - ion is shorter than that of a restriction enzyme.  The result is a more
AB  - homogenous digestion of the DNA throughout the agarose block.  Since the
AB  - concentration of Mg++ in this procedure is usually only 10% or less of that
AB  - normally used, the digestion is easily interrupted by excess EDTA.  We have
AB  - successfully applied this partial digestion technique with EcoRI to obtain
AB  - large human DNA fragments that have been used to construct artificial yeast
AB  - chromosomes (YAC) of several hundred kb in length.
ER  -

TY  - JOUR
AU  - Albertsen, M.
AU  - Hugenholtz, P.
AU  - Skarshewski, A.
AU  - Nielsen, K.L.
AU  - Tyson, G.W.
AU  - Nielsen, P.H.
TI  - Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
JO  - Nat. Biotechnol.
PY  - 2013
SP  - 533
EP  - 538
VL  - 31
AB  - Reference genomes are required to understand the diverse roles of microorganisms in ecology,
AB  - evolution, human and animal health, but most species remain uncultured. Here we present a
AB  - sequence composition-independent approach to recover high-quality microbial genomes from
AB  - deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in
AB  - relative population abundances, were used to assemble 31 bacterial genomes, including rare
AB  - (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were
AB  - assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial
AB  - phylum TM7 and represent the most complete genomes for this phylum to date (relative
AB  - abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential
AB  - coverage binning facilitates recovery of more complete and higher fidelity genome bins than
AB  - other currently used methods, which are primarily based on sequence composition. This approach
AB  - will be an important addition to the standard metagenome toolbox and greatly improve access to
AB  - genomes of uncultured microorganisms.
ER  -

TY  - JOUR
AU  - Albu, R.F.
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 1708
EP  - 1716
VL  - 40
ER  -

TY  - JOUR
AU  - Albu, R.F.
AU  - Zacharias, M.
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study.
JO  - Chembiochem
PY  - 2012
SP  - 1304
EP  - 1311
VL  - 13
AB  - Caulobacter crescentus CcrM is a DNA-(adenine N6)-methyltransferase that methylates adenine in
AB  - the sequence GANTC with high specificity. To
AB  - investigate its mechanism of DNA recognition, we used the crystal
AB  - structure of a related methyltransferase (M1.MboII, which modifies
AB  - GAAGA) as a starting point, and docked into it a DNA substrate to
AB  - identify the protein regions that approach the DNA. After alignment of
AB  - CcrM and M1.MboII, we identified four candidate regions in CcrM to
AB  - contain residues involved in DNA recognition. We mutated 20 amino acid
AB  - residues within these regions, purified the CcrM variants, and
AB  - determined their DNA-binding and catalytic activity on a cognate GANTC
AB  - substrate and on nine near-cognate substrates, each of which contained
AB  - a single base-pair substitution in the recognition sequence.
AB  - Altogether, we identified four residues in two of the regions,
AB  - mutations of which resulted in a strong (>100-fold) reduction of
AB  - methylation activity. Our data show that DNA recognition by CcrM is a
AB  - cooperative process, because disruption of critical contacts led to
AB  - loss of catalytic activity but not to a relaxation in specificity. In
AB  - addition, we identified a change in the readout of the fifth base pair
AB  - in the GANTC sequence with two other CcrM variants that showed smaller
AB  - reductions in overall activity. Based on this and the sequence
AB  - alignment of CcrM with other DNA methyltransferases of same or related
AB  - recognition sequence, we propose roles for these two regions in DNA
AB  - recognition by CcrM.
ER  -

TY  - JOUR
AU  - Albuquerque, G.M.R.
AU  - Souza, E.B.
AU  - Silva, A.M.F.
AU  - Lopes, C.A.
AU  - Boiteux, L.S.
AU  - Fonseca, M.E.N.
TI  - Genome Sequence of Ralstonia pseudosolanacearum Strains with Compatible and Incompatible Interactions with the Major Tomato Resistance Source Hawaii 7996.
JO  - Genome Announcements
PY  - 2017
SP  - e00982
EP  - e00917
VL  - 5
AB  - We report here the complete genome sequences of two Ralstonia pseudosolanacearum  strains,
AB  - isolated from the warm northeast region of Brazil. They display
AB  - divergent (compatible versus incompatible) interactions with the resistant tomato
AB  - line Hawaii 7996. Polymorphisms were detected in a subset of effector genes that
AB  - might be associated with these contrasting phenotypes.
ER  -

TY  - JOUR
AU  - Alcaraz, L.D. et al.
TI  - The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 5803
EP  - 5808
VL  - 105
AB  - The Cuatro Cienegas Basin (CCB) in the central part of the Chihuahan desert (Coahuila, Mexico)
AB  - hosts a wide diversity of microorganisms
AB  - contained within springs thought to be geomorphological relics of an
AB  - ancient sea. A major question remaining to be answered is whether bacteria
AB  - from CCB are ancient marine bacteria that adapted to an oligotrophic
AB  - system poor in NaCl, rich in sulfates, and with extremely low phosphorus
AB  - levels (<0.3 muM). Here, we report the complete genome sequence of
AB  - Bacillus coahuilensis, a sporulating bacterium isolated from the water
AB  - column of a desiccation lagoon in CCB. At 3.35 Megabases this is the
AB  - smallest genome sequenced to date of a Bacillus species and provides
AB  - insights into the origin, evolution, and adaptation of B. coahuilensis to
AB  - the CCB environment. We propose that the size and complexity of the B.
AB  - coahuilensis genome reflects the adaptation of an ancient marine bacterium
AB  - to a novel environment, providing support to a "marine isolation origin
AB  - hypothesis" that is consistent with the geology of CCB. This genomic
AB  - adaptation includes the acquisition through horizontal gene transfer of
AB  - genes involved in phosphorous utilization efficiency and adaptation to
AB  - high-light environments. The B. coahuilensis genome sequence also revealed
AB  - important ecological features of the bacterial community in CCB and offers
AB  - opportunities for a unique glimpse of a microbe-dominated world last seen
AB  - in the Precambrian.
ER  -

TY  - JOUR
AU  - Alcaraz, L.D.
AU  - Moreno-Hagelsieb, G.
AU  - Eguiarte, L.E.
AU  - Souza, V.
AU  - Herrera-Estrella, L.
AU  - Olmedo-Alvarez, G.
TI  - Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics.
JO  - BMC Genomics
PY  - 2010
SP  - 332
EP  - 332
VL  - 11
AB  - BACKGROUND: The presence of Bacillus in very diverse environments reflects
AB  - the versatile metabolic capabilities of a widely distributed genus.
AB  - Traditional phylogenetic analysis based on limited gene sampling is not
AB  - adequate for resolving the genus evolutionary relationships. By
AB  - distinguishing between core and pan-genome, we determined the evolutionary
AB  - and functional relationships of known Bacillus. RESULTS: Our analysis is
AB  - based upon twenty complete and draft Bacillus genomes, including a newly
AB  - sequenced Bacillus isolate from an aquatic environment that we report for
AB  - the first time here. Using a core genome, we were able to determine the
AB  - phylogeny of known Bacilli, including aquatic strains whose position in
AB  - the phylogenetic tree could not be unambiguously determined in the past.
AB  - Using the pan-genome from the sequenced Bacillus, we identified functional
AB  - differences, such as carbohydrate utilization and genes involved in signal
AB  - transduction, which distinguished the taxonomic groups. We also assessed
AB  - the genetic architecture of the defining traits of Bacillus, such as
AB  - sporulation and competence, and showed that less than one third of the B.
AB  - subtilis genes are conserved across other Bacilli. Most variation was
AB  - shown to occur in genes that are needed to respond to environmental cues,
AB  - suggesting that Bacilli have genetically specialized to allow for the
AB  - occupation of diverse habitats and niches. CONCLUSIONS: The aquatic
AB  - Bacilli are defined here for the first time as a group through the
AB  - phylogenetic analysis of 814 genes that comprise the core genome. Our data
AB  - distinguished between genomic components, especially core vs. pan-genome
AB  - to provide insight into phylogeny and function that would otherwise be
AB  - difficult to achieve. A phylogeny may mask the diversity of functions,
AB  - which we tried to uncover in our approach. The diversity of sporulation
AB  - and competence genes across the Bacilli was unexpected based on previous
AB  - studies of the B. subtilis model alone. The challenge of uncovering the
AB  - novelties and variations among genes of the non-subtilis groups still
AB  - remains. This task will be best accomplished by directing efforts toward
AB  - understanding phylogenetic groups with similar ecological niches.
ER  -

TY  - JOUR
AU  - Alegado, R.A.
AU  - Ferriera, S.
AU  - Nusbaum, C.
AU  - Young, S.K.
AU  - Zeng, Q.
AU  - Imamovic, A.
AU  - Fairclough, S.R.
AU  - King, N.
TI  - Complete Genome Sequence of Algoriphagus sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1485
EP  - 1486
VL  - 193
AB  - Bacteria are the primary food source of choanoflagellates, the closest known relatives of
AB  - animals. Studying signaling interactions between the
AB  - Gram-negative Bacteroidetes bacterium Algoriphagus sp. PR1 and its
AB  - predator, the choanoflagellate Salpingoeca rosetta, provides a promising
AB  - avenue for testing hypotheses regarding the involvement of bacteria in
AB  - animal evolution. Here we announce the complete genome sequence of
AB  - Algoriphagus sp. PR1 and initial findings from its annotation.
ER  -

TY  - JOUR
AU  - Alegre, M.T.
AU  - Rodriguez, M.C.
AU  - Mesas, J.M.
TI  - Characterization of pRS5: A theta-type plasmid found in a strain of Pediococcus pentosaceus isolated from wine that can be used to generate cloning vectors for lactic acid bacteria.
JO  - Plasmid
PY  - 2009
SP  - 130
EP  - 134
VL  - 61
AB  - The nucleotide sequence of pRS5 (10153 bp) is reported. Through sequence analysis, 9 open
AB  - reading frames (ORFs) were identified and the
AB  - following features observed: a region likely involved in replication
AB  - whose structural features indicate that pRS5 belongs to the pUCL287
AB  - group of theta-type replicons, and hypothetical proteins putatively
AB  - involved in plasmid copy number control, restriction-modification
AB  - system, toxin-antitoxin system and a putative integrase. Shuttle
AB  - vectors for Escherichia coli and lactic acid bacteria (LAB) as well as
AB  - a small cloning vector for direct use in LAB were constructed using the
AB  - replication region of pRS5. The ability of such vectors to accept and
AB  - express other genes was assessed. All pRS5-derivatives were maintained
AB  - at a high rate over 200 generations without selective pressure.
ER  -

TY  - JOUR
AU  - Alejo-Viderique, A.
AU  - Contreras-Castro, L.
AU  - Felix-Gastelum, R.
AU  - Maldonado, L.A.
AU  - Quintana, E.T.
TI  - Draft Genome Sequence of a Streptomycete Isolated from Potato Common Scab Lesions in the State of Sinaloa, Mexico.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00827
EP  - e00818
VL  - 7
AB  - Streptomyces sp. strain V2 was isolated from potato scab lesions in the state of  Sinaloa,
AB  - Mexico, and appears to be responsible for outbreaks in the area. The
AB  - thaxtomin cluster was found in the approximately 10.2-Mb genome; this cluster is
AB  - associated with potato common scab disease in other potato pathogens.
ER  -

TY  - JOUR
AU  - Aleksandrzak-Piekarczyk, T.
AU  - Koryszewska-Baginska, A.
AU  - Bardowski, J.
TI  - Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK900.
JO  - Genome Announcements
PY  - 2013
SP  - e00640
EP  - e00613
VL  - 1
AB  - Lactobacillus rhamnosus LOCK900 fulfills the criteria required for probiotic strains. In this
AB  - study, we report a whole-genome sequence of this isolate and
AB  - compare it with other L. rhamnosus complete genome sequences already published.
ER  -

TY  - JOUR
AU  - Alencar, V.C.
AU  - Barbosa, D.
AU  - Santos, D.S.
AU  - Oliveira, A.C.
AU  - de Oliveira, R.C.
AU  - Nunes, L.R.
TI  - Genomic Sequencing of Two Coffee-Infecting Strains of Xylella fastidiosa Isolated from Brazil.
JO  - Genome Announcements
PY  - 2014
SP  - e01190
EP  - e01113
VL  - 2
AB  - Here, we describe the draft genome sequences of two Xylella fastidiosa strains: Xf6c and Xf32,
AB  - which have been obtained from infected coffee plants in Brazil,
AB  - and are associated with the disease known as coffee leaf scorch (CLS).
ER  -

TY  - JOUR
AU  - Alenezi, F.N.
AU  - Weitz, H.J.
AU  - Belbahri, L.
AU  - Ben Rebah, H.
AU  - Luptakova, L.
AU  - Jaspars, M.
AU  - Woodward, S.
TI  - Draft Genome Sequence of Aneurinibacillus migulanus Strain Nagano.
JO  - Genome Announcements
PY  - 2015
SP  - e00232
EP  - e00215
VL  - 3
AB  - Aneurinibacillus migulanus is characterized by inhibition of growth of a range of
AB  - plant-pathogenic bacteria and fungi. Here, we report the high-quality draft
AB  - genome sequences of A. migulanus Nagano.
ER  -

TY  - JOUR
AU  - Alenezi, F.N.
AU  - Weitz, H.J.
AU  - Belbahri, L.
AU  - Nidhal, J.
AU  - Luptakova, L.
AU  - Jaspars, M.
AU  - Woodward, S.
TI  - Draft Genome Sequence of Aneurinibacillus migulanus NCTC 7096.
JO  - Genome Announcements
PY  - 2015
SP  - e00234
EP  - e00215
VL  - 3
AB  - Aneurinibacillus migulanus has biocontrol activities against fungal, fungus-like, and
AB  - bacterial plant pathogens with different levels of efficacy depending on the
AB  - target pathogens. Here, we report the high-quality draft genome sequence of A.
AB  - migulanus NCTC 7096.
ER  -

TY  - JOUR
AU  - Aleshkin, G.I.
AU  - Skavronskaya, A.G.
TI  - R.M.EcoRI coding plasmids derived from recombinant R factor.
JO  - Genetika
PY  - 1978
SP  - 1466
EP  - 1469
VL  - 14
AB  - Bacteriophages P1vir and Mu-1 have been used for transductional shortening of a recombinant R
AB  - factor coding for R.M.EcoRI isolated by Yoshimori et al.  P1 shortening made possible the
AB  - isolation of transmissive isogenic plasmids coding for R.M.EcoRI and differing in antibiotic
AB  - resistance, as well as isolation of plasmids differing only in their R.M.EcoRI genes.  Mu-1
AB  - mediated shortening favored the isolation of transmissive R plasmids having lost the
AB  - resistance to chloramphenicol but having all other markers of the recombinant R factor intact.
AB  - The data are interpreted in support of Yoshimori et al.'s supposition concerning the
AB  - existence of R.M.EcoRI coding recombinant R factor of Escherichia coli.
ER  -

TY  - JOUR
AU  - Aleshkin, G.I.
AU  - Strikhanov, S.N.
AU  - Skavronskaya, A.G.
TI  - Plasmid recombination stimulated by restriction endonuclease EcoRI in vivo: formation of recombinant plasmids in recA+-cells of E. coli.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1985
SP  - 15
EP  - 21
VL  - 4
AB  - The possible participation of restriction endonuclease EcoRI in recombination of compatible
AB  - nonhomologous plasmids in E. coli cells has been studied.  To study the process, plasmids RP4
AB  - and R245 have been transferred by conjugation into the recipient cells of E. coli harboring
AB  - one of isogenic plasmids, pSA14 and pSA25, different for the genes coding restriction
AB  - endonuclease EcoRI.  The genetic analysis of transconjugant phenotypes, coded by the plasmids,
AB  - has permitted to register the recombinant plasmids after compatibility of parent plasmids in
AB  - E. coli cells.  Recombination of plasmid RP4 with the plasmid pSA14, carrying EcoRI genes, has
AB  - been registered in E. coli cells, producing the restriction endonuclease, while plasmid
AB  - recombination has not been found in the cells harboring plasmid pSA25, isogenic for all genes,
AB  - except for EcoRI genes, with plasmid pSA14.  Restriction endonuclease EcoRI is concluded to
AB  - stimulate site specific recombination of nonhomologous compatible plasmids in vivo.
AB  - EcoRI-mediated recombination of plasmid R245 with plasmid pSA14 is discussed.
ER  -

TY  - JOUR
AU  - Aleti, G.
AU  - Antonielli, L.
AU  - Corretto, E.
AU  - Nikolic, B.
AU  - Sessitsch, A.
AU  - Brader, G.
TI  - The Draft Genome Sequence of Paenibacillus polymyxa Strain CCI-25 Encompasses High Potential for Secondary Metabolite Production.
JO  - Genome Announcements
PY  - 2016
SP  - e00366
EP  - e00316
VL  - 4
AB  - We report here the draft genome sequence of Paenibacillus polymyxa strain CCI-25, which
AB  - displays strong antifungal and antibacterial activities in vitro The genome
AB  - encompasses nonribosomal peptide synthetases predicted to encode a tridecaptin,
AB  - polymyxin, fusaricidin, an iturin-like synthetase, a lantibiotic similar to
AB  - paenicidin A, as well as a type 1 polyketide synthase.
ER  -

TY  - JOUR
AU  - Alexander, K.A.
AU  - Larsen, M.H.
AU  - Robbe-Austerman, S.
AU  - Stuber, T.P.
AU  - Camp, P.M.
TI  - Draft Genome Sequence of the Mycobacterium tuberculosis Complex Pathogen M. mungi, Identified in a Banded Mongoose (Mungos mungo) in Northern Botswana.
JO  - Genome Announcements
PY  - 2016
SP  - e00471
EP  - e00416
VL  - 4
AB  - Mycobacterium mungi, a Mycobacterium tuberculosis complex pathogen, has emerged in banded
AB  - mongoose in northern Botswana and Northwest Zimbabwe. The pathogen is
AB  - transmitted through infected secretions used in olfactory communication behavior
AB  - (K. A. Alexander, C. E. Sanderson, M. H. Larsen, S. Robbe-Austerman, M. C.
AB  - Williams, and M. V. Palmer, mBio 7(3):e00281-16, 2016,
AB  - http://dx.doi.org/10.1128/mBio.00281-16). We announce here the draft genome
AB  - sequence of this emerging pathogen.
ER  -

TY  - JOUR
AU  - Alexander, S.
AU  - Fazal, M.A.
AU  - Burnett, E.
AU  - Deheer-Graham, A.
AU  - Oliver, K.
AU  - Holroyd, N.
AU  - Parkhill, J.
AU  - Russell, J.E.
TI  - Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.
JO  - Genome Announcements
PY  - 2016
SP  - e00815
EP  - e00816
VL  - 4
AB  - Neisseria weaveri is a commensal organism of the canine oral cavity and an occasional
AB  - opportunistic human pathogen which is associated with dog bite wounds.
AB  - Here we report the first complete genomic sequence of the N. weaveri NCTC13585
AB  - (CCUG30381) strain, which was originally isolated from a patient with a canine
AB  - bite wound.
ER  -

TY  - JOUR
AU  - Alexander, S.
AU  - Fazal, M.A.
AU  - Burnett, E.
AU  - Deheer-Graham, A.
AU  - Oliver, K.
AU  - Holroyd, N.
AU  - Parkhill, J.
AU  - Russell, J.E.
TI  - Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.
JO  - Genome Announcements
PY  - 2016
SP  - e01031
EP  - e01016
VL  - 4
AB  - Plesiomonas shigelloides is a Gram-negative rod within the Enterobacteriaceae family. It is a
AB  - gastrointestinal pathogen of increasing notoriety, often
AB  - associated with diarrheal disease. P. shigelloides is waterborne, and infection
AB  - is often linked to the consumption of seafood. Here, we describe the first
AB  - complete genome for P. shigelloides type strain NCTC10360.
ER  -

TY  - JOUR
AU  - Alexandraki, V.
AU  - Kazou, M.
AU  - Blom, J.
AU  - Pot, B.
AU  - Tsakalidou, E.
AU  - Papadimitriou, K.
TI  - The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 18
EP  - 18
VL  - 12
AB  - Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional
AB  - Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus
AB  - currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest
AB  - chromosome, containing 1,731,838 bp. The annotation of its genome revealed the
AB  - presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and
AB  - 224 potential pseudogenes. A large number of pseudogenes were identified. This
AB  - was also accompanied by the absence of pathogenic features suggesting evolution
AB  - of strain ACA-DC 2 through genome decay processes, most probably due to
AB  - adaptation to the milk ecosystem. Analysis revealed the existence of one complete
AB  - lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide
AB  - cluster, stress response genes and four putative antimicrobial peptides.
AB  - Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only
AB  - one spacer, were predicted indicating low activity or inactivation of the cas
AB  - proteins. Nevertheless, four putative restriction-modification systems were
AB  - determined that may compensate any deficiencies of the CRISPR-cas system.
AB  - Furthermore, whole genome phylogeny indicated three distinct clades within S.
AB  - thermophilus. Comparative analysis among selected strains representative for each
AB  - clade, including strain ACA-DC 2, revealed a high degree of conservation at the
AB  - genomic scale, but also strain specific regions. Unique genes and genomic islands
AB  - of strain ACA-DC 2 contained a number of genes potentially acquired through
AB  - horizontal gene transfer events, that could be related to important technological
AB  - properties for dairy starters. Our study suggests genomic traits in strain ACA-DC
AB  - 2 compatible to the production of dairy fermented foods.
ER  -

TY  - JOUR
AU  - Alexandraki, V.
AU  - Kazou, M.
AU  - Pot, B.
AU  - Tsakalidou, E.
AU  - Papadimitriou, K.
TI  - Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87.
JO  - Genome Announcements
PY  - 2017
SP  - e00868
EP  - e00817
VL  - 5
AB  - Lactobacillus delbrueckii subsp. bulgaricus is widely used in the production of yogurt and
AB  - cheese. In this study, we present the complete genome sequence of L.
AB  - delbrueckii subsp. bulgaricus ACA-DC 87 isolated from traditional Greek yogurt.
AB  - Whole-genome analysis may reveal desirable technological traits of the strain for
AB  - dairy fermentations.
ER  -

TY  - JOUR
AU  - Alexandrino, P.M.
AU  - Mendonca, T.T.
AU  - Guaman, B.L.P.
AU  - Cherix, J.
AU  - Lozano-Sakalauskas, G.C.
AU  - Fujita, A.
AU  - Ramos, F.E.
AU  - Long, P.
AU  - Padilla, G.
AU  - Taciro, M.K.
AU  - Gomez, J.G.
AU  - Silva, L.F.
TI  - Draft Genome Sequence of the Polyhydroxyalkanoate-Producing Bacterium Burkholderia sacchari LMG 19450 Isolated from Brazilian Sugarcane Plantation  Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00313
EP  - e00315
VL  - 3
AB  - Burkholderia sacchari LMG 19450, isolated from the soil of a sugarcane plantation in Brazil,
AB  - accumulates large amounts of polyhydroxyalkanoates from sucrose,
AB  - xylose, other carbohydrates, and organic acids. We present the draft genome
AB  - sequence of this industrially relevant bacterium, which is 7.2 Mb in size and has
AB  - a G+C content of 64%.
ER  -

TY  - JOUR
AU  - Alexeyev, M.F.
AU  - Gunkovskaya, N.V.
AU  - Romanovskaya, V.A.
AU  - Malashenko, Y.R.
TI  - Methylococcus whittenburyi - producer of MwhI, new isoschizomer of HpaI.
JO  - Mikrobiol. Zh.
PY  - 1992
SP  - 70
EP  - 73
VL  - 54
AB  - Type II specific restriction endonucleases (restrictases) draw so much interest not only
AB  - because gene engineering is based on using them but also because they are convenient objects
AB  - to solve the problem of nucleic acid-protein recognition. The list of these enzymes is being
AB  - enlarged, though some of them are more preferable for practical use. HpaI (from Haemophilus
AB  - parainfluenzae) is one such enzyme. A restriction endonuclease has been detected in
AB  - Methylococcus whittenburyi recognizing the same nucleotide sequence as HpaI. The new
AB  - isoschizomer was named MwhI according to the existing nomenclature. As M. whittenburyi (as
AB  - compared to H. parainfluenze) grows on simple mineral medium, is not pathogenic, comprises a
AB  - single enzyme, it might be promising for enzyme production.
ER  -

TY  - JOUR
AU  - Alexiev, A.
AU  - Coil, D.A.
AU  - Badger, J.H.
AU  - Enticknap, J.
AU  - Ward, N.
AU  - Robb, F.T.
AU  - Eisen, J.A.
TI  - Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265.
JO  - Genome Announcements
PY  - 2014
SP  - e00470
EP  - e00414
VL  - 2
AB  - Here we present the complete 1,424,912-bp genome sequence of Coprothermobacter proteolyticus
AB  - DSM 5265, isolated from a thermophilic digester fermenting tannery
AB  - wastes and cattle manure.
ER  -

TY  - JOUR
AU  - Alexiev, A.
AU  - Coil, D.A.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Adams, J.Y.
TI  - Draft Genome Sequence of Klebsiella pneumoniae UCD-JA29 Isolated from a Patient with Sepsis.
JO  - Genome Announcements
PY  - 2016
SP  - e00234
EP  - e00216
VL  - 4
AB  - Here, we present the 6,155,188-bp draft genome sequence of Klebsiella pneumoniae  UCD-JA29,
AB  - isolated from blood cultures from a patient with sepsis at the
AB  - University of California, Davis Medical Center in Sacramento, California, USA.
ER  -

TY  - JOUR
AU  - Alexiev, A.
AU  - Krusor, M.L.
AU  - Jospin, G.
AU  - Lang, J.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina.
JO  - Genome Announcements
PY  - 2016
SP  - e00116
EP  - e00116
VL  - 4
AB  - Here, we present the 4,230,758-bp draft genome for Cobetia sp. UCD-24C. This strain was
AB  - isolated from Zostera marina roots collected in Woods Hole,
AB  - Massachusetts, USA.
ER  -

TY  - JOUR
AU  - Alexiev, A.
AU  - Krusor, M.L.
AU  - Jospin, G.
AU  - Lang, J.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina.
JO  - Genome Announcements
PY  - 2016
SP  - e00010
EP  - e00016
VL  - 4
AB  - Here, we present the draft genome sequences for Pseudoalteromonas sp. strain UCD-33C and
AB  - Pseudoalteromonas lipolytica UCD-48B. Pseudoalteromonas sp. UCD-33C
AB  - was isolated from Zostera marina roots and P. lipolytica UCD-48B from Z. marina
AB  - leaf blades, both collected in Woods Hole, MA. These assemblies contain 4,479,285
AB  - bp and 4,592,435 bp, respectively.
ER  -

TY  - JOUR
AU  - Alfan-Guzman, R.
AU  - Ertan, H.
AU  - Manefield, M.
AU  - Lee, M.
TI  - Genome Sequence of Dehalobacter sp. Strain TeCB1, Able To Respire Chlorinated Benzenes.
JO  - Genome Announcements
PY  - 2017
SP  - e01681
EP  - e01616
VL  - 5
AB  - Dehalobacter sp. strain TeCB1 was isolated from groundwater contaminated with a mixture of
AB  - organohalides and is able to respire 1,2,4,5-tetrachlorobenzene and
AB  - 1,2,4-trichlorobenzene. Here, we report its 3.13-Mb draft genome sequence.
ER  -

TY  - JOUR
AU  - Algire, M.A.
AU  - Montague, M.G.
AU  - Vashee, S.
AU  - Lartigue, C.
AU  - Merryman, C.
TI  - A type III restriction-modification system in Mycoplasma mycoides subsp. capri.
JO  - Open Biology
PY  - 2012
SP  - 120115
EP  - 120115
VL  - 2
AB  - the sequenced genome of Mycoplasma mycoides subsp. capri revealed the presence of a Type III
AB  - restriction-modification system (MmyCI).  The methyltransferase (modification) subunit of
AB  - MmyCI (M.MmyCI) was shown to recognize the sequence 5'-TGAG-3' and methylate the adenine.
AB  - The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide
AB  - repeats that result in a translational termination at a TAA codon immediately beyond the
AB  - repeat region.  This strain does not have MmyCI activity.  A clone was found with 10 AG
AB  - repeats such that the gene is in frame, and this strain has MmyCI activity, suggesting that
AB  - the expression of the MmyCI methyltransferase may be phase variable.
ER  -

TY  - JOUR
AU  - Algowaihi, R.
AU  - Ashgar, S.
AU  - Sirag, B.
AU  - Shalam, S.
AU  - Nassir, A.
AU  - Ahmed, A.
TI  - Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Strain Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.
JO  - Genome Announcements
PY  - 2016
SP  - e00375
EP  - e00316
VL  - 4
AB  - Multidrug-resistant (MDR) Gram-negative infections represent a growing problem and a serious
AB  - global threat. Carbapenem-resistant Klebsiella pneumoniae is
AB  - perhaps cause the most difficult infection to treat and is associated with
AB  - increased morbidity and mortality. Here, we report the draft genome sequence of
AB  - an MDR K. pneumoniae strain isolated from Makkah, Saudi Arabia.
ER  -

TY  - JOUR
AU  - Ali, F.
AU  - Hu, H.
AU  - Xu, P.
AU  - Tang, H.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa FA-HZ1, an Efficient Dibenzofuran-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01634
EP  - e01616
VL  - 5
AB  - Pseudomonas sp. FA-HZ1, an efficient dibenzofuran-degrading bacterium, was isolated from
AB  - landfill leachate. Here, we present the complete genome sequence of
AB  - strain FA-HZ1, which contains only one circular chromosome. The complete genome
AB  - sequence will be essential for revealing the molecular mechanisms of dibenzofuran
AB  - degradation.
ER  -

TY  - JOUR
AU  - Ali, M.
AU  - Haroon, M.F.
AU  - Narita, Y.
AU  - Zhang, L.
AU  - Rangel, S.D.
AU  - Okabe, S.
AU  - Saikaly, P.E.
TI  - Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium 'Candidatus Brocadia sp. 40'.
JO  - Genome Announcements
PY  - 2016
SP  - e01377
EP  - e01316
VL  - 4
AB  - The anaerobic ammonium-oxidizing (anammox) bacterium 'Candidatus Brocadia sp. 40'
AB  - demonstrated the fastest growth rate compared to others in this taxon. Here, we
AB  - report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565
AB  - gene-coding regions, 41 tRNAs, and a single rrn operon.
ER  -

TY  - JOUR
AU  - Ali, S.A.
AU  - Kumar, S.
AU  - Mohanty, A.K.
AU  - Behare, P.
TI  - Draft Genome Sequence of Lactobacillus fermentum NCDC 400, Isolated from a Traditional Indian Dairy Product.
JO  - Genome Announcements
PY  - 2018
SP  - e01492
EP  - e01417
VL  - 6
AB  - We announce here the draft genome sequence of Lactobacillus fermentum NCDC 400, a potential
AB  - probiotic strain isolated from a traditional Indian dairy product. The genome size of
AB  - Lactobacillus fermentum NCDC 400 is 1.89 Mb, and the assembled sequence consists of 185
AB  - contigs joined into 138 scaffolds.
ER  -

TY  - JOUR
AU  - Alic, S.
AU  - Naglic, T.
AU  - Llop, P.
AU  - Toplak, N.
AU  - Koren, S.
AU  - Ravnikar, M.
AU  - Dreo, T.
TI  - Draft Genome Sequences of Dickeya sp. Isolates B16 (NIB Z 2098) and S1 (NIB Z 2099) Causing Soft Rot of Phalaenopsis Orchids.
JO  - Genome Announcements
PY  - 2015
SP  - e00973
EP  - e00915
VL  - 3
AB  - The genus Dickeya contains bacteria causing soft rot of economically important crops and
AB  - ornamental plants. Here, we report the draft genome sequences of two Dickeya sp. isolates from
AB  - rotted leaves of Phalaenopsis orchids.
ER  -

TY  - JOUR
AU  - Aliyu, H.
AU  - De Maayer, P.
AU  - Rees, J.
AU  - Tuffin, M.
AU  - Cowan, D.A.
TI  - Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain  AN1.
JO  - Genome Announcements
PY  - 2014
SP  - e00197
EP  - e00114
VL  - 2
AB  - Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being
AB  - tolerant of low temperatures, high salt concentrations,
AB  - and high alkalinity. Here we report the draft genome sequence of this strain.
ER  -

TY  - JOUR
AU  - Alkahem, A.T.H.
AU  - Rhoads, D.D.
AU  - Barabote, R.D.
TI  - Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e00588
EP  - e00517
VL  - 5
AB  - The draft genome of Anoxybacillus sp. strain UARK-01, a novel lignin-utilizing thermophilic
AB  - soil bacterium, represents the first sequence of an Anoxybacillus
AB  - isolate from the United States. The genome was sequenced using the Illumina MiSeq
AB  - platform, de novo assembled using SeqMan NGen, and annotated at NCBI. The genome
AB  - sequence revealed genes for laccase and lignocellulose degradation enzymes.
ER  -

TY  - JOUR
AU  - Alkhalili, R.N.
AU  - Hatti-Kaul, R.
AU  - Canback, B.
TI  - Genome Sequence of Geobacillus sp. Strain ZGt-1, an Antibacterial Peptide-Producing Bacterium from Hot Springs in Jordan.
JO  - Genome Announcements
PY  - 2015
SP  - e00799
EP  - e00715
VL  - 3
AB  - This paper reports the draft genome sequence of the firmicute Geobacillus sp. strain ZGt-1, an
AB  - antibacterial peptide producer isolated from the Zara hot spring
AB  - in Jordan. This study is the first report on genomic data from a thermophilic
AB  - bacterial strain isolated in Jordan.
ER  -

TY  - JOUR
AU  - Allam, M.
AU  - Joseph, L.
AU  - Ismail, F.
AU  - Said, H.
AU  - Ismail, N.A.
AU  - Ismail, A.
AU  - Mtshali, S.
AU  - Mnyameni, F.
AU  - Goussard, P.
AU  - Pekeur, J.C.
AU  - Lourens, A.
AU  - Omar, S.V.
TI  - Whole-Genome Sequence of a Mycobacterium goodii Isolate from a Pediatric Patient  in South Africa.
JO  - Genome Announcements
PY  - 2018
SP  - e01478
EP  - e01417
VL  - 6
AB  - We describe here the draft genome sequence of a Mycobacterium goodii isolate from a pediatric
AB  - patient in Western Cape, South Africa. To our knowledge, this is the
AB  - second reported genome of this rapidly growing nontuberculous mycobacterial
AB  - species.
ER  -

TY  - JOUR
AU  - Allam, M.
AU  - Tau, N.
AU  - Smouse, S.L.
AU  - Mtshali, P.S.
AU  - Mnyameni, F.
AU  - Khumalo, Z.T.H.
AU  - Ismail, A.
AU  - Govender, N.
AU  - Thomas, J.
AU  - Smith, A.M.
TI  - Whole-Genome Sequences of Listeria monocytogenes Sequence Type 6 Isolates Associated with a Large Foodborne Outbreak in South Africa, 2017 to 2018.
JO  - Genome Announcements
PY  - 2018
SP  - e00538
EP  - e00518
VL  - 6
AB  - We report whole-genome sequences for 10 Listeria monocytogenes sequence type 6 isolates
AB  - associated with a large listeriosis outbreak in South Africa, which
AB  - occurred over the period of 2017 to 2018. The possibility of listeriosis
AB  - spreading beyond South Africa's borders as a result of exported contaminated food
AB  - products prompted us to make the genome sequences publicly available.
ER  -

TY  - JOUR
AU  - Allan, B.W.
TI  - The dynamic origin of sequence discrimination by the EcoRI DNA methyltransferase.
JO  - Diss. Abstr.
PY  - 1999
SP  - 3407B
EP  - 3407B
VL  - 59
AB  - All living cells use DNA modifying enzymes to maintain or expand the information encoded
AB  - within the genome.  These enzymes catalyze the chemical transformation of sterically occluded
AB  - target DNA residues within a huge excess of nontarget DNA.  Enzyme-DNA complexes reveal
AB  - striking distortions of DNA structure such as DNA bending and base flipping; yet, the
AB  - mechanism whereby DNA distortion modulates sequence specificity is only now being elucidated.
AB  - Intriguing mechanistic questions remain unresolved.  Do DNA modifying enzymes capture
AB  - transient structural intermediates or actively induce the conformational changes required for
AB  - DNA binding and catalysis?  Determination of the temporal correlation between the individual
AB  - steps in the reaction pathway provides a means to discern the origin of sequence
AB  - discrimination.  For the EcoRI DNA methyltransferase nearly absolute synchrony between DNA
AB  - binding and base flipping transitions are revealed during both complex assembly and
AB  - disassembly.  Because the rate of product formation under presteady-state conditions is
AB  - determined not by the methylation reaction, but rather by the pre-catalytic isomerization of
AB  - the complex, the base flipping transition is the selection gate whereby the commitment to
AB  - catalysis is manifested.  Our characterization of a methyltransferase mutant which unlike the
AB  - wild type methyltransferase displays no detectable DNA bending, shows that slowing the rate of
AB  - an obligate pre-catalytic isomerization can result in enhanced discrimination for an
AB  - induced-fit enzyme.  The recent extension of the experimental methodologies developed in this
AB  - work to other base flipping enzymes is providing fundamental information concerning the
AB  - integration of DNA distortion and enzyme specificity for other crucial enzymes that modify or
AB  - repair the DNA.  Finally, the high signal to noise, solution-based nature, and millisecond
AB  - timing resolution of this enabling technology is compatible with the rapid throughput
AB  - screening of protein-DNA interactions.
ER  -

TY  - JOUR
AU  - Allan, B.W.
AU  - Beechem, J.M.
AU  - Lindstrom, W.M.
AU  - Reich, N.O.
TI  - Direct real time observation of base flipping by the EcoRI DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 2368
EP  - 2373
VL  - 273
AB  - DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzyme
AB  - specificity because catalysis requires the extrahelical stabilization of the target base
AB  - within the enzyme active site.  The energetics and kinetics of base flipping by the EcoRI DNA
AB  - methyltransferase were investigated by two methods.  First, equilibrium dissociation constants
AB  - (KD/DNA) were determined for the binding of the methyltransferase to DNA containing abasic
AB  - sites or base analogs incorporated at the target base.  Consistent with a base flipping
AB  - mechanism, tighter binding to oligonucleotides containing destabilized target base pairs was
AB  - observed.  Second, total intensity stopped flow fluorescence measurements of DNA containing
AB  - 2-aminopurine allowed presteady-state real time observation of the base flipping transition.
AB  - Following the rapid formation of an enzyme-DNA collision complex, a biphasic increase in total
AB  - intensity was observed.  The fast phase dominated the total intensity increase with a rate
AB  - nearly identical to k(methylation) determined by rapid chemical quench-flow techniques.  The
AB  - restacking of the extrahelical base also revealed biphasic kinetics with the recovered
AB  - amplitudes from these off-rate experiments matching very closely to those observed during the
AB  - base unstacking process.  These results provide the first direct and continuous observation of
AB  - base flipping and show that at least two distinct conformation transitions occurred at the
AB  - flipped base subsequent to complex formation.  Furthermore, our results suggest that the
AB  - commitment to catalysis during the methylation of the target site is not determined at the
AB  - level of the chemistry step but rather is mediated by prior intramolecular isomerization
AB  - within the enzyme-DNA complex.
ER  -

TY  - JOUR
AU  - Allan, B.W.
AU  - Garcia, R.
AU  - Maegley, K.
AU  - Mort, J.
AU  - Wong, D.
AU  - Lindstrom, W.
AU  - Beechem, J.M.
AU  - Reich, N.O.
TI  - DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 19269
EP  - 19275
VL  - 274
AB  - EcoRI DNA methyltransferase was previously shown to bend its cognate DNA sequence by 52
AB  - degrees and stabilize the target adenine in an extrahelical orientation. We describe the
AB  - characterization of an EcoRI DNA methyltransferase mutant in which histidine 235 was
AB  - selectively replaced with asparagine. Steady-state kinetic and thermodynamic parameters for
AB  - the H235N mutant revealed only minor functional consequences: DNA binding affinity (KDDNA) was
AB  - reduced 10-fold, and kcat was decreased 30%. However, in direct contrast to the wild type
AB  - enzyme, DNA bending within the mutant enzyme-DNA complexes was not observed by scanning force
AB  - microscopy. The bending-deficient mutant showed enhanced discrimination against the
AB  - methylation at nontarget sequence DNA. This enhancement of enzyme discrimination was
AB  - accompanied by a change in the rate-limiting catalytic step. No presteady-state burst of
AB  - product formation was observed, indicating that the chemistry step (or prior event) had become
AB  - rate-limiting for methylation. Direct observation of the base flipping transition showed that
AB  - the lack of burst kinetics was entirely due to slower base flipping. The combined data show
AB  - that DNA bending contributes to the correct assembly of the enzyme-DNA complex to accelerate
AB  - base flipping and that slowing the rate of this precatalytic isomerization can enhance
AB  - specificity.
ER  -

TY  - JOUR
AU  - Allan, B.W.
AU  - Reich, N.O.
TI  - Targeted base stacking disruption by the EcoRI DNA methyltransferase.
JO  - Biochemistry
PY  - 1996
SP  - 14757
EP  - 14762
VL  - 35
AB  - We describe a novel fluorescence-based assay for detecting DNA conformational alterations
AB  - within enzyme--DNA complexes.  The target adenine for EcoRI DNA methyltransferase to the
AB  - duplex binding site results in a 14-fold increase in fluorescence intensity with a 10 nm blue
AB  - shift.  The fluorescence is ~50% of that observed with equimolar free nucleoside, consistent
AB  - with extrahelical stabilization of the target base in the enzyme--DNA complex.  The shift in
AB  - lambda/max further implies the base is placed into a low dielectric environment.  For
AB  - adenine-specific DNA methyltransferases, a hydrophobic pocket composed of highly conserved
AB  - amino acids lies proximal to the cofactor binding site.  Substitution of 2-aminopurine
AB  - adjacent to the target base also results in detectable changes in fluorescence emission
AB  - following complex formation with the methyltransferase.  Thus, other classes of enzymes
AB  - hypothesized to utilize base flipping can be investigated by this method.
ER  -

TY  - JOUR
AU  - Allan, B.W.
AU  - Reich, N.O.
AU  - Beechem, J.M.
TI  - Measurement of the absolute temporal coupling between DNA binding and base flipping.
JO  - Biochemistry
PY  - 1999
SP  - 5308
EP  - 5314
VL  - 38
AB  - The absolute temporal couplings between DNA binding and base flipping were examined for the
AB  - EcoRI DNA methyltransferase.  The binding event (monitored using rhodamine-x fluorescence
AB  - anisotropy) was monophasic with a second-order on-rate of 1.1 x 10^7 M-1 s-1 <- kon <- 2.25 x
AB  - 10^7 M-1 s-1.  Base-flipping kinetics (monitored using 2-aminopurine fluorescence intensity)
AB  - were essentially synchronous with the binding kinetics, with less than a 4 ms delay between
AB  - enzyme binding and target base flipping.  The 4 ms delay translates into a base-flipping rate
AB  - of at least 195 s-1, when the data are analyzed in terms of a sequential DNA binding and
AB  - base-flipping reaction mechanism.  Synchrony of binding and base flipping was only observed
AB  - during the first 80% of the reaction, and an additional 20% base-flipping signal occurred well
AB  - after DNA binding was complete.  This additional 2AP fluorescence change, with an effective
AB  - rate of 0.55 s-1, is an intramolecular isomerization reaction which greatly accelerates the
AB  - dissociation of the enzyme from DNA.  The correlation between the dissociation of the
AB  - enzyme-DNA complex and the restacking of the extrahelical base also revealed a very tight
AB  - coupling of these two events.  Both dissociation and base restacking were found to be
AB  - biphasic.  These data are consistent with the following mechanism.  The initial binding rate
AB  - and base-flipping rates map very closely with previously determined pre-steady-state
AB  - burst-rate kinetics for methyl transfer.  Hence, binding, flipping, and methylation appear to
AB  - occur in nearly a single concerted step.  The bound complex then slowly isomerizes (0.1 s-1)
AB  - to a distinct configuration that accelerates the product-release phase of the reaction.  The
AB  - product-release enzyme configuration dissociates from DNA approximately 8 times faster than
AB  - the initial bound complex (0.18 s-1 vs. 0.024 s-1).  When the enzyme dissociates from the DNA
AB  - along the product-release pathway, the target base remains in an extrahelical conformation and
AB  - restacks at a rate of only 0.6 s-1 .  This "multicolor" fluorescence kinetic approach directly
AB  - measures the absolute temporal correlation between DNA binding and base flipping, with
AB  - millisecond timing resolution.  The data reveal that even when the B-DNA structure is altered
AB  - in a radical manner (e.g., via base flipping), enzymes can perform this operation in a highly
AB  - efficient, if not completely concerted manner.
ER  -

TY  - JOUR
AU  - Allan, B.W.
AU  - Reich, N.O.
AU  - Beechem, J.M.
TI  - Simultaneous real-time measurement of binding base-flipping, and dissociation base unflipping in EcoRI DNA methyltransferase.
JO  - Biophys. J.
PY  - 1998
SP  - A69
EP  - A69
VL  - 74
AB  - Many DNA binding proteins generate large changes in the conformation of DNA upon interaction.
AB  - High signal-to-noise data of the exact correlation in-time between the binding event and DNA
AB  - conformational change, would allow a much deeper understanding of this process.  In this
AB  - study, "doubly-labeled" 2-color fluorescent DNA has been synthesized and utilized in
AB  - stopped-flow fluorescence experiments, allowing the simultaneous measurement of DNA binding
AB  - (via anisotropy changes of 5'-Rhodamine-X labeled 14mers; red-signal) and internal
AB  - base-flipping (via changes in the fluorescence intensity of 2-aminopurine at the target
AB  - methylation site; blue signal) (see figure for end-points; up arrow, down arrow indicates
AB  - protein addition).  The binding-rate (kon = 1.6 x 10^7M-1 s-1) and base-flipping rates in
AB  - EcoRI MTase were found to be almost absolutely correlated, whereas differences in off-rate and
AB  - "unflipping" were detected.
ER  -

TY  - JOUR
AU  - Allard, M.W.
AU  - Luo, Y.
AU  - Strain, E.
AU  - Li, C.
AU  - Keys, C.E.
AU  - Son, I.
AU  - Stones, R.
AU  - Musser, S.M.
AU  - Brown, E.W.
TI  - High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach.
JO  - BMC Genomics
PY  - 2012
SP  - 32
EP  - 32
VL  - 13
AB  - BACKGROUND: Next-Generation Sequencing (NGS) is increasingly being used as a
AB  - molecular epidemiologic tool for discerning ancestry and traceback of the most
AB  - complicated, difficult to resolve bacterial pathogens. Making a linkage between
AB  - possible food sources and clinical isolates requires distinguishing the suspected
AB  - pathogen from an environmental background and placing the variation observed into
AB  - the wider context of variation occurring within a serovar and among other closely
AB  - related foodborne pathogens. Equally important is the need to validate these high
AB  - resolution molecular tools for use in molecular epidemiologic traceback. Such
AB  - efforts include the examination of strain cluster stability as well as the
AB  - cumulative genetic effects of sub-culturing on these clusters. Numerous isolates
AB  - of S. Montevideo were shot-gun sequenced including diverse lineage
AB  - representatives as well as numerous replicate clones to determine how much
AB  - variability is due to bias, sequencing error, and or the culturing of isolates.
AB  - All new draft genomes were compared to 34 S. Montevideo isolates previously
AB  - published during an NGS-based molecular epidemiological case study. RESULTS:
AB  - Intraserovar lineages of S. Montevideo differ by thousands of SNPs, that are only
AB  - slightly less than the number of SNPs observed between S. Montevideo and other
AB  - distinct serovars. Much less variability was discovered within an individual S.
AB  - Montevideo clade implicated in a recent foodborne outbreak as well as among
AB  - individual NGS replicates. These findings were similar to previous reports
AB  - documenting homopolymeric and deletion error rates with the Roche 454 GS Titanium
AB  - technology. In no case, however, did variability associated with sequencing
AB  - methods or sample preparations create inconsistencies with our current
AB  - phylogenetic results or the subsequent molecular epidemiological evidence gleaned
AB  - from these data. CONCLUSIONS: Implementation of a validated pipeline for NGS data
AB  - acquisition and analysis provides highly reproducible results that are stable and
AB  - predictable for molecular epidemiological applications. When draft genomes are
AB  - collected at 15x-20x coverage and passed through a quality filter as part of a
AB  - data analysis pipeline, including sub-passaged replicates defined by a few SNPs,
AB  - they can be accurately placed in a phylogenetic context. This reproducibility
AB  - applies to all levels within and between serovars of Salmonella suggesting that
AB  - investigators using these methods can have confidence in their conclusions.
ER  -

TY  - JOUR
AU  - Allard, M.W.
AU  - Luo, Y.
AU  - Strain, E.
AU  - Pettengill, J.
AU  - Timme, R.
AU  - Wang, C.
AU  - Li, C.
AU  - Keys, C.E.
AU  - Zheng, J.
AU  - Stones, R.
AU  - Wilson, M.R.
AU  - Musser, S.M.
AU  - Brown, E.W.
TI  - On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.
JO  - PLoS ONE
PY  - 2013
SP  - E55254
EP  - E55254
VL  - 8
AB  - Facile laboratory tools are needed to augment identification in contamination
AB  - events to trace the contamination back to the source (traceback) of Salmonella
AB  - enterica subsp. enterica serovar Enteritidis (S. Enteritidis). Understanding the
AB  - evolution and diversity within and among outbreak strains is the first step
AB  - towards this goal. To this end, we collected 106 new S. Enteriditis isolates
AB  - within S. Enteriditis Pulsed-Field Gel Electrophoresis (PFGE) pattern JEGX01.0004
AB  - and close relatives, and determined their genome sequences. Sources for these
AB  - isolates spanned food, clinical and environmental farm sources collected during
AB  - the 2010 S. Enteritidis shell egg outbreak in the United States along with
AB  - closely related serovars, S. Dublin, S. Gallinarum biovar Pullorum and S.
AB  - Gallinarum. Despite the highly homogeneous structure of this population, S.
AB  - Enteritidis isolates examined in this study revealed thousands of SNP differences
AB  - and numerous variable genes (n = 366). Twenty-one of these genes from the
AB  - lineages leading to outbreak-associated samples had nonsynonymous (causing amino
AB  - acid changes) changes and five genes are putatively involved in known Salmonella
AB  - virulence pathways. While chromosome synteny and genome organization appeared to
AB  - be stable among these isolates, genome size differences were observed due to
AB  - variation in the presence or absence of several phages and plasmids, including
AB  - phage RE-2010, phage P125109, plasmid pSEEE3072_19 (similar to pSENV), plasmid
AB  - pOU1114 and two newly observed mobile plasmid elements pSEEE1729_15 and
AB  - pSEEE0956_35. These differences produced modifications to the assembled bases for
AB  - these draft genomes in the size range of approximately 4.6 to 4.8 mbp, with S.
AB  - Dublin being larger ( approximately 4.9 mbp) and S. Gallinarum smaller (4.55 mbp)
AB  - when compared to S. Enteritidis. Finally, we identified variable S. Enteritidis
AB  - genes associated with virulence pathways that may be useful markers for the
AB  - development of rapid surveillance and typing methods, potentially aiding in
AB  - traceback efforts during future outbreaks involving S. Enteritidis PFGE pattern
AB  - JEGX01.0004.
ER  -

TY  - JOUR
AU  - Allard, M.W.
AU  - Muruvanda, T.
AU  - Strain, E.
AU  - Timme, R.
AU  - Luo, Y.
AU  - Wang, C.
AU  - Keys, C.E.
AU  - Payne, J.
AU  - Cooper, T.
AU  - Luong, K.
AU  - Song, Y.
AU  - Chin, C.S.
AU  - Korlach, J.
AU  - Roberts, R.J.
AU  - Evans, P.
AU  - Musser, S.M.
AU  - Brown, E.W.
TI  - Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.
JO  - Genome Announcements
PY  - 2014
SP  - e00293
EP  - e00214
VL  - 2
AB  - Volume 1, no. 2, e00081-13, 2013.  Page 1: The article byline should read as given above.
AB  - Page 2: The following should be added to the Acknowledgments.  "Research reported in this
AB  - publication was supported by the Small Business Innovation Research Program (NIGMS) of the
AB  - National Institutes of Health under award number R44GM105125 to R.J.R.  The content is solely
AB  - the responsibility of the authors and does not necessarily represent the official views of the
AB  - National Institutes of Health."
ER  -

TY  - JOUR
AU  - Allard, M.W.
AU  - Muruvanda, T.
AU  - Strain, E.
AU  - Timme, R.
AU  - Luo, Y.
AU  - Wang, C.
AU  - Keys, C.E.
AU  - Payne, J.
AU  - Cooper, T.
AU  - Luong, K.
AU  - Song, Y.
AU  - Chin, C.S.
AU  - Korlach, J.
AU  - Roberts, R.J.
AU  - Evans, P.
AU  - Musser, S.M.
AU  - Brown, E.W.
TI  - Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992.
JO  - Genome Announcements
PY  - 2013
SP  - e00081
EP  - e00013
VL  - 1
AB  - We report a closed genome of Salmonella enterica subsp. enterica serovar Javiana  (S.
AB  - Javiana). This serotype is a common food-borne pathogen and is often associated with fresh-cut
AB  - produce. Complete (finished) genome assemblies will support pilot studies testing the utility
AB  - of next-generation sequencing (NGS) technologies in public health laboratories.
ER  -

TY  - JOUR
AU  - Allen, E.E.
AU  - Tyson, G.W.
AU  - Whitaker, R.J.
AU  - Detter, J.C.
AU  - Richardson, P.M.
AU  - Banfield, J.F.
TI  - Genome dynamics in a natural archaeal population.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 1883
EP  - 1888
VL  - 104
AB  - Evolutionary processes that give rise to, and limit, diversification within
AB  - strain populations can be deduced from the form and distribution of genomic
AB  - heterogeneity. The extent of genomic change that distinguishes the acidophilic
AB  - archaeon Ferroplasma acidarmanus fer1 from an environmental population of the
AB  - same species from the same site, fer1(env), was determined by comparing the
AB  - 1.94-megabase (Mb) genome sequence of the isolate with that reconstructed from 8
AB  - Mb of environmental sequence data. The fer1(env) composite sequence sampled
AB  - approximately 92% of the isolate genome. Environmental sequence data were also
AB  - analyzed to reveal genomic heterogeneity within the coexisting, coevolving
AB  - fer1(env) population. Analyses revealed that transposase movement and the
AB  - insertion and loss of blocks of novel genes of probable phage origin occur
AB  - rapidly enough to give rise to heterogeneity in gene content within the local
AB  - population. Because the environmental DNA was derived from many closely related
AB  - individuals, it was possible to quantify gene sequence variability within the
AB  - population. All but a few gene variants show evidence of strong purifying
AB  - selection. Based on the small number of distinct sequence types and their
AB  - distribution, we infer that the population is undergoing frequent genetic
AB  - recombination, resulting in a mosaic genome pool that is shaped by selection. The
AB  - larger genetic potential of the population relative to individuals within it and
AB  - the combinatorial process that results in many closely related genome types may
AB  - provide the basis for adaptation to environmental fluctuations.
ER  -

TY  - JOUR
AU  - Allen, M.J.
AU  - Tait, K.
AU  - Muhling, M.
AU  - Weynberg, K.
AU  - Bradley, C.
AU  - Trivedi, U.
AU  - Gharbi, K.
AU  - Nissimov, J.
AU  - Mavromatis, K.
AU  - Jensen, C.N.
AU  - Grogan, G.
AU  - Ali, S.T.
TI  - Genome Sequence of Stenotrophomonas maltophilia PML168, Which Displays Baeyer-Villiger Monooxygenase Activity.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4753
EP  - 4754
VL  - 194
AB  - Stenotrophomonas maltophilia PML168 was isolated from Wembury Beach on the English Coast from
AB  - a rock pool following growth and selection on agar plates.
AB  - Here we present the permanent draft genome sequence, which has allowed prediction
AB  - of function for several genes encoding enzymes relevant to industrial
AB  - biotechnology, including a novel flavoprotein monooxygenase.
ER  -

TY  - JOUR
AU  - Allen-Daniels, M.J.
AU  - Serrano, M.G.
AU  - Pflugner, L.P.
AU  - Fettweis, J.M.
AU  - Prestosa, M.A.
AU  - Koparde, V.N.
AU  - Brooks, J.P.
AU  - Strauss, J.F. III
AU  - Romero, R.
AU  - Chaiworapongsa, T.
AU  - Eschenbach, D.A.
AU  - Buck, G.A.
AU  - Jefferson, K.K.
TI  - Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intra-amniotic infection.
JO  - Am. J. Obstet. Gynecol.
PY  - 2015
SP  - 779.e1
EP  - 779.e13
VL  - 212
AB  - OBJECTIVE: Microbial invasion of the amniotic cavity is associated with
AB  - spontaneous preterm labor and adverse pregnancy outcome, and Mycoplasma hominis
AB  - often is present. However, the pathogenic process by which M hominis invades the
AB  - amniotic cavity and gestational tissues, often resulting in chorioamnionitis and
AB  - preterm birth, remains unknown. We hypothesized that strains of M hominis vary
AB  - genetically with regards to their potential to invade and colonize the amniotic
AB  - cavity and placenta. STUDY DESIGN: We sequenced the entire genomes of 2 amniotic
AB  - fluid isolates and a placental isolate of M hominis from pregnancies that
AB  - resulted in preterm births and compared them with the previously sequenced genome
AB  - of the type strain PG21. We identified genes that were specific to the amniotic
AB  - fluid/placental isolates. We then determined the microbial burden and the
AB  - presence of these genes in another set of subjects from whom samples of amniotic
AB  - fluid had been collected and were positive for M hominis. RESULTS: We identified
AB  - 2 genes that encode surface-located membrane proteins (Lmp1 and Lmp-like) in the
AB  - sequenced amniotic fluid/placental isolates that were truncated severely in PG21.
AB  - We also identified, for the first time, a microbial gene of unknown function that
AB  - is referred to in this study as gene of interest C that was associated
AB  - significantly with bacterial burden in amniotic fluid and the risk of preterm
AB  - delivery in patients with preterm labor. CONCLUSION: A gene in M hominis was
AB  - identified that is associated significantly with colonization and/or infection of
AB  - the upper reproductive tract during pregnancy and with preterm birth.
ER  -

TY  - JOUR
AU  - Allet, B.
TI  - Fragments produced by cleavage of lambda deoxyribonucleic acid with the Hemophilus parainfluenzae restriction enzyme HpaII.
JO  - Biochemistry
PY  - 1973
SP  - 3972
EP  - 3977
VL  - 12
AB  - One of the restricting enzymes extracted from Hemophilus parainfluenzae, HpaII,
AB  - is shown to cleave lambda DNA at more than 50 sites.  The resulting DNA
AB  - fragments have been prepared from a variety of deletion or
AB  - deletion-substitution mutants of lambda, and analyzed by polyacrylamide gel
AB  - electrophoresis.  The major DNA segments (larger than 0.3 Mdalton) produced by
AB  - digestion of lambda DNA have been mapped and many of the cleavage sites in the
AB  - immunity region, in the b2 region, and to the right of the immunity region have
AB  - been identified.
ER  -

TY  - JOUR
AU  - Allet, B.
AU  - Jeppesen, P.G.N.
AU  - Katagiri, K.J.
AU  - Delius, H.
TI  - Mapping the DNA fragments produced by cleavage of lambda DNA with endonuclease RI.
JO  - Nature
PY  - 1973
SP  - 120
EP  - 123
VL  - 241
AB  - None
ER  -

TY  - JOUR
AU  - Allet, B.
AU  - Rochaix, J.-D.
TI  - Structure analysis at the ends of the intervening DNA sequences in the chloroplast 23S ribosomal genes of C. reinhardii.
JO  - Cell
PY  - 1979
SP  - 55
EP  - 60
VL  - 18
AB  - All of the chloroplast 23S ribosomal genes of C. reinhardii are interrupted by a 0.87 kb
AB  - sequence.  We have sequenced the DNA across the two ends of this intervening element.  In
AB  - parallel, we have examined the nucleotide sequences in the corresponding part of the 23S
AB  - ribosomal RNA.  This allowed us to locate precisely the boundaries between the coding (that
AB  - is, transcribed into mature 23S rRNA) and the noncoding DNA.  The results show that the
AB  - intervening sequence is flanked by two identical sets of 3 bp (5'-CGT) oriented as direct
AB  - repeats.  In addition, a sequence of 5 bp (5'-CGTGA) lies exactly next to one end and is
AB  - found very close (16 bp) to the other end, in the coding part of the gene.  These two sets are
AB  - also oriented as direct repeats.  Finally, sequences near one end of the intervening element
AB  - are found with a few alterations near the other end, but in an inverted orientation.  Possible
AB  - interpretations of these results are discussed.
ER  -

TY  - JOUR
AU  - Allison, D.P.
AU  - Kerper, P.S.
AU  - Doktycz, M.J.
AU  - Spain, J.A.
AU  - Modrich, P.
AU  - Larimer, F.W.
AU  - Thundat, T.
TI  - Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 8826
EP  - 8829
VL  - 93
AB  - Direct imaging with the atomic force microscope has been used to identify specific nucleotide
AB  - sequences in plasmid DNA molecules.  This was accomplished using EcoRI(Gln-111), a mutant of
AB  - the restriction enzyme that has a 1000-fold greater binding affinity than the wild-type enzyme
AB  - but with cleavage rate constants reduced by a factor of 10^4.  ScaI-linearized plasmids with
AB  - single (pBS+) and double (pGEM-luc and pSV-beta-galactosidase) EcoRI recognition sites were
AB  - imaged, and the bound enzyme was localized to a 50- to 100-nt resolution.  The high affinity
AB  - for the EcoRI binding site exhibited by this mutant endonuclease, coupled with an observed low
AB  - level of nonspecific binding, should prove valuable for physically mapping large DNA clones by
AB  - direct atomic force microscope imaging.
ER  -

TY  - JOUR
AU  - Allison, G.E.
AU  - Angeles, D.
AU  - Tran-Dinh, N.
AU  - Verma, N.K.
TI  - Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri.
JO  - J. Bacteriol.
PY  - 2002
SP  - 1974
EP  - 1987
VL  - 184
AB  - Bacteriophage SfV is a temperate serotype-converting phage of Shigella flexneri. SfV encodes
AB  - the factors involved in type V O-antigen
AB  - modification, and the serotype conversion and integration-excision
AB  - modules of the phage have been isolated and characterized. We now
AB  - report on the complete sequence of the SfV genome (37,074 bp). A total
AB  - of 53 open reading frames were predicted from the nucleotide sequence,
AB  - and analysis of tile corresponding proteins was used to construct a
AB  - functional map. The general organization of the genes in the SfV genome
AB  - is similar to that of bacteriophage X, and numerous features of the
AB  - sequence are described. The superinfection immunity system of SfV
AB  - includes a lambda-like repression system and a P4-like transcription
AB  - termination mechanism. Sequence analysis also suggests that SfV encodes
AB  - multiple DNA methylases, and experiments confirmed that orf-41 encodes
AB  - a Dam methylase. Studies conducted to determine if the phage-encoded
AB  - methylase confers host DNA methylation showed that the two S. flexneri
AB  - strains analyzed encode their own Dam methylase. Restriction mapping
AB  - and sequence analysis revealed that the phage genome has cos sites at
AB  - the termini. The tail assembly and structural genes of SfV show
AB  - homology to those of phage Mu and Mu-like prophages in the genome of
AB  - Escherichia coli O157:H7 and Haemophilus influenzae. Significant
AB  - homology (30% of the genome in total) between sections of the early,
AB  - regulatory, and structural regions of the SfV genome and the e14 and
AB  - KpLE1 prophages in the E. coli K-12 genome were noted, suggesting that
AB  - these three phages have common evolutionary origins.
ER  -

TY  - JOUR
AU  - Allison, G.E.
AU  - Klaenhammer, T.R.
TI  - Phage resistance mechanisms in lactic acid bacteria.
JO  - Int. Dairy Journal
PY  - 1998
SP  - 207
EP  - 226
VL  - 8
AB  - Dairy fermentations involving Lactococcus lactis and more recently Streptococcus thermophilus,
AB  - are commonly attacked by bacteriophages.  Efforts to protect these dairy starter cultures have
AB  - resulted in a significant body of knowledge about the bacteriophages, their interactions with
AB  - the host, and natural phage defense mechanisms that have evolved within bacteria operating
AB  - under the most dynamic and devastating phage environment faced by industrial fermentations.
AB  - This paper will overview this area and discuss the novel genetic approaches that are now being
AB  - investigated in an effort to provide long term phage protection to dairy starter cultures hat
AB  - are used extensively in the industry. A review.
ER  -

TY  - JOUR
AU  - Allison, L.
AU  - Yee, C.N.
TI  - Restriction site mapping is in separation theory.
JO  - Comput. Appl. Biosci.
PY  - 1988
SP  - 97
EP  - 101
VL  - 4
AB  - A computer algorithm for restriction-site mapping consists of a generator of
AB  - partial maps and a consistency checker.  This paper examines consistency
AB  - checking and argues that a method based on separation theory extracts the
AB  - maximum amount of information from fragment lengths in digest data.  It results
AB  - in the minimum number of false maps being generated.
ER  -

TY  - JOUR
AU  - Allnutt, T.R.
AU  - Bradbury, M.I.
AU  - Fanning, S.
AU  - Chandry, P.S.
AU  - Fox, E.M.
TI  - Draft Genome Sequences of 15 Isolates of Listeria monocytogenes Serotype 1/2a, Subgroup ST204.
JO  - Genome Announcements
PY  - 2016
SP  - e00935
EP  - e00916
VL  - 4
AB  - Listeria monocytogenes sequence type 204 (ST204) strains have been isolated from  a range of
AB  - food, environmental, and clinical sources in Australia. This study
AB  - describes the draft genome sequences of 15 isolates collected from meat and dairy
AB  - associated sources.
ER  -

TY  - JOUR
AU  - Allue-Guardia, A.
AU  - Echazarreta, M.
AU  - Koenig, S.S.K.
AU  - Klose, K.E.
AU  - Eppinger, M.
TI  - Closed Genome Sequence of Vibrio cholerae O1 El Tor Inaba Strain A1552.
JO  - Genome Announcements
PY  - 2018
SP  - e00098
EP  - e00018
VL  - 6
AB  - Vibrio cholerae is a Gram-negative waterborne human pathogen and the causative agent of
AB  - cholera. Here, we present the complete genome sequence of the seventh
AB  - pandemic O1 biovar El Tor Inaba strain A1552 isolated in 1992. This clinical
AB  - strain has served as an important model strain for studying cholera pathogenicity
AB  - traits.
ER  -

TY  - JOUR
AU  - Alm, E.
AU  - Advani, A.
AU  - Brave, A.
AU  - Wahab, T.
TI  - Draft Genome Sequence of Strain R13-38 from a Francisella tularensis Outbreak in Sweden.
JO  - Genome Announcements
PY  - 2015
SP  - e01517
EP  - e01514
VL  - 3
AB  - We have whole-genome sequenced a Francisella tularensis subsp. holarctica (also known as type
AB  - B) strain from an outbreak in Sweden in 2013, derived from a privately owned well for drinking
AB  - water.
ER  -

TY  - JOUR
AU  - Alm, R.A.
AU  - Ling, L.-S.L.
AU  - Moir, D.T.
AU  - King, B.L.
AU  - Brown, E.D.
AU  - Doig, P.C.
AU  - Smith, D.R.
AU  - Noonan, B.
AU  - Guild, B.C.
AU  - deJonge, B.L.
AU  - Carmel, G.
AU  - Tummino, P.J.
AU  - Caruso, A.
AU  - Uria-Nickelsen, M.
AU  - Mills, D.M.
AU  - Ives, C.
AU  - Gibson, R.
AU  - Merberg, D.
AU  - Mills, S.
TI  - Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.
JO  - Nature
PY  - 1999
SP  - 176
EP  - 180
VL  - 397
AB  - Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the
AB  - gastric mucosa, where it appears to persist throughout the host's life unless the patient is
AB  - treated.  Colonization induces chronic gastric inflammation which can progress to a variety of
AB  - diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer
AB  - and mucosal-associated lymphoma.  Strain-specific genetic diversity has been proposed to be
AB  - involved in the organism's ability to cause different diseases or even be beneficial to the
AB  - infected host and to participate in the lifelong chronicity of infection.  Here we compare the
AB  - complete genomic sequences of two untreated H. pylori isolates.  This is, to our knowledge,
AB  - the first such genomic comparison.  H. pylori was believed to exhibit a large degree of
AB  - genomic and allelic diversity, but we find that the overall genomic organization, gene order
AB  - and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite
AB  - similar.  Between 6 to 7% of the genes are specific to each strain, with almost half of these
AB  - genes being clustered in a single hypervariable region. Full author list: Alm, R.A., Ling,
AB  - L.-S.L., Moir, D.T., King, B.L., Brown, E.D., Doig, P.C., Smith, D.R., Noonan, B., Guild,
AB  - B.C., deJonge, B.L., Carmel, G., Tummino, P.J., Caruso, A., Uria-Nickelsen, M., Mills, D.M.,
AB  - Ives, C., Gibson, R., Merberg, D., Mills, S.
ER  -

TY  - JOUR
AU  - Alm, R.A.
AU  - Trust, T.J.
TI  - Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes.
JO  - J. Mol. Med.
PY  - 1999
SP  - 834
EP  - 846
VL  - 77
AB  - Infection with Helicobacter pylori has been linked to numerous severe gastroduodenal diseases
AB  - including peptic ulcer and gastric cancer. Several techniques have
AB  - been used to measure the genetic heterogeneity of H. pylori at several different levels and to
AB  - determine whether there is any correlation with severity of disease. The
AB  - availability of two completed genome sequences from unrelated strains (J99 and 26,695) has
AB  - allowed an analysis of the level of diversity from a large-scale yet detailed
AB  - perspective. Although the two chromosomes are organized differently in a limited number of
AB  - discrete regions, the genome size and gene order of these two "high-virulence"
AB  - (cagA+ and vacA+) H. pylori isolates was found to be highly similar. The regions of
AB  - organizational difference are associated with insertion sequences, DNA
AB  - restriction/modification genes, repeat sequences, or a combination of the above. A significant
AB  - level of variation at the nucleotide level is seen across the genome, providing an
AB  - explanation for why the nucleotide-based typing techniques have such high discriminatory power
AB  - among independent H. pylori isolates. This nucleotide variation together
AB  - with the organizational rearrangements appears to have provided an over-estimation of the gene
AB  - order diversity of H. pylori as assessed by pulse-field gel electrophoresis.
AB  - Functional assignments are assigned to approximately only 60% of the gene products in each
AB  - strain, with one-half of the remaining gene products of unknown function having
AB  - homologues in other bacteria, while the remainder appear to be H. pylori-specific. Between 6%
AB  - and 7% of the coding capacity of each strain are genes that are absent from the
AB  - other strain, with almost one-half of these strain-specific genes located in a single
AB  - hypervariable region called the plasticity zone. The majority of the strain-specific genes in
AB  - each strain are also H. pylori-specific, with no homologues being identified in the public
AB  - databases. Significantly, over one-half of the functionally assigned strain-specific
AB  - genes in both H. pylori J99 and 26695 encode DNA restriction/modification enzymes. Analysis of
AB  - the level of conservation between orthologues from the two strains indicates
AB  - that the H. pylori specific genes have a lower level of conservation than those orthologues to
AB  - which a putative function can be assigned. The plasticity zone represents one of
AB  - several regions across each genome that is comprised of lower (G+C)% content DNA, some of
AB  - which has been detected in self-replicating plasmids, suggesting that both
AB  - horizontal transfer from other species and plasmid integration are responsible for the
AB  - strain-specific diversity at this locus. These analyses have yielded results with
AB  - important implications for understanding the genetic diversity of H. pylori and its associated
AB  - diseases, and imply a need to reassess the respective roles of bacterial and host
AB  - factors in H. pylori associated diseases.
ER  -

TY  - JOUR
AU  - Almeida, E.L.
AU  - Margassery, L.M.
AU  - Kennedy, J.
AU  - Dobson, A.D.W.
TI  - Draft Genome Sequence of the Antimycin-Producing Bacterium Streptomyces sp. Strain SM8, Isolated from the Marine Sponge Haliclona simulans.
JO  - Genome Announcements
PY  - 2018
SP  - e01535
EP  - e01517
VL  - 6
AB  - Streptomyces sp. strain SM8, isolated from Haliclona simulans, possesses antifungal and
AB  - antibacterial activities and inhibits the calcineurin pathway in
AB  - yeast. The draft genome sequence is 7,145,211 bp, containing 5,929 predicted
AB  - coding sequences. Several secondary metabolite biosynthetic gene clusters are
AB  - present, encoding known and novel metabolites, including antimycin.
ER  -

TY  - JOUR
AU  - Almeida, E.L.
AU  - Margassery, L.M.
AU  - O'Leary, N.
AU  - Dobson, A.D.W.
TI  - Draft Genome Sequence of Pseudomonas putida CA-3, a Bacterium Capable of Styrene  Degradation and Medium-Chain-Length Polyhydroxyalkanoate Synthesis.
JO  - Genome Announcements
PY  - 2018
SP  - e01534
EP  - e01517
VL  - 6
AB  - Pseudomonas putida strain CA-3 is an industrial bioreactor isolate capable of synthesizing
AB  - biodegradable polyhydroxyalkanoate polymers via the metabolism of
AB  - styrene and other unrelated carbon sources. The pathways involved are subject to
AB  - regulation by global cellular processes. The draft genome sequence is 6,177,154
AB  - bp long and contains 5,608 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Almeida, F.
AU  - Medeiros, M.I.
AU  - Rodrigues, D.P.
AU  - Payne, J.
AU  - Timme, R.E.
AU  - Allard, M.W.
AU  - Falcao, J.P.
TI  - Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e00892
EP  - e00816
VL  - 4
AB  - Salmonellosis is an important health problem worldwide and Salmonella enterica serovar
AB  - Typhimurium is one of the most common isolated serovars. Here, we
AB  - reported the draft genomes of 40 S Typhimurium strains isolated from humans and
AB  - food in Brazil. These draft genomes will improve phylogenetic analysis and will
AB  - help enhance our understanding of strains of this serovar isolated in Brazil.
ER  -

TY  - JOUR
AU  - Almeida, N.F.
AU  - Yan, S.
AU  - Lindeberg, M.
AU  - Studholme, D.J.
AU  - Schneider, D.J.
AU  - Condon, B.
AU  - Liu, H.
AU  - Viana, C.J.
AU  - Warren, A.
AU  - Evans, C.
AU  - Kemen, E.
AU  - Maclean, D.
AU  - Angot, A.
AU  - Martin, G.B.
AU  - Jones, J.D.
AU  - Collmer, A.
AU  - Setubal, J.C.
AU  - Vinatzer, B.A.
TI  - A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.
JO  - Mol. Plant Microbe Interact.
PY  - 2009
SP  - 52
EP  - 62
VL  - 22
AB  - Diverse gene products including phytotoxins, pathogen-associated molecular
AB  - patterns, and type III secreted effectors influence interactions between
AB  - Pseudomonas syringae strains and plants, with additional yet
AB  - uncharacterized factors likely contributing as well. Of particular
AB  - interest are those interactions governing pathogen-host specificity.
AB  - Comparative genomics of closely related pathogens with different host
AB  - specificity represents an excellent approach for identification of genes
AB  - contributing to host-range determination. A draft genome sequence of
AB  - Pseudomonas syringae pv. tomato T1, which is pathogenic on tomato but
AB  - nonpathogenic on Arabidopsis thaliana, was obtained for this purpose and
AB  - compared with the genome of the closely related A. thaliana and tomato
AB  - model pathogen P. syringae pv. tomato DC3000. Although the overall genetic
AB  - content of each of the two genomes appears to be highly similar, the
AB  - repertoire of effectors was found to diverge significantly. Several P.
AB  - syringae pv. tomato T1 effectors absent from strain DC3000 were confirmed
AB  - to be translocated into plants, with the well-studied effector AvrRpt2
AB  - representing a likely candidate for host-range determination. However, the
AB  - presence of avrRpt2 was not found sufficient to explain A. thaliana
AB  - resistance to P. syringae pv. tomato T1, suggesting that other effectors
AB  - and possibly type III secretion system-independent factors also play a
AB  - role in this interaction.
ER  -

TY  - JOUR
AU  - Almeida, S. et al.
TI  - The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 29
EP  - 29
VL  - 11
AB  - Corynebacterium pseudotuberculosis strain VD57 (Cp_VD57), a highly virulent, nonmotile,
AB  - non-sporulating, and a mesophilic bacterium, was isolated from a
AB  - goat's granulomatous lesion in the municipality of Juazeiro, Bahia State, Brazil.
AB  - Here, we describe a set of features of the strain, together with the details of
AB  - its complete genome sequence and annotation. The genome comprises of a 2.5 Mbp
AB  - long, single circular genome with 2,101 protein-coding genes, 12 rRNA, 49 tRNA
AB  - and 47 pseudogenes and a G + C content of 52.85 %. Genetic variation was detected
AB  - in Cp_VD57 using C. pseudotuberculosis strain 1002 as reference, wherein small
AB  - genomic insertions and deletions were identified. The comparative analysis of the
AB  - genome sequence provides means to better understand the host pathogen
AB  - interactions of this strain and can also help us to understand the molecular and
AB  - genetic basis of virulence of this bacterium.
ER  -

TY  - JOUR
AU  - Almeida, S.
AU  - Loureiro, D.
AU  - Portela, R.W.
AU  - Mariano, D.C.
AU  - Sousa, T.J.
AU  - Pereira, F.L.
AU  - Dorella, F.A.
AU  - Carvalho, A.F.
AU  - Moura-Costa, L.F.
AU  - Leal, C.A.
AU  - Figueiredo, H.C.
AU  - Meyer, R.
AU  - Azevedo, V.
TI  - Complete Genome Sequence of the Attenuated Corynebacterium pseudotuberculosis Strain T1.
JO  - Genome Announcements
PY  - 2016
SP  - e00947
EP  - e00916
VL  - 4
AB  - We present here the genome sequence of the attenuated Corynebacterium pseudotuberculosis
AB  - strain T1. The sequencing was performed with an Ion Torrent
AB  - Personal Genome Machine platform. The genome is a circular chromosome of
AB  - 2,337,201 bp, with a G+C content of 52.85% and a total of 2,125 coding sequences
AB  - (CDSs), 12 rRNAs, 49 tRNAs, and 24 pseudogenes.
ER  -

TY  - JOUR
AU  - Almstrand, R.
AU  - Pinto, A.J.
AU  - Figueroa, L.A.
AU  - Sharp, J.O.
TI  - Draft Genome Sequence of a Novel Desulfobacteraceae Member from a Sulfate-Reducing Bioreactor Metagenome.
JO  - Genome Announcements
PY  - 2016
SP  - e01540
EP  - e01515
VL  - 4
AB  - Sulfate-reducing bacteria are important players in the global sulfur cycle and of considerable
AB  - commercial interest. The draft genome sequence of a sulfate-reducing
AB  - bacterium of the family Desulfobacteraceae, assembled from a sulfate-reducing
AB  - bioreactor metagenome, indicates that heavy-metal- and acid-resistance traits of
AB  - this organism may be of importance for its application in acid mine drainage
AB  - mitigation.
ER  -

TY  - JOUR
AU  - Alonso-Carmona, S.
AU  - Vera-Gargallo, B.
AU  - de la Haba, R.R.
AU  - Ventosa, A.
AU  - Sandoval-Trujillo, H.
AU  - Ramirez-Duran, N.
TI  - Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide  Synthase and Nonribosomal Peptide Synthetase Systems.
JO  - Genome Announcements
PY  - 2017
SP  - e00392
EP  - e00317
VL  - 5
AB  - The draft genome sequence of Saccharomonospora sp. strain LRS4.154, a moderately  halophilic
AB  - actinobacterium, has been determined. The genome has 4,860,108 bp, a
AB  - G+C content of 71.0%, and 4,525 open reading frames (ORFs). The clusters of PKS
AB  - and NRPS genes, responsible for the biosynthesis of a large number of
AB  - biomolecules, were identified in the genome.
ER  -

TY  - JOUR
AU  - Alonso-Vega, P.
AU  - Normand, P.
AU  - Bacigalupe, R.
AU  - Pujic, P.
AU  - Lajus, A.
AU  - Vallenet, D.
AU  - Carro, L.
AU  - Coll, P.
AU  - Trujillo, M.E.
TI  - Genome Sequence of Micromonospora lupini Lupac 08, Isolated from Root Nodules of  Lupinus angustifolius.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4135
EP  - 4135
VL  - 194
AB  - Micromonospora strains have been isolated from diverse niches, including soil, water, and
AB  - marine sediments and root nodules of diverse symbiotic plants. In this
AB  - work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated
AB  - from root nodules of the wild legume Lupinus angustifolious.
ER  -

TY  - JOUR
AU  - Alouane, T.
AU  - Uwingabiye, J.
AU  - Lemnouer, A.
AU  - Lahlou, L.
AU  - Laamarti, M.
AU  - Kartti, S.
AU  - Benhrif, O.
AU  - El Misbahi, H.
AU  - Frikh, M.
AU  - Benlahlou, Y.
AU  - Bssaibis, F.
AU  - El Abbassi, S.
AU  - Kabbage, S.
AU  - Maleb, A.
AU  - Elouennass, M.
AU  - Ibrahimi, A.
TI  - First Whole-Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Moroccan Hospital Floor.
JO  - Genome Announcements
PY  - 2017
SP  - e00298
EP  - e00217
VL  - 5
AB  - This report describes the whole-genome shotgun sequences of two multidrug-resistant
AB  - Acinetobacter baumannii strains, ABE8_07 and ABE12_M,
AB  - isolated from a Moroccan hospital floor. These two genome sequences will initiate
AB  - the study and characterization of the Acinetobacter baumannii genome in Morocco.
ER  -

TY  - JOUR
AU  - Aloui, A.
AU  - Tagourti, J.
AU  - El May, A.
AU  - Petit, D.J.
AU  - Landoulsi, A.
TI  - The effect of methylation on some biological parameters in Salmonella enterica serovar Typhimurium.
JO  - Pathol. Biol. (Paris)
PY  - 2011
SP  - 192
EP  - 198
VL  - 59
AB  - Cell growth is tightly coupled to DNA replication and its methylation [Proc Nail Acad Sci US A
AB  - 93 (1996) 12206-12211]. In a culture medium,
AB  - growing of Salmonella Typhimurium (S. Typhimurium) mutant cells
AB  - (dam(-)) decreased (2.5 fold) relative to the wild type strain
AB  - (dam(+)). In this study, we show that the reason for this growth
AB  - deficiency is due to the DNA methylation. The absence of a Dam
AB  - methyltransferase protein results in poor growth efficiency and
AB  - disturbs the synchrony of replication initiation in vivo, as evaluated
AB  - by flow cytometry. On the other hand, we show that lack of methylation
AB  - could increase the DNA response to thermal stress (decreasing the DNA
AB  - melting temperature, T-m), and the reason for this effect is due to the
AB  - methylation status and not to the number of guanine and cytosine bases
AB  - (G + C) in the duplex DNA. Our results show that methylation is an
AB  - epigenetic factor that may play a key role in the cell growth, the
AB  - synchrony of DNA replication [C R Biologies 330 (2007) 576-580] and the
AB  - stress protection.
ER  -

TY  - JOUR
AU  - Aloyo, M.C.
AU  - Campbell, D.
AU  - Combates, N.J.
AU  - Gonzalez, J.
AU  - Kwok, Y.
AU  - Sheardy, R.D.
AU  - Winkle, S.A.
TI  - Restriction enzymes have altered cleavage rates at sites near certain sequences.
JO  - Biophys. J.
PY  - 1993
SP  - A280
EP  - A280
VL  - 64
AB  - Under appropriate environmental conditions, e.g. supercoiled DNA, 50-100 uM cobalt hexamine,
AB  - the DNA sequence (CG)4 forms non-B or Z-type structures. Restriction enzymes, e.g. BglI,
AB  - EcoRV, HaeIII, MboI, NotI, PstI, TaqI, cutting at sites up to circa 50 base pairs from
AB  - inserted (CG)4 segments show enhanced cleavage rates (in the presence of cobalt hexamine)
AB  - relative to cleavage rates for DNA fragments not containing the (CG)4. We have previously
AB  - shown that the sequence TCTTG is a hot spot for the binding of the carcinogen
AB  - N-acetoxy-N-acetyl-2-aminofluorene. Restriction enzymes cleaving near an inserted TCTTG
AB  - segment have decreased reaction rates. Gel retardation binding studies and exonuclease
AB  - footprinting studies suggest that the observed alterations in restriction enzyme reaction
AB  - rates arise from changes in the binding of the restriction enzyme to DNA when either (CG)4 or
AB  - TCTTG segments are present. These studies suggest that certain sequences can modulate DNA
AB  - functions.
ER  -

TY  - JOUR
AU  - Alpert, C.A.
AU  - Crutz-Le, C.A.M.
AU  - Malleret, C.
AU  - Zagorec, M.
TI  - Characterization of a theta-type plasmid from Lactobacillus sakei: a potential basis for low-copy-number vectors in lactobacilli.
JO  - Appl. Environ. Microbiol.
PY  - 2003
SP  - 5574
EP  - 5584
VL  - 69
AB  - The complete nucleotide sequence of the 13-kb plasmid pRV500, isolated from Lactobacillus
AB  - sakei RV332, was determined. Sequence analysis enabled
AB  - the identification of genes coding for a putative type I
AB  - restriction-modification system, two genes coding for putative
AB  - recombinases of the integrase family, and a region likely involved in
AB  - replication. The structural features of this region, comprising a putative
AB  - ori segment containing 11- and 22-bp repeats and a repA gene coding for a
AB  - putative initiator protein, indicated that pRV500 belongs to the pUCL287
AB  - subfamily of theta-type replicons. A 3.7-kb fragment encompassing this
AB  - region was fused to an Escherichia coli replicon to produce the shuttle
AB  - vector pRV566 and was observed to be functional in L. sakei for plasmid
AB  - replication. The L. sakei replicon alone could not support replication in
AB  - E. coli. Plasmid pRV500 and its derivative pRV566 were determined to be at
AB  - very low copy numbers in L. sakei. pRV566 was maintained at a reasonable
AB  - rate over 20 generations in several lactobacilli, such as Lactobacillus
AB  - curvatus, Lactobacillus casei, and Lactobacillus plantarum, in addition to
AB  - L. sakei, making it an interesting basis for developing vectors. Sequence
AB  - relationships with other plasmids are described and discussed.
ER  -

TY  - JOUR
AU  - Alt, D.P.
AU  - Wilson-Welder, J.H.
AU  - Bayles, D.O.
AU  - Cameron, C.
AU  - Adler, B.
AU  - Bulach, D.M.
AU  - Seemann, T.
AU  - Lehane, M.J.
AU  - Haines, L.R.
AU  - Darby, A.C.
AU  - Hall, N.
AU  - Radford, A.D.
AU  - Zuerner, R.L.
TI  - Complete Genome Sequence of Leptospira interrogans Serovar Bratislava, Strain PigK151.
JO  - Genome Announcements
PY  - 2015
SP  - e00678
EP  - e00615
VL  - 3
AB  - Leptospira interrogans serovar Bratislava infection occurs in multiple domestic and wildlife
AB  - species and is associated with poor reproductive performance in
AB  - swine and horses. We present the complete genome assembly of strain PigK151
AB  - comprising two chromosomes, CI (4.457 Mbp) and CII (358 kbp).
ER  -

TY  - JOUR
AU  - Altermann, E.
AU  - Russell, W.M.
AU  - Azcarate-Peril, M.A.
AU  - Barrangou, R.
AU  - Buck, B.L.
AU  - McAuliffe, O.
AU  - Souther, N.
AU  - Dobson, A.
AU  - Duong, T.
AU  - Callanan, M.
AU  - Lick, S.
AU  - Hamrick, A.
AU  - Cano, R.
AU  - Klaenhammer, T.R.
TI  - Inaugural Article: From the Cover: Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 3906
EP  - 3912
VL  - 102
AB  - Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially
AB  - since 1972. The complete genome is 1,993,564 nt and
AB  - devoid of plasmids. The average GC content is 34.71% with 1,864 predicted
AB  - ORFs, of which 72.5% were functionally classified. Nine phage-related
AB  - integrases were predicted, but no complete prophages were found. However,
AB  - three unique regions designated as potential autonomous units (PAUs) were
AB  - identified. These units resemble a unique structure and bear
AB  - characteristics of both plasmids and phages. Analysis of the three PAUs
AB  - revealed the presence of two R/M systems and a prophage maintenance system
AB  - killer protein. A spacers interspersed direct repeat locus containing 32
AB  - nearly perfect 29-bp repeats was discovered and may provide a unique
AB  - molecular signature for this organism. In silico analyses predicted 17
AB  - transposase genes and a chromosomal locus for lactacin B, a class II
AB  - bacteriocin. Several mucus- and fibronectin-binding proteins, implicated
AB  - in adhesion to human intestinal cells, were also identified. Gene clusters
AB  - for transport of a diverse group of carbohydrates, including
AB  - fructooligosaccharides and raffinose, were present and often accompanied
AB  - by transcriptional regulators of the lacI family. For protein degradation
AB  - and peptide utilization, the organism encoded 20 putative peptidases,
AB  - homologs for PrtP and PrtM, and two complete oligopeptide transport
AB  - systems. Nine two-component regulatory systems were predicted, some
AB  - associated with determinants implicated in bacteriocin production and acid
AB  - tolerance. Collectively, these features within the genome sequence of L.
AB  - acidophilus are likely to contribute to the organisms' gastric survival
AB  - and promote interactions with the intestinal mucosa and microbiota.
ER  -

TY  - JOUR
AU  - Althabegoiti, M.J.
AU  - Lozano, L.
AU  - Torres-Tejerizo, G.
AU  - Ormeno-Orrillo, E.
AU  - Rogel, M.A.
AU  - Gonzalez, V.
AU  - Martinez-Romero, E.
TI  - Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6651
EP  - 6652
VL  - 194
AB  - Here we present the genome sequence of Rhizobium grahamii CCGE502. R. grahamii groups with
AB  - other newly described broad-host-range species, which are not very
AB  - efficient Phaseolus vulgaris symbionts, with a wide geographic distribution and
AB  - which constitutes a novel Rhizobium clade.
ER  -

TY  - JOUR
AU  - Altin, G.
AU  - Nikerel, E.
AU  - Sahin, F.
TI  - Draft Genome Sequence of Magnesium-Dissolving Lactococcus garvieae A1, Isolated from Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00386
EP  - e00317
VL  - 5
AB  - The probiotic bacterium Lactococcus garvieae A1, isolated from soil, is interesting for
AB  - biomining applications. Here, we report the draft genome sequence
AB  - and annotation of this strain, with a focus on metal transporter enzymes.
ER  -

TY  - JOUR
AU  - Altintas, M.M.
AU  - Ozer, N.
AU  - Ulgen, K.O.
TI  - Purification of TaqI endonuclease from Thermus aquaticus.
JO  - J. Chromatogr. A
PY  - 1998
SP  - 373
EP  - 381
VL  - 828
AB  - A purification procedure for the thermostable restriction enzyme TaqI was developed using
AB  - high-performance ion-exchange liquid chromatography.  The effects of various operating
AB  - conditions on the separation behavior of TaqI endonuclease from the cell extracts were
AB  - investigated for optimization and scaling up.  The separation of the enzyme by HPLC was found
AB  - to be strongly dependent on the sample volume, slope of linear gradient and order of the
AB  - ion-exchange columns.  The final yield of the enzyme is also dependent to a great extent upon
AB  - the number of fractionation steps employed to purify the enzyme.  In the present study, 4000 U
AB  - TaqI endonuclease per mg. Protein was recovered from 2g Thermus aquaticus cells with a
AB  - two-step purification protocol in one day.  The purification factor was 24.  Compared to other
AB  - classical methods of purification reported in literature with 4,000 or 32,000 U enzyme from
AB  - 200 g of Thermus aquaticus cells, HPLC yielded 190,000 U enzyme from 200g cells using cation
AB  - and anion HPLC  columns sequentially and thus resulted in a higher efficiency.
ER  -

TY  - JOUR
AU  - Altintas, M.M.
AU  - Ulgen, K.O.
TI  - Growth of Thermus aquaticus and its TaqI endonuclease production.
JO  - Acta Biotechnol.
PY  - 1999
SP  - 45
EP  - 56
VL  - 19
AB  - The culture behavior of Thermus aquaticus was characterized.  The response of the bacterium to
AB  - various carbon (tryptone, glucose, glycerol) and nitrogen sources (yeast extract, NaNO3,
AB  - (NH4)2SO4, leucine, thymine, thiamine, glutamic acid) was studied.  Amino acids did not
AB  - support growth, but Castenholz salt medium supplemented with yeast extract and glucose or
AB  - tryptone resulted in good growth and production.  A suitable medium composition giving the
AB  - highest biomass concentration and enzyme yield was developed.  The simple medium containing
AB  - TYE-NaCl resulted in the highest biomass concentration, whereas Castenholz mineral medium
AB  - supplemented with tryptone and yeast extract gave the highest specific activity and enzyme
AB  - yield.  The effect of inoculum age and size on growth was also investigated in order to
AB  - improve the yield and process consistency.  The use of shake flasks inoculated with
AB  - precultures at their early or late stationary phase resulted in the same biomass concentration
AB  - (0.560+- 0.015 g/l) and similar maximum specific growth rates (0.258 +- 0.003 h-1).  Inoculum
AB  - sizes between 1 and 2.5 percent were optimal for cell growth.  As the other papers on
AB  - thermophilic microorganisms, including the T. aquaticus YT-1 strain, gave qualitative
AB  - information on growth, the results presented here cannot be compared with others on a
AB  - quantitative basis.  TaqI endonuclease was purified using a 5 step protocol including cell
AB  - disruption, adsorption, precipitation, column chromatography and final dialysis.  The enriched
AB  - fraction had a specific activity of 33,600 U TaqI endonuclease per mg protein.
ER  -

TY  - JOUR
AU  - Altman, D.R. et al.
TI  - Genome plasticity of agr-defective Staphylococcus aureus during clinical infection.
JO  - Infect. Immun.
PY  - 2018
SP  - e00331
EP  - e00318
VL  - 86
AB  - Therapy for bacteremia caused by Staphylococcus aureus is often ineffective, even
AB  - when treatment conditions are optimal according to experimental protocols.
AB  - Adapted subclones, such as those bearing mutations that attenuate agr-mediated
AB  - virulence activation, are associated with persistent infection and patient
AB  - mortality. To identify additional alterations in agr-defective mutants, we
AB  - sequenced and assembled the complete genomes of clone pairs from colonizing and
AB  - infected sites of several patients in whom S. aureus demonstrated a within-host
AB  - loss of agr function. We report that events associated with agr inactivation
AB  - result in agr-defective blood and nares strain pairs that are enriched in
AB  - mutations compared to pairs from wild-type controls. The random distribution of
AB  - mutations between colonizing and infecting strains from the same patient, and
AB  - between strains from different patients, suggests that much of the genetic
AB  - complexity of agr-defective strains result from prolonged infection or
AB  - therapy-induced stress. However, in one of the agr-defective infecting strains,
AB  - multiple genetic changes resulted in increased virulence in a murine model of
AB  - bloodstream infection, bypassing the mutation of agr and raising the possibility
AB  - that some changes were selected. Expression profiling correlated the elevated
AB  - virulence of this agr-defective mutant to restored expression of the
AB  - agr-regulated ESAT6-like Type VII secretion system, a known virulence factor.
AB  - Thus, additional mutations outside the agr locus can contribute to
AB  - diversification and adaptation during infection by S. aureusagr mutants
AB  - associated with poor patient outcome.
ER  -

TY  - JOUR
AU  - Altschmied, J.
AU  - Volff, J.
AU  - Winkler, C.
AU  - Gutbrod, H.
AU  - Korting, C.
AU  - Pagany, M.
AU  - Schartl, M.
TI  - Primary structure and expression of the Xiphophorus DNA-(cytosine-5)-methyltransferase XDNMT-1.
JO  - Gene
PY  - 2000
SP  - 75
EP  - 82
VL  - 249
AB  - Small aquarium fishes become increasingly important in the study of normal vertebrate
AB  - development and disease. Differential DNA methylation might play a role in these processes. In
AB  - the teleost Xiphophorus, a well-established animal model for melanoma formation,
AB  - tumour-specific hypomethylation of the melanoma-inducing gene ONC-Xmrk has been observed. We
AB  - have isolated a cDNA for the DNA-(cytosine-5)-methyltransferase XDNMT-1 from this organism,
AB  - which encodes the first full-length protein from a fish species. Linkage analysis showed that
AB  - Xdnmt-1 is different from the Xiphophorus tumour suppressor R, which is involved in the
AB  - transcriptional repression of the ONC-Xmrk melanoma oncogene in healthy fish. As methylation
AB  - has been implicated in the regulation of ONC-Xmrk expression, XDNMT-1 might play a role by
AB  - acting up- or downstream of R. Expression analysis demonstrated that the Xdnmt-1 transcript is
AB  - present in all adult tissues and cell lines tested. However, developing embryos show a
AB  - spatially and temporally regulated expression pattern suggesting that the enzyme might play a
AB  - role during development in fish.
ER  -

TY  - JOUR
AU  - Alvarez, C.
AU  - Kukutla, P.
AU  - Jiang, J.
AU  - Yu, W.
AU  - Xu, J.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain Ag1, Isolated from the Midgut of  the Malaria Mosquito Anopheles gambiae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5449
EP  - 5449
VL  - 194
AB  - A Pseudomonas sp. bacterium was isolated from the midguts of Anopheles gambiae mosquitoes.
AB  - Here we present the annotated Pseudomonas sp. draft genome sequence
AB  - as a contribution to the efforts of characterization of the mosquito gut
AB  - microbiome.
ER  -

TY  - JOUR
AU  - Alvarez, M.A.
AU  - Chater, K.F.
AU  - Rosario, M.R.
TI  - Complex transcription of an operon encoding the Sall restriction-modification system of Streptomyces albus G.
JO  - Mol. Microbiol.
PY  - 1993
SP  - 243
EP  - 252
VL  - 8
AB  - High-resolution S1 nuclease mapping of mRNA synthesized in vivo, in vitro run-off
AB  - transcription with RNA polymerase from Streptomyces lividans and gene fusions were used to
AB  - analyse the transcriptional organization of the Sall restriction-modification system of
AB  - Streptomyces albus G. The sallR and sallM genes that encode the restriction endonuclease and
AB  - its cognate methyltransferase constitute an operon which is mainly transcribed from sal-pR1, a
AB  - promoter located immediately upstream of sallR, with two possible minor promoters further
AB  - upstream. Another promoter, sal-pM, is within the 3' end of the sallR coding region, and
AB  - allows expression of the modification gene in the absence of sal-pR1. The sal-pM promoter
AB  - might be involved in the establishment of modification prior to restriction endonuclease
AB  - activity. Sequences upstream of the apparent transcriptional start sites for sal-pR1 and
AB  - sal-pM show similarity with the -10 region of typical vegetatively expressed eubacterial
AB  - promoters, but appropriately centered -35 regions are absent.
ER  -

TY  - JOUR
AU  - Alvarez, M.A.
AU  - Gomez, A.
AU  - Gomez, P.
AU  - Brooks, J.E.
AU  - Rodicio, M.R.
TI  - Comparative analysis of expression of the SalI restriction-modification system in Escherichia coli and Streptomyces.
JO  - Mol. Gen. Genet.
PY  - 1996
SP  - 74
EP  - 80
VL  - 253
AB  - The salIR and salIM genes encode the endonuclease and methyltransferase components of the SalI
AB  - restriction-modification system from Streptomyces albus G.  Expression of the salI genes in
AB  - Escherichia coli was investigated and major differences with Streptomyces were found.  In E.
AB  - coli there is no detectable expression of the salIR gene due to inactivity of the sal-pR
AB  - promoter region.  In the natural host of the system this region directs transcription of the
AB  - salI genes as a bicistronic message.  In contrast to salIR, salIM is transcribed in the
AB  - heterologous host from a promoter within the salI DNA.  Since sal-pR is not active, the gene
AB  - cannot be expressed as part of the salI operon.  It is probably transcribed from sal-pM, a
AB  - promoter internal to the operon which allows independent expression of the modification gene
AB  - in Streptomyces.  Replacement of sal-pR by the strong pLac promoter allows expression of salIR
AB  - in E. coli and enhances expression of salIM.  The resulting strain produces about 10 times
AB  - more endonuclease than a Streptomyces clone containing the SalI system under the control of
AB  - sal-pR.
ER  -

TY  - JOUR
AU  - Alvarez, M.A.
AU  - Gomez, A.
AU  - Gomez, P.
AU  - Rodicio, M.R.
TI  - Expression of the SalI restriction-modification system of Streptomyces albus G in Escherichia coli.
JO  - Gene
PY  - 1995
SP  - 231
EP  - 232
VL  - 157
AB  - The salIR and salIM genes of Streptomyces albus G encode the restriction endonuclease (ENase)
AB  - and DNA methyltransferase (MTase) of the SalI restriction-modification (R-M) system.  In S.
AB  - albus G, the genes constitute an operon that is mainly transcribed from a promoter located
AB  - upstream from SalIR, the first gene of the operon.  In addition, a second promoter, at the 3'
AB  - end of SalIR, allows independent transcription of the MTase gene.  Expression of salIR and
AB  - salIM in Escherichia coli was investigated.  The ENase gene was not expressed in the
AB  - heterologous host, probably due to inactivity of the main promoter of the salI operon.  In
AB  - contrast to salIR, salIM was functional in E. coli.  Preliminary S1 nuclease mapping
AB  - experiments suggest that the alternative promoter of the MTase gene can initiate transcription
AB  - in the heterologous, as well as in the homologous host.
ER  -

TY  - JOUR
AU  - Alvarez, N.
AU  - Haft, D.
AU  - Hurtado, U.A.
AU  - Robledo, J.
AU  - Rouzaud, F.
TI  - Whole-Genome Sequence of a Beijing Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Buenaventura, Colombia.
JO  - Genome Announcements
PY  - 2016
SP  - e01549
EP  - e01515
VL  - 4
AB  - Extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) has been reported  to the WHO
AB  - by 100 countries, including Colombia. An estimated 9.0% of people with
AB  - multidrug-resistant TB have XDR-TB. We report the genome sequence of a Beijing
AB  - XDR-TB clinical isolate from Buenaventura, Colombia. The genome sequence is
AB  - composed of 4,298,162 bp with 4,359 genes.
ER  -

TY  - JOUR
AU  - Alvarez, N.
AU  - Haft, D.
AU  - Hurtado, U.A.
AU  - Robledo, J.
AU  - Rouzaud, F.
TI  - Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellin, Colombia.
JO  - Genome Announcements
PY  - 2016
SP  - e00566
EP  - e00516
VL  - 4
AB  - Colombia is one of the 105 countries that has reported at least one case of extensively
AB  - drug-resistant tuberculosis (XDR-TB). The Mycobacterium tuberculosis
AB  - Haarlem genotype is ubiquitous worldwide. Here, we report the high-quality draft
AB  - genome sequence of a Colombian Haarlem XDR-TB clinical isolate composed of
AB  - 4,329,127 bp with 4,386 genes.
ER  -

TY  - JOUR
AU  - Alvarez, N.
AU  - Haft, D.
AU  - Hurtado, U.A.
AU  - Robledo, J.
AU  - Rouzaud, F.
TI  - Whole-Genome Sequencing of Two Latin American-Mediterranean Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates from Medellin,  Colombia.
JO  - Genome Announcements
PY  - 2016
SP  - e00192
EP  - e00116
VL  - 4
AB  - Colombia, with a tuberculosis incidence of 33 cases per 100,000 population, is one of the
AB  - countries that have reported extensively drug-resistant Mycobacterium
AB  - tuberculosis (XDR-TB). We report the high-quality draft genome sequences of two
AB  - Latin American-Mediterranean XDR-TB clinical isolates (TBR-152 and TBR-175),
AB  - comprising 4,303,775 bp and 4,330,115 bp, respectively.
ER  -

TY  - JOUR
AU  - Alvarez-Fraga, L.
AU  - Lopez, M.
AU  - Merino, M.
AU  - Rumbo-Feal, S.
AU  - Tomas, M.
AU  - Bou, G.
AU  - Poza, M.
TI  - Draft Genome Sequence of the Biofilm-Hyperproducing Acinetobacter baumannii Clinical Strain MAR002.
JO  - Genome Announcements
PY  - 2015
SP  - e00824
EP  - e00815
VL  - 3
AB  - We report the draft genome sequence of Acinetobacter baumannii strain MAR002, a
AB  - biofilm-hyperproducing clinical strain isolated during the study CP/09/0033
AB  - (GEIH/REIPI-Ab2010, Spain). The genome of A. baumannii MAR002 has an approximate
AB  - length of 3,717,929 bp and 3,300 protein-coding sequences, with a C+G content of
AB  - 39.09%.
ER  -

TY  - JOUR
AU  - Alvarez-Ponce, D.
AU  - Weitzman, C.L.
AU  - Tillett, R.L.
AU  - Sandmeier, F.C.
AU  - Tracy, C.R.
TI  - High quality draft genome sequences of Mycoplasma agassizii strains PS6(T) and 723 isolated from Gopherus tortoises with upper respiratory tract disease.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 12
EP  - 12
VL  - 13
AB  - Mycoplasma agassizii is one of the known causative agents of upper respiratory tract disease
AB  - (URTD) in Mojave desert tortoises (Gopherus agassizii) and in
AB  - gopher tortoises (Gopherus polyphemus). We sequenced the genomes of M. agassizii
AB  - strains PS6(T) (ATCC 700616) and 723 (ATCC 700617) isolated from the upper
AB  - respiratory tract of a Mojave desert tortoise and a gopher tortoise,
AB  - respectively, both with signs of URTD. The PS6(T) genome assembly was organized
AB  - in eight scaffolds, had a total length of 1,274,972 bp, a G + C content of
AB  - 28.43%, and contained 979 protein-coding genes, 13 pseudogenes and 35 RNA genes.
AB  - The 723 genome assembly was organized in 40 scaffolds, had a total length of
AB  - 1,211,209 bp, a G + C content of 28.34%, and contained 955 protein-coding genes,
AB  - seven pseudogenes, and 35 RNA genes. Both genomes exhibit a very similar
AB  - organization and very similar numbers of genes in each functional category. Pairs
AB  - of orthologous genes encode proteins that are 93.57% identical on average.
AB  - Homology searches identified a putative cytadhesin. These genomes will enable
AB  - studies that will help understand the molecular bases of pathogenicity of this
AB  - and other Mycoplasma species.
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Kohler, E.
AU  - Selent, U.
AU  - Thielking, V.
AU  - Wolfes, H.
AU  - Pingoud, A.
TI  - The recognition of DNA by the EcoRV restriction endonuclease: Accuracy and cation dependence.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1991
SP  - 627
EP  - 627
VL  - 372
AB  - In order to investigate the accuracy of the EcoRV restriction endonuclease we have synthesized
AB  - 20 single stranded oligodeoxynucleotides similarly as described for EcoRI recently. These can
AB  - be hybridized to give a set of double stranded substrates comprising the canonical recognition
AB  - sequence, the 9 sequences deviating from it by one base pair (star substrates) or the 18
AB  - sequences with all possible mismatched base pairs within the recognition sequence (mismatch
AB  - substrates).
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Pingoud, A.
AU  - Haupt, W.
AU  - Langowski, J.
AU  - Peters, F.
AU  - Maass, G.
AU  - Wolff, C.
TI  - The influence of sequences adjacent to the recognition site on the cleavage of oligodeoxynucleotides by the EcoRI endonuclease.
JO  - Eur. J. Biochem.
PY  - 1984
SP  - 83
EP  - 92
VL  - 140
AB  - We have investigated the influence of the nucleotide sequence adjacent to the
AB  - recognition site on the rate of cleavage of DNA by the restriction endonuclease
AB  - EcoRI.  For this purpose two decadeoxynucleotides, d(G-G-G-A-A-T-T-C-t-T) (Ia)
AB  - and d(A-A-G-A-A-t-T-C-C-C) (Ib) were synthesized.  The duplex Ia Ib is cleaved
AB  - by EcoRI preferentially in the dA-rich strand (approximately 10 times over the
AB  - dG-rich strand).  The individual nucleotides Ia and Ib are also cleaved by
AB  - EcoRI, Ib at a higher rate than Ia and both at a lower rate than Ia Ib.  The
AB  - temperature dependence of the reaction rate shows that only double-stranded
AB  - oligodeoxynucleotides are substrates for the EcoRI endonuclease.  We have,
AB  - furthermore, synthesized oligomers of d(G-G-A-A-T-T-C-C), which contain two,
AB  - three and four EcoRI sites, respectively.  These oligodeoxynucleotides are
AB  - preferentially cleaved at the sites next to the 5' end, where the recognition
AB  - site is only flanked by one dG dC base pair, in contrast to the other sites
AB  - which are flanked by three such pairs.  These data indicate that sequences
AB  - adjacent to the recognition site influence the rate of cleavage: dA dT base
AB  - pairs enhance and dG dC base pairs slow down the hydrolytic activity of the
AB  - EcoRI endonuclease.
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Pingoud, A.
AU  - Langowski, J.
AU  - Urbanke, C.
AU  - Maass, G.
TI  - Two identical subunits of the EcoRI restriction endonuclease co-operate in the binding and cleavage of the palindromic substrate.
JO  - Eur. J. Biochem.
PY  - 1982
SP  - 139
EP  - 142
VL  - 124
AB  - The cleavage of radioactively labelled double-stranded d(G-G-A-A-T-T-C-C) was
AB  - studied in single turnover experiments with substrate and enzyme both being in
AB  - the micromolar range.  The reaction rate was found to increase with enzyme
AB  - concentration until a ratio of one tetrameric enzyme to two double-stranded
AB  - substrates was reached, further increase of the enzyme concentration then leads
AB  - to a sharp decline of the reaction rate.  These findings are interpreted in the
AB  - following manner.  (a) Two subunits of the EcoRI endonuclease co-operate in
AB  - binding and possibly also in cleaving the palindromic substrate.  (b) The
AB  - enzymatic action of the EcoRI endonuclease is inhibited by excess enzyme,
AB  - possibly due to unspecific binding of the enzyme-substrate complex.  The
AB  - self-inhibition of EcoRI endonuclease has also been observed with
AB  - macromolecular substrates.
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Ruter, T.
AU  - Geiger, R.
AU  - Fliess, A.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymatic activity, not the preference of this restriction endonuclease for cleavage within the site GAATTC.
JO  - Biochemistry
PY  - 1989
SP  - 2678
EP  - 2684
VL  - 28
AB  - According to the X-ray structure analysis of an EcoRI-oligodeoxynucleotide
AB  - complex [McClarin et al. (1986) Science 234, 1526], sequence specificity is
AB  - mediated by 12 hydrogen bonds, 6 from each of the two identical subunits of the
AB  - dimeric enzyme to the recognition site -GAATTC-: Arg200 forms two hydrogen
AB  - bonds with guanine, while Glu144 and Arg145 form four hydrogen bonds to
AB  - adjacent adenine residues.  Changing the hydrogen-bonding potential at the
AB  - recognition site without perturbing the rest of the interface should lead to
AB  - the recognition of degenerate sequences [Rosenberg et al. (1987) in Protein
AB  - Engineering (Oxender, D.L., & Fox, C.F., Eds.) pp 237-250, Liss, New York].  We
AB  - have shown previously that replacing Glu144 by Gln and Arg145 by Lys affects
AB  - the activity of the enzyme, not, however, its specificity [Wolfes et al. (1986)
AB  - Nucleic Acids Res. 14, 9063].  We show now that mutation of Arg200 to Lys, the
AB  - double mutation Glu144Arg145 to GlnLys, and the triple mutation
AB  - Glu144Arg145Arg200 to GlnLysLys do not lead to a detectable degeneracy of the
AB  - specificity of cleavage by EcoRI but significantly impair the catalytic
AB  - activity of this enzyme.  A detailed analysis of the steady-state kinetics of
AB  - cleavage of pUC8 DNA and a tridecadeoxynucleotide substrate demonstrates that
AB  - the reduction in activity for all DNA binding site mutants investigated so far
AB  - is mainly due to a decrease in Kcat, with the exception of the Arg200 to Lys
AB  - mutant, which is only impaired in its Km.  This observation is confirmed by
AB  - nitrocellulose filter experiments which show that this mutant has a lower
AB  - affinity toward oligodeoxynucleotide substrates than the other DNA binding site
AB  - mutants and a much lower affinity than wild-type EcoRI.  While these and
AB  - previous data clearly demonstrate that Glu144, Arg145, and Arg200 are essential
AB  - for efficient substrate binding and catalysis, their involvement in the
AB  - specific recognition is more intricate than proposed on the basis of the X-ray
AB  - structure analysis.  Our results also suggest that the specificity of EcoRI
AB  - cannot easily be relaxed, and in particular not without affecting its activity.
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Selent, U.
AU  - Wolfes, H.
TI  - Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.
JO  - Biochemistry
PY  - 1995
SP  - 11191
EP  - 11197
VL  - 34
AB  - In order to investigate the accuracy of the EcoRV restriction endonuclease, we have
AB  - synthesized a set of double-stranded oligodeoxynucleotides comprising the canonical
AB  - recognition sequence, the 9 star sequences (i.e., sequences deviating by one base pair from
AB  - the canonical sequence), and the 18 mismatch sequences (i.e. sequences deviating by one base
AB  - from the canonical sequence).  For each individual single strand of all these 28 substrates we
AB  - have measured the rate of phosphodiester bond cleavage under normal buffer conditions.
AB  - Double-strand cleavage of star substrates is at least 5 orders of magnitude slower than
AB  - cleavage of the canonical substrate.  In contrast, most of the mismatch substrates are
AB  - accepted more readily.  In the absence of the essential cofactor Mg2+, EcoRV binds weakly but
AB  - equally to the canonical and degenerate substrates (i.e., KDiss is in the micromolar range).
AB  - However, the inactive catalytic site mutant D90A in the presence of Mg2+ binds the canonical
AB  - substrate 1-2 orders of magnitude better than degenerate substrates.  Therefore, the EcoRV
AB  - endonuclease needs the essential cofactor Mg2+ to create thermodynamic discrimination between
AB  - degenerate and canonical sites.  But the main discrimination is kinetically controlled and
AB  - takes place during cleavage.  While in the canonical substrate both single strands are cleaved
AB  - with an equal velocity, in all other substrates one single strand is cleaved faster than the
AB  - other one, resulting in a dissociation of the enzyme from the DNA between the two cuts.  In
AB  - vivo this may lead to repair of the erroneous cleavage site by DNA ligases.  The order of
AB  - single-strand nicking together with the division of base contacts on both subunits suggests
AB  - that correct recognition by one subunit triggers cleavage by the other one.
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Thielking, V.
AU  - Selent, U.
AU  - Kohler, E.
AU  - Wolfes, H.
AU  - Pingoud, A.
TI  - The recognition of DNA by the EcoRV restriction endonuclease:  accuracy and cation dependence.
JO  - J. Biomol. Struct. Dyn.
PY  - 1991
SP  - a007
EP  - a007
VL  - 8
AB  - None
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Urbanke, C.
AU  - Fliess, A.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - Fluorescence stopped-flow kinetics of the cleavage of synthetic oligodeoxynucleotides by the EcoRI restriction endonuclease.
JO  - Biochemistry
PY  - 1989
SP  - 7879
EP  - 7888
VL  - 28
AB  - We have investigated in fluorescence stopped-flow and temperature-jump
AB  - experiments the EcoRI-catalyzed cleavage of synthetic palindromic
AB  - tridecadeoxynucleotides which contain the EcoRI site but differ in the flanking
AB  - sequences.  The overall reaction can be resolved in several reactions which
AB  - were analyzed by a nonlinear least-squares fitting procedure on the
AB  - experimental data.  The result of this analysis is a minimal scheme that
AB  - describes the overall reaction in terms of the rate constants of the individual
AB  - reactions.  According to this scheme EcoRI and the tridecadeoxynucleotide
AB  - substrates associate in the presence of Mg2+ in a nearly diffusion-controlled
AB  - process.  This is followed by a reaction which is or includes the cleavage of
AB  - the first phosphodiester bond.  There is no indication for a time-resolved
AB  - conformational transition prior to catalysis.  After cleavage of the first
AB  - strand, dissociation of the nicked double strand can occur, which then
AB  - rearranges to the original palindromic double-stranded substrate and is bound
AB  - again by the enzyme.  Alternatively, the nicked double strand can be cleaved in
AB  - the second strand.  This reaction is followed by product release from the
AB  - enzyme.  The magnitude of the individual rate constants depends on the
AB  - substrate used; the differences explain the preference of EcoRI for substrates
AB  - that contain AT as compared to GC base pairs next to the recognition site.
ER  -

TY  - JOUR
AU  - Alves, J.
AU  - Vennekohl, P.
TI  - Protein engineering of restriction enzymes.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 393
EP  - 411
VL  - 14
AB  - Restriction endonucleases are among the most accurate enzymes known.  Consequently, changing
AB  - their very high sequence specificity is one of the scientific goals in studying these enzymes.
AB  - This review focuses on protein engineering regarding Type II restriction enzymes.  They
AB  - comprise the vast majority of the about 3600 entities listed in REBASE today, although the
AB  - number of those studied in detail is far smaller.  First, we will discuss different approaches
AB  - to changing the recognition of a given sequence starting with rational design using
AB  - site-directed mutagenesis and progressing to random mutagenesis combined with in vivo
AB  - selection.  Then, we will describe attempts to lengthen the recognition sequence by designing
AB  - additional enzyme contacts to DNA.  As the dimeric nature of all restriction enzymes doubles
AB  - the effect of each amino acid exchange, we will also discuss engineering of subunit
AB  - composition.  Finally, we will speculate on possible future directions of protein engineering
AB  - of restriction enzymes.
ER  -

TY  - JOUR
AU  - Alves, J.M.
AU  - Serrano, M.G.
AU  - Maia-da-Silva, F.
AU  - Voegtly, L.J.
AU  - Matveyev, A.V.
AU  - Teixeira, M.M.
AU  - Camargo, E.P.
AU  - Buck, G.A.
TI  - Genome evolution and phylogenomic analysis of candidatus kinetoplastibacterium, the betaproteobacterial endosymbionts of strigomonas and angomonas.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 338
EP  - 350
VL  - 5
AB  - It has been long known that insect-infecting trypanosomatid flagellates from the genera
AB  - Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or
AB  - TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based
AB  - on previous analyses of other bacterial endosymbiont genomes from other lineages, a
AB  - stereotypical path of genome evolution in such bacteria over the duration of their association
AB  - with the eukaryotic host has been characterized. In this work, we sequence and analyze the
AB  - genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic
AB  - analyses with all available Betaproteobacteria, and compare the TPEs with their nearest
AB  - betaproteobacterial relatives. We also identify a number of housekeeping and central
AB  - metabolism genes that seem to have undergone positive selection. Our genome structure analyses
AB  - show total synteny among the five TPEs despite millions of years of divergence, and that this
AB  - lineage follows the common path of genome evolution observed in other endosymbionts of diverse
AB  - ancestries.
AB  - As previously suggested by cell biology and biochemistry experiments, Ca.
AB  - Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis
AB  - of compounds needed by their hosts. We have also shown that metabolic and informational genes
AB  - related to the cooperation with the host are overrepresented amongst genes shown to be under
AB  - positive selection. Finally, our phylogenomic analysis shows that, while being in the
AB  - Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are
AB  - not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.
ER  -

TY  - JOUR
AU  - Alves, J.T.
AU  - Veras, A.A.
AU  - Cavalcante, A.L.
AU  - de Sa, P.H.
AU  - Dias, L.M.
AU  - Guimaraes, L.C.
AU  - Morais, E.
AU  - Silva, A.G.
AU  - Azevedo, V.
AU  - Ramos, R.T.
AU  - Silva, A.
AU  - Carneiro, A.R.
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain PA01, Isolated from Sheep in Para, Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01664
EP  - e01615
VL  - 4
AB  - Corynebacterium pseudotuberculosis is the etiological agent of caseous lymphadenitis disease.
AB  - In this work, we present the first complete genome
AB  - sequence of Corynebacterium pseudotuberculosis strain PA01, isolated in northern
AB  - Brazil from an infected sheep. The genome length is 2,337,920 bp, and 2,003
AB  - coding sequences (CDS), 12 rRNAs, and 49 tRNAs were predicted.
ER  -

TY  - JOUR
AU  - Alzhanov, D.T.
AU  - Alzhanova, D.V.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Thermophilic strain Bacillus species AA contains several site-specific endonucleases.
JO  - Biokhimiia
PY  - 1998
SP  - 636
EP  - 645
VL  - 63
AB  - Thermophilic strain Bacillus species AA contains several site-specific endonucleases and three
AB  - of them have been identified.  BspAAI recognizes the sequence 5'-C/TCGAG-3' and cleaves it
AB  - after the first "C" forming 4-nucleotide 5'-ends and is an isoschizomer of XhoI.  BspAAII
AB  - recognizes the sequence 5'-T/CTAGA-3' and cleaves it after the first "T" forming
AB  - 4-nucleotide 5'-ends and is an isoschizomer of XbaI.  BspAAIII recognizes the sequence
AB  - 5'-GGATCC-3' and is an isomer of BamHI.  The optimal temperature and pH values are 42-48 C
AB  - and 7.0-8.0, respectively.
ER  -

TY  - JOUR
AU  - Alzhanova, D.V.
AU  - Alzhanov, D.T.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Isolation and characterization of site-specific endonuclease Bsp123I from thermophilic strain Bacillus species 123.
JO  - Biokhimiia
PY  - 1998
SP  - 207
EP  - 211
VL  - 63
AB  - The preparation of site-specific endonuclease Bsp123I was isolated and purified from the
AB  - thermophilic strain Bacillus species 123.  Endonuclease Bsp123I recognizes the sequence CGCG
AB  - and cleaves it in the middle between nucleotides G and C, producing blunt ends.  Thus, Bsp123I
AB  - is an isoschizomer of FnuDII.  The maximal activity of the enzyme is displayed at 42 C, pH
AB  - 8.0, 100mM NaCl, 10mM MgCl2.
ER  -

TY  - JOUR
AU  - Amachawadi, R.G.
AU  - Thomas, M.
AU  - Nagaraja, T.G.
AU  - Scaria, J.
TI  - Genome Sequences of Salmonella enterica subsp. enterica Serovar Lubbock Strains Isolated from Liver Abscesses of Feedlot Cattle.
JO  - Genome Announcements
PY  - 2016
SP  - e00319
EP  - e00316
VL  - 4
AB  - The genome sequencing of 13 Salmonella enterica subsp. enterica serovar Lubbock strains
AB  - isolated from liver abscesses of feedlot cattle is reported here. The
AB  - availability of these genomes will help to further understand the etiologic role
AB  - of Salmonella strains in liver abscesses of cattle and will serve as references
AB  - in microbial trace-back studies to improve food safety.
ER  -

TY  - JOUR
AU  - Amadio, A.F.
AU  - Amigo, N.
AU  - Puebla, A.F.
AU  - Farber, M.D.
AU  - Cataldi, A.A.
TI  - Draft Genome Sequences of Escherichia coli O157:H7 Strains Rafaela_II (Clade 8) and 7.1_Anguil (Clade 6) from Cattle in Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e00617
EP  - e00615
VL  - 3
AB  - Escherichia coli O157:H7 is a major etiologic agent of diseases in humans that cause diarrhea,
AB  - hemorrhagic colitis, and hemolytic-uremic syndrome. Here, we
AB  - report the draft genome sequences of two strains isolated from cattle that had
AB  - high levels of Shiga toxin 2 and high lethality in mice.
ER  -

TY  - JOUR
AU  - Amadio, A.F.
AU  - Benintende, G.B.
AU  - Zandomeni, R.O.
TI  - Complete sequence of three plasmids from Bacillus thuringiensis INTA-FR7-4 environmental isolate and comparison with related plasmids from the Bacillus cereus group.
JO  - Plasmid
PY  - 2009
SP  - 172
EP  - 182
VL  - 62
AB  - Bacillus thuringiensis is an insect pathogen used worldwide as a
AB  - bioinsecticide. It belongs to the Bacillus cereus sensu lato group as well
AB  - as Bacillus anthracis and B. cereus. Plasmids from this group of organisms
AB  - have been implicated in pathogenicity as they carry the genes responsible
AB  - for different types of diseases that affect mammals and insects. Some
AB  - plasmids, like pAW63 and pBT9727, encode a functional conjugation
AB  - machinery allowing them to be transferred to a recipient cell. They also
AB  - share extensive homology with the non-functional conjugation apparatus of
AB  - pXO2 from B. anthracis. In this study we report the complete sequence of
AB  - three plasmids from an environmental B. thuringiensis isolate from
AB  - Argentina, obtained by a shotgun sequencing method. We obtained the
AB  - complete nucleotide sequence of plasmids pFR12 (12,095bp), pFR12.5
AB  - (12,459bp) and pFR55 (55,712bp) from B. thuringiensis INTA-FR7-4. pFR12
AB  - and pFR12.5 were classified as cryptic as they do not code for any obvious
AB  - functions besides replication and mobilization. Both small plasmids were
AB  - classified as RCR plasmids due to similarities with the replicases they
AB  - encode. Plasmid pFR55 showed a structural organization similar to that
AB  - observed for plasmids pAW63, pBT9727 and pXO2. pFR55 also shares a tra
AB  - region with these plasmids, containing genes related to T4SS and
AB  - conjugation. A comparison between pFR55 and conjugative plasmids led to
AB  - the postulation that pFR55 is a conjugative plasmid. Genes related to
AB  - replication functions in pFR55 are different to those described for
AB  - plasmids with known complete sequences. pFR55 is the first completely
AB  - sequenced plasmid with a replication machinery related to that of ori44.
AB  - The analysis of the complete sequence of plasmids from an environmental
AB  - isolate of B. thuringiensis permitted the identification of a near
AB  - complete conjugation apparatus in pFR55, resembling those of plasmids
AB  - pAW63, pBT9727 and pXO2. The availability of this sequence is a step
AB  - forward in the study of the molecular basis of the conjugative process in
AB  - Gram positive bacteria, particularly due to the similarity with known
AB  - conjugation systems. It is also a contribution to the expansion of the
AB  - non-pathogenic B. cereus plasmid gene pool.
ER  -

TY  - JOUR
AU  - Amano, N.
AU  - Yamamuro, A.
AU  - Miyahara, M.
AU  - Kouzuma, A.
AU  - Abe, T.
AU  - Watanabe, K.
TI  - Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2018
SP  - 1118
EP  - 1122
VL  - 68
AB  - Abacterial strain, designated MMFC1(T), was isolated from a methanol-fed
AB  - microbial fuel cell that had been inoculated with sludge obtained from a
AB  - wastewater-treatmentfacility in a chemical plant. The strain grows by fermenting
AB  - methanol to produce acetate under anaerobic conditions, while homoacetogenic
AB  - growth is not observed. MMFC1(T) also grows on pyruvate and lactate but not on
AB  - sugars and other organic acids. Cells are curved rods and motile, have
AB  - peritrichous flagella, and form endospores. The genome sequence of strain
AB  - MMFC1(T) supports the physiological data. Phylogenetic analysis based on the 16S
AB  - rRNA gene sequence shows that strain MMFC1(T) is affiliated with the family
AB  - Sporomusaceae, while the closest relative is Sporomusa ovata with
AB  - nucleotide-sequencesimilarity of 93.5 %. Major fatty acids are iso-C13 : 0 3-OH,
AB  - C16 : 1omega9 and iso-C17 : 0. On the basis of its physiological, genomic and
AB  - phylogenetic features, a novel genus and species are proposed to accommodate
AB  - strain MMFC1(T), with the name Methylomusa anaerophila gen. nov., sp. nov. The
AB  - type strain of Methylomusa anaerophila is MMFC1(T) (=JCM 31821(T) = KCTC
AB  - 15592(T)).
ER  -

TY  - JOUR
AU  - Amaral, G.R.
AU  - Silva, B.S.
AU  - Santos, E.O.
AU  - Dias, G.M.
AU  - Lopes, R.M.
AU  - Edwards, R.A.
AU  - Thompson, C.C.
AU  - Thompson, F.L.
TI  - Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2759
EP  - 2760
VL  - 194
AB  - Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome
AB  - of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number
AB  - of coding sequences (CDS) is 6,359, as determined according to the Rapid
AB  - Annotation using Subsystem Technology (RAST) server. The number of ribosomal
AB  - genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A
AB  - contains genes related to virulence and fitness, including a complete
AB  - proteorhodopsin cluster, complete type II and III secretion systems, incomplete
AB  - type I, IV, and VI secretion systems, a hemolysin, and CTXPhi.
ER  -

TY  - JOUR
AU  - Amari, M.
AU  - Laguerre, S.
AU  - Vuillemin, M.
AU  - Robert, H.
AU  - Loux, V.
AU  - Klopp, C.
AU  - Morel, S.
AU  - Gabriel, B.
AU  - Remaud-Simeon, M.
AU  - Gabriel, V.
AU  - Moulis, C.
AU  - Fontagne-Faucher, C.
TI  - Genome Sequence of Weissella confusa LBAE C39-2, Isolated from a Wheat Sourdough.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1608
EP  - 1609
VL  - 194
AB  - Weissella confusa is a rod-shaped heterofermentative lactic acid bacterium from the family of
AB  - Leuconostocaceae. Here we report the draft genome sequence of the
AB  - strain W. confusa LBAE C39-2 isolated from a traditional French wheat sourdough.
ER  -

TY  - JOUR
AU  - Amaro, F.
AU  - Gilbert, J.A.
AU  - Owens, S.
AU  - Trimble, W.
AU  - Shuman, H.A.
TI  - Whole-Genome Sequence of the Human Pathogen Legionella pneumophila Serogroup 12 Strain 570-CO-H.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1613
EP  - 1614
VL  - 194
AB  - We present the genomic sequence of the human pathogen Legionella pneumophila serogroup 12
AB  - strain 570-CO-H (ATCC 43290), a clinical isolate from the Colorado
AB  - Department of Health, Denver, CO. This is the first example of a genome sequence
AB  - of L. pneumophila from a serogroup other than serogroup 1. We highlight the
AB  - similarities and differences relative to six genome sequences that have been
AB  - reported for serogroup 1 strains.
ER  -

TY  - JOUR
AU  - Ambalam, P.
AU  - Pithva, S.
AU  - Kothari, C.
AU  - Kothari, R.
AU  - Parmar, N.
AU  - Nathani, N.M.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Dave, J.M.
AU  - Vyas, B.R.
TI  - Insight into the Draft Genome Sequence of Human Isolate Lactobacillus rhamnosus LR231, a Bacterium with Probiotic Potential.
JO  - Genome Announcements
PY  - 2014
SP  - e00111
EP  - e00114
VL  - 2
AB  - Lactobacillus rhamnosus strain LR231 was isolated from the feces of healthy human subjects. It
AB  - is observed to be a potential probiotic strain, having a broad
AB  - spectrum of antimicrobial activity against a wide range of human pathogens and
AB  - food pathogens. Here, we provide the 2.59-Mb draft genome sequence of L.
AB  - rhamnosus LR231.
ER  -

TY  - JOUR
AU  - Ambrosini, A.
AU  - Sant'Anna, F.H.
AU  - de Souza, R.
AU  - Tadra-Sfeir, M.
AU  - Faoro, H.
AU  - Alvarenga, S.M.
AU  - Pedrosa, F.O.
AU  - Souza, E.M.
AU  - Passaglia, L.M.
TI  - Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.
JO  - Genome Announcements
PY  - 2015
SP  - e00245
EP  - e00215
VL  - 3
AB  - Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to
AB  - promote plant growth and N uptake. The genome of the isolate has
AB  - approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting
AB  - characteristics, such as nitrate reduction and ammonification and
AB  - iron-siderophore uptake.
ER  -

TY  - JOUR
AU  - Amin, O.
AU  - Fardeau, M.L.
AU  - Valette, O.
AU  - Hirschler-Rea, A.
AU  - Barbe, V.
AU  - Medigue, C.
AU  - Vacherie, B.
AU  - Ollivier, B.
AU  - Bertin, P.N.
AU  - Dolla, A.
TI  - Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale  Lam5(T).
JO  - Genome Announcements
PY  - 2013
SP  - e00114
EP  - e00112
VL  - 1
AB  - Here, we report the draft genome sequence of Desulfotomaculum hydrothermale, a
AB  - sulfate-reducing, spore-forming bacterium isolated from a Tunisian hot spring. The genome is
AB  - composed of 2.7 Mb, with a G+C content of 49.48%, and it contains 2,643 protein-coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Amin, S.
AU  - Shah, B.
AU  - Jain, K.
AU  - Patel, A.
AU  - Patel, N.
AU  - Joshi, C.G.
AU  - Madamwar, D.
TI  - Draft Genome Sequence of Achromobacter sp. Strain DMS1, Capable of Degrading Polyaromatic Hydrocarbons Isolated from the Industrially Perturbed Environment of Amlakhadi Canal, India.
JO  - Genome Announcements
PY  - 2015
SP  - e01264
EP  - e01215
VL  - 3
AB  - Here, we report the draft genome sequence of Achromobacter sp. strain DMS1, which is 4.9 Mbp
AB  - and has 3,727 coding sequences (CDSs), and is capable of degrading xenobiotic compounds and
AB  - harboring genes for aromatic hydrocarbon metabolism. Its genome will unravel the basic
AB  - mechanism involved in bioremediation of anthropogens.
ER  -

TY  - JOUR
AU  - Amitsur, M.
AU  - Benjamin, S.
AU  - Rosner, R.
AU  - Chapman-Shimshoni, D.
AU  - Meidler, R.
AU  - Blanga, S.
AU  - Kaufmann, G.
TI  - Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite.
JO  - Mol. Microbiol.
PY  - 2003
SP  - 129
EP  - 143
VL  - 50
AB  - The bacterial tRNALys-specific anticodon nuclease is known as a phage T4 exclusion system. In
AB  - the uninfected host cell anticodon nuclease is kept
AB  - latent due to the association of its core protein PrrC with the DNA
AB  - restriction-modification endonuclease EcoprrI. Stp, the T4-encoded peptide
AB  - inhibitor of EcoprrI activates the latent enzyme. Previous in vitro work
AB  - indicated that the activation by Stp is sensitive to DNase and requires
AB  - added nucleotides. Biochemical and mutational data reported here suggest
AB  - that Stp activates the latent holoenzyme when its EcoprrI component is
AB  - tethered to a cognate DNA substrate. Moreover, the activation is driven by
AB  - GTP hydrolysis, possibly mediated by the NTPase domain of PrrC. The data
AB  - also reveal that Stp can be replaced as the activator of latent anticodon
AB  - nuclease by certain pyrimidine nucleotides, the most potent of which is
AB  - dTTP. The activation by dTTP likewise requires an EcoprrI DNA substrate
AB  - and GTP hydrolysis but involves a different form of the latent
AB  - holoenzyme/DNA complex. Moreover, whereas Stp relays its activating effect
AB  - through EcoprrI, dTTP targets PrrC. The activation of the latent enzyme by
AB  - a normal cell constituent hints that anticodon nuclease plays additional
AB  - roles, other than warding off phage T4 infection.
ER  -

TY  - JOUR
AU  - Amitsur, M.
AU  - Morad, I.
AU  - Chapman-Shimshoni, D.
AU  - Kaufmann, G.
TI  - HSD restriction-modification proteins partake in latent anticodon nuclease.
JO  - EMBO J.
PY  - 1992
SP  - 3129
EP  - 3134
VL  - 11
AB  - Phage T4-induced anticodon nuclease triggers cleavage-ligation of the host tRNALys. The enzyme
AB  - is encoded in latent form by the optional Escherichia coli locus prr and is activated by the
AB  - product of the phage stp gene. Anticodon nuclease latency is attributed to the masking of the
AB  - core function prrC by flanking elements homologous with type I restriction -modification genes
AB  - (prrA-hsdM and prrD-hadR). Activation of anticodon nuclease in extracts of uninfected prr+
AB  - cells required synthetic Stp, ATP and GTP and appeared to depend on endogenous DNA. Stp could
AB  - be substituted by a small, heat-stable E. coli factor, hinting that anticodon nuclease may be
AB  - mobilized in cellular situations other thant T4 infection. Hsd antibodies recognized the
AB  - anticodon nuclease holoenzyme but not the prrC-encoded core. Taken together, these data
AB  - indicate that Hsd proteins partake in the latent ACNase complex where they mask the core
AB  - factor PrrC. Presumable, this making interaction is disrupted by Stp in conjunction with Hsd
AB  - ligands. The Hsd-PrrC interaction may signify coupling and mutal enhancement of two
AB  - prokaryotic restriction systems operating at the DNA and tRNA levels.
ER  -

TY  - JOUR
AU  - Amran, F.
AU  - Mohd, K.M.K.
AU  - Mohamad, S.
AU  - Mat, R.A.
AU  - Ahmad, N.
AU  - Goris, M.G.
AU  - Muhammad, A.H.
AU  - Noor, H.N.A.
TI  - Draft Genome Sequence of Leptospira interrogans Serovar Bataviae Strain LepIMR 22 Isolated from a Rodent in Johor, Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00956
EP  - e00916
VL  - 4
AB  - Leptospira interrogans serovar Bataviae was recently identified as one of the persistent
AB  - Leptospira serovars in Malaysia. Here, we report the draft genome
AB  - sequence of the L. interrogans serovar Bataviae strain LepIMR 22 isolated from
AB  - kidney of a rodent in Johor, Malaysia.
ER  -

TY  - JOUR
AU  - An, L.
AU  - Li, Y.
AU  - Chen, Z.
AU  - Chang, D.
AU  - Zhang, X.
AU  - Guo, Y.
AU  - Wang, J.
AU  - Li, T.
AU  - Dai, W.
AU  - Liu, C.
TI  - Genome Sequence of Enterococcus faecium Strain LCT-EF297, Which Has Specific Biochemical Features.
JO  - Genome Announcements
PY  - 2014
SP  - e00102
EP  - e00114
VL  - 2
AB  - An Enterococcus faecium strain was sent into space on the Shenzhou-VIII craft. After space
AB  - flight, the strain E. faecium LCT-EF297 was selected based on its
AB  - metabolic properties.
ER  -

TY  - JOUR
AU  - An, R.
AU  - Lin, P.
AU  - Bougouffa, S.
AU  - Essack, M.
AU  - Boxrud, D.
AU  - Bajic, V.B.
AU  - Vidovic, S.
TI  - Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts.
JO  - Genome Announcements
PY  - 2018
SP  - e01550
EP  - e01517
VL  - 6
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen.
AB  - Occasionally, it is involved in invasive infections, leading to a high
AB  - mortality rate. Here, we present the draft genome sequences of four S Enteritidis
AB  - strains obtained from human and avian hosts that had been involved in bacteremia,
AB  - gastroenteritis, and primary infections.
ER  -

TY  - JOUR
AU  - An, T.T.
AU  - Picardal, F.W.
TI  - Draft Genome Sequence of Desulfocarbo indianensis SCBM, a New Genus of Sulfate-Reducing Bacteria, Isolated from Water Extracted from an Active Coalbed Methane Gas Well.
JO  - Genome Announcements
PY  - 2015
SP  - e00970
EP  - e00915
VL  - 3
AB  - We used Illumina MiSeq technology to sequence the whole genome of Desulfocarbo indianensis
AB  - SCBM, a new genus of sulfate-reducing bacteria isolated from a coal bed in Indiana, USA. This
AB  - draft genome represents the first sequenced genome of the genus Desulfocarbo and the second
AB  - known genome of the order Desulfarculales.
ER  -

TY  - JOUR
AU  - Anand, S.
AU  - Sangwan, N.
AU  - Lata, P.
AU  - Kaur, J.
AU  - Dua, A.
AU  - Singh, A.K.
AU  - Verma, M.
AU  - Kaur, J.
AU  - Khurana, J.P.
AU  - Khurana, P.
AU  - Mathur, S.
AU  - Lal, R.
TI  - Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4471
EP  - 4472
VL  - 194
AB  - Sphingobium indicum B90A, an efficient degrader of hexachlorocyclohexane (HCH) isomers, was
AB  - isolated in 1990 from sugarcane rhizosphere soil in Cuttack, India.
AB  - Here we report the draft genome sequence of this bacterium, which has now become
AB  - a model system for understanding the genetics, biochemistry, and physiology of
AB  - HCH degradation.
ER  -

TY  - JOUR
AU  - Ancora, M.
AU  - Marcacci, M.
AU  - Orsini, M.
AU  - Zilli, K.
AU  - Di Giannatale, E.
AU  - Garofolo, G.
AU  - Camma, C.
TI  - Complete Genome Sequence of a Brucella ceti ST26 Strain Isolated from a Striped Dolphin (Stenella coeruleoalba) on the Coast of Italy.
JO  - Genome Announcements
PY  - 2014
SP  - e00068
EP  - e00014
VL  - 2
AB  - Brucella spp. are important pathogens affecting a wide range of terrestrial and aquatic
AB  - animals. We report the complete and annotated genome sequence of Brucella
AB  - ceti ST26 strain TE10759-12, isolated from a striped dolphin (Stenella
AB  - coeruleoalba) stranded along the Italian shoreline in March of 2012.
ER  -

TY  - JOUR
AU  - Anda, M.
AU  - Ohtsubo, Y.
AU  - Okubo, T.
AU  - Sugawara, M.
AU  - Nagata, Y.
AU  - Tsuda, M.
AU  - Minamisawa, K.
AU  - Mitsui, H.
TI  - Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2015
SP  - 14343
EP  - 14347
VL  - 112
AB  - rRNA is essential for life because of its functional importance in protein synthesis. The rRNA
AB  - (rrn) operon encoding 16S, 23S, and 5S rRNAs is
AB  - located on the main chromosome in all bacteria documented to date and is frequently used as a
AB  - marker of chromosomes. Here, our genome analysis of a plant-associated alphaproteobacterium,
AB  - Aureimonas sp. AU20, indicates that this strain has its sole rrn operon on a small (9.4 kb),
AB  - high-copy-number replicon. We designated this unusual replicon carrying the rrn operon on the
AB  - background of an rrn-lacking chromosome (RLC) as the rrn-plasmid. Four of 12 strains close to
AB  - AU20 also had this RLC/rrn-plasmid organization. Phylogenetic analysis showed that those
AB  - strains having the RLC/rrn-plasmid organization represented one cladewithin the genus
AB  - Aureimonas. Our finding introduces a previously unaddressed viewpoint into studies of
AB  - genetics, genomics, and evolution in microbiology and biology in general.
ER  -

TY  - JOUR
AU  - Andersen, M.T.
AU  - Liefting, L.W.
AU  - Havukkala, I.
AU  - Beever, R.E.
TI  - Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.
JO  - BMC Genomics
PY  - 2013
SP  - 529
EP  - 529
VL  - 14
AB  - Background: 'Candidatus Phytoplasma australiense' is associated with at least nine diseases
AB  - in Australia and New Zealand. The impact of this
AB  - phytoplasma is considerable, both economically and environmentally. The
AB  - genome of a NZ isolate was sequenced in an effort to understand its
AB  - pathogenicity and ecology. Comparison with a closely related Australian
AB  - isolate enabled us to examine mechanisms of genomic
AB  - rearrangement.Results: The complete genome sequence of a strawberry
AB  - lethal yellows (SLY) isolate of 'Candidatus Phytoplasma australiense'
AB  - was determined. It is a circular genome of 959,779 base pairs with 1126
AB  - predicted open reading frames. Despite being 80 kbp larger than another
AB  - 'Ca. Phytoplasma australiense' isolate PAa, the variation between
AB  - housekeeping genes was generally less than 1% at a nucleotide level.
AB  - The difference in size between the two isolates was largely due to the
AB  - number and size of potential mobile units (PMUs), which contributed to
AB  - some changes in gene order. Comparison of the genomes of the two
AB  - isolates revealed that the highly conserved 5' UTR of a putative
AB  - DNA-directed RNA polymerase seems to be associated with insertion and
AB  - rearrangement events. Two types of PMUs have been identified on the
AB  - basis of the order of three to four conserved genes, with both PMUs
AB  - appearing to have been present in the last common ancestor of 'Ca.
AB  - Phytoplasma asteris' and 'Ca. Phytoplasma australiense'. Comparison
AB  - with other phytoplasma genomes showed that modification methylases
AB  - were, in general, species-specific. A putative methylase (xorIIM) found
AB  - in 'Ca. Phytoplasma australiense' appeared to have no analogue in any
AB  - other firmicute, and we believe has been introduced by way of lateral
AB  - gene transfer. A putative retrostransposon (ltrA) analogous to that
AB  - found in OY-M was present in both isolates, although all examples in
AB  - PAa appear to be fragments. Comparative analysis identified highly
AB  - conserved 5' and 3' UTR regions of ltrA, which may indicate how the
AB  - gene is excised and inserted.Conclusions: Comparison of two assembled
AB  - 'Ca. Phytoplasma australiense' genomes has shown they possess a high
AB  - level of plasticity. This comparative analysis has yielded clues as to
AB  - how rearrangements occur, and the identification of sets of genes that
AB  - appear to be associated with these events.
ER  -

TY  - JOUR
AU  - Andersen, P.S.
AU  - Stegger, M.
AU  - Aziz, M.
AU  - Contente-Cuomo, T.
AU  - Gibbons, H.S.
AU  - Keim, P.
AU  - Sokurenko, E.V.
AU  - Johnson, J.R.
AU  - Price, L.B.
TI  - Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.
JO  - Genome Announcements
PY  - 2013
SP  - e00988
EP  - e00913
VL  - 1
AB  - We report the complete genome sequence, including five complete plasmid sequences, of
AB  - Escherichia coli ST131 isolate JJ1886. The isolate was obtained in
AB  - 2007 in the United States from a patient with fatal urosepsis and belongs to the
AB  - virulent, CTX-M-15-producing H30-Rx sublineage.
ER  -

TY  - JOUR
AU  - Anderson, B.
AU  - McDonald, G.
TI  - Construction of DNA libraries of A-T rich organisms using EcoRI star activity.
JO  - Anal. Biochem.
PY  - 1993
SP  - 325
EP  - 327
VL  - 211
AB  - Construction of genomic or expression libraries involves size fractionation of the DNA to be
AB  - cloned by one of several methods. Methods of fractionation include mechanical shearing,
AB  - digestion with DNAse, or digestion with restriction endonucleases that cleave frequently
AB  - within a genome (i.e., Sau3AI). The latter method is most frequently used for practical
AB  - reasons. Near-random cleavage is best obtained by partial digestion with an enzyme that most
AB  - frequently cleaves a given genome. The frequency of cleavage of each restriction endonuclease
AB  - within a given genome is dependent on the G + C content of each individual organism.
AB  - Therefore, a restriction endonuclease with an A-T rich recognition sequence would be preferred
AB  - when cloning DNA from organisms with A-T rich genomes. We describe the use of EcoRI star
AB  - activity to generate near-random DNA, from A-T rich genomes, for cloning. Expression/genomic
AB  - libraries for three A-T rich bacteria were easily and successfully constructed using this
AB  - method.
ER  -

TY  - JOUR
AU  - Anderson, E.S.
AU  - Felix, A.
TI  - Variation in Vi-Phage II of Salmonella typhi.
JO  - Nature
PY  - 1952
SP  - 492
EP  - 494
VL  - 170
AB  - The recent description of phenotypic variation in bacteriophages by Luria and
AB  - Bertani has prompted us to publish the results of experiments carried out in
AB  - 1947 which show analogous features.  The object of the work was primarily to
AB  - investigate the possibility of tracing a specific Vi-phage type of Salmonella
AB  - typhi in which "degraded" variants had arisen (see Craigie and Felix).  It was
AB  - hoped also to gain more information about the mechanism of "degradation" of
AB  - cultures and the processes concerned in the adaptation of Vi-phage II of
AB  - Craigie and Yen to the specific Vi-types of S. typhi.  Degradation in a
AB  - spsecific Vi-type can take all forms from the appeaerance of minor
AB  - cross-reactions with heterologous phages, typical of partly degraded strains,
AB  - to the full susceptibility to all adapted phages which characterizes Type A.
ER  -

TY  - JOUR
AU  - Anderson, E.S.
AU  - Threlfall, E.J.
AU  - Carr, J.M.
AU  - Savoy, L.G.
TI  - Bacteriophage restriction in Salmonella typhimurium by R factors and transfer factors.
JO  - J. Hyg. (Lond)
PY  - 1973
SP  - 619
EP  - 619
VL  - 71
AB  - A total of 2716 R factors and transfer factors isolated from Escherichia coli
AB  - and Salmonellas of human and animal origin were studied for their
AB  - phage-restrictive effects in Salmonella typhimurium phage type 36.  All of 1402
AB  - wild fi+ factors were non-restricting.  The F factor of E. coli K12 was unique
AB  - among the F-like factors tested in that it inhibited lysis of type 36 by one
AB  - typing phage.  In contrast, eleven distinct changes in the phage type of 36
AB  - were produced by fi- I-like factors.  I-like plasmids can thus be subdivided by
AB  - this method.  I-like R factors and transfer factors from human and animal
AB  - enterobacteria were categorized by their phage-restrictive effects in type 36.
AB  - Factors resembling delta in this respect predominated among fi- I-like factor
AB  - from human E. coli and S. typhimurium and from porcine E. coli.  delta-like and
AB  - ColI-like fi-factors were equally distributed in bovine S. typhimurium.
AB  - ColI-like factors were commonest in bovine and avian E. coli.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 83
EP  - 92
VL  - 9
AB  - Frateuria aurantia (ex Kondo and Ameyama 1958) Swings et al. 1980 is a member of  the
AB  - bispecific genus Frateuria in the family Xanthomonadaceae, which is already
AB  - heavily targeted for non-type strain genome sequencing. Strain Kondo 67(T) was
AB  - initially (1958) identified as a member of 'Acetobacter aurantius', a name that
AB  - was not considered for the approved list. Kondo 67(T) was therefore later
AB  - designated as the type strain of the newly proposed acetogenic species Frateuria
AB  - aurantia . The strain is of interest because of its triterpenoids (hopane
AB  - family). F. aurantia Kondo 67(T) is the first member of the genus Frateura whose
AB  - genome sequence has been deciphered, and here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a
AB  - part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of Methanothermus fervidus type strain (V24S).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 315
EP  - 324
VL  - 3
AB  - Methanothermus fervidus Stetter 1982 is the type strain of the genus
AB  - Methanothermus. This hyperthermophilic genus is of a thought to be endemic in
AB  - Icelandic hot springs. M. fervidus was not only the first characterized organism
AB  - with a maximal growth temperature (97 degrees C) close to the boiling point of
AB  - water, but also the first archaeon in which a detailed functional analysis of its
AB  - histone protein was reported and the first one in which the function of
AB  - 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T)
AB  - is of interest because of its very low substrate ranges, it grows only on H(2) +
AB  - CO(2). This is the first completed genome sequence of the family
AB  - Methanothermaceae. Here we describe the features of this organism, together with
AB  - the complete genome sequence and annotation. The 1,243,342 bp long genome with
AB  - its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of Staphylothermus hellenicus P8.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 12
EP  - 20
VL  - 5
AB  - Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum
AB  - Crenarchaeota. Strain P8(T) is the type strain of the species and
AB  - was isolated from a shallow hydrothermal vent system at Palaeochori Bay, Milos,
AB  - Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the
AB  - features of this organism together with the complete genome sequence and
AB  - annotation. The 1,580,347 bp genome with its 1,668 protein-coding and 48 RNA
AB  - genes was sequenced as part of a DOE Joint Genome Institute (JGI) Laboratory
AB  - Sequencing Program (LSP) project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of Ferroglobus placidus AEDII12DO.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 50
EP  - 60
VL  - 5
AB  - Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum
AB  - Euryarchaeota. Strain AEDII12DO is the type strain of the species and was
AB  - isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a
AB  - hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety
AB  - of aromatic compounds as electron donors. Here we describe the features of this
AB  - organism together with the complete genome sequence and annotation. The 2,196,266
AB  - bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of
AB  - a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of Halorhabdus utahensis type strain (AX-2).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 218
EP  - 225
VL  - 1
AB  - Halorhabdus utahensis Waino et al. 2000 is the type species of the genus, which is of
AB  - phylogenetic interest because of its location on one of the deepest
AB  - branches within the very extensive euryarchaeal family Halobacteriaceae. H.
AB  - utahensis is a free-living, motile, rod shaped to pleomorphic, Gram-negative
AB  - archaeon, which was originally isolated from a sediment sample collected from the
AB  - southern arm of Great Salt Lake, Utah, USA. When grown on appropriate media, H.
AB  - utahensis can form polyhydroxybutyrate (PHB). Here we describe the features of
AB  - this organism, together with the complete genome sequence, and annotation. This
AB  - is the first complete genome sequence of the a member of halobacterial genus
AB  - Halorhabdus, and the 3,116,795 bp long single replicon genome with its 3027
AB  - protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 210
EP  - 220
VL  - 7
AB  - Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class
AB  - Sphingobacteriia that is poorly characterized at the genome
AB  - level, thus far. N. soli strain JS13-8(T) is of interest for its ability to
AB  - produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T)
AB  - is only the second genome sequence of a type strain from the family
AB  - Chitinophagaceae to be published, and the first one from the genus Niabella. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 4,697,343 bp long chromosome with its 3,931
AB  - protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria
AB  - andArchaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 1
EP  - 13
VL  - 6
AB  - Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which
AB  - comprises five species of the order Clostridiales.
AB  - Sulfobacillus species are of interest for comparison to other sulfur and iron
AB  - oxidizers and also have biomining applications. This is the first completed
AB  - genome sequence of a type strain of the genus Sulfobacillus, and the second
AB  - published genome of a member of the species S. acidophilus. The genome, which
AB  - consists of one chromosome and one plasmid with a total size of 3,557,831 bp
AB  - harbors 3,626 protein-coding and 69 RNA genes, and is a part of the
AB  - GenomicEncyclopedia ofBacteria andArchaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 174
EP  - 184
VL  - 6
AB  - Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of
AB  - interest for its ability to anaerobically degrade aromatic compounds and
AB  - for its production of volatile sulfur compounds through a unique pathway. The
AB  - genome of H. foetida strain TMBS4(T) is the first to be sequenced for a
AB  - representative of the class Holophagae. Here we describe the features of this
AB  - organism, together with the complete genome sequence (improved high quality
AB  - draft), and annotation. The 4,127,237 bp long chromosome with its 3,615
AB  - protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 155
EP  - 164
VL  - 6
AB  - Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae,
AB  - a family in the phylum Thermodesulfobacteria that is
AB  - currently poorly characterized at the genome level. Members of this phylum are of
AB  - interest because they represent a distinct, deep-branching, Gram-negative
AB  - lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate
AB  - reducer isolated from a deep-sea hydrothermal vent. Here we describe the features
AB  - of this organism, together with the complete genome sequence, and annotation. The
AB  - 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of Halopiger xanaduensis type strain (SH-6T).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 31
EP  - 42
VL  - 6
AB  - Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the
AB  - euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the
AB  - type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake
AB  - Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile
AB  - requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the
AB  - 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of
AB  - a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse
AB  - haloarchaeal genomes.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 322
EP  - 330
VL  - 4
AB  - Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus
AB  - Nitratifractor, a member of the family Nautiliaceae. The species is of interest
AB  - because of its high capacity for nitrate reduction via conversion to N(2) through
AB  - respiration, which is a key compound in plant nutrition. The strain is also of
AB  - interest because it represents the first mesophilic and facultatively anaerobic
AB  - member of the Epsilonproteobacteria reported to grow on molecular hydrogen. This
AB  - is the first completed genome sequence of a member of the genus Nitratifractor
AB  - and the second sequence from the family Nautiliaceae. The 2,101,285 bp long
AB  - genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I. et al.
TI  - Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 381
EP  - 392
VL  - 4
AB  - Pyrolobus fumarii Blochl et al. 1997 is the type species of the genus Pyrolobus,  which
AB  - belongs to the crenarchaeal family Pyrodictiaceae. The species is a
AB  - facultatively microaerophilic non-motile crenarchaeon. It is of interest because
AB  - of its isolated phylogenetic location in the tree of life and because it is a
AB  - hyperthermophilic chemolithoautotroph known as the primary producer of organic
AB  - matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest
AB  - optimal growth temperature of all life forms on earth (106 degrees C). This is
AB  - the first completed genome sequence of a member of the genus Pyrolobus to be
AB  - published and only the second genome sequence from a member of the family
AB  - Pyrodictiaceae. Although Diversa Corporation announced the completion of
AB  - sequencing of the P. fumarii genome on September 25, 2001, this sequence was
AB  - never released to the public. The 1,843,267 bp long genome with its 1,986
AB  - protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Anderson, I.J. et al.
TI  - Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1.
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 189
EP  - 196
VL  - 1
AB  - Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order
AB  - Methanomicrobiales within the archaeal phylum Euryarchaeota. The type
AB  - strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri
AB  - is of phylogenetic interest because at the time the sequencing project began only
AB  - one genome had previously been sequenced from the order Methanomicrobiales. We
AB  - report here the complete genome sequence of M. marisnigri type strain JR1 and its
AB  - annotation. This is part of a Joint Genome Institute 2006 Community Sequencing
AB  - Program to sequence genomes of diverse Archaea.
ER  -

TY  - JOUR
AU  - Anderson, I.J. et al.
TI  - The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.
JO  - BMC Genomics
PY  - 2009
SP  - 145
EP  - 145
VL  - 10
AB  - BACKGROUND: Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the
AB  - archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing
AB  - crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the
AB  - three genomes. RESULTS: The 1.57 Mbp genome of the hyperthermophilic crenarchaeote
AB  - Staphylothermus marinus has been completely sequenced. The main energy generating pathways
AB  - likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S.
AB  - marinus possesses several enzymes not present in other crenarchaeotes including a sodium
AB  - ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus
AB  - lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that
AB  - have been sequenced -- Thermofilum pendens and Hyperthermus butylicus. Instead it has three
AB  - operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in
AB  - sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H.
AB  - butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for
AB  - potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has
AB  - adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor
AB  - environment, and S. marinus lies between these two extremes. CONCLUSION: The three
AB  - heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs.
AB  - marine, via their transporter content, and they have also adapted to environments with
AB  - differing levels of nutrients. Despite the fact that they all use sulfur as an electron
AB  - acceptor, they are likely to have different pathways for sulfur reduction.
ER  -

TY  - JOUR
AU  - Anderson, I.J. et al.
TI  - Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 70
EP  - 70
VL  - 11
AB  - Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The
AB  - type strain ACAM 34 was isolated from Deep Lake, Antarctica.
AB  - H. lacusprofundi is of phylogenetic interest because it is distantly related to
AB  - the haloarchaea that have previously been sequenced. It is also of interest
AB  - because of its psychrotolerance. We report here the complete genome sequence of
AB  - H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a
AB  - 2006 Joint Genome Institute Community Sequencing Program project to sequence
AB  - genomes of diverse Archaea.
ER  -

TY  - JOUR
AU  - Anderson, I.J.
AU  - Sieprawska-Lupa, M.
AU  - Goltsman, E.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Glavina Del Rio, T.
AU  - Tice, H.
AU  - Dalin, E.
AU  - Barry, K.
AU  - Pitluck, S.
AU  - Hauser, L.
AU  - Land, M.
AU  - Lucas, S.
AU  - Richardson, P.
AU  - Whitman, W.B.
AU  - Kyrpides, N.C.
TI  - Complete genome sequence of Methanocorpusculum labreanum type strain Z.
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 197
EP  - 203
VL  - 1
AB  - Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within
AB  - the archaeal kingdom Euryarchaeota. The type strain Z
AB  - was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in
AB  - Los Angeles, California. M. labreanum is of phylogenetic interest because at the
AB  - time the sequencing project began only one genome had previously been sequenced
AB  - from the order Methanomicrobiales. We report here the complete genome sequence of
AB  - M. labreanum type strain Z and its annotation. This is part of a 2006 Joint
AB  - Genome Institute Community Sequencing Program project to sequence genomes of
AB  - diverse Archaea.
ER  -

TY  - JOUR
AU  - Anderson, I.J.
AU  - Sun, H.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Glavina Del Rio, T.
AU  - Tice, H.
AU  - Dalin, E.
AU  - Lucas, S.
AU  - Barry, K.
AU  - Land, M.
AU  - Richardson, P.
AU  - Huber, H.
AU  - Kyrpides, N.C.
TI  - Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1.
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 183
EP  - 188
VL  - 1
AB  - Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within
AB  - the archaeal phylum Crenarchaeota. S. marinus is a
AB  - hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was
AB  - isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has
AB  - also been isolated from a hydrothermal vent on the East Pacific Rise. We report
AB  - the complete genome of S. marinus strain F1, the type strain of the species. This
AB  - is the fifth reported complete genome sequence from the order Desulfurococcales.
ER  -

TY  - JOUR
AU  - Anderson, J.E.
TI  - Restriction endonucleases and modification methylases.
JO  - Curr. Opin. Struct. Biol.
PY  - 1993
SP  - 24
EP  - 30
VL  - 3
AB  - Restriction endonucleases and modification methylases offer excellent systems for studying
AB  - protein-DNA interactions. The past year has seen the experimental verification of some aspects
AB  - of the catalytic mechanisms of both types of enzyme. The first structures of methylases were
AB  - determined and a number of endonuclease structures should become available soon.
ER  -

TY  - JOUR
AU  - Anderson, M.T.
AU  - Mitchell, L.A.
AU  - Zhao, L.
AU  - Mobley, H.L.
TI  - Citrobacter freundii fitness during bloodstream infection.
JO  - Sci. Rep.
PY  - 2018
SP  - 11792
EP  - 11792
VL  - 8
AB  - Sepsis resulting from microbial colonization of the bloodstream is a serious
AB  - health concern associated with high mortality rates. The objective of this study
AB  - was to define the physiologic requirements of Citrobacter freundii in the
AB  - bloodstream as a model for bacteremia caused by opportunistic Gram-negative
AB  - pathogens. A genetic screen in a murine host identified 177 genes that
AB  - contributed significantly to fitness, the majority of which were broadly
AB  - classified as having metabolic or cellular maintenance functions. Among the
AB  - pathways examined, the Tat protein secretion system conferred the single largest
AB  - fitness contribution during competition infections and a putative Tat-secreted
AB  - protein, SufI, was also identified as a fitness factor. Additional work was
AB  - focused on identifying relevant metabolic pathways for bacteria in the
AB  - bloodstream environment. Mutations that eliminated the use of glucose or mannitol
AB  - as carbon sources in vitro resulted in loss of fitness in the murine model and
AB  - similar results were obtained upon disruption of the cysteine biosynthetic
AB  - pathway. Finally, the conservation of identified fitness factors was compared
AB  - within a cohort of Citrobacter bloodstream isolates and between Citrobacter and
AB  - Serratia marcescens, the results of which suggest the presence of conserved
AB  - strategies for bacterial survival and replication in the bloodstream environment.
ER  -

TY  - JOUR
AU  - Anderson, M.T.
AU  - Mitchell, L.A.
AU  - Zhao, L.
AU  - Mobley, H.L.T.
TI  - Capsule Production and Glucose Metabolism Dictate Fitness during Serratia marcescens Bacteremia.
JO  - MBio
PY  - 2017
SP  - e00740
EP  - e00717
VL  - 8
AB  - Serratia marcescens is an opportunistic pathogen that causes a range of human
AB  - infections, including bacteremia, keratitis, wound infections, and urinary tract
AB  - infections. Compared to other members of the Enterobacteriaceae family, the
AB  - genetic factors that facilitate Serratia proliferation within the mammalian host
AB  - are less well defined. An in vivo screen of transposon insertion mutants
AB  - identified 212 S. marcescens fitness genes that contribute to bacterial survival
AB  - in a murine model of bloodstream infection. Among those identified, 11 genes were
AB  - located within an 18-gene cluster encoding predicted extracellular polysaccharide
AB  - biosynthesis proteins. A mutation in the wzx gene contained within this locus
AB  - conferred a loss of fitness in competition infections with the wild-type strain
AB  - and a reduction in extracellular uronic acids correlating with capsule loss. A
AB  - second gene, pgm, encoding a phosphoglucomutase exhibited similar
AB  - capsule-deficient phenotypes, linking central glucose metabolism with capsule
AB  - production and fitness of Serratia during mammalian infection. Further evidence
AB  - of the importance of central metabolism was obtained with a pfkA glycolytic
AB  - mutant that demonstrated reduced replication in human serum and during murine
AB  - infection. An MgtB magnesium transporter homolog was also among the fitness
AB  - factors identified, and an S. marcescens mgtB mutant exhibited decreased growth
AB  - in defined medium containing low concentrations of magnesium and was outcompeted
AB  - ~10-fold by wild-type bacteria in mice. Together, these newly identified genes
AB  - provide a more complete understanding of the specific requirements for S.
AB  - marcescens survival in the mammalian host and provide a framework for further
AB  - investigation of the means by which S. marcescens causes opportunistic
AB  - infections.IMPORTANCESerratia marcescens is a remarkably prolific organism that
AB  - replicates in diverse environments, including as an opportunistic pathogen in
AB  - human bacteremia. The genetic requirements for S. marcescens survival in the
AB  - mammalian bloodstream were defined in this work by transposon insertion
AB  - sequencing. In total, 212 genes that contribute to bacterial fitness were
AB  - identified. When sorted via biological function, two of the major fitness
AB  - categories identified herein were genes encoding capsule polysaccharide
AB  - biogenesis functions and genes involved in glucose utilization. Further
AB  - investigation determined that certain glucose metabolism fitness genes are also
AB  - important for the generation of extracellular polysaccharides. Together, these
AB  - results identify critical biological processes that allow S. marcescens to
AB  - colonize the mammalian bloodstream.
ER  -

TY  - JOUR
AU  - Andersson, S.G.E.
AU  - Zomorodipour, A.
AU  - Andersson, J.O.
AU  - Sicheritz-Ponten, T.
AU  - Alsmark, U.C.M.
AU  - Podowski, R.M.
AU  - Naslund, A.K.
AU  - Eriksson, A.-S.
AU  - Winkler, H.H.
AU  - Kurland, C.G.
TI  - The genome sequence of Rickettsia prowazekii and the origin of mitochondria.
JO  - Nature
PY  - 1998
SP  - 133
EP  - 140
VL  - 396
AB  - We describe here the complete genome sequence (1,111,523 base pairs) of the obligate
AB  - intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus.  This
AB  - genome contains 834 protein-coding genes.  The functional profiles of these genes show
AB  - similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are
AB  - found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding
AB  - components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R.
AB  - prowazekii.  In effect, ATP production in Rickettsia is the same as that in mitochondria.
AB  - Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and
AB  - nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria.  Such
AB  - genes seem to have been replaced by homologues in the nuclear (host) genome.  The R.
AB  - prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a
AB  - microbial genome.  Such non-coding sequences may be degraded remnants of 'neutralized' genes
AB  - that await elimination from the genome.  Phylogenetic analyses indicate that R. prowazekii is
AB  - more closely related to mitochondria than is any other microbe studied so far.
ER  -

TY  - JOUR
AU  - Ando, T.
TI  - Novel DNA enzymes:  specificity and application.
JO  - Reports Inst. Phys. Chem. Res.
PY  - 1985
SP  - 239
EP  - 255
VL  - 61
AB  - None
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Aras, R.
AU  - Kusugami, K.
AU  - Peek, R.M.
AU  - Blaser, M.J.
AU  - Wassenaar, T.M.
TI  - Presence of hrgA and hrgB (iceA2) differentially associated with Helicobacter pylori virulence.
JO  - Gastroenterology
PY  - 2003
SP  - A272
EP  - A273
VL  - 124
AB  - In the hpyI and hpyIII loci of Helicobacter pylori, the restriction endonuclease-encoding gene
AB  - of these Restriction-Modification (R-M)
AB  - systems can be replaced by a specific non-related gene: hrgA can
AB  - replace hpyIIIR, and hrgB (formerly called iceA2) can replace hpyIR.
AB  - Thus, there are 2 genotypes for each locus, either bearing or lacking
AB  - the R-gene. Although both hrgB and hrgA have been associated with H.
AB  - pylori virulence, we now examined the correlation between the hpyI and
AB  - hpyIII genotypes with pathogenicity in greater detail. 174 H. pylori
AB  - strains were assessed for sensitivity to MboI (indicative of hpyIIIM
AB  - activity) and NlaIII (for hpyIM) digestion. Presence of hpyIIIR or
AB  - hrgA, of hpyIR (iceA1) or hrgB, and of cagA and vacA was determined by
AB  - PCR and/or LIPA. The induction of IL-8 in co-cultured AGS cells was
AB  - determined for representative strains. We assessed the correlation
AB  - between genotypes, clinical features, and IL-8 induction. In all
AB  - strains examined, hrgA was found to be mutually exclusive with hpyIIIR,
AB  - and iceA1 with hrgB; the presence of hrgA and hrgB were independent.
AB  - HpyIM and HpyIIIM activities were detected in 100% and 95%,
AB  - respectively, of the strains studied. Among 132 Asian strains, the
AB  - combination hpyIIIR/iceA1 is the most common genotype (52%) and
AB  - hrgA/hrgB is least (4%) common, whereas in 42 Western strains
AB  - hpyIIIR/hrgB (40%), and hrgA/hrgB (31%) are the most common. The 33
AB  - strains with iceA1 induced significantly more IL-8 (median 1483 pg/ml,
AB  - range 287-2898) (p = 0.03) than 30 strains with hrgB (median 955 pg/ml,
AB  - range 151-2452), whereas there was no difference in relation to the
AB  - hpyIII locus. In Asian strains from gastric cancer patients (n=43, all
AB  - cagA positive and vacA s1), 41% were hrgA and 20% were hrgB. This is an
AB  - overrepresentation of hrgA, but not of hrgB, compared with non-gastric
AB  - cancer diseases. Although gastric cancer strains from Western countries
AB  - were not available for analysis, in patients with duodenal or gastric
AB  - ulcer, hrgA but not hrgB was overrepresented (71%) compared to
AB  - non-ulcer dyspepsia (39%, p<0.05) isolates. Conclusion: In this study,
AB  - hrgA presence correlates with H. pylori clinical outcome, whereas iceA1
AB  - presence was associated with enhanced IL-8 induction.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Aras, R.A.
AU  - Kusugami, K.
AU  - Blaser, M.J.
AU  - Wassenaar, T.M.
TI  - Evolutionary history of hrgA, which replaces the restriction gene hpyIIIR in the hpyIII locus of Helicobacter pylori.
JO  - J. Bacteriol.
PY  - 2003
SP  - 295
EP  - 301
VL  - 185
AB  - A recently identified Helicobacter pylori gene, hrgA, was previously reported to be present in
AB  - 70 (33%) of 208 strains examined (T. Ando, T. M.
AB  - Wassenaar, R. M. Peek, R. A. Aras, A. I. Tschumi, L.-J. Van Doorn, K.
AB  - Kusugami, and M. J. Blaser, Cancer Res. 62:2385-2389, 2002). Sequence
AB  - analysis of nine such strains indicated that in each strain hrgA replaced
AB  - hpyIIIR, which encodes a restriction endonuclease and which, together with
AB  - the gene for its cognate methyltransferase, constitutes the hpyIII locus.
AB  - As a consequence of either the hrgA insertion or independent mutations,
AB  - hpyIIIM function was lost in 11 (5%) of the 208 strains examined,
AB  - rendering chromosomal DNA sensitive to MboI digestion. The evolutionary
AB  - history of the locus containing either hpyIII or hrgA was reconstructed.
AB  - By homologous recombination involving flanking sequences, hrgA and hpyIIIR
AB  - can replace one another in the hpyIII locus, and there is simultaneous
AB  - replacement of several flanking genes. These findings, combined with the
AB  - hpyIM/iceA2 locus discovered previously, suggest that the two most
AB  - strongly conserved methylase genes of H. pylori, hpyIIIM and hpyIM, are
AB  - both preceded by alternative genes that compete for presence at their
AB  - loci.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Hayase, E.
AU  - Ikawa, S.
AU  - Shibata, T.
TI  - Site-specific restriction endodeoxyribonucleases in Bacilli.
JO  - Microbiology-1982
PY  - 1982
SP  - 66
EP  - 70
VL  - 0
AB  - Biochemical studies on the biological phenomena of restriction and modification
AB  - of phages have resulted in the discovery of site-specific endonucleases (type
AB  - II restriction endonucleases) that cleave double-stranded DNA at or near
AB  - nucleotide sequences specific to each enzyme.  Site-specific endonucleases have
AB  - been widely used as tools for research in molecular biology, particularly that
AB  - on recombinant DNA.  During restriction and modification of phage Phi105C, we
AB  - previously observed that Bacillus subtilis (including B. amyloliquefaciens) had
AB  - site-specific restriction endonucleases BamNI and BamNx, which recognize  5'
AB  - G^G A T C C 3' and 5' G^G A C C 3' 3' C C T A G^G 5'     3' C C T G^G5'
AB  - respectively, and cut the phosphodiester bonds as indicated by arrows.  We
AB  - have, since then, systematically screened strains of Bacilli for site-specific
AB  - endonucleases.  In this paper, we describe related biochemical studies.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Ishiguro, K.
AU  - Watanabe, O.
AU  - Miyake, N.
AU  - Kato, T.
AU  - Hibi, S.
AU  - Mimura, S.
AU  - Nakamura, M.
AU  - Miyahara, R.
AU  - Ohmiya, N.
AU  - Niwa, Y.
AU  - Goto, H.
TI  - Restriction-modification systems may be associated with Helicobacter pylori virulence.
JO  - J. Gastroenterol. Hepatol.
PY  - 2010
SP  - S95
EP  - S98
VL  - 25
AB  - Restriction-modification (R-M) systems are exclusive to unicellular organisms and ubiquitous
AB  - in the bacterial world. Bacteria use R-M
AB  - systems as a defense against invasion by foreign DNA. Analysis of the
AB  - genome sequences of Helicobacter pylori strains 26 695 and J99
AB  - identified an extraordinary number of genes with homology to R-M genes
AB  - in other bacterial species. All H. pylori strains possess their own
AB  - unique complement of active R-M systems. All of the methylases that
AB  - have been studied so far were present in all major human population
AB  - groupings, suggesting that their horizontal acquisition pre-dated the
AB  - separation of these populations. The two most strongly conserved
AB  - methylase genes of H. pylori, hpy IM and hpy IIIM, are both preceded by
AB  - alternative genes that compete for presence at their loci, and
AB  - furthermore these genes may be associated with H. pylori pathogenicity.
AB  - Further study should investigate the roles of H. pylori R-M systems.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Peek, R.M. Jr.
AU  - Kusugami, K.
AU  - Van Doorn, L.-J.
AU  - Wassenaar, T.
AU  - Kim, S.-K.
AU  - Blaser, M.J.
TI  - H. pylori strains with the novel gene MboX are correlated with gastric cancer in Asian patients.
JO  - Gastroenterology
PY  - 2001
SP  - A652
EP  - A652
VL  - 120
AB  - Background: H. pylori exhibits substantial genomic diversity that at least in part influences
AB  - clinical outcome.  Type II restriction-modification (R-M) systems are highly diverse between
AB  - strains, a characteristic unique for H. pylori.  HpyIII, a restriction enzyme found in H.
AB  - pylori, is highly homologous to MboI, which recognizes GATC.  We sought to determine the
AB  - variability of hpyIII R-M genotypes in H. pylori strains and whether differences are linked to
AB  - geographic origin or clinical features.  Method: We examined 228 strains (US 50, South America
AB  - 12, Europe 15, Asia 147, Oceana 4), by assessing digestion of chromosomal DNA by MboI, and by
AB  - performing PCR for hpyIII.  We assessed the correlation between hpyIII status, other
AB  - genotypes, and clinical features among 182 strains (50 US, 85 Japan, 28 China, and 19 Korea).
AB  - cagA, vacA, and iceA status were determined by PCR and LIPA.  Results: Eleven (5%) of 228
AB  - strains tested were MboI-sensitive, and by PCR, 10 (91%) of these 11 did not have hpyIIIR.  In
AB  - these 10 strains, we identified a novel gene (that we termed MboX) in the hpyIII position,
AB  - followed by the cognate methylase, hpyIIIM.  MboX has substantial homology with C. jejuni
AB  - Cj1602, but no function is known for either.  Strain 88-29 which is Mbo-I-sensitive, possesses
AB  - hpyIII, but the upstream promoter is truncated.  We next examined the hpyIII locus in 217
AB  - MboI-resistant strains, and found that 148 (68%) have hpyIIIR, and 69 (32%) have MboX.  In
AB  - Western countries, MboX is more prevalent (55%) than in Asia (25%) (p<0.0001, c2).  In Asia,
AB  - MboX is more prevalent among gastric cancer patients (18/43; 42%) than non-cancer patients
AB  - (14/89; 16%) (p=0.001, c2).  Al 132 Asian strains tested were cagA+, but among US strains,
AB  - MboX is more prevalent in those that are cagA+ (19/29; 63%) than cagA (7/20; 35%) (p=0.04,
AB  - c2).  In vitro, MboX can be replaced by hpyIIIR, and vice versa, by homologous recombination.
AB  - Conclusion: The hpyIII locus may contain either hpyIIIR or MboX, followed by hpyIIIM.  MboX is
AB  - a novel strain-specific gene that is associated with gastric cancer among H. pylori isolates
AB  - from Asian patients.  If this observation is confirmed, MboX may be used in the future to
AB  - identify individuals of higher gastric cancer risk.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Shibata, T.
TI  - Host-controlled modification and restriction and the relating enzymes in Bacillus subtilis and other Bacillus strains.
JO  - Tanpakushitsu Kakusan Koso
PY  - 1977
SP  - 1012
EP  - 1019
VL  - 22
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Shibata, T.
AU  - Kazami, J.
TI  - Restriction endonucleases.
JO  - Tanpakushitsu Kakusan Koso
PY  - 1985
SP  - 1429
EP  - 1444
VL  - 30
AB  - Review - in Japanese
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Wassenaar, T.M.
AU  - Peek, R.M. Jr.
AU  - Aras, R.A.
AU  - Tschumi, A.I.
AU  - van Doorn, L.-Jan.
AU  - Kusugami, K.
AU  - Blaser, M.J.
TI  - A Helicobacter pylori restriction endonuclease-replacing gene, hrgA, is associated with gastric cancer in Asian strains.
JO  - Cancer Res.
PY  - 2002
SP  - 2385
EP  - 2389
VL  - 62
AB  - The sensitivity of Helicobacter pylori chromosomal DNA to MboI digestion was investigated in
AB  - 208 strains from several continents. Only
AB  - 11 (5%) of the strains were sensitive to MboI, and it was hypothesized that
AB  - HpyIII, a type II restriction/modification enzyme with sequence
AB  - homology to MboI, mediated the protection. This was confirmed by PCR
AB  - analysis of the gene locus of hpyIII, normally composed of hpyIIIR and
AB  - hpyIIIM. In all but one strain sensitive to MboI, no PCR product of
AB  - hpyIIIR was obtained. In contrast, all strains yielded a product for
AB  - hpyIIIM, independent of MboI phenotype. Further examination of the
AB  - hpyIII locus in strains lacking a hpyIIIR PCR product identified a
AB  - novel gene, hrgA, upstream of hpyIIIM. All 208 strains examined had
AB  - either hpyIIIR or hrgA, but not both, upstream of hpyIIIM. Although
AB  - hrgA has homology with a Campylobacter jejuni gene (Cj1602), its
AB  - function is not known. In Western countries, hrgA was more prevalent
AB  - (53%) than in Asia (25%; P<0.0001, chi2). In Asia, hrgA was more
AB  - prevalent among gastric cancer patients (18 of 43; 42%) than among
AB  - noncancer patients (16 of 95; 17%; P=0.001, chi2). All 143 Asian
AB  - strains tested were cagA+, but among Western strains, hrgA was more
AB  - prevalent in cagA+ strains (26 of 42; 62%) than in cagA- strains (9 of
AB  - 23; 39%; P=0.04, chi2). In coculture with epithelial cells, hpyIIIR and
AB  - hrgA strains did not show any significant differences in interleukin-8
AB  - induction and apoptosis. Although a direct function for hrgA in
AB  - virulence could not be demonstrated, our data indicate that hrgA is a
AB  - strain-specific gene that might be associated with gastric cancer among
AB  - H. pylori isolates from Asian patients.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Wassenaar, T.M.
AU  - Peek, R.M.
AU  - Aras, R.A.
AU  - Kusugami, K.
AU  - van Doom, L.
AU  - Blaser, M.J.
TI  - hypX shares a genomic locus with the restriction endonuclease gene hpyIIIR in Helicobacter pylori.
JO  - Int. J. Med. Microbiol.
PY  - 2001
SP  - 28
EP  - 28
VL  - 291S
AB  - A novel gene, hypX, with potential predictive value to differentiate virulence amongst
AB  - cagA-positive H. pylori strains has been identified.  This gene may replace hpyIIIR, a
AB  - restriction endonuclease that, together with its methyltransferase, constitutes the hpyIII
AB  - locus, which is homologous to the MboI R-M system.  hypX has substantial homology with Cj1602
AB  - in C. jejuni, but the function for both is unknown.  From 208 strains examined, originating
AB  - from several continents, hypX and hpyIIIR were found to be mutually exclusive in the hpyIII
AB  - locus.  Of the 138 strains bearing hpyIIIR, which we designated Type I, 137 (99%) are Mbo-I
AB  - resistant.  Of the 70 strains bearing hypX, or Type II, 14% are MboI-sensitive.  Type I and
AB  - Type II strains were compared for linkage to geographic origin or clinical features.  In
AB  - Western countries, hypX is more prevalent (53%) than in Asian (25%) (p is less than or equal
AB  - to 0.001, c2).  In Asian, hypX is more prevalent among gastric cancer patients (18/43; 42%)
AB  - than non-cancer patients (16/95; 17%) (p=0.001, X2).  All 143 Asian strains tested were cagA+
AB  - strains (24/39; 62%) than in cagA- strains (9/22; 41%) (p=0.04, X2).  Although a direct
AB  - function for phpX in virulence was not examined, we postulate that hypX is a strain-specific
AB  - marker that might be associated with gastric cancer among H. pylori isolates from Asian
AB  - patients.  Gene -specific assays for hypX may provide tools to identify individuals of higher
AB  - gastric cancer risk in populations in which cagA-positive strains predominate.
ER  -

TY  - JOUR
AU  - Ando, T.
AU  - Xu, Q.
AU  - Torres, M.
AU  - Kusugami, K.
AU  - Israel, D.A.
AU  - Blaser, M.J.
TI  - Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 1052
EP  - 1065
VL  - 37
AB  - Helicobacter pylori cells are naturally competent for the uptake of both plasmid and
AB  - chromosomal DNA. However, we demonstrate that there are strong barriers to transformation of
AB  - H. pylori strains by plasmids derived from unrelated strains. We sought to determine the
AB  - molecular mechanisms underlying these barriers. Transformation efficiency was assessed using
AB  - pHP1, an Escherichia coli-H. pylori shuttle vector conferring kanamycin resistance.
AB  - Transformation of 33 H. pylori strains was attempted with pHP1 purified from either E. coli or
AB  - H. pylori, and was successfully introduced into only 11 strains. Digestion of H. pylori
AB  - chromosomes with different restriction endonucleases (REs) showed that DNA methylation
AB  - patterns vary substantially among strains. The strain most easily transformed, JP26, was found
AB  - to have extremely low endogenous RE activity and to lack a restriction-modification (R-M)
AB  - system, homologous to MboI, which is highly conserved among H. pylori strains. When we
AB  - introduced this system to JP26, pHP1 from MboI.M+ JP26, but not from wild-type JP26,
AB  - transformed MboI R-M+ JP26 and heterologous MboI R-M+ wild-type H. pylori strains. Parallel
AB  - studies with pHP1 from dam+ and dam- E. coli strains confirmed these findings. These data
AB  - indicate that the endogenous REs of H. pylori strains represent a critical barrier to
AB  - interstrain plasmid transfer among H. pylori.
ER  -

TY  - JOUR
AU  - Andreeva, I.S.
AU  - Afinogenova, G.N.
AU  - Lebedev, I.R.
AU  - Nadolinnaya, I.G.
AU  - Pustoshilova, N.M.
TI  - Kpn378I - a type II restriction endonuclease from Klebsiella pneumoniae.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1991
SP  - 31
EP  - 32
VL  - 2
AB  - A strain of Klebsiella pneumoniae isolated from the air showed the presence of
AB  - a type II restriction endonuclease. Selection for clones that would not form
AB  - capsula resulted in the isolation of a non-pathogenic subclone. The yield of
AB  - the highly purified enzyme is 40,000 units per g of cells. Judging from the
AB  - fragmentation pattern of lambda phage DNA, the sequence specificity of
AB  - R.Kpn378I is indistinguishable from that of SacII endonuclease. Optimal
AB  - reaction conditions are: 50-70mM NaCl/KCl, 10 mM MgCl2, pH 7.5-8.5, 37C. Unlike
AB  - SacII, Kpn378I is not inhibited by NaCl or KCl at concentrations up to 120mM.
ER  -

TY  - JOUR
AU  - Andreeva, I.S.
AU  - Afinogenova, G.N.
AU  - Lebedev, L.R.
AU  - Pustoshilova, N.M.
AU  - Gordienko, N.Y.
AU  - Maistrenko, G.G.
TI  - Site specific restriction endonuclease Rme21I from Rhizobium meliloti.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1991
SP  - 30
EP  - 31
VL  - 0
AB  - A new site specific restriction endonuclease Rme21I from Rhizobium meliloti has
AB  - been shown to recognize the following nucleotide sequence 5'-ATCGAT-3' in the
AB  - doublestranded DNA.  Thus, the enzyme is a true isoschizomer of the restriction
AB  - endonucleases Bsu15I and ClaI.
ER  -

TY  - JOUR
AU  - Andreevskaya, M.
AU  - Hultman, J.
AU  - Johansson, P.
AU  - Laine, P.
AU  - Paulin, L.
AU  - Auvinen, P.
AU  - Bjorkroth, J.
TI  - Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 40
EP  - 40
VL  - 11
AB  - Leuconostoc gelidum subsp. gasicomitatum is a predominant lactic acid bacterium (LAB) in
AB  - spoilage microbial communities of different kinds of modified-atmosphere
AB  - packaged (MAP) food products. So far, only one genome sequence of a
AB  - poultry-originating type strain of this bacterium (LMG 18811(T)) has been
AB  - available. In the current study, we present the completely sequenced and
AB  - functionally annotated genome of strain KG16-1 isolated from a vegetable-based
AB  - product. In addition, six other vegetable-associated strains were sequenced to
AB  - study possible 'niche' specificity suggested by recent multilocus sequence
AB  - typing. The genome of strain KG16-1 consisted of one circular chromosome and
AB  - three plasmids, which together contained 2,035 CDSs. The chromosome carried at
AB  - least three prophage regions and one of the plasmids encoded a galactan
AB  - degradation cluster, which might provide a survival advantage in plant-related
AB  - environments. The genome comparison with LMG 18811(T) and six other vegetable
AB  - strains suggests no major differences between the meat- and vegetable-associated
AB  - strains that would explain their 'niche' specificity. Finally, the comparison
AB  - with the genomes of other leuconostocs highlights the distribution of
AB  - functionally interesting genes across the L. gelidum strains and the genus
AB  - Leuconostoc.
ER  -

TY  - JOUR
AU  - Andres, S.
AU  - Skoglund, A.
AU  - Nilsson, C.
AU  - Krabbe, M.
AU  - Bjorkholm, B.
AU  - Engstrand, L.
TI  - Type I Restriction-Modification Loci Reveal High Allelic Diversity in Clinical Helicobacter pylori Isolates.
JO  - Helicobacter
PY  - 2010
SP  - 114
EP  - 125
VL  - 15
AB  - Background: A remarkable variety of restriction-modification (R-M) systems is
AB  - found in Helicobacter pylori. Since they encompass a large portion of
AB  - the strain-specific H. pylori genes and therefore contribute to genetic
AB  - variability, they are suggested to have an impact on disease outcome.
AB  - Type I R-M systems comprise three different subunits and are the most
AB  - complex of the three types of R-M systems.
AB  - Aims:
AB  - We investigated the genetic diversity and distribution of type I
AB  - R-M systems in clinical isolates of H. pylori.
AB  - Material and methods:
AB  - Sixty-one H. pylori isolates from a Swedish hospital based
AB  - case-control study and 6 H. pylori isolates of a Swedish
AB  - population-based study were analyzed using polymerase chain reaction
AB  - for the presence of the three R-M systems' subunits. Representative
AB  - gene variants were sequenced.
AB  - Results:
AB  - Although the hsdM and hsdR genes appeared conserved in our clinical
AB  - H. pylori isolates, the sequences of the hsdS loci were highly
AB  - variable. Despite their sequence diversity, the genes per se were
AB  - present at high frequencies. We identified a number of novel allelic
AB  - hsdS variants, which are distinct from corresponding hsdS loci in the
AB  - sequenced H. pylori strains 26695, J99 and HPAG1. In analyses of paired
AB  - H. pylori isolates, obtained from the same individuals with a 4-year
AB  - interval, we observed genetic modifications of hsdS genes in patients
AB  - with atrophic gastric mucosa.
AB  - Discussion:
AB  - We propose that the genetic variability of hsdS genes in a
AB  - bacterial population will give rise to new specificities of these
AB  - enzymes, which might lead to adaptation to an ever-changing gastric
AB  - environment.
ER  -

TY  - JOUR
AU  - Andres-Barrao, C.
AU  - Falquet, L.
AU  - Calderon-Copete, S.P.
AU  - Descombes, P.
AU  - Ortega, P.R.
AU  - Barja, F.
TI  - Genome sequence of high acetic acid resistant bacteria: Gluconacetobacter europaeus LMG 18890T, Gluconacetobacter europaeus LMG 18494 (references  strains), Gluconacetobacter europaeus 5P3 and Gluconacetobacter oboediens  174Bp2 (isolated from vinegar).
JO  - J. Bacteriol.
PY  - 2011
SP  - 2670
EP  - 2671
VL  - 193
AB  - Bacteria of the genus Gluconacetobacter are usually involved in the industrial production of
AB  - vinegars with high acetic acid concentration. We
AB  - describe here the genome sequence of three Gluconacetobacter europaeus
AB  - strains, a very common bacterial species from industrial fermenters, as
AB  - well as of a Gluconacetobacter oboediens strain.
ER  -

TY  - JOUR
AU  - Andrews, K.T.
AU  - Patel, B.K.C.
AU  - Clarke, F.M.
TI  - FgoI, a type II restriction endonuclease from the thermoanaerobe Fervidobacterium gondwanense AB39T.
JO  - Anaerobe
PY  - 1998
SP  - 227
EP  - 232
VL  - 4
AB  - Restriction endonuclease activity was detected in 11 out of 13 Fervidobacterium isolates,
AB  - including F. islandicum H21T, F. gondwanense AB39T, and nine other Fervidobacterium-like
AB  - strains isolated from the Great Artesian Basin of Australia.  The restriction endonuclease
AB  - from F. gondwanense AB39T was partially purified and designated FgoI.  FgoI recognized a 4
AB  - nucleotide sequence 5'-CTAG-3' and cleaved between nucleotides C and T to produce a 2 base
AB  - 5' overhang (5'C/TAG-3').  As predicted from the enzyme recognition and cleavage
AB  - specificity, FgoI was found to cleave phage DNA 13 times, phiX174 three times, pBR322 five
AB  - times, pUC18 four times, and pSK six times.  FgoI exhibited a broad temperature optimum range
AB  - (between 60 to 70oC) and was active at pH 6.5 to 8.5, but not at pH 9.0.  Manganese could
AB  - replace magnesium as a cofactor for activity, but not cobalt chloride, calcium chloride,
AB  - cupric chloride, or zinc chloride.  The restriction endonuclease was completely inactivated by
AB  - phenol/chloroform extraction and was heat inactivated at 80 C for 60 min or at 100 C for 15
AB  - min.  FgoI has been identified as a heat stable isoschizomer of the Type II restriction
AB  - endonucleases, MaeI and BfaI.
ER  -

TY  - JOUR
AU  - Andriashvili, I.A.
AU  - Kvachadze, L.I.
AU  - Vashakidze, R.P.
AU  - Adamiya, R.S.
AU  - Chanishvili, T.G.
TI  - Molecular mechanism of the protection of phage DNA from restriction endonuclease of Staphylococcus aureus cells.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1986
SP  - 43
EP  - 45
VL  - 0
AB  - A representative of the group of virulent staphylococcal bacteriophages Sb-I is
AB  - not limited by the systems of host specificity of DNA in reproduction in
AB  - Staphylococcus aureus cells.  It was also shown that the DNA of this phage is
AB  - not subjected to fragmentation by Sau3A and other restriction endonucleases
AB  - specific for the GATC site.  By restriction analysis of cloned fragments of
AB  - phage DNA in the plasmid pBR322, replicated in E. coli HB101, it was
AB  - established that virus-specific protection is determined by the absence of a
AB  - GATC site in the phage genome.  The evolutionary nature of the elimination of
AB  - the recognition site in the DNA of virulent staphylophages as a method of
AB  - protection from the main type of restriction of the phage DNA in S. aureus
AB  - cells is discussed.
ER  -

TY  - JOUR
AU  - Andrievskaia, O.
AU  - Duceppe, M.O.
AU  - Lloyd, D.
TI  - Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada.
JO  - Genome Announcements
PY  - 2018
SP  - e00258
EP  - e00218
VL  - 6
AB  - Mycobacterium bovis is the causative agent of bovine tuberculosis, an infectious  disease that
AB  - affects both animals and humans and thus presents a risk to public
AB  - health and the livestock industry. Here, we report the genome sequences of five
AB  - Mycobacterium bovis strains that represent major genotype clusters observed in
AB  - farmed animals and wildlife in Canada.
ER  -

TY  - JOUR
AU  - Andryuschenko, S.V.
AU  - Zdvizhkova, I.A.
AU  - Perunova, N.B.
AU  - Bukharin, O.V.
TI  - Draft Genome Sequence of Klebsiella pneumoniae Strain ICIS-278_PBV, Isolated from the Feces of a Healthy 59-Year-Old Man from Orenburg, Russia.
JO  - Genome Announcements
PY  - 2018
SP  - e00576
EP  - e00518
VL  - 6
AB  - This report describes the draft genome sequence of Klebsiella pneumoniae strain ICIS-278_PBV,
AB  - isolated from the feces of a healthy 59-year-old man from Orenburg,
AB  - Russia. The size of the genome was 5,584,615 bp (57.2% G+C content). Annotation
AB  - revealed 5,302 coding sequences, including 5,254 proteins, 23 rRNA genes, and 81
AB  - tRNA genes.
ER  -

TY  - JOUR
AU  - Ang, M.Y.
AU  - Dymock, D.
AU  - Tan, J.L.
AU  - Thong, M.H.
AU  - Tan, Q.K.
AU  - Wong, G.J.
AU  - Paterson, I.C.
AU  - Choo, S.W.
TI  - Genome Sequence of Parvimonas micra Strain A293, Isolated from an Abdominal Abscess from a Patient in the United Kingdom.
JO  - Genome Announcements
PY  - 2013
SP  - e01025
EP  - e01013
VL  - 1
AB  - Parvimonas micra is an important oral microbe that has the ability to grow and proliferate
AB  - within oral biofilms and is involved in periodontal disease, leading
AB  - to gingival bleeding, gingival recession, alveolar bone loss, and tooth mobility.
AB  - However, occasionally these normally oral pathogens can cause infections at other
AB  - sites in the body. We present the genome sequence of Parvimonas micra strain
AB  - A293, a smooth Parvimonas micra strain isolated from an abdominal abscess from a
AB  - patient at Barts Hospital, London, United Kingdom.
ER  -

TY  - JOUR
AU  - Ang, M.Y.
AU  - Dymock, D.
AU  - Tan, J.L.
AU  - Thong, M.H.
AU  - Tan, Q.K.
AU  - Wong, G.J.
AU  - Paterson, I.C.
AU  - Choo, S.W.
TI  - Genome Sequence of Fusobacterium nucleatum Strain W1481, a Possible New Subspecies Isolated from a Periodontal Pocket.
JO  - Genome Announcements
PY  - 2014
SP  - e00009
EP  - e00014
VL  - 2
AB  - Fusobacterium nucleatum is a bacterial species commonly detected in dental plaque within the
AB  - human oral cavity, with some strains associated with periodontal
AB  - disease, one of the most common clinical bacterial infections in the human body.
AB  - The exact mechanisms of its pathogenesis are still not completely understood. In
AB  - this study, we present the genome sequence and annotation of F. nucleatum strain
AB  - W1481, isolated from a periodontal pocket of a dental patient at the University
AB  - of Bristol, United Kingdom, the 16S rRNA gene sequencing of which showed it to be
AB  - markedly different from the five previously named subspecies.
ER  -

TY  - JOUR
AU  - Angelakis, E.
AU  - Bibi, F.
AU  - Ramasamy, D.
AU  - Azhar, E.I.
AU  - Jiman-Fatani, A.A.
AU  - Aboushoushah, S.M.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Caputo, A.
AU  - Yasir, M.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 8
EP  - 8
VL  - 9
AB  - Clostridium saudii strain JCC(T) sp. nov. is the type strain of C. saudii sp. nov., a new
AB  - species within the genus Clostridia. This strain, whose genome is
AB  - described here, was isolated from a fecal sample collected from an obese
AB  - 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C.
AB  - saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of
AB  - this organism, together with the complete genome sequence and annotation. The
AB  - 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes,
AB  - including 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Angelov, A.
AU  - Liebl, S.
AU  - Ballschmiter, M.
AU  - Bomeke, M.
AU  - Lehmann, R.
AU  - Liesegang, H.
AU  - Daniel, R.
AU  - Liebl, W.
TI  - Genome Sequence of the Polysaccharide-Degrading, Thermophilic Anaerobe Spirochaeta thermophila DSM 6192.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6492
EP  - 6493
VL  - 192
AB  - Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade
AB  - various alpha- and beta-linked sugar polymers, including
AB  - cellulose. We report here the complete genome sequence of S. thermophila
AB  - DSM 6192, which is the first genome sequence of a thermophilic,
AB  - free-living member of the Spirochaetes phylum. The genome data reveal a
AB  - high density of genes encoding enzymes from more than 30 glycoside
AB  - hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose
AB  - degradation, and indicate the presence of a novel carbohydrate-binding
AB  - module.
ER  -

TY  - JOUR
AU  - Angelov, A.
AU  - Voss, J.
AU  - Liebl, W.
TI  - Characterization of Plasmid pPO1 from the Hyperacidophile Picrophilus oshimae.
JO  - Archaea
PY  - 2011
SP  - 723604
EP  - 723604
VL  - 0
AB  - Picrophilus oshimae and Picrophilus torridus are free-living, moderately thermophilic and
AB  - acidophilic organisms from the lineage of
AB  - Euryarchaeota. With a pH optimum of growth at pH 0.7 and the ability to
AB  - even withstand molar concentrations of sulphuric acid, these organisms
AB  - represent the most extreme acidophiles known. So far, nothing is known
AB  - about plasmid biology in these hyperacidophiles. Also, there are no
AB  - genetic tools available for this genus. We have mobilized the 7.6 Kbp
AB  - plasmid from P. oshimae in E. coli by introducing origin-containing
AB  - transposons and described the plasmid in terms of its nucleotide
AB  - sequence, copy number in the native host, mode of replication, and
AB  - transcriptional start sites of the encoded ORFs. Plasmid pPO1 may
AB  - encode a restriction/modification system in addition to its replication
AB  - functions. The information gained from the pPO1 plasmid may prove
AB  - useful in developing a cloning system for this group of extreme
AB  - acidophiles.
ER  -

TY  - JOUR
AU  - Anglana, M.
AU  - Bacchetti, S.
TI  - Construction of a recombinant adenovirus for efficient delivery of the I-SceI yeast endonuclease to human cells and its application in the in vivo cleavage of chromosomes to expose new potential telomeres.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 4276
EP  - 4281
VL  - 27
AB  - We have constructed a replication-defective adenovirus vector encoding the yeast I- SceI
AB  - endonuclease under the control of the murine cytomegalovirus immediate-early gene promoter
AB  - (AdM SceI) for efficient delivery of this enzyme to mammalian cells.  We present evidence of
AB  - AdM SceI-mediated I-Sce I protein expression and cleavage activity in replication-permissive
AB  - 293 cells, and of cleavage of chromosomes in vivo in both 293 cells and in non-permissive
AB  - human cells. We have exploited this system for the generation of chromosomes capped by
AB  - artificial telomeric sequences in cells with integrated plasmids containing telomeric DNA
AB  - arrays adjacent to an I-SceI recognition site. The properties of the AdM SceI virus described
AB  - here make it a useful tool for studying biological processes involving induction of DNA
AB  - breaks, recombination and gene targeting in cells grown in culture and in vivo.
ER  -

TY  - JOUR
AU  - Aniello, F.
AU  - Locascio, A.
AU  - Fucci, L.
AU  - Geraci, G.
AU  - Branno, M.
TI  - Isolation of cDNA clones encoding DNA methyltransferase of sea urchin P. lividus: expression during embryonic development.
JO  - Gene
PY  - 1996
SP  - 57
EP  - 61
VL  - 178
AB  - A full-length cDNA, encoding a DNA (cytosine-5)-methyltransferase has been assembled from a
AB  - series of overlapping cDNA clones isolated from P. lividus sea urchin embryo cDNA libraries.
AB  - The cDNA contains 103 bp 5'-UTR, 4839 bp open reading frame corresponding to a 1612 amino
AB  - acids protein and 2240 bp 3'-UTR including a terminal 18-bp poly(A) tail.  Both the cDNA and
AB  - the encoded protein are the longest so far reported for DNA Mtases.  The protein shows five
AB  - distinct and sequential regions of identity with the other animal DNA Mtases, with values of
AB  - identity from zero to 80%.  Northern blot analyses reveal a single RNA band of about 7.5 kb in
AB  - length showing a highly regulated concentration pattern during development with peak value at
AB  - the four blastomere stage.
ER  -

TY  - JOUR
AU  - Aniello, F.
AU  - Villano, G.
AU  - Corrado, M.
AU  - Locascio, A.
AU  - Russo, M.T.
AU  - D'Aniello, S.D.
AU  - Francone, M.
AU  - Fucci, L.
AU  - Branno, M.
TI  - Structural organization of the sea urchin DNA (cytosine-5)-methyltransferase gene and characterization of five alternative spliced transcripts.
JO  - Gene
PY  - 2003
SP  - 1
EP  - 9
VL  - 302
AB  - Sea urchin DNA (cytosine-5)-methyltransferase (Dnmt1) that is responsible for maintenance of
AB  - DNA methylation patterns clearly shares similarity with
AB  - various Dnmt1s identified in vertebrates. In this study, we determined the
AB  - structure of the sea urchin Dnmt1 gene by screening a genomic library of
AB  - the sea urchin Paracentrotus lividus with the complementary DNA (cDNA) as
AB  - probe. Analysis of the positive clones demonstrated that the Dnmt1 gene
AB  - consists of 34 exons and 33 introns spanning a distance of 35 kb. All
AB  - exon-intron junction sequences agree with the GT/AG consensus with the
AB  - exception of the 3' acceptor site of intron 8 where CT replaces AG
AB  - consensus.The differences in the total number of exons between sea urchin
AB  - and mouse genes reside mainly in the N-terminal region of the protein
AB  - (exons 5-7 of the sea urchin, exons 5-12 of the mouse) where there is very
AB  - low similarity in the amino acid sequence.By reverse
AB  - transcription-polymerase chain reaction using oligonucleotides spanning
AB  - different regions of the cDNA we carried out a comprehensive analysis of
AB  - alternative splicing of the Dnmt1 messenger RNA (mRNA) in sea urchin
AB  - embryos at different stages of development. We demonstrated the presence
AB  - of at least five alternative spliced mRNAs that are regulated during
AB  - development and are translated in truncated or deleted proteins.
ER  -

TY  - JOUR
AU  - Anjum, A.
AU  - Brathwaite, K.J.
AU  - Aidley, J.
AU  - Connerton, P.L.
AU  - Cummings, N.J.
AU  - Parkhill, J.
AU  - Connerton, I.
AU  - Bayliss, C.D.
TI  - Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni  strain NCTC11168.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 4581
EP  - 4594
VL  - 44
AB  - Phase-variable restriction-modification systems are a feature of a diverse range  of bacterial
AB  - species. Stochastic, reversible switches in expression of the
AB  - methyltransferase produces variation in methylation of specific sequences.
AB  - Phase-variable methylation by both Type I and Type III methyltransferases is
AB  - associated with altered gene expression and phenotypic variation. One
AB  - phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual
AB  - Type IIG restriction-modification system in which the endonuclease and
AB  - methyltransferase are encoded by a single gene. Using both inhibition of
AB  - restriction and PacBio-derived methylome analyses of mutants and phase-variants,
AB  - the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically
AB  - methylate adenine in 5'CCCGA and 5'CCTGA sequences. Alterations in the levels of
AB  - specific transcripts were detected using RNA-Seq in phase-variants and mutants of
AB  - cj0031c but these changes did not correlate with observed differences in
AB  - phenotypic behaviour. Alterations in restriction of phage growth were also
AB  - associated with phase variation (PV) of cj0031c and correlated with presence of
AB  - sites in the genomes of these phages. We conclude that PV of a Type IIG
AB  - restriction-modification system causes changes in site-specific methylation
AB  - patterns and gene expression patterns that may indirectly change adaptive traits.
ER  -

TY  - JOUR
AU  - Ankrah, N.Y.
AU  - Lane, T.
AU  - Budinoff, C.R.
AU  - Hadden, M.K.
AU  - Buchan, A.
TI  - Draft Genome Sequence of Sulfitobacter sp. CB2047, a Member of the Roseobacter Clade of Marine Bacteria, Isolated from an Emiliania huxleyi Bloom.
JO  - Genome Announcements
PY  - 2014
SP  - e01125
EP  - e01114
VL  - 2
AB  - We announce the draft genome sequence of Sulfitobacter sp. strain CB2047, a marine bacterium
AB  - of the Roseobacter clade, isolated from a phytoplankton bloom.
AB  - The genome encodes pathways for the catabolism of aromatic compounds as well as
AB  - transformations of carbon monoxide and sulfur species. The strain also encodes a
AB  - prophage as well as the gene transfer agent (GTA), both of which are prevalent
AB  - among members of the Rhodobacterales order.
ER  -

TY  - JOUR
AU  - Ankri, S.
AU  - Reyes, O.
AU  - Leblon, G.
TI  - Improved electro-transformation of highly DNA-restrictive corynebacteria with DNA extracted from starved Escherichia coli.
JO  - FEMS Microbiol. Lett.
PY  - 1996
SP  - 247
EP  - 251
VL  - 140
AB  - Differences of up to 33,000-fold in electro-transformability of highly DNA restrictive
AB  - corynebacteria are observed in the DNA of a shuttle plasmid extracted from Escherichia coli
AB  - hosts propagated in different nutritional conditions.  Growth of the host in minimal medium
AB  - increases plasmid transformability is reverted by supplementing with methionine, an obligate
AB  - S-adenosyl-methionine (SAM) precursor.  This suggests that an E. coli nutritionally modulated
AB  - SAM-dependent DNA-methyltransferase may be involved in this phenomenon.
ER  -

TY  - JOUR
AU  - Annapurna, K.
AU  - Govindasamy, V.
AU  - Sharma, M.
AU  - Rajrana, Y.
AU  - Swarnalakshmi, K.
AU  - Paul, S.
AU  - Ghosh, A.
AU  - Chikara, S.K.
TI  - Draft Genome Sequence of Pseudomonas stutzeri Strain KMS 55, an Endophytic Diazotroph Isolated from Rice Roots.
JO  - Genome Announcements
PY  - 2017
SP  - e00972
EP  - e00917
VL  - 5
AB  - Pseudomonas stutzeri strain KMS 55 (MTCC 12703) is an isolate from the root tissues of rice
AB  - (Oryza sativa L.) that displays a high biological nitrogen
AB  - fixation ability. Here, we report the complete genome sequence of this strain,
AB  - which contains 4,637,820 bp, 4,289 protein-coding genes, 5,006 promoter
AB  - sequences, 62 tRNAs, a single copy of 5S-16S-23S rRNA, and a genome average GC
AB  - content of 51.18%. Analysis of the ~4.64-Mb genome sequence will give support to
AB  - increased understanding of the genetic determinants of host range, endophytic
AB  - colonization behavior, endophytic nitrogen fixation, and other plant-beneficial
AB  - roles of Pseudomonas stutzeri.
ER  -

TY  - JOUR
AU  - Anselmo, A.
AU  - Buttinelli, G.
AU  - Ciammaruconi, A.
AU  - Midulla, F.
AU  - Nicolai, A.
AU  - Fortunato, A.
AU  - Palozzi, A.
AU  - Fillo, S.
AU  - Lista, F.
AU  - Stefanelli, P.
TI  - Draft Genome Sequence of a Bordetella pertussis Strain with the Virulence-Associated Allelic Variant ptxP3, Isolated in Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00944
EP  - e00915
VL  - 3
AB  - Despite a universal immunization program, pertussis has persisted and resurged, and is of
AB  - particular concern for infants in terms of morbidity and mortality. Here, we report the genome
AB  - sequence of a Bordetella pertussis strain with the virulence-associated allelic variant ptxP3,
AB  - isolated from a 45-day-old infant.
ER  -

TY  - JOUR
AU  - Anselmo, A.
AU  - Ciammaruconi, A.
AU  - Carannante, A.
AU  - Neri, A.
AU  - Fazio, C.
AU  - Fortunato, A.
AU  - Palozzi, A.M.
AU  - Vacca, P.
AU  - Fillo, S.
AU  - Lista, F.
AU  - Stefanelli, P.
TI  - Draft Genome Sequence of Neisseria gonorrhoeae Sequence Type 1407, a Multidrug-Resistant Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00903
EP  - e00915
VL  - 3
AB  - Gonorrhea may become untreatable due to the spread of resistant or multidrug-resistant
AB  - strains. Cefixime-resistant gonococci belonging to sequence
AB  - type 1407 have been described worldwide. We report the genome sequence of
AB  - Neisseria gonorrhoeae strain G2891, a multidrug-resistant isolate of sequence
AB  - type 1407, collected in Italy in 2013.
ER  -

TY  - JOUR
AU  - Anton, B.P.
TI  - Phylogenomic analysis of Escherichia coli methyltransferases and characterization of a novel subfamily of enzymes performing methyl transfer.
JO  - Ph.D. Thesis, Boston University
PY  - 2011
SP  - 1
EP  - 271
AB  - Methyltransferases, which catalyze the transfer of a methyl group from the donor
AB  - S-adenosyl-L-methionine to a substrate molecule, are an ancient superfamily of enzymes
AB  - comprising significant sequence and structural diversity.  They are involved with nearly every
AB  - conceivable biological process, having evolved to perform this same biochemical reaction on a
AB  - wide variety of substrates including DNA, RNA, proteins, lipids, and small molecules.
AB  - Identifying sequence-structure-function relationships within this superfamily presents
AB  - considerable challenges, and this thesis comprises several computational and experimental
AB  - projects directed towards that end.  We examined different types of prokaryotic
AB  - methyltransferases by phylogenetic profiling and comparative genomic approaches, finding that
AB  - those involved with translation exhibit relatively low rates of gene loss and horizontal
AB  - exchange.  DNA methyltransferases, by contrast, undergo frequent horizontal exchange and are
AB  - not vertically inherited for long periods of time.  We found the model organism Escherichia
AB  - coli K-12 encodes a total of 48 known and 14 probable methyltransferases, and we mined the
AB  - literature to identify methylation activities for which the enzyme responsible was unknown.
AB  - Careful comparison of these two data sets enabled predictions of the activities of many of the
AB  - uncharacterized methyltransferases. We validated one of these predictions by mass
AB  - spectrometry, showing that the yliG gene product (renamed RimO) modifies a universally
AB  - conserved aspartic acid residue in ribosomal protein S12.  This modification (-SCH3 addition)
AB  - involves a radical-SAM mediated sulfur insertion as well as a methylation reaction.  RimO thus
AB  - belongs to a unique methyltransferase subfamily called methylthiotransferases (MTTases), and
AB  - we showed phylogenetically that MTTases comprise four subclades, of which RimO orthologs form
AB  - one.  We predicted substrates for the two remaining uncharacterized subclades and validated
AB  - one of these predictions, showing that YqeV of B. subtilis methylthiolates specific tRNA
AB  - adenosine residues. Despite acting on different substrates (protein vs. tRNA), all found
AB  - MTTase subclades share a surprisingly high degree of sequence similarity in the predicted
AB  - substrate-binding region.  We used this similarity to computationally identify candidate
AB  - residues involved with substrate specificity.  These proteins exhibit a novel protein fold
AB  - compared to other methyltransferases, and we present preliminary biochemical results that shed
AB  - light on the nature of the methylation reaction carried out by RimO.
ER  -

TY  - JOUR
AU  - Anton, B.P.
AU  - Fomenkov, A.
AU  - Raleigh, E.A.
AU  - Berkmen, M.
TI  - Complete Genome Sequence of the Engineered Escherichia coli SHuffle Strains and Their Wild-Type Parents.
JO  - Genome Announcements
PY  - 2016
SP  - e00230
EP  - e00216
VL  - 4
AB  - SHuffle strains are genetically engineeredEscherichia colistrains that are capable of
AB  - oxidizing cysteines within proteins to form disulfide bonds. Here we
AB  - present the complete genome of both the K-12 and B versions of SHuffle strains
AB  - along with their parental ancestors. These strains have been of significant use
AB  - to both the general scientific community and the biotech industry, interested in
AB  - producing novel disulfide-bonded proteins that were hitherto unable to be
AB  - expressed in standardE. coliexpression strains.
ER  -

TY  - JOUR
AU  - Anton, B.P.
AU  - Harhay, G.P.
AU  - Smith, T.P.
AU  - Blom, J.
AU  - Roberts, R.J.
TI  - Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi.
JO  - PLoS ONE
PY  - 2016
SP  - e0161499
EP  - e0161499
VL  - 11
AB  - We examined and compared both the methylomes and the modification-related gene content of four
AB  - sequenced strains of Bibersteinia trehalosi isolated from the
AB  - nasopharyngeal tracts of Nebraska cattle with symptoms of bovine respiratory
AB  - disease complex. The methylation patterns and the encoded DNA methyltransferase
AB  - (MTase) gene sets were different between each strain, with the only common
AB  - pattern being that of Dam (GATC). Among the observed patterns were three novel
AB  - motifs attributable to Type I restriction-modification systems. In some cases the
AB  - differences in methylation patterns corresponded to the gain or loss of MTase
AB  - genes, or to recombination at target recognition domains that resulted in changes
AB  - of enzyme specificity. However, in other cases the differences could be
AB  - attributed to differential expression of the same MTase gene across strains. The
AB  - most obvious regulatory mechanism responsible for these differences was slipped
AB  - strand mispairing within short sequence repeat regions. The combined action of
AB  - these evolutionary forces allows for alteration of different parts of the
AB  - methylome at different time scales. We hypothesize that pleiotropic
AB  - transcriptional modulation resulting from the observed methylomic changes may be
AB  - involved with the switch between the commensal and pathogenic states of this
AB  - common member of ruminant microflora.
ER  -

TY  - JOUR
AU  - Anton, B.P.
AU  - Heiter, D.F.
AU  - Benner, J.S.
AU  - Hess, E.J.
AU  - Greenough, L.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Brooks, J.E.
TI  - Cloning and characterization of the BglII restriction-modification system reveals a possible evolutionary footprint.
JO  - Gene
PY  - 1997
SP  - 19
EP  - 27
VL  - 187
AB  - BglII, a type II restriction-modification (R-M) system from Bacillus globigii, recognizes the
AB  - sequence 5'-AGATCT-3'.  The system has been cloned into E. coli in multiple steps: first the
AB  - methyltransferase (Mtase) gene, bglIIM, was cloned from B. globigii RUB561, a variant
AB  - containing an inactivated endonuclease (Enase) gene (bglIIR).  Next the ENase protein (R.
AB  - BglII) was purified to  homogeneity from RUB562, a strain expressing the complete R-M system.
AB  - Oligonucleotide probes specific for the 5' end of the gene were then synthesized and used to
AB  - locate bglIIR, and the gene was isolated and cloned in a subsequent step.  The nucleotide
AB  - sequence of the system has been determined, and several interesting features have been found.
AB  - The genes are tandemly arranged, with bglIIR preceding bglIIM.  The amino acid sequence of
AB  - M.BglII is compared to those of other known MTases.  A third gene encoding a protein with
AB  - sequence similarity to known C elements of other R-M sysems is found upstream of bglIIR.  This
AB  - is the first instance of a C gene being associated with an R-M system where the R and M genes
AB  - are collinear.  In addition, open reading frames (ORFs) resembling genes involved with DNA
AB  - mobility are found in close association with BglII.  These may shed light on the evolution of
AB  - the R-M system.
ER  -

TY  - JOUR
AU  - Anton, B.P.
AU  - Mongodin, E.F.
AU  - Agrawal, S.
AU  - Fomenkov, A.
AU  - Byrd, D.R.
AU  - Roberts, R.J.
AU  - Raleigh, E.A.
TI  - Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.
JO  - PLoS ONE
PY  - 2015
SP  - E0127446
EP  - E0127446
VL  - 10
AB  - We report the complete sequence of ER2796, a laboratory strain of Escherichia
AB  - coli K-12 that is completely defective in DNA methylation. Because of its lack of
AB  - any native methylation, it is extremely useful as a host into which heterologous
AB  - DNA methyltransferase genes can be cloned and the recognition sequences of their
AB  - products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT)
AB  - sequencing. The genome was itself sequenced from a long-insert library using the
AB  - SMRT platform, resulting in a single closed contig devoid of methylated bases.
AB  - Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows
AB  - an essentially co-linear relationship with no major rearrangements despite many
AB  - generations of laboratory manipulation. The comparison revealed a total of 41
AB  - insertions and deletions, and 228 single base pair substitutions. In addition,
AB  - the long-read approach facilitated the surprising discovery of four gene
AB  - conversion events, three involving rRNA operons and one between two cryptic
AB  - prophages. Such events thus contribute both to genomic homogenization and to
AB  - bacteriophage diversification. As one of relatively few laboratory strains of E.
AB  - coli to be sequenced, the genome also reveals the sequence changes underlying a
AB  - number of classical mutant alleles including those affecting the various native
AB  - DNA methylation systems.
ER  -

TY  - JOUR
AU  - Anton, B.P.
AU  - Raleigh, E.A.
TI  - Complete Genome Sequence of NEB 5-alpha, a Derivative of Escherichia coli K-12 DH5alpha.
JO  - Genome Announcements
PY  - 2016
SP  - e01245
EP  - e01216
VL  - 4
AB  - Escherichia coli K-12 DH5alpha is one of the most popular and widely available laboratory
AB  - strains, but, surprisingly, no complete genome sequence has been
AB  - publicly available. Here, we report the complete, finished sequence of NEB
AB  - 5-alpha (DH5alpha fhuA2). It should serve as a useful reference for researchers
AB  - working with DH5alpha.
ER  -

TY  - JOUR
AU  - Anton, B.P.
AU  - Raleigh, E.A.
TI  - Transposon-mediated linker insertion scanning mutagenesis of the Escherichia coli McrA endonuclease.
JO  - J. Bacteriol.
PY  - 2004
SP  - 5699
EP  - 5707
VL  - 186
AB  - McrA is one of three functions that restrict modified foreign DNA in Escherichia coli K-12,
AB  - affecting both methylated and hydroxymethylated
AB  - substrates. We present here the first systematic analysis of the
AB  - functional organization of McrA by using the GPS-LS insertion scanning
AB  - system. We collected in-frame insertions of five amino acids at 46
AB  - independent locations and C-terminal truncations at 20 independent
AB  - locations in the McrA protein. Each mutant was assayed for in vivo
AB  - restriction of both methylated and hydroxymethylated bacteriophage
AB  - (M.HpaII-modified lambda and T4gt, respectively) and for induction of the
AB  - E. coli SOS response in the presence of M.HpaII methylation, indicative of
AB  - DNA damage. Our findings suggest the presence of an N-terminal DNA-binding
AB  - domain and a C-terminal catalytic nuclease domain connected by a linker
AB  - region largely tolerant of amino acid insertions. DNA damage inflicted by
AB  - a functional C-terminal domain is required for restriction of phage T4gt.
AB  - Disruption of the N-terminal domain abolishes restriction of both
AB  - substrates. Surprisingly, truncation mutations that spare the N-terminal
AB  - domain do not mediate DNA damage, as measured by SOS induction, but
AB  - nevertheless partially restrict M.HpaII-modified lambda in vivo. We
AB  - suggest a common explanation for this "restriction without damage" and a
AB  - similar observation seen in vivo with McrB, a component of another of the
AB  - modified-DNA restriction functions. Briefly, we propose that unproductive
AB  - site-specific binding of the protein to a vulnerable position in the
AB  - lambda genome disrupts the phage development program at an early stage. We
AB  - also identified a single mutant, carrying an insertion in the N-terminal
AB  - domain, which could fully restrict lambda but did not restrict T4gt at
AB  - all. This mutant may have a selective impairment in substrate recognition,
AB  - distinguishing methylated from hydroxymethylated substrates. The study
AB  - shows that the technically easy insertion scanning method can provide a
AB  - rich source of functional information when coupled with effective
AB  - phenotype tests.
ER  -

TY  - JOUR
AU  - Antonenko, V.
AU  - Pawlow, V.
AU  - Heesemann, J.
AU  - Rakin, A.
TI  - Characterization of a novel unique restriction-modification system from Yersinia enterocolitica O:8 1B.
JO  - FEMS Microbiol. Lett.
PY  - 2003
SP  - 249
EP  - 252
VL  - 219
AB  - Genetic manipulations with enteropathogenic Yersinia enterocolitica O:8 are complicated by the
AB  - presence of an efficient PstI-like YenI
AB  - restriction-modification (R-M) system. We have characterized the YenI R-M
AB  - system in Y. enterocolitica O:8, biotype 1B. A 5039 bp DNA fragment of the
AB  - pSAK2 recombinant plasmid carrying the yenI locus was used to determine
AB  - the nucleotide sequence. DNA sequence analysis identified a single 2481 bp
AB  - open reading frame (ORF) that encodes an 826 amino acid large polypeptide
AB  - having an apparent molecular mass of 93 kDa. The N-terminal part of the
AB  - YenI ORF has 45 and 40% identity to PstI and BsuI methyltransferases
AB  - (MTases), respectively; while the C-terminal part depicts 55 and 45%
AB  - identity to endonucleases (ENases) of both isoschyzomeric enzymes. The
AB  - yenI gene was cloned into pT7-5 plasmid and has been shown to encode a
AB  - single polypeptide of expected molecular mass. A specific recognition
AB  - sequence, typical to the type II R-M systems and single peptide
AB  - organization, typical to type IV R-M systems, make YenI unique among known
AB  - restriction-modification systems. We have constructed a truncated
AB  - recombinant variant of YenI enzyme, which conserved only MTase activity,
AB  - and that can be applied to YenI methylation of the DNA to be transformed
AB  - into Y. enterocolitica O:8 biotype 1B strains.
ER  -

TY  - JOUR
AU  - Antonopoulos, D.A.
AU  - Nelson, K.E.
AU  - Morrison, M.
AU  - White, B.A.
TI  - Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization.
JO  - Environ. Microbiol.
PY  - 2004
SP  - 335
EP  - 346
VL  - 6
AB  - Two closely related strains of the Gram-positive, cellulolytic ruminal
AB  - bacterium Ruminococcus flavefaciens were compared at the genomic level by
AB  - suppressive subtractive hybridization. The two strains investigated in
AB  - this study differ by 1.94% in their respective 16S rDNA genes. Three
AB  - hundred and eighty-four PCR-amplified products were cloned and then
AB  - screened for their strain identity by dot blot hybridization. Based on
AB  - redundancy percentages of the clones sequenced, 9.5% of the genome of the
AB  - R. flavefaciens FD-1 strain is not present in the JM1 strain. The majority
AB  - of identities of individual cloned subtracted products (642 bp average
AB  - length) bore no relation to deposited sequences in GenBank (42% of the
AB  - subtracted library), whereas of those with putative assigned functions 7%
AB  - are loosely associated with fibre-degradation, 6% with insertion elements,
AB  - transposons and phage-like ORFs, 5% with cell membrane associated proteins
AB  - and 3% with signal transduction. Subtracted sequences were then
AB  - supplemented with the draft (2 x coverage) genome sequence of R.
AB  - flavefaciens FD-1 to indicate potential regions of rearrangement within
AB  - the genome, including a novel insertion sequence.
ER  -

TY  - JOUR
AU  - Antoshkina, N.V.
AU  - Vorob'eva, L.I.
AU  - Bur'ianov, Ia.I.
TI  - [Methylcobalamin-dependent enzymatic methylation of DNA in a cell-free extract of Propionibacterium shermanii].
JO  - Mikrobiologiia
PY  - 1981
SP  - 631
EP  - 635
VL  - 50
AB  - The regulation of the functional activity of Propionibacterium shermanii cells by cobalamin is
AB  - accompanied by an increase in the methylation of their DNA at the
AB  - cytosine residue: the DNA from B12-deficient cells is undermethylated as compared
AB  - with the DNA from control cells, i. e. cells synthesizing corrinoids. The results
AB  - of in vitro experiments make it possible to correlate this phenomenon with the
AB  - capability of DNA methylases from B12-deficient and control cells to function
AB  - with different donors of methyl groups. Just as the enzymes methylating adenine
AB  - and cytosine in B12-deficient cells, adenine DNA methylase from cells
AB  - synthesizing corrinoids is active in vitro with S-adenosylmethionine. Cytosine
AB  - DNA methylase from P. shermanii control cells is inactive with
AB  - S-adenosylmethionine and transfers methyl groups only in the presence of
AB  - cobalamins.
ER  -

TY  - JOUR
AU  - Antoshkina, N.V.
AU  - Vorob'eva, L.I.
AU  - Iordan, E.P.
TI  - [Participation of methylcobalamin in the methylation of Propionibacterium shermanii DNA].
JO  - Mikrobiologiia
PY  - 1979
SP  - 217
EP  - 221
VL  - 48
AB  - Propionibacterium shermanii is characterized by a high content of 5-methylcytosine (5 MC). The
AB  - level of 5-MC in B12-deficient cells of the culture
AB  - is twice as low as in the control. The in vitro treatment of DNA isolated from
AB  - the B12-deficient cells with methyl-cobalamin in the presence of the extract of
AB  - control cells possessing the activity of DNA-methylase increases the content of
AB  - 5-MC to the control level. No additional methylation of DNA in vitro takes place
AB  - in the absence of the methylase system and in the presence of other forms of
AB  - corrynoids. The methylating activity is displayed either in the presence of
AB  - methionine or without it. The inhibitor of methylcobalamin, i.e.
AB  - diftorchlormethyl-cobalamin, blocks methylation of DNA. Small quantities of
AB  - S-adenosylmethionine are necessary for the reaction of methylation.
ER  -

TY  - JOUR
AU  - Antunes, A.
AU  - Alam, I.
AU  - Bajic, V.B.
AU  - Stingl, U.
TI  - Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the  Shaban Deep in the Red Sea.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4555
EP  - 4556
VL  - 193
AB  - We present the genome of Salinisphaera shabanensis isolated from a brine-seawater interface
AB  - and representing a new order within the
AB  - Gammaproteobacteria. Adaptations to physicochemical and nutrient
AB  - availability fluctuation include six genes encoding heavy metal
AB  - translocating P-type ATPases, multiple genes involved in iron-uptake,
AB  - siderophore production and poly-beta-hydroxybutyrate synthesis.
ER  -

TY  - JOUR
AU  - Antunes, A.
AU  - Alam, I.
AU  - Bajic, V.B.
AU  - Stingl, U.
TI  - Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4553
EP  - 4554
VL  - 193
AB  - We present the draft genome of Halorhabdus tiamatea, the first member of the Archaea ever
AB  - isolated from a deep-sea anoxic brine. Genome comparison
AB  - with H. utahensis, revealed some striking differences, including marked
AB  - increase in genes associated with trans-membrane transport, and putative
AB  - genes for a trehalose synthase and a lactate-dehydrogenase.
ER  -

TY  - JOUR
AU  - Antunes, A.
AU  - Alam, I.
AU  - El Dorry, H.
AU  - Siam, R.
AU  - Robertson, A.
AU  - Bajic, V.B.
AU  - Stingl, U.
TI  - Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4551
EP  - 4552
VL  - 193
AB  - We present the draft genome of Haloplasma contractile, isolated from a deep-sea brine and
AB  - representing a new order between Firmicutes and
AB  - Mollicutes. Its complex morphology with contractile protrusions might be
AB  - strongly influenced by the presence of seven MreB/Mbl homologs, which
AB  - appear to be the highest copy number ever reported.
ER  -

TY  - JOUR
AU  - Antwerpen, M.
AU  - Elschner, M.
AU  - Gaede, W.
AU  - Schliephake, A.
AU  - Grass, G.
AU  - Tomaso, H.
TI  - Genome Sequence of Bacillus anthracis Strain Stendal, Isolated from an Anthrax Outbreak in Cattle in Germany.
JO  - Genome Announcements
PY  - 2016
SP  - e00219
EP  - e00216
VL  - 4
AB  - In July 2012, an anthrax outbreak occurred among cattle in northern Germany resulting in ten
AB  - losses. Here, we report the draft genome sequence ofBacillus
AB  - anthracisstrain Stendal, isolated from one of the diseased cows.
ER  -

TY  - JOUR
AU  - Antwerpen, M.
AU  - Georgi, E.
AU  - Zimmermann, P.
AU  - Hoermansdorfer, S.
AU  - Meyer, H.
AU  - Grass, G.
TI  - Draft Genome Sequence of Strain BF-4, a Lysinibacillus-Like Bacillus Isolated during an Anthrax Outbreak in Bavaria.
JO  - Genome Announcements
PY  - 2014
SP  - e00918
EP  - e00914
VL  - 2
AB  - We report the draft genome sequence of Lysinibacillus sp. strain BF-4. Strain BF-4 has a
AB  - notably small genome for a free-living bacillus, with a size of 2.63
AB  - Mbp. In agreement with phenotypic observations, the genome lacks genes essential
AB  - for endospore formation.
ER  -

TY  - JOUR
AU  - Antwerpen, M.
AU  - Proenca, D.N.
AU  - Ruckert, C.
AU  - Licht, K.
AU  - Kalinowski, J.
AU  - Hanczaruk, M.
AU  - Tiemann, C.
AU  - Grass, G.
TI  - Draft Genome Sequence of Bacillus anthracis BF-1, Isolated from Bavarian Cattle.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6360
EP  - 6361
VL  - 194
AB  - Bacillus anthracis BF-1 was isolated from a cow in Bavaria (Germany) that had succumbed to
AB  - anthrax. Here, we report the draft genome sequence of this strain,
AB  - which belongs to the European B2 subclade of B. anthracis. The closest
AB  - phylogenetic neighbor of strain BF-1 is a strain isolated from cattle in France.
ER  -

TY  - JOUR
AU  - Antwerpen, M.
AU  - Wolfel, R.
AU  - Grass, G.
TI  - Genome Sequence of Historical Bacillus anthracis Strain Tyrol 4675 Isolated from  a Bovine Anthrax Case in Austria.
JO  - Genome Announcements
PY  - 2017
SP  - e00002
EP  - e00017
VL  - 5
AB  - In 1988, an outbreak of anthrax occurred among cattle in the Austrian state of Tyrol. Since
AB  - then, Austria has been declared anthrax-free. Here, we report the
AB  - draft genome sequence of one of these last outbreak strains, Bacillus anthracis
AB  - Tyrol 4675, isolated from a diseased cow.
ER  -

TY  - JOUR
AU  - Antwerpen, M.H.
AU  - Schacht, E.
AU  - Kaysser, P.
AU  - Splettstoesser, W.D.
TI  - Complete Genome Sequence of a Francisella tularensis subsp. holarctica Strain from Germany Causing Lethal Infection in Common Marmosets.
JO  - Genome Announcements
PY  - 2013
SP  - e00135
EP  - e00112
VL  - 1
AB  - Here, we describe the genome sequence of the Francisella tularensis subsp. holarctica strain
AB  - F92, belonging to the Franco-Iberian subgroup. This strain
AB  - represents the first-time isolate of this subgroup in Germany and was obtained
AB  - from naturally infected marmosets.
ER  -

TY  - JOUR
AU  - Anvar, S.Y.
AU  - Frank, J.
AU  - Pol, A.
AU  - Schmitz, A.
AU  - Kraaijeveld, K.
AU  - den Dunnen, J.T.
AU  - Op den Camp, H.J.
TI  - The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.
JO  - BMC Genomics
PY  - 2014
SP  - 914
EP  - 914
VL  - 15
AB  - Background: Aerobic methanotrophs can grow in hostile volcanic environments and use methane as
AB  - their sole source of energy. The discovery of three verrucomicrobial Methylacidiphilum strains
AB  - has revealed diverse metabolic pathways used by these methanotrophs, including mechanisms
AB  - through which methane is oxidized. The basis of a complete understanding of these processes
AB  - and of how these bacteria evolved and are able to thrive in such extreme environments
AB  - partially resides in the complete characterization of their genome and its
AB  - architecture.Results: In this study, we present the complete genome sequence of
AB  - Methylacidiphilum fumariolicum SolV, obtained using Pacific Biosciences single-molecule
AB  - real-time (SMRT) sequencing technology. The genome assembles to a single 2.5 Mbp chromosome
AB  - with an average GC content of 41.5%. The genome contains 2,741 annotated genes and 314
AB  - functional subsystems including all key metabolic pathways that are associated with
AB  - Methylacidiphilum strains, including the CBB pathway for CO2 fixation. However, it does not
AB  - encode the serine cycle and ribulose monophosphate pathways for carbon fixation. Phylogenetic
AB  - analysis of the particulate methane mono-oxygenase operon separates the Methylacidiphilum
AB  - strains from other verrucomicrobial methanotrophs. RNA-Seq analysis of cell cultures growing
AB  - in three different conditions revealed the deregulation of two out of three pmoCAB operons. In
AB  - addition, genes involved in nitrogen fixation were upregulated in cell cultures growing in
AB  - nitrogen fixing conditions, indicating the presence of active nitrogenase. Characterization of
AB  - the global methylation state of M. fumariolicum SolV revealed methylation of adenines and
AB  - cytosines mainly in the coding regions of the genome. Methylation of adenines was
AB  - predominantly associated with 5'-(m6)ACN(4)GT-3' and 5'-CC(m6)AN(5)CTC-3'
AB  - methyltransferase recognition motifs whereas methylated cytosines were not associated with any
AB  - specific motif.Conclusions: Our findings provide novel insights into the global methylation
AB  - state of verrucomicrobial methanotroph M. fumariolicum SolV. However, partial conservation of
AB  - methyltransferases between M. fumariolicum SolV and M. infernorum V4 indicates potential
AB  - differences in the global methylation state of Methylacidiphilum strains. Unravelling the M.
AB  - fumariolicum SolV genome and its epigenetic regulation allow for robust characterization of
AB  - biological processes that are involved in oxidizing methane. In turn, they offer a better
AB  - understanding of the evolution, the underlying physiological and ecological properties of SolV
AB  - and other Methylacidiphilum strains.
ER  -

TY  - JOUR
AU  - Aoki, A.
AU  - Suetake, I.
AU  - Miyagawa, J.
AU  - Fujio, T.
AU  - Chijiwa, T.
AU  - Sasaki, H.
AU  - Tajima, S.
TI  - Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3506
EP  - 3512
VL  - 29
AB  - We have purified GST-fused recombinant mouse Dnmt3a and three isoforms of mouse Dnmt3b to near
AB  - homogeneity. Dnmt3b3, an isoform of Dnmt3b, did not have DNA methylation activity.  Dnmt3a,
AB  - Dnmt3b1 or Dnmt3b2 showed similar activity toward poly(dG-dC)-poly(dG-dC) for measuring de
AB  - novo methylation activity, and toward poly(dI-dC)-poly(dI-dC) for measuring total activity.
AB  - This indicates that the enzymes are de novo-type DNA methyltransferases. The enzyme activity
AB  - was inhibited by NaCl or KCl at concentrations >100 mM. The kinetic parameter, K(m)(AdoMet),
AB  - for Dnmt3a, Dnmt3b1 and Dnmt3b2 was 0.4, 1.2 and 0.9 microM when poly(dI-dC)-poly(dI-dC) was
AB  - used, and 0.3, 1.2 and 0.8 microM when poly(dG-dC)-poly(dG-dC) was used, respectively. The
AB  - K(m)(DNA) values for Dnmt3a, Dnmt3b1 and Dnmt3b2 were 2.7, 1.3 and 1.5 microM when
AB  - poly(dI-dC)-poly(dI-dC) was used, and 3.5, 1.0 and 0.9 microM when poly(dG-dC)-poly(dG-dC) was
AB  - used, respectively. For the methylation specificity, Dnmt3a significantly methylated CpG >>
AB  - CpA. On the other hand, Dnmt3b1 methylated CpG > CpT >/= CpA. Immuno-purified Dnmt3a,
AB  - Myc-tagged and overexpressed in HEK 293T cells, methylated CpG >> CpA > CpT. Neither Dnmt3a
AB  - nor Dnmt3b1 methylated the first cytosine of CpC.
ER  -

TY  - JOUR
AU  - Aoki, K.
AU  - Harada, S.
AU  - Yahara, K.
AU  - Ishii, Y.
AU  - Motooka, D.
AU  - Nakamura, S.
AU  - Akeda, Y.
AU  - Iida, T.
AU  - Tomono, K.
AU  - Iwata, S.
AU  - Moriya, K.
AU  - Tateda, K.
TI  - Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.
JO  - Antimicrob. Agents Chemother.
PY  - 2018
SP  - e02091
EP  - e02017
VL  - 62
AB  - Although KPC enzymes are most common among carbapenemases produced by
AB  - Enterobacter cloacae complex globally, the epidemiology varies from one country
AB  - to another. While previous studies have suggested that IMP enzymes are most
AB  - common in Japan, detailed analysis has been scarce thus far. Here, we carried out
AB  - a molecular epidemiological study and plasmid analysis of IMP-1-producing E.
AB  - cloacae complex isolates collected from three hospitals in central Tokyo using
AB  - whole-genome sequencing. Seventy-one isolates were classified into several
AB  - sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei
AB  - ST78. Isolates of ST78 were divided into three clades by core-genome single
AB  - nucleotide polymorphism (SNP)-based phylogenetic analysis. Whereas isolates of
AB  - clade 3 were isolated from only one hospital, isolates of clade 1 and 2 were
AB  - identified from multiple hospitals. Ten of 12 clade 1 isolates and 1 of 4 clade 2
AB  - isolates carried blaIMP-1 on IncHI2 plasmids, with high similarity of genetic
AB  - structures. In addition, these plasmids shared backbone structures with IncHI2
AB  - plasmids carrying blaIMP reported from other countries of the Asia-Pacific
AB  - region. All isolates of clade 3 except one carried blaIMP-1 in In1426 on IncW
AB  - plasmids. An isolate of clade 3, which lacked IncW plasmids, carried blaIMP-1 in
AB  - In1426 on an IncFIB plasmid. These observations suggest that IMP-producing E.
AB  - cloacae complex isolates with a diversity of host genomic backgrounds have spread
AB  - in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids
AB  - toward this phenomenon.
ER  -

TY  - JOUR
AU  - Aoki, T.
AU  - Teru, Y.
AU  - Morimoto, N.
AU  - Kono, T.
AU  - Sakai, M.
AU  - Takano, T.
AU  - Hawke, J.P.
AU  - Fukuda, Y.
AU  - Takeyama, H.
AU  - Hikima, J.I.
TI  - Complete Genome Sequence of Photobacterium damselae subsp. piscicida Strain OT-51443 Isolated from Yellowtail (Seriola quinqueradiata) in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e00404
EP  - e00417
VL  - 5
AB  - Pseudotuberculosis caused by infection of Photobacterium damselae subsp. piscicida has caused
AB  - serious economic damages to aquaculture farms worldwide.
AB  - Here, the whole-genome sequence of P. damselae subsp. piscicida strain OT-51443,
AB  - isolated in Japan, was determined and suggests that this genome consists of two
AB  - chromosomes and five plasmids.
ER  -

TY  - JOUR
AU  - Aoyagi, T.
AU  - Koike, H.
AU  - Morita, T.
AU  - Sato, Y.
AU  - Habe, H.
AU  - Hori, T.
TI  - Draft Genome Sequence of Geobacter pelophilus Strain Dfr2, a Ferric Iron-Reducing Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00537
EP  - e00517
VL  - 5
AB  - Here, we report a draft genome sequence of Geobacter pelophilus strain Dfr2, a ferric
AB  - iron-reducing bacterium. This genome information will further our
AB  - understanding of the mechanisms underlying electron transfer from microorganisms
AB  - to ferric iron oxides.
ER  -

TY  - JOUR
AU  - Aparicio, J.F.
AU  - Barbes, C.
AU  - Hardisson, C.
AU  - Sanchez, J.
TI  - Sensitivity to phages of Streptomyces coelicolor strains harbouring type II restriction endonucleases.
JO  - Microbiol. Sem.
PY  - 1990
SP  - 71
EP  - 75
VL  - 6
AB  - The role of type II restriction endonucleases in phage development in two
AB  - different strains of Streptomyces coelicolor has been analyzed.  Two of ten
AB  - phages tested (PhiA4 and R4c1) presented a low efficiency of plating (e.o.p.)
AB  - in the studied strains.  The isolation of host-range mutants of PhiA4 and R4c1,
AB  - with improved e.o.p. and higher adsorption capability in these two bacterial
AB  - strains, suggests that the presence of host endonucleases is not the main
AB  - barrier for these phages, but rather adsorption inability.
ER  -

TY  - JOUR
AU  - Arabyan, N.
AU  - Huang, B.C.
AU  - Weimer, B.C.
TI  - Amylases and Their Importance during Glycan Degradation: Genome Sequence Release  of Salmonella Amylase Knockout Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00355
EP  - e00317
VL  - 5
AB  - Amylases catalyze the cleavage of alpha-d-1,4 and alpha-d-1,6-glycosidic bonds in starch and
AB  - related carbohydrates. Amylases are widely distributed in nature and
AB  - are important in carbohydrate metabolism. This is the release of four single and
AB  - two double deletions in Salmonella enterica serovar Typhimurium LT2 that are
AB  - important for glycan degradation during infection.
ER  -

TY  - JOUR
AU  - Arabyan, N.
AU  - Huang, B.C.
AU  - Weimer, B.C.
TI  - Draft Genome Sequences of Salmonella Lysozyme Gene Knockout Mutants.
JO  - Genome Announcements
PY  - 2017
SP  - e00519
EP  - e00517
VL  - 5
AB  - Lysozyme enzymes hydrolyze the beta-1,4-glycosidic bond in oligosaccharides. These enzymes are
AB  - part of a broad group of glucoside hydrolases that are poorly
AB  - characterized; however, they are important for growth and are being recognized as
AB  - emerging virulence factors. This is the release of four
AB  - lysozyme-encoding-gene-deletion mutants in Salmonella enterica serovar
AB  - Typhimurium LT2.
ER  -

TY  - JOUR
AU  - Arabyan, N.
AU  - Huang, B.C.
AU  - Weimer, B.C.
TI  - Draft Genome Sequences of Salmonella enterica Serovar Typhimurium LT2 with Deleted Chitinases That Are Emerging Virulence Factors.
JO  - Genome Announcements
PY  - 2017
SP  - e00659
EP  - e00617
VL  - 5
AB  - Chitinases are glycosyl hydrolases that catalyze the hydrolysis of the beta-1,4 linkages in
AB  - complex carbohydrates and those that contain GlcNAc. These enzymes
AB  - are considered emerging virulence factors during infection because the host
AB  - glycan changes. This is the release of four single chitinase deletion mutants in
AB  - Salmonella enterica serovar Typhimurium LT2.
ER  -

TY  - JOUR
AU  - Arabyan, N.
AU  - Weis, A.M.
AU  - Huang, B.C.
AU  - Weimer, B.C.
TI  - Implication of Sialidases in Salmonella Infection: Genome Release of Sialidase Knockout Strains from Salmonella enterica Serovar Typhimurium LT2.
JO  - Genome Announcements
PY  - 2017
SP  - e00341
EP  - e00317
VL  - 5
AB  - Sialidases, which are widely distributed in nature, cleave the alpha-ketosidic bond of
AB  - terminal sialic acid residue. These emerging virulence factors degrade
AB  - the host glycan. We report here the release of seven sialidase and one sialic
AB  - acid transporter deletion in Salmonella enterica serovar Typhimurium strain LT2,
AB  - which are important in cellular invasion during infection.
ER  -

TY  - JOUR
AU  - Arahal, D.R.
AU  - Pujalte, M.J.
AU  - Rodrigo-Torres, L.
TI  - Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the  family Rhodobacteraceae.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 21
EP  - 21
VL  - 11
AB  - Nereida ignava strain 2SM4(T) (= CECT 5292(T) = DSM 16309(T) = CIP 108404(T) = CCUG 49433(T))
AB  - is a marine bacterium belonging to the Roseobacter group of the
AB  - family Rhodobacteraceae within the class Alphaproteobacteria. The strain was
AB  - isolated from sea water surrounding cultivated oysters 2-3 miles off the
AB  - Mediterranean coast near Valencia (Spain) and was phylogenetically related to
AB  - uncultured clones of gall symbiont bacteria of some species of Prionitis alga.
AB  - Here we describe the genome sequence and annotation of this organism, the type
AB  - strain of the single species of this genus. The genome comprised 2,888,349 bp,
AB  - 2,872 protein-coding genes and 52 RNA genes. The annotation revealed the capacity
AB  - to produce bacteriocins, vitamins and auxins. Besides, it contained sulfur
AB  - cycling related genes.
ER  -

TY  - JOUR
AU  - Arahal, D.R.
AU  - Rodrigo-Torres, L.
AU  - Lucena, T.
AU  - Pujalte, M.J.
TI  - Draft Genome Sequences of Vibrio renopiscarius Strains CECT 8603T and CECT 8604,  Two Marine Gammaproteobacteria Isolated from Cultured Gilthead Sea Bream (Sparus   aurata).
JO  - Genome Announcements
PY  - 2015
SP  - e00099
EP  - e00015
VL  - 3
AB  - Vibrio renopiscarius DCR 1-4-2(T) (CECT 8603(T)) and DCR 1-4-12 (CECT 8604) were  isolated
AB  - from healthy gilthead sea bream (Sparus aurata) from Mediterranean fish
AB  - farms (Castellon, Spain). Their draft genome sequences (30 and 44 contigs,
AB  - respectively) have 4.3 Mbp and a G+C content of 45.2 mol% and contain almost
AB  - 3,700 protein-encoding genes.
ER  -

TY  - JOUR
AU  - Arahal, D.R.
AU  - Shao, Z.
AU  - Lai, Q.
AU  - Pujalte, M.J.
TI  - Draft Genome Sequence of Actibacterium mucosum KCTC 23349, a Marine Alphaproteobacterium with Complex Ionic Requirements Isolated from Mediterranean   Seawater at Malvarrosa Beach, Valencia, Spain.
JO  - Genome Announcements
PY  - 2014
SP  - e00486
EP  - e00414
VL  - 2
AB  - Strain R46 (CECT 7668; KCTC 23349), a nomenclatural type of Actibacterium mucosum, was
AB  - isolated from surface seawater collected at Malvarrosa Beach
AB  - (Valencia, Spain) in July 2008. The draft genome sequence of strain R46
AB  - (approximately 3.72 Mbp) contains 22 scaffolds and 3,619 protein-encoding genes, with a G+C
AB  - content of 60.8 mol%.
ER  -

TY  - JOUR
AU  - Arai, H.
AU  - Kanbe, H.
AU  - Ishii, M.
AU  - Igarashi, Y.
TI  - Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter  thermophilus TK-6.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2651
EP  - 2652
VL  - 192
AB  - Hydrogenobacter thermophilus is a thermophilic, obligately chemolithoautotrophic and aerobic
AB  - hydrogen-oxidizing bacterium. It is
AB  - unique in its ability to fix carbon dioxide via the reductive
AB  - tricarboxylic acid cycle under aerobic conditions. It utilizes molecular
AB  - hydrogen, elemental sulfur, or thiosulfate as the sole energy source.
AB  - Here, we report the complete genome sequence of H. thermophilus TK-6.
ER  -

TY  - JOUR
AU  - Arai, H.
AU  - Shomura, Y.
AU  - Higuchi, Y.
AU  - Ishii, M.
TI  - Complete Genome Sequence of a Moderately Thermophilic Facultative Chemolithoautotrophic Hydrogen-Oxidizing Bacterium, Hydrogenophilus  thermoluteolus TH-1.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00857
EP  - e00818
VL  - 7
AB  - Hydrogenophilus spp., which are moderately thermophilic aerobic betaproteobacteria, are widely
AB  - distributed in geothermal environments. They fix
AB  - carbon dioxide via the Calvin-Benson-Bassham cycle and exhibit rapid autotrophic
AB  - growth using hydrogen as an energy source. Here, we report the complete genome
AB  - sequence of Hydrogenophilus thermoluteolus strain TH-1.
ER  -

TY  - JOUR
AU  - Arai, T.
AU  - Aoki, T.
TI  - New R plasmid-mediated restriction-modification system of deoxyribonucleic acid conferred by group E R plasmids.
JO  - J. Bacteriol.
PY  - 1977
SP  - 529
EP  - 531
VL  - 130
AB  - A new R plasmid-mediated restriction-modification system of deoxyribonucleic
AB  - acid was identified.  This system is specific for group E plasmids which have
AB  - been detected in unidentified marine Vibrio fish pathogens.
ER  -

TY  - JOUR
AU  - Aranda, J.
AU  - Roca, M.
AU  - Lopez-Canut, V.
AU  - Tunon, I.
TI  - Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris.
JO  - J. Phys. Chem. B
PY  - 2010
SP  - 8467
EP  - 8473
VL  - 114
AB  - In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position
AB  - catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular
AB  - mechanics (QM/MM) methods.   A reaction model was prepared by placing a single cytosine base
AB  - in the active site of the enzyme. In this model the exocyclic amino group of the base
AB  - establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl
AB  - oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from AdoMet to
AB  - the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to
AB  - Asp96. Different timings for the proton transfers and methylation steps have been explored at
AB  - the AM1/MM and B3LYP/MM levels including localization and characterization of stationary
AB  - structures. At our best estimate the reaction proceeds by means of a simultaneous but
AB  - asynchronous proton transfer from Ser53 to Asp96 and from N4 of cytosine to Ser53 followed by
AB  - a direct methyl transfer from AdoMet to the exocyclic N4 of cytosine.
ER  -

TY  - JOUR
AU  - Aranda, J.
AU  - Roca, M.
AU  - Tunon, I.
TI  - Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight.
JO  - Org. Biomol. Chem.
PY  - 2012
SP  - 5395
EP  - 5400
VL  - 10
AB  - M. PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes
AB  - methylation of cytosine at the N4 position. This enzyme
AB  - also displays promiscuous activity catalyzing methylation of adenine at
AB  - the N6 position. In this work we use QM/MM methods to investigate the
AB  - reaction mechanism of this promiscuous activity. We found that N6
AB  - methylation in M. PvuII takes place by means of a stepwise mechanism in
AB  - which deprotonation of the exocyclic amino group is followed by the
AB  - methyl transfer. Deprotonation involves two residues of the active
AB  - site, Ser53 and Asp96, while methylation takes place directly from the
AB  - AdoMet cofactor to the target nitrogen atom. The same reaction
AB  - mechanism was described for cytosine methylation in the same enzyme,
AB  - while the reversal timing, that is methylation followed by
AB  - deprotonation, has been described in M. TaqI, an enzyme that catalyzes
AB  - the N6-adenine DNA methylation from Thermus aquaticus. These
AB  - mechanistic findings can be useful to understand the evolutionary paths
AB  - followed by N-methyltransferases.
ER  -

TY  - JOUR
AU  - Aranda, J.
AU  - Zinovjev, K.
AU  - Roca, M.
AU  - Tunon, I.
TI  - Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase.
JO  - J. Am. Chem. Soc.
PY  - 2014
SP  - 16227
EP  - 16239
VL  - 136
AB  - M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a
AB  - methyl group from S-adenosyl-L-methionine to the N6 position of an adenine, a process
AB  - described only in prokaryotes. We have used full atomistic classical molecular dynamics
AB  - simulations to explore the protein-SAM-DNA ternary complex where the target adenine is flipped
AB  - out into the active site. Key protein DNA interactions established by the target adenine in
AB  - the active site are described in detail. The relaxed structure was used for a combined quantum
AB  - mechanics/molecular mechanics exploration of the reaction mechanism using the string method.
AB  - According to our free energy calculations the reaction takes place through a stepwise
AB  - mechanism where the methyl transfer precedes the abstraction of the proton from the exocyclic
AB  - amino group. The methyl transfer is the rate-determining step, and the obtained free energy
AB  - barrier is in good agreement with the value derived from the experimental rate constant. Two
AB  - possible candidates to extract the leftover proton have been explored: a water molecule found
AB  - in the active site and Asn105, a residue activated by the hydrogen bonds formed through the
AB  - amide hydrogens. The barrier for the proton abstraction is smaller when Asn105 acts as a base.
AB  - The reaction mechanisms can be different in other N6-DNA-methyltransferases, as determined
AB  - from the exploration of the reaction mechanism in the Asn105Asp M.TaqI mutant.
ER  -

TY  - JOUR
AU  - Aranda, J.
AU  - Zinovjev, K.
AU  - Swiderek, K.
AU  - Roca, M.
AU  - Tunon, I.
TI  - Molecular dynamics and QM/MM free energy profiles of cytosine C5-methyltransferase M.Hhai.
JO  - FEBS J.
PY  - 2013
SP  - 105
EP  - 105
VL  - 280
AB  - The target of this work is the study of mechanism of the reaction catalyzed by M.Hhai, an
AB  - enzyme that belongs to the restriction-modification system of the bacterium Haemophilus
AB  - haemolyticus which catalyzes the methyl transfer from S-adenosil-L-metionine to C5 position of
AB  - a cytosine base of DNA, working at the 5'-GCGC-3' sequence generating C5-methyl-cytosine.
AB  - The X-Ray structure of the enzyme complexed with SAM and a DNA sequence was the starting point
AB  - of our simulations.  We performed all calculations considering the whole enzymatic and DNA
AB  - environment and the solvation effect by including the enzyme in a orthorhombic box of TIP3P
AB  - water molecules of 88 x 87 x 99 A of side, including sodium counterions to neutralize the
AB  - charge of the system.  Using the NAMD program we equilibrated the system by means of 10 ns of
AB  - classical molecular dynamics with the AMBER force field, employing periodic boundary
AB  - conditions, Ewald summations, a temperature of 300 K and a time step of 1 fs.  We then
AB  - performed 100 ns MD simulaton in order to analyze the most important interactions formed
AB  - between the enzyme and DNA, the interactions within the active site, how the unpaired base is
AB  - stabilized and how the DNA helix accommodates the great perturbation that a flipped out base
AB  - means for its structure.  To analyse the chemical reaction we performed 500 ps of quantum
AB  - mechanics/molecular mechanics (QM/MM) MD simulation at 300 K using Dynamo program.  Quantum
AB  - subsystem was treated using the AM1 semiempirical hamiltonian adding corrections at the
AB  - M062x/6-311 + G level.  By means of the on-the-fly string method the minimum free energy path
AB  - for each step of the reaction was obtained.  Then, the path collective variable was defined
AB  - along these paths, to obtain the potential of mean force using umbrella sampling.
ER  -

TY  - JOUR
AU  - Aras, R.A.
TI  - Helicobacter pylori regulates hpyII restriction-modification function using gene deletion and horizontal reacquisition.
JO  - Int. J. Med. Microbiol.
PY  - 2001
SP  - 95
EP  - 95
VL  - 291S
AB  - Helicobacter pylori possess strain-specific complements of functional restriction-modification
AB  - systems.  The large number of R-M's homologous to those in other bacterial species and their
AB  - strain-specificity suggests that H. pylori may have horizontally acquired these genes.  A type
AB  - IIs R-M system, HpyII, was active in 2 of the 6 H. pylori strains studied.  We now demonstrate
AB  - that in most strains lacking HpyII.M function there is complete absence of the R-M system.
AB  - Direct DNA repeats of 80-bp flanking the hpyII R-M system allow its deletion, resulting in an
AB  - "empty-site" genotype.  We show that strains possessing this empty-site genotype and strains
AB  - with a full but inactive hpyII R-M can reacquire the hpyII R-M cassette and functional
AB  - activity through natural transformation by DNA from the parental R+M+ strain.  Identical
AB  - isolates divergent for the presence of an active HpyII R-M pose different restriction barriers
AB  - to transformation by foreign DNA.  That H. pylori can regulate HpyII R-M function through
AB  - deletion or mutation, and subsequent horizontal reacquisition of the hpyII R-M cassette
AB  - providing an example of a novel mechanism for R-M regulation, supports the hypothesis that H.
AB  - pylori populations use mutation and transformation to regulate gene function.
ER  -

TY  - JOUR
AU  - Aras, R.A.
AU  - Blaser, M.J.
TI  - Conservation of a type IIs restriction-modification system in Helicobacter pylori with homology to the MboII R-M system in Moraxella bovis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2000
SP  - 290
EP  - 291
VL  - 100
AB  - Bacteria use restriction and modification systems as a defense against invasion from foreign
AB  - DNA.  Comparison of the genomes from Helicobacter pylori strains 26695 and J99 identified a
AB  - number of strain-specific R-M systems.  Here we show the conservation of a type IIs R-M system
AB  - among 18 H. pylori strains and its possible involvement in horizontal gene transfer.  Strain
AB  - 26695 has a potential type IIs R-M system that has homology to the Moraxella bovis MboII R-M
AB  - system, which recognizes the non-palindromic sequence GAAGA.  PCR analysis of 17 other strains
AB  - show that 10 contain a complete R-M system, 2 contain partial R-M systems and 5 contain no R-M
AB  - system.  Sequence analysis of the 5' end of the restriction endonuclease subunit from 7
AB  - different strains shows predominantly synonymous variations in codon usage; indicating the
AB  - locus is under substantial selective pressure.  For all strains except J188, which has a
AB  - nonfunctional RE subunit, presence of both methyltransferases (MTs) correlates with protection
AB  - of genomic DNA from MboII digestion, implying that the MTs are responsible for modification of
AB  - the sequence GAAGA.  G+C content and phylogenetic analysis indicates that the H. pylori type
AB  - IIs R-M system may have been acquired through horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Aras, R.A.
AU  - Small, A.J.
AU  - Ando, T.
AU  - Blaser, M.J.
TI  - Horizontal transfer of the Helicobacter pylori restriction-modification system, HpyII, by a conjugation-like mechanism.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 165
EP  - 166
VL  - 102
AB  - Helicobacter pylori, gram-negative, curved bacteria that colonize the human gastric mucosa,
AB  - possess a large number of genes for
AB  - restriction-modification (R-M) systems, and essentially every strain
AB  - possesses a unique complement of functional and partial R-M systems.
AB  - Nearly half of the H. pylori strains studied possess an active, type
AB  - IIs R-M system, HpyII, with the recognition sequence GAAGA.
AB  - Recombination between direct repeats that flank the R-M allows for its
AB  - deletion whereas strains lacking hpyIIRM can acquire this cassette
AB  - through natural transformation. We now asked whether strains lacking
AB  - HpyII R-M activity can acquire an active 4.8 kb hpyIIRM cassette
AB  - (containing a kanamycin resistance (aphA) marker) through a
AB  - DNase-resistant mechanism. We found that hpyIIRM strains 6c and J166
AB  - acquired an hpyIIRM cassette from strain 6a, through a DNase-resistant
AB  - mechanism, if strains are isogenic (6a fwdarw 6c;
AB  - frequency=3.5e-7+-4.0e-7), but not if strains are non-isogenic (6a
AB  - fwdarw J166; frequency<1.8e-8). The frequency of conjugation-like
AB  - transfer of a point mutation conferring streptomycin resistance was not
AB  - significantly (p=0.47) different for isogenic
AB  - (frequency=2.7e-6+-2.3e-6) and non-isogenic (frequency=1.6e-6+-4.8e-7)
AB  - strains. A non-isogenic strain, J188, containing a full but inactive
AB  - hpyIIRM reactivated its HpyII R-M through natural transformation
AB  - (frequency=2.4e-7+-1.5e-7) but not through conjugation-like
AB  - (frequency<6.6e-8), horizontal acquisition of a functional hpyIIRM.
AB  - Strain J188 was transformed with the hpyIIRM cassette at a
AB  - significantly (p<0.05) lower frequency then was the isogenic 6a strain
AB  - (frequency=7.9e-6+-2.0e-6). These data indicate that a conjugation-like
AB  - mechanism contributes to the transfer of large (4.8 kb) fragments of
AB  - chromosomal DNA between H. pylori strains and that inactive or partial
AB  - R-M systems may act as contingency genes that can be reactivated upon
AB  - recombination with a functional allele. That functional R-M systems
AB  - appear to restrict acquisition of chromosomal DNA suggests that there
AB  - is a double-stranded DNA intermediate in the H. pylori uptake process.
ER  -

TY  - JOUR
AU  - Aras, R.A.
AU  - Small, A.J.
AU  - Ando, T.
AU  - Blaser, M.J.
TI  - Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing strains.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 5391
EP  - 5397
VL  - 30
AB  - Helicobacter pylori, bacteria that colonize the human gastric mucosa, possess a large number
AB  - of genes for restriction-modification (R-M) systems, and essentially, every strain possesses a
AB  - unique complement of functional and partial R-M systems. Nearly half of the H.pylori strains
AB  - studied possess an active type IIs R-M system, HpyII, with the recognition sequence GAAGA.
AB  - Recombination between direct repeats that flank the R-M cassette allows for its deletion
AB  - whereas strains lacking hpyIIRM can acquire this cassette through natural transformation. We
AB  - asked whether strains lacking HpyII R-M activity can acquire an active hpyIIRM cassette
AB  - [containing a 1.4 kb kanamycin resistance (aphA) marker], whether such acquisition is DNase
AB  - sensitive or resistant and whether restriction barriers limit acquisition of chromosomal DNA.
AB  - Our results indicate that natural transformation and conjugation-like mechanisms may
AB  - contribute to the transfer of large (4.8 kb) insertions of chromosomal DNA between H.pylori
AB  - strains, that inactive or partial R-M systems can be reactivated upon recombination with a
AB  - functional allele, consistent with their being contingency genes, and that H.pylori R-M
AB  - diversity limits acquisition of chromosomal DNA fragments of 1 kb.
ER  -

TY  - JOUR
AU  - Aras, R.A.
AU  - Takata, T.
AU  - Ando, T.
AU  - van der Ende, A.
AU  - Blaser, M.J.
TI  - Regulation of the HpyII restriction-modification system of Helicobacter pylori by gene deletion and horizontal reconstitution.
JO  - Mol. Microbiol.
PY  - 2001
SP  - 369
EP  - 382
VL  - 42
AB  - Helicobacter pylori, Gram-negative, curved bacteria colonizing the human stomach, possess
AB  - strain-specific complements of functional
AB  - restriction-modification (R-M) systems. Restriction-modification
AB  - systems have been identified in most bacterial species studied and are
AB  - believed to have evolved to protect the host genome from invasion by
AB  - foreign DNA. The large number of R-Ms homologous to those in other
AB  - bacterial species and their strain-specificity suggest that H. pylori
AB  - may have horizontally acquired these genes. A type IIs
AB  - restriction-modification system, hpyIIRM, was active in two out of the
AB  - six H. pylori strains studied. We demonstrate now that in most strains
AB  - lacking M.HpyII function, there is complete absence of the R-M system.
AB  - Direct DNA repeats of 80 bp flanking the hpyIIRM system allow its
AB  - deletion, resulting in an 'empty-site' genotype. We show that strains
AB  - possessing this empty-site genotype and strains with a full but
AB  - inactive hpyIIRM can reacquire the hpyIIRM cassette and functional
AB  - activity through natural transformation by DNA from the parental R-M+
AB  - strain. Identical isolates divergent for the presence of an active
AB  - HpyII R-M pose different restriction barriers to transformation by
AB  - foreign DNA. That H. pylori can lose HpyII R-M function through
AB  - deletion or mutation, and can horizontally reacquire the hpyIIRM
AB  - cassette, is, in composite, a novel mechanism for R-M regulation,
AB  - supporting the general hypothesis that H. pylori populations use
AB  - mutation and transformation to regulate gene function.
ER  -

TY  - JOUR
AU  - Aras, R.A.
AU  - Takata, T.
AU  - van der Ende, A.
AU  - Blaser, M.J.
TI  - Helicobacter pylori variants from a single host that differ in the presence of the hpyII restriction-modification system.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 296
EP  - 296
VL  - 101
AB  - Helicobacter pylori are gram-negative, curved bacteria that reside in the human gastric
AB  - mucosa. Sequencing of two independent H. pylori
AB  - strains, 26695 and J99, identified an extraordinary number of
AB  - restriction-modification (R-M) genes. Many are strain-specific, have
AB  - deviant G+C content, and are associated with genomic rearrangements,
AB  - suggesting their horizontal acquisition from other bacteria. Strain
AB  - 26695 possesses a type IIs R-M system, hpyII R-M, with homology to the
AB  - Moraxella bovis MboII R-M system, recognizing the sequence GAAGA. Since
AB  - genomic analysis identified 80-nucleotide direct repeats flanking the
AB  - 26695 R-M system that could permit deletion of intervening regions, we
AB  - searched for isolates from a single host that differ in hpyII R-M
AB  - status. The resistance of an isolate's DNA to MboII digestion was used
AB  - to indicate the presence of the hpyII R-M system. From a Dutch patient,
AB  - we found two isolates that differed. Using primers specific for
AB  - different regions of the hpyII R-M, all expected PCR products were
AB  - present for the resistant isolate (2a), but were absent for the
AB  - sensitive isolate (2b). PCR using primers that flank the repeat
AB  - sequences amplified a 3.5 kb PCR product in strain 2a (consistent with
AB  - a full hpyII R-M system), and an "empty-site" (276bp) product in strain
AB  - 2b (consistent with deletion of the R-M system and one repeat);
AB  - sequencing of the "empty-site" product confirmed the deletion. That the
AB  - strains had identical RAPD and RFLP profiles and were otherwise
AB  - identical in susceptibility to 13 other restriction enzymes indicate
AB  - that they are clonal variants rather than different strains. Parallel
AB  - results were found for paired isolates obtained from one of the
AB  - patient's daughters. The isolation from a single host of clonal
AB  - variants divergent in hpyII R-M status, coupled with the sequence data
AB  - suggest deletion in vivo, findings consistent with the hypothesis of
AB  - R-M system mobility within H. pylori.
ER  -

TY  - JOUR
AU  - Araujo, C.L.
AU  - Dias, L.M.
AU  - Veras, A.A.
AU  - Alves, J.T.
AU  - Cavalcante, A.L.
AU  - Dowson, C.G.
AU  - Azevedo, V.
AU  - Ramos, R.T.
AU  - Silva, A.
AU  - Carneiro, A.R.
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis 262 Biovar equi Isolated from Cow Milk.
JO  - Genome Announcements
PY  - 2016
SP  - e00176
EP  - e00116
VL  - 4
AB  - We report the complete genome sequence ofCorynebacterium pseudotuberculosis262, isolated from
AB  - a bovine host.C. pseudotuberculosisis an etiological agent of
AB  - diseases with medical and veterinary relevance. The genome contains 2,325,749 bp,
AB  - 52.8% G+C content, 2,022 coding sequences (CDS), 50 pseudogenes, 48 tRNAs, and 12
AB  - rRNAs.
ER  -

TY  - JOUR
AU  - Araujo, F.A.
AU  - Marques, J.M.
AU  - de Moura, V.A.
AU  - Schneider, M.P.
AU  - Andrade, S.S.
AU  - Lima, A.C.
AU  - Guimaraes, L.C.
AU  - Folador, A.R.
AU  - Silva, A.
AU  - Ramos, R.T.
TI  - Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA07 Biovar ovis, Isolated from a Sheep Udder in Amazonia.
JO  - Genome Announcements
PY  - 2017
SP  - e00040
EP  - e00017
VL  - 5
AB  - In this work, we present the draft genome sequence of Corynebacterium pseudotuberculosis
AB  - strain PA07 biovar ovis, isolated from a caseous secretion
AB  - from a sheep udder in Para, Brazil. The genome contains 2,320,235 bp, 52.2% G+C
AB  - content, 2,191 coding sequences (CDSs), five pseudogenes, 48 tRNAs, and three
AB  - rRNAs.
ER  -

TY  - JOUR
AU  - Araujo, F.D.
AU  - Croteau, S.
AU  - Slack, A.D.
AU  - Milutinovic, S.
AU  - Bigey, P.
AU  - Price, G.B.
AU  - Zannis-Hajopoulos, M.
AU  - Szyf, M.
TI  - The dnmt1 target recognition domain resides in the n terminus.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 6930
EP  - 6936
VL  - 276
AB  - DNA-cytosine-5-methyltransferase 1 (DNMT1) is the enzyme believed to be responsible for
AB  - maintaining the epigenetic information encoded by DNA methylation patterns. The target
AB  - recognition domain of DNMT1, the domain responsible for recognizing hemimethylated CGs, is
AB  - unknown. However, based on homology with bacterial cytosine DNA methyltransferases it has been
AB  - postulated that the entire catalytic domain, including the target recognition domain, is
AB  - localized to 500 amino acids at the C terminus of the protein. The N-terminal domain has been
AB  - postulated to have a regulatory role, and it has been suggested that the mammalian DNMT1 is a
AB  - fusion of a prokaryotic methyltransferase and a mammalian DNA-binding protein. Using a
AB  - combination of in vitro translation of different DNMT1 deletion mutant peptides and a
AB  - solid-state hemimethylated substrate, we show that the target recognition domain of DNMT1
AB  - resides in the N terminus (amino acids 122-417) in proximity to the proliferating cell nuclear
AB  - antigen binding site. Hemimethylated CGs were not recognized specifically by the postulated
AB  - catalytic domain. We have previously shown that the hemimethylated substrates utilized here
AB  - act as DNMT1 antagonists and inhibit DNA replication. Our results now indicate that the
AB  - DNMT1-PCNA interaction can be disrupted by substrate binding to the DNMT1 N terminus. These
AB  - results point toward new directions in our understanding of the structure-function of DNMT1.
ER  -

TY  - JOUR
AU  - Araujo, F.D.
AU  - Knox, J.D.
AU  - Ramchandrani, S.
AU  - Pelletier, R.
AU  - Bigey, P.
AU  - Price, G.
AU  - Szyf, M.
AU  - Zannis-Hadjopoulos, M.
TI  - Identification of initiation sites for DNA replication in the human dnmt1 (DNA-methyltransferase) locus.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 9335
EP  - 9341
VL  - 274
AB  - Vertebrates have developed multiple mechanisms to coordinate the replication of epigenetic and
AB  - genetic information.  Dnmt1 encodes the maintenance enzyme DNA-methyltransferase, which is
AB  - responsible for propagating the DNA methylation pattern and the epigenetic information that it
AB  - encodes during replication.  Direct sequence analysis and bisulfite mapping of the 5' region
AB  - of DNA-methyltransferase 1 have indicated the presence of many sequence elements associated
AB  - with previously characterized origins of DNA replication.  This study tests the hypothesis
AB  - that the dnmt1 region containing these elements is an origin of replication in human cells.
AB  - First, we demonstrate that a vector containing this dnmt1 sequence is able to support
AB  - autonomous replication when transfected into HeLa cells.  Second, using a gel retardation
AB  - assay, we show that it contains a site for binding of origin-rich sequences binding activity,
AB  - a recently purified replication protein.  Finally, using competitive polymerase chain
AB  - reaction, we show that replication initiates in this region in vivo.  Based on these lines of
AB  - evidence, we propose that initiation sites for DNA replication are located between the first
AB  - intron and exon 7 of the human dnmt1 locus.
ER  -

TY  - JOUR
AU  - Aravind, L.
AU  - Makarova, K.S.
AU  - Koonin, E.V.
TI  - Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3417
EP  - 3432
VL  - 28
AB  - Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer
AB  - analysis of the structural and evolutionary relationships of HJRs and related nucleases
AB  - suggests that the HJR function has evolved independently from at least four distinct
AB  - structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA. The
AB  - endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very
AB  - short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by
AB  - far a greater diversity of nucleases than previously suspected. This fold unifies archaeal
AB  - HJRs, repair nucleases such as RecB and Vsr, restriction enzymes and a variety of predicted
AB  - nucleases whose specific activities remain to be determined. Within the RNase H fold a new
AB  - family of predicted HJRs, which is nearly ubiquitous in bacteria, was discovered, in addition
AB  - to the previously characterized RuvC family. The proteins of this family, typified by
AB  - Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but
AB  - could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of
AB  - phage T4 is shown to serve as a structural template for many nucleases, including McrA and
AB  - other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a
AB  - distinct metal-dependent nuclease fold. As a result of this analysis, the principal HJRs are
AB  - now known or confidently predicted for all bacteria and archaea whose genomes have been
AB  - completely sequenced, with many species encoding multiple potential HJRs. Horizontal gene
AB  - transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene
AB  - displacement seem to have been major forces in the evolution of HJRs and related nucleases. A
AB  - remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi,
AB  - which does not possess any of the typical HJRs, but instead encodes, in its chromosome and
AB  - each of the linear plasmids, members of the lambda exonuclease family predicted to function as
AB  - HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their
AB  - near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease
AB  - fold and the RNase H fold have probably been acquired from bacteria via horizontal gene
AB  - transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains
AB  - uncertain; this function could be performed by topoisomerase IB or by a novel, so far
AB  - undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes
AB  - of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes
AB  - has probably played a major role in the evolution of this class of enzymes. This analysis
AB  - resulted in the prediction of numerous previously unnoticed nucleases, some of which are
AB  - likely to be new restriction enzymes.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host-controlled variation.
JO  - Bacteriophage Lambda
PY  - 1971
SP  - 83
EP  - 96
VL  - 0
AB  - About twenty years ago a number of similar observations were made in work with various
AB  - bacteriophage species.  They showed that the host range of a given phage preparation depended
AB  - on the bacterial strain in which the phage had last propagated.  This effect was called
AB  - host-controlled variation to distinguish its host-dependent and thus genetically unstable
AB  - nature from persistent hereditary chcanges such as are found in host-range mutants.  Many
AB  - examples now are known to reflect the phenomena described in this chapter:  strain-specific
AB  - restriction and modification of DNA.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Genetic Variation and Molecular Evolution.
JO  - Encyclopedia of Molecular Cell Biology and Molecular Medicine.
PY  - 2004
SP  - 331
EP  - 352
VL  - 5
AB  - The comparison of DNA sequences of genes and entire genomes offers interesting insights into
AB  - the possible evolutionary relatedness of genetic information of living organisms.  Together
AB  - with a relatively rich database from experimental microbial genetics, conclusions can be drawn
AB  - on the molecular mechanisms by which genetic variations are spontaneously generated.  A number
AB  - of different specific mechanisms contribute to the overall mutagenesis.  These mechanisms are
AB  - here grouped into three natural strategies of the spontaneous generation of genetic
AB  - variations: local changes of DNA sequences, intragenomic rearrangement of DNA segments, and
AB  - acquisition of foreign DNA by horizontal gene transfer.  These three strategies have different
AB  - qualities with regard to their contributions to the evolutionary process.  As a general rule,
AB  - none of the known mechanisms producing genetic variants is clearly directed.  Rather, the
AB  - resulting alterations in the inherited genomes are more random.  In addition, usually only a
AB  - minority of resulting variants provide a selective advantage.  Interestingly, in most of the
AB  - molecular mechanisms involved, the products of so-called evolution genes are involved as
AB  - generators of genetic variation and/or as modulators of the frequencies of genetic variation.
AB  - Products of evolution genes work in tight collaboration with nongenetic factors such as
AB  - structural flexibilities and chemical instabilities of molecules, chemical and physical
AB  - mutagens, and random encounter.  All of these aspects contributing to the spontaneous
AB  - generation of genetic variations together form the core of the theory of molecular evolution.
AB  - This theory brings neo-Darwinism to the molecular level.  In view of the increasing evidence
AB  - coming particularly from microbial genetics, knowledge of molecular evolution can be seen as a
AB  - confirmation of Darwinism at the level of biologically active molecules, in particular,
AB  - nucleic acids and proteins.  Philosophical and practical implications of this knowledge will
AB  - be briefly discussed.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - On the generation of genetic diversity in microorganisms.
JO  - Proc. Indian Natn. Sci. Acad.
PY  - 1994
SP  - 357
EP  - 364
VL  - B60
AB  - Bacterial genetics strongly influenced the development of molecular genetic strategies and
AB  - techniques now available to study gene structure and functions of practically any living
AB  - organisms.  It also revealed natural processes of horizontal gene transfer (transformation,
AB  - conjugation, phage-mediated transduction) as well as systems (e.g. restriction-modification
AB  - systems) to hold such gene transfer in tolerably low frequencies to ensure a certain degree of
AB  - genetic stability.  Work with bacterial and bacteriophage systems has helped to unravel both
AB  - homologous and non-homologous enzyme-mediated recombination processes at the molecular level.
AB  - The acquired knowledge now helps to understand molecular processes contributing to the
AB  - generation of genetic variation, especially DNA rearrangements resulting from transposition
AB  - and from site-specific recombination which sometimes occurs at secondary crossing-over sites.
AB  - Present knowledge on the genetic plasticity of haploid microorganisms offers insights into
AB  - the molecular basis for the natural interplay between mutagenesis and selection.  This
AB  - approach greatly profits from the short generation times and relatively small genome sizes of
AB  - haploid microorganisms which allows one to investigate population genetic questions and to
AB  - draw conclusions on the mechanisms of evolutionary processes.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - DNA Modification and Restriction.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 1974
SP  - 1
EP  - 37
VL  - 14
AB  - The reader of the scientific literature may have had his attention attracted
AB  - recently to a growing number of highly interesting reports on research on DNA
AB  - restriction endonucleases and DNA modification methylases.  A striking
AB  - illustration is the November 1972 issue of the Proceedings of the National
AB  - Academy of Sciences of the United States of America:  it contains seven papers
AB  - on restriction endonucleases, and none of the 16 authors signed more than one
AB  - of these papers.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host-controlled modification of bacteriophage.
JO  - Annu. Rev. Microbiol.
PY  - 1965
SP  - 365
EP  - 378
VL  - 19
AB  - Host-controlled modification of viruses is a general term applied to those
AB  - cases in which passage through certain host strains imparts one or more new,
AB  - nonheritable properties to the virus without altering its genetic information
AB  - content.  The terms of host-induced modification, host-controlled variation, or
AB  - host-induced variation are sometimes used as synonyms to designate the same
AB  - phenomena.  However, we would like to recommend the use of "host-controlled
AB  - modification," at least for the cases discussed in this paper, since control
AB  - mechanisms are involved here rather than induction phenomena and since the term
AB  - "variation" may erroneously suggest some change in the genetic message.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Strain-specific restriction and modification of DNA.
JO  - Bull. Schweiz. Akad. Med. Wiss.
PY  - 1970
SP  - 99
EP  - 100
VL  - 25
AB  - Experimental investigation of the molecular mechanism of host-controlled
AB  - modification of bacteriophages has led to the discovery of very interesting
AB  - bacterial enzyme systems.  Each of these systems has a specific restriction
AB  - enzyme (endonuclease) and a specific modification enzyme (DNA methylase).  Both
AB  - enzymes appear to work with high affinity on the same position of DNA.  This
AB  - point of affinity consists of a quite definite sequence of 6 to 9 DNA base
AB  - pairs.  The recognition of the point of affinity by the enzymes is taken over
AB  - by a gene product as the common factor for both enzyme activities.  The genetic
AB  - basis of the activities, the enzymes themselves and the substrate can be
AB  - experimentally investigated and offer the molecular biologist an interesting
AB  - model of the specific interaction of enzymes with nucleic acids.  The
AB  - biological significance of DNA restriction lies in an effective defence
AB  - mechanism against infection with foreign genetic material.  For a detailed
AB  - account of the present knownledge on this subject, the reader is referred to a
AB  - review by Arber and Linn (Ann. Rev. Biochem. 38, 467[1969].
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host-controlled modification of DNA.
JO  - Naturwissenschaften
PY  - 1969
SP  - 155
EP  - 160
VL  - 56
AB  - None
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Promotion and limitation of genetic exchange.
JO  - Science
PY  - 1979
SP  - 361
EP  - 365
VL  - 205
AB  - None
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Specificites biologiques de l'acide desoxyribonucleique.
JO  - Pathol. Microbiol. (Basel)
PY  - 1962
SP  - 668
EP  - 681
VL  - 25
AB  - A new biological specificity of phage DNA molecules is described, which is
AB  - distinct from the genetic specificity of DNA residing in the base sequence.
AB  - Unlike the genetic specificity this newly discovered "host specificity" is not
AB  - multiplied as DNA replicates, but is nevertheless shown to be fixed firmly to
AB  - the DNA molecule and so to be transferred into progeny molecules jointly with
AB  - the parental DNA material.  Production of DNA host specificity is governed both
AB  - by the bacterial genome and by episomes which are present in the cell.  Host
AB  - specificity apparently exists not only on phage DNA but as well on the DNA of
AB  - the host itself.  It is thought to be the element changed in "host controlled
AB  - modification" of phage and also the element recognized by restricting hosts
AB  - which degrade nonadapted, infecting DNA.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli V. The role of Methionine in the Production of Host Specificity.
JO  - J. Mol. Biol.
PY  - 1965
SP  - 247
EP  - 256
VL  - 11
AB  - Bacteriophage lambda grown in auxotrophic met-, pro- or arg- strains of
AB  - Escherichia coli K12 in the presence of the required amino acids show an
AB  - efficiency of plating of approximately 1 on E. coli strains K12 and C.
AB  - However, if met- cells are deprived of methionine during a portion of the
AB  - latent period, the efficiency of plating of the progeny phage is lower on the
AB  - host K12 than on strain C.  Similar results are obtained with met- auxotrophs
AB  - of strains B and K12 (P1); deprivation of methionine during the latent period
AB  - results in the production of phage with lower efficiency of plating on the host
AB  - strain than on strain C.  Such an effect is not observed following a similar
AB  - starvation for proline or arginine.  These results suggest that methionine is
AB  - specifically required for the production of host specificity of DNA.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host-controlled restriction and modification of bacteriophage.
JO  - Symp. Soc. Gen. Microbiol.
PY  - 1968
SP  - 295
EP  - 314
VL  - 18
AB  - Viral properties have frequently been reported to undergo non-heritable changes
AB  - upon passage through certain host strains.  But very little was known about the
AB  - molecular mechanisms forming the basis of such host-controlled modifications,
AB  - when we started in 1960 to investigate one particular virus-host system.  This
AB  - work, carried out with bacteriophage lambda and a few host strains all derived
AB  - from Escherichia coli, soon revealed the existence of a highly specific
AB  - recognition mechanism able to screen infecting and intracellular DNA molecules
AB  - for absence or presence on these molecules of a host-specific stamp.  This has
AB  - more recently been identified as nucleotide methylation.  It is the scope of my
AB  - contribution to this symposium to lay out the crucial experiments and arguments
AB  - that lead to the present understanding of this system, which may be interpreted
AB  - as serving the cell as a defense mechanism against infection with foreign
AB  - genetic material.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli.   9. Host-controlled modification of bacteriophage fd.
JO  - J. Mol. Biol.
PY  - 1966
SP  - 483
EP  - 496
VL  - 20
AB  - Host-controlled modification is shown to occur with four related male-specific
AB  - bacteriophage strains containing single-stranded DNA: fd,f1,M13 and F12.  All
AB  - four phages are restricted and modified in bacteria with B host specificity,
AB  - the first three also in P1-lysogenic cells.  None of the phages is restricted
AB  - in strains with K host specificity or carrying the episome RTF-2.  The
AB  - bacterial characters rB mB which control the B host specificity of lambda DNA,
AB  - are also responsible for restriction and modification of phage fd.  The
AB  - apparent difference in K restriction, which is encountered by lambda, but not
AB  - by fd, is thought to find its explanation in the small molecular size of fd
AB  - DNA, on which K specificity sites might be lacking.  Indeed, restriction and
AB  - modification act on the DNA of fd:  DNA from fd phages which infect restricting
AB  - host cells is partially broken down to acid-soluble products.  On the other
AB  - hand, one-cycle growth of fd.B on non-restricting and non-modifying Kr-m-
AB  - bacteria yields, among a majority of progeny of fd.Kr-m- phage, some phage
AB  - particles with parental B host specificity, and they also have parental DNA as
AB  - shown by density labelling of the infecting phage.  The efficiency of such
AB  - transfer of parental fd.B DNA was found to be 0.12 if measured after 18 minutes
AB  - incubation of the infected cells.  The implication of this transfer on the
AB  - mechanism of phage DNA replication is discussed.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli.  III.  Effects on transduction mediated by lambda dg.
JO  - Virology
PY  - 1964
SP  - 173
EP  - 182
VL  - 23
AB  - Transducing phage lambda dg carrying bacterial gal markers shows the same
AB  - effects of host-controlled modification as does normal lambda.  Phage grown on
AB  - Escherichia coli K12 is restricted (not accepted) on E. coli B and K12(P1), and
AB  - phage grown on B is restricted on K12 and K12(P1) independently of whether the
AB  - gal markers of lambda dg originated from the K12 or B chromosome.  Transduction
AB  - to a restricting host yields a very low proportion of gal+ transductants, which
AB  - are mostly heterogenotes.  Superinfecting restricted lambda phage does not
AB  - exert helper functions for lysogenization or reproduction of nonrestricted
AB  - lambda dg particles.  In cells infected with restricted lambda dg and
AB  - superinfected with nonrestricted lambda, a greatly increased transduction
AB  - frequency is observed, probably due to marker rescue.  A small helper effect is
AB  - observed in cells infected with restricted lambda dg and restricted lambda,
AB  - presumably caused by help in lysogenization in those few cells which accept the
AB  - infecting lambda dg.  For nonrestricting hosts it is known that ultraviolet
AB  - irradiated lambda dg no longer transduces by lysogenization but by stable
AB  - integration of the gal markers into the bacterial chromosome.  The same
AB  - behavior is found for restricting recipients.  Here, the maximum number of
AB  - stable transductants is not notably higher than the number of heterogenotic
AB  - transductants obtained on the same bacteria infected with nonirradiated lambda
AB  - dg.  This is in agreement with the notion that most of the restricted genomes
AB  - are degraded after their injection.  Particles giving rise to stable
AB  - transduction show a very low UV sensitivity.  The ease with which stable
AB  - transduction occurs probably reflects the degree of homology between endo- and
AB  - exogenotic gal regions.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - What is the function of DNA restriction enzymes?
JO  - Trends Biochem. Sci.
PY  - 1977
SP  - N176
EP  - N178
VL  - 2
AB  - None
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Origin and properties of type A host specificity in Escherichia coli.
JO  - Pathol. Microbiol. (Basel)
PY  - 1969
SP  - 147
EP  - 147
VL  - 34
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Restriction Enzymes: From Their Discovery to Their Applications.
JO  - Biovalley Monographs
PY  - 2012
SP  - 33
EP  - 38
VL  - 3
AB  - As a contribution to the history of science, the discovery and the functions of bacterial
AB  - restriction endonucleases, as well as their
AB  - applications in molecular genetic analysis and in biotechnological
AB  - innovations, including genetic engineering, are described here from the
AB  - personal viewpoint of the author.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Roots, strategies and prospects of functional genomics - functional genomics, human genome, bioinformatic software and polymerase chain  reaction; a review.
JO  - Curr. Sci.
PY  - 2002
SP  - 826
EP  - 828
VL  - 83
AB  - AUTHOR ABSTRACT - This essay traces,the historical development of classical and molecular
AB  - genetics from their early roots to the actual
AB  - research strategies and their prospects. Attention is also given to the
AB  - risk evaluation of genetic engineering by comparing designed genetic
AB  - alterations with the spontaneous genetic variation known to form the
AB  - substrate for biological evolution. DERWENT ABSTRACT: Roots, strategies
AB  - and prospects of functional genomics was discussed with respect to
AB  - historical development of classical molecular genetics from their early
AB  - roots to the actual research strategies and their prospects. Classical
AB  - genetics has its roots in the 19th century, when Gregor Mendel carried
AB  - out experiments with peas displaying phenotypically distinct traits
AB  - which got inherited to the progeny. However, efficient methods to
AB  - experimentally determine large extents of such sequences were still
AB  - missing. In the 1950s and 1960s it also became clear that bacteria
AB  - succeed by a number of different strategies to hold the frequency of
AB  - acquisition of foreign genetic information low. One of these strategies
AB  - is the widely encountered phenomenon of restriction and modification of
AB  - DNA. Restriction-modification systems allow bacteria to specifically
AB  - distinguish foreign DNA from the cell's own DNA. As a consequence,
AB  - foreign DNA becomes cleaved into fragments upon its entry into the
AB  - cell. In 1970 investigators succeeded in preparing recombinant DNA
AB  - molecules in vitro and to get them replicated after their transfer into
AB  - appropriate host cells. In these experiments plasmids and viral genomes
AB  - served as gene vectors into which fragments of DNA, often prepared by
AB  - restriction cleavage, were spliced. In 1990s, the gateway to the
AB  - determination of the nucleotide sequences of entire genomes was thus
AB  - open. More recently, the DNA sequences of several eukaryotic organisms
AB  - were published, including the human genome of about three billion base
AB  - pairs(3 pages)
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Genetically encoded generators of genetic variants.
JO  - J. Proteomics
PY  - 2009
SP  - 836
EP  - 837
VL  - 72
AB  - Several specific molecular mechanisms contribute to the generation of genetic variants at low
AB  - rates. Some of these mechanisms involve the action of specific gene products as variation
AB  - generators. We discuss here known as well as still hypothetical ways by which natural reality
AB  - may succeed to keep the rates of genetic variation at low levels that insure a relatively high
AB  - genetic stability of the individual organisms.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Elements in microbial evolution.
JO  - J. Mol. Evol.
PY  - 1991
SP  - 4
EP  - 12
VL  - 33
AB  - Spontaneous mutation, selection, and isolation are key elements in biological evolution.
AB  - Molecular genetic approaches reveal a multitude of different mechanisms by which spontaneous
AB  - mutants arise. Many of these mechanisms depend on enzymes, which often do not act fully at
AB  - random on the DNA, although a large number of sites of action can be observed. Of particular
AB  - interest in this respect are DNA rearrangement processes, e.g., by transposition and by
AB  - site-specific recombination systems. The development of gene functions has thus to be seen as
AB  - the result of both DNA rearrangement processes and sequence alterations brought about by
AB  - nucleotide substitutions and small local deletions, insertions, and duplications. Prokaryotic
AB  - microorganisms are particularly appropriate for studying the effects of spontaneous mutation
AB  - and thus microbial evolution, as they have haploid genomes, so that genetic alterations become
AB  - rapidly apparent phenotypically. In addition, bacteria and their viruses and plasmids have
AB  - relatively small genomes and short generation times, which also facilitate research on
AB  - evolutionary processes. Besides the strategy of development of gene functions in the vertical
AB  - transmission of genomes from generation to generation, the acquisition of short DNA segments
AB  - from other organisms appears to be an important strategy in microbial evolution. In this
AB  - process of horizontal evolution natural vector DNA molecules are often involved. Because of
AB  - acquisition barriers, the acquisition strategy works best for relatively small DNA segments,
AB  - hence at the level of domains, single genes, or at most operons. Among the many enzymes and
AB  - functional systems involved in vertical and horizontal microbial evolution, some may serve
AB  - primarily for essential life functions in each individual and only secondarily contribute to
AB  - evolution.Others, however, might serve primarily for evolution and thus exert their biological
AB  - functions at the level of populations rather than at that of a single organism.
ER  -

TY  - JOUR
AU  - Arber, W.
TI  - Genetic variation: molecular mechanisms and impact on microbial evolution.
JO  - FEMS Microbiol. Rev.
PY  - 2000
SP  - 1
EP  - 7
VL  - 24
AB  - On the basis of established knowledge of microbial genetics one can distinguish three major
AB  - natural strategies in the spontaneous
AB  - generation of genetic variations in bacteria. These strategies are: (1)
AB  - small local changes in the nucleotide sequence of the genome, (2)
AB  - intragenomic reshuffling of segments of genomic sequences and (3) the
AB  - acquisition of DNA sequences from another organism. The three general
AB  - strategies differ in the quality of their contribution to microbial
AB  - evolution. Besides a number of non-genetic factors, various specific
AB  - gene products are involved in the generation of genetic variation and
AB  - in the modulation of the fequency of genetic variation. The underlying
AB  - genes are called evolution genes. They act for the benefit of the
AB  - biological evolution of populations as opposed to the action of
AB  - housekeeping genes and accessory genes which are for the benefit of
AB  - individuals. Examples of evolution genes acting as variation generators
AB  - are found in the transposition of mobile genetic elements and in
AB  - so-called site-specific recombination systems. DNA repair systems and
AB  - restriction-modification systems are examples of modulators of the
AB  - frequency of genetic variation. The involvement of bacterial viruses
AB  - and of plasmids in DNA reshuffling and in horizontal gene transfer is a
AB  - hint for their evolutionary functions. Evolution genes are thought to
AB  - undergo biological evolution themselves, but natural selection for
AB  - their functions is indirect, at the level of populations, and is called
AB  - second-order selection. In spite of an involvement of gene products in
AB  - the generation of genetic variations, evolution genes do not
AB  - programmatically direct evolution towards a specific goal. Rather, a
AB  - steady interplay between natural selection and mixed populations of
AB  - genetic variants gives microbial evolution its direction.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Dussoix, D.
TI  - Host Specificity of DNA Producted by Escherichia Coli:  I. Host controlled modification of bacteriophage lambda.
JO  - J. Mol. Biol.
PY  - 1962
SP  - 18
EP  - 36
VL  - 5
AB  - Lambda bacteriophage particles carry a "host specificity" determined by the
AB  - bacterial strains on which they were produced.  Upon infection of a different
AB  - bacterial host (1) the phage DNA may be either accepted or rejected on the
AB  - basis of this specificity, (2) if accepted, the phage multiplies and progeny
AB  - phage are produced.  Those progeny to which the parental phage DNA molecule is
AB  - transferred, in either conserved or semi-conserved form, also receive the
AB  - parental phage host specificity.  All progeny containing only newly synthesized
AB  - DNA receive only the specificity of the new bacterial host.  It is concluded
AB  - that host specificity is carried on the bacteriophage DNA.  Phage P1, present
AB  - in a bacterial cell as either prophage or vegetative phage, imparts to lambda
AB  - DNA multiplying in the same cell a host specificity over and above that
AB  - determined by the host itself.  Such P1-induced specificity can be impressed
AB  - equally well onto replicating and non-replicating lambda DNA.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Hattman, S.
AU  - Dussoix, D.
TI  - On the host-controlled modification of bacteriophage lambda.
JO  - Virology
PY  - 1963
SP  - 30
EP  - 35
VL  - 21
AB  - Phage lambda.C, grown on Escherichia coli strain C, is restricted on E. coli
AB  - strains K12, K12(P1) and B251, and its DNA is broken down after injection into
AB  - these bacteria strains.  Phage lambda.K(P1)-that is, grown on K12 or K12(P1)-is
AB  - accepted by C, but undergoes host controlled modification upon reproduction in
AB  - C (Weigle and Bertani, 1953).  In a one-cycle growth of lambda.K(P1) on E. coli
AB  - C, parental DNA and host specificity undergo linked transfer into the progeny.
AB  - Thus, host specificity is a property of the DNA molecule, as was previously
AB  - shown for phage lambda in another host system (Arber and Dussoix, 1962).  Host
AB  - specificity is serially transferable, and the probability of transfer to the
AB  - progeny is constant for any given DNA strand under given experimental
AB  - conditions.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Kuhnlein, U.
TI  - Mutational loss of B-specific restriction of the bacteriophage fd.
JO  - Pathol. Microbiol. (Basel)
PY  - 1967
SP  - 946
EP  - 952
VL  - 30
AB  - Bacteriophage fd undergoes host-controlled restriction and modification in
AB  - strains of E. coli B: non modified phage fd.O plates with a probability of only
AB  - 7 x 10-4 on B strains 2027.  Phage mutants u1 were isolated showing an
AB  - efficiency of plating of 3 x 10-2 on B.  Starting from such intermediately
AB  - restricted fd genomes, completely unrestricted double mutants, u1, u2 were
AB  - found.  No notable changes in the physiological properties of the mutants were
AB  - observed.  The stepwise loss of restriction is taken as an evidence that the fd
AB  - DNA molecule carries two B-specific sites, which are most probably determined
AB  - by a specific base sequence, in confirmation of findings made before upon
AB  - methylation analysis of fd DNA.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Kuhnlein, U.
TI  - Repair and modification of genetic material:  DNA modification and restriction.
JO  - Int. Congr. Biochem.
PY  - 1970
SP  - 180
EP  - 180
VL  - 8
AB  - B-specific modification enzyme has been partly purified from extracts of
AB  - Escherichia coli strain B.  This enzyme specifically methylates unmodified DNA
AB  - and thereby renders the DNA resistant to cleavage by endonuclease R.B.
AB  - S-adenosylmethionine is the methyl donor, and the product of the reaction is
AB  - 6-methylaminopurine.  These observations confirm older in vivo results on the
AB  - chemical nature of strain-specific modification.  Quantitatively, each fully
AB  - modified specificity site on the DNA contains two methylated bases, one on each
AB  - strand.  At the genetic level, two independent systems of host specificity have
AB  - been found to reside in strains of E. coli 15.  One of these systems, called A,
AB  - has its genetic determinants located on the bacterial chromosome, linked to the
AB  - thr region.  This observation suggests its relation to the K- and B-specificity
AB  - types.  The genetic basis for the 15-specific and modification, on the other
AB  - hand, resides on a plasmid which by a number of criteria is shown to be related
AB  - to phage P1.  In particular, P1 and the plasmid in question seem to possess
AB  - homologous replicators.  In vivo complementation data obtained with various
AB  - restriction- and modification-deficient mutants measure the functional
AB  - relatedness of the various host specificity systems.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Linn, S.
TI  - DNA modification and restriction.
JO  - Annu. Rev. Biochem.
PY  - 1969
SP  - 467
EP  - 500
VL  - 38
AB  - In this review, we have subdivided the discussion on DNA modification and
AB  - restriction into three convenient (if somewhat arbitrary) areas of study:  (a)
AB  - the enzymatic activities in vivo and in vitro; (b) the substrate, with the
AB  - characterization of "specificity sites" as particular regions on DNA molecules
AB  - showing affinity for modification and restriction activities; and (c) the
AB  - genetic determinants for the enzymatic activities.  Limitations of length
AB  - necessitate the consideration of only those experimental observations which
AB  - seem to us the most relevant for the understanding of the phenomena.
AB  - Previously published reviews may fill some of the gaps that will appear, but
AB  - for the remaining ones we must refer the reader to the original literature.  In
AB  - particular, we regret the omission of studies made with bacterial strains other
AB  - than E. coli, although many of these systems seem strongly related in their
AB  - fundamental properties to those discussed here.  Finaly, the thoroughly
AB  - explored restriction by E. coli of unglucosylated T-even phage must also be
AB  - omitted.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Morse, M.L.
TI  - Host specificity of DNA produced by Escherichia coli.  VI.  Effects on bacterial conjugation.
JO  - Genetics
PY  - 1965
SP  - 137
EP  - 148
VL  - 51
AB  - Bacterial host cells endow the DNA of bacteriophage lambda and that of the
AB  - transducing phage lambda with host specificity (Arber and Dussoix 1962; Arber
AB  - 1964).  This label on the DNA plays an important role in phage infection.  In
AB  - the absence of the required host specificity, the bacteria degrade the DNA of
AB  - the infecting phage, which is then said to be restricted (Dussoix and Arber
AB  - 1962).  Preliminary evidence has been given by Arber and Dussoix (1961) and
AB  - Arber (1962) that bacterial DNA is also subject to this same control mechanism.
AB  - The enzymatic system endowing lambda DNA with host specificity would thus act
AB  - on the host DNA as well, and the host specificity could play a role in the
AB  - decision of whether DNA transferred in conjugation from male to female bacteria
AB  - is accepted or rejected.  This last action can be checked by measuring the
AB  - frequency of formation of recombinants, provided other factors antagonistic to
AB  - genetic integration, such as nonhomology of the male and female DNA molecules,
AB  - are also considered.  The present paper gives an account of experiments carried
AB  - out to investigate restriction in bacterial conjugation involving Hfr, F+,
AB  - F-gal+, F-lac+ and (RTF)+ donor strains.  Since our first experiments the
AB  - results have been confirmed and extended by various other investigators (Boice
AB  - and Luria 1963; Hoekstra and De Haan 1963; Glover, Schell, Symonds and Stacey
AB  - 1963; Pittard 1964; Boyer 1964).
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Rifat, A.
AU  - Wauters-Willems, D.
AU  - Kuhnlein, U.
TI  - Host specificity of DNA produced by Escherichia coli.
JO  - Mol. Gen. Genet.
PY  - 1972
SP  - 195
EP  - 207
VL  - 115
AB  - Bacteria with A-specific restriction plate unmodified phage lambda with an
AB  - efficiency of 10-2.  One mutational event can produce restriction insensitive
AB  - (sAo) mutants of lambda.  These differ from the original sA form of lambda by
AB  - no other property than their response to A-host specificity.  Two-parental
AB  - phage crosses involving sA and sAo, respectively, as non-selective marker
AB  - allowed to map sA between genes cII and O.  These data indicate that sA is the
AB  - only site on lambda DNA with affinity for A-specific restriction.  Lambda DNA
AB  - is thus an interesting substrate in in vitro A-specific restriction and
AB  - modification.  Using an assay based on the infectivity of lambda DNA on
AB  - helper-infected bacteria, A-specific modification activity was found in
AB  - partially purified sonicates of bacteria with A-host specificity.  In parallel
AB  - to modification, 3H-methyl label from S-adenosylmethionine, the only cofactor
AB  - required for modification, was transferred to unmodified lambda DNA.  No
AB  - association of radioactivity was observed in control experiments with DNA from
AB  - either modified lambda.A or from a lambda sAo mutant.  These data suggest that
AB  - A-specific modification is brought about by DNA methylation and that the sAo
AB  - mutation not only abolished the affinity for A-specific restriction, but also
AB  - for A-specific modification.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Smith, J.D.
TI  - Kinetics of reproduction of nucleic acids and their role in biosynthesis of proteins.
JO  - Int. Congr. Microbiol.
PY  - 1966
SP  - 5
EP  - 5
VL  - 5
AB  - Various filamentous, male specific phages containing single stranded DNA
AB  - undergo host-controlled modification in E. coli B and in P1 lysogenic bacteria.
AB  - The B-specific modification is directed by those gene regions of E. coli which
AB  - also are responsible for host-controlled modification of DNA of the bacterial
AB  - host itself, and of other phages such as lambda.  Study of restriction and
AB  - modification with phage fd reveals:  (1) a correlation between restriction in
AB  - phage reproduction and appearance of acid soluble breakdown products from the
AB  - infecting DNA molecule; (2) a correlation between occurrence of modification
AB  - and a distinct increase in the level of 6-methylaminopurine carried by the
AB  - phage DNA.  E. coli K12 does not restrict phage fd, nor does fd-K show a higher
AB  - level of methylated bases than fd grown on mutants of K12 which are deficient
AB  - in providing bacterial DNA with K-specific modification.  Absence of K-specific
AB  - sites on the small DNA molecule (about 4500 nucleotides) of phage fd could
AB  - reasonably explain these facts.  Bacteria of strain K12 infected at very low
AB  - multiplicity with 2H and 15N density labelled fdB liberate, among early progeny
AB  - phage, particles which still have the parental B-specific modification and
AB  - carry heavy, parental DNA molecules wrapped into light, new phage proteins.
AB  - This finding, besides confirming that host specificity of phage fd is closely
AB  - associated with the DNA molecule, demonstrates that single stranded DNA
AB  - molecules of infecting fd phage have a fair chance to be transferred into phage
AB  - progeny particles.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Wauters-Willems, D.
TI  - Host specificity of DNA produced by Escherichia coli. XII.  The two restriction and modification systems of strain 15T-.
JO  - Mol. Gen. Genet.
PY  - 1970
SP  - 203
EP  - 217
VL  - 108
AB  - E. coli 15T- carries two distinct sets of DNA restriction and modification
AB  - activities.  The genetic information for system A is contained in the bacterial
AB  - chromosome and linked to the thr region.  This fact suggests host specificity A
AB  - to be related to those of strains K and B.  The genes controlling system 15 are
AB  - on a plasmid which is related to phage P1: it competes with P1 for stable
AB  - inheritance in the carried state and it genetically recombines with P1.  This
AB  - recombination may produce plasmid genomes with newly assorted characters.  One
AB  - of them is an active, P1-like prophage with the 15-specific instead of the
AB  - parental P1-specific restriction and modification characters.  Superinfection
AB  - of 15T- with P1 may also result in curing of the bacteria from the restriction
AB  - plasmid.  Both A- and 15-specific restrictions and modifications act on
AB  - bacterial DNA, on the DNA of various sex factors and on the DNA of certain
AB  - bacteriophages, e.g. of phage lambda.  Phage 82 DNA is sensitive only to
AB  - 15-specific restriction, but not to A-specific restriction.  Independently of
AB  - the A- and 15-specific restrictions, the growth of phage lambdain E. coli 15T-
AB  - encounters another limitation of yet unknown nature.  No such limitation is
AB  - observed either with phage 82 or with mutants of lambda occurring at a
AB  - frequency of about 10-5.
ER  -

TY  - JOUR
AU  - Arber, W.
AU  - Yuan, R.
AU  - Bickle, T.A.
TI  - Strain-specific modification and restriction of DNA in bacteria.
JO  - Post Synthetic Modification of Macromolecules.  Symposium at 9th FEBS Meeting, Budapest. 1974
PY  - 1975
SP  - 3
EP  - 22
VL  - 34
AB  - Within the last few years bacterial restriction endonucleases have become an
AB  - important tool in genetic, structural and functional studies of DNA.  Many of
AB  - these enzymes reproducibly cleave large double-stranded DNA molecules at sites
AB  - determined by particular nucleotide sequences.  This yields unique populations
AB  - of smaller fragments.  Since the site of cleavage is usually unique for each
AB  - restriction endonclease, any genome can in principle be cleaved by application
AB  - of one or several properly chosen enzyme preparations into DNA fragments of any
AB  - desired length and containing any desired genetic message.  These possibilities
AB  - have attracted widespread attention to the molecular mechanism of these
AB  - enzymes, in particular their interaction with their DNA substrate.  Bacterial
AB  - strains producing restriction endonucleases must necessarily have developed a
AB  - mechanism to protect their own DNA from intracellular cleavage.  In those
AB  - strains studied up to date, this protection is brought about by the enzymatic
AB  - methylation of specific nucleotides and is generally known as strain-specific
AB  - modification of DNA.  This modification related methylation which usually
AB  - represents only a fraction of the methylated bases in DNA clearly defines one
AB  - of the roles of DNA methylation, that is to protect the nucleic acid from
AB  - specific endonucleolytic cleavage.  On the other hand, the biological role of
AB  - strain-specific restriction of DNA is generally believed to reside in a
AB  - primitive system of immunity of bacteria against invasion by foreign genetic
AB  - material.  Bacterial strains not possessing any known restriction-modification
AB  - system (R-M system) are perfectly viable.  Therefore, restriction appears to be
AB  - a dispensable function.  Nevertheless, many naturally occurring bacterial
AB  - strains do possess one or several independent R-M systems, which suggests that
AB  - restriction is not absolutely worthless to bacteria.  A closer look at several
AB  - R-M systems allows us to distinguish two general types of mechanisms.  These
AB  - were tentatively called type I and type II by Boyer (1971).  It is the object
AB  - of our contribution to this symposium to discuss the present state of knowledge
AB  - concerning these two types of restriction and modification mechanisms, and we
AB  - would like to do so by presenting selected examples rather than by strictly
AB  - defining the types.  It is quite likely that future studies may reveal other
AB  - mechanisms with distinctly different features.  Recently published reviews in
AB  - this field were written by Boyer (1971), Meselson et al. (1972) and Arber
AB  - (1974).  The nomenclature used follows the recommendations made by Arber and
AB  - Linn (1969), Smith and Nathans (1973) and Arber (1974).
ER  -

TY  - JOUR
AU  - Arbulu, S.
AU  - Frantzen, C.
AU  - Lohans, C.T.
AU  - Cintas, L.M.
AU  - Herranz, C.
AU  - Holo, H.
AU  - Diep, D.B.
AU  - Vederas, J.C.
AU  - Hernandez, P.E.
TI  - Draft Genome Sequence of the Bacteriocin-Producing Strain Enterococcus faecium M3K31, Isolated from Griffon Vultures (Gyps fulvus subsp. fulvus).
JO  - Genome Announcements
PY  - 2016
SP  - e00055
EP  - e00016
VL  - 4
AB  - Enterococcus faeciumM3K31 is a bacteriocinogenic lactic acid bacterium (LAB) isolated from
AB  - griffon vulture (Gyps fulvussubsp.fulvus) feces. The draft genome
AB  - sequence of this strain provides genetic data that support its biotechnological
AB  - potential.
ER  -

TY  - JOUR
AU  - Arbulu, S.
AU  - Jimenez, J.J.
AU  - Borrero, J.
AU  - Sanchez, J.
AU  - Frantzen, C.
AU  - Herranz, C.
AU  - Nes, I.F.
AU  - Cintas, L.M.
AU  - Diep, D.B.
AU  - Hernandez, P.E.
TI  - Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos).
JO  - Genome Announcements
PY  - 2016
SP  - e00663
EP  - e00616
VL  - 4
AB  - Here, we report the draft genome sequence of Enterococcus faecalis DBH18, a bacteriocinogenic
AB  - lactic acid bacterium (LAB) isolated from mallard ducks (Anas
AB  - platyrhynchos). The assembly contains 2,836,724 bp, with a G+C content of 37.6%.
AB  - The genome is predicted to contain 2,654 coding DNA sequences (CDSs) and 50 RNAs.
ER  -

TY  - JOUR
AU  - Archer, C.T.
AU  - Kim, J.F.
AU  - Jeong, H.
AU  - Park, J.H.
AU  - Vickers, C.E.
AU  - Lee, S.Y.
AU  - Nielsen, L.K.
TI  - The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli.
JO  - BMC Genomics
PY  - 2011
SP  - 9
EP  - 9
VL  - 12
AB  - biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory
AB  - purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe
AB  - strain that can utilize sucrose as a carbon source.  Lifecycle analysis has demonstrated that
AB  - sucrose from sugarcane is a preferred carbon source for industrial
AB  - bioprocesses.  Results: We have sequenced and annotated the genome of E. coli W. The
AB  - chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2
AB  - (5,360 bp), are also present. W has unique features relative to other sequenced laboratory
AB  - strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than
AB  - A. W also grows on a much broader range of carbon sources than does K-12.
AB  - A genome-scale reconstruction was developed and validated in order to interrogate metabolic
AB  - properties.  Conclusions: The genome of W is more similar to commensal and pathogenic B1
AB  - strains than phylogroup A strains, and therefore has greater utility for comparative analyses
AB  - with these strains. W should therefore be the strain of choice, or 'type strain' for group
AB  - B1 comparative analyses. The genome annotation and tools created here
AB  - are expected to allow further utilization and development of E. coli W as an industrial
AB  - organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction
AB  - allow it to more accurately define E. coli metabolism relative to previous models.
ER  -

TY  - JOUR
AU  - Arden, S.B.
AU  - Barksdale, L.
TI  - Restriction and modification and the phage typing of true Corynebacteria.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1971
SP  - 181
EP  - 181
VL  - 71
AB  - Corynebacterium ulcerans, strain 603, neither restricts nor modifies phages Z
AB  - and Zv.  However, C. diphtheriae, strain C7, C. ovis, strain 21, and C.
AB  - belfanti, strain 1030, each produces a distinct restricting endonuclease.
AB  - These we have designated r1, r2, r3, respectively.  Each is in turn linked to a
AB  - distinct host controlled modification which specifically and epigenetically
AB  - renders the phage DNA immune to the action of restricting enzyme.  These are
AB  - designated m1, m2 and m3.  Thus, whereas strain 603 is m0r0, nonrestricting
AB  - nonmodifying, strain C7 is m1r1.  Stocks of Zv phage produced in C7 have the m1
AB  - phenotype.  By preparing phage stocks of m0, m1, m2 and m3 phenotypes the
AB  - discriminatory powers of these phages have been extended when used in
AB  - conjunction with bar mutation and lysogenic immunity in a system of phage
AB  - typing.  This system allows for distinguishing between each of 21 bacteria,
AB  - some of which differ from one another by only one gene; some by one prophage.
AB  - Since the host strains require methionine, certain comparisons between the
AB  - basis for the modification in Zv and that reported for lambda can be made.
ER  -

TY  - JOUR
AU  - Ardley, J.
AU  - Tian, R.
AU  - Howieson, J.
AU  - Yates, R.
AU  - Brau, L.
AU  - Han, J.
AU  - Lobos, E.
AU  - Huntemann, M.
AU  - Chen, A.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 5
EP  - 5
VL  - 9
AB  - Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing
AB  - microsymbionts of species of the African crotalarioid genus Listia. Strain
AB  - WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in
AB  - 2002 from a Listia bainesii root nodule collected at Estcourt Research Station in
AB  - South Africa. Here we describe the features of Methylobacterium sp. WSM2598,
AB  - together with information and annotation of a high-quality draft genome sequence.
AB  - The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains
AB  - 7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome
AB  - is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E
AB  - ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB)
AB  - project.
ER  -

TY  - JOUR
AU  - Ardley, J.
AU  - Tian, R.
AU  - O'Hara, G.
AU  - Seshadri, R.
AU  - Reddy, T.B.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Howieson, J.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a  microsymbiont isolated from Medicago polymorpha growing in alkaline soil.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 126
EP  - 126
VL  - 10
AB  - Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can
AB  - exist as a soil saprophyte or as a legume microsymbiont of Medicago
AB  - species. WSM244 was isolated in 1979 from a nodule recovered from the roots of
AB  - the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer,
AB  - Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced
AB  - to date. It is effective at fixing nitrogen with M. polymorpha L., as well as
AB  - with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M.
AB  - scutellata (L.) Mill., M. tornata (L.) Mill. and M. truncatula Gaertn. This
AB  - strain is also effective with the perennial M. sativa L. Here we describe the
AB  - features of E. medicae WSM244, together with genome sequence information and its
AB  - annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into
AB  - 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only
AB  - encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
AB  - Nodule Bacteria (GEBA-RNB) project proposal.
ER  -

TY  - JOUR
AU  - Areechon, N.
AU  - Kannika, K.
AU  - Hirono, I.
AU  - Kondo, H.
AU  - Unajak, S.
TI  - Draft Genome Sequences of Streptococcus agalactiae Serotype Ia and III Isolates from Tilapia Farms in Thailand.
JO  - Genome Announcements
PY  - 2016
SP  - e00122
EP  - e00116
VL  - 4
AB  - Streptococcus agalactiaeserotypes Ia and III were isolated from infected tilapia  in cage and
AB  - pond culture farms in Thailand during 2012 to 2014, in which
AB  - pathogenicity analysis demonstrated that serotype III showed higher virulence
AB  - than serotype Ia. Here, we report the draft genome sequencing of piscineS.
AB  - agalactiaeserotypes Ia and III.
ER  -

TY  - JOUR
AU  - Arena, F.
AU  - Henrici, De.A.L.
AU  - Pieralli, F.
AU  - Di Pilato, V.
AU  - Giani, T.
AU  - Torricelli, F.
AU  - D'Andrea, M.M.
AU  - Rossolini, G.M.
TI  - Draft Genome Sequence of the First Hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a Bloodstream Infection.
JO  - Genome Announcements
PY  - 2015
SP  - e00952
EP  - e00915
VL  - 3
AB  - Klebsiella quasipneumoniae is a recently described species, formerly identified as K.
AB  - pneumoniae phylogroup KpII. Information on pathogenic and virulence potential of this species
AB  - are lacking. We sequenced the genome of a hypermucoviscous K. quasipneumoniae clinical isolate
AB  - showing a virulence genes content (allABCDRS, kfuABC, and mrkABCDFHIJ) peculiar to
AB  - hypervirulent K. pneumoniae strains.
ER  -

TY  - JOUR
AU  - Arens, J.C.
AU  - Haltli, B.
AU  - Kerr, R.G.
TI  - Draft Genome Sequence of Kitasatospora griseola Strain MF730-N6, a Bafilomycin, Terpentecin, and Satosporin Producer.
JO  - Genome Announcements
PY  - 2015
SP  - e00208
EP  - e00215
VL  - 3
AB  - We report here the draft genome sequence of Kitasatospora griseola strain MF730-N6, a known
AB  - producer of bafilomycin, terpentecin, and satosporins. The
AB  - current assembly comprises 8 contigs covering 7.97 Mb. Genome annotation revealed
AB  - 7,225 protein coding sequences, 100 tRNAs, 40 rRNA genes, and 23 secondary
AB  - metabolite biosynthetic gene clusters.
ER  -

TY  - JOUR
AU  - Argast, G.M.
AU  - Stephens, K.M.
AU  - Emond, M.J.
AU  - Monnat, R.J. Jr.
TI  - I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 345
EP  - 353
VL  - 280
AB  - Plasmid libraries containing partially randomized cleavage sites for the eukaryotic homing
AB  - endonucleases I-PpoI and I-CreI were constructed, and sites that could be cleaved by I-PpoI or
AB  - I-CreI were selectively recovered by successive cycles of cleavage and gel separation followed
AB  - by religation and growth in Escherichia coli.  Twenty-one different I-PpoI-sensitive homing
AB  - sites, including the native homing site, were isolated.  These sites were identical at four
AB  - nucleotide positions within the 15 bp homing site, had a restricted pattern of base
AB  - substitutions at the remaining 11 positions and displayed a preference for purines flanking
AB  - the top strand of the homing site sequence.  Twenty-one different I-CreI-sensitive homing
AB  - sites, including the native site, were isolated.  Ten nucleotide positions were identical in
AB  - homing site variants that were I-CreI-sensitive and required the addition of SDS for efficient
AB  - cleavage product release.  Four of those ten positions were identical in homing sites that did
AB  - not require SDS for product release.  There was a preference for pyrimidines flanking the top
AB  - strand of the homing site sequence.  Three of the 24 I-CreI homing site nucleotide positions
AB  - apparently lacked informational content, i.e. were permissive of cleavage when occupied by any
AB  - nucleotide.  These results suggest that I-PpoI and I-CreI make a larger number of DNA-protein
AB  - contacts across their homing site sequences, and that different subsets of these contacts may
AB  - be sufficient to maintain a high degree of sequence-specific homing site recognition and
AB  - cleavage.  The sequential enrichment protocol we used should be useful for defining the
AB  - sequence degeneracy and informational content of other homing endonuclease target sites.
ER  -

TY  - JOUR
AU  - Argemi, X.
AU  - Martin, V.
AU  - Loux, V.
AU  - Dahyot, S.
AU  - Lebeurre, J.
AU  - Guffroy, A.
AU  - Martin, M.
AU  - Velay, A.
AU  - Keller, D.
AU  - Riegel, P.
AU  - Hansmann, Y.
AU  - Paul, N.
AU  - Prevost, G.
TI  - Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 0
EP  - 0
VL  - 9
AB  - Coagulase negative staphylococci are normal inhabitant of the human skin flora
AB  - that account for an increasing number of infections, particularly
AB  - hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most
AB  - virulent species causing various infections with clinical characteristics close
AB  - to what clinicians usually observe with Staphylococcus aureus and both bacteria
AB  - share more than 70% of their genome. Virulence of S. aureus relies on a large
AB  - repertoire of virulence factors, many of which are encoded on mobile genetic
AB  - elements. S. lugdunensis also bears various putative virulence genes but only one
AB  - complete genome with extensive analysis has been published with one prophage
AB  - sequence (phiSL2) and a unique plasmid was previously described. In this study,
AB  - we performed de novo sequencing, whole genome assembly and annotation of seven
AB  - strains of S. lugdunensis from VISLISI clinical trial. We searched for the
AB  - presence of virulence genes and mobile genetics elements using bioinformatics
AB  - tools. We identified four new prophages, named phiSL2 to phiSL4, belonging to the
AB  - Siphoviridae class and five plasmids, named pVISLISI_1 to pVISLISI_5. Three
AB  - plasmids are homologous to known plasmids that include, amongst others, one S.
AB  - aureus plasmid. The two other plasmids were not described previously. This study
AB  - provides a new context for the study of S. lugdunensis virulence suggesting the
AB  - occurrence of several genetic recombination' with other staphylococci.
ER  -

TY  - JOUR
AU  - Argos, P.
TI  - Evidence for a repeating domain in type I restriction enzymes.
JO  - EMBO J.
PY  - 1985
SP  - 1351
EP  - 1355
VL  - 4
AB  - The primary structures of the recognition subunit (hsdS) in type I restriction
AB  - enzymes from three isolates of Escherichia coli were compared and aligned by
AB  - use of amino acid physical properties.  A repeating domain was found in each of
AB  - the subunits suggesting a pseudo-dimeric structure.  Secondary structure
AB  - predictions delineated two helical regions in each domain which suggested that
AB  - the recognition subunits may act in a fashion similar to that proposed for
AB  - repressor and activator molecules; namely, interaction with double-stranded DNA
AB  - through helices and in two successive major grooves on the same DNA side.  One
AB  - helical motif could provide the specific recognition site and the other, the
AB  - restriction site.
ER  -

TY  - JOUR
AU  - Arimondo, P.B.
TI  - IDENTIFICATION AND DESIGN OF NEW C5-DNA METHYLTRANSFERASE INHIBITORS AND THEIR BIOLOGICAL ACTIVITY.
JO  - Anticancer Res.
PY  - 2014
SP  - 5813
EP  - 5814
VL  - 34
AB  - DNA methylation is involved in the regulation of gene expression and plays an important role
AB  - in normal developmental processes and disease.  In particular, the epigenetic landscape is
AB  - altered in cancers where abnormal hypermethylation leads to silencing of certain genes such as
AB  - tumor suppressor genes.  In mammals, DNA methyltransferases are the enzymes responsible for
AB  - DNa methylation on the position 5 of cytidine in a CpG context.  Few direct enzyme inhibitors
AB  - are known and those have several drawbacks.  In order to identify novel inhibitors, we
AB  - developed three chemical strategies.  First a fluorescene High-Throughput Screening for the
AB  - inhibition of the murine catalytic Dnmt3a/3L complex on the chemical library of the Museum
AB  - Naturelle d'Historie Naturelle and found twelve hits with low micromolar activities.
AB  - Interestingly, they showed little cytotoxicity.  Dichlone, a small halogenated naphthoquinone,
AB  - classically used as pesticide and fungicide, showed the lowest Ec50 at 460 NM.  Two molecules
AB  - including Dichlone, efficiently reactivated YFP gene expression in a stable HEK293 cell line
AB  - by promoter demethylation.  Their efficacy was comparable to the DNMT inhibitor of reference
AB  - 5-azecytidine.  Second, based on molecular modeling studies of quinolone inhibitor SGI1027 in
AB  - the crystal structure of M.HhaI C5 DNA methyltransferase, suggesting that the quinolone and
AB  - the aminopyridimine are important for the interaction with the substrates and the protein, we
AB  - synthesized twenty five new derivatives.
ER  -

TY  - JOUR
AU  - Arivett, B.A.
AU  - Fiester, S.E.
AU  - Ream, D.C.
AU  - Centron, D.
AU  - Ramirez, M.S.
AU  - Tolmasky, M.E.
AU  - Actis, L.A.
TI  - Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00212
EP  - e00215
VL  - 3
AB  - Acinetobacter baumannii is a bacterial pathogen with serious implications on human health, due
AB  - to increasing reports of multidrug-resistant strains isolated
AB  - from patients. Total DNA from the multidrug-resistant A. baumannii strain A155
AB  - clinical isolate was sequenced to greater than 65x coverage, providing
AB  - high-quality contig assemblies.
ER  -

TY  - JOUR
AU  - Arivett, B.A.
AU  - Ream, D.C.
AU  - Fiester, S.E.
AU  - Kidane, D.
AU  - Actis, L.A.
TI  - Draft Genome Sequences of Pseudomonas aeruginosa Isolates from Wounded Military Personnel.
JO  - Genome Announcements
PY  - 2016
SP  - e00829
EP  - e00816
VL  - 4
AB  - Pseudomonas aeruginosa, a Gram-negative bacterium that causes severe hospital-acquired
AB  - infections, is grouped as an ESKAPE (Enterococcus faecium,
AB  - Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii,
AB  - Pseudomonas aeruginosa, and Enterobacter species) pathogen because of its
AB  - extensive drug resistance phenotypes and effects on human health worldwide. Five
AB  - multidrug resistant P. aeruginosa strains isolated from wounded military
AB  - personnel were sequenced and annotated in this work.
ER  -

TY  - JOUR
AU  - Arivett, B.A.
AU  - Ream, D.C.
AU  - Fiester, S.E.
AU  - Kidane, D.
AU  - Actis, L.A.
TI  - Draft Genome Sequences of Escherichia coli Isolates from Wounded Military Personnel.
JO  - Genome Announcements
PY  - 2016
SP  - e00828
EP  - e00816
VL  - 4
AB  - Members of the Escherichia coli bacterial family have been grouped as ESKAPE (Enterococcus
AB  - faecium, Staphylococcus aureus, Klebsiella pneumoniae,
AB  - Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species)
AB  - pathogens because of their extensive drug resistance phenotypes and increasing
AB  - threat to human health. The genomes of six extended-spectrum beta-lactamase
AB  - (ESBL)-producing E. coli strains isolated from wounded military personnel were
AB  - sequenced and annotated.
ER  -

TY  - JOUR
AU  - Arivett, B.A.
AU  - Ream, D.C.
AU  - Fiester, S.E.
AU  - Kidane, D.
AU  - Actis, L.A.
TI  - Draft Genome Sequences of Acinetobacter baumannii Isolates from Wounded Military  Personnel.
JO  - Genome Announcements
PY  - 2016
SP  - e00773
EP  - e00716
VL  - 4
AB  - Acinetobacter baumannii is a Gram-negative bacterium capable of causing hospital-acquired
AB  - infections that has been grouped with Enterococcus faecium,
AB  - Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii,
AB  - Pseudomonas aeruginosa, and Enterobacter species as ESKAPE pathogens because of
AB  - their extensive drug resistance phenotypes and increasing risk to human health.
AB  - Twenty-four multidrug-resistant A. baumannii strains isolated from wounded
AB  - military personnel were sequenced and annotated.
ER  -

TY  - JOUR
AU  - Arivett, B.A.
AU  - Ream, D.C.
AU  - Fiester, S.E.
AU  - Mende, K.
AU  - Murray, C.K.
AU  - Thompson, M.G.
AU  - Kanduru, S.
AU  - Summers, A.M.
AU  - Roth, A.L.
AU  - Zurawski, D.V.
AU  - Actis, L.A.
TI  - Draft Genome Sequences of Klebsiella pneumoniae Clinical Type Strain ATCC 13883 and Three Multidrug-Resistant Clinical Isolates.
JO  - Genome Announcements
PY  - 2015
SP  - e01385
EP  - e01314
VL  - 3
AB  - Klebsiella pneumoniae is a Gram-negative human pathogen capable of causing hospital-acquired
AB  - infections with an increasing risk to human health. The total
AB  - DNA from four clinically relevant strains was sequenced to >100x coverage,
AB  - providing high-quality genome assemblies for K. pneumoniae strains ATCC 13883,
AB  - KP4640, 101488, and 101712.
ER  -

TY  - JOUR
AU  - Armalyte, E.
AU  - Bujnicki, J.M.
AU  - Giedriene, J.
AU  - Gasiunas, G.
AU  - Kosinski, J.
AU  - Lubys, A.
TI  - Mva1269I: A monomeric type IIS restriction endonuclease from micrococcus varians with two EcoRI- and FokI-like catalytic domains.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 41584
EP  - 41594
VL  - 280
AB  - Type II restriction endonuclease Mva1269I recognizes an asymmetric DNa sequence 5'-GAATGCN*
AB  - -3'/5' -NG* CATTC-3' and cuts top and bottom DNA strands at positions, indicated by the "*"
AB  - symbol.  Most restriction endonucleases require dimerization to cleave both strands of DNA.
AB  - We found that Mva1269I is a monomer both in solution and upon binding of cognate DNA.  Protein
AB  - fold-recognition analysis revealed that Mva1269I comprises two "PD-(D/E)XK" domains.  The
AB  - N-terminal domain is related to the 5'-GAATTC-3'-specific restriction endonuclease EcoRI,
AB  - whereas the C-terminal one resembles the nonspecific nuclease domain is related to the
AB  - 5'-GAATTC-3'-specific restriction endonuclease EcoRI, whereas the C-terminal one resembles
AB  - the nonspecific nuclease domain of restriction endonuclease FokI.  Inactivation of the
AB  - C-terminal catalytic site transformed Mva1269I into a very active bottom strand-nicking
AB  - enzyme, whereas mutants in the N-terminal domain nicked the top strand, but only at elevated
AB  - enzyme concentrations.  We found that the cleavage of the bottom strand is a prerequisite for
AB  - the cleavage of the top strand.  We suggest that Mva1269I evolved the ability to recognize and
AB  - to cleave its asymmetrical target by a fusion of an EcoRI-like domain, which incises the
AB  - bottom strand within the target, and a FokI-like domain that completes the cleavage within the
AB  - nonspecific region outside the target sequence.  Our results have implications for the
AB  - molecular evolution of restriction endonucleases, as well as for perspectives of engineering
AB  - new restriction and nicking enzymes with asymmetric target sites.
ER  -

TY  - JOUR
AU  - Armbrust, E.V. et al.
TI  - The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.
JO  - Science
PY  - 2004
SP  - 79
EP  - 86
VL  - 306
AB  - Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are
AB  - responsible for approximately 20% of global carbon
AB  - fixation. We report the 34 million-base pair draft nuclear genome of the
AB  - marine diatom Thalassiosira pseudonana and its 129 thousand-base pair
AB  - plastid and 44 thousand-base pair mitochondrial genomes. Sequence and
AB  - optical restriction mapping revealed 24 diploid nuclear chromosomes. We
AB  - identified novel genes for silicic acid transport and formation of
AB  - silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes
AB  - for several types of polyunsaturated fatty acids, use of a range of
AB  - nitrogenous compounds, and a complete urea cycle, all attributes that
AB  - allow diatoms to prosper in aquatic environments.
ER  -

TY  - JOUR
AU  - Armbruster, C.E.
AU  - Smith, S.N.
AU  - Johnson, A.O.
AU  - DeOrnellas, V.
AU  - Eaton, K.A.
AU  - Yep, A.
AU  - Mody, L.
AU  - Wu, W.
AU  - Mobley, H.L.
TI  - The Pathogenic Potential of Proteus mirabilis is Enhanced by Other Uropathogens During Polymicrobial Urinary Tract Infection.
JO  - Infect. Immun.
PY  - 2017
SP  - e00808
EP  - e00816
VL  - 85
AB  - Urinary catheter use is prevalent in health care settings, and polymicrobial
AB  - colonization by urease-positive organisms, such as Proteus mirabilis and
AB  - Providencia stuartii, commonly occurs with long-term catheterization. We
AB  - previously demonstrated that coinfection with P. mirabilis and P. stuartii
AB  - increased overall urease activity in vitro and disease severity in a model of
AB  - urinary tract infection (UTI). In this study, we expanded these findings to a
AB  - murine model of catheter-associated UTI (CAUTI), delineated the contribution of
AB  - enhanced urease activity to coinfection pathogenesis, and screened for enhanced
AB  - urease activity with other common CAUTI pathogens. In the UTI model, coinfected
AB  - mice exhibited higher urine pH values, urolithiasis, bacteremia, and more
AB  - pronounced tissue damage and inflammation compared to single infections, despite
AB  - having a similar bacterial burden within the urinary tract. The presence of P.
AB  - stuartii, regardless of urease production by this organism, was sufficient to
AB  - enhance P. mirabilis urease activity and increase disease severity, and enhanced
AB  - urease activity was the predominant factor driving tissue damage and
AB  - dissemination of both organisms to the bloodstream during coinfection. These
AB  - findings were largely recapitulated in the CAUTI model. Other uropathogens also
AB  - enhanced P. mirabilis urease activity in vitro, including recent clinical
AB  - isolates of Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, and
AB  - Pseudomonas aeruginosa. We therefore conclude that the underlying mechanism of
AB  - enhanced urease activity may represent a widespread target for limiting
AB  - detrimental consequences of polymicrobial catheter colonization, particularly by
AB  - P. mirabilis and other urease-positive bacteria.
ER  -

TY  - JOUR
AU  - Armitano, R.I.
AU  - Zerbetto, De.P.G.
AU  - Matteo, M.J.
AU  - Revale, S.
AU  - Romero, S.
AU  - Traglia, G.M.
AU  - Catalano, M.
TI  - Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease.
JO  - Genome Announcements
PY  - 2013
SP  - e00700
EP  - e00713
VL  - 1
AB  - Helicobacter pylori colonizes the human gastric mucosa, leading to a spectrum of  gastric
AB  - diseases in susceptible populations. Here we announce the draft genome
AB  - sequences of strains HPARG8G and HPARG63. The data for both genome sequences
AB  - provide insights regarding the diversity in gene content and rearrangement of the
AB  - genomic islands commonly harbored by H. pylori.
ER  -

TY  - JOUR
AU  - Armstrong, K.
AU  - Bauer, W.R.
TI  - Preferential site-dependent cleavage by restriction endonuclease PstI.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 993
EP  - 1007
VL  - 10
AB  - The four identical recognition sites for the restriction endonuclease PstI in
AB  - purified plasmid pSM1 DNA I are cleaved at markedly different rates.  The order
AB  - and relative frequencies of cleavage at these four PstI sites have been
AB  - determined from the order of appearance of partial cleavage products and from
AB  - an analysis of production of specific unit length linear molecules.  The same
AB  - pattern of preferential cleavage is also found when linear, nicked circular, or
AB  - relaxed closed circular forms of the same plasmid DNA are used as substrates
AB  - for PstI.  Inspection of the nucleotide sequences immediately adjoining each of
AB  - the PstI sites suggests that the presence of adjacent runs of G-C base pairs
AB  - confers significant resistance to cleavage.
ER  -

TY  - JOUR
AU  - Armstrong, K.A.
AU  - Bauer, W.R.
TI  - Site-dependent cleavage of pBR322 DNA by restriction endonuclease HinfI.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 4109
EP  - 4126
VL  - 11
AB  - Cleavage of pBR322 DNA I by the restriction endonuclease HinfI is preferentially inhibited at
AB  - specific HinfI cleavage sites.  These sites in pBR322 DNA I have been identified and ordered
AB  - with respect to the frequency with which they are cleaved.  The HinfI site most resistant to
AB  - cleavage in pBR322 DNA I is unique in that runs of G-C base pairs are immediately adjacent on
AB  - both sides.  Two differently permuted linear (DNA III) species were produced by cleavage with
AB  - two different restriction endonucleases, PstI and AvaI.  Only one of these linear molecules,
AB  - that produced by PstI, exhibits the same preferential cleavage pattern as DNA I.  The second
AB  - linear species, that arising from AvaI digestion, shows pronounced relative inhibition of
AB  - cleavage at the HinfI sites nearest the ends of the molecule (100 and 120 base pairs away,
AB  - respectively).  This result suggests that proximity to the termini of a linear DNA molecule
AB  - might also influence preferential cleavage.  The possibility of formation of stem-loop
AB  - structures does not appear to influence preferential cleavage by HinfI.
ER  -

TY  - JOUR
AU  - Arnold, H.P.
AU  - Ziese, U.
AU  - Zillig, W.
TI  - SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus.
JO  - Virology
PY  - 2000
SP  - 409
EP  - 416
VL  - 272
AB  - We describe a novel virus, SNDV (Sulfolobus neozealandicus droplet-shaped virus), of the
AB  - crenarchaeotal archaeon Sulfolobus, which was found in a carrier state in a Sulfolobus strain
AB  - isolated from a field sample from New Zealand. SNDV particles are droplet-shaped and densely
AB  - covered by thin tail fibers at their pointed ends. The virion consists of a core and a coat.
AB  - The latter has the appearance of a beehive and has a surface that is either helically ribbed
AB  - or a stack of hoops. The genome is cccDNA of 20 kb, which is modified by dam-like methylation.
AB  - It is cleaved by only a few type II restriction enzymes e.g., DpnI but not MboI, demonstrating
AB  - an N(6)-methylation of the adenine residue in GATC sequences. The DNA-modifying system
AB  - differentiates between virus and host. We postulate a virus-encoded methylase that is active
AB  - on hemimethylated DNA. The host range of SNDV is confined to few Sulfolobus strains from New
AB  - Zealand.  The virus persists in an unstable carrier state rather than as a prophage. Due to
AB  - its uniqueness we propose to assign it to a novel virus family termed Guttaviridae.
ER  -

TY  - JOUR
AU  - Arnold, J.W.
AU  - Monteagudo-Mera, A.
AU  - Altermann, E.
AU  - Cadenas, M.B.
AU  - Thompson, A.L.
AU  - Azcarate-Peril, M.A.
TI  - Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants.
JO  - Genome Announcements
PY  - 2017
SP  - e00107
EP  - e00117
VL  - 5
AB  - Probiotics provide health benefits to their hosts, including modulation of host immune
AB  - response, inhibition of colonization by pathogens, modulation of the gut
AB  - microbiota, and epithelial barrier enhancement. Here, we present the draft genome
AB  - sequences of two newly isolated Lactobacillus rhamnosus strains of probiotic
AB  - potential from healthy human infants.
ER  -

TY  - JOUR
AU  - Arnold, M.
AU  - Wibberg, D.
AU  - Blom, J.
AU  - Schatschneider, S.
AU  - Winkler, A.
AU  - Kutter, Y.
AU  - Ruckert, C.
AU  - Albersmeier, A.
AU  - Albaum, S.
AU  - Goesmann, A.
AU  - Zange, S.
AU  - Heesemann, J.
AU  - Puhler, A.
AU  - Hogardt, M.
AU  - Vorholter, F.J.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic  ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum.
JO  - Genome Announcements
PY  - 2015
SP  - e00680
EP  - e00615
VL  - 3
AB  - Pseudomonas aeruginosa is an opportunistic pathogen that typically infects patients with a
AB  - compromised immune defense. Here, we present the improved 6.5-Mb
AB  - draft genome of strain WS136, an ExoS-positive and ExoU-negative highly cytotoxic
AB  - chronic wound isolate recovered from pyoderma gangrenosum of a patient who
AB  - received bone marrow transplantation.
ER  -

TY  - JOUR
AU  - Arnould, S.
AU  - Chames, P.
AU  - Perez, C.
AU  - Lacroix, E.
AU  - Duclert, A.
AU  - Epinat, J.C.
AU  - Stricher, F.
AU  - Petit, A.S.
AU  - Patin, A.
AU  - Guillier, S.
AU  - Rolland, S.
AU  - Prieto, J.
AU  - Blanco, F.J.
AU  - Bravo, J.
AU  - Montoya, G.
AU  - Serrano, L.
AU  - Duchateau, P.
AU  - Paques, F.
TI  - Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 443
EP  - 458
VL  - 355
AB  - The last decade has seen the emergence of a universal method for precise and efficient genome
AB  - engineering. This method relies on the use of sequence-specific endonucleases such as homing
AB  - endonucleases. The structures of several of these proteins are known, allowing for
AB  - site-directed mutagenesis of residues essential for DNA binding. Here, we show that a
AB  - semi-rational approach can be used to derive hundreds of novel proteins from I-CreI, a homing
AB  - endonuclease from the LAGLIDADG family. These novel endonucleases display a wide range of
AB  - cleavage patterns in yeast and mammalian cells that in most cases are highly specific and
AB  - distinct from I-CreI. Second, rules for protein/DNA interaction can be inferred from
AB  - statistical analysis. Third, novel endonucleases can be combined to create heterodimeric
AB  - protein species, thereby greatly enhancing the number of potential targets. These results
AB  - describe a straightforward approach for engineering novel endonucleases with tailored
AB  - specificities, while preserving the activity and specificity of natural homing endonucleases,
AB  - and thereby deliver new tools for genome engineering.
ER  -

TY  - JOUR
AU  - Arnould, S.
AU  - Delenda, C.
AU  - Grizot, S.
AU  - Desseaux, C.
AU  - Paques, F.
AU  - Silva, G.H.
AU  - Smith, J.
TI  - The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy.
JO  - Protein Eng. Des. Sel.
PY  - 2011
SP  - 27
EP  - 31
VL  - 24
AB  - Meganucleases (MNs) are highly specific enzymes that can induce homologous recombination in
AB  - different types of cells, including
AB  - mammalian cells. Consequently, these enzymes are used as scaffolds for
AB  - the development of custom gene-targeting tools for gene therapy or
AB  - cell-line development. Over the past 15 years, the high resolution
AB  - X-ray structures of several MNs from the LAGLIDADG family have improved
AB  - our understanding of their protein-DNA interaction and mechanism of DNA
AB  - cleavage. By developing and utilizing high-throughput screening methods
AB  - to test a large number of variant-target combinations, we have been
AB  - able to re-engineer scores of I-CreI derivatives into custom enzymes
AB  - that target a specific DNA sequence of interest. Such customized MNs,
AB  - along with wild-type ones, have allowed for exploring a large range of
AB  - biotechnological applications, including protein-expression cell-line
AB  - development, genetically modified plants and animals and therapeutic
AB  - applications such as targeted gene therapy as well as a novel class of
AB  - antivirals.
ER  -

TY  - JOUR
AU  - Arnould, S.
AU  - Perez, C.
AU  - Cabaniols, J.-P.
AU  - Smith, J.
AU  - Gouble, A.
AU  - Grizot, S.
AU  - Epinat, J.-C.
AU  - Duclert, A.
AU  - Duchateau, P.
AU  - Paques, F.
TI  - Engineered I-Crel derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 49
EP  - 65
VL  - 371
AB  - Meganucleases are sequence-specific endonucleases which recognize large (> 12 bp) target sites
AB  - in living cells and can stimulate homologous
AB  - gene targeting by a 1000-fold factor at the cleaved locus. We have
AB  - recently described a combinatorial approach to redesign the I-Crel
AB  - meganuclease DNA-binding interface, in order to target chosen
AB  - sequences. However, engineering was limited to the protein regions
AB  - shown to directly interact with DNA in a base-specific manner. Here, we
AB  - take advantage of I-Crel natural degeneracy, and of additional
AB  - refinement steps to extend the number of sequences that can be
AB  - efficiently cleaved. We searched the sequence of the human XPC gene,
AB  - involved in the disease Xeroderma Pigmentosum (XP), for potential
AB  - targets, and chose three sequences that differed from the I-Crel
AB  - cleavage site over their entire length, including the central four
AB  - base-pairs, whose role in the DNA/protein recognition and cleavage
AB  - steps remains very elusive. Two out of these targets could be cleaved
AB  - by engineered I-Crel derivatives, and we could improve the activity of
AB  - weak novel meganucleases, to eventually match the activity of the
AB  - parental I-Crel scaffold. The novel proteins maintain a narrow cleavage
AB  - pattern for cognate targets, showing that the extensive redesign of the
AB  - I-Crel protein was not made at the expense of its specificity. Finally,
AB  - we used a chromosomal reporter system in CHO-K1 cells to compare the
AB  - gene targeting frequencies induced by natural and engineered
AB  - meganucleases. Tailored I-Crel derivatives cleaving sequences from the
AB  - XPC gene were found to induce high levels of gene targeting, similar to
AB  - the I-Crel scaffold or the I-SceI "gold standard". This is the first
AB  - time an engineered homing endonuclease has been used to modify a
AB  - chromosomal locus.
ER  -

TY  - JOUR
AU  - Arraj, J.A.
AU  - Marinus, M.G.
TI  - Phenotypic reversal in dam mutants of Escherichia coli K-12 by a recombinant plasmid containing the dam+ gene.
JO  - J. Bacteriol.
PY  - 1983
SP  - 562
EP  - 565
VL  - 153
AB  - A recombinant plasmid, pMQ3, carrying the dam gene of Escherichia coli K-12, was constructed
AB  - and transformed into dam+ and dam- strains. Both dam- and dam+ strains containing pMQ3 showed
AB  - a wild phenotype for all traits, including mutation rate, except for a 10-fold increase in DNA
AB  - adenine methylase activity.
ER  -

TY  - JOUR
AU  - Arraj, J.A.
AU  - Wu, T.-H.
AU  - Marinus, M.G.
TI  - Expression of a DNA methylation (dam) gene in Escherichia coli K-12.
JO  - Curr. Microbiol.
PY  - 1990
SP  - 133
EP  - 136
VL  - 20
AB  - Plasmid pMQ3, carrying the dam gene of Escherichia coli on a 6.1 Kb fragment, shows a tenfold
AB  - increase in relative DNA adenine methylase activity, while plasmid pdam118, with a 1.14 Kb dam
AB  - insert, shows only a twofold increase, although both plasmids were derived from plasmid
AB  - pLC13-42. Since a copy number effect did not seem to be the cause of this difference, we have
AB  - subcloned pMQ3 in order to determine whether the additional chromosomal DNA present in this
AB  - plasmid is responsible for the enhancement of methylase activity. We show that the 346 base
AB  - pairs upstream of dam contain sequences necessary for expression. DNA sequence analysis has
AB  - revealed that in pdam 118 only the 118 bases 5' to the dam gene are present in other
AB  - constructs and that the additional upstream material is pBR322 DNA. This shows that pdam118
AB  - carries a DNA duplication.
ER  -

TY  - JOUR
AU  - Arrand, J.R.
AU  - Myers, P.A.
AU  - Roberts, R.J.
TI  - A new restriction endonuclease from Streptomyces albus G.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 127
EP  - 135
VL  - 118
AB  - A restriction endonuclease, SalI, has been partially purified from Streptomyces
AB  - albus G.  This enzyme cleaves adenovirus-2 DNA at three sites, bacteriophage
AB  - lambda DNA at two sites, but does not cleave simian virus 40 DNA or PhiX174
AB  - DNA.  It recognizes the sequence 5'-G^T-C-G-A-C-3' 3'-C-A-G-C-T-^G-5' and cuts
AB  - at the siteds indicated by the arrows.  An endonuclease (XamI) with similar
AB  - specificity has also been isolated from Xanthomonas amaranthicola.
ER  -

TY  - JOUR
AU  - Arsene-Ploetze, F. et al.
TI  - Structure, function, and evolution of the Thiomonas spp. genome.
JO  - PLoS Genet.
PY  - 2010
SP  - e1000859
EP  - e1000859
VL  - 6
AB  - Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich
AB  - acid mine drainage (AMD).  The genome of one of these strains, Thiomonas sp. 3As, was
AB  - sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to
AB  - survive and grow in its highly toxic environment. In order to explore genomic diversity as
AB  - well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH)
AB  - approach was used on eight different strains of the Thiomonas genus, including five strains of
AB  - the same species. Our results suggest that the Thiomonas genome has evolved through the gain
AB  - or loss of genomic islands and that this evolution is influenced by the specific environmental
AB  - conditions in which the strains live.
ER  -

TY  - JOUR
AU  - Artyukhin, A.B.
AU  - Woo, Y.H.
TI  - DNA extraction method with improved efficiency and specificity using DNA methyltransferase and 'click' chemistry.
JO  - Anal. Biochem.
PY  - 2012
SP  - 169
EP  - 174
VL  - 425
AB  - In an attempt to develop an alternative method to extract DNA from complex samples with much
AB  - improved sensitivity and efficiency, here we
AB  - report a proof-of-concept work for a new DNA extraction method using
AB  - DNA methyltransferase (Mtase) and 'click' chemistry. According to our
AB  - preliminary data, the method has improved the current methods by (i)
AB  - employing a DNA-specific enzyme, TaqI DNA Mtase, for improved
AB  - selectivity, and by (ii) capturing the DNA through covalent bond to the
AB  - functionalized surface, enabling a broad range of treatments yielding
AB  - the final sample DNA with minimal loss and higher purity such that it
AB  - will be highly compatible with downstream analyses. By employing Mtase,
AB  - a highly DNA specific and efficient enzyme, and click chemistry, we
AB  - demonstrated that as little as 0.1 fg of lambda-DNA (close to copy
AB  - number 1) was captured on silica (Si)-based beads by forming a covalent
AB  - bond between an azide group on the surface and the propargyl moiety on
AB  - the DNA. This method holds promise in versatile applications where
AB  - extraction of minute amounts of DNA plays critical roles such as basic
AB  - and applied molecular biology research, bioforensic and biosecurity
AB  - sciences, and state-of-the-art detection methods.
ER  -

TY  - JOUR
AU  - Arushothy, R.
AU  - Ahmad, N.
AU  - Amran, F.
AU  - Hashim, R.
AU  - Samsuddin, N.
AU  - Che, A.C.R.
TI  - Draft Genome Sequence of a Highly Resistant Streptococcus pneumoniae Serotype 15A Strain Isolated from Blood.
JO  - Genome Announcements
PY  - 2018
SP  - e00167
EP  - e00118
VL  - 6
AB  - After the introduction of the pneumococcal conjugate vaccine in Malaysia in recent years, the
AB  - emergence of nonvaccine serotypes is of concern, particularly
AB  - the antibiotic-resistant strains, with an increase specifically in serotype 15A.
AB  - Here, we report the draft genome sequence of Streptococcus pneumoniae strain
AB  - SS40_16, isolated from the blood sample of a 19-month-old female in 2016. SS40_16
AB  - is a multidrug-resistant strain with resistance to penicillin (MIC, >/=2
AB  - microg/ml), tetracycline, and trimethoprim-sulfamethoxazole. The strain belongs
AB  - to serotype 15A and sequence type 1591 (ST1591).
ER  -

TY  - JOUR
AU  - Arutyunyan, E.E.
AU  - Gonchar, N.A.
AU  - Gruber, I.M.
AU  - Nikolskaya, N.I.
TI  - Purification and characterization of DNA methyltransferase Sau6782 of Staphylococcus aureus.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1992
SP  - 26
EP  - 29
VL  - 11-1
ER  -

TY  - JOUR
AU  - Arutyunyan, E.E.
AU  - Gonchar, N.A.
AU  - Levchenko, I.Y.
AU  - Gruber, I.M.
AU  - Nikolskaya, I.I.
TI  - Isoelectrofocusing of methylation and restriction enzymes of Staphylococcus aureus 6782.
JO  - Biokhimiia
PY  - 1991
SP  - 281
EP  - 288
VL  - 56
AB  - The behaviour of methylation and restriction enzymes of Staphylococcus aureus
AB  - 6782 during their isoelectrofocusing on ampholines was studied.  It was found
AB  - that the R.Sau6782I enzyme is represented by two isoforms, RI and RII, with
AB  - isoelectric points of 4.2 and 7.9, respectively.  Data from isoelectrofocusing
AB  - analysis suggest that RI and RII are devoid of the relaxed specificity found in
AB  - the original preparation.  It was shown that the relaxed specificity is also
AB  - inherent in the isoschizomeric enzyme, R.Sau3AI.  Isoelectrofocusing of the
AB  - original preparation of R.Sau3AI, as is the case for R.Sau6782I, allows the
AB  - identification of two peaks, RI and RII, and the separation of each peak from
AB  - the trace activity.  Multiple forms of DNA-methylase of the Sau6782I type are
AB  - represented by four isoenzymes possessing acidic properties.  The method allows
AB  - one to single out from the total methylase pool a modifying methylase with pI
AB  - (3.9) that is close to that of R.Sau6782I and thus the enzyme cannot serve for
AB  - correct separation of restriction and methylation enzymes of Sau6782I.
ER  -

TY  - JOUR
AU  - Arutyunyan, E.E.
AU  - Gruber, I.M.
AU  - Polyachenko, V.M.
AU  - Kvachadze, L.J.
AU  - Andriashvili, I.A.
AU  - Chanishvili, T.G.
AU  - Nikolskaya, I.I.
TI  - Restricting Endonuclease SAU 6782.
JO  - Vopr. Med. Khim.
PY  - 1985
SP  - 127
EP  - 132
VL  - 31
AB  - Data are described on identification, isolation and purification of restricting
AB  - endonuclease Sau 6782 as well as on estimation of the enzyme recognition site.
AB  - Conditions were developed for growing of Staphylococcus aureus 6782 strain,
AB  - which enabled to produce a maximal yield of the restricting activity containing
AB  - minimal level of nucleases.  The procedure for isolation and purification of
AB  - restrictase Sau 6782 involved affinity chromatography on Blue Sepharose and
AB  - cation exchange chromatography on phosphocellulose PII.  The enzyme preparation
AB  - obtained was free from impurities of unspecific nucleases.  The yield of the
AB  - Sau 6782 restrictase constituted 1,0 un from 1 g of the culture cells.
AB  - Restrictase Sau 6782 recognized the nucleotide sequence 5'...GATC...3' and was
AB  - the isoshizomere of the Sau 3A enzyme.
ER  -

TY  - JOUR
AU  - Arutyunyan, E.E.
AU  - Gruber, I.M.
AU  - Polyachenko, V.M.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Isolation of methylases from Sau 6782 strain.
JO  - Vopr. Med. Khim.
PY  - 1990
SP  - 75
EP  - 79
VL  - 36
AB  - A heterogenous profile of methylases was found in S. aureus 6782.  A procedure
AB  - was developed for isolation of individual methylases from Sau 6782, free of Sau
AB  - 6782 restrictases and unspecific nucleases, by means of hydrophobic
AB  - chromatography on phenyl-Sepharose.  Ion exchange, affinity chromatographies
AB  - and gel filtration were also used for isolation of the Sau 6782 methylases.
AB  - But this technique was of limited suitability for isolation of individual
AB  - methylating enzymes of the Sau 6782 type because it did not allow the complete
AB  - separation of these methylases from contaminating enzymes of DNA degradation.
AB  - Effects of salts, glycerol and Triton X-100 on activity of total preparation of
AB  - methylases Sau 6782 were studied.  Na+ and K+ chlorides, ammonium sulfate at
AB  - concentrations 0.4 M and higher as well as Triton X-100 reversibly inhibited
AB  - the methylase activity followed by complete reduction up to initial level after
AB  - dialysis.  Glycerol at 60% concentration activated Sau 6782 methylases by 50%
AB  - and stabilized the enzyme.
ER  -

TY  - JOUR
AU  - Arwert, F.
AU  - Rutberg, L.
TI  - Restriction and modification in Bacillus subtilis.  Induction of a modifying activity in Bacillus subtilis 168.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 175
EP  - 177
VL  - 133
AB  - Bacillus subtilis strain 5GR will restrict and modify phage SPO2 previously grown in strain
AB  - 168.  SPO2 grown in 168 pretreated with Mitomycin C is less restricted by 5GR.  Strain MB500
AB  - is temperature inducible for the defective PBSX prophage.  SPO2 grown in MB500 at inducing
AB  - temperature is less restricted by 5GR compared to phage grown in MB500 at non-inducing
AB  - temperature.  It is suggested that strain 168 carries genetic determinants for modification of
AB  - SPO2 DNA, and that those determinants may be associated with the defective phage PBSX.
ER  -

TY  - JOUR
AU  - Arya, G.
AU  - Petronella, N.
AU  - Crosthwait, J.
AU  - Carrillo, C.D.
AU  - Shwed, P.S.
TI  - Draft Genome Sequence of Bacillus megaterium Type Strain ATCC 14581.
JO  - Genome Announcements
PY  - 2014
SP  - e01124
EP  - e01114
VL  - 2
AB  - Bacillus megaterium is a Gram-positive, rod-shaped, spore-forming bacterium of
AB  - biotechnological importance. Here, we report a 5.7-Mbp draft genome sequence of
AB  - B. megaterium ATCC 14581, which is the type strain of the species.
ER  -

TY  - JOUR
AU  - Aryantini, N.P.
AU  - Prajapati, J.B.
AU  - Urashima, T.
AU  - Fukuda, K.
TI  - Complete Genome Sequence of Lactobacillus fermentum MTCC 25067 (Formerly TDS030603), a Viscous Exopolysaccharide-Producing Strain Isolated from Indian  Fermented Milk.
JO  - Genome Announcements
PY  - 2017
SP  - e00091
EP  - e00017
VL  - 5
AB  - Lactobacillus fermentum MTCC 25067 (formerly TDS030603) is capable of producing a highly
AB  - viscous slime exopolysaccharide. We report here the complete genome
AB  - sequence of the strain, which was deciphered by using PacBio single-molecule
AB  - real-time sequencing technology.
ER  -

TY  - JOUR
AU  - Asahina, A.Y.
AU  - Hadfield, M.G.
TI  - Complete Genome Sequence of Cellulophaga lytica HI1 Using PacBio Single-Molecule  Real-Time Sequencing.
JO  - Genome Announcements
PY  - 2014
SP  - e01148
EP  - e01114
VL  - 2
AB  - We report here the complete genome sequence of Cellulophaga lytica HI1 isolated from a
AB  - seawater table located at the Kewalo Marine Laboratory (Honolulu, HI).
AB  - This is the first complete de novo genome assembly of C. lytica HI1 using PacBio
AB  - single-molecule real-time (SMRT) sequencing, which resulted in a single scaffold
AB  - of 3.8 Mb.
ER  -

TY  - JOUR
AU  - Asahina, A.Y.
AU  - Hadfield, M.G.
TI  - Draft Genome Sequence of Pseudoalteromonas luteoviolacea HI1, Determined Using Roche 454 and PacBio Single-Molecule Real-Time Hybrid Sequencing.
JO  - Genome Announcements
PY  - 2015
SP  - e01590
EP  - e01514
VL  - 3
AB  - We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain HI1
AB  - using Roche 454 and PacBio single-molecule real-time hybrid-sequencing analysis. This strain
AB  - is of biological importance since it has  the capacity to induce the settlement and
AB  - metamorphosis of the serpulid polychaete Hydroides elegans and the coral Pocillopora
AB  - damicornis.
ER  -

TY  - JOUR
AU  - Asahina, Y.
AU  - Shiroma, A.
AU  - Nakano, K.
AU  - Tamotsu, H.
AU  - Ashimine, N.
AU  - Shinzato, M.
AU  - Minami, M.
AU  - Shimoji, M.
AU  - Nakanishi, T.
AU  - Ohki, S.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Kobayashi, M.
AU  - Hagi, T.
AU  - Moriya, N.
AU  - Suzuki, C.
AU  - Tajima, A.
AU  - Nomura, M.
AU  - Hirano, T.
TI  - Complete Genome Sequence of Lactobacillus paracasei EG9, a Strain Accelerating Free Amino Acid Production during Cheese Ripening.
JO  - Genome Announcements
PY  - 2018
SP  - e00627
EP  - e00618
VL  - 6
AB  - Lactobacillus paracasei EG9 is a strain isolated from well-ripened cheese and accelerates free
AB  - amino acid production during cheese ripening. Its complete
AB  - genome sequence was determined using the PacBio RS II platform, revealing a
AB  - single circular chromosome of 2,927,257 bp, a G+C content of 46.59%, and three
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Asai, A.
AU  - Hirai, H.
AU  - Bodell, W.J.
AU  - Hoshino, T.
TI  - Restriction endonuclease recognition and Southern hybridization of bromodeoxyuridine-substituted genomic DNA.
JO  - Cell Prolif.
PY  - 1993
SP  - 271
EP  - 280
VL  - 26
AB  - Human glioma cell lines exposed to various concentrations of bromodeoxyuridine (BrdUrd) were
AB  - studied to determine the effect of BrdUrd substitution on restriction endonuclease recognition
AB  - and Southern hybridization of genomic DNA. BrdUrd substitution had no effect on the
AB  - recognition of restriction endonucleases. When the exposure to BrdUrd was 2 h or less and the
AB  - BrdUrd substitution rate was less than 40%, there was no difference in the density of
AB  - hybridized bands after Southern hybridization using human non-recombinant complementary DNA as
AB  - a probe. Hybridization was suppressed significantly by exposures longer than 24 h or BrdUrd
AB  - substitution rates greater than 40%. These results suggest that the Brdurd substitution rate
AB  - and the exposure time to BrdUrd influence the hybridization reaction by a DNA probe. Brief
AB  - exposure (up to 2 h) to BrdUrd does not influence restriction endonuclease recognition or
AB  - Southern hybridization of genomic DNA.
ER  -

TY  - JOUR
AU  - Asakura, H.
AU  - Ikeda, T.
AU  - Yamamoto, S.
AU  - Kabeya, H.
AU  - Sugiyama, H.
AU  - Takai, S.
TI  - Draft Genome Sequence of Five Shiga Toxin-Producing Escherichia coli Strains Isolated from Wild Deer in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01455
EP  - e01416
VL  - 5
AB  - Shiga toxin-producing Escherichia coli (STEC) is one of the major foodborne pathogens. Having
AB  - observed the wide distribution of this pathogen in wild deer,
AB  - we report here the draft genome sequence of five STEC strains isolated from wild
AB  - deer (Cervus nippon yesoensis) in Hokkaido, Japan.
ER  -

TY  - JOUR
AU  - Asakura, H.
AU  - Takahashi, N.
AU  - Yamamoto, S.
AU  - Maruyama, H.
TI  - Draft Genome Sequence of Campylobacter jejuni CAM970 and C. coli CAM962, Associated with a Large Outbreak of Foodborne Illness in Fukuoka, Japan, in 2016.
JO  - Genome Announcements
PY  - 2017
SP  - e00508
EP  - e00517
VL  - 5
AB  - Here, we report the draft genome sequences of Campylobacter jejuni CAM970 and C.  coli CAM962,
AB  - which were associated with a large outbreak of foodborne illness
AB  - originating from undercooked chicken sushi in Fukuoka, Japan, in May 2016. Their
AB  - genome sizes were 1,690,901 and 1,704,736 bp, with 22 and 23 rRNAs, 9 and 9
AB  - tRNAs, and 411x and 419x coverage for C. jejuni CAM970 and C. coli CAM962,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Asakura, H.
AU  - Yamamoto, S.
AU  - Momose, Y.
AU  - Kato, H.
AU  - Iwaki, M.
AU  - Shibayama, K.
TI  - Genome Sequence of Clostridium botulinum Strain Adk2012 Associated with a Foodborne Botulinum Case in Tottori, Japan, in 2012.
JO  - Genome Announcements
PY  - 2017
SP  - e00872
EP  - e00817
VL  - 5
AB  - We report here a draft genome sequence of Clostridium botulinum Adk2012 responsible for a
AB  - foodborne botulism case that occurred in Tottori, Japan, in
AB  - 2012. Its genome size was 2,904,173 bp, with 46 rRNAs and 54 tRNAs, at a coverage
AB  - of 14.5x.
ER  -

TY  - JOUR
AU  - Asakura, Y.
AU  - Kobayashi, I.
TI  - From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene  complex.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3021
EP  - 3031
VL  - 37
AB  - Genetically programmed cell deaths play important roles in unicellular prokaryotes. In
AB  - postsegregational killing, loss of a gene complex from a
AB  - cell leads to its descendants' deaths. With type II
AB  - restriction-modification gene complexes, such death is triggered by
AB  - restriction endonuclease's attacks on under-methylated chromosomes. Here,
AB  - we examined how the Escherichia coli transcriptome changes after loss of
AB  - PaeR7I gene complex. At earlier time points, activation of SOS genes and
AB  - sigma(E)-regulon was noticeable. With time, more SOS genes,
AB  - stress-response genes (including sigma(S)-regulon, osmotic-, oxidative-
AB  - and periplasmic-stress genes), biofilm-related genes, and many hitherto
AB  - uncharacterized genes were induced, and genes for energy metabolism,
AB  - motility and outer membrane biogenesis were repressed. As expected from
AB  - the activation of sigma(E)-regulon, the death was accompanied by cell
AB  - lysis and release of cellular proteins. Expression of several
AB  - sigma(E)-regulon genes indeed led to cell lysis. We hypothesize that some
AB  - signal was transduced, among multiple genes involved, from the damaged
AB  - genome to the cell surface and led to its disintegration. These results
AB  - are discussed in comparison with other forms of programmed deaths in
AB  - bacteria and eukaryotes.
ER  -

TY  - JOUR
AU  - Asakura, Y.
AU  - Kojima, H.
AU  - Kobayashi, I.
TI  - Evolutionary genome engineering using a restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 9034
EP  - 9046
VL  - 39
AB  - Modification of complex microbial cellular processes is often necessary to obtain organisms
AB  - with particularly favorable characteristics, but such
AB  - experiments can take many generations to achieve. In the present article,
AB  - we accelerated the experimental evolution of Escherichia coli populations
AB  - under selection for improved growth using one of the
AB  - restriction-modification systems, which have shaped bacterial genomes.
AB  - This resulted in faster evolutionary changes in both the genome and
AB  - bacterial growth. Transcriptome/genome analysis at various stages enabled
AB  - prompt identification of sequential genome rearrangements and dynamic
AB  - gene-expression changes associated with growth improvement. The changes
AB  - were related to cell-to-cell communication, the cell death program, as
AB  - well as mass production and energy consumption. These observed changes
AB  - imply that improvements in microorganism population growth can be achieved
AB  - by inactivating the cellular mechanisms regulating fraction of active
AB  - cells in a population. Some of the mutations were shown to have additive
AB  - effects on growth. These results open the way for the application of
AB  - evolutionary genome engineering to generate organisms with desirable
AB  - properties.
ER  -

TY  - JOUR
AU  - Asamizu, E.
AU  - Sato, S.
AU  - Kaneko, T.
AU  - Nakamura, Y.
AU  - Kotani, H.
AU  - Miyajima, N.
AU  - Tabata, S.
TI  - Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones.
JO  - DNA Res.
PY  - 1998
SP  - 379
EP  - 391
VL  - 5
AB  - A total of 17 Pl and TAC clones each representing an assigned region of
AB  - chromosome 5 were isolated from P1 and TAC genomic libraries of
AB  - Arabidopsis thaliana Columbia, and their nucleotide sequences were
AB  - determined. The length of the clones sequenced in this study summed up to
AB  - 1,081,958 bp. As we have previously reported the sequence of 9,072,622 bp
AB  - by analysis of 125 P1 and TAC clones, the total length of the sequences of
AB  - chromosome 5 determined so far is now 10,154,580 bp. The sequences were
AB  - subjected to similarity search against protein and EST databases and
AB  - analysis with computer programs for gene modeling. As a consequence, a
AB  - total of 253 potential protein-coding genes with known or predicted
AB  - functions were identified. The positions of exons, which do not show
AB  - apparent similarity to known genes were also assigned using computer
AB  - programs for exon prediction. The average density of the genes identified
AB  - in this study was 1 gene per 4277 bp. Introns were observed in 74% of the
AB  - potential protein genes, and the average number per gene and the average
AB  - length of the introns were 4.3 and 168 bp, respectively. The sequence data
AB  - and gene information are available on the World Wide Web database KAOS
AB  - (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ER  -

TY  - JOUR
AU  - Aserse, A.A.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Whitman, W.B.
AU  - Lindstrom, K.
TI  - Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T).
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 74
EP  - 74
VL  - 12
AB  - The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11(T), was isolated from a
AB  - nodule of the leguminous tree Erythrina brucei native to
AB  - Ethiopia. The type strain 10.1601/nm.1463
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T), was isolated from the
AB  - nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11(T) and
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T) were sequenced by DOE-JGI
AB  - and deposited at the DOE-JGI genome portal as well as at the European Nucleotide
AB  - Archive. The genome of ERR11(T) is 9,163,226 bp in length and has 102 scaffolds,
AB  - containing 8548 protein-coding and 86 RNA genes. The
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T) genome is arranged in 108
AB  - scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA
AB  - genes. Both genomes contain symbiotic genes, which are homologous to the genes
AB  - found in the complete genome sequence of 10.1601/nm.24498
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 (T). The genes encoding for
AB  - nodulation and nitrogen fixation in ERR11(T) showed high sequence similarity with
AB  - homologous genes found in the draft genome of peanut-nodulating 10.1601/nm.27386
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DLMG+26795 (T). The nodulation genes
AB  - nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11(T) and
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 (T) are organized in a similar
AB  - way to the homologous genes identified in the genomes of
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+110 (T), 10.1601/nm.25806
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and 10.1601/nm.1462
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+05525. The genomes harbor hupSLCFHK
AB  - and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps
AB  - rhizobia to uptake hydrogen released by the N2-fixation process and genes
AB  - encoding denitrification functions napEDABC and norCBQD for nitrate and nitric
AB  - oxide reduction, respectively. The genome of ERR11(T) also contains nosRZDFYLX
AB  - genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of
AB  - housekeeping genes, the novel species, which contains eight strains formed a
AB  - unique group close to the 10.1601/nm.25806 branch. Genome Average Nucleotide
AB  - Identity (ANI) calculated between the genome sequences of ERR11(T) and closely
AB  - related sequences revealed that strains belonging to 10.1601/nm.25806 branch
AB  - (10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 and
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615), were the closest strains to
AB  - the strain ERR11(T) with 95.2% ANI. Type strain ERR11(T) showed the highest DDH
AB  - predicted value with 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 (58.5%),
AB  - followed by 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 (53.1%). Nevertheless,
AB  - the ANI and DDH values obtained between ERR11(T) and
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+15615 or
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DUSDA+4 were below the cutoff values (ANI
AB  - >/= 96.5%; DDH >/= 70%) for strains belonging to the same species, suggesting
AB  - that ERR11(T) is a new species. Therefore, based on the phylogenetic analysis,
AB  - ANI and DDH values, we formally propose the creation of 10.1601/nm.30737 sp. nov.
AB  - with strain ERR11(T) (10.1601/strainfinder?urlappend=%3Fid%3DHAMBI+3532
AB  - (T)=10.1601/strainfinder?urlappend=%3Fid%3DLMG+30162 (T)) as the type strain.
ER  -

TY  - JOUR
AU  - Aserse, A.A.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Whitman, W.B.
AU  - Lindstrom, K.
TI  - Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 14
EP  - 14
VL  - 12
AB  - Rhizobium aethiopicum sp. nov. is a newly proposed species within the genus Rhizobium. This
AB  - species includes six rhizobial strains; which were isolated from
AB  - root nodules of the legume plant Phaseolus vulgaris growing in soils of Ethiopia.
AB  - The species fixes nitrogen effectively in symbiosis with the host plant P.
AB  - vulgaris, and is composed of aerobic, Gram-negative staining, rod-shaped
AB  - bacteria. The genome of type strain HBR26T of R. aethiopicum sp. nov. was one of
AB  - the rhizobial genomes sequenced as a part of the DOE JGI 2014 Genomic
AB  - Encyclopedia project designed for soil and plant-associated and newly described
AB  - type strains. The genome sequence is arranged in 62 scaffolds and consists of
AB  - 6,557,588 bp length, with a 61% G + C content and 6221 protein-coding and 86 RNAs
AB  - genes. The genome of HBR26T contains repABC genes (plasmid replication genes)
AB  - homologous to the genes found in five different Rhizobium etli CFN42T plasmids,
AB  - suggesting that HBR26T may have five additional replicons other than the
AB  - chromosome. In the genome of HBR26T, the nodulation genes nodB, nodC, nodS, nodI,
AB  - nodJ and nodD are located in the same module, and organized in a similar way as
AB  - nod genes found in the genome of other known common bean-nodulating rhizobial
AB  - species. nodA gene is found in a different scaffold, but it is also very similar
AB  - to nodA genes of other bean-nodulating rhizobial strains. Though HBR26T is
AB  - distinct on the phylogenetic tree and based on ANI analysis (the highest value
AB  - 90.2% ANI with CFN42T) from other bean-nodulating species, these nod genes and
AB  - most nitrogen-fixing genes found in the genome of HBR26T share high identity with
AB  - the corresponding genes of known bean-nodulating rhizobial species (96-100%
AB  - identity). This suggests that symbiotic genes might be shared between
AB  - bean-nodulating rhizobia through horizontal gene transfer. R. aethiopicum sp.
AB  - nov. was grouped into the genus Rhizobium but was distinct from all recognized
AB  - species of that genus by phylogenetic analyses of combined sequences of the
AB  - housekeeping genes recA and glnII. The closest reference type strains for HBR26T
AB  - were R. etli CFN42T (94% similarity of the combined recA and glnII sequences) and
AB  - Rhizobium bangladeshense BLR175T (93%). Genomic ANI calculation based on
AB  - protein-coding genes also revealed that the closest reference strains were R.
AB  - bangladeshense BLR175T and R. etli CFN42T with ANI values 91.8 and 90.2%,
AB  - respectively. Nevertheless, the ANI values between HBR26T and BLR175T or CFN42T
AB  - are far lower than the cutoff value of ANI (> = 96%) between strains in the same
AB  - species, confirming that HBR26T belongs to a novel species. Thus, on the basis of
AB  - phylogenetic, comparative genomic analyses and ANI results, we formally propose
AB  - the creation of R. aethiopicum sp. nov. with strain HBR26T (=HAMBI 3550T=LMG
AB  - 29711T) as the type strain. The genome assembly and annotation data is deposited
AB  - in the DOE JGI portal and also available at European Nucleotide Archive under
AB  - accession numbers FMAJ01000001-FMAJ01000062.
ER  -

TY  - JOUR
AU  - Ashapkin, V.V.
AU  - Kutueva, L.I.
AU  - Vanyushin, B.F.
TI  - Is the cytosine DNA methyltransferase gene MET1 regulated by DNA methylation in Arabidopsis thaliana plants?
JO  - Genetika
PY  - 2011
SP  - 279
EP  - 288
VL  - 47
AB  - The methylation patterns of the MET1 gene in organs of Arabidopsis thaliana were studied by
AB  - Southern blot hybridization of DNA samples
AB  - hydrolyzed with differentially methylation-sensitive restriction
AB  - endonucleases. A highly methylated on internal cytosine residue CCGG
AB  - site was found 1.5 kb upstream of the gene, whereas CCGG sites located
AB  - in more proximal parts of the 5'-flanking region and the gene itself
AB  - are essentially unmethylated. This methylation pattern was observed in
AB  - different organs of plants belonging to two different ecotypes as well
AB  - as in different transgenic plant lines. The methylation level of a CCGG
AB  - site in exon 3 (2.1 kb from the gene's 5'-end) occurred to be variable
AB  - between different transgenic plant lines and two ecotypes studied.
AB  - Transcription levels of the MET1 gene vary slightly in organs of
AB  - wild-type plants without any obvious correlation with its methylation.
AB  - The transgenic antisense MET1 constructs expressed in plant genome do
AB  - affect both MET1 methylation and its transcription but again without
AB  - any obvious correlation. The comparative investigation of transcription
AB  - levels of different genes of cytosine DNA methyltransferase family MET
AB  - (MET1, MET2a, MET2b, MET3) and their methylation patterns shows that
AB  - there may exist some mechanisms defending the most actively transcribed
AB  - gene MET1 of this family from methylation mediated silencing. In
AB  - contrast to DRM2 gene we could not find any adenine methylated GATC
AB  - sites in the MET1 gene.
ER  -

TY  - JOUR
AU  - Ashapkin, V.V.
AU  - Kutueva, L.I.
AU  - Vanyushin, B.F.
TI  - The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues.
JO  - FEBS Lett.
PY  - 2002
SP  - 367
EP  - 372
VL  - 532
AB  - The methylation patterns of cytosine and adenine residues in the Arabidopsis thaliana gene for
AB  - domains rearranged methyltransferase (DRM2) were studied in wild-type and several transgene
AB  - plant lines containing antisense fragments of the cytosine DNA-methyltransferase gene METI
AB  - under the control of copper-inducible promoters. It was shown that the promoter region of the
AB  - DRM2 gene is mostly unmethylated at the internal cytosine residue in CCGG sites whereas the
AB  - 3'-end proximal part of the gene coding region is highly methylated. The DRM2 gene was found
AB  - to be also methylated at adenine residues in some GATC sequences. Cytosine methylation in CCGG
AB  - sites and adenine methylation in GATC sites in the DRM2 gene are variable between wild-type
AB  - and different transgenic plants. The induction of antisense METI constructs with copper ions
AB  - in transgene plants in most cases leads to further alterations in the DRM2 gene methylation
AB  - patterns.
ER  -

TY  - JOUR
AU  - Ashraf, M.
AU  - Altschuler, M.
AU  - Galasinski, S.
AU  - Griffiths, T.D.
TI  - Alteration of gene expression by restriction enzymes electroporated into plant cells.
JO  - Mutat. Res.
PY  - 1993
SP  - 75
EP  - 82
VL  - 302
AB  - The alteration in the expression of a B-glucuronidase (GUS) reporter gene was used to monitor
AB  - the effect of restriction endonuclease electroporated into the tobacco (Nicotiana tabacum L.)
AB  - protoplasts. Restriction enzyme (RE) HindIII which does not have a recognition site within the
AB  - gene cassette, had little effect on enzyme activity. In contrast restriction endonucleases
AB  - HaeIII and Sau3AI which possess 8 and 16 recognition sites in the GUS cassette, were found to
AB  - reduce the enzyme activity by 89% and 94% respectively when compared to control
AB  - electroporations. Restriction-site mutation analysis (RSM) and Southern blot analysis
AB  - indicated the enzymatic degradation of GUS coding sequence by the REs HaeIII and Sau3AI.
AB  - Results of this study suggest that on electroporation, REs can enter into plant cells and
AB  - alter the expression of the GUS gene. The alteration of gene expression is thus correlated
AB  - with the digestion of GUS template DNA. Future applications of this technique could include
AB  - addressing fundamental questions with regard to DNA repair, site-specific recombination,
AB  - identifying mutations, insertional mutagenesis, enhancement of stable transformation and gene
AB  - tagging in plants.
ER  -

TY  - JOUR
AU  - Ashworth, J.
AU  - Havranek, J.J.
AU  - Duarte, C.M.
AU  - Sussman, D.
AU  - Monnat, R.J.
AU  - Stoddard, B.L.
AU  - Baker, D.
TI  - Computational redesign of endonuclease DNA binding and cleavage specificity.
JO  - Nature
PY  - 2006
SP  - 656
EP  - 659
VL  - 441
AB  - The reprogramming of DNA-binding specificity is an important challenge for computational
AB  - protein design that tests current understanding of
AB  - protein - DNA recognition, and has considerable practical relevance for
AB  - biotechnology and medicine(1-6). Here we describe the computational
AB  - redesign of the cleavage specificity of the intron-encoded homing
AB  - endonuclease I-MsoI(7) using a physically realistic atomic-level
AB  - forcefield(8,9). Using an in silico screen, we identified single
AB  - base-pair substitutions predicted to disrupt binding by the wild-type
AB  - enzyme, and then optimized the identities and conformations of clusters
AB  - of amino acids around each of these unfavourable substitutions using
AB  - Monte Carlo sampling(10). A redesigned enzyme that was predicted to
AB  - display altered target site specificity, while maintaining wild-type
AB  - binding affinity, was experimentally characterized. The redesigned
AB  - enzyme binds and cleaves the redesigned recognition site similar to
AB  - 10,000 times more effectively than does the wild-type enzyme, with a
AB  - level of target discrimination comparable to the original endonuclease.
AB  - Determination of the structure of the redesigned nuclease-recognition
AB  - site complex by X-ray crystallography confirms the accuracy of the
AB  - computationally predicted interface. These results suggest that
AB  - computational protein design methods can have an important role in the
AB  - creation of novel highly specific endonucleases for gene therapy and
AB  - other applications.
ER  -

TY  - JOUR
AU  - Ashworth, J.
AU  - Taylor, G.K.
AU  - Havranek, J.J.
AU  - Quadri, S.A.
AU  - Stoddard, B.L.
AU  - Baker, D.
TI  - Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 5601
EP  - 5608
VL  - 38
AB  - Site-specific homing endonucleases are capable of inducing gene conversion via homologous
AB  - recombination. Reprogramming their cleavage specificities
AB  - allows the targeting of specific biological sites for gene correction or
AB  - conversion. We used computational protein design to alter the cleavage
AB  - specificity of I-MsoI for three contiguous base pair substitutions,
AB  - resulting in an endonuclease whose activity and specificity for its new
AB  - site rival that of wild-type I-MsoI for the original site. Concerted
AB  - design for all simultaneous substitutions was more successful than a
AB  - modular approach against individual substitutions, highlighting the
AB  - importance of context-dependent redesign and optimization of protein-DNA
AB  - interactions. We then used computational design based on the crystal
AB  - structure of the designed complex, which revealed significant
AB  - unanticipated shifts in DNA conformation, to create an endonuclease that
AB  - specifically cleaves a site with four contiguous base pair substitutions.
AB  - Our results demonstrate that specificity switches for multiple concerted
AB  - base pair substitutions can be computationally designed, and that
AB  - iteration between design and structure determination provides a route to
AB  - large scale reprogramming of specificity.
ER  -

TY  - JOUR
AU  - Asim, M.
AU  - Chikara, S.K.
AU  - Ghosh, A.
AU  - Vudathala, S.
AU  - Romero-Gallo, J.
AU  - Krishna, U.S.
AU  - Wilson, K.T.
AU  - Israel, D.A.
AU  - Peek, R.M. Jr.
AU  - Chaturvedi, R.
TI  - Draft Genome Sequence of Gerbil-Adapted Carcinogenic Helicobacter pylori Strain 7.13.
JO  - Genome Announcements
PY  - 2015
SP  - e00641
EP  - e00615
VL  - 3
AB  - We report here the draft genome sequence of Helicobacter pylori strain 7.13, a gerbil-adapted
AB  - strain that causes gastric cancer in gerbils. Strain 7.13 is
AB  - derived from clinical strain B128, isolated from a patient with a duodenal ulcer.
AB  - This study reveals genes associated with the virulence of the strain.
ER  -

TY  - JOUR
AU  - Aslam, F.
AU  - Yasmin, A.
AU  - Thomas, T.
TI  - Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae MB373, an Effective Bioremediator.
JO  - Genome Announcements
PY  - 2016
SP  - e01068
EP  - e01016
VL  - 4
AB  - Klebsiella quasipneumoniae subsp. similipneumoniae MB373 was isolated from effluent of the
AB  - Hattar Industrial Estate, Haripur, Pakistan. K. quasipneumoniae
AB  - subsp. similipneumoniae has few cultivated/characterized members so far.
AB  - Whole-genome sequencing revealed its potential for metal and toxin resistance,
AB  - which further elucidated various enzymatic processes for the degradation of
AB  - xenobiotics, illuminating its bioremediation applications.
ER  -

TY  - JOUR
AU  - Asmar, S.
AU  - Phelippeau, M.
AU  - Robert, C.
AU  - Croce, O.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T.
JO  - Genome Announcements
PY  - 2015
SP  - e00878
EP  - e00815
VL  - 3
AB  - The Mycobacterium bohemicum strain is a nontuberculosis species mainly responsible for
AB  - pediatric cervical lymphadenitis. The draft genome of M.
AB  - bohemicum DSM 44277(T) comprises 5,097,190 bp exhibiting a 68.64% G+C content,
AB  - 4,840 protein-coding genes, and 75 predicted RNA genes.
ER  -

TY  - JOUR
AU  - Asmar, S.
AU  - Rascovan, N.
AU  - Robert, C.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098.
JO  - Genome Announcements
PY  - 2015
SP  - e01274
EP  - e01215
VL  - 3
AB  - Mycobacterium peregrinum is a nonpigmented rapid growing nontuberculosis species  belonging to
AB  - the Mycobacterium fortuitum group. The draft genome of M. peregrinum
AB  - type I CSUR P2098 comprises 7,109,836 bp exhibiting a 66.23% G+C content, 6,894
AB  - protein-coding genes, and 100 predicted RNA genes. Its genome analysis suggests
AB  - this species differs from Mycobacterium senegalense.
ER  -

TY  - JOUR
AU  - Asmar, S.
AU  - Rascovan, N.
AU  - Robert, C.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium acapulcensis Strain CSURP1424.
JO  - Genome Announcements
PY  - 2016
SP  - e00836
EP  - e00816
VL  - 4
AB  - Mycobacterium acapulcensis is a rapidly growing scotochromogenic acid-fast bacillus. The draft
AB  - genome of M. acapulcensis CSURP1424 comprises 5,290,974 bp,
AB  - exhibiting a 66.67% G+C content, 4,870 protein-coding genes, and 71 predicted RNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Asmar, S.
AU  - Rascovan, N.
AU  - Robert, C.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium mucogenicum Strain CSUR P2099.
JO  - Genome Announcements
PY  - 2015
SP  - e01369
EP  - e01315
VL  - 3
AB  - Mycobacterium mucogenicum is a rapid-growing, nontuberculosis Mycobacterium species. The draft
AB  - genome of M. mucogenicum CSUR P2099 comprises 6,210,127 bp
AB  - exhibiting a 67.2% G+C content, 6,003 protein-coding genes, and 91 predicted RNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Asmar, S.
AU  - Robert, C.
AU  - Croce, O.
AU  - Caputo, A.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T.
JO  - Genome Announcements
PY  - 2015
SP  - e01314
EP  - e01315
VL  - 3
AB  - Mycobacterium neworleansense is a rapid growing nontuberculosis species belonging to the
AB  - Mycobacterium fortuitum complex. The draft genome of M. neworleansense
AB  - ATCC 49404(T) comprises 6,287,317 bp exhibiting a 66.85% G+C content, 5,997
AB  - protein-coding genes, and 89 predicted RNA genes.
ER  -

TY  - JOUR
AU  - Assis-das-Gracas, D.
AU  - Thiago-Juca-Ramos, R.
AU  - Vieira-Araujo, A.C.
AU  - Zahlouth, R.
AU  - Ribeiro-Carneiro, A.
AU  - Souza-Lopes, T.
AU  - Azevedo-Barauna, R.
AU  - Azevedo, V.
AU  - Cruz-Schneider, M.P.
AU  - Pellizari, V.H.
AU  - Silva, A.
TI  - Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area.
JO  - Genome Announcements
PY  - 2013
SP  - e00271
EP  - e00213
VL  - 1
AB  - Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order,
AB  - which is known for its broad catabolic range among
AB  - methanogens and is widespread throughout diverse environments. The draft genome of the strain
AB  - presented here was cultivated from sediment samples collected from the Tucurui hydroelectric
AB  - power station reservoir.
ER  -

TY  - JOUR
AU  - Astolfi, M.C.T.
AU  - Carvalho, E.B.S.
AU  - de Barros, A.M.
AU  - Pinto, M.V.
AU  - de Lacerda, L.B.
AU  - Nogueira, V.B.
AU  - Lopes, E.F.
AU  - Astolfi-Filho, S.
TI  - Draft Genome Sequence of the Novel Enterobacter cloacae Strain amazonensis, a Highly Heavy Metal-Resistant Bacterium from a Contaminated Stream in Amazonas,  Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00450
EP  - e00418
VL  - 6
AB  - Here, we report the draft genome of the Enterobacter cloacae strain amazonensis,  a bacterium
AB  - highly resistant to mercury that was isolated from a metal- and
AB  - sewage-contaminated stream in Amazonas, Brazil. The exploration of the 5.0-Mb
AB  - genome revealed 104 genes encoding resistance to toxic compounds and heavy
AB  - metals, highlighting the potential biotechnological applications of this strain.
ER  -

TY  - JOUR
AU  - Aswani, V.
AU  - Mau, B.
AU  - Shukla, S.K.
TI  - Complete Genome Sequence of Staphylococcus aureus MCRF184, a Necrotizing Fasciitis-Causing Methicillin-Sensitive Sequence Type 45 Staphylococcus Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00374
EP  - e00316
VL  - 4
AB  - We report here the complete genome sequence of a highly virulent methicillin-sensitive
AB  - Staphylococcus aureus strain, MCRF184, belonging to
AB  - sequence type 45. This staphylococcal strain was isolated from a surgical biopsy
AB  - specimen from a patient with necrotizing fasciitis.
ER  -

TY  - JOUR
AU  - Atack, J.M.
AU  - Srikhanta, Y.N.
AU  - Fox, K.L.
AU  - Jurcisek, J.A.
AU  - Brockman, K.L.
AU  - Clark, T.A.
AU  - Boitano, M.
AU  - Power, P.M.
AU  - Jen, F.E.
AU  - McEwan, A.G.
AU  - Grimmond, S.M.
AU  - Smith, A.L.
AU  - Barenkamp, S.J.
AU  - Korlach, J.
AU  - Bakaletz, L.O.
AU  - Jennings, M.P.
TI  - A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae.
JO  - Nat. Commun.
PY  - 2015
SP  - 7828
EP  - 7828
VL  - 6
AB  - Non-typeable Haemophilus influenzae contains an N(6)-adenine DNA-methyltransferase (ModA) that
AB  - is subject to phase-variable expression (random
AB  - ON/OFF switching). Five modA alleles, modA2, modA4, modA5, modA9 and modA10,
AB  - account for over two-thirds of clinical otitis media isolates surveyed. Here, we
AB  - use single molecule, real-time (SMRT) methylome analysis to identify the
AB  - DNA-recognition motifs for all five of these modA alleles. Phase variation of
AB  - these alleles regulates multiple proteins including vaccine candidates, and key
AB  - virulence phenotypes such as antibiotic resistance (modA2, modA5, modA10),
AB  - biofilm formation (modA2) and immunoevasion (modA4). Analyses of a modA2 strain
AB  - in the chinchilla model of otitis media show a clear selection for ON switching
AB  - of modA2 in the middle ear. Our results indicate that a biphasic epigenetic
AB  - switch can control bacterial virulence, immunoevasion and niche adaptation in an
AB  - animal model system.
ER  -

TY  - JOUR
AU  - Atack, J.M.
AU  - Tan, A.
AU  - Bakaletz, L.O.
AU  - Jennings, M.P.
AU  - Seib, K.L.
TI  - Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies.
JO  - Trends Microbiol.
PY  - 2018
SP  - 715
EP  - 726
VL  - 26
AB  - A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that
AB  - control expression of multiple genes via epigenetic mechanisms. These randomly switching
AB  - regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and
AB  - antibiotic resistance. Individual phase-variable genes can be identified in silico as they
AB  - contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats
AB  - (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled
AB  - genes do not contain any easily identifiable features. The study of DNA methyltransferase
AB  - specificity using Single-Molecule, Real-Time (SMRT) sequencing and methylome analysis has
AB  - rapidly advanced the analysis of phasevarions by allowing methylomics to be combined with
AB  - whole-transcriptome/proteome analysis to comprehensively characterize these systems in a
AB  - number of important bacterial pathogens.
ER  -

TY  - JOUR
AU  - Atack, J.M.
AU  - Weinert, L.A.
AU  - Tucker, A.W.
AU  - Husna, A.U.
AU  - Wileman, T.M.
AU  - Hadjirin, N.F.
AU  - Hoa, N.T.
AU  - Parkhill, J.
AU  - Maskell, D.J.
AU  - Blackall, P.J.
AU  - Jennings, M.P.
TI  - Streptococcus suis contains multiple phase-variable methyltransferases that show  a discrete lineage distribution.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 11466
EP  - 11476
VL  - 46
AB  - Streptococcus suis is a major pathogen of swine, responsible for a number of chronic and acute
AB  - infections, and is also emerging as a major zoonotic pathogen, particularly in South-East
AB  - Asia. Our study of a diverse population of S. suis shows that this organism contains both Type
AB  - I and Type III phase-variable methyltransferases. In all previous examples, phase-variation of
AB  - methyltransferases results in genome wide methylation differences, and results in differential
AB  - regulation of multiple genes, a system known as the phasevarion (phase-variable regulon). We
AB  - hypothesized that each variant in the Type I and Type III systems encoded a methyltransferase
AB  - with a unique specificity, and could therefore control a distinct phasevarion, either by
AB  - recombination-driven shuffling between different specificities (Type I) or by biphasic on-off
AB  - switching via simple sequence repeats (Type III). Here, we present the identification of the
AB  - target specificities for each Type III allelic variant from S. suis using single-molecule,
AB  - real-time methylome analysis. We demonstrate phase-variation is occurring in both Type I and
AB  - Type III methyltransferases, and show a distinct association between methyltransferase type
AB  - and presence, and population clades. In addition, we show that the phase-variable Type I
AB  - methyltransferase was likely acquired at the origin of a highly virulent zoonotic
AB  - sub-population.
ER  -

TY  - JOUR
AU  - Atack, J.M.
AU  - Yang, Y.
AU  - Seib, K.L.
AU  - Zhou, Y.
AU  - Jennings, M.P.
TI  - A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 3532
EP  - 3542
VL  - 46
AB  - Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on
AB  - and off. This process is called phase variation. Several phase-variable N6-adenine
AB  - DNA-methyltransferases from Type III restriction-modification systems have been reported in
AB  - bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA
AB  - methylation pattern, leading to changes in gene expression. These epigenetic regulatory
AB  - systems are called phasevarions - phase-variable regulons. The extent of these phase-variable
AB  - genes in the bacterial kingdom is unknown. Here, we interrogated a database of
AB  - restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in
AB  - mod genes that encode Type III N6-adenine DNA-methyltransferases. We report that 17.4% of Type
AB  - III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been
AB  - previously identified. The newly discovered examples are widely distributed and include many
AB  - examples in opportunistic pathogens as well as in environmental species. In many cases,
AB  - multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions
AB  - in some species. We found several new types of phase-variable mod genes, including the first
AB  - example of a phase-variable methyltransferase in pathogenic Escherichia coli. Phasevarions are
AB  - a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Atanasiu, C.
AU  - Byron, O.
AU  - McMiken, H.
AU  - Sturrock, S.S.
AU  - Dryden, D.T.F.
TI  - Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3059
EP  - 3068
VL  - 29
AB  - The product of gene 0.3 of bacterlophage T7, ocr, is a potent inhibitor of type I DNA
AB  - restriction and modification enzymes. We have used
AB  - biophysical methods to examine the mass, stability, shape and surface
AB  - charge distribution of ocr. Ocr is a dimeric protein with hydrodynamic
AB  - behaviour equivalent to a prolate ellipsoid of axial ratio 4.3 +/-
AB  - 0.7:1 and mass of 27 kDa. The protein is resistant to denaturation but
AB  - removal of the C-terminal region reduces stability substantially. Six
AB  - amino acids, N4, D25, N43, D62, S68 and W94, are all located on the
AB  - surface of the protein and N4 and S68 are also located at the interface
AB  - between the two 116 amino acid monomers. Negatively charged amino acid
AB  - side chains surround W94 but these side chains are not part of the
AB  - highly acidic C-terminus after W94. Ocr is able to displace a short DNA
AB  - duplex from the binding site of a type I enzyme with a dissociation
AB  - constant of the order of 100 pM or better. These results suggest that
AB  - ocr is of a suitable size and shape to effectively block the DNA
AB  - binding site of a type I enzyme and has a large negatively charged
AB  - patch on its surface. This charge distribution may be complementary to
AB  - the charge distribution within the DNA binding site of type I DNA
AB  - restriction and modification enzymes.
ER  -

TY  - JOUR
AU  - Atanasiu, C.
AU  - Su, T.-J.
AU  - Sturrock, S.S.
AU  - Dryden, D.T.F.
TI  - Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3936
EP  - 3944
VL  - 30
AB  - The ocr protein, the product of gene 0.3 of bacteriophage T7, is a structural mimic of the
AB  - phosphate backbone of B-form DNA. In total it mimics 22 phosphate groups over 24 bp of DNA.
AB  - This mimicry allows it to block DNA binding by type I DNA restriction enzymes and to inhibit
AB  - these enzymes. We have determined that multiple ocr dimers can bind stoichiometrically to the
AB  - archetypal type I enzyme, EcoKI. One dimer binds to the core methyltransferase and two to the
AB  - complete bifunctional restriction and modification enzyme. Ocr can also bind to the component
AB  - subunits of EcoKI. Binding affinity to the methyltransferase core is extremely strong with a
AB  - large favourable enthalpy change and an unfavourable entropy change. This strong interaction
AB  - prevents the dissociation of the methyltransferase which occurs upon dilution of the enzyme.
AB  - This stabilisation arises because the interaction appears to involve virtually the entire
AB  - surface area of ocr and leads to the enzyme completely wrapping around ocr.
ER  -

TY  - JOUR
AU  - Athanasiadis, A.
AU  - Gregoriu, M.
AU  - Thanos, D.
AU  - Kokkinidis, M.
AU  - Papamatheakis, J.
TI  - Complete nucleotide sequence of the PvuII restriction enzyme gene from Proteus vulgaris.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6434
EP  - 6434
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Athanasiadis, A.
AU  - Kokkinidis, M.
TI  - Purification, crystallization and preliminary X-ray diffraction studies of the PvuII endonuclease.
JO  - J. Mol. Biol.
PY  - 1991
SP  - 451
EP  - 453
VL  - 222
AB  - The PvuII endonuclease (PvuIIR) is a restriction enzyme from a type II
AB  - restriction-modification system of Proteus vulgaris coded on plasmid pPvu1.
AB  - The protein recognizes the DNA sequence 5' CAG'CTG 3' and shows no sequence
AB  - homology to other restriction enzymes.  This makes PvuIIR an interesting
AB  - subject for structural determination.  A purification procedure was developed
AB  - that yields milligram quantitites of the PvuIIR from plasmids expressed in the
AB  - Escherichia coli strain HB101.  The protein was crystallized using ammonium
AB  - sulphate as precipitant.  The crystals are orthorhombic, space group P2(1)2(1)2
AB  - with cell dimensions: a=84.2 Angstrom, b=106.2 Angstrom, c=46.9 Angstrom.  The
AB  - asymmetric unit contains one PvuIIR dimer.  Diffraction extends to 2.3
AB  - Angstrom, so the crystals may permit structural determination at atomic
AB  - resolution.
ER  -

TY  - JOUR
AU  - Athanasiadis, A.
AU  - Papanikolau, Y.
AU  - Rina, M.
AU  - Papadovasilaki, M.
AU  - Dauter, Z.
AU  - Petratos, K.
AU  - Bouriotis, V.
AU  - Kokkindis, M.
TI  - Purification, crystallization and preliminary x-ray analysis of the M.BseCI DNA methyltransferase from Bacillus stearothermophilus.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 1997
SP  - 477
EP  - 479
VL  - 53
AB  - The DNA methyltransferase M.BseCI from B. stearothermophilus methylates the N6 atom of the 3'
AB  - adenine in the sequence 5'-ATCGAT-3'.  The 579-residue protein has been isolated and
AB  - crystallized using seeding and microdialysis techniques.  The crystals are monoclinic, space
AB  - group P21 with cell dimensions a=53.7, b=85.7, c=151.8A and b=95.1o, two molecules in the
AB  - asymmetric unit and diffract to at least 2.5A resolution.
ER  -

TY  - JOUR
AU  - Athanasiadis, A.
AU  - Vlassi, M.
AU  - Kotsifaki, D.
AU  - Tucker, P.A.
AU  - Wilson, K.S.
AU  - Kokkinidis, M.
TI  - Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.
JO  - Nat. Struct. Biol.
PY  - 1994
SP  - 469
EP  - 475
VL  - 1
AB  - The crystal structure of the dimeric PvuII restriction endonuclease (R.PvuII) has been
AB  - determined at a resolution of 2.4 angstroms. The protein has a mixed a/b architecture and
AB  - consists of two subdomains. Despite a lack of sequence homology, extensive structural
AB  - similarities exist between one R.PvuII subdomain and the DNA-binding subdomain of EcoRV
AB  - endonuclease (R.EcoRV); the dimerization subdomains are unrelated. Within the similar domains,
AB  - flexible segments of R.PvuII are topologically equivalent to the DNA-binding turns of R.EcoRV;
AB  - potential catalytic residues can be deduced from the structural similarities to R.EcoRV.
AB  - Conformational flexibility is important for the interaction with DNA. A possible
AB  - classification of endonuclease structures on the basis of the positions of the scissile
AB  - phosphates is discussed.
ER  -

TY  - JOUR
AU  - Atkins, L.M.
AU  - Holder, M.E.
AU  - Ajami, N.J.
AU  - Metcalf, G.A.
AU  - Weissenberger, G.M.
AU  - Wang, M.
AU  - Vee, V.
AU  - Han, Y.
AU  - Muzny, D.M.
AU  - Gibbs, R.A.
AU  - Petrosino, J.F.
TI  - High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain OR96-0246.
JO  - Genome Announcements
PY  - 2015
SP  - e00898
EP  - e00815
VL  - 3
AB  - The bacterial pathogen Francisella tularensis was recently renewed as a tier-one  select
AB  - agent. F. tularensis subsp. tularensis (type A) and holarctica (type B)
AB  - are of clinical relevance. Here, we report the complete genome of a virulent F.
AB  - tularensis type B strain and describe its usefulness in comparative genomics.
ER  -

TY  - JOUR
AU  - Attar, N.
TI  - SMRT-seq reveals an epigenetic switch.
JO  - Nat. Rev. Microbiol.
PY  - 2016
SP  - 546
EP  - 546
VL  - 14
AB  - Streptococcus pneumonia uses genetic diversification as a strategy to achieve phenotypic
AB  - plasticity.  For example, DNA inversion of the hsdS genes of type I restriction-modification
AB  - systems determines whether S. pneumonia forms opaque or transparent colonies, which have
AB  - different colonization and virulence characteristics.  Zhang and colleagues now use
AB  - single-molecule, real-time sequencing to show the allelic variation of hsdS that results from
AB  - site-specific recombination forms part of an epigenetic switch.
ER  -

TY  - JOUR
AU  - Attie, O.
AU  - Jayaprakash, A.
AU  - Shah, H.
AU  - Paulsen, I.T.
AU  - Morino, M.
AU  - Takahashi, Y.
AU  - Narumi, I.
AU  - Sachidanandam, R.
AU  - Satoh, K.
AU  - Ito, M.
AU  - Krulwich, T.A.
TI  - Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934.
JO  - Genome Announcements
PY  - 2014
SP  - e01175
EP  - e01114
VL  - 2
AB  - Bacillus alcalophilus AV1934, isolated from human feces, was described in 1934 before
AB  - microbiome studies and recent indications of novel potassium ion coupling
AB  - to motility in this extremophile. Here, we report draft sequences that will
AB  - facilitate an examination of whether that coupling is part of a larger cycle of
AB  - potassium ion-coupled transporters.
ER  -

TY  - JOUR
AU  - Attwood, G.T.
AU  - Kelly, W.J.
AU  - Altermann, E.H.
AU  - Leahy, S.C.
TI  - Analysis of the Methanobrevibacter ruminantium draft genome: understanding methanogen biology to inhibit their action in the rumen.
JO  - Aust. J. Exp. Agr.
PY  - 2008
SP  - 83
EP  - 88
VL  - 48
AB  - Methane is produced in the foregut (rumen) of ruminants by methanogens, which act as terminal
AB  - reducers of carbon in the rumen system. The
AB  - multistep methanogenesis pathway is well elucidated, mainly from the
AB  - study of non-rumen methanogens, but the adaptations that allow
AB  - methanogens to grow and persist in the rumen are not well understood.
AB  - The Pastoral Greenhouse Gas Research Consortium is sequencing the
AB  - genome of Methanobrevibacter ruminantium, a prominent methanogen in New
AB  - Zealand ruminants, as part of a project to mitigate greenhouse gases.
AB  - The genome is similar to 3.0Mb in size with a guanine-cytosine (GC)
AB  - content of 33.68%. All of the components of the methanogenesis pathway
AB  - have been identified and comparison of these gene sequences with those
AB  - from Methanothermobacter thermoautotrophicus and Methanosphaera
AB  - stadtmanae indicates that methanogenesis gene organisation is conserved
AB  - within the Methanobacteriales. The genome of M. ruminantium contains a
AB  - prophage sequence (designated phi mru) with distinct functional modules
AB  - encoding phage integration, DNA replication and packaging, capsid
AB  - proteins and lysis functions. A low GC region found at the distal end
AB  - of the phage sequence harbours a putative DNA restriction/modification
AB  - system which might provide additional protection against foreign DNA.
AB  - The genome also contains many large surface proteins with
AB  - characteristics that indicate that they may mediate association with
AB  - other rumen microbes. Approximately half of the genes identified within
AB  - the genome have no known function. Determining the function of these
AB  - new genes will assist in de. ning the role of M. ruminantium in methane
AB  - formation in the rumen and help identify means to control methane
AB  - emissions from ruminant animals.
ER  -

TY  - JOUR
AU  - Atyame, C.M.
AU  - Delsuc, F.
AU  - Pasteur, N.
AU  - Weill, M.
AU  - Duron, O.
TI  - Diversification of Wolbachia endosymbiont in the Culex pipiens mosquito.
JO  - Mol. Biol. Evol.
PY  - 2011
SP  - 2761
EP  - 2772
VL  - 28
AB  - The alpha-proteobacteria Wolbachia are among the most common intracellular bacteria and have
AB  - recently emerged as important drivers of arthropod biology. Wolbachia commonly act as
AB  - reproductive parasites in arthropods by inducing cytoplasmic incompatibility (CI), a type of
AB  - conditional sterility between hosts harboring incompatible infections. In this study, we
AB  - examined the evolutionary histories of Wolbachia infections, known as wPip, in the common
AB  - house mosquito Culex pipiens, which exhibits the greatest variation in CI crossing patterns
AB  - observed in any insect. We first investigated a panel of twenty wPip strains for their genetic
AB  - diversity through a multi-locus scheme combining thirteen Wolbachia genes. Because Wolbachia
AB  - depend primarily on maternal transmission for spreading within arthropod populations, we also
AB  - studied the variability in the co-inherited Cx. pipiens mitochondria. In total, we identified
AB  - fourteen wPip haplotypes, which all share a monophyletic origin and clearly cluster into five
AB  - distinct wPip groups. The diversity of Cx. pipiens mitochondria was extremely reduced, which
AB  - is likely a consequence of cytoplasmic hitchhiking driven by a unique and recent Wolbachia
AB  - invasion. Phylogenetic evidence indicates that wPip infections and mitochondrial DNA have
AB  - co-diverged through stable co-transmission within the cytoplasm and shows that a rapid
AB  - diversification of wPip has occurred. The observed pattern demonstrates that a considerable
AB  - degree of Wolbachia diversity can evolve within a single host species over short evolutionary
AB  - periods. In addition, multiple signatures of recombination were found in most wPip genomic
AB  - regions, leading us to conclude that the mosaic nature of wPip genomes may play a key role in
AB  - their evolution.
ER  -

TY  - JOUR
AU  - Atyame, C.M.
AU  - Duron, O.
AU  - Tortosa, P.
AU  - Pasteur, N.
AU  - Fort, P.
AU  - Weill, M.
TI  - Multiple Wolbachia determinants control the evolution of cytoplasmic incompatibilities in Culex pipiens mosquito populations.
JO  - Mol. Ecol.
PY  - 2011
SP  - 286
EP  - 298
VL  - 20
AB  - Wolbachia are maternally inherited endosymbionts that can invade arthropod
AB  - populations through manipulation of their reproduction. In mosquitoes,
AB  - Wolbachia induce embryonic death, known as cytoplasmic incompatibility
AB  - (CI), whenever infected males mate with females either uninfected or
AB  - infected with an incompatible strain. Although genetic determinants of CI
AB  - are unknown, a functional model involving the so-called mod and resc
AB  - factors has been proposed. Natural populations of Culex pipiens mosquito
AB  - display a complex CI relationship pattern associated with the highest
AB  - Wolbachia (wPip) genetic polymorphism reported so far. We show here that
AB  - C. pipiens populations from La Reunion, a geographically isolated island
AB  - in the southwest of the Indian Ocean, are infected with genetically
AB  - closely related wPip strains. Crossing experiments reveal that these
AB  - Wolbachia are all mutually compatible. However, crosses with genetically
AB  - more distant wPip strains indicate that Wolbachia strains from La Reunion
AB  - belong to at least five distinct incompatibility groups (or crossing
AB  - types). These incompatibility properties which are strictly independent
AB  - from the nuclear background, formally establish that in C. pipiens, CI is
AB  - controlled by several Wolbachia mod/resc factors.
ER  -

TY  - JOUR
AU  - Auad, L.
AU  - Peril, M.A.A.
AU  - de Ruiz Holgado, A.A.P.
AU  - Raya, R.R.
TI  - Evidence of a restriction/modification system in Lactobacillus delbrueckii subsp. lactis CNRZ 326.
JO  - Curr. Microbiol.
PY  - 1998
SP  - 271
EP  - 273
VL  - 36
AB  - Lactobacillus delbrueckii subsp. lactis (Lb. lactis) CNRZ 326 is widely used in the
AB  - propagation of Lb. delbrueckii bacteriophages.  In this study, evidence is presented that this
AB  - strain possesses a restriction-modification system. The mitomycin C-induced temperate
AB  - bacteriophage lb539 has a reduced efficiency of plaquing (EOP) on CNRZ 326 cells (EOP=10^-3),
AB  - but after several passages on this strain, or on the indicator strain Lb. lactis LKT, the
AB  - recovered phages (phages lb539.326 and lb539.LKT) have an EOP equal to 1.  Restrictive
AB  - development on CNRZ 326 was also observed after phage lb539.326 was propagated on the strain
AB  - Lb. lactis CRL 934.  The R/M system was also active against the virulent Lb. delbrueckii phage
AB  - ll-h.  Plasmid DNA was not detected in CNRZ 326, which suggests that the R/M system described
AB  - is chromosomally encoded.
ER  -

TY  - JOUR
AU  - Aubert, E.
AU  - Spurgeon, S.
AU  - Ray, W.
AU  - Davies, J.
TI  - Purification and characterization of an isoschizomer of SphI from Bacillus circulans.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6152
EP  - 6152
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Aubin, G.G.
AU  - Kambarev, S.
AU  - Bemer, P.
AU  - Lawson, P.A.
AU  - Corvec, S.
TI  - Draft Genome Sequence of Highly Rifampin-Resistant Propionibacterium namnetense NTS 31307302T Isolated from a Patient with a Bone Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e00819
EP  - e00816
VL  - 4
AB  - Propionibacterium namnetense was recently described as a potential bone pathogen, which is
AB  - closely related to Propionibacterium acnes, a skin commensal
AB  - microorganism. Here, we report the draft genome sequence of the highly
AB  - rifampin-resistant strain NTS 31307302(T) isolated from a patient with a tibia
AB  - infection.
ER  -

TY  - JOUR
AU  - Aubin, G.G.
AU  - Kambarev, S.
AU  - Guillouzouic, A.
AU  - Khammari, A.
AU  - Dreno, B.
AU  - Corvec, S.
TI  - Draft Genome Sequence of an Erythromycin-Resistant Propionibacterium acnes Isolate Recovered from Folliculitis of the Scalp.
JO  - Genome Announcements
PY  - 2017
SP  - e01490
EP  - e01416
VL  - 5
AB  - Propionibacterium acnes is now well-known and recognized for its implication in the
AB  - pathogenesis of acne vulgaris. Here, we report the draft genome sequence of
AB  - an erythromycin-resistant P. acnes strain isolated from a case of folliculitis of
AB  - the scalp belonging to phylotype IA1 and sequence type 18 (ST18).
ER  -

TY  - JOUR
AU  - Aubin, G.G.
AU  - Kambarev, S.
AU  - Guillouzouic, A.
AU  - Lepelletier, D.
AU  - Bemer, P.
AU  - Corvec, S.
TI  - Draft Genome Sequences of Four Propionibacterium acnes Strains Isolated from Implant-Related Infections.
JO  - Genome Announcements
PY  - 2016
SP  - e01395
EP  - e01316
VL  - 4
AB  - Propionibacterium acnes was previously described as a potential implant-related pathogen.
AB  - Here, we report the draft genome sequence of four P. acnes strains,
AB  - isolated from spine material, hip arthroplasty, and knee arthroplasty infections
AB  - in France belonging to different sequence types (ST18, ST27, and ST36).
ER  -

TY  - JOUR
AU  - Aubol, B.E.
AU  - Reich, N.O.
TI  - Murine DNA cytosine C5-methyltransferase: in vitro studies of de novo methylation spreading.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2003
SP  - 209
EP  - 214
VL  - 310
AB  - The preference of murine DNA (cytosine-5)-methyltransferase (Dnmt1) for single stranded DNA
AB  - substrates is increased up to 50-fold by the presence
AB  - of a proximal 5-methyl cytosine (5(me)C). This modulation is
AB  - distance-dependent and is due to an enhanced binding affinity and minor
AB  - changes in catalytic efficiency. No modulation was observed with double
AB  - stranded DNA. Modulation requires that the 5(me)C moiety be attached to
AB  - the DNA strand containing the CpG methylation target. Our results support
AB  - a model in which 5(me)C binding by the enzyme occurs to at least one site
AB  - outside the region involved in CpG recognition. No modulation in response
AB  - to 5(me)C is observed with the bacterial enzyme M.SssI, which lacks the
AB  - large N-terminal regulatory domain found in Dnmt1. We suggest that this
AB  - allosteric modulation involves the N-terminal domain of Dnmt1.
ER  -

TY  - JOUR
AU  - Aubol, B.E.
AU  - Reich, N.O.
TI  - Exploring the N-terminal function of murine methyltransferase.
JO  - ACS Abstracts
PY  - 1999
SP  - 453
EP  - 453
VL  - 217
AB  - The mammalian DNA methyltransferase methylates specific cytosine residues on the host genome.
AB  - DNA methylation is essential for development, gene regulation, and aberrant DNA methylation
AB  - leads to tumorgenesis.  We are using a highly homogeneous preparation of the murine DCMTase to
AB  - gain basic insights into its function, and the design of novel anti-cancer strategies.
AB  - DCMTase contains a large, poorly characterized N-terminal domain not found in bacterial
AB  - enzymes that have similar functions.  This domain binds zinc with characteristics of a zinc
AB  - finger.  We have probed the affect of zinc binding on numerous aspects of DCMTase functions.
AB  - Methylation spreading, activation by adjacent 5-methylcytosine residues with single stranded
AB  - DNA as a substrate, is one of these functions, and is of particular interest.  This activation
AB  - may lead to the process of "methylation spreading" and our approach will determine if the zinc
AB  - plays a role in this regulation of enzyme function.
ER  -

TY  - JOUR
AU  - Auchtung, T.A.
AU  - Holder, M.E.
AU  - Gesell, J.R.
AU  - Ajami, N.J.
AU  - Duarte, R.T.
AU  - Itoh, K.
AU  - Caspi, R.R.
AU  - Petrosino, J.F.
AU  - Horai, R.
AU  - Zarate-Blades, C.R.
TI  - Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse.
JO  - Genome Announcements
PY  - 2016
SP  - e00114
EP  - e00116
VL  - 4
AB  - Turicibacterbacteria are commonly detected in the gastrointestinal tracts and feces of humans
AB  - and animals, but their phylogeny, ecological role, and pathogenic
AB  - potential remain unclear. We present here the first complete genome sequence
AB  - ofTuricibactersp. strain H121, which was isolated from the feces of a mouse line
AB  - contaminated following germ-free derivation.
ER  -

TY  - JOUR
AU  - Audic, S.
AU  - Lescot, M.
AU  - Claverie, J.M.
AU  - Cloeckaert, A.
AU  - Zygmunt, M.S.
TI  - The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella.
JO  - BMC Evol. Biol.
PY  - 2011
SP  - 200
EP  - 200
VL  - 11
AB  - ABSTRACT: BACKGROUND: Since the discovery of the Malta fever agent,
AB  - Brucella melitensis, in the 19th century, six terrestrial
AB  - mammal-associated Brucella species were recognized over the next century.
AB  - More recently the number of novel Brucella species has increased and among
AB  - them, isolation of species B. pinnipedialis and B. ceti from marine
AB  - mammals raised many questions about their origin as well as on the
AB  - evolutionary history of the whole genus. RESULTS: We report here on the
AB  - first complete genome sequence of a Brucella strain isolated from marine
AB  - mammals, Brucella pinnipedialis strain B2/94. A whole gene-based
AB  - phylogenetic analysis shows that five main groups of host-associated
AB  - Brucella species rapidly diverged from a likely free-living ancestor close
AB  - to the recently isolated B. microti. However, this tree lacks the
AB  - resolution required to resolve the order of divergence of those groups.
AB  - Comparative analyses focusing on a) genome segments unshared between B.
AB  - microti and B. pinnipedialis, b) gene deletion/fusion events and c)
AB  - positions and numbers of Brucella specific IS711 elements in the available
AB  - Brucella genomes provided enough information to propose a branching order
AB  - for those five groups. CONCLUSIONS: In this study, it appears that the
AB  - closest relatives of marine mammal Brucella sp. are B. ovis and Brucella
AB  - sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B.
AB  - abortus strains, and finally the group consisting of B. suis strains,
AB  - including B. canis and the group consisting of the single B. neotomae
AB  - species. We were not able, however, to resolve the order of divergence of
AB  - the two latter groups.
ER  -

TY  - JOUR
AU  - Audic, S.
AU  - Lescot, M.
AU  - Claverie, J.M.
AU  - Scholz, H.C.
TI  - Brucella microti: the genome sequence of an emerging pathogen.
JO  - BMC Genomics
PY  - 2009
SP  - 352
EP  - 352
VL  - 10
AB  - ABSTRACT: BACKGROUND: Using a combination of pyrosequencing and
AB  - conventional Sanger sequencing, the complete genome sequence of the
AB  - recently described novel Brucella species, Brucella microti, was
AB  - determined. B. microti is a member of the genus Brucella within the
AB  - Alphaproteobacteria, which consists of medically important highly
AB  - pathogenic facultative intracellular bacteria. In contrast to all other
AB  - Brucella species, B. microti is a fast growing and biochemically very
AB  - active microorganism with a phenotype more similar to that of
AB  - Ochrobactrum, a facultative human pathogen. The atypical phenotype of B.
AB  - microti prompted us to look for genomic differences compared to other
AB  - Brucella species and to look for similarities with Ochrobactrum. RESULTS:
AB  - The genome is composed of two circular chromosomes of 2,117,050 and
AB  - 1,220,319 base pairs. Unexpectedly, we found that the genome sequence of
AB  - B. microti is almost identical to that of Brucella suis 1330 with an
AB  - overall sequence identity of 99.84% in aligned regions. The most
AB  - significant structural difference between the two genomes is a
AB  - bacteriophage-related 11,742 base pairs insert only present in B. microti.
AB  - However, this insert is unlikely to have any phenotypical consequence.
AB  - Only four protein coding genes are shared between B. microti and
AB  - Ochrobactrum anthropi but impaired in other sequenced Brucella. The most
AB  - noticeable difference between B. microti and other Brucella species was
AB  - found in the sequence of the 23S ribosomal RNA gene. This unusual
AB  - variation could have pleiotropic effects and explain the fast growth of B.
AB  - microti. CONCLUSIONS: Contrary to expectations from the phenotypic
AB  - analysis, the genome sequence of B. microti is highly similar to that of
AB  - known Brucella species, and is remotely related to the one of O. anthropi.
AB  - How the few differences in gene content between B. microti and B. suis
AB  - 1330 could result in vastly different phenotypes remains to be elucidated.
AB  - This unexpected finding will complicate the task of identifying virulence
AB  - determinants in the Brucella genus. The genome sequence of B. microti will
AB  - serve as a model for differential expression analysis and complementation
AB  - studies. Our results also raise some concerns about the importance given
AB  - to phenotypical traits in the definition of bacterial species.
ER  -

TY  - JOUR
AU  - Audisio, M.C.
AU  - Albarracin, L.
AU  - Torres, M.J.
AU  - Saavedra, L.
AU  - Hebert, E.M.
AU  - Villena, J.
TI  - Draft Genome Sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, Novel Potential Probiotic Strains for Honeybees (Apis  mellifera L.).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00975
EP  - e00918
VL  - 7
AB  - This report describes the draft genome sequences of Lactobacillus salivarius A3iob and
AB  - Lactobacillus johnsonii CRL1647, probiotic strains isolated from the
AB  - gut of honeybee Apis mellifera workers. The reads were generated by a
AB  - whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were
AB  - assembled into contigs with total sizes of 2,054,490 and 2,137,413 bp for the
AB  - A3iob and CRL1647 strains, respectively. The draft genome sequences of L.
AB  - salivarius A3iob and L. johnsonii CRL1647 will be useful for further studies of
AB  - the specific genetic features of these strains and for understanding the
AB  - mechanisms of their probiotic properties.
ER  -

TY  - JOUR
AU  - Auer, B.
AU  - Schweiger, M.
TI  - Evidence that Escherichia coli virus T1 induces a DNA methyltransferase.
JO  - J. Virol.
PY  - 1984
SP  - 588
EP  - 590
VL  - 49
AB  - DNA of Escherichia coli virus T1 is resistant to MboI cleavage and appears
AB  - to be heavily methylated.  Analysis of methylation by the isoschizomeric restriction
AB  - enzymes Sau3AI and DpnI revealed that recognition sites for E. coli DNA adenine
AB  - methylase (dam methylase) are methylated.  The same methylation pattern was found for
AB  - virus T1 DNA grown on an E. coli dam host, indicating a T1-specific DNA
AB  - methyltransferase.
ER  -

TY  - JOUR
AU  - Auffret, P.
AU  - Segura, A.
AU  - Bertin, Y.
AU  - Klopp, C.
AU  - Bouchez, O.
AU  - Kerouredan, M.
AU  - Bibbal, D.
AU  - Brugere, H.
AU  - Forano, E.
TI  - Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France.
JO  - Genome Announcements
PY  - 2017
SP  - e01097
EP  - e01017
VL  - 5
AB  - Enterohemorrhagic Escherichia coli (EHEC) with serotype O157:H7 is a major foodborne pathogen.
AB  - Here, we report the draft genome sequence of EHEC O157:H7
AB  - strain MC2 isolated from cattle in France. The assembly contains 5,400,376 bp
AB  - that encoded 5,914 predicted genes (5,805 protein-encoding genes and 109 RNA
AB  - genes).
ER  -

TY  - JOUR
AU  - Augelletti, F.
AU  - Tremblay, J.
AU  - Agathos, S.N.
AU  - Stenuit, B.
TI  - Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e00249
EP  - e00218
VL  - 6
AB  - We report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium
AB  - sp. strain LB126. The genes involved in the upper biodegradation
AB  - pathway of fluorene are located on a plasmid, and the lower pathway that
AB  - generates tricarboxylic acid cycle intermediates is initiated by the
AB  - meta-cleavage of protocatechuic acid that is chromosomally encoded.
ER  -

TY  - JOUR
AU  - Auger, S.
AU  - Galleron, N.
AU  - Segurens, B.
AU  - Dossat, C.
AU  - Bolotin, A.
AU  - Wincker, P.
AU  - Sorokin, A.
TI  - Complete Genome Sequence of the Highly Hemolytic Strain Bacillus cereus F837/76.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1630
EP  - 1630
VL  - 194
AB  - Highly hemolytic strain Bacillus cereus F837/76 was isolated in 1976 from a contaminated
AB  - prostate wound. The complete nucleotide sequence of this strain
AB  - reported here counts nearly 36,500 single-nucleotide differences from the closest
AB  - sequenced strain, Bacillus thuringiensis Al Hakam. F827/76 also contains a 10-kb
AB  - plasmid that was not detected in the Al Hakam strain.
ER  -

TY  - JOUR
AU  - Augustyniak, D.
AU  - Seredynski, R.
AU  - McClean, S.
AU  - Roszkowiak, J.
AU  - Roszniowski, B.
AU  - Smith, D.L.
AU  - Drulis-Kawa, Z.
AU  - Mackiewicz, P.
TI  - Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution.
JO  - Sci. Rep.
PY  - 2018
SP  - 4955
EP  - 4955
VL  - 8
AB  - Moraxella catarrhalis is a common human respiratory tract pathogen. Its virulence
AB  - factors associated with whole bacteria or outer membrane vesicles (OMVs) aid
AB  - infection, colonization and may induce specific antibodies. To investigate
AB  - pathogen-host interactions, we applied integrated bioinformatic and
AB  - immunoproteomic (2D-electrophoresis, immunoblotting, LC-MS/MS) approaches. We
AB  - showed that OMV proteins engaged exclusively in complement evasion and
AB  - colonization strategies, but not those involved in iron transport and metabolism,
AB  - are major targets for cross-reacting antibodies produced against phylogenetically
AB  - divergent M. catarrhalis strains. The analysis of 31 complete genomes of M.
AB  - catarrhalis and other Moraxella revealed that OMV protein-coding genes belong to
AB  - 64 orthologous groups, five of which are restricted to M. catarrhalis. This
AB  - species showed a two-fold increase in the number of OMV protein-coding genes
AB  - relative to its ancestors and animal-pathogenic Moraxella. The appearance of
AB  - specific OMV factors and the increase in OMV-associated virulence proteins during
AB  - M. catarrhalis evolution is an interesting example of pathogen adaptation to
AB  - optimize colonization. This precisely targeted cross-reactive immunity against M.
AB  - catarrhalis may be an important strategy of host defences to counteract this
AB  - phenomenon. We demonstrate that cross-reactivity is closely associated with the
AB  - anti-virulent antibody repertoire which we have linked with adaptation of this
AB  - pathogen to the host.
ER  -

TY  - JOUR
AU  - Aung, H.L.
AU  - Tun, T.
AU  - Permina, E.
AU  - Nyunt, W.W.
AU  - Aung, S.T.
AU  - Thinn, K.K.
AU  - Crump, J.A.
AU  - Cook, G.M.
TI  - Draft Genome Sequences of Two Drug-Resistant Mycobacterium tuberculosis Isolates  from Myanmar.
JO  - Genome Announcements
PY  - 2016
SP  - e00850
EP  - e00816
VL  - 4
AB  - Multidrug-resistant tuberculosis (MDR-TB) and lately, extensively drug-resistant  TB (XDR-TB)
AB  - are increasing global health concerns. Here, we present the genome
AB  - sequences of two MDR-TB isolates from Myanmar, one of 27 countries with a high
AB  - MDR-TB burden, and describe a number of mutations consistent with these being
AB  - XDR-TB isolates.
ER  -

TY  - JOUR
AU  - Aurass, P.
AU  - Karste, S.
AU  - Trost, E.
AU  - Glaeser, S.P.
AU  - Kampfer, P.
AU  - Flieger, A.
TI  - Genome Sequence of Paracoccus contaminans LMG 29738T, Isolated from a Water Microcosm.
JO  - Genome Announcements
PY  - 2017
SP  - e00487
EP  - e00417
VL  - 5
AB  - We announce here the complete genome sequence of Paracoccus contaminans LMG 29738T, which we
AB  - recently isolated from a contaminated water microcosm. The
AB  - genome consists of a 2.94-Mb chromosome and a 94-kb plasmid. To our knowledge, we
AB  - provide the first DNA methylation analysis of a Paracoccus species.
ER  -

TY  - JOUR
AU  - Avalos, M.
AU  - Boetzer, M.
AU  - Pirovano, W.
AU  - Arenas, N.E.
AU  - Douthwaite, S.
AU  - van Wezel, G.P.
TI  - Complete Genome Sequence of Escherichia coli AS19, an Antibiotic-Sensitive Variant of E. coli Strain B REL606.
JO  - Genome Announcements
PY  - 2018
SP  - e00385
EP  - e00318
VL  - 6
AB  - The chemically mutagenized Escherichia coli strain AS19 was isolated on the basis of its
AB  - enhanced sensitivity to different antibiotics, in particular to
AB  - actinomycin. The strain was later modified to study rRNA modifications that
AB  - confer antibiotic resistance. Here, we present the genome sequence of the variant
AB  - E. coli AS19-RrmA().
ER  -

TY  - JOUR
AU  - Avasthi, T.S.
AU  - Devi, S.H.
AU  - Taylor, T.D.
AU  - Kumar, N.
AU  - Baddam, R.
AU  - Kondo, S.
AU  - Suzuki, Y.
AU  - Lamouliatte, H.
AU  - Megraud, F.
AU  - Ahmed, N.
TI  - Genomes of the two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908, obtained from a  single patient.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3385
EP  - 3386
VL  - 193
AB  - The diverse clinical outcomes of colonization by Helicobacter pylori reflect need to
AB  - understand genomic rearrangements enabling the bacterium
AB  - to adapt to host niches and exhibit varied colonization/virulence
AB  - potential. We describe genome sequences of the two serial isolates, H.
AB  - pylori 2017 and 2018 (the chronological sub-clones of H. pylori 908),
AB  - cultured in 2003 from corpus and antrum, respectively, of an African
AB  - patient who suffered from recrudescent duodenal ulcer disease. The genome
AB  - sequences when compared with the genome of parent strain, HP 908 (isolated
AB  - from antrum of the same patient in 1994) revealed genomic alterations
AB  - relevant in virulence optimization or host-specific adaptation.
ER  -

TY  - JOUR
AU  - Avasthi, T.S.
AU  - Kumar, N.
AU  - Baddam, R.
AU  - Hussain, A.
AU  - Nandanwar, N.
AU  - Jadhav, S.
AU  - Ahmed, N.
TI  - Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4272
EP  - 4273
VL  - 193
AB  - Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a
AB  - significant environmental prevalence due to
AB  - contamination by human and animal excreta. In developing countries, UPEC
AB  - assumes importance in certain dwellings because of poor community/personal
AB  - hygiene and exposure to contaminated water or soil. We report the complete
AB  - genome sequence of E. coli strain NA114 from India, a UPEC strain with a
AB  - multidrug resistance phenotype and the capacity to produce
AB  - extended-spectrum beta-lactamase. The genome sequence and comparative
AB  - genomics emanating from it will be significant in under-standing the
AB  - genetic makeup of diverse UPEC strains and in boosting the development of
AB  - new diagnostics/vaccines.
ER  -

TY  - JOUR
AU  - Avci, B.
AU  - Hahnke, R.L.
AU  - Chafee, M.
AU  - Fischer, T.
AU  - Gruber-Vodicka, H.
AU  - Tegetmeyer, H.E.
AU  - Harder, J.
AU  - Fuchs, B.M.
AU  - Amann, R.I.
AU  - Teeling, H.
TI  - Genomic and physiological analyses of 'Reinekea forsetii' reveal a versatile opportunistic lifestyle during spring algae blooms.
JO  - Environ. Microbiol.
PY  - 2017
SP  - 1209
EP  - 1221
VL  - 19
AB  - Gammaproteobacterial Reinekea spp. were detected during North Sea spring algae
AB  - blooms in the years 2009-2012, with relative abundances of up to 16% in the
AB  - bacterioplankton. Here, we explore the ecophysiology of 'R. forsetii' strain
AB  - Hel1_31_D35 that was isolated during the 2010 spring bloom using (i) its manually
AB  - annotated, high-quality closed genome, (ii) re-analysis of in situ data from the
AB  - 2009-2012 blooms and (iii) physiological tests. High resolution analysis of 16S
AB  - rRNA gene sequences suggested that 'R. forsetii' dominated Reinekea populations
AB  - during these blooms. This was corroborated by retrieval of almost complete
AB  - Hel1_31_D35 genomes from 2009 and 2010 bacterioplankton metagenomes. Strain
AB  - Hel1_31_D35 can use numerous low-molecular weight substrates including diverse
AB  - sugar monomers, and few but relevant algal polysaccharides such as mannan,
AB  - alpha-glucans, and likely bacterial peptidoglycan. It oxidizes thiosulfate to
AB  - sulfate, and ferments under anoxic conditions. The strain can attach to algae and
AB  - thrives at low phosphate concentrations as they occur during blooms. Its genome
AB  - encodes RTX toxin and secretion proteins, and in cultivation experiments
AB  - Hel1_31_D35 crude cell extracts inhibited growth of a North Sea Polaribacter
AB  - strain. Our data suggest that the combination of these traits make strain
AB  - Hel1_31_D35 a versatile opportunist that is particularly competitive during
AB  - spring phytoplankton blooms.
ER  -

TY  - JOUR
AU  - Avendano-Herrera, R.
AU  - Poblete-Morales, M.
TI  - Genome Sequence of Streptococcus phocae subsp. phocae Strain ATCC 51973T Isolated from a Harbor Seal (Phoca vitulina).
JO  - Genome Announcements
PY  - 2015
SP  - e01307
EP  - e01315
VL  - 3
AB  - Streptococcus phocae subsp. phocae is a pathogen that affects different pinniped  and
AB  - mammalian species. This announcement reports the genome sequence of the type
AB  - strain ATCC 51973 isolated in Norway from clinical specimens of harbor seal
AB  - (Phoca vitulina), revealing interesting genes related to possible virulence
AB  - factors.
ER  -

TY  - JOUR
AU  - Avendano-Herrera, R.
AU  - Suarez, R.
AU  - Lazo, E.
AU  - Bravo, D.
AU  - Llegues, K.O.
AU  - Romalde, J.L.
AU  - Godoy, M.G.
TI  - Genome Sequence of Streptococcus phocae subsp. salmonis Strain C-4T, Isolated from Atlantic Salmon (Salmo salar).
JO  - Genome Announcements
PY  - 2014
SP  - e01269
EP  - e01214
VL  - 2
AB  - Streptococcus phocae subsp. salmonis is a fish pathogen that has an important impact on the
AB  - Chilean salmon industry. Here, we report the genome sequence of the
AB  - type strain C-4(T) isolated from Atlantic salmon (Salmo salar), showing a number
AB  - of interesting features and genes related to its possible virulence factors.
ER  -

TY  - JOUR
AU  - Aw, Y.K.
AU  - Ong, K.S.
AU  - Yule, C.M.
AU  - Gan, H.M.
AU  - Lee, S.M.
TI  - Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e01024
EP  - e01014
VL  - 2
AB  - We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range
AB  - antimicrobial activity, isolated from tropical peat swamp soil. Genes
AB  - involved in antimicrobial biosynthesis are found to be present in this genome.
ER  -

TY  - JOUR
AU  - Axelsson, L.
AU  - Rud, I.
AU  - Naterstad, K.
AU  - Blom, H.
AU  - Renckens, B.
AU  - Boekhorst, J.
AU  - Kleerebezem, M.
AU  - van Hijum, S.
AU  - Siezen, R.J.
TI  - Genome Sequence of the Naturally Plasmid-Free Lactobacillus plantarum Strain NC8  (CCUG 61730).
JO  - J. Bacteriol.
PY  - 2012
SP  - 2391
EP  - 2392
VL  - 194
AB  - Lactobacillus plantarum is a highly versatile lactic acid bacterium found in various
AB  - ecological niches, such as fermented vegetable, meat, and dairy products
AB  - and the gastrointestinal tract. We sequenced the genome of L. plantarum NC8, a
AB  - naturally plasmid-free strain, which has been used as a model strain in many
AB  - laboratories worldwide.
ER  -

TY  - JOUR
AU  - Axenov-Gribanov, D.V.
AU  - Tokovenko, B.T.
AU  - Rebets, Y.V.
AU  - Voytsekhovskaya, I.V.
AU  - Shatilina, Z.M.
AU  - Protasov, E.S.
AU  - Luzhetskyy, A.N.
AU  - Timofeyev, M.A.
TI  - Draft Genome Sequence of Streptomyces sp. Strain IB2014011-1, Isolated from Trichoptera sp. Larvae of Lake Baikal.
JO  - Genome Announcements
PY  - 2017
SP  - e00062
EP  - e00017
VL  - 5
AB  - Unique ecosystems with specific environmental conditions have been proven to be a promising
AB  - source for isolation of new actinobacterial strains. Ancient Lake
AB  - Baikal is one of the greatest examples of an ecosystem with high species
AB  - biodiversity and endemicity caused by long-lasting isolated evolution and stable
AB  - environmental conditions. Herein we report the draft genome sequence of
AB  - Streptomyces sp. strain IB2014011-1, which was isolated from insect Trichoptera
AB  - sp. larvae collected at the bottom of Lake Baikal.
ER  -

TY  - JOUR
AU  - Aya-Castaneda, M.R.
AU  - Sarnacki, S.H.
AU  - Noto-Llana, M.
AU  - Lopez-Guerra, A.G.
AU  - Giacomodonato, M.N.
AU  - Cerquetti, M.C.
TI  - Dam methylation is required for efficient biofilm production in Salmonella enterica serovar Enteritidis.
JO  - Int. J. Food Microbiol.
PY  - 2015
SP  - 15
EP  - 22
VL  - 193
AB  - The ecological success of Salmonella enterica to survive in different environments is due, in
AB  - part, to the ability to form biofilms, something which is especially important for food
AB  - industry. The aim of the current study was to evaluate the involvement of Dam methylation in
AB  - biofilm production in S. Enteritidis strains. The ability to generate biofilms was analyzed in
AB  - wild type and dam mutant strains. In S. Enteritidis, the absence of Dam affected the capacity
AB  - to develop pellicles at the air-liquid interface and reduced the ability to form biofilm on
AB  - polystyrene surfaces.,Curli and cellulose production, determined by Congo red and calcofluor
AB  - assays, were affected in dam mutant strains. Relative quantitative real-time PCR experiments
AB  - showed that the expression of csgD and csgA genes is reduced in mutants lacking dam gene with
AB  - respect to the wild type strains, whereas transcript levels of bcsA are not affected in the
AB  - absence of Dam. To our knowledge, this is the first report on the participation of Dam
AB  - methylation on biofilm production in Enteritidis or any other serovar of S. enterica. Results
AB  - presented here suggest that changes in gene expression required for biofilm production are
AB  - finely regulated by Dam methylation. Thus, Dam methylation could modulate csgD expression and
AB  - upregulate the expression of factors related with biofilm production, including curli and
AB  - cellulose. This study contributes to the understanding of biofilm regulation in Salmonella
AB  - spp. and to the design of new strategies to prevent food contamination and humans and animals
AB  - infections.
ER  -

TY  - JOUR
AU  - Ayala, D.I.
AU  - Cook, P.W.
AU  - Campos, D.L.
AU  - Brashears, M.M.
AU  - den Bakker, H.
AU  - Nightingale, K.K.
TI  - Draft Genome Sequence of Lactobacillus salivarius L28 Isolated from Ground Beef.
JO  - Genome Announcements
PY  - 2017
SP  - e00955
EP  - e00917
VL  - 5
AB  - In this report, we describe the draft genome sequence of a newly discovered probiotic strain,
AB  - Lactobacillus salivarius L28. L. salivarius L28 demonstrates
AB  - antagonistic effects against human foodborne pathogens, including Escherichia
AB  - coli O157:H7, Salmonella spp., and Listeria monocytogenes, in coculture
AB  - experiments and food matrices.
ER  -

TY  - JOUR
AU  - Ayala, D.I.
AU  - Cook, P.W.
AU  - Campos, D.L.
AU  - Franco, J.G.
AU  - Brashears, M.M.
AU  - den Bakker, H.
AU  - Nightingale, K.K.
TI  - Draft Genome Sequence of Enterococcus faecium Strain J19, Isolated from Cabbage.
JO  - Genome Announcements
PY  - 2018
SP  - e00213
EP  - e00218
VL  - 6
AB  - Herein, we report the draft genome sequence of a newly discovered probiotic strain,
AB  - Enterococcus faecium J19, which was isolated from cabbage. Strain J19 has
AB  - shown antagonistic effects against the human foodborne pathogen Listeria
AB  - monocytogenes in coculture and in different food matrices.
ER  -

TY  - JOUR
AU  - Ayala, M.
AU  - Segovia, C.
AU  - Rojas, R.
AU  - Miranda, C.
AU  - Santander, J.
TI  - Draft Genome Sequence of Epilithonimonas sp. FP211-J200, Isolated from an Outbreak Episode on a Rainbow Trout (Oncorhynchus mykiss) Farm.
JO  - Genome Announcements
PY  - 2017
SP  - e00819
EP  - e00817
VL  - 5
AB  - Here, we report the draft genome sequence of Epilithonimonas sp. FP211-J200, isolated from
AB  - rainbow trout head kidney cells. The size of the genome is
AB  - 4,110,772 bp, with a G+C content of 37.1%. The Epilithonimonas sp. FP211-J200
AB  - genome has genes related to tetracycline and beta-lactam resistance. This is the
AB  - first reported Epilithonimonas species genome isolated from a fish host.
ER  -

TY  - JOUR
AU  - Ayalew, S.
AU  - Confer, A.W.
AU  - Hansen, R.D.
AU  - Couger, M.B.
TI  - Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH.
JO  - Genome Announcements
PY  - 2017
SP  - e01721
EP  - e01716
VL  - 5
AB  - Here, we report the genome sequence of Mannheimia haemolytica serotype 1 strain 16041065 BH,
AB  - which was recently isolated from a Midwestern calf that died due to
AB  - Mannheimia haemolytica-induced pneumonia. This genome comprised a total of 2.7
AB  - Mb, with an N50 of 122 kb, and maintained hemolytic activity when grown on blood
AB  - heart infusion agar supplemented with 5% sheep's blood.
ER  -

TY  - JOUR
AU  - Ayalew, S.
AU  - Confer, A.W.
AU  - Hansen, R.D.
AU  - Couger, M.B.
TI  - Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH.
JO  - Genome Announcements
PY  - 2017
SP  - e01720
EP  - e01716
VL  - 5
AB  - We report here the draft genome sequence of a spontaneous nonhemolytic mutant of  Mannheimia
AB  - haemolytica 16041065 GH. This mutant arose during routine passage and
AB  - was devoid of hemolytic activity on standard blood agars. This genome sequence
AB  - had a total size of 2.7 Mb with an N50 of 117 kb.
ER  -

TY  - JOUR
AU  - Ayano, H.
AU  - Kuroda, M.
AU  - Soda, S.
AU  - Ike, M.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.
JO  - Genome Announcements
PY  - 2014
SP  - e00368
EP  - e00314
VL  - 2
AB  - Pseudomonas aeruginosa strain RB is a bacterium capable of synthesizing cadmium selenide
AB  - (CdSe) nanoparticles and was isolated from a soil sample. Here, we
AB  - present the draft genome sequence of P. aeruginosa strain RB. To the best of our
AB  - knowledge, this is the first report of a draft genome of a CdSe-synthesizing
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Ayarza, J.M.
AU  - Figuerola, E.L.
AU  - Erijman, L.
TI  - Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e01073
EP  - e01013
VL  - 2
AB  - The genus Sediminibacterium comprises species present in diverse natural and engineered
AB  - environments. Here, we report for the first time the genome sequences
AB  - of the type strain Sediminibacterium salmoneum NJ-44 (NBRC 103935) and
AB  - Sediminibacterium sp. strain C3 (BNM541), isolated from activated sludge, a
AB  - valuable model for the study of substrate-dependent autoaggregation.
ER  -

TY  - JOUR
AU  - Aylward, F.O. et al.
TI  - Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.
JO  - Genome Announcements
PY  - 2013
SP  - e0023912
EP  - e0023912
VL  - 1
AB  - Serratia sp. strain FGI 94 was isolated from a fungus garden of the leaf-cutter ant Atta
AB  - colombica. Analysis of its 4.86-Mbp chromosome will help advance our
AB  - knowledge of symbiotic interactions and plant biomass degradation in this ancient
AB  - ant-fungus mutualism.
ER  -

TY  - JOUR
AU  - Aylward, F.O. et al.
TI  - Complete Genome of Enterobacteriaceae Bacterium Strain FGI 57, a Strain Associated with Leaf-Cutter Ant Fungus Gardens.
JO  - Genome Announcements
PY  - 2013
SP  - e00238
EP  - e00212
VL  - 1
AB  - The Enterobacteriaceae bacterium strain FGI 57 was isolated from a fungus garden  of the
AB  - leaf-cutter ant Atta colombica. Analysis of its single 4.76-Mbp chromosome
AB  - will shed light on community dynamics and plant biomass degradation in ant fungus
AB  - gardens.
ER  -

TY  - JOUR
AU  - Azarinskas, A.
AU  - Maneliene, Z.
AU  - Jakubauskas, A.
TI  - Hin4II, a new prototype restriction endonuclease from Haemophilus influenzae RFL4: Discovery, cloning and expression in Escherichia coli.
JO  - J. Biotechnol.
PY  - 2006
SP  - 288
EP  - 296
VL  - 123
AB  - The genes encoding restriction-modification system of unknown specificity Hin4II from
AB  - Haemophilus influenzae RFL4 were cloned in
AB  - Escherichia coli and sequenced. The Hin4II system comprises three
AB  - tandemly arranged genes coding for m6A DNA methyltransferase, m5C DNA
AB  - methyltransferase and restriction endonuclease, respectively.
AB  - Restriction endonuclease was expressed in E. coli and purified to
AB  - apparent homogeneity. The DNA recognition sequence and cleavage
AB  - positions were determined. R.Hin4II recognizes the novel
AB  - non-palindromic sequence 5'-CCTTC-3' and cleaves the DNA 6 and 5 nt
AB  - downstream in the top and bottom strand, respectively. The new
AB  - prototype restriction endonuclease Hin4II was classified as a potential
AB  - candidate of HNH nuclease family after comparison against SMART
AB  - database. An amino acid sequence motif 297H-X-14-N-X-8-H of Hin4II was
AB  - proposed as forming a putative catalytic center.
ER  -

TY  - JOUR
AU  - Azarov, D.
AU  - Goncharov, A.
AU  - Karaseva, A.
AU  - Brodina, T.
AU  - Lebedeva, E.
AU  - Taranenko, I.
AU  - Feting, A.
AU  - Bakaev, M.
AU  - Brusina, E.
AU  - Zueva, L.
TI  - Draft Genome Sequence of a Multidrug-Resistant Nosocomial Serratia marcescens Strain That Persisted in a Hospital in Kemerovo, Russian Federation.
JO  - Genome Announcements
PY  - 2017
SP  - e01764
EP  - e01716
VL  - 5
AB  - Serratia marcescens is a frequent cause of health care-associated infections and  has led to
AB  - multiple outbreaks. Here, we report the draft genome of a
AB  - multidrug-resistant S. marcescens strain 189 which was isolated in 2012 as a
AB  - predominant clone in a neonatal hospital in Kemerovo.
ER  -

TY  - JOUR
AU  - Azcarate-Peril, M.A.
AU  - Altermann, E.
AU  - Goh, Y.J.
AU  - Tallon, R.
AU  - Sanozky-Dawes, R.B.
AU  - Pfeiler, E.A.
AU  - O'Flaherty, S.
AU  - Buck, B.L.
AU  - Dobson, A.
AU  - Duong, T.
AU  - Miller, M.J.
AU  - Barrangou, R.
AU  - Klaenhammer, T.R.
TI  - Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 4610
EP  - 4625
VL  - 74
AB  - This study presents the complete genome sequence of Lactobacillus gasseri ATCC 33323, a
AB  - neotype strain of human origin and a native
AB  - species found commonly in the gastrointestinal tracts of neonates and
AB  - adults. The plasmid-free genome was 1,894,360 bp in size and predicted
AB  - to encode 1,810 genes. The GC content was 35.3%, similar to the GC
AB  - content of its closest relatives, L. johnsonii NCC 533 (34%) and L.
AB  - acidophilus NCFM (34%). Two identical copies of the prophage LgaI
AB  - (40,086 bp), of the Sfi11-like Siphoviridae phage family, were
AB  - integrated tandomly in the chromosome. A number of unique features were
AB  - identified in the genome of L. gasseri that were likely acquired by
AB  - horizontal gene transfer and may contribute to the survival of this
AB  - bacterium in its ecological niche. L. gasseri encodes two restriction
AB  - and modification systems, which may limit bacteriophage infection. L.
AB  - gasseri also encodes an operon for production of heteropolysaccharides
AB  - of high complexity. A unique alternative sigma factor was present
AB  - similar to that of B. caccae ATCC 43185, a bacterial species isolated
AB  - from human feces. In addition, L. gasseri encoded the highest number of
AB  - putative mucus-binding proteins (14) among lactobacilli sequenced to
AB  - date. Selected phenotypic characteristics that were compared between
AB  - ATCC 33323 and other human L. gasseri strains included carbohydrate
AB  - fermentation patterns, growth and survival in bile,,oxalate
AB  - degradation, and adhesion to intestinal epithelial cells, in vitro. The
AB  - results from this study indicated high intraspecies variability from a
AB  - genome encoding traits important for survival and retention in the
AB  - gastrointestinal tract.
ER  -

TY  - JOUR
AU  - Azeddoug, H.
AU  - Hubert, J.
AU  - Reysset, G.
TI  - Restriction endonuclease in Clostridium acetobutylicum strain NI-4081.
JO  - Clinical and Molecular Aspects of Anaerobes
PY  - 1990
SP  - 249
EP  - 250
VL  - 0
AB  - That a restriction-modification system may exist in Clostridium acetobutylicum
AB  - strain NI-4081 was suggested by the observation that the efficiency of plasmid
AB  - transformation was dependent upon the DNA source of the replicon, and by
AB  - difficulties encountered in gene cloning experiments with DNA of heterologous
AB  - Clostridia.  These findings led us to search for restriction endonuclease and
AB  - methylase activities in strain NI-4081.
ER  -

TY  - JOUR
AU  - Azeddoug, H.
AU  - Hubert, J.
AU  - Reysset, G.
TI  - Characterization of a methyl-specific restriction system in Clostridium acetobutylicum strain N1-4081.
JO  - FEMS Microbiol. Lett.
PY  - 1989
SP  - 323
EP  - 326
VL  - 65
AB  - A type II restriction endonuclease, named CacI, was detected in Clostridium acetobutylicum
AB  - strain N1-4081. CacI cleaved the tetranucleotide sequence [5'-GATC-3']. The modification
AB  - system consisted of the methylation of the adenine present in this sequence. CacI, an
AB  - isoschizomer of MboI, is inactive on dam methylated substrates.
ER  -

TY  - JOUR
AU  - Azeddoug, H.
AU  - Reysset, G.
TI  - Recognition sequence of a new methyl-specific restriction system from Clostridium acetobutylicum strain ABKn8.
JO  - FEMS Microbiol. Lett.
PY  - 1991
SP  - 153
EP  - 156
VL  - 78
AB  - A new type II restriction endonuclease, named CacII was detected in Clostridium
AB  - acetobutylicum strain ABKn8.  CacII cleaved the hexanucleotide sequence
AB  - [5'-GCN^NGC-3'] and generated blunt ends.  Up to now no isoschizomer of CacII
AB  - has been described. Note that the name of this enzyme has been changed to
AB  - Cac8I.
ER  -

TY  - JOUR
AU  - Azeddoug, H.
AU  - Reysset, G.
AU  - Sebald, M.
TI  - Characterization of restriction endonuclease BfrBI from Bacteroides fragilis strains BE3 and AIP 10006.
JO  - FEMS Microbiol. Lett.
PY  - 1992
SP  - 133
EP  - 136
VL  - 95
AB  - A new type II restriction endonuclease, named BfrBI, was detected in two stains of Bacteroides
AB  - fragilis, BE3 and AIP 10006 (NCTC 9343T). The enzyme BfrBI, an isoschizomer of NsiI and Ava
AB  - III, recognized the hexanucleotide sequence [5'-ATG CAT-3'], with a cleavage site generating
AB  - blunt ends.
ER  -

TY  - JOUR
AU  - Azevedo, A.C.
AU  - Bento, C.B.
AU  - Ruiz, J.C.
AU  - Queiroz, M.V.
AU  - Mantovani, H.C.
TI  - Draft Genome Sequence of Streptococcus equinus (Streptococcus bovis) HC5, a Lantibiotic Producer from the Bovine Rumen.
JO  - Genome Announcements
PY  - 2015
SP  - e00085
EP  - e00015
VL  - 3
AB  - Streptococcus equinus (Streptococcus bovis) HC5 is a bacteriocinogenic lactic acid bacterium
AB  - with simple growth requirements. The draft genome sequence of S.
AB  - equinus HC5 consists of 1,846,241 bp, with a G+C content of 37.04%. In silico
AB  - analysis indicated that S. equinus HC5 might be useful to control bacteria that
AB  - are detrimental to livestock animals.
ER  -

TY  - JOUR
AU  - Azevedo-Antunes, C.
AU  - Richardson, E.J.
AU  - Quick, J.
AU  - Fuentes-Utrilla, P.
AU  - Isom, G.L.
AU  - Goodall, E.C.
AU  - Moller, J.
AU  - Hoskisson, P.A.
AU  - Mattos-Guaraldi, A.L.
AU  - Cunningham, A.F.
AU  - Loman, N.J.
AU  - Sangal, V.
AU  - Burkovski, A.
AU  - Henderson, I.R.
TI  - Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319.
JO  - Genome Announcements
PY  - 2018
SP  - e01566
EP  - e01517
VL  - 6
AB  - The genome sequence of the human pathogen Corynebacterium diphtheriae bv. mitis strain ISS
AB  - 3319 was determined and closed in this study. The genome is estimated to have 2,404,936 bp
AB  - encoding 2,257 proteins. This strain also possesses a plasmid of 1,960 bp.
ER  -

TY  - JOUR
AU  - Aziz, S.
AU  - Mast, Y.
AU  - Wohlleben, W.
AU  - Gross, H.
TI  - Draft Genome Sequence of the Pristinamycin-Producing Strain Streptomyces sp. SW4, Isolated from Soil in Nusa Kambangan, Indonesia.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00912
EP  - e00918
VL  - 7
AB  - Streptomyces sp. strain SW4 exhibited broad-spectrum antibacterial activity toward
AB  - Gram-positive and Gram-negative pathogens. The 7.5-Mb draft genome
AB  - sequence gives insight into the complete secondary metabolite production capacity
AB  - and reveals genes putatively responsible for its antibacterial activity.
ER  -

TY  - JOUR
AU  - Azizbekyan, R.R.
AU  - Rebentish, B.A.
AU  - Netyksa, E.M.
TI  - Bacillus thuringiensis restrictase sensitive to dam-methylation.
JO  - Biotekhnologiya
PY  - 1988
SP  - 197
EP  - 198
VL  - 4
AB  - A new restriction enzyme from Bacillus thuringiensis is described. It is an isoschizomer of
AB  - ClaI and is sensitive to dam methylation.
ER  -

TY  - JOUR
AU  - Azizbekyan, R.R.
AU  - Rebentish, B.A.
AU  - Netyksa, E.M.
AU  - Bychkova, M.A.
AU  - Bolotin, A.P.
TI  - Site-specific restriction endonuclease from Bacillus thuringiensis var. Kumantoenis.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1992
SP  - 13
EP  - 15
VL  - 1-2
AB  - Site-specific restriction endonucleases are widely used in recombinant DNA technology for the
AB  - construction of various molecular vectors. Possessing different specificity toward definite
AB  - nucleotide sequences, they permit the construction of recombinant DNA molecules for their
AB  - subsequent introduction into cells and yet, the presence of restriction-modification systems
AB  - in the cells of the recipient bacteria limit the effectiveness of the introduction of foreign
AB  - DNA. Recent investigations on site-specific restriction endonucleases have been conducted
AB  - along two lines: the search for new restriction-modification systems and the search for
AB  - recipients lacking restriction endonucleases. The entoropathogenic bacteria Bacillus
AB  - thuringiensis, which produce a crystalline protein endotoxin, are finding wide use as
AB  - ecologically safe biological insecticides. Earlier we detected restriction endonucleases of
AB  - various specificity in the cells of strains of various B. thuringiensis serovariants. In the
AB  - course of genetic manipulations with B. thuringiensis (H18) strain 4W1, we found that this
AB  - strain limits the development of certain phages. In this work we studied the mechanism of the
AB  - limitation of phage development and isolated two site-specific endonucleases from cells of the
AB  - strain 4W1.
ER  -

TY  - JOUR
AU  - Azizbekyan, R.R.
AU  - Rebentish, B.A.
AU  - Stepanova, T.V.
AU  - Netyksa, E.M.
AU  - Bychkova, M.A.
TI  - Site specific restriction endonuclease from a Bacillus thuringiensis strain.
JO  - Dokl. Akad. Nauk.
PY  - 1984
SP  - 742
EP  - 744
VL  - 274
AB  - Site-specific restriction endonucleases are used in recombinant DNA methodology
AB  - for the construction of recombinant DNAs and the creation of strains that
AB  - produce biologically active compounds on the basis of them.  The second aspect
AB  - of the use of restriction endonucleases is due to the possibility of their use
AB  - for blocking the expression of foreign genetic information; in particular,
AB  - restriction systems can be introduced into strains that produce biologically
AB  - active compounds to increase their resistance to infection by bacteriophages.
ER  -

TY  - JOUR
AU  - Azorin, F.
AU  - Hahn, R.
AU  - Rich, A.
TI  - Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 5714
EP  - 5718
VL  - 81
AB  - Plasmids containing (C-G)n inserts have been used to study the inhibition of cleavage by
AB  - restriction endonucleases due to Z-DNA formation in negatively supercoiled plasmids.  The
AB  - enzyme BssHII, which recognizes G-C-G-C-G-C, is strongly inhibited when the insert forms
AB  - Z-DNA.  The BamHI recognition sequence (G-G-A-T-C-C) was placed in four different positions
AB  - near the B-Z junction and the inhibition of BamHI cleavage was determined as a function of
AB  - negative superhelical density.  Formation of Z-DNA in the (C-G)n insert inhibited cleavage by
AB  - BamHI when its recognition sequence was located immediately adjacent to the insert or four
AB  - base pairs away from it.  However, no inhibition was found when the BamHI recognition site was
AB  - eight base pairs away.  These experiments help to define the limits of the structural
AB  - perturbation associated with the B-Z junction.
ER  -

TY  - JOUR
AU  - Azuma, Y.
AU  - Hosoyama, A.
AU  - Matsutani, M.
AU  - Furuya, N.
AU  - Horikawa, H.
AU  - Harada, T.
AU  - Hirakawa, H.
AU  - Kuhara, S.
AU  - Matsushita, K.
AU  - Fujita, N.
AU  - Shirai, M.
TI  - Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5768
EP  - 5783
VL  - 37
AB  - Acetobacter species have been used for brewing traditional vinegar and are
AB  - known to have genetic instability. To clarify the mutability, Acetobacter
AB  - pasteurianus NBRC 3283, which forms a multi-phenotype cell complex, was
AB  - subjected to genome DNA sequencing. The genome analysis revealed that
AB  - there are more than 280 transposons and five genes with hyper-mutable
AB  - tandem repeats as common features in the genome consisting of a 2.9-Mb
AB  - chromosome and six plasmids. There were three single nucleotide mutations
AB  - and five transposon insertions in 32 isolates from the cell complex. The
AB  - A. pasteurianus hyper-mutability was applied for breeding a
AB  - temperature-resistant strain grown at an unviable high-temperature (42
AB  - degrees C). The genomic DNA sequence of a heritable mutant showing
AB  - temperature resistance was analyzed by mutation mapping, illustrating that
AB  - a 92-kb deletion and three single nucleotide mutations occurred in the
AB  - genome during the adaptation. Alpha-proteobacteria including A.
AB  - pasteurianus consists of many intracellular symbionts and parasites, and
AB  - their genomes show increased evolution rates and intensive genome
AB  - reduction. However, A. pasteurianus is assumed to be a free-living
AB  - bacterium, it may have the potentiality to evolve to fit in natural niches
AB  - of seasonal fruits and flowers with other organisms, such as yeasts and
AB  - lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Azwani, F.
AU  - Suzuki, K.
AU  - Honjyo, M.
AU  - Tashiro, Y.
AU  - Futamata, H.
TI  - Draft Genome Sequence of Comamonas testosteroni R2, Consisting of Aromatic Compound Degradation Genes for Phenol Hydroxylase.
JO  - Genome Announcements
PY  - 2017
SP  - e00875
EP  - e00817
VL  - 5
AB  - Comamonas testosteroni strain R2 was isolated from a continuous culture enriched  by a low
AB  - concentration of phenol-oxygenating activities with low Ks values (below
AB  - 1 muM). The draft genome sequence of C. testosteroni strain R2 reported here may
AB  - contribute to determining the phenol degradation gene cluster.
ER  -

TY  - JOUR
AU  - Baar, C.
AU  - Eppinger, M.
AU  - Raddatz, G.
AU  - Simon, J.
AU  - Lanz, C.
AU  - Klimmek, O.
AU  - Nandakumar, R.
AU  - Gross, R.
AU  - Rosinus, A.
AU  - Keller, H.
AU  - Jagtap, P.
AU  - Linke, B.
AU  - Meyer, F.
AU  - Lederer, H.
AU  - Schuster, S.C.
TI  - Complete genome sequence and analysis of Wolinella succinogenes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 11690
EP  - 11695
VL  - 100
AB  - To understand the origin and emergence of pathogenic bacteria, knowledge of the genetic
AB  - inventory from their nonpathogenic relatives is a prerequisite.
AB  - Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes, which is
AB  - closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter
AB  - jejuni, was determined. Despite being considered nonpathogenic to its bovine
AB  - host, W. succinogenes holds an extensive repertoire of genes homologous to known
AB  - bacterial virulence factors. Many of these genes have been acquired by lateral
AB  - gene transfer, because part of the virulence plasmid pVir and an N-linked
AB  - glycosylation gene cluster were found to be syntenic between C. jejuni and
AB  - genomic islands of W. succinogenes. In contrast to other host-adapted bacteria,
AB  - W. succinogenes does harbor the highest density of bacterial sensor kinases found
AB  - in any bacterial genome to date, together with an elaborate signaling circuitry
AB  - of the GGDEF family of proteins. Because the analysis of the W. succinogenes
AB  - genome also revealed genes related to soil- and plant-associated bacteria such as
AB  - the nif genes, W. succinogenes may represent a member of the epsilon
AB  - proteobacteria with a life cycle outside its host.
ER  -

TY  - JOUR
AU  - Baaziz, H.
AU  - Lemaire, O.N.
AU  - Jourlin-Castelli, C.
AU  - Iobbi-Nivol, C.
AU  - Mejean, V.
AU  - Alatou, R.
AU  - Fons, M.
TI  - Draft Genome Sequence of Shewanella algidipiscicola H1, a Highly Chromate-Resistant Strain Isolated from Mediterranean Marine Sediments.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00905
EP  - e00918
VL  - 7
AB  - The ability of different Shewanella spp. to convert heavy metals and toxic substances into
AB  - less toxic products by using them as electron acceptors has led
AB  - to their use in environmental clean-up strategies. We present here the draft
AB  - genome sequence of Shewanella algidipiscicola H1, a strain resistant to high
AB  - concentrations of chromates.
ER  -

TY  - JOUR
AU  - Baba, T.
AU  - Bae, T.
AU  - Schneewind, O.
AU  - Takeuchi, F.
AU  - Hiramatsu, K.
TI  - Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity    islands.
JO  - J. Bacteriol.
PY  - 2008
SP  - 300
EP  - 310
VL  - 190
AB  - Strains of Staphylococcus aureus, an important human pathogen, display up to 20%  variability
AB  - in their genome sequence, and most sequence information is available
AB  - for human clinical isolates that have not been subjected to genetic analysis of
AB  - virulence attributes. S. aureus strain Newman, which was also isolated from a
AB  - human infection, displays robust virulence properties in animal models of disease
AB  - and has already been extensively analyzed for its molecular traits of
AB  - staphylococcal pathogenesis. We report here the complete genome sequence of S.
AB  - aureus Newman, which carries four integrated prophages, as well as two large
AB  - pathogenicity islands. In agreement with the view that S. aureus Newman prophages
AB  - contribute important properties to pathogenesis, fewer virulence factors are
AB  - found outside of the prophages than for the highly virulent strain MW2. The
AB  - absence of drug resistance genes reflects the general antibiotic-susceptible
AB  - phenotype of S. aureus Newman. Phylogenetic analyses reveal clonal relationships
AB  - between the staphylococcal strains Newman, COL, NCTC8325, and USA300 and a
AB  - greater evolutionary distance to strains MRSA252, MW2, MSSA476, N315, Mu50, JH1,
AB  - JH9, and RF122. However, polymorphism analysis of two large pathogenicity islands
AB  - distributed among these strains shows that the two islands were acquired
AB  - independently from the evolutionary pathway of the chromosomal backbones of
AB  - staphylococcal genomes. Prophages and pathogenicity islands play central roles in
AB  - S. aureus virulence and evolution.
ER  -

TY  - JOUR
AU  - Baba, T.
AU  - Kuwahara-Arai, K.
AU  - Uchiyama, I.
AU  - Takeuchi, F.
AU  - Ito, T.
AU  - Hiramatsu, K.
TI  - Complete genome sequence of Macrococcus caseolyticus strain JSCS5402, reflecting the ancestral genome of the human-pathogenic staphylococci.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1180
EP  - 1190
VL  - 191
AB  - We isolated the methicillin-resistant Macrococcus caseolyticus strain JCSC5402 from animal
AB  - meat in a supermarket and determined its whole-genome
AB  - nucleotide sequence. This is the first report on the genome analysis of a
AB  - macrococcal species that is evolutionarily closely related to the human
AB  - pathogens Staphylococcus aureus and Bacillus anthracis. The essential
AB  - biological pathways of M. caseolyticus are similar to those of
AB  - staphylococci. However, the species has a small chromosome (2.1 MB) and
AB  - lacks many sugar and amino acid metabolism pathways and a plethora of
AB  - virulence genes that are present in S. aureus. On the other hand, M.
AB  - caseolyticus possesses a series of oxidative phosphorylation machineries
AB  - that are closely related to those in the family Bacillaceae. We also
AB  - discovered a probable primordial form of a Macrococcus methicillin
AB  - resistance gene complex, mecIRAm, on one of the eight plasmids harbored by
AB  - the M. caseolyticus strain. This is the first finding of a
AB  - plasmid-encoding methicillin resistance gene. Macrococcus is considered to
AB  - reflect the genome of ancestral bacteria before the speciation of
AB  - staphylococcal species and may be closely associated with the origin of
AB  - the methicillin resistance gene complex of the notorious human pathogen
AB  - methicillin-resistant S. aureus.
ER  -

TY  - JOUR
AU  - Baba, T.
AU  - Takeuchi, F.
AU  - Kuroda, M.
AU  - Yuzawa, H.
AU  - Aoki, K.
AU  - Oguchi, A.
AU  - Nagai, Y.
AU  - Iwama, N.
AU  - Asano, K.
AU  - Naimi, T.
AU  - Kuroda, H.
AU  - Cui, L.
AU  - Yamamoto, K.
AU  - Hiramatsu, K.
TI  - Genome and virulence determinants of high virulence community-acquired MRSA.
JO  - Lancet
PY  - 2002
SP  - 1819
EP  - 1827
VL  - 359
AB  - BACKGROUND: A new type of meticillin-resistant Staphylococcus aureus (MRSA), designated
AB  - community-acquired MRSA, is becoming increasingly
AB  - noticeable in the community, some strains of which cause fatal infections
AB  - in otherwise healthy individuals. By contrast with hospital-acquired MRSA,
AB  - community-acquired MRSA is more susceptible to non beta-lactam antibiotics.
AB  - We investigated the high virulence potential of certain strains of this
AB  - bacterium. METHODS: We ascertained the whole genome sequence of MW2, a
AB  - strain of community-acquired MRSA, by shotgun cloning and sequencing. MW2
AB  - caused fatal septicaemia and septic arthritis in a 16-month-old girl in
AB  - North Dakota, USA, in 1998. The genome of this strain was compared with
AB  - those of hospital-acquired MRSA strains, including N315 and Mu50.
AB  - FINDINGS: Meticillin resistance gene (mecA) in MW2 was carried by a novel
AB  - allelic form (type IVa) of staphylococcal cassette chromosome mec
AB  - (SCCmec), by contrast with type II in N315 and Mu50. Type IVa SCCmec did
AB  - not carry any of the multiple antibiotic resistance genes reported in type
AB  - II SCCmec. By contrast, 19 additional virulence genes were recorded in the
AB  - MW2 genome. All but two of these virulence genes were noted in four of the
AB  - seven genomic islands of MW2. INTERPRETATION: MW2 carried a range of
AB  - virulence and resistance genes that was distinct from those displayed on
AB  - the chromosomes of extant S aureus strains. Most genes were carried by
AB  - specific allelic forms of genomic islands in the MW2 chromosome. The
AB  - combination of allelic forms of genomic islands is the genetic basis that
AB  - determines the pathogenicity of medically important phenotypes of S
AB  - aureus, including those of community-acquired MRSA strains.
ER  -

TY  - JOUR
AU  - Babbar, A.
AU  - Nitsche-Schmitz, D.P.
AU  - Pieper, D.H.
AU  - Barrantes, I.
TI  - Draft Genome Sequence of Streptococcus dysgalactiae subsp. equisimilis Strain C161L1 Isolated in Vellore, India.
JO  - Genome Announcements
PY  - 2017
SP  - e00336
EP  - e00317
VL  - 5
AB  - Streptococcus dysgalactiae subsp. equisimilis belongs to the beta-hemolytic group C and G
AB  - pyogenic group of streptococci. Here, we report the draft genome of the
AB  - S. dysgalactiae subsp. equisimilis strain C161L1 from Vellore, a region in
AB  - southern India with a high incidence rate of S. dysgalactiae subsp. equisimilis
AB  - infection. This genome is 2.1 Mb long, with a 39.82% G+C content, and encodes
AB  - 2,022 genes.
ER  -

TY  - JOUR
AU  - Babcock, M.J.
AU  - Schottel, J.L.
TI  - SsbI, an isoschizomer of HindIII isolated from Streptomyces scabies.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 3457
EP  - 3457
VL  - 19
AB  - SsbI is a restriction endonuclease identified in cell lysates of the soil
AB  - bacterium Streptomyces scabies, isolate FL1.  SsbI was partially purified by
AB  - DEAE-Sephadex chromatography to remove contaminating nuclease activity.  The
AB  - partially purified SsbI fraction was used to determine the recognition sequence
AB  - and the cleavage site for the endonuclease.
ER  -

TY  - JOUR
AU  - Babic, A.C.
AU  - Little, E.J.
AU  - Manohar, V.M.
AU  - Bitinaite, J.
AU  - Horton, N.C.
TI  - DNA Distortion and Specificity in a Sequence-Specific Endonuclease.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 186
EP  - 204
VL  - 383
AB  - Five new structures of the Q138F HincII enzyme bound to a total of three different DNA
AB  - sequences and three different metal ions (Ca(2+), Mg(2+),
AB  - and Mn(2+)) are presented. While previous structures were produced from
AB  - soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new
AB  - structures are derived from cocrystallization with Ca(2+), Mg(2+), or
AB  - Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product
AB  - complex of Q138F HincII with cleaved DNA. Binding studies and a crystal
AB  - structure show how Ca(2+) allows trapping of a Q138F HincII complex with
AB  - noncognate DNA in a catalytically incompetent conformation. Many Q138F
AB  - HincII/DNA structures show asymmetry, despite the binding of a symmetric
AB  - substrate by a symmetric enzyme. The various complexes are fit into a
AB  - model describing the different conformations of the DNA-bound enzyme and
AB  - show how DNA conformational energetics determine DNA-cleavage rates by the
AB  - Q138F HincII enzyme.
ER  -

TY  - JOUR
AU  - Babinger, P.
AU  - Volkl, R.
AU  - Cakstina, I.
AU  - Maftei, A.
AU  - Schmitt, R.
TI  - Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri.
JO  - Plant Mol. Biol.
PY  - 2007
SP  - 325
EP  - 336
VL  - 63
AB  - DNA methylation plays an important role in the gene-silencing network of higher eukaryotes. We
AB  - have analyzed the 21.5-kb maintenance
AB  - methyltransferase (M-MTase) gene, met1, of the multicellular green alga
AB  - Volvox carteri. The met1 transcript was detected only during the period
AB  - when DNA replication and cell division are taking place. It encodes a
AB  - 238 kDa protein containing eight C-terminal activity domains typical of
AB  - M-MTases, plus upstream DNA-binding domains including the ProDom domain
AB  - PD003757, which experimental analyses in animal systems have indicated
AB  - is required for targeting the enzyme to DNA-replication foci. Several
AB  - insertions of unknown function make Volvox Met1 the largest known
AB  - member of the Met1/Dnmt1 family. Here we also show that several
AB  - endogenous transposon families are CpG-methyated in Volvox, which we
AB  - think causes them to be inactive. This view is supported by the
AB  - observation that an in vitro CpG-methylated gene introduced into Volvox
AB  - was maintained in the methylated and silent state over > 100
AB  - generations. Thus, we believe that Met1 recognizes and perpetuates the
AB  - in vitro methylation signal, and that the silencing machinery is then
AB  - able to transduce such a methylation-only signal into a stable
AB  - heterochromatic (and silent) state.
ER  -

TY  - JOUR
AU  - Babkina, O.V.
AU  - Chutko, C.A.
AU  - Shashkov, A.A.
AU  - Dzhidzhoev, M.S.
AU  - Eritja, R.
AU  - Gromova, E.S.
TI  - Iodouracil-mediated photocrosslinking of DNA to EcoRII restriction endonuclease in catalytic conditions.
JO  - Photochem. Photobiolog.
PY  - 2002
SP  - 636
EP  - 640
VL  - 1
AB  - We used a XeCl excimer laser with 50 ns pulses, a frequency of 0.3 Hz and a wavelength of 308
AB  - nm in appropriate conditions for the photocrosslinking
AB  - of EcoRII restriction endonuclease to a 14-mer DNA duplex, containing a
AB  - 5-iodo-2'-deoxyuridine residue (IdU). IdU replaced the thymidine residue
AB  - within the EcoRII recognition sequence 5'-CCT/AGG. The binding of EcoRII
AB  - endonuclease to the IdU-containing DNA duplex was analyzed by gel
AB  - retardation assay in the presence of Ca2+ or Mg2+ ions. Photocrosslinking
AB  - of EcoRII to the IdU-containing DNA duplex occurred in a pre-reactive
AB  - complex formed in the presence of Ca2+ ions. Photocrosslinking yields as a
AB  - function of time and UV-laser light intensity were studied.
ER  -

TY  - JOUR
AU  - Babkina, O.V.
AU  - Evstafieva, A.G.
AU  - Chichkova, N.V.
AU  - Vartapetian, A.B.
AU  - Muller, S.
AU  - Baskunov, V.B.
AU  - Petrauskene, O.V.
AU  - Kochetkov, S.N.
AU  - Gromova, E.S.
TI  - Recombinant components of the EcoRII restriction-modification system: Restriction endonuclease can interact with DNA-RNA duplexes.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 1065
EP  - 1073
VL  - 34
AB  - To obtain recombinant restriction endonuclease (R) and methylase (M) of the EcoRII
AB  - restriction-modification system, bacterial strains
AB  - overproducing their functional hexahistidine derivatives were
AB  - constructed. Active full-length EcoRII was produced only in cells
AB  - that also expressed M.EcoRII from a multicopy plasmid. Recombinant
AB  - EcoRII bound with hybrid DNA-RNA duplexes.
ER  -

TY  - JOUR
AU  - Babkina, O.V.
AU  - Petrauskene, O.V.
AU  - Gromova, E.S.
TI  - Restriction endonuclease EcoRII hydrolyzes one of the two DNA restriction sites forming the catalytic complex.
JO  - Mol. Biol. (Mosk)
PY  - 1998
SP  - 793
EP  - 796
VL  - 32
AB  - Hydrolysis of 71-mer substrates containing two EcoRII recognition sites was considered in
AB  - order to investigate the two-site mechanism of DNA recognition, which implies the presence in
AB  - the catalytic complex of four internucleotide bonds cleavable by the enzyme.  It is shown that
AB  - the enzyme hydrolyzes only two phosphodiester bonds in one enzyme-substrate complex.  To find
AB  - out whether both bonds belong to one and the same or different recognition sites, scissile
AB  - phosphodiester bonds in one of the recognition sites in the 71-mer duplexes were replaced with
AB  - nonscissile pyrophosphate bonds alternatively or in both strands simultaneously.  This allowed
AB  - one to preclude hydrolysis of the corresponding bonds.  It is shown that endonuclease EcoRII
AB  - cleaves simultaneously two internucleotide phosphodiester bonds belonging to the same
AB  - recognition site.
ER  -

TY  - JOUR
AU  - Baby, V.
AU  - Matteau, D.
AU  - Knight, T.F.
AU  - Rodrigue, S.
TI  - Complete Genome Sequence of the Mesoplasma florum W37 Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00879
EP  - e00813
VL  - 1
AB  - Mesoplasma florum is a small-genome fast-growing mollicute that is an attractive  model for
AB  - systems and synthetic genomics studies. We report the complete
AB  - 825,824-bp genome sequence of a second representative of this species, M. florum
AB  - strain W37, which contains 733 predicted open reading frames and 35 stable RNAs.
ER  -

TY  - JOUR
AU  - Bachi, B.
AU  - Reiser, J.
AU  - Pirrotta, V.
TI  - Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 143
EP  - 163
VL  - 128
AB  - EcoP1 is a restriction modification enzyme encoded by bacteriophage P1.  It
AB  - requires ATP for cleavage and S-adenosyl methionine for methylation of DNA.  We
AB  - have mapped the sites of both cleavage and methylation in simian virus 40 DNA
AB  - and determined their sequences.  The enzyme methylates the sequence A-G-mA-C-C
AB  - and cuts the DNA 25 to 27 base-pairs form the site of methylation in the 3'
AB  - direction, with a two to four base-pair stagger between cuts.  Consistent with
AB  - the fact that the methylation sequence is asymmetric, the enzyme methylates
AB  - only one strand in vitro.  One variant of simian virus 40 has acquired an
AB  - additional EcoP1 methylation and cleavage site by changing a A-G-A-A-C sequence
AB  - to A-G-A-C-C.
ER  -

TY  - JOUR
AU  - Bachman, K.E.
AU  - Rountree, M.R.
AU  - Baylin, S.B.
TI  - Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 32282
EP  - 32287
VL  - 276
AB  - We demonstrate that the recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, like
AB  - DNMT1, repress transcription in a methylation-independent manner. Dnmt3a and Dnmt3b repress
AB  - transcription primarily through a plant homeodomain-like motif that is shared with the ATRX
AB  - protein but is not present in DNMT1. Unlike DNMT1, which localizes to replication foci during
AB  - S-phase in murine embryonic fibroblasts, Dnmt3a co-localizes with heterochromatin protein 1
AB  - alpha (HP1 alpha) and methyl-CpG binding proteins throughout the cell cycle to
AB  - late-replicating pericentromeric heterochromatin. In contrast to Dnmt3a, Dnmt3b remained
AB  - diffuse in the nucleus of embryonic fibroblasts at all cell cycle stages. However, Dnmt3a and
AB  - Dnmt3b co-localize to these pericentromeric heterochromatin regions in murine embryonic stem
AB  - cells. This finding is important to the fact that mutations in DNMT3B are found in the
AB  - developmental syndrome, ICF (immunodeficiency, centromeric heterochromatin instability, and
AB  - facial anomalies), which involves extensive loss of methylation from pericentromeric regions.
AB  - The localization of Dnmt3a and Dnmt3b was unaffected in Dnmt1 null embryonic stem cells, which
AB  - lose the majority of methylation at pericentromeric major satellite repeats, suggesting that
AB  - these enzymes are not dependent upon preexisting methylation for their targeting. DNMT1 is
AB  - then positioned to reestablish transcriptionally repressive chromatin as cells replicate,
AB  - while Dnmt3a and Dnmt3b may help to establish such chromatin in late S-phase and maintain this
AB  - repressive heterochromatin throughout the cell cycle in a developmentally and/or cell type
AB  - manner.
ER  -

TY  - JOUR
AU  - Backman, K.
TI  - A cautionary note on the use of certain restriction endonucleases with methylated substrates.
JO  - Gene
PY  - 1980
SP  - 169
EP  - 171
VL  - 11
AB  - Methylation of adenine and cytosine residues in DNA isolated from common strains of
AB  - Escherichia coli K-12 can render that DNA resistant to cleavage by certain restriction
AB  - endonucleases at those sites at which the recognition sequence for such an endonuclease
AB  - overlaps (but does not include) a sequence recognized by methylases specified by the dam or
AB  - dcm gene.
ER  -

TY  - JOUR
AU  - Backus, L.
AU  - Wels, M.
AU  - Boekhorst, J.
AU  - Dijkstra, A.R.
AU  - Beerthuyzen, M.
AU  - Kelly, W.J.
AU  - Siezen, R.J.
AU  - van Hijum, S.A.
AU  - Bachmann, H.
TI  - Draft Genome Sequences of 24 Lactococcus lactis Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e01737
EP  - e01716
VL  - 5
AB  - The lactic acid bacterium Lactococcus lactis is widely used for the production of fermented
AB  - dairy products. Here, we present the draft genome sequences of 24 L.
AB  - lactis strains isolated from different environments and geographic locations.
ER  -

TY  - JOUR
AU  - Bacolla, A.
AU  - Pradhan, S.
AU  - Larson, J.E.
AU  - Roberts, R.J.
AU  - Wells, R.D.
TI  - Recombinant Human DNA (Cytosine-5) Methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the Fragile X CGG.CCG sequence.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 18605
EP  - 18613
VL  - 276
AB  - Steady-state kinetic analyses revealed that the methylation reaction of the human DNA
AB  - (cytosine-5) methyltransferase 1 (DNMT1) is repressed by the N-terminal domain comprising the
AB  - first 501 amino acids, and that repression is relieved when methylated DNA binds to this
AB  - region. DNMT1 lacking the first 501 amino acids retains its preference for hemimethylated DNA.
AB  - The methylation reaction proceeds by a sequential mechanism, and either substrate
AB  - (S-adenosyl-l-methionine and unmethylated DNA) may be the first to bind to the active site.
AB  - However, initial binding of S-adenosyl-l-methionine is preferred. The binding affinities of
AB  - DNA for both the regulatory and the catalytic sites increase in the presence of methylated CpG
AB  - dinucleotides and vary considerably (more than one hundred times) according to DNA sequence.
AB  - DNA topology strongly influences the reaction rates, which increased with increasing negative
AB  - superhelical tension. These kinetic data are consistent with the role of DNMT1 in maintaining
AB  - the methylation patterns throughout development and suggest that the enzyme may be involved in
AB  - the etiology of fragile X, a syndrome characterized by de novo methylation of a greatly
AB  - expanded CGG.CCG triplet repeat sequence.
ER  -

TY  - JOUR
AU  - Bacolla, A.
AU  - Pradhan, S.
AU  - Roberts, R.J.
AU  - Wells, R.D.
TI  - Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated DNA.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 33011
EP  - 33019
VL  - 274
AB  - Initial velocity determinations were conducted with human DNA (cytosine-5) methyltransferase
AB  - (DNMT1) on unmethylated and hemimethylated DNA templates in order to assess the mechanism of
AB  - the reaction. Initial velocity data with DNA and S-adenosylmethionine (AdoMet) as variable
AB  - substrates and product inhibition studies with methylated DNA and S-adenosylhomocysteine
AB  - (AdoHcy) were obtained and evaluated as double-reciprocal plots. These relationships were
AB  - linear for plasmid DNA, exon-1 from the imprinted small nuclear ribonucleoprotein-associated
AB  - polypeptide N, (CGG.CCG)(12), (m(5)CGG.CCG)(12), and (CGG.CCG)(73) but were not linear for
AB  - (CGG.Cm(5)CG)(12). Inhibition by AdoHcy was apparently competitive versus AdoMet and
AB  - uncompetitive/noncompetitive versus DNA at </=20 microM AdoMet. Addition of the product
AB  - (methylated DNA) to unmethylated plasmid DNA increased V(max(app)) resulting in mixed
AB  - stimulation and inhibition. Velocity equations indicated a two-step mechanism as follows:
AB  - first, activation of DNMT1 by methylated DNA that bound to an allosteric site, and second, the
AB  - addition of AdoMet and DNA to the catalytic site. The preference of DNMT1 for hemimethylated
AB  - DNA may be the result of positive cooperativity of AdoMet binding mediated by allosteric
AB  - activation by the methylated CG steps. We propose that this activation plays a role in vivo in
AB  - the regulation of maintenance methylation.
ER  -

TY  - JOUR
AU  - Badalamenti, J.P.
AU  - Bond, D.R.
TI  - Complete Genome of Geobacter pickeringii G13T, a Metal-Reducing Isolate from Sedimentary Kaolin Deposits.
JO  - Genome Announcements
PY  - 2015
SP  - e00038
EP  - e00015
VL  - 3
AB  - We used PacBio sequencing to assemble the genome of the pristine freshwater isolate Geobacter
AB  - pickeringii G13(T) into a single 3,618,700-bp circular
AB  - chromosome polished to 99.999% accuracy (quality value [QV], 50). This isolate
AB  - shares several features with other Geobacter spp., including genes for
AB  - degradation of aromatics and an abundance of multiheme c-type cytochromes.
ER  -

TY  - JOUR
AU  - Badalamenti, J.P.
AU  - Erickson, J.D.
AU  - Salomon, C.E.
TI  - Complete Genome Sequence of Streptomyces albus SM254, a Potent Antagonist of Bat  White-Nose Syndrome Pathogen Pseudogymnoascus destructans.
JO  - Genome Announcements
PY  - 2016
SP  - e00290
EP  - e00216
VL  - 4
AB  - We sequenced and annotated the complete 7,170,504-bp genome of a novel secondary
AB  - metabolite-producingStreptomycesstrain,Streptomyces albusSM254, isolated from
AB  - copper-rich subsurface fluids at ~220-m depth within the Soudan Iron Mine
AB  - (Soudan, MN, USA).
ER  -

TY  - JOUR
AU  - Badalamenti, J.P.
AU  - Hunter, R.C.
TI  - Complete Genome Sequence of Achromobacter xylosoxidans MN001, a Cystic Fibrosis Airway Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00947
EP  - e00915
VL  - 3
AB  - The genome of Achromobacter xylosoxidans MN001, a strain isolated from sputum derived from an
AB  - adult cystic fibrosis patient, was sequenced using combined
AB  - single-molecule real-time and Illumina sequencing. Assembly of the complete
AB  - genome resulted in a 5,876,039-bp chromosome, representing the smallest A.
AB  - xylosoxidans genome sequenced to date.
ER  -

TY  - JOUR
AU  - Badalamenti, J.P.
AU  - Krajmalnik-Brown, R.
AU  - Torres, C.I.
AU  - Bond, D.R.
TI  - Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e00039
EP  - e00015
VL  - 3
AB  - We sequenced and annotated genomes of two haloalkaliphilic Deltaproteobacteria,
AB  - Geoalkalibacter ferrihydriticus Z-0531(T) (DSM 17813) and Geoalkalibacter
AB  - subterraneus Red1(T) (DSM 23483). During assembly, we discovered that the DSMZ
AB  - stock culture of G. subterraneus was contaminated. We reisolated G. subterraneus
AB  - in axenic culture and redeposited it in DSMZ and JCM.
ER  -

TY  - JOUR
AU  - Baddam, R.
AU  - Kumar, N.
AU  - Thong, K.L.
AU  - Ngoi, S.T.
AU  - Teh, C.S.
AU  - Yap, K.P.
AU  - Chai, L.C.
AU  - Avasthi, T.S.
AU  - Ahmed, N.
TI  - Genetic Fine Structure of a Salmonella enterica Serovar Typhi Strain Associated with the 2005 Outbreak of Typhoid Fever in Kelantan, Malaysia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3565
EP  - 3566
VL  - 194
AB  - Among enteric pathogens, Salmonella enterica serovar Typhi is responsible for the largest
AB  - number of food-borne outbreaks and fatalities. The ability of the
AB  - pathogen to cause systemic infection for extended durations leads to a high cost
AB  - of disease control. Chronic carriers play important roles in the evolution of
AB  - Salmonella Typhi; therefore, identification and in-depth characterization of
AB  - isolates from clinical cases and carriers, especially those from zones of
AB  - endemicity where the pathogen has not been extensively studied, are necessary.
AB  - Here, we describe the genome sequence of the highly virulent Salmonella Typhi
AB  - strain BL196/05 isolated during the outbreak of typhoid in Kelantan, Malaysia, in
AB  - 2005. The whole-genome sequence and comparative genomics of this strain should
AB  - enable us to understand the virulence mechanisms and evolutionary dynamics of
AB  - this pathogen in Malaysia and elsewhere.
ER  -

TY  - JOUR
AU  - Baddam, R.
AU  - Thong, K.L.
AU  - Avasthi, T.S.
AU  - Shaik, S.
AU  - Yap, K.P.
AU  - Teh, C.S.
AU  - Chai, L.C.
AU  - Kumar, N.
AU  - Ahmed, N.
TI  - Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New  Guinea.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5122
EP  - 5123
VL  - 194
AB  - Many of the developing countries of the Southeast Asian region are significantly  affected by
AB  - endemic typhoid fever, possibly as a result of marginal living
AB  - standards. It is an important public health problem in countries such as Papua
AB  - New Guinea, which is geographically close to some of the foci of endemicity in
AB  - Asia. The severity of the disease varies in different regions, and this may be
AB  - attributable to genetic diversity among the native strains. Genome sequence data
AB  - on strains from different countries are needed to clearly understand their
AB  - genetic makeup and virulence potential. We describe the genomes of two Salmonella
AB  - Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in
AB  - Papua New Guinea. We discuss in brief the underlying sequencing methodology,
AB  - assembly, genome statistics, and important features of the two draft genomes,
AB  - which form an essential step in our functional molecular infection epidemiology
AB  - program centering on typhoid fever. The comparative genomics of these and other
AB  - isolates would enable us to identify genetic rearrangements and mechanisms
AB  - responsible for endemicity and the differential severity of pathogenic
AB  - salmonellae in Papua New Guinea and elsewhere.
ER  -

TY  - JOUR
AU  - Badger, J.H. et al.
TI  - Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter  crescentus.
JO  - J. Bacteriol.
PY  - 2006
SP  - 6841
EP  - 6850
VL  - 188
AB  - The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an
AB  - asymmetric manner rather than by binary fission and are of
AB  - interest as simple models of development. Prior to this work, the only
AB  - member of this group for which genome sequence was available was the model
AB  - freshwater organism Caulobacter crescentus. Here we describe the genome
AB  - sequence of Hyphomonas neptunium, a marine member of the DPB that differs
AB  - from C. crescentus in that H. neptunium uses its stalk as a reproductive
AB  - structure. Genome analysis indicates that this organism shares more genes
AB  - with C. crescentus than it does with Silicibacter pomeroyi (a closer
AB  - relative according to 16S rRNA phylogeny), that it relies upon a
AB  - heterotrophic strategy utilizing a wide range of substrates, that its cell
AB  - cycle is likely to be regulated in a similar manner to that of C.
AB  - crescentus, and that the outer membrane complements of H. neptunium and C.
AB  - crescentus are remarkably similar. H. neptunium swarmer cells are highly
AB  - motile via a single polar flagellum. With the exception of cheY and cheR,
AB  - genes required for chemotaxis were absent in the H. neptunium genome.
AB  - Consistent with this observation, H. neptunium swarmer cells did not
AB  - respond to any chemotactic stimuli that were tested, which suggests that
AB  - H. neptunium motility is a random dispersal mechanism for swarmer cells
AB  - rather than a stimulus-controlled navigation system for locating specific
AB  - environments. In addition to providing insights into bacterial
AB  - development, the H. neptunium genome will provide an important resource
AB  - for the study of other interesting biological processes including
AB  - chromosome segregation, polar growth, and cell aging.
ER  -

TY  - JOUR
AU  - Badhai, J.
AU  - Narayan, K.D.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Gulbenkiania indica Strain HT27T (DSM 17901T) Isolated from a Sulfur Spring in India.
JO  - Genome Announcements
PY  - 2016
SP  - e00830
EP  - e00816
VL  - 4
AB  - Gulbenkiania indica strain HT27(T) was isolated from a sulfur spring. Here, we report the
AB  - first representative draft genome sequence of a type strain of the
AB  - genus Gulbenkiania The estimated genome is 2.8 Mb, with 2,713 protein-coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Badhai, J.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Chelatococcus sambhunathii Strain HT4T (DSM 18167T) Isolated from a Hot Spring in India.
JO  - Genome Announcements
PY  - 2016
SP  - e00825
EP  - e00816
VL  - 4
AB  - The moderately thermophilic bacterium Chelatococcus sambhunathii strain HT4(T) was isolated
AB  - from hot spring sediment. Based upon the draft genome sequence, the
AB  - genome is 4.4 Mb and encodes 4,147 proteins.
ER  -

TY  - JOUR
AU  - Badhai, J.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Rhizobiumpusense Strain NRCPB10T (LMG 25623T) Isolated from Rhizosphere Soil of Chickpeas (Cicer arietinum L.) Grown in India.
JO  - Genome Announcements
PY  - 2017
SP  - e00282
EP  - e00217
VL  - 5
AB  - Rhizobium pusense strain NRCPB10T was isolated from rhizosphere soil of chickpeas (Cicer
AB  - arietinum L.). Based upon the draft genome sequence, the genome is 5.28 Mb
AB  - and encodes 5,064 proteins.
ER  -

TY  - JOUR
AU  - Badie, G.
TI  - Role of DNA adenine methylase in regulation of bacterial gene expression, virulence, and the elicitation of immune responses.
JO  - Ph.D. Thesis, Univ. of California, Santa Barbara
PY  - 2005
SP  - 1
EP  - 149
AB  - The threat of emerging infectious diseases and bio-warfare agents has underscored the need for
AB  - development of safe and effective anti-microbial therapies.  One viable approach to address
AB  - this issue is through protective vaccination, which second to water sanitation, is the
AB  - principal method for reduction of morbidity and mortality worldwide.  This dissertation
AB  - describes the role of the DNA adenine methylase as a global regulator of bacterial virulence
AB  - and the utility of Dam-based technology for the development of live-attenuated vaccines that
AB  - elicit potent states of immunity against a variety of infectious agents.  Dam is a highly
AB  - conserved enzyme found in many pathogens, and is involved in a variety of cellular processes
AB  - including the regulation of bacterial virulence and elicitation of protective immune
AB  - responses.  Work presented in this dissertation has further evaluated the role of Dam in
AB  - regulation of several virulence factors in Salmonella typhimurium and Yersinia
AB  - pseudotuberculosis.  Studies in Yersinia revealed that Dam overproduction alters the stringent
AB  - regulation of many virulence factors, including a principal Yersinia immunogen, LcrV, and an
AB  - actin cytotoxin, YopE.  Dysregulation of these virulence factors may be the mechanism by which
AB  - dam mutants elicit protective immunity against Yersinia infections in vaccinated hosts.  In
AB  - Salmonella, Dam regulates the expression of several virulence genes as well.  Moreover,
AB  - expression of these genes was differentially affected by altered Dam levels in closely-related
AB  - pathogenic and non-pathogenic strains of Salmonella.  These data suggest that differential
AB  - gene regulation, rather than gross genomic differences contributes to the virulence
AB  - disparities observed between these pathogenic and non-pathogenic isolates.  Finally, by
AB  - expressing reovirus antigens in Salmonella, the possibility of using Dam-based vaccines as
AB  - carriers of foreign antigens was investigated.  Effective live-attenuated carrier vaccines
AB  - could be used to protect hosts from a variety of diseases for which no therapy is currently
AB  - available.  Investigating the role of Dam in regulation of virulence factors in pathogens such
AB  - as Salmonella and Yersinia will not only help decipher its role in regulation of virulence in
AB  - other pathogens, but will also help design new vaccines that provide potent immunity against a
AB  - wide range of infectious diseases that threaten the safety of public health worldwide.
ER  -

TY  - JOUR
AU  - Badie, G.
AU  - Heithoff, D.M.
AU  - Mahan, M.J.
TI  - LcrV synthesis is altered by DNA adenine methylase overproduction in Yersinia pseudotuberculosis and is required to confer immunity in  vaccinated hosts.
JO  - Infect. Immun.
PY  - 2004
SP  - 6707
EP  - 6710
VL  - 72
AB  - Yersinia pseudotuberculosis mutants that overproduce the DNA adenine methylase (Dam(OP)
AB  - Yersinia) are attenuated, confer robust protective
AB  - immune responses, and synthesize or secrete several Yersinia outer
AB  - proteins (Yops) under conditions that are nonpermissive for synthesis
AB  - and secretion in wild-type strains. To understand the molecular basis
AB  - of immunity elicited by Dam(OP) Yersinia, we investigated the effects
AB  - of Dam overproduction on the synthesis and localization of a principal
AB  - Yersinia immunogen, LcrV, a low-calcium-responsive virulence factor
AB  - involved in Yop synthesis, localization, and suppression of host
AB  - inflammatory activities. Dam overproduction relaxed the stringent
AB  - temperature and calcium regulation of LcrV synthesis. Moreover, the
AB  - LcrV-dependent synthesis and localization of the actin cytotoxin, YopE,
AB  - were shown to be relaxed in Dam(OP) cells, suggesting that the
AB  - synthesis and localization of Yops can occur via both LcrV-dependent
AB  - and -independent mechanisms. Last, the immunity conferred by Dam(OP)
AB  - Yersinia was strictly dependent on the presence of LcrV, which may
AB  - result from its role (i) as an immunogen, (ii) as an immunomodullator
AB  - of host anti-inflammatory activities, or (iii) in the altered synthesis
AB  - and localization of Yops that could contribute to immunogen repertoire
AB  - expansion.
ER  -

TY  - JOUR
AU  - Badie, G.
AU  - Heithoff, D.M.
AU  - Sinsheimer, R.L.
AU  - Mahan, M.J.
TI  - Altered Levels of Salmonella DNA Adenine Methylase Are Associated with Defects in Gene Expression, Motility, Flagellar Synthesis, and Bile  Resistance in the Pathogenic Strain 14028 but Not in the Laboratory Strain  LT2.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1556
EP  - 1564
VL  - 189
AB  - Comparative genomic analysis has revealed limited strain diversity between Salmonella
AB  - pathogenic and nonpathogenic isolates. Thus, some of the
AB  - relative virulence and host-immune response disparities may be credited to
AB  - differential gene regulation rather than gross differences in genomic
AB  - content. Here we show that altered levels of Salmonella DNA adenine
AB  - methylase (Dam) resulted in acute defects in virulence-associated gene
AB  - expression, motility, flagellin synthesis, and bile resistance in the
AB  - Salmonella pathogenic strain 14028 but not in avirulent laboratory strain
AB  - LT2. The defects in motility exhibited by 14028 in response to altered Dam
AB  - levels was not dependent on the presence of the regulatory protein, RpoS.
AB  - The transitioning between flagellar types (phase variation) was also
AB  - differentially regulated in 14028 versus LT2 in response to dam levels,
AB  - resulting in distinct differences in flagellin expression states. These
AB  - data suggest that differential gene regulation may contribute to the
AB  - relative virulence disparities observed between Salmonella serovars that
AB  - are closely related at the DNA level.
ER  -

TY  - JOUR
AU  - Badran, S.
AU  - Morales, N.
AU  - Schick, P.
AU  - Jacoby, B.
AU  - Villella, W.
AU  - Lorenz, T.
TI  - Complete Genome Sequence of the Bacillus pumilus Phage Leo2.
JO  - Genome Announcements
PY  - 2018
SP  - e00066
EP  - e00018
VL  - 6
AB  - Bacillus spp. are ubiquitous Gram-positive microbes with many ecological and symbiotic
AB  - interactions and can be pathogens. Phage Leo2 was found to infect a
AB  - Bacillus pumilus strain isolated from soil. The sequence of phage Leo2 revealed
AB  - 74 genes; 31% of the genes have associated functions, and 67% of coding regions
AB  - are unidentified open reading frames.
ER  -

TY  - JOUR
AU  - Badrun, R.
AU  - Abu, B.N.
AU  - Laboh, R.
AU  - Redzuan, R.
AU  - Bala, J.I.
TI  - Draft Genome Sequence of Blood Disease Bacterium A2 HR-MARDI, a Pathogen Causing  Banana Bacterial Wilt.
JO  - Genome Announcements
PY  - 2017
SP  - e00408
EP  - e00417
VL  - 5
AB  - Blood disease bacterium A2 HR-MARDI was isolated from banana plants infected with banana blood
AB  - disease and which were planted in Kuala Kangsar, Malaysia. Here, we
AB  - report a draft genome sequence of blood disease bacterium A2 HR-MARDI, which
AB  - could provide important information on the virulence mechanism of this pathogen.
ER  -

TY  - JOUR
AU  - Bae, H.
AU  - Kim, K.P.
AU  - Lee, J.I.
AU  - Song, J.G.
AU  - Kil, E.J.
AU  - Kim, J.S.
AU  - Kwon, S.T.
TI  - Characterization of DNA polymerase from the hyperthermophilic archaeon Thermococcus marinus and its application to PCR.
JO  - Extremophiles
PY  - 2009
SP  - 657
EP  - 667
VL  - 13
AB  - The family B DNA polymerase gene from the archaeon Thermococcus marinus (Tma) contains a long
AB  - open reading frame of 3,939 bp that encodes 1,312
AB  - amino acid residues. The gene is split by one intervening sequence that
AB  - forms a continuous open reading frame with the two polymerase exteins. In
AB  - this study, the Tma DNA polymerase gene both with (precursor form) and
AB  - without (mature form) its intein was expressed in Escherichia coli,
AB  - purified by heat treatment and HiTrap Heparin HP column chromatography and
AB  - characterized. Primary sequence analysis of the mature Tma polymerase
AB  - showed high sequence identity with DNA polymerases in the genus
AB  - Thermococcus. The expressed precursor form was easily spliced during
AB  - purification steps. The molecular mass of the purified Tma DNA polymerases
AB  - is about 90 kDa, as estimated by SDS-PAGE. Both Tma DNA polymerases showed
AB  - the same properties. PCR performed with this enzyme was found to be
AB  - optimal in the presence of 50 mM Tris-HCl (pH 8.4), 40 mM KCl, 12.5 mM
AB  - (NH(4))(2)SO(4,) 2 mM MgCl(2,) 0.05% Triton X-100 and 0.0075% BSA.
AB  - Furthermore, long-range PCR and time-saving PCR were performed using
AB  - various specific ratios of Taq and Tma DNA polymerases (Tma plus DNA
AB  - polymerase).
ER  -

TY  - JOUR
AU  - Bae, H.
AU  - Kim, K.P.
AU  - Song, J.M.
AU  - Kim, J.H.
AU  - Yang, J.S.
AU  - Kwon, S.T.
TI  - Characterization of intein homing endonuclease encoded in the DNA polymerase gene of Thermococcus marinus.
JO  - FEMS Microbiol. Lett.
PY  - 2009
SP  - 180
EP  - 188
VL  - 297
AB  - The DNA polymerase gene of Thermococcus marinus (Tma) contains an intein inserted at the pol-b
AB  - site that possesses a 1611-bp ORF encoding
AB  - a 537-amino acid residue. The LAGLIDADG motif, often found in
AB  - site-specific DNA endonucleases, was detected within the amino acid
AB  - sequence of the intein. The intein endonuclease, denoted as PI-Tma, was
AB  - purified as a naturally spliced product from the expression of the
AB  - complete DNA polymerase gene in Escherichia coli. PI-Tma cleaved
AB  - intein-less DNA sequences, leaving four-base-long, 3'-hydroxyl
AB  - overhangs with 5'-phosphate. Nonpalindromic recognition sequences 19 bp
AB  - long were also identified using partially complementary oligonucleotide
AB  - pair sequences inserted into the plasmid pET-22b(+). Cleavage by PI-Tma
AB  - was optimal when present in 50 mM glycine-NaOH (pH 10.5), 150 mM KCl
AB  - and 12 mM MgCl2 at 70 degrees C.
ER  -

TY  - JOUR
AU  - Bae, M.
AU  - Par, J.-O.
AU  - Hwang, H.-Y.
AU  - Yim, J.
TI  - Purification and characterization of a restriction endonuclease from Streptomyces exfoliatus.
JO  - Korean J. Microbiol.
PY  - 1993
SP  - 544
EP  - 549
VL  - 31
AB  - Thirty strains of Streptomyces sp. isolated from soil samples were screened for the presence
AB  - of site-specific endonuclease.  One strain among them showed endonuclease activity to cleave
AB  - lambda DNA.  This study describes the purification and characterization of a site-specific
AB  - restriction endonuclease SexIII from Streptomyces exfoliatus.  The purification procedure
AB  - includes streptomycin sulfate treatment, DEAE-cellulose, hydroxylapatite, phosphocellulose P11
AB  - column chromatography.  This enzyme required high Mg2+ concentration (20-40 mM), and showed
AB  - maximal activity at neutral pH(7-8) in the absence of NaCl.  The enzyme did not require salt
AB  - for its activity and was inhibited by over 75 mM NaCl.  SexIII cut lambda DNA and plasmid
AB  - pBluescript, recognized the hexanucleotide sequence 5'-CCGC/GG-3', and proved to be an
AB  - isoschizomer of SacII.
ER  -

TY  - JOUR
AU  - Bae, M.
AU  - Song, E.-S.
TI  - Purification of restriction endonuclease, SdiI, from Steptomyces diastatochromogenes.
JO  - Korean J. Microbiol.
PY  - 1994
SP  - 297
EP  - 300
VL  - 32
AB  - About thirty bacterial strains of Actinomycetes, isolated from the soil, were examined for the
AB  - presence of restriction endonuclease activity.  Streptomyces diastatochromogenes, which was
AB  - identified previously, was found to contain restriction endonuclease activity.  The
AB  - purification of this enzyme, SdiI, was carried out via streptomycin sulfate precipitation and
AB  - ammonium sulfate fractionation followed by hydroxylapatite column chromatography.  Sephacryl
AB  - S-200 HR column chromatography and a second hydroxylapatite column chromatography.
AB  - SDS-polyacrylamide gel electrophoresis of the active protein (purified from various column
AB  - chromatography) resulted in 35,000 Da protein.
ER  -

TY  - JOUR
AU  - Bae, M.
AU  - Song, E.-S.
AU  - Hwang, H.-Y.
AU  - Yim, J.
TI  - Characterization of the restriction endonuclease, SdiI, from Streptomyces diastatochromogenes.
JO  - Korean J. Microbiol.
PY  - 1994
SP  - 301
EP  - 305
VL  - 32
AB  - In catalytic properties of the restriction endonuclease, SdiI, which was purified from
AB  - Streptomyces diastatochromogenes, this enzyme was active over a wide pH range between 7.0 and
AB  - 12.5 and up to 60oC and 500 mM NaCl.  It was stable between 20oC and 60oC, and MgCl2 is
AB  - essential for endonuclease activity.  The restriction map of lambda DNA which was obtained by
AB  - double digestion with various enzymes suggested that SdiI was an isoschizomer of XhoI.  From
AB  - the determination of the restriction site, based on DNA sequencing, the recognition and
AB  - cleavage specificity of SdiI was concluded to be
AB  - 5'-C/TCGA G-3'
AB  - 3'-G AGCT/C-5'.
ER  -

TY  - JOUR
AU  - Bae, M.
AU  - Suh, W.-N.
AU  - Park, J.-O.
AU  - Kim, H.T.
AU  - Lee, K.-J.
TI  - Numerical identification of Streptomyces sp. 58 producing restriction endonuclease SexIII, a novel isoschizomer of SacII.
JO  - Korean J. Microbiol.
PY  - 1993
SP  - 465
EP  - 470
VL  - 31
AB  - Numerical identification was carried out for an isolate of Streptomyces sp. 58 producing a new
AB  - restriction endonuclease SexIII.  Fifty taxonomic unit characters were tested and the data
AB  - were analyzed numerically using the TAXON program.  The isolate was identified to the major 5
AB  - of Streptomyces.  Therefore, it was concluded that the isolate was identified to be a member
AB  - of Streptomyces exfoliatus.
ER  -

TY  - JOUR
AU  - Bae, M.
AU  - Suh, W.-N.
AU  - Song, E.-S.
AU  - Lee, K.-J.
TI  - Numerical identification of a Streptomyces strain producing restriction endonuclease SdiI.
JO  - Korean J. Appl. Microbiol. Biotechnol.
PY  - 1994
SP  - 126
EP  - 133
VL  - 22
AB  - Numerical identification was applied for Streptomyces sp. 264, an isolate producing a new
AB  - restriction endonuclease SdiI. The restriction enzyme would appear to be an isoschizomer of
AB  - XhoI. Fifty taxonomic unit characters were tested and the data obtained were analyzed
AB  - numerically by using the TAXON program. The isolate was identified to be the major cluster 19
AB  - of Streptomyces and best matched to S. diastatochromogenes. It was, therefore, concluded that
AB  - the isolate was identified to be a member of Streptomyces diastatochromogenes.
ER  -

TY  - JOUR
AU  - Bae, M.
AU  - Yun, M.-S.
AU  - Kim, H.-T.
AU  - Lee, K.-J.
TI  - Numerical identification of a Streptomyces strain producing a thermotolerable restriction endonuclease SviI.
JO  - Korean J. Appl. Microbiol. Biotechnol.
PY  - 1993
SP  - 299
EP  - 305
VL  - 21
AB  - Numerical identification was carried out for an isolate of Streptomyces D2-5 producing a new
AB  - restriction endonuclease SviI. Fifty taxonomic unit characters were tested and the data were
AB  - analyzed numerically using the TAXON program. The isolate was best matched to Streptomyces
AB  - violochromogenes in the major cluster 18 of Streptomyces. Therefore, it was concluded that the
AB  - isolate was identified to be a member of Streptomyces violochromogenes.
ER  -

TY  - JOUR
AU  - Baek, K.
AU  - Chung, E.J.
AU  - Choi, G.G.
AU  - Nam, Y.H.
AU  - Choi, A.
TI  - Draft Genome Sequence of Deinococcus koreensis SJW1-2(T), a Gamma Radiation-Resistant Bacterium Isolated from River Water.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00894
EP  - e00818
VL  - 7
AB  - Deinococcus koreensis SJW1-2(T) was isolated from river water and was observed to be highly
AB  - resistant to gamma radiation. In this study, we report a draft genome
AB  - sequence which revealed that SJW1-2(T) possesses genes involved in nucleotide
AB  - excision repair. The primary genomic information will aid in elucidating the DNA
AB  - repair mechanism during ionizing radiation.
ER  -

TY  - JOUR
AU  - Bag, S.
AU  - Ghosh, T.S.
AU  - Das, B.
TI  - Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult.
JO  - Genome Announcements
PY  - 2017
SP  - e00834
EP  - e00817
VL  - 5
AB  - Prevotella copri, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated
AB  - with the human gastrointestinal tract and influences host physiology,
AB  - immunity, and metabolic pathways. In the present study, we report the draft
AB  - genome sequence of P. copri isolated from the gut of a healthy Indian adult.
ER  -

TY  - JOUR
AU  - Bag, S.
AU  - Ghosh, T.S.
AU  - Das, B.
TI  - Whole-Genome Sequence of Bifidobacterium longum Strain Indica, Isolated from the  Gut of a Healthy Indian Adult.
JO  - Genome Announcements
PY  - 2017
SP  - e01017
EP  - e01017
VL  - 5
AB  - Bifidobacterium longum, a Gram-positive rod-shaped anaerobic bacterium, inhabits  the human
AB  - gastrointestinal tract and contributes significantly to oligosaccharide
AB  - production, amino acid metabolism, and protection against intestinal
AB  - inflammation. Here, we report the whole-genome sequence of B. longum, which was
AB  - isolated from the gastrointestinal tract of a healthy Indian adult.
ER  -

TY  - JOUR
AU  - Bag, S.
AU  - Ghosh, T.S.
AU  - Das, B.
TI  - Whole-Genome Sequence of a Megasphaera elsdenii Strain Isolated from the Gut of a Healthy Indian Adult Subject.
JO  - Genome Announcements
PY  - 2017
SP  - e01033
EP  - e01017
VL  - 5
AB  - Megasphaera elsdenii has been previously reported in the gut of ruminating animals. Its role
AB  - as an animal probiotic is being investigated, specifically from
AB  - the perspective of enhancing animal productivity. Herein, we report the draft
AB  - genome sequence of M. elsdenii strain indica isolated from the stool sample of a
AB  - healthy Indian subject.
ER  -

TY  - JOUR
AU  - Bag, S.
AU  - Ghosh, T.S.
AU  - Das, B.
TI  - Complete Genome Sequence of Faecalibacterium prausnitzii Isolated from the Gut of a Healthy Indian Adult.
JO  - Genome Announcements
PY  - 2017
SP  - e01286
EP  - e01217
VL  - 5
AB  - Faecalibacterium prausnitzii is the most abundant (~4%) member of the phylum Firmicutes found
AB  - in the colon of healthy humans. It is a strict anaerobe and
AB  - plays an important role in intestinal homeostasis. Here, we report the complete
AB  - genome sequence of F. prausnitzii strain Indica.
ER  -

TY  - JOUR
AU  - Bag, S.
AU  - Ghosh, T.S.
AU  - Das, B.
TI  - Complete Genome Sequence of Collinsella aerofaciens Isolated from the Gut of a Healthy Indian Subject.
JO  - Genome Announcements
PY  - 2017
SP  - e01361
EP  - e01317
VL  - 5
AB  - Collinsella aerofaciens, a rod-shaped nonmotile obligate anaerobe, is the most abundant
AB  - actinobacterium in the gastrointestinal tract of healthy humans. An
AB  - altered abundance of C. aerofaciens may be linked with several health disorders,
AB  - including irritable bowel syndrome. In the present study, we report the complete
AB  - genome sequence of C. aerofaciens strain indica.
ER  -

TY  - JOUR
AU  - Bahari, Z.M.
AU  - Ibrahim, Z.
AU  - Jaafar, J.
AU  - Shahir, S.
TI  - Draft Genome Sequence of Arsenic-Resistant Microbacterium sp. Strain SZ1 Isolated from Arsenic-Bearing Gold Ores.
JO  - Genome Announcements
PY  - 2017
SP  - e01183
EP  - e01117
VL  - 5
AB  - Microbacterium sp. strain SZ1 isolated from gold ores of a Malaysia gold mine was found to be
AB  - highly resistant to arsenic. Here, we report the draft genome sequence of SZ1, which may
AB  - provide further insights into understanding its arsenic resistance mechanism. In this draft
AB  - genome, a complete set of ars operons and two additional scattered ars genes were encoded.
ER  -

TY  - JOUR
AU  - Bahr, M.
TI  - Biophysical characterization and biochemical direction of methyltransferase-DNA-interactions.
JO  - Ph.D. Thesis, Germany
PY  - 2009
SP  - 1
EP  - 192
ER  -

TY  - JOUR
AU  - Bahrami, T.
AU  - Zarvandi, S.
AU  - De Mot, R.
AU  - Gross, H.
AU  - Changi-Ashtiani, M.
AU  - Shahani, T.
AU  - Rokni-Zadeh, H.
TI  - Draft Genome Sequence of Pseudomonas gingeri Strain LMG 5327, the Causative Agent of Ginger Blotch in Agaricus bisporus.
JO  - Genome Announcements
PY  - 2018
SP  - e00196
EP  - e00118
VL  - 6
AB  - The draft genome sequence of Pseudomonas gingeri LMG 5327 (NCPPB 3146), the causative agent of
AB  - ginger blotch in Agaricus bisporus, is reported. Together with
AB  - another mushroom pathogen, Pseudomonas agarici, it belongs to a distinct
AB  - phylogenomic group.
ER  -

TY  - JOUR
AU  - Bai, J.
AU  - He, Z.
TI  - Mammalian DNA methylase.
JO  - Shengli Kexue Jinzhan
PY  - 1997
SP  - 67
EP  - 69
VL  - 28
ER  -

TY  - JOUR
AU  - Bai, Y.
AU  - Muller, D.B.
AU  - Srinivas, G.
AU  - Garrido-Oter, R.
AU  - Potthoff, E.
AU  - Rott, M.
AU  - Dombrowski, N.
AU  - Munch, P.C.
AU  - Spaepen, S.
AU  - Remus-Emsermann, M.
AU  - Huttel, B.
AU  - McHardy, A.C.
AU  - Vorholt, J.A.
AU  - Schulze-Lefert, P.
TI  - Functional overlap of the Arabidopsis leaf and root microbiota.
JO  - Nature
PY  - 2015
SP  - 364
EP  - 369
VL  - 528
AB  - Roots and leaves of healthy plants host taxonomically structured bacterial
AB  - assemblies, and members of these communities contribute to plant growth and
AB  - health. We established Arabidopsis leaf- and root-derived microbiota culture
AB  - collections representing the majority of bacterial species that are reproducibly
AB  - detectable by culture-independent community sequencing. We found an extensive
AB  - taxonomic overlap between the leaf and root microbiota. Genome drafts of 400
AB  - isolates revealed a large overlap of genome-encoded functional capabilities
AB  - between leaf- and root-derived bacteria with few significant differences at the
AB  - level of individual functional categories. Using defined bacterial communities
AB  - and a gnotobiotic Arabidopsis plant system we show that the isolates form
AB  - assemblies resembling natural microbiota on their cognate host organs, but are
AB  - also capable of ectopic leaf or root colonization. While this raises the
AB  - possibility of reciprocal relocation between root and leaf microbiota members,
AB  - genome information and recolonization experiments also provide evidence for
AB  - microbiota specialization to their respective niche.
ER  -

TY  - JOUR
AU  - Baik, S.C.
AU  - Lee, W.K.
AU  - Song, J.Y.
AU  - Choi, Y.J.
AU  - Rye, B.D.
AU  - Choi, S.H.
AU  - Cho, M.J.
AU  - Rhee, K.H.
TI  - Purification and characterization of type II restriction endonuclease (HpyI) of Helicobacter pylori.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1998
SP  - 120
EP  - 120
VL  - 0
AB  - This study describes the purification and characterization of type II restriction endonuclease
AB  - of Helicobacter pylori, a Gram-negative spiral bacterium associated with type B gastritis,
AB  - peptic ulcer, and gastric cancer in human.  Helicobacter pylori cytosol was subjected to
AB  - polyethyleneimine treatment, salt precipitation, heparin-sepharose column chromatography, and
AB  - fast protein liquid chromatography using Resource Q column and Mono Q column to purify the
AB  - type II restriction endonuclease.  HpyI was characterized to recognize the sequence
AB  - 5'-GT(G/C)AC-3', yielding 5-base 5' protruding ends.  The restriction sequence was
AB  - identical to that of Tsp45I.  The molecular weight of native protein was estimated to be 22
AB  - kDa by size exclusion chromatography of FPLC.  The enzyme exhibited its maximal activity in
AB  - the presence of 10-20 mM NaCl, but was inhibited completely in the presence of NaCl more than
AB  - 80 mM.  The enzyme showed its maximal activity in the presence of 1-10 mM MgCl2.  The optimal
AB  - pH and temperature for enzyme activity was pH 9.0 and 37E, respectively.  MnCl2 could not
AB  - substitute for MgCl2 in reaction mixture.  And addition of YA-mercaptoethanol and bovine serum
AB  - albumin in reaction mixture led to loss of enzyme activity of HpyI.  HpyI was confirmed to
AB  - digest genomic DNAs of enteric bacteria to less than 1 kb while it could not cut the genomic
AB  - DNAs of Helicobacter pylori isolates.  Eighty HpyI restriction sites were found in the whole
AB  - genome sequence of H. pylori reported by the Institute for Genomic Research, which are less
AB  - than 2.5% of estimated numbers of HpyI restriction sites in the whole genome.  The pBR322 DNA
AB  - that was treated with the crude extract of H. pylori cytosol in the presence of 0.3 mM
AB  - S-adenosylmethionine was partially protected from HpyI restriction.  Therefore, the enzymatic
AB  - activity in the crude extract is likely a DNA methyltransferase.  H. pylori DNA is supposed to
AB  - be protected from HpyI restriction by the rareness of HpyI restriction sites and methylation
AB  - of the site.  Taken together, HpyI might be the one of the barriers preventing the
AB  - introduction of foreign DNAs into H. pylori.
ER  -

TY  - JOUR
AU  - Bailey, A.C.
AU  - Kellom, M.
AU  - Poret-Peterson, A.T.
AU  - Noonan, K.
AU  - Hartnett, H.E.
AU  - Raymond, J.
TI  - Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah.
JO  - Genome Announcements
PY  - 2014
SP  - e01199
EP  - e01114
VL  - 2
AB  - Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain
AB  - appears to be capable of chemotaxis and exopolysaccharide synthesis
AB  - for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate
AB  - reduction pathway as well as a TCA cycle, making it a facultative anaerobe.
ER  -

TY  - JOUR
AU  - Bailey, A.C.
AU  - Kellom, M.
AU  - Poret-Peterson, A.T.
AU  - Noonan, K.
AU  - Hartnett, H.E.
AU  - Raymond, J.
TI  - Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.
JO  - Genome Announcements
PY  - 2014
SP  - e01198
EP  - e01114
VL  - 2
AB  - Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain
AB  - appears to be capable of chemotaxis and biofilm production. The BSC154
AB  - genome contains iron siderophore production, nitrate reduction, mixed
AB  - acid-butanediol fermentation, and assimilatory and dissimilatory sulfate
AB  - metabolism pathways.
ER  -

TY  - JOUR
AU  - Bailey, A.C.
AU  - Kellom, M.
AU  - Poret-Peterson, A.T.
AU  - Noonan, K.
AU  - Hartnett, H.E.
AU  - Raymond, J.
TI  - Draft Genome Sequence of Microvirga sp. Strain BSC39, Isolated from Biological Soil Crust of Moab, Utah.
JO  - Genome Announcements
PY  - 2014
SP  - e01197
EP  - e01114
VL  - 2
AB  - Microvirga sp. BSC39 was isolated from a biological soil crust near Moab, Utah. The strain
AB  - appears to be capable of chemotaxis and exopolysaccharide synthesis
AB  - for biofilm adhesion. The BSC39 genome contains iron siderophore uptake and
AB  - hydrolysis enzymes; however, it lacks siderophore synthesis pathways, suggesting
AB  - the uptake of siderophores produced by neighboring microbes.
ER  -

TY  - JOUR
AU  - Bailey, C.R.
AU  - Winstanley, D.J.
TI  - Inhibition of restriction in Streptomyces clavuligerus by heat treatment.
JO  - J. Gen. Microbiol.
PY  - 1986
SP  - 2945
EP  - 2947
VL  - 132
AB  - Inefficient transformation of Streptomyces clavuligerus protoplasts by DNA from
AB  - the plasmid pIJ702, isolated from S. lividans, was attributed to restriction in
AB  - view of the observation that efficient transformation was observed using
AB  - modified pIJ702 (isolated from S. clavuligerus).  The restriction system could
AB  - be partially inhibited by treating protoplasts at 45C prior to transformation.
AB  - This treatment increased the transformation frequencies of pIJ702 DNA by
AB  - 100-fold and was used to introduce other plasmids into S. clavuligerus.
ER  -

TY  - JOUR
AU  - Bailey, T.W.
AU  - do Nascimento, N.C.
AU  - Bhunia, A.K.
TI  - Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype.
JO  - Genome Announcements
PY  - 2017
SP  - e01324
EP  - e01317
VL  - 5
AB  - Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we  performed
AB  - whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b)
AB  - using Illumina sequencing. The sequence showed 94.5% identity with strain F2365,
AB  - serotype 4b, and 90.6% with EGD-e, serotype 1/2a.
ER  -

TY  - JOUR
AU  - Bair, C.L.
AU  - Black, L.W.
TI  - A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 768
EP  - 778
VL  - 366
AB  - The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel
AB  - type IV modification-dependent restriction
AB  - nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine
AB  - (HMC) DNAs. The protein products GmrS (36 kDa) and GmrD (27 kDa) were
AB  - purified and found to be inactive separately, but together degraded
AB  - several different glc-HMC modified DNAs (T4, T2 and T6). The GMR enzyme is
AB  - able to degrade both alpha-glucosy-HMC T4 DNA and beta-glucosyl-HMC T4
AB  - DNA, whereas no activity was observed against non-modified DNAs including
AB  - unmodified T4 cytosine (C) DNA or non-glucosylated T4 HMC DNA. Enzyme
AB  - activity requires NTP, favors UTP, is stimulated by calcium, and initially
AB  - produces 4 kb DNA fragments that are further degraded to low molecular
AB  - mass products. The enzyme is inhibited by the T4 phage internal protein I*
AB  - (IPI*) to which it was found to bind. Overall activities of the purified
AB  - GmrSD enzyme are in good agreement with the properties of the cloned gmr
AB  - genes in vivo and suggest a restriction enzyme specific for sugar modified
AB  - HMC DNAs. IPI* thus represents a third generation bacteriophage defense
AB  - against restriction nucleases of the Gmr type.
ER  -

TY  - JOUR
AU  - Bair, C.L.
AU  - Black, L.W.
TI  - Setting the phage for evolution: The mechanism of host exclusion of bacteriophage T4 IPI.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2004
SP  - 392
EP  - 392
VL  - 104
AB  - Interaction of bacteria and phages has led to the evolution of complex phage exclusion systems
AB  - and cognate exclusion avoidance mechanisms.  Chief among these are restriction-modification
AB  - system enzymes that attack the invading phage DNA and against which phages employ various
AB  - strategies including DNA modification.  The T-even phages of the myoviridae utilize extended
AB  - DNA modifications to host RMS's with base methylations, 100% hydroxymethylated-cytosine, and
AB  - alpha-, beta-, and other-glucosylated HmC derivaties.  The injected DNA-bound T4 IPI protein
AB  - (~350 molecules/DNA), nonessential in most hosts, has been shown to be necessary for
AB  - productive T4 infection of the pathogenic E. coli K isolate CT596.  This host has now been
AB  - shown to harbor a prophage that encodes the RMS genes gIBEGs (36.649 kb) and gIBEGd (26.854
AB  - kb), with 65% and 48% identity to H. pylori sequences of unknown function that have been
AB  - cloned and shown to be necessary and sufficient to restrict T4 DNA lacking IPI.
AB  - GpIBEGs/gpIBEGd encode a novel Type IV RMS that, unlike previously discovered E. coli
AB  - restriction systems, is able to digest the glucosylated-HmC T4 DNA, and is apparently
AB  - physically blocked from its recognition sequence by the presence of IPI on the DNA.  Active
AB  - tag derivatized forms of the two proteins have been purified to near homogeneity.  The
AB  - proteins are  inactive separately, but together degrade in apparently non-sequence-specific
AB  - manner glucosylated-HmC DNA substrates, with no activity against non-modified templates such
AB  - as T4 C-DNA.  The activity is stimulated by 1-2mM GTP and this effect is inhibited by excess
AB  - ATP.  It appears that this bacterial restriction system has evolved specifically to combat
AB  - infections by T-even phages.  Pursuing this struggle, the T-evens have evolved a highly
AB  - diverse and, in some cases, expanded family of capsid-targeted internal protein I (IPI) locus
AB  - gene products that may specifically shield the diverse modifications of their HmC residues
AB  - from IBEG family RMS's.
ER  -

TY  - JOUR
AU  - Bair, C.L.
AU  - Rifat, D.
AU  - Black, L.W.
TI  - Exclusion of Glucosyl-Hydroxymethylcytosine DNA Containing Bacteriophages Is Overcome by the Injected Protein Inhibitor IPI*.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 779
EP  - 789
VL  - 366
AB  - The Escherichia coli isolate CT596 excludes infection by the Myoviridae T4 ip1(-) phage that
AB  - lacks the encapsidated IPI* protein normally injected into the host with the phage DNA.
AB  - Screening of a CT596 genomic library identified adjacent genes responsible for this exclusion,
AB  - gmrS (942 bp) and gmrD (708 bp) that are encoded by a cryptic prophage DNA. The two genes are
AB  - necessary and sufficient to confer upon a host the ability to exclude infection by T4 ip1(-)
AB  - phage and other glucosyl-hydroxymethylcytosine (glc-HMC) Tevens lacking the ip1 gene, yet
AB  - allow infection by phages with non-glucoslyated cytosine (C) DNA that lack the ip1 gene. A
AB  - plasmid expressing the ip1 gene product, IPI*, allows growth of Tevens lacking ip1 on E. coli
AB  - strains carrying the cloned gmrS/gmrD genes. Members of the Teven family carry a diverse and,
AB  - in some cases, expanded set of ip1 locus genes. In vivo analysis suggests a family of gmr
AB  - genes that specifically target sugar-HMC modified DNA have evolved to exclude Teven phages,
AB  - and these exclusion genes have in turn been countered by a family of injected exclusion
AB  - inhibitors that likely help determine the host range of different glc-HMC phages.
ER  -

TY  - JOUR
AU  - Bajpai, A.
AU  - Shende, K.K.
AU  - Meena, N.
AU  - Suravajhala, P.
AU  - Medicherla, K.M.
AU  - Johri, B.N.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas protegens Strain BNJ-SS-45, Isolated from Rhizosphere Soil of Wheat (Triticum  aestivum).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00926
EP  - e00918
VL  - 7
AB  - Here, we present the draft genome sequence of Pseudomonas protegens strain BNJ-SS-45, which
AB  - was isolated from wheat rhizosphere. The genome is assembled
AB  - with 7,116,445 bp with a GC content of 63.34% consisting of 32 scaffolds. The
AB  - genome is useful in prediction of secondary metabolites, particularly rhizoxin,
AB  - pyoverdine, and bacteriocin.
ER  -

TY  - JOUR
AU  - Bakenhus, I.
AU  - Voget, S.
AU  - Poehlein, A.
AU  - Brinkhoff, T.
AU  - Daniel, R.
AU  - Simon, M.
TI  - Genome sequence of Planktotalea frisia type strain (SH6-1(T)), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton  bloom.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 7
EP  - 7
VL  - 13
AB  - Planktotalea frisia SH6-1(T) Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a
AB  - planktonic marine bacterium isolated during a phytoplankton bloom from
AB  - the southern North Sea. It belongs to the Roseobacter group within the
AB  - alphaproteobacterial family Rhodobacteraceae. Here we describe the draft genome
AB  - sequence and annotation of the type strain SH6-1(T). The genome comprises
AB  - 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome
AB  - sequence provides evidence for at least three extrachromosomal elements, encodes
AB  - genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV
AB  - secretion system. This indicates not only adaptation to a free-living lifestyle
AB  - of P. frisia but points also to interactions with prokaryotic or eukaryotic
AB  - organisms.
ER  -

TY  - JOUR
AU  - Baker, B.J.
AU  - Comolli, L.R.
AU  - Dick, G.J.
AU  - Hauser, L.J.
AU  - Hyatt, D.
AU  - Dill, B.D.
AU  - Land, M.L.
AU  - Verberkmoes, N.C.
AU  - Hettich, R.L.
AU  - Banfield, J.F.
TI  - Enigmatic, ultrasmall, uncultivated Archaea.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 8806
EP  - 8811
VL  - 107
AB  - Metagenomics has provided access to genomes of as yet uncultivated microorganisms
AB  - in natural environments, yet there are gaps in our knowledge-particularly for
AB  - Archaea-that occur at relatively low abundance and in extreme environments.
AB  - Ultrasmall cells (<500 nm in diameter) from lineages without cultivated
AB  - representatives that branch near the crenarchaeal/euryarchaeal divide have been
AB  - detected in a variety of acidic ecosystems. We reconstructed composite,
AB  - near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN
AB  - (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples
AB  - and a biofilm filtrate. Genes of two lineages are among the smallest yet
AB  - described, enabling a 10% higher coding density than found genomes of the same
AB  - size, and there are noncontiguous genes. No biological function could be inferred
AB  - for up to 45% of genes and no more than 63% of the predicted proteins could be
AB  - assigned to a revised set of archaeal clusters of orthologous groups. Some core
AB  - metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of
AB  - genes have the highest sequence identity to bacterial genes, and 12 belong to
AB  - clusters of orthologous groups that were previously exclusive to bacteria. A
AB  - small subset of 3D cryo-electron tomographic reconstructions clearly show
AB  - penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances
AB  - extended from cells of the archaeal order Thermoplasmatales. Interspecies
AB  - interactions, the presence of a unique internal tubular organelle [Comolli, et
AB  - al. (2009) ISME J 3:159-167], and many genes previously only affiliated with
AB  - Crenarchaea or Bacteria indicate extensive unique physiology in organisms that
AB  - branched close to the time that Cren- and Euryarchaeotal lineages diverged.
ER  -

TY  - JOUR
AU  - Baker, D.
TI  - Proteins by design.
JO  - The Scientist
PY  - 2006
SP  - 26
EP  - 32
VL  - 20
AB  - Imagine having the power to create a brand new protein - biosensor for any small molecule,
AB  - say, or a novel enzyme - on demand.  It's not pure fantasy.  Computational structural biology
AB  - is poised to put this power into our hands.  Along with a team of research groups around the
AB  - world, we have begun designing novel proteins and folds from scratch, computing amino acid
AB  - sequences that will fold to create enzymatic activities never before seen in nature.  The
AB  - possibilities are limited only by our imaginations: Picture an endonuclease designed to thwart
AB  - malaria, molecular sensors for bioterror agents, or a vaccine that HIV is less likely to
AB  - evolve around.  The mechanics of these engineering feats are closely related, perhaps not
AB  - surprisingly, to their logical inverse: structure prediction.  Scientists have for years tried
AB  - to develop methods for predicting a protein's structure simply from its amino acid sequence.
AB  - Imagine that in the time it takes to sequence the genome of an organism, scientists could also
AB  - characterize the structure of each of its proteins.  This would unveil biomolecular
AB  - interactions, structural homologies, functional roles, and potential drug targets that might
AB  - never be found from gene sequence alone.  Although there is still a long way to go, with
AB  - improvements to algorithms and increases in computing power, exciting progress is being made
AB  - in both prediction and design.
ER  -

TY  - JOUR
AU  - Baker, D.J.
AU  - Hardy, T.A.
AU  - Smith, S.S.
TI  - The influence of the dT.dG mispair on the activity of the human DNA (cytosine-5) methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1987
SP  - 596
EP  - 602
VL  - 146
AB  - Synthetic oligodeoxynucleotides containing a dT-dG mispair at a centrally located d(pCG) dimer
AB  - are methylated at a moderate rate by highly purified human DNA (cytosine-5) methyltransferase
AB  - (E.C.2.1.1.37). The presence of a mispaired dT in one strand induced the enzyme to
AB  - preferentially methylate the opposite strand.
ER  -

TY  - JOUR
AU  - Baker, D.J.
AU  - Kan, J.L.C.
AU  - Smith, S.S.
TI  - Recognition of structural perturbations in DNA by human DNA(cytosine-5)methyltransferase.
JO  - Gene
PY  - 1988
SP  - 207
EP  - 210
VL  - 74
AB  - We have used oligodeoxynucleotides to study DNA methyltransferase activity on several types of
AB  - DNA structure in which the cytosine is mispaired to test these predictions. These sequences,
AB  - 30 nt in length, containing either C-C or A-C mismatches have been studied in detail. In both
AB  - cases mispaired cytosines are selectively enhanced as acceptors of DNA methylation. Our
AB  - findings with the C-C mispair are illustrative. A kinetic comparison showed that a duplex
AB  - containing a C-C mispair was methylated about seven-fold faster than a complementary
AB  - unmethylated duplex of otherwise identical sequence. Autoradiographic analysis of the
AB  - enzymatically methylated product showed that the methyl groups were applied to each of the
AB  - cytosines in the mismatch with about equal efficiency. MspI (but not HpaII) was able to
AB  - partially cleave the duplex structure containing the mismatch, suggesting that there is a
AB  - dynamic equilibrium in solution between structures like those shown in Fig. 1. The d(pCCGG)
AB  - recognition site is regenerated in structures (2) and (4).
ER  -

TY  - JOUR
AU  - Baker, D.J.
AU  - Laayoun, A.
AU  - Smith, S.S.
TI  - Transition state analogs as affinity labels for human DNA methyltransferases.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1993
SP  - 864
EP  - 871
VL  - 196
AB  - A new class of affinity labels has been developed for human DNA (cytosine-5)
AB  - methyltransferases. These oligodeoxynucleotides contain 5-fluorodeoxycytidine at a mispair
AB  - within the recognition motif of the human enzyme. They were not effectively recognized by
AB  - bacterial methyltransferases. They can be viewed as analogs of the intermediates transiently
AB  - produced by methyltransferases during catalysis. Affinity labelling patterns suggest that both
AB  - the structurally induced activity and the methyl-directed activity of the human enzymes
AB  - operate by the same mechanism and reside on the same polypeptide chains.
ER  -

TY  - JOUR
AU  - Baker, K.S.
AU  - Parkhill, J.
AU  - Thomson, N.R.
TI  - Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.
JO  - Genome Announcements
PY  - 2015
SP  - e00393
EP  - e00315
VL  - 3
AB  - Shigella flexneri is a diarrheal pathogen that causes a large disease burden worldwide. We
AB  - sequenced the genome of the publicly available type strain (S.
AB  - flexneri 2a strain 24570) of this bacterial species to increase its utility as a
AB  - reference. We present genome assembly results and comparisons with other
AB  - reference strains.
ER  -

TY  - JOUR
AU  - Bakh, N.L.
AU  - Semina, I.E.
TI  - Obtaining the preparations of immobilized restrictases SalI and PvuII.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1985
SP  - 32
EP  - 34
VL  - 2
AB  - Conditions for the immobilization of specific endonucleases SalI and PvuII on
AB  - BrCN-activated Sepharose 4B have been selected.  Some physico-chemical
AB  - properties of the preparations of immobilized restrictases SalI and PvuII have
AB  - been characterized.  The specific and general activity values of the
AB  - preparations thus obtained have been established.  The immobilized enzymes have
AB  - been used for the multiple restriction of the DNA of phage lambda and the DNA
AB  - of Neisseria meningitidis.
ER  -

TY  - JOUR
AU  - Bakh, N.L.
AU  - Tsvetkova, N.V.
AU  - Semina, I.E.
AU  - Tarasov, A.P.
AU  - Mileikovskaya, M.M.
AU  - Gruber, I.M.
AU  - Polyachenko, V.M.
AU  - Romanenko, E.E.
TI  - Isolation and Purification of Restriction Endonuclease PmiI from Pseudomonas Mirabilis 1667.
JO  - Antibiot. Med. Biotekhnol.
PY  - 1985
SP  - 342
EP  - 344
VL  - 30
AB  - A new restriction endonuclease PmiI was detected in Proteus mirabilis 1667.
AB  - The enzyme hydrolyzes DNA of the phage lambda into 10 electrophoretically
AB  - separating fragments with molecular weights of 1.3-7.9 mD.  With the use of
AB  - two-stage chromatography on sepharose and phosphocellulose it is possible to
AB  - obtain restriction endonuclease PmiI free of the admixtures of ballast
AB  - proteins, nonspecific nucleases and phosphatases.
ER  -

TY  - JOUR
AU  - Bakhrat, A.
AU  - Baranes, K.
AU  - Krichevsky, O.
AU  - Rom, I.
AU  - Schlenstedt, G.
AU  - Pietrokovski, S.
AU  - Raveh, D.
TI  - Nuclear import of Ho endonuclease utilizes two nuclear localization signals and four importins of the ribosomal import system.
JO  - J. Biol. Chem.
PY  - 2006
SP  - 12218
EP  - 12226
VL  - 281
AB  - Activity of Ho, the yeast mating switch endonuclease, is restricted to a narrow time window of
AB  - the cell cycle. Ho is unstable and despite
AB  - being a nuclear protein is exported to the cytoplasm for proteasomal
AB  - degradation. We report here the molecular basis for the highly
AB  - efficient nuclear import of Ho and the relation between its short
AB  - half-life and passage through the nucleus. The Ho nuclear import
AB  - machinery is functionally redundant, being based on two bipartite
AB  - nuclear localization signals, recognized by four importins of the
AB  - ribosomal import system. Ho degradation is regulated by the DNA damage
AB  - response and Ho retained in the cytoplasm is stabilized, implying that
AB  - Ho acquires its crucial degradation signals in the nucleus. Ho arose by
AB  - domestication of a fungal VMA1 intein. A comparison of the primary
AB  - sequences of Ho and fungal VMA1 inteins shows that the Ho nuclear
AB  - localization signals are highly conserved in all Ho proteins, but are
AB  - absent from VMA1 inteins. Thus adoption of a highly efficient import
AB  - strategy occurred very early in the evolution of Ho. This may have been
AB  - a crucial factor in establishment of homothallism in yeast, and a key
AB  - event in the rise of the Saccharomyces sensu stricto.
ER  -

TY  - JOUR
AU  - Bakhrat, A.
AU  - Jurica, M.S.
AU  - Stoddard, B.L.
AU  - Raveh, D.
TI  - Homology modeling and mutational analysis of Ho endonuclease of yeast.
JO  - Genetics
PY  - 2004
SP  - 721
EP  - 728
VL  - 166
AB  - Ho endonuclease is a LAGLIDADG homing endonuclease that initiates mating-type interconversion
AB  - in yeast. Ho is encoded by a free-standing
AB  - gene but shows 50% primary sequence similarity to the intein
AB  - (protein-intron encoded) PI-SceI. Ho is unique among LAGLIDADG
AB  - endonucleases in having a 120-residue C-terminal putative zinc finger
AB  - domain. The crystal structure of PI-SceI revealed a bipartite enzyme
AB  - with a protein-splicing domain (Hint) and intervening endonuclease
AB  - domain. We made a homology model for Ho on the basis of the PI-SceI
AB  - structure and performed mutational analysis of putative critical
AB  - residues, using a mating-type switch as a bioassay for activity and
AB  - GFP-fusion proteins to detect nuclear localization. We found that
AB  - residues of the N-terminal sequence of the Hint domain are important
AB  - for Ho activity, in particular the DNA recognition region. C-terminal
AB  - residues of the Hint domain are dispensable for Ho activity; however,
AB  - the C-terminal putative zinc finger domain is essential. Mutational
AB  - analysis indicated that residues in Ho that are conserved relative to
AB  - catalytic, active-site residues in PI-SceI and other related homing
AB  - endonucleases are essential for Ho activity. Our results indicate that
AB  - in addition to the conserved catalytic residues, Hint domain residues
AB  - and the zinc finger domain have evolved a critical role in Ho activity.
ER  -

TY  - JOUR
AU  - Baksi, K.
AU  - Rogerson, D.L.
AU  - Rushizky, G.W.
TI  - Rapid, single-step purification of restriction endonucleases on Cibacron blue F3GA-agarose.
JO  - Biochemistry
PY  - 1978
SP  - 4136
EP  - 4139
VL  - 17
AB  - After sonication and high-speed centrifugation, crude extracts of B.
AB  - amyloliquefaciens, P. alcalifaciens, X. holicola, and B. globiggi were absorbed
AB  - on the dye Cibacron blue F3GA covalently cross-linked to agarose.  The
AB  - restriction endonucleases BamHI, PalI, XhoI, and BglI together with BglII were
AB  - isolated by elution of the dye column with linear gradients to 0.5 M NaCl.  The
AB  - enzymes so purified were free of contaminating nucleic acids and other
AB  - nucleases and were sufficiently concentrated for direct, specific DNA
AB  - hydrolysis.
ER  -

TY  - JOUR
AU  - Baksi, K.
AU  - Rushizky, G.W.
TI  - Rapid purification of restriction endonucleases on Cibacron Blue F3GA.
JO  - Fed. Proc.
PY  - 1978
SP  - 1414
EP  - 1414
VL  - 37
AB  - At present, purification of Type II restriction nucleases involves, after cell
AB  - breakage and high-speed centrifugation, at least two more steps: DNA removal
AB  - and column chromatography of the enzyme(s).  We show that the high-speed
AB  - supernatant may be directly adsorbed on Cibacron Blue F3GA covalently
AB  - cross-linked to agarose (CB) and restriction enzymes eluted with linear
AB  - gradients from 0-0.5 M NaCl.  Per gram of frozen cells, 700 or more units of
AB  - Bgl (I and II), Xho (I and II) and PalI were so isolated, free of contaminating
AB  - nuclease activity as judged by electrophoresis of lambda DNA digests on 1.4%
AB  - agarose gels.  The oligonucleotide band patterns observed agreed with those
AB  - reported by others for the purified enzymes.  While the content of restriction
AB  - nuclease activity varied between different batches of frozen cells, the
AB  - recovery of enzyme activity islated by CB chromatography is comparable to that
AB  - obtained by other procedures.  The extent of purification (Lowry protein) was
AB  - 55-fold (PalI).  Purified AluI, BamHI, XhoI and HaeIII (the isoschizomer of
AB  - PalI) (N.E. Biolabs) were similarly bound on and eluted by serum albumin at 5
AB  - mg/ml or calf thymus nucleic acid at 125 microgram/ml.
ER  -

TY  - JOUR
AU  - Baksi, K.
AU  - Rushizky, G.W.
TI  - Purification of the restriction endonuclease PalI.
JO  - Anal. Biochem.
PY  - 1979
SP  - 207
EP  - 212
VL  - 99
AB  - The restriction endonuclease PalI was purified from Providencia alcalifaciens 1650-fold with a
AB  - yield of 33%.  The purified protein moved as a single band upon polyacrylamide gel
AB  - electrophoresis.  When this was carried out in the presence of sodium dodecyl sulfate, a
AB  - molecular weight of 31,000 was obtained for PalI.  Gel filtration through Sephacryl S200 gave
AB  - molecular weights ranging from 44,000 to 53,000 when 58 to 1870 ng/ml enzyme were used,
AB  - respectively.  Other properties of the enzyme are described.
ER  -

TY  - JOUR
AU  - Bakthavatchalam, Y.D.
AU  - Veeraraghavan, B.
AU  - Peter, J.V.
AU  - Rajinikanth, J.
AU  - Inbanathan, F.Y.
AU  - Devanga, R.N.K.
AU  - Rajamani, S.S.K.
TI  - Novel Observations in 11 Heteroresistant Vancomycin-Intermediate Methicillin-Resistant Staphylococcus aureus Strains from South India.
JO  - Genome Announcements
PY  - 2016
SP  - e01425
EP  - e01416
VL  - 4
AB  - We report here the draft genome sequences of 11 heteroresistant vancomycin-intermediate
AB  - Staphylococcus aureus (hVISA) strains from bloodstream infection. All strains harbor mutations
AB  - in vraSR, graSR, walKR, and/or tcaRAB and are often implicated as the frequently mutated
AB  - candidate genes in hVISA phenotypes.
ER  -

TY  - JOUR
AU  - Bala, M.
AU  - Kumar, S.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38.
JO  - Genome Announcements
PY  - 2013
SP  - e0013913
EP  - e0013913
VL  - 1
AB  - We report the 6.1-Mb genome sequence of Rhodococcus ruber strain BKS 20-38, isolated from the
AB  - palm tree rhizosphere soil of Bhitarkanika National Park,
AB  - Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of
AB  - 6,126,900 bp, with a G+C content of 69.72%, 5,716 protein-coding genes, and 49
AB  - RNAs.
ER  -

TY  - JOUR
AU  - Bala, M.
AU  - Kumar, S.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40.
JO  - Genome Announcements
PY  - 2013
SP  - e0012813
EP  - e0012813
VL  - 1
AB  - We report the 5.8-Mb genome sequence of Rhodococcus qingshengii strain BKS 20-40, isolated
AB  - from a palm tree rhizosphere soil sample from Bhitarkanika National
AB  - Park, Odisha, India. The strain is capable of degrading cholesterol moiety. The
AB  - draft genome of strain BKS 20-40 consists of 6,601,618 bp, with 62.4% G+C
AB  - content.
ER  -

TY  - JOUR
AU  - Balabanov, V.P.
AU  - Kotova, V.Y.
AU  - Kholodii, G.Y.
AU  - Mindlin, S.Z.
AU  - Zavilgelsky, G.B.
TI  - A novel gene, ardD, determines antirestriction activity of the non-conjugative transposon Tn5053 and is located antisense within the tniA gene.
JO  - FEMS Microbiol. Lett.
PY  - 2012
SP  - 55
EP  - 60
VL  - 337
AB  - The mercury-resistance transposon Tn5053 inhibits restriction activity of the type I
AB  - restriction-modification endonuclease EcoKI in
AB  - Escherichia coli K12 cells. This is the first report of antirestriction
AB  - activity of a non-conjugative transposon. The gene (ardD) coding for
AB  - the antirestriction protein has been cloned. The ardD gene is located
AB  - within the tniA gene, coding for transposase, on the complementary
AB  - strand. The direction of transcription is opposite to transcription of
AB  - the tniA gene.
ER  -

TY  - JOUR
AU  - Balabanov, V.P.
AU  - Pustovoit, K.S.
AU  - Zavilgelsky, G.B.
TI  - Comparative analysis of antirestriction activity of the ArdA and ArdB proteins encoded by genes of the R64 transmissible plasmid (IncI1).
JO  - Mol. Biol. (Mosk)
PY  - 2012
SP  - 269
EP  - 275
VL  - 46
AB  - Antirestriction proteins ArdA and ArdB are specific inhibitors of type I
AB  - restriction-modification enzymes. The ardA and yfeB (ardB) genes were cloned from the
AB  - transmissible plasmid R64 in the pUC18 and pZE21 vectors. The R64 ArdA and ArdB proteins were
AB  - shown to inhibit only restriction activity of the type I restriction-modification enzyme
AB  - (EcoKI) in Escherichia coli K12 cells. In contrast to ArdA, ArdB inhibited EcoKI restriction
AB  - activity only at a high intracellular concentration. Antirestriction activity of ArdB did not
AB  - depend on the ClpXP protease. The yfeB (ardB) gene of the R64 plasmid is transcribed from a
AB  - weak promoter located upstream of yfeA.
ER  -

TY  - JOUR
AU  - Balachandran, M.
AU  - Riley, M.C.
AU  - Bemis, D.A.
AU  - Kania, S.A.
TI  - Complete Genome Sequence of Staphylococcus aureus Strain Wood 46.
JO  - Genome Announcements
PY  - 2017
SP  - e00087
EP  - e00017
VL  - 5
AB  - Here, we report the first complete genome sequence of the Staphylococcus aureus strain Wood
AB  - 46. Wood 46 has played an important role in understanding the
AB  - virulence and pathogenesis of S. aureus infections. This report will assist
AB  - efforts in vaccine development against methicillin-resistant S. aureus (MRSA)
AB  - infections.
ER  -

TY  - JOUR
AU  - Balado, M.
AU  - Lemos, M.L.
AU  - Osorio, C.R.
TI  - Integrating conjugative elements of the SXT/R391 family from fish-isolated Vibrios encode restriction-modification systems that confer resistance to bacteriophages.
JO  - FEMS Microbiol. Ecol.
PY  - 2013
SP  - 457
EP  - 467
VL  - 83
AB  - Integrating conjugative elements (ICEs) of the SXT/R391 family have been described in Vibrios,
AB  - mainly Vibrio cholerae, and other bacteria
AB  - as carriers of variable gene content conferring adaptive advantages
AB  - upon their hosts, including antimicrobial resistance and motility
AB  - regulation. However, our knowledge on their host range and ecological
AB  - significance is still limited. Here, we report the identification and
AB  - characterization of ICEVspPor3 and ICEValSpa1, two novel ICEs of the
AB  - SXT/R391 family from fish-isolated Vibrio splendidus and Vibrio
AB  - alginolyticus, respectively. We found that ICEVspPor3 carries
AB  - tetracycline and HgCl2 resistance determinants and can be transferred
AB  - by conjugation to Escherichia coli and to several species of marine
AB  - bacteria including some of the major bacterial fish pathogens in marine
AB  - aquaculture, whereas ICEValSpa1 lacks resistance genes. Interestingly,
AB  - both ICEs harbor genes encoding distinct restrictionmodification (RM)
AB  - systems. We demonstrate here that these RM systems, when expressed in
AB  - E. coli, confer protection to infection by T1 bacteriophage and by
AB  - environmental water bacteriophages. Our results provide evidences that
AB  - the variable gene content of ICEs of the SXT/R391 family encodes
AB  - fitness functions beyond those related to antimicrobial resistance and
AB  - motility regulation and suggest that the host range of these elements
AB  - in the marine environment might be broader than expected.
ER  -

TY  - JOUR
AU  - Balaji, V.
AU  - Rajenderan, S.
AU  - Anandan, S.
AU  - Biswas, I.
TI  - Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Clinical Strains Isolated from Southern India.
JO  - Genome Announcements
PY  - 2015
SP  - e01010
EP  - e01015
VL  - 3
AB  - Acinetobacter baumannii is an emerging nosocomial pathogen causing infections worldwide. In
AB  - this study, we determined the genome sequences of two multidrug-resistant A. baumannii
AB  - clinical strains isolated from a hospital in southern India. Genome analyses indicate that
AB  - both the strains harbor numerous horizontally transferred genetic elements and antibiotic
AB  - resistance cassettes.
ER  -

TY  - JOUR
AU  - Balakhonov, S.V.
AU  - Mironova, L.V.
AU  - Basov, E.A.
AU  - Gladkikh, A.S.
AU  - Afanasev, M.V.
AU  - Ganin, V.S.
AU  - Urbanovich, L.Y.
AU  - Sidorova, E.A.
TI  - Whole-Genome Sequencing of a Vibrio cholerae El Tor Strain Isolated in the Imported Cholera Focus in Siberia.
JO  - Genome Announcements
PY  - 2015
SP  - e01550
EP  - e01514
VL  - 3
AB  - The draft genome sequence of Vibrio cholerae O1 strain I-1263, isolated from a patient in the
AB  - imported focus in Siberia, was determined. The established
AB  - structural features of the mobile genetic elements indicate stage-by-stage
AB  - formation of a highly pathogenic V. cholerae clone and promote understanding of
AB  - the mechanisms of evolutionary pathogen transformations.
ER  -

TY  - JOUR
AU  - Balakrishna, P.A.
AU  - Jaya, K.A.
AU  - Thulasi, K.
AU  - Reghunathan, D.
AU  - Prasannakumar, M.
AU  - Kumarapillai, H.
TI  - Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage.
JO  - Genome Announcements
PY  - 2017
SP  - e01072
EP  - e01017
VL  - 5
AB  - Bacillus aryabhattai PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated
AB  - from domestic sewerage. Here, we report the 4.19-Mb draft
AB  - genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This
AB  - sequence will be helpful in the study of the high-level PHB accumulation
AB  - mechanism of the strain.
ER  -

TY  - JOUR
AU  - Balcarova, A.
AU  - Mrazek, J.
AU  - Kleinwachter, W.
AU  - Brabec, V.
TI  - Cleavage by restriction enzymes of DNA modified with the antitumour drug cis-diamminedichloroplatinum (II).
JO  - Gen. Physiol. Biophys.
PY  - 1992
SP  - 579
EP  - 588
VL  - 11
AB  - The effect of binding of an antitumour drug cis-diamminedichloroplatinum (II)
AB  - (cis-[Pt(NH3)2Cl2]) to DNA on cutting effectiveness of BamHI, EcoRI, and SalI restriction
AB  - endonucleases was quantitatively determined. The platinum complex inhibits the cleavage of
AB  - plasmid pHC624 DNA linearized by BglI restrictase. From the present results we conclude that
AB  - the yield of restriction endonuclease cleavage is also lowered if the platinum complex is
AB  - bound outside the recognition DNA sequence of these enzymes. We propose that the origin of
AB  - platinum adducts on DNA outside the recognition sequence can decrease the yield of restriction
AB  - enzyme cleavage via inducing a conformational perturbation in the DNA recognition sequence of
AB  - these enzymes and also via inhibition of the linear diffusion of these enzymes on DNA.
ER  -

TY  - JOUR
AU  - Baldauf, F.
AU  - Kiss, A.
TI  - Expression of cloned gene for methyltransferase from Bacillus subtilis bacteriophage SPbetaB.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1985
SP  - 26
EP  - 28
VL  - 2
AB  - Expression of the methyltransferase gene from Bacillus subtilis lysogenizing phage SPbetaB was
AB  - studied by analyzing the sensitivity of the hybrid plasmid DNAs to restriction by the enzymes
AB  - BspRI, HpaII and MspI.  This gene produces the methylase M.BsuPbetaBI with specificity for
AB  - 5'-GGCC.  The fragment carrying the SPbetaB derived gene also directs the synthesis in E.
AB  - coli of a second methylase activity (M.BsuPbetaBII) with 5'-CCGG specificity.  Indirect
AB  - evidence suggests that the two SPbetaB modification activities are encoded by the same gene.
ER  -

TY  - JOUR
AU  - Baldwin, D.N.
AU  - Shepherd, B.
AU  - Kraemer, P.
AU  - Hall, M.K.
AU  - Sycuro, L.K.
AU  - Pinto-Santini, D.M.
AU  - Salama, N.R.
TI  - Identification of Helicobacter pylori genes that contribute to stomach colonization.
JO  - Infect. Immun.
PY  - 2007
SP  - 1005
EP  - 1016
VL  - 75
AB  - Chronic infection of the human stomach by Helicobacter pylori leads to a variety of
AB  - pathological sequelae, including peptic ulcer and gastric
AB  - cancer, resulting in significant human morbidity and mortality. Several
AB  - genes have been implicated in disease related to H. pylori infection,
AB  - including the vacuolating cytotoxin and the cag pathogenicity island.
AB  - Other factors important for the establishment and maintenance of infection
AB  - include urease enzyme production, motility, iron uptake, and stress
AB  - response. We utilized a C57BL/6 mouse infection model to query a
AB  - collection of 2,400 transposon mutants in two different bacterial strain
AB  - backgrounds for H. pylori genetic loci contributing to colonization of the
AB  - stomach. Microarray-based tracking of transposon mutants allowed us to
AB  - monitor the behavior of transposon insertions in 758 different gene loci.
AB  - Of the loci measured, 223 (29%) had a predicted colonization defect. These
AB  - included previously described H. pylori virulence genes, genes implicated
AB  - in virulence in other pathogenic bacteria, and 81 hypothetical proteins.
AB  - We have retested 10 previously uncharacterized candidate colonization gene
AB  - loci by making independent null alleles and have confirmed their
AB  - colonization phenotypes by using competition experiments and by
AB  - determining the dose required for 50% infection. Of the genetic loci
AB  - retested, 60% have strain-specific colonization defects, while 40% have
AB  - phenotypes in both strain backgrounds for infection, highlighting the
AB  - profound effect of H. pylori strain variation on the pathogenic potential
AB  - of this organism.
ER  -

TY  - JOUR
AU  - Baldwin, G.S.
AU  - Gormley, N.A.
AU  - Halford, S.E.
TI  - Manganese(II) as a probe for the mechanism and specificity of restriction endonucleases.
JO  - Metal Ions in Biological Systems, Vol. 37: Manganese and its role in Biological Processes.
PY  - 2000
SP  - 345
EP  - 364
VL  - 37
AB  - A review of the role of metal ions in DNA cleavage by restriction enzymes and the experimental
AB  - possibilities offered by substituting manganese for magnesium.
ER  -

TY  - JOUR
AU  - Baldwin, G.S.
AU  - Halford, S.E.
TI  - Rapid reaction kinetics on the EcoRV restriction endonuclease.
JO  - Biochem. Soc. Trans.
PY  - 1994
SP  - 300S
EP  - 300S
VL  - 22
AB  - The EcoRV restriction endonuclease cleaves DNA between the central TpA step of its 6 bp
AB  - recognition sequence (GATATC) leaving blunt ends. It utilizes Mg2+ as its sole cofactor in the
AB  - hydrolysis of the phosphodiester backbone. Previous studies have provided a wealth of
AB  - information on the structure and function of the EcoRV restriction endonuclease. Perhaps the
AB  - most surprising aspect of EcoRV's properties is that it binds all DNA sequences with equal
AB  - affinity, yet it cleaves its target sequence with a 10^6 fold preference over the next best
AB  - site. The very high degree of specificity exhibited by EcoRV is thus derived from catalysis,
AB  - as opposed to sequence specific DNA binding. Nearly all of these previous studies were
AB  - performed under steady state conditions, and have consequently provided little insight into
AB  - the reaction pathway. We have used rapid reaction techniques under single turnover conditions
AB  - to resolve intermediates in the reaction pathway with the aim of determining the mechanism of
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Baldwin, G.S.
AU  - Kelly, S.M.
AU  - Price, N.C.
AU  - Wilson, G.W.
AU  - Connolly, B.A.
AU  - Artymiuk, P.J.
AU  - Hornby, D.P.
TI  - Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 545
EP  - 553
VL  - 235
AB  - The interaction of one of the two DNA methyltransferases encoded by the HgaI restriction and
AB  - modification system, M.HgaI-2, with substrates and substrate analogues is described. Circular
AB  - dichroism spectroscopy has been used to demonstrate that addition of the methyl donor,
AB  - S-adenosyl-L-methionine and the inhibitory substrate analogue sinefungin, both induce
AB  - conformational transitions in the protein in the absence of DNA. Moreover, the addition of DNA
AB  - is shown to enhance the apparent secondary structure of M.HgaI-2 whilst addition of sinefungin
AB  - or S-adenosyl-L-methionine reduces apparent secondary structure. The circular dichroism
AB  - spectrum of the abortive complex between the enzyme, DNA and sinefungin is dominated by the
AB  - conformational properties of the binary complex of enzyme and sinefungin alone. Addition of a
AB  - specific oligodeoxynucleotide duplex in which the target cytosine is replaced by a
AB  - pyrimidinone, leads to a further ligand induced conformational transition as determined by
AB  - electrophoretic analysis. The addition of sinefungin, or S-adenosyl-L-methionine, to M.HgaI-2
AB  - bound to the reactive oligodeoxynucleotide duplex, leads to yet another conformational
AB  - transition in the protein as determined by the differential susceptibility of ternary and
AB  - binary complexes to proteolysis. These experiments identify at least six ligand-inducible
AB  - conformational states of M.HgaI-2 and, in view of the sequence similarity amongst this class
AB  - of enzymes, suggest that conformational flexibility is a general feature of C-5
AB  - cytosine-specific DNA methyltransferases. Moreover, the substitution of the target cytosine by
AB  - a pyrimidinone mimics the effect of 5-azacytosine incorporation into DNA.
ER  -

TY  - JOUR
AU  - Baldwin, G.S.
AU  - Sessions, R.B.
AU  - Erskine, S.G.
AU  - Halford, S.E.
TI  - DNA cleavage by the EcoRV restriction endonuclease: Roles in divalent metal ions in specificity and catalysis.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 87
EP  - 103
VL  - 288
AB  - The roles of divalent metal ions in DNA cleavage by the EcoRV endonuclease were studied by
AB  - using Co2+ or Mn2+ as substitutes for the natural cofactor Mg2+.  In steady-state experiments
AB  - with a 12 bp oligonucleotide substrate, Co2+ yielded a similar turnover rate to that with
AB  - Mg2+, but Mn2+ gave a slower rate.  Single turnovers of EcoRV on this substrate were analyzed
AB  - by stopped-flow and quench-flow methods, to determine the rates for the formation of the
AB  - ternary enzyme-DNA-metal complex, the hydrolysis of the phosphodiester bonds and the
AB  - dissociation of the cleaved DNA.  With Co2+, all three steps had similar rates to those with
AB  - Mg2+.  In contrast, Mn2+ gave a faster rate for phosphodiester hydrolysis than either Mg2+ or
AB  - Co2+, but a slower rate for product dissociation, thus accounting for its low turnover rate.
AB  - Single turnovers on plasmids also yielded faster rates for substrate hydrolysis with Mn2+
AB  - compared to Mg2+ and Co2+.  Since Mn2+ gave the most rapid rates for the hydrolytic step,
AB  - despite being less electronegative than Co2+, the function of the metal ion at the active site
AB  - of EcoRV cannot be just the polarization of the scissile phosphate.  Moreover, the minimal
AB  - scheme for the Co2+-catalysed reaction requires two metal ions for DNA cleavage.  The metal
AB  - ions seem to be involved in the precise positioning of both the substrate and the water that
AB  - acts as the attacking nucleophile and in activating that water molecule.  A model is presented
AB  - to account for how two metal ions might fulfil these functions.
ER  -

TY  - JOUR
AU  - Baldwin, G.S.
AU  - Vipond, I.B.
AU  - Halford, S.E.
TI  - Rapid reaction analysis of the catalytic cycle of the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1995
SP  - 705
EP  - 714
VL  - 34
AB  - We have used the intrinsic tryptophan fluorescence of the EcoRV restriction endonuclease to
AB  - monitor changes in protein conformation during binding and cleavage of a duplex
AB  - oligodeoxynucleotide substrate. Appropriate conditions for single-turnover reactions were
AB  - first determined by steady-state kinetics. When single turnovers were monitored by
AB  - stopped-flow fluorescence, the mixing together of EcoRV oligonucleotide and MgCl2 resulted in
AB  - a rapid increase in tryptophan fluorescence followed by a slow decrease. Further analysis by
AB  - order-of-mixing and quench experiments showed that the transient increase in fluorescence was
AB  - due to a conformational change coupled to DNA binding, while the subsequent decay was
AB  - concomitant with phosphodiester hydrolysis. The rate of the latter step varied with the
AB  - concentration of Mg2+ ions, but another Mg2+-dependent transition was observed upon the
AB  - addition of MgCl2 to a preformed enzyme--DNA complex. These results lead to a reaction scheme
AB  - in which one Mg2+ binds to the active site prior to phosphodiester hydrolysis but a second
AB  - Mg2+ is then needed to carry out the hydrolytic reaction. This scheme is correlated to the
AB  - crystal structures of the EcoRV endonuclease and its complexes with DNA and Mg2+ ions.
ER  -

TY  - JOUR
AU  - Bale, A.
AU  - d'Alarcao, M.
AU  - Marinus, M.G.
TI  - Characterization of DNA adenine methylation mutants of Escherichia coli K12.
JO  - Mutat. Res.
PY  - 1979
SP  - 157
EP  - 165
VL  - 59
AB  - The phenotypic traits of 7 independently isolated dam mutants of Escherichia coli have been
AB  - examined. The mutant strains differ from the wildtype in the following respects: (1) decreased
AB  - DNA adenine methylase activity in vivo and in vitro; (2) a 14--85-fold increase in spontaneous
AB  - mutability; (3) decreased survival after ultraviolet irradiation; (4) a 10--21-fold increase
AB  - in spontaneous induction of lambda phage from lysogens; (5) a 3--17-fold increase in the level
AB  - of recombination; and (6) inviability of double mutants containing dam- and recB- or recC-.
AB  - Unmethylated fd phage chromosomes are able to replicate normally in dam- mutants. A mutant
AB  - strain in which the dcm gene is deleted is viable, showing that the dcm gene product is
AB  - dispensible for growth.
ER  -

TY  - JOUR
AU  - Balendiran, K.
AU  - Bonventre, J.
AU  - Knott, R.
AU  - Jack, W.
AU  - Benner, J.
AU  - Schildkraut, I.
AU  - Anderson, J.E.
TI  - Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site.
JO  - Proteins
PY  - 1994
SP  - 77
EP  - 79
VL  - 19
AB  - We have overexpressed the type II restriction endonuclease PvuII (R.PvuII) in E. coli,
AB  - prepared large amounts of the homogeneous enzyme, and crystallized it with an oligonucleotide
AB  - carrying a PvuII recognition site. The cocrystals are orthorhombic space group P212121 with
AB  - cell constants a = 95.8 A, b = 86.3 A, c = 48.5 A, and diffract X-rays to at least 2.7 A.
AB  - There is a complex of two protein subunits and one oligonucleotide duplex in the asymmetric
AB  - unit.
ER  -

TY  - JOUR
AU  - Balganesh, T.S.
AU  - Reiners, L.
AU  - Lauster, R.
AU  - Noyer-Weidner, M.
AU  - Wilke, K.
AU  - Trautner, T.A.
TI  - Construction and use of chimeric SPR/Phi3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.
JO  - EMBO J.
PY  - 1987
SP  - 3543
EP  - 3549
VL  - 6
AB  - Multispecific DNA methyltransferases (Mtases) of temperate Bacillus subtilis
AB  - phages SPR and Phi3T methylate the internal cytosine of the sequence GGCC.
AB  - They differ in their capacity to methylate additional sequences.  These are
AB  - CCGG anad CC(A/T)GG in SPR and GCNGC in Phi3T.  Introducing unique restriction
AB  - sites at equivalent locations within the two genes facilitated the construction
AB  - of chimeric genes.  These expressed Mtase activity at a level comparable to
AB  - that of the parental genes.  The methylation specificity of chimeric enzymes
AB  - was correlated with the location of chimeric fusions.  This analysis, which
AB  - also included the use of mutant genes, showed that domains involved in the
AB  - recognition of target sequences unique to each enezyme [CCGG, CC(A/T)GG or
AB  - GCNGC] are represented by the central non-conserved parts of the proteins,
AB  - whilst recognition of the sequence (GGCC), which is a target for both enzymes,
AB  - is determined by an adjacent conserved region.
ER  -

TY  - JOUR
AU  - Baliga, N.S.
AU  - Bonneau, R.
AU  - Facciotti, M.T.
AU  - Pan, M.
AU  - Glusman, G.
AU  - Deutsch, E.W.
AU  - Shannon, P.
AU  - Chiu, Y.
AU  - Weng, R.S.
AU  - Gan, R.R.
AU  - Hung, P.
AU  - Date, S.V.
AU  - Marcotte, E.
AU  - Hood, L.
AU  - Ng, W.V.
TI  - Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea.
JO  - Genome Res.
PY  - 2004
SP  - 2221
EP  - 2234
VL  - 14
AB  - We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a
AB  - halophilic archaeal isolate from the Dead Sea. The genome
AB  - is organized into nine circular replicons of varying G+C compositions
AB  - ranging from 54% to 62%. Comparison of the genome architectures of
AB  - Halobacterium sp. NRC-1 and H. marismortui suggests a common ancestor for
AB  - the two organisms and a genome of significantly reduced size in the
AB  - former. Both of these halophilic archaea use the same strategy of high
AB  - surface negative charge of folded proteins as means to circumvent the
AB  - salting-out phenomenon in a hypersaline cytoplasm. A multitiered
AB  - annotation approach, including primary sequence similarities, protein
AB  - family signatures, structure prediction, and a protein function
AB  - association network, has assigned putative functions for at least 58% of
AB  - the 4242 predicted proteins, a far larger number than is usually achieved
AB  - in most newly sequenced microorganisms. Among these assigned functions
AB  - were genes encoding six opsins, 19 MCP and/or HAMP domain signal
AB  - transducers, and an unusually large number of environmental response
AB  - regulators-nearly five times as many as those encoded in Halobacterium sp.
AB  - NRC-1-suggesting H. marismortui is significantly more physiologically
AB  - capable of exploiting diverse environments. In comparing the physiologies
AB  - of the two halophilic archaea, in addition to the expected extensive
AB  - similarity, we discovered several differences in their metabolic
AB  - strategies and physiological responses such as distinct pathways for
AB  - arginine breakdown in each halophile. Finally, as expected from the larger
AB  - genome, H. marismortui encodes many more functions and seems to have fewer
AB  - nutritional requirements for survival than does Halobacterium sp. NRC-1.
ER  -

TY  - JOUR
AU  - Ball, C.A.
AU  - Osuna, R.
AU  - Ferguson, K.C.
AU  - Johnson, R.C.
TI  - Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1992
SP  - 8043
EP  - 8056
VL  - 174
AB  - Fis is a small basic DNA-binding protein from Escherichia coli that was identified because of
AB  - its role in site-specific DNA recombination
AB  - reactions. Recent evidence indicates that Fis also participates in
AB  - essential cell processes such as rRNA and tRNA transcription and
AB  - chromosomal DNA replication. In this report, we show that Fis levels vary
AB  - dramatically during the course of cell growth and in response to changing
AB  - environmental conditions. When stationary-phase cells are subcultured into
AB  - a rich medium, Fis levels increase from less than 100 to over 50,000
AB  - copies per cell prior to the first cell division. As cells enter
AB  - exponential growth, nascent synthesis is largely shut off, and
AB  - intracellular Fis levels decrease as a function of cell division. Fis
AB  - synthesis also transiently increases when exponentially growing cells are
AB  - shifted to a richer medium. The magnitude of the peak of Fis synthesis
AB  - appears to reflect the extent of the nutritional upshift. fis mRNA levels
AB  - closely resemble the protein expression pattern, suggesting that
AB  - regulation occurs largely at the transcriptional level. Two RNA
AB  - polymerase-binding sites and at least six high-affinity Fis-binding sites
AB  - are present in the fis promoter region. We show that expression of the fis
AB  - operon is negatively regulated by Fis in vivo and that purified Fis can
AB  - prevent stable complex formation by RNA polymerase at the fis promoter in
AB  - vitro. However, autoregulation only partially accounts for the expression
AB  - pattern of Fis. We suggest that the fluctuations in Fis levels may serve
AB  - as an early signal of a nutritional upshift and may be important in the
AB  - physiological roles Fis plays in the cell.
ER  -

TY  - JOUR
AU  - Ball, N.
AU  - Streeter, S.D.
AU  - Kneale, G.G.
AU  - McGeehan, J.E.
TI  - Structure of the restriction-modification controller protein C.Esp1396I.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2009
SP  - 900
EP  - 905
VL  - 65
AB  - The controller protein of the Esp1396I restriction-modification (R-M) system binds
AB  - differentially to three distinct operator sequences
AB  - upstream of the methyltransferase (M) and endonuclease (R) genes to
AB  - regulate the timing of gene expression. The crystal structure of a
AB  - complex of the protein with two adjacent operator DNA sequences has
AB  - been reported; however, the structure of the free protein has not yet
AB  - been determined. Here, the crystal structure of the free protein is
AB  - reported, with seven dimers in the asymmetric unit. Two of the 14
AB  - monomers show an alternative conformation to the major conformer in
AB  - which the side chains of residues 43-46 in the loop region flanking the
AB  - DNA-recognition helix are displaced by up to 10 A. It is proposed that
AB  - the adoption of these two conformational states may play a role in
AB  - DNA-sequence promiscuity. The two alternative conformations are also
AB  - found in the R35A mutant structure, which is otherwise identical to the
AB  - native protein. Comparison of the free and bound protein structures
AB  - shows a 1.4 A displacement of the recognition helices when the dimer is
AB  - bound to its DNA target.
ER  -

TY  - JOUR
AU  - Ball, N.J.
AU  - McGeehan, J.E.
AU  - Streeter, S.D.
AU  - Thresh, S.J.
AU  - Kneale, G.G.
TI  - The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 10532
EP  - 10542
VL  - 40
AB  - Controller (C) proteins regulate the expression of restriction-modification (RM)  genes in a
AB  - wide variety of RM systems. However, the RM system Esp1396I is of
AB  - particular interest as the C protein regulates both the restriction endonuclease
AB  - (R) gene and the methyltransferase (M) gene. The mechanism of this finely tuned
AB  - genetic switch depends on differential binding affinities for the promoters
AB  - controlling the R and M genes, which in turn depends on differential DNA sequence
AB  - recognition and the ability to recognize dual symmetries. We report here the
AB  - crystal structure of the C protein bound to the M promoter, and compare the
AB  - binding affinities for each operator sequence by surface plasmon resonance.
AB  - Comparison of the structure of the transcriptional repression complex at the M
AB  - promoter with that of the transcriptional activation complex at the R promoter
AB  - shows how subtle changes in protein-DNA interactions, underpinned by small
AB  - conformational changes in the protein, can explain the molecular basis of
AB  - differential regulation of gene expression.
ER  -

TY  - JOUR
AU  - Balmain, A.
TI  - Exploring the bowels of DNA methylation.
JO  - Curr. Biol.
PY  - 1995
SP  - 1013
EP  - 1016
VL  - 5
AB  - The role DNA methylation is thought to have in cancer has become increasingly complex.  In the
AB  - late 1970s and early 1980s, it was shown that methylation of CpG sites in DNA can exert a
AB  - negative influence on gene expression.  Treatment of fibroblastic 10T1/2 cells in culture with
AB  - demethylating agents, such as 5-azacytidine, facilitated the emergence of novel muscle or
AB  - brain-related cell types, presumably by removing methyl groups from developmentally important
AB  - genes, allowing their expression.  One of the genes responsible for the myogenesis programme,
AB  - MyoD, was subsequently found to be methylated in the original 10T1/2 cells, but became
AB  - demethylated (and expressed) in their muscle progeny.  Relevance to cancer development was
AB  - suggested by the observation that tumour cells tend to have hypomethylated DNA, and
AB  - consequently begin to express genes that could confer a growth advantage.  Obligingly, some
AB  - genes that are hypomethylated in cancers turned out to be oncogenes, completing a satisfying
AB  - hypothetical loop.  This concept gained further support with the observation that carcinogenic
AB  - alkylating agents can induce DNA hypomethylation, in addition to their known mutagenic
AB  - effects, possibly by preventing cytosine methylation at sites adjacent to O6-alkylguanosine
AB  - residues.  The conclusion to be drawn from these studies was that hypomethylation of tumour
AB  - DNA would allow uncontrolled or aberrant oncogene expression, with obvious advantages for
AB  - tumour cell growth.
ER  -

TY  - JOUR
AU  - Baltrus, D.A.
AU  - Amieva, M.R.
AU  - Covacci, A.
AU  - Lowe, T.M.
AU  - Merrell, D.S.
AU  - Ottemann, K.M.
AU  - Stein, M.
AU  - Salama, N.R.
AU  - Guillemin, K.
TI  - The complete genome sequence of Helicobacter pylori strain G27.
JO  - J. Bacteriol.
PY  - 2009
SP  - 447
EP  - 448
VL  - 191
AB  - Helicobacter pylori is a gram-negative pathogen that colonizes the stomachs of over half the
AB  - world's population and causes a spectrum of gastric diseases
AB  - including gastritis, ulcers, and gastric carcinoma. The H. pylori species
AB  - exhibits unusually high levels of genetic variation between strains. Here we
AB  - announce the complete genome sequence of H. pylori strain G27, which has been
AB  - used extensively in H. pylori research.
ER  -

TY  - JOUR
AU  - Baltrus, D.A.
AU  - Nishimura, M.T.
AU  - Romanchuk, A.
AU  - Chang, J.H.
AU  - Mukhtar, M.S.
AU  - Cherkis, K.
AU  - Roach, J.
AU  - Grant, S.R.
AU  - Jones, C.D.
AU  - Dangl, J.L.
TI  - Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates.
JO  - PLoS Pathog.
PY  - 2011
SP  - e1002132
EP  - e1002132
VL  - 7
AB  - Closely related pathogens may differ dramatically in host range, but the
AB  - molecular, genetic, and evolutionary basis for these differences remains unclear.
AB  - In many Gram- negative bacteria, including the phytopathogen Pseudomonas
AB  - syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental
AB  - in structuring host range, and exhibit wide diversity between strains. To capture
AB  - the dynamic nature of virulence gene repertoires across P. syringae, we screened
AB  - 11 diverse strains for novel TTE families and coupled this nearly saturating
AB  - screen with the sequencing and assembly of 14 phylogenetically diverse isolates
AB  - from a broad collection of diseased host plants. TTE repertoires vary
AB  - dramatically in size and content across all P. syringae clades; surprisingly few
AB  - TTEs are conserved and present in all strains. Those that are likely provide
AB  - basal requirements for pathogenicity. We demonstrate that functional divergence
AB  - within one conserved locus, hopM1, leads to dramatic differences in
AB  - pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be
AB  - used to identify functionally critical residues of TTEs. The dynamism of the TTE
AB  - repertoire is mirrored by diversity in pathways affecting the synthesis of
AB  - secreted phytotoxins, highlighting the likely role of both types of virulence
AB  - factors in determination of host range. We used these 14 draft genome sequences,
AB  - plus five additional genome sequences previously reported, to identify the core
AB  - genome for P. syringae and we compared this core to that of two closely related
AB  - non-pathogenic pseudomonad species. These data revealed the recent acquisition of
AB  - a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes
AB  - a type IV secretion system and a diverse set of unknown proteins, which
AB  - dramatically increases both the genomic content of these strains and the
AB  - pan-genome of the species.
ER  -

TY  - JOUR
AU  - Baltrus, D.A.
AU  - Yourstone, S.
AU  - Lind, A.
AU  - Guilbaud, C.
AU  - Sands, D.C.
AU  - Jones, C.D.
AU  - Morris, C.E.
AU  - Dangl, J.L.
TI  - Draft Genome Sequences of a Phylogenetically Diverse Suite of Pseudomonas syringae Strains from Multiple Source Populations.
JO  - Genome Announcements
PY  - 2014
SP  - e01195
EP  - e01113
VL  - 2
AB  - Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of
AB  - Pseudomonas syringae, obtained from numerous environmental sources
AB  - and geographically proximate crop species. Overall, these sequences provide a
AB  - wealth of information about the differences (or lack thereof) between isolates
AB  - from disease outbreaks and those from other sources.
ER  -

TY  - JOUR
AU  - Baltz, R.H.
AU  - McHenney, M.A.
TI  - Transduction of plasmid DNA in Streptomyces spp.
JO  - Genetics and Molecular Biology of Industrial Microorganisms
PY  - 1989
SP  - 163
EP  - 167
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Ban, C.
AU  - Yang, W.
TI  - Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases.
JO  - EMBO J.
PY  - 1998
SP  - 1526
EP  - 1534
VL  - 17
AB  - MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA
AB  - mismatch repair to correct mistakes made during DNA replication in Escherichia coli.  MutH
AB  - cleaves a newly synthesized and unmethylated daughter strand 5' to the sequence d(GATC) in a
AB  - hemi-methylated duplex.  Activation of MutH requires the recognition of a DNA mismatch by MutS
AB  - and MutL.  We have crystallized MutH in two space groups and solved the structures at 1.7 and
AB  - 2.3 Angstrom resolution, respectively.  The active site of MutH is located at an interface
AB  - between two subdomains that pivot relative to one another, as revealed by comparison of the
AB  - crystal structures, and this presumably regulates the nuclease activity.  The relative motion
AB  - of the two subdomains in MutH correlates with the position of a protruding C-terminal helix.
AB  - This helix appears to act as a molecular lever through which MutS and MutL may communicate the
AB  - detection of a DNA mismatch and activate MutH.  With sequence homology to Sau3AI and
AB  - structural similarity to PvuII endonuclease, MutH is clearly related to these enzymes by
AB  - divergent evolution, and this suggests that type II restriction endonucleases evolved from a
AB  - common ancestor.
ER  -

TY  - JOUR
AU  - Ban, E.
AU  - Yoshida, Y.
AU  - Wakushima, M.
AU  - Wajima, T.
AU  - Hamabata, T.
AU  - Ichikawa, N.
AU  - Abe, H.
AU  - Horiguchi, Y.
AU  - Hara-Kudo, Y.
AU  - Kage-Nakadai, E.
AU  - Yamamoto, T.
AU  - Wada, T.
AU  - Nishikawa, Y.
TI  - Characterization of unstable pEntYN10 from enterotoxigenic Escherichia coli (ETEC) O169:H41.
JO  - Virulence
PY  - 2015
SP  - 735
EP  - 744
VL  - 6
AB  - Enterotoxigenic Escherichia coli (ETEC) serotype O169:H41 has been an extremely
AB  - destructive epidemic ETEC type worldwide. The strain harbors a large unstable
AB  - plasmid that is regarded as responsible for its virulence, although its etiology
AB  - has remained unknown. To examine its genetic background specifically on the
AB  - unstable retention and responsibility in the unique adherence to epithelial cells
AB  - and enterotoxin production, the complete sequence of a plasmid, pEntYN10,
AB  - purified from the serotype strain was determined. The length is 145,082 bp; its
AB  - GC content is 46.15%. It contains 182 CDSs, which include 3 colonization factors
AB  - (CFs), an enterotoxin, and large number of insertion sequences. The repertory of
AB  - plasmid stability genes was extraordinarily scant. Uniquely, results showed that
AB  - 3 CFs, CS6, CS8 (CFA/III)-like, and K88 (F4)-like were encoded redundantly in the
AB  - plasmid with unique variations among previously known subtypes. These three CFs
AB  - preserved their respective gene structures similarly to those of other ETEC
AB  - strains reported previously with unique sequence variations respectively. It is
AB  - particularly interesting that the K88-like gene cluster of pEntYN10 had 2
AB  - paralogous copies of faeG, which encodes the major component of fimbrial
AB  - structure. It remains to be verified how the unique variations found in the CFs
AB  - respectively affect the affinity to infected cells, host range, and virulence of
AB  - the ETEC strain.
ER  -

TY  - JOUR
AU  - Banas, J.A.
AU  - Biswas, S.
AU  - Zhu, M.
TI  - Effects of DNA Methylation on Expression of Virulence Genes in Streptococcus mutans.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 7236
EP  - 7242
VL  - 77
AB  - Bacteria produce a variety of enzymes capable of methylating DNA. In many species, the
AB  - majority of adenine methylation is accomplished by
AB  - the DNA adenine methylase Dam. In Escherichia coli the Dam methylase
AB  - plays roles in the initiation of replication, mismatch repair, and gene
AB  - regulation. In a number of other bacterial species, mutation or
AB  - overexpression of Dam leads to attenuation of virulence. Homologues of
AB  - the dam gene exist in some members of the Firmicutes, including
AB  - Streptococcus mutans, a dental pathogen. An S. mutans strain
AB  - inactivated in the dam gene (SMU.504; here designated damA) was
AB  - engineered, and phenotypes linked to cariogenicity were examined. A
AB  - prominent observation was that the damA mutant produced greater amounts
AB  - of glucan than the parental strain. Real-time PCR confirmed
AB  - upregulation of gtfB. To determine whether other loci were affected by
AB  - the damA mutation, a microarray analysis was carried out. Seventy genes
AB  - were upregulated at least 2-fold in the damA mutant, and 33 genes were
AB  - downregulated at least 2-fold. In addition to gtfB (upregulated
AB  - 2.6-fold; 1.7-fold when measured by real-time PCR), other upregulated
AB  - virulence factors included gbpC (upregulated 2.1-fold) and loci
AB  - predicted to encode bacteriocins (upregulated 2- to 7-fold). Various
AB  - sugar transport operons were also upregulated, the most extreme being
AB  - the cellobiose operon (upregulated nearly 40-fold). Expression of sacB,
AB  - encoding fructosyltransferase, was downregulated 2.4-fold. The sequence
AB  - 5'-GATC-3' appeared to constitute the recognition sequence for
AB  - methylation. These results provide evidence that DNA methylation in S.
AB  - mutans has a global effect on gene expression, including that of genes
AB  - associated with cariogenic potential.
ER  -

TY  - JOUR
AU  - Banas, J.A.
AU  - Ferretti, J.J.
AU  - Progulske-Fox, A.
TI  - Identification and sequence analysis of a methylase gene in Porphyromonas gingivalis.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4189
EP  - 4192
VL  - 19
AB  - A gene from the periodontal organism Porphyromonas gingivalis has been identified as encoding
AB  - a DNA methylase. The gene, referred to as pgiIM, has been sequenced and found to contain a
AB  - reading frame of 864 basepairs. The putative amino acid sequence of the encoded methylase was
AB  - 288 amino acids, and shared 47% and 31% homology with the Streptococcus pneumoniae DpnII and
AB  - E. coli Dam methylases, respectively. The activity and specificity of the PgiI methylase
AB  - (M.PgiI) was confirmed by cloning the gene into a dam- strain of E. coli (JM110) and
AB  - performing a restriction analysis on the isolated DNA with enzymes whose activities depended
AB  - upon the methylation state of the DNA. The data indicated that M.PgiI, like DpnII and Dam,
AB  - methylated the adenine residue within the sequence 5'-GATC-3'.
ER  -

TY  - JOUR
AU  - Banas, J.A.
AU  - Ferretti, J.J.
AU  - Progulske-Fox, A.
TI  - Identification of a methylase gene in Porphyromonas gingivalis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - 174
EP  - 174
VL  - 91
AB  - Sequence analysis of a portion of the P. gingivalis genome revealed an open reading frame
AB  - which encoded a protein whose putative amino acid sequence shared approximately fifty percent
AB  - and thirty percent identity with the Streptococcus pneumoniae Dpn methylase and Escherichia
AB  - coli Dam methylase, respectively. The P. gingivalis methylase was cloned into pUC18 and
AB  - transformed into E. coli JM110 (dam). Plasmid DNA isolated from transformants could be cut
AB  - with DpnI which only cuts at methylated 5'-GATC-3' sites, but not with NdeII which will not
AB  - cut at methylated 5'-GATC-3' sites. The methylase was expressed in both orientations. These
AB  - results suggest that the gene cloned from P. gingivalis specifies an adenine methylase that
AB  - recognizes the sequence 5'-GATC-3'.
ER  -

TY  - JOUR
AU  - Banavali, N.K.
AU  - MacKerell, A.D. Jr.
TI  - Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 141
EP  - 160
VL  - 319
AB  - Structural distortions of DNA are essential for its biological function due to the genetic
AB  - information of DNA not being physically accessible in the duplex state. Base flipping is one
AB  - of the simplest structural distortions of DNA and may represent an initial event in strand
AB  - separation required to access the genetic code. Flipping is also utilized by DNA-modifying and
AB  - repair enzymes to access specific bases. It is typically thought that base flipping (or
AB  - base-pair opening) occurs via the major groove whereas minor groove flipping is only possible
AB  - when mediated by DNA-binding proteins. Here, umbrella sampling with a novel center-of-mass
AB  - pseudodihedral reaction coordinate was used to calculate the individual potentials of mean
AB  - force (PMF) for flipping of the Watson-Crick (WC) paired C and G bases in the CCATGCGCTGAC DNA
AB  - dodecamer. The novel reaction coordinate allowed explicit investigation of the complete
AB  - flipping process via both the minor and major groove pathways. The minor and major groove
AB  - barriers to flipping are similar for C base flipping while the major groove barrier is
AB  - slightly lower for G base flipping. Minor groove flipping requires distortion of the WC
AB  - partner while the flipping base pulls away from its partner during major groove flipping. The
AB  - flipped states are represented by relatively flat free energy surfaces, with a small, local
AB  - minimum observed for the flipped G base. Conserved patterns of phosphodiester backbone
AB  - dihedral distortions during flipping indicate their essential role in the flipping process.
AB  - During flipping, the target base tracks along the respective grooves, leading to
AB  - hydrogen-bonding interactions with neighboring base-pairs. Such hydrogen-bonding interactions
AB  - with the neighboring sequence suggest a novel mechanism of sequence dependence in DNA
AB  - dynamics.
ER  -

TY  - JOUR
AU  - Bancroft, I.
AU  - Smith, R.J.
TI  - An analysis of restriction endonuclease sites in cyanophages infecting the heterocystous cyanobacteria Anabaena and Nostoc.
JO  - J. Gen. Virol.
PY  - 1988
SP  - 739
EP  - 743
VL  - 69
AB  - An analysis of restriction endonuclease cleavage of DNA isolated from cyanophages that infect
AB  - Anabaena and Nostoc species of cyanobacteria has provided evidence for counter-selection of
AB  - restriction endonuclease sites. These include sites containing subsequences which are
AB  - methylated by host (Anabaena PCC 7120) methylase(s) akin to the dam and dcm enzymes of
AB  - Escherichia coli. Other sites which are counter-selected have no common sequence structure.
AB  - The latter include those of the endogenous restriction endonucleases of the host, but other
AB  - absent sequences are not attributable to isoschizomers of any known Anabaena or Nostoc
AB  - restriction endonuclease. The cyanophages differ in their tolerance to DNA methylation.
AB  - Isolates A-4L, AN-13 and AN-23 do not tolerate adenosine methylation in the GATC sequence
AB  - whereas two cyanophages, A-1L and AN-10 (which are related) do tolerate dam-like methylation
AB  - of this sequence. In addition, A-1L allows cytosine methylation at GGCC sequences, but AN-10
AB  - has counter-selected these sequences and the remaining sites are not methylated. Analysis of
AB  - native and cloned A-4L DNA suggests that counter-selection has occurred against all sequences
AB  - which would be methylated by the host at either adenosine or cytosine nucleotides.
ER  -

TY  - JOUR
AU  - Bandaru, B.
TI  - Study of cytosine to thymine mutations at the sites of dcm and M.HpaII methyltransferases.
JO  - Diss. Abstr.
PY  - 1996
SP  - 2535B
EP  - 2536B
VL  - 57
AB  - It has been proposed that sites of methylation are "hotspots" for C to T mutations in
AB  - bacterial and human genomes.  I have developed a very sensitive genetic reversion assay that
AB  - quantifies the frequency of C to T mutations at various methylation sites and the repair of
AB  - resulting mismatches by DNA repair processes in Escherichia coli.  I have demonstrated that
AB  - the presence of HpaII methyltransferase (Mtase) in E. coli causes a substantial increase in C
AB  - to T mutations at CG sites.  This is similar to the known mutagenic effects of E. coli MTase
AB  - Dcm within its own recognition sequence.  Using this genetic system, I have tested a homolog
AB  - of an E. coli DNA repair gene in Haemophilus parainfluenzae for antimutagenic activity.
AB  - Unexpectedly, the homology was found to have little effect on the reversion frequency.  Using
AB  - this system, I have also shown that in vitro HpaII and SssI Mtases can convert cytosine to
AB  - uracil.  These studies define 5-methylcytosine as an intrinsic mutagen and further elaborate
AB  - the mutagenic potential of cytosine Mtases.  Multi-copy clones of E. coli DNA cytosine
AB  - methyltransferases (C5 Mtases) Dcm and M.EcoRII cause ~50 fold increase in C to T mutations at
AB  - their canonical site of methylation, 5'-CmeCAGG (meC is 5-methylcytosine).  I have observed
AB  - that these plasmids also cause transition mutations at the second cytosine in the sequences
AB  - CCGGG at ~10-fold lower frequency.  Similarly, M.HpaII was found to cause a significant
AB  - increase in C to T mutations at a CCAG site -- in addition to causing mutations at its
AB  - canonical site of methylation, CCGG.  Using a plasmid that substantially overprodces M.EcoRII,
AB  - I have shown that in vivo methylation at CCSGG (S is C or G) and other non-canonical sites
AB  - could be detected using a gel electrophoretic assay.  There is a direct correlation between
AB  - the level of M.EcoRII activity in cells, the extent of methylation at non-canonical sites and
AB  - frequency of mutations at these same sites.  Overproduction of M.EcoRII in cells also causes
AB  - degradation of DNA and induction of the SOS response.  I have shown that in vitro, M.EcoRII
AB  - methylates an oligonucleotide duplex containing a CCGGG site at a slow rate suggesting that
AB  - overproduction of the enzyme is essential for significant amounts of such methylation to
AB  - occur.  Together these results show that C5 Mtases occasionally methylate cellular DNA at
AB  - non-canonical sites and suggest that in E. coli methylation-specific restriction systems and
AB  - DNA mismatch correction systems may have evolved to accommodate this fact.  These results also
AB  - suggest that mutational effects of cytosine methyltransferases may be much broader than
AB  - previously imagined.
ER  -

TY  - JOUR
AU  - Bandaru, B.
AU  - Gopal, J.
AU  - Bhagwat, A.S.
TI  - Overproduction of DNA cytosine methyltransferases causes methylation and C-T mutations at non-canonical sites.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 7851
EP  - 7859
VL  - 271
AB  - Multicopy clones of Escherichia coli cytosine methyltransferases Dcm and EcoRII methylase (M.
AB  - EcoRII) cause ~50-fold increase in C-T mutations at their canonical site of methylation.
AB  - 5'-CmeCAGG (meC is 5-methylcytosine).  These plasmids also cause transition mutations at the
AB  - second cytosine in the sequences CCGGG at ~10-fold lower frequency.  Similarly, M.HpaII was
AB  - found to cause a significant increase in C-T mutations at a CCAG site, in addition to causing
AB  - mutations at its canonical site of methylation, CCGG.  Using a plasmid that substantially
AB  - overproduces M.EcoRII, in vivo methylation at CCSGG (S is C or G) and other noncanonical sites
AB  - could be detected using a gel electrophoretic assay.  There is a direct correlation between
AB  - the level of M.EcoRII activity in cells, the extent of methylation at non-canonical sites and
AB  - frequency of mutations at these same sites.  Overproduction of M.EcoRII in cells also causes
AB  - degradation of DNA and induction of the SOS response.  In vitro, M. EcoRII methylates an
AB  - oligonucleotide duplex containing a CCGGG site at a slow rate, suggesting that overproduction
AB  - of the enzyme is essential for significant amounts of such methylation to occur.  Together
AB  - these results show that cytosine methyltransferases occasionally methylate cellular DNA at
AB  - non-canonical sites and suggest that in E. coli, methylation-specific restriction systems and
AB  - sequence specificity of the DNA mismatch correction systems may have evolved to accommodate
AB  - this fact.  These results also suggest that mutational effects of cytosine methyltransferases
AB  - may be much broader than previously imagined.
ER  -

TY  - JOUR
AU  - Bandaru, B.
AU  - Wyszynski, M.
AU  - Bhagwat, A.S.
TI  - HpaII methyltransferase is mutagenic in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1995
SP  - 2950
EP  - 2952
VL  - 177
AB  - A genetic reversion assay to study C-to-T mutations within CG sites in DNA is described. It
AB  - was used to demonstrate that the presence of HpaII methyltransferase (MTase) in Escherichia
AB  - coli causes a substantial increase in C-to-T mutations at CG sites. This is similar to the
AB  - known mutagenic effects of E. coli MTase Dcm within its own recognition sequence. With this
AB  - genetic system, a homolog of an E. coli DNA repair gene in Haemophilus parainfluenzae was
AB  - tested for antimutagenic activity. Unexpectedly, the homolog was found to have little effect
AB  - on the reversion frequency. The system was also used to show that HpaII and SssI MTases can
AB  - convert cytosine to uracil in vitro. These studies define 5-methylcytosine as an intrinsic
AB  - mutagen and further elaborate the mutagenic potential of cytosine MTases.
ER  -

TY  - JOUR
AU  - Bandyopadhyay, P.K.
AU  - Studier, F.W.
AU  - Hamilton, D.L.
AU  - Yuan, R.
TI  - Inhibition of the type I restriction-modification enzymes EcoB and EcoK by the gene 0.3 protein of bacteriophage T7.
JO  - J. Mol. Biol.
PY  - 1985
SP  - 567
EP  - 578
VL  - 182
AB  - The gene 0.3 protein of bacteriophage T7 is a potent inhibitor of the
AB  - restriction-modification enzymes EcoB and EcoK, both in vivo and in vitro.  We have
AB  - analyzed the ability of purified 0.3 protein to inhibit different steps in the reactions of
AB  - EcoB
AB  - and EcoK with DNA.  Most of our experiments were done with EcoK, but selected tests
AB  - with EcoB indicate that the two enzymes are affected by 0.3 protein in the same way.
AB  - Purified 0.3 protein binds tightly to free enzyme, apparently to one of the small subunits,
AB  - and prevents it from binding to DNA.  If EcoK is allowed to form specific recognition
AB  - complexes with unmodified DNA before 0.3 protein is added, relatively low levels of 0.3
AB  - protein prevent the nuclease activity that would otherwise appear upon addition of ATP, but
AB  - considerably higher levels are needed to prevent formation of filter-binding complexes or
AB  - ATPase activity.  This, together with other results, suggests that the binding site for 0.3
AB  - protein is protected in recognition complexes and in the early stages of the ATP-stimulated
AB  - reactions, but that it becomes accessible again before cleavage of the DNA, perhaps after
AB  - the translocation step.  If added after the nuclease reaction is substantially over, 0.3
AB  - protein
AB  - has little effect on ATPase activity, and indeed, the subunit having the binding site for 0.3
AB  - protein apparently dissociates from the enzyme-DNA complex.  The methylase activity of
AB  - EcoK on hemi-methylated recognition sites is strongly inhibited by 0.3 protein added at any
AB  - stage of the reaction.
ER  -

TY  - JOUR
AU  - Bandyopadhyay, R.
AU  - Das, J.
TI  - The DNA adenine methyltransferase-encoding gene (dam) of Vibrio cholerae.
JO  - Gene
PY  - 1994
SP  - 67
EP  - 71
VL  - 140
AB  - The DNA adenine methyltransferase (MTase)-encoding gene (dam) of Vibrio cholerae, an organism
AB  - belonging to the family Vibrionaceae, has been cloned and the complete nucleotide (nt)
AB  - sequence determined. V. cholerae dam encodes a 21.5-kDa protein and is directly involved in
AB  - methyl-directed DNA mismatch repair. It can substitute for the Escherichia coli enzyme and can
AB  - suppress the phenotypic traits associated with E. coli dam mutants. Overproduction of V.
AB  - cholerae Dam MTase does not result in hypermutability in either V. cholerae or E. coli cells.
AB  - Overproduction of V. cholerae Dam in a pUC plasmid, however, fails to suppress the
AB  - 2-aminopurine (2-AP0-sensitive phenotype of E. coli dam mutants. Homology between the nt and
AB  - deduced amino acid (aa) sequences of the E. coli and V. cholerae dam genes is only 30-35%.
ER  -

TY  - JOUR
AU  - Bandyopadhyay, R.
AU  - Sengupta, A.
AU  - Das, J.
TI  - A mutation in the dam gene of Vibrio cholerae: 2-aminopurine sensitivity with intact GATC methylase activity.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1989
SP  - 561
EP  - 567
VL  - 165
AB  - Vibrio cholerae mutants sensitive to 2-aminopurine (2AP) but with DNA adenine methylase
AB  - activity similar to parental cells have been isolated. The mutant strains were sensitive to
AB  - ultraviolet light (UV), methyl methane sulphonate (MMS) and 9-aminoacridine. The spontaneous
AB  - mutation frequency of the mutants were not significantly affected. Attempts to isolate dam V.
AB  - cholerae cells by screening 2AP sensitive cells have not been successful. All of the mutant
AB  - phenotypes could be suppressed by introducing the plasmid pRB103 carrying the dam gene of
AB  - Escherichia coli into the mutant cells.
ER  -

TY  - JOUR
AU  - Bandyopadhyay, S.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Pannonibacter indicus Strain HT23T (DSM 23407T), a Highly Arsenate-Tolerant Bacterium Isolated from a Hot Spring in India.
JO  - Genome Announcements
PY  - 2017
SP  - e00283
EP  - e00217
VL  - 5
AB  - Pannonibacter indicus strain HT23T, a highly arsenate-tolerant bacterium, was isolated from a
AB  - tropical hot spring. The estimated genome is 4.2 Mb with 3,818
AB  - protein-coding sequences containing putative genes, some of which are involved in
AB  - arsenate resistance.
ER  -

TY  - JOUR
AU  - Banerjee, A.
AU  - Halder, U.
AU  - Chaudhry, V.
AU  - Varshney, R.K.
AU  - Mantri, S.
AU  - Bandopadhyay, R.
TI  - Draft Genome Sequence of the Nonpathogenic, Thermotolerant, and Exopolysaccharide-Producing Bacillus anthracis Strain PFAB2 from Panifala Hot Water Spring in West Bengal, India.
JO  - Genome Announcements
PY  - 2016
SP  - e01346
EP  - e01316
VL  - 4
AB  - Bacillus anthracis is the causative agent of fatal anthrax in both animals and humans. It is
AB  - prevalently pathogenic. Here, we present a Bacillus anthracis PFAB2 strain from a relatively
AB  - unexplored Panifala hot water spring in West Bengal, India. It is nonpathogenic,
AB  - exopolysaccharide producing, and thermotolerant in nature.
ER  -

TY  - JOUR
AU  - Banerjee, A.
AU  - Rao, D.N.
TI  - Functional analysis of an acid adaptive DNA adenine methyltransferase from Helicobacter pylori 26695.
JO  - PLoS ONE
PY  - 2011
SP  - e16810
EP  - e16810
VL  - 6
AB  - HP0593 DNA-(N(6)-adenine)-methyltransferase (HP0593 MTase) is a member of a Type  III
AB  - restriction-modification system in Helicobacter pylori strain 26695. HP0593
AB  - MTase has been cloned, overexpressed and purified heterologously in Escherichia
AB  - coli. The recognition sequence of the purified MTase was determined as
AB  - 5'-GCAG-3'and the site of methylation was found to be adenine. The activity of
AB  - HP0593 MTase was found to be optimal at pH 5.5. This is a unique property in
AB  - context of natural adaptation of H. pylori in its acidic niche. Dot-blot assay
AB  - using antibodies that react specifically with DNA containing m6A modification
AB  - confirmed that HP0593 MTase is an adenine-specific MTase. HP0593 MTase occurred
AB  - as both monomer and dimer in solution as determined by gel-filtration
AB  - chromatography and chemical-crosslinking studies. The nonlinear dependence of
AB  - methylation activity on enzyme concentration indicated that more than one
AB  - molecule of enzyme was required for its activity. Analysis of initial velocity
AB  - with AdoMet as a substrate showed that two molecules of AdoMet bind to HP0593
AB  - MTase, which is the first example in case of Type III MTases. Interestingly,
AB  - metal ion cofactors such as Co(2+), Mn(2+), and also Mg(2+) stimulated the HP0593
AB  - MTase activity. Preincubation and isotope partitioning analyses clearly indicated
AB  - that HP0593 MTase-DNA complex is catalytically competent, and suggested that DNA
AB  - binds to the MTase first followed by AdoMet. HP0593 MTase shows a distributive
AB  - mechanism of methylation on DNA having more than one recognition site.
AB  - Considering the occurrence of GCAG sequence in the potential promoter regions of
AB  - physiologically important genes in H. pylori, our results provide impetus for
AB  - exploring the role of this DNA MTase in the cellular processes of H. pylori.
ER  -

TY  - JOUR
AU  - Banerjee, S.
AU  - Chowdhury, R.
TI  - An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae.
JO  - Microbiology
PY  - 2006
SP  - 1055
EP  - 1062
VL  - 152
AB  - 5-Methyl cytosine (m5C was detected in genomic DNA of the enteric pathogen Vibrio cholerae by
AB  - HPLC analysis and immunoblotting with
AB  - m5C-specific antibody. Although cleavage with the restriction
AB  - endonuclease EcoRII revealed the absence of a Dcm homologue in V.
AB  - cholerae, analysis of the genome sequence indicated the presence of a
AB  - gene, designated in this study as vchM, which encodes a DNA
AB  - (cytosine-5-)-methyltransferase (m5C-MTase) designated M.Vch. M.Vch is
AB  - not associated with a restriction endonuclease or a mismatch very short
AB  - patch repair (Vsr)-like endonuclease and is hence an 'orphan' or
AB  - solitary MTase, although analysis of a phylogenetic tree indicated that
AB  - related cytosine MTases are all components of restriction-modification
AB  - systems. M.Vch recognizes and methylates the first 5' C in the
AB  - degenerate sequence 5'-RCCGGY-3'. RT-PCR analysis suggested that vchM
AB  - gene expression is increased during the stationary phase of growth.
AB  - During stationary phase, the spontaneous mutation frequency in the V.
AB  - cholerae wild-type strain was significantly higher than in the
AB  - corresponding vchM mutant strain, suggesting that the presence of M.Vch
AB  - and the absence of a very short patch (VSP) repair-like system imposes
AB  - upon V. cholerae a mutator phenotype.
ER  -

TY  - JOUR
AU  - Banerjee, S.
AU  - Fisher, O.
AU  - Lohia, A.
AU  - Ankri, S.
TI  - Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix  attachment region (S/MAR).
JO  - Mol. Biochem. Parasitol.
PY  - 2005
SP  - 91
EP  - 97
VL  - 139
AB  - The protozoan parasite Entamoeba histolytica express a cytosine-5 DNA methyltransferase
AB  - (Ehmeth) that belongs to the DNMT2 protein family.
AB  - The biological function of members of this DNMT2 family is unknown. In
AB  - the present study, we have demonstrated that Ehmeth is a nuclear matrix
AB  - protein. Indeed, we showed by south-western analysis and yeast
AB  - one-hybrid system that Ehmeth binds to EhMRS2, a DNA element which
AB  - contains the eukaryotic consensus scaffold/inatrix attachment regions
AB  - (S/MAR) bipartite recognition sequences. S/MARs have been implicated in
AB  - a variety of important functions, such as genome organization and gene
AB  - expression. The methylation status of cytosine located within EhMRS2
AB  - was analyzed by bisulfite genomic sequencing. We observed the presence
AB  - of methylated cytosine within the 3'-end of EhMRS2. These data provide
AB  - the first evidence that a member of the DNMT2 family interacts with a
AB  - S/MAR containing DNA element.
ER  -

TY  - JOUR
AU  - Banerjee, S.
AU  - Petronella, N.
AU  - Chew, L.C.
AU  - Farber, J.
TI  - Draft Genome Sequences of Four Vibrio parahaemolyticus Isolates from Clinical Cases in Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e01482
EP  - e01414
VL  - 3
AB  - Vibrio parahaemolyticus is a leading cause of bacterial gastroenteritis following ingestion of
AB  - contaminated seafood. This report presents the draft genome
AB  - sequences of four clinical strains of V. parahaemolyticus isolated in Canada. All
AB  - four strains lack traditional pathogenic markers and possess uniquely individual
AB  - characteristics identified using other typing criteria.
ER  -

TY  - JOUR
AU  - Banfalvi, G.
AU  - Sarkar, N.
TI  - Effect of mercury substitution of DNA on its susceptibility to cleavage by restriction endonucleases.
JO  - DNA Cell Biol.
PY  - 1995
SP  - 445
EP  - 450
VL  - 14
AB  - Mercurated DNA was synthesized in vitro by substituting Hg-dCTP or Hg-dUMP for dCTP in one
AB  - strand of M13mp8DNA in a DNA polymerase I reaction. Restriction enzymes, including SmaI, PstI,
AB  - BamHI, HindIII, and HincII, were completely inactive when their recognition sites were fully
AB  - substituted with Hg-dCMP, while Hg-dUMP containing DNA was hydrolyzed to some extent. Under
AB  - conditions favoring star activities, or when DNA was substituted with a low level of
AB  - mercury-nucleotide, DNA was cleaved by restriction enzymes. Susceptibility to degrading and
AB  - synthesizing enzymes and insensitivity to restriction endonucleases of fully mercurated DNA
AB  - makes mercuration an attractive molecular "tag" for in vitro manipulation and selective
AB  - isolation of Hg-DNA.
ER  -

TY  - JOUR
AU  - Banfield, J.F.
AU  - Anantharaman, K.
AU  - Williams, K.H.
AU  - Thomas, B.C.
TI  - Complete 4.55-Megabase-Pair Genome of 'Candidatus Fluviicola riflensis,' Curated  from Short-Read Metagenomic Sequences.
JO  - Genome Announcements
PY  - 2017
SP  - e01299
EP  - e01217
VL  - 5
AB  - We report the 4.55-Mbp genome of 'Candidatus Fluviicola riflensis' (Bacteroidetes) that was
AB  - manually curated to completion from Illumina data. 'Ca
AB  - Fluviicola riflensis' is a facultative anaerobe. Its ability to grow over a range
AB  - of O2 levels may favor its proliferation in an aquifer adjacent to the Colorado
AB  - River in the United States.
ER  -

TY  - JOUR
AU  - Bang, M.S.
AU  - Jeong, H.W.
AU  - Lee, Y.J.
AU  - Lee, S.J.
AU  - Lee, S.C.
AU  - Shin, J.I.
AU  - Oh, C.H.
TI  - Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_02, Isolated from Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Poly-gamma-Glutamic Acid Activity.
JO  - Genome Announcements
PY  - 2018
SP  - e00525
EP  - e00518
VL  - 6
AB  - The complete genome sequence of Bacillus subtilis strain DKU_NT_02, isolated from traditional
AB  - Korean food using soybeans (chung-gook-jang), is presented here. This
AB  - strain was chosen to help identify genetic factors with high-quality
AB  - poly-gamma-glutamic acid (gammaPGA) activity.
ER  -

TY  - JOUR
AU  - Bang, M.S.
AU  - Jeong, H.W.
AU  - Lee, Y.J.
AU  - Oh, H.Y.
AU  - Lee, S.J.
AU  - Shim, M.S.
AU  - Shin, J.I.
AU  - Oh, C.H.
TI  - Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang).
JO  - Genome Announcements
PY  - 2017
SP  - e00769
EP  - e00717
VL  - 5
AB  - Here, we report the whole-genome sequence of Bacillus subtilis strain DKU_NT_01 isolated from
AB  - traditional Korean food containing soybean (chung-gook-jang). The
AB  - de novo genome of Bacillus subtilis strain DKU_NT_01 has one contig and G+C
AB  - content of 55.4%, is 4,954,264 bp in length, and contains 5,011 coding sequences
AB  - (CDSs).
ER  -

TY  - JOUR
AU  - Bangera, S.R.
AU  - Umakanth, S.
AU  - Mukhopadhyay, A.K.
AU  - Leekitcharoenphon, P.
AU  - Chowdhury, G.
AU  - Hendriksen, R.S.
AU  - Ballal, M.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from India.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00990
EP  - e00918
VL  - 7
AB  - Salmonella enterica subsp. enterica serotype Typhimurium sequence type 313 (ST313) is most
AB  - commonly associated with invasive nontyphoidal Salmonella disease
AB  - in Africa among patients with HIV infection and malignancy. Here, we report a
AB  - draft genome sequence of S. Typhimurium ST313, isolated from an elderly
AB  - immunosuppressed patient from India with non-Hodgkins lymphoma.
ER  -

TY  - JOUR
AU  - Banks, D.J.
AU  - Porcella, S.F.
AU  - Barbian, K.D.
AU  - Beres, S.B.
AU  - Philips, L.E.
AU  - Voyich, J.M.
AU  - DeLeo, F.R.
AU  - Martin, J.M.
AU  - Somerville, G.A.
AU  - Musser, J.M.
TI  - Progress toward Characterization of the Group A Streptococcus Metagenome: Complete Genome Sequence of a Macrolide-Resistant Serotype M6 Strain.
JO  - J. Infect. Dis.
PY  - 2004
SP  - 727
EP  - 738
VL  - 190
AB  - We describe the genome sequence of a macrolide-resistant strain (MGAS10394) of serotype M6
AB  - group A Streptococcus (GAS). The genome is
AB  - 1,900,156 bp in length, and 8 prophage-like elements or remnants compose
AB  - 12.4% of the chromosome. A 8.3-kb prophage remnant encodes the SpeA4
AB  - variant of streptococcal pyrogenic exotoxin A. The genome of strain
AB  - MGAS10394 contains a chimeric genetic element composed of prophage genes
AB  - and a transposon encoding the mefA gene conferring macrolide resistance.
AB  - This chimeric element also has a gene encoding a novel surface-exposed
AB  - protein (designated "R6 protein"), with an LPKTG cell-anchor motif located
AB  - at the carboxyterminus. Surface expression of this protein was confirmed
AB  - by flow cytometry. Humans with GAS pharyngitis caused by serotype M6
AB  - strains had antibody against the R6 protein present in convalescent, but
AB  - not acute, serum samples. Our studies add to the theme that GAS
AB  - prophage-encoded extracellular proteins contribute to host-pathogen
AB  - interactions in a strain-specific fashion.
ER  -

TY  - JOUR
AU  - Banks, D.J.
AU  - Porcella, S.F.
AU  - Barbian, K.D.
AU  - Martin, J.M.
AU  - Musser, J.M.
TI  - Structure and distribution of an unusual chimeric genetic element encoding macrolide resistance in phylogenetically diverse clones of group A Streptococcus.
JO  - J. Infect. Dis.
PY  - 2003
SP  - 1899
EP  - 1909
VL  - 188
AB  - The resistance of group A Streptococcus (GAS) to macrolide antibiotics is now a worldwide
AB  - problem. Preliminary sequencing of the genome of an
AB  - erythromycin-resistant serotype M6 clone that was responsible for a
AB  - pharyngitis outbreak in Pittsburgh, Pennsylvania, was conducted to
AB  - determine the structure of the genetic element containing the mefA gene,
AB  - which encodes a macrolide efflux protein. The mefA gene is associated with
AB  - a 58.8-kb chimeric genetic element composed of a transposon inserted into
AB  - a prophage. This element also encodes a putative extracellular protein
AB  - with a cell-wall anchoring motif (LPKTG) located at the carboxyterminus.
AB  - The mefA element was present in phylogenetically diverse GAS strains
AB  - isolated throughout the United States. Culture supernatants, prepared
AB  - after mitomycin C treatment, of a strain representing the outbreak clone
AB  - contained mefA element DNA in a DNAse-resistant form. Together, these data
AB  - provide new information about the molecular genetic basis of macrolide
AB  - resistance and dissemination in GAS strains.
ER  -

TY  - JOUR
AU  - Bannam, T.L.
AU  - Teng, W.L.
AU  - Bulach, D.
AU  - Lyras, D.
AU  - Rood, J.I.
TI  - Functional Identification of Conjugation and Replication Regions of the Tetracycline Resistance Plasmid pCW3 from Clostridium perfringens.
JO  - J. Bacteriol.
PY  - 2006
SP  - 4942
EP  - 4951
VL  - 188
AB  - Clostridium perfringens causes fatal human infections, such as gas
AB  - gangrene, as well as gastrointestinal diseases in both humans and animals.
AB  - Detailed molecular analysis of the tetracycline resistance plasmid pCW3
AB  - from C. perfringens has shown that it represents the prototype of a unique
AB  - family of conjugative antibiotic resistance and virulence plasmids. We
AB  - have identified the pCW3 replication region by deletion and transposon
AB  - mutagenesis and showed that the essential rep gene encoded a basic protein
AB  - with no similarity to any known plasmid replication proteins. An 11-gene
AB  - conjugation locus containing 5 genes that encoded putative proteins with
AB  - similarity to proteins from the conjugative transposon Tn916 was
AB  - identified, although the genes' genetic arrangements were different.
AB  - Functional genetic studies demonstrated that two of the genes in this
AB  - transfer clostridial plasmid (tcp) locus, tcpF and tcpH, were essential
AB  - for the conjugative transfer of pCW3, and comparative analysis confirmed
AB  - that the tcp locus was not confined to pCW3. The conjugation region was
AB  - present on all known conjugative plasmids from C. perfringens, including
AB  - an enterotoxin plasmid and other toxin plasmids. These results have
AB  - significant implications for plasmid evolution, as they provide evidence
AB  - that a nonreplicating Tn916-like element can evolve to become the
AB  - conjugation locus of replicating plasmids that carry major virulence genes
AB  - or antibiotic resistance determinants.
ER  -

TY  - JOUR
AU  - Bannam, T.L.
AU  - Yan, X.X.
AU  - Harrison, P.F.
AU  - Seemann, T.
AU  - Keyburn, A.L.
AU  - Stubenrauch, C.
AU  - Weeramantri, L.H.
AU  - Cheung, J.K.
AU  - McClane, B.A.
AU  - Boyce, J.D.
AU  - Moore, R.J.
AU  - Rood, J.I.
TI  - Necrotic Enteritis-Derived Clostridium perfringens Strain with Three Closely Related Independently Conjugative Toxin and Antibiotic Resistance Plasmids.
JO  - MBio
PY  - 2011
SP  - e00190
EP  - e00111
VL  - 2
AB  - The pathogenesis of avian necrotic enteritis involves NetB, a pore-forming
AB  - toxin produced by virulent avian isolates of Clostridium perfringens type
AB  - A. To determine the location and mobility of the netB structural gene, we
AB  - examined a derivative of the tetracycline-resistant necrotic enteritis
AB  - strain EHE-NE18, in which netB was insertionally inactivated by the
AB  - chloramphenicol and thiamphenicol resistance gene catP. Both tetracycline
AB  - and thiamphenicol resistance could be transferred either together or
AB  - separately to a recipient strain in plate matings. The separate
AB  - transconjugants could act as donors in subsequent matings, which
AB  - demonstrated that the tetracycline resistance determinant and the netB
AB  - gene were present on different conjugative elements. Large plasmids were
AB  - isolated from the transconjugants and analyzed by high-throughput
AB  - sequencing. Analysis of the resultant data indicated that there were
AB  - actually three large conjugative plasmids present in the original strain,
AB  - each with its own toxin or antibiotic resistance locus. Each plasmid
AB  - contained a highly conserved 40-kb region that included plasmid
AB  - replication and transfer regions that were closely related to the 47-kb
AB  - conjugative tetracycline resistance plasmid pCW3 from C. perfringens. The
AB  - plasmids were as follows: (i) a conjugative 49-kb tetracycline resistance
AB  - plasmid that was very similar to pCW3, (ii) a conjugative 82-kb plasmid
AB  - that contained the netB gene and other potential virulence genes, and
AB  - (iii) a 70-kb plasmid that carried the cpb2 gene, which encodes a
AB  - different pore-forming toxin, beta2 toxin. IMPORTANCE: The anaerobic
AB  - bacterium Clostridium perfringens can cause an avian gastrointestinal
AB  - disease known as necrotic enteritis. Disease pathogenesis is not well
AB  - understood, although the plasmid-encoded pore-forming toxin NetB, is an
AB  - important virulence factor. In this work, we have shown that the plasmid
AB  - that carries the netB gene is conjugative and has a 40-kb region that is
AB  - very similar to replication and transfer regions found within each of the
AB  - sequenced conjugative plasmids from C. perfringens. We also showed that
AB  - this strain contained two additional large plasmids that were also
AB  - conjugative and carried a similar 40-kb region. One of these plasmids
AB  - encoded beta2 toxin, and the other encoded tetracycline resistance. To our
AB  - knowledge, this is the first report of a bacterial strain that carries
AB  - three closely related but different independently conjugative plasmids.
AB  - These results have significant implications for our understanding of the
AB  - transmission of virulence and antibiotic resistance genes in pathogenic
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Bannantine, J.P.
AU  - Bayles, D.O.
AU  - Robbe-Austerman, S.
AU  - Burrell, A.M.
AU  - Stabel, J.R.
TI  - Draft Genome Sequence of a Mycobacterium avium Complex Isolate from a Broadbill Bird.
JO  - Genome Announcements
PY  - 2014
SP  - e01268
EP  - e01213
VL  - 2
AB  - We report the draft genome sequence of a Mycobacterium avium complex isolate. This isolate has
AB  - an estimated genome size of 5.1 Mb with an average GC content of
AB  - 68.9% and is predicted to carry 4,497 protein-encoding genes and 317 pseudogenes.
ER  -

TY  - JOUR
AU  - Bannantine, J.P.
AU  - Li, L.
AU  - Mwangi, M.
AU  - Cote, R.
AU  - Raygoza, G.J.A.
AU  - Kapur, V.
TI  - Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk.
JO  - Genome Announcements
PY  - 2014
SP  - e01252
EP  - e01213
VL  - 2
AB  - Mycobacterium avium subsp. paratuberculosis is the etiologic agent of Johne's disease in
AB  - ruminants and has also been associated with human Crohn's disease. We
AB  - report the complete genome sequence of M. avium subsp. paratuberculosis, isolated
AB  - from the breast milk of a Crohn's disease patient. This sequence has high
AB  - identity with characterized strains recovered from cattle.
ER  -

TY  - JOUR
AU  - Bannister, D.
TI  - Analysis of an R+ strain carrying two fi- sex factors.
JO  - J. Gen. Microbiol.
PY  - 1970
SP  - 273
EP  - 281
VL  - 61
AB  - An Escherichia coli K12 strain, J5-3 (R313), was presumed to carry a fi-R factor, R313, which
AB  - determined resistance to the drugs tetracycline, streptomycin and sulphonamide, and also
AB  - determined a host specificity, hsII.  When this strain was used as a donor of drug resistance,
AB  - separation of R factor-carried determinants was observed in ex-conjugants.  Resistance to Tc
AB  - and hsII character were not separated, nor was resistance to Sm separated from resistance to
AB  - Su, but separation of these two pairs of characters was observed.  Tetracycline-sensitive
AB  - segregants, obtained by penicillin selection, were resistant to Sm and Su, but had lost the
AB  - hsII character.  Similarly, segregants for selected sensitivity to Su were sensitive to Sm,
AB  - but resistant to Tc and hsII+.  The same pattern of separation of characters was also observed
AB  - when drug resistance was transduced with phage PI, with the additional finding that the Sm and
AB  - Su resistant transductants lacked sex factor activity.  The resistance to Sm carried by these
AB  - transductants could be mobilized by an fi-R factor, R143.  Explanations of this behavior are
AB  - considered, including the possibility that the strain J5-3 (R313) had carried two fi-R
AB  - factors.  This explanation would also require that the transduction of an R factor by phage PI
AB  - is not always complete.
ER  -

TY  - JOUR
AU  - Bannister, D.
AU  - Glover, S.W.
TI  - Restriction and modification of bacteriophages by R+ strains of Escherichia coli K12.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1968
SP  - 735
EP  - 738
VL  - 30
AB  - None
ER  -

TY  - JOUR
AU  - Bannister, D.
AU  - Glover, S.W.
TI  - The isolation and properties of non-restricting mutants of two different host specificities associated with drug resistance factors.
JO  - J. Gen. Microbiol.
PY  - 1970
SP  - 63
EP  - 71
VL  - 61
AB  - Non-restricting (r-) mutants of two different host specificities carried by
AB  - resistance transfer factors have been isolated.  As previously found with other
AB  - host specificities, the non-restricting mutants were of two phenotypes:  those
AB  - that retained the ability to modify DNA, and those which had lost the ability
AB  - to modify DNA.  These mutants were tested for complementation with wild-type
AB  - host specificities carried either on the Escherichia coli chromosome, on
AB  - resistance transfer factors, or on the phage PI.  No complementation was
AB  - observed and possible explanations for this finding are considered.
ER  -

TY  - JOUR
AU  - Bao, G.
AU  - Wang, R.
AU  - Zhu, Y.
AU  - Dong, H.
AU  - Mao, S.
AU  - Zhang, Y.
AU  - Chen, Z.
AU  - Li, Y.
AU  - Ma, Y.
TI  - Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5007
EP  - 5008
VL  - 193
AB  - Clostridium acetobutylicum is an important microorganism for solvent production. We report the
AB  - complete genome sequence of C. acetobutylicum
AB  - DSM 1731, a genome with multi-replicon architecture. Comparison with the
AB  - sequenced type strain C. acetobutylicum ATCC 824, the genome of strain
AB  - DSM1731 harbors a 1.7 kb insertion and a novel 11.1 kb plasmid, which
AB  - might be acquired during evolution.
ER  -

TY  - JOUR
AU  - Bao, G.
AU  - Zhang, Y.
AU  - Du, C.
AU  - Chen, Z.
AU  - Li, Y.
AU  - Cao, Z.
AU  - Ma, Y.
TI  - Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production.
JO  - Genome Announcements
PY  - 2013
SP  - e00074
EP  - e00012
VL  - 1
AB  - Klebsiella oxytoca is an important microorganism for nitrogen fixation and chemical
AB  - production. Here, we report an annotated draft genome of K. oxytoca
AB  - strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs,
AB  - which provides a genetic basis for a better understanding of the physiology of
AB  - this species.
ER  -

TY  - JOUR
AU  - Bao, H.X.
AU  - Tang, L.
AU  - Yu, L.
AU  - Wang, X.Y.
AU  - Li, Y.
AU  - Deng, X.
AU  - Li, Y.G.
AU  - Li, A.
AU  - Zhu, D.L.
AU  - Johnston, R.N.
AU  - Liu, G.R.
AU  - Feng, Y.
AU  - Liu, S.L.
TI  - Differential efficiency in exogenous DNA acquisition among closely related Salmonella strains: implications in bacterial speciation.
JO  - BMC Microbiol.
PY  - 2014
SP  - 157
EP  - 157
VL  - 14
AB  - BACKGROUND: Acquisition of exogenous genetic material is a key event in bacterial
AB  - speciation. It seems reasonable to assume that recombination of the incoming DNA
AB  - into genome would be more efficient with higher levels of relatedness between the
AB  - DNA donor and recipient. If so, bacterial speciation would be a smooth process,
AB  - leading to a continuous spectrum of genomic divergence of bacteria, which,
AB  - however, is not the case as shown by recent findings. The goal of this study was
AB  - todetermine if DNA transfer efficiency is correlated with the levels of sequence
AB  - identity. RESULTS: To compare the relative efficiency of exogenous DNA
AB  - acquisition among closely related bacteria, we carried out phage-mediated
AB  - transduction and plasmid-mediated transformation in representative Salmonella
AB  - strains with different levels of relatedness. We found that the efficiency was
AB  - remarkably variable even among genetically almost identical bacteria. Although
AB  - there was a general tendency that more closely related DNA donor-recipient pairs
AB  - had higher transduction efficiency, transformation efficiency exhibited over a
AB  - thousand times difference among the closely related Salmonella strains.
AB  - CONCLUSION: DNA acquisition efficiency is greatly variable among bacteria that
AB  - have as high as over 99% identical genetic background, suggesting that bacterial
AB  - speciation involves highly complex processes affected not only by whether
AB  - beneficial exogenous DNA may exist in the environment but also the "readiness" of
AB  - the bacteria to accept it.
ER  -

TY  - JOUR
AU  - Bao, P.
AU  - Su, J.Q.
AU  - Hu, Z.Y.
AU  - Haggblom, M.M.
AU  - Zhu, Y.G.
TI  - Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 646
EP  - 654
VL  - 9
AB  - Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to
AB  - reduce nitrate and selenite and for its resistance to arsenic
AB  - under anaerobic conditions. Here we describe some key features of this organism,
AB  - together with the complete genome sequence and annotation. The 3,575,797 bp long
AB  - chromosome with its 3,454 protein-coding and 70 RNA genes, and the information
AB  - gained from its sequence will be relevant to the elucidation of
AB  - microbially-mediated transformations of nitrogen, selenium and arsenic in paddy
AB  - soil.
ER  -

TY  - JOUR
AU  - Bao, Q.
AU  - Tian, Y.
AU  - Li, W.
AU  - Xu, Z.
AU  - Xuan, Z.
AU  - Hu, S.
AU  - Dong, W.
AU  - Yang, J.
AU  - Chen, Y.
AU  - Xue, Y.
AU  - Xu, Y.
AU  - Lai, X.
AU  - Huang, L.
AU  - Dong, X.
AU  - Ma, Y.
AU  - Ling, L.
AU  - Tan, H.
AU  - Chen, R.
AU  - Wang, J.
AU  - Yu, J.
AU  - Yang, H.
TI  - A complete sequence of the T. tengcongensis genome.
JO  - Genome Res.
PY  - 2002
SP  - 689
EP  - 700
VL  - 12
AB  - Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic
AB  - eubacterium that was isolated from a freshwater hot spring in Tengchong,
AB  - China. Using a whole-genome-shotgun method, we sequenced its 2,689,445-bp
AB  - genome from an isolate, MB4(T) (Genbank accession no. AE008691). The
AB  - genome encodes 2588 predicted coding sequences (CDS). Among them, 1764
AB  - (68.2%) are classified according to homology to other documented proteins,
AB  - and the rest, 824 CDS (31.8%), are functionally unknown. One of the
AB  - interesting features of the T. tengcongensis genome is that 86.7% of its
AB  - genes are encoded on the leading strand of DNA replication. Based on
AB  - protein sequence similarity, the T. tengcongensis genome is most similar
AB  - to that of Bacillus halodurans, a mesophilic eubacterium, among all fully
AB  - sequenced prokaryotic genomes up to date. Computational analysis on genes
AB  - involved in basic metabolic pathways supports the experimental discovery
AB  - that T. tengcongensis metabolizes sugars as principal energy and carbon
AB  - source and utilizes thiosulfate and element sulfur, but not sulfate, as
AB  - electron acceptors. T. tengcongensis, as a gram-negative rod by empirical
AB  - definitions (such as staining), shares many genes that are characteristics
AB  - of gram-positive bacteria whereas it is missing molecular components
AB  - unique to gram-negative bacteria. A strong correlation between the G + C
AB  - content of tDNA and rDNA genes and the optimal growth temperature is found
AB  - among the sequenced thermophiles. It is concluded that thermophiles are a
AB  - biologically and phylogenetically divergent group of prokaryotes that have
AB  - converged to sustain extreme environmental conditions over evolutionary
AB  - timescale. Full author list: Bao, Q., Tian, Y., Li, W., Xu, Z., Xuan, Z., Hu, S., Dong, W.,
AB  - Yang, J., Chen, Y., Xue, Y., Xu, Y., Lai, X., Huang, L., Dong, X., Ma, Y., Ling, L., Tan, H.,
AB  - Chen, R., Wang, J., Yu, J., Yang, H.
ER  -

TY  - JOUR
AU  - Bao, W.
AU  - Zhou, Y.
AU  - Jiang, J.
AU  - Xu, Z.
AU  - Hou, L.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of Raoultella ornithinolytica Strain S12, a Lignin-Degrading Bacterium Isolated from Forest Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00104
EP  - e00115
VL  - 3
AB  - We report the complete genome sequence of Raoultella ornithinolytica strain S12,  isolated
AB  - from a soil sample collected from areas bordering rotten wood and wet
AB  - soil on Mt. Zijin, Nanjing. The complete genome of this bacterium may contribute
AB  - toward the discovery of efficient lignin-degrading pathways.
ER  -

TY  - JOUR
AU  - Bao, Y.
AU  - Higgins, L.
AU  - Zhang, P.
AU  - Chan, S.H.
AU  - Laget, S.
AU  - Sweeney, S.
AU  - Lunnen, K.
AU  - Xu, S.Y.
TI  - Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants.
JO  - Protein Expr. Purif.
PY  - 2008
SP  - 42
EP  - 52
VL  - 58
AB  - BmrI (ACTGGG N5/N4) is one of the few metal-independent restriction endonucleases (REases)
AB  - found in bacteria. The BmrI
AB  - restriction-modification system was cloned by the methylase selection
AB  - method, inverse PCR, and PCR. BmrI REase shows significant amino acid
AB  - sequence identity to BfiI and a putative endonuclease MspBNCORF3798 from
AB  - the sequenced Mesorhizobium sp. BNC1 genome. The EDTA-resistant BmrI REase
AB  - was successfully over-expressed in a pre-modified E. coli strain from
AB  - pET21a or pBAC-expIQ vectors. The recombinant BmrI REase shows strong
AB  - promiscuous activity (star activity) in NEB buffers 1, 4, and an EDTA
AB  - buffer. Star activity was diminished in buffers with 100-150mM NaCl and
AB  - 10mM MgCl(2). His-tagged BmrI192, the N-terminal cleavage domain of BmrI,
AB  - was expressed in E. coli and purified from inclusion bodies. The refolded
AB  - BmrI192 protein possesses non-specific endonuclease activity. BmrI192
AB  - variants with a single Ser to Cys substitution (S76C or S90C) and BmrI200
AB  - (T200C) with a single Cys at the C-terminal end were also constructed and
AB  - purified. BmrI200 digests both single-strand (ss) and double-strand (ds)
AB  - DNA and the nuclease activity on ss DNA is at least 5-fold higher than
AB  - that on ds DNA. The Cys-containing BmrI192 and BmrI200 nuclease variants
AB  - may be useful for coupling to other DNA binding elements such as synthetic
AB  - zinc fingers, thio-containing locked nucleic acids (LNA) or peptide
AB  - nucleic acids (PNA).
ER  -

TY  - JOUR
AU  - Bao, Y.
AU  - Kwok, A.H.
AU  - He, L.
AU  - Jiang, J.
AU  - Huang, Z.
AU  - Leung, F.C.
AU  - Sheng, X.
TI  - Complete Genome Sequence of Dyella jiangningensis Strain SBZ3-12, Isolated from the Surfaces of Weathered Rock.
JO  - Genome Announcements
PY  - 2014
SP  - e00416
EP  - e00414
VL  - 2
AB  - Dyella jiangningensis strain SBZ3-12 can weather biotite and release Al and Fe from biotite
AB  - under nutrient-poor conditions. Here, we report the first complete
AB  - genome sequence of D. jiangningensis strain SBZ3-12, which may facilitate a
AB  - better understanding of the molecular mechanism behind mineral weathering.
ER  -

TY  - JOUR
AU  - Bao, Y.
AU  - Liang, Z.
AU  - Booyjzsen, C.
AU  - Mayfield, J.A.
AU  - Li, Y.
AU  - Lee, S.W.
AU  - Ploplis, V.A.
AU  - Song, H.
AU  - Castellino, F.J.
TI  - Unique Genomic Arrangements in an Invasive Serotype M23 strain of Streptococcus pyogenes Identify Genes that Induce Hypervirulence.
JO  - J. Bacteriol.
PY  - 2014
SP  - 4089
EP  - 4102
VL  - 196
AB  - The first genome sequence of a Group A Streptococcus pyogenes M23 (emm23)
AB  - serotype (M23ND), isolated from an invasive human infection, has been completed.
AB  - This opacity factor-negative (SOF-) strain is composed of a circular chromosome
AB  - of 1,846,477 bp. Gene profiling showed that this strain contained six
AB  - phage-encoded and 24 chromosomally-inherited well-known virulence factors, as
AB  - well as 11 pseudogenes. The bacterium has acquired four large prophage elements,
AB  - PhiM23ND.1-4, harboring genes encoding streptococcal superantigen (ssa),
AB  - streptococcal pyrogenic exotoxins (spe) C, H, and I, and DNases spd1 and spd3,
AB  - with phage integrase genes present at one flank of each phage insertion,
AB  - suggesting that the phages were integrated by horizontal gene transfer.
AB  - Comparative analyses revealed unique large-scale genomic rearrangements that
AB  - differ from previously sequenced GAS strains. These rearrangements resulted in an
AB  - imbalanced genomic architecture and translocations of chromosome-encoded
AB  - virulence genes. The covS sensor in M23ND was identified as a pseudogene,
AB  - resulting in attenuation of speB function and increased expression of the
AB  - chromosomal virulence factors, mga, emm23, scpA, fibronectin-binding proteins
AB  - (sfb1 and fbp54), streptolysin O (slo), hyaluronic acid capsule (hasA),
AB  - streptokinase (ska), and a 2 DNases (spd and spd3), which were verified by PCR.
AB  - These genes are responsible for facilitating host epithelial cell binding and
AB  - and/or immune evasion, thus further contributing to the virulence of M23ND. In
AB  - conclusion, strain M23ND has become highly pathogenic as the result of a
AB  - combination of multiple genetic factors, particularly gene composition and
AB  - mutations, prophage integrations, unique genomic rearrangements, and regulated
AB  - expression of critical virulence factors.
ER  -

TY  - JOUR
AU  - Bao, Y.J.
AU  - Liang, Z.
AU  - Mayfield, J.A.
AU  - Donahue, D.L.
AU  - Carothers, K.E.
AU  - Lee, S.W.
AU  - Ploplis, V.A.
AU  - Castellino, F.J.
TI  - Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity.
JO  - J. Bacteriol.
PY  - 2016
SP  - 1712
EP  - 1724
VL  - 198
AB  - The genome of an invasive skin-tropic strain (AP53) of serotype M53 Group
AB  - AStreptococcus pyogenes(GAS) is composed of a circular chromosome of 1,860,554
AB  - bp, and encodes genetic markers for infection at skin locales,viz,emmgene-family
AB  - Pattern D and FCT type-3. Through genome-scale comparisons of AP53 with other GAS
AB  - genomes, we identified 596 candidate SNPs that reveal a potential genetic basis
AB  - for skin tropism. The genome of AP53 differed by approximately 30 point mutations
AB  - from a noninvasive Pattern D M53 strain (Alab49), four of which are located in
AB  - virulence genes. One pseudogene, yielding an inactive sensor kinase (CovS-) of
AB  - the two-component transcriptional regulator, CovRS, a major determinant for
AB  - invasiveness, severely attenuated expression of the secreted cysteine protease,
AB  - SpeB, and enhanced expression of the hyaluronic acid capsule, as compared to the
AB  - isogenic noninvasive AP53/CovS+ The collagen-binding protein transcript,sclB,
AB  - differed in the number of 5' -pentanucleotide repeats in the signal peptides of
AB  - AP53 and Alab49 (9vs15), translating into different lengths of their signal
AB  - peptides, which nonetheless maintained a full-length translatable coding frame.
AB  - Further, the GAS AP53 acquired two phages that are absent in Alab49. One such
AB  - phage (PhiAP53.2) contains the known virulence factor superantigen exotoxin gene
AB  - tandem,speK-slaA Overall, we conclude that this bacterium has evolved in multiple
AB  - ways, including mutational variations of regulatory genes, short tandem repeat
AB  - polymorphisms, large-scale genomic alterations, and acquisition of phages, all of
AB  - which may be involved in shaping the adaptation of GAS in specific infectious
AB  - environments and contribute to its enhanced virulence. IMPORTANCE: Infectious
AB  - strains ofS. pyogenes(GAS) are classified by their serotypes, relating to the
AB  - surface M-protein, theemm-like subfamily pattern, and their tropicity toward
AB  - nasopharynx and/or skin. It is generally agreed that M-proteins from Pattern D
AB  - strains, which also directly bind human host plasminogen, are skin-tropic. We
AB  - have sequenced and characterized the genome of an invasive Pattern D GAS strain
AB  - (AP53) in comparison to a very similar strain (Alab49) that is noninvasive, and
AB  - developed a genomic rationale as to possible reasons for the skin tropicity of
AB  - these two strains and the greater invasiveness of AP53.
ER  -

TY  - JOUR
AU  - Bao, Z.
AU  - Shinoda, R.
AU  - Minamisawa, K.
TI  - Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root  in a Low-Nitrogen Paddy Field.
JO  - Genome Announcements
PY  - 2016
SP  - e00932
EP  - e00916
VL  - 4
AB  - N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies.
AB  - We report here the draft genome sequence of Methylosinus sp. strain
AB  - 3S-1 isolated from rice root in a paddy field without N fertilizer input.
ER  -

TY  - JOUR
AU  - Baptista, J.P.
AU  - Sanches, P.P.
AU  - Teixeira, G.M.
AU  - Morey, A.T.
AU  - Tavares, E.R.
AU  - Yamada-Ogatta, S.F.
AU  - da Rocha, S.P.D.
AU  - Hungria, M.
AU  - Ribeiro, R.A.
AU  - Balbi-Pena, M.I.
AU  - Chideroli, R.T.
AU  - Pereira, U.P.
AU  - de Oliveira, A.G.
TI  - Complete Genome Sequence of Bacillus velezensis LABIM40, an Effective Antagonist  of Fungal Plant Pathogens.
JO  - Genome Announcements
PY  - 2018
SP  - e00595
EP  - e00518
VL  - 6
AB  - Bacillus velezensis strain LABIM40 holds high potential for biological control of plant
AB  - pathogens. Its complete genome contains one chromosome of 3,972,310 bp with
AB  - 3,777 DNA coding sequences and displays 33 gene clusters potentially involved in
AB  - the suppression of fungal pathogens.
ER  -

TY  - JOUR
AU  - Barak-Gavish, N.
AU  - Frada, M.J.
AU  - Lee, P.A.
AU  - DiTullio, G.R.
AU  - Ku, C.
AU  - Malitsky, S.
AU  - Aharoni, A.
AU  - Green, S.J.
AU  - Kartvelishvily, E.
AU  - Sheyn, U.
AU  - Schatz, D.
AU  - Vardi, A.
TI  - Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP.
JO  - Sci. Adv.
PY  - 2018
SP  - eaau5716
EP  - eaau5716
VL  - 4
AB  - Emiliania huxleyi is a bloom-forming microalga that affects the global sulfur cycle by
AB  - producing large amounts of
AB  - dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide.
AB  - Top-down regulation of
AB  - E. huxleyi blooms has been attributed to viruses and grazers; however, the possible
AB  - involvement of algicidal bacteria
AB  - in bloom demise has remained elusive. We demonstrate that a Roseobacter strain, Sulfitobacter
AB  - D7, that we isolated
AB  - from a North Atlantic E. huxleyi bloom, exhibited algicidal effects against E. huxleyi upon
AB  - coculturing. Both the alga
AB  - and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore
AB  - establishing this host-pathogen
AB  - system as an attractive, ecologically relevant model for studying algal-bacterial interactions
AB  - in the
AB  - oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce
AB  - high amounts of
AB  - methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific
AB  - response, in which
AB  - E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter
AB  - D7 infection. Intriguingly,
AB  - exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in an
AB  - algal
AB  - strain typically resistant to the bacterial pathogen. This enhanced virulence was highly
AB  - specific to DMSP compared
AB  - to addition of propionate and glycerol which had no effect on bacterial virulence. We propose
AB  - a novel function for
AB  - DMSP, in addition to its central role in mutualistic interactions among marine organisms, as a
AB  - mediator of bacterial
AB  - virulence that may regulate E. huxleyi blooms.
ER  -

TY  - JOUR
AU  - Baranasic, D.
AU  - Gacesa, R.
AU  - Starcevic, A.
AU  - Zucko, J.
AU  - Blazic, M.
AU  - Horvat, M.
AU  - Gjuracic, K.
AU  - Fujs, S.
AU  - Hranueli, D.
AU  - Kosec, G.
AU  - Cullum, J.
AU  - Petkovic, H.
TI  - Draft Genome Sequence of Streptomyces rapamycinicus Strain NRRL 5491, the Producer of the Immunosuppressant Rapamycin.
JO  - Genome Announcements
PY  - 2013
SP  - e00581
EP  - e00513
VL  - 1
AB  - Streptomyces rapamycinicus strain NRRL 5491 produces the important drug rapamycin. It has a
AB  - large genome of 12.7 Mb, of which over 3 Mb consists of 48
AB  - secondary metabolite biosynthesis clusters.
ER  -

TY  - JOUR
AU  - Baranasic, D.
AU  - Zucko, J.
AU  - Nair, M.
AU  - Pain, A.
AU  - Long, P.F.
AU  - Hranueli, D.
AU  - Cullum, J.
AU  - Starcevic, A.
TI  - Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements.
JO  - Genome Announcements
PY  - 2014
SP  - e00517
EP  - e00514
VL  - 2
AB  - The genome sequence of Streptomyces rimosus R6-500, an industrially improved strain which
AB  - produces high titers of the important antibiotic oxytetracycline, is
AB  - reported, as well as the genome sequences of two derivatives arising due to the
AB  - genetic instability of the strain.
ER  -

TY  - JOUR
AU  - Baranova, N.B.
AU  - Malygina, T.Y.
AU  - Medvedeva, E.S.
AU  - Boulygina, E.A.
AU  - Siniagina, M.N.
AU  - Dramchini, M.A.
AU  - Prottoy, R.A.
AU  - Mouzykantov, A.A.
AU  - Davydova, M.N.
AU  - Chernova, O.A.
AU  - Chernov, V.M.
TI  - Genome Sequences of Acholeplasma laidlawii Strains with Increased Resistance to Tetracycline and Melittin.
JO  - Genome Announcements
PY  - 2018
SP  - e01446
EP  - e01417
VL  - 6
AB  - Acholeplasma laidlawii is a well-suited model for studying the molecular basis for adapting
AB  - mollicutes to environmental conditions. Here, we present the
AB  - whole-genome sequences of two strains of A. laidlawii with increased resistance
AB  - to tetracycline and melittin.
ER  -

TY  - JOUR
AU  - Barany, F.
TI  - A genetic system for isolation and characterization of TaqI restriction endonuclease mutants.
JO  - Gene
PY  - 1987
SP  - 13
EP  - 27
VL  - 56
AB  - The gene encoding TaqI restriction endonuclease has been subcloned downstream
AB  - from an inducible phoA promoter.  Certain strains of Escherichia coli remain
AB  - viable when endonuclease is expressed, even in the absence of (protective)
AB  - methylation.  Infecting lambda phage DNA is not restricted in vivo.  One E.
AB  - coli strain, MM294, exhibited a temperature-sensitive phenotype when TaqI
AB  - endonuclease was induced.  This allowed for design of an in vivo plate assay
AB  - for identification of specially constructed two-codon insertion mutants in the
AB  - endonuclease gene.  These mutants exhibited a wide range of in vitro
AB  - activities, including wild-type activity, greater activity in low-salt buffer,
AB  - and sequence-specific nicking activity.
ER  -

TY  - JOUR
AU  - Barany, F.
TI  - The TaqI star reaction:  strand preferences reveal hydrogen-bond donor and acceptor sites in canonical sequence recognition.
JO  - Gene
PY  - 1988
SP  - 149
EP  - 165
VL  - 65
AB  - TaqI endonuclease recognizes and cleaves its canonical sequence, TCGA, with complete fidelity
AB  - under standard conditions. In the presence of some organic solvents, TaqI endonuclease
AB  - introduced additional single-strand and double-strand cuts at sequences termed TaqI star
AB  - sites. Using middle-labeled DNA, the relative rates of cleavage of each strand were
AB  - simultaneously determined for several star sites. These star recognition sequences differed
AB  - from the canonical sequence by a single base, and all potential star sites were either nicked
AB  - or cleaved. Star sites within the middle labeled substrate represented ten of the twelve
AB  - possible star sequences for each strand. For each group of identical star sites, one strand
AB  - was consistently preferred for cleavage. Based on these preferences, a model for TaqI
AB  - recognition of the TCGA sequence is proposed. According to this model, sequence discrimination
AB  - is mediated by eight hydrogen bonds formed between TaqI and the cognate nucleotides within the
AB  - major groove.
ER  -

TY  - JOUR
AU  - Barany, F.
TI  - Isolation and characterization of TaqI restriction endonuclease mutants.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 82
EP  - 82
VL  - 13A
AB  - The gene encoding the TaqI restriction endonuclease (recognition sequence T^CGA) has been
AB  - subcloned downstream of an inducible phoA promoter, and overproduced to 30% of cellular
AB  - proteins. E. coli cells remain viable at 37C when endonuclease is expressed, even in the
AB  - absence of (protective) methylation. Analysis of wild type TaqI endonuclease star activity
AB  - (cleavage at closely related sequences) revealed that for a particular star site, one strand
AB  - of the DNA duplex was preferentially cleaved. Based on these preferences, a model is proposed
AB  - that sequence specific discrimination is mediated by 8 hydrogen bonds formed by TaqI and
AB  - specific base groups in the major groove. Using a strain that produces beta-galactosidase upon
AB  - DNA damage, and a temperature dependent in vivo plate assay as screens, over two dozen
AB  - two-codon insertion mutants have been isolated. These are being characterized with respect to
AB  - in vitro canonical site activity, DNA binding using gel mobility shifts, and star site
AB  - activity.
ER  -

TY  - JOUR
AU  - Barany, F.
TI  - How TaqI endonuclease recognizes its cognate sequence.
JO  - Gene
PY  - 1988
SP  - 63
EP  - 65
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Barany, F.
TI  - Two codon insertion mutagenesis of the TaqI restriction endonuclease.
JO  - J. Cell Biochem. Suppl.
PY  - 1987
SP  - 240
EP  - 240
VL  - 11C
AB  - Recently, the thermophilic TaqI restriction endonuclease and corresponding
AB  - methylase (recognition sequence TCGA) have been cloned.  The endonuclease gene
AB  - has been subcloned under inducible control of an alkaline phosphatase promoter,
AB  - in a small high copy plasmid.  Surprisingly, E. coli cells overproducing TaqI
AB  - endonuclese are still viable at 37C, even in the absence of (protective)
AB  - methylation.  Indeed, neither transforming DNA nor infecting lambda phage are
AB  - restricted by cells harboring TaqI.  However, certain cells harboring this
AB  - plasmid are barely viable at 42C, and this phenotype has been exploited as a
AB  - plate assay for in vivo TaqI endonuclease activity.  Single stranded hexameric
AB  - linkers were inserted into the endonuclease gene using biological selection,
AB  - and the resultant two codon insertion mutants were assayed in vitro for TaqI
AB  - endonuclease activity.  A wide range of enzymatic activity was observed, from
AB  - wild type activity (3 mutants), slight temperature dependency (2 mutants),
AB  - moderate activity (2 mutants), greater activity in low salt buffers (2
AB  - mutants), nicking activity ( 1 mutant), to no activity (2 mutants, and 2 small
AB  - in-1. Slatko, B., Movan, L., Jager, T., Benner, J., Simcox, T., & Wilson, G.
AB  - Ms in preparation 1986.  2. Barany, F. (1985) Proc. Natl. Acad. Sci. USA
AB  - 82:4202-4206.
ER  -

TY  - JOUR
AU  - Barany, F.
TI  - Overproduction, purification and crystallization of TaqI restriction endonuclease.
JO  - Gene
PY  - 1988
SP  - 167
EP  - 177
VL  - 65
AB  - Under phoA promoter control, TaqI endonuclease was overproduced to 5% of
AB  - Escherichia coli cellular proteins.  This was achieved by fusing the
AB  - endonuclease gene to the first four codons of the alkaline phosphatase signal
AB  - sequence.  For maximal overproduction (30% of cellular proteins), a putative
AB  - 14-bp hairpin within the endonuclease coding sequence was replaced with
AB  - degenerate codons  In addition, TaqI methylase was required to protect host
AB  - DNA.  The endonuclease was purified in sufficient amounts for crystallization.
ER  -

TY  - JOUR
AU  - Barany, F.
AU  - Danzitz, M.
AU  - Zebala, J.
AU  - Mayer, A.
TI  - Cloning and sequencing of genes encoding the TthHB8I restriction and modification enzymes: comparison with the isoschizomeric TaqI enzymes.
JO  - Gene
PY  - 1992
SP  - 3
EP  - 12
VL  - 112
AB  - Genes encoding the TthHB8I restriction and modification (R-M) system from
AB  - Thermus thermophilus HB8 (recognition sequence T^CGA) were cloned in
AB  - Escherichia coli.  The genes have the same transcriptional orientation, with
AB  - the last 13 codons of the methyltransferase (MTase) overlapping the first 13
AB  - codons of the endonuclease (ENase).  Nucleotide sequence analysis of the TthB8I
AB  - ENase revealed a single chain of 263 amino acid (aa) residues that share a 77%
AB  - identity with the corrected isoschizomeric TaqI ENase.  Likewise, the Tth MTase
AB  - (428 aa) shares a 79% identity with the corrected sequence of the TaqI MTase.
AB  - This high degree of aa conservation suggests a common origin between the Taq
AB  - and Tth R-M systems.  However, codon usage and G + C content for the R-M genes
AB  - differed markedly from that of other cloned Thermus genes.  This suggests that
AB  - these R-M genes were only recently introduced into the genus Thermus.
ER  -

TY  - JOUR
AU  - Barany, F.
AU  - Slatko, B.
AU  - Danzitz, M.
AU  - Cowburn, D.
AU  - Schildkraut, I.
AU  - Wilson, G.G.
TI  - The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap.
JO  - Gene
PY  - 1992
SP  - 91
EP  - 95
VL  - 112
AB  - The nucleotide sequence of the genes encoding methyltransferase TaqI (M.TaqI)
AB  - and restriction endonuclease TaqI (R.TaqI) with the recognition sequence, TCGA,
AB  - were analyzed in clones isolated from independent libraries.  The genes,
AB  - originally reported as 363 and 236 codons long [Slatko et al., Nucleic Acids
AB  - Res. 15 (1987) 9781-9796] were determined as 421 and 263 codons long,
AB  - respectively.  The C terminus of the taqIM gene overlaps the N terminus of the
AB  - taqIR gene by 13 codons, as observed with the isoschizomeric TthHB8I
AB  - restriction-modification system [Barany et al., Gene 112 (1992) 13-20].
AB  - Removal of the overlapping codons did not interfere with in vivo M.TaqI
AB  - activity.  We postulate the overlap plays a role in regulating taqIR
AB  - expression.
ER  -

TY  - JOUR
AU  - Barany, F.
AU  - Zebala, J.
TI  - Correlation between insertion mutant activities and amino acid sequence identities of the TaqI and TthHB8 restriction endonucleases.
JO  - Gene
PY  - 1992
SP  - 13
EP  - 20
VL  - 112
AB  - A two-codon insertion mutagenesis method has been generalized.  Over two dozen
AB  - insertion mutants throughout the gene encoding TaqI restriction endonuclease
AB  - were constructed and activity was characterized.  All mutants with activity
AB  - either cleaved or nicked the canonical T^CGA recognition sequence.  Some
AB  - insertion mutants created duplication of gene regions, termed Gemini proteins,
AB  - which still retained activity.  The correlation between mutants with poor
AB  - activity and the regions of shared amino identity between the isoschizomeric
AB  - Taq I and TthHB8I suggests these regions are involved in DNA recognition and/or
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Baranyi, U.
AU  - Klein, R.
AU  - Lubitz, W.
AU  - Kruger, D.H.
AU  - Witte, A.
TI  - The archaeal halophilic virus-encoded Dam-like methyltransferase M.Phi Ch1-I methylates adenine residues and complements dam mutants in the low salt environment of Escherichia coli.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 1168
EP  - 1179
VL  - 35
AB  - The genome of the archaeal virus phi Ch1, infecting Natrialba magadii (formerly
AB  - Natronobacterium magadii), is composed of 58.5 kbp linear ds
AB  - DNA. Virus particles contain several RNA species in sizes of 100-800
AB  - nucleotides. A fraction of phi Ch1 genomes is modified within
AB  - 5'-GATC-3' and related sequences, as determined by various restriction
AB  - enzyme digestion analyses. High performance liquid chromatography
AB  - revealed a fifth base, in addition to the four nucleosides, which was
AB  - identified as N-6-methyladenosine. Genetic analyses and subsequent
AB  - sequencing led to the identification of a DNA (N-6-adenine)
AB  - methyltransferase (mtase) gene. The protein product was designated
AB  - M.phi Ch1-I. By the localization of the most conserved motifs (a DPPY
AB  - motif occurring before FxGxG), the enzyme was placed within the
AB  - beta-subgroup of the (N-6-adenine) methyltransferase class. The mtase
AB  - gene of phi Ch1 was classified as a 'late' gene, as determined by
AB  - measuring the kinetics of mRNA and protein expression in N. magadii
AB  - during the lytic cycle of phi Ch1. After infection of cells, M.phi
AB  - Ch1-I mRNA and protein could be detected in lower amounts than in the
AB  - situation of virus induction from lysogenic cells. Consequently, only
AB  - about 5% of the phi Ch1 progeny genomes after infection of N. magadii
AB  - carry the M.phi Ch1-I methylation in contrast to 50% of virus genomes
AB  - generated by induction of phi Ch1-lysogenic N. magadii cells.
AB  - Heterologous expression of the mtase from a halophile with 3 M
AB  - cytoplasmic salt concentration showed an unexpected feature: the
AB  - protein was active in the low environment of Escherichia coli and was
AB  - able to methylate DNA in vivo. Interestingly, it seemed to exhibit a
AB  - higher sequence specificity in E. coli that resulted in adenine
AB  - methylation exclusively in the sequence 5'-GATC-3'. Additionally,
AB  - expression of M.phi Ch1-I in dam(-) E. coli cells led to a complete
AB  - substitution of the function of M.Dam in DNA mismatch repair.
ER  -

TY  - JOUR
AU  - Baranzoni, G.M.
AU  - Fratamico, P.M.
AU  - Kim, G.H.
AU  - Reichenberger, E.R.
AU  - Funk, J.A.
AU  - Manning, S.D.
AU  - Bosilevac, J.M.
TI  - Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources.
JO  - Genome Announcements
PY  - 2017
SP  - e01214
EP  - e01217
VL  - 5
AB  - Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne pathogens that can be
AB  - carried by various animals. The swine STEC population is partially
AB  - composed of host-specific strains that are often not well characterized. In this
AB  - work, the genome sequences of a number of swine STEC strains are presented.
ER  -

TY  - JOUR
AU  - Baranzoni, G.M.
AU  - Fratamico, P.M.
AU  - Reichenberger, E.R.
AU  - Kim, G.H.
AU  - Breidt, F.
AU  - Kay, K.
AU  - Oh, D.H.
TI  - Complete Genome Sequences of Escherichia coli O157:H7 Strains SRCC 1675 and 28RC, Which Vary in Acid Resistance.
JO  - Genome Announcements
PY  - 2016
SP  - e00743
EP  - e00716
VL  - 4
AB  - The level of acid resistance among Escherichia coli O157:H7 strains varies, and strains with
AB  - higher resistance to acid may have a lower infectious dose. The
AB  - complete genome sequences belonging to two strains of Escherichia coli O157:H7
AB  - with different levels of acid resistance are presented here.
ER  -

TY  - JOUR
AU  - Barau, J.
AU  - Teissandier, A.
AU  - Zamudio, N.
AU  - Roy, S.
AU  - Nalesso, V.
AU  - Herault, Y.
AU  - Guillou, F.
AU  - Bourc'his, D.
TI  - The DNA methyltransferase DNMT3C protects male germ cells from transposon activity.
JO  - Science
PY  - 2016
SP  - 909
EP  - 912
VL  - 354
AB  - DNA methylation is prevalent in mammalian genomes and plays a central role in the epigenetic
AB  - control of development. The mammalian DNA methylation machinery is
AB  - thought to be composed of three DNA methyltransferase enzymes (DNMT1, DNMT3A, and
AB  - DNMT3B) and one cofactor (DNMT3L). Here, we describe the discovery of Dnmt3C, a
AB  - de novo DNA methyltransferase gene that evolved via a duplication of Dnmt3B in
AB  - rodent genomes and was previously annotated as a pseudogene. We show that DNMT3C
AB  - is the enzyme responsible for methylating the promoters of evolutionarily young
AB  - retrotransposons in the male germ line and that this specialized activity is
AB  - required for mouse fertility. DNMT3C reveals the plasticity of the mammalian DNA
AB  - methylation system and expands the scope of the mechanisms involved in the
AB  - epigenetic control of retrotransposons.
ER  -

TY  - JOUR
AU  - Barauna, R.A.
AU  - Guimaraes, L.C.
AU  - Veras, A.A.
AU  - de Sa, P.H.
AU  - Gracas, D.A.
AU  - Pinheiro, K.C.
AU  - Silva, A.S.
AU  - Folador, E.L.
AU  - Benevides, L.J.
AU  - Viana, M.V.
AU  - Carneiro, A.R.
AU  - Schneider, M.P.
AU  - Spier, S.J.
AU  - Edman, J.M.
AU  - Ramos, R.T.
AU  - Azevedo, V.
AU  - Silva, A.
TI  - Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California.
JO  - Genome Announcements
PY  - 2014
SP  - e00977
EP  - e00914
VL  - 2
AB  - The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion
AB  - Personal Genome Machine (PGM) platform, and showed a size of
AB  - 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These
AB  - results will serve as a basis for further studies on the pathogenicity of C.
AB  - pseudotuberculosis bv. equi.
ER  -

TY  - JOUR
AU  - Barauna, R.A.
AU  - Ramos, R.T.
AU  - Veras, A.A.
AU  - de Sa, P.H.
AU  - Guimaraes, L.C.
AU  - das Gracas, D.A.
AU  - Carneiro, A.R.
AU  - Edman, J.M.
AU  - Spier, S.J.
AU  - Azevedo, V.
AU  - Silva, A.
TI  - Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 16
EP  - 16
VL  - 12
AB  - The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium
AB  - pseudotuberculosis biovar equi were sequenced on the Ion Torrent
AB  - PGM platform, completely assembled, and their gene content and structure were
AB  - analyzed. The strains were isolated from horses with distinct signs of infection,
AB  - including ulcerative lymphangitis, external abscesses on the chest, or internal
AB  - abscesses on the liver, kidneys, and lungs. The average size of the genomes was
AB  - 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences
AB  - (CDSs). An optical map of the MB11 strain generated using the KpnI restriction
AB  - enzyme showed that the approach used to assemble the genome was satisfactory,
AB  - producing good alignment between the sequence observed in vitro and that obtained
AB  - in silico. In the resulting Neighbor-Joining dendrogram, the C.
AB  - pseudotuberculosis strains sequenced in this study were clustered into a single
AB  - clade supported by a high bootstrap value. The structural analysis showed that
AB  - the genomes of the MB11 and MB14 strains were very similar, while the MB30 and
AB  - MB66 strains had several inverted regions. The observed genomic characteristics
AB  - were similar to those described for other strains of the same species, despite
AB  - the number of inversions found. These genomes will serve as a basis for
AB  - determining the relationship between the genotype of the pathogen and the type of
AB  - infection that it causes.
ER  -

TY  - JOUR
AU  - Barauna, R.A.
AU  - Ramos, R.T.
AU  - Veras, A.A.
AU  - Pinheiro, K.C.
AU  - Benevides, L.J.
AU  - Viana, M.V.
AU  - Guimaraes, L.C.
AU  - Edman, J.M.
AU  - Spier, S.J.
AU  - Azevedo, V.
AU  - Silva, A.
TI  - Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.
JO  - PLoS ONE
PY  - 2017
SP  - E0170676
EP  - E0170676
VL  - 12
AB  - Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on
AB  - the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp.
AB  - This bacterium is the causative agent of disease known as "pigeon fever" which
AB  - commonly affects horses worldwide. The pangenome of biovar equi was calculated
AB  - and two phylogenomic approaches were used to identify clustering patterns within
AB  - Corynebacterium genus. Furthermore, other comparative analyses were performed
AB  - including the prediction of genomic islands and prophages, and SNP-based
AB  - phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two
AB  - distinct clades, one formed by nitrate non-reducing species (biovar ovis) and
AB  - another formed by nitrate-reducing species (biovar equi). In the latter group,
AB  - the strains isolated from California were more related to each other, while the
AB  - strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A
AB  - total of 1,355 core genes were identified, corresponding to 42.5% of the
AB  - pangenome. This pangenome has one of the smallest core genomes described in the
AB  - literature, suggesting a high genetic variability of biovar equi of C.
AB  - pseudotuberculosis. The analysis of the similarity between the resistance islands
AB  - identified a higher proximity between the strains that caused more severe
AB  - infectious conditions (infection in the internal organs). Pathogenicity islands
AB  - were largely conserved between strains. Several genes that modulate the
AB  - pathogenicity of C. pseudotuberculosis were described including peptidases,
AB  - recombination enzymes, micoside synthesis enzymes, bacteriocins with
AB  - antimicrobial activity and several others. Finally, no genotypic differences were
AB  - observed between the strains that caused the three different types of infection
AB  - (external abscess formation, infection with abscess formation in the internal
AB  - organs, and ulcerative lymphangitis). Instead, it was noted that there is a
AB  - higher phenetic correlation between strains isolated at California compared to
AB  - the other strains. Additionally, high variability of resistance islands suggests
AB  - gene acquisition through several events of horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Barbato, M.
AU  - Mapelli, F.
AU  - Chouaia, B.
AU  - Crotti, E.
AU  - Daffonchio, D.
AU  - Borin, S.
TI  - Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean  Sea.
JO  - Genome Announcements
PY  - 2015
SP  - e01424
EP  - e01415
VL  - 3
AB  - We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a
AB  - hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying
AB  - diesel oil as the sole carbon source. This strain contains multiple putative
AB  - genes associated with hydrocarbon degradation pathways and that are highly
AB  - similar to those described in A. dieselolei type strain B5.
ER  -

TY  - JOUR
AU  - Barbau-Piednoir, E.
AU  - Bertrand, S.
AU  - Roosens, N.H.
AU  - De Keersmaecker, S.C.
TI  - Genome Sequence of the Salmonella enterica subsp. enterica Serovar Namur Strain 05-2929, Lacking the Salmonella Atypical Fimbrial Operon.
JO  - Genome Announcements
PY  - 2014
SP  - e00299
EP  - e00214
VL  - 2
AB  - This paper announces the genome sequence and annotation of Salmonella enterica subsp. enterica
AB  - serovar Namur strain 05-2929. S. Namur is a new serovar (39:z4,z23:-) that was isolated from a
AB  - patient with salmonellosis in 2005 in Namur, Belgium, and has been identified as lacking the
AB  - Salmonella atypical fimbrial (saf) operon.
ER  -

TY  - JOUR
AU  - Barbau-Piednoir, E.
AU  - De Keersmaecker, S.C.
AU  - Wuyts, V.
AU  - Gau, C.
AU  - Pirovano, W.
AU  - Costessi, A.
AU  - Philipp, P.
AU  - Roosens, N.H.
TI  - Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain  2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive.
JO  - Genome Announcements
PY  - 2015
SP  - e00214
EP  - e00215
VL  - 3
AB  - This paper announces the genome sequence and annotation of the genetically modified (GM)
AB  - Bacillus subtilis strain 2014-3557 overproducing riboflavin
AB  - (vitamin B2). This GM-strain is unauthorized in the European Union. Nevertheless,
AB  - it has been isolated from a lot of vitamin B2 (riboflavin) 80% feed grade
AB  - imported to Europe from China.
ER  -

TY  - JOUR
AU  - Barbe, V.
AU  - Bouzon, M.
AU  - Mangenot, S.
AU  - Badet, B.
AU  - Poulain, J.
AU  - Segurens, B.
AU  - Vallenet, D.
AU  - Marliere, P.
AU  - Weissenbach, J.
TI  - Complete Genome Sequence of Streptomyces cattleya NRRL 8057, a Producer of Antibiotics and Fluorometabolites.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5055
EP  - 5056
VL  - 193
AB  - Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of
AB  - the rare bacteria known to synthesize fluorinated
AB  - metabolites. The genome consists of two linear replicons. The genes
AB  - involved in fluorine metabolism and in the biosynthesis of the antibiotic
AB  - thienamycin were mapped on both replicons.
ER  -

TY  - JOUR
AU  - Barbe, V.
AU  - Vallenet, D.
AU  - Fonknechten, N.
AU  - Kreimeyer, A.
AU  - Oztas, S.
AU  - Labarre, L.
AU  - Cruveiller, S.
AU  - Robert, C.
AU  - Duprat, S.
AU  - Wincker, P.
AU  - Ornston, L.N.
AU  - Weissenbach, J.
AU  - Marliere, P.
AU  - Cohen, G.N.
AU  - Medigue, C.
TI  - Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 5766
EP  - 5779
VL  - 32
AB  - Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to
AB  - representatives of the well-characterized Pseudomonas
AB  - aeruginosa and Pseudomonas putida. Unlike these bacteria, the
AB  - Acinetobacter ADP1 is highly competent for natural transformation which
AB  - affords extraordinary convenience for genetic manipulation. The circular
AB  - chromosome of the Acinetobacter ADP1, presented here, encodes 3325
AB  - predicted coding sequences, of which 60% have been classified based on
AB  - sequence similarity to other documented proteins. The close evolutionary
AB  - proximity of Acinetobacter and Pseudomonas species, as judged by the
AB  - sequences of their 16S RNA genes and by the highest level of bidirectional
AB  - best hits, contrasts with the extensive divergence in the GC content of
AB  - their DNA (40 versus 62%). The chromosomes also differ significantly in
AB  - size, with the Acinetobacter ADP1 chromosome <60% of the length of the
AB  - Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1
AB  - revealed genes for metabolic pathways involved in utilization of a large
AB  - variety of compounds. Almost all of these genes, with orthologs that are
AB  - scattered in other species, are located in five major 'islands of
AB  - catabolic diversity', now an apparent 'archipelago of catabolic
AB  - diversity', within one-quarter of the overall genome. Acinetobacter ADP1
AB  - displays many features of other aerobic soil bacteria with metabolism
AB  - oriented toward the degradation of organic compounds found in their
AB  - natural habitat. A distinguishing feature of this genome is the absence of
AB  - a gene corresponding to pyruvate kinase, the enzyme that generally
AB  - catalyzes the terminal step in conversion of carbohydrates to pyruvate for
AB  - respiration by the citric acid cycle. This finding supports the view that
AB  - the cycle itself is centrally geared to the catabolic capabilities of this
AB  - exceptionally versatile organism.
ER  -

TY  - JOUR
AU  - Barber, R.D.
AU  - Zhang, L.
AU  - Harnack, M.
AU  - Olson, M.V.
AU  - Kaul, R.
AU  - Ingram-Smith, C.
AU  - Smith, K.S.
TI  - Complete genome sequence of Methanosaeta concilii, a specialist in aceticlastic methanogenesis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3668
EP  - 3669
VL  - 193
AB  - Complete genome sequence of Methanosaeta concilii, a specialist in Aceticlastic
AB  - Methanogenesis.
AB  - episome, has been determined and exhibits considerable differences in gene
AB  - content from that of Methanosaeta thermophila.
ER  -

TY  - JOUR
AU  - Barbes, C.
AU  - Hardisson, C.
AU  - Novella, I.S.
AU  - Yebra, M.J.
AU  - Sanchez, J.
TI  - DNA-methyltransferase activities in Streptomyces antibioticus.
JO  - FEMS Microbiol. Lett.
PY  - 1988
SP  - 59
EP  - 64
VL  - 55
AB  - Several DNA methyltransferases have been detected in Streptomyces antibioticus ETHZ 7451.  One
AB  - of these enzymes was purified and partially characterized from crude extracts of Streptomyces
AB  - antibioticus ETHZ 7451.  This enzyme only methylates the adenine residues of DNA.  However,
AB  - lambda and pBR322 DNAs were not protected in vitro with the methylase, indicating that the
AB  - enzyme does not seem to form part of a restriction-modification system.  Remarkably, the
AB  - efficiency of the enzyme is significantly higher on the DNA isolated from aerial mycelium than
AB  - from substrate mycelium in S. antibioticus.
ER  -

TY  - JOUR
AU  - Barbes, C.
AU  - Sanchez, J.
AU  - Yebra, M.J.
AU  - Robert-Gero, M.
AU  - Hardisson, C.
TI  - Effects of sinefungin and S-adenosylhomocysteine on DNA and protein methyltransferases from Streptomyces and other bacteria.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 239
EP  - 244
VL  - 69
AB  - Sinefungin is a naturally occurring nucleoside isolated from cultures of
AB  - Streptomyces griseolus and S. incarnatus.  It is structurally related to
AB  - S-adenosyl-methionine (SAM) and S-adenosyl-L-homocysteine (SAH).  Its effect
AB  - and level of action on prokaryotes has not been studied with the same detail as
AB  - with eukaryotic cells.  In this report we describe the effect of sinefungin and
AB  - SAH on several Streptomyces methyltransferases (DNA and protein MTases) and on
AB  - other bacterial DNA-MTases.  Protein MTases are resistant to sinefungin,
AB  - whereas DNA-MTases are inhibited.  Adenine MTases however, seem more sensitive
AB  - to this analogue than cytosine MTases.
ER  -

TY  - JOUR
AU  - Barbeyron, T.
AU  - Kean, K.
AU  - Forterre, P.
TI  - DNA adenine methylation of GATC sequences appeared recently in the Escherichia coli lineage.
JO  - J. Bacteriol.
PY  - 1984
SP  - 586
EP  - 590
VL  - 160
AB  - We have examined the presence of methylated adenine at GATC sequences (Dam phenotype) in the
AB  - DNA of 23 eubacteria and 13 archaebacteria by using isoschizomer restriction enzymes. We have
AB  - found a completely Dam+ phenotype in bacteria of nine genera related to the families
AB  - Enterobacteriaceae, Parvobacteriaceae, and Vibrionaceae, and in the five cyanobacteria tested.
AB  - We have found a partial Dam+ phenotype in the two archaebacteria Halobacterium saccharovorum
AB  - and Methanobacterium sp. strain Ivanov. All of the other archaebacteria (three genera) and
AB  - eubacteria (nine genera) tested were Dam-. Phylogenetic analysis, based on the evolutionary
AB  - tree of Fox et al., indicates that dam methylation in the Escherichia coli lineage appeared
AB  - recently in bacterial evolution and is restricted to a small range of closely related
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Barbier, F.
AU  - Ruppe, E.
AU  - Hernandez, D.
AU  - Lebeaux, D.
AU  - Francois, P.
AU  - Felix, B.
AU  - Desprez, A.
AU  - Maiga, A.
AU  - Woerther, P.L.
AU  - Gaillard, K.
AU  - Jeanrot, C.
AU  - Wolff, M.
AU  - Schrenzel, J.
AU  - Andremont, A.
AU  - Ruimy, R.
TI  - Methicillin-resistant coagulase-negative staphylococci in the community: high homology of SCCmec IVa between Staphylococcus epidermidis and major clones of methicillin-resistant Staphylococcus aureus.
JO  - J. Infect. Dis.
PY  - 2010
SP  - 270
EP  - 281
VL  - 202
AB  - BACKGROUND: Data on community spread of methicillin-resistant
AB  - coagulase-negative staphylococci (MR-CoNS) are scarce. We assessed their
AB  - potential role as a reservoir of staphylococcal cassette chromosome mec
AB  - (SCCmec) IVa, the leading SCCmec subtype in community-acquired
AB  - methicillin-resistant Staphylococcus aureus (CA-MRSA). METHODS: Nasal
AB  - carriage of MR-CoNS was prospectively investigated in 291 adults at
AB  - hospital admission. MR-CoNS were characterized by SCCmec typing,
AB  - long-range polymerase chain reaction (PCR) for SCCmec IV, and
AB  - multiple-locus variable-number tandem repeat analysis (MLVA) for
AB  - Staphylococcus epidermidis (MRSE) strains. Three SCCmec IVa elements were
AB  - fully sequenced. RESULTS: The carriage rate of MR-CoNS was 19.2% (25.9%
AB  - and 16.5% in patients with and patients without previous exposure to the
AB  - health care system, respectively; P = .09). MR-CoNS strains (n = 83,
AB  - including 58 MRSE strains with highly heterogeneous MLVA patterns) carried
AB  - SCCmec type IVa (n = 9, all MRSE), other SCCmec IV subtypes (n = 9,
AB  - including 7 MRSE), other SCCmec types (n = 15), and nontypeable SCCmec (n
AB  - = 50). Long-range PCR indicated structural homology between SCCmec IV in
AB  - MRSE and that in MRSA. Complete sequences of SCCmec IVa from 3 MRSE
AB  - strains were highly homologous to those available for CA-MRSA, including
AB  - major clones USA300 and USA400. CONCLUSIONS: MR-CoNS are probably
AB  - disseminated in the community, notably in subjects without previous
AB  - exposure to the health care system. MRSE, the most prevalent species, may
AB  - act as a reservoir of SCCmec IVa for CA-MRSA.
ER  -

TY  - JOUR
AU  - Barbier, P.
AU  - Houel, A.
AU  - Loux, V.
AU  - Poulain, J.
AU  - Bernardet, J.F.
AU  - Touchon, M.
AU  - Duchaud, E.
TI  - Complete Genome Sequence of Flavobacterium indicum GPSTA100-9T, Isolated from Warm Spring Water.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3024
EP  - 3025
VL  - 194
AB  - We report here the complete annotated genome sequence of Flavobacterium indicum CIP 109464(T)
AB  - (= GPTSA100-9(T)), isolated from warm spring water in Assam, India.  The genome sequence of F.
AB  - indicum revealed a number of interesting features and genes in relation to its environmental
AB  - lifestyle.
ER  -

TY  - JOUR
AU  - Barbosa, B.G.
AU  - Fernandez-Garcia, L.
AU  - Gato, E.
AU  - Lopez, M.
AU  - Blasco, L.
AU  - Leao, R.S.
AU  - Albano, R.M.
AU  - Fernandez, B.
AU  - Cuenca, F.F.
AU  - Pascual, A.
AU  - Bou, G.
AU  - Marques, E.A.
AU  - Tomas, M.
TI  - Genome Sequence of Airborne Acinetobacter sp. Strain 5-2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri.
JO  - Genome Announcements
PY  - 2016
SP  - e01343
EP  - e01316
VL  - 4
AB  - Acinetobacter spp. are found in 53% of air colonization samples from the hospital environment.
AB  - In this work, we sequenced all the genome of airborne Acinetobacter
AB  - sp. strain 5-2Ac02. We found important features at the genomic level in regards
AB  - to the rhizome. By phylogenetic analysis, A. towneri was the species most closely
AB  - related to Acinetobacter sp. 5-2Ac02.
ER  -

TY  - JOUR
AU  - Barbosa, P.
AU  - Leao, C.
AU  - Usie, A.
AU  - Amaro, A.
AU  - Botelho, A.
AU  - Pinto, C.
AU  - Inacio, J.
AU  - Stevenson, K.
AU  - Ramos, A.M.
TI  - Draft Genome Sequence of a Rare Pigmented Mycobacterium avium subsp. paratuberculosis Type C Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e01066
EP  - e01017
VL  - 5
AB  - Mycobacterium avium subsp. paratuberculosis is the causative agent of paratuberculosis. We
AB  - report here the draft genome sequence of a rare pigmented M.
AB  - avium subsp. paratuberculosis type C strain, comprising 58 contigs and having a
AB  - genome size of 4,851,414 bp. The genome will assist in the execution of
AB  - pigmentation and virulence studies on this mycobacterium.
ER  -

TY  - JOUR
AU  - Barbour, A.G.
TI  - Chromosome and Plasmids of the Tick-Borne Relapsing Fever Agent Borrelia hermsii.
JO  - Genome Announcements
PY  - 2016
SP  - e00528
EP  - e00516
VL  - 4
AB  - The zoonotic pathogen Borrelia hermsii bears its multiple paralogous genes for variable
AB  - antigens on several linear plasmids. Application of combined long-read
AB  - and short-read next-generation sequencing provided complete sequences for
AB  - antigen-encoding plasmids as well as other linear and circular plasmids and the
AB  - linear chromosome of the genome.
ER  -

TY  - JOUR
AU  - Barbour, A.G.
AU  - Campeau, M.S.
TI  - Genome Sequence of Borrelia parkeri, an Agent of Enzootic Relapsing Fever in Western North America.
JO  - Genome Announcements
PY  - 2014
SP  - e00018
EP  - e00014
VL  - 2
AB  - Borrelia parkeri is a relapsing fever agent that rarely causes human infection, unlike other
AB  - North American species. B. parkeri strain HR1 was isolated from
AB  - Ornithodoros parkeri ticks. The sequences of its linear chromosome and large
AB  - plasmid were determined by next-generation sequencing. These confirmed its closer
AB  - relatedness to Borrelia turicatae than to Borrelia hermsii.
ER  -

TY  - JOUR
AU  - Barcus, V.A.
AU  - Murray, N.E.
TI  - Barriers to recombination: restriction.
JO  - Population Genetics of Bacteria
PY  - 1995
SP  - 31
EP  - 58
VL  - 0
AB  - The biological barrier provided by restriction is far from complete, and it can be quantified
AB  - by determining the titre of unmodified phages on the restricting strain relative to the titre
AB  - on a non-restricting strain.  For phage genomes with small numbers of targets, the barrier
AB  - increases with target number, as witnessed by a decrease in the efficiency of plating (eop).
AB  - Foreign DNA can be recognized and attacked by restriction endonucleases irrespective of its
AB  - mode of entry into the cell and nature has many tricks for combating restriction.
AB  - Nevertheless, a recipient strain with a restriction system is endowed with a potential barrier
AB  - to the intrusion of large DNA molecules should these molecules include the relevant, but
AB  - unmodified, target sequences.  Whether or not the cutting of larger DNA molecules into smaller
AB  - ones is necessarily a barrier to genetic recombination is of critical concern, since DNA
AB  - breaks can be substrates for recombination.  The restriction of foreign DNA is dependent on
AB  - the donor bacterium lacking a modification system that protects its DNA against attack by a
AB  - restriction system present within a recipient cell.  Any evaluation of the importance of
AB  - restriction to the transfer of genetic information requires an awareness of the diversity of
AB  - restriction specificities within a bacterial species.  This review considers what is known
AB  - about the diversity of restriction systems within the Enterobacteriaceae, but most
AB  - particularly within the best studied species, Escherichia coli.  In the absence of any truly
AB  - systematic analyses, the focus will be primarily on screens for chromosomally encoded
AB  - restriction and modification (R-M) systems.
ER  -

TY  - JOUR
AU  - Barcus, V.A.
AU  - Titheradge, A.J.B.
AU  - Murray, N.E.
TI  - The diversity of alleles at the hsd locus in natural populations of Escherichia coli.
JO  - Genetics
PY  - 1995
SP  - 1187
EP  - 1197
VL  - 140
AB  - In enteric bacteria three discrete families of type I restriction and modification systems
AB  - (IA, IB and ID) are encoded by alleles of the serB-linked hsd locus.  Probes specific for each
AB  - of the three families were used to monitor the distribution of related systems in 37 of the
AB  - 72 wild-type Escherichia coli strains comprising the ECOR collection.  All 25 members of group
AB  - A in this collection were screened; 12 were probe-positive, nine have hsd genes in the IA
AB  - family, two in the IB and one in the ID.  Twelve strains, representing all groups other than
AB  - A, were screened; five were probe-positive, one has hsd genes in the IA family, one in the IB
AB  - and three in the ID.  The type ID genes are the first representatives of this family in E.
AB  - coli, the probe-negative strains could have alternative families of hsd genes.  The type IA
AB  - and IB systems added at least five new specificities to the five already identified in natural
AB  - isolates of E. coli.  The distribution of alleles is inconsistant with the dendrogram of the
AB  - bacterial strains derived from other criteria.  This discrepancy and the dissimilar coding
AB  - sequences of allelic hsd genes both imply lateral transfer of hsd genes.
ER  -

TY  - JOUR
AU  - Barke, J.
AU  - Seipke, R.F.
AU  - Gruschow, S.
AU  - Heavens, D.
AU  - Drou, N.
AU  - Bibb, M.J.
AU  - Goss, R.J.
AU  - Yu, D.W.
AU  - Hutchings, M.I.
TI  - A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus.
JO  - BMC Biol.
PY  - 2010
SP  - 109
EP  - 109
VL  - 8
AB  - BACKGROUND: Attine ants live in an intensely studied tripartite mutualism
AB  - with the fungus Leucoagaricus gongylophorus, which provides food to the
AB  - ants, and with antibiotic-producing actinomycete bacteria. One hypothesis
AB  - suggests that bacteria from the genus Pseudonocardia are the sole,
AB  - co-evolved mutualists of attine ants and are transmitted vertically by the
AB  - queens. A recent study identified a Pseudonocardia-produced antifungal,
AB  - named dentigerumycin, associated with the lower attine Apterostigma
AB  - dentigerum consistent with the idea that co-evolved Pseudonocardia make
AB  - novel antibiotics. An alternative possibility is that attine ants sample
AB  - actinomycete bacteria from the soil, selecting and maintaining those
AB  - species that make useful antibiotics. Consistent with this idea, a
AB  - Streptomyces species associated with the higher attine Acromyrmex
AB  - octospinosus was recently shown to produce the well-known antifungal
AB  - candicidin. Candicidin production is widespread in environmental isolates
AB  - of Streptomyces, so this could either be an environmental contaminant or
AB  - evidence of recruitment of useful actinomycetes from the environment. It
AB  - should be noted that the two possibilities for actinomycete acquisition
AB  - are not necessarily mutually exclusive. RESULTS: In order to test these
AB  - possibilities we isolated bacteria from a geographically distinct
AB  - population of A. octospinosus and identified a candicidin-producing
AB  - Streptomyces species, which suggests that they are common mutualists of
AB  - attine ants, most probably recruited from the environment. We also
AB  - identified a Pseudonocardia species in the same ant colony that produces
AB  - an unusual polyene antifungal, providing evidence for co-evolution of
AB  - Pseudonocardia with A. octospinosus. CONCLUSIONS: Our results show that a
AB  - combination of co-evolution and environmental sampling results in the
AB  - diversity of actinomycete symbionts and antibiotics associated with attine
AB  - ants.
ER  -

TY  - JOUR
AU  - Barker, D.
AU  - Hoff, M.
AU  - Oliphant, A.
AU  - White, R.
TI  - A second type II restriction endonuclease from Thermus aquaticus with an unusual sequence specificity.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 5567
EP  - 5581
VL  - 12
AB  - A type II restriction endonuclease activity free of TaqI was prepared from Thermus aquaticus
AB  - YT.  The fraction contains two endonucleolytic components with apparently different
AB  - specificities, however the major activity is sufficiently dominant to allow partial digestion
AB  - analysis of the position of recognition sites.  A precise determination of the location of
AB  - cleavage sites in pBR322 DNA and a computer-aided search for regions of homology in the
AB  - vicinity of the cut sites indicate that this enzyme recognizes the nonpalindromic sequences
AB  - GACCGA or CACCCA.  Other related sequences are not cleaved, in particular, GACCCA and CACCGA,
AB  - indicating that the enzyme requires the identity of nucleotides in the first and fifth
AB  - positions, a type of specificity that has not been previously reported.  The position of
AB  - cleavage is located outside of the site and is represented as:
AB  - 5'-GACCGANNNNNNNNN^NN-3'
AB  - 3'-CTGGCTNNNNNNNNN^NN-5'.
ER  -

TY  - JOUR
AU  - Barker, E.N.
AU  - Helps, C.R.
AU  - Peters, I.R.
AU  - Darby, A.C.
AU  - Radford, A.D.
AU  - Tasker, S.
TI  - Complete Genome Sequence of Mycoplasma haemofelis, a Hemotropic Mycoplasma.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2060
EP  - 2061
VL  - 193
AB  - Here, we present the genome sequence of Mycoplasma haemofelis strain Langford 1, representing
AB  - the first hemotropic mycoplasma (hemoplasma)
AB  - species to be completely sequenced and annotated. Originally isolated from
AB  - a cat with hemolytic anemia, this strain induces severe hemolytic anemia
AB  - when inoculated into specific-pathogen-free-derived cats. The genome
AB  - sequence has provided insights into the biology of this uncultivatable
AB  - hemoplasma and has identified potential molecular mechanisms underlying
AB  - its pathogenicity.
ER  -

TY  - JOUR
AU  - Barlow, D.P.
TI  - Methylation and imprinting: from host defense to gene regulation?
JO  - Science
PY  - 1993
SP  - 309
EP  - 310
VL  - 260
ER  -

TY  - JOUR
AU  - Barlow, R.S.
AU  - Gobius, K.S.
TI  - Diverse class 2 integrons in bacteria from beef cattle sources.
JO  - J. Antimicrob. Chemother.
PY  - 2006
SP  - 1133
EP  - 1138
VL  - 58
AB  - OBJECTIVES: The purpose of this study was to determine the diversity of class 2 integrons in
AB  - bacteria isolated from beef cattle sources. METHODS:
AB  - The variable regions of a subset of 11 class 2 integron-containing
AB  - bacteria were analysed by PCR and DNA sequencing for the presence of novel
AB  - rearrangements. RESULTS: A total of six different class 2 integron arrays
AB  - were identified and four of these were fully characterized. Three of the
AB  - four arrays characterized have been previously described; however the
AB  - remaining array is unlike previously described class 2 integrons. The
AB  - novel class 2 integron was found in Providencia stuartii and contains an
AB  - apparently functional class 2 integrase. Examination of the variable
AB  - region of the P. stuartii integron identified nine open reading frames,
AB  - mostly of unknown function, and represents the first report of a class 2
AB  - integron without inserted antibiotic resistance gene cassettes.
AB  - CONCLUSIONS: This study has identified a novel class 2 integron found in
AB  - P. stuartii that contains an apparently functional naturally occurring
AB  - class 2 integrase. Further investigation of this novel class 2 integron is
AB  - required to determine the impact of a functional class 2 integrase upon
AB  - the evolution of class 2 integrons.
ER  -

TY  - JOUR
AU  - Barnaba, T.J.
AU  - Gangiredla, J.
AU  - Mammel, M.K.
AU  - Lacher, D.W.
AU  - Elkins, C.A.
AU  - Lampel, K.A.
AU  - Whitehouse, C.A.
AU  - Tartera, C.
TI  - Draft Genome Sequences of Bifidobacterium Strains Isolated from Dietary Supplements and Cultured Food Products.
JO  - Genome Announcements
PY  - 2018
SP  - e00610
EP  - e00618
VL  - 6
AB  - Here, we present the genome sequences of 23 Bifidobacterium isolates from several commercially
AB  - available dietary supplements and cultured food products. Strains of
AB  - this genus are natural inhabitants of the mammalian mouth, gastrointestinal
AB  - tract, and vagina. Some species are considered beneficial to human health.
ER  -

TY  - JOUR
AU  - Barnes, A.C.
AU  - Delamare-Deboutteville, J.
AU  - Gudkovs, N.
AU  - Brosnahan, C.
AU  - Morrison, R.
AU  - Carson, J.
TI  - Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection.
JO  - Microbial Genomics
PY  - 2016
SP  - E000095
EP  - E000095
VL  - 2
AB  - Yersinia ruckeri is a salmonid pathogen with widespread distribution in
AB  - cool-temperate waters including Australia and New Zealand, two isolated
AB  - environments with recently developed salmonid farming industries. Phylogenetic
AB  - comparison of 58 isolates from Australia, New Zealand, USA, Chile, Finland and
AB  - China based on non-recombinant core genome SNPs revealed multiple deep-branching
AB  - lineages, with a most recent common ancestor estimated at 18 500 years BP (12
AB  - 355-24 757 95% HPD) and evidence of Australasian endemism. Evolution within the
AB  - Tasmanian Atlantic salmon serotype O1b lineage has been slow, with 63 SNPs
AB  - describing the variance over 27 years. Isolates from the prevailing lineage are
AB  - poorly/non-motile compared to a lineage pre-vaccination, introduced in 1997,
AB  - which is highly motile but has not been isolated since from epizootics. A
AB  - non-motile phenotype has arisen independently in Tasmania compared to Europe and
AB  - USA through a frameshift in fliI, encoding the ATPase of the flagella cluster. We
AB  - report for the first time lipopolysaccharide O-antigen serotype O2 isolates in
AB  - Tasmania. This phenotype results from deletion of the O-antigen cluster and
AB  - consequent loss of high-molecular-weight O-antigen. This phenomenon has occurred
AB  - independently on three occasions on three continents (Australasia, North America
AB  - and Asia) as O2 isolates from the USA, China and Tasmania share the O-antigen
AB  - deletion but occupy distant lineages. Despite the European and North American
AB  - origins of the Australasian salmonid stocks, the lineages of Y. ruckeri in
AB  - Australia and New Zealand are distinct from those of the northern hemisphere,
AB  - suggesting they are pre-existing ancient strains that have emerged and evolved
AB  - with the introduction of susceptible hosts following European colonization.
ER  -

TY  - JOUR
AU  - Barnes, G.
AU  - Rine, J.
TI  - Regulated expression of endonuclease EcoRI in Saccharomyces cerevisiae: Nuclear entry and biological consequences.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1985
SP  - 1354
EP  - 1358
VL  - 82
AB  - In an investigation to determine how proteins are localized within the nucleus
AB  - of a cell, we demonstrate that the restriction endonuclease EcoRI is able to
AB  - enter and function within the nucleus of Saccharomyces cerevisiae when this
AB  - prokaryotic protein is synthesized in vivo.  The EcoRI endonuclease was
AB  - produced in yeast under the transcriptional control of a regulated yeast
AB  - promoter by ligating a DNA fragment containing only coding sequences for the
AB  - endonuclease to the promoter element of the yeast GAL1 gene (the structural
AB  - gene for galactokinase, EC 2.7.1.6).  Yeast cells harboring a plasmid
AB  - containing this promoter-gene fusion are able to grow under conditions that
AB  - repress transcription from the Gal1 promoter.  However, under inducing
AB  - conditions, these yeast cells are unable to grow.  Moreover, rad52 mutants,
AB  - which are deficient in the repair of double-strand breaks, are more sensitive
AB  - to the presence of the promoter-gene fusion plasmid than are wild-type cells.
AB  - We demonstrate that the EcoRI endonuclease activity is present in lysates
AB  - prepared from yeast transformants grown under conditions that induce
AB  - transcription of GAL1, but this activity is not detectable in cells grown under
AB  - conditions that repress transcription from the promoter.  Furthermore, analysis
AB  - of yeast chromosomal DNA shows that the endonuclease enters the yeast nucleus
AB  - and cleaves DNA specifically at EcoRI recognition sites.
ER  -

TY  - JOUR
AU  - Barnes, H.E.
AU  - Liu, G.
AU  - Weston, C.Q.
AU  - King, P.
AU  - Pham, L.K.
AU  - Waltz, S.
AU  - Helzer, K.T.
AU  - Day, L.
AU  - Sphar, D.
AU  - Yamamoto, R.T.
AU  - Forsyth, R.A.
TI  - Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases.
JO  - PLoS ONE
PY  - 2014
SP  - e109061
EP  - e109061
VL  - 9
AB  - To improve the metagenomic analysis of complex microbiomes, we have repurposed restriction
AB  - endonucleases as methyl specific DNA binding proteins. As an example, we use DpnI immobilized
AB  - on magnetic beads. The ten minute extraction technique allows specific binding of genomes
AB  - containing the DpnI G(m6) ATC motif common in the genomic DNA of many bacteria including
AB  - gamma-proteobacteria. Using synthetic genome mixtures, we demonstrate 80% recovery of
AB  - Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 mu g of
AB  - human DNA background. Binding is very specific with less than 0.5% of human DNA bound. Next
AB  - Generation Sequencing of input and enriched synthetic mixtures results in over 100-fold
AB  - enrichment of target genomes relative to human and plant DNA. We also show comparable
AB  - enrichment when sequencing complex microbiomes such as those from creek water and human
AB  - saliva. The technique can be broadened to other restriction enzymes allowing for the selective
AB  - enrichment of trace and unculturable organisms from complex microbiomes and the stratification
AB  - of organisms according to restriction enzyme enrichment.
ER  -

TY  - JOUR
AU  - Barony, G.M.
AU  - Tavares, G.C.
AU  - Pereira, F.L.
AU  - Carvalho, A.F.
AU  - Dorella, F.A.
AU  - Leal, C.A.G.
AU  - Figueiredo, H.C.P.
TI  - Large-scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms.
JO  - Sci. Rep.
PY  - 2017
SP  - 13538
EP  - 13538
VL  - 7
AB  - Streptococcus agalactiae is a major pathogen and a hindrance on tilapia farming
AB  - worldwide. The aims of this work were to analyze the genomic evolution of
AB  - Brazilian strains of S. agalactiae and to establish spatial and temporal
AB  - relations between strains isolated from different outbreaks of streptococcosis. A
AB  - total of 39 strains were obtained from outbreaks and their whole genomes were
AB  - sequenced and annotated for comparative analysis of multilocus sequence typing,
AB  - genomic similarity and whole genome multilocus sequence typing (wgMLST). The
AB  - Brazilian strains presented two sequence types, including a newly described ST,
AB  - and a non-typeable lineage. The use of wgMLST could differentiate each strain in
AB  - a single clone and was used to establish temporal and geographical correlations
AB  - among strains. Bayesian phylogenomic analysis suggests that the studied Brazilian
AB  - population was co-introduced in the country with their host, approximately 60
AB  - years ago. Brazilian strains of S. agalactiae were shown to be heterogeneous in
AB  - their genome sequences and were distributed in different regions of the country
AB  - according to their genotype, which allowed the use of wgMLST analysis to track
AB  - each outbreak event individually.
ER  -

TY  - JOUR
AU  - Barra, R.
AU  - Chiong, M.
AU  - Gonzalez, E.
AU  - Vasquez, C.
TI  - A DNA-modification methylase from Bacillus stearothermophilus V.
JO  - Biochem. J.
PY  - 1988
SP  - 699
EP  - 703
VL  - 255
AB  - A type II modification methylase (M.BstVI) was partially purified from the
AB  - thermophilic bacterium Bacillus stearothermophilus V.  The methylase catalyses
AB  - the transfer of methyl groups from S-adenosyl-L-methionine to unmodified
AB  - double-stranded DNA.  The product of methylation was identified by paper
AB  - chromatography as N6-methyladenine.  Since M.BstVI protects DNA against
AB  - cleavage by BstVI and XhoI restriction endonucleases, it follows that it
AB  - methylates the adenine residue in the sequence 5'-C-T-C-G-A-G-3'.
ER  -

TY  - JOUR
AU  - Barrado, L.
AU  - Viedma, E.
AU  - Vindel, A.
AU  - Otero, J.R.
AU  - Chaves, F.
TI  - Draft Genome Sequence of Strain SA_ST125_MupR of Methicillin-Resistant Staphylococcus aureus ST125, a Major Clone in Spain.
JO  - Genome Announcements
PY  - 2013
SP  - e00588
EP  - e00513
VL  - 1
AB  - Here, we report the draft genome sequence of a methicillin-resistant Staphylococcus aureus
AB  - (MRSA) strain with high-level mupirocin resistance
AB  - (SA_ST125_MupR), isolated from a patient with recurrent bacteremia. This strain
AB  - belonged to sequence type ST125, which was responsible for more than 50% of the
AB  - health care-associated infections caused by MRSA in Spain.
ER  -

TY  - JOUR
AU  - Barragan, V.
AU  - Sahl, J.W.
AU  - Wiggins, K.
AU  - Chiriboga, J.
AU  - Salinas, A.
AU  - Cantos, N.E.
AU  - Loor, M.N.
AU  - Intriago, B.I.
AU  - Morales, M.
AU  - Trueba, G.
AU  - Pearson, T.
TI  - Draft Genome Sequence of the First Pathogenic Leptospira Isolates from Ecuador.
JO  - Genome Announcements
PY  - 2016
SP  - e00271
EP  - e00216
VL  - 4
AB  - Pathogenic Leptospira spp. cause leptospirosis upon contact with mucosa through wounds or
AB  - ingestion, leading to headaches, fever, jaundice, kidney or liver
AB  - failure, or death in about 1.3 million people each year. Here, we present the
AB  - draft genomes of one L. santarosai isolate and two L. interrogans isolates from
AB  - Ecuador.
ER  -

TY  - JOUR
AU  - Barrangou, R.
AU  - Briczinski, E.P.
AU  - Traeger, L.L.
AU  - Loquasto, J.R.
AU  - Richards, M.
AU  - Horvath, P.
AU  - Coute-Monvoisin, A.C.
AU  - Leyer, G.
AU  - Rendulic, S.
AU  - Steele, J.L.
AU  - Broadbent, J.R.
AU  - Oberg, T.
AU  - Dudley, E.G.
AU  - Schuster, S.
AU  - Romero, D.A.
AU  - Roberts, R.F.
TI  - Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.
JO  - J. Bacteriol.
PY  - 2009
SP  - 4144
EP  - 4151
VL  - 191
AB  - Bifidobacteria are important members of the human gut flora, especially in infants.
AB  - Comparative genomic analysis of two Bifidobacterium animalis
AB  - subsp. lactis strains revealed evolution by internal deletion of
AB  - consecutive spacer-repeat units within a novel clustered regularly
AB  - interspaced short palindromic repeat locus, which represented the largest
AB  - differential content between the two genomes. Additionally, 47 single
AB  - nucleotide polymorphisms were identified, consisting primarily of
AB  - nonsynonymous mutations, indicating positive selection and/or recent
AB  - divergence. A particular nonsynonymous mutation in a putative glucose
AB  - transporter was linked to a negative phenotypic effect on the ability of
AB  - the variant to catabolize glucose, consistent with a modification in the
AB  - predicted protein transmembrane topology. Comparative genome sequence
AB  - analysis of three Bifidobacterium species provided a core genome set of
AB  - 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome
AB  - sequences of the intestinal bacterium B. animalis subsp. lactis provide
AB  - insights into rapid genome evolution and the genetic basis for adaptation
AB  - to the human gut environment, notably with regard to catabolism of dietary
AB  - carbohydrates, resistance to bile and acid, and interaction with the
AB  - intestinal epithelium. The high degree of genome conservation observed
AB  - between the two strains in terms of size, organization, and sequence is
AB  - indicative of a genomically monomorphic subspecies and explains the
AB  - inability to differentiate the strains by standard techniques such as
AB  - pulsed-field gel electrophoresis.
ER  -

TY  - JOUR
AU  - Barrangou, R.
AU  - van der Oost, J.
TI  - Bacteriophage exclusion, a new defense system.
JO  - EMBO J.
PY  - 2015
SP  - 134
EP  - 135
VL  - 34
AB  - The ability to withstand viral predation is critical for survival of most microbes.
AB  - Accordingly, a plethora of phage resistance
AB  - systems has been identified in bacterial genomes (Labrie et al, 2010), including
AB  - restriction-modification systems (R-M) (Tock
ER  -

TY  - JOUR
AU  - Barras, F.
AU  - Marinus, M.G.
TI  - The great GATC:  DNA methylation in E. coli.
JO  - Trends Genet.
PY  - 1989
SP  - 139
EP  - 143
VL  - 5
AB  - In Escherichia coli the methylation of the adenine in the sequence 5'-GATC-3' is catalysed
AB  - by the dam gene product, a DNA adenine methylase. We review the proposed roles for this
AB  - methylation, and the sequence it modifies, in mismatch repair, DNA-protein interaction, gene
AB  - expression, the initiation of chromosome replication, chromosome segregation, chromosome
AB  - structure and the occurrence of mutational hotspots.
ER  -

TY  - JOUR
AU  - Barreau, G.
AU  - Tompkins, T.A.
AU  - de Carvalho, V.G.
TI  - Draft Genome Sequence of Probiotic Strain Pediococcus acidilactici MA18/5M.
JO  - J. Bacteriol.
PY  - 2012
SP  - 901
EP  - 901
VL  - 194
AB  - Pediococcus acidilactici MA18/5M is a commercially available probiotic that is widely used in
AB  - swine, poultry, aquaculture feeds, and human
AB  - dietary supplements. We prepared a genome sequence for this strain
AB  - consisting of 2 scaffolds totaling 1,992,928 bases including gaps for a
AB  - total of 3,346 bases and a G+C content of 42%.
ER  -

TY  - JOUR
AU  - Barreiro, C. et al.
TI  - Draft Genome of Streptomyces tsukubaensis NRRL 18488, the Producer of the Clinically Important Immunosuppressant Tacrolimus (FK506).
JO  - J. Bacteriol.
PY  - 2012
SP  - 3756
EP  - 3757
VL  - 194
AB  - The macrocyclic polyketide tacrolimus (FK506) is a potent immunosuppressant that  prevents
AB  - T-cell proliferation produced solely by Streptomyces species. We report
AB  - here the first draft genome sequence of a true FK506 producer, Streptomyces
AB  - tsukubaensis NRRL 18488, the first tacrolimus-producing strain that was isolated
AB  - and that contains the full tacrolimus biosynthesis gene cluster.
ER  -

TY  - JOUR
AU  - Barrera, C.
AU  - Valot, B.
AU  - Rognon, B.
AU  - Zaugg, C.
AU  - Monod, M.
AU  - Millon, L.
TI  - Draft Genome Sequence of the Principal Etiological Agent of Farmer's Lung Disease, Saccharopolyspora rectivirgula.
JO  - Genome Announcements
PY  - 2014
SP  - e01340
EP  - e01314
VL  - 2
AB  - Saccharopolyspora rectivirgula is the main cause of farmer's lung disease. The development of
AB  - recombinant antigens to standardize the serodiagnosis of the
AB  - disease requires knowledge of the S. rectivirgula genome. We sequenced the genome
AB  - of an environmental strain, S. rectivirgula DSM 43113. A total of 3,221 proteins
AB  - were found to be encoded in a short 3.9-Mb genome.
ER  -

TY  - JOUR
AU  - Barrero, R.A.
AU  - Moolhuijzen, P.
AU  - Indjein, L.
AU  - Venus, B.
AU  - Keeble-Gagnere, G.
AU  - Power, J.
AU  - Bellgard, M.I.
AU  - Lew-Tabor, A.E.
TI  - Draft Genome Sequences of Campylobacter fetus subsp. venerealis bv. venerealis Strain B6 and bv. intermedius Strain 642-21.
JO  - Genome Announcements
PY  - 2014
SP  - e00943
EP  - e00914
VL  - 2
AB  - Campylobacter fetus subsp. venerealis is an important venereal pathogen. We sequenced the
AB  - genomes of Campylobacter fetus subsp. venerealis bv. venerealis
AB  - strain B6 and bv. intermedius strain 642-21. The genetic variability of these
AB  - Australian strains will facilitate the study of mechanisms of geographical
AB  - adaptation of these pathogens that impact livestock.
ER  -

TY  - JOUR
AU  - Barreto-Hernandez, E.
AU  - Falquet, L.
AU  - Reguero, M.T.
AU  - Mantilla, J.R.
AU  - Valenzuela, E.M.
AU  - Gonzalez, E.
AU  - Cepeda, A.
AU  - Escalante, A.
TI  - Draft Genome Sequences of Multidrug-Resistant Acinetobacter sp. Strains from Colombian Hospitals.
JO  - Genome Announcements
PY  - 2013
SP  - e00868
EP  - e00813
VL  - 1
AB  - The draft genome sequences of the strains Acinetobacter baumannii 107m, Acinetobacter
AB  - nosocomialis 28F, and Acinetobacter pittii 42F, isolated from
AB  - Colombian hospitals, are reported here. These isolates are causative of
AB  - nosocomial infections and are classified as multidrug resistant, as they showed
AB  - resistance to four different antibiotic groups.
ER  -

TY  - JOUR
AU  - Barretto, C.
AU  - Alvarez-Martin, P.
AU  - Foata, F.
AU  - Renault, P.
AU  - Berger, B.
TI  - Genome Sequence of the Lantibiotic Bacteriocin Producer Streptococcus salivarius  Strain K12.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5959
EP  - 5960
VL  - 194
AB  - Streptococcus salivarius is a prevalent commensal species of the oropharyngeal tract. S.
AB  - salivarius strain K12 is an isolate from the saliva of a healthy child,
AB  - used as an oral probiotic. Here, we report its genome sequence, i.e., the full
AB  - sequence of the 190-kb megaplasmid pSsal-K12 and a high-quality draft 2.2-Gb
AB  - chromosomal sequence.
ER  -

TY  - JOUR
AU  - Barretto, C.
AU  - Ngom-Bru, C.
AU  - Genevaz, A.
AU  - Fournier, C.
AU  - Moine, D.
AU  - Kassam, M.
AU  - Iltis, A.
AU  - Sagory-Zalkind, P.
AU  - Ciron, P.E.
AU  - Faucherand, G.
AU  - Descombes, P.
AU  - Duboux, S.
TI  - Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068).
JO  - Genome Announcements
PY  - 2016
SP  - e01254
EP  - e01216
VL  - 4
AB  - Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the
AB  - Nestle Culture Collection. Here, we disclose its full 1.9-Gb
AB  - genome sequence comprising one chromosome with no plasmid.
ER  -

TY  - JOUR
AU  - Barshevsky, T.
AU  - Benner, J.S.
TI  - Site-directed mutagenesis of the EcoRV methylase for the study of the functional role of the conserved sequences in N6-adenine methylases.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 211
EP  - 211
VL  - 13D
AB  - EcoRV methylase has been used as a model system to investigate the function of the conserved
AB  - sequences in N6-adenine methylases. The EcoRV methylase gene was subcloned and the methylase
AB  - protein was purified by multiple chromatographic steps. The highly conserved DPPY potein
AB  - sequence in the EcoRV methylase was changed using site-directed oligonucleotide mutagenesis in
AB  - both conservative and radical ways. We produced protein sequence changes at the D, the first P
AB  - and the Y so that the predicted secondary and unknown tertiary structures of this region were
AB  - not only gently perturbed but also disrupted. The EcoRV methylase with the first change (DPPY
AB  - to EPPY) was subcloned back into a modified pUC19 vector. This change produced a methylase
AB  - which unlike the wild-type enzyme does not fully methylate in vivo the genomic or vector DNA.
AB  - We are examining the catalytic properties of the wild-type EcoRV methylase and some
AB  - mutagenized methylase proteins. Also efforts will be made to determine whether SAM or DNA
AB  - binding, if any, remains in mutant methylases.
ER  -

TY  - JOUR
AU  - Barsomian, J.M.
AU  - Card, C.O.
AU  - Wilson, G.G.
TI  - Cloning of the HhaI and HinPI restriction-modification systems.
JO  - Gene
PY  - 1988
SP  - 5
EP  - 7
VL  - 74
AB  - The genes for the HhaI (Roberts et al., 1976) and HinPI (Roberts, 1987)
AB  - restriction-modification (R-M) systems have been cloned in pBR322.  The HhaI
AB  - system was isolated on a 9-kb PstI fragment, and the HinPI system was isolated
AB  - on two PstI fragments of 1.5 and 4.6 kb in length.  The clones were isolated by
AB  - selecting for recombinant molecules that had protectively modified themselves.
AB  - The HhaI and HinPI R-M systems recognize the same sequence, GCGC, but
AB  - hybridization between the DNA fragments encoding them does not take place.
AB  - Note:  this should be HinP1I.
ER  -

TY  - JOUR
AU  - Bart, A.
TI  - Genetic variation in Neisseria meningitidis.
JO  - Ph.D. Thesis, Univ. Amsterdam, Netherlands
PY  - 1999
SP  - 1
EP  - 115
AB  - Neisseria meningitidis or meningococcus is a Gram-negative diplococcus that is a member of the
AB  - family of the Neisseriaceae, belonging to the beta subdivision of the proteobacteria.  The
AB  - genus Neisseria includes closely related species.  These diplococci are primarily commensals
AB  - of the mucous membranes of mammals.  N. meningitidis and N. gonorrhoeae, are well-known
AB  - pathogens of man, although various Neisseria species are opportunistic pathogens (e.g. N.
AB  - flavescens and N. lactamica).  The meningococcus, usually carried in the nasopharynx and
AB  - oroparynx of humans, is distinguished from other Neisseria species on the basis of its sugar
AB  - metabolism.  The Neisseria are usually described as being immobile, though a recent report
AB  - suggests that they may display "twitching motility".
ER  -

TY  - JOUR
AU  - Bart, A.
AU  - Dankert, J.
AU  - van der Ende, A.
TI  - Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone.
JO  - FEMS Microbiol. Lett.
PY  - 2000
SP  - 111
EP  - 114
VL  - 188
AB  - Neisseria meningitidis may cause meningitis and septicemia.  Since the early 1980s, an
AB  - increased incidence of meningococcal disease has been caused by the lineage III clone in many
AB  - countries in Europe and in New Zealand.  We hypothesized that lineage III meningococci have
AB  - specific DNA sequences, providing an opportunity to facilitate epidemiological studies by
AB  - detecting lineage III isolates rapidly.  Applying representational difference analysis on one
AB  - lineage III tester strain and two non-lineage III driver strains, we identified three lineage
AB  - III-specific sequences, probably part of a single locus encoding a restriction modification
AB  - system.  A PCR based on one of these sequences identified lineage III meningococcal isolates
AB  - with a sensitivity of 100% and a specificity of 93%, which is superior to the serological
AB  - identification of lineage III isolates.
ER  -

TY  - JOUR
AU  - Bart, A.
AU  - Dankert, J.
AU  - van der Ende, A.
TI  - Operator sequences for the regulatory proteins of restriction modification systems.
JO  - Mol. Microbiol.
PY  - 1999
SP  - 1275
EP  - 1281
VL  - 31
AB  - For some type II restriction modification systems, it has been shown that transcription of the
AB  - methylase gene and the restriction endonuclease gene is regulated by the control gene product.
AB  - In these systems, C is located directly upstream of R, and in most systems M is located
AB  - divergently from CR.  The control element is a short (~80 amino acids) protein containing a
AB  - helix-turn-helix DNA-binding motif, distantly related to the well-known phage lambda cl
AB  - regulator.
ER  -

TY  - JOUR
AU  - Bart, A.
AU  - Pannekoek, Y.
AU  - Dankert, J.
AU  - van der Ende, A.
TI  - NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain.
JO  - Infect. Immun.
PY  - 2001
SP  - 1816
EP  - 1820
VL  - 69
AB  - Neisseria meningitidis is a gram-negative bacterium that may cause meningitis, sepsis, or
AB  - both. The increase in the incidence of
AB  - meningococcal disease in various countries in the past 2 decades is
AB  - mainly due the genotypically related lineage III meningococci. The
AB  - chromosomal DNA differences between lineage III strains and non-lineage
AB  - III strains were identified using representational difference analysis.
AB  - Thus, a 1.8-kb locus that is specific for lineage III meningococci was
AB  - identified. The locus contains three open reading frames encoding the
AB  - NmeSI restriction-modification system. The methyltransferase gene was
AB  - cloned and expressed in Escherichia coli. Site AGTACT was found to be
AB  - modified by the enzyme. In conclusion, lineage III strains differ from
AB  - endemic strains by the presence of a specific restriction-modification
AB  - system. This restriction-modification system may contribute to the
AB  - clonal and hypervirulent character of lineage III strains by
AB  - influencing horizontal gene transfer and transcription.
ER  -

TY  - JOUR
AU  - Bart, A.
AU  - Pannekoek, Y.
AU  - Dankert, J.
AU  - van der Ende, A.
TI  - The NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria  meningitidis strain.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 303
EP  - 303
VL  - 101
AB  - Neisseria meningitidis is a Gram-negative bacterium that may cause meningitis, sepsis or both.
AB  - In the past two decades, an increase in the
AB  - incidence of meningococcal disease in the Netherlands and various other
AB  - countries has been observed. This increase is mainly due to the
AB  - genotypically related lineage III meningococci. We hypothesize that a
AB  - genetic trait is responsible for the observed clonal and hypervirulent
AB  - phenotype of lineage III strains. Chromosomal DNA differences between
AB  - lineage III strains and non-lineage III strains were identified using
AB  - representational difference analysis. Thus, a 1.8 kb locus that is
AB  - specific for lineage III meningococci was identified. The locus
AB  - contains three open reading frames encoding the NmeSI restriction
AB  - modification system. The methyltransferase gene was cloned and
AB  - expressed in Escherichia coli. The site AGTACT was found to be
AB  - N4-cytosine modified by the recombinant enzyme. Chromosomal DNA of
AB  - lineage III strains was shown to be methylated at AGTACT sequences, in
AB  - contrast to DNA of non-lineage III strains. In conclusion, lineage III
AB  - strains differ from endemic strains by the presence of a specific
AB  - restriction modification system, causing differential methylation of
AB  - chromosomal DNA. The restriction modification system may contribute to
AB  - the clonal and hypervirulent character of lineage III strains by
AB  - influencing horizontal gene transfer and transcription.
ER  -

TY  - JOUR
AU  - Bart, A.
AU  - van Passel, M.W.
AU  - van Amsterdam, K.
AU  - van der Ende, A.
TI  - Direct detection of methylation in genomic DNA.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - e124
EP  - e124
VL  - 33
AB  - The identification of methylated sites on bacterial genomic DNA would be a useful tool to
AB  - study the major roles of DNA methylation in prokaryotes: distinction of
AB  - self and nonself DNA, direction of post-replicative mismatch repair, control of
AB  - DNA replication and cell cycle, and regulation of gene expression. Three types of
AB  - methylated nucleobases are known: N6-methyladenine, 5-methylcytosine and
AB  - N4-methylcytosine. The aim of this study was to develop a method to detect all
AB  - three types of DNA methylation in complete genomic DNA. It was previously shown
AB  - that N6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be
AB  - detected by intersequence trace comparison of methylated and unmethylated DNA. We
AB  - extended this method to include N4-methylcytosine detection in both in vitro and
AB  - in vivo methylated DNA. Furthermore, application of intersequence trace
AB  - comparison was extended to bacterial genomic DNA. Finally, we present evidence
AB  - that intrasequence comparison suffices to detect methylated sites in genomic DNA.
AB  - In conclusion, we present a method to detect all three natural types of DNA
AB  - methylation in bacterial genomic DNA. This provides the possibility to define the
AB  - complete methylome of any prokaryote.
ER  -

TY  - JOUR
AU  - Bart, M.J.
AU  - van der Heide, H.G.
AU  - Zeddeman, A.
AU  - Heuvelman, K.
AU  - van Gent, M.
AU  - Mooi, F.R.
TI  - Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic ptxP3 Lineage.
JO  - Genome Announcements
PY  - 2015
SP  - e01394
EP  - e01315
VL  - 3
AB  - Pathogen adaptation has contributed to the resurgence of pertussis. To facilitate our
AB  - understanding of this adaptation we report here 11 completely closed and
AB  - annotated Bordetella pertussis genomes representing the pandemic ptxP3 lineage.
AB  - Our analyses included six strains which do not produce the vaccine components
AB  - pertactin and/or filamentous hemagglutinin.
ER  -

TY  - JOUR
AU  - Bart, M.J.
AU  - van Gent, M.
AU  - van der Heide, H.G.
AU  - Boekhorst, J.
AU  - Hermans, P.
AU  - Parkhill, J.
AU  - Mooi, F.R.
TI  - Comparative genomics of prevaccination and modern Bordetella pertussis strains.
JO  - BMC Genomics
PY  - 2010
SP  - 627
EP  - 627
VL  - 11
AB  - BACKGROUND: Despite vaccination since the 1950s, pertussis has persisted and
AB  - resurged. It remains a major cause of infant death worldwide and is the most
AB  - prevalent vaccine-preventable disease in developed countries. The resurgence of
AB  - pertussis has been associated with the expansion of Bordetella pertussis strains
AB  - with a novel allele for the pertussis toxin (Ptx) promoter, ptxP3, which have
AB  - replaced resident ptxP1 strains. Compared to ptxP1 strains, ptxP3 produce more
AB  - Ptx resulting in increased virulence and immune suppression. To elucidate how B.
AB  - pertussis has adapted to vaccination, we compared genome sequences of two ptxP3
AB  - strains with four strains isolated before and after the introduction vaccination.
AB  - RESULTS: The distribution of SNPs in regions involved in transcription and
AB  - translation suggested that changes in gene regulation play an important role in
AB  - adaptation. No evidence was found for acquisition of novel genes. Modern strains
AB  - differed significantly from prevaccination strains, both phylogenetically and
AB  - with respect to particular alleles. The ptxP3 strains were found to have diverged
AB  - recently from modern ptxP1 strains. Differences between ptxP3 and modern ptxP1
AB  - strains included SNPs in a number of pathogenicity-associated genes. Further,
AB  - both gene inactivation and reactivation was observed in ptxP3 strains relative to
AB  - modern ptxP1 strains. CONCLUSIONS: Our work suggests that B. pertussis adapted by
AB  - successive accumulation of SNPs and by gene (in)activation. In particular changes
AB  - in gene regulation may have played a role in adaptation.
ER  -

TY  - JOUR
AU  - Bart, M.J.
AU  - Zeddeman, A.
AU  - van der Heide, H.G.
AU  - Heuvelman, K.
AU  - van Gent, M.
AU  - Mooi, F.R.
TI  - Complete Genome Sequences of Bordetella pertussis Isolates B1917 and B1920, Representing Two Predominant Global Lineages.
JO  - Genome Announcements
PY  - 2014
SP  - e01301
EP  - e01314
VL  - 2
AB  - Bordetella pertussis is the causative agent of pertussis, a disease which has resurged despite
AB  - vaccination. We report the complete, annotated genomes of
AB  - isolates B1917 and B1920, representing two lineages predominating globally in the
AB  - last 50 years. The B1917 lineage has been associated with the resurgence of
AB  - pertussis in the 1990s.
ER  -

TY  - JOUR
AU  - Bartee, L.
AU  - Bender, J.
TI  - Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 2127
EP  - 2134
VL  - 29
AB  - In Arabidopsis a SWI2/SNF2 chromatin remodeling factor-related protein DDM1 and a cytosine
AB  - methyltransferase MET1 are required for maintenance of genomic cytosine methylation. Mutations
AB  - in either gene cause global demethylation. In this work we have assessed the effects of these
AB  - mutations on the PAI tryptophan biosynthetic gene family, which consists of four densely
AB  - methylated genes arranged as a tail-to-tail inverted repeat plus two unlinked singlet genes.
AB  - The methylation mutations caused only partial demethylation of the PAI loci: ddm1 had a strong
AB  - effect on the singlet genes but a weaker effect on the inverted repeat, whereas met1 had a
AB  - stronger effect on the inverted repeat than on the singlet genes. The double ddm1 met1 mutant
AB  - also displayed partial demethylation of the PAI genes, with a pattern similar to the ddm1
AB  - single mutant. To determine the relationship between partial methylation and expression for
AB  - the singlet PAI2 gene we constructed a novel reporter strain of Arabidopsis in which PAI2
AB  - silencing could be monitored by a blue fluorescent plant phenotype diagnostic of tryptophan
AB  - pathway defects. This reporter strain revealed that intermediate levels of methylation
AB  - correlate with intermediate suppression of the fluorescent phenotype.
ER  -

TY  - JOUR
AU  - Bartee, L.
AU  - Malagnac, F.
AU  - Bender, J.
TI  - Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.
JO  - Genes Dev.
PY  - 2001
SP  - 1753
EP  - 1758
VL  - 15
AB  - Plants maintain cytosine methylation at CG and non-CG residues to control gene expression and
AB  - genome stability. In a screen for Arabidopsis mutants that alter methylation and silencing of
AB  - a densely methylated endogenous reporter gene, we recovered 11 loss-of-function alleles in the
AB  - CMT3 chromomethylase gene. The cmt3 mutants displayed enhanced expression and reduced
AB  - methylation of the reporter, particularly at non-CG cytosines. CNG methylation was also
AB  - reduced at repetitive centromeric sequences. Thus, CMT3 is a key determinant for non-CG
AB  - methylation. The lack of CMT homologs in animal genomes could account for the observation that
AB  - in contrast to plants, animals maintain primarily CG methylation.
ER  -

TY  - JOUR
AU  - Bartelme, R.P.
AU  - Barbier, P.
AU  - Lipscomb, R.S.
AU  - LaPatra, S.E.
AU  - Newton, R.J.
AU  - Evenhuis, J.P.
AU  - McBride, M.J.
TI  - Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain MS-FC-4.
JO  - Genome Announcements
PY  - 2018
SP  - e00429
EP  - e00418
VL  - 6
AB  - Flavobacterium columnare MS-FC-4 is a highly virulent genetic group 1 (formerly genomovar I)
AB  - strain isolated from rainbow trout (Oncorhynchus mykiss). The draft
AB  - genome consists of three contigs totaling 3,449,277 bp with 2,811 predicted open
AB  - reading frames. F. columnare MS-FC-4 is a model strain for functional genomic
AB  - analyses.
ER  -

TY  - JOUR
AU  - Bartelme, R.P.
AU  - Newton, R.J.
AU  - Zhu, Y.
AU  - Li, N.
AU  - LaFrentz, B.R.
AU  - McBride, M.J.
TI  - Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain C#2.
JO  - Genome Announcements
PY  - 2016
SP  - e00624
EP  - e00616
VL  - 4
AB  - Flavobacterium columnare is a Gram-negative bacterial pathogen that causes columnaris disease
AB  - of freshwater fish. Flavobacterium columnare strain C#2 was
AB  - isolated from a diseased warm-water fish and is typed as genomovar II. The genome
AB  - consists of a single 3.33-Mb circular chromosome with 2,689 predicted coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Bartels, M.D.
AU  - Hansen, L.H.
AU  - Boye, K.
AU  - Sorensen, S.J.
AU  - Westh, H.
TI  - An Unexpected Location of the Arginine Catabolic Mobile Element (ACME) in a USA300-Related MRSA StrainJ3 region.
JO  - PLoS ONE
PY  - 2011
SP  - e16193
EP  - e16193
VL  - 6
AB  - In methicillin resistant Staphylococcus aureus (MRSA), the arginine catabolic mobile element
AB  - (ACME) was initially described in USA300 (t008-ST8) where it is located downstream of the
AB  - staphylococcal cassette chromosome mec (SCCmec). A common health-care associated MRSA in
AB  - Copenhagen, Denmark (t024-ST8) is clonally related to USA300 and is frequently PCR
AB  - positive for the ACME specific arcA-gene. This study is the first to describe an ACME element
AB  - upstream of the SCCmec in MRSA. By traditional SCCmec typing schemes, the SCCmec of t024-ST8
AB  - strain M1 carries SCCmec IVa, but full sequencing of the cassette revealed that the entire J3
AB  - region had no homology to published SCCmec IVa. Within the J3 region of M1 was a 1705 bp
AB  - sequence only similar to a sequence in S. haemolyticus strain JCSC1435 and 2941 bps with no
AB  - homology found in GenBank. In addition to the usual direct repeats (DR) at each extremity of
AB  - SCCmec, M1 had two new DR between the orfX gene and the J3 region of the SCCmec. The region
AB  - between the orfX DR (DR1) and DR2 contained the ccrAB4 genes. An ACME II-like element was
AB  - located between DR2 and DR3. The entire 26,468 bp sequence between DR1 and DR3 was highly
AB  - similar to parts of the ACME composite island of S. epidermidis strain ATCC12228. Sequencing
AB  - of an ACME negative t024-ST8 strain (M299) showed that DR1 and the sequence between DR1 and
AB  - DR3 was missing. The finding of a mobile ACME II-like element inserted downstream of orfX and
AB  - upstream of SCCmec indicates a novel recombination between staphylococcal species.
ER  -

TY  - JOUR
AU  - Bartoli, C.
AU  - Carrere, S.
AU  - Lamichhane, J.R.
AU  - Varvaro, L.
AU  - Morris, C.E.
TI  - Whole-Genome Sequencing of 10 Pseudomonas syringae Strains Representing Different Host Range Spectra.
JO  - Genome Announcements
PY  - 2015
SP  - e00379
EP  - e00315
VL  - 3
AB  - Pseudomonas syringae is a ubiquitous bacterium that readily persists in environmental habitats
AB  - as a saprophyte and also is responsible for numerous
AB  - diseases of crops. Here, we report the whole-genome sequences of 10 strains
AB  - isolated from both woody and herbaceous plants that will contribute to the
AB  - elucidation of the determinants of their host ranges.
ER  -

TY  - JOUR
AU  - Barton, J.K.
TI  - Transition metal complexes in the design of synthetic restriction enzymes.
JO  - ACS Abstracts
PY  - 1988
SP  - 44
EP  - 44
VL  - 195
AB  - Restriction endonucleases recognize specific double-stranded DNA sequences and
AB  - cleave both strands to yield 5'phosphate and 3'hydroxyl termini.  Coordination
AB  - complexes have now been designed which simulate specific binding and catalytic
AB  - features of restriction endonucleases.  Based upon a matching of shapes and
AB  - symmetries, phenanthroline derivatives of ruthenium complexes have been
AB  - prepared which recognize a variety of distinct conformations along the strand.
AB  - Transition metal complexes may be converted to novel DNA cleaving molecules by
AB  - tethering of polyamine arms onto the DNA binding moiety.  These polyamine arms,
AB  - directed to the sugar-phosphate backbone provide chelating centers for divalent
AB  - metal ions such as Zn2+, Cd2+, and Pb2+, and upon activation with these metal
AB  - ions, double-stranded hydrolytic cleavage of the phosphodiester linkages is
AB  - observed.  Aspects of both binding specificity and reactivity of the metal
AB  - complexes with DNA will be described.
ER  -

TY  - JOUR
AU  - Barton, J.K.
AU  - Basile, L.A.
AU  - Paranawithana, S.R.
TI  - The presence of zinc in the restriction enzyme EcoRI*.
JO  - J. Biol. Chem.
PY  - 1982
SP  - 7911
EP  - 7914
VL  - 257
AB  - We have determined that the restriction endonuclease EcoRI contains 1.0 +- 0.1
AB  - eq of zinc/monomeric enzyme.  DNA cleavage by EcoRI is inhibited by
AB  - orthophenanthroline after preincubation of the enzyme with the chelating agent.
AB  - A similar inhibition by the nonchelating meta-phenanthroline is not seen.  The
AB  - sensitivity of the inhibition by the neutral ligand ortho-phenanthroline to
AB  - preincubation is consistent with the tightly bound and inaccessible nature of
AB  - the metal site.  Extensive dialysis against the ortho-phenanthroline inhibitor
AB  - leads to the release of the bound metal with the concomitant loss of enzyme
AB  - activity.  The tightly bound Zn2+ cation, then, appears to be necessary for
AB  - enzyme function.  The finding of zinc in EcoRI further illustrates the ubiquity
AB  - of Zn2+ to DNA-protein complexes.
ER  -

TY  - JOUR
AU  - Barton, J.K.
AU  - Paranawithana, S.R.
TI  - Restriction endonuclease EcoRI alters the Enantiomeric Preference of Chiral Metallointercalators for DNA:  an illustration of a protein-induced DNA conformational change.
JO  - Biochemistry
PY  - 1986
SP  - 2205
EP  - 2211
VL  - 25
AB  - A conformational change in the DNA plasmid ColE1 appears to occur upon specific
AB  - binding of the restriction endonuclese EcoRI.  Enzyme association alters the
AB  - chiral discrimination found in binding metallointercalators to DNA sites.  The
AB  - complexes tris(1,10-phenanthroline) ruthenium(II), Ru(phen) 32+, and
AB  - tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III), Co(DIP)33+, in general, bind
AB  - stereoselectively to DNA helices, with enantiomers processing the D
AB  - configuration bound preferentially by right-handed B-DNA.  In the presence of
AB  - EcoRI, however, this enantioselectivity is altered.  The chiral intercalators,
AB  - at micromolar concentrations, inhibit the reaction of EcoRI, but for each
AB  - enantiomeric pair it is the K enantiomer, which binds only poorly to a B-DNA
AB  - helix, that inhibits EcoRI preferentially.  Kinetic studies in the presence of
AB  - K in the presence of K-Ru(DIP)32+ indicate that the enzyme inhibition occurs as
AB  - a result of the K enantiomer binding to the enzyme-DNA complex as well as to
AB  - the free enzyme.  Furthermore, photolytic strand cleavage experiments using
AB  - Co(DIP)33+ indicate that the metal complex interacts directly at the
AB  - protein-bound DNA site.  Increasing concentrations of bound EcoRI stimulate
AB  - photoactivated cleavage of the DNA helix by K-Co(DIP)33+, until a protein
AB  - concentration is reached where specific DNA recognition sites are saturated
AB  - with enzyme.  Thus, although K-Co(DIP)33+ does not bind closely to the DNA in
AB  - the absence of enzyme, specific binding of EcoRI appears to alter the DNA
AB  - structure so as to permit the close association of the K isomer to the DNA
AB  - helix.  Mapping experiments demonstrate that this association leads to
AB  - photocleavage of DNA by the cobalt complex at or very close to the EcoRI
AB  - recognition site.  This study provides evidence that in solution, under
AB  - enzymatic conditions, a DNA-binding protein may distort the DNA helical
AB  - structure and further illustrates how small molecular probes of DNA
AB  - conformation might be used in examining the structure of protein-bound DNA
AB  - sites.
ER  -

TY  - JOUR
AU  - Baryshev, M.M.
AU  - Buryanov, Y.I.
AU  - Kosykh, V.G.
AU  - Bayev, A.A.
TI  - Isolation, purification and some properties of restrictase and methylase BstNI from Bacillus stearothermophilus.
JO  - Biokhimiia
PY  - 1989
SP  - 1894
EP  - 1903
VL  - 54
AB  - Restriction-methylation enzymes BstNI from Bacillus stearothermophilus were
AB  - isolated and purified.  These enzymes are related to a new class of
AB  - restriction-methylation enzymes of the second type, whose modifying component
AB  - is N4-cytosine-DNA-methylase.  Both enzymes recognize the DNA sequence
AB  - CC(A/T)GG.  Restrictase BstNI is a protein made up of one subunit with a
AB  - molecular mass of 25 kDa.  The temperature optima for restrictase and methylase
AB  - BstNI are around 60C.  Possible uses of BstNI restriction-methylation enzymes
AB  - for the analysis of cytosine methylation in bacterial and higher plant DNA are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Barzel, A.
AU  - Privman, E.
AU  - Peeri, M.
AU  - Naor, A.
AU  - Shachar, E.
AU  - Burstein, D.
AU  - Lazary, R.
AU  - Gophna, U.
AU  - Pupko, T.
AU  - Kupiec, M.
TI  - Native homing endonucleases can target conserved genes in humans and in animal models.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 6646
EP  - 6659
VL  - 39
AB  - In recent years, both homing endonucleases (HEases) and zinc-finger nucleases (ZFNs) have been
AB  - engineered and selected for the targeting of
AB  - desired human loci for gene therapy. However, enzyme engineering is
AB  - lengthy and expensive and the off-target effect of the manufactured
AB  - endonucleases is difficult to predict. Moreover, enzymes selected to
AB  - cleave a human DNA locus may not cleave the homologous locus in the
AB  - genome of animal models because of sequence divergence, thus hampering
AB  - attempts to assess the in vivo efficacy and safety of any engineered
AB  - enzyme prior to its application in human trials. Here, we show that
AB  - naturally occurring HEases can be found, that cleave desirable human
AB  - targets. Some of these enzymes are also shown to cleave the homologous
AB  - sequence in the genome of animal models. In addition, the distribution
AB  - of off-target effects may be more predictable for native HEases. Based
AB  - on our experimental observations, we present the HomeBase algorithm,
AB  - database and web server that allow a high-throughput computational
AB  - search and assignment of HEases for the targeting of specific loci in
AB  - the human and other genomes. We validate experimentally the predicted
AB  - target specificity of candidate fungal, bacterial and archaeal HEases
AB  - using cell free, yeast and archaeal assays.
ER  -

TY  - JOUR
AU  - Barzilai, R.
TI  - SV40 DNA:  Quantitative conversion of closed circular to open circular form by an ethidium bromide-restricted endonuclease.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 739
EP  - 742
VL  - 74
AB  - Closed circular molecules of SV40 DNA can be quantitatively converted to the
AB  - open circular form by digestion with endonucleases in the presence of ethidium
AB  - bromide.  Under these conditions almost no molecules were digested beyond the
AB  - open circular form, whereas in the absence of the dye the DNA was completely
AB  - fragmented.
ER  -

TY  - JOUR
AU  - Basavanna, U.
AU  - Gonzalez-Escalona, N.
AU  - Timme, R.
AU  - Datta, S.
AU  - Schoen, B.
AU  - Brown, E.W.
AU  - Zink, D.
AU  - Sharma, S.K.
TI  - Draft Genome Sequence of a Clostridium botulinum Isolate from Water Used for Cooling at a Plant Producing Low-Acid Canned Foods.
JO  - Genome Announcements
PY  - 2013
SP  - e00200
EP  - e00212
VL  - 1
AB  - Clostridium botulinum is a pathogen of concern for low-acid canned foods. Here we report draft
AB  - genomes of a neurotoxin-producing C. botulinum strain isolated from
AB  - water samples used for cooling low-acid canned foods at a canning facility. The
AB  - genome sequence confirmed that this strain belonged to C. botulinum serotype B1,
AB  - albeit with major differences, including thousands of unique single nucleotide
AB  - polymorphisms (SNPs) compared to other genomes of the same serotype.
ER  -

TY  - JOUR
AU  - Basco, M.D.S.
AU  - Revollo, J.R.
AU  - McKinzie, P.B.
AU  - Agnihothram, S.
AU  - Kothari, A.
AU  - Saccente, M.
AU  - Hart, M.E.
TI  - Draft Genome Sequences of Two Staphylococcus aureus Strains Isolated in Succession from a Case of Bacteremia.
JO  - Genome Announcements
PY  - 2017
SP  - e00259
EP  - e00217
VL  - 5
AB  - Staphylococcus aureus strains MEH1 and MEH7 were successively isolated from the blood of a
AB  - patient with recurrent bacteremia. The submitted draft genomes of
AB  - strains MEH1 and MEH7 are 2,914,972 and 2,911,704 bp, respectively.
ER  -

TY  - JOUR
AU  - Bashir, A. et al.
TI  - A hybrid approach for the automated finishing of bacterial genomes.
JO  - Nat. Biotechnol.
PY  - 2012
SP  - 701
EP  - 707
VL  - 30
AB  - Advances in DNA sequencing technology have improved our ability to characterize
AB  - most genomic diversity. However, accurate resolution of large structural events
AB  - is challenging because of the short read lengths of second-generation
AB  - technologies. Third-generation sequencing technologies, which can yield longer
AB  - multikilobase reads, have the potential to address limitations associated with
AB  - genome assembly. Here we combine sequencing data from second- and
AB  - third-generation DNA sequencing technologies to assemble the two-chromosome
AB  - genome of a recent Haitian cholera outbreak strain into two nearly finished
AB  - contigs at >99.9% accuracy. Complex regions with clinically relevant structure
AB  - were completely resolved. In separate control assemblies on experimental and
AB  - simulated data for the canonical N16961 cholera reference strain, we obtained 14
AB  - scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of
AB  - greater than 1 kb for the simulated data, which allowed us to correct several
AB  - errors in contigs assembled from the short-read data alone. This work provides a
AB  - blueprint for the next generation of rapid microbial identification and
AB  - full-genome assembly.
ER  -

TY  - JOUR
AU  - Bashir, A.
AU  - Attie, O.
AU  - Sullivan, M.
AU  - Sebra, R.
AU  - Singh, K.V.
AU  - Altman, D.
AU  - Pak, T.
AU  - Dutta, J.
AU  - Chacko, K.
AU  - Webster, E.
AU  - Lewis, M.
AU  - Hamula, C.
AU  - Delli-Carpini, K.W.
AU  - Murray, B.E.
AU  - Kasarskis, A.
AU  - van Bakel, H.
AU  - Huprikar, S.
TI  - Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient.
JO  - PLoS ONE
PY  - 2017
SP  - e0170449
EP  - e0170449
VL  - 12
AB  - In a liver transplant recipient with vancomycin-resistant Enterococcus (VRE) surgical site and
AB  - bloodstream infection, a combination of pulsed-field gel
AB  - electrophoresis, multilocus sequence typing, and whole genome sequencing
AB  - identified that donor and recipient VRE isolates were highly similar when
AB  - compared to time-matched hospital isolates. Comparison of de novo assembled
AB  - isolate genomes was highly suggestive of transplant transmission rather than
AB  - hospital-acquired transmission and also identified subtle internal rearrangements
AB  - between donor and recipient missed by other genomic approaches. Given the
AB  - improved resolution, whole-genome assembly of pathogen genomes is likely to
AB  - become an essential tool for investigation of potential organ transplant
AB  - transmissions.
ER  -

TY  - JOUR
AU  - Bashtrykov, P.
AU  - Jankevicius, G.
AU  - Jurkowska, R.Z.
AU  - Ragozin, S.
AU  - Jeltsch, A.
TI  - The UHRF1 Protein Stimulates the Activity and Specificity of the Maintenance DNA Methyltransferase DNMT1 by an Allosteric Mechanism.
JO  - J. Biol. Chem.
PY  - 2014
SP  - 4106
EP  - 4115
VL  - 289
AB  - The ubiquitin-like, containing PHD and RING finger domains protein 1 (UHRF1) is essential for
AB  - maintenance DNA methylation by DNA methyltransferase 1 (DNMT1). UHRF1 has been shown to
AB  - recruit DNMT1 to replicated DNA by the ability of its SET and RING-associated (SRA) domain to
AB  - bind to hemimethylated DNA. Here, we demonstrate that UHRF1 also increases the activity of
AB  - DNMT1 by almost 5-fold. This stimulation is mediated by a direct interaction of both proteins
AB  - through the SRA domain of UHRF1 and the replication focus targeting sequence domain of DNMT1,
AB  - and it does not require DNA binding by the SRA domain. Disruption of the interaction between
AB  - DNMT1 and UHRF1 by replacement of key residues in the replication focus targeting sequence
AB  - domain led to a strong reduction of DNMT1 stimulation. Additionally, the interaction with
AB  - UHRF1 increased the specificity of DNMT1 for methylation of hemimethylated CpG sites. These
AB  - findings show that apart from the targeting of DNMT1 to the replicated DNA UHRF1 increases the
AB  - activity and specificity of DNMT1, thus exerting a multifaceted influence on the maintenance
AB  - of DNA methylation.
ER  -

TY  - JOUR
AU  - Bashtrykov, P.
AU  - Ragozin, S.
AU  - Jeltsch, A.
TI  - Mechanistic details of the DNA recognition by the Dnmt1 DNA methyltransferase.
JO  - FEBS Lett.
PY  - 2012
SP  - 1821
EP  - 1823
VL  - 586
AB  - A recently solved Dnmt1-DNA crystal structure revealed several enzyme-DNA contacts and large
AB  - structural rearrangements of the DNA at
AB  - the target site, including the flipping of the non-target strand base
AB  - of the base pair flanking the CpG site and formation of a non-canonical
AB  - base pair between the non-target strand Gua and the flanking base pair.
AB  - Here, we show that the contacts of the enzyme to the target base and
AB  - the Gua:5mC base pair that are observed in the structure are very
AB  - important for catalytic activity. The contacts to the non-target strand
AB  - Gua are not important since its exchange by Ade stimulated activity.
AB  - Except target base flipping, we could not find evidence that the DNA
AB  - rearrangements have a functional role.
ER  -

TY  - JOUR
AU  - Baskunov, V.B.
AU  - Subach, F.V.
AU  - Kolbanovskiy, A.
AU  - Kolbanovskiy, M.
AU  - Eremin, S.A.
AU  - Johnson, F.
AU  - Bonala, R.
AU  - Geacintov, N.E.
AU  - Gromova, E.S.
TI  - Effects of benzo[a]pyrene-deoxyguanosine lesions on DNA methylation catalyzed by EcoRII DNA methyltransferase and on DNA cleavage effected  by EcoRII restriction endonuclease.
JO  - Biochemistry
PY  - 2005
SP  - 1054
EP  - 1066
VL  - 44
AB  - DNA methylation is an important cellular mechanism for controlling gene expression. Whereas
AB  - the mutagenic properties of many DNA adducts, e.g.,
AB  - those arising from polycyclic aromatic hydrocarbons, have been widely
AB  - studied, little is known about their influence on DNA methylation. We
AB  - have constructed site-specifically modified 18-mer oligodeoxynucleotide
AB  - duplexes containing a pair of stereoisomeric adducts derived from a
AB  - benzo[a]pyrene-derived diol epoxide [(+)- and
AB  - (-)-r7,t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, or
AB  - B[a]PDE] bound to the exocyclic amino group of guanine. The adducts,
AB  - either (+)- or (-)-trans-anti-B[a]P-N-2-dG (G*), positioned either at
AB  - the 5'-side or the 3'-side deoxyguanosine residue in the recognition
AB  - sequence of EcoRII restriction-modification enzymes (5'-...CCA/TGG...)
AB  - were incorporated into 18-mer oligodeoxynucleotide duplexes. The
AB  - effects of these lesions on complex formation and the catalytic
AB  - activity of the EcoRII DNA methyltransferase (M.EcoRII) and EcoRII
AB  - restriction endonuclease (R.EcoRII) were investigated. The M.EcoRII
AB  - catalyzes the transfer of a methyl group to the C5 position of the
AB  - 3'-side cytosine of each strand of the recognition sequence, whereas
AB  - R.EcoRII catalyzes cleavage of both strands. The binding of R.EcoRII to
AB  - the oligodeoxynucleotide duplexes and the catalytic cleavage were
AB  - completely abolished when G* was positioned at the 3'-side dG position
AB  - (5'-...CCTGG*...). When G* was at the 5'-side dG position, binding was
AB  - moderately diminished, but cleavage was completely blocked. In the case
AB  - of M.EcoRII, binding is diminished by factors of 5-30 but the catalytic
AB  - activity was either abolished or reduced 4-80-fold when the adducts
AB  - were located at either position. Somewhat smaller effects were observed
AB  - with hemimethylated oligodeoxynucleotide duplexes. These findings
AB  - suggest that epigenetic effects, in addition to genotoxic effects, need
AB  - to be considered in chemical carcinogenesis initiated by B[a]PDE, since
AB  - the inhibition of methylation may allow the expression of genes that
AB  - promote tumor development.
ER  -

TY  - JOUR
AU  - Basnakyan, A.G.
AU  - Votrin, I.I.
TI  - Restriction endonucleases as a possible factor in the evolution of DNA nucleotide composition.
JO  - Zh. Evol. Biokhim. Fiziol.
PY  - 1983
SP  - 20
EP  - 24
VL  - 19
AB  - On the basis of a statistical analysis of the nucleotide and codogenic
AB  - composition of the sites for restriction endonucleases of type II it was
AB  - concluded that restriction endoncleases may perform an evolutionary function as
AB  - catalysts of the site-specific accumulation of the bacterial pre-genome in
AB  - parallel with a change in its nucleotide composition in the direction of its
AB  - enrichment with AT pairs and the amino acid composition of the proteins in the
AB  - direction of a decrease in the content of alanine, arginine, proline and
AB  - glycine.
ER  -

TY  - JOUR
AU  - Basra, P.
AU  - Koziol, A.
AU  - Wong, A.
AU  - Carrillo, C.D.
TI  - Complete Genome Sequences of Citrobacter braakii Strains GTA-CB01 and GTA-CB04, Isolated from Ground Beef.
JO  - Genome Announcements
PY  - 2015
SP  - e01307
EP  - e01314
VL  - 3
AB  - Citrobacter braakii is a Gram-negative bacterium belonging to the Enterobacteriaceae family.
AB  - Here, we report 5.2- and 5.0-Mb genome assemblies for
AB  - C. braakii strains GTA-CB01 and GTA-CB04, respectively.
ER  -

TY  - JOUR
AU  - Bassi, D.
AU  - Fontana, C.
AU  - Gazzola, S.
AU  - Pietta, E.
AU  - Puglisi, E.
AU  - Cappa, F.
AU  - Cocconcelli, P.S.
TI  - Draft Genome Sequence of Clostridium tyrobutyricum Strain UC7086, Isolated from Grana Padano Cheese with Late-Blowing Defect.
JO  - Genome Announcements
PY  - 2013
SP  - e00614
EP  - e00613
VL  - 1
AB  - Clostridium tyrobutyricum is considered the main agent of late-blowing defect in  the
AB  - production of hard cheese. Here, we described the draft genome sequences and
AB  - annotation of C. tyrobutyricum strain UC7086, which was isolated from Grana
AB  - Padano cheese with blowing defect, and C. tyrobutyricum DSM 2637 type strain in a
AB  - comparative study.
ER  -

TY  - JOUR
AU  - Bassil, N.M.
AU  - Lloyd, J.R.
TI  - Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus.
JO  - Genome Announcements
PY  - 2017
SP  - e01493
EP  - e01416
VL  - 5
AB  - The draft genomes of the alkaliphilic, anaerobic bacteria, Anaerobacillus arseniciselenatis,
AB  - A. alkalidiazotrophicus, and A. alkalilacustris, and a novel
AB  - closely related isolate of the Anaerobacillus genus are reported here. These
AB  - assembled genomes will help identify, at the molecular level, the phenotypic
AB  - differences between the species of this poorly characterized genus.
ER  -

TY  - JOUR
AU  - Bassing, C.H.
AU  - Kim, Y.-G.
AU  - Li, L.
AU  - Chandrasegaran, S.
TI  - Overproduction, purification and characterization of M.HinfI methyltransferase and its deletion mutant.
JO  - Gene
PY  - 1992
SP  - 83
EP  - 88
VL  - 113
AB  - We have used the polymerase chain reaction to alter transcriptional and translational signals
AB  - surrounding the hinfIM gene [encoding M.HinfI methyltransferase (MTase)] so as to achieve
AB  - overexpression in Escherichia coli. The PCR-generated hinfIM gene was subcloned in a
AB  - high-expression vector under control of the hybrid trp-lac promoter. In addition, the positive
AB  - retroregulator stem-loop sequence derived from the crystal protein-encoding gene of Bacillus
AB  - thuringiensis was inserted downstream from hinfIM. Using a similar approach, we have also
AB  - constructed overproducer clones of a deletion mutant of M.HinfI MTase that has 97 amino acids
AB  - from the C terminus deleted. The plasmid from the mutant clones is fully protected from HinfI
AB  - restriction endonuclease digestion. It appears that the functional properties (recognition and
AB  - catalytic functions) are encoded within this mutant gene. The overproducer clones yield the
AB  - wild type (wt) and the mutant enzymes to about 10% of total cellular protein upon induction
AB  - with 1 mM IPTG. The wt M.HinfI and the mutant MTase were purified to near electrophoretic
AB  - homogeneity by phosphocellulose, DEAE and gel chromatography. Their monomer sizes by
AB  - SDS/polyacrylamide-gel electrophoresis are 43 kDa and 31 kDa, respectively, in good agreement
AB  - with that predicted from the nucleotide sequence. DNA methylation experiments with purified
AB  - enzymes using single-strand and double-strand M13mp18 DNA substrates indicate that while wt
AB  - enzyme methylates both forms of DNA substrates, the mutant enzyme appears to preferentially
AB  - methylate ss DNA substrate.
ER  -

TY  - JOUR
AU  - Bateman, A.C.
AU  - Perez-Osorio, A.C.
AU  - Li, Z.
AU  - Tran, M.
AU  - Greninger, A.L.
TI  - Conservation and Recombination in the Genome Sequence of Haemophilus influenzae Type f WAPHL1.
JO  - Genome Announcements
PY  - 2017
SP  - e00929
EP  - e00917
VL  - 5
AB  - We report here the second draft genome sequence of a bloodstream isolate of Haemophilus
AB  - influenzae serotype f. Three discrete 3.1- to 7.8-kb sites contained
AB  - 80% of the variability in the genome, consistent with recombination in known
AB  - virulence factors.
ER  -

TY  - JOUR
AU  - Bateman, M.D.
AU  - de Vries, S.P.W.
AU  - Gupta, S.
AU  - Guardabassi, L.
AU  - Cavaco, L.M.
AU  - Grant, A.J.
AU  - Holmes, M.A.
TI  - Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum beta-Lactamase Isolate Derived from Feces of a Healthy Pig.
JO  - Genome Announcements
PY  - 2017
SP  - e00595
EP  - e00517
VL  - 5
AB  - We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27,
AB  - phylogenetic group D) and its six plasmids, isolated from a healthy pig, as
AB  - determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of
AB  - 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes.
ER  -

TY  - JOUR
AU  - Bates, P.J.
AU  - Hammond, G.B.
AU  - Xu, B.
AU  - Aponte, J.C.
AU  - Malik, M.T.
AU  - Martin, A.N.
AU  - Choi, E.W.
AU  - Thomas, S.D.
AU  - Casson, L.K.
AU  - Trent, J.O.
TI  - Discovery of XB05, a potent antiproliferative agent and novel non-nucleoside inhibitor of DNA methyltransferase 1.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 2008
SP  - 783
EP  - 783
VL  - 49
AB  - While investigating the biological properties of fluorine-containing organic molecules, we
AB  - recently identified a novel small molecule, named XB05, which has tumor-selective
AB  - antiproliferative activity. The molecule was submitted to the Developmental Therapeutics
AB  - Program (DTP) at the National Cancer Institute (NCI) for testing in the 60 human tumor cell
AB  - line screen. The results confirmed that XB05 has potent activity against a diverse range of
AB  - cancer cell lines and also revealed an unusual activity profile, with a more than 1000-fold
AB  - difference in GI50 values between the most and least sensitive lines. For example, colon,
AB  - brain, renal, prostate and breast tumor cells were particularly sensitive to XB05, whereas
AB  - other tumor types were substantially less responsive. The GI50 values for the sensitive cell
AB  - lines were in the 10 - 100 nM range.
AB  - We analyzed the DTP data using the on-line COMPARE program, which allows comparison of the
AB  - activity profile with the 43,000 compounds in the public database and which has been validated
AB  - as grouping together agents with similar mechanisms of action, irrespective of their
AB  - structure. When we used XB05 as a COMPARE seed, we found a strong correlation (Pearson
AB  - coefficient 0.82) with a compound known as halomon.
AB  - Halomon is a marine-derived natural product, which has promising anticancer activity. However,
AB  - its development has been severely limited because attempts to re-isolate it from its natural
AB  - source or to develop an efficient synthesis have not enabled production of sufficient compound
AB  - for testing. Halomon was recently reported to be an inhibitor of human DNA methyltransferase 1
AB  - (DNMT1), the enzyme responsible for maintaining DNA methylation after each cell division.
AB  - DNMT1 is considered an attractive target for epigenetic therapy of cancer because
AB  - methylation-induced silencing of tumor suppressor genes occurs frequently in cancer cells.
AB  - XB05 has now been tested in various cell-free and cell-based assays of DNA methylation. We
AB  - find that it is a potent inhibitor of recombinant DNMT1 activity in vitro, with an IC50 of 10
AB  - nM. Moreover, XB05 could reactivate expression of several silenced tumor suppressor genes in
AB  - cancer cells at concentrations of 100 nM or less.
AB  - In conclusion, XB05 is a novel agent with potent antiproliferative activity against cell lines
AB  - derived from common cancers and a new type of DNMT1 inhibitor. XB05 is a mechanistic mimic of
AB  - a natural product named halomon, but, in contrast to halomon, XB05 can be easily and
AB  - inexpensively synthesized in large quantities. XB05 may also have substantial advantages over
AB  - other existing DNMT inhibitors such as 5-azacytidine and decitabine. XB05 is more active than
AB  - these agents in cell-free or cell-based DNMT assays and will likely be less toxic because it
AB  - cannot be incorporated into DNA. Also, whereas 5-azacytidine and decitabine are rapidly
AB  - degraded in aqueous solutions, XB05 appears to be completely stable.
ER  -

TY  - JOUR
AU  - Bath, A.J.
AU  - Milsom, S.E.
AU  - Gormley, N.A.
AU  - Halford, S.E.
TI  - Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 4024
EP  - 4033
VL  - 277
AB  - Type IIs restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA
AB  - strands at fixed positions, typically several base pairs away from the recognition site.
AB  - These enzymes are generally monomers that transiently associate to form dimmers to cleave both
AB  - strands.  Their reactions could involve bridging interactions between two copies of their
AB  - recognition sequence.  To examine this possibility, several type IIs enzymes were tested
AB  - against substrates with either one or two target sites.  Some of the enzymes cleaved the DNA
AB  - with two target sites at the same rate as that with one site, but most cut their two-site
AB  - substrate more rapidly than the one-site DNA.  In some cases, the two sites were cut
AB  - sequentially, at rates that were equal to each other but that exceeded the rate on the
AB  - one-site DNA.  In another case, the DNA with two sites was cleaved rapidly at one site, but
AB  - the residual site was cleaved at a much slower rate.  In a further example, the two sites were
AB  - cleaved concertedly to give directly the final products cut at both sites.  Many type IIs
AB  - enzymes thus interact with two copies of their recognition sequence before cleaving DNA,
AB  - although via several different mechanisms.
ER  -

TY  - JOUR
AU  - Batista, B.D.
AU  - Taniguti, L.M.
AU  - Almeida, J.R.
AU  - Azevedo, J.L.
AU  - Quecine, M.C.
TI  - Draft Genome Sequence of Multitrait Plant Growth-Promoting Bacillus sp. Strain RZ2MS9.
JO  - Genome Announcements
PY  - 2016
SP  - e01402
EP  - e01416
VL  - 4
AB  - Bacillus sp. strain RZ2MS9 is a multitrait soybean and maize growth-promoting bacterium
AB  - isolated in Brazil from guarana's rhizosphere. Here, we present the draft genome sequence of
AB  - RZ2MS9 and its genes involved in many features related to plant growth promotion.
ER  -

TY  - JOUR
AU  - Batista, B.D.
AU  - Taniguti, L.M.
AU  - Monteiro-Vitorello, C.B.
AU  - Azevedo, J.L.
AU  - Quecine, M.C.
TI  - Draft Genome Sequence of Burkholderia ambifaria RZ2MS16, a Plant Growth-Promoting Rhizobacterium Isolated from Guarana, a Tropical Plant.
JO  - Genome Announcements
PY  - 2016
SP  - e00125
EP  - e00116
VL  - 4
AB  - Burkholderia ambifaria strain RZ2MS16 was isolated from the rhizosphere of Amazon guarana in
AB  - Brazil. This bacterium exhibits a remarkable capacity to promote the
AB  - growth of corn and soybean. Here, we report the draft genome sequence of RZ2MS16
AB  - and some genes related to multiple traits involved in plant growth promotion.
ER  -

TY  - JOUR
AU  - Batista, D.F.
AU  - Freitas, N.O.C.
AU  - Leite, L.R.
AU  - Varani, A.M.
AU  - Araujo, F.M.
AU  - Salim, A.
AU  - Almeida, A.M.
AU  - Ribeiro, S.A.
AU  - Oliveira, G.C.
AU  - Barrow, P.A.
AU  - Berchieri, J.A.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Gallinarum Biovar Pullorum Strain FCAV198, a Brazilian Chicken Pathogen.
JO  - Genome Announcements
PY  - 2014
SP  - e00028
EP  - e00014
VL  - 2
AB  - Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum is a bird-restricted
AB  - pathogen which causes pullorum disease. The strain FCAV198 was
AB  - isolated from a pool of chicken ovaries in Brazil, and its genome may be helpful
AB  - for studies involving molecular mechanisms related to pathogenesis and other
AB  - related applications.
ER  -

TY  - JOUR
AU  - Battisti, J.M.
AU  - Minnick, M.F.
TI  - Development of a system for genetic manipulation of Bartonella bacilliformis.
JO  - Appl. Environ. Microbiol.
PY  - 1999
SP  - 3441
EP  - 3448
VL  - 65
AB  - Lack of a system for site-specific genetic manipulation has severely hindered studies on the
AB  - molecular biology of all Bartonella species. We report the first site-specific mutagenesis and
AB  - complementation for a Bartonella species. A highly transformable strain of B. bacilliformis,
AB  - termed JB584, was isolated and found to exhibit a significant increase in transformation
AB  - efficiency with the broad-host-range plasmid pBBR1MCS-2, relative to wild-type strains.
AB  - Restriction analyses of genomic preparations with the methylation-sensitive restriction
AB  - enzymes ClaI and StuI suggest that strain JB584 possesses a dcm methylase mutation that
AB  - contributes to its enhanced transformability. A suicide plasmid, pUB1, which contains a
AB  - polylinker, a pMB1 replicon, and a nptI kanamycin resistance cassette, was constructed. An
AB  - internal 508-bp fragment of the B. bacilliformis flagellin gene (fla) was cloned into pUB1 to
AB  - generate pUB508, a fla-targeting suicide vector. Introduction of pUB508 into JB584 by
AB  - electroporation generated eight Kan(r) clones of B. bacilliformis.  Characterization of one of
AB  - these strains, termed JB585, indicated that allelic exchange between pUB508 and fla had
AB  - occurred. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis,
AB  - immunoblotting, and electron microscopy showed that synthesis of flagellin encoded by fla and
AB  - secretion/assembly of flagella were abolished.  Complementation of fla in trans was
AB  - accomplished with a pBBR1MCS recombinant containing the entire wild-type fla gene (pBBRFLAG).
AB  - These data conclusively show that inactivation of fla results in a bald, nonmotile phenotype
AB  - and that pMB1 and REP replicons make suitable B. bacilliformis suicide and shuttle vectors,
AB  - respectively. When used in conjunction with the highly transformable strain JB584, this system
AB  - for site-specific genetic manipulation and complementation provides a new venue for studying
AB  - the molecular biology of B. bacilliformis.
ER  -

TY  - JOUR
AU  - Batzilla, J.
AU  - Hoper, D.
AU  - Antonenka, U.
AU  - Heesemann, J.
AU  - Rakin, A.
TI  - Complete Genome Sequence of Yersinia enterocolitica subsp. palearctica Serogroup O:3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2067
EP  - 2067
VL  - 193
AB  - We report here the first finished and annotated genome sequence of a representative of the
AB  - most epidemiologically successful Yersinia group, Y.
AB  - enterocolitica subsp. palearctica strain Y11, serotype O:3, biotype 4.
AB  - This strain is a certified type strain of the German DSMZ collection (DSM
AB  - no. 13030; Yersinia enterocolitica subsp. palearctica) that was isolated
AB  - from the stool of a human patient (H. Neubauer, S. Aleksic, A. Hensel, E.
AB  - J. Finke, and H. Meyer. Int. J. Med. Microbiol. 290:61-64, 2000).
ER  -

TY  - JOUR
AU  - Baubec, T.
AU  - Colombo, D.F.
AU  - Wirbelauer, C.
AU  - Schmidt, J.
AU  - Burger, L.
AU  - Krebs, A.R.
AU  - Akalin, A.
AU  - Schubeler, D.
TI  - Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
JO  - Nature
PY  - 2015
SP  - 243
EP  - 247
VL  - 520
AB  - DNA methylation is an epigenetic modification associated with transcriptional repression of
AB  - promoters and is essential for mammalian development. Establishment
AB  - of DNA methylation is mediated by the de novo DNA methyltransferases DNMT3A and
AB  - DNMT3B, whereas DNMT1 ensures maintenance of methylation through replication.
AB  - Absence of these enzymes is lethal, and somatic mutations in these genes have
AB  - been associated with several human diseases. How genomic DNA methylation patterns
AB  - are regulated remains poorly understood, as the mechanisms that guide recruitment
AB  - and activity of DNMTs in vivo are largely unknown. To gain insights into this
AB  - matter we determined genomic binding and site-specific activity of the mammalian
AB  - de novo DNA methyltransferases DNMT3A and DNMT3B. We show that both enzymes
AB  - localize to methylated, CpG-dense regions in mouse stem cells, yet are excluded
AB  - from active promoters and enhancers. By specifically measuring sites of de novo
AB  - methylation, we observe that enzymatic activity reflects binding. De novo
AB  - methylation increases with CpG density, yet is excluded from nucleosomes.
AB  - Notably, we observed selective binding of DNMT3B to the bodies of transcribed
AB  - genes, which leads to their preferential methylation. This targeting to
AB  - transcribed sequences requires SETD2-mediated methylation of lysine 36 on histone
AB  - H3 and a functional PWWP domain of DNMT3B. Together these findings reveal how
AB  - sequence and chromatin cues guide de novo methyltransferase activity to ensure
AB  - methylome integrity.
ER  -

TY  - JOUR
AU  - Baumgart, M. et al.
TI  - Corynebacterium glutamicum chassis C1*: Building and testing a novel platform host for synthetic biology and industrial biotechnology.
JO  - ACS Synth. Biol.
PY  - 2017
SP  - 132
EP  - 144
VL  - 7
AB  - Targeted top-down strategies for genome reduction are considered to have a high
AB  - potential for providing robust basic strains for synthetic biology and industrial
AB  - biotechnology. Recently, we created a library of 26 genome-reduced strains of
AB  - Corynebacterium glutamicum carrying broad deletions in single gene clusters and
AB  - showing wild-type-like biological fitness. Here, we proceeded with combinatorial
AB  - deletions of these irrelevant gene clusters in two parallel orders, and the
AB  - resulting library of 28 strains was characterized under various environmental
AB  - conditions. The final chassis strain C1* carries a genome reduction of 13.4% (412
AB  - deleted genes) and shows wild-type-like growth behavior in defined medium with
AB  - d-glucose as carbon and energy source. Moreover, C1* proves to be robust against
AB  - several stresses (including oxygen limitation) and shows long-term growth
AB  - stability under defined and complex medium conditions. In addition to providing a
AB  - novel prokaryotic chassis strain, our results comprise a large strain library and
AB  - a revised genome annotation list, which will be valuable sources for future
AB  - systemic studies of C. glutamicum.
ER  -

TY  - JOUR
AU  - Baumgart, M.
AU  - Unthan, S.
AU  - Ruckert, C.
AU  - Sivalingam, J.
AU  - Grunberger, A.
AU  - Kalinowski, J.
AU  - Bott, M.
AU  - Noack, S.
AU  - Frunzke, J.
TI  - Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 6006
EP  - 6015
VL  - 79
AB  - The activity of bacteriophages and phage-related mobile elements is a major
AB  - source for genome rearrangements and genetic instability of their bacterial
AB  - hosts. The genome of the industrial amino acid producer Corynebacterium
AB  - glutamicum ATCC 13032 contains three prophages (CGP1-3) of so far unknown
AB  - functionality. Several phage genes are regularly expressed and the large prophage
AB  - CGP3 ( approximately 190 kbp) has recently been shown to be induced under certain
AB  - stress conditions. Here, we present the construction of MB001, a prophage-free
AB  - variant of C. glutamicum ATCC 13032 with a 6 % reduced genome. This strain does
AB  - not show any unfavorable properties during extensive phenotypic characterization
AB  - under various standard and stress conditions. As expected, we observed an
AB  - improved growth and fitness of MB001 under SOS-response inducing conditions that
AB  - trigger CGP3 induction in the wild type strain. Further studies revealed that
AB  - MB001 has a significantly increased transformation efficiency and produced about
AB  - 30 % more of the heterologous model protein eYFP, presumably as a consequence of
AB  - an increased plasmid copy number. These effects were attributed to the loss of
AB  - the restriction-modification system (cg1996-98) located within CGP3. The deletion
AB  - of the prophages without any negative effect results in a novel platform strain
AB  - for metabolic engineering and represents a useful step towards the construction
AB  - of a C. glutamicum chassis genome of strain ATCC 13032 for biotechnological
AB  - applications and synthetic biology.
ER  -

TY  - JOUR
AU  - Baumstark, B.R.
AU  - Roberts, R.J.
AU  - RajBhandary, U.L.
TI  - Use of short synthetic DNA duplexes as substrates for the restriction endonucleases HpaII and MnoI.
JO  - J. Biol. Chem.
PY  - 1979
SP  - 8943
EP  - 8950
VL  - 254
AB  - In an attempt to determine whether cleavage by restriction enzymes is specified solely by the
AB  - nucleotide sequence at the recognition site or whether additional factors (e.g. the size of
AB  - the DNA or partial disruption of the DNA helix to form cruciform structures) are involved in
AB  - recognition, two restriction enzymes, HpaII and MnoI, were tested for their ability to cleave
AB  - synthetic DNA duplexes of limited size and well-defined sequence.  DNA duplexes ranging from 6
AB  - to 13 base pairs in length were shown to be recognized with high efficiency by HpaII and were
AB  - cleaved specifically within the HpaII recognition sequence.  5' d-C^C-G-G 3'  3' G-G-C^C-d
AB  - 5'.  HpaII was totally inactive against single-stranded DNA; therefore, both strands of the
AB  - DNA duplex are necessary for cleavage to occur.  In two of the DNA duplexes, the recognition
AB  - sequences were located at the end of a base paired region and were thus almost certainly
AB  - present in the form of a linear duplex.  The fact that HpaII could cleave these duplexes
AB  - suggests that the information for HpaII recognition resides in the nucleotide sequence alone.
AB  - By incubation of these synthetic duplexes with restriction nuclease from MnoI we have shown
AB  - that the cleavage site for MnoI is identical with that of HpaII.  Although HpaII and MnoI
AB  - nucleases are isoschizomers, they do difer somewhat in their mode of action on the short
AB  - synthetic DNA duplexes.  With the duplexes used as substrates, it was found that whereas the
AB  - HpaII nuclease preferentially cleaved the pyrimidine-rich strand (3 to 4 times over the
AB  - purine-rich strand), the MnoI nuclease cleaved both strands at an equal rate.
ER  -

TY  - JOUR
AU  - Baxter, B.K.
AU  - Topal, M.D.
TI  - Formation of a cleavasome: enhancer DNA-2 stabilizes an active conformation of NaeI dimer.
JO  - Biochemistry
PY  - 1993
SP  - 8291
EP  - 8298
VL  - 32
AB  - Cleavage of DNA by NaeI-type restriction enzymes is stimulated by a DNA element with affinity
AB  - for the activator site of the enzyme: a cleavage-enhancer DNA element. Measurements of the
AB  - mobility of NaeI activity in comparison with protein standards on gel permeation columns and
AB  - glycerol gradients demonstrated that NaeI, without enhancer, can form a 70,000 MW dimer. The
AB  - dimer, however is inactive: it could not cleave the resistant NaeI site in M13mp18 DNA in the
AB  - absence of enhancer. In cleavage assays, enhancer stimulated either DNA nicking or DNA
AB  - cleavage, depending upon NaeI concentration, and reduced the NaeI concentration required for
AB  - the transition from nicking to cleavage activity. A gel mobility-shift assay of the
AB  - interaction of NaeI with enhancer showed the formation of two complexes. Results using
AB  - different sized DNAs and different percentage acrylamide gels for gel mobility-shift analysis
AB  - implied that the two complexes were caused by NaeI monomer and dimer structures rather than
AB  - one and two DNA binding. Dimer formation increased with the affinity of enhancer for NaeI. UV
AB  - cross-linking captured the NaeI-enhancer complex; electrophoretic analysis of the cross-linked
AB  - products showed NaeI dimer bound to enhancer. These results imply a model for cleavage
AB  - enhancement in which enhancer binding stabilizes an active NaeI dimer conformation
AB  - (cleavasome) that cleaves both DNA strands before dissociating.
ER  -

TY  - JOUR
AU  - Baxter, S.
AU  - Lambert, A.R.
AU  - Kuhar, R.
AU  - Jarjour, J.
AU  - Kulshina, N.
AU  - Parmeggiani, F.
AU  - Danaher, P.
AU  - Gano, J.
AU  - Baker, D.
AU  - Stoddard, B.L.
AU  - Scharenberg, A.M.
TI  - Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 7985
EP  - 8000
VL  - 40
AB  - Although engineered LAGLIDADG homing endonucleases (LHEs) are finding increasing  applications
AB  - in biotechnology, their generation remains a challenging,
AB  - industrial-scale process. As new single-chain LAGLIDADG nuclease scaffolds are
AB  - identified, however, an alternative paradigm is emerging: identification of an
AB  - LHE scaffold whose native cleavage site is a close match to a desired target
AB  - sequence, followed by small-scale engineering to modestly refine recognition
AB  - specificity. The application of this paradigm could be accelerated if methods
AB  - were available for fusing N- and C-terminal domains from newly identified LHEs
AB  - into chimeric enzymes with hybrid cleavage sites. Here we have analyzed the
AB  - structural requirements for fusion of domains extracted from six single-chain
AB  - I-OnuI family LHEs, spanning 40-70% amino acid identity. Our analyses demonstrate
AB  - that both the LAGLIDADG helical interface residues and the linker peptide
AB  - composition have important effects on the stability and activity of chimeric
AB  - enzymes. Using a simple domain fusion method in which linker peptide residues
AB  - predicted to contact their respective domains are retained, and in which limited
AB  - variation is introduced into the LAGLIDADG helix and nearby interface residues,
AB  - catalytically active enzymes were recoverable for approximately 70% of domain
AB  - chimeras. This method will be useful for creating large numbers of chimeric LHEs
AB  - for genome engineering applications.
ER  -

TY  - JOUR
AU  - Bayliss, C.D.
AU  - Bidmos, F.A.
AU  - Anjum, A.
AU  - Manchev, V.T.
AU  - Richards, R.L.
AU  - Grossier, J.P.
AU  - Wooldridge, K.G.
AU  - Ketley, J.M.
AU  - Barrow, P.A.
AU  - Jones, M.A.
AU  - Tretyakov, M.V.
TI  - Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of  population structure during host colonization.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 5876
EP  - 5889
VL  - 40
AB  - Phase variation of surface structures occurs in diverse bacterial species due to  stochastic,
AB  - high frequency, reversible mutations. Multiple genes of Campylobacter
AB  - jejuni are subject to phase variable gene expression due to mutations in polyC/G
AB  - tracts. A modal length of nine repeats was detected for polyC/G tracts within C.
AB  - jejuni genomes. Switching rates for these tracts were measured using
AB  - chromosomally-located reporter constructs and high rates were observed for cj1139
AB  - (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased
AB  - mutability 10-fold and changed the mutational pattern from predominantly
AB  - insertions to mainly deletions. Using a multiplex PCR, major changes were
AB  - detected in 'on/off' status for some phase variable genes during passage of C.
AB  - jejuni in chickens. Utilization of observed switching rates in a stochastic,
AB  - theoretical model of phase variation demonstrated links between mutability and
AB  - genetic diversity but could not replicate observed population diversity. We
AB  - propose that modal repeat numbers have evolved in C. jejuni genomes due to
AB  - molecular drivers associated with the mutational patterns of these polyC/G
AB  - repeats, rather than by selection for particular switching rates, and that
AB  - factors other than mutational drift are responsible for generating genetic
AB  - diversity during host colonization by this bacterial pathogen.
ER  -

TY  - JOUR
AU  - Bayliss, C.D.
AU  - Callaghan, M.J.
AU  - Moxon, E.R.
TI  - High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness  of Haemophilus influenzae.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 4046
EP  - 4059
VL  - 34
AB  - Phase variable restriction-modification (R-M) systems are widespread in Eubacteria.
AB  - Haemophilus influenzae encodes a phase variable homolog of
AB  - Type III R-M systems. Sequence analysis of this system in 22 non-typeable
AB  - H.influenzae isolates revealed a hypervariable region in the central
AB  - portion of the mod gene whereas the res gene was conserved. Maximum
AB  - likelihood (ML) analysis indicated that most sites outside this
AB  - hypervariable region experienced strong negative selection but evidence of
AB  - positive selection for a few sites in adjacent regions. A phylogenetic
AB  - analysis of 61 Type III mod genes revealed clustering of these
AB  - H.influenzae mod alleles with mod genes from pathogenic Neisseriae and,
AB  - based on sequence analysis, horizontal transfer of the mod-res complex
AB  - between these species. Neisserial mod alleles also contained a
AB  - hypervariable region and all mod alleles exhibited variability in the
AB  - repeat tract. We propose that this hypervariable region encodes the target
AB  - recognition domain (TRD) of the Mod protein and that variability results
AB  - in alterations to the recognition sequence of this R-M system. We argue
AB  - that the high allelic diversity and phase variable nature of this R-M
AB  - system have arisen due to selective pressures exerted by diversity in
AB  - bacteriophage populations but also have implications for other fitness
AB  - attributes of these bacterial species.
ER  -

TY  - JOUR
AU  - Bayona-Bafaluy, M.P.
AU  - Blits, B.
AU  - Battersby, B.J.
AU  - Shoubridge, E.A.
AU  - Moraes, C.T.
TI  - Rapid directional shift of mitochondrial DNA heteroplasmy in animal tissues by a mitochondrially targeted restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 14392
EP  - 14397
VL  - 102
AB  - Frequently, mtDNA with pathogenic mutations coexist with wild-type genomes (mtDNA
AB  - heteroplasmy). Mitochondrial dysfunction and disease ensue only
AB  - when the proportion of mutated mtDNAs is high, thus a reduction in this
AB  - proportion should provide an effective therapy for these disorders. We
AB  - developed a system to decrease specific mtDNA haplotypes by expressing a
AB  - mitochondrially targeted restriction endonuclease, ApaLI, in cells of
AB  - heteroplasmic mice. These mice have two mtDNA haplotypes, of which only
AB  - one contains an ApaLI site. After transfection of cultured hepatocytes
AB  - with mitochondrially targeted ApaLI, we found a rapid, directional, and
AB  - complete shift in mtDNA heteroplasmy (2-6 h). We tested the efficacy of
AB  - this approach in vivo, by using recombinant viral vectors expressing the
AB  - mitochondrially targeted ApaLI. We observed a significant shift in mtDNA
AB  - heteroplasmy in muscle and brain transduced with recombinant viruses. This
AB  - strategy could prevent disease onset or reverse clinical symptoms in
AB  - patients harboring certain heteroplasmic pathogenic mutations in mtDNA.
ER  -

TY  - JOUR
AU  - Bayot-Custodio, A.N.
AU  - Alcantara, E.P.
AU  - Zulaybar, T.O.
TI  - Draft Genome Sequence of Insecticidal Streptomyces sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines.
JO  - Genome Announcements
PY  - 2014
SP  - e00448
EP  - e00414
VL  - 2
AB  - A draft genome sequence of a Streptomyces sp. isolated from mangrove soil in Cebu,
AB  - Philippines, is described here. This isolate produced compounds with
AB  - contact insecticidal activity against important corn pests. The genome contains
AB  - 7,479,793 bp (in 27 scaffolds), 6,297 predicted genes, and 29 secondary
AB  - metabolite biosynthetic gene clusters.
ER  -

TY  - JOUR
AU  - Beaber, J.W.
AU  - Hochhut, B.
AU  - Waldor, M.K.
TI  - Genomic and Functional Analyses of SXT, an Integrating Antibiotic Resistance Gene Transfer Element Derived from Vibrio cholerae.
JO  - J. Bacteriol.
PY  - 2002
SP  - 4259
EP  - 4269
VL  - 184
AB  - SXT is representative of a family of conjugative-transposon-like mobile
AB  - genetic elements that encode multiple antibiotic resistance genes. In
AB  - recent years, SXT-related conjugative, self-transmissible integrating
AB  - elements have become widespread in Asian Vibrio cholerae. We have
AB  - determined the 100-kb DNA sequence of SXT. This element appears to be a
AB  - chimera composed of transposon-associated antibiotic resistance genes
AB  - linked to a variety of plasmid- and phage-related genes, as well as to
AB  - many genes from unknown sources. We constructed a nearly comprehensive set
AB  - of deletions through the use of the one-step chromosomal gene inactivation
AB  - technique to identify SXT genes involved in conjugative transfer and
AB  - chromosomal excision. SXT, unlike other conjugative transposons, utilizes
AB  - a conjugation system related to that encoded by the F plasmid. More than
AB  - half of the SXT genome, including the composite transposon-like structure
AB  - that contains its antibiotic resistance genes, was not required for its
AB  - mobility. Two SXT loci, designated setC and setD, whose predicted amino
AB  - acid sequences were similar to those of the flagellar regulators FlhC and
AB  - FlhD, were found to encode regulators that activate the transcription of
AB  - genes required for SXT excision and transfer. Another locus, designated
AB  - setR, whose gene product bears similarity to lambdoid phage CI repressors,
AB  - also appears to regulate SXT gene expression.
ER  -

TY  - JOUR
AU  - Bean, D.C.
AU  - Wigmore, S.M.
AU  - Wareham, D.W.
TI  - Draft Genome Sequence of a Canine Isolate of Methicillin-Resistant Staphylococcus haemolyticus.
JO  - Genome Announcements
PY  - 2017
SP  - e00146
EP  - e00117
VL  - 5
AB  - Staphylococcus haemolyticus strain SW007 was isolated from a nasal swab taken from a healthy
AB  - dog. The isolate is resistant to methicillin, mupirocin,
AB  - macrolides, and sulfonamides. The SW007 draft genome is 2,325,410 bp and contains
AB  - 2,277 coding sequences, including 60 tRNAs and nine complete rRNA-coding regions.
ER  -

TY  - JOUR
AU  - Bean, D.C.
AU  - Wigmore, S.M.
AU  - Wareham, D.W.
TI  - Draft Genome Sequence of Staphylococcus cohnii subsp. urealyticus Isolated from a Healthy Dog.
JO  - Genome Announcements
PY  - 2017
SP  - e01628
EP  - e01616
VL  - 5
AB  - Staphylococcus cohnii subsp. urealyticus strain SW120 was isolated from the ear swab of a
AB  - healthy dog. The isolate is resistant to methicillin and fusidic acid.
AB  - The SW120 draft genome is 2,805,064 bp and contains 2,667 coding sequences,
AB  - including 58 tRNAs and nine complete rRNA coding regions.
ER  -

TY  - JOUR
AU  - Beare, P.A.
AU  - Jeffrey, B.M.
AU  - Martens, C.A.
AU  - Heinzen, R.A.
TI  - Draft Genome Sequences of Three Coxiella burnetii Strains Isolated from Q Fever Patients.
JO  - Genome Announcements
PY  - 2017
SP  - e00986
EP  - e00917
VL  - 5
AB  - In the current study, we determined the draft genome sequences of three Coxiella  burnetii
AB  - human disease isolates. The Coxiella burnetii Turkey (RSA315) and Dyer
AB  - (RSA345) strains were isolated from acute Q fever patients, while the Ko (Q229)
AB  - strain was isolated from a Q fever endocarditis patient.
ER  -

TY  - JOUR
AU  - Beare, P.A.
AU  - Jeffrey, B.M.
AU  - Martens, C.A.
AU  - Heinzen, R.A.
TI  - Draft Genome Sequences of the Avirulent Coxiella burnetii Dugway 7D77-80 and Dugway 7E65-68 Strains Isolated from Rodents in Dugway, Utah.
JO  - Genome Announcements
PY  - 2017
SP  - e00984
EP  - e00917
VL  - 5
AB  - Here, we present the draft genome sequences of the Coxiella burnetii Dugway 7D77-80 and Dugway
AB  - 7E65-68 strains, which were isolated from rodents in Dugway,
AB  - UT, in the 1950s. The strains reside in a distinct genomic group of C. burnetii
AB  - and are considered avirulent despite having the largest genomes of the Coxiella
AB  - genus.
ER  -

TY  - JOUR
AU  - Beare, P.A.
AU  - Jeffrey, B.M.
AU  - Martens, C.A.
AU  - Pearson, T.
AU  - Heinzen, R.A.
TI  - Draft Genome Sequences of Historical Strains of Coxiella burnetii Isolated from Cow's Milk and a Goat Placenta.
JO  - Genome Announcements
PY  - 2017
SP  - e00985
EP  - e00917
VL  - 5
AB  - Here, we report draft genome sequences of historical strains of Coxiella burnetii derived from
AB  - cow's milk and the placenta of a goat that had aborted. The
AB  - California and Ohio milk strains display a different sequence type than do
AB  - contemporary milk strains.
ER  -

TY  - JOUR
AU  - Beary, T.P.
AU  - Braymer, H.D.
AU  - Achberger, E.C.
TI  - Evidence of participation of McrBs in McrBC restriction in Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1997
SP  - 7768
EP  - 7775
VL  - 179
AB  - The McrBC restriction system has the ability to restrict DNA containing
AB  - 5-hydroxymethylcytosine, N4-methylcytosine, and 5-methylcytosine at specific sequences.  The
AB  - mcrB gene produces two gene products.  The complete mcrB open reading frame produces a 51-kDa
AB  - protein (McrBL) and a 33-kDa protein (McrBS).  The smaller McrB polypeptide is produced from
AB  - an in-frame, internal translational start site in the mcrB gene.  The McrBs is unknown,
AB  - although there has been speculation that it plays some role in the modulation of McrBC
AB  - restriction.  Studies of the function of McrBs have been challenging since it is produced in
AB  - frame with McrBL.  In this study, we tested the effects of underproduction (via antisense RNA)
AB  - and overproduction (via gene dosage) of mcrBC gene products on restriction levels of the
AB  - mcrBC+ strain JM107.  Among the parameters monitoredwas the induction of SOS responses, which
AB  - indicate DNA damage.  Evidence from this study suggests that McrBS is necessary for
AB  - stabilization of the McrBC restriction complex in vivo.
ER  -

TY  - JOUR
AU  - Beary, T.P.
AU  - Ross, T.K.
AU  - Braymer, H.D.
AU  - Achberger, E.C.
TI  - Characterization of genes involved in the McrB restriction system of Escherichia coli K12.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 180
EP  - 180
VL  - 89
AB  - The McrB system of E. coli K12 restricts DNA modified at the sequence 'GmC'.
AB  - Two of the genes involved in the restriction of 5-methylcytosine
AB  - (5mC)-containing DNA are mcrB and mcrC.  The nucleic acid sequences of these
AB  - genes were used to predict open reading frames encoding peptides consistent
AB  - with the 51-kilodalton (kDa) mcrB gene product and the 39-kDa mcrC gene
AB  - product.  Based on the nucleotide sequence and the analysis of frameshift
AB  - mutations within the mcrB gene, an internal, in phase translational start was
AB  - identified specifying a peptide of 33 kDa.  It has been shown that the genetic
AB  - components required for the restriction of DNA containing 5mC are different
AB  - than those for the restriction of nonglucosylated hydroxymethylcytosine
AB  - (hmC)-containing T4 phage DNA.  The possible involvement of the 33-kDa peptide
AB  - in the control of the 5mC-specific and hmC-specific activities was examined.
AB  - We found evidence for genetic elements downstream of the mcrC gene that
AB  - influence the restriction of DNA containing modified cytosine residues.
ER  -

TY  - JOUR
AU  - Beatson, S.A. et al.
TI  - Molecular analysis of the asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.
JO  - Infect. Immun.
PY  - 2015
SP  - 1749
EP  - 1764
VL  - 83
AB  - Urinary tract infections (UTIs) are among the most common infectious diseases of
AB  - humans, with Escherichia coli responsible for >80% of all cases. One extreme of
AB  - UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier
AB  - state that resembles commensalism. To understand the evolution and molecular
AB  - mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was
AB  - sequenced. Analysis of the complete genome indicated that it most resembles E.
AB  - coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight
AB  - prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and
AB  - contains genes encoding a number of UTI-associated virulence factors, namely, Afa
AB  - (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin.
AB  - We demonstrated that the presence of this island in VR50 confers its ability to
AB  - colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was
AB  - attenuated in a mouse model of UTI in vivo. We established that Afa is the
AB  - island-encoded factor responsible for this phenotype using two independent
AB  - deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE
AB  - displayed significantly decreased ability to adhere to human bladder epithelial
AB  - cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder
AB  - colonization compared to wild-type VR50, similar to the colonization level of the
AB  - GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like
AB  - strain that has acquired fitness factors that facilitate colonization of the
AB  - human bladder.
ER  -

TY  - JOUR
AU  - Beatson, S.A.
AU  - Das-Gracas-de-Luna, M.
AU  - Bachmann, N.L.
AU  - Alikhanm, N.F.
AU  - Hanksm, K.R.
AU  - Sullivanm, M.J.
AU  - Weem, B.A.
AU  - Freitas-Almeida, A.C.
AU  - Dos Santos, P.A.
AU  - de Melo, J.T.
AU  - Squire, D.J.
AU  - Cunningham, A.F.
AU  - Fitzgerald, J.R.
AU  - Henderson, I.R.
TI  - Genome sequence of the emerging pathogen Aeromonas caviae.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1286
EP  - 1287
VL  - 193
AB  - Aeromonas caviae is a Gram-negative, motile and rod-shaped facultative anaerobe that is
AB  - increasingly being recognised as a cause of diarrhea in  children. Here we present the first
AB  - genome sequence of an A. caviae strain  which was isolated as the sole pathogen from a child
AB  - with profuse diarrhea.
ER  -

TY  - JOUR
AU  - Beattie, K.L.
AU  - Wakil, A.E.
AU  - Driggers, P.H.
TI  - Action of restriction endonucleases on transforming DNA of Haemophilus influenzae.
JO  - J. Bacteriol.
PY  - 1982
SP  - 332
EP  - 337
VL  - 152
AB  - Cleavage of DNA from Haemophilus influenzae with restriction endonucleases
AB  - caused inactivation of transforming ability to an extent that depended on the
AB  - genetic marker and the enzyme.  The rate of inactivation, but not the final
AB  - level of survival, depended on the concentration of enzyme in the restriction
AB  - digest.  In general, the greatest extent of inactivation of transforming
AB  - activity was obtained with endonucleases that are known to produce the shortest
AB  - fragments.  We electrophoresed restriction digests of H. influenzae DNA in
AB  - agarose gels and assayed transforming activity of DNA extracted from gel
AB  - slices.  In this way, we determined the lengths of restriction fragments that
AB  - contain genetic markers of H. influenzae.  For the marker that we studied most
AB  - thoroughly (nov), the shortest restriction fragment that possessed detectable
AB  - transforming activity was a 0.9-kilobase pair fragment produced by endonuclease
AB  - R - PstI.  The shortest marker-bearing restriction fragment that retained
AB  - substantial transforming activity (50% of value for undigested DNA) was a
AB  - 2.1-kilobase pair EcoRI fragment bearing the kan marker.  Among marker-bearing
AB  - restriction fragments 1 to 4 kilobase pairs in length, survival of transforming
AB  - activity varied 10,000-fold.  We relate these observations to the recent
AB  - finding by Sisco and Smith (Proc. Natl. Acad. Sci. USA 76: 972-976, 1979) that
AB  - efficient entry of DNA into competent H. influenzae cells appears to require
AB  - the presence of a recognition sequence that is scattered throughout the
AB  - Haemophilus genome in many more copies than in unrelated genomes.
ER  -

TY  - JOUR
AU  - Beaty, J.S.
AU  - Mclean-Bowen, C.A.
AU  - Brown, L.R.
TI  - BvuI: a site-specific endonuclease from Bacillus vulgatis.
JO  - Gene
PY  - 1982
SP  - 61
EP  - 67
VL  - 18
AB  - A site-specific endodeoxyribonuclease was partially purified from an extract of
AB  - osmotically shocked spheroplasts of a Bacillus vulgatis strain; the enzyme has
AB  - been designated BvuI and its activity was characterized.  The locations of
AB  - BvuI-generated cleavages on bacteriophage lambda and M13 derivatives mp7, mp8
AB  - and mp9, SV40 and pBR322 DNA molecules were determined.  BvuI was shown to
AB  - recognize the DNA sequence	5'-G-Pu-G-C-Py-^C-3'	3'-C-^Py-C-G-Pu-G-5'and cleaves
AB  - it at the positions indicated by arrows.  Two identical BvuI recognition sites
AB  - separated by fourteen nucleotide pairs were shown to occur within the
AB  - tetracycline resistance gene of pBR322; BvuI should be used for molecular
AB  - cloning in that plasmid vector.
ER  -

TY  - JOUR
AU  - Beauchamp, J.M.
AU  - Leveque, R.M.
AU  - Dawid, S.
AU  - DiRita, V.J.
TI  - Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2017
SP  - E8053
EP  - E8061
VL  - 114
AB  - Campylobacter jejuni, a leading cause of bacterial gastroenteritis, is naturally  competent.
AB  - Like many competent organisms, C. jejuni restricts the DNA that can be
AB  - used for transformation to minimize undesirable changes in the chromosome.
AB  - Although C. jejuni can be transformed by C. jejuni-derived DNA, it is poorly
AB  - transformed by the same DNA propagated in Escherichia coli or produced with PCR.
AB  - Our work indicates that methylation plays an important role in marking DNA for
AB  - transformation. We have identified a highly conserved DNA methyltransferase,
AB  - which we term Campylobacter transformation system methyltransferase (ctsM), which
AB  - methylates an overrepresented 6-bp sequence in the chromosome. DNA derived from a
AB  - ctsM mutant transforms C. jejuni significantly less well than DNA derived from
AB  - ctsM+ (parental) cells. The ctsM mutation itself does not affect transformation
AB  - efficiency when parental DNA is used, suggesting that CtsM is important for
AB  - marking transforming DNA, but not for transformation itself. The mutant has no
AB  - growth defect, arguing against ongoing restriction of its own DNA. We further
AB  - show that E. coli plasmid and PCR-derived DNA can efficiently transform C. jejuni
AB  - when only a subset of the CtsM sites are methylated in vitro. A single
AB  - methylation event 1 kb upstream of the DNA involved in homologous recombination
AB  - is sufficient to transform C. jejuni, whereas otherwise identical unmethylated
AB  - DNA is not. Methylation influences DNA uptake, with a slight effect also seen on
AB  - DNA binding. This mechanism of DNA discrimination in C. jejuni is distinct from
AB  - the DNA discrimination described in other competent bacteria.
ER  -

TY  - JOUR
AU  - Beaulaurier, J.
AU  - Zhang, X.S.
AU  - Zhu, S.
AU  - Sebra, R.
AU  - Rosenbluh, C.
AU  - Deikus, G.
AU  - Shen, N.
AU  - Munera, D.
AU  - Waldor, M.K.
AU  - Chess, A.
AU  - Blaser, M.J.
AU  - Schadt, E.E.
AU  - Fang, G.
TI  - Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.
JO  - Nat. Commun.
PY  - 2015
SP  - 7438
EP  - 7438
VL  - 6
AB  - Beyond its role in host defense, bacterial DNA methylation also plays important roles in the
AB  - regulation of gene expression, virulence and antibiotic resistance.
AB  - Bacterial cells in a clonal population can generate epigenetic heterogeneity to
AB  - increase population-level phenotypic plasticity. Single molecule, real-time
AB  - (SMRT) sequencing enables the detection of N6-methyladenine and
AB  - N4-methylcytosine, two major types of DNA modifications comprising the bacterial
AB  - methylome. However, existing SMRT sequencing-based methods for studying bacterial
AB  - methylomes rely on a population-level consensus that lacks the single-cell
AB  - resolution required to observe epigenetic heterogeneity. Here, we present SMALR
AB  - (single-molecule modification analysis of long reads), a novel framework for
AB  - single molecule-level detection and phasing of DNA methylation. Using seven
AB  - bacterial strains, we show that SMALR yields significantly improved resolution
AB  - and reveals distinct types of epigenetic heterogeneity. SMALR is a powerful new
AB  - tool that enables de novo detection of epigenetic heterogeneity and empowers
AB  - investigation of its functions in bacterial populations.
ER  -

TY  - JOUR
AU  - Beaulaurier, J.
AU  - Zhu, S.
AU  - Deikus, G.
AU  - Mogno, I.
AU  - Zhang, X.S.
AU  - Davis-Richardson, A.
AU  - Canepa, R.
AU  - Triplett, E.W.
AU  - Faith, J.J.
AU  - Sebra, R.
AU  - Schadt, E.E.
AU  - Fang, G.
TI  - Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.
JO  - Nat. Biotechnol.
PY  - 2017
SP  - 61
EP  - 69
VL  - 36
AB  - Shotgun metagenomics methods enable characterization of microbial communities in  human
AB  - microbiome and environmental samples. Assembly of metagenome sequences does not output whole
AB  - genomes, so computational binning methods have been developed to cluster sequences into genome
AB  - 'bins'. These methods exploit sequence composition, species abundance, or chromosome
AB  - organization but cannot fully distinguish closely related species and strains. We present a
AB  - binning method that incorporates bacterial DNA methylation signatures, which are detected
AB  - using single-molecule real-time sequencing. Our method takes advantage of these endogenous
AB  - epigenetic barcodes to resolve individual reads and assembled contigs into species- and
AB  - strain-level bins. We validate our method using synthetic and real microbiome sequences. In
AB  - addition to genome binning, we show that our method links plasmids and other mobile genetic
AB  - elements to their host species in a real microbiome sample. Incorporation of DNA methylation
AB  - information into shotgun metagenomics analyses will complement existing methods to enable more
AB  - accurate sequence binning.
ER  -

TY  - JOUR
AU  - Beaulieu, N.
AU  - Morin, S.
AU  - Chute, I.C.
AU  - Robert, M.-F.
AU  - Nguyen, H.
AU  - MacLeod, A.R.
TI  - An essential role for DNA methyltransferase DNMT3B in cancer cell survival.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 28176
EP  - 28181
VL  - 277
AB  - Abnormal methylation and associated silencing of tumor suppressor genes is a common feature of
AB  - many types of cancers. The observation of persistent methylation in human cancer cells lacking
AB  - the maintenance methyltransferase DNMT1 suggests the involvement of other DNA
AB  - methyltransferases in gene silencing in cancer. To test this hypothesis, we have evaluated
AB  - methylation and gene expression in cancer cells specifically depleted of DNMT3A or DNMT3B, de
AB  - novo methyltransferases that are expressed in adult tissues. Here we have shown that depletion
AB  - of DNMT3B, but not DNMT3A, induced apoptosis of human cancer cells but not normal cells.
AB  - DNMT3B depletion reactivated methylation-silenced gene expression but did not induce global or
AB  - juxtacentromeric satellite demethylation as did specific depletion of DNMT1. Furthermore, the
AB  - effect of DNMT3B depletion was rescued by exogenous expression of either of the splice
AB  - variants DNMT3B2 or DNMT3B3 but not DNMT1. These results indicate that DNMT3B has significant
AB  - site selectivity that is distinct from DNMT1, regulates aberrant gene silencing, and is
AB  - essential for cancer cell survival.
ER  -

TY  - JOUR
AU  - Beck, C.
AU  - Cranz, S.
AU  - Solmaz, M.
AU  - Roth, M.
AU  - Jeltsch, A.
TI  - How does a DNA interacting enzyme change its specificity during molecular evolution? A site-directed mutagenesis study at the DNA binding site of the DNA-(adenine-N(6))-methyltransferase EcoRV.
JO  - Biochemistry
PY  - 2001
SP  - 10956
EP  - 10965
VL  - 40
AB  - The EcoRV DNA-(adenine-N6)-methyltransferase (MTase) recognizes GATATC sequences and modifies
AB  - the first adenine residue within this site. Parts of its DNA interface show high sequence
AB  - homology to DNA MTases of the dam family which recognize and modify GATC sequences. A
AB  - phylogenetic analysis of M.EcoRV and dam-MTases suggests that EcoRV arose in evolution from a
AB  - primordial dam-MTase in agreement with the finding that M.EcoRV also methylates GATC sites
AB  - albeit at a strongly reduced rate. GATCTC sites that deviate in only one position from the
AB  - EcoRV sequence are preferred over general dam sites. We have investigated by site-directed
AB  - mutagenesis the function of 17 conserved and nonconserved residues within three loops flanking
AB  - the DNA binding cleft of M.EcoRV. M.EcoRV contacts the GATATC sequence with two highly
AB  - cooperative recognition modules. The contacts to the GAT-part of the recognition sequence are
AB  - formed by residues conserved between dam MTases and M.EcoRV. Mutations at these positions lead
AB  - to an increase in the discrimination between GATATC and GATC substrates. Our data show that
AB  - the change in sequence specificity from dam (GATC) to EcoRV (GATATC) was accompanied by the
AB  - generation of a second recognition module that contacts the second half of the target
AB  - sequence. The new DNA contacts are formed by residues from all three loops that are not
AB  - conserved between M.EcoRV and dam MTases. Mutagenesis at important residues within this module
AB  - leads to variants that show a decreased ability to recognize the TC-part of the GATATC
AB  - sequence.
ER  -

TY  - JOUR
AU  - Beck, C.
AU  - Jeltsch, A.
TI  - Probing the DNA interface of the EcoRV DNA-(adenine-N6)-methyltransferase by site-directed mutagenesis, fluorescence spectroscopy, and UV cross-linking.
JO  - Biochemistry
PY  - 2002
SP  - 14103
EP  - 14110
VL  - 41
AB  - The EcoRV DNA-(adenine-N6)-methyltransferase recognizes GATATC sites and methylates the DNA as
AB  - indicated. It is related to the large family of dam methyltransferases which modify GATC
AB  - sites. We have studied the interaction of DNA with M.EcoRV and 12 M.EcoRV variants using
AB  - oligonucleotides containing 2-aminopurine as a fluorescence probe in equilibrium and
AB  - stopped-flow DNA binding studies and 5-iododeoxyuracil for UV cross-linking. M.EcoRV binds to
AB  - DNA in a multistep binding reaction, including two different conformations of the specific
AB  - enzyme-DNA complex, and induces a strong conformational change of the DNA at the fourth
AB  - position of the recognition site. Mutations at residues forming contacts to the GAT part of
AB  - the recognition site reduce the stability of both specific enzyme-DNA complexes. Two enzyme
AB  - variants which fail to recognize the ATC part do not induce the deformation of the DNA which
AB  - explains why they cannot interact properly with the recognition site. Other mutations at
AB  - residues which interact with the ATC part selectively reduce the stability of the second
AB  - enzyme-DNA complex. These results show that when approaching the DNA M.EcoRV first contacts
AB  - the GAT part of the target site. Since the residues mediating these contacts are conserved
AB  - among M.EcoRV and dam MTases, the kinetics of formation of the enzyme-DNA complex correspond
AB  - to the evolutionary history of the protein. Whether the observation that evolutionarily
AB  - conserved contacts are formed early during complex formation is a general rule for DNA
AB  - interacting enzymes or proteins that change their specificity during evolution remains to be
AB  - seen.
ER  -

TY  - JOUR
AU  - Beck, M.H.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Draft Genome Sequence of the Strict Anaerobe Clostridium homopropionicum LuHBu1 (DSM 5847).
JO  - Genome Announcements
PY  - 2015
SP  - e01112
EP  - e01115
VL  - 3
AB  - Here, we report the draft genome sequence of Clostridium homopropionicum LuHBu1 (DSM 5847(T)),
AB  - a strictly anaerobic bacterium, which performs propionate fermentation and is capable of
AB  - growing with 2-, 3-, or 4-hydroxybutyrate as its sole substrate. The genome consists of a
AB  - single chromosome of 3.65 Mb.
ER  -

TY  - JOUR
AU  - Beck, M.H.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Draft Genome Sequence of the Strict Anaerobe Clostridium neopropionicum X4 (DSM 3847T).
JO  - Genome Announcements
PY  - 2016
SP  - e00209
EP  - e00216
VL  - 4
AB  - Here, we report the draft genome sequence ofClostridium neopropionicumX4 (DSM 3847(T)), a
AB  - strictly anaerobic bacterium capable of fermenting ethanol and CO2to
AB  - propionate, acetate, and propanol. The genome consists of a single chromosome
AB  - (3.19 Mb).
ER  -

TY  - JOUR
AU  - Beck, R.
AU  - Burtscher, H.
TI  - Introduction of arbitrary sequences into genes by use of class IIs restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 886
EP  - 887
VL  - 22
AB  - Introduction of additional nucleotides or modification of sequences at locations where no
AB  - convenient restriction endonuclease recognition site is available can be rather difficult,
AB  - especially if one has to conserve a particular reading frame and new cleavage sites cannot
AB  - simply be generated by taking advantage of the degeneracy of the genetic code. Overlap
AB  - extension can be very useful, however it has some limitations in fragment length and it can
AB  - take some time to find optimal conditions for a particular reaction. Using inverse primers to
AB  - amplify small plasmids followed by blunt-end ligation also has some restrictions (e.g.
AB  - amplification of a longer DNA sequence than necessary; use of polymerases with proof-reading
AB  - activity). We wanted to insert a DNA sequence coding for four histidine residues and an
AB  - enterokinase cleavage site between the signal sequence and the mature sequence of human
AB  - placental alkaline phosphatase for purification. We added the enterokinase recognition site in
AB  - order to allow regeneration of the authentic N-terminus of the enzyme. Here we describe a
AB  - convenient way to achieve this, using class IIs restriction endonucleases. Class IIs
AB  - restriction endonucleases cut DNA several nucleotides away from their recognition site
AB  - irrespective of the interventing sequence. This can be exploited to generate arbitrary sticky
AB  - ends for in-frame fusion of DNA sequences, combining two PCR reactions with a simple cloning
AB  - step.
ER  -

TY  - JOUR
AU  - Becker, L.
AU  - Bunk, B.
AU  - Eller, C.
AU  - Steglich, M.
AU  - Pfeifer, Y.
AU  - Werner, G.
AU  - Nubel, U.
TI  - Complete Genome Sequence of a CTX-M-15-Producing Klebsiella pneumoniae Outbreak Strain from Multilocus Sequence Type 514.
JO  - Genome Announcements
PY  - 2015
SP  - e00742
EP  - e00715
VL  - 3
AB  - We report here the genome sequence of a multidrug-resistant Klebsiella pneumoniae strain,
AB  - which caused an outbreak in a neonatal ward in 2011. The genome consists
AB  - of a single chromosome (5,278 kb) and three plasmids (362 kb, 5 kb, and 4 kb).
ER  -

TY  - JOUR
AU  - Becker, M.M.
AU  - Lesser, D.
AU  - Kurpiewski, M.
AU  - Baranger, A.
AU  - Jen-Jacobson, L.
TI  - Ultraviolet footprinting accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1988
SP  - 6247
EP  - 6251
VL  - 85
AB  - The UV footprinting technique has been used to detect contacts between EcoRI
AB  - endonuclease and its recognition sequence at single nucleotide resolution.
AB  - Comparison of the UV-footprinting results to the published crystal structure of
AB  - the EcoRI endonuclease-DNA complex allows us to determine how UV light detects
AB  - protein-DNA contacts.  We find that kinking of the DNA helix in the complex
AB  - greatly enhances the UV photoreactivity of DNA at the site of the kink.  In
AB  - contrast to kinking, contacts between the endonuclease and the DNA bases
AB  - inhibit the UV photoreactivity of DNA.  Similar analysis of a proteolytically
AB  - modified endonuclease that exhibits the same sequence specificity as wild-type
AB  - enzyme but that does not cleave DNA supports these conclusions.  Furthermore,
AB  - detection of enhanced photoreactivity at the same kink in the modified
AB  - enzyme-DNA complex allows us to conclude that the loss of cleavage activity by
AB  - the modified endonuclease is not due to its failure to kink DNA.
ER  -

TY  - JOUR
AU  - Bedford, D.J.
AU  - Laity, C.
AU  - Buttner, M.J.
TI  - Two genes involved in the phase-variable phi C31 resistance mechanism of Streptomyces coelicolor A3(2).
JO  - J. Bacteriol.
PY  - 1995
SP  - 4681
EP  - 4689
VL  - 177
AB  - The phage growth limitation (Pgl) system of Streptomyces coelicolor confers resistance to phi
AB  - C31 and its homoimmune phages. The positions of the pgl genes
AB  - within a 16-kb clone of S. coelicolor DNA were defined by subcloning, insertional
AB  - inactivation, and deletion mapping. Nucleotide sequencing and functional analysis
AB  - identified two genes, pglY and pglZ, required for the Pgl+ (phage-resistant)
AB  - phenotype. pglY and pglZ, which may be translationally coupled, are predicted to
AB  - encode proteins with M(r)S of 141,000 and 104,000, respectively. Neither protein
AB  - shows significant similarity to other known proteins, but PglY has a putative
AB  - ATP/GTP binding motif. The pglY and pglZ genes are cotranscribed from a single
AB  - promoter which appears to be constitutive and is not induced by phage infection.
ER  -

TY  - JOUR
AU  - Beer, H.D.
AU  - Maschke, H.E.
AU  - Schugerl, K.
TI  - Continuous production of restriction endonucleases: continuous two-stage cultivation with E. coli JM103; continuous cell disintegration and purification by affinity chromatography.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1992
SP  - 220
EP  - 225
VL  - 38
AB  - The optimization of the production of recombinant DNA-derived proteins in Escherichia coli was
AB  - investigated. We chose restriction endonucleases EcoRI and EcoRV from E. coli as model
AB  - proteins, despite the observation that overproduction can result in a toxic effect to the
AB  - cells. The enzymes were expressed as fusion proteins consisting of protein A from
AB  - Staphylococcus aureus and the desired enzymes in order to facilitate purification. The
AB  - expression of the fusion protein was induced by a temperature shift using the PR promoter of
AB  - phage lambda regulated by the repressor plasmid pRK248cI. Data from batch fermentations
AB  - provided the basis for planning a continuous two-stage fermentation. The EcoRI enzyme activity
AB  - was investigated as a function of the induction time after cell disintegration and allowed an
AB  - estimation of yield of the continuous culture. Plasmid instability, which was only observed
AB  - under continuous conditions, could be prevented by adding tetracycline (resistance of the
AB  - repressor plasmid) to the medium. We established a continuous cell disintegration system and
AB  - purified the fusion protein semicontinuously by affinity chromatography. The biological
AB  - activity of the fusion protein was the same as the native endonuclease so there was no need
AB  - for cleavage of the fusion protein and the product could be used without further processing.
ER  -

TY  - JOUR
AU  - Begley, T.J.
AU  - Cunningham, R.P.
TI  - Methanobacterium thermoformicicum thymine DNA mismatch glycosylase: conversion of an N-glycosylase to an AP lyase.
JO  - Protein Eng.
PY  - 1999
SP  - 333
EP  - 340
VL  - 12
AB  - The thymine DNA mismatch glycosylase from Methanobacterium thermoformicicum, a member of the
AB  - endonuclease III family of repair proteins, excises the pyrimidine base from T-G and U-G
AB  - mismatches. Unlike endonuclease III, it does not cleave the phosphodiester backbone by a
AB  - beta-elimination reaction. This cleavage event has been attributed to a nucleophilic attack by
AB  - the conserved Lys120 of endonuclease III on the aldehyde group at C1' of the deoxyribose and
AB  - subsequent Schiff base formation. The inability of TDG to perform this beta-elimination event
AB  - appears to be due to the presence of a tyrosine residue at the position equivalent to Lys120
AB  - in endonuclease III. The purpose of this work was to investigate the requirements for AP lyase
AB  - activity. We replaced Tyr126 in TDG with a lysine residue to determine if this replacement
AB  - would yield an enzyme with an associated AP lyase activity capable of removing a mismatched
AB  - pyrimidine. We observed that this replacement abolishes the glycosylase activity of TDG but
AB  - does not affect substrate recognition. It does, however, convert the enzyme into an AP lyase.
AB  - Chemical trapping assays show that this cleavage proceeds through a Schiff base intermediate
AB  - and suggest that the amino acid at position 126 interacts with C1' on the deoxyribose sugar.
ER  -

TY  - JOUR
AU  - Begley, T.J.
AU  - Haas, B.J.
AU  - Morales, J.C.
AU  - Kool, E.T.
AU  - Cunningham, R.P.
TI  - Kinetics and binding of the tymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates.
JO  - DNA Repair
PY  - 2003
SP  - 107
EP  - 120
VL  - 2
AB  - We have examined the removal of thymine residues from T-G mismatches in DNA by the thymine-DNA
AB  - mismatch glycosylase from Methanobacterium thermoautrophicum (Mig-Mth), within the context of
AB  - the base excision repair (BER) pathway, to investigate why this glycosylase has such low
AB  - activity in vitro. Using single-turnover kinetics and steady-state kinetics, we calculated the
AB  - catalytic and product dissociation rate constants for Mig-Mth, and determined that Mig-Mth is
AB  - inhibited by product apyrimidinic (AP) sites in DNA. Electrophoretic mobility shift assays
AB  - (EMSA) provide evidence that the specificity of product binding is dependent upon the base
AB  - opposite the AP site. The binding of Mig-Mth to DNA containing the non-cleavable substrate
AB  - analogue difluorotoluene (F) was also analyzed to determine the effect of the opposite base on
AB  - Mig-Mth binding specificity for substrate-like duplex DNA. The results of these experiments
AB  - support the idea that opposite strand interactions play roles in determining substrate
AB  - specificity. Endonuclease IV, which cleaves AP sites in the next step of the BER pathway, was
AB  - used to analyze the effect of product removal on the overall rate of thymine hydrolysis by
AB  - Mig-Mth. Our results support the hypothesis that endonuclease IV increases the apparent
AB  - activity of Mig-Mth significantly under steady-state conditions by preventing reassociation of
AB  - enzyme to product.
ER  -

TY  - JOUR
AU  - Behar, A.
AU  - McCormick, L.J.
AU  - Perlman, S.J.
TI  - Rickettsia felis infection in a common household insect pest, Liposcelis bostrychophila (Psocoptera: Liposcelidae).
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 2280
EP  - 2285
VL  - 76
AB  - Many species of Rickettsia are well-known mammalian pathogens transmitted
AB  - by blood-feeding arthropods. However, molecular surveys are continually
AB  - uncovering novel Rickettsia species, often in unexpected hosts, including
AB  - many arthropods that do not feed on blood. This study reports a systematic
AB  - molecular characterization of a Rickettsia infecting the psocid Liposcelis
AB  - bostrychophila (Psocoptera: Liposcelidae), a common and cosmopolitan
AB  - household pest. Surprisingly, the psocid Rickettsia is shown to be
AB  - Rickettsia felis, a human pathogen transmitted by fleas that causes
AB  - serious morbidity and occasional mortality. The plasmid from the psocid R.
AB  - felis was sequenced and was found to be virtually identical to the one in
AB  - R. felis from fleas. As Liposcelis insects are often intimately associated
AB  - with humans and other vertebrates, it is speculated that they acquired R.
AB  - felis from fleas. Whether the R. felis in psocids causes disease in
AB  - vertebrates is not known and warrants further study.
ER  -

TY  - JOUR
AU  - Behera, B.K.
AU  - Das, P.
AU  - Maharana, J.
AU  - Paria, P.
AU  - Mandal, S.N.
AU  - Meena, D.K.
AU  - Sharma, A.P.
AU  - Jayarajan, R.
AU  - Dixit, V.
AU  - Verma, A.
AU  - Vellarikkal, S.K.
AU  - Scaria, V.
AU  - Sivasubbu, S.
AU  - Rao, A.R.
AU  - Mohapatra, T.
TI  - Draft Genome Sequence of the Extremely Halophilic Bacterium Halomonas salina Strain CIFRI1, Isolated from the East Coast of India.
JO  - Genome Announcements
PY  - 2015
SP  - e01321
EP  - e01314
VL  - 3
AB  - Halomonas salina strain CIFRI1 is an extremely salt-stress-tolerant bacterium isolated from
AB  - the salt crystals of the east coast of India. Here we report the
AB  - annotated 3.45-Mb draft genome sequence of strain CIFRI1 having 86 contigs with
AB  - 3,139 protein coding loci, including 62 RNA genes.
ER  -

TY  - JOUR
AU  - Behr, J.
AU  - Geissler, A.J.
AU  - Schmid, J.
AU  - Zehe, A.
AU  - Vogel, R.F.
TI  - The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr.
JO  - PLoS ONE
PY  - 2016
SP  - E0152747
EP  - E0152747
VL  - 11
AB  - As the number of bacterial genomes increases dramatically, the demand for easy to
AB  - use tools with transparent functionality and comprehensible output for applied
AB  - comparative genomics grows as well. We present BlAst Diagnostic Gene findEr
AB  - (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for
AB  - the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG
AB  - identification settings can be modified easily and installing and running BADGE
AB  - does not require specific bioinformatics skills. During the BADGE run the user is
AB  - informed step by step about the DMG finding process, thus making it easy to
AB  - evaluate the impact of chosen settings and options. On the basis of an example
AB  - with relevance for beer brewing, being one of the oldest biotechnological
AB  - processes known, we show a straightforward procedure, from phenotyping, genome
AB  - sequencing, assembly and annotation, up to a discriminant marker gene PCR assay,
AB  - making comparative genomics a means to an end. The value and the functionality of
AB  - BADGE were thoroughly examined, resulting in the successful identification and
AB  - validation of an outstanding novel DMG (fabZ) for the discrimination of harmless
AB  - and harmful contaminations of Pediococcus damnosus, which can be applied for
AB  - spoilage risk determination in breweries. Concomitantly, we present and compare
AB  - five complete P. damnosus genomes sequenced in this study, finding that the
AB  - ability to produce the unwanted, spoilage associated off-flavor diacetyl is a
AB  - plasmid encoded trait in this important beer spoiling species.
ER  -

TY  - JOUR
AU  - Behrens, B.
AU  - Noyer-Weidner, M.
AU  - Pawlek, B.
AU  - Lauster, R.
AU  - Balganesh, T.S.
AU  - Trautner, T.A.
TI  - Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages.
JO  - EMBO J.
PY  - 1987
SP  - 1137
EP  - 1142
VL  - 6
AB  - B. subtilis phage Rho11s codes for a multispecific DNA methyltransferase
AB  - (Mtase) which methylates cytosine within the sequences GGCC and GAGCTC.  The
AB  - Mtase gene of Rho11s was isolated and sequenced.  It has 1509 bp, corresponding
AB  - to 503 amino acids (aa).  The enzyme's Mr of 57.2 kd predicted from the
AB  - nucleotide sequence was verified by direct Mr determinations of the Mtase.  A
AB  - comparison of the aa sequence of the Rho11s Mtase with those of related phages
AB  - SPR and Phi3T, which differ in their methylation potential, revealed
AB  - generalities in the building plan of such enzymes.  At least 70% of the aa of
AB  - each enzyme are contained in two regions of 243 and 109 aa at the N and C
AB  - termini respectively, which are highly conserved among the three enzymes.  In
AB  - each enzyme, variable sequences separate the conserved regions.  Variability is
AB  - generated through the single or multiple use of related and unrelated sequence
AB  - motifs.  We propose that the recognition of those DNA target sequences, which
AB  - are unique for each of the three enzymes, is determined by these variable
AB  - regions.  Evolutionary relationships between the three enzymes are discussed.
ER  -

TY  - JOUR
AU  - Behrens, B.
AU  - Pawlek, B.
AU  - Morelli, G.
AU  - Trautner, T.A.
TI  - Restriction and modification in Bacillus subtilis:  construction of hybrid lambda and SPP1 phages containing a DNA methyltransferase gene from B. subtilis phage SPR.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 10
EP  - 16
VL  - 189
AB  - The gene of B. subtilis phage SPR, specifying DNA methyltransferase activity
AB  - was identified within a 3.1 Md EcoRI fragment of SPR DNA.  This fragment was
AB  - cloned in E. coli using a lambda insertion vector.  A 1.25 Md PstI fragment
AB  - with this gene was subsequently derived from the lambda/SPR hybrid phage and
AB  - subcloned in B. subtilis using a new SPP1 vector, whose construction is
AB  - described.
ER  -

TY  - JOUR
AU  - Behrens, W.
AU  - Bonig, T.
AU  - Suerbaum, S.
AU  - Josenhans, C.
TI  - Genome Sequence of Helicobacter pylori hpEurope Strain N6.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3725
EP  - 3726
VL  - 194
AB  - Helicobacter pylori colonizes about half of the world's population. It is a causative agent
AB  - of stomach diseases, including malignant tumors. We report the
AB  - genome sequence of strain N6, which is widely used in H. pylori research and
AB  - appreciated for its large cell size and high transformation efficiency.
ER  -

TY  - JOUR
AU  - Beja, O.
AU  - Aravind, L.
AU  - Koonin, E.V.
AU  - Suzuki, M.T.
AU  - Hadd, A.
AU  - Nguyen, L.P.
AU  - Jovanovich, S.B.
AU  - Gates, C.M.
AU  - Feldman, R.A.
AU  - Spudich, J.L.
AU  - Spudich, E.N.
AU  - DeLong, E.F.
TI  - Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
JO  - Science
PY  - 2000
SP  - 1902
EP  - 1906
VL  - 289
AB  - Extremely halophilic archaea contain retinal-binding integral membrane
AB  - proteins called bacteriorhodopsins that function as light-driven proton
AB  - pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic
AB  - membrane potential in response to light have been demonstrated only in
AB  - halophilic archaea. We describe here a type of rhodopsin derived from
AB  - bacteria that was discovered through genomic analyses of naturally
AB  - occuring marine bacterioplankton. The bacterial rhodopsin was encoded in
AB  - the genome of an uncultivated gamma-proteobacterium and shared highest
AB  - amino acid sequence similarity with archaeal rhodopsins. The protein was
AB  - functionally expressed in Escherichia coli and bound retinal to form an
AB  - active, light-driven proton pump. The new rhodopsin exhibited a
AB  - photochemical reaction cycle with intermediates and kinetics
AB  - characteristic of archaeal proton-pumping rhodopsins. Our results
AB  - demonstrate that archaeal-like rhodopsins are broadly distributed among
AB  - different taxa, including members of the domain Bacteria. Our data also
AB  - indicate that a previously unsuspected mode of bacterially mediated
AB  - light-driven energy generation may commonly occur in oceanic surface
AB  - waters worldwide.
ER  -

TY  - JOUR
AU  - Bekal, S.
AU  - Lin, A.
AU  - Vincent, A.
AU  - Berry, C.
AU  - Gilmour, M.
AU  - Fournier, E.
AU  - Cote, J.C.
AU  - Tremblay, C.
TI  - Draft Genome Sequence of a Necrotoxigenic Escherichia coli Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e01152
EP  - e01115
VL  - 3
AB  - Here, we present the draft genome sequence of a necrotoxigenic Escherichia coli strain
AB  - isolated from a patient following a very rapidly evolving, lethal necrotizing fasciitis.
ER  -

TY  - JOUR
AU  - Beker, M.
AU  - Rose, S.
AU  - Lykkebo, C.A.
AU  - Douthwaite, S.
TI  - Integrative and Conjugative Elements (ICEs) in Pasteurellaceae Species and Their  Detection by Multiplex PCR.
JO  - Front. Microbiol.
PY  - 2018
SP  - 1329
EP  - 1329
VL  - 9
AB  - Strains of the Pasteurellaceae bacteria Pasteurella multocida and Mannheimia haemolytica are
AB  - major etiological agents of bovine respiratory disease (BRD).
AB  - Treatment of BRD with antimicrobials is becoming more challenging due to the
AB  - increasing occurrence of resistance in infecting strains. In Pasteurellaceae
AB  - strains exhibiting resistance to multiple antimicrobials including
AB  - aminoglycosides, beta-lactams, macrolides and sulfonamides, the resistance
AB  - determinants are often chromosomally encoded within integrative and conjugative
AB  - elements (ICEs). To gain a more comprehensive picture of ICE structures, we
AB  - sequenced the genomes of six strains of P. multocida and four strains of M.
AB  - haemolytica; all strains were independent isolates and eight of them were
AB  - multiple-resistant. ICE sequences varied in size from 49 to 79 kb, and were
AB  - comprised of an array of conserved genes within a core region and varieties of
AB  - resistance genes within accessory regions. These latter regions mainly account
AB  - for the variation in the overall ICE sizes. From the sequence data, we developed
AB  - a multiplex PCR assay targeting four conserved core genes required for
AB  - integration and maintenance of ICE structures. Application of this assay on 75
AB  - isolates of P. multocida and M. haemolytica reveals how the presence and
AB  - structures of ICEs are related to their antibiotic resistance phenotypes. The
AB  - assay is also applicable to other members of the Pasteurellaceae family including
AB  - Histophilus somni and indicates how clustering and dissemination of the
AB  - resistance genes came about.
ER  -

TY  - JOUR
AU  - Bekker, O.B.
AU  - Klimina, K.M.
AU  - Vatlin, A.A.
AU  - Zakharevich, N.V.
AU  - Kasianov, A.S.
AU  - Danilenko, V.N.
TI  - Draft Genome Sequence of Streptomyces fradiae ATCC 19609, a Strain Highly Sensitive to Antibiotics.
JO  - Genome Announcements
PY  - 2014
SP  - e01247
EP  - e01214
VL  - 2
AB  - We report here a sequence of the genome of the Streptomyces fradiae ATCC 19609 strain,
AB  - initially isolated from the soil, which produces tylosin. S. fradiae is
AB  - highly sensitive to different classes of antibiotics, compared to the
AB  - sensitivities of other bacteria. We have identified 9 groups of genes directly or
AB  - indirectly involved in the resistome formation.
ER  -

TY  - JOUR
AU  - Belavin, P.A.
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - A simple technique for detection of restriction endonucleases in bacterial colonies.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1988
SP  - 121
EP  - 124
VL  - 24
AB  - A simple technique is proposed for detection of bacterial restriction
AB  - endonucleases.  Analysis is performed directly in the cells from colonies
AB  - cultivated on Petri dishes.  The cells collected with an inoculation loop are
AB  - treated with lysozyme and Triton X-100.  After centrifugation the supernatant
AB  - is tested for endonuclease activity.  The technique enables up to 100 colonies
AB  - to be tested in 3-4 hr.
ER  -

TY  - JOUR
AU  - Belavin, P.A.
AU  - Gorbunov, Y.A.
AU  - Malygin, E.G.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
TI  - Substrate specificity of DNA methylase from Flavobacterium okeanokoites.
JO  - Bioorg. Khim.
PY  - 1989
SP  - 417
EP  - 418
VL  - 15
AB  - The specificity of DNA methylase M.FokI towards oligonucleotides containing the
AB  - sequence 5' GGATG was investigated, and N6-methyladenine in the GGATG chain was
AB  - shown to be the only product of the modification.
ER  -

TY  - JOUR
AU  - Belbahri, L.
AU  - Alenezi, F.N.
AU  - Luptakova, L.
AU  - Rateb, M.E.
AU  - Woodward, S.
TI  - Complete Genome Sequence of Aneurinibacillus migulanus E1, a Gramicidin S- and d-Phenylalanyl-l-Propyl Diketopiperazine-Deficient Mutant.
JO  - Genome Announcements
PY  - 2015
SP  - e01441
EP  - e01415
VL  - 3
AB  - We report here the complete genome sequence of the Aneurinibacillus migulanus E1  mutant
AB  - deficient in gramicidin S (GS) and d-phenylalanyl-l-propyl
AB  - diketopiperazine (DKP) formation. The genome consists of a circular chromosome
AB  - (6,301,904 bp, 43.20% G+C content) without any plasmid. The complete genome
AB  - sequence enables further investigation of the biosynthetic mechanism and the
AB  - biological function of gramicidin S.
ER  -

TY  - JOUR
AU  - Belcaid, M.
AU  - Kang, Y.
AU  - Tuanyok, A.
AU  - Hoang, T.T.
TI  - Complete Genome Sequence of Burkholderia cepacia Strain LO6.
JO  - Genome Announcements
PY  - 2015
SP  - e00587
EP  - e00515
VL  - 3
AB  - Burkholderia cepacia strain LO6 is a betaproteobacterium that was isolated from a cystic
AB  - fibrosis patient. Here we report the 6.4 Mb draft genome sequence
AB  - assembled into 2 contigs. This genome sequence will aid the transcriptomic
AB  - profiling of this bacterium and help us to better understand the mechanisms
AB  - specific to pulmonary infections.
ER  -

TY  - JOUR
AU  - Belduz, A.O.
AU  - Canakci, S.
AU  - Chan, K.G.
AU  - Kahar, U.M.
AU  - Chan, C.S.
AU  - Yaakop, A.S.
AU  - Goh, K.M.
TI  - Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 70
EP  - 70
VL  - 10
AB  - Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many
AB  - biotechnological applications. Anoxybacillus ayderensis AB04(T)
AB  - (= NCIMB 13972(T) = NCCB 100050(T)) was isolated from the Ayder hot spring in
AB  - Rize, Turkey, and is one of the earliest described Anoxybacillus type strains.
AB  - The present work reports the cellular features of A. ayderensis AB04(T), together
AB  - with a high-quality draft genome sequence and its annotation. The genome is
AB  - 2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and
AB  - 103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome
AB  - annotation of strain AB04(T), we identified genes encoding various glycoside
AB  - hydrolases that are important for carbohydrate-related industries, which we
AB  - compared with those of other, sequenced Anoxybacillus spp. Insights into
AB  - under-explored industrially applicable enzymes and the possible applications of
AB  - strain AB04(T) were also described.
ER  -

TY  - JOUR
AU  - Beletskaya, I.V.
AU  - Zakharova, M.V.
AU  - Shlyapnikov, M.G.
AU  - Semenova, L.M.
AU  - Solonin, A.S.
TI  - DNA methylation at the CfrBI site is involved in expression control in the CfrBI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3817
EP  - 3822
VL  - 28
AB  - We have previously found that genes of the CfrBI restriction-modification (R-M) system from
AB  - Citrobacter freundii are oriented divergently and that their promoter regions overlap. The
AB  - overlapping promoters suggest regulation of gene expression at the transcriptional level. In
AB  - this study the transcription regulation of CfrBI R-M genes was analyzed in vivo and in vitro
AB  - in Escherichia coli. It was shown that in the presence of CfrBI methyltransferase (M.CfrBI),
AB  - cell galactokinase activity decreases 10-fold when the galactokinase gene (galK) is under the
AB  - control of the cfrBIM promoter and increases 20-fold when galK is under the control of the
AB  - cfrBIR promoter. The CfrBI site, proven to be unique for the entire CrfBI R-M gene sequence,
AB  - is located in the -35 cfrBIM promoter region and is in close vicinity of the -10 cfrBIR
AB  - promoter region. A comparison of the cfrBIM and the cfrBIR promoter activities in the in vitro
AB  - transcription system using methylated and unmethylated DNA fragments as templates demonstrated
AB  - that the efficiency of CfrBI R-M gene transcription is regulated by enzymatic modification at
AB  - the N-4-position of cytosine bases of the CfrBI site by M.CfrBI.  From the results of the in
AB  - vivo and in vitro experiments we suggest a new model of gene expression regulation in type II
AB  - R-M systems.
ER  -

TY  - JOUR
AU  - Beletskii, A.
AU  - Bhagwat, A.S.
TI  - Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 13919
EP  - 13924
VL  - 93
AB  - Cytosines in single-stranded DNA deaminate to uracils at 140 times the rate for cytosines in
AB  - double-stranded DNA.  If resulting uracils are not replaced with cytosine, C to T mutations
AB  - occur.  These facts suggest that cellular processes such as transcription that create
AB  - single-stranded DNA should promote C to T mutations.  We tested this hypothesis with the
AB  - Escherichia coli tac promoter and found that induction of transcription causes ~4-fold
AB  - increase in the frequency of C to U or 5-methylcytosine to T deaminations in the
AB  - nontranscribed strand.  Excess mutations caused by C to U deaminations were reduced, but not
AB  - eliminated, by uracil-DNA glycosylase.  Similarly, mutations caused by 5-methylcytosine to T
AB  - deaminations were only partially reduced by the very short-patch repair process in E. coli.
AB  - These effects are unlikely to be caused by differential repair of the two strands, and our
AB  - results suggest that all actively transcribed genes in E. coli should acquire more C to T
AB  - mutations in the nontranscribed strand.
ER  -

TY  - JOUR
AU  - Belfort, M.
TI  - Back to Basics: Structure, function, evolution and application of homing endonucleases and inteins.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 1
EP  - 10
VL  - 16
AB  - "It is a profound and necessary truth that the deep things in science are not found because
AB  - they are useful; they are found because it was possible to find them." (Robert Oppenheimer,
AB  - 1904-1967).  Oppenheimer's words resonate with this book's theme, which is how both applied
AB  - and theoretical science can emanate from answers to basic questions - whether they are being
AB  - asked to model organisms or in test tubes - about molecular structure and mechanism.  Thus,
AB  - fundamental work on DNA, RNA and proteins, which encode or constitute homing endonucleases and
AB  - inteins, is leading to refined theories of evolution in prokaryotes and eukaryotes on the one
AB  - hand, and the development of laboratory tools and health-care reagents on the other.  Homing
AB  - endonucleases and inteins, sometimes referred to as "protein introns", are linked at many
AB  - levels.  First, homing endonucleases are frequently encoded by introns that self-splice at the
AB  - RNA level, in analogy to inteins that self-splice at the protein level. Second, homing
AB  - endonucleases similar to those encoded by introns are often found embedded within and
AB  - co-translated with inteins.  Third, both types of intervening sequence are mobile elements,
AB  - capable of movement from genome to genome.  Fourth, the endonuclease component of both introns
AB  - and inteins imparts their mobility.  Fifth, each of these mobile intervening sequences is
AB  - thought to have originated from invasion of the gene encoding the self-splicing element, the
AB  - intron or intein, by an endonuclease gene, the primordial mobile element.  The final unifying
AB  - theme is the exploitation of introns, inteins and homing endonucleases by chemists,
AB  - geneticists, structural biologists and engineers, to generate reagents and tools that are
AB  - useful in basic research, biotechnology and medicine. This chapter serves as an introduction
AB  - to the volume entitled Homing Endonucleases and Inteins, which provides a wonderful
AB  - illustration of the point that fundamental studies of structure and mechanism fuel
AB  - evolutionary theory and technology development alike.
ER  -

TY  - JOUR
AU  - Belfort, M.
TI  - Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.
JO  - Genes Dev.
PY  - 2003
SP  - 2860
EP  - 2863
VL  - 17
AB  - Homing endonucleases are enzymes that are typically encoded by intervening sequences of
AB  - various kinds -- introns that splice at the RNA level, or inteins that splice at the protein
AB  - level.  The endonucleases function primarily to mobilize these elements, which are often
AB  - self-splicing, by facilitating their integration to new sites in DNA.  Because these sites are
AB  - most often allelic intronless or inteinless sites, this form of mobility is termed homing, and
AB  - the target sequences are termed homing sites.  Homing endonucleases sometimes do double duty,
AB  - also functioning as maturases, which promote RNA splicing.  Maturases are usually intron
AB  - specific, and act as cofactors that bind their intron-containing precursor RNA to facilitate
AB  - splicing.  Nevertheless, catalysis required for splicing remains a property of the RNA.
ER  -

TY  - JOUR
AU  - Belfort, M.
AU  - Bonocora, R.P.
TI  - Homing Endonucleases: From Genetic Anomalies to Programmable Genomic Clippers.
JO  - Methods Mol. Biol.
PY  - 2014
SP  - 1
EP  - 26
VL  - 1123
AB  - Homing endonucleases are strong drivers of genetic exchange and horizontal transfer of both
AB  - their own genes and their local genetic environment. The mechanisms that govern the function
AB  - and evolution of these genetic oddities have been well documented over the past few decades at
AB  - the genetic, biochemical, and structural levels. This wealth of information has led to the
AB  - manipulation and reprogramming of the endonucleases and to their exploitation in genome
AB  - editing for use as therapeutic agents, for insect vector control and in agriculture. In this
AB  - chapter we summarize the molecular properties of homing endonucleases and discuss their
AB  - strengths and weaknesses in genome editing as compared to other site-specific nucleases such
AB  - as zinc finger endonucleases, TALEN, and CRISPR-derived endonucleases.
ER  -

TY  - JOUR
AU  - Belfort, M.
AU  - Edgell, D.
AU  - Shub, D.
AU  - Van Roey, P.
AU  - Derbyshire, V.
TI  - A multicomponent, multifunctional intron endonuclease, I-TevI.
JO  - J. Biomol. Struct. Dyn.
PY  - 2003
SP  - 834
EP  - 835
VL  - 20
AB  - I-TevI is a homing endonuclease that is encoded by and promotes the mobility of the td intron
AB  - of phage T4.  This 28-kD protein is remarkable in that it is site specific, yet recognizes a
AB  - target site of ~37 bp in a sequence-tolerant fashion.  The enzyme consists of two functionally
AB  - distinct domains, an N-terminal catalytic domain connected by a 75-amino acid linker.  What
AB  - has previously been defined as the DNA-binding domain has an extended structure consisting of
AB  - three distinct modules which contact ~20 bp of the homing site: A Zn finger, an alpha-helix
AB  - and a small helix-turn-helix subdomain.  It is now known that the zinc finger is not required
AB  - for DNA binding or catalysis, but rather is a spring-like component of the linker that directs
AB  - the catalytic domain to cleave the homing site at a fixed distance from the intron insertion
AB  - site.  In contrast, the catalytic domain, which contains the conserved GIY-YIG motif
AB  - characteristic of this family of homing endonucleases, is a compactly folded structure.  It is
AB  - provocative that there are similarities in the three-dimensional arrangement of the
AB  - catalytically important residues and the cation-binding site with those of I-PpoI, a member of
AB  - this His-Cys-box family of homing endonucleases.  These results suggest the possibility of
AB  - mechanistic relationships among these different families of enzymes, but whether this
AB  - represents convergent or divergent evolution is not known.  Regardless, the picture that has
AB  - built is one of a catalytic GIY-YIG cartridge that has become associated with modules that
AB  - direct DNA binding and distance measurement.  Surprisingly, the DNA-binding domain has
AB  - recently been shown to interact with regulatory sequences upstream of the I-TevI gene, such
AB  - that I-TevI acts as a repressor of its own synthesis.  Thus, I-TevI is a multicomponent,
AB  - multifunctional molecule that has evolved site-specific cleavage and autorepression functions
AB  - to maximize the invasiveness and persistence of its host intron.
ER  -

TY  - JOUR
AU  - Belfort, M.
AU  - Perlman, P.S.
TI  - Mechanisms of intron mobility.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 30237
EP  - 30240
VL  - 270
AB  - Group I and group II introns, which splice via RNA-catalyzed pathways, can invade DNA
AB  - sequences by virtue of proteins expressed from open reading frames (ORFs) contained within
AB  - them.  These intron products are endonucleases in the case of group I introns and reverse
AB  - transcriptases (RTs) with associated endonuclease activity in the case of the group II
AB  - introns.  Two kinds of mobility reactions will be considered for each intron type: homing into
AB  - cognate intronless alleles and transposition to non-allelic sites.
ER  -

TY  - JOUR
AU  - Belfort, M.
AU  - Reaban, M.E.
AU  - Coetzee, T.
AU  - Dalgaard, J.Z.
TI  - Prokaryotic introns and inteins: a panoply of form and function.
JO  - J. Bacteriol.
PY  - 1995
SP  - 3897
EP  - 3903
VL  - 177
AB  - Following their initial discovery, introns and RNA splicing were considered, along with the
AB  - nuclear envelope, as characteristics that distinguish eukaryotes from prokaryotes (the
AB  - eubacteria, referred to simply as bacteria, and the archaebacteria, referred to as archaea).
AB  - This dogma became shaky with the identification of putative introns in tRNA genes of archaea
AB  - and finally crumbled with the discovery of self-splicing group I introns in the phages of
AB  - purple bacteria, which was followed by the discovery of group I and group II introns in
AB  - bacterial cells. Another breakthrough was the recent discovery of a nuclear pre-mRNA-like
AB  - intron in a bacterial plasmid. The variety of intervening sequences (IVSs) that span the
AB  - phylogenetic spectrum was further extended by the discovery of inteins, elements that can
AB  - splice at the protein level, in eukaryotes, archaea, and bacteria. This minireview will
AB  - illustrate that interrupted genes can no longer be considered the province of eukaryotes, but
AB  - rather than many forms of IVSs are phylogenetically diverse, occurring also in bacterial and
AB  - archaeal genomes.
ER  -

TY  - JOUR
AU  - Belfort, M.
AU  - Roberts, R.J.
TI  - Homing endonucleases: keeping the house in order.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3379
EP  - 3388
VL  - 25
AB  - Homing endonucleases are rare-cutting enzymes encoded by introns and inteins.  They have
AB  - striking structural and functional properties that distinguish them from restriction enzymes.
AB  - Nomenclature conventions analogous to those for restriction enzymes have been developed for
AB  - the homing endonucleases.  Recent progress in understanding the structure and function of the
AB  - four families of homing enzymes is reviewed.  Of particular interest are the first reported
AB  - structures of homing endonucleases of the LAGLIDADG family.  The exploitation of the homing
AB  - enzymes in genome analysis and recombination research is also summarized.  Finally, the
AB  - evolution of homing endonucleases is considered, both at the structure-function level and in
AB  - terms of their persistence in widely divergent biological systems.
ER  -

TY  - JOUR
AU  - Belfort, M.
AU  - Van Roey, P.
AU  - Derbyshire, V.
TI  - Modular assembly of a multi-functional homing endonuclease.
JO  - J. Biomol. Struct. Dyn.
PY  - 2005
SP  - 809
EP  - 809
VL  - 22
AB  - Homing endonucleases are usually encoded within self-splicing introns or inteins, and are
AB  - found in all three biological kingdoms.  The endonuclease genes and their host intron or
AB  - intein are composite selfish genetic elements that spread between related genomes by a process
AB  - called homing.  The homing pathway is initiated by the endonuclease binding to a sequence, the
AB  - homing site, centered on the intron insertion site of intronless alleles.  The role of the
AB  - homing endonuclease is limited to introduction of a double-strand break close to the intron
AB  - IS.  I-TevI, a member of the GIY-YIG family of homing endonucleases, is a site-specific yet
AB  - sequence tolerant enzyme.  It is remarkably extended molecule consisting of a well-folded
AB  - catalytic domain connected to a series of sub-domains by extended regions.  These include a
AB  - Zn-finger, a minor-goove binding helix and a helix-turn-helix subdomain.  The modular nature
AB  - of the enzyme is pertinent to the evolution of homing endonucleases.  We have begun to assess
AB  - the role of each subdomain in endonuclease function.  Most interestingly, we have found that
AB  - the Zn-finger subdomain does not play a role in substrate DNA binding.  Rather it is required
AB  - for positioning the catalytic domain at a set distance from the primary binding site for
AB  - cleavage to occur.  The next challenge is trying to understand the nature of the linker that
AB  - connects the catalytic and DNA-binding domains and how it interacts with the Zn-finger to
AB  - mediate distance determination.  In addition, recent work has shown that the enzyme is
AB  - bi-functional and can act as an auto-repressor.  It can bind to a site present in its promoter
AB  - region that exhibits sequence similarity to its homing site, but does not cleave the DNA.  It
AB  - is the very modular nature of the enzyme, with distinct sequence requirements for binding and
AB  - cleavage, that facilitates its bifunctionality by binding in the absence of cleavage, leading
AB  - to transcriptional repression.
ER  -

TY  - JOUR
AU  - Belguesmia, Y.
AU  - Leclere, V.
AU  - Duban, M.
AU  - Auclair, E.
AU  - Drider, D.
TI  - Draft Genome Sequence of Enterococcus faecalis DD14, a Bacteriocinogenic Lactic Acid Bacterium with Anti-Clostridium Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e00695
EP  - e00617
VL  - 5
AB  - We report the draft genome sequence of Enterococcus faecalis DD14, a strain isolated from
AB  - meconium of a healthy newborn at Roubaix Hospital (France). The
AB  - strain displayed antagonism against a set of Gram-positive bacteria through
AB  - concomitant production of lactic acid and bacteriocin. The genome has a size of
AB  - 2,893,365 bp and a 37.3% G+C ratio and is predicted to contain at least 2,755
AB  - coding sequences and 62 RNAs.
ER  -

TY  - JOUR
AU  - Belinsky, S.A.
AU  - Nikula, K.J.
AU  - Baylin, S.B.
AU  - Issa, J.-P.
TI  - A microassay for measuring cytosine DNA methyltransferase activity during tumor progression.
JO  - Toxicol. Lett.
PY  - 1995
SP  - 335
EP  - 340
VL  - 82
AB  - The cytosine DNA methyltransferase (MT) enzyme, which catalyzes DNA
AB  - methylation at CpG sites, is overexpressed at the mRNA level during the progressive stages of
AB  - colon cancer.  This paper describes the adaptation of a sensitive microassay for determining
AB  - MT
AB  - enzyme activity during tumor progression in human colon and murine lung.  MT activity was
AB  - progressively elevated in mucosa from familial adenomatosis polyposis patients, mucosa
AB  - adjacent
AB  - to cancers, and in colonic adenocarcinomas when compared to colonic mucosa from control
AB  - patients.  In addition, the activity of this enzyme was increased in alveolar type II but not
AB  - Clara
AB  - cells isolated from A/J mice following carcinogen exposure and continued to increase during
AB  - tumor
AB  - progression.  The use of a microassay for measuring MT activity indicates that changes in
AB  - enzyme
AB  - activity were in general agreement with previous findings of increased MT mRNA levels during
AB  - colon cancer progression and also implicates the involvement of this pathway in lung cancer
AB  - development.
ER  -

TY  - JOUR
AU  - Belinsky, S.A.
AU  - Nikula, K.J.
AU  - Baylin, S.B.
AU  - Issa, J.-P.J.
TI  - Increased cytosine DNA-methyltransferase activity is target-cell-specific and an early event in lung cancer.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 4045
EP  - 4050
VL  - 93
AB  - The association between increased DNA-methyltransferase (DNA-MTase) activity
AB  - and tumor development suggests a fundamental role for this enzyme in the initiation and
AB  - progression of cancer.  A true functional role for DNA-MTase in the neoplastic process would
AB  - be
AB  - further substantiated if the target cells affected by the initiating carcinogen exhibit
AB  - changes in
AB  - enzyme activity.  This hypothesis was addressed by examining DNA-MTase activity in alveolar
AB  - type II (target) and Clara (nontarget) cells from A/J and C3H mice that exhibit high and low
AB  - susceptibility, respectively, for lung tumor formation.  Increased DNA-MTase activity was
AB  - found
AB  - only in the target alveolar type II cells of the susceptible A.J mouse and caused a marked
AB  - increase
AB  - in overall DNA methylation in these cells.  Both DNA-MTase and DNA methylation changes were
AB  - detected 7 days after carcinogen exposure and, thus, were early events in neoplastic
AB  - evolution.
AB  - Increased gene expression was also detected by RNA in situ hybridization in hypertrophic
AB  - alveolar
AB  - type II cells of carcinogen-treated A/J mice, indicating that elevated levels of expression
AB  - may be a
AB  - biomarker for premalignancy.  Enzyme activity increased incrementally during lung cancer
AB  - progression and coincided with increased expression of the DNA-MTase gene in hyperplasias,
AB  - adenomas, and carcinomas.  Thus, these results indicate that early increases in DNA-MTase
AB  - activity are strongly associated with neoplastic development and constitute a key step in
AB  - carcinogenesis.  The detection of premalignant lung disease through increased DNA-MTase
AB  - expression and the possibility of blocking the deleterious effects of this change with
AB  - specific
AB  - inhibitors will offer new intervention strategies for lung cancer.
ER  -

TY  - JOUR
AU  - Belkebir, A.
AU  - Azeddoug, H.
TI  - Purification and characterization of SepII a new restriction endonuclease from Staphylococcus epidermidis.
JO  - Microbiol. Res.
PY  - 2012
SP  - 90
EP  - 94
VL  - 167
AB  - A Type II restriction enzyme SepII has been purified to apparent homogeneity from the
AB  - gram-positive coccus,Staphylococcus epidermidis.
AB  - The purification included an ammonium sulfate precipitation followed by
AB  - Q-sepharose, heparin-sepharose and MonoQ column chromatography on an
AB  - FPLC system. SDS-PAGE analysis showed a denatured molecular weight of
AB  - 29 kDa. The effects of temperature, pH, NaCl, Mn2+,Ca2+, and Mg2+ ion
AB  - concentrations were studied to determine the optimal reaction
AB  - conditions. The enzyme exhibits near maximal levels of activity between
AB  - pH 8-10, at 10-20 mM MgCl2, 100-150 mM NaCl and 1 mM DTT. The results
AB  - also show that in NEB Buffer 3 the enzyme is active over a broad
AB  - temperature range from 0 to 70 degrees C, and in the absence of DNA,
AB  - enzyme thermostability is observed up to 50 degrees C for 20 min, while
AB  - most of the original activity is conserved in 50% glycerol for weeks at
AB  - room temperature. Single and double digestion in presence of commercial
AB  - restriction enzymes of known DNA substrates (lambda, pBR322, pET21,
AB  - pTrcHisB, pPB67) showed that the purified SepII recognized and cleaved
AB  - the same site as EcoRV. Genomic DNA modification status was also
AB  - determined.
ER  -

TY  - JOUR
AU  - Belkebir, A.
AU  - Azeddoug, H.
TI  - Metal ion dependence of DNA cleavage by SepMI and EhoI restriction endonucleases.
JO  - Microbiol. Res.
PY  - 2013
SP  - 99
EP  - 105
VL  - 168
AB  - Most of type II restriction endonucleases show an absolute requirement for divalent metal ions
AB  - as cofactors for DNA cleavage. While Mg2+ is
AB  - the natural cofactor other metal ions can substitute it and mediate the
AB  - catalysis, however Ca2+ (alone) only supports DNA binding. To
AB  - investigate the role of Mg2+ in DNA cleavage by restriction
AB  - endonucleases, we have studied the Mg2+ and Mn2+ concentration
AB  - dependence of DNA cleavage by SepMI and EhoI. Digestion reactions were
AB  - carried out at different Mg2+ and Mn2+ concentrations at constant ionic
AB  - strength. These enzymes showed different behavior regarding the ions
AB  - requirement, SepMI reached near maximal level of activity between 10
AB  - and 20 mM while no activity was detected in the presence of Mn2+ and in
AB  - the presence of Ca2+ cleavage activity was significantly decreased.
AB  - However, EhoI was more highly active in the presence of Mn2+ than in
AB  - the presence of Mg2+ and can be activated by Ca2+. Our results propose
AB  - the two-metal ion mechanism for EhoI and the one-metal ion mechanism
AB  - for SepMI restriction endonuclease. The analysis of the kinetic
AB  - parameters under steady state conditions showed that SepMI had a K-m
AB  - value for pTrcHisB DNA of 6.15 nM and a V-max of 1.79 x 10(-2) nM
AB  - min(-1), while EhoI had a K-m for pUC19 plasmid of 8.66 nM and a V-max
AB  - of 2 x 10(-2) nM min(-1). (C) 2012 Elsevier GmbH. All rights reserved.
ER  -

TY  - JOUR
AU  - Belkhelfa, S.
AU  - Labadie, K.
AU  - Cruaud, C.
AU  - Aury, J.M.
AU  - Roche, D.
AU  - Bouzon, M.
AU  - Salanoubat, M.
AU  - Doring, V.
TI  - Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland.
JO  - Genome Announcements
PY  - 2018
SP  - e00018
EP  - e00018
VL  - 6
AB  - Methylobacterium extorquens TK 0001 (DSM 1337, ATCC 43645) is an aerobic pink-pigmented
AB  - facultative methylotrophic alphaproteobacterium isolated from soil
AB  - in Poland. Here, we report the whole-genome sequence and annotation of this
AB  - organism, which consists of a single 5.71-Mb chromosome.
ER  -

TY  - JOUR
AU  - Bell, D.C.
AU  - Cupples, C.G.
TI  - Very-Short-Patch Repair in Escherichia coli Requires the dam Adenine Methylase.
JO  - J. Bacteriol.
PY  - 2001
SP  - 3631
EP  - 3635
VL  - 183
AB  - Strains of Escherichia coli which lack the dam-encoded adenine methylase are mutators due to a
AB  - reduction in the efficiency of postreplication mismatch repair. In this study, we show that
AB  - Dam(-) strains are also defective in very-short-patch repair, the system which corrects T/G
AB  - mismatches arising from the deamination of 5-methylcytosine. This defect is associated with
AB  - decreased levels of Vsr, the endonuclease which initiates short-patch repair. We also show
AB  - that production of the dcm-encoded cytosine methylase is unaffected in Dam(-) strains. Since
AB  - the dcm and vsr genes are cotranscribed, the regulation of Vsr by Dam is probably
AB  - posttranscriptional.
ER  -

TY  - JOUR
AU  - Bell, K.S. et al.
TI  - Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 11105
EP  - 11110
VL  - 101
AB  - The bacterial family Enterobacteriaceae is notable for its well studied human pathogens,
AB  - including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains
AB  - several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium,
AB  - Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot
AB  - and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced
AB  - enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic
AB  - traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains
AB  - an overrepresentation of pathogenicity determinants, including possible horizontally acquired
AB  - gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To
AB  - investigate whether these gene clusters play a role in the disease process, an arrayed set of
AB  - insertional mutants was generated, and mutations were identified. Plant bioassays showed that
AB  - these mutants were significantly reduced in virulence, demonstrating both the presence of
AB  - novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding
AB  - our understanding of phytopathogenicity in the Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Bell-Pedersen, D.
AU  - Quirk, S.
AU  - Clyman, J.
AU  - Belfort, M.
TI  - Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3763
EP  - 3770
VL  - 18
AB  - Although mobility of the phylogenetically widespread group I introns appears to be
AB  - mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of
AB  - the td and sunY introns are different from their eukaryotic counterparts. Most notably, they
AB  - cleave at a distance from the intron insertion sites. The td enzyme was shown to cleave 23-26
AB  - nt 5' and the sunY endonuclease 13-15 nt 3' to the intron insertion site to generate 3-nt or
AB  - 2-nt 3'-OH extensions, respectively. The absolute coconversion of exon markers between the
AB  - distant cleavage and insertion sites is consistent with the double-strand-break repair model
AB  - for intron mobility. As a further critical test of the model we have demonstrated that the
AB  - mobility event is independent of DNA sequences that encode the catalytic intron core
AB  - structure. Thus, in derivatives in which the lacZ or kanR coding sequences replace the intron,
AB  - these marker genes are efficiently inserted into intron-minus alleles when the cognate
AB  - endonuclease is provided in trans. The process is therefore endonuclease-dependent, rather
AB  - than dependent on the intron per se. These findings, which imply that the endonucleases rather
AB  - than the introns themselves were the primordial mobile elements, are incorporated into a model
AB  - for the evolution of mobile introns.
ER  -

TY  - JOUR
AU  - Bell-Pedersen, D.
AU  - Quirk, S.M.
AU  - Aubrey, M.
AU  - Belfort, M.
TI  - A site-secific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4.
JO  - Gene
PY  - 1989
SP  - 119
EP  - 126
VL  - 82
AB  - The product of the td intron open reading frame (ORF) of phage T4 is required for
AB  - high-frequency transfer of the intervening sequence from intron-plus (In+) to intron-minus
AB  - (In-) alleles. In vivo studies have demonstrated that the td ORF product targets cleavage of
AB  - td In- DNA, and that cleavage is correlated with intron inheritance [Quirk et al., Cell 56
AB  - (1989) 455-465]. In the present study we show by in vitro synthesis of the td intron ORF
AB  - product, that the protein possesses endonuclease activity and efficiently cleaves
AB  - double-stranded DNA at or near the site of intron integration. In addition, we demonstrate
AB  - that intron insertion is accompanied by co-conversion of the flanking exon sequences.
AB  - Co-conversion of markers within 50 nt surrounding the site of intron insertion occurred at a
AB  - high frequency (80-100%), and decreased at greater distance from the intervening sequence.
AB  - Co-conversion may provide a mechanism for maintaining exon-intron RNA contacts required for
AB  - accurate splicing of the relocated intron. Cleavage of target DNA by an intron endonuclease
AB  - and co-conversion of flanking exon sequences are both features associated with mobile introns
AB  - of eukaryotes, indicating a common mechanism for intron transfer in the eukaryotic kingdoms.
ER  -

TY  - JOUR
AU  - Bell-Pedersen, D.
AU  - Quirk, S.M.
AU  - Bryk, M.
AU  - Belfort, M.
TI  - I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1991
SP  - 7719
EP  - 7723
VL  - 88
AB  - Mobility of the phage T4 td intron depends on activity of an intron-encoded endonuclease
AB  - (I-TevI), which cleaves a homologous intronless (delta-In) target gene. The double-strand
AB  - break initiates a recombination event that leads to intron transfer. We found previously that
AB  - I-TevI cleaves td-delta-IN target DNA 23-26 nucleotides upstream of the intron insertion site.
AB  - DNase I-footprinting experiments and gel-shift assays indicate that I-TevI makes primary
AB  - contacts around the intron insertion site. A synthetic DNA duplex spanning the insertion site
AB  - but lacking the cleavage site was shown to bind I-TevI specifically, and when cloned, to
AB  - direct cleavage into vector sequences. The behavior of the cloned duplex and that of deletion
AB  - and insertion mutants support a primary role for sequences surrounding the insertion site in
AB  - directing I-TevI binding, conferring cleavage ability, and determining cleavage polarity. On
AB  - the other hand, sequences around the cleavage site were shown to influence cleavage efficiency
AB  - and cut-site selection. The role of cleavage-site sequences in determining cleavage distance
AB  - argues against a strict "ruler" mechanism for cleavage by I-TevI. The complex nature of the
AB  - homing site recognized by this unusual type of endonuclease is considered in the context of
AB  - intron spread.
ER  -

TY  - JOUR
AU  - Bellaiche, Y.
AU  - Mogila, V.
AU  - Perrimon, N.
TI  - I-SceI endonuclease, a new tool for studying DNA double-strand break repair mechanisms in Drosophila.
JO  - Genetics
PY  - 1999
SP  - 1037
EP  - 1044
VL  - 152
AB  - As a step toward the development of a homologous recombination system in Drosophila, we have
AB  - developed a methodology to target double-strand breaks (DSBs) to a specific position in the
AB  - Drosophila genome. This method uses the mitochondrial endonuclease I-SceI that recognizes and
AB  - cuts an 18-bp restriction site. We find that >6% of the progeny derived from males that carry
AB  - a marker gene bordered by two I-SceI sites and that express I-SceI in their germ line lose the
AB  - marker gene. Southern blot analysis and sequencing of the regions surrounding the I-SceI sites
AB  - revealed that in the majority of the cases, the introduction of DSBs at the I-SceI sites
AB  - resulted in the complete deletion of the marker gene; the other events were associated with
AB  - partial deletion of the marker gene. We discuss a number of applications for this novel
AB  - technique, in particular its use to study DSB repair mechanisms.
ER  -

TY  - JOUR
AU  - Bellamy, S.R.
AU  - Kovacheva, Y.S.
AU  - Zulkipli, I.H.
AU  - Halford, S.E.
TI  - Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5443
EP  - 5453
VL  - 37
AB  - Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA.
AB  - Binding studies often employ Ca(2+) as a substitute for
AB  - Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI
AB  - endonuclease requires divalent metal ions to bind DNA but, in contrast to
AB  - many systems where Ca(2+) mimics Mg(2+), Ca(2+) causes SfiI to bind DNA
AB  - almost irreversibly. Equilibrium binding by wild-type SfiI cannot be
AB  - conducted with Mg(2+) present as the DNA is cleaved so, to study the
AB  - effect of Mg(2+) on DNA binding, two catalytically-inactive mutants were
AB  - constructed. The mutants bound DNA in the presence of either Ca(2+) or
AB  - Mg(2+) but, unlike wild-type SfiI with Ca(2+), the binding was reversible.
AB  - With both mutants, dissociation was slow with Ca(2+) but was in one case
AB  - much faster with Mg(2+). Hence, Ca(2+) can affect DNA binding differently
AB  - from Mg(2+). Moreover, SfiI is an archetypal system for DNA looping; on
AB  - DNA with two recognition sites, it binds to both sites and loops out the
AB  - intervening DNA. While the dynamics of looping cannot be measured with
AB  - wild-type SfiI and Ca(2+), it becomes accessible with the mutant and
AB  - Mg(2+).
ER  -

TY  - JOUR
AU  - Bellamy, S.R.
AU  - Milsom, S.E.
AU  - Kovacheva, Y.S.
AU  - Sessions, R.B.
AU  - Halford, S.E.
TI  - A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 1169
EP  - 1183
VL  - 373
AB  - While many Type II restriction enzymes are dimers with a single DNA-binding cleft between the
AB  - subunits, SfiI is a tetramer of identical
AB  - subunits. Two of its subunits (a dimeric unit) create one DNA-binding
AB  - cleft, and the other two create a second cleft on the opposite side of the
AB  - protein. The two clefts bind specific DNA cooperatively to give a complex
AB  - of SfiI with two recognition sites. This complex is responsible for
AB  - essentially all of the DNA-cleavage reactions by SfiI: virtually none is
AB  - due to the complex with one site. The communication between the
AB  - DNA-binding clefts was examined by disrupting one of the very few polar
AB  - interactions in the otherwise hydrophobic interface between the dimeric
AB  - units: a tyrosine hydroxyl was removed by mutation to phenylalanine. The
AB  - mutant protein remained tetrameric in solution and could bind two DNA
AB  - sites. But instead of being activated by binding two sites, like wild-type
AB  - SfiI, it showed maximal activity when bound to a single site and had a
AB  - lower activity when bound to two sites. This interaction across the dimer
AB  - interface thus enforces in wild-type SfiI a cooperative transition between
AB  - inactive and active states in both dimers, but without this interaction as
AB  - in the mutant protein, a single dimer can undergo the transition to give a
AB  - stable intermediate with one inactive dimer and one active dimer.
ER  -

TY  - JOUR
AU  - Bellamy, S.R.
AU  - Mina, P.
AU  - Retter, S.E.
AU  - Halford, S.E.
TI  - Fidelity of DNA Sequence Recognition by the SfiI Restriction Endonuclease Is Determined by Communications between Its Two DNA-Binding Sites.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 557
EP  - 563
VL  - 384
AB  - The SfiI restriction endonuclease is a tetramer in which two subunits form a dimeric unit that
AB  - contains one DNA binding cleft and the other two
AB  - subunits contain a second cleft on the opposite side of the protein. Full
AB  - activity requires both clefts to be filled with its recognition sequence:
AB  - SfiI has low activity when bound to one site. The ability of SfiI to
AB  - cleave non-cognate sites, one base pair different from the true site, was
AB  - initially tested on substrates that lacked specific sites but which
AB  - contained either one or multiple non-cognate sites. No cleavage of the DNA
AB  - with one non-cognate site was detected, while a small fraction of the DNA
AB  - with multiple sites was nicked. The alternative sequences were, however,
AB  - cleaved in both strands, albeit at low levels, when the DNA also carried
AB  - either a recognition site for SfiI or the termini generated by SfiI.
AB  - Further tests employed a mutant of SfiI, altered at the dimer interface,
AB  - which was known to be more active than wild-type SfiI when bound to a
AB  - single site. This mutant similarly failed to cleave DNA with one
AB  - non-cognate site, but cleaved the substrates with multiple non-cognate
AB  - sites more readily than did the native enzyme. To cleave additional sites,
AB  - SfiI thus needs to interact concurrently with either two non-cognate sites
AB  - or one non-cognate and one cognate site (or the termini thereof), yet this
AB  - arrangement is still restrained from cleaving the alternative site unless
AB  - the communication pathway between the two DNA-binding clefts is disrupted.
ER  -

TY  - JOUR
AU  - Bellamy, S.R.W.
AU  - Milsom, S.E.
AU  - Scott, D.J.
AU  - Daniels, L.E.
AU  - Wilson, G.G.
AU  - Halford, S.E.
TI  - Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 641
EP  - 653
VL  - 348
AB  - BbvCI cleaves an asymmetric DNA sequence, 5'-CC^TCAGC-3'/5'-GC^TGAGG-3', as indicated.
AB  - While many Type II
AB  - restriction enzymes consist of identical subunits, BbvCI has two
AB  - different subunits: R-1, which acts at GC^TGAGG; and R-2,
AB  - which acts at CC^TCAGC. Some mutants of BbvCI with defects
AB  - in one subunit either R1-R2+ or R1+R2-, cleave only one strand, that
AB  - attacked by the native subunit. In analytical ultracentrifugation at
AB  - various concentrations of protein, wild-type and mutant BbvCI enzymes
AB  - aggregated extensively, but are R1R2 heterodimers at the concentrations
AB  - used in DNA cleavage reactions. On a plasmid with one recognition site,
AB  - wild-type BbvCI cleaved both strands before dissociating from the DNA,
AB  - while the R1-R2+ and R1+R2- mutants acted almost exclusively on their
AB  - specified strands, albeit at relatively slow rates. During the
AB  - wild-type reaction, the DNA is cleaved initially in one strand, mainly
AB  - that targeted by the R, subunit. The other strand is then cleaved
AB  - slowly by R-2 before the enzyme dissociates from the DNA. Hence, the
AB  - nicked form accumulates as a transient intermediate. This behaviour
AB  - differs from that of many other restriction enzymes, which cut both
AB  - strands at equal rates. However, the activities of the R-1(+) and
AB  - R-2(+) subunits in the wild-type enzyme can differ from their
AB  - activities in the R1+R2- and R1-R2+ mutants. Each active site in BbvCI
AB  - therefore influences the other.
ER  -

TY  - JOUR
AU  - Belland, R.J.
AU  - Morrison, S.G.
AU  - Hogan, D.
TI  - A phase-variable type III restriction-modification system in Neisseria gonorrhoeae.
JO  - Abs. Tenth Int. Conf. Pathogenegic Neisseria
PY  - 1996
SP  - 360
EP  - 361
VL  - 0
AB  - Neisseria gonorrhoeae possesses a number of type II restriction/modification systems but
AB  - characteristically expresses fewer restriction enzyme activities than corresponding
AB  - methyltransferases.  Methyltransferase specificities have been identified for S.NgoI
AB  - (PuGCGCPy), S.NgoII (GGCC), S.NgoIII (CCGCGG), S.NgoIV (GCCGGC), S.NgoV (GGNNCC), S.NgoVI
AB  - (GATC), S.NgoVII (GC[C/G]GC), S.NgoVIII (TCACC) of purified methyltransferase which recognizes
AB  - the sequence GTAN5CTC (S.NgoIX).  Restriction enzymes have been detected which correspond to
AB  - the sequences for NgoI, II, III, IV, and IX in various strains.  We have identified the genes
AB  - encoding a type III restriction modification system present in all strains of N. gonorrhoeae
AB  - tested.  Sequence analysis of the ngoX locus from strain MS11 indicate the predicted protein
AB  - for the restriction enzyme (NgoX.R) is 59% identical to the restriction enzyme of the P1
AB  - system.  The modification enzyme (NgoX.M) is predicted to be 38% identical to the modification
AB  - enzyme of the P1 system. The postulated 5' region of the ngoX.M gene is unusual in that the
AB  - predicted start codon is followed by a series of direct pentameric repeats reminiscent of the
AB  - signal-peptide encoding region of neisserial opa genes, responsible for regulating expression
AB  - of opa genes by "phase variation".  The ngoX.M gene of strain MS11 contains eight repeat
AB  - elements (an out-of-frame configuration) while strain FA228 contains twelve repeat elements
AB  - (an in-frame configuration).  Mutations constructed in Escherichia coli and returned to the
AB  - gonococcal chromosome by allelic replacement indicate that the ngoX.M gene is expressed in
AB  - strain FA228 but not in strain MS11 but the gene is phase-variable from both the on and off
AB  - configurations.  Phase variation cannot be detected in the viable cell population in wild-type
AB  - strains.  Purified heterodimeric NgoX enzyme is active against DNA purified from strains MS11
AB  - mk (no expression of NgoX.M) and FA228 ngoX.M::lacZ but not strain FA228 (expresses NgoX.M).
ER  -

TY  - JOUR
AU  - Bellemare, G.
AU  - Potvin, C.
TI  - Classification of type-II restriction endonucleases and cloning of non-identical cohesive-end fragments without self-polymerization using nonpalindromic oligodeoxyribonucleotide adapters.
JO  - Gene
PY  - 1991
SP  - 67
EP  - 74
VL  - 101
AB  - Enzymatic partial filling-in of recessed 3'-end sequences, left after digestion
AB  - of DNA by the restriction endonucleases (ENases) Sau3AI and SalI, with the
AB  - Klenow fragment of E. coli DNA polymerase I allows the forced ligation of the
AB  - resulting fragments; this technology is already used for subcloning and for
AB  - genomic bank construction.  To simplify and generalize its utilization,
AB  - class-II ENases have been arranged into 16 different families according to the
AB  - composition of the 5'-protruding sequences present after cleavage.  Moreover,
AB  - this system was extended to allow the joining of noncompatible ends by the use
AB  - of nonpalindromic complementary oligodeoxyribonucleotides (NPCOs) containing
AB  - two nucleotides protruding at each 5' end.  The use of these synthetic adapters
AB  - maintains all the advantages of the initial gap-filling cloning technique: only
AB  - one insert can be cloned per vector molecule and no self-ligation or
AB  - -polymerization can occur with any of the DNA molecules involved.  Only 22 such
AB  - oligodeoxyribonucleotides are needed to generate the 60 NPCO pairs necessary to
AB  - ligate to each other any member of twelve ENase families when the regeneration
AB  - of ENase recognition sites is not required.
ER  -

TY  - JOUR
AU  - Beller, H.R.
AU  - Chain, P.S.
AU  - Letain, T.E.
AU  - Chakicherla, A.
AU  - Larimer, F.W.
AU  - Richardson, P.M.
AU  - Coleman, M.A.
AU  - Wood, A.P.
AU  - Kelly, D.P.
TI  - The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans.
JO  - J. Bacteriol.
PY  - 2006
SP  - 1473
EP  - 1488
VL  - 188
AB  - The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become
AB  - available for an obligately chemolithoautotrophic,
AB  - sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the
AB  - 2,909,809-bp genome will facilitate our molecular and biochemical
AB  - understanding of the unusual metabolic repertoire of this bacterium,
AB  - including its ability to couple denitrification to sulfur-compound
AB  - oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II)
AB  - and U(IV), and to oxidize mineral electron donors. Notable genomic
AB  - features include (i) genes encoding c-type cytochromes totaling 1 to 2
AB  - percent of the genome, which is a proportion greater than for almost all
AB  - bacterial and archaeal species sequenced to date, (ii) genes encoding two
AB  - [NiFe]hydrogenases, which is particularly significant because no
AB  - information on hydrogenases has previously been reported for T.
AB  - denitrificans and hydrogen oxidation appears to be critical for anaerobic
AB  - U(IV) oxidation by this species, (iii) a diverse complement of more than
AB  - 50 genes associated with sulfur-compound oxidation (including sox genes,
AB  - dsr genes, and genes associated with the AMP-dependent oxidation of
AB  - sulfite to sulfate), some of which occur in multiple (up to eight) copies,
AB  - (iv) a relatively large number of genes associated with inorganic ion
AB  - transport and heavy metal resistance, and (v) a paucity of genes encoding
AB  - organic-compound transporters, commensurate with obligate
AB  - chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans
AB  - will enable elucidation of the mechanisms of aerobic and anaerobic
AB  - sulfur-compound oxidation by beta-proteobacteria and will help reveal the
AB  - molecular basis of this organism's role in major biogeochemical cycles
AB  - (i.e., those involving sulfur, nitrogen, and carbon) and groundwater
AB  - restoration.
ER  -

TY  - JOUR
AU  - Bellgard, M.I.
AU  - Wanchanthuek, P.
AU  - La, T.
AU  - Ryan, K.
AU  - Moolhuijzen, P.
AU  - Albertyn, Z.
AU  - Shaban, B.
AU  - Motro, Y.
AU  - Dunn, D.S.
AU  - Schibeci, D.
AU  - Hunter, A.
AU  - Barrero, R.
AU  - Phillips, N.D.
AU  - Hampson, D.J.
TI  - Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.
JO  - PLoS ONE
PY  - 2009
SP  - E4641
EP  - E4641
VL  - 4
AB  - Brachyspira hyodysenteriae is an anaerobic intestinal spirochete that
AB  - colonizes the large intestine of pigs and causes swine dysentery, a
AB  - disease of significant economic importance. The genome sequence of B.
AB  - hyodysenteriae strain WA1 was determined, making it the first
AB  - representative of the genus Brachyspira to be sequenced, and the
AB  - seventeenth spirochete genome to be reported. The genome consisted of a
AB  - circular 3,000,694 base pair (bp) chromosome, and a 35,940 bp circular
AB  - plasmid that has not previously been described. The spirochete had 2,122
AB  - protein-coding sequences. Of the predicted proteins, more had similarities
AB  - to proteins of the enteric Escherichia coli and Clostridium species than
AB  - they did to proteins of other spirochetes. Many of these genes were
AB  - associated with transport and metabolism, and they may have been gradually
AB  - acquired through horizontal gene transfer in the environment of the large
AB  - intestine. A reconstruction of central metabolic pathways identified a
AB  - complete set of coding sequences for glycolysis, gluconeogenesis, a
AB  - non-oxidative pentose phosphate pathway, nucleotide metabolism,
AB  - lipooligosaccharide biosynthesis, and a respiratory electron transport
AB  - chain. A notable finding was the presence on the plasmid of the genes
AB  - involved in rhamnose biosynthesis. Potential virulence genes included
AB  - those for 15 proteases and six hemolysins. Other adaptations to an enteric
AB  - lifestyle included the presence of large numbers of genes associated with
AB  - chemotaxis and motility. B. hyodysenteriae has diverged from other
AB  - spirochetes in the process of accommodating to its habitat in the porcine
AB  - large intestine.
ER  -

TY  - JOUR
AU  - Bello-Akinosho, M.
AU  - Adeleke, R.
AU  - Swanevelder, D.
AU  - Thantsha, M.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain 10-1B, a Polycyclic Aromatic Hydrocarbon Degrader in Contaminated Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00325
EP  - e00315
VL  - 3
AB  - Pseudomonas sp. strain 10-1B was isolated from artificially polluted soil after selective
AB  - enrichment. Its draft genome consists of several predicted genes that
AB  - are involved in the hydroxylation of the aromatic ring, which is the
AB  - rate-limiting step in the biodegradation of polycyclic aromatic hydrocarbons.
ER  -

TY  - JOUR
AU  - Bellon, B.
TI  - Construction of restriction maps.
JO  - Comput. Appl. Biosci.
PY  - 1988
SP  - 111
EP  - 116
VL  - 4
AB  - A computer program is described, which constructs maps of restriction
AB  - endonuclease cleavage sites in linear or circular DNA molecules, given the
AB  - fragment lengths in single and double digestions with two enzymes.  The
AB  - algorithm is based upon a partition method and a very simple rule to chain
AB  - fragments.  The program is written in Prolog II.
ER  -

TY  - JOUR
AU  - Bellstein, F.
AU  - Dreiseikelmann, B.
TI  - Temperate bacteriophage Phi O18P from an Aeromonas media isolate: Characterization and complete genome sequence.
JO  - Virology
PY  - 2008
SP  - 25
EP  - 29
VL  - 373
AB  - group of 74 Aeromonas isolates from surface water of three ponds in Bielefeld, Germany was
AB  - screened for prophage induction after UV
AB  - irradiation. The phage Phi O18P was induced from the Aeromonas media
AB  - isolate O18. Phi O18P belongs to the Myoviridae phage family. The
AB  - complete nucleotide sequence of the double stranded DNA genome
AB  - ofbacteriophage Phi O18P consists of 33,985 bp. The genome has 5'
AB  - protruding cohesive ends of 16 bases. On the Phi O18P genome 46 open
AB  - reading frames (orfs) were identified which are organized in the
AB  - modules integration and regulation, replication, head, packaging, tail
AB  - and lysis. Additionally the phage DNA includes a methylase gene.
AB  - Comparison of the genome architecture with those of other
AB  - bacteriophages revealed significant similarities to the P2 phage family
AB  - and especially to the prophages of Aeromonas salmonicida and the Vibrio
AB  - cholerae phage K139.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Delver, E.P.
TI  - A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 785
EP  - 787
VL  - 23
AB  - Antirestriction proteins Ard encoded by some self-transmissible plasmids specifically inhibit
AB  - restriction by members of all three families of type I restriction-modification (R-M) systems
AB  - in E. coli. Recently, we have identified the amino acid region, 'antirestriction' domain,
AB  - that is conserved within different plasmid and phage T7-encoded antirestriction proteins and
AB  - may be involved in interaction with the type I R-M systems. In this paper we demonstrate that
AB  - this amino acid sequence shares considerable similarity with a well-known conserved sequence
AB  - (the Argos repeat) found in the DNA sequence specificity (S) polypeptides of type I systems.
AB  - We suggest that the presence of these similar motifs in restriction and antirestriction
AB  - proteins may give a structural basis for their interaction and that the antirestriction action
AB  - of Ard proteins may be a result of the competition between the 'antirestriction' domains of
AB  - Ard proteins and the similar conserved domains of the S subunits that are believed to play a
AB  - role in the subunit assembly of type I R-M systems.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Delver, E.P.
AU  - Agafonova, O.V.
AU  - Belogurova, N.G.
AU  - Lee, L.Y.
AU  - Kado, C.I.
TI  - Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa has a high similarity to the "Protein Transport" domain of TraC1 primase of promiscuous plasmid RP4.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 969
EP  - 977
VL  - 296
AB  - The IncW plasmid pSa contains the gene ard encoding an antirestriction function that is
AB  - specific for type I restriction and modification systems. The nucleotide
AB  - sequence of ard was determined and an appropriate polypeptide of about 33 kDa was identified
AB  - in Escherichia coli T7 expression system. Analysis of deduced amino acid
AB  - sequence of Ard encoded by pSa revealed that this protein has no significant similarities with
AB  - the known Ard proteins (ArdA and ArdB types) except the "antirestriction"
AB  - motif (14 amino acid residues in length) conserved for all known Ard proteins. This finding
AB  - suggests that pSa Ard may be classified as a new type of Ard proteins which we
AB  - designated ArdC. The remarkable feature of ArdC is that it has a high degree of similarity
AB  - (about 38 % identity) to the N-terminal region of RP4 TraC1 primase which
AB  - includes about 300 amino acid residues and seems to be essential for binding to the
AB  - single-stranded DNA and TraC1 protein transport to the recipient cells during the
AB  - conjugal transfer of plasmid DNA. ArdC also binds to single-stranded DNA. In addition, this
AB  - protein is able in vitro to protect the single-stranded but not double-stranded
AB  - plasmid DNA against the activity of type II restriction endonuclease HhaI that cleaves both
AB  - single and double-stranded DNA. We suggest that like TraC1, ArdC would be
AB  - transported as a result of their interaction with the single-stranded DNA of transferred
AB  - plasmid strand during conjugative passage through the cell envelope to the recipient
AB  - bacterium. Such properties of ArdC protein might be useful to protect immediately the incoming
AB  - single-stranded DNA from the host endonucleases.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Delver, E.P.
AU  - Rodzevich, O.V.
TI  - Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences.
JO  - J. Bacteriol.
PY  - 1993
SP  - 4843
EP  - 4850
VL  - 175
AB  - The Inc plasmid pKM101 (a derivative of R46) encodes the antirestriction protein ArdB
AB  - (alleviation of restriction of DNA) in addition to another antirestriction protein, ArdA,
AB  - described previously. The relevant gene, ardB was located in the leading region of pKM101,
AB  - about 7 kb from oriT. The nucleotide sequence of ardB was determined, and an appropriate
AB  - polypeptide was identified in maxicells of Escherichia coli. Like ArdA, ArdB efficiently
AB  - inhibits restriction by members of the three known families of type I systems of E. coli and
AB  - only slightly affects the type II enzymes, EcoRI. However, in contrast to ArdA, ArdB is
AB  - ineffective against the modification activity of the type I (EcoK) system. Comparison of
AB  - deduced amino acid sequences of ArdA and ArdB revealed only one small region of similarity
AB  - (nine residues), suggesting that this region may be somehow involved in the interaction with
AB  - the type I restriction systems. We also found that the expression of both ardA and ardB genes
AB  - is controlled jointly by two pKM101-encoded proteins, ArdK and ArdR, with molecular weights of
AB  - about 15,000 and 20,000 respectively. The finding that the sequences immediately upstream of
AB  - ardA and ardB share about 94% identity over 218 bp suggests that their expression may be
AB  - controlled by ArdK and ArdR at the transcriptional level. Deletion studies and promoter probe
AB  - analysis of these sequences revealed the regions responsible for the action of ArdK and ArdR
AB  - as regulatory proteins. We propose that both types of antirestriction proteins may play a
AB  - pivotal role in overcoming the host restriction barrier by self-transmissible broad-host-range
AB  - plasmids. It seems likely that the ardKR-dependent regulatory system serves in this case as a
AB  - genetic switch that controls the expression of plasmid-encoded antirestriction functions
AB  - during mating.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Delver, E.P.
AU  - Rodzevich, O.V.
TI  - IncN plasmid pKM101 and IncI1 Plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions.
JO  - J. Bacteriol.
PY  - 1992
SP  - 5079
EP  - 5085
VL  - 174
AB  - The IncN plasmid pKM101 (a derivative of R46), like the the IncI1 plasmid ColIb-P9, carries a
AB  - gene (ardA, for alleviation of restriction of DNA) encoding an antirestriction function, ardA
AB  - was located about 4 kb from the origin of transfer, in the region transferred early during
AB  - bacterial conjugation. The nucleotide sequence of ardA was determined, and an appropriate
AB  - polypeptide with the predicted molecular weight of about 19,500 was identified in maxicells of
AB  - Escherichia coli. Comparison of the deduced amino acid sequences of the antirestriction
AB  - proteins of the unrelated plasmids pKM101 and ColIb (ArdA and Ard, respectively) revealed that
AB  - these proteins have about 60% identify. Like ColIb ard, pMK101 ArdA specifically inhibits both
AB  - the restriction and modification activities of five type I systems of E. coli tested and does
AB  - not influence type III (EcoPI) restriction or the 5-methylcytosine-specific restriction
AB  - systems McrA and McrBC. However, in contrast to ColIb ard, pKM101 ArdA is effective against
AB  - the type II enzyme EcoRI. The Ard proteins are believed to overcome the host restriction
AB  - barrier during bacterial conjugation. We have also identified two other genes of pKM101, ardR
AB  - and ardK, which seem to control ardA activity and ardA-medicated lethality, respectively. Our
AB  - findings suggest that ardR may serve as a genetic switch that determines whether the ard-A
AB  - encoded antirestriction function is induced during mating.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Efimova, E.P.
AU  - Delver, E.P.
AU  - Zavilgelsky, G.B.
TI  - Alleviation of type I restriction in Escherichia coli: Effect of 2-amino-purine and 5-bromouracil.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1987
SP  - 34
EP  - 40
VL  - 12
AB  - 2-aminopurine and 5-bromouracil, strong mutagens of the base analog type, were found to induce
AB  - efficiently the alleviation of type I restriction in Escherichia coli.  2-AP induced
AB  - restriction alleviation occurs in recA, lexA and mut- mutants, but no additional relief of
AB  - restriction is registered in dam- bacteria in the presence of sublethal 2-AP concentrations.
AB  - 2-AP specifically alleviates type I restriction in Escherichia coli (EcoA, EcoB, EcoD, and
AB  - EcoK) and does not affect restriction system of types II (EcoRI) and III (EcoPI).  We suggest
AB  - that 2-AP-induced mismatches and other replication errors may be signals inducing restriction
AB  - alleviation in Escherichia coli.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Efimova, E.P.
AU  - Delver, E.P.
AU  - Zavilgelsky, G.B.
TI  - Alleviation of I type restriction in E. coli: Effect of a dam mutation.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1987
SP  - 10
EP  - 16
VL  - 9
AB  - The host-controlled EcoK-restriction of unmodified phages lambda.0 and T7 ocr, is 100-fold
AB  - alleviated in dam- mutants of E. coli.  In addition the EcoK modification activity is
AB  - considerably decreased in dam- strains.  Type I and III restriction (EcoB, EcoD, EcoK and
AB  - EcoPI) were relieved in dam- mutants, but no alleviation of EcoRI restriction occurred in dam-
AB  - strains.  We interpret the alleviation of the type I restriction in dam- mutants as a
AB  - consequence of induction of the function, which interferes with the type I restriction
AB  - systems.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Yussifov, T.N.
AU  - Kotova, V.U.
AU  - Zavilgelsky, G.B.
TI  - The novel gene(s) ARD of plasmid pKM101: alleviation of EcoK restriction.
JO  - Mol. Gen. Genet.
PY  - 1985
SP  - 509
EP  - 513
VL  - 198
AB  - The host-controlled K restriction of unmodified phage lambda was 10-100 fold
AB  - alleviated in the wild-type strain E.coli K12, carrying plasmid pKM101 of
AB  - incompability group N.  pKM101-mediated release of K restriction was also
AB  - observed in lexA-, recA-, and recB- strains of E.coli K12.  By restriction
AB  - mapping Tn5 insertions in pKM101, which reduced pKM101-mediated alleviation of
AB  - restriction, were shown to be located within the BglIIB fragment approximately
AB  - 11kb anticlockwise from the RI site of pKM101.  We have termed the gene(s)
AB  - promoting the alleviation of K restriction of phage lambda ard (alleviation of
AB  - restriction of DNA).  It was shown (1) that ard function affected only the EcoK
AB  - restriction system and not the EcoB, EcoRI, EcoRIII, or EcoPI systems, (2) ard
AB  - gene(s) did not mediate EcoK type modification of lambda DNA and did not
AB  - increase the modification activity of the EcoK system in a way similar to that
AB  - observed with gene ral of bacteriophage lambda.
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Zavilgelskii, G.B.
TI  - Effect of plasmid pKM101 on the K-specific restriction-modification of bacteriophage lambda DNA.
JO  - Dokl. Akad. Nauk.
PY  - 1983
SP  - 738
EP  - 741
VL  - 269
ER  -

TY  - JOUR
AU  - Belogurov, A.A.
AU  - Zavilgelsky, G.B.
TI  - The repair of the interstrand cross links in DNA: Role of restriction system K.
JO  - Mol. Biol. (Mosk)
PY  - 1979
SP  - 160
EP  - 168
VL  - 13
AB  - The interstrand cross links formed in the DNA after psoralen plus light treatment of bacteria
AB  - E. coli K12 and bacteriophage lambda are repaired by the restriction and modification system
AB  - K.  Strain E. coli C, which does not have the restriction and modification system is 2 times
AB  - more sensitive to psoralen plus light treatment, than the wild type E. coli K12.  But these
AB  - strains are equally sensitive to inactivation by UV-light (254 nm).  By studying the
AB  - sedimentation of bacterial DNA in alkaline sucrose it was found that cells of E. coli C are
AB  - deficieint in filling of gaps, appearing in parental DNA after enzymatic excision of the arms
AB  - of cross links.  In experiments with bacteriophage lambda (W-reactivation,
AB  - prophage-reactivation), treated by psoralen plus light, it was shown that E. coli C and
AB  - mutants of E. coli K12 rR-mR+/- are deficient in non-recombination lexA-dependent repair of
AB  - cross links.  The function of restriction and recognition of restriction and modification
AB  - system are essential for repair of cross links.  It is suggested that the restriction and
AB  - modification system K acts either as a regulatory protein or as a protector of single-stranded
AB  - regions of DNA against nuclease attack.
ER  -

TY  - JOUR
AU  - Belova, T.S.
AU  - Surikov, N.N.
AU  - Prozorov, A.A.
TI  - Transformation and transduction of Bacillus subtilis strains possessing the BsuR system of restriction-modification by nonmodified and modified plasmid pUB110 DNA.
JO  - Genetika
PY  - 1981
SP  - 794
EP  - 800
VL  - 17
AB  - Plasmid pUB110 DNA is restricted and modified during transformation of Bacillus subtilis cells
AB  - possessing the BsuR system of restriction-modification.  Restriction has comparatively little
AB  - influence on the frequency of plasmid transformation only reducing it 20 times.  The frequency
AB  - of transduction of nonmodified plasmid DNA into modifying recipient cells, using phage Ar9 is
AB  - also reduced a little.  The frequency of transduction of chromosomal markers is much more
AB  - lowered under the same experimental conditions.
ER  -

TY  - JOUR
AU  - Beltramo, C.
AU  - Oraby, M.
AU  - Bourel, G.
AU  - Garmyn, D.
AU  - Guzzo, J.
TI  - A new vector, pGID052, for genetic transfer in Oenococcus oeni.
JO  - FEMS Microbiol. Lett.
PY  - 2004
SP  - 53
EP  - 60
VL  - 236
AB  - Despite the large number of techniques available for the transformation of
AB  - bacteria, several species are still resistant to the introduction of
AB  - foreign DNA. Oenococcus oeni are among the organisms that are particularly
AB  - refractory to transformation. However, conjugal experiments from
AB  - Lactococcus lactis to O. oeni with a new plasmid, pGID052, were performed
AB  - via mobilization with success. This plasmid, a derivative of pORI19,
AB  - encompasses: (i) the oriT of pIP501, which permitted the transfer to O.
AB  - oeni, (ii) the replication genes of a native Leuconostoc citreum plasmid.
AB  - Frequencies of 10(-7) conjugants per recipient were found. The transfer
AB  - did not affect the structure of this low-copy-number plasmid. Moreover,
AB  - pGID052 seems segregationally stable and could be used in the future as an
AB  - expression vector.
ER  -

TY  - JOUR
AU  - Ben Hania, W.
AU  - Fadhlaoui, K.
AU  - Brochier-Armanet, C.
AU  - Persillon, C.
AU  - Postec, A.
AU  - Hamdi, M.
AU  - Dolla, A.
AU  - Ollivier, B.
AU  - Fardeau, M.L.
AU  - Le Mer, J.
AU  - Erauso, G.
TI  - Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in  Tunisia.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 12
EP  - 12
VL  - 10
AB  - Mesotoga strain PhosAc3 was the first mesophilic cultivated member of the order Thermotogales.
AB  - This genus currently contain two described species, M. prima and
AB  - M. infera. Strain PhosAc3, isolated from a Tunisian digestor treating
AB  - phosphogypsum, is phylogenetically closely related to M. prima strain
AB  - MesG1.Ag.4.2(T). Strain PhosAc3 has a genome of 3.1 Mb with a G+C content of
AB  - 45.2%. It contains 3,051 protein-coding genes of which 74.6% have their best
AB  - reciprocal BLAST hit in the genome of the type species, strain MesG1.Ag.4.2(T).
AB  - For this reason we propose to assign strain PhosAc3 as a novel ecotype of the
AB  - Mesotoga prima species. However, in contrast with the M. prima type strain, (i)
AB  - it does not ferment sugars but uses them only in the presence of elemental sulfur
AB  - as terminal electron acceptor, (ii) it produces only acetate and CO2 from sugars,
AB  - whereas strain MesG1.Ag.4.2(T) produces acetate, butyrate, isobutyrate,
AB  - isovalerate, 2-methyl-butyrate and (iii) sulfides are also end products of the
AB  - elemental sulfur reduction in theses growth conditions.
ER  -

TY  - JOUR
AU  - Ben Hania, W.
AU  - Joseph, M.
AU  - Schumann, P.
AU  - Bunk, B.
AU  - Fiebig, A.
AU  - Sproer, C.
AU  - Klenk, H.P.
AU  - Fardeau, M.L.
AU  - Spring, S.
TI  - Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 7
EP  - 7
VL  - 10
AB  - During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat
AB  - of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central
AB  - Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor
AB  - was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity
AB  - value of 90% with the novel strain and thus was only distantly related. A
AB  - comprehensive polyphasic study including determination of the complete genome
AB  - sequence was initiated to characterize the novel isolate. Cells of strain
AB  - L21-RPul-D2(T) had a size of 0.2 - 0.25 x 8-9 mum, were helical, motile, stained
AB  - Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions
AB  - for growth were 35 degrees C, a salinity of 50 g/l NaCl and a pH around 7.0.
AB  - Preferred substrates for growth were carbohydrates and a few carboxylic acids.
AB  - The novel strain had an obligate fermentative metabolism and produced ethanol,
AB  - acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain
AB  - L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major
AB  - cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar
AB  - lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified
AB  - phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained
AB  - L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The
AB  - complete genome sequence was determined and annotated. The genome comprised one
AB  - circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding
AB  - genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C
AB  - content was determined from the genome sequence as 51.9 mol%. There were no
AB  - predicted genes encoding cytochromes or enzymes responsible for the biosynthesis
AB  - of respiratory lipoquinones. Based on significant differences to the uncultured
AB  - type species of the genus Spirochaeta, S. plicatilis, as well as to any other
AB  - phylogenetically related cultured species it is suggested to place strain
AB  - L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for
AB  - which the name Salinispira pacifica gen. nov., sp. nov. is proposed.
ER  -

TY  - JOUR
AU  - Ben Zakour, N.L.
AU  - Bannoehr, J.
AU  - van den Broek, A.H.
AU  - Thoday, K.L.
AU  - Fitzgerald, J.R.
TI  - Complete genome sequence of the canine pathogen Staphylococcus pseudintermedius.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2363
EP  - 2364
VL  - 193
AB  - We report the first whole genome sequence for a clinical isolate of Staphylococcus
AB  - pseudintermedius (ED99), the major pathogen responsible for canine bacterial pyoderma. S.
AB  - pseudintermedius contains numerous mobile genetic elements, and encodes an array of putative
AB  - virulence factors including superantigenic, cytolytic and exfoliative toxins, and cell-wall
AB  - associated surface proteins.
ER  -

TY  - JOUR
AU  - Ben-Hattar, J.
AU  - Jiricny, J.
TI  - Effect of cytosine methylation on the cleavage of oligonucleotide duplexes with restriction endonucleases HpaII and MspI.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4160
EP  - 4160
VL  - 16
AB  - the pattern of eucaryotic DNA methylation is commonly determined by restriction
AB  - analysis with methylation-sensitive enzymes.  Due to the likely biological
AB  - significance of hemimethylated CpG dinucleotides, we investigated the MspI and
AB  - HpaII hydrolysis of synthetic 29-mer oligos (Fig. 1a), unmethylated,
AB  - hemimethylated or fully-methylated at the internal C residue of their
AB  - recognition site CCGG.  As shown in Fig. 1b, MspI cleaved all the four
AB  - substrates, irrespective of their state of methylation.  HpaII failed to digest
AB  - the symmetrically-methylated duplex (mC29/mC33), while the unmethylated duplex
AB  - (C29/C33) was completely and efficiently digested.  Surprisingly, neither
AB  - cleavage nor nicking of the unmethylated strand were observed with the
AB  - hemimethylated substrates.  These results demonstrate that the use of HpaII in
AB  - the search for regions of active, unmethylated chromatin would fail to identify
AB  - hemimethylated CpG sites, recently shown to be involved in the process of
AB  - transcriptional gene activation.
ER  -

TY  - JOUR
AU  - Benachour, A.
AU  - Frere, J.
AU  - Novel, G.
TI  - pUCL287 plasmid from Tetragenococcus halophila (Pediococcus halophilus) ATCC 33315 represents a new theta-type replicon family of lactic acid bacteria.
JO  - FEMS Microbiol. Lett.
PY  - 1995
SP  - 167
EP  - 175
VL  - 128
AB  - A cryptic plasmid, pUCL287, was isolated from Tetragenococcus halophila
AB  - (Pediococcus halophilus) ATCC 33315. It had a theta-type mechanism of
AB  - replication in its natural host. Its minimal replicon, Rep287, was
AB  - isolated on a 1.6-kb EcoRI fragment. The Rep287 host range included the
AB  - genera Pediococcus, Enterococcus, Lactobacillus and Leuconostoc but not
AB  - genus Lactococcus. Plasmids hybridizing to pUCL287 are rare among lactic
AB  - acid bacteria. As assessed by hybridization, Rep287 is dissimilar to pAM
AB  - beta 1, pIP501 and pUCL22, representatives of the most common theta-type
AB  - replicon groups in Gram-positive bacteria. Therefore, pUCL287 appears to
AB  - represent a new theta-type replicon family from lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Benahmed, F.H.
AU  - Gopinath, G.R.
AU  - Harbottle, H.
AU  - Cotta, M.A.
AU  - Luo, Y.
AU  - Henderson, C.
AU  - Teri, P.
AU  - Soppet, D.
AU  - Rasmussen, M.
AU  - Whitehead, T.R.
AU  - Davidson, M.
TI  - Draft Genome Sequences of Streptococcus bovis Strains ATCC 33317 and JB1.
JO  - Genome Announcements
PY  - 2014
SP  - e01012
EP  - e01014
VL  - 2
AB  - We report the draft genome sequences of Streptococcus bovis strain ATCC 33317 (CVM42251)
AB  - isolated from cow dung and strain JB1 (CVM42252) isolated from a cow
AB  - rumen in 1977. The strains were sequenced using the Genome Sequencer FLX 454
AB  - system. The genome sizes are approximately 2 Mb and 2.2 Mb, respectively.
ER  -

TY  - JOUR
AU  - Benahmed, F.H.
AU  - Gopinath, G.R.
AU  - Wang, H.
AU  - Jean-Gilles, B.J.
AU  - Grim, C.
AU  - Cheng, C.M.
AU  - McClelland, M.
AU  - Ayers, S.
AU  - Abbott, J.
AU  - Desai, P.
AU  - Frye, J.G.
AU  - Weinstock, G.
AU  - Hammack, T.S.
AU  - Hanes, D.E.
AU  - Rasmussen, M.A.
AU  - Davidson, M.K.
TI  - Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Cubana Strains Isolated from Agricultural Sources.
JO  - Genome Announcements
PY  - 2014
SP  - e01184
EP  - e01113
VL  - 2
AB  - We report the draft genomes of Salmonella enterica subsp. enterica serovar Cubana strain
AB  - CVM42234, isolated from chick feed in 2012, and S. Cubana strain 76814,
AB  - isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 bp,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Benamar, S.
AU  - Cassir, N.
AU  - Caputo, A.
AU  - Cadoret, F.
AU  - La Scola, B.
TI  - Complete Genome Sequence of Clostridium septicum Strain CSUR P1044, Isolated from the Human Gut Microbiota.
JO  - Genome Announcements
PY  - 2016
SP  - e00922
EP  - e00916
VL  - 4
AB  - Clostridium septicum is one of the first pathogenic anaerobes to be identified. Here, we
AB  - announce the genome draft sequence of C. septicum strain CSUR P1044
AB  - isolated from the gut of a healthy adult. Its chromosome genome consists of 3.2
AB  - Mbp with a plasmid of 32 Kbp. C. septicum strain CSUR P1044 has a G+C content of
AB  - 27.5%, and is composed of 3,125 protein-coding genes together with 103 RNA genes,
AB  - including 22 rRNA genes.
ER  -

TY  - JOUR
AU  - Benamar, S.
AU  - Cassir, N.
AU  - La Scola, B.
TI  - Genome Sequence of a Clostridium neonatale Strain Isolated in a Canadian Neonatal Intensive Care Unit.
JO  - Genome Announcements
PY  - 2016
SP  - e01431
EP  - e01415
VL  - 4
AB  - Clostridium neonatale is a Gram-positive endospore-forming obligate anaerobe first isolated
AB  - from the feces of premature neonates during an intensive care unit
AB  - outbreak of necrotizing enterocolitis (NEC) in a Canadian neonatal intensive care
AB  - unit. Here, we announce the genome draft sequence of this bacterium. It is
AB  - composed of 4,710,818 bp and contains 4,169 protein-coding genes and 80 RNA
AB  - genes, including 11 rRNA genes.
ER  -

TY  - JOUR
AU  - Benamar, S.
AU  - La Scola, B.
AU  - Croce, O.
TI  - Genome Sequence of Afipia felis Strain 76713, Isolated in Hospital Water Using an Amoeba Co-Culture Procedure.
JO  - Genome Announcements
PY  - 2014
SP  - e01367
EP  - e01314
VL  - 2
AB  - Afipia felis is a Gram-negative alphaproteobacterium originally described as the  agent of
AB  - cat-scratch disease (CSD). We sequenced the genome from a strain of A.
AB  - felis, which was recovered from a hospital water sample using an amoebal
AB  - co-culture procedure. It is composed of 3,989,646 bp, with a G+C content of
AB  - 61.27% and encodes 4,068 protein-coding genes and 53 RNA genes.
ER  -

TY  - JOUR
AU  - Benbadis, L.
AU  - Faelen, M.
AU  - Slos, P.
AU  - Fazel, A.
AU  - Mercenier, A.
TI  - Characterization and comparison of virulent bacteriophages of Streptococcus thermophilus isolated from yogurt.
JO  - Biochimie
PY  - 1990
SP  - 855
EP  - 862
VL  - 72
AB  - Seven virulent bacteriophages of Streptococcus thermophilus were characterized at the
AB  - molecular level and classified into 2 subgroups (A and B) by DNA/DNA hybridization experiments
AB  - and analysis of their structural proteins. Two representatives of subgroups A and B were
AB  - compared to 3 representatives of Neve's subgroups I, II and III (Neve et al, 1989) by
AB  - Southern blot experiments. These isometric-headed phages possess a double-stranded DNA genome
AB  - varying between 30-44 kilobase (kb) pairs. Subgroup A is composed of 3 phages (phi 57 as
AB  - representative) with similar structural proteins as determined by sodium dodecyl
AB  - sulfate-polyacrylamide gel (SDS-PAGE) electrophoresis (estimated molecular weight of 31,000
AB  - and 27,500 for phage phi 57 and 32,000 and 27,000 for the 2 others). A common structural
AB  - protein of 43,000 was found for phages of subgroup B. Phages phi 57(subgroup D) and a10/J9 or
AB  - PO (Neve's subgroups I or II, respectively) belonged to the same subgroup as determined by
AB  - DNA/DNA hybridization experiments. Partial DNA homology was detected among all the phages
AB  - tested except for phage phi ST27 of AW Jarvis. Phage-host interactions were also investigated
AB  - by cross-propagation of the 7 studied phages on different indicator strains. A complete lack
AB  - of correlation existed between the DNA homology grouping of the phages and their host range.
AB  - Various restriction-modification systems were detected in some of the Streptococcus
AB  - thermophilus strains.
ER  -

TY  - JOUR
AU  - Benbadis, L.
AU  - Garel, J.R.
AU  - Hartley, D.L.
TI  - Purification, properties, and sequence specificity of SslI, a new type II restriction endonuclease from Streptococcus salivarius subsp. thermophilus.
JO  - Appl. Environ. Microbiol.
PY  - 1991
SP  - 3677
EP  - 3678
VL  - 57
AB  - SslI, a type II restriction endonuclease, was purified from Streptococcus
AB  - salivarius subsp. thermophilus strain BSN 45.  SslI is an isoschizomer of
AB  - BstNI.  SslI activity was maximum at pH 8.8, 0 to 50 mM NaCl, 2 to 8 mM Mg2+,
AB  - and 42C.  Activity against phage DNA in vitro was demonstrated.
ER  -

TY  - JOUR
AU  - Bench, S.R.
AU  - Hanson, T.E.
AU  - Williamson, K.E.
AU  - Ghosh, D.
AU  - Radosovich, M.
AU  - Wang, K.
AU  - Wommack, K.E.
TI  - Metagenomic characterization of Chesapeake Bay virioplankton.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 7629
EP  - 7641
VL  - 73
AB  - Viruses are ubiquitous and abundant throughout the biosphere. In marine systems,
AB  - virus-mediated processes can have significant impacts on microbial diversity and on global
AB  - biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To
AB  - address this shortcoming, a metagenomic library was constructed from Chesapeake Bay
AB  - virioplankton. The resulting sequences constitute the largest collection of long-read
AB  - double-stranded DNA (dsDNA) viral metagenome data reported to date. BLAST homology comparisons
AB  - showed that Chesapeake Bay virioplankton contained a high proportion of unknown (homologous
AB  - only to environmental sequences) and novel (no significant homolog) sequences. This analysis
AB  - suggests that dsDNA viruses are likely one of the largest reservoirs of unknown genetic
AB  - diversity in the biosphere. The taxonomic origin of BLAST homologs to viral library sequences
AB  - agreed well with reported abundances of cooccurring bacterial subphyla within the estuary and
AB  - indicated that cyanophages were abundant. However, the low proportion of Siphophage homologs
AB  - contradicts a previous assertion that this family comprises most bacteriophage diversity.
AB  - Identification and analyses of cyanobacterial homologs of the psbA gene illustrated the value
AB  - of metagenomic studies of virioplankton. The phylogeny of inferred PsbA protein sequences
AB  - suggested that Chesapeake Bay cyanophage strains are endemic in that environment.  The ratio
AB  - of psbA homologous sequences to total cyanophage sequences in the metagenome indicated that
AB  - the psbA gene may be nearly universal in Chesapeake Bay cyanophage genomes. Furthermore, the
AB  - low frequency ofpsbD homologs in the library supports the prediction that Chesapeake Bay
AB  - cyanophage populations are dominated by Podoviridae.
ER  -

TY  - JOUR
AU  - Bendall, M.L.
AU  - Luong, K.
AU  - Wetmore, K.M.
AU  - Blow, M.
AU  - Korlach, J.
AU  - Deutschbauer, A.
AU  - Malmstrom, R.R.
TI  - Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.
JO  - J. Bacteriol.
PY  - 2013
SP  - 4966
EP  - 4974
VL  - 195
AB  - We performed whole genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine
AB  - its possible role in regulating gene expression and other
AB  - cellular processes. Single-Molecule Real Time (SMRT) sequencing revealed
AB  - extensive methylation of adenine (N6mA) throughout the genome. These methylated
AB  - bases were located in five sequence motifs, including three novel targets for
AB  - Type I restriction/modification enzymes. The sequence motifs targeted by putative
AB  - methyltranferases were determined via SMRT sequencing of gene knockout mutants.
AB  - In addition, we found S. oneidensis MR-1 cultures grown under various culture
AB  - conditions displayed different DNA methylation patterns. However, the small
AB  - number of differentially methylated sites could not be directly linked to the
AB  - much larger number of differentially expressed genes in these conditions,
AB  - suggesting DNA methylation is not a major regulator of gene expression in S.
AB  - oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of
AB  - replication indicate DNA methylation may regulate genome replication in a manner
AB  - similar to that seen in Escherichia coli. Furthermore, comparative analyses
AB  - suggest that many Gammaproteobacteria, including all members of the
AB  - Shewanellaceae family, may also utilize DNA methylation to regulate genome
AB  - replication.
ER  -

TY  - JOUR
AU  - Bender, J.
TI  - A vicious cycle: RNA silencing and DNA methylation in plants.
JO  - Cell
PY  - 2001
SP  - 129
EP  - 132
VL  - 106
AB  - Several new studies have stimulated intense interest in understanding the mechanism and
AB  - evolutionary significance of RNA silencing, the targeted degradation of RNA.  RNA silencing is
AB  - typically triggered by double-stranded RNA (dsRNA).  The dsRNA trigger is diced into very
AB  - small species of 21-25 nt (siRNAs), which then guide sequence-specific cleavage of other
AB  - homologous RNAs, such as messenger RNAs.  Thus, both the trigger and target RNAs are
AB  - ultimately destroyed.  This mechanism occurs in eukaryotic organisms as diverse as the
AB  - laboratory plant Arabidopsis thaliana, nematode worms, and mice.  It is speculated that RNA
AB  - silencing exists as a defense against invasive dsRNA species such as RNA viruses.  In fact,
AB  - plants can recover from infection by RNA viruses via RNA silencing.  RNA silencing might also
AB  - have a role in developmental regulation.  Furthermore, RNA silencing induced by injected dsRNA
AB  - or dsRNA expressed from a transgene provides a powerful tool for reverse genetics in animals
AB  - and plants.
ER  -

TY  - JOUR
AU  - Bender, J.K.
AU  - Fiedler, S.
AU  - Klare, I.
AU  - Werner, G.
TI  - Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3.
JO  - Genome Announcements
PY  - 2015
SP  - e01275
EP  - e01215
VL  - 3
AB  - The genome sequence of the commensal and widely used laboratory strain
AB  - Enterococcus faecium 64/3 was resolved by means of PacificBioscience and Illumina
AB  - whole-genome sequencing. The genome comprises 2,575,333 bp with 2,382 coding
AB  - sequences as assigned by NCBI.
ER  -

TY  - JOUR
AU  - Bendiks, Z.A.
AU  - Lang, J.M.
AU  - Darling, A.E.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2013
SP  - e0012013
EP  - e0012013
VL  - 1
AB  - Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU,  a member of
AB  - the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8
AB  - scaffolds). This strain was isolated from a residential toilet as part of an
AB  - undergraduate student research project to sequence reference genomes of microbes
AB  - from the built environment.
ER  -

TY  - JOUR
AU  - Bendjama, E.
AU  - Loucif, L.
AU  - Diene, S.M.
AU  - Michelle, C.
AU  - Gacemi-Kirane, D.
AU  - Rolain, J.M.
TI  - Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1352
EP  - 1365
VL  - 9
AB  - Paucisalibacillus algeriensis strain EB02(T) is the type strain of Paucisalibacillus
AB  - algeriensis sp. nov., a new species within the genus
AB  - Paucisalibacillus. This strain, whose genome is described here, was isolated from
AB  - soil sample from the hypersaline lake Ezzemoul Sabkha in northeastern Algeria.
AB  - Paucisalibacillus algeriensis is a Gram-positive and strictly aerobic bacterium.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 4,006,766 bp long genome (1 chromosome but no
AB  - plasmid) exhibits a low G+C content of 36% and contains 3,956 protein-coding and
AB  - 82 RNA genes, including 9 rRNA genes.
ER  -

TY  - JOUR
AU  - Bendjama, E.
AU  - Loucif, L.
AU  - Diene, S.M.
AU  - Michelle, C.
AU  - Gacemi-Kirane, D.
AU  - Rolain, J.M.
TI  - Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1046
EP  - 1061
VL  - 9
AB  - Strain EB01(T) sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species
AB  - within the genus Bacillus. This strain, whose genome is described here,
AB  - was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in
AB  - northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic
AB  - Gram-positive bacillus. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 5,269,577 bp long genome
AB  - contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes.
ER  -

TY  - JOUR
AU  - Beneduzi, A.
AU  - Campos, S.
AU  - Ambrosini, A.
AU  - de Souza, R.
AU  - Granada, C.
AU  - Costa, P.
AU  - Arruda, L.
AU  - Moreira, F.
AU  - Vargas, L.K.
AU  - Weiss, V.
AU  - Tieppo, E.
AU  - Faoro, H.
AU  - de Souza, E.M.
AU  - Pedrosa, F.O.
AU  - Passaglia, L.M.
TI  - Genome Sequence of the Diazotrophic Gram-Positive Rhizobacterium Paenibacillus riograndensis SBR5T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6391
EP  - 6392
VL  - 193
AB  - Paenibacillus riograndensis SBR5(T), a nitrogen-fixing Gram-positive rhizobacterium isolated
AB  - from a wheat field in the south of Brazil, has a
AB  - great potential for agricultural applications due to its plant growth
AB  - promotion effects. Here we present the draft genome sequence of P.
AB  - riograndensis SBR5(T). Its 7.37-Mb genome encodes determinants of the
AB  - diazotrophic lifestyle and plant growth promotion, such as nitrogen
AB  - fixation, antibiotic resistance, nitrate utilization, and iron uptake.
ER  -

TY  - JOUR
AU  - Benetti, R.
AU  - Gonzalo, S.
AU  - Jaco, I.
AU  - Munoz, P.
AU  - Gonzalez, S.
AU  - Schoeftner, S.
AU  - Murchison, E.
AU  - Andl, T.
AU  - Chen, T.
AU  - Klatt, P.
AU  - Li, E.
AU  - Serrano, M.
AU  - Millar, S.
AU  - Hannon, G.
AU  - Blasco, M.A.
TI  - A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases (vol 15, pg 268, 2008).
JO  - Nat. Struct. Mol. Biol.
PY  - 2008
SP  - 998
EP  - 998
VL  - 15
AB  - Dicer initiates RNA interference by generating small RNAs involved in various silencing
AB  - pathways.  Dicer participates in centromeric silencing, but its role in the epigenetic
AB  - regulation of other chromatin domains has not been explored.  Here we show that Dicer1
AB  - deficiency in Mus musculus leads to decreased DNA methylation, concomitant with increased
AB  - telomere recombination and telomere elongation.  These DNA-methylation defects correlate with
AB  - decreased expression of Dnmt1, Dnmt3a and Dnmt3b DNA methyltransferases, and methylation
AB  - levels can be recoverd by their overexpression.  We identify the retinoblastoma-like 2 protein
AB  - as responsible for decreased Dnmt expression in Dicer1-null cells, suggesting the existence of
AB  - Dicer-dependent small RNAs that target Rbl2.  We identify the miR-290 cluster as being
AB  - downregulated in Dicer1-deficient cells and show that it silences Rbl2, thereby controlling
AB  - Dnmt expression.  These results identify a pathway by which miR-290 directly regulates
AB  - Rbl2-dependent Dnmt expression, indirectly affecting telomere-length homeostasis.
ER  -

TY  - JOUR
AU  - Benevides, L.J. et al.
TI  - Genome Sequence of Corynebacterium ulcerans Strain FRC11.
JO  - Genome Announcements
PY  - 2015
SP  - e00112
EP  - e00115
VL  - 3
AB  - Here, we present the genome sequence of Corynebacterium ulcerans strain FRC11. The genome
AB  - includes one circular chromosome of 2,442,826 bp (53.35% G+C content),
AB  - and 2,210 genes were predicted, 2,146 of which are putative protein-coding genes,
AB  - with 12 rRNAs and 51 tRNAs; 1 pseudogene was also identified.
ER  -

TY  - JOUR
AU  - Bengelsdorf, F.R.
AU  - Poehlein, A.
AU  - Esser, C.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Complete Genome Sequence of the Acetogenic Bacterium Moorella thermoacetica DSM 2955T.
JO  - Genome Announcements
PY  - 2015
SP  - e01157
EP  - e01115
VL  - 3
AB  - Here, we report the complete genome sequence of Moorella thermoacetica DSM 2955(T), an
AB  - acetogenic bacterium, which uses the Wood-Ljungdahl pathway for reduction of H2 + CO2 or CO.
AB  - The genome consists of a single circular chromosome  (2.62 Mb).
ER  -

TY  - JOUR
AU  - Bengelsdorf, F.R.
AU  - Poehlein, A.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of the Acetogenic Bacterium Butyribacterium methylotrophicum DSM  3468T.
JO  - Genome Announcements
PY  - 2016
SP  - e01338
EP  - e01316
VL  - 4
AB  - Butyribacterium methylotrophicum DSM 3468T is an acetogenic methylotrophic, anaerobic, carbon
AB  - monoxide-oxidizing bacterium that produces acetate, butyrate,
AB  - and butanol. The genome consists of a single chromosome (4.3 Mb) and harbors
AB  - 3,989 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Bengelsdorf, F.R.
AU  - Poehlein, A.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of the Acetogenic Bacterium Oxobacter pfennigii DSM 3222T.
JO  - Genome Announcements
PY  - 2015
SP  - e01408
EP  - e01415
VL  - 3
AB  - Here, we report the draft genome sequence of Oxobacter pfennigii DSM 3222(T), an  anaerobic,
AB  - acetogenic, carbon monoxide-oxidizing, and butyrate-producing
AB  - bacterium. The genome consists of a chromosome with a size of 4.49 Mbp.
ER  -

TY  - JOUR
AU  - Benight, A.S.
AU  - Gallo, F.J.
AU  - Paner, T.M.
AU  - Bishop, K.D.
AU  - Faldasz, B.D.
AU  - Lane, M.J.
TI  - Sequence context and DNA reactivity: Application to sequence-specific cleavage of DNA.
JO  - Adv. Biophys. Chem.
PY  - 1995
SP  - 1
EP  - 55
VL  - 5
AB  - Reactions between duplex DNA and ligands are largely dictated and mediated by the interplay of
AB  - the structural, thermodynamic, and dynamic characteristics of DNA and the recognition
AB  - mechanisms of reacting ligands.  Ligands that bind to DNA span a broad range of sizes from
AB  - small cations to large proteins and assembled protein aggregates.  As might be expected, a
AB  - wide variety of experimental strategies have been exploited to examine the sequence
AB  - specificity, or lack thereof, exhibited by ligands that interact with DNA.  Sequence-dependent
AB  - variations in local conformation and charge configuration along DNA are thought to be the
AB  - principal means by which ligands discriminate between various DNA sequences.  In efforts to
AB  - define the thermodynamic basis of such sequence-specific discrimination, a variety of
AB  - parameters have been evaluated from studies of DNA alone and ligand/DNA complexes.
ER  -

TY  - JOUR
AU  - Benkovic, S.J.
AU  - Baker, S.J.
AU  - Alley, M.R.K.
AU  - Woo, Y.H.
AU  - Zhang, Y.K.
AU  - Akama, T.
AU  - Mao, W.M.
AU  - Baboval, J.
AU  - Rajagopalan, P.T.R.
AU  - Wall, M.
AU  - Kahng, L.S.
AU  - Tavassoli, A.
AU  - Shapiro, L.
TI  - Identification of borinic esters as inhibitors of bacterial cell growth and bacterial methyltransferases, CcrM and MenH.
JO  - J. Med. Chem.
PY  - 2005
SP  - 7468
EP  - 7476
VL  - 48
AB  - As bacteria continue to develop resistance toward current antibiotics, we find ourselves in a
AB  - continual battle to identify new antibacterial agents and targets. We report herein a class of
AB  - boron-containing compounds termed borinic esters that have broad spectrum antibacterial
AB  - activity with minimum inhibitory concentrations (MIC) in the low microgram/mL range. These
AB  - compounds were identified by screening for inhibitors against Caulobacter crescentus CcrM, an
AB  - essential DNA methyltransferase from gram negative alpha-proteobacteria. In addition, we
AB  - demonstrate that borinic esters inhibit menaquinone methyltransferase in gram positive
AB  - bacteria using a new biochemical assay for MenH from Bacillus subtilis. Our data demonstrate
AB  - the potential for further development of borinic esters as antibacterial agents as well as
AB  - leads to explore more specific inhibitors against two essential bacterial enzymes.
ER  -

TY  - JOUR
AU  - Bennett, G.M.
AU  - Abba, S.
AU  - Kube, M.
AU  - Marzachi, C.
TI  - Complete Genome Sequences of the Obligate Symbionts 'Candidatus Sulcia muelleri'  and 'Ca. Nasuia deltocephalinicola' from the Pestiferous Leafhopper Macrosteles  quadripunctulatus (Hemiptera: Cicadellidae).
JO  - Genome Announcements
PY  - 2016
SP  - e01604
EP  - e01615
VL  - 4
AB  - Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus
AB  - (Hemiptera: Cicadellidae), were fully sequenced. 'Candidatus
AB  - Sulcia muelleri' and 'Ca. Nasuia deltocephalinicola' represent two of the
AB  - smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome
AB  - sequences are nearly identical to strains reported from the closely related host
AB  - species, M. quadrilineatus.
ER  -

TY  - JOUR
AU  - Bennett, S.P.
TI  - Restriction enzymes with asymmetrical recognition sites.
JO  - Diss. Abstr.
PY  - 1988
SP  - 722B
EP  - 722B
VL  - 49
AB  - The class II restriction endonucleases, CauI and CauII, recognize the DNA
AB  - sequences, 5'-GG(A/T)CC-3' and 5' -CC(C/G)GG-3', respectively.  Both of these
AB  - enzymes have been purified to homogeneity.  Molecular weight measurements
AB  - indicate that the active form of the CauI enzyme is a dimer of identical
AB  - protein subunits (of Mr 2x27,500).  In contrast, CauII appears to be a
AB  - heterologous dimer made up of different protein subunits (one of Mr 31,500 and
AB  - one of Mr 29,000).  Kinetic studies using the replicative DNA (RFI) of phage
AB  - PhiX174 as substrate, suggest that CauI and CauII cleave duplex DNA by a
AB  - concerted mechanism, in which both strands of the DNA are cut within the
AB  - lifetimes of a single enzyme-DNA complex.  Each endonuclease shows the same
AB  - activity towards its recognition site on both the supercoiled and relaxed forms
AB  - of PhiX174 RFDNA.  This implies that the unwinding of the DNA plays no
AB  - significant role in either the CauI or CauII cleavage reaction.  In standard
AB  - reactions, CauI and CauII display high specificities towards their recognition
AB  - sequences.  However, in the presence of dimethyl sulphoxide and at high pH,
AB  - each enzyme cleaves DNA at sites that differ from its recognition sequence by
AB  - one nucleotide.  The CauII enzyme cleaves DNA to generate fragments of DNA that
AB  - have at their 5' terminal, single nucleotide extensions of either 5' C or 5'G.
AB  - Ligation of these fragments generates cytosine:cytosine in duplex DNA.
ER  -

TY  - JOUR
AU  - Bennett, S.P.
TI  - Restriction enzymes with asymmetrical recognition sites.
JO  - Ph.D. Thesis, University of Bristol, UK
PY  - 1987
SP  - 1
EP  - 196
AB  - The class-II restriction endonucleases, CauI and CauII, recognize the DNA
AB  - sequences, 5'-GG(A/T)CC-3' and 5'-CC(C/G)GG-3', respectively.  Both of these
AB  - enzymes have been purified to homogeneity.  Molecular weight measurements
AB  - indicate that the active form of the CauI enzyme is a dimer of identical
AB  - protein subunits (of Mr 2 x 27500).  In contrast, CauII appears to be a
AB  - heterologous dimer made up of different protein subunits (one of Mr 31500 and
AB  - one of Mr 29000).  Kinetic studies using the replicative DNA (RFI) of phage
AB  - PhiX174 as substrate, suggest that CauI and CauII cleave duplex DNA by a
AB  - concerted mechanism, in which both strands of the DNA are cut within the
AB  - lifetime of a single enzyme-DNA complex.  Each endonuclease shows the same
AB  - activity towards its recognition site on both the supercoiled and relaxed forms
AB  - of PhiX174 RFDNA.  This implies that the unwinding of the DNA plays no
AB  - significant role in either the CauI or CauII cleavage reaction.  In standard
AB  - reactions, CauI and CauII display high specificities towards their recognition
AB  - sequences.  However, in the presence of dimethyl sulphoxide and at high pH,
AB  - each enzyme cleaves DNA at sites that differ from its recognition sequence by
AB  - one nucleotide.  The CauII enzyme cleaves DNA to generate fragments that have
AB  - at their 5' termini, single nucleotide extensions of either 5'C or 5'G.
AB  - Ligation of these fragments generates cytosine:cytosine in duplex DNA.
ER  -

TY  - JOUR
AU  - Bennett, S.P.
AU  - Halford, S.E.
TI  - Mechanism and specificity of two restriction enzymes, CauI and CauII, that recognize asymmetrical DNA sequences.
JO  - DNA-ligand interactions: from drugs to proteins.
PY  - 1987
SP  - 239
EP  - 250
AB  - Type II restriction endonucleases are enzymes that recognize specific nucleotide sequences on
AB  - duplex DNA and cleave both strands of the duplex at fixed locations relative to their
AB  - recognition sites.  The only co-factor that they need is Mg2+, while type I and type III
AB  - restriction enzymes also need ATP and S-adenosyl methionine for maximal activity.  Type I and
AB  - type III enzymes also differ from type II by cleaving DNA at variable distances from their
AB  - recognition sites.  Hence, the study of type II restriction enzymes was initially motivated by
AB  - their unique applications in the analysis of DNA and in the construction of recombinant DNA
AB  - molecules.  However, these enzymes also provide examples of DNA-protein interactions whose
AB  - mechanisms are amenable to molecular analysis.
ER  -

TY  - JOUR
AU  - Bennett, S.P.
AU  - Halford, S.E.
TI  - Cytosine: cytosine formed in duplex DNA by the ligation of NciI- or CauII-cleaved DNA.
JO  - Biochem. Soc. Trans.
PY  - 1986
SP  - 259
EP  - 259
VL  - 14
AB  - The type II restriction endonucleases, CauII and its isoschizomer NciI, recognize the sequence
AB  - 5'-C-C/-G-G-G-3' 3'-G-G-C/-C-C-5' on duplex DNA and cleave each strand at the sites marked
AB  - by arrows.  Hence these enzymes generate fragments of double-stranded DNA that have single
AB  - nucleotide 5' extensions of either G or C.  The DNA ligase encoded by bacteriophage T4 can
AB  - ligate DNA molecules that have either cohesive termini (due to single-strand extensions) or
AB  - blunt ends.  The efficiency of blunt-end ligations is usually low but can be increased by
AB  - adding polyethylene glycol to the reactions.
ER  -

TY  - JOUR
AU  - Bennett, S.P.
AU  - Halford, S.E.
TI  - Recognition of DNA by Type II restriction enzymes.
JO  - Curr. Top. Cell. Regul.
PY  - 1989
SP  - 57
EP  - 104
VL  - 30
AB  - A review
ER  -

TY  - JOUR
AU  - Bennke, C.M.
AU  - Kruger, K.
AU  - Kappelmann, L.
AU  - Huang, S.
AU  - Gobet, A.
AU  - Schuler, M.
AU  - Barbe, V.
AU  - Fuchs, B.M.
AU  - Michel, G.
AU  - Teeling, H.
AU  - Amann, R.I.
TI  - Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic.
JO  - Environ. Microbiol.
PY  - 2016
SP  - 4456
EP  - 4470
VL  - 18
AB  - Marine Bacteroidetes have pronounced capabilities of degrading high molecular
AB  - weight organic matter such as proteins and polysaccharides. Previously we
AB  - reported on 76 Bacteroidetes-affiliated fosmids from the North Atlantic Ocean's
AB  - boreal polar and oligotrophic subtropical provinces. Here, we report on the
AB  - analysis of further 174 fosmids from the same libraries. The combined,
AB  - re-assembled dataset (226 contigs; 8.8 Mbp) suggests that planktonic
AB  - Bacteroidetes at the oligotrophic southern station use more peptides and
AB  - bacterial and animal polysaccharides, whereas Bacteroidetes at the polar station
AB  - (East-Greenland Current) use more algal and plant polysaccharides. The latter
AB  - agrees with higher abundances of algae and terrigenous organic matter, including
AB  - plant material, at the polar station. Results were corroborated by in-depth
AB  - bioinformatic analysis of 14 polysaccharide utilisation loci from both stations,
AB  - suggesting laminarin-specificity for four and specificity for sulfated xylans for
AB  - two loci. In addition, one locus from the polar station supported use of
AB  - non-sulfated xylans and mannans, possibly of plant origin. While peptides likely
AB  - represent a prime source of carbon for Bacteroidetes in open oceans, our data
AB  - suggest that as yet unstudied clades of these Bacteroidetes have a surprisingly
AB  - broad capacity for polysaccharide degradation. In particular, laminarin-specific
AB  - PULs seem widespread and thus must be regarded as globally important.
ER  -

TY  - JOUR
AU  - Benomar, N.
AU  - Abriouel, H.
AU  - Lee, H.
AU  - Cho, G.S.
AU  - Huch, M.
AU  - Pulido, R.P.
AU  - Holzapfel, W.H.
AU  - Galvez, A.
AU  - Franz, C.M.
TI  - Genome Sequence of Weissella thailandensis fsh4-2.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5868
EP  - 5868
VL  - 193
AB  - Weissella thailandensis fsh4-2 is a heterofermentative lactic acid bacterium isolated from the
AB  - Korean fermented seafood condiment jeotkal.
AB  - Here we report the draft genome sequence of W. thailandensis fsh4-2 (1,651
AB  - genes, 1,436 encoding known proteins, 183 encoding unknown proteins, 32
AB  - RNA genes), which consists of 50 large contigs of >100 bp.
ER  -

TY  - JOUR
AU  - Bens, C.C.
AU  - Voss, A.
AU  - Klaassen, C.H.
TI  - Presence of a novel DNA methylation enzyme in methicillin-resistant Staphylococcus aureus isolates associated with pig farming leads to  uninterpretable results in standard pulsed-field gel electrophoresis  analysis.
JO  - J. Clin. Microbiol.
PY  - 2006
SP  - 1875
EP  - 1876
VL  - 44
AB  - Genomic DNA from methicillin-resistant Staphylococcus aureus isolates recovered from pigs and
AB  - their caretakers proved resistant to SmaI
AB  - digestion, leading to uninterpretable results in standard pulsed-field gel
AB  - electrophoresis. This is the result of a yet unknown
AB  - restriction/methylation system in the genus Staphylococcus with the
AB  - recognition sequence CCNGG.
ER  -

TY  - JOUR
AU  - Benson, M.A.
AU  - Ohneck, E.A.
AU  - Ryan, C.
AU  - Alonzo, F. III
AU  - Smith, H.
AU  - Narechania, A.
AU  - Kolokotronis, S.O.
AU  - Satola, S.W.
AU  - Uhlemann, A.C.
AU  - Sebra, R.
AU  - Deikus, G.
AU  - Shopsin, B.
AU  - Planet, P.J.
AU  - Torres, V.J.
TI  - Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.
JO  - Mol. Microbiol.
PY  - 2014
SP  - 664
EP  - 681
VL  - 93
AB  - Staphylococcus aureus has evolved as a pathogen that causes a range of diseases
AB  - in humans. There are two dominant modes of evolution thought to explain most of
AB  - the virulence differences between strains. First, virulence genes may be acquired
AB  - from other organisms. Second, mutations may cause changes in the regulation and
AB  - expression of genes. Here we describe an evolutionary event in which
AB  - transposition of an IS element has a direct impact on virulence gene regulation
AB  - resulting in hypervirulence. Whole-genome analysis of a methicillin-resistant S.
AB  - aureus (MRSA) strain USA500 revealed acquisition of a transposable element
AB  - (IS256) that is absent from close relatives of this strain. Of the multiple
AB  - copies of IS256 found in the USA500 genome, one was inserted in the promoter
AB  - sequence of repressor of toxins (Rot), a master transcriptional regulator
AB  - responsible for the expression of virulence factors in S. aureus. We show that
AB  - insertion into the rot promoter by IS256 results in the derepression of cytotoxin
AB  - expression and increased virulence. Taken together, this work provides new
AB  - insight into evolutionary strategies by which S. aureus is able to modify its
AB  - virulence properties and demonstrates a novel mechanism by which horizontal gene
AB  - transfer directly impacts virulence through altering toxin regulation.
ER  -

TY  - JOUR
AU  - Bentley, S.D. et al.
TI  - Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
JO  - Nature
PY  - 2002
SP  - 141
EP  - 147
VL  - 417
AB  - Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous
AB  - bacteria responsible for producing most natural antibiotics used in human and veterinary
AB  - medicine.  Here we report the 8,667,507 base pair linear chromosome of this organism,
AB  - containing the largest number of genes so far discovered in a bacterium.  The 7,825 predicted
AB  - genes include more than 20 clusters coding for known or predicted secondary metabolites.  The
AB  - genome contains an unprecedented proportion of regulatory genes, predominantly those likely to
AB  - be involved in responses to external stimuli and stresses, and many duplicated gene sets that
AB  - may represent 'tissue-specific' isoforms operating in different phases of colonial
AB  - development, a unique situation for a bacterium.  An ancient synteny was revealed between the
AB  - central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium
AB  - tuberculosis and Corynebacterium diphtheriae.  The genome sequence will greatly increase our
AB  - understanding of microbial life in the soil as well as aiding the generation of new drug
AB  - candidates by genetic engineering.
ER  -

TY  - JOUR
AU  - Bentley, S.D. et al.
TI  - Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei.
JO  - Lancet
PY  - 2003
SP  - 637
EP  - 644
VL  - 361
AB  - BACKGROUND: Whipple's disease is a rare multisystem chronic infection, involving the
AB  - intestinal tract as well as various other organs. The
AB  - causative agent, Tropheryma whipplei, is a Gram-positive bacterium about
AB  - which little is known. Our aim was to investigate the biology of this
AB  - organism by generating and analysing the complete DNA sequence of its
AB  - genome. METHODS: We isolated and propagated T whipplei strain TW08/27 from
AB  - the cerebrospinal fluid of a patient diagnosed with Whipple's disease. We
AB  - generated the complete sequence of the genome by the whole genome shotgun
AB  - method, and analysed it with a combination of automatic and manual
AB  - bioinformatic techniques. FINDINGS: Sequencing revealed a condensed 925938
AB  - bp genome with a lack of key biosynthetic pathways and a reduced capacity
AB  - for energy metabolism. A family of large surface proteins was identified,
AB  - some associated with large amounts of non-coding repetitive DNA, and an
AB  - unexpected degree of sequence variation. INTERPRETATION: The genome
AB  - reduction and lack of metabolic capabilities point to a host-restricted
AB  - lifestyle for the organism. The sequence variation indicates both known
AB  - and novel mechanisms for the elaboration and variation of surface
AB  - structures, and suggests that immune evasion and host interaction play an
AB  - important part in the lifestyle of this persistent bacterial pathogen.
ER  -

TY  - JOUR
AU  - Bentzon-Tilia, M.
AU  - Riemann, L.
AU  - Gram, L.
TI  - Draft Genome Sequence of Hoeflea sp. Strain BAL378, a Potential Producer of Bioactive Compounds.
JO  - Genome Announcements
PY  - 2014
SP  - e01213
EP  - e01214
VL  - 2
AB  - Some phytoplankton-associated marine bacteria produce bioactive compounds. Members of the
AB  - genus Hoeflea may be examples of such bacteria; however, data
AB  - describing their metabolisms are scarce. Here, we report the draft genome
AB  - sequence of Hoeflea sp. strain BAL378, a putative producer of bacteriocins,
AB  - polyketides, and auxins, as demonstrated by genome mining.
ER  -

TY  - JOUR
AU  - Benzinger, R.
TI  - Restriction of infectious bacteriophage fd DNA's and an assay for in vitro host-controlled restriction and modification.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1968
SP  - 1294
EP  - 1299
VL  - 59
AB  - Arber has shown that bacteriophage fd, which contains single-stranded circular
AB  - DNA (Marvin and Schaller) is restricted by E. coli B and E. coli (P1)+.  This
AB  - report presents detailed data on the restriction of both the infectious,
AB  - single-stranded fd-phage DNA and the infectious, double-stranded fd-replicative
AB  - form (RF) DNA.  It also describes an infectivity assay for in vitro
AB  - host-controlled restriction and modification.  This assay has been used to find
AB  - restriction enzymes in fractionated extracts of E. coli.
ER  -

TY  - JOUR
AU  - Bera, A.K.
AU  - Das, B.
AU  - Chattopadhyay, S.
AU  - Dasgupta, C.
TI  - Refolding of denatured restriction endonucleases with ribosomal preparations from Methanosarcina barkeri.
JO  - Biochem. Mol. Biol. Int.
PY  - 1994
SP  - 315
EP  - 323
VL  - 32
AB  - Two restriction endonucleases, EcoRI and HindIII were denatured by guanidine HCl or by storing
AB  - at room temperature (28oC) for several days. The activity of these enzymes could be restored
AB  - by incubating with ribosomal preparations from an archaebacterium Methanosarcina barkeri.
AB  - These results hint at a possible role of ribosomal preparations in folding polypeptides and
AB  - could be useful in working with restriction enzymes in experiments on genetic engineering and
AB  - molecular biology.
ER  -

TY  - JOUR
AU  - Berben, T.
AU  - Sorokin, D.Y.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Kyrpides, N.
AU  - Goodwin, L.A.
AU  - Woyke, T.
AU  - Muyzer, G.
TI  - Complete genome sequence of type strain ARh 1, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a  Kenyan soda lake.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 105
EP  - 105
VL  - 10
AB  - Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile,
AB  - Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated
AB  - from samples of haloalkaline soda lakes. It derives energy from the oxidation of
AB  - reduced sulfur compounds and is notable for its ability to grow on thiocyanate as
AB  - its sole source of electrons, sulfur and nitrogen. The full genome consists of
AB  - 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This
AB  - organism was sequenced as part of the community science program at the DOE Joint
AB  - Genome Institute.
ER  -

TY  - JOUR
AU  - Berben, T.
AU  - Sorokin, D.Y.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Kyrpides, N.
AU  - Goodwin, L.A.
AU  - Woyke, T.
AU  - Muyzer, G.
TI  - Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 85
EP  - 85
VL  - 10
AB  - Thioalkalivibrio thiocyanoxidans strain ARh 2(T) is a sulfur-oxidizing bacterium  isolated
AB  - from haloalkaline soda lakes. It is a motile, Gram-negative member of
AB  - the Gammaproteobacteria. Remarkable properties include the ability to grow on
AB  - thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of
AB  - growth at salinities of up to 4.3 M total Na(+). This draft genome sequence
AB  - consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616
AB  - protein-coding and 61 RNA-coding genes. This organism was sequenced as part of
AB  - the Community Science Program of the DOE Joint Genome Institute.
ER  -

TY  - JOUR
AU  - Berben, T.
AU  - Sorokin, D.Y.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Kyrpides, N.
AU  - Goodwin, L.A.
AU  - Woyke, T.
AU  - Muyzer, G.
TI  - Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of  complete denitrification.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 84
EP  - 84
VL  - 10
AB  - Thioalkalivibrio thiocyanodenitrificans strain ARhD 1(T) is a motile, Gram-negative bacterium
AB  - isolated from soda lakes that belongs to the
AB  - Gammaproteobacteria. It derives energy for growth and carbon fixation from the
AB  - oxidation of sulfur compounds, most notably thiocyanate, and so is a
AB  - chemolithoautotroph. It is capable of complete denitrification under anaerobic
AB  - conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds,
AB  - containing 3558 protein-coding and 121 RNA genes. T. thiocyanodenitrificans ARhD
AB  - 1(T) was sequenced as part of the DOE Joint Genome Institute Community Science
AB  - Program.
ER  -

TY  - JOUR
AU  - Berdis, A.J.
AU  - Lee, I.
AU  - Coward, J.K.
AU  - Stephens, C.
AU  - Wright, R.
AU  - Shapiro, L.
AU  - Benkovic, S.J.
TI  - A cell cycle-regulated adenine DNA methyltransferase from Caulobacter crescentus processively methylates GANTC sites on hemimethylated DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 2874
EP  - 2879
VL  - 95
AB  - The kinetic properties of an adenine DNA methyltransferase involved in cell cycle regulation
AB  - of Caulobacter crescentus have been elucidated by using defined unmethylated or hemimethylated
AB  - DNA substrates.  Catalytic efficiency is significantly enhanced with a DNAHM substrate.
AB  - Biphasic kinetic behavior during methyl incorporation is observed when unmethylated or DNAHM
AB  - substrates are used, indicating that a step after chemistry limits enzyme turnover and is most
AB  - likely the release of enzyme from methylated DNA product.  The enzyme is thermally inactivated
AB  - at 30oC within 20 min; this process substantially decreased in the presence of saturating
AB  - concentrations of DNAHM, suggesting that the enzyme preferentially binds DNA before
AB  - S-adenosylmethionine.  The activity of the enzyme shows an unusual sensitivity to salt levels,
AB  - apparently dissociating more rapidly from methylated DNA product as the salt level is
AB  - decreased.  The enzyme acts processively during methylation of specific DNA sequences,
AB  - indicating a preferred order of product release in which S-adenosylhomocysteine is released
AB  - from enzyme before fully methylated DNA.  The kinetic behavior and activity of the enzyme are
AB  - consistent with the temporal constraints during the cell cycle-regulated methylation of newly
AB  - replicated chromosomal DNA.
ER  -

TY  - JOUR
AU  - Berendsen, E.M.
AU  - Wells-Bennik, M.H.
AU  - Krawczyk, A.O.
AU  - de Jong, A.
AU  - van Heel, A.
AU  - Eijlander, R.T.
AU  - Kuipers, O.P.
TI  - Draft Genome Sequences of 10 Bacillus subtilis Strains That Form Spores with High or Low Heat Resistance.
JO  - Genome Announcements
PY  - 2016
SP  - e00124
EP  - e00116
VL  - 4
AB  - Here, we report the draft genome sequences of 10 isolates of Bacillus subtilis, a spore
AB  - forming Gram-positive bacterium. The strains were selected from food
AB  - products and produced spores with either high or low heat resistance.
ER  -

TY  - JOUR
AU  - Berendsen, E.M.
AU  - Wells-Bennik, M.H.
AU  - Krawczyk, A.O.
AU  - de Jong, A.
AU  - van Heel, A.
AU  - Holsappel, S.
AU  - Eijlander, R.T.
AU  - Kuipers, O.P.
TI  - Draft Genome Sequences of Seven Thermophilic Spore-Forming Bacteria Isolated from Foods That Produce Highly Heat-Resistant Spores, Comprising Geobacillus spp.,  Caldibacillus debilis, and Anoxybacillus flavithermus.
JO  - Genome Announcements
PY  - 2016
SP  - e00105
EP  - e00116
VL  - 4
AB  - Here, we report the draft genomes of five strains of Geobacillus spp., one Caldibacillus
AB  - debilis strain, and one draft genome of Anoxybacillus flavithermus,
AB  - all thermophilic spore-forming Gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Berenger, B.
AU  - Chen, J.
AU  - Bernier, A.M.
AU  - Bernard, K.
TI  - Draft Whole-Genome Sequence of a Catalase-Negative Staphylococcus aureus subsp. aureus (Sequence Type 25) Strain Isolated from a Patient with Endocarditis and Septic Arthritis.
JO  - Genome Announcements
PY  - 2016
SP  - e01442
EP  - e01416
VL  - 4
AB  - Staphylococcus aureus strains without catalase activity are rare, challenging to  identify
AB  - with conventional biochemical methods, and, despite a supposed decreased pathogenicity, can
AB  - still cause disease. The first whole-genome sequence of a catalase-negative S. aureus isolate
AB  - causing severe recurrent invasive infection with two novel missense mutations in the katA gene
AB  - is reported here.
ER  -

TY  - JOUR
AU  - Berent, L.M.
AU  - Messick, J.B.
TI  - Physical Map and Genome Sequencing Survey of Mycoplasma haemofelis (Haemobartonella felis).
JO  - Infect. Immun.
PY  - 2003
SP  - 3657
EP  - 3662
VL  - 71
AB  - Mycoplasma haemofelis is an uncultivable red-cell pathogen of cats.
AB  - Isolated M. haemofelis DNA was used to create a bacterial artificial
AB  - chromosome library and physical map. Random sequencing of this material
AB  - revealed 75 genes that had not been previously reported for M. haemofelis
AB  - or any other hemotrophic mycoplasma.
ER  -

TY  - JOUR
AU  - Beres, S.B.
AU  - Richter, E.W.
AU  - Nagiec, M.J.
AU  - Sumby, P.
AU  - Porcella, S.F.
AU  - DeLeo, F.R.
AU  - Musser, J.M.
TI  - Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 7059
EP  - 7064
VL  - 103
AB  - In recent years we have studied the relationship between strain genotypes and patient
AB  - phenotypes in group A Streptococcus (GAS), a model human
AB  - bacterial pathogen that causes extensive morbidity and mortality
AB  - worldwide. We have concentrated our efforts on serotype M3 organisms
AB  - because these strains are common causes of pharyngeal and invasive
AB  - infections, produce unusually severe invasive infections, and can exhibit
AB  - epidemic behavior. Our studies have been hindered by the lack of
AB  - genome-scale phylogenies of multiple GAS strains and whole-genome
AB  - sequences of multiple serotype M3 strains recovered from individuals with
AB  - defined clinical phenotypes. To remove some of these impediments, we
AB  - sequenced to closure the genome of four additional GAS strains and
AB  - conducted comparative genomic resequencing of 12 contemporary serotype M3
AB  - strains representing distinct genotypes and phenotypes. Serotype M3
AB  - strains are a single phylogenetic lineage. Strains from asymptomatic
AB  - throat carriers were significantly less virulent for mice than
AB  - sterile-site isolates and evolved to a less virulent phenotype by multiple
AB  - genetic pathways. Strain persistence or extinction between epidemics was
AB  - strongly associated with presence or absence, respectively, of the
AB  - prophage encoding streptococcal pyrogenic exotoxin A. A serotype M3 clone
AB  - significantly underrepresented among necrotizing fasciitis cases has a
AB  - unique frameshift mutation that truncates MtsR, a transcriptional
AB  - regulator controlling expression of genes encoding iron-acquisition
AB  - proteins. Expression microarray analysis of this clone confirmed
AB  - significant alteration in expression of genes encoding iron metabolism
AB  - proteins. Our analysis provided unprecedented detail about the molecular
AB  - anatomy of bacterial strain genotype-patient phenotype relationships.
ER  -

TY  - JOUR
AU  - Beres, S.B.
AU  - Sesso, R.
AU  - Pinto, S.W.
AU  - Hoe, N.P.
AU  - Porcella, S.F.
AU  - Deleo, F.R.
AU  - Musser, J.M.
TI  - Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: new information about an old disease.
JO  - PLoS ONE
PY  - 2008
SP  - E3026
EP  - E3026
VL  - 3
AB  - Outbreaks of disease attributable to human error or natural causes can provide
AB  - unique opportunities to gain new information about host-pathogen interactions and
AB  - new leads for pathogenesis research. Poststreptococcal glomerulonephritis (PSGN),
AB  - a sequela of infection with pathogenic streptococci, is a common cause of
AB  - preventable kidney disease worldwide. Although PSGN usually occurs after
AB  - infection with group A streptococci, organisms of Lancefield group C and G also
AB  - can be responsible. Despite decades of study, the molecular pathogenesis of PSGN
AB  - is poorly understood. As a first step toward gaining new information about PSGN
AB  - pathogenesis, we sequenced the genome of Streptococcus equi subsp. zooepidemicus
AB  - strain MGCS10565, a group C organism that caused a very large and unusually
AB  - severe epidemic of nephritis in Brazil. The genome is a circular chromosome of
AB  - 2,024,171 bp. The genome shares extensive gene content, including many virulence
AB  - factors, with genetically related group A streptococci, but unexpectedly lacks
AB  - prophages. The genome contains many apparently foreign genes interspersed around
AB  - the chromosome, consistent with the presence of a full array of genes required
AB  - for natural competence. An inordinately large family of genes encodes secreted
AB  - extracellular collagen-like proteins with multiple integrin-binding motifs. The
AB  - absence of a gene related to speB rules out the long-held belief that
AB  - streptococcal pyrogenic exotoxin B or antibodies reacting with it singularly
AB  - cause PSGN. Many proteins previously implicated in GAS PSGN, such as
AB  - streptokinase, are either highly divergent in strain MGCS10565 or are not more
AB  - closely related between these species than to orthologs present in other
AB  - streptococci that do not commonly cause PSGN. Our analysis provides a comparative
AB  - genomics framework for renewed appraisal of molecular events underlying APSGN
AB  - pathogenesis.
ER  -

TY  - JOUR
AU  - Beres, S.B.
AU  - Sylva, G.L.
AU  - Barbian, K.D.
AU  - Lei, B.
AU  - Hoff, J.S.
AU  - Mammarella, N.D.
AU  - Liu, M.-Y.
AU  - Smoot, J.C.
AU  - Porcella, S.F.
AU  - Parkins, L.D.
AU  - Campbell, D.S.
AU  - Smith, T.M.
AU  - McCormick, J.K.
AU  - Leung, D.Y.M.
AU  - Schlievert, P.M.
AU  - Musser, J.M.
TI  - Genome sequence of a serotype M3 strain of group A Streptococcus: Phage-encoded toxins, the high-virulence phenotype, and clone emergence.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 10078
EP  - 10083
VL  - 99
AB  - Genome sequences are available for many bacterial strains, but there has been little progress
AB  - in using these data to understand the molecular basis of pathogen emergence and differences in
AB  - strain virulence. Serotype M3 strains of group A Streptococcus (GAS) are a common cause of
AB  - severe invasive infections with unusually high rates of morbidity and mortality. To gain
AB  - insight into the molecular basis of this high-virulence phenotype, we sequenced the genome of
AB  - strain MGAS315, an organism isolated from a patient with streptococcal toxic shock syndrome.
AB  - The genome is composed of 1,900,521 bp, and it shares approximately 1.7 Mb of related genetic
AB  - material with genomes of serotype M1 and M18 strains. Phage-like elements account for the
AB  - great majority of variation in gene content relative to the sequenced M1 and M18 strains.
AB  - Recombination produces chimeric phages and strains with previously uncharacterized arrays of
AB  - virulence factor genes. Strain MGAS315 has phage genes that encode proteins likely to
AB  - contribute to pathogenesis, such as streptococcal pyrogenic exotoxin A (SpeA) and SpeK,
AB  - streptococcal superantigen (SSA), and a previously uncharacterized phospholipase A(2)
AB  - (designated Sla).  Infected humans had anti-SpeK, -SSA, and -Sla antibodies, indicating that
AB  - these GAS proteins are made in vivo.  SpeK and SSA were pyrogenic and toxic for rabbits.
AB  - Serotype M3 strains with the phage-encoded speK and sla genes increased dramatically in
AB  - frequency late in the 20th century, commensurate with the rise in invasive disease caused by
AB  - M3 organisms. Taken together, the results show that phage-mediated recombination has played a
AB  - critical role in the emergence of a new, unusually virulent clone of serotype M3 GAS.
ER  -

TY  - JOUR
AU  - Berg, D.E.
AU  - Hoffman, P.S.
AU  - Appelmelk, B.J.
AU  - Kusters, J.G.
TI  - The Helicobacter pylori genome sequence: genetic factors for long life in the gastric mucosa.
JO  - Trends Microbiol.
PY  - 1997
SP  - 468
EP  - 474
VL  - 5
AB  - The complete DNA sequence of the chromosome of a strain of Helicobacter pylori was released in
AB  - mid-1997 by The Institute for Genomic Research, a long-awaited and warmly welcomed event that
AB  - should greatly stimulate research on this pathogen and benefit public health.  Infection by H,
AB  - pylori occurs in more than half of all people worldwide and is a major cause of severe
AB  - gastritis and peptic ulcer disease and an early risk factor for gastric cancer, although most
AB  - infections are asymptomatic and some might even be beneficial.  H. pylori is Gram-negative,
AB  - fastidious in its nutritional requirements and microaerophilic: it chronically infects human
AB  - gastric epithelial cell surfaces and the overlying mucin layer.  Although some infections are
AB  - cleared spontaneously after a brief acute phase, many last for years or decades, and it is
AB  - these infections that are most often implicated in overt disease.
ER  -

TY  - JOUR
AU  - Berg-Miller, M.E.
AU  - Antonopoulos, D.A.
AU  - Rincon, M.T.
AU  - Band, M.
AU  - Bari, A.
AU  - Akraiko, T.
AU  - Hernandez, A.
AU  - Thimmapuram, J.
AU  - Henrissat, B.
AU  - Coutinho, P.M.
AU  - Borovok, I.
AU  - Jindou, S.
AU  - Lamed, R.
AU  - Flint, H.J.
AU  - Bayer, E.A.
AU  - White, B.A.
TI  - Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.
JO  - PLoS ONE
PY  - 2009
SP  - E6650
EP  - E6650
VL  - 4
AB  - BACKGROUND: Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which
AB  - forms a multi-enzyme cellulosome complex that could play an integral role in the ability of
AB  - this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types
AB  - involved in plant cell wall degradation is essential for gaining a better understanding of the
AB  - cellulolytic capabilities of this organism as well as highlighting potential enzymes for
AB  - application in improvement of livestock nutrition and for conversion of cellulosic biomass to
AB  - liquid fuels. METHODOLOGY/PRINCIPAL FINDINGS: The R. flavefaciens FD-1 genome was sequenced to
AB  - 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into
AB  - 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes
AB  - ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was
AB  - detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was
AB  - further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including
AB  - previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing
AB  - ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs),
AB  - polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that
AB  - contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome
AB  - revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated,
AB  - 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three
AB  - multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of
AB  - up-regulation. CONCLUSIONS/SIGNIFICANCE: The genomic evidence indicates that R. flavefaciens
AB  - FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a
AB  - cellulosome architecture. Functional analysis of the genome has revealed that the growth
AB  - substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as
AB  - well as expression and assembly of key cellulosomal enzyme components.
ER  -

TY  - JOUR
AU  - Berg-Miller, M.E.
AU  - Yeoman, C.J.
AU  - Chia, N.
AU  - Tringe, S.G.
AU  - Angly, F.E.
AU  - Edwards, R.A.
AU  - Flint, H.J.
AU  - Lamed, R.
AU  - Bayer, E.A.
AU  - White, B.A.
TI  - Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
JO  - Environ. Microbiol.
PY  - 2012
SP  - 207
EP  - 227
VL  - 14
AB  - Viruses are the most abundant biological entities on the planet and play an
AB  - important role in balancing microbes within an ecosystem and facilitating
AB  - horizontal gene transfer. Although bacteriophages are abundant in rumen
AB  - environments, little is known about the types of viruses present or their
AB  - interaction with the rumen microbiome. We undertook random pyrosequencing of
AB  - virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and
AB  - analysed the resulting data using comparative metagenomics. A high level of
AB  - diversity was observed with up to 28,000 different viral genotypes obtained from
AB  - each environment. The majority (~78%) of sequences did not match any previously
AB  - described virus. Prophages outnumbered lytic phages approximately 2:1 with the
AB  - most abundant bacteriophage and prophage types being associated with members of
AB  - the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling
AB  - based on SEED subsystems revealed an enrichment of sequences with putative
AB  - functional roles in DNA and protein metabolism, but a surprisingly low proportion
AB  - of sequences assigned to carbohydrate and amino acid metabolism. We expanded our
AB  - analysis to include previously described metagenomic data and 14 reference
AB  - genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were
AB  - detected in most of the microbial genomes, suggesting previous interactions
AB  - between viral and microbial communities.
ER  -

TY  - JOUR
AU  - Berge, T.
AU  - Ellis, D.J.
AU  - Dryden, D.T.F.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy.
JO  - Biophys. J.
PY  - 2000
SP  - 479
EP  - 484
VL  - 79
AB  - Bacterial type I restriction/modification systems are capable of performing multiple actions
AB  - in response to the methylation pattern on
AB  - their DNA recognition sequences. The enzymes making up these systems
AB  - serve to protect the bacterial cells against viral infection by binding
AB  - to their recognition sequences on the invading DNA and degrading it
AB  - after extensive ATP-driven translocation, DNA cleavage has been thought
AB  - to occur as the result of a collision between two translocating enzyme
AB  - complexes. Using atomic force microscopy (AFM), we show here that EcoKI
AB  - dimerizes rapidly when bound to a plasmid containing two recognition
AB  - sites for the enzyme. Dimerization proceeds in the absence of ATP and
AB  - is also seen with an EcoKI mutant (K477R) that is unable to translocate
AB  - DNA. Only monomers are seen when the enzyme complex binds to a plasmid
AB  - containing a single recognition site. Based on our results, we propose
AB  - that the binding of EcoKI to specific DNA target sequences is
AB  - accompanied by a conformational change that leads rapidly to
AB  - dimerization. This event is followed by ATP-dependent translocation and
AB  - cleavage of the DNA.
ER  -

TY  - JOUR
AU  - Bergemann, A.D.
AU  - Whitley, J.C.
AU  - Finch, L.R.
TI  - Taxonomic significance of differences in DNA methylation within the Mycoplasma mycoides cluster' detected with restriction endonucleases MboI and DpnI.
JO  - Lett. Appl. Microbiol.
PY  - 1990
SP  - 48
EP  - 51
VL  - 11
AB  - DNA from 22 strains belonging to the Mycoplasma mycoides cluster was tested for
AB  - methylation of adenine in GATC sequences by its resistance or susceptibility to
AB  - digestion by the restriction endonucleases MboI, which is inhibited by the
AB  - methylation, or DpnI, which requires the methylation.  Strains of bovine
AB  - serogroup 7, M. mycoides subsp. mycoides SC, and some M. mycoides subsp. capri
AB  - strains plus M. capricolum strain Cal Kid lacked the methylation, whereas other
AB  - strains of M. mycoides subsp. capri and of M. capricolum, plus the F38-like and
AB  - M. mycoides subsp. mycoides LC strains, possessed it.  We conclude that this
AB  - simple test could provide a valuable criterion in identifying these
AB  - mycoplasmas.
ER  -

TY  - JOUR
AU  - Berger, S.
AU  - Alauzet, C.
AU  - Aissa, N.
AU  - Henard, S.
AU  - Rabaud, C.
AU  - Bonnet, R.
AU  - Lozniewski, A.
TI  - Characterization of a new blaOXA-48-carrying Plasmid in Enterobacteriaceae.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 4064
EP  - 4067
VL  - 57
AB  - In this work we characterized a new 160-kb blaOXA-48-harboring IncL/M-type
AB  - plasmid, isolated from a Klebsiella pneumoniae strain from France. Moreover, we
AB  - report the transfer of a 60-kb OXA-48 encoding plasmid from Klebsiella pneumoniae
AB  - to other Enterobacteriaceae in two patients.
ER  -

TY  - JOUR
AU  - Berger, S.
AU  - Frank, J.
AU  - Dalcin, M.P.
AU  - Jetten, M.S.M.
AU  - Welte, C.U.
TI  - High-Quality Draft Genome Sequence of 'Candidatus Methanoperedens sp.' Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an  Anoxic Bioreactor.
JO  - Genome Announcements
PY  - 2017
SP  - e01159
EP  - e01117
VL  - 5
AB  - The high-quality draft genome of 'Candidatus Methanoperedens sp.' strain BLZ2, a
AB  - nitrate-reducing archaeon anaerobically oxidizing methane, is presented. The
AB  - genome was obtained from an enrichment culture and measures 3.74 Mb. It harbors
AB  - two nitrate reductase gene clusters, an ammonium-forming nitrite reductase, and
AB  - the complete reverse methanogenesis pathway. Methane that escapes to the
AB  - atmosphere acts as a potent greenhouse gas. Global methane emissions are
AB  - mitigated by methanotrophs, which oxidize methane to CO2 'Candidatus
AB  - Methanoperedens spp.' are unique methanotrophic archaea that can perform
AB  - nitrate-dependent anaerobic oxidation of methane. A high-quality draft genome
AB  - sequence of only 85 contigs from this archaeon is presented here.
ER  -

TY  - JOUR
AU  - Berger, S.L.
TI  - Expanding the potential of restriction endonucleases: Use of hapaxoterministic enzymes.
JO  - Anal. Biochem.
PY  - 1994
SP  - 1
EP  - 8
VL  - 222
AB  - A new class of restriction endonucleases called hapoxoterministic enzymes, hapaxomers for
AB  - short, has been defined. A hapaxomer cleaves DNA outside the recognition site or within an
AB  - interrupted "palindrome" at bases which are not specified producing fragments with asymmetric,
AB  - staggered ends. Such termini are unique; in the general case, the protrusions of a fragment
AB  - obtained with the aid of a hapaxomer cannot self-hybridize, nor can the fragment be ligated to
AB  - the vast majority of other fragments produced by the same enzyme. When the fragments generated
AB  - by a hapaxoterministic enzyme are mixed, they can reassemble in only one configuration--that
AB  - of the original structure from which they were derived. Hapaxomers, then, are characterized
AB  - not by their recognition sites, which may be symmetric or asymmetric, but by their cleavage
AB  - sites. The ability to reunite once-contiguous fragments efficiently means that hapaxomers
AB  - cleaving DNA at many locations are virtually equivalent to restriction enzymes cutting at
AB  - unique sites. These properties can be exploited for applications such as site-specific
AB  - mutagenesis or the isolation of large intact DNA fragments.
ER  -

TY  - JOUR
AU  - Berger, S.L.
TI  - Gene modification with hapaxoterministic restriction enzymes.
JO  - Methods Mol. Biol.
PY  - 2001
SP  - 443
EP  - 458
VL  - 160
AB  - Subcloning can be extraordinarily easy or extremely difficult.  The simplest case requires
AB  - cleavage of the desired fragment from the DNA in which it is located with one or two
AB  - restriction enzymes, cleavage of the plasmid that will serve as the ultimate recipient with
AB  - the same enzymes, and ligation of the fragment to the plasmid.  In a somewhat more complicated
AB  - version of simple cloning, the investigator uses the polymerase chain reaction to amplify the
AB  - DNA to be subcloned.  In this case, restriction sites can be incorporated into the primers
AB  - used for PCR, generating products with the desired restriction sites located near the ends of
AB  - the newly synthesized DNA.  After cleavage of those sites, the fragment is ready for insertion
AB  - into an appropriately cut vector.  The major disadvantage of the method is the need for
AB  - sequencing the amplified material, because even the best of the thermostable polymerases makes
AB  - mistakes that might render the DNA useless for the anticipated application.
ER  -

TY  - JOUR
AU  - Bergerat, A.
AU  - Guschlbauer, W.
TI  - The double role of methyl donor and allosteric effector of S-adenosyl-methionine for Dam methylase of E. coli.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4369
EP  - 4375
VL  - 18
AB  - The turnover of DNA-adenine-methylase of E. coli strongly decreases when the temperature is
AB  - lowered. This has allowed us to study the binding of Dam methylase on 14 bp DNA fragments at
AB  - 0C by gel retardation in the presence of Ado-Met, but without methylation taking place. The
AB  - enzyme can bind nonspecific DNA with low affinity. Binding to the specific sequence occurs in
AB  - the absence of S-adenosylmethionine (Ado-Met), but is activated by the presence of the methyl
AB  - donor. The two competitive inhibitors of Ado-Met, sinefungin and S-adenosyl-homocysteine, can
AB  - neither activate this binding to DNA by themselves, nor inhibit this activation by Ado-Met.
AB  - This suggests that Ado-Met could bind to Dam methylase in two different environments. In one
AB  - of them, it could play the role of an allosteric effector which would reinforce the affinity
AB  - of the enzyme for the GATC site. The analogues can not compete for such binding. In the other
AB  - environment Ado-Met would be in the catalytic site and could be exchanged by its analogues. We
AB  - have also visualized conformational changes in Dam methylases induced by the simultaneous
AB  - binding of Ado-Met and the specific target sequence of the enzyme, by an anomaly of migration
AB  - and partial resistance to proteolytic treatment of the ternary complex Ado-Met/Dam
AB  - methylase/GATC.
ER  -

TY  - JOUR
AU  - Bergerat, A.
AU  - Guschlbauer, W.
AU  - Fazakerley, G.V.
TI  - Allosteric and catalytic binding of S-adenosylmethionine to Escherichia coli DNA adenine methyltransferase monitored by 3H NMR.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1991
SP  - 6394
EP  - 6397
VL  - 88
AB  - Adenine methylation of GATC sequences in DNA is carried out by the DNA adenine
AB  - methyltransferase with the methyl group source being the cofactor
AB  - S-adenosylmethionine.  We report 3H NMR studies on the interaction of DNA
AB  - adenine methyltransferase with S-adenosylmethionine and the reaction when the
AB  - ternary complex is formed with an oligonucleotide containing a GATC site.  The
AB  - methylation reaction was also studied in the presence of a competitive
AB  - inhibitor and this showed two successive stages involved in the methylation and
AB  - tw sites of binding for S-adenosylmethionine.
ER  -

TY  - JOUR
AU  - Bergerat, A.
AU  - Kriebardis, A.
AU  - Guschlbauer, W.
TI  - Preferential site-specific hemimethylation of GATC sites in pBR322 DNA by dam methyltransferase from Escherichia coli.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 4064
EP  - 4070
VL  - 264
AB  - The methylation pattern of the 22 GATC sites of pBR322 (dam-) by Dam methyltransferase from
AB  - Escherichia coli has been studied. Preferential hemimethylation took place at positions 3042
AB  - and 349. It was found that these preferential methylations were the same in supercoiled
AB  - circular and linear DNAs. The flanking regions of these preferentially methylated sites
AB  - contain three GC pairs on one side and two AT pairs and one GC pair on the other. This
AB  - preferential methylation was confirmed on a 126-base pair oligonucleotide containing two GATC
AB  - sites with different flanking sequences. The next sites methylated were, in both cases, the
AB  - first GATC site on the AT-rich side, although the orientation was different. The rapid
AB  - methylation of a second and third neighboring GATC site on the same plasmid suggests a
AB  - processive mechanism. The implications of the orientation of hemimethylation are discussed in
AB  - the context of the recognition of a palindromic target site by a monomeric DNA-binding
AB  - protein.
ER  -

TY  - JOUR
AU  - Bergez, P.
AU  - Doignon, F.
AU  - Crouzet, M.
TI  - The sequence of a 44,420 bp fragment located on the left arm of chromosome XIV from Saccharomyces cerevisiae.
JO  - Yeast
PY  - 1995
SP  - 967
EP  - 974
VL  - 11
AB  - We have determined the complete nucleotide sequence of a 44 420 bp DNA fragment from
AB  - chromosome XIV of Saccharomyces cerevisiae. The sequence data revealed 23 open reading frames
AB  - (ORFs) larger than 300 bp, covering 73.5% of the sequence. The ORFs N2418, N2428, N2441, N2474
AB  - and N2480 correspond to previously sequenced S. cerevisiae genes coding respectively for the
AB  - mitochondrial import protein Mas5, the nucleolar protein Nop2, the outer mitochondrial
AB  - membrane porin Por1, the cytochrome c oxidase polypeptide VA precursor CoxA and the yeast
AB  - protein tyrosine phosphatase Msg5. Translation products of three other ORFs N2406, N2411 and
AB  - N2430 exhibit similarity to previously known S. cerevisiae proteins: the ribosomal protein
AB  - YL9A, the protein Nca3 involved in the mitochondrial expression of subunits 6 and 8 of the ATP
AB  - synthase and actin; in addition N2505 presents strong similarity to an ORF of chromosome IX.
AB  - The predicted protein products of ORFs N2417 and N2403 present similarities with domains from
AB  - proteins of other organisms: the Candida maltosa cycloheximide-resistance protein, the human
AB  - interleukin enhancer-binding factor (ILF-2). The 12 remaining ORFs show no significant
AB  - similarity to known proteins. In addition, we have detected a DNA region very similar to the
AB  - yeast transposon Ty 1-15 of which insertion has disrupted a tRNA(Asp) gene.
ER  -

TY  - JOUR
AU  - Berglund, E.C.
AU  - Frank, A.C.
AU  - Calteau, A.
AU  - Vinnere, P.O.
AU  - Granberg, F.
AU  - Eriksson, A.S.
AU  - Naslund, K.
AU  - Holmberg, M.
AU  - Lindroos, H.
AU  - Andersson, S.G.
TI  - Run-off Replication of Host-Adaptability Genes is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii.
JO  - PLoS Genet.
PY  - 2009
SP  - e1000546
EP  - e1000546
VL  - 5
AB  - The genus Bartonella comprises facultative intracellular bacteria adapted to mammals,
AB  - including previously recognized and emerging human pathogens. We report the 2,341,328 bp
AB  - genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild
AB  - rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher
AB  - copy numbers of genes for putative host-adaptability factors than the related human-specific
AB  - pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using
AB  - hybridization to a microarray designed for the B. grahamii genome, we observed a massive,
AB  - putatively phage-derived run-off replication of this region. We also identified a novel gene
AB  - transfer agent, which packages the bacterial genome, with an over-representation of the
AB  - amplified DNA, in 14 kb pieces. This is the first observation associating the products of
AB  - run-off replication with a gene transfer agent. Because of the high concentration of gene
AB  - clusters for host-adaptation proteins in the amplified region, and since the genes encoding
AB  - the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize
AB  - that these systems are driven by selection. We propose that the coupling of run-off
AB  - replication with gene transfer agents promotes diversification and rapid spread of
AB  - host-adaptability factors, facilitating host shifts in Bartonella.
ER  -

TY  - JOUR
AU  - Bergman, Y.
AU  - Mostoslavsky, R.
TI  - DNA demethylation: Turning genes on.
JO  - Biol. Chem.
PY  - 1998
SP  - 401
EP  - 407
VL  - 379
AB  - The regulation of eukaryotic gene expression is a complicated process involving the
AB  - interaction of a large number of transacting factors with specific cis-regulatory elements.
AB  - DNA methylation plays a role in this scheme by acting in cis to modulate protein-DNA
AB  - interactions.  Several lines of evidence indicate that methylation serves to silence
AB  - transcription, mainly through indirect mechanisms involving the assembly of repressive
AB  - nucleoprotein complexes.  DNA demethylation is mostly an active enzymatic process, controlled
AB  - by cis regulatory elements which provide binding sites for trans demethylation factors.  In
AB  - the immune system DNA methylation plays multiple roles, such as regulating both gene
AB  - expression and gene rearrangement.
ER  -

TY  - JOUR
AU  - Bergottini, V.M.
AU  - Filippidou, S.
AU  - Junier, T.
AU  - Johnson, S.
AU  - Chain, P.S.
AU  - Otegui, M.B.
AU  - Zapata, P.D.
AU  - Junier, P.
TI  - Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.).
JO  - Genome Announcements
PY  - 2015
SP  - e00239
EP  - e00215
VL  - 3
AB  - Kosakonia radicincitans strain YD4 is a rhizospheric isolate from yerba mate (Ilex
AB  - paraguariensis St. Hill.) with plant growth-promoting effects on this crop.
AB  - Genes involved in different plant growth-promoting activities are present in this
AB  - genome, suggesting its potential as a bioinoculant for yerba mate.
ER  -

TY  - JOUR
AU  - Bergsveinson, J.
AU  - Pittet, V.
AU  - Ewen, E.
AU  - Baecker, N.
AU  - Ziola, B.
TI  - Genome Sequence of Rapid Beer-Spoiling Isolate Lactobacillus brevis BSO 464.
JO  - Genome Announcements
PY  - 2015
SP  - e01411
EP  - e01415
VL  - 3
AB  - The genome of brewery-isolate Lactobacillus brevis BSO 464 was sequenced and assembly produced
AB  - a chromosome and eight plasmids. This bacterium tolerates
AB  - dissolved CO2/pressure and can rapidly spoil packaged beer. This genome is useful
AB  - for analyzing the genetics associated with beer spoilage by lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Bergsveinson, J.
AU  - Thomson, E.
AU  - Jacoby, D.
AU  - Coady, Y.
AU  - Ziola, B.
TI  - Genome Sequence of Megasphaera cerevisiae NSB1, a Bacterium Isolated from a Canning Line and Able To Grow in Beer with High Alcohol Content.
JO  - Genome Announcements
PY  - 2017
SP  - e01686
EP  - e01616
VL  - 5
AB  - The genome sequence of the brewery isolate Megasphaera cerevisiae NSB1 was determined. Strain
AB  - NSB1 tolerates 5% (vol/vol) alcohol, which is higher than
AB  - previously reported for M. cerevisiae The NSB1 genome will help elucidate
AB  - genetics required for alcohol tolerance and niche adaptation of this
AB  - Gram-negative beer-spoilage bacterium.
ER  -

TY  - JOUR
AU  - Berkhout, B.
AU  - van Wamel, J.
TI  - Accurate scanning of the BssHII endonuclease in search for its DNA cleavage site.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 1837
EP  - 1840
VL  - 271
AB  - A facilitated diffusion mechanism has been proposed to account for the kinetic efficiency with
AB  - which restriction endonucleases are able to locate DNA recognition sites.  Such a mechanism
AB  - involves the initial formation of the DNA, with the subsequent diffusion of the protein along
AB  - the DNA helix until either a recognition site is located or the protein dissociates into
AB  - solution.  Protein translocation may be facilitated by either sliding along the DNA, hopping
AB  - to nearby sites, or intersegment transfer over larger distances.  Previous analyses of the
AB  - manner in which restriction enzymes cleave DNA substrates did rule out the latter mechanism.
AB  - To discriminate between protein sliding or scanning and protein hopping, we designed a unique
AB  - DNA template with three overlapping, mutually exclusive recognition sites for the BssHII
AB  - endonuclease.  Analysis of the cleavage pattern demonstrated efficient usage of both external
AB  - sites, whereas the centrally located site was not efficiently cleaved.  These results confirm
AB  - that linear diffusion of the BssHII enzyme occurs by scanning along the DNA.  Furthermore, the
AB  - scanning enzyme was found to stop and cleave at the first site encountered.  Thus, a sliding
AB  - restriction endonuclease recognizes cleavage sites with high fidelity, without skipping of
AB  - potential sites.
ER  -

TY  - JOUR
AU  - Berkner, K.L.
AU  - Folk, W.R.
TI  - The effects of substituted pyrimidines in DNAs on cleavage by sequence-specific endonucleases.
JO  - J. Biol. Chem.
PY  - 1979
SP  - 2551
EP  - 2560
VL  - 254
AB  - The rates of cleavage of DNAs containing substituents at position 5 of thymine
AB  - or cytosine have been measured for a variety of sequence-specific
AB  - endonucleases, so as to determine which features in the DNA sequence are being
AB  - probed.  Phage PhiE DNA fully substituted with 5-hydroxymethyluracil is cleaved
AB  - more slowly by enzymes whose recognition sequences contain A-T base pairs than
AB  - are DNAs containing thymine, but both types of DNA are cleaved at similar rates
AB  - by enzymes recognizing sequences composed only of G-C base pairs.  Phage PBS2
AB  - DNA with uracil completely substituted for thymine is cleaved slowly by several
AB  - enzymes which recognize sequences containing A-T base pairs (endonucleases
AB  - HpaI, HindII, and HindIII), while the rates of cleavage by other enzymes
AB  - (endonucleases EcoRI and BamHI) are not affected.  Phage lambda- and P22 DNAs
AB  - containing 5-bromouracil are cleaved more slowly by several enzymes
AB  - (endonucleases HindIII, HpaI, BamHI) than are thymine-containing DNAs.  Enzymes
AB  - that recognize sequence isomers with the composition G:C:2A:2T (endonucleases
AB  - EcoRI, HpaI, HindIII) are not equally affected by substitution at position 5 of
AB  - thymine, suggesting that they differ in their contacts with A-T base pairs.
AB  - DNA containing glucosylated 5-hydroxymethylcytosine in place of cytosine is
AB  - resistant to cleavage by all the endonucleases examined.
ER  -

TY  - JOUR
AU  - Berkner, K.L.
AU  - Folk, W.R.
TI  - Overmethylation of DNAs by the EcoRI methylase.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 435
EP  - 450
VL  - 5
AB  - EcoRI methylase is able to catalyze methyl incorporation into DNA at sequences
AB  - other than the canonical EcoRI site.  At high enzyme concentrations and over a
AB  - wide range of pH and ionic strengths, EcoRI methylase modifies polyoma DNA
AB  - (which contains one EcoRI site) at a number of sites.  This modification
AB  - prevents EcoRI endonuclease activity, and thus is presumably at or near the
AB  - EcoRI sequences (5')NAATTN.
ER  -

TY  - JOUR
AU  - Berkner, K.L.
AU  - Folk, W.R.
TI  - EcoRI cleavage and methylation of DNAs containing modified pyrimidines in the recognition sequence.
JO  - J. Biol. Chem.
PY  - 1977
SP  - 3185
EP  - 3193
VL  - 252
AB  - The effects of substituents at position 5 in the pyrimidine ring of a variety
AB  - of phage DNAs upon EcoRI endonuclease and methylase activities have been
AB  - examined.  The replacement of cytidine in DNA with glucosylated
AB  - hydroxymethylcytidine confers resistance to cleavage by the EcoRI endonuclease.
AB  - Substitution of thymidine in DNA by hydroxymethyluridine (a change in the
AB  - methyl at position 5 of thymidine for a hydroxymethyl) lowers the maximal
AB  - velocity of endonucleolytic cleavage 20-fold, but has no detectble effect upon
AB  - the Km.  Substitution of thymidine in DNA by uridine (a change in the methyl at
AB  - position 5 of thymidine for a hydrogen atom) has no effect upon either the
AB  - maximal velocity or the Km.  The effect of these modifications upon EcoRI
AB  - methylase activity was markedly different.  DNA containing glucosylated
AB  - hydroxymethylcytidine is methylated as well as normal DNA.  DNA containing
AB  - uridine or hydroxymethyluridine, in place of thymidine, is much more poorly
AB  - methylated than normal DNA.  These different sensitivities of the EcoRI
AB  - endonuclease and methylase to modifications in the pyrimidine rings of DNA
AB  - suggest there are significant differences in the manner by which these enzymes
AB  - recognize and bind to the canonical EcoRI sequence.
ER  -

TY  - JOUR
AU  - Berkner, K.L.
AU  - Folk, W.R.
TI  - Quantitation of the various termini generated by Type II restriction endonucleases using the polynucleotide kinase exchange reaction.
JO  - J. Biol. Chem.
PY  - 1979
SP  - 2561
EP  - 2564
VL  - 254
AB  - Parameters of the polynucleotide kinase-catalyzed exchange reaction between [gamma32P]ATP and
AB  - 5'-phosphoryl DNAs have been measured with the termini generated by the following
AB  - endonucleases: EcoRI (Berkner, K.L. and Folk, W.R. (1977) J. Biol. Chem. 252:3176-3184),
AB  - HpaII, BamHI, and HindIII (external termini); HindII and HpaI (blunt termini); HaeII and HhaI
AB  - (internal termini). In every case, exchange is reproducible and proportional to the number of
AB  - termini. However, in most cases, the exchange reaction does not proceed to the theoretical
AB  - maximum. External termini and single-stranded DNAs are labeled more rapidly and to
AB  - approximately 5-fold higher levels than blunt or internal termini. Concentrations of 100 to
AB  - 200 micromolar ADP and 12 micromolar ATP are optimal for labeling all types of termini with
AB  - the exchange reaction.
ER  -

TY  - JOUR
AU  - Berkner, K.L.
AU  - Folk, W.R.
TI  - An assay for the rates of cleavage of specific sites in DNA by restriction endonucleases:  Its use to study the cleavage of phage lambda DNA by EcoRI and phage P22 DNA containing thymine or 5-bromouracil by HindIII.
JO  - Anal. Biochem.
PY  - 1983
SP  - 446
EP  - 456
VL  - 129
AB  - A method to measure the rates of cleavage of specific sites in DNAs by restriction
AB  - endonucleases is described.  Partial digests are prepared by incubating DNAs with limiting
AB  - amounts of endonuclease.  The termini generated by cleavage are labeled with 32P by the
AB  - polynucleotide kinase-exchange reaction.  The labeled termini are then identified by
AB  - completing the digestion with the same endonuclease and separating the products by gel
AB  - electrophoresis. As the products of complete digestion of DNA are often easily separated and
AB  - can be unequivocally identified, this procedure permits comparison of the rates of cleavage of
AB  - specific sites in DNAs:  furthermore, because detection of the products of cleavage utilizes
AB  - radioautography and does not depend upon their size, or amount, only small amounts of DNA need
AB  - to be utilized.  This method has been used to examine the cleavage of phgae lambda DNA by
AB  - EcoRI endonuclease, and to demonstrate that 5-bromouracil substitution in phage P22 DNA
AB  - reduces the rate of cleavage of most sites by HindIII endonuclease approximately threefold and
AB  - the rate of cleavage of one site approximately tenfold.
ER  -

TY  - JOUR
AU  - Berkyurek, A.C.
AU  - Suetake, I.
AU  - Arita, K.
AU  - Takeshita, K.
AU  - Nakagawa, A.
AU  - Shirakawa, M.
AU  - Tajima, S.
TI  - The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA.
JO  - J. Biol. Chem.
PY  - 2014
SP  - 379
EP  - 386
VL  - 289
AB  - Dnmt1 is responsible for the maintenance DNA methylation during replication to propagate
AB  - methylation patterns to the next generation. The replication foci targeting sequence (RFTS),
AB  - which plugs the catalytic pocket, is necessary for recruitment of Dnmt1 to the replication
AB  - site. In the present study we found that the DNA methylation activity of Dnmt1 was DNA
AB  - length-dependent and scarcely methylated 12-bp short hemi-methylated DNA. Contrarily, the
AB  - RFTS-deleted Dnmt1 and Dnmt1 mutants that destroyed th hydrogen bonds between the RFTS and
AB  - catalytic domain showed significant DNA methylation activity even toward 12-bp hemi-methylated
AB  - DNA. The DNA methylation activity of the RFTS-deleted Dnmt1 toward 12-bp hemi-methylated DNA
AB  - was strongly inhibited on the addition of RFTS, but to a lesser extent by Dnmt1 harboring the
AB  - mutations that impair the hydrogen bond formation. The SRA domain of Uhrf1, which is a
AB  - prerequisite factor for maintenance methylation and selectively binds to hemi-methylated DNA,
AB  - stimulated  the DNA methylation activity of Dnmt1. The SRA to Dnmt1 concentration ratio was
AB  - the determinant for the maximum stimulation. In addition, a mutant SRA, which had lost the DNA
AB  - binding activity but was able to bind to Dnmt1, stimulated the DNA methylation activity of
AB  - Dnmt1. The results indicate that the DNA methylation activity of Dnmt1 was stimulated on the
AB  - direct interaction of the SRA and Dnmt1. The SRA facilitated acceptance of the 12-bp
AB  - fluorocytosine-containing DNA by the catalytic center. We propose t hat the SRA removes the
AB  - RFTS plug from the catalytic pocket to facilitate DNA acceptance by the catalytic center.
ER  -

TY  - JOUR
AU  - Berland, J.L.
AU  - de Carvalho, F.M.
AU  - de Almeida, L.G.
AU  - Bablishvili, N.
AU  - Gauthier, M.
AU  - Paranhos-Baccala, G.
AU  - de Vasconcelos, A.T.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain G-12-005.
JO  - Genome Announcements
PY  - 2014
SP  - e00385
EP  - e00314
VL  - 2
AB  - Infection caused by drug-resistant Mycobacterium tuberculosis is a growing concern, especially
AB  - in eastern Europe. We report an annotated draft genome
AB  - sequence of M. tuberculosis strain G-12-005 obtained from a patient in Georgia.
ER  -

TY  - JOUR
AU  - Berlin, Y.A.
AU  - Butkus, V.V.
TI  - Synthesis of oligodeoxynucleotides containing the sequence GGTACC and their interaction with KpnI restriction endonuclease.
JO  - Bioorg. Khim.
PY  - 1981
SP  - 1224
EP  - 1232
VL  - 7
AB  - It has been shown that in the phosphotriester synthesis of
AB  - oligodeoxynucleotides the simultaneous use of a dimethoxytrityl and a levulinyl
AB  - residue to protect the 5'-OH and 3'-OH, respectively, permits the growth of the
AB  - oligonucleotide chain in both directions: 3' 5 5' and 5' 5 3'.  Using this
AB  - approach, the oligodeoxynucleotides GGTACC, GGTACCGG, CCGGTACC, and CCGGTACCGG
AB  - containing the recognition site for KpnI restriction endonuclease have been
AB  - synthesized.  In a study of their interaction with this restrictase it has been
AB  - found that for the normal functioning of the enzyme the GGTACC site in its
AB  - substrate must be flanked in both chains from the 5'-end and in at least one
AB  - chain from the 3'-end.
ER  -

TY  - JOUR
AU  - Berna, L.
AU  - Iraola, G.
AU  - Greif, G.
AU  - Coitinho, C.
AU  - Rivas, C.M.
AU  - Naya, H.
AU  - Robello, C.
TI  - Whole-Genome Sequencing of an Isoniazid-Resistant Clinical Isolate of Mycobacterium tuberculosis Strain MtURU-002 from Uruguay.
JO  - Genome Announcements
PY  - 2014
SP  - e00655
EP  - e00614
VL  - 2
AB  - The incidence of tuberculosis in Uruguay has been effectively reduced to <30 per  100,000
AB  - population, although an increase in nonrisk populations in the last few
AB  - years is evident. Here, we present the genome sequence of Mycobacterium
AB  - tuberculosis strain MtURU-002 isolated from a patient showing bilateral pulmonary
AB  - tuberculosis that was resistant to isoniazid.
ER  -

TY  - JOUR
AU  - Bernacchia, G.
AU  - Para, A.
AU  - Pedrali-Noy, G.
AU  - Cella, R.
TI  - Isolation of a cDNA coding for DNA (cytosine-5)-methyltransferase (Accession No. AJ002140) from Lycopersicon esculentum.
JO  - Plant Physiol.
PY  - 1998
SP  - 446
EP  - 446
VL  - 116
ER  -

TY  - JOUR
AU  - Bernacchia, G.
AU  - Primo, A.
AU  - Giorgetti, L.
AU  - Pitto, L.
AU  - Cella, R.
TI  - Carrot DNA-methyltransferase is encoded by two classes of genes with differing patterns of expression.
JO  - Plant J.
PY  - 1998
SP  - 317
EP  - 329
VL  - 13
AB  - In the present study, the isolation and characterization of two distinct cDNAs that code for
AB  - carrot DNA (cytosine-5)-methyltransferase (DNA-METase) are reported.  The screening of a cDNA
AB  - library with a carrot genomic DNA fragment, previously obtained by PCR using degenerate
AB  - primers, has led to the isolation of clones that belong to two distinct classes of genes (Met1
AB  - and Met2) which differ in sequence and size.  Met1-5 and Met2-21 derived amino acid sequences
AB  - are more than 85% identical for most of the polypeptide and completely diverge at the
AB  - N-terminus.  The larger size of the Met2-21 cDNA is due to the presence of nearly perfect
AB  - fivefold repeat of a 171 bp sequence present only once in the Met1-5 cDNA.  Northern  and in
AB  - situ hybridization analyses with young carrot plants and somatic embryos indicate that both
AB  - genes are maximally expressed in proliferating cells (suspension cells, meri-stems and leaf
AB  - primordia), but differ quantitatively and spatially in their mode of expression.  Polyclonal
AB  - antibodies were raised in rabbit using fusion proteins corresponding to the regulatory and
AB  - catalytic regions of the most highly expressed gene (Met1-5).  In nuclear carrot extracts,
AB  - both antibodies were found to recognize a band of about 200 kDa along with some additional
AB  - bands of lower size.  These results provide the first direct demonstration that DNA-METases of
AB  - a higher eukaryote are encoded by a gene family.
ER  -

TY  - JOUR
AU  - Bernal, J.F.
AU  - Donado-Godoy, P.
AU  - Arevalo, A.
AU  - Duarte, C.
AU  - Realpe, M.E.
AU  - Diaz, P.L.
AU  - Gomez, Y.
AU  - Rodriguez, F.
AU  - Agarwala, R.
AU  - Landsman, D.
AU  - Marino-Ramirez, L.
TI  - Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain.
JO  - Genome Announcements
PY  - 2016
SP  - e00130
EP  - e00116
VL  - 4
AB  - Campylobacter coli is considered one of the main causes of food-borne illness worldwide. We
AB  - report here the whole-genome sequence of multidrug-resistant
AB  - Campylobacter coli strain COL B1-266, isolated from the Colombian poultry chain.
AB  - The genome sequences encode genes for a variety of antimicrobial resistance
AB  - genes, including aminoglycosides, beta-lactams, lincosamides, fluoroquinolones,
AB  - and tetracyclines.
ER  -

TY  - JOUR
AU  - Bernal, J.F.
AU  - Donado-Godoy, P.
AU  - Valencia, M.F.
AU  - Leon, M.
AU  - Gomez, Y.
AU  - Rodriguez, F.
AU  - Agarwala, R.
AU  - Landsman, D.
AU  - Marino-Ramirez, L.
TI  - Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial  Resistance Monitoring Program in Colombia.
JO  - Genome Announcements
PY  - 2016
SP  - e00131
EP  - e00116
VL  - 4
AB  - Campylobacter coli, along with Campylobacter jejuni, is a major agent of gastroenteritis and
AB  - acute enterocolitis in humans. We report the whole-genome
AB  - sequences of two multidrug-resistance C. coli strains, isolated from the
AB  - Colombian poultry chain. The isolates contain a variety of antimicrobial
AB  - resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and
AB  - tetracycline.
ER  -

TY  - JOUR
AU  - Bernal, W.M.
AU  - Raven, N.D.H.
AU  - Williams, R.A.D.
TI  - Restriction endonuclease from Thermus ruber.
JO  - Proceedings 14th Int. Congress Microbiol.
PY  - 1986
SP  - 204
EP  - 204
VL  - 0
AB  - Chromosomal DNA purified from some strains ascribed to the genus Thermus were
AB  - digestable by restriction endonuclease TaqI, indicating that these strains do
AB  - not possess the TaqI restriction-modification system.  These strains were
AB  - tested for the possession of restriction enzymes with potentially novel sites
AB  - of recognition and cleavage.  Thermus ruber BKMB-1258 has a restriction enzyme
AB  - designated TruI, which was separated from other nucleases by phosphocellulose
AB  - column chromatography.  From digestion patterns of DNA from bacteriophage
AB  - lambda and phiX174 RF, and plasmids pBR322 and pAT153, the recognition sequence
AB  - of TruI was identified as GG(A/T)CC, which is the same as for AvaII.  This was
AB  - confirmed by TruI-AvaII double digests.
ER  -

TY  - JOUR
AU  - Bernal-Bayard, J.
AU  - Gomez-Valero, L.
AU  - Wessel, A.
AU  - Khanna, V.
AU  - Bouchier, C.
AU  - Ghigo, J.M.
TI  - Short genome report of cellulose-producing commensal Escherichia coli 1094.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 13
EP  - 13
VL  - 13
AB  - Bacterial surface colonization and biofilm formation often rely on the production of an
AB  - extracellular polymeric matrix that mediates cell-cell and cell-surface
AB  - contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria
AB  - cellulose is often the main component of the extracellular matrix. Here we report
AB  - the complete genome sequence of the cellulose producing strain E. coli 1094 and
AB  - compare it with five other closely related genomes within E. coli phylogenetic
AB  - group A. We present a comparative analysis of the regions encoding genes
AB  - responsible for cellulose biosynthesis and discuss the changes that could have
AB  - led to the loss of this important adaptive advantage in several E. coli strains.
AB  - Data deposition: The annotated genome sequence has been deposited at the European
AB  - Nucleotide Archive under the accession number PRJEB21000.
ER  -

TY  - JOUR
AU  - Bernan, V.
AU  - Sznyter, L.A.
AU  - Vaccaro, C.M.
AU  - Jager-Quinton, T.
AU  - Wilson, G.
AU  - Brooks, J.E.
TI  - Cloning and characterization of the SphI restriction-modification system from S. phaeochromogenes.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 206
EP  - 206
VL  - 89
AB  - SphI, a Type II restriction-modification system from the actinomycete
AB  - Streptomyces phaeochromogenes, recognizes the sequence GCATGC.  The
AB  - endonuclease cleaves at GCATG^C leaving a 3'four base overhang.  A 5.4kb insert
AB  - carrying the methylase gene has been cloned into the PstI site of pBR322 and
AB  - expressed in E. coli at a low level as evidenced by incomplete modification of
AB  - chromosomal DNA and lack of modification of phage DNA in vivo.  The clone has
AB  - no endonuclease activity.  The plasmid has been extensively mapped; deletion
AB  - subcloning has been used to locate the methylase gene.  The entire 5.4kb
AB  - methylase fragment has also been cloned into the Streptomyces promoter-probe
AB  - plasmids, pIJ486 and pIJ487 and the low copy Streptomyces vector, pIJ922.
AB  - Expression of the SphI methylase gene will be discussed.
ER  -

TY  - JOUR
AU  - Berndt, C.
AU  - Meier, P.
AU  - Wackernagel, W.
TI  - DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300.
JO  - Microbiology
PY  - 2003
SP  - 895
EP  - 901
VL  - 149
AB  - Natural transformation is a mechanism for intra- and interspecific transfer of chromosomal DNA
AB  - in Pseudomonas stutzeri. During this process a
AB  - single strand derived from duplex DNA is transported into the cytoplasm
AB  - and recombined with resident DNA. By electroporation, which introduces
AB  - duplex DNA into cells, 100-fold lower transformation frequencies of P.
AB  - stutzeri JM300 were observed with shuttle vector or broad-host-range
AB  - plasmid DNA when the plasmids had replicated in Escherichia coli and not
AB  - in P. stutzeri JM300. Moreover, the natural transformation with cloned
AB  - chromosomal P. stutzeri JM300 DNA was reduced about 40-fold when the DNA
AB  - had not been propagated in P. stutzeri JM300 but in E. coli. Restriction
AB  - was also active during natural transformation by single-stranded DNA.
AB  - Restriction during natural transformation and electroporation was
AB  - abolished in mutants isolated from mutagenized JM300 cells after applying
AB  - a multiple plasmid electroporation strategy for the enrichment of
AB  - restriction-defective strains. The mutants had retained the ability for
AB  - DNA modification. The P. stutzeri strain ATCC 17587 was found to have no
AB  - restriction-modification system as seen in JM300. It is discussed whether
AB  - restriction during natural transformation acts at presynaptic or
AB  - postsynaptic stages of transforming DNA. Restriction as a barrier to
AB  - transformation apparently contributes to sexual isolation and therefore
AB  - may promote speciation in the highly diverse species P. stutzeri.
ER  -

TY  - JOUR
AU  - Bernick, D.L.
AU  - Karplus, K.
AU  - Lui, L.M.
AU  - Coker, J.K.
AU  - Murphy, J.N.
AU  - Chan, P.P.
AU  - Cozen, A.E.
AU  - Lowe, T.M.
TI  - Complete genome sequence of Pyrobaculum oguniense.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 336
EP  - 345
VL  - 6
AB  - Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot
AB  - spring in Japan. Here we describe its main chromosome of 2,436,033 bp,
AB  - with three large-scale inversions and an extra-chromosomal element of 16,887 bp.
AB  - We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome,
AB  - including nine H/ACA-like small RNA, 83 predicted C/D box small RNA, and 47
AB  - transfer RNA genes. Comparative analyses with the closest known relative, the
AB  - anaerobe Pyrobaculum arsenaticum from Italy, reveals unexpectedly high synteny
AB  - and nucleotide identity between these two geographically distant species. Deep
AB  - sequencing of a mixture of genomic DNA from multiple cells has illuminated some
AB  - of the genome dynamics potentially shared with other species in this genus.
ER  -

TY  - JOUR
AU  - Bernier, A.M.
AU  - Bernard, K.
TI  - Draft Genome Sequences of Microbacterium hominis LCDC-84-0209T Isolated from a Human Lung Aspirate and Microbacterium laevaniformans LCDC 91-0039 Isolated from   a Human Blood Culture.
JO  - Genome Announcements
PY  - 2016
SP  - e00989
EP  - e00916
VL  - 4
AB  - Draft genomes for Microbacterium hominis 84-0209(T) and M. laevaniformans 91-0039 were
AB  - studied. Genome sizes (bps, [G+C contents]) were 3,506,522 (70.96%) and
AB  - 2,999,965 (69.51%), respectively. Annotation revealed: (M. hominis) three rRNA
AB  - sequences, 45 tRNA genes, and 3,218 coding sequences; (M. laevaniformans) three
AB  - rRNA sequences, 49 tRNA genes, and 2,874 coding sequences.
ER  -

TY  - JOUR
AU  - Bernier, A.M.
AU  - Bernard, K.
TI  - Draft Genome Sequence of Trueperella bernardiae LCDC 89-0504T, Isolated from a Human Blood Culture.
JO  - Genome Announcements
PY  - 2016
SP  - e01634
EP  - e01615
VL  - 4
AB  - We report here the draft genome sequence of Trueperella bernardiae LCDC 89-0504(T), an
AB  - organism linked to mild to severe infections in humans and
AB  - animals. The genome size is 2,028,874 bp, with a G+C content of 65.44%.
AB  - Annotation of the genome revealed 5 rRNA sequences, 48 tRNA genes, and 1,762
AB  - coding sequences.
ER  -

TY  - JOUR
AU  - Bernier, A.M.
AU  - Bernard, K.
TI  - Draft Genome Sequence for the Type Strain of Corynebacterium afermentans LCDC 88-0199T, Isolated from a Human Blood Culture.
JO  - Genome Announcements
PY  - 2016
SP  - e00661
EP  - e00616
VL  - 4
AB  - A draft genome for Corynebacterium afermentans LCDC 88-0199(T) was investigated.  The size of
AB  - the genome was 2,345,615 bp with an observed G+C content of 64.85%.
AB  - Annotation revealed 2 rRNA sequences, 54 tRNA genes, and 2,164 coding sequences.
AB  - Genome coverage was 85x and consisted of 24 contigs with an N50 of 187,988 bp.
ER  -

TY  - JOUR
AU  - Bernier, A.M.
AU  - Peters, G.A.
AU  - Bernard, K.
TI  - Whole-Genome Sequences of Four Corynebacterium CDC Group F-1 Strains Isolated from Urine.
JO  - Genome Announcements
PY  - 2017
SP  - e01537
EP  - e01516
VL  - 5
AB  - Three draft and one complete genome sequence from strains isolated from urine and consistent
AB  - with Corynebacterium CDC group F-1 were assembled and studied. Genome
AB  - sizes ranged between 2.3 and 2.44 Mb, with G+C content between 60.4% and 60.7%.
ER  -

TY  - JOUR
AU  - Bernstein, R.L.
AU  - Dharmgrongartama, B.
AU  - Srinivasan, P.R.
TI  - Altered P2 bacteriophage restriction in E. coli B.
JO  - Fed. Proc.
PY  - 1970
SP  - 860
EP  - 860
VL  - 29
AB  - P2 phage grown on E. coli C (P2.C) grows very well in E. coli C but is highly
AB  - restricted in E. coli B.  The plating efficiences of P2.C with E. coli C and E.
AB  - coli B grown in nutrient broth are of the order of 1 and 10-7, respectively.
AB  - This retriction can be altered by changing the growth conditions of E. coli B.
AB  - Thus growth on salts-glucose medium gives a 100-fold increase in plating
AB  - efficiency compared to cultures grown in enriched broth.  When E. coli B is
AB  - grown in salts-glucose medium supplemented with amino acids, purines,
AB  - pyrimidines, and vitamins, the higher P2.C plating efficiencies are found only
AB  - with those cultures not supplemented with methionine.  Conditions which lead to
AB  - the depletion of intracellular methionine or S-adenosylmethionine in the
AB  - prototrophic E. coli B further increase the P2.C plating efficiencies.  Plating
AB  - efficiency can also be raised by infection with T3 phage.  However, infection
AB  - with T3 mutants unable to produce the T3-specific early enzyme which cleaves
AB  - S-adenosylmethionine does not alter the plating efficiency.  These results
AB  - suggest that S-adenosylmethionine is involved in the mechanism of restriction
AB  - of P2 phage.
ER  -

TY  - JOUR
AU  - Bertalan, M. et al.
TI  - Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5.
JO  - BMC Genomics
PY  - 2009
SP  - 450
EP  - 450
VL  - 10
AB  - BACKGROUND: Gluconacetobacter diazotrophicus Pal5 is an endophytic diazotrophic bacterium that
AB  - lives in association with sugarcane plants. It has important
AB  - biotechnological features such as nitrogen fixation, plant growth promotion,
AB  - sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the
AB  - occurrence of bacteriocins. RESULTS: Gluconacetobacter diazotrophicus Pal5 is the
AB  - third diazotrophic endophytic bacterium to be completely sequenced. Its genome is
AB  - composed of a 3.9 Mb chromosome and 2 plasmids of 16.6 and 38.8 kb, respectively.
AB  - We annotated 3,938 coding sequences which reveal several characteristics related
AB  - to the endophytic lifestyle such as nitrogen fixation, plant growth promotion,
AB  - sugar metabolism, transport systems, synthesis of auxin and the occurrence of
AB  - bacteriocins. Genomic analysis identified a core component of 894 genes shared
AB  - with phylogenetically related bacteria. Gene clusters for gum-like polysaccharide
AB  - biosynthesis, tad pilus, quorum sensing, for modulation of plant growth by indole
AB  - acetic acid and mechanisms involved in tolerance to acidic conditions were
AB  - identified and may be related to the sugarcane endophytic and plant-growth
AB  - promoting traits of G. diazotrophicus. An accessory component of at least 851
AB  - genes distributed in genome islands was identified, and was most likely acquired
AB  - by horizontal gene transfer. This portion of the genome has likely contributed to
AB  - adaptation to the plant habitat. CONCLUSION: The genome data offer an important
AB  - resource of information that can be used to manipulate plant/bacterium
AB  - interactions with the aim of improving sugarcane crop production and other
AB  - biotechnological applications.
ER  -

TY  - JOUR
AU  - Bertani, G.
AU  - Bassi, D.
AU  - Gatti, M.
AU  - Cocconcelli, P.S.
AU  - Neviani, E.
TI  - Draft Genome Sequence of Lactobacillus helveticus Strain Lh 12 Isolated from Natural Whey Starter.
JO  - Genome Announcements
PY  - 2018
SP  - e00139
EP  - e00118
VL  - 6
AB  - Lactobacillus helveticus is a lactic acid bacterium widely used in cheese-making  and for the
AB  - production of bioactive peptides from milk proteins. Here, we
AB  - describe the draft genome sequence and annotation of L. helveticus strain Lh 12
AB  - isolated from natural whey starter used in the production of Grana Padano cheese.
ER  -

TY  - JOUR
AU  - Bertani, G.
AU  - Weigle, J.J.
TI  - Host controlled variation in bacterial viruses.
JO  - J. Bacteriol.
PY  - 1953
SP  - 113
EP  - 121
VL  - 65
AB  - Passage through new hosts or new tissues is a widely used method for altering
AB  - the properties of viruses.  In some instances selection of spontaneous mutants
AB  - has been demonstrated to be the mechanism causing the variation (Luria, 1945).
AB  - Nonhereditary mechanisms sometimes have been postulated, but since no such case
AB  - has been analyzed sufficiently, it is often assumed that selection of mutants
AB  - is the only possible mechanism.  A detailed analysis of two cases of variation
AB  - in two different bacterial viruses is reported in this paper.  In both these
AB  - cases we are dealing with nonheritable alterations stemming directly from
AB  - passage through a new host and not with mutations.  A somewhat similar case of
AB  - host controlled variation involving other bacterial viruses has been reported
AB  - recently by Luria and Human (1952).
ER  -

TY  - JOUR
AU  - Bertani, I.
AU  - Passos-da-Silva, D.
AU  - Abbruscato, P.
AU  - Piffanelli, P.
AU  - Venturi, V.
TI  - Draft Genome Sequence of the Plant Pathogen Dickeya zeae DZ2Q, Isolated from Rice in Italy.
JO  - Genome Announcements
PY  - 2013
SP  - e00905
EP  - e00913
VL  - 1
AB  - Dickeya zeae is an emerging rice (Oryza sativa) pathogen causing bacterial foot rot. Related
AB  - pathogens affect maize (Zea mays) and potato (Solanum tuberosum) and
AB  - a variety of important ornamental and floral plants. Here, we present the draft
AB  - genome sequence of D. zeae DZ2Q, an isolate obtained from rice grown in Italy.
ER  -

TY  - JOUR
AU  - Bertelli, C.
AU  - Collyn, F.
AU  - Croxatto, A.
AU  - Ruckert, C.
AU  - Polkinghorne, A.
AU  - Kebbi-Beghdadi, C.
AU  - Goesmann, A.
AU  - Vaughan, L.
AU  - Greub, G.
TI  - The Waddlia Genome: A Window into Chlamydial Biology.
JO  - PLoS ONE
PY  - 2010
SP  - e10890
EP  - e10890
VL  - 5
AB  - Growing evidence suggests that a novel member of the Chlamydiales order, Waddlia chondrophila,
AB  - is a potential agent of miscarriage in humans and abortion in ruminants. Due to the lack of
AB  - genetic tools to manipulate chlamydia, genomic analysis is proving to be the most incisive
AB  - tool in stimulating investigations into the biology of these obligate intracellular
AB  - bacteria. 454/Roche and Solexa/Illumina technologies were thus used to sequence and assemble
AB  - de novo the full genome of the first representative of the Waddliaceae family, W.
AB  - chondrophila. The bacteria possesses a 291169312bp chromosome and a 159593 bp low-copy number
AB  - plasmid that might integrate into the bacterial chromosome. The Waddlia genome displays
AB  - numerous repeated sequences indicating different genome dynamics from classical chlamydia
AB  - which almost completely lack repetitive elements. Moreover, W. chondrophila exhibits many
AB  - virulence factors also present in classical chlamydia, including a functional type III
AB  - secretion system, but also a large complement of specific factors for resistance to host or
AB  - environmental stresses. Large families of outer membrane proteins were identified indicating
AB  - that these highly immunogenic proteins are not Chlamydiaceae specific and might have been
AB  - present in their last common ancestor.  Enhanced metabolic capability for the synthesis of
AB  - nucleotides, amino acids, lipids and other co-factors suggests that the common ancestor of the
AB  - modern Chlamydiales may have been less dependent on their eukaryotic host. The fine-detailed
AB  - analysis of biosynthetic pathways brings us closer to possibly developing a synthetic medium
AB  - to grow W. chondrophila, a critical step in the development of genetic tools. As a whole, the
AB  - availability of the W. chondrophila genome opens new possibilities in Chlamydiales research,
AB  - providing new insights into the evolution of members of the order Chlamydiales and the biology
AB  - of the Waddliaceae.
ER  -

TY  - JOUR
AU  - Bertelli, C.
AU  - Goesmann, A.
AU  - Greub, G.
TI  - Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance.
JO  - Genome Announcements
PY  - 2014
SP  - e00949
EP  - e00914
VL  - 2
AB  - Criblamydia sequanensis is an amoeba-resisting bacterium recently isolated from the Seine
AB  - River. This Chlamydia-related bacterium harbors a genome of
AB  - approximately 3 Mbp and a megaplasmid of 89,525 bp. The plasmid encodes several
AB  - efflux systems and an operon for arsenite resistance. This first genome sequence
AB  - within the Criblamydiaceae family enlarges our view on the evolution and the
AB  - ecology of this important bacterial clade largely understudied so far.
ER  -

TY  - JOUR
AU  - Bertinuson, A.
AU  - Illingworth, C.A.
AU  - Otto, C.J.
AU  - Hornemann, U.
TI  - An apparently restriction deficient mutant of Streptomyces achromogenes var streptozoticus can be transformed by plasmid pIJ350.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1984
SP  - H74
EP  - H74
VL  - 84
AB  - We have isolated a mutant of S. achromogenes var streptozoticus (SAS) which
AB  - differed from wild type in respect to digestion of chromosomal DNA by NaeI and
AB  - susceptibility to phage infection.  While DNA of SAS was resistant to digestion
AB  - by NaeI, the DNA of mutant AB301 was NaeI-sensitive.  We found that AB301 could
AB  - be infected by 4 phages to which wild type SAS was resistant.  We were able to
AB  - transform AB301 with plasmid pIJ350 (confirmed by mini-prepping transformants),
AB  - although we had never successfully transformed wild type SAS with this or any
AB  - other plasmid.  The DNA of pIJ 350 and phages PhiCC 53, PhiCC 55, and PhiCC 57
AB  - was cut by NaeI, but that of phage PhiCC 26 was not.  We suggest that
AB  - restriction by NaeI is one barrier to transformation in SAS and that loss of
AB  - this barrier (and additional possible restriction barriers) contributed to the
AB  - successful transformation of this previously recalcitrant species.
ER  -

TY  - JOUR
AU  - Bertolini, C.
AU  - van Aerle, R.
AU  - Lampis, S.
AU  - Moore, K.A.
AU  - Paszkiewicz, K.
AU  - Butler, C.S.
AU  - Vallini, G.
AU  - van der Giezen, M.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e00331
EP  - e00314
VL  - 2
AB  - Stenotrophomonas maltophilia strain SeITE02 was isolated from the rhizosphere of  the
AB  - selenium-hyperaccumulating legume Astragalus bisculcatus. In this report, we
AB  - provide the 4.56-Mb draft genome sequence of S. maltophilia SeITE02, a
AB  - gammaproteobacterium that can withstand high concentrations of selenite and
AB  - reduce these to elemental selenium.
ER  -

TY  - JOUR
AU  - Bertschinger, J.
AU  - Neri, D.
TI  - Covalent DNA display as a novel tool for directed evolution of proteins in vitro.
JO  - Protein Eng. Des. Sel.
PY  - 2004
SP  - 699
EP  - 707
VL  - 17
AB  - We present a novel method for the directed evolution of polypeptides, which combines in vitro
AB  - compartmentalization and covalent DNA display. A
AB  - library of linear DNA fragments is co-packaged with an in vitro
AB  - transcription/translation mixture in the compartments of a water-in-oil
AB  - emulsion. Experimental conditions are adjusted so that, in most cases, one
AB  - compartment contains one DNA molecule. The DNA fragments encode fusion
AB  - proteins containing a DNA-methyltransferase (M.Hae III), which can form a
AB  - covalent bond with a 5-fluorodeoxycytidine base at the extremity of the
AB  - DNA fragment. The resulting library of DNA-protein fusions is extracted
AB  - from the emulsion and DNA molecules displaying a protein with desired
AB  - binding properties are selected from the pool of DNA-protein fusions by
AB  - affinity panning on target antigens. We applied this methodology in model
AB  - selection experiments, using specific ligands for the capture of peptides
AB  - and globular proteins bound to DNA. We observed enrichment factors
AB  - >1000-fold for selections performed in separate emulsions and up to
AB  - 150-fold for selections performed using mixtures of DNA molecules. M.Hae
AB  - III could be fused to small globular proteins (such as calmodulin and
AB  - fibronectin domains), which are ideally suited for the generation of
AB  - combinatorial libraries and for the isolation of novel binding
AB  - specificities.
ER  -

TY  - JOUR
AU  - Bertuzzi, A.S.
AU  - Guinane, C.M.
AU  - Crispie, F.
AU  - Kilcawley, K.N.
AU  - McSweeney, P.L.H.
AU  - Rea, M.C.
TI  - Genome Sequence of Staphylococcus saprophyticus DPC5671, a Strain Isolated from Cheddar Cheese.
JO  - Genome Announcements
PY  - 2017
SP  - e00193
EP  - e00117
VL  - 5
AB  - The draft genome sequence of Staphylococcus saprophyticus DPC5671, isolated from  cheddar
AB  - cheese, was determined. S. saprophyticus is a common Gram-positive
AB  - bacterium detected on the surface of smear-ripened cheese and other fermented
AB  - foods.
ER  -

TY  - JOUR
AU  - Berube, P.M. et al.
TI  - Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.
JO  - Sci. Data
PY  - 2018
SP  - 180154
EP  - 180154
VL  - 5
AB  - Prochlorococcus and Synechococcus are the dominant primary producers in marine
AB  - ecosystems and perform a significant fraction of ocean carbon fixation. These
AB  - cyanobacteria interact with a diverse microbial community that coexists with
AB  - them. Comparative genomics of cultivated isolates has helped address questions
AB  - regarding patterns of evolution and diversity among microbes, but the fraction
AB  - that can be cultivated is miniscule compared to the diversity in the wild. To
AB  - further probe the diversity of these groups and extend the utility of reference
AB  - sequence databases, we report a data set of single cell genomes for 489
AB  - Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190
AB  - additional microorganisms from a diverse range of bacterial, archaeal, and viral
AB  - groups. Many of these uncultivated single cell genomes are derived from samples
AB  - obtained on GEOTRACES cruises and at well-studied oceanographic stations, each
AB  - with extensive suites of physical, chemical, and biological measurements. The
AB  - genomic data reported here greatly increases the number of available
AB  - Prochlorococcus genomes and will facilitate studies on evolutionary biology,
AB  - microbial ecology, and biological oceanography.
ER  -

TY  - JOUR
AU  - Besaury, L.
AU  - Amato, P.
AU  - Sancelme, M.
AU  - Delort, A.M.
TI  - Draft Genome Sequence of Pseudomonas syringae PDD-32b-74, a Model Strain for Ice-Nucleation Studies in the Atmosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e00742
EP  - e00717
VL  - 5
AB  - We report here the whole genome sequence of Pseudomonas syringae PDD-32b-74, a
AB  - gammaproteobacterium isolated from cloud water. This microorganism is equipped
AB  - with ice-nucleation protein and biosurfactant genes that could potentially be
AB  - involved in physicochemical processes in the atmosphere and clouds.
ER  -

TY  - JOUR
AU  - Besaury, L.
AU  - Amato, P.
AU  - Wirgot, N.
AU  - Sancelme, M.
AU  - Delort, A.M.
TI  - Draft Genome Sequence of Pseudomonas graminis PDD-13b-3, a Model Strain Isolated  from Cloud Water.
JO  - Genome Announcements
PY  - 2017
SP  - e00464
EP  - e00417
VL  - 5
AB  - The whole genome of Pseudomonas graminis PDD-13b-3, a strain of bacteria isolated from cloud
AB  - water, was sequenced. This showed that this microorganism is equipped
AB  - with genes that could potentially be involved in its survival in the atmosphere
AB  - and clouds: those for oxidative stress and carbon starvation responses, DNA
AB  - repair, and iron uptake.
ER  -

TY  - JOUR
AU  - Besnier, C.E.
AU  - Kong, H.
TI  - Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state.
JO  - EMBO Rep.
PY  - 2001
SP  - 782
EP  - 786
VL  - 2
AB  - N.Bst NBI is a nicking endonuclease that recognizes the sequence GAGTC and nicks one DNA
AB  - strand specifically. The Type IIs endonuclease, Mly I, also recognizes GAGTC, but cleaves both
AB  - DNA strands. Sequence comparisons revealed significant similarities between N.Bst NBI and Mly
AB  - I. Previous studies showed that Mly I dimerizes in the presence of a cognate DNA, whereas
AB  - N.Bst NBI remains a monomer. This suggests that dimerization may be required for
AB  - double-stranded cleavage. To test this hypothesis, we used a multiple alignment to design
AB  - mutations to disrupt the dimerization function of Mly I. When Tyr491 and Lys494 were both
AB  - changed to alanine, the mutated endonuclease, N.Mly I, no longer formed a dimer and cleaved
AB  - only one DNA strand specifically. Thus, we have shown that changing the oligomerization state
AB  - of an enzyme changes its enzymatic function. This experiment also established a protocol that
AB  - could be applied to other Type IIs endonucleases in order to generate more novel nicking
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Bessen, D.E.
AU  - Kumar, N.
AU  - Hall, G.S.
AU  - Riley, D.R.
AU  - Luo, F.
AU  - Lizano, S.
AU  - Ford, C.N.
AU  - McShan, W.M.
AU  - Nguyen, S.V.
AU  - Dunning-Hotopp, J.C.
AU  - Tettelin, H.
TI  - Whole Genome Association Study on Tissue Tropism Phenotypes in Group A Streptococcus.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6651
EP  - 6663
VL  - 193
AB  - Group A Streptococcus (GAS) has a rich evolutionary history of horizontal transfer among its
AB  - core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological
AB  - phenotypes. To further our understanding of the molecular basis for ecological phenotypes,
AB  - comparative genomic hybridization of a set of 97 diverse strains to a GAS pan-genome
AB  - microarray was undertaken, and the association of accessory genes with emm genotypes that
AB  - define tissue tropisms for infection was determined. Of the 22 non-prophage, accessory gene
AB  - regions (AGRs) identified, only three AGRs account for all statistically significant linkage
AB  - disequilibrium among strains having the genotypic biomarkers for throat versus skin infection
AB  - specialist. Networked evolution and population structure analysis of loci representing each of
AB  - the AGRs reveals that most strains with the skin specialist and generalist biomarkers form
AB  - discrete clusters, whereas strains with the throat specialist biomarker are highly diverse. To
AB  - identify co-inherited and co-selected accessory genes, the strength of genetic associations
AB  - was determined for all possible pair wise combinations of accessory genes among the 97 GAS
AB  - strains. Accessory genes showing very strong associations provide the basis for an
AB  - evolutionary model, which reveals that a major transition between many throat and skin
AB  - specialist haplotypes correlates with the gain or loss of genes encoding fibronectin-binding
AB  - proteins. This study employs a novel synthesis of tools to help delineate the major genetic
AB  - changes associated with key adaptive shifts in an extensively recombined bacterial species.
ER  -

TY  - JOUR
AU  - Bestor, T.
TI  - Structure of mammalian DNA methyltransferase as deduced from the inferred amino acid sequence and direct studies of the protein.
JO  - Biochem. Soc. Trans.
PY  - 1988
SP  - 944
EP  - 947
VL  - 16
AB  - DNA (cytosine-5)-methyltransferase establishes and maintains methylation patterns in the
AB  - genome of higher eukaryotes.  This enzyme has been purified, and the cDNA which encodes it has
AB  - been cloned and sequenced.  DNA MeTase appears to contain a large (1000 amino acid) N-terminal
AB  - domain that contains potential metal-binding sites.  This domain appears to contain a series
AB  - of five to seven structural units of Mr about 20,000, since post-translational processing in
AB  - vivo or partial proteolysis of the purified protein in vitro leads to the production of a
AB  - series of catalytically active species differing in Mr by units of 20,000.  The N-terminal
AB  - domain is fused to a small (570 amino acid) C-terminal domain that is related to bacterial
AB  - type II cytosine methyltransferases.  The relevance of these findings for the biological
AB  - function of DNA MeTase is discussed.
ER  -

TY  - JOUR
AU  - Bestor, T.
TI  - Supercoiling-dependent sequence specificity of mammalian DNA mthyltransferase.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3835
EP  - 3843
VL  - 15
AB  - Negative supercoiling of substrate DNA dramatically alters the in vitro sequence specificity
AB  - of mammalian DNA methyltransferase.  This result suggests in vivo site selection by DNA MeTase
AB  - could be regulated by conformational information in the form of alternative secondary
AB  - structures indicated in DNA by local supercoiling or by the binding of specific nuclear
AB  - proteins.  DNA in the left-handed Z-form is shown not to be a substrate for mammalian DNA
AB  - MeTase.  The sensitivity of DNA MeTase to DNA structure may also make it useful as a probe for
AB  - sequences which undergo supercoiling-dependent structural transitions in vitro.
ER  -

TY  - JOUR
AU  - Bestor, T.
AU  - Laudano, A.
AU  - Mattaliano, R.
AU  - Ingram, V.
TI  - Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells.
JO  - J. Mol. Biol.
PY  - 1988
SP  - 971
EP  - 983
VL  - 203
AB  - A cDNA encoding DNA (cytosine-5)-methyltransferase (DNA MTase) of mouse cells has been cloned
AB  - and sequenced.  The nucleotide sequence contains an open reading frame sufficient to encode a
AB  - polypeptide of 1573 amino acid residues, which is close to the apparent size of the largest
AB  - species of DNA MTase found in mouse cells.  The carboxylterminal 570 amino acid residues of
AB  - the inferred protein sequence shows striking similarities to bacterial type II DNA cytosine
AB  - methyltransferases and appears to represent a catalytic methyltransferase domain.  The
AB  - amino-terminal portion of the molecule may be involved in regulating the activity of the
AB  - carboxyl-terminal methyltransferase domain, since antibodies directed against a peptide
AB  - sequence located within this region inhibits transmethylase activity in vitro.  A 5200 base
AB  - DNA MTase-specific mRNA was found to be expressed in all mouse cell types tested, and cell
AB  - lines known to have different genomic methylation patterns were found to contain DNA MTase
AB  - proteins of similar or identical sizes and de novo sequence specificities.  The implications
AB  - of these findings for an understanding of the mechanisms involved in the establishment and
AB  - maintenance of methylation patterns are discussed.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
TI  - DNA methyltransferases in mammalian development and genome defense.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 61
EP  - 76
VL  - 0
AB  - The mammalian genome is modified by the addition of about 3 x 10^7 methyl groups, all at the 5
AB  - position of cytosine and most at 5'-CpG-3' dinucleotides.  Methylation patterns are
AB  - transmitted by clonal inheritance and increase the information content of the genome;
AB  - transcription is repressed when CpG sites within promoters are methylated.  Cytosine
AB  - methylation is dangerous: 5-methylcytosine (m5C) is the major endogenous mutagen (deamination
AB  - results in C-T transition mutations at CpG sites, which account for about one-third of all
AB  - mutations in humans, and tumor suppressor genes are frequently inactivated by ectopic de novo
AB  - methylation of promoter regions.  However, there must be benefits that yield a net selective
AB  - advantage.  This is shown by the retention of cytosine methylation by virtually all organisms
AB  - with genomes of more than 5 x 10^8 bp and by the fact that perturbations of methylation
AB  - patterns are lethal to mouse embryos and to differentiated cells.  Severe developmental
AB  - abnormalities are seen when m5C levels are reduced in Arabidopsis as the result of mutations
AB  - at uncharacterized loci or by expression of a DNA methyltransferase antisense construct.
AB  - Although methylation patterns clearly play an essential role in large-genome eukaryotes, the
AB  - nature of that role is not understood.  It is argued here that an understanding of the
AB  - regulation of de novo methylation will reveal the biological function of methylation patterns.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
TI  - Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain.
JO  - EMBO J.
PY  - 1992
SP  - 2611
EP  - 2617
VL  - 11
AB  - Mammalian DNA (cytosine-5) methyltransferase contains a C-terminal domain that is closely
AB  - related to bacterial cytosine-5 restriction methyltransferases. This methyltransferase domain
AB  - is linked to a large N-terminal domain. It is shown here that the N-terminal domain contains a
AB  - Zn binding site and that the N- and C-terminal domains can be separated by cleavage with
AB  - trypsin or Staphylococcus aureus protease V8; the protease V8 cleavage site was determined by
AB  - Edman degradation to lie 10 residues C-terminal of the run of alternating lysyl and glycyl
AB  - residues which joins the two domains and six residues N-terminal of the first sequence motif
AB  - conserved between the mammalian and bacterial cytosine methyltransferases. While the intact
AB  - enzyme had little activity on unmethylated DNA substrates, cleavage between the domains caused
AB  - a large stimulation of the initial velocity of methylation of unmethylated DNA without
AB  - substantial change in the rate of methylation of hemimethylated DNA. These findings indicate
AB  - that the N-terminal domain of DNA methyltransferase ensures the clonal propagation of
AB  - methylation patterns through inhibition of the de novo activity of the C-terminal domain.
AB  - Mammalian DNA methyltransferase is likely to have arisen via fusion of a prokaryotic-like
AB  - restriction methyltransferase and an unrelated DNA binding protein. Stimulation of the de novo
AB  - activity of DNA methyltransferase by proteolytic cleavage in vivo may contribute to the
AB  - process of ectopic methylation observed in the DNA of aging animals, tumors and in lines of
AB  - cultured cells.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
TI  - DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes.
JO  - Philos. Trans. R. Soc. Lond. B. Biol. Sci.
PY  - 1990
SP  - 179
EP  - 187
VL  - 326
AB  - The amino acid sequence of mammalian DNA methyltransferase has been deduced from the
AB  - nucleotide sequence of a cloned cDNA. It appears that the mammalian enzyme arose during
AB  - evolution via fusion of a prokaryotic restriction methyltransferase gene and a second gene of
AB  - unknown function. Mammalian DNA methyltransferase currently comprises an N-terminal domain of
AB  - about 1000 amino acids that may have a regulatory role and a C-terminal 570 amino acid domain
AB  - that retains similarities to bacterial restriction methyltransferases. The sequence
AB  - similarities among mammalian and bacterial DNA cytosine methyltransferases suggest a common
AB  - evolutionary origin. DNA methylation is uncommon among those eukaryotes having genomes of less
AB  - than 108 base pairs, but nearly universal among large-genome eukaryotes. This and other
AB  - considerations make it likely that sequence inactivation by DNA methylation has evolved to
AB  - compensate for the expansion of the genome that has accompanied the development of higher
AB  - plants and animals. As methylated sequences are usually propagated in the repressed,
AB  - nuclease-insensitive state, it is likely that DNA methylation compartmentalizes the genome to
AB  - facilitate gene regulation by reducing the total amount of DNA sequence that must be scanned
AB  - by DNA-binding regulatory proteins. DNA methylation is involved in immune recognition in
AB  - bacteria but appears to regulate the structure and expression of the genome in complex higher
AB  - eukaryotes. I suggest that the DNA-methylating system of mammals was derived from that of
AB  - bacteria by way of a hypothetical intermediate that carried out selective de novo methylation
AB  - of exogenous DNA and propagated the methylated DNA in the repressed state within its own
AB  - genome. During the evolution of complex plants and animals the inactivating effects of DNA
AB  - methylation spread to extraneous cellular sequences, such as highly repetitive DNA and
AB  - transposable elements, and later to tissue-specific genes. Modern large-genome eukaryotes have
AB  - adapted a primitive prokaryotic immune system to enable them to manage a genome that has
AB  - expanded more than 1000-fold as a result of accumulation of extraneous sequences and
AB  - tissue-specific genes.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
TI  - The DNA methyltransferases of mammals.
JO  - Hum. Mol. Genet.
PY  - 2000
SP  - 2395
EP  - 2402
VL  - 9
AB  - The biological significance of 5-methylcytosine was in doubt for many years, but is no longer,
AB  - Through targeted mutagenesis in mice it has
AB  - been learnt that every protein shown by biochemical tests to be
AB  - involved in the establishment, maintenance or interpretation of genomic
AB  - methylation patterns is encoded by an essential gene. A human genetic
AB  - disorder (ICF syndrome) has recently been shown to be caused by
AB  - mutations in the DNA methyltransferase 3B (DNMT3B) gene, A second human
AB  - disorder (Rett syndrome) has been found to result from mutations in the
AB  - MECP2 gene, which encodes a protein that binds to methylated DNA.
AB  - Global genome demethylation caused by targeted mutations in the DNA
AB  - methyltransferase-l (Dnmt1) gene has shown that cytosine methylation
AB  - plays essential roles in X-inactivation, genomic imprinting and genome.
AB  - stabilization. The majority of genomic 5-methylcytosine is now known to
AB  - enforce the transcriptional silence of the enormous burden of
AB  - transposons and retroviruses that have accumulated in the mammalian
AB  - genome. It has also become clear that programmed changes in methylation
AB  - patterns are less important in the regulation of mammalian development
AB  - than was previously believed. Although a number of outstanding
AB  - questions have yet to be answered (one of these questions involves the
AB  - nature of the cues that designate sites for methylation at particular
AB  - stages of gametogenesis and early development), studies of DNA
AB  - methyltransferases are likely to provide further insights into the
AB  - biological functions of genomic methylation patterns.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
TI  - Cloning of a mammalian DNA methyltransferase.
JO  - Gene
PY  - 1988
SP  - 9
EP  - 12
VL  - 74
AB  - Cloning and sequencing of cDNA clones has shown that mammalian DNA
AB  - (cytosine-5)-methyltransferase comprises a 1000-amino acid (aa) N-terminal
AB  - region of unknown function and a 570-aa C-terminal region that is clearly
AB  - related to bacterial Type II cytosine restriction methyltransferases.  These
AB  - findings indicate that the mammalian enzyme contains at least two structural
AB  - domains and suggest a common evolutionary origin for mammalian and prokaryotic
AB  - DNA (cytosine-5)-methyltransferases.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
TI  - Methylation patterns in the vertebrate genome.
JO  - J. NIH Res.
PY  - 1993
SP  - 57
EP  - 60
VL  - 5
AB  - The estimated amount of DNA in a mammalian cell is 6x109 base pairs, the equivalent of more
AB  - than 2 m of linear DNA. Cells of some amphibians and vascular plants contain even larger
AB  - amounts. However, only a small fraction of the genome is available for interaction with
AB  - transcription factors that regulate gene expression, and the accessibility of specific
AB  - sequences to these factors appears to be controlled in large part by methylation at the 5
AB  - position of cytosine residues in 5'-CpG-3' dinucleotides. Most DNA in large-genome
AB  - eukaryotes is methylated and inaccessible to the transcription apparatus, whereas promoter
AB  - regions are normally unmethylated and accessible to regulatory factors. Methylation of
AB  - promoter regions prevents transcription, as in the case of genes inactivated by genomic
AB  - imprinting and those on the inactive X chromosome. Programmed changes in the methylation
AB  - status of DNA may also be involved in the regulation of tissue-specific genes during
AB  - development, although this hypothesis remains controversial. Another unsolved question concern
AB  - the ways in which sex-and tissue-specific methylation patterns are established during
AB  - gametogenesis and early development; this is an important issue for human health because
AB  - certain human diseases are likely to involve defective establishment or maintenance of genomic
AB  - methylation patterns.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
AU  - Ingram, V.M.
TI  - Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1983
SP  - 5559
EP  - 5563
VL  - 80
AB  - Dye-ligand chromatography on Cibacron blue F3GA-agarose has been used to resolve two species
AB  - of DNA (cytosine-5-)-methyltransferase from nuclear
AB  - extracts of uninduced Friend murine erythroleukemia cells. Each species
AB  - has been highly purified; the activities in the first and second peaks
AB  - were associated with polypeptides of Mr 150,000 and 175,000, respectively.
AB  - Analysis of substrate specificity with synthetic DNAs and restriction
AB  - fragments of phi X174 replicative form DNA and pBR322 DNA showed that
AB  - neither enzyme had dependence on the sequence context of CpG
AB  - dinucleotides; poly(dG-dC) had the greatest methyl-accepting activity of
AB  - any unmethylated DNA substrate tested. De novo methylation by both enzymes
AB  - was inefficient relative to methylation of hemimethylated sites.
AB  - Methyl-accepting activity was strongly dependent on DNA chain length. This
AB  - observation suggests that binding to DNA, followed by one-dimensional
AB  - diffusion of enzyme along the DNA molecule, is important in the mechanism
AB  - by which DNA methyltransferase locates its recognition sites.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
AU  - Ingram, V.M.
TI  - Growth-dependent expression of multiple species of DNA methyltransferase in murine erythroleukemia cells.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1985
SP  - 2674
EP  - 2678
VL  - 82
AB  - Friend murine erythroleukemia cells were found to contain three distinct species of DNA
AB  - (cytosine-5-)-methyltransferase whose relative proportions were a characteristic function of
AB  - the proliferative state of the cells.  Rapidly proliferating cells contained a Mr 190,000
AB  - species of DNA MeTase, whereas cells in the late logarithmic/early plateau phase of cellular
AB  - growth contained two species of Mr 150,000 and 175,000 (DNA MeTases I and II); stationary
AB  - phase cells contained primarily DNA MeTase I.  The three species of DNA MeTase displayed
AB  - structural similarities, as determined by analysis of partial proteolysis products, and have
AB  - similar de novo sequence specificites in transmethylation reactions involving purified enzyme
AB  - and prokaryotic DNA.  The different relative proportions of the enzymes in cells under
AB  - different growth conditions suggest that the three species of DNA MeTase fulfill different
AB  - roles in processes leading to the perpetuation of DNA methylation patterns.
ER  -

TY  - JOUR
AU  - Bestor, T.H.
AU  - Verdine, G.L.
TI  - DNA methyltransferases.
JO  - Curr. Opin. Cell Biol.
PY  - 1994
SP  - 380
EP  - 389
VL  - 6
AB  - Mammals have long been known to tag their DNA by the addition of methyl groups to cytosine
AB  - residues. Only quite recently, however, has the functional significance of DNA methylation
AB  - established a firm footing. Evidence now indicates that DNA methylation is essential for
AB  - development, and is involved in both programmed and ectopic gene inactivation. Recent
AB  - structural and mechanistic work on bacterial cytosine-5-methyltransferases has provided much
AB  - insight into the function of the carboxy-terminal catalytic domain of eukaryotic
AB  - cytosine-5-methyltransferases; evidence is emerging that the amino-terminal domain targets the
AB  - enzyme to the replication machinery and may be involved in sensing the pre-existing
AB  - methylation state of the DNA.
ER  -

TY  - JOUR
AU  - Bethke, J.
AU  - Yanez, A.J.
AU  - Avendano-Herrera, R.
TI  - Comparative Genomic Analysis of Two Chilean Renibacterium salmoninarum Isolates and the type strain ATCC 33209T.
JO  - Genome Biol. Evol.
PY  - 2018
SP  - 1816
EP  - 1822
VL  - 10
AB  - Renibacterium salmoninarum, a slow-growing facultative intracellular pathogen
AB  - belonging to the high C + G content Actinobacteria phylum, is the causative agent
AB  - of bacterial kidney disease, a progressive granulomatous infection affecting
AB  - salmonids worldwide. This Gram-positive bacterium has existed in the Chilean
AB  - salmonid industry for >30 years, but little or no information is available
AB  - regarding the virulence mechanisms and genomic characteristics of Chilean
AB  - isolates. In this study, the genomes of two Chilean isolates (H-2 and DJ2R) were
AB  - sequenced, and a search was conducted for genes and proteins involved in
AB  - virulence and pathogenicity, and we compare with the type strain ATCC 33209 T
AB  - genome. The genome sizes of H-2 and DJ2R are 3,155,332 bp and 3,155,228 bp,
AB  - respectively. They genomes presented six ribosomal RNA, 46 transcription RNA, and
AB  - 25 noncodingRNA, and both had the same 56.27% G + C content described for the
AB  - type strain ATCC 33209 T. A total of 3,522 and 3,527 coding sequences were found
AB  - for H-2 and DJ2R, respectively. Meanwhile, the ATCC 33209 T type strain had 3,519
AB  - coding sequences. The in silico genome analysis revealed a genes related to
AB  - tricarboxylic acid cycle, glycolysis, iron transport and others metabolic
AB  - pathway. Also, the data indicated that R salmoninarum may have a variety of
AB  - possible virulence-factor and antibiotic-resistance strategies. Interestingly,
AB  - many of genes had high identities with Mycobacterium species, a known pathogenic
AB  - Actinobacteria bacterium. In summary, this study provides the first insights into
AB  - and initial steps towards understanding the molecular basis of antibiotic
AB  - resistance, virulence mechanisms and host/environment adaptation in two Chilean
AB  - R. salmoninarum isolates that contain proteins of which were similar to those of
AB  - Mycobacterium. Furthermore, important information is presented that could
AB  - facilitate the development of preventive and treatment measures against R.
AB  - salmoninarum in Chile and worldwide.
ER  -

TY  - JOUR
AU  - Betlach, M.
AU  - Hershfield, V.
AU  - Chow, L.
AU  - Brown, W.
AU  - Goodman, H.
AU  - Boyer, H.W.
TI  - A restriction endonuclease analysis of the bacterial plasmid controlling the ecoRI restriction and modification of DNA.
JO  - Fed. Proc.
PY  - 1976
SP  - 2037
EP  - 2043
VL  - 35
AB  - Genetic analyses of DNA restriction and modification mechanisms have been encumbered by the
AB  - inability to rigorously select for mutant phenotypes associated
AB  - with these systems. The application of restriction endonucleases has now proved
AB  - to be a successful approach to the genetic analyses of small genomes that are
AB  - recalcitrant to the more standard genetic techniques. Restriction endonucleases
AB  - EcoRI and HindIII were used to analyze the structure of the plasmid genome
AB  - responsible for the EcoRI restriction endonuclease and modification methylase.
AB  - This plasmid in the original clinical isolate of Escherichia coli appears to be
AB  - identical to the ColE 1 plasmid except for a 1.95 kilobase pair segment which
AB  - contains these genes. A preliminary restriction map of this plasmid is presented.
ER  -

TY  - JOUR
AU  - Bettegowda, C.
AU  - Huang, X.
AU  - Lin, J.
AU  - Cheong, I.
AU  - Kohli, M.
AU  - Szabo, S.A.
AU  - Zhang, X.
AU  - Diaz, L.A. Jr.
AU  - Velculescu, V.E.
AU  - Parmigiani, G.
AU  - Kinzler, K.W.
AU  - Vogelstein, B.
AU  - Zhou, S.
TI  - The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.
JO  - Nat. Biotechnol.
PY  - 2006
SP  - 1573
EP  - 1580
VL  - 24
AB  - Bacteriolytic anti-cancer therapies employ attenuated bacterial strains that selectively
AB  - proliferate within tumors. Clostridium novyi-NT spores
AB  - represent one of the most promising of these agents, as they generate
AB  - potent anti-tumor effects in experimental animals. We have determined the
AB  - 2.55-Mb genomic sequence of C. novyi-NT, identifying a new type of
AB  - transposition and 139 genes that do not have homologs in other bacteria.
AB  - The genomic sequence was used to facilitate the detection of transcripts
AB  - expressed at various stages of the life cycle of this bacterium in vitro
AB  - as well as in infections of tumors in vivo. Through this analysis, we
AB  - found that C. novyi-NT spores contained mRNA and that the spore
AB  - transcripts were distinct from those in vegetative forms of the bacterium.
ER  -

TY  - JOUR
AU  - Bettina, A.M.
AU  - Doing, G.
AU  - O'Brien, K.
AU  - Perron, G.G.
AU  - Jude, B.A.
TI  - Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates  Cultured from the Hudson Valley Watershed.
JO  - Genome Announcements
PY  - 2018
SP  - e01426
EP  - e01417
VL  - 6
AB  - Investigation of the Hudson Valley watershed reveals many violacein-producing bacteria. These
AB  - are of interest for their biotherapeutic potential in treating
AB  - chytrid infections of amphibians. The draft whole-genome sequences for seven
AB  - Janthinobacterium isolates with a variety of phenotypes are provided in this
AB  - study.
ER  -

TY  - JOUR
AU  - Betts, M.N.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes).
JO  - Genome Announcements
PY  - 2015
SP  - e01209
EP  - e01215
VL  - 3
AB  - Here, we present the draft genome of Planomicrobium glaciei, a member of the phylum
AB  - Firmicutes, found at the University of California Davis. Paired-end, 300-bp reads were
AB  - generated on an Illumina MiSeq. The assembly consists of 3,925,122 bp, contained in 109
AB  - contigs, with a G+C content of 46.7%.
ER  -

TY  - JOUR
AU  - Beuck, C.
AU  - Singh, I.
AU  - Bhattacharya, A.
AU  - Hecker, W.
AU  - Parmar, V.S.
AU  - Seitz, O.
AU  - Weinhold, E.
TI  - Polycyclic Aromatic DNA-base surrogates: High-affinity binding to an adenine-specific base-flipping DNA methyltransferase.
JO  - Angew. Chem. Int. Ed. Engl.
PY  - 2003
SP  - 3958
EP  - 3960
VL  - 42
AB  - DNA methylation is an important biological event that serves diverse cellular functions such
AB  - as protection against endogenous restriction endonucleases, direction of DNA-mismatch repair,
AB  - as well as regulation of gene expression and DNA replication.  DNA methylation is catalyzed by
AB  - DNA methyltransferases (MTases), which bind to specific DNA sequences and transfer a methyl
AB  - group from S-adenosyl-L-methionine to the exocyclic amino groups of adenine or cytosine or to
AB  - C5 of cytosine.  Interestingly, methylation is commenced by flipping the target nucleotide
AB  - completely out of the helix.  The energy cost for disrupting Watson-Crick hydrogen bonds and
AB  - base-stacking interactions is mainly compensated by specific binding of the target bases
AB  - within the active sites of the enzymes and by stabilizing the formed apparent abasic site.
AB  - Three different mechanisms of abasic-site stabilization have been observed in crystal
AB  - structures of DNA MTases complexed with DNA.  The cytosine-specific DNA MTases M.HhaI and
AB  - M.HaeIII either only insert an amino acid side chain into the opened space or insert an amino
AB  - acid side chain in addition to rearranging the base pairing.  This is in contrast to the
AB  - adenine-specific DNA MTase M.TaqI.  In this case, the formed unpaired partner base is inserted
AB  - into the opened space, resulting in interstrand stacking.
ER  -

TY  - JOUR
AU  - Beukers, A.G.
AU  - Zaheer, R.
AU  - Goji, N.
AU  - Cook, S.R.
AU  - Amoako, K.K.
AU  - Chaves, A.V.
AU  - Ward, M.P.
AU  - McAllister, T.A.
TI  - Draft Genome Sequence of an Enterococcus thailandicus Strain Isolated from Bovine Feces.
JO  - Genome Announcements
PY  - 2016
SP  - e00576
EP  - e00516
VL  - 4
AB  - Here, we report the first draft genome sequence of Enterococcus thailandicus isolated from the
AB  - feces of feedlot cattle in Southern Alberta.
ER  -

TY  - JOUR
AU  - Beurmann, S.
AU  - Videau, P.
AU  - Ushijima, B.
AU  - Smith, A.M.
AU  - Aeby, G.S.
AU  - Callahan, S.M.
AU  - Belcaid, M.
TI  - Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from Kane'ohe Bay, O'ahu, Hawaii.
JO  - Genome Announcements
PY  - 2015
SP  - e01396
EP  - e01314
VL  - 3
AB  - Pseudoalteromonas sp. strain OCN003 is a marine gammaproteobacterium that was isolated from a
AB  - diseased colony of the common Hawaiian reef coral, Montipora capitata, found on a reef
AB  - surrounding Moku o Lo'e in Kane'ohe Bay, Hawaii. Here, we report the complete genome of
AB  - Pseudoalteromonas sp. strain OCN003.
ER  -

TY  - JOUR
AU  - Beutin, L.
AU  - Hammerl, J.A.
AU  - Strauch, E.
AU  - Reetz, J.
AU  - Dieckmann, R.
AU  - Kelner-Burgos, Y.
AU  - Martin, A.
AU  - Miko, A.
AU  - Strockbine, N.A.
AU  - Lindstedt, B.A.
AU  - Horn, D.
AU  - Monse, H.
AU  - Huettel, B.
AU  - Muller, I.
AU  - Stuber, K.
AU  - Reinhardt, R.
TI  - Spread of a Distinct Stx2-Encoding Phage Prototype among Escherichia coli O104:H4 Strains from Outbreaks in Germany, Norway, and Georgia.
JO  - J. Virol.
PY  - 2012
SP  - 10444
EP  - 10455
VL  - 86
AB  - Shiga toxin 2 (Stx2)-producing Escherichia coli (STEC) O104:H4 caused one of the
AB  - world's largest outbreaks of hemorrhagic colitis and hemolytic uremic syndrome in
AB  - Germany in 2011. These strains have evolved from enteroaggregative E. coli (EAEC)
AB  - by the acquisition of the Stx2 genes and have been designated enteroaggregative
AB  - hemorrhagic E. coli. Nucleotide sequencing has shown that the Stx2 gene is
AB  - carried by prophages integrated into the chromosome of STEC O104:H4. We studied
AB  - the properties of Stx2-encoding bacteriophages which are responsible for the
AB  - emergence of this new type of E. coli pathogen. For this, we analyzed Stx
AB  - bacteriophages from STEC O104:H4 strains from Germany (in 2001 and 2011), Norway
AB  - (2006), and the Republic of Georgia (2009). Viable Stx2-encoding bacteriophages
AB  - could be isolated from all STEC strains except for the Norwegian strain. The Stx2
AB  - phages formed lysogens on E. coli K-12 by integration into the wrbA locus,
AB  - resulting in Stx2 production. The nucleotide sequence of the Stx2 phage P13374 of
AB  - a German STEC O104:H4 outbreak was determined. From the bioinformatic analyses of
AB  - the prophage sequence of 60,894 bp, 79 open reading frames were inferred.
AB  - Interestingly, the Stx2 phages from the German 2001 and 2011 outbreak strains
AB  - were found to be identical and closely related to the Stx2 phages from the
AB  - Georgian 2009 isolates. Major proteins of the virion particles were analyzed by
AB  - mass spectrometry. Stx2 production in STEC O104:H4 strains was inducible by
AB  - mitomycin C and was compared to Stx2 production of E. coli K-12 lysogens.
ER  -

TY  - JOUR
AU  - Beutin, L.
AU  - Kruger, U.
AU  - Krause, G.
AU  - Miko, A.
AU  - Martin, A.
AU  - Strauch, E.
TI  - Evaluation of major types of Shiga toxin 2E-producing Escherichia coli bacteria present in food, pigs, and the environment as potential pathogens for humans.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 4806
EP  - 4816
VL  - 74
AB  - Shiga toxin 2e (Stx2e)-producing strains from food (n = 36), slaughtered
AB  - pigs (n = 25), the environment (n = 21), diseased pigs (n = 19), and
AB  - humans (n = 9) were investigated for production of Stx2e by enzyme-linked
AB  - immunosorbent assay, for virulence markers by PCR, and for their serotypes
AB  - to evaluate their role as potential human pathogens. Stx2e production was
AB  - low in 64% of all 110 strains. Stx2e production was inducible by mitomycin
AB  - C but differed considerably between strains. Analysis by nucleotide
AB  - sequencing and transcription of stx(2e) genes in high- and
AB  - low-Stx2e-producing strains showed that toxin production correlated with
AB  - transcription rates of stx(2e) genes. DNA sequences specific for the int,
AB  - Q, dam, and S genes of the stx(2e) bacteriophage P27 were found in 109
AB  - strains, indicating cryptic P27-like prophages, although 102 of these were
AB  - not complete for all genes tested. Genes encoding intimin (eae),
AB  - enterohemorrhagic Escherichia coli hemolysin (ehx), or other stx(1) or
AB  - stx(2) variants were not found, whereas genes for heat-stable enterotoxins
AB  - STI, STII, or EAST1 were present in 54.5% of the strains. Seven major
AB  - serotypes that were associated with diseased pigs (O138:H14, O139:H1, and
AB  - O141:H4) or with slaughter pigs, food, and the environment (O8:H4, O8:H9,
AB  - O100:H30, and O101:H9) accounted for 60% of all Stx2e strains. The human
AB  - Stx2e isolates did not belong to these major serotypes of Stx2e strains,
AB  - and high production of Stx2e in human strains was not related to diarrheal
AB  - disease. The results from this study and other studies do not point to
AB  - Stx2e as a pathogenicity factor for diarrhea and hemolytic uremic syndrome
AB  - in humans.
ER  -

TY  - JOUR
AU  - Bevan, M. et al.
TI  - Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana.
JO  - Nature
PY  - 1998
SP  - 485
EP  - 488
VL  - 391
AB  - The plant Arabidopsis thaliana has become an important model species for the study of many
AB  - aspects of plant biology.  The relatively small size of the nuclear genome and the
AB  - availability of extensive physical maps of the five chromosomes provide a feasible basis for
AB  - initiating sequencing of the five chromosomes.  The YAC-based physical map of chromosome 4 was
AB  - used to construct a sequence-ready map of cosmid and BAC clones covering a 1.9-megabase
AB  - contiguous region, and the sequence of this region is reported here.  Analysis of the sequence
AB  - revealed an average gene density of one gene every 4.8 kilobases, and 54% of the predicted
AB  - genes had significant similarity to known genes.  Other interesting features were found, such
AB  - as the sequence of a disease-resistance gene locus, the distribution of retroelements, the
AB  - frequent occurrence of clustered gene families, and the sequence of several classes of genes
AB  - not previously encountered in plants.
ER  -

TY  - JOUR
AU  - Bey, S.J.
AU  - Tsou, M.F.
AU  - Huang, C.H.
AU  - Yang, C.C.
AU  - Chen, C.W.
TI  - The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid.
JO  - Microbiology
PY  - 2000
SP  - 911
EP  - 922
VL  - 146
AB  - The chromosome of Streptomyces lividans shares 15.4 kb homology with one end of the linear
AB  - plasmid SLP2, consisting of a 10.1 kb terminal sequence
AB  - followed by the 5.3 kb transposable element Tn4811. The 10.1 kb terminal
AB  - sequence was determined. The mean G+C content of this sequence is 67.9
AB  - mol% with a striking G vs C bias in the last kb. The terminal 232 nt
AB  - contained 10 palindromic sequences with potential to form complex
AB  - secondary structures. One typical Streptomyces coding sequence (designated
AB  - ORF1) of 2643 bp was predicted in the determined sequence. The amino acid
AB  - sequence of the ORF1 product contained a DEAH helicase motif, and
AB  - exhibited similarity to type I restriction enzyme HsdR subunits in the
AB  - database, suggesting a possible role in replication of the telomeres.
AB  - However, all the ORF1 sequences on the chromosome and SLP2 could be
AB  - simultaneously knocked out by targeted recombination without affecting the
AB  - viability of the cells and the linearity of the chromosome and SLP2. This
AB  - ruled out ORF1 as an essential component in the maintenance of the linear
AB  - chromosome and plasmids.
ER  -

TY  - JOUR
AU  - Beye, M.
AU  - Bakour, S.
AU  - Labas, N.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Actinobaculum massiliense Strain FC3.
JO  - Genome Announcements
PY  - 2016
SP  - e01537
EP  - e01515
VL  - 4
AB  - Actinobaculum massiliense strain FC3 was isolated from the urine of a patient with acute
AB  - cystitis. The 2.06-Mb genome of strain FC3 contains 17 toxin/antitoxin
AB  - modules and 9 bacteriocin-encoding genes that may play a role in virulence. The
AB  - genome also exhibits 693 genes acquired by lateral gene transfer.
ER  -

TY  - JOUR
AU  - Beye, M.
AU  - Bakour, S.
AU  - Traore, S.I.
AU  - Rathored, J.
AU  - Labas, N.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 8
EP  - 8
VL  - 13
AB  - We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola
AB  - strain SIT8 (= CSUR P1560). This strain, whose genome is
AB  - described here, was isolated from the fecal flora of a healthy 28-month-old
AB  - Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid)
AB  - contains 2354 protein-coding and 46 RNA genes, including four rRNA genes.
ER  -

TY  - JOUR
AU  - Beyersmann, P.G.
AU  - Chertkov, O.
AU  - Petersen, J.
AU  - Fiebig, A.
AU  - Chen, A.
AU  - Pati, A.
AU  - Ivanova, N.
AU  - Lapidus, A.
AU  - Goodwin, L.A.
AU  - Chain, P.
AU  - Detter, J.C.
AU  - Rohde, M.
AU  - Gronow, S.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Simon, M.
AU  - Goker, M.
AU  - Klenk, H.P.
AU  - Brinkhoff, T.
TI  - Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 403
EP  - 419
VL  - 8
AB  - In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine
AB  - Roseobacter clade, which, in turn, belongs to the class
AB  - Alphaproteobacteria. The genus Phaeobacter is well known for members that produce
AB  - various secondary metabolites. Here we report of putative quorum sensing systems,
AB  - based on the finding of six N-acyl-homoserine lactone synthetases, and show that
AB  - the blue color of P. caeruleus is probably due to the production of the secondary
AB  - metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on
AB  - other bacteria. In this study the genome of the type strain DSM 24564(T) was
AB  - sequenced, annotated and characterized. The 5,344,419 bp long genome with its
AB  - seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted
AB  - function) and 108 RNA genes.
ER  -

TY  - JOUR
AU  - Beylefeld, A.
AU  - Abolnik, C.
TI  - Complete Genome Sequence of Mycoplasma pullorum Isolated from Domestic Chickens.
JO  - Genome Announcements
PY  - 2017
SP  - e01647
EP  - e01616
VL  - 5
AB  - The 1,007,172-bp complete genome of Mycoplasma pullorum strain B359_6, isolated from domestic
AB  - chickens, has been sequenced, assembled, and annotated.
ER  -

TY  - JOUR
AU  - Beylot, B.
AU  - Spassky, A.
TI  - Chemical probing shows that the intron-encoded endonuclease I-SceI distorts DNA through binding in monomeric form to its homing site.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 25243
EP  - 25253
VL  - 276
AB  - Despite its small size (27.6 kDa), the group I intron-encoded I-SceI endonuclease initiates
AB  - intron homing by recognizing and specifically cleaving a large intronless DNA sequence. Here,
AB  - we used gel shift assays and footprinting experiments to analyze the interaction between
AB  - I-SceI and its target. I-SceI was found to bind to its substrate in monomeric form.
AB  - Footprinting using DNase I, hydroxyl radical, phenanthroline copper complexes, UV/DH-MePyPs
AB  - photosensitizer, and base-modifying reagents revealed the asymmetric nature of the interaction
AB  - and provided a first glimpse into the architecture of the complex. The protein interacts in
AB  - the minor and major grooves and distorts DNA at three distinct sites: one at the intron
AB  - insertion site and the other two, respectively, downstream (-8, -9) and upstream (+9, +10)
AB  - from this site. The protein appears to stabilize the DNA curved around it by bridging the
AB  - minor groove on one face of the helix. The scissile phosphates would lie on the outside of the
AB  - bend, facing in the same direction relative to the DNA helical axis, as expected for an
AB  - endonuclease that generates 3' overhangs. An internally consistent model is proposed in which
AB  - the protein would take advantage of the concerted flexibility of the DNA sequence to induce a
AB  - synergistic binding/kinking process, resulting in the correct positioning of the enzyme active
AB  - site.
ER  -

TY  - JOUR
AU  - Bezuidt, O.K.
AU  - Gomri, M.A.
AU  - Pierneef, R.
AU  - Van Goethem, M.W.
AU  - Kharroub, K.
AU  - Cowan, D.A.
AU  - Makhalanyane, T.P.
TI  - Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 68
EP  - 68
VL  - 11
AB  - The members of the genus Thermoactinomyces are known for their protein degradative capacities.
AB  - Thermoactinomyces sp. strain AS95 is a Gram-positive
AB  - filamentous bacterium, isolated from moderately saline water in the Thamelaht
AB  - region of Algeria. This isolate is a thermophilic aerobic bacterium with the
AB  - capacity to produce extracellular proteolytic enzymes. This strain exhibits up to
AB  - 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA
AB  - gene sequence similarity. Here we report on the phenotypic features of
AB  - Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its
AB  - annotation. The genome of this strain is 2,558,690 bp in length (one chromosome,
AB  - but no plasmid) with an average G + C content of 47.95 %, and contains 2550
AB  - protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases.
ER  -

TY  - JOUR
AU  - Bezuidt, O.K.
AU  - Makhalanyane, T.P.
AU  - Gomri, M.A.
AU  - Kharroub, K.
AU  - Cowan, D.A.
TI  - Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria.
JO  - Genome Announcements
PY  - 2015
SP  - e01447
EP  - e01415
VL  - 3
AB  - Geobacillus spp. are potential sources of novel enzymes, such as those involved in the
AB  - degradation of recalcitrant polymers. Here, we report a Geobacillus genome
AB  - that may help reveal genomic differences between this strain and publicly
AB  - available representatives of the same genus from diverse niches.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
TI  - Restriction enzymes: Properties and Use.
JO  - Methods Enzymol.
PY  - 1992
SP  - 199
EP  - 224
VL  - 216
AB  - Most experiments in molecular biology involve the use of restriction enzymes (REs) at some
AB  - stage of the experiment. The ability of these enzymes to cut DNA at a specific sequence of
AB  - bases has greatly stimulated the growth of recombinant DNA technology. The popularity of these
AB  - enzymes is, in part, due to their wide commercial availability and the simplicity of their
AB  - use. Over 1900 REs are known and of these 275 are available from companies based around the
AB  - world. The purpose of this chapter is to list all commercially available enzymes, to describe
AB  - their general properties, the basic procedures for their use, and ways of troubleshooting
AB  - problems encountered in their use. Although the number of enzymes being discussed is large, a
AB  - few simple rules apply to virtually all the enzymes. One of the aims of this chapter is to
AB  - show that most enzymes can be used successfully without the help of pre-made kits, colorful
AB  - charts, complex buffers, or specialized equipment. Some of this ground has been covered in
AB  - previous reviews by Fuchs and Blakesley, Brooks, and Roberts and Macelis.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Beletskii, A.
TI  - Transcription is intrinsically mutagenic: Direct correlation between transcription and C to U or 5meC to T deaminations in the non-transcribed strand.
JO  - FASEB J.
PY  - 1996
SP  - A962
EP  - A962
VL  - 10
AB  - Among mutations induced by external agents, more mutations occur in the
AB  - non-transcribed than the transcribed strand.  This strand bias occurs because of preferential
AB  - repair of the transcribed strand.  We have now shown that there is also a strand bias in the
AB  - spontaneous process of hydrolytic deamination of cytosine and 5-methylcytosine (5meC)
AB  - and it causes accumulation of C to T mutations in the non-transcribed strand.  To
AB  - demonstrate this, we used a genetic reversion system involving a transcriptionally regulated
AB  - kanamycin-resistance gene.  Induction of transcription increased the frequency of
AB  - conversion of target C to T only when it was present in the non-transcribed strand.  We
AB  - conclude that the mutations occur as a result of deamination of C or 5meC because
AB  - mismatch correction processes that repair U:G and T:G mismatches partially suppress the
AB  - mutations.  Further, methylation of target cytosine increases frequency of mutations -
AB  - consistent with the higher rate of hydrolytic deamination of 5meC compared to C.  The
AB  - non-transcribed strand suffers more deaminations probably because it is in single-stranded
AB  - state during transcription, and deamination of cytosines in single-stranded DNA is ~1000
AB  - times the rate in double-stranded DNA.  Because transcription requires separation of the
AB  - two DNA strands, we suggest that similar strand bias in hydrolytic deamination of C and
AB  - 5meC must exist in all transcription events.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Gabbara, S.
TI  - The mechanism of activation of EcoRII endonuclease.
JO  - FASEB J.
PY  - 1992
SP  - A281
EP  - A281
VL  - 6
AB  - EcoRII is unusual among restriction enzymes in that it requires a high density
AB  - of its sites [sequence- 5'-CC(A/T)GG-3'] in a DNA for efficient cleavage.
AB  - Substrates such as phage T3 and T7 that contain only a few well separated sites
AB  - for the enzyme are cut poorly, while DNAs that contain several sites for the
AB  - enzyme are cut efficiently.  Interestingly, pBR322, pUC119 or short
AB  - oligonucleotide duplexes containing a single site for the enzyme can activate
AB  - the enzyme to cut poor substrates.  We are investigating the mechanism of this
AB  - activation using short oligonucleotide duplexes.  We have shown that activator
AB  - short duplexes are themselves cleaved poorly by the enzyme despite the fact
AB  - that the enzyme binds to the duplexes efficiently.  Thus, binding of the enzyme
AB  - to the substrate is not sufficient for cleavage.  As expected, pUC119 DNA can
AB  - activate EcoRII to cut these duplexes.  We have also shown that the inefficient
AB  - step in the reaction is not the release of the product after catalysis.
AB  - Interestingly, the efficiency of cleavage of a duplex increases with its
AB  - concentration in the reaction, ie. a duplex can act as its own activator.
AB  - Further, at high concentrations, a duplex can activate the enzyme to cut
AB  - another duplex.  Our results show that EcoRII endonuclease resembles
AB  - recombinational enzymes such as gamma/delta resolvase and phage lambda Int
AB  - protein in that it requires the simultaneous binding of two DNA molecules for
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Johnson, B.
AU  - Weule, K.
AU  - Roberts, R.J.
TI  - Primary sequence of the EcoRII endonuclease and properties of its fusions with beta-galactosidase.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 767
EP  - 773
VL  - 265
AB  - The EcoRII endonuclease cleaves DNA containing the sequence CC(A/T)GG before the first
AB  - cytosine. The methylation of the second cytosine in the sequence by either the EcoRII
AB  - methylase or Dcm, a chromosomally coded protein in Escherichia coli, inhibits the cleavage.
AB  - The gene for the EcoRII endonuclease was mapped by analysis of derivatives containing linker
AB  - insertions, transposon insertions, and restriction fragment deletions. Surprisingly, plasmids
AB  - carrying the wild-type endonuclease gene and the EcoRII methylase gene interrupted by
AB  - transposon insertions appeared to be lethal to dcm+ strains of E. coli. We conclude that not
AB  - all the EcoRII/Dcm recognition sites in the cellular DNA are methylated in dcm+ strains. The
AB  - DNA sequence of a 1650-base pair fragment containing the endonuclease gene was determined. It
AB  - revealed an open reading frame that could code for a 45.6-kDa protein. This predicted size is
AB  - consistent with the known size of the endonuclease monomer (44 kDa). The endonuclease and
AB  - methylase genes appear to be transcribed convergently from separate promoters. The reading
AB  - frame of the endonuclease gene was confirmed at three points by generating random protein
AB  - fusions between the endonuclease and beta-galactosidase, followed by an analysis of the
AB  - sequence at the junctions. One of these fusions is missing 18 COOH-terminal amino acids of the
AB  - endonuclease but still displays significant ability to restrict incoming phage in addition to
AB  - beta-galactosidase activity. No striking similarity between the sequence of the endonuclease
AB  - and any other protein in the PIR data base was found. The knowledge of the primary sequence of
AB  - the endonuclease and the availability of the various constructs involving its gene should be
AB  - helpful in the study of the interaction of the enzyme with its substrate DNA.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - McClelland, M.
TI  - DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1663
EP  - 1668
VL  - 20
AB  - A base mismatch correction process in E. coli K-12 called Very Short Patch (VSP) repair
AB  - corrects T:G mismatches to C:G when found in certain sequence contexts. Two of the substrate
AB  - mismatches (5'-CTWGG/3'-GGW'CC; W = A or T) occur in the context of cytosine methylation in
AB  - DNA and reduce the mutagenic effects of 5-methylcytosine deamination to thymine. However, VSP
AB  - repair is also known to repair T:G mismatches that are not expected to arise from
AB  - 5-methylcytosine deamination (example--CTAG/GGT-C). In these cases, if the original base pair
AB  - were a T:A, VSP repair would cause a T to C transition. We have carried out Markov chain
AB  - analysis of an E. coli sequence database to determine if repair at the latter class of sites
AB  - has altered the abundance of the relevant tetranucleotides. The results are consistent with
AB  - the prediction that VSP repair would tend to deplete the genome of the 'T' containing
AB  - sequences (example--CTAG), while enriching it for the corresponding 'C' containing sequences
AB  - (CCAG). Further, they provide an explanation for the known scarcity of CTAG containing
AB  - restriction enzyme sites among the genomes of enteric bacteria and identify VSP repair as a
AB  - force in shaping the sequence composition of bacterial genomes.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Person, S.
TI  - Structure and properties of the region of homology between plasmids pMB1 and ColE1.
JO  - Mol. Gen. Genet.
PY  - 1981
SP  - 505
EP  - 507
VL  - 182
AB  - Physical maps of the two independently isolated Escherichia coli plasmids, pMB1
AB  - and Co1E1, were prepared with 13 restriction endonucleases and compared.  A 5.1
AB  - kilobase continuous region covering 55% of pMB1 and 75% of Co1E1 was found to
AB  - have similar, but non-identical, restriction maps.  The differences in the maps
AB  - of this region probably arose by localized mutational events rather than by
AB  - major sequence rearrangements.  The F-factor was found to mobilize pMB1
AB  - efficiently for conjugal transfer.  A region on pMB1 required for its
AB  - F-mediated transfer was mapped.  Results of our study combined with results of
AB  - other investigators suggest that pMB1 and Co1E1 share functional properties
AB  - such as colicin production, colicin immunity, mode of replication, and
AB  - mobilization by the F-factor, and that the sequences required to code these
AB  - functions are contained within the 5.1 kilobase homologous region.  A
AB  - nomenclature for the genes encoding restriction and modification enzymes is
AB  - proposed.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Roberts, R.J.
TI  - Genetic analysis of the 5-azacytidine sensitivity of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1987
SP  - 1537
EP  - 1546
VL  - 169
AB  - DNA containing 5-azacytidine (5-azaC) has been shown to form stable detergent-resistent
AB  - complexes with cytosine methylases. We reasoned that if 5-azaC treatment causes protein-DNA
AB  - cross-links in vivo, then mutations in DNA repair and recombination genes may increase the
AB  - sensitivity of a cell to 5-azaC. We found that although recA (defective) and lexA
AB  - (induction-negative) mutants of Escherichia coli were very sensitive to the drug, mutations in
AB  - uvrA and ung genes had little effect on cell lethality. The sensitivity of recA strains to
AB  - 5-azaC was dose dependent and was enhanced by the overproduction of a DNA cytosine methylase
AB  - in the cell. Unexpectedly, a strain of E. coli carrying a recA mutation and a deletion of the
AB  - DNA cystosine methylase gene (dcm) was found to be significantly sensitive to 5-azaC. Study of
AB  - mutations in the pyrimidine salvage pathway of E. coli suggests that direct phosphorylation of
AB  - 5-azaC, rather than phosphorylation of its degradation products, is largely responsible for
AB  - the lethal effects of the drug. The addition of uracil to the growth medium had little effect
AB  - on cell lethality of recA mutants, but it partially reversed the inhibition of cell growth
AB  - caused by 5-azaC. This reversal of the bacteriostatic effects of the drug could not be
AB  - achieved by adding cytosine or orotic acid to the growth medium and required the presence of
AB  - functional UMP-pyrophosphorylase (gene upp) in the cell.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Sohail, A.
AU  - Lieb, M.
TI  - The ability of DCM and EcoRII methylases to methylate CC(A/T)GG sequences is not sufficient for their participation in very short patch repair at the same sites.
JO  - J. Cell Biochem. Suppl.
PY  - 1988
SP  - 282
EP  - 282
VL  - 12A
AB  - E. coli has the ability to correct mismatches such as -CTAGG- -CTTGG- -GGTCC- -GGACC- to
AB  - restore CC(A/T)GG sites by a mechanism called very short patch (VSP) repair. It also codes for
AB  - a DNA cytosine methylase, Dcm, that methylates the second cytosine within CC(A/T)GG sequence
AB  - at its C5 position. Several mutations in dcm that lack the ability to methylate are defective
AB  - in VSP repair as well, suggesting a role for dcm in VSP repair. We have isolated a deletion
AB  - mutant of dcm that is active in methylation, but inactive in VSP repair. Another strain of E.
AB  - coli carries the restriction-modification system EcoRII that includes a DNA methylase with the
AB  - same sequence specificity as Dcm. The two enzymes methylate the same cytosine in the sequence
AB  - at the identical position, but EcoRII methylase cannot complement dcm mutations defective in
AB  - VSP repair. This is despite the fact that the two methylases share signficant sequence
AB  - homology. It appears that the two methylases have evolved to perform separate functions in the
AB  - cell.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Sohail, A.
AU  - Lieb, M.
TI  - Methylation abilities of EcoRII and DCM methylases are not sufficient for their involvement in very short patch repair.
JO  - UCLA Symp. Mol. Cell. Biol.
PY  - 1988
SP  - 173
EP  - 178
VL  - 83
AB  - Dcm, a methylase coded by a chromosomal gene in E. coli K-12, methylates the second cytosine
AB  - in the sequence CC(A/T)GG. E. coli can repair mismatches in DNA such as -CTAGG- or -CTTGG-
AB  - -GGTCC- -GGACC- in favor of the lower strand, creating CC(A/T)GG sites. This is called very
AB  - short patch (VSP) repair. Mutation dcm6 destroys the ability of the cell to methylate DNA and
AB  - to repair mismatches of the kind mentioned above. The methylase in the
AB  - restriction-modification system EcoRII recognizes and methylates the same sequence as Dcm. We
AB  - have found that the gene for the EcoRII methylase is closely related to dcm. Despite these
AB  - similarities, EcoRII methylase cannot complement the dcm6 mutation for VSP repair. We have
AB  - also studied the ability of certain deletion derivatives of the cloned dcm gene to complement
AB  - the dcm6 mutation. At least two deletions complement the mutation for methylation but not for
AB  - repair. A mutated methylase may lose a role in DNA repair without losing its methylating
AB  - ability.
ER  -

TY  - JOUR
AU  - Bhagwat, A.S.
AU  - Sohail, A.
AU  - Roberts, R.J.
TI  - Cloning and characterization of the dcm locus of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1986
SP  - 751
EP  - 755
VL  - 166
AB  - The dcm locus of Escherichia coli K-12 has been shown to code for a methylase that methylates
AB  - the second cytosine within the sequence 5'-CC(A/T)GG-3'. This sequence is also recognized by
AB  - the EcoRII restriction-modification system coded by the E. coli plasmid N3. The methylase
AB  - within the EcoRII system methylates the same cytosine as the dcm protein. We have isolated,
AB  - from a library of E. coli K-12 DNA, two overlapping clones that carry the dcm locus. We show
AB  - that the two clones carry overlapping sequences that are present in a dcm+ strain, but are
AB  - absent in a dcm deletion strain. We also show that the cloned gene codes for a methylase, that
AB  - it complements mutations in the EcoRII methylase, and that it protects EcoRII recognition
AB  - sites from cleavage by the EcoRII endonuclease. We found no phage restriction activity
AB  - associated with the dcm clones.
ER  -

TY  - JOUR
AU  - Bhalla, A.
AU  - Kainth, A.S.
AU  - Sani, R.K.
TI  - Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1.
JO  - Genome Announcements
PY  - 2013
SP  - e00595
EP  - e00513
VL  - 1
AB  - Geobacillus sp. strain WSUCF1 is a thermophilic spore-forming member of the phylum Firmicutes,
AB  - isolated from a soil sample collected from the compost
AB  - facility. We report the draft genome sequence of this isolate with an estimated
AB  - genome size of 3.4 Mb. The genome sequence of this isolate revealed several genes
AB  - encoding glycoside hydrolases, making it a potential candidate for plant biomass
AB  - degradation.
ER  -

TY  - JOUR
AU  - Bhandare, S.G.
AU  - Warry, A.
AU  - Emes, R.D.
AU  - Hooton, S.P.T.
AU  - Barrow, P.A.
AU  - Atterbury, R.J.
TI  - Complete Genome Sequences of Vibrio cholerae-Specific Bacteriophages 24 and X29.
JO  - Genome Announcements
PY  - 2017
SP  - e01013
EP  - e01017
VL  - 5
AB  - The complete genomes of two Vibrio cholerae bacteriophages of potential interest  for cholera
AB  - bacteriophage (phage) therapy were sequenced and annotated. The
AB  - genome size of phage 24 is 44,395 bp encoding 71 putative proteins, and that of
AB  - phage X29 is 41,569 bp encoding 68 putative proteins.
ER  -

TY  - JOUR
AU  - Bharadwaj, Sv.V.
AU  - Shrivastav, A.
AU  - Dubey, S.
AU  - Ghosh, T.
AU  - Paliwal, C.
AU  - Maurya, R.
AU  - Mishra, S.
TI  - Draft Genome Sequence of Halomonas hydrothermalis MTCC 5445, Isolated from the West Coast of India.
JO  - Genome Announcements
PY  - 2015
SP  - e01419
EP  - e01414
VL  - 3
AB  - We announce here the draft genome sequence of Halomonas hydrothermalis MTCC 5445, a halophilic
AB  - bacterium of the class Gammaproteobacteria. It was isolated from the
AB  - sea coast of Aadri, Veraval, Gujarat, India. Its genome contains genes for
AB  - polyhydroxybutyrate (PHB), a biodegradable polymer that can be used as a
AB  - substitute for petroleum plastics.
ER  -

TY  - JOUR
AU  - Bharat, A.
AU  - Martin, I.
AU  - Demczuk, W.
AU  - Allen, V.
AU  - Haldane, D.
AU  - Hoang, L.
AU  - Mulvey, M.R.
TI  - Complete Genome Sequences of Neisseria gonorrhoeae with Coresistance to First-Line Antimicrobials.
JO  - Genome Announcements
PY  - 2016
SP  - e00966
EP  - e00916
VL  - 4
AB  - Neisseria gonorrhoeae strains with coresistance to the first-line antimicrobial treatments
AB  - azithromycin and ceftriaxone are an emerging public health threat.
AB  - Here, we present the complete genome sequences of three strains of N.
AB  - gonorrhoeae, including one susceptible strain and two strains with coresistance
AB  - to ceftriaxone and azithromycin.
ER  -

TY  - JOUR
AU  - Bhat, A.
AU  - Tamuli, R.
AU  - Kasbekar, D.P.
TI  - Genetic Transformation of Neurospora tetrasperma, Demonstration of Repeat-Induced Point Mutation (RIP) in Self-Crosses and a Screen for Recessive RIP-Defective Mutants.
JO  - Genetics
PY  - 2004
SP  - 1155
EP  - 1164
VL  - 167
AB  - The pseudohomothallic fungus Neurospora tetrasperma is naturally resistant
AB  - to the antibiotic hygromycin. We discovered that mutation of its erg-3
AB  - (sterol C-14 reductase) gene confers a hygromycin-sensitive phenotype that
AB  - can be used to select transformants on hygromycin medium by
AB  - complementation with the N. crassa erg-3+ and bacterial hph genes.
AB  - Cotransformation of hph with PCR-amplified DNA of other genes enabled us
AB  - to construct strains duplicated for the amplified DNA. Using
AB  - transformation we constructed self-fertile strains that were homoallelic
AB  - for an ectopic erg-3+ transgene and a mutant erg-3 allele at the
AB  - endogenous locus. Self-crosses of these strains yielded erg-3 mutant
AB  - ascospores that produced colonies with the characteristic morphology on
AB  - Vogel's sorbose agar described previously for erg-3 mutants of N. crassa.
AB  - The mutants were generated by repeat-induced point mutation (RIP), a
AB  - genome defense process that causes numerous G:C to A:T mutations in
AB  - duplicated DNA sequences. Homozygosity for novel recessive RIP-deficient
AB  - mutations was signaled by self-crosses of erg-3-duplication strains that
AB  - fail to produce erg-3 mutant progeny. Using this assay we isolated a
AB  - UV-induced mutant with a putative partial RIP defect. RIP-induced mutants
AB  - were isolated in rid-1 and sad-1, which are essential genes, respectively,
AB  - for RIP and another genome defense mechanism called meiotic silencing by
AB  - unpaired DNA.
ER  -

TY  - JOUR
AU  - Bhatia, U.
AU  - Robison, K.
AU  - Gilbert, W.
TI  - Dealing with database explosion: A cautionary note.
JO  - Science
PY  - 1997
SP  - 1724
EP  - 1725
VL  - 276
AB  - Carol J. Bult et al. Report the first entire archaea genome sequence of Methanococcus
AB  - jannashii (Mja).  Because the initial gene assignments were conservative, we anticipated that
AB  - much interesting biological information would be missing.  We searched the database for
AB  - additional open reading frames, and found 15 ORFs: four within intergenic regions (1 through
AB  - M4, Table 1); five overlapping with previously identified ORFs but that read off in a
AB  - different frame (M5 through M9, Table 1); and six that are extended or truncated as a result
AB  - of potential frameshifts (M10 through M15, Table 2).  Although the potential frameshifts we
AB  - describe might be bona fide, it cannot be ruled out that they represent actual sequencing
AB  - artifacts.  Erroneous sequences in public databases are a substantial problem and have been
AB  - estimated to be in the range of 0.37 to 2.9 errors per 1000 nucleotides, making data
AB  - interpretation sometimes difficult.  This is especially true, for example, in studies that
AB  - utilize protein and DNA sequence information to estimate evolutionary distances.  It is not
AB  - known how the error rate in this study compares with error rates in the database, but a
AB  - previous study suggests that error rates generally vary between 1 in 5000 to 1 in 10,000
AB  - nucleotides.
ER  -

TY  - JOUR
AU  - Bhatnagar, S.
AU  - Badger, J.H.
AU  - Madupu, R.
AU  - Khouri, H.M.
AU  - O'Connor, E.M.
AU  - Robb, F.T.
AU  - Ward, N.L.
AU  - Eisen, J.A.
TI  - Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria).
JO  - Genome Announcements
PY  - 2015
SP  - e01490
EP  - e01414
VL  - 3
AB  - Here, we present the complete genome sequence of Thermodesulfobacterium commune DSM 2178(T) of
AB  - the phylum Thermodesulfobacteria.
ER  -

TY  - JOUR
AU  - Bhatnagar, S.
AU  - Badger, J.H.
AU  - Madupu, R.
AU  - Khouri, H.M.
AU  - O'Connor, E.M.
AU  - Robb, F.T.
AU  - Ward, N.L.
AU  - Eisen, J.A.
TI  - Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae).
JO  - Genome Announcements
PY  - 2015
SP  - e01489
EP  - e01414
VL  - 3
AB  - Here, we present the complete 2,003,803-bp genome of a sulfate-reducing thermophilic
AB  - bacterium, Thermodesulfovibrio yellowstonii strain DSM 11347(T).
ER  -

TY  - JOUR
AU  - Bhattacharjee, S.K.
AU  - Mahajan, S.K.
TI  - The origin of adaptive mutations: Explaining the mutational spectra of Lac+ revertants of the Escherichia coli strain FC40.
JO  - Curr. Sci.
PY  - 1998
SP  - 583
EP  - 590
VL  - 74
AB  - Reversion of lacI33-lacZ frameshift mutation to produce Lac+ colonies takes place by
AB  - demonstrably different mechanisms in growing and starving cultures of strains (such as FC40)
AB  - harboring this mutation.  The revertants appear to arise in starving cells only under
AB  - conditions where they can immediately promote growth.  This is reminiscent of Lamarckism.
AB  - Here we propose a mutagenic mechanism which is Darwinian inasmuch as it is blind to the
AB  - adaptive fitness of the mutants but can explain the mutational spectra seen in C40 and certain
AB  - other strains.  This mechanism can produce mutations only in the neighborhood of a
AB  - methylatable cytosine.
ER  -

TY  - JOUR
AU  - Bhattacharya, P.
AU  - Barnebey, A.
AU  - Zemla, M.
AU  - Goodwin, L.
AU  - Auer, M.
AU  - Yannone, S.M.
TI  - Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 74
EP  - 74
VL  - 10
AB  - Thermoanaerobacter thermohydrosulfuricus BSB-33 is a thermophilic gram positive obligate
AB  - anaerobe isolated from a hot spring in West Bengal, India. Unlike other
AB  - T. thermohydrosulfuricus strains, BSB-33 is able to anaerobically reduce Fe(III)
AB  - and Cr(VI) optimally at 60 degrees C. BSB-33 is the first Cr(VI) reducing T.
AB  - thermohydrosulfuricus genome sequenced and of particular interest for
AB  - bioremediation of environmental chromium contaminations. Here we discuss features
AB  - of T. thermohydrosulfuricus BSB-33 and the unique genetic elements that may
AB  - account for the peculiar metal reducing properties of this organism. The T.
AB  - thermohydrosulfuricus BSB-33 genome comprises 2597606 bp encoding 2581 protein
AB  - genes, 12 rRNA, 193 pseudogenes and has a G + C content of 34.20 %. Putative
AB  - chromate reductases were identified by comparative analyses with other
AB  - Thermoanaerobacter and chromate-reducing bacteria.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.
AU  - Dubey, A.K.
TI  - Metabolic burden as reflected by maintenance coefficient of recombinant Escherichia coli overexpressing target gene.
JO  - Biotechnol. Lett.
PY  - 1995
SP  - 1155
EP  - 1160
VL  - 17
AB  - Metabolic burden as a consequence of the overexpression of a target gene in a recombinant
AB  - strain of E. coli 1727 has been analyzed with respect to the maintenance energy coefficient
AB  - (m).  The values of 'm' for the host, uninduced recombinant and IPTG induced recombinant
AB  - were determined to be 0.12, 0.17 and 0.32 g.g-1.h-1 respectively.  Transient plasmid
AB  - instability and a nearly 33% fall in maximum specific growth rate were observed under
AB  - conditions of enhanced requirements for maintenance energy.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - The N-terminus of m5C-DNA methyltransferase MspI is involved in its topoisomerase activity.
JO  - Eur. J. Biochem.
PY  - 2002
SP  - 2491
EP  - 2497
VL  - 269
AB  - DNA cytosine methyltransferase MspI (M.MspI) must require a different type of interaction of
AB  - protein with DNA from other bacterial DNA
AB  - cytosine methyltransferases (m5C-MTases) to evoke the topoisomerase
AB  - activity that it possesses in addition to DNA-methylation ability. This
AB  - may require a different structural organization in the solution phase
AB  - from the reported consensus structural arrangement for m5C-MTases.
AB  - Limited proteolysis of M.MspI, however, generates two peptide
AB  - fragments, a large one (p26) and a small one (p18), consistent with
AB  - reported m5C-MTase structures. Examination of the amino-acid sequence
AB  - of M.MspI revealed similarity to human topoisomerase I at the
AB  - N-terminus. Alignment of the amino-acid sequence of M.MspI also
AB  - uncovered similarity (residues 245-287) to the active site of human DNA
AB  - ligase I. To evaluate the role of the N-terminus of M.MspI,
AB  - 2-hydroxy-5-nitrobenzyl bromide (HNBB) was used to truncate M.MspI
AB  - between residues 34 and 35. The purified HNBB-truncated protein has a
AB  - molecular mass of approximately 45 kDa, retains DNA binding and
AB  - methyltransferase activity, but does not possess topoisomerase
AB  - activity. These findings were substantiated using a purified
AB  - recombinant MspI protein with the N-terminal 34 amino acids deleted.
AB  - Changing the N-terminal residues Trp34 and Tyr74 to alanine results in
AB  - abolition of the topoisomerase I activity while the methyltransferase
AB  - activity remains intact.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - Transient DNA binding by a proteolytic peptide from m5C-DNA methyltransferase MspI.
JO  - J. Biochem. Mol. Biol. Biophys.
PY  - 2002
SP  - 357
EP  - 364
VL  - 6
AB  - A peptide fragment (p26) generated as a result of limited tryptic proteolysis of
AB  - methyltransferase MspI retains transient but non-specific DNA binding capability. The
AB  - transient DNA binding by p26 was characterized with respect to physicochemical factors.
AB  - Limited proteolysis was performed to probe gross structural deviation from the reported
AB  - two-domain organization for m5C-MTases, in light of topoisomerase activity shown by MspI,
AB  - resulted in two peptide fragments; a large fragment p26 and a small fragment p18, consistent
AB  - with the other reported m5C-MTase structures. The purified large peptide fragment p26, spans
AB  - between 6 and 251 in the amino acid sequence of M.MspI. The peptide p26 does not bind
AB  - S-adenosylmethionine, although in the intact protein the AdoMet binding region can be mapped
AB  - to a region in the protein that is present in this peptide. Such transient DNA binding has not
AB  - been reported for other protolytic product of any other m5C-DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - Effects of dissolved oxygen and oxygen mass transfer on overexpression of target gene in recombinant E. coli.
JO  - Enzyme Microb. Technol.
PY  - 1997
SP  - 355
EP  - 360
VL  - 20
AB  - Overexpression of target gene (MspI methylase) in recombinant Escherichia coli has been
AB  - studied in response to dissolved oxygen mass transfer.  The rate of target gene expression
AB  - attained its maximum value (2.67 U mg^-1p^-1h^-1) when the culture was induced with 1 mM
AB  - isopropyl-beta-D-thiogalactopyranoside (IPTG) in the mid-exponential phase of growth.  The
AB  - maximum value of 6.7 x 10^2 U mg^-1p^-1 for the target gene expression was attained in about 3
AB  - h of postinduction cultivation.  An oxygen-sufficient condition (0.22 mmoles l^-1) was
AB  - necessary to obtain optimal expression and cell productivity.  Expression of the target gene
AB  - upon induction was accompanied by an increase in oxygen uptake rate (OUR) of the cells and
AB  - decrease in dissolved oxygen (DO) concentration in the cultivation broth.  Volumetric oxygen
AB  - transfer coefficient (Kla) of 61 h^-1 was optimum for cell productivity of uninduced culture
AB  - while that for the induced culture was 84 h^-1 which was optimum for foreign protein synthesis
AB  - also.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - High-level expression of a heterologous gene in Escherichia coli in response to carbon-nitrogen source and C/N ration in a batch bioreactor.
JO  - Biotechnol. Prog.
PY  - 1997
SP  - 151
EP  - 155
VL  - 13
AB  - Overexpression of the target gene in a recombinant strain of Escherichia coli has been
AB  - analyzed in view of changes in the carbon-nitrogen source and as a function of C/N ratio.  The
AB  - rate of target gene expression varied over a range of 200%, and the yield coefficient for the
AB  - target gene product changed over 400% with change in carbon source at 10 gL^-1 in M9 medium.
AB  - With variation in nitrogen, source, however, only marginal changes (10-15%) occurred in these
AB  - parameters of overexpression.  Higher concentration, for example 2.5 g L^-1, of any nitrogen
AB  - source adversely affected heterologous expression as rate of target gene expression declined
AB  - in the range 35%-50% and the yield coefficient of foreign protein decreased between 45% and
AB  - 60%.  A C/N ratio of 15 was found to be optimum for both parameters for overexpression and
AB  - host specific parameters such as specific growth rate and observed yield coefficient for
AB  - cellular growth.  An analysis with respect to temperature and pH revealed that host and
AB  - expression parameters were quite susceptible to changes in these factors.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - Kinetic mechanism of cytosine DNA methyltransferase MspI.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 14743
EP  - 14749
VL  - 274
AB  - A kinetic analysis of MspI DNA methyltransferase (M.MspI) is presented. The enzyme catalyzes
AB  - methylation of lambda-DNA, a 50-kilobase pair linear molecule with multiple M.MspI-specific
AB  - sites, with a specificity constant (kcat/KM) of 0.9 x 10^8 M-1 s-1. But the values of the
AB  - specificity constants for the smaller DNA substrates (121 and 1459 base pairs (bp)) with
AB  - single methylation target or with multiple targets (sonicated lambda-DNA) were less by an
AB  - order of magnitude. Product inhibition of the M.MspI-catalyzed methylation reaction by
AB  - methylated DNA is competitive with respect to DNA and noncompetitive with respect to
AB  - S-adenosylmethionine (AdoMet). The S-adenosylhomocysteine inhibition of the methylation
AB  - reaction is competitive with respect to AdoMet and uncompetitive with respect to DNA. The
AB  - presteady state kinetic analysis showed a burst of product formation when AdoMet was added to
AB  - the enzyme preincubated with the substrate DNA. The burst is followed by a constant rate of
AB  - product formation (0.06 mol per mol of enzyme s-1) which is similar to catalytic constants
AB  - (kcat = approximately 0.056 s-1) measured under steady state conditions. The isotope exchange
AB  - in chasing the labeled methyltransferase-DNA complex with unlabeled DNA and AdoMet leads to a
AB  - reduced burst as compared with the one involving chase with labeled DNA and AdoMet. The enzyme
AB  - is capable of exchanging tritium at C-5 of target cytosine in the substrate DNA in the absence
AB  - of cofactor AdoMet. The kinetic data are consistent with an ordered Bi Bi mechanism for the
AB  - M.MspI-catalyzed DNA methylation where DNA binds first.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - Preparation and properties of restriction endonuclease SphI coupled to a nylon fabric filter.
JO  - Biotechnol. Appl. Biochem.
PY  - 1994
SP  - 141
EP  - 146
VL  - 20
AB  - A procedure has been devised for covalent coupling of SphI, a type II restriction endonuclease
AB  - (EC 3.1.2.1.4) from Streptomyces phaeochromogenes, to a nylon-fabric filter.  Immobilized SphI
AB  - preparations were characterized with respect to operational parameters, re-usability and
AB  - stability during storage.  It is shown that immobilization of SphI on nylon filter discs did
AB  - not affect the enzymic behavior of the enzyme, but did enhance its thermal stability.  The
AB  - rates of inactivation of free and bound SphI at 45oC were determined to be 5.0 h-1 and 3.0 h-1
AB  - respectively.  The membrane-bound preparations could be stored for over 2 months at 4oC
AB  - without significant loss of activity, compared with free enzyme, which had lost most of its
AB  - activity during this period.  The insolubilized R. SphI could be used up to three times.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - Amino acid residues involved in catalysis and DNA binding by cytosine DNA methyltransferase MspI.
JO  - J. Biochem. Mol. Biol. Biophys.
PY  - 2000
SP  - 109
EP  - 120
VL  - 4
AB  - Chemical modifications of chosen amino acid residues: arginine, histidine, cysteine, glycine
AB  - and tryptophan have been attempted to investigate their role in catalysis and DNA binding by
AB  - MspI DNA methyltransferase (M.MspI).  The catalytic inactivation following modifications of
AB  - two arginine and three histidine moieties was a consequence of loss of DNA binding property of
AB  - the methyltransferase.  Modification of a single cysteine residue completely abolished the
AB  - ability of M.MspI to transfer a methyl group but there was no loss of DNA binding activity.
AB  - While tryptophan had no apparent functional role, glycine was critical for AdoMet binding and
AB  - target base methylation by the M.MspI.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Dubey, A.K.
TI  - Expression parameters for target gene cloned in Escherichia coli in response to phosphate supply.
JO  - Biotechnol. Lett.
PY  - 1996
SP  - 1145
EP  - 1148
VL  - 18
AB  - A recombinant strain of E. coli 1727 overexpressed a target gene at enhanced levels when
AB  - supplied with an excess of inorganic phosphate.  The rate of target gene expression, the yield
AB  - coefficient for the target gene product and the plasmid copy number increased significantly:
AB  - 50%, 100% and 40% respectively at 125 mM excess phosphate.  This was, however, accompanied by
AB  - a 26% decrease in the specific growth rate and 30% in the cellular growth yield coefficient.
ER  -

TY  - JOUR
AU  - Bhattacharya, S.K.
AU  - Ramchandani, S.
AU  - Cervoni, N.
AU  - Szyf, M.
TI  - A mammalian protein with specific demethylase activity for mCpG DNA.
JO  - Nature
PY  - 1999
SP  - 579
EP  - 583
VL  - 397
AB  - DNA-methylation patterns are important for regulating genome functions, and are determined by
AB  - the enzymatic processes of methylation and demethylation.  The demethylating enzyme has now
AB  - been identified; a mammalian complementary DNA encodes a methyl-CpG-binding domain, bears a
AB  - demethylase activity that transforms methylated cytosine bases to cytosine, and demethylates a
AB  - plasmid when the cDNA is translated or transiently transfected into human embryonal kidney
AB  - cells in vitro.  The discovery of this DNA demethylase should provide a basis for the
AB  - molecular and developmental analysis of the role of DNA methylation and demethylation.
ER  -

TY  - JOUR
AU  - Bhattacharyya, S.
AU  - Chandrababunaidu, M.M.
AU  - Sen, D.
AU  - Panda, A.
AU  - Ghorai, A.
AU  - Bhan, S.
AU  - Sanghi, N.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of Exopolysaccharide-Producing Cyanobacterium Aphanocapsa montana BDHKU 210001.
JO  - Genome Announcements
PY  - 2015
SP  - e00057
EP  - e00015
VL  - 3
AB  - We report for the first time the draft genome sequence of Aphanocapsa montana BDHKU 210001, a
AB  - halotolerant cyanobacterium isolated from India. This is a marine
AB  - exopolysaccharide (EPS)-producing cyanobacterium. The genome of this species is
AB  - assembled into 11.50 million bases, with 296 scaffolds carrying approximately
AB  - 7,296 protein-coding genes.
ER  -

TY  - JOUR
AU  - Bhave, N.
AU  - Woodhead, J.L.
AU  - Malcolm, A.D.B.
TI  - Cation-dependence of the restriction endodeoxyribonuclease EcoRI.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 634
EP  - 634
VL  - 8
AB  - The restriction endodeoxyribonucleases and DNA methylases provide excellent examples for the
AB  - enzymologist of highly specific protein-nucleic acid interactions.  The endodeoxyribonuclease
AB  - EcoRI is comparatively easy to prepare, and is therefore among the best studied of these
AB  - restriction enzymes.  It is unusual (although not unique) in that its recognition sequence
AB  - depends on the exact assay conditions.  At low pH and high ionic strength the enzyme
AB  - recognizes the DNA sequence.
ER  -

TY  - JOUR
AU  - Bheemanaik, S.
AU  - Bujnicki, J.M.
AU  - Nagaraja, V.
AU  - Rao, D.N.
TI  - Functional analysis of amino acid residues at the dimerisation interface of Kpnl DNA methyltransferase.
JO  - Biol. Chem.
PY  - 2006
SP  - 515
EP  - 523
VL  - 387
AB  - KpnI DNA-(N-6-adenine) methyltransferase (M.Kpnl) recognises the sequence 5'-GGTACC-3' and
AB  - transfers the methyl group from
AB  - S-adenosyl-L-methionine (AdoMet) to the N6 position of the adenine
AB  - residue in each strand. Earlier studies have shown that M.Kpnl exists
AB  - as a dimer in solution, unlike most other MTases. To address the
AB  - importance of dimerisation for enzyme function, a three-dimensional
AB  - model of M.Kpnl was obtained based on protein fold-recognition
AB  - analysis, using the crystal structures of M.Rsrl and M.MbollA as
AB  - templates. Residues l146, l161 and Y167, the side chains of which are
AB  - present in the putative dimerisation interface-in the model, were
AB  - targeted for site-directed mutagenesis. Methylation and in vitro
AB  - restriction assays showed that the mutant MTases are catalytically
AB  - inactive. Mutation at the l146 position resulted in complete disruption
AB  - of the dimer. The replacement of l146 led to drastically reduced DNA
AB  - and cofactor binding. Substitution of l161 resulted in weakening of the
AB  - interaction between monomers, leading to both monomeric and dimeric
AB  - species. Steady-state fluorescence measurements showed that the
AB  - wild-type KpnI MTase induces structural distortion in bound DNA, while
AB  - the mutant MTases do not. The results establish that monomeric MTase is
AB  - catalytically inactive and that dimerisation is an essential event for
AB  - M.Kpnl to catalyse the methyl transfer reaction.
ER  -

TY  - JOUR
AU  - Bheemanaik, S.
AU  - Chandrashekaran, S.
AU  - Nagaraja, V.
AU  - Rao, D.N.
TI  - Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 7863
EP  - 7874
VL  - 278
AB  - KpnI DNA-(N(6)-adenine)-methyltransferase (KpnI MTase) is a member of a
AB  - restriction-modification (R-M) system in Klebsiella pneumoniae and
AB  - recognizes the sequence 5'-GGTACC-3'. It modifies the recognition sequence
AB  - by transferring the methyl group from S-adenosyl-l-methionine (AdoMet) to
AB  - the N(6) position of adenine residue. KpnI MTase occurs as a dimer in
AB  - solution as shown by gel filtration and chemical cross-linking analysis.
AB  - The nonlinear dependence of methylation activity on enzyme concentration
AB  - indicates that the functionally active form of the enzyme is also a dimer.
AB  - Product inhibition studies with KpnI MTase showed that
AB  - S-adenosyl-l-homocysteine is a competitive inhibitor with respect to
AB  - AdoMet and noncompetitive inhibitor with respect to DNA. The methylated
AB  - DNA showed noncompetitive inhibition with respect to both DNA and AdoMet.
AB  - A reduction in the rate of methylation was observed at high concentrations
AB  - of duplex DNA. The kinetic analysis where AdoMet binds first followed by
AB  - DNA, supports an ordered bi bi mechanism. After methyl transfer,
AB  - methylated DNA dissociates followed by S-adenosyl-l-homocysteine.
AB  - Isotope-partitioning analysis showed that KpnI MTase-AdoMet complex is
AB  - catalytically active.
ER  -

TY  - JOUR
AU  - Bheemanaik, S.
AU  - Reddy, Y.V.R.
AU  - Rao, D.N.
TI  - Structure, function and mechanism of exocyclic DNA methyltransferases.
JO  - Biochem. J.
PY  - 2006
SP  - 177
EP  - 190
VL  - 399
AB  - DNA MTases (methyltransferases) catalyse the transfer of methyl groups to DNA from AdoMet
AB  - (S-adenosyl-L-methionine) producing AdoHcy
AB  - (S-adenosyl-L-homocysteine) and methylated DNA. The C-5 and N-4
AB  - positions of cytosine and N-6 position of adenine are the target sites
AB  - for methylation. All three methylation patterns are found in
AB  - prokaryotes, whereas cytosine at the C-5 position is the only
AB  - methylation reaction that is known to occur in eukaryotes. In general,
AB  - MTases are two-domain proteins comprising one large and one small
AB  - domain with the DNA-binding cleft located at the domain interface. The
AB  - striking feature of all, the structurally characterized DNA MTases is
AB  - that they share a common core structure referred to as an
AB  - 'AdoMet-dependent MTase fold'. DNA methylation has been reported to be
AB  - essential for bacterial virulence, and it has been suggested that DNA
AB  - adenine MTases (Dams) could be potential targets for both vaccines and
AB  - antimicrobials. Drugs that block Dam could slow down bacterial growth
AB  - and therefore drug-design initiatives could result in a whole new
AB  - generation of antibiotics. The transfer of larger chemical entities in
AB  - A MTase-catalysed reaction has been reported and this represents an
AB  - interesting challenge for bio-organic chemists. In general, amino
AB  - MTases could therefore be used as delivery systems for fluorescent or
AB  - other reporter groups on to DNA. This is one of the potential
AB  - applications of DNA MTases towards developing non-radioactive DNA
AB  - probes and these could have interesting applications in molecular
AB  - biology. Being nucleotide-sequence-specific, DNA MTases provide
AB  - excellent model systems for studies on protein-DNA interactions. The
AB  - focus of this review is on the chemistry, enzymology and structural
AB  - aspects of exocyclic amino MTases.
ER  -

TY  - JOUR
AU  - Bheemanaik, S.
AU  - Reddy, Y.V.R.
AU  - Rao, D.N.
TI  - Structure, function and mechanism of exocyclic DNA methyltransferases (vol 399, pg 177, 2006).
JO  - Biochem. J.
PY  - 2006
SP  - 543
EP  - 543
VL  - 399
AB  - In Table 2, the Kd(DNA) values for the enzyme M.EcoRI were incorrect.  The correct table
AB  - appears here.
ER  -

TY  - JOUR
AU  - Bheemanaik, S.
AU  - Sistla, S.
AU  - Krishnamurthy, V.
AU  - Sampath, A.
AU  - Desirazu, N.R.
TI  - Kinetics of methylation by EcoP1I DNA methyltransferase.
JO  - Enzyme Res.
PY  - 2010
SP  - 302731
EP  - 302731
VL  - 2010
AB  - EcoP1I DNA MTase (M.EcoP1I), an N6-adenine MTase from bacteriophage P1, is a part of the
AB  - EcoP1I restriction-modification
AB  - (R-M) system which belongs to the Type III R-M system. It recognizes the sequence
AB  - 5'-AGACC-3' and methylates the internal adenine. M.EcoP1I requires Mg2+ for the transfer of
AB  - methyl groups to DNA. M.EcoP1I is shown to exist as dimer in solution, and even at high salt
AB  - concentrations (0.5M) the dimeric M.EcoP1I does not dissociate into monomers suggesting a
AB  - strong interaction
AB  - between the monomer subunits. Preincubation and isotope partitioning studies with M.EcoP1I
AB  - indicate a kinetic mechanism where the duplex DNA binds first followed by AdoMet.
AB  - Interestingly, M.EcoP1I methylates DNA substrates in the presence of Mn2+ and Ca2+ other than
AB  - Mg2+ with varying affinities. Amino acid analysis and methylation assays in the presence of
AB  - metal ions suggest that M.EcoP1I has indeed two metal ion-binding sites [358ID(x)n . . .
AB  - ExK401 and 600DxDxD604 motif]. EcoP1I DNA MTase catalyzes the transfer of methyl groups using
AB  - a distributive mode of methylation on DNA containing more than one recognition site. A
AB  - chemical modification of EcoP1I DNA MTase using N-ethylmaleimide resulted in an irreversible
AB  - inactivation of enzyme activity suggesting the possible role of cysteine residues in
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Bhotra, T.
AU  - Singh, D.V.
TI  - Whole-Genome Sequence of Vibrio alginolyticus Isolated from the Mucus of the Coral Fungia danai in the Andaman Sea, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00339
EP  - e00316
VL  - 4
AB  - Vibrio alginolyticus, a halophilic Gram-negative bacterium, which is found in temperate marine
AB  - and estuarine environments, is known to cause infections in
AB  - humans and other organisms. We sequenced the genome of
AB  - sulfamethoxazole-trimthoprim-positive V. alginolyticus strain 4-19 isolated from
AB  - the mucus of the coral Fungia danai in the Andaman Sea, India.
ER  -

TY  - JOUR
AU  - Bhowmick, S.
AU  - Malar, M.
AU  - Das, A.
AU  - Kumar-Thakur, B.
AU  - Saha, P.
AU  - Das, S.
AU  - Rashmi, H.M.
AU  - Batish, V.K.
AU  - Grover, S.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of Lactobacillus casei Lbs2.
JO  - Genome Announcements
PY  - 2014
SP  - e01326
EP  - e01314
VL  - 2
AB  - We report here a 3.2-Mb draft assembled genome of Lactobacillus casei Lbs2. The bacterium
AB  - shows probiotic and immunomodulatory activities. The genome assembly
AB  - and annotation will help to identify molecules and pathways responsible for
AB  - interaction between the host immune system and the microbe.
ER  -

TY  - JOUR
AU  - Bhugra, B.
AU  - Voelker, L.L.
AU  - Zou, N.
AU  - Yu, H.
AU  - Dybvig, K.
TI  - Mechanism of antigenic variation in Mycoplasma pulmonis: interwoven, site-specific DNA inversions.
JO  - Mol. Microbiol.
PY  - 1995
SP  - 703
EP  - 714
VL  - 18
AB  - The chromosome of the murine pathogen Mycoplasma pulmonis undergoes rearrangements at a high
AB  - frequency.  We show that some of these rearrangements regulate the phase-variable expression
AB  - of a cluster of genes (the vsa locus) that encode the variable V-1 surface antigens.  Only one
AB  - vsa gene is associated with an expression site; the other vsa genes are transcriptionally
AB  - silent.  The silent genes lack the 5' end region (promoter and ribosome-binding site) that is
AB  - present in the expressed gene, and DNA rearrangements regulate gene expression by reassorting
AB  - the 5' end region from an expressed gene with the 3' end region from a previously silent
AB  - gene.  All vsa rearrangements identified so far are site-specific DNA inversions that occur
AB  - between copies of a specific 34bp sequence that is conserved in each vsa gene.  Interestingly,
AB  - DNA inversions within the vsa locus apparently occur in concert with inversion of the hsd1
AB  - element, which regulates restriction and modification activity in M. pulmonis.
ER  -

TY  - JOUR
AU  - Bian, F.
AU  - Qin, Q.L.
AU  - Xie, B.B.
AU  - Shu, Y.L.
AU  - Zhang, X.Y.
AU  - Yu, Y.
AU  - Chen, B.
AU  - Chen, X.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Complete Genome Sequence of Seawater Bacterium Glaciecola nitratireducens FR1064T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7006
EP  - 7007
VL  - 193
AB  - Glaciecola nitratireducens strain FR1064(T) was isolated from seawater and described as a new
AB  - species by Baik et al. in 2006. The genome size is
AB  - about 1.01 to 1.26 Mb smaller than two reported Glaciecola genomes,
AB  - indicating the gain or loss of large genome segments in the evolution of
AB  - Glaciecola strains.
ER  -

TY  - JOUR
AU  - Bian, F.
AU  - Xie, B.B.
AU  - Qin, Q.L.
AU  - Shu, Y.L.
AU  - Zhang, X.Y.
AU  - Yu, Y.
AU  - Chen, B.
AU  - Chen, X.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Genome sequences of six pseudoalteromonas strains isolated from arctic sea ice.
JO  - J. Bacteriol.
PY  - 2012
SP  - 908
EP  - 909
VL  - 194
AB  - Yu et al. (Polar Biol. 32:1539-1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic
AB  - sea ice. We sequenced the genomes of six of these
AB  - strains, which are affiliated to different Pseudoalteromonas species based
AB  - on 16S rRNA gene sequences, facilitating the study of physiology and
AB  - adaptation of Arctic sea ice Pseudoalteromonas strains.
ER  -

TY  - JOUR
AU  - Bian, J.
AU  - Li, C.
TI  - Disruption of a Type II Endonuclease (TDE0911) Enables Treponema denticola ATCC 35405 To Accept an Unmethylated Shuttle Vector.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 4573
EP  - 4578
VL  - 77
AB  - The oral spirochete Treponema denticola is associated with human periodontal disease. T.
AB  - denticola ATCC 35405 and ATCC 33520 are two
AB  - routinely used laboratory strains. Compared to T. denticola ATCC 33520,
AB  - ATCC 35405 is more virulent but less accessible to genetic
AB  - manipulations. For instance, the shuttle vectors of ATCC 33520 cannot
AB  - be transformed into strain ATCC 35405. The lack of a shuttle vector has
AB  - been a barrier to study the biology and virulence of T. denticola ATCC
AB  - 35405. In this report, we hypothesize that T. denticola ATCC 35405 may
AB  - have a unique DNA restriction-modification (R-M) system that prevents
AB  - it from accepting the shuttle vectors of ATCC 33520 (e. g., the shuttle
AB  - plasmid pBFC). To test this hypothesis, DNA restriction digestion, PCR,
AB  - and Southern blot analyses were conducted to identify the differences
AB  - between the R-M systems of these two strains. DNA restriction digestion
AB  - analysis of these strains showed that only the cell extract from ATCC
AB  - 35405 was able to digest pBFC. Consistently, PCR and Southern blot
AB  - analyses revealed that the genome of T. denticola ATCC 35405 encodes
AB  - three type II endonucleases that are absent in ATCC 33520. Among these
AB  - three endonucleases, TDE0911 was predicted to cleave unmethylated
AB  - double-stranded DNA and to be most likely responsible for the cleavage
AB  - of unmethylated pBFC. In agreement with this prediction, the mutant of
AB  - TDE0911 failed to cleave unmethylated pBFC plasmid, and it could accept
AB  - the unmethylated shuttle vector. The study described here provides us
AB  - with a new tool and strategy to genetically manipulate T. denticola, in
AB  - particular ATCC 35405, and other strains that may carry similar
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Bianco, P.R.
AU  - Hurley, E.M.
TI  - The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 837
EP  - 859
VL  - 352
AB  - Type I restriction endonuclease holoenzymes contain methylase (M), restriction (R) and
AB  - specificity (S) subunits, present in an M-2:R-2:S-1
AB  - stoichiometry. These enzymes bind to specific DNA sequences and
AB  - translocate dsDNA in an ATP-dependent manner toward the holoenzyme
AB  - anchored at the recognition sequence. Once translocation is impeded,
AB  - DNA restriction, which functions to protect the host cell from invading
AB  - DNA, takes place. Translocation and DNA cleavage are afforded by the
AB  - two diametrically opposed R-subunits. To gain insight into the
AB  - mechanism of translocation, a detailed characterization of the ATPase
AB  - activity of EcoR124I was done. Results show that following recognition
AB  - sequence binding, ATP hydrolysis-coupled, bidirectional DNA
AB  - translocation by EcoR124I ensues, with the R-subunits transiently
AB  - disengaging, on average, every 515 bp. Macroscopic processivity of
AB  - 2031( 184) bp is maintained, as the R-subunits remain in close
AB  - proximity to the DNA through association with the methyltransferase.
AB  - Transient uncoupling of ATP hydrolysis from translocation results in
AB  - 3.1( 0.4) ATP molecules being hydrolyzed per base-pair translocated
AB  - per R-subunit. This is the first clear demonstration of the coupling of
AB  - ATP hydrolysis to dsDNA translocation, albeit inefficient. Once
AB  - translocation is impeded on supercoiled DNA, the DNA is cleaved. DNA
AB  - cleavage inactivates the EcoR124I holoenzyme partially and reversibly,
AB  - which explains the stoichiometric behaviour of type I restriction
AB  - enzymes. Inactivated holoenzyme remains bound to the DNA at the
AB  - recognition sequence and immediately releases the nascent ends. The
AB  - release of nascent ends was demonstrated using a novel,
AB  - fluorescence-based, real-time assay that takes advantage of the ability
AB  - of the Escherichia coli RecBCD enzyme to unwind restricted dsDNA. The
AB  - resulting unwinding of EcoR124I-restricted DNA by RecBCD reveals
AB  - coordination between the restriction-modification and recombination
AB  - systems that functions to destroy invading DNA efficiently. In
AB  - addition, we demonstrate the displacement of EcoR124I following DNA
AB  - cleavage by the translocating RecBCD enzyme, resulting in the
AB  - restoration of catalytic function to EcoR124I.
ER  -

TY  - JOUR
AU  - Bianco, P.R.
AU  - Xu, C.
AU  - Chi, M.
TI  - Type I restriction endonucleases are true catalytic enzymes.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3377
EP  - 3390
VL  - 37
AB  - Type I restriction endonucleases are intriguing, multifunctional complexes that restrict DNA
AB  - randomly, at sites distant from the target sequence.
AB  - Restriction at distant sites is facilitated by ATP hydrolysis-dependent,
AB  - translocation of double-stranded DNA towards the stationary enzyme bound
AB  - at the recognition sequence. Following restriction, the enzymes are
AB  - thought to remain associated with the DNA at the target site, hydrolyzing
AB  - copious amounts of ATP. As a result, for the past 35 years type I
AB  - restriction endonucleases could only be loosely classified as enzymes
AB  - since they functioned stoichiometrically relative to DNA. To further
AB  - understand enzyme mechanism, a detailed analysis of DNA cleavage by the
AB  - EcoR124I holoenzyme was done. We demonstrate for the first time that type
AB  - I restriction endonucleases are not stoichiometric but are instead
AB  - catalytic with respect to DNA. Further, the mechanism involves formation
AB  - of a dimer of holoenzymes, with each monomer bound to a target sequence
AB  - and, following cleavage, each dissociates in an intact form to bind and
AB  - restrict subsequent DNA molecules. Therefore, type I restriction
AB  - endonucleases, like their type II counterparts, are true enzymes. The
AB  - conclusion that type I restriction enzymes are catalytic relative to DNA
AB  - has important implications for the in vivo function of these previously
AB  - enigmatic enzymes.
ER  -

TY  - JOUR
AU  - Bianconi, I.
AU  - D'Arcangelo, S.
AU  - Benedet, M.
AU  - Bailey, K.E.
AU  - Esposito, A.
AU  - Piffer, E.
AU  - Mariotto, A.
AU  - Baldo, E.
AU  - Dinnella, G.
AU  - Gualdi, P.
AU  - Schinella, M.
AU  - Donati, C.
AU  - Jousson, O.
TI  - Draft Genome Sequences of 40 Pseudomonas aeruginosa Clinical Strains Isolated from the Sputum of a Single Cystic Fibrosis Patient Over an 8-Year Period.
JO  - Genome Announcements
PY  - 2016
SP  - e01205
EP  - e01216
VL  - 4
AB  - We report draft genome sequences of 40 Pseudomonas aeruginosa strains, isolated from the
AB  - sputum of a single cystic fibrosis patient over eight years. Analyses
AB  - indicated a correlation between multidrug-resistant phenotypes and population
AB  - structure. Our data provide new insights into the mechanisms leading to
AB  - acquisition of antibiotic resistance in P. aeruginosa.
ER  -

TY  - JOUR
AU  - Bickle, T.
AU  - Arber, W.
TI  - Host-controlled restriction and modification of filamentous I- and F-specific bacteriophages.
JO  - Virology
PY  - 1969
SP  - 605
EP  - 607
VL  - 39
AB  - In the study of strain-specific DNA restriction and modification, the DNA
AB  - molecules of small bacteriophages have proved very useful, particularly those
AB  - possessing only one sitie of affinity for the enzymes of a given restriction
AB  - and modification system.  The male specific phage fd and other small phages
AB  - closely related to fd undergo host-controlled modification in E. coli B, and
AB  - some are also modified in P1-lysogenic strains.  However, they are not
AB  - restricted in E. coli K12 or in strains carrying two other specificity systems,
AB  - as shown here, probably because their DNA lacks the appropriate specificity
AB  - sites.  With the aim of finding small phages restricted by host specificity
AB  - systems to which fd does not respond, we have screened other filamentous
AB  - bacteriophages for their responses to these sytems, including the two
AB  - I-specific phages If1 and If2 and two additional F-specific phages, Ec9 and HR.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
TI  - The ATP-dependent restriction enzymes.
JO  - Nucleases
PY  - 1993
SP  - 89
EP  - 109
VL  - 0
AB  - *
AB  -   I. Introduction
AB  - 
AB  -  II. Type I restriction enzymes
AB  -         A. Occurrences
AB  -         B. Structural genes
AB  -         C. Family relationships among type I restriction enzymes
AB  -             1. DNA and protein sequence homologies within families
AB  -             2. DNA and protein sequence homologies between families
AB  -         D. Evolution of DNA sequence specificity in type I enzymes
AB  -             1. By homologous recombination
AB  -             2. By unequal crossing over
AB  -             3. By transposition
AB  -         E. Enzyme structure and mechanisms
AB  -             1. Enzyme structures
AB  -             2. Enzyme mechanisms
AB  - 
AB  - III. Type III restriction enzymes
AB  -         A. Occurrence
AB  -         B. Genetics
AB  -         C. Enzyme mechanism
AB  -         D. DNA cleavage
AB  - 
AB  -  IV. Concluding remarks
AB  - 
ER  -

TY  - JOUR
AU  - Bickle, T.A.
TI  - The ATP-dependent restriction endonucleases.
JO  - Nucleases
PY  - 1982
SP  - 85
EP  - 108
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Bickle, T.A.
TI  - DNA restriction and modification systems.
JO  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
PY  - 1987
SP  - 692
EP  - 696
VL  - 1
AB  - The phenomenon of DNA restriction and modification was discovered in
AB  - Escherichia coli more than three decades ago by Bertani and Weigle in the
AB  - course of experiments with the phages P2 and lambda.  They found that phages
AB  - grown on E. coli K-12 plated with equal efficiency on strains K-12 and C, but
AB  - the converse was not true:  phage grown on E. coli C plated with high
AB  - efficiency on E. coli C but poorly on E. coli K-12.  Moreover, a single cycle
AB  - of growth in E. coli C was sufficient to remove the ability to grow well in E.
AB  - coli K-12.  The molecular explanation for this Lamarckian effect came from a
AB  - series of experiments conducted in Arber's laboratory in the 1960s.  The DNA of
AB  - phage grown in E. coli C is degraded by a DNA sequence-specific endonuclese
AB  - present in E. coli K-12.  When the phage are grown in E. coli K-12, the DNA is
AB  - protected from the endonuclease because a DNA methylase present in E. coli K-12
AB  - and absent from E. coli C methylates the sequences recognized by the
AB  - endonuclease, rendering them resistant to digestion.  Arber coined the term
AB  - host-controlled restriction and modification of DNA to describe this
AB  - phenomenon.  The endonuclease involved is a restriction endonuclease, and the
AB  - methylase is a modification methylase.  The primary function of the
AB  - modification methylase is to protect the cell's own genome from restriction.
AB  - Restriction and modification systems (R-M systems) are common throughout the
AB  - procaryotic world, and this chapter will focus on those systems that have been
AB  - found in E. coli, Salmonella typhimurium, and their close relatives.  Several
AB  - comprehensive reviews on restriction and modification have been published
AB  - recently.  These reviews should be consulted for details of the enzymology of
AB  - R-M systems and for references to the early literature.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
TI  - Restricting restriction.
JO  - Mol. Microbiol.
PY  - 2004
SP  - 3
EP  - 5
VL  - 51
AB  - Systems biology is a new, fashionable and well-funded discipline, which to quote from a recent
AB  - review aims to 'examine the structure and dynamics of cellular and organismal function, raher
AB  - than the characteristics of isolated parts of a cell or organism . . . '.  Systems biology
AB  - will do this by profiting from the vast amounts of biological information that are available
AB  - in the genomics era and make extensive use of computer modelling.  But: 'many breakthroughs
AB  - in experimental devices, advanced software and analytical methods are required before the
AB  - achievements of system biology can live up to their much-touted potential'.  This edition of
AB  - Molecular Microbiology contains a paper that is the product of traditional experimental
AB  - biology but which could serve as a test case for systems biology.  The paper shows how
AB  - bacteria integrate such disparate subsystems as DNA restriction, homologous recombination and
AB  - regulated proteolysis to protect their chromosomes from degradation.  When systems biology can
AB  - predict this level of choreography, it will be a mature discipline.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
TI  - Adenosine triphosphate-requiring restriction enzymes.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 396
EP  - 397
VL  - 8
AB  - None
ER  -

TY  - JOUR
AU  - Bickle, T.A.
TI  - Phage introns on the hop: an alternative view.
JO  - Curr. Biol.
PY  - 1992
SP  - 150
EP  - 151
VL  - 2
AB  - The nuclease encoded by a rare bacteriophage intron is very similar to one class of bacterial
AB  - restriction enzyme, and may provide clues as to the co-evolution of host and phage.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
AU  - Brack, C.
AU  - Yuan, R.
TI  - ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1978
SP  - 3099
EP  - 3103
VL  - 75
AB  - ATP induces a conformational change in the Escherichia coli K-12 restriction
AB  - enzyme that allows it to discriminate between unmodified and modified DNA
AB  - recognition sequences.  This conformational change does not require ATP
AB  - hydrolysis.  However, ATP hydrolysis is a requirement for DNA cleavage.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
AU  - Ineichen, K.
TI  - The DNA sequence recognised by BglI.
JO  - Gene
PY  - 1980
SP  - 205
EP  - 212
VL  - 9
AB  - The restriction enzyme BglI recognizes the DNA sequence: 5'-GCCNNNN^NGGC-3'
AB  - 3'-CGGN^NNNNCCG-5' and cleaves it in the position shown by the arrows to leave
AB  - 3' single-stranded protrusions three bases long.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
AU  - Kruger, D.H.
TI  - Biology of DNA Restriction.
JO  - Microbiol. Rev.
PY  - 1993
SP  - 434
EP  - 450
VL  - 57
AB  - *
AB  - Introduction
AB  - Type I R-M Systems
AB  - Type I Systems Form Families of Related Enzymes
AB  - Structure of hsd Genes
AB  - Evolution of DNA Sequence Recognition by Recombination between hsdS Genes
AB  - Mutations Affecting Modification Activity
AB  - Type II R-M Systems
AB  - Evolutionary Aspects
AB  - Control of Expression of Type II RM Genes
AB  - Cytosine Can Be Methylated on Either C-5 or N4: Consequences for Mutagenesis
AB  - Type II Restriction Endonuclease That Require Two Recognition Sites for Cleavage
AB  - What is the Function of Type IIS Enzymes?
AB  - Type III R-M Systems
AB  - Genetics of Type III Systems
AB  - DNA Recognition by Type III Enzymes:
AB  -    Different Sequence Requirements for Restriction and Modification
AB  - Sty LTI System
AB  - Restriction Systems Specific and Modified DNA
AB  - DpnI and DpnII
AB  - Rediscovery of Methyl-Directed Restriction in E. coli
AB  - McrBC
AB  - McrA
AB  - Mrr
AB  - Phage Antirestriction
AB  - Recent Developments
AB  - "Nature Red in Tooth and Claw": The case of Phage T4
AB  - Concluding Remarks
AB  - Acknowledgments
AB  - References
AB  - 
ER  -

TY  - JOUR
AU  - Bickle, T.A.
AU  - Pirrotta, V.
AU  - Imber, R.
TI  - A simple, general procedure for purifying restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 2561
EP  - 2572
VL  - 4
AB  - A simple, general method for purifying restriction endonucleases is described.
AB  - The method employs precipitation of nucleic acids from crude extracts with
AB  - polyethyleneimine followed by affinity chromatography on columns of heparin
AB  - covalently linked to agarose.  Most of the sixteen enzymes tested could be
AB  - purified to a degree sufficient for DNA sequencing work by this method
AB  - sometimes supplemented by at most one step of ion exchange chromatography.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
AU  - Pirrotta, V.
AU  - Imber, R.
TI  - Purification and properties of the BglI and II endonucleases.
JO  - Methods Enzymol.
PY  - 1980
SP  - 132
EP  - 138
VL  - 65
AB  - The presence of two distinct restriction endonucleases in Bacillus globigii,
AB  - BglI and II, was first reported by Wilson and Young.
ER  -

TY  - JOUR
AU  - Bickle, T.A.
AU  - Streiff, M.
TI  - Methods for purification of restriction enzymes.
JO  - Nucleic Acid Biochem.
PY  - 1983
SP  - 1
EP  - 8
VL  - B510
AB  - None
ER  -

TY  - JOUR
AU  - Biddle, A.S. et al.
TI  - The complete genome sequence of Clostridium indolis DSM 755(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1089
EP  - 1104
VL  - 9
AB  - Clostridium indolis DSM 755(T) is a bacterium commonly found in soils and the feces of birds
AB  - and mammals. Despite its prevalence, little is known about the
AB  - ecology or physiology of this species. However, close relatives, C.
AB  - saccharolyticum and C. hathewayi, have demonstrated interesting metabolic
AB  - potentials related to plant degradation and human health. The genome of C.
AB  - indolis DSM 755(T) reveals an abundance of genes in functional groups associated
AB  - with the transport and utilization of carbohydrates, as well as citrate, lactate,
AB  - and aromatics. Ecologically relevant gene clusters related to nitrogen fixation
AB  - and a unique type of bacterial microcompartment, the CoAT BMC, are also detected.
AB  - Our genome analysis suggests hypotheses to be tested in future culture based work
AB  - to better understand the physiology of this poorly described species.
ER  -

TY  - JOUR
AU  - Bidle, K.D.
AU  - Lee, S.
AU  - Marchant, D.R.
AU  - Falkowski, P.G.
TI  - Fossil genes and microbes in the oldest ice on earth.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 13455
EP  - 13460
VL  - 104
AB  - Although the vast majority of ice that formed on the Antarctic continent over the past 34
AB  - million years has been lost to the oceans, pockets of
AB  - ancient ice persist in the Dry Valleys of the Transantarctic Mountains.
AB  - Here we report on the potential metabolic activity of microbes and the
AB  - state of community DNA in ice derived from Mullins and upper Beacon
AB  - Valleys. The minimum age of the former is 100 ka, whereas that of the
AB  - latter is approximately 8 Ma, making it the oldest known ice on Earth. In
AB  - both samples, radiolabeled substrates were incorporated into
AB  - macromolecules, and microbes grew in nutrient-enriched meltwaters, but
AB  - metabolic activity and cell viability were critically compromised with
AB  - age. Although a 16S rDNA-based community reconstruction suggested
AB  - relatively low bacterial sequence diversity in both ice samples,
AB  - metagenomic analyses of community DNA revealed many diverse orthologs to
AB  - extant metabolic genes. Analyses of five ice samples, spanning the last 8
AB  - million years in this region, demonstrated an exponential decline in the
AB  - average community DNA size with a half-life of approximately 1.1 million
AB  - years, thereby constraining the geological preservation of microbes in icy
AB  - environments and the possible exchange of genetic material to the oceans.
ER  -

TY  - JOUR
AU  - Biedrzycka, I.
AU  - Sektas, M.
AU  - Kaczorowski, T.
TI  - Characterization of pEC156, a ColE1-type plasmid from Escherichia coli E1585-68 that carries genes of the EcoVIII restriction-modification system.
JO  - Plasmid
PY  - 2001
SP  - 161
EP  - 161
VL  - 45
AB  - Type II restriction-modification systems are common in prokaryotes.  It is believed that they
AB  - evolved to protect these organisms against viral invasion.  Genes encoding R-M systems are
AB  - often present on natural plasmids which may facilitate the spread of these systems among
AB  - bacteria by horizontal gene transfer.  It has been shown that the genes coding for R-M systems
AB  - can increase the stability of the plasmids which carry them.  Bacterial strains isolated from
AB  - clinical specimens are especially abundant in plasmids.  Some of them possess Hsd (host
AB  - specificity for DNA) plasmids carrying R-M systems.  The strain of E. coli E1585-68 used in
AB  - our study was isolated from a patient in England in 1973, and since then it has often been
AB  - used as a reference strain for the E. coli O156 serotype.  Later it was discovered that this
AB  - strain possesses a natural plasmid (pEC156), carrying genes for the EcoVIII R-M system, a
AB  - HindIII isoschizomer.  The complete 4312-bp sequence of the plasmid pEC156 has been
AB  - determined.  The plasmid, numbering 20 copies per cell, has been sequenced on both strands and
AB  - the sequence has been deposited in GenBank (Accession No. AF158026).  The pEC156 plasmid
AB  - carries genes encoding the EcoVIII R-M system - an isoschizomer of HindIII from Haemophilus
AB  - influenzae.  Nucleotide sequence analysis of pEC156 suggests that this plasmid possesses a
AB  - ColE1 replicon.  It consists of an origin of replication and two untranslated genes encoding
AB  - RNAI and RNAII, both involved in the regulation of plasmid DNA replication.  The replication
AB  - region also contains a gene, encoding a 64-amino-acid Rom-like (RNA one modulator) peptide,
AB  - which presumably is involved in the negative regulation of plasmid pEC156 replication by
AB  - stabilizing the NRAI-RNAII complex.  The DNA sequence homologous to the rom region of ColE1
AB  - plasmids was also identified.  The stable maintenance of ColE1 plasmids in bacteria depends on
AB  - the existence of cis-acting cer locus, which ensures that at cell division each daughter cell
AB  - receives at least one copy of the plasmid.  Computational analysis of pEC156 nucleotide
AB  - sequence revealed the presence of a DNA region that has high homology to the cer locus of
AB  - ColE1 plasmid.  The replication of all ColE1-type plasmids is dependent on the activity of E.
AB  - coli DNA polymerase I.  It was shown that pEC156 derivatives carrying antibiotic resistance
AB  - genes failed to replicate in an E. coli polA12(ts) mutant at 43oC.  It was also shown that the
AB  - pEC156 plasmid copy number increase after treating bacteria with chloramphenicol and decrease
AB  - in E. coli pcnB80 mutant.  The pEC156 plasmid carries the genes encoding the EcoVIII R-M
AB  - system belonging to type II family.  This system consists of two separate enzymes: an
AB  - endonuclease and cognate methyltransferase.  The first of them is the EcoVIII endonuclease
AB  - which recognizes specific nucleotide sequence and is capable of cleaving two strands of DNA at
AB  - the recognition site, between two adenine residues in the recognition site:
AB  - A'A/AGCT-3'/3'TTCGA/A.  the second component is the methyltransferase, which protects
AB  - bacterial DNA against cleavage by cognate endonuclease.  Both proteins have been purified and
AB  - characterized.
ER  -

TY  - JOUR
AU  - Bielas, J.H.
AU  - Loeb, L.A.
TI  - Quantification of random genomic mutations.
JO  - Nat. Methods
PY  - 2005
SP  - 285
EP  - 290
VL  - 2
AB  - Cancer cells contain numerous clonal mutations. It has been theorized that malignant cells
AB  - sustain an elevated mutation rate and, as a consequence, harbor yet larger numbers of random
AB  - point mutations. Testing this hypothesis has been precluded by lack of an assay to measure
AB  - random mutations-that is, mutations that occur in only one or a few cells of a population. We
AB  - have established a method that has permitted us to detect and identify rare random mutations
AB  - in human cells, at a frequency of 1 per 10(8) base pairs. The assay is based on gene capture,
AB  - by hybridization with a uracil-containing probe, followed by magnetic separation. Mutations
AB  - that render the mutational target sequence non-cleavable by a restriction enzyme are
AB  - quantified by dilution to single molecules and real-time quantitative PCR amplification. The
AB  - assay can be extended to quantify mutation in any DNA-based organism, at different sites in
AB  - the genome, in introns and exons, in unselected and selected genes, and in proliferating and
AB  - quiescent cells.
ER  -

TY  - JOUR
AU  - Bier, F.F.
AU  - Kleinjung, F.
AU  - Schmidt, P.M.
AU  - Scheller, F.W.
TI  - Determination of the turnover number of the restriction endonuclease EcoRI using evanescent wave technology.
JO  - Anal. Bioanal. Chem.
PY  - 2002
SP  - 308
EP  - 313
VL  - 372
AB  - Binding and catalytic activity of the type II restriction endonuclease EcoRI on immobilized
AB  - DNA has been observed in real time using three different evanescent wave biosensors and two
AB  - different immobilization techniques.  The method gives direct access to the turnover number
AB  - (kcat) without the necessity for the determination of any concentration or activity.  The
AB  - combination of different evanescent wave techniques gives access to the catalytic mechanism
AB  - and allows the determination of the rate limiting step.
ER  -

TY  - JOUR
AU  - Bigey, P.
AU  - Knox, J.D.
AU  - Croteau, S.
AU  - Bhattacharya, S.K.
AU  - Theberge, J.
AU  - Szyf, M.
TI  - Modified oligonucleotides as bona fide antagonists of proteins interacting with DNA.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 4594
EP  - 4606
VL  - 274
AB  - The study of the biological role of DNA methyltransferase has been impeded by the lack of
AB  - direct and specific inhibitors.  This report describes the design of potent DNA based
AB  - antagonists of DNA MeTase and their utilization to define the interactions of DNA MeTase with
AB  - its substrate and to study its biological role.  We demonstrate that the size, secondary
AB  - structure, hemimethylation, and phosphorothioate modification strongly affect the antagonists
AB  - interaction with DNA MeTase whereas base substitutions do not have a significant effect.  To
AB  - study whether DNA MeTase is critical for cellular transformation, human lung non-small
AB  - carcinoma cells were treated with the DNA MeTase antagonists.  Ex vivo, hairpin inhibitors of
AB  - DNA MeTase are localized to the cell nucleus in lung cancer cells.  They inhibit DNA MeTase,
AB  - cell growth, and anchorage independent growth (an indicator of tumorigenesis in cell culture)
AB  - in a dose-dependent manner.  The inhibitors developed in this study are the first documented
AB  - example of direct inhibitors of DNA MeTase in living cells and of modified oligonucleotides as
AB  - bona fide antagonists of critical cellular proteins.
ER  -

TY  - JOUR
AU  - Bigey, P.
AU  - Ramchandani, S.
AU  - Theberge, J.
AU  - Araujo, F.D.
AU  - Szyf, M.
TI  - Transcriptional regulation of the human DNA methyltransferase (dnmt1) gene.
JO  - Gene
PY  - 2000
SP  - 407
EP  - 418
VL  - 242
AB  - DNA methylation is an important component of the epigenetic control of genome functions.
AB  - Understanding the regulation of the DNA Methyltransferase (dnmt1) gene expression is critical
AB  - for comprehending how DNA methylation is coordinated with other critical biological
AB  - processes. In this paper, we investigate the transcriptional regulatory
AB  - region of the human dnmt1 gene using a combination of RACE, RNase
AB  - protection analysis and CAT assays. We identified one major and three
AB  - minor transcription initiation sites in vivo (P1-P4), which are
AB  - regulated by independent enhancers and promoter sequences. The minimal
AB  - promoter elements of P1, P2 and P4 are mapped within 256 bp upstream of
AB  - their respective transcription initiation sites. P1 is nested within a
AB  - CC-rich area, similar to other housekeeping genes, whereas P2-P4 are
AB  - found in CG-poor areas. Three c-Jun-dependent enhancers are located
AB  - downstream to P1 and upstream to P2-P4, thus providing a molecular
AB  - explanation for the responsiveness of dnmt1 to oncogenic signals that
AB  - are mediated by the Ras-c-Jun oncogenic signaling pathway.
ER  -

TY  - JOUR
AU  - Bigger, C.H.
AU  - Murray, K.
AU  - Murray, N.E.
TI  - Recognition sequence of a restriction enzyme.
JO  - Nature New Biol.
PY  - 1973
SP  - 7
EP  - 10
VL  - 244
AB  - Restriction endonuclease EcoRII makes about twenty double-stranded breaks per
AB  - molecule of lambda h80 DNA.  The 5'- terminal sequences are pC-C-A-G-G and
AB  - pC-C-T-G-G.  These are complementary and rotationally symmetrical, showing how
AB  - the enzyme may produce DNA fragments with short cohesive ends.
ER  -

TY  - JOUR
AU  - Bikandi, J.
AU  - San, M.R.
AU  - Rementeria, A.
AU  - Garaizar, J.
TI  - In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.
JO  - Bioinformatics
PY  - 2004
SP  - 798
EP  - 799
VL  - 20
AB  - We have developed a website, www.in-silico.com, which runs a software program that performs
AB  - three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR
AB  - amplification, amplified fragment length polymorphism (AFLP-PCR) and endonuclease restriction.
AB  - For PCR, after selection of the genome and introduction of primers, fragment size, DNA
AB  - sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is
AB  - computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP-PCR
AB  - analyzes similar parameters, and includes a suggestion tool providing a list of commercial
AB  - restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease
AB  - restriction analysis of complete genomes and plasmids calculates the number of restriction
AB  - sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed
AB  - field gel electrophoresis image and restriction maps are illustrated. Other tools that have
AB  - been included in this site are ORF search by name and DNA to protein translation as well as
AB  - restriction digestion of user-defined DNA sequences. AVAILABILITY: This is a new molecular
AB  - biology resource freely available over the Internet at http://www.in-silico.com
ER  -

TY  - JOUR
AU  - Bilcock, D.T.
AU  - Daniels, L.E.
AU  - Bath, A.J.
AU  - Halford, S.E.
TI  - Reactions of type II restriction endonucleases with 8-base pair recognition sites.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 36379
EP  - 36386
VL  - 274
AB  - Type II restriction endonucleases usually recognize 4-6-base pair (bp) sites on DNA and cleave
AB  - each site in a separate reaction.  A few type II endonucleases have 8-bp recognition sites,
AB  - but these seem unsuited for restriction, since their sites are rare on most DNA. Moreover,
AB  - only one endonuclease that recognizes a target containing 8 bp has been examined to date, and
AB  - this enzyme, SfiI, needs two copies of this site for its DNA cleavage reaction. In this study,
AB  - several endonucleases with 8-bp sites were tested on plasmids that have either one or two
AB  - copies of the relevant sequence to determine if they also need two sites. SgfI, SrfI, FseI,
AB  - PacI, PmeI, Sse8781I, and SdaI all acted through equal and independent reactions at each site.
AB  - AscI cleaved the DNA with one site at the same rate as that with two sites but acted
AB  - processively on the latter. In contrast, SgrAI showed a marked preference for the plasmid with
AB  - two sites and cleaved both sites on this DNA in a concerted manner, like SfiI. Endonucleases
AB  - that require two copies of an 8-bp sequence may be widespread in nature, where, despite this
AB  - seemingly inappropriate requirement, they may function in DNA restriction.
ER  -

TY  - JOUR
AU  - Bilcock, D.T.
AU  - Halford, S.E.
TI  - DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli.
JO  - Mol. Microbiol.
PY  - 1999
SP  - 1243
EP  - 1254
VL  - 31
AB  - In contrast to many type II restriction enzymes, dimeric proteins that cleave DNA at
AB  - individual recognition sites 4-6 bp long, the SfiI endonuclease is a tetrameric protein that
AB  - binds to two copies of an elongated sequence before cutting the DNA at both sites.  The mode
AB  - of action of the SfiI endonuclease thus seems more appropriate for DNA rearrangements than for
AB  - restriction. To elucidate its biological function, strains of Escherichia coli expressing the
AB  - SfiI restriction-modification system were transformed with plasmids carrying SfiI sites. The
AB  - SfiI system often failed to restrict the survival of a plasmid with one SfiI site, but
AB  - plasmids with two or more sites were restricted efficiently.  Plasmids containing methylated
AB  - SfiI sites were not restricted.  No rearrangements of the plasmids carrying SfiI sites were
AB  - detected among the transformants.  Hence, provided the target DNA contains at least two
AB  - recognition sites, SfiI displays all of the hallmarks of a restriction-modification system as
AB  - opposed to a recombination system in E. coli cells.,  The properties of the system in vivo
AB  - match those of the enzyme in vitro.  For both restriction in vivo and DNA cleavage in vitro,
AB  - SfiI operates best with two recognition sites on the same DNA.
ER  -

TY  - JOUR
AU  - Biller, S.J.
AU  - Coe, A.
AU  - Martin-Cuadrado, A.B.
AU  - Chisholm, S.W.
TI  - Draft Genome Sequence of Alteromonas macleodii Strain MIT1002, Isolated from an Enrichment Culture of the Marine Cyanobacterium Prochlorococcus.
JO  - Genome Announcements
PY  - 2015
SP  - e00967
EP  - e00915
VL  - 3
AB  - Alteromonas spp. are heterotrophic gammaproteobacteria commonly found in marine environments.
AB  - We present here the draft genome sequence of Alteromonas macleodii  MIT1002, which was
AB  - isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus NATL2A. This
AB  - genome contains a mixture of features previously seen only within either the 'surface' or
AB  - 'deep' Alteromonas ecotype.
ER  -

TY  - JOUR
AU  - Billings, A.F.
AU  - Fortney, J.L.
AU  - Hazen, T.C.
AU  - Simmons, B.
AU  - Davenport, K.W.
AU  - Goodwin, L.
AU  - Ivanova, N.
AU  - Kyrpides, N.C.
AU  - Mavromatis, K.
AU  - Woyke, T.
AU  - DeAngelis, K.M.
TI  - Genome sequence and description of the anaerobic lignin-degrading bacterium sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 106
EP  - 106
VL  - 10
AB  - Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a
AB  - proposed novel species of the Tolumonas genus. This strain was isolated
AB  - from tropical rainforest soils based on its ability to utilize lignin as a sole
AB  - carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore
AB  - forming, Gram-negative rods that are oxidase and catalase negative. The genome
AB  - for this isolate was sequenced and returned in seven unique contigs totaling
AB  - 3.6Mbp, enabling the characterization of several putative pathways for lignin
AB  - breakdown. Particularly, we found an extracellular peroxidase involved in lignin
AB  - depolymerization, as well as several enzymes involved in beta-aryl ether bond
AB  - cleavage, which is the most abundant linkage between lignin monomers. We also
AB  - found genes for enzymes involved in ferulic acid metabolism, which is a common
AB  - product of lignin breakdown. By characterizing pathways and enzymes employed in
AB  - the bacterial breakdown of lignin in anaerobic environments, this work should
AB  - assist in the efficient engineering of biofuel production from lignocellulosic
AB  - material.
ER  -

TY  - JOUR
AU  - Billington, S.J.
AU  - Huggins, A.S.
AU  - Johanesen, P.A.
AU  - Crellin, P.K.
AU  - Cheung, J.K.
AU  - Katz, M.E.
AU  - Wright, C.L.
AU  - Haring, V.
AU  - Rood, J.I.
TI  - Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin.
JO  - Infect. Immun.
PY  - 1999
SP  - 1277
EP  - 1286
VL  - 67
AB  - The vrl locus is preferentially associated with virulent isolates
AB  - of the ovine footrot pathogen, Dichelobacter nodosus. The complete
AB  - nucleotide sequence of this 27.1-kb region has now been determined. The
AB  - data reveal that the locus has a G+C content much higher than the rest
AB  - of the D. nodosus chromosome and contains 22 open reading frames (ORFs)
AB  - encoding products including a putative adenine-specific methylase, two
AB  - potential DEAH ATP-dependent helicases, and two products with sequence
AB  - similarity to a bacteriophage resistance system. These ORFs are all in
AB  - the same orientation, and most are either overlapping or separated by
AB  - only a few nucleotides, suggesting that they comprise an operon and are
AB  - translationally coupled. Expression vector studies have led to the
AB  - identification of proteins that correspond to many of these ORFs. These
AB  - data, in combination with evidence of insertion of vrl into the 3' end
AB  - of an ssrA gene, are consistent with the hypothesis that the vrl locus
AB  - was derived from the insertion of a bacteriophage or plasmid into the
AB  - D. nodosus genome.
ER  -

TY  - JOUR
AU  - Billington, S.J.
AU  - Jost, B.H.
TI  - Multiple genetic elements carry the tetracycline resistance gene, tet(W) in the animal pathogen, Arcanobacterium pyogenes.
JO  - Antimicrob. Agents Chemother.
PY  - 2006
SP  - 3580
EP  - 3587
VL  - 50
AB  - The tet(W) gene is associated with tetracycline resistance in a wide range
AB  - of bacterial species, including obligately anaerobic rumen bacteria and
AB  - isolates from the human gut and oral mucosa. However, little is known
AB  - about how this gene is disseminated and the types of genetic elements it
AB  - is carried on. We examined tetracycline-resistant isolates of the animal
AB  - commensal and opportunistic pathogen Arcanobacterium pyogenes, all of
AB  - which carried tet(W), and identified three genetic elements designated
AB  - ATE-1, ATE-2, and ATE-3. These elements were found in 25%, 35%, and 60% of
AB  - tetracycline-resistant isolates, respectively, with some strains carrying
AB  - both ATE-2 and ATE-3. ATE-1 shows characteristics of a mobilizable
AB  - transposon, and the tet(W) genes from strains carrying this element can be
AB  - transferred at low frequencies between A. pyogenes strains. ATE-2 has
AB  - characteristics of a simple transposon, carrying only the resistance gene
AB  - and a transposase, while in ATE-3, the tet(W) gene is associated with a
AB  - streptomycin resistance gene that is 100% identical at the DNA level with
AB  - the aadE gene from the Campylobacter jejuni plasmid pCG8245. Both ATE-2
AB  - and ATE-3 show evidence of being carried on larger genetic elements, but
AB  - conjugation to other strains was not observed under the conditions tested.
AB  - ATE-1 was preferentially associated with A. pyogenes strains of bovine
AB  - origin, while ATE-2 and ATE-3 elements were primarily found in porcine
AB  - isolates, suggesting that these elements may circulate in different
AB  - environments. In addition, four alleles of the tet(W) gene, primarily
AB  - associated with different elements, were detected among A. pyogenes
AB  - isolates.
ER  -

TY  - JOUR
AU  - Bina, J.E.
AU  - Nano, F.
AU  - Hancock, R.E.W.
TI  - Utilization of alkaline phosphatase fusions to identify secreted proteins, including potential efflux proteins and virulence factors from Helicobacter pylori.
JO  - FEMS Microbiol. Lett.
PY  - 1997
SP  - 63
EP  - 68
VL  - 148
AB  - The targeted genomic strategy of random fusions to a partial gene encoding
AB  - a signal sequence-deficient fragment of bacterial alkaline phosphatase was
AB  - utilized to screen for secreted proteins in Helicobacter pylori. The
AB  - rationale for targeting extracytoplasmic proteins was based on the
AB  - hypothesis that most virulence factors and vaccine candidates are secreted
AB  - or exported proteins. In addition, extracytosolic proteins represent good
AB  - potential targets for drug intervention since they are in general more
AB  - accessible to drugs than are cytoplasmically localized proteins. The
AB  - application of this strategy to H. pylori allowed the identification of
AB  - putative virulence factors and novel targets for drug intervention
AB  - including four putative antibiotic efflux genes. The strategy used here is
AB  - rapid and technically simple, relatively inexpensive, adaptable to a wide
AB  - variety of microbes and genetic systems, and selects for expressed and
AB  - accessible proteins.
ER  -

TY  - JOUR
AU  - Binetti, A.G.
AU  - Suarez, V.B.
AU  - Tailliez, P.
AU  - Reinheimer, J.A.
TI  - Characterization of spontaneous phage-resistant variants of Streptococcus thermophilus by randomly amplified polymorphic DNA analysis and identification of phage-resistance mechanisms.
JO  - Int. Dairy Journal
PY  - 2007
SP  - 1115
EP  - 1122
VL  - 17
AB  - A total of 100 spontaneous phage-resistant mutants isolated from nine commercial Streptococcus
AB  - thermophilus strains were characterized
AB  - preliminarily by randomly amplified polymorphic DNA (RAPD) and the
AB  - nature of their phage-resistance mechanisms was investigated. Only for
AB  - mutants isolated from one strain, free phages were detected in their
AB  - culture supernatants when these were titrated on the sensitive strain,
AB  - suggesting that the mutants could have acquired the resistance
AB  - phenotype by integrating the phage in their genomes (lysogeny).
AB  - Adsorption interference was observed in the derivatives isolated from
AB  - two strains. For mutants isolated from two other strains.
AB  - restriction-modification (R-M) type systems were detected. In one of
AB  - these cases, R-M was probably combined with another intracellular
AB  - anti-phage system. In most cases, the molecular profiles (RAPD
AB  - fingerprints) obtained with four arbitrary primers showed a high
AB  - similarity among parent strains and their respective phage-resistant
AB  - mutants. Some of these mutants were identified as potentially improved
AB  - strains for industrial use.
ER  -

TY  - JOUR
AU  - Bingham, A.H.A.
AU  - Atkinson, T.
TI  - Restriction endonucleases and modification methylases in bacteria.
JO  - Biochem. Soc. Trans.
PY  - 1978
SP  - 315
EP  - 324
VL  - 6
AB  - There are three mechanisms by which foreign DNA may enter a prokaryotic organism: conjugation
AB  - between Gram-negative bacteria, uptake of exogenous DNA (transformation) and infection by
AB  - viral (bacteriophage) nucleic acid.  The interaction between a bacteriophage and its host
AB  - bacterial cell has been extensively investigated.  A bacterium can restrict phage infection
AB  - through its ability to degrade the infectious DNA on entry into the cell.  This is achieved by
AB  - site-specific deoxyriboendonucleases, called restriction endonucleases, that cleave DNA into a
AB  - limited, but defined, number of fragments, which are then susceptible to exonuclease attack.
AB  - The bacterium can prevent cleavage of its chromosomal DNA by site-specific methylation of the
AB  - nucleotide bases, for which another activity, the DNA-modification methylase, is responsible.
AB  - The modification methylase can also modify bacteriophage DNA on entry into the cell, thus
AB  - making the modified phage DNA resistant to the action of the restriction endonuclease.
AB  - Although the modification methylase protects the host bacterial chromosome, it can also afford
AB  - protection to the invading phage DNA; as a result, phages grown in a given bacterial strain
AB  - are insensitive to restriction by that strain. A review.
ER  -

TY  - JOUR
AU  - Bingham, A.H.A.
AU  - Atkinson, T.
AU  - Sciaky, D.
AU  - Roberts, R.J.
TI  - A specific endonuclease from Bacillus caldolyticus.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 3457
EP  - 3467
VL  - 5
AB  - The purification and characterization of a new restriction endonuclease, BclI,
AB  - from the extreme thermophile Bacillus caldolyticus is reported.  This enzyme
AB  - recognizes the sequence 5'-T^-G-A-T-C-A-3' 3'-A-C-T-A-G^-T-5' and cleaves at
AB  - the positions indicated by the arrows.
ER  -

TY  - JOUR
AU  - Bingham, A.H.A.
AU  - Darbyshire, J.
TI  - Isolation of two restriction endonucleases from Chloroflexus aurantiacus (CauI, CauII).
JO  - Gene
PY  - 1982
SP  - 87
EP  - 91
VL  - 18
AB  - The purification and characterization of two restriction endonucleases from the
AB  - photosynthetic gliding bacterium Chloroflexus aurantiacus are described.
ER  -

TY  - JOUR
AU  - Bingham, A.H.A.
AU  - Sharman, A.F.
AU  - Atkinson, T.
TI  - The purification of restriction endonuclease EcoRI by precipitation involving polyethyleneimine.
JO  - FEBS Lett.
PY  - 1977
SP  - 250
EP  - 256
VL  - 76
AB  - The restriction endonuclease EcoRI from an Escherichia coli containing the
AB  - plasmid pMB 1,3 or 4 is widely used in the analysis and manipulation of DNA
AB  - molecules.  The enzyme has been used in the physical mapping of viral genomes
AB  - and mitochondrial DNA, the preliminary analysis of DNA molecules and since
AB  - cleavage with EcoRI yields cohesive terminii, in the in vitro construction of
AB  - recombinant DNA molecules.  Homogeneous enzyme preparations are not essential
AB  - for the in vitro analysis and manipulation of DNA molecules; a preparation
AB  - completely free of contaminating non-specific nucleases is adequate for most
AB  - experiments.  There are several published procedures for the puruification of
AB  - EcoRI, however they all suffer from two major disadvantages, the large number
AB  - of steps involved in the preparation of exonuclease-free material and the poor
AB  - yields of the enzyme finally obtained.  The use of polyethyleneimine (PEI) for
AB  - the removal of nucleic acids from microbial extracts was demonstrated by
AB  - Atkinson and Jack, and it was found that if this procedure was carried out
AB  - under conditions of low ionic strength with an extract of E. coli RY13 the
AB  - EcoRI activity precipitated with the PEI-DNA complex.  This paper describes a
AB  - rapid, two step method for the purification of exonuclease-free EcoRI
AB  - restriction endonuclease in high yield, based on elution of the enzyme from a
AB  - PEI precipitated DNA-enzyme complex.  The preparation of other restriction
AB  - endonucleases using a similar technique is also discussed.
ER  -

TY  - JOUR
AU  - Binh, T.T.
AU  - Suzuki, R.
AU  - Kwon, D.H.
AU  - Yamaoka, Y.
TI  - Complete Genome Sequence of a Metronidazole-Resistant Helicobacter pylori Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00051
EP  - e00015
VL  - 3
AB  - We report here the complete genome sequence of a metronidazole-resistant Helicobacter pylori
AB  - strain (MET(r)). The MET(r) strain was obtained under
AB  - exposure of H. pylori 26695 on agar plates with low metronidazole concentrations.
AB  - The genome data provide insight into the genomic changes of H. pylori under
AB  - selection by metronidazole in vitro.
ER  -

TY  - JOUR
AU  - Binh, T.T.
AU  - Suzuki, R.
AU  - Shiota, S.
AU  - Kwon, D.H.
AU  - Yamaoka, Y.
TI  - Complete Genome Sequences of Helicobacter pylori Clarithromycin-Resistant Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00912
EP  - e00913
VL  - 1
AB  - We report the complete genome sequences of two Helicobacter pylori clarithromycin-resistant
AB  - strains. Clarithromycin (CLR)-resistant strains were
AB  - obtained under the exposure of H. pylori strain 26695 on agar plates with low
AB  - clarithromycin concentrations. The genome data provide insights into the genomic
AB  - changes of H. pylori under selection by clarithromycin in vitro.
ER  -

TY  - JOUR
AU  - Bini, E. et al.
TI  - Complete genome sequence of Desulfurispirillum indicum stain S5.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 371
EP  - 378
VL  - 5
AB  - Desulfurispirillum indicum strain S5T is a strictly anaerobic bacterium isolated from river
AB  - se-diment in Chennai, India. D. indicum belongs to the deep branching phylum of
AB  - Chrysioge-netes, which currently only includes three other cultured species. Strain S5T is the
AB  - type strain of the species and it is capable of growth using selenate, selenite, arsenate,
AB  - nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619
AB  - proteins and 49 RNA genes, and the information gained from its sequence will be relevant to
AB  - the elucidation of mi-crobially-mediated transformations of arsenic and selenium, in addition
AB  - to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.
ER  -

TY  - JOUR
AU  - Biniszkiewicz, D.
AU  - Cesnaviciene, E.
AU  - Shub, D.A.
TI  - Self-splicing group I intron in cyanobacterial initiator methionine tRNA: evidence for lateral transfer of introns in bacteria.
JO  - EMBO J.
PY  - 1994
SP  - 4629
EP  - 4635
VL  - 13
AB  - A group I self-splicing intron has been found in the anticodon loop of
AB  - tRNA(fMet) genes in three cyanobacterial genera: Dermocarpa, Scytonema and
AB  - Synechocystis; it is absent in nine others. The Synechocystis intron is
AB  - also interrupted by an open reading frame (ORF) of 150 codons. Of these
AB  - three bacteria, only Scytonema also contains the group I intron that has
AB  - previously been reported in tRNA(Leu) (UAA) genes in both cyanobacteria
AB  - and chloroplasts. The presence of an ORF in the tRNA(fMet) intron, the
AB  - sporadic distribution of the intron among cyanobacteria and the lack of
AB  - correlation between relatedness of the intron sequences and the bacteria
AB  - in which they reside, are all consistent with recent introduction of this
AB  - intron by lateral transfer.
ER  -

TY  - JOUR
AU  - Bioteau, A.
AU  - Huguet, K.
AU  - Burrus, V.
AU  - Banerjee, S.
TI  - Genome Sequence of a Canadian Vibrio parahaemolyticus Isolate with Unique Mobilizing Capacity.
JO  - Genome Announcements
PY  - 2018
SP  - e00520
EP  - e00518
VL  - 6
AB  - Vibrio parahaemolyticus is a clinically significant marine bacterium implicated in
AB  - gastroenteritis among consumers of raw or undercooked seafood. This report
AB  - presents the whole-genome sequence of a unique strain of V. parahaemolyticus
AB  - isolated from oysters harvested in Canada.
ER  -

TY  - JOUR
AU  - Bircakova, M.
AU  - Truksa, M.
AU  - Scouten, W.H.
TI  - Oriented immobilization of restriction endonuclease EcoRI.
JO  - J. Mol. Recognit.
PY  - 1996
SP  - 683
EP  - 690
VL  - 9
AB  - Two activated matrices have been developed to determine whether immobilization chemistry can
AB  - be used to orient proteins on a support.  Restriction endonuclease EcoRI from Escherichia coli
AB  - RY13 (E.C.3.1.23.13) was used as a model in these studies.  Thiol-activated Sephadex G-10 was
AB  - used to couple the EcoRI endonuclease through its free sulfhydryl, while amino-activated
AB  - Sephadex G-10 was used to couple it randomly through its free carboxyl groups.  To determine
AB  - whether the enzyme was immobilized randomly or specifically, both lower and higher molecular
AB  - weight substrates were used.  The polymerase chain reaction amplified multiple cloning site
AB  - region of pBluescript KS obtained using T3 and T7 primers was considered as the small
AB  - substrate.  The plasmid Sp64 containing firefly luciferase gene was the large substrate.
AB  - Immobilized EcoRI preparations were characterized with respect to repeated usage and storage
AB  - stability.  The EcoRI immobilized on thiopropyl-Sepharose 4B could be stored for over 14 days
AB  - at 4oC without observable loss of activity.  In an independent experiment the same gel was
AB  - used thrice repeatedly without any discernible loss of activity.
ER  -

TY  - JOUR
AU  - Bird, A.
TI  - The essentials of DNA methylation.
JO  - Cell
PY  - 1992
SP  - 5
EP  - 8
VL  - 70
AB  - An obstacle to progress in understanding eukaryotic DNA methylation has been the lack of a
AB  - good genetic system - the most favorable eukaryotes for genetic analysis (yeasts,
AB  - Caenorhabditis, Drosophila) have no detectable methylation in their genomes. Not only has this
AB  - hampered progress, but the clear evidence for life without methylation that these organisms
AB  - provide has raised questions about the relevance of the whole phenomenon. The current status
AB  - of methylation is reviewed.
ER  -

TY  - JOUR
AU  - Bird, A.
TI  - DNA methylation de novo.
JO  - Science
PY  - 1999
SP  - 2287
EP  - 2288
VL  - 286
AB  - In an ideal world, biological processes would be understood at the molecular level by first
AB  - identifying all the participating components and then by deducing their roles in the system
AB  - through experiment.  In reality, knowledge of each component is hard-won, and the temptation
AB  - to assume that the key players are those that are currently known, ever-present.  Fortunately,
AB  - as human cDNA sequencing approaches saturation, candidate components in mammalian systems are
AB  - becoming easier to find.  One beneficiary is the field of DNA methylation in which researchers
AB  - study the shutting down of gene expression through the addition of methyl groups to cytosine
AB  - bases in the DNA.  Few players are more important in this arena than DNA methyltransferases,
AB  - the enzymes responsible for methylating DNA.  Thanks to DNA sequence databases, a clutch of
AB  - new Dnmts as well as proteins that bind methylated C bases have recently been uncovered.
AB  - Three recent papers make clear that several of these newly recognized Dnmts are capable of de
AB  - novo DNA methylation (that is, addition of methyl groups to DNA that has not been methylated
AB  - before).  The new work demonstrates the crucial importance of an appropriately methylated
AB  - genome for successful embryonic development.
ER  -

TY  - JOUR
AU  - Bird, A.
AU  - Taggart, M.
AU  - Frommer, M.
AU  - Miller, O.J.
AU  - Macleod, D.
TI  - A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA.
JO  - Cell
PY  - 1985
SP  - 91
EP  - 99
VL  - 40
AB  - About 1% of the mouse genome is cleaved by HpaII to give a discrete fraction on
AB  - gels.  The nonmethylated fraction is present in all tested tissues, including
AB  - sperm, and contains HpaII sites at about 15 times their frequency in bulk DNA.
AB  - About 80% of the fraction is composed of sequences that occur once or a few
AB  - times per genome; the remainder is largely rDNA.  Unlike bulk DNA, the fraction
AB  - is not deficient in CpG, and this may be directly due to the lack of
AB  - methylation.  Genomic mapping of three nonribosomal fragments showed that they
AB  - are part of islands of DNA within which nonmethylated HpaII and HhaI sites are
AB  - highly concentrated.  We estimate about 30,000 islands per haploid genome and
AB  - discuss evidence that many may be associated with genes.
ER  -

TY  - JOUR
AU  - Bird, A.P.
TI  - Gene number, noise reduction and biological complexity.
JO  - Trends Genet.
PY  - 1995
SP  - 94
EP  - 100
VL  - 11
AB  - Preliminary estimates suggest that gene number, and hence biological complexity, increased
AB  - suddenly at two periods of macroevolutionary change (the origin of eukaryotes and the origin
AB  - of vertebrates), but otherwise remained relatively constant. As the genome is in constant
AB  - flux, what normally constrains the number of different genes that an organism can retain?
AB  - Here, I suggest that an important limitation on gene number is the efficiency of mechanisms
AB  - that reduce transcriptional background noise. The appearance of both eukaryotes and
AB  - vertebrates coincided with novel mechanisms of noise reduction.
ER  -

TY  - JOUR
AU  - Bird, A.P.
AU  - Taggart, M.H.
AU  - Smith, B.A.
TI  - Methylated and unmethylated DNA compartments in the sea urchin genome.
JO  - Cell
PY  - 1979
SP  - 889
EP  - 901
VL  - 17
AB  - Sea urchin (Echinus esculentus) DNA has been separated into high and low molecular weight
AB  - fractions by digestion with the mCpG-sensitive restriction endonucleases HpaII, HhaI and AvaI.
AB  - The separation was due to differences in methylation at the recognition sequences for these
AB  - enzymes because an mCpG-insensitive isoschizomer of HpaII (MspI digested HpaII-resistant DNA
AB  - to low molecular weight, showing that many HapII sites were in fact present in this fraction;
AB  - and because 3H-methyl methionine administered to embryos was incorporated into the high
AB  - molecular weight HpaII-, HhaI- and AvaI-resistant fraction, but not significantly into the low
AB  - molecular weight fraction. The fraction resistant to HpaII, HhaI and AvaI amounted to about
AB  - 401f the total DNA. It consisted of long sequence tracts between 15 and well over 50 kb in
AB  - length, in which many sites for each of these enzymes were methylated consecutively. The
AB  - remaining 600f the genome, (m-), was not significantly methylated. Methylated and unmethylated
AB  - fractions were considered to be subfractions of the genome because enriched unique sequences
AB  - from one fraction cross-reassociated poorly with the other fraction and specific sequences
AB  - were found in either (m+) or (m-) but not in both (see below). Similar (m+) and (m-)
AB  - compartments were found in embryos, germ cells and adult somatic tissues. Furthermore, we
AB  - found no evidence for changes in the sequence composition of (m+) or (m-) between sperm,
AB  - embryo or intestine DNAs, although low levels of exchange would not have been detected. Using
AB  - cloned Echinus histone DNA, heterologous 5S DNA and ribosomal DNA probes, we have found that
AB  - each of these gene families belongs to the unmethylated DNA compartment in all the tissues
AB  - examined. In particular, there was no detectable methylation of histone DNA either in early
AB  - embryos, which are thought to be actively transcribing the bulk of histone genes, or in sperm
AB  - and gastrulae, in which most histone genes are not being transcribed. In contrast to these
AB  - gene families, sequences complementary to an internally repetitious Echinus DNA clone were
AB  - found primarily in the methylated DNA compartment. nt.
ER  -

TY  - JOUR
AU  - Bird, A.P.
AU  - Wolffe, A.P.
TI  - Methylation-induced repression - belts, braces, and chromatin.
JO  - Cell
PY  - 1999
SP  - 451
EP  - 454
VL  - 99
AB  - DNA methylation is essential for development in the mouse and plays an important role in
AB  - inactivation of the X-chromosome and genomic imprinting.  It may also contribute to
AB  - immobilization of mammalian transposons, suppression of transcriptional noise, and the control
AB  - of tissue-specific gene expression, but decisive evidence on these points is lacking.  The
AB  - theme that is common to all these phenomena is transcriptional repression.  Work on animals,
AB  - plants, and fungi now leaves little doubt that gene silencing is a major biological
AB  - consequence of DNA methylation.
ER  -

TY  - JOUR
AU  - Birdsell, D.N.
AU  - Antwerpen, M.
AU  - Keim, P.
AU  - Hanczaruk, M.
AU  - Foster, J.T.
AU  - Sahl, J.W.
AU  - Wagner, D.M.
AU  - Grass, G.
TI  - Draft Genome Sequences of Two Bulgarian Bacillus anthracis Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00152
EP  - e00113
VL  - 1
AB  - Bacillus anthracis strains previously isolated from Bulgaria form a unique subcluster within
AB  - the A1.a cluster that is typical for isolates from southeastern
AB  - Europe. Here, we report the draft genome sequences of two Bulgarian B. anthracis
AB  - strains belonging to the A branch (A.Br.)008/009 canonical single nucleotide
AB  - polymorphism (SNP) group of the major A branch.
ER  -

TY  - JOUR
AU  - Birkeland, N.K.
AU  - Schonheit, P.
AU  - Poghosyan, L.
AU  - Fiebig, A.
AU  - Klenk, H.P.
TI  - Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 79
EP  - 79
VL  - 12
AB  - Archaeoglobus fulgidus is the type species of genus Archaeoglobus Stetter 1998, a
AB  - hyperthermophilic sulfate reducing group within the Archaeoglobi class of the
AB  - euryarchaeota phylum. Members of this genus grow heterotrophically or
AB  - chemolithoautotrophically with sulfate or thiosulfate as electron acceptors.
AB  - Except for A. fulgidus strain 7324 and the candidate species 'Archaeoglobus
AB  - lithotrophicus', which both originate from deep oil-fields, the other members of
AB  - this genus have been recovered from marine hydrothermal systems. Here we describe
AB  - the features of the A. fulgidus strain 7324 genome as compared to the A. fulgidus
AB  - VC16 type strain. The 2.3 Mbp genome sequence of strain 7324 shares about 93.5%
AB  - sequence identity with that of strain VC16(T) but is about 138 Kbp longer, which
AB  - is mostly due to two large 'insertions' carrying one extra cdc6 (cell-cycle
AB  - control protein 6) gene, extra CRISPR elements and mobile genetic elements, a
AB  - high-GC ncRNA gene (hgcC) and a large number of hypothetical gene functions. A
AB  - comparison with four other Archaeoglobus spp. genomes identified 1001 core
AB  - Archaeoglobus genes and more than 2900 pan-genome orthologous genes.
ER  -

TY  - JOUR
AU  - Biro, J.C.
AU  - Biro, J.M.
TI  - Frequent occurrence of recognition site-like sequences in the restriction endonucleases.
JO  - BMC Bioinformatics
PY  - 2004
SP  - 30
EP  - 30
VL  - 5
AB  - BACKGROUND: There are two different theories about the development of the genetic code. Woese
AB  - suggested that it was developed in connection with the
AB  - amino acid repertoire, while Crick argued that any connection between
AB  - codons and amino acids is only the result of an "accident". This question
AB  - is fundamental to understand the nature of specific protein-nucleic acid
AB  - interactions. RESULTS: The nature of specific protein-nucleic acid
AB  - interaction between restriction endonucleases (RE) and their recognition
AB  - sequences (RS) was studied by bioinformatics methods. It was found that
AB  - the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly
AB  - high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p
AB  - < 0.001 respectively, n = 7). There is an extensive conservation of these
AB  - RS-like sequences in RE isoschizomers. A review of the seven available
AB  - crystallographic studies showed that the amino acids coded by codons that
AB  - are subsets of recognition sequences were often closely located to the RS
AB  - itself and they were in many cases directly adjacent to the codon-like
AB  - triplets in the RS.  Fifty-five examples of this codon-amino acid
AB  - co-localization are found and analyzed, which represents 41.5% of total
AB  - 132 amino acids which are localized within 8 angstroms distance to the C1' atoms
AB  - in the DNA. The average distance between the closest atoms in the codons
AB  - and amino acids is 5.5 +/- 0.2 A (mean +/- S.E.M, n = 55), while the
AB  - distance between the nitrogen and oxygen atoms of the co-localized
AB  - molecules is significantly shorter, (3.4 +/- 0.2 A, p < 0.001, n = 15),
AB  - when positively charged amino acids are involved. This is indicating that
AB  - an interaction between the nucleic- and amino acids might occur.
AB  - CONCLUSION: We interpret these results in favor of Woese and suggest that
AB  - the genetic code is "rational" and there is a stereospecific relationship
AB  - between the codes and the amino acids.
ER  -

TY  - JOUR
AU  - Bischofberger, N.
AU  - Ng, P.G.
AU  - Webb, T.R.
AU  - Matteucci, M.D.
TI  - Cleavage of single stranded oligonucleotides by EcoRI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 709
EP  - 716
VL  - 15
AB  - The 31mer 5'-TCA ACG CTA GAA TTC GGA TCC ATC GCT TGG T, the complementary 33mer
AB  - 5'-CCA AGC GAT GGA TCC GAA TTC TAG CGT TGA GAT, the 40 mer 5'-GGC CAG GAT GGT
AB  - GAA GAA TTC GAT CCG GTA CGT AGC TAA G, and the complementary 42mer 5'-TAC TTA
AB  - GCT ACG TAC CGG ATC GAA TTC TTC ACC ATC CTG GCC were synthesized and their
AB  - reactivity towards EcoRI was studied.  It was found that the 31mer and the
AB  - 40mer were cleaved at a comparable rate to the 31mer-33mer hybrid and the
AB  - 40mer-42mer hybrid, respectively.  The rate of cleavage of the 33mer and the
AB  - 42mer was an order of magnitude lower.  To rule out possible intermolecular
AB  - duplex formation, the 33mer was immobilized on cellulose by ligation and
AB  - labelled with a 32P-dCTP using Klenow fragment of E. coli DNA polymerase.
AB  - EcoRI cleaved this immobilized oligomer into specific fragments.
ER  -

TY  - JOUR
AU  - Bishnoi, U.
AU  - Polson, S.W.
AU  - Sherrier, D.J.
AU  - Bais, H.P.
TI  - Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent.
JO  - Genome Announcements
PY  - 2015
SP  - e00696
EP  - e00615
VL  - 3
AB  - Bacillus subtilis, which belongs to the phylum Firmicutes, is the most widely studied
AB  - Gram-positive model organism. It is found in a wide variety of
AB  - environments and is particularly abundant in soils and in the gastrointestinal
AB  - tracts of ruminants and humans. Here, we present the complete genome sequence of
AB  - the newly described B. subtilis strain UD1022. The UD1022 genome consists of a
AB  - 4.025-Mbp chromosome, and other major findings from our analysis will provide
AB  - insights into the genomic basis of it being a plant growth-promoting
AB  - rhizobacterium (PGPR) with biocontrol potential.
ER  -

TY  - JOUR
AU  - Bishop, J.O.
TI  - A DNA sequence cleaved by restriction endonuclease R.EcoRI in only one strand.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 545
EP  - 559
VL  - 128
AB  - Restriction endonuclease EcoRI cuts both strands of the DNA sequence GAATTC
AB  - generating two separate frayed ends (Hedgpeth et al., 1972).  Here it is shown
AB  - that under standard digestion conditions, the enzyme also attacks the sequence
AB  - GAATTA, but cuts only one strand.  The resulting nick is an efficient
AB  - initiation point for DNA synthesis by Escherichia coli DNA polymerase I,
AB  - allowing the selective labelling of one strand of the DNA duplex.  In buffers
AB  - of low molarity and high pH (8.5), EcoRI cleaves sequences with the form NAATTN
AB  - (Polisky et al., 1975).  Thus it seems that under both sets of conditions the
AB  - enzyme recognizes the four-base-pair core sequence AATT, and that its ability
AB  - to cleave different adjacent phosphodiester bonds varies with pH and ionic
AB  - strength.
ER  -

TY  - JOUR
AU  - Bishop-Lilly, K.A.
AU  - Frey, K.G.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Chertkov, O.
AU  - Freitas, T.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Minogue, T.D.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ.
JO  - Genome Announcements
PY  - 2014
SP  - e01084
EP  - e01014
VL  - 2
AB  - Salmonella enterica constitutes a group of enteric pathogens with a broad host range,
AB  - including humans, reptiles, and birds. S. enterica subsp. enterica is a
AB  - common cause of inflammatory diarrhea in humans. We present the draft genome of
AB  - S. enterica subsp. enterica serovar Enteritidis strain SEJ, including a 59-kbp
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Bishop-Lilly, K.A.
AU  - Johnson, S.L.
AU  - Verratti, K.
AU  - Luu, T.
AU  - Khiani, A.
AU  - Awosika, J.
AU  - Mokashi, V.P.
AU  - Chain, P.S.
AU  - Sozhamannan, S.
TI  - Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00893
EP  - e00814
VL  - 2
AB  - We present draft genome sequences of 15 clinical Vibrio isolates of various serogroups. These
AB  - are valuable data for use in studying Vibrio cholerae genetic
AB  - diversity, epidemic potential, and strain attribution.
ER  -

TY  - JOUR
AU  - Bist, P.
AU  - Madhusoodanan, U.K.
AU  - Rao, D.N.
TI  - A mutation in the Mod subunit of EcoP15I restriction enzyme converts the DNA methyltransferase to a site-specific endonuclease.
JO  - J. Biol. Chem.
PY  - 2007
SP  - 3520
EP  - 3530
VL  - 282
AB  - A closer inspection of the amino acid sequence of EcoP15I DNA methyltransferase revealed a
AB  - region of similarity to the PDXn(D/E)XK
AB  - catalytic site of type II restriction endonucleases, except for methionine
AB  - in EcoP15I DNA methyltransferase instead of proline. Substitution of
AB  - methionine at position 357 by proline converts EcoP15I DNA
AB  - methyltransferase to a site-specific endonuclease. EcoP15I-M357P DNA
AB  - methyltransferase specifically binds to the recognition sequence
AB  - 5'-CAGCAG-3' and cleaves DNA asymmetrically EcoP151-M357P.DNA
AB  - methyltransferase specifically binds to the recognition sequence
AB  - 5'-CAGCAG-3' and cleaves DNA asymmetrically, 5'-CAGCAG(N)(10)-3', as
AB  - indicated by the arrows, in presence of magnesium ions.
ER  -

TY  - JOUR
AU  - Bist, P.
AU  - Rao, D.N.
TI  - Identification and mutational analysis of Mg2+ binding site in EcoP15I DNA methyltransferase: involvement in target base eversion.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 41837
EP  - 41848
VL  - 278
AB  - EcoP15I DNA methyltransferase catalyzes the transfer of the methyl group of
AB  - S-adenosyl-l-methionine to the N6 position of the second adenine within
AB  - the double-stranded DNA sequence 5'-CAGCAG-3'. To achieve catalysis, the
AB  - enzyme requires a magnesium ion. Binding of magnesium to the enzyme
AB  - induces significant conformational changes as monitored by circular
AB  - dichroism spectroscopy. EcoP15I DNA methyltransferase was rapidly
AB  - inactivated by micromolar concentrations of ferrous sulfate in the
AB  - presence of ascorbate at pH 8.0. The inactivated enzyme was cleaved into
AB  - two fragments with molecular masses of 36 and 35 kDa. Using this affinity
AB  - cleavage assay, we have located the magnesium binding-like motif to amino
AB  - acids 355-377 of EcoP15I DNA methyltransferase. Sequence homology
AB  - comparisons between EcoP15I DNA methyltransferase and other restriction
AB  - endonucleases allowed us to identify a PD(X)n(D/E)XK-like sequence as the
AB  - putative magnesium ion binding site. Point mutations generated in this
AB  - region were analyzed for their role in methyltransferase activity, metal
AB  - coordination, and substrate binding. Although the mutant
AB  - methyltransferases bind DNA and S-adenosyl-l-methionine as well as the
AB  - wild-type enzyme does, they are inactive primarily because of their
AB  - inability to flip the target base. Collectively, these data are consistent
AB  - with the fact that acidic amino acid residues of the region 355-377 in
AB  - EcoP15I DNA methyltransferase are important for the critical positioning
AB  - of magnesium ions for catalysis. This is the first example of
AB  - metal-dependent function of a DNA methyltransferase. These findings
AB  - provide impetus for exploring the role(s) of metal ions in the structure
AB  - and function of DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Bist, P.
AU  - Sistla, S.
AU  - Krishnamurthy, V.
AU  - Acharya, A.
AU  - Chandrakala, B.
AU  - Rao, D.N.
TI  - S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 93
EP  - 109
VL  - 310
AB  - The requirement of S-adenosyl-L-methionine (AdoMet) in the cleavage reaction carried out by
AB  - type III restriction-modification enzymes has
AB  - been investigated. We show that DNA restriction by EcoPI restriction
AB  - enzyme does not take place in the absence of exogenously added AdoMet.
AB  - Interestingly, the closely related EcoP15I enzyme has endogenously
AB  - bound AdoMet and therefore does not require the addition of the
AB  - cofactor for DNA cleavage. By employing a variety of AdoMet analogs,
AB  - which differ structurally from AdoMet, this study demonstrates that the
AB  - carboxyl group and any substitution at the epsilon carbon of methionine
AB  - is absolutely essential for DNA cleavage. Such analogs could bring
AB  - about the necessary conformational change(s) in the enzyme, which make
AB  - the enzyme proficient in DNA cleavage. Our studies, which include
AB  - native polyacrylamide gel electrophoresis, molecular size exclusion
AB  - chromatography, UV, fluorescence and circular dichroism spectroscopy,
AB  - clearly demonstrate that the holoenzyme and apoenzyme forms of EcoP15I
AB  - restriction enzyme have different conformations. Furthermore, the Res
AB  - and Mod subunits of the EcoP15I restriction enzyme can be separated by
AB  - gel filtration chromatography in the presence of 2 M NaCl.
AB  - Reconstitution experiments, which involve mixing of the isolated
AB  - subunits, result in an apoenzyme form, which is restriction proficient
AB  - in the presence of AdoMet. However, mixing the Res subunit with Mod
AB  - subunit deficient in AdoMet binding does not result in a functional
AB  - restriction enzyme. These observations are consistent with the fact
AB  - that AdoMet is required for DNA cleavage. In vivo complementation of
AB  - the defective mod allele with a wild-type mod allele showed that an
AB  - active restriction enzyme could be formed. Furthermore, we show that
AB  - while the purified c2-134 mutant restriction enzyme is unable to cleave
AB  - DNA, the c2-440 mutant enzyme is able to cleave DNA albeit poorly.
AB  - Taken together, these results suggest that AdoMet binding causes
AB  - conformational changes in the restriction enzyme and is necessary to
AB  - bring about DNA cleavage.
ER  -

TY  - JOUR
AU  - Biswas, R.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Palaniappan, K.
AU  - Varghese, N.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.B.K.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Ivanova, N.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Guss, A.M.
TI  - Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate-  and Butanol-Producing Thermophile.
JO  - Genome Announcements
PY  - 2018
SP  - e01411
EP  - e01417
VL  - 6
AB  - Thermoanaerobacterium sp. strain RBIITD was isolated from contaminated rich growth medium at
AB  - 55 degrees C in an anaerobic chamber. It primarily produces
AB  - butyrate as a fermentation product from plant biomass-derived sugars. The
AB  - whole-genome sequence of the strain is 3.4 Mbp, with 3,444 genes and 32.48% GC
AB  - content.
ER  -

TY  - JOUR
AU  - Biswas, R.K.
AU  - Kock, M.M.
AU  - Adelowotan, T.
AU  - Strasheim, W.
AU  - Mahomed, T.G.
AU  - Salawu, A.
AU  - Ehlers, M.M.
TI  - Draft Genome Sequences of Five Clinical Methicillin-Resistant Staphylococcus aureus Isolates and a Methicillin-Resistant Staphylococcus epidermidis Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00836
EP  - e00815
VL  - 3
AB  - We report the complete draft genome sequences of five individually isolated strains of
AB  - methicillin-resistant Staphylococcus aureus (MRSA) and a
AB  - Staphylococcus epidermidis strain. These clinically important isolates have
AB  - staphylococcal cassette chromosome mec type A, while Panton-Valentine leukocidin
AB  - (PVL) toxin coding genes were present in MRSA isolates only.
ER  -

TY  - JOUR
AU  - Biswas, S.
AU  - Biswas, I.
TI  - Complete Genome Sequence of Lactobacillus rhamnosus Strain LRB.
JO  - Genome Announcements
PY  - 2016
SP  - e01208
EP  - e01216
VL  - 4
AB  - Lactobacillus rhamnosus is a Gram-positive facultative heterofermentative lactic  acid
AB  - bacterium. It is often isolated from the gastrointestinal tract, mouth,
AB  - vagina, and fermented dairy products. We have isolated the L. rhamnosus strain
AB  - LRB from a healthy baby tooth that had naturally fallen out. Here, we report the
AB  - annotated whole-genome sequence of LRB.
ER  -

TY  - JOUR
AU  - Biswas, S.
AU  - Biswas, I.
TI  - Complete Genome Sequence of Streptococcus mutans GS-5, a Serotype c Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4787
EP  - 4788
VL  - 194
AB  - Streptococcus mutans, a principal causative agent of dental caries, is considered to be the
AB  - most cariogenic among all oral streptococci. Of the four S. mutans
AB  - serotypes (c, e, f, and k), serotype c strains predominate in the oral cavity.
AB  - Here, we present the complete genome sequence of S. mutans GS-5, a serotype c
AB  - strain originally isolated from human carious lesions, which is extensively used
AB  - as a laboratory strain worldwide.
ER  -

TY  - JOUR
AU  - Bitinaite, J.
AU  - Grigaite, R.
AU  - Maneliene, Z.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Esp3I - a novel type IIs restriction endonuclease from Hafnia alvei that recognizes the sequence 5'-CGTCTC(N)1/5-3' .
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 5076
EP  - 5076
VL  - 19
AB  - A new type IIs restriction endonuclease, Esp3I, has been isolated from Hafnia
AB  - alvei RFL3*.  Esp3I recognizes the non-palindromic sequence 5'-CGTCTC-3' and
AB  - cleaves DNA one nucleotide to the right from the noted recognition strand.
ER  -

TY  - JOUR
AU  - Bitinaite, J.
AU  - Maneliene, Z.
AU  - Menkevicius, S.
AU  - Klimasauskas, S.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Alw26I, Eco31I and Esp3I - type IIs methyltransferases modifying cytosine and adenine in complementary strands of the target DNA.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4981
EP  - 4985
VL  - 20
AB  - *The specificity of three DNA methyltransferases M.Alw261, M.Eco31I and M.Esp3I,
AB  - isolated from Acinetobacter lwoffi RFL26, Escherichia coli RFL31 and Hafnia
AB  - alvei RFL3+, respectively, was determined. All the enzymes methylate both
AB  - strands of asymmetric recognition sites yielding m5C in the top-strand and
AB  - m6A in the bottom-strand, as below: 
AB  - 
AB  -    5'-GTm5CTC      5'-GGTm5CTC     5'-CGTm5CTC 
AB  -    3'-Cm6AGAG      3'-CCm6AGAG     3'-GCm6AGAG
AB  -    (M.Alw26I)      (M.Eco31I)      (M.Esp3I)
AB  - are the first members of type IIs methyltransferases that modify different
AB  - types of nucleotides in the recognition sequence.
AB  - 
ER  -

TY  - JOUR
AU  - Bitinaite, J.
AU  - Mitkaite, G.
AU  - Dauksaite, V.
AU  - Jakubauskas, A.
AU  - Timinskas, A.
AU  - Vaisvila, R.
AU  - Lubys, A.
AU  - Janulaitis, A.
TI  - Evolutionary relationship of Alw261, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences.
JO  - Mol. Genet. Genomics
PY  - 2002
SP  - 664
EP  - 672
VL  - 267
AB  - Type II restriction endonucleases (ENases) have served as models for understanding the
AB  - enzyme-based site-specific cleavage of DNA. Using the
AB  - knowledge gained from the available crystal structures, a number of
AB  - attempts have been made to alter the specificity of ENases by
AB  - mutagenesis. The negative results of these experiments argue that the
AB  - three-dimensional structure of DNA-ENase complexes does not provide
AB  - enough information to enable us to understand the interactions between
AB  - DNA and ENases in detail. This conclusion calls for alternative
AB  - approaches to the study of structure-function relationships related to
AB  - the specificity of ENases. Comparative analysis of ENases that manifest
AB  - divergent substrate specificities, but at the same time are
AB  - evolutionarily related to each other, may be helpful in this respect.
AB  - The success of such studies depends to a great extent on the
AB  - availability of related ENases that recognise partially overlapping
AB  - nucleotide sequences (e.g. sets of enzymes that bind to recognition
AB  - sites of increasing length). In this study we report the cloning and
AB  - sequence analysis of genes for three Type I IS restriction-modification
AB  - (RM) systems. The genes encoding the ENases Alw26I, Eco31I and Esp3I
AB  - (whose recognition sequences are 5'-GTCTC-3', 5'-GGTCTC-3' and
AB  - 5'-CGTCTC-3'. respectively) and their accompanying methyltransferases
AB  - (MTases) have been cloned and the deduced amino acid sequences of their
AB  - products have been compared. In pairwise comparisons, the degree of
AB  - sequence identity between Alw261, Eco31I and Esp3I ENases is higher
AB  - than that observed hitherto among ENases that recognise partially
AB  - overlapping nucleotide sequences. The sequences of Alw26I, Eco31I and
AB  - Esp3I also reveal identical mosaic patterns of sequence conservation,
AB  - which supports the idea that they are evolutionarily related and
AB  - suggests that they should show a high level of structural similarity.
AB  - Thus these ENases represent very attractive models for the study of the
AB  - molecular basis of variation in the specific recognition of DNA
AB  - targets. The corresponding MTases are represented by proteins of
AB  - unusual structural and functional organisation. Both M.Alw26I and
AB  - M.Esp3I are represented by a single bifunctional protein, which is
AB  - composed of an m6A-MTase domain fused to aN m5C-MTase domain. In
AB  - contrast, two separate genes encode the m6A-MTase and m5C-MTase in
AB  - the Eco31I RM system. Among the known bacterial m5C-MTases, the m5C-MTases of M.Alw26I,
AB  - M.Eco31I and M.Esp3I represent unique examples of
AB  - the circular permutation of their putative target recognition domains
AB  - together with the conserved motifs IX and X.
ER  -

TY  - JOUR
AU  - Bitinaite, J.
AU  - Schildkraut, I.
TI  - Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 1164
EP  - 1169
VL  - 99
AB  - The primary target of SgrAI restriction endonuclease is a multiple sequence of the form
AB  - 5'-Cpu^CCGGPyG. Previous work had indicated that SgrAI must bind two recognition sites
AB  - simultaneously for catalysis [Bilcock, D. T., Daniels, L. E., Bath, A. J. & Halford, S. E.
AB  - (1999) J. Biol. Chem. 274, 36379-36386]. In the present study, SgrAI is shown to cleave not
AB  - only its canonical sequences, but also the sequences 5'-CPuCCGGPy(A,T,C) and 5'-CPuCCGGGG,
AB  - both referred to as secondary sequences. On plasmid pSK7, SgrAI cleaves secondary sites
AB  - 26-fold slower than the canonical site. However, the same plasmid, but without the canonical
AB  - site, is cleaved 200-fold slower. We show that DNA termini generated by cleaving the canonical
AB  - site for SgrAI assist in the cleavage of secondary sites. The SgrAI-termini in cis with
AB  - respect to secondary site are markedly preferred over those in trans. The SgrAI-termini
AB  - provided in a form of oligonucleotide duplex are also shown to stimulate canonical site
AB  - cleavage. At a 40-fold molar excess of the SgrAI-termini over substrate, the SgrAI specificity
AB  - is shown to improve by two orders of magnitude, because of concurrent 10-fold increase in the
AB  - cleavage of canonical site and 50-fold decrease in the cleavage of secondary sites. The
AB  - unconventional reaction pathway by which SgrAI utilizes the self-generated DNA termini to
AB  - cleave its DNA targets has not been observed hitherto among type II restriction endonucleases.
AB  - Based on our work and previous reports, a pathway of DNA binding and cleavage by the SgrAI
AB  - restriction endonuclease is proposed.
ER  -

TY  - JOUR
AU  - Bitinaite, J.
AU  - Wah, D.A.
AU  - Aggarwal, A.K.
AU  - Schildkraut, I.
TI  - FokI dimerization is required for DNA cleavage.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 10570
EP  - 10575
VL  - 95
AB  - FokI is a type IIs restriction endonuclease comprised of a DNA recognition domain and a
AB  - catalytic domain.  The structural similarity of the FokI catalytic domain to the type II
AB  - restriction endonuclease BamHI monomer suggested that the FokI catalytic domains may dimerize.
AB  - In addition, the FokI structure, presented in an accompanying paper in this issue of
AB  - Proceedings, reveals a dimerization interface between catalytic domains.  We provide evidence
AB  - here that FokI catalytic domain must dimerize for DNA cleavage to occur.  First, we show that
AB  - the rate of DNA cleavage catalyzed by various concentrations of FokI are not directly
AB  - proportional to the protein concentration, suggesting a cooperative effect for DNA cleavage.
AB  - Second, we constructed a FokI variant, FokN13Y, which is unable to bind the FokI recognition
AB  - sequence but when mixed with wild-type FokI increases the rate of DNA cleavage.  Additionally,
AB  - the FokI catalytic domain that lacks the DNA binding domain was shown to increase the rate of
AB  - wild-type FokI cleavage of DNA.  We also constructed an FokI variant, FokD483A, R487A, which
AB  - should be defective for dimerization because the altered residues reside at the putative
AB  - dimerization interface.  Consistent with the FokI dimerization model, the variant FokD483A,
AB  - R487A revealed greatly impaired DNA cleavage.  Based on our work and previous reports, we
AB  - discuss a pathway of DNA binding, dimerization, and cleavage by FokI endonuclease.
ER  -

TY  - JOUR
AU  - Bitinaite, J.B.
AU  - Klimasauskas, S.J.
AU  - Butkus, V.V.
AU  - Janulaitis, A.
TI  - Characterization of restriction-modification enzymes Cfr13I from Citrobacter freundii RFL13.
JO  - FEBS Lett.
PY  - 1985
SP  - 509
EP  - 513
VL  - 182
AB  - This communication describes some properties of R.Cfr13I and M.Cfr13I, isolated from
AB  - Citrobacter freundii RFL13. R.Cfr13I restriction enzyme recognizes the 5'-G^GNCC sequence and
AB  - cleaves, as indicated by the arrow. M.Cfr13I methylase modifies the internal cytosine
AB  - producing m5C (5'-GGNm5CC). R.Cfr13I is sensitive not only to this type of substrate
AB  - modification but also to hemimethylation in overlapping sites by M.Cfr10I (internal cytosine
AB  - of R.Cfr13I recognition is methylated) and M.HpaII (external cytosine is methylated). From
AB  - these results the sensitivity of R.Cfr13I to methylation by dcm methylase of E.coli in
AB  - overlapping sites is deduced.
ER  -

TY  - JOUR
AU  - Bittar, F.
AU  - Bibi, F.
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Azhar, E.I.
AU  - Jiman-Fatani, A.A.
AU  - Al-Ghamdi, A.K.
AU  - Nguyen, T.T.
AU  - Yasir, M.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 47
EP  - 47
VL  - 10
AB  - Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah,
AB  - Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a
AB  - 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically
AB  - closest species with standing nomenclature. Moreover, the strain JCE(T) presents many
AB  - phenotypic differences, when it is compared to other Bacillus species, and shows a low
AB  - MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely
AB  - that this strain represents a new species. Here we describe the features of this  organism,
AB  - together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1
AB  - chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA
AB  - genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than
AB  - 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the
AB  - strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming
AB  - again its new species status. On the basis of these polyphasic data made of phenotypic and
AB  - genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the
AB  - strain JCE(T).
ER  -

TY  - JOUR
AU  - Bitzer, A.S.
AU  - Garbeva, P.
AU  - Silby, M.W.
TI  - Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand  Dune in the Netherlands.
JO  - Genome Announcements
PY  - 2014
SP  - e00094
EP  - e00014
VL  - 2
AB  - Pedobacter sp. strain V48 participates in an interaction with Pseudomonas fluorescens which
AB  - elicits interaction-induced phenotypes. We report the draft
AB  - genome sequence of Pedobacter sp. V48, consisting of 6.46 Mbp. The sequence will
AB  - contribute to improved understanding of the genus and facilitate genomic analysis
AB  - of the model interspecies interaction with P. fluorescens.
ER  -

TY  - JOUR
AU  - Bjerga, G.E.
AU  - Hjerde, E.
AU  - De Santi, C.
AU  - Williamson, A.K.
AU  - Smalas, A.O.
AU  - Willassen, N.P.
AU  - Altermark, B.
TI  - High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 676
EP  - 686
VL  - 9
AB  - Here we report the 8 Mb high quality draft genome of Streptomyces sp. strain AW19M42, together
AB  - with specific properties of the organism and the generation,
AB  - annotation and analysis of its genome sequence. The genome encodes 7,727 putative
AB  - open reading frames, of which 6,400 could be assigned with COG categories. Also,
AB  - 62 tRNA genes and 8 rRNA operons were identified. The genome harbors several gene
AB  - clusters involved in the production of secondary metabolites. Functional
AB  - screening of the isolate was positive for several enzymatic activities, and some
AB  - candidate genes coding for those activities are listed in this report. We find
AB  - that this isolate shows biotechnological potential and is an interesting target
AB  - for bioprospecting.
ER  -

TY  - JOUR
AU  - Bjorkholm, B.M.
AU  - Guruge, J.L.
AU  - Oh, J.D.
AU  - Syder, A.J.
AU  - Salama, N.
AU  - Guillemin, K.
AU  - Falkow, S.
AU  - Nilsson, C.
AU  - Falk, P.G.
AU  - Engstrand, L.
AU  - Gordon, J.I.
TI  - Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a  correlation between host responses and HsdS components of type I  restriction-modification systems.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 34191
EP  - 34197
VL  - 277
AB  - Helicobacter pylori infects the stomachs of half of all humans. It has a relatively benign
AB  - relationship with most hosts but produces severe
AB  - pathology, including gastric cancer, in others. Identifying the relative
AB  - contributions of host, microbial, and environmental factors to the outcome
AB  - of infection has been challenging. Here we describe one approach for
AB  - identifying microbial genes that affect the magnitude of host responses to
AB  - infection. Single colony purified H. pylori isolates were obtained from 25
AB  - cases and 71 controls in a Swedish case-control study of gastric cancer.
AB  - Strains were first phenotyped based on their ability to produce adhesins
AB  - that recognize two classes of human gastric epithelial receptors. Thirteen
AB  - binding strains and two non-binding controls were then subjected to whole
AB  - genome genotyping using H. pylori DNA microarrays. A cohort of "variable"
AB  - genes was identified based on a microarray-determined call of "absent" in
AB  - at least one member of the strain panel. Each strain was subsequently
AB  - introduced into two types of germ-free transgenic mice, each programmed to
AB  - express a different host factor postulated to pose increased risk for
AB  - development of severe pathology. Expression of biomarkers of host defense
AB  - was quantitated 4 weeks after inoculation, and the magnitude of the
AB  - response correlated with bacterial genotype. The proportion of genes
AB  - encoding HsdS homologs (specificity subunit of heterooligomeric type I
AB  - restriction-modification systems) was significantly higher in the pool of
AB  - 18 variable genes whose presence directly correlated with a robust host
AB  - response than their proportion in the remaining 352 members of the
AB  - variable gene pool. This suggests that the functions of these HsdS
AB  - homologs may include control of expression of microbial determinants that
AB  - affect the extent of gastric responses to this potentially virulent
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Bjornsdottir-Butler, K.
AU  - Leon, M.S.
AU  - Benner, R.A. Jr.
TI  - Draft Genome Sequences of Histamine-Producing Morganella psychrotolerans Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e01001
EP  - e01016
VL  - 4
AB  - Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a
AB  - leading cause of fish poisoning in the United States. We report here
AB  - the first draft genomes of three histamine-producing Morganella psychrotolerans
AB  - strains, isolated from tuna and mahi-mahi.
ER  -

TY  - JOUR
AU  - Bjornsdottir-Butler, K.
AU  - McCarthy, S.A.
AU  - Dunlap, P.V.
AU  - Timme, R.E.
AU  - Benner, R.A. Jr.
TI  - Draft Genome Sequences of Histamine-Producing Photobacterium kishitanii and Photobacterium angustum, Isolated from Albacore (Thunnus alalunga) and Yellowfin   (Thunnus albacares) Tuna.
JO  - Genome Announcements
PY  - 2015
SP  - e00400
EP  - e00415
VL  - 3
AB  - Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a
AB  - leading cause of fish poisoning in the United States. We report here
AB  - the draft genome sequences of four histamine-producing (HP) Photobacterium
AB  - kishitanii strains and nine HP Photobacterium angustum strains isolated from
AB  - tuna.
ER  -

TY  - JOUR
AU  - Bjornsdottir-Butler, K.
AU  - Sanchez, L.M.
AU  - Dunlap, P.V.
AU  - Benner, R.A. Jr.
TI  - Draft Genome Sequences of Histamine- and Non-Histamine-Producing Photobacterium Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e01008
EP  - e01016
VL  - 4
AB  - Histamine-producing bacteria (HPBs) have recently been identified from the marine environment.
AB  - The identification and characterization of HPBs is important to
AB  - developing effective mitigation strategies for scombrotoxin fish poisoning. We
AB  - report here the draft genomes of seven histamine-producing and two
AB  - non-histamine-producing marine Photobacterium strains.
ER  -

TY  - JOUR
AU  - Blakely, G.W.
AU  - Murray, N.E.
TI  - Control of the endonuclease activity of type I restriction-modification systems is required to maintain chromosome integrity following  homologous recombination.
JO  - Mol. Microbiol.
PY  - 2006
SP  - 883
EP  - 893
VL  - 60
AB  - A type I restriction-modification enzyme will bind to an unmethylated target sequence in DNA
AB  - and, while still bound to the target,
AB  - translocate DNA through the protein complex in both directions. DNA
AB  - breakage occurs when two translocating complexes collide. However, if
AB  - type I restriction-modification systems bind to unmodified target
AB  - sequences within the resident bacterial chromosome, as opposed to
AB  - incoming 'foreign' DNA, their activity is curtailed; a process known as
AB  - restriction alleviation (RA). We have identified two genes in
AB  - Escherichia coli, rnhA and recG, mutations in which lead to the
AB  - alleviation of restriction. Induction of RA in response to these
AB  - mutations is consistent with the production of unmodified target
AB  - sequences following DNA synthesis associated with both homologous
AB  - recombination and R-loop formation. This implies that a normal function
AB  - of RA is to protect the bacterial chromosome when recombination
AB  - generates unmodified products. For EcoKI, our experiments demonstrate
AB  - the contribution of two pathways that serve to protect unmodified DNA
AB  - in the bacterial chromosome: the primary pathway in which ClpXP
AB  - degrades the restriction endonucleas and a mechanism dependent on the
AB  - lar gene within Rac, a resident, defective prophage of E. coli K-12.
AB  - Previously, the potential of the second pathway has only been
AB  - demonstrated when expression of lar has been elevated. Our data
AB  - identify the effect of lar from the repressed prophage.
ER  -

TY  - JOUR
AU  - Blakesley, R.W.
TI  - Restriction endonuclease:  cleavage, ligation, and sensitivity.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 51
EP  - 102
VL  - 5
AB  - Restriction endonucleases are important tools for the molecular biologist.
AB  - These enzymes are routinely used to subdivide DNA molecules in a very specific,
AB  - predictable fashion, allowing one to isolate certain regions for study.  DNA
AB  - sequencing, cloning, mapping, hybridization, and genome characterization are
AB  - some of the more common procedures incorporating restriction endonuclease
AB  - treated DNA.  The characteristics of the restriction endonucleases and their
AB  - reactions have been reviewed.  A comprehensive listing of the enzymes and the
AB  - diversity of microbiological sources appears in this volume.  Informative
AB  - tables on some characteristics of restriction endonucleases have appeared
AB  - elsewhere.  Tabulated in this chapter are a number of facts frequently used
AB  - when planning experiments that utilize restriction endonucleases.  The final
AB  - table summarizes a number of general characteristics of the enzyme which should
AB  - be valuable when designing complex strategies or trouble-shooting unexpected
AB  - results.
ER  -

TY  - JOUR
AU  - Blakesley, R.W.
TI  - Restriction endonuclease: specificities, diversities and computer analysis.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 1
EP  - 43
VL  - 1
AB  - I. Introduction II. Table I: DNA cleavage frequency for restriction
AB  - endonucleases with known recognition sequences III. Table II: DNA cleavage
AB  - frequency for restriction endonucleases with undetermined recognition sequences
AB  - IV. Table III: Microorganisms as sources for restriction endonucleases V. Table
AB  - IV: Reaction conditions for certain restriction endonucleases VI. Table V:
AB  - Restriction endonuclease cross reference: Tables I-IV, references VII. Table
AB  - VI: Restriction endonuclease site combinations for ligation.
ER  -

TY  - JOUR
AU  - Blakesley, R.W.
AU  - Dodgson, J.B.
AU  - Nes, I.F.
AU  - Wells, R.D.
TI  - Duplex regions in "single-stranded" PhiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegyptius.
JO  - J. Biol. Chem.
PY  - 1977
SP  - 7300
EP  - 7306
VL  - 252
AB  - DNA from bacteriophage PhiX174 is cleaved by several DNA restriction
AB  - endonucleases.  We wish to determine whether or not the recognition sites are
AB  - within duplex regions in this single-stranded DNA.  We report here the
AB  - influence of two perturbants of duplex DNA structure, temperature and
AB  - actinomycin, on the cleavage of PhiX174 (single-stranded, circular) DNA and its
AB  - double-stranded, replicative form (RF DNA) by the restriction endonuclease,
AB  - HaeIII.  The conditions for optimal rates of cleavage for the (+)-strand and RF
AB  - DNA's by HaeIII were virtually identical (25 mM Tris/HCl, pH 7.5; 5 mM MgCl2;
AB  - 30 mM NaCl).  At 37C, RF DNA was cleaved 16 times faster than (+)-strand DNA.
AB  - When the initial rates of reaction for both DNA's were measured as a function
AB  - of temperature of incubation, the maximum rates occurred at 72C and 47C for the
AB  - RF and (+)-strand DNA's, respectively.  At 10-15C above the respective maxima,
AB  - the rates fell to zero.  Near the temperature optima, a preferential
AB  - disappearance of certain fragments with temperature occurred with (+)-strand,
AB  - but not with RF DNA.  These results indicate that the HaeIII restriction sites
AB  - in PhiX174 (+)-strand DNA are located in several different, noncontiguous,
AB  - duplex regions with different sequence-dependent tM values.  The rate of
AB  - cleavage of each DNA was also inhibited by actinomycin; 50% inhibition occurred
AB  - at a molar ratio (actinomycin/nucleotide) of 1.2 for RF and 0.04 for (+)-strand
AB  - DNA.  Netropson, which, like actinomycin binds only to duplex DNA, inhibited
AB  - the cleavage of both DNA's.  The restriction endonuclease HhaI, gave results
AB  - similar to those found for HaeIII.  RF DNA was cleaved once by the restriction
AB  - endonuclease, PstI; (+)-strand DNA was not cleaved.  This result for (+)-strand
AB  - would be expected if intramolecular base-pairing were required for cleavage.
AB  - RF and (+)-strand DNA's were also cleaved by MboI and HinfI.  Neither DNA was
AB  - cleaved by BamHI, SmaI, or SalI.  These results indicate that certain DNA
AB  - restriction endonucleases cleave "single-stranded" viral DNA's at duplex
AB  - regions.
ER  -

TY  - JOUR
AU  - Blakesley, R.W.
AU  - Wells, R.D.
TI  - Single-stranded DNA from PhiX174 and M13 is cleaved by certain restriction endonucleases.
JO  - Nature
PY  - 1975
SP  - 421
EP  - 422
VL  - 257
AB  - During a systematic survey of the substrate specificities of a variety of
AB  - restriction endonucleases, it was discovered that the Haemophilus aegyptius
AB  - restriction endonuclease III (HaeIII) specifically cleaved 'single-stranded'
AB  - DNA from PhiX174 and M13.  Since these DNAs are not doubled-stranded and
AB  - restriction enzymes recognize duplex DNA with twofold sequence symmetry, this
AB  - result was unexpected.  This finding is significant with regard to the
AB  - conformation of single-stranded viral DNA as well as the biochemical mechanism
AB  - and physiological role of restriction enzymes.
ER  -

TY  - JOUR
AU  - Blakeway, L.V.
AU  - Power, P.M.
AU  - Jen, F.E.
AU  - Worboys, S.R.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Bakaletz, L.O.
AU  - Jennings, M.P.
AU  - Peak, I.R.
AU  - Seib, K.L.
TI  - ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media.
JO  - FASEB J.
PY  - 2014
SP  - 5197
EP  - 5207
VL  - 28
AB  - Moraxella catarrhalis is a significant cause of otitis media and exacerbations of
AB  - chronic obstructive pulmonary disease. Here, we characterize a phase-variable DNA
AB  - methyltransferase (ModM), which contains 5'-CAAC-3' repeats in its open reading
AB  - frame that mediate high-frequency mutation resulting in reversible on/off
AB  - switching of ModM expression. Three modM alleles have been identified (modM1-3),
AB  - with modM2 being the most commonly found allele. Using single-molecule, real-time
AB  - (SMRT) genome sequencing and methylome analysis, we have determined that the
AB  - ModM2 methylation target is 5'-GARm6AC-3', and 100% of these sites are methylated
AB  - in the genome of the M. catarrhalis 25239 ModM2 on strain. Proteomic analysis of
AB  - ModM2 on and off variants revealed that ModM2 regulates expression of multiple
AB  - genes that have potential roles in colonization, infection, and protection
AB  - against host defenses. Investigation of the distribution of modM alleles in a
AB  - panel of M. catarrhalis strains, isolated from the nasopharynx of healthy
AB  - children or middle ear effusions from patients with otitis media, revealed a
AB  - statistically significant association of modM3 with otitis media isolates. The
AB  - modulation of gene expression via the ModM phase-variable regulon (phasevarion),
AB  - and the significant association of the modM3 allele with otitis media, suggests a
AB  - key role for ModM phasevarions in the pathogenesis of this organism.-Blakeway, L.
AB  - V., Power, P. M., Jen, F. E.-C., Worboys, S. R., Boitano, M., Clark, T. A.,
AB  - Korlach, J., Bakaletz, L. O., Jennings, M. P., Peak, I. R., Seib, K. L. ModM DNA
AB  - methyltransferase methylome analysis reveals a potential role for Moraxella
AB  - catarrhalis phasevarions in otitis media.
ER  -

TY  - JOUR
AU  - Blanc, V.
AU  - Gil, P.
AU  - Bamas-Jacques, N.
AU  - Lorenzon, S.
AU  - Zagorec, M.
AU  - Schleuniger, J.
AU  - Bisch, D.
AU  - Blanche, F.
AU  - Debussche, L.
AU  - Crouzet, J.
AU  - Thibaut, D.
TI  - Identification and analysis of genes from Streptomyces pristinaespiralis encoding enzymes involved in the biosynthesis of the 4-dimethylamino-L-phenylalanine precursor of pristinamycin I.
JO  - Mol. Microbiol.
PY  - 1997
SP  - 191
EP  - 202
VL  - 23
AB  - Four pap genes (papA, papB, papC, papM) were found by sequencing near to snbA, a Streptomyces
AB  - pristinaespiralis gene which was previously shown to encode one of the pristinamycin I (PI)
AB  - synthetases. Analysis of the homologies observed from the deduced amino acid sequences
AB  - suggested that these four genes could be involved in the biosynthesis of the PI precursor
AB  - 4-dimethylamino-L-phenylalanine (DMPAPA). This was first verified when disruption of papA in
AB  - S. pristinaespiralis led to a PI- phenotype, which was reversed by the addition of DMPAPA into
AB  - the culture medium. Further confirmation was obtained when papM was overexpressed in
AB  - Escherichia coli and the corresponding protein purified to homogeneity. It catalysed the two
AB  - successive N-methylation steps of 4-amino-L-phenylalanine leading to DMPAPA via
AB  - 4-methylamino-L-phenylalanine. These results allowed us to assign a function to each of the
AB  - four pap genes and to propose a biosynthetic pathway for DMPAPA.
ER  -

TY  - JOUR
AU  - Blanck, A.
AU  - Gluck, B.
AU  - Wartbichler, R.
AU  - Bender, S.
AU  - Poll, M.
AU  - Brandl, A.
TI  - Activity of restriction enzymes in a PCR mix.
JO  - Biochemica
PY  - 1995
SP  - 14
EP  - 14
VL  - 2
AB  - By cutting PCR products with restriction enzymes, the resulting DNA fragments can be cloned
AB  - directionally into vector DNA.  Alternatively, researchers can use this cleavage procedure to
AB  - verify that the DNA of interest has been successfully amplified or even to show a Restriction
AB  - Fragment Length Polymorphism (RFLP) in the amplified fragments.  For maximum convenience, the
AB  - restriction enzyme digest would be performed directly in the PCR mix, without prior
AB  - purification of the amplified fragment.  To investigate which restriction enzymes show
AB  - sufficient activity to be used directly in the PCR mix, we performed an activity test with 50
AB  - selected restriction enzymes.
ER  -

TY  - JOUR
AU  - Blanco-Massani, M.
AU  - Klumpp, J.
AU  - Widmer, M.
AU  - Lehmann, R.P.
AU  - Schuppler, M.
TI  - Chromosomal Sil system contributes to silver resistance in E. coli ATCC 8739.
JO  - Biometals
PY  - 2018
SP  - 1101
EP  - 1114
VL  - 31
AB  - The rise of antibiotic resistance in pathogenic bacteria is endangering the efficacy of
AB  - antibiotics, which consequently results in greater use of silver as a biocide. Chromosomal
AB  - mapping of the Cus system or plasmid encoded Sil system and their relationship with silver
AB  - resistance was studied for several gram-negative bacteria. However, only few reports
AB  - investigated silver detoxification mediated by the Sil system integrated in Escherichia coli
AB  - chromosome. Accordingly, this work aimed to study the Sil system in E. coli ATCC 8739 and to
AB  - produce evidence for its role in silver resistance development. Silver resistance was induced
AB  - in E. coli ATCC 8739 by stepwise passage in culture media containing increasing concentrations
AB  - of AgNO3. The published genome of E. coli ATCC 8739 contains a region showing strong homology
AB  - to the Sil system genes. The role of this region in E. coli ATCC 8739 was assessed by
AB  - monitoring the expression of silC upon silver stress, which resulted in a 350-fold increased
AB  - expression. De novo sequencing of the whole genome of a silver resistant strain derived from
AB  - E. coli ATCC 8739 revealed mutations in ORFs putative for SilR and CusR. The silver resistant
AB  - strain (E. coli AgNO3R) showed constitutive expression of silC which posed a cost of fitness
AB  - resulting in retarded growth. Furthermore, E. coli AgNO3R exhibited cross-resistance to
AB  - ciprofloxacin and a slightly increased tolerance to ampicillin. This study demonstrates that
AB  - E. coli is able to develop resistance to silver, which may pose a threat towards an effective
AB  - use of silver compounds as antiseptics.
ER  -

TY  - JOUR
AU  - Blanga-Kanfi, S.
AU  - Amitsur, M.
AU  - Azem, A.
AU  - Kaufmann, G.
TI  - PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 3209
EP  - 3219
VL  - 34
AB  - The tRNA(Lys) anticodon nuclease PrrC is associated in latent form with the type Ic DNA
AB  - restriction endonuclease EcoprrI and activated by a phage
AB  - T4-encoded inhibitor of EcoprrI. The activation also requires the
AB  - hydrolysis of GTP and presence of dTTP and is inhibited by ATP. The
AB  - N-proximal NTPase domain of PrrC has been implicated in relaying the
AB  - activating signal to a C-proximal anticodon nuclease site by interacting
AB  - with the requisite nucleotide cofactors [Amitsur et al. (2003) Mol.
AB  - Microbiol., 50, 129-143]. Means described here to bypass PrrC's
AB  - self-limiting translation and thermal instability allowed purifying an
AB  - active mutant form of the protein, demonstrating its oligomeric structure
AB  - and confirming its anticipated interactions with the nucleotide cofactors
AB  - of the activation reaction. Mutagenesis and chemical rescue data shown
AB  - implicate the C-proximal Arg320, Glu324 and, possibly, His356 in anticodon
AB  - nuclease catalysis. This triad exists in all the known PrrC homologs but
AB  - only some of them feature residues needed for tRNA(Lys) recognition by the
AB  - Escherichia coli prototype. The differential conservation and consistent
AB  - genetic linkage of the PrrC proteins with EcoprrI homologs portray them as
AB  - a family of restriction RNases of diverse substrate specificities that are
AB  - mobilized when an associated DNA restriction nuclease is compromised.
ER  -

TY  - JOUR
AU  - Blanks, R.
AU  - McLaughlin, L.W.
TI  - An oligodeoxynucleotide affinity column for the isolation of sequence specific DNA binding proteins.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 10283
EP  - 10299
VL  - 16
AB  - A nucleic acid affinity matrix containing a short oligodeoxynucleotide ligand
AB  - has been prepared as an example of a material which can be used for the rapid
AB  - and effective isolation of sequence specific DNA binding proteins.  Two
AB  - complementary oligodeoxynucleotides have been employed, one of which contains a
AB  - small 5'-spacer arm with a terminal thiol group.  Using this terminal thiol
AB  - group, the ligand can be covalently coupled to Tresyl-activated Sepharose 4B or
AB  - Epoxy-activated Sepharose 6B via a thioether linkage.  This approach allows the
AB  - specific attachment of the nucleic acid ligand via its 5'-terminus to the
AB  - insoluble matrix.  The double stranded affinity material was obtained by
AB  - annealing of the complementary DNA fragment.  As an example, we have used an
AB  - eicosomer affinity column containing the sequence d(GAATTC) for the isolation
AB  - of the EcoRI restriction endonuclease.  Using a single column, the enzyme could
AB  - be isolated by eluting the column with a single step or multistep gradient of
AB  - increasing salt concentration.  The enzyme was purified to 75%-85% homogeneity
AB  - with yields of 0.1 mg to 0.2 mg from 0.5 g of cell paste.
ER  -

TY  - JOUR
AU  - Blasche, S.
AU  - Kim, Y.
AU  - Patil, K.R.
TI  - Draft Genome Sequence of Corynebacterium kefirresidentii SB, Isolated from Kefir.
JO  - Genome Announcements
PY  - 2017
SP  - e00877
EP  - e00817
VL  - 5
AB  - The genus Corynebacterium includes Gram-positive species with a high G+C content. We report
AB  - here a novel species, Corynebacterium kefirresidentii SB, isolated from
AB  - kefir grains collected in Germany. Its draft genome sequence was remarkably
AB  - dissimilar (average nucleotide identity, 76.54%) to those of other
AB  - Corynebacterium spp., confirming that this is a unique novel species.
ER  -

TY  - JOUR
AU  - Blaschitz, M.
AU  - Lepuschitz, S.
AU  - Wagner, L.
AU  - Allerberger, F.
AU  - Indra, A.
AU  - Ruppitsch, W.
AU  - Huhulescu, S.
TI  - Draft Genome Sequence of a Vancomycin-Resistant and Vancomycin-Dependent Enterococcus faecium Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00059
EP  - e00016
VL  - 4
AB  - Vancomycin-resistant enterococci have emerged as major nosocomial pathogens worldwide. While
AB  - antimicrobial pressure promotes nosocomial colonization with
AB  - these enterococci, prolonged exposure to vancomycin may foster the transition
AB  - from vancomycin resistance to vancomycin dependence. Here, we report the draft
AB  - genome sequence of a vancomycin-dependentEnterococcus faeciumisolate showing
AB  - partial teicoplanin dependence.
ER  -

TY  - JOUR
AU  - Blaschke, U.
AU  - Skiebe, E.
AU  - Kaatz, M.
AU  - Higgins, P.G.
AU  - Pfeifer, Y.
AU  - Wilharm, G.
TI  - Complete Genome Sequencing of Acinetobacter sp. Strain LoGeW2-3, Isolated from the Pellet of a White Stork, Reveals a Novel Class D Beta-Lactamase Gene.
JO  - Genome Announcements
PY  - 2018
SP  - e01405
EP  - e01417
VL  - 6
AB  - Whole-genome sequencing of Acinetobacter sp. strain LoGeW2-3, isolated from the pellet of a
AB  - white stork (Ciconia ciconia), reveals the presence of a plasmid of
AB  - 179,399 bp encoding a CRISPR-Cas (clustered regularly interspaced short
AB  - palindromic repeats and associated genes) system of the I-F type, and the
AB  - chromosomally encoded novel class D beta-lactamase OXA-568.
ER  -

TY  - JOUR
AU  - Blaschke, U.
AU  - Wilharm, G.
TI  - Complete Genome Sequence of Acinetobacter sp. Strain NCu2D-2 Isolated from a Mouse.
JO  - Genome Announcements
PY  - 2017
SP  - e01415
EP  - e01416
VL  - 5
AB  - Whole-genome sequencing of Acinetobacter sp. strain NCu2D-2, isolated from the trachea of a
AB  - mouse, revealed the presence of a plasmid of 309,964 bp with little
AB  - overall similarity to known plasmids and enriched in insertion sequences (ISs)
AB  - closely related to IS elements known from the nosocomial pathogen Acinetobacter
AB  - baumannii.
ER  -

TY  - JOUR
AU  - Blasiak, J.
AU  - Kowalik, J.
TI  - Interaction between organophosphorus compounds and DNA assayed by the restriction endonuclease EcoRI.
JO  - Acta Univ. Lodz. Folia Biochim. Biophys.
PY  - 1998
SP  - 61
EP  - 67
VL  - 13
AB  - Restriction endonucleases due to the nature of their action may provide information on the
AB  - location or the sequence specificity of a compound that binds to DNA.  On the other hand, the
AB  - action of the enzymes may be disturbed by compounds that have an ability to methylate DNA
AB  - bases.  The latter feature can be considered as a simple method for primary selection of
AB  - potentially genotoxic compounds.  In the present work we investigated the action of
AB  - restriction endonuclease EcoRI on DNA which had been incubated with some organophosphorus
AB  - agents.  PUC19 plasmid DNA at a concentration of 78 microgram/ml was incubated for 72 h with
AB  - organophosphorus insecticides parathion, methylparathion and their main metabolites: paraoxon
AB  - and methylparaoxon, respectively, at a concentration of 300 microM.  After incubation
AB  - non-bound insecticides were removed and DNA was subjected to 1 h incubation with the
AB  - restriction endonuclease EcoRI and electrophoresed in 0.8% agarose gel.  The organophosphorus
AB  - compound methylparaoxon evoked unwinding of supercoiled DNA and the action of EcoRI on the DNA
AB  - was disturbed that was displayed in changes in restriction pattern.
ER  -

TY  - JOUR
AU  - Blattler, M.O.
AU  - Wenz, C.
AU  - Pingoud, A.
AU  - Benner, S.A.
TI  - Distorting duplex DNA by dimethylenesulfone substitution: A new class of "transition state analog" inhibitors for restriction enzymes.
JO  - J. Am. Chem. Soc.
PY  - 1998
SP  - 2674
EP  - 2675
VL  - 120
AB  - After they bind (but before they cleave) duplex DNA, some restriction enzymes (such as EcoRV
AB  - and EcoRI) distort the duplex.  The distorted duplex is not, of course, in its ground-state
AB  - conformation; it requires "binding energy" to bend DNA.  Thus, an analogue of DNA that
AB  - generates this distortion in the unbound state (without altering other features of the
AB  - substrate that are recognized by the enzyme) should bind to these restriction enzymes with a
AB  - higher affinity than the DNA substrate itself.  This is, of course, the principle underlying
AB  - transition-state analogues generally, which approximate in structure the "distorted"
AB  - transition state (or a distorted high-energy intermediate) for an enzymatic reaction.
ER  -

TY  - JOUR
AU  - Blattner, F.R.
AU  - Plunkett, G. III
AU  - Bloch, C.A.
AU  - Perna, N.T.
AU  - Burland, V.
AU  - Riley, M.
AU  - Collado-Vides, J.
AU  - Glasner, J.D.
AU  - Rode, C.K.
AU  - Mayhew, G.F.
AU  - Gregor, J.
AU  - Davis, N.W.
AU  - Kirkpatrick, H.A.
AU  - Goeden, M.A.
AU  - Rose, D.J.
AU  - Mau, B.
AU  - Shao, Y.
TI  - The complete genome sequence of Escherichia coli K-12.
JO  - Science
PY  - 1997
SP  - 1453
EP  - 1462
VL  - 277
AB  - The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding
AB  - genes annotated, 38 percent have no attributed function.  Comparison with five other sequenced
AB  - microbes reveals ubiquitous as well as narrowly distributed gene families; many families of
AB  - similar genes within E. coli are also evident.  The largest family of paralogous proteins
AB  - contains 80 ABC transporters.  The genome as a whole is strikingly organized with respect to
AB  - the local direction of replication; guanines, oligonucleotides possibly related to replication
AB  - and recombination, and most genes are so oriented.  The genome also contains insertion
AB  - sequence elements, phage remnants, and many other patches of unusual composition indicating
AB  - genome plasticity through horizontal transfer.
ER  -

TY  - JOUR
AU  - Bleckwedel, J.
AU  - Teran, L.C.
AU  - Bonacina, J.
AU  - Saavedra, L.
AU  - Mozzi, F.
AU  - Raya, R.R.
TI  - Draft Genome Sequence of the Mannitol-Producing Strain Lactobacillus mucosae CRL573.
JO  - Genome Announcements
PY  - 2014
SP  - e01292
EP  - e01214
VL  - 2
AB  - Lactobacillus mucosae CRL573, isolated from child fecal samples, efficiently converts fructose
AB  - and/or sucrose into the low-calorie sugar mannitol when
AB  - cultured in modified MRS medium at pH 5.0. Also, the strain is capable of
AB  - producing bacteriocin. The draft genome sequence of this strain with potential
AB  - industrial applications is presented here.
ER  -

TY  - JOUR
AU  - Blom, J.
AU  - Rueckert, C.
AU  - Niu, B.
AU  - Wang, Q.
AU  - Borriss, R.
TI  - The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1845
EP  - 1846
VL  - 194
AB  - The genome of the rhizobacterium Bacillus amyloliquefaciens subsp. plantarum CAU  B946 was
AB  - 4.02 Mb in size and harbored 3,823 genes (coding sequences [CDS]). Nine
AB  - giant gene clusters were dedicated to nonribosomal synthesis of antimicrobial
AB  - compounds. Remarkably, strain CAU B946 possessed a gene cluster involved in
AB  - synthesis of iturin A.
ER  -

TY  - JOUR
AU  - Bloodworth, R.A.
AU  - Selin, C.
AU  - Lopez, De.V.M.A.
AU  - Drevinek, P.
AU  - Galanternik, L.
AU  - Degrossi, J.
AU  - Cardona, S.T.
TI  - Draft Genome Sequences of Burkholderia contaminans, a Burkholderia cepacia Complex Species That Is Increasingly Recovered from Cystic Fibrosis Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e00766
EP  - e00715
VL  - 3
AB  - Burkholderia contaminans belongs to the Burkholderia cepacia complex (BCC), a group of
AB  - bacteria that are ubiquitous in the environment and capable of infecting
AB  - the immunocompromised and people with cystic fibrosis. We report here draft
AB  - genome sequences for the B. contaminans type strain LMG 23361 and an Argentinian
AB  - cystic fibrosis sputum isolate.
ER  -

TY  - JOUR
AU  - Blouin, Y.
AU  - Platonov, M.E.
AU  - Pourcel, C.
AU  - Evseeva, V.V.
AU  - Afanas'ev, M.V.
AU  - Balakhonov, S.V.
AU  - Anisimov, A.P.
AU  - Vergnaud, G.
TI  - Draft Genome Sequences of Two Yersinia pseudotuberculosis ST43 (O:1b) Strains, B-7194 and B-7195.
JO  - Genome Announcements
PY  - 2013
SP  - e00510
EP  - e00513
VL  - 1
AB  - We report the first draft genome sequences of two Yersinia pseudotuberculosis sequence type 43
AB  - (ST43) (O:1b) strains, B-7194 and B-7195, isolated in Russia.
AB  - The total lengths of the assemblies are 4,427,121 bp and 4,608,472 bp, and 3,819
AB  - and 4,018 coding sequences, respectively, were predicted within the genomes.
ER  -

TY  - JOUR
AU  - Blow, F.
AU  - Gioti, A.
AU  - Starns, D.
AU  - Ben-Yosef, M.
AU  - Pasternak, Z.
AU  - Jurkevitch, E.
AU  - Vontas, J.
AU  - Darby, A.C.
TI  - Draft Genome Sequence of the Bactrocera oleae Symbiont 'Candidatus Erwinia dacicola'.
JO  - Genome Announcements
PY  - 2016
SP  - e00896
EP  - e00816
VL  - 4
AB  - 'Candidatus Erwinia dacicola' is a Gammaproteobacterium that forms a symbiotic association
AB  - with the agricultural pest Bactrocera oleae Here, we present a 2.1-Mb
AB  - draft hybrid genome assembly for 'Ca. Erwinia dacicola' generated from
AB  - single-cell and metagenomic data.
ER  -

TY  - JOUR
AU  - Blow, F.
AU  - Vontas, J.
AU  - Darby, A.C.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia SBo1 Isolated from Bactrocera oleae.
JO  - Genome Announcements
PY  - 2016
SP  - e00905
EP  - e00916
VL  - 4
AB  - Bacteria of the genus Stenotrophomonas are ubiquitous in the environment and are  increasingly
AB  - associated with insects. Stenotrophomonas maltophilia SBo1 was
AB  - cultured from the gut of Bactrocera oleae The draft genome sequence presented
AB  - here will inform future investigations into the nature of the interaction between
AB  - insects and their microbiota.
ER  -

TY  - JOUR
AU  - Blow, F.
AU  - Vontas, J.
AU  - Darby, A.C.
TI  - Draft Genome Sequence of Chryseobacterium Strain CBo1 Isolated from Bactrocera oleae.
JO  - Genome Announcements
PY  - 2017
SP  - e00177
EP  - e00117
VL  - 5
AB  - Bacteria of the genus Chryseobacterium have previously been identified as mutualists of plants
AB  - and insects. Chryseobacterium strain CBo1 was cultured from
AB  - the gut of the agricultural pest Bactrocera oleae and its whole genome sequenced.
AB  - This genomic resource will aid investigations into the transition of microbes
AB  - between plant and invertebrate hosts.
ER  -

TY  - JOUR
AU  - Blow, M.J. et al.
TI  - The Epigenomic Landscape of Prokaryotes.
JO  - PLoS Genet.
PY  - 2016
SP  - e1005854
EP  - e1005854
VL  - 12
AB  - DNA methylation acts in concert with restriction enzymes to protect the integrity of
AB  - prokaryotic genomes. Studies in a limited number of organisms suggest that
AB  - methylation also contributes to prokaryotic genome regulation, but the prevalence
AB  - and properties of such non-restriction-associated methylation systems remain
AB  - poorly understood. Here, we used single molecule, real-time sequencing to map DNA
AB  - modifications including m6A, m4C, and m5C across the genomes of 230 diverse
AB  - bacterial and archaeal species. We observed DNA methylation in nearly all (93%)
AB  - organisms examined, and identified a total of 834 distinct reproducibly
AB  - methylated motifs. This data enabled annotation of the DNA binding specificities
AB  - of 620 DNA Methyltransferases (MTases), doubling known specificities for
AB  - previously hard to study Type I, IIG and III MTases, and revealing their
AB  - extraordinary diversity. Strikingly, 48% of organisms harbor active Type II
AB  - MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases
AB  - are present in diverse bacterial and archaeal phyla and show motif specificities
AB  - and methylation patterns consistent with functions in gene regulation and DNA
AB  - replication. Our results reveal the pervasive presence of DNA methylation
AB  - throughout the prokaryotic kingdoms, as well as the diversity of sequence
AB  - specificities and potential functions of DNA methylation systems.
ER  -

TY  - JOUR
AU  - Blum, E.
AU  - Horst, G.
AU  - Kroger, M.
TI  - PCR directed preparation and single step purification of highly active histidine-tagged restriction endonuclease HgiBI (GGWCC).
JO  - J. Biochem. Biophys. Methods
PY  - 1994
SP  - 113
EP  - 121
VL  - 29
AB  - The polymerase-chain-reaction technique is used to produce fusion proteins via deletion of any
AB  - intervening piece of DNA. Here a stretch of six histidine codons is fused to the 3'-terminus
AB  - of any defined gene using a standard plasmid vector or a derivative thereof. The advantage
AB  - over existing methods is that no other amino acids besides the six histidines are added to the
AB  - protein terminus and only one oligonucleotide needs to be synthesized as special primer. Genes
AB  - of interest must only be cloned in the correct orientation into a universal multilinker. Using
AB  - just one specific primer derived from the 3'-terminus of the gene and one standard primer
AB  - derived from the six histidine codons the fusion is performed by amplifying the entire vector
AB  - system as described for inverse PCR. As an example, we report on the modification and
AB  - purification of the restriction endonuclease HgiBI (GGWCC). Enzymatically active protein was
AB  - obtained in a single step purification under nondenaturing conditions with a purity greater
AB  - than 95% according to polyacrylamide gel electrophoresis.
ER  -

TY  - JOUR
AU  - Blum, E.
AU  - Horst, G.
AU  - Kroger, M.
TI  - PCR-directed preparation and single-step purification of highly active histidine-tagged restriction endonuclease HgiBI (GGWCC).
JO  - Gene
PY  - 1995
SP  - 107
EP  - 108
VL  - 157
AB  - The polymerase chain reaction was used to produce His6 fusion proteins via deletion of an
AB  - intervening piece of DNA.  The generally applicable method was performed using a standard
AB  - primer with the advantage that the fusion does not produce additional amino acids.  In a
AB  - single-step purification highly purified, enzymatically active restriction endonuclease was
AB  - obtained.
ER  -

TY  - JOUR
AU  - Blum, S.
AU  - Sela, N.
AU  - Heller, E.D.
AU  - Sela, S.
AU  - Leitner, G.
TI  - Genome Analysis of Bovine-Mastitis-Associated Escherichia coli O32:H37 Strain P4.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3732
EP  - 3732
VL  - 194
AB  - Escherichia coli is a major pathogen of bovine intramammary infections. Here we report the
AB  - first draft of the genome sequence of the E. coli O32:H37 P4 strain,
AB  - which is widely used in experimental bovine mastitis studies.
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
TI  - The PvuII restriction-modification system:  cloning, characterization and use in revealing in E. coli barrier to certain methylases or methylated DNAs.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 227
EP  - 245
VL  - 5
AB  - The physiology of the type II restriction-modification systems (RMS2s) is not
AB  - yet understood in detail.  Relatively few RMS2s have actually been demonstrated
AB  - to carry out the role for which they were named:  restriction of DNA entry into
AB  - the cell through selective endonuclease action.  On the other hand, there are
AB  - numerous examples of DNA methylases, biochemically identical to RMS2 enzymes
AB  - but apparently lacking a cognate endonuclease activity, for which no role has
AB  - yet been discovered.  Our limited knowledge in this area has hindered attempts
AB  - to understand why the genes for certain RMS2s have been difficult to clone and
AB  - express.  Several basic questions remain to be answered regarding the
AB  - regulation of and sequence recognition by RMS2 enzymes.  Also, does the
AB  - methylase of a newly introduced RMS2 have to fully protect the DNA of its new
AB  - host before the endonuclease gene is expressed, or can the cell repair a
AB  - significant amount of endonucleolytic damage?  And what are the effects of a
AB  - foreign DNA methylase on the cell?  We have cloned and characterized the genes
AB  - for the PvuII RMS2 from Proteus vulgaris and, in the course of studies designed
AB  - to examine their regulation, found that the majority of E. coli strains tested
AB  - are poorly transformed by these genes.  We found that this effect is due to the
AB  - PvuII methylase, not to the endonuclease, and that DNAs methyolated by the
AB  - PvuII methylase also transform most tested strains poorly.  Others have found
AB  - this effect with several other DNA methylases, and it has raised new questions
AB  - about gene cloning procedures and about E. coli physiology.
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
TI  - E. coli can restrict methylated DNA and may skew genomic libraries.
JO  - Trends Biotechnol.
PY  - 1986
SP  - 302
EP  - 305
VL  - 4
AB  - None
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
TI  - Cloning and restriction of methylated DNA in Escherichia coli.
JO  - BRL Focus
PY  - 1989
SP  - 41
EP  - 46
VL  - 11
AB  - A review of mcr systems.
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - A Taq attack displaces bases.
JO  - Nat. Struct. Biol.
PY  - 2001
SP  - 101
EP  - 103
VL  - 8
AB  - The cocrystal structure of TaqI DNA methyltransferase in complex with its specific DNA
AB  - substrate adds to the growing list of structurally confirmed DNA base-flipping enzymes, and
AB  - provides a basis for the general mechanism of AdoMet-dependent DNA N-methylation.
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
AU  - Cotterman, M.M.
TI  - Isolation of mutants in a DNA methyltransferase through mcr-B-mediated restriction.
JO  - Gene
PY  - 1988
SP  - 271
EP  - 273
VL  - 74
AB  - A procedure has been developed that permits the positive selection of mutants
AB  - in a DNA methyltransferase (MTase) gene.  The stringency of this selection can
AB  - be varied so as to yield null mutants only, or a mixture of null and partially
AB  - defective mutants.  The procedure was developed with the PvuII MTase gene
AB  - (pvuIIM), which was subcloned into a bacteriophage Lambda vector.  Growth of
AB  - this lambda pvuIIM construct on an mcrB+ host selected for non-methylating
AB  - mutants, and the stringency of selection was proportional to the number of
AB  - consecutive lytic cycles.  Many cytosine MTases have been found to generate
AB  - substrates for mcrB-mediated restriction, and this procedure should be
AB  - applicable to a number of cytosine MTase genes.
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
AU  - Gregory, S.A.
AU  - Cooperider, J.S.
TI  - Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1985
SP  - 501
EP  - 509
VL  - 164
AB  - A 4.84 kilobasepair plasmid was isolated from Proteus vulgaris (ATCC 13315) and
AB  - cloned into the plasmid vector pBR322.  Plasmid pBR322 contains substrate sites
AB  - for the restriction endonucleases PvuI and PvuII.  The recombinant plasmids
AB  - were resistant to in vitro cleavage by PvuII but not PvuI endonuclease and were
AB  - found to cause production of PvuII endonuclease or methylase activity or both
AB  - in Escherichia coli strain HB101.  The approximate endonuclease and methylase
AB  - gene boundaries were determined through subcloning, Bal31 resection,
AB  - insertional inactivation, DNA-dependent translation, and partial DNA
AB  - sequencing.  The two genes are adjacent and appear to be divergently
AB  - transcribed.  Most E. coli strains tested were poorly transformed by the
AB  - recombinant plasmids, and this was shown by subcloning and insertional
AB  - inactivation to be due to the dPvuII methylase gene.  At a low freqency, stable
AB  - methylase-producing transformants of a "methylase-sensitive" strain were
AB  - obtained, and efficiently-transformed cell mutants were isolated from them.
ER  -

TY  - JOUR
AU  - Blumenthal, R.M.
AU  - Vijesurier, R.M.
AU  - Carlock, L.
AU  - Dunbar, J.C.
TI  - C.PvuII, an unusual transcriptional activator conserved among restriction-modification systems.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1999
SP  - 354
EP  - 354
VL  - 99
AB  - The pvuII restriction-modification system is a type II system, which means that its
AB  - restriction endonuclease and modification methyltransferase are independently active proteins.
AB  - Because the PvuII genes are carried on a plasmid their expression must be regulated such that
AB  - movement into a new host cell is initially followed by expression of the methyltransferase
AB  - gene alone, so that the new host's DNA is protected before endonuclease activity appears.
AB  - Previous studies have identified a regulatory gene (pvuIIC) between the divergently-oriented
AB  - genes for the restriction endonuclease (pvuIIM), with pvuIIC in the same orientation as and
AB  - partially overlapping pvuIIR.  The product of pvuIIC, C.PvuII, was found to act in trans and
AB  - to be required for expression of pvuIIR.  We have demonstrated that premature expression of
AB  - pvuIIC prevents establishment of the PvuII genes, consistent with the model that requiring
AB  - C.PvuII for pvuIIR expression provides a timing delay essential for protection of the new
AB  - host's DNA.  We find that the opposing pvuIIC and pvuIIM transcripts overlap by over 60
AB  - nucleotides at their 5' ends, raising the possibility that their hybridization might play a
AB  - regulatory role.  We furthermore characterize the action of C.PvuII, demonstrating that it is
AB  - a sequence-specific DNA-binding protein that binds the DNA just upstream of the pvuIIC
AB  - promoter and stimulates transcription of both pvuIIC and pvuIIR into a polycistronic mRNA. The
AB  - location of CoPvuII binding immediately adjacent to the pvuIIC transcriptional stating points
AB  - is highly unusual among transcriptional activators.  Another surprise is that we found no
AB  - evidence for a pvuIIR-specific promoter, leaving open the question of whether the endonuclease
AB  - gene is actually expressed (if at low levels) as early in establishment as the
AB  - methyltransferase gene.  We are exploring the role of predicted hairpins in the mRNA just
AB  - upstream of pvuIIR, one of which would obstruct the Shine-Dalgarno sequence and might be used
AB  - to delay the appearance of endonuclease activity.
ER  -

TY  - JOUR
AU  - Blumer-Schuette, S.E. et al.
TI  - Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis,  Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis,  Caldicellulosiruptor owensensis, and Cal.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1483
EP  - 1484
VL  - 193
AB  - The genus Caldicellulosiruptor contains the most thermophilic, plant biomass-degrading
AB  - bacteria isolated to date. Previously, genome sequences
AB  - from three cellulolytic members of this genus were reported (C.
AB  - saccharolyticus, C. bescii, and C. obsidiansis). To further explore the
AB  - physiological and biochemical basis for polysaccharide degradation within
AB  - this genus, five additional genomes were sequenced: C. hydrothermalis, C.
AB  - kristjanssonii, C. kronotskyensis, C. lactoaceticus, and C. owensensis.
AB  - Taken together, the seven completed and one draft-phase
AB  - Caldicellulosiruptor genomes suggest that, while central metabolism is
AB  - highly conserved, significant differences in glycoside hydrolase
AB  - inventories and numbers of carbohydrate transporters exist, a finding
AB  - which likely relates to variability observed in plant biomass degradation
AB  - capacity.
ER  -

TY  - JOUR
AU  - Bobst, A.M.
AU  - Pauly, G.T.
AU  - Keyes, R.S.
AU  - Bobst, E.V.
TI  - Enzymatic sequence-specific spin labeling of a DNA fragment containing the recognition sequence of EcoRI endonuclease.
JO  - FEBS Lett.
PY  - 1988
SP  - 33
EP  - 36
VL  - 228
AB  - Deoxyuridine analogs spin labeled in position 5 have been enzymatically
AB  - incorporated sequence specifically into an oligodeoxyribonucleotide to form a
AB  - spin-labeled 26-mer.  The 26-mer contains the EcoRI-binding site and two labels
AB  - which are located symmetrically close to the binding site.  The labels are
AB  - separated from one another far beyond the Heisenberg spin-exchange distance.
AB  - The local base motion as determined by ESR spectroscopy is of the order of 4 ns
AB  - in the oligonucleotide duplex.  This is the same value as reported earlier for
AB  - local T motions in polynucleotide duplexes, thereby providing direct
AB  - experimental evidence that the ESR line shape of spin levels covalently
AB  - attached to nucleic acids depends primarily on the local dynamics of the
AB  - nucleic acid building blocks.
ER  -

TY  - JOUR
AU  - Boch, J.
AU  - Bonas, U.
TI  - Xanthomonas AvrBs3 family-type III effectors: discovery and function.
JO  - Annu. Rev. Phytopathol.
PY  - 2010
SP  - 419
EP  - 436
VL  - 48
AB  - Xanthomonads are bacterial plant pathogens that cause diseases on many plant species,
AB  - including important crops. Key to pathogenicity of most Xanthomonas
AB  - pathovars is a Hrp-type III secretion (T3S) system that translocates effector
AB  - proteins into plant cells. Within the eukaryotic cell, the effectors are thought
AB  - to perform a variety of tasks to support bacterial virulence, proliferation, and
AB  - dissemination. We are only beginning to understand the host targets of different
AB  - effectors. The largest effector family found in Xanthomonas spp. is the
AB  - AvrBs3/PthA or TAL (transcription activator-like) family. TAL effectors act as
AB  - transcriptional activators in the plant cell nucleus. Specificity of TAL
AB  - effectors is determined by a novel modular DNA-binding domain. Here, we describe
AB  - the discovery of TAL effectors and their structure, activity, and host targets.
ER  -

TY  - JOUR
AU  - Bochow, S.
AU  - Elliman, J.
AU  - Owens, L.
TI  - Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio harveyi myovirus like.
JO  - J. Appl. Microbiol.
PY  - 2012
SP  - 1001
EP  - 1013
VL  - 113
AB  - The adenine methyltransferase (DAM) gene methylates GATC sequences that have been demonstrated
AB  - in various bacteria to be a powerful gene
AB  - regulator functioning as an epigenetic switch, particularly with
AB  - virulence gene regulation. However, overproduction of DAM can lead to
AB  - mutations, giving rise to variability that may be important for
AB  - adaptation to environmental change. While most bacterial hosts carry a
AB  - DAM gene, not all bacteriophage carry this gene. Currently, there is no
AB  - literature regarding the role DAM plays in life cycle regulation of
AB  - bacteriophage. Vibriocampbellii strain 642 carries the bacteriophage
AB  - Vibrioharveyi myovirus like (VHML) that has been proven to increase
AB  - virulence. The complete genome sequence of VHML bacteriophage revealed
AB  - a putative adenine methyltransferase gene. Using VHML, a new model of
AB  - phage life cycle regulation, where DAM plays a central role between the
AB  - lysogenic and lytic states, will be hypothesized. In short, DAM
AB  - methylates the rha antirepressor gene and once methylation is removed,
AB  - homologous CI repressor protein becomes repressed and non-functional
AB  - leading to the switching to the lytic cycle. Greater understanding of
AB  - life cycle regulation at the genetic level can, in the future, lead to
AB  - the genesis of chimeric bacteriophage with greater control over their
AB  - life cycle for their safe use as probiotics within the aquaculture
AB  - industry.
ER  -

TY  - JOUR
AU  - Bochtler, M.
TI  - Indirect DNA Sequence Readout by LAGLIDADG Homing Endonucleases.
JO  - Structure
PY  - 2016
SP  - 839
EP  - 840
VL  - 24
AB  - In this issue of Structure, Lambert et al. (2016) describe extensive structural and functional
AB  - work on meganucleases, the group of homing endonucleases most
AB  - commonly adapted to genome engineering applications. The data are of interest to
AB  - structural biologists, evolutionary biologists, protein designers, and genome
AB  - engineers.
ER  -

TY  - JOUR
AU  - Bochtler, M.
AU  - Szczepanowski, R.H.
AU  - Tamulaitis, G.
AU  - Grazulis, S.
AU  - Czapinska, H.
AU  - Manakova, E.
AU  - Siksnys, V.
TI  - Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
JO  - EMBO J.
PY  - 2006
SP  - 2219
EP  - 2229
VL  - 25
AB  - Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the
AB  - outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily
AB  - related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt
AB  - 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A
AB  - resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that
AB  - Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases
AB  - in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces
AB  - a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile
AB  - phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two
AB  - enzymes can use a conserved DNA recognition module, yet recognize different sequences, and
AB  - form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the
AB  - first example of a restriction endonuclease that flips nucleotides to achieve specificity for
AB  - its recognition site.
ER  -

TY  - JOUR
AU  - Bocklage, H.
AU  - Heeger, K.
AU  - Muller-Hill, B.
TI  - Cloning and characterization of the MboII restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 1007
EP  - 1013
VL  - 19
AB  - The two genes encoding the class IIS restriction-modification system MboII from
AB  - Moraxella bovis were cloned separately in two compatible plasmids and expressed
AB  - in E. coli RR1DeltaM15.  The nucleotide sequences of the MboII endonuclease
AB  - (R.MboII) and methylase (M.MboII) genes were determined and the putative start
AB  - codon of R.MboII was confirmed by amino acid sequence analysis.  The mboIIR
AB  - gene specifies a protein of 110 amino acids (MW:48,617) while the mboIIM gene
AB  - codes for a putative 260-residue polypeptide (MW:30,077).  Both genes are
AB  - aligned in the same orientation.  The coding region of the methylase gene ends
AB  - 11 bp upstream of the start codon of the restrictase gene.  Comparing the amino
AB  - acid sequence of M.MboII with sequences of other N6 adenine methyltransferases
AB  - reveals a significant homology to M.RsrI, M.HinfI and M.DpnA.  Furthermore,
AB  - M.MboII shows homology to the N4-cytosine methyltransferase BamHI.
ER  -

TY  - JOUR
AU  - Bocsanczy, A.M.
AU  - Huguet-Tapia, J.C.
AU  - Norman, D.J.
TI  - Whole-Genome Sequence of Ralstonia solanacearum P673, a Strain Capable of Infecting Tomato Plants at Low Temperatures.
JO  - Genome Announcements
PY  - 2014
SP  - e00106
EP  - e00114
VL  - 2
AB  - Ralstonia solanacearum is the causal agent of bacterial wilt, one of the most destructive
AB  - bacterial plant diseases. We present the whole-genome sequence of the
AB  - strain P673 (phylotype IIB, sequevar 4). This strain is capable of producing
AB  - disease in tomato plants at low temperatures. P673 has 311 unique genes.
ER  -

TY  - JOUR
AU  - Bodaker, I.
AU  - Sharon, I.
AU  - Suzuki, M.T.
AU  - Feingersch, R.
AU  - Shmoish, M.
AU  - Andreishcheva, E.
AU  - Sogin, M.L.
AU  - Rosenberg, M.
AU  - Maguire, M.E.
AU  - Belkin, S.
AU  - Oren, A.
AU  - Beja, O.
TI  - Comparative community genomics in the Dead Sea: an increasingly extreme environment.
JO  - ISME J.
PY  - 2010
SP  - 399
EP  - 407
VL  - 4
AB  - Owing to the extreme salinity ( approximately 10 times saltier than the
AB  - oceans), near toxic magnesium levels (approximately 2.0 M Mg(2+)), the
AB  - dominance of divalent cations, acidic pH (6.0) and high-absorbed radiation
AB  - flux rates, the Dead Sea represents a unique and harsh ecosystem. Measures
AB  - of microbial presence (microscopy, pigments and lipids) indicate that
AB  - during rare bloom events after exceptionally rainy seasons, the microbial
AB  - communities can reach high densities. However, most of the time, when the
AB  - Dead Sea level is declining and halite is precipitating from the water
AB  - column, it is difficult to reliably measure the presence of microorganisms
AB  - and their activities. Although a number of halophilic Archaea have been
AB  - previously isolated from the Dead Sea, polar lipid analyses of biomass
AB  - collected during Dead Sea blooms suggested that these isolates were not
AB  - the major components of the microbial community of these blooms. In this
AB  - study, in an effort to characterize the perennial microbial community of
AB  - the Dead Sea and compare it with bloom assemblages, we performed
AB  - metagenomic analyses of concentrated biomass from hundreds of liters of
AB  - brine and of microbial material from the last massive Dead Sea bloom. The
AB  - difference between the two conditions was reflected in community
AB  - composition and diversity, in which the bloom was different and less
AB  - diverse from the residual brine population. The distributional patterns of
AB  - microbial genes suggested Dead Sea community trends in mono- and divalent
AB  - cation metabolisms as well as in transposable elements. This may indicate
AB  - possible mechanisms and pathways enabling these microbes to survive in
AB  - such a harsh environment.
ER  -

TY  - JOUR
AU  - Boden, R. et al.
TI  - Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7001
EP  - 7002
VL  - 193
AB  - Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of
AB  - the Gammaproteobacteria, isolated from coastal
AB  - seawater. Here we present the complete genome sequence of this strain, the
AB  - first available from an aerobic marine methanotroph.
ER  -

TY  - JOUR
AU  - Boden, R.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Kelly, D.P.
AU  - Murrell, J.C.
AU  - Schafer, H.
TI  - Draft genome sequence of the chemolithoheterotrophic halophilic methylotroph Methylophaga thiooxydans DMS010.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3154
EP  - 3155
VL  - 193
AB  - Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of
AB  - methylotrophic growth on a range of one-carbon
AB  - compounds as well as chemolithoheterotrophic growth at the expense of
AB  - thiosulfate. Here we present the draft genome sequence of Methylophaga
AB  - thiooxydans DMS010 (DSM 22068(T), VKM B2586(T)), the type strain of the
AB  - species, which has allowed prediction of the genes involved in one-carbon
AB  - metabolism, nitrogen metabolism and other aspects of central metabolism.
ER  -

TY  - JOUR
AU  - Boden, R.
AU  - Hutt, L.P.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Palaniappan, K.
AU  - Varghese, N.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.
AU  - Ngan, C.Y.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Woyke, T.
AU  - Kyrpides, N.
TI  - Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately  thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 74
EP  - 74
VL  - 11
AB  - Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a
AB  - sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at
AB  - Bath, United Kingdom and is an obligate chemolithoautotroph growing at the
AB  - expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp.
AB  - Here we report the genome sequence, annotation and characteristics. The genome
AB  - comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the
AB  - transaldolase variant of the Calvin-Benson-Bassham cycle were identified along
AB  - with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal
AB  - oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and
AB  - ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in
AB  - pathways of arsenic and cadmium resistance were found. Evidence of horizontal
AB  - gene transfer accounting for 5.9 % of the protein-coding genes was found,
AB  - including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath,
AB  - isolated from the same spring. A sox gene cluster was found, similar in structure
AB  - to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus
AB  - and Paracoccus denitrificans, an additional gene between soxA and soxB was found,
AB  - annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich
AB  - pathway of thiosulfate oxidation (encoded by sox) is not used in
AB  - Thermithiobacillus spp., the role of the operon (if any) in this species remains
AB  - unknown. We speculate that DUF302 and sox genes may have a role in periplasmic
AB  - trithionate oxidation.
ER  -

TY  - JOUR
AU  - Bodi-Winn, C.
AU  - Dzink-Fox, J.
AU  - Feng, Y.
AU  - Shen, Z.
AU  - Bakthavatchalu, V.
AU  - Fox, J.G.
TI  - Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus).
JO  - Genome Announcements
PY  - 2017
SP  - e01435
EP  - e01416
VL  - 5
AB  - In collaboration with the CDC's Streptococcus Laboratory, we report here the whole-genome
AB  - sequences of seven Streptococcus agalactiae bacteria isolated from laboratory-reared
AB  - Long-Evans rats. Four of the S. agalactiae isolates were associated with morbidity accompanied
AB  - by endocarditis, metritis, and fatal septicemia, providing an opportunity for comparative
AB  - genomic analysis of this opportunistic pathogen.
ER  -

TY  - JOUR
AU  - Bodilis, J.
AU  - Youenou, B.
AU  - Briolay, J.
AU  - Brothier, E.
AU  - Favre-Bonte, S.
AU  - Nazaret, S.
TI  - Draft Genome Sequences of Stenotrophomonas maltophilia Strains Sm32COP, Sm41DVV,  Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, Isolated from Different Manures in   France.
JO  - Genome Announcements
PY  - 2016
SP  - e00841
EP  - e00816
VL  - 4
AB  - Stenotrophomonas maltophilia is a major opportunistic human pathogen responsible  for
AB  - nosocomial infections. Here, we report the draft genome sequences of Sm32COP,
AB  - Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different
AB  - manures in France, which provide insights into the genetic determinism of
AB  - intrinsic or acquired antibiotic resistance in this species.
ER  -

TY  - JOUR
AU  - Bodnar, J.W.
AU  - Zempsky, W.
AU  - Warder, D.
AU  - Bergson, C.
AU  - Ward, D.C.
TI  - Effect of nucleotide analogs on the cleavage of DNA by the restriction enzymes AluI, DdeI, HinfI, RsaI, and TaqI.
JO  - J. Biol. Chem.
PY  - 1983
SP  - 15206
EP  - 15213
VL  - 258
AB  - The cleavage of specific DNA sequences by the restriction endonucleases AluI,
AB  - DdeI, HinfI, RsaI, and TaqI has been studied by monitoring the effect of
AB  - various nucleotide modifications on the rate of DNA digestion.  Bacteriophage
AB  - fd DNA was completely substituted in one strand with a single nucleotide
AB  - analog, using an in vitro primed DNA synthesis reaction on a single-stranded
AB  - viral DNA template.  Twelve deoxynucleotide analogs were incorporated into
AB  - these DNA substrates:  2-aminopurine, 2,6-diaminopurine, deoxytubercidin,
AB  - deoxyuridine, 5-bromodeoxyuridine, 5-allylamine deoxyuridine, 5-biotinyl
AB  - deoxyuridine, deoxypseudouridine, deoxyinosine, 8-azadeoxyguanosine,
AB  - 5-iododeoxycytidine, and 5-bromodeoxycytidine.  The restriction enzymes tested
AB  - varied considerably in their ability to digest hemi-substituted DNAs containing
AB  - these modified nucleotides.  Structural alterations in the base pairs
AB  - immediately adjacent to the phosphodiester bonds cleaved by the enzyme reduced
AB  - the rate of enzyme activity most dramatically, and in most cases more than a
AB  - single determinant on each base pair altered activity.  Interactions with
AB  - nucleotides outside the recognition site seem to have little importance in the
AB  - binding or catalytic activity of these enzymes.
ER  -

TY  - JOUR
AU  - Bogdanova, E.
AU  - Djordjevic, M.
AU  - Papapanagiotou, I.
AU  - Heyduk, T.
AU  - Kneale, G.
AU  - Severinov, K.
TI  - Transcription regulation of the type II restriction-modification system AhdI.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 1429
EP  - 1442
VL  - 36
AB  - The Restriction-modification system AhdI contains two convergent transcription units, one with
AB  - genes encoding methyltransferase subunits M and S and another with genes encoding the
AB  - controller (C) protein and the restriction endonuclease (R). We show that AhdI transcription
AB  - is controlled by two independent regulatory loops that are well-optimized to ensure successful
AB  - establishment in a naive bacterial host. Transcription from the strong MS promoter is
AB  - attenuated by methylation of an AhdI site overlapping the -10 element of the promoter.
AB  - Transcription from the weak CR promoter is regulated by the C protein interaction with two
AB  - DNA-binding sites. The interaction with the promoter-distal high-affinity site activates
AB  - transcription, while interaction with the weaker promoter-proximal site represses it. Because
AB  - of high levels of cooperativity, both C protein-binding sites are always occupied in the
AB  - absence of RNA polymerase, raising a question how activated transcription is achieved. We
AB  - develop a mathematical model that is in quantitative agreement with the experiment and
AB  - indicates that RNA polymerase outcompetes C protein from the promoter-proximal-binding site.
AB  - Such an unusual mechanism leads to a very inefficient activation of the R gene transcription,
AB  - which presumably helps control the level of the endonuclease in the cell.
ER  -

TY  - JOUR
AU  - Bogdanova, E.
AU  - Zakharova, M.
AU  - Streeter, S.
AU  - Taylor, J.
AU  - Heyduk, T.
AU  - Kneale, G.
AU  - Severinov, K.
TI  - Transcription regulation of restriction-modification system Esp1396I.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3354
EP  - 3366
VL  - 37
AB  - The convergently transcribed restriction (R) and methylase (M) genes of the
AB  - Restriction-Modification system Esp1396I are tightly regulated by a
AB  - controller (C) protein that forms part of the CR operon. We have mapped
AB  - the transcriptional start sites from each promoter and examined the
AB  - regulatory role of C.Esp1396I in vivo and in vitro. C-protein binding at
AB  - the CR and M promoters was analyzed by DNA footprinting and a range of
AB  - biophysical techniques. The distal and proximal C-protein binding sites at
AB  - the CR promoter are responsible for activation and repression,
AB  - respectively. In contrast, a C-protein dimer binds to a single site at the
AB  - M-promoter to repress the gene, with an affinity much greater than for the
AB  - CR promoter. Thus, during establishment of the system in a naive host, the
AB  - activity of the M promoter is turned off early, preventing excessive
AB  - synthesis of methylase. Mutational analysis of promoter binding sites
AB  - reveals that the tetranucleotide inverted repeats long believed to be
AB  - important for C-protein binding to DNA are less significant than
AB  - previously thought. Instead, symmetry-related elements outside of these
AB  - repeats appear to be critical for the interaction and are discussed in
AB  - terms of the recent crystal structure of C.Esp139I bound to the CR
AB  - promoter.
ER  -

TY  - JOUR
AU  - Bogdanove, A.J. et al.
TI  - Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5450
EP  - 5464
VL  - 193
AB  - Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300
AB  - plant species. The broad host range of the genus
AB  - contrasts with stringent host and tissue specificity for individual
AB  - species and pathovars. Whole-genome sequences of Xanthomonas campestris
AB  - pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256,
AB  - pathogens that infect the mesophyll tissue of the leading models for plant
AB  - biology, Arabidopsis thaliana and rice, respectively, were determined and
AB  - provided insight into the genetic determinants of host and tissue
AB  - specificity. Comparisons were made with genomes of closely related strains
AB  - that infect the vascular tissue of the same hosts and across a larger
AB  - collection of complete Xanthomonas genomes. The results suggest a model in
AB  - which complex sets of adaptations at the level of gene content account for
AB  - host specificity and subtler adaptations at the level of amino acid or
AB  - noncoding regulatory nucleotide sequence determine tissue specificity.
ER  -

TY  - JOUR
AU  - Bogdanove, A.J.
AU  - Bohm, A.
AU  - Miller, J.C.
AU  - Morgan, R.D.
AU  - Stoddard, B.L.
TI  - Engineering altered protein-DNA recognition specificity.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 4845
EP  - 4871
VL  - 46
AB  - Protein engineering is used to generate novel protein folds and assemblages, to impart new
AB  - properties and functions onto existing proteins, and to enhance our
AB  - understanding of principles that govern protein structure. While such approaches
AB  - can be employed to reprogram protein-protein interactions, modifying protein-DNA
AB  - interactions is more difficult. This may be related to the structural features of
AB  - protein-DNA interfaces, which display more charged groups, directional hydrogen
AB  - bonds, ordered solvent molecules and counterions than comparable protein
AB  - interfaces. Nevertheless, progress has been made in the redesign of protein-DNA
AB  - specificity, much of it driven by the development of engineered enzymes for
AB  - genome modification. Here, we summarize the creation of novel DNA specificities
AB  - for zinc finger proteins, meganucleases, TAL effectors, recombinases and
AB  - restriction endonucleases. The ease of re-engineering each system is related both
AB  - to the modularity of the protein and the extent to which the proteins have
AB  - evolved to be capable of readily modifying their recognition specificities in
AB  - response to natural selection. The development of engineered DNA binding proteins
AB  - that display an ideal combination of activity, specificity, deliverability, and
AB  - outcomes is not a fully solved problem, however each of the current platforms
AB  - offers unique advantages, offset by behaviors and properties requiring further
AB  - study and development.
ER  -

TY  - JOUR
AU  - Bogdarina, I.G.
AU  - Burianov, I.I.
AU  - Baev, A.A.
TI  - DNA modification in vitro by E. coli C and E. coli MRE 600 DNA-cytosine-methyltransferases: increased resistance of bacteriophage lambda DNA to the RII restriction system.
JO  - Dokl. Akad. Nauk.
PY  - 1977
SP  - 498
EP  - 501
VL  - 233
ER  -

TY  - JOUR
AU  - Bogdarina, I.G.
AU  - Buryanov, Y.I.
AU  - Bayev, A.A.
TI  - Isolation and properties of DNA-cytosine-methyltransferase EcoRII and E. coli K12.
JO  - Biokhimiia
PY  - 1979
SP  - 440
EP  - 452
VL  - 44
AB  - The methods of isolation and partial purification of two DNA-cytosine-methylases EcoRII and E.
AB  - coli K12 are described.  After chromatography on phosphocellulose the enzymes were purified
AB  - 100-fold, the yield being 30%.  Further purification of the enzymes was performed by
AB  - sedimentation in a sucrose concentration gradient.  Both enzymes have native molecular weights
AB  - of 50,000; DC-methylase from E. coli K12 may simultaneously occur in the forms with molecular
AB  - weights of 70,000, 90,000 and 110,000.  Both DC-methylases modify identical nucleotide
AB  - sequences of DNA, have equal numbers of methylation sites in phage lambda DNA and provide in
AB  - vitro a complete protection of phage lambda DNA against restriction endonuclease EcoRII.
AB  - DC-methylases E. coli K12 and EcoRII differ in their chromatographic behavior on
AB  - phosphocellulose and capacity to form complexes with the cell DNA-adenine-methylase.
ER  -

TY  - JOUR
AU  - Bogdarina, I.G.
AU  - Buryanov, Y.I.
AU  - Bayev, A.A.
TI  - Isolation and properties of DNA-cytosine-methyl-transferase from Escherichia coli C.
JO  - Mol. Biol. (Mosk)
PY  - 1979
SP  - 281
EP  - 291
VL  - 13
AB  - The method of isolation and partial purification of DNA-cytosine-methyltransferase from E.
AB  - coli C is described.  The enzyme underwent approximately 100-fold purification.  The obtained
AB  - preparation of DC-methylase can be additionally considerably purified by sedimentation in
AB  - sucrose gradient.  Native molecular weight of DC-methylase from E. coli C is 70,000.  The
AB  - activity of the enzyme does not depend on Mg2+ ions.  The DC-methylase from E. coli C provides
AB  - DNA of lambda phage in vitro with full resistance against restriction endonuclease EcoRII.  In
AB  - DNA methylated by DC-methylase the modified cytosine, mainly in C-MC and C-MC-T sequences,
AB  - corresponds to the pyrimidine sequences of specific site EcoRII.  DNA of lambda.B phage
AB  - contains approximately 80 sites for modification by DC-methylase E. coli C.  The results
AB  - obtained point to the same specificity in vitro of DNA-cytosine-methylase E. coli C and
AB  - DNA-methylase EcoRII.
ER  -

TY  - JOUR
AU  - Bogdarina, I.G.
AU  - Nadirova, I.M.
AU  - Buryanov, Y.I.
TI  - A technique for the detection of new strains producing enzymes involved in DNA modification and restriction - isoschizomers and isomethylomers of the known restrictases and methylases.
JO  - Mikrobiologiia
PY  - 1986
SP  - 699
EP  - 700
VL  - 55
AB  - The paper describes a technique for the detection of new strains producing enzymes which
AB  - mediate DNA modification and restriction, and isoschizomers and isomethylomers of the known
AB  - restriction endonucleases and methylases.  Three Bacillus subtilis strains whose DNA carries a
AB  - BamHI modification have been found.  Two of these strains exert the restrictase activity with
AB  - an R.BamHI specificity.
ER  -

TY  - JOUR
AU  - Bogdarina, I.G.
AU  - Reuter, M.
AU  - Kruger, D.H.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.A.
TI  - Methylation of DNA of phages T3 and T7 by various types of DNA-adenine methylases and inhibition of the EcoK methylase by the ocR+ protein.
JO  - Dokl. Akad. Nauk.
PY  - 1983
SP  - 234
EP  - 237
VL  - 273
AB  - In recent years interest in the study of the role of site-specific DNA methylation in cells of
AB  - prokaryotes, eukaryotes, and their viruses in the regulation of gene activity has increased
AB  - substantially. It is known that the manifestation of the activity of the ocR+ gene of
AB  - bacteriophages T3 and T7 in infected Escherichia coli cells suppresses the restriction and
AB  - modification of the virus DNA by Type I enzymes, and, moreover, the methylation of
AB  - bacteriophage T3 DNA does not occur at all, as a result of breakdown of the intracellular
AB  - S-adenosyl-L-methionine by SAMase (S-adenosyl-L-methionine hydrolase), which is also coded by
AB  - the gene 0.3 of phage T3. In view of this it is of interest to study the methylation of DNA of
AB  - phages T3 and T7 by DNA-adenine methylases EcoK and EcoDam in vivo and to determine the
AB  - influence of the ocR gene on the activity of these enzymes. For this purpose we determined the
AB  - number of CH3 groups incorporated into the phage genome by various DNA methylases in vitro to
AB  - determine the number of recognition sites in their DNA that are not methylated in vivo.
ER  -

TY  - JOUR
AU  - Bogdarina, I.G.
AU  - Vagabova, L.M.
AU  - Buryanov, Y.I.
TI  - DNA-cytosine methylation in E. coli MRE 600 cells.
JO  - FEBS Lett.
PY  - 1976
SP  - 177
EP  - 180
VL  - 68
AB  - Two DNA-cytosine methyltransferases (Dcm I and II) modifying cytosine in different nucleotide
AB  - sequences have been isolated from E. coli MRE 600 cells. Physiological role of these
AB  - methylases is still unknown but it is possible that one of them is connected with the DNA
AB  - modification and restriction system. This supposition is supported by the fact that the main
AB  - targets in DNA fro Dcm II are the pyrimidine sequences C-m5C and C-m5C-T (m5C:
AB  - 5-methylcytosine) identical to pyrimidine fragments in DNA sequences, which are methylated by
AB  - DNA methylase of resistance factor RII. The work presents the data on in vivo methylation of
AB  - cytosine in E. coli MRE 600 DNA and we describe a new method for separate determination of Dcm
AB  - I and Dcm II action in the cell. Structural peculiarities of nucleotide sequences recognized
AB  - by two enzymes constitute the basis of this method. More that 90% of cytosine modified by Dcm
AB  - I appears in the sequence Pu-m5C-C-Pu and about 30% of cytosine methylated by Dcm II is
AB  - detected in the sequence Pu-C-m5C-Pu. So, separate determination of Dcm I and Dcm II activity
AB  - in the cell is based on quantitative estimation of 5-methylcytosine content at 5'- and
AB  - 3'-termini of Pu-C-C-Pu- sequences of E. coli MRE 600 DNA.
ER  -

TY  - JOUR
AU  - Bohle, H.
AU  - Henriquez, P.
AU  - Grothusen, H.
AU  - Navas, E.
AU  - Bustamante, F.
AU  - Bustos, P.
AU  - Mancilla, M.
TI  - The Genome Sequence of an Oxytetracycline-Resistant Isolate of the Fish Pathogen  Piscirickettsia salmonis Harbors a Multidrug Resistance Plasmid.
JO  - Genome Announcements
PY  - 2017
SP  - e01571
EP  - e01516
VL  - 5
AB  - The amount of antibiotics needed to counteract frequent piscirickettsiosis outbreaks is a
AB  - major concern for the Chilean salmon industry. Resistance to
AB  - antibiotics may contribute to this issue. To understand the genetics underlying
AB  - Piscirickettsia salmonis-resistant phenotypes, the genome of AY3800B, an
AB  - oxytetracycline-resistant isolate bearing a multidrug resistance plasmid, is
AB  - presented here.
ER  -

TY  - JOUR
AU  - Bohle, H.
AU  - Henriquez, P.
AU  - Grothusen, H.
AU  - Navas, E.
AU  - Sandoval, A.
AU  - Bustamante, F.
AU  - Bustos, P.
AU  - Mancilla, M.
TI  - Comparative Genome Analysis of Two Isolates of the Fish Pathogen Piscirickettsia  salmonis from Different Hosts Reveals Major Differences in Virulence-Associated  Secretion Systems.
JO  - Genome Announcements
PY  - 2014
SP  - e01219
EP  - e01214
VL  - 2
AB  - Outbreaks caused by Piscirickettsia salmonis are one of the major threats to the
AB  - sustainability of the Chilean salmon industry. We report here the annotated draft
AB  - genomes of two P. salmonis isolates recovered from different salmonid species. A
AB  - comparative analysis showed that the number of virulence-associated secretion
AB  - systems constitutes a main genomic difference.
ER  -

TY  - JOUR
AU  - Bohm, M.E.
AU  - Huptas, C.
AU  - Krey, V.M.
AU  - Scherer, S.
TI  - Draft Genome Sequence of Bacillus cytotoxicus CVUAS 2833, a Very Close Relative to Type Strain NVH 391-98 Isolated from a Different Location.
JO  - Genome Announcements
PY  - 2015
SP  - e00901
EP  - e00915
VL  - 3
AB  - We report the draft genome sequence of Bacillus cytotoxicus CVUAS 2833, isolated  from potato
AB  - puree in Germany (2007), which is-despite its clearly different
AB  - source-very similar to the type strain B. cytotoxicus NVH 391-98 isolated in
AB  - France (average nucleotide identity, 99.5%).
ER  -

TY  - JOUR
AU  - Boinett, C.J.
AU  - Harris, S.R.
AU  - Langridge, G.C.
AU  - Trainor, E.A.
AU  - Merkel, T.J.
AU  - Parkhill, J.
TI  - Complete Genome Sequence of Bordetella pertussis D420.
JO  - Genome Announcements
PY  - 2015
SP  - e00657
EP  - e00615
VL  - 3
AB  - Bordetella pertussis is the causative agent of whooping cough, a highly contagious, acute
AB  - respiratory illness that has seen resurgence despite the use of
AB  - vaccines. We present the complete genome sequence of a clinical strain of B.
AB  - pertussis, D420, which is representative of a currently circulating clade of this
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Bokor, A.A.
AU  - van Kan, J.A.
AU  - Poulter, R.T.
TI  - Sexual mating of Botrytis cinerea illustrates PRP8 intein HEG activity.
JO  - Fungal. Genet. Biol.
PY  - 2010
SP  - 392
EP  - 398
VL  - 47
AB  - Strains of Botrytis cinerea are polymorphic for the presence of an intein in the Prp8 gene
AB  - (intein +/-). The intein encodes a homing endonuclease
AB  - (HEG). During meiosis in an intein +/- heterozygote, the homing
AB  - endonuclease initiates intein 'homing' by inducing gene conversion. In
AB  - such meioses, the homing endonuclease triggers gene conversion of the
AB  - intein together with its flanking sequences into the empty allele. The
AB  - efficiency of gene conversion of the intein was found to be 100%. The
AB  - extent of flanking sequence affected by the gene conversion varied in
AB  - different meioses. A survey of the inteins and flanking sequences of a
AB  - group B. cinerea isolates indicates that there are two distinct variants
AB  - of the intein both of which have active HEGs. The survey also suggests
AB  - that the intein has been actively homing during the evolution of the
AB  - species and that the PRP8 intein may have entered the species by
AB  - horizontal transfer.
ER  -

TY  - JOUR
AU  - Boland, M.J.
TI  - Identification and characterization of interactions between de novo DNA methyltransferase 3b and thymine-DNA glycosylase.
JO  - Ph.D. Thesis, University of Nebraska, USA
PY  - 2007
SP  - 1
EP  - 141
AB  - The majority of methylation found in the vertebrate genome occurs at carbon 5 of the cytosine
AB  - pyrimidine ring within CpG dinucleotides.  DNA methylation patterns are established during
AB  - early embryogenesis by the de novo methyltransferases, Dnmt3a and Dnmt3b.  These patterns play
AB  - a large role in genetic commitment and cellular differentiation via the heritable repression
AB  - of certain developmental programs.  An important in vivo function of Dnmt3b is methylation of
AB  - the centromeric and pericentromeric satellite repeats, regions of heterochromatin that are
AB  - rich in methylated CpG sites.  Methylation of these repeats contributes to the higher-order
AB  - heterochromatin structure that is essential to maintain genomic stability, repression of
AB  - aberrant mitotic recombination and assurance of proper chromosome segregation.  Mutations that
AB  - ablate Dnmt3b activity, exemplified by those found in the autosomal recessive genetic
AB  - disorder, ICF syndrome, lead to hypomethylation of the pericentromeric satellite repeats
AB  - resulting in chromatin decondensationa nd enhanced chromosomal rearrangements.  A significant
AB  - source of endogenous DNa damage is the spontaneous hydrolytic deamination of cytosine and
AB  - 5-methylcytosine to uracil and thymidine, thereby generating U.G and T.C mismatches,
AB  - respectively.  If these promutagenic lesions are not repaired, C - T transition mutations
AB  - occur during replication.  Mechanisms to repair such damage have evolved in the form of
AB  - mismatch-specific DNA glycosylases.  G/T mismatch-specific thymine-DNA glycosylase initiates
AB  - post-replicative base excision repair at G.G and U.G mismatches ultimately leading to
AB  - reformation of the original C.G base pair.  Tdg was isolated as a positive protein interactor
AB  - with Dnmt3b in a yeast two-hybrid screen.  Subsequently, interaction between the endogenous
AB  - proteins was demonstrated.  It was determined that Dnmt3b and Tdg are targeted to genomic
AB  - regions of heterochromatin.  the regions/domains of Dnmt3b that mediate the interaction with
AB  - Tdg were determined to be regions that have been previously identified as necessary for
AB  - targeting Dnmt3b to pericentromeric heterochromatin.  A t.G mismatch repair assay utilizing ES
AB  - cells nullizygous for different DNA methyltransferases was developed to study the effect of
AB  - DNA methyltransferases on base excision repair.  Results of these experiments suggest that DNA
AB  - methyltransferases potentiate T.G mismatch repair.  During this course of investigation, it
AB  - was determined that a putative RNA component is essential for proper T.G mismatch repair.
ER  -

TY  - JOUR
AU  - Boland, M.J.
AU  - Christman, J.K.
TI  - Mammalian DNA methyltransferases Catalytic mechanism, structure, and functions.
JO  - Nutrients and Epigenetics
PY  - 2009
SP  - 37
EP  - 65
VL  - 0
AB  - 5-Methylcytosine was first detected in mammalian DNA 60 years ago and within six years, it was
AB  - demonstrated that the only dinucleotide with significant 5mC content was 5mC,G.  It took
AB  - almost another decade to determine that cytosine residues were enzymatically methylated after
AB  - incorporation into DNA, establishing the basis for epigenetic modulation of gene expression.
AB  - The first demonstrations that inhibition of DNA methylation could induce differentiation of
AB  - cultured cells were published in the late 1970s.  Since then, it has become increasingly clear
AB  - that DNA methylation plays a number of important roles in cellular homeostasis and regulation
AB  - of normal mammalian development.  Methylation of DNA promotes genomic stability through
AB  - repression of mitotic recombination and transposition, assuring proper chromatid segregation
AB  - and maintenance of higher-order heterochromatin structure.  Genomic methylation patterns also
AB  - play a crucial role during embryogenesis, leading to temporal transcriptional repression of
AB  - critical developmental programs during cellular differentiation through its ability to
AB  - regulate chromatin structure.  Additionally, DNA methylation is integral to the processes of
AB  - genomic imprinting and gene dosage compensation in females through inactivation of one X
AB  - chromosome.  A variety of tumors exhibit aberrant DNA methylation patterns.  The most common
AB  - change is an early global loss or reduction in DNA methylation, that is hypomethylation.  This
AB  - is followed by localized promoter hypermethylation of tumor-suppressor genes.
ER  -

TY  - JOUR
AU  - Boland, M.J.
AU  - Christman, J.K.
TI  - A novel interaction between thymine DNA-glycosylase and the de novo methyltransferase, Dnmt3b.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 2005
SP  - 645
EP  - 645
VL  - 46
AB  - DNA methylation patterns are established shortly before gastrulation by the de novo
AB  - methyltransferases, Dnmt3a and Dnmt3b.  The majority of methylation found in the vertebrate
AB  - genome occurs at carbon 5 of cytosine (m5C) within CpG dinucleotides.  These patterns are
AB  - thought to set the stage for genetic commitment and cellular differentiation.  Aberrant DNA
AB  - methylation has been implicated in cancer and certain genetic diseases.  An important in vivo
AB  - function of Dnmt3b is methylation of the pericentric heterochromatin major satellite repeats.
AB  - DNA methylation of these repeats contributes to the higher-order chromatin structure necessary
AB  - for genome stability and proper sister chromatid segregation during mitosis.  Mutations that
AB  - ablate Dnmt3b activity such as those found in the rare recessive genetic disorder, ICF
AB  - syndrome lead to hypomethylation of the pericentric satellite repeats.  This results in
AB  - chromatin decondensation and enhanced chromosomal rearrangements.  Analogous chromosomal
AB  - abnormalities have been observed in breast carcinoma, ovarian epithelial carcinoma, and
AB  - pediatric Wilms tumors although they have not been directly attributed to Dnmt3b malfunction.
AB  - Dnmt3b is composed of multiple domains, suggesting it can form interactions with many
AB  - proteins.  In order to further elucidate how de novo methylation is regulated, we initiated a
AB  - search for proteins that interact with Dnmt3b.  Using Dnmt3b as bait in a yeast two-hybrid
AB  - screen of a murine embryonic cDNA library, we isolated thymine DNA-glycosylase (Tdg) as a
AB  - positive protein interactor.  This interaction has been confirmed by coimmunoprecipitation. We
AB  - show that both the catalytic domain and the PWWP domain of Dnmt3b are able to interact with
AB  - Tdg.  In addition, we demonstrate an in vivo nuclear interaction between Tdg and Dnmt3b in HEK
AB  - 293T cells using confocal microscopy.  The interaction between Dnmt3b and Tdg is enhanced in
AB  - mitotic cells and can be induced by arresting cells in mitosis with the cell cycle inhibitors
AB  - vinblastine and demecolcine.  Spontaneous hydrolytic deamination of C or m5C residues within a
AB  - CpG dinucleotide results in U:G or T:G mismatches, respectively.  Mechanisms to repair such
AB  - damage have evolved in the form of mismatch-specific DNA glycosylases.  Tdg initiates the base
AB  - excision repair of T:G and U:G mismatches leading to reformation of a C:G base pair.  The
AB  - evidence presented here supports the hypothesis that the association of Dnmt3b and Tdg
AB  - promotes genomic stability and reduces the incidence of pericentromeric heterochromatin
AB  - rearrangement through repair of T:G and/or U:G mismatches followed by or simultaneous with
AB  - methylation of the repaired product, thereby restoring the original methylation status at that
AB  - locus.  Supported by NIH R21-CA91315 to JKC.
AB  - Note: Our subsequent studies of endogenous interactions between Dnmt3b and Tdg in murine P19
AB  - cells did not confirm the enhancement of interaction between these enzymes during mitosis.
AB  - This suggests that the result reported above may be the result of an elevated,
AB  - non-physiological level of exogenously expressed Dnmt3b and Tdg.
ER  -

TY  - JOUR
AU  - Boland, M.J.
AU  - Christman, J.K.
TI  - Characterization of Dnmt3b:Thymine-DNA Glycosylase Interaction and Stimulation of Thymine Glycosylase-Mediated Repair by DNA  Methyltransferase(s) and RNA.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 492
EP  - 504
VL  - 379
AB  - Methylation of cytosine residues in CpG dinucleotides plays an important role in epigenetic
AB  - regulation of gene expression and chromatin
AB  - structure/stability in higher eukaryotes. DNA methylation patterns are
AB  - established and maintained at CpG dinucleotides by DNA methyltransferases
AB  - (Dnmt1, Dnmt3a, and Dnmt3b). In mammals and many other eukaryotes, the CpG
AB  - dinucleotide is underrepresented in the genome. This loss is postulated to
AB  - be the result of unrepaired deamination of cytosine and 5-methylcytosine
AB  - to uracil and thymine, respectively. Two thymine glycosylases are believed
AB  - to reduce the impact of 5-methylcytosine deamination. G/T
AB  - mismatch-specific thymine-DNA glycosylase (Tdg) and methyl-CpG binding
AB  - domain protein 4 can both excise uracil or thymine at U.G and T.G
AB  - mismatches to initiate base excision repair. Here, we report the
AB  - characterization of interactions between Dnmt3b and both Tdg and
AB  - methyl-CpG binding domain protein 4. Our results demonstrate (1) that both
AB  - Tdg and Dnmt3b are colocalized to heterochromatin and (2) reduction of T.G
AB  - mismatch repair efficiency upon loss of DNA methyltransferase expression,
AB  - as well as a requirement for an RNA component for correct T.G mismatch
AB  - repair.
ER  -

TY  - JOUR
AU  - Bolduc, J.M.
AU  - Spiegel, P.C.
AU  - Chatterjee, P.
AU  - Brady, K.L.
AU  - Downing, M.E.
AU  - Caprara, M.G.
AU  - Waring, R.B.
AU  - Stoddard, B.L.
TI  - Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.
JO  - Genes Dev.
PY  - 2003
SP  - 2875
EP  - 2888
VL  - 17
AB  - We determined the crystal structure of a bifunctional group I intron splicing factor and
AB  - homing endonuclease, termed the I-AniI maturase, in
AB  - complex with its DNA target at 2.6 A resolution. The structure
AB  - demonstrates the remarkable structural conservation of the beta-sheet
AB  - DNA-binding motif between highly divergent enzyme subfamilies. DNA
AB  - recognition by I-AniI was further studied using nucleoside deletion and
AB  - DMS modification interference analyses. Correlation of these results with
AB  - the crystal structure provides information on the relative importance of
AB  - individual nucleotide contacts for DNA recognition. Alignment and modeling
AB  - of two homologous maturases reveals conserved basic surface residues,
AB  - distant from the DNA-binding surface, that might be involved in RNA
AB  - binding. A point mutation that introduces a single negative charge in this
AB  - region uncouples the maturase and endonuclease functions of the protein,
AB  - inhibiting RNA binding and splicing while maintaining DNA binding and
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Bolhuis, H.H.
AU  - Palm, P.P.
AU  - Wende, A.A.
AU  - Falb, M.M.
AU  - Rampp, M.M.
AU  - Rodriguez-Valera, F.F.
AU  - Pfeiffer, F.F.
AU  - Oesterhelt, D.D.
TI  - The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity.
JO  - BMC Genomics
PY  - 2006
SP  - 169
EP  - 169
VL  - 7
AB  - ABSTRACT: BACKGROUND: The square halophilic archaeon Haloquadratum walsbyi dominates
AB  - NaCl-saturated and MgCl2 enriched aquatic ecosystems, which
AB  - imposes a serious desiccation stress, caused by the extremely low water
AB  - activity. The genome sequence was analyzed and physiological and physical
AB  - experiments were carried out in order to reveal how H. walsbyi has
AB  - specialized into its narrow and hostile ecological niche and found ways to
AB  - cope with the desiccation stress. RESULTS: A rich repertoire of proteins
AB  - involved in phosphate metabolism, phototrophic growth and extracellular
AB  - protective polymers, including the largest archaeal protein (9159 amino
AB  - acids), a homolog to eukaryotic mucins, are amongst the most outstanding
AB  - features. A relatively low GC content (47.9%), 15-20% less than in other
AB  - halophilic archaea, and one of the lowest coding densities (76.5%) known
AB  - for prokaryotes might be an indication for the specialization in its
AB  - unique environment CONCLUSIONS: Although no direct genetic indication was
AB  - found that can explain how this peculiar organism retains its square
AB  - shape, the genome revealed several unique adaptive traits that allow this
AB  - organism to thrive in its specific and extreme niche.
ER  -

TY  - JOUR
AU  - Bolker, M.
AU  - Bohnert, H.U.
AU  - Braun, K.H.
AU  - Gorl, J.
AU  - Kahmann, R.
TI  - Tagging pathogenicity genes in Ustilago maydis by restriction enzyme-mediated integration (REMI).
JO  - Mol. Gen. Genet.
PY  - 1995
SP  - 547
EP  - 552
VL  - 248
AB  - In the maize pathogenic fungus Ustilago maydis integration of transforming DNA at homologous
AB  - or heterologous sites is often accompanied by duplications of the DNA.  We show that it is
AB  - possible to generate single-copy integration events with high efficiency by restriction
AB  - enzyme-mediated integration (REMI).  In about 50% of cases, a plasmid that contains a single
AB  - BamHI site is integrated at chromosomal BamHI sites, if BamHI is added to the transformation
AB  - mixtures.  In the other cases it appears that integration events have also occurred
AB  - preferentially at BamHI sites, but without restoration of the recognition sites.  Using REMI
AB  - we have generated approximately 1000 insertion mutants.  Pathogenicity tests demonstrated that
AB  - about 1-2% of these mutants were unable to induce symptoms when tested in planta.  For two of
AB  - the mutants we have shown that the phenotype is linked to the insertion event.
ER  -

TY  - JOUR
AU  - Bollmann, A. et al.
TI  - Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 469
EP  - 482
VL  - 7
AB  - Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to
AB  - the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia
AB  - oxidation is the first step of nitrification, an important process in the global
AB  - nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas
AB  - sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low
AB  - ammonium and can be found in freshwater environments around the world. The
AB  - 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA
AB  - genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.
ER  -

TY  - JOUR
AU  - Bolot, S.
AU  - Cerutti, A.
AU  - Carrere, S.
AU  - Arlat, M.
AU  - Fischer-Le, S.M.
AU  - Portier, P.
AU  - Poussier, S.
AU  - Jacques, M.A.
AU  - Noel, L.D.
TI  - Genome Sequences of the Race 1 and Race 4 Xanthomonas campestris pv. campestris Strains CFBP 1869 and CFBP 5817.
JO  - Genome Announcements
PY  - 2015
SP  - e01023
EP  - e01015
VL  - 3
AB  - Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The
AB  - draft genome sequences of strains CFBP 1869 and CFBP 5817 have  been determined and are the
AB  - first ones corresponding to race 1 and race 4 strains, which have a predominant agronomic and
AB  - economic impact on cabbage cultures worldwide.
ER  -

TY  - JOUR
AU  - Bolot, S.
AU  - Guy, E.
AU  - Carrere, S.
AU  - Barbe, V.
AU  - Arlat, M.
AU  - Noel, L.D.
TI  - Genome Sequence of Xanthomonas campestris pv. campestris Strain Xca5.
JO  - Genome Announcements
PY  - 2013
SP  - e00032
EP  - e00012
VL  - 1
AB  - An annotated high-quality draft genome sequence for Xanthomonas campestris pv. campestris race
AB  - 1 strain Xca5 (originally described as X. campestris pv.
AB  - armoraciae), the causal agent of black rot on Brassicaceae plants, has been
AB  - determined. This genome sequence is a valuable resource for comparative genomics
AB  - within the campestris pathovar.
ER  -

TY  - JOUR
AU  - Bolot, S.
AU  - Munoz, B.A.
AU  - Cunnac, S.
AU  - Ortiz, E.
AU  - Szurek, B.
AU  - Noel, L.D.
AU  - Arlat, M.
AU  - Jacques, M.A.
AU  - Gagnevin, L.
AU  - Portier, P.
AU  - Fischer-Le, S.M.
AU  - Carrere, S.
AU  - Koebnik, R.
TI  - Draft Genome Sequence of the Xanthomonas cassavae Type Strain CFBP 4642.
JO  - Genome Announcements
PY  - 2013
SP  - e00679
EP  - e00613
VL  - 1
AB  - We report the draft genome sequence of the Xanthomonas cassavae type strain CFBP  4642, the
AB  - causal agent of bacterial necrosis on cassava plants. These data will
AB  - allow the comparison of this nonvascular pathogen with the vascular pathogen
AB  - Xanthomonas axonopodis pv. manihotis, both infecting the same host, which will
AB  - facilitate the development of diagnostic tools.
ER  -

TY  - JOUR
AU  - Bolot, S.
AU  - Roux, B.
AU  - Carrere, S.
AU  - Jiang, B.L.
AU  - Tang, J.L.
AU  - Arlat, M.
AU  - Noel, L.D.
TI  - Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16.
JO  - Genome Announcements
PY  - 2013
SP  - e00465
EP  - e00413
VL  - 1
AB  - Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The
AB  - draft genome sequences of three strains (CN14, CN15, and CN16)
AB  - that are highly aggressive on Arabidopsis have been determined. These genome
AB  - sequences present an unexpected genomic diversity in X. campestris pv.
AB  - campestris, which will be valuable for comparative analyses.
ER  -

TY  - JOUR
AU  - Bolotin, A.
AU  - de Wouters, T.
AU  - Schnupf, P.
AU  - Bouchier, C.
AU  - Loux, V.
AU  - Rhimi, M.
AU  - Jamet, A.
AU  - Dervyn, R.
AU  - Boudebbouze, S.
AU  - Blottiere, H.M.
AU  - Sorokin, A.
AU  - Snel, J.
AU  - Cerf-Bensussan, N.
AU  - Gaboriau-Routhiau, V.
AU  - van de Guchte, M.
AU  - Maguin, E.
TI  - Genome Sequence of 'Candidatus Arthromitus' sp. Strain SFB-Mouse-NL, a Commensal  Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions.
JO  - Genome Announcements
PY  - 2014
SP  - e00705
EP  - e00714
VL  - 2
AB  - 'Candidatus Arthromitus' sp. strain SFB-mouse-NL (SFB, segmented filamentous bacteria) is a
AB  - commensal bacterium necessary for inducing the postnatal
AB  - maturation of homeostatic innate and adaptive immune responses in the mouse gut.
AB  - Here, we report the genome sequence of this bacterium, which sets it apart from
AB  - earlier sequenced mouse SFB isolates.
ER  -

TY  - JOUR
AU  - Bolotin, A.
AU  - Quinquis, B.
AU  - Ehrlich, S.D.
AU  - Sorokin, A.
TI  - Complete Genome Sequence of Lactococcus lactis subsp. cremoris A76.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1241
EP  - 1242
VL  - 194
AB  - We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy
AB  - strain isolated from a cheese production outfit. Genome analysis detected
AB  - two contiguous islands fitting to the L. lactis subsp. lactis rather than to the
AB  - L. lactis subsp. cremoris lineage. This indicates the existence of genetic
AB  - exchange between the diverse subspecies, presumably related to the technological
AB  - process.
ER  -

TY  - JOUR
AU  - Bolotin, A.
AU  - Wincker, P.
AU  - Mauger, S.
AU  - Jaillon, O.
AU  - Malarme, K.
AU  - Weissenbach, J.
AU  - Ehrlich, S.D.
AU  - Sorokin, A.
TI  - The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403.
JO  - Genome Res.
PY  - 2001
SP  - 731
EP  - 753
VL  - 11
AB  - Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the
AB  - genus Streptococcus and is the most commonly used cheese starter. It is also the
AB  - best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain
AB  - IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire
AB  - genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310
AB  - proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion
AB  - sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of
AB  - the sequenced strain may be a product of recent recombination between two closely related
AB  - genomes. A complete set of late competence genes is present, indicating the ability of L.
AB  - lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for
AB  - fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of
AB  - genetic information from Lactococcus to gram-negative enteric bacteria of
AB  - Salmonella-Escherichia group.
ER  -

TY  - JOUR
AU  - Boltner, D.
AU  - MacMahon, C.
AU  - Pembroke, J.T.
AU  - Strike, P.
AU  - Osborn, A.M.
TI  - R391: a Conjugative Integrating Mosaic Comprised of Phage, Plasmid, and Transposon Elements.
JO  - J. Bacteriol.
PY  - 2002
SP  - 5158
EP  - 5169
VL  - 184
AB  - The conjugative, chromosomally integrating element R391 is the archetype
AB  - of the IncJ class of mobile genetic elements. Originally found in a South
AB  - African Providencia rettgeri strain, R391 carries antibiotic and mercury
AB  - resistance traits, as well as genes involved in mutagenic DNA repair.
AB  - While initially described as a plasmid, R391 has subsequently been shown
AB  - to be integrated into the bacterial chromosome, employing a phage-like
AB  - integration mechanism closely related to that of the SXT element from
AB  - Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence
AB  - of R391 has revealed a mosaic structure consisting of elements originating
AB  - in bacteriophages and plasmids and of transposable elements. A total of 96
AB  - open reading frames were identified; of these, 30 could not be assigned a
AB  - function. Sequence similarity suggests a relationship of large sections of
AB  - R391 to sequences from Salmonella, in particular those corresponding to
AB  - the putative conjugative transfer proteins, which are related to the
AB  - IncHI1 plasmid R27. A composite transposon carrying the kanamycin
AB  - resistance gene and a novel insertion element were identified. Challenging
AB  - the previous assumption that IncJ elements are plasmids, no plasmid
AB  - replicon was identified on R391, suggesting that they cannot replicate
AB  - autonomously.
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Comer, M.
AU  - Kessler, C.
TI  - Asp700I, a novel isoschizomer of XmnI from Achromobacter species 700 recognizing 5'-GAANN/NNTTC-3'.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8879
EP  - 8879
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Holtke, H.-J.
AU  - Schmitz, G.G.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - AspHI, a novel isoschizomer of HgiAI from Achromobacter species H recognizing 5'-GWGCW/C-3'.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9500
EP  - 9500
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Kaluza, K.
AU  - Herz, M.J.
AU  - Berger, G.
AU  - Kessler, C.
AU  - Schmitz, G.
TI  - Screening for novel type II restriction endonucleases.
JO  - Fresenius Z. Anal. Chem.
PY  - 1988
SP  - 376
EP  - 376
VL  - 330
AB  - Site specific endonucleases have become indispensable tools for recombinant DNA
AB  - techniques.  Although to date the recognition sequences for 115 different class
AB  - II restriction endonucleases have been reported, additional enzymes with novel
AB  - specificities are required for the analysis and manipulation of DNA.  We have
AB  - examined a wide variety of bacteria for the presence of class II restriction
AB  - endonucleases.  Our aim was to find novel specific activities, to purity and
AB  - characterize the enzymes and to determine the specificities in respect to their
AB  - recognition sequence and cleavage position.  Hewre we give an overview on the
AB  - occurance of class II enzymes in various microorganisms tested and describe a
AB  - new class IIS enzyme discovered in Kluyvera species 632.
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Nesch, G.
AU  - Comer, M.J.
AU  - Wolf, W.
AU  - Kessler, C.
TI  - Asp718 from a non-pathogenic species of the genus Achromobacter: a KpnI isoschizomer generating DNA-fragments with 5'-protruding ends.
JO  - FEBS Lett.
PY  - 1985
SP  - 130
EP  - 134
VL  - 182
AB  - A new type II restriction endonuclease Asp718 has been isolated from the
AB  - non-pathogenic species of Achromobacter 718.  This novel enzyme, an
AB  - isoschizomer of KpnI, recognizes and cleaves specifically within the nucleotide
AB  - sequence:5'-G^GTAC-C-3'3'-C-CATG^G-5'In contrast to KpnI, Asp718 generates
AB  - fragments with 5'-protruding single-stranded ends.  These 5'-terminal
AB  - extensions of the Asp718 fragments may be efficiently labeled with T4
AB  - polynucleotide kinase, whereas the recessed 3'-ends are suitable substrates for
AB  - the terminal labeling reaction applying Klenow enzyme.  The presence of only
AB  - one restriction activity in this Achromobacter strain facilitates the
AB  - preparation of Asp718 free of other contaminating site-specific nucleases which
AB  - could interfere with the in vitro digestion of DNA.
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Reischl, U.
AU  - Holtke, H.-J.
AU  - Schmitz, G.G.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - EclXI, a novel isoschizomer of XmaIII from Enterobacter cloacae 590 recognizing 5'-C/GGCCG-3' .
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 381
EP  - 381
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Schmitz, G.G.
AU  - Jarsch, M.
AU  - Comer, M.J.
AU  - Kessler, C.
TI  - Ksp632I: a novel class IIS restriction endonuclease from Kluyvera species 632 with the asymmetric hexanucleotide recognition sequence: 5'-CTCTTCN^-3' 3'-GAGAAGNNNN^-5' .
JO  - Gene
PY  - 1988
SP  - 31
EP  - 43
VL  - 66
AB  - A new class-IIS restriction endonuclease, Ksp632I, with novel sequence
AB  - specificity has been discovered in a non-pathogenic species of Kluyvera.  The
AB  - presence of only a single site-specific activity in this Kluyvera sp. strain
AB  - 632 enables Ksp632I to be isolated in highly purified form free of
AB  - contaminating nucleases.  Ksp632I recognition sites and cleavage positions were
AB  - deduced using experimental and computer-assisted mapping and sequencing.  The
AB  - cleavage specificity corresponds to the sequence 5'-CTCTTCN^NNN-N-3'
AB  - 3'-GAGAAGN-NNN^N-5' The enzyme recognizes an asymmetric hexanucleotide sequence
AB  - and cleaves in the presence of Mg2+ ions specific phosphodiester bonds in both
AB  - DNA strands, 1 and 4 nucleotides distal to the recognition sequence.  The
AB  - staggered cuts generate 5'-protruding ends with single-stranded
AB  - 5'-phosphorylated trinucleotides.  Several slow cleavage sites for Ksp632I were
AB  - observed on lambda cI857 Sam7 DNA.  Ksp632I may complement other class-IIS
AB  - enzymes in the universal restriction approach and may serve as a tool for
AB  - generating defined unidirectional deletions or insertions.
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Schmitz, G.G.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - KspI, a novel isoschizomer of SacII from Kluyvera species recognizing 5'-CCGC/GG-3'.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9476
EP  - 9476
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Bolton, B.J.
AU  - Schmitz, G.G.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - AspI, a novel isoschizomer of Tht111l from Achromobacter species 699 recognizing 5'-GACN/NNGTC-3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3422
EP  - 3422
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Bomar, L.
AU  - Stephens, W.Z.
AU  - Nelson, M.C.
AU  - Velle, K.
AU  - Guillemin, K.
AU  - Graf, J.
TI  - Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract.
JO  - Genome Announcements
PY  - 2013
SP  - e00800
EP  - e00813
VL  - 1
AB  - Aeromonas veronii strain Hm21 was isolated from the digestive tract of the medicinal leech
AB  - Hirudo verbana and has been used to identify genes that are
AB  - important for host colonization. This species is also a symbiont in the gut of
AB  - zebrafish and is a pathogen of mammals and fish. We present here a 4.68-Mbp draft
AB  - genome sequence for Hm21.
ER  -

TY  - JOUR
AU  - Bomholt, C.
AU  - Glaub, A.
AU  - Gravermann, K.
AU  - Albersmeier, A.
AU  - Brinkrolf, K.
AU  - Ruckert, C.
AU  - Tauch, A.
TI  - Whole-Genome Sequence of the Clinical Strain Corynebacterium argentoratense DSM 44202, Isolated from a Human Throat Specimen.
JO  - Genome Announcements
PY  - 2013
SP  - e00793
EP  - e00713
VL  - 1
AB  - Corynebacterium argentoratense is part of the human skin microbiota and is occasionally
AB  - detected in the upper respiratory tract of patients suffering from
AB  - tonsillitis. The complete DNA sequence of the type strain DSM 44202 comprises
AB  - 2,031,902 bp, yielding the smallest genome sequenced thus far for a
AB  - corynebacterium associated with humans.
ER  -

TY  - JOUR
AU  - Bonacina, J.
AU  - Saavedra, L.
AU  - Suarez, N.E.
AU  - Sesma, F.
TI  - Draft Genome Sequence of the Nonstarter Bacteriocin-Producing Strain Enterococcus mundtii CRL35.
JO  - Genome Announcements
PY  - 2014
SP  - e00444
EP  - e00414
VL  - 2
AB  - Enterococcus mundtii CRL35 is a bacteriocinogenic strain isolated from an artisanal cheese of
AB  - northwestern Argentina. Here we report its draft genome
AB  - sequence, consisting of 82 contigs. In silico genomic analysis of
AB  - biotechnological properties was performed to determine the potential of this
AB  - microorganism to be used in a food model system.
ER  -

TY  - JOUR
AU  - Bonaldo, M.F.
AU  - Lennon, G.
AU  - Soares, M.B.
TI  - Normalization and subtraction: two approaches to facilitate gene discovery.
JO  - Genome Res.
PY  - 1996
SP  - 791
EP  - 806
VL  - 6
AB  - Large-scale sequencing of cDNAs randomly picked from libraries has proven
AB  - to be a very powerful approach to discover (putatively) expressed
AB  - sequences that, in turn, once mapped, may greatly expedite the process
AB  - involved in the identification and cloning of human disease genes.
AB  - However, the integrity of the data and the pace at which novel sequences
AB  - can be identified depends to a great extent on the cDNA libraries that are
AB  - used. Because altogether, in a typical cell, the mRNAs of the prevalent
AB  - and intermediate frequency classes comprise as much as 50-65% of the total
AB  - mRNA mass, but represent no more than 1000-2000 different mRNAs, redundant
AB  - identification of mRNAs of these two frequency classes is destined to
AB  - become overwhelming relatively early in any such random gene discovery
AB  - programs, thus seriously compromising their cost-effectiveness. With the
AB  - goal of facilitating such efforts, previously we developed a method to
AB  - construct directionally cloned normalized cDNA libraries and applied it to
AB  - generate infant brain (INIB) and fetal liver/spleen (INFLS) libraries,
AB  - from which a total of 45,192 and 86,088 expressed sequence tags,
AB  - respectively, have been derived. While improving the representation of the
AB  - longest cDNAs in our libraries, we developed three additional methods to
AB  - normalize cDNA libraries and generated over 35 libraries, most of which
AB  - have been contributed to our integrated Molecular Analysis of Genomes and
AB  - Their Expression (IMAGE) Consortium and thus distributed widely and used
AB  - for sequencing and mapping. In an attempt to facilitate the process of
AB  - gene discovery further, we have also developed a subtractive hybridization
AB  - approach designed specifically to eliminate (or reduce significantly the
AB  - representation of) large pools of arrayed and (mostly) sequenced clones
AB  - from normalized libraries yet to be (or just partly) surveyed. Here we
AB  - present a detailed description and a comparative analysis of four methods
AB  - that we developed and used to generate normalize cDNA libraries from human
AB  - (15), mouse (3), rat (2), as well as the parasite Schistosoma mansoni (1).
AB  - In addition, we describe the construction and preliminary characterization
AB  - of a subtracted liver/spleen library (INFLS-SI) that resulted from the
AB  - elimination (or reduction of representation) of -5000 INFLS-IMAGE clones
AB  - from the INFLS library.
ER  -

TY  - JOUR
AU  - Bonamy, C.
AU  - Guyonvarch, A.
AU  - Ryes, O.
AU  - David, F.
AU  - Leblon, G.
TI  - Interspecies electro-transformation in Corynebacteria.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 263
EP  - 270
VL  - 66
AB  - Plasmid DNA was efficiently electro-transformed into intact cells of nine Corynebacteria
AB  - strains belonging to Brevibacterium lactofermentum, Brevibacterium flavum, Corynebacterium
AB  - glutamicum and Corynebacterium melassecola.  Relationships were explored between
AB  - transformation efficiency and parameters such as electric field strength and pulse length, DNA
AB  - concentration, physiological state and concentration of the cells.  In optimal conditions,
AB  - more than 10^7 transformants per microgram of DNA could be obtained.  Electrotransformation
AB  - with plasmid DNA isolated from different sources indicates that DNA modification may play a
AB  - role in transformation efficiency.
ER  -

TY  - JOUR
AU  - Bonfils, C.
AU  - Beaulieu, N.
AU  - Chan, E.
AU  - Cotton-Montpetit, J.
AU  - MacLeod, A.R.
TI  - Characterization of the human DNA methyltransferase splice variant dnmt1b.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 10754
EP  - 10760
VL  - 275
AB  - Tissue- and gene-specific patterns of cytosine-DNA methylation are characteristic features of
AB  - vertebrate genomes. The generation and proper maintenance of DNA methylation patterns are
AB  - essential for embryonic development, as demonstrated by the lethal phenotypes of mice with
AB  - either a targeted disruption of Dnmt1, the gene responsible for the maintenance of DNA
AB  - methylation, or targeted disruption of Dnmt3a or Dnmt3b, the genes involved in generation of
AB  - newly formed methylation patterns. Recently, a novel mRNA, Dnmt1b, resulting from alternative
AB  - splicing of Dnmt1 was identified (Hsu, D. W., Lin, M. J., Lee, T. L., Wen, S. C., Chen, X.,
AB  - and Shen, C. K., (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9751-9756). The abundance of
AB  - Dnmt1b mRNA was estimated by semiquantitative reverse transcription polymerase chain reaction
AB  - and was suggested to encode a major C-5 DNA methyltransferase isoform. Here we report
AB  - characterization of this novel DNA methyltransferase transcript, Dnmt1b, and its protein
AB  - product in human cell lines and in freshly isolated human peripheral blood mononuclear cells.
AB  - The abundance of Dnmt1b transcript, as determined by quantitative RNase protection analysis,
AB  - was determined to range from 6% to 25% of Dnmt1 in human cells. Second generation antisense
AB  - inhibitors targeted to the 5'- and 3'-ends of Dnmt1 inhibited the accumulation of both Dnmt1
AB  - and Dnmt1b in cells. Dnmt1b protein purified from a baculovirus expression system was
AB  - demonstrated to be a functional DNA methyltransferase, and to have Michaelis constants for
AB  - both DNA and S-adenosyl-L-methionine similar to baculovirus-expressed Dnmt1. However,
AB  - antibodies raised against Dnmt1b epitopes demonstrated that Dnmt1b protein was present at
AB  - approximately 2-5% of the level of Dnmt1 and therefore represents only a minor DNA
AB  - methyltransferase isoform in human cells.
ER  -

TY  - JOUR
AU  - Bonitz, S.G.
AU  - Coruzzi, G.
AU  - Thalenfeld, B.E.
AU  - Tzagoloff, A.
TI  - Assembly of the mitochondrial membrane system.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 11927
EP  - 11941
VL  - 255
AB  - The oxi3 locus of yeast mitochondrial DNA has been sequenced in Saccharomyces cerevisiae
AB  - D273-10B. The sequence was obtained from the mitochondrial genomes of a series of cytoplasmic
AB  - "petite" mutants selected for the retention of genetic markers in the oxi3 locus. The oxi3
AB  - locus has been ascertained to code for Subunit 1 of cytochrome oxidase. The Subunit 1 gene is
AB  - 9,979 nucleotides long, consisting of seven to eight exons that account for only 16% of the
AB  - gene sequence. The coding sequences have been identified on the basis of protein sequence
AB  - homology with Subunit 1 of human cytochrome oxidase. The yeast Subunit 1 is 510 amino acid
AB  - residues long and has a molecular weight of 56,000. In addition to the exon sequences, the
AB  - Subunit I gene contains six to seven introns. The first four introns have long reading frames
AB  - that are continuous with the exon coding sequences. These reading frames are potentially
AB  - capable for coding for basic proteins with molecular weights ranging from 30,000 to 80,000.
AB  - The first two introns of the gene have a sequence homology of 50%, while the reading frame of
AB  - the fourth intron is 70% homologous with an intron of the apocytochrome b gene. At least five
AB  - stable transcripts have been found by Northern blot hybridizations with single-stranded DNA
AB  - probes containing either exon or intron sequences. A 1.9-kilobase transcript hybridizes only
AB  - with probes from the exon regions of the gene. This RNA species has been tentatively
AB  - identified as the fully processed messenger of Subunit 1. Other transcripts are detected with
AB  - intron probes. Three transcripts with sizes of 2.5, 2.4, and 0.85 kilobases appear to be
AB  - stable excision products from the first, second, and fifth introns.
ER  -

TY  - JOUR
AU  - Bonnassie, S.
AU  - Burini, J.-F.
AU  - Oreglia, J.
AU  - Trautwetter, A.
AU  - Patte, J.-C.
AU  - Sicard, A.M.
TI  - Transfer of plasmid DNA to Brevibacterium lactofermentum by electrotransformation.
JO  - J. Gen. Microbiol.
PY  - 1990
SP  - 2107
EP  - 2112
VL  - 136
AB  - The Escherichia coli-Brevibacterium lactofermentum shuttle vector pBLA was introduced into
AB  - intact cells of B. lactofermentum by electrotransformation.  Several parameters of this
AB  - procedure such as voltage and cell concentration were analysed.  Optimal conditions gave an
AB  - efficiency of 10^6 transformants per microgram of DNA.  Two recalcitrant strains could be
AB  - electrotransformed when an ampicillin pretreatment step was used.  Electrotransformation
AB  - experiments using DNAse or different structural forms of plasmid DNA showed that the
AB  - electrotransformation process is quite different from natural transformation involving
AB  - competence development.  Restriction-modification-proficient B. lactofermentum could be
AB  - efficiently electrotransformed with pBLA DNA isolated from E. coli.  This
AB  - restriction-modification system therefore seems to be overcome by electrotransformation.  Thus
AB  - electrotransformation may efficiently replace the protoplast bacterial transformation method.
ER  -

TY  - JOUR
AU  - Bonnassie, S.
AU  - Oreglia, J.
AU  - Trautwetter, A.
AU  - Sicard, A.M.
TI  - Isolation and characterization of a restriction and modification deficient mutant of Brevibacterium lactofermentum.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 143
EP  - 146
VL  - 72
AB  - In order to facilitate genetic engineering in amino-acid producing bacteria we
AB  - have isolated two restriction-deficient Brevibacterium lactofermentum strains.
AB  - They have been selected for their ability to obtain a high yield of plaques
AB  - from CL31 phage which was grown on Corynebacterium lilium.  These mutant
AB  - strains do not restrict either phage DNA by transfection or DNA from the
AB  - shuttle vector pBLA extracted from Escherichia coli by protoplast
AB  - transformation.  These mutants have also lost modification activity.  We also
AB  - report the presence of a restriction modification system in C. lilium ATCC
AB  - 15990.
ER  -

TY  - JOUR
AU  - Bonnet, I.
AU  - Biebricher, A.
AU  - Porte, P.L.
AU  - Loverdo, C.
AU  - Benichou, O.
AU  - Voituriez, R.
AU  - Escude, C.
AU  - Wende, W.
AU  - Pingoud, A.
AU  - Desbiolles, P.
TI  - Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 4118
EP  - 4127
VL  - 36
AB  - The restriction endonuclease EcoRV can rapidly locate a short recognition site within long
AB  - non-cognate DNA using 'facilitated diffusion'. This
AB  - process has long been attributed to a sliding mechanism, in which the
AB  - enzyme first binds to the DNA via nonspecific interaction and then moves
AB  - along the DNA by 1D diffusion. Recent studies, however, provided evidence
AB  - that 3D translocations (hopping/jumping) also help EcoRV to locate its
AB  - target site. Here we report the first direct observation of sliding and
AB  - jumping of individual EcoRV molecules along nonspecific DNA. Using
AB  - fluorescence microscopy, we could distinguish between a slow 1D diffusion
AB  - of the enzyme and a fast translocation mechanism that was demonstrated to
AB  - stem from 3D jumps. Salt effects on both sliding and jumping were
AB  - investigated, and we developed numerical simulations to account for both
AB  - the jump frequency and the jump length distribution. We deduced from our
AB  - study the 1D diffusion coefficient of EcoRV, and we estimated the number
AB  - of jumps occurring during an interaction event with nonspecific DNA. Our
AB  - results substantiate that sliding alternates with hopping/jumping during
AB  - the facilitated diffusion of EcoRV and, furthermore, set up a framework
AB  - for the investigation of target site location by other DNA-binding
AB  - proteins.
ER  -

TY  - JOUR
AU  - Bonnin, R.A.
AU  - Girlich, D.
AU  - Imanci, D.
AU  - Dortet, L.
AU  - Naas, T.
TI  - Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.
JO  - Genome Announcements
PY  - 2015
SP  - e01340
EP  - e01315
VL  - 3
AB  - We provide here the first genome sequence of a Serratia rubidaea isolate, a
AB  - human-opportunistic pathogen. This reference sequence will permit a comparison of
AB  - this species with others of the Serratia genus.
ER  -

TY  - JOUR
AU  - Bonnin, R.A.
AU  - Nordmann, P.
AU  - Carattoli, A.
AU  - Poirel, L.
TI  - Comparative genomics of IncL/M-type plasmids; evolution by acquisition of resistance genes and insertion sequences.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 674
EP  - 676
VL  - 57
AB  - IncL/M-type plasmids R446b and R471a were originally isolated from Morganella
AB  - morganii (formerly Proteus morganii) as the first members of the IncL/M group of
AB  - multidrug resistance (MDR) plasmids (6, 7)....
ER  -

TY  - JOUR
AU  - Bonnin, R.A.
AU  - Poirel, L.
AU  - Carattoli, A.
AU  - Nordmann, P.
TI  - Characterization of an IncFII Plasmid Encoding NDM-1 from Escherichia coli ST131.
JO  - PLoS ONE
PY  - 2012
SP  - E34752
EP  - E34752
VL  - 7
AB  - BACKGROUND: The current spread of the gene encoding the metallo-ss-lactamase
AB  - NDM-1 in Enterobacteriaceae is linked to a variety of surrounding genetic
AB  - structures and plasmid scaffolds. METHODOLOGY: The whole sequence of plasmid
AB  - pGUE-NDM carrying the bla(NDM-1) gene was determined by high-density
AB  - pyrosequencing and a genomic comparative analysis with other bla(NDM-1)-negative
AB  - IncFII was performed. PRINCIPAL FINDINGS: Plasmid pGUE-NDM replicating in
AB  - Escherichia coli confers resistance to many antibiotic molecules including
AB  - beta-lactams, aminoglycosides, trimethoprim, and sulfonamides. It is 87,022 bp
AB  - in-size and carries the two beta-lactamase genes bla(NDM-1) and bla(OXA-1),
AB  - together with three aminoglycoside resistance genes aacA4, aadA2, and aacC2.
AB  - Comparative analysis of the multidrug resistance locus contained a module
AB  - encompassing the bla(NDM-1) gene that is actually conserved among different
AB  - structures identified in other enterobacterial isolates. This module was
AB  - constituted by the bla(NDM-1) gene, a fragment of insertion sequence ISAba125 and
AB  - a bleomycin resistance encoding gene. SIGNIFICANCE: This is the first
AB  - characterized bla(NDM-1)-carrying IncFII-type plasmid. Such association between
AB  - the bla(NDM-1) gene and an IncFII-type plasmid backbone is extremely worrisome
AB  - considering that this plasmid type is known to spread efficiently, as examplified
AB  - with the worldwide dissemination of bla(CTX-M-15)-borne IncFII plasmids.
ER  -

TY  - JOUR
AU  - Bonnin, R.A.
AU  - Poirel, L.
AU  - Nordmann, P.
AU  - Eikmeyer, F.G.
AU  - Wibberg, D.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - Complete sequence of broad-host-range plasmid pNOR-2000 harbouring the metallo-beta-lactamase gene blaVIM-2 from Pseudomonas aeruginosa.
JO  - J. Antimicrob. Chemother.
PY  - 2013
SP  - 1060
EP  - 1065
VL  - 68
AB  - OBJECTIVES: Metallo-beta-lactamases (MBLs) are increasingly reported not only in
AB  - Enterobacteriaceae but also in Pseudomonas spp. These enzymes hydrolyse all
AB  - beta-lactams, including carbapenems, and are not inhibited by beta-lactamase
AB  - inhibitors. The aim of this study was to fully characterize a plasmid bearing the
AB  - bla(VIM-2) MBL gene identified in a Pseudomonas aeruginosa isolate. METHODS: This
AB  - plasmid was fully sequenced by high-density pyrosequencing and annotated using
AB  - the GenDB version 2.0 annotation tool. The evaluation of the broad-host-range
AB  - replication of the pNOR-2000 replication initiation gene was assessed using
AB  - electro-transformation and conjugation assays and the distribution of this
AB  - replicase gene was evaluated using an international collection of VIM-producing
AB  - Pseudomonas spp. RESULTS: Analysis of the 21 880 bp sequence of pNOR-2000
AB  - revealed a truncated and non-functional transfer operon, in addition to novel
AB  - genes encoding a serine protease and toxin/antitoxin addiction systems. This
AB  - broad-host-range plasmid shares high gene synteny with part of the mobile genomic
AB  - island pKLC102 identified in P. aeruginosa strain C. CONCLUSIONS: We report here
AB  - the complete nucleotide sequence of plasmid pNOR-2000 from a P. aeruginosa
AB  - clinical isolate harbouring the integron-located MBL gene bla(VIM-2).
ER  -

TY  - JOUR
AU  - Bonnist, E.Y.M.
AU  - Liebert, K.
AU  - Dryden, D.T.F.
AU  - Jeltsch, A.
AU  - Jones, A.C.
TI  - Using the fluorescence decay of 2-aminopurine to investigate conformational change in the recognition sequence of the EcoRV DNA-(adenine-N6)-methyltransferase on enzyme binding.
JO  - Biophys. Chem.
PY  - 2012
SP  - 28
EP  - 34
VL  - 160
AB  - The EcoRV DNA methyltransferase methylates the first adenine in the GATATC recognition
AB  - sequence. It is presumed that methylation proceeds
AB  - by a nucleotide flipping mechanism but no crystal structure is
AB  - available to confirm this. A popular solution-phase assay for
AB  - nucleotide flipping employs the fluorescent adenine analogue,
AB  - 2-aminopurine (2AP), substituted at the methylation target site; a
AB  - substantial increase in fluorescence intensity on enzyme binding
AB  - indicates flipping. However, this appeared to fail for M.EcoRV, since
AB  - 2AP substituted for the non-target adenine in the recognition sequence
AB  - showed a much greater intensity increase than 2AP at the target site.
AB  - This anomaly is resolved by recording the fluorescence decay of 2AP
AB  - which shows that the target 2AP is indeed flipped by the enzyme, but
AB  - its fluorescence is quenched by interaction with aromatic residues in
AB  - the catalytic site, whereas bending of the duplex at the non-target
AB  - site alleviates inter-base quenching and exposes the 2AP to solvent.
ER  -

TY  - JOUR
AU  - Bonocora, R.P.
AU  - Belfort, M.
TI  - Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein.
JO  - Methods Mol. Biol.
PY  - 2014
SP  - 55
EP  - 67
VL  - 1123
AB  - Mapping the precise position of endonucleolytic cleavage sites is a fundamental experimental
AB  - technique used to describe the function of a homing endonuclease. However, these proteins are
AB  - often recalcitrant to cloning and over-expression in biological systems because of toxicity
AB  - induced by spurious DNA cleavage events. In this chapter we outline the steps to successfully
AB  - express a homing endonuclease in vitro and use this product in nucleotide-resolution cleavage
AB  - assays.
ER  -

TY  - JOUR
AU  - Bonocora, R.P.
AU  - Shub, D.A.
TI  - A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages.
JO  - J. Bacteriol.
PY  - 2004
SP  - 8153
EP  - 8155
VL  - 186
AB  - Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive
AB  - bacteria. However, among the phages of
AB  - enteric and other gram-negative proteobacteria, introns have been
AB  - encountered only in phage T4 and several of its close relatives. Here we
AB  - report the insertion of a self-splicing group I intron in the coding
AB  - sequence of the DNA polymerase genes of PhiI and W31, phages that are
AB  - closely related to T7. The introns belong to subgroup IA2 and both contain
AB  - an open reading frame, inserted into structural element P6a, encoding a
AB  - protein belonging to the HNH family of homing endonucleases. The introns
AB  - splice efficiently in vivo and self-splice in vitro under mild conditions
AB  - of ionic strength and temperature. We conclude that there is no barrier
AB  - for maintenance of group I introns in phages of proteobacteria.
ER  -

TY  - JOUR
AU  - Bonocora, R.P.
AU  - Shub, D.A.
TI  - A likely pathway for formation of mobile group I introns.
JO  - Curr. Biol.
PY  - 2009
SP  - 223
EP  - 228
VL  - 19
AB  - Mobile group I introns are RNA splicing elements that have been invaded by endonuclease genes.
AB  - These endonucleases facilitate intron mobility by a
AB  - unidirectional, duplicative gene-conversion process known as homing [1].
AB  - Survival of the invading endonuclease depends upon its ability to promote
AB  - intron mobility. Therefore, the endonuclease must either quickly change
AB  - its cleavage specificity to match the site of intron insertion, or it must
AB  - already be preadapted to cleave this sequence. Here we show that the group
AB  - I intron in the DNA polymerase gene of T7-like bacteriophage PhiI is
AB  - mobile, dependent upon its intronic HNH homing endonuclease gene, I-TslI.
AB  - We also show that gene 5.3 of phage T3, located adjacent to its intronless
AB  - DNA polymerase gene, is a homologous homing endonuclease gene whose
AB  - protein product initiates efficient spread of gene 5.3 into empty sites in
AB  - related phages. Both of these endonucleases cleave intronless DNA
AB  - polymerase genes at identical positions. This shared feature between an
AB  - intronic and free-standing endonuclease is unprecedented. Based on this
AB  - evidence, we propose that introns and their homing endonucleases evolve
AB  - separately to target the same highly conserved sequences, uniting
AB  - afterwards to create a composite mobile element.
ER  -

TY  - JOUR
AU  - Bonocora, R.P.
AU  - Shub, D.A.
TI  - A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes.
JO  - Mol. Microbiol.
PY  - 2001
SP  - 1299
EP  - 1306
VL  - 39
AB  - Open reading frames (ORFs) are frequently inserted into group I self-splicing introns. These
AB  - ORFs encode either maturases that are
AB  - required for splicing of the intron or DNA endonucleases that promote
AB  - intron mobility. A self-splicing intron in the tRNA(fMet) gene of
AB  - Synechocystis PCC 6803, which has been proposed to have moved laterally
AB  - within the cyanobacteria, contains an ORF that is unrelated to known
AB  - intron-encoded endonucleases or maturases. Here, using an in vitro
AB  - transcription-translation system, we show that this intronic ORF
AB  - encodes a double-strand DNA endonuclease, I-Ssp6803I. I-Ssp6803I
AB  - cleaves each strand of the intronless tRNA(fMet) gene adjacent to the
AB  - anticodon triplet leaving 3 bp 3' extensions and has no activity at
AB  - intron-exon boundaries. Using an in vitro cleavage assay and scanning
AB  - deletion mutants of the intronless target site, the minimal recognition
AB  - site was determined to be a partially palindromic 20 bp region
AB  - encompassing the entire anticodon stem and loop of the tRNA(fMet) gene.
AB  - I-Ssp6803I represents a novel intron-encoded DNA endonuclease and is
AB  - the first example of a chromosomally encoded group I intron
AB  - endonuclease in bacteria.
ER  -

TY  - JOUR
AU  - Booker, A.E.
AU  - Johnston, M.D.
AU  - Daly, R.A.
AU  - Wrighton, K.C.
AU  - Wilkins, M.J.
TI  - Draft Genome Sequences of Multiple Frackibacter Strains Isolated from Hydraulically Fractured Shale Environments.
JO  - Genome Announcements
PY  - 2017
SP  - e00608
EP  - e00617
VL  - 5
AB  - The genomes of three novel Frackibacter strains (WG11, WG12, and WG13) were sequenced. These
AB  - strains were isolated from hypersaline fluid collected from a
AB  - hydraulically fractured natural gas well. These genomes provide information on
AB  - the mechanisms necessary for growth in these environments and offer insight into
AB  - interactions with other community members.
ER  -

TY  - JOUR
AU  - Boon, E.M.
AU  - Salas, J.E.
AU  - Barton, J.K.
TI  - An electrical probe of protein-DNA interactions on DNA-modified surfaces.
JO  - Nat. Biotechnol.
PY  - 2002
SP  - 282
EP  - 286
VL  - 20
AB  - DNA charge transport chemistry is found to provide a sensitive method for probing
AB  - protein-dependent changes in DNA structure and enzymatic reactions. Here we describe the
AB  - development of an electrochemical assay of protein binding to DNA-modified electrodes based
AB  - upon the detection of associated perturbations in DNA base stacking. Gold electrode surfaces
AB  - that were modified with loosely packed DNA duplexes, covalently crosslinked to a redox-active
AB  - intercalator and containing the binding site of the test protein, were constructed. Charge
AB  - transport through DNA as a function of protein binding was then assayed. Substantial
AB  - attenuation in current is seen in the presence of the base-flipping enzymes HhaI methylase and
AB  - uracil DNA glycosylase, as well as with TATA-binding protein. When restriction endonuclease
AB  - PvuII (R.PvuII) binds to its methylated target, little base-stacking perturbation occurs and
AB  - little diminution in current flow is observed. Importantly, the kinetics of restriction by
AB  - R.PvuII of its nonmethylated target is also easily monitored electrochemically. This approach
AB  - should be generally applicable to assaying protein--DNA interactions and reactions on
AB  - surfaces.
ER  -

TY  - JOUR
AU  - Boonma, P.
AU  - Spinler, J.K.
AU  - Qin, X.
AU  - Jittaprasatsin, C.
AU  - Muzny, D.M.
AU  - Doddapaneni, H.
AU  - Gibbs, R.
AU  - Petrosino, J.
AU  - Tumwasorn, S.
AU  - Versalovic, J.
TI  - Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 744
EP  - 754
VL  - 9
AB  - Lactobacillus rhamnosus is a facultative, lactic acid bacterium in the phylum Firmicutes.
AB  - Lactobacillus spp. are generally considered beneficial, and specific
AB  - strains of L. rhamnosus are validated probiotics. We describe the draft genomes
AB  - of three L. rhamnosus strains (L31, L34, and L35) isolated from the feces of Thai
AB  - breastfed infants, which exhibit anti-inflammatory properties in vitro. The three
AB  - genomes range between 2.8 - 2.9 Mb, and contain approximately 2,700 protein
AB  - coding genes.
ER  -

TY  - JOUR
AU  - Boonmak, C.
AU  - Takahasi, Y.
AU  - Morikawa, M.
TI  - Draft Genome Sequence of Geobacillus thermoleovorans Strain B23.
JO  - Genome Announcements
PY  - 2013
SP  - e00944
EP  - e00913
VL  - 1
AB  - Here, we report the draft genome sequence of Geobacillus thermoleovorans strain B23, which was
AB  - isolated from a deep subterranean petroleum reservoir in Japan. An
AB  - array of genes related to unique long-chain alkane degradation pathways in G.
AB  - thermoleovorans B23 has been identified by whole-genome analyses of this strain.
ER  -

TY  - JOUR
AU  - Borase, H.P.
AU  - Patil, C.D.
AU  - Salunkhe, R.B.
AU  - Suryawanshi, R.K.
AU  - Salunke, B.K.
AU  - Patil, S.V.
TI  - Inhibition of restriction endonucleases by biofunctionalized silver nanoparticles: An in vitro study.
JO  - Mater. Lett.
PY  - 2014
SP  - 24
EP  - 26
VL  - 134
AB  - Ecofriendly synthesis of metal nanoparticles and their unique properties hold promise for
AB  - innovative therapeutic applications. In the present study, rapid, novel, low cost method for
AB  - synthesis of silver nanoparticles (AgNPs) using aqueous leaves extract of medicinal plant
AB  - Euphorbia heterophylla (E. heterophylla) is reported. AgNPs synthesized by plant extract
AB  - exhibited absorption peak at 422 nm in UV-vis spectroscopy. Transmission electron microscopy
AB  - micrographs revealed presence of AgNPs with average size of 13 nm with grain and triangular
AB  - shapes. Fourier Transform Infrared Spectroscopy analysis revealed role of leaves metabolites
AB  - as reducing and capping agent in synthesis of AgNPs. X ray diffraction pattern and selected
AB  - area electron diffraction study confirmed crystalline nature of AgNPs. Inhibition of DNA
AB  - cutting activity of restriction endonucleases (EcoRI, HindIII and BamHI) by biofunctionalized
AB  - AgNPs in agarose gel electrophoresis is first time reported in the present study. This
AB  - potential of AgNPs can be useful for enhancing effectiveness of phage therapy by acting as
AB  - synergistic cocktail with bacteriophages to kill bacteria via inhibition of their restriction
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Borck, K.
AU  - Beggs, J.D.
AU  - Brammar, W.J.
AU  - Hopkins, A.S.
AU  - Murray, N.E.
TI  - The construction in vitro of transducing derivatives of phage lambda.
JO  - Mol. Gen. Genet.
PY  - 1976
SP  - 199
EP  - 207
VL  - 146
AB  - Methods are described for the construction of plaque-forming, transducing
AB  - derivatives of phage lambda, using appropriate receptor genomes and fragments
AB  - of DNA generated by the restriction enzymes endo R.EcoRI and endo R.HindIII.
AB  - The general properties of the transducing derivatives are described and
AB  - discussed.  Plaque-forming phages carrying the E. coli trp, his, cysB, thyA,
AB  - supD, supE, supF, hsd, tna and lig genes have been isolated.
ER  -

TY  - JOUR
AU  - Borek, E.
AU  - Srinivasan, P.R.
TI  - The methylation of nucleic acids.
JO  - Annu. Rev. Biochem.
PY  - 1966
SP  - 275
EP  - 298
VL  - 35
AB  - The evidence for the methylation of nucleic acids at the macromolecular level
AB  - has been presented in several review articles and, therefore, will not be
AB  - repeated here.  The biochemistry of the phenomenon will be emphasized in this
AB  - article and the biological implications in a companion article in which all
AB  - alterations of macromolecules effected by enzymes will be reviewed.
ER  -

TY  - JOUR
AU  - Boreskov, Y.G.
AU  - Titeeva, G.R.
AU  - Berlin, Y.A.
TI  - Synthetic oligodeoxynucleotides in studying MspI restriction endonuclease.
JO  - Bioorg. Khim.
PY  - 1988
SP  - 333
EP  - 339
VL  - 14
AB  - Interaction of MspI restriction endonuclease with a series of
AB  - oligodeoxynucleotides varying in stability of secondary structure and in
AB  - location of the restriction site, has been studied.  It is shown that a
AB  - functionally active MspI site must be double-stranded and flanked from both
AB  - sides.  Separate MspI cleavage of dodecanucleotides dCGACCCGGGATC and
AB  - dGATCCCGGGTCG is inhibited by the reaction products as well as by
AB  - non-homological hexanucleotides dGGTACC and dGGATCC (but not by dCGGCGC).
AB  - Polyethylene glycol in low concentrations (1-3%) promotes and in higher
AB  - concentrations (7-14%) inhibits the cleavage.  A scheme of MspI functioning is
AB  - suggested including the enzyme's step-by-step recognition of the restriction
AB  - site and its nonspecific interaction with flanking segments of DNA, which leads
AB  - to formation of the productive complex.
ER  -

TY  - JOUR
AU  - Borgaro, J.G.
AU  - Benner, N.
AU  - Zhu, Z.Y.
TI  - Fidelity Index Determination of DNA Methyltransferases.
JO  - PLoS ONE
PY  - 2013
SP  - e63866
EP  - e63866
VL  - 8
AB  - DNA methylation is the most frequent form of epigenetic modification in the cell, which
AB  - involves gene regulation in eukaryotes and protection
AB  - against restriction enzymes in prokaryotes. Even though many
AB  - methyltransferases exclusively modify their cognate sites, there have
AB  - been reports of those that exhibit promiscuity. Previous experimental
AB  - approaches used to characterize these methyltransferases do not provide
AB  - the exact concentration at which off-target methylation occurs. Here,
AB  - we present the first reported fidelity index (FI) for a number of DNA
AB  - methyltransferases. We define the FI as the ratio of the highest amount
AB  - of methyltransferase that exhibits no star activity (off-target
AB  - effects) to the lowest amount that exhibits complete modification of
AB  - the cognate site. Of the methyltransferases assayed, M. MspI and M.
AB  - AluI exhibited the highest fidelity of >= 250 and >= 500, respectively,
AB  - and do not show star activity even at very high concentrations. In
AB  - contrast, M. HaeIII, M.EcoKDam and M. BamHI have the lowest fidelity of
AB  - 4, 4 and 2, respectively, and exhibit star activity at concentrations
AB  - close to complete methylation of the cognate site. The fidelity indexes
AB  - provide vital information on the usage of methyltransferases and are
AB  - especially important in applications where site specific methylation is
AB  - required.
ER  -

TY  - JOUR
AU  - Borgaro, J.G.
AU  - Zhu, Z.
TI  - Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 4198
EP  - 4206
VL  - 41
AB  - In T4 bacteriophage, 5-hydroxymethylcytosine (5hmC) is incorporated into DNA during
AB  - replication. In response, bacteria may have developed
AB  - modification-dependent type IV restriction enzymes to defend the cell from
AB  - T4-like infection. PvuRts1I was the first identified restriction enzyme to
AB  - exhibit specificity toward hmC over 5-methylcytosine (5mC) and cytosine. By using
AB  - PvuRts1I as the original member, we identified and characterized a number of
AB  - homologous proteins. Most enzymes exhibited similar cutting properties to
AB  - PvuRts1I, creating a double-stranded cleavage on the 3' side of the modified
AB  - cytosine. In addition, for efficient cutting, the enzymes require two cytosines
AB  - 21-22-nt apart and on opposite strands where one cytosine must be modified.
AB  - Interestingly, the specificity determination unveiled a new layer of complexity
AB  - where the enzymes not only have specificity for 5-beta-glucosylated hmC
AB  - (5betaghmC) but also 5-alpha-glucosylated hmC (5alphaghmC). In some cases, the
AB  - enzymes are inhibited by 5betaghmC, whereas in others they are inhibited by
AB  - 5alphaghmC. These observations indicate that the position of the sugar ring
AB  - relative to the base is a determining factor in the substrate specificity of the
AB  - PvuRts1I homologues. Lastly, we envision that the unique properties of select
AB  - PvuRts1I homologues will permit their use as an additive or alternative tool to
AB  - map the hydroxymethylome.
ER  -

TY  - JOUR
AU  - Borges, K.M.
AU  - Wetterhahn, K.E.
TI  - Chromium Bound to DNA alters cleavage by restriction endonucleases.
JO  - Chem. Res. Toxicol.
PY  - 1991
SP  - 638
EP  - 641
VL  - 4
AB  - None
ER  -

TY  - JOUR
AU  - Bork, P.
AU  - Ouzounis, C.
AU  - Casari, G.
AU  - Schneider, R.
AU  - Sander, C.
AU  - Dolan, M.
AU  - Gilbert, W.
AU  - Gillevet, P.M.
TI  - Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology.
JO  - Mol. Microbiol.
PY  - 1995
SP  - 955
EP  - 967
VL  - 16
AB  - We report on the analysis of 214kb of the parasitic eubacterium Mycoplasma capricolum
AB  - sequenced by genomic walking techniques. The 287 putative proteins detected to date represent
AB  - about half of the estimated total number of 500 predicted for this organism. A large fraction
AB  - of these (75%) can be assigned a likely function as a result of similarity searches. Several
AB  - important features of the functional organization of this small genome are already apparent.
AB  - Among these are (i) the expected relatively large number of enzymes involved in metabolic
AB  - transport and activation, for efficient use of host cell nutrients; (ii) the presence of
AB  - anabolic enzymes; (iii) the unexpected diversity of enzymes involved in DNA replication and
AB  - repair; and (iv) a sizeable number of orthologues (82 so far) in Escherichia coli. This survey
AB  - is beginning to provide a detailed view of how M. capricolum manages to maintain essential
AB  - cellular processes with a genome much smaller than that of its bacterial relatives.
ER  -

TY  - JOUR
AU  - Borneman, A.R.
AU  - Bartowsky, E.J.
AU  - McCarthy, J.
AU  - Chambers, P.J.
TI  - Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2010
SP  - 681
EP  - 691
VL  - 86
AB  - Many bacteria display substantial intra-specific genomic diversity that
AB  - produces significant phenotypic variation between strains of the same
AB  - species. Understanding the genetic basis of these strain-specific
AB  - phenotypes is especially important for industrial microorganisms where
AB  - these characters match individual strains to specific industrial
AB  - processes. Oenococcus oeni, a bacterium used during winemaking, is one
AB  - such industrial species where large numbers of strains show significant
AB  - differences in commercially important industrial phenotypes. To ascertain
AB  - the basis of these phenotypic differences, the genomic content of ten wine
AB  - strains of O. oeni were mapped by array-based comparative genome
AB  - hybridization (aCGH). These strains comprised a genomically diverse group
AB  - in which large sections of the reference genome were often absent from
AB  - individual strains. To place the aCGH results in context, whole genome
AB  - sequence was obtained for one of these strains and compared with two
AB  - previously sequenced, unrelated strains. While the three strains shared a
AB  - core group of conserved ORFs, up to 10% of the coding potential of any one
AB  - strain was specific to that isolate. The genome of O. oeni is therefore
AB  - likely to be much larger than that present in any single strain and it is
AB  - these strain-specific regions that are likely to be responsible for
AB  - differences in industrial phenotypes.
ER  -

TY  - JOUR
AU  - Boronin, A.M.
AU  - Kochetkov, V.V.
AU  - Kulakov, L.A.
AU  - Tusupbekova, G.A.
AU  - Alieva, R.M.
TI  - PaeD253 restriction-modification system determined by pBS253 biodegradation plasmid of Pseudomonas aeruginosa.
JO  - Dokl. Akad. Nauk.
PY  - 1989
SP  - 1472
EP  - 1474
VL  - 304
AB  - None
ER  -

TY  - JOUR
AU  - Borowczyk, E.
AU  - Mohan, K.N.
AU  - D'Aiuto, L.
AU  - Cirio, M.C.
AU  - Chaillet, J.R.
TI  - Identification of a region of the DNMT1 methyltransferase that regulates the maintenance of genomic imprints.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 20806
EP  - 20811
VL  - 106
AB  - Reprogramming of DNA methylation patterns during mammalian preimplantation development
AB  - involves the concurrent maintenance of
AB  - methylation on differentially methylated domains (DMDs) of imprinted
AB  - genes and a marked reduction of global (non-DMD) genomic methylation.
AB  - In the developing mammalian embryo, one allele of a DMD is
AB  - unmethylated, and the opposite parental allele is methylated, having
AB  - inherited this methylation from the parental gamete. The maintenance of
AB  - DMDs is important for monoallelic imprinted gene expression and normal
AB  - development of the embryo. Because the DNMT1 cytosine methyltransferase
AB  - governs maintenance methylation in mammals, rearrangements of non-DMD,
AB  - but not DMD methylation in preimplantation embryos suggest that the
AB  - preimplantation DNMT1-dependent maintenance mechanism specifically
AB  - targets DMD sequences. We explored this possibility using an engineered
AB  - mouse ES cell line to screen for mutant DNMT1 proteins that protect
AB  - against the loss of DMD and/or global (non-DMD) methylation in the
AB  - absence of the wild-type endogenous DNMT1 methyltransferase. We
AB  - identified DNMT1 mutants that were defective in maintenance of
AB  - either-DMD and/or non-DMD methylation. Among these, one mutant
AB  - maintained non-DMD methylation but not imprinted DMD methylation and
AB  - another mutant maintained just DMD methylation. The mutated amino acids
AB  - of these mutants reside in a mammal-specific, disordered region near
AB  - the amino terminus of DNMT1. These findings suggest that DNMT1
AB  - participates in epigenetic reprogramming through its ability to
AB  - distinguish different categories of methylated sequences.
ER  -

TY  - JOUR
AU  - Borowiak, M.
AU  - Fischer, J.
AU  - Baumann, B.
AU  - Hammerl, J.A.
AU  - Szabo, I.
AU  - Malorny, B.
TI  - Complete Genome Sequence of a VIM-1-Producing Salmonella enterica subsp. enterica Serovar Infantis Isolate Derived from Minced Pork Meat.
JO  - Genome Announcements
PY  - 2018
SP  - e00327
EP  - e00318
VL  - 6
AB  - Carbapenems are considered last-resort antibiotics used to treat human infections caused by
AB  - multidrug-resistant bacteria. In 2011, VIM-1 carbapenemase-producing
AB  - Salmonella enterica subsp. enterica serovar Infantis strains were isolated from
AB  - livestock for the first time in Germany. Here, we announce the complete genome
AB  - sequence of the first German blaVIM-1-harboring Salmonella Infantis isolate
AB  - (15-SA01028) originating from food.
ER  -

TY  - JOUR
AU  - Borowiak, M.
AU  - Hammerl, J.A.
AU  - Fischer, J.
AU  - Szabo, I.
AU  - Malorny, B.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Paratyphi B Sequence Type 28 Harboring mcr-1.
JO  - Genome Announcements
PY  - 2017
SP  - e00991
EP  - e00917
VL  - 5
AB  - In 2015, plasmid-mediated colistin resistance was reported to be caused by a mobilized
AB  - phosphoethanolamine transferase gene (mcr-1) in Enterobacteriaceae
AB  - Here, we announce the complete genome sequence of the earliest
AB  - d-tartrate-fermenting Salmonella enterica subsp. enterica serovar Paratyphi B
AB  - isolate harboring mcr-1 from the collection of the German National Reference
AB  - Laboratory for Salmonella.
ER  -

TY  - JOUR
AU  - Borowka, P.
AU  - Lach, J.
AU  - Bakula, Z.
AU  - van Ingen, J.
AU  - Safianowska, A.
AU  - Brzostek, A.
AU  - Dziadek, J.
AU  - Strapagiel, D.
AU  - Jagielski, T.
TI  - Draft Genome Sequences of Mycobacterium kansasii Clinical Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00406
EP  - e00417
VL  - 5
AB  - Mycobacterium kansasii is a nontuberculous mycobacterial (NTM) pathogen, frequently isolated
AB  - from clinical samples and responsible for a large part of NTM
AB  - infections in the human population. Here, we report the draft genome sequences of
AB  - 12 M. kansasii strains isolated from clinical and host-associated sources from
AB  - the Netherlands, Germany, and Poland.
ER  -

TY  - JOUR
AU  - Borrel, G.
AU  - Harris, H.M.
AU  - Parisot, N.
AU  - Gaci, N.
AU  - Tottey, W.
AU  - Mihajlovski, A.
AU  - Deane, J.
AU  - Gribaldo, S.
AU  - Bardot, O.
AU  - Peyretaillade, E.
AU  - Peyret, P.
AU  - O'Toole, P.W.
AU  - Brugere, J.F.
TI  - Genome Sequence of 'Candidatus Methanomassiliicoccus intestinalis' Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces.
JO  - Genome Announcements
PY  - 2013
SP  - e00453
EP  - e00413
VL  - 1
AB  - 'Candidatus Methanomassiliicoccus intestinalis' Issoire-Mx1 is a methanogenic archaeon found
AB  - in the human gut and is a representative of the novel order of
AB  - methanogens related to Thermoplasmatales. Its complete genome sequence is
AB  - presented here.
ER  -

TY  - JOUR
AU  - Borrel, G.
AU  - Harris, H.M.
AU  - Tottey, W.
AU  - Mihajlovski, A.
AU  - Parisot, N.
AU  - Peyretaillade, E.
AU  - Peyret, P.
AU  - Gribaldo, S.
AU  - O'Toole, P.W.
AU  - Brugere, J.F.
TI  - Genome Sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6944
EP  - 6945
VL  - 194
AB  - We report the draft genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a
AB  - methanogen present in the human gut. It was enriched from human feces
AB  - under anaerobic conditions with methanol as the substrate. Its circular genome,
AB  - of around 1.7 Mb, contains genes needed for methylotrophic methanogenesis from
AB  - methanol and tri-, di-, and monomethylamine.
ER  -

TY  - JOUR
AU  - Borriss, M.
AU  - Lombardot, T.
AU  - Glockner, F.O.
AU  - Becher, D.
AU  - Albrecht, D.
AU  - Schweder, T.
TI  - Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b.
JO  - Extremophiles
PY  - 2007
SP  - 95
EP  - 104
VL  - 11
AB  - Virion DNA of bacteriophage 11b (phi 11b), which infects a psychrophilic Flavobacterium
AB  - isolate from Arctic sea-ice, was
AB  - determined to consist of 36,012 bp. With 30.6% its GC content
AB  - corresponds to that of host-genus species and is the lowest of all
AB  - phages of Gram-negative bacteria sequenced so far. Similarities of
AB  - several of 65 predicted ORFs, genome organization and phylogeny suggest
AB  - an affiliation to 'mesophilic' nonmarine siphoviruses, e.g. to
AB  - bacteriophages SPP1 and HK97. Early genes presumably encode an
AB  - essential recombination factor (ERF), a single strand binding (SSB)
AB  - protein, an endonuclease, and a DNA methylase. The late gene segment is
AB  - likely to contain a terminase, portal, minor head, protease and a major
AB  - capsid gene. Five ORFs exhibited similarities to Bacteroidetes species
AB  - and seem to reflect the host specificity of the phage. Among
AB  - PAGE-separated virion proteins that were identified by MALDI-ToF mass
AB  - spectrometry are the portal, the major capsid, and a putative conserved
AB  - tail protein. The phi 11b genome is the first to be described of a
AB  - cultivated virus infecting a psychrophilic host as well as a
AB  - Bacteroidetes bacterium.
ER  -

TY  - JOUR
AU  - Borriss, R.
AU  - Chen, X.
AU  - Rueckert, C.
AU  - Blom, J.
AU  - Becker, A.
AU  - Baumgarth, B.
AU  - Fan, B.
AU  - Pukall, R.
AU  - Schumann, P.
AU  - Sproer, C.
AU  - Junge, H.
AU  - Vater, J.
AU  - Puhler, A.
AU  - Klenk, H.P.
TI  - Relationship of Bacillus amyloliquefaciens clades associated with strains DSM7T and FZB42: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and plantarum subsp. nov. based on their discriminating complete genome sequences.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2011
SP  - 1786
EP  - 1801
VL  - 61
AB  - The whole genome sequenced rhizobacterium FZB42 (Chen et al., 2007) and other plant-associated
AB  - Bacillus strains either designated as Bacillus amyloliquefaciens or Bacillus subtilis are used
AB  - commercially to promote growth and health of crop plants. Previous investigations revealed
AB  - that the strains represent an own ecotype related to B. amyloliquefaciens, however its exact
AB  - taxonomic position remains elusive (Reva et al., 2004). Here we have demonstrated ability to
AB  - colonize Arabidopsis roots for a group of Bacillus strains, closely related to FZB42.
AB  - According to their phenotypic traits the strains were similar to Bacillus amyloliquefaciens
AB  - DSM 7T, but differed considerably in DNA sequences of the genes encoding 16S rRNA, gyrase
AB  - subunit A (gyrA), and histidine kinase (cheA) from the type strain. Phylogenetic analysis
AB  - performed with partial 16S rRNA, gyrA, and cheA sequences revealed that plant-associated
AB  - Bacillus strains including FZB42 form a lineage, which can be discriminated from the cluster
AB  - of strains closely related to B. amyloliquefaciens DSM 7T. DNA-DNA hybridization (DDH)
AB  - performed with genomic DNAs from DSM 7T and FZB42 yielded 63.7 to 71.2 % homology. As
AB  - complementary approach, we used several genomic methods, as direct whole genome comparison,
AB  - digital DDH, and microarray-based comparative genomic hybridization (M-CGH). Plant-associated
AB  - strains were discriminated from DSM 7T and B. subtilis type strain by their different
AB  - potential to synthesize non-ribosomally lipopeptides and polyketides. According to the
AB  - differences found in marker gene sequences and the whole genomes, we propose the two B.
AB  - amyloliquefaciens subspecies, 'plantarum' for their plant-associated, and
AB  - 'amyloliquefaciens', for their non-plant associated representatives. This is in line with
AB  - results of DDH, MCGH, and the MALDI TOF mass spectrometry of cellular components which are
AB  - justifying that both ecovars represent two different subspecies.
ER  -

TY  - JOUR
AU  - Borst, L.B.
AU  - Suyemoto, M.M.
AU  - Scholl, E.H.
AU  - Fuller, F.J.
AU  - Barnes, H.J.
TI  - Comparative genomic analysis identifies divergent genomic features of pathogenic Enterococcus cecorum including a type IC CRISPR-Cas system, a capsule locus, an epa-like locus, and putative host tissue binding proteins.
JO  - PLoS ONE
PY  - 2015
SP  - E0121294
EP  - E0121294
VL  - 10
AB  - Enterococcus cecorum (EC) is the dominant enteric commensal of adult chickens and
AB  - contributes to the gut consortia of many avian and mammalian species. While EC
AB  - infection is an uncommon zoonosis, like other enterococcal species it can cause
AB  - life-threating nosocomial infection in people. In contrast to other enterococci
AB  - which are considered opportunistic pathogens, emerging pathogenic strains of EC
AB  - cause outbreaks of musculoskeletal disease in broiler chickens. Typical morbidity
AB  - and mortality is comparable to other important infectious diseases of poultry. In
AB  - molecular epidemiologic studies, pathogenic EC strains were found to be
AB  - genetically clonal. These findings suggested acquisition of specific virulence
AB  - determinants by pathogenic EC. To identify divergent genomic features and
AB  - acquired virulence determinants in pathogenic EC; comparative genomic analysis
AB  - was performed on genomes of 3 pathogenic and 3 commensal strains of EC.
AB  - Pathogenic isolates had smaller genomes with a higher GC content, and they
AB  - demonstrated large regions of synteny compared to commensal isolates. A molecular
AB  - phylogenetic analysis demonstrated sequence divergence in pathogenic EC genomes.
AB  - At a threshold of 98% identity, 414 predicted proteins were identified that were
AB  - highly conserved in pathogenic EC but not in commensal EC. Among these, divergent
AB  - CRISPR-cas defense loci were observed. In commensal EC, the type IIA arrangement
AB  - typical for enterococci was present; however, pathogenic EC had a type IC locus,
AB  - which is novel in enterococci but commonly observed in streptococci. Potential
AB  - mediators of virulence identified in this analysis included a polysaccharide
AB  - capsular locus similar to that recently described for E. faecium, an epa-like
AB  - locus, and cell wall associated proteins which may bind host extracellular
AB  - matrix. This analysis identified specific genomic regions, coding sequences, and
AB  - predicted proteins which may be related to the divergent evolution and increased
AB  - virulence of emerging pathogenic strains of EC.
ER  -

TY  - JOUR
AU  - Bose, S.
AU  - Mukherjee, T.
AU  - Sen, U.
AU  - Roy, C.
AU  - Rameez, M.J.
AU  - Ghosh, W.
AU  - Mukhopadhyay, S.K.
TI  - Genome Sequence of the Multiple-Protease-Producing Strain Geobacillus thermoleovorans N7, a Thermophilic Bacterium Isolated from Paniphala Hot Spring,   West Bengal, India.
JO  - Genome Announcements
PY  - 2016
SP  - e01202
EP  - e01216
VL  - 4
AB  - Here, we present the draft genome sequence of Geobacillus thermoleovorans strain  N7 (MCC
AB  - 3175), isolated from Paniphala Hot Spring, West Bengal, India, which
AB  - contains genes that encode several industrially and medically important
AB  - thermostable enzymes like neutral protease, xylose isomerase, rhamnogalacturonan
AB  - acetylesterase, nitrate and nitrite reductase, l-asparaginase, glutaminase, and
AB  - RNase P.
ER  -

TY  - JOUR
AU  - Bosi, E.
AU  - Fondi, M.
AU  - Orlandini, V.
AU  - Perrin, E.
AU  - Maida, I.
AU  - de Pascale, D.
AU  - Tutino, M.L.
AU  - Parrilli, E.
AU  - Lo, G.A.
AU  - Filloux, A.
AU  - Fani, R.
TI  - The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.
JO  - BMC Genomics
PY  - 2017
SP  - 93
EP  - 93
VL  - 18
AB  - BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms
AB  - to study the biological mechanisms involved in the adaptation to
AB  - cold conditions. A remarkable feature shared by these bacteria is their ability
AB  - to produce secondary metabolites with a strong antimicrobial and antitumor
AB  - activity. Despite their biotechnological relevance, representatives of this genus
AB  - are still lacking (with few exceptions) an extensive genomic characterization,
AB  - including features involved in the evolution of secondary metabolites production.
AB  - Indeed, biotechnological applications would greatly benefit from such analysis.
AB  - RESULTS: Here, we analyzed the genomes of 38 strains belonging to different
AB  - Pseudoalteromonas species and isolated from diverse ecological niches, including
AB  - extreme ones (i.e. Antarctica). These sequences were used to reconstruct the
AB  - largest Pseudoalteromonas pangenome computed so far, including also the two main
AB  - groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The
AB  - downstream analyses were conducted to describe the genomic diversity, both at
AB  - genus and group levels. This allowed highlighting a remarkable genomic
AB  - heterogeneity, even for closely related strains. We drafted all the main
AB  - evolutionary steps that led to the current structure and gene content of
AB  - Pseudoalteromonas representatives. These, most likely, included an extensive
AB  - genome reduction and a strong contribution of Horizontal Gene Transfer (HGT),
AB  - which affected biotechnologically relevant gene sets and occurred in a
AB  - strain-specific fashion. Furthermore, this study also identified the genomic
AB  - determinants related to some of the most interesting features of the
AB  - Pseudoalteromonas representatives, such as the production of secondary
AB  - metabolites, the adaptation to cold temperatures and the resistance to abiotic
AB  - compounds. CONCLUSIONS: This study poses the bases for a comprehensive
AB  - understanding of the evolutionary trajectories followed in time by this peculiar
AB  - bacterial genus and for a focused exploitation of their biotechnological
AB  - potential.
ER  -

TY  - JOUR
AU  - Bosma, E.F.
AU  - Koehorst, J.J.
AU  - van Hijum, S.A.
AU  - Renckens, B.
AU  - Vriesendorp, B.
AU  - van de Weijer, A.H.
AU  - Schaap, P.J.
AU  - de Vos, W.M.
AU  - van der Oost, J.
AU  - van Kranenburg, R.
TI  - Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 52
EP  - 52
VL  - 11
AB  - Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of
AB  - sugars that can be derived from lignocellulosic feedstocks. Being
AB  - genetically accessible, it is a potential new host for biotechnological
AB  - production of green chemicals from renewable resources. We determined the
AB  - complete genomic sequence of the B. smithii type strain DSM 4216(T), which
AB  - consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a
AB  - 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880
AB  - genes. Genome annotation via RAST was complemented by a protein domain analysis.
AB  - Some unique features of B. smithii central metabolism in comparison to related
AB  - organisms included the lack of a standard acetate production pathway with no
AB  - apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes,
AB  - while acetate was the second fermentation product.
ER  -

TY  - JOUR
AU  - Bosse, J.T.
AU  - Chaudhuri, R.R.
AU  - Li, Y.
AU  - Leanse, L.G.
AU  - Fernandez, C.R.
AU  - Coupland, P.
AU  - Holden, M.T.
AU  - Bazzolli, D.M.
AU  - Maskell, D.J.
AU  - Tucker, A.W.
AU  - Wren, B.W.
AU  - Rycroft, A.N.
AU  - Langford, P.R.
TI  - Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical  Isolate of Actinobacillus pleuropneumoniae.
JO  - Genome Announcements
PY  - 2016
SP  - e01667
EP  - e01615
VL  - 4
AB  - We report here the complete annotated genome sequence of a clinical serovar 8 isolate
AB  - Actinobacillus pleuropneumoniae MIDG2331. Unlike the serovar 8 reference
AB  - strain 405, MIDG2331 is amenable to genetic manipulation via natural
AB  - transformation as well as conjugation, making it ideal for studies of gene
AB  - function.
ER  -

TY  - JOUR
AU  - Botelho, A.M.
AU  - Costa, M.O.
AU  - Beltrame, C.O.
AU  - Ferreira, F.A.
AU  - Cortes, M.F.
AU  - Bandeira, P.T.
AU  - Lima, N.C.
AU  - Souza, R.C.
AU  - Almeida, L.G.
AU  - Vasconcelos, A.T.
AU  - Nicolas, M.F.
AU  - Figueiredo, A.M.
TI  - Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of  the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 34
EP  - 34
VL  - 11
AB  - Staphylococcus aureus is a versatile Gram-positive coccus frequently found colonizing the skin
AB  - and nasal membranes of humans. The acquisition of the
AB  - staphylococcal cassette chromosome mec was a major milestone in the evolutionary
AB  - path of methicillin-resistant S. aureus. This genetic element carries the mecA
AB  - gene, the main determinant of methicillin resistance. MRSA is involved in a
AB  - plethora of opportunistic infectious diseases. The accessory gene regulator is
AB  - the major S. aureus quorum sensing system, playing an important role in
AB  - staphylococcal virulence, including the development of biofilms. We report the
AB  - complete genome sequence (NCBI BioProject ID: PRJNA264181) of the
AB  - methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a variant of the
AB  - ST239 lineage that presents with a natural attenuation of agr-RNAIII
AB  - transcription and a moderate accumulation of biofilm.
ER  -

TY  - JOUR
AU  - Bothma, L.
AU  - Gonzalez-Ibeas, D.
AU  - Mienie, C.
AU  - Bezuidenhout, C.C.
AU  - Adeleke, R.
TI  - Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Strain WG49 and Escherichia coli Strain WG5 Used in South Africa for Phage Detection in Water Samples.
JO  - Genome Announcements
PY  - 2018
SP  - e00372
EP  - e00318
VL  - 6
AB  - Salmonella enterica subsp. enterica serovar Typhimurium WG49 is widely used for enumeration of
AB  - F-specific RNA (F-RNA) coliphages in water. Escherichia coli WG5
AB  - is broadly used for the detection and enumeration of somatic coliphages in water
AB  - samples. We report here the genome sequences of these bacterial strains used in
AB  - South Africa under ISO methods 10705-1 and 10705-2.
ER  -

TY  - JOUR
AU  - Bottacini, F.
AU  - Dal Bello, F.
AU  - Turroni, F.
AU  - Milani, C.
AU  - Duranti, S.
AU  - Foroni, E.
AU  - Viappiani, A.
AU  - Strati, F.
AU  - Mora, D.
AU  - van Sinderen, D.
AU  - Ventura, M.
TI  - Complete Genome Sequence of Bifidobacterium animalis subsp. lactis BLC1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6387
EP  - 6388
VL  - 193
AB  - Bifidobacterium animalis subsp. lactis BLC1 is a probiotic bacterium that is widely exploited
AB  - by food industries as the active ingredient of various
AB  - functional foods. Here we report the complete genome sequence of B.
AB  - animalis subsp. lactis BLC1, which is expected to provide insights into
AB  - the biology of this health-promoting microorganism and improve our
AB  - understanding of its phylogenetic relatedness with other members of the B.
AB  - animalis subsp. lactis taxon.
ER  -

TY  - JOUR
AU  - Bottacini, F.
AU  - Milani, C.
AU  - Turroni, F.
AU  - Sanchez, B.
AU  - Foroni, E.
AU  - Duranti, S.
AU  - Serafini, F.
AU  - Viappiani, A.
AU  - Strati, F.
AU  - Ferrarini, A.
AU  - Delledonne, M.
AU  - Henrissat, B.
AU  - Coutinho, P.
AU  - Fitzgerald, G.F.
AU  - Margolles, A.
AU  - van Sinderen, D.
AU  - Ventura, M.
TI  - Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut.
JO  - PLoS ONE
PY  - 2012
SP  - E44229
EP  - E44229
VL  - 7
AB  - Bifidobacteria are known as anaerobic/microaerophilic and fermentative
AB  - microorganisms, which commonly inhabit the gastrointestinal tract of various
AB  - animals and insects. Analysis of the 2,167,301 bp genome of Bifidobacterium
AB  - asteroides PRL2011, a strain isolated from the hindgut of Apis mellifera var.
AB  - ligustica, commonly known as the honey bee, revealed its predicted capability for
AB  - respiratory metabolism. Conservation of the latter gene clusters in various B.
AB  - asteroides strains enforces the notion that respiration is a common metabolic
AB  - feature of this ancient bifidobacterial species, which has been lost in currently
AB  - known mammal-derived Bifidobacterium species. In fact, phylogenomic based
AB  - analyses suggested an ancient origin of B. asteroides and indicates it as an
AB  - ancestor of the genus Bifidobacterium. Furthermore, the B. asteroides PRL2011
AB  - genome encodes various enzymes for coping with toxic products that arise as a
AB  - result of oxygen-mediated respiration.
ER  -

TY  - JOUR
AU  - Bottacini, F.
AU  - Morrissey, R.
AU  - Roberts, R.J.
AU  - James, K.
AU  - van Breen, J.
AU  - Egan, M.
AU  - Lambert, J.
AU  - van Limpt, K.
AU  - Knol, J.
AU  - Motherway, M.O.
AU  - van Sinderen, D.
TI  - Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 1860
EP  - 1877
VL  - 46
AB  - Bifidobacterium breve represents one of the most abundant bifidobacterial species in the
AB  - gastro-intestinal tract of breast-fed infants, where their presence is
AB  - believed to exert beneficial effects. In the present study whole genome
AB  - sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing
AB  - platform, combined with comparative genome analysis allowed the most extensive
AB  - genetic investigation of this taxon. Our findings demonstrate that genes encoding
AB  - Restriction/Modification (R/M) systems constitute a substantial part of the B.
AB  - breve variable gene content (or variome). Using the methylome data generated by
AB  - SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq)
AB  - and comparative genome analysis, we were able to detect methylation recognition
AB  - motifs and assign these to identified B. breve R/M systems, where in several
AB  - cases such assignments were confirmed by restriction analysis. Furthermore, we
AB  - show that R/M systems typically impose a very significant barrier to genetic
AB  - accessibility of B. breve strains, and that cloning of a
AB  - methyltransferase-encoding gene may overcome such a barrier, thus allowing future
AB  - functional investigations of members of this species.
ER  -

TY  - JOUR
AU  - Bottacini, F.
AU  - O'Connell-Motherway, M.
AU  - Casey, E.
AU  - McDonnell, B.
AU  - Mahony, J.
AU  - Ventura, M.
AU  - van Sinderen, D.
TI  - Discovery of a conjugative megaplasmid in Bifidobacterium breve.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 166
EP  - 176
VL  - 81
AB  - Bifidobacterium breve is a common and sometimes very abundant inhabitant of the human gut.
AB  - Genome sequencing of B. breve JCM 7017 revealed the presence of an extrachromosomal element,
AB  - designated pMP7017 consisting of more than 190 kb, thus representing the first reported
AB  - bifidobacterial megaplasmid. In silico characterization of this element revealed several
AB  - genomic features supporting a stable establishment of the megaplasmid in its host, illustrated
AB  - by predicted CRISPR-Cas functions that are known to protect the host against intrusion of
AB  - foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer
AB  - apparatus and consistent with this notion we demonstrate conjugal transfer of pMP7017 to
AB  - representative strains of B. breve and B. longum subsp.
AB  - longum. We furthermore demonstrate the presence of a megaplasmid with homology to
AB  - pMP7017 in three B. longum subsp. longum strains.
ER  -

TY  - JOUR
AU  - Bottacini, F.
AU  - O'Connell-Motherway, M.
AU  - Kuczynski, J.
AU  - O'Connell, K.J.
AU  - Serafini, F.
AU  - Duranti, S.
AU  - Milani, C.
AU  - Turroni, F.
AU  - Lugli, G.A.
AU  - Zomer, A.
AU  - Zhurina, D.
AU  - Riedel, C.
AU  - Ventura, M.
AU  - van Sinderen, D.
TI  - Comparative genomics of the Bifidobacterium breve taxon.
JO  - BMC Genomics
PY  - 2014
SP  - 170
EP  - 170
VL  - 15
AB  - BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the
AB  - gastrointestinal tract (GIT) of a broad range of hosts, where their presence is
AB  - positively correlated with the host's health status. In this study, we assessed
AB  - the genomes of thirteen representatives of Bifidobacterium breve, which is not
AB  - only a frequently encountered component of the (adult and infant) human gut
AB  - microbiota, but can also be isolated from human milk and vagina. RESULTS: In
AB  - silico analysis of genome sequences from thirteen B. breve strains isolated from
AB  - different environments (infant and adult faeces, human milk, human vagina) shows
AB  - that the genetic variability of this species principally consists of hypothetical
AB  - genes and mobile elements, but, interestingly, also genes correlated with the
AB  - adaptation to host environment and gut colonization. These latter genes specify
AB  - the biosynthetic machinery for sortase-dependent pili and exopolysaccharide
AB  - production, as well as genes that provide protection against invasion of foreign
AB  - DNA (i.e. CRISPR loci and restriction/modification systems), and genes that
AB  - encode enzymes responsible for carbohydrate fermentation. Gene-trait matching
AB  - analysis showed clear correlations between known metabolic capabilities and
AB  - characterized genes, and it also allowed the identification of a gene cluster
AB  - involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS: Genome
AB  - analysis of thirteen representatives of the B. breve species revealed that the
AB  - deduced pan-genome exhibits an essentially close trend. For this reason our
AB  - analyses suggest that this number of B. breve representatives is sufficient to
AB  - fully describe the pan-genome of this species. Comparative genomics also
AB  - facilitated the genetic explanation for differential carbon source utilization
AB  - phenotypes previously observed in different strains of B. breve.
ER  -

TY  - JOUR
AU  - Bottagisio, M.
AU  - Soggiu, A.
AU  - Lovati, A.B.
AU  - Toscano, M.
AU  - Piras, C.
AU  - Romano, C.L.
AU  - Bonizzi, L.
AU  - Roncada, P.
AU  - Drago, L.
TI  - Draft Genome Sequence of Staphylococcus epidermidis Clinical Strain GOI1153754-03-14 Isolated from an Infected Knee Prosthesis.
JO  - Genome Announcements
PY  - 2017
SP  - e00378
EP  - e00317
VL  - 5
AB  - We announce the draft genome sequence of Staphylococcus epidermidis clinical strain
AB  - GOI1153754-03-14, isolated from an infected orthopedic prosthesis. The
AB  - reported genomic sequence will provide valuable information concerning the
AB  - mechanisms of the biofilm formation on metallic implants.
ER  -

TY  - JOUR
AU  - Botterman, J.
AU  - Zabeau, M.
TI  - High-level production of the EcoRI endonuclease under the control of the pL promoter of bacteriophage lambda.
JO  - Gene
PY  - 1985
SP  - 229
EP  - 239
VL  - 37
AB  - Escherichia coli strains overproducing the EcoRI restriction endonuclease have
AB  - been constructed, using lambda pL promoter expression vectors.  In a first step
AB  - we constructed endRI::lacZ gene fusions by fusing the N-terminal part of the
AB  - endRI gene with a lacZ gene fragment, whereafter the hybrid gene was positioned
AB  - randomly under the control of the pL promoter to optimize the level of
AB  - expression.  These plasmids direct the synthesis of large amounts of fusion
AB  - protein approaching 30% of the total cellular protein content.  In most cases
AB  - the overproduced protein forms enzymatically inactive intracellular aggregates.
AB  - The position of the promoter in front of the hybrid gene had little effect on
AB  - the level of expression, except in fusions directly affecting the
AB  - ribosome-binding site (RBS).  In a second step, several of these promoter-gene
AB  - configurations were used to reconstruct the intact endRI gene in appropriate
AB  - hosts producing EcoRI methylase and cI-coded repressor.  The levels of EcoRI
AB  - endonuclease overproduction were similar to that obtained for the corresponding
AB  - fusion protein, despite the fourfold difference in protein size.  Intracellular
AB  - precipitation was also observed with the overproduced EcoRI endonuclease.
ER  -

TY  - JOUR
AU  - Botterman, J.
AU  - Zabeau, M.
TI  - High-level production of the restriction endonucleases EcoRI and EcoRV in Escherichia coli.
JO  - Arch. Int. Physiol. Biochim.
PY  - 1985
SP  - S38
EP  - S38
VL  - 93
AB  - Type II restriction and modification systems constitute an attractive system for analysis of
AB  - sequence-specific DNA-protein interaction.  These systems comprise a site-specific
AB  - endonuclease, which recognizes short target sequences in DNA at which they produce double
AB  - stranded cleavages, and a companion methylase, which specifically modifies this target
AB  - sequence to protect the host's DNA against degradation by the endonuclease.  However, the
AB  - limited available quantitites and elaborate purification procedures of these proteins hinder
AB  - biochemical and crystallographic studies.  The EcoRI and EcoRV restriction and modification
AB  - system have been cloned and characterized.  The development of a versatile plasmid expression
AB  - vector system based on the strong pL and pR promoters which are negatively regulated by the cI
AB  - repressor of phage lambda, made it possible to construct strains overproducing the enzymes.
AB  - The expression can be experimentally controlled in strains producing a temperature-sensitive
AB  - repressor (cIts), which is readily switched off and on at respectively low (28C) and high
AB  - temperatures (42C).  Since restriction endonucleases are potentially lethal to the cell, a
AB  - strategy was developed in which the expression of the EcoRI endonuclease (endRI) was first
AB  - optimized in an inactive form: an endRI-lacZ hybrid gene was randomly positioned downstream
AB  - from the pL promoter.  Optimal promoter-gene configurations were used to reconstruct the
AB  - intact gene under pL promoter control in appropriate hosts producing EcoRI methylase and cI
AB  - repressor.  Production levels of the EcoRI endonuclease reached 30% total cellular protein
AB  - content upon temperature induction, yielding after purification 5mg/g cells pure active
AB  - enzyme. Similar optimization of the expression of the EcoRV endonuclease yielded only moderate
AB  - levels of synthesis (2-5% total cellular protein content), which was nonetheless useful for
AB  - purification (1mg/g cells).  Further improvements of the ribosome binding site gave better
AB  - production.  Moreover, deletion of a putative regulatory signal downstream of the gene led to
AB  - increased levels of enzyme synthesis and indicated a possible mechanism for regulation of
AB  - prokaryotic gene expression, in which protein synthesis is modulated at the level of
AB  - translation initiation. (1) J. Botterman and M. Zabeau, Gene, in press. (2) J. Botterman, D.
AB  - DeBuyser, J. Spriet, M. Zabeau and G. Vansteenkiste, Biotechnology and Bioengineering, in
AB  - press. (3) L. Bougueleret, M. Tenchini, J. Botterman and M. Zabeau, Nucl. Acids Res., in
AB  - press. (4) J. Botterman, E. DeAlmeida, L. Bougueleret and M. Zabeau, UCLA Symposia on
AB  - Molecular and Cellular Biology 1985.
ER  -

TY  - JOUR
AU  - Bouam, A.
AU  - Levasseur, A.
AU  - Bonnet, M.
AU  - Borand, L.
AU  - Van Goethem, C.
AU  - Drancourt, M.
AU  - Godreuil, S.
TI  - Complete Genome Sequence of Mycobacterium sp. Strain 3519A.
JO  - Genome Announcements
PY  - 2018
SP  - e01565
EP  - e01517
VL  - 6
AB  - Mycobacterium sp. strain 3519A is a nontuberculous mycobacterium isolated from sputum from a
AB  - Cambodian patient with a pulmonary infection. We report here the
AB  - first complete 7.3-Mbp-long genome sequence of Mycobacterium sp. 3519A with
AB  - 66.35% GC content, encoding 7,029 protein-coding genes, 50 tRNAs, and 5 rRNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Bouam, A.
AU  - Levasseur, A.
AU  - Bonnet, M.
AU  - Borand, L.
AU  - Van Goethem, C.
AU  - Drancourt, M.
AU  - Godreuil, S.
TI  - Complete Genome Sequence of Mycobacterium sp. Strain 4858.
JO  - Genome Announcements
PY  - 2018
SP  - e01604
EP  - e01617
VL  - 6
AB  - Mycobacterium sp. strain 4858 is a nontuberculous mycobacterium isolated from sputum in a
AB  - Cambodian patient with a pulmonary infection. We report the first
AB  - complete 5.6-Mbp-long genome sequence of Mycobacterium strain 4858, with 68.24%
AB  - GC content, carrying 5,255 protein-coding genes, 47 tRNAs, and 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Bouam, A.
AU  - Levasseur, A.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium porcinum CSURP1564.
JO  - Genome Announcements
PY  - 2018
SP  - e00291
EP  - e00218
VL  - 6
AB  - Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for
AB  - opportunistic infections. The 7,025,616-bp draft genome of M.
AB  - porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding
AB  - genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its
AB  - assignment to the Mycobacterium fortuitum complex.
ER  -

TY  - JOUR
AU  - Bouam, A.
AU  - Levasseur, A.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium setense CSUR47.
JO  - Genome Announcements
PY  - 2018
SP  - e01415
EP  - e01417
VL  - 6
AB  - Mycobacterium setense CSUR47 is a rapidly growing Mycobacterium species strain isolated from
AB  - pus collected from a left maxillary sinus in Marseille, France.
AB  - Here, we report the complete 6,278,097-bp genome sequence of M. setense CSUR47,
AB  - which exhibits a 66.40% GC content and encodes 5,863 protein-coding genes, 48
AB  - tRNAs, and 9 rRNAs.
ER  -

TY  - JOUR
AU  - Bouam, A.
AU  - Robert, C.
AU  - Croce, O.
AU  - Levasseur, A.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium boenickei CIP 107829.
JO  - Genome Announcements
PY  - 2017
SP  - e00292
EP  - e00217
VL  - 5
AB  - Mycobacterium boenickei is a rapidly growing mycobacterium isolated for the first time from a
AB  - leg wound in the United States. Its 6,506,908-bp draft genome
AB  - exhibits a 66.77% G+C content, 6,279 protein-coding genes, and 59 predicted RNA
AB  - genes. In silico DNA-DNA hybridization confirms its assignment to the
AB  - Mycobacterium fortuitum complex.
ER  -

TY  - JOUR
AU  - Bouam, A.
AU  - Robert, C.
AU  - Levasseur, A.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium colombiense.
JO  - Genome Announcements
PY  - 2017
SP  - e00119
EP  - e00117
VL  - 5
AB  - Mycobacterium colombiense is a rapidly growing mycobacterium initially isolated from the blood
AB  - of an HIV-positive patient in Colombia. Its 5,854,893-bp draft
AB  - genome exhibits a G+C content of 67.64%, 5,233 protein-coding genes, and 54
AB  - predicted RNA genes.
ER  -

TY  - JOUR
AU  - Bouchard, D.
AU  - Peton, V.
AU  - Almeida, S.
AU  - Le Marechal, C.
AU  - Miyoshi, A.
AU  - Azevedo, V.
AU  - Berkova, N.
AU  - Rault, L.
AU  - Francois, P.
AU  - Schrenzel, J.
AU  - Even, S.
AU  - Hernandez, D.
AU  - Le Loir, Y.
TI  - Genome Sequence of Staphylococcus aureus Newbould 305, a Strain Associated with Mild Bovine Mastitis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6292
EP  - 6293
VL  - 194
AB  - Staphylococcus aureus is a major etiological agent of mastitis in ruminants. We report here
AB  - the genome sequence of bovine strain Newbould 305, isolated in the
AB  - 1950s in a case of bovine mastitis and now used as a model strain able to
AB  - reproducibly induce chronic mastitis in cows.
ER  -

TY  - JOUR
AU  - Bouche, J.P.C.
TI  - Isolation and in vitro restriction of unmethylated DNA from Escherichia coli K.
JO  - Biochim. Biophys. Acta
PY  - 1974
SP  - 135
EP  - 142
VL  - 366
AB  - A previous report (Bouche, J.P.C. (1973) J. Bacteriol. 115, 752-761) has
AB  - presented evidence that a part of the DNA synthesized in a methionine starved
AB  - dnaB mutant after return to the permissive temperature is completely or almost
AB  - completely unmethylated.  We describe here the isolation of this DNA, and
AB  - either its methylation in vitro by Escherichia coli K methylases, or its
AB  - restriction by endonucleases K and RI from E. coli, and dII from Haemophilus
AB  - influenzae.  These experiments show that this DNA not only lacks methylation
AB  - due to the general (non-modifying) methylases, but also due to the K
AB  - modifiction methylase.  Furthermore, the levels of restriction of this DNA were
AB  - found to be equivalent to those of an E. coli K DNA deficient only in
AB  - modification.  We conclude that there is no significant overlap in vitro
AB  - between the sequence specificities of major non-modifying methylases and of the
AB  - endonucleases tested.
ER  -

TY  - JOUR
AU  - Boucher, I.
AU  - Emond, E.
AU  - Parrot, M.
AU  - Moineau, S.
TI  - DNA sequence analysis of three Lactococcus lactis plasmids encoding phage resistance mechanisms.
JO  - J. Dairy Sci.
PY  - 2001
SP  - 1610
EP  - 1620
VL  - 84
AB  - The three Lactococcus lactis plasmids pSRQ700, pSRQ800, and pSRQ900 encode the previously
AB  - described anti-phage resistance mechanisms
AB  - LlaDCHI, AbiK, and AbiQ, respectively. Since these plasmids are likely
AB  - to be introduced into industrial Lactococcus lactis strains used to
AB  - manufacture commercial fermented dairy products, their complete DNA
AB  - sequences were determined and analyzed. The plasmids pSRQ700 (7784 bp),
AB  - pSRQ800 (7858 bp), and pSRQ900 (10,836 bp) showed a similar genetic
AB  - organization including a common lactococcal theta-type replicon. A
AB  - second replication module showing features of the pMV158 family of
AB  - rolling circle replicons was also found on pSRQ700. The theta
AB  - replication regions of the three plasmids were associated with two
AB  - additional coding regions, one of which encodes for HsdS, the
AB  - specificity subunit of the type I restriction/modification system. When
AB  - introduced into L. lactis IL1403, the HsdS of pSRQ800 and pSRQ900
AB  - conferred a weak resistance against phage P008 (936 species). These
AB  - results indicated that both HsdS subunits can complement the
AB  - chromosomally encoded type I restriction/modification system in IL1403.
AB  - The genes involved in the phage resistance systems LlaDCHI, AbiK, and
AB  - AbiQ were found in close proximity to and downstream of the replication
AB  - modules. In pSRQ800 and pSRQ900, transfer origins and putative tyrosine
AB  - recombinases were found upstream of the theta replicons. Genes encoding
AB  - recombination proteins were also found on pSRQ700. Finally, open
AB  - reading frames associated with bacteriocin production were found on
AB  - pSRQ900, but no anti-lactococcal activity was detected. Based on our
AB  - current knowledge, these three plasmids are safe and suitable for
AB  - food-grade applications.
ER  -

TY  - JOUR
AU  - Boucher, Y.
AU  - Nesbo, C.L.
AU  - Joss, M.J.
AU  - Robinson, A.
AU  - Mabbutt, B.C.
AU  - Gillings, M.R.
AU  - Doolittle, W.F.
AU  - Stokes, H.W.
TI  - Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio.
JO  - BMC Evol. Biol.
PY  - 2006
SP  - 3
EP  - 3
VL  - 6
AB  - ABSTRACT: BACKGROUND: Integrons are genetic elements capable of the
AB  - acquisition, rearrangement and expression of genes contained in gene
AB  - cassettes. Gene cassettes generally consist of a promoterless gene
AB  - associated with a recombination site known as a 59-base element (59-be).
AB  - Multiple insertion events can lead to the assembly of large
AB  - integron-associated cassette arrays. The most striking examples are found
AB  - in Vibrio, where such cassette arrays are widespread and can range from 30
AB  - kb to 150 kb. Besides those found in completely sequenced genomes, no such
AB  - array has yet been recovered in its entirety. We describe an approach to
AB  - systematically isolate, sequence and annotate large integron gene cassette
AB  - arrays from bacterial strains. RESULTS: The complete Vibrio sp. DAT722
AB  - integron cassette array was determined through the streamlined approach
AB  - described here. To place it in an evolutionary context, we compare the
AB  - DAT722 array to known vibrio arrays and performed phylogenetic analyses
AB  - for all of its components (integrase, 59-be sites, gene cassette encoded
AB  - genes). It differs extensively in terms of genomic context as well as gene
AB  - cassette content and organization. The phylogenetic tree of the 59-be
AB  - sites collectively found in the Vibrio gene cassette pool suggests
AB  - frequent transfer of cassettes within and between Vibrio species, with
AB  - slower transfer rates between more phylogenetically distant relatives. We
AB  - also identify multiple cases where non-integron chromosomal genes seem to
AB  - have been assembled into gene cassettes and others where cassettes have
AB  - been inserted into chromosomal locations outside integrons. CONCLUSIONS:
AB  - Our systematic approach greatly facilitates the isolation and annotation
AB  - of large integrons gene cassette arrays. Comparative analysis of the
AB  - Vibrio sp. DAT722 integron obtained through this approach to those found
AB  - in other vibrios confirms the role of this genetic element in promoting
AB  - lateral gene transfer and suggests a high rate of gene gain/loss relative
AB  - to most other loci on vibrio chromosomes. We identify a relation between
AB  - the phylogenetic distance separating two species and the rate at which
AB  - they exchange gene cassettes, interactions between the non-mobile portion
AB  - of bacterial genomes and the vibrio gene cassette pool as well as
AB  - intragenomic translocation events of integrons in vibrios.
ER  -

TY  - JOUR
AU  - Bougueleret, L.
AU  - Schwarzstein, M.
AU  - Tsugita, A.
AU  - Zabeau, M.
TI  - Characterization of the genes coding for the EcoRV restriction and modification system of Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 3659
EP  - 3677
VL  - 12
AB  - A plasmid encoding the recently described Eco RV restriction and modification system has been
AB  - isolated and characterized.  This plasmid, pLB1, is 6.2 kb long and carries only the EcoRV
AB  - genes.  A subclone of 3 kb has been inserted in pBR322.  The relative positions of the
AB  - endonuclease and the methylase genes were determined by the construction of a set of
AB  - overlapping deletions generated by Bal31 resection.  The DNA sequence of a 2.2 kb fragment
AB  - containing the two genes was determined.  The two genes are transcribed divergently from a 310
AB  - bp region and the assignment of the coding region has been confirmed by direct aminoacid
AB  - sequence analysis.  Possible mechanisms of the regulation of the endonuclease gene expression
AB  - at the translational level are proposed and discussed.
ER  -

TY  - JOUR
AU  - Bougueleret, L.
AU  - Tenchini, M.L.
AU  - Botterman, J.
AU  - Zabeau, M.
TI  - Overproduction of the EcoRV endonuclease and methylase.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 3823
EP  - 3839
VL  - 13
AB  - Strains overproducing the EcoRV endonuclease and methylase have been obtained by inserting
AB  - each of the two genes in expression vectors containing the lambda PL promoter.  The methylase
AB  - is overproduced to a level reaching 5-10% of the total cellular proteins, which represents a
AB  - 50-100 fold increase.  A 30 fold overproduction of endonuclease was achieved by randomly
AB  - positioning the EcoRV gene downstream of the lambda PL promoter.  The situation in the
AB  - endonuclease overproducing clone resembles that encountered in maxi-cells.  The strains
AB  - described here allowed a quick purification of both enzymes in sufficient amounts for
AB  - crystallisation attempts.
ER  -

TY  - JOUR
AU  - Boujelben, I.
AU  - Yarza, P.
AU  - Almansa, C.
AU  - Villamor, J.
AU  - Maalej, S.
AU  - Anton, J.
AU  - Santos, F.
TI  - Virioplankton community structure in Tunisian solar salterns.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 7429
EP  - 7437
VL  - 78
AB  - The microbial community inhabiting Sfax solar salterns on the east coast of
AB  - Tunisia has been studied by means of different molecular and culture-dependent
AB  - tools that have unveiled the presence of novel microbial groups as well as a
AB  - community structure different from that of other coastal hypersaline
AB  - environments. We have focused on the study of the viral assemblages of these
AB  - salterns and their changes along the salinity gradient and over time. Viruses
AB  - from three ponds (C4, M1, and TS) encompassing salinities from moderately
AB  - hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in
AB  - May and October 2009 and analyzed by transmission electron microscopy (TEM) and
AB  - pulsed-field gel electrophoresis (PFGE). Additionally, for all three October
AB  - samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end
AB  - sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios,
AB  - increased along the salinity gradient, with around 10(10) virus-like particles
AB  - (VLPs)/ml in close-to-saturation ponds, which represents the highest viral
AB  - concentration reported so far for aquatic systems. Four distinct morphologies
AB  - could be observed with TEM (spherical, tailed, spindled, and filamentous) but
AB  - with various proportions in the different samples. Metagenomic analyses indicated
AB  - that every pond harbored a distinct viral assemblage whose G+C content could be
AB  - roughly correlated with that of the active part of the microbial community that
AB  - may have constituted the putative hosts. As previously reported for hypersaline
AB  - metaviromes, most sequences did not have matches in the databases, although some
AB  - were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide
AB  - frequency analyses indicated that (i) factors additional to salinity could be
AB  - structuring viral communities and (ii) every metavirome had unique gene contents
AB  - and dinucleotide frequencies. Comparison with hypersaline metaviromes available
AB  - in the databases indicated that the viral assemblages present in
AB  - close-to-saturation environments located thousands of kilometers apart presented
AB  - some common traits among them in spite of their differences regarding the
AB  - putative hosts. A small core metavirome for close-to-saturation systems was found
AB  - that contained 7 sequences of around 100 nucleotides (nt) whose function was not
AB  - hinted at by in silico search results, although it most likely represents
AB  - properties essential for hyperhalophilic viruses.
ER  -

TY  - JOUR
AU  - Boukerb, A.M.
AU  - Marti, R.
AU  - Cournoyer, B.
TI  - Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade.
JO  - Genome Announcements
PY  - 2015
SP  - e01366
EP  - e01315
VL  - 3
AB  - Draft genome sequences of three P. aeruginosa strains from the PA7 clade are presented here.
AB  - Their lengths are 6.36 (EML528), 6.44 (EML545), and 6.33 Mb
AB  - (EML548). Comparisons with the PA7 genome showed 5,113 conserved coding sequences
AB  - (CDSs), and significant numbers of strain-specific CDSs. Their analysis will
AB  - improve our understanding of this highly divergent clade.
ER  -

TY  - JOUR
AU  - Bourbonniere, M.
AU  - Nalbantoglu, J.
TI  - The restriction enzyme AlwNI is blocked by overlapping methylation.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4774
EP  - 4774
VL  - 19
AB  - Most strains of E. coli contain two sequence specific methylases, Dam and Dcm. The adenine
AB  - residue of the sequence GATC is methylated at the N6 position by the Dam methylase whereas the
AB  - Dcm methylase recognizes the sequences CC(A/T)GG methylating the internal cytosine at the C5
AB  - position. The commercially available restriction enzyme AlwNI (New England Biolabs) has a
AB  - recognition sequence CAGNNN^CTG and is a useful enzyme for creating deletions. One site
AB  - AGCCCCTGgcaa is a potential dcm site and AlwNI cleavage at this site is blocked by dcm
AB  - methylation.
ER  -

TY  - JOUR
AU  - Bourchis, D.
AU  - Bestor, T.H.
TI  - Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L.
JO  - Nature
PY  - 2004
SP  - 96
EP  - 99
VL  - 431
AB  - Mammalian genomes employ heritable cytosine methylation in the long-term silencing of
AB  - retrotransposons and genes subject to genomic imprinting and X chromosome inactivation. Little
AB  - is known of the mechanisms that direct cytosine methylation to specific sequences. Here we
AB  - show that DNA methyltransferase 3-like (Dnmt3L (ref. 1)) is expressed in testes during a brief
AB  - perinatal period in the non-dividing precursors of spermatogonial stem cells at a stage where
AB  - retrotransposons undergo de novo methylation. Deletion of the Dnmt3L gene prevented the de
AB  - novo methylation of both long-terminal-repeat (LTR) and non-LTR retrotransposons, which were
AB  - transcribed at high levels in spermatogonia and spermatocytes. Loss of Dnmt3L from early germ
AB  - cells also caused meiotic failure in spermatocytes, which do not express Dnmt3L. Whereas
AB  - dispersed repeated sequences were demethylated in mutant germ cells, tandem repeats in
AB  - pericentric regions were methylated normally. This result indicates that the Dnmt3L protein
AB  - might have a function in the de novo methylation of dispersed repeated sequences in a
AB  - premeiotic genome scanning process that occurs in male germ cells at about the time of birth.
ER  -

TY  - JOUR
AU  - Bourchis, D.
AU  - Xu, G.-L.
AU  - Lin, C.-S.
AU  - Bollman, B.
AU  - Bestor, T.H.
TI  - Dnmt3L and the establishment of maternal genomic imprints.
JO  - Science
PY  - 2001
SP  - 2536
EP  - 2539
VL  - 294
AB  - Complementary sets of genes are epigenetically silenced in male
AB  - and female gametes in a process termed genomic imprinting. The Dnmt3L gene
AB  - is expressed during gametogenesis at stages where genomic imprints are
AB  - established. Targeted disruption of Dnmt3L caused azoospermia in homozygous
AB  - males, and heterozygous progeny of homozygous females died before
AB  - midgestation. Bisulfite genomic sequencing of DNA from oocytes and embryos
AB  - showed that removal of Dnmt3L prevented methylation of sequences that are
AB  - normally maternally methylated. The defect was specific to imprinted
AB  - regions, and global genome methylation levels were not affected. Lack of
AB  - maternal methylation imprints in heterozygous embryos derived from
AB  - homozygous mutant oocytes caused biallelic expression of genes that are
AB  - normally expressed only from the allele of paternal origin. The key
AB  - catalytic motifs characteristic of DNA cytosine methyltransferases have
AB  - been lost from Dnmt3L, and the protein is more likely to act as a regulator
AB  - of imprint establishment than as a DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Bourges, A.C.
AU  - Torres, M.O.E.
AU  - Ghosh, A.
AU  - Tadesse, W.M.
AU  - Declerck, N.
AU  - Aertsen, A.
AU  - Royer, C.A.
TI  - High pressure activation of the Mrr restriction endonuclease in Escherichia coli  involves tetramer dissociation.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 5323
EP  - 5332
VL  - 45
AB  - A sub-lethal hydrostatic pressure (HP) shock of approximately 100 MPa elicits a RecA-dependent
AB  - DNA damage (SOS) response in Escherichia coli K-12, despite the
AB  - fact that pressure cannot compromise the covalent integrity of DNA. Prior screens
AB  - for HP resistance identified Mrr (Methylated adenine Recognition and
AB  - Restriction), a Type IV restriction endonuclease (REase), as instigator for this
AB  - enigmatic HP-induced SOS response. Type IV REases tend to target modified DNA
AB  - sites, and E. coli Mrr activity was previously shown to be elicited by expression
AB  - of the foreign M.HhaII Type II methytransferase (MTase), as well. Here we
AB  - measured the concentration and stoichiometry of a functional GFP-Mrr fusion
AB  - protein using in vivo fluorescence fluctuation microscopy. Our results
AB  - demonstrate that Mrr is a tetramer in unstressed cells, but shifts to a dimer
AB  - after HP shock or co-expression with M.HhaII. Based on the differences in
AB  - reversibility of tetramer dissociation observed for wild-type GFP-Mrr and a
AB  - catalytic mutant upon HP shock compared to M.HhaII expression, we propose a model
AB  - by which (i) HP triggers Mrr activity by directly pushing inactive Mrr tetramers
AB  - to dissociate into active Mrr dimers, while (ii) M.HhaII triggers Mrr activity by
AB  - creating high affinity target sites on the chromosome, which pull the equilibrium
AB  - from inactive tetrameric Mrr toward active dimer.
ER  -

TY  - JOUR
AU  - Bourgogne, A. et al.
TI  - Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF.
JO  - Genome Biology
PY  - 2008
SP  - R110
EP  - R110
VL  - 9
AB  - BACKGROUND: Enterococcus faecalis has emerged as a major hospital
AB  - pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF,
AB  - which is commonly used for molecular manipulation and virulence studies.
AB  - RESULTS: The 2,739,625 base pair chromosome of OG1RF was found to contain
AB  - approximately 232 kilobases unique to this strain compared to V583, the
AB  - only publicly available sequenced strain. Almost no mobile genetic
AB  - elements were found in OG1RF. The 64 areas of divergence were classified
AB  - into three categories. First, OG1RF carries 39 unique regions, including 2
AB  - CRISPR loci and a new WxL locus. Second, we found nine replacements where
AB  - a sequence specific to V583 was substituted by a sequence specific to
AB  - OG1RF. For example, the iol operon of OG1RF replaces a possible prophage
AB  - and the vanB transposon in V583. Finally, we found 16 regions that were
AB  - present in V583 but missing from OG1RF, including the proposed
AB  - pathogenicity island, several probable prophages, and the cpsCDEFGHIJK
AB  - capsular polysaccharide operon. OG1RF was more rapidly but less frequently
AB  - lethal than V583 in the mouse peritonitis model and considerably
AB  - outcompeted V583 in a murine model of urinary tract infections.
AB  - CONCLUSION: E. faecalis OG1RF carries a number of unique loci compared to
AB  - V583, but the almost complete lack of mobile genetic elements demonstrates
AB  - that this is not a defining feature of the species. Additionally, OG1RF's
AB  - effects in experimental models suggest that mediators of virulence may be
AB  - diverse between different E. faecalis strains and that virulence is not
AB  - dependent on the presence of mobile genetic elements.
ER  -

TY  - JOUR
AU  - Bouriotis, V.
AU  - Zafeiropoulos, A.
AU  - Clonis, Y.D.
TI  - High-performance liquid chromatography for the purification of restriction endonucleases, application to BanII, SacI, and SphI.
JO  - Anal. Biochem.
PY  - 1987
SP  - 127
EP  - 134
VL  - 160
AB  - Conventional fractionation methods are time consuming, thus they prolong the
AB  - time required to process low-stability restriction enzymes.  We now report a
AB  - rapid and effective two-step chromatographic method that affords high purity
AB  - endonucleases in a short time.  Accordingly, an inexpensive chromatographic
AB  - adsorbent such as phosphocellulose or dyed agarose in the first step is coupled
AB  - to a high-performance ion exchanger, namely, MonoQ, in the second step.  The
AB  - purification schemes reported here are now in routine use to prepare
AB  - high-purity BanII, SacI, and SphI as judged by the "overdigestion" and
AB  - "cut-ligate-recut" stringent quality tests.
ER  -

TY  - JOUR
AU  - Bourniquel, A.A.
AU  - Bickle, T.A.
TI  - Complex restriction enzymes: NTP-driven molecular motors.
JO  - Biochimie
PY  - 2002
SP  - 1047
EP  - 1059
VL  - 84
AB  - Survival is assuredly the prime directive for all living organisms either as individuals or as
AB  - a species. One of the main challenges encountered by bacterial populations is the danger of
AB  - bacteriophage attacks, since infection of a single bacterium may rapidly propagate, decimating
AB  - the entire population. In order to protect themselves against this acute threat, bacteria have
AB  - developed an array of defence mechanisms, which range from preventing the infection itself via
AB  - interference with bacteriophage adsorption to the cell surface and prevention of phage DNA
AB  - injection, to degradation of the injected phage DNA. This last defence mechanism is catalysed
AB  - by the bacterial restriction-modification (R-M) systems, and in particular, by nucleoside
AB  - 5'-triphosphate (NTP)-dependent restriction enzymes, e.g. type I and type III R-M systems or
AB  - the modification-dependent endonucleases. Type I and type III restriction systems have dual
AB  - properties. They may either act as methylases and protect the host's own DNA against
AB  - restriction by methylating specific residues, or they catalyse ATP-dependent endonuclease
AB  - activity so that invading foreign DNA lacking the host-specific methylation is degraded. These
AB  - defence mechanism systems are further complemented by the presence of methylation-dependent,
AB  - GTP-dependent endonucleases that restricts specifically methylated DNA. Although all three
AB  - types of endonucleases are structurally very different, they share a common functional
AB  - mechanism. They recognise and bind to specific DNA sequences but do not cleave DNA within
AB  - those target sites. They belong to the general class of DNA motor proteins, which use the free
AB  - energy associated with nucleoside 5'-triphosphate hydrolysis to translocate DNA so that the
AB  - subsequent DNA cleavage event occurs at a distance from the endonuclease recognition site.
AB  - Moreover, DNA cleavage appears to be a random process triggered upon stalling of the DNA
AB  - translocation process and requiring dimerisation of the bound endonucleases for a concerted
AB  - break of both DNA strands. In this review, we present a detailed description and analysis of
AB  - the functional mechanism of the three known NTP-dependent restriction systems: type I and type
AB  - III restriction-modification enzymes, as well as the methylation-dependent McrBC endonuclease.
ER  -

TY  - JOUR
AU  - Bourniquel, A.A.
AU  - Casey, M.G.
AU  - Mollet, B.
AU  - Pridmore, R.D.
TI  - DNA sequence and functional analysis of Lactobacillus delbrueckii subsp. lactis plasmids pN42 and pJBL2.
JO  - Plasmid
PY  - 2002
SP  - 153
EP  - 157
VL  - 47
AB  - The plasmids pN42 and pJBL2 were isolated from the Lactobacillus delbrueckii subsp. lactis
AB  - strains NCC88 and JCL414. DNA sequence determination and bioinformatic analysis revealed a
AB  - strikingly conserved genetic organization containing five major, highly conserved open reading
AB  - frames (ORFs). Transformation studies indicated that ORF2 (consisting of a primase fused to a
AB  - replicative DNA helicase), ori, and ORF3 constitute the minimal requirements for replication
AB  - of pN42 in the heterologous host Lactococcus lactis. The ORF1's are predicted to encode type
AB  - I restriction-modification (R-M) system HsdS subunits with different specificities on either
AB  - plasmid, suggesting that these plasmids may be involved in host defense by expanding their
AB  - host R-M system repertoire. These plasmids constitute the basis for the construction of novel
AB  - L. delbrueckii vectors.
ER  -

TY  - JOUR
AU  - Bourniquel, A.A.
AU  - Mollet, B.
AU  - Bickle, T.A.
TI  - Type I restriction-modification systems from Lactobacillus delbrueckii subsp. lactis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 238
EP  - 238
VL  - 102
AB  - Background: Lactobacillus delbrueckii subsp. lactis is a lactic acid bacterium used worldwide
AB  - for the production of Swiss-type hard cheeses.
AB  - Whereas other dairy starters, e.g. Lactococcus lactis or Streptococcus
AB  - thermophilus, are highly susceptible to bacteriophage infections, very
AB  - few phages are known to target L. delbrueckii ssp. suggesting these
AB  - bacteria possess a very active and reliable/versatile endogenous
AB  - defense mechanism. Type I restriction-modification (R-M) systems are
AB  - acknowledged defense mechanisms that depend on the generation of novel
AB  - specificities for adaptability. Methods: Type I R-M hsd (host
AB  - specificity for DNA) gene clusters were isolated from two strains of L.
AB  - delbrueckii subsp. lactis, sequenced and characterized. In vivo
AB  - transcription of the identified genes was verified by Northern
AB  - blotting. The hsdR (restriction), hsdM (modification) and hsdS
AB  - (specificity of DNA binding) genes were cloned into expression vectors
AB  - for overexpression in Escherichia coli. The expressed proteins were
AB  - purified, tested for activity and their recognition sites determined.
AB  - Results: Both L. delbrueckii subsp. lactis strains examined possess
AB  - type I R-M systems. The two hsd clusters (apprx8 kb) share a similar
AB  - genetic organization consisting of: (i) the hsdR, hsdM and hsdS genes
AB  - coding for a type I restriction enzyme, (ii) a second hsdS gene with a
AB  - truncated 5'-end, and (iii) a gene similar to phage integrases. The
AB  - HsdR and HsdM snbunits on both strains are highly conserved (98%
AB  - identity), whereas the hsds genes code for subunits with different
AB  - specificities i.e. the two type I restriction enzymes have different
AB  - recognition sites. Conclusion: Until recently, research on type I R-M
AB  - systems focused on the enterobacteriaceae group in which hsd genes are
AB  - but slightly conserved in-between strains. In the gram-positive
AB  - bacterium L. delbrueckii subsp. lactis type I R-M genes are
AB  - well-conserved, genetic variability being limited to the DNA binding
AB  - domains of hsdS determining enzyme specificity. The presence of
AB  - truncated hsdS and integrases genes in the hsd clusters suggests that
AB  - novel specificities might be generated by domain shuffling.
ER  -

TY  - JOUR
AU  - Boussemaer, J.P.
AU  - Schrauwen, P.P.
AU  - Sourrouille, J.L.
AU  - Guy, P.
TI  - Multiple modification/restriction systems in lactic streptococci and their significance in defining a phage-typing system.
JO  - J. Dairy Res.
PY  - 1980
SP  - 401
EP  - 409
VL  - 47
AB  - The reactions between 6 strains of mesophilic lactic steptococci and their respective phages
AB  - were studied quantitatively. Of 30 nonhomologous reactions, the bacteria were fully sensitive
AB  - in 4 and restricted the phages in 23. A mathematical model was developed that was used to
AB  - identify at least 4 and probably 5 modification restriction (M/R) systems of which up to 3
AB  - were found in the same strain. The model was based on 24 measued values and correctly
AB  - predicted the values of 5 others. One of the 3 negative reactions was shown to be due to a
AB  - restriction beyond the limit of detection, a second was due to lysogeny or lack of adsorption,
AB  - but was shown to have the predicted value when the homologous phage was modified on the host
AB  - of the challenging phage. In the last reaction a measurable restriction was predicted, but
AB  - could not be proven by means of a modified phage. These results suggest M/R to be one of the
AB  - main defenses of the lactic streptococci against their phages. They explaim why host range is
AB  - not a useful criterion in the classification of phages and suggest a rational approach to the
AB  - definition of a starter rotation.
ER  -

TY  - JOUR
AU  - Boutibonnes, P.
TI  - Cell death in bacterial populations: caused or programmed?  Accepted or deliberate?
JO  - Med. Sci. (Paris)
PY  - 1997
SP  - 73
EP  - 80
VL  - 13
AB  - In bacterial cells, plasmids are stabilized by numerous different mechanisms.  Here we
AB  - describe three different ways which mediate plasmid maintenance by selectively killing plasmid
AB  - free cells.  In the first system, plasmid genes encode a stable toxic protein (or the stable
AB  - corresponding mRNA) and an unstable antidote (or a small unstable antisense RNA which inhibits
AB  - the translation of the messenger).  The expression of the lethality is regulated
AB  - post-translationally (e.g. ccd system from plasmid F in Escherichia coli) or
AB  - post-transcriptionally (e.g. hok system from plasmid R1 in E. coli).  In the second system
AB  - (e.g. rm genes of Pseudomonas aeruginosa R7) plasmid genes encode a stable type II restriction
AB  - enzyme and the unstable cognate methylase which offers protection from endonucleolytic attack
AB  - by the restriction enzyme.  The third system is composed of a complex operon (e.g. MccB17
AB  - system in E. coli) whose genes encode the synthesis and maturation of a cytotoxic protein and
AB  - for a polypeptide which confers resistance or immunity to the killer cell by an unknown
AB  - mechanism.  The plasmid-free cells are killed by the cytotoxic protein excreted by bacteria
AB  - carrying the plasmid.  The set of two or more genes carried by a plasmid responsible for the
AB  - lethal consequences of plasmid loss can be viewed as an addiction module or a selfish symbiote
AB  - according to Yarmolinsky and Naito, respectively; the loss of these genomic units lead the
AB  - cells to an unavoidable death.
ER  -

TY  - JOUR
AU  - Bowden, K.E.
AU  - Weigand, M.R.
AU  - Peng, Y.
AU  - Cassiday, P.K.
AU  - Sammons, S.
AU  - Knipe, K.
AU  - Rowe, L.A.
AU  - Loparev, V.
AU  - Sheth, M.
AU  - Weening, K.
AU  - Tondella, M.L.
AU  - Williams, M.M.
TI  - Genome Structural Diversity among 31 Bordetella pertussis Isolates from Two Recent U.S. Whooping Cough Statewide Epidemics.
JO  - mSphere
PY  - 2016
SP  - e00036
EP  - e00016
VL  - 1
AB  - During 2010 and 2012, California and Vermont, respectively, experienced statewide epidemics of
AB  - pertussis with differences seen in the demographic affected, case clinical presentation, and
AB  - molecular epidemiology of the circulating strains. To overcome limitations of the current
AB  - molecular typing methods for pertussis, we utilized whole-genome sequencing to gain a broader
AB  - understanding of how current circulating strains are causing large epidemics. Through the use
AB  - of combined next-generation sequencing technologies, this study compared de novo,
AB  - single-contig genome assemblies from 31 out of 33 Bordetella pertussis isolates collected
AB  - during two separate pertussis statewide epidemics and 2 resequenced vaccine strains. Final
AB  - genome architecture assemblies were verified with whole-genome optical mapping. Sixteen
AB  - distinct genome rearrangement profiles were observed in epidemic isolate genomes, all of which
AB  - were distinct from the genome structures of the two resequenced vaccine strains. These
AB  - rearrangements appear to be mediated by repetitive sequence elements, such as high-copy-number
AB  - mobile genetic elements and rRNA operons. Additionally, novel and previously identified single
AB  - nucleotide polymorphisms were detected in 10 virulence-related genes in the epidemic isolates.
AB  - Whole-genome variation analysis identified state-specific variants, and coding regions bearing
AB  - nonsynonymous mutations were classified into functional annotated orthologous groups.
AB  - Comprehensive studies on whole genomes are needed to understand the resurgence of pertussis
AB  - and develop novel tools to better characterize the molecular epidemiology of evolving B.
AB  - pertussis populations. IMPORTANCE Pertussis, or whooping cough, is the most poorly controlled
AB  - vaccine-preventable bacterial disease in the United States, which has experienced a resurgence
AB  - for more than a decade. Once viewed as a monomorphic pathogen, B. pertussis strains
AB  - circulating during epidemics exhibit diversity visible on a genome structural level,
AB  - previously undetectable by traditional sequence analysis using short-read technologies. For
AB  - the first time, we combine short- and long-read sequencing platforms with restriction optical
AB  - mapping for single-contig, de novo assembly of 31 isolates to investigate two geographically
AB  - and temporally independent U.S. pertussis epidemics. These complete genomes reshape our
AB  - understanding of B. pertussis evolution and strengthen molecular epidemiology toward one day
AB  - understanding the resurgence of pertussis.
ER  -

TY  - JOUR
AU  - Bowen, L.M.
AU  - Dupureur, C.M.
TI  - Investigation of restriction enzyme cofactor requirements: A relationship between metal ion properties and sequence specificity.
JO  - Biochemistry
PY  - 2003
SP  - 12643
EP  - 12653
VL  - 42
AB  - Restriction enzymes are important model systems for understanding the mechanistic
AB  - contributions of metal ions to nuclease activity. These
AB  - systems are unique in that they combine distinct functions which have been
AB  - shown to depend on metal ions: high-affinity DNA binding,
AB  - sequence-specific recognition of DNA, and Mg(II)-dependent phosphodiester
AB  - cleavage. While Ca(II) and Mn(II) are commonly used to promote DNA binding
AB  - and cleavage, respectively, the metal ion properties that are critical to
AB  - the support of these functions are not clear. To address this question, we
AB  - assessed the abilities of a series of metal ions to promote DNA binding,
AB  - sequence specificity, and cleavage in the representative PvuII
AB  - endonuclease. Among the metal ions tested [Ca(II), Sr(II), Ba(II),
AB  - Eu(III), Tb(III), Cd(II), Mn(II), Co(II), and Zn(II)], only Mn(II) and
AB  - Co(II) were similar enough to Mg(II) to support detectable cleavage
AB  - activity. Interestingly, cofactor requirements for the support of DNA
AB  - binding are much more permissive; the survey of DNA binding cofactors
AB  - indicated that Cd(II) and the heavier and larger alkaline earth metal ions
AB  - Sr(II) and Ba(II) were effective cofactors, stimulating DNA binding
AB  - affinity 20-200-fold. Impressively, the trivalent lanthanides Tb(III) and
AB  - Eu(III) promoted DNA binding as efficiently as Ca(II), corresponding to an
AB  - increase in affinity over 1000-fold higher than that observed under
AB  - metal-free conditions. The trend for DNA binding affinity supported by
AB  - these ions suggests that ionic radius and charge are not critical to the
AB  - promotion of DNA binding. To examine the role of metal ions in sequence
AB  - discrimination, we determined specificity factors
AB  - [K(a)(specific)/K(a)(nonspecific)] in the presence of Cd(II), Ba(II), and
AB  - Tb(III). Most interestingly, all of these ions compromised sequence
AB  - specificity to some degree compared to Ca(II), by either increased
AB  - affinity for a noncognate sequence, decreased affinity for the cognate
AB  - sequence, or both. These results suggest that while amino acid-base
AB  - contacts are important for specificity, the properties of metal ion
AB  - cofactors at the catalytic site are also critical for sequence
AB  - discrimination. This insight is invaluable to our efforts to understand
AB  - and subsequently design sequence-specific nucleases.
ER  -

TY  - JOUR
AU  - Bowen, L.M.
AU  - Muller, G.
AU  - Riehl, J.P.
AU  - Dupureur, C.M.
TI  - Lanthanide spectroscopic studies of the dinuclear and Mg(II)-dependent PvuII restriction endonuclease.
JO  - Biochemistry
PY  - 2004
SP  - 15286
EP  - 15295
VL  - 43
AB  - Type II restriction enzymes are homodimeric systems that bind four to eight base pair
AB  - palindromic recognition sequences of DNA and catalyze
AB  - metal ion-dependent phosphodiester cleavage. While Mg(II) is required
AB  - for cleavage in these enzymes, in some systems Ca(II) promotes avid
AB  - substrate binding and sequence discrimination. These properties make
AB  - them useful model systems for understanding the roles of alkaline earth
AB  - metal ions in nucleic acid processing. We have previously shown that
AB  - two Ca(II) ions stimulate DNA binding by Pvull endonuclease and that
AB  - the trivalent lanthanide ions Tb(III) and Eu(III) support subnanomolar
AB  - DNA binding in this system. Here we capitalize on this behavior,
AB  - employing a unique combination of luminescence spectroscopy and DNA
AB  - binding assays to characterize Ln(III) binding behavior by this enzyme.
AB  - Upon excitation of tyrosine residues, the emissions of both Tb(III) and
AB  - Eu(III) are enhanced severalfold. This enhancement is reduced by the
AB  - addition of a large excess of Ca(II), indicating that these ions bind
AB  - in the active site. Poor enhancements and affinities in the presence of
AB  - the active site variant E68A indicate that Glu68 is an important
AB  - Ln(III) ligand, similar to that observed with Ca(II), Mg(II), and
AB  - Mn(II). At low micromolar Eu(III) concentrations in the presence of
AB  - enzyme (10-20 muM), Eu(III) excitation F-7(0) --> D-5(0) spectra yield
AB  - one dominant peak at 579.2 nm. A second, smaller peak at 579.4 nm is
AB  - apparent at high Eu(III) concentrations (150 muM). Titration data for
AB  - both Tb(III) and Eu(III) fit well to a two-site model featuring a
AB  - strong site (K-d = 1-3 muM) and a much weaker site (K-d approximate to
AB  - 100-200 muM). Experiments with the E68A variant indicate that the Glu68
AB  - side chain is not required for the binding of this second Ln(III)
AB  - equivalent; however, the dramatic increase in DNA binding affinity
AB  - around 100 muM Ln(III) for the wild-type enzyme and metal-enhanced
AB  - substrate affinity for E68A are consistent with functional relevance
AB  - for this weaker site. This discrimination of sites should make it
AB  - possible to use lanthanide substitution and lanthanide spectroscopy to
AB  - probe individual metal ion binding sites, thus adding an important tool
AB  - to the study of restriction enzyme structure and function.
ER  -

TY  - JOUR
AU  - Bower, E.K.M.
AU  - Cooper, L.P.
AU  - Roberts, G.A.
AU  - White, J.H.
AU  - Luyten, Y.
AU  - Morgan, R.D.
AU  - Dryden, D.T.F.
TI  - A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification  enzymes.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 9067
EP  - 9080
VL  - 46
AB  - Restriction Modification (RM) systems prevent the invasion of foreign genetic material into
AB  - bacterial cells by restriction and protect the host's genetic
AB  - material by methylation. They are therefore important in maintaining the
AB  - integrity of the host genome. RM systems are currently classified into four types
AB  - (I to IV) on the basis of differences in composition, target recognition,
AB  - cofactors and the manner in which they cleave DNA. Comparing the structures of
AB  - the different types, similarities can be observed suggesting an evolutionary link
AB  - between these different types. This work describes the 'deconstruction' of a
AB  - large Type I RM enzyme into forms structurally similar to smaller Type II RM
AB  - enzymes in an effort to elucidate the pathway taken by Nature to form these
AB  - different RM enzymes. Based upon the ability to engineer new enzymes from the
AB  - Type I 'scaffold', an evolutionary pathway and the evolutionary pressures
AB  - required to move along the pathway from Type I RM systems to Type II RM systems
AB  - are proposed. Experiments to test the evolutionary model are discussed.
ER  -

TY  - JOUR
AU  - Bowman, J.P.
TI  - Draft Genome Sequence of the Psychrophilic Gliding Species Gelidibacter algens ACAM 536.
JO  - Genome Announcements
PY  - 2016
SP  - e00908
EP  - e00916
VL  - 4
AB  - A draft genome sequence was obtained from the type strain of Gelidibacter algens  (ACAM 536).
AB  - This species was isolated from sea-ice diatom assemblages collected
AB  - from Ellis Fjord, Eastern Antarctica. The genome of ACAM 536 is a single circular
AB  - chromosome with an estimated size of 4.50 Mbp.
ER  -

TY  - JOUR
AU  - Bown, L.
AU  - Bignell, D.R.D.
TI  - Draft Genome Sequence of the Plant Pathogen Streptomyces sp. Strain 11-1-2.
JO  - Genome Announcements
PY  - 2017
SP  - e00968
EP  - e00917
VL  - 5
AB  - Streptomyces sp. strain 11-1-2 is a Gram-positive filamentous bacterium that was  isolated
AB  - from a common scab lesion on a potato tuber. The strain is highly
AB  - pathogenic to plants but does not produce the virulence-associated Streptomyces
AB  - phytotoxin thaxtomin A. Here, we report the draft genome sequence of Streptomyces
AB  - sp. 11-1-2.
ER  -

TY  - JOUR
AU  - Boybek, A.
AU  - Ray, T.D.
AU  - Evans, M.C.
AU  - Dyson, P.J.
TI  - Novel site-specific DNA modification in Streptomyces: analysis of preferred intragenic modification sites present in a 5.7 kb amplified DNA sequence.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 3364
EP  - 3371
VL  - 26
AB  - Both Streptomyces lividans and Streptomyces avermitilis encode similar systems of
AB  - post-replicative DNA modification which act site-specifically on closely opposed
AB  - guanines on either strand. The modifications can be detected since they react in
AB  - vitro with an oxidative derivative of Tris, resulting in strand cleavage.
AB  - Previous analysis of the preferred modification site of plasmid pIJ101 indicated
AB  - that extensive amounts of flanking sequence, including direct and inverted repeat
AB  - structures, are required to direct modification in vivo within a central 6 bp
AB  - palindrome. We have now examined the preferred modification sites of a
AB  - chromosomal element, the 5.7 kb amplified DNA sequence (ADS5.7) found in certain
AB  - S. lividans mutants. In contrast to the pIJ101 site, each of the ADS5. 7sites is
AB  - intragenic and modified with a 10-fold reduced frequency. However, similar
AB  - extents of flanking sequence are required for authentic double-strand
AB  - modification; deletion mutants exhibited different modification profiles,
AB  - including displaced double-stranded or single-stranded modi-fication. Comparison
AB  - of different modification sites reveals conservation of the central core
AB  - sequence, but no significant similarities between flanking sequences. Enhanced
AB  - modification was detected in a cloned region of the ADS5.7, suggesting that local
AB  - DNA topology, probably influenced by both DNA supercoiling and the nature of
AB  - flanking sequences, can influence the modifying activity.
ER  -

TY  - JOUR
AU  - Boyd, A.C.
AU  - Charles, I.G.
AU  - Keyte, J.W.
AU  - Brammar, W.J.
TI  - Isolation and computer-aided characterization of MmeI, a Type II restriction endonuclease from Methylophilus methylotrophus.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 5255
EP  - 5274
VL  - 14
AB  - A Type II restriction endonuclease, MmeI, has been purified from the obligate
AB  - methylotroph, Methylophilus methylotrophus.  The enzyme was shown to have the
AB  - non-palindromic recognition sequence 5' - T C C Pu A C (N) 20- 3' 3' - A G G Py
AB  - T G (N) 18 - 5' and to cleave (as indicated) on the 3' side, generating a two
AB  - nucleotide 3' projection.  Determination of the recognition sequence was
AB  - achieved using two new computer programs; RECOG, which predicts recognition
AB  - sequences from the pattern of restriction fragments obtained from DNAs of known
AB  - sequence, and GELSIM, which generates graphical simulations of DNA band
AB  - patterns obtained by gel electrophoresis of restriction digests of sequenced
AB  - DNA molecules.
ER  -

TY  - JOUR
AU  - Boyd, D.A.
AU  - Mataseje, L.F.
AU  - Pelude, L.
AU  - Mitchell, R.
AU  - Bryce, E.
AU  - Roscoe, D.
AU  - Embree, J.
AU  - Katz, K.
AU  - Kibsey, P.
AU  - Lavallee, C.
AU  - Simor, A.E.
AU  - Taylor, G.
AU  - Turgeon, N.
AU  - Langley, J.M.
AU  - Amaratunga, K.
AU  - Mulvey, M.R.
TI  - Results from the Canadian Nosocomial Infection Surveillance Program for detection of carbapenemase-producing Acinetobacter spp. in Canadian hospitals, 2010-16.
JO  - J. Antimicrob. Chemother.
PY  - 2018
SP  - 0
EP  - 0
VL  - 0
AB  - Objectives: Globally there is an increased prevalence of carbapenem-resistant
AB  - Acinetobacter spp. (CRAs) and carbapenemase-producing Acinetobacter spp. (CPAs)
AB  - in the hospital setting. This increase prompted the Canadian Nosocomial Infection
AB  - Surveillance Program (CNISP) to conduct surveillance of CRA colonizations and
AB  - infections identified from patients in CNISP-participating hospitals between 2010
AB  - and 2016. Methods: Participating acute care facilities across Canada submitted
AB  - CRAs from 1 January 2010 to 31 December 2016. Patient data were collected from
AB  - medical records using a standardized questionnaire. WGS was conducted on all CRAs
AB  - and data underwent single nucleotide variant analysis, resistance gene detection
AB  - and MLST. Results: The 7 year incidence rate of CRA was 0.02 per 10 000 patient
AB  - days and 0.015 per 1000 admissions, with no significant increase observed over
AB  - the surveillance period (P > 0.73). Ninety-four CRA isolates were collected from
AB  - 58 hospitals, of which 93 (98.9%) were CPA. Carbapenemase OXA-235 group (48.4%)
AB  - was the most common due to two separate clusters, followed by the OXA-23 group
AB  - (41.9%). Patients with a travel history were associated with 38.8% of CRA cases.
AB  - The all-cause 30 day mortality rate for infected cases was 24.4 per 100 CRA
AB  - cases. Colistin was the most active antimicrobial agent (95.8% susceptibility).
AB  - Conclusions: CRA remains uncommon in Canadian hospitals and the incidence did not
AB  - increase from 2010 to 2016. Almost half of the cases were from two clusters
AB  - harbouring OXA-235-group enzymes. Previous medical treatment during travel
AB  - outside of Canada was common.
ER  -

TY  - JOUR
AU  - Boye, E.
AU  - Lobner-Olesen, A.
TI  - The role of dam methyltransferase in the control of DNA replication in E. coli.
JO  - Cell
PY  - 1990
SP  - 981
EP  - 989
VL  - 62
AB  - The timing and control of initiation of DNA replication in E. coli was studied under
AB  - conditions where the cellular level of dam methyltransferase was controlled by a
AB  - temperature-inducible promoter. Flow cytometry was used to demonstrate that the synchrony of
AB  - initiation at the several origins within each cell was critically dependent on the level of
AB  - dam methyltransferase. Initiations were shown to be synchronous only in a narrow temperature
AB  - range. The data are explained by a model where a newly replicated and therefore hemimethylated
AB  - oriC is inert for reinitiation. Such a model may be applicable to eukaryotic cells, where
AB  - classes of origins are initiated in synchrony and only once per cell cycle.
ER  -

TY  - JOUR
AU  - Boye, E.
AU  - Marinus, M.G.
AU  - Lobner-Olesen, A.
TI  - Quantitation of Dam methyltransferase in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1992
SP  - 1682
EP  - 1685
VL  - 174
AB  - An antiserum against Escherichia coli Dam methyltransferase has been developed in rabbits and
AB  - employed to detect and quantitate the enzyme in immunoblots. A wild-type, rapidly growing E.
AB  - coli cell (doubling time = 30 min) was found to contain about 130 molecules of Dam
AB  - methyltransferase.
ER  -

TY  - JOUR
AU  - Boyer, H.
TI  - Genetic control of restriction and modification in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1964
SP  - 1652
EP  - 1660
VL  - 88
AB  - Bacterial crosses with K-12 strains of Escherichia coli as Hfr donors (Hfr
AB  - Hayes, Hfr Cavalli, and Hfr P4X-6) and B/r strains of E. coli as F- recipients
AB  - were found to differ from crosses between K-12 Hfr donors and K-12 F-
AB  - recipients in two ways:  (i) recombinants (leu,pro, lac, and gal) did not
AB  - appear at discrete time intervals but did appear simultaneously 30 min after
AB  - matings were initiated, and (ii) the linkage of unselected markers to selected
AB  - markers was reduced.  Integration of a genetic region linked to the threonine
AB  - locus of K-12 into the B/r genome resulted in a hybrid which no longer gave
AB  - anomalous results in conjugation experiments.  A similar region of the B strain
AB  - was introduced into the K-12 strain, which then behaved as a typical B F-
AB  - recipient.  These observations are interpreted as the manifestation of
AB  - host-controlled modification and restriction on the E. coli chromosome.  This
AB  - was verified by experiments on the restriction and modification of the
AB  - bacteriophage lambda, F-lac, F-gal, and sex-factor, F1.  It was found that the
AB  - genetic region that controlled the mating responses of the K-12 and B/r strains
AB  - also controlled the modification and restriction properties of these two
AB  - strains.  The genes responsible for the restricting and modifying properties of
AB  - the K-12 and B strains of E. coli were found to be allelic, linked to each
AB  - other, and linked to the threonine locus.
ER  -

TY  - JOUR
AU  - Boyer, H.
AU  - Scibienski, E.
AU  - Slocum, H.
AU  - Roulland-Dussoix, D.
TI  - The in vitro restriction of the replicative form of W.T. and mutant fd phage DNA.
JO  - Virology
PY  - 1971
SP  - 703
EP  - 710
VL  - 46
AB  - Tritium- and 32P-labeled replicative form DNA of wild-type and restriction-site
AB  - mutants of the male specific phage fd were used as substrates for purified
AB  - Escherichia coli B restriction endonuclease and the products of the reaction
AB  - were analyzed by zonal centrifugation.  The products of the
AB  - endonuclease-treated unmodified wild-type RF DNA were found to be two fragments
AB  - about one-third and two-thirds the size of the genome.  The product of the
AB  - endonuclease-treated unmodified RF DNA of mutants partially resistant to in
AB  - vivo restriction was a single linear molecule.  The unmodified RF of phage
AB  - mutants totally resistant to in vivo restriction was undegraded by the E. coli
AB  - B restriction endonuclease.  These observations confirm the hypothesis of Arber
AB  - and Kuhnlein (1967) that the wild-type phage genome has two sites (each of
AB  - which consists of a limited sequence of base pairs), sensitive to the E. coli B
AB  - restriction endonuclease and mutational alteration of one or both sites results
AB  - in mutants either partially or completely resistant to E. coli B restriction.
AB  - All of the seven independently altered sites were found to be insensitive to
AB  - both steps of the restriction endonuclease attack; i.e., no single strand
AB  - phosphodiester bond cleavages were detected.  However, by using nitrocellulose
AB  - membrane filters to measure the interaction of the B restriction endonuclease
AB  - with fd RF DNA, we found that one of the mutant RF formed measurable amounts of
AB  - enzyme-substrate complexes.  In one other case no measurable complexes were
AB  - formed between the endonuclease and a mutant restriction site.  This suggests
AB  - that the restriction endonuclease relies on the proper sequence of base pairs
AB  - for recognition (formation of enzyme-substrate complex) and for the enzymatic
AB  - cleavage of phosphodiester bonds.
ER  -

TY  - JOUR
AU  - Boyer, H.W.
TI  - DNA restriction and modification mechanisms in bacteria.
JO  - Annu. Rev. Microbiol.
PY  - 1971
SP  - 153
EP  - 176
VL  - 25
AB  - The restriction and modification of DNA as currently understood was first
AB  - recognized as a unique biological mechanism because of the effect it has on the
AB  - ability of a bacteriophage to propagate on related bacterial strains.  Similar
AB  - observations were made prior to these reports, but they were never clearly
AB  - defined or pursued on an experimental basis.  The restriction and modification
AB  - of phage lambda by several host specificities found in E. coli has been
AB  - extensively exploited and has led to the general concept that two enzymes, an
AB  - endonuclease and a methylase, are responsible for the restriction and
AB  - modification of DNA.  The restriction endonuclease makes a double-strand
AB  - scission at a specific sequence of base pairs if it is unmodified, and the
AB  - modification methylase modifies this sequence of base pairs to render it
AB  - insensitive to the restriction endonuclease.  This mechanism (hs) appears to be
AB  - quite general in bacteria, but it should be pointed out that some restriction
AB  - and modification systems (e.g., the restriction and modification of T-even
AB  - phages, 87) could have a different molecular basis.  The plan of this review is
AB  - to treat the restriction and modification of DNA as a general bacterial
AB  - mechanism.  Emphasis will be placed on the two types of hs mechanisms
AB  - associated with E. coli, and two models of protein-polynucleotide interaction
AB  - are presented to account for the two types of restriction and modification
AB  - mechanisms.
ER  -

TY  - JOUR
AU  - Boyer, H.W.
TI  - Restriction and modification of DNA: enzymes and substrates.
JO  - Fed. Proc.
PY  - 1974
SP  - 1125
EP  - 1127
VL  - 33
AB  - A great deal of interest in the restriction and modification of DNA has been
AB  - generated in the past few years and a symposium devoted to some aspects of this
AB  - biological mechanism was part of the 1973 Federation Meeting.
ER  -

TY  - JOUR
AU  - Boyer, H.W.
AU  - Chow, L.T.
AU  - Dugaiczyk, A.
AU  - Hedgpeth, J.
AU  - Goodman, H.M.
TI  - DNA substrate site for the EcoRII restriction endonuclease and modification methylase.
JO  - Nature New Biol.
PY  - 1973
SP  - 40
EP  - 43
VL  - 244
AB  - The same nucleotide sequence in double stranded DNA restricted in double
AB  - stranded DNA restricted by the EcoRII restriction endonuclease is methylated by
AB  - the EcoRII modification methylase.  The EcoRII endonucleolytic cleavages
AB  - generate DNA fragments with cohesive termini.
ER  -

TY  - JOUR
AU  - Boyer, H.W.
AU  - Greene, P.J.
AU  - Meagher, R.B.
AU  - Betlach, M.C.
AU  - Russel, D.
AU  - Goodman, H.M.
TI  - The methylation of DNA as the biochemical basis of host controlled modification of DNA in bacteria.
JO  - FEBS J.
PY  - 1975
SP  - 23
EP  - 37
VL  - 34
AB  - In 1962 the work of Arber and Dussoix (Arber and Dussoix, 1962; Dussoix and
AB  - Arber, 1962) provided the conceptual framework for the study of the enzymatic
AB  - basis of the host controlled modification and restriction of bacteriophage
AB  - lambda.  Restriction and modification of phage lambda had received scant
AB  - attention until this time, probably because of its peripheral role to the ideas
AB  - occupying the attention of most molecular biologists of the time.  It had been
AB  - a long established fact that when a bacterial virus had been propagated on one
AB  - bacterial host, it would have a low efficiency of plating after infection of a
AB  - related host strain (for reviews see Arber and Linn, 1969; Boyer, 1971;
AB  - Meselson et al., 1972).  However, after one round of replication on the new
AB  - host, the few virus particles which were propagated would be modified in some
AB  - way to have the capacity to subsequently plate on that strain with a high
AB  - efficiency of plating (see Table 1).
ER  -

TY  - JOUR
AU  - Boyer, H.W.
AU  - Roulland-Dussoix, D.
TI  - A complementation analysis of the restriction and modification of DNA in Escherichia coli.
JO  - J. Mol. Biol.
PY  - 1969
SP  - 459
EP  - 472
VL  - 41
AB  - A complementation analysis of host-controlled modification and restriction of
AB  - DNA by Escherichia coli has been carried out by examining the restriction and
AB  - modification phenotypes of partial, permanent diploids containing various
AB  - arrangements of wild type and mutant restriction and modification alleles.
AB  - Intercistronic complementation was observed between three classes of
AB  - restriction and modification mutants of E. coli B, indicating that at least
AB  - three cistrons (the ram cistrons) are involved in the genetic control of the
AB  - restriction and modification of DNA.  Mutations in one cistron (ramA) result in
AB  - a loss of restriction activity but not in modification activity (r-m+).
AB  - Mutations in a second cistron (ramC) result in a loss of restriction and
AB  - modification activities (r-m-).  Mutations in  third cistron result in a loss
AB  - of modification activity and appear to be lethal unless accompanied by a
AB  - mutation in the ramA or ramC cistrons.  A fourth class of mutations, which are
AB  - linked to the other ram cistrons and are expressed phenotypically as r-m-
AB  - mutants, are trans dominant to the wild-type ram alleles.  It is not known if
AB  - this latter class of mutants represents a fourth cistron of the ram locus.
AB  - Complementation was observed between E. coli K12 and B ramA and ramC mutations
AB  - and the host specificity of the restored restriction activity was dependent on
AB  - an intact ramC cistron.  However, complementation was not detected between the
AB  - P1 and K12 or P1 and B ram alleles.  A general model for the genetic control of
AB  - the restriction and modification properties of E. coli strains and their
AB  - episomes is presented.
ER  -

TY  - JOUR
AU  - Boyer, M.
AU  - Yutin, N.
AU  - Pagnier, I.
AU  - Barrassi, L.
AU  - Fournous, G.
AU  - Espinosa, L.
AU  - Robert, C.
AU  - Azza, S.
AU  - Sun, S.
AU  - Rossmann, M.G.
AU  - Suzan-Monti, M.
AU  - La Scola, B.
AU  - Koonin, E.V.
AU  - Raoult, D.
TI  - Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 21848
EP  - 21853
VL  - 106
AB  - Giant viruses such as Mimivirus isolated from amoeba found in aquatic habitats show biological
AB  - sophistication comparable to that of simple cellular life forms and seem to evolve by similar
AB  - mechanisms, including extensive gene duplication and horizontal gene transfer (HGT), possibly
AB  - in part through a viral parasite, the virophage. We report here the isolation of "Marseille"
AB  - virus, a previously uncharacterized giant virus of amoeba. The virions of Marseillevirus
AB  - encompass a 368-kb genome, a minimum of 49 proteins, and some messenger RNAs. Phylogenetic
AB  - analysis of core genes indicates that Marseillevirus is the prototype of a family of
AB  - nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes. The genome repertoire of the virus
AB  - is composed of typical NCLDV core genes and genes apparently obtained from eukaryotic hosts
AB  - and their parasites or symbionts, both bacterial and viral. We propose that amoebae are
AB  - "melting pots" of microbial evolution where diverse forms emerge, including giant viruses with
AB  - complex gene repertoires of various origins.
ER  -

TY  - JOUR
AU  - Boyle, B.
AU  - Fernandez, L.
AU  - Laroche, J.
AU  - Kukavica-Ibrulj, I.
AU  - Mendes, C.M.
AU  - Hancock, R.W.
AU  - Levesque, R.C.
TI  - Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates with Phenotypes of Polymyxin B Adaptation and Inducible Resistance.
JO  - J. Bacteriol.
PY  - 2012
SP  - 529
EP  - 530
VL  - 194
AB  - Clinical 'superbug' isolates of Pseudomonas aeruginosa were previously observed to be
AB  - resistant to several antibiotics, including polymyxin B,
AB  - and/or to have a distinct, reproducible adaptive polymyxin resistance
AB  - phenotype, identified by observing 'skipped' wells (appearance of extra
AB  - turbid wells) during broth microdilution testing. Here we report the
AB  - complete assembled draft genome sequences of three such polymyxin
AB  - resistant P. aeruginosa strains (9BR, 19BR, and 213BR).
ER  -

TY  - JOUR
AU  - Boyle, B.
AU  - Vaillancourt, K.
AU  - Bonifait, L.
AU  - Charette, S.J.
AU  - Gottschalk, M.
AU  - Grenier, D.
TI  - Genome Sequence of the Swine Pathogen Streptococcus suis Serotype 2 Strain S735.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6343
EP  - 6344
VL  - 194
AB  - Streptococcus suis is a major swine pathogen responsible for significant, worldwide economic
AB  - losses in the swine industry, in addition to being an emerging
AB  - zoonotic agent. Strains of serotype 2 are the most commonly associated with
AB  - infections causing meningitis, endocarditis, and septicemia. Here we present the
AB  - genome sequence of S. suis serotype 2 strain S735.
ER  -

TY  - JOUR
AU  - Bozic, D.
AU  - Grazulis, S.
AU  - Siksnys, V.
AU  - Huber, R.
TI  - Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 176
EP  - 186
VL  - 255
AB  - The X-ray crystal structure of Citrobacter freundii restriction endonuclease Cfr10I has been
AB  - determined at a resolution of 2.15 Angstroms by multiple isomorphous replacement methods and
AB  - refined to an R-factor of 19.64%.  The structure of Cfr10I represents the first structure of a
AB  - restriction endonuclease recognizing a degenerate nucleotide sequence.  Structural comparison
AB  - of Cfr10I with previously solved structures of other restriction enzymes suggests that
AB  - recognition of specific sequence occurs through contacts in the major and the minor grooves of
AB  - DNA.  The arrangement of the putative active site residues shows some striking differences
AB  - from previously described restriction endonucleases and supports a two-metal-ion mechanism of
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Braasch, J.L.
AU  - Lapin, C.N.
AU  - Dowd, S.E.
AU  - McLaughlin, R.W.
TI  - Draft Genome Sequence of Robinsoniella peoriensis Strain WTD, Isolated from the Fecal Material of a Wood Turtle.
JO  - Genome Announcements
PY  - 2015
SP  - e01444
EP  - e01414
VL  - 3
AB  - Here, we report the draft genome of Robinsoniella peoriensis strain WTD, which was isolated
AB  - from the fecal material of a wood turtle. The genome size was
AB  - 7,391,415 bp with 41.1 mol% G+C.
ER  -

TY  - JOUR
AU  - Brabec, V.
AU  - Balcarova, Z.
TI  - Restriction-enzyme cleavage of DNA modified by platinum (II) complexes.
JO  - Eur. J. Biochem.
PY  - 1993
SP  - 183
EP  - 187
VL  - 216
AB  - The effect of binding of cis-diamminedichloroplatinum(II), its trans isomer and
AB  - diethylenetriaminechloroplatinum(II) chloride to DNA on the splicing effectiveness of BamHI,
AB  - EcoRI and SalI restriction endonucleases has been determined by means of gel electrophoresis.
AB  - All three platinum complexes inhibit the cleavage of linearized plasmid DNA. In addition, the
AB  - three platinum complexes bound to DNA constitute a barrier across which the linear diffusion
AB  - of EcoRI on DNA is difficult. We interpret these findings to mean that the splicing
AB  - effectiveness of restriction enzymes is influenced by bifunctional and monofunctional DNA
AB  - adducts of platinum via both steric interference and DNA conformational distortions. Whereas
AB  - the platinum adducts in the restriction sites or in their very closed proximity inhibit the
AB  - cleavage, the lesions occurring a greater distance from the restriction site can slow down the
AB  - process of the localization of recognition sequences.
ER  -

TY  - JOUR
AU  - Brack, C.
AU  - Eberle, H.
AU  - Bickle, T.A.
AU  - Yuan, R.
TI  - Mapping of recognition sites for the restriction endonuclease from Escherichia coli K12 on bacteriophage PM2 DNA.
JO  - J. Mol. Biol.
PY  - 1976
SP  - 583
EP  - 593
VL  - 108
AB  - Two different methods have been used to locate the recognition sites for the
AB  - restriction endonuclease from Escherichia coli K12 on the genome of
AB  - bacteriophage PM2.  The first method employs purified fragments of PM2 DNA
AB  - produced by digestion with HindIII.  The fragments are tested for their ability
AB  - to support the ATPase activity of the enzyme or, alternatively, to inhibit it
AB  - in the presence of intact substrate DNA.  In this way, recognition sites were
AB  - assigned to the HindIII fragments 2, 6 and 7.  An independent approach involved
AB  - the study of complexes between the enzyme and either the HindIII fragments or
AB  - linear DNA produced by cleavage of PM2 DNA at the unique site for HpaII.
AB  - Electron microscopic analysis of such preparations allowed mapping of the three
AB  - recognition sites to 40, 60 and 62 map units from the HpaII cleavage site.
ER  -

TY  - JOUR
AU  - Bradbury, M.
AU  - Greenfield, P.
AU  - Midgley, D.
AU  - Li, D.
AU  - Tran-Dinh, N.
AU  - Vriesekoop, F.
AU  - Brown, J.L.
TI  - Draft Genome Sequence of Clostridium sporogenes PA 3679, the Common Nontoxigenic  Surrogate for Proteolytic Clostridium botulinum.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1631
EP  - 1632
VL  - 194
AB  - Clostridium sporogenes PA 3679 is widely used as a nontoxigenic surrogate for proteolytic
AB  - strains of Clostridium botulinum in the derivation and validation of
AB  - thermal processes in food. Here we report the draft assembly and annotation of
AB  - the C. sporogenes PA 3679 genome. Preliminary analysis demonstrates a high degree
AB  - of relatedness between C. sporogenes PA 3679 and sequenced strains of proteolytic
AB  - C. botulinum.
ER  -

TY  - JOUR
AU  - Braesel, J.
AU  - Crnkovic, C.M.
AU  - Kunstman, K.J.
AU  - Green, S.J.
AU  - Maienschein-Cline, M.
AU  - Orjala, J.
AU  - Murphy, B.T.
AU  - Eustaquio, A.S.
TI  - Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete.
JO  - J. Nat. Prod.
PY  - 2018
SP  - 2057
EP  - 2068
VL  - 81
AB  - Actinomycete bacteria isolated from freshwater environments are an unexplored
AB  - source of natural products. Here we report the complete genome of the Great
AB  - Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural
AB  - product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced
AB  - using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to
AB  - close remaining gaps. All identified biosynthetic gene clusters (BGCs) were
AB  - manually curated. Five known BGCs were identified encoding desferrioxamine,
AB  - alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and
AB  - diazepinomicin, which is currently in phase II clinical trials to treat
AB  - Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006
AB  - is indeed a producer of diazepinomicin and at yields higher than previously
AB  - reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were
AB  - transcriptionally active under the culture condition tested. Orphan BGCs include
AB  - an enediyne polyketide synthase and an uncharacteristically large, 36-module
AB  - polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics
AB  - system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in
AB  - the future. This study is one of the few attempts to report the biosynthetic
AB  - capacity of a freshwater-derived actinomycete and highlights this resource as a
AB  - potential reservoir for new natural products.
ER  -

TY  - JOUR
AU  - Braga, E.A.
AU  - Nosikov, V.V.
AU  - Polyanovsky, O.L.
TI  - The use of antibiotics actinomycin D and distamycin A for mapping of phage lambda HindIII fragments.
JO  - FEBS Lett.
PY  - 1976
SP  - 91
EP  - 95
VL  - 70
AB  - The antibiotics distamycin A and actinomycin D interact with double-stranded
AB  - DNA forming noncovalently bound complexes.  This interaction is rather
AB  - selective: distamycin forms complexes preferentially with d(A/T) rich regions
AB  - whereas actinomycin binds d(G/C) rich regions of DNA.  This property has
AB  - offered a possibility to use these antibiotics for effective and highly
AB  - selective protection of the cleavage sites recognized by restriction
AB  - endonucleases.  The recognition site of endo R. HindIII 5'AAGCTT 3'TTCGAA may
AB  - be protected by both actinomycin D and distamycin A as long as it contains TT
AB  - and GC sequences favourable for interaction of distamycin and actinomycin with
AB  - template DNA.  It has been demonstrated that different EcoRI recognition sites
AB  - on lambda DNA may be effectively blocked by different antibiotic concentrations
AB  - due to the peculiarities of the environment of different recognition sites.  In
AB  - the present paper it is shown that certain endo R. HindIII sites of phage
AB  - lambda DNA may be effectively protected with actinomycin whereas some other
AB  - sites are protected with distamycin.  This allows us to obtain a set of larger
AB  - overlapping fragments of DNA (hereafter we shall term them as distamycin and
AB  - actinomycin protected fragments) and to establish the location of all HindIII
AB  - fragments on the physical map of phage lambda DNA.  The data reported here and
AB  - earlier lead to a conclusion that the antibiotics may be useful for DNA mapping
AB  - and for obtaining new vector molecules.
ER  -

TY  - JOUR
AU  - Braga, E.A.
AU  - Nosikov, V.V.
AU  - Tanyashin, V.I.
AU  - Zhuze, A.L.
AU  - Polyanovskii, O.L.
TI  - Limitation of the action of restriction endonucleases by antibiotics bound to DNA.
JO  - Dokl. Akad. Nauk.
PY  - 1975
SP  - 707
EP  - 710
VL  - 225
AB  - The effect of the antibiotics distamycin A and actinomycin D on the splitting
AB  - of DNA by restriction endonucleases was studied.  Electrophoresis showed that
AB  - antibiotics binding with DNA can compete with the corresponding enzymes.  Their
AB  - selectivity was determined by the nucleotide sequence of the recognition
AB  - section for the enzyme and also the immediate neighbourhood of these DNA
AB  - sections.  With EcoRI and phage lambda DNA it was shown that distamycin A
AB  - limited the number of sections split by restriction endonuclease.
ER  -

TY  - JOUR
AU  - Bragin, E.Y.
AU  - Shtratnikova, V.Y.
AU  - Dovbnya, D.V.
AU  - Schelkunov, M.I.
AU  - Pekov, Y.A.
AU  - Malakho, S.G.
AU  - Egorova, O.V.
AU  - Ivashina, T.V.
AU  - Sokolov, S.L.
AU  - Ashapkin, V.V.
AU  - Donova, M.V.
TI  - Comparative analysis of genes encoding key steroid core oxidation enzymes in fast-growing Mycobacterium spp. strains.
JO  - J. Steroid Biochem. Mol. Biol.
PY  - 2013
SP  - 41
EP  - 53
VL  - 138
AB  - A comparative genome analysis of Mycobacterium spp. VKM Ac-1815D, 1816D and 1817D
AB  - strains used for efficient production of key steroid intermediates
AB  - (androst-4-ene-3,17-dione, AD, androsta-1,4-diene-3,17-dione, ADD, 9alpha-hydroxy
AB  - androst-4-ene-3,17-dione, 9-OH-AD) from phytosterol has been carried out by deep
AB  - sequencing. The assembled contig sequences were analyzed for the presence
AB  - putative genes of steroid catabolism pathways. Since
AB  - 3-ketosteroid-9alpha-hydroxylases (KSH) and 3-ketosteroid-Delta(1)-dehydrogenase
AB  - (Delta(1) KSTD) play key role in steroid core oxidation, special attention was
AB  - paid to the genes encoding these enzymes. At least three genes of Delta(1) KSTD
AB  - (kstD), five genes of KSH subunit A (kshA), and one gene of KSH subunit B of
AB  - 3-ketosteroid-9alpha-hydroxylases (kshB) have been found in Mycobacterium sp. VKM
AB  - Ac-1817D. Strains of Mycobacterium spp. VKM Ac-1815D and 1816D were found to
AB  - possess at least one kstD, one kshB and two kshA genes. The assembled genome
AB  - sequence of Mycobacterium sp. VKM Ac-1817D differs from those of 1815D and 1816D
AB  - strains, whereas these last two are nearly identical, differing by 13 single
AB  - nucleotide substitutions (SNPs). One of these SNPs is located in the coding
AB  - region of a kstD gene and corresponds to an amino acid substitution Lys (135) in
AB  - 1816D for Ser (135) in 1815D. The findings may be useful for targeted genetic
AB  - engineering of the biocatalysts for biotechnological application.
ER  -

TY  - JOUR
AU  - Brahmachari, S.K.
AU  - Shouche, Y.S.
AU  - Cantor, C.R.
AU  - McClelland, M.
TI  - Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation.
JO  - J. Mol. Biol.
PY  - 1987
SP  - 201
EP  - 211
VL  - 193
AB  - pBR322 form V DNA is a highly torsionally strained molecule with a linking
AB  - number of zero.  We have used sequence-specific DNA methylases as probes for
AB  - B-DNA in this molecule, exploiting the inability of methylases to methylate
AB  - single-stranded DNA and Z-DNA, both of which are known to occur in form V DNA.
AB  - Some sequences in form V DNA were shown to be totally in the B-form, others
AB  - were totally in an altered, unmethylatable conformation, while still other
AB  - sites appeared to exist partly in altered and partly in normal B-conformation.
AB  - Some potential Z-forming sequences (alternating pyrimidine/purine) of less than
AB  - seven base-pairs were not in the Z conformation in form V DNA, whereas others
AB  - did adopt an altered structure, indicating a modulating influence of flanking
AB  - sequences.  Furthermore, regions of imperfect alternating pyrimidine/purine
AB  - structure were sometimes capable of adopting an altered structure.  In
AB  - addition, some regions of altered structure had no apparent Z-forming
AB  - sequences, nor were they in polypurine stretches, which have also been proposed
AB  - to form left-handed DNA.  These non-B-DNA conformations may represent novel
AB  - left-handed helical structures or sequences that become single stranded under
AB  - torsional strain.  Long regions of either altered (unmethylatable) DNA or B-DNA
AB  - were not always observed.  In fact, one region showed three transitions between
AB  - B-like DNA and altered structure within 26 base-pairs.
ER  -

TY  - JOUR
AU  - Braid, M.D.
AU  - Silhavy, J.L.
AU  - Kitts, C.L.
AU  - Cano, R.J.
AU  - Howe, M.M.
TI  - Complete Genomic Sequence of Bacteriophage B3, a Mu-Like Phage of Pseudomonas aeruginosa.
JO  - J. Bacteriol.
PY  - 2004
SP  - 6560
EP  - 6574
VL  - 186
AB  - Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In
AB  - this report, we present the complete DNA sequence and annotation of the B3
AB  - genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp
AB  - long with a G+C content of 63.3%. The genome contains 59 proposed open
AB  - reading frames (ORFs) organized into at least three operons. Of these
AB  - ORFs, the predicted proteins from 41 ORFs (68%) display significant
AB  - similarity to other phage or bacterial proteins. Many of the predicted B3
AB  - proteins are homologous to those encoded by the early genes and head genes
AB  - of Mu and Mu-like prophages found in sequenced bacterial genomes. Only two
AB  - of the predicted B3 tail proteins are homologous to other
AB  - well-characterized phage tail proteins; however, several Mu-like prophages
AB  - and transposable phage D3112 encode approximately 10 highly similar
AB  - proteins in their predicted tail gene regions. Comparison of the B3
AB  - genomic organization with that of Mu revealed evidence of multiple genetic
AB  - rearrangements, the most notable being the inversion of the proposed B3
AB  - immunity/early gene region, the loss of Mu-like tail genes, and an extreme
AB  - leftward shift of the B3 DNA modification gene cluster. These differences
AB  - illustrate and support the widely held view that tailed phages are genetic
AB  - mosaics arising by the exchange of functional modules within a diverse
AB  - genetic pool.
ER  -

TY  - JOUR
AU  - Brambila-Tapia, A.J.
AU  - Poot-Hernandez, A.C.
AU  - Perez-Rueda, E.
AU  - Rodriguez-Vazquez, K.
TI  - Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics.
JO  - Indian J. Microbiol.
PY  - 2016
SP  - 134
EP  - 141
VL  - 56
AB  - DNA methylation plays an important role in gene expression and virulence in some  pathogenic
AB  - bacteria. In this report, we describe DNA methyltransferases (MTases)
AB  - present in human pathogenic bacteria and compared them with related species,
AB  - which are not pathogenic or less pathogenic, based in comparative genomics. We
AB  - performed a search in the KEGG database of the KEGG database orthology groups
AB  - associated with adenine and cytosine DNA MTase activities (EC: 2.1.1.37, EC:
AB  - 2.1.1.113 and EC: 2.1.1.72) in 37 human pathogenic species and 18 non/less
AB  - pathogenic relatives and performed comparisons of the number of these MTases
AB  - sequences according to their genome size, the DNA MTase type and with their
AB  - non-less pathogenic relatives. We observed that Helicobacter pylori and Neisseria
AB  - spp. presented the highest number of MTases while ten different species did not
AB  - present a predicted DNA MTase. We also detected a significant increase of adenine
AB  - MTases over cytosine MTases (2.19 vs. 1.06, respectively, p < 0.001). Adenine
AB  - MTases were the only MTases associated with restriction modification systems and
AB  - DNA MTases associated with type I restriction modification systems were more
AB  - numerous than those associated with type III restriction modification systems
AB  - (0.84 vs. 0.17, p < 0.001); additionally, there was no correlation with the
AB  - genome size and the total number of DNA MTases, indicating that the number of DNA
AB  - MTases is related to the particular evolution and lifestyle of specific species,
AB  - regulating the expression of virulence genes in some pathogenic bacteria.
ER  -

TY  - JOUR
AU  - Brambilla, E. et al.
TI  - Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 203
EP  - 211
VL  - 3
AB  - Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus.
AB  - The strain was originally isolated from an offshore oil field from
AB  - the Gulf of Guinea. Members of the genus Methanoplanus are of interest because
AB  - they play an important role in the carbon cycle and also because of their
AB  - significant contribution to the global warming by methane emission in the
AB  - atmosphere. Like other archaea of the family Methanomicrobiales, the members of
AB  - the genus Methanoplanus are able to use CO(2) and H(2) as a source of carbon and
AB  - energy; acetate is required for growth and probably also serves as carbon source.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. This is the first complete genome sequence of a member
AB  - of the family Methanomicrobiaceae and the sixth complete genome sequence from the
AB  - order Methanomicrobiales. The 2,843,290 bp long genome with its 2,824
AB  - protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Brammar, W.J.
AU  - Murray, N.E.
AU  - Winton, S.
TI  - Restriction of lambda trp bacteriophages by Escherichia coli K.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 633
EP  - 647
VL  - 90
AB  - trp-transducing derivatives of phage lambda have been used to study Escherichia
AB  - coli K specific restriction in vivo.  The expression of the trp genes from
AB  - unmodified phages during infection of a rec+, restricting host is eliminated by
AB  - restriction.  In a K-restricting recB,C host, where degradation of restricted
AB  - phage DNA is prevented, expression of the trp genes is little affected by the
AB  - presence of a single unmodified, K-restriction recognition site, even when that
AB  - site is within the trpE gene.  RI restriction, in contrast to K restriction,
AB  - prevents trp gene expression in a recB,C host when the restriction target is
AB  - between the trp genes and the relevant promoter.  The presence of two
AB  - K-restriction recognition sites in a lambda trp phage can have a marked effect
AB  - on trp gene expression.  This effect can be interpreted as the result of
AB  - preferential breakage between the two restriction recognition sites.  We
AB  - conclude that K restriction does not break susceptible DNA at, or even
AB  - preferentially near, a restriction recognition sequence.
ER  -

TY  - JOUR
AU  - Brancaccio, V.F.
AU  - Zhurina, D.S.
AU  - Riedel, C.U.
TI  - Tough nuts to crack Site-directed mutagenesis of bifidobacteria remains a challenge.
JO  - Bioengineered
PY  - 2013
SP  - 197
EP  - 202
VL  - 4
AB  - Most members of the genus Bifidobacterium are commensals of the human gastrointestinal tract
AB  - and some strains were shown to exert beneficial effects on their host. Based on these effects
AB  - and due to their status as GRAS (generally recognized as safe) microorganisms, specific
AB  - strains of bifidobacteria are marketed as probiotics. Despite their important role in food and
AB  - dairy industries, the mechanisms responsible for the probiotic effects of bifidobacteria are
AB  - mostly unknown. Over the last decade, the genomes of a large number of bifidobacteria have
AB  - been sequenced and analyzed. This has yielded a number of genes and their products that are
AB  - speculated to contribute to the probiotic effects of bifidobacteria. The gold standard to
AB  - demonstrate a role for specific genes is the analysis of mutants. At present, only a small
AB  - number of mutants of bifidobacteria have been generated by targeted mutagenesis. This is owed
AB  - to the genetic inaccessibility of most strains and a lack of appropriate molecular tools.
AB  - Successful generation of mutants of bifidobacteria was achieved by various methods including
AB  - classical suicide vector strategies, increase of transformation efficiencies by methylation of
AB  - plasmids and the use of temperature-sensitive vectors. In this commentary, we will describe
AB  - the methods successfully used for mutagenesis of bifidobacteria and discuss their advantages
AB  - and limitations.
ER  -

TY  - JOUR
AU  - Brandt, J.U.
AU  - Jakob, F.
AU  - Behr, J.
AU  - Geissler, A.J.
AU  - Vogel, R.F.
TI  - Dissection of exopolysaccharide biosynthesis in Kozakia baliensis.
JO  - Microb. Cell Fact.
PY  - 2016
SP  - 170
EP  - 170
VL  - 15
AB  - BACKGROUND: Acetic acid bacteria (AAB) are well known producers of commercially
AB  - used exopolysaccharides, such as cellulose and levan. Kozakia (K.) baliensis is a
AB  - relatively new member of AAB, which produces ultra-high molecular weight levan
AB  - from sucrose. Throughout cultivation of two K. baliensis strains (DSM 14400, NBRC
AB  - 16680) on sucrose-deficient media, we found that both strains still produce high
AB  - amounts of mucous, water-soluble substances from mannitol and glycerol as (main)
AB  - carbon sources. This indicated that both Kozakia strains additionally produce new
AB  - classes of so far not characterized EPS. RESULTS: By whole genome sequencing of
AB  - both strains, circularized genomes could be established and typical EPS forming
AB  - clusters were identified. As expected, complete ORFs coding for levansucrases
AB  - could be detected in both Kozakia strains. In K. baliensis DSM 14400 plasmid
AB  - encoded cellulose synthase genes and fragments of truncated levansucrase operons
AB  - could be assigned in contrast to K. baliensis NBRC 16680. Additionally, both K.
AB  - baliensis strains harbor identical gum-like clusters, which are related to the
AB  - well characterized gum cluster coding for xanthan synthesis in Xanthomanas
AB  - campestris and show highest similarity with gum-like heteropolysaccharide (HePS)
AB  - clusters from other acetic acid bacteria such as Gluconacetobacter diazotrophicus
AB  - and Komagataeibacter xylinus. A mutant strain of K. baliensis NBRC 16680 lacking
AB  - EPS production on sucrose-deficient media exhibited a transposon insertion in
AB  - front of the gumD gene of its gum-like cluster in contrast to the wildtype
AB  - strain, which indicated the essential role of gumD and of the associated gum
AB  - genes for production of these new EPS. The EPS secreted by K. baliensis are
AB  - composed of glucose, galactose and mannose, respectively, which is in agreement
AB  - with the predicted sugar monomer composition derived from in silico genome
AB  - analysis of the respective gum-like clusters. CONCLUSIONS: By comparative sugar
AB  - monomer and genome analysis, the polymeric substances secreted by K. baliensis
AB  - can be considered as unique HePS. Via genome sequencing of K. baliensis DSM 14400
AB  - + NBRC 16680 we got first insights into the biosynthesis of these novel HePS,
AB  - which is related to xanthan and acetan biosynthesis. Consequently, the present
AB  - study provides the basis for establishment of K. baliensis strains as novel
AB  - microbial cell factories for biotechnologically relevant, unique polysaccharides.
ER  -

TY  - JOUR
AU  - Brandt, J.U.
AU  - Jakob, F.
AU  - Geissler, A.J.
AU  - Behr, J.
AU  - Vogel, R.F.
TI  - Multiple Genome Sequences of Heteropolysaccharide-Forming Acetic Acid Bacteria.
JO  - Genome Announcements
PY  - 2017
SP  - e00185
EP  - e00117
VL  - 5
AB  - We report here the complete genome sequences of the acetic acid bacteria (AAB) Acetobacter
AB  - aceti TMW 2.1153, A. persici TMW 2.1084, and Neoasaia chiangmaiensis
AB  - NBRC 101099, which secrete biotechnologically relevant heteropolysaccharides
AB  - (HePSs) into their environments. Upon genome sequencing of these AAB strains, the
AB  - corresponding HePS biosynthesis pathways were identified.
ER  -

TY  - JOUR
AU  - Branger, M.
AU  - Hauer, A.
AU  - Michelet, L.
AU  - Karoui, C.
AU  - Cochard, T.
AU  - De Cruz, K.
AU  - Henault, S.
AU  - Boschiroli, M.L.
AU  - Biet, F.
TI  - Draft Genome Sequence of Mycobacterium bovis Strain D-10-02315 Isolated from Wild Boar.
JO  - Genome Announcements
PY  - 2016
SP  - e01268
EP  - e01216
VL  - 4
AB  - Mycobacterium bovis is the etiologic agent of bovine tuberculosis, a chronic infectious
AB  - disease, affecting livestock, wild animals, and sometimes humans. We
AB  - report the draft genome sequence of a Mycobacterium bovis strain isolated from
AB  - wild boar of spoligotype SB0120 (or BCG-like) also present in wildlife-livestock
AB  - multi-host systems.
ER  -

TY  - JOUR
AU  - Branger, M.
AU  - Hauer, A.
AU  - Michelet, L.
AU  - Karoui, C.
AU  - Cochard, T.
AU  - De Cruz, K.
AU  - Henault, S.
AU  - Boschiroli, M.L.
AU  - Biet, F.
TI  - Draft Genome Sequences of Three Mycobacterium bovis Strains Identified in Cattle  and Wildlife in France.
JO  - Genome Announcements
PY  - 2017
SP  - e00410
EP  - e00417
VL  - 5
AB  - Mycobacterium bovis is the etiologic agent of bovine tuberculosis, a chronic infectious
AB  - disease affecting livestock, wild animals, and sometimes humans. We
AB  - report here three draft genome sequences of Mycobacterium bovis strains of
AB  - spoligotypes SB0821 and SB0134, isolated from wildlife but circulating in
AB  - wildlife-livestock multihost systems, and SB0121, circulating exclusively in
AB  - cattle.
ER  -

TY  - JOUR
AU  - Brank, A.S.
TI  - Development and characterization of DNA methyltransferase inhibitors.
JO  - Diss. Abstr.
PY  - 2001
SP  - 5291
EP  - 529B
VL  - 61
AB  - Enzymatic methylation of carbon 5 of cytosine bases is an epigenetic modification that is
AB  - implicated in the silencing of tumor suppressor genes in various forms of cancer.  As a
AB  - potential therapeutic approach for the treatment of such tumors, the goal of this project was
AB  - to develop direct, mechanism-based inhibitors of mammalian DNA (cytosine-C5)-methyltransferase
AB  - (DNMT1), which is the enzyme responsible for the maintenance of established methylation
AB  - patterns in the genome.  The inhibition of the bacterial DNA (Cytosine-C5)-methyltransferase,
AB  - HhaI methyltransferase (M.HhaI), was initially examined because of the large volume of
AB  - structural information reported for this enzyme and because of the high degree of homology
AB  - between catalytic domains of M.HhaI and DNMT1.  The oligodeoxyribonucleotide (ODN) inhibitor
AB  - containing an abasic site in the target position (normally occupied by cytosine) was the most
AB  - potent inhibitor of M.HhaI in comparison to a variety of other ODN inhibitors containing other
AB  - modified target bases.  In addition to this potent inhibition, correlations were found between
AB  - binding of M.HhaI to the most potent ODN inhibitors and the ability of these ODNs to induce a
AB  - major M.HhaI conformational change.  Analysis of the catalytic efficiency of purified,
AB  - recombinant DNMTI (rD-NMT1) with a variety of substrates revealed the preference of rDNMT1 for
AB  - single-stranded substrates that formed stem-loop structures containing DNMT1 recognition
AB  - sites.  These ODNs were substituted with various potential inhibitory target bases and were
AB  - tested for the ability to inhibit rDNMT1 activity.  Of the inhibitors tested, ODNs containing
AB  - abasic target sites were again found to be the most potent inhibitors and were also found to
AB  - induce a dramatic conformational change of DNMT1.  In conclusion, the results show that ODNs
AB  - containing an abasic target site are potent inhibitors of DNMT1 activity, which may be
AB  - effective in vivo inhibitors of DNMT1 and potential therapeutic agents for treatment of
AB  - cancer.
ER  -

TY  - JOUR
AU  - Brank, A.S.
AU  - Eritja, R.
AU  - Garcia, R.
AU  - Marquez, V.
AU  - Christman, J.
TI  - Inhibition of HhaI DNA (cytosine-C5) methyltransferase by oligodeoxyribonucleotides containing 5-Aza-2'-deoxycytidine: Examination of the intertwined roles of co-factor, target, transition state structure and enzyme conformation.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 53
EP  - 67
VL  - 323
AB  - The presence of 5-azacytosine (ZCyt) residues in DNA leads to potent inhibition of DNA
AB  - (cytosine-C5) methyltranferases (C5-MTases) in vivo and in vitro. Enzymatic methylation of
AB  - cytosine in mammalian DNA is an epigenetic modification that can alter gene activity and
AB  - chromosomal stability, influencing both differentiation and tumorigenesis. Thus, it is
AB  - important to understand the critical mechanistic determinants of ZCyt's inhibitory action.
AB  - Although several DNA C5-MTases have been reported to undergo essentially irreversible binding
AB  - to ZCyt in DNA, there is little agreement as to the role of AdoMet and/or methyl transfer in
AB  - stabilizing enzyme interactions with ZCyt. Our results demonstrate that formation of stable
AB  - complexes between HhaI methyltransferase (M.HhaI) and oligodeoxyribonucleotides containing
AB  - ZCyt at the target position for methylation (ZCyt-ODNs) occurs in both the absence and
AB  - presence of co-factors, AdoMet and AdoHcy. Both binary and ternary complexes survive SDS-PAGE
AB  - under reducing conditions and take on a compact conformation that increases their
AB  - electrophoretic mobility in comparison to free M.HhaI. Since methyl transfer can occur only in
AB  - the presence of AdoMet, these results suggest (1) that the inhibitory capacity of ZCyt in DNA
AB  - is based on its ability to induce a stable, tightly closed conformation of M.HhaI that
AB  - prevents DNA and co-factor release and (2) that methylation of ZCyt in DNA is not required for
AB  - inhibition of M.HhaI.
ER  -

TY  - JOUR
AU  - Brank, A.S.
AU  - Van Bemmel, D.M.
AU  - Christman, J.K.
TI  - Optimization of baculovirus-mediated expression and purification of  hexahistidine-tagged murine DNA (cytosine-C5)-methyltransferase-1 in   Spodoptera frugiperda 9 cells.
JO  - Protein Expr. Purif.
PY  - 2002
SP  - 31
EP  - 40
VL  - 25
AB  - Enzymatic DNA methylation of carbon 5 of cytosines is an epigenetic  modification that plays a
AB  - role in regulating gene expression,
AB  - differentiation, and tumorigenesis. DNA (cytosine-C5)-methyltransferase-1
AB  - is the enzyme responsible for maintaining established methylation patterns
AB  - during replication in mammalian cells. It is composed of a large (approximately 1100 amino
AB  - acids (a.a.)) amino-terminal region containing many putative
AB  - regulatory domains and a smaller (approximately 500 a.a.) carboxy-terminal
AB  - region containing conserved, catalytic domains. In this study, murine DNA
AB  - (cytosine C5)-methyltransferase-1, fused to an amino-terminal
AB  - hexahistidine tag, was expressed by infecting Spodoptera frugiperda cells
AB  - for 46 h with a recombinant baculovirus carrying the DNA
AB  - (cytosine-C5)-methyltransferase-1 cDNA. A total of 3 X 10^8 infected S.
AB  - frugiperda cells yielded approximately 1 mg of full-length,
AB  - hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1, which was
AB  - purified approximately 450-fold from RNase-treated S. frugiperda cell extracts
AB  - by nickel affinity chromatography. The characterization of
AB  - hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 through DNA
AB  - methylation and inhibitor-binding assays indicated that the purified
AB  - enzyme had at least a 30-fold higher catalytic efficiency with
AB  - hemimethylated double-stranded oligodeoxyribonucleotide substrates than
AB  - unmethylated substrates and was most active with small
AB  - oligodeoxyribonucleotide substrates with a capacity for forming stem-loop
AB  - structures. The expression and purification procedures reported here
AB  - differ significantly from the original reports of baculovirus-mediated
AB  - hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 expression and
AB  - purification by nickel affinity chromatography and provide a consistent
AB  - yield of active enzyme.
ER  -

TY  - JOUR
AU  - Brankatschk, K.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Smits, T.H.
AU  - Duffy, B.
TI  - Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp. enterica Serovar Weltevreden.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2066
EP  - 2066
VL  - 193
AB  - The genome of Salmonella enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1
AB  - was sequenced. The genome sequence of this
AB  - fresh-vegetable isolate from Scandinavia will be useful for the
AB  - elucidation of plant host factors in comparison to other serovars of S.
AB  - enterica subsp. enterica.
ER  -

TY  - JOUR
AU  - Brassard, S.
AU  - Paquet, H.
AU  - Roy, P.H.
TI  - A transposon-like sequence adjacent to the AccI restriction-modification operon.
JO  - Gene
PY  - 1995
SP  - 69
EP  - 72
VL  - 157
AB  - We have cloned and sequenced the accIRM genes from Weeksella zoohelcum (the original
AB  - identification of this strain as Acinetobacter calcoaceticus was incorrect).  Our sequence
AB  - differs in the coding regions from a previously published sequence by the addition of three
AB  - nucleotides near the 3' end of the DNA methyltransferase-encoding gene (accIM).  We have
AB  - sequenced approx. 3 kb beyond this operon.  Two genes were found, convergently transcribed
AB  - with the R-M operon.  The first of these genes encodes a protein which shows significant
AB  - similarity to the recombinases of the phage integrase family.  The W. zoohelcum recombinase
AB  - may function as a transposon resolvase, as in Tn4430.  The recombinase-encoding gene is
AB  - followed by a putative transposase (Tnp), which is in turn followed by a terminator which is
AB  - predicted to be Rho-dependent for the recombinase-Tnp operon and Rho-independent for the
AB  - convergent R-M operon.  Since the G+C content of the two operons is notably different, it is
AB  - possible that the terminator is at the extremity of the mobile element and serves to protect
AB  - it from incoming transcription.
ER  -

TY  - JOUR
AU  - Brathwaite, K.J.
AU  - Siringan, P.
AU  - Moreton, J.
AU  - Wilson, R.
AU  - Connerton, I.F.
TI  - Complete Genome Sequence of Universal Bacteriophage Host Strain Campylobacter jejuni subsp. jejuni PT14.
JO  - Genome Announcements
PY  - 2013
SP  - e00969
EP  - e00913
VL  - 1
AB  - Campylobacter jejuni strain PT14 is a clinical isolate previously used to propagate
AB  - bacteriophages in the United Kingdom phage typing scheme. The strain
AB  - has proven useful in the isolation of Campylobacter bacteriophages from several
AB  - sources, and it functions as a model host in phage therapy experiments with
AB  - poultry and poultry meat.
ER  -

TY  - JOUR
AU  - Braun, B.
AU  - Kunzel, S.
AU  - Schroder, J.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of Actinobacterial Strain Kineosporia sp. R_H_3, a Neutrophilic Iron-Depositing Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00335
EP  - e00318
VL  - 6
AB  - The draft genome sequence of a neutrophilic iron-depositing actinobacterial strain,
AB  - Kineosporia sp. R_H_3, is reported here. Detailed analysis of the genome
AB  - can elucidate the role of specific cytochromes for Fe oxidation and how this
AB  - organism might receive energy from Fe oxidation. To date, this is the second
AB  - publicly available genome sequence of a Kineosporia strain.
ER  -

TY  - JOUR
AU  - Braun, B.
AU  - Kunzel, S.
AU  - Schroder, J.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of Strain R_RK_3, an Iron-Depositing Isolate of the Genus Rhodomicrobium, Isolated from a Dewatering Well of an Opencast Mine.
JO  - Genome Announcements
PY  - 2017
SP  - e00864
EP  - e00817
VL  - 5
AB  - Rhodomicrobium sp. strain R_RK_3 is an iron-depositing bacterium from which we report the
AB  - draft genome. This strain was isolated from ochrous depositions of a
AB  - mining well pump in Germany. The Illumina NextSeq technique was used to sequence
AB  - the genome of the strain.
ER  -

TY  - JOUR
AU  - Braun, B.
AU  - Kunzel, S.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of the Gram-Positive Neutrophilic Iron-Precipitating Kineosporia sp. Strain A_224.
JO  - Genome Announcements
PY  - 2017
SP  - e00763
EP  - e00717
VL  - 5
AB  - We report here the draft genome sequence of the neutrophilic iron-precipitating Kineosporia
AB  - sp. strain A_224. Analysis of the predicted genes may improve our
AB  - knowledge of its role in ochrous formations in natural and technical water
AB  - systems. This is the first public genome sequence of a Kineosporia aurantiaca
AB  - strain.
ER  -

TY  - JOUR
AU  - Braun, B.
AU  - Kunzel, S.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of Strain B 225, an Iron-Depositing Isolate of the Genus Novosphingobium.
JO  - Genome Announcements
PY  - 2018
SP  - e00325
EP  - e00318
VL  - 6
AB  - Here, we report the draft genome sequence of Novosphingobium sp. strain B 225, an
AB  - iron-depositing bacterium isolated from a phenazone-amended naturally grown
AB  - biofilm. This biofilm was grown in the Unteres Odertal National Park, Germany.
AB  - Illumina NextSeq sequencing was used to determine the genome of the strain.
ER  -

TY  - JOUR
AU  - Braun, B.
AU  - Kunzel, S.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of Ideonella sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm.
JO  - Genome Announcements
PY  - 2017
SP  - e00803
EP  - e00817
VL  - 5
AB  - Here, we report the draft genome sequence of the betaproteobacterium Ideonella sp. strain
AB  - A_228. This isolate, obtained from a bog iron ore-containing
AB  - floodplain area in Germany, provides valuable information about the genetic
AB  - diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq
AB  - technique was used to sequence the draft genome sequence of the strain.
ER  -

TY  - JOUR
AU  - Braun, B.
AU  - Szewzyk, U.
TI  - Complete Genome Sequence of 'Candidatus Viadribacter manganicus' Isolated from a  German Floodplain Area.
JO  - Genome Announcements
PY  - 2016
SP  - e00897
EP  - e00816
VL  - 4
AB  - Iron- and manganese-depositing bacteria occur in many soils and all water systems, and their
AB  - biogenic depositions of ochre in technical systems may cause
AB  - severe clogging problems and monetary losses. 'Candidatus Viadribacter
AB  - manganicus' is a small coccoid, iron- and manganese-depositing bacterium isolated
AB  - from the Lower Oder Valley National Park, Germany.
ER  -

TY  - JOUR
AU  - Braun, D.R.
AU  - Chevrette, M.G.
AU  - Acharya, D.
AU  - Currie, C.R.
AU  - Rajski, S.R.
AU  - Ritchie, K.B.
AU  - Bugni, T.S.
TI  - Complete Genome Sequence of Dietzia sp. Strain WMMA184, a Marine Coral-Associated Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e01582
EP  - e01517
VL  - 6
AB  - Dietzia sp. strain WMMA184 was isolated from the marine coral Montastraea faveolata as part of
AB  - ongoing drug discovery efforts. Analysis of the 4.16-Mb
AB  - genome provides information regarding interspecies interactions as it pertains to
AB  - the regulation of secondary metabolism and natural product biosynthesis
AB  - potential.
ER  -

TY  - JOUR
AU  - Braun, D.R.
AU  - Chevrette, M.G.
AU  - Acharya, D.D.
AU  - Currie, C.R.
AU  - Rajski, S.R.
AU  - Bugni, T.S.
TI  - Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00077
EP  - e00018
VL  - 6
AB  - Micromonospora sp. strain WMMA1996 was isolated in 2013 off the coast of the Florida Keys,
AB  - United States, from a marine sponge as part of bacterial
AB  - coculture-based drug discovery initiatives. Analysis of the approximately 6.44-Mb
AB  - genome reveals this microbe's potential role in the discovery of new drugs.
ER  -

TY  - JOUR
AU  - Braun, J.
TI  - Structural study of the inhibition of DNA (cytosine-5) methyltransferases by original non-nucleoside inhibitors.
JO  - Chim. Nouv.
PY  - 2010
SP  - 20
EP  - 22
VL  - 28
ER  -

TY  - JOUR
AU  - Bravo, J.I.
AU  - Lozano, G.L.
AU  - Handelsman, J.
TI  - Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e01535
EP  - e01516
VL  - 5
AB  - Flavobacterium johnsoniae CI04 was coisolated with Bacillus cereus from a root of a
AB  - field-grown soybean plant in Arlington, WI, and selected as a model for
AB  - studying commensalism between members of the Cytophaga-Flavobacterium-Bacteroides
AB  - group and B. cereus Here we report the draft genome sequence of F. johnsoniae
AB  - CI04 obtained by Illumina sequencing.
ER  -

TY  - JOUR
AU  - Brawand, S.G.
AU  - Rychener, L.
AU  - Schwendener, S.
AU  - Pantucek, R.
AU  - Perreten, V.
TI  - Complete Genome Sequence of the Type Strain of Macrococcus canis.
JO  - Genome Announcements
PY  - 2018
SP  - e01507
EP  - e01517
VL  - 6
AB  - The first complete genome sequence of the recently described Macrococcus canis species has
AB  - been determined for the strain KM45013(T) (=DSM 101690(T) = CCOS 969(T) = CCUG 68920(T) = CCM
AB  - 8748(T)). The strain was isolated from a dog with rhinitis and contains a putative
AB  - gamma-hemolysin and a mecB-carrying staphylococcal cassette chromosome mec element
AB  - (SCCmecKM45013).
ER  -

TY  - JOUR
AU  - Brawer, R.
AU  - Batista, F.D.
AU  - Burrone, O.
AU  - Sordelli, D.O.
AU  - Cerquetti, M.C.
TI  - The dam methyltransferase of a Salmonella typhimurium insertion mutant.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1996
SP  - 500
EP  - 500
VL  - 96
AB  - A Salmonella typhimurium temperature-sensitive (ts) mutant was obtained after
AB  - transposition mutagenesis with a miniTn10dTc element.  This mutant replicated well at 28oC but
AB  - showed impaired growth at 37oC on LB agar.  Microscopic analysis revealed that the mutant
AB  - produced filaments when cultured at 37oC.  Sequences flanking the insertion site were cloned
AB  - by a
AB  - "jumping PCR" technique.  Sequencing data demonstrated that the miniTn10d Tc was inserted at
AB  - position 804 of the dam gene.  The Dam protein, coded by dam, methylates adenines in 5'-
AB  - GATC-3' sequences.  The miniTn10d Tc insertion created a stop codon truncating the
AB  - translation
AB  - of the Dam last 10 amino acids.  The insertion site GGCTCTGTA was duplicated due to the
AB  - transposition.  DNA digestion with MboI, DpnI and Sau3AI showed that the mutant genomic DNA
AB  - contained methylated and unmethylated GATC sites.  The S. typhimurium wt dam gene showed
AB  - 82% and 92% homology in their nucleotide and deduced amino acid sequences, respectively, with
AB  - the E. coli dam gene.  Mutant transformation with pTP166, which overproduces E. coli Dam,
AB  - complemented the mutant phenotype.  We also constructed a recombinant plasmid (pDeldam)
AB  - which mimics the deletion produced by the miniTn10d Tc insertion.  The pDeldam was used to
AB  - transform an E. coli dam mutant.  The transformants showed a ts phenotype identical to that of
AB  - the
AB  - S. typhimurium insertion mutant.  We conclude that deletion of the last 10 amino acids from
AB  - protein Dam diminished the methylase activity and conferred a ts phenotype.
ER  -

TY  - JOUR
AU  - Brawer, R.
AU  - Batista, F.D.
AU  - Burrone, O.R.
AU  - Sordelli, D.O.
AU  - Cerquetti, M.C.
TI  - A temperature-sensitive DNA adenine methyltransferase mutant of Salmonella typhimurium.
JO  - Arch. Microbiol.
PY  - 1998
SP  - 530
EP  - 533
VL  - 169
AB  - A temperature-sensitive mutant of Salmonella typhimurium was isolated earlier after transposon
AB  - mutagenesis with Tn10dTet.  The mutant D220 grows well at 28 C but has a lower growth rate and
AB  - forms filaments at 37 C.  Transposon-flanking fragments of mutant D220 DNA were cloned and
AB  - sequenced.  The transposon was inserted in the dam gene between positions 803 and 804
AB  - (assigned allele number: dam-231::Tn10dTet) and resulted in a predicted ten-amino-acid-shorter
AB  - Dam protein.  The insertion created a stop codon that led to a truncated Dam protein with a
AB  - temperature-sensitive phenotype.  The insertion dam-231::Tn10dTet resulted in a dam "leaky"
AB  - phenotype since methylated and unmethylated adenines in GATC sequences were present.  In
AB  - addition, the dam-231::Tn10dTet insertion rendered dam mutants temperature-sensitive for
AB  - growth depending upon the genetic background of the S. typhimurium strain.  The wild-type dam
AB  - gene of S. typhimurium exhibited 82% identity with the Escherichia coli dam gene.
ER  -

TY  - JOUR
AU  - Breakwell, D.P.
AU  - Barrus, E.Z.
AU  - Benedict, A.B.
AU  - Brighton, A.K.
AU  - Fisher, J.N.
AU  - Gardner, A.V.
AU  - Kartchner, B.J.
AU  - Ladle, K.C.
AU  - Lunt, B.L.
AU  - Merrill, B.D.
AU  - Morrell, J.D.
AU  - Burnett, S.H.
AU  - Grose, J.H.
TI  - Genome Sequences of Five B1 Subcluster Mycobacteriophages.
JO  - Genome Announcements
PY  - 2013
SP  - e00968
EP  - e00913
VL  - 1
AB  - Mycobacteriophages infect members of the Mycobacterium genus in the phylum Actinobacteria and
AB  - exhibit remarkable diversity. Genome analysis groups the
AB  - thousands of known mycobacteriophages into clusters, of which the B1 subcluster
AB  - is currently the third most populous. We report the complete genome sequences of
AB  - five additional members of the B1 subcluster.
ER  -

TY  - JOUR
AU  - Brede, D.A.
AU  - Snipen, L.G.
AU  - Ussery, D.W.
AU  - Nederbragt, A.J.
AU  - Nes, I.F.
TI  - Complete genome sequence of the commensal Enterococcus faecalis 62 isolated from a healthy Norwegian infant.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2377
EP  - 2378
VL  - 193
AB  - The genome of Enterococcus faecalis 62, a commensal isolate from a healthy Norwegian infant,
AB  - revealed multiple adaptive traits to the gastro intestinal tract (GIT) environment and the
AB  - milk containing diet of a breast fed infant. Adaptation to a commensal existence was
AB  - emphasized by lactose and other carbohydrate metabolism genes within genomic islands
AB  - accompanied by the absence of virulence traits.
ER  -

TY  - JOUR
AU  - Breider, S. et al.
TI  - Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 687
EP  - 703
VL  - 9
AB  - Leisingera nanhaiensis DSM 24252(T) is a Gram-negative, motile, rod-shaped marine
AB  - Alphaproteobacterium, isolated from sandy marine sediments. Here we present the
AB  - non-contiguous genome sequence and annotation together with a summary of the
AB  - organism's phenotypic features. The 4,948,550 bp long genome with its 4,832
AB  - protein-coding and 64 RNA genes consists of one chromosome and six
AB  - extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and
AB  - 35 kb, respectively. The analysis of the genome showed that DSM 24252(T)
AB  - possesses all genes necessary for dissimilatory nitrite reduction, and the strain
AB  - was shown to be facultatively anaerobic, a deviation from the original
AB  - description that calls for an emendation of the species. Also present in the
AB  - genome are genes coding for a putative prophage, for gene-transfer agents and for
AB  - the utilization of methylated amines. Phylogenetic analysis and intergenomic
AB  - distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
ER  -

TY  - JOUR
AU  - Breitbart, M.
AU  - Haynes, M.
AU  - Kelley, S.
AU  - Angly, F.
AU  - Edwards, R.A.
AU  - Felts, B.
AU  - Mahaffy, J.M.
AU  - Mueller, J.
AU  - Nulton, J.
AU  - Rayhawk, S.
AU  - Rodriguez-Brito, B.
AU  - Salamon, P.
AU  - Rohwer, F.
TI  - Viral diversity and dynamics in an infant gut.
JO  - Res. Microbiol.
PY  - 2008
SP  - 367
EP  - 373
VL  - 159
AB  - Metagenomic sequencing of DNA viruses from the feces of a healthy week-old
AB  - infant revealed a viral community with extremely low diversity. The
AB  - identifiable sequences were dominated by phages, which likely influence
AB  - the diversity and abundance of co-occurring microbes. The most abundant
AB  - fecal viral sequences did not originate from breast milk or formula,
AB  - suggesting a non-dietary initial source of viruses. Certain sequences were
AB  - stable in the infant's gut over the first 3 months of life, but microarray
AB  - experiments demonstrated that the overall viral community composition
AB  - changed dramatically between 1 and 2 weeks of age.
ER  -

TY  - JOUR
AU  - Breitbart, M.
AU  - Hewson, I.
AU  - Felts, B.
AU  - Mahaffy, J.M.
AU  - Nulton, J.
AU  - Salamon, P.
AU  - Rohwer, F.
TI  - Metagenomic analyses of an uncultured viral community from human feces.
JO  - J. Bacteriol.
PY  - 2003
SP  - 6220
EP  - 6223
VL  - 185
AB  - Here we present the first metagenomic analyses of an uncultured viral community from human
AB  - feces, using partial shotgun sequencing. Most of the
AB  - sequences were unrelated to anything previously reported. The recognizable
AB  - viruses were mostly siphophages, and the community contained an estimated
AB  - 1,200 viral genotypes.
ER  -

TY  - JOUR
AU  - Breitbart, M.
AU  - Salamon, P.
AU  - Andresen, B.
AU  - Mahaffy, J.M.
AU  - Segall, A.M.
AU  - Mead, D.
AU  - Azam, F.
AU  - Rohwer, F.
TI  - Genomic analysis of uncultured marine viral communities.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 14250
EP  - 14255
VL  - 99
AB  - Viruses are the most common biological entities in the oceans by an order of magnitude.
AB  - However, very little is known about their diversity. Here we report a genomic analysis of two
AB  - uncultured marine viral communities. Over 65% of the sequences were not significantly similar
AB  - to previously reported sequences, suggesting that much of the diversity is previously
AB  - uncharacterized. The most common significant hits among the known sequences were to viruses.
AB  - The viral hits included sequences from all of the major families of dsDNA tailed phages, as
AB  - well as some algal viruses. Several independent mathematical models based on the observed
AB  - number of contigs predicted that the most abundant viral genome comprised 2-3% of the total
AB  - population in both communities, which was estimated to contain between 374 and 7,114 viral
AB  - types. Overall, diversity of the viral communities was extremely high. The results also showed
AB  - that it would be possible to sequence the entire genome of an uncultured marine viral
AB  - community.
ER  -

TY  - JOUR
AU  - Bremer, M.C.D.
AU  - Gimble, F.S.
AU  - Thorner, J.
AU  - Smith, C.L.
TI  - VDE endonuclease cleaves Saccharomyces cerevisiae genomic DNA at a single site: physical mapping of the VMA1 gene.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5484
EP  - 5484
VL  - 20
AB  - A DNA endonuclease, VDE, is derived from the VMA1 gene product of the yeast Saccharomyces
AB  - cerevisiae and is related to other nucleases involved in nucleic acid rearrangements. Analysis
AB  - of two cleavages sites showed that VDE recognizes an extended sequence,
AB  - 5'=TATSYATGYYGGGTGY^GGRG-AARKMGKKAAWGAAAWG-3', and leaves a staggered double-strand break
AB  - with 4-bp 3'-hydroxyl overhangs. Cleavage of one site in the VMA1(delta)vde allele
AB  - (previously deleted for the segment encoding VDE) during meiosis of a heterozygous diploid
AB  - initiates a gene conversion event that transforms the mutant allele into a full-length VMA1
AB  - gene. Here VDE cleavage of this same site in vitro was used to physically map the VMA1 locus.
ER  -

TY  - JOUR
AU  - Brendler, T.
AU  - Austin, S.
TI  - Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences.
JO  - EMBO J.
PY  - 1999
SP  - 2304
EP  - 2310
VL  - 18
AB  - The SeqA protein binds to the post-replicative forms of the origins of replication of the
AB  - Escherichia coli chromosome (oriC) and the P1 plasmid (P1oriR) at hemimethylated GATC adenine
AB  - methylation sites.  It appears to regulate replication by preventing premature reinitiation.
AB  - However, SeqA binding is not exclusive to replication origins: different fragments with
AB  - hemimethylated GATC sites can bind SeqA in vitro when certain rules apply.  Most notably, more
AB  - than one such site must be present on a bound fragment.  The protein appears to recognize
AB  - individual hemimethylated sites, but must undergo an obligate cooperative interaction with a
AB  - nearby found protein for stable binding.  SeqA contacts both DNA strands in a discrete patch
AB  - at each hemimethylated GATC sequence.  All four GATC bases are contacted and are essential for
AB  - binding.  Although the recognized sequence is symmetrical, the footprint on the methylated
AB  - strand is always broader, suggesting that the bound protein is positioned asymmetrically with
AB  - its orientation dictated by the position of the unique methyl group.  Studies of alternative
AB  - spacings and relative orientations of adjacent sites suggest that each site may be recognized
AB  - by a symmetrical dimer with an induced asymmetry in one of the subunits similar to that seen
AB  - with certain type II restriction endonucleases.
ER  -

TY  - JOUR
AU  - Brennan, C.A.
AU  - Gumport, R.I.
TI  - T4 RNA ligase catalyzed synthesis of base analogue-containing oligodeoxyribonucleotides and a characterization of their thermal stabilities.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 8665
EP  - 8684
VL  - 13
AB  - Self-complementary oligodeoxyribonucleotides containing the base analogues
AB  - 2-aminopurine, 2,6-diaminopurine, N6-methyladenine, uracil, and 5-bromouracil
AB  - were synthesized by a general method that allows incorporation of the analogues
AB  - at specific positions.  The method uses chemically synthesized partial
AB  - sequences but circumvents the need for protected base analogues by
AB  - incorporating their unprotected 3',5'-bisphosphate derivatives enzymatically.
AB  - T4 RNA ligase was used to add the analogues to the oligodeoxyribonucleotides
AB  - with yields from 54 to greater than 95 percent.  Oligodeoxyribonucleotides were
AB  - joined to the oligodeoxyribonucleotides containing the analogues at their
AB  - 3'-termini in yields from 22 to 81 percent.  The high yields obtained in these
AB  - joinings suggest that RNA ligase should be of general use for the specific
AB  - incorporation of other deoxyribonucleoside analogues into
AB  - oligodeoxyribonucleotides.  The oligodeoxyribonucleotides containing the base
AB  - analogues were characterized by their mobilities during HPLC, nucleoside
AB  - compositions, sequences, and thermal stabilities.
ER  -

TY  - JOUR
AU  - Brennan, C.A.
AU  - Van Cleve, M.D.
AU  - Gumport, R.I.
TI  - The effects of base analogue substitutions on the methylation by the EcoRI modification methylase of octadeoxyribonucleotides containing modified EcoRI recognition sequences.
JO  - J. Biol. Chem.
PY  - 1986
SP  - 7279
EP  - 7286
VL  - 261
AB  - We have examined the DNA-protein interactions involved in the recognition of a
AB  - specific hexameric sequence, GAATTC, by the EcoRI modification methylase by
AB  - using derivatives of an oligodeoxyribonucleotide that contain a variety of base
AB  - analogues.  The base analogues 2-aminopurine, 5-bromocytosine, 5-bromouracil,
AB  - 2,6-diaminopurine, hypoxanthine, 5-methylcytosine, N6-methyladenine, and uracil
AB  - were incorporated as single substitutions into the octadeoxyribonucleotide
AB  - d(pG-G-A-A-T-T-C-C).  The effects of the substitutions on the ability of the
AB  - enzyme to methylate the modified substrates were monitored by determining the
AB  - steady state kinetic values of the reaction in the presence of the cosubstrate,
AB  - S-adenosylmethionine.  The substitutions resulted in effects ranging from
AB  - complete inactivity to enhanced reactivity.  The enzyme exhibited
AB  - Michaelis-Menten kinetics with those analogues that were active, whereas the
AB  - octanucleotides containing hypoxanthine at the guanine site, N6-methyladenine
AB  - at the first or 2-aminopurine at the second adenine site, or uracil at the
AB  - second thymine site were completely inactive.  The results are discussed in
AB  - terms of the possible interactions between the methylase and its recognition
AB  - sequence.  In addition, the interactions are compared to those of the EcoRI
AB  - restriction endonuclease, which has been similarly tested with the same
AB  - analogue oligonucleotides.  The results of that study are reported in an
AB  - accompanying paper.  Although both enzymes recognize the same sequence, they do
AB  - so in different ways.
ER  -

TY  - JOUR
AU  - Brennan, C.A.
AU  - Van Cleve, M.D.
AU  - Gumport, R.I.
TI  - The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences.
JO  - J. Biol. Chem.
PY  - 1986
SP  - 7270
EP  - 7278
VL  - 261
AB  - It has been proposed that recognition of specific DNA sequences by proteins is
AB  - accomplished by hydrogen bond formation between the protein and particular
AB  - groups that are accessible in the major and minor grooves of the DNA.  We have
AB  - examined the DNA-protein interactions involved in the recognition of the
AB  - hexameric DNA sequence, GAATTC, by the EcoRI restriction endonuclease by using
AB  - derivatives of an oligodeoxyribonucleotide that contain a variety of base
AB  - analogues.  The base analogues hypoxanthine, 2-aminopurine, 2,6-diaminopurine,
AB  - N6-methyladenine, 5-bromouracil, uracil, 5-bromocytosine, and 5-methylcytosine
AB  - were incorporated as single substitutions into the octadeoxyribonucleotide
AB  - d(pG-G-A-A-T-T-C-C).  The effects of the substitutions on the interactions
AB  - between the EcoRI endonuclease and its recognition sequence were monitored by
AB  - determining the steady state kinetic values of the hydrolysis reaction.  The
AB  - substitutions resulted in effects that varied from complete inactivity to
AB  - enhanced reactivity.  The enzyme exhibited Michaelis-Menten kinetics with those
AB  - substrates that were reactive, whereas octanucleotide analoguues containing
AB  - N6-methyladenine at either adenine position, uracil at the second thymine
AB  - position, of 5-bromocytosine or 5-methylcytosine at the cytosine position were
AB  - unreactive.  The results are discussed in terms of possible effects on the
AB  - interactions between the enzyme and its recognition site during the reaction.
AB  - An accompanying paper presents the results of a similar study using these
AB  - oligonucleotides with the EcoRI modification methylase.
ER  -

TY  - JOUR
AU  - Brennan, M.A.
AU  - Trachtenberg, A.M.
AU  - McClelland, W.D.
AU  - MacLea, K.S.
TI  - Genome Sequence of Oceanimonas doudoroffii ATCC 27123T.
JO  - Genome Announcements
PY  - 2017
SP  - e00996
EP  - e00917
VL  - 5
AB  - Oceanimonas doudoroffii ATCC 27123T is an obligately aerobic Gram-negative rod of the class
AB  - Gammaproteobacteria It was first isolated from surface seawater off the
AB  - coast of Oahu, HI, USA, in 1972. The predicted genome size is 3,832,938 bp (G+C
AB  - content, 60.03%), which contains 3,524 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Brenneman, M.
AU  - Gimble, F.S.
AU  - Wilson, J.H.
TI  - Stimulation of intrachromosomal homologous recombination in human cells by electroporation with site-specific endonucleases.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 3608
EP  - 3612
VL  - 93
AB  - In somatic mammalian cells, homologous recombination is a rare event.  To study
AB  - the effects of chromosomal breaks on frequency of homologous recombination, site-specific
AB  - endonucleases were introduced into human cells by electroporation.  Cell lines with a partial
AB  - duplication within the HPRT (hypoxanthine phosphoribosyltransferase) gene were created through
AB  - gene targeting.  Homologous, intrachromosomal recombination between the repeated regions of
AB  - the gene can reconstruct a functioning, wild-type gene.  Treatment of thse cells with the
AB  - restriction
AB  - endonuclease XbaI, which has a recognition site within the repeated region of HPRT homology,
AB  - increased the frequency of homologous recombination by more than 10-fold.  Recombination
AB  - frequency was similarly increased by treatment with the rare-cutting yeast endonuclease
AB  - PI-SceI
AB  - when a cleavage site was placed within the repeated region of HPRT.  In contrast, four
AB  - restriction
AB  - enzymes that cut at positions either outside of the repeated regions or between them produced
AB  - no
AB  - change in recombination frequency.  The results suggest that homologous recombination between
AB  - intrachromosomal repeats can be specificially initiated by a double-strand break occurring
AB  - within
AB  - regions of homology, consistent with the predictions of a double-strand-break-repair model.
ER  -

TY  - JOUR
AU  - Brenner, C.
AU  - Fuks, F.
TI  - DNA methyltransferases: Facts, clues, mysteries.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 2006
SP  - 45
EP  - 66
VL  - 301
AB  - DNA methylation plays a pivotal role during development in mammals and is central to
AB  - transcriptional silencing. The DNA methyltransferases
AB  - (DNMTs) are responsible for the generation of genomic methylation
AB  - patterns leading to gene silencing, but the underlying molecular basis
AB  - remains largely shrouded in mystery. Here we review our current
AB  - understanding of the mechanisms by which DNMTs repress transcription
AB  - and how they are targeted to preferred DNA sequences. Emerging evidence
AB  - points to an essential and intricate web of interactions between DNMTs
AB  - and the chromatin environment in which they function. The recent
AB  - identification of novel transcription factors recruiting the DNMTs may
AB  - open new avenues of research into the origin of DNA methylation
AB  - patterns. Thanks to these emerging clues, researchers have begun to
AB  - lift the veil on the multi-faceted DNMTs, but there remains fascinating
AB  - work ahead for whoever wants to fully understand DNMTs and their role
AB  - in the mammalian cell.
ER  -

TY  - JOUR
AU  - Brenner, E.V.
AU  - Brouchkov, A.V.
AU  - Kurilshikov, A.M.
AU  - Griva, G.I.
AU  - Kashuba, E.
AU  - Kashuba, V.I.
AU  - Melefors, O.
AU  - Repin, V.E.
AU  - Melnikov, V.P.
AU  - Vlassov, V.V.
TI  - Draft Genome Sequence of Bacillus cereus Strain F, Isolated from Ancient Permafrost.
JO  - Genome Announcements
PY  - 2013
SP  - e00561
EP  - e00513
VL  - 1
AB  - Bacillus cereus strain F was isolated and cultured from a sample of permafrost, aged
AB  - presumably about 3 million years, on the Mammoth Mountain (62 degrees 56'N,
AB  - 133 degrees 59'E). These genome data provide the basis to investigate Bacillus
AB  - cereus F, identified as a long-term survivor of the extremely cold and close
AB  - environment.
ER  -

TY  - JOUR
AU  - Brenner, V.
AU  - Focht, D.D.
TI  - Cloning of the Type II methyltransferase from chlorobenzoate degrader Pseudomonas putida P111.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 459
EP  - 459
VL  - 94
AB  - Pseudomonas putida P111 is able to utilize a broad range of mono-, di-, and trichlorinated
AB  - benzoates for growth. Phenotypical varient of this strain, designated P111B, was isolated to
AB  - enable the cloning of the gene complex specifying degradation of ortho-chlorinated benzoates
AB  - which was found on the indigenous plasmid pPB111. However, the cloning of this gene(s) was
AB  - hampered by the presence of the Type II restriction and modification (R-M) system, designed
AB  - PpuI, detected on the same plasmid. The R-M system has the same specificity as the R-M system
AB  - EcoRI, e.g. the restriction endonuclease and the methylase both recognize the sequence
AB  - G/AATTC. The gene for the methyltransferase PpuI was cloned into a broad host range cosmid
AB  - pLAFR3, in selection step including the transformation of DNA isolated from all recombinant
AB  - clones, and predigested thoroughly with EcoRI restriction endonuclease. Thus, only the DNA
AB  - from recombinants protected by the methyltransferase PpuI was not linearized and was able to
AB  - transform the recipient strain E. coli HB101. The region containing the gene for the
AB  - methyltransferase PpuI was further subcloned and reintroduced into the cosmid pLAFR3. The
AB  - isoschizomer enzymes recognizing the sequence G/AATTC were found in two reports on conjugative
AB  - plasmids (EcoRI, RrsII), therefore the comparison of their sequences may be an important
AB  - evolutionary development.
ER  -

TY  - JOUR
AU  - Brenner, V.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Cloning and nucleotide sequence of the gene encoding the EcaI DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 355
EP  - 359
VL  - 18
AB  - The gene coding for the GGTNACC specific EcaI DNA methyltransferase (M.EcaI)
AB  - has been cloned in E. coli from Enterobacter cloacae and its nucleotide
AB  - sequence has been determined.  The ecaIM gene codes for a protein of 452 amino
AB  - acids (Mr:51,111).  It was determined that M.EcaI is an adenine
AB  - methyltransferase.  M.EcaI shows limited amino acid sequence similarity to
AB  - other adenine methyltransferases.  A clone that expresses EcaI
AB  - methyltransferase at high level was constructed.
ER  -

TY  - JOUR
AU  - Brenot, A.
AU  - Werts, C.
AU  - Ottone, C.
AU  - Sertour, N.
AU  - Charon, N.W.
AU  - Postic, D.
AU  - Baranton, G.
AU  - Saint, G.I.
TI  - First evidence for a restriction-modification system in Leptospira sp.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 139
EP  - 143
VL  - 201
AB  - The LE1 leptophage exhibited a host range restricted to the saprophytic Leptospira hiflexa
AB  - [Saint Girons et al., Res. Microbiol. 141 (1990)
AB  - 1131-1133] and mainly to the Patoc 1 strain (hereafter called PFRA)
AB  - kept in the Paris, France collection. Results of titration of LEI
AB  - lysates indicated the presence of a host-controlled modification and
AB  - restriction system within PUSA (Patoc 1 strain maintained in the
AB  - Morgantown, WV, USA collection) that was absent in PFRA. Because
AB  - genomic DNA of PITAL (Patoc 1 strain maintained in Trieste, Italy)
AB  - appeared smeared in pulsed field gel electrophoresis (PFGE), this
AB  - strain is likely to contain nucleases that are activated upon DNA
AB  - isolation. Moreover, comparative Nod digestions of PUSA and PFRA DNAs,
AB  - as visualized by PFGE, indicated that PUSA belonged to a different
AB  - serovar than PFRA. Finally, 16S ribosomal sequence analysis indicated
AB  - that PUSA belonged to the saprophytic Leptospira meyeri species, while
AB  - PITAL and PFRA appertained to L. biflexa. The evolutionary significance
AB  - and the importance of the restriction and modification enzymes or
AB  - non-specific nucleases within strains for genetic experiments are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Brensing-Kuppers, J.
AU  - Reischl, U.
AU  - Schmitz, G.S.
AU  - Kaluza, K.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - McrI:  a novel class-II restriction endonuclease from Micrococcus cryophilus recognizing 5'-CGRY/CG-3'.
JO  - FEBS Lett.
PY  - 1990
SP  - 218
EP  - 222
VL  - 264
AB  - A new class-II restriction endonuclease, McrI, with a novel sequence
AB  - specificity as isolated from the Gram-positive eubacterium Micrococcus
AB  - cryophilus.  McrI recognizes the palindromic hexanucleotide sequence
AB  - 5'-CGRY^CG-3'
AB  - 3'-GC^YRGC-5'.  The novel enzyme in the presence of Mg2+-ions cleaves
AB  - specifically both strands as indicated by the arrows.  The staggered cuts
AB  - generate 3'-protruding ends with single-stranded 5'-RY-3' dinucleotide
AB  - extensions.  The McrI recognition sequence was deduced from mapping data on
AB  - DNAs of bacteriophages PhiX174 RF and M13mp18 RF characterized by one and four
AB  - cleavage sites, respectively.  The cut positions within both strands of the
AB  - recognition sequence were determined in sequencing experiments by analyzing
AB  - hydrolysis of phosphodiester bonds within a polylinker region of M13mp18 RF DNA
AB  - containing an additional McrI recognition site including treatment with T4 DNA
AB  - polymerase.  The novel enzyme may be a useful tool for cloning experiments by
AB  - completion of the enzymes EclXI (5'-C/GGCCG-3'), NotI (5'-GC/GGCCGC-3'), PvuI
AB  - (5'-CGAT/CG-3') as well as EaeI (5'-Y/GGCCR-3') and XhoII (5'-Y/GATCR-3')
AB  - characterized by partly identical sequence specificities.
ER  -

TY  - JOUR
AU  - Brevnov, M.G.
AU  - Gritsenko, O.M.
AU  - Mikhailov, S.N.
AU  - Efimtseva, E.V.
AU  - Ermolinsky, B.S.
AU  - Van Aeroschot, A.
AU  - Herdewijn, P.
AU  - Repyk, A.V.
AU  - Gromova, E.S.
TI  - DNA duplexes with reactive dialdehyde groups as novel reagents for cross-linking to restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3302
EP  - 3309
VL  - 25
AB  - To create new, effective reagents for affinity modification of restriction-modification
AB  - enzymes, a regio-selective method for reactive dialdehyde group incorporation into
AB  - oligonucleotides, based on insertion of a 1-beta-D-galactopyranosylthymine residue, has been
AB  - developed.  We synthesized DNA duplex analogs of the substrates of the EcoRII and MvaI R-M
AB  - enzymes that contained a galactose or periodate-oxidized galactose residue as single
AB  - substituents either in the center of the EcoRII (MvaI) recognition site or in the flanking
AB  - nucleotide sequence.  The dependence of binding, cleavage and methylation of these substrate
AB  - analogs on the modified sugar location in the duplex was determined.  Cross-linking of the
AB  - reagents to the enzymes under different conditions was examined.  M.EcoRII covalent attachment
AB  - to periodate-oxidized substrate analogs proceeded in a specific way and to a large extent
AB  - depended on the location of the reactive dialdehyde group in the substrate.  The yield of
AB  - covalent attachment to a DNA duplex with a dialdehyde group in the flanking sequence with
AB  - EcoRII or MvaI methylases was 9-20% and did not exceed 4% for R.EcoRII.
ER  -

TY  - JOUR
AU  - Brevnov, M.G.
AU  - Kubareva, E.A.
AU  - Romanova, E.A.
AU  - Volkov, E.M.
AU  - Karyagina, A.S.
AU  - Nikolskaya, I.I.
AU  - Gromova, E.S.
TI  - Interaction of the MvaI and SsoII methyltransferases with DNAs altered at the central base pair of the recognition sequence.
JO  - Gene
PY  - 1995
SP  - 149
EP  - 152
VL  - 157
AB  - The interaction of the MvaI and SsoII DNA methyltransferases (MTases; M.MvaI and M.SsoII,
AB  - respectively) with a set of synthetic DNA duplexes, containing an M.MvaI and an M.SsoII
AB  - recognition site (CCWGG), was investigated.  In these DNA duplexes dA or dT of the recognition
AB  - site was replaced by nucleoside analogs with modified sugar moieties and heterocyclic bases
AB  - (2'-deoxy-2'-fluorouridine (flU), 1-(b-D-2'-deoxy-threo-pentofuranosyl) thymine (xT),
AB  - 1-(b-D-3'-deoxy-threo-pentofuranosyl)uracil (tU)), or by 1,3-propanediol (Prd).  A new
AB  - approach for monitoring methylation of each strand of DNA duplexes by MTases was developed.
AB  - It allowed the determination of the influence of the modification in one DNA strand on the
AB  - methylation of the other.  In most cases, for both M.MvaI and M.SsoII, sugar analog-containing
AB  - duplexes showed inhibition of methylation of only the modified strand.  Prd-containing DNA
AB  - duplexes were not substrates for M.MvaI.  M.SsoII did not methylate DNA duplexes in which the
AB  - dT residue was replaced by Prd.
ER  -

TY  - JOUR
AU  - Brevnov, M.G.
AU  - Kubareva, E.A.
AU  - Volkov, E.M.
AU  - Romanova, E.A.
AU  - Oretskaya, T.S.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Influence of a single modification of the DNA sugar-phosphate backbone on the functioning of restriction endonucleases EcoRII, MvaI, and BstNI.
JO  - Mol. Biol. (Mosk)
PY  - 1995
SP  - 1294
EP  - 1300
VL  - 29
AB  - Oligonucleotide duplexes containing modified nucleoside residues
AB  - 1-(2'-deoxy-betaD-threo-pentofuranosyl)thymine (xT) or
AB  - 1-(3'-deoxy-betaD-threo-pentofuranosyl)uracil (tU) in the center of the recognition site for
AB  - EcoRII, MvaI, and BstNI (CCWGG) were constructed and examined in respect of their
AB  - physicochemical and substrate properties.  The restriction endonucleases proved to differ in
AB  - their sensitivity to the resulting conformational distortions.  For the first time with
AB  - EcoRII, the xT-containing analog turned out to be a much better substrate and, moreover, an
AB  - activator of the enzyme.
ER  -

TY  - JOUR
AU  - Brewer, R.J.M.
AU  - Haskett, T.L.
AU  - Ramsay, J.P.
AU  - O'Hara, G.W.
AU  - Terpolilli, J.J.
TI  - Complete Genome Sequence of Mesorhizobium ciceri bv. biserrulae WSM1497, an Efficient Nitrogen-Fixing Microsymbiont of the Forage Legume Biserrula pelecinus.
JO  - Genome Announcements
PY  - 2017
SP  - e00902
EP  - e00917
VL  - 5
AB  - We report here the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain
AB  - WSM1497, the efficient nitrogen-fixing microsymbiont and
AB  - commercial inoculant in Australia of the forage legume Biserrula pelecinus The
AB  - genome consists of 7.2 Mb distributed across a single chromosome (6.67 Mb) and a
AB  - single plasmid (0.53 Mb).
ER  -

TY  - JOUR
AU  - Brezellec, P.
AU  - Hoebeke, M.
AU  - Hiet, M.S.
AU  - Pasek, S.
AU  - Ferat, J.L.
TI  - DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance.
JO  - Bioinformatics
PY  - 2006
SP  - 1935
EP  - 1941
VL  - 22
AB  - Motivation: The Dam methyltransferase (DamMT) activity, broadly distributed in association
AB  - with restriction endonucleases, as part of
AB  - the restriction-modification defense systems, has evolved to become
AB  - intimately associated with essential biological functions in a few
AB  - organisms. In Escherichia coli, DamMT is involved in multiple aspects
AB  - of DNA maintenance, replication initiation, daughter chromosome
AB  - segregation, DNA mismatch repair, gene expression control, etc.
AB  - The participation of DamMT in such a diverse set of functions
AB  - required that other genes adapted, or emerged through evolution, in
AB  - response to the DamMT-induced modification of the genomic environment.
AB  - One example is SeqA, a protein that senses the methylation status of
AB  - the origin of replication of the chromosome to control the timing of
AB  - replication initiation.
AB  - Interestingly, seqA is only present in a few DamMT-specifying
AB  - proteobacteria. This observation led us to hypothesize that other
AB  - genes, specifying related functions, might also be found in these
AB  - organisms. To test this hypothesis, we implemented a large-scale
AB  - comparative genomic screen meant to identify genes specifying DNA
AB  - methylation sensing domains, probably involved in DNA maintenance
AB  - functions.
AB  - Results: We carried out a phylogenetic analysis of DamMT,
AB  - identifying two contrasting behaviors of the protein. Based on this
AB  - phylogeny, we defined precisely a set of genomes, in which the protein
AB  - activity is likely to be involved in DNA maintenance functions, the
AB  - 'resident' dam genomes. We defined a second set of genomes, in which
AB  - DamMT is not resident. We developed a new tool, 'DomainSieve', in
AB  - order to screen these two sets for protein domains that are strictly
AB  - associated with 'resident' dam genomes.
AB  - This approach was rewarding and generated a list of genes, among
AB  - which some, at least, specify activities with clear linkage to
AB  - DamMT-dependent DNA methylation and DNA maintenance.
ER  -

TY  - JOUR
AU  - Brickner, M.
AU  - Chmielewski, J.
TI  - Inhibiting the dimeric restriction endonuclease EcoRI using interfacial helical peptides.
JO  - Chem. Biol.
PY  - 1998
SP  - 339
EP  - 343
VL  - 5
AB  - Many enzymes are active only in a dimeric form, including a variety of type II restriction
AB  - endonucleases.  Disruption of subunit interactions is therefore a potential method for
AB  - multimeric enzyme inhibition.  EcoRI is a homodimeric restriction endonuclease, the dimeric
AB  - interface of which consists of a four-helix bundle.  We set out to design helical peptides to
AB  - interact with this interface and block dimer formation, thus rendering EcoRI inactive.  Here
AB  - we describe two synthetic, helical peptides based on the interfacial region of EcoRI.  Both
AB  - peptides inhibit the enzyme, but the peptide derived from the alpha4 helix of EcoRI had both a
AB  - higher helical content and better efficacy than a variant peptide, alpha4(Leu), that has three
AB  - lle-Leu mutations (IC50 values of 27 microM and 90 microM, and helical contents of 29% and
AB  - 10%, respectively).  Size-exclusion chromatography confirmed that the alpha4 peptide disrupted
AB  - dimerization of EcoRI, and circular dichroism indicated that EcoRI remained folded upon
AB  - binding to alpha4.  Inhibition with alpha4 and alpha4(Leu) was shown to be specific for EcoRI,
AB  - as the dimeric restriction enzyme PvuII was not affected by the peptides.
ER  -

TY  - JOUR
AU  - Bridger, S.L.
AU  - Lancaster, W.A.
AU  - Poole, F.L.I.I.
AU  - Schut, G.J.
AU  - Adams, M.W.
TI  - Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4097
EP  - 4106
VL  - 194
AB  - The model archaeon Pyrococcus furiosus grows optimally near 100 degrees C on carbohydrates and
AB  - peptides. Its genome sequence (NCBI) was determined 12 years
AB  - ago. A genetically tractable strain, COM1, was very recently reported, and here
AB  - we describe its genome sequence. Of 1,909,827 bp in size, it is 1,571 bp longer
AB  - (0.1%) than the reference NCBI sequence. The COM1 genome contains numerous
AB  - chromosomal rearrangements, deletions, and single base changes. COM1 also has 45
AB  - full or partial insertion sequences (ISs) compared to 35 in the reference NCBI
AB  - strain, and these have resulted in the direct deletion or insertional
AB  - inactivation of 13 genes. Another seven genes were affected by chromosomal
AB  - deletions and are predicted to be nonfunctional. In addition, the amino acid
AB  - sequences of another 102 of the 2,134 predicted gene products are different in
AB  - COM1. These changes potentially impact various cellular functions, including
AB  - carbohydrate, peptide, and nucleotide metabolism; DNA repair; CRISPR-associated
AB  - defense; transcriptional regulation; membrane transport; and growth at 72 degrees
AB  - C. For example, the IS-mediated inactivation of riboflavin synthase in COM1
AB  - resulted in a riboflavin requirement for growth. Nevertheless, COM1 grew on
AB  - cellobiose, malto-oligosaccharides, and peptides in complex and minimal media at
AB  - 98 and 72 degrees C to the same extent as did both its parent strain and a new
AB  - culture collection strain (DSMZ 3638). This was in spite of COM1 lacking several
AB  - metabolic enzymes, including nonphosphorylating glyceraldehyde-3-phosphate
AB  - dehydrogenase and beta-glucosidase. The P. furiosus genome is therefore of high
AB  - plasticity, and the availability of the COM1 sequence will be critical for the
AB  - future studies of this model hyperthermophile.
ER  -

TY  - JOUR
AU  - Briers, Y.
AU  - Klumpp, J.
AU  - Schuppler, M.
AU  - Loessner, M.J.
TI  - Genome Sequence of Listeria monocytogenes Scott A, a Clinical Isolate from a Food-Borne Listeriosis Outbreak.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4284
EP  - 4285
VL  - 193
AB  - Listeria monocytogenes is an opportunistic food-borne pathogen and the causative agent of
AB  - listeriosis in animals and humans. We present the
AB  - genome sequence of Listeria monocytogenes Scott A, a widely distributed
AB  - and frequently used serovar 4b clinical isolate from the 1983 listeriosis
AB  - outbreak in Massachusetts.
ER  -

TY  - JOUR
AU  - Briggs, R.E.
AU  - Tatum, F.M.
TI  - Characterization of a restriction endonuclease from Pasteurella haemolytica serotype A1 and construction of a gene-replacement Aroa mutant.
JO  - Haemophilus, Actinobacillus and Pasteurella
PY  - 1995
SP  - 221
EP  - 222
VL  - 0
AB  - A new restriction endonuclease, PhaI, was isolated from P. haemolytica
AB  - serotype
AB  - 1, strain NADC D60, obtained from pneumonic bovine lung.  PhaI recognizes the 5 base
AB  - non-
AB  - palindromic sequences 5'-GCATC-3' and 5'-GATGC-3'.  Cleavage occurs 5 bases 3'
AB  - from the
AB  - former recognition site and 9 bases 5' from the latter.  A gene encoding for a
AB  - methyltransferase
AB  - which protects against PhaI cleavage was cloned from P. haemolytica into E. coli.
AB  - Whereas
AB  - unmethylated plasmid DNA containing a P. haemolytica origin of replication was unable to
AB  - transform P. haemolytica when introduced by electroporation, the same plasmid DNA
AB  - obtained
AB  - from E. coli which contained cloned PhaI methyltransferase could do so.  The aroA gene of
AB  - P.
AB  - haemolytica serotype A1 was cloned and sequenced.  A P. haemolytica ampicillin-
AB  - resistance
AB  - fragment was cloned into the unique NdeI site of aroA.  A hybrid plasmid was constructed
AB  - by
AB  - joining the aroA replacement plasmid with the 4.2 kb P. haemolytica plasmid which
AB  - encodes
AB  - streptomycin resistance.  Following PhaI methylation, the hybrid plasmid was introduced
AB  - into P.
AB  - haemolytica by electroporation.  Allelic exchange between the replacement plasmid and
AB  - chromosome of P. haemolytica gave rise to an ampicillin-resistant mutant which was
AB  - unable to
AB  - grow on medium deficient in tryptophan.  Although transformation efficiency with
AB  - methylated
AB  - hybrid plasmid was <10^3/ug, the hybrid was capable of unstable replication in P.
AB  - haemolytica, so
AB  - this system may be suitable for construction of additional gene-replacement mutants.
ER  -

TY  - JOUR
AU  - Briggs, R.E.
AU  - Tatum, F.M.
TI  - Generation and molecular characterization of new temperature-sensitive plasmids intended for genetic engineering of Pasteurellaceae.
JO  - Appl. Environ. Microbiol.
PY  - 2005
SP  - 7187
EP  - 7195
VL  - 71
AB  - Temperature-sensitive (TS) plasmids were generated through chemical mutagenesis of a
AB  - derivative of the streptomycin resistance parent plasmid pD70, isolated from Mannheimia
AB  - hemolytica serotype 1. Three TS plasmids which failed to replicate at or above 42 degrees C in
AB  - M. hemolytica but which were fully functional below 31 degrees C were selected for further
AB  - analysis. Two of the TS plasmids were shown by sequencing to possess unique single-base-pair
AB  - mutations. The third TS plasmid contained a unique base pair substitution and a second
AB  - mutation that had been previously identified. These mutations were clustered within a 200-bp
AB  - region of the presumed plasmid origin of replication. Site-directed single-nucleotide
AB  - substitutions were introduced into the wild-type pD70 origin of replication to confirm that
AB  - mutations identified by sequencing had conferred thermoregulated replication. Deletion
AB  - analysis on the wild-type pD70 plasmid replicon revealed that approximately 720 bp are
AB  - necessary for plasmid maintenance. Replication of the TS plasmids was thermoregulated in
AB  - Pasteurella multocida and Haemophilus somnus as well. To consistently transform H. somnus with
AB  - TS plasmid, in vitro DNA methylation with commercially available HhaI methyltransferase was
AB  - necessary to protect against the organism's restriction enzyme HsoI (recognition sequence
AB  - 5'-GCGC-3') characterized herein.
ER  -

TY  - JOUR
AU  - Briggs, R.E.
AU  - Tatum, F.M.
AU  - Casey, T.A.
AU  - Frank, G.H.
TI  - Characterization of a restriction endonuclease, PhaI, from Pasteurella haemolytica Serotype A1 and protection of heterologous DNA by a cloned PhaI methyltransferase gene.
JO  - Appl. Environ. Microbiol.
PY  - 1994
SP  - 2006
EP  - 2010
VL  - 60
AB  - Pasteurella haemolytica is the leading cause of economic loss to the beef cattle industry in
AB  - the United States and an important etiologic agent worldwide. Study of P. haemolytica is
AB  - hindered by researchers' inability to genetically manipulate the organism. A new restriction
AB  - endonuclease, PhaI, an isoschizomer of SfaNI (R.J. Roberts, Methods Enzymol. 65:19-36, 1980),
AB  - was isolated from P. haemolytica serotype I, strain NADC-D60, obtained from pneumonic bovine
AB  - lung, PhaI recognizes the 5-base nonpalindromic sequences 5'-GCATC-3' and 5'-GATGC-3'.
AB  - Cleavage occurs 5 bases 3' from the former recognition site and 9 bases 5' from the latter
AB  - recognition site. A gene encoding a methyltransferase which protects against PhaI cleavage was
AB  - cloned from P. haemolytica NADC-D60 into Escherichia coli. Whereas unmethylated plasmid DNA
AB  - containing a P. haemolytica origin of replication was unable to transform P. haemolytica when
AB  - introduced by electroporation, the same plasmid DNA obtained from E. coli which contained a
AB  - cloned PhaI methyltransferase gene could do so. The data indicate that PhaI is an effective
AB  - barrier to the introduction and establishment of exogenous DNA in P. haemolytica.
ER  -

TY  - JOUR
AU  - Briggs, R.E.
AU  - Tatum, F.M.
AU  - Casey, T.A.
AU  - Frank, G.H.
TI  - Characterization of a restriction endonuclease, PhaI, from Pasteurella haemolytica serotype A1 and protection of heterologous DNA by cloned PhaI methyltransferase.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 132
EP  - 132
VL  - 94
AB  - Pasteurella haemolytica is the leading cause of economic loss to the beef cattle industry in
AB  - the US, and an important etiologic agent worldwide. Study of P. haemolytica is hindered by
AB  - researchers' inability to genetically manipulate the organism. A new restriction
AB  - endonuclease, PhaI, an isoschizomer of SfaNI, was isolated from Pasteurella haemolytica
AB  - serotype 1, strain NADC-D60, obtained from pneumonic bovine lung. PhaI recognizes the 5 base
AB  - non-palindromic sequences 5'-GCATC-3' and 5'-GATGC-3'. Cleavage occurs 5 bases 3' from
AB  - the former recognition site and 9 bases 5' from the latter recognition site. A gene encoding
AB  - for a methyltransferase which protects against PhaI cleavage was cloned from P. haemolytica
AB  - NADC-D60 into E. coli. Whereas unmethylated plasmid DNA containing a P. haemolytica origin of
AB  - replication was unable to transform P. haemolytica when introduced by electroporation, the
AB  - same plasmid DNA obtained from E. coli which contained cloned PhaI methyltransferase could do
AB  - so. The data indicate that PhaI is an effective barrier to the introduction and establishment
AB  - of exogenous DNA in P. haemolytica.
ER  -

TY  - JOUR
AU  - Bringel, F. et al.
TI  - Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21.
JO  - Genome Announcements
PY  - 2017
SP  - e00622
EP  - e00617
VL  - 5
AB  - The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from
AB  - samples of environments contaminated with halogenated pollutants
AB  - and capable of using dichloromethane as its sole carbon and energy source, was
AB  - determined.
ER  -

TY  - JOUR
AU  - Brinkley, C.
AU  - Burland, V.
AU  - Keller, R.
AU  - Rose, D.J.
AU  - Boutin, A.T.
AU  - Klink, S.A.
AU  - Blattner, F.R.
AU  - Kaper, J.B.
TI  - Nucleotide Sequence Analysis of the Enteropathogenic Escherichia coli Adherence Factor Plasmid pMAR7.
JO  - Infect. Immun.
PY  - 2006
SP  - 5408
EP  - 5413
VL  - 74
AB  - The complete nucleotide sequence was determined for pMAR7, an
AB  - enteropathogenic Escherichia coli (EPEC) adherence factor (EAF) plasmid
AB  - that contains genes encoding a type IV attachment pilus (Bfp) and the
AB  - global virulence regulator per. Prototypic EAF plasmid pMAR7 is
AB  - self-transmissible, unlike the smaller EAF plasmid pB171, which has no
AB  - genes encoding conjugative functions. The tra locus, a highly conserved
AB  - 33-kb segment found in pMAR7, is similar to the tra (conjugation) region
AB  - of the F plasmid. ISEc13 copies flanking the pMAR7 tra region could
AB  - potentially mobilize or delete the tra genes. Hybridization of 134 EPEC
AB  - strains showed that a complete tra region is present only in strains of
AB  - the EPEC1 clonal group. This study confirms EPEC's potential for
AB  - dissemination of virulence attributes by horizontal transfer of the EAF
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Brinkley, P.
AU  - Bautista, D.S.
AU  - Graham, F.L.
TI  - The cleavage site of restriction endonuclease MnlI.
JO  - Gene
PY  - 1991
SP  - 267
EP  - 268
VL  - 100
AB  - The cleavage site generated by restriction endonuclease MnlI has the structure:
AB  - 5'-CCTC(N)7-3'
AB  - 3'-GGAG(N)6-5'  with one-nucleotide 3' overhang.
ER  -

TY  - JOUR
AU  - Brinkrolf, K.
AU  - Schneider, J.
AU  - Knecht, M.
AU  - Ruckert, C.
AU  - Tauch, A.
TI  - Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear  Fluid from a Child with Otitis Media.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5968
EP  - 5969
VL  - 194
AB  - Turicella otitidis is an unusual corynebacterium with a controversial role in otitis media in
AB  - children. Metabolic capabilities deduced from the draft genome
AB  - indicate its adaptation to habitats on the human skin and in the intestine. The
AB  - lack of candidate virulence factors implies that T. otitidis has a low pathogenic
AB  - potential.
ER  -

TY  - JOUR
AU  - Brizendine, A.M.
AU  - Rousseau, S.
AU  - Hernandez, A.C.
AU  - Kuty, E.G.F.
TI  - Complete Genome Sequence of Bacillus megaterium Siphophage Stahl.
JO  - Genome Announcements
PY  - 2015
SP  - e00857
EP  - e00815
VL  - 3
AB  - Stahl is a siphophage active against Bacillus megaterium, a Gram-positive bacterium often used
AB  - as a model system in research and as a protein production
AB  - strain in industrial applications. Here, we present the complete annotated genome
AB  - of phage Stahl and describe its major features.
ER  -

TY  - JOUR
AU  - Brnakova, Z.
AU  - Farkasovska, J.
AU  - Godany, A.
TI  - The use of bacteriophages in eliminating polyresistant strains of Staphylococcus aureus and Streptococcus agalactiae.
JO  - Folia Microbiol. (Praha)
PY  - 2005
SP  - 187
EP  - 194
VL  - 50
AB  - Temperate bacteriophages were induced in and released from isolates of Staphylococcus aureus
AB  - and Streptococcus agalactiae using mitomycin C. Various specific indicator cultures were
AB  - tested for providing clear plaques after phage infection. Specific lytic mixture of
AB  - bacteriophages was prepared using the induced, modified and laboratory variants of phages.
AB  - Under laboratory conditions, the mixture eliminated all isolates from the tested collection of
AB  - microorganisms. The restriction barrier of some bacterial isolates to bacteriophage infection
AB  - was overcome either by UV irradiation or in vitro modification of bacteriophage DNA with
AB  - specific methyltransferases. Conjugative R plasmids, capable of replication in G(+) and G(-)
AB  - bacteria, were detected and isolated from S. aureus and S. agalactiae antibiotic-resistant
AB  - strains.
ER  -

TY  - JOUR
AU  - Broadbent, J.R.
AU  - Hughes, J.E.
AU  - Welker, D.L.
AU  - Tompkins, T.A.
AU  - Steele, J.L.
TI  - Complete Genome Sequence for Lactobacillus helveticus CNRZ 32, an Industrial Cheese Starter and Cheese Flavor Adjunct.
JO  - Genome Announcements
PY  - 2013
SP  - e00590
EP  - e00513
VL  - 1
AB  - Lactobacillus helveticus is a lactic acid bacterium widely used in the manufacture of cheese
AB  - and for production of bioactive peptides from milk
AB  - proteins. We present the complete genome sequence for L. helveticus CNRZ 32, a
AB  - strain particularly recognized for its ability to reduce bitterness and
AB  - accelerate flavor development in cheese.
ER  -

TY  - JOUR
AU  - Broadbent, J.R.
AU  - Neeno-Eckwall, E.C.
AU  - Stahl, B.
AU  - Tandee, K.
AU  - Cai, H.
AU  - Morovic, W.
AU  - Horvath, P.
AU  - Heidenreich, J.
AU  - Perna, N.T.
AU  - Barrangou, R.
AU  - Steele, J.L.
TI  - Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation.
JO  - BMC Genomics
PY  - 2012
SP  - 533
EP  - 533
VL  - 13
AB  - BACKGROUND: The broad ecological distribution of L. casei makes it an insightful
AB  - subject for research on genome evolution and lifestyle adaptation. To explore
AB  - evolutionary mechanisms that determine genomic diversity of L. casei, we
AB  - performed comparative analysis of 17 L. casei genomes representing strains
AB  - collected from dairy, plant, and human sources. RESULTS: Differences in L. casei
AB  - genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220
AB  - accessory genes. Extrapolation of pan-genome data indicates L. casei has a
AB  - supragenome approximately 3.2 times larger than the average genome of individual
AB  - strains. Evidence suggests horizontal gene transfer from other bacterial species,
AB  - particularly lactobacilli, has been important in adaptation of L. casei to new
AB  - habitats and lifestyles, but evolution of dairy niche specialists also appears to
AB  - involve gene decay. CONCLUSIONS: Genome diversity in L. casei has evolved through
AB  - gene acquisition and decay. Acquisition of foreign genomic islands likely confers
AB  - a fitness benefit in specific habitats, notably plant-associated niches. Loss of
AB  - unnecessary ancestral traits in strains collected from bacterial-ripened cheeses
AB  - supports the hypothesis that gene decay contributes to enhanced fitness in that
AB  - niche. This study gives the first evidence for a L. casei supragenome and
AB  - provides valuable insights into mechanisms for genome evolution and lifestyle
AB  - adaptation of this ecologically flexible and industrially important lactic acid
AB  - bacterium. Additionally, our data confirm the Distributed Genome Hypothesis
AB  - extends to non-pathogenic, ecologically flexible species like L. casei.
ER  -

TY  - JOUR
AU  - Broadbent, S.E.
AU  - Balbontin, R.
AU  - Casadesus, J.
AU  - Marinus, M.G.
AU  - van der Woude, M.
TI  - YhdJ, a Nonessential CcrM-Like DNA Methyltransferase of Escherichia coli and Salmonella enterica.
JO  - J. Bacteriol.
PY  - 2007
SP  - 4325
EP  - 4327
VL  - 189
AB  - The Caulobacter crescentus DNA adenine methyltransferase CcrM and its homologs in the
AB  - alpha-Proteobacteria are essential for viability. CcrM is
AB  - 34% identical to the yhdJ gene products of Escherichia coli and Salmonella
AB  - enterica. This study provides evidence that the E. coli yhdJ gene encodes
AB  - a DNA adenine methyltransferase. In contrast to an earlier report,
AB  - however, we show that yhdJ is not an essential gene in either E. coli or
AB  - S. enterica.
ER  -

TY  - JOUR
AU  - Broberg, C.A.
AU  - Palacios, M.
AU  - Miller, V.L.
TI  - Whole-Genome Draft Sequences of Three Multidrug-Resistant Klebsiella pneumoniae Strains Available from the American Type Culture Collection.
JO  - Genome Announcements
PY  - 2013
SP  - e00312
EP  - e00313
VL  - 1
AB  - Infection with multidrug-resistant Klebsiella pneumoniae is a significant problem worldwide,
AB  - requiring a better understanding of how various strains are able to
AB  - defeat current antibiotic therapies and cause disease. Here, we report the draft
AB  - genome sequences of three K. pneumoniae strains harboring the SHV-18, KPC-2, or
AB  - NDM-1 beta-lactamases.
ER  -

TY  - JOUR
AU  - Broberg, C.A.
AU  - Wu, W.
AU  - Cavalcoli, J.D.
AU  - Miller, V.L.
AU  - Bachman, M.A.
TI  - Complete Genome Sequence of Klebsiella pneumoniae Strain ATCC 43816 KPPR1, a Rifampin-Resistant Mutant Commonly Used in Animal, Genetic, and Molecular Biology  Studies.
JO  - Genome Announcements
PY  - 2014
SP  - e00924
EP  - e00914
VL  - 2
AB  - Klebsiella pneumoniae is an urgent public health threat due to the spread of
AB  - carbapenem-resistant strains causing serious, and frequently fatal, infections.
AB  - To facilitate genetic, molecular, and immunological studies of this pathogen, we
AB  - report the complete chromosomal sequence of a genetically tractable, prototypical
AB  - strain used in animal models.
ER  -

TY  - JOUR
AU  - Brocchi, M.
AU  - de Vasconcelos, A.T.R.
AU  - Zaha, A.
TI  - Restriction-modification systems in Mycoplasma spp.
JO  - Genet. Mol. Biol.
PY  - 2007
SP  - 236
EP  - 244
VL  - 30
AB  - Restriction and Modification (R-M) systems are present in all Mycoplasma species sequenced so
AB  - far. The presence of these genes poses
AB  - barriers to gene transfer and could protect the cell against phage
AB  - infections. The number and types of R-M genes between different
AB  - Mycoplasma species are variable, which is characteristic of a
AB  - polymorphism. The majority of the CDSs code for Type III R-M systems
AB  - and particularly for methyltransferase enzymes, which suggests that
AB  - functions other than the protection against the invasion of
AB  - heterologous DNA may exist. A possible function of these enzymes could
AB  - be the protection against the invasion of other but similar R-M
AB  - systems. In Mycoplasma hyopneumoniae strain J, three of the putative
AB  - methyltransferase genes were clustered in a region forming a genomic
AB  - island. Many R-M CDSs were mapped in the vicinity of transposable
AB  - elements suggesting an association between these genes and reinforcing
AB  - the idea of R-M systems as mobile selfish DNA. Also, many R-M genes
AB  - present repeats within their coding sequences, indicating that their
AB  - expression is under the control of phase variation mechanisms.
AB  - Altogether, these data suggest that R-M systems are a remarkable
AB  - characteristic of Mycoplasma species and are probably involved in the
AB  - adaptation of these bacteria to different environmental conditions.
ER  -

TY  - JOUR
AU  - Brockes, J.P.
TI  - Nucleotide sequences at the sites of action of the deoxyribonucleic acid modification enzyme of bacteriophage P1.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 437
EP  - 443
VL  - 88
AB  - Labelled oligonucleotides have been fractionated from DNAase digests of phage
AB  - lambda DNA that had been methylated with the phage P1 modification enzyme and
AB  - S-[methyl-14C]adenosyl-L-methionine.  The longest sequences established are the
AB  - tetranucleotides pG-A*-T-C and pA*-T-C-T, which, together with the other
AB  - sequences determined, particularly pA*-G-A, show that the modification enzyme,
AB  - M.EcoP1, methylates adenine residues within defined sequences and suggest that
AB  - the oligonucleotide sequence recognized by this enzyme is the hexanucleotide
AB  - pA-G-A-T-C-T.  The duplex formed by base-pairing this hexanucleotide with its
AB  - complementary sequence resembles the recognition sequence for several
AB  - restriction enzymes in being bisected by an axis of 2-fold rotational symmetry.
ER  -

TY  - JOUR
AU  - Brockes, J.P.
TI  - The deoxyribonucleic acid-modification enzyme of bacteriophage P1. Subunit structure.
JO  - Biochem. J.
PY  - 1973
SP  - 629
EP  - 633
VL  - 133
AB  - The bacteriophage P1 modification enzyme was purified 1400-fold from induced
AB  - lysogens of a thermoinducible mutant of bacteriophage P1.  The most purified
AB  - fraction, when analysed by polyacrylamide-gel electropohoresis in sodium
AB  - dodecyl sulphate, showed two principal stained bands.  The two bands
AB  - co-sedimented in a glycerol gradient with the modification activity, at a rate
AB  - which, when compared with the rate of sedimentation of marker proteins,
AB  - corresponds to a sedimentation coefficient in water of 6S.  The mobilities of
AB  - the bands on sodium dodecyl sulphate-polyacrylamide-gel electrophoresis
AB  - corresponded to polypeptides of molecular weight 70000 and 45000 and they were
AB  - present in equimolar amounts.  It was concluded that the 6S species of the
AB  - enzyme is a dimer of unlike subunits.
ER  -

TY  - JOUR
AU  - Brockes, J.P.
AU  - Brown, P.R.
AU  - Murray, K.
TI  - The deoxyribonucleic acid modification enzyme of bacteriophage P1: Purification and properties.
JO  - Biochem. J.
PY  - 1972
SP  - 1
EP  - 10
VL  - 127
AB  - The bacteriophage P1 modification enzyme, assayed by the specific methylation
AB  - of unmodified bacteriophage 82 DNA, has been purified 500-fold from a
AB  - bacteriophage P1 lysogen of Escherichia coli.  The enzyme catalyses the
AB  - incorporation of approximately 20-24 methyl groups per bacteriophage 82 DNA
AB  - molecule.  The sole product of methylation is 6-methylaminopurine.  Methylation
AB  - of unmodified bacteriophage DNA confers protection against a challenge by
AB  - purified bacteriophage P1 restriction enzyme.  The pH optimum is 6.0-6.25: the
AB  - apparent Km for S-adenosyl-L-methionine is 5 microM.
ER  -

TY  - JOUR
AU  - Brok-Volchanskaya, V.S.
AU  - Kadyrov, F.A.
AU  - Sivogrivov, D.E.
AU  - Kolosov, P.M.
AU  - Sokolov, A.S.
AU  - Shlyapnikov, M.G.
AU  - Kryukov, V.M.
AU  - Granovsky, I.E.
TI  - Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 2094
EP  - 2105
VL  - 36
AB  - Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own
AB  - genes and the flanking sequences by cleaving the
AB  - recipient DNA. Bacteriophage T4 segB gene, which is located in a
AB  - cluster of tRNA genes, encodes a protein of unknown function,
AB  - homologous to homing endonucleases of the GIY-YIG family. We
AB  - demonstrate that SegB protein is a site-specific endonuclease, which
AB  - produces mostly 3 2-nt protruding ends at its DNA cleavage site.
AB  - Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp
AB  - sequence. It contains 11-bp conserved sequence, which corresponds to a
AB  - conserved motif of tRNA TC stem-loop, whereas the remainder of the
AB  - recognition site is rather degenerate. T4-related phages T2L, RB1 and
AB  - RB3 contain tRNA gene regions that are homologous to that of phage T4
AB  - but lack segB gene and several tRNA genes. In co-infections of phages
AB  - T4 and T2L, segB gene is inherited with nearly 100 of efficiency. The
AB  - preferred inheritance depends absolutely on the segB gene integrity and
AB  - is accompanied by the loss of the T2L tRNA gene region markers. We
AB  - suggest that SegB is a homing endonuclease that functions to ensure
AB  - spreading of its own gene and the surrounding tRNA genes among
AB  - T4-related phages.
ER  -

TY  - JOUR
AU  - Brolund, A.
AU  - Franzen, O.
AU  - Melefors, O.
AU  - Tegmark-Wisell, K.
AU  - Sandegren, L.
TI  - Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing.
JO  - PLoS ONE
PY  - 2013
SP  - E65793
EP  - E65793
VL  - 8
AB  - Infections caused by Extended spectrum beta-lactamase (ESBL)-producing E. coli
AB  - are an emerging global problem, threatening the effectiveness of the extensively
AB  - used beta-lactam antibiotics. ESBL dissemination is facilitated by plasmids,
AB  - transposons, and other mobile elements. We have characterized the plasmid content
AB  - of ESBL-producing E. coli from human urinary tract infections. Ten diverse
AB  - isolates were selected; they had unrelated pulsed-field gel electrophoresis
AB  - (PFGE) types (<90% similarity), were from geographically dispersed locations and
AB  - had diverging antibiotic resistance profiles. Three isolates belonged to the
AB  - globally disseminated sequence type ST131. ESBL-genes of the CTX-M-1 and CTX-M-9
AB  - phylogroups were identified in all ten isolates. The plasmid content (plasmidome)
AB  - of each strain was analyzed using a combination of molecular methods and
AB  - high-throughput sequencing. Hidden Markov Model-based analysis of unassembled
AB  - sequencing reads was used to analyze the genetic diversity of the plasmid samples
AB  - and to detect resistance genes. Each isolate contained between two and eight
AB  - distinct plasmids, and at least 22 large plasmids were identified overall. The
AB  - plasmids were variants of pUTI89, pKF3-70, pEK499, pKF3-140, pKF3-70, p1ESCUM,
AB  - pEK204, pHK17a, p083CORR, R64, pLF82, pSFO157, and R721. In addition, small
AB  - cryptic high copy-number plasmids were frequent, containing one to seven open
AB  - reading frames per plasmid. Three clustered groups of such small cryptic plasmids
AB  - could be distinguished based on sequence similarity. Extrachromosomal prophages
AB  - were found in three isolates. Two of them resembled the E. coli P1 phage and one
AB  - was previously unknown. The present study confirms plasmid multiplicity in
AB  - multi-resistant E. coli. We conclude that high-throughput sequencing successfully
AB  - provides information on the extrachromosomal gene content and can be used to
AB  - generate a genetic fingerprint of possible use in epidemiology. This could be a
AB  - valuable tool for tracing plasmids in outbreaks.
ER  -

TY  - JOUR
AU  - Bromberg, S.
AU  - Pratt, K.
AU  - Hattman, S.
TI  - Sequence specificity of DNA adenine methylase in the protozoan Tetrahymena thermophila.
JO  - J. Bacteriol.
PY  - 1982
SP  - 993
EP  - 996
VL  - 150
AB  - The sequence specificity of the Tetrahymena DNA-adenine methylase was determined by
AB  - nearest-neighbor analyses of in vivo and in vitro methylated DNA.  In vivo all four common
AB  - bases were found to the 5' side of N6-methyladenine, but only thymidine was 3'.  Homologous
AB  - DNA already methylated in vivo and heterologous Micrococcus luteus DNA were methylated in
AB  - vitro by a partially purified DNA-adenine methylase activity isolated from Terrahymena
AB  - macronuclei.  The in vitro-methylated sequence differed from the in vivo sequence in that both
AB  - thymidine and cytosine were 3' nearest neighbors of N6-methyladenine.
ER  -

TY  - JOUR
AU  - Bromfield, E.S.P.
AU  - Cloutier, S.
AU  - Tambong, J.T.
AU  - Tran-Thi, T.V.
TI  - Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential.
JO  - Syst. Appl. Microbiol.
PY  - 2017
SP  - 440
EP  - 447
VL  - 40
AB  - An assessment was made of the evolutionary relationships of soybean nodulating
AB  - bacteria associated with legumes native to eastern Canada to identify potential
AB  - new sources of soybean inoculant strains. Short season soybeans were used to
AB  - selectively trap bacteria from root zone soils of four native legume species.
AB  - Screening of more than 800 bacterial isolates from soybean root nodules by
AB  - analysis of recA gene sequences followed by analyses of selected genotypes using
AB  - six core and two symbiosis (nodC and nifH) gene sequences permitted
AB  - identification of diverse taxa that included eight novel and four named
AB  - Bradyrhizobium species as well as lineages attributed to the genera Afipia and
AB  - Tardiphaga. Plant tests showed that symbionts related to four named species as
AB  - well as a novel Bradyrhizobium lineage were highly efficient with regard to
AB  - nitrogen fixation on soybeans relative to an inoculant strain. A new symbiovar
AB  - (sv. septentrionalis) is proposed based on a group of four novel Bradyrhizobium
AB  - spp. that possess distinctive nodC and nifH gene sequences and symbiotic
AB  - characteristics. Evidence is provided for horizontal transfer of sv.
AB  - septentrionalis symbiosis genes between novel Bradyrhizobium spp., a process that
AB  - rendered recipient bacteria ineffective on soybeans. Diverse lineages of
AB  - non-symbiotic and symbiotic Bradyrhizobium spp. co-occured within monophyletic
AB  - clusters in a phylogenetic tree of concatenated core genes, suggesting that loss
AB  - and/or gain of symbiosis genes has occurred in the evolutionary history of the
AB  - bacterial genus. Our data suggest that symbiont populations associated with
AB  - legumes native to eastern Canada harbour elite strains of Bradyrhizobium for
AB  - soybean inoculation.
ER  -

TY  - JOUR
AU  - Bron, P.A.
AU  - Lee, I.C.
AU  - Backus, L.
AU  - van Hijum, S.A.
AU  - Wels, M.
AU  - Kleerebezem, M.
TI  - Draft Genome Sequence of Lactobacillus plantarum SF2A35B.
JO  - Genome Announcements
PY  - 2016
SP  - e01638
EP  - e01615
VL  - 4
AB  - The lactic acid bacterium Lactobacillus plantarum is intensively studied as a model probiotic
AB  - species. Here, we present the draft genome sequence of the
AB  - exopolysaccharide-producing strain SF2A35B.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Horz, W.
TI  - Purification and properties of the Bsu endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 112
EP  - 132
VL  - 65
AB  - For various reasons Bacillus subtilis is an attractive organism to study
AB  - restriction and modification.  It is easy to grow and to manipulate, has a
AB  - fairly detailed genetic map, and, most important, possesses a simple
AB  - transformation/transfection system.  This enables the introduction of
AB  - biologically active DNA into cells of defined R-M background, and the analysis
AB  - of its fate.  In addition, the effects of in vitro treatments of biologically
AB  - active DNA with restriction and modification enzymes can conveniently be
AB  - studied by means of transformation and transfection.  Restriction and
AB  - modification in B. subtilis were demonstrated some years ago.  A site-specific
AB  - type II restriction endonuclease, Bsu, has been purified and characterized from
AB  - B. subtilis strain R.  The enzyme cleaves susceptible DNAs in the middle of the
AB  - tetranucleotide sequence 5'GGCC3'.  Resistance to Bsu is conferred to DNA by
AB  - the modification methylase from the same strain, which methylates the internal
AB  - C residues of the recognition sequence.  We will describe the purification and
AB  - properties of Bsu.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Janniere, L.
AU  - Ehrlich, S.D.
TI  - Restriction and modification in Bacillus subtilis Marburg 168:  Target sites and effects on plasmid transformation.
JO  - Mol. Gen. Genet.
PY  - 1988
SP  - 186
EP  - 189
VL  - 211
AB  - The effects of the restriction system of Bacillus subtilis strain M on plasmid
AB  - transformation were studied.  Plasmid pHV1401 DNA prepared from B. subtilis
AB  - transformed the restriction-proficient M strain 100 times more efficiently than
AB  - the DNA prepared from Escherichia coli, while the two DNA preparations
AB  - transformed restriction-deficient derivatives of that strain with similar
AB  - efficiencies.  This indicates that transformation with pHV1401 is sensitive to
AB  - the M restriction system.  pHV1401 contains three CTCGAG (XhoI sites).
AB  - Successive removal of these abolished the effect of restriction.  This
AB  - indicates that the XhoI sites are the targets for the M restriction system.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Luxen, E.
AU  - Trautner, T.A.
TI  - Restriction and modification in B. subtilis:  the role of homology between donor and recipient DNA in transformation and transfection.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 111
EP  - 117
VL  - 179
AB  - Non-modified DNAs from phages SPO2 and Phi105, and prophage DNAs extracted from
AB  - lysogens carrying these phages, were used to transfect isogenic r-m- B.
AB  - subtilis recipients which were either non-lysogenic, or had been lysogenized
AB  - with a homologous or a non-homologous phage.  Restriction of transfecting phage
AB  - and prophage DNA occurred in non-lysogenic recipients and in recipients
AB  - lysogenic for a non-homologous phage.  No effect of restriction was observed
AB  - when phage or prophage DNA was used to transfect recipients carrying a
AB  - homologous prophage.  This is analogous to the absence of restriction in
AB  - transformation and indicates that in B. subtilis the distinction between
AB  - transforming and transfecting DNA is not made at the initial stages of DNA
AB  - uptake and processing, but rather at later stages, where recognition of
AB  - homologous regions in donor and recipient DNA plays an important role.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Luxen, E.
AU  - Venema, G.
TI  - Resistance of bacteriophage H1 to restriction and modification by Bacillus subtilis R.
JO  - J. Virol.
PY  - 1983
SP  - 703
EP  - 708
VL  - 46
AB  - H1, a 5-hydroxymethyluracil (HMU)-containing Bacillus subtilis bacteriophage,
AB  - was neither restricted nor modified upon infection of B. subtilis R cells.  In
AB  - vitro, H1 DNA was not restricted by BsuR under standard conditions (200 mM
AB  - salt), although the expected frequency of -GGCC- cleavage sites was
AB  - approximately 250.  However, four specific sites were cleaved under nonstandard
AB  - conditions (low salt or high pH) or in the presence of organic solvents, like
AB  - dimethyl sulfoxide and glycerol.  After the substitution of thymine for HMU by
AB  - DNA cloning in B. subtilis, a BsuR cleavage site was restricted and modified
AB  - under standard conditions.  No additional sites were detected after
AB  - shotgun-cloning of about 11% of the chromosome.  The nucleotide sequence of a
AB  - cleavage site was found to be
AB  - 5'..C-A-Hmu-A-A-C-Hmu-Hmu-Hmu-G-G-C-C-Hmu-A-G-..3', which shows the presence of
AB  - a bona fide BsuR (GGCC) recognition sequence, flanked by (Hmu-A)-rich
AB  - sequences.  The results suggested that the resistance of H1 to restriction and
AB  - modification by B. subtilis R was due to (i) a strong bias against the
AB  - GGCC-recognition sequence and (ii) protection of the four remaining GGCC sites
AB  - as a consequence of HMU-A base pairs flanking the sites.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Luxen, E.
AU  - Venema, G.
TI  - Restriction and modification in Bacillus subtilis: Effects on transfection under marker rescue conditions.
JO  - J. Virol.
PY  - 1982
SP  - 357
EP  - 364
VL  - 42
AB  - The role of homology between donor and recipient DNAs in the protection of transfecting DNA
AB  - against restriction by competent Bacillus subtilis R cells was studied under marker rescue
AB  - conditions with modified helper phage.  By comparing restriction under conditions of
AB  - preinfection marker rescue and superinfection marker rescue, the significance of DNA homology
AB  - during the initial stages of DNA processing by competent cells could be studied.  The results
AB  - showed that in both preinfection and superinfection, complete protection against restriction
AB  - of transfectants produced via rescue by the modified homologous helper chromosome occurred.
AB  - Even up to 90 min after entry, DNA entering the helper-mediated pathway of transfection was
AB  - not affected by restriction.  The significance of these findings is discussed in the general
AB  - context of the role of DNA homology between donor and recipient on the fate of donor DNA in
AB  - competent B. subtilis, in particular in relation to the effects on restriction.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Luxen, E.
AU  - Venema, G.
TI  - Restriction of hemimethylated DNA by the Bacillus subtilis R system.
JO  - Mol. Gen. Genet.
PY  - 1984
SP  - 370
EP  - 373
VL  - 195
AB  - The effects of restriction by the BsuR system on hemimethylated SPP1 DNA were investigated.
AB  - In vitro, single-stranded nicks were introduced in the nonmodified strand of the
AB  - hemimethylated DNA at the same sites as recognized in nonmodified homoduplex DNA.
AB  - Transfection with BsuR-treated hemimethylated DNA was severely reduced.  In vivo, transfection
AB  - with hemimethylated DNA was also severely reduced in competent B. subtilis R cells.  In
AB  - contrast, transfection of protoplasts of the R strain with this DNA was not affected.  The
AB  - apparent restriction by competent cells was attributed to the special mode of processing of
AB  - transfecting DNA.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Luxen, E.
AU  - Venema, G.
AU  - Trautner, T.
TI  - Restriction and modification in B. subtilis:  Effects on transformation and transfection with native and single-stranded DNA.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 103
EP  - 110
VL  - 179
AB  - The effects of restriction in vivo by competent B. subtilis R cells and in
AB  - vitro by purified endonuclease BsuR on transformation and transfection with
AB  - native and denatured DNA were investigated.  The results show that
AB  - transformation by either native, or denatured DNA is not affected by
AB  - restriction, whereas transfection both with native and denatured SPP1 DNA is
AB  - severely restricted.  In contrast to the results obtained in vivo, the
AB  - biological activity of native and denatured transforming DNA is destroyed by
AB  - BsuR in vitro, as is the transfecting activity of native and denatured SPP1
AB  - DNA.  The sensitivity of denatured DNA, either with mixtures of the
AB  - complementary strands or with separated single strands alone, is significantly
AB  - lower than that of native DNA.  The results are discussed in the context of
AB  - possible mechanisms underlying the different responses of transforming and
AB  - transfecting DNA to in vivo restriction by B. subtilis R cells.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Murray, K.
TI  - Restriction and modification in B. subtilis: Nucleotide sequence recognized by restriction endonuclease R.BsuR from strain R.
JO  - Mol. Gen. Genet.
PY  - 1975
SP  - 25
EP  - 33
VL  - 143
AB  - Restriction endonuclease R from Bacillus subtilis strain R cleaves nonmodified
AB  - SPP1 DNA in approximately 80, and lambda DNA in about 200 different sites.  DNA
AB  - digests with this endonuclease and with endonuclease HaeIII from Haemophilus
AB  - aegyptius show identical fragmentation patterns on gel electrophoresis,
AB  - indicating that the two enzymes recognize the same nucleotide sequence.  The
AB  - polynucleotide kinase reaction was used in conjunction with two-dimensional
AB  - ionophoretic nucleotide mapping methods to identify the 5'-nucleotide sequences
AB  - at the sites of cleavage by the B. subtilis restriction endonuclease.  The
AB  - results show that the recognition sequence is 5' N-G-G^C-C-N- 3' 3'
AB  - N-C-C^G-G-N- 5' where arrows indicate the point of strand scission.  Each of
AB  - the four possible nucleotides can occur in the positions flanking the
AB  - recognition site.
ER  -

TY  - JOUR
AU  - Bron, S.
AU  - Murray, K.
AU  - Trautner, T.A.
TI  - Restriction and Modification in B. subtilis:  Purification and General Properties of a Restriction Endonuclease from Strain R.
JO  - Mol. Gen. Genet.
PY  - 1975
SP  - 13
EP  - 23
VL  - 143
AB  - All Bacillus subtilis R-type strains showing the phenomena of restriction and
AB  - modification contain an endonuclease that inactiviates in vitro the biological
AB  - activity of a variety of DNAs lacking R-specific modification, such as
AB  - transfecting SPP1, SPO2 and Phi-105 DNA, and transforming B. subtilis 168-type
AB  - DNA.  The corresponding DNAs carrying R-specific modification are resistant to
AB  - the enzyme.  The enzyme has been purified approximately 400-fold and is
AB  - essentially free from contaminating double strand-directed unspecific exo- or
AB  - endonuclease activity.  Only Mg2+ is required as cofactor.  The substrate DNAs
AB  - are cleaved at specific sites.  The double-stranded fragments produced from
AB  - SPP1 DNA (molecular weight 2.5 x 107) have an average molecular weight of about
AB  - 300,000.
ER  -

TY  - JOUR
AU  - Bronnec, V.
AU  - Haddad, N.
AU  - Cruveiller, S.
AU  - Hernould, M.
AU  - Tresse, O.
AU  - Zagorec, M.
TI  - Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis.
JO  - Genome Announcements
PY  - 2016
SP  - e00120
EP  - e00116
VL  - 4
AB  - In this study, we describe the draft genome sequence of aCampylobacter jejuniclinical isolate
AB  - issued from a French patient suffering from severe
AB  - campylobacteriosis. This atypical strain is characterized by an unusual
AB  - resistance to oxygen and the ability to grow under an aerobic atmosphere, a
AB  - characteristic as-of-yet unique to this species.
ER  -

TY  - JOUR
AU  - Brooks, J.
AU  - Hattman, S.
TI  - Location of the DNA-adenine methylase gene on the genetic map of phage T2.
JO  - Virology
PY  - 1973
SP  - 285
EP  - 288
VL  - 55
AB  - The location of the gene controlling DNA-adenine methylase activity is reported to be in the
AB  - region between genes 49 and rI on the T2 genetic map. A new nomenclature is proposed to
AB  - describe the various phage types affected by mutations in the methylase gene.
ER  -

TY  - JOUR
AU  - Brooks, J.
AU  - Masurekar, M.
AU  - Hattman, S.
TI  - In vitro methylation of phage lambda.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1975
SP  - 225
EP  - 225
VL  - 75
AB  - Phage T2 produces an adenine-specific DNA methylase. Certain mutants (designated damh) produce
AB  - an altered enzyme which methylates various forms of T2 DNA to higher extents than does the
AB  - wild-type (dam+) enzyme. The higher methylation by damh protects nonglucosylated T2 DNA
AB  - against P1-restriction. We have studied in vitro methylation of phage lambda DNA by the dam+
AB  - and damh enzymes (using both crude extracts and highly purified enzyme preparations). DNA from
AB  - lambda grown in Escherichia coli strain K (=lambda.K DNA) is methylated to a two-fold greater
AB  - extent by the damh enzyme; ca.150 and ca.300 MeAde residues per lambda DNA are produced by
AB  - dam+ and damh, respectively (the same stoichiometry is observed with lambda.K(P1)DNA).
AB  - Following methylation by dam+ enzyme there is no change in the ability of lambda.K DNA to
AB  - transfect spheroplasts derived from E. coli K or K(P1); the relative transfecting titer
AB  - remains ca.10000 fold higher on K than K(P1). In contrast, methylation by the damh enzyme
AB  - resulted in a 1000 to 10000 fold increase in transfection ability on K(P1) spheroplasts; the
AB  - transfection efficiency on K(P1) was 20 to 40% that observed on K (under similar conditions
AB  - lambda.K(P1) DNA transfected both spheroplast preparations equally well). Thus, the damh
AB  - methylase recognizes more sites on lambda DNA than the dam+ enzyme; the additional methylation
AB  - protects against P1-restriction.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
TI  - Properties and uses of restriction endonucleases.
JO  - Methods Enzymol.
PY  - 1987
SP  - 113
EP  - 129
VL  - 152
AB  - This chapter focuses on the properties and uses of restriction endonucleases.
AB  - The large battery of endonucleases now commercially available will first be
AB  - described in terms of nomenclature and properties.  The next section will cover
AB  - basic methods for their use in mapping and genetic engineering experiments, and
AB  - a final section will focus on the more detailed aspects of selecting
AB  - endonucleases for generating ends compatible with subsequent steps of
AB  - construction.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
TI  - A comparative study of the wild type and mutant forms of phage T2 DNA-adenine methylase.
JO  - Ph.D. Thesis, University of Rochester
PY  - 1977
SP  - 1
EP  - 188
AB  - Bacteriophage T2 produces an adenine-specific DNA methylase.  Certain mutants (designated
AB  - damh) produce an altered enzyme which methylates T2 DNA to a higher extent than does the wild
AB  - type (dam+) enzyme.  The higher methylation by the damh enzyme protects nonglucosylated phage
AB  - against P1 restriction.  The position of the T2 dam gene on the phage genetic map was
AB  - determined by a series of three-factor crosses.  The gene was located between the 49 and rI
AB  - loci on the map.  The kinetics of enzyme production were also studied: under the conditions
AB  - used, overproduction of methylase activity could not be achieved by blocking DNA synthesis.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Benner, J.S.
AU  - Heiter, D.F.
AU  - Silber, K.R.
AU  - Sznyter, L.A.
AU  - Jager-Quinton, T.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Wilson, G.G.
AU  - Nwankwo, D.O.
TI  - Cloning the BamHI restriction modification system.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 979
EP  - 997
VL  - 17
AB  - BamHI, a Type II restriction modification system from Bacillus amyloliquefaciens H recognizes
AB  - the sequence GGATCC. The methylase and endonuclease genes have been cloned into E. coli in
AB  - separate steps; the clone is able to restrict unmodified phage. Although within the clone the
AB  - methylase and endonuclease genes are present on the same pACYC184 vector, the system can be
AB  - maintained in E. coli only with an additional copy of the methylase gene present on a separate
AB  - vector. The initial selection for BamHI methylase activity also yielded a second BamHI
AB  - methylase gene which is not homologous in DNA sequence and hybridizes to different genomic
AB  - restriction fragments than does the endonuclease-linked methylase gene. Finally, the
AB  - interaction of the BamHI system with the E. coli Dam and the Mcr A and B functions, have been
AB  - studied and are reported here.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Benner, J.S.
AU  - Silber, K.R.
AU  - Heiter, D.F.
AU  - Sznyter, L.A.
AU  - Jager-Quinton, T.
AU  - Wilson, G.G.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Nwankwo, D.O.
TI  - Cloning and characterization of the BamHI restriction modification system.
JO  - Gene
PY  - 1988
SP  - 13
EP  - 13
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Blumenthal, R.M.
AU  - Gingeras, T.R.
TI  - The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 837
EP  - 851
VL  - 11
AB  - The E. coli dam (DNA adenine methylase) enzyme is known to methylate the sequence GATC. A
AB  - general method for cloning sequence-specific DNA methylase genes was used to isolate the dam
AB  - gene on a 1.14 kb fragment, inserted in the plasmid vector pBR322. Subsequent restriction
AB  - mapping and subcloning experiments established a set of approximate boundaries of the gene.
AB  - The nucleotide sequence of the dam gene was determined, and analysis of that sequence revealed
AB  - a unique open reading frame which corresponded in length to that necessary to code for a
AB  - protein the size of dam. Amino acid composition derived from this sequence corresponds closely
AB  - to the amino acid composition of the purified dam protein. Enzymatic and DNA:DNA hybridization
AB  - methods were used to investigate the possible presence of dam genes in a variety of
AB  - prokaryotic organisms.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Hattman, S.
TI  - In vitro methylation of bacteriophage lambda DNA by wild type (dam+) mutant (damh) forms of the phage T2 DNA adenine methylase.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 381
EP  - 394
VL  - 126
AB  - The wild-type (dam+) and mutant (damh) forms of the bacteriophage T2 DNA adenine methylase
AB  - have been partially purified; these enzymes methylate the sequence, 5'...G-A-Py...3'
AB  - (Hattman et al., 1978a). However, in vitro methylation studies using phage lambda DNA revealed
AB  - the following: (1) T2 dam+ and damh enzymes differ in their ability to methylate lambda DNA;
AB  - under identical reaction conditions the T2 damh enzyme methylated lambda DNA to a higher level
AB  - than did the dam+ enzyme. However, the respective methylation sites are equally distributed on
AB  - the l and r strands. (2) Methylation with T2 damh, but not T2 dam+ protected lambda against P1
AB  - restriction. This was demonstrated by transfection of Escherichia coli (P1) spheroplasts and
AB  - by cleavage with R.EcoP1. (3) T2 dam+ and damh were similarly capable of methylating G-A-T-C
AB  - sequences on lambda DNA; e.g. k-dam3 DNA (contains no N6-methyladenine) methylated with either
AB  - enzyme was made resistant to cleavage by R.DpnII. In contrast, only the T2 damh modified DNA
AB  - was resistant to further methylation by M.EcoP1 (which methylates the sequence
AB  - 5'...A-G-A-C-Py...3'; Hattman et al., 1978b). (4) lambda.dam3 DNA was partially methylated
AB  - to the same level with T2 dam+ or T2 damh; the two enzymes producted different patterns of
AB  - G-A-C versus G-A-T methylation. We propose that the T2 dam+ enzyme methylates G-A-C sequences
AB  - less efficiently than the T2 damh methylase; this property does not entirely account for the
AB  - large difference in methylation levels produced by the two enzymes.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Nathan, P.D.
AU  - Landry, D.
AU  - Sznyter, L.A.
AU  - Waite-Rees, P.
AU  - Ives, C.L.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Benner, J.S.
TI  - Characterization of the cloned BamHI restriction modification system:  its nucleotide sequence, properties of the methylase, and expression in heterologous hosts.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 841
EP  - 850
VL  - 19
AB  - The BamHI restriction modification system was previously cloned into E. coli and maintained
AB  - with an extra copy of the methylase gene on a high copy vector (Brooks et al, (1989) Nucl.
AB  - Acids Res. 17, 979-997). The nucleotide sequence of a 3014 bp region containing the
AB  - endonuclease (R) and methylase (M) genes has now been determined. The sequence predicts a
AB  - methylase protein of 423 amino acids, Mr 49,527, and an endonuclease protein of 213 amino
AB  - acids, Mr 24,570. Between the two genes is a small open reading frame capable of encoding a
AB  - 102 amino acid protein, Mr 13,351. The M.BamHI enzyme has been purified from a high expression
AB  - clone, its amino terminal sequence determined, and the nature of its substrate modification
AB  - studied. The BamHI methylase modifies the internal C within its recognition sequence at the N4
AB  - position. Comparisons of the deduced amino acid sequence of M.BamHI have been made with those
AB  - available for other DNA methylases: among them, several contain five distinct regions, 12 to
AB  - 22 amino acids in length, of pronounced sequence similarity. Finally, stability and expression
AB  - of the BamHI system in both E. coli and B. subtilis have been studied. The results suggest R
AB  - and M expression are carefully regulated in a natural host like B. subtilis.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Nwankwo, D.
AU  - Sznyter, L.
AU  - Jager, T.
AU  - Wilson, G.
AU  - Heiter, D.
AU  - Slatko, B.
AU  - Benner, J.
TI  - Cloning of the BamHI restriction-modification system.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1987
SP  - 154
EP  - 154
VL  - 87
AB  - BamHI, a TypeII restriction-modification system from Bacillus
AB  - amyloliquefaciens, recognizes the sequence GGATCC.  The system has been cloned
AB  - into E. coli in two steps.  First the methylase gene was cloned into pBR322 and
AB  - a derivative expressing higher levels was constructed using a pUC vector.  The
AB  - endonuclease gene was then located using Southern blot analyses; HindIII
AB  - fragments large enough to contain the endonuclease gene were cloned into
AB  - pACYC184, introduced into a host containing the methylase gene and screened for
AB  - endonuclease activity.  Both genes are stably maintained in E. coli on separate
AB  - but compatible plasmids.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Roberts, R.J.
TI  - Modification profiles of bacterial genomes.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 913
EP  - 934
VL  - 10
AB  - DNAs were prepared from twenty-six bacterial species and digested with a
AB  - variety of restriction endonucleases to determine what modifications the DNAs
AB  - carry.  Several general conclusions could be made: 1) First, in no instance was
AB  - the DNA of a restriction enzyme strain cleaved by its own restriction enzyme.
AB  - 2) The specificity of the DNA modification was the same as that of its
AB  - restriction counterpart; there were no cases of the DNAs being modified against
AB  - a less specific class of restriction enzymes. 3) In most (but not all) cases,
AB  - the resistance of a bacterium's DNA to its own restriction enzyme could be
AB  - generalized to include resistance to all other restriction enzymes with the
AB  - same specificity (isoschizomers).  4) DNA modified within the central tetramer
AB  - of a recognition sequence is usually protected against cleavage by all related
AB  - hexameric enzymes possessing that central tetramer.  Only three families of DNA
AB  - presented in this study disobey this rule.  5) Finally, a significant number of
AB  - cases emerge where bacterial DNA carries a modification but no corresponding
AB  - restriction endonuclease activity.
ER  -

TY  - JOUR
AU  - Brooks, J.E.
AU  - Sznyter, L.
AU  - Vaccaro, C.
AU  - Arnaud, M.
AU  - Jager-Quinton, T.
AU  - Wilson, G.
AU  - Moran, L.
AU  - Slatko, B.
AU  - Bernan, V.
TI  - Cloning and characterization of the SphI restriction modification system from Streptomyces phaeochromogenes.
JO  - J. Cell Biochem. Suppl.
PY  - 1990
SP  - 106
EP  - 106
VL  - 14A
AB  - SphI, a Type II restriction modification from Streptomyces phaeochromogenes,
AB  - recognizes the sequence GCATGC.  The endonuclease cleaves at GCATG^C to
AB  - generate a 3' four base overhang.  A 5.4 kb PstI fragment from the S.
AB  - phaeochromogenes genome has been cloned into pBR322 and shown to express the
AB  - SphI methylase at low level in E. coli.  Clones carrying the fragment have no
AB  - endonuclease activity.  Extensive mapping and subcloning have been used to
AB  - determine the position and orientation of the m gene.  The nucleotide sequence
AB  - of the region is now being determined.  The entire 5.4 kb fragment and also
AB  - various restriction fragments have been transferred into S. lividans on pIJ486,
AB  - pIJ487 and also the low copy vector pIJ922.  Their expression in Streptomyces
AB  - will be discussed.
ER  -

TY  - JOUR
AU  - Brooks, S.L.
AU  - Van Hamme, J.D.
TI  - Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5492
EP  - 5493
VL  - 194
AB  - Here we present a whole-genome shotgun sequence of Rhodococcus species strain JVH1, an
AB  - organism capable of degrading a variety of organosulfur compounds. In
AB  - particular, JVH1 is able to selectively cleave carbon-sulfur bonds within alkyl
AB  - chains. A large number of oxygenases were identified, consistent with other
AB  - members of the genus.
ER  -

TY  - JOUR
AU  - Brouwer, M.S.
AU  - Allan, E.
AU  - Mullany, P.
AU  - Roberts, A.P.
TI  - Draft Genome Sequence of the Nontoxigenic Clostridium difficile Strain CD37.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2125
EP  - 2126
VL  - 194
AB  - Here we report the draft genome sequence of Clostridium difficile strain CD37, the first
AB  - nontoxigenic strain sequenced. Every sequenced strain of Clostridium
AB  - difficile has been shown to contain multiple different mobile genetic elements.
AB  - The draft genome sequence of strain CD37 reveals the presence of two putative
AB  - conjugative transposons.
ER  -

TY  - JOUR
AU  - Brovedan, M.
AU  - Marchiaro, P.M.
AU  - Moran-Barrio, J.
AU  - Revale, S.
AU  - Cameranesi, M.
AU  - Brambilla, L.
AU  - Viale, A.M.
AU  - Limansky, A.S.
TI  - Draft Genome Sequence of Acinetobacter bereziniae HPC229, a Carbapenem-Resistant  Clinical Strain from Argentina Harboring blaNDM-1.
JO  - Genome Announcements
PY  - 2016
SP  - e00117
EP  - e00116
VL  - 4
AB  - We report here the draft genome sequence of an NDM-1-producing Acinetobacter bereziniae
AB  - clinical strain, HPC229. This strain harbors both plasmid and
AB  - chromosomal resistance determinants toward different beta-lactams and
AB  - aminoglycosides as well as several types of multidrug efflux pumps, most likely
AB  - representing an adaptation strategy for survival under different environments.
ER  -

TY  - JOUR
AU  - Brown, C.J.
AU  - Sen, D.
AU  - Yano, H.
AU  - Bauer, M.L.
AU  - Rogers, L.M.
AU  - Van der Auwera, G.A.
AU  - Top, E.M.
TI  - Diverse broad-host-range plasmids from freshwater carry few accessory genes.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 7684
EP  - 7695
VL  - 79
AB  - Broad-host-range self-transferable plasmids are known to facilitate bacterial
AB  - adaptation by spreading genes between phylogenetically distinct hosts. These
AB  - plasmids typically have a conserved backbone region and a variable accessory
AB  - region that encodes host-beneficial traits. We do not know, however, how well
AB  - plasmids that do not encode accessory functions can survive in nature. The goal
AB  - of this study was to characterize the backbone and accessory gene content of
AB  - plasmids that were captured from freshwater sources without selecting for a
AB  - particular phenotype or cultivating their host. To do this, triparental matings
AB  - were used such that the only required phenotype was the plasmid's ability to
AB  - mobilize a nonconjugative plasmid. Based on complete genome sequences of 10
AB  - plasmids, only 5 carried identifiable accessory gene regions, and none carried
AB  - antibiotic resistance genes. The plasmids belong to four known incompatibility
AB  - groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of
AB  - the plasmids were shown to have a broad host range, being able to transfer into
AB  - alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic
AB  - resistance genes, we resampled one of the sites and compared the proportion of
AB  - captured plasmids that conferred antibiotic resistance to their hosts with the
AB  - proportion of such plasmids captured from the effluent of a local wastewater
AB  - treatment plant. Few of the captured plasmids from either site encoded antibiotic
AB  - resistance. A high diversity of plasmids that encode no or unknown accessory
AB  - functions is thus readily found in freshwater habitats. The question remains how
AB  - the plasmids persist in these microbial communities.
ER  -

TY  - JOUR
AU  - Brown, C.T.
AU  - Hug, L.A.
AU  - Thomas, B.C.
AU  - Sharon, I.
AU  - Castelle, C.J.
AU  - Singh, A.
AU  - Wilkins, M.J.
AU  - Williams, K.H.
AU  - Banfield, J.F.
TI  - rRNA introns, odd ribosomes, and small enigmatic genomes across a large radiation of phyla.
JO  - Nature
PY  - 2015
SP  - 208
EP  - 208
VL  - 523
AB  - Aprominent feature of the bacterial domain is a radiation of major
AB  - lineages that are defined as candidate phyla because they lack isolated
AB  - representatives. Bacteria from these phyla occur in diverse
AB  - environments1 and are thought to mediate carbon and hydrogen
AB  - cycles2. Genomic analyses of a few representatives suggested that
AB  - metabolic limitations have prevented their cultivation2-6. Here we
AB  - reconstructed 8 complete and 789 draft genomes from bacteria
AB  - representing.35 phyla and documented features that consistently
AB  - distinguish these organisms from other bacteria. We infer that this
AB  - group, which may comprise .15% of the bacterial domain, has
AB  - shared evolutionary history, and describe it as the candidate phyla
AB  - radiation (CPR). All CPR genomes are small and most lack numerous
AB  - biosynthetic pathways. Owing to divergent 16S ribosomal
AB  - RNA (rRNA) gene sequences, 50-100% of organisms sampled
AB  - from specific phyla would evade detection in typical cultivationindependent
AB  - surveys. CPR organisms often have self-splicing
AB  - introns and proteins encoded within their rRNA genes, a feature
AB  - rarely reported in bacteria. Furthermore, they have unusual ribosome
AB  - compositions. All are missing a ribosomal protein often
AB  - absent in symbionts, and specific lineages are missing ribosomal
AB  - proteins and biogenesis factors considered universal in bacteria.
AB  - This implies different ribosome structures and biogenesis mechanisms,
AB  - and underlines unusual biology across a large part of the
AB  - bacterial domain.
ER  -

TY  - JOUR
AU  - Brown, D.R.
AU  - May, M.
AU  - Michaels, D.L.
AU  - Barbet, A.F.
TI  - Genome Annotation of Five Mycoplasma canis Strains.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4138
EP  - 4139
VL  - 194
AB  - To understand its potential to cause invasive disease, the genome of Mycoplasma canis strain
AB  - PG14(T) from a dog's throat was compared to those of isolates from
AB  - the genital tract or brain of dogs. The average nucleotide identity between
AB  - strain pairs is 98%, and their genome annotations are similar.
ER  -

TY  - JOUR
AU  - Brown, F.L.
AU  - Musich, P.R.
AU  - Maio, J.
TI  - Cae I: an endonuclease isolated from the African green monkey with properties indicating site-specific cleavage of homologous and heterologous mammalian DNA.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 1093
EP  - 1107
VL  - 5
AB  - Component a DNA is a highly repetitive sequence that comprises nearly a quarter of the African
AB  - green monkey (Ceropithecus aethiops) genome.  A previous microbial restriction enzyme analysis
AB  - showed that the repeat structure of component a DNA is based upon a nonomeric unit of 176  - 4
AB  - base-pairs.  An endonuclease, provisionally termed CaeI, has been isolated from African green
AB  - monkey teste that cleaves component a DNA into multimeric segments based upon the same repeat
AB  - periodicity as that revealed by microbial restriction enzymes. The primary sites of CaeI
AB  - cleavage in the component a sequence appear to be 120 +- 6 base-pairs distant from the HindIII
AB  - sites and 73 +- 6 base-pairs distant from the EcoRI* sites.  CaeI has been partially
AB  - characterized with special reference to the effects of ATP and S-adenosylmethionine on the
AB  - cleavage of component a DNA.  CaeI may be a member of a class of similar site-specific
AB  - nucleases present in mammalian cells. CaeI also cleave mouse satellite DNA into a multimeric
AB  - series of discrete segments: the periodicty of this series is shorter than that revealed by
AB  - EcoRII restriction analysis of mouse satellite DNA.
ER  -

TY  - JOUR
AU  - Brown, L.M.
AU  - Gunasekera, T.S.
AU  - Bowen, L.L.
AU  - Ruiz, O.N.
TI  - Draft Genome Sequence of Rhodovulum sp. Strain NI22, a Naphthalene-Degrading Marine Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01475
EP  - e01414
VL  - 3
AB  - Rhodovulum sp. strain NI22 is a hydrocarbon-degrading member of the genus Rhodovulum. The
AB  - draft genome of Rhodovulum sp. NI22 is 3.8 Mb in size, with 3,756
AB  - coding sequences and 64.4% G+C content. The catechol and gentisate pathways for
AB  - naphthalene degradation are predicted to be present in Rhodovulum sp. NI22.
ER  -

TY  - JOUR
AU  - Brown, L.M.
AU  - Gunasekera, T.S.
AU  - Ruiz, O.N.
TI  - Draft Genome Sequence of Pseudomonas stutzeri Strain 19, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2017
SP  - e01373
EP  - e01317
VL  - 5
AB  - Pseudomonas stutzeri strain 19 is a Gram-negative bacterium capable of degrading  aromatic
AB  - hydrocarbons. The draft genome of P. stutzeri 19 is estimated to be 5.1
AB  - Mb, containing 4,652 protein-coding genes and a G+C content of 63.3%. Multiple
AB  - genes responsible for the degradation of aromatics are present in this strain.
ER  -

TY  - JOUR
AU  - Brown, L.M.
AU  - Gunasekera, T.S.
AU  - Ruiz, O.N.
TI  - Draft Genome Sequence of Nocardioides luteus Strain BAFB, an Alkane-Degrading Bacterium Isolated from JP-7-Polluted Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e01529
EP  - e01516
VL  - 5
AB  - Nocardioides luteus strain BAFB is a Gram-positive bacterium that efficiently degrades C8 to
AB  - C11 alkanes aerobically. The draft genome of N. luteus BAFB is
AB  - 5.76 Mb in size, with 5,358 coding sequences and 69.9% G+C content. The genes
AB  - responsible for alkane degradation are present in this strain.
ER  -

TY  - JOUR
AU  - Brown, L.M.
AU  - Gunasekera, T.S.
AU  - Ruiz, O.N.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa ATCC 33988, a Bacterium Highly Adapted to Fuel-Polluted Environments.
JO  - Genome Announcements
PY  - 2014
SP  - e01113
EP  - e01114
VL  - 2
AB  - Pseudomonas aeruginosa ATCC 33988 is highly adapted to grow in jet and diesel fuel, with a
AB  - defined regulation of adaptive genes and metabolization of
AB  - n-alkanes. The draft genome of strain ATCC 33988 is 6.4 Mb in size, with 5,975
AB  - coding sequences and 66.3% G+C content, and it is highly similar to that of the
AB  - clinical strain P. aeruginosa PAO1.
ER  -

TY  - JOUR
AU  - Brown, L.M.
AU  - Gunasekera, T.S.
AU  - Striebich, R.C.
AU  - Ruiz, O.N.
TI  - Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00622
EP  - e00616
VL  - 4
AB  - Gordonia sihwensis strain 9 is a Gram-positive bacterium capable of efficient aerobic
AB  - degradation of branched and normal alkanes. The draft genome of G.
AB  - sihwensis S9 is 4.16 Mb in size, with 3,686 coding sequences and 68.1% G+C
AB  - content. Alkane monooxygenase and P-450 cytochrome genes required for alkane
AB  - degradation are predicted in G. sihwensis S9.
ER  -

TY  - JOUR
AU  - Brown, N.L.
TI  - Sequence determination of restriction-endonuclease recognition sites.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 398
EP  - 399
VL  - 8
AB  - Restriction endonucleases are widely used in the study of the physical structure of DNA
AB  - molecules, and in the genetic manipulation of DNA molecules in vitro.  They also provided
AB  - interesting and useful model systems for the study of protein-DNA interactions.  A knowledge
AB  - of the DNA sequence that is recognized by a restriction endonuclease, and of the structure of
AB  - the termini of the DNA fragments, is essential to the prediction of the uses to which the
AB  - enzyme may be put.
ER  -

TY  - JOUR
AU  - Brown, N.L.
AU  - Hutchison, C.A. III
AU  - Smith, M.
TI  - The specific non-symmetrical sequence recognized by restriction endonuclease MboII.
JO  - J. Mol. Biol.
PY  - 1980
SP  - 143
EP  - 148
VL  - 140
AB  - The restriction endonuclease MboII, isolated from Moraxella bovis (ATCC 10900),
AB  - cleaves bacteriophage PhiX174am3 replicative form I DNA into ten fragments.
AB  - The physical map of these fragments has been aligned with the sequence of
AB  - PhiX174 DNA.  There is no sequence with 2-fold rotational symmetry common to
AB  - the region of all ten cleavage sites.  However, the non-symmetrical sequence
AB  - 5'-G-A-A-G-A-3' 3'-C-T-T-C-T-5' occurs near to each cleavage site.  Precise
AB  - mapping of the cleavages in both DNA strands at several sites places the cuts
AB  - eight nucleotides to the right of the upper sequence and seven nucleotides to
AB  - the right of the lower sequence.
ER  -

TY  - JOUR
AU  - Brown, N.L.
AU  - McClelland, M.
AU  - Whitehead, P.R.
TI  - HgiAI: A restriction endonuclease from Herpetosiphon giganteus HP1023.
JO  - Gene
PY  - 1980
SP  - 49
EP  - 68
VL  - 9
AB  - A new class II restriction endonuclease, HgiAI has been partially purified from
AB  - Herpetosiphon giganteus HP1023.  The enzyme activity has been characterized and
AB  - shown to recognize the family of related hexanucleotide sequences 5'-G
AB  - (A/T)-G-C-(A/T)^C-3' 3'-C^(A/T)-C-G-(A/T)-G-5' where the second and fifth
AB  - nucleotide pairs are A:T pairs in either orientation.  Cleavage occurs as
AB  - shown, to give DNA fragments with 3'-terminal tetranucleotide extensions.  The
AB  - recognition sites of the enzymes SacI and SStI (GAGCT^C) form a subset of the
AB  - recognition site of HgiAI.  One of the four possible tetranucleotide
AB  - 3'-extenions (cohesive ends), generated by HgiAI is identical with those
AB  - generated by SacI and SstI, another is identical with that of PstI.  HgiAI
AB  - should be useful for molecular cloning.
ER  -

TY  - JOUR
AU  - Brown, N.L.
AU  - Smith, M.
TI  - A general method for defining restriction enzyme cleavage and recognition sites.
JO  - Methods Enzymol.
PY  - 1980
SP  - 391
EP  - 404
VL  - 65
AB  - Class II restriction endonucleases cleave double-stranded DNA into specific
AB  - fragments.  These enzymes are powerful tools for the dissection of DNA, and
AB  - they are essential for the construction of recombinant DNA molecules and for
AB  - DNA sequence determination.
ER  -

TY  - JOUR
AU  - Brown, N.L.
AU  - Smith, M.
TI  - The mapping and sequence determination of the single site in PhiX174am3 replicative form DNA cleaved by restriction endonuclease PstI.
JO  - FEBS Lett.
PY  - 1976
SP  - 284
EP  - 287
VL  - 65
AB  - A large number of restriction endonucleases have now been isolated from
AB  - prokaryotes.  We have tested some of these enzymes on the covalently-closed
AB  - replicative form (RFI) of PhiX174am3 DNA.  The restriction endonuclease from
AB  - Providencia stuarti 164 (PstI) was found to convert RFI DNA to a linear form of
AB  - apparent unit length. In this paper we describe the mapping of the single PstI
AB  - site in PhiX174am3 RFI DNA and the determination of the sequence cleaved.  This
AB  - is the symmetrical hexanucleotide sequence: 5'-C-T-G-C-A-^G-3'
AB  - 3'-G-^A-C-G-T-C-5' The methods used to determine the sequence recognised by
AB  - PstI and the site of cleavage within that sequence are novel, and should be of
AB  - general use.
ER  -

TY  - JOUR
AU  - Brown, N.L.
AU  - Smith, M.
TI  - Cleavage specificity of the restriction endonuclease isolated from Haemophilus gallinarum (HgaI).
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1977
SP  - 3213
EP  - 3216
VL  - 74
AB  - The nucleotide sequences in the replicative form (duplex) of PhiX174 DNA around
AB  - six sites cut by HgaI, a restriction endonuclease from Haemophilus gallinarum,
AB  - have been compared.  The enzyme produces a staggered cleavage resulting in a
AB  - pentanucleotide 5'-terminal extension.  The sequences within and immediately
AB  - surrounding the pentanucleotide cleavage site have no obvious relationship.
AB  - However, the sequence 5'-G-A-C-G-C-3' 3'-C-T-G-C-G-5' occurs five nucleotide
AB  - pairs to the left of the cut in the upper strand and 10 nucleotide pairs to the
AB  - left of the cut in the lower strand and, therefore, is believed to constitute
AB  - the recognition in which recognition and cleavage sites lack 2-fold rotational
AB  - symmetry.  The method used to define the cleavage site is of general
AB  - applicability.
ER  -

TY  - JOUR
AU  - Brown, N.P.
AU  - Sander, C.
AU  - Bork, P.
TI  - Frame: detection of genomic sequencing errors.
JO  - Bioinformatics
PY  - 1998
SP  - 367
EP  - 371
VL  - 14
AB  - Motivation: The underlying error rate for genomic sequencing sometimes results in the
AB  - introduction of artificial frameshifts and in-frame stop codons into putative protein encoding
AB  - genes.  Severe errors are then introduced into the inferred transcripts through
AB  - mis-translation or premature termination.  Results: We describe a system for screening
AB  - segments of DNA for frameshift and in-frame stop errors in coding regions.  The method is
AB  - based on homology matching using blastx to compare all six reading frames of the query
AB  - nucleotide sequence against selected protein sequence databases.  Fragments of protein
AB  - matching neighboring regions of the query DNA are united and extended laterally to define
AB  - candidate open reading frames, within which, frameshifts and stops are identified.  Suitable
AB  - targets include prokaryotic or other intron-free genomic sequence and complementary DNA's.
AB  - As an example of its use, we report here two frameshifted ORFs that deviate from the original
AB  - TIGR sequence annotations for the recently released Helicobacter pylori genome.  Availability:
AB  - The tool is accessible via the URL http://www.sander.ebi.ac.uk/frame/.  Contact:
AB  - brown@ebi.ac.uk.
ER  -

TY  - JOUR
AU  - Brown, S.D. et al.
TI  - Genome Sequence of the Mercury-Methylating Strain Desulfovibrio desulfuricans ND132.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2078
EP  - 2079
VL  - 193
AB  - Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB)
AB  - capable of producing methylmercury (MeHg), a potent human
AB  - neurotoxin. The mechanism of methylation by this and other organisms is
AB  - unknown. We present the 3.8-Mb genome sequence to provide further insight
AB  - into microbial mercury methylation.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Begemann, M.B.
AU  - Mormile, M.R.
AU  - Wall, J.D.
AU  - Han, C.S.
AU  - Goodwin, L.A.
AU  - Pitluck, S.
AU  - Land, M.L.
AU  - Hauser, L.J.
AU  - Elias, D.A.
TI  - Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing bacterium Halanaerobium hydrogenoformans.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3682
EP  - 3683
VL  - 193
AB  - Halanaerobium hydrogenoformans is an alkaliphilic bacterium capable of biohydrogen production
AB  - at pH 11 and 7% (w/v) salt. We present the 2.6 Mb
AB  - genome sequence to provide insights into its physiology and potential for
AB  - bioenergy applications.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Hurt, R.A. Jr.
AU  - Gilmour, C.C.
AU  - Elias, D.A.
TI  - Draft genome sequences for three mercury-methylating, sulfate-reducing bacteria.
JO  - Genome Announcements
PY  - 2013
SP  - e00618
EP  - e00613
VL  - 1
AB  - The genetic basis for bacterial mercury methylation has been described recently.  For insights
AB  - into the physiology of mercury-methylating bacteria, we present
AB  - genome sequences for Desulfococcus multivorans strain DSM 2059, Desulfovibrio
AB  - alkalitolerans strain DSM 16529, and Desulfovibrio species strain X2.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Jun, S.
TI  - Complete Genome Sequence of Escherichia coli NCM3722.
JO  - Genome Announcements
PY  - 2015
SP  - e00879
EP  - e00815
VL  - 3
AB  - Escherichia coli NCM3722 is a prototrophic K-12 strain with robust physiologic phenotypes. We
AB  - report the complete 4,678,045-bp chromosome and 67,545-bp F-like
AB  - plasmid of this unique model organism.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Klingeman, D.M.
AU  - Lu, T.Y.
AU  - Johnson, C.M.
AU  - Utturkar, S.M.
AU  - Land, M.L.
AU  - Schadt, C.W.
AU  - Doktycz, M.J.
AU  - Pelletier, D.A.
TI  - Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2383
EP  - 2384
VL  - 194
AB  - Rhizobium sp. strain PDO1-076 is a plant-associated bacterium isolated from Populus deltoides,
AB  - and its draft genome sequence is reported.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Lamed, R.
AU  - Morag, E.
AU  - Borovok, I.
AU  - Shoham, Y.
AU  - Klingeman, D.M.
AU  - Johnson, C.M.
AU  - Yang, Z.
AU  - Land, M.L.
AU  - Utturkar, S.M.
AU  - Keller, M.
AU  - Bayer, E.A.
TI  - Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3290
EP  - 3291
VL  - 194
AB  - Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic
AB  - bacterium capable of directly converting cellulosic substrates into
AB  - ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain, AD2,
AB  - played pivotal roles in describing the original cellulosome concept. We present
AB  - their draft genome sequences.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Palumbo, A.V.
AU  - Panikov, N.
AU  - Ariyawansa, T.
AU  - Klingeman, D.M.
AU  - Johnson, C.M.
AU  - Land, M.L.
AU  - Utturkar, S.M.
AU  - Epstein, S.S.
TI  - Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3279
EP  - 3280
VL  - 194
AB  - Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained
AB  - from the Field Research Center (FRC) in Oak Ridge, TN. It was
AB  - characterized as a bacterium tolerant to heavy metals, such as uranium, nickel,
AB  - cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome
AB  - sequence.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Podar, M.
AU  - Klingeman, D.M.
AU  - Johnson, C.M.
AU  - Yang, Z.K.
AU  - Utturkar, S.M.
AU  - Land, M.L.
AU  - Mosher, J.J.
AU  - Hurt, R.A. Jr.
AU  - Phelps, T.J.
AU  - Palumbo, A.V.
AU  - Arkin, A.P.
AU  - Hazen, T.C.
AU  - Elias, D.A.
TI  - Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5147
EP  - 5148
VL  - 194
AB  - Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical
AB  - sites since the recent isolation of the type strain. We present the
AB  - genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome
AB  - sequences for two new strains with different abilities to reduce iron, chromate,
AB  - and uranium.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Utturkar, S.M.
AU  - Arkin, A.P.
AU  - Deutschbauer, A.M.
AU  - Elias, D.A.
AU  - Hazen, T.C.
AU  - Chakraborty, R.
TI  - Draft Genome Sequence for Desulfovibrio africanus Strain PCS.
JO  - Genome Announcements
PY  - 2013
SP  - e00144
EP  - e00113
VL  - 1
AB  - Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated
AB  - from sediment from Paleta Creek, San Diego, CA. Strain PCS is
AB  - capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is
AB  - predicted to produce methylmercury. We present the D. africanus PCS genome
AB  - sequence.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Utturkar, S.M.
AU  - Klingeman, D.M.
AU  - Johnson, C.M.
AU  - Martin, S.L.
AU  - Land, M.L.
AU  - Lu, T.Y.
AU  - Schadt, C.W.
AU  - Doktycz, M.J.
AU  - Pelletier, D.A.
TI  - Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus  deltoides.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5991
EP  - 5993
VL  - 194
AB  - To aid in the investigation of the Populus deltoides microbiome, we generated draft genome
AB  - sequences for 21 Pseudomonas strains and 19 other diverse bacteria
AB  - isolated from Populus deltoides roots. Genome sequences for isolates similar to
AB  - Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium,
AB  - Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium,
AB  - Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Utturkar, S.M.
AU  - Magnuson, T.S.
AU  - Ray, A.E.
AU  - Poole, F.L.
AU  - Lancaster, W.A.
AU  - Thorgersen, M.P.
AU  - Adams, M.W.
AU  - Elias, D.A.
TI  - Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology.
JO  - Genome Announcements
PY  - 2014
SP  - e00881
EP  - e00814
VL  - 2
AB  - Pelosinus species can reduce metals such as Fe(III), U(VI), and Cr(VI) and have been isolated
AB  - from diverse geographical regions. Five draft genome sequences have
AB  - been published. We report the complete genome sequence for Pelosinus sp. strain
AB  - UFO1 using only PacBio DNA sequence data and without manual finishing.
ER  -

TY  - JOUR
AU  - Brown, S.D.
AU  - Wall, J.D.
AU  - Kucken, A.M.
AU  - Gilmour, C.C.
AU  - Podar, M.
AU  - Brandt, C.C.
AU  - Teshima, H.
AU  - Detter, J.C.
AU  - Han, C.S.
AU  - Land, M.L.
AU  - Lucas, S.
AU  - Han, J.
AU  - Pennacchio, L.
AU  - Nolan, M.
AU  - Pitluck, S.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Palumbo, A.V.
AU  - Elias, D.A.
TI  - Genome Sequence of the Mercury-Methylating and Pleomorphic Desulfovibrio africanus strain Walvis Bay.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4037
EP  - 4038
VL  - 193
AB  - Desulfovibrio africanus strain Walvis Bay is an anaerobic sulfate-reducing bacterium (SRB)
AB  - capable of producing methylmercury (MeHg), a potent human
AB  - neurotoxin. The mechanism of methylation by this and other organisms is
AB  - unknown. We present the 4.2 Mb genome sequence to provide further insight
AB  - into microbial mercury methylation and sulfate-reducing bacteria.
ER  -

TY  - JOUR
AU  - Brown, T.A.
TI  - Restriction and modification.
JO  - Essential Molecular Biology
PY  - 1991
SP  - 260
EP  - 284
VL  - 2
AB  - *
AB  - 1. Restriction endonucleases. Almost 1500 restriction endonucleases are now known and over 150
AB  - are commercially-available. Complete lists plus details of restriction sites and reaction
AB  - conditions have been published.
AB  - 
AB  - 2. Site-specific methylases. At the last count 117 site-specific methylases had been
AB  - characterized. A full list including recognition sequences and other relevant information is
AB  - available.
AB  - 
AB  - 3. Restriction fragment patterns. Restriction fragments are frequently used as size markers
AB  - for agarose and polyacrylamide gel electrophoresis. Figures 1-6 are restriction endonuclease
AB  - digests that have been computer-generated assuming that all digests are run in 1.4% agarose.
AB  - The scale on the left is in base-pairs.
AB  - 
ER  -

TY  - JOUR
AU  - Brown, W.M.
AU  - Vinograd, J.
TI  - Restriction endonuclease cleavage maps of animal mitochondrial DNAs.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1974
SP  - 4617
EP  - 4621
VL  - 71
AB  - The restriction endonuclease, HindIII, gives rise to three fragments in each of
AB  - the three mitochondrial DNAs isolated from the established mammalian cell lines
AB  - LA9 (mouse), HeLa (human), and BSC-1 (African green monkey).  The restriction
AB  - endonuclease, EcoRI gives rise to three fragments in mitochondrial DNA from
AB  - HeLa and to two in DNAs form LA9 and BSC-1.  The sizes and the orders of the
AB  - fragments in the respective genomes have been determined with data obtained
AB  - from the electron microscope.  The origin and the direction of replication have
AB  - been designated in each of the cleavage maps.  Polyacrylamide gel
AB  - electrophoretic analyses demonstrated that additional fragments not detectable
AB  - in the electron microscope and larger than 50 nucleotide pairs were not
AB  - present.
ER  -

TY  - JOUR
AU  - Browne, A.S.
AU  - Biggs, P.J.
AU  - Elliott, A.
AU  - Jaros, P.
AU  - French, N.P.
AU  - Midwinter, A.C.
TI  - Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand.
JO  - Genome Announcements
PY  - 2018
SP  - e00300
EP  - e00318
VL  - 6
AB  - Escherichia coli bacteria commonly colonize the gastrointestinal tracts of farmed ruminants.
AB  - Cattle are a well-recognized reservoir of zoonotic E. coli; we report
AB  - here, however, the draft genome sequences of three diarrheagenic E. coli strains
AB  - isolated from farmed red deer (Cervus elaphus) in the Manawatu region of New
AB  - Zealand.
ER  -

TY  - JOUR
AU  - Brownlee, C.
TI  - Danna and Nathans: Restriction enzymes and the boon to modern molecular biology.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 5909
EP  - 5909
VL  - 102
AB  - In 1971, a paper published in PNAS helped jump-start the era of modern molecular biology and
AB  - biotechnology, eventually giving rise to many of the genetic advances that seem so commonplace
AB  - today.  The article, written by Academy member Daniel Nathans and his then graduate student,
AB  - Kathleen Danna, exposed the marvelous utility of restriction enzymes.  In the accompanying
AB  - Perspective highlighting this classic work of scientific literature, Rich Roberts provides a
AB  - historial account of the scientific discoveries leading up to the PNAS paper and the
AB  - unparalleled scientific advances made after its publication.
ER  -

TY  - JOUR
AU  - Bruce, T.
AU  - Leite, F.G.
AU  - Tschoeke, D.A.
AU  - Miranda, M.
AU  - Pereira, N. Jr.
AU  - Valle, R.
AU  - Thompson, C.C.
AU  - Thompson, F.L.
TI  - Exploring the Genome of a Butyric Acid Producer, Clostridium butyricum INCQS635.
JO  - Genome Announcements
PY  - 2014
SP  - e01169
EP  - e01114
VL  - 2
AB  - The draft genome sequence of Clostridium butyricum INCQS635 was obtained by means of ion
AB  - sequencing. The genome provides further insight into the genetic
AB  - repertoire involved with metabolic pathways related to the fermentation of
AB  - different compounds and organic solvents synthesis (i.e., butyric acid) with
AB  - biofuel applications.
ER  -

TY  - JOUR
AU  - Brueckner, B.
AU  - Kuck, D.
AU  - Lyko, F.
TI  - DNA methyltransferase inhibitors for cancer therapy.
JO  - Cancer J.
PY  - 2007
SP  - 17
EP  - 22
VL  - 13
AB  - Aberrant DNA methylation patterns, including hypermethylation of tumor suppressor genes, have
AB  - been described in many human cancers. These epigenetic mutations can be reversed by DNA
AB  - methyltransferase inhibitors, which provide novel opportunities for cancer therapy. Clinical
AB  - concepts for epigenetic therapies are currently being developed by using azanucleosides for
AB  - the treatment of leukemias and other tumors. These trials will greatly benefit from the
AB  - inclusion of molecular markers for monitoring epigenetic changes in patients and for
AB  - maximizing biologic responses. In addition, novel inhibitors need to be developed that result
AB  - in a direct and specific inhibition of DNA methyltransferase activity. Several recent
AB  - developments indicate that rational design of small molecule DNA methyltransferase inhibitors
AB  - is feasible and that this approach can result in the establishment of novel drug candidates.
AB  - The use of novel DNA methyltransferase inhibitors in clinical trials that allow monitoring of
AB  - drug-induced DNA methylation changes should provide the foundation for improved epigenetic
AB  - cancer therapies.
ER  -

TY  - JOUR
AU  - Bruffaerts, N.
AU  - Vluggen, C.
AU  - Duytschaever, L.
AU  - Mathys, V.
AU  - Saegerman, C.
AU  - Chapeira, O.
AU  - Huygen, K.
TI  - Genome Sequences of Four Strains of Mycobacterium avium subsp. hominissuis, Isolated from Swine and Humans, Differing in Virulence in a Murine Intranasal  Infection Model.
JO  - Genome Announcements
PY  - 2016
SP  - e00533
EP  - e00516
VL  - 4
AB  - This paper announces the genome sequences of four strains of Mycobacterium avium  subsp.
AB  - hominissuis, isolated from cases of lymphadenopathy in swine and humans,
AB  - differing in virulence in a murine intranasal infection model.
ER  -

TY  - JOUR
AU  - Bruggemann, H.
AU  - Baumer, S.
AU  - Fricke, W.F.
AU  - Wiezer, A.
AU  - Liesegang, H.
AU  - Decker, I.
AU  - Herzberg, C.
AU  - Martinez-Arias, R.
AU  - Merkl, R.
AU  - Henne, A.
AU  - Gottschalk, G.
TI  - The genome sequence of Clostridium tetani, the causative agent of tetanus disease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 1316
EP  - 1321
VL  - 100
AB  - Tetanus disease is one of the most dramatic and globally prevalent diseases of humans and
AB  - vertebrate animals, and has been reported for over
AB  - 24 centuries. The manifestation of the disease, spastic paralysis, is
AB  - caused by the second most poisonous substance known, the tetanus toxin,
AB  - with a human lethal dose of approximately 1 ng/kg. Fortunately, this
AB  - disease is successfully controlled through immunization with tetanus
AB  - toxoid; nevertheless, according to the World Health Organization, an
AB  - estimated 400,000 cases still occur each year, mainly of neonatal tetanus.
AB  - The causative agent of tetanus disease is Clostridium tetani, an anaerobic
AB  - spore-forming bacterium, whose natural habitat is soil, dust, and
AB  - intestinal tracts of various animals. Here we report the complete genome
AB  - sequence of toxigenic C. tetani E88, a variant of strain Massachusetts.
AB  - The genome consists of a 2,799,250-bp chromosome encoding 2,372 ORFs. The
AB  - tetanus toxin and a collagenase are encoded on a 74,082-bp plasmid,
AB  - containing 61 ORFs. Additional virulence-related factors could be
AB  - identified, such as an array of surface-layer and adhesion proteins (35
AB  - ORFs), some of them unique to C. tetani. Comparative genomics with the
AB  - genomes of Clostridium perfringens, the causative agent of gas gangrene,
AB  - and Clostridium acetobutylicum, a nonpathogenic solvent producer, revealed
AB  - a remarkable capacity of C. tetani: The organism can rely on an extensive
AB  - sodium ion bioenergetics. Additional candidate genes involved in the
AB  - establishment and maintenance of a pathogenic lifestyle of C. tetani are
AB  - presented.
ER  -

TY  - JOUR
AU  - Bruggemann, H.
AU  - Henne, A.
AU  - Hoster, F.
AU  - Liesegang, H.
AU  - Wiezer, A.
AU  - Strittmatter, A.
AU  - Hujer, S.
AU  - Durre, P.
AU  - Gottschalk, G.
TI  - The Complete Genome Sequence of Propionibacterium Acnes, a Commensal of Human Skin.
JO  - Science
PY  - 2004
SP  - 671
EP  - 673
VL  - 305
AB  - Propionibacterium acnes is a major inhabitant of adult human skin, where it resides within
AB  - sebaceous follicles, usually as a harmless commensal although it has been implicated in acne
AB  - vulgaris formation. The entire genome sequence of this Gram positive bacterium encodes 2333
AB  - putative genes and revealed numerous gene products involved in degrading host molecules,
AB  - including sialidases, neuraminidases, endoglycoceramidases, lipases, and pore forming factors.
AB  - Surface associated and other immunogenic factors have been identified, which might be involved
AB  - in triggering acne inflammation and other P. acnes associated diseases.
ER  -

TY  - JOUR
AU  - Brumm, P.
AU  - Land, M.L.
AU  - Hauser, L.J.
AU  - Jeffries, C.D.
AU  - Chang, Y.J.
AU  - Mead, D.A.
TI  - Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 81
EP  - 81
VL  - 10
AB  - Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park,
AB  - Montana, USA under permit from the National Park Service. The
AB  - genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute
AB  - and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes
AB  - and average nucleotide identity, Geobacillus sp. Y412MC52 and the related
AB  - Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus.
AB  - The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of
AB  - 3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057
AB  - bp and an average G + C content of 45 %. Y412MC52 possesses arabinan,
AB  - arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of
AB  - hemicellulose from biomass. Transport and utilization clusters are also present
AB  - for other carbohydrates including starch, cellobiose, and alpha- and
AB  - beta-galactooligosaccharides.
ER  -

TY  - JOUR
AU  - Brumm, P.J.
AU  - Land, M.L.
AU  - Mead, D.A.
TI  - Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 33
EP  - 33
VL  - 11
AB  - Geobacillus sp. WCH70 was one of several thermophilic organisms isolated from hot composts in
AB  - the Middleton, WI area. Comparison of 16 S rRNA sequences showed the
AB  - strain may be a new species, and is most closely related to G. galactosidasius
AB  - and G. toebii. The genome was sequenced, assembled, and annotated by the DOE
AB  - Joint Genome Institute and deposited at the NCBI in December 2009 (CP001638). The
AB  - genome of Geobacillus species WCH70 consists of one circular chromosome of
AB  - 3,893,306 bp with an average G + C content of 43 %, and two circular plasmids of
AB  - 33,899 and 10,287 bp with an average G + C content of 40 %. Among sequenced
AB  - organisms, Geobacillus sp. WCH70 shares highest Average Nucleotide Identity (86
AB  - %) with G. thermoglucosidasius strains, as well as similar genome organization.
AB  - Geobacillus sp. WCH70 appears to be a highly adaptable organism, with an
AB  - exceptionally high 125 annotated transposons in the genome. The organism also
AB  - possesses four predicted restriction-modification systems not found in other
AB  - Geobacillus species.
ER  -

TY  - JOUR
AU  - Brumm, P.J.
AU  - Land, M.L.
AU  - Mead, D.A.
TI  - Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 73
EP  - 73
VL  - 10
AB  - Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated
AB  - from Obsidian Hot Spring, Yellowstone National Park, Montana,
AB  - USA under permit from the National Park Service. Comparison of 16 S rRNA
AB  - sequences confirmed the classification of the strain as a G. thermoglucosidasius
AB  - species. The genome was sequenced, assembled, and annotated by the DOE Joint
AB  - Genome Institute and deposited at the NCBI in December 2011 (CP002835). The
AB  - genome of G. thermoglucosidasius C56-YS93 consists of one circular chromosome of
AB  - 3,893,306 bp and two circular plasmids of 80,849 and 19,638 bp and an average G +
AB  - C content of 43.93 %. G. thermoglucosidasius C56-YS93 possesses a xylan
AB  - degradation cluster not found in the other G. thermoglucosidasius sequenced
AB  - strains. This cluster appears to be related to the xylan degradation cluster
AB  - found in G. stearothermophilus. G. thermoglucosidasius C56-YS93 possesses two
AB  - plasmids not found in the other two strains. One plasmid contains a novel gene
AB  - cluster coding for proteins involved in proline degradation and metabolism, the
AB  - other contains a collection of mostly hypothetical proteins.
ER  -

TY  - JOUR
AU  - Brumm, P.J.
AU  - Monsma, S.
AU  - Keough, B.
AU  - Jasinovica, S.
AU  - Ferguson, E.
AU  - Schoenfeld, T.
AU  - Lodes, M.
AU  - Mead, D.A.
TI  - Complete Genome Sequence of Thermus aquaticus Y51MC23.
JO  - PLoS ONE
PY  - 2015
SP  - e0138674
EP  - e0138674
VL  - 10
AB  - Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser  Basin of
AB  - Yellowstone National Park. Remarkably, this T. aquaticus strain is able
AB  - to grow anaerobically and produces multiple morphological forms. Y51MC23 is a
AB  - Gram-negative, rod-shaped organism that grows well between 50 degrees C and 80
AB  - degrees C with maximum growth rate at 65 degrees C to 70 degrees C. Growth
AB  - studies suggest that Y51MC23 primarily scavenges protein from the environment,
AB  - supported by the high number of secreted and intracellular proteases and
AB  - peptidases as well as transporter systems for amino acids and peptides. The
AB  - genome was assembled de novo using a 350 bp fragment library (paired end
AB  - sequencing) and an 8 kb long span mate pair library. A closed and finished genome
AB  - was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of
AB  - 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on
AB  - megaplasmids were identified on the chromosome. The Y51MC23 genome contains two
AB  - full and two partial prophage as well as numerous CRISPR loci. The high identity
AB  - and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is
AB  - interesting, given the 8,800 km separation of the two hot springs from which they
AB  - were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple
AB  - morphologies present in cultures. The use of fluorescence microscopy reveals new
AB  - details about these unusual morphological features, including the presence of
AB  - multiple types of large and small spheres, often forming a confluent layer of
AB  - spheres. Many of the spheres appear to be formed not from cell envelope or outer
AB  - membrane components as previously believed, but from a remodeled peptidoglycan
AB  - cell wall. These complex morphological forms may serve multiple functions in the
AB  - survival of the organism, including food and nucleic acid storage as well as
AB  - colony attachment and organization.
ER  -

TY  - JOUR
AU  - Bruna, R.E.
AU  - Revale, S.
AU  - Garcia, V.E.
AU  - Mariscotti, J.F.
TI  - Draft Whole-Genome Sequence of Serratia marcescens Strain RM66262, Isolated from  a Patient with a Urinary Tract Infection.
JO  - Genome Announcements
PY  - 2015
SP  - e01423
EP  - e01415
VL  - 3
AB  - Serratia marcescens strains are ubiquitous bacteria isolated from environmental niches and
AB  - also constitute emergent nosocomial opportunistic pathogens. Here, we
AB  - report on the draft genome sequence of S. marcescens strain RM66262, which was
AB  - isolated from a patient with urinary tract infection in the Bacteriology Service
AB  - of the Rosario National University, Rosario, Argentina.
ER  -

TY  - JOUR
AU  - Brunder, W.
AU  - Karch, H.
AU  - Schmidt, H.
TI  - Complete sequence of the large virulence plasmid pSFO157 of the sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H(-) strain 3072/96.
JO  - Int. J. Med. Microbiol.
PY  - 2006
SP  - 467
EP  - 474
VL  - 296
AB  - The large virulence plasmid pSFO157 of sorbitol-fermenting E. coli
AB  - O157:H(-) strain 3072/96 has a size of 121,239bp and contains 96 open
AB  - reading frames >50bp. It is therefore 29,162bp larger (ca. 32%) than
AB  - plasmid pO157 of E. coli O157:H7 strain EDL933. Major differences between
AB  - the plasmids are the absence of katP, espP, and toxB in pSFO157 and,
AB  - instead of these, the presence of the sfp fimbriae gene cluster and a
AB  - large part of an F-plasmid transfer region, the latter accounting for most
AB  - of the additional DNA. The differences in the order of the genes and their
AB  - composition, as well as the presence of a number of replication-associated
AB  - genes and mobile genetic elements suggests that the large E. coli O157
AB  - virulence plasmids have a complex evolutionary origin.
ER  -

TY  - JOUR
AU  - Brunet-Galmes, I.
AU  - Busquets, A.
AU  - Pena, A.
AU  - Gomila, M.
AU  - Nogales, B.
AU  - Garcia-Valdes, E.
AU  - Lalucat, J.
AU  - Bennasar, A.
AU  - Bosch, R.
TI  - Complete Genome Sequence of the Naphthalene-Degrading Bacterium Pseudomonas stutzeri AN10 (CCUG 29243).
JO  - J. Bacteriol.
PY  - 2012
SP  - 6642
EP  - 6643
VL  - 194
AB  - Pseudomonas stutzeri AN10 (CCUG 29243) can be considered a model strain for aerobic
AB  - naphthalene degradation. We report the complete genome sequence of this
AB  - bacterium. Its 4.71-Mb chromosome provides insights into other biodegradative
AB  - capabilities of strain AN10 (i.e., benzoate catabolism) and suggests a high
AB  - number of horizontal gene transfer events.
ER  -

TY  - JOUR
AU  - Bruno, D.D.C.F.
AU  - Bartelli, T.F.
AU  - Briones, M.R.S.
TI  - Genome Sequence of a Staphylococcus epidermidis Strain (GTH12) Associated with Candida albicans SC5314 Cultured under Hypoxia at 37 degrees C in Glycerol for 12 Weeks.
JO  - Genome Announcements
PY  - 2018
SP  - e00533
EP  - e00518
VL  - 6
AB  - Polymicrobial infections with mixed-species biofilms are important health problems because of
AB  - increased antimicrobial resistance and worse patient outcomes
AB  - than with monomicrobial infections. Here, we present the whole-genome sequence of
AB  - Staphylococcus epidermidis strain GTH12, which was cocultured with the yeast
AB  - Candida albicans SC5314 (generating C. albicans strain SC5314 GTH12), thus
AB  - providing genomic information on polymicrobial infections.
ER  -

TY  - JOUR
AU  - Bruno-Barcena, J.M.
AU  - Chinn, M.S.
AU  - Grunden, A.M.
TI  - Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide.
JO  - Genome Announcements
PY  - 2013
SP  - e00628
EP  - e00613
VL  - 1
AB  - Clostridium autoethanogenum is an anaerobic, autotrophic acetogen that is capable of
AB  - converting CO and CO2 into ethanol and acetate. Here we report the draft
AB  - genome sequence of C. autoethanogenum JA1-1 strain DSM 10061 (4.5 Mbp; G+C
AB  - content, 37.5%) and the findings obtained from annotation of the genome sequence.
ER  -

TY  - JOUR
AU  - Bryanskaya, A.V.
AU  - Rozanov, A.S.
AU  - Logacheva, M.D.
AU  - Kotenko, A.V.
AU  - Peltek, S.E.
TI  - Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation).
JO  - Genome Announcements
PY  - 2014
SP  - e01098
EP  - e01014
VL  - 2
AB  - The Geobacillus icigianus G1w1(T) strain was isolated from sludge samples of unnamed vaporing
AB  - hydrothermal (97 degrees capital ES, Cyrillic) outlets situated
AB  - in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve,
AB  - Kamchatka, Russian Federation; 54 degrees 25'51.40'N, 160 degrees 7'41.40'E).
AB  - The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes.
ER  -

TY  - JOUR
AU  - Bryant, D.A.
AU  - Costas, A.M.
AU  - Maresca, J.A.
AU  - Chew, A.G.
AU  - Klatt, C.G.
AU  - Bateson, M.M.
AU  - Tallon, L.J.
AU  - Hostetler, J.
AU  - Nelson, W.C.
AU  - Heidelberg, J.F.
AU  - Ward, D.M.
TI  - Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium.
JO  - Science
PY  - 2007
SP  - 523
EP  - 526
VL  - 317
AB  - Only five bacterial phyla with members capable of chlorophyll (Chl)-based
AB  - phototrophy are presently known. Metagenomic data from the phototrophic
AB  - microbial mats of alkaline siliceous hot springs in Yellowstone National
AB  - Park revealed the existence of a distinctive bacteriochlorophyll
AB  - (BChl)-synthesizing, phototrophic bacterium. A highly enriched culture of
AB  - this bacterium grew photoheterotrophically, synthesized BChls a and c
AB  - under oxic conditions, and had chlorosomes and type 1 reaction centers.
AB  - "Candidatus Chloracidobacterium thermophilum" is a BChl-producing member
AB  - of the poorly characterized phylum Acidobacteria.
ER  -

TY  - JOUR
AU  - Bryk, M.
AU  - Belisle, M.
AU  - Mueller, J.E.
AU  - Belfort, M.
TI  - Selection of a remote cleavage site by I-TevI, the td intron-encoded endonuclease.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 197
EP  - 210
VL  - 247
AB  - I-TevI, a double-strand DNA endonuclease involved in the mobility of the td intron of phage
AB  - T4, is highly unusual in that it binds and cleaves intronless td alleles (td homing sites) in
AB  - a site-specific but sequence-tolerant manner. The endonuclease binds to sequences flanking the
AB  - intron insertion site and near the remote cleavage site, located 23 and 25 nucleotides away on
AB  - the top and bottom strands, respectively. Mapping studies indicate that I-TevI has both
AB  - sequence and distance sensors that function during cut-site selection. Although I-TevI
AB  - cleavage of many insertion and deletion variants of the homing site is impaired, double-strand
AB  - breaks are generated at positions that collectively span two turns of the helix, indicating
AB  - that the interaction is extraordinarily flexible. However, the endonuclease does exhibit
AB  - spacing preferences between its binding domains, and sequence preferences near the cleavage
AB  - site, with the G:C pair at -23 implicated as a cleavage determinant. Furthermore, I-TevI
AB  - appears to function through interactions across the minor groove at the cleavage site, as it
AB  - does at the intron insertion site, and to be capable of cleaving sequentially, first on the
AB  - bottom and then on the top strand. These properties of I-TevI are incorporated in a model
AB  - wherein the endonuclease effects distant cleavage via a flexible hinge.
ER  -

TY  - JOUR
AU  - Bryk, M.
AU  - Quirk, S.M.
AU  - Mueller, J.E.
AU  - Loizos, N.
AU  - Lawrence, C.
AU  - Belfort, M.
TI  - The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target.
JO  - EMBO J.
PY  - 1993
SP  - 2141
EP  - 2149
VL  - 12
AB  - I-TevI, a double-strand DNA endonuclease encoded by the mobile td intron of phage T4, has
AB  - specificity for the intronless td allele. Genetic and physical studies indicate that the
AB  - enzyme makes extensive contact with its DNA substrate over at least three helical turns and
AB  - around the circumference of the helix. Remarkably, no single nucleotide within a 48 bp region
AB  - encompassing this interaction domain is essential for cleavage. Although two subdomains (DI
AB  - and DII) contain preferred sequences, a third domain (DIII), a primary region of contact with
AB  - the enzyme, displays much lower sequence preference. While DII and DIII suffice for
AB  - recognition and binding of I-TevI, all three domains are important for formation of a
AB  - cleavage-competent complex. Mutational, footprinting and interference studies indicate
AB  - predominant interactions of I-TevI across the minor groove and phosphate backbone of the DNA.
AB  - Contacts appear not to be at the single nucleotide level; rather redundant interactions and/or
AB  - structural recognition are implied. These unusual properties provide a basis for understanding
AB  - how I-TevI recognizes T-even phage DNA, which is heavily modified in the major groove. These
AB  - recognition characteristics may increase the range of natural substrates available to the
AB  - endonuclease, thereby extending the invasive potential of the mobile intron.
ER  -

TY  - JOUR
AU  - Brzezinski, R.
AU  - Piekarowicz, A.
TI  - Steps in the reaction mechanism of the Haemophilus influenzae Rf restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1982
SP  - 615
EP  - 627
VL  - 154
AB  - HinfIII is a restriction modification enzyme isolated from Haemophilus
AB  - influenzae strain Rf. It requires ATP for cleavage and S-adenosyl-L-methionine
AB  - for methylation of DNA.  S-Adenosyl-L-methionine acts as an allosteric effector
AB  - in the endonuclease reaction.  The enzyme forms a complex with unmodified DNA
AB  - in the absence of ATP and S-adenosyl-L-methionine.  This complex is sensitive
AB  - to inhibition by heparin.  S-Adenosyl-L-methionine is required for the
AB  - formation of a complex that is insensitive to such inhibition.  ATP acts as an
AB  - allosteric effector of HinfIII, and induces DNA cleavage followed probably by
AB  - the release of the enzyme from the DNA.
ER  -

TY  - JOUR
AU  - Brzuszkiewicz, E.
AU  - Bruggemann, H.
AU  - Liesegang, H.
AU  - Emmerth, M.
AU  - Olschlager, T.
AU  - Nagy, G.
AU  - Albermann, K.
AU  - Wagner, C.
AU  - Buchrieser, C.
AU  - Emody, L.
AU  - Gottschalk, G.
AU  - Hacker, J.
AU  - Dobrindt, U.
TI  - How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 12879
EP  - 12884
VL  - 103
AB  - Uropathogenic Escherichia coli (UPEC) strain 536 (O6:K15:H31) is one of the model organisms of
AB  - extraintestinal pathogenic E. coli (ExPEC). To
AB  - analyze this strain's genetic basis of urovirulence, we sequenced the
AB  - entire genome and compared the data with the genome sequence of UPEC
AB  - strain CFT073 (O6:K2:H1) and to the available genomes of nonpathogenic E.
AB  - coli strain MG1655 (K-12) and enterohemorrhagic E. coli. The genome of
AB  - strain 536 is approximately 292 kb smaller than that of strain CFT073.
AB  - Genomic differences between both UPEC are mainly restricted to large
AB  - pathogenicity islands, parts of which are unique to strain 536 or CFT073.
AB  - Genome comparison underlines that repeated insertions and deletions in
AB  - certain parts of the genome contribute to genome evolution. Furthermore,
AB  - 427 and 432 genes are only present in strain 536 or in both UPEC,
AB  - respectively. The majority of the latter genes is encoded within smaller
AB  - horizontally acquired DNA regions scattered all over the genome. Several
AB  - of these genes are involved in increasing the pathogens' fitness and
AB  - adaptability. Analysis of virulence-associated traits expressed in the two
AB  - UPEC O6 strains, together with genome comparison, demonstrate the marked
AB  - genetic and phenotypic variability among UPEC. The ability to accumulate
AB  - and express a variety of virulence-associated genes distinguishes ExPEC
AB  - from many commensals and forms the basis for the individual virulence
AB  - potential of ExPEC. Accordingly, instead of a common virulence mechanism,
AB  - different ways exist among ExPEC to cause disease.
ER  -

TY  - JOUR
AU  - Brzuszkiewicz, E.
AU  - Schulz, T.
AU  - Rydzewski, K.
AU  - Daniel, R.
AU  - Gillmaier, N.
AU  - Dittmann, C.
AU  - Holland, G.
AU  - Schunder, E.
AU  - Lautner, M.
AU  - Eisenreich, W.
AU  - Luck, C.
AU  - Heuner, K.
TI  - Legionella oakridgensis ATCC 33761 genome sequence and phenotypic characterization reveals its replication capacity in amoebae.
JO  - Int. J. Med. Microbiol.
PY  - 2013
SP  - 514
EP  - 528
VL  - 303
AB  - Legionella oakridgensis is able to cause Legionnaires' disease, but is less
AB  - virulent compared to L. pneumophila strains and very rarely associated with human
AB  - disease. L. oakridgensis is the only species of the family legionellae which is
AB  - able to grow on media without additional cysteine. In contrast to earlier
AB  - publications, we found that L. oakridgensis is able to multiply in amoebae. We
AB  - sequenced the genome of L. oakridgensis type strain OR-10 (ATCC 33761). The
AB  - genome is smaller than the other yet sequenced Legionella genomes and has a
AB  - higher G+C-content of 40.9%. L. oakridgensis lacks a flagellum and it also lacks
AB  - all genes of the flagellar regulon except of the alternative sigma-28 factor FliA
AB  - and the anti-sigma-28 factor FlgM. Genes encoding structural components of type
AB  - I, type II, type IV Lvh and type IV Dot/Icm, Sec- and Tat-secretion systems could
AB  - be identified. Only a limited set of Dot/Icm effector proteins have been
AB  - recognized within the genome sequence of L. oakridgensis. Like in L. pneumophila
AB  - strains, various proteins with eukaryotic motifs and eukaryote-like proteins were
AB  - detected. We could demonstrate that the Dot/Icm system is essential for
AB  - intracellular replication of L. oakridgensis. Furthermore, we identified new
AB  - putative virulence factors of Legionella.
ER  -

TY  - JOUR
AU  - Brzuszkiewicz, E.
AU  - Waschkowitz, T.
AU  - Wiezer, A.
AU  - Daniel, R.
TI  - Complete Genome Sequence of the B12-Producing Shimwellia blattae Strain DSM 4481, Isolated from a Cockroach.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4436
EP  - 4436
VL  - 194
AB  - Here we announce the complete genome sequence of the coenzyme B(12)-producing enteric
AB  - bacterium Shimwellia blattae (formerly Escherichia blattae). The genome
AB  - consists of a single chromosome (4,158,636 bp). The genome size is smaller than
AB  - that of most other enteric bacteria. Genome comparison revealed significant
AB  - differences from the Escherichia coli genome.
ER  -

TY  - JOUR
AU  - Bucci, C.
AU  - Lavitola, A.
AU  - Salvatore, P.
AU  - Del Giudice, L.
AU  - Massardo, D.R.
AU  - Bruni, C.B.
AU  - Alifano, P.
TI  - Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype.
JO  - Mol. Cell
PY  - 1999
SP  - 435
EP  - 445
VL  - 3
AB  - Expression of serogroup B meningococcal capsular polysaccharide undergoes frequent phase
AB  - variation involving reversible frameshift mutations within a homopolymeric repeat in the siaD
AB  - gene. A high rate of phase variation is the consequence of a biochemical defect in
AB  - methyl-directed mismatch repair. The mutator phenotype is associated to the absence of DNA
AB  - adenine methyltransferase (Dam) activity in all pathogenic isolates and in 50% of commensal
AB  - strains. Analysis of the meningococcal dam gene region revealed that in all Dam- strains a
AB  - gene encoding a putative restriction endonuclease (drg) that cleaves only the methylated DNA
AB  - sequence 5'-GmeATC-3' replaced the dam gene. Insertional inactivation of the dam and/or drg
AB  - genes indicated that high rates of phase variation and hypermutator phenotype are caused by
AB  - absence of a functional dam gene.
ER  -

TY  - JOUR
AU  - Buchmann, A.
AU  - Eitel, M.
AU  - Koch, P.
AU  - Schwarz, P.N.
AU  - Stegmann, E.
AU  - Wohlleben, W.
AU  - Wolanski, M.
AU  - Krawiec, M.
AU  - Zakrzewska-Czerwinska, J.
AU  - Mendez, C.
AU  - Botas, A.
AU  - Nunez, L.E.
AU  - Moris, F.
AU  - Cortes, J.
AU  - Gross, H.
TI  - High-Quality Draft Genome Sequence of the Actinobacterium Nocardia terpenica IFM  0406, Producer of the Immunosuppressant Brasilicardins, Using Illumina and PacBio  Technologies.
JO  - Genome Announcements
PY  - 2016
SP  - e01391
EP  - e01316
VL  - 4
AB  - The bacterium Nocardia terpenica IFM 0406 is known as the producer of the immunosuppressant
AB  - brasilicardin A. Here, we report the completely sequenced
AB  - genome of strain IFM 0406, which facilitates the heterologous expression of the
AB  - brasilicardin biosynthetic gene cluster but also unveils the intriguing
AB  - biosynthetic capacity of the strain to produce secondary metabolites.
ER  -

TY  - JOUR
AU  - Buchrieser, C.
AU  - Glaser, P.
AU  - Rusniok, C.
AU  - Nedjari, H.
AU  - D'Hauteville, H.
AU  - Kunst, F.
AU  - Sansonetti, P.
AU  - Parsot, C.
TI  - The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 760
EP  - 771
VL  - 38
AB  - Bacteria of Shigella spp. are the causative agents of shigellosis. The
AB  - virulence traits of these pathogens include their ability to enter into
AB  - epithelial cells and induce apoptosis in macrophages. Expression of these
AB  - functions requires the Mxi-Spa type III secretion apparatus and the
AB  - secreted IpaA-D proteins, all of which are encoded by a virulence plasmid.
AB  - In wild-type strains, the activity of the secretion apparatus is tightly
AB  - regulated and induced upon contact of bacteria with epithelial cells. To
AB  - investigate the repertoire of proteins secreted by Shigella flexneri in
AB  - conditions of active secretion, we determined the N-terminal sequence of
AB  - 14 proteins that are secreted by a mutant in which secretion was
AB  - deregulated. Sequencing of the virulence plasmid pWR100 of the S. flexneri
AB  - strain M90T (serotype 5) has allowed us to identify the genes encoding
AB  - these secreted proteins and suggests that approximately 25 proteins are
AB  - secreted by the type III secretion apparatus. Analysis of the G+C content
AB  - and the relative positions of genes and open reading frames carried by the
AB  - plasmid, together with information concerning the localization and
AB  - function of encoded proteins, suggests that pWR100 contains blocks of
AB  - genes of various origins, some of which were initially carried by four
AB  - different plasmids.
ER  -

TY  - JOUR
AU  - Buddruhs, N.
AU  - Chertkov, O.
AU  - Petersen, J.
AU  - Fiebig, A.
AU  - Chen, A.
AU  - Pati, A.
AU  - Ivanova, N.
AU  - Lapidus, A.
AU  - Goodwin, L.A.
AU  - Chain, P.
AU  - Detter, J.C.
AU  - Gronow, S.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Goker, M.
AU  - Brinkhoff, T.
AU  - Klenk, H.P.
TI  - Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the  Roseobacter clade.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 128
EP  - 141
VL  - 9
AB  - Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the
AB  - type species of the genus Leisingera. The genus belongs to the
AB  - Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed
AB  - lineage in marine environments. Leisingera and particularly L.
AB  - methylohalidivorans strain MB2(T) is of special interest due to its
AB  - methylotrophy. Here we describe the complete genome sequence and annotation of
AB  - this bacterium together with previously unreported aspects of its phenotype. The
AB  - 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists
AB  - of three replicons, a single chromosome and two extrachromosomal elements with
AB  - sizes of 221 kb and 285 kb.
ER  -

TY  - JOUR
AU  - Budiharjo, A.
AU  - Jeong, H.
AU  - Wulandari, D.
AU  - Lee, S.
AU  - Ryu, C.M.
TI  - Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant  against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java,  Indonesia.
JO  - Genome Announcements
PY  - 2017
SP  - e01388
EP  - e01317
VL  - 5
AB  - Bacillus altitudinis P-10 was isolated from the rhizosphere of rice grown in an organic rice
AB  - field and provides strong antagonism against the bacterial blight
AB  - caused by Xanthomonas oryzae pv. oryzae in rice. Herein, we provide the complete
AB  - genome sequence and a possible explanation of the antibiotic function of the P-10
AB  - strain.
ER  -

TY  - JOUR
AU  - Budker, V.G.
AU  - Degtyarev, S.K.
AU  - Sokolov, A.V.
TI  - Cleavage of DNA adsorbed on the surface of phospholipid membranes by Type II restriction endonucleases.
JO  - Biokhimiia
PY  - 1986
SP  - 1496
EP  - 1498
VL  - 51
AB  - The hydrolysis of phage lambda DNA by restriction endonucleases of type II in the presence of
AB  - model membranes from egg phosphatidylcholine was studied.  It was shown that the degree of
AB  - hydrolysis of DNA by the enzymes BspI, PstI, and BamHI under these conditions is sharply
AB  - reduced.  This is not associated with irreversible inactivation of the enzymes in their
AB  - interaction with the membrane.  The most probable explanation for the inhibition of DNA
AB  - hydrolysis in the presence of phospholipid vesicles is a change in the substrate properties of
AB  - the DNA as a result of its adsorption on the surface of the phospholipid membrane with the
AB  - participation of Mg2+ ions.
ER  -

TY  - JOUR
AU  - Budroni, S.
AU  - Siena, E.
AU  - Dunning, H.J.C.
AU  - Seib, K.L.
AU  - Serruto, D.
AU  - Nofroni, C.
AU  - Comanducci, M.
AU  - Riley, D.R.
AU  - Daugherty, S.C.
AU  - Angiuoli, S.V.
AU  - Covacci, A.
AU  - Pizza, M.
AU  - Rappuoli, R.
AU  - Moxon, E.R.
AU  - Tettelin, H.
AU  - Medini, D.
TI  - Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 4494
EP  - 4499
VL  - 108
AB  - Molecular data on a limited number of chromosomal loci have shown that the population of
AB  - Neisseria meningitidis (Nm), a deadly human pathogen, is
AB  - structured in distinct lineages. Given that the Nm population undergoes
AB  - substantial recombination, the mechanisms resulting in the evolution of
AB  - these lineages, their persistence in time, and the implications for the
AB  - pathogenicity of the bacterium are not yet completely understood. Based on
AB  - whole-genome sequencing, we show that Nm is structured in phylogenetic
AB  - clades. Through acquisition of specific genes and through insertions and
AB  - rearrangements, each clade has acquired and remodeled specific genomic
AB  - tracts, with the potential to impact on the commensal and virulence
AB  - behavior of Nm. Despite this clear evidence of a structured population, we
AB  - confirm high rates of detectable recombination throughout the whole Nm
AB  - chromosome. However, gene conversion events were found to be longer within
AB  - clades than between clades, suggesting a DNA cleavage mechanism associated
AB  - with the phylogeny of the species. We identify 22 restriction modification
AB  - systems, probably acquired by horizontal gene transfer from outside of the
AB  - species/genus, whose distribution in the different strains coincides with
AB  - the phylogenetic clade structure. We provide evidence that these
AB  - clade-associated restriction modification systems generate a differential
AB  - barrier to DNA exchange consistent with the observed population structure.
AB  - These findings have general implications for the emergence of lineage
AB  - structure and virulence in recombining bacterial populations, and they
AB  - could provide an evolutionary framework for the population biology of a
AB  - number of other bacterial species that show contradictory population
AB  - structure and dynamics.
ER  -

TY  - JOUR
AU  - Buell, C.R. et al.
TI  - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 10181
EP  - 10186
VL  - 100
AB  - We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae
AB  - pathovar tomato DC3000 (DC3000), which is pathogenic
AB  - on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases)
AB  - contains a circular chromosome and two plasmids, which collectively encode
AB  - 5,763 ORFs. We identified 298 established and putative virulence genes,
AB  - including several clusters of genes encoding 31 confirmed and 19 predicted
AB  - type III secretion system effector proteins. Many of the virulence genes
AB  - were members of paralogous families and also were proximal to mobile
AB  - elements, which collectively comprise 7% of the DC3000 genome. The
AB  - bacterium possesses a large repertoire of transporters for the acquisition
AB  - of nutrients, particularly sugars, as well as genes implicated in
AB  - attachment to plant surfaces. Over 12% of the genes are dedicated to
AB  - regulation, which may reflect the need for rapid adaptation to the diverse
AB  - environments encountered during epiphytic growth and pathogenesis.
AB  - Comparative analyses confirmed a high degree of similarity with two
AB  - sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet
AB  - revealed 1,159 genes unique to DC3000, of which 811 lack a known function.
ER  -

TY  - JOUR
AU  - Buera, M.P.
AU  - Rossi, S.
AU  - Moreno, S.
AU  - Chirife, J.
TI  - DSC confirmation that vitrification is not necessary for stabilization of the restriction enzyme EcoRI dried with saccharides.
JO  - Biotechnol. Prog.
PY  - 1999
SP  - 577
EP  - 579
VL  - 15
AB  - The glass transition temperature (Tg) of preparations of the restriction enzyme EcoRI,
AB  - vacuum-dried in the presence of sucrose, trehalose, or raffinose, was determined using
AB  - differential scanning calorimetry.  Tg values were well below those expected for low-moisture
AB  - sucrose, trehalose, or raffinose, and this was attributed to the presence of glycerol (a
AB  - plasticizer), which was a main component of the restriction enzyme preparation.  This was
AB  - verified by determining the glass transition temperature of glycerol, which was found to be
AB  - (onset value) -77 C.  Present results confirmed that vitrification (i.e., glass formation) was
AB  - not necessary for enzyme protection in present low-moisture saccharide systems.  As shown in
AB  - previous work, the enzyme EcoRI was very stable when stored at 37/45 C in spite of the fact
AB  - that sugar matrices were completely rubbery, as unequivocally demonstrated in the present
AB  - work.
ER  -

TY  - JOUR
AU  - Bugarel, M.
AU  - den Bakker, H.C.
AU  - Nightingale, K.K.
AU  - Brichta-Harhay, D.M.
AU  - Edrington, T.S.
AU  - Loneragan, G.H.
TI  - Two Draft Genome Sequences of a New Serovar of Salmonella enterica, Serovar Lubbock.
JO  - Genome Announcements
PY  - 2015
SP  - e00215
EP  - e00215
VL  - 3
AB  - Salmonella enterica is principally a foodborne pathogen that shows considerable serovar
AB  - diversity. In this report, we present two draft genome sequences of
AB  - Salmonella enterica subsp. enterica serovar Lubbock, a novel serovar.
ER  -

TY  - JOUR
AU  - Bugreev, D.V.
AU  - Nevinsky, G.A.
TI  - Possibilities of the method of step-by-step complication of ligand structure in studies of protein-nucleic acid interactions: mechanisms of functioning of some replication, repair, topoisomerization, and restriction enzymes.
JO  - Biokhimiia
PY  - 1999
SP  - 291
EP  - 305
VL  - 64
AB  - X-Ray structure analysis is one of the most informative methods for investigation of enzymes.
AB  - However, it does not provide quantitative estimation of the relative efficiency of formation
AB  - of contacts revealed by this method, and when interpreting the data this does not allow taking
AB  - into account the relative contribution of some specific and nonspecific interactions to the
AB  - total affinity of nucleic acids (NA) to enzymes. This often results in unjustified
AB  - overestimation of the role of specific enzyme--NA contacts in affinity and specificity of
AB  - enzyme action. In recent years we have developed new approaches to analysis of the mechanisms
AB  - of protein--nucleic acid interactions allowing quantitative estimation of the relative
AB  - contribution of virtually every nucleotide unit (including individual structural elements) to
AB  - the total affinity of enzymes to long DNA and RNA molecules. It is shown that the interaction
AB  - between enzymes and NA on the molecular level can be successfully analyzed by the methods of
AB  - synthesis and analysis, that is, step-by-step simplification or complication of the structure
AB  - of a long NA-ligand. This approach allows the demonstration that complex formation including
AB  - formation of contacts between enzymes and specific NA units can provide neither high affinity
AB  - of the enzymes to NA nor the specificity of their action. Using a number of
AB  - sequence-independent replication and repair enzymes specifically recognizing a modified unit
AB  - in DNA and also some sequence-dependent topoisomerization and restriction enzymes as examples,
AB  - it was shown that virtually all nucleotide units within the DNA binding cleft interact with
AB  - the enzyme, and high affinity mainly (up to 5-7 of 7-10 orders of magnitude) is provided by
AB  - many weak additive interactions between these enzymes and various structural elements of the
AB  - individual NA nucleotide units. At the same time, the relative contribution of specific
AB  - interactions to the total affinity of NA is rather small and does not exceed 1-2 orders of
AB  - magnitude. Specificity of enzyme action is provided by the stages of the enzyme-dependent NA
AB  - adaptation to the optimal conformation and directly of catalysis: kcat increases by 3-7 orders
AB  - of magnitude when changing from nonspecific to specific NA. In the present work we summarized
AB  - our experience in studies of enzymes by the method of step-by-step complication of the ligand
AB  - structure and performed a detailed analysis of the features of this approach and its
AB  - possibilities for the study of protein--nucleic acid interactions on the molecular level.
ER  -

TY  - JOUR
AU  - Bugrysheva, J.V.
AU  - Cherney, B.
AU  - Sue, D.
AU  - Conley, A.B.
AU  - Rowe, L.A.
AU  - Knipe, K.M.
AU  - Frace, M.A.
AU  - Loparev, V.N.
AU  - Avila, J.R.
AU  - Anderson, K.
AU  - Hodge, D.R.
AU  - Pillai, S.P.
AU  - Weigel, L.M.
TI  - Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67).
JO  - Genome Announcements
PY  - 2016
SP  - e01294
EP  - e01216
VL  - 4
AB  - We report here the complete annotated genome sequence of the Burkholderia stabilis type strain
AB  - ATCC BAA-67. There were three circular chromosomes with a
AB  - combined size of 8,527,947 bp and G+C composition of 66.4%. These characteristics
AB  - closely resemble the genomes of other sequenced members of the Burkholderia
AB  - cepacia complex.
ER  -

TY  - JOUR
AU  - Bugrysheva, J.V.
AU  - Sue, D.
AU  - Hakovirta, J.
AU  - Loparev, V.N.
AU  - Knipe, K.
AU  - Sammons, S.A.
AU  - Ranganathan-Ganakammal, S.
AU  - Changayil, S.
AU  - Srinivasamoorthy, G.
AU  - Weil, M.R.
AU  - Tatusov, R.L.
AU  - Gee, J.E.
AU  - Elrod, M.G.
AU  - Hoffmaster, A.R.
AU  - Weigel, L.M.
TI  - Finished Annotated Genome Sequence of Burkholderia pseudomallei Strain Bp1651, a  Multidrug-Resistant Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e01427
EP  - e01415
VL  - 3
AB  - Burkholderia pseudomallei strain Bp1651, a human isolate, is resistant to all clinically
AB  - relevant antibiotics. We report here on the finished genome sequence
AB  - assembly and annotation of the two chromosomes of this strain. This genome
AB  - sequence may assist in understanding the mechanisms of antimicrobial resistance
AB  - for this pathogenic species.
ER  -

TY  - JOUR
AU  - Buhk, H.-J.
AU  - Behrens, B.
AU  - Tailor, R.
AU  - Wilke, K.
AU  - Prada, J.J.
AU  - Gunthert, U.
AU  - Noyer-Weidner, M.
AU  - Jentsch, S.
AU  - Trautner, T.A.
TI  - Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR.
JO  - Gene
PY  - 1984
SP  - 51
EP  - 61
VL  - 29
AB  - Bacillus subtilis phage SPR codes for a DNA methyltransferase (Mtase) which
AB  - methylates the 5' cytosine in the sequence GGCC and both cytosies in the
AB  - sequence CCGG.  A 2126-bp fragment of SPR DNA containing the Mtase gene has
AB  - been sequenced.  This fragment has only one significant open reading frame of
AB  - 1347 bp, which corresponds to the Mtase gene.  Within the sequence the Mtase
AB  - promoter has been defined by S1 mapping.  The size of the SPR Mtase predicted
AB  - from the deduced amino acid composition is 49.9 kDal.  This is in agreement
AB  - with both the Mr of the purified enzyme and with that of the SPR Mtase gene
AB  - product identified here by minicell technique.  Base changes leading to mutants
AB  - affected in Mtase activity were localized within the Mtase gene.
ER  -

TY  - JOUR
AU  - Buhler, R.
AU  - Yuan, R.
TI  - Characterization of a restriction enzyme from Escherichia coli K carrying a mutation in the modification subunit.
JO  - J. Biol. Chem.
PY  - 1978
SP  - 6756
EP  - 6760
VL  - 253
AB  - The restriction enzyme from a restriction and modification-deficient strain of
AB  - Escherichia coli K mutated in the modification gene (hsdM) has been purified
AB  - using an in vitro complementation assay with a mutant restriction enzyme from a
AB  - strain lacking only restriction.  The restriction enzyme from the hsdM mutant
AB  - lacks all of the activities that are associated with the wild type enzyme:
AB  - binding of unmodified DNA to filters, cleavage, or methylation of unmodified
AB  - DNA and ATP hydrolysis.  It is shown that the enzyme from this hsdM mutant
AB  - cannot bind S-adenosylmethionine, an allosteric effector in the restriction
AB  - reaction.  In the absence of enzyme activation by S-adenosylmethionine, no
AB  - binding to unmodified DNA takes place.  A comparison with other mutant
AB  - restriction enzymes allows us to outline the biochemical role of the subunits
AB  - of the E. coli K restriction endonuclease.
ER  -

TY  - JOUR
AU  - Buhnik-Rosenblau, K.
AU  - Danin-Poleg, Y.
AU  - Elgavish, S.
AU  - Kashi, Y.
TI  - Draft Genome Sequence of Lactobacillus johnsonii Strain 16, Isolated from Mice.
JO  - Genome Announcements
PY  - 2015
SP  - e01141
EP  - e01115
VL  - 3
AB  - Here, we report the genome sequence of Lactobacillus johnsonii, a member of the gut
AB  - lactobacilli. This draft genome of L. johnsonii strain 16 isolated from C57BL/6J mice enables
AB  - the identification of bacterial genes responsible for host-specific gut persistence.
ER  -

TY  - JOUR
AU  - Bui, L.M.G.
AU  - Kidd, S.P.
TI  - A full genomic characterization of the development of a stable Small Colony Variant cell-type by a clinical Staphylococcus aureus strain.
JO  - Infect. Genet. Evol.
PY  - 2015
SP  - 345
EP  - 355
VL  - 36
AB  - A key to persistent and recurrent Staphylococcus aureus infections is its ability to adapt to
AB  - diverse and toxic conditions. This ability includes a switch into a
AB  - biofilm or to the quasi-dormant Small Colony Variant (SCV). The development and
AB  - molecular attributes of SCVs have been difficult to study due to their rapid
AB  - reversion to their parental cell-type. We recently described the unique induction
AB  - of a matrix-embedded and stable SCV cell-type in a clinical S. aureus strain
AB  - (WCH-SK2) by growing the cells with limiting conditions for a prolonged
AB  - timeframe. Here we further study their characteristics. They possessed an
AB  - increased viability in the presence of antibiotics compared to their non-SCV
AB  - form. Their stability implied that there had been genetic changes; we therefore
AB  - determined both the genome sequence of WCH-SK2 and its stable SCV form at a
AB  - single base resolution, employing Single Molecular Real-Time (SMRT) sequencing
AB  - that enabled the methylome to also be determined. The genetic features of WCH-SK2
AB  - have been identified; the SCCmec type, the pathogenicity and genetic islands and
AB  - virulence factors. The genetic changes that had occurred in the stable SCV form
AB  - were identified; most notably being in MgrA, a global regulator, and RsbU, a
AB  - phosphoserine phosphatase within the regulatory pathway of the sigma factor SigB.
AB  - There was a shift in the methylomes of the non-SCV and stable SCV forms. We have
AB  - also shown a similar induction of this cell-type in other S. aureus strains and
AB  - performed a genetic comparison to these and other S. aureus genomes. We
AB  - additionally map RNAseq data to the WCH-SK2 genome in a transcriptomic analysis
AB  - of the parental, SCV and stable SCV cells. The results from this study represent
AB  - the unique identification of a suite of epigenetic, genetic and transcriptional
AB  - factors that are implicated in the switch in S. aureus to its persistent SCV
AB  - form.
ER  -

TY  - JOUR
AU  - Bujan, N.
AU  - Lasa, A.
AU  - E-Toranzo, A.
AU  - Magarinos, B.
TI  - Draft Genome Sequence of the Fish Strain Edwardsiella tarda NCIMB 2034.
JO  - Genome Announcements
PY  - 2017
SP  - e00359
EP  - e00317
VL  - 5
AB  - Edwardsiella tarda is an important pathogen for fish. The strain NCIMB 2034, obtained from the
AB  - National Collection of Industrial Food and Marine Bacteria, was
AB  - isolated from unknown diseased fish in the United States. The draft genome
AB  - sequence has 3.79 Mb with a G+C content of 57.1% and >3,340 protein-coding genes.
ER  -

TY  - JOUR
AU  - Bujan, N.
AU  - Toranzo, A.E.
AU  - Magarinos, B.
TI  - Draft Genome Sequence of Edwardsiellapiscicida Strain ACC35.1 Isolated from Diseased Turbot (Scophthalmus maximus) in Europe.
JO  - Genome Announcements
PY  - 2017
SP  - e01626
EP  - e01616
VL  - 5
AB  - Edwardsiella piscicida is a bacterial fish pathogen with a high degree of virulence. The
AB  - strain ACC35.1 was isolated from diseased turbot in Europe. The
AB  - draft genome sequence comprises 3.84 Mb with a G+C content of 59.8% and >3,450
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Molecular phylogenetics of restriction endonucleaseses.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 63
EP  - 93
VL  - 14
AB  - 1. Discovery and classification of restriction enzymes.  The phenomenon of restriction and
AB  - modification was first discovered in the early 1950s.  It was observed that certain strains of
AB  - bacteria inhibited (restricted) the growth of bacteriophages previously propagated on a
AB  - different strain.  In the early 1960s, it was found that the restriction is due to the
AB  - enzymatic cleavage of the phage DNA by sequence-specific endonucleases (REases), which are
AB  - sensitive to covalent modification of bases in the target sequence.  Some of the REases
AB  - produced discrete DNA fragments upon cleavage.  This property proved very useful for analyzing
AB  - and rearranging DNA, which soon prompted the rapid development of genetic engineering
AB  - techniques as well as the search for more REases with novel recognition sequences.  It was in
AB  - the mid-1970s when cloning of R-M enzymes themselves began.  It was found that most of
AB  - restriction enzymes are genetically linked with modification enzymes of cognate specificity,
AB  - forming R-M systems, but a few solitary enzymes were also characterized.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.
JO  - J. Mol. Evol.
PY  - 2000
SP  - 39
EP  - 44
VL  - 50
AB  - To date all attempts to derive a phyletic relationship among restriction endonucleases
AB  - (ENases) from multiple sequence alignments have been limited by extreme divergence of these
AB  - enzymes.  Based on the approach of Johnson et al. (1990), I report for the first time the
AB  - evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison
AB  - of atomic coordinates of structurally characterized enzymes. The results presented are in
AB  - harmony with previous comparisons obtained by crystallographic analyses. It is shown that
AB  - lambda-exonuclease initially diverged from the common ancestor and then two "endonucleolytic"
AB  - families branched out, separating "blunt end cutters" from "5' four-base overhand cutters."
AB  - These data may contribute to a better understanding of ENases and encourage the use of
AB  - structure-based methods for inference of phylogenetic relationship among extremely divergent
AB  - proteins. In addition, the comparison of three-dimensional structures of ENase-like domains
AB  - provides a platform for further clustering analyses of sequence similarities among different
AB  - branches of this large protein family, rational choice of homology modeling templates, and
AB  - targets for protein engineering.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.
JO  - Acta Microbiol. Pol.
PY  - 2001
SP  - 219
EP  - 231
VL  - 50
AB  - Sau3AI is a type II endonuclease that cleaves GATC sequences, producing sticky ends with
AB  - 4-nucleotide 5'-overhangs.  Its activity is inhibited by cytosine C5-methylation within the
AB  - target sequence.  In the N-terminus, Sau3AI exhibits sequence similarity to the GATC-specific
AB  - single-strand nicking endonuclease MutH implicated in mismatch repair.  Sequence analysis of
AB  - Sau3AI and its homologs reveals that Sau3AI possesses an additional MutH-like domain in the
AB  - C-terminus.  Structure prediction suggests that the C-terminal domain lacks the endonuclease
AB  - active site but retains all putative DNA-binding elements.  As an illustration of these
AB  - findings, a model of quaternary structure of Sau3AI complexed with the target DNA is
AB  - presented.  These predictions have implications for evolution, structure and function of
AB  - bacterial DNA repair enzymes and restriction endonucleases.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Comparison of protein structures reveals monophyletic origin of AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.
JO  - In Silico Biology
PY  - 1999
SP  - 175
EP  - 182
VL  - 1
AB  - Phylogenetic analysis of the S-adenosyl-L-methionine-dependent methyltransferases was
AB  - performed based on similarity of positions of main chain alpha-carbon atoms in published
AB  - structures of members of this superfamily.  The evolutionary tree was inferred and the problem
AB  - of mono/polyphyletic origin of DNA methyltransferases from the Rossmann-fold enzymes was
AB  - solved, bridging two seemingly antithetical hypotheses.  The comparison of protein structures
AB  - provides evidence for an evolutionary link between widely diverged subfamilies of RNA and DNA
AB  - N6-adenine methyltransferases and argues against the close homology of N6-adenine and
AB  - N4-cytosine methyltransferases, apparent from biochemical data and comparison of fragments of
AB  - sequences.  Such evolutionary analysis of methyltransferases has never been published yet in
AB  - the literature and will guide further phylogenetical studies based on both sequence and
AB  - structure comparison.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Sequence permutations in the molecular evolution of DNA methyltransferases.
JO  - BMC Evol. Biol.
PY  - 2002
SP  - 3
EP  - 3
VL  - 2
AB  - BACKGROUND: DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit
AB  - sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the
AB  - catalytic subdomain, and the target recognition domain (TRD), several classes of permutants
AB  - have been proposed. The majority of known DNA MTases fall into the alpha, beta, and gamma
AB  - classes. There is only one member of the zeta class known and no members of the delta and
AB  - epsilon classes have been identified to date. Two mechanisms of permutation have been
AB  - proposed: one involving gene duplication and in-frame fusion, and the other involving inter-
AB  - and intragenic shuffling of gene segments. RESULTS: Two novel cases of sequence permutation in
AB  - DNA MTases implicated in restriction-modification systems have been identified, which suggest
AB  - that members of the delta and zeta classes (M.MwoI and M.TvoORF1413P, respectively) evolved
AB  - from beta-class MTases. This is the first identification of the delta-class MTase and the
AB  - second known zeta-class MTase (the first zeta-class member among DNA:m4C and m6A-MTases).
AB  - CONCLUSIONS: Fragmentation of a DNA MTase gene may result from attack of nucleases, for
AB  - instance when the RM system invades a new cell. Its reassembly into a functional form, the
AB  - order of motifs notwithstanding, may be strongly selected for, if the cognate ENase gene
AB  - remains active and poses a threat to the host's chromosome. The "cut-and-paste" mechanism is
AB  - proposed for beta-delta permutation, which is non-circular and involves relocation of one
AB  - segment of a gene. The circular beta-zeta permutation may be explained both by gene
AB  - duplication or shuffling of gene fragments. These two mechanisms are not mutually exclusive
AB  - and probably both played a role in the evolution of permuted DNA MTases.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Crystallographic and bioinformatic studies on restriction endonucleases: Inference of evolutionary relationships in the 'midnight zone' of homology.
JO  - Curr. Protein Pept. Sci.
PY  - 2003
SP  - 327
EP  - 337
VL  - 4
AB  - Type II restriction endonucleases (ENases) cleave DNA with remarkable sequence specificity.
AB  - Their discovery in 1970 and studies on molecular
AB  - genetics and biochemistry carried out over the past four decades laid
AB  - foundations for recombinant DNA techniques. Today, restriction enzymes are
AB  - indispensable tools in molecular biology and molecular medicine and a
AB  - paradigm for proteins that specifically interact with DNA as well as a
AB  - challenging target for protein engineering. The
AB  - sequence-structure-function relationships for these proteins are therefore
AB  - of central interest in biotechnology. However, among numerous ENase
AB  - sequences, only a few exhibit statistically significant similarity in
AB  - pairwise comparisons, which was initially interpreted as evidence for the
AB  - lack of common origin. Nevertheless, X-ray crystallographic studies of
AB  - seemingly dissimilar type II ENases demonstrated that they share a common
AB  - structural core and metal-binding/catalytic site, arguing for extreme
AB  - divergence rather than independent evolution. A similar nuclease domain
AB  - has been also identified in various enzymes implicated in DNA repair and
AB  - recombination. Ironically, following the series of crystallographic
AB  - studies suggesting homology of all type II ENases, bioinformatic studies
AB  - provided evidence that some restriction enzymes are in fact diverged
AB  - members of unrelated nuclease superfamilies: Nuc, HNH and GIY-YIG. Hence,
AB  - the restriction enzymes as a whole, represent a group of functionally
AB  - similar proteins, which evolved on multiple occasions and subsequently
AB  - diverged into the "midnight zone" of homology, where common origins within
AB  - particular groups can be inferred only from structure-guided comparisons.
AB  - The structure-guided approaches used for this purpose include:
AB  - identification of functionally important residues using superposition of
AB  - atomic coordinates, alignment of sequence profiles enhanced by secondary
AB  - structures, fold recognition, and homology modeling. This review covers
AB  - recent results of comparative analyses of restriction enzymes from the
AB  - four currently known superfamilies of nucleases with distinct folds, using
AB  - crystallographic and bioinformatic methods, with the emphasis on
AB  - theoretical predictions and their experimental validation by site-directed
AB  - mutagenesis and biochemical analyses of the mutants.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?
JO  - Int. J. Biol. Macromol.
PY  - 2000
SP  - 195
EP  - 204
VL  - 27
AB  - This work presents a full tertiary model of the M.BssHII methyltransferase (MTase) complexed
AB  - with substrate DNA and cofactor
AB  - S-adenosyl-L-methionine, built by homology modelling based on
AB  - previously solved complete structures of DNA MTases M.HaeIII and
AB  - M.HhaI. M.BssHII and the template proteins show high sequence
AB  - similarity, which indicates that they are evolutionary related.
AB  - However, they are topologically different: M.BssHII is a circularly
AB  - permuted variant of template MTases (Xu et al. Nucleic Acids Res.
AB  - 1997,25:3991). The model developed in this work will be a good starting
AB  - point and valuable help in designing mutagenesis experiments to better
AB  - understand the biological function of methyltransferases and the
AB  - process of domain swapping.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
TI  - Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons.
JO  - Acta Biochim. Pol.
PY  - 2001
SP  - 935
EP  - 967
VL  - 48
AB  - Restriction-modification (RM) systems comprise two opposing enzymatic activities: a
AB  - restriction endonuclease, that targets specific DNA
AB  - sequences and performs endonucleolytic cleavage, and a modification
AB  - methyltransferase that renders these sequences resistant to cleavage.
AB  - Studies on molecular genetics and biochemistry of RM systems have been
AB  - carried out over the past four decades, laying foundations for modern
AB  - molecular biology and providing important models for mechanisms of
AB  - highly specific protein-DNA interactions. Although the number of known,
AB  - relevant sequences 3D structures of RM proteins is growing steadily, we
AB  - do not fully understand their functional diversities from an
AB  - evolutionary perspective and we are not yet able to engineer new
AB  - sequence specificities based on rational approaches. Recent findings on
AB  - the evolution of RM systems and on their structures and mechanisms of
AB  - action have led to a picture in which conserved modules with defined
AB  - function are shared between different RM proteins and other enzymes
AB  - involved in nucleic acid biochemistry. On the other hand, it has been
AB  - realized that some of the modules have been replaced in the evolution
AB  - by unrelated domains exerting similar function. The aim of this review
AB  - is to give a survey on the recent progress in the field of structural
AB  - phylogeny of RM enzymes with special emphasis on studies of
AB  - sequence-structure-function relationships and emerging potential
AB  - applications in biotechnology.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Feder, M.
AU  - Ayres, C.L.
AU  - Redman, K.L.
TI  - Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 2453
EP  - 2463
VL  - 32
AB  - Three types of methyltransferases (MTases) generate 5-methylpyrimidine in nucleic acids,
AB  - forming m5U in RNA, m5C in RNA and m5C in DNA. The DNA:m5C
AB  - MTases have been extensively studied by crystallographic, biophysical,
AB  - biochemical and computational methods. On the other hand, the
AB  - sequence-structure-function relationships of RNA:m5C MTases remain
AB  - obscure, as do the potential evolutionary relationships between the three
AB  - types of 5-methylpyrimidine-generating enzymes. Sequence analyses and
AB  - homology modeling of the yeast tRNA:m5C MTase Trm4p (also called Ncl1p)
AB  - provided a structural and evolutionary platform for identification of
AB  - catalytic residues and modeling of the architecture of the RNA:m5C MTase
AB  - active site. The analysis led to the identification of two invariant
AB  - residues that are important for Trm4p activity in addition to the
AB  - conserved Cys residues in motif IV and motif VI that were previously found
AB  - to be critical. The newly identified residues include a Lys residue in
AB  - motif I and an Asp in motif IV. A conserved Gln found in motif X was found
AB  - to be dispensable for MTase activity. Locations of essential residues in
AB  - the model of Trm4p are in very good agreement with the X-ray structure of
AB  - an RNA:m5C MTase homolog PH1374. Theoretical and experimental analyses
AB  - revealed that RNA:m5C MTases share a number of features with either
AB  - RNA:m5U MTases or DNA:m5C MTases, which suggested a tentative phylogenetic
AB  - model of relationships between these three classes of 5-methylpyrimidine
AB  - MTases. We infer that RNA:m5C MTases evolved from RNA:m5U MTases by
AB  - acquiring an additional Cys residue in motif IV, which was adapted to
AB  - function as the nucleophilic catalyst only later in DNA:m5C MTases,
AB  - accompanied by loss of the original Cys from motif VI, transfer of a
AB  - conserved carboxylate from motif IV to motif VI and sequence permutation.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Feder, M.
AU  - Radlinska, M.
AU  - Blumenthal, R.M.
TI  - Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the  human mRNA:m6A methyltransferase.
JO  - J. Mol. Evol.
PY  - 2002
SP  - 431
EP  - 444
VL  - 55
AB  - MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyltransferase
AB  - (MTase), an enzyme that sequence-specifically
AB  - methylates adenines in pre-mRNAs. The physiological importance yet
AB  - limited understanding of MT-A70 and its apparent lack of similarity to
AB  - other known RNA MTases combined to make this protein an attractive
AB  - target for bioinformatic analysis. The sequence of MT-A70 was subjected
AB  - to extensive in silico analysis to identify orthologous and paralogous
AB  - polypeptides. This analysis revealed that the MT-A70 family comprises
AB  - four subfamilies with varying degrees of interrelatedness. One
AB  - subfamily is a small group of bacterial DNA:m6A MTases. The other three
AB  - subfamilies are paralogous eukaryotic lineages, two of which have not
AB  - been associated with MTase activity but include proteins having
AB  - substantial regulatory effects. Multiple sequence alignments and
AB  - structure prediction for members of all four subfamilies indicated a
AB  - high probability that a consensus MTase fold domain is present.
AB  - Significantly, this consensus fold shows the permuted topology
AB  - characteristic of the beta class of MTases, which to date has only been
AB  - known to include DNA MTases.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
TI  - Molecular phylogenetics of DNA 5mC-methyltransferases.
JO  - Acta Microbiol. Pol.
PY  - 1999
SP  - 19
EP  - 30
VL  - 48
AB  - We have identified a total of 88 members of the DNA-(cytosine-5) methyltransferase (5mC MTase)
AB  - family whose sequences have been deposited in the databases. The results of a comparison of
AB  - these sequences is presented in the form of an alignment-based phylogenetic tree and sequence
AB  - logos for 10 conserved motifs. Phylogenetic analysis showed that members of the family
AB  - aggregate into subfamilies which are usually consistent with their target specificity.
AB  - However, it was also shown that similar target specificity does not necessarily imply close
AB  - homology of the catalytic domain of MTases, which strongly supports the hypothesis that target
AB  - recognition evolved independently of catalytic properties. This analysis also indicate that
AB  - the 5mC MTase was present in the cenancestor (last common ancestor) of eubacteria,
AB  - archaebacteria, and eukaryotes. The phylogeny of the 5mC MTases catalytic domain provides the
AB  - basis for establishing the patterns of evolutionary change that characterize this family of
AB  - proteins with conserved structural core and variable and mobile modules not directly involved
AB  - in formation of the active site.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
TI  - Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 4501
EP  - 4509
VL  - 27
AB  - DNA N4-cytosine methyltransferases (N4mC MTases) are a family of S -adenosyl-L-methionine
AB  - (AdoMet)-dependent MTases. Members of this family were previously found to share nine
AB  - conserved sequence motifs, but the evolutionary basis of these similarities has never been
AB  - studied in detail. We performed phylogenetic analysis of 37 known and potential new family
AB  - members from the multiple sequence alignment using distance matrix, parsimony and maximum
AB  - likelihood approaches to infer the evolutionary relationship among the N4mC MTases and
AB  - classify them into groups of orthologs. All the treeing algorithms employed as well as results
AB  - of exhaustive sequence database searching support a scenario, in which the majority of N4mC
AB  - MTases, except for M.BalI and M.BamHI, arose by divergence from a common ancestor.
AB  - Interestingly, MTases M.BalI and M.BamHI apparently originated from N6-adenine MTases and
AB  - represent the most recent addendum to the N4mC MTase family. In addition to the previously
AB  - reported nine sequence motifs, two more conserved sequence patches were detected. Phylogenetic
AB  - analysis also provided the evidence for massive horizontal transfer of MTase genes, presumably
AB  - with the whole restriction-modification systems, between Bacteria and Archaea.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
TI  - Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria  monocytogenes Phage A118, a close homolog of M.NgoMXV.
JO  - Acta Microbiol. Pol.
PY  - 2001
SP  - 155
EP  - 160
VL  - 50
AB  - A homolog of M.NgoMXV DNA:M4C methyltransferase has been identified among the open reading
AB  - frames deduced from the genomic sequence of Listeria monocytogenes phage A118.  The gene
AB  - coding for this putative protein has been cloned in Escherichia coli and its enzymatic
AB  - activity in vivo in this host have been analyzed.  Remarkably, although M.NgoMXV and
AB  - M.LmoA118I exhibit high sequence similarity (58% identical and 19% conservatively substituted
AB  - residues), their target preferences differ: both proteins exhibit "relaxed" sequence
AB  - specificity, but while M.LmoA118I more efficiently methylates GGCC sites, it seems to target
AB  - only a subset of CCWGG sites methylated by M.NgoMXV.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
TI  - Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases?  A hypothesis.
JO  - Life
PY  - 1999
SP  - 247
EP  - 249
VL  - 48
AB  - Previous comparative studies revealed close similarity among various groups of
AB  - S-adenosyl-L-methionine-dependent methyltransferases, indicating their common evolutionary
AB  - origin.  We present evidence for a remarkable similarity between the sequence and predicted
AB  - structure of HemK (a widespread family of putative proteins encoded in genomes from bacteria
AB  - to humans) and the catalytic domain of the gamma-subfamily of adenine-specific DNA MTases
AB  - (N6mA MTases).  We predict the structure and function of the putative catalytic domain of HemK
AB  - proteins and speculate that the target-recognizing function may be conferred by the N-terminal
AB  - variable region.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
AU  - Rychlewski, L.
TI  - Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to beta beta alpha-Me endonucleases.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 1280
EP  - 1281
VL  - 37
AB  - Using a novel FFAS algorithm for supersensitive sequence comparison and fold recognition, we
AB  - have identified a domain in the 5-methylcytosine-specific restriction enzyme (ENase) McrA from
AB  - Escherichia coli that is common to the beta beta alpha-Me superfamily of nucleases.  We
AB  - carried out extensive threading of the McrA sequence onto the known protein structures and
AB  - detected a high compatibility with conformation assumed by the DNase domain of colicins E7 and
AB  - E9, although it displays no significant similarity to the sequences of these proteins.  The
AB  - model presented reveals that McrA shares a putative zinc finger with homologous group II
AB  - intron maturases and the more remotely related coliphage T4 endonuclease VII, despite the fact
AB  - that this structure is absent from colicins.  This is the first robust structure prediction of
AB  - an ENase ever performed.  It strongly suggests that ENases do not all share the same
AB  - three-dimensional fold and, as a functional class of proteins, they should be regarded as
AB  - products of convergent evolution.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
AU  - Zaleski, P.
AU  - Piekarowicz, A.
TI  - Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
JO  - Acta Biochim. Pol.
PY  - 2001
SP  - 969
EP  - 983
VL  - 48
AB  - In this paper we report cloning and experimental characterization of the DNA adenine
AB  - methyltransferase (dam) gene from Haemophilus
AB  - influenzae and comparison of its product with the Dam protein from the
AB  - lysogenic phage of H. influenzae, HP1. Molecular modeling of M.HinDam
AB  - and M.HP1Dam was carried out, providing a framework for a comparative
AB  - analysis of these enzymes and their close homologs in the structural
AB  - context. Both proteins share the common fold and essential
AB  - cofactor-binding and catalytic residues despite overall divergence.
AB  - However, subtle but significant differences in the cofactor-binding
AB  - pocket have been identified. Moreover, while M.HinDam seems to contact
AB  - its target DNA sequence using a number of loops, most of them are
AB  - missing from M.HP1Dam. Analysis of both MTases suggests that their
AB  - catalytic activity was derived from a common ancestor, but similar
AB  - sequence specificities arose by convergence.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Rotkiewicz, P.
AU  - Kolinski, A.
AU  - Rychlewski, L.
TI  - Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
JO  - Protein Eng.
PY  - 2001
SP  - 717
EP  - 721
VL  - 14
AB  - Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind
AB  - prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain
AB  - (CD) of the I-TevI homing endonuclease, a representative of the GIY-YIG superfamily of homing
AB  - endonucleases. The secondary structure of the I-TevI CD has been determined using NMR
AB  - spectroscopy, but computational sequence analysis failed to detect any protein of known
AB  - tertiary structure related to the GIY-YIG nucleases (Kowalski et al., Nucleic Acids Res.,
AB  - 1999, 27, 2115-2125). To provide further insight into the structure-function relationships of
AB  - all GIY-YIG superfamily members, including the recently described subfamily of type II
AB  - restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9-11), we incorporated
AB  - the experimentally determined and predicted secondary and tertiary restraints in a reduced
AB  - (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated
AB  - annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available
AB  - experimental data to be put into a structural context and suggests that the GIY-YIG domain may
AB  - dimerize in order to bring together the conserved residues of the active site.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Rychlewski, L.
TI  - The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis.
JO  - Virus Genes
PY  - 2001
SP  - 219
EP  - 230
VL  - 22
AB  - The PD-(D/E)XK superfamily of deoxyribonucleases (Enases) comprises restriction endonucleases,
AB  - exonucleases and nicking enzymes, which share a common fold and the architecture of the active
AB  - site.  Their extreme divergence generally hampers identification of novel members based solely
AB  - on sequence comparisons.  Here we report a remote similarity between the phage lambda
AB  - exonuclease (lambda-exo), branching out early in the evolutionary history of Enases, with the
AB  - family of alkaline exonucleases encoded by various viruses infecting higher Eukaryota.  The
AB  - predicted structural compatibility and the conservation of the functionally important residues
AB  - between AE and Enases strongly suggest a distant evolutionary relationship between these
AB  - proteins.  According to the results of extensive sequence database mining, sequence/structure
AB  - threading and molecular modeling it is plausible that the AE proteins with lambda-exo and some
AB  - other putative phage-encoded exonucleases form a distinct subfamily of PD-(D/E)XK Enases.  The
AB  - phylogenetic history of this subfamily is inferred using sequence alignment and distance
AB  - matrix methods.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Rychlewski, L.
TI  - Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs.
JO  - Gene
PY  - 2001
SP  - 183
EP  - 191
VL  - 267
AB  - The Escherichia coli K-12 restriction enzyme Mrr recognizes and cleaves N6-methyladenine- and
AB  - 5-methylcytosine-containing DNA. Its amino acid sequence has been subjected to structure
AB  - prediction and comparison with other sequences from publicly available sources. The results
AB  - obtained suggest that Mrr and related putative endonucleases possess a cleavage domain typical
AB  - for all the so far structurally characterized type II restriction enzymes, however with an
AB  - unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active
AB  - site. The 'missing' acidic side chain was instead found anchored in a different, unusual
AB  - position, suggesting that Mrr represents a third topological variant of the endonuclease
AB  - active site in addition to the two alternatives determined previously (Skirgaila et al., 1998.
AB  - J. Mol. Biol. 279, 473-481). One of the newly identified putative endonucleases from the Mrr
AB  - family is composed of two diverged cleavage domains, which possess both the 'typical' D-EXK
AB  - and the 'Mrr-like' D-QXK variants of the active site. Among the Mrr homologs there are also
AB  - proteins from yeast, in which restriction phenotype has not been observed, suggesting that the
AB  - free-standing Eukaryotic PD-(D/E)XK superfamily members might be implicated in other cellular
AB  - processes involving enzymatic DNA cleavage.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Rychlewski, L.
TI  - Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.
JO  - Protein Sci.
PY  - 2001
SP  - 656
EP  - 660
VL  - 10
AB  - The tRNA splicing endoribonuclease EndA from Methanococcus jannaschii is a homotetramer formed
AB  - via heterologous interaction between the two pairs of homodimers. Each monomer consists of two
AB  - alpha/beta domains, the N-terminal domain (NTD) and the C-terminal domain (CTD) containing the
AB  - RNase A-like active site. Comparison of the EndA coordinates with the publicly available
AB  - protein structure database revealed the similarity of both domains to site-specific
AB  - deoxyribonucleases: the NTD to the LAGLIDADG family and the CTD to the PD-(D/E)XK family.
AB  - Superposition of the NTD on the catalytic domain of LAGLIDADG homing endonucleases allowed a
AB  - suggestion to be made about which amino acid residues of the tRNA splicing nuclease might
AB  - participate in formation of a presumptive cryptic deoxyribonuclease active site. On the other
AB  - hand, the CTD and PD-(D/E)XK endonucleases, represented by restriction enzymes and a phage
AB  - lambda exonuclease, were shown to share extensive similarities of the structural framework, to
AB  - which entirely different active sites might be attached in two alternative locations. These
AB  - findings suggest that EndA evolved from a fusion protein with at least two distinct
AB  - endonuclease activities: the ribonuclease, which made it an essential "antitoxin" for the
AB  - cells whose RNA genes were interrupted by introns, and the deoxyribonuclease, which provided
AB  - the means for homing-like mobility. The residues of the noncatalytic CTDs from the positions
AB  - corresponding to the catalytic side chains in PD-(D/E)XK deoxyribonucleases map to the surface
AB  - at the opposite side to the tRNA binding site, for which no function has been implicated. Many
AB  - restriction enzymes from the PD-(D/E)XK superfamily might have the potential to maintain an
AB  - additional active or binding site at the face opposite the deoxyribonuclease active site, a
AB  - property that can be utilized in protein engineering.
ER  -

TY  - JOUR
AU  - Bujnicki, J.M.
AU  - Rychlewski, L.
AU  - Radlinska, M.
TI  - Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.
JO  - Trends Biochem. Sci.
PY  - 2001
SP  - 9
EP  - 11
VL  - 26
AB  - Using algorithms for protein sequence analysis we predict that some of the canonical type II
AB  - and type IIS restriction enzymes have an active site with a substantially different
AB  - architecture and fold from the "typical" PD-(D/E)xK superfamily.  These results suggest that
AB  - they are related to nucleases from the HNH and GIY-YIG superfamilies.
ER  -

TY  - JOUR
AU  - Bulach, D.M.
AU  - Zuerner, R.L.
AU  - Wilson, P.
AU  - Seemann, T.
AU  - McGrath, A.
AU  - Cullen, P.A.
AU  - Davis, J.
AU  - Johnson, M.
AU  - Kuczek, E.
AU  - Alt, D.P.
AU  - Peterson-Burch, B.
AU  - Coppel, R.L.
AU  - Rood, J.I.
AU  - Davies, J.K.
AU  - Adler, B.
TI  - Genome reduction in Leptospira borgpetersenii reflects limited transmission potential.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 14560
EP  - 14565
VL  - 103
AB  - Leptospirosis is one of the most common zoonotic diseases in the world, resulting in high
AB  - morbidity and mortality in humans and affecting global
AB  - livestock production. Most infections are caused by either Leptospira
AB  - borgpetersenii or Leptospira interrogans, bacteria that vary in their
AB  - distribution in nature and rely on different modes of transmission. We
AB  - report the complete genomic sequences of two strains of L. borgpetersenii
AB  - serovar Hardjo that have distinct phenotypes and virulence. These two
AB  - strains have nearly identical genetic content, with subtle frameshift and
AB  - point mutations being a common form of genetic variation. Starkly limited
AB  - regions of synteny are shared between the large chromosomes of L.
AB  - borgpetersenii and L. interrogans, probably the result of frequent
AB  - recombination events between insertion sequences. The L. borgpetersenii
AB  - genome is approximately 700 kb smaller and has a lower coding density than
AB  - L. interrogans, indicating it is decaying through a process of insertion
AB  - sequence-mediated genome reduction. Loss of gene function is not random
AB  - but is centered on impairment of environmental sensing and metabolite
AB  - transport and utilization. These features distinguish L. borgpetersenii
AB  - from L. interrogans, a species with minimal genetic decay and that
AB  - survives extended passage in aquatic environments encountering a mammalian
AB  - host. We conclude that L. borgpetersenii is evolving toward dependence on
AB  - a strict host-to-host transmission cycle.
ER  -

TY  - JOUR
AU  - Bulanenkova, S.
AU  - Kotova, E.
AU  - Snezhkov, E.
AU  - Akopov, S.
AU  - Nikolaev, L.
AU  - Sverdlov, E.
TI  - Dam methylase accessibility as an instrument for analysis of mammalian chromatin structure.
JO  - FEBS J.
PY  - 2012
SP  - 493
EP  - 493
VL  - 279
AB  - The study of regulatory mechanisms operating at the level of the chromatin fiber is one of the
AB  - rapidly developing fields of modern molecular biology.  Changes in chromatin condensation
AB  - state is one of the main regulatory mechanisms of cell functions, such as transcription,
AB  - replication, DNA repair, and other processes. The lack of information on dynamic behavior of
AB  - extended chromatin regions leads to a gap in our understanding of mechanisms of coordinated
AB  - expression regulation of gene ensembles.  Chromatin structure analysis is in many cases based
AB  - on the accessibility of chromatin DNA to modifying agents.  The main benefits are granted by
AB  - in vivo detecting agents such as Dam methylase, for example.  For a 140 kb human genome locus,
AB  - an analysis of the distribution of Dam methylase accessible sites, DNase I sensitive and
AB  - resistant regions, and acetylated histone H3 molecules was performed and compared with
AB  - transcriptional activity of the genes within the locus.  It was demonstrated that promoter
AB  - regions of all highly and moderately transcribed genes are highly accessible to methylation by
AB  - Dam methylase.  In contrast, promoters of non-transcribed genes showed a very low extent of
AB  - Dam methylation.  Some highly Dam methylase accessible regions are present in the intergenic
AB  - regions of the locus suggesting that the latter contain either unidentified non-coding
AB  - transcripts or extended regulatory elements like locus control regions.
ER  -

TY  - JOUR
AU  - Bulgari, D.
AU  - Minio, A.
AU  - Casati, P.
AU  - Quaglino, F.
AU  - Delledonne, M.
AU  - Bianco, P.A.
TI  - Curtobacterium sp. Genome Sequencing Underlines Plant Growth Promotion-Related Traits.
JO  - Genome Announcements
PY  - 2014
SP  - e00592
EP  - e00514
VL  - 2
AB  - Endophytic bacteria are microorganisms residing in plant tissues without causing  disease
AB  - symptoms. Here, we provide the high-quality genome sequence of
AB  - Curtobacterium sp. strain S6, isolated from grapevine plant. The genome assembly
AB  - contains 2,759,404 bp in 13 contigs and 2,456 predicted genes.
ER  -

TY  - JOUR
AU  - Bulkacz, J.
AU  - Roulland-Dussoix, D.
AU  - Boyer, H.W.
TI  - Deoxyribonucleic acid modification by intermediate-type modification mutants of Escherichia coli K-12 and B.
JO  - J. Bacteriol.
PY  - 1975
SP  - 1395
EP  - 1402
VL  - 124
AB  - The modification of bacteriophages grown on r-m+- restriction and modification
AB  - mutants of Escherichia coli K-12 or B appears to be related to the number of
AB  - restriction-specific sites in the viral genome.  Bacteriophage fd and its
AB  - mutant U1 fd, which carry two and one B-specific sites, respectively, are not
AB  - modified in vivo by rB-mB+- mutant strains.  In vitro treatment of fd RF.B+-
AB  - deoxyribonucleic acid (DNA) or U1 fd RF.B+- DNA by endo R.EcoB results in
AB  - cleavage of the substrate DNA.  Lambda bacteriophge, after growth in r-m+-
AB  - mutant host strains (k.K+- or k.B+-), is partially protected from in vivo
AB  - degradation by wild-type homospecific strains.  Its efficiency of plating on
AB  - these strains is approximately 10-2.  However, a hybrid Phi80-lambda phage
AB  - which carries only one K-specific site (skk-1) is not modified by rK-mK+-
AB  - strains.  Labeled DNAs from k.B+- and k.K+- phages were used as substrates for
AB  - endo R.Eco B and endo R.Eco K nucleases.  Zonal centrifugation analysis of the
AB  - products of the reactions indicate that rK-mK+- mutants do not protect lambda
AB  - DNA from in vitro degradation by endo R.EcoK.  In contrast, rB-mB+- mutants
AB  - appear to partially protect lambda DNA from attack by endo R.Eco B.
ER  -

TY  - JOUR
AU  - Bulkowska, U.
AU  - Ishikawa, T.
AU  - Kurlandzka, A.
AU  - Trzcinska-Danielewicz, J.
AU  - Derlacz, R.
AU  - Fronk, J.
TI  - Expression and of murine DNA methyltransferases Dnmt1 and Dnmt3a in the yeast Saccharomyces cerevisiae.
JO  - Yeast
PY  - 2007
SP  - 871
EP  - 882
VL  - 24
AB  - Murine DNA methyltransferases Dnmt1 and Dnmt3a were expressed in the yeast Saccharomyces
AB  - cerevisiae. Adjustment to yeast preferences of the
AB  - nucleotide sequences upstream and downstream of the translation
AB  - initiation sites of both cDNAs was needed to obtain significant levels
AB  - of the methyltransferases. Both proteins were correctly localized to
AB  - the nucleus and their presence had no measurable influence on the
AB  - functioning of yeast cells. Both Dnmt1 and Dnmt3a expressed in yeast
AB  - cells were enzymatically active in vitro, and in vivo in the genomic
AB  - DNA of the transgenic S. cerevisiae ca. 0.06% and 0.4%, respectively,
AB  - of cytosines became methylated. This level of DNA methylation is about
AB  - 100- to 10-fold less than that observed in mammalian cells. The
AB  - constructed system may be used to investigate the in vivo specificity
AB  - of individual mammalian DNA methyltransferases and to search for
AB  - additional factors needed to allow more efficient in vivo methylation
AB  - of chromatincontained DNA and to study their mechanism of action.
ER  -

TY  - JOUR
AU  - Bull, J.J.
AU  - Vimr, E.R.
AU  - Molineux, I.J.
TI  - A tale of tails: Sialidase is key to success in a model of phage therapy against K1-capsulated Escherichia coli.
JO  - Virology
PY  - 2010
SP  - 79
EP  - 86
VL  - 398
AB  - Prior studies treating mice infected with Escherichia coli O18:K1:H7 observed that phages
AB  - requiring the K1 capsule for infection (K1-dep) were superior to capsule-independent (K1-ind)
AB  - phages. We show that three K1-ind phages all have low fitness when grown on cells in serum
AB  - whereas fitnesses of four K1-dep phages were high. The difference is serum-specific, as
AB  - fitnesses in broth overlapped. Sialidase activity was associated with all K1-dep virions
AB  - tested but no K1-ind virions, a phenotype supported by sequence analyses. Adding endosialidase
AB  - to cells infected with K1-ind phage increased fitness in serum by enhancing productive
AB  - infection after adsorption. We propose that virion sialidase activity is the primary
AB  - determinant of high fitness on cells grown in serum, and thus in a mammalian host. Although
AB  - the benefit of sialidase is specific to K1-capsulated bacteria, this study may provide a
AB  - scientific rationale for selecting phages for therapeutic use in many systemic infections.
ER  -

TY  - JOUR
AU  - Bull, L.N.
AU  - Hewitt, J.E.
AU  - Cox, D.R.
AU  - Myers, R.M.
TI  - Sensitivity of HincII to CpG methylation.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2021
EP  - 2021
VL  - 21
AB  - Restriction fragment length polymorphism (RFLP) analysis in human genetics can be confounded
AB  - by the sensitivity of restriction enzymes to cytosine methylation that occurs at many
AB  - cytosine-guanine (CpG) dinucleotides. Previous reports provided conflicting information on the
AB  - sensitivity of HincII to C methylation (1-3). We identified alleles at a chromosome 4p16 locus
AB  - that were inherited in a non-Mendelian manner due to inhibition of HincII cleavage by CpG
AB  - methylation. We confirmed that cleavage by HincII, whose recognition sequence is
AB  - 5'GTPyPuAC3', is inhibited by the presence of 5-methyl-cytosine at the terminal base of its
AB  - recognition site.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
TI  - Cloning of the SA system for the restriction and modification of DNA from Salmonella typhimurium into phage lambda.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 224
EP  - 224
VL  - 94
AB  - The Salmonella typhimurium SA system of genes for the restriction and modification of DNA (R-M
AB  - system), the first such system recognized in this organism, has been cloned. Selection for the
AB  - SA genes has been difficult since all SA E. coli/Salmonella hybrids derived years ago failed
AB  - to express either SA restriction or modification when tested at this time. However, such a
AB  - hybrid between E. coli and Salmonella typhi, designated LB4019, was found still to express SA
AB  - restriction and modification. Several libraries consisting of partial SauIIIA digests of
AB  - genomic S. typhimurium DNA ligated to phageEMBL4 and amplified on the non-restriction,
AB  - non-modifying strain of E. coli NM477, were plated out on a lawn of LB4019. All plaques which
AB  - were produced on LB4019 were picked, plated out on NM477 and the efficiencies of plating (eop)
AB  - on LB4019 determined. From one library, a number of plaques plated out at eop of 1. In
AB  - addition, plaques that gave significantly higher eop than unmodified phageEMBL on LB4019 (1 x
AB  - 10-3) were isolated. The phages fell into four groups relative to their eop on LB4019. Group 1
AB  - clones consistently plated with an eop of 1.0, group 2 an eop of about 0.5, group 3 an eop of
AB  - about 0.2 and group 4 an eop of about 0.02. The cloning of these apparently partially
AB  - SA-modified clones in addition to the completely SA-modified clones was unexpected and is
AB  - unique to this system. Restriction analysis indicates that the sizes of the fragments cloned
AB  - in the four groups are similar. A molecular and genetic analysis of representative clones is
AB  - in progress.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Colson, C.
TI  - DNA restriction and modification systems in Salmonella.  III.  SP, a Salmonella potsdam system allelic to the SB system in Salmonella typhimurium.
JO  - Mol. Gen. Genet.
PY  - 1975
SP  - 177
EP  - 188
VL  - 139
AB  - By screening 42 Salmonella strains with P3, a temperate bacteriophage with an
AB  - unusally wide host range, five new DNA restriction and modification systems
AB  - (R-M systems) were identified in five different serotypes in Kauffmann-White
AB  - group C.  One of these systems, SP, in a Pl-sensitive strain of S. potsdam, was
AB  - analyzed genetically by Pl transduction methods in which SP was transferred
AB  - into S. typhimurium and E. coli/S. typhimurium hybrids.  It was found that the
AB  - genes of the SP system were allelic and functionally homologous to the genes of
AB  - the SB system of S. typhimurium.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Colson, C.
AU  - Neufeld, B.
TI  - Deoxyribonucleic acid restriction and modification systems in Salmonella:  chromosomally located systems of different serotypes.
JO  - J. Bacteriol.
PY  - 1980
SP  - 275
EP  - 292
VL  - 141
AB  - With the use of four different phages, Salmonella strains representing 85 different serotypes
AB  - were examined to determine their restriction-modification phenotype.  They fell into one of
AB  - three groups on this basis:  group 1, those which lacked the common LT system; group 2, those
AB  - in which only the LT system could be recognized; and group 3, those which possessed the LT
AB  - system and at least one other system shown with some serotypes to be closely linked to serB.
AB  - The specificity of the serB-linked restricted-modification system was unique for each
AB  - serotype, but different strains of the same serotype expressed the same specificity.  Two of
AB  - the systems were shown to behave in genetic crosses as functional alleles of the S.
AB  - typhimurium SB system.  It is possible that these serB-linked restriction-modification systems
AB  - constitute a large multiallelic series of genes extending throughout the Salmonella genus and
AB  - Escherichia coli.  We suggest that the division of the Salmonella into the three
AB  - restriction-modification groups may be significant in defining a biological grouping of the
AB  - different serotypes within the genus which may ultimately be useful in describing the
AB  - Salmonella species.  From the genetic relatedness between the genes of some of the Salmonella
AB  - restriction-modification systems with those of the E. coli systems, we deduce that the
AB  - restriction endonucleases produced by the Salmonella serB-linked systems are of type I.
AB  - Determination of the nucleotide sequences of the recognition sites of the restriction
AB  - endonucleases of selected Salmonella systems should further our understanding of specificity
AB  - with these enzymes.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Colson, C.
AU  - van Pel, A.
TI  - DNA restriction and modification systems in Salmonella. SQ, a new system derived by recombination between the SB system of Salmonella typhimurium and the SP system of Salmonella potsdam.
JO  - J. Gen. Microbiol.
PY  - 1976
SP  - 166
EP  - 172
VL  - 95
AB  - As a result of PI-mediated cotransduction with serB from Salmonella potsdam to
AB  - the Escherichia coli/Salmonella typhimurium hybrid 4617, one recombinant,
AB  - L4004, was isolated which had a restriction-modification (R-M) system different
AB  - from the SB and SP systems of its parents, and was designated SQ.  The genes of
AB  - complementation experiments to be functionally related to those of the K system
AB  - of E. coli.  Evidence that the SQ system in L4004 arose as the result of a
AB  - recombination event within the hsdS genes of SB and SP is discussed.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Harding, G.
TI  - Cryptic genes for the restriction and modification of DNA in Salmonella typhi and Salmonella gallinarum.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1996
SP  - 258
EP  - 258
VL  - 96
AB  - Salmonella typhi and Salmonella gallinarum fail to express the StyLTI and StyII
AB  - genes for the restriction and modification of DNA which are expressed by other Salmonella
AB  - serotypes.  S. typhi transformed by either pRUCL531 with the S. typhimurium StyLTI restriction
AB  - and modification genes or pXC1 with the StyLTIII modification gene, has a reduced ability to
AB  - propagate within human Mac6 macrophage-like cells.  In P1 transductions from S. typhi to an E.
AB  - coli/Salmonella StyLTIII+ recipient, the "lack of expression" of StyLTIII is co-transduced
AB  - with
AB  - serB to 17% of recombinants.  These observations prompted us to investigate whether S. typhi
AB  - and
AB  - S. gallinarum might possess cryptic StyLTI or StyLTIII systems of genes.  We isolated a 1.8kb
AB  - DNA sequence which included the end of the modification gene and the beginning of the
AB  - restriction
AB  - gene of StyLTI, and a 2.6 kb sequence which included parts of the StyLTIII modification and
AB  - specificity genes, and used them as probes in Southern hybridizations to genomic DNA of S.
AB  - typhi
AB  - and S. gallinarum.  The DNA of both serotypes hybridized strongly to both probes.  Thus, S.
AB  - typhi and S. gallinarum both possess cryptic StyLTI and StyLTIII R-M genes.  Since pRUCL531-
AB  - and pXC1-transformed S. typhi have reduced growth parameters in Mac6, it is likely that the S.
AB  - typhi cryptic R-M genes are concerned with the ability of this serotype to propagate within
AB  - human
AB  - macrophages.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Nutter, R.L.
TI  - Host-induced modification of Salmonella potsdam bacteriophage P3 by growth in E. coli.
JO  - Bacteriol. Proc.
PY  - 1969
SP  - 157
EP  - 157
VL  - 69
AB  - The temperate Salmonella potsdam bacteriophage P3 lyses E. coli K and E. coli C
AB  - with high efficiency.  Growth of P3 in either E. coli K (producing phage P3.K)
AB  - or E. coli C (phage P3-C) modified the phage so that its original Salmonella
AB  - host is now insensitive, but the phage retains the ability to grow on either
AB  - strain of E. coli.  P3, therefore, propagated on S. potsdam (phage P3.S) has an
AB  - unrestricted host range, while P3.K and P3.C are restricted.  Rare P3.K and
AB  - P3.C phages (10-6) will grow on the original Salmonella host producing
AB  - unrestricted phages identical to P3.S.  E. coli is readily lysogenized by P3.S,
AB  - in which it is also inducible by UV light.  Phages grown either on Salmonella
AB  - or E. coli appear to be serologically identical, although comparison of the
AB  - rates of neutralization suggest that slight structural changes of the phage
AB  - particle may have occurred in E. coli, rendering P3.K and P3.C more susceptible
AB  - than P3.S to neutralization by antiserum produced against P3.S.  These and
AB  - other results indicate that a host-induced modification of the Salmonella phage
AB  - P3.S occurs by growth in E. coli K or E. coli C.  Similar results have been
AB  - obtained for the related Salmonella phage P9a.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Rajadas, P.T.
TI  - Evidence of additional families of TypeI hsd genes concerned with the restriction and modification of DNA in Salmonella.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1987
SP  - 154
EP  - 154
VL  - 87
AB  - Hybridization and complementation experiments have shown that serB-linked genes
AB  - for the restriction and modification of DNA in E. coli and Salmonella comprise
AB  - at least two "families".  A third "family" consists of genes on a plasmid.  We
AB  - have prepared DNA probes from the cloned genes of the two chromosomal
AB  - families--hsdSB and hsdSP from the first family and hsdA from the second
AB  - family.  In addition we prepared a probe from the hsdSEN genes (from S.
AB  - enteritidis) which we had earlier cloned in phage lambda and subcloned into
AB  - pUC18 and whose family relationship was unknown.  With each of these probes
AB  - radioactively labelled with 32P and Southern gel transfer, we have performed a
AB  - series of hybridization experiments with the DNA from six E. coli/Salmonella
AB  - hybrids possessing the serB-linked hsd genes from a Salmonella serotype.
AB  - Neither of the two probes from the first family nor the A probe of the second
AB  - family hybridized with the DNA from any of the hybrids.  The SEN probe
AB  - hybridized with DNA from only two of the six hybrids.  Thus additional families
AB  - of the Type1 hsd genes must exist in Salmonella.
ER  -

TY  - JOUR
AU  - Bullas, L.R.
AU  - Ryu, J.-I.
TI  - Salmonella typhimurium LT2 strains which are r- m+ for all three chromosomally located systems of DNA restriction and modification.
JO  - J. Bacteriol.
PY  - 1983
SP  - 471
EP  - 474
VL  - 156
AB  - We describe the derivation of two strains of Salmonella typhimurium LT2 which are r- m+ for
AB  - all three of the known chromosomal genes for the restriction and modification of DNA, hsdLT,
AB  - hsdSA, and hsdSB; the strains were designated LB5000 and LB5010.  LB5000 is a smooth
AB  - derivative sensitive to phage P22; LB5010 is a galE strain sensitive to phage P1.
ER  -

TY  - JOUR
AU  - Bult, C.J. et al.
TI  - Complete genome sequence of the Methanogenic archaeon, Methanococcus jannaschii.
JO  - Science
PY  - 1996
SP  - 1058
EP  - 1073
VL  - 273
AB  - The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus
AB  - jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by
AB  - whole-genome random sequencing.  A total of 1738 predicted protein coding genes were
AB  - identified; however, only a minority of those (38 percent) could be assigned a putative
AB  - cellular role with high confidence.  Although the majority of genes related to energy
AB  - production, cell division, and metabolism in M. jannaschii are most similar to those found in
AB  - Bacteria, most of the genes involved in transcription, translation, and replication in M.
AB  - jannaschii are more similar to those found in Eukaryotes.
ER  -

TY  - JOUR
AU  - Buluwela, L.
AU  - Malcolm, A.D.B.
AU  - Coleman, D.V.
AU  - Gardner, S.D.
TI  - The use of the restriction endonuclease DdeI for mapping related DNAs.
JO  - Biosci. Rep.
PY  - 1981
SP  - 223
EP  - 228
VL  - 1
AB  - Restriction endonuclease mapping of BK virus strain GS using DdeI has allowed
AB  - us to correct and extend the previously published map.
ER  -

TY  - JOUR
AU  - Bulyk, M.L.
AU  - Gentalen, E.
AU  - Lockhart, D.J.
AU  - Church, G.M.
TI  - Quantifying DNA-protein interactions by double-stranded DNA arrays.
JO  - Nat. Biotechnol.
PY  - 1999
SP  - 573
EP  - 577
VL  - 17
AB  - We have created double-stranded oligonucleotide arrays to perform highly parallel
AB  - investigations of DNA-protein interactions.  Arrays of single-stranded DNA oligonucleotides,
AB  - synthesized by a combination of photolithography and solid-state chemistry, have been used for
AB  - a variety of applications, including large-scale mRNA expression monitoring, genotyping, and
AB  - sequence-variation analysis. We converted a single-stranded to a double-stranded array by
AB  - synthesizing a constant sequence at every position on an array and then annealing and
AB  - enzymatically extending a complementary primer. The efficiency of second-strand synthesis was
AB  - demonstrated by incorporation of fluorescently labeled dNTPs (2'-deoxyribonucleoside
AB  - 5'-triphosphates) and by terminal transferase addition of a fluorescently labeled ddNTP. The
AB  - accuracy of second-strand synthesis was demonstrated by digestion of the arrayed
AB  - double-stranded DNA (dsDNA) on the array with sequence-specific restriction enzymes. We showed
AB  - dam methylation of dsDNA arrays by digestion with DpnI, which cleaves when its recognition
AB  - site is methylated. This digestion demonstrated that the dsDNA arrays can be further
AB  - biochemically modified and that the DNA is accessible for interaction with DNA-binding
AB  - proteins. This dsDNA array approach could be extended to explore the spectrum of
AB  - sequence-specific protein binding sites in genomes.
ER  -

TY  - JOUR
AU  - Bumgardner, E.
AU  - Bey, R.F.
AU  - Kittichotirat, W.
AU  - Bumgarner, R.E.
AU  - Lawrence, P.K.
TI  - Genome Sequences of Seven Mycoplasma hyosynoviae Strains Isolated from the Joint  Tissue of Infected Swine (Sus scrofa).
JO  - Genome Announcements
PY  - 2014
SP  - e00552
EP  - e00514
VL  - 2
AB  - Mycoplasma hyosynoviae is a Gram-negative bacterium that can cause debilitating arthritis in
AB  - swine. Currently, there are no M. hyosynoviae genome sequences in
AB  - the GenBank database, which makes it impossible to understand its pathogenesis,
AB  - nutrition, or colonization characteristics, or to devise an effective strategy
AB  - for its control. Here, we report the genome sequences of seven strains of M.
AB  - hyosynoviae. Within each genome, several virulence factors were identified that
AB  - may prove important in the pathogenesis of M. hyosynoviae-mediated arthritis and
AB  - serve as potential virulence markers that may be critical in vaccine development.
ER  -

TY  - JOUR
AU  - Bunina, Z.F.
AU  - Kramarov, V.M.
AU  - Mazanov, A.L.
AU  - Pachkunov, D.M.
AU  - Smolianinov, V.V.
AU  - Matvienko, N.N.
TI  - BbvII:  A new site-specific endonuclease from Bacillus brevis 80.
JO  - Bioorg. Khim.
PY  - 1983
SP  - 1578
EP  - 1580
VL  - 9
AB  - BbvII, a new site-specific endonuclease, has been isolated from Bacillus brevis
AB  - 80 by gel-filtration and chromatography on heparin-Sepharose.  The endonuclease
AB  - recognizes a non-symmetrical sequence 5'-GTGTTC-3'/3'-CAGAAG-5' in
AB  - double-stranded DNA and cleaves DNA in both strands outside the recognition
AB  - sequence.
ER  -

TY  - JOUR
AU  - Bunina, Z.F.
AU  - Kramarov, V.M.
AU  - Smolyaninov, V.V.
AU  - Tolstova, L.A.
TI  - XphI - A new sequence-specific endonuclease from Xanthomonas phaseoli.
JO  - Bioorg. Khim.
PY  - 1984
SP  - 1333
EP  - 1335
VL  - 10
AB  - A sequence-specific endonuclease XphI was purified by chromatography on
AB  - Ultrogel AcA-44 and phosphocellulose.  The final preparation is free of
AB  - admixtures of non-specific nucleases.  It is demonstrated that endonuclease
AB  - XphI recognized 5'-CTGCAG-3' sequence like endonuclease PstI.  According to gel
AB  - filtration data, the molecular mass of endonuclease is 47000+2000.  DNA
AB  - methylated by methylases which block its hydrolysis by endonuclease PstI, is
AB  - also resistant to the cleavage by endonuclease XphI.
ER  -

TY  - JOUR
AU  - Bunina, Z.F.
AU  - Smolyaninov, V.V.
TI  - Dynamics of site-specific endonuclease accumulation in Caryophanon latum L. cells.
JO  - Biotekhnologiya
PY  - 1988
SP  - 621
EP  - 623
VL  - 4
AB  - None
ER  -

TY  - JOUR
AU  - Bunting, K.A.
AU  - Roe, S.M.
AU  - Headley, A.
AU  - Brown, T.
AU  - Savva, R.
AU  - Pearl, L.H.
TI  - Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 1633
EP  - 1639
VL  - 31
AB  - Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate
AB  - nucleotide excision repair of G:T mismatches arising
AB  - by deamination of 5-methyl-cytosines in specific regulatory sequences. We
AB  - have now determined the structure of the archetypal dcm-Vsr endonuclease
AB  - from Escherichia coli bound to the cleaved authentic
AB  - hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3'
AB  - 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of
AB  - a 12mer oligonucleotide into a continuous nicked DNA superhelix. The
AB  - structure reveals the presence of a Hoogsteen base pair within the
AB  - deaminated recognition sequence and the substantial distortions of the DNA
AB  - that accompany Vsr binding to product sites.
ER  -

TY  - JOUR
AU  - Buongiorno, J.
AU  - Bird, J.T.
AU  - Krivushin, K.
AU  - Oshurkova, V.
AU  - Shcherbakova, V.
AU  - Rivkina, E.M.
AU  - Lloyd, K.G.
AU  - Vishnivetskaya, T.A.
TI  - Draft Genome Sequence of Antarctic Methanogen Enriched from Dry Valley Permafrost.
JO  - Genome Announcements
PY  - 2016
SP  - e01362
EP  - e01316
VL  - 4
AB  - A genomic reconstruction belonging to the genus Methanosarcina was assembled from metagenomic
AB  - data from a methane-producing enrichment of Antarctic permafrost.
AB  - This is the first methanogen genome reported from permafrost of the Dry Valleys
AB  - and can help shed light on future climate-affected methane dynamics.
ER  -

TY  - JOUR
AU  - Burall, L.S.
AU  - Grim, C.
AU  - Gopinath, G.
AU  - Laksanalamai, P.
AU  - Datta, A.R.
TI  - Whole-Genome Sequencing Identifies an Atypical Listeria monocytogenes Strain Isolated from Pet Foods.
JO  - Genome Announcements
PY  - 2014
SP  - e01243
EP  - e01214
VL  - 2
AB  - Four Listeria isolates, including an atypical strain, were isolated from various  pet foods
AB  - and sequenced. We report here the draft genome sequences of these
AB  - isolates and a comparative genomic analysis with a closely related human clinical
AB  - isolate. An analysis of the atypical strain identified a frameshift mutation in
AB  - the prfA gene.
ER  -

TY  - JOUR
AU  - Burbank, D.E.
AU  - Shields, S.L.
AU  - Schuster, A.M.
AU  - Van Etten, J.L.
TI  - 5-Azacytidine-resistant mutants of Chlorella Virus IL-3A.
JO  - Virology
PY  - 1990
SP  - 311
EP  - 315
VL  - 176
AB  - Many dsDNA-containing viruses which infect the unicellular, eukaryotic
AB  - Chlorella-like green alga strain NC64A encode for DNA methyltransferases and
AB  - DNA site-specific (restriction) endonucleases.  We have hypothesized that these
AB  - endonucleases help degrade host DNA permitting deoxynucleotides to recycle into
AB  - virus DNA.  This hypothesis was tested by isolating deletion mutants of
AB  - Chlorella virus IL-3A lacking functional genes for the cytosine
AB  - methyltransferase M.CviJI and the cognate site-specific endonuclease CviJI.
AB  - The growth and burst sizes of the mutants and parent virus were identical.
AB  - Also host nuclear and chloroplast DNAs disappeared from infected cells at the
AB  - same rates.  Thus M.CviJI and CviJI activities are not required for IL-3A
AB  - replication and CviJI activity is not essential for host DNA degradation.
ER  -

TY  - JOUR
AU  - Burckhardt, J.
AU  - Weisemann, J.
AU  - Hamilton, D.L.
AU  - Yuan, R.
TI  - Complexes formed between the restriction endonuclease EcoK and heteroduplex DNA.
JO  - J. Mol. Biol.
PY  - 1981
SP  - 425
EP  - 440
VL  - 153
AB  - The complexes between the Escherichia coli K restriction endonuclease and
AB  - heteroduplex DNA (one strand methylated and one unmethylated) have been
AB  - characterized and shown to have different properties from those formed with
AB  - unmodified DNA.  The nature of the heteroduplex complex appears to commit the
AB  - enzyme to its methylase mode.
ER  -

TY  - JOUR
AU  - Burckhardt, J.
AU  - Weisemann, J.
AU  - Yuan, R.
TI  - Characterization of the DNA methylase activity of the restriction enzyme from Escherichia coli K.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 4024
EP  - 4032
VL  - 256
AB  - The restriction endonuclease from Escherichia coli K is a multifunctional
AB  - protein which efficiently methylates heteroduplex DNA (one strand modified and
AB  - one strand unmodified) in the presence of S-adenosylmethionine (AdoMet), ATP,
AB  - and Mg2+.  The methylase activity is catalytic, and seems to modify different
AB  - heteroduplex host specificity sites for E. coli K with equal efficiency.
ER  -

TY  - JOUR
AU  - Burenina, O.Y.
AU  - Fedotova, E.A.
AU  - Ryazanova, A.Y.
AU  - Protsenko, A.S.
AU  - Zakharova, M.V.
AU  - Karyagina, A.S.
AU  - Solonin, A.S.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - Peculiarities of the Regulation of Gene Expression in the Ecl18kI RestrictionModification System.
JO  - Acta Naturae
PY  - 2013
SP  - 70
EP  - 80
VL  - 5
AB  - Transcription regulation in bacterial restriction-modification (R-M) systems is an important
AB  - process, which provides coordinated expression levels of tandem enzymes, DNA methyltransferase
AB  - (MTase) and restriction endonuclease (RE) protecting cells against penetration of alien DNA.
AB  - The present study focuses on (cytosine-5)-DNA methyltransferase Ecl18kI (M. Ecl18kI), which is
AB  - almost identical to DNA methyltransferase SsoII (M. SsoII) in terms of its structure and
AB  - properties. Each of these enzymes inhibits expression of the intrinsic gene and activates
AB  - expression of the corresponding RE gene via binding to the regulatory site in the promoter
AB  - region of these genes. In the present work, complex formation of M. Ecl18kI and RNA polymerase
AB  - from Escherichia.oli with the promoter regions of the MTase and RE genes is studied. The
AB  - mechanism of regulation of gene expression in the Ecl18kI R-M system is thoroughly
AB  - investigated. M. Ecl18kI and RNA polymerase are shown to compete for binding to the promoter
AB  - region. However, no direct contacts between M. Ecl18kI and RNA polymerase are detected. The
AB  - properties of M. Ecl18kI and M. SsoII mutants are studied. Amino acid substitutions in the
AB  - N-terminal region of M. Ecl18kI, which performs the regulatory function, are shown to
AB  - influence not only M. Ecl18kI capability to interact with the regulatory site and to act as a
AB  - transcription factor, but also its ability to bind and methylate the substrate DNA. The loss
AB  - of methylation activity does not prevent MTase from performing its regulatory function and
AB  - even increases its affinity to the regulatory site. However, the presence of the domain
AB  - responsible for methylation in the M. Ecl18kI molecule is necessary for M. Ecl18kI to perform
AB  - its regulatory function.
ER  -

TY  - JOUR
AU  - Burger, K.J.
AU  - Schinzel, R.
TI  - Restriction endonuclease BglI as a tool for in vitro reconstruction and recombination of plasmid and bacteriophage genomes.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 269
EP  - 274
VL  - 189
AB  - The restriction endonuclease BglI produces different individual fragment ends from different
AB  - cut sites.  This property has allowed us to reconstruct efficiently several commonly used
AB  - plasmid and bacteriophage genomes and a number of recombinant plasmids containing up to seven
AB  - BglI restriction sites from their constituent BglI fragments.  It is demonstrated that in
AB  - vitro reconstitution from BglI fragments can be used to create, in a simple way, recombinant
AB  - DNA molecules by recombining in vitro BglI fragments from different mutated or otherwise
AB  - related genomes.  Further applications of the method are discussed.
ER  -

TY  - JOUR
AU  - Burgers, W.A.
AU  - Blanchon, L.
AU  - Pradhan, S.
AU  - de Launoit, Y.
AU  - Kouzarides, T.
AU  - Fuks, F.
TI  - Viral oncoproteins target the DNA methyltransferases.
JO  - Oncogene
PY  - 2007
SP  - 1650
EP  - 1655
VL  - 26
AB  - Small DNA tumour viruses have evolved a number of mechanisms to drive nondividing cells into S
AB  - phase. Virally encoded oncoproteins such as
AB  - adenovirus E1A and human papillomavirus (HPV) E7 can bind an array of
AB  - cellular proteins to override proliferation arrest. The DNA
AB  - methyltransferase Dnmt1 is the major mammalian enzyme responsible for
AB  - maintaining CpG methylation patterns in the cell following replication.
AB  - One of the hallmarks of tumour cells is disrupted DNA methylation
AB  - patterns, highlighting the importance of the proper regulation of DNA
AB  - methyltransferases in normal cell proliferation. Here, we show that
AB  - adenovirus 5 E1A and HPV-16 E7 associate in vitro and in vivo with the
AB  - DNA methyltransferase Dnmt1. Consistent with this interaction, we find
AB  - that E1A and E7 can purify DNA methyltransferase activity from nuclear
AB  - extracts. These associations are direct and mediated by the extreme
AB  - N-terminus of E1A and the CR3 zinc-finger domain of E7. Furthermore, we
AB  - find that a point mutant at leucine 20 of E1A, a residue known to be
AB  - critical for its transformation functions, is unable to bind Dnmt1 and
AB  - DNA methyltransferase activity. Finally, both E1A and E7 can stimulate
AB  - the methyltransferase activity of Dnmt1 in vitro. Our results provide
AB  - the first indication that viral oncoproteins bind and regulate Dnmt1
AB  - enzymatic activity. These observations open up the possibility that
AB  - this association may be used to control cellular proliferation pathways
AB  - and suggest a new mechanism by which small DNA tumour viruses can steer
AB  - cells through the cell cycle.
ER  -

TY  - JOUR
AU  - Burgess, S.A.
AU  - Cox, M.P.
AU  - Flint, S.H.
AU  - Lindsay, D.
AU  - Biggs, P.J.
TI  - Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.
JO  - Genome Announcements
PY  - 2015
SP  - e00939
EP  - e00915
VL  - 3
AB  - Three strains of Geobacillus stearothermophilus (designated A1, P3, and D1) were  isolated
AB  - from a New Zealand milk powder manufacturing plant. Here, we describe their draft genome
AB  - sequences. This information provided the first genomic insights into the nature of G.
AB  - stearothermophilus strains present in the milk powder manufacturing environment.
ER  -

TY  - JOUR
AU  - Burghartz, M.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Voget, S.
AU  - Daniel, R.
AU  - Overmann, J.
AU  - Jahn, M.
TI  - Complete Genome Sequence of the Urethral Catheter Isolate Myroides sp. A21.
JO  - Genome Announcements
PY  - 2015
SP  - e00068
EP  - e00015
VL  - 3
AB  - Myroides sp. A21, isolated from a urethral catheterized patient without symptoms  of a urinary
AB  - tract infection in Germany, proved to be extensively drug resistant.
AB  - Here, we report the 4.16-Mb complete genome sequence of strain A21, carrying
AB  - unusual pathogenicity islands and explaining the features of multidrug
AB  - resistance.
ER  -

TY  - JOUR
AU  - Burguener, G.F.
AU  - Maldonado, M.J.
AU  - Revale, S.
AU  - Fernandez, Do.P.D.
AU  - Rascovan, N.
AU  - Vazquez, M.
AU  - Farias, M.E.
AU  - Marti, M.A.
AU  - Turjanski, A.G.
TI  - Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna.
JO  - Genome Announcements
PY  - 2014
SP  - e01096
EP  - e01013
VL  - 2
AB  - Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from
AB  - Laguna Antofalla in the Argentinian Puna. The draft genome sequence
AB  - suggests the presence of potent enzyme candidates that are essential for survival
AB  - under multiple environmental extreme conditions, such as high UV radiation,
AB  - elevated salinity, and the presence of critical arsenic concentrations.
ER  -

TY  - JOUR
AU  - Burkhart, J.G.
AU  - Burkhart, B.A.
AU  - Sampson, K.
AU  - Malling, H.V.
TI  - Evidence for a previously undetected CpG methyl-directed restriction system in E.coli.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4368
EP  - 4368
VL  - 20
ER  -

TY  - JOUR
AU  - Burks, J.N.
AU  - Wujick, C.T.
AU  - Marshall, L.M.
AU  - Kozarov, E.V.
AU  - Progulske-Fox, A.
TI  - Function of the porphyromonas gingivalis DNA adenine methylase in the expression of virulence.
JO  - J. Dent. Res.
PY  - 2002
SP  - A
EP  - 497
VL  - 81
AB  - Objectives: DNA adenine methylases (dam) modify specific sequences of DNA and thus regulate
AB  - the expression of certain genes in many species of bacteria.  Therefore, the dam gene is a
AB  - prime target for the development of broad-spectrum antibiotics and vaccines.  Our lab has
AB  - previously identified pgiM, a Porphyromonas gingivalis 381 (P. gingivalis) dam gene that
AB  - restores wild-type function to an Escherichia coli dam- mutant.  Recently, it was shown that
AB  - the dam gene of Salmonella typhimurium (S. typhimurium) regulates the expression of virulence
AB  - genes activated by the global regulator, PhoP.  dam-, avirulent strains of S. typhimurium
AB  - showed complete restoration of virulence when complemented with the S. typhimurium dam gene.
AB  - We hypothesized that pgiM may play a similar role in the regulation of virulence in P.
AB  - gingivalis.  Methods: To test this theory, we constructed the dam complementation plasmid,
AB  - pDC1. pDC1 is a derivative of pWKS30, a modified version of pBluescriptIIks, and contains a
AB  - 1.1 kb region of P. gingivalis DNA harboring pgiM.  Subsequently, we transformed the non-polar
AB  - dam- mutant S. typhimurium MT2188D232 with pDC1.  Transformed cells were plated onto Luria
AB  - Bertani agar plates containing 50 ug/ml of ampicillin.  Analysis of plasmid preps performed on
AB  - five of the resulting clones confirmed the presence of pDC1.  Next, the complemented S.
AB  - typhimurium mutant clones were plated onto Luria Bertani agar plates containing 0.6 mg/ml of
AB  - 2-aminopurine.  In addition, we used a 5' truncated form of pgiM in a single crossover
AB  - through homologous recombination, to construct a P. gingivalis dam- mutant.  Results: The
AB  - complemented clones grew on 2-aminopurine, indicating a restoration of the dam gene adenine
AB  - methylase in P. gingivalis irulence.  Conclusion: This data demonstrates that the P. ginivalis
AB  - dam gene can functionally complement the S. typhimurium dam gene.
ER  -

TY  - JOUR
AU  - Burland, V.
AU  - Plunkett, G. III
AU  - Sofia, H.J.
AU  - Daniels, D.L.
AU  - Blattner, F.R.
TI  - Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 2105
EP  - 2119
VL  - 23
AB  - The 338.5 kb of the Escherichia coli genome described here together with previously described
AB  - segments bring the total of contiguous finished sequence of this genome to >1 Mb.  Of 319 open
AB  - reading frames found in this 338.5 kb segment, 147 (46%) are potential new genes.  The
AB  - positions of several genes which had been previously located here by mapping or partial
AB  - sequencing have been confirmed.  Several ORFs have functions suggested by similarities to
AB  - other characterized genes but cannot be assigned with certainty.  Fifteen of the ORFs of
AB  - unknown function had been previously sequenced.  Eight transfer RNAs are encoded in the region
AB  - and there are two grey holes in which no features were found.  The attachment site for phage
AB  - P4 and three insertion sequences were located.  The region was also analyzed for chi sites,
AB  - bend sites, REP elements and other repeats.  A computer search identified potential promoters
AB  - and tentative transcription units were assigned.  The occurrence of the rare tetramer CTAG was
AB  - analyzed in 1.6 Mb of contiguous E. coli sequence.  Hypotheses addressing the rarity and
AB  - distribution of CTAG are discussed.
ER  -

TY  - JOUR
AU  - Burland, V.
AU  - Shao, Y.
AU  - Perna, N.T.
AU  - Plunkett, G.
AU  - Sofia, H.J.
AU  - Blattner, F.R.
TI  - The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 4196
EP  - 4204
VL  - 26
AB  - The complete DNA sequence of pO157, the large virulence plasmid of EHEC strain O157:H7 EDL
AB  - 933, is presented.  The 92 kb F-like plasmid is composed of segments of putative virulence
AB  - genes in a framework of replication and maintenance regions, with seven insertion sequence
AB  - elements, located mostly at the boundaries of the virulence segments.  One hundred open
AB  - reading frames were identified, of which 19 were previously sequenced potential virulence
AB  - genes.  Forty-two ORFs were sufficiently similar to known proteins for suggested functions to
AB  - be assigned, and 22 had no convincing similarity with any known proteins.  Of the newly
AB  - identified genes, an unusually large ORF of 3169 amino acids has a putative cytotoxin active
AB  - site shared with the large clostridial toxin (LCT) family and proteins such as ToxA and B of
AB  - Clostridium difficile.  A conserved motif was detected that links the large ORF and the LCT
AB  - proteins with the OCH1 family of glycosyltransferases.  In the complete sequence, the mosaic
AB  - form can be observed at the levels of base composition, codon usage and gene organization.
AB  - Insights were obtained from patterns of DNA composition as well as the pathogenic and
AB  - 'housekeeping' gene segments.  Evolutionary trees built from shared plasmid maintenance
AB  - genes show that even these genes have heterogeneous origins.
ER  -

TY  - JOUR
AU  - Burns, B.P.
AU  - Gudhka, R.K.
AU  - Neilan, B.A.
TI  - Genome Sequence of the Halophilic Archaeon Halococcus hamelinensis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2100
EP  - 2101
VL  - 194
AB  - Halococcus hamelinensis was isolated from hypersaline stromatolites in Shark Bay, Australia.
AB  - Here we report the genome sequence (3,133,046 bp) of H. hamelinensis,
AB  - which provides insights into the ecology, evolution, and adaptation of this novel
AB  - microorganism.
ER  -

TY  - JOUR
AU  - Burrus, V.
AU  - Bontemps, C.
AU  - Decaris, B.
AU  - Guedon, G.
TI  - Characterization of a novel type II restriction-modification system, Sth368I, encoded by the integrative element ICESt1 of Streptococcus thermophilus CNRZ368.
JO  - Appl. Environ. Microbiol.
PY  - 2001
SP  - 1522
EP  - 1528
VL  - 67
AB  - A novel type II restriction and modification (R-M) system, Sth368I, which confers resistance
AB  - to ST84, was found in Streptococcus thermophilus CNRZ368 but not in the very closely related
AB  - strain A054. Partial sequencing of the integrative conjugative element ICESt1, carried by S.
AB  - thermophilus CNRZ368 but not by A054, revealed a divergent cluster of two genes, sth368IR and
AB  - sth368IM. The protein sequence encoded by sth368IR is related to the type II endonucleases
AB  - R.LlaKR2I and R.Sau3AI, which recognize and cleave the sequence 5'-GATC-3'. The protein
AB  - sequence encoded by sth368IM is very similar to numerous type II 5-methylcytosine
AB  - methyltransferases, including M.LlaKR2I and M.Sau3AI. Cell extracts of CNRZ368 but not A054
AB  - were found to cleave at the GATC site. Furthermore, the C residue of the sequence 5'-GATC-3'
AB  - was found to be methylated in CNRZ368 but not in A054. Cloning and integration of a copy of
AB  - sth368IR and sth368IM in the A054 chromosome confers on this strain phenotypes similar to
AB  - those of CNRZ368, i.e., phage resistance, endonuclease activity of cell extracts, and
AB  - methylation of the sequence 5'-GATC-3'. Disruption of sth368IR removes resistance and
AB  - restriction activity. We conclude that ICESt1 encodes an R-M system, Sth368I, which recognizes
AB  - the sequence 5'-GATC-3' and is related to the Sau3AI and LlaKR2I restriction systems.
ER  -

TY  - JOUR
AU  - Burrus, V.
AU  - Quezada-Calvillo, R.
AU  - Marrero, J.
AU  - Waldor, M.K.
TI  - SXT-Related Integrating Conjugative Element in New World Vibrio cholerae.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 3054
EP  - 3057
VL  - 72
AB  - SXT-related integrating conjugative elements (ICEs) became prevalent in
AB  - Asian Vibrio cholerae populations after V. cholerae O139 emerged. Here, we
AB  - describe an SXT-related ICE, ICEVchMex1, in a Mexican environmental V.
AB  - cholerae isolate. Identification of ICEVchMex1 represents the first
AB  - description of an SXT-related ICE in the Western Hemisphere. The
AB  - significant differences between the SXT and ICEVchMex1 genomes suggest
AB  - that these ICEs have evolved independently.
ER  -

TY  - JOUR
AU  - Burstein, D.
AU  - Amaro, F.
AU  - Zusman, T.
AU  - Lifshitz, Z.
AU  - Cohen, O.
AU  - Gilbert, J.A.
AU  - Pupko, T.
AU  - Shuman, H.A.
AU  - Segal, G.
TI  - Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.
JO  - Nat. Genet.
PY  - 2016
SP  - 167
EP  - 175
VL  - 48
AB  - Infection by the human pathogen Legionella pneumophila relies on the translocation of
AB  - approximately 300 virulence proteins, termed effectors, which
AB  - manipulate host cell processes. However, almost no information exists regarding
AB  - effectors in other Legionella pathogens. Here we sequenced, assembled and
AB  - characterized the genomes of 38 Legionella species and predicted their effector
AB  - repertoires using a previously validated machine learning approach. This analysis
AB  - identified 5,885 predicted effectors. The effector repertoires of different
AB  - Legionella species were found to be largely non-overlapping, and only seven core
AB  - effectors were shared by all species studied. Species-specific effectors had
AB  - atypically low GC content, suggesting exogenous acquisition, possibly from the
AB  - natural protozoan hosts of these species. Furthermore, we detected numerous new
AB  - conserved effector domains and discovered new domain combinations, which allowed
AB  - the inference of as yet undescribed effector functions. The effector collection
AB  - and network of domain architectures described here can serve as a roadmap for
AB  - future studies of effector function and evolution.
ER  -

TY  - JOUR
AU  - Burt, A.
AU  - Koufopanou, V.
TI  - Homing endonuclease genes: the rise and fall and rise again of a selfish element.
JO  - Curr. Opin. Genet. Dev.
PY  - 2004
SP  - 609
EP  - 615
VL  - 14
AB  - Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving
AB  - chromosomes that do not contain them and then getting copied across to the broken chromosome
AB  - as a byproduct of the repair process. The success of this strategy will depend on the
AB  - opportunities for homing - in other words, the frequency with which HEG(+) and HEG(-)
AB  - chromosomes come into contact - which varies widely among host taxa. HEGs are also unusual in
AB  - that the selection pressure for endonuclease function disappears if they become fixed in a
AB  - population, which makes them susceptible to degeneration and imposes a need for regular
AB  - horizontal transmission between species. HEGs will be selected to reduce the harm done to the
AB  - host organism, and this is expected to influence the evolution of their sequence specificity
AB  - and maturase functions. HEGs may also be domesticated by their hosts, and are currently being
AB  - put to human uses.
ER  -

TY  - JOUR
AU  - Bury, C.
AU  - Garman, E.F.
AU  - Ginn, H.M.
AU  - Ravelli, R.B.
AU  - Carmichael, I.
AU  - Kneale, G.
AU  - McGeehan, J.E.
TI  - Radiation damage to nucleoprotein complexes in macromolecular crystallography.
JO  - J. Synchrotron. Radiat.
PY  - 2015
SP  - 213
EP  - 224
VL  - 22
AB  - Significant progress has been made in macromolecular crystallography over recent  years in
AB  - both the understanding and mitigation of X-ray induced radiation damage
AB  - when collecting diffraction data from crystalline proteins. In contrast, despite
AB  - the large field that is productively engaged in the study of radiation chemistry
AB  - of nucleic acids, particularly of DNA, there are currently very few X-ray
AB  - crystallographic studies on radiation damage mechanisms in nucleic acids.
AB  - Quantitative comparison of damage to protein and DNA crystals separately is
AB  - challenging, but many of the issues are circumvented by studying pre-formed
AB  - biological nucleoprotein complexes where direct comparison of each component can
AB  - be made under the same controlled conditions. Here a model protein-DNA complex
AB  - C.Esp1396I is employed to investigate specific damage mechanisms for protein and
AB  - DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy).
AB  - In order to allow a quantitative analysis of radiation damage sites from a
AB  - complex series of macromolecular diffraction data, a computational method has
AB  - been developed that is generally applicable to the field. Typical specific damage
AB  - was observed for both the protein on particular amino acids and for the DNA on,
AB  - for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds.
AB  - Strikingly the DNA component was determined to be far more resistant to specific
AB  - damage than the protein for the investigated dose range. At low doses the protein
AB  - was observed to be susceptible to radiation damage while the DNA was far more
AB  - resistant, damage only being observed at significantly higher doses.
ER  -

TY  - JOUR
AU  - Buryanov, Y.
AU  - Shevchuk, T.
TI  - The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology.
JO  - Anal. Biochem.
PY  - 2005
SP  - 1
EP  - 11
VL  - 338
AB  - Prokaryotic DNA methyltransferases (MTases) are used as experimental and research tools in
AB  - molecular biology and molecular genetics due to
AB  - their ability to recognize and transfer methyl groups to target bases
AB  - in specific DNA sequences. As a practical tool, prokaryotic DNA MTases
AB  - can be used in recombinant DNA technology for in vitro alteration and
AB  - enhancing of cleavage specificity of restriction endonucleases. The
AB  - ability of prokaryotic DNA MTases to methylate cytosine residues in
AB  - specific sequences, which are also methylated in eukaryotic DNA, makes
AB  - it possible to use them as analytical reagent for determination of the
AB  - site-specific level of methylation in eukaryotic DNA. In vivo DNA
AB  - methylation by prokaryotic DNA MTases is used in different techniques
AB  - for probing chromatin structure and protein-DNA interactions.
AB  - Additional prospects are opened by development of the methods of DNA
AB  - methylation targeted to predetermined DNA sequences by fusion of DNA
AB  - MTases to DNA binding proteins. This review will discuss the
AB  - application of prokaryotic DNA MTases of Type II in the methods and
AB  - approaches mentioned above.
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Baryshev, M.M.
AU  - Kosykh, V.G.
AU  - Bayev, A.A.
TI  - The purification and characterization of BstNI modification methylase.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 211
EP  - 211
VL  - 13D
AB  - We have isolated and purified the BstNI modification methylase (M.BstNI) from
AB  - Bacillus stearothermophilus.  This enzyme catalyses the transfer of methyl
AB  - groups from AdoMet to CC(A/T)GG DNA sequences yielding N4-methylcytosine.  This
AB  - modification renders the DNA resistant to cleavage by both BstNI and EcoRII
AB  - restriction endonucleases.  At the same time M.BstNI is able to modify the DNA
AB  - previously methylated by EcoRII methylase while the DNA methylated by M.BstNI
AB  - is resistant to EcoRII methylation.  This property of two methylases can be
AB  - used for analysis of the 5-methylcytosine presence in plant DNA in the
AB  - CC(A/T)GG sequence.  We have partially purified M.BstNI by DEAE-cellulose,
AB  - phosphocellulose and hydroxylapatite column chromatography.  The enzyme has a
AB  - molecular weight of 60 kD as determined by gel-filtration and
AB  - SDS-polyacrylamide gel electrophoresis.  E. coli clones were isolated from
AB  - libraries of B. stearothermophilus DNA fragments in pUC19 by selecting for
AB  - self-modified molecules that were resistant to BstNI endonuclease digestion.
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Bogdarina, I.G.
AU  - Bayev, A.A.
TI  - Site specificity and chromatographic properties of E. coli K12 and EcoRII DNA-cytosine methylases.
JO  - FEBS Lett.
PY  - 1978
SP  - 251
EP  - 254
VL  - 88
AB  - It has been shown that DNA methylation in vitro by DNA-cytosine methylase from E. coli K12
AB  - provides phage lambda DNA with complete resistance against EcoRII restriction endonuclease.
AB  - E. coli C DNA-cytosine methylase and E. coli MRE 600 DNA-cytosine methylase II also provide
AB  - lambda DNA with resistance against RII restriction in transfection experiments.  It is likely
AB  - that all these DNA-cytosine methylases can display the same or overlapping site specificity as
AB  - EcoRII DNA methylase.  For E. coli MRE 600 DNA-cytosine methylase II and E. coli C
AB  - DNA-cytosine methylation in vivo the major targets in DNA are the dinucleotide C-m5C and
AB  - trinucleotide C-m5C-T (m5C:5-methylcytosine).  These pyrimidine fragments of DNA are identical
AB  - to pyrimidine sequences of the DNA site modified by EcoRII DNA methylase:
AB  - 5'...C-m5C-A-G-G...3'  3'...G-G-T-m5C-C...5' However, the pattern of DNA modification in
AB  - vitro by E. coli K12 DNA-cytosine methylase and RII DNA methylase and the only major target
AB  - sequences C-m5C-T for these two enzymes do not correspond to the in vivo methylation pattern
AB  - of E. coli K12 DNA and to the mode of RII DNA methylase action.  The aim of this communication
AB  - is the additional analysis of DNA sequences methylated in vitro by RII and E. coli K12
AB  - DNA-cytosine methylases.  The results reported here show that E. coli K12 DNA-cytosine
AB  - methylase and RII DNA methylase display the same site specificity which is identical to that
AB  - of E. coli C and E. coli MRE 600 DNA-cytosine methylases.  Our data on chromatographic
AB  - behavior of RII DNA methylase on phosphocellulose differ from those in (1).
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Bogdarina, I.G.
AU  - Vagabova, L.M.
TI  - DNA-cytosine methylation in Escherichia coli MRE 600 cells.
JO  - Dokl. Akad. Nauk.
PY  - 1976
SP  - 976
EP  - 978
VL  - 230
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Bogdarina, I.T.
AU  - Baev, A.A.
TI  - Isolation of DNA-cytosine methyltransferases from E. coli B (RII), E. coli K12 and E. coli K12 (RII).  Analysis of nucleotide sequences anlayzed in vitro.
JO  - Dokl. Akad. Nauk.
PY  - 1977
SP  - 465
EP  - 468
VL  - 237
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Kholodkov, O.A.
AU  - Bogdarina, I.G.
AU  - Neserenko, V.F.
AU  - Zakharchenko, V.N.
AU  - Chernov, A.P.
TI  - On the ability of E. coli DNA methylases to modify denatured DNA's.
JO  - Biokhimiia
PY  - 1983
SP  - 1752
EP  - 1754
VL  - 48
AB  - Adenine and cytosine DNA methylases from different strains of E. coli are able to methylate
AB  - denaturated and single-stranded DNA's.
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Nesterenko, V.F.
AU  - Dyacheniko, G.P.
AU  - Korunskii, O.F.
AU  - Skryabin, G.K.
TI  - Specificity of different fractions of DNA-cytosine-methylase from Escherichia coli MRE 600.
JO  - Dokl. Akad. Nauk.
PY  - 1976
SP  - 228
EP  - 231
VL  - 227
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Nesterenko, V.F.
AU  - Kosykh, V.G.
AU  - Baev, A.A.
TI  - Different molecular structure of DNA methylases EcoRII and Eco MRE600 dcmII.
JO  - Dokl. Akad. Nauk.
PY  - 1981
SP  - 495
EP  - 497
VL  - 257
AB  - The cells of most strains of Escherichia coli contain DNA methylases that exhibit site
AB  - specificity of the methylase EcoRII. DNA methylases of the EcoRII type provide the host
AB  - chromosome with complete protection against the restriction endonuclease EcoRII and the
AB  - rapidly amplified DNAs of phages and plasmids with partial protection against this
AB  - endonuclease. In contrast to the plasmid nature of the enzymes of modification and restriction
AB  - of EcoRII, DNA methylases of the EcoRII type are determined by a chromosomal gene of E. coli,
AB  - and there is no corresponding restriction endonuclease in E. coli cells.
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Nesterenko, V.F.
AU  - Vagabova, L.M.
TI  - The presence of two DNA-cytosine methylases in cells of Escherichia coli MRE600.
JO  - Dokl. Akad. Nauk.
PY  - 1976
SP  - 1472
EP  - 1475
VL  - 227
AB  - None
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Shevchuk, T.V.
TI  - DNA methyltransferases and structural-functional specificity of eukaryotic DNA modification.
JO  - Biochemistry
PY  - 2005
SP  - 730
EP  - 742
VL  - 70
AB  - Properties of the main families of mammalian, plant, and fungal DNA methyltransferases are
AB  - considered. Structural-functional specificity of
AB  - eukaryotic genome sequences methylated by DNA methyltransferases is
AB  - characterized. The total methylation of cytosine in DNA sequences is
AB  - described, as well as its relation with RNA interference. Mechanisms of
AB  - regulation of expression and modulation of DNA methyltransferase
AB  - activity in the eukaryotic cell are discussed.
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Zakharchenko, N.S.
AU  - Shevchuk, T.V.
AU  - Bogdarina, I.G.
TI  - Effect of the M.EcoRII methyltransferase-encoding gene on the phenotype of Nicotiana tabacum transgenic cells.
JO  - Gene
PY  - 1995
SP  - 283
EP  - 287
VL  - 157
AB  - The EcoRII DNA methyltransferase (M.EcoRII; MTase) modifies a cytosine in the DNA sequence
AB  - CCWGG which contains a CNG methylation motif characteristic of plant DNA.  The gene (ecoRIIM)
AB  - encoding this MTase has been cloned into the T-DNA of the wild-type Agrobacterium Ti-plasmid
AB  - pTiC58 downstream from the plant expression nopaline synthase-encoding gene promoter.
AB  - Nicotiana tabacum cells have been transformed with Agrobacterium tumefaciens harboring this
AB  - recombinant Ti-plasmid.  The primary transformed tabacco tissue line has given rise to novel
AB  - stable lines which are morphologically distinctive.  Southern hybridization analysis of all
AB  - transformed tissue lines has shown the presence, in each of them, of ecoRIIM.  The tissue
AB  - studied differed in morphology in callus culture, dependence on phytohormones and the ability
AB  - to synthesize nopaline.
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Zakharenko, V.N.
AU  - Baev, A.A.
TI  - Isolation, purification and properties of adenine DNA methylase Eco dam.
JO  - Dokl. Akad. Nauk.
PY  - 1981
SP  - 1492
EP  - 1495
VL  - 259
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Zinovev, V.V.
AU  - Gorbunov, Y.A.
AU  - Tuzikov, F.V.
AU  - Rechkunova, N.I.
AU  - Malygin, E.G.
AU  - Bayev, A.A.
TI  - Interaction of the Eco Dam methyltransferase with synthetic oligodeoxyribonucleotides.
JO  - Gene
PY  - 1988
SP  - 67
EP  - 69
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Buryanov, Y.I.
AU  - Zinoviev, V.V.
AU  - Vienozhinskis, M.T.
AU  - Malygin, E.G.
AU  - Nesterenko, V.F.
AU  - Popov, S.G.
AU  - Gorbunov, Y.A.
TI  - Does the DNA methylase Eco dam pair nucleotide sequences to form site-specific duplexes?
JO  - FEBS Lett.
PY  - 1984
SP  - 166
EP  - 168
VL  - 168
AB  - The Eco dam methylase is active on denatured DNA and single-stranded synthetic
AB  - oligonucleotides containing GATC sites.  The results suggest that on interaction with
AB  - single-stranded oligonucleotides the Eco dam methylase is able to form a duplex structure
AB  - within the GATC site, and that this duplex site is a substrate for enzyme.
ER  -

TY  - JOUR
AU  - Busch, A.
AU  - Ryll, M.
AU  - Immel, A.
AU  - Kornell, S.
AU  - Krause-Kyora, B.
AU  - Tomaso, H.
AU  - Hotzel, H.
TI  - Draft Genome Sequence of Riemerella anatipestifer Isolate 17CS0503.
JO  - Genome Announcements
PY  - 2018
SP  - e00274
EP  - e00218
VL  - 6
AB  - Riemerella anatipestifer is a Gram-negative bacterium belonging to the family
AB  - Flavobacteriaceae It is primarily associated with acute septicemia in younger
AB  - birds. The R. anatipestifer isolate 17CS0503 described here was isolated from a
AB  - Peking duck (Anas platyrhynchos domesticus) in Hannover, Germany, in 1999.
ER  -

TY  - JOUR
AU  - Busch, A.
AU  - Thomas, P.
AU  - Myrtennas, K.
AU  - Forsman, M.
AU  - Braune, S.
AU  - Runge, M.
AU  - Tomaso, H.
TI  - High-Quality Draft Genome Sequence of Francisella tularensis subsp. holarctica Strain 08T0073 Isolated from a Wild European Hare.
JO  - Genome Announcements
PY  - 2017
SP  - e01577
EP  - e01516
VL  - 5
AB  - Here, we report a high-quality draft genome sequence of Francisella tularensis subsp.
AB  - holarctica strain 08T0073, isolated from the cadaver of a wild European
AB  - hare (Lepus europaeus) found near Helmstedt, Lower Saxony, Germany, in 2007. In
AB  - Germany, infected hares are a major source of tularemia in humans.
ER  -

TY  - JOUR
AU  - Busche, T.
AU  - Novakova, R.
AU  - Al'Dilaimi, A.
AU  - Homerova, D.
AU  - Feckova, L.
AU  - Rezuchova, B.
AU  - Mingyar, E.
AU  - Csolleiova, D.
AU  - Bekeova, C.
AU  - Winkler, A.
AU  - Sevcikova, B.
AU  - Kalinowski, J.
AU  - Kormanec, J.
AU  - Ruckert, C.
TI  - Complete Genome Sequence of Streptomyces lavendulae subsp. lavendulae CCM 3239 (Formerly 'Streptomyces aureofaciens CCM 3239'), a Producer of the Angucycline-Type Antibiotic Auricin.
JO  - Genome Announcements
PY  - 2018
SP  - e00103
EP  - e00118
VL  - 6
AB  - Streptomyces lavendulae subsp. lavendulae CCM 3239 produces the angucycline antibiotic auricin
AB  - and was thought to be the type strain of Streptomyces
AB  - aureofaciens We report the complete genome sequence of this strain, which
AB  - consists of a linear chromosome and the linear plasmid pSA3239, and demonstrate
AB  - it to be S. lavendulae subsp. lavendulae.
ER  -

TY  - JOUR
AU  - Busquets, A. et al.
TI  - Draft Genome Sequence of Pseudomonas azotifigens Strain DSM 17556T (6H33bT), a Nitrogen Fixer Strain Isolated from a Compost Pile.
JO  - Genome Announcements
PY  - 2013
SP  - e00893
EP  - e00813
VL  - 1
AB  - Pseudomonas azotifigens strain 6H33b(T) is a nitrogen fixer isolated from a hyperthermal
AB  - compost pile in 2005 by Hatayama and collaborators. Here we report
AB  - the draft genome, which has an estimated size of 5.0 Mb, exhibits an average G+C
AB  - content of 66.73%, and is predicted to encode 4,536 protein-coding genes and 100
AB  - RNA genes.
ER  -

TY  - JOUR
AU  - Busquets, A.
AU  - Pena, A.
AU  - Gomila, M.
AU  - Bosch, R.
AU  - Nogales, B.
AU  - Garcia-Valdes, E.
AU  - Lalucat, J.
AU  - Bennasar, A.
TI  - Genome Sequence of Pseudomonas stutzeri Strain JM300 (DSM 10701), a Soil Isolate  and Model Organism for Natural Transformation.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5477
EP  - 5478
VL  - 194
AB  - Pseudomonas stutzeri strain JM300 (DSM 10701) is a denitrifying soil isolate and  a model
AB  - organism for natural transformation in bacteria. Here we report the first
AB  - complete genome sequence of JM300, the reference strain of genomovar 8 for the
AB  - species.
ER  -

TY  - JOUR
AU  - Busquets, A.
AU  - Pena, A.
AU  - Gomila, M.
AU  - Mayol, J.
AU  - Bosch, R.
AU  - Nogales, B.
AU  - Garcia-Valdes, E.
AU  - Bennasar, A.
AU  - Lalucat, J.
TI  - Draft Genome Sequence of Pseudomonas stutzeri Strain B1SMN1, a Nitrogen-Fixing and Naphthalene-Degrading Strain Isolated from Wastewater.
JO  - Genome Announcements
PY  - 2013
SP  - e00584
EP  - e00513
VL  - 1
AB  - Pseudomonas stutzeri strain B1SMN1 is a naphthalene-degrading and simultaneously
AB  - nitrogen-fixing strain isolated from a wastewater sample taken at a lagooning
AB  - treatment plant in Menorca (Balearic Islands, Spain). Here we report the draft
AB  - genome sequence of P. stutzeri B1SMN1. It is composed of a chromosome of an
AB  - estimated size of 5.2 Mb and two plasmids of 44,324 bp and 56,118 bp.
ER  -

TY  - JOUR
AU  - Busslinger, M.
AU  - deBoer, E.
AU  - Wright, S.
AU  - Grosveld, F.G.
AU  - Flavell, R.A.
TI  - The sequence GGCmCGG is resistant to MspI cleavage.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 3559
EP  - 3569
VL  - 11
AB  - MspI essentially fails to cut the sequence GGCmCGG at enzyme concentrations
AB  - which give total digestion of CCGG, CmCGG and GGCCGG sites.  This result
AB  - explains why certain sites in mammalian DNA are resistant to both MspI and HhaI
AB  - and shows that this results from an idiosyncracy of MspI rather than a novel
AB  - form of DNA methylation at this site in mammalian cells.
ER  -

TY  - JOUR
AU  - Bustos, P.
AU  - Santamaria, R.I.
AU  - Perez-Carrascal, O.M.
AU  - Acosta, J.L.
AU  - Lozano, L.
AU  - Juarez, S.
AU  - Martinez-Flores, I.
AU  - Martinez-Romero, E.
AU  - Cevallos, M.A.
AU  - Romero, D.
AU  - Davila, G.
AU  - Vinuesa, P.
AU  - Miranda, F.
AU  - Ormeno, E.
AU  - Gonzalez, V.
TI  - Complete Genome Sequences of Three Rhizobium gallicum Symbionts Associated with Common Bean (Phaseolus vulgaris).
JO  - Genome Announcements
PY  - 2017
SP  - e00030
EP  - e00017
VL  - 5
AB  - The whole-genome sequences of three strains of Rhizobium gallicum reported here support the
AB  - concept that the distinct nodulation host ranges displayed by the
AB  - symbiovars gallicum and phaseoli can be largely explained by different symbiotic
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Bitinaite, J.
AU  - Kersulyte, D.
AU  - Janulaitis, A.
TI  - A new restriction endonuclease Eco31I recognizing a non-palindromic sequence.
JO  - Biochim. Biophys. Acta
PY  - 1985
SP  - 208
EP  - 212
VL  - 826
AB  - A restriction endonuclease with a novel site-specificity has been isolated from the
AB  - Escherichia coli strain RFL31.  The nucleotide sequences around a single Eco311 cut on pBR322
AB  - DNA and two cuts of lambda DNA have been compared.  A common 5'GAGACC/3'CTCTGG sequence
AB  - occurs near each cleavage site.  Precise mapping of the cleavages in both DNA strands places
AB  - the cuts five nucleotides to the left of the upper sequence and one nucleotide to the left of
AB  - the lower sequence.  This enabled us to deduce the following recognition and cleavage
AB  - specificity of Eco31I:
AB  - 5' GGTCTCN/
AB  - 3' CCAGAGN NNNN/.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Kazlauskiene, R.
AU  - Gilvonauskaite, R.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - Determination of substrate specificity of restriction endonuclease Eco78I.
JO  - Bioorg. Khim.
PY  - 1985
SP  - 1572
EP  - 1573
VL  - 11
AB  - The recognition sequence and cleavage point of restriction endonuclease Eco78I
AB  - have been determined at 5'-GGCG^CC-.  There are several known enzymes
AB  - recognizing the same sequence, although the prototype NarI and isoschizomers
AB  - NdaI and NunII cleave the substrate to produce 5'-protruding ends, whereas
AB  - cleavage with isoschizomer BbeI results in 3'-protruding ends.  Therefore,
AB  - restrictase Eco78I, generating flush ends, may be regarded as an enzyme with
AB  - new specificity among the restriction endonucleases recognizing the
AB  - 5'-GGCGCC-sequence.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Klimasauskas, S.
AU  - Kersulyte, D.
AU  - Vaitkevicius, D.
AU  - Lebionka, A.
AU  - Janulaitis, A.
TI  - Investigation of restriction-modification enzymes from M. varians RFL19 with a new type of specificity toward modification of substrate.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 5727
EP  - 5746
VL  - 13
AB  - The characterization of MvaI restriction-modification enzymes, isolated from Micrococcus
AB  - varians RFL19, is reported. Both enzymes recognize the 5'CC^(A/T)GG nucleotide sequence. The
AB  - endonuclease cleaves the sequence at the position indicated by the arrow, whereas the
AB  - methylase modifies the internal cytosine, yielding N4-methylcytosine. This type of
AB  - modification protects the substrate from R.MvaI cleavage. 5-methylcytosine in the same
AB  - position of the recognition sequence does not protect the substrate from R.MvaI cleavage.
AB  - R.MvaI proved to be the first example of a restriction endonuclease differentiating the
AB  - position of the methyl group in the heterocyclic ring of cytosine, located in the same site of
AB  - the recognition sequence. M.MvaI modifies DNA dcm+ in vitro yielding N4, 5-dimethylcytosine.
AB  - N4-methylcytosine cannot be differentiated from cytosine using the Maxam-Gilbert DNA
AB  - sequencing procedure.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Klimasauskas, S.
AU  - Petrauskiene, L.
AU  - Maneliene, Z.
TI  - The effects of N4- and C5-methylation of cytosine on DNA physical properties and restriction endonuclease action.
JO  - Metabolism and Enzymology of Nucleic Acids
PY  - 1987
SP  - 119
EP  - 127
VL  - 6
AB  - Not long ago a new type of methylase, generating N4-methylcytosine (4mC) in DNA
AB  - was isolated in our laboratory from Bacillus centrosporus (Janulaitis et al.,
AB  - 1983).  At present a number of the 4mC type methylases are isolated (Janulaitis
AB  - et al., 1984; Butkus et al., 1985,1987) and a wide spread of N4-methylcytosine
AB  - in DNA of thermophilic and mesophilic bacteria is well documented (Ehrlich et
AB  - al., 1985,1987).  Since the two methylated cytosine bases occurred in native
AB  - DNA, a comparison of the effects of N4- and C5-methylation on DNA
AB  - physico-chemical properties and enzyme action seems to be of great interest.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Klimasauskas, S.
AU  - Petrauskiene, L.
AU  - Maneliene, Z.
AU  - Janulaitis, A.
AU  - Minchenkova, L.E.
AU  - Schyolkina, A.K.
TI  - Synthesis and physical characterization of DNA fragments containing N4-methylcytosine and 5-methylcytosine.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 8467
EP  - 8478
VL  - 15
AB  - The synthesis of N4-methyl-2'-deoxycytidine and its fully protected
AB  - mononucleotide, suitable for the oligonucleotide synthesis by phosphotriester
AB  - method is described.  A set of octanucleotides -d(CGCGCGCG), d(CG5mCGCGCG),
AB  - d(CG4mCGCGCG) and dodecanucleotides -d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC),
AB  - d(GGA4mCCCGGGTCC) has been synthesized in a solution.  Physical
AB  - characterization of the oligonucleotide duplexes by means of UV and CD
AB  - spectrometry provides the evidence that 4mC similarly to 5mC favours the B-->Z
AB  - transition, although both of these methylated cytosines inhibit the B-->A
AB  - conformational change.  N4-Methylcytosine in contrast to 5-methylcytosine
AB  - reduces the DNA double helix thermal stability.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Klimasauskas, S.
AU  - Petrauskiene, L.
AU  - Maneliene, Z.
AU  - Lebionka, A.
AU  - Janulaitis, A.
TI  - Interaction of AluI, Cfr6I and PvuII restriction-modification enzymes with substrates containing either N4-methylcytosine or 5-methylcytosine.
JO  - Biochim. Biophys. Acta
PY  - 1987
SP  - 201
EP  - 207
VL  - 909
AB  - The cleavage specificity of R.Cfr6I, an isoschizomer of PvuII restriction
AB  - endonuclease was determined to be 5'CAG^CTG and the methylation specificity of
AB  - Cfr6I and PvuII methylases, 5'CAG4mCTG.  Thus, M.Cfr6I and M.PvuII are new
AB  - additions to the list of methylases with N4-methylcytosine specificity.
AB  - Neither of the above RM enzymes acts on the substrates containing either
AB  - N4-methylcytosine or 5-methylcytosine in a cognate methylation position.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Klimasauskas, S.
AU  - Petrauskiene, L.
AU  - Maneliene, Z.
AU  - Minchenkova, L.E.
AU  - Schyolkina, A.K.
AU  - Janulaitis, A.
TI  - The effects of N4- and C5-methylation of cytosine on DNA physical properties and restriction endonuclease action.
JO  - Metabolism and Enzymology of Nucleic Acids
PY  - 1988
SP  - 73
EP  - 78
VL  - 7
AB  - Not long ago a new type of methylase, generating N4-methylcytosine (4mC) in DNA
AB  - was isolated in our laboratory from Bacillus centrosporus (Janulaitis et al.,
AB  - 1983).  At present a number of the 4mC type methylases are isolated (Janulaitis
AB  - et al., 1984; Butkus et al., 1985; 1987) and the widespread occurrence of
AB  - N4-methylcytosine in DNA of thermophilic and mesophilic bacteria is documented
AB  - (Ehrlich et al., 1985, 1987).  Since the two methylated cytosine bases occur in
AB  - native DNA, a comparison of the effects of N4- and C5-methylation on DNA
AB  - physico-chemical properties and enzyme action seems to be of great interest.
ER  -

TY  - JOUR
AU  - Butkus, V.
AU  - Petrauskiene, L.
AU  - Maneliene, Z.
AU  - Klimasauskas, S.
AU  - Laucys, V.
AU  - Janulaitis, A.
TI  - Cleavage of methylated CCCGGG sequences containing either N4-methylcytosine or 5-methylcytosine with MspI, HpaII, SmaI, XmaI and Cfr9I restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 7091
EP  - 7102
VL  - 15
AB  - The cleavage specificity of R.Cfr9I was determined to be C/CCGGG whereas the
AB  - methylation specificity of M.Cfr9I was C4mCCGGG.  The action of MspI, HpaII,
AB  - SmaI, XmaI and Cfr9I restriction endonucleases on an unmethylated parent
AB  - d(GGACCCGGGTCC) dodecanucleotide duplex and a set of oligonucleotide duplexes,
AB  - containing all possible substitutions of either 4mC or 5mC for C in the CCCGGG
AB  - sequence, was investigated.  It was found that 4mC methylation, in contrast to
AB  - 5mC, renders the CCCGGG site resistant to practically all the investigated
AB  - endonucleases.  The cleavage of methylated substrates with restriction
AB  - endonucleases is discussed.
ER  -

TY  - JOUR
AU  - Butkus, V.V.
AU  - Klimasauskas, S.J.
AU  - Janulaitis, A.
TI  - Analysis of products of DNA modification by methylases:  A procedure for the determination of 5- and N4-methylcytosines in DNA.
JO  - Anal. Biochem.
PY  - 1985
SP  - 194
EP  - 198
VL  - 148
AB  - Although many different methods are used for the identification of methylated heterocyclic
AB  - bases in DNA not all of them possess the ability to discriminate N4-methylcytosine (m4C) and
AB  - 5-methylcytosine (m5C).  Therefore, some of the methods need additional reexamination.  This
AB  - paper reinvestigates some chromatographic systems (thin-layer chromatography, paper
AB  - chromatography, electrophoresis) most widely used in the analysis of minor bases occuring in
AB  - nucleic acids according to their ability to separate m4C and m5C.  A simple procedure for the
AB  - preparation of the sample and a chromatographic system for its analysis was developed.  The
AB  - recommended chromatographic systems may be used for the simultaneous separation of not only
AB  - m4C and m5C but also both methylated cytosines together with N6-methyladenine and
AB  - 7-methylguanine.
ER  -

TY  - JOUR
AU  - Butkus, V.V.
AU  - Petrusyte, M.P.
AU  - Janulaitis, A.
TI  - Determination of substrate specificity of Eco47I and Eco52I restriction endonucleases.
JO  - Bioorg. Khim.
PY  - 1985
SP  - 987
EP  - 988
VL  - 11
AB  - Cleavage sites for Eco47I and Eco52I restriction endonucleases, which are
AB  - isoschizomers of AvaII and XmaIII, respectively, have been structurally
AB  - elucidated.
ER  -

TY  - JOUR
AU  - Butler, C.A.
AU  - Gotschlich, E.C.
TI  - High-frequency mobilization of broad-host-range plasmids into Neisseria gonorrhoeae requires methylation in the donor.
JO  - J. Bacteriol.
PY  - 1991
SP  - 5793
EP  - 5799
VL  - 173
AB  - Antibiotic resistance in Neisseria gonorrhoeae has been associated with the
AB  - acquisition of R plasmids from heterologous organisms.  The broad-host-range
AB  - plasmids of incompatibility groups P (IncP) and Q (IncQ) have played a role in
AB  - this genetic exchange in nature.  We have utilized derivatives of RSF1010
AB  - (IncQ) and RP1 (IncP) to demonstrate that the plethora of restriction barriers
AB  - associated with the gonococci markedly reduces mobilization of plasmids from
AB  - Escherichia coli into strains F62 and PGH 3-2.  Partially purified restriction
AB  - endonucleases from these gonococcal strains can digest RSF1010 in vitro.
AB  - Protection of RSF1010-km from digestion by gonococcal enzymes purified from
AB  - strain F62 is observed when the plasmid is isolated from E. coli containing a
AB  - coresident plasmid, pCAL7.  Plasmid pCAL7 produces a 5'-mCG-3' cytosine
AB  - methylase (M.SssI).  The M.SssI methylase only partially protects RSF1010-km
AB  - from digestion by restriction enzymes from strain PGH 3-2.  Total protection of
AB  - RSF1010-km from PGH 3-2 restriction requires both pCAL7 and a second coresident
AB  - plasmid, pFnuDI, which produces a 5'-GGmCC-3' cytosine methylase.  When both
AB  - F62 and PGH 3-2 are utilized as recipients in heterospecific matings with E.
AB  - coli, mobilization of RSF1010 from strains containing the appropriate
AB  - methylases into the gonococci occurs at frequencies 4 orders of magnitude
AB  - higher than from strains without the methylases.  Thus, protection of RSF1010
AB  - from gonococcal restriction enzymes in vitro correlates with an increase in the
AB  - conjugal frequency.  These data indicate that restriction is a major barrier
AB  - against efficient conjugal transfer between N. gonorrhoeae and heterologous
AB  - hosts.
ER  -

TY  - JOUR
AU  - Butler, D.
AU  - Fitzgerald, G.F.
TI  - Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503.
JO  - J. Bacteriol.
PY  - 2001
SP  - 4668
EP  - 4673
VL  - 183
AB  - ScrFI is a type II restriction-modification system from Lactococcus lactis which recognizes
AB  - the nucleotide sequence 5'-CC^NGG-3', cleaving at the point indicated by the arrow, and it
AB  - comprises an endonuclease gene that is flanked on either side by genes encoding two
AB  - 5-methylcytosine methylases. An open reading frame (orfX) of unknown function is located
AB  - immediately upstream of these genes. In this study Northern analysis was performed, and it
AB  - revealed that orfX, scrFIBM, and scrFIR are cotranscribed as a single polygenic mRNA molecule,
AB  - while scrFIAM is transcribed independently. 5' extension analysis indicated that the start
AB  - site for the scrFIAM promoter was a thymine located 4 bp downstream of the -10 motif. The
AB  - transcriptional start site for the orfX promoter was also found to be a thymine which is more
AB  - atypically located 24 bp downstream of the -10 motif proximal to the start codon. A
AB  - helix-turn-helix motif was identified at the N-terminal end of one of the methylases
AB  - (M.ScrFIA). In order to determine if this motif played a role in regulation of the ScrFI
AB  - locus, M.ScrFIA was purified. It was then employed in gel retardation assays using fragments
AB  - containing the two promoters found on the ScrFI operon, one located upstream of orfX and the
AB  - other located just upstream of scrFIAM. M.ScrFIA was found to bind to the promoter region
AB  - upstream of the gene encoding it, indicating that it may have a regulatory role. In further
AB  - studies the two putative promoters were introduced into a vector (pAK80) upstream of a
AB  - promoterless lacZ gene, and cloned fragments of the ScrFI locus were introduced in trans with
AB  - each of these promoter constructs to investigate the effect on promoter activity. These
AB  - results implicated M.ScrFIA in regulation of both promoters on the ScrFI locus.
ER  -

TY  - JOUR
AU  - Butler, M.I.
AU  - Stockwell, P.A.
AU  - Black, M.A.
AU  - Day, R.C.
AU  - Lamont, I.L.
AU  - Poulter, R.T.M.
TI  - Pseudomonas syringae pv. actinidiae from Recent Outbreaks of Kiwifruit Bacterial Canker Belong to Different Clones that Originated in China.
JO  - PLoS ONE
PY  - 2013
SP  - e57464
EP  - e57464
VL  - 8
AB  - A recently emerged plant disease, bacterial canker of kiwifruit (Actinidia deliciosa and A.
AB  - chinensis), is caused by Pseudomonas syringae pv. actinidiae (PSA).  The disease was first
AB  - reported in China nad Japan in the 1980s.  A severe breakout of PSA began in Italy in 2008 and
AB  - has spread to other European countries.  PSA was found in both New Zealand and Chile in 2010.
AB  - To study the evolution of the pathogen and analyse the transmission of PSA between countries,
AB  - genomes of strands from China and Japan (where the genus Actinidia is endemic)m Italy, New
AB  - Zealand and Chile were sequenced.  The genomes of PSA strains are very similar.  However, all
AB  - strains from New Zealand share several single nucleotide polymorphisms (SNPs) that distinguish
AB  - them from all other PSA strains.  Similarly, all the PSA strains from the 2008 Italian
AB  - outbreak form a distinct clonal group and those from Chile form a third group.  In addition to
AB  - the rare SNPs present in the core genones, there is abundant genetic diversity in a genomic
AB  - island that is part of the accessory genome.  The island from several Chinese strains is
AB  - almost identical to the island present in the New Zealand strains. The island from a different
AB  - Chinese strain is identical to the island prsent in the strains from the recent Italian
AB  - outbreak.  The Chilean strains of PSA carry a third variant of this island.  These genome
AB  - islands are integrative conjugative elements (ICEs).  Sequencing of these ICEs provides
AB  - evidence of three recent horizontal transmissions of ICE from other strains of Pseudomonas
AB  - syringae to PSA.  The analyses of the core genome SNPs and the ICEs, combined with disease
AB  - history, all support the hypothesis of an independent Chinese origin for both the Italian and
AB  - the New Zealand outbreaks and suggest the Chilean strains also originate from China.
ER  -

TY  - JOUR
AU  - Butler, R.R.I.I.I.
AU  - Soomer-James, J.T.A.
AU  - Frenette, M.
AU  - Pombert, J.F.
TI  - Complete Genome Sequences of Two Human Oral Microbiome Commensals, Streptococcus  salivarius ATCC 25975 and S. salivarius ATCC 27945.
JO  - Genome Announcements
PY  - 2017
SP  - e00536
EP  - e00517
VL  - 5
AB  - Streptococcus salivarius strains are significant contributors to the human oral microbiome.
AB  - Some possess unique fimbriae that give them the ability to
AB  - coaggregate and colonize particular oral structures. We present here the complete
AB  - genomes of Streptococcus salivarius Lancefield K-/K+ strains ATCC 25975 and ATCC
AB  - 27945, which can and cannot, respectively, produce fimbriae.
ER  -

TY  - JOUR
AU  - Butler, R.R.I.I.I.
AU  - Wang, J.
AU  - Stark, B.C.
AU  - Pombert, J.F.
TI  - Complete Genome Sequences of Two Interactive Moderate Thermophiles, Paenibacillus napthalenovorans 32O-Y and Paenibacillus sp. 32O-W.
JO  - Genome Announcements
PY  - 2016
SP  - e01717
EP  - e01715
VL  - 4
AB  - Microorganisms with the capability to desulfurize petroleum are in high demand with escalating
AB  - restrictions currently placed on fuel purity. Thermophilic
AB  - desulfurizers are particularly valuable in high-temperature industrial
AB  - applications. We report the whole-genome sequences of Paenibacillus
AB  - napthalenovorans 32O-Y and Paenibacillus sp. 32O-W, which can and cannot,
AB  - respectively, metabolize dibenzothiophene.
ER  -

TY  - JOUR
AU  - Butler-Wu, S.M.
AU  - Sengupta, D.J.
AU  - Kittichotirat, W.
AU  - Matsen, F.A.
AU  - Bumgarner, R.E.
TI  - Genome sequence of a novel species, Propionibacterium humerusii.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3678
EP  - 3678
VL  - 193
AB  - As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes,
AB  - we have produced a draft genome sequence of a
AB  - novel Propionibacterium species that is closely related to, yet distinct
AB  - (by sequence) from P. acnes. We have tentatively named this new species
AB  - Propionibacterium humerusii.
ER  -

TY  - JOUR
AU  - Butterer, A.
AU  - Pernstich, C.
AU  - Smith, R.M.
AU  - Sobott, F.
AU  - Szczelkun, M.D.
AU  - Toth, J.
TI  - Type III restriction endonucleases are heterotrimeric: comprising one helicase-nuclease subunit and a dimeric methyltransferase that binds only one  specific DNA.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 5139
EP  - 5150
VL  - 42
AB  - Fundamental aspects of the biochemistry of Type III restriction endonucleases remain
AB  - unresolved despite being characterized by numerous research groups in the
AB  - past decades. One such feature is the subunit stoichiometry of these
AB  - hetero-oligomeric enzyme complexes, which has important implications for the
AB  - reaction mechanism. In this study, we present a series of results obtained by
AB  - native mass spectrometry and size exclusion chromatography with multi-angle light
AB  - scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I,
AB  - EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry
AB  - of specific DNA (sDNA) binding by EcoP15I and EcoPI. Our data are also consistent
AB  - with a model where ATP hydrolysis activated by recognition site binding leads to
AB  - release of the enzyme from the site, dissociation from the substrate via a free
AB  - DNA end and cleavage of the DNA. These results are discussed critically in the
AB  - light of the published literature, aiming to resolve controversies and discuss
AB  - consequences in terms of the reaction mechanism.
ER  -

TY  - JOUR
AU  - Byrne-Bailey, K.G.
AU  - Coates, J.D.
TI  - Complete Genome Sequence of the Anaerobic Perchlorate-Reducing Bacterium Azospira suillum Strain PS.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2767
EP  - 2768
VL  - 194
AB  - Azospira suillum strain PS (formally Dechlorosoma suillum strain PS) is a metabolically
AB  - versatile betaproteobacterium first identified for its ability to
AB  - grow by dissimilatory reduction of perchlorate and chlorate [denoted
AB  - (per)chlorate]. Together with Dechloromonas species, these two genera represent
AB  - the dominant (per)chlorate-reducing bacteria in mesophilic freshwater
AB  - environments. In addition to (per)chlorate reduction, A. suillum is capable of
AB  - the anaerobic oxidation of humic substances and is the first anaerobic
AB  - nitrate-dependent Fe(II) oxidizer outside the Diaphorobacter and Acidovorax
AB  - genera for which there is a completed genome sequence.
ER  -

TY  - JOUR
AU  - Byrne-Bailey, K.G.
AU  - Weber, K.A.
AU  - Chair, A.H.
AU  - Bose, S.
AU  - Knox, T.
AU  - Spanbauer, T.L.
AU  - Chertkov, O.
AU  - Coates, J.D.
TI  - Completed genome sequence of the anaerobic iron oxidizing bacterium Acidovorax ebreus strain TPSY.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1475
EP  - 1476
VL  - 192
AB  - Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for
AB  - which there is a completed genome sequence. Preliminary protein annotation revealed an
AB  - organism optimized for survival in a complex environmental system. Here, we briefly report the
AB  - completed and annotated genome sequence of strain TPSY.
ER  -

TY  - JOUR
AU  - Byrne-Bailey, K.G.
AU  - Weber, K.A.
AU  - Coates, J.D.
TI  - Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2400
EP  - 2401
VL  - 194
AB  - Pseudogulbenkiania ferrooxidans strain 2002 was isolated as a lithoautotrophic,
AB  - Fe(II)-oxidizing, nitrate-reducing bacterium. Phylogenetically, it is in a clade
AB  - within the family Neisseriaceae in the order Nessieriales of the class
AB  - Betaproteobacteria. It is anticipated that comparative genomic analysis of this
AB  - strain with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in the
AB  - elucidation of the genetics and biochemistry underlying this critically important
AB  - geochemical metabolism.
ER  -

TY  - JOUR
AU  - Byrne-Bailey, K.G.
AU  - Wrighton, K.C.
AU  - Melnyk, R.A.
AU  - Agbo, P.
AU  - Hazen, T.C.
AU  - Coates, J.D.
TI  - Complete genome sequence of the electricity-producing Thermincola potens strain JR.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4078
EP  - 4079
VL  - 192
AB  - Thermincola potens strain JR is one of the first Gram-positive dissimilatory metal reducing
AB  - bacteria (DMRB) for which there is a draft
AB  - genome sequence. Consistent with the physiology of this organism,
AB  - preliminary annotation revealed an abundance of multi-heme c-type
AB  - cytochromes that are putatively associated with the periplasm and cell
AB  - surface in a Gram-positive bacterium. Here we report the draft genome
AB  - sequence of strain JR.
ER  -

TY  - JOUR
AU  - Cab-Barrera, E.L.
AU  - Barrera-Saldana, H.A.
TI  - A general method to optimize the amount of enzyme in restriction and DNA modification reactions using the beta galactosidase blue-white plaques assay.
JO  - Biotechniques
PY  - 1989
SP  - 132
EP  - 135
VL  - 7
AB  - We propose a simple and economical method for assaying the activity of
AB  - restriction and other modifying enzymes.  The method involves assaying the use
AB  - of the blue and white colored phenotypes of bacterial colonies obtained by
AB  - digesting the polylinker sequence of M13 bacteriophage vectors followed by
AB  - transformation in appropriate strains on X-gal/IPTG plates.  In conjunction
AB  - with restriction enzymes and DNA ligases, the method can evaluate polymerase
AB  - activity and can be applied to test 3'-5' exonuclease activities such as that
AB  - of T4 DNA polymerase, without having to use expensive radioisotopes.  We
AB  - describe its application in the assessment of restriction enzymes, DNA ligase
AB  - and DNA polymerase activities.
ER  -

TY  - JOUR
AU  - Caballero, J.I.
AU  - Zerillo, M.M.
AU  - Snelling, J.
AU  - Boucher, C.
AU  - Tisserat, N.
TI  - Genome Sequence of Xanthomonas arboricola pv. Corylina, Isolated from Turkish Filbert in Colorado.
JO  - Genome Announcements
PY  - 2013
SP  - e00246
EP  - e00213
VL  - 1
AB  - Previously, we reported the isolation of a bacterium producing leaf spots in Turkish filbert.
AB  - Here, we present the draft genome assembly of the bacterium identified as Xanthomonas
AB  - arboricola pv. corylina. To our knowledge, this is the first published genome of this pathovar
AB  - of X. arboricola.
ER  -

TY  - JOUR
AU  - Cabria, G.L.
AU  - Argayosa, V.B.
AU  - Lazaro, J.E.
AU  - Argayosa, A.M.
AU  - Arcilla, C.A.
TI  - Draft Genome Sequence of Haloalkaliphilic Exiguobacterium sp. Strain AB2 from Manleluag Ophiolitic Spring, Philippines.
JO  - Genome Announcements
PY  - 2014
SP  - e00840
EP  - e00814
VL  - 2
AB  - Exiguobacterium sp. AB2 is a haloalkaliphilic bacterium isolated from a hyperalkaline spring
AB  - in Manleluag, Pangasinan, Philippines. Sequencing of
AB  - bacterial DNA assembled a 2.85 MB draft genome. Analysis suggests the presence of
AB  - genes for tolerance to stresses such as elevated pH and salt concentrations and
AB  - toxic metals.
ER  -

TY  - JOUR
AU  - Caceres, O.
AU  - Montenegro, J.
AU  - Padilla, C.
AU  - Tarazona, D.
AU  - Bailon, H.
AU  - Garcia, P.
AU  - Cespedes, M.
AU  - Valencia, P.
AU  - Guio, H.
TI  - Whole-Genome Sequencing and Comparative Analysis of Yersinia pestis, the Causative Agent of a Plague Outbreak in Northern Peru.
JO  - Genome Announcements
PY  - 2013
SP  - e00249
EP  - e00212
VL  - 1
AB  - The plague is a zoonotic disease caused by the bacterium . Here, we report the complete genome
AB  - sequence of the strain INS, which was isolated from swollen lymph
AB  - gland aspirate (bubo aspirate) of an infected patient from a pneumonic outbreak
AB  - in 2010 in northern Peru.
ER  -

TY  - JOUR
AU  - Cadillo-Quiroz, H.
AU  - Browne, P.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Detter, C.
AU  - Yavitt, J.B.
AU  - Zinder, S.H.
TI  - Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland.
JO  - Genome Announcements
PY  - 2015
SP  - e01280
EP  - e01215
VL  - 3
AB  - Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C(T),
AB  - a methanogen isolated from a minerotrophic fen. This is the
AB  - first genome report of the Methanosphaerula genus, within the Methanoregulaceae
AB  - family, in the Methanomicrobiales order. E1-9C(T) relatives are found in a wide
AB  - range of ecological and geographical settings.
ER  -

TY  - JOUR
AU  - Cadillo-Quiroz, H.
AU  - Didelot, X.
AU  - Held, N.L.
AU  - Herrera, A.
AU  - Darling, A.
AU  - Reno, M.L.
AU  - Krause, D.J.
AU  - Whitaker, R.J.
TI  - Patterns of gene flow define species of thermophilic archaea.
JO  - PLoS Biology
PY  - 2012
SP  - E1001265
EP  - E1001265
VL  - 10
AB  - Despite a growing appreciation of their vast diversity in nature, mechanisms of
AB  - speciation are poorly understood in Bacteria and Archaea. Here we use
AB  - high-throughput genome sequencing to identify ongoing speciation in the
AB  - thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene
AB  - flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia,
AB  - demonstrate higher levels of gene flow within than between two persistent,
AB  - coexisting groups, demonstrating that these microorganisms fit the biological
AB  - species concept. Furthermore, rates of gene flow between two species are
AB  - decreasing over time in a manner consistent with incipient speciation. Unlike
AB  - other microorganisms investigated, we do not observe a relationship between
AB  - genetic divergence and frequency of recombination along a chromosome, or other
AB  - physical mechanisms that would reduce gene flow between lineages. Each species
AB  - has its own genetic island encoding unique physiological functions and a unique
AB  - growth phenotype that may be indicative of ecological specialization. Genetic
AB  - differentiation between these coexisting groups occurs in large genomic
AB  - "continents," indicating the topology of genomic divergence during speciation is
AB  - not uniform and is not associated with a single locus under strong diversifying
AB  - selection. These data support a model where species do not require physical
AB  - barriers to gene flow but are maintained by ecological differentiation.
ER  -

TY  - JOUR
AU  - Cai, H.
AU  - Chen, F.
TI  - Genome Sequence of the Proteorhodopsin-Containing Bacterium Flavobacterium sp. Strain TH167, Isolated from Cyanobacterial Aggregates in a Eutrophic Lake.
JO  - Genome Announcements
PY  - 2018
SP  - e00217
EP  - e00218
VL  - 6
AB  - Flavobacterium is the most abundant group of bacteria within the cyanobacterial aggregates in
AB  - Lake Taihu, China. Here, we present the genome sequence and
AB  - annotation of Flavobacterium sp. strain TH167. Genome analysis revealed the
AB  - presence of a proteorhodopsin-encoding sequence, together with its
AB  - retinal-producing pathway, indicating a putative photoheterotrophic lifestyle
AB  - that generates energy from light.
ER  -

TY  - JOUR
AU  - Cai, H.
AU  - Zeng, Y.
TI  - High-quality draft genome sequence of Aquidulcibacter paucihalophilus TH1-2(T) isolated from cyanobacterial aggregates in a eutrophic lake.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 69
EP  - 69
VL  - 12
AB  - Aquidulcibacter paucihalophilus TH1-2(T) is a member of the family Caulobacteraceae within
AB  - Alphaproteobacteria isolated from cyanobacterial
AB  - aggregates in a eutrophic lake. The draft genome comprises 3,711,627 bp and 3489
AB  - predicted protein-coding genes. The genome of strain TH1-2(T) has 270 genes
AB  - encoding peptidases. And metallo and serine peptidases were found most
AB  - frequently. A high number of genes encoding carbohydrate active enzymes (141
AB  - CAZymes) also present in strain TH1-2(T) genome. Among CAZymes, 47 glycoside
AB  - hydrolase families, 37 glycosyl transferase families, 38 carbohydrate esterases
AB  - families, nine auxiliary activities families, seven carbohydrate-binding modules
AB  - families, and three polysaccharide lyases families were identified. Accordingly,
AB  - strain TH1-2(T) has a high number of transporters (91), the dominated ones are
AB  - ATP-binding cassette transporters (61) and TonB-dependent transporters (28).
AB  - Major TBDTs are Group I, which consisted of transporters for various types of
AB  - dissolved organic matter. These genome features indicate adaption to
AB  - cyanobacterial aggregates microenvironments.
ER  -

TY  - JOUR
AU  - Cai, L.
AU  - Shao, M.F.
AU  - Zhang, T.
TI  - Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and  sulfur-oxidizing chemolithoautotroph isolated from marine sediment.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1302
EP  - 1310
VL  - 9
AB  - Here, we report a type strain AST-10 representing a novel species Sulfurimonas hongkongensis
AB  - within Epsilonproteobacteria, which is involved in marine
AB  - sedimentary sulfur oxidation and denitrification. Strain AST-10(T) (= DSM
AB  - 22096(T) = JCM 18418(T)) was isolated from the coastal sediment at the Kai Tak
AB  - Approach Channel connected to Victoria Harbour in Hong Kong. It grew
AB  - chemolithoautotrophically using thiosulfate, sulfide or hydrogen as the sole
AB  - electron donor and nitrate as the electron acceptor under anoxic conditions. It
AB  - was rod-shaped and grew at 15-35 degrees C (optimum at 30 degrees C), pH 6.5-8.5
AB  - (optimum at 7.0-7.5), and 10-60 g L(-1) NaCl (optimum at 30 g L(-1)). Genome
AB  - sequencing and annotation of strain AST-10(T) showed a 2,302,023 bp genome size,
AB  - with 34.9% GC content, 2,290 protein-coding genes, and 42 RNA genes, including 3
AB  - rRNA genes.
ER  -

TY  - JOUR
AU  - Cai, L.
AU  - Tan, D.
AU  - Aibaidula, G.
AU  - Dong, X.R.
AU  - Chen, J.C.
AU  - Tian, W.D.
AU  - Chen, G.Q.
TI  - Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships.
JO  - Microb. Cell Fact.
PY  - 2011
SP  - 88
EP  - 88
VL  - 10
AB  - BACKGROUND: Halophilic bacteria have shown their significance in industrial
AB  - production of polyhydroxyalkanoates (PHA) and are gaining more attention for
AB  - genetic engineering modification. Yet, little information on the genomics and PHA
AB  - related genes from halophilic bacteria have been disclosed so far. RESULTS: The
AB  - draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of
AB  - great potential for industrial production of short-chain-length
AB  - polyhydroxyalkanoates (PHA), was analyzed through computational methods to reveal
AB  - the osmoregulation mechanism and the evolutionary relationship of the enzymes
AB  - relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA
AB  - and osmolytes were annotated and studied in silico. Although PHA synthase,
AB  - depolymerase, regulator/repressor and phasin were all involved in PHA metabolic
AB  - pathways, they demonstrated different horizontal gene transfer (HGT) events
AB  - between the genomes of different strains. In contrast, co-occurrence of ectoine
AB  - genes in the same genome was more frequently observed, and ectoine genes were
AB  - more likely under coincidental horizontal gene transfer than PHA related genes.
AB  - In addition, the adjacent organization of the homologues of PHA synthase phaC1
AB  - and PHA granule binding protein phaP was conserved in the strain TD01, which was
AB  - also observed in some halophiles and non-halophiles exclusively from
AB  - gamma-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp.
AB  - TD01 did not show obvious inclination towards acidity relative to non-halophilic
AB  - Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the
AB  - accumulation of organic osmolytes to ions in order to balance the intracellular
AB  - osmotic pressure with the environment. CONCLUSIONS: The accessibility of genome
AB  - information would facilitate research on the genetic engineering of halophilic
AB  - bacteria including Halomonas sp. TD01.
ER  -

TY  - JOUR
AU  - Cai, L.
AU  - Zhang, T.
TI  - Genome of Bacillus macauensis ZFHKF-1, a Long-Chain-Forming Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4780
EP  - 4780
VL  - 194
AB  - Here, we report the draft genome sequence of Bacillus macauensis ZFHKF-1, a novel long-chain
AB  - bacterium previously isolated and identified by us (Zhang T, Fan XJ,
AB  - Hanada S, Kamagata Y, Fang HHP, J. Syst. Evol. Microbiol. 56:349-353, 2006). The
AB  - genome provides basic genetic information to understand this particular species
AB  - and explore the potential mechanism of long-chain formation. The type strain is
AB  - ZFHKF-1 (= JCM 13285 = DSM 17262).
ER  -

TY  - JOUR
AU  - Cai, L.
AU  - Zheng, S.W.
AU  - Shen, Y.J.
AU  - Zheng, G.D.
AU  - Liu, H.T.
AU  - Wu, Z.Y.
TI  - Complete genome sequence provides insights into the biodrying-related microbial function of Bacillus thermoamylovorans isolated from sewage sludge biodrying material.
JO  - Bioresource Technology
PY  - 2018
SP  - 141
EP  - 149
VL  - 260
AB  - To enable the development of microbial agents and identify suitable candidate
AB  - used for biodrying, the existence and function of Bacillus thermoamylovorans
AB  - during sewage sludge biodrying merits investigation. This study isolated a strain
AB  - of B. thermoamylovorans during sludge biodrying, submitted it for complete genome
AB  - sequencing and analyzed its potential microbial functions. After biodrying, the
AB  - moisture content of the biodrying material decreased from 66.33% to 50.18%, and
AB  - B. thermoamylovorans was the ecologically dominant Bacillus, with the primary
AB  - annotations associated with amino acid transport and metabolism (9.53%) and
AB  - carbohydrate transport and metabolism (8.14%). It contains 96
AB  - carbohydrate-active- enzyme-encoding gene counts, mainly distributed in glycoside
AB  - hydrolases (33.3%) and glycosyl transferases (27.1%). The virulence factors are
AB  - mainly associated with biosynthesis of capsule and polysaccharide capsule. This
AB  - work indicates that among the biodrying microorganisms, B. thermoamylovorans has
AB  - good potential for degrading recalcitrant and readily degradable components, thus
AB  - being a potential microbial agent used to improve biodrying.
ER  -

TY  - JOUR
AU  - Cai, M.
AU  - Chen, W.M.
AU  - Nie, Y.
AU  - Chi, C.Q.
AU  - Wang, Y.N.
AU  - Tang, Y.Q.
AU  - Li, G.Y.
AU  - Wu, X.L.
TI  - Complete Genome Sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4538
EP  - 4539
VL  - 193
AB  - Amycolicicoccus subflavus DQS3-9A1(T) , isolated from crude oil polluted soil in the Daqing
AB  - Oilfield in China , is a type strain of a newly
AB  - published novel species in the novel genus Amycolicicoccus. Here we report
AB  - the complete genome of DQS3-9A1(T) and genes associated with oil-polluted
AB  - environment.
ER  -

TY  - JOUR
AU  - Cai, Q.
AU  - Ye, X.
AU  - Chen, B.
AU  - Zhang, B.
TI  - Complete Genome Sequence of Exiguobacterium sp. Strain N4-1P, a Psychrophilic Bioemulsifier Producer Isolated from a Cold Marine Environment in North Atlantic   Canada.
JO  - Genome Announcements
PY  - 2017
SP  - e01248
EP  - e01217
VL  - 5
AB  - Here, we present the complete genome sequence of Exiguobacterium sp. strain N4-1P, a
AB  - psychrophilic bacterium that produces bioemulsifier, isolated for the
AB  - first time from petroleum hydrocarbon-contaminated sediment samples from
AB  - shoreline Newfoundland, Canada. Many strains of the genus Exiguobacterium are
AB  - extremophiles and have properties of biotechnological interest.
ER  -

TY  - JOUR
AU  - Cai, W.
AU  - Srivastava, S.K.
AU  - Stulberg, M.J.
AU  - Nakhla, M.K.
AU  - Rascoe, J.
TI  - Draft Genome Sequences of Two Dickeya dianthicola Isolates from Potato.
JO  - Genome Announcements
PY  - 2018
SP  - e00115
EP  - e00118
VL  - 6
AB  - Here, we report two annotated draft genome sequences of Dickeya dianthicola isolates from
AB  - potatoes collected in Delaware and West Virginia. The genomes of
AB  - strains DE440 and WV516 show 99% similarity to each other and 96% and 95%
AB  - similarity to the European strains IPO 980 and RNS04.9, respectively.
ER  -

TY  - JOUR
AU  - Cai, W.
AU  - Yan, Z.
AU  - Rascoe, J.
AU  - Stulberg, M.J.
TI  - Draft Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' Strain TX1712  from Citrus in Texas.
JO  - Genome Announcements
PY  - 2018
SP  - e00554
EP  - e00518
VL  - 6
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain TX1712, obtained
AB  - from a Texas citrus tree, is reported here. Strain TX1712 has a draft
AB  - genome size of 1,203,333 bp, a G+C content of 36.4%, 1,230 predicted open reading
AB  - frames, and 41 RNAs and comprises 97.4% of the psy62 reference genome.
ER  -

TY  - JOUR
AU  - Cai, X.
AU  - Kang, X.
AU  - Xi, H.
AU  - Liu, C.
AU  - Xue, Y.
TI  - Complete Genome Sequence of the Endophytic Biocontrol Strain Bacillus velezensis  CC09.
JO  - Genome Announcements
PY  - 2016
SP  - e01048
EP  - e01016
VL  - 4
AB  - Bacillus velezensis is a heterotypic synonym of B. methylotrophicus, B. amyloliquefaciens
AB  - subsp. plantarum, and Bacillus oryzicola, and has been used to
AB  - control plant fungal diseases. In order to fully understand the genetic basis of
AB  - antimicrobial capacities, we did a complete genome sequencing of the endophytic
AB  - B. velezensis strain CC09. Genes tightly associated with biocontrol ability,
AB  - including nonribosomal peptide synthetases, polyketide synthetases, iron
AB  - acquisition, colonization, and volatile organic compound synthesis were
AB  - identified in the genome.
ER  -

TY  - JOUR
AU  - Cailliez-Grimal, C.
AU  - Chaillou, S.
AU  - Anba-Mondoloni, J.
AU  - Loux, V.
AU  - Afzal, M.I.
AU  - Rahman, A.
AU  - Kergourlay, G.
AU  - Champomier-Verges, M.C.
AU  - Zagorec, M.
AU  - Dalgaard, P.
AU  - Leisner, J.J.
AU  - Prevost, H.
AU  - Revol-Junelles, A.M.
AU  - Borges, F.
TI  - Complete Chromosome Sequence of Carnobacterium maltaromaticum LMA 28.
JO  - Genome Announcements
PY  - 2013
SP  - e00115
EP  - e00112
VL  - 1
AB  - Within the lactic acid bacterium genus Carnobacterium, Carnobacterium maltaromaticum is one of
AB  - the most frequently isolated species from natural
AB  - environments and food. It potentially plays a major role in food product
AB  - biopreservation. We report here on the 3.649-Mb chromosome sequence of C.
AB  - maltaromaticum LMA 28, which was isolated from ripened soft cheese.
ER  -

TY  - JOUR
AU  - Cajo, G.C.
AU  - Brcic-Kostic, K.
AU  - Ivancic, I.
AU  - Trgovcevic, Z.
AU  - Salaj-Smic, E.
TI  - Inactivation of the EcoKI restriction in UV-irradiated Escherichia coli: The role of RecBCD enzyme.
JO  - Periodicum Biologorum
PY  - 2001
SP  - 157
EP  - 161
VL  - 103
AB  - Background and Purpose: UV-induced restriction alleviation (UV-induced RA) has been known for
AB  - a long time, but the mechanism underlying this
AB  - phenomenon is not known. UV-induced RA depends on the induction of the
AB  - SOS response and on the functional recBCD genes. The experiments
AB  - described in this study attempt to clarify the role of the RecBCD
AB  - enzyme in UV-induced RA
AB  - Materials and Methods: Restriction alleviation (RA) is expressed as
AB  - the efficiency of plating unmodified lambda virC.0 on UV-irradiated
AB  - bacteria relative to the phage titer on E. coli C00r(k)(-)m(k)(-),
AB  - lacking the EcoKI restriction-modification system.
AB  - Results and Conclusions: Alleviation of EcoKI restriction following
AB  - induction of the SOS response and its dependence on RecBDC enzyme after
AB  - UV irradiation (UV induced RA) was further characterized. We examined
AB  - the efficiency of plating unmodified lambda (RA) in bacteria with
AB  - modified activities of RecBCD enzyme, i.e. in a recD mutant, in
AB  - bacteria producing the truncated RecB(1.929) polypeptide instead of
AB  - wild-type RecB and in a Gam(+)- producing strain in which the RecBCD
AB  - enzyme interacts with the Gam protein of phage lambda It follows from
AB  - the results presented here that the helicase activity of the RecBCD
AB  - enzyme is involved in UV-induced RA.
ER  -

TY  - JOUR
AU  - Cajthamlova, K.
AU  - Sisakova, E.
AU  - Weiser, J.
AU  - Weiserova, M.
TI  - Phosphorylation of type IA restriction-modification complex enzyme EcoKI on the HsdR subunit.
JO  - FEMS Microbiol. Lett.
PY  - 2007
SP  - 171
EP  - 177
VL  - 270
AB  - Phosphorylation of Type I restriction-modification (R-M) enzymes EcoKI, EcoAI, and EcoR124I -
AB  - representatives of IA, IB, and IC families,
AB  - respectively - was analysed in vivo by immunoblotting of endogenous
AB  - phosphoproteins isolated from Escherichia coli strains harbouring the
AB  - corresponding hsd genes, and in vitro by a phosphorylation assay using
AB  - protein kinase present in subcellular fractions of E. coli. From all
AB  - three R-M enzymes, the HsdR subunit of EcoKI system was the only
AB  - subunit that was phosphorylated. Further, evidence is presented that
AB  - HsdR is phosphorylated in vivo only when coproduced with HsdM and HsdS
AB  - subunits - as part of assembled EcoKI restriction endonuclease, while
AB  - the individually produced HsdR subunit is not phosphorylated. In vitro
AB  - phosphorylation of the HsdR subunit of purified EcoKI endonuclease
AB  - occurs on Thr, and is strictly dependent on the addition of a catalytic
AB  - amount of cytoplasmic fraction isolated from E. coli. So far this is
AB  - the first case of phosphorylation of a Type I R-M enzyme reported.
ER  -

TY  - JOUR
AU  - Cal, S.
AU  - Connolly, B.A.
TI  - DNA distortion and base flipping by the EcoRV DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 1997
SP  - 490
EP  - 496
VL  - 272
AB  - The EcoRV DNA methyltransferase introduces a CH3 group at the 6-amino position of the first dA
AB  - in the duplex sequence d(GATATC).  It has previously been reported that the methylase contacts
AB  - the four phosphates (pNpNpGpA) at, and preceding, the 5'-end of the recognition sequence as
AB  - well as the single dG in this sequence.  To study the possible role of the dA and T bases
AB  - within the ATAT sequence, interference studies have been carried out using
AB  - diethylpyrocarbonate and osmium tetroxide.  The methylase bound very strongly to
AB  - hemimethylated oligonucleotides modified at the second AT, of the ATAT sequence, in the
AB  - unmethylated strand of the duplex.  This probably arises because these modifications
AB  - facilitate DNA distortion that follows the binding of the nucleic acid to the protein.
AB  - Oligonucleotides containing modified bases at both the target dA base and its complementary T
AB  - were used to determine whether this dA methylase flips out its target base in a similar manner
AB  - to that observed for dC DNA methylases.  In binary EcoRV methylase-DNA complexes, analogues
AB  - that weakened the base pair caused an increase in affinity between the protein and the nucleic
AB  - acid.  In contrast, in ternary EcoRV methylase-DNA-sinefungin (an analogue of the natural
AB  - co-factor, S-adenosyl-L-methionine (AdoMet)) complexes, only small differences in affinity
AB  - were observed between the normal dA-T base pair and the analogues.  These results are almost
AB  - identical to those seen with DNA dC methylases and support a base-flipping mechanism for DNA
AB  - dA methylases.
ER  -

TY  - JOUR
AU  - Cal, S.
AU  - Connolly, B.A.
TI  - The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 1008
EP  - 1015
VL  - 271
AB  - The EcoRV methyltransferase modifies DNA by the introduction of a methyl group at the 6-NH2
AB  - position of the first deoxyadenosine in GATATC sequences.  The enzyme forms a stable and
AB  - specific complex with GATATC sequences in the presence of a nonreactive analogue, such as
AB  - sinefungin, of its natural cofactor S-adenosyl-L-methionine.  Using circular permutation band
AB  - mobility shift analysis (in which the distance between the GATATC sequence and the end of the
AB  - DNA is varied) of protein-DNA-cofactor complexes we have shown the methylase induces a bend of
AB  - just over 60o in the bound DNA.  This was confirmed by phasing analysis, in which the spacing
AB  - between the GATATC site and a poly(dA) tract is varied through a helical turn, which showed
AB  - that the orientation of the induced curve was toward the major groove.  There was no
AB  - significant difference in the bend angle measured using unmethylated GATATC sequences and
AB  - hemimethylated sequences which contain G6-MeATATC in one strand only.  These are the natural
AB  - substrates for the enzyme.  The EcoRV endonuclease, a very well characterized protein, served
AB  - as a positive control.  DNA bending by this protein has been previously determined both by
AB  - crystallographic and solution methods.  The two proteins bend DNA toward the major groove but
AB  - the bend angle produced by the methylase, slightly greater than 60o, is a little larger than
AB  - that observed with the endonuclease, which is approximately 44o.
ER  -

TY  - JOUR
AU  - Calarco, J.P.
AU  - Martienssen, R.A.
TI  - Imprinting: DNA Methyltransferases Illuminate Reprogramming.
JO  - Curr. Biol.
PY  - 2012
SP  - R929
EP  - R931
VL  - 22
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
TI  - Complete Genome Sequence of Kocuria palustris MU14/1.
JO  - Genome Announcements
PY  - 2015
SP  - e01195
EP  - e01115
VL  - 3
AB  - Presented here is the first completely assembled genome sequence of Kocuria palustris, an
AB  - actinobacterial species with broad ecological distribution. The single, circular chromosome of
AB  - K. palustris MU14/1 comprises 2,854,447 bp, has a  G+C content of 70.5%, and contains a
AB  - deduced gene set of 2,521 coding sequences.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
TI  - Genome Sequence of Mycoplasma putrefaciens Type Strain KS1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6094
EP  - 6094
VL  - 193
AB  - Mycoplasma putrefaciens is a causative agent of contagious agalactia in goats. Reported herein
AB  - is the complete genome sequence of the M.
AB  - putrefaciens type strain KS1.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
TI  - Complete Genome Sequence of Mycoplasma bovoculi Strain M165/69T (ATCC 29104).
JO  - Genome Announcements
PY  - 2014
SP  - e00115
EP  - e00114
VL  - 2
AB  - Bovine ocular infections compromise animal health and result in significant economic losses.
AB  - Mycoplasma bovoculi is an etiological agent of conjunctivitis.
AB  - Presented here is the 760,240-bp complete genome sequence of the M. bovoculi type
AB  - strain M165/69(T). An analysis of the deduced proteome provides insights into the
AB  - adherence and antigenic variation mechanisms of the strain.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
TI  - Complete Genome Sequence of Mycoplasma hominis Strain Sprott (ATCC 33131), Isolated from a Patient with Nongonococcal Urethritis.
JO  - Genome Announcements
PY  - 2015
SP  - e00771
EP  - e00715
VL  - 3
AB  - Presented here is the complete and annotated genome sequence of Mycoplasma hominis Sprott
AB  - (ATCC 33131). The chromosome comprises 695,214 bp, which is
AB  - approximately 30 kb larger than the syntenic genome of M. hominis PG21(T).
AB  - Tetracycline resistance of strain Sprott is most probably conferred by the tetM
AB  - determinant, harbored on a mosaic transposon-like structure.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
TI  - Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements.
JO  - Genome Announcements
PY  - 2015
SP  - e01582
EP  - e01514
VL  - 3
AB  - The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene
AB  - content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a
AB  - strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma
AB  - arthritidis MAV-1. Comparative analysis with the  genome of M. hominis PG21(T) reveals
AB  - distinctive arrangements of repeat-containing surface proteins.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Fox, L.K.
TI  - Complete Genome Sequence of the Bovine Mastitis Pathogen Mycoplasma californicum  Strain ST-6T (ATCC 33461T).
JO  - Genome Announcements
PY  - 2014
SP  - e00648
EP  - e00614
VL  - 2
AB  - Mycoplasma californicum is one of several mycoplasmal species associated with bovine mastitis.
AB  - The complete genome sequence of 793,841 bp has been determined
AB  - and annotated for the M. californicum ST-6 type strain, providing a resource for
AB  - the identification of surface antigens and putative pathoadaptive features.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Fry, P.R.
AU  - Hsieh, H.Y.
AU  - Perry, J.
AU  - Stewart, G.C.
AU  - Scholl, D.T.
AU  - Messier, S.
AU  - Middleton, J.R.
TI  - Draft Genome Sequence of Bovine Mastitis Isolate Staphylococcus agnetis CBMRN 20813338.
JO  - Genome Announcements
PY  - 2014
SP  - e00883
EP  - e00814
VL  - 2
AB  - Presented here is a draft genome sequence for Staphylococcus agnetis CBMRN 20813338, isolated
AB  - from a lactating dairy cow with subclinical mastitis. The
AB  - genome is approximately 2,416 kb and has 35.79% G+C content. Analysis of the
AB  - deduced open reading frame (ORF) set identified candidate virulence attributes in
AB  - addition to potential molecular targets for species identification.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Heidari, M.B.
AU  - McIntosh, M.A.
TI  - Complete Genome Sequence of Mycoplasma flocculare Strain Ms42T (ATCC 27399T).
JO  - Genome Announcements
PY  - 2015
SP  - e00124
EP  - e00115
VL  - 3
AB  - Mycoplasma flocculare is a commensal or low-virulence pathogen of swine. The complete
AB  - 778,866-bp genome sequence of M. flocculare strain Ms42(T) has been
AB  - determined, enabling further comparison to genomes of the closely related
AB  - pathogen Mycoplasma hyopneumoniae. The absence of the p97 and glpD genes may
AB  - contribute to the attenuated virulence of M. flocculare.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Hsieh, H.Y.
AU  - Adkins, P.R.
AU  - Stewart, G.C.
AU  - Middleton, J.R.
TI  - Sequence Analysis of Staphylococcus hyicus ATCC 11249T, an Etiological Agent of Exudative Epidermitis in Swine, Reveals a Type VII Secretion System Locus and a Novel 116-Kilobase Genomic Island Harboring Toxin-Encoding Genes.
JO  - Genome Announcements
PY  - 2015
SP  - e01525
EP  - e01514
VL  - 3
AB  - Staphylococcus hyicus is the primary etiological agent of exudative epidermitis in swine.
AB  - Analysis of the complete genome sequence of the type strain revealed a  locus encoding a type
AB  - VII secretion system and a large chromosomal island harboring the genes encoding exfoliative
AB  - toxin ExhA and an EDIN toxin homolog.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Hsieh, H.Y.
AU  - Perry, J.
AU  - Stewart, G.C.
AU  - Middleton, J.R.
TI  - Draft Genome Sequence of Staphylococcus simulans UMC-CNS-990, Isolated from a Case of Chronic Bovine Mastitis.
JO  - Genome Announcements
PY  - 2013
SP  - e01037
EP  - e01013
VL  - 1
AB  - Coagulase-negative staphylococci are frequently isolated from cases of subclinical bovine
AB  - mastitis. Reported here is a draft genome sequence of
AB  - Staphylococcus simulans UMC-CNS-990, an isolate recovered from a chronic
AB  - intramammary infection of a Holstein cow. Unexpectedly, a cluster of genes
AB  - encoding gas vesicle proteins was found within the 2,755-kb genome.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Hsieh, H.Y.
AU  - Perry, J.
AU  - Stewart, G.C.
AU  - Middleton, J.R.
TI  - Genome Sequence Analysis of Staphylococcus equorum Bovine Mastitis Isolate UMC-CNS-924.
JO  - Genome Announcements
PY  - 2013
SP  - e00840
EP  - e00813
VL  - 1
AB  - Intramammary infections in dairy cattle are frequently caused by staphylococci, resulting in
AB  - mastitis and associated economic losses. A draft genome sequence was
AB  - determined for Staphylococcus equorum UMC-CNS-924, isolated from the milk of a
AB  - Holstein cow, to better understand the genetic basis of its pathogenesis and
AB  - adaptation to the bovine mammary gland.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Martin, N.T.
AU  - Mhlanga-Mutangadura, T.
AU  - Reilly, T.J.
TI  - Draft Genome Sequence of Moraxella bovoculi Strain 237T (ATCC BAA-1259T) Isolated from a Calf with Infectious Bovine Keratoconjunctivitis.
JO  - Genome Announcements
PY  - 2014
SP  - e00612
EP  - e00614
VL  - 2
AB  - Moraxella bovoculi is a recently identified species, recovered from the bovine eye, which is
AB  - under investigation as an etiological agent of infectious bovine
AB  - keratoconjunctivitis. A draft genome sequence of the Moraxella bovoculi type
AB  - strain 237(T) has been determined to identify features that may be important
AB  - during host colonization.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Mhlanga-Mutangadura, T.
AU  - Reilly, T.J.
TI  - Genome Sequence of Actinobacillus suis Type Strain ATCC 33415T.
JO  - Genome Announcements
PY  - 2014
SP  - e00926
EP  - e00914
VL  - 2
AB  - The assembled and annotated genome of Actinobacillus suis ATCC 33415(T) is reported here. The
AB  - 2,501,598-bp genome encodes 2,246 open reading frames (ORFs)
AB  - with strain variable incursion of an integrative conjugative element into a tRNA
AB  - locus. Comparative analysis of the deduced gene set should inform our
AB  - understanding of pathogenesis, genomic plasticity, and serotype variation.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Nagaraja, T.G.
AU  - Stewart, G.C.
TI  - Draft Genome Sequence of Fusobacterium necrophorum subsp. funduliforme Bovine Liver Abscess Isolate B35.
JO  - Genome Announcements
PY  - 2014
SP  - e00412
EP  - e00414
VL  - 2
AB  - Fusobacterium necrophorum is a Gram-negative anaerobic bacterium that causes foot rot and
AB  - liver abscesses in cattle. F. necrophorum subsp. necrophorum and the less
AB  - virulent organism F. necrophorum subsp. funduliforme are recognized. We present
AB  - here a draft genome sequence of the bovine liver abscess isolate F. necrophorum
AB  - subsp. funduliforme strain B35, which affords a genomic perspective of virulence
AB  - and bovine adaptation.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Rosales, R.S.
AU  - Ellis, R.J.
AU  - Nicholas, R.A.
TI  - Genome Sequence of Mycoplasma hyorhinis Strain GDL-1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1848
EP  - 1848
VL  - 194
AB  - Mycoplasma hyorhinis impacts swine health and production in many countries, either as a
AB  - primary pathogen or as a component of a polymicrobial infection.
AB  - Isolates of this species are also common contaminants of tissue culture lines.
AB  - The genome sequence of the cell culture isolate M. hyorhinis GDL-1 is presented
AB  - herein.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Kent, B.N.
AU  - Foecking, M.F.
TI  - Complete Genome Sequence of Mycoplasma yeatsii Strain GM274B (ATCC 43094).
JO  - Genome Announcements
PY  - 2015
SP  - e00328
EP  - e00315
VL  - 3
AB  - Mycoplasma yeatsii is a goat mycoplasma species that, although an obligate parasite,
AB  - accommodates this lifestyle as an inapparent commensalist.
AB  - High-frequency transformation has also been reported for this species. The
AB  - complete 895,051-bp genome sequence of strain GM274B has been determined,
AB  - enabling an analysis of the features of this potential cloning host.
ER  -

TY  - JOUR
AU  - Calcutt, M.J.
AU  - Szikriszt, B.
AU  - Poti, A.
AU  - Molnar, J.
AU  - Gervai, J.Z.
AU  - Tusnady, G.E.
AU  - Foecking, M.F.
AU  - Szuts, D.
TI  - Genome Sequence Analysis of Mycoplasma sp. HU2014, Isolated from Tissue Culture.
JO  - Genome Announcements
PY  - 2015
SP  - e01086
EP  - e01015
VL  - 3
AB  - The draft genome sequence of a novel Mycoplasma strain, designated Mycoplasma sp. HU2014, has
AB  - been determined. The genome comprises 1,084,927 nucleotides and was obtained from a
AB  - mycoplasma-infected culture of chicken DT40 cells. Phylogenetic analysis places this taxon in
AB  - a group comprising the closely related species Mycoplasma yeatsii and Mycoplasma cottewii.
ER  -

TY  - JOUR
AU  - Caldelari, I.
AU  - Chane-Woon-Ming, B.
AU  - Noirot, C.
AU  - Moreau, K.
AU  - Romby, P.
AU  - Gaspin, C.
AU  - Marzi, S.
TI  - Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001.
JO  - Genome Announcements
PY  - 2017
SP  - e00783
EP  - e00717
VL  - 5
AB  - Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for  a wide range
AB  - of infections from minor skin abscesses to life-threatening
AB  - diseases. Here, we report the draft genome assembly and current annotation of the
AB  - HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a
AB  - positive activator of SigB).
ER  -

TY  - JOUR
AU  - Calderon, C.E.
AU  - Ramos, C.
AU  - de Vicente, A.
AU  - Cazorla, F.M.
TI  - Comparative Genomic Analysis of Pseudomonas chlororaphis PCL1606 Reveals New Insight into Antifungal Compounds Involved in Biocontrol.
JO  - Mol. Plant Microbe Interact.
PY  - 2015
SP  - 249
EP  - 260
VL  - 28
AB  - Pseudomonas chlororaphis PCL1606 is a rhizobacterium that has biocontrol activity
AB  - against many soilborne phytopathogenic fungi. The whole genome sequence of this
AB  - strain was obtained using the Illumina Hiseq 2000 sequencing platform and was
AB  - assembled using SOAP denovo software. The resulting 6.66-Mb complete sequence of
AB  - the PCL1606 genome was further analyzed. A comparative genomic analysis using 10
AB  - plant-associated strains within the fluorescent Pseudomonas group, including the
AB  - complete genome of P. chlororaphis PCL1606, revealed a diverse spectrum of traits
AB  - involved in multitrophic interactions with plants and microbes as well as
AB  - biological control. Phylogenetic analysis of these strains using eight
AB  - housekeeping genes clearly placed strain PCL1606 into the P. chlororaphis group.
AB  - The genome sequence of P. chlororaphis PCL1606 revealed the presence of sequences
AB  - that were homologous to biosynthetic genes for the antifungal compounds 2-hexyl,
AB  - 5-propyl resorcinol (HPR), hydrogen cyanide, and pyrrolnitrin; this is the first
AB  - report of pyrrolnitrin encoding genes in this P. chlororaphis strain. Single-,
AB  - double-, and triple-insertional mutants in the biosynthetic genes of each
AB  - antifungal compound were used to test their roles in the production of these
AB  - antifungal compounds and in antagonism and biocontrol of two fungal pathogens.
AB  - The results confirmed the function of HPR in the antagonistic phenotype and in
AB  - the biocontrol activity of P. chlororaphis PCL1606.
ER  -

TY  - JOUR
AU  - Calero-Delgado, B.
AU  - Martin-Platero, A.M.
AU  - Perez-Pulido, A.J.
AU  - Benitez-Cabello, A.
AU  - Casimiro-Soriguer, C.S.
AU  - Martinez-Bueno, M.
AU  - Arroyo-Lopez, F.N.
AU  - Rodriguez-Gomez, F.
AU  - Bautista-Gallego, J.
AU  - Garrido-Fernandez, A.
AU  - Jimenez-Diaz, R.
TI  - Draft Genome Sequences of Six Lactobacillus pentosus Strains Isolated from Brines of Traditionally Fermented Spanish-Style Green Table Olives.
JO  - Genome Announcements
PY  - 2018
SP  - e00379
EP  - e00318
VL  - 6
AB  - Here, we report the genome sequences of six Lactobacillus pentosus strains isolated from
AB  - traditional noninoculated Spanish-style green table olive brines.
AB  - The total genome sizes varied between 3.77 and 4.039 Mbp. These genome sequences
AB  - will assist in revealing the genes responsible for both technological and
AB  - probiotic properties of these strains.
ER  -

TY  - JOUR
AU  - Califano, G.
AU  - Franco, T.
AU  - Goncalves, A.C.
AU  - Castanho, S.
AU  - Soares, F.
AU  - Ribeiro, L.
AU  - Mata, L.
AU  - Costa, R.
TI  - Draft Genome Sequence of Aliivibrio fischeri Strain 5LC, a Bacterium Retrieved from Gilthead Sea Bream (Sparus aurata) Larvae Reared in Aquaculture.
JO  - Genome Announcements
PY  - 2015
SP  - e00593
EP  - e00515
VL  - 3
AB  - To shed light on the putative host-mediated lifestyle of the quintessential marine symbiont
AB  - Aliivibrio fischeri, and on the symbiosis versus potentially
AB  - pathogenic features of bacteria associated with farmed fish, we report the draft
AB  - genome sequence of A. fischeri strain 5LC, a bacterium retrieved from gilthead
AB  - sea bream (Sparus aurata) larvae.
ER  -

TY  - JOUR
AU  - Calisto, R.M.
AU  - Pich, O.Q.
AU  - Pinol, J.
AU  - Fita, I.
AU  - Querol, E.
AU  - Carpena, X.
TI  - Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 749
EP  - 762
VL  - 351
AB  - The crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 peptide, determined by
AB  - multiple anomalous dispersion and refined at
AB  - poly 2.3 angstrom resolution, reveals the organization of S subunits
AB  - from the Type I restriction and modification system. The structure
AB  - consists of two globular domains, with about 150 residues each,
AB  - separated by a pair of 40 residue long antiparallel alpha-helices. The
AB  - globular domains correspond to the variable target recognition domains
AB  - (TRDs), as previously defined for S subunits on sequence analysis,
AB  - while the two helices correspond to the central (CRI) and C-terminal
AB  - (CR2) conserved regions, respectively. The structure of the MG438
AB  - subunit presents an overall cyclic topology with an intramolecular
AB  - 2-fold axis that superimposes the N and the C-half parts, each half
AB  - containing a globular domain and a conserved helix. TRDs are found to
AB  - be structurally related with the small domain of the Type II N6-adenine
AB  - DNA MTase TaqI. These relationships together with the structural
AB  - peculiarities of MG438, in particular the presence of the
AB  - intramolecular quasi-symmetry, allow the proposal of a model for S
AB  - subunits recognition of their DNA targets in agreement with previous
AB  - experimental results. In the crystal, two subunits of MG438 related by
AB  - a crystallographic 2-fold axis present a large contact area mainly
AB  - involving the symmetric interactions of a cluster of exposed
AB  - hydrophobic residues. Comparison with the recently reported structure
AB  - of an S subunit from the archaea Methanococcus jannaschii highlights
AB  - the structural features preserved despite a sequence identity below
AB  - 20%, but also reveals important differences in the globular domains and
AB  - in their disposition with respect to the conserved regions.
ER  -

TY  - JOUR
AU  - Callahan, S.J.
AU  - Luyten, Y.A.
AU  - Gupta, Y.K.
AU  - Wilson, G.G.
AU  - Roberts, R.J.
AU  - Morgan, R.D.
AU  - Aggarwal, A.K.
TI  - Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities.
JO  - PLoS Biology
PY  - 2016
SP  - e1002442
EP  - e1002442
VL  - 14
AB  - The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities
AB  - has long been a goal of modern biology. The recently discovered
AB  - Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a
AB  - shared target recognition domain provides a framework for engineering such new
AB  - specificities. However, a lack of structural information on Type IIL enzymes has
AB  - limited the repertoire that can be rationally engineered. We report here a
AB  - crystal structure of MmeI in complex with its DNA substrate and an
AB  - S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first
AB  - time the interactions that underlie MmeI-DNA recognition and methylation
AB  - (5'-TCCRAC-3'; R = purine) and provides a molecular basis for changing
AB  - specificity at four of the six base pairs of the recognition sequence
AB  - (5'-TCCRAC-3'). Surprisingly, the enzyme is resilient to specificity changes at
AB  - the first position of the recognition sequence (5'-TCCRAC-3'). Collectively, the
AB  - structure provides a basis for engineering further derivatives of MmeI and
AB  - delineates which base pairs of the recognition sequence are more amenable to
AB  - alterations than others.
ER  -

TY  - JOUR
AU  - Callahan, S.J.
AU  - Morgan, R.D.
AU  - Jain, R.
AU  - Townson, S.A.
AU  - Wilson, G.G.
AU  - Roberts, R.J.
AU  - Aggarwal, A.K.
TI  - Crystallization and preliminary crystallographic analysis of the type IIL restriction enzyme MmeI in complex with DNA.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2011
SP  - 1262
EP  - 1265
VL  - 67
AB  - Type IIL restriction enzymes have rejuvenated the search for user-specified DNA binding and
AB  - cutting. By aligning and contrasting the
AB  - highly comparable amino-acid sequences yet diverse recognition
AB  - specificities across the family of enzymes, amino acids involved in DNA
AB  - binding have been identified and mutated to produce alternative binding
AB  - specificities. To date, the specificity of MmeI (a type IIL restriction
AB  - enzyme) has successfully been altered at positions 3, 4 and 6 of the
AB  - asymmetric TCCRAC (where R is a purine) DNA-recognition sequence. To
AB  - further understand the structural basis of MmeI DNA-binding
AB  - specificity, the enzyme has been crystallized in complex with its DNA
AB  - substrate. The crystal belonged to space group P1, with unit-cell
AB  - parameters a = 61.73, b = 94.96, c = 161.24 angstrom, alpha = 72.79,
AB  - beta = 89.12, gamma = 71.68 degrees, and diffracted to 2.6 angstrom
AB  - resolution when exposed to synchrotron radiation. The structure
AB  - promises to reveal the basis of MmeI DNA-binding specificity and will
AB  - complement efforts to create enzymes with novel specificities.
ER  -

TY  - JOUR
AU  - Callanan, M.
AU  - Kaleta, P.
AU  - O'Callaghan, J.
AU  - O'Sullivan, O.
AU  - Jordan, K.
AU  - McAuliffe, O.
AU  - Sangrador-Vegas, A.
AU  - Slattery, L.
AU  - Fitzgerald, G.F.
AU  - Beresford, T.
AU  - Ross, R.P.
TI  - Genome sequence of Lactobacillus helveticus: an organism distinguished by selective gene loss and IS element expansion.
JO  - J. Bacteriol.
PY  - 2008
SP  - 727
EP  - 735
VL  - 190
AB  - Mobile genetic elements are major contributing factors to the generation of genetic diversity
AB  - in prokaryotic organisms. For example insertion
AB  - sequence (IS) elements have been shown to specifically contribute to niche
AB  - adaptation by promoting a variety of genetic rearrangements. The complete
AB  - genome sequence of the cheese culture Lactobacillus helveticus DPC 4571
AB  - was determined and revealed significant conservation when compared to
AB  - three non-dairy gut lactobacilli. Despite originating from significantly
AB  - different environments, 65-75% of genes were conserved between the
AB  - commensal and dairy lactobacilli which allowed key niche-specific gene
AB  - sets to be described. However, the primary distinguishing feature was two
AB  - hundred and thirteen IS elements in the DPC 4571 genome, ten times more
AB  - than the other lactobacilli. Moreover, genome alignments revealed an
AB  - unprecedented level of genome stability between these four Lactobacillus
AB  - species considering the number of IS elements in the L. helveticus genome.
AB  - Comparative analysis also indicated that the IS elements were not the
AB  - primary agents of niche adaptation for the L. helveticus genome. A clear
AB  - bias towards the loss of genes reported to be important for gut
AB  - colonization was observed for the cheese culture but there was no clear
AB  - evidence of IS-associated gene deletion and decay for the majority of
AB  - genes lost. Furthermore, an extraordinary level of sequence diversity
AB  - exists between copies of certain IS elements in the DPC 4571 genome
AB  - indicating they may represent an ancient component of the L. helveticus
AB  - genome. These data suggests a special unobtrusive relationship between the
AB  - DPC 4571 genome and its mobile DNA complement.
ER  -

TY  - JOUR
AU  - Calleja, F.
AU  - Dekker, B.M.M.
AU  - Coursin, T.
AU  - de Waard, A.
TI  - A new sequence specific endonuclease EspI, of cyanobacterial origin.
JO  - FEBS Lett.
PY  - 1984
SP  - 69
EP  - 72
VL  - 178
AB  - The isolation of a new sequence-specific endonuclease from a unicellular
AB  - cyanobacterium is described.  This enzyme specifically cleaves the nucleotide
AB  - sequence GC^TNAGC.
ER  -

TY  - JOUR
AU  - Calleja, F.
AU  - Tandeau de Marsac, N.
AU  - Coursin, T.
AU  - van Ormondt, H.
AU  - de Waard, A.
TI  - A new endonuclease recognizing the deoxynucleotide sequence C^CNNGG from the cyanobacterium Synechocystis 6701.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 6745
EP  - 6751
VL  - 13
AB  - A new sequence-specific endonuclease from the cyanobacterium Synechocystis
AB  - species PCC 6701 has been purified and characterized.  This enzyme, SecI, is
AB  - unique in recognizing the nucleotide sequence: 5' -C^C N N G G-3'3' -G G N N
AB  - C^C-5'	and cleaves it at the position indicated by the ^ symbol.  Two other
AB  - restriction endonucleases, SecII and SecIII, found in this organism are
AB  - isoschizomers of MspI and MstII, respectively.
ER  -

TY  - JOUR
AU  - Callow, P.
AU  - Sukhodub, A.
AU  - Taylor, J.E.
AU  - Kneale, G.G.
TI  - Shape and Subunit Organisation of the DNA Methyltransferase M.AhdI by Small-angle Neutron Scattering.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 177
EP  - 185
VL  - 369
AB  - Type I restriction-modification (R-M) systems encode multisubunit/multidomain enzymes. Two
AB  - genes (M and S) are required to form
AB  - the methyltransferase (MTase) that methylates a specific base within the
AB  - recognition sequence and protects DNA from cleavage by the endonuclease.
AB  - The DNA methyltransferase M.AhdI is a 170 kDa tetramer with the
AB  - stoichiometry M(2)S(2) and has properties typical of a type I MTase. The
AB  - M.AhdI enzyme has been prepared with deuterated S subunits, to allow
AB  - contrast variation using small-angle neutron scattering (SANS) methods.
AB  - The SANS data were collected in a number of (1)H:(2)H solvent contrasts to
AB  - allow matching of one or other of the subunits in the multisubunit enzyme.
AB  - The radius of gyration (R(g)) and maximum dimensions (D(max)) of the M
AB  - subunits in situ in the multisubunit enzyme (50 A and 190 A, respectively)
AB  - are close of those of the entire MTase (51 A and 190 A). In contrast, the
AB  - S subunits in situ have experimentally determined values of R(g)=35 A and
AB  - D(max)=110 A, indicating their more central location in the enzyme. Ab
AB  - initio reconstruction methods yield a low-resolution structural model of
AB  - the shape and subunit organization of M.AhdI, in which the Z-shaped
AB  - structure of the S subunit dimer can be discerned. In contrast, the M
AB  - subunits form a much more elongated and extended structure. The core of
AB  - the MTase comprises the two S subunits and the globular regions of the two
AB  - M subunits, with the extended portion of the M subunits most probably
AB  - forming highly mobile regions at the outer extremities, which collapse
AB  - around the DNA when the MTase binds.
ER  -

TY  - JOUR
AU  - Callow, P.
AU  - Timmins, P.
AU  - Kneale, G.
TI  - Preliminary neutron scattering studies of the Type I restriction-modification enzyme M.Ahdl.
JO  - Phys. Rev., B Condens. Matter
PY  - 2006
SP  - 853
EP  - 855
VL  - 385-386
AB  - Type I restriction-modification (R-M) systems encode multisubunit/multidomain enzymes. Two
AB  - genes (M and S) are required to
AB  - form the 160kDa methyltransferase that methylates a specific base
AB  - within the recognition sequence and protects DNA from cleavage by the
AB  - endonuclease. Small angle neutron scattering (SANS) revealed an
AB  - unusually large structural change in the EcoR124l methyltransferase
AB  - following DNA binding; this involves a major repositioning of the
AB  - subunits of the enzyme, resulting in a 60 angstrom reduction in the
AB  - dimensions of the enzyme on forming a complex with DNA. The related
AB  - methyltransferase M.Ahdl, with stoichiometry M2S2 has been prepared in
AB  - two protonated/deuterated states (S and M subunits protonated, S
AB  - deuterated and M protonated) for which SANS data have been collected in
AB  - a number of H:D solvent contrasts. The contrast match point of the
AB  - selectively deuterated enzyme confirms the successful reconstitution of
AB  - the enzyme with deuterated S subunits. Ab initio shape determination
AB  - using this contrast matched data is in progress to determine the
AB  - subunit organization of M.Ahdl and the large change in structure that
AB  - occurs on DNA binding.
ER  -

TY  - JOUR
AU  - Calmann, M.A.
AU  - Marinus, M.G.
TI  - Regulated expression of the Escherichia coli dam gene.
JO  - J. Bacteriol.
PY  - 2003
SP  - 5012
EP  - 5014
VL  - 185
AB  - Regulated expression of the Escherichia coli dam gene has been achieved with the araBAD
AB  - promoter lacking a ribosome binding site. Cultures of dam
AB  - mutants containing plasmid pMQ430 show no detectable methylation in the
AB  - absence of arabinose and complete methylation in its presence. Dam
AB  - methyltransferase is a substrate for the Lon protease.
ER  -

TY  - JOUR
AU  - Calva, E.
AU  - Silva, C.
AU  - Zaidi, M.B.
AU  - Sanchez-Flores, A.
AU  - Estrada, K.
AU  - Silva, G.G.
AU  - Soto-Jimenez, L.M.
AU  - Wiesner, M.
AU  - Fernandez-Mora, M.
AU  - Edwards, R.A.
AU  - Vinuesa, P.
TI  - Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype.
JO  - Genome Announcements
PY  - 2015
SP  - e00663
EP  - e00615
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated  in 2005 in
AB  - the state of Yucatan, Mexico, from a human systemic infection. The
AB  - YU39 strain is representative of the multidrug-resistant emergent sequence type
AB  - 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and
AB  - seven plasmids.
ER  -

TY  - JOUR
AU  - Calvin-Koons, M.D.
AU  - Blumenthal, R.M.
TI  - Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system.
JO  - Gene
PY  - 1995
SP  - 73
EP  - 79
VL  - 157
AB  - Plasmid pPvu1 from Proteus vulgaris carries the genes of the PvuII restriction-modification
AB  - system.  This report focuses on physical and functional features of the 4.84-kb plasmid, which
AB  - shows a composite genetic architecture.  Plasmid pPvu1 has a replication origin and an
AB  - incompatibility locus that each function in Escherichia coli, and an apparent cer
AB  - recombination site.  The replication origin includes a possible RNAI gene, and the
AB  - incompatibility locus closely resembles a rom gene.  These loci show substantial sequence
AB  - similarity to corresponding loci from the E. coli plasmids P15A, ColEI and pSC101, and closely
AB  - flank the PvuII genes.  The close association between a recombinational locus and the PvuII
AB  - genes has implications for their mobility.
ER  -

TY  - JOUR
AU  - Cameron, D.R.
AU  - Jiang, J.H.
AU  - Abbott, I.J.
AU  - Spelman, D.W.
AU  - Peleg, A.Y.
TI  - Draft Genome Sequences of Clinical Daptomycin-Nonsusceptible Methicillin-Resistant Staphylococcus aureus Strain APS211 and Its  Daptomycin-Susceptible Progenitor APS210.
JO  - Genome Announcements
PY  - 2015
SP  - e00568
EP  - e00515
VL  - 3
AB  - To assess the genetic factors contributing to daptomycin resistance in Staphylococcus aureus,
AB  - the draft genome of a clinically derived
AB  - daptomycin-nonsusceptible isolate APS211 was generated and compared to the draft
AB  - sequence of its susceptible progenitor strain APS210. Four genetic differences
AB  - were identified including a previously described mutation within the mprF gene.
ER  -

TY  - JOUR
AU  - Cameron, D.R.
AU  - Jiang, J.H.
AU  - Hassan, K.A.
AU  - Elbourne, L.D.
AU  - Tuck, K.L.
AU  - Paulsen, I.T.
AU  - Peleg, A.Y.
TI  - Insights on virulence from the complete genome of Staphylococcus capitis.
JO  - Front. Microbiol.
PY  - 2015
SP  - 980
EP  - 980
VL  - 6
AB  - Staphylococcus capitis is an opportunistic pathogen of the coagulase negative
AB  - staphylococci (CoNS). Functional genomic studies of S. capitis have thus far been
AB  - limited by a lack of available complete genome sequences. Here, we determined the
AB  - closed S. capitis genome and methylome using Single Molecule Real Time (SMRT)
AB  - sequencing. The strain, AYP1020, harbors a single circular chromosome of 2.44 Mb
AB  - encoding 2304 predicted proteins, which is the smallest of all complete
AB  - staphylococcal genomes sequenced to date. AYP1020 harbors two large mobile
AB  - genetic elements; a plasmid designated pAYP1020 (59.6 Kb) and a prophage,
AB  - PhiAYP1020 (48.5 Kb). Methylome analysis identified significant adenine
AB  - methylation across the genome involving two distinct methylation motifs (1972
AB  - putative 6-methyladenine (m6A) residues identified). Putative adenine
AB  - methyltransferases were also identified. Comparative analysis of AYP1020 and the
AB  - closely related CoNS, S. epidermidis RP62a, revealed a host of virulence factors
AB  - that likely contribute to S. capitis pathogenicity, most notably genes important
AB  - for biofilm formation and a suite of phenol soluble modulins (PSMs); the
AB  - expression/production of these factors were corroborated by functional assays.
AB  - The complete S. capitis genome will aid future studies on the evolution and
AB  - pathogenesis of the coagulase negative staphylococci.
ER  -

TY  - JOUR
AU  - Camiolo, S.
AU  - Porceddu, A.
AU  - Ruiu, L.
TI  - Genome Sequence of Brevibacillus laterosporus UNISS 18, a Pathogen of Mosquitoes  and Flies.
JO  - Genome Announcements
PY  - 2017
SP  - e00419
EP  - e00417
VL  - 5
AB  - The entomopathogenic properties of Brevibacillus laterosporus UNISS 18 against insects are
AB  - well documented. Here, we report the whole-genome sequence of this
AB  - strain, which revealed the presence of several insecticide action-related genes.
AB  - The deriving genetic information will help to elucidate the mechanisms underlying
AB  - strain specificity and virulence against diverse target pests.
ER  -

TY  - JOUR
AU  - Campbell, B.J.
AU  - Smith, J.L.
AU  - Hanson, T.E.
AU  - Klotz, M.G.
AU  - Stein, L.Y.
AU  - Lee, C.K.
AU  - Wu, D.
AU  - Robinson, J.M.
AU  - Khouri, H.M.
AU  - Eisen, J.A.
AU  - Cary, S.C.
TI  - Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola.
JO  - PLoS Genet.
PY  - 2009
SP  - e1000362
EP  - e1000362
VL  - 5
AB  - Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some
AB  - sites maintain conditions that may have favored the
AB  - formation and evolution of cellular life. Vents are typified by rapid
AB  - fluctuations in temperature and redox potential that impose a strong
AB  - selective pressure on resident microbial communities. Nautilia
AB  - profundicola strain Am-H is a moderately thermophilic, deeply-branching
AB  - Epsilonproteobacterium found free-living at hydrothermal vents and is a
AB  - member of the microbial mass on the dorsal surface of vent polychaete,
AB  - Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola
AB  - uncovered adaptations to the vent environment--some unique and some shared
AB  - with other Epsilonproteobacterial genomes. The major findings included:
AB  - (1) a diverse suite of hydrogenases coupled to a relatively simple
AB  - electron transport chain, (2) numerous stress response systems, (3) a
AB  - novel predicted nitrate assimilation pathway with hydroxylamine as a key
AB  - intermediate, and (4) a gene (rgy) encoding the hallmark protein for
AB  - hyperthermophilic growth, reverse gyrase. Additional experiments indicated
AB  - that expression of rgy in strain Am-H was induced over 100-fold with a 20
AB  - degrees C increase above the optimal growth temperature of this bacterium
AB  - and that closely related rgy genes are present and expressed in bacterial
AB  - communities residing in geographically distinct thermophilic environments.
AB  - N. profundicola, therefore, is a model Epsilonproteobacterium that
AB  - contains all the genes necessary for life in the extreme conditions widely
AB  - believed to reflect those in the Archaean biosphere--anaerobic, sulfur,
AB  - H2- and CO2-rich, with fluctuating redox potentials and temperatures. In
AB  - addition, reverse gyrase appears to be an important and common adaptation
AB  - for mesophiles and moderate thermophiles that inhabit ecological niches
AB  - characterized by rapid and frequent temperature fluctuations and, as such,
AB  - can no longer be considered a unique feature of hyperthermophiles.
ER  -

TY  - JOUR
AU  - Campedelli, I.
AU  - Florez, A.B.
AU  - Salvetti, E.
AU  - Delgado, S.
AU  - Orru, L.
AU  - Cattivelli, L.
AU  - Alegria, A.
AU  - Felis, G.E.
AU  - Torriani, S.
AU  - Mayo, B.
TI  - Draft Genome Sequence of Three Antibiotic-Resistant Leuconostoc mesenteroides Strains of Dairy Origin.
JO  - Genome Announcements
PY  - 2015
SP  - e01018
EP  - e01015
VL  - 3
AB  - Leuconostoc mesenteroides is a lactic acid bacterium (LAB) commonly associated with fermented
AB  - foods. Here, we report the genome sequence of three selected dairy strains, showing atypical
AB  - antibiotic resistances (AR). Genome analysis provided a better understanding of the genetic
AB  - bases of AR in Leuconostoc and its potential  transferability among foodborne bacteria.
ER  -

TY  - JOUR
AU  - Campellone, K.G.
AU  - Roe, A.J.
AU  - Lobner-Olesen, A.
AU  - Murphy, K.C.
AU  - Magoun, L.
AU  - Brady, M.J.
AU  - Donohue-Rolfe, A.
AU  - Tzipori, S.
AU  - Gally, D.L.
AU  - Leong, J.M.
AU  - Marinus, M.G.
TI  - Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157 : H7.
JO  - Mol. Microbiol.
PY  - 2007
SP  - 1468
EP  - 1481
VL  - 63
AB  - Enterohaemorrhagic Escherichia coli (EHEC) are highly infectious pathogens capable of causing
AB  - severe diarrhoeal illnesses. As a critical
AB  - step during their colonization, EHEC adhere intimately to intestinal
AB  - epithelial cells and generate F-actin 'pedestal' structures that
AB  - elevate them above surrounding cell surfaces. Intimate adhesion and
AB  - pedestal formation result from delivery of the EHEC type III secretion
AB  - system (TTSS) effector proteins Tir and EspF(U) into the host cell and
AB  - expression of the bacterial outer membrane adhesin, intimin. To
AB  - investigate a role for DNA methylation during the regulation of
AB  - adhesion and pedestal formation in EHEC, we deleted the dam (DNA
AB  - adenine methyltransferase) gene from EHEC O157:H7 and demonstrate that
AB  - this mutation results in increased interactions with cultured host
AB  - cells. EHEC Delta dam exhibits dramatically elevated levels of
AB  - adherence and pedestal formation when compared with wild-type EHEC, and
AB  - expresses significantly higher protein levels of intimin, Tir and
AB  - EspF(U). Analyses of GFP fusions, Northern blotting, reverse
AB  - transcription polymerase chain reaction, and microarray experiments
AB  - indicate that the abundance of Tir in the dam mutant is not due to
AB  - increased transcription levels, raising the possibility that Dam
AB  - methylation can indirectly control protein expression by a
AB  - post-transcriptional mechanism. In contrast to other dam-deficient
AB  - pathogens, EHEC Delta dam is capable of robust intestinal colonization
AB  - of experimentally infected animals.
ER  -

TY  - JOUR
AU  - Campione-Piccardo, J.
AU  - Moro, R.
TI  - Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions.
JO  - Comput. Appl. Biosci.
PY  - 1988
SP  - 215
EP  - 216
VL  - 4
AB  - A program has been developed for the modelling of modifications in DNA ends,
AB  - for the construction of ligated junctions, and for the analysis in these
AB  - junctions of new restriction enzyme recognition sequences.  This program allows
AB  - the analysis of restriction enzyme specificities in ligated junctions of
AB  - cohesive or blunt DNA ends.  Cohesive ends are considered in their natural
AB  - configuration or after modification by possible blunt-ending procedures.  The
AB  - program also allows the modelling of partial filling-in for 5'-single-stranded
AB  - ends.   This program has proven useful for the design of sequences with new
AB  - restriction sites or to predict or confirm the sequences of junctions created
AB  - by the ligation of modified ends.
ER  -

TY  - JOUR
AU  - Campioni, F.
AU  - Cao, G.
AU  - Kastanis, G.
AU  - Sanchez, L.M.
AU  - Bergamini, A.M.M.
AU  - Rodrigues, D.D.P.
AU  - Allard, M.W.
AU  - Falcao, J.P.
TI  - Draft Genome Sequences of 256 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Humans, Food, Chickens, and Farm Environments  in Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00399
EP  - e00317
VL  - 5
AB  - Salmonella enterica subsp. enterica serovar Enteritidis emerged in the late 1980s as the most
AB  - isolated Salmonella serovar worldwide. Here, we report the draft
AB  - genomes of 256 S Enteritidis strains isolated from humans, food, chickens, and
AB  - farm environments in Brazil. These draft genomes will help enhance our
AB  - understanding of this serovar in Brazil.
ER  -

TY  - JOUR
AU  - Campioni, F.
AU  - Vilela, F.P.
AU  - Cao, G.
AU  - Kastanis, G.
AU  - Miller, D.
AU  - Sanchez, L.M.
AU  - Tiba-Casas, M.R.
AU  - Fernandes, S.A.
AU  - Rodrigues, D.D.P.
AU  - Costa, R.G.
AU  - Allard, M.W.
AU  - Falcao, J.P.
TI  - Draft Genome Sequences of 112 Salmonella enterica Serovar Dublin Strains Isolated from Humans and Animals in Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00405
EP  - e00418
VL  - 6
AB  - Salmonella enterica serovar Dublin is a strongly adapted serovar that causes enteritis and/or
AB  - systemic disease in cattle and results in high rates of
AB  - mortality. Here, we report the draft genome sequences of 112 S. Dublin strains
AB  - isolated from humans and animals in Brazil. These draft genome sequences will
AB  - help enhance our understanding of this serovar in Brazil.
ER  -

TY  - JOUR
AU  - Campos, F.S.
AU  - Santos, G.R.
AU  - Nascimento, V.L.
AU  - Correia, R.F.T.
AU  - Cangussu, A.S.R.
AU  - Hoffmann, K.
AU  - Oliveira, E.E.
AU  - Ribeiro, B.M.
AU  - Aguiar, R.W.S.
TI  - Genome Sequence of a New Siphoviridae Phage Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain.
JO  - Genome Announcements
PY  - 2018
SP  - e01606
EP  - e01617
VL  - 6
AB  - During the fermentation process, Bacillus thuringiensis (Bt) phages can result in bacterial
AB  - death and decreased yield. In this work, we describe the genome of a
AB  - new phage related to the Siphoviridae viral family from a Brazilian strain of Bt
AB  - which showed high nucleotide sequence identity to the genomes of phages phi4l1
AB  - and BtCS33.
ER  -

TY  - JOUR
AU  - Campos-Guillen, J.
AU  - Caballero, P.J.
AU  - Cruz, M.J.A.
AU  - Molina, V.C.
AU  - Salas, R.L.M.
AU  - Limpens, G.C.
AU  - Garcia, S.I.
AU  - Hernandez, R.M.R.
AU  - Soto, A.G.
AU  - Cruz, H.A.
AU  - Saldana, G.C.
AU  - Romero, G.S.
AU  - Pastrana, M.X.
AU  - Alvarez, H.E.
AU  - Gosar, M.
AU  - Dizdarevic, T.
TI  - Draft Genome Sequence of the Mercury-Resistant Bacterium Acinetobacter idrijaensis Strain MII, Isolated from a Mine-Impacted Area, Idrija, Slovenia.
JO  - Genome Announcements
PY  - 2014
SP  - e01177
EP  - e01114
VL  - 2
AB  - We report here the first draft assembly for the genome of Acinetobacter idrijaensis strain
AB  - MII, isolated from the Idrija mercury mine area (Slovenia).
AB  - This strain shows a strikingly high tolerance to mercury, and the genome sequence
AB  - shows genes involved in the mechanisms for heavy metal tolerance pathways and
AB  - multidrug efflux pumps.
ER  -

TY  - JOUR
AU  - Campoy, S.
AU  - Aranda, J.
AU  - Alvarez, G.
AU  - Barbe, J.
AU  - Llagostera, M.
TI  - Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 3154
EP  - 3160
VL  - 72
AB  - A temperate bacteriophage (F108) has been isolated through mitomycin C
AB  - induction of a Pasteurella multocida serogroup A strain. F108 has a
AB  - typical morphology of the family Myoviridae, presenting a hexagonal head
AB  - and a long contractile tail. F108 is able to infect all P. multocida
AB  - serogroup A strains tested but not those belonging to other serotypes.
AB  - Bacteriophage F108, the first P. multocida phage sequenced so far,
AB  - presents a 30,505-bp double-stranded DNA genome with cohesive ends
AB  - (CTTCCTCCCC cos site). The F108 genome shows the highest homology with
AB  - those of Haemophilus influenzae HP1 and HP2 phages. Furthermore, an F108
AB  - prophage attachment site in the P. multocida chromosome has been
AB  - established to be inside a gene encoding tRNA(Leu). By using several
AB  - chromosomal markers that are spread along the P. multocida chromosome, it has been
AB  - demonstrated that F108 is able to perform generalized transduction. This fact, together with
AB  - the absence of pathogenic genes in the F108 genome, makes this bacteriophage a valuable tool
AB  - for P.multocida genetic manipulation.
ER  -

TY  - JOUR
AU  - Campoy, S.
AU  - Mazon, G.
AU  - de Henestrosa, A.R.F.
AU  - Llagostera, M.
AU  - Monteiro, P.B.
AU  - Barbe, J.
TI  - A new regulatory DNA motif of the gamma subclass proteobacteria: identification of the LexA protein binding site of the plant pathogen  Xylella fastidiiosa.
JO  - Microbiology
PY  - 2002
SP  - 3583
EP  - 3597
VL  - 148
AB  - Escherichia coli LexA protein is the repressor of a gene network whose members are directly
AB  - involved in the repair of damaged DNA and in the
AB  - survival of bacterial cells until DNA lesions have been eliminated. The
AB  - lexA gene is widely present in bacteria, although the sequences of only
AB  - three LexA-binding sites are known: Gram-positive, alpha Proteobacteria
AB  - and some members of gamma Proteobacteria represented by E. coli. Taking
AB  - advantage of the fact that the genome sequence of the plant-pathogenic
AB  - bacterium Xylella fastidiosa has been determined, its lexA gene has
AB  - been cloned and overexpressed in E. coli to purify its product. After
AB  - demonstration that X. fastidiosa lexA and recA genes are
AB  - co-transcribed, gel mobility shift assays and directed mutagenesis
AB  - experiments using the promoter of the lexA-recA transcriptional unit
AB  - demonstrated that the X. fastidiosa LexA protein specifically binds the
AB  - imperfect palindrome TTAGN(6)TACTA. This is the first LexA binding
AB  - sequence identified in the gamma Proteobacteria differing from the E.
AB  - coli-like LexA box. Although a computational search has revealed the
AB  - presence of TTAGN(6)TACTA-like motifs upstream of X. fastidiosa genes
AB  - other than lxA, X. fastidiosa LexA only binds the promoter of one of
AB  - them, XF2313, encoding a putative DNA-modification methylase. Moreover,
AB  - X. fastidiosa LexA protein does not bind any of the other genes whose
AB  - homologues are regulated by the LexA repressor in E. coli (uvrA, uvrB,
AB  - ssb, ruvAB, ftsK, dinG, recN and ybfE). RTPCR quantitative analysis has
AB  - also demonstrated that lexA-recA and XF2313 genes, as well as the X.
AB  - fastidiosa genes which are homologues to those of E. coli belonging to
AB  - the LexA regulon, with the exception of ssb, are DNA damage-inducible
AB  - in X. fastidiosa.
ER  -

TY  - JOUR
AU  - Camus, J.C.
AU  - Pryor, M.J.
AU  - Medigue, C.
AU  - Cole, S.T.
TI  - Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.
JO  - Microbiology
PY  - 2002
SP  - 2967
EP  - 2973
VL  - 148
AB  - Original genome annotations need to be regularly updated if the information they contain is to
AB  - remain accurate and relevant. Here the
AB  - complete re-annotation of the genome sequence of Mycobacterium
AB  - tuberculosis strain H37Rv is presented almost 4 years after the first
AB  - submission. Eighty-two new protein-coding sequences (CDS) have been
AB  - included and 22 of these have a predicted function. The majority were
AB  - identified by manual or automated re-analysis of the genome and most of
AB  - them were shorter than the 100 codon cut-off used in the initial genome
AB  - analysis. The functional classification of 643 CDS has been changed based
AB  - principally on recent sequence comparisons and new experimental data from
AB  - the literature. More than 300 gene names and over 1000 targeted citations
AB  - have been added and the lengths of 60 genes have been modified. Presently,
AB  - it is possible to assign a function to 2058 proteins (52% of the 3995
AB  - proteins predicted) and only 376 putative proteins share no homology with
AB  - known proteins and thus could be unique to M. tuberculosis.
ER  -

TY  - JOUR
AU  - Canevari, C.A.B.
AU  - Nishibe, C.
AU  - Moura, A.
AU  - de Alencar, A.P.
AU  - de Azevedo, I.M.
AU  - Hodon, M.A.
AU  - Mota, P.M.
AU  - Sales, E.B.
AU  - Fonseca, J.A.A.
AU  - Almeida, N.F.
AU  - Araujo, F.R.
TI  - Draft Genome Sequence of Mycobacterium bovis Strain AN5, Used for Production of Purified Protein Derivative.
JO  - Genome Announcements
PY  - 2014
SP  - e00277
EP  - e00214
VL  - 2
AB  - Mycobacterium bovis strain AN5 has been used to produce purified protein derivative (PPD) for
AB  - the intradermal test for bovine tuberculosis since it was introduced in 1948. This work
AB  - reports the draft genome sequence of M. bovis AN5, which is used for the production of bovine
AB  - PPD in Brazil, as well as comparisons to other strains of M. bovis and Mycobacterium
AB  - tuberculosis.
ER  -

TY  - JOUR
AU  - Canosi, U.
AU  - Luder, G.
AU  - Trautner, T.A.
AU  - Bron, S.
TI  - Restriction and modification in B. subtilis:  effects on plasmid transformation.
JO  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection
PY  - 1981
SP  - 179
EP  - 187
VL  - 0
AB  - In previous communications in this series we have demonstrated that bacterial
AB  - transformation is resistent to restriction, whereas transfection is susceptible
AB  - to restriction.  To explain this difference in the behaviour of the two kinds
AB  - of DNA we have postulated that both transforming and transfecting DNA are first
AB  - converted to single stranded DNA molecules in the course of DNA processing.
AB  - Such single stranded transforming DNA would then hybridize to modified host DNA
AB  - of complementary polarity to form donor/recipient complex.  This
AB  - donor/recipient complex represents DNA heterozygous with respect to
AB  - methylation.  It would be highly reactive to become totally modified and hence
AB  - resistant to restriction.  In transfection, DNA/DNA hybridization would be
AB  - between complementary strands of opposite polarity derived from different
AB  - transfecting phage DNA molecules.  These molecules would be double stranded,
AB  - nonmodified in the pairing regions and would hence be substrates for the
AB  - restriction enzyme.  Major support for this interpretation came from
AB  - experiments in which we had demonstrated that transfection of lysogenic cells
AB  - with homologus phage DNA was insensitive to restriction.  This result pointed
AB  - to the important role played by homology between donor and recipient DNA in the
AB  - establishment of DNA taken up by restricting cells.
ER  -

TY  - JOUR
AU  - Cantalupo, G.
AU  - Bucci, C.
AU  - Salvatore, P.
AU  - Pagliarulo, C.
AU  - Roberti, V.
AU  - Lavitola, A.
AU  - Bruni, C.B.
AU  - Alifano, P.
TI  - Evolution and function of the Neisserial dam-replacing gene.
JO  - FEBS Lett.
PY  - 2001
SP  - 178
EP  - 183
VL  - 495
AB  - Phase variation through slippage-like mechanisms involving homopolymeric tracts depends in
AB  - part on the absence of Dam-methylase in
AB  - several pathogenic isolates of Neisseria meningitidis, In Dam-defective
AB  - strains drg (dam-replacing gene), flanked by pseudo-transposable small
AB  - repeated elements (SREs), replaced dam. We demonstrate that drg encodes
AB  - a restriction endonuclease (NmeBII) that cleaves 5'-GmeATC-3'. drg is
AB  - also present in 50% of Neisseria lactamica strains, but in most of them
AB  - it is inactive because of the absence of an SRE-providing, promoter.
AB  - This is associated with the presence of GATmeC suggesting an
AB  - alternative restriction-modification system (RM) specific for
AB  - 5'-GATC-3', similar to Sau3AI-RM of Staphylococcus aureus 3A.
AB  - Lactococcus lactis KR2 and Listeria monocytogenes.
ER  -

TY  - JOUR
AU  - Cao, B.
AU  - Chen, C.
AU  - DeMott, M.S.
AU  - Cheng, Q.
AU  - Clark, T.A.
AU  - Xiong, X.
AU  - Zheng, X.
AU  - Butty, V.
AU  - Levine, S.S.
AU  - Yuan, G.
AU  - Boitano, M.
AU  - Khai, L.
AU  - Song, Yi.
AU  - Zhou, X.
AU  - Deng, Z.
AU  - Turner, S.W.
AU  - Korlach, J.
AU  - You, D.
AU  - Wang, L.
AU  - Chen, S.
AU  - Dedon, P.C.
TI  - Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.
JO  - Nat. Commun.
PY  - 2014
SP  - 3951
EP  - 3951
VL  - 5
AB  - Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and
AB  - often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli
AB  - B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other
AB  - PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes
AB  - of B7A and FF75 with > 90% agreement: single molecule, real-time sequencing and deep
AB  - sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of
AB  - G(ps)AAC/G(ps)TTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT
AB  - in FF75 occurs as a single-strand modification at C(ps)CA, again with only 14% of 160,541
AB  - sites modified. Single-molecule analysis indicates that modification could be partial at any
AB  - particular genomic site even with active restriction by DndF-H, with direct interaction of
AB  - modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results
AB  - point to highly unusual target selection by PT-modification proteins and rule out known R-M
AB  - mechanisms.
ER  -

TY  - JOUR
AU  - Cao, B.
AU  - Ma, T.
AU  - Ren, Y.
AU  - Ren, Y.
AU  - Li, G.
AU  - Li, P.
AU  - Guo, X.
AU  - Ding, P.
AU  - Feng, L.
TI  - Complete Genome Sequence of Pusillimonas sp. T7-7, a cold-tolerate diesel oil-degrading bacterium isolated from the Bohai Sea in China.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4021
EP  - 4022
VL  - 193
AB  - Pusillimonas sp. T7-7 is a diesel oil-degrading cold-tolerate bacterium isolated from the
AB  - benthal mud of petroleum-contaminated site in Bohai Sea,
AB  - China. We present here the complete genome sequence of T7-7. Genome
AB  - analysis revealed many features of typical marine bacteria including the
AB  - absence of intact sugar metabolic pathways, the presence of glyoxylate and
AB  - gluconeogenesis pathways, and the abilities for nitrate assimilation and
AB  - denitrification, as well as sulfate reduction and sulfite oxidation.
AB  - Presence of novel genes for the degradation of diesel oils was suggested.
ER  -

TY  - JOUR
AU  - Cao, Bo.
AU  - Cheng, Q.
AU  - Gu, C.
AU  - Yao, F.
AU  - DeMott, M.S.
AU  - Zheng, X.
AU  - Deng, Z.
AU  - Dedon, P.C.
AU  - You, D.
TI  - Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate- based restriction system in Salmonella.
JO  - Mol. Microbiol.
PY  - 2014
SP  - 776
EP  - 785
VL  - 93
AB  - Prokaryotes protect their genomes from foreign DNA with a diversity of defence mechanisms,
AB  - including a widespread restriction-modification (R-M) system involving phosphorothioate (PT)
AB  - modification of the DNA backbone. Unlike classical R-M systems, highly partial PT modification
AB  - of consensus motifs in bacterial genomes suggests an unusual mechanism of PT-dependent
AB  - restriction. In Salmonella enterica, PT modification is mediated by four genes dptB-E, while
AB  - restriction involves additional three genes dptF-H. Here, we performed a series of studies to
AB  - characterize the PT-dependent restriction, and found that it presented several features
AB  - distinct with traditional R-M systems. The presence of restriction genes in a PT-deficient
AB  - mutant was not lethal, but instead resulted in several pathological phenotypes. Subsequent
AB  - transcriptional profiling revealed the expression of > 600 genes was affected by restriction
AB  - enzymes in cells lacking PT, including induction of bacteriophage, SOS response and DNA
AB  - repair-related genes. These transcriptional responses are consistent with the observation that
AB  - restriction enzymes caused extensive DNA cleavage in the absence of PT modifications in vivo.
AB  - However, overexpression of restriction genes was lethal to the host in spite of the presence
AB  - PT modifications. These results point to an unusual mechanism of PT-dependent DNA cleavage by
AB  - restriction enzymes in the face of partial PT modification.
ER  -

TY  - JOUR
AU  - Cao, D.
TI  - Cosolute effects as probes of the role of water in DNA binding and catalysis by three restriction endonucleases.
JO  - Ph.D. Thesis, University of Pittsburgh
PY  - 2002
SP  - 283
EP  - 283
AB  - Site-specific protein-DNA interactions play important roles in many cellular processes and are
AB  - regulated by many factors, including the amount and type of cytoplasmic solutes.  In this work
AB  - I use restriction endonucleases EcoRI, BamHI and EcoRV endonucleases as models to probe the
AB  - role of water in formation of protein-DNA complexes and to understand how osmolytes
AB  - (cosolutes) promote protein-DNA association.  We observe that many cosolutes facilitate
AB  - specific binding of protein to DNA; however the extent of the effect depends on the
AB  - physico-chemical properties of the cosolute.  Our data show conclusively that cosolute effects
AB  - are best understood from the perspective of 'preferential interaction' rather than those of
AB  - 'osmotic stress' or 'excluded volume effects.  Because we find that triethylene glycol is
AB  - nearly completely excluded from the macromolecular surfaces, we use the dependence of the
AB  - equilibrium association of protein and DNA on TEG concentration to estimate that 430, 350 and
AB  - 450 molecules of H2O are released upon formation of specific EcoRI, BamHI and EcoRV complexes,
AB  - respectively.  The flanking sequence surrounding the specific site affects binding free energy
AB  - but does not affect water stoichiometry.  We show that binding to nonspecific sites involves
AB  - little water release whereas binding to miscognate sites (one incorrect base pair) entails
AB  - intermediate water release.  Thus a massive amount of water release is a thermodynamic
AB  - signature for the formation of the specific complex.  In addition, the experimental
AB  - determination of water release permits us to establish for the first time that the hydrophobic
AB  - effect can provide as much as -80 Kcal/mol, more than half of the driving force for specific
AB  - binding.  There is no dependence on cosolute concentration for cleavage of specific sites.
AB  - This implies that there is no additional release of water in achieving the specific transition
AB  - state complex; thus the specific recognition complex closely resembles the transition-state
AB  - complex.  By contrast, cosolutes enhance the cleavage of miscognate sites; we infer that the
AB  - rearrangements required of the adaptive miscognate complex to achieve the transition state are
AB  - accompanied by further release of water.
ER  -

TY  - JOUR
AU  - Cao, D.
AU  - Ju, Z.
AU  - Gao, C.
AU  - Mei, X.
AU  - Fu, D.
AU  - Zhu, H.
AU  - Luo, Y.
AU  - Zhu, B.
TI  - Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum.
JO  - Gene
PY  - 2014
SP  - 230
EP  - 237
VL  - 550
AB  - Recent studies have reported that decreased level of DNA cytosine methylation in the global
AB  - genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening.
AB  - However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and
AB  - demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases
AB  - were identified in tomato genome, which probably contributed to DNA cytosine methylation level
AB  - in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were
AB  - classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their
AB  - structure and genomic localization was also performed in this paper. According to online
AB  - RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L)
AB  - were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly
AB  - changed during tomato fruit development and ripening. Furthermore, all these five gene
AB  - expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment,
AB  - indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In
AB  - addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the
AB  - nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this
AB  - paper provided a framework for gene discovery and functional characterization of C5-MTases and
AB  - DNA demethylases in other Solanaceae species.
ER  -

TY  - JOUR
AU  - Cao, G.
AU  - Allard, M.W.
AU  - Hoffmann, M.
AU  - Monday, S.R.
AU  - Muruvanda, T.
AU  - Luo, Y.
AU  - Payne, J.
AU  - Rump, L.
AU  - Meng, K.
AU  - Zhao, S.
AU  - McDermott, P.F.
AU  - Brown, E.W.
AU  - Meng, J.
TI  - Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport.
JO  - Genome Announcements
PY  - 2015
SP  - e00027
EP  - e00015
VL  - 3
AB  - Multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Newport has been a
AB  - long-standing public health concern in the United States. We present the complete sequences of
AB  - six IncA/C plasmids from animal-derived MDR S. Newport  ranging from 80.1 to 158.5 kb. They
AB  - shared a genetic backbone with S. Newport IncA/C plasmids pSN254 and pAM04528.
ER  -

TY  - JOUR
AU  - Cao, G.
AU  - Ju, W.
AU  - Rump, L.
AU  - Zhao, S.
AU  - Zou, L.
AU  - Wang, C.
AU  - Strain, E.
AU  - Luo, Y.
AU  - Timme, R.
AU  - Allard, M.
AU  - Brown, E.
AU  - Meng, J.
TI  - Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli  Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00200
EP  - e00213
VL  - 1
AB  - Shiga toxin-producing Escherichia coli (STEC) causes severe illness in humans, including
AB  - hemorrhagic colitis and hemolytic uremic syndrome. A parallel
AB  - evolutionary model was proposed in which E. coli strains of distinct phylogenies
AB  - independently integrate Shiga toxin-encoding genes and evolve into STEC. We
AB  - report the draft genomes of two emerging non-O157 STEC strains.
ER  -

TY  - JOUR
AU  - Cao, G.
AU  - Liu, Y.
AU  - Liu, G.
AU  - Wang, J.
AU  - Wang, G.
TI  - Draft genome sequence of pseudomonas strain p818, isolated from glyphosate-polluted soil.
JO  - Genome Announcements
PY  - 2013
SP  - e01079
EP  - e01013
VL  - 1
AB  - Pseudomonas strain P818 was isolated from glyphosate-polluted soil in China. This bacterium
AB  - presents a capacity for high glyphosate tolerance. We present the draft
AB  - genome sequence of the strain Pseudomonas P818. The genes involved in the
AB  - glyphosate tolerance were identified. This genomic information will facilitate
AB  - the study of glyphosate tolerance mechanisms.
ER  -

TY  - JOUR
AU  - Cao, G.
AU  - Zhang, J.
AU  - Xu, X.
AU  - Jin, H.
AU  - Yang, X.
AU  - Pan, H.
AU  - Allard, M.
AU  - Brown, E.
AU  - Meng, J.
TI  - Whole-Genome Sequences of 12 Clinical Strains of Listeria monocytogenes.
JO  - Genome Announcements
PY  - 2015
SP  - e01203
EP  - e01214
VL  - 3
AB  - Listeria monocytogenes is a foodborne pathogen of global concern due to the high mortality
AB  - rate among immunocompromised patients. Whole-genome sequences of 12 strains of L.
AB  - monocytogenes from humans were reported. The availability of these  genomes should provide
AB  - useful information on the evolutionary history and genetic diversity of L. monocytogenes.
ER  -

TY  - JOUR
AU  - Cao, G.
AU  - Zhao, S.
AU  - Strain, E.
AU  - Luo, Y.
AU  - Timme, R.
AU  - Wang, C.
AU  - Brown, E.
AU  - Meng, J.
AU  - Allard, M.
TI  - Draft Genome Sequences of Eight Salmonella enterica Serotype Newport Strains from Diverse Hosts and Locations.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5146
EP  - 5146
VL  - 194
AB  - Salmonellosis is a major contributor to the global public health burden. Salmonella enterica
AB  - serotype Newport has ranked among three Salmonella serotypes
AB  - most commonly associated with food-borne outbreaks in the United States. It was
AB  - thought to be polyphyletic and composed of independent lineages. Here we report
AB  - draft genomes of eight strains of S. Newport from diverse hosts and locations.
ER  -

TY  - JOUR
AU  - Cao, G.
AU  - Zhong, C.
AU  - Zong, G.
AU  - Fu, J.
AU  - Liu, Z.
AU  - Zhang, G.
AU  - Qin, R.
TI  - Complete Genome Sequence of Streptomyces clavuligerus F613-1, an Industrial Producer of Clavulanic Acid.
JO  - Genome Announcements
PY  - 2016
SP  - e01020
EP  - e01016
VL  - 4
AB  - Streptomyces clavuligerus strain F613-1 is an industrial strain with high-yield clavulanic
AB  - acid production. In this study, the complete genome sequence of S.
AB  - clavuligerus strain F613-1 was determined, including one linear chromosome and
AB  - one linear plasmid, carrying numerous sets of genes involving in the biosynthesis
AB  - of clavulanic acid.
ER  -

TY  - JOUR
AU  - Cao, H.
AU  - Shimura, Y.
AU  - Masanobu, K.
AU  - Yin, Y.
TI  - Draft Genome Sequence of the Toxic Bloom-Forming Cyanobacterium Aphanizomenon flos-aquae NIES-81.
JO  - Genome Announcements
PY  - 2014
SP  - e00044
EP  - e00014
VL  - 2
AB  - Aphanizomenon flos-aquae is a toxic filamentous cyanobacterium that causes water  blooms in
AB  - freshwaters across the globe. We present the draft genome sequence of
AB  - the A. flos-aquae strain NIES-81, which was determined by 454 pyrosequencing
AB  - technology. The draft genome is ~5.7 Mb, containing 5,802 predicted
AB  - protein-coding genes and 58 RNA genes, with a G+C content of 38.5%.
ER  -

TY  - JOUR
AU  - Cao, J.
AU  - Maignien, L.
AU  - Shao, Z.
AU  - Alain, K.
AU  - Jebbar, M.
TI  - Genome Sequence of the Piezophilic, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio indicus J2T.
JO  - Genome Announcements
PY  - 2016
SP  - e00214
EP  - e00216
VL  - 4
AB  - The complete genome sequence ofDesulfovibrio indicusJ2(T), a member of the
AB  - familyDesulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes
AB  - 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding
AB  - genes. The genome is consistent with a heterotrophic, anaerobic lifestyle
AB  - including the sulfate reduction pathway.
ER  -

TY  - JOUR
AU  - Cao, W.
TI  - Binding kinetics and footprinting of TaqI endonuclease: Effects of metal cofactors on sequence-specific interactions.
JO  - Biochemistry
PY  - 1999
SP  - 8080
EP  - 8087
VL  - 38
AB  - Restriction endonucleases achieve sequence-specific recognition and strand cleavage through
AB  - the interplay of base, phosphate backbone, and metal cofactor interactions. In this study, we
AB  - investigate the binding kinetics of TaqI endonuclease using the wild-type enzyme and a binding
AB  - proficient, catalysis deficient mutant TaqI-D137A both in the absence of a metal cofactor and
AB  - in the presence of Mg2+ or Ca2+. As demonstrated by gel mobility shift analyses, TaqI
AB  - endonuclease requires a metal cofactor for achieving high-affinity specific binding to its
AB  - cognate sequence, TCGA. In the absence of a metal cofactor, the enzyme binds all DNA sequences
AB  - (TaqI cognate site, star site, and nonspecific site) with essentially equal affinity, thereby
AB  - exhibiting little discrimination. The dissociation constant of the cognate sequence in the
AB  - presence of Mg2+ at 60 degrees C is 0.26 nM, a value comparable to our previously reported Km
AB  - of 0.5 nM measured under steady-state conditions. The TaqI-TCGA-Mg2+ complex is stable, with a
AB  - half-life of 21 min at 60 degrees C. The boundary of the protein-DNA interface is approximated
AB  - to be about 18 bp as determined by DNase I footprinting. Data from this study support the
AB  - notion that a metal cofactor plays a critical role for achieving sequence-specific
AB  - discrimination in a subset of nucleases, including TaqI, EcoRV, and others.
ER  -

TY  - JOUR
AU  - Cao, W.
AU  - Barany, F.
TI  - Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 33002
EP  - 33010
VL  - 273
AB  - Metal cofactors (Mg2+ and Mn2+) modulate both specific DNA binding and strand cleavage in the
AB  - TaqI endonuclease.  This work attempts to establish the structural basis of TaqI-DNA-metal2+
AB  - interactions using an affinity cleavage technique.  The protein was cleaved by localized
AB  - hydroxyl radicals generated by oxidizing Fe2+ within the metal binding sites.  Cleavage
AB  - fragments were separated by SDS-polyacrylamide gel electrophoresis, and cleavage sites were
AB  - determined using micropeptide sequencing.  Eleven amino acid residues in the vicinity of
AB  - cleavage sites were selected for site-directed mutagenesis.  The negative charge at Asp137 is
AB  - essential for DNA cleavage but not required for sequence specific binding.  Mutations at
AB  - Asp142 abolish both specific binding and catalysis, except for D142E, which converts TaqI into
AB  - a completely Mn2+-dependent endonuclease.  The positive charge at Lys158 appears to be
AB  - important for both specific binding and catalysis.  Mutations at other sites affect binding
AB  - and/or catalysis to different degrees, except Trp113 and Glu135, which appear to be
AB  - nonessential for the TaqI enzyme activity.  The critical residues for TaqI function are
AB  - distinct from the PDX14-20(E/D)XK catalytic motif elucidated from other endonucleases.
ER  -

TY  - JOUR
AU  - Cao, W.
AU  - Lu, J.
TI  - Exploring the catalytic center of TaqI endonuclease: rescuing catalytic activity by double mutations and Mn(2+).
JO  - Biochim. Biophys. Acta
PY  - 2001
SP  - 253
EP  - 260
VL  - 1546
AB  - TaqI is a metal-dependent endonuclease that recognizes T^CGA, with the arrow
AB  - indicating the cleavage site. Mutations at K158 render the enzyme inactive and mutations at
AB  - K157 significantly reduce DNA cleavage activity (W. Cao and F. Barany (1998) J. Biol. Chem.
AB  - 273, 33002-33010). Aspartate, glutamate, and histidine substitutions were made at K158 in the
AB  - wild-type and K157S mutant TaqI endonuclease to understand the functional organization of the
AB  - active site. None of the mutants was active with Mg(2+), but the DNA cleavage activities were
AB  - partly rescued by Mn(2+) for K157S-K158E and K157S-K158H mutants. The rescuing effects were
AB  - observed with Mn(2+) but not with other divalent cations. K157S-K158E required higher Mn(2+)
AB  - concentrations than the wild-type enzyme for DNA cleavage activity, suggesting that a Mn(2+)
AB  - ion is weakly bound at the 158 position. The need to neutralize K157 to recover the catalytic
AB  - activity of K158E and K158H indicates that K158 and K157 may interact functionally. In analogy
AB  - with EcoRV, Ca(2+) stimulated Mn(2+)-mediated cleavage for the wild-type TaqI, suggesting the
AB  - existence of at least two metal ions at the catalytic center. A catalytic mechanism involving
AB  - two metal ions and the K157-K158 pair is proposed for TaqI endonuclease.
ER  -

TY  - JOUR
AU  - Cao, W.
AU  - Lu, J.
AU  - Barany, F.
TI  - Nucleotide sequences and gene organization of TaqI endonuclease isoschizomers from Thermus sp. SM32 and Thermus filiformis Tok6AI.
JO  - Gene
PY  - 1997
SP  - 205
EP  - 214
VL  - 197
AB  - Eight TaqI isoschizomer genes, two from Yellowstone National Park, one from Japan, two from
AB  - New Zealand, two from Portugal, and one from the Azores (1000 miles west of Portugal), were
AB  - PCR-amplified and sequenced.  Sequence alignment of isoschizomers isolated from close
AB  - geographical locations shows identical or almost identical protein sequences, while
AB  - isoschizomers from distant sites demonstrate considerable diversity, ranging from 54 to 75% in
AB  - amino acid identity.  Accordingly, these isoschizomers were arranged into four geographical
AB  - groups, i.e., USA as represented by Thermus aquaticus YT1, Japan by Thermus thermophilus HB8,
AB  - New Zealand by thermus filiformis Tok5AI, Portugal by Thermus sp. SM32.  The complete ORFs of
AB  - two new representative genes, tfiTok6AII and tsp32IR, were obtained by bubble PCR.  Unlike
AB  - M.TaqI-R.TaqI and M.TthHB81-R.TthHB8I which exhibit an unusual 13-codon overlap, the methylase
AB  - and endonuclease genes are each separated by 15 nucleotides in the TfiTok6AII and Tsp32IR
AB  - restriction-modification systems.  Phylogenetic analysis suggests that initially TfiTok6AII
AB  - diverged from a common ancestor, then Tsp32IR branched out, and finally TaqI and TthHB8I
AB  - diverged from each other during evolution.
ER  -

TY  - JOUR
AU  - Cao, W.
AU  - Lu, J.
AU  - Welch, S.G.
AU  - Williams, R.A.D.
AU  - Barany, F.
TI  - Cloning and thermostability of TaqI endonuclease isoschizomers from Thermus species SM32 and Thermus filiformis Tok6A1.
JO  - Biochem. J.
PY  - 1998
SP  - 425
EP  - 431
VL  - 333
AB  - Two TaqI endonuclease (hereafter referred to as TaqI) isoschizomer genes, tsp32IR from Thermus
AB  - species SM32 of Azores and tfiTok6A1I from T. filiformis Tok6A1 of New Zealand, were cloned in
AB  - Escherichia coli.  The overexpressed enzymes were partly purified and their thermostability
AB  - was determined.  In the medium-salt buffer, Tsp32IR, TfiTok6A1I and one previously cloned TaqI
AB  - isoschizomer (TthHB8I) were more thermostable than TaqI.  Tsp32IR remained partly active up to
AB  - 90 C in the low-salt buffer.  Six amino acid residues that are identical in the three high
AB  - thermostability isoschizomers (Tsp32IR, TfiTok6A1I and TthHB8I) but differ in TaqI might
AB  - provide added rigidity for thermostabilization.  These include four proline residues located
AB  - in or near loop regions, and one alanine and one arginine located at helix regions in the
AB  - predicted TaqI endonuclease secondary structure.  The possible role of these residues in
AB  - thermostabilization was evaluated by mutagenizing the TaqI enzyme.  Mutants generated at these
AB  - six positions were less thermostable than wild-type TaqI.  The results suggest that the
AB  - surrounding sequence or structural context might be as important as the mutation itself.
ER  -

TY  - JOUR
AU  - Cao, W.
AU  - Mayer, A.N.
AU  - Barany, F.
TI  - Stringent and relaxed specificities of TaqI endonuclease: interactions with metal cofactors and DNA sequences.
JO  - Biochemistry
PY  - 1995
SP  - 2276
EP  - 2283
VL  - 34
AB  - We have studied the roles of metal cofactors Mg2+ and Mn2+ in modulating substrate
AB  - specificities during the enzymatic cycle of TaqI endonuclease using steady state and
AB  - single-turnover kinetics. In the presence of Mg2+, stringent discrimination of TaqI against
AB  - single base-pair changes (star sites) is manifested by the loss of tight, specific binding in
AB  - the early stage of the enzymatic cycle. In the presence of Mn2+, relaxed specificity for a
AB  - star site sequence is attributed to formation of three distinct classes of the ternary
AB  - complexes: the highly activated TaqI-cognate-Mn2+ complex; the partially activated
AB  - TaqI-star-Mn2+-complex; and the ground state, inactive TaqI-nonspecific-Mn2+ complex. In
AB  - addition to a high affinity for a TaqI-DNA complex, Mn2+ also binds to TaqI in a
AB  - DNA-independent fashion. This may facilitate enzyme activation, which could account for the
AB  - observed relaxation in substrate specificity. Thus, the TaqI-DNA-Mn2+ could be formed by
AB  - either of two pathways: TaqI binding to DNA followed by the binding of Mn2+ or TaqI first
AB  - binding to Mn2+ followed by the addition of DNA. The inactive, nonspecific TaqI-star-Mg2+
AB  - complex virtually prohibits transition state interactions, but a TaqI-star-Mn2+ complex
AB  - attains a measurable single-turnover rate. In the late stages of the enzymatic cycle, high
AB  - affinity of Mn2+ to a TaqI-DNA complex and to the TaqI enzyme may also account for a slower
AB  - rate of product release.
ER  -

TY  - JOUR
AU  - Cao, X.
AU  - Li, Z.
AU  - Lou, Z.
AU  - Fu, B.
AU  - Liu, Y.
AU  - Shang, Y.
AU  - Jing, Z.
AU  - Zhou, J.
TI  - Whole-Genome Sequences of Brucella melitensis Strain QY1, Isolated from Sheep in  Gansu, China.
JO  - Genome Announcements
PY  - 2017
SP  - e00896
EP  - e00817
VL  - 5
AB  - The facultative intracellular Gram-negative bacterium Brucella melitensis causes  brucellosis
AB  - in domestic and wild mammals, and it is a dominant pathogen
AB  - responsible for human disease. This study reports the whole-genome sequencing of
AB  - B. melitensis strain QY1, isolated from sheep suffering from abortion and
AB  - arthritis in 2015 in Gansu, China.
ER  -

TY  - JOUR
AU  - Cao, X.
AU  - Li, Z.
AU  - Lou, Z.
AU  - Fu, B.
AU  - Liu, Y.
AU  - Shang, Y.
AU  - Zhou, J.
AU  - Jing, Z.
TI  - Whole-Genome Sequences of Brucella melitensis Strain QH61, Isolated from Yak in Qinghai, China.
JO  - Genome Announcements
PY  - 2018
SP  - e01422
EP  - e01417
VL  - 6
AB  - The facultative intracellular Gram-negative bacterium Brucella melitensis causes  brucellosis
AB  - in domestic and wild mammals. Brucella melitensis QH61 was isolated
AB  - from a yak suffering from abortion in 2015 in Qinghai, China. Here, we report the
AB  - whole-genome sequence of B. melitensis strain QH61.
ER  -

TY  - JOUR
AU  - Cao, X.
AU  - Springer, N.M.
AU  - Muszynski, M.G.
AU  - Phillips, R.L.
AU  - Kaeppler, S.
AU  - Jacobsen, S.E.
TI  - Conserved plant genes with similarity to mammalian de novo DNA methyltransferases.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 4979
EP  - 4984
VL  - 97
AB  - DNA methylation plays a critical role in controlling states of gene activity in most
AB  - eukaryotic organisms, and it is essential for proper growth and development. Patterns of
AB  - methylation are established by de novo methyltransferases and maintained by maintenance
AB  - methyltransferase activities. The Dnmt3 family of de novo DNA methyltransferases has recently
AB  - been characterized in animals. Here we describe DNA methyltransferase genes from both
AB  - Arabidopsis and maize that show a high level of sequence similarity to Dnmt3, suggesting that
AB  - they encode plant de novo methyltransferases. Relative to all known eukaryotic
AB  - methyltransferases, these plant proteins contain a novel arrangement of the motifs required
AB  - for DNA methyltransferase catalytic activity. The N termini of these methyltransferases
AB  - contain a series of ubiquitin-associated (UBA) domains. UBA domains are found in several
AB  - ubiquitin pathway proteins and in DNA repair enzymes such as Rad23, and they may be involved
AB  - in ubiquitin binding. The presence of UBA domains provides a possible link between DNA
AB  - methylation and ubiquitin/proteasome pathways.
ER  -

TY  - JOUR
AU  - Cao, X.F.
AU  - Aufsatz, W.
AU  - Zilberman, D.
AU  - Mette, M.F.
AU  - Huang, M.S.
AU  - Matzke, M.
AU  - Jacobsen, S.E.
TI  - Role of the DRM and CMT3 Methyltransferases in RNA-directed DNA methylation.
JO  - Curr. Biol.
PY  - 2003
SP  - 2212
EP  - 2217
VL  - 13
AB  - RNA interference is a conserved process in which double-stranded RNA is processed into 21-25
AB  - nucleotide siRNAs that trigger posttranscriptional
AB  - gene silencing. In addition, plants display a phenomenon termed
AB  - RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to
AB  - silenced RNA is de novo methylated at its cytosine residues. This
AB  - methylation is not only at canonical CpG sites but also at cytosines in
AB  - CpNpG and asymmetric sequence contexts. In this report, we study the role
AB  - of the DRM and CMT3 DNA methyltransferase genes in the initiation and
AB  - maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance
AB  - of preestablished RNA-directed CpG methylation. However, drm mutants
AB  - showed a nearly complete loss of asymmetric methylation and a partial loss
AB  - of CpNpG methylation. The remaining asymmetric and CpNpG methylation was
AB  - dependent on the activity of CMT3, showing that DRM and CMT3 act
AB  - redundantly to maintain non-CpG methylation. These DNA methyltransferases
AB  - appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants
AB  - show a lack of non-CpG methylation but elevated levels of siRNAs. Finally,
AB  - we demonstrate that DRM activity is required for the initial establishment
AB  - of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric
AB  - sites.
ER  -

TY  - JOUR
AU  - Cao, X.F.
AU  - Jacobsen, S.E.
TI  - Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing.
JO  - Curr. Biol.
PY  - 2002
SP  - 1138
EP  - 1144
VL  - 12
AB  - Proper DNA methylation patterning requires the complementary processes of de novo methylation
AB  - (the initial methylation of unmethylated DNA
AB  - sequences) and maintenance methylation (the faithful replication of
AB  - preexisting methylation). Arabidopsis has two types of
AB  - methyltransferases with demonstrated maintenance activity: MET1, which
AB  - maintains CpG methylation [1-3] and is homologous to mammalian DNMT1,
AB  - and CHROMOMETHYLASE 3 (CMT3), which maintains CpNpG (N = A, T, C, or G)
AB  - methylation [3,4] and is unique to the plant kingdom. Here we describe
AB  - loss-of-function mutations in the Arabidopsis DOMAINS REARRANGED
AB  - METHYLASE (DRM) genes [5] and provide evidence that they encode de novo
AB  - methyltransferases. drm1 drm2 double mutants retained preexisting CpG
AB  - methylation at the endogenous FWA locus but blocked de novo CpG
AB  - methylation that is normally associated with FWA transgene silencing.
AB  - Furthermore, drm1 drm2 double mutants blocked de novo CpNpG and
AB  - asymmetric methylation and gene silencing of the endogenous SUPERMAN
AB  - (SUP) gene, which is normally triggered by an inverted SUP repeat.
AB  - However, drm1 drm2 double mutants did not show reactivation of
AB  - previously established SUPERMAN epigenetic silenced alleles. Thus, drm
AB  - mutants prevent the establishment but not the maintenance of gene
AB  - silencing at FWA and SUP, suggesting that the DRMs encode the major de
AB  - novo methylation enzymes affecting these genes.
ER  -

TY  - JOUR
AU  - Cao, X.F.
AU  - Jacobsen, S.E.
TI  - Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 16491
EP  - 16498
VL  - 99
AB  - Many plant, animal, and fungal genomes contain cytosine DNA methylation in asymmetric sequence
AB  - contexts (CpHpH, H = A, T, C). Although the enzymes responsible for this methylation are
AB  - unknown, it has been assumed that asymmetric methylation is maintained by the persistent
AB  - activity of de novo methyltransferases (enzymes capable of methylating previously unmodified
AB  - DNA). We recently reported that the domains rearranged methylase (DRM) genes are required for
AB  - de novo DNA methylation in Arabidopsis thaliana because drm1 drm2 double mutants lack the de
AB  - novo methylation normally associated with transgene silencing. In this study, we have used
AB  - bisulfite sequencing and Southern blot analysis to examine the role of the DRM loci in the
AB  - maintenance of asymmetric methylation. At some loci, drm1 drm2 double mutants eliminated all
AB  - asymmetric methylation. However, at the SUPERMAN locus, asymmetric methylation was only
AB  - completely abolished in drm1 drm2 chromomethylase 3 (cmt3) triple mutant plants. drm1 drm2
AB  - double mutants also showed a strong reduction of CpNpG (n = A, T, C, or G) methylation at some
AB  - loci, but not at others. The drm1 drm2 cmt3 triple mutant plants did not affect CpG
AB  - methylation at any locus tested, suggesting that the primary CpG methylases are encoded by the
AB  - MET1 class of genes. Although neither the drm1 drm2 double mutants nor the cmt3 single mutants
AB  - show morphological defects, drm1 drm2 cmt3 triple mutant plants show pleiotropic effects on
AB  - plant development. Our results suggest that the DRM and CMT3 genes act in a partially
AB  - redundant and locus-specific manner to control asymmetric and CpNpG methylation.
ER  -

TY  - JOUR
AU  - Cao, X.M.
AU  - Chen, T.
AU  - Xu, L.Z.
AU  - Yao, L.S.
AU  - Qi, J.
AU  - Zhang, X.L.
AU  - Yan, Q.L.
AU  - Deng, Y.H.
AU  - Guo, T.Y.
AU  - Wang, J.
AU  - Hu, K.X.
AU  - Xu, B.L.
TI  - Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain SH04, Isolated from Chrysomya megacephala Collected from Pudong International Airport  in China.
JO  - Genome Announcements
PY  - 2013
SP  - e0011913
EP  - e0011913
VL  - 1
AB  - Wohlfahrtiimonas chitiniclastica bacilli that live in the larvae of a parasitic fly were
AB  - recently isolated and are speculated to be the cause of fulminant
AB  - sepsis. Here we report and analyze the complete genome sequence of
AB  - Wohlfahrtiimonas chitiniclastica strain SH04. No complete genome sequence of a
AB  - Wohlfahrtiimonas chitiniclastica isolate has been documented previously.
ER  -

TY  - JOUR
AU  - Cao, Y.
AU  - Liu, X.F.
AU  - Zhang, H.L.
AU  - Chen, Y.J.
AU  - Hu, C.J.
TI  - Draft Genome Sequence of the Human-Pathogenic Bacterium Vibrio alginolyticus E0666.
JO  - Genome Announcements
PY  - 2013
SP  - e00686
EP  - e00613
VL  - 1
AB  - Vibrio alginolyticus is a Gram-negative halophilic bacterium with worldwide distribution. In
AB  - this work, we report the draft genome sequence of a V.
AB  - alginolyticus strain (E0666) isolated from Epinephelus coioides ascites in the
AB  - Shantou city of Guangdong Province, China.
ER  -

TY  - JOUR
AU  - Cao, Y.
AU  - Tian, B.
AU  - Liu, Y.
AU  - Cai, L.
AU  - Wang, H.
AU  - Lu, N.
AU  - Wang, M.
AU  - Shang, S.
AU  - Luo, Z.
AU  - Shi, J.
TI  - Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance.
JO  - Genome Announcements
PY  - 2013
SP  - e00125
EP  - e00113
VL  - 1
AB  - Ralstonia solanacearum strain FQY_4 was isolated from a bacterial wilt nursery, which is used
AB  - for breeding crops for Ralstonia resistance in China. Here, we
AB  - report the complete genome sequence of FQY_4 and its comparison with other
AB  - published R. solanacearum genomes, especially with the strains GMI1000 and Y45 in
AB  - the same group.
ER  -

TY  - JOUR
AU  - Capowski, E.E.
AU  - Wells, J.M.
AU  - Karrer, K.M.
TI  - Maintenance of methylation patterns in Tetrahymena thermophila.
JO  - Gene
PY  - 1988
SP  - 103
EP  - 104
VL  - 74
AB  - Historically, the maintenance of methylation paterns in differentiated cells has been
AB  - attributed to the action of a methyltransferase that functions after DNA replication and whose
AB  - target is palindromic, hemimethylated sites. This maintenance methyltransferase is thought to
AB  - methylate the daughter strand of newly replicated DNA, thus retaining the pattern of the
AB  - parent through successive divisions. We have begun a molecular anlaysis of the maintenance of
AB  - methylation patterns during somatic proliferation in the ciliated protozoan Tetrahymena
AB  - thermophila. The data we have accumulated indicate that this process is more complex than a
AB  - semiconservative copying model.
ER  -

TY  - JOUR
AU  - Capozzi, V.
AU  - Russo, P.
AU  - Lamontanara, A.
AU  - Orru, L.
AU  - Cattivelli, L.
AU  - Spano, G.
TI  - Genome Sequences of Five Oenococcus oeni Strains Isolated from Nero Di Troia Wine from the Same Terroir in Apulia, Southern Italy.
JO  - Genome Announcements
PY  - 2014
SP  - e01077
EP  - e01014
VL  - 2
AB  - Oenococcus oeni is the principal lactic acid bacterium responsible for malolactic fermentation
AB  - in wine. Here, we announce the genome sequences of five O. oeni
AB  - strains isolated from Nero di Troia wine undergoing spontaneous malolactic
AB  - fermentation, and we report, for the first time, several genome sequences of
AB  - strains isolated from the same terroir.
ER  -

TY  - JOUR
AU  - Cappelletti, M.
AU  - Di Gennaro, P.
AU  - D'Ursi, P.
AU  - Orro, A.
AU  - Mezzelani, A.
AU  - Landini, M.
AU  - Fedi, S.
AU  - Frascari, D.
AU  - Presentato, A.
AU  - Zannoni, D.
AU  - Milanesi, L.
TI  - Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds.
JO  - Genome Announcements
PY  - 2013
SP  - e00657
EP  - e00613
VL  - 1
AB  - Rhodococcus sp. strain BCP1 cometabolizes chlorinated compounds and mineralizes a broad range
AB  - of alkanes, as it is highly tolerant to them. The high-quality draft
AB  - genome sequence of Rhodococcus sp. strain BCP1, consisting of 6,231,823 bp, with
AB  - a G+C content of 70.4%, 5,902 protein-coding genes, and 58 RNA genes, is
AB  - presented here.
ER  -

TY  - JOUR
AU  - Carasso, E.
AU  - Salmon-Divon, M.
AU  - Carmeli, Y.
AU  - Banin, E.
AU  - Navon-Venezia, S.
TI  - Draft Genome Sequences of Two Multidrug-Resistant Extended-Spectrum-beta-Lactamase-Producing Klebsiella pneumoniae Strains Causing   Bloodstream Infections.
JO  - Genome Announcements
PY  - 2016
SP  - e01533
EP  - e01515
VL  - 4
AB  - Multidrug-resistant (MDR) Klebsiella pneumoniae has become a major contributor to nosocomial
AB  - bloodstream infections. Here, we report the draft genome sequences of
AB  - two MDR extended-spectrum-beta-lactamase-producing strains causing bloodstream
AB  - infections. These sequenced genomes display a wide-spectrum virulence arsenal and
AB  - will help us understand the genomic basis of K. pneumoniae virulence.
ER  -

TY  - JOUR
AU  - Carattoli, A.
AU  - Villa, L.
AU  - Poirel, L.
AU  - Bonnin, R.A.
AU  - Nordmann, P.
TI  - Evolution of IncA/C blaCMY-2-Carrying Plasmids by Acquisition of the blaNDM-1 Carbapenemase Gene.
JO  - Antimicrob. Agents Chemother.
PY  - 2012
SP  - 783
EP  - 786
VL  - 56
AB  - The bla(NDM-1) gene has been reported to be often located on broad-host-range
AB  - plasmids of the IncA/C type in clinical but also environmental bacteria recovered
AB  - from the New Delhi, India, area. IncA/C-type plasmids are the main vehicles for
AB  - the spread of the cephalosporinase gene bla(CMY-2), frequently identified in the
AB  - United States, Canada, and Europe. In this study, we completed the sequence of
AB  - IncA/C plasmid pNDM-KN carrying the bla(NDM-1) gene, recovered from a Klebsiella
AB  - pneumoniae isolate from Kenya. This sequence was compared with those of three
AB  - IncA/C-type reference plasmids from Escherichia coli, Yersinia ruckeri, and
AB  - Photobacterium damselae. Comparative analysis showed that the bla(NDM-1) gene was
AB  - located on a widely diffused plasmid scaffold known to be responsible for the
AB  - spread of bla(CMY-2)-like genes and consequently for resistance to broad-spectrum
AB  - cephalosporins. Considering that IncA/C plasmids possess a broad host range, this
AB  - scaffold might support a large-scale diffusion of the bla(NDM-1) gene among
AB  - Gram-negative rods.
ER  -

TY  - JOUR
AU  - Carballeira, N.
AU  - Jorge, Y.
AU  - Guerra, M.
AU  - Madrazo, J.J.
AU  - Lleonart, R.
AU  - Silva, A.
AU  - Garcia, O.
AU  - De La Fuente, J.
AU  - Herrera, L.
TI  - Cloning and characterization of the PvuII restriction-modification system in Proteus vulgaris.  Purification of recombinant restrictase.
JO  - Biotecnol. Apl.
PY  - 1990
SP  - 167
EP  - 175
VL  - 7
AB  - The PvuII restriction-modification system (RMS) from P. vulgaris was cloned and
AB  - expressed restrictase and methylase were studied in different E. coli strains.
AB  - Only the E. coli strain HB101 (mcrB-) was efficiently transformed by plasmids
AB  - carrying the RMSII PvuII.  A new procedure for the purification of recombinant
AB  - PvuII restrictase was applied, using ion exchange chromatography.  The methods
AB  - described in this paper allow the obtention of high amounts of PvuII
AB  - restrictase free of contaminants.
ER  -

TY  - JOUR
AU  - Carbonari, C.C.
AU  - Fittipaldi, N.
AU  - Teatero, S.
AU  - Athey, T.B.
AU  - Pianciola, L.
AU  - Masana, M.
AU  - Melano, R.G.
AU  - Rivas, M.
AU  - Chinen, I.
TI  - Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina.
JO  - Genome Announcements
PY  - 2016
SP  - e01341
EP  - e01316
VL  - 4
AB  - Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human
AB  - infections and outbreaks. In this work, we report the availability
AB  - of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in
AB  - Argentina.
ER  -

TY  - JOUR
AU  - Carbone, I.
AU  - Anderson, J.B.
AU  - Kohn, L.M.
TI  - A group-I intron in the mitochondrial small subunit ribosomal RNA gene of Sclerotinia sclerotiorum.
JO  - Curr. Genet.
PY  - 1995
SP  - 166
EP  - 176
VL  - 27
AB  - A 1,380-bp intervening sequence within the mitochondrial small subunit
AB  - ribosomal RNA (mt SSU rRNA) gene of the fungus Sclerotinia sclerotiorum
AB  - has been sequenced and identified as a group-I intron. This is the first
AB  - report of an intron in the mt SSU rRNA gene. The intron shows close
AB  - similarity in secondary structure to the subgroup-IC2 introns from
AB  - Podospora (ND3i1, ND5i2, and COIi5) and Neurospora (ND5i1). The intron has
AB  - an open reading frame (ORF) that encodes a putative protein of 420 amino
AB  - acids which contains two copies of the LAGLI-DADG motif. The ORF belongs
AB  - to a family of ORFs identified in Podospora (ND3i1, ND4Li1, ND4Li2, ND5i2,
AB  - and COIi5) and Neurospora (ND5i1). The putative 420-aa polypeptide is also
AB  - similar to a site-specific endonuclease in the chloroplast large subunit
AB  - ribosomal RNA (LSU rRNA) gene of the green alga Chlamydomonas eugametos.
AB  - In each clone of S. sclerotiorum examined, including several clones which
AB  - were sampled over a 3-year period from geographically separated sites, all
AB  - isolates either had the intron or lacked the intron within the mt SSU rRNA
AB  - gene. Screening by means of Southern hybridization and PCR amplification
AB  - detected the intron in the mt SSU rRNA genes of S. minor, S. trifoliorum
AB  - and Sclerotium cepivorum, but not in other members of the Sclerotiniaceae,
AB  - such as Botrytis anamorphs of Botryotinia spp., or in other ascomycetous
AB  - and basidiomycetous fungi.
ER  -

TY  - JOUR
AU  - Card, C.O.
AU  - Wilson, G.G.
AU  - Weule, K.
AU  - Hasapes, J.
AU  - Kiss, A.
AU  - Roberts, R.J.
TI  - Cloning and characterization of the HpaII methylase gene.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1377
EP  - 1383
VL  - 18
AB  - The HpaII restriction-modification system from Haemophilus parainfluenzae
AB  - recognizes the DNA sequence CCGG.  The gene for the HpaII methylase has been
AB  - cloned into E. coli and its nucleotide sequence has been determined.  The DNA
AB  - of the clones is fully protected against cleavage by the HpaII restriction
AB  - enzyme in vitro, indicating that the methylase gene is active in E. coli.  The
AB  - clones were isolated in an McrA- strain of E. coli; attempts to isolate them in
AB  - an McrA+ strain were unsuccessful.  The clones do not express detectable HpaII
AB  - restriction endonuclease activity, suggesting that either the endonuclease gene
AB  - is not expressed well in E. coli, or that it is not present in its entirety in
AB  - any of the clones that we have isolated.  The derived amino acid sequence of
AB  - the HpaII methylase shows overall similarity to other cytosine methylases.  It
AB  - bears a particularly close resemblance to the sequences of the HhaI, BsuFI and
AB  - MspI methylases.  When compared with three other methylases that recognize
AB  - CCGG, the variable region of the HpaII methylase, which is believed to be
AB  - responsible for sequence specific recognition, shows some similarity to the
AB  - corresponding regions of the BsuFI and MspI methylases, but is rather
AB  - dissimilar to that of the SPR methylase.
ER  -

TY  - JOUR
AU  - Cardenas, J.P.
AU  - Lazcano, M.
AU  - Ossandon, F.J.
AU  - Corbett, M.
AU  - Holmes, D.S.
AU  - Watkin, E.
TI  - Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647.
JO  - Genome Announcements
PY  - 2014
SP  - e01153
EP  - e01114
VL  - 2
AB  - The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are  described
AB  - here. An analysis of the predicted genes enriches our knowledge of the
AB  - molecular basis of iron oxidation, improves our understanding of its role in
AB  - industrial bioleaching, and suggests how it is adapted to live at extremely low
AB  - pH.
ER  -

TY  - JOUR
AU  - Cardinali-Rezende, J.
AU  - Alexandrino, P.M.
AU  - Nahat, R.A.
AU  - Sant'Ana, D.P.
AU  - Silva, L.F.
AU  - Gomez, J.G.
AU  - Taciro, M.K.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain LFM046, a Producer of Medium-Chain-Length Polyhydroxyalkanoate.
JO  - Genome Announcements
PY  - 2015
SP  - e00966
EP  - e00915
VL  - 3
AB  - Pseudomonas sp. LFM046 is a medium-chain-length polyhydroxyalkanoate (PHAMCL) producer capable
AB  - of using various carbon sources (carbohydrates, organic acids,
AB  - and vegetable oils) and was first isolated from sugarcane cultivation soil in
AB  - Brazil. The genome sequence was found to be 5.97 Mb long with a G+C content of
AB  - 66%.
ER  -

TY  - JOUR
AU  - Cardinali-Rezende, J.
AU  - Nahat, R.A.
AU  - Guzman, M.C.W.
AU  - Carreno, F.C.R.
AU  - Silva, L.F.
AU  - Taciro, M.K.
AU  - Gomez, J.G.
TI  - Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating  Strain Isolated from Peru.
JO  - Genome Announcements
PY  - 2016
SP  - e01598
EP  - e01515
VL  - 4
AB  - Halomonas sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic
AB  - heterotrophic bacterium accumulating poly-3-hydroxybutyrate and
AB  - poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from different carbon sources. Here,
AB  - we report the draft genome sequence of this isolate, which was found to be
AB  - 3,665,487 bp long, with a G+C content of 68%.
ER  -

TY  - JOUR
AU  - Cardoso, M.C.
AU  - Leonhardt, H.
TI  - DNA methyltransferase is actively retained in the cytoplasm during early development.
JO  - J. Cell Biol.
PY  - 1999
SP  - 25
EP  - 32
VL  - 147
AB  - The overall DNA methylation level sharply decreases from the zygote to the blastocyst stage
AB  - despite the presence of high levels of DNA methyltransferase (Dnmt1). Surprisingly, the enzyme
AB  - is localized in the cytoplasm of early embryos despite the presence of several functional
AB  - nuclear localization signals. We mapped a region in the NH(2)-terminal, regulatory domain of
AB  - Dnmt1 that is necessary and sufficient for cytoplasmic retention during early development.
AB  - Altogether, our results suggest that Dnmt1 is actively retained in the cytoplasm, which
AB  - prevents binding to its DNA substrate in the nucleus and thereby contributes to the erasure of
AB  - gamete-specific epigenetic information during early mammalian development.
ER  -

TY  - JOUR
AU  - Cardozo, F.A.
AU  - Alfonso, V.N.C.
AU  - Zimpel, C.K.
AU  - Pessoa, A.
AU  - Rivera, I.N.
TI  - Draft Genome Sequence of Aeromonas caviae CH129, a Marine-Derived Bacterium Isolated from the Coast of Sao Paulo State, Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01336
EP  - e01316
VL  - 4
AB  - We report here the draft genome sequence of Aeromonas caviae CH129, a marine-derived bacterium
AB  - isolated from the coast of Sao Paulo state, Brazil.
AB  - Genomic analysis revealed genes encoding enzymes involved in binding, transport,
AB  - and chitin metabolism and different virulence-associated factors.
ER  -

TY  - JOUR
AU  - Cardozo, F.A.
AU  - Zimpel, C.K.
AU  - Guimaraes, A.M.
AU  - Pessoa, A.
AU  - Rivera, I.N.
TI  - Draft Genome Sequence of Marine-Derived Aeromonas caviae CHZ306, a Potential Chitinase Producer Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01293
EP  - e01216
VL  - 4
AB  - We report here a draft genome sequence of Aeromonas caviae CHZ306, a marine-derived bacterium
AB  - with the ability to hydrolyze chitin and express high
AB  - levels of chitinases. The assembly resulted in 65 scaffolds with approximately
AB  - 4.78 Mb. Genomic analysis revealed different genes encoding chitin-degrading
AB  - enzymes that can be used for chitin derivative production.
ER  -

TY  - JOUR
AU  - Carignani, G.
AU  - Groudinsky, O.
AU  - Frezza, D.
AU  - Schiavon, E.
AU  - Bergantino, E.
AU  - Slonimski, P.P.
TI  - An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae.
JO  - Cell
PY  - 1983
SP  - 733
EP  - 742
VL  - 35
AB  - We have localized ten oxi3- mutations in the first, ai1, intron of the coxI gene.  All are
AB  - splicing deficient, being unable to excise the intron.  Complementation experiments disclose
AB  - several domains in the intron ai1: the 5'-proximal and 3'-proximal domains harbor
AB  - cis-dominant mutations, while trans-recessive ones are located in the intron's open reading
AB  - frame.  Comprehensive analyses of allele-specific polypeptides accumulating in mutants show
AB  - that they result from the translation of the intron's ORF;  We conclude that a specific mRNA
AB  - maturase involved in splicing of oxidase mRNA is encoded by the intron ai1 in a manner similar
AB  - to the cytochrome b mRNA maturase.
ER  -

TY  - JOUR
AU  - Carkaci, D.
AU  - Dargis, R.
AU  - Nielsen, X.C.
AU  - Skovgaard, O.
AU  - Fuursted, K.
AU  - Christensen, J.J.
TI  - Complete Genome Sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi  CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG  4311T.
JO  - Genome Announcements
PY  - 2016
SP  - e00302
EP  - e00316
VL  - 4
AB  - Strains belonging to the genus ITALIC! Aerococcusare causative agents of human and animal
AB  - infections, including urogenital infections, bacteremia/septicemia,
AB  - and infective endocarditis. This study reports the first fully closed and
AB  - complete genome sequences of six type strains belonging to the genus ITALIC!
AB  - Aerococcususing a combination of Illumina HiSeq and PacBio sequencing
AB  - technologies.
ER  -

TY  - JOUR
AU  - Carl, G.
AU  - Jackel, C.
AU  - Grutzke, J.
AU  - Hertwig, S.
AU  - Grobbel, M.
AU  - Malorny, B.
AU  - Rau, J.
AU  - Kasbohrer, A.
AU  - Hammerl, J.A.
TI  - Complete Genome Sequence of the Temperate Klebsiella pneumoniae Phage KPP5665-2.
JO  - Genome Announcements
PY  - 2017
SP  - e01118
EP  - e01117
VL  - 5
AB  - We describe here the genome sequence of the novel temperate Klebsiella pneumoniae phage
AB  - KPP5665-2 isolated from a Klebsiella pneumoniae strain recovered from milk
AB  - in Germany in 2016. The phage exhibited a narrow host range and a siphoviridal
AB  - morphology. KPP5665-2-related prophage sequences were detected in whole-genome
AB  - sequencing (WGS) data of various Klebsiella species isolates.
ER  -

TY  - JOUR
AU  - Carle, P.
AU  - Saillard, C.
AU  - Carrere, N.
AU  - Carrere, S.
AU  - Duret, S.
AU  - Eveillard, S.
AU  - Gaurivaud, P.
AU  - Gourgues, G.
AU  - Gouzy, J.
AU  - Salar, P.
AU  - Verdin, E.
AU  - Breton, M.
AU  - Blanchard, A.
AU  - Laigret, F.
AU  - Bove, J.M.
AU  - Renaudin, J.
AU  - Foissac, X.
TI  - Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 3420
EP  - 3426
VL  - 76
AB  - The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific
AB  - libraries of the Spiroplasma citri genome yielded 77
AB  - chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome.
AB  - The largest chromosomal contigs were positioned on the physical and
AB  - genetic maps constructed from pulsed-field gel electrophoresis and
AB  - Southern blot hybridizations. Thirty-eight contigs were annotated,
AB  - resulting in 1,908 predicted coding sequences (CDS) representing an
AB  - overall coding density of only 74%. Cellular processes, cell metabolism,
AB  - and structural-element CDS account for 29% of the coding capacity, CDS of
AB  - external origin such as viruses and mobile elements account for 24% of the
AB  - coding capacity, and CDS of unknown function account for 47% of the coding
AB  - capacity. Among these, 21% of the CDS group into 63 paralog families. The
AB  - organization of these paralogs into conserved blocks suggests that they
AB  - represent potential mobile units. Phage-related sequences were
AB  - particularly abundant and include plectrovirus SpV1 and SVGII3 and
AB  - lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to
AB  - four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were
AB  - detected. Similarity analyses showed that 21% of chromosomal CDS were
AB  - truncated compared to their bacterial orthologs. Transmembrane domains,
AB  - including signal peptides, were predicted for 599 CDS, of which 58 were
AB  - putative lipoproteins. S. citri has a Sec-dependent protein export
AB  - pathway. Eighty-four CDS were assigned to transport, such as
AB  - phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding
AB  - cassette (ABC), and other transporters. Besides glycolytic and ATP
AB  - synthesis pathways, it is noteworthy that S. citri possesses a nearly
AB  - complete pathway for the biosynthesis of a terpenoid.
ER  -

TY  - JOUR
AU  - Carlier, A.
AU  - Agnoli, K.
AU  - Pessi, G.
AU  - Suppiger, A.
AU  - Jenul, C.
AU  - Schmid, N.
AU  - Tummler, B.
AU  - Pinto-Carbo, M.
AU  - Eberl, L.
TI  - Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate.
JO  - Genome Announcements
PY  - 2014
SP  - e00298
EP  - e00214
VL  - 2
AB  - The Burkholderia cepacia complex (BCC) is a group of related bacterial species that are
AB  - commonly isolated from environmental samples. Members of the BCC can cause respiratory
AB  - infections in cystic fibrosis patients and immunocompromised individuals. We report here the
AB  - genome sequence of Burkholderia cenocepacia H111, a well-studied model strain of the BCC.
ER  -

TY  - JOUR
AU  - Carlson, K.
AU  - Kosturko, L.D.
TI  - Endonuclease II of coliphage T4: a recombinase disguised as a restriction endonuclease?
JO  - Mol. Microbiol.
PY  - 1998
SP  - 671
EP  - 676
VL  - 27
AB  - Endo ll shares with restriction endonucleases the property of cleaving foreign DNA while
AB  - leaving the endonuclease-encoding genome intact, ensuring the survival of one DNA species in
AB  - the cell.  In addition, in vivo Endo ll cleaves a specific DNA sequence and cleavage is
AB  - context dependent.  These context effects extend over at least 1000 bp, largely limiting
AB  - cleavage to once within this distance.  Like homing endonucleases, in vivo Endo ll recognizes
AB  - a long, asymmetric and degenerate consensus sequence which has two distinct parts.
AB  - Recognition of one part of the consensus sequence involves base-specific bonds, and
AB  - recognition of the other involves sequence-dependent helical structure.  Endo ll fulfils an
AB  - obvious short-term survival role in ensuring the dominance of phase DNA in an infected cell,
AB  - but may also have a long-term evolutionary role, producing gene-size fragments of foreign DNA
AB  - to be enrolled in the phage genetic repertoire.
ER  -

TY  - JOUR
AU  - Carlson, K.
AU  - Krabbe, M.
AU  - Nystrom, A.C.
AU  - Kosturko, L.D.
TI  - DNA determinants of restriction.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 8908
EP  - 8918
VL  - 268
AB  - Endonuclease II of coliphage T4 is necessary for the in vivo restriction of plasmid DNA in
AB  - phage-infected cells. Double-stranded restriction cleavage at 12 sites in pBR322 commenced
AB  - before 10-min postinfection with T4 at 37C and proceeded more slowly in the presence of
AB  - competing phage DNA than in its absence, utilizing the same sites in both cases; in a 200-base
AB  - pair segment of the plasmid, single stranded nicks also were frequent. The plasmid sites were
AB  - cleaved with a speed that varied with the site, yielding frequencies of cleavage at different
AB  - sites varying between 10 and 90%, at 50-min postinfection. All sites contained good matches to
AB  - a consensus, 5'-GRCCGCNTYGC-3', most frequently cleaved around the variable central base
AB  - pair, generating fragments with blunt ends or 1-2-base 5' overhangs. Using the frequency of
AB  - cleavage to determine a weighted consensus, a larger sequence, 5'-CGRCCGCNTTGSYNGC-3' was
AB  - identified. Thus, DNA sequence elements 3' to the cut site appear important for rapid
AB  - cleavage. Several models describing the sequence-dependent structure of DNA suggest structural
AB  - anomalies around the cleavage sites. The endonuclease II restriction system is most similar to
AB  - type II systems, although it differs from known type II systems in several respects.
ER  -

TY  - JOUR
AU  - Carlson, K.
AU  - Raleigh, E.A.
AU  - Hattman, S.
TI  - Restriction and Modification.
JO  - Molecular Biology of Bacteriophage T4
PY  - 1994
SP  - 369
EP  - 381
AB  - A host-parasite interaction is an intricate balance of mutual attack and defense.  Several
AB  - nucleases and other proteins encoded by Escherichia coli and T4 are involved in restriction
AB  - and modification, processes in which an organism causes degradation of "foreign" DNA while
AB  - modifying its own DNA to provide "immunity" to the restriction endonuclease(s).  Restriction
AB  - endonucleases encoded by the host (E. coli, EcoK or EcoB, Mcr {Rgl}, and Mrr) and its prophage
AB  - symbiont phage P1 (EcoP1) may restrict infecting phage DNA; in addition, E. coli exonuclease V
AB  - (ExoV; the RecBCD enzyme) and possibly endonuclease I may degrade phage DNA as it enters the
AB  - cell.  Phage-encoded nucleases, on the other hand, with endonuclease II (EndoII) as a crucial
AB  - participant, cause the restriction cleavage and ultimate breakdown of host DNA and other
AB  - cytosine-containing DNA in the cell.  The reutilization of host-derived nucleotides via a
AB  - "nucleotide scavenge pathway" permits the production of about 20 phage equivalents of phage
AB  - DNA per host genome scavenged.  Scavenging host DNA breakdown products this way undoubtedly is
AB  - evolutionarily advantageous to the phage when nutrients are limited.
ER  -

TY  - JOUR
AU  - Carlson, K.
AU  - Wiberg, J.S.
TI  - In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments.
JO  - J. Virol.
PY  - 1983
SP  - 18
EP  - 30
VL  - 48
AB  - Mutants of bacteriophage T4D that are defective in genes 42 (dCMP hydroxymethylase), 46 (DNA
AB  - exonuclease), and 56 (dCTPase) produce limited amounts of phage DNA in Escherichia coli B. In
AB  - this DNA, glucosylated 5-hydroxymethylcytosine is completely replaced by cytosine. We found
AB  - that this DNA rapidly becomes fragmented in vivo to at least 16 discrete bands as visualized
AB  - on agarose gels subjected to electrophoresis. The sizes of the fragments ranged from more than
AB  - 20 to less than 2 kilobase pairs. When DNAs from two of these bands were radioactively labeled
AB  - in vitro by nick translation and hybridized to XbaI restriction fragments of
AB  - cytosine-containing T4 DNA, evidence was obtained that the two bands are genetically distinct,
AB  - i.e., they contain DNA from different parts of the T4 genome. Mutational inactivation of T4
AB  - endonuclease II (gene denA) prevented the fragmentation. Three different mutations in T4
AB  - endonuclease IV (gene denB) caused the same minor changes in the pattern of fragments. We
AB  - conclude that T4 endonuclease II is required, and endonuclease IV is involved to a minor
AB  - extent, in the in vivo production of these cytosine-containing T4 DNA fragments. We view these
AB  - DNA fragments as "restriction fragments" since they represent degradation products of DNA
AB  - "foreign" to T4, they are of discrete size, and they are genetically distinct. Thus, this
AB  - report may represent the first, direct in vivo demonstration of discretely sized genetically
AB  - distinct DNA restriction fragments.
ER  -

TY  - JOUR
AU  - Carlson, L.L.
AU  - Page, A.W.
AU  - Bestor, T.H.
TI  - Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting.
JO  - Genes Dev.
PY  - 1992
SP  - 2536
EP  - 2541
VL  - 6
AB  - Preimplantation mouse embryos contain very high levels of DNA methyltransferase activity. We
AB  - show here that the form of DNA methyltransferase (DNA MTase) in early embryos differs from the
AB  - form found in other cells and tissues by a slightly higher mobility on gel electrophoresis.
AB  - Levels of DNA MTase were found to be very high throughout preimplantation development even
AB  - though levels of 5-methylcytosine (m5C)in nuclear DNA are known to undergo a substantial
AB  - decline in the same period. Confocal laser scanning microscopy of mouse embryos stained with
AB  - DNA MTase-specific antibodies showed striking developmentally regulated changes in the
AB  - distribution of DNA MTase. From the oocyte stage to the four-cell-stage, most DNA MTase was
AB  - concentrated in peripheral cytoplasm, and nuclei did not contain detectable DNA MTase. In
AB  - four-and eight-cell embryos, DNA MTase was seen in cytoplasmic granules; and in eight-cell
AB  - embryos, DNA MTase was also present in large amounts in nuclei. Nuclei of blastocysts stained
AB  - only faintly, whereas the cytoplasmic granules remained prominent. Paradoxically, DNA MTase
AB  - was found to be at its highest levels in nuclei at a developmental stage where levels of m5C
AB  - in DNA are decreasing most rapidly. Changes in methylation patterns in preimplanation embryos
AB  - are therefore proposed to be under the control of unidentified regulatory factors rather than
AB  - DNA MTase itself; these regulatory factors could be members of the group that contains the
AB  - products of the Ssm-1 and Imp-1 genes, which are involved in the regulation of genomic
AB  - imprinting.
ER  -

TY  - JOUR
AU  - Carneiro, A.R. et al.
TI  - Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6689
EP  - 6690
VL  - 194
AB  - Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from
AB  - microbial mats of Lake Fryxell in Antarctica. Many organisms of the
AB  - genus Exiguobacterium are extremophiles and have properties of biotechnological
AB  - interest, e.g., the capacity to adapt to cold, which make this genus a target for
AB  - discovering new enzymes, such as lipases and proteases, in addition to improving
AB  - our understanding of the mechanisms of adaptation and survival at low
AB  - temperatures. This study presents the genome of E. antarcticum B7, isolated from
AB  - a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.
ER  -

TY  - JOUR
AU  - Carneiro, A.R.
AU  - Juca, R.R.T.
AU  - Barauna, R.A.
AU  - de Sa, P.H.
AU  - Marinho, A.D.
AU  - Barbosa, S.
AU  - Pereira, A.
AU  - Alves, A.
AU  - Egas, C.
AU  - Correia, A.
AU  - Henriques, I.
AU  - Silva, A.
TI  - Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater.
JO  - Genome Announcements
PY  - 2013
SP  - e00971
EP  - e00913
VL  - 1
AB  - Serratia fonticola is a Gram-negative bacterium with a wide distribution in aquatic
AB  - environments. On some occasions, it has also been regarded as a
AB  - significant human pathogen. In this work, we report the first draft genome
AB  - sequence of an S. fonticola strain (LMG 7882T), which was isolated from
AB  - freshwater.
ER  -

TY  - JOUR
AU  - Carney, J.G.
AU  - Trachtenberg, A.M.
AU  - Rheaume, B.A.
AU  - Linnane, J.D.
AU  - Pitts, N.L.
AU  - Mykles, D.L.
AU  - MacLea, K.S.
TI  - Genome Sequence of a Marine Spirillum, Oceanospirillum multiglobuliferum ATCC 33336T, Isolated from Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e00396
EP  - e00317
VL  - 5
AB  - Oceanospirillum multiglobuliferum ATCC 33336T is a motile gammaproteobacterium with bipolar
AB  - tufted flagella, noted for its low salt tolerance compared to other
AB  - marine spirilla. This strain was originally isolated from the putrid infusions of
AB  - Crassostrea gigas near Hiroshima, Japan. This paper presents a draft genome
AB  - sequence for O. multiglobuliferum ATCC 33336T.
ER  -

TY  - JOUR
AU  - Carnilli, R.
AU  - Del Grosso, M.
AU  - Lannelli, F.
AU  - Pantostil, A.
TI  - New genetic element carrying the erythromycin resistance determinant erm (TR) in Streptococcus pneumoniae.
JO  - Antimicrob. Agents Chemother.
PY  - 2008
SP  - 619
EP  - 625
VL  - 52
AB  - erm(A) subclass erm(TR), a common macrolide resistance determinant in Streptococcus pyogenes
AB  - but quite rare in Streptococcus pneumoniae, was
AB  - found in a clinical S. pneumoniae isolate (AP200) from Italy. In this
AB  - isolate, erm(TR) was found included in a genetic element approximately
AB  - 56 kb in size that did not appear to be conjugative but could be
AB  - transferred by transformation. An erm (TR)-containing DNA fragment of
AB  - approximately 10 kb was sequenced and 12 open reading frames (ORFs)
AB  - were identified. Upstream of erm(TR), a regulatory protein of the TOR
AB  - family and the two components of an efflux pump of the ABC type were
AB  - found. Downstream of erm(TR), there were ORFs homologous to a
AB  - spectinomycin phosphotransferase, transposases, and a relaxase. Since
AB  - the genomic sequence of S. pyogenes MGAS10750 carrying erm(TR) became
AB  - available, comparison between the erm (TR) -containing genetic elements
AB  - in AP200 and in MGAS10750 was performed. The region flanking erm(TR) in
AB  - MGAS10750 showed identity with AP200 for 10 ORFs out of 12. PCR mapping
AB  - using primers designed on the sequence of MGAS10750 confirmed that
AB  - AP200 carries a genetic element similar to that of MGAS10750. In AP200
AB  - the genetic element was inserted inside an ORF homologous to spr0790 of
AB  - S. pneumoniae R6, coding for a type I restriction modification system.
AB  - Homologies between the insertion sites in AP200 and MGAS10750 consisted
AB  - of eight conserved nucleotides, of which three were duplicated, likely
AB  - representing target site duplication. The structure of the erm
AB  - (TR)-carrying genetic element shows characteristics of a
AB  - transposon/prophage remnant chimera. In AP200 this genetic element was
AB  - designated Tn1806.
ER  -

TY  - JOUR
AU  - Caro-Quintero, A.
AU  - Auchtung, J.
AU  - Deng, J.
AU  - Brettar, I.
AU  - Hofle, M.
AU  - Tiedje, J.M.
AU  - Konstantinidis, K.T.
TI  - Genome Sequencing of Five Shewanella baltica Strains Recovered from the Oxic-Anoxic Interface of the Baltic Sea.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1236
EP  - 1236
VL  - 194
AB  - Here we describe five Shewanella baltica genomes recovered from the same sample,  as well as
AB  - 12 years apart from the same sampling station. These genomes expand
AB  - the collection of previously sequenced S. baltica strains and represent a
AB  - valuable resource for assessing the role of environmental settings on genome
AB  - adaptation.
ER  -

TY  - JOUR
AU  - Carotti, D.
AU  - Funiciello, S.
AU  - Lavia, P.
AU  - Caiafa, P.
AU  - Strom, R.
TI  - Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase.
JO  - Biochemistry
PY  - 1996
SP  - 11660
EP  - 11667
VL  - 35
AB  - We have characterized the inhibition exerted by histone H1 on the activity of human placenta
AB  - DNA (cytosine-5-)-methyltransferase.  Our experiments demonstrate that the extent of
AB  - inhibition depends on the DNA base composition, AT-rich substrates being more severely
AB  - affected than GC-rich substrates and CpG-rich islands.  With bacterial SssI methylase, the
AB  - effect is completely reversed since its activity on AT-rich substrates undergoes a 4-5-fold
AB  - stimulation upon the addition of H1.  Poly(L-lysine) mimicks H1 effects, suggesting an
AB  - essential role of lysine residues in both the inhibitory and stimulatory effects of H1.  By
AB  - comparison of the different behaviors of the two enzymes, the inhibitory effect over the
AB  - eukaryotic enzyme might be accounted for by hypothesizing a competition between minor
AB  - groove-binding motifs (SPKK-like) present in placenta methylase as well as in histone H1.
ER  -

TY  - JOUR
AU  - Carotti, D.
AU  - Funiciello, S.
AU  - Palitti, F.
AU  - Strom, R.
TI  - Influence of pre-existing methylation on the de novo activity of eukaryotic DNA methyltransferase.
JO  - Biochemistry
PY  - 1998
SP  - 1101
EP  - 1108
VL  - 37
AB  - Aberrant de novo methylation of CpG island DNA sequences has been observed in cultured cell
AB  - lines or upon malignant transformation but the mechanisms underlying this phenomenon are
AB  - poorly understood.  Using eukaryotic DNA (cytosine-5)-methyltransferase (of both human and
AB  - murine origin), we have studied the in vitro methylation pattern of three CpG islands.  Such
AB  - sequences are intrinsically poor substrates of the enzyme, yet are efficiently methylated when
AB  - a small amount of 5-methylcytosine is randomly introduced by the M.SssI prokaryotic DNA
AB  - (cytosine-5)-methyltransferase prior to in vitro methylation by the eukaryotic enzyme.  A
AB  - stimulation was also found with several other double-stranded DNA substrates, either natural
AB  - or of synthetic origin, such as poly(dG-dC).poly(dG-dC).  An A+T-rich plasmid, pHbbeta1S,
AB  - showed an initial stimulation, followed by a severe inhibition of the activity of DNA
AB  - (cytosine-5)-methyltransferase.  Methylation of poly(dI-dC).poly(dI-dC) was instead inhibited
AB  - by pre-existing 5-methylcytosines.  The extent of stimulation observed with
AB  - poly(dG-dC).poly(dG-dC) depends on both the number and the distribution of the
AB  - 5-methylcytosine residues, which probably must not be too closely spaced for the stimulatory
AB  - effect to be exerted.  The activity of the M.SssI prokaryotic DNA methyltransferase was not
AB  - stimulated, but was inhibited by pre-methylation on either poly(dG-dC).poly(dG-dC) or
AB  - poly(dI-dC).poly(dI-dC).  The prokaryotic and eukaryotic DNA methyltransferases also differed
AB  - in sensitivity to poly(dG-m5dC).poly(dG-m5dC), which is highly inhibitory for eukaryotic
AB  - enzymes and almost ineffective on prokaryotic enzymes.
ER  -

TY  - JOUR
AU  - Carpenter, M.
AU  - Divvela, P.
AU  - Pingoud, V.
AU  - Bujnicki, J.
AU  - Bhagwat, A.S.
TI  - Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 3762
EP  - 3770
VL  - 34
AB  - Hydrolytic deamination of cytosines in DNA creates uracil and, if unrepaired, these lesions
AB  - result in C to T mutations. We have suggested
AB  - previously that a possible way in which cells may prevent or reduce this
AB  - chemical reaction is through the binding of proteins to DNA. We use a
AB  - genetic reversion assay to show that a restriction enzyme, PspGI, protects
AB  - cytosines within its cognate site, 5'-CCWGG (W is A or T), against
AB  - deamination under conditions where no DNA cleavage can occur. It decreases
AB  - the rate of cytosine deamination to uracil by 7-fold. However, the same
AB  - protein dramatically increases the rate of deaminations within the site
AB  - 5'-CCSGG (S is C or G) by approximately 15-fold. Furthermore, a similar
AB  - increase in cytosine deaminations is also seen with a catalytically
AB  - inactive mutant of the enzyme showing that endonucleolytic ability of the
AB  - protein is dispensable for its mutagenic action. The sequences of the
AB  - mutants generated in the presence of PspGI show that only one of the
AB  - cytosines in CCSGG is predominantly converted to thymine. Our results are
AB  - consistent with PspGI 'sensitizing' the cytosine in the central base pair
AB  - in CCSGG for deamination. Remarkably, PspGI sensitizes this base for
AB  - damage despite its inability to form stable complexes at CCSGG sites.
AB  - These results can be explained if the enzyme has a transient interaction
AB  - with this sequence during which it flips the central cytosine out of the
AB  - helix. This prediction was validated by modeling the structure of
AB  - PspGI-DNA complex based on the structure of the related enzyme Ecl18kI
AB  - which is known to cause base-flipping.
ER  -

TY  - JOUR
AU  - Carpenter, M.A.
TI  - Studies of base flipping by the Pyrococcus species GI-H restriction-modification system.
JO  - Ph.D. Thesis, Wayne State Univ., Detroit, MI, USA
PY  - 2008
AB  - Water is the single most DNA damaging agent that cells regularly encounter.  Water induces DNA
AB  - damage by a variety of mechanisms including depurination, depyrimidination, and deamination.
AB  - Figure 1 shows some of the most frequently observed types of DNA damage.  Depurination and
AB  - depyrimidination occur when a water molecular attacks at the C1' of deoxyribose kicking the
AB  - DNA base off in an Sn2 type substitution.  Depurination occurs at a very high rate, inducing
AB  - an estimated 18,000 abasic sites per cell, per day in a typical human cell.  Depyrimidination
AB  - occurs about 300 fold less frequently than depurination.  Repair of abasic sites in
AB  - Escherichia coli is similar to Base Excision Repair except that the abasic site is caused by
AB  - hydrolytic attack of water and not by a DNA glycosylase.
ER  -

TY  - JOUR
AU  - Carpenter, M.A.
AU  - Bhagwat, A.S.
TI  - DNA base flipping by both members of the PspGI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 5417
EP  - 5425
VL  - 36
AB  - The PspGI restriction-modification system recognizes the sequence CCWGG. R.PspGI cuts DNA
AB  - before the first C in the cognate sequence and M.PspGI is
AB  - thought to methylate N4 of one of the cytosines in the sequence. M.PspGI
AB  - enhances fluorescence of 2-aminopurine in DNA if it replaces the second C
AB  - in the sequence, while R.PspGI enhances fluorescence when the fluorophore
AB  - replaces adenine in the central base pair. This strongly suggests that the
AB  - methyltransferase flips the second C in the recognition sequence, while
AB  - the endonuclease flips both bases in the central base pair out of the
AB  - duplex. M.PspGI is the first N4-cytosine MTase for which biochemical
AB  - evidence for base flipping has been presented. It is also the first type
AB  - IIP methyltransferase whose catalytic activity is strongly stimulated by
AB  - divalent metal ions. However, divalent metal ions are not required for its
AB  - base-flipping activity. In contrast, these ions are required for both base
AB  - flipping and catalysis by the endonuclease. The two enzymes have similar
AB  - temperature profiles for base flipping and optimal flipping occurs at
AB  - temperatures substantially below the growth temperature of the source
AB  - organism for PspGI and for the catalytic activity of endonuclease. We
AB  - discuss the implications of these results for DNA binding by these enzymes
AB  - and their evolutionary origin.
ER  -

TY  - JOUR
AU  - Carpenter, S.
AU  - Mishra, P.
AU  - Ghoshal, C.
AU  - Dash, P.
AU  - Wang, L.
AU  - Midha, S.
AU  - Laha, G.S.
AU  - Lore, J.
AU  - Kositratana, W.
AU  - Singh, N.
AU  - Singh, K.
AU  - Patil, P.
AU  - Oliva, R.
AU  - Patarapuwadol, S.
AU  - Bogdanove, A.J.
AU  - Rai, R.
TI  - A strain of an emerging Indian pathotype of Xanthomonas oryzae pv. oryzae defeats the rice bacterial blight resistance gene xa13 without inducing a clade III SWEET gene and is nearly identical to a recent Thai isolate.
JO  - bioRxiv
PY  - 2018
SP  - 0
EP  - 0
VL  - 0
AB  - The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription
AB  - activator-like
AB  - effectors (TALEs) that bind and activate host susceptibility (S) genes important for disease.
AB  - Clade III
AB  - SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces
AB  - TALE
AB  - activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been
AB  - effectively
AB  - deployed. However, strains that defeat both resistance genes individually were recently
AB  - reported in India
AB  - and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one
AB  - such
AB  - strain from each country and examined the encoded TALEs. Strikingly, the two strains are
AB  - clones, sharing
AB  - nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough
AB  - to be
AB  - effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian
AB  - strain.
AB  - The Indian strain induced no clade III SWEET in plants harbouring xa13, indicating a pathogen
AB  - adaptation
AB  - that relieves dependence on these genes for susceptibility. The findings open a door to
AB  - mechanistic
AB  - understanding of the role SWEET genes play in susceptibility and illustrate the importance of
AB  - complete
AB  - genome sequence-based monitoring of Xoo populations in developing varieties with effective
AB  - disease
AB  - resistance.
AB  - Key
ER  -

TY  - JOUR
AU  - Carraro, N.
AU  - Sauve, M.
AU  - Matteau, D.
AU  - Lauzon, G.
AU  - Rodrigue, S.
AU  - Burrus, V.
TI  - Development of pVCR94DeltaX from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids.
JO  - Front. Microbiol.
PY  - 2014
SP  - 44
EP  - 44
VL  - 5
AB  - Antibiotic resistance has grown steadily in Vibrio cholerae over the last few
AB  - decades to become a major threat in countries affected by cholera. Multi-drug
AB  - resistance (MDR) spreads among clinical and environmental V. cholerae strains by
AB  - lateral gene transfer often mediated by integrative and conjugative elements
AB  - (ICEs) of the SXT/R391 family. However, in a few reported but seemingly isolated
AB  - cases, MDR in V. cholerae was shown to be associated with other
AB  - self-transmissible genetic elements such as conjugative plasmids. IncA/C
AB  - conjugative plasmids are often found associated with MDR in isolates of
AB  - Enterobacteriaceae. To date, IncA/C plasmids have not been commonly found in V.
AB  - cholerae or other species of Vibrio. Here we present a detailed analysis of
AB  - pVCR94DeltaX derived from pVCR94, a novel IncA/C conjugative plasmid identified
AB  - in a V. cholerae clinical strain isolated during the 1994 Rwandan cholera
AB  - outbreak. pVCR94 was found to confer resistance to sulfamethoxazole,
AB  - trimethoprim, ampicillin, streptomycin, tetracycline, and chloramphenicol and to
AB  - transfer at very high frequency. Sequence analysis revealed its mosaic nature as
AB  - well as high similarity of the core genes responsible for transfer and
AB  - maintenance with other IncA/C plasmids and ICEs of the SXT/R391 family. Although
AB  - IncA/C plasmids are considered a major threat in antibiotics resistance, their
AB  - basic biology has received little attention, mostly because of the difficulty to
AB  - genetically manipulate these MDR conferring elements. Therefore, we developed a
AB  - convenient derivative from pVCR94, pVCR94Delta X, a 120.5-kb conjugative plasmid
AB  - which only codes for sulfamethoxazole resistance. Using pVCR94Delta X, we
AB  - identified the origin of transfer (oriT) and discovered an essential gene for
AB  - transfer, both located within the shared backbone, allowing for an annotation
AB  - update of all IncA/C plasmids. pVCR94Delta X may be a useful model that will
AB  - provide new insights on the basic biology of IncA/C conjugative plasmids.
ER  -

TY  - JOUR
AU  - Carrasco, G.
AU  - Monzon, S.
AU  - Jimenez, P.
AU  - Cuesta, I.
AU  - Bartolome-Alvarez, J.
AU  - Valdezate, S.
TI  - First Draft Genome Sequence of a Clinical Strain of Nocardia cerradoensis.
JO  - Genome Announcements
PY  - 2017
SP  - e00551
EP  - e00517
VL  - 5
AB  - This paper reports the first draft genome sequence for a strain of Nocardia cerradoensis
AB  - obtained from an immunocompetent patient with a knee infection. The
AB  - 8.2-Mb genome has 8,329 coding sequences, including intrinsic resistance genes,
AB  - biosynthetic gene clusters for polyketide synthase and nonribosomal peptide
AB  - synthase, virulence genes, and prophages.
ER  -

TY  - JOUR
AU  - Carraway, M.
AU  - Youderian, P.
AU  - Marinus, M.G.
TI  - Spontaneous mutations occur near dam recognition sites in a dam- Escherichia coli host.
JO  - Genetics
PY  - 1987
SP  - 343
EP  - 347
VL  - 116
AB  - The mismatch repair system of Escherichia coli K12 removes mispaired bases from DNA. Mismatch
AB  - repair can occur on either strand of DNA if it lacks N6-methyladenines within
AB  - 5'-GATC-3'sequences. In hemimethylated heteroduplexes, repair occurs preferentially on the
AB  - unmethylated strand. If both strands are fully methylated, repair is inhibited. Mutant (dam-)
AB  - strains of E. coli defective in the adenine methylase that recognizes 5'-GATC-3' sequences
AB  - (Dam), and therefore defective in mismatch repair, show increased spontaneous mutation rates
AB  - compared to otherwise isogenic dam+ hosts. We have isolated and characterized 91 independent
AB  - mutations that arise as a consequence of the Dam- defect in a plasmid-borne phage P22
AB  - repressor gene, mnt. The majority of these mutations are A:T----G:C transitions that occur
AB  - within six base pairs of the two 5'-GATC-3' sequences in the mnt gene. In contrast, the
AB  - spectrum of mnt- mutations in a dam+ host is comprised of a majority of insertions of IS
AB  - elements and deletions that do not cluster near Dam recognition sites. These results show that
AB  - Dam-directed post-replicative mismatch repair plays a significant role in the rectification of
AB  - potential transition mutations in vivo, and suggest that sequences associated with Dam
AB  - recognition sites are particularly prone to replication or repair errors.
ER  -

TY  - JOUR
AU  - Carrias, A.
AU  - Welch, T.J.
AU  - Waldbieser, G.C.
AU  - Mead, D.A.
AU  - Terhune, J.S.
AU  - Liles, M.R.
TI  - Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri.
JO  - Virol. J.
PY  - 2011
SP  - 6
EP  - 6
VL  - 8
AB  - BACKGROUND: The bacterial pathogen Edwardsiella ictaluri is a primary
AB  - cause of mortality in channel catfish raised commercially in aquaculture
AB  - farms. Additional treatment and diagnostic regimes are needed for this
AB  - enteric pathogen, motivating the discovery and characterization of
AB  - bacteriophages specific to E. ictaluri. RESULTS: The genomes of three
AB  - Edwardsiella ictaluri-specific bacteriophages isolated from geographically
AB  - distant aquaculture ponds, at different times, were sequenced and
AB  - analyzed. The genomes for phages eiAU, eiDWF, and eiMSLS are 42.80 kbp,
AB  - 42.12 kbp, and 42.69 kbp, respectively, and are greater than 95% identical
AB  - to each other at the nucleotide level. Nucleotide differences were mostly
AB  - observed in non-coding regions and in structural proteins, with
AB  - significant variability in the sequences of putative tail fiber proteins.
AB  - The genome organization of these phages exhibit a pattern shared by other
AB  - Siphoviridae. CONCLUSIONS: These E. ictaluri-specific phage genomes reveal
AB  - considerable conservation of genomic architecture and sequence identity,
AB  - even with considerable temporal and spatial divergence in their isolation.
AB  - Their genomic homogeneity is similarly observed among E. ictaluri
AB  - bacterial isolates. The genomic analysis of these phages supports the
AB  - conclusion that these are virulent phages, lacking the capacity for
AB  - lysogeny or expression of virulence genes. This study contributes to our
AB  - knowledge of phage genomic diversity and facilitates studies on the
AB  - diagnostic and therapeutic applications of these phages.
ER  -

TY  - JOUR
AU  - Carrick, K.L.
AU  - Topal, M.D.
TI  - Amino Acid Substitutions at Position 43 of NaeI Endonuclease - Evidence for Changes in NaeI Structure.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 9733
EP  - 9739
VL  - 278
AB  - NaeI endonuclease contains a 10-amino acid region with sequence similarity to the active site
AB  - KXDG motif of DNA ligase except for leucine (Leu-43) in
AB  - NaeI ((43)LXDG(46)). Changing Leu-43 to lysine abolishes the NaeI
AB  - endonuclease activity and replaces it with topoisomerase and recombinase
AB  - activities. Here we report the results of substituting Leu-43 with
AB  - alanine, arginine, asparagine, glutamate, and histidine. Quantitating
AB  - specific activities and DNA binding values for the mutant proteins
AB  - determined the range of amino acids at position 43 that alter NaeI
AB  - mechanism. Substituting alanine, asparagine, glutamate, and histidine for
AB  - Leu-43 maintained endonuclease activity, but at a lower level. On the
AB  - other hand, substituting positively charged arginine, like lysine at
AB  - position 43, converted NaeI to a topoisomerase with no observable
AB  - double-strand cleavage activity. The specific activities of NaeI-43K and
AB  - NaeI-43R and their relative sensitivities to salt, the
AB  - topoisomerase-inhibiting drug
AB  - N-[4-(9-acridinylamino)-3-methoxyphenyl]methane-sulfonamide (amsacrine)
AB  - and single-stranded DNA showed that the two activities are similar. The
AB  - effect of placing a positive charge at position 43 on NaeI structure was
AB  - determined by measuring (for NaeI and NaeI-43K) relative susceptibilities
AB  - to proteolysis, UV, circular dichroism spectra, and temperature melting
AB  - transitions. The results provide evidence that a positive charge at
AB  - position 43 induces dramatic changes in NaeI structure that affect both
AB  - the Endo and Topo domains of NaeI. The identification of four putative DNA
AB  - ligase motifs in NaeI leads us to speculate that structural changes that
AB  - superimpose these motifs on the ligase structure may account for the
AB  - changes in activity.
ER  -

TY  - JOUR
AU  - Carrington, M.
AU  - Doro, E.
AU  - Forlenza, M.
AU  - Wiegertjes, G.F.
AU  - Kelly, S.
TI  - Transcriptome Sequence of the Bloodstream Form of Trypanoplasma borreli, a Hematozoic Parasite of Fish Transmitted by Leeches.
JO  - Genome Announcements
PY  - 2017
SP  - e01712
EP  - e01716
VL  - 5
AB  - Here, we report a transcriptome sequence of Trypanoplasma borreli isolated from its natural
AB  - host, the common carp, Cyprinus carpio The transcriptome allows an
AB  - analysis of abundant cell surface proteins and acts as a comparator for
AB  - understanding the evolution and pathogenicity of other Kinetoplastida, including
AB  - several that infect humans.
ER  -

TY  - JOUR
AU  - Carrion, V.J.
AU  - Cordovez, V.
AU  - Tyc, O.
AU  - Etalo, D.W.
AU  - de Bruijn, I.
AU  - de Jager, V.C.
AU  - Medema, M.H.
AU  - Eberl, L.
AU  - Raaijmakers, J.M.
TI  - Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.
JO  - ISME J.
PY  - 2018
SP  - 23072321
EP  - 23072321
VL  - 12
AB  - Disease-suppressive soils are ecosystems in which plants suffer less from root
AB  - infections due to the activities of specific microbial consortia. The
AB  - characteristics of soils suppressive to specific fungal root pathogens are
AB  - comparable to those of adaptive immunity in animals, as reported by Raaijmakers
AB  - and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species
AB  - involved in the soil suppressiveness are largely unknown. Previous taxonomic and
AB  - metatranscriptome analyses of a soil suppressive to the fungal root pathogen
AB  - Rhizoctonia solani revealed that members of the Burkholderiaceae family were more
AB  - abundant and more active in suppressive than in non-suppressive soils. Here,
AB  - isolation, phylogeny, and soil bioassays revealed a significant
AB  - disease-suppressive activity for representative isolates of Burkholderia
AB  - pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P.
AB  - terricola. In vitro antifungal activity was only observed for P. graminis.
AB  - Comparative genomics and metabolite profiling further showed that the antifungal
AB  - activity of P. graminis PHS1 was associated with the production of sulfurous
AB  - volatile compounds encoded by genes not found in the other four genera.
AB  - Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide
AB  - reductase and a cysteine desulfurase, resulted in a loss of antifungal activity
AB  - both in vitro and in situ. These results indicate that specific members of the
AB  - Burkholderiaceae family contribute to soil suppressiveness via the production of
AB  - sulfurous volatile compounds.
ER  -

TY  - JOUR
AU  - Carroll, R.K.
AU  - Burda, W.N.
AU  - Roberts, J.C.
AU  - Peak, K.K.
AU  - Cannons, A.C.
AU  - Shaw, L.N.
TI  - Draft Genome Sequence of Strain CBD-635, a Methicillin-Resistant Staphylococcus aureus USA100 Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e00491
EP  - e00413
VL  - 1
AB  - We present the draft genome sequence of methicillin-resistant Staphylococcus aureus strain
AB  - CBD-635, from the USA100 lineage. This is a sepsis isolate obtained
AB  - from Tampa General Hospital. This strain is spa type t003 and multilocus sequence
AB  - typing (MLST) type ST5, and it has been used by our group in the study of novel
AB  - antimicrobial chemotherapeutics.
ER  -

TY  - JOUR
AU  - Carruthers, M.D.
AU  - Harding, C.M.
AU  - Baker, B.D.
AU  - Bonomo, R.A.
AU  - Hujer, K.M.
AU  - Rather, P.N.
AU  - Munson, R.S. Jr.
TI  - Draft Genome Sequence of the Clinical Isolate Acinetobacter nosocomialis Strain M2.
JO  - Genome Announcements
PY  - 2013
SP  - e00906
EP  - e00913
VL  - 1
AB  - We report the 3.78-Mbp high-quality draft assembly of the genome from a clinical  isolate of
AB  - Acinetobacter nosocomialis called strain M2 (previously known as
AB  - Acinetobacter baumannii strain M2).
ER  -

TY  - JOUR
AU  - Carter, A.T.
AU  - Pearson, B.M.
AU  - Crossman, L.C.
AU  - Drou, N.
AU  - Heavens, D.
AU  - Baker, D.
AU  - Febrer, M.
AU  - Caccamo, M.
AU  - Grant, K.A.
AU  - Peck, M.W.
TI  - Complete Genome Sequence of proteolytic Clostridium botulinum type A5 (B3') Strain H04402 065.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2351
EP  - 2352
VL  - 193
AB  - H04402 065 is one of a very small group of strains of proteolytic Clostridium botulinum that
AB  - form type A5 neurotoxin. Here, we report the complete 3.9 Mb genome sequence and annotation of
AB  - strain H04402 065, which was isolated from a botulism patient in the UK in 2004.
ER  -

TY  - JOUR
AU  - Carter, J.A.
AU  - Chater, K.F.
AU  - Bruton, C.J.
AU  - Brown, N.L.
TI  - A comparison of DNA cleavage by the restriction enzymes SalPI and PstI.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 4943
EP  - 4954
VL  - 8
AB  - Methods for obtaining highly active, exonuclease-free, stable preparations of
AB  - the Streptomyces albus P restriction enzyme SalPI are described.  SalPI and its
AB  - isoschizomer PstI (from the taxonomically distant Providencia stuartii 164)
AB  - both cleave their recognition sequence (5'-CTGCAG-3') to generate fragments
AB  - terminating in tetranucleotide 3' extensions whose sequence is 5'-TGCA-3'.
AB  - Bacteriophage R4G2 DNA, protected against SalPI cleavage by pregrowth on S.
AB  - albus P, is also protected against PstI cleavage; and total DNA of both S.
AB  - albus P and P. stuartii 164 is resistant to cleavage by both enzymes.
ER  -

TY  - JOUR
AU  - Carter, J.M.
AU  - Friedrich, N.C.
AU  - Kleinstiver, B.
AU  - Edgell, D.R.
TI  - Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 306
EP  - 321
VL  - 374
AB  - GIY-YIG homing endonucleases are modular enzymes consisting of a well-defined N-terminal
AB  - catalytic domain connected to a variable
AB  - C-terminal DNA-binding domain. Previous studies have revealed that the
AB  - role of the DNA-binding domain is to recognize and bind intronless DNA
AB  - substrate, positioning the N-terminal catalytic domain such that it is
AB  - poised to generate a staggered double-strand break by an unknown
AB  - mechanism. Interactions of the N-terminal catalytic domain with intronless
AB  - substrate are therefore a critical step in the reaction pathway but have
AB  - been difficult to define. Here, we have taken advantage of the reduced
AB  - activity of I-BmoI, an isoschizomer of the well-studied bacteriophage T4
AB  - homing endonuclease I-TevI, to examine double-strand break formation by
AB  - I-BmoI. We present evidence demonstrating that I-BmoI generates a
AB  - double-strand break by two sequential but chemically independent nicking
AB  - reactions where divalent metal ion is a limiting factor in top-strand
AB  - nicking. We also show by in-gel footprinting that contacts by the I-BmoI
AB  - catalytic domain induce significant minor groove DNA distortions that
AB  - occur independently of bottom-strand nicking. Bottom-strand contacts are
AB  - critical for accurate top-strand nicking, whereas top-strand contacts have
AB  - little influence on the accuracy of bottom-strand nicking. We discuss our
AB  - results in the context of current models of GIY-YIG endonuclease function,
AB  - with emphasis on the role of divalent metal ion and strand-specific
AB  - contacts in regulating the activity of a single active site to generate a
AB  - staggered double-strand break.
ER  -

TY  - JOUR
AU  - Carter, L.
AU  - Chase, H.R.
AU  - Choi, H.
AU  - Jun, S.
AU  - Park, J.
AU  - Jeong, S.
AU  - Kim, M.
AU  - Han, K.
AU  - Lee, C.
AU  - Jeong, H.
AU  - Finkelstein, S.
AU  - Negrete, F.
AU  - Cinar, H.N.
AU  - Tall, B.D.
AU  - Gopinath, G.R.
TI  - Draft Genome Sequences of Enterotoxigenic Bacillus cereus Strains Obtained from Powdered Infant Formula.
JO  - Genome Announcements
PY  - 2017
SP  - e01644
EP  - e01616
VL  - 5
AB  - We introduce the draft genome sequences of five enterotoxigenic Bacillus cereus strains: Bc
AB  - 12, Bc 67, Bc 111, Bc 112, and Bc 113, which were obtained from
AB  - powdered infant formula. The genome sizes of the strains ranged from 5.5 to 5.8
AB  - Mb, and the G+C contents were ~35.2%.
ER  -

TY  - JOUR
AU  - Carter, M.Q.
AU  - Pham, A.
TI  - Complete Genome Sequence of a Natural Escherichia coli O145:H11 Isolate That Belongs to Phylogroup A.
JO  - Genome Announcements
PY  - 2018
SP  - e00349
EP  - e00318
VL  - 6
AB  - Escherichia coli O145:H11 strain RM14721 was originally isolated from wildlife feces near a
AB  - leafy greens-growing region in Yuma, AZ. This strain was initially
AB  - positive for stx1; however, in subsequent cultures, stx1 was not detected by PCR.
AB  - Here, we report the complete genome sequence and annotation of RM14721.
ER  -

TY  - JOUR
AU  - Carter, M.Q.
AU  - Pham, A.
TI  - Complete Genome Sequences of Two Atypical Enteropathogenic Escherichia coli O145  Environmental Strains.
JO  - Genome Announcements
PY  - 2018
SP  - e00418
EP  - e00418
VL  - 6
AB  - Escherichia coli O145 strains RM14715 and RM14723 were isolated from wildlife feces near a
AB  - leafy greens-growing region in Yuma, Arizona. Both strains carry a
AB  - distinct genotype compared with the E. coli O145 strains isolated from Salinas
AB  - Valley, California. Here we report complete genome sequences and annotations of
AB  - RM14715 and RM14723.
ER  -

TY  - JOUR
AU  - Carter, M.Q.
AU  - Pham, A.
AU  - Huynh, S.
AU  - He, X.
TI  - Complete Genome Sequence of a Shiga Toxin-Producing Enterobacter cloacae Clinical Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00883
EP  - e00817
VL  - 5
AB  - Enterobacter cloacae strain M12X01451 was isolated from a patient with mild diarrhea. This
AB  - strain produces a novel subtype of Shiga toxin 1, Stx1e. The
AB  - Stx1e-converting prophage in strain M12X01451 is stable and can infect other
AB  - bacteria following induction. Here we report the complete genome sequence and
AB  - annotation of strain M12X01451.
ER  -

TY  - JOUR
AU  - Carvin, C.D.
AU  - Dhasarathy, A.
AU  - Friesenhahn, L.B.
AU  - Jessen, W.J.
AU  - Kladde, M.P.
TI  - Targeted cytosine methylation for in vivo detection of protein-DNA interactions.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 7743
EP  - 7748
VL  - 100
AB  - We report a technique, named targeted gene methylation (TAGM), for identifying in vivo
AB  - protein-binding sites in chromatin. M.CviPI, a
AB  - cytosine-5 DNA methyltransferase recognizing GC sites, is fused to a
AB  - DNA-binding factor enabling simultaneous detection of targeted
AB  - methylation, factor footprints, and chromatin structural changes by
AB  - bisulfite genomic sequencing. Using TAGM with the yeast transactivator
AB  - Pho4, methylation enrichments of up to 34- fold occur proximal to native
AB  - Pho4-binding sites. Additionally, significant selective targeting of
AB  - methylation is observed several hundred nucleotides away, suggesting the
AB  - detection of long-range interactions due to higher-order chromatin
AB  - structure. In contrast, at an extragenic locus lacking Pho4-binding sites,
AB  - methylation levels are at the detection limit at early times after Pho4
AB  - transactivation. Notably, substantial amounts of methylation are targeted
AB  - by Pho4-M.CviPI under repressive conditions when most of the
AB  - transactivator is excluded from the nucleus. Thus, TAGM enables rapid
AB  - detection of DNA-protein interactions even at low occupancies and has
AB  - potential for identifying factor targets at the genome-wide level.
AB  - Extension of TAGM from yeast to vertebrates, which use methylation to
AB  - initiate and propagate repressed chromatin, could also provide a valuable
AB  - strategy for heritable inactivation of gene expression.
ER  -

TY  - JOUR
AU  - Carvin, C.D.
AU  - Parr, R.D.
AU  - Kladde, M.P.
TI  - Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 6493
EP  - 6501
VL  - 31
AB  - Cytosine-5 DNA methylation is a critical signal defining heritable epigenetic states of
AB  - transcription. As aberrant methylation patterns often
AB  - accompany disease states, the ability to target cytosine methylation to
AB  - preselected regions could prove valuable in re-establishing proper gene
AB  - regulation. We employ the strategy of targeted gene methylation in yeast,
AB  - which has a naturally unmethylated genome, selectively directing de novo
AB  - DNA methylation via the fusion of C5 DNA methyltransferases to
AB  - heterologous DNA-binding proteins. The zinc-finger proteins Zif268 and
AB  - Zip53 can target DNA methylation by M.CviPI or M.SssI 5-52 nt from single
AB  - zinc-factor binding sites. Modification at specific GC (M.CviPI) or CG
AB  - (M.SssI) sites is enhanced as much as 20-fold compared with strains
AB  - expressing either the free enzyme or a fusion protein with the zinc-finger
AB  - protein moiety unable to bind to DNA. Interestingly, methylation is also
AB  - selectively targeted as far as 353 nt from the zinc-finger protein binding
AB  - sites, possibly indicative of looping, nucleosomes or higher-order
AB  - chromatin structure. These data demonstrate that methylation can be
AB  - targeted in vivo to a potentially broad range of sequences using
AB  - specifically engineered zinc-finger proteins. Further more, the selective
AB  - targeting of methylation by zinc-finger proteins demonstrates that binding
AB  - of distinct classes of factors can be monitored in living cells.
ER  -

TY  - JOUR
AU  - Casadesus, J.
AU  - Low, D.
TI  - Epigenetic gene regulation in the bacterial world.
JO  - Microbiol. Mol. Biol. Rev.
PY  - 2006
SP  - 830
EP  - 856
VL  - 70
AB  - Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the
AB  - epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA
AB  - adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA
AB  - adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock
AB  - animals, including pathogenic Escherichia coh, Salmonella, Vibrio, Yersinia, Haemophilus, and
AB  - Brucella. In Alphaproteobactetia, methylation of adenine at GANTC sites by the CcrM methylase
AB  - regulates the cell cycle and couples gene transcription to DNA replication. In
AB  - Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals
AB  - for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage
AB  - genomes, transposase activity, and regulation of gene expression. Transcriptional repression
AB  - by Dam methylation appears to be more common than transcriptional activation. Certain
AB  - promoters are active only during the hemimethylation interval that follows DNA replication;
AB  - repression is restored when the newly synthesized DNA strand is methylated In the E. coli
AB  - genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding
AB  - proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA
AB  - methylation patterns to daughter cells and can give rise to distinct epigenetic states, each
AB  - propagated by a positive feedback loop. Switching between alternative DNA methylation patterns
AB  - can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of
AB  - eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns
AB  - governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding
AB  - virulence-related cell surface functions.
ER  -

TY  - JOUR
AU  - Casadesus, J.
AU  - Torreblanca, J.
TI  - Methylation-related epigenetic signals in bacterial DNA.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 141
EP  - 153
AB  - The term "epigenetic signals"  may seem extraneous to the life-style of bacteria, because the
AB  - classic concept of epigenetics has been applied to the changes in gene expression that govern
AB  - differentiation and development.  However, because differentiation is often associated with
AB  - changes in DNA or chromatin structure, DNA modification has provided an attractive model for
AB  - the study of epigenetic regulation.
ER  -

TY  - JOUR
AU  - Casale, A.
AU  - Clark, S.
AU  - Grasso, M.
AU  - Kryschuk, M.
AU  - Ritzer, L.
AU  - Trudeau, M.
AU  - Williams, L.E.
TI  - Complete Genome Sequence of Escherichia coli ML35.
JO  - Genome Announcements
PY  - 2018
SP  - e00034
EP  - e00018
VL  - 6
AB  - We report here the complete genome sequence of Escherichia coli strain ML35. We assembled
AB  - PacBio reads into a single closed contig with 169x mean coverage and
AB  - then polished this contig using Illumina MiSeq reads, yielding a 4,918,774-bp
AB  - sequence with 50.8% GC content.
ER  -

TY  - JOUR
AU  - Cascales, D.
AU  - Guijarro, J.A.
AU  - Reimundo, P.
AU  - Garcia-Torrico, A.I.
AU  - Mendez, J.
TI  - Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 150, Isolated from Diseased Rainbow Trout.
JO  - Genome Announcements
PY  - 2016
SP  - e01331
EP  - e01316
VL  - 4
AB  - We present here the draft genome of a pathogenic Yersinia ruckeri strain, isolated from
AB  - rainbow trout (Oncorhynchus mykiss) affected by enteric redmouth
AB  - disease. The chromosome has 3,826,775 bp, a GC content of 46.88%, and is
AB  - predicted to contain 3,538 coding sequences. The data will be useful for
AB  - comparative pathogenicity studies.
ER  -

TY  - JOUR
AU  - Caserta, M.
AU  - Zacharias, W.
AU  - Nwankwo, D.
AU  - Wilson, G.G.
AU  - Wells, R.D.
TI  - Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase.
JO  - J. Biol. Chem.
PY  - 1987
SP  - 4770
EP  - 4777
VL  - 262
AB  - A 1476-base pair DNA fragment from Haemophilus haemolyticus containing the HhaI
AB  - methyltransferase gene was isolated from a cell library and cloned into pBR322.
AB  - The nucleotide sequence of this fragment was determined.  The structural gene
AB  - is 981 nucleotides in length coding for a protein of 327 amino acids (Mr
AB  - 37,000).  The translational start signal (ATG) is preceded by the putative
AB  - ribosome-binding site (TAAG).  Recombinant plasmids containing the
AB  - 1476-basepair fragment are completely methylated when isolated from Escherichia
AB  - coli, as judged by their insusceptibility to the HhaI restriction endonuclease.
AB  - However, the presence of an active HhaI methylase gene in certain E. coli
AB  - stsrains results in a very poor yield of transformants and/or in
AB  - vivo-originated deletions due to the Rgl functions of these hosts.  The in vivo
AB  - transcription and initiation sites have been identified by S1 protection and
AB  - primer-extension experiments using specific probes with total RNA prepared from
AB  - E. coli cells (HB101 or RR1) which tolerate the expression of MHhaI.
ER  -

TY  - JOUR
AU  - Casey, A.
AU  - McAuliffe, O.
AU  - Coffey, A.
AU  - Hunt, K.
AU  - Fanning, S.
AU  - Fox, E.
AU  - Jordan, K.
TI  - Complete Genome Sequence of Listeria monocytogenes Strain DPC6895, a Serotype 1/2b Isolate from Bovine Raw Milk.
JO  - Genome Announcements
PY  - 2015
SP  - e00629
EP  - e00615
VL  - 3
AB  - Listeria monocytogenes is a foodborne pathogen and is the causative agent of listeriosis among
AB  - humans and animals. The draft genome sequence of L.
AB  - monocytogenes DPC6895, a serotype 1/2b strain isolated from the raw milk of a cow
AB  - with subclinical bovine mastitis, is reported.
ER  -

TY  - JOUR
AU  - Casey, A.
AU  - McAuliffe, O.
AU  - Fox, E.M.
AU  - Leong, D.
AU  - Gahan, C.G.
AU  - Jordan, K.
TI  - Draft Genome Sequences of Listeria monocytogenes Serotype 4b Strains 944 and 2993 and Serotype 1/2c Strains 198 and 2932.
JO  - Genome Announcements
PY  - 2016
SP  - e00482
EP  - e00416
VL  - 4
AB  - Listeria monocytogenes is a foodborne pathogen and the causative agent of listeriosis among
AB  - humans and animals. The draft genome sequences of L.
AB  - monocytogenes serotype 4b strains 944 and 2993 and serotype 1/2c strains 198 and
AB  - 2932 are reported here.
ER  -

TY  - JOUR
AU  - Casjens, S.
AU  - Hayden, M.
AU  - Jackson, E.
AU  - Deans, R.
TI  - Additional restriction endonuclease cleavage sites on the bacteriophage P22 genome.
JO  - J. Virol.
PY  - 1983
SP  - 864
EP  - 867
VL  - 45
AB  - We present complete restriction endonuclease cleavage site maps of the
AB  - bacteriophage P22 chromosome for 16 enzymes with six base recognition
AB  - sequences, thereby positioning 116 new sites on the chromosome.  Twenty-four
AB  - such restriction maps for P22 DNA, containing 162 sites, have now been
AB  - completed, and three enzymes were found that did not cut P22 DNA.  Our results
AB  - are consistent with the ideas that ClaI does not cleave the methylated
AB  - recognition sequence ATCGMeAT or MeATCGAT and StuI does not cleave the
AB  - methylated recognition sequence AGGCMeCT.
ER  -

TY  - JOUR
AU  - Casjens, S.
AU  - Palmer, N.
AU  - van Vugt, R.
AU  - Huang, W.M.
AU  - Stevenson, B.
AU  - Rosa, P.
AU  - Lathigra, R.
AU  - Sutton, G.
AU  - Peterson, J.
AU  - Dodson, R.J.
AU  - Haft, D.
AU  - Hickey, E.
AU  - Gwinn, M.
AU  - White, O.
AU  - Fraser, C.M.
TI  - A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 490
EP  - 516
VL  - 35
AB  - We have determined that Borrelia burgdorferi strain B31 MI carries 21
AB  - extrachromosomal DNA elements, the largest number known for any bacterium.
AB  - Among these are 12 linear and nine circular plasmids, whose sequences
AB  - total 610 694 bp. We report here the nucleotide sequence of three linear
AB  - and seven circular plasmids (comprising 290 546 bp) in this infectious
AB  - isolate. This completes the genome sequencing project for this organism;
AB  - its genome size is 1 521 419 bp (plus about 2000 bp of undetermined
AB  - telomeric sequences). Analysis of the sequence implies that there has been
AB  - extensive and sometimes rather recent DNA rearrangement among a number of
AB  - the linear plasmids. Many of these events appear to have been mediated by
AB  - recombinational processes that formed duplications. These many regions of
AB  - similarity are reflected in the fact that most plasmid genes are members
AB  - of one of the genome's 161 paralogous gene families; 107 of these gene
AB  - families, which vary in size from two to 41 members, contain at least one
AB  - plasmid gene. These rearrangements appear to have contributed to a
AB  - surprisingly large number of apparently non-functional pseudogenes, a very
AB  - unusual feature for a prokaryotic genome. The presence of these damaged
AB  - genes suggests that some of the plasmids may be in a period of rapid
AB  - evolution. The sequence predicts 535 plasmid genes >/=300 bp in length
AB  - that may be intact and 167 apparently mutationally damaged and/or
AB  - unexpressed genes (pseudogenes). The large majority, over 90%, of genes on
AB  - these plasmids have no convincing similarity to genes outside Borrelia,
AB  - suggesting that they perform specialized functions.
ER  -

TY  - JOUR
AU  - Casjens, S.
AU  - Winn-Stapley, D.A.
AU  - Gilcrease, E.B.
AU  - Morona, R.
AU  - Kuhlewein, C.
AU  - Chua, J.E.
AU  - Manning, P.A.
AU  - Inwood, W.
AU  - Clark, A.J.
TI  - The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 379
EP  - 394
VL  - 339
AB  - Shigella flexneri temperate bacteriophage Sf6 is of interest in part because its
AB  - prophageexpresses the oac gene that alters the antigenic
AB  - properties of the surface O-antigen polysaccharide of its host bacterium.
AB  - We have determined the complete sequence of its 39,044 bp genome. The
AB  - sequence shows that Sf6 is a member of the canonical lambdoid phage group,
AB  - and like other phages of this type has a highly mosaic genome. It has
AB  - chromosomal regions that encode proteins >80% identical with at least 15
AB  - different previously characterized lambdoid phages and prophages, but 43%
AB  - of the genome, including the virion assembly genes, is homologous to the
AB  - genome of one phage, HK620. An analysis of the nucleotide differences
AB  - between Sf6 and HK620 indicates that even these similar regions are highly
AB  - mosaic. This mosaicism suggests ways in which the virion structural
AB  - proteins might interact with each other. The Sf6 early operons are
AB  - arranged like a typical lambdoid phage, with "boundary sequences" often
AB  - found between functional modules in the "metabolic" genome domain. By
AB  - virtue of high degree of similarity in the encoding genes and their DNA
AB  - target sites, we predict that the integrase, early transcription
AB  - anti-terminator, CI and Cro repressors, and CII protein of Sf6 have DNA
AB  - binding specificities very similar to the homologous proteins encoded byphages HK620, lambda,
AB  - 434 and P22, respectively. The late operon contains
AB  - two tRNA genes. The Sf6 terminase genes are unusual. Analysis of in vivo
AB  - initiation of the DNA packaging series showed that the Sf6 apparatus that
AB  - recognizes DNA for packaging appears to cleave DNA for initiation of
AB  - packaging series at many sites within a large region of about 1800 bp that
AB  - includes a possible pac site. This is unlike previously characterized
AB  - phage packaging mechanisms.
ER  -

TY  - JOUR
AU  - Casjens, S.R.
AU  - Fraser-Liggett, C.M.
AU  - Mongodin, E.F.
AU  - Qiu, W.G.
AU  - Dunn, J.J.
AU  - Luft, B.J.
AU  - Schutzer, S.E.
TI  - Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1489
EP  - 1490
VL  - 193
AB  - Human Lyme disease is caused by a number of related Borrelia burgdorferi sensu lato species.
AB  - We report here the complete genome sequence of
AB  - Borrelia sp. isolate SV1 from Finland. This isolate is to date the closest
AB  - known relative of B. burgdorferi sensu stricto, but it is sufficiently
AB  - genetically distinct from that species that it and its close relatives
AB  - warrant its candidacy for new-species status. We suggest that this isolate
AB  - should be named 'Borrelia finlandensis.'
ER  -

TY  - JOUR
AU  - Casjens, S.R.
AU  - Gilcrease, E.B.
AU  - Huang, W.M.
AU  - Bunny, K.L.
AU  - Pedulla, M.L.
AU  - Ford, M.E.
AU  - Houtz, J.M.
AU  - Hatfull, G.F.
AU  - Hendrix, R.W.
TI  - The pKO2 Linear Plasmid Prophage of Klebsiella oxytoca.
JO  - J. Bacteriol.
PY  - 2004
SP  - 1818
EP  - 1832
VL  - 186
AB  - Temperate bacteriophages with plasmid prophages are uncommon in nature, and of these only
AB  - phages N15 and PY54 are known to have a linear plasmid prophage with closed hairpin telomeres.
AB  - We report here the complete nucleotide sequence of the 51,601-bp Klebsiella oxytoca linear
AB  - plasmid pKO2, and we demonstrate experimentally that it is also a prophage. We call this
AB  - bacteriophage phiKO2. An analysis of the 64 predicted phiKO2 genes indicate that it is a
AB  - fairly close relative of phage N15; they share a mosaic relationship that is typical of
AB  - different members of double-stranded DNA tailed-phage groups. Although the head, tail shaft,
AB  - and lysis genes are not recognizably homologous between these phages, other genes such as the
AB  - plasmid partitioning, replicase, prophage repressor, and protelomerase genes (and their
AB  - putative targets) are so similar that we predict that they must have nearly identical DNA
AB  - binding specificities. The phiKO2 virion is unusual in that its phage lambda-like tails have
AB  - an exceptionally long (3,433 amino acids) central tip tail fiber protein. The phiKO2 genome
AB  - also carries putative homologues of bacterial dinI and umuD genes, both of which are involved
AB  - in the host SOS response. We show that these divergently transcribed genes are regulated by
AB  - LexA protein binding to a single target site that overlaps both promoters.
ER  -

TY  - JOUR
AU  - Casjens, S.R.
AU  - Mongodin, E.F.
AU  - Qiu, W.G.
AU  - Dunn, J.J.
AU  - Luft, B.J.
AU  - Fraser-Liggett, C.M.
AU  - Schutzer, S.E.
TI  - Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6995
EP  - 6996
VL  - 193
AB  - Human Lyme disease is commonly caused by several species of spirochetes in the Borrelia genus.
AB  - In Eurasia these species are largely Borrelia afzelii,
AB  - B. garinii, B. burgdorferi, and B. bavariensis sp. nov. Whole-genome
AB  - sequencing is an excellent tool for investigating and understanding the
AB  - influence of bacterial diversity on the pathogenesis and etiology of Lyme
AB  - disease. We report here the whole-genome sequences of four isolates from
AB  - two of the Borrelia species that cause human Lyme disease, B. afzelii
AB  - isolates ACA-1 and PKo and B. garinii isolates PBr and Far04.
ER  -

TY  - JOUR
AU  - Caspers, M.P.
AU  - Boekhorst, J.
AU  - Abee, T.
AU  - Siezen, R.J.
AU  - Kort, R.
TI  - Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.
JO  - Genome Announcements
PY  - 2013
SP  - e00010
EP  - e00013
VL  - 1
AB  - Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy
AB  - products. We isolated the thermophilic strain TNO-09.006 from a
AB  - milk-processing plant, and we report the complete genome of this isolate
AB  - consisting of a single chromosome of 2.65 Mb.
ER  -

TY  - JOUR
AU  - Caspers, M.P.
AU  - Boekhorst, J.
AU  - de Jong, A.
AU  - Kort, R.
AU  - Nierop, G.M.
AU  - Abee, T.
TI  - Draft Genome Sequences of Four Thermophilic Spore Formers Isolated from a Dairy-Processing Environment.
JO  - Genome Announcements
PY  - 2016
SP  - e00757
EP  - e00716
VL  - 4
AB  - Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy
AB  - products. Here, we report draft genome sequences of four thermophilic
AB  - strains from a milk-processing plant or standard milk, namely, a Geobacillus
AB  - thermoglucosidans isolate (TNO-09.023), Geobacillus stearothermophilus
AB  - TNO-09.027, and two Anoxybacillus flavithermus isolates (TNO-09.014 and
AB  - TNO-09.016).
ER  -

TY  - JOUR
AU  - Casselli, T.
AU  - Tourand, Y.
AU  - Scheidegger, A.
AU  - Arnold, W.K.
AU  - Proulx, A.
AU  - Stevenson, B.
AU  - Brissette, C.A.
TI  - DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi.
JO  - J. Bacteriol.
PY  - 2018
SP  - e00395
EP  - e00318
VL  - 200
AB  - Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially
AB  - detrimental foreign DNA. Recent evidence suggests that DNA
AB  - methylation by the methyltransferase (MTase) components of RM systems can also
AB  - have effects on transcriptome profiles. The type strain of the causative agent of
AB  - Lyme disease, Borrelia burgdorferi B31, possesses two RM systems with
AB  - N6-methyladenosine (m6A) MTase activity, which are encoded by the bbe02 gene
AB  - located on linear plasmid lp25 and bbq67 on lp56. The specific recognition and/or
AB  - methylation sequences had not been identified for either of these B. burgdorferi
AB  - MTases, and it was not previously known whether these RM systems influence
AB  - transcript levels. In the current study, single-molecule real-time sequencing was
AB  - utilized to map genome-wide m6A sites and to identify consensus modified motifs
AB  - in wild-type B. burgdorferi as well as MTase mutants lacking either the bbe02
AB  - gene alone or both bbe02 and bbq67 genes. Four novel conserved m6A motifs were
AB  - identified and were fully attributable to the presence of specific MTases.
AB  - Whole-genome transcriptome changes were observed in conjunction with the loss of
AB  - MTase enzymes, indicating that DNA methylation by the RM systems has effects on
AB  - gene expression. Genes with altered transcription in MTase mutants include those
AB  - involved in vertebrate host colonization (e.g., rpoS regulon) and acquisition
AB  - by/transmission from the tick vector (e.g., rrp1 and pdeB). The results of this
AB  - study provide a comprehensive view of the DNA methylation pattern in B.
AB  - burgdorferi, and the accompanying gene expression profiles add to the emerging
AB  - body of research on RM systems and gene regulation in bacteria.IMPORTANCE Lyme
AB  - disease is the most prevalent vector-borne disease in North America and is
AB  - classified by the Centers for Disease Control and Prevention (CDC) as an emerging
AB  - infectious disease with an expanding geographical area of occurrence. Previous
AB  - studies have shown that the causative bacterium, Borrelia burgdorferi, methylates
AB  - its genome using restriction modification systems that enable the distinction
AB  - from foreign DNA. Although much research has focused on the regulation of gene
AB  - expression in B. burgdorferi, the effect of DNA methylation on gene regulation
AB  - has not been evaluated. The current study characterizes the patterns of DNA
AB  - methylation by restriction modification systems in B. burgdorferi and evaluates
AB  - the resulting effects on gene regulation in this important pathogen.
ER  -

TY  - JOUR
AU  - Cassir, N.
AU  - Croce, O.
AU  - Pagnier, I.
AU  - Benamar, S.
AU  - Couderc, C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 794
EP  - 806
VL  - 9
AB  - Bacteroides neonati strain MS4(T), is the type strain of Bacteroides neonati sp.  nov., a new
AB  - species within the genus Bacteroides. This strain, whose genome is
AB  - described here, was isolated from a premature neonate stool sample. B. neonati
AB  - strain MS4(T) is an obligate anaerobic Gram-negative bacillus. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and
AB  - contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes.
ER  -

TY  - JOUR
AU  - Castel, A.L.
AU  - Nakamori, M.
AU  - Thornton, C.A.
AU  - Pearson, C.E.
TI  - Identification of restriction endonucleases sensitive to 5-cytosine methylation at non-CpG sites, including expanded (CAG)n/(CTG)n repeats.
JO  - EPIGENETICS
PY  - 2011
SP  - 417
EP  - 421
VL  - 6
AB  - Most epigenetic studies assess methylation of 5'-CpG-3' sites but recent evidence indicates
AB  - that non-CpG cytosine methylation occurs at
AB  - high levels in humans and other species. This is most prevalent at
AB  - 5'-CHG-3', where H = A, C or T, and it preferentially occurs at
AB  - 5'-CpA-3' and 5'-CpT-3' sites. With the goal of facilitating the
AB  - detection of non-CpG methylation, the restriction endonucleases ApeKI,
AB  - BbvI, EcoP15I, Fnu4HI, MwoI and TseI were assessed for their
AB  - sensitivity to 5-methylcytosine at GpCpA, GpCpT, GpCpC or GpCpG sites,
AB  - where methylation is catalyzed by the DNA 5-cytosine 5'-GpC-3'
AB  - methyltransferase M.CviPI. We tested a variety of sequences including
AB  - various plasmid-based sites, a cloned disease-associated (CAG)83 center
AB  - dot(CTG)83 repeat and in vitro synthesized tracts of only (CAG)500
AB  - center dot(CTG) 500 or (CAG)800 center dot(CTG)800. The repeat tracts
AB  - are enriched for the preferred CpA and CpT motifs. We found that none
AB  - of the tested enzymes can cleave their recognition sequences when they
AB  - are 5'-GpC-3' methylated. A genomic site known to convert its non-CpG
AB  - methylation levels upon C2C12 differentiation was confirmed through the
AB  - use of these enzymes. These enzymes can be useful in rapidly and easily
AB  - determining the most common non-CpG methylation status in various
AB  - sequence contexts, as well as at expansions of (CAG) n.(CTG) n repeat
AB  - tracts associated with diseases like myotonic dystrophy and Huntington
AB  - disease.
ER  -

TY  - JOUR
AU  - Castelan-Vega, J.A.
AU  - Jimenez-Alberto, A.
AU  - Ribas-Aparicio, R.M.
TI  - Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA.
JO  - J. Mol. Model.
PY  - 2010
SP  - 1213
EP  - 1222
VL  - 16
AB  - M.HgiDII is a methyltransferase (MTase) from Herpetosiphon giganteus that recognizes the
AB  - sequence GTCGAC. This enzyme belongs to a group of
AB  - MTases that share a high degree of amino acid similarity, albeit none
AB  - of them has been thoroughly characterized. To study the catalytic
AB  - mechanism of M.HgiDII and its interactions with DNA, we performed
AB  - molecular dynamics simulations with a homology model of M.HgiDII
AB  - complexed with DNA and S-adenosyl-methionine. Our results indicate that
AB  - M.HgiDII may not rely only on Glu119 to activate the cytosine ring,
AB  - which is an early step in the catalysis of cytosine methylation;
AB  - apparently, Arg160 and Arg162 may also participate in the activation by
AB  - interacting with cytosine O2. Another residue from the catalytic site,
AB  - Val118, also played a relevant role in the catalysis of M.HgiDII.
AB  - Val118 interacted with the target cytosine and kept water molecules
AB  - from accessing the region of the catalytic pocket where Cys79 interacts
AB  - with cytosine, thus preventing water-mediated disruption of
AB  - interactions in the catalytic site. Specific recognition of DNA was
AB  - mediated mainly by amino acids of the target recognition domain,
AB  - although some amino acids (loop 80-88) of the catalytic domain may also
AB  - contribute to DNA recognition. These interactions involved direct
AB  - contacts between M.HgiDII and DNA, as well as indirect contacts through
AB  - water bridges. Additionally, analysis of sequence alignments with
AB  - closely related MTases helped us to identify a motif in the TRD of
AB  - M.HgiDII that may be relevant to specific DNA recognition.
ER  -

TY  - JOUR
AU  - Castellano, S.
AU  - Kuck, D.
AU  - Sala, M.
AU  - Novellino, E.
AU  - Lyko, F.
AU  - Sbardella, G.
TI  - Constrained analogues of procaine as novel small molecule inhibitors of DNA methyltransferase-1.
JO  - J. Med. Chem.
PY  - 2008
SP  - 2321
EP  - 2325
VL  - 51
AB  - Constrained analogues of procaine were synthesized, and their inhibiting activity against
AB  - DNMT1 was tested. Among them, the most
AB  - potent compound, derivative 3b, was also able to induce a recognizable
AB  - demethylation of chromosomal satellite repeats in HL60 human myeloid
AB  - leukemia cells and thus represents a lead compound for the development
AB  - of a novel class of non-nucleoside DNMT1 inhibitors.
ER  -

TY  - JOUR
AU  - Casteneda-Ruelas, G.M.
AU  - Carreon-Gaxiola, C.
AU  - Castelan-Sanchez, H.G.
AU  - Acatzi-Silva, A.
AU  - Romero-Martinez, S.
AU  - Garcia-Molina, A.
AU  - Jimenez-Edeza, M.
TI  - Draft Genome Sequences of 18 Salmonella enterica subsp. enterica Serovar Oranienburg Strains Isolated from Rivers in Northwestern Mexico.
JO  - Genome Announcements
PY  - 2017
SP  - e01585
EP  - e01516
VL  - 5
AB  - Salmonella enterica subsp. enterica serovar Oranienburg is recognized as a foodborne pathogen
AB  - widely distributed in the environment. Here, we report 18
AB  - draft genomes of S Oranienburg strains isolated from rivers in the northwestern
AB  - region of Mexico.
ER  -

TY  - JOUR
AU  - Castignetti, D.
AU  - Polley, N.
AU  - Putonti, C.
TI  - Draft Genome Sequence of the Siderophore-Degrading Soil Bacterium Mesorhizobium loti Strain LU.
JO  - Genome Announcements
PY  - 2018
SP  - e00029
EP  - e00018
VL  - 6
AB  - Here, we present the draft genome of Mesorhizobium loti strain LU, a soil bacterium capable of
AB  - degrading the trihydroxamate siderophore deferrioxamine B to
AB  - its constituent monohydroxamic acids. Genome size was 6,399,828 bp, with a GC
AB  - content of 61.5%. This draft genome consists of 35 scaffolds, with an N50 of
AB  - 389,921 bp.
ER  -

TY  - JOUR
AU  - Castillo, A.
AU  - Peterson, S.
TI  - The role of GATC flanking sequences in the methylation efficiency of Escherichia coli DNA adenine methyltransferase.
JO  - FASEB J.
PY  - 2009
SP  - 482.3
EP  - 482.3
VL  - 23
AB  - Escherichia coli DNA adenine methyltransferase (Dam) methylates the adenine in GATC sequences.
AB  - The enzyme plays a crucial role in the
AB  - timing of DNA replication, gene regulation, and mismatch repair. Many
AB  - genes that Dam regulates are involved in pathogenesis. Previous in
AB  - vitro studies showed that certain GATC sites were preferentially
AB  - methylated depending upon the GATC flanking sequences. Sites rich in
AB  - A/T base pairs tend to be less preferred than those rich in G/C. Poorly
AB  - preferred GATC sites as determined by in vitro studies are also
AB  - undermethylated in vivo. The lack of methylation at these sites is
AB  - often important for the expression of pathogenic genes. Our goal is to
AB  - determine if GATC flanking sequences affect Dam methylation efficiency
AB  - at certain sites in vivo. We hypothesize that the same trend will hold
AB  - true in vivo and G/C rich flanking sequences will be preferred.
AB  - dam-minus cells were transformed with a plasmid containing the dam gene
AB  - under control of the arabinose promoter. After growth at low
AB  - concentrations of Dam we isolated the plasmid and observed the
AB  - methylation levels of GATC sites. We found that a GATC with G/C rich
AB  - flanking sequences was preferentially methylated compared to a
AB  - consecutive GATC with A/T rich flanking sequences. Our studies will
AB  - help in understanding how Dam is able to discriminate between GATC
AB  - sites in vivo which is important for its various roles, particularly
AB  - gene regulation.
ER  -

TY  - JOUR
AU  - Castillo, D.
AU  - D'Alvise, P.
AU  - Kalatzis, P.G.
AU  - Kokkari, C.
AU  - Middelboe, M.
AU  - Gram, L.
AU  - Liu, S.
AU  - Katharios, P.
TI  - Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens.
JO  - Genome Announcements
PY  - 2015
SP  - e00729
EP  - e00715
VL  - 3
AB  - We announce the draft genome sequences of Vibrio alginolyticus strains V1 and V2, isolated
AB  - from juvenile Sparus aurata and Dentex dentex, respectively, during
AB  - outbreaks of vibriosis. The genome sequences are 5,257,950 bp with a G+C content
AB  - of 44.5% for V. alginolyticus V1 and 5,068,299 bp with a G+C content of 44.8% for
AB  - strain V2. These genomes provide further insights into the putative virulence
AB  - factors, prophage carriage, and evolution of this opportunistic marine pathogen.
ER  -

TY  - JOUR
AU  - Castillo, D.
AU  - D'Alvise, P.
AU  - Middelboe, M.
AU  - Gram, L.
AU  - Liu, S.
AU  - Kalatzis, P.G.
AU  - Kokkari, C.
AU  - Katharios, P.
TI  - Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5.
JO  - Genome Announcements
PY  - 2015
SP  - e01062
EP  - e01015
VL  - 3
AB  - Vibrio harveyi is an important marine pathogen that is responsible for vibriosis  outbreaks in
AB  - cultured fish and invertebrates worldwide. Here, we announce the draft genome sequences of V.
AB  - harveyi strains VH2 and VH5, isolated from farmed juvenile Seriola dumerili during outbreaks
AB  - of vibriosis in Crete, Greece.
ER  -

TY  - JOUR
AU  - Castillo, D.
AU  - Gram, L.
AU  - Dailey, F.E.
TI  - Genome Sequences of Shewanella baltica and Shewanella morhuae Strains Isolated from the Gastrointestinal Tract of Freshwater Fish.
JO  - Genome Announcements
PY  - 2018
SP  - e00541
EP  - e00518
VL  - 6
AB  - We present here the genome sequences of Shewanella baltica strain CW2 and Shewanella morhuae
AB  - strain CW7, isolated from the gastrointestinal tract of
AB  - Salvelinus namaycush (lean lake trout) and Coregonus clupeaformis (whitefish),
AB  - respectively. These genome sequences provide insights into the niche adaptation
AB  - of these specific species in freshwater systems.
ER  -

TY  - JOUR
AU  - Castillo, D.
AU  - Gram, L.
AU  - Dailey, F.E.
TI  - Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands.
JO  - Genome Announcements
PY  - 2018
SP  - e00277
EP  - e00218
VL  - 6
AB  - We present here the whole-genome sequence of Shewanella sp. WE21, an unusual omega-3 fatty
AB  - acid-producing bacterium isolated from the gastrointestinal tract
AB  - of the freshwater fish Sander vitreus (walleye). This genome contains a number of
AB  - unique, large genomic islands with genes not present in other Shewanella
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Castillo, D.
AU  - Jun, J.W.
AU  - D'Alvise, P.
AU  - Middelboe, M.
AU  - Gram, L.
AU  - Liu, S.
AU  - Katharios, P.
TI  - Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece.
JO  - Genome Announcements
PY  - 2015
SP  - e00731
EP  - e00715
VL  - 3
AB  - Vibrio parahaemolyticus is an important foodborne pathogen responsible for gastroenteritis
AB  - outbreaks globally. It has also been identified as an important
AB  - pathogen in aquatic organisms. Here, we report a draft genome sequence of V.
AB  - parahaemolyticus, strain VH3, isolated from farmed juvenile greater amberjack,
AB  - Seriola dumerili, in Greece.
ER  -

TY  - JOUR
AU  - Castillo, D.
AU  - Vandieken, V.
AU  - Engelen, B.
AU  - Engelhardt, T.
AU  - Middelboe, M.
TI  - Draft Genome Sequences of Six Vibrio diazotrophicus Strains Isolated from Deep Subsurface Sediments of the Baltic Sea.
JO  - Genome Announcements
PY  - 2018
SP  - e00081
EP  - e00018
VL  - 6
AB  - We present here the draft genome sequences of six Vibrio diazotrophicus strains,  which were
AB  - isolated from deep subseafloor sediments of the Baltic Sea. The
AB  - genomic sequences contained several virulence and antibiotic resistance genes.
AB  - These genome sequences provide insights into the genetic composition and
AB  - evolution of the genus Vibrio in marine environments.
ER  -

TY  - JOUR
AU  - Castillo, V.G.A.
AU  - Poehlein, A.
TI  - Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T.
JO  - Genome Announcements
PY  - 2016
SP  - e00444
EP  - e00416
VL  - 4
AB  - Here, we report the draft genome sequence of Moorella mulderi DSM 14980(T), a thermophilic
AB  - acetogenic bacterium, which is able to grow autotrophically on H2
AB  - plus CO2 using the Wood-Ljungdahl pathway. The genome consists of a circular
AB  - chromosome (2.99 Mb).
ER  -

TY  - JOUR
AU  - Castrillo, M.L.
AU  - Bich, G.A.
AU  - Modenutti, C.
AU  - Turjanski, A.
AU  - Zapata, P.D.
AU  - Villalba, L.L.
TI  - First Whole-Genome Shotgun Sequence of a Promising Cellulase Secretor, Trichoderma koningiopsis Strain POS7.
JO  - Genome Announcements
PY  - 2017
SP  - e00823
EP  - e00817
VL  - 5
AB  - Trichoderma koningiopsis strain POS7 produces significantly large amounts of cellulase enzymes
AB  - in solid-state fermentation. The Illumina-based sequence
AB  - analysis reveals an approximate genome size of 36.6 Mbp, with a G+C content of
AB  - 48.82% for T. koningiopsis POS7. Based on ab initio prediction, 12,661 coding
AB  - genes were annotated.
ER  -

TY  - JOUR
AU  - Castro, M.
AU  - Moya-Beltran, A.
AU  - Covarrubias, P.C.
AU  - Gonzalez, M.
AU  - Cardenas, J.P.
AU  - Issotta, F.
AU  - Nunez, H.
AU  - Acuna, L.G.
AU  - Encina, G.
AU  - Holmes, D.S.
AU  - Johnson, D.B.
AU  - Quatrini, R.
TI  - Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366).
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 77
EP  - 77
VL  - 12
AB  - Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic
AB  - sulfur-oxidizer, with potential importance in the bioleaching of
AB  - sulfidic metal ores, first described in the 1980s. Here we present the draft
AB  - genome sequence of Acidithiobacillus albertensis DSM 14366(T), thereby both
AB  - filling a long-standing gap in the genomics of the acidithiobacilli, and
AB  - providing further insight into the understanding of the biology of the non
AB  - iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is
AB  - 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149
AB  - protein-coding predicted genes. The Whole Genome Shotgun project was deposited in
AB  - DDBJ/EMBL/GenBank under the accession MOAD00000000.
ER  -

TY  - JOUR
AU  - Castro, W.O.
AU  - Lima, A.R.
AU  - Moraes, P.H.
AU  - Siqueira, A.S.
AU  - Aguiar, D.C.
AU  - Barauna, A.R.
AU  - Martins, L.C.
AU  - Fuzii, H.T.
AU  - de Lima, C.P.
AU  - Vianez-Junior, J.L.
AU  - Nunes, M.R.
AU  - Dall'Agnol, L.T.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of Microcystis aeruginosa CACIAM 03, a Cyanobacterium Isolated from an Amazonian Freshwater Environment.
JO  - Genome Announcements
PY  - 2016
SP  - e01299
EP  - e01216
VL  - 4
AB  - Given its toxigenic potential, Microcystis aeruginosa is an important bloom-forming
AB  - cyanobacterium. Here, we present a draft genome and annotation of
AB  - the strain CACIAM 03, which was isolated from an Amazonian freshwater
AB  - environment.
ER  -

TY  - JOUR
AU  - Castro, W.O.
AU  - Torres-Ballesteros, A.M.
AU  - Nakayama, C.R.
AU  - Melo, I.S.
AU  - Pellizari, V.H.
AU  - Silva, A.
AU  - Ramos, R.T.
TI  - Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga.
JO  - Genome Announcements
PY  - 2014
SP  - e00812
EP  - e00814
VL  - 2
AB  - Organisms in the Haloferax genus are extreme halophiles that grow in environments with pH
AB  - values between 4 and 12, and temperatures between 0 degrees C and 60
AB  - degrees C. In the present study, a draft of the first Haloferax sp. strain ATB1
AB  - genome isolated from the region of Cariri (in Paraiba State, Brazil) is
AB  - presented.
ER  -

TY  - JOUR
AU  - Castro-Jaimes, S.
AU  - Salgado-Camargo, A.D.
AU  - Grana-Miraglia, L.
AU  - Lozano, L.
AU  - Bocanegra-Ibarias, P.
AU  - Volkow-Fernandez, P.
AU  - Silva-Sanchez, J.
AU  - Castillo-Ramirez, S.
AU  - Cevallos, M.A.
TI  - Complete Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Isolate Obtained from a Mexican Hospital (Sequence Type 422).
JO  - Genome Announcements
PY  - 2016
SP  - e00583
EP  - e00516
VL  - 4
AB  - Acinetobacter baumannii has emerged as a dangerous nosocomial pathogen, particularly for
AB  - severely ill patients in intensive care units and patients with
AB  - hematologic malignancies. Here, we present the complete genome sequence of a
AB  - multidrug-resistant A. baumannii isolate, recovered from a Mexican hospital and
AB  - classified as sequence type 422 according to the multilocus sequence typing
AB  - Pasteur scheme.
ER  -

TY  - JOUR
AU  - Castro-Nallar, E.
AU  - Valenzuela, S.L.
AU  - Baquedano, S.
AU  - Sanchez, C.
AU  - Fernandez, F.
AU  - Trombert, A.N.
TI  - Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection.
JO  - Genome Announcements
PY  - 2017
SP  - e00379
EP  - e00317
VL  - 5
AB  - We present draft genome sequences of five Enterococcus species from patients suspected of
AB  - Clostridium difficile infection. Genome completeness was confirmed
AB  - by presence of bacterial orthologs (97%). Gene searches using Hidden-Markov
AB  - models revealed that the isolates harbor between seven and 11 genes involved in
AB  - antibiotic resistance to tetracyclines, beta-lactams, and vancomycin.
ER  -

TY  - JOUR
AU  - Castronovo, M.
AU  - Radovic, S.
AU  - Grunwald, C.
AU  - Casalis, L.
AU  - Morgante, M.
AU  - Scoles, G.
TI  - Control of Steric Hindrance on Restriction Enzyme Reactions with Surface-Bound DNA Nanostructures.
JO  - Nano Lett.
PY  - 2008
SP  - 4140
EP  - 4145
VL  - 8
AB  - To understand better enzyme/DNA interactions and to design innovative detectors based on DNA
AB  - nanoarrays, we need to study the effect of
AB  - nanometric confinement on the biochemical activity of the DNA
AB  - molecules. We focus on the study of the restriction enzyme reactions
AB  - (Dpnll within DNA nanostructures on flat gold films by atomic force
AB  - microscopy (AFM). Typically we work with a few patches of DNA self
AB  - assembled monolayers (SAMs) that are hundred nm in size and are
AB  - lithographically fabricated within alkylthiol SAMs by AFM nanografting.
AB  - We start by nanografting a few patches of a single-stranded DNA (ssDNA)
AB  - molecule of 44 base pairs (bps) with a 4 bps recognition sequence
AB  - (specific for Dpnll in the middle. Afterwards, reaction-ready DNA
AB  - nanopatches are obtained by hybridization with a complementary 44bps
AB  - ssDNA sequence. The enzymatic reactions were carried out over
AB  - nanopatches with different density. By carrying out AFM height
AB  - measurements, we are able to show that the capability of the Dpnll
AB  - enzyme to reach and react at the recognition site is easily varied by
AB  - controlling the DNA packing in the nanostructures. We have found strong
AB  - evidence that inside our ordered DNA nanostructures the enzyme (that
AB  - works as a dimer) can operate down to the limit in which the space
AB  - between adjacent DNA molecules is equal to the size of the DNA/enzyme
AB  - complex. Similar experiments were carried out with a DNA sequence
AB  - without the recognition site, clearly finding that in that case the
AB  - enzymatic reaction did not lead to digestion of the molecules. These
AB  - findings suggest that it is possible to tune the efficiency of an
AB  - enzymatic reaction on a surface by controlling the steric hindrance
AB  - inside the DNA nanopatches without vary any further physical or
AB  - chemical variable. These findings are opening the door to novel
AB  - applications in both the fields of biosensing and fundamental
AB  - biophysics.
ER  -

TY  - JOUR
AU  - Catania, J.
AU  - Keenan, B.C.
AU  - Margison, G.P.
AU  - Fairweather, D.S.
TI  - Determination of 5-methylcytosine by acid hydrolysis of DNA with hydrofluoric acid.
JO  - Anal. Biochem.
PY  - 1987
SP  - 347
EP  - 351
VL  - 167
AB  - Quantitation of 5-methylcytosine in DNA after acid hydrolysis has been
AB  - inaccurate because deamination of cytosine and 5-methylcytosine occurs during
AB  - the hydrolysis procedure.  There is little information in the literature
AB  - regarding the use of hydrofluoric acid (HF) for DNA hydrolysis and we have
AB  - therefore undertaken a systematic study of this process.  The
AB  - deoxyribonucleotides of cytosine and 5-methylcytosine were shown not to undergo
AB  - detectable levels of deaminatiton during prolonged periods (up to 24 h) at 80C
AB  - in 48% HF.  Kinetic studies show that the release of purine and pyrimidine
AB  - bases was complete by 4 h under these conditons.  Analysis of the
AB  - 5-methylcytosine content of DNA from various tissues gave levels that were very
AB  - close to the values reported in the literature.  This method is ideally suited
AB  - for the determination of the overall cytosine methylation levels in DNA.
ER  -

TY  - JOUR
AU  - Catcheside, D.E.A.
TI  - A restriction and modification model for the initiation and control of recombination in Neurospora.
JO  - Genet. Res.
PY  - 1986
SP  - 157
EP  - 165
VL  - 47
AB  - It is hypothesized that the products of Neurospora rec+ genes mask
AB  - recombinators such as cog by modifying DNA and that unmodified recombinators
AB  - act as recognition sites for an endonuclease with scission properties like
AB  - those of the type I restriction enzymes found in E. coli.  These cut the DNA in
AB  - both strands at some variable distance from a recognition site.  Repair of a
AB  - two strand gap initiated in this way would require DNA synthesis using the
AB  - information contained in the homologous DNA duplex, leading to gene conversion.
AB  - Crossing over could follow from resolution of two Holliday structures formed
AB  - during gap repair.  The hypothesis explains the polarity in the frequency of
AB  - conversion events across genetic loci, the observation that chromosomes
AB  - carrying recombinators are more often converted than is the homologue, and how
AB  - recombinators can initiate conversion at a distance, as suggested by the
AB  - pattern of conversion events in the his-3 locus in crosses heterozygous for the
AB  - translocation TM429.
ER  -

TY  - JOUR
AU  - Catterall, J.F.
AU  - Lees, N.D.
AU  - Welker, N.E.
TI  - Restriction and modification in Thermophilic bacilli.
JO  - Microbiology-1976
PY  - 1976
SP  - 358
EP  - 366
VL  - 0
AB  - Over the past several years we have been engaged in an effort to develop transformation in B.
AB  - stearothermophilus.  Until recently these studies have met with little success.  During this
AB  - time, however, a transfection system was established.  This system requires a 'helper phage'
AB  - which may facilitate adsorption and/or uptake of the bacteriophage DNA from the environment.
AB  - While studying the uptake and expression of infectious phage DNA, we observed that the
AB  - efficiency of transfection varied as much as 1,000-fold depending upon the strain in which the
AB  - phage were propagated.  These results suggested the presence of a restriction and modification
AB  - system.  This hypothesis was verified when we identified, by efficiency of plating (EOP)
AB  - studies, classical restriction and modification systems in these strains.  In this
AB  - communication, we describe preliminary studies on the restriction and modification systems in
AB  - B. stearothermophilus.
ER  -

TY  - JOUR
AU  - Catterall, J.F.
AU  - Welker, N.E.
TI  - Purification and Properties of the Bst1503 Endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 167
EP  - 170
VL  - 65
AB  - Site-specific endonucleases have become invaluable to the study of the
AB  - structure and function of DNA from both prokaryotic and eukaryotic organisms.
AB  - Some enzymes of this class, the restriction endonucleases, have been shown to
AB  - have a specific in vivo  function acting to protect bacterial cells from
AB  - infection.  An associated enzyme, a modification methylase, must be present in
AB  - cells producing a restriction enzyme to protect cellular DNA from digestion.
AB  - It has recently been shown that restriction enzymes may be capable of promoting
AB  - site-specific recombination in vivo.  The obligate thermophile Bacillus
AB  - stearothermophilus  exhibited typical host-specific restriction and
AB  - modification during infection by thermophilic bacteriophages.  A restriction
AB  - endonuclease (endo R.Bst15035) was purified from B. stearothermophilus strain
AB  - 1503-4R.6  The purified Bst1503 retains its thermostability and is optimally
AB  - active at temperatures near the optimal growth temperature of the organism.
AB  - The enzyme is stable to long incubation at 65C in the absence of substrate and
AB  - forms limit digests after similar incubations in the presence of DNA.  Bst1503
AB  - is also stable to long term storage at 5C.
ER  -

TY  - JOUR
AU  - Catterall, J.F.
AU  - Welker, N.E.
TI  - Reduced efficiency of transfection in Bacillus stearothermophilus with modified phage DNA.
JO  - Mol. Genetics Bulletin
PY  - 1974
SP  - 9
EP  - 10
VL  - 37
AB  - The infection of B. stearothermophilus, strain 4S with the thermophilic phage
AB  - TP-IC or TP-84 DNA requires the presence of helper phage TP-12.  The mechanism
AB  - by which the helper phage initiates transfection is unknown.
ER  -

TY  - JOUR
AU  - Catterall, J.F.
AU  - Welker, N.E.
TI  - Isolation and properties of a thermostable restriction endonuclease (Endo R.Bst1503) .
JO  - J. Bacteriol.
PY  - 1977
SP  - 1110
EP  - 1120
VL  - 129
AB  - A restriction endonuclease was isolated from Bacillus stearothermophilus
AB  - 1503-4R (Bst1503) and purified to homogeneity.  The enzyme required Mg2+ ion as
AB  - a cofactor.  Bst1503 exhibited maximal activity between pH 7.5 and 8.0 between
AB  - 60 and 65C, and with about 0.2mM Mg2+.  Bst1503 was not inactivated after
AB  - exposure at 55 or 65C for up to 10h.  After 2h of incubation at 70C.  Bst1503
AB  - was inactivated by 65%.  Bst1503 was rapidly inactivated at 75C.  A single
AB  - protein-staining band having a molecular weight of 46,000 was obseved when
AB  - Bst1503 was analyzed by sodium dodecyl sufate-polyacrylamide gel
AB  - electrophoresis.  The enzyme was found to exist in two active forms, the
AB  - predominating form with an S value of 8.3 (180,000) and the second form with an
AB  - S value of 5.4 (96,000).  No conversion between the 8.3S and 5.4S forms was
AB  - observed after storage.  Bst1503 recognized six sites in TP-1C deoxyribonucleic
AB  - acid (DNA), one site in pSC101 and simian virus 40 DNAs, and three sites in
AB  - kvir DNA.  Bst1503 and BamHI were determined to be isoschizomers.  The effect
AB  - of temperatures on the activity and stability of BamHI was determined.
ER  -

TY  - JOUR
AU  - Catto, L.E.
AU  - Bellamy, S.R.
AU  - Retter, S.E.
AU  - Halford, S.E.
TI  - Dynamics and consequences of DNA looping by the FokI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 2073
EP  - 2081
VL  - 36
AB  - Genetic events often require proteins to be activated by interacting with two DNA sites,
AB  - trapping the intervening DNA in a loop. While much is known about looping equilibria, only a
AB  - few studies have examined DNA-looping dynamics experimentally. The restriction enzymes that
AB  - cut DNA after interacting with two recognition sites, such as FokI, can be used to exemplify
AB  - looping reactions. The reaction pathway for FokI on a supercoiled DNA with two sites was
AB  - dissected by fast kinetics to reveal, in turn: the initial binding of a protein monomer to
AB  - each site; the protein-protein association to form the dimer, trapping the loop; the
AB  - subsequent phosphodiester hydrolysis step. The DNA motion that juxtaposes the sites ought on
AB  - the basis of Brownian dynamics to take approximately 2 ms, but loop capture by FokI took 230
AB  - ms. Hence, DNA looping by FokI is rate limited by protein association rather than DNA
AB  - dynamics. The FokI endonuclease also illustrated activation by looping: it cut looped DNA 400
AB  - times faster than unlooped DNA.
ER  -

TY  - JOUR
AU  - Catto, L.E.
AU  - Ganguly, S.
AU  - Milsom, S.E.
AU  - Welsh, A.J.
AU  - Halford, S.E.
TI  - Protein assembly and DNA looping by the FokI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 1711
EP  - 1711
VL  - 34
AB  - The FokI restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands
AB  - at fixed positions upstream of the site. The sequence is contacted by a single monomer of the
AB  - protein, but the monomer has only one catalytic centre and forms a dimer to cut both strands.
AB  - FokI is also known to cleave DNA with two copies of its site more rapidly than DNA with one
AB  - copy. To discover how FokI acts at a single site and how it acts at two sites, its reactions
AB  - were examined on a series of plasmids with either one recognition site or with two sites
AB  - separated by varied distances, sometimes in the presence of a DNA-binding defective mutant of
AB  - FokI. These experiments showed that, to cleave DNA with one site, the monomer bound to that
AB  - site associates via a weak protein-protein interaction with a second monomer that remains
AB  - detached from the recognition sequence. Nevertheless, the second monomer catalyses
AB  - phosphodiester bond hydrolysis at the same rate as the DNA-bound monomer. On DNA with two
AB  - sites, two monomers of FokI interact strongly, as a result of being tethered to the same
AB  - molecule of DNA, and sequester the intervening DNA in a loop.
ER  -

TY  - JOUR
AU  - Caulfield, T.
AU  - Medina-Franco, J.L.
TI  - Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A.
JO  - J. Struct. Biol.
PY  - 2011
SP  - 185
EP  - 191
VL  - 176
AB  - DNA methyltransferases (DNMTs) are involved in epigenetic regulation of the genome and are
AB  - promising targets for therapeutic intervention in
AB  - cancer and other diseases. Until now, very limited information is
AB  - available concerning the molecular dynamics of DNMTs. The natural
AB  - product nanaomycin A is the first selective inhibitor of DNMT3B that
AB  - induce genomic demethylation. Herein we report long (>100 ns) molecular
AB  - dynamics simulations for human DNMT3B bound to nanaomycin A with and
AB  - without the presence of the cofactor S-adenosyl-L-methionine (SAM). We
AB  - concluded that SAM favors the binding of nanaomycin A to DNMT3B. Key
AB  - interactions of nanaomycin A with DNMT3B involve long lasting
AB  - interactions with Arg731, Arg733, Arg832, and the catalytic Cys651.
AB  - Results further support the previous hypothesis that nanaomycin A has
AB  - key interactions with amino acid residues involved in the mechanism of
AB  - methylation. This work represents one of the first molecular dynamics
AB  - studies of DNMT3B. Results of this work shed light on the structure and
AB  - binding recognition process of a key epigenetic enzyme with a small
AB  - molecule inhibitor.
ER  -

TY  - JOUR
AU  - Cavalca, L.
AU  - Corsini, A.
AU  - Andreoni, V.
AU  - Muyzer, G.
TI  - Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater.
JO  - Genome Announcements
PY  - 2013
SP  - e01072
EP  - e01013
VL  - 1
AB  - Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp.
AB  - strain 2WW, which consists of a 4.15-Mb chromosome and contains
AB  - different genes that are involved in arsenic transformations.
ER  -

TY  - JOUR
AU  - Cavalcante, A.L.
AU  - Dias, L.M.
AU  - Alves, J.T.
AU  - Veras, A.A.
AU  - Guimaraes, L.C.
AU  - Rocha, F.S.
AU  - Gala-Garcia, A.
AU  - Retamal, P.
AU  - Ramos, R.T.
AU  - Azevedo, V.
AU  - Silva, A.
AU  - Carneiro, A.R.
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain E19, Isolated from a Horse in Chile.
JO  - Genome Announcements
PY  - 2015
SP  - e01385
EP  - e01315
VL  - 3
AB  - Corynebacterium pseudotuberculosis is related to several diseases infecting horses and small
AB  - ruminants, causing economic losses to agribusiness. Here, we
AB  - present the genome sequence of C. pseudotuberculosis strain E19. The genome
AB  - includes one circular chromosome 2,367,956 bp (52.1% G+C content), with 2,112
AB  - genes predicted, 12 rRNAs, and 48 tRNAs.
ER  -

TY  - JOUR
AU  - Caverly, L.J.
AU  - Spilker, T.
AU  - LiPuma, J.J.
TI  - Complete Genome Sequences of 17 Rapidly Growing Nontuberculous Mycobacterial Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e01009
EP  - e01016
VL  - 4
AB  - We report the complete genome sequences of 17 rapidly growing nontuberculous mycobacterial
AB  - (NTM) strains, including 16 Mycobacterium abscessus complex strains
AB  - and one M. immunogenum strain. These sequences add value to studies of the
AB  - genetic diversity of rapidly growing NTM strains recovered from human specimens.
ER  -

TY  - JOUR
AU  - Caverly, L.J.
AU  - Spilker, T.
AU  - LiPuma, J.J.
TI  - Complete Genome Sequence of Mycobacterium abscessus subsp. bolletii.
JO  - Genome Announcements
PY  - 2016
SP  - e00543
EP  - e00516
VL  - 4
AB  - We report the complete genome sequence of a Mycobacterium abscessus subsp. bolletii isolate
AB  - recovered from a sputum culture from an individual with cystic
AB  - fibrosis. This sequence is the first completed whole-genome sequence of M.
AB  - abscessus subsp. bolletii and adds value to studies of M. abscessus complex
AB  - genomics.
ER  -

TY  - JOUR
AU  - Cayley, S.
AU  - Record, M.T.
TI  - Anions affect the in vitro function of endonuclease EcoRI.
JO  - J. Cell Biochem. Suppl.
PY  - 1987
SP  - 204
EP  - 204
VL  - 11C
AB  - Environmental variables dictate the stability and function of protein-DNA
AB  - interactions in vitro.  For instance, increasing the in vitro K+ concentration
AB  - drastically affects both the rate and extent of the formation of EcoRI-DNA
AB  - complexes (1).  Here we show the critical importance of anionic solution
AB  - components in determining the functional activity of EcoRI.  K+ and glutamate
AB  - are the predominant intracellular ionic species in E. coli and the in vivo
AB  - concentrations of these ions can accumulate to greater than 0.9 and 0.25 M,
AB  - respectively, as part of the osmotic adaptability of the organism.  Comparison
AB  - of the extent of DNA cutting by EcoRI as a function of KCl or KGlu
AB  - concentration in vitro indicates the rate of cleavage is not only highly
AB  - sensitive to the K+ concentration but also to the types and concentrations of
AB  - anions present.  Interestingly, substitution of glu- increases the rate of DNA
AB  - dramatically in solutions of high K+ content.  Since Cl- is not a primary anion
AB  - in E. coli, the results in KGlu are more likely to reflect the physiological
AB  - function of the enzyme.  Our studies indicate that anions drastically affect
AB  - the stability and function of protein-DNA interactions.  Kinetic studies
AB  - therefore provide insight into the determinants of complex formation not
AB  - obtainable from structural studies alone.
ER  -

TY  - JOUR
AU  - Cazalet, C.
AU  - Gomez-Valero, L.
AU  - Rusniok, C.
AU  - Lomma, M.
AU  - Dervins-Ravault, D.
AU  - Newton, H.J.
AU  - Sansom, F.M.
AU  - Jarraud, S.
AU  - Zidane, N.
AU  - Ma, L.
AU  - Bouchier, C.
AU  - Etienne, J.
AU  - Hartland, E.L.
AU  - Buchrieser, C.
TI  - Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires' disease.
JO  - PLoS Genet.
PY  - 2010
SP  - e1000851
EP  - e1000851
VL  - 6
AB  - Legionella pneumophila and L. longbeachae are two species of a large genus of bacteria that
AB  - are ubiquitous in nature. L. pneumophila is mainly found
AB  - in natural and artificial water circuits while L. longbeachae is mainly
AB  - present in soil. Under the appropriate conditions both species are human
AB  - pathogens, capable of causing a severe form of pneumonia termed
AB  - Legionnaires' disease. Here we report the sequencing and analysis of four
AB  - L. longbeachae genomes, one complete genome sequence of L. longbeachae
AB  - strain NSW150 serogroup (Sg) 1, and three draft genome sequences another
AB  - belonging to Sg1 and two to Sg2. The genome organization and gene content
AB  - of the four L. longbeachae genomes are highly conserved, indicating strong
AB  - pressure for niche adaptation. Analysis and comparison of L. longbeachae
AB  - strain NSW150 with L. pneumophila revealed common but also unexpected
AB  - features specific to this pathogen. The interaction with host cells shows
AB  - distinct features from L. pneumophila, as L. longbeachae possesses a
AB  - unique repertoire of putative Dot/Icm type IV secretion system substrates,
AB  - eukaryotic-like and eukaryotic domain proteins, and encodes additional
AB  - secretion systems. However, analysis of the ability of a dotA mutant of L.
AB  - longbeachae NSW150 to replicate in the Acanthamoeba castellanii and in a
AB  - mouse lung infection model showed that the Dot/Icm type IV secretion
AB  - system is also essential for the virulence of L. longbeachae. In contrast
AB  - to L. pneumophila, L. longbeachae does not encode flagella, thereby
AB  - providing a possible explanation for differences in mouse susceptibility
AB  - to infection between the two pathogens. Furthermore, transcriptome
AB  - analysis revealed that L. longbeachae has a less pronounced biphasic life
AB  - cycle as compared to L. pneumophila, and genome analysis and electron
AB  - microscopy suggested that L. longbeachae is encapsulated. These
AB  - species-specific differences may account for the different environmental
AB  - niches and disease epidemiology of these two Legionella species.
ER  -

TY  - JOUR
AU  - Cazalet, C.
AU  - Rusniok, C.
AU  - Bruggemann, H.
AU  - Zidane, N.
AU  - Magnier, A.
AU  - Ma, L.
AU  - Tichit, M.
AU  - Jarraud, S.
AU  - Bouchier, C.
AU  - Vandenesch, F.
AU  - Kunst, F.
AU  - Etienne, J.
AU  - Glaser, P.
AU  - Buchrieser, C.
TI  - Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity.
JO  - Nat. Genet.
PY  - 2004
SP  - 1165
EP  - 1173
VL  - 36
AB  - Legionella pneumophila, the causative agent of Legionnaires' disease, replicates as an
AB  - intracellular parasite of amoebae and persists in the
AB  - environment as a free-living microbe. Here we have analyzed the complete
AB  - genome sequences of L. pneumophila Paris (3,503,610 bp, 3,077 genes), an
AB  - endemic strain that is predominant in France, and Lens (3,345,687 bp,
AB  - 2,932 genes), an epidemic strain responsible for a major outbreak of
AB  - disease in France. The L. pneumophila genomes show marked plasticity, with
AB  - three different plasmids and with about 13% of the sequence differing
AB  - between the two strains. Only strain Paris contains a type V secretion
AB  - system, and its Lvh type IV secretion system is encoded by a 36-kb region
AB  - that is either carried on a multicopy plasmid or integrated into the
AB  - chromosome. Genetic mobility may enhance the versatility of L.
AB  - pneumophila. Numerous genes encode eukaryotic-like proteins or motifs that
AB  - are predicted to modulate host cell functions to the pathogen's advantage.
AB  - The genome thus reflects the history and lifestyle of L. pneumophila, a
AB  - human pathogen of macrophages that coevolved with fresh-water amoebae.
ER  -

TY  - JOUR
AU  - Ccorahua-Santo, R.
AU  - Cervantes, M.
AU  - Duran, Y.
AU  - Aguirre, M.
AU  - Marin, C.
AU  - Ramirez, P.
TI  - Draft Genome Sequence of Klebsiella michiganensis 3T412C, Harboring an Arsenic Resistance Genomic Island, Isolated from Mine Tailings in Peru.
JO  - Genome Announcements
PY  - 2017
SP  - e00611
EP  - e00617
VL  - 5
AB  - An arsenic resistance genomic island in the bacterium Klebsiella michiganensis 3T412C was
AB  - isolated from mine tailings from Peru. This genomic island confers
AB  - adaptation to extreme environments with high concentrations of arsenic. Isolate
AB  - 3T412C contained a complete set of genes involved in resistance to arsenic. This
AB  - operon is surrounded by putative genes for resistance to other heavy metals.
ER  -

TY  - JOUR
AU  - Ceccaldi, A.
AU  - Rajavelu, A.
AU  - Champion, C.
AU  - Rampon, C.
AU  - Jurkowska, R.
AU  - Jankevicius, G.
AU  - Senamaud-Beaufort, C.
AU  - Ponger, L.
AU  - Gagey, N.
AU  - Ali, H.D.
AU  - Tost, J.
AU  - Vriz, S.
AU  - Ros, S.
AU  - Dauzonne, D.
AU  - Jeltsch, A.
AU  - Guianvarc'h, D.
AU  - Arimondo, P.B.
TI  - C5-DNA Methyltransferase Inhibitors: From Screening to Effects on Zebrafish Embryo Development.
JO  - Chembiochem
PY  - 2011
SP  - 1337
EP  - 1345
VL  - 12
AB  - DNA methylation is involved in the regulation of gene expression and plays an important role
AB  - in normal developmental processes and diseases,
AB  - such as cancer. DNA methyltransferases are the enzymes responsible for
AB  - DNA methylation on the position 5 of cytidine in a CpG context. In
AB  - order to identify and characterize novel inhibitors of these enzymes,
AB  - we developed a fluorescence-based throughput screening by using a short
AB  - DNA duplex immobilized on 96-well plates. We have screened 114 flavones
AB  - and flavanones for the inhibition of the murine catalytic Dnmt3a/3L
AB  - complex and found 36 hits with IC50 values in the lower micromolar and
AB  - high nanomolar ranges. The assay, together with inhibition tests on two
AB  - other methyltransferases, structure-activity relationships and docking
AB  - studies, gave insights on the mechanism of inhibition. Finally, two
AB  - derivatives effected zebrafish embryo development, and induced a global
AB  - demethylation of the genome, at doses lower than the control drug,
AB  - 5-azacytidine.
ER  -

TY  - JOUR
AU  - Ceccaldi, A.
AU  - Rajavelu, A.
AU  - Ragozin, S.
AU  - Senamaud-Beaufort, C.
AU  - Bashtrykov, P.
AU  - Testa, N.
AU  - Dali-Ali, H.
AU  - Maulay-Bailly, C.
AU  - Amand, S.
AU  - Guianvarc'h, D.
AU  - Jeltsch, A.
AU  - Arimondo, P.B.
TI  - Identification of Novel Inhibitors of DNA Methylation by Screening of a Chemical Library.
JO  - ACS Chem. Biol.
PY  - 2013
SP  - 543
EP  - 548
VL  - 8
AB  - In order to discover new inhibitors of the DNA methyltransferase 3A/3L complex, we used a
AB  - medium-throughput nonradioactive screen on a random
AB  - collection of 1120 small organic compounds. After a primary hit
AB  - detection against DNA methylation activity of the murine Dnmt3A/3L
AB  - catalytic complex, we further evaluated the EC50 of the 12 most potent
AB  - hits as well as their cytotoxicity on DU145 prostate cancer cultured
AB  - cells. Interestingly, most of the inhibitors showed low micromolar
AB  - activities and little cytotoxicity. Dichlone, a small halogenated
AB  - naphthoquinone, classically used as pesticide and fungicide, showed the
AB  - lowest EC50 at 460 nM. We briefly assessed the selectivity of a subset
AB  - of our new inhibitors against hDNMT1 and bacterial Dnmts, including M.
AB  - SssI and EcoDam, and the protein lysine methyltransferase PKMT G9a and
AB  - the mode of inhibition. Globally, the tested molecules showed a clear
AB  - preference for the DNA methyltransferases, but poor selectivity among
AB  - them. Two molecules including Dichlone efficiently reactivated YFP gene
AB  - expression in a stable HEK293 cell line by promoter demethylation.
AB  - Their efficacy was comparable to the DNMT inhibitor of reference
AB  - 5-azacytidine.
ER  -

TY  - JOUR
AU  - Cecchini, D.
AU  - Laville, E.
AU  - Laguerre, S.
AU  - Robe, P.
AU  - Leclerc, M.
AU  - Dore, J.
AU  - Henrissat, B.
AU  - Remaud-Simeon, M.
AU  - Monsan, P.
AU  - Potocki-Veronese, G.
TI  - Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.
JO  - PLoS ONE
PY  - 2013
SP  - e72766
EP  - e72766
VL  - 8
AB  - The human intestine hosts a complex bacterial community that plays a major role in nutrition
AB  - and in maintaining human health. A functional metagenomic approach was used to explore the
AB  - prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two
AB  - metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for
AB  - hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides,
AB  - xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones,
AB  - selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in
AB  - total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic
AB  - degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which
AB  - we provided the first experimental proof of function. Twenty of these proteins are encoded by
AB  - genes that are also present in the gut metagenome of at least 100 subjects, whatever are their
AB  - ages or their geographical origin. The sequence taxonomic assignment indicated that still
AB  - unknown bacteria, for which neither culture conditions nor genome sequence are available,
AB  - possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results
AB  - expand the vision on how prebiotics are metabolized along the intestine, and open new
AB  - perspectives for the design of functional foods.
ER  -

TY  - JOUR
AU  - Cech, D.
AU  - Pein, C.-D.
TI  - The influence of modifications on the cleavage of oligonucleotide duplexes by EcoRII and MvaI endonucleases.
JO  - Nucleosides and Nucleotides
PY  - 1988
SP  - 585
EP  - 588
VL  - 7
AB  - To study the interaction of the restriction endonucleases MvaI and EcoRII with DNA we have
AB  - synthesized some modified oligonucleotides. The results of hydrolysis demonstrate that both
AB  - enzymes cleave their substrate by different mechanisms.
ER  -

TY  - JOUR
AU  - Cedar, H.
AU  - Solage, A.
AU  - Glaser, G.
AU  - Razin, A.
TI  - Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI.
JO  - Nucleic Acids Res.
PY  - 1979
SP  - 2125
EP  - 2132
VL  - 6
AB  - The extent of methylation of the internal C in the sequence CCGG in DNA from
AB  - various eukaryotic sources has been determined using the restriction enzyme
AB  - MspI known to be specific for this sequence.  The methylation of the CCGG
AB  - sequence is reflected in the restriction pattern obtained by DNA treated with
AB  - MspI and its isoschizomer HpaII and analyzed by gel electrophoresis.  A direct
AB  - method for detection of 5-methylcytosine in the sequence CCGG has been deviced.
AB  - DNA fragments obtained with MspI were radioactively labeled at their 5' ends
AB  - and subsequently degraded to the corresponding 5'-deoxyribonucleoside
AB  - monophosphates.  5 methylcytidylic acid has been found in most of the 5' ends
AB  - of MspI fragments of calf thymus DNA (about 90%) indicating heavy methylation
AB  - of the sequence CCGG in calf thymus DNA.  The results also reveal a symmetric
AB  - methylation of both strands at this sequence in calf thymus DNA.  In contrast,
AB  - the CCGG sequence in other eukaryotic DNAs from organisms like Neurospora,
AB  - Drosophila and Herpes virus proved to be undermethylated at this sequence.
ER  -

TY  - JOUR
AU  - Cedar, H.
AU  - Verdine, G.L.
TI  - The amazing demethylase.
JO  - Nature
PY  - 1999
SP  - 568
EP  - 569
VL  - 397
AB  - DNA methylation is important for mediating repression of gene expression during mammalian
AB  - development.  But although much is known about how methyl groups are added to DNA, little has
AB  - been done to work out how they are taken off.  In an exciting article on page 579 of this
AB  - issue, Bhattacharya et al. report that they have cloned a hitherto unknown gene which codes
AB  - for a protein with a remarkable property - it can catalyse demethylation by directly removing
AB  - methyl groups from 5-methyl-cytosine residues in DNA.
ER  -

TY  - JOUR
AU  - Centeno-Leija, S.
AU  - Vinuesa, P.
AU  - Rodriguez-Pena, K.
AU  - Trenado-Uribe, M.
AU  - Cardenas-Conejo, Y.
AU  - Serrano-Posada, H.
AU  - Rodriguez-Sanoja, R.
AU  - Sanchez, S.
TI  - Draft Genome Sequence of an Endophytic Actinoplanes Species, Encoding Uncommon trans-Acyltransferase Polyketide Synthases.
JO  - Genome Announcements
PY  - 2016
SP  - e00164
EP  - e00116
VL  - 4
AB  - Actinoplanesis an endophytic actinobacterium isolated from the medicinal plantAmphipterygium
AB  - adstringens The strain draft genome sequence reveals a gene
AB  - cluster involved in the biosynthesis of a hybridtrans-acyltransferase (AT)
AB  - polyketide, an unconventional bioactive metabolite never reported before in the
AB  - genusActinoplanes.
ER  -

TY  - JOUR
AU  - Centorame, P.
AU  - Acciari, V.A.
AU  - Orsini, M.
AU  - Torresi, M.
AU  - Iannetti, L.
AU  - Angius, A.
AU  - Di Giammartino, D.
AU  - Prencipe, V.A.
AU  - Migliorati, G.
TI  - Whole-Genome Sequence of Listeria monocytogenes Serovar 4b Strain IZSAM_Lm_hs2008, Isolated from a Human Infection in Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00053
EP  - e00015
VL  - 3
AB  - Listeria monocytogenes is one of the most important foodborne pathogens. In this  report, we
AB  - present the complete and annotated genome of L. monocytogenes sequence
AB  - type 06 (ST06) serovar 4b strain IZSAM_Lm_hs2008, isolated from an adult
AB  - immunocompetent patient who developed the disease and died.
ER  -

TY  - JOUR
AU  - Cerdeira, L.
AU  - Fernandes, M.R.
AU  - Francisco, G.R.
AU  - Bueno, M.F.
AU  - Ienne, S.
AU  - Souza, T.A.
AU  - de Oliveira, G.D.
AU  - Lincopan, N.
TI  - Draft Genome Sequence of a Hospital-Associated Clone of Klebsiella pneumoniae ST340/CC258 Coproducing RmtG and KPC-2 Isolated from a Pediatric Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e01130
EP  - e01116
VL  - 4
AB  - We report here the draft genome sequence of a Klebsiella pneumoniae strain 1194/11, belonging
AB  - to the hospital-associated sequence type 340 (ST340; clonal
AB  - complex CC258), isolated from a catheter tip culture from a pediatric patient.
AB  - The multidrug-resistant strain coproduced the 16S rRNA methyltransferase rRNA
AB  - RmtG and beta-lactamases KPC-2 and CTX-M-15.
ER  -

TY  - JOUR
AU  - Cerdeira, L.T. et al.
TI  - Complete genome sequence of Corynebacterium pseudotuberculosis strain CIP 52.97, isolated from a horse in Kenya.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7025
EP  - 7026
VL  - 193
AB  - In this work, we report the whole-genome sequence of Corynebacterium
AB  - pseudotuberculosis bv. equi strain CIP 52.97 (Collection Institut Pasteur),
AB  - isolated in 1952 from a case of ulcerative lymphangitis in a Kenyan horse, which
AB  - has evidently caused significant losses to agribusiness. Therefore, obtaining
AB  - this genome will allow the detection of important targets for postgenomic
AB  - studies, with the aim of minimizing problems caused by this microorganism.
ER  -

TY  - JOUR
AU  - Cerdeira, L.T. et al.
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6420
EP  - 6421
VL  - 193
AB  - In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis
AB  - PAT10 isolate, collected from a lung abscess in an
AB  - Argentine sheep in Patagonia, whose pathogen also required an
AB  - investigation of its pathogenesis. Thus, the analysis of the genome
AB  - sequence offers a means to better understanding of the molecular and
AB  - genetic basis of virulence of this bacterium.
ER  -

TY  - JOUR
AU  - Cerdeno-Tarraga, A.M. et al.
TI  - The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 6516
EP  - 6523
VL  - 31
AB  - Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod
AB  - belonging to the genus Corynebacterium and the
AB  - actinomycete group of organisms. The organism produces a potent
AB  - bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which
AB  - causes the symptoms of diphtheria. This potentially fatal infectious
AB  - disease is controlled in many developed countries by an effective
AB  - immunisation programme. However, the disease has made a dramatic return in
AB  - recent years, in particular within the Eastern European region. The
AB  - largest, and still on-going, outbreak since the advent of mass
AB  - immunisation started within Russia and the newly independent states of the
AB  - former Soviet Union in the 1990s. We have sequenced the genome of a UK
AB  - clinical isolate (biotype gravis strain NCTC13129), representative of the
AB  - clone responsible for this outbreak. The genome consists of a single
AB  - circular chromosome of 2 488 635 bp, with no plasmids. It provides
AB  - evidence that recent acquisition of pathogenicity factors goes beyond the
AB  - toxin itself, and includes iron-uptake systems, adhesins and fimbrial
AB  - proteins. This is in contrast to Corynebacterium's nearest sequenced
AB  - pathogenic relative, Mycobacterium tuberculosis, where there is little
AB  - evidence of recent horizontal DNA acquisition. The genome itself shows an
AB  - unusually extreme large-scale compositional bias, being noticeably higher
AB  - in G+C near the origin than at the terminus.
ER  -

TY  - JOUR
AU  - Cerdeno-Tarraga, A.M. et al.
TI  - Extensive DNA inversions in the B. fragilis genome control variable gene expression.
JO  - Science
PY  - 2005
SP  - 1463
EP  - 1465
VL  - 307
AB  - The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and
AB  - inhabitant of the normal human colonic microbiota, exhibits
AB  - considerable within-strain phase and antigenic variation of surface
AB  - components. The complete genome sequence has revealed an unusual breadth
AB  - (in number and in effect) of DNA inversion events that potentially control
AB  - expression of many different components, including surface and secreted
AB  - components, regulatory molecules, and restriction-modification proteins.
AB  - Invertible promoters of two different types (12 group 1 and 11 group 2)
AB  - were identified. One group has inversion crossover (fix) sites similar to
AB  - the hix sites of Salmonella typhimurium. There are also four independent
AB  - intergenic shufflons that potentially alter the expression and function of
AB  - varied genes. The composition of the 10 different polysaccharide
AB  - biosynthesis gene clusters identified (7 with associated invertible
AB  - promoters) suggests a mechanism of synthesis similar to the O-antigen
AB  - capsules of Escherichia coli.
ER  -

TY  - JOUR
AU  - Cermak, T.
AU  - Doyle, E.L.
AU  - Christian, M.
AU  - Wang, L.
AU  - Zhang, Y.
AU  - Schmidt, C.
AU  - Baller, J.A.
AU  - Somia, N.V.
AU  - Bogdanove, A.J.
AU  - Voytas, D.F.
TI  - Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - E82
EP  - E82
VL  - 39
AB  - TALENs are important new tools for genome engineering. Fusions of transcription
AB  - activator-like (TAL) effectors of plant pathogenic Xanthomonas spp. to the FokI
AB  - nuclease, TALENs bind and cleave DNA in pairs. Binding specificity is determined
AB  - by customizable arrays of polymorphic amino acid repeats in the TAL effectors. We
AB  - present a method and reagents for efficiently assembling TALEN constructs with
AB  - custom repeat arrays. We also describe design guidelines based on naturally
AB  - occurring TAL effectors and their binding sites. Using software that applies
AB  - these guidelines, in nine genes from plants, animals and protists, we found
AB  - candidate cleavage sites on average every 35 bp. Each of 15 sites selected from
AB  - this set was cleaved in a yeast-based assay with TALEN pairs constructed with our
AB  - reagents. We used two of the TALEN pairs to mutate HPRT1 in human cells and ADH1
AB  - in Arabidopsis thaliana protoplasts. Our reagents include a plasmid construct for
AB  - making custom TAL effectors and one for TAL effector fusions to additional
AB  - proteins of interest. Using the former, we constructed de novo a functional
AB  - analog of AvrHah1 of Xanthomonas gardneri. The complete plasmid set is available
AB  - through the non-profit repository AddGene and a web-based version of our software
AB  - is freely accessible online.
ER  -

TY  - JOUR
AU  - Cerquetti, M.C.
AU  - Brawer, R.
AU  - Gherardi, M.M.
AU  - Sordelli, D.O.
TI  - Location of aroB and dam genes in the Salmonella typhimurium chromosome.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1997
SP  - 318
EP  - 318
VL  - 97
AB  - Enterobacteria possess a functional dam methylase.  The dam gene of Escherichia coli in min 74
AB  - is part of an operon that includes at least 3 other genes, aroK, aroB and urf74.3, and the
AB  - distance between aroB and dam is less than 2 Kbp.  The dam gene of Salmonella typhimurium has
AB  - been positioned on the chromosomal map in homology to E. coli.  We have recently isolated an
AB  - insertional dam::Tn10dTc mutant of S. typhimurium.  Cotransduction frequencies of aroB and
AB  - dam::Tn10tDc found in S. typhimurium (40%) do not agree with a map distance of 2 Kbp between
AB  - these two genes, oligonucleotides matching E. coli aroB (ECaroB), S. typhimurium aroB
AB  - (STaroB), E. coli dam (Ecdam) and S. typhimurium dam (Stdam) sequences were synthesized and
AB  - tested as opposing PCR primers in the amplification of S. typhimurium and E. coli DNA.  ECaroB
AB  - and Ecdam oligonucleotide primers produced a band of the expected size (1.6 Kbp) in the
AB  - amplification of E. coli DNA.  A band of similar size was obtained using ECaroB and STdam as
AB  - primers in the amplification of E. coli DNA.  No specific PCR product was yielded when STaroB
AB  - and STdam were tested as primers in the amplification of S. typhimurium DNA.  These results
AB  - support the hypothesis that there are differences between E. coli and S. typhimurium in this
AB  - region of the chromosome.
ER  -

TY  - JOUR
AU  - Cerquetti, M.C.
AU  - Brawer, R.
AU  - Gherardi, M.M.
AU  - Sordelli, D.O.
TI  - Map position of the dam gene in Salmonella typhimurium.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1996
SP  - 491
EP  - 491
VL  - 96
AB  - Escherichia coli and Salmonella typhimurium DNA is methylated in the adenine
AB  - residue in the sequence 5'-GATC-3'.  The DNA adenine methylase (dam) gene of E. coli is
AB  - located
AB  - at 74 min in a multicistronic operon containing aroK and aroB among other genes.  The S.
AB  - typhimurium dam gene has not been mapped yet, although a gene order similar to that of E. coli
AB  - (cys-G-dam-aroB) has been suggested.  The recently isolated dam::Tn10dTc mutant of S.
AB  - typhimurium enabled us to locate the dam gene more precisely.  Transductional crosses were
AB  - carried out using bacteriophage P22 lysates.  Double mutants of S. typhimurium DM6
AB  - [csG::Tn5(Kan)-aroB] and DM53 (aroB-dam::Tn10dTc) were constructed in order to perform
AB  - three-factor crosses.  Strain DM6 was transduced with a lysate grown on the dam::Tn10dTC
AB  - mutant and a total of 129 tetracycline resistant (TetR) transductants were analyzed.  More
AB  - than half
AB  - (51%) of the TetR transductants maintained the cys- aro- phenotype, 42% were cys+ aro+, 5%
AB  - were cys+ aro- and 2% were cys+ aro+.  DM53 was transduced with phage propagated on S.
AB  - typhimurium ompR::Tn5.  Kanamycin resistant transductants were screened for sensitivity to 2
AB  - aminopurine (2AP) and aro+ phenotype.  Eighty-three percent of the 72 KanR transductants were
AB  - aro- and resistant to 2AP, 13% were aro- and sensitive to 2AP, and 3% were sensitive to 2 AP
AB  - and
AB  - aro-.  Our data support the order: cysG-aroB-dam-ompR on the S. typhimurium genetic map.
ER  -

TY  - JOUR
AU  - Cerra, J.
AU  - Donohue, H.
AU  - Kral, A.
AU  - Oser, M.
AU  - Rostkowski, L.
AU  - Zappia, L.
AU  - Williams, L.E.
TI  - Complete Genome Sequence of Pseudomonas sp. Strain NC02, Isolated from Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e00033
EP  - e00018
VL  - 6
AB  - We report here the complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil
AB  - in eastern Massachusetts. We assembled PacBio reads into a
AB  - single closed contig with 132x mean coverage and then polished this contig using
AB  - Illumina MiSeq reads, yielding a 6,890,566-bp sequence with 61.1% GC content.
ER  -

TY  - JOUR
AU  - Cerritelli, S.
AU  - Springhorn, S.S.
AU  - Lacks, S.A.
TI  - DpnA, a methylase for single-strand DNA in the DpnII restriction system, and its biological function.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1989
SP  - 9223
EP  - 9227
VL  - 86
AB  - The two DNA-adenine methylases encoded by the DpnII restriction gene cassette
AB  - were purified, and their activities were compared on various DNA substrates.
AB  - DpnA was able to methylate single-strand DNA and double-strand DNA, whereas
AB  - DpnM methylated only double-strand DNA.  Although both enzymes act at
AB  - 5'-GATC-3' in DNA, DpnA can also methylate sequences altered in the guanine
AB  - position, but at a lower rate.  A deletion mutation in the dpnA gene was
AB  - constructed and transferred to the chromosome.  Transmission by way of the
AB  - transformation pathway of methylated and unmethylated plasmids to dpnA mutant
AB  - and wild-type recipients was examined.  The mutant cells restricted
AB  - unmethylated donor plasmid establishment much more strongly than did wild-type
AB  - cells.  In the wild type, the single strands of donor plasmid DNA that enter by
AB  - the transformation pathway are apparently methylated by DpnA prior to
AB  - conversion of the plasmid to a double-strand form, in which the plasmid would
AB  - be susceptible to the DpnII endonuclease.  The biological function of DpnA may,
AB  - therefore, be the enhancement of plasmid transfer to DpnII-containing strains
AB  - of Streptococcus pneumoniae.
ER  -

TY  - JOUR
AU  - Cerritelli, S.
AU  - White, S.W.
AU  - Lacks, S.A.
TI  - Crystallization of the DpnM methylase from the DpnII restriction system of Streptococcus pneumoniae.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 841
EP  - 842
VL  - 207
AB  - Three proteins, two DNA methylases and an endonuclease, from the DpnII
AB  - restriction system of Streptococcus pneumoniae recognize the DNA sequence 5'
AB  - GATC 3' but have very different amino acid sequences, which make them
AB  - interesting subjects for structural determination.  A purification procedure
AB  - was developed that conveniently yields milligram amounts of the DpnM methylase.
AB  - The DpnM protein tends to precipitate at reduced ionic strength, and this
AB  - property was exploited to yield well-formed bipyramidal crystals.  By X-ray
AB  - diffraction, the crystals of DpnM were found to be orthorhombic, with cell
AB  - dimensions a=56.9 angstrom, b=68.2 angstrom, c=84.5 angstrom; systematic
AB  - absences identify the space group as P2/1 2/1 2/1.  Diffraction extends beyond
AB  - 3 angstrom, so the crystals may allow structural determination at atomic
AB  - resolution.
ER  -

TY  - JOUR
AU  - Cerritelli, S.
AU  - White, S.W.
AU  - Springhorn, S.S.
AU  - Lacks, S.A.
TI  - Two DNA methylases in the DpnII restriction system of Streptococcus pneumoniae.
JO  - FASEB J.
PY  - 1990
SP  - A2295
EP  - A2295
VL  - 4
AB  - The DpnII cassette contains three genes, dpnM, dpnA and dpnB, that encode,
AB  - respectively, two DNA methylases, DpnM and DpnA, and the DpnII endonuclease.
AB  - The two DNA-adenine methyltransferases were purified and characterized.  DpnM
AB  - methylates only double-strand DNA at 5'-GATC-3'.  It is the major DNA
AB  - methylating activity in S. pneumoniae and is homologous to the Dam methylase of
AB  - Escherichia coli.  We have obtained crystals of DpnM methylase suitable for
AB  - diffraction analysis.  At present we are in the process of determining the
AB  - crystal structure using the multiwavelength anomalous dispersion procedure.
AB  - DpnA, the other methylase in the DpnII restriction system, methylates
AB  - single-strand and double-strand DNA, although it is more active in methylating
AB  - DNA in single-strand form.  A deletion mutant in the dpnA gene was constructed
AB  - and introduced into the chromosome.  The mutant cells have reduced ability to
AB  - establish unmethylated donor plasmid, as compared to wild-type cells.  The role
AB  - of DpnA may be to methylate the single strands of donor plasmid DNA that enter
AB  - the cell by the transformation pathway, thereby protecting the subsequent
AB  - reconstructed plasmid from DpnII endonuclease cleavage.  The biological
AB  - function of DpnA, therefore, may be the enhancement of plasmid transfer to
AB  - DpnII-containing strains of S. pneumoniae.
ER  -

TY  - JOUR
AU  - Cerveny, J.
AU  - Sinetova, M.A.
AU  - Zavrel, T.
AU  - Los, D.A.
TI  - Mechanisms of High Temperature Resistance of Synechocystis sp. PCC 6803: An Impact of Histidine Kinase 34.
JO  - Life
PY  - 2015
SP  - 676
EP  - 699
VL  - 5
AB  - Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying
AB  - responses and acclimation to different abiotic stresses. Changes in
AB  - transcriptome, proteome, lipidome, and photosynthesis in response to short term
AB  - heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is
AB  - shown to play an important role in mediating such response. Corresponding data on
AB  - long term responses, however, are fragmentary and vary depending on parameters of
AB  - experiments and methods of data collection, and thus are hard to compare. In
AB  - order to elucidate how the early stress responses help cells to sustain long-term
AB  - heat stress, as well as the role of Hik34 in prolonged acclimation, we examined
AB  - the resistance to long-term heat stress of wild-type and DeltaHik34 mutant of
AB  - Synechocystis. In this work, we were able to precisely control the long term
AB  - experimental conditions by cultivating Synechocystis in automated
AB  - photobioreactors, measuring selected physiological parameters within a time range
AB  - of minutes. In addition, morphological and ultrastructural changes in cells were
AB  - analyzed and western blotting of individual proteins was used to study the heat
AB  - stress-affected protein expression. We have shown that the majority of wild type
AB  - cell population was able to recover after 24 h of cultivation at 44 degrees C. In
AB  - contrast, while DeltaHik34 mutant cells were resistant to heat stress within its
AB  - first hours, they could not recover after 24 h long high temperature treatment.
AB  - We demonstrated that the early induction of HspA expression and maintenance of
AB  - high amount of other HSPs throughout the heat incubation is critical for
AB  - successful adaptation to long-term stress. In addition, it appears that histidine
AB  - kinase Hik34 is an essential component for the long term high temperature
AB  - resistance.
ER  -

TY  - JOUR
AU  - Cervoni, N.
AU  - Bhattacharya, S.
AU  - Szyf, M.
TI  - DNA demethylase is a processive enzyme.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 8363
EP  - 8366
VL  - 274
AB  - DNA methylation patterns are generated during development by a sequence of methylation and
AB  - demethylation events.  We have recently demonstrated that mammals bear a bona fide demethylase
AB  - enzyme that removes methyl groups from methylated cytosines.  A general genome wide
AB  - demethylation occurs early in development and in differentiating cell lines.  This manuscript
AB  - tests the hypothesis that the demethylase enzyme is a processive enzyme.  Using bisulfite
AB  - mapping, this report demonstrates that demethylase is a processive enzyme and that the
AB  - rate-limiting step in demethylation is the initiation of demethylation.  Initiation of
AB  - demethylation is determined by the properties of the sequence.  Once initiated, demethylation
AB  - progresses processively.  We suggest that these data provide a molecular explanation for
AB  - global hypomethylation.
ER  -

TY  - JOUR
AU  - Cervoni, N.
AU  - Szyf, M.
TI  - Demethylase activity is directed by histone acetylation.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 40778
EP  - 40787
VL  - 276
AB  - Mammalian genomes are compartmentalized into dense inactive chromatin that is hypermethylated
AB  - and active open chromatin that is hypomethylated. It is generally accepted that this bimodal
AB  - pattern of methylation is established during development and is then faithfully inherited
AB  - through subsequent cell divisions by a maintenance DNA methyltransferase (DNMT1). The pattern
AB  - of methylation is believed to direct local histone acetylation states. In contrast to this
AB  - well accepted consensus, we show here using a transient transfection model that an active
AB  - demethylase is involved in shaping patterns of methylation in somatic cells.  Demethylase
AB  - activity is directed by the state of histone acetylation, and therefore, the resulting
AB  - methylation pattern is determined by local histone acetylation states contrary to the accepted
AB  - model. Our data support a new model suggesting that the pattern of methylation is maintained
AB  - by a dynamic balance of methylation and demethylation activities and the local state of
AB  - histone acetylation. This provides a simple mechanism for explaining why active genes are not
AB  - methylated.
ER  -

TY  - JOUR
AU  - Cesnaviciene, E.
AU  - Mitkaite, G.
AU  - Stankevicius, K.
AU  - Janulaitis, A.
AU  - Lubys, A.
TI  - Esp1396I restriction-modification system: Structural organization and mode of regulation.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 743
EP  - 749
VL  - 31
AB  - Esp1396I restriction-modification (RM) system recognizes an interrupted palindromic DNA
AB  - sequence 5'-CCA(N)(5)TGG-3'. The Esp1396I RM system was
AB  - found to reside on pEsp1396, a 5.6 kb plasmid naturally occurring in
AB  - Enterobacter sp. strain RFL1396. The nucleotide sequence of the entire
AB  - 5622 bp pEsp1396 plasmid was determined on both strands. Identified genes
AB  - for DNA methyltransferase (esp1396IM) and restriction endonuclease
AB  - (esp1396IR) are transcribed convergently. The restriction endonuclease
AB  - gene is preceded by the small ORF (esp1396IC) that possesses a strong
AB  - helix-turn-helix motif and resembles regulatory proteins found in PvuII,
AB  - BamHI and few other RM systems. Gene regulation studies revealed that
AB  - C.Esp1396I acts as both a repressor of methylase expression and an
AB  - activator of regulatory protein and restriction endonuclease expression.
AB  - Our data indicate that C protein from Esp1396I RM system activates the
AB  - expression of the Enase gene, which is co-transcribed from the promoter of
AB  - regulatory gene, by the mechanism of coupled translation.
ER  -

TY  - JOUR
AU  - Cesnaviciene, E.E.
AU  - Petrusyte, M.M.
AU  - Kazlauskiene, R.R.
AU  - Maneliene, Z.
AU  - Timinskas, A.
AU  - Lubys, A.
AU  - Janulaitis, A.
TI  - Characterization of AloI, a Restriction-modification System of a New Type.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 205
EP  - 216
VL  - 314
AB  - We report the properties of the new AloI restriction and modification enzyme from
AB  - Acinetobacter lwoffi Ks 4-8 that recognizes the DNA target 5' GGA(N)(6)GTTC3' (complementary
AB  - strand 5' GAAC(N)(6)TCC3'), and the nucleotide sequence of the gene encoding this enzyme.
AB  - AloI is a bifunctional large polypeptide (deduced M(r) 143 kDa) revealing both DNA
AB  - endonuclease and methyltransferase activities. Depending on reaction cofactors, AloI cleaves
AB  - double-stranded DNA on both strands, seven bases on the 5' side, and 12-13 bases on the 3'
AB  - side of its recognition sequence, and modifies adenine residues in both DNA strands in the
AB  - target sequence yielding N6-methyladenine. For cleavage activity AloI maintains an absolute
AB  - requirement for Mg(2+) and does not depend on or is stimulated by either ATP or
AB  - S-adenosyl-l-methionine. Modification function requires the presence of
AB  - S-adenosyl-l-methionine and is stimulated by metal ions (Ca(2+)). The C-terminal and central
AB  - parts of the protein were found to be homologous to certain specificity (HsdS) and
AB  - modification (HsdM) subunits of type I R-M systems, respectively. The N-terminal part of the
AB  - protein possesses the putative endonucleolytic motif DX(n)EXK of restriction endonucleases.
AB  - The deduced amino acid sequence of AloI shares significant homology with polypeptides encoding
AB  - HaeIV and CjeI restriction-modification proteins at the N-terminal and central, but not at the
AB  - C-terminal domains. The organization of AloI implies that its evolution involved fusion of an
AB  - endonuclease and the two subunits, HsdM and HsdS, of type I restriction enzymes. According to
AB  - the structure and function properties AloI may be regarded as one more representative of a
AB  - newly emerging group of HaeIV-like restriction endonucleases. Discovery of these enzymes opens
AB  - new opportunities for constructing restriction endonucleases with a new specificity.
ER  -

TY  - JOUR
AU  - Cha, I.T.
AU  - Lee, M.H.
AU  - Kim, B.Y.
AU  - Cho, Y.J.
AU  - Kim, D.W.
AU  - Yim, K.J.
AU  - Song, H.S.
AU  - Seo, M.J.
AU  - Rhee, J.K.
AU  - Choi, J.S.
AU  - Choi, H.J.
AU  - Yoon, C.
AU  - Roh, S.W.
AU  - Nam, Y.D.
TI  - Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 49
EP  - 49
VL  - 10
AB  - Haloterrigena jeotgali is a halophilic archaeon within the family Natrialbaceae that was
AB  - isolated from shrimp jeotgal, a traditional Korean salt-fermented food.  A29(T) is the type
AB  - strain of H. jeotgali, and is a Gram-negative staining, non-motile, rod-shaped archaeon that
AB  - grows in 10 %-30 % (w/v) NaCl. We present the annotated H. jeotgali A29(T) genome sequence
AB  - along with a summary of its features. The 4,131,621 bp genome with a GC content of 64.9 %
AB  - comprises 4,215 protein-coding genes and 127 RNA genes. The sequence can provide useful
AB  - information on genetic mechanisms that enable haloarchaea to endure a hypersaline environment.
ER  -

TY  - JOUR
AU  - Chaboki, K.M.
TI  - Characterization of a restriction endonuclease isolated from Bacillus subtilis F2.
JO  - Biophys. J.
PY  - 2001
SP  - 282A
EP  - 282A
VL  - 80
AB  - The usefulness of restriction systems with their high substrate specificities for ds-DNA, and
AB  - the processing of the free or packaged DNA during uptake into Bacillus subtilis cells made us
AB  - study the restriction enzyme activity of one of our laboratory isolate, Bacillus subtilis F2
AB  - which has been used for the propagation of the newly isolated PAK phage. During the life cycle
AB  - of PAK phage in Bacillus subtilis F2 host, it has been noticed that DNA of the phage gets
AB  - fragmented in vivo, therefore, it becomes important to explore the endonuclease activity in
AB  - this strain.  A cell bound enzyme was isolated from Bacillus subtilis F2, and was
AB  - characterized in a crude extract of the bacterial cell pellet.  The enzyme was shown to have
AB  - endonuclease activity on bacteriophage lambda DNA and other DNA as well.  Interestingly,
AB  - lambda DNA seems to have very few cut sites.  Another important characteristic of this enzyme
AB  - is it has an optimum pH shifted toward alkaline range, which is 8.5, among 182 known
AB  - restriction enzymes.  The optimum temperature was found to be 40 C.  It seems to work at high
AB  - salt concentration.  Lysates extracted at pH 6 and 6.5 have shown endonuclease activity with a
AB  - new profile of lambda DNA fragmentation of lysate extracted at pH 7.5.  Hence BsuF2 is a type
AB  - II restriction enzyme it seems to have high potential to be used as a genetic tool in
AB  - molecular biology.
ER  -

TY  - JOUR
AU  - Chacon-Vargas, K.
AU  - Chirino, A.A.
AU  - Davis, M.M.
AU  - Debler, S.A.
AU  - Haimer, W.R.
AU  - Wilbur, J.J.
AU  - Mo, X.
AU  - Worthing, B.W.
AU  - Wainblat, E.G.
AU  - Zhao, S.
AU  - Gibbons, J.G.
TI  - Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960.
JO  - Genome Announcements
PY  - 2017
SP  - e00562
EP  - e00517
VL  - 5
AB  - Zymomonas mobilis subsp. mobilis is an efficient ethanol producer with application for
AB  - industrial production of biofuel. To supplement existing Z.
AB  - mobilis genomic resources and to facilitate genomic research, we used Oxford
AB  - Nanopore and Illumina sequencing to assemble the complete genome of the beer
AB  - spoilage isolate Z. mobilis subsp. mobilis strain NRRL B-1960.
ER  -

TY  - JOUR
AU  - Chagas, F.O.
AU  - Ruzzini, A.C.
AU  - Bacha, L.V.
AU  - Samborskyy, M.
AU  - Conti, R.
AU  - Pessotti, R.C.
AU  - de Oliveira, L.G.
AU  - Clardy, J.
AU  - Pupo, M.T.
TI  - Genome Sequence of Streptomyces sp. Strain RTd22, an Endophyte of the Mexican Sunflower.
JO  - Genome Announcements
PY  - 2016
SP  - e00693
EP  - e00616
VL  - 4
AB  - We report here the complete genome sequence of Streptomyces sp. strain RTd22, an  endophytic
AB  - actinobacterium that was isolated from the roots of the Mexican
AB  - sunflower Tithonia diversifolia The bacterium's 11.1-Mb linear chromosome is
AB  - predicted to encode a large number of unknown natural products.
ER  -

TY  - JOUR
AU  - Chahar, S.
AU  - Elsawy, H.
AU  - Ragozin, S.
AU  - Jeltsch, A.
TI  - Changing the DNA Recognition Specificity of the EcoDam DNA-(Adenine-N6)-Methyltransferase by Directed Evolution.
JO  - J. Mol. Biol.
PY  - 2010
SP  - 79
EP  - 88
VL  - 395
AB  - EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the
AB  - Escherichia coli genome. We have changed the target
AB  - specificity of EcoDam from GATC to GATT by directed evolution, combining
AB  - different random mutagenesis methods with restriction protection at GATT
AB  - sites for selection and screening. By co-evolution of an enzyme library
AB  - and a substrate library, we identified GATT as the best non-GATC site and
AB  - discover a double mutation, R124S/P134S, as the first step to increase
AB  - enzyme activity at GATT sites. After four generations of mutagenesis and
AB  - selection, we obtained enzyme variants with new specificity for GATT.
AB  - While the wild-type EcoDam shows no detectable activity at GATT sites in
AB  - E. coli cells, some variants prefer methylation at GATT over GATC sites by
AB  - about 10-fold in cells. In vitro DNA methylation kinetics carried out
AB  - under single-turnover conditions using a hemimethylated GATC and a GATT
AB  - oligonucleotide substrate confirmed that the evolved proteins prefer
AB  - methylation of GATT sites to a similar degree. They show up to 1600-fold
AB  - change in specificity in vitro and methylate the new GATT target site with
AB  - 20% of the rate of GATC methylation by the wild-type enzyme, indicating
AB  - good activity. We conclude that the new methyltransferases are fully
AB  - functional in vivo and in vitro but show a new target-site specificity.
ER  -

TY  - JOUR
AU  - Chai, B.
AU  - Wang, H.
AU  - Chen, X.
TI  - Draft Genome Sequence of High-Melanin-Yielding Aeromonas media Strain WS.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6693
EP  - 6694
VL  - 194
AB  - We sequenced the genome of the high-melanin-yielding Aeromonas media strain WS and then
AB  - analyzed genes potentially involved in melanin formation. The 4.2-Mb
AB  - draft genome carries multiple genes responsible for pyomelanin synthesis and
AB  - other candidate genes identified in our separate study, which have no homolog in
AB  - other strains of Aeromonas species.
ER  -

TY  - JOUR
AU  - Chaillet, R.
AU  - Cirio, C.
AU  - Navara, C.
TI  - The somatic form of the mouse Dnmt1 maintenance methyltransferase is expressed throughout preimplantation development.
JO  - Biol. Reprod.
PY  - 2007
SP  - 90
EP  - 90
VL  - SI
AB  - The inheritance of gametic epigenetic modifications of DNA is essential to the process of
AB  - genomic imprinting, which in turn is essential for normal mammalian development. Patterns of
AB  - CpG dinucleotide methylation on imprinted genes appear during gametogenesis due to the action
AB  - of de novo cytosine methyltransferase activity. Although the inheritance of these methylation
AB  - patterns during post-implantation development is due to the potent maintenance
AB  - methyltransferase activity of the somatic form of the Dnmt1 cytosine methyltransferase
AB  - (Dnmt1s), the molecular mechanism for maintaining imprinted methylation patterns during
AB  - preimplantation development remains largely unknown. The goal of this study was to determine
AB  - if Dnmt1s is a possible candidate enzyme for this mechanism by determining if Dnmt1s is
AB  - expressed in wild-type preimplantation embryos. For these studies we used the UPT82 rabbit
AB  - polyclonal antibody, which recognizes epitopes specific to Dnmt1s protein, but does not detect
AB  - the shorter, oocyte-specific Dnmt1o protein.  Improved, sensitive techniques of Dnmt1s
AB  - immunodetection with UPT82 were used. On immunoblots of extracts from 100 staged oocytes or
AB  - staged embryos, UPT82 detects Dnmt1s in fully-grown oocyte (GV and MII stages), and in embryos
AB  - at the 1-cell, 2-cell, 4-cell, 8-cell, morula and blastocyst stages. Using immunostaining and
AB  - confocal microscopy, we showed that Dnmt1s is present in the cytoplasm at all stages, and in
AB  - the nuclei of all stages except the 1-cell, pronuclear-stage embryos. Dnmt1s also failed to
AB  - appear in the maternal and paternal pronuclei even in pronuclear-stage embryos derived from
AB  - mouse strains that overexpress Dnmt1s in oocytes, and show greatly increased cytoplasmic
AB  - Dnmt1s staining. Because DNA replication is very likely to have been completed at the time of
AB  - pronuclear membrane breakdown, these observations indicate that DNA replicated at the first
AB  - embryonic cell cycle is probably not exposed to Dnmt1s until well after the replication event.
AB  - Using crosses between wild-type mice and mice carrying the Dnmt1V allele, which express only
AB  - the Dnmt1o form of Dnmt1, we showed that Dnmt1s protein expressed in 1-cell and 2-cell embryos
AB  - is derived from the oocyte, whereas Dnmt1s expressed afterwards is synthesized de novo during
AB  - embryogenesis.  These findings indicate that Dnmt1s is expressed in all diploidnuclear stages
AB  - of mouse preimplantation embryos, and suggest therefore that Dnmt1s is a strong candidate for
AB  - the maintenance methyltransferase activity required for the inheritance of methylation
AB  - imprints in the early mouse embryo.
ER  -

TY  - JOUR
AU  - Chain, P.
AU  - Lamerdin, J.
AU  - Larimer, F.
AU  - Regala, W.
AU  - Lao, V.
AU  - Land, M.
AU  - Hauser, L.
AU  - Hooper, A.
AU  - Klotz, M.
AU  - Norton, J.
AU  - Sayavedra-Soto, L.
AU  - Arciero, D.
AU  - Hommes, N.
AU  - Whittaker, M.
AU  - Arp, D.
TI  - Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea.
JO  - J. Bacteriol.
PY  - 2003
SP  - 2759
EP  - 2773
VL  - 185
AB  - Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can
AB  - derive all its energy and reductant for
AB  - growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea
AB  - participates in the biogeochemical N cycle in the process of
AB  - nitrification. Its genome consists of a single circular chromosome of
AB  - 2,812,094 bp. The GC skew analysis indicates that the genome is divided
AB  - into two unequal replichores. Genes are distributed evenly around the
AB  - genome, with approximately 47% transcribed from one strand and
AB  - approximately 53% transcribed from the complementary strand. A total of
AB  - 2,460 protein-encoding genes emerged from the modeling effort, averaging
AB  - 1,011 bp in length, with intergenic regions averaging 117 bp. Genes
AB  - necessary for the catabolism of ammonia, energy and reductant generation,
AB  - biosynthesis, and CO(2) and NH(3) assimilation were identified. In
AB  - contrast, genes for catabolism of organic compounds are limited. Genes
AB  - encoding transporters for inorganic ions were plentiful, whereas genes
AB  - encoding transporters for organic molecules were scant. Complex repetitive
AB  - elements constitute ca. 5% of the genome. Among these are 85 predicted
AB  - insertion sequence elements in eight different families. The strategy of
AB  - N. europaea to accumulate Fe from the environment involves several classes
AB  - of Fe receptors with more than 20 genes devoted to these receptors.
AB  - However, genes for the synthesis of only one siderophore, citrate, were
AB  - identified in the genome. This genome has provided new insights into the
AB  - growth and metabolism of ammonia-oxidizing bacteria.
ER  -

TY  - JOUR
AU  - Chain, P.S. et al.
TI  - Inaugural Article: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 15280
EP  - 15287
VL  - 103
AB  - Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated
AB  - biphenyl-degrader, has one of the two largest known
AB  - bacterial genomes and is the first nonpathogenic Burkholderia isolate
AB  - sequenced. From an evolutionary perspective, we find significant
AB  - differences in functional specialization between the three replicons of
AB  - LB400, as well as a more relaxed selective pressure for genes located on
AB  - the two smaller vs. the largest replicon. High genomic plasticity,
AB  - diversity, and specialization within the Burkholderia genus are
AB  - exemplified by the conservation of only 44% of the genes between LB400 and
AB  - Burkholderia cepacia complex strain 383. Even among four B. xenovorans
AB  - strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely
AB  - explained by our findings that >20% of the LB400 sequence was recently
AB  - acquired by means of lateral gene transfer. Although a range of genetic
AB  - factors associated with in vivo survival and intercellular interactions
AB  - are present, these genetic factors are likely related to niche breadth
AB  - rather than determinants of pathogenicity. The presence of at least eleven
AB  - "central aromatic" and twenty "peripheral aromatic" pathways in LB400,
AB  - among the highest in any sequenced bacterial genome, supports this
AB  - hypothesis. Finally, in addition to the experimentally observed redundancy
AB  - in benzoate degradation and formaldehyde oxidation pathways, the fact that
AB  - 17.6% of proteins have a better LB400 paralog than an ortholog in a
AB  - different genome highlights the importance of gene duplication and
AB  - repeated acquirement, which, coupled with their divergence, raises
AB  - questions regarding the role of paralogs and potential functional
AB  - redundancies in large-genome microbes.
ER  -

TY  - JOUR
AU  - Chain, P.S.
AU  - Comerci, D.J.
AU  - Tolmasky, M.E.
AU  - Larimer, F.W.
AU  - Malfatti, S.A.
AU  - Vergez, L.M.
AU  - Aguero, F.
AU  - Land, M.L.
AU  - Ugalde, R.A.
AU  - Garcia, E.
TI  - Whole-genome analyses of speciation events in pathogenic Brucellae.
JO  - Infect. Immun.
PY  - 2005
SP  - 8353
EP  - 8361
VL  - 73
AB  - Despite their high DNA identity and a proposal to group classical Brucella species as biovars
AB  - of Brucella melitensis, the commonly recognized Brucella species can be distinguished by
AB  - distinct biochemical and fatty acid characters, as well as by a marked host range (e.g.,
AB  - Brucella suis for swine, B. melitensis for sheep and goats, and Brucella abortus for cattle).
AB  - Here we present the genome of B. abortus 2308, the virulent prototype biovar 1 strain, and its
AB  - comparison to the two other human pathogenic Brucella species and to B. abortus field isolate
AB  - 9-941. The global distribution of pseudogenes, deletions, and insertions supports previous
AB  - indications that B. abortus and B. melitensis share a common ancestor that diverged from B.
AB  - suis. With the exception of a dozen genes, the genetic complements of both B. abortus strains
AB  - are identical, whereas the three species differ in gene content and pseudogenes. The pattern
AB  - of species-specific gene inactivations affecting transcriptional regulators and outer membrane
AB  - proteins suggests that these inactivations may play an important role in the establishment of
AB  - host specificity and may have been a primary driver of speciation in the genus Brucella.
AB  - Despite being nonmotile, the brucellae contain flagellum gene clusters and display
AB  - species-specific flagellar gene inactivations, which lead to the putative generation of
AB  - different versions of flagellum-derived structures and may contribute to differences in host
AB  - specificity and virulence. Metabolic changes such as the lack of complete metabolic pathways
AB  - for the synthesis of numerous compounds (e.g., glycogen, biotin, NAD, and choline) are
AB  - consistent with adaptation of brucellae to an intracellular life-style.
ER  -

TY  - JOUR
AU  - Chain, P.S.
AU  - Hu, P.
AU  - Malfatti, S.A.
AU  - Radnedge, L.
AU  - Larimer, F.
AU  - Vergez, L.M.
AU  - Worsham, P.
AU  - Chu, M.C.
AU  - Andersen, G.L.
TI  - Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen.
JO  - J. Bacteriol.
PY  - 2006
SP  - 4453
EP  - 4463
VL  - 188
AB  - Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed
AB  - study at the molecular level. To further investigate
AB  - the genomic diversity among this group and to help characterize lineages
AB  - of the plague organism that have no sequenced members, we present here the
AB  - genomes of two isolates of the "classical" antiqua biovar, strains Antiqua
AB  - and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb
AB  - and encode 4,138 and 3,956 open reading frames, respectively. Though both
AB  - strains belong to one of the three classical biovars, they represent
AB  - separate lineages defined by recent phylogenetic studies. We compare all
AB  - five currently sequenced Y. pestis genomes and the corresponding features
AB  - in Yersinia pseudotuberculosis. There are strain-specific rearrangements,
AB  - insertions, deletions, single nucleotide polymorphisms, and a unique
AB  - distribution of insertion sequences. We found 453 single nucleotide
AB  - polymorphisms in protein-coding regions, which were used to assess the
AB  - evolutionary relationships of these Y. pestis strains. Gene reduction
AB  - analysis revealed that the gene deletion processes are under selective
AB  - pressure, and many of the inactivations are probably related to the
AB  - organism's interaction with its host environment. The results presented
AB  - here clearly demonstrate the differences between the two biovar antiqua
AB  - lineages and support the notion that grouping Y. pestis strains based
AB  - strictly on the classical definition of biovars (predicated upon two
AB  - biochemical assays) does not accurately reflect the phylogenetic
AB  - relationships within this species. A comparison of four virulent Y. pestis
AB  - strains with the human-avirulent strain 91001 provides further insight
AB  - into the genetic basis of virulence to humans.
ER  -

TY  - JOUR
AU  - Chain, P.S.
AU  - Lang, D.M.
AU  - Comerci, D.J.
AU  - Malfatti, S.A.
AU  - Vergez, L.M.
AU  - Shin, M.
AU  - Ugalde, R.A.
AU  - Garcia, E.
AU  - Tolmasky, M.E.
TI  - Genome of Ochrobactrum anthropi ATCC 49188T, a Versatile Opportunistic Pathogen and Symbiont of Several Eukaryotic Hosts.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4274
EP  - 4275
VL  - 193
AB  - Ochrobactrum anthropi is a common soil alphaproteobacterium that colonizes a wide spectrum of
AB  - organisms and is being increasingly recognized as an
AB  - opportunistic human pathogen. Potentially life-threatening infections,
AB  - such as endocarditis, are included in the list of reported O. anthropi
AB  - infections. These reports, together with the scant number of studies and
AB  - the organism's phylogenetic proximity to the highly pathogenic brucellae,
AB  - make O. anthropi an attractive model of bacterial pathogenicity. Here we
AB  - report the genome sequence of the type strain O. anthropi ATCC 49188,
AB  - which revealed the presence of two chromosomes and four plasmids.
ER  -

TY  - JOUR
AU  - Chain, P.S.G. et al.
TI  - Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 13826
EP  - 13831
VL  - 101
AB  - Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged
AB  - recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic
AB  - relationship, they differ radically in their pathogenicity and transmission. Here, we report
AB  - the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome
AB  - comparisons with available Y. pestis sequences. Analyses of identified differences across a
AB  - panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that,
AB  - together with the two Y. pestis-specific plasmids, to our knowledge, represent the only new
AB  - genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis. In
AB  - contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y.
AB  - pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer
AB  - function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and
AB  - reductive evolution through massive gene loss, resulting in elimination and modification of
AB  - preexisting gene expression pathways, appear to be more important than acquisition of genes in
AB  - the evolution of Y. pestis. These results provide a sobering example of how a highly virulent
AB  - epidemic clone can suddenly emerge from a less virulent, closely related progenitor.
ER  -

TY  - JOUR
AU  - Chakrabortti, A.
AU  - Li, J.
AU  - Liang, Z.X.
TI  - Draft Genome Sequence of Nocardia jinanensis, an Opportunistic Bacterial Pathogen That Causes Cellulitis.
JO  - Genome Announcements
PY  - 2016
SP  - e00593
EP  - e00516
VL  - 4
AB  - The draft genome sequence of Nocardia jinanensis, an opportunistic pathogen that  can cause
AB  - skin infections, reveals genes that may contribute to the lifestyle and
AB  - pathogenicity of N. jinanensis The genome also reveals the biosynthetic capacity
AB  - of N. jinanensis in producing mycolic acids, siderophores, and other polyketide
AB  - and nonribosomal peptide-derived secondary metabolites.
ER  -

TY  - JOUR
AU  - Chakraborty, R.
AU  - Woo, H.
AU  - Dehal, P.
AU  - Walker, R.
AU  - Zemla, M.
AU  - Auer, M.
AU  - Goodwin, L.A.
AU  - Kazakov, A.
AU  - Novichkov, P.
AU  - Arkin, A.P.
AU  - Hazen, T.C.
TI  - Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 23
EP  - 23
VL  - 12
AB  - Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground
AB  - water in several DOE sites, including Hanford 100 H area. In order to
AB  - stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate
AB  - hydrogen release compound was injected into the chromium contaminated aquifer.
AB  - Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted
AB  - in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was
AB  - isolated using acetate as the electron donor and is a complete denitrifier.
AB  - Experiments with anaerobic washed cell suspension of strain RCH2 revealed it
AB  - could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a
AB  - combination of Illumina and 454 sequencing technologies and contained a circular
AB  - chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2
AB  - with six other fully sequenced P. stutzeri strains revealed most genomic regions
AB  - are conserved, however strain RCH2 has an additional 244 genes, some of which are
AB  - involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex
AB  - formation.
ER  -

TY  - JOUR
AU  - Challacombe, J.F. et al.
TI  - Complete genome sequence of Halorhodospira halophila SL1.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 206
EP  - 214
VL  - 8
AB  - Halorhodospira halophila is among the most halophilic organisms known. It is an obligately
AB  - photosynthetic and anaerobic purple sulfur bacterium that exhibits
AB  - autotrophic growth up to saturated NaCl concentrations. The type strain H.
AB  - halophila SL1 was isolated from a hypersaline lake in Oregon. Here we report the
AB  - determination of its entire genome in a single contig. This is the first genome
AB  - of a phototrophic extreme halophile. The genome consists of 2,678,452 bp,
AB  - encoding 2,493 predicted genes as determined by automated genome annotation. Of
AB  - the 2,407 predicted proteins, 1,905 were assigned to a putative function. Future
AB  - detailed analysis of this genome promises to yield insights into the halophilic
AB  - adaptations of this organism, its ability for photoautotrophic growth under
AB  - extreme conditions, and its characteristic sulfur metabolism.
ER  -

TY  - JOUR
AU  - Challacombe, J.F.
AU  - Duncan, A.J.
AU  - Brettin, T.S.
AU  - Bruce, D.
AU  - Chertkov, O.
AU  - Detter, J.C.
AU  - Han, C.S.
AU  - Misra, M.
AU  - Richardson, P.
AU  - Tapia, R.
AU  - Thayer, N.
AU  - Xie, G.
AU  - Inzana, T.J.
TI  - Complete Genome Sequence of Haemophilus somnus (Histophilus somni) Strain 129Pt and Comparison to Haemophilus ducreyi 35000HP and Haemophilus  influenzae Rd.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1890
EP  - 1898
VL  - 189
AB  - Haemophilus somnus can be either a commensal of bovine mucosal surfaces or an opportunistic
AB  - pathogen. Pathogenic strains of H. somnus are a
AB  - significant cause of systemic disease in cattle. We report the genome
AB  - sequence of H. somnus 129Pt, a nonpathogenic commensal preputial isolate,
AB  - and the results of a genome-wide comparative analysis of H. somnus 129Pt,
AB  - Haemophilus influenzae Rd, and Haemophilus ducreyi 35000HP. We found
AB  - unique genes in H. somnus 129Pt involved in lipooligosaccharide
AB  - biosynthesis, carbohydrate uptake and metabolism, cation transport, amino
AB  - acid metabolism, ubiquinone and menaquinone biosynthesis, cell surface
AB  - adhesion, biosynthesis of cofactors, energy metabolism, and electron
AB  - transport. There were also many genes in common among the three organisms.
AB  - Our comparative analyses of H. somnus 129Pt, H. influenzae Rd, and H.
AB  - ducreyi 35000HP revealed similarities and differences in the numbers and
AB  - compositions of genes involved in metabolism, host colonization, and
AB  - persistence. These results lay a foundation for research on the host
AB  - specificities and niche preferences of these organisms. Future comparisons
AB  - between H. somnus 129Pt and virulent strains will aid in the development
AB  - of protective strategies and vaccines to protect cattle against H. somnus
AB  - disease.
ER  -

TY  - JOUR
AU  - Challacombe, J.F.
AU  - Petersen, J.M.
AU  - Gallegos-Graves, V.
AU  - Hodge, D.
AU  - Pillai, S.
AU  - Kuske, C.R.
TI  - Whole genome relationships among Francisella bacteria of diverse origin define new species and provide specific regions for detection.
JO  - Appl. Environ. Microbiol.
PY  - 2017
SP  - e02589
EP  - e02516
VL  - 83
AB  - Francisella tularensis is a highly virulent zoonotic pathogen that causes
AB  - tularemia and, because of weaponization efforts in past world wars, is considered
AB  - a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be
AB  - confounded by the presence of uncharacterized, closely related organisms. Through
AB  - DNA-based diagnostics and environmental surveys, novel clinical and environmental
AB  - Francisella isolates have been obtained in recent years. Here we present 7 new
AB  - Francisella genomes and a comparison of their characteristics to each other and
AB  - to 24 publicly available genomes as well as a comparative analysis of 16S rRNA
AB  - and sdhA genes from over 90 Francisella strains. Delineation of new species in
AB  - bacteria is challenging, especially when isolates having very close genomic
AB  - characteristics exhibit different physiological features-for example, when some
AB  - are virulent pathogens in humans and animals while others are nonpathogenic or
AB  - are opportunistic pathogens. Species resolution within Francisella varies with
AB  - analyses of single genes, multiple gene or protein sets, or whole-genome
AB  - comparisons of nucleic acid and amino acid sequences. Analyses focusing on single
AB  - genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide
AB  - [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons
AB  - (nucleotide and protein) gave congruent results, but with different levels of
AB  - discrimination confidence. We designate four new species within the genus;
AB  - Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov.
AB  - (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella
AB  - frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative
AB  - framework to discern species and virulence features of newly detected Francisella
AB  - bacteria. IMPORTANCE: DNA-based detection and sequencing methods have identified
AB  - thousands of new bacteria in the human body and the environment. In most cases,
AB  - there are no cultured isolates that correspond to these sequences. While
AB  - DNA-based approaches are highly sensitive, accurately assigning species is
AB  - difficult without known near relatives for comparison. This ambiguity poses
AB  - challenges for clinical cases, disease epidemics, and environmental surveillance,
AB  - for which response times must be short. Many new Francisella isolates have been
AB  - identified globally. However, their species designations and potential for
AB  - causing human disease remain ambiguous. Through detailed genome comparisons, we
AB  - identified features that differentiate F. tularensis from clinical and
AB  - environmental Francisella isolates and provide a knowledge base for future
AB  - comparison of Francisella organisms identified in clinical samples or
AB  - environmental surveys.
ER  -

TY  - JOUR
AU  - Chambaud, I.
AU  - Heilig, R.
AU  - Ferris, S.
AU  - Barbe, V.
AU  - Samson, D.
AU  - Galisson, F.
AU  - Moszer, I.
AU  - Dybvig, K.
AU  - Wroblewski, H.
AU  - Viari, A.
AU  - Rocha, E.P.C.
AU  - Blanchard, A.
TI  - The complete genome sequence of the murine respiratory pathogen  Mycoplasma pulmonis.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 2145
EP  - 2153
VL  - 29
AB  - Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name,
AB  - mycoplasmas) and responsible for murine respiratory
AB  - diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome
AB  - with a G + C content of 26.6 mol%, i.e. the lowest
AB  - reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative
AB  - coding sequences (CDSs) covering 91.4% of its length
AB  - and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of
AB  - hypothetical proteins, leaving 204 CDSs without significant
AB  - database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The
AB  - replication origin oriC was localized by sequence
AB  - analysis and by using the G + C skew method. Sequence polymorphisms within stretches of
AB  - repeated nucleotides generate phase-variable protein
AB  - antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in
AB  - major M. pulmonis surface antigens. Furthermore, a
AB  - hemolysin, secreted nucleases and a glycoprotease are predicted virulence factors.
AB  - Surprisingly, several of the genes previously reported to be
AB  - essential for a self-replicating minimal cell are missing in the M. pulmonis genome although
AB  - this one is larger than the other mycoplasma genomes fully
AB  - sequenced until now.
ER  -

TY  - JOUR
AU  - Chames, P.
AU  - Epinat, J.C.
AU  - Guillier, S.
AU  - Patin, A.
AU  - Lacroix, E.
AU  - Paques, F.
TI  - In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - e178
EP  - e178
VL  - 33
AB  - Homing endonucleases, endonucleases capable of recognizing long DNA sequences, have been shown
AB  - to be a tool of choice for precise and efficient genome engineering. Consequently, the
AB  - possibility to engineer novel endonucleases with tailored specificities is under strong
AB  - investigation. In this report, we present a simple and efficient method to select
AB  - meganucleases from libraries of variants, based on their cleavage properties. The method has
AB  - the advantage of directly selecting for the ability to induce double-strand break induced
AB  - homologous recombination in a eukaryotic environment. Model selections demonstrated high
AB  - levels of enrichments. Moreover, this method compared favorably with phage display for
AB  - enrichment of active mutants from a mutant library. This approach makes possible the
AB  - exploration of large sequence spaces and thereby represents a valuable tool for genome
AB  - engineering.
ER  -

TY  - JOUR
AU  - Champion, C.
AU  - Guianvarc'h, D.
AU  - Senamaud-Beaufort, C.
AU  - Jurkowska, R.Z.
AU  - Jeltsch, A.
AU  - Ponger, L.
AU  - Arimondo, P.B.
AU  - Guieysse-Peugeot, A.L.
TI  - Mechanistic Insights on the Inhibition of C5 DNA Methyltransferases by Zebularine.
JO  - PLoS ONE
PY  - 2010
SP  - e12388
EP  - e12388
VL  - 5
AB  - In mammals DNA methylation occurs at position 5 of cytosine in a CpG context and regulates
AB  - gene expression. It plays an important role in
AB  - diseases and inhibitors of DNA methyltransferases (DNMTs)-the enzymes
AB  - responsible for DNA methylation-are used in clinics for cancer therapy.
AB  - The most potent inhibitors are 5-azacytidine and 5-azadeoxycytidine.
AB  - Zebularine (1-(beta-D-ribofuranosyl)-2(1H)-pyrimidinone) is another
AB  - cytidine analog described as a potent inhibitor that acts by forming a
AB  - covalent complex with DNMT when incorporated into DNA. Here we bring
AB  - additional experiments to explain its mechanism of action. First, we
AB  - observe an increase in the DNA binding when zebularine is incorporated
AB  - into the DNA, compared to deoxycytidine and 5-fluorodeoxycytidine,
AB  - together with a strong decrease in the dissociation rate. Second, we
AB  - show by denaturing gel analysis that the intermediate covalent complex
AB  - between the enzyme and the DNA is reversible, differing thus from
AB  - 5-fluorodeoxycytidine. Third, no methylation reaction occurs when
AB  - zebularine is present in the DNA. We confirm that zebularine exerts its
AB  - demethylation activity by stabilizing the binding of DNMTs to DNA,
AB  - hindering the methylation and decreasing the dissociation, thereby
AB  - trapping the enzyme and preventing turnover even at other sites.
ER  -

TY  - JOUR
AU  - Champion, M.D. et al.
TI  - Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies.
JO  - PLoS Pathog.
PY  - 2009
SP  - e1000459
EP  - e1000459
VL  - 5
AB  - Tularemia is a geographically widespread, severely debilitating, and occasionally lethal
AB  - disease in humans. It is caused by infection by a
AB  - gram-negative bacterium, Francisella tularensis. In order to better
AB  - understand its potency as an etiological agent as well as its potential
AB  - as a biological weapon, we have completed draft assemblies and report
AB  - the first complete genomic characterization of five strains belonging
AB  - to the following different Francisella subspecies (subsp.): the F.
AB  - tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica
AB  - FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and
AB  - GA99-3549 strains. Here, we report the sequencing of these strains and
AB  - comparative genomic analysis with recently available public Francisella
AB  - sequences, including the rare F. tularensis subsp. mediasiatica FSC147
AB  - strain isolate from the Central Asian Region. We report evidence for
AB  - the occurrence of large-scale rearrangement events in strains of the
AB  - holarctica subspecies, supporting previous proposals that further
AB  - phylogenetic subdivisions of the Type B clade are likely. We also find
AB  - a significant enrichment of disrupted or absent ORFs proximal to
AB  - predicted breakpoints in the FSC022 strain, including a genetic
AB  - component of the Type I restriction-modification defense system. Many
AB  - of the pseudogenes identified are also disrupted in the closely related
AB  - rarely human pathogenic F. tularensis subsp. mediasiatica FSC147
AB  - strain, including modulator of drug activity B (mdaB) (FTT0961), which
AB  - encodes a known NADPH quinone reductase involved in oxidative stress
AB  - resistance. We have also identified genes exhibiting sequence
AB  - similarity to effectors of the Type III (T3SS) and components of the
AB  - Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c),
AB  - is disrupted in F. tularensis subsp. mediasiatica and has recently been
AB  - shown to mediate bacterial pathogen survival in host organisms. Our
AB  - findings suggest that in addition to the duplication of the Francisella
AB  - Pathogenicity Island, and acquisition of individual loci, adaptation by
AB  - gene loss in the more recently emerged tularensis, holarctica, and
AB  - mediasiatica subspecies occurred and was distinct from evolutionary
AB  - events that differentiated these subspecies, and the novicida
AB  - subspecies, from a common ancestor. Our findings are applicable to
AB  - future studies focused on variations in Francisella subspecies
AB  - pathogenesis, and of broader interest to studies of genomic
AB  - pathoadaptation in bacteria.
ER  -

TY  - JOUR
AU  - Chan, G.F.
AU  - Gan, H.M.
AU  - Rashid, N.A.
TI  - Genome Sequence of Citrobacter sp. Strain A1, a Dye-Degrading Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5485
EP  - 5486
VL  - 194
AB  - Citrobacter sp. strain A1, isolated from a sewage oxidation pond, is a facultative aerobe and
AB  - mesophilic dye-degrading bacterium. This organism degrades
AB  - azo dyes efficiently via azo reduction and desulfonation, followed by the
AB  - successive biotransformation of dye intermediates under an aerobic environment.
AB  - Here we report the draft genome sequence of Citrobacter sp. A1.
ER  -

TY  - JOUR
AU  - Chan, G.F.
AU  - Gan, H.M.
AU  - Rashid, N.A.
TI  - Genome Sequence of Enterococcus sp. Strain C1, an Azo Dye Decolorizer.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5716
EP  - 5717
VL  - 194
AB  - Enterococcus sp. strain C1 is a facultative anaerobe which was coisolated with Citrobacter sp.
AB  - strain A1 from a sewage oxidation pond. Strain C1 could degrade
AB  - azo dyes very efficiently via azo reduction and desulfonation in a
AB  - microaerophilic environment. Here the draft genome sequence of Enterococcus sp.
AB  - C1 is reported.
ER  -

TY  - JOUR
AU  - Chan, H.-Y.
AU  - Chan, Y.-C.
AU  - Kam, K.-M.
AU  - Shaw, P.-C.
TI  - Isolation and characterization of restriction endonuclease EclHKI from an Enterobacter cloacae strain.
JO  - World J. Microbiol. Biotechnol.
PY  - 1994
SP  - 30
EP  - 32
VL  - 10
AB  - An Enterobacter cloacae strain, producing restriction enzyme EclHKI, was isolated from a
AB  - decaying potato. The enzyme is an isoschizomer of Eam1105I, which recognizes and cleaves
AB  - GACNNN^NNGTC. EclHKI was produced at high activity (40000 U/g wet cells) and was purified from
AB  - contaminants which interfere with restriction digestion by passing the cell lysate through
AB  - DEAE-Sephacel and heparin columns. Activity was optimal at 37oC in a medium salt buffer.
ER  -

TY  - JOUR
AU  - Chan, J.
AU  - Halachev, M.
AU  - Yates, E.
AU  - Smith, G.
AU  - Pallen, M.
TI  - Whole-Genome Sequence of the Emerging Pathogen Mycobacterium abscessus Strain 47J26.
JO  - J. Bacteriol.
PY  - 2012
SP  - 549
EP  - 549
VL  - 194
AB  - Mycobacterium abscessus is a rapidly growing environmental mycobacterium commonly found in
AB  - soil and water which is often also associated with
AB  - infections in humans, particularly of the lung. We report herein the draft
AB  - genome sequence of M. abscessus strain 47J26.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Chen, J.W.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Chan, X.Y.
TI  - Draft Genome Sequence of Lysinibacillus sp. Strain A1, Isolated from Malaysian Tropical Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00095
EP  - e00015
VL  - 3
AB  - In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from
AB  - tropical soil. Analysis of its genome sequence shows the presence
AB  - of a gene encoding for a putative peptidase responsible for nitrogen compounds.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Chen, J.W.
AU  - Tee, K.K.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Chan, X.Y.
TI  - Whole-Genome Analysis of Quorum-Sensing Burkholderia sp. Strain A9.
JO  - Genome Announcements
PY  - 2015
SP  - e00063
EP  - e00015
VL  - 3
AB  - Burkholderia spp. rely on N-acyl homoserine lactone as quorum-sensing signal molecules which
AB  - coordinate their phenotype at the population level. In this work,
AB  - we present the whole genome of Burkholderia sp. strain A9, which enables the
AB  - discovery of its N-acyl homoserine lactone synthase gene.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Chin, P.S.
AU  - Tee, K.K.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Sheng, K.Y.
TI  - Draft Genome Sequence of Aeromonas caviae Strain L12, a Quorum-Sensing Strain Isolated from a Freshwater Lake in Malaysia.
JO  - Genome Announcements
PY  - 2015
SP  - e00079
EP  - e00015
VL  - 3
AB  - Here, we present the draft genome sequence of Aeromonas caviae strain L12, which  shows
AB  - quorum-sensing activity. The availability of this genome sequence is
AB  - important to the research of the quorum-sensing regulatory system in this
AB  - isolate.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Chong, T.M.
AU  - Adrian, T.G.
AU  - Kher, H.L.
AU  - Hong, K.W.
AU  - Grandclement, C.
AU  - Faure, D.
AU  - Yin, W.F.
AU  - Dessaux, Y.
TI  - Whole-Genome Sequence of Stenotrophomonas maltophilia ZBG7B Reveals Its Biotechnological Potential.
JO  - Genome Announcements
PY  - 2015
SP  - e01442
EP  - e01415
VL  - 3
AB  - Stenotrophomonas maltophilia ZBG7B was isolated from vineyard soil of Zellenberg, France.
AB  - Here, we present the draft genome sequence of this bacterial strain,
AB  - which has facilitated the prediction of function for several genes encoding
AB  - biotechnologically important enzymes, such as xylosidase, xylanase, laccase, and
AB  - chitinase.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Kher, H.L.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Tan, K.H.
TI  - Analysis of Pectate Lyase Genes in Dickeya chrysanthemi Strain L11, Isolated from a Recreational Lake in Malaysia: a Draft Genome Sequence Perspective.
JO  - Genome Announcements
PY  - 2015
SP  - e00145
EP  - e00115
VL  - 3
AB  - Dickeya chrysanthemi is well known as a plant pathogen that caused major blackleg in the
AB  - European potato industry in the 1990s. D. chrysanthemi strain L11 was
AB  - discovered in a recreational lake in Malaysia. Here, we present its draft genome
AB  - sequence.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Ng, K.T.
AU  - Pang, Y.K.
AU  - Chong, T.M.
AU  - Kamarulzaman, A.
AU  - Yin, W.F.
AU  - Tee, K.K.
TI  - Genome Anatomy of Streptococcus parasanguinis Strain C1A, Isolated from a Patient with Acute Exacerbation of Chronic Obstructive Pulmonary Disease, Reveals Unusual  Genomic Features.
JO  - Genome Announcements
PY  - 2015
SP  - e00541
EP  - e00515
VL  - 3
AB  - Streptococcus parasanguinis causes invasive diseases. However, the mechanism by which it
AB  - causes disease remains unclear. Here, we describe the complete genome
AB  - sequence of S. parasanguinis C1A, isolated from a patient diagnosed with an acute
AB  - exacerbation of chronic obstructive pulmonary disease. Several genes that might
AB  - be associated with pathogenesis are also described.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Sulaiman, J.
AU  - Yong, D.A.
AU  - Tee, K.K.
AU  - Yin, W.F.
AU  - Priya, K.
TI  - Draft Genome Perspective of Staphylococcus saprophyticus Strain SU8, an N-Acyl Homoserine Lactone-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01097
EP  - e01015
VL  - 3
AB  - Staphylococcus saprophyticus strain SU8 was isolated from a pristine water source in Malaysia
AB  - and it exhibited degradation of N-hexanoylhomoserine lactone. Here we report the draft genome
AB  - sequence of S. saprophyticus strain SU8 to further understand its quorum quenching abilities.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Tan, K.H.
AU  - Yin, W.F.
AU  - Tan, J.Y.
TI  - Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi.
JO  - Genome Announcements
PY  - 2014
SP  - e01339
EP  - e01314
VL  - 2
AB  - We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from
AB  - pickled mackerel sashimi, sequenced by third-generation sequencing
AB  - technology. To the best of our knowledge, this is the first documentation that
AB  - reports the complete genome of Cedecea neteri.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Tan, W.S.
TI  - Genomic Insights of Pectobacterium carotovorum Strain M022 Quorum-Sensing Activity through Whole-Genome Sequencing.
JO  - Genome Announcements
PY  - 2015
SP  - e01554
EP  - e01514
VL  - 3
AB  - Pectobacterium carotovorum is known to cause serious damage to various major crops worldwide.
AB  - Here, we report the draft genome of Pectobacterium carotovorum
AB  - strain M022, a freshwater isolate from a Malaysian waterfall, which has been
AB  - reported as a plant pathogen and is able to communicate with N-acylhomoserine
AB  - lactone-mediated quorum sensing.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Tan, W.S.
TI  - Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 40
EP  - 40
VL  - 12
AB  - Cedecea neteri M006 is a rare bacterium typically found as an environmental isolate from the
AB  - tropical rainforest Sungai Tua waterfall (Gombak, Selangor,
AB  - Malaysia). It is a Gram-reaction-negative, facultative anaerobic, bacillus. Here,
AB  - we explore the features of Cedecea neteri M006, together with its genome sequence
AB  - and annotation. The genome comprised 4,965,436 bp with 4447 protein-coding genes
AB  - and 103 RNA genes.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Tan, W.S.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Mumahad, Y.N.Y.
TI  - Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila Strain M062, Isolated from Freshwater.
JO  - Genome Announcements
PY  - 2015
SP  - e00100
EP  - e00115
VL  - 3
AB  - Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft
AB  - whole-genome sequence of a freshwater isolate from Malaysia, A.
AB  - hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported
AB  - here.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Tee, K.K.
AU  - Yin, W.F.
AU  - Tan, J.Y.
TI  - Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste.
JO  - Genome Announcements
PY  - 2014
SP  - e01276
EP  - e01214
VL  - 2
AB  - Pluralibacter gergoviae FB2, a bacterial strain isolated from packed food, has been found to
AB  - exhibit quorum-quenching properties. Hence, we report the first,
AB  - complete genome of P. gergoviae sequenced using the Pacific Biosciences
AB  - single-molecule, real-time (SMRT) platform.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Wong, C.S.
AU  - Yin, W.F.
AU  - Chan, X.Y.
TI  - Draft Genome Sequence of Quorum-Sensing and Quorum-Quenching Pseudomonas aeruginosa Strain MW3a.
JO  - Genome Announcements
PY  - 2014
SP  - e00258
EP  - e00214
VL  - 2
AB  - Pseudomonas aeruginosa has a broad range of habitation, from aquatic environments to human
AB  - lungs. The coexistence of quorum-sensing and quorum-quenching activities occurs in P.
AB  - aeruginosa strain MW3a. In this work, we present the draft genome sequence of P. aeruginosa
AB  - MW3a, an interesting bacterium isolated from a marine environment.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Yin, W.F.
AU  - Goh, S.Y.
TI  - Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site.
JO  - Genome Announcements
PY  - 2014
SP  - e00427
EP  - e00414
VL  - 2
AB  - Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from
AB  - soil. Here, we report the complete genome sequence of P. pnomenusa
AB  - strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS
AB  - SMRT) sequencer high-resolution technology.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Yin, W.F.
AU  - Lim, Y.L.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Strain YL84, a Quorum-Sensing  Strain Isolated from Compost.
JO  - Genome Announcements
PY  - 2014
SP  - e00246
EP  - e00214
VL  - 2
AB  - Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was
AB  - isolated from compost. This strain was found to be a chitinase-producing quorum-sensing
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Yin, W.F.
AU  - Tee, K.K.
AU  - Chang, C.Y.
AU  - Priya, K.
TI  - Pandoraea sp. Strain E26: Discovery of Its Quorum-Sensing Properties via Whole-Genome Sequence Analysis.
JO  - Genome Announcements
PY  - 2015
SP  - e00565
EP  - e00515
VL  - 3
AB  - We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former
AB  - landfill site, sequenced by the Illumina MiSeq platform. This genome
AB  - sequence will be useful to further understand the quorum-sensing system of this
AB  - isolate.
ER  -

TY  - JOUR
AU  - Chan, K.G.
AU  - Yunos, N.Y.
TI  - Whole-Genome Sequencing Analysis of Chromobacterium piscinae Strain ND17, a Quorum-Sensing Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00081
EP  - e00016
VL  - 4
AB  - Here, we report the draft genome sequence of Chromobacterium piscinae strain ND17. This
AB  - bacterium was isolated from a fresh water sample in Malaysia and
AB  - exhibits quorum-sensing activity. This first draft genome of C. piscinae strain
AB  - ND17 will pave the way to future studies of the quorum-sensing properties of this
AB  - isolate.
ER  -

TY  - JOUR
AU  - Chan, Q.W.
AU  - Cornman, R.S.
AU  - Birol, I.
AU  - Liao, N.Y.
AU  - Chan, S.K.
AU  - Docking, T.R.
AU  - Jackman, S.D.
AU  - Taylor, G.A.
AU  - Jones, S.J.
AU  - de Graaf, D.C.
AU  - Evans, J.D.
AU  - Foster, L.J.
TI  - Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.
JO  - BMC Genomics
PY  - 2011
SP  - 450
EP  - 450
VL  - 12
AB  - BACKGROUND: As scientists continue to pursue various 'omics-based research, there
AB  - is a need for high quality data for the most fundamental 'omics of all: genomics.
AB  - The bacterium Paenibacillus larvae is the causative agent of the honey bee
AB  - disease American foulbrood. If untreated, it can lead to the demise of an entire
AB  - hive; the highly social nature of bees also leads to easy disease spread, between
AB  - both individuals and colonies. Biologists have studied this organism since the
AB  - early 1900s, and a century later, the molecular mechanism of infection remains
AB  - elusive. Transcriptomics and proteomics, because of their ability to analyze
AB  - multiple genes and proteins in a high-throughput manner, may be very helpful to
AB  - its study. However, the power of these methodologies is severely limited without
AB  - a complete genome; we undertake to address that deficiency here. RESULTS: We used
AB  - the Illumina GAIIx platform and conventional Sanger sequencing to generate a
AB  - 182-fold sequence coverage of the P. larvae genome, and assembled the data using
AB  - ABySS into a total of 388 contigs spanning 4.5 Mbp. Comparative genomics analysis
AB  - against fully-sequenced soil bacteria P. JDR2 and P. vortex showed that regions
AB  - of poor conservation may contain putative virulence factors. We used GLIMMER to
AB  - predict 3568 gene models, and named them based on homology revealed by BLAST
AB  - searches; proteases, hemolytic factors, toxins, and antibiotic resistance enzymes
AB  - were identified in this way. Finally, mass spectrometry was used to provide
AB  - experimental evidence that at least 35% of the genes are expressed at the protein
AB  - level. CONCLUSIONS: This update on the genome of P. larvae and annotation
AB  - represents an immense advancement from what we had previously known about this
AB  - species. We provide here a reliable resource that can be used to elucidate the
AB  - mechanism of infection, and by extension, more effective methods to control and
AB  - cure this widespread honey bee disease.
ER  -

TY  - JOUR
AU  - Chan, S.-H.
AU  - Zhu, Z.
AU  - Van Etten, J.L.
AU  - Xu, S.-Y.
TI  - Cloning of CviPII nicking and modification system from chlorella virus Nys-1 and application of Nt.CviPII in random DNA amplification.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 6187
EP  - 6199
VL  - 32
AB  - The cloning and expression of the CviPII DNA nicking and modification system encoded by
AB  - chlorella virus NYs-1 is described. The system consists of a co-linear MTase encoding gene
AB  - (cviPIIM) and a nicking endonuclease encoding gene (cviPIINt) separated by 12 nt. M.CviPII
AB  - possesses eight conserved amino acid motifs (I to VIII) typical of C5 MTases, but, like
AB  - another chlorella virus MTase M.CviJI, lacks conserved motifs IX and X. In addition to
AB  - modification of the first cytosine in CCD (D = A, G or T) sequences, M.CviPII modifies both
AB  - the first two cytosines in CCAA and CCCG sites as well. Nt.CviPII has significant amino acid
AB  - sequence similarity to Type II restriction endonuclease CviJI that recognizes an overlapping
AB  - sequence (RG^CY). Nt.CviPII was expressed in Escherichia coli with or without a His-tag in a
AB  - host pre-modified by M.CviPII. Recombinant Nt.CviPII recognizes the DNA sequence CCD and
AB  - cleaves the phosphodiester bond 5' of the first cytosine while the other strand of DNA at
AB  - this site is not affected. Nt.CviPII displays site preferences with CCR (R = A or G) sites
AB  - preferred over CCT sites. Nt.CviPII is active from 16 to 65 degrees C with a temperature
AB  - optimum of 30-45 degrees C. Nt.CviPII can be used to generate single-stranded DNAs (ssDNAs)
AB  - for isothermal strand-displacement amplification. Nt.CviPII was used in combination with Bst
AB  - DNA polymerase I large fragment to rapidly amplify anonymous DNA from genomic DNA or from a
AB  - single bacterial colony.
ER  -

TY  - JOUR
AU  - Chan, S.H.
AU  - Bao, Y.
AU  - Ciszak, E.
AU  - Laget, S.
AU  - Xu, S.Y.
TI  - Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 6238
EP  - 6248
VL  - 35
AB  - Creating endonucleases with novel sequence specificities provides more possibilities to
AB  - manipulate DNA. We have created a chimeric endonuclease
AB  - (CH-endonuclease) consisting of the DNA cleavage domain of BmrI
AB  - restriction endonuclease and C.BclI, a controller protein of the BclI
AB  - restriction-modification system. The purified chimeric endonuclease,
AB  - BmrI198-C.BclI, cleaves DNA at specific sites in the vicinity of the
AB  - recognition sequence of C.BclI. Double-strand (ds) breaks were observed at
AB  - two sites: 8 bp upstream and 18 bp within the C-box sequence. Using DNA
AB  - substrates with deletions of C-box sequence, we show that the chimeric
AB  - endonuclease requires the 5' half of the C box only for specific cleavage.
AB  - A schematic model is proposed for the mode of protein-DNA binding and DNA
AB  - cleavage. The present study demonstrates that the BmrI cleavage domain can
AB  - be used to create combinatorial endonucleases that cleave DNA at specific
AB  - sequences dictated by the DNA-binding partner. The resulting endonucleases
AB  - will be useful in vitro and in vivo to create ds breaks at specific sites
AB  - and generate deletions.
ER  -

TY  - JOUR
AU  - Chan, S.H.
AU  - Opitz, L.
AU  - Higgins, L.
AU  - O'loane, D.
AU  - Xu, S.-Y.
TI  - Cofactor Requirement of HpyAV Restriction Endonuclease.
JO  - PLoS ONE
PY  - 2010
SP  - e9071
EP  - e9071
VL  - 5
AB  - Background: Helicobacter pylori is the etiologic agent of common gastritis and a risk factor
AB  - for gastric cancer. It is also one of the richest sources of Type II restriction-modification
AB  - (R-M) systems in microorganisms. Principal/Findings: We have cloned, expressed and purified a
AB  - new restriction endonuclease HpyAV from H. pylori strain 26695. We determined the HpyAV DNA
AB  - recognition sequence and cleavage site as CCTTC 6/5. In addition, we found that HpyAV has a
AB  - unique metal ion requirement: its cleavage activity is higher with transition metal ions than
AB  - in Mg++. The special metal ion requirement of HpyAV can be attributed to the presence of a HNH
AB  - catalytic site similar to ColE9 nuclease instead of the canonical PD-X-D/EXK catalytic site
AB  - found in many other REases. Site-directed mutagenesis was carried out to verify the catalytic
AB  - residues of HpyAV. Mutation of the conserved metal-binding Asn311 and His320 to alanine
AB  - eliminated cleavage activity. HpyAV variant H295A displayed approximately 1% of wt activity.
AB  - Conclusions/Significance: Some HNH-type endonucleases have unique metal ion cofactor
AB  - requirement for optimal activities. Homology modeling and site-directed mutagenesis confirmed
AB  - that HpyAV is a member of the HNH nuclease family. The identification of catalytic residues in
AB  - HpyAV paved the way for further engineering of the metal binding site. A survey of sequenced
AB  - microbial genomes uncovered 10 putative R-M systems that show high sequence similarity to the
AB  - HpyAV system, suggesting lateral transfer of a prototypic HpyAV-like R-M system among these
AB  - microorganisms.
ER  -

TY  - JOUR
AU  - Chan, S.H.
AU  - Stoddard, B.L.
AU  - Xu, S.Y.
TI  - Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 1
EP  - 18
VL  - 39
AB  - Restriction endonucleases (REases) are highly specific DNA scissors that have facilitated the
AB  - development of modern molecular biology. Intensive studies of double strand (ds) cleavage
AB  - activity of Type IIP REases, which recognize 4-8 bp palindromic sequences, have revealed a
AB  - variety of mechanisms of molecular recognition and catalysis. Less well-studied are REases
AB  - which cleave only one of the strands of dsDNA, creating a nick instead of a ds break.
AB  - Naturally occurring nicking endonucleases (NEases) range from frequent cutters such as
AB  - Nt.CviPII (;CCD; ; denotes the cleavage site) to rare-cutting homing endonucleases (HEases)
AB  - such as I-HmuI. In addition to these bona fida NEases, individual subunits of some
AB  - heterodimeric Type IIS REases have recently been shown to be natural NEases. The discovery and
AB  - characterization of more REases that recognize asymmetric sequences, particularly Types IIS
AB  - and IIA REases, has revealed recognition and cleavage mechanisms drastically different from
AB  - the canonical Type IIP mechanisms, and has allowed researchers to engineer highly
AB  - strand-specific NEases. Monomeric LAGLIDADG HEases use two separate catalytic sites for
AB  - cleavage. Exploitation of this characteristic has also resulted in useful nicking HEases. This
AB  - review aims at providing an overview of the cleavage mechanisms of Types IIS and IIA REases
AB  - and LAGLIDADG HEases, the engineering of their nicking variants, and the applications of
AB  - NEases and nicking HEases.
ER  -

TY  - JOUR
AU  - Chan, S.H.
AU  - Zhu, Z.Y.
AU  - Dunigan, D.D.
AU  - Van Etten, J.L.
AU  - Xu, S.Y.
TI  - Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences.
JO  - Protein Expr. Purif.
PY  - 2006
SP  - 138
EP  - 150
VL  - 49
AB  - Chlorella virus NY-2A has a large, highly methylated dsDNA genome (45% of the cytosines are
AB  - 5-methylcytosine and 37% of the adenines are
AB  - N-6-methyladenine). Here, we report the cloning, expression, and
AB  - characterization of the NY-2A-encoded CviQII nicking-modification (N-M)
AB  - system. The nicking endonuclease, Nt.CviQII, recognizes R down arrow AG
AB  - (R = A or G, down arrow indicating cleavage site) sequences and cleaves
AB  - the phosphodiester bond 5' to the adenosine. Because of the difficulty
AB  - in cloning and expressing the wild-type Nt.CviQII, C-terminal
AB  - truncation mutants were generated and full-length Nt.CviQII was
AB  - reconstructed by intein-mediated peptide ligation. The truncation
AB  - mutants and the reconstructed full-length Nt.CviQII have the same
AB  - recognition and cleavage specificity as the native enzyme. Full-length
AB  - and truncated Nt.CviQII produced by a cell-free
AB  - transcription/translation system have similar reaction rates. The
AB  - methyltransferase, M.CviQII, was also cloned and expressed. It modifies
AB  - the adenine in AG doublets of DNA in vitro and in vivo in Escherichia
AB  - coli. To our knowledge, M.CviQII is the first adenine methyltransferase
AB  - that recognizes a dinucleotide. Therefore, M.CviQII may be a useful
AB  - reagent for blocking endonuclease cleavage when restriction sites
AB  - overlap with AG sequences.
ER  -

TY  - JOUR
AU  - Chan, S.W.-L.
AU  - Zilberman, D.
AU  - Xie, Z.
AU  - Johansen, L.K.
AU  - Carrington, J.C.
AU  - Jacobsen, S.E.
TI  - RNA silencing genes control de novo DNA methylation.
JO  - Science
PY  - 2004
SP  - 1336
EP  - 1336
VL  - 303
AB  - Cytosine DNA methylation silences harmful DNAs such as transposons and retroviruses.
AB  - Maintenance DNA methyltransferases propagate pre-existing DNA methylation in the CG sequence
AB  - context by methylating hemi-methylated sites after DNA replication.  Much less is understood
AB  - about how invasive DNAs are initially recognized and how de novo DNA methyltransferases of the
AB  - DNMT3 family (DRM1 and DRM2 in the plant Arabidopsis thaliana) are directed to unmethylated
AB  - loci to initiate gene silencing.
ER  -

TY  - JOUR
AU  - Chan, W.Y.
AU  - Dietel, K.
AU  - Lapa, S.V.
AU  - Avdeeva, L.V.
AU  - Borriss, R.
AU  - Reva, O.N.
TI  - Draft Genome Sequence of Bacillus atrophaeus UCMB-5137, a Plant Growth-Promoting  Rhizobacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00233
EP  - e00213
VL  - 1
AB  - Bacillus atrophaeus UCMB-5137 shows an extraordinary activity in root colonization and plant
AB  - and crop protection. Its draft genome sequence comprises
AB  - 21 contigs of 4.11 Mb, harboring 4,167 coding sequences (CDS). The genome carries
AB  - several genes encoding antimicrobial lipopeptides and polyketides. Multiple
AB  - horizontally acquired genes of possible importance for plant colonization were
AB  - also found.
ER  -

TY  - JOUR
AU  - Chan, X.Y.
AU  - Chen, J.W.
AU  - Adrian, T.G.
AU  - Hong, K.W.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia.
JO  - Genome Announcements
PY  - 2017
SP  - e00067
EP  - e00017
VL  - 5
AB  - Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In  this study,
AB  - the genome of marine Bacillus sp. strain G3(2015) was sequenced using
AB  - MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome
AB  - annotation.
ER  -

TY  - JOUR
AU  - Chan, X.Y.
AU  - Chua, K.H.
AU  - Puthucheary, S.D.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Draft Genome Sequence of an Aeromonas sp. Strain 159 Clinical Isolate That Shows  Quorum-Sensing Activity.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6350
EP  - 6350
VL  - 194
AB  - Aeromonas is a pathogenic organism that is often found to infect humans. Here we  report the
AB  - draft genome of a clinical isolate in Malaysia, Aeromonas sp. strain
AB  - 159, which shows N-acylhomoserine lactone production. In the draft genome of
AB  - strain 159, luxI and luxR homologue genes were found to be located at contig 47,
AB  - and these genes are believed to be important for the quorum-sensing system
AB  - present in this pathogen.
ER  -

TY  - JOUR
AU  - Chan, X.Y.
AU  - Chua, K.H.
AU  - Yin, W.F.
AU  - Puthucheary, S.D.
AU  - Chan, K.G.
TI  - Whole-Genome Analysis of Aeromonas hydrophila Strain 187, Exhibiting Quorum-Sensing Activity.
JO  - Genome Announcements
PY  - 2014
SP  - e01360
EP  - e01314
VL  - 2
AB  - Aeromonas hydrophila is a quorum-sensing (QS) bacterium that causes diarrhea in humans upon
AB  - infection. Here, we report the genome of pathogenic Aeromonas
AB  - hydrophila strain 187, which possesses a QS gene responsible for signaling
AB  - molecule N-acyl homoserine lactone (AHL) synthesis and has been found to be
AB  - located at contig 36.
ER  -

TY  - JOUR
AU  - Chan, Y.
AU  - Ma, A.P.
AU  - Lacap-Bugler, D.C.
AU  - Huo, Y.B.
AU  - Keung, L.W.
AU  - Leung, F.C.
AU  - Watt, R.M.
TI  - Complete Genome Sequence for Treponema sp. OMZ 838 (ATCC 700772, DSM 16789), Isolated from a Necrotizing Ulcerative Gingivitis Lesion.
JO  - Genome Announcements
PY  - 2014
SP  - e01333
EP  - e01314
VL  - 2
AB  - The oral treponeme bacterium Treponema sp. OMZ 838 was originally isolated from a human
AB  - necrotizing ulcerative gingivitis (NUG) lesion. Its taxonomic status
AB  - remains uncertain. The complete genome sequence length was determined to be
AB  - 2,708,067 bp, with a G+C content of 44.58%, and 2,236 predicted coding DNA
AB  - sequences (CDS).
ER  -

TY  - JOUR
AU  - Chan, Y.-S.
AU  - Takeuchi, R.
AU  - Jarjour, J.
AU  - Huen, D.S.
AU  - Stoddard, B.L.
AU  - Russell, S.
TI  - The Design and In Vivo Evaluation of Engineered I-OnuI-Based Enzymes for HEG Gene Drive.
JO  - PLoS ONE
PY  - 2013
SP  - e74254
EP  - e74254
VL  - 8
AB  - The homing endonuclease gene (HEG) drive system, a promising genetic approach for controlling
AB  - arthropod populations, utilises engineered nucleases to spread deleterious mutations that
AB  - inactivate individual genes throughout a target population. Previous work with a naturally
AB  - occurring LAGLIDADG homing endonuclease (I-SceI) demonstrated its feasibility in both
AB  - Drosophila and Anopheles. Here we report on the next stage of this strategy: the redesign of
AB  - HEGs with customized specificity in order to drive
ER  -

TY  - JOUR
AU  - Chand, M.K.
AU  - Nirwan, N.
AU  - Diffin, F.M.
AU  - van Aelst, K.
AU  - Kulkarni, M.
AU  - Pernstich, C.
AU  - Szczelkun, M.D.
AU  - Saikrishnan, K.
TI  - Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes.
JO  - Nat. Chem. Biol.
PY  - 2015
SP  - 870
EP  - 877
VL  - 11
AB  - Production of endonucleolytic double-strand DNA breaks requires separate strand cleavage
AB  - events. Although catalytic mechanisms for simple, dimeric endonucleases
AB  - are known, there are many complex nuclease machines that are poorly understood.
AB  - Here we studied the single polypeptide Type ISP restriction-modification (RM)
AB  - enzymes, which cleave random DNA between distant target sites when two enzymes
AB  - collide after convergent ATP-driven translocation. We report the 2.7-A resolution
AB  - X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the
AB  - helicase-like ATPase and nuclease are located upstream of the direction of
AB  - translocation, an observation inconsistent with simple nuclease-domain
AB  - dimerization. Using single-molecule and biochemical techniques, we demonstrate
AB  - that each ATPase remodels its DNA-protein complex and translocates along DNA
AB  - without looping it, leading to a collision complex in which the nuclease domains
AB  - are distal. Sequencing of the products of single cleavage events suggests a
AB  - previously undescribed endonuclease model, where multiple, stochastic
AB  - strand-nicking events combine to produce DNA scission.
ER  -

TY  - JOUR
AU  - Chander, A.M.
AU  - Kaur, G.
AU  - Nair, R.G.
AU  - Dhawan, D.K.
AU  - Kochhar, R.
AU  - Mayilraj, S.
AU  - Bhadada, S.K.
TI  - Genome Sequencing of Serinicoccus chungangensis Strain CD08_5 Isolated from Duodenal Mucosa of a Celiac Disease Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e00043
EP  - e00016
VL  - 4
AB  - For the first time, we report here the 3.5-Mb genome of Serinicoccus chungangensis strain
AB  - CD08_5, isolated from duodenal mucosa from a celiac disease
AB  - (CD) patient. The specific annotations obtained revealed genes associated with
AB  - virulence, disease, and defense, which predict its probable role in the
AB  - pathogenesis of CD.
ER  -

TY  - JOUR
AU  - Chander, A.M.
AU  - Kumari, M.
AU  - Kochhar, R.
AU  - Dhawan, D.K.
AU  - Bhadada, S.K.
AU  - Mayilraj, S.
TI  - Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient.
JO  - Genome Announcements
PY  - 2017
SP  - e01158
EP  - e01117
VL  - 5
AB  - We report here the 3.8-Mb genome sequence of Kocuria polaris strain CD08_4, an isolate from
AB  - the duodenal mucosa of a celiac disease patient. The genome consists
AB  - of specific virulence determinant genes, antibiotic resistance genes, genes for
AB  - coping with oxidative stress, and genes responsible for iron acquisition and
AB  - metabolism, suggestive of its pathogenic attributes.
ER  -

TY  - JOUR
AU  - Chander, A.M.
AU  - Nair, R.G.
AU  - Kaur, G.
AU  - Kochhar, R.
AU  - Mayilraj, S.
AU  - Dhawan, D.K.
AU  - Bhadada, S.K.
TI  - Genome Sequence of Kocuria palustris Strain CD07_3 Isolated from the Duodenal Mucosa of a Celiac Disease Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e00210
EP  - e00216
VL  - 4
AB  - We report here the 2.8-Mb genome of Kocuria palustris strain CD07_3 isolated from the duodenal
AB  - mucosa of a celiac disease (CD) patient. The genome of the bacterium
AB  - consists of specific virulence factor genes and antibiotic resistance genes that
AB  - depict its pathogenic potential.
ER  -

TY  - JOUR
AU  - Chandrababunaidu, M.M.
AU  - Sen, D.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of Filamentous Marine Cyanobacterium Lyngbya confervoides Strain BDU141951.
JO  - Genome Announcements
PY  - 2015
SP  - e00066
EP  - e00015
VL  - 3
AB  - Lyngbya confervoides strain BDU141951 is a fast-growing, unicellular, marine, nonheterocystous
AB  - cyanobacterium forming long unbranched filaments inside sheaths.
AB  - Here, we report the draft genome assembly of Lyngbya confervoides BDU141951 for
AB  - the first time. The genome size is 8,799,693 bp and has 6,093 putative
AB  - protein-coding genes assembled into 298 scaffolds.
ER  -

TY  - JOUR
AU  - Chandrababunaidu, M.M.
AU  - Singh, D.
AU  - Sen, D.
AU  - Bhan, S.
AU  - Das, S.
AU  - Gupta, A.
AU  - Adhikary, S.P.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of Tolypothrix boutellei Strain VB521301.
JO  - Genome Announcements
PY  - 2015
SP  - e00001
EP  - e00015
VL  - 3
AB  - We report here the draft genome sequence of the filamentous nitrogen-fixing cyanobacterium
AB  - Tolypothrix boutellei strain VB521301. The organism is lipid rich  and hydrophobic and
AB  - produces polyunsaturated fatty acids which can be harnessed for industrial purpose. The draft
AB  - genome sequence assembled into 11,572,263 bp with 70 scaffolds and 7,777 protein coding genes.
ER  -

TY  - JOUR
AU  - Chandrasegaran, S.
AU  - Carroll, D.
TI  - Origins of Programmable Nucleases for Genome Engineering.
JO  - J. Mol. Biol.
PY  - 2016
SP  - 963
EP  - 989
VL  - 428
AB  - Genome engineering with programmable nucleases depends on cellular responses to a targeted
AB  - double-strand break (DSB). The first truly targetable reagents were the
AB  - zinc finger nucleases (ZFNs) showing that arbitrary DNA sequences could be
AB  - addressed for cleavage by protein engineering, ushering in the breakthrough in
AB  - genome manipulation. ZFNs resulted from basic research on zinc finger proteins
AB  - and the FokI restriction enzyme (which revealed a bipartite structure with a
AB  - separable DNA-binding domain and a non-specific cleavage domain). Studies on the
AB  - mechanism of cleavage by 3-finger ZFNs established that the preferred substrates
AB  - were paired binding sites, which doubled the size of the target sequence
AB  - recognition from 9 to 18bp, long enough to specify a unique genomic locus in
AB  - plant and mammalian cells. Soon afterwards, a ZFN-induced DSB was shown to
AB  - stimulate homologous recombination in cells. Transcription activator-like
AB  - effector nucleases (TALENs) that are based on bacterial TALEs fused to the FokI
AB  - cleavage domain expanded this capability. The fact that ZFNs and TALENs have been
AB  - used for genome modification of more than 40 different organisms and cell types
AB  - attests to the success of protein engineering. The most recent technology
AB  - platform for delivering a targeted DSB to cellular genomes is that of the
AB  - RNA-guided nucleases, which are based on the naturally occurring Type II
AB  - prokaryotic CRISPR-Cas9 system. Unlike ZFNs and TALENs that use protein motifs
AB  - for DNA sequence recognition, CRISPR-Cas9 depends on RNA-DNA recognition. The
AB  - advantages of the CRISPR-Cas9 system-the ease of RNA design for new targets and
AB  - the dependence on a single, constant Cas9 protein-have led to its wide adoption
AB  - by research laboratories around the world. These technology platforms have
AB  - equipped scientists with an unprecedented ability to modify cells and organisms
AB  - almost at will, with wide-ranging implications across biology and medicine.
AB  - However, these nucleases have also been shown to cut at off-target sites with
AB  - mutagenic consequences. Therefore, issues such as efficacy, specificity and
AB  - delivery are likely to drive selection of reagents for particular purposes. Human
AB  - therapeutic applications of these technologies will ultimately depend on risk
AB  - versus benefit analysis and informed consent.
ER  -

TY  - JOUR
AU  - Chandrasegaran, S.
AU  - Lunnen, K.D.
AU  - Smith, H.O.
AU  - Wilson, G.G.
TI  - Cloning and sequencing the HinfI restriction and modification genes.
JO  - Gene
PY  - 1988
SP  - 387
EP  - 392
VL  - 70
AB  - The HinfI restriction and modification genes were cloned on a 3.9-kb PstI
AB  - fragment inserted into the PstI site of plasmid pBR322.  Both genes are
AB  - confined to an internal 2.3-kb BclI-AvaI subfragment.  This subfragment was
AB  - sequenced.  Two large open reading frames (ORF's) are present.  ORF1 codes for
AB  - the methylase [predicted 359 amino acids (aa)] and ORF2 codes for the
AB  - endonuclease (predicted 252 or 272 aa).
ER  -

TY  - JOUR
AU  - Chandrasegaran, S.
AU  - Smith, H.O.
TI  - Amino acid sequence homologies among twenty-five restriction endonucleases and methylases.
JO  - Structure and Expression. From Proteins to Ribosomes.
PY  - 1988
SP  - 149
EP  - 156
VL  - 1
AB  - The amino acid sequences of 17 DNA methylases were compared. They show extensive homologies
AB  - that tend to cluster in distinct groups sharing similar DNA recognition sequences. Altogether
AB  - they fall into 5 groups: (I) M.Dam(GATC), M.DpnII(GATC), M.T4(GATC), and M.EcoRV(GATATC) show
AB  - extensive homology (28% to 34%). (II) M.HinfI(GANTC) and M.HhaII(GANTC) are 18.8% homologous
AB  - in 128 amino acids of their amino-terminal regions. (III) M.TaqI(TCGA), M.CviBIII(TCGA),
AB  - M.PaeR7I(CTCGAG) and M.PstI(CTGCAG) show regions of homology ranging from 103 to 128 residues
AB  - in length with amino acid sequence identities of 22% to 28%. (IV) M.BspRI(GGCC),
AB  - M.BsuRI(GGCC), M.SPR(GGCC, CCGG, CC(A/T)GG), M.EcoRII(CC(A/T)GG), M.Phi3T(GGCC,GCNGC) and
AB  - M.HhaI(GCGC) show extensive homologies ranging from 22% to 66% in regions ranging from 25% to
AB  - 100% of their lengths. (V)M.EcoRI is not homologous to any of the above. All the 11 DNA
AB  - adenine methylases contain a conserved DPPY or NPPY sequence within the homologous segments.
AB  - This motif is probably involved in adenine recognition and AdoMet binding at the position of
AB  - methylation. Three short regions of high homology were identified in the 6 cytosine
AB  - methylases, namely the PC, ENVK, and RER homologies. The PC motif is believed to be involved
AB  - in the catalytic mechanism of the cytosine methylases. Eight restriction enzyme sequences were
AB  - also compared. No clearly significant homologies were observed. The restriction enzymes did
AB  - not show homology to the methylases.
ER  -

TY  - JOUR
AU  - Chandrasegaran, S.
AU  - Smith, H.O.
AU  - Amzel, M.L.
AU  - Ysern, X.
TI  - Preliminary x-ray diffraction analysis of HhaII endonuclease-DNA cocrystals.
JO  - Proteins
PY  - 1986
SP  - 263
EP  - 266
VL  - 1
AB  - HhaII restriction endonuclease purified from an overproducing recombinant E.
AB  - coli clone has been cocrystallized with a heptanucleotide duplex,
AB  - d-GGAGTCC:GGACTCC.  The cocrystals are monoclonic and belong to the space group
AB  - C2.  The unit cell dimensions are a = 199.0+/-1.0 angstrom, b = 100.0+/-0.5
AB  - angstrom, c = 80.3+/-0.4 angstrom, and b = 101.0+/-1.0o.  There appear to be
AB  - two dimers per asymmetric unit and the crystals diffract to 4-angstrom
AB  - resolution.
ER  -

TY  - JOUR
AU  - Chandrasegaran, S.
AU  - Smith, J.
TI  - Chimeric restriction enzymes: What is next?
JO  - Biol. Chem.
PY  - 1999
SP  - 841
EP  - 848
VL  - 380
AB  - Chimeric restriction enzymes are a novel class of engineered nucleases in which the
AB  - non-specific DNA cleavage domain of Fokl (a type IIS restriction endonuclease) is fused to
AB  - other DNA-binding motifs. The latter include the three common eukaryotic DNA-binding motifs,
AB  - namely the helix-turn-helix motif, the zinc finger motif and the basic helix-loop-helix
AB  - protein containing a leucine zipper motif. Such chimeric nucleases have been shown to make
AB  - specific cuts in vitro very close to the expected recognition sequences. The most important
AB  - chimeric nucleases are those based on zinc finger DNA-binding proteins because of their
AB  - modular structure. Recently, one such chimeric nuclease, Zif-QQR-F(N) was shown to find and
AB  - cleave its target in vivo. This was tested by microinjection of DNA substrates and the enzyme
AB  - into frog oocytes (Carroll et al., 1999). The injected enzyme made site-specific double-strand
AB  - breaks in the targets even after assembly of the DNA into chromatin. In addition, this
AB  - cleavage activated the target molecules for efficient homologous recombination. Since the
AB  - recognition specificity of zinc fingers can be manipulated experimentally, chimeric nucleases
AB  - could be engineered so as to target a specific site within a genome. The availability of such
AB  - engineered chimeric restriction enzymes should make it feasible to do genome engineering, also
AB  - commonly referred to as gene therapy.
ER  -

TY  - JOUR
AU  - Chandrasegaran, S.
AU  - Wu, L.P.
AU  - Valda, E.
AU  - Smith, H.O.
TI  - Overproduction and purification of the M.HhaII methyltransferase from Haemophilus haemolyticus.
JO  - Gene
PY  - 1988
SP  - 15
EP  - 21
VL  - 74
AB  - The HhaII methyltransferase gene from Haemophilus haemolyticus was subcloned in
AB  - an expression vector under control of the hybrid trp-lac promoter.  Induction
AB  - with isopropyl-Beta-D-thiogalactopyranoside results in overproduction of the
AB  - methyltransferase to about 3% of total cellular protein.  The methyltransferase
AB  - was purified to near electrophoretic homogeneity by phosphocellulose, DEAE, and
AB  - gel chromatography.  Its monomer Mr by sodium dodecyl sulfate-polyacrylamide
AB  - gel electrophoresis is 25 kDa, in good agreement with that predicted from the
AB  - nucleotide sequence.  Crystals of the methyltransferase were obtained in the
AB  - presence of a two-fold molar excess of the duplex oligodeoxynucleotide
AB  - substrate 5'd-GGACTCC/CCTGAGG.
ER  -

TY  - JOUR
AU  - Chandrasekhar, K.
AU  - Raman, R.
TI  - Restriction enzyme HincII is sensitive to methylation of cytosine that occurs 5' to the recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 1045
EP  - 1046
VL  - 24
AB  - In this paper we demonstrate that the HincII restriction endonuclease, in addition to being
AB  - sensitive to methylation of the 3' A and C residues, is also sensitive to methylation of a
AB  - cytosine immediately 5' to the recognition sequence.  Having encountered this property in
AB  - one of the sites in the mouse c-fos gene, we confirmed the sensitivity of HincII to the 5'
AB  - cytosine methylation in in vitro methylated pUC12, pBR322 and pfos-1 plasmids.
ER  -

TY  - JOUR
AU  - Chandrashekaran, S.
AU  - Babu, P.
AU  - Nagaraja, V.
TI  - Purification and characterization of restriction endonuclease BasI from Bacillus species.
JO  - J. Biochem. Mol. Biol. Biophys.
PY  - 1999
SP  - 225
EP  - 229
VL  - 3
AB  - After screening a variety of bacteria from soil for the DNA cleavage activity, a type II
AB  - restriction endonuclease, BasI was isolated and characterized from a Bacillus species.  Using
AB  - the purified enzyme the recognition sequence was determined.  The enzyme functions efficiently
AB  - at low ionic strength, narrow pH range and at the optimum temperature of 30oC.
ER  -

TY  - JOUR
AU  - Chandrashekaran, S.
AU  - Babu, P.
AU  - Nagaraja, V.
TI  - Characterization of DNA binding activities of over-expressed KpnI restriction endonuclease and modification methylase.
JO  - J. Biosci.
PY  - 1999
SP  - 269
EP  - 277
VL  - 24
AB  - The genes encoding the KpnI restriction endonuclease and methyltransferase from Klebsiella
AB  - pneumoniae have been cloned and expressed in Escherichia coli using a two plasmid strategy.
AB  - The gene for KpnI methylase with its promoter was cloned and expressed in pACYC184.  Even
AB  - though the methylase clone is in a low copy number plasmid pACMK, high level expression of
AB  - methylase is achieved.  A hyper-expressing clone of KpnI endonuclease, pETRK was engineered by
AB  - cloning the R gene into the T7 expression system.  This strategy resulted in over-expression
AB  - of KpnI endonuclease to about 15-30% of cellular protein.  Both the enzymes were purified
AB  - using a single chromatographic step to apparent homogeneity.  The yield of purified
AB  - endonuclease and methylase from one liter of culture was approximately 30 and 6 mg
AB  - respectively.  Electrophoretic mobility shift assays show that both the enzymes are capable of
AB  - binding to specific recognition sequence in the absence of any cofactors.  The complexes of
AB  - KpnI methyl transferase and endonuclease with their cognate site exhibit distinctive behavior
AB  - with respect to ionic requirement.
ER  -

TY  - JOUR
AU  - Chandrashekaran, S.
AU  - Manjunatha, U.H.
AU  - Nagaraja, V.
TI  - KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3148
EP  - 3155
VL  - 32
AB  - The molecular basis of the interaction of KpnI restriction endonuclease (REase) and the
AB  - corresponding methyltransferase (MTase) at their cognate recognition sequence is investigated
AB  - using a range of footprinting techniques. DNase I protection analysis with the REase reveals
AB  - the protection of a 14-18 bp region encompassing the hexanucleotide recognition sequence. The
AB  - MTase, in contrast, protects a larger region. KpnI REase contacts two adjacent guanine
AB  - residues and the single adenine residue in both the strands within the recognition sequence
AB  - 5'-GGTACC-3', inferred by dimethylsulfate (DMS) protection, interference and missing
AB  - nucleotide interference analysis. In contrast, KpnI MTase does not show elaborate
AB  - base-specific contacts. Ethylation interference analysis also showed the differential
AB  - interaction of REase and MTase with phosphate groups of three adjacent bases on both strands
AB  - within the recognition sequence. The single thymine residue within the sequence is hyper-
AB  - reactive to the permanganate oxidation, consistent with MTase-induced base flipping. The REase
AB  - on the other hand does not show any major DNA distortion. The results demonstrate that the
AB  - differences in the molecular interaction pattern of the two proteins at the same recognition
AB  - sequence reflect the contrasting chemistry of DNA cleavage and methylation catalyzed by these
AB  - two dissimilar enzymes, working in combination as constituents of a cellular defense strategy.
ER  -

TY  - JOUR
AU  - Chandrashekaran, S.
AU  - Saravanan, M.
AU  - Radha, D.R.
AU  - Nagaraja, V.
TI  - Ca2+-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 49736
EP  - 49740
VL  - 279
AB  - The characteristic feature of type II restriction endonucleases (REases) is their exquisite
AB  - sequence specificity and obligate Mg2+
AB  - requirement for catalysis. Efficient cleavage of DNA only in the
AB  - presence of Ca2+ ions, comparable with that of Mg2+, is previously not
AB  - described. Most intriguingly, KpnI REase exhibits Ca2+-dependent
AB  - specific DNA cleavage. Moreover, the enzyme is highly promiscuous in
AB  - its cleavage pattern on plasmid DNAs in the presence of Mn2+ or Mg2+,
AB  - with the complete suppression of promiscuous activity in the presence
AB  - of Ca2+. KpnI methyltransferase does not exhibit promiscuous activity
AB  - unlike its cognate REase. The REase binds to oligonucleotides
AB  - containing canonical and mapped noncanonical sites with comparable
AB  - affinities. However, the extent of cleavage is varied depending on the
AB  - metal ion and the sequence. The ability of the enzyme to be promiscuous
AB  - or specific may reflect an evolutionary design. Based on the results,
AB  - we suggest that the enzyme KpnI represents an REase evolving to attain
AB  - higher sequence specificity from an ancient nonspecific nuclease.
ER  -

TY  - JOUR
AU  - Chandrashekaran, S.
AU  - Shankar, A.B.
AU  - Babu, P.
AU  - Paul, B.D.
AU  - Nagaraja, V.
TI  - Identification and characterization of a type II restriction endonuclease, StrI from Streptomyces thermodiastaticus.
JO  - Curr. Sci.
PY  - 1999
SP  - 273
EP  - 276
VL  - 77
AB  - A new type II restriction endonuclease, StrI has been identified from Streptomyces
AB  - thermodiastaticus.  The enzyme has been purified using three column chromatography steps.  The
AB  - enzyme recognizes a hexanucleotide sequence and cleaves DNA 5'-C/TCGAG-3' as indicated.  The
AB  - optimum temperature, pH, and cation requirements for the enzyme activity were determined.
ER  -

TY  - JOUR
AU  - Chandrashekharan, S.
AU  - Paul, B.D.
AU  - Nagaraja, V.
TI  - Design of a novel regulatory circuit for expression of restriction endonucleases.
JO  - Biol. Chem.
PY  - 1998
SP  - 579
EP  - 582
VL  - 379
AB  - We have developed a new strategy with a very tight control for the expression of cloned genes.
AB  - The system employed here is the T7 promoter-based expression system in which transcription
AB  - activator protein C of bacteriophage Mu (Mu C) has been cloned to serve as a repressor in the
AB  - regulatory circuit.  The system also includes pLysE, which encodes T7 lysozyme, an inhibitor
AB  - of T7 RNA polymerase.  This ensures tight regulation of cloned genes in the uninduced state.
AB  - Upon induction, the expressed Mu C protein binds to its cognate site thereby repressing lys
AB  - transcription driven by the tet promoter.  In order to evaluate the tight control achieved in
AB  - the system, and to check leaky expression, if any, we have cloned the gene for the SmaI
AB  - restriction endonuclease without its cognate methylase.  For this purpose, a dicistronic unit
AB  - was constructed by cloning the smaIR gene downstream of the Mu C gene.  SmaI expression was
AB  - observed only in the induced cell extracts, demonstrating a tight control.  The system could
AB  - be used to express the genes of other cloned restriction enzymes and has the potential for
AB  - general applications.
ER  -

TY  - JOUR
AU  - Chang, D.
AU  - Zhu, Y.
AU  - Chen, J.
AU  - Fang, X.
AU  - Li, T.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Su, L.
AU  - Xu, G.
AU  - Wang, Y.
AU  - Chen, Z.
AU  - Liu, C.
TI  - Draft Genome Sequences and Annotation of Enterococcus faecium Strain LCT-EF20.
JO  - Genome Announcements
PY  - 2013
SP  - e00083
EP  - e00012
VL  - 1
AB  - The space environment is reported to cause biological alterations in microorganisms, such as
AB  - growth, drug resistance, and virulence. Here, we present the model of Enterococcus faecium to
AB  - investigate the effects of space conditions on the microbe and on the whole-genome sequences
AB  - of the strain LCT-EF20 after being exposed to space flight.
ER  -

TY  - JOUR
AU  - Chang, D.
AU  - Zhu, Y.
AU  - Fang, X.
AU  - Li, T.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Su, L.
AU  - Liu, Y.
AU  - Jiang, X.
AU  - Wang, L.
AU  - Guo, N.
AU  - Liu, C.
TI  - Draft Genome Sequences of the Enterococcus faecium Strain LCT-EF258.
JO  - Genome Announcements
PY  - 2013
SP  - e00147
EP  - e00112
VL  - 1
AB  - The space environment has been shown to affect microbes by altering various features,
AB  - including morphology, growth rate, metabolism, virulence, drug
AB  - resistance, and gene expression and mutation. Here we present the draft genome
AB  - sequence of the Enterococcus faecium strain LCT-EF258, derived from the E.
AB  - faecium strain CGMCC 1.1736, which was exposed to 17-day space flight.
ER  -

TY  - JOUR
AU  - Chang, D.
AU  - Zhu, Y.
AU  - Zou, Y.
AU  - Fang, X.
AU  - Li, T.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Su, L.
AU  - Xia, J.
AU  - Yang, R.
AU  - Fang, C.
AU  - Liu, C.
TI  - Draft Genome Sequence of Enterococcus faecium Strain LCT-EF90.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3556
EP  - 3557
VL  - 194
AB  - Enterococcus faecium is an opportunistic human pathogen, found widely in the human
AB  - gastrointestinal tract, and can also be isolated from a variety of plants,
AB  - animals, insects, and other environmental sources. Here, we present the fine
AB  - draft genome sequence of E. faecium LCT-EF90.
ER  -

TY  - JOUR
AU  - Chang, D.H.
AU  - Jin, T.E.
AU  - Rhee, M.S.
AU  - Jeong, H.
AU  - Kim, S.
AU  - Kim, B.C.
TI  - Draft Genome Sequence of Bordetella trematum Strain HR18.
JO  - Genome Announcements
PY  - 2015
SP  - e01357
EP  - e01314
VL  - 3
AB  - The genus Bordetella is reportedly a human or animal pathogen and environmental microbe. We
AB  - report the draft genome sequence of Bordetella trematum strain HR18,
AB  - which was isolated from the rumen of Korean native cattle (Hanwoo; Bos taurus
AB  - coreanae). It is the first genome sequence of a Bordetella sp. isolated from the
AB  - rumen of cattle.
ER  -

TY  - JOUR
AU  - Chang, D.H.
AU  - Rhee, M.S.
AU  - Jeong, H.
AU  - Kim, S.
AU  - Kim, B.C.
TI  - Draft Genome Sequence of Acinetobacter sp. HR7, Isolated from Hanwoo, Korean Native Cattle.
JO  - Genome Announcements
PY  - 2015
SP  - e01358
EP  - e01314
VL  - 3
AB  - Acinetobacter species have been reported as opportunistic pathogens. Here, we report the draft
AB  - genome sequence of Acinetobacter sp. HR7 isolated from the rumen
AB  - of cannulated Korean native cattle (Hanwoo; Bos taurus coreanae).
ER  -

TY  - JOUR
AU  - Chang, H.K.
AU  - Zylstra, G.J.
AU  - Chae, J.C.
TI  - Genome Sequence of n-Alkane-Degrading Hydrocarboniphaga effusa Strain AP103T (ATCC BAA-332T).
JO  - J. Bacteriol.
PY  - 2012
SP  - 5120
EP  - 5120
VL  - 194
AB  - Hydrocarboniphaga effusa strain AP103(T) (ATCC BAA-332(T)) is a member of the
AB  - Gammaproteobacteria utilizing n-alkanes as the sole source of carbon and energy.
AB  - Here we report the draft genome sequence of AP103(T), which consists of 5,193,926
AB  - bp with a G + C content of 65.18%.
ER  -

TY  - JOUR
AU  - Chang, S.
AU  - Cohen, S.N.
TI  - In vivo site-specific genetic recombination promoted by the EcoRI restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1977
SP  - 4811
EP  - 4815
VL  - 74
AB  - Site-specific genetic recombination promoted in vivo by the EcoRI endonuclease
AB  - has been demonstrated by using constructed hybrid plasmids in which the
AB  - chloramphenicol resistance gene was inactivated by insertion of DNA fragments
AB  - at an EcoRI site within the gene.  Such recombination can involve either the
AB  - joining of intracellularly generated cohesive termini of the same DNA fragment
AB  - or intermolecular ligation of different DNA fragments.  DNA cleavage and
AB  - ligation in vivo are precise: recombinant DNA molecules show functional
AB  - continuity of the gene sequence cleaved by the enzyme and regeneration of
AB  - nucleotide recognition sites for both the EcoRI endonuclease and the EcoRI DNA
AB  - methylase.  In other experiments, EcoRI-generated fragments of eukaryotic DNA
AB  - that had not been modified by the Escherichia coli K methylase were shown to be
AB  - taken up by bacterial cells and to undergo intracellular ligation to segments
AB  - of bacterial plasmid DNA.
ER  -

TY  - JOUR
AU  - Chang, S.
AU  - Zhang, G.
AU  - Chen, X.
AU  - Long, H.
AU  - Wang, Y.
AU  - Chen, T.
AU  - Liu, G.
TI  - The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 45
EP  - 45
VL  - 12
AB  - Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil
AB  - as sole carbon and energy source at 15 degrees C. The genome of
AB  - Pedobacter steynii DX4 has been sequenced and served as basis for analysis its
AB  - metabolic mechanism. It is the first genome of crude oil degrading strain in
AB  - Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and
AB  - encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4
AB  - has cold shock proteins, abundant response regulators for cell motility, and
AB  - enzymes involved in energy conversion and fatty acid metabolism. The genomic
AB  - characteristics could provide information for further study of oil-degrading
AB  - microbes for recovery of crude oil polluted environment.
ER  -

TY  - JOUR
AU  - Chang, S.H.
AU  - Cho, S.T.
AU  - Chen, C.L.
AU  - Yang, J.Y.
AU  - Kuo, C.H.
TI  - Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches' Broom Disease in Taiwan.
JO  - Genome Announcements
PY  - 2015
SP  - e01398
EP  - e01315
VL  - 3
AB  - The bacterial genus 'Candidatus Phytoplasma' contains a group of insect-transmitted plant
AB  - pathogens in the class Mollicutes. Here, we report a
AB  - draft genome assembly and annotation of strain NCHU2014, which belongs to the
AB  - 16SrII-A subgroup within this genus and is associated with purple coneflower
AB  - witches' broom disease in Taiwan.
ER  -

TY  - JOUR
AU  - Chang, Y.C.
AU  - Sawada, K.
AU  - Kim, E.S.
AU  - Jung, K.
AU  - Kikuchi, S.
TI  - Whole-Genome Sequence of Aquamicrobium sp. Strain SK-2, a Polychlorinated Biphenyl-Utilizing Bacterium Isolated from Sewage Sludge.
JO  - Genome Announcements
PY  - 2015
SP  - e00439
EP  - e00415
VL  - 3
AB  - Here, we report the whole-genome sequence of Aquamicrobium sp. strain SK-2, a bacterium which
AB  - can use 2,2',4,4',5,5'-hexachlorobiphenyl as the sole carbon
AB  - source for its growth. An approximately 9.23-Mb genome sequence of SK-2 will
AB  - greatly facilitate research efforts regarding the study of the polychlorinated
AB  - biphenyl (PCB) degradation mechanism.
ER  -

TY  - JOUR
AU  - Chang, Y.J. et al.
TI  - Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 97
EP  - 111
VL  - 5
AB  - Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the  genus
AB  - Ktedonobacter, which in turn is the type genus of the family
AB  - Ktedonobacteraceae, the type family of the order Ktedonobacterales within the
AB  - class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares
AB  - some morphological features with the actinobacteria, it is of special interest
AB  - because it was the first cultivated representative of a deep branching
AB  - unclassified lineage of otherwise uncultivated environmental phylotypes
AB  - tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous,
AB  - non-motile, spore-forming Gram-positive heterotroph was isolated from soil in
AB  - Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten
AB  - contigs and is the first reported genome sequence from a member of the class
AB  - Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the
AB  - largest prokaryotic genome reported so far. It comprises a large number of
AB  - over-represented COGs, particularly genes associated with transposons, causing
AB  - the genetic redundancy within the genome being considerably larger than expected
AB  - by chance. This work is a part of the Genomic Encyclopedia of Bacteria and
AB  - Archaea project.
ER  -

TY  - JOUR
AU  - Chang, Y.J. et al.
TI  - Complete genome sequence of Acidaminococcus fermentans type strain (VR4).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 1
EP  - 14
VL  - 3
AB  - Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and
AB  - is of phylogenetic interest because of its isolated
AB  - placement in a genomically little characterized region of the Firmicutes. A.
AB  - fermentans is known for its habitation of the gastrointestinal tract and its
AB  - ability to oxidize trans-aconitate. Its anaerobic fermentation of glutamate has
AB  - been intensively studied and will now be complemented by the genomic basis. The
AB  - strain described in this report is a nonsporulating, nonmotile, Gram-negative
AB  - coccus, originally isolated from a pig alimentary tract. Here we describe the
AB  - features of this organism, together with the complete genome sequence, and
AB  - annotation. This is the first complete genome sequence of a member of the family
AB  - Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101
AB  - protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Chanto, G.
AU  - Occhialini, A.
AU  - Gras, N.
AU  - Alm, R.A.
AU  - Megraud, F.
AU  - Marais, A.
TI  - Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori.
JO  - Microbiology
PY  - 2002
SP  - 3671
EP  - 3680
VL  - 148
AB  - Helicobacter pylori is a Gram-negative bacterium that is associated with
AB  - the development of peptic ulcers and gastric carcinoma in humans. This
AB  - species appears to be one of the most genetically variable bacteria
AB  - described to date. The overall level of heterogeneity within strains of
AB  - this organism was determined by comparing the genome sequences of two
AB  - reference strains, J99 and 26695. The aim of this study was to measure the
AB  - genetic diversity within strains of H. pylori by looking for
AB  - strain-specific genes in nine H. pylori strains isolated from patients
AB  - suffering from chronic gastritis (n=3), duodenal ulcers (n=3) or gastric
AB  - cancer (n=3). Seven loci that contained strain-specific genes in strains
AB  - J99 and 26695 were studied. These regions were subsequently amplified from
AB  - most of the clinical isolates studied and their sequences were determined.
AB  - ORFs were predicted from the sequence data and were compared to sequences
AB  - within the databases. The results showed that the genes flanking the ORFs
AB  - specific to either strain J99 or strain 26695 were also present in a
AB  - similar configuration in the genomes of the nine clinical isolates.
AB  - Moreover, in most regions, ORFs homologous to those found in the
AB  - corresponding loci in the two reference strains were detected. However, in
AB  - 10 regions, genes similar to those located at another locus in the genome
AB  - of J99 or 26695 were found. Finally, six strain-specific genes were
AB  - identified in three regions of three of the H. pylori strains isolated
AB  - from patients with duodenal ulcers (n=2) and gastric cancer (n=1). Of
AB  - these six genes, five were putative genes and one was an orthologue of a
AB  - gene encoding a transposase in Thermotoga maritima. However, no
AB  - association with disease was found for these genes.
ER  -

TY  - JOUR
AU  - Chapartegui-Gonzalez, I.
AU  - Lazaro-Diez, M.
AU  - Redondo-Salvo, S.
AU  - Alted-Perez, L.
AU  - Ocejo-Vinyals, J.G.
AU  - Navas, J.
AU  - Ramos-Vivas, J.
TI  - Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 Isolated from Human Urine.
JO  - Genome Announcements
PY  - 2017
SP  - e00658
EP  - e00617
VL  - 5
AB  - Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report
AB  - here its complete genome assembly using PacBio single-molecule
AB  - real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular
AB  - contig of 112 kb. About 3,953 protein-coding genes are predicted from this
AB  - assembly.
ER  -

TY  - JOUR
AU  - Chapelais-Baron, M.
AU  - Goubet, I.
AU  - Duchaud, E.
AU  - Rosenfeld, E.
TI  - Draft Genome Sequence of the Iridescent Marine Bacterium Cellulophaga lytica CECT 8139.
JO  - Genome Announcements
PY  - 2017
SP  - e00811
EP  - e00817
VL  - 5
AB  - Some species of the genus Cellulophaga have been reported as having biotechnological interests
AB  - and noteworthy physiological properties. We report
AB  - here the draft genome sequence of Cellulophaga lytica CECT 8139, a bacterium that
AB  - produces an intensely iridescent colony biofilm on agar surfaces.
ER  -

TY  - JOUR
AU  - Chaplin, A.V.
AU  - Efimov, B.A.
AU  - Khokhlova, E.V.
AU  - Kafarskaia, L.I.
AU  - Tupikin, A.E.
AU  - Kabilov, M.R.
AU  - Shkoporov, A.N.
TI  - Draft Genome Sequence of Coprobacter fastidiosus NSB1T.
JO  - Genome Announcements
PY  - 2014
SP  - e00122
EP  - e00114
VL  - 2
AB  - Coprobacter fastidiosus is a Gram-negative obligate anaerobic bacterium belonging to the
AB  - phylum Bacteroidetes. In this work, we report the draft genome sequence of
AB  - C. fastidiosus strain NSB1(T) isolated from human infant feces.
ER  -

TY  - JOUR
AU  - Chaplin, A.V.
AU  - Shkoporov, A.N.
AU  - Efimov, B.A.
AU  - Pikina, A.P.
AU  - Borisova, O.Y.
AU  - Gladko, I.A.
AU  - Postnikova, E.A.
AU  - Lordkipanidze, A.E.
AU  - Kafarskaia, L.I.
TI  - Draft Genome Sequence of Lactobacillus fermentum NB-22.
JO  - Genome Announcements
PY  - 2015
SP  - e00896
EP  - e00815
VL  - 3
AB  - We announce here a draft genome sequence of Lactobacillus fermentum NB-22, a strain isolated
AB  - from human vaginal microbiota. The assembled sequence consists of
AB  - 190 contigs, joined into 137 scaffolds, and the total size is 2.01 Mb.
ER  -

TY  - JOUR
AU  - Chapman, J.A. et al.
TI  - The dynamic genome of Hydra.
JO  - Nature
PY  - 2010
SP  - 592
EP  - 596
VL  - 464
AB  - The freshwater cnidarian Hydra was first described in 1702 and has been the object of study
AB  - for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery
AB  - of asexual reproduction of an animal by budding, the first description of regeneration in an
AB  - animal, and successful transplantation of tissue between animals. Today, Hydra is an important
AB  - model for studies of axial patterning, stem cell biology and regeneration. Here we report the
AB  - genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella
AB  - vectensis and other animals. The Hydra genome has been shaped by bursts of transposable
AB  - element expansion, horizontal gene transfer, trans-splicing, and simplification of gene
AB  - structure and gene content that parallel simplification of the Hydra life cycle. We also
AB  - report the sequence of the genome of a novel bacterium stably associated with H.
AB  - magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on
AB  - the evolution of epithelia, contractile tissues, developmentally regulated transcription
AB  - factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
ER  -

TY  - JOUR
AU  - Charette, S.J.
AU  - Brochu, F.
AU  - Boyle, B.
AU  - Filion, G.
AU  - Tanaka, K.H.
AU  - Derome, N.
TI  - Draft Genome Sequence of the Virulent Strain 01-B526 of the Fish Pathogen Aeromonas salmonicida.
JO  - J. Bacteriol.
PY  - 2012
SP  - 722
EP  - 723
VL  - 194
AB  - Aeromonas salmonicida is an important fish pathogen, mainly of salmonids. This bacterium
AB  - causes a disease named furunculosis, which is particularly
AB  - detrimental for the aquaculture industry. Here, we present the draft
AB  - genome sequence of A. salmonicida 01-B526, a strain isolated from a brook
AB  - trout that is more virulent than A. salmonicida reference strain A449, for
AB  - which a genome sequence is available.
ER  -

TY  - JOUR
AU  - Charlop-Powers, Z.
AU  - Banik, J.J.
AU  - Owen, J.G.
AU  - Craig, J.W.
AU  - Brady, S.F.
TI  - Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis.
JO  - ACS Chem. Biol.
PY  - 2013
SP  - 138
EP  - 143
VL  - 8
AB  - The cloning of DNA directly from environmental samples provides a means to
AB  - functionally access biosynthetic gene clusters present in the genomes of the
AB  - large fraction of bacteria that remains recalcitrant to growth in the laboratory.
AB  - Herein, we demonstrate a method by which complementation of phosphopantetheine
AB  - transferase deletion mutants can be used to restore siderophore biosynthesis and
AB  - to therefore selectively enrich eDNA libraries for nonribosomal peptide
AB  - synthetase (NRPS) and polyketide synthase (PKS) gene sequences to unprecedented
AB  - levels. The common use of NRPS/PKS-derived siderophores across bacterial taxa
AB  - makes this method generalizable and should allow for the facile selective
AB  - enrichment of NRPS/PKS-containing biosynthetic gene clusters from large
AB  - environmental DNA libraries using a wide variety of phylogenetically diverse
AB  - bacterial hosts.
ER  -

TY  - JOUR
AU  - Chase, H.R.
AU  - Eberl, L.
AU  - Stephan, R.
AU  - Jeong, H.
AU  - Lee, C.
AU  - Finkelstein, S.
AU  - Negrete, F.
AU  - Gangiredla, J.
AU  - Patel, I.
AU  - Tall, B.D.
AU  - Gopinath, G.R.
AU  - Lehner, A.
TI  - Draft Genome Sequence of Cronobacter sakazakii GP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato's Rhizoplane/Rhizosphere Continuum.
JO  - Genome Announcements
PY  - 2017
SP  - e00723
EP  - e00717
VL  - 5
AB  - We present here the draft genome of Cronobacter sakazakii GP1999, a sequence type 145 strain
AB  - isolated from the rhizosphere of tomato plants. Assembly and
AB  - annotation of the genome resulted in a genome of 4,504,670 bp in size, with 4,148
AB  - coding sequences, and a GC content of 56.8%.
ER  -

TY  - JOUR
AU  - Chase, H.R.
AU  - Gopinath, G.R.
AU  - Gangiredla, J.
AU  - Patel, I.R.
AU  - Kothary, M.H.
AU  - Carter, L.
AU  - Sathyamoorthy, V.
AU  - Lee, B.
AU  - Park, E.
AU  - Yoo, Y.J.
AU  - Chung, T.J.
AU  - Choi, H.
AU  - Jun, S.
AU  - Park, J.
AU  - Jeong, S.
AU  - Kim, M.
AU  - Reich, F.
AU  - Klein, G.
AU  - Tall, B.D.
TI  - Genome Sequences of Malonate-Positive Cronobacter sakazakii Serogroup O:2, Sequence Type 64 Strains CDC 1121-73 and GK1025, Isolated from Human Bronchial  Wash and a Powdered Infant Formula Manufacturing Plant.
JO  - Genome Announcements
PY  - 2016
SP  - e01072
EP  - e01016
VL  - 4
AB  - We introduce draft genome sequences of strains CDC1121-73 (human bronchial wash isolate) and
AB  - GK1025 (powdered infant formula manufacturing facility isolate),
AB  - which are both malonate-positive Cronobacter sakazakii serogroup O:2, sequence
AB  - type 64. Assemblies for these strains have sizes of 4,442,307 and 4,599,266 bp
AB  - and % G+C contents of 56.9 and 56.7, respectively.
ER  -

TY  - JOUR
AU  - Chastain-Gross, R.P.
AU  - Xie, G.
AU  - Belanger, M.
AU  - Kumar, D.
AU  - Whitlock, J.A.
AU  - Liu, L.
AU  - Raines, S.M.
AU  - Farmerie, W.G.
AU  - Daligault, H.E.
AU  - Han, C.S.
AU  - Brettin, T.S.
AU  - Progulske-Fox, A.
TI  - Genome Sequence of Porphyromonas gingivalis Strain 381.
JO  - Genome Announcements
PY  - 2017
SP  - e01467
EP  - e01416
VL  - 5
AB  - Porphyromonas gingivalis is associated with both oral and systemic diseases. Strain-specific
AB  - P. gingivalis invasion phenotypes do not reliably predict disease
AB  - presentation during in vivo studies. Here, we present the genome sequence of 381,
AB  - a common laboratory strain, with a single contig of 2,378,872 bp and a G+C
AB  - content of 48.36%.
ER  -

TY  - JOUR
AU  - Chater, K.F.
TI  - Some Recent Developments in Streptomyces Genetics.
JO  - Genetics of Industrial Microorganisms
PY  - 1979
SP  - 123
EP  - 133
VL  - 0
AB  - This review will be concerned with "nonchromosomal" genetics.  The omission of
AB  - normal chromosomal genetics does not reflect a decline in its importance, but
AB  - rather the absence of major advances since previous reviews, with the important
AB  - exception of the development of protoplast fusion, which is dealt with by D.A.
AB  - Hopwood elsewhere in this volume.  My approach is to consider what is known
AB  - about the occurrence and genetic determination of "nonessential" (and therefore
AB  - possibly plasmid-specified) functions in streptomycetes, and then to discuss
AB  - aspects of plasmids and temperate phages relevant to the development of
AB  - potential "recombinant DNA" systems in streptomycetes.
ER  -

TY  - JOUR
AU  - Chater, K.F.
TI  - Streptomyces Phages and Their Applications to Streptomyces Genetics.
JO  - The Bacteria
PY  - 1986
SP  - 119
EP  - 158
VL  - 9
AB  - Interest in Streptomyces phages was first caused by the occasional infestation
AB  - of early antibiotic fermentation cultures.  The economic loss caused by lysed
AB  - fermentation cultures was occasionally significant so that even today there is
AB  - sometimes opposition to the import of Streptomyces phages into laboratories
AB  - attached to production plants.  However, it is now clear that laboratory
AB  - varieties of Streptomyces phages can be contained in the laboratory and turned
AB  - to good account.  Many industrial laboratories are beginning to exploit them.
AB  - This chapter is an account of recent developments in the study of Streptomyces
AB  - phages and their use in genetic manipulation.  Its starting point is a fairly
AB  - comprehensive review written several years ago (Lomovskaya et al., 1980);
AB  - information given in detail there will be only briefly summarized here.  The
AB  - most conspicuous advances since that time have been in, or have resulted from,
AB  - the use of Streptomyces phages as DNA cloning vectors.  Techniques for
AB  - isolating, assaying, and propagating Streptomyces phages from soil and from
AB  - lysogens differ only in minor detail (related to the host's mycelial growth
AB  - habit) from those used for eubacterial phages, which they resemble closely in
AB  - structure and biology (Lomovskaya et al., 1980).  This resemblance is not
AB  - surprising, since the gross molecular biology of streptomycetes is similar to
AB  - that of other gram-positive bacteria.  Of course, there are interesting
AB  - differences between streptomycetes and other bacteria (e.g., in morphology,
AB  - antibiotic production, and high G + C content in DNA), and it is mainly as
AB  - agents to help our understanding of the genetic basis of these phenomena that
AB  - Streptomyces phages have come to be important topics of research.  Streptomyces
AB  - phages are not the only tools available for such a purpose.  Some species of
AB  - Streptomyces, notably S. coelicolor A3(2), have good chromosomal genetics
AB  - (Hopwood, 1967; Hopwood et al., 1973; Hopwood and Chater, 1974; Hopwood and
AB  - Merrick, 1977; Rhodes, this volume).  Highly efficient generalized
AB  - recombination through protoplast fusion (Hopwood et al., 1977; Baltz, 1978) is
AB  - broadly applicable to Streptomyces.  Transformation for chromosomal markers by
AB  - liposome-entrapped DNA (Makins and Holt, 1981) has been reported for these
AB  - gram-positive bacteria.  Moreover, an almost extravagant range of plasmid DNA
AB  - cloning vectors for Streptomyces has come into use (reviewed by Chater et al.,
AB  - 1982a; Hopwood and Chater, 1982; Chater, 1983; Bib et al., 1983; Hopwood et
AB  - al., this volume).  Streptomyces genetics has been the subject of two recent
AB  - reviews (Chater and Hopwood, 1984; Hopwood and Chater, 1984).	This chapter will
AB  - be almost wholly concerned with temperate phages (reflecting the bias in
AB  - published data), and in particular with UC31, which is the most studied
AB  - Streptomyces phage.
ER  -

TY  - JOUR
AU  - Chater, K.F.
TI  - Restriction in Streptomyces.
JO  - Nocardia and Streptomyces. Proceedings of the International Symposium on Nocardia and Streptomyces. Warsaw Oct 4-8 1978
PY  - 1978
SP  - 303
EP  - 311
VL  - 0
AB  - Restriction has been the subject of authoritative recent reviews, and I will
AB  - give only a short introduction to it before pointing out its interest for the
AB  - Streptomyces geneticist.  Many bacteria possess restriction enzymes, which are
AB  - endodeoxy-ribonucleases that recognize specific short nucleotide sequences in
AB  - double-stranded DNA and cleave both strands.  The cleavage sites may, like the
AB  - recognition site, be specific (class II enzymes) or non-specific (class I
AB  - enzymes).  The only co-factor required for class II enzymes is Mg++, whereas
AB  - class I enzymes usually require ATP, Mg++ and S-adenosyl methionine.
AB  - Restriction enzymes are obligatorily accompanied by so-called modifying enzymes
AB  - that protect the cell's own DNA from endonucleolytic cleavage, by specific
AB  - recognition and modification of the same sites as are recognized by the
AB  - restriction enzyme.  Different species or even different wild-type isolates of
AB  - the same species usually have restriction-modification (R-M) systems with
AB  - different specificities.  Consequently DNA transferred from one species or
AB  - strain to another, for example in phage infection or bacterial mating, will
AB  - often be unprotected against endonucleolytic breakdown on entering the new host
AB  - and may thus be inactivated.  In the case of a phage, a lower efficiency of
AB  - plating (e.o.p.) restriction is observed on the second host.  However, incoming
AB  - foreign DNA is also subject to host-specific modification, and if this is
AB  - achieved before restriction, that DNA molecule is safe from endonucleolytic
AB  - cleavage and retains its biological activity.  In the case of phage DNA the
AB  - normal infective cycle ensues, detectable by plaque formation.  The recognition
AB  - sites of type II enzymes are invariably palindromic, showing 2-fold rotational
AB  - symmetry.  Moreover, cleavage been due to restriction or perhaps to
AB  - inefficiency of pair formation between the species.  The e.o.p. of the
AB  - temperate phage VP5 was therefore tested on the two strains and was shown to be
AB  - independent of the previous host used for its propagation.  Either an R-M
AB  - system was absent or, if it existed, VP5 was not susceptible to it.  It
AB  - therefore seems that an R-M system which has recently been identified in S.
AB  - albus G, and which will be described later, is the only one yet identified in
AB  - Streptomycetes.
ER  -

TY  - JOUR
AU  - Chater, K.F.
TI  - Actinophage DNA.
JO  - Dev. Ind. Microbiol.
PY  - 1980
SP  - 65
EP  - 74
VL  - 21
AB  - Actinophage DNA is considered largely in relation to its possible uses in
AB  - genetic engineering.  The G + C contents (determined by density) varied from 55
AB  - to 69%.  The no. of target sites for various restriction enzymes bore some
AB  - relation to base composition, high G + C content correlating with high
AB  - frequencies of SalGI sites and very low frequencies of sites for EcoRI,
AB  - HindIII, and HpaI.  Sites for BamHI and SalPI were absent from most actinophage
AB  - DNA tested regardless of its base composition.  A transfection procedure was
AB  - characterized, in which plaques could be visualised in soft agar overlays to
AB  - which had been added actinophage DNA and protoplasts previously mixed in the
AB  - presence of polyethylene glycol.  The procedure was effective with DNA of VP5,
AB  - UC32, R4, U448, and S14 and protoplasts of Streptomyces coelicolor A3(2) or S.
AB  - lividans 66.  	Deletion mutants of several phages (detected by virtue of their
AB  - resistance to chelating agents) were obtained both spontaneously and after
AB  - transfection of protoplasts with phage DNA pretreated with EcoRI and DNA
AB  - ligase.  One deletion mutant of phage R4 lacked the single EcoRI target site,
AB  - which is therefore dispensable and available as a DNA cloning site.  The
AB  - occurrence of chelating-agent-resistant deletion mutants of some actinophages
AB  - suggested that packaging of their DNA involved staggered, site-specific cutting
AB  - of concatameric DNA.  This was corroborated by evidence that UC31, SH10, and
AB  - probably R4 DNA molecules possess cohesive ends.
ER  -

TY  - JOUR
AU  - Chater, K.F.
TI  - A site-specific endodeoxyribonuclease from Streptomyces albus CMI 52766 sharing site-specificity with Providencia stuartii endonuclease PstI.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 1989
EP  - 1998
VL  - 4
AB  - A class II site-specific endodeoxyribonuclease (SalPI) was identified in
AB  - cell-free extracts of Streptomyces albus CMI 52766 after high speed
AB  - centrifugation and fractionation through BioGel A0.5M.  SalPI cleaves lambda
AB  - DNA into at least 18 fragments.  Five cleavage sites were located in the linear
AB  - lambda map by the use of double and triple restriction enzyme digests involving
AB  - EcoRI, HindIII, SalGI and another new Streptomyces enzyme, SacI.  The results
AB  - were indistinguishable from those previously obtained for a Providencia
AB  - stuartii enzyme, PstI, by Smith, Blattner & Davies (Nucl. Acids Res. 1976 3:
AB  - 343).  SalPI and PstI were shown by a double digest test to have the same site
AB  - specificity.  None of 34 phages tested was obviously restricted by S. albus CMI
AB  - 52766, and correspondingly DNA from two of them was not cleaved in vitro by
AB  - SalPI.  DNA from a Streptomyces phage that does not form plaques on S. albus
AB  - CMI 52766, and plasmid SCP2 DNA from S. coelicolor A3(2), were both cleaved.
ER  -

TY  - JOUR
AU  - Chater, K.F.
AU  - Carter, A.T.
TI  - A New, Wide Host-range, Temperate Bacteriophage (R4) of Streptomyces and its Interaction with some Restriction-Modification Systems.
JO  - J. Gen. Microbiol.
PY  - 1979
SP  - 431
EP  - 442
VL  - 115
AB  - A new temperate phage, R4, of Streptomyces was isolated from soil on a restriction-deficient
AB  - mutant of S. albus G.  In its morphology, adsorption properties and growth kinetics R4
AB  - resembled other temperate phages of Streptomyces though its requirements for Ca2+ and Mg2+
AB  - were higher than usual. It was unable to form plaques above 34.5 C.  R4-mediated transduction
AB  - was not detected.  Unlike other Streptomyces temperate phages, R4 had a wide host-range, which
AB  - correlated better with the absence of detectable class II restriction enzymes than with
AB  - conventional taxonomic divisions.  Many of the sensitive strains [but not, apparently, S.
AB  - coelicolor A3(2)] could be lysogenized. With the wild-type R4, plaques were obtained on S.
AB  - albus G only after growth on a restriction-deficient, modification-proficient mutant, and then
AB  - only at a very low efficiency of plating.  All of these plaques were of a mutant type (R4G)
AB  - which (unlike the parental R4 phage) showed conventional patterns of restriction-modification
AB  - in the S. albus G (SalGI) and S. albus P (SalPI) systems.  R4G mutants, but not R4, were
AB  - sensitive to a restriction-modification system present in two S. rimosus strains (2251 and
AB  - NRRL 2234).  DNA from SalGI-unmodified (but not from modified) R4 or R4G was cleaved by SalGI
AB  - into more than 30 fragments (mean size 1.35 kilobases; summed molecular weight (30.02x10^6).
AB  - R4 DNA was cleaved at one site by EcoRI, at one site by SalPI (0 PstI), and not at all by
AB  - HindIII or BamHI.
ER  -

TY  - JOUR
AU  - Chater, K.F.
AU  - Carter, A.T.
TI  - Restriction of a bacteriophage in Streptomyces albus P (CMI 52766) by Endonuclease SalPI.
JO  - J. Gen. Microbiol.
PY  - 1978
SP  - 181
EP  - 185
VL  - 109
AB  - Restriction has been hard to show in streptomycetes.  For example, in
AB  - Streptomyces coelicolor A3(2) (a strain sensitive to many actinophages),
AB  - restriction could be demonstrated only in a hybrid strain (S. coelicolor A3(2)
AB  - X S. griseus kr.15) which possessed phage receptors from S. griseus kr.15 and a
AB  - restriction system from S. coelicolor A3(2) (Lomovskaya et al., 1977). This
AB  - paper reports the restriction and modification by S. albus P of a wide
AB  - host-range temperate Streptomyces phage, R4, and it is shown that the agent of
AB  - restriction is the endonuclease SalPI.
ER  -

TY  - JOUR
AU  - Chater, K.F.
AU  - Wilde, L.C.
TI  - Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.
JO  - J. Bacteriol.
PY  - 1976
SP  - 644
EP  - 650
VL  - 128
AB  - The bacteriophage Pa16, isolated from soil on Streptomyces albus G, was
AB  - restricted when transferred from an alternative host back to S. albus G.
AB  - Extracted unmodified Pa16 deoxyribonucleic acid was cleaved at a single site by
AB  - a cell-free extract of S. albus G.  Fractions cleaving Pa16 deoxyribonucleic
AB  - acid contained the endonuclease SalI first described by J. Arrand, P. Myers,
AB  - and R.J. Roberts (unpublished data).  A mutant of S. albus G was isolated which
AB  - was defective in both restriction and modification of Pa16.  This mutant lacked
AB  - SalI activity.  It is concluded that SalI is the agent of restriction of Pa16
AB  - by S. albus G.
ER  -

TY  - JOUR
AU  - Chater, K.F.
AU  - Wilde, L.C.
TI  - Streptomyces albus G Mutants Defective in the SalGI Restriction-Modification System.
JO  - J. Gen. Microbiol.
PY  - 1980
SP  - 323
EP  - 334
VL  - 116
AB  - Streptomyces albus G mutants (at least 12 of which were independent) defective
AB  - in SalGI-mediated restriction (R-) were isolated after mutagenesis.  Some of
AB  - them lacked detectable SalGI activity in cell-free extracts.  Some were also
AB  - partially or completely defective in SalGI-associated modification (M-).  Loss
AB  - of restriction rendered S. albus G sensitive to many phages to which it was
AB  - normally totally resistant.  DNA from one such phage had many SalGI target
AB  - sites (means, one site per 1.35 kilobases).  A mutant was isolated which was
AB  - heat-sensitive for growth, apparently because it was restriction-proficient but
AB  - temperature-sensitive for modification.  At a rather high frequency, this
AB  - mutant generated spontaneous heat-tolerant derivatives which were nearly all
AB  - R-.  Such R- mutants were always M- rather than being temperature-sensitive for
AB  - modification.  In a limited genetic analysis, the determinants of restriction
AB  - and modification did not recombine with each other, and since there was no
AB  - reassortment of these phenotypes among the parental output of crosses it
AB  - appeared that the determinants were located close together on the chromosome.
ER  -

TY  - JOUR
AU  - Chatterjee, D.
AU  - Thakur, A.R.
AU  - Raychaudhuri, S.
TI  - Draft Genome Sequence of Ammonia-Producing Acinetobacter sp. Strain MCC2139 from  Dairy Effluent.
JO  - Genome Announcements
PY  - 2013
SP  - e00410
EP  - e00413
VL  - 1
AB  - We report the draft genome sequence of an ammonia-producing, esculin-hydrolyzing,
AB  - catalase-positive, gram-negative bacterium, Acinetobacter sp. strain MCC2139.
AB  - This bacterium, isolated from dairy sludge and with optimum growth at 37 degrees
AB  - C, has a genome size of 2,967,280 bp with a G+C content of 42.3%.
ER  -

TY  - JOUR
AU  - Chatterjee, D.K.
AU  - Hammond, A.W.
AU  - Blakesley, R.W.
AU  - Adams, S.M.
AU  - Gerard, G.F.
TI  - Genetic organization of the KpnI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6505
EP  - 6509
VL  - 19
AB  - The KpnI restriction-modification (KpnI RM) system was previously cloned and
AB  - expressed in E. coli.  The nucleotide sequences of the KpnI endonuclease
AB  - (R.KpnI) and methylase (M.KpnI) genes have now been determined.  The sequence
AB  - of the amino acid residues predicted from the endonuclease gene DNA sequence
AB  - and the sequence of the first 12 NH2-terminal amino acids determined from the
AB  - purified endonuclease protein were identical.  The KpnIR gene specifies a
AB  - protein of 218 amino acids (MW:25,115), while the KpnIM gene coes for a protein
AB  - of 417 amino acids (MW:47,582).  The two genes transcribe divergently with an
AB  - intergenenic region of 167 nucleotides containing the putative promoter regions
AB  - for both genes.  No protein sequence similarity was detected between R.KpnI and
AB  - M.KpnI.  Comparison of the amino acid sequence of M.KpnI with sequences of
AB  - various methylases revealed a significant homology to N6-adenine methylases, a
AB  - partial homology to N4-cytosine methylases, and no homology to C5-methylases.
ER  -

TY  - JOUR
AU  - Chatterjee, P.
AU  - Brady, K.L.
AU  - Solem, A.
AU  - Ho, Y.
AU  - Caprara, M.G.
TI  - Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 239
EP  - 251
VL  - 329
AB  - A large number of group I introns encode a family of homologous proteins that either promote
AB  - intron splicing (maturases) or are site-specific DNA
AB  - endonucleases that function in intron mobility (a process called
AB  - "homing"). Genetic studies have shown that some of these proteins have
AB  - both activities, yet how a single protein carries out both functions
AB  - remains obscure. The similarity between respective DNA-binding sites and
AB  - the RNA structure near the 5' and 3' splice sites has fueled speculation
AB  - that such proteins may use analogous interactions to perform both
AB  - functions. The Aspergillus nidulans mitochondrial COB group I intron
AB  - encodes a bi-functional protein, I-AniI, that has both RNA maturase and
AB  - site-specific DNA endonuclease activities in vitro. Here, we show that
AB  - I-AniI shows distinctive features of the endonuclease family to which it
AB  - belongs, including highly specific, tight binding and sequential DNA
AB  - strand cleavage. Competition experiments demonstrate that I-AniI binds the
AB  - COB intron RNA even in saturating concentrations of its DNA target site
AB  - substrate, suggesting that the protein has a separate binding site for
AB  - RNA. In addition, we provide evidence that two different DNA-binding site
AB  - mutants of I-AniI have little effect on the protein's RNA maturation
AB  - activity. Since RNA splicing is likely a secondary adaptation of the
AB  - protein, these observations support a model in which homing endonucleases
AB  - may have developed maturase function by utilizing a hitherto
AB  - "non-functional" protein surface.
ER  -

TY  - JOUR
AU  - Chaturvedi, D.
AU  - Chakravorty, M.
TI  - Restriction-modification system in bacteriophage MB78.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2003
SP  - 884
EP  - 890
VL  - 303
AB  - Restriction-modification system is present in bacteria to protect the cells against phage
AB  - infection. Interestingly, the bacteriophage MB78, a
AB  - virulent phage of Salmonella typhimurium possesses
AB  - restriction-modification system. Permissive host transformed with plasmid
AB  - having the genomic fragment of MB78 carrying the putative
AB  - restriction-modification genes severely restrict the growth of the phage
AB  - 9NA. Growth of phage MB78 is also restricted to some extent. However, the
AB  - temperate phage P22 is not restricted at all. Cloning of the the putative
AB  - restriction-modification genes has been done in both orientations in
AB  - different vectors. The clones carrying the genes in the same orientation
AB  - as that of the lacZ in pUC19 are mostly unstable. However, those are
AB  - stable when cloned in opposite orientation. Viability of the transformants
AB  - is strain-, orientation-, and medium-dependent. The two genes have also
AB  - been cloned individually/separately. Hosts carrying only the modification
AB  - gene do not restrict growth of phages while the hosts carrying only the
AB  - restriction gene do. The former produces stable transformants while the
AB  - latter produces very unstable transformants which were viable only upto 36
AB  - h or so. The colonies carrying modification gene were normal looking while
AB  - those carrying the restriction gene were tiny, flat, and looked distressed
AB  - resembling very much the clones carrying bacterial
AB  - restriction-modification system. Amplification of the genes and subsequent
AB  - cloning in expression vector will be carried out for characterization of
AB  - the enzymes.
ER  -

TY  - JOUR
AU  - Chaturvedi, D.
AU  - Chakravorty, M.
TI  - Identification of an unusual restriction-modification system in bacteriophage MB78.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A171
EP  - A171
VL  - 28
AB  - A restriction-modification system has been identified in bacteriophage MB78, a virulent phage
AB  - of Salmonella typhimurium isolated in this laboratory.  Genomic fragment of MB78 carrying the
AB  - corresponding genes has been cloned in both orientations in pUC19.  The clones carrying the
AB  - genes in the same orientation as that of the lacZ are mostly unstable.  However, those cloned
AB  - in opposite orientation are stable.  Viability of transformants is strain-, orientation- and
AB  - medium-dependent.  To clone the genes for restriction and modification enzymes separately, the
AB  - genomic fragment containing the restriction-modification system was subcloned using AccI and
AB  - SmaI enzymes.  One set of subclones contained active methylase gene, while the others
AB  - contained an active endonuclease gene as well as truncated (inactive) methylase gene.  The
AB  - former are stable and normal looking while the latter are unstable and looked distressed.
AB  - Both the genes have been sequenced.  The methylase and restriction genes (only 228 and 333 bp
AB  - respectively) are unusually small in comparison to respective bacterial genes.
ER  -

TY  - JOUR
AU  - Chau, M.L. et al.
TI  - Group B Streptococcus Infections Caused by Improper Sourcing and Handling of Fish for Raw Consumption, Singapore, 2015-2016.
JO  - Emerg. Infect. Dis.
PY  - 2017
SP  - 1982
EP  - 1990
VL  - 23
AB  - We assessed microbial safety and quality of raw fish sold in Singapore during 2015-2016 to
AB  - complement epidemiologic findings for an outbreak of infection with group B Streptococcus
AB  - serotype III sequence type (ST) 283 associated with raw fish consumption. Fish-associated
AB  - group B Streptococcus ST283 strains included strains nearly identical (0-2 single-nucleotide
AB  - polymorphisms) with the human outbreak strain, as well as strains in another distinct ST283
AB  - clade (57-71 single-nucleotide polymorphisms). Our investigations highlight the risk for
AB  - contamination of freshwater fish (which are handled and distributed separately from saltwater
AB  - fish sold as sashimi) and the need for improved hygienic handling of all fish for raw
AB  - consumption. These results have led to updated policy and guidelines regarding the sale of
AB  - ready-to-eat raw fish dishes in Singapore.
ER  -

TY  - JOUR
AU  - Chaudhuri, P.
AU  - Goswami, T.T.K.
AU  - Lalsiamthara, J.
AU  - Kaur, G.
AU  - Vishnu, U.S.
AU  - Sankarasubramanian, J.
AU  - Gunasekaran, P.
AU  - Rajendhran, J.
TI  - Draft Genome Sequence of the Intermediate Rough Vaccine Strain Brucella abortus S19Deltaper Mutant.
JO  - Genome Announcements
PY  - 2015
SP  - e01336
EP  - e01315
VL  - 3
AB  - Here, we report the genome sequence of the intermediate rough vaccine strain mutant, Brucella
AB  - abortus S19Deltaper. The length of the draft genome was
AB  - 3,271,238 bp, with 57.2% G+C content. A total of 3,204 protein-coding genes and
AB  - 56 RNA genes were predicted.
ER  -

TY  - JOUR
AU  - Chaudhuri, R.R. et al.
TI  - Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.
JO  - PLoS ONE
PY  - 2010
SP  - e8801
EP  - e8801
VL  - 5
AB  - BACKGROUND: Escherichia coli can experience a multifaceted life, in some cases acting as a
AB  - commensal while in other cases causing intestinal and/or
AB  - extraintestinal disease. Several studies suggest enteroaggregative E. coli
AB  - are the predominant cause of E. coli-mediated diarrhea in the developed
AB  - world and are second only to Campylobacter sp. as a cause of
AB  - bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a
AB  - predominant cause of persistent diarrhea in the developing world where
AB  - infection has been associated with malnourishment and growth retardation.
AB  - METHODS: In this study we determined the complete genomic sequence of E.
AB  - coli 042, the prototypical member of the enteroaggregative E. coli, which
AB  - has been shown to cause disease in volunteer studies. We performed genomic
AB  - and phylogenetic comparisons with other E. coli strains revealing
AB  - previously uncharacterised virulence factors including a variety of
AB  - secreted proteins and a capsular polysaccharide biosynthetic locus. In
AB  - addition, by using Biolog Phenotype Microarrays we have provided a full
AB  - metabolic profiling of E. coli 042 and the non-pathogenic lab strain E.
AB  - coli K-12. We have highlighted the genetic basis for many of the metabolic
AB  - differences between E. coli 042 and E. coli K-12. CONCLUSION: This study
AB  - provides a genetic context for the vast amount of experimental and
AB  - epidemiological data published thus far and provides a template for future
AB  - diagnostic and intervention strategies.
ER  -

TY  - JOUR
AU  - Chaudhuri, S.R.
TI  - Draft Genome Sequence of an Industrially Important Bacillus sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00867
EP  - e00816
VL  - 4
AB  - Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-,
AB  - gelatinase-, and catalase-producing, Gram-positive diplobacillus (Bacillus sp. SM1 strain
AB  - MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk
AB  - fabric as well as Ramie fiber. The genome comprises 1.76 Mb with a GC content of 34.5%.
ER  -

TY  - JOUR
AU  - Chauhan, A.
AU  - Green, S.
AU  - Pathak, A.
AU  - Thomas, J.
AU  - Venkatramanan, R.
TI  - Whole-genome sequences of five oyster-associated bacteria show potential for crude oil hydrocarbon degradation.
JO  - Genome Announcements
PY  - 2013
SP  - e00802
EP  - e00813
VL  - 1
AB  - Draft genome sequences of oyster-associated Pseudomonas stutzeri strain MF28, P.  alcaligenes
AB  - strain OT69, P. aeruginosa strain WC55, Stenotrophomonas maltophilia
AB  - strain MF89, and Microbacterium maritypicum strain MF109 are reported.
AB  - Genome-wide surveys of these isolates suggest that the oyster microbiome, which
AB  - remains largely understudied, has a strong potential to degrade crude oil.
ER  -

TY  - JOUR
AU  - Chauhan, A.
AU  - Layton, A.C.
AU  - Williams, D.
AU  - Smartt, A.E.
AU  - Ripp, S.
AU  - Karpinets, T.V.
AU  - Brown, S.D.
AU  - Sayler, G.S.
TI  - Draft Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading, Genetically Engineered Bioluminescent Bioreporter Pseudomonas fluorescens  HK44.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5009
EP  - 5009
VL  - 193
AB  - Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based
AB  - bioluminescent bioreporter. Here we report the draft genome
AB  - sequence of strain HK44. Annotation of  approximately 6.1 Mb sequence
AB  - indicates that 30% of the traits are unique and distributed over 5 genomic
AB  - islands, a prophage and two plasmids.
ER  -

TY  - JOUR
AU  - Chauhan, D.
AU  - Srivastava, P.A.
AU  - Yennamalli, R.M.
AU  - Priyadarshini, R.
TI  - Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a  Freshwater Wetland.
JO  - Genome Announcements
PY  - 2017
SP  - e00754
EP  - e00717
VL  - 5
AB  - Deinococcus indicus strain DR1, a red-pigmented, arsenic- and radiation-resistant bacterium,
AB  - was isolated from a water sample of the Dadri wetland, Uttar Pradesh,
AB  - India. Here, we report a draft genome sequence of this strain, which may provide
AB  - useful information regarding the genes and pathways involved in heavy-metal
AB  - bioremediation.
ER  -

TY  - JOUR
AU  - Chauhan, H.C.
AU  - Patel, B.K.
AU  - Chandel, B.S.
AU  - Patel, K.B.
AU  - Patel, A.C.
AU  - Shrimali, M.D.
AU  - Patel, S.S.
AU  - Bhagat, A.G.
AU  - Rajgor, M.
AU  - Patel, M.A.
AU  - Patel, M.
AU  - Kala, J.
AU  - Patel, B.
TI  - Complete Genome Sequence of Brucella abortus SKN 13 Isolated from Placenta of Aborted Cattle in Gujarat, India.
JO  - Genome Announcements
PY  - 2016
SP  - e01123
EP  - e01116
VL  - 4
AB  - Brucella abortus is generally known to cause brucellosis in cattle and buffalo. Here, we
AB  - report the draft genome sequence of Brucella abortus SKN 13, isolated
AB  - from aborted cattle placenta in the area of Gujarat, India, providing precious
AB  - resources for comparative genomic analyses of Brucella field strains.
ER  -

TY  - JOUR
AU  - Chauthaiwale, V.M.
AU  - Vyas, P.R.
AU  - Deshpande, V.V.
TI  - Genetic transformation of Chainia and heat attenuation of its restriction system.
JO  - Can. J. Microbiol.
PY  - 1991
SP  - 713
EP  - 715
VL  - 37
AB  - A PEG-mediated transformation system for Chainia (NCL 82-5-1) was developed
AB  - using a broad host range Streptomyces vector, pIJ702.  Protoplasts prepared
AB  - from Chainia (NCL 81-5-1) were regenerated with 5% efficiency.  Transformation
AB  - of the protoplasts with pIJ702 gave 10-20 transformants/microgram DNA.  The low
AB  - efficiency of transformation is attributed to a restriction system in Chainia;
AB  - this could be inhibited by treating the protoplasts at 42C for 10 min just
AB  - before transformation.  The yield of transformants increased 100-fold when
AB  - pIJ702 was modified by passage in Chainia.  Because the plasmid replicon was
AB  - functional in Chainia and the modified plasmid was stably maintained, the
AB  - transformation system should be useful for self-cloning in Chainia NCL 82-5-1
AB  - of the many commercially important enzymes this strain is known to produce.
ER  -

TY  - JOUR
AU  - Chavez, S.L.
AU  - Pera, R.A.R.
TI  - Identification of the De Novo DNA Methyltransferase, DNMT3A2, as a Novel Regulator of Germ Cell Development.
JO  - Reprod. Sci.
PY  - 2011
SP  - 172A
EP  - 172A
VL  - 18
AB  - The methylation of DNA is mediated by a family of DNA methyltransferases which play a role in
AB  - the establishment and/or maintenance of DNA methylation patterns.  Previously, it was shown
AB  - that the targeted disruption of both active isoforms of the de novo methyltransferase, Dnmt3a,
AB  - in germ cells by conditional mouse knockout technology resulted in aberrant gametogenesis.
AB  - The aim of this study was to evaluate the expression and function of DNMT3A in human fetal
AB  - gonads and human embryonic stem cell (hESC)-derived germ cell differentiation.  In addition,
AB  - the role of Dnmt3a in mouse primordial germ cells isolated from fetal gonads throughout
AB  - development and in mouse embryonic germ cells, the pluripotent cells that PGCs form in vitro,
AB  - was also investigated.
ER  -

TY  - JOUR
AU  - Chavez-Bueno, S.
AU  - Day, M.W.
AU  - Toby, I.T.
AU  - Akins, D.R.
AU  - Dyer, D.W.
TI  - Genome Sequence of SCB34, a Sequence Type 131 Multidrug-Resistant Escherichia coli Isolate Causing Neonatal Early-Onset Sepsis.
JO  - Genome Announcements
PY  - 2014
SP  - e00514
EP  - e00514
VL  - 2
AB  - SCB34 is a sequence type 131, highly invasive, multidrug-resistant Escherichia coli isolate
AB  - that produced neonatal bacteremia. Whole-genome sequencing was
AB  - performed using a 250-bp library on the Illumina MiSeq platform; 5,910,264 reads
AB  - were assembled de novo using the A5 assembly pipeline. The total contig length
AB  - was 5,227,742 bp; the RAST server was used for annotation.
ER  -

TY  - JOUR
AU  - Che, J.
AU  - Liu, B.
AU  - Lin, Y.
AU  - Tang, W.
AU  - Tang, J.
TI  - Draft Genome Sequence of Biocontrol Bacterium Brevibacillus brevis Strain FJAT-0809-GLX.
JO  - Genome Announcements
PY  - 2013
SP  - e00160
EP  - e00113
VL  - 1
AB  - Brevibacillus brevis strain FJAT-0809-GLX had significant inhibition on many plant and animal
AB  - pathogens. The draft genome sequence of B. brevis FJAT-0809-GLX
AB  - is 6 Mb in size and consists of 5,677 genes (protein-coding sequences [CDS]),
AB  - with an average length of 933 bp and a G+C content of 47.30%. Compared with the
AB  - published B. brevis strain NBRC 100599, 618 specific genes were identified in the
AB  - strain FJAT-0809-GLX.
ER  -

TY  - JOUR
AU  - Che, S.
AU  - Song, L.
AU  - Song, W.
AU  - Yang, M.
AU  - Liu, G.
AU  - Lin, X.
TI  - Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G.
JO  - Genome Announcements
PY  - 2013
SP  - e00725
EP  - e00713
VL  - 1
AB  - Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King
AB  - George Island, Antarctica, which can produce lipolytic enzymes
AB  - at low temperatures. The genomics information of this strain will facilitate the
AB  - study of the physiology, cold adaptation properties, and evolution of this genus.
ER  -

TY  - JOUR
AU  - Checinska, S.A.
AU  - Singh, N.K.
AU  - Allen, J.E.
AU  - Thissen, J.
AU  - Jaing, C.
AU  - Venkateswaran, K.
TI  - Draft Genome Sequences of Biosafety Level 2 Opportunistic Pathogens Isolated from the Environmental Surfaces of the International Space Station.
JO  - Genome Announcements
PY  - 2016
SP  - e01263
EP  - e01216
VL  - 4
AB  - The draft genome sequences of 20 biosafety level 2 (BSL-2) opportunistic pathogens isolated
AB  - from the environmental surfaces of the International Space
AB  - Station (ISS) were presented. These genomic sequences will help in understanding
AB  - the influence of microgravity on the pathogenicity and virulence of these strains
AB  - when compared with Earth strains.
ER  -

TY  - JOUR
AU  - Chedin, F.
TI  - The DNMT3 Family of Mammalian De Novo DNA Methyltransferases.
JO  - Prog. Mol. Biol. Transl. Sci.
PY  - 2011
SP  - 255
EP  - 285
VL  - 101
AB  - The deposition of DNA methylation at promoters of transposons, X-linked genes, imprinted
AB  - genes, and other lineage-specific genes is clearly
AB  - associated with long-term transcriptional silencing. Thus, DNA
AB  - methylation represents a key layer of epigenetic information in mammals
AB  - that is required for embryonic development, germline differentiation,
AB  - and, as shown more recently, for the function and maturation of
AB  - neuronal tissues. The DNMT3A, DNMT3B, and DNMT3L proteins are primarily
AB  - responsible for the establishment of genomic DNA methylation patterns
AB  - and, as such, play an important role in human developmental,
AB  - reproductive, and mental health. Progress in our understanding of this
AB  - important protein family has been rapid in recent years and has been
AB  - accompanied by stunning developments in the analysis of the human DNA
AB  - methylome in multiple cell types. This review focuses on recent
AB  - developments in the characterization of the DNMT3 family of DNA
AB  - methyltransferases at the biochemical, structural, and functional
AB  - levels. Interconnections between the DNA-based and histone-based layers
AB  - of epigenetic information are particularly highlighted, as it is now
AB  - clear that de now methylation occurs chiefly in the context of
AB  - nucleosomal templates.
ER  -

TY  - JOUR
AU  - Chedin, F.
AU  - Lieber, M.R.
AU  - Hsieh, C.L.
TI  - The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 16916
EP  - 16921
VL  - 99
AB  - Dnmt3L is required for the establishment of maternal methylation imprints at imprinting
AB  - centers (ICs). Dnmt3L, however, lacks the conserved
AB  - catalytic domain common to DNA methyltransferases. In an attempt to define
AB  - its function, we coexpressed DNMT3L with each of the two known de novo
AB  - methyltransferases, Dnmt3a and DNMT3B, in human cells and monitored de
AB  - novo methylation by using replicating minichromosomes carrying various ICs
AB  - as targets. Coexpression of DNMT3L with DNMT3B led to little or no change
AB  - in target methylation. However, coexpression of DNMT3L with Dnmt3a
AB  - resulted in a striking stimulation of de novo methylation by Dnmt3a.
AB  - Stimulation was observed at maternally methylated ICs such as small
AB  - nuclear ribonucleoprotein polypeptide N (SNRPN), Snrpn, and Igf2rAir, as
AB  - well as at various nonimprinted sequences present on the episomes.
AB  - Stimulation of Dnmt3a by DNMT3L was also observed at endogenous sequences
AB  - in the genome. Therefore, DNMT3L acts as a general stimulatory factor for
AB  - de novo methylation by Dnmt3a. The implications of these findings for the
AB  - function of DNMT3L and Dnmt3a in DNA methylation and genomic imprinting
AB  - are discussed.
ER  -

TY  - JOUR
AU  - Chee, J.L.
AU  - Ravins, M.
AU  - Hanski, E.
AU  - Chen, S.L.
TI  - Complete Genome Sequence of Streptococcus pyogenes emm14 JS95, a Necrotizing Fasciitis Strain Isolated in Israel.
JO  - Genome Announcements
PY  - 2017
SP  - e00025
EP  - e00017
VL  - 5
AB  - Here, we report the complete genome sequence of the Streptococcus pyogenes emm14  strain JS95,
AB  - isolated from a patient with necrotizing fasciitis. The
AB  - streptococcal invasion locus (sil), the first quorum-sensing system characterized
AB  - in S. pyogenes, was identified in this strain.
ER  -

TY  - JOUR
AU  - Cheevadhanarak, S. et al.
TI  - Draft genome sequence of Arthrospira platensis C1 (PCC9438).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 43
EP  - 53
VL  - 6
AB  - Arthrospira platensis is a cyanobacterium that is extensively cultivated outdoors on a large
AB  - commercial scale for consumption as a food for humans and animals. It can be grown in
AB  - monoculture under highly alkaline conditions, making it attractive for industrial production.
AB  - Here we describe the complete genome sequence of A. platensis C1 strain and its annotation.
AB  - The A. platensis C1 genome contains 6,089,210 bp including 6,108 protein-coding genes and 45
AB  - RNA genes, and no plasmids. The genome information has been used for further comparative
AB  - analysis, particularly of metabolic pathways, photosynthetic efficiency and barriers to gene
AB  - transfer.
ER  -

TY  - JOUR
AU  - Chekireb, D.
AU  - Crovadore, J.
AU  - Brachmann, A.
AU  - Chablais, R.
AU  - Cochard, B.
AU  - Lefort, F.
TI  - Whole-Genome Sequences of 14 Strains of Bradyrhizobium canariense and 1 Strain of Bradyrhizobium japonicum Isolated from Lupinus spp. in Algeria.
JO  - Genome Announcements
PY  - 2017
SP  - e00676
EP  - e00617
VL  - 5
AB  - We report here the whole-genome sequences of 14 strains of Bradyrhizobium canariense, isolated
AB  - from root nodules of Lupinus microanthus and Lupinus
AB  - angustifolius, and 1 strain of Bradyrhizobium japonicum isolated from root
AB  - nodules from Lupinus angustifolius in Algeria. These sequences add to the known
AB  - diversity of this agronomically important genus.
ER  -

TY  - JOUR
AU  - Cheleuitte-Nieves, C.
AU  - Gulvik, C.A.
AU  - Humrighouse, B.W.
AU  - Bell, M.E.
AU  - Villarma, A.
AU  - Westblade, L.F.
AU  - Lipman, N.S.
AU  - Fischetti, V.A.
AU  - McQuiston, J.R.
TI  - Draft Reference Genome Sequence of Corynebacterium mastitidis 16-1433, Isolated from a Mouse.
JO  - Genome Announcements
PY  - 2018
SP  - e00050
EP  - e00018
VL  - 6
AB  - We report here a nearly complete draft genome sequence for a Corynebacterium mastitidis
AB  - isolate from a mouse. The total read coverage is 198x, and the genome
AB  - size is 2,264,319 bp with a 69.04% GC content. This genome complements the only
AB  - other genome available for C. mastitidis, which was obtained from a sheep.
ER  -

TY  - JOUR
AU  - Chen, A.
AU  - Powell, L.M.
AU  - Dryden, D.T.F.
AU  - Murray, N.E.
AU  - Brown, T.
TI  - Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 1177
EP  - 1183
VL  - 23
AB  - The specificity (S) subunit of the restriction enzyme EcoKI imparts specificity for the
AB  - sequence AAC(N6)GTGC. Substitution of thymine with bromodeoxyuridine in a 25 bp DNA duplex
AB  - containing this sequence stimulated UV light-induced covalent cross-linking to the S subunit.
AB  - Crosslinking occurred only at the residue complementary to the first adenine in the AAC
AB  - sequence, demonstrating a close contact between the major groove at this sequence and the S
AB  - subunit. Peptide sequencing of a proteolytically-digested, crosslinked complex identified
AB  - tyrosine 27 in the S subunit as the site of crosslinking. This is consistent with the role of
AB  - the N-terminal domain of the S subunit in recognizing the AAC sequence. Tyrosine 27 is
AB  - conserved in the S subunits of the three type I enzymes that share the sequence AA in the
AB  - trinucleotide component of their target sequence. This suggests that tyrosine 27 may make a
AB  - similar DNA contact in these other enzymes.
ER  -

TY  - JOUR
AU  - Chen, B.S.
AU  - Otten, L.G.
AU  - Resch, V.
AU  - Muyzer, G.
AU  - Hanefeld, U.
TI  - Draft genome sequence of Rhodococcus rhodochrous strain ATCC 17895.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 175
EP  - 184
VL  - 9
AB  - Rhodococcus rhodochrous ATCC 17895 possesses an array of mono- and dioxygenases,  as well as
AB  - hydratases, which makes it an interesting organism for biocatalysis.
AB  - R. rhodochrous is a Gram-positive aerobic bacterium with a rod-like morphology.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 6,869,887 bp long genome contains 6,609
AB  - protein-coding genes and 53 RNA genes. Based on small subunit rRNA analysis, the
AB  - strain is more likely to be a strain of Rhodococcus erythropolis rather than
AB  - Rhodococcus rhodochrous.
ER  -

TY  - JOUR
AU  - Chen, Bi.-F.
AU  - Chan, W.-Yee.
TI  - The de novo DNA methyltransferase DNMT3A in development and cancer.
JO  - EPIGENETICS
PY  - 2014
SP  - 669
EP  - 677
VL  - 9
AB  - DNA methylation, one of the best-characterized epigenetic modifications, plays essential roles
AB  - in development, aging and diseases. The de novo DNA methyltransferase DNMT3A is responsible
AB  - for the establishment of de novo genomic DNA methylation patterns and, as such, involved in
AB  - normal development as well as in many diseases including cancer. In recent years, our
AB  - understanding of this important protein has made significant progress, which was facilitated
AB  - by stunning development in the analysis of the DNA methylome of multiple organs and cell
AB  - types. In this review, recent developments in the characterization of DNMT3A were discussed
AB  - with special emphasis on the roles of DNMT3A in development and cancer.
ER  -

TY  - JOUR
AU  - Chen, C. et al.
TI  - A Glimpse of Streptococcal Toxic Shock Syndrome from Comparative Genomics of S. suis 2 Chinese Isolates.
JO  - PLoS ONE
PY  - 2007
SP  - e315
EP  - e315
VL  - 2
AB  - BACKGROUND: Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen, causing
AB  - more than 200 cases of severe human infection worldwide,
AB  - with the hallmarks of meningitis, septicemia, arthritis, etc. Very
AB  - recently, SS2 has been recognized as an etiological agent for
AB  - streptococcal toxic shock syndrome (STSS), which was originally associated
AB  - with Streptococcus pyogenes (GAS) in Streptococci. However, the molecular
AB  - mechanisms underlying STSS are poorly understood. METHODS AND FINDINGS: To
AB  - elucidate the genetic determinants of STSS caused by SS2, whole genome
AB  - sequencing of 3 different Chinese SS2 strains was undertaken. Comparative
AB  - genomics accompanied by several lines of experiments, including
AB  - experimental animal infection, PCR assay, and expression analysis, were
AB  - utilized to further dissect a candidate pathogenicity island (PAI). Here
AB  - we show, for the first time, a novel molecular insight into Chinese
AB  - isolates of highly invasive SS2, which caused two large-scale human STSS
AB  - outbreaks in China. A candidate PAI of approximately 89 kb in length,
AB  - which is designated 89K and specific for Chinese SS2 virulent isolates,
AB  - was investigated at the genomic level. It shares the universal properties
AB  - of PAIs such as distinct GC content, consistent with its pivotal role in
AB  - STSS and high virulence. CONCLUSIONS: To our knowledge, this is the first
AB  - PAI candidate from S. suis worldwide. Our finding thus sheds light on STSS
AB  - triggered by SS2 at the genomic level, facilitates further understanding
AB  - of its pathogenesis and points to directions of development on some
AB  - effective strategies to combat highly pathogenic SS2 infections.
ER  -

TY  - JOUR
AU  - Chen, C.
AU  - Ai, L.
AU  - Zhou, F.
AU  - Wang, L.
AU  - Zhang, H.
AU  - Chen, W.
AU  - Guo, B.
TI  - Complete genome sequence of the probiotic bacterium Lactobacillus casei LC2W.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3419
EP  - 3420
VL  - 193
AB  - Lactobacillus casei LC2W, a patented probiotic strain (EP 164209630B1), is isolated from
AB  - Chinese traditional dairy products and has been implemented
AB  - in the industrial production as starter cultures. Here we present the
AB  - complete genome sequence of LC2W and the identification of a gene cluster
AB  - implicated in the biosynthesis of exopolysaccharides.
ER  -

TY  - JOUR
AU  - Chen, C.
AU  - Kittichotirat, W.
AU  - Chen, W.
AU  - Downey, J.S.
AU  - Bumgarner, R.
TI  - Genome Sequence of a Serotype b Non-JP2 Aggregatibacter actinomycetemcomitans Strain, ANH9381, from a Periodontally Healthy Individual.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1837
EP  - 1837
VL  - 194
AB  - Gram-negative Aggregatibacter actinomycetemcomitans can be distinguished (based on the
AB  - promoter structure of the leukotoxin operon) into JP2 and non-JP2
AB  - genotypes, with the former found to be more pathogenic than the latter. Here we
AB  - report the first complete genome sequence of a serotype b non-JP2 strain of A.
AB  - actinomycetemcomitans.
ER  -

TY  - JOUR
AU  - Chen, C.
AU  - Kittichotirat, W.
AU  - Chen, W.
AU  - Downey, J.S.
AU  - Si, Y.
AU  - Bumgarner, R.
TI  - Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2643
EP  - 2644
VL  - 192
AB  - The major clonal lineages of the Gram-negative periodontal pathogen Aggregatibacter
AB  - actinomycetemcomitans include serotype a, b, and c
AB  - strains. Here, we report the draft genome sequence of a naturally
AB  - competent serotype a strain, D7S-1, isolated from a patient with
AB  - aggressive periodontitis.
ER  -

TY  - JOUR
AU  - Chen, C.
AU  - Kittichotirat, W.
AU  - Si, Y.
AU  - Bumgarner, R.
TI  - Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7378
EP  - 7379
VL  - 191
AB  - Aggregatibacter actinomycetemcomitans is a major etiological agent of periodontitis. Here we
AB  - report the complete genome sequence of a serotype c strain D11S-1, which was recovered from
AB  - the subgingival plaque of a patient diagnosed with generalized aggressive periodontitis.
ER  -

TY  - JOUR
AU  - Chen, C.
AU  - Sun, L.
TI  - Draft Genome Sequence of Exiguobacterium sp. HVEsp1, a Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent in the Okinawa Trough.
JO  - Genome Announcements
PY  - 2017
SP  - e00253
EP  - e00217
VL  - 5
AB  - We report here the draft genome sequence of Exiguobacterium sp. HVEsp1, a thermophilic
AB  - bacterium isolated from a deep-sea hydrothermal vent. The estimated
AB  - genome size of this strain is 2,838,499 bp with a G+C content of 48.2%. The
AB  - genome sequence data provide valuable information that will facilitate studies on
AB  - the adaptation mechanisms of bacteria living in deep-sea hydrothermal vents.
ER  -

TY  - JOUR
AU  - Chen, C.
AU  - Wang, L.
AU  - Chen, S.
AU  - Wu, X.
AU  - Gu, M.
AU  - Chen, X.
AU  - Jiang, S.
AU  - Wang, Y.
AU  - Deng, Z.
AU  - Dedon, P.C.
AU  - Chen, S.
TI  - Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2017
SP  - 4501
EP  - 4506
VL  - 114
AB  - Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical
AB  - structures and biological functions of DNA modifications in restriction-modification (R-M) and
AB  - basic genetic processes. Here, we describe the discovery of shared consensus sequences for two
AB  - seemingly unrelated DNA modification systems, 6mA methylation and phosphorothioation (PT), in
AB  - which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of
AB  - DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing
AB  - PT-based R-M genes, revealed d(GPS6mA) dinucleotides in the GPS6mAAC consensus representing
AB  - approximately 5% of the 1,100 to 1,300 PT-modified d(GPSA) motifs per genome, with 6mA arising
AB  - from a yet-to-be-identified methyltransferase. To further explore PT and 6mA in another
AB  - consensus sequence, GPS6mATC, we engineered a strain of E. coli HST04 to express Dnd genes
AB  - from Hahella chejuensis KCTC2396 (PT in GPSATC) and Dam methyltransferase from E. coli DH10B
AB  - (6mA in G6mATC). Based on this model, in vitro studies revealed reduced Dam activity in
AB  - GPSATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA
AB  - revealed 6mA in all 2,058 GPSATC sites (5% of 37,698 total GATC sites). This model system also
AB  - revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited
AB  - to discover that 6mA can substitute for PT to confer resistance to restriction by the DndFGH
AB  - system. These results point to complex but unappreciated interactions between DNA modification
AB  - systems and raise the possibility of coevolution of interacting systems to facilitate the
AB  - function of each.
ER  -

TY  - JOUR
AU  - Chen, C.-H.B.
AU  - Sigman, D.S.
TI  - Chemical Conversion of a DNA-binding protein into a site-specific nuclease.
JO  - Science
PY  - 1987
SP  - 1197
EP  - 1201
VL  - 237
AB  - The tryptophan gene (trp) repressor of Escherichia coli has been converted into
AB  - a site-specific nuclease by covalently attaching it to the
AB  - 1,10-phenanthroline-copper complex.  In its cuprous form, the coordination
AB  - complex with hydrogen peroxide as a coreactant cleaves DNA by oxidatively
AB  - attacking the deoxyribose moiety.  The chemistry for the attachment of
AB  - 1,10-phenanthroline to the trp repressor involves modification of lysyl
AB  - residues with iminothiolane followed by alkylation of the resulting sulfhydryl
AB  - groups with 5-iodoacetamido-1,10-phenanthroline.  The modified trp repressor
AB  - cleaves the operators of aroH and trpEDCBA upon the addition of cupric ion and
AB  - thiol in a reaction dependent on the corepressor L-tryptophan.  Scission was
AB  - restricted to the binding site for the repressor, defined by deoxyribonuclease
AB  - I footprinting.  Since DNA-binding proteins have recognition sequences
AB  - approximately 20 base pairs long, the nucleolytic activities derived from them
AB  - could be used to isolate long DNA fragments for sequencing or chromosomal
AB  - mapping.
ER  -

TY  - JOUR
AU  - Chen, C.-K.
AU  - Boucle, C.M.
AU  - Blaschek, H.P.
TI  - Factors involved in the transformation of previously non-transformable Clostridium perfringens type B.
JO  - FEMS Microbiol. Lett.
PY  - 1996
SP  - 185
EP  - 191
VL  - 140
AB  - The pre-shock incubation of cells plus DNA and the methylation state of plasmid DNA were found
AB  - to play a role in the electroporation-based transformation of Clostridium perfringens 3626B.
AB  - Following pre-shock incubation, the highest number of C. perfringens 3626B transformants was
AB  - obtained when plasmid pGK201 was both dam+ dcm+ modified, while no transformants were obtained
AB  - when pGK201 was not methylated or only dcm methylated.  This is consistent with the
AB  - observation that plasmid pGK201 was protected against digestion by C. perfringens 3626B
AB  - cell-associated nucleases for up to 3 min when methylated by both methylases.  C. perfringens
AB  - 3626B was successfully transformed only within a narrow cell recovery rate window.  The ermAM
AB  - gene associated with pGK201 and pAK102 was found to integrate into the chromosome of C.
AB  - perfringens strains 13A and 3626B.
ER  -

TY  - JOUR
AU  - Chen, C.C.
AU  - Hsia, K.C.
AU  - Huang, C.T.
AU  - Wong, W.W.
AU  - Yen, M.Y.
AU  - Li, L.H.
AU  - Lin, K.Y.
AU  - Chen, K.W.
AU  - Li, S.Y.
TI  - Draft Genome Sequence of a Dominant Multidrug-resistant Neisseria gonorrhoeae strain TCDC-NG08107 from Sexual Network at High Risk of  Acquiring Human Immunodeficiency Virus and Syphilis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1788
EP  - 1789
VL  - 193
AB  - Neisseria gonorrhoeae infection is the second major cause of sexually transmitted diseases
AB  - worldwide. Development of resistance to multiple classes of antimicrobials in N. gonorrhoeae
AB  - has compromised treatment and disease control. Herein, we report the availability of the draft
AB  - genome sequence of a multidrug-resistant N. gonorrhoeae isolate, TCDC-NG08107, which spread in
AB  - groups of men who have sex with men (MSM) in Taiwan.
ER  -

TY  - JOUR
AU  - Chen, C.C.
AU  - Lin, Y.C.
AU  - Sheng, W.H.
AU  - Chen, Y.C.
AU  - Chang, S.C.
AU  - Hsia, K.C.
AU  - Liao, M.H.
AU  - Li, S.Y.
TI  - Genome Sequence of a Dominant Multidrug-resistant Acinetobacter baumannii strain TCDC-AB0715.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2361
EP  - 2362
VL  - 193
AB  - Acinetobacter baumannii has emerged as a significant nosocomial pathogen worldwide. The
AB  - increasing trend of carbapenem and fluoroquinolone resistance in A. baumannii severely limits
AB  - the usage of therapeutic antimicrobial agents. Here, we report the genome sequence of a
AB  - multidrug-resistant A. baumannii strain TCDC-AB0715 harboring both blaOXA-23 and blaOXA-66.
ER  -

TY  - JOUR
AU  - Chen, C.C.
AU  - Wang, K.Y.
AU  - Shen, C.K.J.
TI  - DNA 5-Methylcytosine Demethylation Activities of the Mammalian DNA Methyltransferases.
JO  - J. Biol. Chem.
PY  - 2013
SP  - 9084
EP  - 9091
VL  - 288
AB  - Methylation at the 5-position of DNA cytosine on the vertebrate genomes is accomplished by the
AB  - combined catalytic actions of three DNA
AB  - methyltransferases (DNMTs), the de novo enzymes DNMT3A and DNMT3B and
AB  - the maintenance enzyme DNMT1. Although several metabolic routes have
AB  - been suggested for demethylation of the vertebrate DNA, whether active
AB  - DNA demethylase(s) exist has remained elusive. Surprisingly, we have
AB  - found that the mammalian DNMTs, and likely the vertebrates DNMTs in
AB  - general, can also act as Ca2+ ion- and redox state-dependent active DNA
AB  - demethylases. This finding suggests new directions for reinvestigation
AB  - of the structures and functions of these DNMTs, in particular their
AB  - roles in Ca2+ ion-dependent biological processes, including the
AB  - genome-wide/local DNA demethylation during early embryogenesis, cell
AB  - differentiation, neuronal activity-regulated gene expression, and
AB  - carcinogenesis.
ER  -

TY  - JOUR
AU  - Chen, C.C.
AU  - Wang, K.Y.
AU  - Shen, C.K.J.
TI  - The Mammalian de Novo DNA Methyltransferases DNMT3A and DNMT3B Are Also DNA 5-Hydroxymethylcytosine Dehydroxymethylases.
JO  - J. Biol. Chem.
PY  - 2012
SP  - 33116
EP  - 33121
VL  - 287
AB  - For cytosine (C) demethylation of vertebrate DNA, it is known that the TET proteins could
AB  - convert 5-methyl C (5-mC) to 5-hydroxymethyl C
AB  - (5-hmC). However, DNA dehydroxymethylase(s), or enzymes able to
AB  - directly convert 5-hmC to C, have been elusive. We present in vitro
AB  - evidence that the mammalian de novo DNA methyltransferases DNMT3A and
AB  - DNMT3B, but not the maintenance enzyme DNMT1, are also redox-dependent
AB  - DNA dehydroxymethylases. Significantly, intactness of the C methylation
AB  - catalytic sites of these de novo enzymes is also required for their
AB  - 5-hmC dehydroxymethylation activity. That DNMT3A and DNMT3B function
AB  - bidirectionally both as DNA methyltransferases and as
AB  - dehydroxymethylases raises intriguing and new questions regarding the
AB  - structural and functional aspects of these enzymes and their regulatory
AB  - roles in the dynamic modifications of the vertebrate genomes during
AB  - development, carcinogenesis, and gene regulation.
ER  -

TY  - JOUR
AU  - Chen, C.J.
AU  - Unger, C.
AU  - Hoffmann, W.
AU  - Lindsay, J.A.
AU  - Huang, Y.C.
AU  - Gotz, F.
TI  - Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage.
JO  - PLoS ONE
PY  - 2013
SP  - E63210
EP  - E63210
VL  - 8
AB  - Sequence type (ST) 59 is an epidemic lineage of community-associated (CA)
AB  - methicillin-resistant Staphylococcus aureus (MRSA) isolates. Taiwanese CA-MRSA
AB  - isolates belong to ST59 and can be grouped into 2 distinct clones, a virulent
AB  - Taiwan clone and a commensal Asian-Pacific clone. The Taiwan clone carries the
AB  - Panton-Valentine leukocidin (PVL) genes and the staphylococcal chromosomal
AB  - cassette mec (SCCmec) VT, and is frequently isolated from patients with severe
AB  - disease. The Asian-Pacific clone is PVL-negative, carries SCCmec IV, and a
AB  - frequent colonizer of healthy children. Isolates of both clones were
AB  - characterized by their ability to adhere to respiratory A549 cells, cytotoxicity
AB  - to human neutrophils, and nasal colonization of a murine and murine sepsis
AB  - models. Genome variation was determined by polymerase chain reaction of selected
AB  - virulence factors and by multi-strain whole genome microarray. Additionally, the
AB  - expression of selected factors was compared between the 2 clones. The Taiwan
AB  - clone showed a much higher cytotoxicity to the human neutrophils and caused more
AB  - severe septic infections with a high mortality rate in the murine model. The
AB  - clones were indistinguishable in their adhesion to A549 cells and persistence of
AB  - murine nasal colonization. The microarray data revealed that the Taiwan clone had
AB  - lost the o3-prophage that integrates into the beta-hemolysin gene and includes
AB  - staphylokinase- and enterotoxin P-encoding genes, but had retained the genes for
AB  - human immune evasion, scn and chps. Production of the virulence factors did not
AB  - differ significantly in the 2 clonal groups, although more alpha-toxin was
AB  - expressed in Taiwan clone isolates from pneumonia patients. In conclusion, the
AB  - Taiwan CA-MRSA clone was distinguished by enhanced virulence in both humans and
AB  - an animal infection model. The evolutionary acquisition of PVL, the higher
AB  - expression of alpha-toxin, and possibly the loss of a large portion of the
AB  - beta-hemolysin-converting prophage likely contribute to its higher pathogenic
AB  - potential than the Asian-Pacific clone.
ER  -

TY  - JOUR
AU  - Chen, C.J.
AU  - Wu, T.L.
AU  - Lu, P.L.
AU  - Chen, Y.T.
AU  - Fung, C.P.
AU  - Chuang, Y.C.
AU  - Lin, J.C.
AU  - Siu, L.K.
TI  - Closely Related NDM-1-Encoding Plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.
JO  - PLoS ONE
PY  - 2014
SP  - E104899
EP  - E104899
VL  - 9
AB  - OBJECTIVE: Two plasmids carrying blaNDM-1 isolated from carbapenem-resistant
AB  - Klebsiella pneumoniae (CR-KP) and carbapenem-resistant Escherichia coli (CR-EC)
AB  - were sequenced. CR-KP and CR-EC were isolated from two Taiwanese patients without
AB  - travel histories. METHODS: Complete sequencing of the plasmids (pLK75 and pLK78)
AB  - was conducted using a shotgun approach. Annotation of the contigs was performed
AB  - using the RAST Server, followed by manual inspection and correction. RESULTS:
AB  - These similar plasmids were obtained from two patients with overlapping stays at
AB  - the same hospital. The pLK75 and pLK78 plasmids were 56,489-bp and 56,072-bp in
AB  - length, respectively. Plasmid annotation revealed a common backbone similar to
AB  - the IncN plasmid pR46. The regions flanking the blaNDM-1 genes in these plasmids
AB  - were very similar to plasmid pNDM-HU01 in Japan, which contains a complex class 1
AB  - integron located next to an ISCR1 element. The ISCR1 element has been suggested
AB  - to provide a powerful mechanism for mobilising antibiotic resistance genes.
AB  - CONCLUSION: Two indigenous NDM-1-producing Enterobacteriaceae cases were
AB  - identified for the first time in Taiwan, highlighting the alarming introduction
AB  - of NDM-1-producing Enterobacteriaceae in this region.
ER  -

TY  - JOUR
AU  - Chen, C.Y.
AU  - Wu, K.M.
AU  - Chang, Y.C.
AU  - Chang, C.H.
AU  - Tsai, H.C.
AU  - Liao, T.L.
AU  - Liu, Y.M.
AU  - Chen, H.J.
AU  - Shen, A.B.
AU  - Li, J.C.
AU  - Su, T.L.
AU  - Shao, C.P.
AU  - Lee, C.T.
AU  - Hor, L.I.
AU  - Tsai, S.F.
TI  - Comparative genome analysis of Vibrio vulnificus, a marine pathogen.
JO  - Genome Res.
PY  - 2003
SP  - 2577
EP  - 2587
VL  - 13
AB  - The halophile Vibrio vulnificus is an etiologic agent of human mortality from seafood-borne
AB  - infections. We applied whole-genome sequencing and
AB  - comparative analysis to investigate the evolution of this pathogen. The
AB  - genome of biotype 1 strain, V. vulnificus YJ016, was sequenced and
AB  - includes two chromosomes of estimated 3377 kbp and 1857 kbp in size, and a
AB  - plasmid of 48,508 bp. A super-integron (SI) was identified, and the SI
AB  - region spans 139 kbp and contains 188 gene cassettes. In contrast to
AB  - non-SI sequences, the captured gene cassettes are unique for any given
AB  - Vibrio species and are highly variable among V. vulnificus strains.
AB  - Multiple rearrangements were found when comparing the 5.3-Mbp V.
AB  - vulnificus YJ016 genome and the 4.0-Mbp V. cholerae El Tor N16961 genome.
AB  - The organization of gene clusters of capsular polysaccharide, iron
AB  - metabolism, and RTX toxin showed distinct genetic features of V.
AB  - vulnificus and V. cholerae. The content of the V. vulnificus genome
AB  - contained gene duplications and evidence of horizontal transfer, allowing
AB  - for genetic diversity and function in the marine environment. The genomic
AB  - information obtained in this study can be applied to monitoring vibrio
AB  - infections and identifying virulence genes in V. vulnificus.
ER  -

TY  - JOUR
AU  - Chen, D.
TI  - Chemical modification of restriction endonuclease Bsp63I and its substrate.
JO  - Hunan Jiaoyu Xueyuan Xuebao
PY  - 1997
SP  - 91
EP  - 94
VL  - 15
AB  - This paper reports on a study of the chemical modification of Bsp63I and its substrate by
AB  - using group modification reagents.  The results show that the sulfhydryl group and the lysine
AB  - residue are possibly the necessary group in the active center of Bsp63I.  The base sequence of
AB  - d(GC), which is in the recognition sequence of Bsp63I, plays an important role in the
AB  - catalysis of Bsp63I.
ER  -

TY  - JOUR
AU  - Chen, D.
AU  - Liu, B.
AU  - Zhu, Y.
AU  - Wang, J.
AU  - Chen, Z.
AU  - Che, J.
AU  - Zheng, X.
AU  - Chen, X.
TI  - Complete Genome Sequence of Ralstonia solanacearum FJAT-1458, a Potential Biocontrol Agent for Tomato Wilt.
JO  - Genome Announcements
PY  - 2017
SP  - e00070
EP  - e00017
VL  - 5
AB  - An avirulent strain of Ralstonia solanacearum FJAT-1458 was isolated from a living tomato.
AB  - Here, we report the complete R. solanacearum FJAT-1458 genome
AB  - sequence of 6,059,899 bp and 5,241 genes. This bacterial strain is a potential
AB  - candidate as a biocontrol agent in the form of a plant vaccine for bacterial
AB  - wilt.
ER  -

TY  - JOUR
AU  - Chen, D.
AU  - Liu, B.
AU  - Zhu, Y.
AU  - Zhang, H.
AU  - Chen, Z.
AU  - Zheng, X.
AU  - Xiao, R.
AU  - Chen, Y.
TI  - Complete Genome Sequence of Ralstonia solanacearum FJAT-91, a High-Virulence Pathogen of Tomato Wilt.
JO  - Genome Announcements
PY  - 2017
SP  - e00900
EP  - e00917
VL  - 5
AB  - Ralstonia solanacearum FJAT-91, which displays higher virulence toward plants belonging to the
AB  - family Solanaceae, was isolated from a wilted tomato plant
AB  - vessel in Fujian province, southeast China. Here, we report the complete genome
AB  - sequence of R. solanacearum FJAT-91 using long-read single-molecule PacBio
AB  - sequencing technology. The genome comprises a 3,873,214-bp circular chromosome
AB  - and a 2,000,873-bp circular megaplasmid with an overall G+C content of 66.85%.
ER  -

TY  - JOUR
AU  - Chen, D.
AU  - Liu, Q.
AU  - Chen, X.
AU  - Zhao, X.
AU  - Chen, Y.
TI  - The inhibition of restriction endonuclease PvuII cleavage activity by methylation outside its recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 5703
EP  - 5705
VL  - 19
AB  - The recombinant plasmid pGEM4Z-ras DNA which was methylated on dam and dcm sites outside the
AB  - PvuII recognition sequence was digested with restriction endonuclease PvuII, and one of the
AB  - three PvuII sites was about 16-fold less efficient to cleave than either of the other two. On
AB  - the contrary, the three PvuII sites were cleaved at about the same rate on the unmethylated
AB  - DNA molecule. The results show that the cleavage inhibition of the methylated DNA on the
AB  - certain PvuII site was caused by methylation outside the PvuII recognition sequence. Maybe an
AB  - adjacent methylated dam site *A was responsible for the less efficient cleavage. This
AB  - observation suggests that methylation outside the recognition sequence may be considered a new
AB  - factor in the kinetic experiment of restriction endonuclease.
ER  -

TY  - JOUR
AU  - Chen, D.
AU  - Sun, M.
AU  - Liu, Y.
AU  - Shi, G.
AU  - Chen, Y.
TI  - Molecular mechanism of the inhibitory effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage activity.
JO  - Chinese Sci. Bull.
PY  - 1998
SP  - 47
EP  - 53
VL  - 43
AB  - In 1991, we found that methylation outside the PvuII recognition sequence could partially
AB  - inhibit its cleavage activity.  To clarify the molecular mechanism, three plasmids with
AB  - different methylation states were constructed.  Then, together with the original one, four
AB  - plasmids were digested with different amounts of PvuII.  Results show that methylation on both
AB  - sites results in 90% inhibition; moving the methylated site one base further away decreases
AB  - the inhibitory effect to about 30%; with the adjacent dam methylation site eliminated, the
AB  - inhibitory effect disappears.  The data suggest that the inhibition of cleavage activity
AB  - caused by outside methylation is not "all or none", and the degree of inhibition is dependent
AB  - on the position and the number of methylated bases.
ER  -

TY  - JOUR
AU  - Chen, F.
AU  - Wang, H.
AU  - Cao, Y.
AU  - Li, X.
AU  - Wang, G.
TI  - High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 59
EP  - 59
VL  - 10
AB  - Arenimonas donghaensis is the type species of genus Arenimonas which belongs to family
AB  - Xanthomonadaceae within Gammaproteobacteria. In this study, a total of five type strains of
AB  - Arenimonas were sequenced. The draft genomic information of  A. donghaensis DSM 18148(T) is
AB  - described and compared with other four genomes of  Arenimonas. The genome size of A.
AB  - donghaensis DSM 18148(T) is 2,977,056 bp distributed in 51 contigs, containing 2685
AB  - protein-coding genes and 49 RNA genes.
ER  -

TY  - JOUR
AU  - Chen, F.
AU  - Yang, Z.
AU  - Yan, M.
AU  - Alvarado, J.B.
AU  - Wang, G.
AU  - Benner, S.A.
TI  - Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 3949
EP  - 3961
VL  - 39
AB  - To explore the possibility of using restriction enzymes in a synthetic biology based on
AB  - artificially expanded genetic information systems
AB  - (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to
AB  - digest DNA duplexes containing recognition sites where individual Cs and
AB  - Gs were replaced by the AEGIS nucleotides Z and P [respectively,
AB  - 6-amino-5-nitro-3-(1'-beta-d-2'-deoxyribofuranosyl)-2(1H)-pyridone and
AB  - 2-amino-8-(1'-beta-d-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4
AB  - (8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond
AB  - donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed
AB  - us to classify type-II REases into five groups based on their performance,
AB  - and to infer some specifics of their interactions with functional groups
AB  - in the major and minor grooves of the target DNA. For three enzymes among
AB  - these 24 where crystal structures are available (BcnI, EcoO109I and NotI),
AB  - these interactions were modeled. Further, we applied a type-II REase to
AB  - quantitate the fidelity polymerases challenged to maintain in a DNA duplex
AB  - C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds
AB  - tools that are able to manipulate this expanded genetic alphabet in vitro,
AB  - provides some structural insights into the working of restriction enzymes,
AB  - and offers some preliminary data needed to take the next step in synthetic
AB  - biology to use an artificial genetic system inside of living bacterial
AB  - cells.
ER  -

TY  - JOUR
AU  - Chen, F.J.
AU  - Lauderdale, T.L.
AU  - Wang, L.S.
AU  - Huang, I.W.
TI  - Complete Genome Sequence of Staphylococcus aureus Z172, a Vancomycin-Intermediate and Daptomycin-Nonsusceptible Methicillin-Resistant Strain Isolated in Taiwan.
JO  - Genome Announcements
PY  - 2013
SP  - e01011
EP  - e01013
VL  - 1
AB  - We report the complete genome sequence of Z172, a representative strain of sequence type
AB  - 239-staphylococcal cassette chromosome mec type III (ST239-SCCmec
AB  - type III) hospital-associated methicillin-resistant Staphylococcus aureus in
AB  - Taiwan. Strain Z172 also exhibits a vancomycin-intermediate and
AB  - daptomycin-nonsusceptible phenotype.
ER  -

TY  - JOUR
AU  - Chen, G.
AU  - Murdoch, R.W.
AU  - Mack, E.E.
AU  - Seger, E.S.
AU  - Loffler, F.E.
TI  - Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00897
EP  - e00817
VL  - 5
AB  - Dehalobacterium formicoaceticum utilizes dichloromethane as the sole energy source in defined
AB  - anoxic bicarbonate-buffered mineral salt medium. The products
AB  - are formate, acetate, inorganic chloride, and biomass. The bacterium's genome was
AB  - sequenced using PacBio, assembled, and annotated. The complete genome consists of
AB  - one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Chen, G.C.C.
AU  - Brown, A.
AU  - Lema, M.W.
TI  - Restriction endonuclease activities in the legionellae.
JO  - Can. J. Microbiol.
PY  - 1986
SP  - 591
EP  - 593
VL  - 32
AB  - Studies of the restriction-modification system of bacteria led to the discovery
AB  - of a number of endonucleases which recognize and cleave specific DNA base
AB  - sequences.  These recognition sequences often consist of short palindromes and,
AB  - in a number of instances, several different enzymes have been found with the
AB  - same site specificity (isochizomers).  Because of their specificity,
AB  - restriction endonucleases have been useful for the construction of recombinant
AB  - DNA molecules and for DNA sequencing.  This system for detecting and destroying
AB  - "foreign" DNA is found in such taxonomically diverse organisms as
AB  - Acinetobacter, Nocardia, Nostoc, and Thermoplasma.  It is, therefore, not
AB  - surprising to find restriction endonucleases in new groups of organisms as they
AB  - are studied.  Because of differences in the recipient ability of several
AB  - legionellae (Chen et al. 1984), we examined these strains for the presence of
AB  - these enzymes.  We now report that several different restriction activities are
AB  - present in various legionellae strains.
ER  -

TY  - JOUR
AU  - Chen, H.
AU  - Brinkac, L.M.
AU  - Mishra, P.
AU  - Li, N.
AU  - Lymperopoulou, D.S.
AU  - Dickerson, T.L.
AU  - Gordon-Bradley, N.
AU  - Williams, H.N.
AU  - Badger, J.H.
TI  - Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 11
EP  - 11
VL  - 10
AB  - Bacteriovorax is the halophilic genus of the obligate bacterial predators, Bdellovibrio and
AB  - like organisms. The predators are known for their unique
AB  - biphasic life style in which they search for and attack their prey in the free
AB  - living phase; penetrate, grow, multiply and lyse the prey in the intraperiplasmic
AB  - phase. Bacteriovorax isolates representing four phylogenetic clusters were
AB  - selected for genomic sequencing. Only one type strain genome has been published
AB  - so far from the genus Bacteriovorax. We report the genomes from non-type strains
AB  - isolated from aquatic environments. Here we describe and compare the genomic
AB  - features of the four strains, together with the classification and annotation.
ER  -

TY  - JOUR
AU  - Chen, H.-P.
AU  - Zhu, S.-H.
AU  - Casabon, I.
AU  - Hallam, S.J.
AU  - Crocker, F.H.
AU  - Mohn, W.W.
AU  - Indest, K.J.
AU  - Eltis, L.D.
TI  - Genomic and Transcriptomic Studies of an RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine)-Degrading Actinobacterium.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 7798
EP  - 7800
VL  - 78
AB  - Whole genome sequencing, transcriptomic analyses and metabolic reconstruction were used to
AB  - investigate Gordonia sp. KTR9s ability to catabolize a range of compounds including explosives
AB  - and steroids. Aspects of this mycolic acid-containing actinobacteriums catabolic potential
AB  - were experimentally verified and compared with those of rhodococci and mycobacteria.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Fang, Q.
TI  - Whole-Genome Sequencing Analysis of Methicillin-Resistant Staphylococcus simulans Causing Surgical Site Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e00555
EP  - e00516
VL  - 4
AB  - Staphylococcus simulans is a normal part of the microbiota in humans and animals  and is
AB  - rarely associated with human invasive infections. We present here the
AB  - genome sequence of S. simulans CJ16, which caused the first case of surgical site
AB  - infection. Adhesion proteins, including fibronectin-binding protein (FnbA),
AB  - elastin-binding protein (EbpS), and cell wall-anchored protein (SasA, SasF, and
AB  - SasH), were detected in the genome, which might promote the survival of S.
AB  - simulans on human skin and pathogenesis of infections.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Herzenberg, L.A.
AU  - Herzenberg, L.A.
TI  - Heparin inhibits EcoRI endonuclease cleavage of DNA at certain EcoRI sites.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3255
EP  - 3255
VL  - 18
AB  - Studies presented here demonstrate that heparin inhibits EcoRI endonuclease
AB  - cleavage of DNA whereas related proteoglycans show no effect.  The inhibition
AB  - occurs at particular EcoRI sites that are near or overlap with palindromic
AB  - sequences in the murine lambda5 and Lyt-2 genes.  Endogenous heparin from
AB  - peritoneal mast cells co-isolates with DNA and inhibits digestion of peritoneal
AB  - cell DNA at the inhibitable sites.  Digestion of spleen DNA is inhibited at the
AB  - same sites when commerical heparin is added prior to digestion.  In both cases,
AB  - the inhibition is abolished by pre-treating the DNA with heparinase.  Thus,
AB  - potential artifacts in restriction fragment length analyses could occur with
AB  - DNA isolated either from cells that are naturally rich in heparin or from cells
AB  - to which heparin has been added, e.g., as an anticoagulant.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Huang, H.
AU  - Chang, C.J.
AU  - Stenger, D.C.
TI  - Draft Genome Sequence of Xylella fastidiosa subsp. multiplex Strain Griffin-1 from Quercus rubra in Georgia.
JO  - Genome Announcements
PY  - 2013
SP  - e00756
EP  - e00713
VL  - 1
AB  - The draft genome sequence of Xylella fastidiosa subsp. multiplex strain Griffin-1, isolated
AB  - from a red oak tree (Quercus rubra) in Georgia, is reported
AB  - here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of
AB  - 51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames
AB  - and 50 RNA genes.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Li, Y.
AU  - Zhang, K.
AU  - Wang, H.
TI  - Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5alpha.
JO  - Genome Announcements
PY  - 2018
SP  - e00097
EP  - e00018
VL  - 6
AB  - The genomes of many strains of Escherichia coli have been sequenced, as this organism is a
AB  - classic model bacterium. Here, we report the genome sequence of
AB  - Escherichia coli DH5alpha, which is resistant to a T4 bacteriophage (CCTCC AB
AB  - 2015375), while its other homologous E. coli strains, such as E. coli BL21,
AB  - DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of
AB  - the genome of the DH5alpha strain, along with comparative analysis of its genome
AB  - sequence along with other sequences of E. coli strains, may help to reveal the
AB  - bacteriophage resistance mechanism of E. coli.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Wang, X.
AU  - Zhu, S.
AU  - Chen, Y.
AU  - Yang, J.
TI  - Complete Genome Sequence of Alteromonas stellipolaris LMG 21856, a Budding Brown  Pigment-Producing Oligotrophic Bacterium Isolated from the Southern Ocean.
JO  - Genome Announcements
PY  - 2016
SP  - e00137
EP  - e00116
VL  - 4
AB  - Here, we report the complete genome sequence ofAlteromonas stellipolarisLMG 21856, which was
AB  - isolated from seawater collected from the Southern Ocean.A.
AB  - stellipolarisLMG 21856 is a budding, psychrotrophic, brown pigment-producing, and
AB  - oligotrophic bacterium.The complete genome of this bacterium contains 4,686,200
AB  - bp, with a G+C content of 43.6%.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Wu, F.
AU  - Zheng, Z.
AU  - Deng, X.
AU  - Burbank, L.P.
AU  - Stenger, D.C.
TI  - Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag's Leap.
JO  - Genome Announcements
PY  - 2016
SP  - e00240
EP  - e00216
VL  - 4
AB  - ITALIC! Xylella fastidiosasubsp. ITALIC! fastidiosacauses Pierce's disease of grapevine.
AB  - Presented here is the draft genome sequence of the Stag's Leap strain,
AB  - previously used in pathogenicity/virulence assays to evaluate grapevine germplasm
AB  - bearing Pierce's disease resistance and a phenotypic assessment of knockout
AB  - mutants to determine gene function.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Xia, Y.
AU  - Cheng, C.
AU  - Fang, C.
AU  - Shan, Y.
AU  - Jin, G.
AU  - Fang, W.
TI  - Genome sequence of a non-pathogenic Listeria monocytogenes serovar 4a strain M7.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5019
EP  - 5020
VL  - 193
AB  - This report presents the complete and annotated genome sequence of a naturally non-pathogenic
AB  - Listeria monocytogenes serovar 4a strain M7, isolated from cow's milk in Zhejiang province,
AB  - China.
ER  -

TY  - JOUR
AU  - Chen, J.
AU  - Xie, G.
AU  - Han, S.
AU  - Civerolo, E.L.
TI  - Two whole genome sequences of Xylella fastidiosa (strains M12 and M23) causing almond leaf scorch disease in California.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4534
EP  - 4534
VL  - 192
AB  - Xylella fastidiosa is a Gram negative plant pathogenic bacterium causing many economically
AB  - important diseases including almond leaf scorch disease
AB  - (ALSD) in California. Genome information greatly facilitates research in
AB  - this nutritionally fastidious organism. Here we report the complete genome
AB  - sequences of two ALSD strains, M12 and M23 of this bacterium.
ER  -

TY  - JOUR
AU  - Chen, J.H.
AU  - Zhang, J.
AU  - Yang, H.H.
AU  - Fu, F.F.
AU  - Chen, G.N.
TI  - A strategy for development of electrochemical DNA biosensor based on site-specific DNA cleavage of restriction endonuclease.
JO  - Biosensors and Bioelectronics
PY  - 2010
SP  - 144
EP  - 148
VL  - 26
AB  - A new strategy for development of electrochemical DNA biosensor based on site-specific DNA
AB  - cleavage of restriction endonuclease and using
AB  - quantum dots as reporter was reported in this paper The biosensor was
AB  - fabricated by immobilizing a capture hairpin probe, thiolated single
AB  - strand DNA labeled with biotin group, on a gold electrode BfuCl
AB  - nuclease, which is able to specifically cleave only double strand DNA
AB  - but not single strand DNA, was used to reduce background current and
AB  - Improve the sensitivity We demonstrated that the capture hairpin probe
AB  - can be cleaved by BfuCl nuclease in the absence of target DNA, but
AB  - cannot be cleaved in the presence of target DNA. The difference before
AB  - and after enzymatic cleavage was then monitored by electrochemical
AB  - method after the quantum dots were dissolved from the hybrids Our
AB  - results suggested that the usage of BfuCl nuclease obviously Improved
AB  - the sensitivity and selectivity of the biosensor. We successfully
AB  - applied this method to the sequence-selective discrimination between
AB  - perfectly matched and mismatched target DNA including a single-base
AB  - mismatched target DNA, and detected as low as 3 3 x 10(-14) M of
AB  - complementary target DNA Furthermore, our above strategy was also
AB  - verified with fluorescent method by designing a fluorescent molecular
AB  - beacon (MB), which combined the capture hairpin probe and a pair of
AB  - fluorophore (TAMRA) and quencher (DABCYL) The fluorescent results are
AB  - consistent with that of electroanalysis, further indicating that the
AB  - proposed new strategy indeed works as we expected.
ER  -

TY  - JOUR
AU  - Chen, J.W.
AU  - Chan, K.G.
TI  - Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones, Isolated from Malaysian Tropical Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6331
EP  - 6331
VL  - 194
AB  - Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows
AB  - N-acylhomoserine lactone-degrading activity. Here, we present its draft
AB  - genome sequence. A putative quorum-quenching gene was identified based on the
AB  - genome sequence analysis of strain A8. To the best of our knowledge, this is the
AB  - first genome announcement of a member from the genus of Dyella, and this is also
AB  - the first work that reports the quorum-quenching activity of Dyella japonica.
ER  -

TY  - JOUR
AU  - Chen, J.W.
AU  - Gan, H.M.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Genome Sequence of Roseomonas sp. Strain B5, a Quorum-Quenching N-Acylhomoserine  Lactone-Degrading Bacterium Isolated from Malaysian Tropical Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6681
EP  - 6682
VL  - 194
AB  - Roseomonas sp. strain B5 was isolated from Malaysian tropical soil that showed
AB  - N-acylhomoserine lactone degradation. This is the first genome announcement of a
AB  - member from the genus of Roseomonas and the first report on the quorum-quenching
AB  - activity of Roseomonas spp.
ER  -

TY  - JOUR
AU  - Chen, K.
AU  - Reuter, M.
AU  - Sanghvi, B.
AU  - Roberts, G.A.
AU  - Cooper, L.P.
AU  - Tilling, M.
AU  - Blakely, G.W.
AU  - Dryden, D.T.F.
TI  - ArdA proteins from different mobile genetic elements can bind to the EcoKI Type I DNA methyltransferase of E. coli K12.
JO  - Biochim. Biophys. Acta
PY  - 2014
SP  - 505
EP  - 511
VL  - 1844
AB  - Anti-restriction and anti-modification (anti-RM) is the ability to prevent cleavage by DNA
AB  - restriction-modification (RM) systems of foreign DNA entering a new bacterial host. The
AB  - evolutionary consequence of anti-RM is the enhanced dissemination of mobile genetic elements.
AB  - Homologues of ArdA anti-RM proteins are encoded by genes present in many mobile genetic
AB  - elements such as conjugative plasmids and transposons within bacterial genomes. The ArdA
AB  - proteins cause anti-RM by mimicking the DNA structure bound by Type I RM enzymes. We have
AB  - investigated ArdA proteins from the genomes of Enterococcus faecalis V583, Staphylococcus
AB  - aureus Mu50 and Bacteroides fragilis NCTC 9343, and compared them to the ArdA protein
AB  - expressed by the conjugative transposon Tn916. We find that despite having very different
AB  - structural stability and secondary structure content, they can all bind to the EcoKI
AB  - methyltransferase, a core component of the EcoKI Type I RM system. This finding indicates that
AB  - the less structured ArdA proteins become fully folded upon binding. The ability of ArdA from
AB  - diverse mobile elements to inhibit Type I RM systems from other bacteria suggests that they
AB  - are an advantage for transfer not only between closely-related bacteria but also between more
AB  - distantly related bacterial species.
ER  -

TY  - JOUR
AU  - Chen, K.
AU  - Roberts, G.A.
AU  - Stephanou, A.S.
AU  - Cooper, L.P.
AU  - White, J.H.
AU  - Dryden, D.T.F.
TI  - Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2010
SP  - 254
EP  - 259
VL  - 398
AB  - We describe the fusion of enhanced green fluorescent protein to the C-terminus of the HsdS DNA
AB  - sequence-specificity subunit of the Type I
AB  - DNA modification methyltransferase M.EcoKI. The fusion expresses well
AB  - in vivo and assembles with the two HsdM modification subunits. The
AB  - fusion protein functions as a sequence-specific DNA methyltransferase
AB  - protecting DNA against digestion by the EcoKI restriction endonuclease.
AB  - The purified enzyme shows Forster resonance energy transfer to
AB  - fluorescently-labelled DNA duplexes containing the target sequence and
AB  - to fluorescently-labelled ocr protein, a DNA mimic that binds to the
AB  - M.EcoKI enzyme. Distances determined from the energy transfer
AB  - experiments corroborate the structural model of M.EcoKI.
ER  -

TY  - JOUR
AU  - Chen, K.
AU  - Stephanou, A.S.
AU  - Roberts, G.A.
AU  - White, J.H.
AU  - Cooper, L.P.
AU  - Houston, P.J.
AU  - Lindsay, J.A.
AU  - Dryden, D.T.
TI  - The Type I Restriction Enzymes as Barriers to Horizontal Gene Transfer: Determination of the DNA Target Sequences Recognised by Livestock-Associated  Methicillin-Resistant Staphylococcus aureus Clonal Complexes 133/ST771 and 398.
JO  - Adv. Exp. Med. Biol.
PY  - 2016
SP  - 81
EP  - 97
VL  - 915
AB  - The Type I DNA restriction-modification (RM) systems of Staphylococcus aureus are known to act
AB  - as a significant barrier to horizontal gene transfer between S.
AB  - aureus strains belonging to different clonal complexes. The livestock-associated
AB  - clonal complexes CC133/771 and CC398 contain Type I RM systems not found in human
AB  - MRSA strains as yet but at some point transfer will occur. When this does take
AB  - place, horizontal gene transfer of resistance will happen more easily between
AB  - these strains. The reservoir of antibiotic resistance, virulence and
AB  - host-adaptation genes present in livestock-associated MRSA will then potentially
AB  - contribute to the development of newly evolving MRSA clones. The target sites
AB  - recognised by the Type I RM systems of CC133/771 and CC398 were identified as
AB  - CAG(N)5RTGA and ACC(N)5RTGA, respectively. Assuming that these enzymes recognise
AB  - the methylation state of adenine, the underlined A and T bases indicate the
AB  - unique positions of methylation. Target methylation points for enzymes from CC1
AB  - were also identified. The methylation points for CC1-1 are CCAY(N)5TTAA and those
AB  - for CC1-2 are CCAY(N)6 TGT with the underline indicating the adenine methylation
AB  - site thus clearing up the ambiguity noted previously (Roberts et al. 2013,
AB  - Nucleic Acids Res 41:7472-7484) for the half sites containing two adenine bases.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Brugger, K.
AU  - Skovgaard, M.
AU  - Redder, P.
AU  - She, Q.
AU  - Torarinsson, E.
AU  - Greve, B.
AU  - Awayez, M.
AU  - Zibat, A.
AU  - Klenk, H.-P.
AU  - Garrett, R.A.
TI  - The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota.
JO  - J. Bacteriol.
PY  - 2005
SP  - 4992
EP  - 4999
VL  - 187
AB  - Sulfolobus acidocaldarius is an aerobic thermoacidophilic crenarchaeon which grows optimally
AB  - at 80 degrees C and pH 2 in terrestrial solfataric springs.  Here, we describe the genome
AB  - sequence of strain DSM639, which has been used for many seminal studies on archaeal and
AB  - crenarchaeal biology.  The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted
AB  - protein-encoding genes.  Many of the smaller genes were identified for the first time on the
AB  - basis of comparison of three Sulfolobus genome sequences.  Of the protein-coding genes, 305
AB  - are exclusive to S.  acidocaldarius and 866 are specific to the Sulfolobus genus.  Moreover,
AB  - 82 genes for untranslated RNAs were identified and annotated.  Owing to the probable absence
AB  - of active autonomous and nonautonomous mobile elements, the genome stability and organization
AB  - of S.  acidocaldarius differ radically from those of Sulfolobus solfataricus and Sulfolobus
AB  - tokodaii.  The S.  acidocaldarius genome contains an integrated, and probably encaptured,
AB  - pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in
AB  - S.  acidocaldarius.  Moreover, it contains genes for a characteristic restriction modification
AB  - system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all
AB  - of which are absent from genomes of other Sulfolobus species.  However, it lacks genes for
AB  - some of their sugar transporters, consistent with it growing on a more limited range of carbon
AB  - sources.  These results, together with the many newly identified protein-coding genes for
AB  - Sulfolobus, are incorporated into a public Sulfolobus database which can be accessed at
AB  - http://dac.molbio.ku.dk/dbs/Sulfolobus.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Chavda, K.D.
AU  - DeLeo, F.R.
AU  - Bryant, K.A.
AU  - Jacobs, M.R.
AU  - Bonomo, R.A.
AU  - Kreiswirth, B.N.
TI  - Genome Sequence of a Klebsiella pneumoniae Sequence Type 258 Isolate with Prophage-Encoded K. pneumoniae Carbapenemase.
JO  - Genome Announcements
PY  - 2015
SP  - e00659
EP  - e00615
VL  - 3
AB  - We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase (KPC)-producing
AB  - sequence type 258 (ST258) K. pneumoniae strain, ST258_FL.
AB  - Uniquely, strain ST258_FL harbors two copies of the blaKPC gene on the
AB  - chromosome, one of which is integrated into a prophage.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Chavda, K.D.
AU  - Fraimow, H.S.
AU  - Mediavilla, J.R.
AU  - Melano, R.G.
AU  - Jacobs, M.R.
AU  - Bonomo, R.A.
AU  - Kreiswirth, B.N.
TI  - Complete nucleotide sequence of blaKPC-4 and blaKPC-5 harboring IncN and IncX plasmids from Klebsiella pneumoniae strains isolated in New Jersey.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 269
EP  - 276
VL  - 57
AB  - Klebsiella pneumoniae carbapenemase (KPC) producing Enterobacteriaceae have
AB  - emerged as major nosocomial pathogens. bla(KPC), commonly located on Tn4401, is
AB  - found in Gram-negative bacterial strains, with the two most common variants,
AB  - bla(KPC-2) and bla(KPC-3), identified in plasmids with diverse genetic
AB  - backgrounds. In this study, we examined bla(KPC-4) and bla(KPC-5) bearing
AB  - plasmids recovered from two K. pneumoniae strains, isolated from a single New
AB  - Jersey hospital in 2005 and 2006, respectively. IncN plasmid pBK31551 is 84kb in
AB  - length, and harbors bla(KPC-4), bla(TEM-1), qnrB2, aac (3)-Ib, aph(3')-I, qacF,
AB  - qacEDelta1, sul and dfrA14, which confer resistance to ss-lactams, quinolones,
AB  - aminoglycosides, quaternary ammonium compounds and co-trimoxazole. The conserved
AB  - regions within pBK31551 are similar to that of other IncN plasmids. Surprisingly,
AB  - analysis of the Tn4401 sequence revealed a large IS110 and Tn6901carrying element
AB  - (8.3kb) inserted into the istA gene, encoding glyoxalase/bleomycin resistance,
AB  - alcohol dehydrogenase and S-formylglutathione hydrolase. Plasmid pBK31567 is 47kb
AB  - in length, and harbors bla(KPC-5), dfrA5, qacEDelta1 and sul1. pBK31567 belongs
AB  - to a novel IncX subgroup (IncX5), and possesses a highly syntenic plasmid
AB  - backbone like other IncX plasmids; however, sequence similarity at the nucleotide
AB  - level is divergent. The bla(KPC-5) gene is carried on a Tn4401 element, and
AB  - differs from the genetic environment of bla(KPC-5) described in Pseudomonas
AB  - aeruginosa strain P28 from Puerto Rico. This study underscores the genetic
AB  - diversity of multidrug resistant plasmids involved in the spread of bla(KPC)
AB  - genes, and highlights the mobility and plasticity of Tn4401. Comparative genomic
AB  - analysis provides new insights into the evolution and dissemination of KPC
AB  - plasmids belonging to different incompatibility groups.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Chavda, K.D.
AU  - Melano, R.G.
AU  - Hong, T.
AU  - Rojtman, A.D.
AU  - Jacobs, M.R.
AU  - Bonomo, R.A.
AU  - Kreiswirth, B.N.
TI  - Molecular Survey of the Dissemination of Two blaKPC-Harboring IncFIA Plasmids in New Jersey and New York Hospitals.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 2289
EP  - 2294
VL  - 58
AB  - Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains have
AB  - spread worldwide and become a major threat in health care facilities.
AB  - Transmission of blaKPC, the plasmid-borne KPC gene, can be mediated by clonal
AB  - spread and horizontal transfer. Here, we report the complete nucleotide sequences
AB  - of two novel blaKPC-3-harboring IncFIA plasmids, pBK30661 and pBK30683. pBK30661
AB  - is 74 kb in length, with a mosaic plasmid structure; it exhibits homologies to
AB  - several other plasmids but lacks the plasmid transfer operon (tra) and the origin
AB  - of transfer (oriT) that are required for plasmid transfer. pBK30683 is a
AB  - conjugative plasmid with a cointegrated plasmid structure, comprising a 72-kb
AB  - element that highly resembles pBK30661 (>99.9% nucleotide identities) and an
AB  - extra 68-kb element that harbors tra and oriT. A PCR scheme was designed to
AB  - detect the distribution of blaKPC-harboring IncFIA (pBK30661-like and
AB  - pBK30683-like) plasmids in a collection of clinical Enterobacteriaceae isolates
AB  - from 10 hospitals in New Jersey and New York. KPC-harboring IncFIA plasmids were
AB  - found in 20% of 491 K. pneumoniae isolates, and all carried blaKPC-3.
AB  - pBK30661-like plasmids were identified mainly in the epidemic sequence type 258
AB  - (ST258) K. pneumoniae clone, while pBK30683-like plasmids were widely distributed
AB  - in ST258 and other K. pneumoniae sequence types and among non-K. pneumoniae
AB  - Enterobacteriaceae species. This suggests that both clonal spread and horizontal
AB  - plasmid transfer contributed to the dissemination of blaKPC-harboring IncFIA
AB  - plasmids in our area. Further studies are needed to understand the distribution
AB  - of this plasmid group in other health care regions and to decipher the origins of
AB  - pBK30661-like and pBK30683-like plasmids.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Chavda, K.D.
AU  - Melano, R.G.
AU  - Jacobs, M.R.
AU  - Koll, B.
AU  - Hong, T.
AU  - Rojtman, A.D.
AU  - Levi, M.H.
AU  - Bonomo, R.A.
AU  - Kreiswirth, B.N.
TI  - Comparative Genomic Analysis of KPC-Encoding pKpQIL-Like Plasmids and Their Distribution in New Jersey and New York Hospitals.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 2871
EP  - 2877
VL  - 58
AB  - The global spread of Klebsiella pneumoniae carbapenemase (KPC) is predominately
AB  - associated with K. pneumoniae strains genotyped as sequence type 258 (ST258). The
AB  - first ST258-associated plasmid, pKpQIL, was described in Israel in 2006, but its
AB  - history in the northeastern United States remains unknown. Six pKpQIL-like
AB  - plasmids from four K. pneumoniae isolates (three ST258 and one ST234), one
AB  - Escherichia coli isolate, and one Enterobacter aerogenes isolate, collected from
AB  - 2003 to 2010 in New York (NY) and New Jersey (NJ) hospitals, were completely
AB  - sequenced. The sequences and overall sizes of the six plasmids are highly similar
AB  - to those of pKpQIL; the major difference is that five of six NJ/NY strains harbor
AB  - blaKPC-2, while pKpQIL contains blaKPC-3. Moreover, a 26.7-kb fragment was
AB  - inverted in pKpQIL-234 (from ST234 K. pneumoniae), while a 14.5-kb region was
AB  - deleted in pKpQIL-Ec (from ST131 E. coli). PCR screening of 284 other clinical K.
AB  - pneumoniae isolates identified 101 (35.6%) harboring pKpQIL-like plasmids from 9
AB  - of 10 surveyed hospitals, demonstrating the wide dissemination of pKpQIL in this
AB  - region of endemicity. Among the positive isolates, 87.1% were typed as ST258 and
AB  - 88.1% carried blaKPC-2. The finding of pKpQIL-like plasmid in this study from
AB  - strains that predate the initial report of KPC in Israel provides evidence that
AB  - pKpQIL may have originated in the United States. Our findings demonstrate that
AB  - pKpQIL plasmids are both spreading clonally in ST258 strains and spreading
AB  - horizontally to different sequence types and species, further highlighting the
AB  - clinical and public health concerns associated with carbapenem resistance.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Hu, H.
AU  - Chavda, K.D.
AU  - Zhao, S.
AU  - Liu, R.
AU  - Liang, H.
AU  - Zhang, W.
AU  - Wang, X.
AU  - Jacobs, M.R.
AU  - Bonomo, R.A.
AU  - Kreiswirth, B.N.
TI  - Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli ST131 strain in China.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 2422
EP  - 2425
VL  - 58
AB  - We report the nucleotide sequence of a novel blaKPC-2-harboring IncNplasmid,
AB  - pECN580, from a multidrug-resistant Escherichia coli ST131 isolate recovered from
AB  - Beijing, China. pECN580 harbors multiple antimicrobial resistance genes,
AB  - including blaKPC-2, blaCTX-M-3, blaTEM-1, aac(6')-Ib-cr, qnrS1, arr-3 and dfrA14
AB  - that confer beta-lactam, aminoglycoside, quinolone, rifampin and trimethoprim
AB  - resistance. The emergence of blaKPC-2-harboring multidrug-resistant plasmid in
AB  - epidemic E. coli ST131 clone poses a significant potential threat for both
AB  - community and hospital settings.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Lin, J.
AU  - Liu, X.
AU  - Pang, X.
AU  - Lin, H.
AU  - Lin, J.
TI  - Transposition of IS elements induced by electroporation of suicide plasmid in Acidithiobacillus caldus.
JO  - Enzyme Microb. Technol.
PY  - 2013
SP  - 165
EP  - 169
VL  - 53
AB  - Transposition insertional mutagenesis of the insertion sequences (IS elements) was discovered
AB  - for the first time in Acidithiobacillus caldus
AB  - (A. caldus), when A. caldus MTH-04 hsdM (type I
AB  - restriction-modification system M-subunit) mutant was constructed by
AB  - electroporation of a suicide plasmid. The IS element, specifically
AB  - inserting into hsdM gene, was analyzed, identified, and named ISAtc2.
AB  - The transposition frequency of ISAtc2 was ranged from 4% to 7%, and no
AB  - reverse mutation occurred in the mutants after 50 generations of
AB  - proliferation without selective pressure. These results revealed that
AB  - transposition of IS elements on A. caldus chromosome could regulate the
AB  - gene expression and metabolic pathways by gene inactivation, gene loss
AB  - and gene acquisition. Therefore, the transposition of IS elements in A.
AB  - caldus may be an important and unique regulation mechanism for
AB  - adaptation to the living condition.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - MacMillan, A.M.
AU  - Chang, W.
AU  - Ezaz-Nikpay, K.
AU  - Lane, W.S.
AU  - Verdine, G.L.
TI  - Direct identification of the active-site nucleophile in a DNA (Cytosine-5)-methyltransferase.
JO  - Biochemistry
PY  - 1991
SP  - 11018
EP  - 11025
VL  - 30
AB  - The overproduction, purification, and determination of the active-site catalytic nucleophile
AB  - of the DNA (cytosine-5)-methyltransferase (DCMtase) enzyme, M.HaeIII are reported. Incubation
AB  - of purified M.HaeIII with an oligodeoxynucleotide specifically modified with the
AB  - mechanism-based inhibitor 5-fluoro-2'-deoxycytidine [Osterman, D.G., et al. (1988)
AB  - Biochemistry 27,5204-5210], in the presence of the cofactor S-adenosyl-L-methionine (AdoMet),
AB  - resulted in the formation of a covalent DNA-M.HaeIII complex, which was purified to
AB  - homogeneity. Characterization of the intact complex showed it to consist of one molecule of
AB  - the FdC-containing duplex oligonucleotide, one molecule of M.HaeIII, and one methyl group
AB  - derived from AdoMet. Exhaustive proteolysis, reduction, and alkylation fof the DNA-M.HaeIII
AB  - complex led to the isolation of two DNA-bound peptides-one each from treatment with Pronase or
AB  - trypsin-which were subjected to peptide sequencing in order to identify the DNA attachment
AB  - site. Both peptides were derived from the region of M.HaeIII containing a Pro-Cys sequence
AB  - that is conserved in all known DCMtases. At the position of this conserved Cys residue
AB  - (Cys71), in the sequence of each peptide, was found an unidentified amino acid residue; all
AB  - other amino acid residues were in accord with the known sequence. It it thus concluded that
AB  - Cys71 of M.HaeIII forms a covalent bond to DNA during catalytic methyl transfer. This finding
AB  - represents a direct experimental verification for the hypothesis that the conserved Cys
AB  - residue of DCMtases is the catalytic nucleophile [Wu, J.C., & Santi, D.V. (1987) J. Biol.
AB  - Chem. 262,4778-4786]. Furthermore, the present studies provide ready access to large
AB  - quantities of a homogeneous, covalent protein-DNA complex that is trapped at an intermediate
AB  - state in catalysis.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - MacMillan, A.M.
AU  - Verdine, G.L.
TI  - Mutational separation of DNA binding from catalysis in a DNA cytosine methyltransferase.
JO  - J. Am. Chem. Soc.
PY  - 1993
SP  - 5318
EP  - 5319
VL  - 115
AB  - Despite the substantial progress made toward understanding sequence-specific recognition of
AB  - DNA by regulatory proteins, the details of catalysis by DNA-modifying proteins remain poorly
AB  - understood. The inherently transient nature of catalytic protein-DNA complexes presents
AB  - problems for their characterization by X-ray crystallography or NMR spectroscopy. Catalytic
AB  - DNA-binding proteins thus present the challenge of discovering how to stall or subvert the
AB  - catalytic process so as to obtain a stable macromolecular complex. In this communication we
AB  - report the use of site-direced mutagenesis to separate catalysis from DNA binding in a DNA
AB  - (cytosine-5)-methyltransferase (DC-Mtase) enzyme.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Mediavilla, J.R.
AU  - Oliveira, D.C.
AU  - Willey, B.M.
AU  - de Lencastre, H.
AU  - Kreiswirth, B.N.
TI  - Multiplex real-time PCR for rapid Staphylococcal cassette chromosome mec typing.
JO  - J. Clin. Microbiol.
PY  - 2009
SP  - 3692
EP  - 3706
VL  - 47
AB  - Rapid identification and typing of methicillin (meticillin)-resistant
AB  - Staphylococcus aureus (MRSA) is important for understanding the molecular
AB  - epidemiology and evolution of MRSA and offers many advantages for
AB  - controlling transmission in both health care and community settings. We
AB  - developed a rapid molecular beacon real-time PCR (MB-PCR) assay for
AB  - staphylococcal cassette chromosome mec (SCCmec) typing. The design of this
AB  - system is based on the established definition of SCCmec types, namely, the
AB  - combination of the mec class complex with the ccr allotype. The assay
AB  - consists of two multiplex panels, the combination of which results in two
AB  - targets (mec class, ccr) for each SCCmec type. MB-PCR panel I targets
AB  - mecA, ccrB2, mecI, and the DeltamecR1-IS1272 junction (mec class B); it
AB  - can definitively identify SCCmec types II and IV. MB-PCR panel II detects
AB  - ccrC, ccrB1, ccrB3, ccrB4, and the DeltamecR1-IS431 junction (mec class
AB  - C2) and is therefore capable of identifying SCCmec types I, III, V, and VI
AB  - in combination with panel I. The method can also detect the recently
AB  - described novel SCCmec type VIII (ccrAB4 with mec class A). Our assay
AB  - demonstrated 100% concordance when applied to 162 MRSA strains previously
AB  - characterized by traditional SCCmec typing schemes. Four geographically
AB  - and temporally diverse S. aureus collections were also successfully
AB  - classified by our assay, along with 1,683 clinical isolates comprising
AB  - both hospital- and community-associated MRSA and methicillin-susceptible
AB  - S. aureus strains. As many as 96 isolates can be classified easily within
AB  - 3 to 4 h, including DNA isolation, PCR cycling, and analysis. The assay is
AB  - rapid, robust, sensitive, and cost-effective, allowing for high-throughput
AB  - SCCmec typing of MRSA isolates.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Mediavilla, J.R.
AU  - Smyth, D.S.
AU  - Chavda, K.D.
AU  - Ionescu, R.
AU  - Roberts, R.B.
AU  - Robinson, D.A.
AU  - Kreiswirth, B.N.
TI  - Identification of a novel transposon (Tn6072) and a truncated staphylococcal cassette chromosome mec element in methicillin-resistant Staphylococcus aureus ST239.
JO  - Antimicrob. Agents Chemother.
PY  - 2010
SP  - 3347
EP  - 3354
VL  - 54
AB  - A novel composite transposon (Tn6072) resembling staphylococcal cassette
AB  - chromosome mercury (SCCHg) was identified in a collection of sequence type
AB  - (ST) 239 methicillin (meticillin)-resistant Staphylococcus aureus (MRSA)
AB  - isolates from Romanian hospitals. Tn6072 is homologous to the 5' region of
AB  - SCCHg found in staphylococcal cassette chromosome mec (SCCmec) type III
AB  - prototype strain 85/2082 but lacks the characteristic mer operon. SCCHg
AB  - has previously been reported to integrate downstream of orfX, at the same
AB  - chromosomal location as SCCmec. Tn6072, by contrast, is demarcated by two
AB  - IS431 elements, flanked by 8-bp direct repeats, and inserted upstream of
AB  - the origin of replication, within an open reading frame homologous to
AB  - SAR2700 of S. aureus strain MRSA252. Analysis of a geographically and
AB  - temporally diverse collection of 111 strains from the ST239 clonal group
AB  - uncovered 11 additional strains harboring Tn6072, demonstrating a
AB  - lineage-specific insertion pattern. Complete sequence analysis of the
AB  - SCCmec regions of two representative Romanian strains (BK16704, BK16691)
AB  - revealed two additional novel structures derived from a type III SCCmec
AB  - background. BK16704 possesses an SCCmec 3A.1.4 structure, with an IS256
AB  - insertion downstream of the right chromosomal junction. In contrast, the
AB  - SCCmec element of BK16691 is truncated downstream of the mec gene complex,
AB  - with a 24-kb deletion encompassing the right chromosomal junction and an
AB  - inverted downstream IS256 element. This structure, tentatively named
AB  - "psiSCCmec16691," confers methicillin resistance but lacks most of the
AB  - J1/J2 region, including the ccr gene complex. Taken together, these
AB  - findings provide evidence for the continuing evolution of SCC elements, as
AB  - well as the ST239 clonal group.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Paulsen, D.B.
AU  - Scruggs, D.W.
AU  - Banes, M.M.
AU  - Reeks, B.Y.
AU  - Lawrence, M.L.
TI  - Alteration of DNA adenine methylase (Dam) activity in Pasteurella multocida causes increased spontaneous mutation frequency and attenuation in mice.
JO  - Microbiology
PY  - 2003
SP  - 2283
EP  - 2290
VL  - 149
AB  - Pasteurella multocida is one of the primary bacterial pathogens associated with bovine
AB  - respiratory disease (BRD) complex. Relatively few virulence
AB  - factors of P. multocida have been characterized, and there is a need for
AB  - improved vaccines for prevention of BRD. In other Gram-negative species,
AB  - DNA adenine methylase (Dam) regulates the expression of virulence genes,
AB  - and appropriate expression of Dam is required for virulence. In this
AB  - study, the authors cloned and sequenced the P. multocida A1 dam gene and
AB  - demonstrated that it is able to restore Dam function in an Escherichia
AB  - coli dam mutant. When P. multocida dam was placed under the control of a
AB  - constitutively expressed promoter on a plasmid, it caused an increased
AB  - spontaneous mutation rate in P. multocida. In addition, the
AB  - plasmid-mediated alteration of Dam production in P. multocida caused it to
AB  - be highly attenuated in mice. These findings indicate that appropriate
AB  - expression of Dam is required for virulence of P. multocida, which is
AB  - believed to be the first report that Dam is required for virulence of a
AB  - species in the Pasteurellaceae. Therefore, Dam may function as a virulence
AB  - gene regulator in the Pasteurellaceae, similar to previously reported
AB  - findings from other Gram-negative species.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Wu, D.
AU  - Cai, X.
AU  - Guo, F.
AU  - Blackall, P.J.
AU  - Xu, X.
AU  - Chen, H.
TI  - Electrotransformation of Haemophilus parasuis with in vitro modified DNA based on a novel shuttle vector.
JO  - Vet. Microbiol.
PY  - 2012
SP  - 310
EP  - 316
VL  - 155
AB  - The objective of the present study was to establish a valid transformation method of
AB  - Haemophilus parasuis, the causative agent of
AB  - Glasser's disease in pigs, using a novel H. parasuis-Escherichia coli
AB  - shuttle vector. A 4.2 kb endogenous plasmid pYC93 was extracted from an
AB  - H. parasuis field isolate and completely sequenced. Analysis of pYC93
AB  - revealed a region approximately 800 bp showing high homology with the
AB  - defined replication origin oriV of pLS88, a native plasmid identified
AB  - in Haemophilus ducreyi. Based on the origin region of pYC93, E. coli
AB  - cloning vector pBluescript SK(+) and the Tn903 derived kanamycin
AB  - cassette, a shuttle vector pSHK4 was constructed by overlapping PCR
AB  - strategy. When electroporation of the 15 H. parasuis serovar reference
AB  - strains and one clinical isolate SH0165 with pSHK4 was performed, only
AB  - one of these strains yielded transformants with an efficiency of 8.5 x
AB  - 10(2) CFUhlg of DNA. Transformation efficiency was notably increased
AB  - (1.3 x 10(5) CFU/mu g of DNA) with vector DNA reisolated from the
AB  - homologous transformants. This demonstrated that
AB  - restriction-modification systems were involved in the barrier to
AB  - transformation of H. parasuis. By utilizing an in vitro DNA
AB  - modification method with cell-free extracts of the host H. parasuis
AB  - strains, 15 out of 16 strains were transformable. The novel shuttle
AB  - vector pSHK4 and the established electrotransformation method
AB  - constitute useful tools for the genetic manipulation of H. parasuis to
AB  - gain a better understanding of the pathogen.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Zhang, D.T.
AU  - Zhang, J.
AU  - Su, Y.A.
AU  - Zhang, H.
TI  - Whole-Genome Sequences of Two Clinical Isolates of Extensively Drug-Resistant Mycobacterium tuberculosis from Zunyi, China.
JO  - Genome Announcements
PY  - 2014
SP  - e00910
EP  - e00914
VL  - 2
AB  - Before 2013, 92 countries reported extensively drug-resistant Mycobacterium tuberculosis cases
AB  - to the WHO. Here, we announce the genome sequences of two
AB  - clinical isolates of extensively drug-resistant tuberculosis (XDR-TB) from Zunyi,
AB  - China. The genome sequences are composed of 4,411,507 bp and 4,411,515 bp with
AB  - 2,210 and 2,071 variants, respectively, when compared to the H37Rv genome.
ER  -

TY  - JOUR
AU  - Chen, L.
AU  - Zou, G.
AU  - Cao, X.
AU  - Rufan, Z.
TI  - The synthesis of nine kinds of oligodeoxynucleotide containing the recognition sequence for PstI and their interaction with enzyme.
JO  - J. Wuhan Univ.
PY  - 1996
SP  - 499
EP  - 506
VL  - 42
AB  - In this paper, nine kinds of oligodeoxynucleotide containing the recognition sequence of
AB  - restriction endonuclease PstI have been synthesized by a solid phase phosphite-triester method
AB  - or a combination of chemical and enzymatic methods.  The results of their enzymatic hydrolysis
AB  - show that the existence of uridine in the recognition sequence of PstI has little influence on
AB  - the cleavage of this strand, but reduces the cleavage rate of its complementary strand; PstI
AB  - cleaves its substrate through  single strand cleavage in two steps.  The minimum PstI
AB  - substrate is an eight to twelve long oligodeoxynucleotide containing its recognition sequence,
AB  - and there is a requirement to the base pair numbers on both sides of PstI recognition
AB  - sequence. The two cytidines in the recognition sequence of PstI don't play the same role in
AB  - enzymatic hydrolysis.
ER  -

TY  - JOUR
AU  - Chen, M.
AU  - Lin, L.
AU  - Zhang, Y.
AU  - Sun, L.
AU  - An, Q.
TI  - Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa.
JO  - Genome Announcements
PY  - 2013
SP  - e00601
EP  - e00613
VL  - 1
AB  - Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the
AB  - pioneer grass Psammochloa villosa, which grows in the moving sand dunes
AB  - of Ordos Plateau, China. The SA2 genome sequence provides the genetic background
AB  - for understanding its endophytic lifestyle and survival in association with grass
AB  - in nitrogen-poor environments.
ER  -

TY  - JOUR
AU  - Chen, M.
AU  - Qin, N.
AU  - Pei, W.
AU  - Li, Q.
AU  - Yang, Q.
AU  - Chen, Y.
AU  - Huang, D.
AU  - Xiang, Y.
AU  - Lin, L.
TI  - Draft Whole-Genome Sequences of Zhihengliuella halotolerans La12 and Microbacterium kitamiense Sa12, Strains with Cellulase Activity, Isolated from  the Qinghai-Tibetan Plateau.
JO  - Genome Announcements
PY  - 2018
SP  - e01531
EP  - e01517
VL  - 6
AB  - We report the complete genome sequences of cellulolytic strains Zhihengliuella halotolerans
AB  - La12 and Microbacterium kitamiense Sa12, which were isolated from
AB  - soil samples collected from the Qinghai-Tibetan Plateau in Western China. The
AB  - final assemblies of La12 and Sa12 comprise 3,712,694 bp, with over 111 contigs,
AB  - and 3,830,439 bp, with over 39 contigs, respectively.
ER  -

TY  - JOUR
AU  - Chen, M.
AU  - Yan, Y.
AU  - Zhang, W.
AU  - Lu, W.
AU  - Wang, J.
AU  - Ping, S.
AU  - Lin, M.
TI  - Complete Genome Sequence of the Type Strain Pseudomonas stutzeri CGMCC 1.1803.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6095
EP  - 6095
VL  - 193
AB  - Here we report the complete genome sequence of Pseudomonas stutzeri strain CGMCC 1.1803
AB  - (equivalent to ATCC 17588), the type strain of P. stutzeri,
AB  - which encodes 4,138 open reading frames on a 4,547,930-bp circular
AB  - chromosome. The CGMCC 1.1803 genome contains genes involved in
AB  - denitrification, benzoate/catechol degradation, chemotaxis, and other
AB  - functions.
ER  -

TY  - JOUR
AU  - Chen, M.
AU  - Zhu, B.
AU  - Lin, L.
AU  - Yang, L.
AU  - Li, Y.
AU  - An, Q.
TI  - Complete genome sequence of Kosakonia sacchari type strain SP1(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1311
EP  - 1318
VL  - 9
AB  - Kosakonia sacchari sp. nov. is a new species within the new genus Kosakonia, which was
AB  - included in the genus Enterobacter. K sacchari is a nitrogen-fixing
AB  - bacterium named for its association with sugarcane (Saccharum officinarum L.). K
AB  - sacchari bacteria are Gram-negative, aerobic, non-spore-forming, motile rods.
AB  - Strain SP1(T) (=CGMCC1.12102(T)=LMG 26783(T)) is the type strain of the K
AB  - sacchari sp. nov and is able to colonize and fix N2 in association with sugarcane
AB  - plants, thus promoting plant growth. Here we summarize the features of strain
AB  - SP1(T) and describe its complete genome sequence. The genome contains a single
AB  - chromosome and no plasmids, 4,902,024 nucleotides with 53.7% GC content, 4,460
AB  - protein-coding genes and 105 RNA genes including 22 rRNA genes, 82 tRNA genes,
AB  - and 1 ncRNA gene.
ER  -

TY  - JOUR
AU  - Chen, M.X.
AU  - Li, H.Y.
AU  - Ye, X.S.
AU  - He, X.Y.
TI  - Draft Genome Sequence of an Extracellular Protease-Producing Bacterium, Stenotrophomonas bentonitica VV6, Isolated from Arctic Seawater.
JO  - Genome Announcements
PY  - 2018
SP  - e01610
EP  - e01617
VL  - 6
AB  - The draft genome sequence of the extracellular protease-producing bacterium Stenotrophomonas
AB  - bentonitica VV6, isolated from Arctic seawater, was established.
AB  - The genome size was approximately 4.365 Mb, with a G+C content of 66.54%, and it
AB  - contains 3,871 predicted protein-coding sequences (CDSs) and 60 tRNAs.
ER  -

TY  - JOUR
AU  - Chen, P.
AU  - den Bakker, H.C.
AU  - Korlach, J.
AU  - Kong, N.
AU  - Storey, D.B.
AU  - Paxinos, E.E.
AU  - Ashby, M.
AU  - Clark, T.
AU  - Luong, K.
AU  - Wiedmann, M.
AU  - Weimer, B.C.
TI  - Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.
JO  - Appl. Environ. Microbiol.
PY  - 2017
SP  - e02091
EP  - e02016
VL  - 83
AB  - Listeria monocytogenes is a bacterial pathogen that is found in a wide variety of
AB  - anthropogenic and natural environments. Genome sequencing technologies are
AB  - rapidly becoming a powerful tool in facilitating our understanding of how
AB  - genotype, classification phenotypes, and virulence phenotypes interact to predict
AB  - the health risks of individual bacterial isolates. Currently, 57 closed L.
AB  - monocytogenes genomes are publicly available, representing three of the four
AB  - phylogenetic lineages, and they suggest that L. monocytogenes has high genomic
AB  - synteny. This study contributes an additional 15 closed L. monocytogenes genomes
AB  - that were used to determine the associations between the genome and methylome
AB  - with host invasion magnitude. In contrast to previous findings, large chromosomal
AB  - inversions and rearrangements were detected in five isolates at the chromosome
AB  - terminus and within rRNA genes, including a previously undescribed inversion
AB  - within rRNA-encoding regions. Each isolate's epigenome contained highly diverse
AB  - methyltransferase recognition sites, even within the same serotype and
AB  - methylation pattern. Eleven strains contained a single chromosomally encoded
AB  - methyltransferase, one strain contained two methylation systems (one system on a
AB  - plasmid), and three strains exhibited no methylation, despite the occurrence of
AB  - methyltransferase genes. In three isolates a new, unknown DNA modification was
AB  - observed in addition to diverse methylation patterns, accompanied by a novel
AB  - methylation system. Neither chromosome rearrangement nor strain-specific patterns
AB  - of epigenome modification observed within virulence genes were correlated with
AB  - serotype designation, clonal complex, or in vitro infectivity. These data suggest
AB  - that genome diversity is larger than previously considered in L. monocytogenes
AB  - and that as more genomes are sequenced, additional structure and methylation
AB  - novelty will be observed in this organism. IMPORTANCE: Listeria monocytogenes is
AB  - the causative agent of listeriosis, a disease which manifests as gastroenteritis,
AB  - meningoencephalitis, and abortion. Among Salmonella, Escherichia coli,
AB  - Campylobacter, and Listeria-causing the most prevalent foodborne
AB  - illnesses-infection by L. monocytogenes carries the highest mortality rate. The
AB  - ability of L. monocytogenes to regulate its response to various harsh
AB  - environments enables its persistence and transmission. Small-scale comparisons of
AB  - L. monocytogenes focusing solely on genome contents reveal a highly syntenic
AB  - genome yet fail to address the observed diversity in phenotypic regulation. This
AB  - study provides a large-scale comparison of 302 L. monocytogenes isolates,
AB  - revealing the importance of the epigenome and restriction-modification systems as
AB  - major determinants of L. monocytogenes phylogenetic grouping and subsequent
AB  - phenotypic expression. Further examination of virulence genes of select outbreak
AB  - strains reveals an unprecedented diversity in methylation statuses despite high
AB  - degrees of genome conservation.
ER  -

TY  - JOUR
AU  - Chen, P.
AU  - Jeannotte, R.
AU  - Weimer, B.C.
TI  - Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier.
JO  - Trends Microbiol.
PY  - 2014
SP  - 292
EP  - 300
VL  - 22
AB  - Epigenetics has an important role for the success of foodborne pathogen persistence in diverse
AB  - host niches. Substantial challenges exist in determining DNA methylation to situation-specific
AB  - phenotypic traits. DNA modification, mediated by restriction-modification systems, functions
AB  - as an immune response against antagonistic external DNA, and bacteriophage-acquired
AB  - methyltransferases (MTase) and orphan MTases - those lacking the cognate restriction
AB  - endonuclease - facilitate evolution of new phenotypes via gene expression modulation via DNA
AB  - and RNA modifications, including methylation and phosphorothioation. Recent establishment of
AB  - large-scale genome sequencing projects will result in a significant increase in genome
AB  - availability that will lead to new demands for data analysis including new predictive
AB  - bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing
AB  - technologies that detect modification coupled with mass spectrometry to discover new adducts
AB  - is a powerful tactic to study bacterial epigenetics, which is poised to make novel and
AB  - far-reaching discoveries that link biological significance and the bacterial epigenome.
ER  -

TY  - JOUR
AU  - Chen, P.
AU  - Kong, N.
AU  - Huang, B.
AU  - Thao, K.
AU  - Ng, W.
AU  - Storey, D.B.
AU  - Arabyan, N.
AU  - Foutouhi, A.
AU  - Foutouhi, S.
AU  - Weimer, B.C.
TI  - 100K Pathogen Genome Project: 306 Listeria Draft Genome Sequences for Food Safety and Public Health.
JO  - Genome Announcements
PY  - 2017
SP  - e00967
EP  - e00916
VL  - 5
AB  - Listeria monocytogenes is a food-associated bacterium that is responsible for food-related
AB  - illnesses worldwide. This is the initial public release of 306 L.
AB  - monocytogenes genome sequences as part of the 100K Pathogen Genome Project. These
AB  - isolates represent global genomic diversity in L. monocytogenes.
ER  -

TY  - JOUR
AU  - Chen, P.
AU  - Li, J.
AU  - Zhao, J.
AU  - He, L.
AU  - Zhang, Z.
TI  - Differential dependence on DNA ligase of type II restriction enzymes: A practical way toward ligase-free DNA automaton.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2007
SP  - 733
EP  - 737
VL  - 353
AB  - DNA computing study is a new paradigm in computer science and biological computing fields. As
AB  - one of DNA computing approaches, DNA automaton is
AB  - composed of the hardware, input DNA molecule and state transition
AB  - molecules. By now restriction enzymes are key hardware for DNA computing
AB  - automaton. It has been found that DNA computing efficiency may be
AB  - independent on DNA ligases when type IIS restriction enzymes like FokI are
AB  - used as hardware. In this study, we compared FokI with four other distinct
AB  - enzymes HgaI, BsmFI, BbsI, and BseMII, and found their differential
AB  - independence on T4 DNA ligase when performing automaton reactions. Since
AB  - DNA automaton is a potential powerful tool to tackle gene relationship in
AB  - genomic network scale, the feasible ligase-free DNA automaton may set an
AB  - initial base to develop functional DNA automata for various DNA technology
AB  - development and implications in genetics study in the near future.
ER  -

TY  - JOUR
AU  - Chen, P.
AU  - Li, S.
AU  - Yan, L.
AU  - Wang, N.
AU  - Yan, X.
AU  - Li, H.
TI  - Draft Genome Sequence of Bacillus subtilis Type Strain B7-S, Which Converts Ferulic Acid to Vanillin.
JO  - Genome Announcements
PY  - 2014
SP  - e00025
EP  - e00014
VL  - 2
AB  - The Bacillus subtilis type strain B7-S was obtained through induction with ferulic acid. Here,
AB  - we present the draft genome of strain B7-S, which contains
AB  - 5,313,924 bp, with a G+C content of 35.8%, 5,135 protein-coding genes, and 40
AB  - tRNA-encoding genes.
ER  -

TY  - JOUR
AU  - Chen, P.C.
AU  - Chen, T.W.
AU  - Han, Y.A.
AU  - Ng, W.V.
AU  - Yang, C.S.
TI  - Complete Genome Sequence of a New Halophilic Archaeon, Haloarcula taiwanensis, Isolated from a Solar Saltern in Southern Taiwan.
JO  - Genome Announcements
PY  - 2018
SP  - e01529
EP  - e01517
VL  - 6
AB  - We report here the completion of the genome sequence of a new species of haloarchaea,
AB  - Haloarcula taiwanensis, isolated in southern Taiwan. The
AB  - 3,721,706-bp genome consisted of chromosome I (2,966,258 bp, 63.6% GC content),
AB  - chromosome II (525,233 bp, 59.6% GC content), plasmid pNYT1 (129,893 bp, 55.3% GC
AB  - content), and plasmid pNYT2 (100,322 bp, 55.7% GC content).
ER  -

TY  - JOUR
AU  - Chen, Q.
AU  - Fischer, J.R.
AU  - Benoit, V.M.
AU  - Dufour, N.P.
AU  - Youderian, P.
AU  - Leong, J.M.
TI  - In Vitro CpG Methylation Increases the Transformation Efficiency of Borrelia burgdorferi Strains Harboring the Endogenous Linear Plasmid lp56.
JO  - J. Bacteriol.
PY  - 2008
SP  - 7885
EP  - 7891
VL  - 190
AB  - Borrelia burgdorferi is the causative agent of Lyme disease, the most common vector-borne
AB  - illness in the Northern hemisphere.
AB  - Low-passage-number infectious strains of B. burgdorferi exhibit
AB  - extremely low transformation efficiencies-so low, in fact, as to hinder
AB  - the genetic study of putative virulence factors. Two putative
AB  - restriction-modification (R-M) systems, BBE02 contained on linear
AB  - plasmid 25 ( lp25) and BBQ67 contained on lp56, have been postulated to
AB  - contribute to this poor transformability. Restriction barriers posed by
AB  - other bacteria have been overcome by the in vitro methylation of DNA
AB  - prior to transformation. To test whether a methylation-sensitive
AB  - restriction system contributes to poor B. burgdorferi transformability,
AB  - shuttle plasmids were treated with the CpG methylase M. SssI prior to
AB  - the electroporation of a variety of strains harboring different
AB  - putative R-M systems. We found that for B. burgdorferi strains that
AB  - harbor lp56, in vitro methylation increased transformation by at least
AB  - 1 order of magnitude. These results suggest that in vitro CpG
AB  - methylation protects exogenous DNA from degradation by an
AB  - lp56-contained R-M system, presumably BBQ67. The utility of in vitro
AB  - methylation for the genetic manipulation of B. burgdorferi was
AB  - exemplified by the ease of plasmid complementation of a B. burgdorferi
AB  - B31 A3 BBK32 kanamycin-resistant ( B31 A3 BBK32:: Kan(r)) mutant,
AB  - deficient in the expression of the fibronectin- and glycosaminoglycan (
AB  - GAG)-binding adhesin BBK32. Consistent with the observation that
AB  - several surface proteins may promote GAG binding, the B. burgdorferi
AB  - B31 A3 BBK32:: Kanr mutant demonstrated no defect in the ability to
AB  - bind purified GAGs or GAGs expressed on the surfaces of cultured cells.
ER  -

TY  - JOUR
AU  - Chen, Q.
AU  - Wang, C.H.
AU  - Deng, S.K.
AU  - Wu, Y.D.
AU  - Li, Y.
AU  - Yao, L.
AU  - Jiang, J.D.
AU  - Yan, X.
AU  - He, J.
AU  - Li, S.P.
TI  - Novel three-component Rieske non-heme iron oxygenase system catalyzing the N-dealkylation of chloroacetanilide herbicides in sphingomonads DC-6 and DC-2.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 5078
EP  - 5085
VL  - 80
AB  - Sphingomonads DC-6 and DC-2 degrade the chloroacetanilide herbicides alachlor,
AB  - acetochlor, and butachlor via N-dealkylation. In this study, we report a
AB  - three-component Rieske non-heme iron oxygenase (RHO) system catalyzing the
AB  - N-dealkylation of these herbicides. The oxygenase component gene cndA is located
AB  - in a transposable element that is highly conserved in the two strains. CndA
AB  - shares 24 to 42% amino acid sequence identities with the oxygenase components of
AB  - some RHOs that catalyze N- or O-demethylation. Two putative [2Fe-2S] ferredoxin
AB  - genes and one glutathione reductase (GR)-type reductase gene were retrieved from
AB  - the genome of each strain. These genes were not located in the immediate vicinity
AB  - of cndA. The four ferredoxins share 64 to 72% amino acid sequence identities to
AB  - the ferredoxin component of dicamba O-demethylase (DMO), and the two reductases
AB  - share 62 to 65% amino acid sequence identities to the reductase component of DMO.
AB  - cndA, the four ferredoxin genes, and the two reductases genes were expressed in
AB  - Escherichia coli, and the recombinant proteins were purified using Ni-affinity
AB  - chromatography. The individual components or the components in pairs displayed no
AB  - activity; the enzyme mixture showed N-dealkylase activities toward alachlor,
AB  - acetochlor, and butachlor only when CndA-His6 was combined with one of the four
AB  - ferredoxins and one of the two reductases, suggesting that the enzyme consists of
AB  - three components, a homo-oligomer oxygenase, a [2Fe-2S] ferredoxin, and a GR-type
AB  - reductase, and CndA has a low specificity for the electron transport component
AB  - (ETC). The N-dealkylase utilizes NADH, but not NADPH, as the electron donor.
ER  -

TY  - JOUR
AU  - Chen, Q.
AU  - Zhou, J.W.
AU  - Wu, S.H.
AU  - Meng, X.H.
AU  - Yu, D.J.
AU  - Wang, X.J.
TI  - Draft Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae XPY20 Collected from a Bloodstream Infection Patient.
JO  - Genome Announcements
PY  - 2018
SP  - e00443
EP  - e00418
VL  - 6
AB  - Bloodstream infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) strains
AB  - have been a severe problem with high clinical costs and high
AB  - mortality rates. The blaKPC-2-producing CRKP strain XPY20 was collected from the
AB  - blood of a patient. The genome characteristics and antimicrobial resistance
AB  - mechanisms were determined using next-generation sequencing.
ER  -

TY  - JOUR
AU  - Chen, Q.Q.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Wang, J.P.
AU  - Che, J.M.
TI  - Draft Genome Sequence of Bacillus tequilensis Strain FJAT-14262a.
JO  - Genome Announcements
PY  - 2015
SP  - e01317
EP  - e01315
VL  - 3
AB  - Bacillus tequilensis FJAT-14262a is a Gram-positive rod-shaped bacterium. Here, we report the
AB  - 4,038,551-bp genome sequence of B. tequilensis FJAT-14262a, which
AB  - will provide useful information for genomic taxonomy and phylogenomics of
AB  - Bacillus.
ER  -

TY  - JOUR
AU  - Chen, S.
AU  - Chen, L.
AU  - Chen, L.
AU  - Ren, X.
AU  - Ge, H.
AU  - Kang, G.
AU  - Sun, S.
AU  - Chen, Z.
AU  - Sun, Y.
AU  - Li, Y.
TI  - Complete Genome Sequence of Lactobacillus reuteri WHH1689, Isolated from Traditional Chinese Highland Barley Wine.
JO  - Genome Announcements
PY  - 2018
SP  - e00425
EP  - e00418
VL  - 6
AB  - Here, we report the complete genome sequence of Lactobacillus reuteri WHH1689, which was
AB  - isolated from traditional Chinese highland barley wine in the Tibetan
AB  - Plateau of China. The genome consists of a circular chromosome (2.04 Mb).
ER  -

TY  - JOUR
AU  - Chen, S.
AU  - Hao, H.
AU  - Zhao, P.
AU  - Gao, P.
AU  - He, Y.
AU  - Ji, W.
AU  - Wang, Z.
AU  - Lu, Z.
AU  - Liu, Y.
AU  - Chu, Y.
TI  - Complete Genome Sequence of Mycoplasma bovis Strain 08M.
JO  - Genome Announcements
PY  - 2017
SP  - e00324
EP  - e00317
VL  - 5
AB  - Mycoplasma bovis is a major bacterial pathogen that can cause respiratory disease, mastitis,
AB  - and arthritis in cattle. We report here the complete and
AB  - annotated genome sequence of M. bovis strain 08M, isolated from a calf lung with
AB  - pneumonia in China.
ER  -

TY  - JOUR
AU  - Chen, S.
AU  - Soehnlen, M.
AU  - Downes, F.P.
AU  - Walker, E.D.
TI  - Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 56
EP  - 56
VL  - 12
AB  - Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high
AB  - mortality rate in immunocompromised patients. We report the draft
AB  - genome sequence of E. meningoseptica Em3, isolated from sputum from a patient
AB  - with multiple underlying diseases. The genome has a length of 4,037,922 bp, a
AB  - GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide
AB  - identity analysis (>95%) assigned the bacterium to the species E. meningoseptica.
AB  - Genome analysis showed presence of the curli formation and assembly operon and a
AB  - gene encoding hemagglutinins, indicating ability to form biofilm. In vitro
AB  - biofilm assays demonstrated that E. meningoseptica Em3 formed more biofilm than
AB  - E. anophelis Ag1 and E. miricola Emi3, both lacking the curli operon. A gene
AB  - encoding thiol-activated cholesterol-dependent cytolysin in E. meningoseptica Em3
AB  - (potentially involved in lysing host immune cells) was also absent in E.
AB  - anophelis Ag1 and E. miricola Emi3. Strain Em3 showed alpha-hemolysin activity on
AB  - blood agar medium, congruent with presence of hemolysin and cytolysin genes.
AB  - Furthermore, presence of heme uptake and utilization genes demonstrated
AB  - adaptations for bloodstream infections. Strain Em3 contained 12 genes conferring
AB  - resistance to beta-lactams, including beta-lactamases class A, class B, and
AB  - metallo-beta-lactamases. Results of comparative genomic analysis here provide
AB  - insights into the evolution of E. meningoseptica Em3 as a pathogen.
ER  -

TY  - JOUR
AU  - Chen, S.
AU  - Soehnlen, M.
AU  - Walker, E.D.
TI  - Genome Sequence of Elizabethkingia meningoseptica EM1, Isolated from a Patient with a Bloodstream Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e01137
EP  - e01116
VL  - 4
AB  - Elizabethkingia meningoseptica EM1 was isolated from a whole-blood sample from a  female
AB  - patient. The draft genome sequence of Em1 contains 4,038,467 bp, with a
AB  - G+C content of 36.37%. A preliminary genome analysis showed that Em1 contains
AB  - genes conferring resistance to beta-lactams. The bacterium has hemolysin genes
AB  - and a set of genes involved in heme uptake and heme utilization, showing its
AB  - potential to cause bloodstream infections. A clustered regularly interspaced
AB  - short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system
AB  - was identified. Average nucleotide identity (ANI) analysis assigned the bacterium
AB  - to the species E. meningoseptica (ANI, >95%). The annotated genome sequence
AB  - provides the genetic basis for revealing its role as a pathogen in humans.
ER  -

TY  - JOUR
AU  - Chen, S.
AU  - Wang, C.
AU  - Li, H.
AU  - Shen, Y.
TI  - Draft Genome Sequence of Haloparvum sedimenti Strain DYS4, the Type Species of the Genus Haloparvum, Isolated from a Salt Mine.
JO  - Genome Announcements
PY  - 2017
SP  - e00770
EP  - e00717
VL  - 5
AB  - Here is the genome sequence of Haloparvum sedimenti DYS4, the type species of the genus
AB  - Haloparvum, isolated from a salt mine. The DNA G+C content of this genome
AB  - was 68.27 mol%. The scaffold N50 was 96,635 bp. The completely sequenced and
AB  - annotated genome is 3,243,052 bp and contains 3,313 genes.
ER  -

TY  - JOUR
AU  - Chen, S.
AU  - Wang, C.
AU  - Zhao, Z.
AU  - Yang, Z.L.
TI  - Genome Sequence of Halorubrum sp. Strain T3, an Extremely Halophilic Archaeon Harboring a Virus-Like Element.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6608
EP  - 6609
VL  - 194
AB  - Halorubrum sp. strain T3, harboring a virus-like element, was isolated from a sample collected
AB  - from a solar saltern in Yunnan, China. Several strains of
AB  - Halorubrum pleomorphic viruses were reported in this genus recently; however, the
AB  - virus-host interaction in haloarchaea remains unclear. To explore this issue,
AB  - here we present the genome sequence of Halorubrum sp. strain T3 (3,168,011 bp,
AB  - 68.48% G+C content).
ER  -

TY  - JOUR
AU  - Chen, S.C.
AU  - Chen, M.F.
AU  - Weng, C.Y.
AU  - Lai, M.C.
AU  - Wu, S.Y.
TI  - Draft Genome Sequence of Methanoculleus sediminis S3FaT, a Hydrogenotrophic Methanogen Isolated from a Submarine Mud Volcano in Taiwan.
JO  - Genome Announcements
PY  - 2016
SP  - e00308
EP  - e00316
VL  - 4
AB  - Here, we announce the genome sequence of ITALIC! Methanoculleus sediminisS3Fa(T)(DSM
AB  - 29354(T)), a strict anaerobic methanoarchaeon, which was
AB  - isolated from sediments near the submarine mud volcano MV4 located offshore in
AB  - southwestern Taiwan. The 2.49-Mb genome consists of 2,459 predicted genes, 3
AB  - rRNAs, 48 tRNAs, and 1 ncRNA. The sequence of this novel strain may provide more
AB  - information for species delineation and the roles that this strain plays in the
AB  - unique marine mud volcano habitat.
ER  -

TY  - JOUR
AU  - Chen, S.L.
AU  - Hung, C.S.
AU  - Xu, J.
AU  - Reigstad, C.S.
AU  - Magrini, V.
AU  - Sabo, A.
AU  - Blasiar, D.
AU  - Bieri, T.
AU  - Meyer, R.R.
AU  - Ozersky, P.
AU  - Armstrong, J.R.
AU  - Fulton, R.S.
AU  - Latreille, J.P.
AU  - Spieth, J.
AU  - Hooton, T.M.
AU  - Mardis, E.R.
AU  - Hultgren, S.J.
AU  - Gordon, J.I.
TI  - Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 5977
EP  - 5982
VL  - 103
AB  - Escherichia coli is a model laboratory bacterium, a species that is widely distributed in the
AB  - environment, as well as a mutualist and pathogen in its human hosts. As such, E. coli
AB  - represents an attractive organism to study how environment impacts microbial genome structure
AB  - and function. Uropathogenic E. coli (UPEC) must adapt to life in several microbial communities
AB  - in the human body, and has a complex life cycle in the bladder when it causes acute or
AB  - recurrent urinary tract infection (UTI). Several studies designed to identify virulence
AB  - factors have focused on genes that are uniquely represented in UPEC strains, whereas the role
AB  - of genes that are common to all E. coli has received much less attention. Here we describe the
AB  - complete 5,065,741-bp genome sequence of a UPEC strain recovered from a patient with an acute
AB  - bladder infection and compare it with six other finished E. coli genome sequences. We searched
AB  - 3,470 ortholog sets for genes that are under positive selection only in UPEC strains. Our
AB  - maximum likelihood-based analysis yielded 29 genes involved in various aspects of cell surface
AB  - structure, DNA metabolism, nutrient acquisition, and UTI. These results were validated by
AB  - resequencing a subset of the 29 genes in a panel of 50 urinary, periurethral, and rectal E.
AB  - coli isolates from patients with UTI. These studies outline a computational approach that may
AB  - be broadly applicable for studying strain-specific adaptation and pathogenesis in other
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Chen, S.L.
AU  - Shapiro, L.
TI  - Identification of long intergenic repeat sequences associated with DNA methylation sites in Caulobacter crescentus and other alpha-proteobacteria.
JO  - J. Bacteriol.
PY  - 2003
SP  - 4997
EP  - 5002
VL  - 185
AB  - A systematic search for motifs associated with CcrM DNA methylation sites revealed four long
AB  - (>100-bp) motifs (CIR sequences) present in up to 21
AB  - copies in Caulobacter crescentus. The CIR1 and CIR2 motifs exhibit a
AB  - conserved inverted repeat organization, with a CcrM site in the center of
AB  - one of the repeats.
ER  -

TY  - JOUR
AU  - Chen, S.L.
AU  - Wu, M.
AU  - Henderson, J.P.
AU  - Hooton, T.M.
AU  - Hibbing, M.E.
AU  - Hultgren, S.J.
AU  - Gordon, J.I.
TI  - Genomic Diversity and Fitness of E. coli Strains Recovered from the Intestinal and Urinary Tracts of Women with Recurrent Urinary Tract Infection.
JO  - Sci. Transl. Med.
PY  - 2013
SP  - 184RA60
EP  - 184RA60
VL  - 5
AB  - Urinary tract infections (UTIs) are common in women, and recurrence is a major
AB  - clinical problem. Most UTIs are caused by uropathogenic Escherichia coli (UPEC).
AB  - UPEC are generally thought to migrate from the gut to the bladder to cause UTI.
AB  - UPEC form specialized intracellular bacterial communities in the bladder
AB  - urothelium as part of a pathogenic mechanism to establish a foothold during acute
AB  - stages of infection. Evolutionarily, such a specific adaptation to the bladder
AB  - environment would be predicted to result in decreased fitness in other habitats,
AB  - such as the gut. To examine this prediction, we characterized 45 E. coli strains
AB  - isolated from the feces and urine of four otherwise healthy women with recurrent
AB  - UTI. Multilocus sequence typing and whole genome sequencing revealed that two
AB  - patients maintained a clonal population in both these body habitats throughout
AB  - their recurrent UTIs, whereas the other two exhibited a wholesale shift in the
AB  - dominant UPEC strain colonizing both sites. In vivo competition studies in mouse
AB  - models, using isolates taken from one of the patients with a wholesale population
AB  - shift, revealed that the strain that dominated her last UTI episode had increased
AB  - fitness in both the gut and the bladder relative to the strain that dominated in
AB  - preceding episodes. Increased fitness correlated with differences in the strains'
AB  - gene repertoires and carbohydrate and amino acid utilization profiles. Thus, UPEC
AB  - appear capable of persisting in both the gut and urinary tract without a fitness
AB  - trade-off, emphasizing the need to widen our consideration of potential
AB  - reservoirs for strains causing recurrent UTI.
ER  -

TY  - JOUR
AU  - Chen, T.
AU  - Li, E.
TI  - Structure and function of eukaryotic DNA methyltransferases.
JO  - Curr. Top. Dev. Biol.
PY  - 2004
SP  - 55
EP  - 89
VL  - 60
AB  - DNA methylation is a common epigenetic modification found in eukaryotic organisms ranging from
AB  - fungi to mammals. Over the past 15 years, a number
AB  - of eukaryotic DNA methyltransferases have been identified from various
AB  - model organisms. These enzymes exhibit distinct biochemical properties and
AB  - biological functions, partly due to their structural differences. The
AB  - highly variable N-terminal extensions of these enzymes harbor various
AB  - evolutionarily conserved domains and motifs, some of which have been shown
AB  - to be involved in functional specializations. DNA methylation has
AB  - divergent functions in different organisms, consistent with the notion
AB  - that it is a dynamically evolving mechanism that can be adapted to fulfill
AB  - various functions. Genetic studies using model organisms have provided
AB  - evidence suggesting the progressive integration of DNA methylation into
AB  - eukaryotic developmental programs during evolution.
ER  -

TY  - JOUR
AU  - Chen, T.
AU  - Ueda, Y.
AU  - Dodge, J.E.
AU  - Wang, Z.
AU  - Li, E.
TI  - Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b.
JO  - Mol. Cell. Biol.
PY  - 2003
SP  - 5594
EP  - 5605
VL  - 23
AB  - We have previously shown that the DNA methyltransferases Dnmt3a and Dnmt3b carry out de novo
AB  - methylation of the mouse genome during early
AB  - postimplantation development and of maternally imprinted genes in the
AB  - oocyte. In the present study, we demonstrate that Dnmt3a and Dnmt3b are
AB  - also essential for the stable inheritance, or "maintenance," of DNA
AB  - methylation patterns. Inactivation of both Dnmt3a and Dnmt3b in embryonic
AB  - stem (ES) cells results in progressive loss of methylation in various
AB  - repeats and single-copy genes. Interestingly, introduction of the Dnmt3a,
AB  - Dnmt3a2, and Dnmt3b1 isoforms back into highly demethylated mutant ES
AB  - cells restores genomic methylation patterns; these isoforms appear to have
AB  - both common and distinct DNA targets, but they all fail to restore the
AB  - maternal methylation imprints. In contrast, overexpression of Dnmt1 and
AB  - Dnmt3b3 failed to restore DNA methylation patterns due to their inability
AB  - to catalyze de novo methylation in vivo. We also show that
AB  - hypermethylation of genomic DNA by Dnmt3a and Dnmt3b is necessary for ES
AB  - cells to form teratomas in nude mice. These results indicate that genomic
AB  - methylation patterns are determined partly through differential expression
AB  - of different Dnmt3a and Dnmt3b isoforms.
ER  -

TY  - JOUR
AU  - Chen, T.
AU  - Ueda, Y.
AU  - Xie, S.
AU  - Li, E.
TI  - A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 38746
EP  - 38754
VL  - 277
AB  - Previous studies have shown that the Dnmt3b gene encodes multiple variants via alternative
AB  - splicing. However, only one form of Dnmt3a has been identified so far. We now report the
AB  - discovery of a small form of Dnmt3a, termed Dnmt3a2, from both human and mouse. The transcript
AB  - encoding Dnmt3a2 is initiated from a downstream intronic promoter. As a result, the Dnmt3a2
AB  - protein lacks the N-terminal 223 (human) or 219 (mouse) amino acid residues of the full length
AB  - Dnmt3a. Recombinant Dnmt3a2 protein displayed similar cytosine methyltransferase activity as
AB  - Dnmt3a in vitro. However, Dnmt3a and Dnmt3a2 exhibited strikingly different subcellular
AB  - localization patterns. Unlike Dnmt3a, which was concentrated on heterochromatin, Dnmt3a2
AB  - displayed a localization pattern suggestive of euchromatin association. Dnmt3a2 is the
AB  - predominant form in embryonic stem cells and embryonal carcinoma cells and can also be
AB  - detected from testis, ovary, thymus, and spleen, whereas Dnmt3a is expressed at low levels
AB  - ubiquitously. Comparison of human embryonal carcinoma cell lines with breast/ovarian cancer
AB  - cell lines indicates that DNMT3A2 expression correlates with high de novo methylation
AB  - activity. These findings suggest that Dnmt3a and Dnmt3a2 may have distinct DNA targets and
AB  - different functions in development.
ER  -

TY  - JOUR
AU  - Chen, W.
AU  - Wang, Y.
AU  - Li, D.
AU  - Li, L.
AU  - Xiao, Q.
AU  - Zhou, Q.
TI  - Draft Genome Sequence of Brevibacillus brevis Strain X23, a Biocontrol Agent against Bacterial Wilt.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6634
EP  - 6635
VL  - 194
AB  - Brevibacillus brevis X23 is an appropriate biocontrol agent against bacterial wilt caused by
AB  - Ralstonia solanacearum. We report herein the draft genome sequence
AB  - (6,566,879 bp) and a circular plasmid (6,600 bp) of B. brevis X23, data which may
AB  - be helpful for mining the antagonistic activity against R. solanacearum.
ER  -

TY  - JOUR
AU  - Chen, X.
AU  - E, Z.
AU  - Gu, D.
AU  - Lv, L.
AU  - Li, Y.
TI  - Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts.
JO  - Genome Announcements
PY  - 2015
SP  - e01084
EP  - e01015
VL  - 3
AB  - Bifidobacteria are one of the most important beneficial bacteria in the gut of mammals and
AB  - insects. We sequenced the genome of B. actinocoloniiforme DSM 22766,  which was isolated from
AB  - the digestive tracts of bumblebees. The genome contains 1,548 protein-coding genes, 49 RNAs
AB  - and two CRISPR repeats.
ER  -

TY  - JOUR
AU  - Chen, X.
AU  - Wang, Z.-C.
TI  - Plant DNA methyltransferase.
JO  - Shengming De Huaxue
PY  - 2009
SP  - 534
EP  - 538
VL  - 29
AB  - The addition of a methyl group to the carbon 5 of cytosine residues is the most common
AB  - modification of DNA in higher plants.  Plant DNA methyltransferases can be divided into three
AB  - classes based on their linear domain arrangement: DNA methyltransferase,
AB  - chromomethyltransferase and domains-rearranged methyltrnasferase.  MET and CMT are responsible
AB  - for the maintenance of methylation, and the latter has been found only in plants presently;
AB  - DRM appears to be the principal de novo methyltransferase.  In this article, the structure,
AB  - function and evolutionary aspects of the main plant DNA methyltransferases are analyzed in
AB  - detail.
ER  -

TY  - JOUR
AU  - Chen, X.
AU  - Zhang, B.
AU  - Zhang, W.
AU  - Wu, X.
AU  - Zhang, M.
AU  - Chen, T.
AU  - Liu, G.
AU  - Dyson, P.
TI  - Genome Sequence of Streptomyces violaceusniger Strain SPC6, a Halotolerant Streptomycete That Exhibits Rapid Growth and Development.
JO  - Genome Announcements
PY  - 2013
SP  - e00494
EP  - e00413
VL  - 1
AB  - Streptomyces violaceusniger strain SPC6 is a halotolerant streptomycete isolated  from the
AB  - Linze desert in China. The strain has a very high growth rate and a
AB  - short life cycle for a streptomycete. For surface-grown cultures, the period from
AB  - spore germination to formation of colonies with mature spore chains is only 2
AB  - days at 37 degrees C. Additionally, the strain is remarkably resistant to
AB  - osmotic, heat, and UV stress compared with other streptomycetes. Analysis of the
AB  - draft genome sequence indicates that the strain has the smallest reported genome
AB  - (6.4 Mb) of any streptomycete. The availability of this genome sequence allows us
AB  - to investigate the genetic basis of adaptation for growth in an extremely arid
AB  - environment.
ER  -

TY  - JOUR
AU  - Chen, X.H. et al.
TI  - Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 1007
EP  - 1014
VL  - 25
AB  - Bacillus amyloliquefaciens FZB42 is a Gram-positive, plant-associated bacterium, which
AB  - stimulates plant growth and produces secondary metabolites that suppress soil-borne plant
AB  - pathogens. Its 3,918-kb genome, containing an estimated 3,693 protein-coding sequences, lacks
AB  - extended phage insertions, which occur ubiquitously in the closely related Bacillus subtilis
AB  - 168 genome. The B. amyloliquefaciens FZB42 genome reveals an unexpected potential to produce
AB  - secondary metabolites, including the polyketides bacillaene and difficidin. More than 8.5% of
AB  - the genome is devoted to synthesizing antibiotics and siderophores by pathways not involving
AB  - ribosomes. Besides five gene clusters, known from B. subtilis to mediate nonribosomal
AB  - synthesis of secondary metabolites, we identified four giant gene clusters absent in B.
AB  - subtilis 168. The pks2 gene cluster encodes the components to synthesize the macrolactin core
AB  - skeleton.
ER  -

TY  - JOUR
AU  - Chen, X.J.
AU  - Han, K.
AU  - Feng, J.
AU  - Zhuo, L.
AU  - Li, Y.J.
AU  - Li, Y.Z.
TI  - The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 1
EP  - 1
VL  - 11
AB  - Myxobacteria, phylogenetically located in the delta division of the Proteobacteria, are well
AB  - known for characterized social behaviors and large
AB  - genomes of more than 9 Mb in size. Myxococcus fulvus is a typical species of the
AB  - genus Myxococcus in the family Myxococcaceae. M. fulvus 124B02, originally
AB  - isolated from a soil sample collected in Northeast China, is the one and only
AB  - presently known myxobacterial strain that harbors an endogenous autonomously
AB  - replicating plasmid, named pMF1. The endogenous plasmid is of importance for
AB  - understanding the genome evolution of myxobacteria, as well as for the
AB  - development of genetic engineering tools in myxobacteria. Here we describe the
AB  - complete genome sequence of this organism. M. fulvus 124B02 consists of a
AB  - circular chromosome with a total length of 11,048,835 bp and a circular plasmid
AB  - of 18,634 bp. Comparative genomic analyses suggest that pMF1 has a longstanding
AB  - sustention within myxobacteria, and probably contributes to the genome expansion
AB  - of myxobacteria.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Chatterjee, S.S.
AU  - Porcella, S.F.
AU  - Yu, Y.S.
AU  - Otto, M.
TI  - Complete Genome Sequence of a Panton-Valentine Leukocidin-Negative Community-Associated Methicillin-Resistant Staphylococcus aureus Strain of Sequence type 72 from Korea.
JO  - PLoS ONE
PY  - 2013
SP  - E72803
EP  - E72803
VL  - 8
AB  - In the past decade, community-associated (CA-) infections with
AB  - methicillin-resistant Staphylococcus aureus (MRSA) have emerged throughout the
AB  - world. Different CA-MRSA strains dominate in different geographical locations.
AB  - Many CA-MRSA lineages contain genes coding for the Panton-Valentine leukocidin.
AB  - However, the role of this leukotoxin in CA-MRSA pathogenesis is still
AB  - controversial. The genome sequences of two key PVL-positive CA-MRSA strains
AB  - (USA300, USA400) have been reported, but we lack information on the more recently
AB  - found PVL-negative CA-MRSA strains. One such strain is the PVL-negative ST72, the
AB  - main cause of CA-MRSA infections in Korea. Here, we report the entire genome
AB  - sequence of CA-MRSA ST72 and analyze its gene content with a focus on virulence
AB  - factors. Our results show that this strain does not have considerable differences
AB  - in virulence factor content compared to other CA-MRSA strains (USA300, USA400),
AB  - indicating that other toxins do not substitute for the lack of PVL in ST72. This
AB  - finding is in accordance with the notion that differential expression of
AB  - widespread virulence determinants, rather than the acquisition of additional
AB  - virulence factors on mobile genetic elements, such as PVL, is responsible for the
AB  - increased virulence of CA- compared to hospital-associated MRSA.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Crosby, H.A.
AU  - Oosthuysen, W.F.I.I.
AU  - Diekema, D.J.
AU  - Kelley, S.T.
AU  - Horswill, A.R.
TI  - Draft Genome Sequence of USA100 Methicillin-Resistant Staphylococcus aureus Strain 209.
JO  - Genome Announcements
PY  - 2018
SP  - e01399
EP  - e01317
VL  - 6
AB  - USA100 strains are significant contributors to the overall burden of health care-associated
AB  - methicillin-resistant Staphylococcus aureus (MRSA) infections.
AB  - Strain 209 is a representative MRSA isolate that serves as a model organism for
AB  - agr type II studies and USA100 virulence assessments. We present a draft genome
AB  - sequence of this strain.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Cui, Y.
AU  - Pu, F.
AU  - Jiang, G.
AU  - Zhao, X.
AU  - Yuan, Y.
AU  - Zhao, W.
AU  - Li, D.
AU  - Liu, H.
AU  - Li, Y.
AU  - Liang, T.
AU  - Xu, L.
AU  - Wang, Y.
AU  - Song, Q.
AU  - Yang, J.
AU  - Liang, L.
AU  - Yang, R.
AU  - Han, L.
AU  - Song, Y.
TI  - Draft genome sequence of an Acinetobacter genomic species 3 strain harboring a blaNDM-1 gene.
JO  - J. Bacteriol.
PY  - 2011
SP  - 204
EP  - 205
VL  - 194
AB  - Here we report the draft genome sequence of one Acinetobacter genomic species 3 strain, D499,
AB  - which harbors the blaNDM-1 gene.  The total length of the assembled genome is 4,103,824 bp,
AB  - and 3,896 coding sequences (CDSs) were predicted within the genome.  A previously unreported
AB  - blaNDM-1-bearing plasmid was identified in this strain.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - He, Y.
AU  - Zhang, B.
AU  - Yang, J.
AU  - Li, W.
AU  - Dong, Z.
AU  - Hu, S.
TI  - Complete Genome Sequence of Alicyclobacillus acidocaldarius Strain Tc-4-1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5602
EP  - 5603
VL  - 193
AB  - Alicyclobacillus acidocaldarius strain Tc-4-1 was initially isolated from a hot spring in
AB  - Tengchong, China. This organism is both thermophilic and
AB  - acidophilic. It can produce heat- and acid-stable enzymes, such as amylase
AB  - and esterase, which may be important in industry. Here we report the whole
AB  - genome sequence of the strain.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Ji, Y.J.
AU  - Roxby, R.
AU  - Conrad, C.
TI  - In vivo expression of single-stranded DNA in mammalian cells with DNA enzyme sequences targeted to C-raf.
JO  - Antisense Nucleic Acid Drug Dev.
PY  - 2000
SP  - 415
EP  - 422
VL  - 10
AB  - The use of antisense oligodeoxynucleotides (AS-ODN) remains a viable method to downregulate
AB  - selected gene function.  However, limitations to the antisense approach remain, such as (1)
AB  - difficulties in delivery of the
AB  - As-ODN into target tissues, (2) instability of As-ODN in vivo, (3) uncertainties about the
AB  - precise mode of action, and (4) toxic effects in animal and human studies.  To circumvent some
AB  - of these difficulties, we designed a vector set that directs the in vivo production of
AB  - single-stranded DNA (ssDNA) of a desired target sequence with limited extraneous vector
AB  - nucleotide sequences.  One plasmid was designed to express Moloney murine leukemia virus
AB  - (MoMuLV) reverse transcriptase (RT).  Another expression plasmid contains the MoMuLV primer
AB  - binding site at the 3' end of its RNA transcript so that an ssDNA would be synthesized by RT
AB  - when both plasmids are cotransfected into cells.  To test this expression system, we
AB  - constructed a plasmid set, pssXA/pssXB that produces ssRNA-cleaving DNA 10-23 enzyme (Santoro,
AB  - S.W. and Joyce, G.F. (1977) Proc. Natl. Acad. Sci. USA 37, 13330-13342).  The DNA enzyme
AB  - sequence was placed between two oligonucleotide arms that are complementary and able to
AB  - specifically target C-raf kinase mRNA.  These plasmids were transfected into the A549 lung
AB  - carcinoma cell line.  Reduced C-raf mRNA levels by up to 34%-36%, as determined by Northern
AB  - blot analysis, were observed in the transfected cells.  Our results demonstrate the
AB  - feasibility of using this novel ssDNA expression system to generate any sequence of interest
AB  - in vivo for antisense, RNA-cleavage DNA enzyme, or triplex-forming strategies.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Mukherjee, S.
AU  - Hoffmann, M.
AU  - Kotewicz, M.L.
AU  - Young, S.
AU  - Abbott, J.
AU  - Luo, Y.
AU  - Davidson, M.K.
AU  - Allard, M.
AU  - McDermott, P.
AU  - Zhao, S.
TI  - Whole Genome Sequencing of a Gentamicin-Resistant Campylobacter coli isolated from United States Retail Meats Reveals Novel Plasmid Mediated Aminoglycoside Resistance Genes.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 5398
EP  - 5405
VL  - 57
AB  - Aminoglycoside resistance in Campylobacter has been routinely monitored in the
AB  - United States in clinical isolates since 1996 and in retail meats since 2002.
AB  - Gentamicin resistance first appeared in a single human isolate of Campylobacter
AB  - coli in 2000 and a single chicken meat isolate in 2007, after which it increased
AB  - rapidly to account for 11.3% human isolates and 12.5% of retail isolates in 2010.
AB  - Pulsed-field gel electrophoresis analysis indicated that gentamicin resistant C.
AB  - coli isolates from retail meat were clonal. We sequenced the genomes of two
AB  - strains in this clone using a next generation sequencing technique in order to
AB  - investigate the genetic basis for the resistance. The gaps of one strain were
AB  - closed using optical mapping and Sanger sequencing, and it is the first completed
AB  - genome of C. coli. The two genomes are highly similar to each other. A
AB  - self-transmissible plasmid carrying multiple antibiotics resistance genes was
AB  - revealed within both genomes, encoding genes resistant to gentamicin, kanamycin,
AB  - streptomycin, streptothricin, and tetracycline. Bioinformatics analysis and
AB  - experimental results showed that gentamicin resistance was due to a
AB  - phosphotransferase gene aph(2')-Ig not described previously. The phylogenetic
AB  - relationship of this newly emerged clone to other Campylobacter sp. was
AB  - determined by whole genome single nucleotide polymorphisms (SNPs) and showed that
AB  - it clustered with the other poultry isolates and was separated from isolates from
AB  - livestock.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Stine, O.C.
AU  - Badger, J.H.
AU  - Gil, A.I.
AU  - Nair, G.B.
AU  - Nishibuchi, M.
AU  - Fouts, D.E.
TI  - Comparative Genomic Analysis of Vibrio parahaemolyticus: Serotype Conversion and Virulence.
JO  - BMC Genomics
PY  - 2011
SP  - 294
EP  - 294
VL  - 12
AB  - BACKGROUND: Vibrio parahaemolyticus is a common cause of foodborne
AB  - disease. Beginning in 1996, a more virulent strain having serotype O3:K6
AB  - caused major outbreaks in India and other parts of the world, resulting in
AB  - the emergence of a pandemic. Other serovariants of this strain emerged
AB  - during its dissemination and together with the original O3:K6 were termed
AB  - strains of the pandemic clone. Two genomes, one of this virulent strain
AB  - and one pre-pandemic strain have been sequenced. We sequenced four
AB  - additional genomes of V. parahaemolyticus in this study that were isolated
AB  - from different geographical regions and time points. Comparative genomic
AB  - analyses of six strains of V. parahaemolyticus isolated from Asia and Peru
AB  - were performed in order to advance knowledge concerning the evolution of
AB  - V. parahaemolyticus; specifically, the genetic changes contributing to
AB  - serotype conversion and virulence. Two pre-pandemic strains and three
AB  - pandemic strains, isolated from different geographical regions, were
AB  - serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The
AB  - sixth pandemic strain sequenced in this study was serotype O4:K68.
AB  - RESULTS: Genomic analyses revealed that the trh+ and tdh+ strains had
AB  - different types of pathogenicity islands and mobile elements as well as
AB  - major structural differences between the tdh pathogenicity islands of the
AB  - pre-pandemic and pandemic strains. In addition, the results of single
AB  - nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between
AB  - O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding
AB  - the O- and K-antigen-encoding gene clusters. The "core" genes of V.
AB  - parahaemolyticus were also compared to those of V. cholerae and V.
AB  - vulnificus, in order to delineate differences between these three
AB  - pathogenic species. Approximately one-half (49-59%) of each species' core
AB  - genes were conserved in all three species, and 14-24% of the core genes
AB  - were species-specific and in different functional categories. CONCLUSIONS:
AB  - Our data support the idea that the pandemic strains are closely related
AB  - and that recent South American outbreaks of foodborne disease caused by V.
AB  - parahaemolyticus are closely linked to outbreaks in India. Serotype
AB  - conversion from O3:K6 to O4:K68 was likely due to a recombination event
AB  - involving a region much larger than the O-antigen- and K-antigen-encoding
AB  - gene clusters. Major differences between pathogenicity islands and mobile
AB  - elements are also likely driving the evolution of V. parahaemolyticus. In
AB  - addition, our analyses categorized genes that may be useful in
AB  - differentiating pathogenic Vibrios at the species level.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Strain, E.A.
AU  - Allard, M.
AU  - Brown, E.W.
TI  - Genome sequences of Listeria monocytogenes strains J1816 and J1-220 associated with human outbreaks.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3424
EP  - 3425
VL  - 193
AB  - Listeria monocytogenes has caused numerous human outbreaks. Here we report draft genomes of L.
AB  - monocytogenes J1816 and J1-220, which belongs to the
AB  - epidemic clone II and epidemic clone IV, respectively. Whole genome
AB  - sequence analysis of these strains provides a tool for studying the
AB  - short-term evolution of these epidemic clones.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Strain, E.A.
AU  - Allard, M.
AU  - Brown, E.W.
TI  - Genome Sequence of Cronobacter sakazakii E899, a Strain Associated with Human Illness.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5861
EP  - 5861
VL  - 193
AB  - Cronobacter has caused numerous illnesses in neonates, infants, and children. Here we report
AB  - the draft genome of Cronobacter sakazakii E899.
AB  - Whole-genome sequence analysis of Cronobacter strains provides a tool for
AB  - understanding the genomic regions specific to each individual species.
ER  -

TY  - JOUR
AU  - Chen, Y.
AU  - Xiang, Y.
AU  - Yuan, R.
AU  - Chai, Y.
TI  - A restriction enzyme-powered autonomous DNA walking machine: its application for a highly sensitive electrochemiluminescence assay of DNA.
JO  - Nanoscale
PY  - 2015
SP  - 981
EP  - 986
VL  - 7
AB  - The construction of a restriction enzyme (Nt. AlwI)-powered DNA walking machine and its
AB  - application for highly sensitive detection of DNA are described. DNA nanostructure tracks
AB  - containing four overhang sequences with electrochemiluminescence (ECL) labels and
AB  - complementary to the walker (target DNA) are self-assembled on the sensing electrode. The
AB  - walker hybridizes with the complementary sequences on the tracks and forms specific
AB  - recognition sites for Nt. AlwI, which cleaves the overhang sequences, releases the ECL labels
AB  - and enables directional movement of the walker along the tracks. The formation of the
AB  - nanostructure tracks and the Nt. AlwI-assisted cleavage of the overhang sequences in the
AB  - presence of the walker are verified by using polyacrylamide gel electrophoresis analysis and
AB  - cyclic voltammetry. The successive movement of the walker on the nanostructure tracks leads to
AB  - continuous removal of massive ECL labels from the sensing electrode, which results in a
AB  - significantly amplified suppression of the ECL emission for highly sensitive detection of
AB  - sequence-specific DNA down to 0.19 pM. Results show that this DNA walking machine can also
AB  - offer single-base mismatch discrimination capability. The successful application of the DNA
AB  - walking machine for sequence-specific DNA detection can thus offer new opportunities for
AB  - molecular machines in biosensing applications.
ER  -

TY  - JOUR
AU  - Chen, Y.H.
AU  - Lin, S.S.
AU  - Shyu, Y.T.
TI  - Revealing the Saline Adaptation Strategies of the Halophilic Bacterium Halomonas beimenensis through High-throughput Omics and Transposon Mutagenesis Approaches.
JO  - Sci. Rep.
PY  - 2017
SP  - 0
EP  - 0
VL  - 7
AB  - Studies on the halotolerance of bacteria are attractive to the fermentation industry. However,
AB  - a lack of sufficient genomic information has precluded an investigation of the halotolerance
AB  - of Halomonas beimenensis. Here, we describe the molecular mechanisms of saline adaptation in
AB  - H. beimenensis based on high-throughput omics and Tn5 transposon mutagenesis. The H.
AB  - beimenensis genome is 4.05 Mbp and contains 3,807 genes, which were sequenced using short and
AB  - long reads obtained via deep sequencing. Sixteen Tn5 mutants with a loss of halotolerance were
AB  - identified. Orthologs of the
AB  - mutated genes, such as nqrA, trkA, atpC, nadA, and gdhB, have significant biological functions
AB  - in sodium efflux, potassium uptake, hydrogen ion transport for energy conversion, and
AB  - compatible solute synthesis, which are known to control halotolerance. Other genes, such as
AB  - spoT, prkA, mtnN, rsbV, lon, smpB, rfbC, rfbP, tatB, acrR1, and lacA, function in cellular
AB  - signaling, quorum sensing, transcription/translation, and cell motility also shown critical
AB  - functions for promoting a halotolerance. In addition, KCl application increased halotolerance
AB  - and potassium-dependent cell motility in a high-salinity environment. Our results demonstrated
AB  - that a combination of omics and mutagenesis could be used to facilitate the mechanistic
AB  - exploitation of saline adaptation in H. beimenensis, which can be applied for
AB  - biotechnological purposes.
ER  -

TY  - JOUR
AU  - Chen, Y.S.
AU  - Lin, H.H.
AU  - Hsueh, P.T.
AU  - Liu, P.J.
AU  - Ni, W.F.
AU  - Chung, W.C.
AU  - Lin, C.P.
AU  - Chen, Y.L.
TI  - Whole-Genome Sequence of an Epidemic Strain of Burkholderia pseudomallei vgh07 in Taiwan.
JO  - Genome Announcements
PY  - 2015
SP  - e00345
EP  - e00315
VL  - 3
AB  - Here, we report the complete genome sequence of B. pseudomallei vgh07. This is an epidemic
AB  - strain that was isolated from a melioidosis patient with
AB  - arthro-osteomyelitis in Taiwan.
ER  -

TY  - JOUR
AU  - Chen, Y.T.
AU  - Lauderdale, T.L.
AU  - Liao, T.L.
AU  - Shiau, Y.R.
AU  - Shu, H.Y.
AU  - Wu, K.M.
AU  - Yan, J.J.
AU  - Su, I.J.
AU  - Tsai, S.F.
TI  - Sequencing and comparative genomic analysis of pK29, a 269-kilobase conjugative plasmid encoding CMY-8 and CTX-M-3 beta-lactamases in  Klebsiella pneumoniae.
JO  - Antimicrob. Agents Chemother.
PY  - 2007
SP  - 3004
EP  - 3007
VL  - 51
AB  - A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced.
AB  - The plasmid harbors multiple antimicrobial
AB  - resistance genes, including those encoding CMY-8 AmpC-type and CTX-M-3
AB  - extended-spectrum beta-lactamases in the common backbone of IncHI2
AB  - plasmids. Mechanisms for dissemination of the resistance genes are
AB  - highlighted in comparative genomic analyses.
ER  -

TY  - JOUR
AU  - Chen, Y.T.
AU  - Liao, T.L.
AU  - Liu, Y.M.
AU  - Lauderdale, T.L.
AU  - Yan, J.J.
AU  - Tsai, S.F.
TI  - Mobilization of qnrB2 and ISCR1 in plasmids.
JO  - Antimicrob. Agents Chemother.
PY  - 2009
SP  - 1235
EP  - 1237
VL  - 53
AB  - The DNA sequences of two IncHI2 plasmids, pEC-IMP and pEC-IMPQ, from
AB  - metallo-beta-lactamase-producing Enterobacter cloacae clinical isolates
AB  - were determined. The two conjugative plasmids are almost identical, but
AB  - pEC-IMPQ carries an additional segment containing an orf513 (ISCR1), a
AB  - truncated 3' conserved sequence, and a qnrB2. Comparative analyses provide
AB  - support for the proposed ISCR1-mediated gene mobilization.
ER  -

TY  - JOUR
AU  - Chen, Y.T.
AU  - Lin, J.C.
AU  - Fung, C.P.
AU  - Lu, P.L.
AU  - Chuang, Y.C.
AU  - Wu, T.L.
AU  - Siu, L.K.
TI  - KPC-2-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan.
JO  - J. Antimicrob. Chemother.
PY  - 2014
SP  - 628
EP  - 631
VL  - 69
AB  - OBJECTIVES: Two plasmids carrying blaKPC-2 isolated from carbapenem-resistant
AB  - Escherichia coli (CR-EC) and carbapenem-resistant Klebsiella pneumoniae (CR-KP),
AB  - respectively, were completely sequenced. The CR-KP strain was selected from an
AB  - outbreak in 2012, and the CR-EC strain was the first blaKPC-2-carrying E. coli
AB  - identified in the same carbapenem resistance monitoring programme in Taiwan.
AB  - METHODS: Antimicrobial susceptibility tests, multilocus sequence typing (MLST)
AB  - and the conjugal transfer of plasmids were performed. Complete sequencing of the
AB  - plasmids was performed using a shotgun approach. RESULTS: The CR-EC and CR-KP
AB  - strains in this study were determined to be ST410 and ST11, respectively, by
AB  - MLST. From CR-EC, we identified a 145 kb conjugative plasmid that carries
AB  - blaKPC-2, blaCMY-2, blaCTX-M-3 and blaTEM-1. The plasmid is a chimera composed of
AB  - three regions related to IncI, IncN and RepFIC replicons. From CR-KP, we
AB  - identified an 86.5 kb plasmid, pKPC-LK30, which carries blaKPC-2 and blaSHV-11.
AB  - The plasmid is very similar to two blaKPC-2-carrying IncFIIK plasmids, but lacks
AB  - one of the replication origins and cannot conjugate. CONCLUSIONS: The differences
AB  - in cross-species transferability of the two plasmids can be explained by genetic
AB  - differences between their backbones and could have resulted in the confined
AB  - blaKPC-2-carrying CR-KP outbreak in Taiwan. Plasmid pKPC-LKEc is the first
AB  - blaKPC-2-carrying plasmid identified from CR-EC in Taiwan. With relatively high
AB  - transferability it should be closely monitored.
ER  -

TY  - JOUR
AU  - Chen, Y.T.
AU  - Peng, H.L.
AU  - Shia, W.C.
AU  - Hsu, F.R.
AU  - Ken, C.F.
AU  - Tsao, Y.M.
AU  - Chen, C.H.
AU  - Liu, C.E.
AU  - Hsieh, M.F.
AU  - Chen, H.C.
AU  - Tang, C.Y.
AU  - Ku, T.H.
TI  - Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes.
JO  - BMC Genomics
PY  - 2012
SP  - S4
EP  - S4
VL  - 13
AB  - BACKGROUND: The opportunistic enterobacterium, Morganella morganii, which can cause
AB  - bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua
AB  - Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative
AB  - care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia.
AB  - M. morganii is sometimes encountered in nosocomial settings and has been causally linked to
AB  - catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary
AB  - tracts, wound infection, and septicaemia. M. morganii infection is associated with a high
AB  - mortality rate, although most patients respond well to appropriate antibiotic therapy. To
AB  - obtain insights into the genome biology of M. morganii and the mechanisms underlying its
AB  - pathogenicity, we used Illumina technology to sequence the genome of the KT strain and
AB  - compared its sequence with the genome sequences of related bacteria. RESULTS: The 3,826,919-bp
AB  - sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding
AB  - sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode
AB  - determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and
AB  - insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition
AB  - system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with
AB  - 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of
AB  - similarity to several systems found in M. morganii. The most striking similarities were found
AB  - in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required
AB  - for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and
AB  - the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes
AB  - analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in
AB  - the other non-Proteeae enterobacterial genomes. CONCLUSIONS: This is the first genome sequence
AB  - of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed
AB  - several pathogenicity-related genes and novel genes not found in the genomes of other members
AB  - of Proteeae. Thus, the genome sequence of M. morganii provides important information
AB  - concerning virulence and determinants of fitness in this pathogen.
ER  -

TY  - JOUR
AU  - Chen, Y.T.
AU  - Shu, H.Y.
AU  - Li, L.H.
AU  - Liao, T.L.
AU  - Wu, K.M.
AU  - Shiau, Y.R.
AU  - Yan, J.J.
AU  - Su, I.J.
AU  - Tsai, S.F.
AU  - Lauderdale, T.L.
TI  - Complete Nucleotide Sequence of pK245, a 98-Kilobase Plasmid Conferring Quinolone Resistance and Extended-Spectrum-beta-Lactamase Activity in a Clinical Klebsiella pneumoniae Isolate.
JO  - Antimicrob. Agents Chemother.
PY  - 2006
SP  - 3861
EP  - 3866
VL  - 50
AB  - A plasmid containing the qnrS quinolone resistance determinant and the
AB  - gene encoding the SHV-2 beta-lactamase has been discovered from a clinical
AB  - Klebsiella pneumoniae strain isolated in Taiwan. The complete 98-kb
AB  - sequence of this plasmid, designated pK245, was determined by using a
AB  - whole-genome shotgun approach. Transfer of pK245 conferred low-level
AB  - resistance to fluoroquinolones in electroporant Escherichia coli epi300.
AB  - The sequence of the immediate region surrounding qnrS in pK245 is nearly
AB  - identical (>99% identity) to those of pAH0376 from Shigella flexneri and
AB  - pINF5 from Salmonella enterica serovar Infantis, the two other
AB  - qnrS-carrying plasmids reported to date, indicating a potential common
AB  - origin. Other genes conferring resistance to aminoglycosides (aacC2, strA,
AB  - and strB), chloramphenicol (catA2), sulfonamides (sul2), tetracycline
AB  - (tetD), and trimethoprim (dfrA14) were also detected in pK245. The dfrA14
AB  - gene is carried on a class I integron. Several features of this plasmid,
AB  - including three separate regions containing putative replicons, a
AB  - partitioning-control system, and a type II restriction modification
AB  - system, suggest that it may be able to replicate and adapt in a variety of
AB  - hosts. Although no critical conjugative genes were detected, multiple
AB  - insertion sequence elements were found scattered throughout pK245, and
AB  - these may facilitate the dissemination of the antimicrobial resistance
AB  - determinants. We conclude that pK245 is a chimera which acquired its
AB  - multiple antimicrobial resistance determinants horizontally from different
AB  - sources. The identification of pK245 plasmid expands the repertoire of the
AB  - coexistence of quinolone and extended-spectrum-beta-lactam resistance
AB  - determinants in plasmids carried by various species of the family
AB  - Enterobacteriaceae in different countries.
ER  -

TY  - JOUR
AU  - Chen, Y.Z.
AU  - Mohan, V.
AU  - Griffey, R.H.
TI  - Spontaneous base flipping in DNA and its possible role in methyltransferase binding.
JO  - Phys. Rev. E
PY  - 2000
SP  - 1133
EP  - 1137
VL  - 62
AB  - Recent crystallographic studies showed that HhaI and other methyltransferases flip their
AB  - target DNA base completely out of a DNA helix.  This base flipping is also a key feature in a
AB  - number of other enzyme-catalyzed processes involving DNA.  The mechanism of base flipping by
AB  - these enzymes remains elusive.  Based on a full atomic level description of bond rotational
AB  - motions we have studied the energetics of flipping a base in a B-DNA duplex in the absence of
AB  - the enzyme.  We have also investigated the effect of the restraints from enzyme-distorted DNA
AB  - backbone on the movement of a flipped base in several methyltransferase bound DNA crystal
AB  - structures.  Our study on crystal B-DNA helices showed that a base could be flipped at an
AB  - energy cost close to the enthalpy observed for base pair opening in premelting thermal
AB  - fluctuations.  This suggests that spontaneous base flipping in DNA due to thermal fluctuation
AB  - may be achieved.  Analysis of several crystal HhaI and HaeIII methyltransferase DNA duplex
AB  - structures showed that the enzyme induced DNA backbone distortion severely restricts the
AB  - movement of the flipped base, which indicates that during base flipping the backbone needs to
AB  - adopt a substantially different conformation than that observed in the x-ray (enzyme-bound)
AB  - structures.  Our results suggest the possible role of thermally induced transient base opening
AB  - in facilitating recognition and binding of methyltransferases and other enzymes.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Chang, D.
AU  - Zou, Y.
AU  - Su, L.
AU  - Zhu, Y.
AU  - Fang, X.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Zhao, J.
AU  - Li, D.
AU  - Fang, C.
AU  - Yang, R.
AU  - Liu, C.
TI  - Genome Sequence of Enterococcus faecium Clinical Isolate LCT-EF128.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4765
EP  - 4765
VL  - 194
AB  - Enterococcus faecium, an opportunistic human pathogen that inhabits the gastrointestinal
AB  - tracts of most mammals, has emerged as an important
AB  - opportunistic nosocomial pathogen and is a prominent cause of multiresistant
AB  - nosocomial infections. Here, we report the draft genome sequence of strain
AB  - LCT-EF128, isolated from clinical specimens.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Gui, J.
AU  - Gao, X.
AU  - Pei, C.
AU  - Hong, Y.
AU  - Zhang, Q.
TI  - Genome architecture changes and major gene variations of Andrias davidianus ranavirus (ADRV).
JO  - Vet. Res.
PY  - 2013
SP  - 101
EP  - 101
VL  - 44
AB  - Ranaviruses are emerging pathogens that have led to global impact and public
AB  - concern. As a rarely endangered species and the largest amphibian in the world,
AB  - the Chinese giant salamander, Andrias davidianus, has recently undergone
AB  - outbreaks of epidemic diseases with high mortality. In this study, we isolated
AB  - and identified a novel ranavirus from the Chinese giant salamanders that
AB  - exhibited systemic hemorrhage and swelling syndrome with high death rate in China
AB  - during May 2011 to August 2012. The isolate, designated Andrias davidianus
AB  - ranavirus (ADRV), not only could induce cytopathic effects in different fish cell
AB  - lines and yield high viral titers, but also caused severely hemorrhagic lesions
AB  - and resulted in 100% mortality in experimental infections of salamanders. The
AB  - complete genome of ADRV was sequenced and compared with other sequenced amphibian
AB  - ranaviruses. Gene content and phylogenetic analyses revealed that ADRV should
AB  - belong to an amphibian subgroup in genus Ranavirus, and is more closely related
AB  - to frog ranaviruses than to other salamander ranaviruses. Homologous gene
AB  - comparisons show that ADRV contains 99%, 97%, 94%, 93% and 85% homologues in RGV,
AB  - FV3, CMTV, TFV and ATV genomes respectively. In addition, several variable major
AB  - genes, such as duplicate US22 family-like genes, viral eukaryotic translation
AB  - initiation factor 2 alpha gene and novel 75L gene with both motifs of nuclear
AB  - localization signal (NLS) and nuclear export signal (NES), were predicted to
AB  - contribute to pathogen virulence and host susceptibility. These findings confirm
AB  - the etiologic role of ADRV in epidemic diseases of Chinese giant salamanders, and
AB  - broaden our understanding of evolutionary emergence of ranaviruses.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Kong, H.
TI  - Isolation and characterization of restriction endonuclease BstYI from Bacillus stearothermophilus Y406.
JO  - FEBS Lett.
PY  - 1988
SP  - 169
EP  - 171
VL  - 234
AB  - BstYI, an isoschizomer of XhoII and MflI, has been purified from Bacillus
AB  - stearothermophilus Y406.  This enzyme recognized 5' Pu^GATCPy 3' in DNA and
AB  - cleaved between Pu and G in this sequence.  BstYI can be easily isolated and
AB  - purified by heparin-agarose column chromatography in a high yield (8000 units
AB  - BstYI can be obtained per g wet wt of cells).
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Kong, H.
AU  - Wang, L.
TI  - Isolation and characterization of restriction endonucleases BstFI and BstSI from Bacillus stearothermophilus.
JO  - J. Fudan Univ. (Natural Sci.)
PY  - 1989
SP  - 363
EP  - 366
VL  - 28
AB  - Two type II restriction endonucleases, BstFI and BstSI, have been isolated from
AB  - Bacillus stearothermophilus FH58 and Bacillus stearothermophilus S183.  The
AB  - recognition sequence and cleavage site of BstFI is A/AGCTT; and C/PyCGPuG in
AB  - BstSI.  Therefore, BstFI is the isoschizomer of HindIII and BstSI is the
AB  - isoschizomer of AvaI.  These two enzymes can be easily purified with
AB  - heparin-agarose.  10,000 units of BstFI and 24,000 units of BstSI can be
AB  - purified per gram wet cell of FH58 or S183, respectively.  They have different
AB  - thermostability.  BstFI and BatSI are stable under incubation at 45C for as
AB  - long as 6 hours.  After 1 h incubation at 50C the relative activity of BstFI
AB  - was reduced by 50%, whereas the relative activity of BstSI was reduced only by
AB  - 10% after 1 h incubation at 70C.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Lei, X.
AU  - Li, Y.
AU  - Zhang, J.
AU  - Zhang, H.
AU  - Yang, L.
AU  - Zheng, W.
AU  - Xu, H.
AU  - Zheng, T.
TI  - Whole-Genome Sequence of Marine Bacterium Phaeodactylibacter xiamenensis Strain KD52, Isolated from the Phycosphere of Microalga Phacodactylum tricornutum.
JO  - Genome Announcements
PY  - 2014
SP  - e01289
EP  - e01214
VL  - 2
AB  - Phaeodactylibacter xiamenensis KD52 is a novel bacterium isolated from a culture  of the alga
AB  - Phaeodactylum tricornutum in Xiamen, Fujian Province, China. Here, we
AB  - present the first draft genome sequence of this strain, which will provide an
AB  - opportunity to further understand the functional genes related to signing for
AB  - nutrition from the host algae and the molecular mechanisms underlying its
AB  - beneficial properties.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Li, Y.
AU  - Chang, D.
AU  - An, L.
AU  - Guo, Y.
AU  - Wang, J.
AU  - Li, T.
AU  - Wang, Y.
AU  - Zhang, X.
AU  - Dai, W.
AU  - Liu, C.
TI  - Draft Genome Sequence of Enterococcus faecium Strain LCT-EF301, Which Shows Changes in Biochemical Metabolism following Space Flight.
JO  - Genome Announcements
PY  - 2014
SP  - e00103
EP  - e00114
VL  - 2
AB  - An Enterococcus faecium strain was sent into space on the Shenzhou-VIII mission.  After the
AB  - space flight, the strain E. faecium LCT-EF301 was isolated and
AB  - sequenced based on the changes to its metabolic properties.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Ou, W.
AU  - Fan, X.
AU  - Cui, G.
AU  - Wang, Q.
AU  - Li, Q.
AU  - Sun, R.
AU  - Wu, X.
AU  - Qin, W.
AU  - Wang, Y.
TI  - Complete Genome Sequences of Two Multidrug-Resistant Mycobacterium tuberculosis Strains Isolated in Guiyang, China.
JO  - Genome Announcements
PY  - 2018
SP  - e01257
EP  - e01217
VL  - 6
AB  - We identified the genome sequences of two Mycobacterium tuberculosis isolates. They were
AB  - resistant to rifampin and isoniazid, as determined by the agar
AB  - proportion method, but were susceptible to isoniazid, as determined by the DNA
AB  - array method. The genome sequences showed that a katG deletion led to the false
AB  - diagnosis of isoniazid resistance by DNA array.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Wen, F.
AU  - Sun, N.
AU  - Zhao, H.
TI  - Directed evolution of homing endonuclease I-SceI with altered sequence specificity.
JO  - Protein Eng. Des. Sel.
PY  - 2009
SP  - 249
EP  - 256
VL  - 22
AB  - Homing endonucleases recognize specific long DNA sequences and catalyze double-stranded breaks
AB  - that significantly stimulate homologous
AB  - recombination, representing an attractive tool for genome targeting and
AB  - editing. We previously described a two-plasmid selection system that
AB  - couples enzymatic DNA cleavage with the survival of host cells, and
AB  - enables directed evolution of homing endonucleases with altered cleavage
AB  - sequence specificity. Using this selection system, we successfully evolved
AB  - mutant I-SceI homing endonucleases with greatly increased cleavage
AB  - activity towards a new target DNA sequence that differs from the wild-type
AB  - cleavage sequence by 4 bp. The most highly evolved mutant showed a
AB  - survival rate approximately 100-fold higher than that of wild-type I-SceI
AB  - enzyme. The degree of selectivity displayed by a mutant isolated from one
AB  - round of saturation mutagenesis for the new target sequence is comparable
AB  - to that of wild-type I-SceI for the natural sequence. These results
AB  - highlight the ability and efficiency of our selection system for
AB  - engineering homing endonucleases with novel DNA cleavage specificities.
AB  - The mutant identified from this study can potentially be used in vivo for
AB  - targeting the new cleavage sequence within genomic DNA.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Wilkins, M.R.
AU  - Hunter, N.
AU  - Nadkarni, M.A.
TI  - Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection.
JO  - Genome Announcements
PY  - 2013
SP  - e00073
EP  - e00012
VL  - 1
AB  - Here we report the draft genomic sequences of two clinical isolates of Lactobacillus rhamnosus
AB  - from infected dental pulps representing the initial stages of infection of pulp tissue. Based
AB  - on 454 FLX+ pyrosequencing, the two clinical isolates infecting vital pulp had a genome length
AB  - of 2.9 Mbp with distinct genomic signatures.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Wojcik, S.F.
AU  - Welker, N.E.
TI  - Genetic analysis of Bacillus stearothermophilus by protoplast fusion.
JO  - J. Bacteriol.
PY  - 1986
SP  - 994
EP  - 1001
VL  - 165
AB  - Efficient and reliable protoplasting, regeneration, and fusion techniques were
AB  - established for the prototrophic strain Bacillus stearothermophilus NUB36.
AB  - Auxotrophic mutants were isolated, and protoplast fusion was used to construct
AB  - isogenic mutant strains and for chromosomal mapping.  Markers were mapped using
AB  - two-, three-, and four-factor crosses.  The order of the markers was
AB  - hom-1-thr-1-his-1-(gly-1 or gly-2)-pur-1-pur-2.  These markers may be analogous
AB  - to hom, thrA, hisA, glyC, and purA markers on the Bacillus subtilis chromosome.
AB  - No analogous pur-1 marker has been reported in B. subtilis.  The relative
AB  - order of three of the markers (hom-1-thr-1-gly-1) was independently confirmed.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Yang, R.
AU  - Chen, B.
AU  - Li, R.
TI  - Restriction and modification in a gram-negative thermophilic bacterium and isolation of restriction endonuclease TspAI.
JO  - J. Fudan Univ. (Natural Sci.)
PY  - 1989
SP  - 96
EP  - 101
VL  - 28
AB  - A restriction endonuclease TspAI had been isolated from the gram-negative and
AB  - flagellate thermophilic bacterium FD230.  TspAI functions upon phage p228 in
AB  - terms of restriction and modification.  By cleaving lambda DNA, pBR322DNA and
AB  - Phi X174 RFDNA-Hae III fragment, it had been identified as a restriction
AB  - endonuclease possessing the same recognition sequence as that of EcoRII, i.e.
AB  - the cleavage site is CCA/TGG.  TspAI could be easily isolated and purified.
AB  - The enzyme was active over a temperature range of 30-80C.  Moreover, it was
AB  - stable at 60C for as long as 30 minutes.
ER  -

TY  - JOUR
AU  - Chen, Z.
AU  - Zhao, H.
TI  - A highly sensitive selection method for directed evolution of homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - e154
EP  - e154
VL  - 33
AB  - Homing endonucleases are enzymes that catalyze DNA sequence specific double-strand breaks and
AB  - can significantly stimulate homologous recombination at these breaks. These enzymes have great
AB  - potential for applications such as gene correction in gene therapy or gene alteration in
AB  - systems biology and metabolic engineering. However, homing endonucleases have a limited
AB  - natural repertoire of target sequences, which severely hamper their applications. Here we
AB  - report the development of a highly sensitive selection method for the directed evolution of
AB  - homing endonucleases that couples enzymatic DNA cleavage with the survival of host cells.
AB  - Using I-SceI as a model homing endonuclease, we have demonstrated that cells with wild-type
AB  - I-SceI showed a high cell survival rate of 80-100% in the presence of the original I-SceI
AB  - recognition site, whereas cells without I-SceI showed a survival rate <0.003%. This system
AB  - should also be readily applicable for directed evolution of other DNA cleavage enzymes.
ER  -

TY  - JOUR
AU  - Chen, Z.-X.
AU  - Riggs, A.D.
TI  - Self-association of human de novo DNA methyltransferases, DNMT3A and DNMT3B.
JO  - Biochem. Cell Biol.
PY  - 2005
SP  - 566
EP  - 566
VL  - 83
AB  - Proper control of cytosine methylation patterns is critical for mammalian development.  Two de
AB  - novo DNA methyltransferases, Dnmt3a and Dnmt3b, are required for the establishment of DNA
AB  - methylation patterns in germ cells and early embryos.  The mechanism by which DNMT3A and
AB  - DNMT3B carry out de novo methylation remains largely unknown.  Here, using the yeast
AB  - two-hybrid system and co-immunoprecipitation analysis, we demonstrate that human DNMT3A and
AB  - DNMT3B are capable of self-association.  Deletion analysis revealed that the C-terminal
AB  - catalytic domain is responsible for self-interaction.  Since most mutations causing
AB  - immunodeficiency, centromeric instability, and facial anomalies syndrome occur in the
AB  - catalytic domain of DNMT3B, we investigated whether these mutations can affect the ability of
AB  - DNMT3B to self-interact.  Two DNMT3B ICF mutants (H814R and D817G) show reduced ability to
AB  - interact with themselves in the yeast two-hybrid system.  In addition, DNMT3A interacts with
AB  - DNMT3B through their C-terminal catalytic domains.  Self-association of the catalytic domain
AB  - may play a role in regulating activity and function of DNMT3 methyltransferases.
ER  -

TY  - JOUR
AU  - Chen, Z.F.
AU  - Pan, X.S.
TI  - Identification of a new type-II restriction enzyme BsrGI from Bacillus stearothermophilus GR75.
JO  - Chinese Sci. Bull.
PY  - 1994
SP  - 526
EP  - 528
VL  - 39
AB  - A new type II restriction endonuclease, BsrGI, has been isolated from Bacillus
AB  - stearothermophilus GR75. BsrGI cleaves T7 DNA at 13 sites, Lambda DNA at 5 sites and M13mp19
AB  - DNA at one site, but does not cleave pBR322 DNA and pUC19 DNA. The position of restriction
AB  - site of BsrGI on M13mp19 DNA was mapped to position 1000 using double digests with restriction
AB  - enzymes AvaII and BsrFI. The recognition sequence and cleavage site of BsrGI on M13mp19 DNA
AB  - was determined directly by using the dideoxynucleotide chain-termination method with a
AB  - synthetic counter-clockwise primer (1190-1175) downstream of the BsrGI restriction site.
AB  - Sequencing data show that the recognition sequence and cleavage site of BsrGI is
AB  - 5'...T/GTACA...3'. Thus this enzyme recognizes the palindromic sequence 5'TGTACA3' and
AB  - cleaves between 5'T and G, generating 5'-protruding single-strand ends 5'GTAC3'.
ER  -

TY  - JOUR
AU  - Chen, Z.X.
AU  - Mann, J.R.
AU  - Hsieh, C.L.
AU  - Riggs, A.D.
AU  - Chedin, F.
TI  - Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family.
JO  - J. Cell. Biochem.
PY  - 2005
SP  - 902
EP  - 917
VL  - 95
AB  - The de novo methyltransferase-like protein, DNMT3L, is required for methylation of imprinted
AB  - genes in germ cells. Although enzymatically
AB  - inactive, human DNMT3L was shown to act as a general stimulatory factor
AB  - for de novo methylation by murine Dnmt3a. Several isoforms of DNMT3A
AB  - and DNMT3B with development-stage and tissue-specific expression
AB  - patterns have been described in mouse and human, thus bringing into
AB  - question the identity of the physiological partner(s) for stimulation
AB  - by DNMT3L. Here, we used an episome-based in vivo methyltransferase
AB  - assay to systematically analyze five isoforms of human DNMT3A and
AB  - DNMT3B for activity and stimulation by human DNMT3L. Our results show
AB  - that human DNMT3A, DNMT3A2, DNMT3B1, and DNMT3B2 are catalytically
AB  - competent, while DNMT3B3 is inactive in our assay. We also report that
AB  - the activity of all four active isoforms is significantly increased
AB  - upon co-expression with DNMT3L, albeit to varying extents. This is the
AB  - first comprehensive description of the in vivo activities of the poorly
AB  - characterized human DNMT3A and DNMT3B isoforms and of their functional
AB  - interactions with DNMT3L. To further elucidate the mechanism by which
AB  - DNMT3L stimulates DNA methylation, we have mapped in detail the domains
AB  - that mediate interaction of human DNMT3L with human DNMT3A and DNMT3B.
AB  - Our results show that the C-terminus of DNMT3L is the only region
AB  - required for interaction with DNMT3A and DNMT3B and that interaction
AB  - takes place through the C-terminal catalytic domain of DNMT3A and
AB  - DNMT3B. The implications of these findings for the regulation of de
AB  - novo methyltransferases and genomic imprinting are discussed.
ER  -

TY  - JOUR
AU  - Cheng, C.K.
AU  - Au, C.H.
AU  - Li, L.
AU  - Nong, W.
AU  - Law, P.T.
AU  - Cheung, W.M.
AU  - Ling, J.M.
AU  - Kwan, H.S.
TI  - Genome Sequences of Salmonella enterica Serotype Typhimurium Blood Clinical Isolate ST4848/06 and Stool Isolate ST1489/06.
JO  - Genome Announcements
PY  - 2013
SP  - e00823
EP  - e00813
VL  - 1
AB  - Salmonella enterica serotype Typhimurium human blood strains isolated from outside Africa are
AB  - rarely sequenced. Here, we report the draft genome sequences
AB  - of two S. Typhimurium clinical strains isolated in the same year, one from blood
AB  - and another from stool, in order to gain insights into the genetic basis leading
AB  - to invasive diseases.
ER  -

TY  - JOUR
AU  - Cheng, D.-F.
AU  - Liu, Q.
AU  - Zhao, X.-L.
AU  - Dong, Y.-S.
AU  - Li, Q.
TI  - Quantitive study on the inhibitive effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage activity.
JO  - Shengwu Huazue Zazhi
PY  - 1996
SP  - 36
EP  - 41
VL  - 12
AB  - The recombinant plasmid pSV2gpt-SV40 ori-antisense-ras (P1) was constructed. Using this
AB  - plasmid as a model, it was confirmed that the DNA methylation outside the recognition sequence
AB  - could inhibit the activity of restriction endonuclease PvuII.  Quantitive observation showed
AB  - that the activity of the PvuII was reduced by 70 percent due to the DNA methylation outside
AB  - the recognition sequence.
ER  -

TY  - JOUR
AU  - Cheng, H.
AU  - Fang, M.X.
AU  - Jiang, X.W.
AU  - Wu, M.
AU  - Zhu, X.F.
AU  - Zheng, G.
AU  - Yang, Z.J.
TI  - Draft Genome Sequence of Amphibacillus jilinensis Y1(T), a Facultatively Anaerobic, Alkaliphilic and Halotolerant Bacterium.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 491
EP  - 499
VL  - 8
AB  - The genus Amphibacillus was established in 1990, and seven additional species were described
AB  - in the past two decades. Amphibacillus jilinensis Y1(T) is a
AB  - facultatively anaerobic and alkaliphilic bacterium isolated from a soda lake in
AB  - China. Here we describe the structural and genetic features of the draft genome
AB  - about the type strain Y1(T) (3,831,075 bp, with a G+C content of 37.27%). This is
AB  - the first genome report of the Amphibacillus genus.
ER  -

TY  - JOUR
AU  - Cheng, H.
AU  - Huo, Y.Y.
AU  - Hu, J.
AU  - Xu, X.W.
AU  - Wu, M.
TI  - High quality draft genome sequence of an extremely halophilic archaeon Natrinema  altunense strain AJ2T.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 25
EP  - 25
VL  - 12
AB  - Natrinema altunense strain AJ2T, a halophilic archaeal strain, was isolated from  a
AB  - high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at
AB  - least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate.
AB  - To understand the genetics underlying its extreme phenotype, we de novo assembled
AB  - the entire genome sequence of AJ2T (=CGMCC 1.3731T=JCM 12890T). We assembled
AB  - 3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC
AB  - content (64.6%). Subsequently we predicted the gene content and generated genome
AB  - annotation to identify the relationship between the epigenetic characteristics
AB  - and genomic features. The genome sequence contains 52 tRNA genes, 3 rRNA genes
AB  - and 4,462 protein-coding genes, 3792 assigned as functional or hypothetical
AB  - proteins in nr database. This Whole Genome Shotgun project was deposited in
AB  - DDBJ/EMBL/GenBank under the accession JNCS00000000. We performed a Bayesian
AB  - (Maximum-Likelihood) phylogenetic analysis using 16S rRNA sequence and obtained
AB  - its relationship to other strains in the Natrinema and Haloterrigena genera. We
AB  - also confirmed the ANI value between every two species of Natrinema and
AB  - Haloterrigena genera. In conclusion, our analysis furthered our understanding of
AB  - the extreme-environment adapted strain AJ2T by characterizing its genome
AB  - structure, gene content and phylogenetic placement. Our detailed case study will
AB  - contribute to our overall understanding of why Natrinema strains can survive in
AB  - such a high-altitude salt lake.
ER  -

TY  - JOUR
AU  - Cheng, H.
AU  - Wu, Y.H.
AU  - Huo, Y.Y.
AU  - Wang, C.S.
AU  - Xu, X.W.
TI  - Draft Genome Sequence of Altererythrobacter marensis DSM 21428T, Isolated from Seawater.
JO  - Genome Announcements
PY  - 2016
SP  - e01607
EP  - e01615
VL  - 4
AB  - Altererythrobacter marensis DSM 21428(T) was isolated from seawater collected around Mara
AB  - Island, South Korea. The genomic characteristics of this strain
AB  - support its potential for alkane-related compound degradation. A. marensis DSM
AB  - 21428(T) has potential applications in bioremediation projects concerning
AB  - offshore petroleum spill prevention and response.
ER  -

TY  - JOUR
AU  - Cheng, J.
AU  - Yang, H.
AU  - Fang, J.
AU  - Ma, L.
AU  - Gong, R.
AU  - Wang, P.
AU  - Li, Z.
AU  - Xu, Y.
TI  - Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.
JO  - Nat. Commun.
PY  - 2015
SP  - 7023
EP  - 7023
VL  - 6
AB  - DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA
AB  - methylation. Here we determined the crystal structure of DNMT1
AB  - in complex with USP7 at 2.9 A resolution. The interaction between the two
AB  - proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues
AB  - within DNMT1's KG linker. This intermolecular interaction is required for
AB  - USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine
AB  - residues impair DNMT1-USP7 interaction and promote the degradation of DNMT1.
AB  - Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and
AB  - decreased total DNMT1 protein. This negative correlation is observed in
AB  - differentiated neuronal cells and pancreatic cancer cells. Our studies reveal
AB  - that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide
AB  - a structural basis for the design of inhibitors, targeting the DNMT1-USP7
AB  - interaction surface for therapeutic applications.
ER  -

TY  - JOUR
AU  - Cheng, S.-C.
AU  - Kim, R.
AU  - King, K.
AU  - Kim, S.-H.
AU  - Modrich, P.
TI  - Isolation of gram quantities of EcoRI restriction and modification enzymes from an overproducing strain.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 11571
EP  - 11575
VL  - 259
AB  - Structural genes for EcoRI restriction endonuclease and modification methylase
AB  - have been inserted into the plasmid vector pKC3 (Shimatake, H., and Rosenberg,
AB  - M. (1981) Nature (Lond.) 292, 128-132 downstream from the bacteriophage
AB  - lambdapL promoter.  Upon induction of pL expression in strains producing a
AB  - thermolabile lambda cI857 repressor, synthesis of EcoRI polypeptides is
AB  - enhanced to the extent that after 4 h they represent several per cent of the
AB  - total cell protein.  Purification of activities overproduced in this manner
AB  - yields preparations of endonuclease and methylase which appear identical to
AB  - those obtained from conventional sources, with overall yields corresponding to
AB  - 0.5 to 0.9 g of each enzyme/kg of cell paste.
ER  -

TY  - JOUR
AU  - Cheng, S.-C.
AU  - Modrich, P.
TI  - Positive-selection cloning vehicle useful for overproduction of hybrid proteins.
JO  - J. Bacteriol.
PY  - 1983
SP  - 1005
EP  - 1008
VL  - 154
AB  - Plasmid pSCC31 contains the EcoRI endonuclease gene downstream from lambda pL.
AB  - It does not yield transformants upon introduction into Escherichia coli unless
AB  - the structural integrity of the endonuclease is destroyed.  This makes it
AB  - useful as a positive-selection cloning vehicle which can be employed for
AB  - regulated overproduction of hybrid proteins.
ER  -

TY  - JOUR
AU  - Cheng, T.
AU  - Lin, P.
AU  - Jin, S.
AU  - Wu, Y.
AU  - Fu, B.
AU  - Long, R.
AU  - Liu, D.
AU  - Guo, Y.
AU  - Peng, L.
AU  - Xia, Q.
TI  - Complete Genome Sequence of Bacillus bombysepticus, a Pathogen Leading to Bombyx  mori Black Chest Septicemia.
JO  - Genome Announcements
PY  - 2014
SP  - e00312
EP  - e00314
VL  - 2
AB  - Bacillus bombysepticus is a Gram-positive spore-forming bacterium. Here, we announce the first
AB  - complete genome sequence of this organism isolated from the
AB  - cadavers of silkworm larvae that had been sick. The genome contains a single
AB  - circular chromosome and a circular plasmid. Analyses of the B. bombysepticus
AB  - genome will provide insights into its pathomechanisms and biology.
ER  -

TY  - JOUR
AU  - Cheng, T.H.
AU  - Saidin, J.
AU  - Danish-Daniel, M.
AU  - Gan, H.M.
AU  - Mat, I.M.N.
AU  - Abu, B.M.F.
AU  - Ismail, N.
TI  - Genome Sequence of Serratia marcescens subsp. sakuensis Strain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis).
JO  - Genome Announcements
PY  - 2018
SP  - e00022
EP  - e00018
VL  - 6
AB  - Serratia marcescens subsp. sakuensis strain K27 was isolated from sponge (Haliclona
AB  - amboinensis). The genome of this strain consists of 5,325,727 bp, with
AB  - 5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for
AB  - the production of amylases, lipases, and proteases. Gene clusters for the
AB  - biosynthesis of nonribosomal peptides and thiopeptide were also identified.
ER  -

TY  - JOUR
AU  - Cheng, V.W.
AU  - Zhang, G.
AU  - Oyedotun, K.S.
AU  - Ridgway, D.
AU  - Ellison, M.J.
AU  - Weiner, J.H.
TI  - Complete Genome of the Solvent-Tolerant Staphylococcus warneri Strain SG1.
JO  - Genome Announcements
PY  - 2013
SP  - e0003813
EP  - e0003813
VL  - 1
AB  - Staphylococcus warneri is a Gram-positive bacterium commonly found in human skin  flora. The
AB  - genome of a laboratory S. warneri isolate, strain SG1, was sequenced
AB  - to explore its mechanism of solvent tolerance and its potential as a chassis for
AB  - biofuel production.
ER  -

TY  - JOUR
AU  - Cheng, W.
AU  - Zhan, G.
AU  - Liu, W.
AU  - Zhu, R.
AU  - Yu, X.
AU  - Li, Y.
AU  - Li, Y.
AU  - Wu, W.
AU  - Wang, X.
TI  - Draft Genome Sequence of Endophytic Herbaspirillum sp. Strain WT00C, a Tea Plant  Growth-Promoting Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01719
EP  - e01716
VL  - 5
AB  - Endophytic Herbaspirillum sp. strain WT00C was isolated from tea plant (Camellia  sinensis
AB  - L.). Here, we report the 6.08 Mb draft genome sequence of this strain,
AB  - providing bioinformation about its agronomic benefits and capability to reduce
AB  - selenate/selenite into red elemental selenium.
ER  -

TY  - JOUR
AU  - Cheng, X.
TI  - Structure and function of DNA methyltransferases.
JO  - Annu. Rev. Biophys. Biomol. Struct.
PY  - 1995
SP  - 293
EP  - 318
VL  - 24
AB  - Perspectives and Overview
AB  - DNA Methylation
AB  - Types of DNA methylation
AB  - C5-cytosine methyltransferases
AB  - Catalytic mechanism
AB  - HhaI methyltransferase
AB  - Crystal Structure of a C5-cytosine Methyltransferase
AB  - General protein topology: a two-domain structure
AB  - Induced fit in Protein-DNA interactions
AB  - Catalytic domain
AB  - DNA-Recognition domain
AB  - Summary and Discussion
AB  - The Catalytic Domain is a Structural Framework for the SAM-dependent Methyltransferases
AB  - TaqI methyltransferase
AB  - Catechol O-methyltransferase
AB  - Common catalytic-domain structure
AB  - N6-adenine and N4-cytosine methylation
AB  - Summary
ER  -

TY  - JOUR
AU  - Cheng, X.
TI  - DNA modification by methyltransferases.
JO  - Curr. Opin. Struct. Biol.
PY  - 1995
SP  - 4
EP  - 10
VL  - 5
AB  - Enzymatic methylation of DNA plays important roles in both prokaryotes and eukaryotes.
AB  - Structural study of the HhaI DNA methyltransferase has provided considerable insight into the
AB  - chemistry of C5-cytosine methylation. The DNA-protein complex reveals a substrate cytosine
AB  - flipped out of the double helix during the reaction, and a novel two-loop DNA-binding motif
AB  - used for both sequence recognition and flipping the base. Structural comparison of HhaI
AB  - C5-cytosine methyltransferase, TaqI N6-adenine methyltransferase, and catechol
AB  - O-methyltransferase reveals a common catalytic domain structure, which might be universal
AB  - among S-adenosyl-L-methionine (SAM)-dependent methyltransferases.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Balendiran, K.
AU  - Schildkraut, I.
AU  - Anderson, J.E.
TI  - Structure of PvuII endonuclease with cognate DNA.
JO  - EMBO J.
PY  - 1994
SP  - 3927
EP  - 3935
VL  - 13
AB  - We have determined the structure of PvuII endonuclease complexed with cognate DNA by X-ray
AB  - crystallography. The DNA substrate is bound with a single homodimeric protein, each subunit of
AB  - which reveals three structural regions. The catalytic region strongly resembles structures of
AB  - other restriction endonucleases, even though these regions have dissimilar primary sequences.
AB  - Comparison of the active site with those of EcoRV and EcoRI endonucleases reveals a conserved
AB  - triplet sequence close to the reactive phosphodiester group and a conserved acidic pair that
AB  - may represent the ligands for the catalytic cofactor Mg2+. The DNA duplex is not significantly
AB  - bent and maintains a B-DNA-like conformation. The subunit interface region of the homodimeric
AB  - protein consists of a pseudo-three-helix bundle. Direct contacts between the protein and the
AB  - base pairs of the PvuII recognition site occur exclusively in the major groove through two
AB  - antiparallel beta strands from the sequence recognition region of the protein. Water-mediated
AB  - contacts are made in the minor grooves to central bases of the site. If restriction enzymes do
AB  - share a common ancestor, as has been proposed, their catalytic regions have been very strongly
AB  - conserved, while their subunit interfaces and DNA sequence recognition regions have undergone
AB  - remarkable structural variation.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Balendiran, K.
AU  - Schildkraut, I.
AU  - Anderson, J.E.
TI  - Crystal stucture of the PvuII restriction endonuclease.
JO  - Gene
PY  - 1995
SP  - 139
EP  - 140
VL  - 157
AB  - Crystal structures have now been determined for the R.PvuII restriction endonuclease as a
AB  - protein-DNA complex and in apo-form.  The structures indicate how the interaction with DNA
AB  - might proceed.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Blumenthal, R.M.
TI  - Finding a basis for flipping bases.
JO  - Structure
PY  - 1996
SP  - 639
EP  - 645
VL  - 4
AB  - Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ('base
AB  - flipping') was first observed in the structure of a DNA methyltransferase.  There is now
AB  - evidence that a variety of proteins use base flipping in their interactions with DNA.  Though
AB  - the mechanism for base flipping is still unclear, we propose a three-step pathway: recognizing
AB  - the target site and increasing the interstrand phosphate-phosphate distance nearby, initiating
AB  - base flipping by protein invasion of the DNA, and trapping the flipped DNA structure.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Blumenthal, R.M.
TI  - Mammalian DNA methyltransferases: A structural perspective.
JO  - Structure
PY  - 2008
SP  - 341
EP  - 350
VL  - 16
AB  - The methylation of mammalian DNA, primarily at CpG dinucleotides, has long been recognized to
AB  - play a major role in controlling gene expression, among other functions.  Given their
AB  - importance, it is surprising how many basic questions remain to be answered about the proteins
AB  - responsible for this methylation and for coordination with the parallel chromatin-marking
AB  - system that operates at the level of histone modification.  This article reviews recent
AB  - studies on, and discusses the resulting biochemical and structural insights into, the DNA
AB  - nucleotide methyltransferase (Dnmt) proteins 1, 3a, 3a2, 3b, and 3L.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Kumar, S.
AU  - Klimasauskas, S.
AU  - Roberts, R.J.
TI  - Crystal structure of the HhaI DNA methyltransferase.
JO  - Cold Spring Harb. Symp. Quant. Biol.
PY  - 1993
SP  - 331
EP  - 338
VL  - 58
AB  - Structures of M.HhaI with AdoMet and M.HhaI, DNA and AdoHcy are described.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Kumar, S.
AU  - Posfai, J.
AU  - Pflugrath, J.W.
AU  - Roberts, R.J.
TI  - Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
JO  - Cell
PY  - 1993
SP  - 299
EP  - 307
VL  - 74
AB  - The first three-dimensional structure of a DNA methyltranferase is presented. The crystal
AB  - structure of the DNA (cytosine-5)-methyltransferase, M.HhaI (recognition sequence: GCGC),
AB  - complexed with S-adenosyl-L-methionine has been determined and refined at 2.5 A resolution.
AB  - The core of the structure is dominated by sequence motifs conserved among all DNA
AB  - (cytosine-5)-methyltransferases, and these are responsible for cofactor binding and
AB  - methyltransferase function.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Kumar, S.
AU  - Sha, M.
AU  - Roberts, R.J.
TI  - Crystal structure of HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
JO  - Acta Crystallogr. A
PY  - 1993
SP  - 61
EP  - 61
VL  - SA49
AB  - DNA methyltransferases are found in organisms ranging from bacteria to mammals. The DNA
AB  - methyltransferase from the bacterium Haemophilus haemolyticus catalyzes the transfer of a
AB  - methyl group from S-adenosyl-L-methionine (AdoMet) to C-5 of the internal cytosine in the DNA
AB  - sequence GCGC. The three dimensional structure of the M.HhaI-AdoMet complex has been
AB  - determined and refined at a resolution of 2.5 A. The structure is the first to be solved for
AB  - any DNA methyltransferase as well as being the first for any methyltransferase that utilizes
AB  - the ubiquitous methyl donor AdoMet. Due to the conserved nature of
AB  - (cytosine-5)-methyltransferases, the information obtained from this structure can be
AB  - generalized to the entire family, including the mammalian CpG methyltransferase.
ER  -

TY  - JOUR
AU  - Cheng, X.
AU  - Roberts, R.J.
TI  - AdoMet-dependent methylation, DNA methyltransferases and base flipping.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3784
EP  - 3795
VL  - 29
AB  - Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by
AB  - X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein
AB  - MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their
AB  - substrates. The MTases share a common core structure of a mixed seven-stranded beta-sheet
AB  - (6|7^5|4|1|2^3|) referred to as an 'AdoMet-dependent MTase fold', with the exception
AB  - of a protein arginine MTase which contains a compact consensus fold lacking the antiparallel
AB  - hairpin strands (6|7^). The consensus fold is useful to identify
AB  - hypothetical MTases during structural proteomics efforts on unannotated proteins. The same
AB  - core structure works for very different classes of MTase including those that act on
AB  - substrates differing in size from small molecules (catechol or glycine) to macromolecules
AB  - (DNA, RNA and protein). DNA MTases use a 'base flipping' mechanism to deliver a specific
AB  - base within a DNA molecule into a typically concave catalytic pocket. Base flipping involves
AB  - rotation of backbone bonds in double-stranded DNA to expose an out-of-stack nucleotide, which
AB  - can then be a substrate for an enzyme-catalyzed chemical reaction. The phenomenon is fully
AB  - established for DNA MTases and for DNA base excision repair enzymes, and is likely to prove
AB  - general for enzymes that require access to unpaired, mismatched or damaged nucleotides within
AB  - base-paired regions in DNA and RNA. Several newly discovered MTase families in eukaryotes (DNA
AB  - 5mC MTases and protein arginine and lysine MTases) offer new challenges in the MTase field.
ER  -

TY  - JOUR
AU  - Cheng, X.D.
AU  - Collins, R.C.
AU  - Jia, D.
AU  - Khan, S.I.
AU  - Horton, J.R.
AU  - Qiu, C.
AU  - Sawada, K.
AU  - Yang, Z.
AU  - Zhang, X.
TI  - Structural and functional analysis of methyltransferases.
JO  - Cell Res.
PY  - 2003
SP  - 408
EP  - 408
VL  - 13
AB  - Our work involves structural characterization of AdoMet-dependent methyltransferases (MTases),
AB  - including enzymes that covalently modify DNA and histones, a process that controls many
AB  - cellular processes by affecting gene expression.  The DNA MTase structure comprises a
AB  - seven-stranded beta sheet, flanked by alpha helices to form a doubly wound open aba sandwich,
AB  - and is
AB  - henceforth referred to as the Class 1 MTase structure.  Many of the known Class I MTases act
AB  - on DNA to regulate gene expression, to repair mutations or to protect against bacterial
AB  - restriction enzymes.  Initially, it was a mystery as to how MTases acted on nucleotides that
AB  - are held inside the DNA duplex by base pairing and stacking -- seemingly inaccessible to the
AB  - active site of an enzyme.  In a process termed 'base flipping', the enzyme simply rotates
AB  - the target DNA on its flanking phosphodiester bonds such that the base projects into the
AB  - catalytic pocket.  Protein arginine MTases (PRMTs) have broad substrates including histones H3
AB  - and H4.  PRMT1 is the predominant PRMT in mammalian cells, accounting for 85% of cellular PRMT
AB  - activity and is essential for early postimplantation development.  The structure of PRMT1
AB  - forms a ring-like dimer, essential for AdoMet binding and enzymatic activity.  The AdoMet
AB  - binding domain is a compact version of the Class I MTase fold.  A recently discovered class of
AB  - these enzymes is the histone lysine MTase family, whose catalytic activity lies within a
AB  - conserved domain, the SET domain.  Using entirely different structural scaffolding, the
AB  - SET-domain MTases bind to a kinked AdoMet molecule on the opposite side of a narrow channel
AB  - from the target nitrogen of the lysine substrate.  The C-terminal tail of the SET domain forms
AB  - a pseudo knot and provides an integral part of the hydrophobic active-site pocket, including
AB  - tyrosine residues implicated in the catalytic mechanism.  On the other hand, not all histone
AB  - lysine MTases contain the SET domain; the yeast Dot1p histone H3-Lys79 MTase belongs to Class
AB  - 1 MTases.
ER  -

TY  - JOUR
AU  - Chenoll, E.
AU  - Codoner, F.M.
AU  - Martinez-Blanch, J.F.
AU  - Acevedo-Pierart, M.
AU  - Ormeno, M.L.
AU  - Ramon, D.
AU  - Genoves, S.
TI  - Complete Genome Sequence of the Probiotic Strain Lactobacillus salivarius LPM01.
JO  - Genome Announcements
PY  - 2016
SP  - e01319
EP  - e01316
VL  - 4
AB  - Lactobacillus salivarius LPM01 (DSM 22150) is a probiotic strain able to improve  health
AB  - status in immunocompromised people. Here, we report its complete genome
AB  - sequence deciphered by PacBio single-molecule real-time (SMRT) technology.
AB  - Analysis of the sequence may provide insights into its functional activity and
AB  - safety assessment.
ER  -

TY  - JOUR
AU  - Chenoll, E.
AU  - Codoner, F.M.
AU  - Martinez-Blanch, J.F.
AU  - Ramon, D.
AU  - Genoves, S.
AU  - Menabrito, M.
TI  - Complete Genome Sequence of Lactobacillus rhamnosus Strain BPL5 (CECT 8800), a Probiotic for Treatment of Bacterial Vaginosis.
JO  - Genome Announcements
PY  - 2016
SP  - e00292
EP  - e00216
VL  - 4
AB  - ITALIC! Lactobacillus rhamnosusBPL5 (CECT 8800), is a probiotic strain suitable for the
AB  - treatment of bacterial vaginosis. Here, we report its complete genome
AB  - sequence deciphered by PacBio single-molecule real-time (SMRT) technology.
AB  - Analysis of the sequence may provide insight into its functional activity.
ER  -

TY  - JOUR
AU  - Chenoll, E.
AU  - Codoner, F.M.
AU  - Silva, A.
AU  - Martinez-Blanch, J.F.
AU  - Martorell, P.
AU  - Ramon, D.
AU  - Genoves, S.
TI  - Draft Genome Sequence of Bifidobacterium animalis subsp. lactis Strain CECT 8145, Able To Improve Metabolic Syndrome In Vivo.
JO  - Genome Announcements
PY  - 2014
SP  - e00183
EP  - e00114
VL  - 2
AB  - Bifidobacterium animalis subsp. lactis strain CECT 8145 is able to reduce body fat content and
AB  - improve metabolic syndrome biomarkers. Here, we report the draft
AB  - genome sequence of this strain, which may provide insights into its safety status
AB  - and functional role.
ER  -

TY  - JOUR
AU  - Chenoll, E.
AU  - Rivero, M.
AU  - Codoner, F.M.
AU  - Martinez-Blanch, J.F.
AU  - Ramon, D.
AU  - Genoves, S.
AU  - Moreno, M.J.A.
TI  - Complete Genome Sequence of Bifidobacterium longum subsp. infantis Strain CECT 7210, a Probiotic Strain Active against Rotavirus Infections.
JO  - Genome Announcements
PY  - 2015
SP  - e00105
EP  - e00115
VL  - 3
AB  - Bifidobacterium longum subsp. infantis CECT 7210 is a probiotic strain able to inhibit
AB  - rotavirus in vitro and protect against viral infection in both cell
AB  - cultures and mice. Here, we report its complete genome sequence, as deciphered by
AB  - PacBio single-molecule real-time (SMRT) technology. An analysis of the sequence
AB  - may provide insights into its functional activity.
ER  -

TY  - JOUR
AU  - Cherepanova, N.A.
AU  - Minero, A.S.
AU  - Rakhimova, A.R.
AU  - Gromova, E.S.
TI  - Mechanism of CpG DNA Methyltransferases M.SssI and Dnmt3a Studied by DNA Containing 2-Aminopurine.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2011
SP  - 619
EP  - 631
VL  - 30
AB  - Murine DNA methyltransferases Dnmt3a-CD and M.SssI from Spiroplasma methylate cytosines at CpG
AB  - sites.  The role of 6-oxo groups of guanines in DNA methylation by these enzymes has been
AB  - studied using DNA substrates, which contained 2-aminopurine at different positions.  Removal
AB  - of the 6-oxo group of the guanine located adjacent to the target cytosine in the CpG site
AB  - dramatically reduces the stability of the methyltransferase-DNA complexes and leads to a
AB  - significant decrease in the methylation.  Apparently, 06 of this guanine is involvd in the
AB  - recognition of CpG sites by the enzymes.  Cooperative binding of Dnmt3a-CD to
AB  - 2-aminopurine-containing DNA and the formation of nonproductive enzyme-substrate complexes
AB  - were observed.
ER  -

TY  - JOUR
AU  - Cherepanova, N.A.
AU  - Zhuze, A.L.
AU  - Gromova, E.S.
TI  - Inhibition of murine DNA methyltransferase Dnmt3a by DNA duplexes containing pyrimidine-2(1H)-one.
JO  - Biochemistry
PY  - 2010
SP  - 1244
EP  - 1256
VL  - 75
AB  - Here we studied the inhibition of the catalytic domain of Dnmt3a methyltransferase (Dnmt3a-CD)
AB  - by DNA duplexes containing the mechanism-based inhibitor pyrimidine-2(1H)-one (P) instead of
AB  - the target cytosine. It has been shown that conjugates of Dnmt3a-CD with P-DNA (DNA containing
AB  - pyrimidine-2(1H)-one) are not stable to heating at 65A degrees C in 0.1% SDS. The yield of
AB  - covalent intermediate increases in the presence of the regulatory factor Dnmt3L. The
AB  - importance of the DNA minor groove for covalent intermediate formation during the methylation
AB  - reaction catalyzed by Dnmt3a-CD has been revealed. P-DNA was shown to inhibit Dnmt3a-CD; the
AB  - IC50 is 830 nM. The competitive mechanism of inhibition of Dnmt3a-CD by P-DNA has been
AB  - elucidated. It is suggested that therapeutic effect of zebularine could be achieved by
AB  - inhibition of not only Dnmt1 but also Dnmt3a.
ER  -

TY  - JOUR
AU  - Chernikova, T.N.
AU  - Kyrpides, N.
AU  - Bargiela, R.
AU  - Woyke, T.
AU  - Shapiro, N.
AU  - Whitman, W.B.
AU  - Golyshin, P.N.
TI  - Draft Genome Sequence of Monaibacterium marinum C7(T), Isolated from Seawater from the Menai Straits, Wales, United Kingdom.
JO  - Genome Announcements
PY  - 2018
SP  - e01444
EP  - e01417
VL  - 6
AB  - Here, we report the draft genome sequence of Monaibacterium marinum C7(T), a strain that
AB  - represents a new member of the Roseobacter clade of the family
AB  - Rhodobacteraceae (Alphaproteobacteria). The genome size of Monaibacterium marinum
AB  - C7(T) is 3.7 Mb (3,734,267 bp), with a G+C content of 58.86%.
ER  -

TY  - JOUR
AU  - Chernov, A.P.
AU  - Kaliman, A.V.
TI  - Some peculiarities of the antirestriction mechanism of bacteriophage T5.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1987
SP  - 14
EP  - 19
VL  - 1
AB  - Data are cited on the peculiarities of the unique antirestriction mechanism (ARM) of
AB  - bacteriophage T5.  Phage T5 is not confined by the restriction systems of the second type,
AB  - EcoRI, EcoRII, and EcoRV, although its ARM does not inactivate the restriction endonucleases
AB  - of these systems.  There is no modification of phage T5 DNA at the EcoRII, EcoRI, and EcoRV
AB  - sites in vivo; consequently, the protection of T5 DNA from the action of restriction
AB  - endonucleases is not based on its modification by the ARM.  The ARM of phage T5 protects only
AB  - its own DNA from restriction and does not protect foreign DNA (from phage lambda).  Four
AB  - recognition sites for restriction endonuclease EcoRV have been mapped in T5 DNA and two sites
AB  - for restriction endonuclease EcoRII and three sites for restriction endonuclease HpaI in FST.
AB  - It was shown that in FST of phage T5 there are two zones with boundaries in the region of 5%
AB  - of the length of T5 DNA.  Introduction of recognition sites for restriction endonucleases by
AB  - mutagenesis into the terminal zone of FST leads to a confinement of the mutant T5 phage by the
AB  - corresponding restriction system, whereas the presence of sites in the second zone of FST does
AB  - not lead to confinement of the phage.  It is suggested that the action of (ARM) of phage T5 is
AB  - based on prevention by the antirestriction protein of contact of the T5 DNA with the enzymes
AB  - of the host restriction systems.
ER  -

TY  - JOUR
AU  - Chernov, A.V.
AU  - Lepikhov, K.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Two site-specific endonucleases from thermophilic strain Bacillus species OV.
JO  - Biokhimiia
PY  - 1996
SP  - 1837
EP  - 1847
VL  - 61
AB  - Two site-specific endonucleases, BspOVI and BspOVII, were isolated from the thermophilic
AB  - strain Bacillus species OV.  The highest activity of both the enzymes was observed at 48 C and
AB  - did not depend on the presence of S-adenosyl-L-methionine and ATP.  BspOVI recognizes the
AB  - sequence 5'-GACNNN/NNGTC-3' 3'-CTGNN/NNNCAG-5' and cleaves it as shown by the arrows.
AB  - Consequently, it is an isoschizomer of Eam1105I and belongs to subclass IIN of endonucleases.
AB  - BspOVI has an increased stability during storage.  The enzyme can be used to create T-vectors
AB  - for direct cloning of PCR products.  BspOVII recognizes and cleaves the sequence
AB  - 5'-AT/CGAT-3' 3'-TAGC/TA-5' and, consequently, it is an isoschizomer of ClaI,.  BspOVII is
AB  - blocked by methylation of adenine inside the recognition site.
ER  -

TY  - JOUR
AU  - Chernov, A.V.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A new site-specific endonuclease-methylase from the thermophilic strain of Bacillus species LU11.
JO  - Biokhimiia
PY  - 1994
SP  - 1714
EP  - 1729
VL  - 59
AB  - A new site-specific endonuclease, BspLU11III, was isolated and purified to homogeneity from
AB  - the thermophilic strain Bacillus species LU11. The enzyme recognizes the 5'-GGGAC-3'
AB  - sequence on double-stranded DNA and cleaves it at two places, 10 and 11 nucleotides from the
AB  - 3'-end of the 5'-GGGAC-3' sequence and 14 and 15 nucleotides from the recognized site along
AB  - the complementary strand. In solution the enzyme is a monomer with molecular mass of about 93
AB  - kD. In the presence of S-adenosylmethionine the enzyme has methylase activity. The adenine
AB  - residue in the recognition site is methylated on one of the DNA strands. The restriction
AB  - activity of BspLU11III does not depend on ATP, but is stimulated by 80 microM
AB  - S-adenosyl-methionine. Mg2+ is required for restriction activity. Star activity is observed in
AB  - the presence of sodium chloride. BspLU11III is not a member of the three main classes of
AB  - endonucleases, but has properties similar to type IV site-specific endonucleases.
ER  -

TY  - JOUR
AU  - Chernov, A.V.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - BspLUII III, a bifunctional restriction and modification enzyme from a thermohilic strain Bacillus species LUII.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 1213
EP  - 1214
VL  - 23
AB  - BspLU11III, an isomer of FinI and BsmFI, was found to cleave DNA at two points 10, 11 and 14,
AB  - 15 bp in the different strands away from the recognition site, and in the presence of SAM it
AB  - exhibits the adenine specific methyltransferase activity.
ER  -

TY  - JOUR
AU  - Chernov, A.V.
AU  - Vollmayr, P.
AU  - Walter, J.
AU  - Trautner, T.A.
TI  - Masc2, a C5-DNA-methyltransferase from Ascobolus immersus with similarity to methyltransferases of higher organisms.
JO  - Biol. Chem.
PY  - 1997
SP  - 1467
EP  - 1473
VL  - 378
AB  - The filamentous fungus Ascobolus immersus represents a eukaryotic model organism to study
AB  - genetic phenomena linked to DNA methylation.  Following our previous characterization of a
AB  - gene, masc1 from A. immersus, encoding the 'de novo' C5-DNA-methyltransferase, we report
AB  - here the identification of a second MTase gene, masc2.  The deduced peptide sequence of Masc2
AB  - is similar to previously identified eukaryotic MTases and distinct from Masc1 by having a
AB  - large N-terminal domain in addition to the ubiquitous C-terminal catalytic domain.  Following
AB  - cloning of the gene, Masc2 was overexpressed and purified.  Masc2 shows MTase activity with
AB  - double stranded DNAs.  Structural and biochemical properties of Masc2 suggest that it may
AB  - function as a 'maintenance' MTase.  With this finding, A. immersus represents so far the
AB  - only eukaryotic organism in which two possibly synergistically operating MTases have been
AB  - identified.
ER  -

TY  - JOUR
AU  - Chernov, A.V.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease BspKT8 from the Thermophile strain Bacillus species KT8.
JO  - Biokhimiia
PY  - 1995
SP  - 1318
EP  - 1325
VL  - 60
AB  - A site-specific endonuclease recognizing the sequence 5'-AAGCTT-3' was isolated and purified
AB  - to homogeneity from the thermophilic strain Bacillus species KT8.  The enzyme, BspKT8, has
AB  - molecular mass 34kD and is a monomeric protein in solution.  The activity of BspKT8 does not
AB  - depend on ATP and is not stimulated by S-adenosyl-L-methionine.  The enzyme has the highest
AB  - activity in the wide temperature range from 37 to 48oC.  DNA is cleaved as indicated by the
AB  - arrows 5'-A/AGCT T-3' 3'-T TCGA/A-5' hence, the enzyme is a class II restriction
AB  - endonuclease and an isoschizomer of HindIII.
ER  -

TY  - JOUR
AU  - Chernuhin, V.A.
AU  - Gonchar, D.A.
AU  - Abdurashidov, M.A.
AU  - Belichenko, O.A.
AU  - Dedkov, V.S.
AU  - Mihnenkova, N.A.
AU  - Lomakovskaja, E.N.
AU  - Udal'cova, S.G.
AU  - Degterev, S.H.
TI  - Cloning and characterization of the novel site-specific, methyl-dependent endonuclease EmlI that recognizse and digests 5mC methylated sequence 5'-G(5mC)/NG(5mC)-3'.
JO  - Acta Naturae
PY  - 2016
SP  - 117
EP  - 125
VL  - 8
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Boltengagen, A.A.
AU  - Tarasova, G.V.
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - New Restriction Endonuclease AluBI from Arthrobacter luteus B - AluI Isoshizomer, nonsensitive to Presence of 5-methylcytosine in the Recognition Sequence AGCT.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2007
SP  - 21
EP  - 27
VL  - 3
AB  - A new restriction endonuclease AluBI has been discovered and characterized. AluBI is an
AB  - isoshizomer of well known restriction endonuclease AluI, which recognizes DNA sequence AGCT.
AB  - Unlike AluI, enzyme AluBI is able to cleave DNA when recognition sequence contains
AB  - 5-methylcytosines. AluBI also cleaves recognition sequence with two methylated cytosines, one
AB  - modified at N4 and other at C5 positions. However, new enzyme doesn't cleave DNA with two
AB  - N4-methylcytosines in the recognition site.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Chmuzh, E.V.
AU  - Tomilova, Y.E.
AU  - Nayakshina, T.N.
AU  - Gonchar, D.A.
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - A novel site-specific endonuclease GluI recognizes methylated DNA sequence 5'-G(5mC)^NG(5mC)-3'/3'-(5mC)GN^(5mC)G.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2007
SP  - 13
EP  - 17
VL  - 3
AB  - A novel site-specific endonuclease GluI from the bacterial strain GL24 has been isolated and
AB  - characterized. The enzyme recognizes methylated DNA sequence
AB  - 5'-G(5mC)^NG(5mC)-3'/3'-(5mC)GN^(5mC)G-5' and cleaves it as it is shown by arrow. Due to
AB  - its ability to cleave only modified DNA GluI may be useful for genetic engineering experiments
AB  - as well as for determination of DNA methylation status in eucaryotes.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Golikova, L.N.
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Kashirina, Y.G.
AU  - Netesova, N.A.
AU  - Degtyarev, S.K.
TI  - M.BstF5I-2 and M.BstF5I-4 DNA methyltransferases from BstF5I restriction-modification system of Bacillus stearothermophilus F5.
JO  - Biokhimiia
PY  - 2003
SP  - 967
EP  - 975
VL  - 68
AB  - The BstF5I restriction-modification system from Bacillus stearothermophilus F5 includes four
AB  - site-specific DNA methyltransferases,
AB  - thus differing from all known restriction-modification systems. Here we
AB  - demonstrated for the first time that one bacterial cell can possess two
AB  - pairs of methylases with identical substrate specificities (methylases
AB  - BstF5I-1 and BstF5I-3 recognize GGATG, whereas methylases BstF5I-2 and
AB  - BstF5I-4 recognize CATCC) that modify adenine residues on both DNA
AB  - strands. Different chromatographic methods provide homogenous preparations
AB  - of methylases BstF5I-2 and BstF5I-4. We estimated the principal kinetic
AB  - parameters of the reaction of transfer of methyl group from the donor
AB  - S-adenosyl-L-methionine to the recognition site 5;-CATCC-3; catalyzed by
AB  - BstF5I-2 and BstF5I-4 DNA [N6-adenine]-methyltransferases from the BstF5I
AB  - restriction-modification system.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Belichenko, O.A.
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Lomakovskaya, E.N.
AU  - Udalyeva, S.G.
AU  - Degtyarev, S.K.
TI  - Cloning and characterization of a new site specific methyl-directed endonuclease ElmI recognizing and cleaving C5-methylated DNA sequence 5'-G(5mC)^NG(5mC)-3'.
JO  - Acta Naturae
PY  - 2016
SP  - 42
EP  - 51
VL  - 28
AB  - As a result of the search of amino acid sequences homologous to MD-endonuclease BisI a
AB  - putative open reading frames of MD-endonucleases have been identified in Enterobacteria
AB  - genomes. A highly conserved DNA primary structure of these open reading frames in different
AB  - genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed creating the
AB  - primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural
AB  - sources.  The DNA fragment about 440 bp in length was amplified by use the genomic DNA of a
AB  - wild E.coli LM N17 strain as a template and was inserted into the pMTL22 vector. The resulting
AB  - endonuclease activity was detected in E.coli ER 2267 strain being transformed with obtained
AB  - construction. A new enzyme named ElmI was purified by chromatographic techniques from
AB  - recombinant strain biomass.  It was found this enzyme like BisI specifically cleaved
AB  - methylated DNA sequence 5'-GCNGC-3' before the central nucleotide N in the case of the
AB  - presence of two 5-methylcytosines within it. However, unlike BisI, ElmI more efficiently
AB  - cleaves this sequence if more than two cytosine residues are methylated.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Kashirina, Y.G.
AU  - Sukhanova, K.S.
AU  - Abdurashitov, M.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Isolation and characterization of biochemical properties of DNA methyltransferase FauIA modifying the second cytosine in the  nonpalindromic sequence 5 '-CCCGC-3 '.
JO  - Biokhimiia
PY  - 2005
SP  - 829
EP  - 837
VL  - 70
AB  - A gene encoding DNA methyltransferase (methylase) FauIA of the restriction-modification system
AB  - FauI from Flavobaclerium aquatile (recognizing sequence 5'-CCCGC-3') was cloned in pJW
AB  - vector. The latter was used for transformation of E. coli RRI cells followed by subsequent
AB  - thermoinduction and biomass elaboration. Highly purified DNA methyltransferase FauIA
AB  - preparation was obtained using chromatography on different sorbents. The molecular mass of the
AB  - isolated enzyme of about 39 kD corresponds to its theoretical value. The enzyme was
AB  - characterized by temperature and pH optima of 33 degrees C and pH 7.5, respectively.
AB  - Methylation of a synthetic oligonucleotide by FauIA methylase followed by its cleavage with
AB  - various restrictases and analysis of the resultant restriction fragments revealed that FauIA
AB  - methylase modified the second cytosine residue in the sequence 5'-CCCGC-3'. Kinetic analysis
AB  - revealed Km and catalytic constant values of 0.16 mu M and 0.05 min(-1), respectively.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Kashirina, Y.G.
AU  - Tomilova, J.E.
AU  - Gonchar, D.A.
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Degtyarev, S.K.
TI  - New Eight Bases Cutter AbsI from Arthrobacter species Recognizes Palindromic DNA Sequence 5'-CC^TCGAGG-3'.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2006
SP  - 29
EP  - 34
VL  - 2
AB  - Bacterial strain Arthrobacter species7M06 producing site-specific endonuclease AbsI has been
AB  - discovered. AbsI recognizes palindromic octanucleotide DNA sequence 5'-CC^TCGAGG-3' and
AB  - hydrolyzes it after second cytosine, producing 5'- sticky ends, which are compatible with
AB  - sticky ends after DNA cleavage by restriction endonucleases XhoI (5'-C^TCGAG-3'), PspXI
AB  - (5'-VC^TCGAGB-3') and SalI (5'-G^TCGAC-3'). Among all known rare-cutting site-specific
AB  - endonucleases AbsI is the only enzyme which has no recognition sequences in standard
AB  - substrates Lambda and T7 DNAs and Adenovirus type 2 DNA.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Kileva, E.V.
AU  - Sokolova, V.A.
AU  - Gonchar, D.A.
AU  - Golikova, L.N.
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Degtyarev, S.K.
TI  - A new methyl-directed site-specific DNA endonuclease MteI cleaves nine nucleotides sequence 5-G(5mC)G(5mC)^NG(5mC)GC-3/3-CG(5mC)GN^(5mC)G(5mC)G-5.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2012
SP  - 16
EP  - 26
VL  - 8
AB  - We have discovered and purified a new methyl-directed site-specific DNA endonuclease MteI from
AB  - bacterial strain Microbacterium testaceum 17B. The enzyme recognizes methylated DNA sequence
AB  - and doesnt cleave unmethylated DNA. MteI is a first methyl-directed site-specific DNA
AB  - endonuclease recognizing a prolonged DNA sequence and its activity depends on a number of
AB  - 5-methycytosines and their positions in the recognition site. MteI cleaves DNA sequence
AB  - 5-G(5mC)G(5mC)NG(5mC)GC-3/3-CG(5mC)GN(5mC)G(5mC)G-5 as indicated by arrows and this
AB  - nonanucleotide is a minimal recognition site. The enzyme activity is significantly higher if
AB  - 5-GC-3 dinucleotides in this site are replaced by 5-G(5mC)-3 dinucleotides and additional
AB  - 5-G(5mC)-3 dinucleotides are present at 5-ends in both DNA strands. Due to an ability to
AB  - cleave only prolonged methylated DNA sequences MteI may find a practical application in the
AB  - molecular biology and epigenetics studies.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Kuznetsov, V.V.
AU  - Gonchar, D.A.
AU  - Kashirina, Y.G.
AU  - Netesova, N.A.
AU  - Degtyarev, S.K.
TI  - Substrate Specificity and Biochemical Properties of M3.BstF5I DNA Methyltransferase from the BstF5I Restriction-Modification System.
JO  - Biochemistry
PY  - 2010
SP  - 63
EP  - 71
VL  - 75
AB  - Optimal conditions for DNA methylation by the M3.BstF5I enzyme from Bacillus
AB  - stearothermophilus and kinetic parameters of lambda phage DNA
AB  - modification and that of a number of oligonucleotide substrates are
AB  - established. Comparison of M1.BstF5I and M3.BstF5I kinetic parameters
AB  - revealed that with similar temperature optima and affinity for DNA,
AB  - M3.BstF5I has nearly fourfold lower turnover number (0.24 min(-1)) and
AB  - modifies the hemimethylated recognition site with lower efficiency
AB  - under optimal conditions than the unmethylated one. In contrast to
AB  - another three methylases of the BstF5I restriction-modification system,
AB  - the M3. BstF5I enzyme is able to optionally modify the noncanonical
AB  - 5'-GGATC-3' DNA sequence with a rate more than one order of magnitude
AB  - lower than the methylation rate of the canonical 5'-GGATG-3'
AB  - recognition site.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Nayakshina, T.N.
AU  - Abdurashitov, M.A.
AU  - Tomilova, Y.E.
AU  - Mezentseva, N.V.
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - A novel restriction endonuclease GlaI recognizes the methylated sequence 5'-G(5mC)^GC-3'.
JO  - Biotekhnologiya
PY  - 2006
SP  - 26
EP  - 30
VL  - 0
AB  - A novel restriction endonuclease GlaI from soil bacterium strain GL29 has been isolated and
AB  - characterized. The enzyme recognizes the methylated DNA sequence 5'-G(m5C)^GC-3' and cleaves
AB  - it as indicated by the arrow. Due to its ability to only cleave modified DNA, GlaI can find a
AB  - practical application in genetic engineering experiments as well as in determination of
AB  - eukaryotic DNA methylation status.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Nayakshina, T.N.
AU  - Gonchar, D.A.
AU  - Tomilova, J.E.
AU  - Tarasova, M.V.
AU  - Dedkov, V.S.
AU  - Mikhenenkova, N.A.
AU  - Degtyarev, S.K.
TI  - A new site-specific methyl-directed DNA endonuclease PkrI recognizes and cuts methylated DNA sequence 5'-GCN^GC-3'/3'-CG^NCG-5' carrying at least three 5-methylcytosines.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2011
SP  - 35
EP  - 42
VL  - 7
AB  - Type II restriction endonucleases are the most known and well studied enzymes among all
AB  - site-specific DNA endonucleases.  As a rule restriction endonuclease and corresponding
AB  - DNA-methyltransferase form restriction-modification system.  RE cleaves foreign DNA at a short
AB  - recognition site, whereas a cognate MTase modifies the same sequence in a host DNA protecting
AB  - it against digestion with RE.  Methyl-directed site-specific endonucleases hydrolyze only
AB  - methylated DNA and their biochemical properties are similar to the restriction endonucleases
AB  - ones.  Recently discovered at SibEnzyme site-specific 5-methylcytosine directed DNA
AB  - endonucleases recognize and cleave different methylated DNA sequences, require only mg2+ ions
AB  - as a cofactor and completely hydrolyze DNA.  Three MD endonucleases BlsI, BisI and GluI
AB  - recognize different variants of methylated 5'-GCNGC-3' sequence and cleave DNA before or
AB  - after N.  In the present work we describe a substrate specificity of new methyl-directed
AB  - DNA-endonuclease PkrI, which recognizes methylated DNA sequence 5'-GCN^GC-3'/3'-CG(down
AB  - arrow)NCG-5' carrying at lest three 5-methylcytosies and cleaves it as indicated by arrows.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Seggewiss, J.
AU  - Kashirina, Y.G.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Purification and properties of recombinant DNA methyltransferase M2.BstSE of the BstSEI nickase-modification system.
JO  - Mol. Biol. (Mosk)
PY  - 2009
SP  - 8
EP  - 15
VL  - 43
AB  - The operon for the Bacillus stearothermophilus SE-589 nickase-modification system (NM.BstSEI,
AB  - recognition site 5'-GAGTC-3')
AB  - includes two DNA methyltransferase (M.) genes, bstSEIM1 and bstSEIM2.
AB  - The gene encoding M2.BstSEI was cloned in pJW and expressed in
AB  - Escherichia coli cells. M2.BstSEI was purified by chromatography and
AB  - displayed maximal activity at 55A degrees C and pH 7.5. The enzyme
AB  - modified adenine in the nickase recognition site 5'-GAGTC-3' and was
AB  - specific for 5'-GASTC-3' substrates. The kinetic parameters of the
AB  - methylation reaction were determined. The catalytic constant was 2.2
AB  - min(-1), and the Michaelis constant was 9.8 nM on T7 DNA and 5.8 mu M
AB  - on SAM.
ER  -

TY  - JOUR
AU  - Chernukhin, V.A.
AU  - Tomilova, J.E.
AU  - Chmuzh, E.V.
AU  - Sokolova, O.O.
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - Site-specific endonuclease BlsI recognizes DNA sequence 5'-G(5mC)N^GC-3' and cleaves it producing 3' sticky ends.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2007
SP  - 28
EP  - 33
VL  - 3
AB  - A bacterial strain Bacillus simplex 23, a producer of a site-specific endonuclease BlsI has
AB  - been discovered. BlsI recognizes the methylated DNA sequence 5'-G(5mC)NGC-3', like the
AB  - earlier described site-specific endonuclease BisI (recognition site 5'-G(5mC)^NGC-3'), but
AB  - differs in positions of DNA cleavage producing 3'-protruding ends. Due to its ability to
AB  - cleave only methylated DNA, enzyme BlsI can find an application in gene engineering works as
AB  - well as in determining the methylation status of eucaryotic DNA.
ER  -

TY  - JOUR
AU  - Cherny, D.I.
AU  - Kurakin, A.V.
TI  - Site-selective targeting of duplex DNA with methyltransferase and biotinylated synthetic reagents.
JO  - Electron Microsc.
PY  - 1994
SP  - 449
EP  - 450
VL  - 3A
AB  - Site-selective interaction of some ligands with duplex DNA may provide
AB  - the tools for developing gene-targeted drugs and for mapping of DNA and genomes.  In
AB  - this study we have examined the interaction of methyltransferase and biotinylated both
AB  - deoxyoligonucleotides and peptide nucleic acid (PNA) with duplex DNA.  It was shown
AB  - that the target sequence can be EM detected via specific complex formation either with the
AB  - enzyme per se or streptavidin as an EM marker.  These approaches allow the study  of the
AB  - site-selective interaction of these ligands with DNA and introduce novel types of sequences
AB  - for mapping of DNA and genomes.
ER  -

TY  - JOUR
AU  - Cherry, J.L.
TI  - Methylation-Induced Hypermutation in Natural Populations of Bacteria.
JO  - J. Bacteriol.
PY  - 2018
SP  - e00371
EP  - e00318
VL  - 200
AB  - Methylation of DNA at the C5 position of cytosine occurs in diverse organisms. This
AB  - modification can increase the rate of C->T transitions at the methylated
AB  - position. In E. coli and related enteric bacteria, the inner C residues of the
AB  - sequence CCWGG (W=A or T) are methylated by the Dcm enzyme. These sites are
AB  - hotspots of mutation during rapid growth in the laboratory, but not in non
AB  - dividing cells, in which repair by the Vsr protein is effective. It has been
AB  - suggested that hypermutation at these sites is a laboratory artifact and does not
AB  - occur in nature. Many other methyltransferases, with a variety of specificities,
AB  - can be found in bacteria, usually associated with restriction enzymes and
AB  - confined to a subset of the population. Their methylation targets are also
AB  - possible sites of hypermutation. Here I show, using whole genome sequence data
AB  - for thousands of isolates, that there is indeed considerable hypermutation at Dcm
AB  - sites in natural populations: their transition rate is approximately eight times
AB  - the average. I also demonstrate hypermutability of targets of restriction
AB  - associated methyltransferases in several distantly related bacteria, ranging from
AB  - a factor of 12 increase in transition rate to a factor of 58. In addition, I
AB  - demonstrate how patterns of hypermutability inferred from massive sequence data
AB  - can be used to determine previously unknown methylation patterns and
AB  - methyltransferase specificities.IMPORTANCE A common type of DNA modification,
AB  - addition of a methyl group to cytosine (C) at carbon atom C5, can greatly
AB  - increase the rate of mutation of the C to a T. In mammals, methylation of CG
AB  - sequences increases the rate of CG->TG mutations. It is unknown whether cytosine
AB  - C5 methylation increases mutation rate in bacteria under natural conditions. I
AB  - show that sites methylated by the Dcm enzyme exhibit an eight fold increase in
AB  - mutation rate in natural bacterial populations. I also show that modifications at
AB  - other sites in various bacteria also increase the mutation rate, in some cases by
AB  - a factor of forty or more. Finally, I demonstrate how this phenomenon can be used
AB  - to infer sequence specificities of methylation enzymes.
ER  -

TY  - JOUR
AU  - Chertkov, O. et al.
TI  - Complete genome sequence of Tolumonas auensis type strain (TA 4).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 112
EP  - 120
VL  - 5
AB  - Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named  species of
AB  - the genus Tolumonas in the family Aeromonadaceae. The strain is of
AB  - interest because of its ability to produce toluene from phenylalanine and other
AB  - phenyl precursors, as well as phenol from tyrosine. This is of interest because
AB  - toluene is normally considered to be a tracer of anthropogenic pollution in
AB  - lakes, but T. auensis represents a biogenic source of toluene. Other than
AB  - Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only
AB  - other member in the family Aeromonadaceae with a completely sequenced type-strain
AB  - genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116
AB  - RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI
AB  - 2008.
ER  -

TY  - JOUR
AU  - Chertkov, O. et al.
TI  - Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 280
EP  - 289
VL  - 2
AB  - Aminobacterium colombiense Baena et al. 1999 is the type species of the genus Aminobacterium.
AB  - This genus is of large interest because of its isolated
AB  - phylogenetic location in the family Synergistaceae, its strictly anaerobic
AB  - lifestyle, and its ability to grow by fermentation of a limited range of amino
AB  - acids but not carbohydrates. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is the second
AB  - completed genome sequence of a member of the family Synergistaceae and the first
AB  - genome sequence of a member of the genus Aminobacterium. The 1,980,592 bp long
AB  - genome with its 1,914 protein-coding and 56 RNA genes is part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Chertkov, O. et al.
TI  - Complete genome sequence of Thermomonospora curvata type strain (B9).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 13
EP  - 22
VL  - 4
AB  - Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This
AB  - genus is of interest because members of this clade are
AB  - sources of new antibiotics, enzymes, and products with pharmacological activity.
AB  - In addition, members of this genus participate in the active degradation of
AB  - cellulose. This is the first complete genome sequence of a member of the family
AB  - Thermomonosporaceae. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 5,639,016 bp long genome
AB  - with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Chertkov, O. et al.
TI  - Complete genome sequence of Hirschia baltica type strain (IFAM 1418T).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 287
EP  - 297
VL  - 5
AB  - The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacte-ria
AB  - isolated from marine environments with striking morphologies and an unusual mode of cell
AB  - growth. Here, we report the complete genome sequence Hirschia baltica, which is only the
AB  - second a member of the Hyphomonadaceae with a published genome sequence. H. bal-tica is of
AB  - special interest because it has a dimorphic life cycle and is a stalked, budding bacte-rium.
AB  - The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 pro-tein-coding
AB  - and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.
ER  -

TY  - JOUR
AU  - Chervaux, C.
AU  - Grimaldi, C.
AU  - Bolotin, A.
AU  - Quinquis, B.
AU  - Legrain-Raspaud, S.
AU  - van Hylckama, V.J.E.
AU  - Denariaz, G.
AU  - Smokvina, T.
TI  - Genome Sequence of the Probiotic Strain Bifidobacterium animalis subsp. lactis CNCM I-2494.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5560
EP  - 5561
VL  - 193
AB  - Bifidobacterium animalis subsp. lactis CNCM I-2494 is part of a commercialized fermented dairy
AB  - product with documented health benefits
AB  - revealed by multiple randomized placebo-controlled clinical trials. Here
AB  - we report the complete genome sequence of this strain, which has a
AB  - circular genome of 1,943,113 bp with 1,660 open reading frames and 4
AB  - ribosomal operons.
ER  -

TY  - JOUR
AU  - Chevalier, B.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - The LAGLIDADG homing endonuclease family.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 33
EP  - 47
VL  - 16
AB  - The LAGLIDADG protein family includes the first identified and biochemically characterized
AB  - intron-encoded proteins, as described in this volume by Dujon.  It has been variously termed
AB  - the "DOD", "Dodecapeptide', "dodecamer", and "decapeptide" endonuclease family, based on the
AB  - conservation of a ten-residue sequence motif.  The LAGLIDADG endonucleases are the most
AB  - diverse of the homing endonuclease families.  Their host range includes the genomes of plant
AB  - and algal chloroplasts, fungal and protozoan mitochondria, bacteria and Archaea.  One reason
AB  - for the wide phylogenetic distribution of LAGLIDADG genes appears to be their remarkable
AB  - ability to invade unrelated types of intervening sequences, including group I introns,
AB  - archaeal introns and inteins.  Descendents of LAGLIDADG homing endonucleases also include the
AB  - yeast HO mating type switch endonuclease, which is encoded by an independent reading frame
AB  - rather than within an intron, but does carry remnants of an inactive intein domain, and
AB  - maturases that assist in RNA splicing.
ER  -

TY  - JOUR
AU  - Chevalier, B.
AU  - Sussman, D.
AU  - Otis, C.
AU  - Noel, A.J.
AU  - Turmel, M.
AU  - Lemieux, C.
AU  - Stephens, K.
AU  - Monnat, R.J.
AU  - Stoddard, B.L.
TI  - Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease.
JO  - Biochemistry
PY  - 2004
SP  - 14015
EP  - 14026
VL  - 43
AB  - The LAGLIDADG homing endonucleases include free-standing homodimers, pseudosymmetric monomers,
AB  - and related enzyme domains embedded within
AB  - inteins. DNA-bound structures of homodimeric I-CreI and monomeric
AB  - I-SceI indicate that three catalytic divalent metal ions are
AB  - distributed across a pair of overlapping active sites, with one shared
AB  - metal participating in both strand cleavage reactions. These structures
AB  - differ in the precise position and binding interactions of the metals.
AB  - We have studied the metal dependence for the I-CreI homodimer using
AB  - site-directed mutagenesis of active site residues and assays of binding
AB  - affinity and cleavage activity. We have also reassessed the binding of
AB  - a nonactivating metal ion (calcium) in the wild-type enzyme-substrate
AB  - complex, and determined the DNA-bound structure of two inactive enzyme
AB  - mutants. The conclusion of these studies is that the catalytic
AB  - mechanism of symmetric LAGLIDADG homing, endonucleases, and probably
AB  - many of their monomeric cousins, involves a canonical two-metal
AB  - mechanism in each of two active sites, which are chemically and
AB  - structurally tethered to one another by a shared metal ion. Failure to
AB  - occupy the shared metal site, as observed in the presence of calcium or
AB  - when the metal-binding side chain from the LAGLIDADG motif (Asp 20) is
AB  - mutated to asparagines, prevents cleavage by the enzyme.
ER  -

TY  - JOUR
AU  - Chevalier, B.
AU  - Turmel, M.
AU  - Lemieux, C.
AU  - Monnat, R.J.
AU  - Stoddard, B.L.
TI  - Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 253
EP  - 269
VL  - 329
AB  - Homing endonucleases are highly specific catalysts of DNA strand breaks that induce the
AB  - transposition of mobile intervening sequences containing
AB  - the endonuclease open reading frame. These enzymes recognize long DNA
AB  - targets while tolerating individual sequence polymorphisms within those
AB  - sites. Sequences of the homing endonucleases themselves diversify to a
AB  - great extent after founding intron invasion events, generating highly
AB  - divergent enzymes that recognize similar target sequences. Here, we
AB  - visualize the mechanism of flexible DNA recognition and the pattern of
AB  - structural divergence displayed by two homing endonuclease isoschizomers.
AB  - We determined structures of I-CreI bound to two DNA target sites that
AB  - differ at eight of 22 base-pairs, and the structure of an isoschizomer,
AB  - I-MsoI, bound to a nearly identical DNA target site. This study
AB  - illustrates several principles governing promiscuous base-pair recognition
AB  - by DNA-binding proteins, and demonstrates that the isoschizomers display
AB  - strikingly different protein/DNA contacts. The structures allow us to
AB  - determine the information content at individual positions in the binding
AB  - site as a function of the distribution of direct and water-mediated
AB  - contacts to nucleotide bases, and provide an evolutionary snapshot of
AB  - endonucleases at an early stage of divergence in their target specificity.
ER  -

TY  - JOUR
AU  - Chevalier, B.S.
AU  - Kortemme, T.
AU  - Chadsey, M.S.
AU  - Baker, D.
AU  - Monnat, R.J.
AU  - Stoddard, B.L.
TI  - Design, activity, and structure of a highly specific artificial endonuclease.
JO  - Mol. Cell
PY  - 2002
SP  - 895
EP  - 905
VL  - 10
AB  - We have generated an artificial highly specific endonuclease by fusing domains of homing
AB  - endonucleases I-Dmol and I-Crel and creating a new 1400
AB  - Angstrom(2) protein interface between these domains. Protein engineering
AB  - was accomplished by combining computational redesign and an in vivo
AB  - protein-folding screen. The resulting enzyme, E-Drel (Engineered
AB  - I-Dmol/I-Crel), binds a long chimeric DNA target site with nanomolar
AB  - affinity, cleaving it precisely at a rate equivalent to its natural
AB  - parents. The structure of an E-Drel/DNA complex demonstrates the accuracy
AB  - of the protein interface redesign algorithm and reveals how catalytic
AB  - function is maintained during the creation of the new endonuclease. These
AB  - results indicate that it may be possible to generate novel highly specific
AB  - DNA binding proteins from homing endonucleases.
ER  -

TY  - JOUR
AU  - Chevalier, B.S.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
JO  - Nat. Struct. Biol.
PY  - 2001
SP  - 312
EP  - 316
VL  - 8
AB  - Homing endonucleases, like restriction enzymes, cleave double-stranded DNA at specific target
AB  - sites. The cleavage mechanism(s) utilized by
AB  - LAGLIDADG endonucleases have been difficult to elucidate; their active
AB  - sites are divergent, and only one low resolution cocrystal structure
AB  - has been determined, Here we report two high resolution structures of
AB  - the dimeric I-CreI homing endonuclease bound to DNA: a substrate
AB  - complex with calcium and a product complex with magnesium, The bound
AB  - metals in both complexes are verified by manganese anomalous difference
AB  - maps, The active sites are positioned close together to facilitate
AB  - cleavage across the DNA minor groove; each contains one metal ion
AB  - bound between a conserved aspartate (Asp 20) and a single scissile
AB  - phosphate. A third metal ion bridges the two active sites. This
AB  - divalent cation is bound between aspartate residues from the active
AB  - site of each subunit and is in simultaneous contact with the scissile
AB  - phosphates of both DNA strands. A metal-bound water molecule acts as
AB  - the nucleophile and is part of an extensive network of ordered water
AB  - molecules that are positioned by enzyme side chains; These structures
AB  - illustrate a unique variant of a two-metal endonuclease mechanism is
AB  - employed by the highly divergent LAGLIDADG enzyme family.
ER  -

TY  - JOUR
AU  - Chevalier, B.S.
AU  - Stoddard, B.L.
TI  - Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3757
EP  - 3774
VL  - 29
AB  - Homing endonucleases confer mobility to their host intervening sequence, either an intron or
AB  - intein, by catalyzing a highly specific double-strand break in a cognate allele lacking the
AB  - intervening sequence. These proteins are characterized by their ability to bind long DNA
AB  - target sites (14-40 bp) and their tolerance of minor sequence changes in these sites. A wealth
AB  - of biochemical and structural data has been generated for these enzymes over the past few
AB  - years. Herein we review our current understanding of homing endonucleases, including their
AB  - diversity and evolution, DNA-binding and catalytic mechanisms, and attempts to engineer them
AB  - to bind novel DNA substrates.
ER  -

TY  - JOUR
AU  - Chi, M.-G.
TI  - Isolation and purification of EcoRI restriction endonuclease.
JO  - Junshi Yixue Kexueyuan Yuankan
PY  - 1995
SP  - 132
EP  - 135
VL  - 19
AB  - EcoRI restriction endonuclease was isolated from Escherichia coli RY13 and K121100.  The
AB  - purification process involved treatment with ammonium sulfate, polyethyleneimine and
AB  - phosphocellulose chromatography.  By this method a highly purified EcoRI restriction
AB  - endonuclease can be prepared.  The enzyme recognizes unique sites on DNA, with the minimal
AB  - recognition site being a hexanucleotide sequence characterized by 2-fold symmetry.  Thus, the
AB  - EcoRI enzyme is one of the simplest sequence-specific DNA enzymes known and is well suited to
AB  - a study of DNA sequence recognition by proteins.
ER  -

TY  - JOUR
AU  - Chiara, M.
AU  - D'Erchia, A.M.
AU  - Manzari, C.
AU  - Minotto, A.
AU  - Montagna, C.
AU  - Addante, N.
AU  - Santagada, G.
AU  - Latorre, L.
AU  - Pesole, G.
AU  - Horner, D.S.
AU  - Parisi, A.
TI  - Draft Genome Sequences of Six Listeria monocytogenes Strains Isolated from Dairy  Products from a Processing Plant in Southern Italy.
JO  - Genome Announcements
PY  - 2014
SP  - e00282
EP  - e00214
VL  - 2
AB  - Here we announce the draft genome sequences of 6 Listeria monocytogenes strains from ricotta
AB  - cheese produced in a dairy processing plant located in southern Italy and potentially involved
AB  - in a multistate outbreak of listeriosis in the United States.
ER  -

TY  - JOUR
AU  - Chibani, C.M.
AU  - Poehlein, A.
AU  - Roth, O.
AU  - Liesegang, H.
AU  - Wendling, C.C.
TI  - Draft Genome Sequence of Vibrio splendidus DSM 19640.
JO  - Genome Announcements
PY  - 2017
SP  - e01368
EP  - e01317
VL  - 5
AB  - Here, we present the draft genome sequence of Vibrio splendidus type strain DSM 19640. V.
AB  - splendidus is an abundant species among coastal vibrioplankton. The
AB  - assembly resulted in a 5,729,362-bp draft genome with 5,032 protein-coding
AB  - sequences, 6 rRNAs, and 117 tRNAs.
ER  -

TY  - JOUR
AU  - Chiciudean, I.
AU  - Nie, Y.
AU  - Tanase, A.M.
AU  - Stoica, I.
AU  - Wu, X.L.
TI  - Complete genome sequence of Tsukamurella sp. MH1, a wide-chain length alkane-degrading actinomycete.
JO  - J. Biotechnol.
PY  - 2017
SP  - 1
EP  - 5
VL  - 268
AB  - Tsukamurella sp. strain MH1, capable to use a wide range of n-alkanes as the only
AB  - carbon source, was isolated from petroleum-contaminated soil (Pitesti, Romania)
AB  - and its complete genome was sequenced. The 4,922,396bp genome contains only one
AB  - circular chromosome with a G+C content of 71.12%, much higher than the type
AB  - strains of this genus (68.4%). Based on the 16S rRNA genes sequence similarity,
AB  - strain MH1 was taxonomically identified as Tsukamurella carboxydivorans. Genome
AB  - analyses revealed that strain MH1 is harboring only one gene encoding for the
AB  - alkB-like hydroxylase, arranged in a complete alkane monooxygenase operon. This
AB  - is the first complete genome of the specie T. carboxydivorans, which will provide
AB  - insights into the potential of Tsukamurella sp. MH1 and related strains for
AB  - bioremediation of petroleum hydrocarbons-contaminated sites and into the
AB  - environmental role of these bacteria.
ER  -

TY  - JOUR
AU  - Chien, H.R.
TI  - Cloning and genetic analysis of restriction and modification systems from Neisseria gonorrhoeae.
JO  - Ph.D. Thesis, University of Maryland, USA
PY  - 1991
SP  - 1
EP  - 126
AB  - Endonucleases with the specificities of S.NgoI and S.NgoIII were isolated from Neisseria
AB  - gonorrhoeae MS11; but the remaining endonucleases with the specificities of S.NgoII, S.NgoIV,
AB  - S.NgoV, S.NgoVI, S.NgoVIII, and S.NgoIX were not produced at detectable levels in MS11. The
AB  - genes encoding the RM NgoMI (recognition sequence GCCGGC), the RM NgoMII (TCACC), and the RM
AB  - NgoMIII (CCGCGG) from gonococcus MS11 were cloned in E. coli. The gene encoding the M.NgoBIII
AB  - (GGNNCC) from gonococcus MUG116 was also cloned. The cloned endonuclease R.NgoMI was purified
AB  - by column chromatography and the cutting site determined to be G/CCGGC. The base methylated in
AB  - the sequence GCCGGC by the M.NgoMI in vivo was determined to be the the first C in the
AB  - sequence GCCGGC. Plasmids encoding M.NgoMI, M.NgoMIII, and M.NgoBIII were restricted when
AB  - these plasmids were used to transform MM294 (mcr+), due to the action of the mcr gene products
AB  - on the methylated DNA. Plasmids encoding for M.NgoMII were not restricted because the mcr gene
AB  - products do not recognize S.NgoMII specificity. The DNA sequence of the NgoMI
AB  - restriction/methylation system was determined and two open reading frames were identified. The
AB  - molecular weight of the purified endonuclease was determined to be 33,000 Dal, and was in good
AB  - agreement with the size predicted from the DNA sequence (31,759 Dal). M.NgoMI contains the
AB  - four conserved domains found in cytosine-specific DNA methylases, however the size and spacing
AB  - between these domains are significantly different from that in the conserved domains in other
AB  - cytosine-specific DNA methylases. Two restriction/modification mutants MUG700 and MUG701 were
AB  - derived from MS11. Mutant MUG700 was RM NgoII negative, while mutant MUG701 was RM NgoMI
AB  - negative, as determined by appropriate endonuclease digestion and Southern hybridizations. The
AB  - RM NgoII and RM NgoMI systems seem involved in regulating the biosynthesis of LOS in N.
AB  - gonorrhoeae. The RM NgoMI system also seems involved in regulating the stability of colony
AB  - morphology. Finally, endonuclease R.NgoII was able to mediate host restriction in N.
AB  - gonorrhoeae, while endonuclease R.NgoMI was not, even though both endonucleases were not
AB  - produced at detectable levels in the strain MS11. [ The enzyme called NgoMI in this abstract
AB  - has been renamed NgoMIV, Jan/1998. ] [ The enzyme called NgoMII in this abstract has been
AB  - renamed NgoMVIII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Chien, M. et al.
TI  - The genomic sequence of the accidental pathogen Legionella pneumophila.
JO  - Science
PY  - 2004
SP  - 1966
EP  - 1968
VL  - 305
AB  - We present the genomic sequence of Legionella pneumophila, the bacterial agent of
AB  - Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated
AB  - fresh water. The genome includes a 45-kilobase pair element that can exist in chromosomal and
AB  - episomal forms, selective expansions of important gene families, genes for unexpected
AB  - metabolic pathways, and previously unknown candidate virulence determinants. We highlight the
AB  - genes that may account for Legionella's ability to survive in protozoa, mammalian
AB  - macrophages, and inhospitable environmental niches and that may define new therapeutic
AB  - targets.
ER  -

TY  - JOUR
AU  - Chien, R.H.
AU  - Stein, D.C.
AU  - Seifert, H.S.
AU  - Floyd, K.
AU  - So, M.
TI  - Cloning and characterization of a restriction and modification system from Neisseria gonorrhoeae strain MS11.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1988
SP  - 213
EP  - 213
VL  - 88
AB  - A type II restriction and modification (R/M) system from Neisseria gonorrhoeae MS11 was cloned
AB  - and expressed in Escherichia coli HB101.  R/M clones were constructed by the partial digestion
AB  - of DNA from MS11 with MboI and HpaII and its insertion into the BamHI and ClaI site of the
AB  - cloning vector pHSS7.  The R/M clone, pCBB49, was identified by its resistance to cleavage
AB  - with NaeI, a restriction enzyme that has 1 site in the cloning vector.  The R/M genes were
AB  - encoded by a 2.5 kb fragment in plasmid pCBB49.1, a deletion derivative of pCBB49.  The
AB  - restriction (NgoMI) and modification (M.NgoMI) enzymes were purified from HB101 (pCBB49.1) by
AB  - column chromatography.  The recognition sequence for NgoMI was GCCGGC.  When plasmid pCBB49.1
AB  - was introduced into HB101 (pFT180), the single NgoMI site of pFT180 was now resistant to
AB  - cleavage by NaeI.  When pCBB49.1 was used to transform E. coli strains ER1563 (mcrB+) and
AB  - ER1562 (mcrB), a two log difference in transformation frequencies was obtained due to the
AB  - action of the mcrB gene product on the methylated DNA.
AB  - [ The enzyme called NgoMI in this abstract has been renamed NgoMIV, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Chies, J.M.
AU  - de O-Dias, A.C.
AU  - Maia, H.M.M.
AU  - Astolfi-Filho, S.
TI  - BanAI a new isoschizomer of the type II restriction endonuclease HaeIII discovered in a Bacillus anthracis isolate from Amazon Basin.
JO  - FEMS Microbiol. Lett.
PY  - 2002
SP  - 97
EP  - 101
VL  - 215
AB  - Bacillus anthracis was isolated and identified from a bacterial collection of samples from the
AB  - Amazon river bank.  Type II restriction endonuclease activity was detected in this prokaryote,
AB  - the enzyme was purified, the molecular mass of the native protein estimated by gel filtration,
AB  - and optima pH, temperature and salt requirements were determined.  Quality control assays
AB  - showed complete absence of 'non-specific nucleases'.  Restriction cleavage analysis and DNA
AB  - sequencing of restriction fragments allowed unequivocal demonstration of 5'-GG/CC-3' as the
AB  - recognition sequence.  This enzyme was named BanAI and is therefore an isoschizomer of the
AB  - prototype restriction endonuclease HaeIII.  This is the first report of a type II restriction
AB  - endonuclease identified, purified from a natural isolate of B. anthracis.
ER  -

TY  - JOUR
AU  - Chies, J.M.
AU  - Dias, A.C.D.O.
AU  - Maia, H.M.M.
AU  - Braga, L.P.D.S.
AU  - Astolfi-Filho, S.
TI  - Isolation and characterization of Bliai, an isoschizomer of CLAI from Bacillus licheniformis.
JO  - Braz. J. Microbiol.
PY  - 2006
SP  - 551
EP  - 555
VL  - 37
AB  - The restriction endonuclease BliAI, an isoschizomer of ClaI, which recognizes the sequence
AB  - 5'-AT down arrow CGAT-3', was purified from a
AB  - natural isolate identified as Bacillus licheniformis. The restriction
AB  - endonuclease was isolated from cell extracts using single-step
AB  - purification by phosphocellulose column chromatography. The restriction
AB  - endonuclease is active at 37 degrees C and over a wide range of pH and
AB  - salt concentration. The molecular weight of the purified restriction
AB  - enzyme is consistent with a value of 39 kDa.
ER  -

TY  - JOUR
AU  - Chik, J.
AU  - Robins, L.
AU  - Stoddard, B.
TI  - Expression and purification of Ltr-II: A homing endonuclease for gene targeting.
JO  - ACS Abstracts
PY  - 2012
SP  - 475
EP  - 475
VL  - 243
AB  - Homing endonucleases are microbial enzymes that selectively form double-stranded breaks in DNA
AB  - and drive gene conversion events via homologous recombination.  One type of homing
AB  - endonuclease conaining the LADLIDADG catalytic motif recognizes long DNA sequences wqith high
AB  - specificity and has successfully been used for targeting genes involved in both medicine
AB  - (genetic diseases) and biotechnology.  LtrII is an intron-encoded LAGLIDADG homing
AB  - endonuclease from the fungus Leptogaphium truncatum.  The results of the overexpression and
AB  - purificaiton of LtrII will be shown.  In addition, initial kinetic results of LtrII with its
AB  - target DNA sequence will be presented.
ER  -

TY  - JOUR
AU  - Chikaev, N.A.
AU  - Baklanov, M.M.
AU  - Ryazankin, I.A.
AU  - Nechaev, Y.S.
TI  - Purification of restriction endonucleases using aqueous two-phase systems.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1987
SP  - 84
EP  - 92
VL  - 23
AB  - A simple procedure was developed for testing and purification of restriction
AB  - endonucleases MspI, PstI, BamHI, PvuI, PvuII that includes biomass destruction,
AB  - fractionation of cell-free extracts in the aqueous two-phase (polyethylene
AB  - glycol-dextran) system and chromatography of phosphocellulose.  Optimal
AB  - conditions for the fractionation of MspI, PstI, BamHI, PvuII, EcoRI, EcoRII,
AB  - BspRI, AluI were chosen.  For separation of PvuI and PvuII gel filtration
AB  - through Biogel A-0.5 m was additionally introduced.
ER  -

TY  - JOUR
AU  - Chilley, P.M.
AU  - Wilkins, B.M.
TI  - Distribution of the ardA family of antirestriction genes on conjugative plasmids.
JO  - Microbiology
PY  - 1995
SP  - 2157
EP  - 2164
VL  - 141
AB  - The ardA gene of I1 plasmid ColIb-P9 was previously shown to alleviate DNA restriction by type
AB  - I enzymes and to promote conjugative transmission of the unmodified plasmid to a restricting
AB  - host. To clarify the ecological role of ardA, its distribution was determined on plasmids from
AB  - 23 incompatibility groups using hybridization to the coding sequence as an assay. Hybridizing
AB  - sequences, shown by nucleotide sequencing to have at least 60% identity with ardA, were
AB  - detected on plasmids belonging to the I complex (IncB, I1 and K), the F complex (IncFV) and
AB  - the IncN group. The ardA homologues were found to specify an antirestriction phenotype which
AB  - was enhanced by genetic depression of the plasmid transfer system. ardA loci map in plasmid
AB  - leading regions but show no consistent association with a particular type of
AB  - origin-of-transfer or a leading region gene of the ssb (single-stranded DNA-binding protein),
AB  - psiB (plasmid SOS inhibition) and hok (host killing) families. It may be significant that
AB  - ardA+ plasmids are authentic enterobacterial plasmids and that type I restriction systems are
AB  - associated historically with members of the Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Chin, V.
AU  - Valinluck, V.
AU  - Magaki, S.
AU  - Ryu, J.
TI  - KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - e138
EP  - e138
VL  - 32
AB  - KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella
AB  - pneumoniae. Here, the KpnBI modification genes were
AB  - cloned into a plasmid using a modification expression screening method.
AB  - The modification genes that consist of both hsdM (2631 bp) and hsdS (1344
AB  - bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These
AB  - two genes overlap by one base and share the same promoter located upstream
AB  - of the hsdM gene. Using recently developed plasmid R-M tests and a
AB  - computer program RM Search, the DNA recognition sequence for the KpnBI
AB  - enzymes was identified as a new 8 nt sequence containing one degenerate
AB  - base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII
AB  - sensitivity tests, the methylation loci were predicted to be the
AB  - italicized third adenine in the 5' specific region and the adenine
AB  - opposite the italicized thymine in the 3' specific region. Combined with
AB  - previous sequence data for hsdR, we concluded that the KpnBI system is a
AB  - typical type I R-M system. The deduced amino acid sequences of the three
AB  - subunits of the KpnBI system show only limited homologies (25 to 33%
AB  - identity) at best, to the four previously categorized type I families (IA,
AB  - IB, IC, and ID). Furthermore, their identity scores to other
AB  - uncharacterized putative genome type I sequences were 53% at maximum.
AB  - Therefore, we propose that KpnBI is the prototype of a new 'type IE'
AB  - family.
ER  -

TY  - JOUR
AU  - Chin, V.R.
AU  - Valinluck, V.
AU  - Ryu, J.
TI  - The KpnBI restriction-modification (R-M) system of Klebsiella pneumoniae strain GM236 is a prototype of a new family of type I R-M  systems.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 404
EP  - 405
VL  - 101
AB  - From genetic evidence, the KpnBI R-M system in Klebsiella pneumoniae strain GM236 was assumed
AB  - to be either a type I or type III R-M system.
AB  - The restriction subunit (hsdR) was previously cloned and sequenced.
AB  - However, it did not show any close homology to the preexisting R-M
AB  - systems. In this project the modification genes of the KpnBI system
AB  - were cloned into a plasmid, pMECA, using a modification expression
AB  - screening method. The modification genes were identified on an 8.2 kb
AB  - EcoRI chromosomal fragment. The complete 8.2 kb fragment was sequenced
AB  - and two open reading frames (ORF) were identified. The first ORF is
AB  - 2,631 bp in length and identified as the hsdM gene based on sequence
AB  - homologies. Similarily, the second ORF, which was 1,344 bp in length
AB  - and overlapped 1 base with the hsdM gene, was identified as the hsdS
AB  - gene. The presence of both hsdM and hsdS genes is a unique
AB  - characteristic of type I R-M systems. Therefore, the KpnBI system was
AB  - concluded to be a type I system. Phage and plasmid modification tests
AB  - as well as complementation tests with the HsdR subunit indicate that
AB  - the modification genes are expressed in both Klebsiella and E. coli
AB  - strains. Since the deduced amino acid sequences of all three subunits
AB  - of the KpnBI did not show sufficient (more than 40%) homologies with
AB  - any of the four categorized type I families (IA, IB, IC, and ID) we
AB  - concluded that KpnBI represents a new type I family. This family was
AB  - subsequently labeled type IE. The DNA recognition sequence of KpnBI
AB  - system has also been elucidated using a plasmid transformation method
AB  - currently developed in our laboratory. A further analysis of the inter-
AB  - and intra-family protein sequence comparisons of the subunits of type I
AB  - enzymes has allowed us to develop a criteria for grouping all the type
AB  - I systems into more than 20 new type I families in addition to the 4
AB  - existing families.
ER  -

TY  - JOUR
AU  - Chinen, A.
AU  - Naito, Y.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Evolution of sequence recognition by restriction-modification enzymes: Selective pressure for specificity decrease.
JO  - Genes Genet. Syst.
PY  - 2000
SP  - 381
EP  - 381
VL  - 75
AB  - Several type II restriction-modification (RM) gene complexes kill host bacterial cells that
AB  - have lost them, through attack on their chromosomal recognition sites.  Two RM gene complexes
AB  - recognizing the same sequence cannot simultaneously enjoy such stabilization through
AB  - post-segregational host killing, because one will defend chromosomal sites from attack by the
AB  - other.  We analyzed intra-host competition between two RM gene complexes when the recognition
AB  - sequence of one is included in that of the other.  When the EcoRII gene complex, recognizing
AB  - 5'CCWGG (W = A, T) is lost from the host, the SsoII gene complex, which recognizes 5'CCNGG
AB  - (N = A, T, G, C) will prevent host death by protecting CCWGG sites on the chromosome.
AB  - However, when the SsoII (CCNGG) gene complex is lost, the EcoRII (CCWGG) gene complex will be
AB  - unable to prevent host death through attack by SsoII on 5'CCSGG (S = C, G) sites.  These
AB  - predictions were verified in our experiments in which we analyzed plasmid maintenance, cell
AB  - growth, cell shape and chromosomal DNA.  Our results demonstrate the presence of selective
AB  - pressure for decrease in the specificity of recognition sequence of RM systems in the absence
AB  - of invading DNA.
ER  -

TY  - JOUR
AU  - Chinen, A.
AU  - Naito, Y.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease.
JO  - Mol. Biol. Evol.
PY  - 2000
SP  - 1610
EP  - 1619
VL  - 17
AB  - Several type II restriction-modification (RM) gene complexes kill host bacterial cells that
AB  - have lost them, through attack on the chromosomal recognition sites of these cells. Two RM
AB  - gene complexes recognizing the same sequence cannot simultaneously enjoy such stabilization
AB  - through post-segregational host killing, because one will defend chromosomal sites from attack
AB  - by the other. In the present work, we analyzed intrahost competition between two RM gene
AB  - complexes when the recognition sequence of one was included in that of the other. When the
AB  - EcoRII gene complex, recognizing 5'-CCWGG (W = A, T), is lost from the host, the SsoII gene
AB  - complex, which recognizes 5'-CCNGG (N = A, T, G, C), will prevent host death by protecting
AB  - CCWGG sites on the chromosome. However, when the SsoII (CCNGG) gene complex is lost, the
AB  - EcoRII (CCWGG) gene complex will be unable to prevent host death through attack by SsoII on
AB  - 5'-CCSGG (S = C, G) sites. These predictions were verified in our experiments, in which we
AB  - analyzed plasmid maintenance, cell growth, cell shape, and chromosomal DNA. Our results
AB  - demonstrate the presence of selective pressure for decrease in the specificity of recognition
AB  - sequence of RM systems in the absence of invading DNA.
ER  -

TY  - JOUR
AU  - Chinen, A.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms.
JO  - Gene
PY  - 2000
SP  - 109
EP  - 121
VL  - 259
AB  - Recent work suggests that restriction-modification gene complexes are mobile genetic elements
AB  - that insert themselves into the genome and cause various genome rearrangements. In the present
AB  - work, the complete genome sequences of Pyrococcus horikoshii and Pyrococcus abyssi, two
AB  - species in a genus of hyperthermophilic archaeon (archaebacterium), were compared to detect
AB  - large genome polymorphisms linked with restriction-modification gene homologs. Sequence
AB  - alignments, GC content analysis, and codon usage analysis demonstrated the diversity of these
AB  - homologs and revealed a possible case of relatively recent acquisition (horizontal transfer).
AB  - In two cases out of the six large polymorphisms identified, there was insertion of a DNA
AB  - segment with a modification gene homolog, accompanied by target deletion (simple
AB  - substitution).  In two other cases, homologous DNA segments carrying a modification gene
AB  - homolog were present at different locations in the two genomes (transposition). In both cases,
AB  - substitution (insertion/deletion) in one of the two loci was accompanied by inversion of the
AB  - adjacent chromosomal segment. In the fifth case, substitution by a DNA segment carrying type I
AB  - restriction, modification, and specificity gene homologs was likewise accompanied by adjacent
AB  - inversion. In the last case, two homologous DNA segments, were found at different loci in the
AB  - two genomes (transposition), but only one of them had insertion of a modification homolog and
AB  - an unknown ORF.  The possible relationship of these polymorphisms to attack by restriction
AB  - enzymes on the chromosome will be discussed.
ER  -

TY  - JOUR
AU  - Chinen, A.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Association of putative restriction modification genes with large genome polymorphisms suggested from comparison of Pyrococcus horikoshii and Pyrococcus abyssi genome sequences.
JO  - Genome Informatics
PY  - 2000
SP  - 339
EP  - 340
VL  - 11
AB  - Restriction-modification (RM) gene complexes encode two enzymatic functions, restriction and
AB  - modification.  A restriction enzyme will recognize a specific sequence in DNA and cut the DNA
AB  - unless it is methylated by a cognate modification enzyme.  RM systems will defend bacterial
AB  - cells by attacking incoming foreign DNA.  It is widely held that bacteria have evolved RM
AB  - systems and maintain them in order to protect their genome from invasion by foreign DNA such
AB  - as bacteriophages and plasmids. We earlier reported that carrying a type II RM gene complex
AB  - can increase the stability of a plasmid because cells that have lost the plasmid die.  From
AB  - this and other observations, it was proposed that the relative frequency of RM gene complexes
AB  - has increased through this post-segregational killing, in competitive exclusion, as well as
AB  - through direct attack on invading DNA.
ER  -

TY  - JOUR
AU  - Chinenova, T.A.
AU  - Mkrtumian, N.M.
AU  - Lomovskaia, N.D.
TI  - [Genetic characteristics of a new phage resistance trait in Streptomyces coelicolor A3(2)].
JO  - Genetika
PY  - 1982
SP  - 1945
EP  - 1952
VL  - 18
AB  - Phage resistance was investigated in the system of Streptomyces coelicolor A3(2) and phi C31
AB  - actinophage. Resistance of A3(2) strain to phi C31 was
AB  - shown to involve a novel mechanism responsible for the arrest of phage
AB  - intracellular growth in the whole cell population. The phage resistance
AB  - character designated Pgl+ (for 'phage growth limiting') is determined by a
AB  - gene located on the A3(2) chromosome. The gene (pgl) controls phage
AB  - 'modification' which results in an inability of phage to lyse lysogenize
AB  - Pgl+ host. Instability of the Pgl+ character was revealed. Pgl+ strains
AB  - segregate Pgl variants at a high frequency, the majority of Pgl strains
AB  - reverting to the initial Pgl+ phenotype with the same high frequency.
AB  - Reversible Pgl+ in equilibrium Pgl transitions are a common feature of
AB  - A3(2) cell population.
ER  -

TY  - JOUR
AU  - Chiou, C.S.
AU  - Li, H.Y.
AU  - Tung, S.K.
AU  - Chen, C.Y.
AU  - Teng, C.H.
AU  - Shu, J.C.
AU  - Tseng, J.T.
AU  - Hsu, C.Y.
AU  - Chen, C.C.
TI  - Identification of prophage gene z2389 in Escherichia coli EDL933 encoding a DNA cytosine methyltransferase for full protection of Notl sites.
JO  - Int. J. Med. Microbiol.
PY  - 2010
SP  - 296
EP  - 303
VL  - 300
AB  - Pulsed-field gel electrophoresis (PFGE) analysis revealed that the genomes of some pathogenic
AB  - Escherichia coli O157:H7 strains, including
AB  - EDL933, were resistant to Noti digestion. An amino acid sequence
AB  - comparison suggested that the z2389 gene carried on prophage CP-933R in
AB  - strain EDL933 is likely to encode a C-5-cytosine methyltransferase. The
AB  - z2389-equivalent gene was found in the Notl-resistant strains tested,
AB  - but it was not detected in the Notl-susceptible strains. PFGE analysis
AB  - of the wild-type EDL933 strain and of a z2389 null mutant revealed that
AB  - z2389 was associated with full genome protection against Notl digestion
AB  - and partial protection against Eagl digestion. In vitro methylation
AB  - experiments with purified recombinant protein demonstrated that Z2389
AB  - is capable of methylating Notl and Eagl sites. Sequencing of
AB  - bisulfite-treated DNA indicated that the methylation occurred at the
AB  - first cytosine residue of the Notl recognition sequence, whereas Eagl
AB  - sites remained unmethylated or were methylated at the first cytosine
AB  - residue. Thus, z2389 encodes a DNA cytosine methyltransferase that
AB  - confers full protection to Notl sites.
ER  -

TY  - JOUR
AU  - Chiou, T.Y.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Hattori, M.
AU  - Takahashi, T.
TI  - Draft Genome Sequence of Lactobacillus farciminis NBRC 111452, Isolated from Koso, a Japanese Sugar-Vegetable Fermented Beverage.
JO  - Genome Announcements
PY  - 2016
SP  - e01514
EP  - e01515
VL  - 4
AB  - Here, we report the draft genome sequence of the Lactobacillus farciminis strain  NBRC 111452,
AB  - isolated from koso, a Japanese sugar-vegetable fermented beverage.
AB  - This genome information is of potential use in studies of Lactobacillus
AB  - farciminis as a probiotic.
ER  -

TY  - JOUR
AU  - Chiriac, C.
AU  - Baricz, A.
AU  - Coman, C.
TI  - Draft Genome Sequence of Janthinobacterium sp. Strain ROICE36, a Putative Secondary Metabolite-Synthesizing Bacterium Isolated from Antarctic Snow.
JO  - Genome Announcements
PY  - 2018
SP  - e01553
EP  - e01517
VL  - 6
AB  - The draft genome assembly of Janthinobacterium sp. strain ROICE36 has 207 contigs, with a
AB  - total genome size of 5,977,006 bp and a G+C content of 62%.
AB  - Preliminary genome analysis identified 5,363 protein-coding genes and a total of
AB  - 7 secondary metabolic gene clusters (encoding bacteriocins, nonribosomal
AB  - peptide-synthetase [NRPS], terpene, hserlactone, and other ketide synthases).
ER  -

TY  - JOUR
AU  - Chirikjian, J.G.
AU  - George, A.
AU  - Smith, L.A.
TI  - Purification of restriction endonucleases including the isolation of a novel activity using affinity chromatography.
JO  - Fed. Proc.
PY  - 1978
SP  - 1415
EP  - 1415
VL  - 37
AB  - We wish to report a new method for purifying EndoRs based on affinity
AB  - fractionation.  To date purification of restriction endonucleases have been
AB  - modifications of few early methods which are often tedious and time consuming.
AB  - We have investigated the use of affinity matrices such as covalently bound
AB  - pyran and Cibacron Blue F3Ga sepharose.  Pyran is a divinyl ether copolymer of
AB  - maleic anhydride which in carboxylic acid solution hydrolyzes to the negatively
AB  - charged polycarboxylic acid that simulates the negatively charged
AB  - phosphodiester bond.  Cibacron Blue F3Ga is a derivative of a sulfonated
AB  - polyaromatic dye and is widely used as a nonspecific affinity matrix.  Both
AB  - matrices have high capacity, rapid development time and yield enzyme free from
AB  - interfering activities.  Using these matrices we have purified several reported
AB  - EndoRs such as BamHI, HinfI, PstI and XbaI.  We have also isolated a new Endo3
AB  - from a clinical isolate H. influenzae Georgetown, which contains two major
AB  - activities: HindGUI which we have temporarily assigned to be an isoschizomer of
AB  - HhaI and HinGUII with the following fragmentation properties: PhiX174, 10;
AB  - SV40, 12-14; lambda >50; and Adeno 2 >50.
ER  -

TY  - JOUR
AU  - Chirikjian, J.G.
AU  - George, J.
TI  - Sequence-specific endonucleases: General properties and specific characteristics.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 73
EP  - 99
VL  - 1
AB  - I. Introduction II. Sequence-specific endonucleases as reagents in molecular biology. III.
AB  - Matrix bound sequence-specific endonucleases IV. General methods for determining
AB  - sequence-specific endonuclease activity. V. Strategies for elucidating the recognition of DNA
AB  - by sequence-specific endonucleases VI. Catalytic diversities among isoschizomers VII. Effect
AB  - of hydrophobic reagents on sequence recognition and catalysis of sequence-specific
AB  - endonucleases VIII. Conclusions
ER  -

TY  - JOUR
AU  - Chistoserdova, L.
AU  - Lapidus, A.
AU  - Han, C.
AU  - Goodwin, L.
AU  - Saunders, L.
AU  - Brettin, T.
AU  - Tapia, R.
AU  - Gilna, P.
AU  - Lucas, S.
AU  - Richardson, P.M.
AU  - Lidstrom, M.E.
TI  - Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy.
JO  - J. Bacteriol.
PY  - 2007
SP  - 4020
EP  - 4027
VL  - 189
AB  - Along with methane, methanol and methylated amines represent important biogenic atmospheric
AB  - constituents; thus, not only methanotrophs but also
AB  - nonmethanotrophic methylotrophs play a significant role in global carbon
AB  - cycling. The complete genome of a model obligate methanol and methylamine
AB  - utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The
AB  - genome is represented by a single circular chromosome of approximately 3
AB  - Mbp, potentially encoding a total of 2,766 proteins. Based on genome
AB  - analysis as well as the results from previous genetic and mutational
AB  - analyses, methylotrophy is enabled by methanol and methylamine
AB  - dehydrogenases and their specific electron transport chain components, the
AB  - tetrahydromethanopterin-linked formaldehyde oxidation pathway and the
AB  - assimilatory and dissimilatory ribulose monophosphate cycles, and by a
AB  - formate dehydrogenase. Some of the methylotrophy genes are present in more
AB  - than one (identical or nonidentical) copy. The obligate dependence on
AB  - single-carbon compounds appears to be due to the incomplete tricarboxylic
AB  - acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate,
AB  - or succinate dehydrogenases are identifiable. The genome of M. flagellatus
AB  - was compared in terms of methylotrophy functions to the previously
AB  - sequenced genomes of three methylotrophs, Methylobacterium extorquens (an
AB  - alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a
AB  - betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a
AB  - gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or
AB  - phylogenetically, the methylotrophy functions in M. flagellatus were more
AB  - similar to those in M. capsulatus and M. extorquens than to the ones in
AB  - the more closely related M. petroleiphilum species, providing the first
AB  - genomic evidence for the polyphyletic origin of methylotrophy in
AB  - Betaproteobacteria.
ER  -

TY  - JOUR
AU  - Chiu, C.H.
AU  - Tang, P.
AU  - Chu, C.
AU  - Hu, S.
AU  - Bao, Q.
AU  - Yu, J.
AU  - Chou, Y.Y.
AU  - Wang, H.S.
AU  - Lee, Y.S.
TI  - The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 1690
EP  - 1698
VL  - 33
AB  - Salmonella enterica serovar Choleraesuis (S.Choleraesuis), a highly invasive serovar among
AB  - non-typhoidal Salmonella, usually causes sepsis or
AB  - extra-intestinal focal infections in humans. S.Choleraesuis infections
AB  - have now become particularly difficult to treat because of the emergence
AB  - of resistance to multiple antimicrobial agents. The 4.7 Mb genome sequence
AB  - of a multidrug-resistant S.Choleraesuis strain SC-B67 was determined.
AB  - Genome wide comparison of three sequenced Salmonella genomes revealed that
AB  - more deletion events occurred in S.Choleraesuis SC-B67 and S.Typhi CT18
AB  - relative to S.Typhimurium LT2. S.Choleraesuis has 151 pseudogenes, which,
AB  - among the three Salmonella genomes, include the highest percentage of
AB  - pseudogenes arising from the genes involved in bacterial chemotaxis
AB  - signal-transduction pathways. Mutations in these genes may increase smooth
AB  - swimming of the bacteria, potentially allowing more effective interactions
AB  - with and invasion of host cells to occur. A key regulatory gene of
AB  - TetR/AcrR family, acrR, was inactivated through the introduction of an
AB  - internal stop codon resulting in overexpression of AcrAB that appears to
AB  - be associated with ciprofloxacin resistance. While lateral gene transfer
AB  - providing basic functions to allow niche expansion in the host and
AB  - environment is maintained during the evolution of different serovars of
AB  - Salmonella, genes providing little overall selective benefit may be lost
AB  - rapidly. Our findings suggest that the formation of pseudogenes may
AB  - provide a simple evolutionary pathway that complements gene acquisition to
AB  - enhance virulence and antimicrobial resistance in S.Choleraesuis.
ER  -

TY  - JOUR
AU  - Chiu, C.M.
AU  - Chang, C.H.
AU  - Pan, S.F.
AU  - Wu, H.C.
AU  - Li, S.W.
AU  - Chang, C.H.
AU  - Lee, Y.S.
AU  - Chiang, C.M.
AU  - Chen, Y.S.
TI  - Draft Genome Sequence of Lactobacillus pobuzihii E100301T.
JO  - Genome Announcements
PY  - 2013
SP  - e00185
EP  - e00113
VL  - 1
AB  - Lactobacillus pobuzihii E100301(T) is a novel Lactobacillus species previously isolated from
AB  - pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically,
AB  - this strain is closest to Lactobacillus acidipiscis, but its phenotypic
AB  - characteristics can be clearly distinguished from those of L. acidipiscis. We
AB  - present the draft genome sequence of strain L. pobuzihii E100301(T).
ER  -

TY  - JOUR
AU  - Chiu, S.H.
AU  - Chen, C.C.
AU  - Wang, L.T.
AU  - Huang, L.
TI  - Whole-Genome Sequencing of Lactobacillus salivarius Strains BCRC 14759 and BCRC 12574.
JO  - Genome Announcements
PY  - 2017
SP  - e01336
EP  - e01317
VL  - 5
AB  - Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing
AB  - strain with potential as a probiotic or
AB  - fermented dairy product. Here, we report the genome sequences of L. salivarius
AB  - BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The
AB  - PacBio RSII sequencing platform was used to obtain high-quality assemblies for
AB  - characterization of this probiotic candidate.
ER  -

TY  - JOUR
AU  - Chiura, H.
AU  - Noro, Y.
AU  - Kanayama, S.
AU  - Ueda, Y.
AU  - Simidu, U.
AU  - Takagi, J.
TI  - Site specific deoxyribonuclease produced by a marine bacterium, Flavobacterium I 16-04.
JO  - Agric. Biol. Chem.
PY  - 1988
SP  - 2107
EP  - 2109
VL  - 52
AB  - Since the discovery of HindII, more than 120 kinds of site-specific
AB  - endodeoxyribonucleases (restriction enzymes) have been isolated from some 600
AB  - species of bacteria and reported.  All of them have been obtained from
AB  - terrestrial bacteria except FokI isolated from a marine bacterium,
AB  - Flavobacterium okeanokoites.  Furthermore, the marine bacteria have not been as
AB  - extensively studied as the terrestrial bacteria.  Under these circumstances, we
AB  - have been attempting to survey site-specific endonucleases in the marine
AB  - bacteria of the laboratory collection of the Ocean Research Institute,
AB  - University of Tokyo.
ER  -

TY  - JOUR
AU  - Chiura, H.X.
AU  - Kamiyama, T.
AU  - Hirano, H.
AU  - Futagami, M.
AU  - Watahiki, M.
AU  - Kobayashi, K.
AU  - Simidu, U.
AU  - Takagi, J.
TI  - Purification and characterization of AspMDI, an isoschizomer of Sau3AI, from a marine bacterium, Alcaligenes sp MD1.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1996
EP  - 1996
VL  - 20
AB  - A new type II restriction endonuclease, Asp MD1, was isolated from a pigmented marine
AB  - bacterium Alcaligenes species MD1 which was collected from the open sea around Taiwan Island.
ER  -

TY  - JOUR
AU  - Chiurillo, M.A.
AU  - Moran, Y.
AU  - Canas, M.
AU  - Valderrama, E.
AU  - Granda, N.
AU  - Sayegh, M.
AU  - Ramirez, J.L.
TI  - Genotyping of virulence-associated genes from biopsy specimens show high genetic diversity of Helicobacter pylori strains infecting patients in Venezuela.
JO  - Int. J. Infect. Dis.
PY  - 2013
SP  - e750
EP  - e756
VL  - 17
AB  - Background: Helicobacter pylori is a major cause of chronic gastritis and an established risk
AB  - factor for gastric adenocarcinoma. This bacterium also exhibits an extraordinarily high
AB  - genetic diversity.
AB  - Methods: The genetic diversity of H. pylori strains from Venezuelan patients with chronic
AB  - gastritis was evaluated by PCR-typing of vacA, cagA, iceA, and babA2 virulence-associated
AB  - genes using DNA extracted directly from biopsies. The nucleotide sequence and prevalence of
AB  - size variants of iceA1, iceA2, and babA2 PCR products were introduced in this analysis.
AB  - Results: The frequency of vacA s1 was associated (p < 0.01) with moderate/severe grades of
AB  - atrophic
AB  - gastritis. The cagA, iceA1, iceA2, and babA2 genotypes were found in 70.6%, 66.4%, 33.6%, and
AB  - 92.3% of strains, respectively. The frequency of iceA2 and its subtype iceA2_D were higher (p
AB  - < 0.015) in cases with moderate/severe granulocytic inflammation. The most prevalent combined
AB  - genotypes were vacA
AB  - s1m1/cagA/iceA1/babA2 (26.3%), vacA s2m2/iceA1/babA2 (19.5%), and vacA s1m1/cagA/iceA2/babA2
AB  - (18.8%). Sequence analysis of iceA1, iceA2, and babA2 PCR-amplified fragments allowed us to
AB  - define allelic variants and to increase the number of genotypes detected (from 19 to 62). A
AB  - phylogenetic tree made with iceA1 sequences showed that the H. pylori strains analyzed here
AB  - were grouped with those of Western origin.
AB  - Conclusions: Our results show that patients from the western region of Venezuela have an
AB  - elevated prevalence of infection with H. pylori strains carrying known virulence genotypes
AB  - with high genetic diversity. This highlights the importance of identifying gene variants for
AB  - an early detection of virulent genotypes.
ER  -

TY  - JOUR
AU  - Chivian, D. et al.
TI  - Environmental genomics reveals a single-species ecosystem deep within Earth.
JO  - Science
PY  - 2008
SP  - 275
EP  - 278
VL  - 322
AB  - DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African
AB  - gold mine was sequenced and assembled into a single,
AB  - complete genome. This bacterium, Candidatus Desulforudis audaxviator,
AB  - composes >99.9% of the microorganisms inhabiting the fluid phase of this
AB  - particular fracture. Its genome indicates a motile, sporulating,
AB  - sulfate-reducing, chemoautotrophic thermophile that can fix its own
AB  - nitrogen and carbon by using machinery shared with archaea. Candidatus
AB  - Desulforudis audaxviator is capable of an independent life-style well
AB  - suited to long-term isolation from the photosphere deep within Earth's
AB  - crust and offers an example of a natural ecosystem that appears to have
AB  - its biological component entirely encoded within a single genome.
ER  -

TY  - JOUR
AU  - Chlebowicz, M.A.
AU  - Nganou, K.
AU  - Kozytska, S.
AU  - Arends, J.P.
AU  - Engelmann, S.
AU  - Grundmann, H.
AU  - Ohlsen, K.
AU  - van Dijl, J.M.
AU  - Buist, G.
TI  - Recombination between ccrC genes in a type V (5C2 and 5) staphylococcal cassette chromosome mec (SCCmec) of Staphylococcus aureus ST398 leads to conversion from methicillin resistance to methicillin susceptibility in vivo.
JO  - Antimicrob. Agents Chemother.
PY  - 2010
SP  - 783
EP  - 791
VL  - 54
AB  - Various types of the staphylococcal cassette chromosome mec (SCCmec) are known to confer
AB  - methicillin resistance on the human pathogen Staphylococcus aureus. Such cassettes are not
AB  - always stably maintained.  The present studies were aimed at identifying the mechanism
AB  - underlying the in vivo conversion of methicillin-resistant S. aureus (MRSA) to
AB  - methicillin-susceptible S. aureus (MSSA) derivatives as encountered in two patients suffering
AB  - from pneumonia and an umbilicus infection, respectively. All MRSA and MSSA isolates identified
AB  - belong to multilocus sequence type (MLST) 398, have spa type t034, and are Panton-Valentine
AB  - leukocidin positive. Sequencing of 27,616 nucleotides from the chromosomal SCCmec insertion
AB  - site in orfX to the hsdR gene for a restriction enzyme revealed a type V (5C2&5) SCCmec.
AB  - Sequence comparisons show that parts of the cassette are highly similar to sequences within
AB  - SCCmec elements from coagulase-negative staphylococci, indicating a possible common origin.
AB  - The cassette investigated contains ccrC-carrying units on either side of its class C2b mec
AB  - gene complex. In vivo loss of the mec gene complex was caused by recombination between the
AB  - recombinase genes ccrC1 allele 8 and ccrC1 allele 10. In vitro, the SCCmec was very stable,
AB  - and low-frequency MRSA-to-MSSA conversion was only observed when MRSA isolates were cultivated
AB  - at 41 degrees C for prolonged periods of time. In this case also, loss of the mec complex was
AB  - due to ccrC gene recombination. Interestingly, the MRSA and MSSA isolates studied displayed no
AB  - detectable differences in competitive growth and virulence, suggesting that the presence of
AB  - the intact type V (5C2&5) SCCmec has no negative bearing on staphylococcal fitness under the
AB  - conditions used.
ER  -

TY  - JOUR
AU  - Chmelo, R.
AU  - Foltz, L.
AU  - Eadie, J.S.
TI  - Determination of restriction enzyme digestion completeness under low target concentration.
JO  - FASEB J.
PY  - 1993
SP  - A1304
EP  - A1304
VL  - 7
AB  - A method for the determination of restriction enzyme digestion efficiency under low target
AB  - concentration is described. Target DNA was serially diluted from 10 to the eleventh power
AB  - molecules to 1 molecule. The DNA was digested with one unit of enzyme for one hour at 37C. The
AB  - digestion was stopped by heating the reaction at 65C for 10 minutes. PCR was performed on the
AB  - restriction digests to assay for completeness. Three primers were used: 2 forward primers and
AB  - 1 reverse primer. When both forward primers are used in conjunction with the reverse primer in
AB  - PCR, products of 523 and 170 base pairs are observed. The restriction site of interest lies
AB  - between the two forward primers. If the enzyme is active at low target concentration, only the
AB  - 170 base pair fragment is detected. Results have indicated that this technique is sensitive to
AB  - detect completeness of a restriction enzyme digestion at low target DNA concentration. This
AB  - protocol can be applicable for testing any restriction enzyme.
ER  -

TY  - JOUR
AU  - Chmiel, A.A.
AU  - Bujnicki, J.M.
AU  - Skowronek, K.J.
TI  - A homology model of restriction endonuclease SfiI in complex with DNA.
JO  - BMC Struct. Biol.
PY  - 2005
SP  - 2
EP  - 2
VL  - 5
AB  - BACKGROUND: Restriction enzymes (REases) are commercial reagents commonly used in recombinant
AB  - DNA technologies. They are attractive models for studying protein-DNA interactions and
AB  - valuable targets for protein engineering. They are, however, extremely divergent: the amino
AB  - acid sequence of a typical REase usually shows no detectable similarities to any other
AB  - proteins, with rare exceptions of other REases that recognize identical or very similar
AB  - sequences. From structural analyses and bioinformatics studies it has been learned that some
AB  - REases belong to at least four unrelated and structurally distinct superfamilies of nucleases,
AB  - PD-DxK, PLD, HNH, and GIY-YIG. Hence, they are extremely hard targets for structure prediction
AB  - and homology-based inference of sequence-function relationships and the great majority of
AB  - REases remain structurally and evolutionarily unclassified. RESULTS: SfiI is a REase which
AB  - recognizes the interrupted palindromic sequence 5'GGCCNNNN--NGGCC3' and generates 3 nt long
AB  - 3' overhangs upon cleavage. SfiI is an archetypal Type IIF enzyme, which functions as a
AB  - tetramer and cleaves two copies of the recognition site in a concerted manner. Its sequence
AB  - shows no similarity to other proteins and nothing is known about the localization of its
AB  - active site or residues important for oligomerization. Using the threading approach for
AB  - protein fold-recognition, we identified a remote relationship between SfiI and BglI, a dimeric
AB  - Type IIP restriction enzyme from the PD-DxK superfamily of nucleases, which recognizes the
AB  - 5'GCCNNNN--NGGC3' sequence and whose structure in complex with the substrate DNA is
AB  - available. We constructed a homology model of SfiI in complex with its target sequence and
AB  - used it to predict residues important for dimerization, tetramerization, DNA binding and
AB  - catalysis. CONCLUSIONS: The bioinformatics analysis suggest that SfiI, a Type IIF enzyme, is
AB  - more closely related to BglI, an "orthodox" Type IIP restriction enzyme, than to any other
AB  - REase, including other Type IIF REases with known structures, such as NgoMIV. NgoMIV and BglI
AB  - belong to two different, very remotely related branches of the PD-DxK superfamily: the
AB  - alpha-class (EcoRI-like), and the beta-class (EcoRV-like), respectively. Thus, our analysis
AB  - provides evidence that the ability to tetramerize and cut the two DNA sequences in a concerted
AB  - manner was developed independently at least two times in the evolution of the PD-DxK
AB  - superfamily of REases. The model of SfiI will also serve as a convenient platform for further
AB  - experimental analyses.
ER  -

TY  - JOUR
AU  - Chmiel, A.A.
AU  - Radlinska, M.
AU  - Pawlak, S.D.
AU  - Krowarsch, D.
AU  - Bujnicki, J.M.
AU  - Skowronek, K.J.
TI  - A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed  mutagenesis and circular dichroism spectroscopy.
JO  - Protein Eng. Des. Sel.
PY  - 2005
SP  - 181
EP  - 189
VL  - 18
AB  - Restriction enzymes (REases) are commercial reagents commonly used in DNA manipulations and
AB  - mapping. They are regarded as very attractive
AB  - models for studying protein-DNA interactions and valuable targets for
AB  - protein engineering. Their amino acid sequences usually show no
AB  - similarities to other proteins, with rare exceptions of other REases
AB  - that recognize identical or very similar sequences. Hence, they are
AB  - extremely hard targets for structure prediction and modeling. NlaIV is
AB  - a Type II REase, which recognizes the interrupted palindromic sequence
AB  - GGNNCC (where N indicates any base) and cleaves it in the middle,
AB  - leaving blunt ends. NlaIV shows no sequence similarity to other
AB  - proteins and virtually nothing is known about its
AB  - sequence-structure-function relationships. Using protein fold
AB  - recognition, we identified a remote relationship between NlaIV and
AB  - EcoRV, an extensively studied REase, which recognizes the GATATC
AB  - sequence and whose crystal structure has been determined. Using the
AB  - 'FRankenstein's monster' approach we constructed a comparative model of
AB  - NlaIV based on the EcoRV template and used it to predict the catalytic
AB  - and DNA-binding residues. The model was validated by site-directed
AB  - mutagenesis and analysis of the activity of the mutants in vivo and in
AB  - vitro as well as structural characterization of the wild-type enzyme
AB  - and two mutants by circular dichroism spectroscopy. The structural
AB  - model of the NlaIV-DNA complex suggests regions of the protein sequence
AB  - that may interact with the 'non-specific' bases of the target and thus
AB  - it provides insight into the evolution of sequence specificity in
AB  - restriction enzymes and may help engineer REases with novel
AB  - specificities. Before this analysis was carried out, neither the
AB  - three-dimensional fold of NlaIV, its evolutionary relationships or its
AB  - catalytic or DNA-binding residues were known. Hence our analysis may be
AB  - regarded as a paradigm for studies aiming at reducing 'white spaces' on
AB  - the evolutionary landscape of sequence-function relationships by
AB  - combining bioinformatics with simple experimental assays.
ER  -

TY  - JOUR
AU  - Chmuzh, E.V.
AU  - Kashirina, J.G.
AU  - Tomilova, J.E.
AU  - Mezentseva, N.V.
AU  - Dedkov, V.S.
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Degtyarev, S.K.
TI  - A Novel Restriction endonuclease BisI from Bacillus subtilis T30, recognizes a methylated DNA sequence 5'- G(m5C)^NGC-3'.
JO  - Biotekhnologiya
PY  - 2005
SP  - 22
EP  - 26
VL  - 3
AB  - Bacillus subtilis strain T30, producing a novel restriction endonuclease Bis I, has been
AB  - isolated and characterized. The enzyme recognizes methylated DNA sequence 5'- G(m5C)^NGC-3'
AB  - and cleaves it as shown by the arrow. Due to cleavage of only modified DNAs Bis I may find a
AB  - practical application in genetic engineering experiments as well as in determination of
AB  - eukaryotic DNA methylation status.
ER  -

TY  - JOUR
AU  - Chmuzh, E.V.
AU  - Kashirina, Y.G.
AU  - Tomilova, Y.E.
AU  - Chernukhin, V.A.
AU  - Okhapkina, S.S.
AU  - Gonchar, D.A.
AU  - Dedkov, V.S.
AU  - Abdurashitov, M.A.
AU  - Degtyarev, S.K.
TI  - The Fsp4HI restriction-modification system: Gene cloning, comparison of protein structures, and biochemical properties of recombinant DNA methyltransferase M.Fsp4HI.
JO  - Mol. Biol. (Mosk)
PY  - 2007
SP  - 43
EP  - 50
VL  - 41
AB  - Genes coding for the Flavobacterium sp. 4H restriction-modification (RM) system, which
AB  - recognizes the sequence 5'-GCNGC-3', were cloned in Escherichia coli ER2267 and sequenced.
AB  - The Fsp4HI RM system includes two genes: one for DNA methyltransferase (M.) and the other for
AB  - restriction endonuclease (R.), immediately following the former in the same direction. The
AB  - genes partly overlap. According to the deduced amino acid sequences, M.Fsp4HI belongs to C5
AB  - DNA methyltransferases, whereas R.Fsp4HI is only slightly similar to some restriction enzymes
AB  - recognizing similar sequences. M.Fsp4HI was purified by column chromatography. The optimal
AB  - conditions for the enzyme are 30 degrees C and pH 7.5. M.Fsp4HI modifies the first cytosine in
AB  - 5'-GCNGC-3'.
ER  -

TY  - JOUR
AU  - Cho, E.
AU  - Park, S.N.
AU  - Kim, H.K.
AU  - Kim, D.S.
AU  - Jung, J.
AU  - Baek, J.H.
AU  - Lim, Y.K.
AU  - Jo, E.
AU  - Choi, M.H.
AU  - Chang, Y.H.
AU  - Shin, Y.
AU  - Paek, J.
AU  - Shin, J.H.
AU  - Kim, J.
AU  - Choi, S.H.
AU  - Park, H.S.
AU  - Kim, H.
AU  - Kook, J.K.
TI  - Draft Genome Sequence of the Novel Peptoniphilus sp. Strain ChDC B134, Isolated from a Human Periapical Abscess Lesion.
JO  - Genome Announcements
PY  - 2013
SP  - e00822
EP  - e00813
VL  - 1
AB  - The genus Peptoniphilus comprises butyrate-producing, nonsaccharolytic species that use
AB  - peptone and amino acids as major energy sources. The novel Peptoniphilus
AB  - sp. strain ChDC B134 (=KCOM 1628) was isolated from a human periapical abscess
AB  - lesion. Here, we report the draft genome sequence of the strain.
ER  -

TY  - JOUR
AU  - Cho, M.-J.
AU  - Park, J.-U.
AU  - Jeon, B.S.
AU  - Pack, J.-W.
AU  - Byun, E.Y.
AU  - Lee, S.-K.
AU  - Park, Y.-H.
AU  - Song, J.-H.
AU  - Lee, W.-K.
AU  - Baik, S.-C.
AU  - Choi, Y.-J.
AU  - Jung, S.-A.
AU  - Choe, M.-Y.
AU  - Choi, S.-H.
AU  - Ko, G.-H.
AU  - Youn, H.-S.
AU  - Rhee, K.-H.
TI  - Characterization of type II restriction endonucleases (Hpy51-I) from Helicobacter pylori strain 51.
JO  - J. Bact. Virol.
PY  - 2001
SP  - 207
EP  - 215
VL  - 31
AB  - This study describes the purification and characterization of a type II restriction
AB  - endonuclease of Helicobacter pylori in order to understand the DNA restriction and
AB  - modification of H. pylori.  H. pylori cell extract was subjected to polyethyleneimine
AB  - treatment, salt precipitation, heparine-sepharose column chromatography, and fast protein
AB  - liquid chromatography using Resource Q column and Mono Q column to purify the type II
AB  - restriction endonuclease.  Hpy51-I was characterized to recognize the sequence
AB  - 5'-GT(G/C)AC-3', yielding 5-base 5' protruding ends.  The restriction sequence was
AB  - identical to that of Tsp45I.  The enzyme exhibited its maximal activity in the presence of
AB  - 10~20 mM NaCl, but was inhibited completely in the presence of more than 80 mM NaCl.  The
AB  - enzyme showed its maximal activity in the presence of 1~10 mM MCl2.  The optimal pH and
AB  - temperature for enzyme activity was pH 9.0 and 37oC, respectively.  MnCl2 could not substitute
AB  - for MgCl2 in reaction mixture.  Addition of beta-mercaptoethanol and bovine serum albumin in
AB  - the reaction mixture led to loss of enzyme activity of Hpy51-I.  The whole cell extract of H.
AB  - pylori strain 51 was confirmed to carry the enzyme activity for methylation of
AB  - Hpy51-I-recognised sequence.  Hpy51-I digested genomic DNAs of enteric bacteria to less than I
AB  - kb while it could not cut the genomic DNAs of H. pylori isolates.  In this study, the type II
AB  - restriction enzyme (Hpy51-I) of H. pylori was identified and its biochemical properties
AB  - characterized, demonstrating that Hpy51-I might be one of the barriers for preventing the
AB  - introduction of foreign DNAs into H. pylori.
ER  -

TY  - JOUR
AU  - Cho, N.H.
AU  - Kim, H.R.
AU  - Lee, J.H.
AU  - Kim, S.Y.
AU  - Kim, J.
AU  - Cha, S.
AU  - Kim, S.Y.
AU  - Darby, A.C.
AU  - Fuxelius, H.H.
AU  - Yin, J.
AU  - Kim, J.H.
AU  - Kim, J.
AU  - Lee, S.J.
AU  - Koh, Y.S.
AU  - Jang, W.J.
AU  - Park, K.H.
AU  - Andersson, S.G.
AU  - Choi, M.S.
AU  - Kim, I.S.
TI  - The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 7981
EP  - 7986
VL  - 104
AB  - Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi
AB  - (previously called Rickettsia tsutsugamushi). The bacterium
AB  - is maternally inherited in trombicuid mites and transmitted to humans by
AB  - feeding larvae. We report here the 2,127,051-bp genome of the Boryong
AB  - strain, which represents the most highly repeated bacterial genome
AB  - sequenced to date. The repeat density of the scrub typhus pathogen is
AB  - 200-fold higher than that of its close relative Rickettsia prowazekii, the
AB  - agent of epidemic typhus. A total of 359 tra genes for components of
AB  - conjugative type IV secretion systems were identified at 79 sites in the
AB  - genome. Associated with these are >200 genes for signaling and host-cell
AB  - interaction proteins, such as histidine kinases, ankyrin-repeat proteins,
AB  - and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi
AB  - genome contains >400 transposases, 60 phage integrases, and 70 reverse
AB  - transcriptases. Deletions and rearrangements have yielded unique gene
AB  - combinations as well as frequent pseudogenization in the tra clusters. A
AB  - comparative analysis of the tra clusters within the genome and across
AB  - strains indicates sequence homogenization by gene conversion, whereas
AB  - complexity, diversity, and pseudogenization are acquired by duplications,
AB  - deletions, and transposon integrations into the amplified segments. The
AB  - results suggest intragenomic duplications or multiple integrations of a
AB  - massively proliferating conjugative transfer system. Diversifying
AB  - selection on host-cell interaction genes along with repeated population
AB  - bottlenecks may drive rare genome variants to fixation, thereby
AB  - short-circuiting selection for low complexity in bacterial genomes.
ER  -

TY  - JOUR
AU  - Cho, S.-H.
AU  - Kang, C.
TI  - DNA sequence-dependent cleavage sites of restriction endonuclease HphI.
JO  - Mol. Cells
PY  - 1990
SP  - 81
EP  - 86
VL  - 1
AB  - A class IIS restriction endonuclease HphI has been known to make a staggered
AB  - cut always at the 8th base pair downstream of its recognition sequence
AB  - 5'GGTGA3', producing one-base 3' protruding ends, regardless of the DNA
AB  - sequence around the cleavage site.  Since the cleavage sites of HphI are
AB  - separate from its recognition sites, the effects of mutations around a cleavage
AB  - site have been studied using a phage SP6 promoter-containing plasmid pSP64
AB  - which has an HphI cleavage site near the transcription initiation site.  The
AB  - exact cutting site of the lower strand was determined to be after the 8th
AB  - nucleotide downstream of the recognition site, indicating a staggered cut at
AB  - the 9th base pair downstream.  In addition, the same cutting site in the
AB  - mutants carrying a few base pair deletions around the cleavage site is shown to
AB  - be shifted.  These variations were not affected by any changes in reaction
AB  - conditions.  These results suggest that the HphI cleavage site shifts depending
AB  - on the DNA sequence, which might affect the DNA helical structure.
ER  -

TY  - JOUR
AU  - Cho, S.T.
AU  - Chen, C.L.
AU  - Yang, Y.
AU  - Wang, T.F.
AU  - Kuo, C.H.
TI  - Draft Genome Sequence of Burkholderia sp. Strain WAC0059, a Bacterium Isolated from the Medicinal Fungus Antrodia cinnamomea.
JO  - Genome Announcements
PY  - 2018
SP  - e00027
EP  - e00018
VL  - 6
AB  - Burkholderia sp. strain WAC0059 was isolated from a fruiting body of the medicinal fungus
AB  - Antrodia cinnamomea collected in Taiwan. Here, we report the
AB  - draft genome sequence of this bacterium to facilitate the investigation of its
AB  - biology.
ER  -

TY  - JOUR
AU  - Cho, S.T.
AU  - Haryono, M.
AU  - Chang, H.H.
AU  - Santos, M.N.M.
AU  - Lai, E.M.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Agrobacterium tumefaciens 1D1609.
JO  - Genome Announcements
PY  - 2018
SP  - e00253
EP  - e00218
VL  - 6
AB  - Agrobacterium tumefaciens 1D1609 is a highly virulent strain isolated from a crown gall tumor
AB  - of alfalfa (Medicago sativa L.). Compared to other
AB  - well-characterized A. tumefaciens strains, such as C58 and Ach5, 1D1609 has a
AB  - distinctive host range. Here, we report its complete genome sequence to
AB  - facilitate future studies.
ER  -

TY  - JOUR
AU  - Cho, Y.J.
AU  - Choi, J.K.
AU  - Kim, J.H.
AU  - Lim, Y.S.
AU  - Ham, J.S.
AU  - Kang, D.K.
AU  - Chun, J.
AU  - Paik, H.D.
AU  - Kim, G.B.
TI  - Genome Sequence of Lactobacillus salivarius GJ-24, a probiotic strain isolated from healthy adult intestine.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5021
EP  - 5022
VL  - 193
AB  - The draft genome sequence of Lactobacillus salivarius GJ-24 isolated from the feces of healthy
AB  - adults was determined. The properties including milk
AB  - fermentation activity and bacteriocin production suggest its potential
AB  - uses as a probiotic lactic acid bacterium and start culture for dairy
AB  - products.
ER  -

TY  - JOUR
AU  - Cho, Y.J.
AU  - Jung, Y.J.
AU  - Hong, S.G.
AU  - Kim, O.S.
TI  - Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium, Janthinobacterium svalbardensis PAMC 27463.
JO  - Genome Announcements
PY  - 2017
SP  - e01178
EP  - e01117
VL  - 5
AB  - We report here the complete genome sequence of Janthinobacterium svalbardensis PAMC 27463
AB  - isolated from a freshwater lake on Barton Peninsula on King George
AB  - Island, Antarctica. The genome consists of a chromosome with 6,274,078 bp which
AB  - contains 5,585 genes, including 121 RNA genes.
ER  -

TY  - JOUR
AU  - Choe, W.
AU  - Chandrasegaran, S.
AU  - Ostermeier, M.
TI  - Protein fragment complementation in M.HhaI DNA methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2005
SP  - 1233
EP  - 1240
VL  - 334
AB  - The 5mC DNA methyltransferase M.HhaI can be split into two individually inactive N- and
AB  - C-terminal fragments that together can form an active
AB  - enzyme in vivo capable of efficiently methylating DNA. This active
AB  - fragment pair was identified by creating libraries of M.HhaI gene
AB  - fragment pairs and then selecting for the pairs that code for an active
AB  - 5mC methyltransferase. The site of bisection for successful protein
AB  - fragment complementation in M.HhaI was in the variable region near the
AB  - target recognition domain between motif VIII and TRD. This same region
AB  - is the location of bifurcation in the naturally split 5mC
AB  - methyltransferase M.AquI, the location for circular permutation in
AB  - M.BssHII, and the location for previously engineered split versions of
AB  - M.BspRI.
ER  -

TY  - JOUR
AU  - Choi, D.H.
AU  - Ahn, C.
AU  - Jang, G.I.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Reddy, T.B.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.
AU  - Markowitz, V.
AU  - Rohde, M.
AU  - Tindall, B.
AU  - Goker, M.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Cho, B.C.
TI  - High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 98
EP  - 98
VL  - 10
AB  - Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class
AB  - Sphingobacteriia. Three species of the genus Gracilimonas have been
AB  - isolated from marine seawater or a salt mine and showed extremely halotolerant
AB  - and mesophilic features, although close relatives are extremely halophilic or
AB  - thermophilic. The type strain of the type species of Gracilimonas, G. tropica
AB  - DSM19535(T), was isolated from a Synechococcus culture which was established from
AB  - the tropical sea-surface water of the Pacific Ocean. The genome of the strain
AB  - DSM19535(T) was sequenced through the Genomic Encyclopedia of Type Strains, Phase
AB  - I: the one thousand microbial genomes project. Here, we describe the genomic
AB  - features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs
AB  - with 3373 protein-coding and 53 RNA genes. The strain seems to adapt to phosphate
AB  - limitation and requires amino acids from external environment. In addition,
AB  - genomic analyses and pasteurization experiment suggested that G. tropica
AB  - DSM19535(T) did not form spore.
ER  -

TY  - JOUR
AU  - Choi, D.H.
AU  - Jang, G.I.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Reddy, T.B.K.
AU  - Mukherjee, S.
AU  - Huntemann, M.
AU  - Varghese, N.
AU  - Ivanova, N.
AU  - Pillay, M.
AU  - Tindall, B.J.
AU  - Goker, M.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Cho, B.C.
TI  - Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 65
EP  - 65
VL  - 12
AB  - The genus Marinobacterium belongs to the family Alteromonadaceae within the class
AB  - Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium
AB  - contains 16 species. Marinobacterium rhizophilum CL-YJ9T was isolated from
AB  - sediment associated with the roots of a plant growing in a tidal flat of
AB  - Youngjong Island, Korea. The genome of the strain CL-YJ9T was sequenced through
AB  - the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report
AB  - the main features of the draft genome of the strain. The 5,364,574 bp long draft
AB  - genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based
AB  - on the genomic analyses, the strain seems to adapt to osmotic changes by
AB  - intracellular production as well as extracellular uptake of compatible solutes,
AB  - such as ectoine and betaine. In addition, the strain has a number of genes to
AB  - defense against oxygen stresses such as reactive oxygen species and hypoxia.
ER  -

TY  - JOUR
AU  - Choi, D.H.
AU  - Kwon, Y.M.
AU  - Kwon, K.K.
AU  - Kim, S.J.
TI  - Complete genome sequence of US6-1.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 107
EP  - 107
VL  - 10
AB  - Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae.
AB  - According to the phylogenetic analysis based on 16S rRNA gene
AB  - sequence of the N. pentaromativorans US6-1T and nine genome-sequenced strains in
AB  - the genus Novosphingobium, the similarity ranged from 93.9 to 99.9 % and the
AB  - highest similarity was found with Novosphingobium sp. PP1Y (99.9 %), whereas the
AB  - ANI value based on genomes ranged from 70.9 to 93 % and the highest value was 93
AB  - %. This microorganism was isolated from muddy coastal bay sediments where the
AB  - environment is heavily polluted by polycyclic aromatic hydrocarbons (PAHs). It
AB  - was previously shown to be capable of degrading multiple PAHs, including
AB  - benzo[a]pyrene. To further understand the PAH biodegradation pathways the
AB  - previous draft genome of this microorganism was revised to obtain a complete
AB  - genome using Illumina MiSeq and PacBio platform. The genome of strain US6-1T
AB  - consists of 5,457,578 bp, which includes the 3,979,506 bp chromosome and five
AB  - megaplasmids. It comprises 5110 protein-coding genes and 82 RNA genes. Here, we
AB  - provide an analysis of the complete genome sequence which enables the
AB  - identification of new characteristics of this strain.
ER  -

TY  - JOUR
AU  - Choi, D.H.
AU  - Ryu, J.Y.
AU  - Kwon, K.K.
AU  - Lee, J.H.
AU  - Kim, C.
AU  - Lee, C.M.
AU  - Noh, J.H.
TI  - Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2(T), a cyanobacterium isolated from seawater of Chuuk lagoon.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 197
EP  - 204
VL  - 9
AB  - A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for  the first
AB  - time. The type strain, KORDI 51-2(T), was isolated from seawater of
AB  - Chuuk lagoon located in a tropical area. Although it belonged to a clade
AB  - exclusively comprised of extremely halotolerant strains by phylogenetic analyses,
AB  - R. lacunae is known to be incapable of growth at high salt concentration over
AB  - 10%. Here we report the main features of the genome of R. lacunae strain KORDI
AB  - 51-2(T). The genome of R. lacunae contains a gene cluster for phosphonate
AB  - utilization encoding three transporters, one regulator and eight C-P lyase
AB  - subunits.
ER  -

TY  - JOUR
AU  - Choi, G.-E.
AU  - Cho, Y.J.
AU  - Koh, W.J.
AU  - Chun, J.
AU  - Cho, S.N.
AU  - Shin, S.J.
TI  - Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii BDT.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2756
EP  - 2757
VL  - 194
AB  - Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and
AB  - infections of the skin and soft tissues. Consistent reports of human infections indicate that
AB  - M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM).
AB  - Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD(T).
ER  -

TY  - JOUR
AU  - Choi, H.S.
AU  - Kwon, M.G.
AU  - Kim, M.S.
AU  - Park, M.A.
AU  - Kim, D.W.
AU  - Park, J.Y.
AU  - Kim, J.S.
AU  - Na, Y.J.
AU  - Kim, M.Y.
AU  - Kim, D.S.
AU  - Chae, S.H.
AU  - Seo, J.S.
TI  - Draft Genome Sequence of Beta-Hemolytic Streptococcus iniae KCTC 11634.
JO  - Genome Announcements
PY  - 2013
SP  - e00897
EP  - e00813
VL  - 1
AB  - Streptococcus iniae is a beta-hemolytic, Gram-positive coccus, which affects a broad range of
AB  - freshwater and marine fish species, causing substantial economic
AB  - losses in the aquaculture industry worldwide. Thus, it is very important to
AB  - derive a complete genome sequence of the bacterium to aid in the development of
AB  - vaccines and methods for preventing fish streptococcosis and zoonotic infections
AB  - in humans. Here, we present the draft genome sequence of S. iniae KCTC 11634
AB  - (1,955,615 bp, with a G+C content of 36.6%), which contains 1,868 putative coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Choi, J.H.
AU  - Sugiura, H.
AU  - Moriuchi, R.
AU  - Kawagishi, H.
AU  - Dohra, H.
TI  - High-Quality Draft Genome Sequence of Burkholderia contaminans CH-1, a Gram-Negative Bacterium That Metabolizes 2-Azahypoxanthine, a Plant  Growth-Regulating Compound.
JO  - Genome Announcements
PY  - 2017
SP  - e01148
EP  - e01117
VL  - 5
AB  - Burkholderia contaminans strain CH-1 converts 2-azahypoxnathine to 2-aza-8-oxohypoxanthine,
AB  - plant growth-regulating compounds, by oxidation. We
AB  - report here the high-quality draft genome sequence of B. contaminans CH-1. The
AB  - genome contains 8,065 protein-coding sequences, including several genes possibly
AB  - involved in metabolizing 2-azahypoxanthine.
ER  -

TY  - JOUR
AU  - Choi, K.D.
AU  - Kim, K.
AU  - Yoo, O.J.
TI  - A new restriction endonuclease from Clostridium thermocellum.
JO  - Sanop Misaengmul Hakhoe Chi
PY  - 1987
SP  - 352
EP  - 355
VL  - 15
AB  - The isolation and characterization of the Type II restriction endonuclease from Clostridium
AB  - thermocellum ATCC 27405 is described. This enzyme (CthI endonuclease) is an isoschizomer of
AB  - BclI endonuclease recognizing 5'-TGATCA-3'. CthI endonuclease requires Mg2+ ion for its
AB  - activity and is maximally active at pH 7.5 to 10.5 in the presence of 0 to 10mM NaCl. CthI
AB  - endonuclease is heat stable and has an optimum temperature of 60C. The activity of CthI enzyme
AB  - is sensitive to dam methylation.
ER  -

TY  - JOUR
AU  - Choi, K.D.
AU  - Yoo, O.J.
TI  - A new restriction endonuclease, CthII, from Clostridium thermocellum ATCC 27405.
JO  - Korean Biochem. J.
PY  - 1990
SP  - 418
EP  - 421
VL  - 23
AB  - A new restriction enzyme has been isolated by DEAE-cellulose and phosphocellulose columns from
AB  - a thermophilic anaerobic bacterium, Clostridium thermocellum ATCC 27405. Following CthI, the
AB  - second peak of sequence specific endonuclease activity was eluted from the phosphocellulose
AB  - column. The enzyme was designated as CthII. The recognition sequence of CthII was determined
AB  - to be the dcm sequence, 5'-CC^(A/T) GG-3' and the cleavage site was indicated by the arrow.
AB  - CthII endonuclease requires Mg2+ ion for its activity and is maximally active at a pH range
AB  - from 8.0 to 9.0. CthII endonuclease is heat stable and has an optimum reaction temperature of
AB  - 55C. Like BstNI and ZanI this enzyme was able to cleave dcm-methylated DNA.
ER  -

TY  - JOUR
AU  - Choi, O.
AU  - Lim, J.Y.
AU  - Seo, Y.S.
AU  - Hwang, I.
AU  - Kim, J.
TI  - Complete Genome Sequence of the Rice Pathogen Pantoea ananatis Strain PA13.
JO  - J. Bacteriol.
PY  - 2012
SP  - 531
EP  - 531
VL  - 194
AB  - Pantoea ananatis is the causative agent of sheath and grain rot in rice. Here, we present the
AB  - complete genome sequence of P. ananatis strain PA13,
AB  - originally isolated from a diseased rice grain.
ER  -

TY  - JOUR
AU  - Choi, S.-H.
TI  - Restriction-modification systems and genetic variability of Xanthomonas oryzae pv.
JO  - Diss. Abstr.
PY  - 1994
SP  - 5462B
EP  - 5463B
VL  - 54
AB  - The XorII methyltransferase gene (xorIIM) and very short patch repair endonuclease gene
AB  - (xorii.vsr) were cloned from Xanthomonas oryzae pv. oryzae, the rice bacterial leaf blight
AB  - pathogen. XorIIM encodes a polypeptide of 47 KD and was identified as a monospecific m5
AB  - cytosine methyltransferase gene. The xorii.vsr encodes a polypeptide of 19.7 KD and the gene
AB  - is similar in sequence and size to the E. coli vsr gene of the DNA cytosine methylase system
AB  - (Dcm). A population of X. oryzae pv. oryzae strains from major rice growing countries in Asia
AB  - was evaluated for the presence or absence of the XorI and XorII restriction-modification (R-M)
AB  - systems. Four clonal populations with the phenotype XorI+II+, XorI-II+, XorI+II-, XorI-II+,
AB  - and XorI-II- were distributed in Asia. The XorII R-M system was predominantly found in
AB  - southeast Asia, whereas the XorI modification system was most prevalent in northeast Asia. DNA
AB  - polymorphisms were observed between strains in genomic sequences containing the XorII R-M
AB  - genes; however, most Philippine strains and all the Indonesian and Korean strains had
AB  - identical patterns. Based on the geographic distribution of both systems and the genome
AB  - organization around the XorII system, I propose that the XorI system originated in northeast
AB  - Asia and moved to southeast Asia, while the XorII system originated in southeast Asia. The
AB  - existence of several phenotypes in some parts of Asia indicate that after movement of the
AB  - systems the populations remained clonal.
AB  - 
AB  - A marker-exchange mutant in which the avirulence gene locus avrXa7 was insertionally
AB  - inactivated was significantly reduced in aggressiveness to susceptible rice cultivars.
AB  - Aggressiveness was restored by complementation with a plasmid bearing the avrXa7 gene. Thus,
AB  - avrXa7 codes for not only resistance-gene-specific avirulence function, but also for
AB  - pathogenicity functions.
AB  - 
ER  -

TY  - JOUR
AU  - Choi, S.C.
AU  - Parker, J.
AU  - Richards, V.P.
AU  - Ross, K.
AU  - Jilly, B.
AU  - Chen, J.
TI  - Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Isolated  from a Respiratory Infection.
JO  - Genome Announcements
PY  - 2014
SP  - e00822
EP  - e00814
VL  - 2
AB  - Next-generation sequencing was used to investigate an unknown clinical respiratory infection.
AB  - This new strain of Streptococcus pneumoniae, ASVL_JC_0001,
AB  - was isolated from a clinical specimen from a patient with bronchitis and
AB  - pulmonary inflammation. The draft genome sequence, obtained with an Illumina
AB  - MiSeq sequencing system, consists of 83 large contigs, a total of 2,092,532 bp
AB  - long, and has a GC content of 40.3%.
ER  -

TY  - JOUR
AU  - Choi, S.H.
AU  - Heo, K.
AU  - Byun, H.M.
AU  - An, W.
AU  - Lu, W.
AU  - Yang, A.S.
TI  - Identification of preferential target sites for human DNA methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 104
EP  - 118
VL  - 39
AB  - DNA methyltransferases (DNMTs) play an important role in establishing and maintaining DNA
AB  - methylation. Aberrant expression of DNMTs and their
AB  - isoforms has been found in many types of cancer, and their contribution to
AB  - aberrant DNA methylation has been proposed. Here, we generated HEK 293T
AB  - cells stably transfected with each of 13 different DNMTs (DNMT1, two
AB  - DNMT3A isoforms, nine DNMT3B isoforms and DNMT3L) and assessed the DNA
AB  - methylation changes induced by each DNMT. We obtained DNA methylation
AB  - profiles of DNA repetitive elements and 1505 CpG sites from 808
AB  - cancer-related genes. We found that DNMTs have specific and overlapping
AB  - target sites and their DNA methylation target profiles are a reflection of
AB  - the DNMT domains. By examining H3K4me3 and H3K27me3 modifications in the
AB  - 808 gene promoter regions using promoter ChIP-on-chip analysis, we found
AB  - that specific de novo DNA methylation target sites of DNMT3A1 are
AB  - associated with H3K4me3 modification that are transcriptionally active,
AB  - whereas the specific target sites of DNMT3B1 are associated with H3K27me3
AB  - modification that are transcriptionally inactive. Our data suggest that
AB  - different DNMT domains are responsible for targeting DNA methylation to
AB  - specific regions of the genome, and this targeting might be associated
AB  - with histone modifications.
ER  -

TY  - JOUR
AU  - Choi, S.H.
AU  - Ji, Y.
AU  - Park, S.
AU  - Mathara, J.
AU  - Holzapfel, W.
AU  - Kang, J.
TI  - Complete Genome Sequence of Lactobacillus rhamnosus BFE5264, Isolated from Maasai Traditional Fermented Milk.
JO  - Genome Announcements
PY  - 2017
SP  - e00563
EP  - e00517
VL  - 5
AB  - Here, we report the complete genome of Lactobacillus rhamnosus BFE5264, which was sequenced
AB  - with the Pacific Biosciences RSII platform. The genome size is 3.01 Mb
AB  - and includes 3,077 annotated coding sequences, including genes associated with
AB  - the promotion of intestinal epithelial homeostasis through specific signaling
AB  - pathways.
ER  -

TY  - JOUR
AU  - Choi, S.H.
AU  - Leach, J.E.
TI  - Identification of the XorII methyltransferase gene and a vsr homolog from Xanthomonas oryzae pv. oryzae.
JO  - Mol. Gen. Genet.
PY  - 1994
SP  - 383
EP  - 390
VL  - 244
AB  - The gene encoding the XorII methyltransferase (M.XorII) was cloned from Xanthomonas oryzae pv.
AB  - oryzae and characterized in Escherichia coli. The M.XorII activity was localized to a 3.1 kb
AB  - BamHI-BstXI fragment, which contained two open reading frames (ORFs) of 1272 nucleotides (424
AB  - amino acids) and 408 nucleotides (136 amino acids). Ten polypeptide domains conserved in other
AB  - M5 cytosine methyltransferases (MTases) were identified in the deduced amino acid sequence of
AB  - the 1272 ORF. E. coli Mrr+ strains were transformed poorly by plasmids containing the XorII
AB  - MTase gene, indicating the presence of at least one MeCG in the recognition sequence for
AB  - M.XorII (CGATCG). The 408 nucleotide ORF was 36% identical at the amino acid level to
AB  - sequences of the E. coli dcm-vsr gene, which is required for very short patch repair. X.
AB  - oryzae pv. oryzae genomic DNA that is resistant to digestion by PvuI and XorII hybridizes with
AB  - a 7.0 kb fragment containing the XorII MTase gene and vsr homolog, whereas DNA from strains
AB  - that lack M.XorII activity do not hybridize with the fragment.
ER  -

TY  - JOUR
AU  - Choi, S.H.
AU  - Vera Cruz, C.M.
AU  - Leach, J.E.
TI  - Distribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia.
JO  - Appl. Environ. Microbiol.
PY  - 1998
SP  - 1663
EP  - 1668
VL  - 64
AB  - The presence or absence of two DNA modification systems, XorI and XorII, in 195 strains of
AB  - Xanthomonas oryzae pv. oryzae collected from different major rice-growing countries of Asia
AB  - was assessed.  All four possible phenotypes (XorI+ XorII+, XorI+ XorII-, XorI- XorII+ and Xor-
AB  - XorII-) were detected in the population at a ratio of approximately 1:2:2:2.  The XorI+ XorII+
AB  - and XorI- XorII+ phenotypes were observed predominantly in strains from southeast Asia
AB  - (Philippines, Malaysia, and Indonesia), whereas strains with the phenotypes XorI- XorII- and
AB  - XorI+ XorII- were distributed in south Asia (India and Nepal) and northeast Asia (China, Korea
AB  - and Japan), respectively.  Based on the prevalence and geographic distribution of the XorI and
AB  - XorII systems, we suggest that the XorI modification system originated in northeast Asia and
AB  - was later introduced to southeast Asia, while the XorII system originated in southeast Asia
AB  - and moved to northeast Asia and south Asia.  Genomic DNA from all tested strains of X. oryzae
AB  - pv. Oryzae that were resistant to digestion by endonuclease XorII or its isoschizomer PvuI
AB  - also hybridized with a 7.0-kb clone that contained the XorII modification system, whereas
AB  - strains that were digested by XorII or PvuI lacked DNA that hybridized with the clone.  Size
AB  - polymorphisms were observed in fragments that hybridized with the 7.0-kb clone.  However, a
AB  - single hybridization pattern generally was found in XorII+ strains within a country,
AB  - indicating clonal maintenance of the XorII methyltransferase gene locus.  The locus was
AB  - monomorphic for X. oryzae pv. Oryzae strains from the Philippines and all strains from
AB  - Indonesia and Korea.
ER  -

TY  - JOUR
AU  - Choi, S.K.
AU  - Jeong, H.
AU  - Kloepper, J.W.
AU  - Ryu, C.M.
TI  - Genome Sequence of Bacillus amyloliquefaciens GB03, an Active Ingredient of the First Commercial Biological Control Product.
JO  - Genome Announcements
PY  - 2014
SP  - e01092
EP  - e01014
VL  - 2
AB  - Bacillus amyloliquefaciens GB03 has been used as a representative commercialized  strain of
AB  - the bacilli for biological control against a broad spectrum of plant
AB  - pathogens and as a bio-fertilizer to promote growth and yield of field crops for
AB  - more than two decades. Herein, we present the genome sequence and a brief
AB  - analysis of strain GB03.
ER  -

TY  - JOUR
AU  - Choi, W.S.
AU  - Kang, S.C.
AU  - Seo, J.S.
AU  - Yoo, O.J.
TI  - Inhibition of SmaI, AvaI, NaeI and XmaI endonuclease activities by the methylation of DNA with HpaII methylase.
JO  - Korean J. Microbiol.
PY  - 1986
SP  - 86
EP  - 90
VL  - 24
AB  - The DNA methylated by HpaII methylase was not cleaved by SmaI, AvaI and NaeI
AB  - endonucleases.  This experimental data could be interpreted as strong evidence
AB  - that SmaI, AvaI and NaeI methylases which yet to be isolated would methylate on
AB  - the inmost cytosine nucleotide within their hexameric recognition sequences.
AB  - The facts that SmaI, AvaI and NaeI endonucleases cannot cleave the DNA
AB  - methylated by HpaII methylase are the valuable informations for protecting DNAs
AB  - upon cleavage reactions by SmaI, AvaI and NaeI endonucleases especially for
AB  - cDNA insertion experiments into vector DNAs using SmaI, AvaI and NaeI
AB  - oligonucleotide linkers.  In the case of XmaI endonuclease, partially cleaved
AB  - DNA fragments were observed although the reaction rate was greatly decreased.
AB  - This result implies that the methylation site of XmaI methylase which is yet to
AB  - be isolated would not be the same as that of HpaII methylase in XmaI sequence.
ER  -

TY  - JOUR
AU  - Choi, Y.
AU  - Shin, H.
AU  - Lee, J.H.
AU  - Ryu, S.
TI  - Identification and characterization of a novel flagellum-dependent Salmonella-infecting bacteriophage, iEPS5.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 4829
EP  - 4837
VL  - 79
AB  - A novel flagellatropic phage of Salmonella enterica serovar Typhimurium called
AB  - iEPS5 was isolated and characterized. iEPS5 has an icosahedral head and a long
AB  - non-contractile tail with a tail fiber. Genome sequencing revealed a
AB  - double-stranded DNA of 59,254 bp having 73 open reading frames (ORFs). To
AB  - identify the receptor for iEPS5, Tn5 transposon insertion mutants of S.
AB  - Typhimurium SL1344 that were resistant to the phage were isolated. All of the
AB  - phage-resistant mutants were found to have mutations in genes involved in
AB  - flagellar formation, suggesting that the flagellum is the adsorption target of
AB  - this phage. Analysis of phage infection using the DeltamotA mutant, which is
AB  - flagellated but non-motile, demonstrated the requirement of flagellar rotation
AB  - for iEPS5 infection. Further analysis of phage infection using the DeltacheY
AB  - mutant revealed that iEPS5 could infect host bacteria only when the flagellum is
AB  - rotating counterclockwise (CCW). These results suggested that the CCW-rotating
AB  - flagellar filament is essential for phage adsorption and required for successful
AB  - infection by iEPS5. In contrast to the well-studied flagellatropic phage Chi,
AB  - iEPS5 cannot infect the DeltafliK mutant that makes a polyhook without a
AB  - flagellar filament, suggesting that these two flagellatropic phages utilize
AB  - different infection mechanisms. Here, we present evidences that iEPS5 may inject
AB  - its DNA into the flagellar filament for infection by assessing DNA transfer from
AB  - SYBR-gold-labeled iEPS5 to the host bacteria.
ER  -

TY  - JOUR
AU  - Choi, Y.-J.
AU  - Kim, S.-J.
AU  - Hwang, H.-Y.
AU  - Yim, J.
AU  - Kim, J.-C.
TI  - Characterization of restriction endonuclease EagBI from Enterobacter agglomerans CBNU45.
JO  - Korean J. Microbiol.
PY  - 1994
SP  - 91
EP  - 95
VL  - 32
AB  - EagBI is a type II restriction endonuclease from Enterobacter agglomerans strain CBNU45
AB  - isolated from soil.  EagBI was partially purified by DEAE-cellulose, phosphocellulose P11 and
AB  - hydroxylapatite column chromatography.  EagBI recognizes and cleaves the sequence
AB  - 5'-CGAT/CG-3' and generates 2-base 3'-protruding cohesive ends.  The optimal reaction
AB  - conditions of EagBI are 10mM Tris-HCl (pH 7.8), 6-10mM MgCl2 at 37oC.  The enzyme is maximally
AB  - active in the absence of NaCl, able to cleave both dam- and dam+ DNAs and sensitive to heat
AB  - treatment (at 65oC for 10 min).  Therefore, although EagBI is an isoschizomer of PvuI, it is
AB  - more useful than PvuI in respect of the NaCl requirement and heat-stability.
ER  -

TY  - JOUR
AU  - Choi, Y.U.
AU  - Kwon, Y.K.
AU  - Ye, B.R.
AU  - Hyun, J.H.
AU  - Heo, S.J.
AU  - Affan, A.
AU  - Yoon, K.T.
AU  - Park, H.S.
AU  - Oh, C.
AU  - Kang, D.H.
TI  - Draft Genome Sequence of Marinobacterium stanieri S30, a Strain Isolated from a Coastal Lagoon in Chuuk State in Micronesia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1260
EP  - 1260
VL  - 194
AB  - In this study, we isolated xylan-degrading bacteria from a coastal lagoon of Micronesia and
AB  - identified the bacteria as Marinobacterium stanieri S30. GSFLX 454
AB  - pyrosequencing and sequence analysis of the M. stanieri S30 genome generated
AB  - 4,007 predicted open reading frames (ORFs) that could be candidate genes for
AB  - producing enzymes with different catalytic functions.
ER  -

TY  - JOUR
AU  - Chollet, A.
AU  - Kawashima, E.
TI  - DNA containing the base analogue 2-aminoadenine:  preparation, use as hybridization probes and cleavage by restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 305
EP  - 317
VL  - 16
AB  - The base analogue 2-aminoadenine (2,6-diaminopurine,D) has been introduced at
AB  - selected positions into synthetic oligodeoxyribonucleotides and DNA by the
AB  - combined use of chemical and enzymatic methods.  2-aminoadenine substitution
AB  - for adenine introduces changes in the minor groove of DNA and creates an
AB  - additional hydrogen bond in the Watson-Crick base pair with thymine.
AB  - Oligonucleotide hybridization probes containing 2-aminoadenine showed increased
AB  - selectivity and hybridization strength during DNA-DNA hybridization to phage or
AB  - genomic target DNA.  Properties of the base analogue with respect to DNA
AB  - modifying enzymes were examined.  2-aminoadenine was used to probe minor groove
AB  - determinants during the treatment of DNA by 12 restriction endonucleases.
AB  - Inhibition of cleavage was found for several restriction enzymes.
ER  -

TY  - JOUR
AU  - Chong, S.
AU  - Shao, Y.
AU  - Paulus, H.
AU  - Benner, J.
AU  - Perler, F.B.
AU  - Xu, M.-Q.
TI  - Protein splicing involving the Saccharomyces cerevisiae VMA intein.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 22159
EP  - 22168
VL  - 271
AB  - Protein splicing involves the excision of an internal protein segment, the intein, from a
AB  - precursor protein and the concomitant ligation of the flanking N- and C-terminal regions.  It
AB  - occurs in mesophilic bacteria, yeast, and thermophilic archaea.  The ability to control
AB  - protein splicing of a thermophilic intein by temperature and pH in a foreign protein context
AB  - facilitated the study of the mechanism of protein splicing in thermophiles.  On the other
AB  - hand, no direct studies have been done on the mechanism of protein splicing in mesophiles.  We
AB  - examined the splicing of a chimeric protein containing the intein of the vacuolar ATPase
AB  - subunit (VMA) of Saccharomyces cerevisiae that involves cysteines rather than serines at the
AB  - reaction center.  The steps in the splicing process were deduced by analyzing intermediates
AB  - and side products that accumulate as a result of amino acid substitutions and were found to be
AB  - analogous to those occurring in thermophiles.  Moreover, appropriate amino acid replacements
AB  - allowed us to develop the first mesophilic in vitro protein splicing system as well as
AB  - strategies for modulating the rate of protein splicing and for converting the splicing
AB  - reaction to an efficient protein cleavage reaction at either splice junction.
ER  -

TY  - JOUR
AU  - Chong, T.M.
AU  - Tung, H.J.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Insights from the Genome Sequence of Quorum-Quenching Staphylococcus sp. Strain AL1, Isolated from Traditional Chinese Soy Sauce Brine Fermentation.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6611
EP  - 6612
VL  - 194
AB  - We report the draft genome sequence of Staphylococcus sp. strain AL1, which degrades
AB  - quorum-sensing molecules (namely, N-acyl homoserine lactones). To the
AB  - best of our knowledge, this is the first documentation that reports the whole
AB  - genome sequence and quorum-quenching activity of Staphylococcus sp. strain AL1.
ER  -

TY  - JOUR
AU  - Chong, T.M.
AU  - Yin, W.F.
AU  - Mondy, S.
AU  - Grandclement, C.
AU  - Dessaux, Y.
AU  - Chan, K.G.
TI  - Heavy-Metal Resistance of a France Vineyard Soil Bacterium, Pseudomonas mendocina Strain S5.2, Revealed by Whole-Genome Sequencing.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6366
EP  - 6366
VL  - 194
AB  - Here we present the draft genome of Pseudomonas mendocina strain S5.2, possessing tolerance to
AB  - a high concentration of copper. In addition to being copper
AB  - resistant, the genome of P. mendocina strain S5.2 contains a number of
AB  - heavy-metal-resistant genes known to confer resistance to multiple heavy-metal
AB  - ions.
ER  -

TY  - JOUR
AU  - Choo, S.W.
AU  - Wong, Y.L.
AU  - Beh, C.Y.
AU  - Lokanathan, N.
AU  - Leong, M.L.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Ngeow, Y.F.
TI  - Whole-Genome Shotgun Sequencing of Mycobacterium abscessus M156, an Emerging Clinical Pathogen in Malaysia.
JO  - Genome Announcements
PY  - 2013
SP  - e00063
EP  - e00012
VL  - 1
AB  - Mycobacterium abscessus is an emerging clinical pathogen commonly associated with
AB  - non-tuberculous mycobacterial infections. We report herein the draft genome of M. abscessus
AB  - strain M156.
ER  -

TY  - JOUR
AU  - Choo, S.W.
AU  - Wong, Y.L.
AU  - Leong, M.L.
AU  - Heydari, H.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Ngeow, Y.F.
TI  - Analysis of the Genome of Mycobacterium abscessus Strain M94 Reveals an Uncommon  Cluster of tRNAs.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5724
EP  - 5724
VL  - 194
AB  - Mycobacterium abscessus is a species of rapidly growing nontuberculous mycobacteria that is
AB  - frequently associated with opportunistic infections in
AB  - humans. Here, we report the annotated genome sequence of M. abscessus strain M94,
AB  - which showed an unusual cluster of tRNAs.
ER  -

TY  - JOUR
AU  - Choo, S.W.
AU  - Wong, Y.L.
AU  - Tan, J.L.
AU  - Ong, C.S.
AU  - Wong, G.J.
AU  - Ng, K.P.
AU  - Ngeow, Y.F.
TI  - Annotated Genome Sequence of Mycobacterium massiliense Strain M154, Belonging to  the Recently Created Taxon Mycobacterium abscessus subsp. bolletii comb. nov.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4778
EP  - 4778
VL  - 194
AB  - Mycobacterium massiliense has recently been proposed as a member of Mycobacterium abscessus
AB  - subsp. bolletii comb. nov. Strain M154, a clinical isolate from the
AB  - bronchoalveolar lavage fluid of a Malaysian patient presenting with lower
AB  - respiratory tract infection, was subjected to shotgun DNA sequencing with the
AB  - Illumina sequencing technology to obtain whole-genome sequence data for
AB  - comparison with other genetically related strains within the M. abscessus species
AB  - complex.
ER  -

TY  - JOUR
AU  - Choo, S.W.
AU  - Wong, Y.L.
AU  - Yusoff, A.M.
AU  - Leong, M.L.
AU  - Wong, G.J.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Ngeow, Y.F.
TI  - Genome Sequence of the Mycobacterium abscessus Strain M93.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3278
EP  - 3278
VL  - 194
AB  - Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is
AB  - frequently associated with opportunistic infections in humans. We report
AB  - herein the draft genome sequence of M. abscessus strain M93.
ER  -

TY  - JOUR
AU  - Choo, S.W.
AU  - Yusoff, A.M.
AU  - Wong, Y.L.
AU  - Wee, W.Y.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Ngeow, Y.F.
TI  - Genome Analysis of Mycobacterium massiliense Strain M172, Which Contains a Putative Mycobacteriophage.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5128
EP  - 5128
VL  - 194
AB  - The genome of Mycobacterium massiliense M172, isolated from a human sputum sample, was
AB  - sequenced using Illumina GA IIX technology and found to contain
AB  - 5,204,460 bp, including putative genes for virulence and antibiotic resistance as
AB  - well as a 92-kb genomic region most likely to correspond to a mycobacteriophage.
ER  -

TY  - JOUR
AU  - Choo, Y.
TI  - Recognition of DNA methylation by zinc fingers.
JO  - Nat. Struct. Biol.
PY  - 1998
SP  - 264
EP  - 265
VL  - 5
AB  - Zinc fingers are small DNA-binding motifs that occur in a large family of eukaryotic
AB  - transcription factors.  The DNA-binding specificity of zinc fingers can be altered by protein
AB  - engineering, for instance using phage display, to create novel protein domains which recognize
AB  - predetermined sequences.  It has been proposed that tailored DNA-binding domains of this type
AB  - can be incorporated into proteins such as restriction enzymes and transcription factors, in
AB  - order to target particular DNA sequences or genes.  The zinc finger domains studied so far -
AB  - whether naturally occurring, designed or selected - can bind specifically to various DNA sites
AB  - containing the four major DNA bases: A, G, C and T.
ER  -

TY  - JOUR
AU  - Choo, Y.
AU  - Isalan, M.
TI  - Advances in zinc finger engineering.
JO  - Curr. Opin. Struct. Biol.
PY  - 2000
SP  - 411
EP  - 416
VL  - 10
AB  - Recently developments have been made in engineering sequence-specific zinc finger DNA-binding
AB  - proteins.  Advances in this area will soon make it routine to target proteins to specific DNA
AB  - sequences associated with any given gene.  The primary interest is in the regulation of gene
AB  - expression using customized transcription factors.  However, modular catalytic domains are
AB  - also being developed in order to engineer chimeric proteins with customized restriction
AB  - enzyme, methylase and integrase activity.
ER  -

TY  - JOUR
AU  - Chopin, A.
AU  - Chopin, M.-C.
AU  - Moillo-Batt, A.
AU  - Langella, P.
TI  - Two plasmid-determined restriction and modification systems in Streptococcus lactis.
JO  - Plasmid
PY  - 1984
SP  - 260
EP  - 263
VL  - 11
AB  - Two restriction and modification systems were found in Streptococcus lactis
AB  - strain IL594 which was found to contain 9 plasmids designated pIL1 to pIL9.  On
AB  - the basis of protoplast-induced curing experiments, we showed that a
AB  - restriction and modification system was related to the presence of pIL6 or
AB  - pIL7.  The pIL-6-determined restriction and modification system was related to
AB  - the presence of pIL6 or pIL7.  The pIL-6-determined restriction and
AB  - modification system was confirmed by cotransfer of the plasmid and of the
AB  - restriction and modification system to a plasmid-free, nonrestricting
AB  - derivative of S. lactis IL594.
ER  -

TY  - JOUR
AU  - Chou, L.F.
AU  - Chen, Y.T.
AU  - Lu, C.W.
AU  - Ko, Y.C.
AU  - Tang, C.Y.
AU  - Pan, M.J.
AU  - Tian, Y.C.
AU  - Chiu, C.H.
AU  - Hung, C.C.
AU  - Yang, C.W.
TI  - Sequence of Leptospira santarosai serovar Shermani genome and prediction of virulence-associated genes.
JO  - Gene
PY  - 2012
SP  - 364
EP  - 370
VL  - 511
AB  - Leptospirosis, a widespread zoonosis, is a re-emerging infectious disease caused
AB  - by pathogenic Leptospira species. In Taiwan, Leptospira santarosai serovar
AB  - Shermani is the most frequently isolated serovar, causing both renal and systemic
AB  - infections. This study aimed to generate a L. santarosai serovar Shermani genome
AB  - sequence and categorize its hypothetical genes, particularly those associated
AB  - with virulence. The genome sequence consists of 3,936,333 nucleotides and 4033
AB  - predicted genes. Additionally, 2244 coding sequences could be placed into
AB  - clusters of orthologous groups and the number of genes involving cell
AB  - wall/membrane/envelope biogenesis and defense mechanisms was higher than that of
AB  - other Leptospira spp. Comparative genetic analysis based on BLASTX data revealed
AB  - that about 73% and 68.8% of all coding sequences have matches to pathogenic L.
AB  - interrogans and L. borgpetersenii, respectively, and about 57.6% to saprophyte L.
AB  - biflexa. Among the hypothetical proteins, 421 have a transmembrane region, 172
AB  - have a signal peptide and 17 possess a lipoprotein signature. According to PFAM
AB  - prediction, 32 hypothetical proteins have properties of toxins and surface
AB  - proteins mediated bacterial attachment, suggesting they may have roles associated
AB  - with virulence. The availability of the genome sequence of L. santarosai serovar
AB  - Shermani and the bioinformatics re-annotation of leptospiral hypothetical
AB  - proteins will facilitate further functional genomic studies to elucidate the
AB  - pathogenesis of leptospirosis and develop leptospiral vaccines.
ER  -

TY  - JOUR
AU  - Chouaia, B.
AU  - Crotti, E.
AU  - Brusetti, L.
AU  - Daffonchio, D.
AU  - Essoussi, I.
AU  - Nouioui, I.
AU  - Sbissi, I.
AU  - Ghodhbane-Gtari, F.
AU  - Gtari, M.
AU  - Vacherie, B.
AU  - Barbe, V.
AU  - Medigue, C.
AU  - Gury, J.
AU  - Pujic, P.
AU  - Normand, P.
TI  - Genome Sequence of Blastococcus saxobsidens DD2, a Stone-Inhabiting Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2752
EP  - 2753
VL  - 194
AB  - Members of the genus Blastococcus have been isolated from sandstone monuments, as well as from
AB  - sea, soil, plant, and snow samples. We report here the genome
AB  - sequence of a member of this genus, Blastococcus saxobsidens strain DD2, isolated
AB  - from below the surface of a Sardinian wall calcarenite stone sample.
ER  -

TY  - JOUR
AU  - Choudhary, M.
AU  - Mackenzie, C.
AU  - Nereng, K.
AU  - Sodergren, E.
AU  - Weinstock, G.M.
AU  - Kaplan, S.
TI  - Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome.
JO  - Microbiology
PY  - 1997
SP  - 3085
EP  - 3099
VL  - 143
AB  - The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1T has two chromosomes, CI
AB  - (approximately 3.0 Mb) and CII (approximately 0.9 Mb). In this study a low-redundancy
AB  - sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library.
AB  - The sum of the lengths of these 23 cosmid inserts was approximately 495 kb, which comprised
AB  - approximately 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each
AB  - run generating 559 +/- 268 bases of sequence to give approximately 640 kb of total sequence.
AB  - After editing, approximately 2.8% bases per run were estimated to be ambiguous. After the
AB  - removal of vector and Escherichia coli sequences, the remaining approximately 565 kb of R.
AB  - sphaeroides sequences were assembled, generating approximately 291 kb of unique sequences.
AB  - BLASTX analysis of these unique sequences suggested that approximately 131 kb (45% of the
AB  - unique sequence) had matches to either known genes, or database ORFs of hypothetical or
AB  - unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of
AB  - these matches represented genes encoding a wide variety of functions, e.g. amino acid
AB  - biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA
AB  - operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA
AB  - sequence which did not yield database matches was then analysed using CODONPREFERENCE from the
AB  - GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could
AB  - encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding
AB  - intergenic DNA. From the data so far obtained, CII does not appear to be specialized for
AB  - encoding any particular metabolic function, physiological state or growth condition. These
AB  - data suggest that CII contains genes which are functionally as diverse as those found on any
AB  - other bacterial chromosome and also contains sequences (pORFs), which may prove to be unique
AB  - to this organism.
ER  -

TY  - JOUR
AU  - Choudhary, M.
AU  - Zanhua, X.
AU  - Fu, Y.X.
AU  - Kaplan, S.
TI  - Genome Analyses of Three Strains of Rhodobacter sphaeroides: Evidence of Rapid Evolution of Chromosome II.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1914
EP  - 1921
VL  - 189
AB  - Three strains of Rhodobacter sphaeroides of diverse origin have been under investigation in
AB  - our laboratory for their genome complexities, including
AB  - the presence of multiple chromosomes and the distribution of essential
AB  - genes within their genomes. The genome of R. sphaeroides 2.4.1 has been
AB  - completely sequenced and fully annotated, and now two additional strains
AB  - (ATCC 17019 and ATCC 17025) of R. sphaeroides have been sequenced. Thus,
AB  - genome comparisons have become a useful approach in determining the
AB  - evolutionary relationships among different strains of R. sphaeroides. In
AB  - this study, the concatenated chromosomal sequences from the three strains
AB  - of R. sphaeroides were aligned, using Mauve, to examine the extent of
AB  - shared DNA regions and the degree of relatedness among their
AB  - chromosome-specific DNA sequences. In addition, the exact intra- and
AB  - interchromosomal DNA duplications were analyzed using Mummer. Genome
AB  - analyses employing these two independent approaches revealed that strain
AB  - ATCC 17025 diverged considerably from the other two strains, 2.4.1 and
AB  - ATCC 17029, and that the two latter strains are more closely related to
AB  - one another. Results further demonstrated that chromosome II
AB  - (CII)-specific DNA sequences of R. sphaeroides have rapidly evolved, while
AB  - CI-specific DNA sequences have remained highly conserved. Aside from the
AB  - size variation of CII of R. sphaeroides, variation in sequence lengths of
AB  - the CII-shared DNA regions and their high sequence divergence among
AB  - strains of R. sphaeroides suggest the involvement of CII in the evolution
AB  - of strain-specific genomic rearrangements, perhaps requiring strains to
AB  - adapt in specialized niches.
ER  -

TY  - JOUR
AU  - Choudhry, S.
TI  - Characterization of new type II restriction endonucleases from bacteria.
JO  - Proc. Pakistan Acad. Sci.
PY  - 1999
SP  - 165
EP  - 171
VL  - 36
AB  - The aim of the present study was to search the available microflora of Pakistan for new type
AB  - II restriction endonucleases.  Twelve bacterial strains from the American Type Culture
AB  - Collection and CAMB Culture Collection were screened for the presence of new type II
AB  - restriction endonucleases.  Two strains, Arthrobacter picolinophilus (ATCC 27854) and
AB  - Pseudomonas aeruginosa Q2 (CAMB 2637) yielded the endonucleases.  The type II restriction
AB  - enzymes isolated and characterized from these strains are designated as ApiI and PaeQI.  These
AB  - enzymes were purified by a combination of gel filtration, ion exchange and affinity
AB  - chromatography.  The DNA sequences recognized by the two enzymes were determined by analysis
AB  - of the fragment patterns generated on different substrate DNAs, Lambda, T7, pUC19, pBR322,
AB  - PhiX174RFI.  The cleavage sites within the recognition sequences were also established by
AB  - primed synthesis.  The newly discovered enzymes ApiI and PaeQI recognize and cleave 4-6
AB  - nucleotide long DNA sequences 5'-CTGCAG-3', 5'-CCGCGG-3', respectively.
ER  -

TY  - JOUR
AU  - Choudhury, J.D.
AU  - Pramanik, A.
AU  - Webster, N.S.
AU  - Llewellyn, L.E.
AU  - Gachhui, R.
AU  - Mukherjee, J.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile.
JO  - Genome Announcements
PY  - 2014
SP  - e00001
EP  - e00014
VL  - 2
AB  - To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled
AB  - Koch's postulates. We report the 4.48-Mbp draft genome sequence of
AB  - this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides
AB  - odorabile. The sequence provides valuable information on sponge-pathogen
AB  - interactions, including the mode of transmission and associated virulence
AB  - factors.
ER  -

TY  - JOUR
AU  - Choudhury, K.
AU  - Leibowitz, M.J.
TI  - Pentamidine-induced Alteration in Restriction Endonuclease Cleavage of Plasmid DNA.
JO  - J. Biomol. Struct. Dyn.
PY  - 2003
SP  - 127
EP  - 134
VL  - 21
AB  - We have used restriction enzymes and DNaseI as probes to determine the specificity of
AB  - pentamidine binding to plasmid DNA. Cleavage of plasmid
AB  - pAZ130 by EcoRI, EcoRV and ApaI is inhibited by pentamidine, cleavage by
AB  - XbaI, NotI and AvaI is unaffected, while cleavage by XhoI, which
AB  - recognizes the same sequence as AvaI, is stimulated. DNaseI footprinting
AB  - of DNA containing these restriction sites revealed that pentamidine
AB  - protection is not strictly limited to AT-rich regions. We suggest that
AB  - perturbation of the DNA micro- environment by pentamidine binding is
AB  - responsible for its effect on nucleases.
ER  -

TY  - JOUR
AU  - Choulika, A.
AU  - Perrin, A.
AU  - Dujon, B.
AU  - Nicolas, J.-F.
TI  - Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae.
JO  - Mol. Cell. Biol.
PY  - 1995
SP  - 1968
EP  - 1973
VL  - 15
AB  - The mitochondrial intron-encoded endonuclease I-SceI of Saccharomyces cerevisiae has an 18-bp
AB  - recognition sequence and, therefore, has a very low probability of cutting DNA, even within
AB  - large genomes.  We demonstrate that double-strand breaks can be initiated by the I-SceI
AB  - endonuclease at a predetermined location in the mouse genome and that the breaks can be
AB  - repaired with a donor molecule homologous with regions flanking the breaks.  This induced
AB  - homologous recombination is approximately 2 orders of magnitude more frequent than spontaneous
AB  - homologous recombination and at least 10 times more frequent than random integration near an
AB  - active promoter.  As a consequence of induced homologous recombination, a heterologous novel
AB  - sequence can be inserted at the site of the break.  This recombination can occur at a variety
AB  - of chromosomal targets in differentiated and multipotential cells.  These results demonstrate
AB  - homologous recombination involving chromosomal DNA by the double-strand break repair mechanism
AB  - in mammals and show the usefulness of very rare cutter endonucleases, such as I-SceI, for
AB  - designing genome rearrangements.
ER  -

TY  - JOUR
AU  - Choulika, A.
AU  - Perrin, A.
AU  - Dujon, B.
AU  - Nicolas, J.-F.
TI  - The yeast I-SceI meganuclease induces site-directed chromosomal recombination in mammalian cells.
JO  - C.R. Acad. Sci. III
PY  - 1994
SP  - 1013
EP  - 1019
VL  - 317
AB  - Double-strand breaks in genomic DNA stimulate recombination.  Until now it was not possible to
AB  - induce in vivo site-directed double-strand breaks in a mammalian chromosomal target.  In this
AB  - article we describe the use of I-SceI meganuclease, a very rare cutter yeast endonuclease, to
AB  - induce site-directed double-strand breaks mediated recombination.  The results demonstrate the
AB  - potential of the I-SceI system for chromosome manipulation in mammalian cells.
ER  -

TY  - JOUR
AU  - Chovatia, M. et al.
TI  - Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 254
EP  - 261
VL  - 1
AB  - Thermanaerovibrio acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 is the type
AB  - species of the genus Thermanaerovibrio and is of phylogenetic interest
AB  - because of the very isolated location of the novel phylum Synergistetes. T.
AB  - acidaminovorans Su883(T) is a Gram-negative, motile, non-spore-forming bacterium
AB  - isolated from an anaerobic reactor of a sugar refinery in The Netherlands. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence, and annotation. This is the first completed genome sequence from a
AB  - member of the phylum Synergistetes. The 1,848,474 bp long single replicon genome
AB  - with its 1765 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Chow, N.A.
AU  - Gade, L.
AU  - Batra, D.
AU  - Rowe, L.A.
AU  - Juieng, P.
AU  - Ben-Ami, R.
AU  - Loparev, V.N.
AU  - Litvintseva, A.P.
TI  - Genome Sequence of a Multidrug-Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel.
JO  - Genome Announcements
PY  - 2018
SP  - e00176
EP  - e00118
VL  - 6
AB  - Candida haemulonii is an emerging multidrug-resistant yeast that can cause invasive
AB  - candidiasis. Here, we report the first genome sequence of C. haemulonii
AB  - (isolate B11899) generated using PacBio sequencing technology. The estimated
AB  - genome size was 13.3 Mb, with a GC content of 45.19%.
ER  -

TY  - JOUR
AU  - Chow, V. et al.
TI  - Complete genome sequence of Paenibacillus sp. strain JDR-2.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 1
EP  - 10
VL  - 6
AB  - Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum
AB  - (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize
AB  - 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A
AB  - basis for this capability was first supported by the identification of genes and
AB  - characterization of encoded enzymes and has been further defined by the sequencing and
AB  - annotation of the complete genome, which we describe. In addition to genes implicated in the
AB  - utilization of a-1,4-xylan, genes have also been identified for the utilization of other
AB  - hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in
AB  - a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874
AB  - genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and
AB  - organization of these genes support a metabolic potential for bioprocessing of hemicellulose
AB  - fractions derived from lignocellulosic resources.
ER  -

TY  - JOUR
AU  - Chowdhury, P.R.
AU  - Boucher, Y.
AU  - Hassan, K.A.
AU  - Paulsen, I.T.
AU  - Stokes, H.W.
AU  - Labbate, M.
TI  - Genome sequence of Vibrio rotiferianus strain DAT722.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3381
EP  - 3382
VL  - 193
AB  - Vibrio rotiferianus is a marine pathogen capable of causing disease in various aquatic
AB  - organisms. We announce the genome sequence of V.
AB  - rotiferianus DAT722, which has a large chromosomal integron containing 116
AB  - gene cassettes and is a model organism for studying the role of this
AB  - system in vibrio evolution.
ER  -

TY  - JOUR
AU  - Chowdhury, P.R.
AU  - Ingold, A.
AU  - Vanegas, N.
AU  - Martinez, E.
AU  - Merlino, J.
AU  - Merkier, A.K.
AU  - Castro, M.
AU  - Rocha, G.G.
AU  - Borthagaray, G.
AU  - Centron, D.
AU  - Toledo, H.B.
AU  - Marquez, C.M.
AU  - Stokes, H.W.
TI  - Dissemination of multiple drug resistance genes by class 1 integrons in Klebsiella pneumoniae isolates from four countries: a comparative study.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 3140
EP  - 3149
VL  - 55
AB  - A comparative genetic analysis of 42 clinical Klebsiella pneumoniae isolates, resistant to two
AB  - or more antibiotics belonging to the broad-spectrum beta-lactam group, sourced from Sydney,
AB  - Australia, and three South American countries is presented. The study focuses on the genetic
AB  - contexts of class 1 integrons, mobilizable genetic elements best known for their role in the
AB  - rapid evolution of antibiotic resistance among Gram-negative pathogens. It was found that the
AB  - class 1 integrons in this cohort were located in a number of different genetic contexts with
AB  - clear regional differences. In Sydney, IS26-associated Tn21-like transposons on IncL/M
AB  - plasmids contribute greatly to the dispersal of integron-associated multiple-drug-resistant
AB  - (MDR) loci. In contrast, in the South American countries, Tn1696-like transposons on an IncA/C
AB  - plasmid(s) appeared to be disseminating a characteristic MDR region. A range of mobile genetic
AB  - elements is clearly being recruited by clinically important mobile class 1 integrons, and
AB  - these elements appear to be becoming more common with time. This in turn is driving the
AB  - evolution of complex and laterally mobile MDR units and may further complicate antibiotic
AB  - therapy.
ER  -

TY  - JOUR
AU  - Christ, C.
AU  - Nelson, M.
TI  - DNA modification methylases:  New uses in the manipulation of DNA.
JO  - Biotechniques
PY  - 1984
SP  - 218
EP  - 221
VL  - 2
AB  - None
ER  -

TY  - JOUR
AU  - Christ, F.
AU  - Schoettler, S.
AU  - Wende, W.
AU  - Steuer, S.
AU  - Pingoud, A.
AU  - Pingoud, V.
TI  - The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate.
JO  - EMBO J.
PY  - 1999
SP  - 6908
EP  - 6916
VL  - 18
AB  - The monomeric homing endonuclease PI-SceI cleaves the two strands of its DNA substrate in a
AB  - concerted manner, which raises the question of whether this enzyme harbours one or two
AB  - catalytic centres. If PI-SceI has only one catalytic centre, one would expect that
AB  - cross-linking enzyme and substrate should prevent reorientation of the enzyme required to
AB  - perform the second cut after having made the first cut: PI-SceI, however, when cross-linked to
AB  - its substrate, is able to cleave both DNA strands. If PI-SceI has two catalytic centres, one
AB  - would expect that it should be possible to inactivate one catalytic centre by mutation and
AB  - obtain a variant with preference for a substrate nicked in one strand; such variants have been
AB  - found. The structural homology between the catalytic domain of PI-SceI having a pseudo 2-fold
AB  - symmetry, and I-CreI, a homodimeric homing endonuclease, suggests that in PI-SceI active site
AB  - I, which attacks the top strand, comprises Asp218, Asp229 and Lys403, while Asp326, Thr341 and
AB  - Lys301 make up active site II, which cleaves the bottom strand. Cleavage experiments with
AB  - modified oligodeoxynucleotides and metal ion mapping experiments demonstrate that PI-SceI
AB  - interacts differently with the two strands at the cleavage position, supporting a model of two
AB  - catalytic centres.
ER  -

TY  - JOUR
AU  - Christ, F.
AU  - Steuer, S.
AU  - Thole, H.
AU  - Wende, W.
AU  - Pingoud, A.
AU  - Pingoud, V.
TI  - A model for the PI-SceIxDNA complex based on multiple base and phosphate backbone-specific photocross-links.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 867
EP  - 875
VL  - 300
AB  - We have synthesized different oligodeoxynucleotides carrying, in single positions of the >36
AB  - bp recognition site of PI-SceI, photoreactive base analogues (5-iododeoxypyrimidines) or
AB  - phosphate modifications (p-azidophenacylphosphorothioates) and used them in photocross-linking
AB  - experiments with PI-SceI to probe the protein-DNA interface of the specific complex between
AB  - the homing endonuclease PI-SceI and its DNA substrate. One base-specific and several
AB  - backbone-specific cross-links were analyzed in detail: the cross-linking positions were
AB  - identified by Edman degradation of isolated cross-linked peptide x oligodeoxynucleotide
AB  - adducts
AB  - and confirmed by site-directed mutagenesis. Based on these results and the crystal structure
AB  - of PI-SceI, a model for the structure of the PI-SceI x DNA complex is proposed.
ER  -

TY  - JOUR
AU  - Christensen, L.F.B.
AU  - Otzen, D.
AU  - Dueholm, M.S.
TI  - High-Quality Draft Genome Sequence of Sphaerisporangium cinnabarinum ATCC 31213.
JO  - Genome Announcements
PY  - 2018
SP  - e00456
EP  - e00418
VL  - 6
AB  - A high-quality draft genome sequence of Sphaerisporangium cinnabarinum ATCC 31213 is presented
AB  - here. This bacterium produces several important bioactive compounds
AB  - and may also produce functional amyloids. This is the first sequenced genome from
AB  - the genus Sphaerisporangium, and it will be essential in determining the nature
AB  - of the potential amyloid protein.
ER  -

TY  - JOUR
AU  - Christensen, L.L.
AU  - Josephsen, J.
TI  - The methyltransferase from the LlaDII restriction-modification system influences the level of expression of its own gene.
JO  - J. Bacteriol.
PY  - 2004
SP  - 287
EP  - 295
VL  - 186
AB  - The type II restriction-modification (R-M) system LlaDII isolated from Lactococcus lactis
AB  - contains two tandemly arranged genes, llaDIIR and llaDIIM, encoding a restriction endonuclease
AB  - (REase) and a methyltransferase (MTase), respectively. Interestingly, two LlaDII recognition
AB  - sites are present in the llaDIIM promoter region, suggesting that they may influence the
AB  - activity of the promoter through methylation status. In this study, separate promoters for
AB  - llaDIIR and llaDIIM were identified, and the regulation of the two genes at the
AB  - transcriptional level was investigated. DNA fragments containing the putative promoters were
AB  - cloned in a promoter probe vector and tested for activity in the presence and absence of the
AB  - active MTase. The level of expression of the MTase was 5- to 10-fold higher than the level of
AB  - expression of the REase. The results also showed that the presence of M.LlaDII reduced the in
AB  - vivo expression of the llaDIIM promoter (P(llaDIIM)) up to 1,000-fold, whereas the activity of
AB  - the llaDIIR promoter (P(llaDIIR)) was not affected. Based on site-specific mutations it was
AB  - shown that both of the LlaDII recognition sites within P(llaDIIM) are required to obtain
AB  - complete repression of transcriptional activity. No regulation was found for llaDIIR, which
AB  - appears to be constitutively expressed.
ER  -

TY  - JOUR
AU  - Christman, J.K.
AU  - Sheikhnejad, G.
AU  - Marasco, C.J.
AU  - Sufrin, J.R.
TI  - 5-methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1995
SP  - 7347
EP  - 7351
VL  - 92
AB  - Methylation of cytosine residues in DNA plays an important role in regulating gene expression
AB  - during vertebrate embryonic development.  Conversely, disruption of normal patterns of
AB  - methylation is common in tumors and occurs early in progression of some human cancers.  In
AB  - vertebrates, it appears that the same DNA methyltransferase maintains preexisting patterns of
AB  - methylation during DNA replication and carries out de novo methylation to create new
AB  - methylation patterns.  There are several indications that inherent signals in DNA structure
AB  - can act in vivo to initiate or block de novo methylation in adjacent DNA regions.  To identify
AB  - sequences capable of enhancing de novo methylation of DNA in vitro, we designed a series of
AB  - oligodeoxyribonucleotide substrates with substrate cytosine residues in different sequence
AB  - contexts.  We obtained evidence that some 5-methylcytosine residues in these single-stranded
AB  - DNAs can stimulate de novo methylation of adjacent sites by murine DNA 5-cytosine
AB  - methyltransferase as effectively as 5-methylcytosine residues in double-stranded DNA stimulate
AB  - maintenance methylation.  This suggests that double-stranded DNA may not be the primary
AB  - natural substrate for de novo methylation and that looped single-stranded structures formed
AB  - during the normal course of DNA replication or repair serve as "nucleation" sites for de novo
AB  - methylation of adjacent DNA regions.
ER  -

TY  - JOUR
AU  - Christopher, L.P.
AU  - Kapatral, V.
AU  - Vaisvil, B.
AU  - Emel, G.
AU  - Deveaux, L.C.
TI  - Draft Genome Sequence of a New Homofermentative, Lactic Acid-Producing Enterococcus faecalis Isolate, CBRD01.
JO  - Genome Announcements
PY  - 2014
SP  - e00147
EP  - e00114
VL  - 2
AB  - We report here the draft genome sequence of the novel homofermentative Enterococcus faecalis
AB  - isolate CBRD01, which is capable of high lactic acid
AB  - productivity and yields, with minimal nutritional requirements. The genome is 2.8
AB  - Mbp, with 37% G+C, and contains genes for two lactate dehydrogenase (LDH) enzymes
AB  - found in related organisms.
ER  -

TY  - JOUR
AU  - Chu, F.K.
AU  - Maley, F.
AU  - Wang, A.-M.
AU  - Pedersen-Lane, J.
AU  - Maley, G.
TI  - Purification and substrate specificity of a T4 phage intron-encoded endonuclease.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6863
EP  - 6869
VL  - 19
AB  - The T4 phage td intron-encoded endonuclease (I-Tev I) cleaves the intron-deleted
AB  - td gene (td-delta-I) 23 nucleotides upstream of the intron insertion site on the noncoding
AB  - strand and
AB  - 25 nucleotides upstream of this site on the coding strand, to generate a 2-base hydroxyl
AB  - overhang
AB  - in the 3' end of each DNA strand.  I-Tev I-157, a truncated form in which slightly more than
AB  - one
AB  - third (88 residues) of the endonuclease is deleted, was purified to homogeneity and shown to
AB  - possess endonuclease activity similar to that of I-Tev I, the full-length enzyme (245
AB  - residues).  The
AB  - minimal length of the td-delta-I gene that was cleaved by I-Tev I and I-Tev I-157 has been
AB  - determined to be exactly 39 basepairs, from -27 (upstream in exon1) to +12 (downstream in
AB  - exon2) relative to the intron insertion site.  Similar to the full-length endonuclease, I-Tev
AB  - I-157 cuts
AB  - the intronless thymidylate synthase genes from such diverse organisms as Escherichia coli,
AB  - Lactobacillus casei and the human.  The position and nature of the in vitro endonucleolytic
AB  - cut in
AB  - these genes are homologous to those in td-delta-I.  Point mutational analysis of the
AB  - td-delta-I
AB  - substrate based on the deduced consensus nucleotide sequence has revealed a very low degree of
AB  - specificity on either side of the cleavage site, for both the full-length and truncated I-Tev
AB  - I.
ER  -

TY  - JOUR
AU  - Chu, F.K.
AU  - Maley, G.
AU  - Pedersen-Lane, J.
AU  - Wang, A.-M.
AU  - Maley, F.
TI  - Characterization of the restriction site of a prokaryotic intron-encoded endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1990
SP  - 3574
EP  - 3578
VL  - 87
AB  - The 1016-base-pair (bp) intron in the T4 bacteriophage thymidylate
AB  - synthase gene (td) contains a 735-bp open reading frame that encodes a protein product
AB  - with endonucleolytic activity.  The endonuclease shows specificity for the intronless form
AB  - of the td gene.  Highly purified endonuclease cleaves the DNA of the intronless form of the
AB  - td gene in vitro at 24 bp upstream of the exon 1-exon 2 junction, generating a 2-base
AB  - staggered cut with 3'-hydroxyl overhangs.  Although the endonuclease cleaves in exon 1, it
AB  - requires some exon 2 sequence for recognition.  The maximum recognition sequence lies in
AB  - an 87-bp stretch, from 52 bp upstream to 35 bp downstream of the cleavage site, ending at
AB  - 11 bp into exon 2.  The td intron endonuclease appears involved in the conversion of the
AB  - intronless form of td to intron-containing td gene in the T-even phages.  A role for intron
AB  - mobility is discussed.
ER  -

TY  - JOUR
AU  - Chu, F.K.
AU  - Maley, G.F.
AU  - Maley, F.
AU  - Belfort, M.
TI  - Intervening sequence in the thymidylate synthase gene of bacteriophage T4.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 3049
EP  - 3053
VL  - 81
AB  - The continuous sequence of 2.3 kilobases in a 3-kilobase DNA fragment encoding the structural
AB  - gene for coliphage T4 thymidylate synthase (5,10-methylenetetrahydrofolate:dUMP
AB  - C-methyltranferase, EC 2.1.1.45) was determined by using the M13 dideoxy chain-termination
AB  - method. From the coding information within this gene and that provided by sequence analysis of
AB  - selected CNBr peptides from the protein product, the primary structure of T4 thymidylate
AB  - synthase was determined. The most significant finding of these studies is the presence of a
AB  - 1017-base-pair interruption two-thirds of the way through the nucleotide sequence of the
AB  - structural gene. The 5'- and 3'-terminal ends of this intron are demarcated by an apparent
AB  - stop and start codon, respectively. The corresponding methionine preceding the second coding
AB  - region of the synthase is not incorporated into the final protein product. Structural evidence
AB  - confirming the presence of the intervening sequence in the phage genome was obtained by
AB  - restriction and hybridization analysis. Support for the presence of the intron was also
AB  - obtained at the functional level by enzyme expression studies using selected td gene
AB  - fragments. This work also confirms the findings of Purohit and Mathews, which reveal that the
AB  - termination codon for the dihydrofolate reductase gene and the triplet intitiating thymidylate
AB  - synthase overlap by a four-base stretch, A-T-G-A. The implications of this unusual gene
AB  - arrangement are discussed.
ER  -

TY  - JOUR
AU  - Chu, F.K.
AU  - Maley, G.F.
AU  - West, D.K.
AU  - Belfort, M.
AU  - Maley, F.
TI  - Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript.
JO  - Cell
PY  - 1986
SP  - 157
EP  - 166
VL  - 45
AB  - The td gene contains a 735 bp open reading frame within its 1017 bp intron. A 12 nucleotide
AB  - stretch may form a stable secondary structure with the putative Shine-Dalgarno sequence of the
AB  - intron open reading frame and thus impair its translation. SP6 RNA polymerase transcripts of
AB  - the td gene synthesized in vitro at 40oC encompass a 2.7 kb primary transcript, a 1.7 kb mRNA,
AB  - and a 1 kb intron RNA. The excised intron RNA consisted of linear and cyclized forms. RNAase H
AB  - studies and resistance of the cyclized intron to linearization by HeLa cell debranching enzyme
AB  - suggest it to be circular. Self-splicing of isolated td primary transcript occurred only
AB  - marginally at 28oC, but increased progressively to 50oC, and required the presence of both
AB  - Mg++ and a guanosine cofactor. An internal guide sequence is evident which may align the 5'
AB  - splice site with the 3' end, presumably for precise exon ligation.
ER  -

TY  - JOUR
AU  - Chu, Y.
AU  - Gao, P.
AU  - Zhao, P.
AU  - He, Y.
AU  - Liao, N.
AU  - Jackman, S.
AU  - Zhao, Y.
AU  - Birol, I.
AU  - Duan, X.
AU  - Lu, Z.
TI  - Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain M1601.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6098
EP  - 6099
VL  - 193
AB  - Mycoplasma capricolum subsp. capripneumoniae is the causative agent of contagious caprine
AB  - pleuropneumonia, a devastating disease of goats listed
AB  - by the World Organization for Animal Health. Here we report the first
AB  - complete genome sequence of this organism (strain M1601, a clinically
AB  - isolated strain from China).
ER  -

TY  - JOUR
AU  - Chua, K.
AU  - Seemann, T.
AU  - Harrison, P.F.
AU  - Davies, J.K.
AU  - Coutts, S.J.
AU  - Chen, H.
AU  - Haring, V.
AU  - Moore, R.
AU  - Howden, B.P.
AU  - Stinear, T.P.
TI  - Complete genome sequence of Staphylococcus aureus strain JKD6159, a unique Australian clone of ST93-IV community methicillin-resistant Staphylococcus  aureus.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5556
EP  - 5557
VL  - 192
AB  - Community methicillin-resistant Staphylococcus aureus (cMRSA) is an emerging issue that has
AB  - resulted in multiple worldwide epidemics. We
AB  - report the first complete genome sequence of an ST93-MRSA-IV clinical
AB  - isolate that caused severe invasive infection and a familial outbreak of
AB  - skin infection. This isolate is a representative of the most common
AB  - Australian clone of cMRSA that is more distantly related to the previously
AB  - sequenced genomes of S. aureus.
ER  -

TY  - JOUR
AU  - Chua, P.
AU  - Yoo, H.S.
AU  - Gan, H.M.
AU  - Lee, S.M.
TI  - Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and  MAEPY2, from Malaysian Landfill Leachate.
JO  - Genome Announcements
PY  - 2014
SP  - e00065
EP  - e00014
VL  - 2
AB  - We report the draft genome sequences of two Paenibacillus species with cellulose-degrading
AB  - abilities isolated from landfill leachate. An array of genes
AB  - putatively involved in cellulose degradation have been identified in both genome
AB  - sequences, which can benefit various biotechnological industries.
ER  -

TY  - JOUR
AU  - Chuah, L.O.
AU  - Yap, K.P.
AU  - Thong, K.L.
AU  - Liong, M.T.
AU  - Ahmad, R.
AU  - Shamila-Syuhada, A.K.
AU  - Rusul, G.
TI  - Genome Sequence of 'Anthococcus,' a Novel Genus of the Family Streptococcaceae Isolated from Flowers.
JO  - Genome Announcements
PY  - 2016
SP  - e01410
EP  - e01416
VL  - 4
AB  - Here, we report the draft whole-genome sequence of 'Anthococcus,' a novel genus of the
AB  - family Streptococcaceae isolated from fresh flowers of a durian (Durio
AB  - zibethinus) tree. The draft genome of Anthococcus sp. strain DF1 contains
AB  - 2,157,756 bp, with a G+C content of 33.0%.
ER  -

TY  - JOUR
AU  - Chuang, L.S.-H.
AU  - Ng, H.-H.
AU  - Chia, J.-N.
AU  - Li, B.F.L.
TI  - Characterisation of independent DNA and multiple Zn-binding domains at the N terminus of human DNA-(cytosine-5) methyltransferase: Modulating the property of a DNA-binding domain by contiguous Zn-binding motifs.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 935
EP  - 948
VL  - 257
AB  - We report here a detailed mapping and characterisation of a DNA-binding domain
AB  - at the N terminus of human DNA-(cytosine-5) methyltransferase.  A small region, B1 (codon 202
AB  - to 369), was first identified by its Zn- and gross DNA-binding properties.  Further
AB  - fine-mapping
AB  - using deletion and point mutation analysis shows that the DNA- and Zn-binding domains involve
AB  - separate peptide motifs, KRRKTTPKEPTEKK (codons 202 to 215) for a bipartite DNA-binding
AB  - oligopeptide (DB1) and Cx2CX13HX2D(X)23EX2EX13CX3H (codons 232 to 297) for possibly
AB  - two contiguous Zn-binding domains (Azn), which can function independently.  However, B1
AB  - (containing DB1 and AZn) differs from DB1 because it does not bind to a 30 base-pair duplex.
AB  - Interestingly, H3 codons 202 to 974, which encloses B1 and B2 (containing the Zn-binding
AB  - CX2CX2CX4CX2CX2C motif from codon 533 to 550) binds preferentially to 0.8 kb duplexes,
AB  - compared with 0.4 and 0.6 kb duplexes.  As the homologous murine B1, which targets the murine
AB  - methylase to replication foci, also binds to DNA and Zn, it is possible that the N terminus of
AB  - mammalian methylase may be involved in sensing the appropriate length of newly synthesized
AB  - DNA before methylation by its C terminus.  This may enable a time delay for the transient
AB  - existence of hemi-methylation sites for their unknown biological functions in mammals.
ER  -

TY  - JOUR
AU  - Chuang, L.S.H.
AU  - Ian, H.-I.
AU  - Koh, T.W.
AU  - Ng, H.-H.
AU  - Xu, G.
AU  - Li, B.F.L.
TI  - Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1.
JO  - Science
PY  - 1997
SP  - 1996
EP  - 2000
VL  - 277
AB  - DNA-(cytosine-5) methyltransferase (MCMT) methylates newly replicated mammalian DNA, but the
AB  - factors regulating this activity are unknown.  Here, MCMT is shown to bind proliferating cell
AB  - nuclear antigen, an auxiliary factor for DNA replication and repair.  Binding of PCNA requires
AB  - amino acids 163 to 174 of MCMT, occurs in intact cells at foci of newly replicated DNA, and
AB  - does not alter MCMT activity.  A peptide derived from the cell cycle regulator p21WAF1 can
AB  - disrupt the MCMT-PCNA interaction, which suggests that p21WAF1 may regulate methylation by
AB  - blocking access of MCMT to PCNA.  MCMT and p21WAF1 may be linked in a regulatory pathway,
AB  - because the extents of their expression are inversely related in both SV40-transformed and
AB  - nontransformed cells.
ER  -

TY  - JOUR
AU  - Chuang, L.S.H.
AU  - Tan, E.H.H.
AU  - Oh, H.K.
AU  - Li, B.F.L.
TI  - Selective depletion of human DNA-methyltransferase DNMT1 proteins by sulfonate-derived methylating agents.
JO  - Cancer Res.
PY  - 2002
SP  - 1592
EP  - 1597
VL  - 62
AB  - 5-Methylcytosine residues in the DNA (DNA methylation) are formed from the transfer of the
AB  - methyl group from S-adenosylmethionine to the C-5
AB  - position of cytosine by the DNA-(cytosine-5) methyltransferases
AB  - (DNMTs). Although regional hypermethylation and global hypomethylation
AB  - of the genome are commonly observed in neoplastic cells, how these
AB  - aberrant methylation patterns occur remains unestablished. We report
AB  - here that sulfonate-derived methylating agents, unlike
AB  - N-methylnitrosourea or iodomethane, are potent in depleting DNMT1
AB  - proteins in human cells, in addition to their DNA-damaging properties.
AB  - Their effects on cellular DNMT1 are time and dosage dependent but
AB  - independent of cell type. Unlike gamma-irradiation, these agents
AB  - apparently do not activate the p53/p21(WAF1) DNA damage response
AB  - pathway to deplete the DNMT1 proteins because cells with wild-type,
AB  - mutated, or inactivated p53 behave similarly. However, cell cycle
AB  - analysis and protease assay studies strongly suggest that
AB  - methylmethanesulfonate may activate a cellular protease to degrade
AB  - DNMT1. These results explain why reported observations on the effect of
AB  - alkylating agents on DNMT1 activities in human cells vary significantly
AB  - and provide a crucial link to understand the mechanism behind genomic
AB  - hypomethylation.
ER  -

TY  - JOUR
AU  - Chuea-Nongthon, C.
AU  - Rodtong, S.
AU  - Yongsawatdigul, J.
AU  - Steele, J.L.
TI  - Draft Genome Sequences of Tetragenococcus muriaticus Strains 3MR10-3 and PMC-11-5 Isolated from Thai Fish Sauce during Natural Fermentation.
JO  - Genome Announcements
PY  - 2017
SP  - e00198
EP  - e00117
VL  - 5
AB  - Tetragenococcus muriaticus strains 3MR10-3 and PMC-11-5 are homofermentative halophilic lactic
AB  - acid bacteria isolated from Thai fish sauce during natural
AB  - fermentation. Their draft genomes were sequenced. Our interest in these organisms
AB  - is related to their impact on fish sauce flavor and their high osmotolerance.
ER  -

TY  - JOUR
AU  - Chugani, S.
AU  - Kim, B.S.
AU  - Phattarasukol, S.
AU  - Brittnacher, M.J.
AU  - Choi, S.H.
AU  - Harwood, C.S.
AU  - Greenberg, E.P.
TI  - Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - E2823
EP  - E2831
VL  - 109
AB  - Quorum sensing allows bacteria to sense and respond to changes in population
AB  - density. Acyl-homoserine lactones serve as quorum-sensing signals for many
AB  - Proteobacteria, and acyl-homoserine lactone signaling is known to control
AB  - cooperative activities. Quorum-controlled activities vary from one species to
AB  - another. Quorum-sensing controls a constellation of genes in the opportunistic
AB  - pathogen Pseudomonas aeruginosa, which thrives in a number of habitats ranging
AB  - from soil and water to animal hosts. We hypothesized that there would be
AB  - significant variation in quorum-sensing regulons among strains of P. aeruginosa
AB  - isolated from different habitats and that differences in the quorum-sensing
AB  - regulons might reveal insights about the ecology of P. aeruginosa. As a test of
AB  - our hypothesis we used RNA-seq to identify quorum-controlled genes in seven P.
AB  - aeruginosa isolates of diverse origins. Although our approach certainly overlooks
AB  - some quorum-sensing-regulated genes we found a shared set of genes, i.e., a core
AB  - quorum-controlled gene set, and we identified distinct, strain-variable sets of
AB  - quorum-controlled genes, i.e., accessory genes. Some quorum-controlled genes in
AB  - some strains were not present in the genomes of other strains. We detected a
AB  - correlation between traits encoded by some genes in the strain-variable subsets
AB  - of the quorum regulons and the ecology of the isolates. These findings indicate a
AB  - role for quorum sensing in extension of the range of habitats in which a species
AB  - can thrive. This study also provides a framework for understanding the molecular
AB  - mechanisms by which quorum-sensing systems operate, the evolutionary pressures by
AB  - which they are maintained, and their importance in disparate ecological contexts.
ER  -

TY  - JOUR
AU  - Chuluunbaatar, T.
AU  - Ivanenko-Johnston, T.
AU  - Fuxreiter, M.
AU  - Meleshko, R.
AU  - Rasko, T.
AU  - Simon, I.
AU  - Heitman, J.
AU  - Kiss, A.
TI  - An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity.
JO  - Biochim. Biophys. Acta
PY  - 2007
SP  - 583
EP  - 594
VL  - 1774
AB  - To test their structural and functional similarity, hybrids were constructed between EcoRI and
AB  - RsrI, two restriction endonucleases recognizing the same DNA sequence and sharing 50% amino
AB  - acid sequence identity. One of the chimeric proteins (EERE), in which the EcoRI segment
AB  - His147-Ala206 was replaced with the corresponding RsrI segment, showed EcoRI/RsrI-specific
AB  - endonuclease activity. EERE purified from inclusion bodies was found to have approximately
AB  - 100-fold weaker activity but higher specific DNA binding affinity, than EcoRI. Increased
AB  - binding is consistent with results of molecular dynamics simulations, which indicate that the
AB  - number of hydrogen bonds formed with the recognition sequence increased in the chimera as
AB  - compared to EcoRI. The success of obtaining an EcoRI-RsrI hybrid endonuclease, which differs
AB  - from EcoRI by 22 RsrI-specific amino acid substitutions and still preserves canonical cleavage
AB  - specificity, is a sign of structural and functional similarity shared by the parental enzymes.
AB  - This conclusion is also supported by computational studies, which indicate that construction
AB  - of the EERE chimera did not induce substantial changes in the structure of EcoRI.
AB  - Surprisingly, the chimeric endonuclease was more toxic to cells not protected by EcoRI
AB  - methyltransferase, than the parental EcoRI mutant. Molecular modelling revealed structural
AB  - alterations, which are likely to impede coupling between substrate recognition and cleavage
AB  - and suggest a possible explanation for the toxic phenotype.
ER  -

TY  - JOUR
AU  - Chun, B.H.
AU  - Lee, S.H.
AU  - Jeon, H.H.
AU  - Kim, D.W.
AU  - Jeon, C.O.
TI  - Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 38
EP  - 38
VL  - 12
AB  - The genome of Leuconostoc suionicum DSM 20241T (=ATCC 9135T = LMG 8159T = NCIMB 6992T) was
AB  - completely sequenced and its fermentative metabolic pathways were
AB  - reconstructed to investigate the fermentative properties and metabolites of
AB  - strain DSM 20241T during fermentation. The genome of L. suionicum DSM 20241T
AB  - consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb)
AB  - with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs.
AB  - Analysis of the metabolic pathways of L. suionicum DSM 20241T revealed that
AB  - strain DSM 20241T performs heterolactic acid fermentation and can metabolize
AB  - diverse organic compounds including glucose, fructose, galactose, cellobiose,
AB  - mannose, sucrose, trehalose, arbutin, salcin, xylose, arabinose and ribose.
ER  -

TY  - JOUR
AU  - Chun, J.H.
AU  - Hong, K.J.
AU  - Cha, S.H.
AU  - Cho, M.H.
AU  - Lee, K.J.
AU  - Jeong, D.H.
AU  - Yoo, C.K.
AU  - Rhie, G.E.
TI  - Complete Genome Sequence of Bacillus anthracis H9401, an Isolate from a Korean Patient with Anthrax.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4116
EP  - 4117
VL  - 194
AB  - Bacillus anthracis H9401 (NCCP 12889) is an isolate from a Korean patient with
AB  - gastrointestinal anthrax. The whole genome of H9401 was sequenced. It is a
AB  - circular chromosome containing 5,480 open reading frames (ORFs) and two plasmids,
AB  - pXO1 containing 202 ORFs and pXO2 containing 110 ORFs. H9401 shows high
AB  - pathogenicity and genome sequence similarity to Ames Ancestor.
ER  -

TY  - JOUR
AU  - Chung, D.
AU  - Cha, M.
AU  - Farkas, J.
AU  - Westpheling, J.
TI  - Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus.
JO  - PLoS ONE
PY  - 2013
SP  - e62881
EP  - e62881
VL  - 8
AB  - The recalcitrance of plant biomass is the most important barrier to its economic  conversion
AB  - by microbes to products of interest. Thermophiles have special
AB  - advantages for biomass conversion and members of the genus Caldicellulosiruptor
AB  - are the most thermophilic cellulolytic microbes known. In this study, we report
AB  - the construction of a replicating shuttle vector for Caldicellulosiruptor species
AB  - based on pBAS2, the smaller of two native C. bescii plasmids. The entire plasmid
AB  - was cloned into an E. coli cloning vector containing a pSC101 origin of
AB  - replication and an apramycin resistance cassette for selection in E. coli. The
AB  - wild-type C. bescii pyrF locus was cloned under the transcriptional control of
AB  - the regulatory region of the ribosomal protein S30EA (Cbes2105), and the
AB  - resulting vector was transformed into a new spontaneous deletion mutant in the
AB  - pyrFA locus of C. bescii that allowed complementation with the pyrF gene alone.
AB  - Plasmid DNA was methylated in vitro with a recently described cognate
AB  - methyltransferase, M.CbeI, and transformants were selected for uracil
AB  - prototrophy. The plasmid was stably maintained in low copy with selection but
AB  - rapidly lost without selection. There was no evidence of DNA rearrangement during
AB  - transformation and replication in C. bescii. A similar approach was used to
AB  - screen for transformability of other members of this genus using M.CbeI to
AB  - overcome restriction as a barrier and was successful for transformation of C.
AB  - hydrothermalis, an attractive species for many applications. Plasmids containing
AB  - a carbohydrate binding domain (CBM) and linker region from the C. bescii celA
AB  - gene were maintained with selection and were structurally stable through
AB  - transformation and replication in C. bescii and E. coli.
ER  -

TY  - JOUR
AU  - Chung, D.
AU  - Farkas, J.
AU  - Huddleston, J.R.
AU  - Olivar, E.
AU  - Westpheling, J.
TI  - Methylation by a Unique alpha-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725.
JO  - PLoS ONE
PY  - 2012
SP  - e43844
EP  - e43844
VL  - 7
AB  - Thermophilic microorganisms capable of using complex substrates offer special advantages for
AB  - the conversion of lignocellulosic biomass to
AB  - biofuels and bioproducts. Members of the Gram-positive bacterial genus
AB  - Caldicellulosiruptor are anaerobic thermophiles with optimum growth
AB  - temperatures between 65 degrees C and 78 degrees C and are the most
AB  - thermophilic cellulolytic organisms known. In fact, they efficiently
AB  - use biomass non-pretreated as their sole carbon source and in
AB  - successive rounds of application digest 70% of total switchgrass
AB  - substrate. The ability to genetically manipulate these organisms is a
AB  - prerequisite to engineering them for use in conversion of these complex
AB  - substrates to products of interest as well as identifying gene products
AB  - critical for their ability to utilize non-pretreated biomass. Here, we
AB  - report the first example of DNA transformation of a member of this
AB  - genus, C. bescii. We show that restriction of DNA is a major barrier to
AB  - transformation (in this case apparently absolute) and that methylation
AB  - with an endogenous unique alpha-class N4-Cytosine methyltransferase is
AB  - required for transformation of DNA isolated from E. coli. The use of
AB  - modified DNA leads to the development of an efficient and reproducible
AB  - method for DNA transformation and the combined frequencies of
AB  - transformation and recombination allow marker replacement between
AB  - non-replicating plasmids and chromosomal genes providing the basis for
AB  - rapid and efficient methods of genetic manipulation.
ER  -

TY  - JOUR
AU  - Chung, D.H.
AU  - Huddleston, J.R.
AU  - Farkas, J.
AU  - Westpheling, J.
TI  - Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes.
JO  - J. Ind. Microbiol. Biotechnol.
PY  - 2011
SP  - 1867
EP  - 1877
VL  - 38
AB  - Potent HaeIII-like DNA restriction activity was detected in cell-free extracts of
AB  - Caldicellulosiruptor bescii DSM 6725 using plasmid DNA
AB  - isolated from Escherichia coli as substrate. Incubation of the plasmid
AB  - DNA in vitro with HaeIII methyltransferase protected it from cleavage
AB  - by HaeIII nuclease as well as cell-free extracts of C. bescii. The gene
AB  - encoding the putative restriction enzyme was cloned and expressed in E.
AB  - coli with a His-tag at the C-terminus. The purified protein was 38 kDa
AB  - as predicted by the 981-bp nucleic acid sequence, was optimally active
AB  - at temperatures between 75 degrees C and 85 degrees C, and was stable
AB  - for more than 1 week when stored at 35 degrees C. The cleavage sequence
AB  - was determined to be 50-GG/CC-30, indicating that CbeI is an
AB  - isoschizomer of HaeIII. A search of the C. bescii genome sequence
AB  - revealed the presence of both a HaeIII-like restriction endonuclease
AB  - (Athe 2438) and DNA methyltransferase (Athe 2437). Preliminary analysis
AB  - of other Caldicellulosiruptor species suggested that this
AB  - restriction/modification activity is widespread in this genus. A
AB  - phylogenetic analysis based on sequence alignment and conserved motif
AB  - searches identified features of CbeI distinct from other members of
AB  - this group and classified CbeI as a member of a novel subfamily of
AB  - HaeIII-like enzymes.
ER  -

TY  - JOUR
AU  - Chung, D.W.
AU  - Farkas, J.
AU  - Westpheling, J.
TI  - Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement.
JO  - Biotechnol. Biofuels.
PY  - 2013
SP  - 16187
EP  - 16187
VL  - 6
AB  - Background: Thermophilic microorganisms have special advantages for the conversion of plant
AB  - biomass to fuels and chemicals. Members of the genus Caldicellulosiruptor are the most
AB  - thermophilic cellulolytic bacteria known. They have the ability to grow on a variety of
AB  - non-pretreated biomass substrates at or near similar to 80 degrees C and hold promise for
AB  - converting biomass to bioproducts in a single step. As for all such relatively uncharacterized
AB  - organisms with desirable traits, the ability to genetically manipulate them is a prerequisite
AB  - for making them useful. Metabolic engineering of pathways for product synthesis is relatively
AB  - simple compared to engineering the ability to utilize non-pretreated biomass. Results: Here we
AB  - report the construction of a deletion of cbeI (Cbes2438), which encodes a restriction
AB  - endonuclease that is as a major barrier to DNA transformation of C. bescii. This is the first
AB  - example of a targeted chromosomal deletion generated by homologous recombination in this genus
AB  - and the resulting mutant, JWCB018 (Delta pyrFA Delta cbeI), is readily transformed by DNA
AB  - isolated from E. coli without in vitro methylation. PCR amplification and sequencing suggested
AB  - that this deletion left the adjacent methyltransferase (Cbes2437) intact. This was confirmed
AB  - by the fact that DNA isolated from JWCB018 was protected from digestion by CbeI and HaeIII.
AB  - Plasmid DNA isolated from C. hydrothermalis transformants were readily transformed into C.
AB  - bescii. Digestion analysis of chromosomal DNA isolated from seven Caldicellulosiruptor species
AB  - by using nine different restriction endonucleases was also performed to identify the
AB  - functional restriction-modification activities in this genus. Conclusion: Deletion of the cbeI
AB  - gene removes a substantial barrier to routine DNA transformation and chromosomal modification
AB  - of C. bescii. This will facilitate the functional analyses of genes as well as metabolic
AB  - engineering for the production of biofuels and bioproducts from biomass. An analysis of
AB  - restriction-modification activities in members of this genus suggests a way forward to
AB  - eliminating restriction as a barrier to DNA transformation and efficient genetic manipulation
AB  - of this important group of hyperthermophiles.
ER  -

TY  - JOUR
AU  - Chung, E.J.
AU  - Choi, G.G.
AU  - Nam, Y.H.
AU  - Choi, A.
TI  - Draft Genome Sequence of Paucibacter aquatile CR182(T), a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea.
JO  - Genome Announcements
PY  - 2018
SP  - e00194
EP  - e00118
VL  - 6
AB  - This report details a draft genome sequence of Paucibacter aquatile CR182(T), isolated from
AB  - river water, which contains 5,523,543 bp, has a G+C content of
AB  - 66.3%, and harbors 4,544 protein-coding genes in 4 contigs. These genome data
AB  - provide insights into the genetic basis of this strain's antibacterial activity
AB  - and adaptive mechanisms.
ER  -

TY  - JOUR
AU  - Chung, G.T.
AU  - Yoo, J.S.
AU  - Oh, H.B.
AU  - Lee, Y.S.
AU  - Cha, S.H.
AU  - Kim, S.J.
AU  - Yoo, C.K.
TI  - The Complete Genome Sequence of Neisseria gonorrhoeae NCCP11945.
JO  - J. Bacteriol.
PY  - 2008
SP  - 6035
EP  - 6036
VL  - 190
AB  - Neisseria gonorrhoeae is an obligate human pathogen that is the etiological agent of
AB  - gonorrhea. We explored variations in genes of a
AB  - multidrug-resistant N. gonorrhoeae Korean patient isolate in an effort to
AB  - understand the prevalence, antibiotic resistance, and importance of
AB  - horizontal gene transfer within this important, naturally competent
AB  - organism. Here we report the complete annotated genome sequence of N.
AB  - gonorrhoeae strain NCCP11945.
ER  -

TY  - JOUR
AU  - Chung, H.M. et al.
TI  - Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas.
JO  - Genome Announcements
PY  - 2017
SP  - e01129
EP  - e01117
VL  - 5
AB  - We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly
AB  - isolated from soil samples, using Mycobacterium
AB  - smegmatis mc(2)155 as the host. Comparative genomic analyses with four previously
AB  - described subcluster L3 phages reveal strong nucleotide similarity and gene
AB  - conservation, with several large insertions/deletions near their right genome
AB  - ends.
ER  -

TY  - JOUR
AU  - Chung, H.Y.
AU  - Kim, Y.T.
AU  - Kim, S.
AU  - Na, E.J.
AU  - Ku, H.J.
AU  - Lee, K.H.
AU  - Heo, S.T.
AU  - Ryu, S.
AU  - Kim, H.
AU  - Choi, S.H.
AU  - Lee, J.H.
TI  - Complete genome sequence of Vibrio vulnificus FORC_017 isolated from a patient with a hemorrhagic rash after consuming raw dotted gizzard shad.
JO  - Gut Pathog.
PY  - 2016
SP  - 22
EP  - 22
VL  - 8
AB  - BACKGROUND: Vibrio vulnificus, a resident in the human gut, is frequently found
AB  - in seafood, causing food-borne illnesses including gastroenteritis and severe
AB  - septicemia. While V. vulnificus has been known to be one of the major food-borne
AB  - pathogens, pathogenicity and virulence factors are not fully understood yet. To
AB  - extend our understanding of the pathogenesis of V. vulnificus at the genomic
AB  - level, the genome of V. vulnificus FORC_017 isolated from a female patient
AB  - experiencing a hemorrhagic rash was completely sequenced and analyzed. RESULTS:
AB  - Three discontinuous contigs were generated from a hybrid assembly using Illumina
AB  - MiSeq and PacBio platforms, revealing that the genome of the FORC_017 consists of
AB  - two circular chromosomes and a plasmid. Chromosome I consists of 3,253,417-bp (GC
AB  - content 46.49 %) containing 2943 predicted open reading frames (ORFs) and
AB  - chromosome II of 1,905,745-bp (GC content 46.90 %) containing 1638 ORFs. The
AB  - plasmid pFORC17 consists of 70,069-bp (GC content 43.77 %) containing 84 ORFs.
AB  - The average nucleotide identity (ANI) value of the FORC_017 and CMCP6 strains was
AB  - 98.53, suggesting that they are closely related. CONCLUSIONS:
AB  - Pathogenesis-associated genes including vvhA, rtx gene cluster, and various
AB  - hemolysin genes were present in FORC_017. In addition, three complete secretion
AB  - systems (Type I, II and VI) as well as iron uptake-related genes for virulence of
AB  - the FORC_017 were detected, suggesting that this strain is pathogenic. Further
AB  - comparative genome analysis revealed that FORC_017 and CMCP6 share major toxin
AB  - genes including vvhA and rtx for pathogenesis activities. The genome information
AB  - of the FORC_017 provides novel insights into pathogenicity and virulence factors
AB  - of V. vulnificus.
ER  -

TY  - JOUR
AU  - Chung, H.Y.
AU  - Lee, K.H.
AU  - Ryu, S.
AU  - Yoon, H.
AU  - Lee, J.H.
AU  - Kim, H.B.
AU  - Kim, H.
AU  - Jeong, H.G.
AU  - Choi, S.H.
AU  - Kim, B.S.
TI  - Genome Sequence of Bacillus cereus FORC_021, a Food-Borne Pathogen Isolated from a Knife at a Sashimi Restaurant.
JO  - J. Microbiol. Biotechnol.
PY  - 2016
SP  - 2030
EP  - 2035
VL  - 26
AB  - Bacillus cereus causes food-borne illness through contaminated foods; therefore,
AB  - its pathogenicity and genome sequences have been analyzed in several studies. We
AB  - sequenced and analyzed B. cereus strain FORC_021 isolated from a sashimi
AB  - restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents,
AB  - 5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico
AB  - DNA-DNA hybridization values, B. cereus ATCC 14579T was closest to FORC_021 among
AB  - the complete genome-sequenced strains. Three major enterotoxins were detected in
AB  - FORC_021. Comparative genomic analysis of FORC_021 with ATCC 14579T revealed that
AB  - FORC_021 harbored an additional genomic region encoding virulence factors, such
AB  - as putative ADP-ribosylating toxin, spore germination protein, internalin, and
AB  - sortase. Furthermore, in vitro cytotoxicity testing showed that FORC_021
AB  - exhibited a high level of cytotoxicity toward INT-407 human epithelial cells.
AB  - This genomic information of FORC_021 will help us to understand its pathogenesis
AB  - and assist in managing food contamination.
ER  -

TY  - JOUR
AU  - Chung, J.H.
AU  - Jeong, H.
AU  - Ryu, C.M.
TI  - Complete Genome Sequences of Enterobacter cancerogenus CR-Eb1 and Enterococcus sp. Strain CR-Ec1, Isolated from the Larval Gut of the Greater Wax Moth, Galleria  mellonella.
JO  - Genome Announcements
PY  - 2018
SP  - e00044
EP  - e00018
VL  - 6
AB  - Enterobacter cancerogenus CR-Eb1 and Enterococcus sp. CR-Ec1 were isolated from the larval gut
AB  - of Galleria mellonella, the greater wax moth. Here, we report the
AB  - completed and annotated genome sequences of insect gut-dwelling bacteria.
ER  -

TY  - JOUR
AU  - Chung, W.C.
AU  - Chen, L.L.
AU  - Lo, W.S.
AU  - Kuo, P.A.
AU  - Tu, J.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Serratia marcescens WW4.
JO  - Genome Announcements
PY  - 2013
SP  - e0012613
EP  - e0012613
VL  - 1
AB  - Serratia marcescens WW4 is a biofilm-forming bacterium isolated from paper machine aggregates.
AB  - Under conditions of phosphate limitation, this bacterium
AB  - exhibits intergeneric inhibition of Pseudomonas aeruginosa. Here, the complete
AB  - genome sequence of S. marcescens WW4, which consists of one circular chromosome
AB  - (5,241,455 bp) and one plasmid (pSmWW4; 3,248 bp), was determined.
ER  -

TY  - JOUR
AU  - Cibulski, S.P.
AU  - Siqueira, F.M.
AU  - Teixeira, T.F.
AU  - Mayer, F.Q.
AU  - Almeida, L.G.
AU  - Roehe, P.M.
TI  - Genome Sequence of Mycoplasma hyorhinis Isolated from Cell Cultures.
JO  - Genome Announcements
PY  - 2016
SP  - e01119
EP  - e01116
VL  - 4
AB  - Mycoplasmas are major contaminants of mammalian cell cultures. Here, the complete genome
AB  - sequence of Mycoplasma hyorhinis recovered from Madin-Darby bovine kidney
AB  - (MDBK) cells is reported.
ER  -

TY  - JOUR
AU  - Cigna, J.
AU  - Raoul-des-Essarts, Y.
AU  - Mondy, S.
AU  - Helias, V.
AU  - Beury-Cirou, A.
AU  - Faure, D.
TI  - Draft Genome Sequences of Pseudomonas fluorescens Strains PA4C2 and PA3G8 and Pseudomonas putida PA14H7, Three Biocontrol Bacteria against Dickeya  Phytopathogens.
JO  - Genome Announcements
PY  - 2015
SP  - e01503
EP  - e01514
VL  - 3
AB  - Pseudomonas fluorescens strains PA4C2 and PA3G8 and Pseudomonas putida strain PA14H7 were
AB  - isolated from potato rhizosphere and show an ability to inhibit the
AB  - growth of Dickeya phytopathogens. Here, we report their draft genome sequences,
AB  - which provide a basis for understanding the molecular mechanisms involved in
AB  - antibiosis against Dickeya.
ER  -

TY  - JOUR
AU  - Cimdins, A.
AU  - Luthje, P.
AU  - Li, F.
AU  - Ahmad, I.
AU  - Brauner, A.
AU  - Romling, U.
TI  - Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.
JO  - Genome Announcements
PY  - 2017
SP  - e01249
EP  - e01216
VL  - 5
AB  - Strains of Escherichia coli exhibit diverse biofilm formation capabilities. E. coli K-12
AB  - expresses the red, dry, and rough (rdar) morphotype below 30 degrees C,
AB  - whereas clinical isolates frequently display the rdar morphotype
AB  - semiconstitutively. We sequenced the genomes of eight E. coli strains to
AB  - subsequently investigate the molecular basis of semiconstitutive rdar morphotype
AB  - expression.
ER  -

TY  - JOUR
AU  - Cimerman, A.
AU  - Arnaud, G.
AU  - Foissac, X.
TI  - Stolbur phytoplasma genome survey achieved using a suppression subtractive hybridization approach with high specificity.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 3274
EP  - 3283
VL  - 72
AB  - Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding
AB  - hemipteran insects. DNA of phytoplasmas is difficult to
AB  - purify because of their exclusive phloem location and low abundance in
AB  - plants. To overcome this constraint, suppression subtractive hybridization
AB  - (SSH) was modified and used to selectively amplify DNA of the stolbur
AB  - phytoplasma infecting a periwinkle plant. Plasmid libraries were
AB  - constructed, and the origins of the DNA inserts were verified by
AB  - hybridization and PCR screenings. After a single round of SSH, there was
AB  - still a significant level of contamination with plant DNA (around 50%).
AB  - However, the modified SSH, which included a second round of subtraction
AB  - (double SSH), resulted in an increased phytoplasma DNA purity (97%).
AB  - Results validated double SSH as an efficient way to produce a genome
AB  - survey for microbial agents unavailable in culture. Assembly of 266 insert
AB  - sequences revealed 181 phytoplasma genetic loci which were annotated.
AB  - Comparative analysis of 113 kbp indicated that among 217 protein coding
AB  - sequences, 83% were homologous to "Candidatus Phytoplasma asteris" (OY-M
AB  - strain) genes, with hits widely distributed along the chromosome. Most of
AB  - the stolbur-specific SSH sequences were orphan genes, with the exception
AB  - of two partial coding sequences encoding proteins homologous to a
AB  - mycoplasma surface protein and riboflavin kinase.
ER  -

TY  - JOUR
AU  - Cinelli, T.
AU  - Moscetti, I.
AU  - Matchi, G.
TI  - PsasM2I, a Type II Restriction-Modification System in Pseudomonas savastanoi pv. savastanoi: Differential Distribution of Carrier Strains in the Environment and the Evolutionary History of Homologous RM Systems in the Pseudomonas syringae Complex.
JO  - Microb. Ecol.
PY  - 2014
SP  - 842
EP  - 858
VL  - 68
AB  - A type II restriction-modification system was
AB  - found in a native plasmid of Pseudomonas savastanoi pv.
AB  - savastanoi MLLI2. Functional analysis of the methyltransferase
AB  - showed that the enzyme acts by protecting the DNA sequence
AB  - CTGCAG from cleavage. Restriction endonuclease
AB  - expression in recombinant Escherichia coli cells resulted in
AB  - mutations in the REase sequence or transposition of insertion
AB  - sequence 1A in the coding sequence, preventing lethal gene
AB  - expression. Population screening detected homologous RM
AB  - systems in other P. savastanoi strains and in the Pseudomonas
AB  - syringae complex. An epidemiological survey carried out by
AB  - sampling olive and oleander knots in two Italian regions
AB  - showed an uneven diffusion of carrier strains, whose presence
AB  - could be related to a selective advantage in maintaining the RM
AB  - system in particular environments or subpopulations. Moreover,
AB  - carrier strains can coexist in the same orchards, plants,
AB  - and knot tissues with non-carriers, revealing unexpected genetic
AB  - variability on a very small spatial scale. Phylogenetic analysis
AB  - of the RM system and housekeeping gene sequences in the
AB  - P. syringae complex demonstrated the ancient acquisition of the
AB  - RM systems. However, the evolutionary history of the gene
AB  - complex also showed the involvement of horizontal gene transfer
AB  - between related strains and recombination events.
ER  -

TY  - JOUR
AU  - Ciranna, A.
AU  - Larjo, A.
AU  - Kivisto, A.
AU  - Santala, V.
AU  - Roos, C.
AU  - Karp, M.
TI  - Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Anaerobic Alkalithermophilic Bacterium Caloramator celer.
JO  - Genome Announcements
PY  - 2013
SP  - e00471
EP  - e00413
VL  - 1
AB  - Caloramator celer strain JW/YL-NZ35 is a Gram-positive thermophilic, alkalitolerant, and
AB  - strictly anaerobic bacterium capable of producing hydrogen
AB  - and ethanol under extreme conditions. The draft genome sequence presented here
AB  - will provide valuable information to further explore the physiology of this
AB  - species and its potential for biofuel production.
ER  -

TY  - JOUR
AU  - Citron, M.
AU  - Velleman, M.
AU  - Schuster, H.
TI  - Three additional operators, Op21, Op68, and Op88, of bacteriophage P1.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 3611
EP  - 3617
VL  - 264
AB  - The repressor of bacteriophage P1, encoded by the c1 gene, is responsible for maintaining the
AB  - P1 prophage in the lysogenic state.  Previously, 11 c1 repressor binding sites or operators
AB  - scattered over the whole genome of P1 have been found.  From sequence analysis an asymmetric,
AB  - 17-base pair consensus sequence, ATTGCTCTAATAAATTT, was derived.  Using a synthetic
AB  - 15-base-long oligodeoxyribonucleotide as operator probe, we have identified three additional
AB  - operators.  We have mapped the operators at the positions 21, 68, and 88 of the P1 genome and
AB  - determined their sequence.  These operators are controlled by c1 because corresponding P1 DNA
AB  - fragments (I) require c1 repressor in vivo in order to be clonable in multicopy plasmids, (ii)
AB  - exhibit a c1-repressible promoter activity, (iii) are retarded by c1 repressor protein during
AB  - electrophoresis, and (iv) contain the 17-base pair consensus sequence with one mismatch base
AB  - each.  Furthermore, we suggest that expression of the DNA adenine methylase (dam) encoded by
AB  - P1 is controlled via Op68.
ER  -

TY  - JOUR
AU  - Claesson, M.J.
AU  - Li, Y.
AU  - Leahy, S.
AU  - Canchaya, C.
AU  - van Pijkeren, J.P.
AU  - Cerdeno-Tarraga, A.M.
AU  - Parkhill, J.
AU  - Flynn, S.
AU  - O'sullivan, G.C.
AU  - Collins, J.K.
AU  - Higgins, D.
AU  - Shanahan, F.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
AU  - O'toole, P.W.
TI  - Multireplicon genome architecture of Lactobacillus salivarius.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 6718
EP  - 6723
VL  - 103
AB  - Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain
AB  - with probiotic characteristics. The 2.13-Mb
AB  - genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb
AB  - megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously
AB  - have not been characterized in lactic acid bacteria or intestinal
AB  - lactobacilli. Annotation of the genome sequence indicated an intermediate
AB  - level of auxotrophy compared with other sequenced lactobacilli. No
AB  - single-copy essential genes were located on the megaplasmid. However,
AB  - contingency amino acid metabolism genes and carbohydrate utilization
AB  - genes, including two genes for completion of the pentose phosphate
AB  - pathway, were megaplasmid encoded. The megaplasmid also harbored genes for
AB  - the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation
AB  - locus, and other genes potentially relevant for probiotic properties. Two
AB  - subspecies of L. salivarius are recognized, salivarius and salicinius, and
AB  - we detected megaplasmids in both subspecies by pulsed-field gel
AB  - electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of
AB  - megaplasmids of widely varying size in L. salivarius suggests a possible
AB  - mechanism for genome expansion or contraction to adapt to different
AB  - environments.
ER  -

TY  - JOUR
AU  - Clancy, C.D.
AU  - Forde, B.M.
AU  - Moore, S.A.
AU  - O'Toole, P.W.
TI  - Draft Genome Sequences of Helicobacter pylori Strains 17874 and P79.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2402
EP  - 2402
VL  - 194
AB  - Helicobacter pylori is a human pathogen that colonizes the human gastric mucosa,  causing
AB  - gastritis, duodenal and gastric ulcers, and gastric carcinoma. Here we
AB  - announce the draft genomes of H. pylori strain 17874, commonly used for studying
AB  - motility, and P79, a strain for which plasmid vectors have been developed.
ER  -

TY  - JOUR
AU  - Clanton, D.J.
AU  - Riggsby, W.S.
AU  - Miller, R.V.
TI  - NgoII, a restriction endonuclease from Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1979
SP  - 1299
EP  - 1307
VL  - 137
AB  - EndoR.NgoII, a class II restriction endonuclease isolated from Neisseria gonorrhoeae, was
AB  - purified to electrophoretic homogeneity.  We were able to separate it from another restriction
AB  - endonuclease of N. gonorrhoeae, NgoI, by phosphocellulose chromatography.  NgoII is an
AB  - isoschizomer of HaeIII, a restriction endonuclease of Haemophilus aegyptius, and was found to
AB  - recognize the deoxyribonucleic acid nucleotide base sequence GGCC.  NgoII was able to digest
AB  - phage lambda deoxyribonucleic acid over a wide pH range, with optimal activity at pH 8.5.  The
AB  - enzyme has an absolute requirement for Mg2+; maximal enzyme activity was observed at 1 mM
AB  - Mg2+.  The active enzyme has a molecular weight of 65,000 and appears to be composed of six
AB  - subunits of identical molecular weight (11,000).  No methylase activity could be detected in
AB  - the purified enzyme preparation.
AB  - [ The enzyme called NgoI in this abstract has been renamed NgoCI, Jan/1998. ]
AB  - [ The enzyme called NgoII in this abstract has been renamed NgoCII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Clanton, D.J.
AU  - Woodward, J.M.
AU  - Miller, R.V.
TI  - Identification of a new sequence-specific endonuclease NgoII, from Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1978
SP  - 270
EP  - 273
VL  - 135
AB  - A class II restriction endonuclease which recognizes the same nucleotide
AB  - sequence as EndoR-HaeIII has been found in four of seven isolates of Neisseria
AB  - gonorrhoeae.
ER  -

TY  - JOUR
AU  - Clark, C.G.
AU  - Chong, P.M.
AU  - McCorrister, S.J.
AU  - Mabon, P.
AU  - Walker, M.
AU  - Westmacott, G.R.
TI  - DNA Sequence Heterogeneity of Campylobacter jejuni CJIE4 Prophages and Expression of Prophage Genes.
JO  - PLoS ONE
PY  - 2014
SP  - E95349
EP  - E95349
VL  - 9
AB  - Campylobacter jejuni carry temperate bacteriophages that can affect the biology
AB  - or virulence of the host bacterium. Known effects include genomic rearrangements
AB  - and resistance to DNA transformation. C. jejuni prophage CJIE1 shows sequence
AB  - variability and variability in the content of morons. Homologs of the CJIE1
AB  - prophage enhance both adherence and invasion to cells in culture and increase the
AB  - expression of a specific subset of bacterial genes. Other C. jejuni temperate
AB  - phages have so far not been well characterized. In this study we describe
AB  - investigations into the DNA sequence variability and protein expression in a
AB  - second prophage, CJIE4. CJIE4 sequences were obtained de novo from DNA sequencing
AB  - of five C. jejuni isolates, as well as from whole genome sequences submitted to
AB  - GenBank by other research groups. These CJIE4 DNA sequences were heterogenous,
AB  - with several different insertions/deletions (indels) in different parts of the
AB  - prophage genome. Two variants of a 3-4 kb region inserted within CJIE4 had
AB  - different gene content that distinguished two major conserved CJIE4 prophage
AB  - families. Additional indels were detected throughout the prophage. Detection of
AB  - proteins in the five isolates characterized in our laboratory in isobaric Tags
AB  - for Relative and Absolute Quantitation (iTRAQ) experiments indicated that
AB  - prophage proteins within each of the two large indel variants were expressed
AB  - during growth of the bacteria on Mueller Hinton agar plates. These proteins
AB  - included the extracellular DNase associated with resistance to DNA transformation
AB  - and prophage repressor proteins. Other proteins associated with known or
AB  - suspected roles in prophage biology were also expressed from CJIE4, including
AB  - capsid protein, the phage integrase, and MazF, a type II toxin-antitoxin system
AB  - protein. Together with the results previously obtained for the CJIE1 prophage
AB  - these results demonstrate that sequence variability and expression of moron genes
AB  - are both general properties of temperate bacteriophages in C. jejuni.
ER  -

TY  - JOUR
AU  - Clark, C.G.
AU  - Ng, L.-K.
TI  - Sequence variability of Campylobacter temperate bacteriophages.
JO  - BMC Microbiol.
PY  - 2008
SP  - 49
EP  - 49
VL  - 8
AB  - Background: Prophages integrated within the chromosomes of Campylobacter jejuni isolates have
AB  - been demonstrated very recently. Prior work with Campylobacter temperate bacteriophages, as
AB  - well as evidence from prophages in other enteric bacteria, suggests these prophages might have
AB  - a
AB  - role in the biology and virulence of the organism. However, very little is known about the
AB  - genetic variability of Campylobacter prophages which, if present, could lead to differential
AB  - phenotypes in isolates carrying the phages versus those that do not. As a first step in the
AB  - characterization of C. jejuni prophages, we investigated the distribution of prophage DNA
AB  - within a C. jejuni population assessed the DNA and protein sequence variability within a
AB  - subset of the putative prophages found.
AB  - Results: Southern blotting of C. jejuni DNA using probes from genes within the three putative
AB  - prophages of the C. jejuni sequenced strain RM 1221 demonstrated the presence of at least one
AB  - prophage gene in a large proportion (27/35) of isolates tested. Of these, 15 were positive for
AB  - 5 or
AB  - more of the 7 Campylobacter Mu-like phage 1 (CMLP 1, also designated Campylobacter jejuni
AB  - integrated element 1, or CJIE 1) genes tested. Twelve of these putative prophages were chosen
AB  - for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage
AB  - demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence.
AB  - Structural and sequence variability, including short insertions, deletions, and allele
AB  - replacements, were found within the prophage genomes, some of which would alter the protein
AB  - products of the ORFs involved. No insertions of novel genes were detected within the sequenced
AB  - regions. The 12
AB  - prophages and RM 1221 had a % G+C very similar to C. jejuni sequenced strains, as well as
AB  - promoter regions characteristic of C. jejuni. None of the putative prophages were successfully
AB  - induced and propagated, so it is not known if they were functional or if they represented
AB  - remnant
AB  - prophage DNA in the bacterial chromosomes.
AB  - Conclusion: These putative prophages form a family of phages with conserved sequences, and
AB  - appear to be adapted to Campylobacter. There was evidence for recombination among groups of
AB  - prophages, suggesting that the prophages had a mosaic structure. In many of these properties,
AB  - the Mu-like CMLP 1 homologs characterized in this study resemble temperate bacteriophages of
AB  - enteric bacteria that are responsible for contributions to virulence and host adaptation.
ER  -

TY  - JOUR
AU  - Clark, J.
AU  - Harrison, J.C.
AU  - Mdegela, R.H.
AU  - March, J.B.
TI  - Extended stability of restriction enzymes at ambient temperatures.
JO  - Biotechniques
PY  - 2000
SP  - 536
EP  - 536
VL  - 29
AB  - The stability of restriction enzymes as supplied by manufacturers without any modification has
AB  - been examined. No reduction in activity
AB  - was observed for three enzymes (HindIII, EcoRI and Tsp5091) held at
AB  - ambient temperature or 4 degrees C for the period of study (12 months),
AB  - while activity was observed for up to 12 weeks after storage at 37
AB  - degrees C, which was considerably better than following desiccation
AB  - with trehalose, a recognized preservation technique. A larger trial of
AB  - 23 different restriction enzymes held at room temperature for one week
AB  - showed that all enzymes retained significant activity. As a practical
AB  - demonstration of the usefulness of this finding, enzymes were posted to
AB  - Africa by conventional mail (cost $1 US) and shown to retain activity
AB  - upon arrival after three weeks in transit (compared to a cost of $1000
AB  - US by cold-chain transportation). Supplying enzymes to third-world
AB  - markets should now be possible by removing the necessity for cold-chain
AB  - transport. After arrival, enzymes can simply be stored in a standard
AB  - domestic refrigerator.
ER  -

TY  - JOUR
AU  - Clark, J.
AU  - Shevchuk, T.
AU  - Kho, M.R.
AU  - Smith, S.S.
TI  - Methods for the design and analysis of oligodeoxynucleotide-based DNA (cytosine-5) methyltransferase inhibitors.
JO  - Anal. Biochem.
PY  - 2003
SP  - 50
EP  - 64
VL  - 321
AB  - Several second-generation inhibitors of DNA (cytosine-5) methyltransferases based on studies
AB  - of modified synthetic
AB  - oligodeoxynucleoides have been described. As an aid to studies of these
AB  - inhibitors, we present an electronic structure-based algorithm that can be
AB  - used as a method for predicting the nature of the expected inhibition by
AB  - any noncytosine nucleotide target. Targeting by the major human enzyme
AB  - (hDnmt1) is governed by the presence of a three-nucleotide motif. In
AB  - hemimethylated DNA, this motif consists of a 5-methylcytosine targeting
AB  - signal that causes the enzyme to probe the opposite strand for a normally
AB  - paired guanosine or inosine residue and attempt to methylate the residue
AB  - 5' to that site. As a demonstration of the method, we apply these rules to
AB  - the design and characterization of a novel oligodeoxynucleotide inhibitor
AB  - of hDnmt1. This inhibitor takes advantage of the three-nucleotide
AB  - recognition motif characteristic of hDnmt1 and shows that the enzyme is
AB  - inhibited in vitro by non-CG methylation which targets the enzyme to
AB  - normally basepaired but unproductive nucleotides such as dG, dA, and dT.
AB  - Kinetic analysis at constant S-adenosyl-L-methionine concentration shows
AB  - that representative inhibitory oligodeoxynucleotides are best viewed as
AB  - weakly productive components of systems containing two DNA substrates.
AB  - This model suggests that the most effective inhibitors are those with very
AB  - low apparent Vmax and very low Km values. Oligodeoxynucleotides containing
AB  - mispaired and unproductive targets such as dG, dA, dT, and dU are also
AB  - inhibitory as secondary substrates for the human enzyme. Biologically,
AB  - fail-safe mechanisms identified by the ab initio approach appear to be
AB  - active in preventing potentially mutagenic deamination of dihydrocytosine
AB  - and enzymatic methylation of dU.
ER  -

TY  - JOUR
AU  - Clark, N.C.
AU  - Zhu, W.
AU  - Patel, J.B.
TI  - Missense Mutation of hsdR-Encoded Type I Restriction Enzyme Implicated in Transfer of Vancomycin-Resistance from Enterococcus to Staphylococcus aureus.
JO  - Abstr. InterSci. Conf. Antimicrob. Agents Chemother.
PY  - 2007
SP  - 83
EP  - 84
VL  - 47
AB  - Background:  Seven vanA-mediated vancomycin-resistant S. aureus (VRSA) cases have been
AB  - reported. To prevent VRSA, it is important to understand the microbiological characteristics
AB  - that allow for transfer of vanA from vancomycin-resistant Enterococcus (VRE) to S. aureus.
AB  - Previously it was reported that S. aureus strain RN4220 readily acquires foreign DNA as a
AB  - result of a missense mutation within the hsdR gene of the Type I restriction-modification
AB  - system. Therefore we investigated the possibility that this mutation may have contributed to
AB  - the transfer of vanA from Enterococcus to S. aureus.
AB  - Methods:  The hsdR gene was amplified using primers, previously described by Waldron and
AB  - Lindsay (2006. J. Bacteriol.), and both strands of this PCR product were sequenced using
AB  - eleven additional primers.  The resulting sequences were compared to those of S. aureus
AB  - 8325-4, the parent strain of RN4220, and the S. aureus COL strain.
AB  - Results:  The hsdR sequences of a VRSA isolate from each case were analyzed. For VRSA 1, 2, 5,
AB  - and 6 no mutation was identified that changes the amino acid sequence. For VRSA 4, a base
AB  - substitution was identified that resulted in a I to F amino acid change at position 774 and
AB  - for VRSA 7, a base substitution resulted in a T to P amino acid change at position 362. For
AB  - VRSA 3 a single-base deletion C, at base position 1382 (codon 461) created a frameshift and a
AB  - premature stop codon at base position 1405. These changes would result in a truncation of the
AB  - restriction enzyme from 930 amino acids to 469 amino acids. This truncation (50% of the
AB  - protein) is less extensive than that reported for S. aureus RN4220 (21%).  Eight other S.
AB  - aureus isolates (1 VRSA and 7 vancomycin-susceptible SA) from the same patient were
AB  - characterized. These isolates were recovered from multiple body sites on different days, but
AB  - were closely related by pulsed-field gel electrophoresis typing.  All 9 S. aureus isolates had
AB  - the same hsdR gene mutation.
AB  - Conclusions:  Three of the seven VRSA isolates has a mutation in the hsdR gene that resulted
AB  - in a protein change. The amino acid substitutions identified in VRSA 4 and 7 have not been
AB  - reported in another S. aureus and the significance of these changes is unknown. The missense
AB  - mutation identified in VRSA 3 and related S. aureus isolates from the same patient likely
AB  - results in a loss of function of the Type I restriction enzyme and may allow this strain to
AB  - more readily acquire foreign DNA than strains with a functional restriction enzyme.
ER  -

TY  - JOUR
AU  - Clark, S.J.
AU  - Harrison, J.
AU  - Paul, C.L.
AU  - Frommer, M.
TI  - High sensitivity mapping of methylated cytosines.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 2990
EP  - 2997
VL  - 22
AB  - An understanding of DNA methylation and its potential role in gene control during development,
AB  - aging and cancer has been hampered by a lack of sensitive methods which can resolve exact
AB  - methylation patterns from only small quantities of DNA. We have now developed a genomic
AB  - sequencing technique which is capable of detecting every methylated cytosine on both strands
AB  - of any target sequence, using DNA isolated from fewer than 100 cells. In this method, sodium
AB  - bisulphite is used to convert cytosine residues to uracil residues in single-stranded DNA,
AB  - under conditions whereby 5-methylcytosine remains non-reactive. The converted DNA is amplified
AB  - with specific primers and sequenced. All the cytosine residues remaining in the sequence
AB  - represent previously methylated cytosines in the genome. The work described has defined
AB  - procedures that maximise the efficiency of denaturation, bisulphite conversion and
AB  - amplification, to permit methylation mapping of single genes from small amounts of genomic
AB  - DNA, readily available from germ cells and early developmental stages.
ER  -

TY  - JOUR
AU  - Clark, T.A.
AU  - Lu, X.
AU  - Luong, K.
AU  - Dai, Q.
AU  - Boitano, M.
AU  - Turner, S.W.
AU  - He, C.
AU  - Korlach, J.
TI  - Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via  Tet1 oxidation.
JO  - BMC Biol.
PY  - 2013
SP  - 4
EP  - 4
VL  - 11
AB  - ABSTRACT: BACKGROUND: DNA methylation serves as an important epigenetic mark in both
AB  - eukaryotic and prokaryotic organisms. In eukaryotes, the most common
AB  - epigenetic mark is 5-methylcytosine, whereas prokaryotes can have
AB  - 6-methyladenine, 4-methylcytosine, or 5-methylcytosine. Single-molecule,
AB  - real-time sequencing is capable of directly detecting all three types of modified
AB  - bases. However, the kinetic signature of 5-methylcytosine is subtle, which
AB  - presents a challenge for detection. We investigated whether conversion of
AB  - 5-methylcytosine to 5-carboxylcytosine using the enzyme Tet1 would enhance the
AB  - kinetic signature, thereby improving detection. RESULTS: We characterized the
AB  - kinetic signatures of various cytosine modifications, demonstrating that
AB  - 5-carboxylcytosine has a larger impact on the local polymerase rate than
AB  - 5-methylcytosine. Using Tet1-mediated conversion, we show improved detection of
AB  - 5-methylcytosine using in vitro methylated templates and apply the method to the
AB  - characterization of 5-methylcytosine sites in the genomes of Escherichia coli
AB  - MG1655 and Bacillus halodurans C-125. CONCLUSIONS: We have developed a method for
AB  - the enhancement of directly detecting 5-methylcytosine during single-molecule,
AB  - real-time sequencing. Using Tet1 to convert 5-methylcytosine to
AB  - 5-carboxylcytosine improves the detection rate of this important epigenetic
AB  - marker, thereby complementing the set of readily detectable microbial base
AB  - modifications, and enhancing the ability to interrogate eukaryotic epigenetic
AB  - markers.
ER  -

TY  - JOUR
AU  - Clark, T.A.
AU  - Murray, I.A.
AU  - Morgan, R.D.
AU  - Kislyuk, A.O.
AU  - Spittle, K.E.
AU  - Boitano, M.
AU  - Fomenkov, A.
AU  - Roberts, R.J.
AU  - Korlach, J.
TI  - Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - e29
EP  - e29
VL  - 40
AB  - DNA methylation is the most common form of DNA modification in prokaryotic and eukaryotic
AB  - genomes. We have applied the method of single-molecule, real-time (SMRT(R)) DNA sequencing
AB  - that is capable of direct detection of modified bases at single-nucleotide resolution to
AB  - characterize the specificity of several bacterial DNA methyltransferases (MTases). In addition
AB  - to previously described SMRT sequencing of N6-methyladenine and 5-methylcytosine, we show that
AB  - N4-methylcytosine also has a specific kinetic signature and is therefore identifiable using
AB  - this approach. We demonstrate for all three prokaryotic methylation types that SMRT sequencing
AB  - confirms the identity and position of the methylated base in cases where the MTase specificity
AB  - was previously established by other methods. We then applied the method to determine the
AB  - sequence context and methylated base identity for three MTases with unknown specificities. In
AB  - addition, we also find evidence of unanticipated MTase promiscuity with some enzymes
AB  - apparently also modifying sequences that are related, but not identical, to the cognate site.
ER  -

TY  - JOUR
AU  - Clark, T.R.
AU  - Noriea, N.F.
AU  - Bublitz, D.C.
AU  - Ellison, D.W.
AU  - Martens, C.
AU  - Lutter, E.I.
AU  - Hackstadt, T.
TI  - Comparative Genome Sequencing of Rickettsia rickettsii Strains Differing in Virulence.
JO  - Infect. Immun.
PY  - 2015
SP  - 1568
EP  - 1576
VL  - 83
AB  - Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of
AB  - Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a
AB  - Guinea pig model of infection, the severity of disease as assessed by fever response varies
AB  - from the most virulent, Sheila Smith, to Iowa which causes no fever. To identify potential
AB  - determinants of virulence in R. rickettsii, the genomes of two additional strains were
AB  - sequenced for comparison to known sequences (CGS). R. rickettsii Morgan and R strains were
AB  - compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith. The
AB  - Montana strains Sheila Smith and R  were found to be highly similar while the Eastern strains
AB  - Iowa and Morgan were most similar to each other. A major surface antigen, rOmpA, is severely
AB  - truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced
AB  - revealing only 7 shared SNP's (4 nonsynonymous) for R and Morgan strains compared to Sheila
AB  - Smith with an additional 17 SNPs identified in Morgan. Another major surface antigen and
AB  - autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta
AB  - fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa
AB  - and Morgan strains and R identical to Sheila Smith. The number of SNPs and
AB  - insertions/deletions between sequences of the two Montana strains and the two Eastern strains
AB  - is low, thus narrowing the field of possible virulence factors.
ER  -

TY  - JOUR
AU  - Clarke, C.M.
AU  - Hartley, B.S.
TI  - Purification, properties and specificity of the restriction endonuclease from Bacillus stearothermophilus.
JO  - Biochem. J.
PY  - 1979
SP  - 49
EP  - 62
VL  - 177
AB  - The restriction endonuclease BstI was purified from 70kg of Bacillus stearothermophilus.  The
AB  - final product is at least 97% pure as judged by sodium dodecyl sulphate/polyacrylamide-gel
AB  - electrophoresis; this major protein species co-migrates with the enzyme activity on native
AB  - polyacrylamide-gel electrophoresis and isoelectric focusing.  Pure restriction endonuclease
AB  - BstI has a subunit mol. wt. of 26000 and is probably a loosely associated dimer. The enzyme
AB  - shows maximum activity at pH values between 7 and 9.5, and in the presence of 0.5-2mM-Mg2+.
AB  - NaCl inhibits the restriction enzymeactivity. Restriction endonuclease BstI cleaves DNA in a
AB  - position identical with that cleaved by endonuclease BamHI (for Bacillus amyloliquefaciens),
AB  - i.e.:
AB  - 5'-G/-G-A-T-C-C-3'
AB  - 3'-C-C-T-A-G/-G-5'.
AB  - In the presence of high concentrations of enzyme, DNA cleavage occurs at secondary sites.
AB  - This side-specificity is enhanced by the addition of glycerol.  Preliminary studies indicate
AB  - that these sites are of the type:
AB  - 5'-/G-A-T-C-3'
AB  - 3'-C-T-A-G/-5'.
ER  -

TY  - JOUR
AU  - Clarke, D.J.
AU  - Chaudhuri, R.R.
AU  - Martin, H.M.
AU  - Campbell, B.J.
AU  - Rhodes, J.M.
AU  - Constantinidou, C.
AU  - Pallen, M.J.
AU  - Loman, N.J.
AU  - Cunningham, A.F.
AU  - Browning, D.F.
AU  - Henderson, I.R.
TI  - Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4540
EP  - 4540
VL  - 193
AB  - Adherent-invasive Escherchia coli strains are increasingly being associated with intestinal
AB  - pathologies. Here we present the genome
AB  - sequence of E. coli HM605, a strain isolated from colonic biopsies of a
AB  - patient with Crohn's disease.
ER  -

TY  - JOUR
AU  - Clarke, N.D.
TI  - A proposed mechanism for the self-splicing of proteins.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 11084
EP  - 11088
VL  - 91
AB  - Intervening protein sequences, called inteins, are intronlike elements that
AB  - are removed posttranslationally, apparently by self-splicing.  The conserved and essential
AB  - residues of precursor proteins consist of an asparagine as the last residue of the intein and
AB  - a
AB  - hydroxyl- or thiol-containing residue immediately following both splice junctions.
AB  - Evidence for a branched intermediate has been reported; however, the chemical nature of
AB  - the branched structure is unclear.  I propose a mechanism that includes the formation of a
AB  - branched structure, provides an explanation for the reversal of branch formation observed
AB  - at high pH, and accounts for each of the essential amino acids.  The branched structure is
AB  - formed by nucleophilic attack of the asparagine side chain on the N-terminal splice
AB  - junction.  The nature of this branched structure is a distinguishing feature of the model and
AB  - can be experimentally tested.
ER  -

TY  - JOUR
AU  - Clarke, S.
AU  - Banfield, K.
TI  - S-Adenosylmethionine-dependent methyltransferases.
JO  - Homocysteine in Health and Disease
PY  - 2001
SP  - 63
EP  - 78
AB  - Mammalian S-adenosylmethionine-dependent methyltransferases each catalyze a reaction, giving
AB  - rise to two products - S-adenosylhomocysteine and one of a variety of methylated biomolecules
AB  - including nucleic acids, proteins, lipids, and small molecules.  S-adenosylhomocysteine is
AB  - subsequently broken down to adenosine and homocysteine by S-adenosylhomocysteine hydrolase.
AB  - The homocysteine formed can be either remethylated to methionine or converted to cysteine via
AB  - cystathionine.  As such, these methyltransferases are bifunctional; they make up an essential
AB  - part of the conduit for the conversion of methionine to cysteine in addition to generating
AB  - methylated products.
ER  -

TY  - JOUR
AU  - Claus, H.
AU  - Friedrich, A.
AU  - Frosch, M.
AU  - Vogel, U.
TI  - Differential distribution of novel restriction-modification systems in clonal lineages of Neisseria meningitidis.
JO  - J. Bacteriol.
PY  - 2000
SP  - 1296
EP  - 1303
VL  - 182
AB  - Using representational difference analysis, we isolated novel meningococcal
AB  - restriction-modification (R-M) systems. NmeBI, which is a homologue of the R-M system HgaI of
AB  - Pasteurella volantium, was present in meningococci of the ET-5 complex and of lineage III.
AB  - NmeAI was found in serogroup A, ET-37 complex, and cluster A4 meningococci. NmeDI was harbored
AB  - by meningococci of the ET-37 complex and of cluster A4, but not by serogroup A meningococci.
AB  - Two of the R-M systems, NmeBI and NmeDI, were located at homologous positions between the
AB  - phenylalanyl-tRNA synthetase genes pheS and pheT, which appeared to be a preferential target
AB  - for the insertion of foreign DNA in meningococci. The distribution of the three R-M systems
AB  - was tested with 103 meningococcal strains comprising 49 sequence types. The vast majority of
AB  - the strains had either NmeBI, NmeAI, or both NmeAI and NmeDI. Using cocultivation experiments,
AB  - we could demonstrate that NmeBI, which was present in ET-5 complex meningococci, was
AB  - responsible for a partial restriction of DNA transfer from meningococci of the ET-37 complex
AB  - to meningococci of the ET-5 complex.
ER  -

TY  - JOUR
AU  - Claus, H.
AU  - Stoevesandt, J.
AU  - Frosch, M.
AU  - Vogel, U.
TI  - Genetic isolation of meningococci of the electrophoretic type 37 complex.
JO  - J. Bacteriol.
PY  - 2001
SP  - 2570
EP  - 2575
VL  - 183
AB  - Neisseria meningitidis (the meningococcus) is a naturally competent bacterial species in which
AB  - intra- and interspecific horizontal gene transfer is a major source of genetic diversity. In
AB  - strains of the electrophoretic type 37 (ET-37) complex and of the A4 cluster, we identified
AB  - genomic DNA coding for a novel restriction-modification system and for the tail of a
AB  - previously unidentified prophage. Furthermore, a novel 7.2-kb DNA segment restricted to clones
AB  - of the ET-37 complex and the A4 cluster was isolated and shown to occur both as a plasmid
AB  - (pJS-B) and as a chromosomal integration. Neither the genomic loci nor pJS-B was present in
AB  - ET-5 complex, lineage 3, or serogroup A meningococci. The differential distribution of the DNA
AB  - segments described herein, as well as of opcA, porB, nmeAI, nmeBI, and nmeDI described
AB  - previously, supports the concept of genetic isolation of hypervirulent lineages responsible
AB  - for most cases of serogroup C disease worldwide.
ER  -

TY  - JOUR
AU  - Clauwers, C.
AU  - Briers, Y.
AU  - Lavigne, R.
AU  - Michiels, C.W.
TI  - Two Complete and One Draft Genome Sequence of Nonproteolytic Clostridium botulinum Type E Strains NCTC 8266, NCTC 8550, and NCTC 11219.
JO  - Genome Announcements
PY  - 2015
SP  - e00083
EP  - e00015
VL  - 3
AB  - Group II (gII) nonproteolytic Clostridium botulinum strains are a major cause of  foodborne
AB  - botulism outbreaks. Here, we report two complete genome sequences of
AB  - gII type E strains NCTC 8266 and NCTC 8550 and one draft genome sequence of type
AB  - E NCTC 11219.
ER  -

TY  - JOUR
AU  - Cleaver, J.E.
AU  - Samson, L.
AU  - Thomas, G.H.
TI  - Restriction enzyme cleavage of ultraviolet-damaged DNA.
JO  - Biochim. Biophys. Acta
PY  - 1982
SP  - 255
EP  - 258
VL  - 697
AB  - SV40 and pBR322 DNAs damaged by ultraviolet light were cleaved abnormally by
AB  - several restriction enzymes because of damage to pyrimidines in the recognition
AB  - sequences.  The use of a tandemly duplicated plasmid provided a particularly
AB  - sensitive target molecule for detecting pyrimidine dimers and other possible
AB  - photoproducts.  The relative efficiency with which cleavage was blocked
AB  - (HindIII>TaqI>BamI>SalI>>HhaI, HaeIII) corresponds approximately to the
AB  - relative frequency of pyrimidine dimer formation in the recognition sequences,
AB  - but at a slightly higher frequency in potential sites for the non-cyclobutane
AB  - T-C product.  The pyrimidine dimers appear to have a range of influence that
AB  - extends 1 to 3 basepairs along the DNA molecule.  These effects provide clues
AB  - to the way DNA damage from mutagens and carcinogens can interfere with specific
AB  - enzyme-DNA interactions.
ER  -

TY  - JOUR
AU  - Clements, J.B.
AU  - Cortini, R.
AU  - Wilkie, N.M.
TI  - Analysis of Herpesvirus DNA Substructure by means of Restriction Endonucleases.
JO  - J. Gen. Virol.
PY  - 1976
SP  - 243
EP  - 256
VL  - 30
AB  - The mol. wt. and molar ratios of the HindIII and HpaI fragments of HSV-1 DNA
AB  - and the EcoRI fragments of HSV-2 DNA have been determined.  Results obtained
AB  - suggest that DNA isolated from both HSV-1 and HSV-2 consists of molecules with
AB  - four different sequence arrangements which are present in similar amounts.  Our
AB  - explanation of the cleavage patterns of these four genome arrangements with the
AB  - different restriction enzymes is presented.  Some of the possible implications
AB  - of these four genome arrangements for genetic recombination are discussed.
ER  -

TY  - JOUR
AU  - Cleto, S.
AU  - Van der Auwera, G.
AU  - Almeida, C.
AU  - Vieira, M.J.
AU  - Vlamakis, H.
AU  - Kolter, R.
TI  - Genome Sequence of Serratia plymuthica V4.
JO  - Genome Announcements
PY  - 2014
SP  - e00340
EP  - e00314
VL  - 2
AB  - Serratia spp. are gammaproteobacteria and members of the family Enterobacteriaceae. Here, we
AB  - announce the genome sequence of Serratia plymuthica
AB  - strain V4, which produces the siderophore serratiochelin and antimicrobial
AB  - compounds.
ER  -

TY  - JOUR
AU  - Clifford, R.J.
AU  - Hang, J.
AU  - Riley, M.C.
AU  - Onmus-Leone, F.
AU  - Kuschner, R.A.
AU  - Lesho, E.P.
AU  - Waterman, P.E.
TI  - Complete Genome Sequence of Providencia stuartii Clinical Isolate MRSN 2154.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3736
EP  - 3737
VL  - 194
AB  - Here we present the complete genome sequence of Providencia stuartii MRSN 2154, isolated from
AB  - an Afghan national. P. stuartii is a Gram-negative bacillus capable
AB  - of causing infections in a wide variety of human tissues. Because Providencia
AB  - readily acquires plasmids bearing drug resistance loci, it is of growing clinical
AB  - significance.
ER  -

TY  - JOUR
AU  - Clum, A. et al.
TI  - Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 38
EP  - 45
VL  - 1
AB  - Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species  of the
AB  - genus, which until recently was the only genus within the actinobacterial
AB  - family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of
AB  - iron pyrite during autotrophic growth in the absence of an enhanced CO(2)
AB  - concentration is characteristic for A. ferrooxidans. Here we describe the
AB  - features of this organism, together with the complete genome sequence, and
AB  - annotation. This is the first complete genome sequence of the order
AB  - Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038
AB  - protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Clum, A. et al.
TI  - Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 308
EP  - 316
VL  - 1
AB  - Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the
AB  - family Planctomycetaceae. Members of this pear- or
AB  - teardrop-shaped bacterium show a clearly visible pointed attachment pole and can
AB  - be distinguished from other Planctomycetes by a lack of true stalks. Strains
AB  - closely related to the species have been isolated from fresh and brackish water,
AB  - as well as from hypersaline lakes. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. This is the
AB  - first completed genome sequence of the order Planctomyces and only the second
AB  - sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long
AB  - genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Clyman, J.
TI  - Some microbes have splicing proteins.
JO  - ASM News
PY  - 1995
SP  - 344
EP  - 347
VL  - 61
AB  - The recent discovery of microbial genes whose products are spliced at the protein level,
AB  - instead of at the mRNA level, adds an unexpected dimension of complexity to the ways in which
AB  - genetic information flows from DNA to protein. These amazing protein elements, discovered
AB  - about 5 years ago and now called inteins, typically catalyze both protein and DNA
AB  - rearrangements.
ER  -

TY  - JOUR
AU  - Clyman, J.
AU  - Belfort, M.
TI  - Trans and cis requirements for intron mobility in a prokaryotic system.
JO  - Genes Dev.
PY  - 1992
SP  - 1269
EP  - 1279
VL  - 6
AB  - Intron mobility requires cleavage of an intronless allele by an intron-encoded endonuclease,
AB  - followed by transfer of the intron into the cleaved recipient.  The mobile phage introns
AB  - provide an opportunity to identify accessory functions involved in the intron inheritance
AB  - process.  To test for trans and cis requirements of mobility in Escherichia coli, we have
AB  - exploited the td intron of phage T4 in both phage T4 and lambda genetic backgrounds.  Mobility
AB  - depends on host or phage recombinase functions, RecA or UvsX, respectively.  The process also
AB  - requires a phage-encoded 5'-->3' exonuclease activity and associated annealing function that
AB  - can be provided by phage lambda.  Finally, host-encoded 3'-->5' exonuclease activities are
AB  - also implicated in intron inheritance.  We demonstrated further that restriction enzymes could
AB  - substitute for the intron-encoded endonuclease, indicating that the endonuclease does not have
AB  - an essential role in recombination.  Neither the precise position nor the nature of the
AB  - double-strand break was critical to intron transfer.  These features provide insight into the
AB  - recombination pathway and are factors impacting on the spread of introns throughout natural
AB  - populations.
ER  -

TY  - JOUR
AU  - Coad, J.E.
AU  - Lander, T.A.
AU  - Litz, C.E.
TI  - Inhibition of restriction endonucleases by common clinical anticoagulants.
JO  - Anal. Biochem.
PY  - 1992
SP  - 368
EP  - 369
VL  - 205
AB  - Anticoagulated peripheral blood and bone marrow provide an accessible source of DNA for
AB  - molecular studies. Successful results in such investigations often depend on full activity of
AB  - labile restriction enzymes. Though occasional studies have shown heparin to be inhibitory, an
AB  - often overlooked cause of enzyme inactivity is the effect of the anticoagulant used in sample
AB  - collection. No systematic study regarding the effect of anticoagulants on restriction enzymes
AB  - or techniques to remove anticoagulant contamination has been reported. The sensitivites of 18
AB  - commonly used restriction endonucleases to sodium heparin, citric acid-sodium citrate-dextrose
AB  - (ACD), and ethylenediaminetetraacetic acid (EDTA) and various methods of decontamination are
AB  - presented.
ER  -

TY  - JOUR
AU  - Coates-Brown, R.
AU  - Horsburgh, M.J.
TI  - Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy  Human Skin.
JO  - Genome Announcements
PY  - 2017
SP  - e01548
EP  - e01516
VL  - 5
AB  - We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus
AB  - hominis determined using the PacBio long-read sequencing platform.
AB  - S. hominis is a major commensal of the skin microflora. This genome sequence adds
AB  - to our understanding of this species and will aid studies of gene traffic between
AB  - staphylococci.
ER  -

TY  - JOUR
AU  - Cocks, B.G.
AU  - Finch, L.R.
TI  - Characterization of a restriction endonuclease from Ureaplasma urealyticum 960 and differences in deoxyribonucleic acid modification of human ureaplasmas.
JO  - Int. J. Syst. Bacteriol.
PY  - 1987
SP  - 451
EP  - 453
VL  - 37
AB  - Uur960I, a restriction endonuclease from Ureaplasma urealyticum 960T, cleaved
AB  - at the sequence 5'-GC/NGC-3' and is thus an isoschizomer of Fnu4HI.  Fnu4HI
AB  - cleaved deoxyribonucleic acid from human ureaplasma serovars I,III, and VI but
AB  - not II, IV, V, VII, VIII (strain 960), and IX.  This grouping of serovars,
AB  - indicative of their deoxyribonucleic acid modification, matches that previously
AB  - reported by others using different criteria.
ER  -

TY  - JOUR
AU  - Coene, M.
AU  - Hoet, P.
AU  - Cocito, C.
TI  - Physical map of Phage 2 C DNA: Evidence for the existence of large redundant ends.
JO  - Eur. J. Biochem.
PY  - 1983
SP  - 69
EP  - 75
VL  - 132
AB  - The chromosome of the Bacillus subtilis phage 2C, a linear molecule of double-stranded DNA of
AB  - about 10^8 Da, in which thymine is completely replaced by hydroxymethyluracil, was cleaved by
AB  - different endonucleases. In some cases restriction segments were much fewer than expected,
AB  - suggesting a possible interference of the unusual base with the recognition mechanism of
AB  - endonucleases. The physical map of 2C DNA was established by use of SalI and HaeIII
AB  - restriction endonucleases, which yielded a limited number of fragments. The expected number of
AB  - fragments was 240 for HaeIII and 23 for SalI; in reality, five segments were observed upon
AB  - cleavage with HaeIII and four with SalI. The terminal fragments of the genome were first
AB  - identified; the other fragments were ordered by hybridization and molecular weight
AB  - determination of restriction fragments obtained by cleavage with the two endonucleases. In
AB  - addition, hybridization of restriction fragments showed the presence of homologous regions at
AB  - the ends of the 2C genome. The structure of these direct repetitive sequences was analyzed by
AB  - cleavage with HaeIII and hybridization with EcoRI restriction fragments. Their size (9.2 MDa)
AB  - was found to be about 1/11 of that of the whole chromosome.
ER  -

TY  - JOUR
AU  - Coetzee, J.N.
AU  - Smit, J.A.
TI  - Restriction without modification of phage 34/13 in a strain of Proteus mirabilis.
JO  - S. Afr. Med. J.
PY  - 1969
SP  - 356
EP  - 356
VL  - 43
AB  - Phage 34/13 prepared on its host strain Proteus mirabilis 13at does not form
AB  - plaques on P. mirabilis strain N6 when serial dilutions are spotted on a lawn
AB  - of the organism.  Low dilutions show areas of clearing due to bacterial lysis
AB  - but no phage capable of forming plaques on N6 is obtained from these zones.
AB  - Phage 34/13 adsorbs to an extent of 99% on strain N6 within 15 min.  With the
AB  - use of 32P-labelled phage 34/13 DNA it is shown that within 15 min. of
AB  - adsorption to N6, 57% of the label is in the medium in the form of acid-soluble
AB  - nucleotides.  This figure is reduced to 11% when the phage adsorbs to its
AB  - normal host 13at and 0.9% when the phage is mixed with a strain of P. mirabilis
AB  - to which it does not adsorb.  This indicates that the DNA of phage 34/13 is
AB  - restricted by strain N6.  The phage DNA which escapes restriction is not
AB  - modified as no plaques are formed.  Phenotypically strain N6 behaves as if its
AB  - genotype is r+m-.  It may be argued that r+m- strains should degrade their own
AB  - DNA and be nonviable.  Strains of this genotype have never been isolated after
AB  - mutagen treatment of wild strains.  Many bacteria which restrict foreign DNA
AB  - owe this property to a prophage.  Strain N6 carries a prophage which on UV
AB  - induction produces a defective phage which manifests itself as a bacteriocin
AB  - which kills strains of P. mirabilis, and this plasmid may contribute to the
AB  - restrictive process.  This has not been proved.  Attempts to isolate mutants of
AB  - phage 34/13 which escape restriction have been unsuccessful.  Fruitless
AB  - attempts have also been made to isolate r-m- or r-m+ mutants of strain N6 which
AB  - would allow plaque formation by the phage.
ER  -

TY  - JOUR
AU  - Coffey, A.
AU  - Ross, R.P.
TI  - Bacteriophage-resistance systems in dairy starter strains: molecular analysis to application.
JO  - Antonie Van Leeuwenhoek
PY  - 2002
SP  - 303
EP  - 321
VL  - 82
AB  - Starter inhibition by bacteriophage infection in dairy fermentations can limit the usage of
AB  - specific bacterial strains used in the
AB  - manufacture of Cheddar, Mozzarella and other cheeses and can result in
AB  - substantial economic losses. A variety of practical measures to
AB  - alleviate the problem of phage infection have been adopted over the
AB  - years but has invariably resulted in a very limited number of strains
AB  - which can withstand intensive usage in industry. The application of
AB  - genetic techniques to improve the phage-resistance of starter cultures
AB  - for dairy fermentations has been intensively studied for the last 20
AB  - years to a point where this approach now has significant potential to
AB  - alleviate the problem. This paper highlights the recent findings and
AB  - developments that have been described in the literature that will have
AB  - an impact on improvement of the phage-resistance of starter cultures.
ER  -

TY  - JOUR
AU  - Coffey, A.
AU  - Stokes, D.
AU  - Fitzgerald, G.F.
AU  - Ross, R.P.
TI  - Traditional and molecular approaches to improving bacteriophage resistance of Cheddar and Mozzarella cheese starters.
JO  - Irish J. Agr. Food Res.
PY  - 2001
SP  - 239
EP  - 270
VL  - 40
AB  - Infection by bacteriophage (bacterial viruses) during dairy fermentations remains a major
AB  - cause of starter culture failure in
AB  - Cheddar and Mozzarella manufacture, often resulting in substantial
AB  - economic losses. A variety of practical measures to alleviate the
AB  - problem of phage infection have been adopted over the years. The
AB  - application of genetic techniques to improve the phage resistance of
AB  - starter cultures for dairy fermentations is currently being explored
AB  - and this approach has significant potential to alleviate the problem.
AB  - This review highlights the significant developments that have been made
AB  - in understanding the interaction between dairy starter cultures and
AB  - bacteriophage in industry. It also describes the exploitation of
AB  - molecular methodology to genetically defend these bacteria from the
AB  - ever-present threat of bacteriophage and the scientific advances, which
AB  - formed the basis for these achievements. Attention is also given to the
AB  - development of food-grade approaches to improve genetic traits of
AB  - industrial starter strains in the context of phage resistance.
ER  -

TY  - JOUR
AU  - Coffey, B.
AU  - Ross, R.P.
AU  - O'Flynn, G.
AU  - O'Sullivan, O.
AU  - Casey, A.
AU  - Callanan, M.
AU  - Coffey, A.
AU  - McAuliffe, O.
TI  - Complete Genome Sequence of vB_EcoM_112, a T-Even-Type Bacteriophage Specific for Escherichia coli O157:H7.
JO  - Genome Announcements
PY  - 2014
SP  - e00393
EP  - e00314
VL  - 2
AB  - Bacteriophage vB_EcoM_112 (formerly e11/2) is an Escherichia coli phage with specificity for
AB  - the O157:H7 serotype. The vB_EcoM_112 genome sequence shares high
AB  - degrees of similarity with the phage T4 genome sequence.
ER  -

TY  - JOUR
AU  - Coffin, S.R.
AU  - Reich, N.O.
TI  - Escherichia coli DNA Adenine Methyltransferase THE STRUCTURAL BASIS OF PROCESSIVE CATALYSIS AND INDIRECT READ-OUT.
JO  - J. Biol. Chem.
PY  - 2009
SP  - 18390
EP  - 18400
VL  - 284
AB  - We have investigated the structural basis of processive GATC methylation by the Escherichia
AB  - coli DNA adenine methyltransferase,
AB  - which is critical in chromosome replication and mismatch repair. We
AB  - determined the contribution of the orthologically conserved phosphate
AB  - interactions involving residues Arg(95), Asn(126), Asn(132), Arg(116),
AB  - and Lys(139), which directly contact the DNA outside the cognate
AB  - recognition site (GATC) to processive catalysis, and that of residue
AB  - Arg(137), which is not conserved and contacts the DNA backbone within
AB  - the GATC sequence. Alanine substitutions at the conserved positions
AB  - have large impacts on processivity yet do not impact k(cat)/K-m(DNA) or
AB  - DNA affinity (K-D(DNA)). However, these mutants cause large preferences
AB  - for GATC sites varying in flanking sequences when considering the
AB  - pre-steady state efficiency constant k(chem)/K-D(DNA). These changes
AB  - occur mainly at the level of the methylation rate constant, which
AB  - results in the observed decreases in processive catalysis. Thus,
AB  - processivity and catalytic efficiency (k(cat)/K-m(DNA)) are uncoupled
AB  - in these mutants. These results reveal that the binding energy involved
AB  - in DNA recognition contributes to the assembly of the active site
AB  - rather than tight binding. Furthermore, the conserved residues
AB  - (Arg(95), Asn(126), Asn(132), and Arg(116)) repress the modulation of
AB  - the response of the enzyme to flanking sequence effects. Processivity
AB  - impacted mutants do not show substrate-induced dimerization as is
AB  - observed for the wild type enzyme. This study describes the structural
AB  - means by which an enzyme that does not completely enclose its substrate
AB  - has evolved to achieve processive catalysis, and how interactions with
AB  - DNA flanking the recognition site alter this processivity.
ER  -

TY  - JOUR
AU  - Coffin, S.R.
AU  - Reich, N.O.
TI  - Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.
JO  - J. Biol. Chem.
PY  - 2008
SP  - 20106
EP  - 20116
VL  - 283
AB  - Escherichia coli DNA adenine methyltransferase (EcoDam) methylates the N-6 position of the
AB  - adenine in the sequence 5'-GATC-3' and plays vital
AB  - roles in gene regulation, mismatch repair, and DNA replication. It
AB  - remains unclear how the small number of critical GATC sites involved in
AB  - the regulation of replication and gene expression are differentially
AB  - methylated, whereas the similar to 20,000 GATCs important for mismatch
AB  - repair and dispersed throughout the genome are extensively methylated.
AB  - Our prior work, limited to the pap regulon, showed that methylation
AB  - efficiency is controlled by sequences immediately flanking the GATC
AB  - sites. We extend these studies to include GATC sites involved in
AB  - diverse gene regulatory and DNA replication pathways as well as sites
AB  - previously shown to undergo differential in vivo methylation but whose
AB  - function remains to be assigned. EcoDam shows no change in affinity
AB  - with variations in flanking sequences derived from these sources, but
AB  - methylation kinetics varied 12-fold. A-tracts immediately adjacent to
AB  - the GATC site contribute significantly to these differences in
AB  - methylation kinetics. Interestingly, only when the poly(A) is located
AB  - 5' of the GATC are the changes in methylation kinetics revealed.
AB  - Preferential methylation is obscured when two GATC sites are positioned
AB  - on the same DNA molecule, unless both sites are surrounded by large
AB  - amounts of nonspecific DNA. Thus, facilitated diffusion and sequences
AB  - immediately flanking target sites contribute to higher order
AB  - specificity for EcoDam; we suggest that the diverse biological roles of
AB  - the enzyme are in part regulated by these two factors, which may be
AB  - important for other enzymes that sequence-specifically modify DNA.
ER  -

TY  - JOUR
AU  - Coffin, S.R.
AU  - Reich, N.O.
TI  - Escherichia coli DNA Adenine Methyltransferase: Intrasite Processivity and Substrate-Induced Dimerization and Activation.
JO  - Biochemistry
PY  - 2009
SP  - 7399
EP  - 7410
VL  - 48
AB  - Methylation of GATC sites in Escherichia coli by DNA adenine methyltransferase (EcoDam) is
AB  - essential for proper DNA replication
AB  - timing, gene regulation, and mismatch repair. The low cellular
AB  - concentration of EcoDam and the high number of GATC sites in the genome
AB  - (similar to 20000) Support the reliance on methylation
AB  - efficiency-enhancing strategies such as extensive intersite
AB  - processivity. Here, we present evidence that EcoDam has evolved other
AB  - unique mechanisms of activation not commonly observed with
AB  - restriction-modification methyltransferases, EcoDam dimerizes oil
AB  - short, synthetic DNA, resulting in enhanced catalysis; however,
AB  - dimerization is not observed on large genomic DNA where the potential
AB  - for intersite processive methylation precludes any
AB  - dimerization-dependent activation. An activated form of the enzyme is
AB  - apparent on large genomic DNA and can also be achieved with high
AB  - concentrations of short, synthetic substrates. We suggest that this
AB  - activation is inherent on polymeric DNA where either multiple GATC
AB  - sites are available for methylation or the partitioning of the enzyme
AB  - onto nonspecific DNA is favored. Unlike other restriction-modification
AB  - methyltransferases, EcoDam carries out intrasite processive catalysis
AB  - whereby the enzyme-DNA complex methylates both strands of an
AB  - unmethylated GATC site prior to dissociation From the DNA. This occurs
AB  - with short 21 bp oligonucleotides and is highly dependent upon salt
AB  - concentrations. Kinetic modeling which invokes enzyme activation by
AB  - both dimerization and excess substrate provides mechanistic insights
AB  - into key regulatory checkpoints for an enzyme involved in multiple,
AB  - diverse biological pathways.
ER  -

TY  - JOUR
AU  - Coffman, G.L.
AU  - Gaubatz, J.W.
AU  - Yielding, K.L.
AU  - Yielding, L.W.
TI  - Demonstration of specific high affinity binding sites in plasmid DNA by photoaffinity labeling with an ethidium analog.
JO  - J. Biol. Chem.
PY  - 1982
SP  - 13205
EP  - 13207
VL  - 257
AB  - We have used photoaffinity labeling of pBR322 DNA with
AB  - 8-azido-3-amino-5ethyl-6-phenylphenanthridinium chloride to demonstrate high affinity ethidium
AB  - binding sites. Plasmid equilibrated with as little as 1 drug/DNA molecule was photoactivated,
AB  - freed of uncomplexed drug by ethanol precipitation, and subjected to restriction analysis.
AB  - There was highly specific, rather than random blockage of HhaI sites (d(GCGC))at low drug
AB  - concentrations. Furthermore, the same 7 new digestion fragments were generated at drug to
AB  - nucleotide ratios ranging from 1:100 to 1:8000. All the new DNA fragments had chain lengths
AB  - greater than the largest HhaI fragment (393 base pairs). At higher ligand concentrations
AB  - closely approximating those needed for equilibrium binding studies, detection of the high
AB  - affinity sites was greatly masked. Drug binding to HhaI restriction fragments which had been
AB  - prepared prior to the action of drug did not induce new bands. Furthermore, the larger DNA
AB  - fragments from drug labeled plasmid were resistant to HhaI digestion over a wide range of
AB  - enzyme concentrations. These findings suggest that ligand binding can be highly selective even
AB  - between sites which have the same tetranucleotide sequence. Therefore, selective drug binding
AB  - must be dictated not only by local base sequence preference, but also by other long range
AB  - parameters.
ER  -

TY  - JOUR
AU  - Cohen, H.M.
AU  - Griffiths, A.D.
AU  - Tawfik, D.S.
AU  - Loakes, D.
TI  - Determinants of cofactor binding to DNA methyltransferases: insights from a systematic series of structural variants of  S-adenosylhomocysteine.
JO  - Org. Biomol. Chem.
PY  - 2005
SP  - 152
EP  - 161
VL  - 3
AB  - S-Adenosylmethionine (AdoMet) is a commonly used cofactor, second only to ATP in the variety
AB  - of reactions in which it participates. It is the
AB  - methyl donor in the majority of methyl transfer reactions, including
AB  - methylation of DNA, RNA, proteins and small molecules. Almost all
AB  - structurally characterised methyltransferases share a conserved
AB  - AdoMet-dependent methyltransferase fold, in which AdoMet is bound in
AB  - the same orientation. Although potential interactions between the
AB  - cofactor and methyltransferases have been inferred from crystal
AB  - structures, there has not been a systematic study of the contributions
AB  - of each functional group to binding. To explore the binding interaction
AB  - we synthesised a series of seven analogues of the methyltransferase
AB  - inhibitor S-adenosylhomocysteine (AdoHcy), each containing a single
AB  - modi cation, and tested them for the ability to inhibit methylation by
AB  - HhaI and HaeIII DNA methyltransferase. Comparison of the K-i values
AB  - highlights the structural determinants for cofactor binding, and
AB  - indicates which nucleoside and amino acid functional groups contribute
AB  - significantly to AdoMet binding. An understanding of the binding of
AB  - AdoHyc to methyltransferases will greatly assist the design of AdoMet
AB  - inhibitors.
ER  -

TY  - JOUR
AU  - Cohen, H.M.
AU  - Tawfik, D.S.
AU  - Griffiths, A.D.
TI  - Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization.
JO  - Protein Eng. Des. Sel.
PY  - 2004
SP  - 3
EP  - 11
VL  - 17
AB  - Engineering the specificity of DNA-modifying enzymes has proven extremely challenging, as
AB  - sequence recognition by these enzymes is poorly understood.  Here we used directed evolution
AB  - to generate a variant of HaeIII methyltransferase that efficiently methylates a novel target
AB  - site.  M.HaeIII methylates the internal cytosine of the canonical sequence GGCC, but there is
AB  - promiscuous methylation of a variety of non-canonical sites, notably AGCC, at a reduced rate.
AB  - Using in vitro compartmentalization, libraries of M.HaeIII genes were selected for the ability
AB  - to efficiently methylate AGCC.  A two-step mutagenesis strategy, involving initial
AB  - randomization of DNA-contracting residues followed by randomization of the loop that lies
AB  - behind these residues, yielded a mutant with a 670-fold improvement in catalytic efficiency
AB  - (kcat/KmDNA) using AGCC and a preference for AGCC over GGCC.  The mutant methylates three
AB  - sites efficiently (AGCC, CGCC and GGCC).  Indeed, it methylates CGCC slightly more efficiently
AB  - than AGCC.  However, the mutant discriminates against other non-canonical sites, including
AB  - TGCC, as effectively as the wild-type enzyme.  This study provides a rate example of a
AB  - laboratory-evolved enzyme whose catalytic efficiency surpasses that of the wild-type enzyme
AB  - with the principal substrate.
ER  -

TY  - JOUR
AU  - Cohen, H.M.
AU  - Tawfik, D.S.
AU  - Griffiths, A.D.
TI  - Promiscuous methylation of non-canonical DNA sites by HaeIII methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3880
EP  - 3885
VL  - 30
AB  - The cytosine C5 methyltransferase M.HaeIII recognises and methylates the central cytosine of
AB  - its canonical site GGCC. Here we report that M.HaeIII can also, with lower efficiency,
AB  - methylate cytosines located in a wide range of non-canonical sequences. Using bisulphite
AB  - sequencing we mapped the methyl-cytosine residues in DNA methylated in vitro and in vivo by
AB  - M.HaeIII. Methyl-cytosine residues were observed in multiple sequence contexts, most commonly,
AB  - but not exclusively, at star sites (sites differing by a single base from the canonical
AB  - sequence). The most frequently used star sites had changes at positions 1 and 4, but there is
AB  - little or no methylation at star sites changed at position 2. The rate of methylation of
AB  - non-canonical sites can be quite significant: a DNA substrate lacking a canonical site was
AB  - methylated by M.HaeIII in vitro at a rate only an order of magnitude slower than an otherwise
AB  - identical substrate containing the canonical site. In vivo methylation of non-canonical sites
AB  - may therefore be significant and may have provided the starting point for the evolution of
AB  - restriction-modification systems with novel sequence specificities.
ER  -

TY  - JOUR
AU  - Cohen, M.F.
AU  - Hu, P.
AU  - Nguyen, M.V.
AU  - Kamennaya, N.
AU  - Brown, N.
AU  - Woyke, T.
AU  - Kyrpides, N.
AU  - Holman, H.Y.
AU  - Torok, T.
TI  - Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1.
JO  - Genome Announcements
PY  - 2015
SP  - e00646
EP  - e00615
VL  - 3
AB  - We present the genome of the cellulose-degrading Cellulomonas sp. strain FA1 isolated from an
AB  - actively serpentinizing highly alkaline spring. Knowledge of
AB  - this genome will enable studies into the molecular basis of plant material
AB  - degradation in alkaline environments and inform the development of lignocellulose
AB  - bioprocessing procedures for biofuel production.
ER  -

TY  - JOUR
AU  - Cohen, N.R.
AU  - Ross, C.A.
AU  - Jain, S.
AU  - Shapiro, R.S.
AU  - Gutierrez, A.
AU  - Belenky, P.
AU  - Li, H.
AU  - Collins, J.J.
TI  - A role for the bacterial GATC methylome in antibiotic stress survival.
JO  - Nat. Genet.
PY  - 2016
SP  - 581
EP  - 586
VL  - 48
AB  - Antibiotic resistance is an increasingly serious public health threat. Understanding pathways
AB  - allowing bacteria to survive antibiotic stress may unveil
AB  - new therapeutic targets. We explore the role of the bacterial epigenome in
AB  - antibiotic stress survival using classical genetic tools and single-molecule
AB  - real-time sequencing to characterize genomic methylation kinetics. We find that
AB  - Escherichia coli survival under antibiotic pressure is severely compromised
AB  - without adenine methylation at GATC sites. Although the adenine methylome remains
AB  - stable during drug stress, without GATC methylation, methyl-dependent mismatch
AB  - repair (MMR) is deleterious and, fueled by the drug-induced error-prone
AB  - polymerase Pol IV, overwhelms cells with toxic DNA breaks. In multiple E. coli
AB  - strains, including pathogenic and drug-resistant clinical isolates, DNA adenine
AB  - methyltransferase deficiency potentiates antibiotics from the beta-lactam and
AB  - quinolone classes. This work indicates that the GATC methylome provides
AB  - structural support for bacterial survival during antibiotic stress and suggests
AB  - targeting bacterial DNA methylation as a viable approach to enhancing antibiotic
AB  - activity.
ER  -

TY  - JOUR
AU  - Cohen-Gihon, I.
AU  - Israeli, O.
AU  - Beth-Din, A.
AU  - Levy, H.
AU  - Cohen, O.
AU  - Shafferman, A.
AU  - Zvi, A.
AU  - Chitlaru, T.
TI  - Whole-Genome Sequencing of the Nonproteolytic Bacillus anthracis V770-NP1-R Strain Reveals Multiple Mutations in Peptidase Loci.
JO  - Genome Announcements
PY  - 2014
SP  - e00075
EP  - e00014
VL  - 2
AB  - We report the draft whole-genome sequence of the nonproteolytic Bacillus anthracis V770-NP1-R
AB  - strain. Compared to those of other B. anthracis strains, the
AB  - genome exhibits unique mutations in multiple targets potentially affecting
AB  - proteolytic functions. One of these mutations is a deletion that disrupts the
AB  - NprR quorum-sensing regulator of the NprA protease.
ER  -

TY  - JOUR
AU  - Cohen-Karni, D.
AU  - Xu, D.
AU  - Apone, L.
AU  - Fomenkov, A.
AU  - Sun, Z.Y.
AU  - Davis, P.J.
AU  - Kinney, S.R.M.
AU  - Yamada-Mabuchi, M.
AU  - Xu, S.Y.
AU  - Davis, T.
AU  - Pradhan, S.
AU  - Roberts, R.J.
AU  - Zheng, Y.
TI  - The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 11040
EP  - 11045
VL  - 108
AB  - MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed
AB  - distance away from the modification site. Here, we
AB  - present the biochemical characterization of several MspJI homologs,
AB  - including FspEI, LpnPI, AspBHI, RlaI, and SgrTI. All of the enzymes
AB  - specifically recognize cytosine C5 modification (methylation or
AB  - hydroxymethylation) in DNA and cleave at a constant distance
AB  - (N-12/N-16) away from the modified cytosine. Each displays its own
AB  - sequence context preference, favoring different nucleotides flanking
AB  - the modified cytosine. By cleaving on both sides of fully modified CpG
AB  - sites, they allow the extraction of 32-base long fragments around the
AB  - modified sites from the genomic DNA. These enzymes provide powerful
AB  - tools for direct interrogation of the epigenome. For example, we show
AB  - that RlaI, an enzyme that prefers (m)CWG but not (m)CpG sites,
AB  - generates digestion patterns that differ between plant and mammalian
AB  - genomic DNA, highlighting the difference between their epigenomic
AB  - patterns. In addition, we demonstrate that deep sequencing of the
AB  - digested DNA fragments generated from these enzymes provides a feasible
AB  - method to map the modified sites in the genome. Altogether, the MspJI
AB  - family of enzymes represent appealing tools of choice for method
AB  - development in DNA epigenetic studies.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Alexiev, A.
AU  - Wallis, C.
AU  - O'Flynn, C.
AU  - Deusch, O.
AU  - Davis, I.
AU  - Horsfall, A.
AU  - Kirkwood, N.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Harris, S.
AU  - Darling, A.E.
TI  - Draft genome sequences of 26 porphyromonas strains isolated from the canine oral  microbiome.
JO  - Genome Announcements
PY  - 2015
SP  - e00187
EP  - e00115
VL  - 3
AB  - We present the draft genome sequences for 26 strains of Porphyromonas (P. canoris, P. gulae,
AB  - P. cangingavalis, P. macacae, and 7 unidentified) and an
AB  - unidentified member of the Porphyromonadaceae family. All of these strains were
AB  - isolated from the canine oral cavity, from dogs with and without early
AB  - periodontal disease.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Badger, J.H.
AU  - Forberger, H.C.
AU  - Riggs, F.
AU  - Madupu, R.
AU  - Fedorova, N.
AU  - Ward, N.
AU  - Robb, F.T.
AU  - Eisen, J.A.
TI  - Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12.
JO  - Genome Announcements
PY  - 2014
SP  - e00109
EP  - e00114
VL  - 2
AB  - Here, we present the complete genome of the extreme thermophile, Dictyoglomus thermophilum
AB  - H-6-12 (phylum Dictyoglomi), which consists of 1,959,987 bp.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Benardini, J.N.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft.
JO  - Genome Announcements
PY  - 2015
SP  - e01360
EP  - e01315
VL  - 3
AB  - Here, we present the draft genome of Bacillus safensis JPL-MERTA-8-2, a strain found in a
AB  - spacecraft assembly cleanroom before launch of the Mars Exploration
AB  - Rovers. The assembly contains 3,671,133 bp in 14 contigs.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Doctor, J.I.
AU  - Lang, J.M.
AU  - Darling, A.E.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2013
SP  - e00172
EP  - e00113
VL  - 1
AB  - Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum
AB  - Actinobacteria, isolated from a restaurant chair cushion. The assembly
AB  - contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado.
JO  - Genome Announcements
PY  - 2015
SP  - e00856
EP  - e00815
VL  - 3
AB  - Here, we present the draft genome of Porphyrobacter mercurialis strain Coronado,  the proposed
AB  - type strain for this species. The assembly contains 3,482,341 bp in
AB  - 10 contigs.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Adams, J.Y.
TI  - Additional Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients.
JO  - Genome Announcements
PY  - 2016
SP  - e01614
EP  - e01615
VL  - 4
AB  - We present the draft genome sequences of eight uropathogenic strains of Escherichia coli
AB  - isolated from blood cultures collected from patients with
AB  - sepsis, an extension of previous sequencing work from the same cohort.
ER  -

TY  - JOUR
AU  - Coil, D.A.
AU  - Lo, J.R.
AU  - Chen, R.
AU  - Ward, N.
AU  - Robb, F.T.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis  Strain DSM 11915.
JO  - Genome Announcements
PY  - 2013
SP  - e00953
EP  - e00913
VL  - 1
AB  - Here we present the draft genome sequence of Chrysiogenes arsenatis strain DSM 11915, only the
AB  - second genome sequence from the phylum Chrysiogenetes. This
AB  - strictly anaerobic organism was isolated from arsenic-contaminated gold mine
AB  - wastewater and respires arsenate or nitrate instead of oxygen. The assembly
AB  - contains 2,824,977 bp in 22 scaffolds.
ER  -

TY  - JOUR
AU  - Coker, O.O.
AU  - Regmi, S.M.
AU  - Suriyaphol, P.
AU  - Chininmanu, K.
AU  - Prammananan, T.
AU  - Chaiprasert, A.
TI  - Whole-Genome Sequence of a Multidrug-Resistant Mycobacterium tuberculosis Beijing Sequence Type 10 Isolate from an Outbreak in Thailand.
JO  - Genome Announcements
PY  - 2014
SP  - e00803
EP  - e00814
VL  - 2
AB  - Infections with the Beijing family of Mycobacterium tuberculosis occur worldwide  and are
AB  - endemic in Asian countries. We present the draft genome sequence of
AB  - DS6701, a multidrug-resistant M. tuberculosis Beijing strain of sequence type 10.
AB  - The isolate is a representative of strains isolated from a multidrug-resistant
AB  - tuberculosis outbreak in Thailand.
ER  -

TY  - JOUR
AU  - Col, B.
AU  - Ozkeserli, Z.
AU  - Kumar, D.
AU  - Ozdag, H.
AU  - Alakoc, Y.D.
TI  - Genome Sequence of the Boron-Tolerant and -Requiring Bacterium Bacillus boroniphilus.
JO  - Genome Announcements
PY  - 2014
SP  - e00935
EP  - e00913
VL  - 2
AB  - Bacillus boroniphilus is a highly boron-tolerant bacterium that also requires this element for
AB  - its growth. The complete genome sequence of B. boroniphilus was
AB  - determined by a combination of shotgun sequencing and paired-end sequencing using
AB  - 454 pyrosequencing technology. A total of 84,872,624 reads from shotgun
AB  - sequencing and a total of 194,092,510 reads from paired-end sequencing were
AB  - assembled using Newbler 2.3. The estimated size of the draft genome is 5.2 Mb.
ER  -

TY  - JOUR
AU  - Colaco, C.
AU  - Sen, S.
AU  - Thangavelu, M.
AU  - Pinder, S.
AU  - Roser, B.
TI  - Extraordinary stability of enzymes dried in trehalose: simplified molecular biology.
JO  - Biotechnology
PY  - 1992
SP  - 1007
EP  - 1011
VL  - 10
AB  - We show that extremely fragile biomolecules such as DNA restriction and modifying enzymes can
AB  - be dried in vitro in the presence of trehalose with no loss of activity, even after prolonged
AB  - storage. A remarkable and unexpected property of the dried enzyme preparations is their
AB  - ability to withstand prolonged exposure to temperatures as high as +70oC. This stability is
AB  - unique to trehalose and is not found with other sugars irrespective of their physical or
AB  - chemical properties. The immediate significance of these observations is the ability to
AB  - convert enzymes used in molecular biology into stable reagents. The indefinite stability and
AB  - high temperature tolerance of these dried enzymes should permit the design of convenient
AB  - formats that may be of particular significance in the automation of genome mapping and
AB  - sequencing projects. The stabilization of a wide range of biomolecules by trehalose also has
AB  - practical implications for a number of areas ranging from basic science, through health care
AB  - and agriculture, to bio-electronics.
ER  -

TY  - JOUR
AU  - Colandene, J.D.
AU  - Topal, M.D.
TI  - The domain organization of NaeI endonuclease: Separation of binding and catalysis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 3531
EP  - 3536
VL  - 95
AB  - NaeI is a remarkable type II restriction endonuclease.  It must bind two recognition sequences
AB  - to cleave DNA, forms a covalent protein-DNA intermediate, and is only 1 aa change away from
AB  - topoisomerase and recombinase activity.  The latter activities apparently derive from
AB  - reactivation of a cryptic DNA ligase active site.  Here, we demonstrate that NaeI has two
AB  - protease-resistant domains, involving approximately the N-terminal and C-terminal halves of
AB  - the protein, linked by a protease-accessible region of 30 aa.  The domains were purified by
AB  - cloning.  The C-terminal domain was shown by gel mobility-shift assay to have approximately
AB  - 8-fold lower DNA-binding ability than intact NaeI.  Analytical ultracentrifugation showed this
AB  - domain to be a monomer in solution.  The N-terminal domain, which contains the catalytic
AB  - region defined by random mutagenesis, do not bind DNA and was a mixture of different-sized
AB  - complexes in solution implying that it mediates self-association.  DNA greatly inhibited
AB  - proteolysis of the linker region.  The results identify the DNA-binding domain, imply that DNA
AB  - cleavage and recognition are independent and separable, and lead us to speculate about a
AB  - cleft-like structure for NaeI.
ER  -

TY  - JOUR
AU  - Colandene, J.D.
AU  - Topal, M.D.
TI  - Evidence for mutations that break communication between the Endo and Topo domains in NaeI endonuclease/topoisomerase.
JO  - Biochemistry
PY  - 2000
SP  - 13703
EP  - 13707
VL  - 2000
AB  - NaeI is a type IIe endonuclease that interacts with two DNA recognition sequences to cleave
AB  - DNA. One DNA sequence serves as a substrate and the other serves to activate cleavage. NaeI is
AB  - divided into two domains whose structures parallel the two functionalities recognized in NaeI,
AB  - endonuclease and topoisomerase. In this study, we report evidence for mutations that break
AB  - interdomain functional communication in a NaeI-DNA complex. Deletion of the initial 124 amino
AB  - acids of the N-terminal domain of NaeI converted NaeI to a monomer, consistent with
AB  - self-association being mediated by the Endo domain.  Deletions within a small region of the
AB  - C-terminal DNA binding domain of NaeI (amino acids 182-192) altered the recognition by NaeI of
AB  - sequences flanking the NaeI recognition sequence. Substituting Ala for Arg182 within this
AB  - region had no apparent effect on DNA binding but greatly reduced the extent of DNA cleavage
AB  - even though it is not part of the catalytic Endo domain. Substituting Ala for Ile185 reduced
AB  - the extent of DNA binding about 1000-fold. Substituting Ala for Lys189 altered flanking
AB  - sequence recognition.  Residues 182-192 are away from the Endo domain responsible for cleavage
AB  - and also face away from the modeled DNA binding faces of the apoprotein crystal structure. We
AB  - propose that residues 182-192 are part of a web that mediates the flow of information between
AB  - the NaeI Endo and Topo domains.
ER  -

TY  - JOUR
AU  - Colasanti, J.
AU  - Sundaresan, V.
TI  - Cytosine methylated DNA synthesized by Taq polymerase used to assay methylation sensitivity of restriction endonuclease HinfI.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 391
EP  - 394
VL  - 19
AB  - We have studied the resistance of cytosine methylated DNA to digestion by the
AB  - restriction endonuclease HinfI, using a simple PCR procedure to synthesize DNA
AB  - of known sequence in which every cytosine is methylated at the 5 position.  We
AB  - find that HinfI cannot digest cytosine methylated DNA at the concentrations
AB  - normally used in restriction digests.  Complete digestion is possible using a
AB  - vast excess of enzyme; under these conditions, the rate of HinfI digestion for
AB  - cytosine methylated DNA is at least 1440-fold slower than for unmethylated DNA.
AB  - The presence of an additional methylated cytosine at the degenerate position
AB  - internal to the recognition sequence does not appear to increase the resistance
AB  - to HinfI digestion.  We also tested HhaII, an isoschizomer of HinfI, and found
AB  - that it is completely inactive on cytosine methylated DNA.  The procedure we
AB  - have used should be of general applicability in determination of the
AB  - methylation sensitivities of other restriction enzymes, as well as studies of
AB  - the effects of methylation on gene expression in direct DNA transfer
AB  - experiments.
ER  -

TY  - JOUR
AU  - Colavecchio, A.
AU  - Leo, V.
AU  - Zaccheo, S.
AU  - Jeukens, J.
AU  - Emond-Rheault, J.G.
AU  - Hamel, J.
AU  - Kukavica-Ibrulj, I.
AU  - Levesque, R.C.
AU  - Goodridge, L.
TI  - Whole-Genome Sequencing of Lactobacillus Species from Two Commercial Probiotic Products.
JO  - Genome Announcements
PY  - 2017
SP  - e01279
EP  - e01217
VL  - 5
AB  - Eight Lactobacillus strains, each intrinsically resistant to an antibiotic, were  isolated
AB  - from two commercial probiotic products. Whole-genome sequencing
AB  - identified two efflux transporters, a multidrug and extrusion protein (MATE)
AB  - efflux transporter, and LmrCD, which may contribute to their intrinsic antibiotic
AB  - resistance and may therefore facilitate their survival in the intestinal
AB  - microbiota following antibiotic therapy.
ER  -

TY  - JOUR
AU  - Cole, S.T. et al.
TI  - Massive gene decay in the leprosy bacillus.
JO  - Nature
PY  - 2001
SP  - 1007
EP  - 1011
VL  - 409
AB  - Leprosy, a chronic human neurological disease, results from infection with the obligate
AB  - intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus.
AB  - Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted
AB  - every effort at culture in the laboratory.  Comparing the 3.27-megabase genome sequence of an
AB  - armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium
AB  - tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme
AB  - case of reductive evolution.  Less than half of the genome contains functional genes but
AB  - pseudogenes, with intact counterparts in M. tuberculosis, abound.  Genome downsizing and the
AB  - current mosaic arrangement appear to have resulted from extensive recombination events between
AB  - dispersed repetitive sequences.  Gene deletion and decay have eliminated many important
AB  - metabolic activities including siderophore production, part of the oxidative and most of the
AB  - microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their
AB  - regulatory circuits.
ER  -

TY  - JOUR
AU  - Cole, S.T. et al.
TI  - Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
JO  - Nature
PY  - 1998
SP  - 537
EP  - 544
VL  - 393
AB  - Countless millions of people have died from tuberculosis, a chronic infectious disease caused
AB  - by the tubercle bacillus.  The complete genome sequence of the best-characterized strain of
AB  - Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our
AB  - understanding of the biology of this slow-growing pathogen and to help the conception of new
AB  - prophylactic and therapeutic interventions.  The genome comprises 4,411,529 base pairs,
AB  - contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected
AB  - in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other
AB  - bacteria in that a very large portion of its coding capacity is devoted to the production of
AB  - enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich
AB  - proteins with a repetitive structure that may represent a source of antigenic variation.
ER  -

TY  - JOUR
AU  - Coleman, M.L.
AU  - Sullivan, M.B.
AU  - Martiny, A.C.
AU  - Steglich, C.
AU  - Barry, K.
AU  - Delong, E.F.
AU  - Chisholm, S.W.
TI  - Genomic islands and the ecology and evolution of Prochlorococcus.
JO  - Science
PY  - 2006
SP  - 1768
EP  - 1770
VL  - 311
AB  - Prochlorococcus ecotypes are a useful system for exploring the origin and function of
AB  - diversity among closely related microbes. The genetic
AB  - variability between phenotypically distinct strains that differ by less
AB  - that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands.
AB  - Island genes appear to have been acquired in part by phage-mediated
AB  - lateral gene transfer, and some are differentially expressed under light
AB  - and nutrient stress. Furthermore, genome fragments directly recovered from
AB  - ocean ecosystems indicate that these islands are variable among
AB  - cooccurring Prochlorococcus cells. Genomic islands in this free-living
AB  - photoautotroph share features with pathogenicity islands of parasitic
AB  - bacteria, suggesting a general mechanism for niche differentiation in
AB  - microbial species.
ER  -

TY  - JOUR
AU  - Coleman, N.V. et al.
TI  - Genome sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3399
EP  - 3400
VL  - 193
AB  - Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and
AB  - energy sources, and is of interest for bioremediation and
AB  - biocatalysis. Sequencing the complete genome of JS614 provides insight
AB  - into the genetic basis of alkene oxidation, supports ongoing research into
AB  - the physiology and biochemistry of growth on ethene and VC, and provides
AB  - biomarkers to facilitate detection of VC/ethene-oxidizers in the
AB  - environment. This is the first genome sequence from the genus
AB  - Nocardioides, and the first genome of a VC/ethene-oxidizing bacterium.
ER  -

TY  - JOUR
AU  - Colleaux, L.
AU  - d'Auriol, L.
AU  - Betermier, M.
AU  - Cottarel, G.
AU  - Jacquier, A.
AU  - Galibert, F.
AU  - Dujon, B.
TI  - Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease.
JO  - Cell
PY  - 1986
SP  - 521
EP  - 533
VL  - 44
AB  - The intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (r1 intron)
AB  - possesses a 235 codon long internal open reading frame (r1 ORF) whose translation product
AB  - determines the duplicative transposition of that intron during crosses between intron-plus
AB  - strains (omega+) and intron-minus ones (omega-). Using site-directed mutagenesis, we have
AB  - constructed a universal code equivalent of the r1 ORF that, under appropriate promoter
AB  - control, allows the overexpression in E. coli of a protein identical to the mitochondrial
AB  - intron encoded "transposase". This protein exhibits a double strand endonuclease activity
AB  - specific for the omega site. This finding demonstrates, for the first time, the enzymatic
AB  - activity of an intron encoded protein whose function is to promote the spreading of that
AB  - intron by generating double strand breaks at a specific sequence within a gene.
ER  -

TY  - JOUR
AU  - Colleaux, L.
AU  - D'Auriol, L.
AU  - Galibert, F.
AU  - Dujon, B.
TI  - Recognition and cleavage site of the intron-encoded omega transposase.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1988
SP  - 6022
EP  - 6026
VL  - 85
AB  - The optional group I intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae
AB  - contains a 235-codon-long open reading frame the translation product of which (the omega
AB  - transposase) catalyzes the formation of a double-strand break within the intron-minus (omega-)
AB  - copies of the same gene. Purified omega transposase generates in vitro a 4-base-pair staggered
AB  - cut with 3' hydroxyl overhangs at the extact position where the intron eventually inserts in
AB  - the gene. Using randomly mutagenized synthetic olitonucleotides, single-base mutants were
AB  - produced at 21 positions around the cleavage site. Experiments with these oligonucleotides
AB  - show that the recognition site extends over an 18-base pair-long sequence within which minimal
AB  - sequence degeneracy is tolerated. The intron-encoded omega transposase is, therefore, one of
AB  - the most specific restriction endonucleases known to date.
ER  -

TY  - JOUR
AU  - Colleaux, L.
AU  - Michel-Wolwertz, M.-R.
AU  - Matagne, R.F.
AU  - Dujon, B.
TI  - The apocytochrome b gene of Chlamydomonas smithii contains a mobile intron related to both Saccharomyces and Neurospora introns.
JO  - Mol. Gen. Genet.
PY  - 1990
SP  - 288
EP  - 296
VL  - 223
AB  - The mitochondrial DNA of the two interfertile algal species Chlamydomonas smithii and
AB  - Chlamydomonas reinhardtii are co-linear with the exception of ca. 1 kb insertion (the alpha
AB  - insert) present in C. smithii DNA only. In vegetative diploids resulting from interspecific
AB  - crosses, mitochondrial genomes are transmitted biparentally except for the alpha insert which
AB  - is transmitted to all C. reinhardtii molecules in a manner reminiscent of the intron-mediated
AB  - conversion event that occurs at the omega locus in yeast mitochondria, under the action of the
AB  - I-SceI endonuclease. Here we report that the alpha insert corresponds to a typical group I
AB  - intron of 1075 bp, inserted within the gene for apocytochrome b and containing a 237 codon
AB  - open reading frame (ORF). We also report the complete sequence of the apocytochrome b gene of
AB  - C. smithii. Comparison with the sequence of the same gene in C. reinhardtii reveals the
AB  - precise intron insertion site. These data, together with the previous genetic data provide the
AB  - first example of intron mobility in mitochondria of the plant kingdom. The product of the
AB  - intronic ORF shows 36% amino acid identity with the I-SceI endonuclease whereas the intron
AB  - ribozyme shows a 60% identity at the nucleotide level with the Neurospora crassa cob 1 intron.
AB  - The possibility of a recent horizontal transfer of introns between fungi and algae is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Collier, D.A.
AU  - Thuong, N.T.
AU  - Helene, C.
TI  - Sequence-specific bifunctional DNA ligands based on triple-helix-forming oligonucleotides inhibit restriction enzyme cleavage under physiological conditions.
JO  - J. Am. Chem. Soc.
PY  - 1991
SP  - 1457
EP  - 1458
VL  - 113
AB  - Intermolecular triplex formation has been demonstrated to inhibit DNA-protein
AB  - interactions by the observation that selective binding of a third strand of DNA
AB  - at the recognition site of restriction/modification enzymes prevents cleavage
AB  - or methylation of the duplex.  Triplex formation has the potential to precisely
AB  - modulate gene expression if targeted at protein binding sites involved in the
AB  - regulation of a specific gene.  Intermolecular triplex formation occurs by
AB  - binding of a homopyrimidine oligonucleotide to the major grrove of a
AB  - homopurine-homopyrimidine stretch of DNA, parallel to the purine strand.
AB  - Sequence specificity results from Hoogsteen pairing between thymine and
AB  - protonated cytosine in the third pyrimidine strand and the Watson-Crick A.T and
AB  - G.C pairs of the duplex, respectively.
ER  -

TY  - JOUR
AU  - Collier, G.B.
TI  - Regulation of intracellular S-adenosyl-L-methionine as a strategy for cloning restriction endonucleases.
JO  - Diss. Abstr.
PY  - 1995
SP  - 73B
EP  - 73B
VL  - 56
AB  - Available strategies to clone restriction endonucleases (REs) are dependent on selection of
AB  - the cognate DNA methyltransferase (Mtase), which are closely linked to the REs.  These
AB  - strategies are indirect and less successful at cloning REs.  Therefore, a novel RE cloning
AB  - strategy was conceived, proposed and developed.  This novel strategy is based on modulating
AB  - the intracellular S-adenosyl-L-methionine (AdoMet) levels.  DNA Mtases require the methyl
AB  - cofactor AdoMet to effect DNA methylation.  By reducing the intracellular AdoMet levels, the
AB  - DNA Mtase is unable to effect DNA methylation.  Restriction endonucleases are present only
AB  - with their cognate DNA methyltransferases to protect the host chromosomal DNA from degradation
AB  - by its own expressed RE genes.  Under reduced levels of AdoMet the DNA Mtase is rendered
AB  - ineffective and the RE will degrade the chromosomal DNA.  To reduce the intracellular AdoMet
AB  - concentrations, several strategies were considered and bacteriophage T3
AB  - S-adenosyl-L-methionine hydrolase (SAMase) was found to be useful for the development of this
AB  - system.  To tightly control the expression of SAMase a novel expression system based on the
AB  - TN10 tetracycline regulation, inducible with heated chlortetracycline, was developed.  The
AB  - effect of SAMase in this system was first optimized by using a cloned M.BamHII (BamHII Mtase)
AB  - to develop conditions to prevent methylation of this plasmid.  This in vivo reduction in DNA
AB  - methylation provides opportunities for cellular studies involved with DNA methylation.  Since
AB  - REs generate double stranded DNA breaks when the DNA is unprotected by the cognate DNA Mtase,
AB  - a system was developed to monitor and assay for these breaks.  A chromosomal
AB  - dinD1::beta-galactosidase promotor gene fusion, induced by double stranded DNA breaks, was P1
AB  - transduced into an appropriate E. coli host.  The tetracycline regulon controlled SAMase was
AB  - supplied on plasmid pACYC184 and the compatible (colE1 replicon) RM.EcoRI plasmid pRI13 was
AB  - also present.  Inducing the expression of SAMase caused the dinD1 promotor to express the
AB  - fused beta-galactosidase, suggesting that the cell was experiencing DNA double strand breaks
AB  - due to the active RE, since the DNA Mtase was affected by reduction of the level of AdoMet.
AB  - This data suggests that this novel cloning strategy is feasible.
ER  -

TY  - JOUR
AU  - Collier, G.B.
AU  - Mattson, T.L.
AU  - Connaughton, J.F.
AU  - Kalloss, W.D.
TI  - Development of a novel screening system for cloning restriction endonucleases.
JO  - FASEB J.
PY  - 1993
SP  - A1303
EP  - A1303
VL  - 7
AB  - We have developed a novel screening system for the cloning of prokaryotic restriction
AB  - endonucleases. This system differs from existing strategies, since it is a screen for the
AB  - restriction endonuclease. Present restriction endonuclease cloning strategies are dependent on
AB  - screening or selecting for the cognate methyltransferase. The cognate methyltransferase
AB  - appears to be necessary to prevent cellular death due to enzymatic cleavage of the host
AB  - chromosomal DNA. This cloning strategy is dependent on modulating the intracellular levels of
AB  - S-adenosyl-L-methionine, the biological methyl donor used by DNA methyltransferases. In the
AB  - presence of a functional restriction endonuclease structural gene and limiting levels of
AB  - S-adenosyl-L-methionine the chromosomal DNA is not methylated but is cleaved, causing cellular
AB  - death or the induction of the SOS response. The methodology of modulating
AB  - S-adenosyl-L-methionine has further application to other cellular phenomena.
ER  -

TY  - JOUR
AU  - Collier, J.
AU  - McAdams, H.H.
AU  - Shapiro, L.
TI  - A DNA methylation ratchet governs progression through a bacterial cell cycle.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 17111
EP  - 17116
VL  - 104
AB  - The Caulobacter cell cycle is driven by a cascade of transient regulators, starting with the
AB  - expression of DnaA in G(1) and ending with the
AB  - expression of the essential CcrM DNA methyltransferase at the completion
AB  - of DNA replication. The timing of DnaA accumulation was found to be
AB  - regulated by the methylation state of the dnaA promoter, which in turn
AB  - depends on the chromosomal position of dnaA near the origin of replication
AB  - and restriction of CcrM synthesis to the end of the cell cycle. The dnaA
AB  - gene is preferentially transcribed from a fully methylated promoter. DnaA
AB  - initiates DNA replication and activates the transcription of the next
AB  - cell-cycle regulator, GcrA. With the passage of the replication fork, the
AB  - dnaA promoter becomes hemimethylated, and DnaA accumulation drops. GcrA
AB  - then activates the transcription of the next cell-cycle regulator, CtrA,
AB  - once the replication fork passes through the ctrA P1 promoter, generating
AB  - two hemimethylated copies of ctrA. The ctrA gene is preferentially
AB  - transcribed from a hemimethylated promoter. CtrA then activates the
AB  - transcription of ccrM, to bring the newly replicated chromosome to the
AB  - fully methylated state, promoting dnaA transcription and the start of a
AB  - new cell cycle. We show that the cell-cycle timing of CcrM is critical for
AB  - Caulobacter fitness. The sequential changes in the chromosomal methylation
AB  - state serve to couple the progression of DNA replication to cell-cycle
AB  - events regulated by the master transcriptional regulatory cascade, thus
AB  - providing a ratchet mechanism for robust cell-cycle control.
ER  -

TY  - JOUR
AU  - Collin, B.
AU  - Pinnell, L.J.
AU  - Tallman, J.J.
AU  - Turner, J.W.
TI  - Draft Genome Sequences of One Marine and One Clinical Vibrio parahaemolyticus Strain, Both Isolated in Sweden.
JO  - Genome Announcements
PY  - 2016
SP  - e01196
EP  - e01116
VL  - 4
AB  - Vibrio parahaemolyticus is the leading bacterial pathogen associated with seafood consumption.
AB  - Here, we report the draft genome sequences of one marine and one
AB  - clinical strain, both isolated in Sweden. These sequences will inform future
AB  - comparative analysis of V. parahaemolyticus in northern Europe.
ER  -

TY  - JOUR
AU  - Collingro, A.
AU  - Kostanjsek, R.
AU  - Toenshoff, E.R.
AU  - Schulz, F.
AU  - Schuster, L.
AU  - Domann, D.
AU  - Horn, M.
TI  - Draft Genome Sequence of 'Candidatus Hepatoplasma crinochetorum' Ps, a Bacterial  Symbiont in the Hepatopancreas of the Terrestrial Isopod Porcellio scaber.
JO  - Genome Announcements
PY  - 2015
SP  - e00674
EP  - e00615
VL  - 3
AB  - 'Candidatus Hepatoplasma crinochetorum' Ps is an extracellular symbiont residing  in the
AB  - hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is
AB  - highly similar to that of the close relative 'Ca. Hepatoplasma crinochetorum' Av
AB  - from Armadillidium vulgare. However, instead of a clustered regularly interspaced
AB  - short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction
AB  - modification system.
ER  -

TY  - JOUR
AU  - Collingro, A.
AU  - Tischler, P.
AU  - Weinmaier, T.
AU  - Penz, T.
AU  - Heinz, E.
AU  - Brunham, R.C.
AU  - Read, T.D.
AU  - Bavoil, P.M.
AU  - Sachse, K.
AU  - Kahane, S.
AU  - Friedman, M.G.
AU  - Rattei, T.
AU  - Myers, G.S.A.
AU  - Horn, M.
TI  - Unity in variety -- the pan-genome of the Chlamydiae.
JO  - Mol. Biol. Evol.
PY  - 2011
SP  - 3253
EP  - 3270
VL  - 28
AB  - Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic
AB  - host cells.  They include important human pathogens such as Chlamydia trachomatis as well as
AB  - symbionts of protozoa.  As these bacteria are experimentally challenging and genetically
AB  - intractable, our knowledge about them is still limited.  In this study, we obtained the genome
AB  - sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99 and Parachlamydia
AB  - acanthamoebae UV-7.  This enabled us to perform the first comprehensive comparative and
AB  - phylogenomic analysis of representative members of four major families of the Chlamydiae,
AB  - including the Chlamydiaceae.  We identifid a surprisingly large core gene set present in all
AB  - genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily
AB  - infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV
AB  - secretion system.  In S. negevensis, the type IV secretion system is encoded on a large
AB  - conjugative plasmid (pSn, 132 kb).  Phylogenetic analyses suggested that a plasmid similar to
AB  - the S. negevensis plasmid was originally acquired by the lst common ancestor of all four
AB  - families and that it was subsequently reduced, integrated into the chromosome, or lost during
AB  - diversification, ultimately giving rise to the extant virulence-associated plasmid of
AB  - pathogenic chlamydiae.  Other virulence factors, including a type III secretion system, are
AB  - conserved among the Chlamydiae to variable degrees, and together with differences in the
AB  - composition of the cell wall, reflect adaptation to different host cells including convergent
AB  - evolution among the four chlamydial families.  Phylogenomic analysis focusing on chlamydial
AB  - proteins with homology to plant proteins provided evidence for the aquisition of 53 chlamydial
AB  - genes by a plant progenitor, lending further support for the hypothesis of an early
AB  - interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
ER  -

TY  - JOUR
AU  - Collins, A.J.
AU  - Nyholm, S.V.
TI  - Draft genome of Phaeobacter gallaeciensis ANG1, a dominant member of the accessory nidamental gland of Euprymna scolopes.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3397
EP  - 3398
VL  - 193
AB  - Phaeobacter gallaeciensis strain ANG1 represents the dominant member of the bacterial
AB  - consortium within the reproductive accessory nidamental
AB  - gland (ANG) of the squid Euprymna scolopes. We present a 4.59Mb assembly
AB  - of its genome, which may provide clues as to how it benefits its host.
ER  -

TY  - JOUR
AU  - Collins, C.
AU  - Kowalski, C.
AU  - Zebrowski, J.
AU  - Tulchinskaya, Y.
AU  - Tai, A.K.
AU  - James-Pederson, M.
AU  - Hirst, R.
TI  - Draft Genome Sequence of Methylobacterium sp. Strain ARG-1 Isolated from the White-Rot Fungus Armillaria gallica.
JO  - Genome Announcements
PY  - 2016
SP  - e00398
EP  - e00316
VL  - 4
AB  - Methylobacterium sp. strain ARG-1 was isolated from a cell culture of hyphal tips of the
AB  - white-rot fungus Armillaria gallica We describe here the sequencing,
AB  - assembly, and annotation of its genome, confirming the presence of genes involved
AB  - in methylotrophy. This is the first genome announcement of a strain of
AB  - Methylobacterium associated with A. gallica.
ER  -

TY  - JOUR
AU  - Collins, E.B.
TI  - Host-controlled variations in bacteriophages active against lactic Streptococci.
JO  - Virology
PY  - 1956
SP  - 261
EP  - 271
VL  - 2
AB  - Certain bacteriophages were very active against some strains of Streptococcus
AB  - cremoris, and restricted in activity against others.  Drastic changes in
AB  - activity were observed after one growth cycle.  The results of adsorption of a
AB  - restricted bacteriophage was either no detected consequence, bacterial death,
AB  - or bacterial death followed by bacteriophage reproduction.  The occurrence of
AB  - each of the last two possibilities was found to be influenced by the
AB  - multiplicity of infection.  Bacteriophage reproduction within the fruitful
AB  - cells of a restrictive host produced progeny that were fully active on the
AB  - cells of that host.  Alteration of the bacteriophgaes appeared limited to
AB  - changes in virulence for particular hosts, the alterations not being
AB  - accompanied by changes in adsorbability or changes in heat resistance.  Both
AB  - the strain of infecting bacteriophage and the particular host were important
AB  - factors in determining the specific virulence of the progeny.
ER  -

TY  - JOUR
AU  - Collins, J.
AU  - Mayer, H.
TI  - Restriction endonucleases or the site-specific DNA endonucleases.
JO  - Arzneimittelforschung
PY  - 1980
SP  - 541
EP  - 547
VL  - 30
AB  - Our present view of the site-specific endonucleases, which appear to be
AB  - ubiquituous in the prokaryote kingdom, is probably heavily distorted by our
AB  - search for tools for recombinant DNA technology.  Only those enzymes having
AB  - recognition sequences in the range of three to seven specific bases have been
AB  - isolated.  Of course the usefulness of these enzymes in the analysis of complex
AB  - genomes, the rise of "reverse genetics", and the immediate breakthroughs in the
AB  - area of gene expression in eukaryotes, particularly the understanding of tumour
AB  - virus RNA processing and gene rearrangements in the expression of
AB  - immunoglobulin genes has dominated the consciousness of the molecular and
AB  - cell-biologists during the last five years.  There is great diversity of
AB  - staggering, symmetry, asymmetry and degeneration in the recognition sequences
AB  - found.  Taking into account also the genetic data on site-specific
AB  - recombination and/or DNA degradation suggests that our present collection of
AB  - endonucleases may only represent a narrow spectrum of specificities on an
AB  - open-ended scale of complexity.  The enzymes themselves provide a rich pool to
AB  - be exploited by the biophysicist and the biochemist to probe the subtleties of
AB  - DNA-protein interaction.
ER  -

TY  - JOUR
AU  - Collins, R.E.
AU  - Rocap, G.
TI  - REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - W58
EP  - W62
VL  - 35
AB  - Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widespread technique
AB  - for rapidly fingerprinting microbial communities.
AB  - Users of T-RFLP frequently overlook the resolving power of well-chosen
AB  - restriction endonucleases and often fail to report how they chose their
AB  - enzymes. REPK (Restriction Endonuclease Picker) assists in the rational
AB  - choice of restriction endonucleases for T-RFLP by finding sets of four
AB  - restriction endonucleases that together uniquely differentiate
AB  - user-designated sequence groups. With REPK, users can provide their own
AB  - sequences (of any gene, not just 16S rRNA), specify the taxonomic rank of
AB  - interest and choose from a number of filtering options to further narrow
AB  - down the enzyme selection. Bug tracking is provided, and the source code
AB  - is open and accessible under the GNU Public License v.2, at
AB  - http://code.google.com/p/repk. The web server is available without access
AB  - restrictions at http://rocaplab.ocean.washington.edu/tools/repk.
ER  -

TY  - JOUR
AU  - Collyn, F.
AU  - Billault, A.
AU  - Mullet, C.
AU  - Simonet, M.
AU  - Marceau, M.
TI  - YAPI, a new Yersinia pseudotuberculosis pathogenicity island.
JO  - Infect. Immun.
PY  - 2004
SP  - 4784
EP  - 4790
VL  - 72
AB  - Pathogenicity islands (PAIs) are chromosomal clusters of pathogen-specific virulence genes
AB  - often found at tRNA loci. In the
AB  - Yersinia pseudotuberculosis 32777 chromosome, we characterized a 98-kb
AB  - segment that has all of the characteristic features of a PAI, including
AB  - insertion in a (phenylalanine) tRNA gene, the presence of a
AB  - bacteriophage-like integrase-encoding gene, and direct repeats at the
AB  - integration sites. The G+C content of the segment ranges from 31 to
AB  - 60%, reflecting a genetic mosaic: this is consistent with the notion
AB  - that the sequences were horizontally acquired. The PAI, termed YAPI
AB  - (for Yersinia adhesion pathogenicity island), carries 95 open reading
AB  - frames and includes (i) the previously described pil operon, encoding a
AB  - type IV pilus that contributes to pathogenicity (F. Collyn et al.,
AB  - Infect. Immun. 70:6196-6205, 2002); (ii) a block of genes potentially
AB  - involved in general metabolism; (iii) a gene cluster for a
AB  - restriction-modification system; and (iv) a large number of mobile
AB  - genetic elements. Furthermore, the PAI can excise itself from the
AB  - chromosome at low frequency and in a precise manner, and deletion does
AB  - not result in a significant decrease of bacterial virulence compared to
AB  - inactivation of the fimbrial gene cluster alone. The prevalence and
AB  - size of the PAI vary from one Y. pseudotuberculosis strain to another,
AB  - and it can be found integrated into either of the two phe tRNA loci
AB  - present on the species' chromosome. YAPI was not detected in the genome
AB  - of the genetically closely related species Y. pestis, whereas a
AB  - homologous PAI is harbored by the Y. enterocolitica chromosome.
ER  -

TY  - JOUR
AU  - Colson, A.M.
AU  - Colson, C.
TI  - Expression of the Escherichia coli K, B and Phage P1 DNA host specificities in Salmonella typhimurium.
JO  - J. Gen. Microbiol.
PY  - 1972
SP  - 123
EP  - 128
VL  - 70
AB  - The Escherichia coli K,B and phage P1 host specificity genes (hsp) were
AB  - introduced into Salmonella typhimurium by means of E. coli Hfr x S. typhimurium
AB  - F- crosses.  The three systems were found to govern modification and
AB  - restriction of phages P22 and L.  The restriction coefficients were comparable
AB  - to that of lambda for the PI system and were lower (about 100) for the K and B
AB  - systems.  Phage grown on hspK+ and hspB+ recombinants was restricted by S.
AB  - typhimurium independently of the restriction governed by the LT system.  This
AB  - observation suggested that S. typhimurium possesses a previously undetected hsp
AB  - locus allelic to those of E. coli K and B.
ER  -

TY  - JOUR
AU  - Colson, A.M.
AU  - Colson, C.
AU  - Van Pel, A.
TI  - Host-controlled restriction mutants of Salmonella typhimurium.
JO  - J. Gen. Microbiol.
PY  - 1969
SP  - 57
EP  - 64
VL  - 58
AB  - Forty-eight independent restriction-deficient mutations of Salmonella typhimurium LT2 were
AB  - isolated by using selective and non-selective methods.  With phage P22 it was shown that some
AB  - mutations affected the restriction capacity only, while others affected both restriction and
AB  - modification.  The host-restriction of S. typhimurium decreased the recovery of F-lac+
AB  - infected cells and decreased the yield of recombinants in bacterial mating and in phage
AB  - P22-mediated transduction.
ER  -

TY  - JOUR
AU  - Colson, C.
TI  - Genetics of R-M systems in Salmonella.
JO  - Heredity
PY  - 1978
SP  - 123
EP  - 123
VL  - 41
AB  - Salmonella typhimurium LT2 and LT7 have three R-M systems coded by chromosomal genes.  Mutants
AB  - with r-m+ and r-m- phenotypes have been isolated for each of them.  All three were first
AB  - detected in Escherichia coli-S. typhimurium hybrids.  System LT was detected when phage P22
AB  - from lac+ hybrids between E. coli Hfr and S. typhimurium LT7 mut (with a mutator gene) was
AB  - plated on wild-type S. typhimurium.  All mutations affecting system LT are closely linked and
AB  - situated between proA and proC.  System LT is present in the many Salmonella serotypes tested,
AB  - with the exception of S. typhi.  System SA was first observed using hybrids with the hsdK
AB  - genes of E. coli: phage L. (closely related to P22) from such hybrids underwent restriction in
AB  - wild-type S. typhimurium, independently of the presence of system LT.  hsdSA is situated
AB  - between pyrB and serB and was first thought to be the Salmonella allele of hsdK and hsdB in E.
AB  - coli.  System SA was found in all S. typhimurium strains tested, but not in other Salmonella
AB  - serotypes.
ER  -

TY  - JOUR
AU  - Colson, C.
AU  - Colson, A.M.
TI  - A new Salmonella typhimurium DNA host specificity.
JO  - J. Gen. Microbiol.
PY  - 1971
SP  - 345
EP  - 351
VL  - 69
AB  - The genetic properties of a new (hspS) host specificity of Salmonella
AB  - typhimurium were investigated using bacteriophage L.  Phage L is a better
AB  - substrate for S-specific restriction than phage P22.  Mutants deficient in
AB  - S-restriction only were found at the same frequency as mutants deficient in
AB  - both restriction and modification.  Crosses between S. typhimurium Hfr and S.
AB  - typhimurium F- or between Escherichia coli and S. typhimurium showed that the S
AB  - system has the same chromosomal location as the K system of E. coli.  The S
AB  - system was introduced in E. coli and found to be effective on phage lambda.
ER  -

TY  - JOUR
AU  - Colson, C.
AU  - Colson, A.M.
AU  - van Pel, A.
TI  - Chromosomal location of host specificity in Salmonella typhimurium.
JO  - J. Gen. Microbiol.
PY  - 1970
SP  - 265
EP  - 271
VL  - 60
AB  - The chromosomal location of the genes for host specificity in Salmonella
AB  - typhimurium has been investigated by F-mediated conjugation using host
AB  - specificity mutants isolated previously.  It was found that the sites of
AB  - mutations leading to two distinct phenotypes r-LTm+LT and r-LTm-LT, are closely
AB  - linked to each other and are located near the marker proC.
ER  -

TY  - JOUR
AU  - Colson, C.
AU  - Glover, S.W.
AU  - Symonds, N.
AU  - Stacey, K.A.
TI  - The location of the genes for host-controlled modification and restriction in Escherichia coli K-12.
JO  - Genetics
PY  - 1965
SP  - 1043
EP  - 1050
VL  - 52
AB  - Recent experiments have clarified certain aspects of the processes of
AB  - modification and restriction by which certain systems of host-controlled
AB  - modification (HCM) operate in Escherichia coli (Arber 1962; Arber and Dussoix
AB  - 1962; Dussoix and Arber 1962; Glover, Schell, Symonds and Stacey 1963).  The
AB  - two aspects of HCM have one thing in common:  they both involve the recognition
AB  - of a particular base sequence in DNA.  However, basically they are very
AB  - different, modification resulting in the addition of certain groups to DNA,
AB  - while restriction leaves unmodified DNA in a condition in which it is open to
AB  - attack by DNase.  This apparent dissimilarity in the processes of restriction
AB  - and modification suggests that they are under independent genetic control.  One
AB  - method of learning more about the genetic control of HCM in this system is to
AB  - analyze it genetically.
ER  -

TY  - JOUR
AU  - Colson, C.
AU  - van Pel, A.
TI  - DNA restriction and modification systems in Salmonella.  I.  SA and SB, two Salmonella typhimurium systems determined by genes with a chromosomal location comparable to that of the Escherichia coli hsd genes.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 325
EP  - 337
VL  - 129
AB  - Haploid hybrids between Salmonella typhimurium Hfr and Escherichia coli F-
AB  - exercise two additive types of restriction and modification (SA and SB) on
AB  - phage lambda.  System SA had been detected previously in S. typhimurium with
AB  - phage L.  Independent mutants in the SA and SB systems were isolated.  P22- and
AB  - P1-mediated transductions in S. typhimurium and in hybrids established that the
AB  - genes governing these systems are independent but linked and situated
AB  - counter-clockwise of ser B on the map, in the order:  pyrB-hsdSA-hsdSB-serB.
ER  -

TY  - JOUR
AU  - Colston, M.J.
AU  - Davis, E.O.
TI  - Homologous recombination, DNA repair and mycobacterial recA genes.
JO  - Tuberculosis: Pathogenesis, Protection, and Control
PY  - 1994
SP  - 217
EP  - 226
VL  - 0
AB  - Bacterial responses to DNA damage are highly conserved.  One system, the
AB  - SOS response, involves the coordinately induced expression of over 20 genes through a
AB  - common regulatory mechanism.  The RecA protein, found in most bacteria, plays a central
AB  - role in the regulation of the SOS response.  In addition to its regulatory function, this
AB  - protein also mediates genetic recombination and DNA repair.  Virtually nothing is known
AB  - about these systems in mycobacteria.  However, since some mycobacteria are intracellular
AB  - pathogens and many of the mechanisms involved in macrophage killing of such pathogens
AB  - require the production of DNA-damaging agents such as peroxide and nitric oxide, DNA
AB  - repair mechanisms are likely to be particularly important for mycobacterial survival.  In
AB  - addition, homologous genetic recombination, a process mediated by RecA, is an important
AB  - technique for the genetic manipulation of bacteria and could play an important role in our
AB  - understanding of gene function.  In this chapter we discuss the mechanisms involved in
AB  - homologous recombination and DNA repair, what is known about these systems in
AB  - mycobacteria, and recent information on the unusual structure of the recA gene in the
AB  - pathogenic mycobacteria.
ER  -

TY  - JOUR
AU  - Colston, S.M.
AU  - Ellis, G.A.
AU  - Kim, S.
AU  - Wijesekera, H.W.
AU  - Leary, D.H.
AU  - Lin, B.
AU  - Kirkup, B.C.
AU  - Hervey, W.J. IV
AU  - Vora, G.J.
TI  - Complete Genome Sequences of Two Bioluminescent Vibrio campbellii Strains Isolated from Biofouling Communities in the Bay of Bengal.
JO  - Genome Announcements
PY  - 2018
SP  - e00422
EP  - e00418
VL  - 6
AB  - Vibrio campbellii is a pathogen of aquatic animals and has been proposed as a bacterial
AB  - partner in the formation of bioluminescent milky seas. We present here
AB  - the complete genome sequences assembled from Illumina and Oxford Nanopore data
AB  - for two bioluminescent Vibrio campbellii strains (BoB-53 and BoB-90) isolated
AB  - from biofouled moorings in the Bay of Bengal.
ER  -

TY  - JOUR
AU  - Colston, S.M.
AU  - Navarro, A.
AU  - Martinez-Murcia, A.J.
AU  - Graf, J.
TI  - Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474(T), Isolated from a Cavern Brook in the Moravia Region of the Czech Republic.
JO  - Genome Announcements
PY  - 2018
SP  - e00227
EP  - e00218
VL  - 6
AB  - Species of the Aeromonas genus can be found in numerous environmental milieus, including
AB  - various water sources, and some species cause disease in animals. We
AB  - present here the draft genome sequence for Aeromonas cavernicola DSM 24474(T), a
AB  - novel species isolated from a freshwater brook within a cavern in the Czech
AB  - Republic.
ER  -

TY  - JOUR
AU  - Colston, S.M.
AU  - Navarro, A.
AU  - Martinez-Murcia, A.J.
AU  - Graf, J.
TI  - Draft Genome Sequence of Aeromonas lusitana sp. nov. Strain DSM 24905(T), Isolated from a Hot Spring in Vila-Real, Portugal.
JO  - Genome Announcements
PY  - 2018
SP  - e00226
EP  - e00218
VL  - 6
AB  - Aeromonas lusitana sp. nov. is an isolate derived from a study aimed at characterizing
AB  - Aeromonas spp. from water sources used for recreation and
AB  - agricultural purposes and assessing the implications these organisms have for
AB  - human and animal health. We present here the 4.52-Mbp draft genome sequence of
AB  - this novel species.
ER  -

TY  - JOUR
AU  - Comai, L.
AU  - Young, K.
AU  - Till, B.J.
AU  - Reynolds, S.
AU  - Greene, E.A.
AU  - Codomo, C.A.
AU  - Enns, L.
AU  - Johnson, J.E.
AU  - Burtner, C.
AU  - Odden, A.
AU  - Henikoff, S.
TI  - Efficient discovery of DNA polymorphisms in natural populations by Ecotilling.
JO  - Plant J.
PY  - 2004
SP  - 778
EP  - 786
VL  - 37
AB  - We have adapted the mutation detection technology used in Targeting Induced Local Lesions in
AB  - Genomes (TILLING) to the discovery of polymorphisms in natural populations.  The genomic DNA
AB  - of a queried individual is mixed with a references DNA and used to amplify a target 1-kbp
AB  - region of DNA with asymmetrically labeled fluorescent primers.  Afer heating and annealing,
AB  - heteroduplexes are nicked at mismatched sites by the endonuclease CEL I and cut strands are
AB  - visualized using Li-cor gel analyzers.  Putative polymorphisms detected in one fluorescence
AB  - channel can be verified by appearance of the opposite cut strand in the other channel.  We
AB  - demonstrated the efficiency of this technology, called Ecotilling, by the discovery in 150+
AB  - individuals of 55 haplotypes in five genes, ranging from sequences differing by a single
AB  - nucleotide polymorphism to those representing complex haplotypes in five genes, ranging from
AB  - sequences differing by a single nucleotide polymorphism to those representing complex
AB  - haplotypes.  The discovered polymorphisms were confirmed by sequencing and included base-pair
AB  - changes, small insertions and deletions, and variation in microsatellite repeat number.
AB  - Ecotilling allows the rapid detection of variation in many individuals and is cost effective
AB  - because only one individual for each haplotype needs to be sequenced.  The technology is
AB  - applicable to any organism including those that are heterozygous and polyploid.
ER  -

TY  - JOUR
AU  - Comandatore, F.
AU  - Gaibani, P.
AU  - Ambretti, S.
AU  - Landini, M.P.
AU  - Daffonchio, D.
AU  - Marone, P.
AU  - Sambri, V.
AU  - Bandi, C.
AU  - Sassera, D.
TI  - Draft Genome of Klebsiella pneumoniae Sequence Type 512, a Multidrug-Resistant Strain Isolated during a Recent KPC Outbreak in Italy.
JO  - Genome Announcements
PY  - 2013
SP  - e00035
EP  - e00012
VL  - 1
AB  - Here, we present the draft genome sequence of Klebsiella pneumoniae subsp. pneumoniae sequence
AB  - type 512 (ST512) isolated during a KPC-producer outbreak. This strain is resistant to
AB  - beta-lactams, cephalosporins, fluoroquinolones, aminoglycosides, macrolides, tetracyclines,
AB  - and carbapenems but susceptible to colistin. The ST512-K30BO genome is composed of 289 contigs
AB  - for 5,392,844 bp with 56.9% G+C content.
ER  -

TY  - JOUR
AU  - Comandatore, F.
AU  - Sassera, D.
AU  - Ambretti, S.
AU  - Landini, M.P.
AU  - Daffonchio, D.
AU  - Marone, P.
AU  - Sambri, V.
AU  - Bandi, C.
AU  - Gaibani, P.
TI  - Draft Genome Sequences of Two Multidrug Resistant Klebsiella pneumoniae ST258 Isolates Resistant to Colistin.
JO  - Genome Announcements
PY  - 2013
SP  - e00113
EP  - e00112
VL  - 1
AB  - Sequence type 258 (ST258) is the most widespread multidrug resistant (MDR) Klebsiella
AB  - pneumoniae strain worldwide. Here, we report the draft genome sequences of two
AB  - colistin-resistant MDR K. pneumoniae ST258 clinical strains isolated from hospital patients in
AB  - Italy. These strains are resistant to beta-lactams, cephalosporins, fluoroquinolones,
AB  - aminoglycosides, macrolides, tetracyclines, carbapenems, and colistin.
ER  -

TY  - JOUR
AU  - Comstock, L.R.
AU  - Rajski, S.R.
TI  - Methyltransferase-directed DNA strand scission.
JO  - J. Am. Chem. Soc.
PY  - 2005
SP  - 14136
EP  - 14137
VL  - 127
AB  - The study of prokaryotic DNA methyltransferases (MTases) has provided significant insight into
AB  - eukaryotic MTases and the important role that methylation plays in mammalian biology.  The
AB  - prokaryotic enzymes M.TaqI, M.EcoRI, and M.HhaI are all capable of using 5'-aziridine
AB  - adenylate 1 in place of (S)-adenosyl-L-methionine in MTase-dependent DNA alkylation reactions.
AB  - By virtue of the C8 azide, 1 is significant because it is capable of converting these DNA
AB  - MTases into azidonucleoside transferases.  Not suprising, DNA modified with 1 is capable of
AB  - undergoing very efficient Staudinger ligation with biotinylated triarylphosphines.
ER  -

TY  - JOUR
AU  - Comstock, L.R.
AU  - Rajski, S.R.
TI  - Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 1644
EP  - 1652
VL  - 33
AB  - Aziridine-based cofactor mimics have been synthesized and are shown to undergo
AB  - methyltransferase-dependent DNA alkylation. Notably, each cofactor
AB  - mimic possesses an azide functionality, to which can be attached an
AB  - assortment of unnatural groups following methyltransferase-dependent DNA
AB  - delivery. DNA duplexes modified with these cofactor mimics are capable of
AB  - undergoing the Staudinger ligation with phosphines tethered to biological
AB  - functionalities following enzymatic modification. This methodology
AB  - provides a new tool by which to selectively modify DNA in a
AB  - methyltransferase-dependent way. The conversion of biological
AB  - methyltransferases into azidonucleosidyl transferases demonstrated here
AB  - also holds tremendous promise as a means of identifying, as yet, unknown
AB  - substrates of methylation.
ER  -

TY  - JOUR
AU  - Conchillo-Sole, O.
AU  - Yero, D.
AU  - Coves, X.
AU  - Huedo, P.
AU  - Martinez-Servat, S.
AU  - Daura, X.
AU  - Gibert, I.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group.
JO  - Genome Announcements
PY  - 2015
SP  - e00611
EP  - e00615
VL  - 3
AB  - We report the draft genome sequence of Stenotrophomonas maltophilia UV74, isolated from a
AB  - vascular ulcer. This draft genome sequence shall contribute to
AB  - the understanding of the evolution and pathogenicity of this species,
AB  - particularly regarding isolates of clinical origin.
ER  -

TY  - JOUR
AU  - Conlan, L.H.
AU  - Dupureur, C.M.
TI  - Dissecting the metal ion dependence of DNA binding by PvuII endonuclease.
JO  - Biochemistry
PY  - 2002
SP  - 1335
EP  - 1342
VL  - 41
AB  - Divalent cations can provide an effective means of modulating the behavior of nucleic acid
AB  - binding proteins. As a result, there is strong interest in understanding the role of metal
AB  - ions in the function of both nucleic acid binding proteins and their enzymes. We have applied
AB  - complementary fluorescence spectroscopic and nitrocellulose filter binding assays to
AB  - quantitate the role of metal ions in mediating DNA binding and sequence specificity by the
AB  - representative PvuII endonuclease. At pH 7.5 in the presence of the catalytically
AB  - nonsupportive Ca(II), this enzyme binds the PvuII target sequence with a K(d) of 50 pM. Under
AB  - strict metal-free conditions, the enzyme exhibits a K(d) of only 300 nM for the cognate
AB  - sequence, an affinity which is weak relative to those measured for other systems in the
AB  - absence of metal ions. This represents a 6000-fold increase in PvuII affinity for cognate DNA
AB  - upon the addition of Ca(II). The pH dependences of both metal ion-dependent and metal
AB  - ion-independent DNA binding are remarkably shallow throughout the physiological range; other
AB  - characterized restriction enzymes exhibit more pronounced pH dependences of DNA binding even
AB  - in the absence of metal ions. Similar measurements with noncognate sequences indicate that
AB  - divalent metal ions are not important to nonspecific DNA binding; K(d) values are
AB  - approximately 200 nM throughout the physiological pH range, a behavior shared with other
AB  - endonucleases. While some of these results extend somewhat the range of expected behavior for
AB  - restriction enzymes, these results indicate that PvuII endonuclease shares with other
AB  - characterized systems a mechanism by which cognate affinity and sequence discrimination are
AB  - most effectively achieved in the presence of divalent metal ions.
ER  -

TY  - JOUR
AU  - Conlan, L.H.
AU  - Jose, T.J.
AU  - Thornton, K.C.
AU  - Dupureur, C.M.
TI  - Modulating restriction endonuclease activities and specificities using neutral detergents.
JO  - Biotechniques
PY  - 1999
SP  - 955
EP  - 960
VL  - 27
AB  - It is well known that type II restriction enzyme activities and specificities can be modulated
AB  - by altering solution conditions. The addition of co-solvents such as dimethyl sulfoxide
AB  - (DMSO), alcohols and polyols can promote star activity, which is the cleavage of non-cognate
AB  - sequences. While neutral detergents are often used to control protein aggregation, little is
AB  - known about the effect of neutral detergents on restriction enzyme activities and
AB  - specificities. We report here that BamHI, BglI, BglII, EcoRI, EcoRV, HindIII, MluI, PvuII,
AB  - SalI and XhoI restriction endonucleases are remarkably tolerant of high concentrations of
AB  - neutral detergents, Triton X-100, CHAPS and octyl glucoside. In most cases, lambda DNA
AB  - cleavage rates were comparable to those observed in the absence of detergent. Indeed, the
AB  - specific activities of SalI and XhoI were appreciably increased in the presence of Triton
AB  - X-100. For all enzymes active in the presence of detergents, sequence specificity toward
AB  - lambda DNA was not compromised. Assays of star cleavage of pUC18 by EcoRI, PvuII and BamHI
AB  - endonucleases in equimolar concentrations of Triton X-100 and sucrose revealed reduced star
AB  - activity in the detergent relative to the sucrose co-solvent. Interestingly, under star
AB  - activity-promoting
AB  - conditions, PvuII endonuclease displayed greater fidelity in Triton X-100 than in conventional
AB  - buffer. Taken altogether, these results suggest that in some cases, neutral detergents can be
AB  - used to manipulate restriction endonuclease reaction rates and specificities.
ER  -

TY  - JOUR
AU  - Conlan, L.M.
TI  - The influence of divalent metal ions on DNA binding and cleavage by the restriction enzyme PvuII endonuclease.
JO  - Ph.D. Thesis, Texas A and M Univ., College Station, TX, USA
PY  - 2002
SP  - 143
EP  - 143
AB  - Divalent metal ions can play an important role in the interactions beween nucleic acids and
AB  - proteins.  Here, PvuII endonuclease is developed as a model system to study DNA binding and
AB  - catalysis as a function of divalent metal ions.  A novel approach of equilibrium binding and
AB  - kinetics of binding and cleavage is used to understand the influence of divalent metal ions on
AB  - DNA recognition and catalysis.  In the presence of calcium, a divalent metal ion that does not
AB  - support catalysis, the  interaction between the specific recognition site and PvuII
AB  - endonuclease has a Kd of 53 +/- 10 pM (pH 7.5, 100 mM NaCl, 10 MM CaCl2).  A 6000 fold
AB  - reduction in the dissociation constant is seen when metal ions are absent.  Specific DNA
AB  - binding interactions exhibit an unusual shallow pH dependence.  Most protein-DNA interactions
AB  - have a more pronounced pH effect.  Nonspecific DNA binding is independent of divalent metal
AB  - ions; exhibiting a Kd near 200 nM (pH 7.5, 100 mM NaCl). Kinetic methods were developed to
AB  - understand how many metal ions are involved with both DNA binding and catalysis.  This work
AB  - presents the first comprehensive kinetic study of a restriction enzyme to show that more than
AB  - one metal ion influences both the DNA cleavage and association rate constants.  Using Ca(II)
AB  - to prevent turnover, the enzyme-DNA association rate constant is metal ion concentration
AB  - dependent, exhibiting a 100 fold increase from metal-free experiments to those done in the
AB  - presence of 10 mM Ca(II).  The association rate constant exhibited cooperative binding of at
AB  - least four metal ions per PvuII endonuclease dimer.  The dissociation rate constant showed a
AB  - shallow Ca(II) concentration dependence.  This provides new evidence that the metal ion
AB  - influence on the DNA dissociation constant is due to alterations in the association rate
AB  - constant.  Hill analysis of the cleavage rate constant as a function of Mg(II) concentration,
AB  - indicates that at least three metal ions per endonuclease dimer are involved in DNA
AB  - hydrolysis.  Combining the knowledge gained from equilibrium and kinetic studies provides
AB  - unique insights on how metal ions influence DNA binding and catalysis for restriction enzymes.
ER  -

TY  - JOUR
AU  - Conlan, S. et al.
TI  - Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.
JO  - Sci. Transl. Med.
PY  - 2014
SP  - 254ra126
EP  - 254ra126
VL  - 6
AB  - Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae
AB  - species may spread resistance to carbapenems, an antibiotic
AB  - class of last resort, thereby rendering common health care-associated infections
AB  - nearly impossible to treat. To determine the diversity of carbapenemase-encoding
AB  - plasmids and assess their mobility among bacterial species, we performed
AB  - comprehensive surveillance and genomic sequencing of carbapenem-resistant
AB  - Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center
AB  - patient population and hospital environment. We isolated a repertoire of
AB  - carbapenemase-encoding Enterobacteriaceae, including multiple strains of
AB  - Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter
AB  - cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing
AB  - with full end-to-end assembly revealed that these organisms carry the carbapenem
AB  - resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacae
AB  - isolated simultaneously from a single patient harbored two different
AB  - carbapenemase-encoding plasmids, indicating that plasmid transfer between
AB  - organisms was unlikely within this patient. We did, however, find evidence of
AB  - horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E.
AB  - cloacae, and C. freundii in the hospital environment. Our data, including full
AB  - plasmid identification, challenge assumptions about horizontal gene transfer
AB  - events within patients and identify possible connections between patients and the
AB  - hospital environment. In addition, we identified a new carbapenemase-encoding
AB  - plasmid of potentially high clinical impact carried by K. pneumoniae, E. coli, E.
AB  - cloacae, and Pantoea species, in unrelated patients and in the hospital
AB  - environment.
ER  -

TY  - JOUR
AU  - Conlan, S.
AU  - Deming, C.
AU  - Tsai, Y.C.
AU  - Lau, A.F.
AU  - Dekker, J.P.
AU  - Korlach, J.
AU  - Segre, J.A.
TI  - Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci.
JO  - Genome Announcements
PY  - 2014
SP  - e01332
EP  - e01314
VL  - 2
AB  - Klebsiella pneumoniae is an important nosocomial pathogen, and multidrug-resistant strains
AB  - have become a worldwide concern. Here, we report the
AB  - complete genome of a K. pneumoniae isolate with chromosomally integrated blaKPC
AB  - genes and a colibactin synthesis locus.
ER  -

TY  - JOUR
AU  - Conlan, S.
AU  - Lau, A.F.
AU  - Palmore, T.N.
AU  - Frank, K.M.
AU  - Segre, J.A.
TI  - Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid.
JO  - Genome Announcements
PY  - 2016
SP  - e00664
EP  - e00616
VL  - 4
AB  - Here, we report the genome sequence of a blaNDM-1-positive Klebsiella pneumoniae  AATZP
AB  - isolate cultured from a perirectal surveillance swab collected upon
AB  - admission of a patient to the NIH Clinical Center in 2014. Genome sequencing of
AB  - this isolate revealed three plasmids, including one carrying the blaNDM-1 gene
AB  - encoding resistance to carbapenems.
ER  -

TY  - JOUR
AU  - Conlan, S.
AU  - Lawrence, C.
AU  - McCue, L.A.
TI  - Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes.
JO  - Appl. Environ. Microbiol.
PY  - 2005
SP  - 7442
EP  - 7452
VL  - 71
AB  - Rhodopseudomonas palustris, an alpha-proteobacterium, carries out three of the chemical
AB  - reactions that support life on this planet: the conversion of sunlight to chemical-potential
AB  - energy; the absorption of carbon dioxide, which it converts to cellular material; and the
AB  - fixation of atmospheric nitrogen into ammonia. Insight into the transcription-regulatory
AB  - network that coordinates these processes is fundamental to understanding the biology of this
AB  - versatile bacterium. With this goal in mind, we predicted regulatory signals genomewide, using
AB  - a two-step phylogenetic-footprinting and clustering process that we had developed previously.
AB  - In the first step, 4,963 putative transcription factor binding sites, upstream of 2,044 genes
AB  - and operons, were identified using cross-species Gibbs sampling. Bayesian motif clustering was
AB  - then employed to group the cross-species motifs into regulons. We have identified 101 putative
AB  - regulons in R. palustris, including 8 that are of particular interest: a photosynthetic
AB  - regulon, a flagellar regulon, an organic hydroperoxide resistance regulon, the LexA regulon,
AB  - and four regulons related to nitrogen metabolism (FixK2, NnrR, NtrC, and sigma54). In some
AB  - cases, clustering allowed us to assign functions to proteins that previously had been
AB  - annotated with only putative functions; we have identified RPA0828 as the organic
AB  - hydroperoxide resistance regulator and RPA1026 as a cell cycle methylase. In addition to
AB  - predicting regulons, we identified a novel inverted repeat that likely forms a highly
AB  - conserved stem-loop and that occurs downstream of over 100 genes.
ER  -

TY  - JOUR
AU  - Connaughton, J.F.
AU  - Kaloss, W.D.
AU  - Vanek, P.G.
AU  - Nardone, G.A.
AU  - Chirikjian, J.G.
TI  - The complete sequence of the Bacillus amyloliquefaciens proviral H2, BamHI methylase gene.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4002
EP  - 4002
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Connaughton, J.F.
AU  - Vanek, P.G.
AU  - Chirikjian, J.G.
TI  - Cloning of the BamHI methyl transferase gene from Bacillus amyloliquefaciens.
JO  - J. Cell Biol.
PY  - 1988
SP  - 535a
EP  - 535a
VL  - 107
AB  - We wish to report the initial characterization of a recombinant clone containing the BamHI
AB  - methylase gene.  Genomic chromosomal DNA purified from Bacillus amyloliquefaciens was
AB  - partially cleaved with HindIII, fractionated by size, and cloned into pSP64.  Plasmid DNA from
AB  - this library was challenged with BamHI endonuclease and transformed into E. coli HB101.  A
AB  - recombinant plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI methylase
AB  - gene based on three independent observations.  Both plasmids were found to be resistent to
AB  - BamHI endonuclease cleavage, and chromosomal DNA isolated from E. coli HB101 cells harboring
AB  - either of the plasmids pBamM6.5 or pBamM2.5 were resistant to cleavage by BamHI endonuclease.
AB  - In addition, DNA isolated from lambda phage passaged through E. coli HB101 containing either
AB  - plasmid were also resistant to BamHI cleavage.  Expression of the BamHI methylase gene is
AB  - dependent on orientation in pSP64.  In these clones preliminary evidence indicates that
AB  - methylase gene expression may be under the direction of the plasmid encoded LacZ promoter.
ER  -

TY  - JOUR
AU  - Connaughton, J.F.
AU  - Vanek, P.G.
AU  - Lee-Lin, S.-Q.
AU  - Chirikjian, J.G.
TI  - Cloning of the BamHI methyltransferase gene from Bacillus amyloliquefaciens.
JO  - Gene Anal. Tech.
PY  - 1988
SP  - 116
EP  - 124
VL  - 5
AB  - We wish to report the initial characterization of a recombinant clone
AB  - containing the BamHI methylase gene.  Genomic chromosomal DNA purified from
AB  - Bacillus amyloliquefaciens was partially cleaved with HindIII, fractionated by
AB  - size, and cloned into pSP64.  Plasmid DNA from this library was challenged with
AB  - BamHI endonuclease and transformed into Escherichia coli HB101.  A recombinant
AB  - plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI
AB  - methylase gene based on three independent observations.  Both plasmids were
AB  - found to be resistant to BamHI endonuclease cleavage, and chromosomal DNA
AB  - isolated from E. coli HB101 cells harboring either of the plasmids pBamM6.5 or
AB  - pBamM2.5 was resistant to cleavage by BamHI endonuclease.  In addition, DNA
AB  - isolated from lambda phage passaged through E. coli HB101 containing either
AB  - plasmid was also resistant to BamHI cleavage.  Expression of the BamHI
AB  - methylase gene is dependent on orientation in pSP64.  In these clones
AB  - preliminary evidence indicates that methylase gene expresion may be under the
AB  - direction of the plasmid encoded LacZ promoter.
ER  -

TY  - JOUR
AU  - Connolly, B.A.
TI  - Assay of restriction endonucleases using oligonucleotides.
JO  - Methods Mol. Biol.
PY  - 1994
SP  - 371
EP  - 383
VL  - 30
AB  - Type II restriction endonucleases cleave double-stranded DNA at sequence-specific sites
AB  - typically 4-6 bp in length. Although large DNA molecules (viral DNA, plasmid DNA, and
AB  - chromosomal DNA) are the physiological substrates for these enzymes, activity is often shown
AB  - with small synthetic oligodeoxynucleotides providing that the recognition sequence is present.
AB  - The use of oligodeoxynucleotide substrates often allows information to be obtained concerning
AB  - the mechanism by which the particular endonuclease recognizes its cognate site so specifically
AB  - and discriminates accurately against all other sequences. Excellent examples include a very
AB  - thorough study with the EcoRI endonuclease that revealed the energetic bases of its
AB  - specificity and experiments with the EcoRV endonuclease using oligodeoxynucleotides containing
AB  - modified bases that demonstrated several direct contacts between enzyme and substrate. Central
AB  - to all these experiments are methods for the assay of the activity a particular restriction
AB  - endonuclease shows toward an oligonucleotide substrate.
ER  -

TY  - JOUR
AU  - Connolly, B.A.
AU  - Eckstein, F.
AU  - Pingoud, A.
TI  - The Stereochemical Course of the Restriction Endonuclease EcoRI-catalyzed reaction.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 10760
EP  - 10763
VL  - 259
AB  - The restriction endonuclease EcoRI hydrolyzes the Rp diastereomer of
AB  - d(pGGsAATTCC), an analogue of d(pGGAATTCC) containing a chiral phosphorothioate
AB  - group at the cleavage site between the deoxyguanosine and the deoxyadenosine
AB  - residues (Connolly, B.A., Potter, B.V.L., Eckstein, F., Pingoud, A. and
AB  - Grotjahn, L. (1984) Biochemistry 23: 3343-3453).  Performing the reaction in
AB  - H2[18]O leads to d(pGG) and the hexanucleotide d([[18]O, S]pAATTCC) which has
AB  - an [18]O-containing phosphorothioate group at the 5' terminus.  Further
AB  - hydrolysis of this hexamer with nuclease P1 yields deoxyadenosine
AB  - 5'-O-[18]O)phosphorothioate which can be stereospecifically phosphorylated with
AB  - adenylate kinase and pyruvate kinase to give Sp-[18]O deoxyadenosine
AB  - 5'-O-(1-thiotriphosphate).  31P NMR spectroscopy shows the oxygen-18 in this
AB  - compound to be in a bridging position between the alpha- and beta-phosphorus
AB  - atoms.  Thus, the hydrolysis reaction catalyzed by EcoRI proceeds with
AB  - inversion of configuration at phosphorus.  This result is compatible with a
AB  - direct enzyme-catalyzed nucleophilic attack of H2O at phosphorus without
AB  - involvement of a covalent enzyme intermediate.
ER  -

TY  - JOUR
AU  - Connolly, B.A.
AU  - Potter, B.V.L.
AU  - Eckstein, F.
AU  - Pingoud, A.
AU  - Grotjahn, L.
TI  - Synthesis and characterization of an octanucleotide containing the EcoRI recognition sequence with a phosphorothioate group at the cleavage site.
JO  - Biochemistry
PY  - 1984
SP  - 3443
EP  - 3453
VL  - 23
AB  - The synthesis and characterization of an octanucleotide, d(GGsAATTCC),
AB  - containing the recognition sequence of the EcoRI restriction endonuclease with
AB  - a phosphorothioate internucleotidic linkage at the cleavage site are described.
AB  - Two approaches for the synthesis of the Rp and Sp diastereomers of this
AB  - octamer by the phosphite method are presented.  The first consists of the
AB  - addition of the sulfur instead of H2O to the phosphite at the appropriate
AB  - position during chain elongation.  This method results in a mixture of
AB  - diastereomers that can be separated by high-performance liquid chromatography
AB  - after 5'-terminal phosphorylation.  The second uses the presynthesized and
AB  - diastereomerically pure dinucleoside phosphorothioate d[Gp(S)A] for the
AB  - addition to the growing oligonucleotide chain as a block.  The products are
AB  - characterized by digestion with nuclease P1, fast atom bombardment mass
AB  - spectrometry, 31P NMR spectroscopy, and conversion to d(GGAATTCC) by
AB  - desulfurization with iodine.  Only the Rp diastereomers of d(GGsAATTCC) and its
AB  - 5'-phosphorylated derivative are cleaved by EcoRI endonuclease.  The rate of
AB  - hydrolysis is slower than that of the unmodified octamer.  The phosphorothioate
AB  - octamer will be useful for the determination of the stereochemical course of
AB  - the EcoRI-catalyzed reaction.
ER  -

TY  - JOUR
AU  - Conrad, M.
AU  - Topal, M.D.
TI  - Modified DNA fragments activate NaeI cleavage of refractory DNA sites.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5127
EP  - 5130
VL  - 20
AB  - Endonuclease NaeI cleaves DNA using a two-site mechanism. The DNA-binding sites are
AB  - nonidentical: they recognize different families of flanking sequences. A unique NaeI site that
AB  - is resistant to cleavage resides in M13 double-stranded DNA. NaeI can be activated to cleave
AB  - this site by small DNA fragments containing one or more NaeI sites. These activators are not
AB  - practical for genetic engineering because unphosphorylated activators that are consumed during
AB  - the cleavage of substrate give ends that may interfere with subsequent ligations. We show that
AB  - a DNA fragment containing phosphorothioate linkages at the NaeI scissile bonds (S-activator)
AB  - is not cleaved by NaeI, even though this S-activator binds to the substrate site. The
AB  - S-activator activates NaeI to cleave M13 DNA under conditions that completely exhaust
AB  - unsubstituted activator. These results demonstrate that activation is not coupled to cleavage
AB  - of activator, that NaeI reverts to its inactive state soon after dissociation of the EA
AB  - complex, and that S-activator makes for a nondepletable activator during prolonged
AB  - incubations.
ER  -

TY  - JOUR
AU  - Conrad, M.
AU  - Topal, M.D.
TI  - DNA and spermidine provide a switch mechanism to regulate the activity of restriction enzyme NaeI.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1989
SP  - 9707
EP  - 9711
VL  - 86
AB  - Sequence-specific DNA-protein interactions are basic to DNA function.  To
AB  - better understand these interactions, we studied the effect of position on
AB  - cleavage of DNA by the type II restriction enzyme (EC 3.1.21.4) NaeI.  We
AB  - discovered two classes of NaeI restriction sites: sites susceptible and sites
AB  - resistant to cleavage.  Kinetic analysis showed that NaeI was activated by DNA
AB  - containing cleavable NaeI sites to rapidly cleave resistant NaeI sites by a
AB  - noncompetitive mechanism with a Km for substrate DNA of about 2 nM and a KA for
AB  - activating DNA of about 6 nM; activation increased catalysis but not substrate
AB  - binding.  Deletion mutagenesis in vitro showed that sequences flanking the NaeI
AB  - recognition site were responsible for the differences between activating and
AB  - nonactivating NaeI sites.  The polyamine spermidine had a dramatic effect on
AB  - the interaction of NaeI with DNA; in the presence of 1 mM spermidine, resistant
AB  - sites were cleaved rapidly and cleavable DNA inhibited cleavage.  The direct
AB  - regulation of enzymatic activity by DNA sequences in trans, and the modulation
AB  - of this regulation by a polyamine that is sensitive to the cell cycle, provides
AB  - a regulatory switch mechanism.  The implications of this switch for biological
AB  - control functions are discussed.
ER  -

TY  - JOUR
AU  - Contreras, S.
AU  - Sagory-Zalkind, P.
AU  - Blanquart, H.
AU  - Iltis, A.
AU  - Morand, S.
TI  - Complete Genome Sequence of Vitreoscilla filiformis (ATCC 15551), Used as a Cosmetic Ingredient.
JO  - Genome Announcements
PY  - 2017
SP  - e00913
EP  - e00917
VL  - 5
AB  - We report the first complete genome sequence of a Vitreoscilla filiformis strain  (ATCC 15551)
AB  - that is used in the cosmetic industry as Vitreoscilla ferment. The
AB  - assembled genome consisted of one chromosome and two plasmids. These data will
AB  - provide valuable information and important insights into the physiology of this
AB  - filamentous organism.
ER  -

TY  - JOUR
AU  - Contreras-Castro, L.
AU  - Maldonado, L.A.
AU  - Quintana, E.T.
AU  - Raggi, L.
AU  - Sanchez-Flores, A.
TI  - Draft Genome Sequence of Two Marine Plantactinospora spp. from the Gulf of California.
JO  - Genome Announcements
PY  - 2018
SP  - e00436
EP  - e00418
VL  - 6
AB  - Plantactinospora sp. strains BB1 and BC1 were isolated in 2009 from sediment samples of the
AB  - Gulf of California from among almost 300 actinobacteria. Genome
AB  - mining of their approximately 8.5-Mb sequences showed the bioprospecting
AB  - potential of these rare actinomycetes, providing an insight to their ecological
AB  - and biotechnological importance.
ER  -

TY  - JOUR
AU  - Cook, L.E.
AU  - Gang, S.S.
AU  - Ihlan, A.
AU  - Maune, M.
AU  - Tanner, R.S.
AU  - McInerney, M.J.
AU  - Weinstock, G.
AU  - Lobos, E.A.
AU  - Gunsalus, R.P.
TI  - Genome Sequence of Acetomicrobium hydrogeniformans OS1.
JO  - Genome Announcements
PY  - 2018
SP  - e00581
EP  - e00518
VL  - 6
AB  - Acetomicrobium hydrogeniformans, an obligate anaerobe of the phylum Synergistetes, was
AB  - isolated from oil production water. It has the unusual ability
AB  - to produce almost 4 molecules H2/molecule glucose. The draft genome of A.
AB  - hydrogeniformans OS1 (DSM 22491(T)) is 2,123,925 bp, with 2,068 coding sequences
AB  - and 60 RNA genes.
ER  -

TY  - JOUR
AU  - Cook, L.J.
AU  - Cox, J.P.L.
TI  - Methylated DNA labels for marking objects.
JO  - Biotechnol. Lett.
PY  - 2003
SP  - 89
EP  - 94
VL  - 25
AB  - We recently described a method for digitally labelling objects with DNA. Here we show that,
AB  - using DNA methyltransferases to create polymorphic DNA
AB  - templates, it is possible to significantly increase the number of labels
AB  - that can be generated by this method. Nine double-stranded DNA templates
AB  - of different length were methylated with either M.HaeIII or M.AluI
AB  - methyltransferase, or both. Different mixtures of methylated and
AB  - unmethylated versions of this template set were used to 'invisibly' label
AB  - paper. The mixtures were eluted from the paper and the methylated status
AB  - of the templates in each mixture successfully determined, and the labels
AB  - read, by digestion with the complementary restriction endonuclease,
AB  - followed by a polymerase chain reaction and agarose gel electrophoresis.
AB  - One methylated DNA label was read after it had been left on paper for two
AB  - months.
ER  -

TY  - JOUR
AU  - Cook, S.N.
AU  - Jack, W.E.
AU  - Xiong, X.
AU  - Danley, L.E.
AU  - Ellman, J.A.
AU  - Schultz, P.G.
AU  - Noren, C.J.
TI  - Photochemically initiated protein splicing.
JO  - Angew. Chem. Int. Ed. Engl.
PY  - 1995
SP  - 1629
EP  - 1630
VL  - 34
AB  - Protein splicing is a post-translational rearrangement process in which an
AB  - internal polypeptide segment (intein) is excised from a primary translation product, with
AB  - concomitant ligation of the flanking polypeptides (exteins).  This process results in the
AB  - production of two protein products from a single precursor polypeptide: the intein (often a
AB  - homing endonuclease thought to initiate lateral transmission of the intein coding sequence)
AB  - and the ligated exteins.
ER  -

TY  - JOUR
AU  - Coolen, J.P.
AU  - Sjodin, A.
AU  - Maraha, B.
AU  - Hajer, G.F.
AU  - Forsman, M.
AU  - Verspui, E.
AU  - Frenay, H.M.
AU  - Notermans, D.W.
AU  - de Vries, M.C.
AU  - Reubsaet, F.A.
AU  - Paauw, A.
AU  - Roeselers, G.
TI  - Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 539
EP  - 547
VL  - 8
AB  - Francisella tularensis is a facultative intracellular bacterium in the class
AB  - Gammaproteobacteria. This strain is of interest because it is the etiologic agent
AB  - of tularemia and a highly virulent category A biothreat agent. Here we describe
AB  - the draft genome sequence and annotation of Francisella tularensis subsp.
AB  - holarctica BD11-00177, isolated from the first case of indigenous tularemia
AB  - detected in The Netherlands since 1953. Whole genome DNA sequence analysis
AB  - assigned this isolate to the genomic group B.FTNF002-00, which previously has
AB  - been exclusively reported from Spain, France, Italy, Switzerland and Germany.
AB  - Automatic annotation of the 1,813,372 bp draft genome revealed 2,103
AB  - protein-coding and 46 RNA genes.
ER  -

TY  - JOUR
AU  - Cooney, C.A.
TI  - The restriction enzyme EheI (GGC/GCC) is sensitive to CpG methylation.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3667
EP  - 3667
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Cooney, C.A.
AU  - Eykholt, R.L.
AU  - Bradbury, E.M.
TI  - Methylation is co-ordinated on the putative replication origins of Physarum ribosomal DNA.
JO  - J. Mol. Biol.
PY  - 1988
SP  - 889
EP  - 901
VL  - 204
AB  - In Physarum polycephalum, the ribosomal DNA is found as 60,000 base-pair palindromes. Each
AB  - rDNA has four symmetrically arranged replication origins flanked by ribosomal RNA genes. A
AB  - particular sequence, the putative replication origin, is repeated at the approximate position
AB  - of each origin and nowhere else in the molecule. On a typical rDNA molecule, only one origin
AB  - is active per replication cycle. We show that both the level and co-ordination of methylation
AB  - result in asymmetrically methylated rDNA molecules that are particularly hypomethylated at one
AB  - of their four putative replication origins. This pattern of methylation on a typical rDNA
AB  - molecule is consistent with a model where hypomethylation is a determinant of origin activity.
ER  -

TY  - JOUR
AU  - Cooper, A.
AU  - Koziol, A.G.
AU  - Carrillo, C.D.
AU  - Lambert, D.
TI  - Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Berta ATCC  8392 and a Nalidixic Acid-Resistant Isolate of This Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00186
EP  - e00116
VL  - 4
AB  - ITALIC! Salmonella entericasubspecies ITALIC! entericaserovar Berta has been isolated in
AB  - multiple animal species and has been implicated in human disease.
AB  - Here, we report a 4.7-Mbp draft genome sequence of ITALIC! S. entericaserovar
AB  - Berta (ATCC strain 8392) and a nalidixic acid-resistant isolate derived from this
AB  - strain.
ER  -

TY  - JOUR
AU  - Cooper, A.
AU  - Lambert, D.
AU  - Koziol, A.G.
AU  - Seyer, K.
AU  - Carrillo, C.D.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Mishmarhaemek Isolated from Bovine Feces.
JO  - Genome Announcements
PY  - 2015
SP  - e01210
EP  - e01215
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Mishmarhaemek is a Gram-negative,
AB  - non-spore-forming, rod-shaped bacterium implicated in human clinical disease. Here, we report
AB  - a 4.8-Mbp draft genome sequence of a nalidixic acid-resistant isolate of S. serovar
AB  - Mishmarhaemek.
ER  -

TY  - JOUR
AU  - Cooper, A.A.
AU  - Chen, Y.-J.
AU  - Lindorfer, M.A.
AU  - Stevens, T.H.
TI  - Protein splicing of the yeast TFP1 intervening protein sequence: a model for self-excision.
JO  - EMBO J.
PY  - 1993
SP  - 2575
EP  - 2583
VL  - 12
AB  - Protein splicing is the protein analogue of RNA splicing in which the
AB  - central portion (spacer) of a protein precursor is excised and the amino- and carboxy-
AB  - terminal portions of the precursor reconnected.  The yeast Tfp1 protein undergoes a rapid
AB  - protein splicing reaction to yield a spliced 69 kDa polypeptide and an excised 50 kDa spacer
AB  - protein.  We have demonstrated that the 69 kDa species arises by reformation of a bona fide
AB  - peptide bond.  Deletion analyses indicate that only sequences in the central spacer protein of
AB  - the Tfp1 precursor are critical for the protein splicing reaction.  A fusion protein in which
AB  - only the Tfp1 spacer domain was inserted into an unrelated protein also underwent efficient
AB  - splicing, demonstrating that all of the information required for protein splicing resides
AB  - within the spacer domain.  Alteration of Tfp1p splice junction residues blocked or
AB  - kinetically impaired protein splicing.  A protein splicing model is presented in which
AB  - asparagine rearrangement initiates the self-excision of the spacer protein from the Tfp1
AB  - precursor.  The Tfp1 spacer protein belongs to a new class of intervening sequences that
AB  - are excised at the protein rather than the RNA level.
ER  -

TY  - JOUR
AU  - Cooper, A.A.
AU  - Stevens, T.H.
TI  - Protein splicing: self-splicing of genetically mobile elements at the protein level.
JO  - Trends Biochem. Sci.
PY  - 1995
SP  - 351
EP  - 356
VL  - 20
AB  - Protein splicing is a newly discovered process that is the protein equivalent
AB  - of RNA splicing.  Protein splicing proceeds through a branched protein intermediate, and
AB  - in vitro studies indicate that the reaction is autocatalytic.  The excised 'intein' proteins
AB  - are
AB  - site-specific DNA endonucleases that catalyze genetic mobility of their DNA coding
AB  - sequence by an 'intein homing' mechanism.
ER  -

TY  - JOUR
AU  - Cooper, A.A.
AU  - Stevens, T.H.
TI  - Protein splicing: Excision of intervening sequences at the protein level.
JO  - Bioessays
PY  - 1993
SP  - 667
EP  - 674
VL  - 15
AB  - Protein splicing is an extraordinary post-translational reaction that removes
AB  - an intact central "spacer" domain (Sp) from precursor proteins (N-Sp-C) while splicing
AB  - together the N- and C-domains of the precursor, via a peptide bond, to produce a new
AB  - protein (N-C).  All of the available data on protein splicing fit a model in which these
AB  - intervening sequences excise at the protein level via a self-splicing mechanism.  Several
AB  - proteins have recently been discovered that undergo protein splicing, and in two such
AB  - cases, the excised spacer protein is an endonuclease.  Such endonucleases are capable of
AB  - conferring genetic mobility upon the intervening sequences that encodes them.  These
AB  - intervening sequences define a new family of mobile genetic elements that are translated yet
AB  - remain phenotypically silent by excising at the protein rather than the RNA level.
ER  -

TY  - JOUR
AU  - Cooper, J.E.
AU  - Feil, E.J.
TI  - The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers?
JO  - Microbiology
PY  - 2006
SP  - 1297
EP  - 1305
VL  - 152
AB  - The ability to make informed decisions on the suitability of alternative marker loci is
AB  - central for population and epidemiological investigations.
AB  - This issue was addressed using Staphylococcus aureus as a model population
AB  - by generating nucleotide sequence data from 33 gene fragments in a
AB  - representative sample of 30 strains. Supplementing the data with
AB  - pre-existing multilocus sequence typing data, an intra-species tree based
AB  - on approximately 17.8 kb of sequence was reconstructed and the goodness of
AB  - fit of each individual gene tree was computed. No strong association was
AB  - noted between gene function per se and phylogenetic reliability, but it is
AB  - suggested that candidate loci should possess at least the average degree
AB  - of nucleotide diversity for all genes in the genome. In the case of S.
AB  - aureus this threshold is >1 % mean pairwise diversity.
ER  -

TY  - JOUR
AU  - Cooper, K.K.
AU  - Cooper, M.A.
AU  - Zuccolo, A.
AU  - Law, B.
AU  - Joens, L.A.
TI  - Complete Genome Sequence of Campylobacter jejuni Strain S3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1491
EP  - 1492
VL  - 193
AB  - Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis in the world;
AB  - however, there is only one complete genome
AB  - sequence of a poultry strain to date. Here we report the complete genome
AB  - sequence and annotation of the second poultry strain, C. jejuni strain S3.
AB  - This strain has been shown to be nonmotile, to be a poor invader in vitro,
AB  - and to be a poor colonizer of poultry after minimal in vitro passage.
ER  -

TY  - JOUR
AU  - Cooper, K.K.
AU  - Mandrell, R.E.
AU  - Louie, J.W.
AU  - Korlach, J.
AU  - Clark, T.A.
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - Chain, P.S.
AU  - Ahmed, S.
AU  - Carter, M.Q.
TI  - Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates  a common evolutionary lineage with Escherichia coli O157:H7.
JO  - BMC Genomics
PY  - 2014
SP  - 17
EP  - 17
VL  - 15
AB  - BACKGROUND: Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli
AB  - (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne
AB  - illness, including hemolytic uremic syndrome have increased worldwide. In fact,
AB  - non-O157 serotypes are now estimated to cause over half of all the Shiga
AB  - toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC
AB  - infections are frequently associated with serotypes O26, O45, O103, O111, O121,
AB  - and O145. Currently, there are no complete genomes for O145 in public databases.
AB  - RESULTS: We determined the complete genome sequences of two O145 strains
AB  - (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a
AB  - Belgium ice-cream-associated outbreak (RM13516). Both strains contain one
AB  - chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514
AB  - and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes
AB  - revealed a large core (5,173 genes) and a considerable amount of strain-specific
AB  - genes. Additionally, the two EcO145 genomes display distinct chromosomal
AB  - architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and
AB  - methylation profile (methylome). Comparative analysis of EcO145 genomes to other
AB  - completely sequenced STEC and other E. coli and Shigella genomes revealed that,
AB  - unlike any other known non-O157 EHEC strain, EcO145 ascended from a common
AB  - lineage with EcO157/EcO55. This evolutionary relationship was further supported
AB  - by the pangenome analysis of the 10 EHEC str ains. Of the 4,192 EHEC core genes,
AB  - EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC
AB  - strains. CONCLUSIONS: Our data provide evidence that EcO145 and EcO157 evolved
AB  - from a common lineage, but ultimately each serotype evolves via a
AB  - lineage-independent nature to EHEC by acquisition of the core set of EHEC
AB  - virulence factors, including the genes encoding Shiga toxin and the large
AB  - virulence plasmid. The large variation between the two EcO145 genomes suggests a
AB  - distinctive evolutionary path between the two outbreak strains. The distinct
AB  - methylome between the two EcO145 strains is likely due to the presence of a
AB  - BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain
AB  - RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic
AB  - alteration in the evolution of individual EHEC strains.
ER  -

TY  - JOUR
AU  - Cooper, K.K.
AU  - Mandrell, R.E.
AU  - Louie, J.W.
AU  - Korlach, J.
AU  - Clark, T.A.
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - Chain, P.S.
AU  - Ahmed, S.
AU  - Carter, M.Q.
TI  - Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin.
JO  - Genome Announcements
PY  - 2014
SP  - e00482
EP  - e00414
VL  - 2
AB  - Escherichia coli O145:H28 strain RM12581 was isolated from bagged romaine lettuce during a
AB  - 2010 U.S. lettuce-associated outbreak. E. coli O145:H28 strain RM12761
AB  - was isolated from ice cream during a 2007 ice cream-associated outbreak in
AB  - Belgium. Here we report the complete genome sequences and annotation of both
AB  - strains.
ER  -

TY  - JOUR
AU  - Cooper, L.P.
AU  - Dryden, D.T.F.
TI  - The domains of a type I DNA methyltransferase: interactions and role in recognition of DNA methylation.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 1011
EP  - 1021
VL  - 236
AB  - The DNA methyltransferases of type I restriction-modification systems are trimeric enzymes
AB  - composed of one DNA specificity (S) subunit and two modification (M) subunits. The S subunit
AB  - contains two large regions, each of which recognizes one part of the split, asymmetrical DNA
AB  - target sequence. Each M subunit contains an amino acid motif for binding the methyl group
AB  - donor and cofactor, S-adenosyl methionine. The EcoKI methyltransferase has a strong preference
AB  - for methylating a hemimethylated DNA target rather than an unmodified target. We have used
AB  - partial proteolytic digestion of EcoKI methyltransferase to generate polypeptide domains that
AB  - we have identified by amino acid sequencing. The S subunit was cut into two large, folded
AB  - domains each containing one DNA binding region. Binding of DNA partially protected the S
AB  - subunit from digestion. The M subunit was also cut into two large domains joined together by a
AB  - short flexible loop, and a C-terminal tail region. The short loop contained part of the
AB  - S-adenosyl methionine binding motif, and cofactor binding protected the loop and the two large
AB  - domains from proteolysis. The C-terminal domain of M remained associated with the N-terminal
AB  - domain of the S subunit even after the rest of the protein had been digested. The conformation
AB  - of the tail region of the M subunit was sensitive to the methylation state of DNA in ternary
AB  - complexes also containing S-adenosyl methionine, and could differentiate between unmethylated
AB  - and hemimethylated DNA substrates.
ER  -

TY  - JOUR
AU  - Cooper, L.P.
AU  - Roberts, G.A.
AU  - White, J.H.
AU  - Luyten, Y.A.
AU  - Bower, E.K.M.
AU  - Morgan, R.D.
AU  - Roberts, R.J.
AU  - Lindsay, J.A.
AU  - Dryden, D.T.F.
TI  - DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 3395
EP  - 3406
VL  - 45
AB  - Staphylococcus aureus displays a clonal population structure in which horizontal  gene
AB  - transfer between different lineages is extremely rare. This is due, in part,
AB  - to the presence of a Type I DNA restriction-modification (RM) system given the
AB  - generic name of Sau1, which maintains different patterns of methylation on
AB  - specific target sequences on the genomes of different lineages. We have
AB  - determined the target sequences recognized by the Sau1 Type I RM systems present
AB  - in a wide range of the most prevalent S. aureus lineages and assigned the
AB  - sequences recognized to particular target recognition domains within the RM
AB  - enzymes. We used a range of biochemical assays on purified enzymes and single
AB  - molecule real-time sequencing on genomic DNA to determine these target sequences
AB  - and their patterns of methylation. Knowledge of the main target sequences for
AB  - Sau1 will facilitate the synthesis of new vectors for transformation of the most
AB  - prevalent lineages of this 'untransformable' bacterium.
ER  -

TY  - JOUR
AU  - Cooper, T.F.
AU  - Heinemann, J.A.
TI  - Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 12643
EP  - 12648
VL  - 97
AB  - Postsegregational killing (PSK) systems consist of a tightly linked toxin-antitoxin pair.
AB  - Antitoxin must be continually produced to prevent
AB  - the longer lived toxin from killing the cell. PSK systems on plasmids
AB  - are widely believed to benefit the plasmid by ensuring its stable
AB  - vertical inheritance. However, experimental tests of this "stability"
AB  - hypothesis were not consistent with its predictions. We suggest an
AB  - alternative hypothesis to explain the evolution of PSK: that PSK
AB  - systems have been selected through benefiting host plasmids in
AB  - environments where plasmids must compete during horizontal
AB  - reproduction. In this "competition" hypothesis, success of PSK
AB  - systems is a consequence of plasmid-plasmid competition, rather than
AB  - from an adaptive plasmid-host relationship. In support of this
AB  - hypothesis, a plasmid-encoded parDE PSK system mediated the exclusion
AB  - of an isogenic Delta parDE plasmid. An understanding of how PSK systems
AB  - influence plasmid success may provide insight into the evolution of
AB  - other determinants (e.g., antibiotic resistance and virulence) also
AB  - rendering a cell potentially dependent on an otherwise dispensable
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of Desulfomicrobium baculatum type strain (X).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 29
EP  - 37
VL  - 1
AB  - Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the
AB  - type genus of the family Desulfomicrobiaceae. It is of phylogenetic
AB  - interest because of the isolated location of the family Desulfomicrobiaceae
AB  - within the order Desulfovibrionales. D. baculatum strain X(T) is a Gram-negative,
AB  - motile, sulfate-reducing bacterium isolated from water-saturated manganese
AB  - carbonate ore. It is strictly anaerobic and does not require NaCl for growth,
AB  - although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is
AB  - respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are
AB  - incompletely oxidized to acetate and CO(2). Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. This is the
AB  - first completed genome sequence of a member of the deltaproteobacterial family
AB  - Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its
AB  - 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of Catenulispora acidiphila type strain (ID 139908).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 119
EP  - 125
VL  - 1
AB  - Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and
AB  - is of interest because of the rather isolated phylogenetic
AB  - location it occupies within the scarcely explored suborder Catenulisporineae of
AB  - the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic
AB  - lifestyle, but can also grow scantly under anaerobic conditions. Under regular
AB  - conditions, C. acidiphilia grows in long filaments of relatively short aerial
AB  - hyphae with marked septation. It is a free living, non motile, Gram-positive
AB  - bacterium isolated from a forest soil sample taken from a wooded area in
AB  - Gerenzano, Italy. Here we describe the features of this organism, together with
AB  - the complete genome sequence and annotation. This is the first complete genome
AB  - sequence of the actinobacterial family Catenulisporaceae, and the 10,467,782 bp
AB  - long single replicon genome with its 9056 protein-coding and 69 RNA genes is a
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of Atopobium parvulum type strain (IPP 1246).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 166
EP  - 173
VL  - 1
AB  - Atopobium parvulum (Weinberg et al. 1937) Collins and Wallbanks 1993 comb. nov. is the type
AB  - strain of the species and belongs to the genomically yet unstudied
AB  - Atopobium/Olsenella branch of the family Coriobacteriaceae. The species A.
AB  - parvulum is of interest because its members are frequently isolated from the
AB  - human oral cavity and are found to be associated with halitosis (oral malodor)
AB  - but not with periodontitis. Here we describe the features of this organism,
AB  - together with the complete genome sequence, and annotation. This is the first
AB  - complete genome sequence of the genus Atopobium, and the 1,543,805 bp long single
AB  - replicon genome with its 1369 protein-coding and 49 RNA genes is part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus  proteolyticus type strain (MRP(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 240
EP  - 250
VL  - 6
AB  - Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one  of currently
AB  - 47 species in the genus Deinococcus within the family
AB  - Deinococcaceae. Strain MRP(T) was isolated from feces of Lama glama and possesses
AB  - extreme radiation resistance, a trait is shares with various other species of the
AB  - genus Deinococcus, with D. proteolyticus being resistant up to 1.5 Mrad of gamma
AB  - radiation. Strain MRP(T) is of further interest for its carotenoid pigment. The
AB  - genome presented here is only the fifth completed genome sequence of a member of
AB  - the genus Deinococcus (and the forth type strain) to be published, and will
AB  - hopefully contribute to a better understanding of how members of this genus
AB  - adapted to high gamma- or UV ionizing-radiation. Here we describe the features of
AB  - this organism, together with the complete genome sequence and annotation. The
AB  - 2,886,836 bp long genome with its four large plasmids of lengths 97 kbp, 132 kbp,
AB  - 196 kbp and 315 kbp harbors 2,741 protein-coding and 58 RNA genes and is a part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 145
EP  - 154
VL  - 6
AB  - Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which
AB  - belongs to the Cytophagaceae, a family that was only recently
AB  - classified to the order Cytophagales in the class Cytophagia. The species is of
AB  - interest because it is able to grow at temperatures as low as 4 degrees C. This
AB  - is the first completed genome sequence of a member of the genus Runella and the
AB  - sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome
AB  - consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0
AB  - kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of the aerobic, heterotrophy Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 21
EP  - 30
VL  - 6
AB  - Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus
AB  - Marinithermus. M. hydrothermalis T1T was the first isolate within the phylum
AB  - "Thermus-Deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea
AB  - water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1T is of
AB  - interest because it may provide a new insight into the ecological significance of the aerobic,
AB  - thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent
AB  - ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus
AB  - and the seventh sequence from the family Thermaceae. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The 2,269,167 bp long
AB  - genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Copeland, A. et al.
TI  - Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 379
EP  - 388
VL  - 5
AB  - Chromohalobacter salexigens is one of nine currently known species of the genus
AB  - Chromoha-lobacter in the family Halomonadaceae. It is the most halotolerant of the so-called
AB  - 'mod-erately halophilic bacteria' currently known and, due to its strong euryhaline
AB  - phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens
AB  - strain 1H11T and Halomonas elongata are the first and the second members of the family
AB  - Halomonada-ceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a
AB  - total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome
AB  - Institute Program DOEM 2004.
ER  -

TY  - JOUR
AU  - Copeland, J.C.
AU  - Bryson, V.
TI  - Restriction in matings of Escherichia coli strain K-12 with strain B.
JO  - Genetics
PY  - 1966
SP  - 441
EP  - 452
VL  - 54
AB  - Restriction in Escherichia coli limits the acceptance of genetic elements such
AB  - as bacteriophage, sex-factor, and donated bacterial chromosomes.  As reported
AB  - in this paper, restriction of K-12 genetic material by strain B is greatest
AB  - early in the mating and later becomes constant.  Unlike restriction in B/r, no
AB  - delay in the appearance of a proximal marker is found.  Also, the linkage
AB  - between markers is not reduced by a constant amount, but is dependent upon the
AB  - distance between the markers.  Restriction in strain B is responsible for only
AB  - part of the reduction in the inheritance of genetic markers from K-12, whereas
AB  - in strain B/r restriction accounts for the entire effect.
ER  -

TY  - JOUR
AU  - Corby-Harris, V.
AU  - Anderson, K.E.
TI  - Draft Genome Sequences of Four Parasaccharibacter apium Strains Isolated from Honey Bees.
JO  - Genome Announcements
PY  - 2018
SP  - e00165
EP  - e00118
VL  - 6
AB  - Parasaccharibacter apium displays multiple ecological strategies in its honey bee host. We
AB  - sequenced the genomes of four strains found in larvae and the adult gut
AB  - in order to better understand its ecology and relationship to other
AB  - Acetobacteraceae The P. apium genome consists of 2,009,892 bp and 1,830
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Corina, L.E.
TI  - Homing endonuclease I-CreII: A novel dual-motif enzyme that catalyzes group I intron homing.
JO  - Ph.D. Thesis, Southwestern Medical Center, Univ. of Texas, USA
PY  - 2005
SP  - 1
EP  - 148
AB  - I-CreII is a homing endonuclease from the Cr.psbA intron of Chlamydomonas reinhardtii.  It
AB  - cleaves the exon 4-exon 5 junction of psbA DNA, thereby inducing a recombination event
AB  - referred to as intron homing.  Homing endonucleases are classified into four main groups based
AB  - on the presence of a catalytic domain unique to each group.  I-CreII is novel in that it
AB  - appears to contain two catalytic domains, an H-N-H and a GIY-YIG.  The role of the puative
AB  - GIY-YIG motif has been questioned, however, because I-CmoeI, a related protein, behaves like
AB  - an H-N-H endonuclease.  Recently, Kim et al. (2005) showed that DNA cleavage by I-CreII leaves
AB  - 2-nt 3' OH overhands, which is a feature unique to GIY-YIG enzymes.  Thus, in order to
AB  - resolve this question, I have performed new biochemical and kinetic analyses of wild-type and
AB  - mutant proteins that have had a conserved residue in one of the motifs substituted with
AB  - alanine.  The results indicate that not only does I-CreII have a functional GIY-YIG motif, but
AB  - the data point to it as the catalytic domain.  From this new perspective, this is also the
AB  - first quantitative study of a GIY-YIG endonuclease.  These data also provide the first direct
AB  - evidence that an H-N-H motif can function primarily in DNA binding rather than catalysis- a
AB  - finding that has implications for transcription factors from lower plants and protists that
AB  - appear to have this motif.
ER  -

TY  - JOUR
AU  - Corina, L.E.
AU  - Qiu, W.
AU  - Desai, A.
AU  - Herrin, D.L.
TI  - Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5810
EP  - 5821
VL  - 37
AB  - Homing endonucleases typically contain one of four conserved catalytic motifs, and other
AB  - elements that confer tight DNA binding. I-CreII, which
AB  - catalyzes homing of the Cr.psbA4 intron, is unusual in containing two
AB  - potential catalytic motifs, H-N-H and GIY-YIG. Previously, we showed that
AB  - cleavage by I-CreII leaves ends (2-nt 3' overhangs) that are
AB  - characteristic of GIY-YIG endonucleases, yet it has a relaxed metal
AB  - requirement like H-N-H enzymes. Here we show that I-CreII can bind DNA
AB  - without an added metal ion, and that it binds as a monomer, akin to
AB  - GIY-YIG enzymes. Moreover, cleavage of supercoiled DNA, and estimates of
AB  - strand-specific cleavage rates, suggest that I-CreII uses a sequential
AB  - cleavage mechanism. Alanine substitution of a number of residues in the
AB  - GIY-YIG motif, however, did not block cleavage activity, although DNA
AB  - binding was substantially reduced in several variants. Substitution of
AB  - conserved histidines in the H-N-H motif resulted in variants that did not
AB  - promote DNA cleavage, but retained high-affinity DNA binding-thus
AB  - identifying it as the catalytic motif. Unlike the non-specific H-N-H
AB  - colicins, however; substitution of the conserved asparagine substantially
AB  - reduced DNA binding (though not the ability to promote cleavage). These
AB  - results indicate that, in I-CreII, two catalytic motifs have evolved to
AB  - play important roles in specific DNA binding. The data also indicate that
AB  - only the H-N-H motif has retained catalytic ability.
ER  -

TY  - JOUR
AU  - Cornelius, A.J.
AU  - Miller, W.G.
AU  - Lastovica, A.J.
AU  - On, S.L.W.
AU  - French, N.P.
AU  - Vandenberg, O.
AU  - Biggs, P.J.
TI  - Complete Genome Sequence of Campylobacter concisus ATCC 33237T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00711
EP  - e00717
VL  - 5
AB  - We report the complete genome sequence of the Campylobacter concisus type strain  ATCC 33237
AB  - and the draft genome sequences of eight additional well-characterized
AB  - C. concisus strains. C. concisus has been shown to be a genetically heterogeneous
AB  - species, and these nine genomes provide valuable information regarding the
AB  - diversity within this taxon.
ER  -

TY  - JOUR
AU  - Cornell, C.R.
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Draft Genome Sequences of Megaplasmid-Bearing Streptomyces sp. Strains BF-3 and 4F, Isolated from the Great Salt Plains of Oklahoma.
JO  - Genome Announcements
PY  - 2018
SP  - e00208
EP  - e00218
VL  - 6
AB  - Draft genome sequences of megaplasmid-bearing Streptomyces sp. strains BF-3 and 4F, isolated
AB  - from the Great Salt Plains of Oklahoma, showed genome sizes of
AB  - 7,950,134 and 7,550,992 bp, respectively. Both genomes revealed the presence of
AB  - genes involved in osmoregulation and stress response, potentially helping their
AB  - survival in such an extreme environment.
ER  -

TY  - JOUR
AU  - Cornell, J.L.
AU  - Breslin, E.
AU  - Schuhmacher, Z.
AU  - Himelright, M.
AU  - Berluti, C.
AU  - Boyd, C.
AU  - Carson, R.
AU  - Del Gallo, E.
AU  - Giessler, C.
AU  - Gilliam, B.
AU  - Heatherly, C.
AU  - Nevin, J.
AU  - Nguyen, B.
AU  - Nguyen, J.
AU  - Parada, J.
AU  - Sutterfield, B.
AU  - Tukruni, M.
AU  - Temple, L.
TI  - Complete Genome Sequence of Bacillus thuringiensis Bacteriophage Smudge.
JO  - Genome Announcements
PY  - 2016
SP  - e00572
EP  - e00516
VL  - 4
AB  - Smudge, a bacteriophage enriched from soil using Bacillus thuringiensis DSM-350 as the host,
AB  - had its complete genome sequenced. Smudge is a myovirus with a
AB  - genome consisting of 292 genes and was identified as belonging to the C1 cluster
AB  - of Bacillus phages.
ER  -

TY  - JOUR
AU  - Cornish-Bowden, A.
TI  - Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 3021
EP  - 3030
VL  - 13
AB  - With the introduction of methods of rapid nucleic acid sequence determination, synthesis of
AB  - mixed oligonucleotide probes and computer-assisted analysis of nucleic acid sequences, the use
AB  - of a single symbol to designate a variety of possible nucleotides at a single position has
AB  - become widespread over the last few years. Whereas the use of, for example, the symbols R and
AB  - Y to designate purine (A or G) and pyrimidine (C or T) ribonucleotides respectively is
AB  - generally accepted, no agreed symbols exist for the other possible combinations. Indeed, a
AB  - plethora of diverse systems have proliferated in the last few years. It is striking that, in
AB  - one extreme case, the combination (C or G) has been represented by at least five different
AB  - symbols. A standardized set of symbols is thus required to prevent confusion.
ER  -

TY  - JOUR
AU  - Corretto, E.
AU  - Antonielli, L.
AU  - Sessitsch, A.
AU  - Compant, S.
AU  - Hofer, C.
AU  - Puschenreiter, M.
AU  - Brader, G.
TI  - Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus  AR33T and comparison with related Actinobacteria.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 2
EP  - 2
VL  - 12
AB  - Agromyces aureus AR33T is a Gram-positive, rod-shaped and motile bacterium belonging to the
AB  - Microbacteriaceae family in the phylum Actinobacteria that was
AB  - isolated from a former zinc/lead mining and processing site in Austria. In this
AB  - study, the whole genome was sequenced and assembled combining sequences obtained
AB  - from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete
AB  - genome sequence which is 4,373,124 bp long and has a GC content of 70.1%.
AB  - Furthermore, we performed a comparative genomic analysis with other related
AB  - organisms: 6 Agromyces spp., 4 Microbacteriaceae spp. and 2 other members of the
AB  - class Actinobacteria.
ER  -

TY  - JOUR
AU  - Corretto, E.
AU  - Antonielli, L.
AU  - Sessitsch, A.
AU  - Kidd, P.
AU  - Weyens, N.
AU  - Brader, G.
TI  - Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments.
JO  - Genome Announcements
PY  - 2015
SP  - e00432
EP  - e00415
VL  - 3
AB  - Microbacterium spp. isolated from heavy metal (HM)-contaminated environments (soil and plants)
AB  - can play a role in mobilization processes and in the
AB  - phytoextraction of HM. Here, we report the whole-genome sequences and annotation
AB  - of 10 Microbacterium spp. isolated from both HM-contaminated and -noncontaminated
AB  - compartments.
ER  -

TY  - JOUR
AU  - Corsini, G.
AU  - Valdes, N.
AU  - Pradel, P.
AU  - Tello, M.
AU  - Cottet, L.
AU  - Muino, L.
AU  - Karahanian, E.
AU  - Castillo, A.
AU  - Gonzalez, A.R.
TI  - Draft Genome Sequence of a Copper-Resistant Marine Bacterium, Pantoea agglomerans Strain LMAE-2, a Bacterial Strain with Potential Use in Bioremediation.
JO  - Genome Announcements
PY  - 2016
SP  - e00525
EP  - e00516
VL  - 4
AB  - Pantoea agglomerans LMAE-2 was isolated from seabed sediment moderately contaminated with
AB  - Cu(2+) Here, we report its draft genome sequence, which has a
AB  - size of 4.98 Mb. The presence of cop genes related with copper homeostasis in its
AB  - genome may explain the resistance and strengthen its potential for use as
AB  - bioremediation agent.
ER  -

TY  - JOUR
AU  - Corvaglia, A.R.
AU  - Francois, P.
AU  - Bertrand, X.
AU  - Quentin, R.
AU  - Hernandez, D.
AU  - van der Mee-Marquet, N.
TI  - Whole-Genome Sequences of Two Staphylococcus aureus ST398 Strains of Human Origin, S94 and S100.
JO  - Genome Announcements
PY  - 2013
SP  - e00691
EP  - e00613
VL  - 1
AB  - Sequence type 398 (ST398) Staphylococcus aureus was originally associated with animal
AB  - infection. We announce the complete genome sequences of two ST398
AB  - methicillin-susceptible S. aureus strains of human origin, S94 and S100. The
AB  - genome sequences assist in the characterization of interesting ST398 features
AB  - related to host specificities.
ER  -

TY  - JOUR
AU  - Corvaglia, A.R.
AU  - Francois, P.
AU  - Hernandez, D.
AU  - Perron, K.
AU  - Linder, P.
AU  - Schrenzel, J.
TI  - A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 11954
EP  - 11958
VL  - 107
AB  - Staphylococcus aureus is an versatile pathogen that can cause life-threatening infections.
AB  - Depending on the clinical setting, up to 50% of S. aureus infections are caused by
AB  - methicillin-resistant strains (MRSA) that in most cases are resistant to many other
AB  - antibiotics, making treatment difficult. The emergence of community-acquired MRSA drastically
AB  - changed the picture by increasing the risk of MRSA infections. Horizontal transfer of genes
AB  - encoding for antibiotic resistance or virulence factors is a major concern of
AB  - multidrug-resistant S. aureus infections and epidemiology. We identified and characterized a
AB  - type III-like restriction system present in clinical S. aureus strains that prevents
AB  - transformation with DNA from other bacterial species. Interestingly, our analysis revealed
AB  - that some clinical MRSA strains are deficient in this restriction system, and thus are
AB  - hypersusceptible to the horizontal transfer of DNA from other species, such as Escherichia
AB  - coli, and could easily acquire a vancomycin-resistance gene from enterococci. Inactivation of
AB  - this restriction system dramatically increases the transformation efficiency of clinical S.
AB  - aureus strains, opening the field of molecular genetic manipulation of these strains using DNA
AB  - of exogenous origin.
ER  -

TY  - JOUR
AU  - Cosate, M.R.
AU  - Soares, S.C.
AU  - Mendes, T.A.
AU  - Raittz, R.T.
AU  - Moreira, E.C.
AU  - Leite, R.
AU  - Fernandes, G.R.
AU  - Haddad, J.P.
AU  - Ortega, J.M.
TI  - Whole-Genome Sequence of Leptospira interrogans Serovar Hardjo Subtype Hardjoprajitno Strain Norma, Isolated from Cattle in a Leptospirosis Outbreak in   Brazil.
JO  - Genome Announcements
PY  - 2015
SP  - e01302
EP  - e01315
VL  - 3
AB  - Leptospirosis is caused by pathogenic bacteria of the genus Leptospira spp. This  neglected
AB  - re-emergent disease has global distribution and relevance in veterinary
AB  - production. Here, we report the whole-genome sequence and annotation of
AB  - Leptospira interrogans serovar Hardjo subtype Hardjoprajitno strain Norma,
AB  - isolated from cattle in a livestock leptospirosis outbreak in Brazil.
ER  -

TY  - JOUR
AU  - Cossio-Bayugar, R.
AU  - Miranda-Miranda, E.
AU  - Arreguin-Perez, C.A.
AU  - Lozano, L.
AU  - Perez-de-la-Rosa, D.
AU  - Rocha-Martinez, M.K.
AU  - Bravo-Diaz, M.A.
AU  - Sachman-Ruiz, B.
TI  - Draft Genome Sequence of Enterococcus casseliflavus PAVET15 Obtained from the Oviduct Infection of the Cattle Tick (Rhipicephalus microplus) in Jiutepec, Morelos, Mexico.
JO  - Genome Announcements
PY  - 2017
SP  - e00196
EP  - e00117
VL  - 5
AB  - Enterococcus spp. are Gram-positive lactic acid-producing bacteria found in the intestinal
AB  - tracts of animals, like mammals, birds, and arthropods. Enterococcus
AB  - spp. may cause oportunistic infections in vertebrate and invertebrate hosts. We
AB  - report here the draft genome sequence of Enterococcus casseliflavus PAVET15
AB  - containing 3,722,480 bp, with 80 contigs, an N50 of 179,476 bp, and 41.93% G+C
AB  - content.
ER  -

TY  - JOUR
AU  - Cosstick, R.
AU  - Li, X.
AU  - Tuli, D.K.
AU  - Williams, D.M.
AU  - Connolly, B.A.
AU  - Newman, P.C.
TI  - Molecular recognition in the minor groove of the DNA helix. Studies on the synthesis of oligonucleotides and polynucleotides containing 3-deaza-2'-deoxyadenosine. Interaction of the oligonucleotides with the restriction endonuclease EcoRV.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4771
EP  - 4778
VL  - 18
AB  - An improved procedure for the preparation of 3-deaza-2'-deoxyadenosine (d3CA)
AB  - is described which is suitable for the synthesis of gram quantities of this
AB  - analogue.  Using phosphoramidite chemistry d3CA has been incorporated into the
AB  - EcoRV restriction endonuclease recognition sequence present in the
AB  - self-complementary dodecamer d(GACGATATCGTC).  The modified oligonucleotides
AB  - have been thoroughly characterised by nucleoside composition analysis, circular
AB  - dichroism and thermal melting studies.  Studies with EcoRV show that
AB  - incorporation of d3CA into either the central or outer dA-dT base-pair results
AB  - in a substantial reduction in the rate of cleavage.  The two-step conversion of
AB  - d3CA to 3-deaza-2'-deoxyadenosine-5'-O-triphosphate (d3CATP) via the
AB  - 5'-O-tosylate is also described.  d3CATP is not a substrate in the
AB  - poly[d(AT)].poly[d(AT)] primed polymerisation for either E. coli DNA polymerase
AB  - I or Micrococcus luteus DNA polymerase.  In a more detailed kinetic analysis
AB  - d3CATP was shown to be a competitive inhibitor of E. coli DNA polymerase I with
AB  - respect to dATP.
ER  -

TY  - JOUR
AU  - Cossu, M.
AU  - Badel, C.
AU  - Catchpole, R.
AU  - Gadelle, D.
AU  - Marguet, E.
AU  - Barbe, V.
AU  - Forterre, P.
AU  - Oberto, J.
TI  - Flipping chromosomes in deep-sea archaea.
JO  - PLoS Genet.
PY  - 2017
SP  - e1006847
EP  - e1006847
VL  - 13
AB  - One of the major mechanisms driving the evolution of all organisms is genomic rearrangement.
AB  - In hyperthermophilic Archaea of the order Thermococcales, large
AB  - chromosomal inversions occur so frequently that even closely related genomes are
AB  - difficult to align. Clearly not resulting from the native homologous
AB  - recombination machinery, the causative agent of these inversions has remained
AB  - elusive. We present a model in which genomic inversions are catalyzed by the
AB  - integrase enzyme encoded by a family of mobile genetic elements. We characterized
AB  - the integrase from Thermococcus nautili plasmid pTN3 and showed that besides
AB  - canonical site-specific reactions, it catalyzes low sequence specificity
AB  - recombination reactions with the same outcome as homologous recombination events
AB  - on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other
AB  - known tyrosine recombinases. Through serial culturing, we showed that the
AB  - integrase-mediated divergence of T. nautili strains occurs at an astonishing
AB  - rate, with at least four large-scale genomic inversions appearing within 60
AB  - generations. Our results and the ubiquitous distribution of pTN3-like integrated
AB  - elements suggest that a major mechanism of evolution of an entire order of
AB  - Archaea results from the activity of a selfish mobile genetic element.
ER  -

TY  - JOUR
AU  - Costa, M.O.
AU  - Beltrame, C.O.
AU  - Ferreira, F.A.
AU  - Botelho, A.M.
AU  - Lima, N.C.
AU  - Souza, R.C.
AU  - de Almeida, L.G.
AU  - Vasconcelos, A.T.
AU  - Nicolas, M.F.
AU  - Figueiredo, A.M.
TI  - Complete Genome Sequence of a Variant of the Methicillin-Resistant Staphylococcus aureus ST239 Lineage, Strain BMB9393, Displaying Superior Ability To Accumulate  ica-Independent Biofilm.
JO  - Genome Announcements
PY  - 2013
SP  - e00576
EP  - e00513
VL  - 1
AB  - Biofilm is considered an important virulence factor in nosocomial infections. Herein, we
AB  - report the complete genome sequence of a variant of
AB  - methicillin-resistant Staphylococcus aureus, strain BMB9393, which is highly
AB  - disseminated in Brazil. This strain belongs to the lineage ST239 and displays
AB  - increased ability to accumulate ica-independent biofilm and to invade human
AB  - epithelial cells.
ER  -

TY  - JOUR
AU  - Costa, N.D.
AU  - Thacker, J.
TI  - The Efficiency of Restriction Endonuclease Digests Determined by PCR.
JO  - Biotechniques
PY  - 1992
SP  - 190
EP  - 190
VL  - 13
AB  - Amplification of DNA by PCR should be stopped by a double-strand break in the template
AB  - molecule. However, in the course of experiments designed to utilize restriction endonucleases
AB  - (RE) to eliminate PCR amplification, we observed that extensive digestion rarely resulted in
AB  - lack of a PCR product. We excluded one possible explanation for this obervation: "jumping" PCR
AB  - where a 5' overhang will give rise to first-round products with short end homologies that may
AB  - hybridize. Polymerization on this substrate would result in a complete template molecule.
AB  - However, this will not occur for a 3' overhang or blunt end, yet we obtained similar
AB  - amplification with DNA cut to give any type of end.
ER  -

TY  - JOUR
AU  - Costa, P.S.
AU  - Tschoeke, D.A.
AU  - Silva, B.S.
AU  - Thompson, F.
AU  - Reis, M.P.
AU  - Chartone-Souza, E.
AU  - Nascimento, A.M.
TI  - Draft Genome Sequence of Micrococcus sp. Strain MS-AsIII-49, an Arsenate-Reducing Isolate from Tropical Metal-Rich Sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e00122
EP  - e00115
VL  - 3
AB  - Micrococcus sp. strain MS-AsIII-49, which was isolated from a tropical metal-polluted stream
AB  - sediment in Brazil, has the ability to reduce AsV to AsIII.
AB  - Analysis of its draft genome revealed 186 contigs with a total size of 2,440,924
AB  - bp encoding several metal resistance genes.
ER  -

TY  - JOUR
AU  - Costa, S.K.
AU  - Donegan, N.P.
AU  - Corvaglia, A.R.
AU  - Francois, P.
AU  - Cheung, A.L.
TI  - Bypassing the restriction system to improve transformation of Staphylococcus epidermidis.
JO  - J. Bacteriol.
PY  - 2017
SP  - e00271
EP  - e00217
VL  - 199
AB  - Staphylococcus epidermidis is the leading cause of infections on indwelling medical devices
AB  - worldwide. Intrinsic antibiotic resistance and vigorous biofilm
AB  - production have rendered these infections difficult to treat and, in some cases,
AB  - require the removal of the offending medical prostheses. With the exception of
AB  - two widely-passaged isolates RP62A and 1457, the pathogenesis of infections
AB  - caused by clinical S. epidermidis strains is poorly understood due to the strong
AB  - genetic barrier that precludes efficient transformation of foreign DNA into
AB  - clinical isolates. The difficulty in transforming clinical S. epidermidis
AB  - isolates is primarily due to the type I and IV restriction modification systems
AB  - which act as genetic barriers. Here, we showed that efficient plasmid
AB  - transformation of clinical S. epidermidis isolates from clonal complexes 2, 10
AB  - and 89 could be realized by employing a plasmid artificial modification (PAM) in
AB  - E. coli DC10B containing a Deltadcm mutation. This transformative technique
AB  - should facilitate our ability to genetically modify clinical isolates of S.
AB  - epidermidis and hence improve our understanding of its pathogenesis in human
AB  - infections.ImportanceStaphylococcus epidermidis is a source of considerable
AB  - morbidity worldwide. The underlying mechanisms contributing to the commensal and
AB  - pathogenic lifestyles of S. epidermidis are poorly understood. Genetic
AB  - manipulations of clinically relevant strains of S. epidermidis are largely
AB  - prohibited due to the presence of a strong restriction barrier. With the
AB  - introductions of the tools presented here, genetic manipulation has now become
AB  - possible with clinically relevant S. epidermidis isolates, thus improving our
AB  - understanding of S. epidermidis as a pathogen.
ER  -

TY  - JOUR
AU  - Costa, W.L.O.
AU  - Alves, J.T.C.
AU  - Dias, L.M.
AU  - Araujo, C.L.A.
AU  - Morais, E.
AU  - Silva, A.G.M.
AU  - Andrade, S.S.
AU  - Ramos, R.T.J.
AU  - Silva, A.
AU  - Folador, A.R.C.
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis PA04, Isolated from the Lymph Node of a Sheep in the Amazon, Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00202
EP  - e00217
VL  - 5
AB  - This study reports the complete genome sequence of Corynebacterium pseudotuberculosis strain
AB  - PA04, isolated from a sheep in the Amazon, Brazil. This
AB  - bacterium is the etiological agent of caseous lymphadenitis. This genome contains
AB  - 2,338,093 bp, 52.2% G+C content, and a total of 2,104 coding sequences (CDSs), 41
AB  - pseudogenes, 12 rRNAs, and 49 tRNAs.
ER  -

TY  - JOUR
AU  - Costello, E.K.
AU  - Sun, C.L.
AU  - Carlisle, E.M.
AU  - Morowitz, M.J.
AU  - Banfield, J.F.
AU  - Relman, D.A.
TI  - Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.
JO  - Sci. Rep.
PY  - 2017
SP  - 3764
EP  - 3764
VL  - 7
AB  - Genital mycoplasmas, which can be vertically transmitted, have been implicated in
AB  - preterm birth, neonatal infections, and chronic lung disease of prematurity. Our
AB  - prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated
AB  - mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we
AB  - characterize the organism's associated community, growth status, metabolic
AB  - potential, and population diversity. Sequencing of genomic DNA from the infant's
AB  - saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we
AB  - recovered three essentially complete (including 'Mnola') and three partial draft
AB  - genomes (including Trichomonas vaginalis). The completed 629,409-bp 'Mnola'
AB  - genome (Candidatus Mycoplasma girerdii str. UC-B3) was distinct at the strain
AB  - level from its closest relative, vaginally-derived Ca. M. girerdii str. VCU-M1,
AB  - which is also associated with T. vaginalis. Replication rate measurements
AB  - indicated growth of str. UC-B3 within the infant. Genes encoding
AB  - surface-associated proteins and restriction-modification systems were especially
AB  - diverse within and between strains. In UC-B3, the population genetic
AB  - underpinnings of phase variable expression were evident in vivo. Unique among
AB  - mycoplasmas, Ca. M. girerdii encodes pyruvate-ferredoxin oxidoreductase and may
AB  - be sensitive to metronidazole. This study reveals a metabolically unique
AB  - mycoplasma colonizing a premature neonate, and establishes the value of
AB  - genome-resolved metagenomics in tracking phase variation.
ER  -

TY  - JOUR
AU  - Cote, V.
AU  - Mercier, J.P.
AU  - Lemieux, C.
AU  - Turmel, M.
TI  - The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I-ChuI).
JO  - Gene
PY  - 1993
SP  - 69
EP  - 76
VL  - 129
AB  - The single group-I intron (ChLSU-1) in the chloroplast (cp) large subunit rRNA-encoding gene
AB  - (rrnL) of the green alga Chlamydomonas humicola is located at a position at which no introns
AB  - have previously been characterized in other systems. In the present study, the nucleotide (nt)
AB  - sequence of this 1118-bp intron was found to contain an internal open reading frame (ORF) that
AB  - potentially encodes a basic protein of 218 amino acid residues. The putative C. humicola
AB  - protein features two copies of the LAGLI-DADG motif and is part of the family of
AB  - intron-encoded proteins comprising the endonucleases (ENases). I-SceI, I-SceI, I-SceIV and
AB  - I-CsmI. Expression of the ChLSU.1 intron ORF in vitro in the presence of a 260-bp DNA fragment
AB  - containing the exon 1-2 junction of an intronless version of the C. humicol rrnL resulted in
AB  - specific cleavage of the DNA fragment very close to the intron insertion site. This novel
AB  - intron-encoded ENase, designated I-ChuI, was also shown to generate a staggered cut with 4-nt
AB  - (CTCG) 3'-OH overhangs 2 bp downstream from the intron insertion site.
ER  -

TY  - JOUR
AU  - Coucheron, D.H.
TI  - Acetobacter strains contain DNA modified at GAATTC and GANTC.
JO  - Can. J. Microbiol.
PY  - 1997
SP  - 456
EP  - 460
VL  - 43
AB  - Total DNAs from nine strains of Acetobacter xylinum, two strains of Acetobacter aceti, and one
AB  - Acetobacter pasteurianus strain were examined for the extent of digestion by various
AB  - restriction endonucleases.  The majority of the endonucleases cleaved the total DNAs with a
AB  - frequency expected from the number of sites present in DNA sequences deposited in the GenBank
AB  - database.  However, the restriction enzyme digestions identified two different genomic DNA
AB  - modifications in Acetobacter.  One sequence-specific modification protected total DNAs from
AB  - seven of the A. xylinum strains against cleavage by EcoRI (GAATTC).  Digestion of total DNAs
AB  - from A. xylinum ATCC 10245 (DNA not cut by EcoRI) and the closely related A. xylinum NRCC
AB  - 17005 (DNA cut by EcoRI) with Tsp509I (AATT) revealed differences in restriction frequencies
AB  - adenine within GAATTC.  Another sequence-specific modification rendered total DNAs from all
AB  - the 12 strains recalcitrant to digestion by HinfI.  The latter modification indicated that
AB  - species of the genus Actobacter contain a solitary DNA methyltransferase that probably
AB  - methylates adenine in GANTC.
ER  -

TY  - JOUR
AU  - Couger, M.B.
AU  - Hanafy, R.A.
AU  - Edens, C.
AU  - Budd, C.
AU  - French, D.P.
AU  - Hoff, W.D.
AU  - Elshahed, M.S.
AU  - Youssef, N.H.
TI  - Draft Genome of the Arthrobacter sp. Strain Edens01.
JO  - Genome Announcements
PY  - 2015
SP  - e01475
EP  - e01415
VL  - 3
AB  - We report the draft genome sequence of Arthrobacter sp. strain Edens01, isolated  from a leaf
AB  - surface of a Rosa hybrid plant as part of the Howard Hughes Medical
AB  - Institute-funded Student Initiated Microbial Discovery (SIMD) project. The genome
AB  - has a total size of 3,639,179 bp and contig N50 of 454,897 bp.
ER  -

TY  - JOUR
AU  - Couger, M.B.
AU  - Hanafy, R.A.
AU  - Mitacek, R.M.
AU  - Budd, C.
AU  - French, D.P.
AU  - Hoff, W.D.
AU  - Elshahed, M.S.
AU  - Youssef, N.H.
TI  - The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.
JO  - Genome Announcements
PY  - 2015
SP  - e01450
EP  - e01415
VL  - 3
AB  - We report the draft genome sequence of Xanthomonas sp. strain Mitacek01, isolated from an
AB  - indoor environment vending machine surface with frequent human use in
AB  - Stillwater, Oklahoma, USA, as part of the Student-Initiated Microbial Discovery
AB  - project. The genome has a total size of 3,617,426 bp and a contig N50 of
AB  - 1,906,967 bp.
ER  -

TY  - JOUR
AU  - Couger, M.B.
AU  - Hurlbut, A.
AU  - Murphy, C.L.
AU  - Budd, C.
AU  - French, D.P.
AU  - Hoff, W.D.
AU  - Elshahed, M.S.
AU  - Youssef, N.H.
TI  - Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01.
JO  - Genome Announcements
PY  - 2015
SP  - e01071
EP  - e01015
VL  - 3
AB  - We report here the draft genome sequence of the environmental isolate Chryseobacterium sp.
AB  - Hurlbut01, isolated from a light switch surface in Stillwater, OK, as part of the
AB  - Student-Initiated Microbial Discovery (SIMD) project. The genome has a size of 3,899,838 bp
AB  - and a contig N50 of 321 kb.
ER  -

TY  - JOUR
AU  - Couger, M.B.
AU  - Wright, A.
AU  - Lutter, E.I.
AU  - Youssef, N.
TI  - Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients.
JO  - Genome Announcements
PY  - 2016
SP  - e01528
EP  - e01515
VL  - 4
AB  - We report here the draft genome sequences of five Pseudomonas aeruginosa isolates obtained
AB  - from sputum samples from two cystic fibrosis patients with chronic
AB  - colonization. These closely related strains harbor 225 to 493 genes absent from
AB  - the P. aeruginosa POA1 genome and contain 178 to 179 virulence factors and 29 to
AB  - 31 antibiotic resistance genes.
ER  -

TY  - JOUR
AU  - Coulby, J.
AU  - Sternberg, N.
TI  - Bacteriophage P1 encodes its own dam methylase.
JO  - Plasmid
PY  - 1987
SP  - 81
EP  - 81
VL  - 17
AB  - The packaging of P1 DNA during its life cycle has been shown to be dependent upon the
AB  - methylation of the adenine residue in the sequence 5'-GATC-3' of the phage packaging site
AB  - (pac).  In vitro studies have shown that unmethylated P1 DNA is not cut at the pac site, and
AB  - the DNA is not packaged into the viral heads.  In an E. coli dam- host, which is unable to
AB  - methylate 5'-GATC-3', P1 phage production lags about 20 min behind that in a dam+ host. This
AB  - delayed production of phage is probably due to a need to synthesize a P1 dam analog before the
AB  - pac site can be cleaved.  To study this process we have begun to characterize the P1 dam gene.
AB  - A 13.5-kb region of P1 DNA was cloned into a lambda vector, and the hybrid was shown to encode
AB  - a dam methylase based on its ability to methylate pBR322 DNA upon infection of an E. coli dam-
AB  - host containing that plasmid.  The P1 dam gene borders the junction of P1 EcoRI fragments 3
AB  - and 8.  This region of the P1 genome is currently being subcloned in order to localize the
AB  - gene.  Following localization the gene will be mutagenized in an effort to further elucidate
AB  - the role of the dam methylase in the P1 life cycle.
ER  -

TY  - JOUR
AU  - Coulby, J.N.
AU  - Sternberg, N.L.
TI  - Characterization of the phage P1 dam gene.
JO  - Gene
PY  - 1988
SP  - 191
EP  - 191
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Coulson, T.J.
AU  - Patten, C.L.
TI  - Complete Genome Sequence of Enterobacter cloacae UW5, a Rhizobacterium Capable of High Levels of Indole-3-Acetic Acid Production.
JO  - Genome Announcements
PY  - 2015
SP  - e00843
EP  - e00815
VL  - 3
AB  - We report the complete genome sequence of Enterobacter cloacae UW5, an indole-3-acetic
AB  - acid-producing rhizobacterium originally isolated from the
AB  - rhizosphere of grass. The 4.9-Mbp genome has a G+C content of 54% and contains
AB  - 4,496 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Coupland, P.
AU  - Chandra, T.
AU  - Quail, M.
AU  - Reik, W.
AU  - Swerdlow, H.
TI  - Direct sequencing of small genomes on the Pacific Biosciences RS without library  preparation.
JO  - Biotechniques
PY  - 2012
SP  - 365
EP  - 372
VL  - 53
AB  - We have developed a sequencing method on the Pacific Biosciences RS sequencer (the PacBio) for
AB  - small DNA molecules that avoids the need for a standard library
AB  - preparation. To date this approach has been applied toward sequencing
AB  - single-stranded and double-stranded viral genomes, bacterial plasmids, plasmid
AB  - vector models for DNA-modification analysis, and linear DNA fragments covering an
AB  - entire bacterial genome. Using direct sequencing it is possible to generate
AB  - sequence data from as little as 1 ng of DNA, offering a significant advantage
AB  - over current protocols which typically require 400-500 ng of sheared DNA for the
AB  - library preparation.
ER  -

TY  - JOUR
AU  - Courties, A.
AU  - Riedel, T.
AU  - Jarek, M.
AU  - Intertaglia, L.
AU  - Lebaron, P.
AU  - Suzuki, M.T.
TI  - Genome Sequence of Strain MOLA814, a Proteorhodopsin-Containing Representative of the Betaproteobacteria Common in the Ocean.
JO  - Genome Announcements
PY  - 2013
SP  - e01062
EP  - e01013
VL  - 1
AB  - Strain MOLA814 is a marine betaproteobacterium that was isolated from seawater in the Beaufort
AB  - Sea. Here, we present its genome sequence and annotation. Genome
AB  - analysis revealed the presence of a proteorhodopsin-encoding sequence together
AB  - with its retinal-producing pathway, indicating that this strain might generate
AB  - energy by using light.
ER  -

TY  - JOUR
AU  - Courtine, D.
AU  - Alain, K.
AU  - Georges, M.
AU  - Bienvenu, N.
AU  - Morrison, H.G.
AU  - Eren, A.M.
AU  - Maignien, L.
TI  - Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9 degrees N.
JO  - Genome Announcements
PY  - 2017
SP  - e01385
EP  - e01317
VL  - 5
AB  - We report the genome sequence of Thermococcus sp. EXT12c isolated from a deep-sea hydrothermal
AB  - vent at the East Pacific Rise 9 degrees N. Microbes in the genus
AB  - Thermococcus are able to grow anaerobically at high temperature, around neutral
AB  - pH, and some of them under high hydrostatic pressure.
ER  -

TY  - JOUR
AU  - Cousin, S.
AU  - Clermont, D.
AU  - Creno, S.
AU  - Ma, L.
AU  - Loux, V.
AU  - Bizet, C.
AU  - Bouchier, C.
TI  - Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76T.
JO  - Genome Announcements
PY  - 2013
SP  - e00660
EP  - e00613
VL  - 1
AB  - We report the draft genome sequence of the type strain Lactobacillus pasteurii CRBIP 24.76,
AB  - which is closely related to L. gigeriorum CRBIP 24.85(T), isolated
AB  - from a chicken crop. The total length of the 29 contigs is about 1.9 Mb, with a
AB  - G+C content of 40% and 1,946 coding sequences.
ER  -

TY  - JOUR
AU  - Cousin, S.
AU  - Creno, S.
AU  - Ma, L.
AU  - Clermont, D.
AU  - Loux, V.
AU  - Bizet, C.
AU  - Bouchier, C.
TI  - Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T, Isolated from Human Intestine.
JO  - Genome Announcements
PY  - 2013
SP  - e00662
EP  - e00613
VL  - 1
AB  - We report the draft genome sequence of the strain Lactobacillus hominis CRBIP 24.179(T),
AB  - isolated from a human clinical sample. The total length of the 28
AB  - contigs is about 1.9 Mb, with a G+C content of 37% and 1,983 coding sequences.
ER  -

TY  - JOUR
AU  - Cousin, S.
AU  - Loux, V.
AU  - Ma, L.
AU  - Creno, S.
AU  - Clermont, D.
AU  - Bizet, C.
AU  - Bouchier, C.
TI  - Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137, Isolated from Thoroughbred Racehorse Feces  and Human Urine, Respectively.
JO  - Genome Announcements
PY  - 2013
SP  - e00663
EP  - e00613
VL  - 1
AB  - We report the draft genome sequences of strain Lactobacillus equicursoris CIP 110162(T),
AB  - isolated from racehorse breed feces, and Lactobacillus sp. strain
AB  - CRBIP 24.137, isolated from human urine; the two strains are closely related. The
AB  - total lengths of the 116 and 62 scaffolds are about 2.157 and 2.358 Mb, with G+C
AB  - contents of 46 and 45% and 2,279 and 2,342 coding sequences (CDSs), respectively.
ER  -

TY  - JOUR
AU  - Cousin, S.
AU  - Ma, L.
AU  - Creno, S.
AU  - Clermont, D.
AU  - Loux, V.
AU  - Bizet, C.
AU  - Bouchier, C.
TI  - Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T, Isolated from a Chicken Crop.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5973
EP  - 5973
VL  - 194
AB  - We report the draft genome of the strain Lactobacillus gigeriorum CRBIP 24.85(T), isolated
AB  - from a chicken crop. The total length of the 60 scaffolds is about 1.9
AB  - Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS).
ER  -

TY  - JOUR
AU  - Cousineau, B.
AU  - Lawrence, S.
AU  - Smith, D.
AU  - Belfort, M.
TI  - Retrotransposition of a bacterial group II intron.
JO  - Nature
PY  - 2000
SP  - 1018
EP  - 1021
VL  - 404
AB  - Self-splicing group II introns may be the evolutionary progenitors of eukaryotic spliceosomal
AB  - introns, but the route by which they invade new chromosomal sites is unknown. To address the
AB  - mechanism by which group II introns are disseminated, we have studied the bacterial L1.LtrB
AB  - intron from Lactococcus lactis. The protein product of this intron, LtrA, possesses maturase,
AB  - reverse transcriptase and endonuclease enzymatic activities. Together with the intron, LtrA
AB  - forms a ribonucleoprotein (RNP) complex which mediates a process known as retrohoming. In
AB  - retrohoming, the intron reverse splices into a cognate intronless DNA site. Integration of a
AB  - DNA copy of the intron is recombinase independent but requires all three activities of LtrA.
AB  - Here we report the first experimental demonstration of a group II intron invading ectopic
AB  - chromosomal sites, which occurs by a distinct retrotransposition mechanism. This
AB  - retrotransposition process is endonuclease-independent and recombinase-dependent, and is
AB  - likely to involve reverse splicing of the intron RNA into cellular RNA targets. These
AB  - retrotranspositions suggest a mechanism by which splicesomal introns may have become widely
AB  - dispersed.
ER  -

TY  - JOUR
AU  - Cousineau, B.
AU  - Smith, D.
AU  - Lawrence-Cavanagh, S.
AU  - Mueller, J.E.
AU  - Yang, J.
AU  - Mills, D.
AU  - Manias, D.
AU  - Dunny, G.
AU  - Lambowitz, A.M.
AU  - Belfort, M.
TI  - Retrohoming of a bacterial group II intron: Mobility via complete reverse splicing, independent of homologous DNA recombination.
JO  - Cell
PY  - 1998
SP  - 451
EP  - 462
VL  - 94
AB  - The mobile group II intron of Lactococcus lactis, Ll.LtrB, provides the opportunity to analyze
AB  - the homing pathway in genetically tractable bacterial systems.  Here, we show that Ll.LtrB
AB  - mobility occurs by an RNA-based retrohoming mechanism in both Escherichia coli and L. lactis.
AB  - Surprisingly, retrohoming occurs efficiently in the absence of RecA function, with a relaxed
AB  - requirement for flanking exon homology and without coconversion of exon markers.  These
AB  - results lead to a model for bacterial retrohoming in which the intron integrates into
AB  - recipient DNA by complete reverse splicing and serves as the template for cDNA synthesis.  The
AB  - retrohoming reaction is completed in unprecedented fashion by a DNA repair event that is
AB  - independent of homologous recombination between the alleles.  Thus, Ll.LtrB has many features
AB  - of retrotransposons, with practical and evolutionary implications.
ER  -

TY  - JOUR
AU  - Coutinho, B.G.
AU  - Passos-da-Silva, D.
AU  - Previato, J.O.
AU  - Mendonca-Previato, L.
AU  - Venturi, V.
TI  - Draft Genome Sequence of the Rice Endophyte Burkholderia kururiensis M130.
JO  - Genome Announcements
PY  - 2013
SP  - e0022512
EP  - e0022512
VL  - 1
AB  - Burkholderia kururiensis M130 is one of the few characterized rice endophytes and was isolated
AB  - from surface-sterilized rice roots. This bacterium shows strong growth-promoting effects,
AB  - being able to increase rice yields. Here we present its draft genome sequence, which contains
AB  - important traits for endophytic life and plant growth promotion.
ER  -

TY  - JOUR
AU  - Couto, N.
AU  - Chlebowicz, M.A.
AU  - Raangs, E.C.
AU  - Friedrich, A.W.
AU  - Rossen, J.W.
TI  - Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun  Metagenomics.
JO  - Genome Announcements
PY  - 2018
SP  - e00036
EP  - e00018
VL  - 6
AB  - The emergence of nosocomial infections by multidrug-resistant Staphylococcus haemolyticus
AB  - isolates has been reported in several European countries. Here, we
AB  - report the first two complete genome sequences of S. haemolyticus sequence type
AB  - 25 (ST25) isolates 83131A and 83131B. Both isolates were isolated from the same
AB  - clinical sample and were first identified through shotgun metagenomics.
ER  -

TY  - JOUR
AU  - Couturier, M.
AU  - Lindas, A.C.
TI  - The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius.
JO  - Front. Microbiol.
PY  - 2018
SP  - 137
EP  - 137
VL  - 9
AB  - DNA methylation is the most common epigenetic modification observed in the genomic DNA (gDNA)
AB  - of prokaryotes and eukaryotes. Methylated nucleobases,
AB  - N(6)-methyl-adenine (m6A), N(4)-methyl-cytosine (m4C), and 5-methyl-cytosine
AB  - (m5C), detected on gDNA represent the discrimination mark between self and
AB  - non-self DNA when they are part of restriction-modification systems in
AB  - prokaryotes (Bacteria and Archaea). In addition, m5C in Eukaryotes and m6A in
AB  - Bacteria play an important role in the regulation of key cellular processes.
AB  - Although archaeal genomes present modified bases as in the two other domains of
AB  - life, the significance of DNA methylations as regulatory mechanisms remains
AB  - largely uncharacterized in Archaea. Here, we began by investigating the DNA
AB  - methylome of Sulfolobus acidocaldarius. The strategy behind this initial study
AB  - entailed the use of combined digestion assays, dot blots, and genome
AB  - resequencing, which utilizes specific restriction enzymes, antibodies
AB  - specifically raised against m6A and m5C and single-molecule real-time (SMRT)
AB  - sequencing, respectively, to identify DNA methylations occurring in exponentially
AB  - growing cells. The previously identified restriction-modification system,
AB  - specific of S. acidocaldarius, was confirmed by digestion assay and SMRT
AB  - sequencing while, the presence of m6A was revealed by dot blot and identified on
AB  - the characteristic Dam motif by SMRT sequencing. No m5C was detected by dot blot
AB  - under the conditions tested. Furthermore, by comparing the distribution of both
AB  - detected methylations along the genome and, by analyzing DNA methylation profiles
AB  - in synchronized cells, we investigated in which cellular pathways, in particular
AB  - the cell cycle, this m6A methylation could be a key player. The analysis of
AB  - sequencing data rejected a role for m6A methylation in another defense system and
AB  - also raised new questions about a potential involvement of this modification in
AB  - the regulation of other biological functions in S. acidocaldarius.
ER  -

TY  - JOUR
AU  - Cowan, G.M.
TI  - New family of Type I restriction and modification systems.
JO  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
PY  - 1988
SP  - 1
EP  - 128
AB  - The chromosomally encoded type I restriction and modification system of Escherichia coli 15T,
AB  - EcoA, behaves physiologically as a type I system, and in genetic crosses the hsdA genes behave
AB  - as alleles of the hsd K genes of the archetypal type I system of E. coli K-12.  However,
AB  - molecular experiments failed to demonstrate relatedness between the A and K systems.  Genes
AB  - (hsdE) related to hsdA on the basis of DNA homology confer a new specificity to a natural
AB  - isolate, E. coli A58.  The genes encoding EcoA and EcoE have an organization which mimics that
AB  - of EcoK: there are three genes in the same order as those encoding EcoK, of which one, hsdS,
AB  - confers the specificity.  The polypeptides of EcoA, EcoE, and CfrA (a new A-like system) show
AB  - structural homology, demonstrated by immunological cross-reactivity.  The evidence presented
AB  - indicates that EcoA and EcoE represent an alternative family of type I restriction and
AB  - modification enzymes.  The recognition sequence of EcoE, 5'-GAG(N7)ATGC-3', is typical of
AB  - type I systems.  Furthermore, heteroduplex analyses and nucleotide sequencing have indicated
AB  - that the specificity genes of the A-like family show two large regions of variable sequence,
AB  - interspersed and flanked by conserved sequences which include a repeated sequence.  Such an
AB  - organization is similar to that of the K family specificity genes.  The hsdS genes of EcoA and
AB  - EcoE show extensive homology throughout the proximal regions: both recognize the trinucleotide
AB  - GAG.  In general no obvious similarity was detected between the primary sequences of the
AB  - specificity polypeptides of the two families, with one remarkable exception: the proximal
AB  - variable domain of the SB specificity polypeptide shows 44% identity to the proximal regions
AB  - of the specificity subunits of both EcoA and EcoE.  Significantly, the StySB enzyme also
AB  - recognizes the trinucleotide GAG.
ER  -

TY  - JOUR
AU  - Cowan, G.M.
TI  - A new family of type I restriction and modification systems.
JO  - Diss. Abstr.
PY  - 1989
SP  - 441
EP  - 441
VL  - 50
AB  - The chromosomally encoded type I restriction and modification system of Escherichia coli 15T-,
AB  - EcoA, behaves physiologically as a type I system, and in genetic crosses the hsd A genes
AB  - behave as alleles of the hsd K genes of the archetypal type I system of E. coli K-12. However,
AB  - molecular experiments failed to demonstrate relatedness between the A and K systems. Genes
AB  - (hsd E) related to hsd A on the basis of DNA homology confer a new specificity to a natural
AB  - isolate, E. coli A58. The genes encoding EcoA and EcoE have an organization which mimics that
AB  - of EcoK: there are three genes in the same order as those encoding EcoK, of which one, hsdS,
AB  - confers the specificity. The polypeptides of EcoA, EcoE, and CfrA (a new A-like system) show
AB  - structural homology, demonstrated by immunological cross-reactivity. The evidence presented
AB  - indicates that EcoA and EcoE represent an alternative family of type I restriction and
AB  - modification enzyme. The recognition sequence of EcoE, 5'-GAG(N7)ATGC-3', is typical of type
AB  - I systems. Furthermore, heteroduplex analyses and nucleotide sequencing have indicated that
AB  - the specificity genes of the A-like family show two large regions of variable sequence,
AB  - interspersed and flanked by conserved sequences which include a repeated sequence. Such an
AB  - organization is similar to that of the K family specificity genes. The hsdS genes of EcoA and
AB  - EcoE show extensive homology throughout the proximal regions: both recognize the trinucleotide
AB  - GAG. In general no obvious similarity was detected between the primary sequences of the
AB  - specificity polypeptides of the two families, with one remarkable exception the proximal
AB  - variable domain of the SB specificity polypeptide shows 44% identity to the proximal regions
AB  - of the specificity subunits of both EcoA and EcoE. Significantly, the StySB enzyme also
AB  - recognizes the trinucleotide GAG.
ER  -

TY  - JOUR
AU  - Cowan, G.M.
AU  - Daniel, A.S.
AU  - Gann, A.A.F.
AU  - Kelleher, J.E.
AU  - Murray, N.E.
TI  - Defining domains in type-I restriction and modification enzymes.
JO  - Gene
PY  - 1988
SP  - 239
EP  - 241
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Cowan, G.M.
AU  - Gann, A.A.F.
AU  - Murray, N.E.
TI  - Conservation of complex DNA recognition domains between families of restriction enzymes.
JO  - Cell
PY  - 1989
SP  - 103
EP  - 109
VL  - 56
AB  - One polypeptide, designated S, confers sequence-specificity to the multisubunit
AB  - type I restriction enzymes.  Two families of such enzymes, K and A, include
AB  - members that recognize diverse, bipartite, target sequences.  The S
AB  - polypeptides of the K family, while having areas of near identity, also contain
AB  - two extensive regions of variable sequence.  We now show that one of these,
AB  - comprising the N-terminal 150 amino acids, specifies recognition of one
AB  - component of the bipartite target sequence.  We have determined the sequence
AB  - recognized by EcoE, a member of the A family.  This sequence, 5'GAG(N7)ATGC,
AB  - has the trinucleotide GAG in common with EcoA and with StySB of the K family.
AB  - We determined the nucleotide sequences of the S genes of EcoA and EcoE, and
AB  - compared their predicted amino acid sequences with each other and with those of
AB  - the five members of the K family.  There is no general sequence similarity
AB  - between families, but the domain of the S polypeptide of StySB, which specifies
AB  - GAG, shows nearly 50 per cent identity with the amino variable region of the S
AB  - polypeptides of EcoA and EcoE.  A complex domain that recognizes and directs
AB  - methylation of GAG is therefore common to enzymes of generally dissimilar amino
AB  - acid sequence.
ER  -

TY  - JOUR
AU  - Cowan, J.A.
TI  - Role of metal ions in promoting DNA binding and cleavage by restriction endonucleases.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 339
EP  - 360
VL  - 14
AB  - While three major classes of restriction endonucleases have been identified (Types I, II, and
AB  - III), Type II are the most straightforward inasmuch as they require divalent magnesium as an
AB  - essential cofactor but have no need for ATP.  A complete classification of Type II restriction
AB  - nucleases has been presented elsewhere and the family is noted for the remarkable specificity
AB  - and simplicity of its function.  These enzymes cleave both strands of double-strand DNA either
AB  - at or near a recognition sequence that tends to be palindromic.  Consequently most restriction
AB  - endonucleases are dimeric and recognize symmetric DNA sequences.  While showing many
AB  - functional similarities in DNA recognition and catalytic cleavage, restriction endonucleases
AB  - also display low sequence homology, and diversity in mechanisms of recognizing DNA target
AB  - sequences and the positioning of metal cofactors.  Such diversity results in subtle variations
AB  - in both protein binding locations and potential functional roles for essential metal cofactors
AB  - that are only now coming under investigation.
ER  -

TY  - JOUR
AU  - Cowley, L.A.
AU  - Petersen, F.C.
AU  - Junges, R.
AU  - Jimenez, M.J.D.
AU  - Morrison, D.A.
AU  - Hanage, W.P.
TI  - Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.
JO  - PLoS Genet.
PY  - 2018
SP  - e1007410
EP  - e1007410
VL  - 14
AB  - Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae
AB  - is thought to be important in the adaptation and
AB  - evolution of this pathogen. While competent pneumococci are able to scavenge DNA
AB  - added to laboratory cultures, large-scale transfers of multiple kb are rare under
AB  - these conditions. We used whole genome sequencing (WGS) to map transfers in
AB  - recombinants arising from contact of competent cells with non-competent 'target'
AB  - cells, using strains with known genomes, distinguished by a total of ~16,000
AB  - SNPs. Experiments designed to explore the effect of environment on large scale
AB  - recombination events used saturating purified donor DNA, short-term cell
AB  - assemblages on Millipore filters, and mature biofilm mixed cultures. WGS of 22
AB  - recombinants for each environment mapped all SNPs that were identical between the
AB  - recombinant and the donor but not the recipient. The mean recombination event
AB  - size was found to be significantly larger in cell-to-cell contact cultures (4051
AB  - bp in filter assemblage and 3938 bp in biofilm co-culture versus 1815 bp with
AB  - saturating DNA). Up to 5.8% of the genome was transferred, through 20
AB  - recombination events, to a single recipient, with the largest single event
AB  - incorporating 29,971 bp. We also found that some recombination events are
AB  - clustered, that these clusters are more likely to occur in cell-to-cell contact
AB  - environments, and that they cause significantly increased linkage of genes as far
AB  - apart as 60,000 bp. We conclude that pneumococcal evolution through homologous
AB  - recombination is more likely to occur on a larger scale in environments that
AB  - permit cell-to-cell contact.
ER  -

TY  - JOUR
AU  - Cox, K.L.
AU  - Baltz, R.H.
TI  - Restriction of bacteriophage plaque formation in Streptomyces spp.
JO  - J. Bacteriol.
PY  - 1984
SP  - 499
EP  - 504
VL  - 159
AB  - Several Streptomyces species that produce restriction endonucleases were
AB  - characterized for their ability to propagate 10 different broad host range
AB  - bacteriophages.  Each species displayed a different pattern of plaque
AB  - formation.  A restrictionless mutant of S. albus G allowed plaque formation by
AB  - all 10 phages, whereas the wildtype strain showed plaques with only 2 phages.
AB  - DNA isolated from three of the phages was analyzed for the presence of
AB  - restriction sites for Streptomyces species-encoded enzymes, and a very strong
AB  - correlation was established between the failure to form plaques on Streptomyces
AB  - species that produced particular restriction enzymes and the presence of the
AB  - corresponding restriction sites in the phage DNA.  Also, the phages that lacked
AB  - restriction sites in their DNA generally formed plaques on the corresponding
AB  - restriction endonuclease-producing hosts at high efficiency.  The DNAs from the
AB  - three phages analyzed also generally contained either many or no restriction
AB  - sites for the Streptomyces species-produced enzymes, suggesting a strong
AB  - evolutionary trend to either eliminate all or tolerate many restriction sites.
AB  - The data indicate that restriction plays a major role in host range
AB  - determination for Streptomyces phages.  Analysis of bacteriophage host ranges
AB  - of many other uncharacterized Streptomyces hosts has identified four relatively
AB  - nonrestricting hosts, at least two of which may be suitable hosts for gene
AB  - cloning.  The data also suggest that several restriction systems remain to be
AB  - identified in the genus Streptomyces.
ER  -

TY  - JOUR
AU  - Cox, R.
AU  - Goorha, S.
AU  - Irving, C.
TI  - Acrolein, a metabolite of cyclophosphamide, alters DNA methylase activity in a non-competitive fashion by reacting with -SH groups of the enzyme.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1987
SP  - 86
EP  - 86
VL  - 28
AB  - Cyclophosphamide induces urinary bladder cancer both in humans and rats. Acrolein, an active
AB  - metabolite of cyclophosphamide, may be responsible for the bladder cancer induced by
AB  - cyclophosphamide.  Experiments are in progress to determine the carcinogenicity of acrolein in
AB  - rat bladder.  Studies have also been initiated to examine the biochemical lesions induced
AB  - following exposure of urothelial cells to acrolein.  In vitro studies on the effect of
AB  - acrolein on DNA methylase, a -SH containing enzyme (R. Cox, Cancer Res., 40:61, 1980), were
AB  - initiated to determine if acrolein might alter the DNA methylation pattern. Acrolein was shown
AB  - to react with the -SH group of cytochrome P450, resulting in inactivation (A.J. Marinello et
AB  - al., Cancer Res., 44:4615, 1984).  DNA methylase was isolated from the liver and urothelium of
AB  - rats and assayed as previously described (R. Cox, Biochem. Int., 5:787, 1982).  Acrolein
AB  - inhibited DNA methylase activity by 50% and 92% at final concentrations of 10 and 100 microM
AB  - acrolein.  Kinetic studies demonstrated non-competitive inhibition wiuth a Ki of 6.7 microM.
AB  - The inhibition of DNA methylase by 20 microM acrolein was restored to 85% of its original
AB  - activity when 100 microM dithiothreitol was added.  As the enzyme concentration was increased,
AB  - the inhibition of DNA methylase by 20 microM acrolein was decreased, whereas increased amounts
AB  - of DNA had no effect.  These data suggest that acrolein is a very good inhibitor of DNA
AB  - methylase, in a non-competitive fashion, by reacting with the -SH groups of the protein.
ER  -

TY  - JOUR
AU  - Cox, R.
AU  - Goorha, S.
AU  - Irving, C.C.
TI  - Inhibition of DNA methylase activity by acrolein.
JO  - Carcinogenesis
PY  - 1988
SP  - 463
EP  - 465
VL  - 9
AB  - Acrolein, a reactive metabolite of cyclophosphamide, may be responsible for bladder cancer
AB  - induced by cyclophosphamide.  DNA methylase was isolated from the liver and urothelium of rats
AB  - by high salt extraction of purified nuclei.  Acrolein at 10 microM inhibited liver and bladder
AB  - DNA methylase activity by 30-50%.  Kinetic studies with the liver enzyme showed a competitive
AB  - type of inhibition with a Ki of 6.7 microM.  Both dithiothreitol and glutathione afforded
AB  - protection to the enzyme when added to the assay.  At near equimolar concentrations of
AB  - glutathione to acrolein, the methylase retained 80-90% activity.  An increase in DNA had no
AB  - effect on the inhibition by acrolein, whereas increased amounts of protein protected against
AB  - acrolein inhibition, suggesting that acrolein reacted with the DNA methylase protein.  On the
AB  - other hand, DNA that had been reacted with acrolein was unable to serve as a substrate for DNA
AB  - methylase.  As the DNA adducts increased the methylation of the DNA decreased.  Thus, acrolein
AB  - has the ability to react with DNA and the DNA methylase protein, either of which results in
AB  - inhibition of DNA methylation.
ER  -

TY  - JOUR
AU  - Coyne, M.J.
AU  - Zitomersky, N.L.
AU  - McGuire, A.M.
AU  - Earl, A.M.
AU  - Comstock, L.E.
TI  - Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut.
JO  - MBio
PY  - 2014
SP  - e01305
EP  - e01314
VL  - 5
AB  - The genome sequences of intestinal Bacteroidales strains reveal evidence of extensive
AB  - horizontal gene transfer. In vitro studies of Bacteroides and other bacteria have addressed
AB  - mechanisms of conjugative transfer and some phenotypic outcomes of these DNA acquisitions in
AB  - the recipient, such as the acquisition of antibiotic resistance. However, few studies have
AB  - addressed the horizontal transfer of genetic elements between bacterial species coresident in
AB  - natural microbial communities, especially microbial ecosystems of humans. Here, we examine the
AB  - genomes of Bacteroidales species from two human adults to identify genetic elements that were
AB  - likely transferred among these Bacteroidales while they were coresident in the intestine.
AB  - Using seven coresident Bacteroidales species from one individual and eight from another, we
AB  - identified five large chromosomal regions, each present in a minimum of three of the
AB  - coresident strains at near 100% DNA identity. These five regions are not found in any other
AB  - sequenced Bacteroidetes genome at this level of identity and are likely all integrative
AB  - conjugative elements (ICEs). Such highly similar and unique regions occur in only 0.4% of
AB  - phylogenetically representative mock communities, providing strong evidence that these five
AB  - regions were transferred between coresident strains in these subjects. In addition to the
AB  - requisite proteins necessary for transfer, these elements encode proteins predicted to
AB  - increase fitness, including orphan DNA methylases that may alter gene expression, fimbriae
AB  - synthesis proteins that may facilitate attachment and the utilization of new substrates,
AB  - putative secreted antimicrobial molecules, and a predicted type VI secretion system (T6SS),
AB  - which may confer a competitive ecological advantage to these strains in their complex
AB  - microbial ecosystem.IMPORTANCE By analyzing Bacteroidales strains coresident in the gut
AB  - microbiota of two human adults, we provide strong evidence for extensive interspecies and
AB  - interfamily transfer of integrative conjug!
AB  - ative el
AB  - ements within the intestinal microbiota of individual humans. In the recipient strain, we show
AB  - that the conjugative elements themselves can be modified by the transposition of insertion
AB  - sequences and retroelements from the recipient's genome, with subsequent transfer of these
AB  - modified elements to other members of the microbiota. These data suggest that the genomes of
AB  - our gut bacteria are substantially modified by other, coresident members of the ecosystem,
AB  - resulting in highly personalized Bacteroidales strains likely unique to that individual. The
AB  - genetic content of these ICEs suggests that their transfer from successful adapted members of
AB  - an ecosystem confers beneficial properties to the recipient, increasing its fitness and
AB  - allowing it to better compete within its particular personalized gut microbial ecosystem.
ER  -

TY  - JOUR
AU  - Craig, J.W.
AU  - Chang, F.Y.
AU  - Kim, J.H.
AU  - Obiajulu, S.C.
AU  - Brady, S.F.
TI  - Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 1633
EP  - 1641
VL  - 76
AB  - The small-molecule biosynthetic diversity encoded within the genomes of
AB  - uncultured bacteria is an attractive target for the discovery of natural
AB  - products using functional metagenomics. Phenotypes commonly associated
AB  - with the production of small molecules, such as antibiosis, altered
AB  - pigmentation, or altered colony morphology, are easily identified from
AB  - screens of arrayed metagenomic library clones. However, functional
AB  - metagenomic screening methods are limited by their intrinsic dependence on
AB  - a heterologous expression host. Toward the goal of increasing the
AB  - small-molecule biosynthetic diversity found in functional metagenomic
AB  - studies, we report the phenotypic screening of broad-host-range
AB  - environmental DNA libraries in six different proteobacteria: Agrobacterium
AB  - tumefaciens, Burkholderia graminis, Caulobacter vibrioides, Escherichia
AB  - coli, Pseudomonas putida, and Ralstonia metallidurans. Clone-specific
AB  - small molecules found in culture broth extracts from pigmented and
AB  - antibacterially active clones, as well as the genetic elements responsible
AB  - for the biosynthesis of these metabolites, are described. The host strains
AB  - used in this investigation provided access to unique sets of clones
AB  - showing minimal overlap, thus demonstrating the potential advantage
AB  - conferred on functional metagenomics through the use of multiple diverse
AB  - host species.
ER  -

TY  - JOUR
AU  - Craig, R.J.
AU  - Arraj, J.A.
AU  - Marinus, M.G.
TI  - Induction of damage inducible (SOS) repair in dam mutants of Escherichia coli exposed to 2-aminopurine.
JO  - Mol. Gen. Genet.
PY  - 1984
SP  - 539
EP  - 540
VL  - 194
AB  - 2-Aminopurine induces damage inducible (SOS) repair in an Escherichia coli dam-4 strain but
AB  - not in a dam-4 mutS456 derivative or in dam+ bacteria.
ER  -

TY  - JOUR
AU  - Crampton, N.
AU  - Roes, S.
AU  - Dryden, D.T.
AU  - Rao, D.N.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes.
JO  - EMBO J.
PY  - 2007
SP  - 3815
EP  - 3825
VL  - 26
AB  - EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined
AB  - orientation separated by up to 3.5 kbp to efficiently
AB  - cleave DNA. The mechanism through which site-bound EcoP15I enzymes
AB  - communicate between the two sites is unclear. Here, we use atomic force
AB  - microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number
AB  - and size distribution of loops formed, we conclude that the loops observed
AB  - do not result from translocation, but are instead formed by a contact
AB  - between site-bound EcoP15I and a nonspecific region of DNA. This
AB  - conclusion is confirmed by a theoretical polymer model. It is further
AB  - shown that translocation must play some role, because when translocation
AB  - is blocked by a Lac repressor protein, DNA cleavage is similarly blocked.
AB  - On the basis of these results, we present a model for restriction by type
AB  - III restriction enzymes and highlight the similarities between this and
AB  - other classes of restriction enzymes.
ER  -

TY  - JOUR
AU  - Crampton, N.
AU  - Yokokawa, M.
AU  - Dryden, D.T.F.
AU  - Edwardson, J.
AU  - Michael, R.
AU  - Desirazu, N.
AU  - Takeyasu, K.
AU  - Yoshimura, S.H.
AU  - Henderson, R.M.
TI  - Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 12755
EP  - 12760
VL  - 104
AB  - Many DNA-modifying enzymes act in a manner that requires communication between two
AB  - noncontiguous DNA sites.  These sites can be brought into contact either by a
AB  - diffusion-mediated chance interaction between enzymes bound at the two sites, or by active
AB  - translocation of the intervening DNA by a site-bound enzyme.  EcoP15I, a type III restriction
AB  - enzyme, needs to interact with two recognition sites separated by up to 3,500 bp before it can
AB  - cleave DNA.  Here, we have studied the behavior of EcoP15I, using a novel fast-scan atomic
AB  - force microscope, which uses a miniaturized cantilever and scan stage to reduce the mechanical
AB  - response time of the cantilever and to prevent the onset of resonant motion at high scan
AB  - speeds.  With this instrument, we were able to achieve scan rates of up to 10 frames per s
AB  - under fluid.  The improved time resolution allowed us to image EcoP15I in real time at scan
AB  - rates of 1-3 frames per s.  EcoP15I translocated DNA in an ATP-dependent manner, at a rate of
AB  - 79 +/- 33 bp/s.  The accumulation of supercoiling, as a consequence of movemennt of EcoP15I
AB  - along the DNA, could also be observed.  EcoP15I bound to its recognition site was also seen to
AB  - make nonspecific contacts with other DNA sites, thus forming DNA loops and reducing the
AB  - distance between the two recognition sites.  On the basis of our results, we conclude that
AB  - EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive
AB  - DNA loop formation and ATPase-driven translocation of the intervening DNA contour.
ER  -

TY  - JOUR
AU  - Cranz, S.
AU  - Beck, C.
AU  - Roth, M.
AU  - Jeltsch, A.
TI  - Molecular enzymology of the adenine-N6 DNA methyltransferase M.EcoRV: Site-directed mutagenesis analysis of DNA sequence and target base recognition.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A309
EP  - A309
VL  - 28
AB  - Methylation of DNA is important in many organisms and essential in mammals.  Nucleobases can
AB  - be methylated at adenine-N6, cytosine-N4 or cytosine-C6 atoms by specific DNA
AB  - methyltransferases.  The M.EcoRV DNA-(adenine-N6)-methyltransferase specifically transfers a
AB  - methyl group from AdoMet to the first adenine within GATATC sequences.  Here, we have
AB  - investigated the target base and DNA sequence recognition by M.EcoRV using site-directed
AB  - mutagenesis.  We show that variants of M.EcoRV in which active site residues are exchanged
AB  - (K16R, Y196W) show a >100 fold altered target base specificity and prefer methylation of
AB  - cytosine residues over adenine residues.  M.EcoRV is closely related to the dam DNA
AB  - methyltransferase which modifies adenine residues within GATC and M.EcoRV also accepts this
AB  - sequence.  To investigate DNA recognition by M.EcoRV, several amino acid residues in putative
AB  - DNA interacting regions were exchanged, i.e. in the variable domain of the enzyme as well as
AB  - at the N-terminus.  The mutants were analyzed with respect to their ability to modify GATATC,
AB  - GATC and GATCTC sequences in order to find out, which part of the recognition sequence is
AB  - contacted by the corresponding amino acid residue.  Our data show that some of the variants
AB  - display an increased specificity N136A, C140A, Lys141, Lys142 and Arg145 are important for DNA
AB  - binding of the enzyme, and that the N-terminal part of the M.EcoRV protein is not only
AB  - involved in AdoMet binding but also in DNA recognition.
ER  -

TY  - JOUR
AU  - Crasta, O.R.
AU  - Folkerts, O.
AU  - Fei, Z.
AU  - Mane, S.P.
AU  - Evans, C.
AU  - Martino-Catt, S.
AU  - Bricker, B.
AU  - Yu, G.
AU  - Du, L.
AU  - Sobral, B.W.
TI  - Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes.
JO  - PLoS ONE
PY  - 2008
SP  - e2193
EP  - e2193
VL  - 3
AB  - The Brucella abortus strain S19, a spontaneously attenuated strain, has been used as a vaccine
AB  - strain in vaccination of cattle against brucellosis
AB  - for six decades. Despite many studies, the physiological and molecular
AB  - mechanisms causing the attenuation are not known. We have applied
AB  - pyrosequencing technology together with conventional sequencing to rapidly
AB  - and comprehensively determine the complete genome sequence of the
AB  - attenuated Brucella abortus vaccine strain S19. The main goal of this
AB  - study is to identify candidate virulence genes by systematic comparative
AB  - analysis of the attenuated strain with the published genome sequences of
AB  - two virulent and closely related strains of B. abortus, 9-941 and 2308.
AB  - The two S19 chromosomes are 2,122,487 and 1,161,449 bp in length. A total
AB  - of 3062 genes were identified and annotated. Pairwise and reciprocal
AB  - genome comparisons resulted in a total of 263 genes that were
AB  - non-identical between the S19 genome and any of the two virulent strains.
AB  - Amongst these, 45 genes were consistently different between the attenuated
AB  - strain and the two virulent strains but were identical amongst the
AB  - virulent strains, which included only two of the 236 genes that have been
AB  - implicated as virulence factors in literature. The functional analyses of
AB  - the differences have revealed a total of 24 genes that may be associated
AB  - with the loss of virulence in S19. Of particular relevance are four genes
AB  - with more than 60 bp consistent difference in S19 compared to both the
AB  - virulent strains, which, in the virulent strains, encode an outer membrane
AB  - protein and three proteins involved in erythritol uptake or metabolism.
ER  -

TY  - JOUR
AU  - Crawford, J.T.
AU  - Cave, M.D.
AU  - Bates, J.H.
TI  - Evidence for plasmid-mediated restriction-modification in Mycobacterium avium intracellulare.
JO  - J. Gen. Microbiol.
PY  - 1981
SP  - 333
EP  - 338
VL  - 127
AB  - Mycobacterium avium intracellular strain LR25 carries three plasmids with
AB  - molecular weights of 11.2, 18.3 and 107 x 10(6) as determined by electron
AB  - microscopy.  A number of phages propagated on Mycobacterium smegmatis ATCC 607
AB  - were tested for their ability to infect strain LR25.  Phage JF2 gave an
AB  - efficiency of plating of 10-4 on strain LR25, but phage JF2 propagated on
AB  - strain LR25 infected strain LR25 and M. smegmatis with equal high efficiency.
AB  - This indicated the presence of a restriction-modification (R-M) system in
AB  - strain LR25 that was not present in M. smegmatis.  Strain LR25 was grown in the
AB  - presence of acriflavine to eliminate the plasmids and tested for sensitivity to
AB  - phage JF2.  One of forty colonies was found to be R-M-deficient.  This strain,
AB  - designated strain LR163, lacks the three plasmids present in strain LR25.  The
AB  - results indicate that the R-M system is plasmid-coded.  Strain LR163 was
AB  - sensitive to several phages to which strain LR25 was resistant and for which we
AB  - were unable to isolate modified phage.  This suggests that some plasmid-coded
AB  - function in addition to restriction is involved.  An R-M system was also
AB  - demonstrated in M. avium intracellulare strain LR131 using phage JF1.  This
AB  - strain does not carry plasmids.
ER  -

TY  - JOUR
AU  - Crawford, M.A. et al.
TI  - Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan.
JO  - Genome Announcements
PY  - 2016
SP  - e01419
EP  - e01416
VL  - 4
AB  - The emergence and spread of colistin resistance among multidrug-resistant (MDR) Klebsiella
AB  - pneumoniae represent a critical threat to global health. Here, we
AB  - report the complete genome sequences of 10 MDR, colistin-susceptible and
AB  - -resistant K. pneumoniae clinical isolates obtained in Pakistan between 2010 and
AB  - 2013.
ER  -

TY  - JOUR
AU  - Cregg, J.M.
AU  - Nguyen, A.H.
AU  - Ito, J.
TI  - DNA modification induced during infection of Bacillus subtilis by phage Phi3T.
JO  - Gene
PY  - 1980
SP  - 17
EP  - 24
VL  - 12
AB  - The DNA of the Bacillus subtilis temperate phage Phi3T is not susceptible to
AB  - cleavage by the restriction endonuclease HaeIII, although it is cut by many
AB  - other restriction enzymes.  The host DNA from uninfected cells is cut by
AB  - HaeIII.  We show that Phi3T DNA propagated in a
AB  - restriction-modification-defective Escherichia coli cell can be digested by
AB  - HaeIII.  Thus, Phi3T DNA does contain the nucleotide recognition sequence of
AB  - HaeIII.  We suggest that this phage induces the modification of its own DNA.
AB  - In support of this mechanism we show that extracts prepared from Phi3T-infected
AB  - cells contain an activity which in the presence of S-adenosyl-L-methionine
AB  - (SAM) can modify lambda DNA against cleavage by HaeIII.  The same in
AB  - vitro-modified DNA is still susceptible to cleavage by other restriction
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Cregg, J.M.
AU  - Stewart, C.R.
TI  - EcoRI cleavage of DNA from Bacillus subtilis phage SPO1.
JO  - Virology
PY  - 1978
SP  - 601
EP  - 605
VL  - 85
AB  - The hydroxymethyluracil-containing DNA of B. subtilis phage SPO1 is cleaved only with low
AB  - efficiency by restriction nuclease EcoRI.  The efficiency is greatly increased by EcoRI*
AB  - conditions, but even under these conditions, the efficiency is less than with
AB  - thymine-containing DNA.  In contrast with their effect on thymine-containing DNA, EcoRI*
AB  - conditions do not appear to increase the number of sites on the SPO1 genome at which cleavage
AB  - takes place.  We describe the fragments produced by a (nearly) limit digest of SPO1 DNA with
AB  - EcoRI and assign most of the known SPO1 cistrons to specific fragments.
ER  -

TY  - JOUR
AU  - Cress, B.F.
AU  - Erkert, K.A.
AU  - Barquera, B.
AU  - Koffas, M.A.
TI  - Draft Genome Sequence of Pseudoalteromonas luteoviolacea Strain B (ATCC 29581).
JO  - Genome Announcements
PY  - 2013
SP  - e0004813
EP  - e0004813
VL  - 1
AB  - We report the 4.049-Mbp high-quality draft assembly of the Pseudoalteromonas luteoviolacea
AB  - strain B (ATCC 29581) genome. This marine species is known to
AB  - biosynthesize several antimicrobial compounds, including the purple pigment
AB  - violacein. Whole-genome sequencing and genome mining will complement experimental
AB  - studies aimed at elucidating novel biosynthetic pathways capable of producing
AB  - pharmaceutically relevant molecules. Based upon 16S rRNA phylogenetic analysis,
AB  - we propose that strain ATCC 29581 be classified as a distinct phylogenetic
AB  - species of the genus Pseudoalteromonas.
ER  -

TY  - JOUR
AU  - Cress, B.F.
AU  - Greene, Z.R.
AU  - Linhardt, R.J.
AU  - Koffas, M.A.
TI  - Draft Genome Sequence of Escherichia coli Strain ATCC 23506 (Serovar O10:K5:H4).
JO  - Genome Announcements
PY  - 2013
SP  - e0004913
EP  - e0004913
VL  - 1
AB  - We report the 5.101-Mbp high-quality draft assembly of the Escherichia coli strain ATCC 23506
AB  - (serovar O10:K5:H4, also known as NCDC Bi 8337-41) genome. This
AB  - uropathogenic strain, commonly referred to as E. coli K5, produces N-acetyl
AB  - heparosan, a glycosaminoglycan-like capsular polysaccharide and precursor to the
AB  - anticoagulant pharmaceutical heparin. Metabolic reconstruction of this genome
AB  - will enable the prediction of gene deletions and overexpressions that lead to
AB  - increased heparosan production.
ER  -

TY  - JOUR
AU  - Cress, B.F.
AU  - Greene, Z.R.
AU  - Linhardt, R.J.
AU  - Koffas, M.A.
TI  - Draft Genome Sequence of Escherichia coli Strain ATCC 23502 (Serovar O5:K4:H4).
JO  - Genome Announcements
PY  - 2013
SP  - e0004613
EP  - e0004613
VL  - 1
AB  - We report the 4.682-Mbp high-quality draft assembly of the Escherichia coli strain ATCC 23502
AB  - (serovar O5:K4:H4, also known as NCDC U1-41) genome. This
AB  - uropathogenic strain, commonly referred to as E. coli K4, produces a
AB  - glycosaminoglycan-like capsular polysaccharide with a backbone similar in
AB  - structure to unsulfated chondroitin, a precursor to the nutraceutically and
AB  - potentially pharmaceutically valuable compound chondroitin sulfate. Metabolic
AB  - reconstruction of this genome will enable prediction of genetic engineering
AB  - strategies leading to increased chondroitin production.
ER  -

TY  - JOUR
AU  - Cress, B.F.
AU  - Linhardt, R.J.
AU  - Koffas, M.A.
TI  - Draft Genome Sequence of Escherichia coli Strain Nissle 1917 (Serovar O6:K5:H1).
JO  - Genome Announcements
PY  - 2013
SP  - e0004713
EP  - e0004713
VL  - 1
AB  - We announce the availability of the 5.023-Mbp high-quality draft assembly of the  Escherichia
AB  - coli strain Nissle 1917 (serovar O6:K5:H1) genome. Short genomic
AB  - segments from this important probiotic strain have been available in public
AB  - databases, but the full genome sequence has remained inaccessible. Thus,
AB  - high-coverage, whole genome sequencing of E. coli Nissle 1917 is presented
AB  - herein. Reannotation and metabolic reconstruction will enable comparative
AB  - genomics analysis and model-guided predictions of genetic manipulations leading
AB  - to increased production of the K5 capsular polysaccharide known as N-acetyl
AB  - heparosan, a precursor to the anticoagulant pharmaceutical heparin.
ER  -

TY  - JOUR
AU  - Criscuolo, A.
AU  - Chesneau, O.
AU  - Clermont, D.
AU  - Bizet, C.
TI  - Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753).
JO  - Genome Announcements
PY  - 2018
SP  - e00222
EP  - e00218
VL  - 6
AB  - Flavobacterium columnare strain PH-97028 (=CIP 109753) is a genomovar III reference strain
AB  - that was isolated from a diseased Ayu fish in Japan. We report
AB  - here the analysis of the first available genomovar III sequence of this species
AB  - to aid in identification, epidemiological tracking, and virulence studies.
ER  -

TY  - JOUR
AU  - Criscuolo, A.
AU  - de la Blanchardiere, A.
AU  - Coeuret, S.
AU  - Passet, V.
AU  - Saguet-Rysanek, V.
AU  - Vergnaud, M.
AU  - Verdon, R.
AU  - Leclercq, A.
AU  - Lecuit, M.
AU  - Brisse, S.
TI  - Draft Genome Sequence of Campylobacter coli Strain IPSID-1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease.
JO  - Genome Announcements
PY  - 2014
SP  - e00079
EP  - e00014
VL  - 2
AB  - The genome sequence and annotation of Campylobacter coli strain IPSID-1 are reported here.
AB  - This bacterial isolate is the first to be cultured from a patient
AB  - with immunoproliferative small intestinal disease (IPSID). The draft genome
AB  - sequence is 1.683 Mb long, comprises 64 contigs, and has 31.26% G+C content.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Hugon, P.
AU  - Lagier, J.C.
AU  - Bibi, F.
AU  - Robert, C.
AU  - Azhar, E.I.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Bacillus simplex Strain P558, Isolated from a Human Fecal Sample.
JO  - Genome Announcements
PY  - 2014
SP  - e01241
EP  - e01214
VL  - 2
AB  - Bacillus simplex strain P558 was isolated from a fecal sample of a 25-year-old Saudi male. We
AB  - sequenced the 5.98-Mb genome of the strain and compared it to that
AB  - of B. simplex strain 1NLA3E.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium vulneris DSM 45247T.
JO  - Genome Announcements
PY  - 2014
SP  - e00370
EP  - e00314
VL  - 2
AB  - We report the draft genome sequence of Mycobacterium vulneris DSM 45247(T) strain, an
AB  - emerging, opportunistic pathogen of the Mycobacterium avium complex.
AB  - The genome described here is composed of 6,981,439 bp (with a G+C content of
AB  - 67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium mageritense DSM 44476T.
JO  - Genome Announcements
PY  - 2014
SP  - e00354
EP  - e00314
VL  - 2
AB  - We report the draft genome sequence of Mycobacterium mageritense strain DSM 44476(T) (CIP
AB  - 104973), a nontuberculosis species responsible for various
AB  - infections. The genome described here is composed of 7,966,608 bp, with a G+C
AB  - content of 66.95%, and contains 7,675 protein-coding genes and 120 predicted RNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium asiaticum Strain DSM 44297.
JO  - Genome Announcements
PY  - 2014
SP  - e00320
EP  - e00314
VL  - 2
AB  - We report the draft genome sequence of Mycobacterium asiaticum strain DSM 44297,  a tropical
AB  - mycobacterium seldom responsible for human infection. The genome of M. asiaticum has a size of
AB  - 5,935,986 bp, with a 66.03% G+C content, encoding 5,591 proteins and 81 RNAs.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium austroafricanum DSM 44191.
JO  - Genome Announcements
PY  - 2014
SP  - e00317
EP  - e00314
VL  - 2
AB  - We announce the draft genome sequence of Mycobacterium austroafricanum DSM 44191(T) (=
AB  - E9789-SA12441(T)), a non-tuberculosis species responsible for opportunistic infection. The
AB  - genome described here has a size of 6,772,357 bp with a G+C content of 66.79% and contains
AB  - 6,419 protein-coding genes and 112 RNA genes.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829.
JO  - Genome Announcements
PY  - 2014
SP  - e00315
EP  - e00314
VL  - 2
AB  - We announce the draft genome sequence of Mycobacterium cosmeticum strain DSM 44829, a
AB  - nontuberculous species responsible for opportunistic infection. The genome described here is
AB  - composed of 6,462,090 bp, with a G+C content of 68.24%. It contains 6,281 protein-coding genes
AB  - and 75 predicted RNA genes.
ER  -

TY  - JOUR
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955.
JO  - Genome Announcements
PY  - 2014
SP  - e00523
EP  - e00514
VL  - 2
AB  - We report the draft genome sequence of Mycobacterium farcinogenes NCTC 10955 (=DSM 43637(T)),
AB  - a nontuberculosis species responsible for bovine farcy. The
AB  - strain described here is composed of 6,139,893 bp, with a G+C content of 65.73%,
AB  - and contains 5,816 protein-coding genes and 76 RNA genes.
ER  -

TY  - JOUR
AU  - Crofts, T.S.
AU  - Wang, B.
AU  - Spivak, A.
AU  - Gianoulis, T.A.
AU  - Forsberg, K.J.
AU  - Gibson, M.K.
AU  - Johnsky, L.A.
AU  - Broomall, S.M.
AU  - Rosenzweig, C.N.
AU  - Skowronski, E.W.
AU  - Gibbons, H.S.
AU  - Sommer, M.O.A.
AU  - Dantas, G.
TI  - Draft Genome Sequences of Three beta-Lactam-Catabolizing Soil Proteobacteria.<jour_book>Genome Announc.
JO  - 
PY  - 2017
SP  - e00653
EP  - e00617
VL  - 5
AB  - Most antibiotics are derived from the soil, but their catabolism there, which is  necessary to
AB  - close the antibiotic carbon cycle, remains uncharacterized. We
AB  - report the first draft genome sequences of soil Proteobacteria identified for
AB  - subsisting solely on beta-lactams as their carbon sources. The genomes encode
AB  - multiple beta-lactamases, although their antibiotic catabolic pathways remain
AB  - enigmatic.
ER  -

TY  - JOUR
AU  - Crombie, A.T.
AU  - Emery, H.
AU  - McGenity, T.J.
AU  - Murrell, J.C.
TI  - Draft Genome Sequences of Three Terrestrial Isoprene-Degrading Rhodococcus Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e01256
EP  - e01217
VL  - 5
AB  - Isoprene is produced in abundance by plants and constitutes a carbon source for microbes. The
AB  - genomes of three isoprene degraders isolated from tree leaves or
AB  - soil from the campus of the University of East Anglia were sequenced. These
AB  - high-GC-content isolates are actinobacteria belonging to the genus Rhodococcus.
ER  -

TY  - JOUR
AU  - Crook, M.B.
AU  - Mitra, S.
AU  - Ane, J.M.
AU  - Sadowsky, M.J.
AU  - Gyaneshwar, P.
TI  - Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74.
JO  - Genome Announcements
PY  - 2013
SP  - e00934
EP  - e00913
VL  - 1
AB  - Rhizobium sp. strain IRBG74 is the first known nitrogen-fixing symbiont in the
AB  - Agrobacterium/Rhizobium clade that nodulates the aquatic legume Sesbania sp. and
AB  - is also a growth-promoting endophyte of wetland rice. Here, we present the
AB  - sequence of the IRBG74 genome, which is composed of a circular chromosome, a
AB  - linear chromosome, and a symbiotic plasmid, pIRBG74a.
ER  -

TY  - JOUR
AU  - Crooks, C.
AU  - Palmer, J.M.
AU  - Lindner, D.L.
TI  - Draft Genome Sequence of Burkholderia cepacia ATCC 17759, a Polyhydroxybutyrate-Co-Valerate Copolymer-Producing Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00348
EP  - e00318
VL  - 6
AB  - Burkholderia cepacia ATCC 17759, isolated from forest soils in Trinidad, accumulates large
AB  - amounts of polyhydroxyalkanoate copolymers when grown on
AB  - xylose, mannose, arabinose, other carbohydrates, and organic acid cosubstrates.
AB  - This 8.72-Mb draft genome sequence of B. cepacia ATCC 17759 will provide better
AB  - insight into this organism's utility in lignocellulose bioconversion.
ER  -

TY  - JOUR
AU  - Crooks, P.A.
AU  - Tribe, M.J.
AU  - Pinney, R.J.
TI  - Inhibition of bacterial DNA cytosine-5-methyltransferase by S-adenosyl-L-homocysteine and some related compounds.
JO  - J. Pharm. Pharmacol.
PY  - 1984
SP  - 85
EP  - 89
VL  - 36
AB  - S-Adenosyl-L-homocysteine and five related compounds have been evaluated as inhibitors of a
AB  - DNA cytosine-5-methyltransferase. DNA methylation was assayed in cell extracts from E. coli
AB  - strain J6-2 dcm+, proficient in DNA cytosine-5-methyltransferase activity, containing
AB  - substrate DNA isolated from E. coli strain J6-2 dcm-, a strain deficient in DNA
AB  - cytosine-5-methyltransferase. S-Adenosyl-L-homocysteine and its 7-deaza analogue,
AB  - S-tubercidinylhomocysteine, were competitive inhibitors of DNA cytosine-5-methyltransferase
AB  - with Ki's of 14.2 and 17.6 microM, respectively, in the above enzyme assay.
ER  -

TY  - JOUR
AU  - Cross, K.L.
AU  - Chirania, P.
AU  - Xiong, W.
AU  - Beall, C.J.
AU  - Elkins, J.G.
AU  - Giannone, R.J.
AU  - Griffen, A.L.
AU  - Guss, A.M.
AU  - Hettich, R.L.
AU  - Joshi, S.S.
AU  - Mokrzan, E.M.
AU  - Martin, R.K.
AU  - Zhulin, I.B.
AU  - Leys, E.J.
AU  - Podar, M.
TI  - Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.
JO  - MBio
PY  - 2018
SP  - e02061
EP  - e02017
VL  - 9
AB  - The human oral microbiota encompasses representatives of many bacterial lineages  that have
AB  - not yet been cultured. Here we describe the isolation and
AB  - characterization of previously uncultured Desulfobulbus oralis, the first
AB  - human-associated representative of its genus. As mammalian-associated microbes
AB  - rarely have free-living close relatives, D. oralis provides opportunities to
AB  - study how bacteria adapt and evolve within a host. This sulfate-reducing
AB  - deltaproteobacterium has adapted to the human oral subgingival niche by
AB  - curtailing its physiological repertoire, losing some biosynthetic abilities and
AB  - metabolic independence, and by dramatically reducing environmental sensing and
AB  - signaling capabilities. The genes that enable free-living Desulfobulbus to
AB  - synthesize the potent neurotoxin methylmercury were also lost by D. oralis, a
AB  - notably positive outcome of host association. However, horizontal gene
AB  - acquisitions from other members of the microbiota provided novel mechanisms of
AB  - interaction with the human host, including toxins like leukotoxin and hemolysins.
AB  - Proteomic and transcriptomic analysis revealed that most of those factors are
AB  - actively expressed, including in the subgingival environment, and some are
AB  - secreted. Similar to other known oral pathobionts, D. oralis can trigger a
AB  - proinflammatory response in oral epithelial cells, suggesting a direct role in
AB  - the development of periodontal disease.IMPORTANCE Animal-associated microbiota
AB  - likely assembled as a result of numerous independent colonization events by
AB  - free-living microbes followed by coevolution with their host and other microbes.
AB  - Through specific adaptation to various body sites and physiological niches,
AB  - microbes have a wide range of contributions, from beneficial to disease causing.
AB  - Desulfobulbus oralis provides insights into genomic and physiological
AB  - transformations associated with transition from an open environment to a
AB  - host-dependent lifestyle and the emergence of pathogenicity. Through a
AB  - multifaceted mechanism triggering a proinflammatory response, D. oralis is a
AB  - novel periodontal pathobiont. Even though culture-independent approaches can
AB  - provide insights into the potential role of the human microbiome 'dark matter,'
AB  - cultivation and experimental characterization remain important to studying the
AB  - roles of individual organisms in health and disease.
ER  -

TY  - JOUR
AU  - Cross, S.H.
AU  - Meehan, R.R.
AU  - Nan, X.
AU  - Bird, A.
TI  - A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins.
JO  - Nat. Genet.
PY  - 1997
SP  - 256
EP  - 259
VL  - 16
AB  - Methylation of cytosines within the sequence CpG is essential for mouse development and has
AB  - been linked to transcriptional suppression in vertebrate systems.  Methyl-CpG binding proteins
AB  - (MeCPs) 1 and 2 bind preferentially to methylated DNA and can inhibit transcription.  The gene
AB  - for MeCP2 has been cloned and a methyl-CpG binding domain within it has been defined.  A
AB  - search of DNA sequence databases with the MBD sequence identified a human cDNA with potential
AB  - to encode an MBD-like region.  Sequencing of the complete cDNA revealed that the open reading
AB  - frame also encodes two cysteine-rich domains that are found in animal DNA methyltransferases
AB  - and in the mammalian HRX protein (also known as MLL and ALL-1).  HRX is related to Drosophila
AB  - trithorax.  The protein, known as Protein Containing MBD (PCM1), was expressed in bacteria and
AB  - shown to bind specifically to methylated DNA.  PCM1 also repressed transcription in vitro in a
AB  - methylation-dependent manner.  A polyclonal antibody raised against the protein was able to
AB  - 'supershift' the native MeCP1 complex from HeLa cells, indicating that PCM1 is a component
AB  - of mammalian MeCP1.
ER  -

TY  - JOUR
AU  - Crossman, L.C. et al.
TI  - A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5822
EP  - 5831
VL  - 192
AB  - In most cases, Escherichia coli exists as a harmless commensal organism, but it may on
AB  - occasion cause intestinal and/or extraintestinal disease.
AB  - Enterotoxigenic E. coli (ETEC) is the predominant cause of E.
AB  - coli-mediated diarrhea in the developing world and is responsible for a
AB  - significant portion of pediatric deaths. In this study, we determined the
AB  - complete genomic sequence of E. coli H10407, a prototypical strain of
AB  - enterotoxigenic E. coli, which reproducibly elicits diarrhea in human
AB  - volunteer studies. We performed genomic and phylogenetic comparisons with
AB  - other E. coli strains, revealing that the chromosome is closely related to
AB  - that of the nonpathogenic commensal strain E. coli HS and to those of the
AB  - laboratory strains E. coli K-12 and C. Furthermore, these analyses
AB  - demonstrated that there were no chromosomally encoded factors unique to
AB  - any sequenced ETEC strains. Comparison of the E. coli H10407 plasmids with
AB  - those from several ETEC strains revealed that the plasmids had a mosaic
AB  - structure but that several loci were conserved among ETEC strains. This
AB  - study provides a genetic context for the vast amount of experimental and
AB  - epidemiological data that have been published.
ER  -

TY  - JOUR
AU  - Crossman, L.C. et al.
TI  - The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug  resistance determinants.
JO  - Genome Biol.
PY  - 2008
SP  - R74
EP  - R74
VL  - 9
AB  - ABSTRACT: BACKGROUND: Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of
AB  - the Xanthomonadaceae. The organism has been
AB  - isolated from both clinical and soil environments in addition to the
AB  - sputum of cystic fibrosis patients and the immunocompromised. Whilst
AB  - relatively distant phylogenetically, the closest sequenced relatives of S.
AB  - maltophilia are the plant pathogenic xanthomonads. RESULTS: The genome of
AB  - the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and
AB  - of high G+C content. The sequence reveals an organism with a remarkable
AB  - capacity for drug and heavy metal resistance. In addition to a number of
AB  - genes conferring resistance to antimicrobial drugs of different classes
AB  - via alternative mechanisms, nine resistance-nodulation-division (RND)-type
AB  - putative antimicrobial efflux systems are present. Functional genomic
AB  - analysis confirms a role in drug resistance for several of the novel RND
AB  - efflux pumps. S. maltophilia possesses potentially mobile regions of DNA
AB  - and encodes a number of pili and fimbriae likely to be involved in
AB  - adhesion and biofilm formation that may also contribute to increased
AB  - antimicrobial drug resistance. CONCLUSION: The panoply of antimicrobial
AB  - drug resistance genes and mobile genetic elements found suggests that the
AB  - organism can act as a reservoir of antimicrobial drug resistance
AB  - determinants in a clinical environment, which is an issue of considerable
AB  - concern.
ER  -

TY  - JOUR
AU  - Croucher, N.J. et al.
TI  - Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection.
JO  - PLoS Genet.
PY  - 2013
SP  - e1003868
EP  - e1100386
VL  - 9
AB  - Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated
AB  - with high mortality rates
AB  - relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81
AB  - draft sequences from clonal
AB  - complex 180, the predominant serotype 3 clone in much of the world, found most sampled
AB  - isolates belonged to a clade
AB  - affected by few diversifying recombinations. However, other isolates indicate significant
AB  - genetic variation has accumulated
AB  - over the clonal complex's entire history. Two closely related genomes, one from the blood and
AB  - another from the
AB  - cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their
AB  - behaviour in a mouse model of
AB  - disease and in their susceptibility to antimicrobials, with at least some of these changes
AB  - attributable to a mutation that upregulated
AB  - the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate
AB  - rapidly through
AB  - small alterations to the genotype.
ER  -

TY  - JOUR
AU  - Croucher, N.J.
AU  - Coupland, P.G.
AU  - Stevenson, A.E.
AU  - Callendrello, A.
AU  - Bentley, S.D.
AU  - Hanage, W.P.
TI  - Diversification of bacterial genome content through distinct mechanisms over different timescales.
JO  - Nat. Commun.
PY  - 2014
SP  - 5471
EP  - 5471
VL  - 5
AB  - Bacterial populations often consist of multiple co-circulating lineages. Determining how such
AB  - population structures arise requires understanding what drives bacterial diversification.
AB  - Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are
AB  - typically characterized by combinations of infrequently transferred stable genomic islands:
AB  - those moving primarily through transformation, along with integrative and conjugative elements
AB  - and phage-related chromosomal islands. The only lineage containing extensive unique sequence
AB  - corresponds to a set of atypical unencapsulated isolates that may represent a distinct
AB  - species. However, prophage content is highly variable even within lineages, suggesting
AB  - frequent horizontal transmission that would necessitate rapidly diversifying antiphage
AB  - mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci
AB  - encoding Type I restriction-modification systems able to change their specificity over short
AB  - timescales through intragenomic recombination are ubiquitous across the collection. Hence
AB  - short-term pneumococcal variation is characterized by movement of phage and intragenomic
AB  - rearrangements, with the slower transfer of stable loci distinguishing lineages.
ER  -

TY  - JOUR
AU  - Croucher, N.J.
AU  - Walker, D.
AU  - Romero, P.
AU  - Lennard, N.
AU  - Paterson, G.K.
AU  - Bason, N.C.
AU  - Mitchell, A.M.
AU  - Quail, M.A.
AU  - Andrew, P.W.
AU  - Parkhill, J.
AU  - Bentley, S.D.
AU  - Mitchell, T.J.
TI  - Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1480
EP  - 1489
VL  - 191
AB  - Streptococcus pneumoniae is a human commensal and pathogen able to cause a variety of diseases
AB  - that annually result in over a million deaths worldwide. The
AB  - S. pneumoniae(Spain23F) sequence type 81 lineage was among the first recognized
AB  - pandemic clones and was responsible for almost 40% of penicillin-resistant
AB  - pneumococcal infections in the United States in the late 1990s. Analysis of the
AB  - chromosome sequence of a representative strain, and comparison with other
AB  - available genomes, indicates roles for integrative and conjugative elements in
AB  - the evolution of pneumococci and, more particularly, the emergence of the
AB  - multidrug-resistant Spain 23F ST81 lineage. A number of recently acquired loci
AB  - within the chromosome appear to encode proteins involved in the production of, or
AB  - immunity to, antimicrobial compounds, which may contribute to the proficiency of
AB  - this strain at nasopharyngeal colonization. However, further sequencing of other
AB  - pandemic clones will be required to establish whether there are any general
AB  - attributes shared by these strains that are responsible for their international
AB  - success.
ER  -

TY  - JOUR
AU  - Crouzier, L.
AU  - Dubois, C.
AU  - Wengel, J.
AU  - Veedu, R.N.
TI  - Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases.
JO  - Bioorg. Med. Chem. Lett.
PY  - 2012
SP  - 4836
EP  - 4838
VL  - 22
AB  - Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far.
AB  - We herein for the first time report cleavage
AB  - by restriction endonuclease of LNA-modified DNA oligonucleotides. The
AB  - experiments revealed that RsaI is an efficient enzyme capable of
AB  - recognizing and cleaving LNA-modified DNA oligonucleotides.
AB  - Furthermore, introduction of LNA nucleotides protects against cleavage
AB  - by the restriction endonucleases PvuII, PstI, SacI, KpnI and EcoRI.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Chablais, R.
AU  - Cochard, B.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Enteractinococcus helveticum sp. nov. Strain UASWS1574 Isolated from Industrial Used Waters.
JO  - Genome Announcements
PY  - 2016
SP  - e00756
EP  - e00716
VL  - 4
AB  - We report here the whole-genome shotgun sequences of the strain UASWS1574 of the  undescribed
AB  - Enteractinococcus helveticum sp. nov., isolated from used water. This
AB  - is the first genome registered for the whole genus.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Chablais, R.
AU  - Cochard, B.
AU  - Schulz, T.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Pseudomonas graminis Strain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland.
JO  - Genome Announcements
PY  - 2016
SP  - e01096
EP  - e01016
VL  - 4
AB  - We report here the whole-genome shotgun sequence of the strain UASWS1507 of the species
AB  - Pseudomonas graminis, isolated in Switzerland from an apple tree. This is
AB  - the first genome registered for this species, which is considered as a potential
AB  - and valuable resource of biological control agents and biofertilizers for
AB  - agriculture.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Chablais, R.
AU  - Cochard, B.
AU  - Schulz, T.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1016, a Potential Symbiotic Biofertilizer for Agriculture.
JO  - Genome Announcements
PY  - 2016
SP  - e01095
EP  - e01016
VL  - 4
AB  - Bradyrhizobium elkanii UASWS1016 has been isolated from a wet oxidation sewage plant in Italy.
AB  - Fully equipped for ammonia assimilation, heavy metal resistances,
AB  - and aromatic compounds degradation, it carries a large type IV secretion system,
AB  - specific of plant-associated microbes. Deprived of toxins, it could be considered
AB  - for agricultural and environmental uses.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Cochard, B.
AU  - Chablais, R.
AU  - Grizard, D.
AU  - Berthon, J.Y.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules.
JO  - Genome Announcements
PY  - 2015
SP  - e01153
EP  - e01115
VL  - 3
AB  - We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant
AB  - nitrifying strain isolated from sewage sludge aerobic granules,  which displays adequate
AB  - genetic equipment for soil depollution, sludge treatment, and biological fertilization in
AB  - agriculture.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Cochard, B.
AU  - Chablais, R.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1015, a Highly Ammonia-Tolerant Nitrifying Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00111
EP  - e00116
VL  - 4
AB  - Bradyrhizobium elkanii UASWS1015 was isolated from a sewage plant in Switzerland. Its genome
AB  - indicates that it is fully equipped for ammonia assimilation and
AB  - aromatic compound degradation, and it displays a large type IV secretion system,
AB  - which characterizes plant-associated microbes. Totally deprived of toxins, it
AB  - could be considered for agricultural and environmental uses.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Tonacini, J.
AU  - Chablais, R.
AU  - Baumgartner, A.
AU  - Schnyder, B.
AU  - Hodille, E.
AU  - Lefort, F.
TI  - Whole-Genome Sequences of 15 Strains of Staphylococcus aureus subsp. aureus Isolated from Foodstuff and Human Clinical Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e00684
EP  - e00615
VL  - 3
AB  - The whole-genome sequences of 15 strains of Staphylococcus aureus (10 strains isolated from
AB  - foodstuff samples in Switzerland and five from human clinical
AB  - samples) were obtained by Illumina sequencing. Most strains fit within the known
AB  - diversity for the species, but one (SA-120) possessed a higher G+C content and a
AB  - higher number of genes than usual.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Calmin, G.
AU  - Tonacini, J.
AU  - Chablais, R.
AU  - Schnyder, B.
AU  - Messelhausser, U.
AU  - Lefort, F.
TI  - Whole-Genome Sequences of Seven Strains of Bacillus cereus Isolated from Foodstuff or Poisoning Incidents.
JO  - Genome Announcements
PY  - 2016
SP  - e00435
EP  - e00416
VL  - 4
AB  - We present here the whole shotgun genome sequences of seven strains of Bacillus cereus
AB  - isolated from foodstuff samples or food poisoning incidents.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Cochard, B.
AU  - Calmin, G.
AU  - Chablais, R.
AU  - Schulz, T.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses.
JO  - Genome Announcements
PY  - 2016
SP  - e01158
EP  - e01116
VL  - 4
AB  - We report here the whole-genome shotgun sequences of the strain UASWS1009 of the  species
AB  - Mesorhizobium hungaricum sp. nov., which are different from any other
AB  - known Mesorhizobium species. This is the first genome registered for this new
AB  - species, which could be considered as a potential resource for agriculture and
AB  - environmental uses.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Cochard, B.
AU  - Calmin, G.
AU  - Chablais, R.
AU  - Schulz, T.
AU  - Lefort, F.
TI  - Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses.
JO  - Genome Announcements
PY  - 2016
SP  - e01136
EP  - e01116
VL  - 4
AB  - We report here the whole-genome shotgun sequence of the strain UASWS0955 of the species
AB  - Pseudomonas xanthomarina, isolated from sewage sludge. This genome was
AB  - obtained with an Illumina MiniSeq and is the second genome registered for this
AB  - species, which is considered as a promising resource for agriculture and
AB  - bioremediation of contaminated soils.
ER  -

TY  - JOUR
AU  - Crovadore, J.
AU  - Xu, S.
AU  - Chablais, R.
AU  - Cochard, B.
AU  - Lukito, D.
AU  - Calmin, G.
AU  - Lefort, F.
TI  - Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant.
JO  - Genome Announcements
PY  - 2017
SP  - e00221
EP  - e00217
VL  - 5
AB  - We report here the draft genome sequence of strain ELI 1980 of Rhodopseudomonas palustris,
AB  - commercialized as a biostimulant for agriculture. The genome was
AB  - reconstructed from the metagenome of a commercial product containing this strain
AB  - as its major component.
ER  -

TY  - JOUR
AU  - Crowe, S.A.
AU  - Hahn, A.S.
AU  - Morgan-Lang, C.
AU  - Thompson, K.J.
AU  - Simister, R.L.
AU  - Lliros, M.
AU  - Hirst, M.
AU  - Hallam, S.J.
TI  - Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans.
JO  - Genome Announcements
PY  - 2017
SP  - e01584
EP  - e01516
VL  - 5
AB  - Here, we report the draft genome sequence of Chlorobium phaeoferrooxidans, a photoferrotrophic
AB  - member of the genus Chlorobium in the phylum Chlorobi This
AB  - genome sequence provides insight into the metabolic capacity that underpins
AB  - photoferrotrophy within low-light-adapted pelagic Chlorobi.
ER  -

TY  - JOUR
AU  - Crowley, S.
AU  - Bottacini, F.
AU  - Mahony, J.
AU  - van Sinderen, D.
TI  - Complete Genome Sequence of Lactobacillus plantarum Strain 16, a Broad-Spectrum Antifungal-Producing Lactic Acid Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00533
EP  - e00513
VL  - 1
AB  - Lactobacillus plantarum strain 16 restricts the growth of various food spoilage fungi and has
AB  - the potential to be used as a biopreservative to improve the shelf
AB  - life of foods. The complete genome sequence contains 3,044,678 bp with a G+C
AB  - content of 44.74% and harbors the largest plasmid complement reported for this
AB  - species to date.
ER  -

TY  - JOUR
AU  - Cruz, A.K.
AU  - Kidane, G.
AU  - Pires, M.Q.
AU  - Rabinovitch, L.
AU  - Guaycurus, T.V.
AU  - Morel, C.M.
TI  - An Sau3AI restriction endonuclease isoschizomer from Bacillus cereus.
JO  - FEBS Lett.
PY  - 1984
SP  - 99
EP  - 102
VL  - 173
AB  - The isolation and characterization of a restriction endonuclease from Bacillus
AB  - cereus 10C 243 are described.  The enzyme recognizes the palindromic sequence
AB  - 5'-G(met-A,A)TC-3' as determined by PEI chromatography of pancreatic DNase,
AB  - snake venom phosphodiesterase digestion products of labelled fragments,
AB  - analysis of restriction digests from normal and N6-methyladenine-free DNA and
AB  - direct sequence analysis of cloned fragments.  The staggered cleavage products
AB  - with 5'-terminal pGATC extensions are efficiently labelled with polynucleotide
AB  - kinase and are easily cloned into BamHI sites.  The enzyme, denoted Bce243, is
AB  - thus an isoschizomer of SauAI.  Its use and potential advantages in
AB  - substituting Sau3AI are discussed.
ER  -

TY  - JOUR
AU  - Cruz, A.K.
AU  - Pires, M.Q.
AU  - Lima, V.G.
AU  - Morel, C.M.
TI  - Restriction endonucleases from microorganisms isolated in Brazil: an isoschizomer of HaeIII from a thermophilic Bacillus sp.
JO  - Braz. J. Med. Biol. Res.
PY  - 1989
SP  - 1321
EP  - 1328
VL  - 22
AB  - The isolation and characterization of a restriction endonuclease from a
AB  - thermophilic strain of Bacillus is described.  The enzyme recognizes the
AB  - palindromic sequence 5' GGCC 3' as determined by PEI-cellulose chromatography
AB  - of pancreatic DNAse and snake venom phosphodiesterase digestion products of
AB  - labelled DNA fragments, analysis of restriction digests and direct sequence
AB  - analysis.  The enzyme, denominated BspBR, is an isoschizomer of HaeIII and
AB  - BspRI.
ER  -

TY  - JOUR
AU  - Cruz-Morales, P.
AU  - Vijgenboom, E.
AU  - Iruegas-Bocardo, F.
AU  - Girard, G.
AU  - Yanez-Guerra, L.A.
AU  - Ramos-Aboites, H.E.
AU  - Pernodet, J.L.
AU  - Anne, J.
AU  - van Wezel, G.P.
AU  - Barona-Gomez, F.
TI  - The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 1165
EP  - 1175
VL  - 5
AB  - The complete genome sequence of the original isolate of the model actinomycete
AB  - Streptomyces lividans 66, also referred to as 1326, was deciphered after a
AB  - combination of next-generation sequencing platforms and a hybrid assembly
AB  - pipeline. Comparative analysis of the genomes of S. lividans 66 and closely
AB  - related strains, including S. coelicolor M145 and S. lividans TK24, was used to
AB  - identify strain-specific genes. The genetic diversity identified included a large
AB  - genomic island with a mosaic structure, present in S. lividans 66 but not in the
AB  - strain TK24. Sequence analyses showed that this genomic island has an anomalous
AB  - (G + C) content, suggesting recent acquisition and that it is rich in
AB  - metal-related genes. Sequences previously linked to a mobile conjugative element,
AB  - termed plasmid SLP3 and defined here as a 94 kb region, could also be identified
AB  - within this locus. Transcriptional analysis of the response of S. lividans 66 to
AB  - copper was used to corroborate a role of this large genomic island, including two
AB  - SLP3-borne "cryptic" peptide biosynthetic gene clusters, in metal homeostasis.
AB  - Notably, one of these predicted biosynthetic systems includes an unprecedented
AB  - nonribosomal peptide synthetase--tRNA-dependent transferase biosynthetic hybrid
AB  - organization. This observation implies the recruitment of members of the
AB  - leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond
AB  - formation within the biosynthesis of natural products. Thus, the genome sequence
AB  - of S. lividans 66 not only explains long-standing genetic and phenotypic
AB  - differences but also opens the door for further in-depth comparative genomic
AB  - analyses of model Streptomyces strains, as well as for the discovery of novel
AB  - natural products following genome-mining approaches.
ER  -

TY  - JOUR
AU  - Csepregi, K.
AU  - Valasek, A.
AU  - Penzes, A.
AU  - Toth, Z.
AU  - Kiss, E.I.
AU  - Kerepesi, I.
AU  - Horvath, B.
AU  - Nagy, I.
AU  - Fekete, C.
TI  - Draft Genome Sequence of an Efficient Antibiotic-Producing Industrial Strain of Saccharomonospora azurea, SZMC 14600.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1263
EP  - 1263
VL  - 194
AB  - Although certain rare actinomycetes have been recognized as prolific sources of bioactive
AB  - natural products, their potential for producing biologically active
AB  - metabolites still remains unexplored. With the aim of gaining global insights
AB  - into the genetic background and the metabolic capability of Saccharomonospora
AB  - azurea SZMC 14600, whole-genome sequencing was performed.
ER  -

TY  - JOUR
AU  - Cserhati, M.
AU  - Kriszt, B.
AU  - Szoboszlay, S.
AU  - Toth, A.
AU  - Szabo, I.
AU  - Tancsics, A.
AU  - Nagy, I.
AU  - Horvath, B.
AU  - Nagy, I.
AU  - Kukolya, J.
TI  - De Novo Genome Project of Cupriavidus basilensis OR16.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2109
EP  - 2110
VL  - 194
AB  - Here we report on the complete genome sequence of Cupriavidus basilensis OR16 NCAIM BO2487.
AB  - The genome of strain OR16 contains 7,534 putative coding sequences,
AB  - including a large set of xenobiotics-degrading genes and a unique glucose
AB  - dehydrogenase gene that is absent from other Cupriavidus genomes.
ER  -

TY  - JOUR
AU  - Csirik, J.
AU  - Magyar, J.
AU  - Polner, G.
TI  - A computer algorithm to determine the recognition site of restriction enzymes.
JO  - Comput. Appl. Biosci.
PY  - 1987
SP  - 245
EP  - 246
VL  - 3
AB  - A new algorithm is proposed to determine the type-II restriction endonucleases'
AB  - recognition site knowing the digested DNA sequence and fragment lengths in an
AB  - actual case.  The algorithm is implemented for the Commodore 64 microcomputer.
ER  -

TY  - JOUR
AU  - Cuadros-Orellana, S.
AU  - Martin-Cuadrado, A.B.
AU  - Legault, B.
AU  - D'Auria, G.
AU  - Zhaxybayeva, O.
AU  - Papke, R.T.
AU  - Rodriguez-Valera, F.
TI  - Genomic plasticity in prokaryotes: the case of the square haloarchaeon.
JO  - ISME J.
PY  - 2007
SP  - 235
EP  - 245
VL  - 1
AB  - The variability in genome content among closely related strains of
AB  - prokaryotes has been one of the most remarkable discoveries of genomics.
AB  - One way to approach the description of this so-called pan-genome is to
AB  - compare one reference strain genome with metagenomic sequences from the
AB  - environment. We have applied this approach to one extreme aquatic habitat,
AB  - saturated brines in a solar saltern. The genome of Haloquadratum walsbyi
AB  - strain DSM 16790 was compared to an environmental metagenome obtained from
AB  - the exact site of its isolation. This approach revealed that some regions
AB  - of the strain genome were scarcely represented in the metagenome. Here we
AB  - have analyzed these genomic islands (GI) in the genome of DSM 16790 and
AB  - compared them with the complete sequence of some fosmids from the
AB  - environmental library. Two of the islands, GI 2 and GI 4, overlapped with
AB  - two large guanine and cytosine (GC)-rich regions that showed evidence of
AB  - high variability through mobile elements. GI 3 seemed to be a phage or
AB  - phage-remnant acquired by the reference genome, but not present in most
AB  - environmental lineages. Most differential gene content was related to
AB  - small molecule transport and detection, probably reflecting adaptation to
AB  - different pools of organic nutrients. GI 1 did not possess traces of
AB  - mobile elements and had normal GC content. This island contained the main
AB  - cluster of cell envelope glycoproteins and the variability found was
AB  - different from the other GIs. Rather than containing different genes it
AB  - consisted of homologs with low similarity. This variation might reflect a
AB  - phage evasion strategy.
ER  -

TY  - JOUR
AU  - Cuculich, P.S.
TI  - Overexpression of E. coli EcoRI modification system enzymes.
JO  - The Nucleus
PY  - 1996
SP  - 8
EP  - 10
VL  - 75
AB  - Escherichia coli RI (EcoRI) DNA restriction and modification enzymes are reponsible for host
AB  - specificity of E. coli.  The restriction endonuclease enzyme recognizes a hexanucleotide
AB  - repeat (5'-GAATTC-3') and cleaves double-stranded DNA in a staggered fashion between the
AB  - guanine and first adenine residues.  The methyltransferase enzyme, or methylase, adds a methyl
AB  - group to the second adenine, nearest the axis of symmetry, leaving the site resistant to
AB  - endonuclease cleavage.  The endonuclease and methylase are two independent proteins which are
AB  - coded for by distinct genes, and will be referred to collectively as the EcoRI modification
AB  - system.
ER  -

TY  - JOUR
AU  - Cue, D.
AU  - Hong, L.
AU  - Hanson, R.S.
AU  - Flickinger, M.C.
TI  - Characterization of a restriction-modification system of the thermotolerant methylotroph Bacillus methanolicus.
JO  - Appl. Environ. Microbiol.
PY  - 1996
SP  - 1107
EP  - 1111
VL  - 62
AB  - We report the isolation of a restriction endonuclease, BmeTI, an isoschizomer of BclI, that
AB  - recognizes the DNA sequence 5' TGATCA 3'.  We also report that BmeTI sites are modified to
AB  - TGm6ATCA.  These findings provide the basis for devising strategies to prevent BmeTI
AB  - restriction of any DNA introduced into Bacillus methanolicus.
ER  -

TY  - JOUR
AU  - Cue, D.
AU  - Lam, H.
AU  - Hanson, R.S.
AU  - Flickinger, M.
TI  - Characterization of a Bacillus methanolicus restriction/modification system.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1995
SP  - 525
EP  - 525
VL  - 95
AB  - A restriction endonuclease (BmeI) has been isolated from the thermotolerant, methylotrophic
AB  - bacterium Bacillus methanolicus.  BmeI is an isoschizomer of BclI, both enzymes cutting within
AB  - the sequence, TGATCA.  The same restriction patterns are evident when phage DNA or
AB  - HindIII-digested phage DNA are incubated with either BmeI or BclI or when phage DNA is
AB  - digested with both BmeI and BclI.  Destruction of the BclI restriction site present in the
AB  - integrational plasmid, pDQ500, resulted in a plasmid pDQ503, that is resistant to cleavage by
AB  - both BmeI and BclI.  The modification specificity of the cognate BmeI methyltransferase was
AB  - determined by Southern blotting of B. methanolicus chromosomal DNA that had been digested with
AB  - PstI and either BclI, DpnI, MboI or Sau3AI and using the cloned B. methanolicus, lysC gene as
AB  - the probe.  The results indicated that the single BmeI restriction site within lysC is
AB  - modified to: TGm6ATCA.  We have successfully transformed B. methanolicus with several plasmid
AB  - and integrational vectors (including pDQ503).  Our results suggest that B. methanolicus
AB  - possesses a single, dominant restriction system or, that if a second restriction system
AB  - exists, that the second restriction endonuclease is an infrequent cutter.
ER  -

TY  - JOUR
AU  - Cui, C.
AU  - Li, P.
AU  - Liu, G.
AU  - Tang, H.
AU  - Lin, K.
AU  - Luo, Q.
AU  - Liu, S.
AU  - Xu, P.
AU  - Liu, Y.
TI  - Genome Sequence of Martelella sp. Strain AD-3, a Moderately Halophilic Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01189
EP  - e01113
VL  - 2
AB  - Martelella sp. strain AD-3, enriched from a petroleum-contaminated site with high salinity,
AB  - can efficiently degrade polycyclic aromatic hydrocarbons. Here, we
AB  - report the 4.75-Mb genome sequence of strain AD-3 with its genetic feature of
AB  - helping to remediate environmental organic pollutants.
ER  -

TY  - JOUR
AU  - Cui, G.-Z.
AU  - Hong, W.
AU  - Zhang, J.
AU  - Li, W.-L.
AU  - Feng, Y.
AU  - Liu, Y.-J.
AU  - Cui, Q.
TI  - Targeted gene engineering in Clostridium cellulolyticum H10 without methylation.
JO  - J. Microbiol. Methods
PY  - 2012
SP  - 201
EP  - 208
VL  - 89
AB  - Genetic engineering of Clostridium cellulolyticum has been developed slowly compared with that
AB  - of other clostridial species, and one of the
AB  - major reasons might be the restriction and modification (RM) system
AB  - which degrades foreign DNA. Here, a putative Mspl endonuclease gene,
AB  - ccel2866, was inactivated by a ClosTron-based gene disruption method.
AB  - The resulting C cellulolyticum mutant H10 Delta mspl lost the Mspl
AB  - endonuclease activity and can accept unmethylated DNA efficiently.
AB  - Following that, an oxygen-independent green fluorescence protein gene
AB  - was introduced into H10 Delta mspl without methylation, generating a
AB  - convenient reporter system to evaluate the expression of heterologous
AB  - protein in C. cellulolyticum by green fluorescence. To further
AB  - demonstrate the efficiency of the H10 Delta mspl, double mutants H10
AB  - Delta mspl Delta ldh and H10 Delta mspl Delta ack were constructed by
AB  - disrupting lactate dehydrogenase gene ccel2485 and acetate kinase gene
AB  - ccel2136 in H10 Delta mspl, respectively, without DNA methylation, and
AB  - the stability of the double mutation was confirmed after the 100th
AB  - generation. The mutant H10 Delta mspl constructed here can be used as a
AB  - platform for further targeted gene manipulation conveniently and
AB  - efficiently. It will greatly facilitate the metabolic engineering of C.
AB  - cellulolyticum aiming at faster cellulose degradation and higher
AB  - biofuel production at the molecular level.
ER  -

TY  - JOUR
AU  - Cui, X.X.
AU  - Davis, G.
TI  - Mobile group II intron targeting: applications in prokaryotes and perspectives in eukaryotes.
JO  - Front. Biosci.
PY  - 2007
SP  - 4972
EP  - 4985
VL  - 12
AB  - Mobile group II introns are ribozymes and use a novel mechanism--target DNA-primed reverse
AB  - transcription--to proliferate in DNA. Group II introns are a unique mobile element for their
AB  - high sequence-specific, yet readily flexible target site recognition. Both the intron RNA and
AB  - the intron-encoded protein (IEP) are involved in target site recognition, and the specificity
AB  - is determined primarily by base pairing between the intron RNA and DNA target. Therefore, the
AB  - intron RNA can be modified according to the desired target sequence for specific gene
AB  - disruption. Group II intron knockout technology is mature in bacteria and is currently being
AB  - developed in eukaryotes. This technology has great potential to revolutionize fields such as
AB  - functional genomics, gene therapy, and cell line engineering.
ER  -

TY  - JOUR
AU  - Cui, Y.
AU  - Cheng, B.
AU  - Meng, Y.
AU  - Li, C.
AU  - Yin, H.
AU  - Xu, P.
AU  - Yang, C.
TI  - Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2.
JO  - Extremophiles
PY  - 2016
SP  - 631
EP  - 639
VL  - 20
AB  - Na(+)/H(+) antiporters play important roles in ion and pH homeostasis. In this
AB  - study, two NhaD homologues that effectively catalyze Na(+)/H(+) antiporter were
AB  - identified from Halomonas sp. Y2, a halotolerant and alkaliphilic strain isolated
AB  - from sodium enriched black liquor. They exhibited high sequence identity of 72 %
AB  - and similar binding affinities for Na(+) and Li(+) translocation, while having
AB  - different pH profiles. Ha-NhaD1 was active at pH 6.0 and most active at pH
AB  - 8.0-8.5, whereas Ha-NhaD2 lacked activity at pH 6.0 but exhibited maximum
AB  - activity at pH 9.5 or higher. Based on multiple alignments, 11 partially
AB  - conserved residues were selected and corresponding mutants were generated for
AB  - Ha-NhaD1. As expected, replacement of most of the hydrophobic residues abolished
AB  - the cation exchange activities. Three serine residues at positions 200, 282 and
AB  - 353 in Ha-NhaD1 were replaceable by alanines with partial retention of activity.
AB  - The S353A mutant exhibited significantly reduced binding affinity for Na(+) and
AB  - Li(+), while S282 mutant exhibited an alkaline shift of about 1.5 pH units, as
AB  - compared to the wild type Ha-NhaD1. Serine at position 282 was predicted to be
AB  - located in transmembrane segment VIII and was found to be important in regulating
AB  - pH sensitivity in concert with flanking residues.
ER  -

TY  - JOUR
AU  - Cui, Z.
AU  - Gao, W.
AU  - Li, Q.
AU  - Xu, G.
AU  - Zheng, L.
TI  - Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Strain Marinobacter nanhaiticus D15-8WT.
JO  - Genome Announcements
PY  - 2013
SP  - e00301
EP  - e00313
VL  - 1
AB  - Marinobacter nanhaiticus strain D15-8W(T) was isolated from a phenanthrene-degrading
AB  - consortium, enriched from sediment of the South China Sea.
AB  - Here, we present the draft genome of strain D15-8W(T), which contains 5,358,309
AB  - bp with a G+C content of 58.53% and contains 4,829 protein-coding genes and 47
AB  - tRNA genes.
ER  -

TY  - JOUR
AU  - Cui, Z.
AU  - Xu, G.
AU  - Li, Q.
AU  - Gao, W.
AU  - Zheng, L.
TI  - Genome Sequence of the Pyrene- and Fluoranthene-Degrading Bacterium Cycloclasticus sp. Strain PY97M.
JO  - Genome Announcements
PY  - 2013
SP  - e00536
EP  - e00513
VL  - 1
AB  - Cycloclasticus sp. strain PY97M was isolated from a phenanthrene-degrading consortium,
AB  - enriched from Yellow Sea sediment of China. Here, we present the
AB  - draft genome sequence of strain PY97M, which contains 2,359,509 bp with a G+C
AB  - content of 41.92% and contains 2, 264 protein-coding genes and 40 tRNAs.
ER  -

TY  - JOUR
AU  - Cuiv, P.O.
AU  - Klaassens, E.S.
AU  - Durkin, A.S.
AU  - Harkins, D.M.
AU  - Foster, L.
AU  - McCorrison, J.
AU  - Torralba, M.
AU  - Nelson, K.E.
AU  - Morrison, M.
TI  - Draft genome sequence of Turicibacter sanguinis PC909 isolated from human faeces.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1288
EP  - 1289
VL  - 193
AB  - While the microbiota resident in the human gut is now known to provide a range of functions
AB  - relevant to host health many of the microbial members of the community have not yet been
AB  - cultured or are represented by a limited number of isolates. We describe here the draft genome
AB  - sequence of Turicibacter sanguinis PC909, isolated from a pooled healthy human faecal sample
AB  - as part of the Australian Human Gut Microbiome Project.
ER  -

TY  - JOUR
AU  - Culley, D.E.
AU  - Shi, L.
AU  - Reed, S.
AU  - Romme, M.
TI  - Genetic and biochemical studies of the transformation barriers present in Shewanella oneidensis MR-1.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2004
SP  - 320
EP  - 320
VL  - 104
AB  - Shewanella oneidensis is able to enzymatically reduce and precipitate a variety of heavy
AB  - metals and is widely investigated for bioremediation of metals and radionuclides.  The
AB  - availability of the complete genome sequence and its ability to grow both aerobically and
AB  - anaerobically makes S. oneidensis MR-1 an extremely useful model system.  However, genetic
AB  - studies of this organism have been slowed by the lack of an efficient transformation system.
AB  - We are utilizing several approaches to investigate the genetic factors influencing
AB  - transformation and to improve the transformation efficiency.  Utilizing a pUC-type plasmid
AB  - isolated from MR-1, we were able to test various competent cell preparation methods,
AB  - electrical parameters, and selection strategies to develop a method that improves
AB  - electroporation efficiencies from less than 105 cfu/ug to almost 108/ug.  However, even these
AB  - improved conditions yielded less than 103/ug when transforming MR-1 with the same plasmid
AB  - isolated from E. coli.  This 100,000-fold reduction in efficiency with unmodified plasmid
AB  - indicates a very active restriction-modification system in MR-1.  Analysis of the genome
AB  - sequence indicates the presence of a dam methylase locus, three type II, and two Type I
AB  - methylases on the chromosome and a Type II methylase on a 160 kb megaplasmid.  The use of a
AB  - Type I restriction inhibitor did not improve transformation, indicating an active Type II
AB  - system.  The Type II system borne on the megaplasmid has high homology to the ClaI restriction
AB  - system, but no effect was observed with either in vivo modification using an E. coli strain
AB  - expressing ClaI methylase (pHS17; NEB) or with in vitro modification of the test plasmid with
AB  - M.TaqI (blocks ClaI cleavage).  One of the chromosomal Type II methylases is located within a
AB  - lambda-like prophage, but is lacking the corresponding restriction subunit.  We are currently
AB  - constructing MR-1 knockout mutants of the restriction subunits from the remaining two loci, as
AB  - well as attempting to modify plasmid DNA in E. coli by co-expression of the corresponding
AB  - Shewanella methylases, in hopes of overcoming the transformation barrier present in S.
AB  - oneidensis.
ER  -

TY  - JOUR
AU  - Cullik, A.
AU  - Pfeifer, Y.
AU  - Prager, R.
AU  - von Baum, H.
AU  - Witte, W.
TI  - A novel IS26 structure surrounds blaCTX-M genes in different plasmids from German clinical Escherichia coli isolates.
JO  - J. Med. Microbiol.
PY  - 2010
SP  - 580
EP  - 587
VL  - 59
AB  - This report focuses on the molecular characterization of 22
AB  - extended-spectrum beta-lactamase-producing Escherichia coli isolates
AB  - collected in a German university hospital during a period of 9 months in
AB  - 2006. Relationship analysis of clinical isolates was done via PFGE,
AB  - multilocus sequence typing, plasmid profiling and additionally PCR for
AB  - bla(ESBL) detection and determination of phylogroups. After conjugal
AB  - transfer, plasmid isolation and subsequent PCR for bla(ESBL) detection and
AB  - determination of incompatibility groups were performed. Using one-primer
AB  - walking, up to 3600 bp upstream and downstream of different bla(CTX-M)
AB  - genes could be sequenced. beta-Lactamases found were TEM-1 (n=14), SHV-5
AB  - (n=1) and a wide variety of CTX-M types (n=21), i.e. CTX-M-15 (n=12),
AB  - CTX-M-1 (n=4), CTX-M-14 (n=2), CTX-M-9 (n=1), CTX-M-3 (n=1) and one new
AB  - type, CTX-M-65 (n=1). In 18 isolates, bla(ESBL) genes were located on
AB  - conjugative plasmids of sizes between 40 and 180 kbp belonging to
AB  - incompatibility groups FII (n=9), N (n=5) and I1 (n=4). bla(CTX-M) was
AB  - found to be associated with the common elements ISEcp1, IS26 and IS903-D,
AB  - but with unusual spacer sequences for ISEcp1 in two isolates. These
AB  - insertion sequences, connected to bla(CTX-M) as well as other genes, were
AB  - located between two IS26 elements in a configuration that has not yet been
AB  - described. The results reveal the emergence of bla(ESBL), predominantly
AB  - bla(CTX-M), located on different plasmids harboured by genotypically
AB  - different E. coli strains. The identical gene arrangement in the
AB  - bla(CTX-M) neighbourhood in plasmids of different incompatibility groups
AB  - indicates a main role of IS26 in distribution of mobile resistance
AB  - elements between different plasmids.
ER  -

TY  - JOUR
AU  - Cummings, D.J.
AU  - McNally, K.L.
AU  - Domenico, J.M.
AU  - Matsuura, E.T.
TI  - The complete DNA sequence of the mitochondrial genome of Podospora anserina.
JO  - Curr. Genet.
PY  - 1990
SP  - 375
EP  - 402
VL  - 17
AB  - The complete 94,192 bp sequence of the mitochondrial genome from race s of
AB  - Podospora anserina is presented (1 kb = 10(3) base pairs). Three regions
AB  - unique to race A are also presented bringing the size of this genome to
AB  - 100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group
AB  - II introns (3 in race A). Analysis shows that the group I introns can be
AB  - categorized according to families both with regard to secondary structure
AB  - and their open reading frames. All identified genes are transcribed from
AB  - the same strand. Except for the lack of ATPase 9, the Podospora genome
AB  - contains the same genes as its fungal counterparts, N. crassa and A.
AB  - nidulans. About 20% of the genome has not yet been identified. DNA
AB  - sequence studies of several excision-amplification plasmids demonstrate a
AB  - common feature to be the presence of short repeated sequences at both
AB  - termini with a prevalence of GGCGCAAGCTC.
ER  -

TY  - JOUR
AU  - Cummings, M.
AU  - Adams, R.L.P.
TI  - Cloning the pea DNA methylase cDNA.
JO  - Biochem. Soc. Trans.
PY  - 1992
SP  - 7s
EP  - 7s
VL  - 21
AB  - Both eukaryotic and prokaryotic cytosine methylases catalyse the transfer of a methyl group
AB  - from S-adenosyl methionine to the 5-position of the cytosine ring in DNA. The cDNA coding for
AB  - mouse and human methylase have been previously cloned. Comparison of the encoded proteins with
AB  - prokaryotic type II cytosine methylase sequences shows that the carboxy terminal one-third of
AB  - the eukaryotic enzymes shares significant homology with the prokaryotic enzymes. The
AB  - arrangement of several sequence motifs has been preserved in the eukaryotic proteins. This
AB  - includes a short amino acid sequence containing a pro-cys dipeptide which has been proved to
AB  - the the catalytic center of at least one bacterial type II methylase.
ER  -

TY  - JOUR
AU  - Cunnac, S.
AU  - Bolot, S.
AU  - Forero, S.N.
AU  - Ortiz, E.
AU  - Szurek, B.
AU  - Noel, L.D.
AU  - Arlat, M.
AU  - Jacques, M.A.
AU  - Gagnevin, L.
AU  - Carrere, S.
AU  - Nicole, M.
AU  - Koebnik, R.
TI  - High-Quality Draft Genome Sequences of Two Xanthomonas citri pv. malvacearum Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00674
EP  - e00613
VL  - 1
AB  - We report high-quality draft genome sequences of two strains (race 18 and 20) of  Xanthomonas
AB  - citri pv. malvacearum, the causal agent of bacterial blight of
AB  - cotton. Comparative genomics will help to decipher mechanisms provoking disease
AB  - and triggering defense responses and to develop new molecular tools for
AB  - epidemiological surveillance.
ER  -

TY  - JOUR
AU  - Cuppels, D.A.
AU  - Van Etten, J.L.
AU  - Lambrecht, P.
AU  - Vidaver, A.K.
TI  - Survey of phytopathogenic pseudomonads for a restriction and modification system active on the double-stranded ribonucleic acid phage Phi-6.
JO  - Curr. Microbiol.
PY  - 1981
SP  - 247
EP  - 249
VL  - 5
AB  - A total of 380 pseudomonad strains from 39 nomenspecies and 41 strains from 7 other bacterial
AB  - genera were screened for a double-stranded ribonucleic acid modification and restriction
AB  - system using the double-stranded ribonucleic acid modification and restriction system using
AB  - the double-stranded ribonucleic acid bacteriophage Phi-6.  Of these 421 strains, 8 showed the
AB  - low plating efficiency (10^-5 to 10^-7) characteristic of such a system.  However, the phage
AB  - propagated in 7 of the 8 were host-range mutants; the remaining strain showed some
AB  - characteristics of a host-modification system but the results were equivocal.
ER  -

TY  - JOUR
AU  - Curcio, M.J.
AU  - Belfort, M.
TI  - Retrohoming: cDNA-mediated mobility.
JO  - Cell
PY  - 1996
SP  - 9
EP  - 12
VL  - 84
AB  - Last year was a vintage year for mobile group II introns.  In 1995 we moved from phenomenology
AB  - to mechanistic insight, from enigmatic observations to a coherent appreciation of process.
AB  - The finding that nucleated our understanding of the group II intron mobility event was the
AB  - appearance of an extraordinary double-strand break in the target DNA: a break that provides an
AB  - initiation site for reverse transcriptase, which mediates group II intron mobility; a break in
AB  - which the excised intron RNA is covalently attached to one of the DNA ends; a break that is
AB  - made by the protein and RNA products of the intron itself, with the RNA believed to be the
AB  - catalyst responsible for one of the DNA strand cleavages.  In this minireview, we piece
AB  - together the puzzle by describing the formation of this remarkable double-strand break, its
AB  - role in group II intron mobility, and the evolutionary implications of the process.  Group II
AB  - introns are catalytic RNAs that, like spliceosomal introns, splice via a lariat intermediate.
AB  - The nuclear pre-mRNA introns are thought to be descended from the group II introns, which are
AB  - found in both pro- and eukaryotes.  The functional domains of the self-splicing group II
AB  - introns are suspected to have evolved to act in trans under the guise of the snRNAs.  The
AB  - mobile group II introns are also phylogenetically linked to retroelements, which may provide
AB  - clues as to how the group II introns have become disseminated.  The mobility of group II
AB  - introns therefore engenders great evolutionary and mechanistic interest.
ER  -

TY  - JOUR
AU  - Cusick, K.D.
AU  - Dale, J.R.
AU  - Little, B.J.
AU  - Biffinger, J.C.
TI  - Draft Genome Sequences of Four Alteromonas macleodii Strains Isolated from Copper Coupons and Grown Long-Term at Elevated Copper Levels.
JO  - Genome Announcements
PY  - 2016
SP  - e01311
EP  - e01316
VL  - 4
AB  - Alteromonas macleodii is a marine bacterium involved in the early stages of biofouling on ship
AB  - hulls treated with copper as an antifouling agent. We report
AB  - here the draft genome sequences of an A. macleodii strain isolated from copper
AB  - coupons and three laboratory mutants grown long-term at elevated copper levels.
ER  -

TY  - JOUR
AU  - Cymerman, I.A.
AU  - Obarska, A.
AU  - Skowronek, K.J.
AU  - Lubys, A.
AU  - Bujnicki, J.M.
TI  - Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
JO  - Proteins
PY  - 2006
SP  - 867
EP  - 876
VL  - 65
AB  - The restriction endonuclease (REase) R. HphI is a Type IIS enzyme that recognizes the
AB  - asymmetric target DNA sequence 5'-GGTGA-3' and in the
AB  - presence of Mg2+ hydrolyzes phosphodiester bonds in both strands of the
AB  - DNA at a distance of 8 nucleotides towards the 3' side of the target,
AB  - producing a 1 nucleotide T-staggered cut in an unspecified sequence at
AB  - this position. REases are typically ORFans that exhibit little
AB  - similarity to each other and to any proteins in the database. However,
AB  - bioinformatics analyses revealed that R.HphI is a member of a
AB  - relatively big sequence family with a conserved C-terminal domain and a
AB  - variable N-terminal domain. We predict that the C-terminal domains of
AB  - proteins from this family correspond to the nuclease domain of the HNH
AB  - superfamily rather than to the most common PD(D/E)XK superfamily of
AB  - nucleases. We constructed a three-dimensional model of the R.HphI
AB  - catalytic domain and validated our predictions by sitedirected
AB  - mutagenesis and studies of DNA-binding and catalytic activities of the
AB  - mutant proteins. We also analyzed the genomic neighborhood of R.HphI
AB  - homologs and found that putative nucleases accompanied by a DNA
AB  - methyltransferase (i.e. predicted REases) do not form a single group on
AB  - a phylogenetic tree, but are dispersed among free-standing putative
AB  - nucleases. This suggests that nucleases from the HNH superfamily were
AB  - independently recruited to become REases in the context of RM systems
AB  - multiple times in the evolution and that members of the HNH superfamily
AB  - may be much more frequent among the so far unassigned REase sequences
AB  - than previously thought.
ER  -

TY  - JOUR
AU  - Czajkowski, R.
AU  - van der Wolf, J.M.
TI  - Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated  from Rotting Potato Tuber Tissue.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6999
EP  - 7000
VL  - 194
AB  - Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward
AB  - blackleg- and soft rot-causing Dickeya sp. biovar 3 ('Dickeya
AB  - solani'). Here, we present the draft genome sequence of strain A30, which has
AB  - been isolated from rotten potato tuber tissue.
ER  -

TY  - JOUR
AU  - Czank, A.
AU  - Hauselmann, R.
AU  - Page, A.W.
AU  - Leonhardt, H.
AU  - Bestor, T.H.
AU  - Schafner, W.
AU  - Hergersberg, M.
TI  - Expression in mammalian cells of a cloned gene encoding murine DNA methyltransferase.
JO  - Gene
PY  - 1991
SP  - 259
EP  - 263
VL  - 109
AB  - Mammalian DNA cytosine-5-methyltransferase (MTase, EC 2.1.1.37) is an essential
AB  - component for establishing and maintaining cell-type specific methylation
AB  - patterns in the genome.  The cDNA for the murine enzyme was previously cloned
AB  - in segments.  We have reconstructed the entire gene, encoding a protein of 1517
AB  - amino acids, from a set of overlapping cDNA clones.  We report the assembly of
AB  - two expression constructs in bacterial/mammalian shuttle vectors.
AB  - Transcription in the first construct (pEMT) is driven by the cytomegalovirus
AB  - enhancer/promoter and encodes a fusion protein with 15 additional aa at the N
AB  - terminus, while the second construct (pJMT) is driven by the simian virus 40
AB  - early promoter/enhancer upstream from the natural ATG codon.
AB  - Immunofluorescence microscopy and immunoblot analysis have shown that both
AB  - constructs direct the synthesis of MTase in COS-1 cells.  Enzyme activity in
AB  - whole-cell lysates of transfected COS-1 cells transfected with pEMT and pJMT
AB  - are on average tenfold and fivefold higher than in controls, respectively.  The
AB  - specific activities of the recombinant and endogenous mouse-cell enzyme are
AB  - similar.  These expression constructs will be of use in studies of DNA
AB  - methylation in mammals.
ER  -

TY  - JOUR
AU  - Czapinska, H.
AU  - Kowalska, M.
AU  - Zagorskaite, E.
AU  - Manakova, E.
AU  - Slyvka, A.
AU  - Xu, S.Y.
AU  - Siksnys, V.
AU  - Sasnauskas, G.
AU  - Bochtler, M.
TI  - Activity and structure of EcoKMcrA.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 9829
EP  - 9841
VL  - 46
AB  - Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent
AB  - restriction endonuclease. We present a
AB  - biochemical characterization of EcoKMcrA that includes the first demonstration of
AB  - its endonuclease activity, small angle X-ray scattering (SAXS) data, and a
AB  - crystal structure of the enzyme in the absence of DNA. Our data indicate that
AB  - EcoKMcrA dimerizes via the anticipated C-terminal HNH domains, which together
AB  - form a single DNA binding site. The N-terminal domains are not homologous to SRA
AB  - domains, do not interact with each other, and have separate DNA binding sites.
AB  - Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest
AB  - that the N-terminal domains can sense the presence and sequence context of
AB  - modified cytosines. Pyrrolocytosine fluorescence data indicate no base flipping.
AB  - In vitro, EcoKMcrA DNA endonuclease activity requires Mn2+ ions, is not strictly
AB  - methyl dependent, and is not observed when active site variants of the enzyme are
AB  - used. In cells, EcoKMcrA specifically restricts DNA that is modified in the
AB  - correct sequence context. This activity is impaired by mutations of the nuclease
AB  - active site, unless the enzyme is highly overexpressed.
ER  -

TY  - JOUR
AU  - D'Afonseca, V.
AU  - Prosdocimi, F.
AU  - Dorella, F.A.
AU  - Pacheco, L.G.
AU  - Moraes, P.M.
AU  - Pena, I.
AU  - Ortega, J.M.
AU  - Teixeira, S.
AU  - Oliveira, S.C.
AU  - Coser, E.M.
AU  - Oliveira, L.M.
AU  - Correa-de-Oliveira, G.
AU  - Meyer, R.
AU  - Miyoshi, A.
AU  - Azevedo, V.
TI  - Survey of genome organization and gene content of Corynebacterium pseudotuberculosis.
JO  - Microbiol. Res.
PY  - 2010
SP  - 312
EP  - 320
VL  - 165
AB  - Corynebacterium pseudotuberculosis is an intracellular pathogen that
AB  - causes Caseous lymphadenitis (CLA) disease in sheep and goats. The
AB  - widespread occurrence and the economic importance of this pathogen have
AB  - prompted investigation of its pathogenesis. We used a genomic library of
AB  - C. pseudotuberculosis to generate 1440 genomic survey sequences (GSSs);
AB  - these were analyzed in silico with bioinformatics tools, using public
AB  - databases for comparative analyses. We employed non-redundant unique
AB  - sequences as a query for BLAST searches against the genome, the translated
AB  - genome and the proteome of four other Corynebacterium species that have
AB  - been completely sequenced. We were able to characterize approximately 8%
AB  - of the genome of C. pseudotuberculosis, including previously undescribed
AB  - functional group genes, based on the COG database; the GSSs classification
AB  - into categories gave 13% information storage and processing, 14% cellular
AB  - processes and 23% metabolism. We found a close relation between C.
AB  - pseudotuberculosis and C. diphtheriae conserved-gene synteny in
AB  - Corynebacteria species.
ER  -

TY  - JOUR
AU  - D'Agostino, N.
AU  - Sorrentino, R.
AU  - Scotti, R.
AU  - Salzano, M.
AU  - Aurilia, V.
AU  - Zaccardelli, M.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA-C16 Isolated from Pea (Pisum sativum L.) Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e01456
EP  - e01416
VL  - 5
AB  - Herein, we report the draft genome sequence of Pseudomonas fluorescens strain CREA-C16, a
AB  - plant growth-promoting rhizobacterium that was isolated from the
AB  - rhizosphere of Pisum sativum L. plants. The genome sequence is ~6 Mb in size,
AB  - with a G+C content of 60.1%, and includes 4,457 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - D'Andrea, M.M.
AU  - Giani, T.
AU  - Henrici, De.A.L.
AU  - Ciacci, N.
AU  - Gniadkowski, M.
AU  - Miriagou, V.
AU  - Torricelli, F.
AU  - Rossolini, G.M.
TI  - Draft Genome Sequence of Proteus mirabilis NO-051/03, Representative of a Multidrug-Resistant Clone Spreading in Europe and Expressing the CMY-16 AmpC-Type  beta-Lactamase.
JO  - Genome Announcements
PY  - 2016
SP  - e01702
EP  - e01715
VL  - 4
AB  - Proteus mirabilis NO-051/03, representative of a multidrug-resistant clone expressing the
AB  - CMY-16 AmpC-type beta-lactamase and circulating in Europe since
AB  - 2003, was sequenced by a MiSeq platform using a paired-end approach. The genome
AB  - was assembled in 100 scaffolds with a total length of 4,197,318 bp. Analysis of
AB  - the draft genome sequence revealed the presence of several acquired resistance
AB  - determinants to beta-lactams, aminoglycosides, phenicols, tetracyclines,
AB  - trimethoprim, and sulfonamides, of one plasmid replicon, and of a type I-E
AB  - clustered regularly interspaced short palindromic repeat (CRISPR)-associated
AB  - protein (Cas) adaptive immune system.
ER  -

TY  - JOUR
AU  - D'Angelo, T.
AU  - Oshone, R.
AU  - Abebe-Akele, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia.
JO  - Genome Announcements
PY  - 2016
SP  - e01000
EP  - e01016
VL  - 4
AB  - Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the
AB  - Casuarinaceae family. Here, we report a 5.2-Mbp draft genome
AB  - sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - D'Angelo, T.
AU  - Oshone, R.
AU  - Abebe-Akele, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence for Frankia sp. Strain EI5c, a Single-Spore Isolate of a Nitrogen-Fixing Actinobacterium, Isolated from the Root Nodules of  Elaeagnus angustifolia.
JO  - Genome Announcements
PY  - 2016
SP  - e00660
EP  - e00616
VL  - 4
AB  - Frankia sp. strain EI5c is a member of Frankia lineage III, which is able to reinfect plants
AB  - of the Eleagnaceae, Rhamnaceae, Myricaceae, and Gymnostoma, as
AB  - well as the genus Alnus Here, we report the 6.6-Mbp draft genome sequence of
AB  - Frankia sp. strain EI5c with a G+C content of 72.14 % and 5,458 candidate
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - D'Arcy, A.
AU  - Brown, R.S.
AU  - Zabeau, M.
AU  - van Resandt, R.W.
AU  - Winkler, F.K.
TI  - Purification and crystallization of the EcoRV restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 1987
EP  - 1990
VL  - 260
AB  - The type II restriction endonuclease EcoRV purified from a genetically
AB  - engineered, overproducing strain has been crystallized.  Four crystal forms all
AB  - obtained by precipitation with polyethylene glycol 4000 have been
AB  - characterized.  Two of these are suitable for high resolution structure
AB  - analysis.  Both are orthorhombic, have space group P2/12/1/2/1 and have similar
AB  - unit cell dimensions of a = 58.2 angstrom, b = 71.7 angstrom, c = 130.6
AB  - angstrom (form A) and a = 59.9 angstrom, b = 74.5 angstrom, c= 121.8 angstrom
AB  - (form B).  They diffract to about 2 angstrom resolution and appear to have one
AB  - dimer of 2 x 29,000 daltons in the asymmetric unit.
ER  -

TY  - JOUR
AU  - D'Argenio, V.
AU  - Petrillo, M.
AU  - Cantiello, P.
AU  - Naso, B.
AU  - Cozzuto, L.
AU  - Notomista, E.
AU  - Paolella, G.
AU  - Di Donato, A.
AU  - Salvatore, F.
TI  - De Novo Sequencing and Assembly of the Whole Genome of Novosphingobium sp. Strain PP1Y.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4296
EP  - 4296
VL  - 193
AB  - Novosphingobium sp. strain PP1Y is a marine bacterium specifically adapted to use fuels as an
AB  - energy source. We sequenced and assembled its entire
AB  - genome using the Roche 454 genome sequencer system, which led to the
AB  - identification of two plasmids and one megaplasmid, besides a 3.9-Mb
AB  - circular chromosome.
ER  -

TY  - JOUR
AU  - D'Auria, G.
AU  - Dzunkova, M.
AU  - Moya, A.
AU  - Tomaska, M.
AU  - Kolosta, M.
AU  - Kmet, V.
TI  - Genome Sequence of Lactobacillus plantarum 19L3, a Strain Proposed as a Starter Culture for Slovenska Bryndza Ovine Cheese.
JO  - Genome Announcements
PY  - 2014
SP  - e00292
EP  - e00214
VL  - 2
AB  - The genome sequence of Lactobacillus plantarum isolated from ovine cheese is presented here.
AB  - This bacterium is proposed as a starter strain, named 19L3, for Slovenska bryndza cheese, a
AB  - traditional Slovak cheese fulfilling European Food Safety Authority (EFSA) requirements.
ER  -

TY  - JOUR
AU  - D'Auria, G.
AU  - Galan, J.C.
AU  - Rodriguez-Alcayna, M.
AU  - Moya, A.
AU  - Baquero, F.
AU  - Latorre, A.
TI  - Complete Genome Sequence of Acidaminococcus intestini RYC-MR95, a Gram-Negative Bacterium from the Phylum Firmicutes.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7008
EP  - 7009
VL  - 193
AB  - Acidaminococcus intestini belongs to the family Acidaminococcaceae, order Selenomonadales,
AB  - class Negativicutes, phylum Firmicutes. Negativicutes
AB  - show the double-membrane system of Gram-negative bacteria, although their
AB  - chromosomal backbone is closely related to that of Gram-positive bacteria
AB  - of the phylum Firmicutes. The complete genome of a clinical A. intestini
AB  - strain is here presented.
ER  -

TY  - JOUR
AU  - D'Auria, G.
AU  - Torrents, E.
AU  - Luquin, M.
AU  - Comas, I.
AU  - Julian, E.
TI  - Draft Genome Sequence of Mycobacterium brumae ATCC 51384.
JO  - Genome Announcements
PY  - 2016
SP  - e00237
EP  - e00216
VL  - 4
AB  - Here, we report the draft genome sequence of Mycobacterium brumae type strain ATCC 51384. This
AB  - is the first draft genome sequence of M. brumae, a
AB  - nonpathogenic, rapidly growing, nonchromogenic mycobacterium, with
AB  - immunotherapeutic capacities.
ER  -

TY  - JOUR
AU  - D'haeseleer, P.
AU  - Johnson, S.L.
AU  - Davenport, K.W.
AU  - Chain, P.S.
AU  - Schoeniger, J.
AU  - Ray, D.
AU  - Sinha, A.
AU  - Williams, K.P.
AU  - Pena, J.
AU  - Branda, S.S.
AU  - El-Etr, S.
TI  - Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6.
JO  - Genome Announcements
PY  - 2016
SP  - e00649
EP  - e00616
VL  - 4
AB  - Here, we present the draft genome sequence of Burkholderia pseudomallei PHLS 6, a virulent
AB  - clinical strain isolated from a melioidosis patient in Bangladesh in 1960. The draft genome
AB  - consists of 39 contigs and is 7,322,181 bp long.
ER  -

TY  - JOUR
AU  - D'Souza, D.R.
AU  - Morgan, R.D.
AU  - Parashar, V.
AU  - Capalash, N.
AU  - Sharma, P.
TI  - Characterization of BflI - a thermostable, Co++-requiring isoschizomer of BsiYI from Anoxybacillus flavithermus.
JO  - World J. Microbiol. Biotechnol.
PY  - 2004
SP  - 593
EP  - 598
VL  - 20
AB  - A thermophile, isolated from geothermal areas in the northern Himalayan region of India, was
AB  - identified by partial 16S rDNA sequence (GenBank
AB  - accession # AF482430) analysis as Anoxybacillus flavithermus. The
AB  - isolate produced BflI (REBASE # 4910), a Type II restriction
AB  - endonuclease, which recognized the sequence 5'-CCNNNN-N/NNGG-3' and was
AB  - the isoschizomer of BsiYI. The enzyme was purified to homogeneity by
AB  - passing through Cibacron Blue F3GA agarose, DEAE-cellulose,
AB  - heparin-agarose and MonoQ FPLC. The purified enzyme (MW 36 kDa) worked
AB  - best at 60 C in Promega's buffer C and preferentially required
AB  - Co++(0.4 mM) as cofactor followed by Mg++ (10 mM) and Mn++ (1 mM). The
AB  - enzyme showed high specific activity and worked in the presence of high
AB  - concentrations of beta-mercaptoethanol (200 mM), Triton-X-100 (25%),
AB  - urea (30%), formamide (6%) and guanidine (40 mM) and showed no star
AB  - activity in the presence of 40% glycerol. In the absence of any
AB  - stabilizing agent, BflI retained t(1/2) for at least 96 h at 37
AB  - degreesC, 6 h at 60 C and 6 months at 4 C. N-terminal
AB  - sequencing showed that its first 10 amino acid residues were
AB  - DFHEDKTIAR.
ER  -

TY  - JOUR
AU  - da Gama, A.M.
AU  - de Almeida, L.G.
AU  - Yamane, T.
AU  - Spira, B.
TI  - Two Draft Genome Sequences of Chromobacterium violaceum Isolates from the Rio Negro.
JO  - Genome Announcements
PY  - 2018
SP  - e01348
EP  - e01317
VL  - 6
AB  - The draft genome sequences of two Chromobacterium violaceum strains isolated from the Rio
AB  - Negro are reported here. These bacteria carry most genetic systems
AB  - associated with the production of bioactive compounds, but unlike other C.
AB  - violaceum strains, they lack a dedicated operon for arsenic resistance.
ER  -

TY  - JOUR
AU  - da Mota, F.F.
AU  - Vollu, R.E.
AU  - Jurelevicius, D.
AU  - Seldin, L.
TI  - Whole-Genome Sequence of Rummeliibacillus stabekisii Strain PP9 Isolated from Antarctic Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00416
EP  - e00416
VL  - 4
AB  - The whole genome of Rummeliibacillus stabekisii PP9, isolated from a soil sample  from
AB  - Antarctica, consists of a circular chromosome of 3,412,092 bp and a circular
AB  - plasmid of 8,647 bp, with 3,244 protein-coding genes, 12 copies of the 16S-23S-5S
AB  - rRNA operon, 101 tRNA genes, and 6 noncoding RNAs (ncRNAs).
ER  -

TY  - JOUR
AU  - da Piedade, I.
AU  - Skive, B.
AU  - Christensen, H.
AU  - Bojesen, A.M.
TI  - Draft Genome Sequence of Streptococcus equi subsp. zooepidemicus Strain S31A1, Isolated from Equine Infectious Endometritis.
JO  - Genome Announcements
PY  - 2013
SP  - e00683
EP  - e00613
VL  - 1
AB  - We present the draft genome sequence of Streptococcus equi subsp. zooepidemicus S31A1, a
AB  - strain isolated from equine infectious endometritis in Denmark.
AB  - Comparative analyses of this genome were done with four published reference
AB  - genomes: S. zooepidemicus strains MGCS10565, ATCC 35246, and H70 and S. equi
AB  - subsp. equi strain 4047.
ER  -

TY  - JOUR
AU  - da Silva, A.C.R. et al.
TI  - Comparison of the genomes of two Xanthomonas pathogens with differing host specificities.
JO  - Nature
PY  - 2002
SP  - 459
EP  - 463
VL  - 417
AB  - The genus Xanthomonas is a diverse and economically important group of bacterial
AB  - phytopathogens, belonging to the gamma-subdivision of the Proteobacteria. Xanthomonas
AB  - axonopodis pv. citri (Xac) causes citrus canker, which affects most commercial citrus
AB  - cultivars, resulting in significant losses worldwide. Symptoms include canker lesions, leading
AB  - to abscission of fruit and leaves and general tree decline. Xanthomonas campestris pv.
AB  - campestris (Xcc) causes black rot, which affects crucifers such as Brassica and Arabidopsis.
AB  - Symptoms include marginal leaf chlorosis and darkening of vascular tissue, accompanied by
AB  - extensive wilting and necrosis. Xanthomonas campestris pv. campestris is grown commercially to
AB  - produce the exopolysaccharide xanthan gum, which is used as a viscosifying and stabilizing
AB  - agent in many industries. Here we report and compare the complete genome sequences of Xac and
AB  - Xcc. Their distinct disease phenotypes and host ranges belie a high degree of similarity at
AB  - the genomic level. More than 80% of genes are shared, and gene order is conserved along most
AB  - of their respective chromosomes. We identified several groups of strain-specific genes, and on
AB  - the basis of these groups we propose mechanisms that may explain the differing host
AB  - specificities and pathogenic processes.
ER  -

TY  - JOUR
AU  - da Silva, F.D.
AU  - Lima, A.R.
AU  - Moraes, P.H.
AU  - Siqueira, A.S.
AU  - Dall'Agnol, L.T.
AU  - Barauna, A.R.
AU  - Martins, L.C.
AU  - Oliveira, K.G.
AU  - de Lima, C.P.
AU  - Nunes, M.R.
AU  - Vianez-Junior, J.L.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00399
EP  - e00316
VL  - 4
AB  - Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known.
AB  - To improve the genomic studies of heterotrophic
AB  - bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of
AB  - Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus
AB  - sp. (cyanobacteria), is presented here.
ER  -

TY  - JOUR
AU  - Da Silva, S.A.C.
AU  - Rodrigues, J.
TI  - Draft Genome Sequence of Shiga Toxin-Producing Escherichia coli Strain D92/09.
JO  - Genome Announcements
PY  - 2015
SP  - e00805
EP  - e00815
VL  - 3
AB  - Escherichia coli is suspected to be involved with Crohn's disease. Adherence and  invasion to
AB  - epithelial cells are properties commonly observed in these bacteria.
AB  - Here, we present a draft genome sequence of E. coli D92/09, a multidrug-resistant
AB  - strain, which besides showing these properties produces Shiga cytotoxin-1 and
AB  - possibly other toxins.
ER  -

TY  - JOUR
AU  - Daas, M.S.
AU  - Rosana, A.R.R.
AU  - Acedo, J.Z.
AU  - Douzane, M.
AU  - Nateche, F.
AU  - Kebbouche-Gana, S.
AU  - Vederas, J.C.
TI  - Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 25
EP  - 25
VL  - 13
AB  - Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form
AB  - parasporal crystals containing proteinaceous toxins. It is a member of the
AB  - Bacillus cereus sensu lato, a group with low genetic diversity but produces
AB  - several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from
AB  - an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and
AB  - biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of
AB  - B. thuringiensis DNG9. The genome encodes several gene inventories for the
AB  - biosynthesis of bioactive compounds such as zwittermycin A, petrobactin,
AB  - insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect
AB  - the genome information of strain DNG9 will provide another model system to study
AB  - pathogenicity against insect pests, plant diseases, and antimicrobial compound
AB  - mining and comparative phylogenesis among the Bacillus cereus sensu lato group.
ER  -

TY  - JOUR
AU  - Daas, M.S.
AU  - Rosana, A.R.R.
AU  - Acedo, J.Z.
AU  - Douzane, M.
AU  - Nateche, F.
AU  - Kebbouche-Gana, S.
AU  - Vederas, J.C.
TI  - Draft Genome Sequence of Bacillus paralicheniformis F47, Isolated from an Algerian Salty Lake.
JO  - Genome Announcements
PY  - 2018
SP  - e00190
EP  - e00118
VL  - 6
AB  - Bacillus paralicheniformis F47 was isolated from a salty lake in Ain Baida-Ouargla, southern
AB  - Algeria. The genome contains genes for the production of
AB  - several bioactive secondary metabolites, including the siderophore bacillibactin,
AB  - the lipopeptides fengycin, surfactin, and lichenysin, the antibiotics bacitracin
AB  - and kanosamine, and a putative circular bacteriocin.
ER  -

TY  - JOUR
AU  - Daas, M.S.
AU  - Rosana, A.R.R.
AU  - Acedo, J.Z.
AU  - Nateche, F.
AU  - Kebbouche-Gana, S.
AU  - Vederas, J.C.
AU  - Case, R.J.
TI  - Draft Genome Sequences of Bacillus cereus E41 and Bacillus anthracis F34 Isolated from Algerian Salt Lakes.
JO  - Genome Announcements
PY  - 2017
SP  - e00383
EP  - e00317
VL  - 5
AB  - Two strains of Bacillus, B. cereus E41 and B. anthracis F34, were isolated from a salt lake in
AB  - Ain M'lila-Oum El Bouaghi, eastern Algeria, and Ain Baida-Ouargla,
AB  - southern Algeria, respectively. Their genomes display genes for the production of
AB  - several bioactive secondary metabolites, including polyhydroxyalkanoate, iron
AB  - siderophores, lipopeptides, and bacteriocins.
ER  -

TY  - JOUR
AU  - Dabe, E.C.
AU  - Kohn, A.B.
AU  - Bobkova, Y.
AU  - Kocot, K.
AU  - Citarella, M.
AU  - Bostwick, C.J.
AU  - Winters, G.C.
AU  - Swalla, B.J.
AU  - Moroz, L.L.
TI  - Epigenomic Signatures in Basal Metazoans: DNA Methyltransferase in Pleurobrachia bachei.
JO  - Integr. Comp. Biol.
PY  - 2013
SP  - E273
EP  - E273
VL  - 53
AB  - DNA methylation is an epigenetic modification crucial to cell differentiation and development.
AB  - In the majority of bilaterians 5-methylcytosine DNA methylation occurs at CpG sites and
AB  - islands controlling gene transcription.  Contrary to Drosophila and C. elegans that have lost
AB  - this machinery, possibly due to their compact genome sizes and short life cycle, here we show
AB  - that the phylum Ctenophora has conserved methylation machinery.  Using the data from the
AB  - recently sequenced genome of Pleurobrachia bachei we cloned DNA 5-cytosine methyltransferase
AB  - (DNMT) and characterized its expression in major developmental stages and adult ctenophores.
AB  - Distinctive mRNA expression in the digestive system, (stomach, pharynx and mouth), tentacles
AB  - and unique patterns in between ciliated comb rows in adult Pleurobrachia collectively suggest
AB  - that DNMT mRNA expression levels are both cell-specific and noticeable in areas of high
AB  - proliferation.  Next using colorimetric ELISA assay for methylated DNA we directly showed that
AB  - DNA methylation does occur in the Pleurobrachia genome, although it was significantly lower
AB  - than in the molluscan (Aplysia) and mammalian (Ratus) nervous tissues. Combined, our data
AB  - suggest that the small genome of the ctenophore Pleurobrachia bachei has functional DNA
AB  - methylation machinery, possibly involved in epigenetic control of somatic cell divisions and
AB  - regulation of mRNA expression at zones of proliferation.
ER  -

TY  - JOUR
AU  - Daboussi, F. et al.
TI  - Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 6367
EP  - 6379
VL  - 40
AB  - The ability to specifically engineer the genome of living cells at precise locations using
AB  - rare-cutting designer endonucleases has broad
AB  - implications for biotechnology and medicine, particularly for
AB  - functional genomics, transgenics and gene therapy. However, the
AB  - potential impact of chromosomal context and epigenetics on designer
AB  - endonuclease-mediated genome editing is poorly understood. To address
AB  - this question, we conducted a comprehensive analysis on the efficacy of
AB  - 37 endonucleases derived from the quintessential I-CreI meganuclease
AB  - that were specifically designed to cleave 39 different genomic targets.
AB  - The analysis revealed that the efficiency of targeted mutagenesis at a
AB  - given chromosomal locus is predictive of that of homologous gene
AB  - targeting. Consequently, a strong genome-wide correlation was apparent
AB  - between the efficiency of targeted mutagenesis (0.1% to similar to 6%)
AB  - with that of homologous gene targeting (0.1% to similar to 15%). In
AB  - contrast, the efficiency of targeted mutagenesis or homologous gene
AB  - targeting at a given chromosomal locus does not correlate with the
AB  - activity of individual endonucleases on transiently transfected
AB  - substrates. Finally, we demonstrate that chromatin accessibility
AB  - modulates the efficacy of rare-cutting endonucleases, accounting for
AB  - strong position effects. Thus, chromosomal context and epigenetic
AB  - mechanisms may play a major role in the efficiency rare-cutting
AB  - endonuclease-induced genome engineering.
ER  -

TY  - JOUR
AU  - Dabrazhynetskaya, A.
AU  - Soika, V.
AU  - Volokhov, D.
AU  - Simonyan, V.
AU  - Chizhikov, V.
TI  - Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050.
JO  - Genome Announcements
PY  - 2014
SP  - e00127
EP  - e00114
VL  - 2
AB  - Mycoplasma hyorhinis is known as one of the most prevalent contaminants of mammalian cell and
AB  - tissue cultures worldwide. Here, we present the complete
AB  - genome sequence of the fastidious M. hyorhinis strain DBS 1050.
ER  -

TY  - JOUR
AU  - Dabul, A.N.
AU  - Kos, V.N.
AU  - Gilmore, M.S.
AU  - Camargo, I.L.
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SA16, Representative of an Endemic Clone from a Brazilian Hospital.
JO  - Genome Announcements
PY  - 2013
SP  - e00754
EP  - e00713
VL  - 1
AB  - Here we report the draft genome sequence of a bloodstream isolate of methicillin-resistant
AB  - Staphylococcus aureus strain SA16. Strain SA16 is a
AB  - sequence type 5 (ST5)-staphylococcal cassette chromosome mec type II (SCCmec II)
AB  - clone and was the most prevalent isolate at a Brazilian hospital during the
AB  - second half of 2009.
ER  -

TY  - JOUR
AU  - Daccord, A.
AU  - Ceccarelli, D.
AU  - Burrus, V.
TI  - Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands.
JO  - Mol. Microbiol.
PY  - 2010
SP  - 576
EP  - 588
VL  - 78
AB  - In vibrios and enterobacteria lateral gene transfer is often facilitated by
AB  - integrating conjugative elements (ICEs) of the SXT/R391 family. SXT/R391 ICEs
AB  - integrate by site-specific recombination into prfC and transfer by conjugation, a
AB  - process that is initiated at a specific locus called the origin of transfer
AB  - (oriT(SXT) ). We identified genomic islands (GIs) harbouring a sequence that
AB  - shares >63% identity with oriT(SXT) in three species of Vibrio. Unlike SXT/R391
AB  - ICEs, these GIs are integrated into a gene coding for a putative stress-induced
AB  - protein and do not appear to carry any gene coding for a conjugative machinery or
AB  - for mobilization proteins. Our results show that SXT/R391 ICEs trigger the
AB  - excision and mediate the conjugative transfer in trans of the three Vibrio GIs at
AB  - high frequency. GIs' excision is independent of the ICE-encoded recombinase and
AB  - is controlled by the ICE-encoded transcriptional activator SetCD, which is
AB  - expressed during the host SOS response. Both mobI and traI, two ICE-borne genes
AB  - involved in oriT recognition, are essential for GIs' transfer. We also found that
AB  - SXT/R391 ICEs mobilize in trans over 1 Mb of chromosomal DNA located 5' of the
AB  - GIs' integration site. Together these results support a novel mechanism of
AB  - mobilization of GIs by ICEs of the SXT/R391 family.
ER  -

TY  - JOUR
AU  - Daebeler, A.
AU  - Herbold, C.W.
AU  - Vierheilig, J.
AU  - Sedlacek, C.J.
AU  - Pjevac, P.
AU  - Albertsen, M.
AU  - Kirkegaard, R.H.
AU  - de la Torre, J.R.
AU  - Daims, H.
AU  - Wagner, M.
TI  - Cultivation and Genomic Analysis of 'Candidatus Nitrosocaldus islandicus,' an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.
JO  - Front. Microbiol.
PY  - 2018
SP  - 193
EP  - 193
VL  - 9
AB  - Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic
AB  - ammonia oxidizers in geothermal environments. Although molecular
AB  - data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus
AB  - clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature
AB  - habitats, only one enrichment culture of an AOA thriving above 50 degrees C has
AB  - been reported and functionally analyzed. In this study, we physiologically and
AB  - genomically characterized a newly discovered thaumarchaeon from the
AB  - deep-branching Nitrosocaldaceae family of which we have obtained a high (
AB  - approximately 85%) enrichment from biofilm of an Icelandic hot spring (73 degrees
AB  - C). This AOA, which we provisionally refer to as 'Candidatus Nitrosocaldus
AB  - islandicus,' is an obligately thermophilic, aerobic chemolithoautotrophic ammonia
AB  - oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures
AB  - between 50 and 70 degrees C. 'Ca. N. islandicus' encodes the expected repertoire
AB  - of enzymes proposed to be required for archaeal ammonia oxidation, but
AB  - unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme
AB  - for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA
AB  - appears to be NO-dependent as 'Ca. N. islandicus' is, like all other tested AOA,
AB  - inhibited by the addition of an NO scavenger. Furthermore, comparative genomics
AB  - revealed that 'Ca. N. islandicus' has the potential for aromatic amino acid
AB  - fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as
AB  - well as a type 3b hydrogenase, which are not present in any other sequenced AOA.
AB  - A further surprising genomic feature of this thermophilic ammonia oxidizer is the
AB  - absence of DNA polymerase D genes - one of the predominant replicative DNA
AB  - polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our
AB  - findings suggest that metabolic versatility and DNA replication might differ
AB  - substantially between obligately thermophilic and other AOA.
ER  -

TY  - JOUR
AU  - Dahai, T.
AU  - Ando, S.
AU  - Takasaki, Y.
AU  - Tadano, J.
TI  - Site-directed mutagenesis of restriction endonuclease HindIII.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1999
SP  - 1703
EP  - 1707
VL  - 63
AB  - Site-directed mutagenesis by inverse PCR was done on the HindIII gene.  Target residues to be
AB  - mutated were chosen according to (i) the fact that a mutant obtained by sodium nitrite
AB  - treatment showed almost no HindIII activity, where Asp-123 was replaced with Asn, and (ii) the
AB  - model proposed by Stahl et al.  Seven kinds of mutants were obtained by PCR, and their
AB  - enzymatic and biochemical properties were examined.  Three mutants, P50S, D108L, and D123N,
AB  - showed fairly low HindIII activity.  On the other hand, the other four, P84Q, E85K, V106E, and
AB  - K125N, retained the activity.  In particular, E86K showed higher activity than the wild type
AB  - enzyme.  This fact was confirmed when activities of the purified wild type and E86K enzymes
AB  - were assayed.  These results coincided fairly well with data using E. coli strains that carry
AB  - the respective mutant plasmids, on their resistance to phage T7 and on growth rate.  We
AB  - conclude that the PE motif at residues 50 and 51, and DXK motif at residues 108-110, are
AB  - responsible for the enzymic reaction of HindIII.
ER  -

TY  - JOUR
AU  - Dahlem, T.J.
AU  - Hoshijima, K.
AU  - Jurynec, M.J.
AU  - Gunther, D.
AU  - Starker, C.G.
AU  - Locke, A.S.
AU  - Weis, A.M.
AU  - Voytas, D.F.
AU  - Grunwald, D.J.
TI  - Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome.
JO  - PLoS Genet.
PY  - 2012
SP  - E1002861
EP  - E1002861
VL  - 8
AB  - The zebrafish is a powerful experimental system for uncovering gene function in
AB  - vertebrate organisms. Nevertheless, studies in the zebrafish have been limited by
AB  - the approaches available for eliminating gene function. Here we present simple
AB  - and efficient methods for inducing, detecting, and recovering mutations at
AB  - virtually any locus in the zebrafish. Briefly, double-strand DNA breaks are
AB  - induced at a locus of interest by synthetic nucleases, called TALENs. Subsequent
AB  - host repair of the DNA lesions leads to the generation of insertion and deletion
AB  - mutations at the targeted locus. To detect the induced DNA sequence alterations
AB  - at targeted loci, genomes are examined using High Resolution Melt Analysis, an
AB  - efficient and sensitive method for detecting the presence of newly arising
AB  - sequence polymorphisms. As the DNA binding specificity of a TALEN is determined
AB  - by a custom designed array of DNA recognition modules, each of which interacts
AB  - with a single target nucleotide, TALENs with very high target sequence
AB  - specificities can be easily generated. Using freely accessible reagents and
AB  - Web-based software, and a very simple cloning strategy, a TALEN that uniquely
AB  - recognizes a specific pre-determined locus in the zebrafish genome can be
AB  - generated within days. Here we develop and test the activity of four TALENs
AB  - directed at different target genes. Using the experimental approach described
AB  - here, every embryo injected with RNA encoding a TALEN will acquire targeted
AB  - mutations. Multiple independently arising mutations are produced in each growing
AB  - embryo, and up to 50% of the host genomes may acquire a targeted mutation. Upon
AB  - reaching adulthood, approximately 90% of these animals transmit targeted
AB  - mutations to their progeny. Results presented here indicate the TALENs are highly
AB  - sequence-specific and produce minimal off-target effects. In all, it takes about
AB  - two weeks to create a target-specific TALEN and generate growing embryos that
AB  - harbor an array of germ line mutations at a pre-specified locus.
ER  -

TY  - JOUR
AU  - Dahms, P.A.
AU  - Martin, A.L.
AU  - Ganz, H.H.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a  Feline Anal Sac.
JO  - Genome Announcements
PY  - 2017
SP  - e00034
EP  - e00017
VL  - 5
AB  - Here, we present the draft genome sequence of Propionibacterium (Cutibacterium) avidum strain
AB  - UCD-PD2. The assembly contains 2,667,287 bp in 51 contigs. The
AB  - strain was isolated from anal sac secretion samples collected from a feral
AB  - domestic cat (Felis catus) as part of a larger project to study the microbiology
AB  - of cats.
ER  -

TY  - JOUR
AU  - Dai, J.
AU  - Wang, S.
AU  - Guerlebeck, D.
AU  - Laturnus, C.
AU  - Guenther, S.
AU  - Shi, Z.
AU  - Lu, C.
AU  - Ewers, C.
TI  - Suppression subtractive hybridization identifies an autotransporter adhesin gene  of E. coli IMT5155 specifically associated with avian pathogenic Escherichia coli  (APEC).
JO  - BMC Microbiol.
PY  - 2010
SP  - 236
EP  - 236
VL  - 10
AB  - BACKGROUND: Extraintestinal pathogenic E. coli (ExPEC) represent a phylogenetically diverse
AB  - group of bacteria which are implicated in a large range
AB  - of infections in humans and animals. Although subgroups of different ExPEC
AB  - pathotypes, including uropathogenic, newborn meningitis causing, and avian
AB  - pathogenic E. coli (APEC) share a number of virulence features, there still might
AB  - be factors specifically contributing to the pathogenesis of a certain subset of
AB  - strains or a distinct pathotype. Thus, we made use of suppression subtractive
AB  - hybridization and compared APEC strain IMT5155 (O2:K1:H5; sequence type complex
AB  - 95) with human uropathogenic E. coli strain CFT073 (O6:K2:H5; sequence type
AB  - complex 73) to identify factors which may complete the currently existing model
AB  - of APEC pathogenicity and further elucidate the position of this avian pathotype
AB  - within the whole ExPEC group. RESULTS: Twenty-eight different genomic loci were
AB  - identified, which are present in IMT5155 but not in CFT073. One of these loci
AB  - contained a gene encoding a putative autotransporter adhesin. The open reading
AB  - frame of the gene spans a 3,498 bp region leading to a putative 124-kDa adhesive
AB  - protein. A specific antibody was raised against this protein and expression of
AB  - the adhesin was shown under laboratory conditions. Adherence and adherence
AB  - inhibition assays demonstrated a role for the corresponding protein in adhesion
AB  - to DF-1 chicken fibroblasts. Sequence analyses revealed that the flanking regions
AB  - of the chromosomally located gene contained sequences of mobile genetic elements,
AB  - indicating a probable spread among different strains by horizontal gene transfer.
AB  - In accordance with this hypothesis, the adhesin was found to be present not only
AB  - in different phylogenetic groups of extraintestinal pathogenic but also of
AB  - commensal E. coli strains, yielding a significant association with strains of
AB  - avian origin. CONCLUSIONS: We identified a chromosomally located autotransporter
AB  - gene in a highly virulent APEC strain which confers increased adherence of a
AB  - non-fimbriated E. coli K-12 strain to a chicken fibroblast cell line. Even though
AB  - flanked by mobile genetic elements and three different genetic regions upstream
AB  - of the gene, most probably indicating horizontal gene transfer events, the
AB  - adhesin gene was significantly linked with strains of avian origin. Due to the
AB  - nucleotide sequence similarity of 98% to a recently published adhesin-related
AB  - gene, located on plasmid pAPEC-O1-ColBM, the name aatA (APEC autotransporter
AB  - adhesin A) was adopted from that study.Our data substantiate that AatA might not
AB  - only be of relevance in APEC pathogenicity but also in facilitating their
AB  - reservoir life style in the chicken intestine, which might pave the way for
AB  - future intestinal preventive strategies.
ER  -

TY  - JOUR
AU  - Dai, K.
AU  - Jin, J.
AU  - Wen, Y.
AU  - Wen, X.
AU  - He, L.
AU  - Cao, S.
AU  - Huang, X.
AU  - Wu, R.
AU  - Zhao, Q.
TI  - Complete Genome Sequence of Highly Virulent Haemophilus parasuis Serotype 11 Strain SC1401.
JO  - Genome Announcements
PY  - 2016
SP  - e00628
EP  - e00616
VL  - 4
AB  - Haemophilus parasuis, a normal Gram-negative bacterium, may cause Glasser's disease and
AB  - pneumonia in pigs. This study aims to identify the genes related to
AB  - natural competence of the serotype 11 strain SC1401, which frequently shows
AB  - competence and high pathogenicity. SC1401 shows many differences from strains
AB  - without natural competence within the molecular basis. We performed complete
AB  - genome sequencing together with restriction modification system analysis to lay
AB  - the foundation for later study.
ER  -

TY  - JOUR
AU  - Dai, L.
AU  - Chai, D.
AU  - Gu, S.Q.
AU  - Gabel, J.
AU  - Noskov, S.Y.
AU  - Blocker, F.J.
AU  - Lambowitz, A.M.
AU  - Zimmerly, S.
TI  - A Three-Dimensional Model of a Group II Intron RNA and Its Interaction with the Intron-Encoded Reverse Transcriptase.
JO  - Mol. Cell
PY  - 2008
SP  - 472
EP  - 485
VL  - 30
AB  - Group II introns are self-splicing ribozymes believed to be the ancestors of spliceosomal
AB  - introns. Many group II introns encode reverse
AB  - transcriptases that promote both RNA splicing and intron mobility to new
AB  - genomic sites. Here we used a circular permutation and crosslinking method
AB  - to establish 16 intramolecular distance relationships within the mobile
AB  - Lactococcus lactis Ll.LtrB-DeltaORF intron. Using these new constraints
AB  - together with 13 established tertiary interactions and eight published
AB  - crosslinks, we modeled a complete three-dimensional structure of the
AB  - intron. We also used the circular permutation strategy to map RNA-protein
AB  - interaction sites through fluorescence quenching and crosslinking assays.
AB  - Our model provides a comprehensive structural framework for understanding
AB  - the function of group II ribozymes, their natural structural variations,
AB  - and the mechanisms by which the intron-encoded protein promotes RNA
AB  - splicing and intron mobility. The model also suggests an arrangement of
AB  - active site elements that may be conserved in the spliceosome.
ER  -

TY  - JOUR
AU  - Dai, Q.
AU  - Restrepo, B.I.
AU  - Porcella, S.F.
AU  - Raffel, S.J.
AU  - Schwan, T.G.
AU  - Barbour, A.G.
TI  - Antigenic variation by Borrelia hermsii occurs through recombination between extragenic repetitive elements on linear plasmids.
JO  - Mol. Microbiol.
PY  - 2006
SP  - 1329
EP  - 1343
VL  - 60
AB  - The relapsing fever agent Borrelia hermsii undergoes multiphasic antigenic variation through
AB  - gene conversion of a unique expression site on a linear plasmid by an archived variable
AB  - antigen gene. To further characterize this mechanism we assessed the repertoire and
AB  - organization of archived variable antigen genes by sequencing approximately 85% of plasmids
AB  - bearing these genes. Most archived genes shared with the expressed gene a less than or equal
AB  - 62 nucleotide (nt) region, the upstream homology sequence (UHS), that surrounded the start
AB  - codon. The 59 archived variable antigen genes were arrayed in clusters with 13 repetitive, 214
AB  - nt long downstream homology sequence (DHS) elements distributed among them. A fourteenth DHS
AB  - element was downstream of the expression locus. Informative nucleotide polymorphisms in UHS
AB  - regions and DHS elements were applied to the analysis of the expression site of relapse
AB  - serotypes from 60 infected mice in a prospective study. For most recombinations, the upstream
AB  - crossover occurred in the UHS's second half, and the downstream crossover was in the DHS's
AB  - second half. Usually the closest archival DHS element was used, but occasionally a more
AB  - distant DHS was employed. The downstream extragenic crossover site in B. hermsii contrasts
AB  - with the downstream extragenic crossover site for antigenic variation in African trypanosomes.
ER  -

TY  - JOUR
AU  - Dai, W.
AU  - Zhu, Y.
AU  - Wang, X.
AU  - Sakenova, N.
AU  - Yang, Z.
AU  - Wang, H.
AU  - Li, G.
AU  - He, J.
AU  - Huang, D.
AU  - Cai, Y.
AU  - Guo, W.
AU  - Wang, Q.
AU  - Feng, T.
AU  - Fan, Q.
AU  - Zheng, T.
AU  - Han, A.
TI  - Draft Genome Sequence of the Bacterium Comamonas aquatica CJG.
JO  - Genome Announcements
PY  - 2016
SP  - e01186
EP  - e01116
VL  - 4
AB  - A Gram-negative bacterial strain, Comamonas aquatica CJG, absorbs low-density lipoprotein but
AB  - not high-density lipoprotein in serum. Here, we report its draft
AB  - genomic sequence of 3,764,434 bp, containing total 3,425 genes, 27% of which
AB  - encode proteins for metabolism and energy conversion, and it is 30% identical to
AB  - the genome of Comamonas testosteroni.
ER  -

TY  - JOUR
AU  - Dai, Y.
AU  - Ni, Z.F.
AU  - Dai, J.
AU  - Zhao, T.
AU  - Sun, Q.X.
TI  - Isolation and expression analysis of genes encoding DNA methyltransferase in wheat (Triticum aestivum L.).
JO  - Biochim. Biophys. Acta
PY  - 2005
SP  - 118
EP  - 125
VL  - 1729
AB  - DNA methylation of cytosine residues, catalyzed by DNA methyltransferases, is suggested to
AB  - play important roles in regulating
AB  - gene expression and plant development. In this study, we isolated four
AB  - wheat cDNA fragments and one cDNA with open reading frame encoding
AB  - putative DNA methyltransferase and designated TaMET1, TaMET2a, TaMET2b,
AB  - TaCMT, TaMET3, respectively. BLASTX searches and phylogenetic analysis
AB  - suggested that five cDNAs belonged to four classes (Dnmt1, Dnmt2, CMT
AB  - and Dnmt3) of DNA methyltransferase genes. TaMET2a encoded a protein of
AB  - 376 aa and contained eight of ten conserved motifs characteristic of
AB  - DNA methyltransferase. Genomic sequence of TaMET2a was obtained and
AB  - found to contain ten introns and eleven exons. The expression analysis
AB  - of the five genes revealed that they were expressed in developing seed,
AB  - during germination and various vegetative tissues, but in quite
AB  - different abundance. It was interesting to note that TaMET1 and TaMET3
AB  - mRNAs were clearly detected in dry seeds. Moreover, the differential
AB  - expression patterns of five genes were observed between wheat hybrid
AB  - and its parents in leaf, stem and root of jointing stage, some were
AB  - up-regulated while some others were down-regulated in the hybrid. We
AB  - concluded that multiple wheat DNA methyltransferase genes were present
AB  - and might play important roles in wheat growth and development.
ER  -

TY  - JOUR
AU  - Daifuku, T.
AU  - Yoshida, T.
AU  - Kitamura, T.
AU  - Kawaichi, S.
AU  - Inoue, T.
AU  - Nomura, K.
AU  - Yoshida, Y.
AU  - Kuno, S.
AU  - Sako, Y.
TI  - Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 5891
EP  - 5898
VL  - 79
AB  - The increasing number of genome sequences of archaea and bacteria show their
AB  - adaptation to different environmental conditions at the genomic level. Aeropyrum
AB  - spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated
AB  - from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a
AB  - coastal solfataric vent. To investigate the adaptation strategy in each habitat,
AB  - we compared the genomes of the two species. Shared genome features were a small
AB  - genome size, a high GC content, and a large portion of orthologous genes (86 to
AB  - 88%). The genomes also showed high synteny. These shared features may have been
AB  - derived from the small number of mobile genetic elements and the lack of a RecBCD
AB  - system, a recombinational enzyme complex. In addition, the specialized physiology
AB  - (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the
AB  - entire-genome similarity. Despite having stable genomes, interference of synteny
AB  - occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A.
AB  - pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short
AB  - palindromic repeat (CRISPR) elements. Spacer sequences derived from the A. camini
AB  - CRISPR showed significant matches with protospacers of the two proviruses
AB  - infecting A. pernix, indicating that A. camini interacted with viruses closely
AB  - related to APSV1 and APOV1. Furthermore, a significant fraction of the
AB  - nonorthologous genes (41 to 45%) were proviral genes or ORFans probably
AB  - originating from viruses. Although the genomes of A. camini and A. pernix were
AB  - conserved, we observed nonsynteny that was attributed primarily to virus-related
AB  - elements. Our findings indicated that the genomic diversification of Aeropyrum
AB  - spp. is substantially caused by viruses.
ER  -

TY  - JOUR
AU  - Daigle, K.
AU  - Shenoy, S.
AU  - Ehrlich, K.
AU  - Gehrke, C.
AU  - Ehrlich, M.
TI  - Restriction at mismatched sites in DNA.
JO  - Fed. Proc.
PY  - 1986
SP  - 1783
EP  - 1783
VL  - 45
AB  - Restriction endonucleases were tested for their ability to catalyze the
AB  - cleavage of mismatch-containing recognition sites in DNA.  These mismatched
AB  - base pairs were T-G, U-G or A-C in covalently closed, circular DNA molecules
AB  - prepared by in vitro extension of chemically synthesized oligonucleotide
AB  - primers annealed to an M13-derived viral DNA.  None of the tested restriction
AB  - enzymes was able to completely cleave the mismatch-containing recognition sites
AB  - of these heteroduplexes at a normal rate.  However, three of them, SmaI, SalI,
AB  - SstI, partially digested certain T-G or U-G-substituted recognition sites under
AB  - standard digestion conditions.  In these digests, there was an accumulation of
AB  - DNA singly nicked at the mismatched recognition site.  The ability of SmaI and
AB  - SstI to partially cleave at a mismatch was shown to depend on the nature and
AB  - position of the mismatch within the corresponding recognition site.  In
AB  - contrast to such partial cleavage, little or no digestion was obtained with
AB  - AccI, HincII, HindIII, and KpnI at their corresponding tested
AB  - mismatch-containing recognition sites.  Therefore, a transition-type
AB  - substitution of only one strand of a recognition site can inhibit restriction
AB  - endonuclease-catalyzed digestion at that site.
ER  -

TY  - JOUR
AU  - Daiyasu, H.
AU  - Komori, K.
AU  - Sakae, S.
AU  - Ishino, Y.
AU  - Toh, H.
TI  - Hjc resolvase is a distantly related member of the type II restriction endonuclease family.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 4540
EP  - 4543
VL  - 28
AB  - Hjc resolvase is an archaeal enzyme involved in homologous DNA recombination at the Holliday
AB  - junction intermediate. However, the structure and the catalytic mechanism of the enzyme have
AB  - not yet been identified.  We performed database searching using the amino acid sequence of the
AB  - enzyme from Pyrococcus furiosus as a query. We detected 59 amino acid sequences showing weak
AB  - but significant sequence similarity to the Hjc resolvase. The detected sequences included
AB  - DpnII, HaeII and Vsr endonuclease, which belong to the type II restriction endonuclease
AB  - family. In addition, a highly conserved region was identified from a multiple alignment of the
AB  - detected sequences, which was similar to an active site of the type II restriction
AB  - endonucleases. We substituted three conserved amino acid residues in the highly conserved
AB  - region of the Hjc resolvase with Ala residues. The amino acid replacements inactivated the
AB  - enzyme. The experimental study, together with the results of the database searching, suggests
AB  - that the Hjc resolvase is a distantly related member of the type II restriction endonuclease
AB  - family. In addition, the results of our database searches suggested that the members of the
AB  - RecB domain superfamily are evolutionarily related to the type II restriction endonuclease
AB  - family.
ER  -

TY  - JOUR
AU  - Dale, C.J.H.
AU  - Moses, E.K.
AU  - Ong, C.C.
AU  - Morrow, C.J.
AU  - Reed, M.B.
AU  - Hasse, D.
AU  - Strugnell, R.A.
TI  - Identification and sequencing of the groE operon and flanking genes of Lawsonia intracellularis: use in phylogeny.
JO  - Microbiology
PY  - 1998
SP  - 2073
EP  - 2084
VL  - 144
AB  - Proliferative enteropathy (PE) is a complex of diseases of commercial importance to the pig
AB  - industry. The obligate intracellular bacterium Lawsonia intracellularis is consistently
AB  - associated with PE and pure cultures of this bacterium have been used to reproduce PE in pigs.
AB  - In this study L. intracellularis bacteria were purified directly from PE-affected tissue. DNA
AB  - extracted from purified bacteria was used to construct a partial genomic library which was
AB  - screened using sera from L. intracellularis-immunized rabbits. Two seroreactive recombinant
AB  - clones were identified, one of which expressed proteins of 10 and 60 kDa. The sequence of the
AB  - insert from this clone, pISI-2, revealed ORFs with sequence similarity to the groES/EL operon
AB  - of Escherichia coli, the 505 ribosomal proteins L21 and L27 of E. coli, a GTP-binding protein
AB  - of Bacillus subtilis and a possible protoporphyrinogen oxidase, HemK, of E. coli. Primers
AB  - designed from unique sequences from the pISI-2 insert amplified DNA from infected, but not
AB  - non-infected, porcine ilea; the amplicon sequence obtained from tissue-cultured L.
AB  - intracellularis was identical to the corresponding sequence in pISI-2, confirming the origin
AB  - of the clone. The sequence of L. intracellularis GroEL and other GroEL sequences in the
AB  - databases were used to construct a partial phylogenetic tree. Analysis of the GroEL sequence
AB  - relationship suggested that L. intracellularis is not significantly related to other organisms
AB  - whose GroEL sequences are held in the databases and supports previous data from 16S sequence
AB  - analyses suggesting that L. intracellularis is a member of a novel group of enteric pathogens.
ER  -

TY  - JOUR
AU  - Dalgaard, J.Z.
TI  - Mobile introns and inteins: friend or foe?
JO  - Trends Genet.
PY  - 1994
SP  - 306
EP  - 307
VL  - 10
AB  - Since the discovery of introns, one question that has puzzled the scientific community has
AB  - been whether these genetic elements are of functional importance to their host organism. One
AB  - theory is that introns are selfish DNA elements whose mobility allows them to overcome
AB  - selection against them. This theory seems especially plausible in the case of mobile group I
AB  - introns, which encode site-specific DNA endonucleases and can invade genomes in a
AB  - site-specific manner via a double-stranded break repair (DSBR) mechanism. Interestingly, it
AB  - has recently been discovered that this mechanism also accounts for the mobility of archael
AB  - introns and inteins, introns that are spliced at the level of the protein, several of which
AB  - have been found in prokaryotic genomes. The discovery that this mechanism of mobility is not
AB  - unique to group I introns and that this family of genetic elements is not limited to the
AB  - genomes of bacteriophages and eurkaryotic nuclear and organelles revives the question of
AB  - whether encoding these 'parasitic' DNA elements confers a selective advantage on the host
AB  - genome.
ER  -

TY  - JOUR
AU  - Dalgaard, J.Z.
AU  - Garrett, R.A.
TI  - Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum.
JO  - Gene
PY  - 1992
SP  - 103
EP  - 110
VL  - 121
AB  - Two archaeal introns have been discovered in the single-copy 23S rRNA-encoding gene of the
AB  - hyperthermophile, Pyrobaculum organotrophum.  After excision from rRNA transcripts, both
AB  - introns circularize and are stably retained in the cell.  Putative proteins encoded by the
AB  - introns and covering most of the intron sequence share a decapeptide motif with proteins
AB  - encoded by another archaeal intron and by group I introns.
ER  -

TY  - JOUR
AU  - Dalgaard, J.Z.
AU  - Garrett, R.A.
AU  - Belfort, M.
TI  - A site-specific endonuclease encoded by a typical archaeal intron.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 5414
EP  - 5417
VL  - 90
AB  - The protein encoded by the archaeal intron in the 23S rRNA gene of the hyperthermophile
AB  - Desulfurococcus mobilis is a double-strand DNase, that like group I intron homing
AB  - endonucleases, is capable of cleaving an intronless allele of the gene. This enzyme, I-Dmo I,
AB  - is unusual among the intron endonucleases in that it is thermostable and is expressed only
AB  - from linear and cyclized intron species and not from the precursor RNA. However, in analogy to
AB  - its eukaryotic counterparts, but unlike the bacteriophage enzymes, I-Dmo I makes a staggered
AB  - double-strand cut that generates 4-nt 3' extensions. Additionally, although the archaeal and
AB  - group I introns have entirely different structural properties and splicing pathways, I-DmoI
AB  - shares sequence similarity, in the form of the LAGLIDADG motif, with group I intron
AB  - endonucleases of eukaryotes. These observations support the independent evolutionary origin of
AB  - endonucleases and intron core elements and are consistent with the invasive potential of
AB  - endonuclease genes.
ER  -

TY  - JOUR
AU  - Dalgaard, J.Z.
AU  - Garrett, R.A.
AU  - Belfort, M.
TI  - Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 28885
EP  - 28892
VL  - 269
AB  - The archaeal intron in the 23 S rRNA gene of the hyperthermophile Desulfurococcus mobilis has
AB  - previously been shown to encode a site-specific DNA endonuclease that contains the LAGLIDADG
AB  - motif. The enzyme, I-DmoI, has been shown to be active in two forms when expressed in vitro,
AB  - from RNAs representing either the linear (I-DmoIl) or circular (I-DmoIc) intron. In this study
AB  - we have overexpressed I-DmoIl and I-DmoIc and purified the enzymes from Escherichia coli. The
AB  - optimal conditions for the enzymatic activity in vitro were determined, and the enzyme was
AB  - used to delimit the recognition boundary on its DNA substrate (14-20 nucleotides), an
AB  - intronless 23 S rRNA gene. Despite belonging to the archaeal kingdom, and being the product of
AB  - a hyperthermophile, I-DmoI shares many properties with LAGLIDADG intron and intein
AB  - endonucleases in other kingdoms. These results support the view that these phylogenetically
AB  - diverse enzymes, which function to mobilize the DNA sequences that encode them, share a common
AB  - ancestry.
ER  -

TY  - JOUR
AU  - Dalgaard, J.Z.
AU  - Klar, A.J.
AU  - Moser, M.J.
AU  - Holley, W.R.
AU  - Chatterjee, A.
AU  - Mian, I.S.
TI  - Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4626
EP  - 4638
VL  - 25
AB  - The LAGLIDADG and HNH families of site-specific DNA endonucleases encoded by viruses,
AB  - bacteriophages as well as archaeal, eucaryotic nuclear and organellar genomes are
AB  - characterized by the sequence motifs 'LAGLIDADG' and 'HNH', respectively.  These
AB  - endonucleases have been shown to occur in different environments: LAGLIDADG endonucleases are
AB  - found in inteins, archaeal and group I introns and as free standing open reading frames; HNH
AB  - endonucleases occur in group I and group II introns and as ORFs.  Here, statistical models
AB  - (hidden Markov models, HMMs) that encompass both the conserved motifs and more variable
AB  - regions of these families have been created and employed to characterize known and potential
AB  - new family members.  A number of new, putative LAGLIDADG and HNH endonucleases have been
AB  - identified including an intein-encoded HNH sequence.  Analysis of an HMM-generated multiple
AB  - alignment of 130 LAGLIDADG family members and the three-dimensional structure of the I-CreI
AB  - endonuclease has enabled definition of the core elements of the repeated domain (~90 residues)
AB  - that is present in this family of proteins.  A conserved negatively charged residue is
AB  - proposed to be involved in catalysis.  Phylogenetic analysis of the two families indicates a
AB  - lack of exchange of endonucleases between different mobile elements (environments) and between
AB  - hosts from different phylogenetic kingdoms.  However, there does appear to have been
AB  - considerable exchange of endonuclease domains amongst elements of the same type. Such events
AB  - are suggested to be important for the formation of elements of new specificity.
ER  -

TY  - JOUR
AU  - Dalgaard, J.Z.
AU  - Silva, G.H.
AU  - Belfort, M.
AU  - Van Roey, P.
TI  - Crystallization and preliminary crystallographic analysis of the archaeal intron-encoded endonuclease I-DmoI.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 1998
SP  - 1435
EP  - 1436
VL  - 54
AB  - Two forms of the archaeal intron-encoded site-specific endonuclease I-DmoI, namely I-DmoIc and
AB  - I-DmoIl, have been purified and crystallized. Crystals of I-DmoIc are rod-shaped and diffract
AB  - to 3.0 A resolution, but further analysis was hampered by twinning. Crystals of I-DmoIl, which
AB  - is a six-amino-acid C-terminal truncation of I-DmoIc, are plate shaped and belong to space
AB  - group C2 with cell parameters a = 93.72, b = 37.03, c = 55.56 A, beta = 113.4 degrees, with
AB  - one molecule per asymmetric unit (Vm = 2.01 A3 Da-1). The crystals diffract to at least 2.3 A
AB  - resolution. A complete native data set has been measured and structure determination is
AB  - on-going.
ER  -

TY  - JOUR
AU  - Dalhoff, C.
AU  - Lukinavicius, G.
AU  - Klimasauskas, S.
AU  - Weinhold, E.
TI  - Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases.
JO  - Nat. Chem. Biol.
PY  - 2006
SP  - 31
EP  - 32
VL  - 2
AB  - S-Adenosyl-L-methionine is the major methyl donor for biological methylation reactions
AB  - catalyzed by methyltransferases.  We report the first chemical synthesis of AdoMet analogs
AB  - with extended carbon chains replacing the methyl group and their evaluation as cofactors for
AB  - all three classes of DNA methyltransferases.  Extended groups containing a double or triple
AB  - bond in the b position to the sulfonium center were transferred onto DNA in a catalytic and
AB  - sequence-specific manner, demonstrating a high utility of such synthetic cofactors for
AB  - targeted functionalization of biopolymers.
ER  -

TY  - JOUR
AU  - Dalhoff, C.
AU  - Lukinavicius, G.
AU  - Klimasauskas, S.
AU  - Weinhold, E.
TI  - Synthesis of S-adenosyl-L-methionine analogs and their use for sequence-specific transalkylation of DNA by methyltransferases.
JO  - Nat. Protoc.
PY  - 2006
SP  - 1879
EP  - 1886
VL  - 1
AB  - Here we describe a one-step synthetic procedure for the preparation of S-adenosyl-L-methionine
AB  - analogs with extended carbon chains replacing the methyl group.  These AdoMet analogs function
AB  - as efficient cofactors for DNA methyltransferases, and we provide a protocol for
AB  - sequence-specific transfer of extended side chains from these AdoMet analogs to DNA by DNA
AB  - MTases.  Direct chemoselective allylation or propargylation of S-adenosyl-L-homocysteine at
AB  - sulfur is achieved under the acidic conditions needed to protect other nucleophilic positions
AB  - in AdoHcy.  The unsaturated bonds in b position to the sulfonium center of the resulting
AB  - AdoMet analogs are designed to stabilize the transition state formed upon DNA MTase-catalyzed
AB  - nucleophilic attack at the carbon next to the sulfonium center and lead to efficient transfer
AB  - of the extended side chains to DNA.  Using these protocols, sequence-specific functionalized
AB  - DNA can be obtained within one to two weeks.
ER  -

TY  - JOUR
AU  - Dalia, A.B.
AU  - Lazinski, D.W.
AU  - Camilli, A.
TI  - Characterization of Undermethylated Sites in Vibrio cholerae.
JO  - J. Bacteriol.
PY  - 2013
SP  - 2389
EP  - 2399
VL  - 195
AB  - The activities of DNA methyltransferases are important for a variety of cellular  functions in
AB  - bacteria. In this study, we developed a modified high-throughput
AB  - technique called methyl homopolymer tail mediated sequencing (methyl HTM-seq) to
AB  - identify the undermethylated sites in the Vibrio cholerae genome for the two DNA
AB  - methyltransferases, Dam, an adenine methyltransferase, and VchM, a cytosine
AB  - methyltransferase, during growth in rich medium in vitro. Many of the
AB  - undermethylated sites occurred in intergenic regions, and for most of these
AB  - sites, we identified the transcription factors responsible for undermethylation.
AB  - This confirmed the presence of previously hypothesized DNA-protein interactions
AB  - for these transcription factors and provided insight into the biological state of
AB  - these cells during growth in vitro. DNA adenine methylation has previously been
AB  - shown to mediate heritable epigenetic switches in gene regulation. However, none
AB  - of the undermethylated Dam sites tested showed evidence of regulation by this
AB  - mechanism. This study is the first to identify undermethylated adenines and
AB  - cytosines genomewide in a bacterium using second-generation sequencing
AB  - technology.
ER  -

TY  - JOUR
AU  - Daligault, H. et al.
TI  - Complete genome sequence of Haliscomenobacter hydrossis type strain (O).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 352
EP  - 360
VL  - 4
AB  - Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus
AB  - Haliscomenobacter, which belongs to order 'Sphingobacteriales'. The species is of
AB  - interest because of its isolated phylogenetic location in the tree of life,
AB  - especially the so far genomically uncharted part of it, and because the organism
AB  - grows in a thin, hardly visible hyaline sheath. Members of the species were
AB  - isolated from fresh water of lakes and from ditch water. The genome of H.
AB  - hydrossis is the first completed genome sequence reported from a member of the
AB  - family 'Saprospiraceae'. The 8,771,651 bp long genome with its three plasmids of
AB  - 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA
AB  - genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Daligault, H.E. et al.
TI  - Genome Assembly of Shigella flexneri ATCC 12022, a Quality Control Reference Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e01052
EP  - e01014
VL  - 2
AB  - Shigella flexneri causes shigellosis, severe and potentially life-threatening diarrhea, and
AB  - accounts for 18% of shigellosis cases in the United States. Here,
AB  - we present the 4.51-Mbp genome assembly of S. flexneri ATCC 12022, a quality
AB  - control and reference strain, in 10 scaffolds.
ER  -

TY  - JOUR
AU  - Daligault, H.E. et al.
TI  - Twenty Whole-Genome Bacillus sp. Assemblies.
JO  - Genome Announcements
PY  - 2014
SP  - e00958
EP  - e00914
VL  - 2
AB  - Bacilli are genetically and physiologically diverse, ranging from innocuous to highly
AB  - pathogenic. Here, we present annotated genome assemblies for 20 strains
AB  - belonging to Bacillus anthracis, B. atrophaeus, B. cereus, B. licheniformis, B.
AB  - macerans, B. megaterium, B. mycoides, and B. subtilis.
ER  -

TY  - JOUR
AU  - Daligault, H.E. et al.
TI  - Genome Assembly of Methicillin-Resistant Quality Control Strain Staphylococcus aureus CDC73-57501 (ATCC 29247).
JO  - Genome Announcements
PY  - 2014
SP  - e00961
EP  - e00914
VL  - 2
AB  - Staphylococcus aureus is a major cause of bacterial infections in the United States, with high
AB  - percentages of serious infections resistant to a variety of
AB  - beta-lactam antibiotics. Here, we present the scaffolded genome assembly into 16
AB  - contigs of S. aureus CDC73-57501 (ATCC 29247), a methicillin-resistant quality
AB  - control strain.
ER  -

TY  - JOUR
AU  - Daligault, H.E. et al.
TI  - Draft Genomes for Eight Burkholderia mallei Isolates from Turkey.
JO  - Genome Announcements
PY  - 2016
SP  - e01234
EP  - e01215
VL  - 4
AB  - Burkholderia mallei, the etiologic agent of glanders, is a Gram-negative, nonmotile,
AB  - facultative intracellular pathogen. Although glanders has been
AB  - eradicated from many parts of the world, the threat of B. mallei being used as a
AB  - weapon is very real. Here we present draft genome assemblies of 8 Burkholderia
AB  - mallei strains that were isolated in Turkey.
ER  -

TY  - JOUR
AU  - Daligault, H.E. et al.
TI  - Whole-Genome Assemblies of 56 Burkholderia Species.
JO  - Genome Announcements
PY  - 2014
SP  - e01106
EP  - e01114
VL  - 2
AB  - Burkholderia is a genus of betaproteobacteria that includes three notable human pathogens: B.
AB  - cepacia, B. pseudomallei, and B. mallei. While B. pseudomallei and
AB  - B. mallei are considered potential biowarfare agents, B. cepacia infections are
AB  - largely limited to cystic fibrosis patients. Here, we present 56 Burkholderia
AB  - genomes from 8 distinct species.
ER  -

TY  - JOUR
AU  - Daligault, H.E. et al.
TI  - Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e01055
EP  - e01014
VL  - 2
AB  - Yersinia spp. are animal pathogens, some of which cause human disease. We sequenced 10
AB  - Yersinia isolates (from six species: Yersinia enterocolitica, Y.
AB  - fredericksenii, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, and Y.
AB  - ruckeri) to high-quality draft or complete status. The genomes range in size from
AB  - 3.77 to 4.94 Mbp.
ER  -

TY  - JOUR
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Li, P.E.
AU  - Meincke, L.
AU  - Munk, A.C.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of Corynebacterium sp. Strain ATCC 6931.
JO  - Genome Announcements
PY  - 2014
SP  - e01074
EP  - e01014
VL  - 2
AB  - The genus Corynebacterium is best known for the pathogen C. diphtheriae; however, it contains
AB  - mostly commensal and nonpathogenic, as well as several opportunistic,
AB  - pathogens. Here, we present the 2.47-Mb scaffolded assembly of the type strain,
AB  - Corynebacterium sp. ATCC 6931 (NCTC 1914), as deposited into GenBank under
AB  - accession number CP008913.
ER  -

TY  - JOUR
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Lo, C.C.
AU  - Meincke, L.
AU  - Munk, A.C.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Klebsiella pneumoniae Type Strain ATCC 13883.
JO  - Genome Announcements
PY  - 2014
SP  - e00939
EP  - e00914
VL  - 2
AB  - Klebsiella pneumoniae is a common cause of antibiotic-resistant bacterial infections in
AB  - immunocompromised individuals. Here, we present the 5.54-Mb
AB  - scaffolded assembly of the type strain K. pneumoniae type strain ATCC 13883, as
AB  - deposited in GenBank under accession no. JOOW00000000.
ER  -

TY  - JOUR
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Lo, C.C.
AU  - Meincke, L.
AU  - Munk, C.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of a Quality Control Reference Isolate, Moraxella catarrhalis Strain ATCC 25240.
JO  - Genome Announcements
PY  - 2014
SP  - e00938
EP  - e00914
VL  - 2
AB  - Generally an opportunistic pathogen in the United States, Moraxella catarrhalis has acquired
AB  - resistance to multiple antibacterial/antimicrobial agents. Here, we
AB  - present the complete 1.9-Mb genome of M. catarrhalis strain ATCC 25240, as
AB  - deposited in NCBI under the accession number CP008804.
ER  -

TY  - JOUR
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Lo, C.C.
AU  - Meincke, L.
AU  - Munk, C.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Bordetella bronchiseptica ATCC 10580, a Historical Canine Clinical Isolate.
JO  - Genome Announcements
PY  - 2014
SP  - e00916
EP  - e00914
VL  - 2
AB  - We present the scaffolded genome of Bordetella bronchiseptica ATCC 10580, assembled into 98
AB  - contigs. This 5.1-Mb assembly (68.2% G+C content) contains
AB  - 4,870 coding regions. The strain was originally isolated from canine lung tissue
AB  - and is used in quality control testing.
ER  -

TY  - JOUR
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Minogue, T.D.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Lo, C.C.
AU  - Meincke, L.
AU  - Munk, A.C.
AU  - Rosenzweig, C.N.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Ralstonia pickettii Type Strain K-288 (ATCC 27853).
JO  - Genome Announcements
PY  - 2014
SP  - e00973
EP  - e00914
VL  - 2
AB  - We present the genome assembly of Ralstonia pickettii K-288 (ATCC 27511), consisting of 27
AB  - contigs placed into a single scaffold. This 4.76-Mbp genome has
AB  - 64.0% G+C content and 4,425 coding sequences. Because this is the type strain,
AB  - inclusion of its data set among other Ralstonia genomes should provide a
AB  - historical genomic perspective.
ER  -

TY  - JOUR
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Minogue, T.D.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Rosenzweig, C.N.
AU  - Scholz, M.
AU  - Teshima, H.
AU  - Johnson, S.L.
TI  - Genome Assembly of Serratia marcescens Type Strain ATCC 13880.
JO  - Genome Announcements
PY  - 2014
SP  - e00967
EP  - e00914
VL  - 2
AB  - Serratia marcescens ATCC 13880 is the type strain of the species and a commonly used quality
AB  - control strain. Here, we present the annotated genome assembly of
AB  - 5.13 Mbp (59.8% G+C content) as submitted to NCBI under accession no.
AB  - JOVM00000000.
ER  -

TY  - JOUR
AU  - Dall'Acqua, W.
AU  - Carter, P.
TI  - Substrate-assisted catalysis: Molecular basis and biological significance.
JO  - Protein Sci.
PY  - 2000
SP  - 1
EP  - 9
VL  - 9
AB  - Substrate-assisted catalysis (SAC) is the process by which a functional group in a substrate
AB  - contributes to catalysis by an enzyme.  SAC has been demonstrated for representatives of three
AB  - major enzyme classes: serine proteases, GTPases, and type II restriction endonucleases, as
AB  - well as lysozyme and hexose-1-phosphate uridylyltransferase.  Morover, structure-based
AB  - predictions of SAC have been made for many additional enzymes.  Examples of SAC include both
AB  - naturally occurring enzymes such as type II restriction endonucleases as well as engineered
AB  - enzymes including serine proteases.  In the latter case, a functional group from a substrate
AB  - can substitute for a catalytic residue replaced by site-directed mutagenesis. From a protein
AB  - engineering perspective, SAC provides a strategy for drastically changing enzyme substrate
AB  - specificity or even the reaction catalyzed.  From a biological viewpoint, SAC contributes
AB  - significantly to the activity of some enzymes and may represent a functional intermediate in
AB  - the evolution of catalysis.  This review focuses on advances in engineering enzyme specificity
AB  - and activity by SAC, together with the biological significance of this phenomenon.
ER  -

TY  - JOUR
AU  - Dall'Agnol, H.
AU  - Nancucheo, I.
AU  - Johnson, D.B.
AU  - Oliveira, R.
AU  - Leite, L.
AU  - Pylro, V.S.
AU  - Holanda, R.
AU  - Grail, B.
AU  - Carvalho, N.
AU  - Nunes, G.L.
AU  - Tzotzos, G.
AU  - Fernandes, G.R.
AU  - Dutra, J.
AU  - Orellana, S.C.
AU  - Oliveira, G.
TI  - Draft Genome Sequence of 'Acidibacillus ferrooxidans' ITV01, a Novel Acidophilic  Firmicute Isolated from a Chalcopyrite Mine Drainage Site in Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01748
EP  - e01715
VL  - 4
AB  - Here, we report the draft genome sequence of 'Acidibacillus ferrooxidans' strain  ITV01, a
AB  - ferrous iron- and sulfide-mineral-oxidizing, obligate heterotrophic, and
AB  - acidophilic bacterium affiliated with the phylum Firmicutes. Strain ITV01 was
AB  - isolated from neutral drainage from a low-grade chalcopyrite from a mine in
AB  - northern Brazil.
ER  -

TY  - JOUR
AU  - Dall'Agnol, R.F.
AU  - Costa, M.R.
AU  - Ribeiro, R.A.
AU  - Delamuta, J.R.
AU  - Chueire, L.M.
AU  - Hungria, M.
TI  - Genome Sequence of Paraburkholderia nodosa Strain CNPSo 1341, a N2-Fixing Symbiont of the Promiscuous Legume Phaseolus vulgaris.
JO  - Genome Announcements
PY  - 2016
SP  - e01073
EP  - e01016
VL  - 4
AB  - Paraburkholderia nodosa CNPSo 1341 is a N2-fixing symbiont of Phaseolus vulgaris  isolated
AB  - from an undisturbed soil of the Brazilian Cerrado. Its draft genome
AB  - contains 8,614,032 bp and 8,068 coding sequences (CDSs). Nodulation and
AB  - N2-fixation genes were clustered in the genome that also contains several genes
AB  - of secretion systems and quorum sensing.
ER  -

TY  - JOUR
AU  - Dalmasso, C.
AU  - Oger, P.
AU  - Courtine, D.
AU  - Georges, M.
AU  - Takai, K.
AU  - Maignien, L.
AU  - Alain, K.
TI  - Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archeon Thermococcus piezophilus CDGST, Able To Grow under Extreme Hydrostatic Pressures.
JO  - Genome Announcements
PY  - 2016
SP  - e00610
EP  - e00616
VL  - 4
AB  - We report the genome sequence of Thermococcus superprofundus strain CDGS(T), a new piezophilic
AB  - and hyperthermophilic member of the order Thermococcales isolated
AB  - from the world's deepest hydrothermal vents, at the Mid-Cayman Rise. The genome
AB  - is consistent with a heterotrophic, anaerobic, and piezophilic lifestyle.
ER  -

TY  - JOUR
AU  - Daly, C.
AU  - Fitzgerald, G.
TI  - Mechanisms of bacteriophage insensitivity in the lactic streptococci.
JO  - Streptococcal Genetics
PY  - 1987
SP  - 259
EP  - 268
VL  - 0
AB  - The mesophilic lactic streptococci, which comprise Streptococcus cremoris, S. lactis, and S.
AB  - lactis subsp. diacetylactis, are of major industrial importance as components of starter
AB  - cultures used in the manufacture of a variety of fermented dairy products, e.g., cheeses,
AB  - lactic butter, cultured buttermilk, sour cream, and quarg.  Bacteriophage attack has been
AB  - recognized since the 1930s as the most serious cause of starter culture inhibition in
AB  - commercial practice.  The consequence may be significant economic loss due to downgrading of
AB  - product or, in severe cases, total loss of the fermentation.  The vulnerability of dairying,
AB  - in contrast to other modern industrial fermentations, to phages exists partly because the
AB  - substrate, milk, cannot be sterilized for biochemical reasons, and in addition, the starter
AB  - culture must perform in large mechanized and automated units that demand consistent,
AB  - predictable acid production to ensure high-quality end products with the desired flavor and
AB  - texture characteristics.
ER  -

TY  - JOUR
AU  - Daly, C.
AU  - Fitzgerald, G.F.
AU  - Davis, R.
TI  - Biotechnology of lactic acid bacteria with special reference to bacteriophage resistance.
JO  - Antonie Van Leeuwenhoek
PY  - 1996
SP  - 99
EP  - 110
VL  - 70
AB  - Lactic acid bacteria play an important role in many food and feed fermentations.  In recent
AB  - years major advances have been made in unravelling the genetic and molecular basis of
AB  - significant industrial traits of lactic acid bacteria.  Bacteriophages which can infect and
AB  - destroy lactic acid bacteria pose a particularly serious threat to dairy fermentations that
AB  - can result in serious economic losses.  Consequently, these organisms and the mechanisms by
AB  - which they interact with their hosts have received much research attention.  This paper
AB  - reviews some of the key discoveries over the years that have led us to our current
AB  - understanding of bacteriophages themselves and the means by which their disruptive influence
AB  - may be minimized.
ER  -

TY  - JOUR
AU  - Daly, M.J.
AU  - Gaidamakova, E.K.
AU  - Matrosova, V.Y.
AU  - Vasilenko, A.
AU  - Zhai, M.
AU  - Leapman, R.D.
AU  - Lai, B.
AU  - Ravel, B.
AU  - Li, S.M.
AU  - Kemner, K.M.
AU  - Fredrickson, J.K.
TI  - Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance.
JO  - PLoS Biology
PY  - 2007
SP  - e92
EP  - e92
VL  - 5
AB  - In the hierarchy of cellular targets damaged by ionizing radiation (IR), classical models of
AB  - radiation toxicity place DNA at the top. Yet, many
AB  - prokaryotes are killed by doses of IR that cause little DNA damage. Here
AB  - we have probed the nature of Mn-facilitated IR resistance in Deinococcus
AB  - radiodurans, which together with other extremely IR-resistant bacteria
AB  - have high intracellular Mn/Fe concentration ratios compared to
AB  - IR-sensitive bacteria. For in vitro and in vivo irradiation, we
AB  - demonstrate a mechanistic link between Mn(II) ions and protection of
AB  - proteins from oxidative modifications that introduce carbonyl groups.
AB  - Conditions that inhibited Mn accumulation or Mn redox cycling rendered D.
AB  - radiodurans radiation sensitive and highly susceptible to protein
AB  - oxidation. X-ray fluorescence microprobe analysis showed that Mn is
AB  - globally distributed in D. radiodurans, but Fe is sequestered in a region
AB  - between dividing cells. For a group of phylogenetically diverse
AB  - IR-resistant and IR-sensitive wild-type bacteria, our findings support the
AB  - idea that the degree of resistance is determined by the level of oxidative
AB  - protein damage caused during irradiation. We present the case that
AB  - protein, rather than DNA, is the principal target of the biological action
AB  - of IR in sensitive bacteria, and extreme resistance in Mn-accumulating
AB  - bacteria is based on protein protection.
ER  -

TY  - JOUR
AU  - Dam, B.
AU  - Kube, M.
AU  - Dam, S.
AU  - Reinhardt, R.
AU  - Liesack, W.
TI  - Complete Sequence Analysis of Two Methanotroph-Specific repABC-Containing Plasmids from Methylocystis sp. Strain SC2.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 4373
EP  - 4379
VL  - 78
AB  - The complete nucleotide sequences of two large, low-copy-number plasmids of 229.6
AB  - kb (pBSC2-1) and 143.5 kb (pBSC2-2) were determined during assembly of the
AB  - whole-genome shotgun sequences of the methane-oxidizing bacterium Methylocystis
AB  - sp. strain SC2. The physical existence of the two plasmids in strain SC2 was
AB  - confirmed by pulsed-field gel electrophoresis followed by Southern hybridization.
AB  - Both plasmids have a conserved replication module of the repABC system and carry
AB  - genes involved in their faithful maintenance and conjugation. In addition, they
AB  - contain genes that might be involved in essential metabolic processes. These
AB  - include several heavy metal resistance genes and copper transport genes in
AB  - pBSC2-1 and a complete nitrous oxide reductase operon and a pmoC singleton in
AB  - pBSC2-2, the latter encoding the PmoC subunit of particulate methane
AB  - monooxygenase.
ER  -

TY  - JOUR
AU  - Damelin, M.
AU  - Bestor, T.H.
TI  - Biological functions of DNA methyltransferase 1 require its methyltransferase activity.
JO  - Mol. Cell. Biol.
PY  - 2007
SP  - 3891
EP  - 3899
VL  - 27
AB  - DNA methyltransferase 1 (DNMT1) has been reported to interact with a wide variety of factors
AB  - and to contain intrinsic transcriptional
AB  - repressor activity. When a conservative point mutation was introduced
AB  - at the key catalytic residue, mutant DNMT1 failed to rescue any of the
AB  - phenotypes of Dnmt1-null embryonic stem (ES) cells, which indicated
AB  - that the biological functions of DNMT1 are exerted through the
AB  - methylation of DNA. ES cells that expressed the mutant protein did not
AB  - survive differentiation. Intracisternal A-particle family
AB  - retrotransposons were no longer methylated and were transcribed at high
AB  - levels. The proper localization of DNMT1 depended on normal genomic
AB  - methylation, and we discuss the implications of this finding for
AB  - epigenetic dysregulation in cancer.
ER  -

TY  - JOUR
AU  - Danaher, R.
AU  - Stein, D.C.
TI  - Characterization of a restriction enzyme isolated from a hydrothermal vent community bacterium, Hyphomonas jannaschiana.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1988
SP  - 213
EP  - 213
VL  - 88
AB  - A restriction endonuclease has been isolated and purified from Hyphomonas
AB  - jannaschiana.  The enzyme, HjaI, was purified using an FPLC equipped with a
AB  - Mono Q column.  Yields of several thousand units of enzyme activity per gram of
AB  - cells were obtained.  Optimal activity was achieved in 25 mM Tris-HCl (pH-7.8),
AB  - 100 mM NaCl, 10 mM MgCl/2, 100 micro g/ml BSA, 2 mM 2-mercaptoethanol at 37C.
AB  - This enzyme was inactivated by incubation at 65C.  By comparing the
AB  - fragmentation patterns of pBR322 and lambda DNA to computer generated patterns
AB  - provided by New England Biolabs, the recognition sequence was found to be
AB  - GATATC.  HjaI is an isoschizomer of EcoRV.  Cleavage of DNA by this enzyme
AB  - produced blunt ended fragments.  Furthermore, DNA isolated from H. jannaschiana
AB  - was not cleaved by EcoRV.
ER  -

TY  - JOUR
AU  - Danaher, R.
AU  - Stein, D.C.
TI  - Characterization of a restriction endonuclease and the cloning of its corresponding DNA methylase from the thermal vent bacterium Hyphomonas jannaschiana.
JO  - Abstr. 1st Intl. Symp. Marine Mol. Biol.
PY  - 1988
SP  - 25
EP  - 25
VL  - 0
AB  - The marine bacterium H. jannaschiana produces a restriction enzyme, HjaI, that
AB  - was purified by column chromatography.  Maximal enzyme activity occurred in 25
AB  - mM Tris-HCl (pH-9.0), 100 mM NaCl, 10 mM MgCl2, 100 micrograms/ml BSA, 2 mM
AB  - 2-mercaptoethanol at 37C.  The recognition sequence was found to be GATATC, as
AB  - determined by comparing banding patterns obtained after digesting lambda DNA
AB  - with those predicted from its DNA sequence.  HjaI produces blunt ended DNA
AB  - fragments, as measured by a digestion/ligation scheme.  DNA isolated from H.
AB  - jannaschiana was not cleaved by EcoRV, an isoschizomer of HjaI.  The
AB  - corresponding methylase (M.HjaI) was cloned into E. coli methylase accepting
AB  - host (DH5 mcr).  H. jannaschiana chromosomal DNA was partially digested with
AB  - and inserted into the PstI site of pBR322.  Plasmid DNA was isolated from the
AB  - entire gene bank, digested with EcoRV, and transformed back into DH5 mcr.
AB  - M.HjaI clones were identified based on their plasmid DNA being partially
AB  - protected against cleavage by EcoRV.  Several plasmids were identified that
AB  - were partially resistant to EcoRV, and all shared a common 8 Kb PstI fragment.
ER  -

TY  - JOUR
AU  - Danaher, R.J.
AU  - Stein, D.C.
TI  - Expression of cloned restriction and modification genes, hjaIRM from Hyphomonas jannaschiana in Escherichia coli.
JO  - Gene
PY  - 1990
SP  - 129
EP  - 133
VL  - 89
AB  - A type-II RM system, HjaI, was identified in the marine bacterium, Hyphomonas
AB  - jannaschiana.  The ENase recognizes GATATC, and DNA fragments generated after
AB  - cleavage with this enzyme contain blunt ends.  A DNA fragment encoding these
AB  - enzymes was cloned and expressed in Escherichia coli, although the level of
AB  - expression of the cloned genes was low.  DNA methylated by M.HjaI was not
AB  - restricted by the Mcr or Mrr restriction systems of E. coli.  Although H.
AB  - jannaschiana is a marine bacterium isolated near the thermal vents on the floor
AB  - of the Pacific Ocean, the biochemical properties of the ENase were similar to
AB  - those of EcoRV, an isoschizomer isolated from E. coli.
ER  -

TY  - JOUR
AU  - Dandare, S.U.
AU  - Skvortsov, T.
AU  - Arkhipova, K.
AU  - Allen, C.C.R.
TI  - Draft Genome Sequence of Rhodococcus sp. Strain NCIMB 12038, a Naphthalene-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e01420
EP  - e01417
VL  - 6
AB  - We report here the draft genome sequence of Rhodococcus sp. strain NCIMB 12038, an
AB  - industrially important bacterium, possessing a large and diverse repertoire of
AB  - genes involved in the biotransformation of various organic compounds, including
AB  - naphthalene.
ER  -

TY  - JOUR
AU  - Dandekar, T.
AU  - Huynen, M.
AU  - Regula, J.T.
AU  - Ueberle, B.
AU  - Zimmermann, C.U.
AU  - Andrade, M.A.
AU  - Doerks, T.
AU  - Sanchez-Pulido, L.
AU  - Snel, B.
AU  - Suyama, M.
AU  - Yuan, Y.P.
AU  - Herrmann, R.
AU  - Bork, P.
TI  - Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3278
EP  - 3288
VL  - 28
AB  - Four years after the original sequence submission, we have re-annotated the genome of
AB  - Mycoplasma pneumoniae to incorporate novel data. The total number of ORFs has been increased
AB  - from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly
AB  - identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from
AB  - 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome
AB  - positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified.
AB  - Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent
AB  - annotation vocabulary has been introduced. Annotation reasoning, annotation categories and
AB  - comparisons to other published data on M. pneumoniae functional assignments are given.
AB  - Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass
AB  - spectrometry as well as gene expression data from this study. Compared to the original
AB  - annotation, we increased the number of proteins with predicted functional features from 349 to
AB  - 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the
AB  - published literature. Furthermore, there are 23 reductions and 30 additions with respect to
AB  - the previous annotation. mRNA expression data support transcription of 184 of the functionally
AB  - unassigned reading frames.
ER  -

TY  - JOUR
AU  - Dang, H.T.
AU  - Yotsumoto, K.
AU  - Enomoto, K.
TI  - Draft Genome Sequence of Violacein-Producing Marine Bacterium Pseudoalteromonas sp. 520P1.
JO  - Genome Announcements
PY  - 2014
SP  - e01346
EP  - e01314
VL  - 2
AB  - Here, we report a draft 5.25-Mb genome sequence of Pseudoalteromonas sp. 520P1, a marine
AB  - violacein-producing bacterium isolated from the Pacific coast of Japan.
AB  - Genome annotation by BLAST searches revealed the presence of one acylhomoserine
AB  - lactone (AHL) synthase (luxI) and five AHL receptor protein (luxR) gene homologs.
ER  -

TY  - JOUR
AU  - Daniel, A.S.
AU  - Fuller-Pace, F.V.
AU  - Legge, D.M.
AU  - Murray, N.E.
TI  - Distribution and diversity of hsd genes in Escherichia coli and other enteric bacteria.
JO  - J. Bacteriol.
PY  - 1988
SP  - 1775
EP  - 1782
VL  - 170
AB  - We screened Salmonella typhimurium, Citrobacter freundii, Klebsiella
AB  - pneumoniae, Shigella boydii, and many isolates of Escherichia coli for DNA
AB  - sequences homologous to those encoding each of two unrelated type I restriction
AB  - and modification systems (EcoK and EcoA).  Both K- and A-related hsd genes were
AB  - identified, but never both in the same strain.  S. typhimurium encodes three
AB  - restriction and modification systems, but its DNA hybridized only to the
AB  - K-specific probe which we know to identify the StySB system.  No homology to
AB  - either probe was detected in the majority of E. coli strains, but in C.
AB  - freundii, we identified homology to the A-specific probe.  We cloned this
AB  - region of the C. freundii genome and showed that it encoded a functional,
AB  - A-related restriction system whose specificity differs from those of known type
AB  - I enzymes.  Sequences immediately flanking the hsdK genes of E.coli K-12 and
AB  - the hsdA genes of E. coli 15T- were shown to be homologous, indicating similar
AB  - or even identical positions in their respective chromosomes.  E. coli C has no
AB  - known restriction system, and the organization of its chromosome is consistent
AB  - with deletion of the three hsd genes and their neighbor, mcrB.
ER  -

TY  - JOUR
AU  - Daniel, D.S.
AU  - Gan, H.M.
AU  - Lee, S.M.
AU  - Dykes, G.A.
AU  - Rahman, S.
TI  - Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins.
JO  - Genome Announcements
PY  - 2017
SP  - e00553
EP  - e00517
VL  - 5
AB  - Enterococcus faecalis is known to cause a variety of nosocomial infections, including urinary
AB  - tract infections. Antibiotic resistance and virulence
AB  - properties in this species are of public concern. The draft genome sequences of
AB  - six E. faecalis strains isolated from clinical and environmental sources in
AB  - Malaysia are presented here.
ER  -

TY  - JOUR
AU  - Daniel, J.J.
AU  - Givan, S.A.
AU  - Brun, Y.V.
AU  - Brown, P.J.
TI  - Draft Genome Sequence of Prosthecomicrobium hirschii ATCC 27832T.
JO  - Genome Announcements
PY  - 2015
SP  - e01355
EP  - e01315
VL  - 3
AB  - We report the draft genome sequence of Prosthecomicrobium hirschii ATCC 27832T, an
AB  - alphaproteobacterium with remarkable cellular morphologies. The chromosome
AB  - comprises 6,484,983 bp in six scaffolds with a G+C content of 69%, and 6,066
AB  - potential coding sequences.
ER  -

TY  - JOUR
AU  - Daniels, J.S.
AU  - Gates, K.S.
TI  - Specificity of DNA cleavage by the type IIs restriction enzyme, HphI.
JO  - ACS Abstracts
PY  - 1994
SP  - 66
EP  - 66
VL  - 208
AB  - Type IIs restriction enzymes are DNA-cleaving proteins that bind to short (4-8 base pair)
AB  - sequences of double-helical DNA and cleave at positions distant from the recognition site.
AB  - HphI is a type IIs restriction enzyme that recognizes the nonpalindromic sequence
AB  - 5'-GGTGA-3' and is reported to hydrolyze the DNA backbone 8/7 base pairs away from the
AB  - recognition site. We will report interesting effects of varying substrate size and sequence on
AB  - the DNA-cleavage reaction of HphI.
ER  -

TY  - JOUR
AU  - Daniels, L.E.
AU  - Wood, K.M.
AU  - Scott, D.J.
AU  - Halford, S.E.
TI  - Subunit assembly for DNA cleavage by restriction endonuclease SgrAI.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 579
EP  - 591
VL  - 327
AB  - The SgrAI endonuclease usually cleaves DNA with two recognition sites more rapidly than DNA
AB  - with one site, often converting the former directly to
AB  - the products cut at both sites. In this respect, SgrAI acts like the
AB  - tetrameric restriction enzymes that bind two copies of their target sites
AB  - before cleaving both sites concertedly. However, by analytical
AB  - ultracentrifugation, SgrAI is a dimer in solution though it aggregates to
AB  - high molecular mass species when bound to its specific DNA sequence. Its
AB  - reaction kinetics indicate that it uses different mechanisms to cleave DNA
AB  - with one and with two SgrAI sites. It cleaves the one-site DNA in the
AB  - style of a dimeric restriction enzyme acting at an individual site,
AB  - mediating neither interactions in trans, as seen with the tetrameric
AB  - enzymes, nor subunit associations, as seen with the monomeric enzymes. In
AB  - contrast, its optimal reaction on DNA with two sites involves an
AB  - association of protein subunits: two dimers bound to sites in cis may
AB  - associate to form a tetramer that has enhanced activity, which then
AB  - cleaves both sites concurrently. The mode of action of SgrAI differs from
AB  - all restriction enzymes characterised previously, so this study extends
AB  - the range of mechanisms known for restriction endonucleases.
ER  -

TY  - JOUR
AU  - Daniels, L.L.
AU  - Wais, A.C.
TI  - Restriction and modification of halophage S45 in Halobacterium.
JO  - Curr. Microbiol.
PY  - 1984
SP  - 133
EP  - 136
VL  - 10
AB  - A newly isolated group B1 bacteriophage, Halophage S45, is restricted and
AB  - modified in vivo by strains of Halobacterium.  Three strain-specific activities
AB  - have been observed.  Two of these occur in the same bacterial strain and appear
AB  - to be due to different kinds of enzymatic activities.  One of the restriction
AB  - specificities is shown to be associated with a strain-specific endonuclease
AB  - active on unmodified halobacterial DNA.
ER  -

TY  - JOUR
AU  - Danilevich, V.N.
AU  - Livshits, V.A.
TI  - The plasmid carrying a temperature-sensitive mutation in the DNA-methylase gene of the PstI system: Effect on host cells at nonpermissive temperature.
JO  - Genetika
PY  - 1999
SP  - 574
EP  - 586
VL  - 35
AB  - Temperature-sensitive (ts) derivatives of plasmid pRMP1, a derivative of PBR322 containing
AB  - restriction and modification (RM) genes of the PstI system, were obtained using hydroxylamine
AB  - mutagenesis. One of the isolated plasmids responsible for the inhibition of Escherichia coli
AB  - cell growth at 42 degrees C, pRMPts, was analyzed in this work. Cells of Rec+ strains carrying
AB  - this plasmid were unable to divide at 42 degrees C and formed long non-septated filaments that
AB  - died upon prolonged cultivation. Cells of the RecA- strains carrying pRMPts did not form
AB  - filaments at 42 degrees C and rapidly disappeared. On agar media with or without ampicillin,
AB  - Rec+ and RecA- strains with this plasmid formed colonies of temperature-resistant (tr)
AB  - derivatives with frequencies ranging from 1.5 x 10^-4 to 4 x 10^-6 in independent clones. The
AB  - structure of plasmids from cells of tr- derivatives of Rec+ and RecA- strains carrying plasmid
AB  - pRMPts was analyzed by the set of restriction enzymes. Reversions to the temperature-resistant
AB  - phenotype were shown to result from the following events: (1) the insertional inactivation of
AB  - the PstI restriction enzyme gene in pRMPts (the insertion of the IS1 element); (2) deletions
AB  - in plasmid DNA fragments that partially or completely cover the restriction enzyme gene; (3)
AB  - point mutations; and (4) others. The effect of the chromosomal sulA mutation on the
AB  - maintenance of the ts-plasmid in bacterial cells was studied at 42 degrees C. High efficiency
AB  - loss of the plasmid was detected in pRMPts-carrying Rec+ cells with the sulA::Tn5 mutation
AB  - grown in liquid and solid nutrient media at this temperature.  Under similar conditions,
AB  - plasmid loss was not detected in SulA+ cells. On the basis of the data obtained, it is
AB  - concluded that the ts-mutation is located in the DNA-methylase gene of plasmid pRMPts. Mutant
AB  - DNA methylase was unable to methylate all sites in the chromosomal DNA at 42 degrees C. Some
AB  - of the unmethylated sites can be digested with the PstI enzyme, which leads to the induction
AB  - of SOS response in Rec+ cells or to total mortality in cells with the recA phenotype.
ER  -

TY  - JOUR
AU  - Danin-Poleg, Y.
AU  - Elgavish, S.
AU  - Raz, N.
AU  - Efimov, V.
AU  - Kashi, Y.
TI  - Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus Biotype 3.
JO  - Genome Announcements
PY  - 2013
SP  - e00136
EP  - e00113
VL  - 1
AB  - We report the first genome sequence of the pathogenic Vibrio vulnificus biotype 3. This draft
AB  - genome sequence of the environmental strain VVyb1(BT3), isolated in
AB  - Israel, provides a representation of this newly emerged clonal group, which
AB  - reveals higher similarity to the clinical strains of biotype 1 than to the
AB  - environmental ones.
ER  -

TY  - JOUR
AU  - Danin-Poleg, Y.
AU  - Raz, N.
AU  - Roig, F.J.
AU  - Amaro, C.
AU  - Kashi, Y.
TI  - Draft Genome Sequence of Environmental Bacterium Vibrio vulnificus CladeA-yb158.
JO  - Genome Announcements
PY  - 2015
SP  - e00754
EP  - e00715
VL  - 3
AB  - We report the genome sequence of the environmental Vibrio vulnificus biotype 1_cladeA. This
AB  - draft genome of the CladeA-yb158 strain, isolated in Israel,
AB  - represents this newly emerged clonal group that contains both clinical and
AB  - environmental strains.
ER  -

TY  - JOUR
AU  - Danish-Daniel, M.
AU  - Gan, H.Y.
AU  - Gan, H.M.
AU  - Saari, N.A.
AU  - Usup, G.
TI  - Genome Sequence of Nitratireductor basaltis Strain UMTGB225, a Marine Bacterium Isolated from a Green Barrel Tunicate in Bidong Island, Malaysia.
JO  - Genome Announcements
PY  - 2014
SP  - e01015
EP  - e01014
VL  - 2
AB  - Nitratireductor basaltis strain UMTGB225 is a Gram-negative bacterium isolated from a marine
AB  - tunicate found in Bidong Island, Terengganu, Malaysia. In this
AB  - study, the genome of Nitratireductor basaltis UMTGB225 was sequenced to gain
AB  - insight into the role of this bacterium and its association with tunicate hosts
AB  - in a coral reef habitat.
ER  -

TY  - JOUR
AU  - Danish-Daniel, M.
AU  - Ming, G.H.
AU  - Mohd, N.M.E.
AU  - Sung, Y.Y.
AU  - Usup, G.
TI  - Genome Sequence of Bacillus sp. Strain UMTAT18 Isolated from the Dinoflagellate Alexandrium tamiyavanichii Found in the Straits of Malacca.
JO  - Genome Announcements
PY  - 2016
SP  - e01106
EP  - e01116
VL  - 4
AB  - Bacillus sp. strain UMTAT18 was isolated from the harmful dinoflagellate Alexandrium
AB  - tamiyavanichii Its genome consists of 5,479,367 bp with 5,546 open
AB  - reading frames, 102 tRNAs, and 29 rRNAs. Gene clusters for biosynthesis of
AB  - nonribosomal peptides, bacteriocin, and lantipeptide were identified. It also
AB  - contains siderophore and genes related to stress tolerance.
ER  -

TY  - JOUR
AU  - Danna, K.
AU  - Nathans, D.
TI  - Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1971
SP  - 2913
EP  - 2917
VL  - 68
AB  - A bacterial restriction endonuclease has been used to produce specific
AB  - fragments of SV40 DNA.  Digestion of DNA from plaque-purified stocks of SV40
AB  - with the restriction endonuclease from Hemophilus influenzae gave ll fragments
AB  - resolvable by polyacrylamide gel electrophoresis, eight of which were equimolar
AB  - with the original DNA.  The fragments ranged from about 6.5 x 10/5 to 7.4 x
AB  - 10/4 daltons, as determined by electron microscopy, DNA content, or
AB  - electrophoretic mobility.
ER  -

TY  - JOUR
AU  - Danna, K.J.
TI  - Daniel Nathans.
JO  - Proc. Amer. Phil. Soc.
PY  - 2010
SP  - 338
EP  - 354
VL  - 154
AB  - Dr. Daniel Nathans, the brilliant and reticent Nobel Prize-winning scientist who was regarded
AB  - by many of his peers as the conscience of the Johns Hopkins University, died on 16 November
AB  - 1999 of leukemia at his home.  He was seventy-one.  Proud and passionate about ideas, Dr.
AB  - Nathans helped Hopkins sustain its sense of tradition during a time that brought wrenching
AB  - changes to academic medical centers.  In addition to reaching and conducting research, Dr.
AB  - Nathans served the university as a valued adviser and interim president.  "He was the wise man
AB  - of the medical center and he was seen that way," said former Hopkins medical dean Michael M.E.
AB  - Johns, now chancellor for health affairs at Emory University in Atlanta.  "He walked quietly
AB  - but carried the responsibility of the respect he had very, very thoughtfully."  Dr. William R.
AB  - Broady, president of the Johns Hopkins University, said, "Dan Nathans was an extraordinary
AB  - human being.  He was brilliant, of course... But as one who had the privilege of knowing Dan
AB  - well, I was always most impressed with the man - modest, soft-spoken, unassuming, even
AB  - self-effacing." Colleagues described Dr. Nathans as a man who taught by example and by
AB  - encouragement, and as a researcher of vision and intellectual vigor.  "The great scientist can
AB  - separate the wheat from the chaff.  One of the great things in research is to know what
AB  - questions to ask, what subjects to focus on," said Dr. Solomon H. Snyder, the director of
AB  - Hopkins's neuroscience department.  "He would ask the very best questions."
ER  -

TY  - JOUR
AU  - Danna, K.J.
AU  - Nathans, D.
TI  - Bidirectional replication of simian virus 40 DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3097
EP  - 3100
VL  - 69
AB  - SV40 (Simian Virus 40) DNA was pulse-labeled with [3H]thymidine in infected
AB  - monkey cells, and the distribution of label within newly completed molecules
AB  - was determined by analysis of specific fragments produced by restriction
AB  - endonuclease from Hemophilus influenzae.  From these data, an order of
AB  - synthesis or temporal order of the fragments was deduced.  Comparison of the
AB  - temporal order with the physical order of the fragments in the SV40 DNA
AB  - molecule indicates a correspondence in thehse orders for two separate groups of
AB  - fragments.  From an analysis of the results, we conclude that SV40 DNA
AB  - replication begins at a specific site and proceeds bidirectionally, terminating
AB  - about halfway around the circular molecule from the initiation point.
ER  -

TY  - JOUR
AU  - Dannheim, H.
AU  - Riedel, T.
AU  - Neumann-Schaal, M.
AU  - Bunk, B.
AU  - Schober, I.
AU  - Sproer, C.
AU  - Chibani, C.M.
AU  - Gronow, S.
AU  - Liesegang, H.
AU  - Overmann, J.
AU  - Schomburg, D.
TI  - Manual curation and reannotation of the genomes of Clostridium difficile 630Deltaerm and C. difficile 630.
JO  - J. Med. Microbiol.
PY  - 2017
SP  - 286
EP  - 293
VL  - 66
AB  - PURPOSE: We resequenced the genome of Clostridium difficile 630Deltaerm (DSM
AB  - 28645), a model strain commonly used for the generation of insertion mutants.
AB  - METHODOLOGY: The genome sequence was obtained by a combination of single-molecule
AB  - real-timeand Illumina sequencing technology. RESULTS: Detailed manual curation
AB  - and comparison to the previously published genomic sequence revealed sequence
AB  - differences including inverted regions and the presence of plasmid pCD630. Manual
AB  - curation of our previously deposited genome sequence of the parental strain 630
AB  - (DSM 27543) led to an improved genome sequence. In addition, the sequence of the
AB  - transposon Tn5397 was completely identified. We manually revised the current
AB  - manual annotation of the initial sequence of strain 630 and modified either gene
AB  - names, gene product names or assigned EC numbers of 57 % of genes. The number of
AB  - hypothetical and conserved hypothetical proteins was reduced by 152. This
AB  - annotation was used as a template to annotate the most recent genome sequences of
AB  - the strains 630Deltaerm and 630. CONCLUSION: Based on the genomic analysis,
AB  - several new metabolic features of C. difficile are proposed and could be
AB  - supported by literature and subsequent experiments.
ER  -

TY  - JOUR
AU  - Dantoft, S.H.
AU  - Bielak, E.M.
AU  - Seo, J.G.
AU  - Chung, M.J.
AU  - Jensen, P.R.
TI  - Complete Genome Sequence of Pediococcus pentosaceus Strain SL4.
JO  - Genome Announcements
PY  - 2013
SP  - e01106
EP  - e01113
VL  - 1
AB  - Pediococcus pentosaceus SL4 was isolated from a Korean fermented vegetable product, kimchi. We
AB  - report here the whole-genome sequence (WGS) of P. pentosaceus
AB  - SL4. The genome consists of a 1.79-Mb circular chromosome (G+C content of 37.3%)
AB  - and seven distinct plasmids ranging in size from 4 kb to 50 kb.
ER  -

TY  - JOUR
AU  - Danzitz, M.J.
TI  - Analysis of a protein: DNA interface; the effect of altered DNA substrates on EcoRI methylase function.
JO  - Diss. Abstr.
PY  - 1993
SP  - 5180B
EP  - 5180B
VL  - 53
AB  - EcoRI methyltransferase (MTase) binds to its double stranded recognition site 5'-GAATTC-3'
AB  - and methylates it at the inner adenosine of each strand using S-adenosyl-L-methionine as the
AB  - methyl donor. The Mtase is unperturbed by hemi-methylation at either inner adenosine in
AB  - synthetic substrates, facilitating the study of substrates harboring modified bases at unique
AB  - positions. Using this strategy the contributions of the N2 amino groups of guanosine and the
AB  - C5 methyl groups of thymine toward specificity were investigated.
AB  - 
AB  - As a result largely of changes in KM-DNA, deoxyinosine substitution for guanosine at either
AB  - position in the M.EcoRI recognition site reduces the specificity constant (kcat/KM-DNA) 13 and
AB  - 39 fold. Thus methylation, which occurs in the major groove, is sensitive to both of these
AB  - minor groove modifications. The specificity constant obtained from the double substituted
AB  - substrate (14 fold below the control) indicates that there may be structural "communication"
AB  - between these sites.
AB  - 
AB  - The MTase is insensitive to removal of either one of the outer methyl groups by substitution
AB  - of deoxyuridine for the outer thymine residues. When either the inner thymine residue opposite
AB  - the hemi-methylation or both inner thymidine residues are substituted with deoxyuridine, the
AB  - KM-DNA is 5 to 10 times larger than for the control substrate leading to a specificity
AB  - constant that is 2 to 9 times larger.
AB  - 
AB  - Comparisons of entropic and enthalpic data clearly show that there are structural
AB  - perturbations within all of these modified substrates.
AB  - 
AB  - The results indicate that not only are there effects of functional group removal on MTase
AB  - function, but also structural change in the substrate beyond the altered residue is observed.
AB  - Substitutions which reduce enzyme specificity were coupled with ones that are fairly silent in
AB  - several different combinations. The resulting substrate could not only regain some of its lost
AB  - specificity, but could also become a better substrate than the control. Thus, structural
AB  - changes within the DNA substrate caused by functional group alterations can have a more
AB  - profound effect on specificity than the removal of a protein:DNA contact.
AB  - 
ER  -

TY  - JOUR
AU  - Danzitz, M.J.
AU  - Reich, N.O.
TI  - Investigations of EcoRI methylase contacts with its DNA substrate.
JO  - ACS Abstracts
PY  - 1988
SP  - 95
EP  - 95
VL  - 196
AB  - The interactions between DNA binding proteins and their DNA substrates have
AB  - been analyzed by many researchers during the past decade.  Much of this
AB  - interest stems from the fact that DNA binding proteins are involved in a myriad
AB  - of biologically significant events.  The monomeric EcoRI methylase recognizes
AB  - the double stranded DNA sequence GAATTC and methylates the second adenine of
AB  - this site.  This methylation event protects the site from cleavage by the
AB  - corresponding dimeric endonuclease.  The portion of the DNA substrate which is
AB  - protected by EcoRI methylase binding has been determined with the use of the
AB  - hydroxyl radical DNA footprinting technique.  The ability of this enzyme to
AB  - discriminate its preferred recognition site from modified sites has also been
AB  - investigated kinetically by comparisons of specificity constants (kcat/Km).
ER  -

TY  - JOUR
AU  - Danzitz, M.J.
AU  - Reich, N.O.
TI  - Characterization of a protein-DNA interface:  DNA substrate functionalties important for EcoRI methylase specificity.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 84
EP  - 84
VL  - 13D
AB  - EcoRI methylase is a monomeric 38,050 dalton enzyme requiring the cofactor
AB  - S-adenosylmethionine (AdoMet) and its DNA substrate for activity.  The methylase recognizes
AB  - the double stranded DNA sequence 5'-GAATTC-3' and methylates the second adenine of each
AB  - strand.  Details about the DNA protein interface of a DNA methylase or any monomeric DNA
AB  - binding protein have yet to be determined.  Hydroxyl radical footprinting experiments of
AB  - recognition site containing oligonucleotides complexed with the methylase alone or with the
AB  - methylase and sinefungin (an AdoMet analog and methylase inhibitor) have been carried out.
AB  - These experiments have shown the sugar phosphate backbone regions in and around the
AB  - recognition site which are protected by the methylase both with and without sinefungin
AB  - present.  Some differences in both the binding pattern and affinity have been observed between
AB  - these complexes.  Specific functionalities have been removed from the substrate at defined
AB  - locations in the recognition site by the incorporation of non-standard nucleotides, such as
AB  - uracil.  The kinetic parameters obtained with these substrates have allowed us to evaluate the
AB  - importance of specific functional groups in substrate recognition (in the uracil example the
AB  - methyl group of each thymidine).  The effect of single asymmetric substitutions on specificity
AB  - and catalysis are being dissected out using this approach.  The thermal denaturation
AB  - characteristics of the modified substrates are being used to probe for additional substrate
AB  - structural changes.
ER  -

TY  - JOUR
AU  - Dar, M.E.
AU  - Bhagwat, A.S.
TI  - Mechanism of expression of DNA repair gene vsr, an Escherichia coli gene that overlaps the DNA cystosine methylase gene, dcm.
JO  - Mol. Microbiol.
PY  - 1993
SP  - 823
EP  - 833
VL  - 9
AB  - The DNA cytosine methylase gene of Escherichia coli, dcm, overlaps an open reading frame (ORF)
AB  - that continues in +1 register past the end of the dcm. This ORF codes for a gene, vsr, that is
AB  - required for a T:G to C:G base mismatch correction process. In this study, mutants that affect
AB  - the level of expression of the two genes were constructed and characterized. Further, a
AB  - previously isolated mutant, dcm-6, was cloned and mutations within it were identified.
AB  - Northern blots were used to identify dcm-specific RNA species in wild type and dcm-6 cells.
AB  - Based on these studies we conclude that there is a six-codon overlap between vsr and dcm. The
AB  - two proteins appear to be made from a single RNA transcript and translation of dcm is required
AB  - for the efficient synthesis of Vsr. Further, Vsr is active by itself and may not be produced
AB  - as a fusion with Dcm. This is the first example of chromosomal genes that overlap in their
AB  - coding regions and produce proteins with distinct functions.
ER  -

TY  - JOUR
AU  - Darii, M.V.
AU  - Cherepanova, N.A.
AU  - Subach, O.M.
AU  - Kirsanova, O.V.
AU  - Rasko, T.
AU  - Slaska-Kiss, K.
AU  - Kiss, A.
AU  - Deville-Bonne, D.
AU  - Reboud-Ravaux, M.
AU  - Gromova, E.S.
TI  - Mutational analysis of the CG recognizing DNA methyltransferase SssI: Insight into enzyme-DNA interactions.
JO  - Biochim. Biophys. Acta
PY  - 2009
SP  - 1654
EP  - 1662
VL  - 1794
AB  - To characterize important steps of DNA methylation by M.SssI, a prokaryotic DNA-(cytosine
AB  - C5)methyltransferase (C5-MTase) sharing the
AB  - specificity of eukaryotic C5-MTases (5'-CG-3'), ten amino acids,
AB  - selected on the basis of sequence alignments and a computational model,
AB  - were subjected to mutational analysis. Wild-type and mutant M.SssI
AB  - variants were studied to determine methylation activity, DNA binding
AB  - affinity, capacity to induce base flipping, and ability to form
AB  - covalent complex with a DNA substrate containing the mechanism-based
AB  - inhibitor 2-pyrimidinone. Wild-type M.SssI induced strong fluorescence
AB  - when bound to substrate DNA containing 2-aminopurine in place of the
AB  - target cytosine, indicating flipping of the target base. Reduced
AB  - fluorescence, moderate, or drastic loss of methyltransferase activity
AB  - and reduced DNA binding suggest the involvement of the conserved 5745
AB  - (motif IV), 8232 (motif VIII, QxRx (R) under bar, and T313 (variable
AB  - region, conserved (T) under barL), as well as of the non-conserved Q147
AB  - in base flipping. Replacement of E186 (motif VI, (E) under bar NV) and
AB  - 8230 (motif VIII, Qx (R) under bar xR) with alanine resulted in loss of
AB  - methyltransferase activity without impairing DNA binding affinity.
AB  - These data are consistent with the catalytic role of E186 and 8230, and
AB  - provide, for the first time, experimental support for the essential
AB  - function of the hitherto not investigated invariant arginine of motif
AB  - VIII in C5-MTases.
ER  -

TY  - JOUR
AU  - Darii, M.V.
AU  - Kirsanova, O.V.
AU  - Drutsa, V.L.
AU  - Kochetkov, S.N.
AU  - Gromova, E.S.
TI  - Isolation and site-directed mutagenesis of DNA methyltransferase SssI.
JO  - Mol. Biol. (Mosk)
PY  - 2007
SP  - 110
EP  - 117
VL  - 41
AB  - Prokaryotic DNA methyltransferase SssI (M.SssI) methylates cytosines at C5 in CpG sequences.
AB  - Bacterial strains that produced M.SssI and its
AB  - mutants as His(6)-tagged proteins were constructed. To verify the role
AB  - of Ser300 in recognizing the CpG sequence by the enzyme, Ser300 was
AB  - replaced by Gly or Pro. The substitutions had virtually no effect on
AB  - DNA binding and methylation by M.SssI apart from a slight decrease in
AB  - binding in the case of S300P. It was assumed that no contact with DNA
AB  - is formed by the side chain of Ser300 and the carbonyl oxygen and amide
AB  - nitrogen of its peptide bonds. In addition, Ala was substituted for
AB  - highly conserved Val188, presumably involved in stabilization of the
AB  - flipped-out cytosine during the reaction. The substitution decreased
AB  - fivefold the dissociation constant of the enzyme-substrate complex and
AB  - halved the initial rate of DNA methylation. Despite the lack of a
AB  - considerable effect of V188A, it was assumed that Val188 does form a
AB  - contact with the target cytosine, but such a contact is formed with Ala
AB  - in the case of the V188A mutant.
ER  -

TY  - JOUR
AU  - Darmon, E.
AU  - Leach, D.R.F.
TI  - Bacterial Genome Instability.
JO  - Microbiol. Mol. Biol. Rev.
PY  - 2014
SP  - 1
EP  - 39
VL  - 78
AB  - Bacterial genomes are remarkably stable from one generation to the next but are plastic on an
AB  - evolutionary time scale, substantially shaped by horizontal gene transfer, genome
AB  - rearrangement, and the activities of mobile DNA elements. This implies the existence of a
AB  - delicate balance between the maintenance of genome stability and the tolerance of genome
AB  - instability. In this review, we describe the specialized genetic elements and the endogenous
AB  - processes that contribute to genome instability. We then discuss the consequences of genome
AB  - instability at the physiological level, where cells have harnessed instability to mediate
AB  - phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer
AB  - has played an important role. Indeed, this ability to share DNA sequences has played a major
AB  - part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes,
AB  - coupled with the vast numbers of bacteria on the planet, substantially limits our ability to
AB  - control disease.
ER  -

TY  - JOUR
AU  - Darrasse, A.
AU  - Bolot, S.
AU  - Serres-Giardi, L.
AU  - Charbit, E.
AU  - Boureau, T.
AU  - Fisher-Le, S.M.
AU  - Briand, M.
AU  - Arlat, M.
AU  - Gagnevin, L.
AU  - Koebnik, R.
AU  - Noel, L.D.
AU  - Carrere, S.
AU  - Jacques, M.A.
TI  - High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119.
JO  - Genome Announcements
PY  - 2013
SP  - e01036
EP  - e01013
VL  - 1
AB  - We report here the high-quality draft genome sequences of two strains of Xanthomonas
AB  - axonopodis pv. glycines, the causal agent of bacterial pustule on
AB  - soybeans. Comparison of these genomes with those of phylogenetically closely
AB  - related pathovars of Xanthomonas spp. will help to understand the mechanisms
AB  - involved in host specificity and adaptation to host plants.
ER  -

TY  - JOUR
AU  - Dartois, V.
AU  - De Backer, O.
AU  - Colson, C.
TI  - Sequence of the Salmonella typhimurium StyLT1 restriction-modification genes: homologies with EcoP1 and EcoP15 type-III R-M systems and presence of helicase domains.
JO  - Gene
PY  - 1993
SP  - 105
EP  - 110
VL  - 127
AB  - The StyLTI restriction-modification (R-M) system of Salmonella typhimurium has recently been
AB  - suggested to belong to the type-III R-M systems [De Backer and Colson. Gene 97 (1991)
AB  - 103-107]. The nucleotide sequences of StyLTI mod and res have been determined. Two closely
AB  - adjacent open reading frames were found 12 bp apart with coding capacities of 651 (Mod) and
AB  - 982 (Res) amino acids (aa), respectively. The genes, lying in the same direction of
AB  - transcription in the mod-res order, are transcribed as distinct units. The deduced aa
AB  - sequences reveal homologies with known type-III enzymes from the Escherichia coli P1 prophage,
AB  - E. coli P15 plasmid and Bacillus cereus chromosome. In addition, the StyLTI restriction
AB  - endonuclease (ENase), like other type-I and type-III ENases, contains sequence motifs
AB  - characteristic of superfamily-II helicases, which may be involved in DNA unwinding at the
AB  - cleavage site.
ER  -

TY  - JOUR
AU  - Darzi, Y.
AU  - Jiao, Y.
AU  - Hasegawa, M.
AU  - Moon, H.
AU  - Nunez, G.
AU  - Inohara, N.
AU  - Raes, J.
TI  - The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity.
JO  - PLoS ONE
PY  - 2016
SP  - E0158866
EP  - E0158866
VL  - 11
AB  - Strain NI1060 is an oral bacterium responsible for periodontitis in a murine
AB  - ligature-induced disease model. To better understand its pathogenicity, we have
AB  - determined the complete sequence of its 2,553,982 bp genome. Although closely
AB  - related to Pasteurella pneumotropica, a pneumonia-associated rodent commensal
AB  - based on its 16S rRNA, the NI1060 genomic content suggests that they are
AB  - different species thriving on different energy sources via alternative metabolic
AB  - pathways. Genomic and phylogenetic analyses showed that strain NI1060 is distinct
AB  - from the genera currently described in the family Pasteurellaceae, and is likely
AB  - to represent a novel species. In addition, we found putative virulence genes
AB  - involved in lipooligosaccharide synthesis, adhesins and bacteriotoxic proteins.
AB  - These genes are potentially important for host adaption and for the induction of
AB  - dysbiosis through bacterial competition and pathogenicity. Importantly, strain
AB  - NI1060 strongly stimulates Nod1, an innate immune receptor, but is defective in
AB  - two peptidoglycan recycling genes due to a frameshift mutation. The in-depth
AB  - analysis of its genome thus provides critical insights for the development of
AB  - NI1060 as a prime model system for infectious disease.
ER  -

TY  - JOUR
AU  - Das, A.
AU  - Panda, A.
AU  - Singh, D.
AU  - Chandrababunaidu, M.M.
AU  - Mishra, G.P.
AU  - Bhan, S.
AU  - Adhikary, S.P.
AU  - Tripathy, S.
TI  - Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278.
JO  - Genome Announcements
PY  - 2015
SP  - e00228
EP  - e00215
VL  - 3
AB  - Scytonema tolypothrichoides VB-61278, a terrestrial cyanobacterium, can be exploited to
AB  - produce commercially important products. Here, we report for the
AB  - first time a 10-Mb draft genome assembly of S. tolypothrichoides VB-61278, with
AB  - 214 scaffolds and 7,148 putative protein-coding genes.
ER  -

TY  - JOUR
AU  - Das, S.
AU  - Pettersson, B.M.
AU  - Behra, P.R.
AU  - Mallick, A.
AU  - Cheramie, M.
AU  - Ramesh, M.
AU  - Shirreff, L.
AU  - DuCote, T.
AU  - Dasgupta, S.
AU  - Ennis, D.G.
AU  - Kirsebom, L.A.
TI  - Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing.
JO  - Sci. Rep.
PY  - 2018
SP  - 12040
EP  - 12040
VL  - 8
AB  - Mycobacterium marinum is the causative agent for the tuberculosis-like disease
AB  - mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its
AB  - geographical distribution, M. marinum is known to occupy diverse fish as hosts.
AB  - However, information about its genomic diversity is limited. Here, we provide the
AB  - genome sequences for 15 M. marinum strains isolated from infected humans and
AB  - fish. Comparative genomic analysis of these and four available genomes of the M.
AB  - marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the
AB  - strains, leading to the conclusion that M. marinum should be divided into two
AB  - different clusters, the "M"- and the "Aronson"-type. We suggest that these two
AB  - clusters should be considered to represent two M. marinum subspecies. Our data
AB  - also show that the M. marinum pan-genome for both groups is open and expanding
AB  - and we provide data showing high number of mutational hotspots in M. marinum
AB  - relative to other mycobacteria such as Mycobacterium tuberculosis. This high
AB  - genomic diversity might be related to the ability of M. marinum to occupy
AB  - different ecological niches.
ER  -

TY  - JOUR
AU  - Das, S.
AU  - Pettersson, B.M.
AU  - Behra, P.R.
AU  - Ramesh, M.
AU  - Dasgupta, S.
AU  - Bhattacharya, A.
AU  - Kirsebom, L.A.
TI  - The Mycobacterium phlei genome: expectations and surprises.
JO  - Genome Biol. Evol.
PY  - 2016
SP  - 975
EP  - 985
VL  - 8
AB  - Mycobacterium phlei, a non-tuberculosis mycobacterial species was first described in 1898-99.
AB  - We present the complete genome sequence for the M. phlei CCUG21000T type strain and the draft
AB  - genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% GC
AB  - content. This is approximately 0.35 Mbps smaller than the previously reported M. phlei RIVM
AB  - draft genome. The size difference is attributed partly to large bacteriophage sequence
AB  - fragments in the M. phlei RIVM genome. Comparative analysis revealed: i) a CRISPR system
AB  - similar to Type-1E (cas3) in M. phlei RIVM; ii) genes involved in polyamine metabolism and
AB  - transport (potAD, potF) that are absent in other mycobacteria, and iii) strain-specific
AB  - variations in the number of sigma-factor genes. Moreover, M. phlei has as many as 82 mce
AB  - (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are
AB  - present in other environmental bacteria including mycobacteria that share similar habitat.
AB  - Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete
AB  - mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and
AB  - Mycobacterium rhodesiae NBB3 while it is more distant to M. smegmatis mc2 155.
ER  -

TY  - JOUR
AU  - Das, S.
AU  - Singh, D.
AU  - Madduluri, M.
AU  - Chandrababunaidu, M.M.
AU  - Gupta, A.
AU  - Adhikary, S.P.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix  campylonemoides Strain VB511288.
JO  - Genome Announcements
PY  - 2015
SP  - e00226
EP  - e00215
VL  - 3
AB  - We report here the draft genome sequence of Tolypothrix campylonemoides VB511288, isolated
AB  - from building facades in Santiniketan, India. The members of this genus
AB  - produce several compounds of commercial importance. The draft assembly is
AB  - 10,627,177 bases in 135 scaffolds, and it contains 7,886 protein-coding genes,
AB  - 994 pseudogenes, 18 rRNA genes, and 76 tRNA genes.
ER  -

TY  - JOUR
AU  - Dassa, B.
AU  - Pietrokovski, S.
TI  - Origin and evolution of inteins and other hint domains.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 211
EP  - 231
VL  - 16
AB  - The intein protein family is part of the Hint superfamily, named after the characteristic
AB  - structure fold first identified in Hedgehog and intein protein domains.  Four characterized
AB  - Hint domain families are currently known: Hog-Hint, intein, and two types of bacterial
AB  - intein-like domains.  Together with sharing the same structural fold and common sequence
AB  - features, Hint domains have similar biochemical activities.  The domains post-translationally
AB  - process the proteins in which they are present by protein-splicing, self-cleavage or ligation
AB  - activities.  Hint domains are 130 to 160 amino acids long, sharing 4-6 conserved sequence
AB  - motifs.  The Hint protein fold is a compact, relatively flat, symmetrical structure, mainly
AB  - composed of b-strands, with its N- and C-termini close together.  Inteins usually include
AB  - additional homing-endonuclease and DNA-binding domains, not necessary for protein splicing,
AB  - which mediate the homing of the intein gene.  Species from the three domains of life, Eukarya,
AB  - Bacteria and Archaea, include Hint domains.  While inteins are apparently limited to
AB  - unicellular eukaryotes and prokaryotes, Hog-Hint domains are present in multicellular animals.
AB  - BIL domains and inteins overlap in their phylogenetic distributions, both are present in
AB  - bacteria, but in different types of proteins.  Data gathered on Hint domains since their
AB  - discovery in 1990 have identified their biochemical activity, their genetics and evolution.
AB  - Apparently, each Hint family has its own distinct biological role.  Nevertheless, many facets
AB  - of Hint domains are still unknown or debated.
ER  -

TY  - JOUR
AU  - Dassa, B.
AU  - Utturkar, S.
AU  - Hurt, R.A.
AU  - Klingeman, D.M.
AU  - Keller, M.
AU  - Xu, J.
AU  - Reddy, Y.H.
AU  - Borovok, I.
AU  - Rozman, G.I.
AU  - Lamed, R.
AU  - Zhivin, O.
AU  - Bayer, E.A.
AU  - Brown, S.D.
TI  - Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603.
JO  - Genome Announcements
PY  - 2015
SP  - e01022
EP  - e01015
VL  - 3
AB  - We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic
AB  - bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate
AB  - cellulosome system, wherein the types of cohesin-dockerin  interactions are opposite of other
AB  - known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions,
AB  - whereas enzymes are integrated via type-II interactions.
ER  -

TY  - JOUR
AU  - Datta, J.
AU  - Ghoshal, K.
AU  - Sharma, S.M.
AU  - Tajima, S.
AU  - Jacob, S.T.
TI  - Biochemical fractionation reveals association of DNA methyltransferase (Dnmt) 3b With Dnmt1 and that of Dnmt 3a with a histone H3 methyltransferase and Hdac1.
JO  - J. Cell. Biochem.
PY  - 2003
SP  - 855
EP  - 864
VL  - 88
AB  - De novo DNA methyltransferases, Dnmt3a and 3b, were purified by fractionation of S-100 extract
AB  - from mouse lymphosarcoma cells through
AB  - several chromatographic matrices followed by glycerol density gradient
AB  - centrifugation. Dnmt3a was separated from Dnmt3b and Dnmt1 in the first
AB  - column, Q-Sepharose whereas Dnmt3b co-purified with Dnmt1 after further
AB  - fractionation through Mono-S and Mono-Q columns and glycerol density
AB  - gradient centrifugation. Following purification, the majority of de novo
AB  - DNA methyltransfearse activity was associated with Dnmt3b/Dnmt1 fractions.
AB  - By contrast, the fractions containing Dnmt3a alone exhibited markedly
AB  - reduced activity, which correlated with diminished expression of this
AB  - isoform in these cells. Histone deacetylase 1(Hdac1) cofractionated with
AB  - Dnmt3a throughout purification whereas Hdac1 was separated from
AB  - Dnmt3b/Dnmt1 following chromatography on Mono-Q column. Dnmt3a purified
AB  - through glycerol gradient centrifugation was also associated with a
AB  - histone H3 methyltransferase (HMTase) activity whereas purified
AB  - Dnmt3b/Dnmt1 was devoid of any HMTase activity. The activity of this
AB  - HMTase was abolished when lysine 9 of N-terminal histone H3 peptide was
AB  - replaced by leucine whereas mutation of lysine 4 to leucine inhibited this
AB  - activity only partially. This is the first report on the identification of
AB  - a few key co-repressors associated with endogenous Dnmt3a and of a complex
AB  - containing Dnmt3b and a minor form of Dnmt1 following extensive
AB  - biochemical fractionation.
ER  -

TY  - JOUR
AU  - Datta, J.
AU  - Majumder, S.
AU  - Bai, S.M.
AU  - Ghoshal, K.
AU  - Kutay, H.
AU  - Smith, D.S.
AU  - Crabb, J.W.
AU  - Jacob, S.T.
TI  - Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells.
JO  - Cancer Res.
PY  - 2005
SP  - 10891
EP  - 10900
VL  - 65
AB  - Dnmt3a and Dnmt3b are de novo DNA methyltransferases that also act as transcriptional
AB  - repressors independent of methyltransferase activity.
AB  - To elucidate the underlying mechanism of transcriptional repression,
AB  - Dnmt3a was purified from mouse lymphosarcoma cells (P1798) by extensive
AB  - fractionation on five different chromatographic matrices followed by
AB  - glycerol density gradient centrifugation. Liquid chromatography
AB  - electrospray tandem mass spectrometry analysis of Dnmt3a-associated
AB  - polypeptides identified the methyl CpG binding protein Mbd3, histone
AB  - deacetylase 1(Hdac1), and components of Brg1 complex (Brg1, Baf155, and
AB  - Baf57) in the purified preparation. Association of Dnmt3a with Mbd3 and
AB  - Brg1 was confirmed by coinummoprecipitation and coimmunolocalization
AB  - studies. Glutathione S-transferase pulldown assay showed that the
AB  - NH2-terminal ATRX homology domain of Dnmt3a interacts with the methyl
AB  - CpG binding domain of Mbd3 and with both bromo and ATPase domains of
AB  - Brg1. Chromatin immunoprecipitation assay revealed that all three
AB  - proteins are associated with transcriptionally silent methylated
AB  - metallothionein (MT-I) promoter in the mouse lymphosarcoma cells. To
AB  - understand the functional significance of their association with the
AB  - promoter, their role on the MT-I promoter activity was analyzed by
AB  - transient transfection assay. The results showed that Mbd3 and Dnmt3a
AB  - specifically inhibited the methylated promoter, and the catalytic
AB  - activity of Dnmt3a was dispensable for the suppression. In contrast,
AB  - the wild-type but not the ATPase-inactive mutant of Brg1 suppressed
AB  - MT-I promoter irrespective of its methylation status, implicating
AB  - involvement of ATP-dependent chromatin remodeling in the process.
AB  - Coexpression of two of the three interacting proteins at a time
AB  - augmented their repressor function. This study shows physical and
AB  - functional interaction of Dnmt3a with components of nucleosome
AB  - remodeling machinery.
ER  -

TY  - JOUR
AU  - Datz, M.
AU  - Janetzki-Mittmann, C.
AU  - Franke, S.
AU  - Gunzer, F.
AU  - Schmidt, H.
AU  - Karch, H.
TI  - Analysis of the enterohemorrhagic Escherichia coli 0157 DNA region containing lambdoid phage gene p and Shiga-like toxin structural genes.
JO  - Appl. Environ. Microbiol.
PY  - 1996
SP  - 791
EP  - 797
VL  - 62
AB  - In this study, we determined the nucleotide sequence of the p gene contained within a 5-kb
AB  - EcoRI restriction fragment cloned from Shiga-like toxin II (SLT-II)-converting phage 933W of
AB  - Escherichia coli O157:H7 strain EDL933. The p gene was 702 bp long and had 95.3% sequence
AB  - similarity to the p gene of phage lambda. Multiple hybridization patterns were obtained when
AB  - genomic DNA fragments were hybridized with both p and slt-I, slt-II, or slt-IIc sequences. All
AB  - O157 isolates also possessed an analog of lambda gene p which was not linked with either slt-I
AB  - or slt-II. Restriction fragment length polymorphism comparisons of clinical O157 isolates and
AB  - derivatives undergoing genotype turnover during infection were made, and loss of large DNA
AB  - fragments that hybridized with slt-II and p sequences was observed. To further analyze the DNA
AB  - region containing the p and slt genes, we amplified fragments by using PCR with one primer
AB  - complementary to p and the other complementary to either the slt-I or the slt-II gene. PCR
AB  - analysis with enterohemorrhagic E. coli O157 and non-O157 strains yielded PCR products that
AB  - varied in size between 5.1 and 7.8 kb. These results suggest that even within O157 isolates,
AB  - the genomes of SLT-converting phages differ.  The methods described here may assist in further
AB  - investigation of SLT-encoding phages and their role in the epidemiology of infection with
AB  - enterohemorrhagic E. coli.
ER  -

TY  - JOUR
AU  - Daujotyte, D.
AU  - Liutkeviciute, Z.
AU  - Tamulaitis, G.
AU  - Klimasauskas, S.
TI  - Chemical mapping of cytosines enzymatically flipped out of the DNA helix.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - e57
EP  - e57
VL  - 36
AB  - Haloacetaldehydes can be employed for probing unpaired DNA structures involving cytosine and
AB  - adenine residues. Using an enzyme that was structurally proven to flip its target cytosine out
AB  - of the DNA helix, the HhaI DNA methyltransferase (M.HhaI), we demonstrate the suitability of
AB  - the chloroacetaldehyde modification for mapping extrahelical (flipped-out) cytosine bases in
AB  - protein-DNA complexes. The generality of this method was verified with two other DNA
AB  - cytosine-5 methyltransferases, M.AluI and M.SssI, as well as with two restriction
AB  - endonucleases, R.Ecl18kI and R.PspGI, which represent a novel class of base-flipping enzymes.
AB  - Our results thus offer a simple and convenient laboratory tool for detection and mapping of
AB  - flipped-out cytosines in protein-DNA complexes.
ER  -

TY  - JOUR
AU  - Daujotyte, D.
AU  - Serva, S.
AU  - Vilkaitis, G.
AU  - Merkiene, E.
AU  - Venclovas, C.
AU  - Klimasauskas, S.
TI  - HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.
JO  - Structure
PY  - 2004
SP  - 1047
EP  - 1055
VL  - 12
AB  - Access to a nucleotide by its rotation out of the DNA helix (base flipping) is used by
AB  - numerous DNA modification and repair enzymes.  Despite extensive studies of the paradigm HhaI
AB  - methyltransferase, initial events leading to base flipping remained elusive.  Here we
AB  - demonstrate that the replacement of the target C:G pair with the 2-aminopurine:T pair in the
AB  - DNA or shortening of the side chain of Gln237 in the protein severely perturb base flipping,
AB  - but retain specific DNA binding.  Kinetic analyses and molecular modeling suggest that a
AB  - steric interaction between the protruding side chain of Gln237 and the target cytosine in
AB  - B-DNA reduces the energy barrier for flipping by 3 kcal/mol.  Subsequent stabilization of an
AB  - open state by further 4 kcal/mol is achieved through specific hydrogen bonding of the side
AB  - chain to the orphan guanine.  Gln237 thus plays a key role in actively opening the target C:G
AB  - pair by a ?push-and-bind? mechanism.
ER  -

TY  - JOUR
AU  - Daujotyte, D.
AU  - Vilkaitis, G.
AU  - Manelyte, L.
AU  - Skalicky, J.
AU  - Szyperski, T.
AU  - Klimasauskas, S.
TI  - Solubility engineering of the HhaI methyltransferase.
JO  - Protein Eng.
PY  - 2003
SP  - 295
EP  - 301
VL  - 16
AB  - DNA methylation is involved in epigenetic control of numerous cellular processes in
AB  - eukaryotes, however, many mechanistic aspects of this
AB  - phenomenon are not yet understood. A bacterial prototype cytosine-C5
AB  - methyltransferase, M.HhaI, serves as a paradigm system for structural and
AB  - mechanistic studies of biological DNA methylation, but further analysis of
AB  - the 37 kDa protein is hampered by its insufficient solubility (0.15 mM).
AB  - To overcome this problem, three hydrophobic patches on the surface of
AB  - M.HhaI that are not involved in substrate interactions were subjected to
AB  - site-specific mutagenesis. Residues M51 or V213 were substituted by polar
AB  - amino acids of a similar size, and/or the C-terminal tetrapeptide FKPY was
AB  - replaced by a single glycine residue (Delta324G). Two out of six mutants,
AB  - delta324G and V213S/delta324G, showed improved solubility in initial
AB  - analyses and were purified to homogeneity using a newly developed
AB  - procedure. Biochemical studies of the engineered methyltransferases showed
AB  - that the deletion mutant delta324G retained identical DNA binding, base
AB  - flipping and catalytic properties as the wild-type enzyme. In contrast,
AB  - the engineered enzyme showed (i) a significantly increased solubility
AB  - (>0.35 mM), (ii) high-quality 2D-[(15)N,(1)H] TROSY NMR spectra, and (iii)
AB  - (15)N spin relaxation times evidencing the presence of a monomeric
AB  - well-folded protein in solution.
ER  -

TY  - JOUR
AU  - Daum, H.A.
AU  - White, H.W.
AU  - Seidell, C.M.
AU  - Johnson, P.A.
TI  - Cloning, restriction digestion and DNA labeling of large DNA fragments (>1 kb) in the presence of remelted SeaPlaque GTG agarose gels.
JO  - Biotechniques
PY  - 1991
SP  - 784
EP  - 790
VL  - 11
AB  - Large DNA fragments (>1 kb), separated in low melting temperature SeaPlaque GTG
AB  - agarose gels, can be enzymatically processed directly in the presence of this
AB  - agarose (in-gel).  Time saving protocols are discussed for in-gel processing of
AB  - large DNA fragments in the presence of remelted SeaPlaque GTG agarose,
AB  - including cloning into pUC18, nick translation, random priming and restriction
AB  - digestion.  These in-gel molecular biology techniques are as efficient as those
AB  - using DNA recovered from agarose.  The effects of UV irradiation, Mg2+
AB  - concentration and agarose concentration on selected in-gel protocols are also
AB  - discussed.
ER  -

TY  - JOUR
AU  - Daum, L.T.
AU  - Bumah, V.V.
AU  - Masson-Meyers, D.S.
AU  - Khubbar, M.
AU  - Rodriguez, J.D.
AU  - Fischer, G.W.
AU  - Enwemeka, C.S.
AU  - Gradus, S.
AU  - Bhattacharyya, S.
TI  - Whole-Genome Sequence for Methicillin-Resistant Staphylococcus aureus Strain ATCC BAA-1680.
JO  - Genome Announcements
PY  - 2015
SP  - e00011
EP  - e00015
VL  - 3
AB  - We report here the whole-genome sequence of the USA300 strain of methicillin-resistant
AB  - Staphylococcus aureus (MRSA), designated ATCC BAA-1680, and
AB  - commonly referred to as community-associated MRSA (CA-MRSA). This clinical MRSA
AB  - isolate is commercially available from the American Type Culture Collection
AB  - (ATCC) and is widely utilized as a control strain for research applications and
AB  - clinical diagnosis. The isolate was propagated in ATCC medium 18, tryptic soy
AB  - agar, and has been utilized as a model S. aureus strain in several studies,
AB  - including MRSA genetic analysis after irradiation with 470-nm blue light.
ER  -

TY  - JOUR
AU  - Davalieva, K.
AU  - Ziberovski, J.
AU  - Efremov, G.D.
TI  - Bme585I [5'-CCCGC(4/6)-3'], a new isoschizomer of restriction endonuclease FauI, isolated from a strain of Bacillus mesentericus.
JO  - Microbiol. Res.
PY  - 2004
SP  - 129
EP  - 133
VL  - 159
AB  - Bme585I is a new member of the restriction endonuclease type IIS family. It was partially
AB  - purified from the heterothrophic, mesophilic
AB  - bacterial strain Bacillus mesentericus 585 by ammonium sulphate
AB  - precipitation and phosphocellulose column chromatography. Bme585I is a
AB  - monomeric protein with a molecular mass of 62 kD. The enzyme is active
AB  - over a broad pH range from 7.0 to 8.8, has a temperature optimum of
AB  - 37 degrees C and tolerance of NaCl. in reaction buffer from 0 to 400 mM.
AB  - Bme585I recognizes the asymmetric sequence 5'-CCCGC(4/6)-3' and is
AB  - therefore an isoschizomer of restriction endonuclease FauI.
ER  -

TY  - JOUR
AU  - Davenport, K.W. et al.
TI  - Whole-genome sequences of nine francisella isolates.
JO  - Genome Announcements
PY  - 2014
SP  - e00941
EP  - e00914
VL  - 2
AB  - Primarily a zoonotic disease, Francisella tularensis is a fastidious intracellular pathogen
AB  - and is listed as a CDC category A pathogen with notably
AB  - high pathogenicity. Here we present the scaffolded genome assemblies of nine
AB  - Francisella strains: eight F. tularensis and one F. philomiragia.
ER  -

TY  - JOUR
AU  - Davenport, K.W.
AU  - Daligault, H.E.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Redden, C.L.
AU  - Rosenzweig, C.N.
AU  - Scholz, M.B.
AU  - Teshima, H.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of Staphylococcus epidermidis AmMS 205.
JO  - Genome Announcements
PY  - 2014
SP  - e01059
EP  - e01014
VL  - 2
AB  - Staphylococcus epidermidis causes a large number of catheter-related sepsis infections
AB  - annually in the United States. We present the 2.54-Mbp complete genome
AB  - assembly of reference strain S. epidermidis AmMS 205, including a single 37.7-kbp
AB  - plasmid. The annotated assembly is available in GenBank under accession numbers
AB  - CP009046 and CP009047.
ER  -

TY  - JOUR
AU  - Davenport, K.W.
AU  - Daligault, H.E.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Li, P.E.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Scholz, M.B.
AU  - Teshima, H.
AU  - Johnson, S.L.
TI  - Whole-Genome Sequence of Listeria monocytogenes Type Strain 53 XXIII.
JO  - Genome Announcements
PY  - 2014
SP  - e00970
EP  - e00914
VL  - 2
AB  - Listeria monocytogenes causes the food-borne illness listeriosis that primarily infects
AB  - 'vulnerable' groups (e.g., elderly adults, pregnant women, very young
AB  - children, and the immunocompromised). We sequenced the genome of L. monocytogenes
AB  - XXIII (ATCC 15313) and assembled it into a single scaffold (three contigs) and
AB  - deposited the annotated assembly into GenBank as accession no. JOOX00000000.
ER  -

TY  - JOUR
AU  - Davenport, K.W.
AU  - Daligault, H.E.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Lo, C.C.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Scholz, M.B.
AU  - Teshima, H.
AU  - Johnson, S.L.
TI  - Complete Genome Sequence of Type Strain Pasteurella multocida subsp. multocida ATCC 43137.
JO  - Genome Announcements
PY  - 2014
SP  - e01070
EP  - e01014
VL  - 2
AB  - Soft-tissue infection by Pasteurella multocida in humans is usually associated with a dog- or
AB  - cat-related injury, and these infections can become aggressive. We
AB  - sequenced the type strain P. multocida subsp. multocida ATCC 43137 into a single
AB  - closed chromosome consisting of 2,271,840 bp (40.4% G+C content), which is
AB  - currently available in the NCBI GenBank under the accession number CP008918.
ER  -

TY  - JOUR
AU  - Davenport, K.W.
AU  - Daligault, H.E.
AU  - Minogue, T.D.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Scholz, M.B.
AU  - Teshima, H.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Delftia acidovorans Type Strain 2167.
JO  - Genome Announcements
PY  - 2014
SP  - e00917
EP  - e00914
VL  - 2
AB  - The Delftia acidovorans 2167 (ATCC 15668, Delftia type strain) genome was sequenced into a
AB  - 6-contig scaffolded assembly of 6.78-Mb. This environmental
AB  - microbe, previously named to both the Comamonas and Pseudomonas genera, is an
AB  - opportunistic pathogen and often the subject of phylogenetic placement debates.
ER  -

TY  - JOUR
AU  - Davenport, K.W.
AU  - Daligault, H.E.
AU  - Minogue, T.D.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Li, P.E.
AU  - Rosenzweig, C.N.
AU  - Scholz, M.B.
AU  - Johnson, S.L.
TI  - Complete Genome Sequence of Stenotrophomonas maltophilia Type Strain 810-2 (ATCC  13637).
JO  - Genome Announcements
PY  - 2014
SP  - e00974
EP  - e00914
VL  - 2
AB  - An emerging nosocomial pathogen, Stenotrophomonas maltophila has a high mortality rate in
AB  - those it infects. Here, we present the complete genome sequence of
AB  - Stenotrophomonas maltophilia 810-2 (ATCC 13637), the type strain of the species.
AB  - The 5-Mb (66.1% G+C content) genome has been deposited in NCBI under accession
AB  - number CP008838.
ER  -

TY  - JOUR
AU  - Davenport, K.W.
AU  - Daligault, H.E.
AU  - Minogue, T.D.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Jaissle, J.G.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Li, P.E.
AU  - Palacios, G.F.
AU  - Scholz, M.B.
AU  - Teshima, H.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Acinetobacter baumannii ATCC 19606.
JO  - Genome Announcements
PY  - 2014
SP  - e00832
EP  - e00814
VL  - 2
AB  - Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome
AB  - assemblies for this organism are needed to aid in detection,
AB  - diagnostic, and treatment technologies. Here we present the improved draft
AB  - assembly of A. baumannii ATCC 19606 in two scaffolds. This 3,953,621-bp genome
AB  - contains 3,750 coding regions and has a 39.1% G+C content.
ER  -

TY  - JOUR
AU  - David, A.
AU  - Bleimling, N.
AU  - Beuck, C.
AU  - Lehn, J.M.
AU  - Weinhold, E.
AU  - Teulade-Fichou, M.P.
TI  - DNA mismatch-specific base flipping by a bisacridine macrocycle.
JO  - Chembiochem
PY  - 2003
SP  - 1326
EP  - 1331
VL  - 4
AB  - Most, if not all, enzymes that chemically modify nucleobases in DNA flip their target base
AB  - from the inside of the double helix into an extrahelical
AB  - position. This energetically unfavorable conformation is partly stabilized
AB  - by specific binding of the apparent abasic site being formed. Thus, DNA
AB  - base-flipping enzymes, like DNA methyltransferases and DNA glycosylases,
AB  - generally bind very strongly to DNA containing abasic sites or abasic-site
AB  - analogues. The macrocyclic bisacridine BisA has previously been shown to
AB  - bind abasic sites. Herein we demonstrate that it is able to specifically
AB  - recognize DNA base mismatches and most likely induces base flipping.
AB  - Specific binding of BisA to DNA mismatches was studied by thermal
AB  - denaturation experiments by using short duplex oligodeoxynucleotides
AB  - containing central TT, TC, or TG mismatches or a TA match. In the presence
AB  - of the macrocycle a strong increase in the melting temperature of up to
AB  - 7.1 degrees C was observed for the mismatch-containing duplexes, whereas
AB  - the melting temperature of the fully matched duplex was unaffected.
AB  - Furthermore, BisA binding induced an enhanced reactivity of the mispaired
AB  - thymine residue in the DNA toward potassium permanganate oxidation. A
AB  - comparable reactivity has previously been observed for a TT target base
AB  - mismatch in the presence of DNA methyltransferase M.TaqI. This similarity
AB  - to a known base-flipping enzyme suggests that insertion of BisA into the
AB  - DNA helix displaces the mispaired thymine residue into an extrahelical
AB  - position, where it should be more prone to chemical oxidation. Thus, DNA
AB  - base flipping does not appear to be limited to DNA-modifying enzymes but
AB  - it is likely to also be induced by a small synthetic molecule binding to a
AB  - thermodynamically weakened site in DNA.
ER  -

TY  - JOUR
AU  - Davidson, F.W.
AU  - Whitney, H.G.
AU  - Tahlan, K.
TI  - Genome Sequences of Klebsiella variicola Isolates from Dairy Animals with Bovine  Mastitis from Newfoundland, Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e00938
EP  - e00915
VL  - 3
AB  - Klebsiella variicola was recently reported as an emerging and/or previously misidentified
AB  - species associated with opportunistic infections in humans. Here, we report the draft genome
AB  - sequences of K. variicola isolates from two animals with clinical mastitis from a dairy farm
AB  - in Newfoundland, Canada.
ER  -

TY  - JOUR
AU  - Davidson, R.M.
AU  - Reynolds, P.R.
AU  - Farias-Hesson, E.
AU  - Duarte, R.S.
AU  - Jackson, M.
AU  - Strong, M.
TI  - Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.
JO  - Genome Announcements
PY  - 2013
SP  - e00617
EP  - e00613
VL  - 1
AB  - Multiple isolates of Mycobacterium abscessus subsp. bolletii, collectively called BRA100, were
AB  - associated with outbreaks of postsurgical skin infections across
AB  - various regions of Brazil from 2003 to 2009. We announce the draft genome
AB  - sequence of a newly sequenced BRA100 strain, M. abscessus subsp. bolletii
AB  - CRM-0020, isolated from a patient in Rio de Janeiro, Brazil.
ER  -

TY  - JOUR
AU  - Davidson, Y.Y.
AU  - Soper, S.A.
AU  - Margolis, S.
AU  - Sander, L.C.
TI  - Immobilization of the restriction enzymes HaeIII and HindIII on porous silica particles via a glutaraldehyde linkage for the micro-digestion of dsDNA with analysis by capillary electrophoresis.
JO  - J. Sep. Sci.
PY  - 2001
SP  - 10
EP  - 16
VL  - 24
AB  - Solid-phase DNA restriction digest reactors have been developed consisting of silica particles
AB  - modified with a covalently tethered
AB  - restriction enzyme. This solid-phase restriction reactor enables
AB  - digestion and separation of minute quantities of DNA with minimal
AB  - reagent consumption. In this study, the restriction enzymes, HaeIII,
AB  - PstI, and HindIII, were successfully immobilized via glutaraldehyde
AB  - linkages to porous silica micro-particles. Studies were carried out to
AB  - examine the impact of immobilization on enzymatic activity. Digestions
AB  - of phiX174-RF DNA phage and SV40 viral DNA were performed with the
AB  - immobilized enzymes by placing the silica particles in solution with
AB  - the target DNA with digestion times of 120 min and 240 min
AB  - respectively. The digests were analyzed off-line using capillary
AB  - electrophoresis (CE) with laser-induced fluorescence (LIF) detection.
AB  - Timed studies were performed to establish optimal conditions for
AB  - complete digestion. Digests utilizing immobilized HaeIII and HindIII
AB  - were similar in composition to homogeneous, free solution digests. PstI
AB  - showed no evidence of activity upon immobilization. The immobilized
AB  - restriction enzymes could also be used for multiple rounds of
AB  - digestion; however, longer incubation times were required for
AB  - successive runs probably due to partial denaturation of the restriction
AB  - enzyme. Digests also were prepared and isolated by use of a simple
AB  - micro-spin column consisting of a layer of immobilized enzyme-coated
AB  - silica on a molecular weight cut-off filter. Using this approach,
AB  - digestion times were comparable to solution digests as previously
AB  - mentioned; however, enzyme reuse and reaction product isolation was
AB  - facilitated.
ER  -

TY  - JOUR
AU  - Davie, J.J.
AU  - Earl, J.
AU  - de Vries, S.P.
AU  - Ahmed, A.
AU  - Hu, F.Z.
AU  - Bootsma, H.J.
AU  - Stol, K.
AU  - Hermans, P.W.
AU  - Wadowsky, R.M.
AU  - Ehrlich, G.D.
AU  - Hays, J.P.
AU  - Campagnari, A.A.
TI  - Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates.
JO  - BMC Genomics
PY  - 2011
SP  - 70
EP  - 70
VL  - 12
AB  - BACKGROUND: M. catarrhalis is a gram-negative, gamma-proteobacterium and
AB  - an opportunistic human pathogen associated with otitis media (OM) and
AB  - exacerbations of chronic obstructive pulmonary disease (COPD). With direct
AB  - and indirect costs for treating these conditions annually exceeding $33
AB  - billion in the United States alone, and nearly ubiquitous resistance to
AB  - beta-lactam antibiotics among M. catarrhalis clinical isolates, a greater
AB  - understanding of this pathogen's genome and its variability among isolates
AB  - is needed. RESULTS: The genomic sequences of ten geographically and
AB  - phenotypically diverse clinical isolates of M. catarrhalis were determined
AB  - and analyzed together with two publicly available genomes. These twelve
AB  - genomes were subjected to detailed comparative and predictive analyses
AB  - aimed at characterizing the supragenome and understanding the metabolic
AB  - and pathogenic potential of this species. A total of 2383 gene clusters
AB  - were identified, of which 1755 are core with the remaining 628 clusters
AB  - unevenly distributed among the twelve isolates. These findings are
AB  - consistent with the distributed genome hypothesis (DGH), which posits that
AB  - the species genome possesses a far greater number of genes than any single
AB  - isolate. Multiple and pair-wise whole genome alignments highlight limited
AB  - chromosomal re-arrangement. CONCLUSIONS: M. catarrhalis gene content and
AB  - chromosomal organization data, although supportive of the DGH, show modest
AB  - overall genic diversity. These findings are in stark contrast with the
AB  - reported heterogeneity of the species as a whole, as wells as to other
AB  - bacterial pathogens mediating OM and COPD, providing important insight
AB  - into M. catarrhalis pathogenesis that will aid in the development of novel
AB  - therapeutic regimens.
ER  -

TY  - JOUR
AU  - Davies, G.P.
AU  - Kemp, P.
AU  - Molineux, I.J.
AU  - Murray, N.E.
TI  - The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 787
EP  - 796
VL  - 292
AB  - EcoKI, a type I restriction enzyme, specifies DNA methyltransferase, ATPase, endonuclease and
AB  - DNA translocation activities. One subunit (HsdR) of the oligomeric enzyme contributes to those
AB  - activities essential for restriction. These activities involve ATP-dependent DNA translocation
AB  - and DNA cleavage. Mutations that change amino acids within recognisable motifs in HsdR impair
AB  - restriction. We have used an in vivo assay to monitor the effect of these mutations on DNA
AB  - translocation. The assay follows the EcoKI-dependent entry of phage T7 DNA from the phage
AB  - particle into the host cell. Earlier experiments have shown that mutations within the seven
AB  - motifs characteristic of the DEAD-box family of proteins that comprise known or putative
AB  - helicases severely impair the ATPase activity of purified enzymes. We find that the mutations
AB  - abolish DNA translocation in vivo. This provides evidence that these motifs are relevant to
AB  - the coupling of ATP hydrolysis to DNA translocation. Mutations that identify an endonuclease
AB  - motif similar to that found at the active site of type II restriction enzymes and other
AB  - nucleases have been shown to abolish DNA nicking activity.  When conservative changes are made
AB  - at these residues, the enzymes lack nuclease activity but retain the ability to hydrolyse ATP
AB  - and to translocate DNA at wild-type levels. It has been speculated that nicking may be
AB  - necessary to resolve the topological problems associated with DNA translocation by type I
AB  - restriction and modification systems. Our experiments show that loss of the nicking activity
AB  - associated with the endonuclease motif of EcoKI has no effect on ATPase activity in vitro or
AB  - DNA translocation of the T7 genome in vivo.
ER  -

TY  - JOUR
AU  - Davies, G.P.
AU  - Martin, I.
AU  - Sturrock, S.S.
AU  - Cronshaw, A.
AU  - Murray, N.E.
AU  - Dryden, D.T.F.
TI  - On the structure and operation of type I DNA restriction enzymes.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 565
EP  - 579
VL  - 290
AB  - Type I DNA restriction enzymes are large, molecular machines possessing DNA methyltransferase,
AB  - ATPase, DNA translocase and endonuclease activities. The ATPase, DNA translocase and
AB  - endonuclease activities are specified by the restriction (R) subunit of the enzyme. We
AB  - demonstrate that the R subunit of the Eco KI type I restriction enzyme comprises several
AB  - different functional domains. An N-terminal domain contains an amino acid motif identical with
AB  - that forming the catalytic site in simple restriction endonucleases, and changes within this
AB  - motif lead to a loss of nuclease activity and abolish the restriction reaction. The central
AB  - part of the R subunit contains amino acid sequences characteristic of DNA helicases. We
AB  - demonstrate, using limited proteolysis of this subunit, that the helicase motifs are contained
AB  - in two domains. Secondary structure prediction of these domains suggests a structure that is
AB  - the same as the catalytic domains of DNA helicases of known structure. The C-terminal region
AB  - of the R subunit can be removed by elastase treatment leaving a large fragment, stable in the
AB  - presence of ATP, which can no longer bind to the other subunits of Eco KI suggesting that this
AB  - domain is required for protein assembly. Considering these results and previous models of the
AB  - methyltransferase part of these enzymes, a structural and operational model of a type I DNA
AB  - restriction enzyme is presented.
ER  -

TY  - JOUR
AU  - Davies, G.P.
AU  - Powell, L.M.
AU  - Webb, J.L.
AU  - Cooper, L.P.
AU  - Murray, N.E.
TI  - EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 4828
EP  - 4836
VL  - 26
AB  - For type I restriction systems, recently determined nucleotide sequences predict conserved
AB  - amino acids in the subunit that is essential for restriction but not modification (HsdR). The
AB  - conserved sequences emphasize motifs characteristic of the DEAD-box family of proteins which
AB  - comprises putative helicases, and they identify a new candidate for motif IV. We provide
AB  - evidence based on an analysis of EcoKI which supports both the relevance of DEAD-box motifs to
AB  - the mechanism of restriction and the new definition of motif IV. Amino acid substitutions
AB  - within the newly identified motif IV and those in six other previously identified DEAD-box
AB  - motifs, but not in the original motif IV, confer restriction-deficient phenotypes. We have
AB  - examined the relevance of the DEAD-box motifs to the restriction pathway by determining the
AB  - steps permitted in vitro by the defective enzymes resulting from amino acid substitutions in
AB  - each of the seven motifs. EcoKI purified from the seven restriction-deficient mutants binds to
AB  - an unmethylated target sequence and, in the presence of AdoMet, responds to ATP by undergoing
AB  - the conformational change essential for the pathway of events leading to DNA cleavage. The
AB  - seven enzymes have little or no ATPase activity and no endonuclease activity, but they retain
AB  - the ability to nick unmodified DNA, though at reduced rates. Nicking of a DNA strand could
AB  - therefore be an essential early step in the restriction pathway, facilitating the
AB  - ATP-dependent translocation of DNA, particularly if this involves DNA helicase activity.
ER  -

TY  - JOUR
AU  - Davies, J.K.
TI  - DNA restriction and modification systems in Neisseria gonorrhoeae.
JO  - Clin. Microbiol. Rev.
PY  - 1989
SP  - S78
EP  - S82
VL  - 2
AB  - A review.  Introduces new nomenclature.
ER  -

TY  - JOUR
AU  - Davies, J.K.
AU  - Normark, S.
TI  - A relationship between plasmid structure, structural lability, and sensitivity to site-specific endonucleases in Neisseria gonorrhoeae.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 251
EP  - 260
VL  - 177
AB  - Nearly all gonococcal strains carry a small "phenotypically cryptic" plasmid of
AB  - approximately 4,200 basepairs.  A detailed physical map of this plasmid has
AB  - been constructed, revealing the presence of numerous putative inverted repeats.
AB  - These studies also revealed the presence on the plasmid of rercognition
AB  - sequences for several site-specific endonucleases (particularly HpaII, MspI and
AB  - AluI) that are particularly resistant to cleavage, and confirmed previous
AB  - reports of structural lability.  Both the sites that are resistant to cleavage,
AB  - and the observed structural variation are association with the inverted
AB  - repetitive sequences.
ER  -

TY  - JOUR
AU  - Davies, M.R.
AU  - Shera, J.
AU  - Van Domselaar, G.H.
AU  - Sriprakash, K.S.
AU  - McMillan, D.J.
TI  - A Novel Integrative Conjugative Element Mediates Genetic Transfer from Group G Streptococcus to Other -Hemolytic Streptococci.
JO  - J. Bacteriol.
PY  - 2009
SP  - 2257
EP  - 2265
VL  - 191
AB  - Lateral gene transfer is a significant contributor to the ongoing
AB  - evolution of many bacterial pathogens, including beta-hemolytic
AB  - streptococci. Here we provide the first characterization of a novel
AB  - integrative conjugative element (ICE), ICESde3396, from Streptococcus
AB  - dysgalactiae subsp. equisimilis (group G streptococcus [GGS]), a bacterium
AB  - commonly found in the throat and skin of humans. ICESde3396 is 64 kb in
AB  - size and encodes 66 putative open reading frames. ICESde3396 shares 38
AB  - open reading frames with a putative ICE from Streptococcus agalactiae
AB  - (group B streptococcus [GBS]), ICESa2603. In addition to genes involves in
AB  - conjugal processes, ICESde3396 also carries genes predicted to be involved
AB  - in virulence and resistance to various metals. A major feature of
AB  - ICESde3396 differentiating it from ICESa2603 is the presence of an 18-kb
AB  - internal recombinogenic region containing four unique gene clusters, which
AB  - appear to have been acquired from streptococcal and nonstreptococcal
AB  - bacterial species. The four clusters include two cadmium resistance
AB  - operons, an arsenic resistance operon, and genes with orthologues in a
AB  - group A streptococcus (GAS) prophage. Streptococci that naturally harbor
AB  - ICESde3396 have increased resistance to cadmium and arsenate, indicating
AB  - the functionality of genes present in the 18-kb recombinogenic region. By
AB  - marking ICESde3396 with a kanamycin resistance gene, we demonstrate that
AB  - the ICE is transferable to other GGS isolates as well as GBS and GAS. To
AB  - investigate the presence of the ICE in clinical streptococcal isolates, we
AB  - screened 69 isolates (30 GGS, 19 GBS, and 20 GAS isolates) for the
AB  - presence of three separate regions of ICESde3396. Eleven isolates
AB  - possessed all three regions, suggesting they harbored ICESde3396-like
AB  - elements. Another four isolates possessed ICESa2603-like elements. We
AB  - propose that ICESde3396 is a mobile genetic element that is capable of
AB  - acquiring DNA from multiple bacterial sources and is a vehicle for
AB  - dissemination of this DNA through the wider beta-hemolytic streptococcal
AB  - population.
ER  -

TY  - JOUR
AU  - Davis, B.M.
AU  - Chao, M.C.
AU  - Waldor, M.K.
TI  - Entering the era of bacterial epigenomics with single molecule real time DNA sequencing.
JO  - Curr. Opin. Microbiol.
PY  - 2013
SP  - 192
EP  - 198
VL  - 16
AB  - DNA modifications, such as methylation guide numerous critical biological processes, yet
AB  - epigenetic information has not routinely been collected as part of
AB  - DNA sequence analyses. Recently, the development of single molecule real time
AB  - (SMRT) DNA sequencing has enabled detection of modified nucleotides (e.g. 6mA,
AB  - 4mC, 5mC) in parallel with acquisition of primary sequence data, based on
AB  - analysis of the kinetics of DNA synthesis reactions. In bacteria, genome-wide
AB  - mapping of methylated and unmethylated loci is now feasible. This technological
AB  - advance sets the stage for comprehensive, mechanistic assessment of the effects
AB  - of bacterial DNA methyltransferases (MTases)-which are ubiquitous, extremely
AB  - diverse, and largely uncharacterized-on gene expression, chromosome structure,
AB  - chromosome replication, and other fundamental biological processes. SMRT
AB  - sequencing also enables detection of damaged DNA and has the potential to uncover
AB  - novel DNA modifications.
ER  -

TY  - JOUR
AU  - Davis, E.O.
AU  - Jenner, P.J.
TI  - Protein splicing -- the lengths some proteins will go to.
JO  - Antonie Van Leeuwenhoek
PY  - 1995
SP  - 131
EP  - 137
VL  - 67
AB  - We review the recently discovered phenomenon of protein splicing which
AB  - is the excision of an inernal protein sequence at the protein level rather than at the RNA
AB  - level. The means by which examples of protein splicing have been idenified are described,
AB  - and the similarities of the internally spliced protein products (or inteins) are discussed.
AB  - Comparisons are made between inteins and group I RNA introns.  We describe the
AB  - evidence supporting excision of inteins by a post-translational autocatalytic reaction of a
AB  - full
AB  - length polypeptide precursor, rather than by RNA splicing.  An examination is made of
AB  - some of the proposed mechanism schemes and the evidence supporting them is presented.
ER  -

TY  - JOUR
AU  - Davis, E.O.
AU  - Jenner, P.J.
AU  - Brooks, P.C.
AU  - Colston, M.J.
AU  - Sedgwick, S.G.
TI  - Protein splicing in the maturation of M. tuberculosis RecA protein: a mechanism for tolerating a novel class of intervening sequence.
JO  - Cell
PY  - 1992
SP  - 201
EP  - 210
VL  - 71
AB  - The M. tuberculosis recA locus comprises an 85 kd open reading frame but produced 38 kd RecA
AB  - and 47 kd products in E. coli. No RNA processing was detected; rather, an 85 kd precursor
AB  - protein was spliced, releasing a 47 kd spacer protein, and joining its terminal fragments to
AB  - form mature RecA protein. "Spacer" protein was also produced in M. tuberculosis and from a
AB  - hybrid spacer-LacZa fusion molecule. Mutagenesis at codon wobble positions at one splice
AB  - junction showed that protein rather than nucleotide sequence determined splicing activity.
AB  - Other mutants defined additional regions needed for splicing and allowed processing to be
AB  - followed. Splicing was essential for RecA activity in E. coli. The possibility that splicing
AB  - is a manifestation of a novel class of genetic element is discussed.
ER  -

TY  - JOUR
AU  - Davis, E.O.
AU  - Sedgwick, S.G.
AU  - Colston, M.J.
TI  - Novel structure of the recA locus of Mycobacterium tuberculosis implies processing of the gene product.
JO  - J. Bacteriol.
PY  - 1991
SP  - 5653
EP  - 5662
VL  - 173
AB  - A fragment of Mycobacterium tuberculosis DNA containing recA-like sequences was identified by
AB  - hybridization with the Escherichia coli recA gene and cloned. Although no expression was
AB  - detected from its own promoter in E. coli, expression from a vector promoter partially
AB  - complemented E. coli recA mutants for recombination, DNA repair, and mutagenesis, but not for
AB  - induction of phage lambda. This clone produced a protein which cross-reacts with antisera
AB  - raised against the E. coli RecA protein and was approximately the same size. However, the
AB  - nucleotide sequence of the cloned fragment revealed the presence of an open reading frame for
AB  - a protein about twice the size of other RecA proteins and the cloned product detected by
AB  - Western blotting (immunoblotting). The predicted M. tuberculosis RecA protein sequence was
AB  - homologous with RecA sequences from other bacteria, but this homology was not dispersed;
AB  - rather it was localized to the first 254 and the last 96 amino acids, with the intervening 440
AB  - amino acids being unrelated. Furthermore, the junctions of homology were in register with the
AB  - uninterrupted sequence of the E. coli RecA protein. Identical restriction fragments were found
AB  - in the genomic DNAs of M. tuberculosis H37Rv and H37Ra and of M. bovis BCG. It is concluded
AB  - that the ancestral recA gene of these species diversified via an insertional mutation of at
AB  - least 1,320 bp of DNA. Possible processing mechanisms for synthesizing a normal-size RecA
AB  - protein from this elongated sequence are discussed.
ER  -

TY  - JOUR
AU  - Davis, E.O.
AU  - Thangaraj, H.S.
AU  - Brooks, P.C.
AU  - Colston, M.J.
TI  - Evidence of selection for protein introns in the recAs of pathogenic mycobacteria.
JO  - EMBO J.
PY  - 1994
SP  - 699
EP  - 703
VL  - 13
AB  - Protein introns are recently discovered genetic elements whose intervening sequences are
AB  - removed from a precursor protein by an unusual protein splicing intron, and the religation of
AB  - the amino- and carboxy-terminal fragments of the precursor. The recA gene of Mycobacterium
AB  - tuberculosis contains one such element and we now show that the other major mycobacterial
AB  - pathogen, Mycobacterium leprae, also possesses a protein intron in its recA, although other
AB  - mycobacterial recA genes do not. However, these two protein introns are different in size,
AB  - sequence and location of insertion of their coding sequences into the recAs of M. tuberculosis
AB  - and M. leprae, indicating that acquisition of the protein introns has occurred independently
AB  - in the two species, and thus suggesting that there has been selection for splicing in the
AB  - maturation of RecA in the pathogenic mycobacteria. The M. leprae protein intron provides an
AB  - example of conditional protein splicing, splicing occurring in M. leprae itself but not when
AB  - expressed in Escherichia coli, unlike most previously described protein introns. These
AB  - observations suggest that protein introns may perform a function for their host, rather than
AB  - being just selfish elements.
ER  -

TY  - JOUR
AU  - Davis, J.
AU  - Hill, R.T.
TI  - Draft Genome Sequence of Hawaiian Sea Slug Symbiont Vibrio sp. Strain ER1A.
JO  - Genome Announcements
PY  - 2014
SP  - e00820
EP  - e00814
VL  - 2
AB  - Bacteria belonging to the genus Vibrio are prevalent in the marine environment and are known
AB  - for forming symbiotic relationships with hosts. Vibrio sp. strain
AB  - ER1A is a dominant symbiont of the Hawaiian sea slug, Elysia rufescens. Here we
AB  - report the draft genome sequence of Vibrio sp. ER1A.
ER  -

TY  - JOUR
AU  - Davis, J.R. et al.
TI  - Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete.
JO  - Genome Announcements
PY  - 2013
SP  - e00416
EP  - e00413
VL  - 1
AB  - We announce the availability of the genome sequence of Streptomyces viridosporus  strain T7A
AB  - ATCC 39115, a plant biomass-degrading actinomycete. This bacterium is
AB  - of special interest because of its capacity to degrade lignin, an underutilized
AB  - component of plants in the context of bioenergy. It has a full complement of
AB  - genes for plant biomass catabolism.
ER  -

TY  - JOUR
AU  - Davis, J.R.
AU  - Goodwin, L.A.
AU  - Woyke, T.
AU  - Teshima, H.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, S.
AU  - Han, J.
AU  - Pitluck, S.
AU  - Nolan, M.
AU  - Mikhailova, N.
AU  - Land, M.L.
AU  - Sello, J.K.
TI  - Genome Sequence of Amycolatopsis sp. Strain ATCC 39116, a Plant Biomass-Degrading Actinomycete.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2396
EP  - 2397
VL  - 194
AB  - We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis
AB  - sp. strain 39116, one of few bacterial species that are known to
AB  - consume the lignin component of plant biomass. This genome sequence will further
AB  - ongoing efforts to use microorganisms for the conversion of plant biomass into
AB  - fuels and high-value chemicals.
ER  -

TY  - JOUR
AU  - Davis, M.
AU  - Guorong, X.
AU  - Glickman, G.
AU  - Reich, N.
TI  - Eludication of sites flanking CpG dinucleotides important in the regulation of mammalian cytosine DNA methyltransferase.
JO  - FASEB J.
PY  - 1993
SP  - A1291
EP  - A1291
VL  - 7
AB  - It is known that methylation of cytosines in eukaryotes occurs only at cytosines within CpG
AB  - dinucleotides. However, not every CpG site in eukaryotic DNA is methylated, giving rise to
AB  - various patterns of methylation for different types of cells and stages of development. How
AB  - this variability is established is not well understood, but methylation of genes at particular
AB  - sites has been shown to inhibit their expression. To examine the possibility that sequences
AB  - flanking CpG dinucleotides act differentially in the regulation of mammalian cytosine
AB  - methyltransferase, a number of dissimilar CpG flanking sequences on various substrates have
AB  - been examined. Through use of gel-shift and methylation data carried out on plasmid pBR322 and
AB  - SV40 viral DNA, sites of facilitated methyltransferase-DNA interaction have been determined.
AB  - Footprinting assays currently being employed will reveal sites critical to recognition and
AB  - catalysis. Characterization of the protein-DNA interactions involved with the mammalian
AB  - methyltransferase may lead to new insights into its gene regulatory mechanism.
ER  -

TY  - JOUR
AU  - Davis, R.
AU  - Hossain, M.J.
AU  - Liles, M.R.
AU  - Panizzi, P.
TI  - Complete Genome Sequence of Staphylococcus aureus Tager 104, a Sequence Type 49 Ancestor.
JO  - Genome Announcements
PY  - 2013
SP  - e00706
EP  - e00713
VL  - 1
AB  - We report here the complete genome sequence of Staphylococcus aureus Tager 104, originally
AB  - isolated from a cutaneous abscess in 1947 by Morris Tager. Sequence
AB  - typing of the strain revealed its membership in sequence type 49 (ST49), a
AB  - previously unknown multilocus sequence type (MLST) in clinical samples.
ER  -

TY  - JOUR
AU  - Davis, R.
AU  - Van der Lelie, D.
AU  - Mercenier, A.
AU  - Daly, C.
AU  - Fitzgerald, G.F.
TI  - ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503: Cloning and Characterization of two ScrFI methylase genes.
JO  - Appl. Environ. Microbiol.
PY  - 1993
SP  - 777
EP  - 785
VL  - 59
AB  - Two genes from the total genomic DNA of dairy starter culture Lactococcus lactis subsp.
AB  - cremoris UC503, encoding ScrFI modification enzymes, have been cloned and expressed in
AB  - Escherichia coli. No homology between the two methyase genes was detected, and inverse
AB  - polymerase chain reaction of flanking chromosomal DNA indicated that both were linked on the
AB  - Lactococcus genome. Neither clone encoded the cognate endonuclease. The DNA sequence of one of
AB  - the methylase genes (encoded by pCI931M) was determined and consisted of an open reading frame
AB  - 1,170 bp long, which could encode a protein of 389 amino acids (Mr,44.5). The amino acid
AB  - sequence contained the highly characteristic motifs of an m5C methylase. Extensive regions of
AB  - homology were observed with the methylases of NlaX, EcoRII, and Dcm.
ER  -

TY  - JOUR
AU  - Davis, R.E.
AU  - Shao, J.
AU  - Dally, E.L.
AU  - Zhao, Y.
AU  - Gasparich, G.E.
AU  - Gaynor, B.J.
AU  - Athey, J.C.
AU  - Harrison, N.A.
AU  - Donofrio, N.
TI  - Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in Zea mays L.
JO  - Genome Announcements
PY  - 2015
SP  - e01216
EP  - e01215
VL  - 3
AB  - Spiroplasma kunkelii causes corn stunt disease of Zea mays L. in the Americas. Here, we report
AB  - the nucleotide sequence of the 1,463,926-bp circular chromosome and four plasmids of strain
AB  - CR2-3x. This information will facilitate studies of Spiroplasma pathogenicity and evolutionary
AB  - adaptations to transkingdom parasitism in plants and insect vectors.
ER  -

TY  - JOUR
AU  - Davis, R.E.
AU  - Shao, J.
AU  - Zhao, Y.
AU  - Gasparich, G.E.
AU  - Gaynor, B.J.
AU  - Donofrio, N.
TI  - Complete Genome Sequence of Spiroplasma citri Strain R8-A2T, Causal Agent of Stubborn Disease in Citrus Species.
JO  - Genome Announcements
PY  - 2017
SP  - e00206
EP  - e00217
VL  - 5
AB  - Spiroplasma citri causes stubborn disease in Citrus spp. and diseases in other plants. Here,
AB  - we report the nucleotide sequence of the 1,599,709-bp circular
AB  - chromosome and two plasmids of S. citri strain R8-A2T This information will
AB  - facilitate analyses to understand spiroplasmal pathogenicity and evolutionary
AB  - adaptations to lifestyles in plants and arthropod hosts.
ER  -

TY  - JOUR
AU  - Davis, R.E.
AU  - Shao, J.
AU  - Zhao, Y.
AU  - Gasparich, G.E.
AU  - Gaynor, B.J.
AU  - Donofrio, N.
TI  - Complete Genome Sequence of Spiroplasma turonicum Strain Tab4cT, a Parasite of a  Horse Fly, Haematopota sp. (Diptera: Tabanidae).
JO  - Genome Announcements
PY  - 2015
SP  - e01367
EP  - e01315
VL  - 3
AB  - Spiroplasma turonicum was isolated from a Haematopota sp. fly in France. We report the
AB  - nucleotide sequence of the circular chromosome of strain Tab4cT. The
AB  - genome information will facilitate evolutionary studies of spiroplasmas,
AB  - including symbionts of insects and ticks and pathogens of plants, insects,
AB  - crustaceans, and humans.
ER  -

TY  - JOUR
AU  - Davis, R.W. IV
AU  - Brannen, A.D.
AU  - Hossain, M.J.
AU  - Monsma, S.
AU  - Bock, P.E.
AU  - Nahrendorf, M.
AU  - Mead, D.
AU  - Lodes, M.
AU  - Liles, M.R.
AU  - Panizzi, P.
TI  - Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains.
JO  - BMC Genomics
PY  - 2016
SP  - 179
EP  - 179
VL  - 17
AB  - BACKGROUND: Staphylococcus aureus (S. aureus) infections range in severity due to
AB  - expression of certain virulence factors encoded on mobile genetic elements (MGE).
AB  - As such, characterization of these MGE, as well as single nucleotide
AB  - polymorphisms, is of high clinical and microbiological importance. To understand
AB  - the evolution of these dangerous pathogens, it is paramount to define reference
AB  - strains that may predate MGE acquisition. One such candidate is S. aureus Tager
AB  - 104, a previously uncharacterized strain isolated from a patient with impetigo in
AB  - 1947. RESULTS: We show here that S. aureus Tager 104 can survive in the
AB  - bloodstream and infect naive organs. We also demonstrate a procedure to construct
AB  - and validate the assembly of S. aureus genomes, using Tager 104 as a
AB  - proof-of-concept. In so doing, we bridged confounding gap regions that limited
AB  - our initial attempts to close this 2.82 Mb genome, through integration of data
AB  - from Illumina Nextera paired-end, PacBio RS, and Lucigen NxSeq mate-pair
AB  - libraries. Furthermore, we provide independent confirmation of our segmental
AB  - arrangement of the Tager 104 genome by the sole use of Lucigen NxSeq libraries
AB  - filled by paired-end MiSeq reads and alignment with SPAdes software. Genomic
AB  - analysis of Tager 104 revealed limited MGE, and a nuSabeta island configuration
AB  - that is reminiscent of other hospital acquired S. aureus genomes. CONCLUSIONS:
AB  - Tager 104 represents an early-branching ancestor of certain hospital-acquired
AB  - strains. Combined with its earlier isolation date and limited content of MGE,
AB  - Tager 104 can serve as a viable reference for future comparative genome studies.
ER  -

TY  - JOUR
AU  - Davis, T.O.
AU  - Henderson, I.
AU  - Brehm, J.K.
AU  - Minton, N.P.
TI  - Development of a transformation and gene reporter system for group II, non-proteolytic Clostridium botulinum type B strains.
JO  - J. Mol. Microbiol. Biotechnol.
PY  - 2000
SP  - 59
EP  - 69
VL  - 2
AB  - Non-proteolytic, Group II strains of Clostridium botulinum are of particular concern to the
AB  - food industry because of their ability to survive and grow in REPFEDs (refrigerated processed
AB  - foods of extended durability). Their analysis would benefit from the availability of a gene
AB  - transfer system. In the present study we have been able, for the first time, to demonstrate
AB  - transformation in a representative Group II strain, ATCC 25765. Initial attempts to transform
AB  - ATCC 25765 with existing clostridial cloning vectors (pMTL540E and pMTL500E) were, however,
AB  - prevented by a restriction barrier. Through a combination of classical and molecular
AB  - approaches we were able to show that strain ATCC 25765 possesses a restriction endonuclease
AB  - (CboI) and a methylase activity (M.CboI) which have the same specificity as MspI and M.MspI,
AB  - respectively. CboI cleaves the palindrome 5'-CCGG-3' to generate a 3'-GC sticky end, whilst
AB  - M.CboI specifically methylates the external C residue. An E. coli host was generated which
AB  - expressed a Bacillus subtilis methylase enzyme (M.BsuFI) with equivalent specificity to
AB  - M.CboI. Plasmids (pMTL540E and pMTL500E) prepared in this strain were subsequently shown to be
AB  - capable of transforming ATCC 25765. The highest frequencies (0.8 X 10^4) transformants per
AB  - microg of DNA) were obtained when cells were cultivated in media supplemented with 1% (w/v)
AB  - glycine, and when the electroporation was undertaken at 10 kV/cm, 25 microF and at 400 ohms.
AB  - Having developed an effective transformation procedure, we went on to construct reporter
AB  - cassettes based on the Thermanaerobacterium sulfurigenes lacZ and the Vibrio fischeri luxAB
AB  - genes. Using the former, and promoter regions isolated from the botulinum toxin genes, we have
AB  - obtained preliminary evidence that reporter genes may be used to evaluate the physiological
AB  - factors that affect toxin production in the food environment.
ER  -

TY  - JOUR
AU  - Davison, J.
AU  - Brunel, F.
TI  - Restriction insensitivity in bacteriophage T5.  I. Genetic characterization of mutants sensitive to EcoRI restriction.
JO  - J. Virol.
PY  - 1979
SP  - 11
EP  - 16
VL  - 29
AB  - Unmodified bacteriophage T5 is able to grow normally on bacterial hosts carrying three
AB  - different Escherichia coli restriction systems, EcoK, EcoPI, and EcoRI.  Under the same
AB  - conditions, the plating efficiency of bacteriophage lambda is less than 10^-9.  At least in
AB  - the case of EcoRI, this lack of in vivo restriction is not due to lack of restriction sites on
AB  - the T5 DNA molecule.  These observations suggest that bacteriophage T5 specifies one or more
AB  - restriction protection systems.  Mutants (ris) of T5 have been isolated which confer
AB  - sensitivity to EcoRI restriction but not to EcoK or EcoPI.  The mutations are located in the
AB  - pre-early region of the genetic map but are too far apart to be alleles of a single gene.
AB  - Complementation studies show that the ris mutants can be helped to grow on the
AB  - EcoRI-restricting host by coinfection with T5+.  This result provides evidence for a
AB  - restriction protection function but does not necessarily show that the ris mutants are
AB  - defective in such a system.
ER  -

TY  - JOUR
AU  - Dawar, C.
AU  - Aggarwal, R.K.
TI  - Draft Genome Sequence of Rhodococcus rhodochrous Strain KG-21, a Soil Isolate from Oil Fields of Krishna-Godavari Basin, India.
JO  - Genome Announcements
PY  - 2015
SP  - e01201
EP  - e01215
VL  - 3
AB  - Here, we present the 6.1-Mb draft genome sequence of Rhodococcus rhodochrous strain KG-21, a
AB  - soil isolate from the oil fields of Krishna-Godavari Basin in Andhra Pradesh, India. This
AB  - genomic resource may help in the identification of the gene(s) involved in hydrocarbon
AB  - degradation and their possible deployment for bioremediation.
ER  -

TY  - JOUR
AU  - Dawar, C.
AU  - Aggarwal, R.K.
TI  - Draft Genome Sequence of Hydrocarbon-Degrading Pseudomonas putida Strain KG-4, Isolated from Soil Samples Collected from Krishna-Godavari Basin in India.
JO  - Genome Announcements
PY  - 2015
SP  - e00590
EP  - e00515
VL  - 3
AB  - We report here the 5.58-Mb draft genome of Pseudomonas putida strain KG-4 obtained from the
AB  - oil fields of the Krishna-Godavari basin, Andhra Pradesh,
AB  - India. The genome sequence is expected to facilitate identification and
AB  - understanding of genes associated with hydrocarbon metabolism, which can help in
AB  - developing strategies for managing oil spills and bioremediation.
ER  -

TY  - JOUR
AU  - Dawoud, T.M.
AU  - Jiang, T.
AU  - Mandal, R.K.
AU  - Ricke, S.C.
AU  - Kwon, Y.M.
TI  - Improving the Efficiency of Transposon Mutagenesis in Salmonella Enteritidis by Overcoming Host-Restriction Barriers.
JO  - Mol. Biotechnol.
PY  - 2014
SP  - 1004
EP  - 1010
VL  - 56
AB  - Transposon mutagenesis using transposome complex is a powerful method for functional genomics
AB  - analysis in diverse bacteria by creating a large number of random mutants to prepare a
AB  - genome-saturating mutant library. However, strong host restriction barriers can lead to
AB  - limitations with species- or strain-specific restriction-modification systems. The purpose of
AB  - this study was to enhance the transposon mutagenesis efficiency of Salmonella Enteritidis to
AB  - generate a larger number of random insertion mutants. Host-adapted Tn5 DNA was used to form a
AB  - transposome complex, and this simple approach significantly and consistently improved the
AB  - efficiency of transposon mutagenesis, resulting in a 46-fold increase in the efficiency as
AB  - compared to non-adapted transposon DNA fragments. Random nature of Tn5 insertions was
AB  - confirmed by high-throughput sequencing of the Tn5-junction sequences. The result based on S.
AB  - Enteritidis in this study should find broad applications in preparing a comprehensive mutant
AB  - library of other species using transposome complex.
ER  -

TY  - JOUR
AU  - Day, J.P.
AU  - Reich, N.O.
AU  - Hager, P.
AU  - Rosenberg, J.
AU  - McClarin, J.A.
AU  - Grable, J.
AU  - Boyer, H.W.
AU  - Greene, P.J.
TI  - Characterization of three EcoRI endonuclease mutants with altered DNA-Protein contacts designed to change specificity.
JO  - J. Cell Biochem. Suppl.
PY  - 1987
SP  - 205
EP  - 205
VL  - 11C
AB  - Mutants of the EcoRI endonuclease were created by site directed mutagenesis in
AB  - an attempt to alter specificity.  The mutations were chosen, based on the
AB  - crystal structure, to change the hydrogen bonding characteristics of the amino
AB  - acid side chains responsible for recognition of the canonical DNA sequence.
AB  - The mutants generated were Glu144->Asp(ED144), Arg145->Lys(RK145), and
AB  - Arg200->Lys(RK200).  These were purified to homogeneity.  We measured kcat and
AB  - Km on pBR322 and pBR322 lacking the RI site.  We also determined the salt and
AB  - pH optima.  All of the mutants cleave the canonical sequence; however, they all
AB  - accumulate the nicked intermediate.  Linear DNA production by ED144 is
AB  - increased at low salt to a nearly wildtype level.  kcat values are well below
AB  - wildtype kcat in RK145 and RK200.  The specificity constants (kcat/Km) are
AB  - different from wildtype.  Canonical to noncanonical kcat/Km ratios indicate
AB  - altered specificity.  Ed144 has increased specificity for the canonical site.
AB  - The rate limiting step in the wildtype is the off rate from nonspecific DNA
AB  - after cleavage.  If this step is also limitiing in the mutants, then hydrogen
AB  - bonds involved in recognition of the canonical site are normally made to some
AB  - extent in nonspecific DNA.  Completely changing specificity is difficult or
AB  - perhaps impossible to accomplish by making a single amino acid change.  One
AB  - might expect enzymes to have a structure resistsant to specificity changes by a
AB  - single amino acid substitution, especially if a specificity change would be a
AB  - lethal event.
ER  -

TY  - JOUR
AU  - Day, M.
AU  - Ibrahim, M.
AU  - Dyer, D.
AU  - Bulla, L. Jr.
TI  - Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD-1.
JO  - Genome Announcements
PY  - 2014
SP  - e00613
EP  - e00614
VL  - 2
AB  - We report here the complete genome sequence of Bacillus thuringiensis subsp. kurstaki strain
AB  - HD-1, which serves as the primary U.S. reference standard for all
AB  - commercial insecticidal formulations of B. thuringiensis manufactured around the
AB  - world.
ER  -

TY  - JOUR
AU  - Day, M.W.
AU  - Jackson, L.A.
AU  - Akins, D.R.
AU  - Dyer, D.W.
AU  - Chavez-Bueno, S.
TI  - Whole-Genome Sequences of the Archetypal K1 Escherichia coli Neonatal Isolate RS218 and Contemporary Neonatal Bacteremia Clinical Isolates SCB11, SCB12, and SCB15.
JO  - Genome Announcements
PY  - 2015
SP  - e01598
EP  - e01514
VL  - 3
AB  - Neonatal bacteremia Escherichia coli strains commonly belong to the K1 capsular type. Their
AB  - ability to cause invasive neonatal disease appears to be determined by other virulence factors
AB  - that have yet to be identified. We report here the genome sequences of four E. coli neonatal
AB  - bacteremia isolates, including that of  the archetypal strain RS218.
ER  -

TY  - JOUR
AU  - Day, R.S.
TI  - UV-induced alleviation of K-specific restriction of bacteriophage lambda.
JO  - J. Virol.
PY  - 1977
SP  - 1249
EP  - 1251
VL  - 21
AB  - A partial release of K-specific restriction of phage lambda grown in
AB  - Escherichia coli C was observed when E. coli K strains AB1157 (having wild-type
AB  - repair of UV-produced DNA damage) and AB1886 (uvrA) were irradiated with UV
AB  - light before infection.  The effect occurred in AB1886 at lower UV fluences
AB  - than it did in AB1157.  Little or no release of restriction was observed when
AB  - AB2463 (recA) or AB2494 (lex-1) was used.  Such release of restriction appears
AB  - to be another of the UV-induced phenomena associated with SOS repair.
ER  -

TY  - JOUR
AU  - de Aguiar, E.L. et al.
TI  - Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of  type Ia isolated from human oropharynx.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 39
EP  - 39
VL  - 11
AB  - Streptococcus agalactiae, also referred to as Group B Streptococcus, is a frequent resident of
AB  - the rectovaginal tract in humans, and a major cause of
AB  - neonatal infection. The pathogen can also infect adults with underlying disease,
AB  - particularly the elderly and immunocompromised ones. In addition, S. agalactiae
AB  - is a known fish pathogen, which compromises food safety and represents a zoonotic
AB  - hazard. This study provides valuable structural, functional and evolutionary
AB  - genomic information of a human S. agalactiae serotype Ia (ST-103) GBS85147 strain
AB  - isolated from the oropharynx of an adult patient from Rio de Janeiro, thereby
AB  - representing the first human isolate in Brazil. We used the Ion Torrent PGM
AB  - platform with the 200 bp fragment library sequencing kit. The sequencing
AB  - generated 578,082,183 bp, distributed among 2,973,022 reads, resulting in an
AB  - approximately 246-fold mean coverage depth and was assembled using the Mira
AB  - Assembler v3.9.18. The S. agalactiae strain GBS85147 comprises of a circular
AB  - chromosome with a final genome length of 1,996,151 bp containing 1,915
AB  - protein-coding genes, 18 rRNA, 63 tRNA, 2 pseudogenes and a G + C content of
AB  - 35.48 %.
ER  -

TY  - JOUR
AU  - de Alencar, S.A.
AU  - Costa, F.S.
AU  - Rodrigues, G.R.
AU  - Barreto, C.C.
TI  - Draft Genome Sequence of a Novel Mucilaginibacter Member Isolated from Brazilian  Amazon Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01033
EP  - e01016
VL  - 4
AB  - Bacteria from the Mucilaginibacter genus are still poorly understood, although their
AB  - importance has been shown by recent reports describing great quantities of
AB  - biofilms produced in their colonies. We report the draft genome sequence of a
AB  - novel Mucilaginibacter member, comprising 8 contigs, totaling 5,478,589 bp and
AB  - 4,876 predicted coding sequences.
ER  -

TY  - JOUR
AU  - de Almeida, J.B.
AU  - de Carvalho, S.P.
AU  - de Freitas, L.M.
AU  - Guimaraes, A.M.
AU  - do Nascimento, N.C.
AU  - Dos Santos, A.P.
AU  - Messick, J.B.
AU  - Timenetsky, J.
AU  - Marques, L.M.
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain LC33  Isolated from Human Breast Milk.
JO  - Genome Announcements
PY  - 2017
SP  - e00154
EP  - e00117
VL  - 5
AB  - Here, we report the draft genome sequence of Staphylococcus aureus strain LC33, isolated from
AB  - human breast milk in Brazil. This microorganism has been typed as
AB  - ST1/t127/sccmecV. To our knowledge, this is the first draft genome sequence of a
AB  - methicillin-resistant S. aureus strain isolated from human breast milk.
ER  -

TY  - JOUR
AU  - de Almeida, L.M.
AU  - Pires, C.
AU  - Cerdeira, L.T.
AU  - de Oliveira, T.G.
AU  - McCulloch, J.A.
AU  - Perez-Chaparro, P.J.
AU  - Sacramento, A.G.
AU  - Brito, A.C.
AU  - da Silva, J.L.
AU  - de Araujo, M.R.
AU  - Lincopan, N.
AU  - Martin, M.J.
AU  - Gilmore, M.S.
AU  - Mamizuka, E.M.
TI  - Complete Genome Sequence of Linezolid-Susceptible Staphylococcus haemolyticus Sh29/312/L2, a Clonal Derivative of a Linezolid-Resistant Clinical Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00494
EP  - e00415
VL  - 3
AB  - We report the whole-genome sequence (WGS) of an in vitro susceptible derivative revertant
AB  - mutant from a bloodstream isolate involved in a nosocomial outbreak in
AB  - Brazil. The WGS comprises 2.5 Mb with 2,500 protein-coding sequences, 16rRNA
AB  - genes, and 60 tRNA genes.
ER  -

TY  - JOUR
AU  - de Andrade-Barboza, S.
AU  - Meygret, A.
AU  - Vincent, P.
AU  - Moullec, S.
AU  - Soriano, N.
AU  - Lagente, V.
AU  - Minet, J.
AU  - Kayal, S.
AU  - Faili, A.
TI  - Complete Genome Sequence of Noninvasive Streptococcus pyogenes M/emm28 Strain STAB10015, Isolated from a Child with Perianal Dermatitis in French Brittany.
JO  - Genome Announcements
PY  - 2015
SP  - e00806
EP  - e00815
VL  - 3
AB  - We report here the complete genome sequence of a noninvasive strain of Streptococcus pyogenes
AB  - M/emm28, isolated from perianal dermatitis in a child. The genome is composed of 1,950,454 bp,
AB  - with a G+C content of 38.2%, and it has 1,925 identified coding sequences and harbors two
AB  - intact prophages and a new integrating conjugative element (ICE).
ER  -

TY  - JOUR
AU  - De Backer, O.
AU  - Colson, C.
TI  - Molecular nature of the restriction-modification system LT of Salmonella typhimurium.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 212
EP  - 212
VL  - 13D
AB  - Restriction-modification (R-M) system LT is present in most Salmonella strains.
AB  - Its genes are chromosomally located near proC.  We have cloned these genes and
AB  - determined some properties of the coded enzymes.  On appropriate S. typhimurium
AB  - strains, the phage vector lambda EMBL4 was very strongly restricted by LT.
AB  - This allowed the selection of a lambda clone carrying the modification gene and
AB  - therefore immune to the LT restriction.  This gene was subcloned into plasmid
AB  - vectors and expressed in E. coli.  A restricting recombinant clone was isolated
AB  - from a plasmid genomic library of S. typhimurium made in a modifying host
AB  - strain.  This clone proved to contain a plasmid harboring the genes coding for
AB  - both restriction and modification activities.  In contrast with other studied
AB  - R-M systems, the introduction of LT genes into a nonmodifying host is lethal,
AB  - probably because of self-restriction of the chromosomal DNA.  The sequence of
AB  - the recognition site of the LT enzymes was found to be 5' GAGAC 3'.  It is
AB  - characteristic of type III R-M systems (5 bp long, asymmetric, adenine present
AB  - on only one strand).  The methylated base is the 5' adenine.
ER  -

TY  - JOUR
AU  - De Backer, O.
AU  - Colson, C.
TI  - Transfer of the genes for the StyLTI restriction-modification system of Salmonella typhimurium to strains lacking modification ability results in death of the recipient cells and degradation of their DNA.
JO  - J. Bacteriol.
PY  - 1991
SP  - 1328
EP  - 1330
VL  - 173
AB  - The genes encoding the restriction-modification system, StyLTI, of Salmonella
AB  - typhimurium were inserted in vivo into the conjugative plasmid pULB21.  This
AB  - allowed us to transfer the StyLTI genes at a very high frequency and to monitor
AB  - the fate of recipient cells after mating.  Transfer of the StyLTI restriction
AB  - and modification genes into a modificationless recipient was lethal and
AB  - resulted in degradation of the cell's DNA.  This indicates that, in contrast to
AB  - any other known restriction-modification systems, StyLTI cannot be established
AB  - after horizontal transfer into a naive host.
ER  -

TY  - JOUR
AU  - De Backer, O.
AU  - Colson, C.
TI  - Two-step cloning and expression in Escherichia coli of the DNA restriction-modification system StyLTI of Salmonella typhimurium.
JO  - J. Bacteriol.
PY  - 1991
SP  - 1321
EP  - 1327
VL  - 173
AB  - The StyLTI restriction-modification system is common to most strains of the
AB  - genus Salmonella, including Salmonella typhimurium.  We report here the
AB  - two-step cloning of the genes controlling the StyLTI system.  The StyLTI
AB  - methylase gene (mod) was cloned first.  Then, the companion endonuclease gene
AB  - (res) was introduced on a compatible vector.  A strain of S. typhimurium
AB  - sensitive to the coliphage lambda was constructed and used to select
AB  - self-modifying recombinant phages from a Res-Mod+ S. typhimurium genomic
AB  - library in the lambda EMBL4 cloning vector.  The methylase gene of one of these
AB  - phages was then subcloned in pBR328 and transferred into Escherichia coli.  In
AB  - the second step, the closely linked endonuclease and methylase genes were
AB  - cloned together on a single DNA fragment inserted in pACYC184 and introduced
AB  - into the Mod+ E. coli strain obtained in the first step.  Attemps to transform
AB  - Mod- E. coli or S. typhimurium strains with this Res+ Mod+ plasmid were
AB  - unsuccessful, whereas transformation of Mod+ strains occured at a normal
AB  - frequency.  This can be understood if the introduction of the StyLTI genes into
AB  - naive hosts is lethal because of degradation of host DNA by restriction
AB  - activity; in contrast to most restriction-modification systems, StyLTI could
AB  - not be transferred into naive hosts without killing them.  In addition, it was
AB  - found that strains containing only the res gene are viable and lack restriction
AB  - activity in the absence of the companion mod gene.  This suggests that
AB  - expression of the StyLTI endonuclease activity requires at least one
AB  - polypeptide involved in the methylation activity, as is the case for types I
AB  - and III restriction-modification systems but not for type II systems.
ER  -

TY  - JOUR
AU  - De Backer, O.
AU  - Colson, C.
TI  - Identification of the recognition sequence for the M.StyLTI methyltransferase of Salmonella typhimurium LT7: an asymmetric site typical of type-III enzymes.
JO  - Gene
PY  - 1991
SP  - 103
EP  - 107
VL  - 97
AB  - The StyLTI restriction-modification (R-M) system is encoded by chromosomal
AB  - genes of Salmonella typhimurium LT7.  We report here the identification of the
AB  - nucleotide (nt) sequence methylated by the StyLTI modification
AB  - methyltransferase (M.StyLTI).  This enzyme was partially purified from an
AB  - Escherichia coli strain expressing the cloned M.StyLTI-encoding gene, but
AB  - lacking StyLTI restriction activity, and used to methylate DNAs of known
AB  - sequence, using S-adenosyl-[methyl-3H]-methionine as the methyl donor.  The
AB  - [3H]methylated DNA was then digested with various endonucleases.  Examination
AB  - of labelled and unlabelled restriction fragments allowed us to map the M.StyLTI
AB  - sites in perfectly defined regions of the DNA.  Comparison of the nt sequences
AB  - of DNA segments with or without M.StyLTI sites permitted us to identify the
AB  - asymmetric and nondegenerate pentanucleotide, 5'-CAG(A*)G-3'/3'-GTCTC-5', as
AB  - the StyLTI sequence.  M.StyLTI was found to methylate only the 3' A (see
AB  - asterisk) in the upper strand of this sequence.  Thus, M.StyLTI recognises and
AB  - methylates the DNA in a manner very similar to that of the three known type-III
AB  - MTases, M.EcoPI, M.EcoP15, and M.HinfIII.  This strongly suggests that StyLTI
AB  - constitutes a fourth type-III R-M system.
ER  -

TY  - JOUR
AU  - de Been, M.
AU  - Lanza, V.F.
AU  - de Toro, M.
AU  - Scharringa, J.
AU  - Dohmen, W.
AU  - Du, Y.
AU  - Hu, J.
AU  - Lei, Y.
AU  - Li, N.
AU  - Tooming-Klunderud, A.
AU  - Heederik, D.J.
AU  - Fluit, A.C.
AU  - Bonten, M.J.
AU  - Willems, R.J.
AU  - de la Cruz, F.
AU  - van Schaik, W.
TI  - Dissemination of cephalosporin resistance genes between Escherichia coli strains  from farm animals and humans by specific plasmid lineages.
JO  - PLoS Genet.
PY  - 2014
SP  - e1004776
EP  - e1004776
VL  - 10
AB  - Third-generation cephalosporins are a class of beta-lactam antibiotics that are often used for
AB  - the treatment of human infections caused by Gram-negative
AB  - bacteria, especially Escherichia coli. Worryingly, the incidence of human
AB  - infections caused by third-generation cephalosporin-resistant E. coli is
AB  - increasing worldwide. Recent studies have suggested that these E. coli strains,
AB  - and their antibiotic resistance genes, can spread from food-producing animals,
AB  - via the food-chain, to humans. However, these studies used traditional typing
AB  - methods, which may not have provided sufficient resolution to reliably assess the
AB  - relatedness of these strains. We therefore used whole-genome sequencing (WGS) to
AB  - study the relatedness of cephalosporin-resistant E. coli from humans, chicken
AB  - meat, poultry and pigs. One strain collection included pairs of human and
AB  - poultry-associated strains that had previously been considered to be identical
AB  - based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance
AB  - gene sequencing. The second collection included isolates from farmers and their
AB  - pigs. WGS analysis revealed considerable heterogeneity between human and
AB  - poultry-associated isolates. The most closely related pairs of strains from both
AB  - sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome.
AB  - In contrast, epidemiologically linked strains from humans and pigs differed by
AB  - only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed
AB  - three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin
AB  - resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types.
AB  - The plasmid backbones within each lineage were virtually identical and were
AB  - shared by genetically unrelated human and animal isolates. Plasmid
AB  - reconstructions from short-read sequencing data were validated by long-read DNA
AB  - sequencing for two strains. Our findings failed to demonstrate evidence for
AB  - recent clonal transmission of cephalosporin-resistant E. coli strains from
AB  - poultry to humans, as has been suggested based on traditional, low-resolution
AB  - typing methods. Instead, our data suggest that cephalosporin resistance genes are
AB  - mainly disseminated in animals and humans via distinct plasmids.
ER  -

TY  - JOUR
AU  - De Bolle, X.
AU  - Bayliss, C.D.
AU  - Field, D.
AU  - van de Ven, T.
AU  - Saunders, N.J.
AU  - Hood, D.W.
AU  - Moxon, E.R.
TI  - The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 211
EP  - 222
VL  - 35
AB  - Haemophilus influenzae is an obligate commensal of the upper respiratory tract of humans that
AB  - uses simple repeats (microsatellites) to alter gene expression. The mod gene of H. influenzae
AB  - strain Rd has homology to DNA methyltransferases of type III restriction/modification systems
AB  - and has 40 tetranucleotide (5'-AGTC) repeats within its open reading frame. This gene was
AB  - found in 21 out of 23 genetically distinct H. influenzae strains, and in 13 of these strains
AB  - the locus contained repeats. H. influenzae strains were constructed in which a lacZ reporter
AB  - was fused to a chromosomal copy of mod downstream of the repeats. Phase variation occurred at
AB  - a high frequency in strains with the wild-type number of repeats. Mutation rates were derived
AB  - for similarly engineered strains, containing different numbers of repeats. Rates increased
AB  - linearly with tract length over the range 17-38 repeat units. The majority of tract
AB  - alterations were insertions or deletions of one repeat unit with a 2:1 bias towards
AB  - contractions of the tract. These results demonstrate the number of repeats to be an important
AB  - determinant of phase variation rate in H. influenzae for a gene containing a microsatellite.
ER  -

TY  - JOUR
AU  - De Carli, S.
AU  - Graf, T.
AU  - Mayer, F.Q.
AU  - Cibulski, S.
AU  - Lehmann, F.K.
AU  - Fonseca, A.S.
AU  - Ikuta, N.
AU  - Lunge, V.R.
TI  - Draft Genome Sequence of a Salmonella enterica subsp. enterica Serovar Gallinarum bv. Gallinarum Isolate Associated with Fowl Typhoid Outbreaks in Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e00019
EP  - e00016
VL  - 4
AB  - Salmonella enterica subsp. enterica serovar Gallinarum bv. Gallinarum strains are bird
AB  - pathogens causing fowl typhoid (FT). Isolate BR_RS12 was obtained from a
AB  - poultry flock with FT in 2014. The sequencing of this genome will enable to track
AB  - the origin of the recent outbreaks in Brazil.
ER  -

TY  - JOUR
AU  - de Carvalho, S.P.
AU  - de Almeida, J.B.
AU  - de Freitas, L.M.
AU  - Guimaraes, A.M.
AU  - do Nascimento, N.C.
AU  - Dos Santos, A.P.
AU  - Messick, J.B.
AU  - Timenetsky, J.
AU  - Marques, L.M.
TI  - Draft Genome Sequences of Two Clinical Methicillin-Resistant Staphylococcus aureus Strains Isolated from Healthy Children in Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00158
EP  - e00117
VL  - 5
AB  - We report here the draft genome sequences of two community-associated methicillin-resistant
AB  - Staphylococcus aureus (CA-MRSA) strains, C18 and C80,
AB  - isolated from healthy children from day care centers. To our knowledge, these are
AB  - the first draft genome sequences of CA-MRSA ST398/CC398/SccmecV and CA-MRSA
AB  - ST5/CC5/SccmecIVa isolated from healthy children in Brazil.
ER  -

TY  - JOUR
AU  - de Diego-Diaz, B.
AU  - Treu, L.
AU  - Campanaro, S.
AU  - da Silva, D.V.
AU  - Basaglia, M.
AU  - Favaro, L.
AU  - Casella, S.
AU  - Squartini, A.
TI  - Genome Sequence of Rhizobium sullae HCNT1 Isolated from Hedysarum coronarium Nodules and Featuring Peculiar Denitrification Phenotypes.
JO  - Genome Announcements
PY  - 2018
SP  - e01518
EP  - e01517
VL  - 6
AB  - The genome sequence of Rhizobium sullae strain HCNT1, isolated from root nodules  of the
AB  - legume Hedysarum coronarium growing in wild stands in Tuscany, Italy, is
AB  - described here. Unlike other R. sullae strains, this isolate features a truncated
AB  - denitrification pathway lacking NO/N2O reductase activity and displaying high
AB  - sensitivity to nitrite under anaerobic conditions.
ER  -

TY  - JOUR
AU  - de Diego-Diaz, B.
AU  - Treu, L.
AU  - Campanaro, S.
AU  - da Silva, D.V.
AU  - Saviane, A.
AU  - Cappellozza, S.
AU  - Squartini, A.
TI  - Genome Sequence of Enterococcus mundtii EM01, Isolated from Bombyx mori Midgut and Responsible for Flacherie Disease in Silkworms Reared on an Artificial Diet.
JO  - Genome Announcements
PY  - 2018
SP  - e01495
EP  - e01417
VL  - 6
AB  - The whole genome sequence of Enterococcus mundtii strain EM01 is reported here. The isolate
AB  - proved to be the cause of flacherie in Bombyx mori To date, the
AB  - genomes of 11 other E. mundtii strains have been sequenced. EM01 is the only
AB  - strain that displayed active pathological effects on its associated animal
AB  - species.
ER  -

TY  - JOUR
AU  - De Feyter, R.
AU  - Gabriel, D.W.
TI  - Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum.
JO  - J. Bacteriol.
PY  - 1991
SP  - 6421
EP  - 6427
VL  - 173
AB  - In vitro-packaged cosmid libraries of DNA from the bacterium Xanthomonas
AB  - campestris pv. malvacearum were restricted 200- to 1,000-fold when introduced
AB  - into Mcr+ strains of Escherichia coli compared with restriction in the Mcr-
AB  - strain HB101.  Restriction was predominantly associated with the mcrBC+ gene in
AB  - E. coli.  A plasmid (pUFR052) encoding the XmaI and XmaIII DNA methylases was
AB  - isolated from an X. campestris pv. malvacearum library by a screening procedure
AB  - utilizing Mcr+ and Mcr- E. coli strains.  Transfer of plasmids from E. coli
AB  - strains to X. campestris pv. malvacearum by conjugation was enhanced by up to
AB  - five orders of magnitude when the donor cells contained pUFR052 as well as the
AB  - plasmid to be transferred.  Subcloning of pUFR052 revealed that at least two
AB  - regions of the plasmid were required for full modification activity.  Use of
AB  - such modifier plasmids is a simple, novel method that may allow the efficient
AB  - introduction of genes into any organism in which restriction systems provide a
AB  - potent barrier to such gene transfer.
ER  -

TY  - JOUR
AU  - de Franca, P.
AU  - Camilo, E.
AU  - Fantinatti-Garboginni, F.
TI  - Draft Genome Sequence of Marinobacter sp. Strain ANT_B65, Isolated from Antarctic Marine Sponge.
JO  - Genome Announcements
PY  - 2018
SP  - e01404
EP  - e01417
VL  - 6
AB  - Marinobacter sp. strain ANT_B65 was isolated from sponge collected in King George Island,
AB  - Antarctica. The draft genome of 4,173,840 bp encodes 3,743 protein-coding
AB  - open reading frames. The genome will provide insights into the strain's potential
AB  - use in the production of natural products.
ER  -

TY  - JOUR
AU  - De Groot, A.
AU  - Dulermo, R.
AU  - Ortet, P.
AU  - Blanchard, L.
AU  - Guerin, P.
AU  - Fernandez, B.
AU  - Vacherie, B.
AU  - Dossat, C.
AU  - Jolivet, E.
AU  - Siguier, P.
AU  - Chandler, M.
AU  - Barakat, M.
AU  - Dedieu, A.
AU  - Barbe, V.
AU  - Heulin, T.
AU  - Sommer, S.
AU  - Achouak, W.
AU  - Jean, A.
TI  - Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium.
JO  - PLoS Genet.
PY  - 2009
SP  - e1000434
EP  - e1000434
VL  - 5
AB  - To better understand adaptation to harsh conditions encountered in hot arid deserts, we report
AB  - the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti
AB  - VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and
AB  - three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its
AB  - 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS
AB  - spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among
AB  - the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown
AB  - function. The alliance of proteomics and genomics highthroughput techniques allowed
AB  - identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted
AB  - orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced
AB  - genes, ddrC and ddrH, and
AB  - identification in D. deserti of supplementary genes involved in manganese import extend our
AB  - knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in
AB  - nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a
AB  - photolyase) were also identified and found to be expressed under standard growth conditions,
AB  - and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient
AB  - import and DNA repair genes are likely important for survival and adaptation of D. deserti to
AB  - its nutrient-poor, dry, and UV-exposed extreme environment.
ER  -

TY  - JOUR
AU  - De Jonckheere, J.F.
TI  - Evidence for the ancestral origin of group I introns in the SSUrDNA of Naegleria spp.
JO  - J. Eukaryot. Microbiol.
PY  - 1994
SP  - 457
EP  - 463
VL  - 41
AB  - The sequence variation within the group I intron in five Naegleria spp. was studied and
AB  - compared with the sequence variation within the flanking small subunit ribosomal DNA.
AB  - Considerable sequence divergence was observed in the introns as well as in the rDNA.  In the
AB  - intron deletions and insertions are only detected in the sequence contributing to the
AB  - secondary structure, not in the open reading frame.  Most of the sequence variation is
AB  - detected in the unpaired loops.  In the case of nucleotide substitution in helices,
AB  - compensating base pair changes were observed.  The sequence variation does not induce
AB  - variation in the secondary structure model.  The phylogenetic tree based on the intron
AB  - sequences is similar to the tree based on the flanking rDNA sequences.  This observation
AB  - indicates that the intron might have been acquired at an early stage in evolution, and lost in
AB  - the majority of Naegleria spp.
ER  -

TY  - JOUR
AU  - de Jong, A.
AU  - van Heel, A.J.
AU  - Montalban-Lopez, M.
AU  - Krawczyk, A.O.
AU  - Berendsen, E.M.
AU  - Wells-Bennik, M.
AU  - Kuipers, O.P.
TI  - Draft Genome Sequences of Five Spore-Forming Food Isolates of Bacillus pumilus.
JO  - Genome Announcements
PY  - 2015
SP  - e01539
EP  - e01514
VL  - 3
AB  - Here, we report the draft genome sequences of five food isolates of Bacillus pumilus, a
AB  - spore-forming Gram-positive bacterium.
ER  -

TY  - JOUR
AU  - de la Campa, A.G.
AU  - Kale, P.
AU  - Springhorn, S.S.
AU  - Lacks, S.A.
TI  - Proteins encoded by the DpnII restriction gene cassette:  Two methylases and an endonuclease.
JO  - J. Mol. Biol.
PY  - 1987
SP  - 457
EP  - 469
VL  - 196
AB  - Proteins encoded by three genes in the DpnII restriction enzyme cassette of
AB  - Streptococcus pneumoniae were purified and characterized.  Large amounts of the
AB  - proteins were produced by subcloning the cassette in an Escherichia coli
AB  - expression system.  All three proteins appear to be dimers composed of
AB  - identical polypeptide subunits.  One is the DpnII endonuclease, and the other
AB  - two are DNA adenine methylases active at 5'GATC3' sites.  Inactivation of
AB  - enzyme activity by insertions into the genes and comparison of the DNA sequence
AB  - with the amino-terminal sequence of amino acid residues in the proteins
AB  - demonstrated the following correspondence between genes and enzymes.  The
AB  - promoter-proximal gene in the operon, dpnM, encodes a 33000 Mr polypeptide that
AB  - gives rise to a potent DNA methylase.  The next gene, dpnA, encodes the 31000
AB  - Mr polypeptide of a weaker and less-specific methylase.  The third gene, dpnB,
AB  - encodes the 34000 Mr polypeptide of the endonuclease.  Although the
AB  - endonuclease polypeptide is initiated from an ordinary ribosome-binding site,
AB  - each of the methylase polypeptides begins at an atypical site with a consensus
AB  - sequence entirely different from that of Shine & Dalgarno.  This presumptive
AB  - novel ribosome-binding site is well recognized in both S. pneumoniae and E.
AB  - coli.
ER  -

TY  - JOUR
AU  - de la Campa, A.G.
AU  - Springhorn, S.S.
AU  - Kale, P.
AU  - Lacks, S.A.
TI  - Proteins encoded by the DpnI restriction gene cassette.
JO  - J. Biol. Chem.
PY  - 1988
SP  - 14696
EP  - 14702
VL  - 263
AB  - Insertion mutations in the DpnI gene cassette of Streptococcus pneumoniae
AB  - indicated that the two genes it contains, dpnC and dpnD, were transcribed from
AB  - an adjacent promoter and that only dpnC was necessary for expression of the
AB  - DpnI endonuclease.  Large amounts of the DpnI endonuclease were produced from
AB  - the cloned cassette in an Escherichia coli expression system, and the enzyme
AB  - was purified to homogeneity.  The DpnI endonuclease is composed of a single
AB  - polypeptide of 30 kDa, which, as shown by NH2-terminal sequencing of the
AB  - protein, is encoded by the entire dpnC open reading frame.  the native protein
AB  - sedimented as a monomer of 30 kDa in 0.5 M NaCl.  A protein composed of a
AB  - 20-kDa polypeptide, which is presumably encoded by dpnD, was also produced in
AB  - large amounts.  It was partially purified, but its function is unknown.
AB  - Examination of the predicted amino acid sequence of DpnI revealed a potential
AB  - metal-containing, DNA-binding finger structure.  It is suggested that this
AB  - structure provides the specificity for recognition of the methylated DNA
AB  - sequence, 5'-GmATC-3', that is cleaved by the DpnI endonuclease.
ER  -

TY  - JOUR
AU  - de la Fuente, J.
AU  - Diez-Delgado, I.
AU  - Contreras, M.
AU  - Vicente, J.
AU  - Cabezas-Cruz, A.
AU  - Manrique, M.
AU  - Tobes, R.
AU  - Lopez, V.
AU  - Romero, B.
AU  - Dominguez, L.
AU  - Garrido, J.M.
AU  - Juste, R.
AU  - Gortazar, C.
TI  - Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae.
JO  - Genome Announcements
PY  - 2015
SP  - e00247
EP  - e00215
VL  - 3
AB  - Here we report the complete genome sequences of field isolates of Mycobacterium bovis and the
AB  - related mycobacterial species, Mycobacterium caprae. The genomes of
AB  - three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with
AB  - different virulence, prevalence, and host distribution phenotypes were sequenced.
ER  -

TY  - JOUR
AU  - de la Haba, R.R.
AU  - Sanchez-Porro, C.
AU  - Leon, M.J.
AU  - Papke, R.T.
AU  - Ventosa, A.
TI  - Draft Genome Sequence of the Moderately Halophilic Bacterium Pseudoalteromonas ruthenica Strain CP76.
JO  - Genome Announcements
PY  - 2013
SP  - e00268
EP  - e00213
VL  - 1
AB  - Pseudoalteromonas ruthenica strain CP76, isolated from a saltern in Spain, is a moderately
AB  - halophilic bacterium belonging to the Gammaproteobacteria. Here we
AB  - report the draft genome sequence, which consists of a 4.0-Mb chromosome, of this
AB  - strain, which is able to produce the extracellular enzyme haloprotease CPI.
ER  -

TY  - JOUR
AU  - De Lencastre, H.
AU  - Wu, S.W.
AU  - Pinho, M.G.
AU  - Ludovice, A.M.
AU  - Filipe, S.
AU  - Gardete, S.
AU  - Sobral, R.
AU  - Gill, S.
AU  - Chung, M.
AU  - Tomasz, A.
TI  - Antibiotic resistance as a stress response: complete sequencing of a large number of chromosomal loci in Staphylococcus aureus strain COL that impact   on the expression of resistance to methicillin.
JO  - Microb. Drug Resist.
PY  - 1999
SP  - 163
EP  - 175
VL  - 5
AB  - Tn551 inactivation has identified several determinants--fem or auxiliary genes--that, in
AB  - addition to the mecA gene, are also critical for the
AB  - expression of high-level and homogeneous resistance to methicillin.
AB  - Genetic and/or biochemical analysis has shown that of the nearly dozen aux
AB  - mutations described so far most are in genes involved in cell wall
AB  - synthesis (murE, pbp2, glmM, glnR, femA/B, llm, etc.) or in complex
AB  - regulatory functions (sigmaB), suggesting that optimal expression of
AB  - resistance may involve the cooperative functioning of a number of genes in
AB  - cell wall metabolism as well as stress response. The exact mechanism of
AB  - these functions is not known. In an attempt to explore this unusual aspect
AB  - of methicillin resistance more fully, a Tn551 transposon library,
AB  - constructed in the background of the highly and homogeneously
AB  - methicillin-resistant Staphylococcus aureus strain COL, was screened for
AB  - all independent insertional mutants in which the level of methicillin
AB  - resistance of the parental strain (MIC, 1,600 microg/ml) was reduced by at
AB  - least 15-fold and up to 500-fold. We now describe the sequencing of 21
AB  - Tn551-inactivated genes and their vicinities in 23 new auxiliary mutants
AB  - that have been studied before. Using the inverted polymerase chain
AB  - reaction (IPCR), we amplified fragments corresponding to the right and
AB  - left junction of the Tn551 insertions, which were then sequenced by primer
AB  - walking. The two largest groups of these new auxiliary genes encoded
AB  - either proteins of unknown functions (6 genes) or showed homology with
AB  - genes encoding proteins involved with putative sensory/regulatory
AB  - activities (7 genes: protein kinases, ABC transporters, and a catabolite
AB  - control protein). Sequencing upstream and downstream allowed the
AB  - identification of a number of additional open reading frames, some of
AB  - which may also include functions relevant for the expression of antibiotic
AB  - resistance.
ER  -

TY  - JOUR
AU  - De Leon, K.B.
AU  - Utturkar, S.M.
AU  - Camilleri, L.B.
AU  - Elias, D.A.
AU  - Arkin, A.P.
AU  - Fields, M.W.
AU  - Brown, S.D.
AU  - Wall, J.D.
TI  - Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably  Competitive Group of Negativicutes in the Firmicutes Phylum.
JO  - Genome Announcements
PY  - 2015
SP  - e01090
EP  - e01015
VL  - 3
AB  - The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in
AB  - Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA
AB  - gene operon and multiple transposase genes with identical sequences resulted in breaks in the
AB  - original draft genome and may suggest genomic instability of JBW45.
ER  -

TY  - JOUR
AU  - De Leon, K.B.
AU  - Young, M.L.
AU  - Camilleri, L.B.
AU  - Brown, S.D.
AU  - Skerker, J.M.
AU  - Deutschbauer, A.M.
AU  - Arkin, A.P.
AU  - Fields, M.W.
TI  - Draft Genome Sequence of Pelosinus fermentans JBW45, Isolated during In Situ Stimulation for Cr(VI) Reduction.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5456
EP  - 5457
VL  - 194
AB  - Pelosinus fermentans JBW45 is an anaerobic, lactate-fermenting bacterium isolated from
AB  - Cr(VI)-contaminated groundwater at the Hanford Nuclear Reservation 100-H site (Washington)
AB  - that was collected after stimulation with a polylactate compound. The genome sequence of this
AB  - organism will provide insight into the metabolic potential of a predominant population during
AB  - stimulation for metal-reducing conditions.
ER  -

TY  - JOUR
AU  - De Leon, M.P.
AU  - Park, A.Y.
AU  - Montecillo, A.D.
AU  - Siringan, M.A.T.
AU  - Rosana, A.R.R.
AU  - Kim, S.G.
TI  - Near-Complete Genome Sequences of Streptomyces sp. Strains AC1-42T and AC1-42W, Isolated from Bat Guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00904
EP  - e00918
VL  - 7
AB  - Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave,
AB  - Mabini, Pangasinan, Philippines, are active against Bacillus
AB  - subtilis subsp. subtilis KCTC 3135(T). The near-complete genome sequences
AB  - reported here represent a possible source of ribosomally synthesized,
AB  - posttranslationally modified peptides, such as lantipeptides, bacteriocins,
AB  - linaridin, and a lasso peptide.
ER  -

TY  - JOUR
AU  - de Lima-Morales, D.
AU  - Chaves-Moreno, D.
AU  - Jarek, M.
AU  - Vilchez-Vargas, R.
AU  - Jauregui, R.
AU  - Pieper, D.H.
TI  - Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.
JO  - Genome Announcements
PY  - 2013
SP  - e00258
EP  - e00213
VL  - 1
AB  - Pseudomonas veronii strain 1YdBTEX2 was isolated from a benzene-contaminated site. Here we
AB  - report the draft genome sequence of 1YdBTEX2 and its genes
AB  - associated with aromatic metabolism. The broad catabolic potential of this strain
AB  - is consistent with the environment from which it was isolated.
ER  -

TY  - JOUR
AU  - de los Reyes-Gavilan, C.G.
AU  - Aparicio, J.F.
AU  - Barbes, C.
AU  - Hardisson, C.
AU  - Sanchez, J.
TI  - An exocytoplasmic endonuclease with restriction function in Streptomyces antibioticus.
JO  - J. Bacteriol.
PY  - 1988
SP  - 1339
EP  - 1345
VL  - 170
AB  - Streptomyces antibioticus produces a strong endo-DNase which is located between
AB  - the cytoplasmic membrane and the cell wall.  All DNA substrates assayed,
AB  - including the chromosomal DNA of this species and several bacteriophage DNAs,
AB  - were completely degraded in vitro by the enzyme.  The rate of synthesis of the
AB  - nuclease depended on the growth medium.  In NBG medium, in which the enzyme is
AB  - not produced, the size of lytic plaques of several actinophages was larger than
AB  - that in GYM or GAE medium, in which synthesis of the nuclease takes place late
AB  - in growth.  In addition, one of the phages assayed, PhiA6, showed a diminution
AB  - of its efficiency of plating in GYM medium with respect to that in NBG medium;
AB  - another phage, PhiA9, grew in NBG medium but not in the other two media.  It is
AB  - postulated that the presence of the host nuclease, together with the capability
AB  - of the particular phage to adsorb on S. antibioticus of different growth
AB  - phases, determines the efficiency of growth and the plaque size of the phages
AB  - on productive media.  This hypothesis was confirmed when the growth of PhiA6
AB  - and PhiA9 in a mutant of S. antibioticus lacking the endonuclease activity was
AB  - analyzed.  It is concluded that the enzyme can assume, under some
AB  - circumstances, a role in in vivo restriction.
ER  -

TY  - JOUR
AU  - de los Reyes-Gavilan, C.G.
AU  - Limsowtin, G.K.Y.
AU  - Sechaud, L.
AU  - Veaux, M.
AU  - Accolas, J.-P.
TI  - Evidence for a plasmid-linked restriction-modification system in Lactobacillus helveticus.
JO  - Appl. Environ. Microbiol.
PY  - 1990
SP  - 3412
EP  - 3419
VL  - 56
AB  - The presence of a restriction-modification (R/M) system against two
AB  - bacteriophages, 328-B1 and hv, was demonstrated in three Lactobacillus
AB  - helveticus strains, CNRZ 1094, CNRZ 1095, and CNRZ 1096.  In addition, the
AB  - burst size of phage 328-B1 in the three restrictive strains CNRZ 1094, CNRZ
AB  - 1095, and CNRZ 1096 was reduced with respect to the values obtained in its
AB  - propagating strain, CNRZ 328.  Heating at 60C did not inactivate the R/M
AB  - system.  Nonrestrictive variants from CNRZ 1094 were easily obtained under
AB  - several culture conditions, but treatment with novobiocin at 42C followed by
AB  - storage at -20C resulted in drastic elimination of the R+/M+ phenotype from all
AB  - clones tested.  Electrophoretic analysis of CNRZ 1084 nonrestrictive variants
AB  - revealed the concomitant loss of a 34-kb plasmid.  Four EcoRI fragments from
AB  - the 34-kb plasmid were cloned in the Escherichia coli vector pACYC184.  The use
AB  - of one or several of these fragments as probes confirmed the plasmidic location
AB  - of the genes responsible for the R/M system.  These probes also showed the
AB  - presence of R/M plasmids in the two other restriction strains, CNRZ 1095 and
AB  - CNRZ 1096.  Lactose-fermenting ability and/or proteolytic capacity was not
AB  - linked to the 34-kb plasmid.
ER  -

TY  - JOUR
AU  - De Luca, S.
AU  - Nicholson, P.
AU  - Magistrali, C.F.
AU  - Garcia-Martin, A.B.
AU  - Rychener, L.
AU  - Zeeh, F.
AU  - Frey, J.
AU  - Perreten, V.
TI  - Transposon-associated lincosamide resistance lnu(C) gene identified in Brachyspira hyodysenteriae ST83.
JO  - Vet. Microbiol.
PY  - 2018
SP  - 51
EP  - 55
VL  - 214
AB  - Treatment of Swine Dysentery (SD) caused by Brachyspira hyodysenteriae (B. hyodysenteriae) is
AB  - carried out using antimicrobials such as macrolides, lincosamides and pleuromutilins leading
AB  - to the selection of resistant strains.  Whole genome sequencing of a multidrug-resistant B.
AB  - hyodysenteriae strain called BH718 belonging to sequence type (ST) 83 revealed the presence of
AB  - the lincosamide resistance gene lnu(C) on the small 1724-bp transposon MTnSag1. The strain
AB  - also contains an A to T substitution at position 2058 (A2058T) in the 23S rRNA gene which is
AB  - known to be associated with macrolide and lincosamide resistance in B. hyodysenteriae. Testing
AB  - of additional strains showed that those containing lnu(C) exhibited a higher minimal
AB  - inhibitory concentration (MIC) of lincomycin
AB  - (MIC64 mg/L) compared to strains lacking lnu(C), even if they also harbor the A2058T mutation.
AB  - Resistance to pleuromutilins could not be explained by the presence of already reported
AB  - mutations in the 23S rRNA gene and in the ribosomal protein L3. This study shows that B.
AB  - hyodysenteriae has the ability to acquire mobile genetic elements conferring resistance to
AB  - antibiotics.
ER  -

TY  - JOUR
AU  - De Maayer, P.
AU  - Chan, W.Y.
AU  - Rezzonico, F.
AU  - Buhlmann, A.
AU  - Venter, S.N.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Frey, J.E.
AU  - Smits, T.H.
AU  - Duffy, B.
AU  - Coutinho, T.A.
TI  - Complete Genome Sequence of Clinical Isolate Pantoea ananatis LMG 5342.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1615
EP  - 1616
VL  - 194
AB  - The enterobacterium Pantoea ananatis is an ecologically versatile species. It has been found
AB  - in the environment, as plant epiphyte and endophyte, as an emerging
AB  - phytopathogen, and as a presumptive, opportunistic human pathogen. Here, we
AB  - report the complete genome sequence of P. ananatis LMG 5342, isolated from a
AB  - human wound.
ER  -

TY  - JOUR
AU  - De Maayer, P.
AU  - Chan, W.Y.
AU  - Venter, S.N.
AU  - Toth, I.K.
AU  - Birch, P.R.
AU  - Joubert, F.
AU  - Coutinho, T.A.
TI  - Genome sequence of Pantoea ananatis LMG20103, the causative agent of Eucalyptus blight and dieback.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2936
EP  - 2937
VL  - 192
AB  - Pantoea ananatis is a Gram-negative plant pathogen that causes disease on a broad range of
AB  - host plants, including pineapple, maize, rice, onion, melons, and Eucalyptus, and has been
AB  - implicated in several cases of human disease. Here, we report the genome sequence of P.
AB  - ananatis LMG20103
AB  - isolated from diseased Eucalyptus in South Africa.
ER  -

TY  - JOUR
AU  - De Maayer, P.
AU  - Williamson, C.E.
AU  - Vennard, C.T.
AU  - Danson, M.J.
AU  - Cowan, D.A.
TI  - Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739.
JO  - Genome Announcements
PY  - 2014
SP  - e00567
EP  - e00514
VL  - 2
AB  - Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are
AB  - therefore of interest in biotechnological applications. Here we report
AB  - the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739
AB  - and CAMR5420.
ER  -

TY  - JOUR
AU  - de Man, T.J.
AU  - Perry, K.A.
AU  - Avillan, J.J.
AU  - Rasheed, J.K.
AU  - Limbago, B.M.
TI  - Draft Genome Sequence of a New Delhi Metallo-beta-Lactamase-5 (NDM-5)-Producing Multidrug-Resistant Escherichia coli Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00017
EP  - e00015
VL  - 3
AB  - A multidrug-resistant Escherichia coli isolate from an abdominal lesion displayed resistance
AB  - to all beta-lactams tested, including carbapenems, in addition to
AB  - macrolides, fluoroquinolones, and tetracycline. Sequence analyses demonstrated
AB  - the presence of blaNDM-5 in addition to at least 13 genes and 6 efflux pumps
AB  - associated with antibiotic resistance.
ER  -

TY  - JOUR
AU  - de Man, T.J.
AU  - Perry, K.A.
AU  - Lawsin, A.
AU  - Coulliette, A.D.
AU  - Jensen, B.
AU  - Toney, N.C.
AU  - Limbago, B.M.
AU  - Noble-Wang, J.
TI  - Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00138
EP  - e00116
VL  - 4
AB  - Mycobacterium wolinskyi is a nonpigmented, rapidly growing nontuberculous mycobacterium
AB  - species that is associated with bacteremia, peritonitis, infections
AB  - associated with implants/prostheses, and skin and soft tissue infections often
AB  - following surgical procedures in humans. Here, we report the first functionally
AB  - annotated draft genome sequence of M. wolinskyi CDC_01.
ER  -

TY  - JOUR
AU  - de Mello, S.S.
AU  - Van Tyne, D.
AU  - Dabul, A.N.
AU  - Gilmore, M.S.
AU  - Camargo, I.L.
TI  - High-Quality Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Enterococcus faecium VRE16.
JO  - Genome Announcements
PY  - 2016
SP  - e00992
EP  - e00916
VL  - 4
AB  - Specific lineages of the commensal bacterium Enterococcus faecium belonging to CC17,
AB  - especially ST412, have been isolated from patients in several hospitals
AB  - worldwide and harbor antibiotic resistance genes and virulence factors. Here, we
AB  - report a high-quality draft genome sequence and highlight features of E. faecium
AB  - VRE16, a representative of this ST.
ER  -

TY  - JOUR
AU  - de Melo, A.G.
AU  - Labrie, S.J.
AU  - Dumaresq, J.
AU  - Roberts, R.J.
AU  - Tremblay, D.M.
AU  - Moineau, S.
TI  - Complete Genome Sequence of Brevibacterium linens SMQ-1335.
JO  - Genome Announcements
PY  - 2016
SP  - e01242
EP  - e01216
VL  - 4
AB  - Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened
AB  - cheeses. The genome of the industrial strain SMQ-1335 was
AB  - sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open
AB  - reading frames, and 61 structural RNAs. A new type I restriction-modification
AB  - system was identified.
ER  -

TY  - JOUR
AU  - De Meyer, S.E.
AU  - Fabiano, E.
AU  - Tian, R.
AU  - Van Berkum, P.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Howieson, J.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 31
EP  - 31
VL  - 10
AB  - Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod
AB  - that was isolated from a root nodule of Parapiptadenia
AB  - rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A
AB  - survey of symbionts of P. rigida in Uruguay demonstrated that this species is
AB  - nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia
AB  - sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this
AB  - host. Currently, the only other sequenced isolate to fix with this host is
AB  - Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was
AB  - selected for sequencing on the basis of its environmental and agricultural
AB  - relevance to issues in global carbon cycling, alternative energy production, and
AB  - biogeochemical importance, and is part of the GEBA-RNB project. Here we describe
AB  - the features of Burkholderia sp. strain UYPR1.413, together with sequence and
AB  - annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in
AB  - 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only
AB  - encoding genes.
ER  -

TY  - JOUR
AU  - De Meyer, S.E.
AU  - Fabiano, E.
AU  - Tian, R.
AU  - Van Berkum, P.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Howieson, J.
AU  - Kyrpides, N.C.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 13
EP  - 13
VL  - 10
AB  - Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod
AB  - that was isolated from a root nodule of Parapiptadenia
AB  - rigida grown in soils from a native forest of Uruguay. Here we describe the
AB  - features of Cupriavidus sp. strain UYPR2.512, together with sequence and
AB  - annotation. The 7,858,949 bp high-quality permanent draft genome is arranged in
AB  - 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only
AB  - encoding genes, and is part of the GEBA-RNB project proposal.
ER  -

TY  - JOUR
AU  - De Meyer, S.E.
AU  - Nguyen, D.T.
AU  - Wang, P.
AU  - Andrews, M.
TI  - Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535T, a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp.
JO  - Genome Announcements
PY  - 2017
SP  - e00958
EP  - e00917
VL  - 5
AB  - We report here the complete genome sequence of Mesorhizobium sophorae ICMP 19535T This strain
AB  - was isolated from Sophora microphylla root nodules and can nodulate
AB  - and fix nitrogen with this host and also with Sophora prostrata, Sophora
AB  - longicarinata, and Clianthus puniceus The genome consists of 8.05 Mb.
ER  -

TY  - JOUR
AU  - De Meyer, S.E.
AU  - Parker, M.
AU  - Van Berkum, P.
AU  - Tian, R.
AU  - Seshadri, R.
AU  - Reddy, T.B.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Kyrpides, N.
AU  - Howieson, J.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of the Mimosa asperata - nodulating  Cupriavidus sp. strain AMP6.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 80
EP  - 80
VL  - 10
AB  - Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that
AB  - was isolated from a root nodule of Mimosa asperata
AB  - collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata
AB  - is the only legume described so far to exclusively associates with Cupriavidus
AB  - symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the
AB  - symbiotic Cupriavidus group and has the capacity to develop an effective
AB  - nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the
AB  - genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic
AB  - trait evolution in this genus and here we describe the general features, together
AB  - with sequence and annotation. The 7,579,563 bp high-quality permanent draft
AB  - genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding
AB  - genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project
AB  - proposal.
ER  -

TY  - JOUR
AU  - De Meyer, S.E.
AU  - Tian, R.
AU  - Seshadri, R.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Yates, R.
AU  - Howieson, J.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 64
EP  - 64
VL  - 10
AB  - Burkholderia dilworthii strain WSM3556(T) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia
AB  - ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in
AB  - October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is
AB  - therefore an ideal candidate for a perennial based agriculture system in Western Australia.
AB  - WSM3556(T) thus represents a potential inoculant quality strain for L. ambigua for which we
AB  - describe the general features, together with genome sequence and annotation. The 7,679,067 bp
AB  - high-quality permanent draft genome is arranged in 140 scaffolds of 141 contigs,  contains
AB  - 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project
AB  - proposal.
ER  -

TY  - JOUR
AU  - De Meyer, S.E.
AU  - Tian, R.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Kyrpides, N.
AU  - Yates, R.
AU  - Howieson, J.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 79
EP  - 79
VL  - 10
AB  - Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod
AB  - that was isolated from an effective N2-fixing root nodule
AB  - of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in
AB  - October 2007. This plant persists in infertile, acidic and deep sandy soils, and
AB  - is therefore an ideal candidate for a perennial based agriculture system in
AB  - Western Australia. Here we describe the features of Burkholderia sp. strain
AB  - WSM4176, which represents a potential inoculant quality strain for L. ambigua,
AB  - together with sequence and annotation. The 9,065,247 bp high-quality-draft genome
AB  - is arranged in 13 scaffolds of 65 contigs, contains 8369 protein-coding genes and
AB  - 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal
AB  - (Project ID 882).
ER  -

TY  - JOUR
AU  - de Oliveira, L.G.
AU  - Tormet, G.G.D.
AU  - Samborsky, M.
AU  - Marcon, J.
AU  - Araujo, W.L.
AU  - de Azevedo, J.L.
TI  - Genome Sequence of Streptomyces wadayamensis Strain A23, an Endophytic Actinobacterium from Citrus reticulata.
JO  - Genome Announcements
PY  - 2014
SP  - e00625
EP  - e00614
VL  - 2
AB  - The actinobacterium Streptomyces wadayamensis A23 is an endophyte of Citrus reticulata that
AB  - produces the antimycin and mannopeptimycin antibiotics, among
AB  - others. The strain has the capability to inhibit Xylella fastidiosa growth. The
AB  - draft genome of S. wadayamensis A23 has ~7.0 Mb and 6,006 protein-coding
AB  - sequences, with a 73.5% G+C content.
ER  -

TY  - JOUR
AU  - de Oliveira-Veras, A.A. et al.
TI  - Draft Genome Sequences of Vibrio fluvialis Strains 560 and 539, Isolated from Environmental Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e01344
EP  - e01314
VL  - 3
AB  - Vibrio fluvialis is a halophilic bacterium found in many environments and is mainly associated
AB  - with sporadic cases and outbreaks of gastroenteritis in humans.
AB  - Here, we describe the genome sequences of environmental strains of V. fluvialis
AB  - 560 (Vf560) and V. fluvialis 539 (Vf539) possessing a variant of the integrative
AB  - and conjugative element (ICE) SXT for the first time in Brazil and South America.
ER  -

TY  - JOUR
AU  - de Padua-Pereira, U. et al.
TI  - Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 188
EP  - 197
VL  - 8
AB  - Streptococcus agalactiae (Lancefield group B; GBS) is the causative agent of
AB  - meningoencephalitis in fish, mastitis in cows, and neonatal sepsis in humans.
AB  - Meningoencephalitis is a major health problem for tilapia farming and is
AB  - responsible for high economic losses worldwide. Despite its importance, the
AB  - genomic characteristics and the main molecular mechanisms involved in virulence
AB  - of S. agalactiae isolated from fish are still poorly understood. Here, we present
AB  - the genomic features of the 1,820,886 bp long complete genome sequence of S.
AB  - agalactiae SA20-06 isolated from a meningoencephalitis outbreak in Nile tilapia
AB  - (Oreochromis niloticus) from Brazil, and its annotation, consisting of 1,710
AB  - protein-coding genes (excluding pseudogenes), 7 rRNA operons, 79 tRNA genes and
AB  - 62 pseudogenes.
ER  -

TY  - JOUR
AU  - de Sa, P.C.
AU  - Da Silva, M.L.
AU  - Carneiro, A.R.
AU  - Gomes, J.C.
AU  - Dias, L.M.
AU  - Alves, J.T.
AU  - De Oliveira, V.A.A.
AU  - Barauna, R.A.
AU  - Das Gracas, D.A.
AU  - Matte, M.H.
AU  - Sato, M.I.
AU  - Hachich, E.M.
AU  - Matte, G.R.
AU  - Ramos, R.T.
AU  - Silva, A.
TI  - Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19.
JO  - Genome Announcements
PY  - 2014
SP  - e01094
EP  - e01014
VL  - 2
AB  - Vibrio cholerae O1 is the causative agent of cholera and is ubiquitous in the aquatic
AB  - environment, while V. cholerae strains non-O1 and non-O139 are recognized
AB  - as causative agents of sporadic and localized outbreaks of diarrhea. Here, we
AB  - report the complete sequence of a non-O1 and non-O139 V. cholerae strain (VCC19),
AB  - which was isolated from the environment in Brazil. The sequence includes the
AB  - integrative conjugative element (ICE). This paper is the first report of the
AB  - presence of such an element in a V. cholerae strain isolated in Brazil.
ER  -

TY  - JOUR
AU  - de Siqueira, K.A.
AU  - Liotti, R.G.
AU  - Mendes, T.A.O.
AU  - Soares, M.A.
TI  - Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.)  Ducke].
JO  - Genome Announcements
PY  - 2018
SP  - e00287
EP  - e00218
VL  - 6
AB  - Pseudomonas sp. strain 382 and Pantoea coffeiphila 342 are two endophytic bacterial strains
AB  - isolated from Paullinia cupana (guarana) seeds. Their draft
AB  - genome sizes were 5.96 and 6.38 Mbp, with 315 and 266 scaffolds and 52% and 62%
AB  - GC content, respectively.
ER  -

TY  - JOUR
AU  - de Siqueira, K.A.
AU  - Mello, I.S.
AU  - Pietro-Souza, W.
AU  - Mendes, T.A.O.
AU  - Soares, M.A.
TI  - Draft Genome Sequence of the Mercury-Resistant Strain Acinetobacter baumannii I43.
JO  - Genome Announcements
PY  - 2018
SP  - e00283
EP  - e00218
VL  - 6
AB  - Here, we report the draft genome sequence of the Acinetobacter baumannii strain I43, which is
AB  - highly resistant to mercury. The Illumina-based sequence analysis
AB  - revealed a genome of approximately 4,520,353 bp composed of 4,091 coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - de Souza, J.A.
AU  - Tieppo, E.
AU  - Magnani, G.S.
AU  - Alves, L.M.
AU  - Cardoso, R.L.
AU  - Cruz, L.M.
AU  - de Oliveira, L.F.
AU  - Raittz, R.T.
AU  - de Souza, E.M.
AU  - Pedrosa, F.O.
AU  - Lemos, E.G.
TI  - Draft Genome Sequence of the Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium elkanii 587.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3547
EP  - 3548
VL  - 194
AB  - The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained
AB  - using Illumina Next-Gen DNA sequencing combined with Sanger
AB  - sequencing. Genes for the pathways involved in biological nitrogen fixation (the
AB  - nif gene cluster), nod genes including nodABC, and genes for the type III protein
AB  - secretion system (T3SS) are present.
ER  -

TY  - JOUR
AU  - de Souza, R.
AU  - Sant'Anna, F.H.
AU  - Ambrosini, A.
AU  - Tadra-Sfeir, M.
AU  - Faoro, H.
AU  - Pedrosa, F.O.
AU  - Souza, E.M.
AU  - Passaglia, L.M.
TI  - Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.
JO  - Genome Announcements
PY  - 2015
SP  - e00249
EP  - e00215
VL  - 3
AB  - Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it
AB  - presents plant growth-promoting abilities. The nutrient uptake in
AB  - rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is
AB  - composed of 5,233,443-bp and harbors 5,079 coding sequences.
ER  -

TY  - JOUR
AU  - de Souza, R.
AU  - Sant'Anna, F.H.
AU  - Ambrosini, A.
AU  - Tadra-Sfeir, M.
AU  - Faoro, H.
AU  - Pedrosa, F.O.
AU  - Souza, E.M.
AU  - Passaglia, L.M.
TI  - Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils.
JO  - Genome Announcements
PY  - 2015
SP  - e00248
EP  - e00215
VL  - 3
AB  - Pseudomonas sp. FeS53a was isolated from the roots of rice plants cultivated in one area with
AB  - a well-established history of iron toxicity. The FeS53a genome
AB  - sequence provides the genetic basis for understanding its lifestyle and survival
AB  - in association with rice in conditions of iron toxicity.
ER  -

TY  - JOUR
AU  - de Souza, V.
AU  - Piro, V.C.
AU  - Faoro, H.
AU  - Tadra-Sfeir, M.Z.
AU  - Chicora, V.K.
AU  - Guizelini, D.
AU  - Weiss, V.
AU  - Vialle, R.A.
AU  - Monteiro, R.A.
AU  - Steffens, M.B.
AU  - Marchaukoski, J.N.
AU  - Pedrosa, F.O.
AU  - Cruz, L.M.
AU  - Chubatsu, L.S.
AU  - Raittz, R.T.
TI  - Draft Genome Sequence of Herbaspirillum huttiense subsp. putei IAM 15032, a Strain Isolated from Well Water.
JO  - Genome Announcements
PY  - 2013
SP  - e00252
EP  - e00212
VL  - 1
AB  - Here we report the one-scaffold draft genome of subsp. strain 7-2 (IAM 15032), which was
AB  - isolated from well water.
ER  -

TY  - JOUR
AU  - de Souza, Y.P.A.
AU  - da Mota, F.F.
AU  - Rosado, A.S.
TI  - Draft Genome Sequence of Geobacillus sp. LEMMY01, a Thermophilic Bacterium Isolated from the Site of a Burning Grass Pile.
JO  - Genome Announcements
PY  - 2017
SP  - e00200
EP  - e00217
VL  - 5
AB  - We report here the 3,586,065-bp draft genome of Geobacillus sp. LEMMY01, which was isolated
AB  - (axenic culture) from a thermophilic chemolitoautotrophic consortium
AB  - obtained from the site of a burning grass pile. The genome contains biosynthetic
AB  - gene clusters coding for secondary metabolites, such as terpene and lantipeptide,
AB  - confirming the biotechnological potential of this strain.
ER  -

TY  - JOUR
AU  - De Vries, D.R.
AU  - Martin, A.L.
AU  - Ganz, H.H.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3.
JO  - Genome Announcements
PY  - 2016
SP  - e01386
EP  - e01316
VL  - 4
AB  - Here, we present the draft genome sequence of Enterococcus faecalis strain UCD-PD3. The
AB  - assembly contains 2,861,314 bp in 73 contigs. This strain was
AB  - isolated from a feral domestic cat (Felis catus) anal sac secretion sample, as
AB  - part of a project on isolating and characterizing the microbes present in feline
AB  - anal sacs.
ER  -

TY  - JOUR
AU  - de Vries, G.E.
AU  - Harms, N.
AU  - Hoogendijk, J.
AU  - Stouthamer, A.H.
TI  - Isolation and characterization of Paracoccus denitrificans mutants with increased conjugation frequencies and pleiotropic loss of a (nGATCn) DNA-modifying property.
JO  - Arch. Microbiol.
PY  - 1989
SP  - 52
EP  - 57
VL  - 152
AB  - A selection scheme was devised to isolate Paracoccus denitrificans mutants with
AB  - increased recipient qualities in transfer experiments, using broad host range
AB  - plasmids.  In some of the mutants obtained, a DNA modifying activity that
AB  - prevents the activity of the restriction endonucleases BamHI and BglII on
AB  - isolated P. denitrificans DNA had simultaneously been lost.  From a detailed
AB  - analysis of the restriction properties of the enzymes Sau3AI, MboI and DpnI, it
AB  - was concluded that a subset of GATC sequences in P. denitrificans DNA may be
AB  - methylated at an unusual position.  It was concluded that P. denitrificans
AB  - possesses at least one potent host-dependent restriction/modification system
AB  - which affects conjugation.  In addition to the class of enhanced transfer
AB  - mutants, at least one other class of enhanced transfer mutants with unknown
AB  - defect(s) was isolated.  Strains, in which the two mutant classes were
AB  - combined, exhibited transfer frequencies which were significantly higher than
AB  - strains containing either mutation alone.  Such double mutant strains appeared
AB  - to be well suited for future experiments like complementation analysis,
AB  - transposon mutagenesis and gene replacement by homologous recombination.
ER  -

TY  - JOUR
AU  - de Vries, H.J.
AU  - Marshall, I.P.G.
AU  - Schreiber, L.
AU  - Plugge, C.M.
TI  - Draft Genome Sequence of Sphingomonas sp. Strain Sph1(2015), Isolated from a Fouled Membrane Filter Used To Produce Drinking Water.
JO  - Genome Announcements
PY  - 2017
SP  - e00517
EP  - e00517
VL  - 5
AB  - We report here the high-quality draft genome sequence of Sphingomonas sp. strain  Sph1(2015),
AB  - isolated from a fouled reverse osmosis membrane used for the
AB  - production of high-quality drinking water. The draft sequence provides insights
AB  - into the modus operandi of this strain to form biofilms on membrane surfaces.
AB  - This knowledge offers tools to develop novel antifouling strategies.
ER  -

TY  - JOUR
AU  - De Vries, N.
AU  - Duinsbergen, D.
AU  - Kuipers, E.J.
AU  - Pot, R.G.J.
AU  - Wiesenekker, P.
AU  - Penn, C.W.
AU  - Van Vliet, A.H.M.
AU  - Vandenbroucke-Grauls, C.M.J.E.
AU  - Kusters, J.G.
TI  - Transcriptional phase variation of a Type III restriction-modification system in Helicobacter pylori.
JO  - J. Bacteriol.
PY  - 2002
SP  - 6615
EP  - 6623
VL  - 184
AB  - Phase variation is important in bacterial pathogenesis, since it generates
AB  - antigenic variation for the evasion of immune responses and provides a
AB  - strategy for quick adaptation to environmental changes. In this study, a
AB  - Helicobacter pylori clone, designated MOD525, was identified that
AB  - displayed phase-variable lacZ expression. The clone contained a
AB  - transcriptional lacZ fusion in a putative type III DNA methyltransferase
AB  - gene (mod, a homolog of the gene JHP1296 of strain J99), organized in an
AB  - operon-like structure with a putative type III restriction endonuclease
AB  - gene (res, a homolog of the gene JHP1297), located directly upstream of
AB  - it. This putative type III restriction-modification system was common in
AB  - H. pylori, as it was present in 15 out of 16 clinical isolates. Phase
AB  - variation of the mod gene occurred at the transcriptional level both in
AB  - clone MOD525 and in the parental H. pylori strain 1061. Further analysis
AB  - showed that the res gene also displayed transcriptional phase variation
AB  - and that it was cotranscribed with the mod gene. A homopolymeric cytosine
AB  - tract (C tract) was present in the 5' coding region of the res gene.
AB  - Length variation of this C tract caused the res open reading frame (ORF)
AB  - to shift in and out of frame, switching the res gene on and off at the
AB  - translational level. Surprisingly, the presence of an intact res ORF was
AB  - positively correlated with active transcription of the downstream mod
AB  - gene. Moreover, the C tract was required for the occurrence of
AB  - transcriptional phase variation. Our finding that translation and
AB  - transcription are linked during phase variation through slipped-strand
AB  - mispairing is new for H. pylori.
ER  -

TY  - JOUR
AU  - de Vries, N.
AU  - Duinsbergen, D.
AU  - Kuipers, E.J.
AU  - Wiesenekker, P.
AU  - Vandenbroucke-Grauls, C.M.
AU  - Kusters, J.G.
TI  - Phase variation in a type III restriction-modification system of Helicobacter pylori.
JO  - Gastroenterology
PY  - 2000
SP  - A736
EP  - A736
VL  - 118
AB  - The on- and off-switching of the expression of virulence factors (phase variation) plays an
AB  - important role in the pathogenesis of many bacterial infections.  LPS phase variation in
AB  - Helicobacter pylori occurs at the translational level and has been studied well.  In contrast,
AB  - phase variation at the transcriptional level has not been demonstrated in H. pylori.
AB  - Therefore, we investigated transcriptional on- and off-switching of gene expression in H.
AB  - pylori.  Methods: A library with random genomic transcriptional lacZ fusions in H. pylori
AB  - strain 1061 (HP1061) was screened for mutants that showed blue and white sectored colonies on
AB  - X-Gal.  As the X-Gal substrate is converted into a blue product when the lacZ gene is
AB  - expressed into the beta-galactosidase, sectored colonies indicate transcriptional phase
AB  - variation.  Results: One HP1061 mutant displayed frequent on- and off-switching of lacZ
AB  - expression.  The on-to-off switch frequency was 2.67%, while the off-to-on frequency was
AB  - 0.75%.  Sequencing revealed that the lacZ gene was fused to a putative type III methylase gene
AB  - (mod).  RNA spot blot hybridization demonstrated that specific lacZ and mod probes bound to
AB  - mRNA from blue colonies, but not to mRNA from white colonies.  This proved that mod switched
AB  - on and off a the transcriptional level.  An open reading frame, encoding a putative type III
AB  - restriction enzyme gene (res), is located immediately upstream of mod and contains a
AB  - polynucleotide C-tract.  This C-tract, which may cause phase variation of res through
AB  - translational frameshifts, might indirectly act on the transcription of mod.  However,
AB  - sequence analysis showed that the number of cytosines in res was not related to the on- or
AB  - off-status of mod. Conclusion: In H. pylori, the putative type III methylase gene, mod,
AB  - displays phase variation at the transcriptional level.  It is known that methylation of
AB  - promoter sequences can affect the transcription of bacterial virulence factors.  We propose a
AB  - specific role of mod and related restriction-modification systems in H. pylori in the
AB  - regulation of virulence genes.
ER  -

TY  - JOUR
AU  - de Vries, N.
AU  - Duinsbergen, D.
AU  - Kuipers, E.J.
AU  - Wiesenekker, P.
AU  - Vandenbroucke-Grauls, C.M.J.
AU  - Kusters, J.G.
TI  - Transcriptional phase variation in a type III restriction modification system of Helicobacter pylori.
JO  - Gut
PY  - 2000
SP  - A17
EP  - A17
VL  - 47
AB  - Phase variation of virulence genes is important in the pathogenesis of many bacterial
AB  - infections.  So far, phase variation at the transcriptional level has not been demonstrated in
AB  - H. pylori.  Here, we report for the first time transcriptional phase variation in H. pylori.
AB  - An H. pylori 1061 library with random genomic transcriptional lacZ fusions was screened for
AB  - transformants showing blue, white and sectored colonies on X-Gal.  This phenotype indicated a
AB  - fusion of lacZ to a gene displaying transcriptional phase variation.  In one transformant
AB  - showing sectored colonies, lacZ was inserted in a putative type III methylase gene (mod).  An
AB  - endonuclease gene (res) was located immediately upstream of mod and contained a C-tract, which
AB  - may cause translational frameshifting.  Blue colonies tended to have 14 Cs, which results in
AB  - the translation of res.  In contrast, white colonies contained C-tract lengths leading to
AB  - disruption of the open reading frame.  RNA spot blots and RT-PCR indicated that mod displayed
AB  - transcriptional phase variation, as mod mRNA was only present in blue colonies, and not in
AB  - white colonies.  Res was transcribed both in blue and in white colonies.  In H. pylori 1061 a
AB  - type III methylase gene displays transcriptional phase variation.  Translational frameshifting
AB  - of the upstream endonuclease gene may be involved in the regulation of mod phase variation.
AB  - Since DNA methylation can affect the transcription of bacterial virulence factors, we propose
AB  - that mod and related restriction-modification systems play a role in the regulation of the
AB  - expression of virulence genes in H. pylori.
ER  -

TY  - JOUR
AU  - de Waard, A.
AU  - Duyvesteyn, M.
TI  - Are sequence-specific deoxyribonucleases of value as taxonomic markers of cyanobacterial species?
JO  - Arch. Microbiol.
PY  - 1980
SP  - 242
EP  - 247
VL  - 128
AB  - Three nucleotide sequence-specific deoxyribonucleases present in extracts of
AB  - Anabaena subcylindrica have been purified and characterized.  Endo R AsuI
AB  - recognizes and cleaves the nucleotide sequence G^GNCC (Hughes et al., 1980)
AB  - while Endo R AsuII and III split the sequences TT^CGAA and GPu^CGPyC,
AB  - respectively (this paper).  An Anabaena strain "Waterbury" converging
AB  - genetically at the 30-35% level with both A. subcylindrica and A. cylindrica
AB  - (as judged by DNA-DNA hybridization in vitro) was shown to possess the
AB  - endonuclease pattern typical for A. cylindrica (de Waard et al., 1978).  The
AB  - usefulness of these specific endonucleases as taxonomic markers for the
AB  - classifiction of cyanobacteria is discussed.
ER  -

TY  - JOUR
AU  - de Waard, A.
AU  - Korsuize, J.
AU  - van Beveren, C.P.
AU  - Maat, J.
TI  - A new sequence-specific endonuclease from Anabaena cylindrica.
JO  - FEBS Lett.
PY  - 1978
SP  - 106
EP  - 110
VL  - 96
AB  - The isolation of sequence-specific endodeoxyribonucleases from the cyanophytes
AB  - Anabaena variabilis (ATCC 27892), Anabaena subcylindrica (CCAP 1403/4b) and
AB  - Anabaena catenula (CCAP 1403/1) has been reported.  We have found a new
AB  - endonuclease from Anabaena cylindrica (CCAP 1403/2a) and describe here the
AB  - procedure of its isolation as well as the elucidation of the nucleotide
AB  - sequences: 5' G Pu ^ C G Py C 3' 3' C Py G C ^ Pu G 5' recognized by the
AB  - purified enzyme AcyI.
ER  -

TY  - JOUR
AU  - de Waard, A.
AU  - van Beveren, C.P.
AU  - Duyvesteyn, M.
AU  - van Ormondt, H.
TI  - Two sequence-specific endonucleases from Anabaena oscillarioides.
JO  - FEBS Lett.
PY  - 1979
SP  - 71
EP  - 76
VL  - 101
AB  - There has been an increasing number of reports on sequence-specific
AB  - endodeoxyribonucleases (endo.R.) in cyanobacteria (blue-green algae).  As their
AB  - cleavage specificities have proven to be different from those of the many
AB  - bacterial restriction enzymes already characterized, these new enzymes have
AB  - been useful additions to the ever expanding endo R. catalog.  We report here
AB  - the isolation of two such endonucleases from one strain of Anabaena
AB  - oscillarioides (AosI and II) which cleave the nucleotide sequences 5'TGC^GCA3'
AB  - and 5'GPu^CGPyC3', respectively.
ER  -

TY  - JOUR
AU  - de Wit, C.M.
AU  - Dekker, B.M.M.
AU  - Neele, A.C.
AU  - de Waard, A.
TI  - Purification and characterization of endonucleases DraII and III from Deinococcus radiophilus.
JO  - FEBS Lett.
PY  - 1985
SP  - 219
EP  - 223
VL  - 180
AB  - Deinococcus radiophilus strain ATCC 27603 contains, apart from endonuclease
AB  - DraI, two additional sequence-specific endonucleases.  These enzymes,
AB  - designated DraII and DraIII, recognize nucleotide sequences with novel
AB  - specificities, PuG^GNCCPy and CACNNN^GTG, respectively.
ER  -

TY  - JOUR
AU  - Dean, A.B.
AU  - Stanger, M.J.
AU  - Dansereau, J.T.
AU  - Van Roey, P.
AU  - Derbyshire, V.
AU  - Belfort, M.
TI  - Zinc finger as distance determinant in the flexible linker of intron  endonuclease I-TevI.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 8554
EP  - 8561
VL  - 99
AB  - l-Tevl, the phage T4 td intron-encoded endonuclease, recognizes a  lengthy DNA target and
AB  - initiates intron mobility by introducing a
AB  - double-strand break in the homing site. The enzyme uses both sequence and
AB  - distance determinants to cleave the DNA 23-25 bp upstream of the intron
AB  - insertion site. l-Tevl consists of an N-terminal catalytic domain and a
AB  - C-terminal DNA-binding domain separated by a long, flexible linker. The
AB  - DNA-binding domain consists of three subdomains: a zinc finger, a
AB  - minor-groove binding a-helix, and a helix-turn-helix. In this study, a
AB  - mutational analysis was undertaken to assess the roles of these subdomains
AB  - in substrate binding and cleavage. Surprisingly, the zinc finger is not
AB  - required for DNA binding or catalysis. Rather, the zinc finger is a
AB  - component of the linker and directs the catalytic domain to cleave the
AB  - homing site at a fixed distance from the intron insertion site. When the
AB  - cleavage site (CS) is shifted outside a given range, wild-type l-Tevl
AB  - defaults to the fixed distance, whereas zinc-finger mutants have lost the
AB  - distance determinant and search out the displaced cleavage sequences.
AB  - Although counterintuitive, a protein containing a 19-aa deletion of the
AB  - zinc finger can extend further than can wild-type l-Tevl to cleave a
AB  - distant CS sequence, and a Cys-to-Ala mutant of the ligands for zinc,
AB  - nominally a longer protein, can retract to cleave at a closer CS sequence.
AB  - Models are presented for the novel function of the zinc finger, as a
AB  - molecular constraint, whereby intramolecular protein-protein interactions
AB  - position the catalytic domain by "catalytic clamp" and/or
AB  - "linker-organizer" mechanisms.
ER  -

TY  - JOUR
AU  - Dean, P.D.C.
AU  - Walker, J.N.B.
TI  - Recent advances in high-performance liquid affinity chromatography columns.
JO  - Biochem. Soc. Trans.
PY  - 1985
SP  - 1055
EP  - 1058
VL  - 13
AB  - For the initial isolation of restriction endonucleases from crude extracts we
AB  - have found that 1 ml of quaternary aminoethyl 'Mono-Q' strong anion-exchange
AB  - column is ideal.  All the restriction enzymes we studies were eluted between
AB  - 0.2 and 0.6m-KCl.  This has enabled us to get to up a rapid screening program
AB  - for novel type-II restriction endonuclease activities.  the profile of enzyme
AB  - activities from an extract of a cyanobacterium Nostoc SA, incubated with lambda
AB  - DNA, shows four separate restriction enzymes of different specificity.  These
AB  - enzyme fractions were separately digested with other DNA substrates.  These and
AB  - other experiments lead us to conclude that the enzymes were NspSAI
AB  - (C-Y-C-G-R-G), NspSAII (G-G-T-N-A-C-C), NspSAIII (C-C-A-T-G-G), NspSAIV
AB  - (G-G-A-T-C-C) and were isoschizomers of AvaI, BstEII, NcoI and BamHI,
AB  - respectively.  The distribution of cytosines and guanines in each cutting site
AB  - is interestingly consistent.  We have found that the purity of these and other
AB  - enzymes after a single Mono Q column step is sufficient not only for
AB  - characterization of their specificity on a series of substrates, but also to
AB  - carry out analysis of the termini of the cutting sites using a modified form of
AB  - M13 sequencing.
ER  -

TY  - JOUR
AU  - Dean, S.N.
AU  - Vora, G.J.
AU  - Walper, S.A.
TI  - Complete Genome Sequence of Lactobacillus acidophilus Strain ATCC 53544.
JO  - Genome Announcements
PY  - 2017
SP  - e01138
EP  - e01117
VL  - 5
AB  - Here we present the complete genome sequence of Lactobacillus acidophilus ATCC 53544. The
AB  - assembly contains 1,991,906 bp and is 99.7% similar to L. acidophilus
AB  - NCFM. This strain was isolated from a rectal swab specimen of an infant and has
AB  - previously been used as a feed supplement for animals.
ER  -

TY  - JOUR
AU  - Deangelis, K.M.
AU  - D'Haeseleer, P.
AU  - Chivian, D.
AU  - Fortney, J.L.
AU  - Khudyakov, J.
AU  - Simmons, B.
AU  - Woo, H.
AU  - Arkin, A.P.
AU  - Davenport, K.W.
AU  - Goodwin, L.
AU  - Chen, A.
AU  - Ivanova, N.
AU  - Kyrpides, N.C.
AU  - Mavromatis, K.
AU  - Woyke, T.
AU  - Hazen, T.C.
TI  - Complete genome sequence of 'Enterobacter lignolyticus' SCF1.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 69
EP  - 85
VL  - 5
AB  - In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated
AB  - 'Enterobacter lignolyticus' SCF1 on minimal media with alkali lignin as
AB  - the sole source of carbon. This organism was isolated anaerobically from tropical
AB  - forest soils collected from the Short Cloud Forest site in the El Yunque National
AB  - Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research
AB  - Station. At this site, the soils experience strong fluctuations in redox
AB  - potential and are net methane producers. Because of its ability to grow on lignin
AB  - anaerobically, we sequenced the genome. The genome of 'E. lignolyticus' SCF1 is
AB  - 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of
AB  - lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in
AB  - culture, and the genome revealed two putative laccases, a putative peroxidase,
AB  - and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single
AB  - gene cluster.
ER  -

TY  - JOUR
AU  - DeBacker, O.
AU  - Chomez, P.
AU  - DePlaen, E.
TI  - Positive selection of recombinant plasmids based on the EcoK restriction activity of Escherichia coli K-12.
JO  - Gene
PY  - 1994
SP  - 197
EP  - 198
VL  - 150
AB  - We have constructed a pTZ19R-derived vector which allows efficient positive selection of
AB  - recombinant plasmids. The system uses the EcoK restriction activity of Escherichia coli K-12
AB  - to select against non-recombinant plasmids. The vector contains an EcoK site which, if deleted
AB  - or disrupted by ligating a DNA fragment, yields recombinant plasmids that are no longer
AB  - suceptible to EcoK restriction when transformed into a restriction-proficient E. coli host.
ER  -

TY  - JOUR
AU  - DeBoy, R.T.
AU  - Mongodin, E.F.
AU  - Fouts, D.E.
AU  - Tailford, L.E.
AU  - Khouri, H.
AU  - Emerson, J.B.
AU  - Mohamoud, Y.
AU  - Watkins, K.
AU  - Henrissat, B.
AU  - Gilbert, H.J.
AU  - Nelson, K.E.
TI  - Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.
JO  - J. Bacteriol.
PY  - 2008
SP  - 5455
EP  - 5463
VL  - 190
AB  - The plant cell wall, which consists of a highly complex array of interconnecting
AB  - polysaccharides, is the most abundant source of organic
AB  - carbon in the biosphere. Microorganisms that degrade the plant cell wall
AB  - synthesize an extensive portfolio of hydrolytic enzymes that display
AB  - highly complex molecular architectures. To unravel the intricate
AB  - repertoire of plant cell wall-degrading enzymes synthesized by the
AB  - saprophytic soil bacterium Cellvibrio japonicus, we sequenced and analyzed
AB  - its genome, which predicts that the bacterium contains the complete
AB  - repertoire of enzymes required to degrade plant cell wall and storage
AB  - polysaccharides. Approximately one-third of these putative proteins (57)
AB  - are predicted to contain carbohydrate binding modules derived from 13 of
AB  - the 49 known families. Sequence analysis reveals approximately 130
AB  - predicted glycoside hydrolases that target the major structural and
AB  - storage plant polysaccharides. In common with that of the colonic
AB  - prokaryote Bacteroides thetaiotaomicron, the genome of C. japonicus is
AB  - predicted to encode a large number of GH43 enzymes, suggesting that the
AB  - extensive arabinose decorations appended to pectins and xylans may
AB  - represent a major nutrient source, not just for intestinal bacteria but
AB  - also for microorganisms that occupy terrestrial ecosystems. The results
AB  - presented here predict that C. japonicus possesses an extensive range of
AB  - glycoside hydrolases, lyases, and esterases. Most importantly, the genome
AB  - of C. japonicus is remarkably similar to that of the gram-negative marine
AB  - bacterium, Saccharophagus degradans 2-40(T). Approximately 50% of the
AB  - predicted C. japonicus plant-degradative apparatus appears to be shared
AB  - with S. degradans, consistent with the utilization of plant-derived
AB  - complex carbohydrates as a major substrate by both organisms.
ER  -

TY  - JOUR
AU  - Debroas, D.
AU  - Humbert, J.F.
AU  - Enault, F.
AU  - Bronner, G.
AU  - Faubladier, F.
AU  - Cornillot, C.
TI  - Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget - France).
JO  - Environ. Microbiol.
PY  - 2009
SP  - 2412
EP  - 2424
VL  - 11
AB  - The main goals of this work were to identify the metabolic pathways of the
AB  - bacterial community in a lacustrine ecosystem and to establish links
AB  - between taxonomic composition and the relative abundances of these
AB  - metabolic pathways. For this purpose, we analysed a 16S rRNA gene library
AB  - obtained by gene amplification together with a sequence library of both
AB  - insert ends on c. 7700 fosmids. Whatever the library used, Actinobacteria
AB  - was the most abundant bacterial group, followed by Proteobacteria and
AB  - Bacteroidetes. Specific aquatic clades such as acI and acIV
AB  - (Actinobacteria) or LD12 and GOBB-C201 (Alphaproteobacteria) were found in
AB  - both libraries. From comparative analysis of metagenomic libraries, the
AB  - metagenome of this lake was characterized by overrepresentation of genes
AB  - involved in the degradation of xenobiotics mainly associated with
AB  - Alphaproteobacteria. Actinobacteria were mainly related to metabolic
AB  - pathways involved in nucleotide metabolism, cofactors, vitamins, energy,
AB  - replication and repair. Betaproteobacteria appeared to be characterized by
AB  - the presence of numerous genes implicated in environmental information
AB  - processing (membrane transport and signal transduction) whereas glycan and
AB  - carbohydrate metabolism pathways were overrepresented in Bacteroidetes.
AB  - These results prompted us to propose hypotheses on the ecological role of
AB  - these bacterial classes in lacustrine ecosystems.
ER  -

TY  - JOUR
AU  - Debrouwere, L.
AU  - Zabeau, M.
AU  - Van Montagu, M.
AU  - Schell, J.
TI  - The ral gene of phage lambda.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 75
EP  - 80
VL  - 179
AB  - The lambda ral function modulates the restriction and modification activities
AB  - of the Escherichia coli K12 and B restriction enzymes (Zabeau et al., 1980).
AB  - In order to further analyse this function, ral deficient mutants have been
AB  - isolated, using a method which exploits the property of the strong mutagen
AB  - N-methyl-N'-nitro-N-nitrosoguanidine (N.G.) to induce multiple closely linked
AB  - mutations.  Hence, mutagenized phages carrying mutations in one locus were
AB  - frequently found to contain additional mutations in adjacent loci.  This very
AB  - efficient mutagenesis procedure enabled us to isolate 27 independent Ral
AB  - deficient mutants.  Seven mutants were found to affect the ral gene directly
AB  - and were located between the genes N and cIII.  Detailed mapping of two of
AB  - these mutants showed that the lambda ral gene is located at position 70.6-70.9%
AB  - on the physical map.  The isolation and characterization of these mutants
AB  - further supports the conclusion that ral is a gene different from the N gene,
AB  - and demonstrates that the ral gene product is responsible for both
AB  - counteracting restriction and enhancing modification.
ER  -

TY  - JOUR
AU  - Debroy, S.
AU  - Bhattacharjee, A.
AU  - Thakur, A.R.
AU  - Raychaudhuri, S.
TI  - Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008.
JO  - Genome Announcements
PY  - 2013
SP  - e00189
EP  - e00112
VL  - 1
AB  - Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus
AB  - sp. strain MCC0008, isolated from a consortium
AB  - enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of
AB  - the genome is 5,609,456 bp, with a G+C content of 35.1%.
ER  -

TY  - JOUR
AU  - Debroy, S.
AU  - Mukherjee, P.
AU  - Roy, S.
AU  - Thakur, A.R.
AU  - Raychaudhuri, S.
TI  - Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009.
JO  - Genome Announcements
PY  - 2013
SP  - e00254
EP  - e00212
VL  - 1
AB  - The draft genome sequence (5,868,741 bp) of a nitrate- and phosphate-removing sp., WBUNB009,
AB  - isolated from a raw sewage canal in nitrate broth (Himedia M439)
AB  - with a G+C content of 34.9% is reported. It removes 60.23% nitrate and 96%
AB  - phosphate within 16 h at 37 degrees C.
ER  -

TY  - JOUR
AU  - Debroy, S.
AU  - Mukherjee, P.
AU  - Roy, S.
AU  - Thakur, A.R.
AU  - Raychaudhuri, S.
TI  - Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004.
JO  - Genome Announcements
PY  - 2013
SP  - e00251
EP  - e00212
VL  - 1
AB  - The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive sp. with optimum
AB  - growth at 37 degrees C and pH 7 in nitrate broth (HiMedia M439)
AB  - isolated from rhizosphere of a water lily, with a genome size of 5,465,157 bp and
AB  - a G+C content of 35.0%, is reported here.
ER  -

TY  - JOUR
AU  - Debruyn, J.M.
AU  - Radosevich, M.
AU  - Wommack, K.E.
AU  - Polson, S.W.
AU  - Hauser, L.J.
AU  - Fawaz, M.N.
AU  - Korlach, J.
AU  - Tsai, Y.C.
TI  - Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum.
JO  - Genome Announcements
PY  - 2014
SP  - e00226
EP  - e00214
VL  - 2
AB  - Bacteria belonging to the phylum Gemmatimonadetes are found in a wide variety of  environments
AB  - and are particularly abundant in soils. Here, we present the complete genome sequence and
AB  - methylation pattern of the newly described Gemmatirosa kalamazoonensis type strain.
ER  -

TY  - JOUR
AU  - Decatur, W.A.
AU  - Johansen, S.
AU  - Vogt, V.M.
TI  - Expression of the Naegleria intron endonuclease is dependent on a functional group I self-cleaving ribozyme.
JO  - RNA
PY  - 2000
SP  - 616
EP  - 627
VL  - 6
AB  - NaSSU1 is a complex nuclear group I intron found in several species of Naegleria, consisting
AB  - of a large self-splicing group I ribozyme (NaGIR2), which itself is interrupted by a small,
AB  - group I-like ribozyme (NaGIR1) and an open reading frame (ORF) coding for a homing
AB  - endonuclease. The GIR1 ribozyme cleaves in vitro transcripts of NaSSU1 at two internal
AB  - processing sites about 400 nt downstream of the 5' end of the intron, proximal to the
AB  - endonuclease ORF. Here we demonstrate that self-cleavage of the excised intron also occurs in
AB  - vivo in Naegleria gruberi, generating an ORF-containing RNA that possesses a short leader with
AB  - a sequence element likely to be involved in gene expression. To assess the functional
AB  - significance of self-cleavage, we constructed a genetic system in Saccharomyces cerevisiae.
AB  - First, a mutant yeast strain was selected with a mutation in all the rRNA genes, rendering the
AB  - rDNA resistant to cleavage by the Naegleria endonuclease. Active endonuclease, which is
AB  - otherwise lethal, could be expressed readily in these cells. Endonuclease activity also could
AB  - be detected in extracts of yeast harboring plasmids in which the endonuclease ORF was embedded
AB  - in its native context in the intron. Analysis of the RNA from these yeast cells showed that
AB  - the excised intron RNA was processed as in N. gruberi. A mutant intron constructed to prevent
AB  - self-cleavage of the RNA failed to express endonuclease activity. These results support the
AB  - hypothesis that the NaGIR1-catalyzed self-cleavage of the intron RNA is a key event in
AB  - expression of the endonuclease.
ER  -

TY  - JOUR
AU  - Deckert, G.
AU  - Warren, P.V.
AU  - Gaasterland, T.
AU  - Young, W.G.
AU  - Lenox, A.L.
AU  - Graham, D.E.
AU  - Overbeek, R.
AU  - Snead, M.A.
AU  - Keller, M.
AU  - Aujay, M.
AU  - Huber, R.
AU  - Feldman, R.A.
AU  - Short, J.M.
AU  - Olson, G.J.
AU  - Swanson, R.V.
TI  - The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.
JO  - Nature
PY  - 1998
SP  - 353
EP  - 358
VL  - 392
AB  - Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic,
AB  - bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The
AB  - complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an
AB  - organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical
AB  - energy source) is encoded within a genome that is only one-third the size of the E. coli
AB  - genome. Metabolic flexibility seems to be reduced as a result of the limited genome size. The
AB  - use of oxygen (albeit at very low concentrations) as an electron acceptor is allowed by the
AB  - presence of a complex respiratory apparatus. Although this organism grows at 95 degrees C, the
AB  - extreme thermal limit of the Bacteria, only a few specific indications of thermophily are
AB  - apparent from the genome. Here we describe the complete genome sequence of 1,551,335 base
AB  - pairs of this evolutionarily and physiologically interesting organism.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
TI  - New DNA methyltransferase M.AjnI from the bacterium Acinetobacter johnsonii R2 produces the 5'-m5CCWGG-3' sequence.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 2010
SP  - 849
EP  - 853
VL  - 46
AB  - Optimum conditions for the activity of the new DNA methylase in cell lysate were determined.
AB  - Methylation of DNAs of bacteriophages lambda
AB  - and T7 and plasmid pBR322 (dcm+) in the 5'-Cm5CWGG-3' region blocked
AB  - M.AjnI activity. The specificity of M.AjnI was determined using lambda
AB  - DNA methylated by this enzyme as well as computer modeling and data on
AB  - the sensitivity of restriction endonucleases Mval, HinfI, and BstMAI to
AB  - methylation.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
TI  - Analysis of specificity of DNA-methyltransferase M.AspS9I in cell lysate by means of restriction endonuclease blocking.
JO  - Biotekhnologiya
PY  - 2009
SP  - 30
EP  - 39
VL  - 0
AB  - Specificity of DNA-methyltransferase M.AspS9I has been determined using cell lysate of
AB  - Arthrobacter species S9.  To this end, we employed methylation sensitivity of restriction
AB  - endonucleases and also modeling of the methylation process.  Modeling consisted of editing DNA
AB  - sequences by substitution of letters for methylated bases and their complementary bases.
AB  - Substrate DNA treated by M.AspS9I were used for studying of sensitivity of some restriction
AB  - endonucleases to methylation.  Thus it was shown that the overlapping dcm-methylation did not
AB  - block the M.AspS9I activity.  The suggested approach can appear universal and simple enough
AB  - for determining DNA-methyltransferases specificity.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
TI  - Defining specificity of DNA methyltransferase M.Bsc4I in cellular lysate by blocking restriction endonucleases and computer modeling.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 2009
SP  - 3
EP  - 8
VL  - 0
AB  - The specificity of DNA methyltransferase M.Bsc4I was determined in cellular lysate of Bacillus
AB  - schlegelii 4.  The methylation sensitivity of restriction endonucleases and methylation
AB  - modeling were used for this purpose.  Modeling consisted of editing DNA sequences using
AB  - replacements of methylated bases and their complementary bases.  Substrate DNA treated with
AB  - M.Bsc4I were used to study the sensitivity of some restrictases to methylation.  It was shown
AB  - that M.Bsc4I methylated 5'-Cm4CNNNNNNNGG-3' and overlapping dcm-methylation blocked its
AB  - activity.  The suggested approach would be universal and simple for determining the
AB  - specificity of DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
TI  - Determining of G+C Content in Bacterial DNA using Restriction Endonucleases.
JO  - Biotekhnologiya
PY  - 2004
SP  - 77
EP  - 82
VL  - 4
AB  - Bacterial DNAs were cleaved by restriction endonucleases (restrictases) recognizing sequences
AB  - of G and C or A and T nucleotides. Experimental curves were obtained for determination G+C
AB  - content in bacterial DNA. The developed express-method is supposed to be helpful for
AB  - restriction cleavage of bacterial lysates DNA, bacteria identification separation of microbial
AB  - isolates in to strains and also for determining DNA methylases.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
TI  - Novel M.BstC8I methyltransferase forms 5'-G(m5C)NNGC-3'. Investigation of restriction endonuclease sensitivity to M.BstC8I methylation.
JO  - Mol. Genet. Microbiol. Virol.
PY  - 2012
SP  - 40
EP  - 47
VL  - 27
AB  - A novel M.BstC8I DNA methylase was detected in cell lysate of Bacillus stearothermophilus C8
AB  - grown on Luria agar at 37A degrees C. DNA
AB  - methylation of bacteriophages lambda and T7 in the 5'-G(m5C)NNGC-3'
AB  - segment blocked the activity of the BstC8I restrictase. The specificity
AB  - of the M.BstC8I was analyzed on methylated lambda DNA and using
AB  - computer modeling and the data on the sensitivity of BstC8I, BsuRI,
AB  - AjnI, and PvuII restrictases to methylation. The sensitivity of a
AB  - number of restrictases to the novel type of methylation was shown. The
AB  - results can be used for study of DNA methylation.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
TI  - New DNA methyltransferase M.AjnI from Acinetobacter johnsonii R2 produces 5'-m5CCWGG-3' sequence.
JO  - Biotekhnologiya
PY  - 2010
SP  - 36
EP  - 40
VL  - 0
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Bondar, T.S.
AU  - Shevchenco, A.V.
AU  - Degtyarev, S.K.
TI  - New rare-cutting restriction endonuclease SmiI from Streptococcus milleri recognizes 5'-ATTT/AAAT-3'.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 2000
SP  - 23
EP  - 27
VL  - 1
AB  - A new restriction endonuclease (restrictase) SmiI of type II was detected in the bacterial
AB  - strain Streptococcus milleri. Cellular lysate enzyme cut T7 and adenovirus-2 DNAs at site
AB  - 5'-ATTT/AAAT-3' but not lambda DNA, which does not contain this sequence. Intensive aeration
AB  - inhibited the growth of S. milleri. The content of restrictase in cells was the greatest
AB  - during the logarithmic growth phase. A total of 20,000 units of SmiI were isolated from 4 g of
AB  - cells by cellular extract fractionation with ammonium sulfate and subsequent chromatography on
AB  - columns with Bio Gel A 0.5 m, heparin agarose, and phosphocellulose. The purified enzyme cut
AB  - the synthetic oligonucleotide duplex in the center of the recognized site 5'-ATTT/AAAT-3'.
AB  - SmiI restrictase is a true isoschizomer of the rare-cutting SwaI enzyme. SmiI belongs to a
AB  - small group of enzymes which recognize octanucleotide sites and can be used for large-block
AB  - fragmentation of DNA. Comparison of specificities of rare-cutting and other restrictases
AB  - suggests that the enzymes recognizing octanucleotides can evolutionarily originate from
AB  - enzymes recognizing both hexanucleotides and tetranucleotides.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - Actinobacillus and Streptococcus: producers of isoschizomers of the restriction endonucleases R.HphI, R.SauI, R.NheI, R.MboI and R.SwaI.
JO  - Biol. Chem.
PY  - 1998
SP  - 573
EP  - 574
VL  - 379
AB  - New restriction endonucleases have been found in microorganisms isolated from the microflora
AB  - of human teeth.  The strain-producers are Actinobacillus suis and Streptococcus milleri.  The
AB  - new enzymes are isoschizomers of the prototypes as follows: AsuHPI-HphI; AsuSAI-SauI;
AB  - AsuNHI-NheI; AsuMBI and SmiMBI-MboI; SmiI-rare-cutter SwaI.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Degtyarev, S.K.
TI  - Detection of restriction endonucleases in Streptomyces and Nocardia cells.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1992
SP  - 309
EP  - 313
VL  - 28
AB  - A simple technique is proposed for the detection of restriction endonucleases in Streptomyces
AB  - and Nocardia cells. The analysis was performed directly in the cells collected from colonies
AB  - cultivated on Petri dishes with an innoculation loop. The cells were treated with lyzozyme,
AB  - EDTA and Triton X-100. The lysates were tested for restriction endonucleases. The technique
AB  - enables the detection of enzymes NcoI, NotI, NruI, Sfr303I, and SfiI in the lysates of the
AB  - respective strains-producers.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Udalyeva, S.G.
AU  - Urumceva, L.A.
AU  - Chernukhin, V.A.
AU  - Mutylo, G.V.
AU  - Degtyarev, S.K.
TI  - Cloning and Study of New DNA Methyltransferase M.FatI Modifying Cytosine in a Recognition Site CATG.
JO  - Res. J. Pharm. Biol. Chem. Sci.
PY  - 2015
SP  - 1341
EP  - 1348
VL  - 6
AB  - A fragment of Flavobacterium aquatile NL3 DNA carrying the gene of DNA methyltransferase
AB  - M.FatI was cloned in pUC19 plasmid. DNA was sequenced and M.FatI gene was analyzed. A
AB  - recombinant strain Esherichia coli was grown up and the enzyme was purified. M.FatI
AB  - specificity was determined by a blocking of some restriction endonucleases and computer
AB  - modeling. It's well known that M.NlaIII produces 5'-C(m6A)TG-3', whereas FatI MTase
AB  - modifies the cytosine residue with formation 5'-(m5C)ATG-3'. The sensitivity of restriction
AB  - endonucleases to FatI-methylation has been studied.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Udalyeva, S.G.
AU  - Urumceva, L.A.
AU  - Chernukhin, V.A.
AU  - Shiryaeva, E.N.
AU  - Degtyarev, S.K.
TI  - Cloning and study of new DNA methyltransferase M.AluBI modifying adenine in a recognition site AGCT.
JO  - Biotecnol. Apl.
PY  - 2015
SP  - 3211
EP  - 3216
VL  - 32
AB  - A fragment of Arthrobacter luteus B DNA carrying the gene of new DNA methyltransferase M.AluBI
AB  - was cloned and expressed in Escherichia coli. The recombinant plasmid pM.AluBI-16 contains the
AB  - M.AluBI gene (1515 bp in length), corresponding to a protein of 504 amino acid residues. The
AB  - amino acid sequence analysis showed that M.AluBI could be an adenine-(N6)-DNA
AB  - methyltransferase. A recombinant strain was grown up and the enzyme was purified by a
AB  - consecutive chromatography on P-11 Phosphocellulose, Heparin-Sepharose, Sephacryl S-200 and
AB  - Hydroxyapatite. M.AluBI specificity was determined by the original method based on blocking of
AB  - restriction endonucleases cleavage of overlapped sites and on computer modeling. It was first
AB  - shown that AluBI MTase modifies the adenine residue with formation of 5&#180;-(m6A)GCT-3&#180;
AB  - as opposed to its prototype, M.AluI, producing 5&#180;-AG(m5C)T-3&#180;. A comparative
AB  - sensitivity analysis of different, well known restriction endonucleases to the methylation by
AB  - M.AluBI and M.AluI was done using &#955; and T7 phage DNA. The newly acquired data on
AB  - methylation sensitivity cold be useful for conducting experiments on DNA digestion with
AB  - restriction endonucleases, and especially with the particular cleavage sensitivity pattern
AB  - generated with the M.AluBI methyltransferase enzyme.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Gonchar, D.A.
AU  - Chernukhin, V.A.
AU  - Abdurashitov, M.A.
AU  - Udalyeva, S.G.
AU  - Urumceva, L.A.
AU  - Degtyarev, S.K.
TI  - New DNA methyltransferase M.AgsI produces TTSA(m6A).
JO  - Biotechnology: an Indian Journal
PY  - 2016
SP  - 100
EP  - 106
VL  - 12
AB  - Agrococcus species 25 DNA was cloned in pUC19 plasmid of Escherichia coli. Cloned DNA fragment
AB  - contained two Opened Reading Frames with 8 amino acid motives which belonged to amino DNA
AB  - methyltransferases. Thus M.AgsI can be the first of subunit adenine-(N6)-DNA
AB  - methyltransferase. The enzyme was purified from the recombinant strain by chromatography on
AB  - P-11 Phosphocellulose, Heparin-Sepharose and Hydroxyapatite. M.AgsI specificity was determined
AB  - by a study of protection of lambda DNA methylated with M.AgsI against cleavage with some
AB  - restriction endonucleases. A sensitivity of restriction endonucleases to M.AgsI-methylation
AB  - was studied.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Kileva, E.V.
AU  - Popichenko, D.V.
AU  - Degtyarev, S.K.
TI  - FatI restriction endonuclease from Flavobacterium aquatile NL3 cleaves DNA at 5'-^CATG-3' site.
JO  - Biotekhnologiya
PY  - 2002
SP  - 3
EP  - 7
VL  - 5
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Djanobilova, Z.K.
AU  - Tarasova, M.V.
TI  - A M.BssECI DNA Methyltransferase Forms 5 '-m4CCNNGG-3 '. Sensitivity of Restriction Endonucleases to the New Methylation.
JO  - Biotekhnologiya
PY  - 2012
SP  - 32
EP  - 42
VL  - 2
AB  - A novel DNA methyltransferase, M.BssECI, has been isolated and purified from Bacillus
AB  - stearothermophilus EC cells. The enzyme methylates a
AB  - surface cytosine residue in a 5'-CCNNGG-3' sequence with the formation
AB  - of N4-methylcytosine, 5'-m4CCNNGG-3'. The approaches to enzyme
AB  - isolation, purification (gel-filtration on a Biogel A-0,5m with the
AB  - following chromatography on benzyl-DEAE-cellulose and
AB  - heparin-Sepharose) and identification of the methylated DNA sequence
AB  - were developed. The optimum conditions and the activity of the novel
AB  - methyltransferase were determined using phage X. DNA on the basis of
AB  - the BssECI restriction endonuclease blockage. A base that was
AB  - methylated within the recognized sequence was detected using the
AB  - [H-3]-labeling of the oligonucleotide duplex. The specificity of
AB  - M.BssECI was investigated using self-methylated Adeno-2 DNA taking into
AB  - account the sensitivity of the BssECI, MvaI and MspI restriction
AB  - endonucleases to methylated DNA; computer modeling was also employed.
AB  - The isolated enzyme can be used in studying of character of DNA
AB  - methylation; in particular, it permitted to distinguish the
AB  - m4C-methylated cytosine from m5C. DNAs of phages lambda and T7
AB  - methylated by M.BssECI were applied to the investigation of the
AB  - sensitivity of some restriction endonucleases to the methylation of
AB  - their recognition sites.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Vlasenko, L.P.
AU  - Tomilova, J.E.
AU  - Kashirina, J.G.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Restriction Endonuclease AjnI from Acinetobacter johnsonii R2, an Isoschizomer of EcoRII, recognizes 5'- CCWGG-3' and cleaves dcm-methylated sites.
JO  - Biotekhnologiya
PY  - 2004
SP  - 19
EP  - 24
VL  - 3
AB  - A producer of restriction endonuclease AjnI has been isolated from natural resources and
AB  - identified as bacterial species Acinetobacter johnsonii R2. The restriction enzyme
AB  - purification and estimation of its activity is described. It has been shown that AjnI produces
AB  - DNA fragments with 5'-CCWGG sticky ends similar to EcoRII, but cleavage is not blocked by
AB  - dcm-methylation. A new restriction endonuclease AjnI may be widely used in genetic
AB  - engineering.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Nayakshina, T.N.
AU  - Popichenko, D.V.
AU  - Degtyarev, S.K.
TI  - Restriction endonuclease BmtI from Bacillus megaterium S2 cleaves DNA at 5'-GCTAG^C-3' site.
JO  - Biotekhnologiya
PY  - 2003
SP  - 11
EP  - 15
VL  - 1
AB  - A new strain producer of a BmtI restriction endonuclease (restrictase) has been found out and
AB  - identified as bacteria species Bacillus
AB  - megaterium S2. The scheme of purification and several characteristics
AB  - of the enzyme are described. BmtI is a heteroschizomer of the well
AB  - known NheI enzyme (recognition sequence 5'-GdwnarwCTAGC-3'). It
AB  - produces DNA fragments with CTAG-3' extending ends. BmtI restrictase
AB  - may be used in genetic engineering.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Prihodko, G.G.
AU  - Puchkova, L.I.
AU  - Serov, G.D.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
TI  - SsrI - a Type II restriction endonuclease from Staphylococcus saprophyticus cells.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1989
SP  - 24
EP  - 27
VL  - 11
AB  - The recognition sequence and cleavage site for restriction endonuclease SsrI have been
AB  - determined, the latter being 5'-GTT^AAC-3'.  The enzyme was isolated from Staphyloccus
AB  - saprophyticus and may be used in DNA investigation instead of its isoschizomer HpaI.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Rechkunova, N.I.
AU  - Prihodko, E.A.
AU  - Kileva, E.V.
AU  - Kusner, Y.S.
AU  - Verchozina, V.A.
AU  - Degtyarev, S.K.
TI  - CciNI, an isoschizomer of NotI from Curtobacterium citreum recognizes 5'-GC/GGCCGC-3'.
JO  - Gene
PY  - 1995
SP  - 99
EP  - 100
VL  - 157
AB  - CciNI, an isoschizomer of NotI, has been isolated from Curtobacterium citreum.  The enzyme
AB  - cleaves within the recognition sequence 5'-GC/GGCCGC-3' as indicated by the slash.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Repin, V.E.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
AU  - Verhosina, V.A.
AU  - Vinogradova, T.P.
TI  - Screening of strains producing restriction endonucleases in Lake Baikal.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1990
SP  - 35
EP  - 37
VL  - 1
AB  - Screening of bacterial strains which produce restriction endonucleases was
AB  - performed.  It was shown that strains Flavobacterium aquatile, Hafnia alvei,
AB  - Acinetobacter calcoaceticus, Pseudomonas gladioli were producers of
AB  - restrictases FauI, HalI and HalII, Aca I, PgaI, respectively.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Sinichkina, S.A.
AU  - Abdurashitov, M.A.
AU  - Popichenko, D.V.
AU  - Degtyarev, S.K.
TI  - Restriction endonucleases FalI and FalII from Flavobacterium aquatile Ob10 recognize 5'-(8/13)AAGN5CTT(13/8)-3' and 5'-CG^CG-3',  respectively.
JO  - Biotekhnologiya
PY  - 2003
SP  - 24
EP  - 29
VL  - 6
AB  - We have isolated from water supplies a strain Flavobacterium aquatile Ob10 which produces two
AB  - restriction endonucleases FalI and FalII.  FalI is a new prototype and recognizes the DNA
AB  - sequence that follows: 5'-(8/13)AAGN5CTT(13/8)-3'.  FalI is stimulated by
AB  - S-adenosylmethionine and cleaves DNA on both sides of its recognition sequence.  Thus, FalI
AB  - belongs to the BcgI-subtype of restriction endonucleases.  The recognition sequence for FalII
AB  - restriction
AB  - endonuclease is 5'-CG/CG-3' and this enzyme is thus an isoschizomer of FnuDII.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Sinichkina, S.A.
AU  - Popichenko, D.V.
AU  - Degtyarev, S.K.
TI  - Restriction endonuclease ZraI from Zoogloea ramigera 11 recognizes 5'-GAC/GTC-3'.
JO  - Biotekhnologiya
PY  - 2001
SP  - 3
EP  - 7
VL  - 6
AB  - A producer of restriction endonuclease (restrictase) from natural isolates has been obtained
AB  - and identified as bacteria species Zoogloea ramigera II, while the restrictase was named ZraI.
AB  - The way of the purification and estimation of the enzyme activity is described.  It was shown
AB  - that ZraI produces blunt ended DNA fragments.  The restrictase is promising for the wide use
AB  - in gene engineering.
ER  -

TY  - JOUR
AU  - Dedkov, V.S.
AU  - Zernov, Y.P.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
TI  - Isolation of aquatic microorganisms producing the restriction endonucleases from the Black Sea.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1990
SP  - 17
EP  - 18
VL  - 0
AB  - 300 clones of microorganisms isolated at different stations and from different
AB  - depths in the Black Sea were screened for restriction endonucleases was found
AB  - in 17 clones screened.  Three of them were identified to be Alteromonas
AB  - haloplanktis Bl. Restriction endonuclease AhaBI is an isoschizomer of Sau96I.
AB  - An identified Alteromonas haloplanktis clone B8 produces AhaB8I restriction
AB  - endonuclease the prototype of which is KpnI.  Of the clones isolated three are
AB  - Moraxella species B4 producing MspB4I restriction endonuclease analogous to
AB  - BanI, three are Bacillus species producing BspB2I and one is Micrococcus lylae
AB  - 113 producing Mly1131 analogue of NarI, six Moraxella species B6 produce
AB  - MspB6I.  The isolated producer strains may be used for isolation of
AB  - above-mentioned restriction endonucleases.
ER  -

TY  - JOUR
AU  - Dedysh, S.N.
AU  - Naumoff, D.G.
AU  - Vorobev, A.V.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Shapiro, N.
AU  - Crombie, A.T.
AU  - Murrell, J.C.
AU  - Kalyuzhnaya, M.G.
AU  - Smirnova, A.V.
AU  - Dunfield, P.F.
TI  - Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase.
JO  - Genome Announcements
PY  - 2015
SP  - e01555
EP  - e01514
VL  - 3
AB  - Methyloferula stellata AR4 is an aerobic acidophilic methanotroph, which, in contrast to most
AB  - known methanotrophs but similar to Methylocella spp., possesses
AB  - only a soluble methane monooxygenase. However, it differs from Methylocella spp.
AB  - by its inability to grow on multicarbon substrates. Here, we report the draft
AB  - genome sequence of this bacterium.
ER  -

TY  - JOUR
AU  - Deep, K.
AU  - Poddar, A.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Anoxybacillus suryakundensis Strain JS1T (DSM 27374T) Isolated from a Hot Spring in Jharkhand, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00824
EP  - e00816
VL  - 4
AB  - Anoxybacillus suryakundensis strain JS1(T), a facultative anaerobic, moderately thermophilic,
AB  - alkalitolerant bacterium, was isolated from a hot spring. The
AB  - estimated genome is 2.6 Mb and encodes 2,668 proteins.
ER  -

TY  - JOUR
AU  - DeFilippes, F.M.
TI  - A simple assay for DNA restriction endonucleases.
JO  - Anal. Biochem.
PY  - 1973
SP  - 637
EP  - 641
VL  - 52
AB  - Recently several groups have used restriction enzymes to produce a limited
AB  - number of unique, double stranded DNA fragments from the genome of SV40 virus
AB  - and the double stranded replicative form of bacteriophage PhiX174.
ER  -

TY  - JOUR
AU  - DeFilippes, F.M.
TI  - A new method for isolation of a restriction enzyme from Haemophilus parainfluenzae.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1974
SP  - 586
EP  - 596
VL  - 58
AB  - A rapid procedure which gives high yields of the restriction enzyme HpaI from
AB  - Hemophilus parainfluenzae is described.  The procedure effectively removes a
AB  - second restriction enzyme HpaII as well as exonucleolytic activity.  The
AB  - optimal ionic conditions for the enzyme are similar to those found for one of
AB  - the enzymes isolated from Hemophilus influenzae.  The enzyme is stable at 37C
AB  - for several hours but it is rapidly inactivated at 60C.  Patterns are presented
AB  - which show the electropohoretic separation of the digestion products of two
AB  - viral DNAs by this enzyme.
ER  -

TY  - JOUR
AU  - Defossez, P.-A.
TI  - Ceci n'est pas une DNMT: Recently discovered functions of DNMT2 and their relation to methyltransferase activity (Comment on DOI 10.1002/bies.201300088).
JO  - Bioessays
PY  - 2013
SP  - 1024
EP  - 1024
VL  - 35
ER  -

TY  - JOUR
AU  - Degnan, P.H.
AU  - Yu, Y.
AU  - Sisneros, N.
AU  - Wing, R.A.
AU  - Moran, N.A.
TI  - Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 9063
EP  - 9068
VL  - 106
AB  - Eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria.
AB  - Hamiltonella defensa, an endosymbiont of
AB  - aphids and other sap-feeding insects, protects its aphid host from attack
AB  - by parasitoid wasps. Thus H. defensa is only conditionally beneficial to
AB  - hosts, unlike ancient nutritional symbionts, such as Buchnera, that are
AB  - obligate. Similar to pathogenic bacteria, H. defensa is able to invade
AB  - naive hosts and circumvent host immune responses. We have sequenced the
AB  - genome of H. defensa to identify possible mechanisms that underlie its
AB  - persistence in healthy aphids and protection from parasitoids. The 2.1-Mb
AB  - genome has undergone significant reduction in size relative to its closest
AB  - free-living relatives, which include Yersinia and Serratia species
AB  - (4.6-5.4 Mb). Auxotrophic for 8 of the 10 essential amino acids, H.
AB  - defensa is reliant upon the essential amino acids produced by Buchnera.
AB  - Despite these losses, the H. defensa genome retains more genes and
AB  - pathways for a variety of cell structures and processes than do obligate
AB  - symbionts, such as Buchnera. Furthermore, putative pathogenicity loci,
AB  - encoding type-3 secretion systems, and toxin homologs, which are absent in
AB  - obligate symbionts, are abundant in the H. defensa genome, as are
AB  - regulatory genes that likely control the timing of their expression. The
AB  - genome is also littered with mobile DNA, including phage-derived genes,
AB  - plasmids, and insertion-sequence elements, highlighting its dynamic nature
AB  - and the continued role horizontal gene transfer plays in shaping it.
ER  -

TY  - JOUR
AU  - deGraaff, J.
AU  - Kreuning, P.C.
AU  - van de Putte, P.
TI  - Host controlled restriction and modification of bacteriophage mu and mu-promoted chromosome mobilization in Citrobacter freundii.
JO  - Mol. Gen. Genet.
PY  - 1973
SP  - 283
EP  - 288
VL  - 123
AB  - Bacteriophage Mu grown on Escherichia coli K12 (Mu.K) is restricted by wild
AB  - type Citrobacter freundii.  In two C. freundii mutants, where the restriction
AB  - of foreign F' factors is absent (de Graaff and Stouthamer, 1971), the
AB  - restriction for Mu.K., although at a lower level, still exists.  Consequently
AB  - two host specificity systems exist in C. freundii, one affecting mainly the
AB  - acceptance of foreign plasmid and chromosomal DNA and one affecting foreign DNA
AB  - of bacteriophage Mu.  Mu is able to lysogenize C. freundii and to induce
AB  - mutations at random in its chromosome.  Furthermore Mu is able to promote the
AB  - mobilization of the C. freundii chromosome in strains carrying F' factors.  Mu
AB  - promoted integration of F ts 114 lac+ into the C. freundii chromosome was
AB  - observed, resulting in the formation of stable Hfr strains.  In this way it is
AB  - possible to devise a method for chromosome transfer in other genera than E.
AB  - coli to which plasmids of E. coli can be transferred, but in which no
AB  - chromosome mobilization is possible because of poor DNA homology between the
AB  - foreign plasmid and the host chromosome.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Abdurashitov, M.A.
AU  - Kolyhalov, A.A.
AU  - Rechkunova, N.I.
TI  - AclI, a new restriction endonuclease from Acinetobacter calcoaceticus recognizing 5'-AA^CGTT-3' .
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3787
EP  - 3787
VL  - 20
AB  - AclI, a new restriction endonuclease, has been purified from Acinetobacter calcoaceticus M4.
AB  - AclI recognizes the sequence 5'AA^CGTT3' and cleaves DNA as indicated. The enzyme was
AB  - purified using the following chromatographic steps: 1) gel-filtration through biogel A-0.5m,
AB  - 2) DEAE-cellulose, 3) phosphocellulose, 4) heparin sepharose.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Belavin, P.A.
AU  - Shishkina, I.G.
AU  - Zarytova, V.F.
AU  - Gavryuchenkova, L.P.
AU  - Morozov, S.M.
TI  - Immobilized oligonucleotides as affinity ligands for restriction endonucleases.
JO  - Bioorg. Khim.
PY  - 1989
SP  - 358
EP  - 362
VL  - 15
AB  - Affinity chromatography of Type IIS restriction endonucleases is proposed. It is shown that
AB  - endonucleases HgaI, FokI, and SfaNI have affinity to the matrix with immobilized
AB  - oligonucleotides which contain the endonuclease's recognition sites resistant to hydrolysis.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Belichenko, O.A.
AU  - Lebedeva, N.A.
AU  - Dedkov, V.S.
AU  - Abdurashitov, M.A.
TI  - BtrI, a novel restriction endonuclease, recognises the non-palindromic sequence 5'-CACGTC(-3/-3)-3'.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - e56
EP  - e56
VL  - 28
AB  - The recognition sequence and cleavage positions of a new restriction endonuclease BtrI
AB  - isolated from Bacillus stearothermophilus SE-U62 have been determined.  BtrI belongs to a rare
AB  - type IIQ of restriction endonucleases, which recognise non-palindromic nucleotide sequences
AB  - and cleave DNA symmetrically within them.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Kolyhalov, A.A.
AU  - Rechkunova, N.I.
AU  - Abdurashitov, M.A.
TI  - AcsI, a new restriction endonuclease from Arthrobacter citreus 310 recognizing 5'-Pu^AATTPy-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3789
EP  - 3789
VL  - 20
AB  - AcsI, an isoschizomer of FsiI, has been purified from Arthrobacter citreus 310. AcsI
AB  - recognizes the sequence 5'Pu^AATTPy3' and cleaves DNA as indicated by the arrow. The enzyme
AB  - was purified using two chromatographic steps: phosphocellulose and heparin sepharose. The
AB  - enzyme was free of contaminating nuclease activity. After 20-fold over-digestion on lambda DNA
AB  - greater than 95% of the DNA fragments can be ligated and then recut by AcsI. Optimal
AB  - conditions for AcsI activity are 10 mM Tris-HCl (pH 8.5), 10 mM MgCl2, 100 mM NaCl at 37C. The
AB  - fragments produced by AcsI digestion of lambda and T7 DNAs match those predicted by cleavage
AB  - at the sequence PuAATTPy.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Kolyhalov, A.A.
AU  - Rechkunova, N.I.
AU  - Dedkov, V.S.
TI  - Determination of substrate specificity of restriction endonuclease FauI.
JO  - Bioorg. Khim.
PY  - 1989
SP  - 130
EP  - 132
VL  - 15
AB  - The recognition sequence and cleavage point of restriction endonuclease FauI
AB  - have been determined as 5'-CCCGC(4/6).  Not being an isoschizomer of any known
AB  - restriction endonuclease, this enzyme may be used in genetic engineering.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Kolyhalov, A.A.
AU  - Rechkunova, N.T.
AU  - Tepavicharova, I.I.
AU  - Mechandjiska, L.I.
AU  - Builieva, E.I.
TI  - Bsp1720I, an isoschizomer of EspI from Bacillus species 1720 recognizing 5'-GC^TNAGC-3'.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2504
EP  - 2504
VL  - 19
AB  - Bsp1720I, an isoschisomer of EspI (1) has been purified from Bacillus species 1720.  Bsp1720I
AB  - recognizes the sequence 5'GC^TNAGC3' and cleaves DNA as indicated by the arrow.  The enzyme
AB  - was purified using the following chromatographic steps: 1) gel-filtration through biogel A0.5
AB  - m, 2) DEAE-cellulose, 3) phosphocellulose.  The enzyme was free of contaminating nuclease
AB  - activity.  After 40-fold overdigestion on lambda DNA greater than 95% of the DNA fragments can
AB  - be ligated and then recut by Bsp1720I.  Optimal conditions for Bsp1720I activity are 20 mM
AB  - Tris-HCl (pH 7.5), 10 mM MgCl2, 100 mM NaCl at 37C. The fragments produced by Bsp1720I
AB  - digestion of lambda DNA match those predicted by cleavage at the sequence GCTNAGC (figure 1,
AB  - lane 2). The cleavage site was determined accordingly to earlier published procedure (2).  DNA
AB  - of pUC 8 with the insert containing a Bsp1720I cleavage site (pVE27) was digested by the
AB  - enzymes XmaI and PvuII; reaction products were labelled with [a-32P]dCTP by Klenow Fragment.
AB  - 350 bp DNA fragment was eluted from gel after electrophoresis in 6% PAAG, its structure and
AB  - Bsp1720I hydrolysis site were determined (figure 2).  The results show that Bsp1720I cleaves
AB  - DNA as indicated by arrows:
AB  - 5'-GC^TNAGC-3'
AB  - 3'-CGANT^CG-5'.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Kolykhalov, A.A.
AU  - Rechkunova, N.I.
AU  - Dedkov, V.S.
AU  - Zhilkin, P.A.
TI  - BsiI - A new unusual restriction endonuclease.
JO  - Mol. Biol. (Mosk)
PY  - 1990
SP  - 244
EP  - 247
VL  - 24
AB  - The restriction endonuclease BsiI from Bacillus sphaericus was isolated.  The
AB  - recognition sequence and cleavage point of enzyme BsiI have been determined as
AB  - C^TCGTG
AB  - GAGCA^C.
AB  - This restriction endonuclease is not an isoschizomer of any known restriction
AB  - endonucleases and differs from other enzymes: it hydrolyses DNA at an
AB  - assymmetrical recognition sequence.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Netesova, N.A.
AU  - Abdurashitov, M.A.
AU  - Shevchenko, A.V.
TI  - Primary structure and strand specificity of BstF5I-1 DNA methyltransferase which recognizes 5'-GGATG-3'.
JO  - Gene
PY  - 1997
SP  - 217
EP  - 219
VL  - 187
AB  - The gene for BstF5I-1 DNA-methyltransferase (Mtase) from Bacillus stearothermophilus F5 (a
AB  - FokI isoschizomer, recognizing 5'-GGATG-3') was cloned and its nucleotide sequence was
AB  - determined.  Analysis of deduced amino acid sequence shows that M.BstF5I-1 belongs to D/21
AB  - class of Mtases and has a little homology with M.FokI.  M.BstF5I-1 modifies only the upper
AB  - strand of the recognition sequence (5'-GGATG-3').
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Netesova, N.A.
AU  - Chizhikov, V.E.
AU  - Abdurashitov, M.A.
TI  - Cloning and characterization of the gene encoding M.FauI DNA methyltransferase.
JO  - Biol. Chem.
PY  - 1998
SP  - 567
EP  - 568
VL  - 379
AB  - The enzymes of the FauI restriction-modification system from the Flavobacterium aquatile
AB  - strain recognize the non-palindromic sequence 5'-CCCGC-3'/3'-GG-GCG-5'.  We have cloned
AB  - the gene encoding the DNA modifying component of this system and determined its nucleotide
AB  - sequence.  The deduced amino acid sequence contains ten conserved motifs characteristic for
AB  - [cytosine-5] DNA methyltransferases.  Part of the gene sequence that encodes the putative
AB  - target recognizing domain of the M.FauI shows some homology with the downstream region, thus
AB  - indicating that duplication of the DNA segment was probably involved in the gene evolution.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Prihodko, G.G.
AU  - Rechkunova, N.I.
TI  - Determination of the substrate specificity of restriction endonuclease SfeI.
JO  - Bioorg. Khim.
PY  - 1988
SP  - 848
EP  - 849
VL  - 14
AB  - The recognition sequence and cleavage site C^TRYAG of a new restriction
AB  - endonuclease SfeI have been determined.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Prikhodko, E.A.
AU  - Prikhodko, G.G.
AU  - Krasnykh, V.N.
TI  - VspI methylase belongs to m6A-gamma class of adenine methylases.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2015
EP  - 2015
VL  - 21
AB  - We have successfully isolated a genomic clone of Vibrio species strain 343 which encodes
AB  - methyltransferases and prevents plasmid and bacterial DNA degredation by restriction
AB  - endonuclease VspI. There are three open reading frames starting from nucleotides #503, #57,
AB  - #812 and ending at #1780, which encode 47.5, 45.5 and 36.1 kd proteins respectively. The
AB  - Shine-Dalgarno signal are present in the last two open reading frames. Gel-filtration of
AB  - native methylase VspI showed a molecular weight of 42.7 kd. Thus, the open reading frame of
AB  - the methylase gene is #557-1780 and it encodes a 408 amino acid protein. The comparison of
AB  - deduced amino acid structure of VspI methylase and others has been done according to
AB  - Klimasauskas et al. According to mutual positions of two conservative domains this enzyme
AB  - belongs to m6A-gamma class. M.VspI has a NPPW-motif instead of an NPPY one, but replacement of
AB  - aromatic amino acid tyrosine by another aromatic amino acid tryptophan might be insignificant.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Prikhodko, E.A.
AU  - Rechkunova, N.I.
AU  - Gorbunov, Y.A.
TI  - Interaction of VspI and Tru9I restriction endonucleases with synthetic oligonucleotides.
JO  - Biochim. Biophys. Acta
PY  - 1993
SP  - 89
EP  - 94
VL  - 1172
AB  - We describe the properties of two new restriction endonucleases VspI and Tru9I which recognize
AB  - sequences AT^TAAT and T^TAA respectively. The molecular weights, subunit structure and
AB  - steady-state kinetic constants of these enzymes for native and modified substrates have been
AB  - determined. We have investigated the interaction of VspI and Tru9I with synthetic
AB  - oligonucleotides containing modifications either within the recognition sites or around them.
AB  - These modifications represent the substitution of different DNA deoxyribonucleosides by
AB  - 1,2-dideoxy-D-ribofuranose, which corresponds to loss of the heterocyclic base while the
AB  - sugar-phosphate chain remains intact. The effects of the substitutions were analyzed by
AB  - determining the steady-state kinetic values of the hydrolysis reaction by VspI and Tru9I. The
AB  - enzymes exhibited Michaelis-Menten kinetics for hydrolyzable substrates. The initial rates
AB  - (Vo) of hydrolysis of modified and unmodified strands of the duplexes varied as a result of
AB  - these substitutions. The substrates for VspI and Tru9I which contain modifications around the
AB  - bond to be hydrolyzed or within the complementary nucleosides were unreactive.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Prikhodko, E.A.
AU  - Rechkunova, N.I.
AU  - Prikhodko, G.G.
AU  - Krasnykh, V.N.
TI  - Biochemical characterization of VspI methyltransferase.
JO  - Gene
PY  - 1995
SP  - 65
EP  - 66
VL  - 157
AB  - The gene (vspIM) encoding VspI methyltransferase (MTase) has previously been cloned and
AB  - sequenced, and shown to belong to the gamma class of m6-adenine MTases.  Here it is shown that
AB  - the MTase modifies the third adenine within the recognition sequence 5'-ATTAAT-3'.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
TI  - Determination of purity of restriction endonucleases.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1988
SP  - 102
EP  - 105
VL  - 14
AB  - A method for the determination of exonucleases and phosphatase impurities in preparations of
AB  - restriction endonucleases using 5'-[32P]-labelled double-stranded 20-base long
AB  - deoxyribooligonucleotides is suggested. Incubation of enzyme with substrate is carried out in
AB  - restriction buffer with subsequent electrophoresis of the reaction mixture in 20%
AB  - polyacrylamide in the presence of 7M urea and autoradiography of the gel.  The percent of
AB  - label in oligonucleotide is determined.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
AU  - Grinev, A.A.
AU  - Dedkov, V.S.
TI  - Determination of substrate specificity of restriction endonucleases Bme18I and Kzo9I.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1989
SP  - 25
EP  - 26
VL  - 15
AB  - The recognition sequence and cleavage point of restriction endonucleases Bme18I and Kzo9I have
AB  - been determined as G^G(A/T) CC and ^GATC, respectively.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
AU  - Kolyhalov, A.A.
AU  - Dedkov, V.S.
AU  - Zhilkin, P.A.
TI  - II-Q restriction endonucleases - new class of type II enzymes.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 5807
EP  - 5810
VL  - 18
AB  - Unique restriction endonucleases Bpu10I and BsiI have been isolated from
AB  - Bacillus pumilus and Bacillus sphaericus, respectively.  The recognition
AB  - sequences and cleavage points of these enzymes have been determined as
AB  - 5'-CC^TNAGC-3'
AB  - 3'-GGANT^CG-5' for Bpu10I
AB  - and
AB  - 5'-C^TCGTG-3'
AB  - 3'-GAGCA^C-5' for BsiI.
AB  - Restriction endonucleases Bpu10I and BsiI represent a new class of enzymes
AB  - which recognize nonpalindromic nucleotide sequences and hydrolyze DNA within
AB  - the recognition sequences may be regarded as quasi-palindromic and the enzymes
AB  - may be designated as type II-Q restriction endonucleases.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
AU  - Netesova, N.A.
AU  - Tchigikov, V.E.
AU  - Malygin, E.G.
AU  - Kochkin, A.V.
AU  - Mikhajlov, V.V.
AU  - Rasskazov, V.A.
TI  - Determination of substrate specificity of restriction endonuclease VneI.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 422
EP  - 423
VL  - 13
AB  - The recognition sequence and cleavage point of restriction endonuclease VneI
AB  - have been determined as 5'-G^TGCAC.  This enzyme is not isoschizomer of any
AB  - known restriction endonucleases and therefore may be widely used in
AB  - investigation of DNA structure.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
AU  - Repin, V.E.
AU  - Kolyhalov, A.A.
AU  - Netesov, S.V.
TI  - The recognition sequence and cleavage point of restriction endonuclease Bse 21 I.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1990
SP  - 138
EP  - 139
VL  - 1
AB  - The recognition sequence and cleavage point of restriction endonuclease Bse21I
AB  - have been determined as 5'-CC^TNAGG.  This enzyme is an isoschizomer of SauI
AB  - and may replace it in investigation of DNA structure.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
AU  - Zernov, Y.P.
AU  - Dedkov, V.S.
AU  - Chizikov, V.E.
AU  - Van Calligan, M.
AU  - Williams, R.
AU  - Murray, E.
TI  - Bsp24I, a new unusual restriction endonuclease.
JO  - Gene
PY  - 1993
SP  - 93
EP  - 95
VL  - 131
AB  - *
AB  - A new restriction endonuclease, Bsp24I, from Bacillus species 24, recognizing:
AB  - 
AB  -    5'-^N8 GACNNNNNNTGGN12^-3'
AB  -    3'-^N13CTGNNNNNNACCN7^-5',
AB  - 
AB  - has been isolated. Its specificity and cleavage points were determined.
AB  - 
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Repin, V.E.
AU  - Rechkunova, N.I.
AU  - Tchigikov, V.E.
AU  - Malygin, E.G.
AU  - Mikhajlov, V.V.
AU  - Rasskazov, V.A.
TI  - Determination of the substrate specificity of restriction endonuclease VspI.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 420
EP  - 421
VL  - 13
AB  - The recognition sequence and cleavage point of restriction endonuclease VspI
AB  - have been determined as 5'-AT^TAAT.  This enzyme is not an isoschizomer of any
AB  - known restriction endonucleases.  DNA pBR322 contains a single VspI recognition
AB  - sequence in position 3539.  Therefore this enzyme may be used for cloning DNA
AB  - in the VspI site in AmpR-gene of pBR322.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Zernov, Y.P.
TI  - Type II restriction enzymes:  Possible evolutionary links between the enzymes and their palindromic tetranucleotide recognition sequences.
JO  - Mol. Biol. (Mosk)
PY  - 1990
SP  - 1393
EP  - 1398
VL  - 24
AB  - The distribution of restriction enzymes with tetranucleotide recognition sequences in nature
AB  - was analyzed.  A rule for the conversion of these recognition sites was formulated, and a
AB  - scheme showing the evolutionary links of restriction enzymes with their palindromic
AB  - tetranucleotide sequences is proposed.
ER  -

TY  - JOUR
AU  - Degtyarev, S.K.
AU  - Zilkin, P.A.
AU  - Prihodko, G.G.
AU  - Repin, V.E.
AU  - Rechkunova, N.I.
TI  - Determination of unusual substrate specificity of restriction endonuclease Bpu10I.
JO  - Mol. Biol. (Mosk)
PY  - 1989
SP  - 1051
EP  - 1056
VL  - 23
AB  - A new enzyme Bpu10I was isolated form Bacillus pumilus.  This enzyme is not an isoschizomer of
AB  - any known restriction endonucleases.  The search of possible recognition sequences was carried
AB  - out in sequences ABCNiDEF (i=0-6) on substrate DNA lambda CI857, T7, pBR322.  The recognition
AB  - sequence and cleavage sites of restriction endonuclease Bpu10I have been determined as
AB  - CC^TNAGC
AB  - GGANT^CG.
ER  -

TY  - JOUR
AU  - Deibert, M.
AU  - Grazulis, S.
AU  - Janulaitis, A.
AU  - Siksnys, V.
AU  - Huber, R.
TI  - Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.
JO  - EMBO J.
PY  - 1999
SP  - 5805
EP  - 5816
VL  - 18
AB  - The MunI restriction enzyme recognizes the palindromic hexanucleotide sequence C/AATTG (the
AB  - '/' indicates the cleavage site).  The crystal structure of its active site mutant D83A
AB  - bound to cognate DNA has been determined at 1.7 A resolution.  Base-specific contacts between
AB  - MunI and DNA occur exclusively in the major groove. While DNA-binding sites of most other
AB  - restriction enzymes are comprised of discontinuous sequence segments, MunI combines all
AB  - residues involved in the base-specific contacts within one short stretch (residues R115-R121)
AB  - located at the N-terminal region of the 3(10)4 helix. The outer CG base pair of the
AB  - recognition sequence is recognized solely by R115 through hydrogen bonds made by backbone and
AB  - side chain atoms to both bases. The mechanism of recognition of the central AATT nucleotides
AB  - by MunI is similar to that of EcoRI, which recognizes the G/AATTC sequence. The local
AB  - conformation of AATT deviates from the typical B-DNA form and is remarkably similar to
AB  - EcoRI-DNA. It appears to be essential for specific hydrogen bonding and recognition by MunI
AB  - and EcoRI.
ER  -

TY  - JOUR
AU  - Deibert, M.
AU  - Grazulis, S.
AU  - Sasnauskas, G.
AU  - Siksnys, V.
AU  - Huber, R.
TI  - Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.
JO  - Nat. Struct. Biol.
PY  - 2000
SP  - 792
EP  - 799
VL  - 7
AB  - The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has
AB  - been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein
AB  - tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure
AB  - of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are
AB  - arranged back to back with two oligonucleotides bound in clefts on opposite sides of the
AB  - tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between
AB  - their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and
AB  - minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of
AB  - NgoMIV. Biochemical experiments show that interactions between the recognition sites within
AB  - the tetramer greatly increase DNA cleavage efficiency.
ER  -

TY  - JOUR
AU  - Deissler, H.
AU  - Genc, B.
AU  - Doerfler, W.
TI  - Restriction endonuclease BsoFI is sensitive to the 5'-methylation of deoxycytidines in its recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 4227
EP  - 4228
VL  - 23
AB  - The isoschizomeric restriction endonucleases Fnu4HI and BsoFI cleave DNA at 5'-GC/NGC-3'
AB  - sequences.  Fnu4HI has been shown to be inhibited by 5'-CG-3' methylation in the sequences
AB  - 5'-GmCGGC-3' or 5'-GCGGmCG-3'.  We have now investigated the methylation sensitivity of
AB  - BsoFI by testing its activity on plasmid DNA 5'-CG-3' methylated with the M.SssI DNA
AB  - methyltransferase or on synthetic (CGG)n repetitive oligodeoxyribonucleotides which have been
AB  - partly or completely C methylated.  The data demonstrate that BsoFI cannot cleave at its
AB  - recognition sequence when it is completely 5'-CG-3' methylated.  These enzymes have proven
AB  - to be useful in analyses of the methylation status in (CGG)n repeats of the human genome.
ER  -

TY  - JOUR
AU  - Deitzler, G.E.
AU  - Ruiz, M.J.
AU  - Lu, W.
AU  - Weimer, C.
AU  - Park, S.
AU  - Robinson, L.S.
AU  - Hallsworth-Pepin, K.
AU  - Wollam, A.
AU  - Mitreva, M.
AU  - Lewis, W.G.
AU  - Lewis, A.L.
TI  - Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e00889
EP  - e00816
VL  - 4
AB  - The vagina is home to a wide variety of bacteria that have great potential to impact human
AB  - health. Here, we announce reference strains (now available through
AB  - BEI Resources) and draft genome sequences for 9 Gram-negative vaginal isolates
AB  - from the taxa Citrobacter, Klebsiella, Fusobacterium, Proteus, and Prevotella.
ER  -

TY  - JOUR
AU  - Deitzler, G.E.
AU  - Ruiz, M.J.
AU  - Weimer, C.
AU  - Park, S.
AU  - Robinson, L.
AU  - Hallsworth-Pepin, K.
AU  - Wollam, A.
AU  - Mitreva, M.
AU  - Lewis, A.L.
AU  - Lewis, W.G.
TI  - Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina.
JO  - Genome Announcements
PY  - 2016
SP  - e00888
EP  - e00816
VL  - 4
AB  - Research on vaginal infections is currently limited by a lack of available fully  sequenced
AB  - bacterial reference strains. Here, we present strains (now available
AB  - through BEI Resources) and genome sequences for a set of 14 vaginal isolates from
AB  - the phylum Firmicutes These genome sequences provide a valuable resource for
AB  - future research in understanding the role of Gram-positive bacteria in vaginal
AB  - health and disease.
ER  -

TY  - JOUR
AU  - DeJonckheere, J.F.
AU  - Brown, S.
TI  - Three different group I introns in the nuclear large subunit ribosomal DNA of the amoeboflagellate Naegleria.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 456
EP  - 461
VL  - 26
AB  - We have amplified the large subunit ribosomal DNA of the 12 described Naegleria spp. and of 34
AB  - other Naegleria lineages that might be distinct species.  Two strains yielded a product that
AB  - is longer than 3 kb, which is the length of the LSUrDNA of all described Naegleria spp.
AB  - Sequencing data revealed that the insert in one of these strains is a group I intron without
AB  - an open reading frame, while the other strain contains two different group I introns, of which
AB  - the second intron has an ORF of 175 amino acids.  In the latter ORF there is a conserved
AB  - His-Cys box as in the homing endonucleases present in group I introns in the small subunit
AB  - ribosomal DNA of Naegleria spp.  Although the group I introns in the LSUrDNA differ in
AB  - sequence, they are more related to each other than they are to the group I introns in the
AB  - SSUrDNA of Naegleria spp.  The three group I introns in the LSUrDNA in Naegleria are at
AB  - different locations and are probably acquired by horizontal transfer, contrary to the SSUrDNA
AB  - group I introns in this genus which are of ancestral origin and are transmitted vertically.
ER  -

TY  - JOUR
AU  - Del Castillo, C.S.
AU  - Hikima, J.I.
AU  - Jang, H.B.
AU  - Nho, S.W.
AU  - Jung, T.S.
AU  - Wongtavatchai, J.
AU  - Kondo, H.
AU  - Hirono, I.
AU  - Takeyama, H.
AU  - Aoki, T.
TI  - Comparative sequence analysis of a multi-drug resistant plasmid from Aeromonas hydrophila.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 120
EP  - 129
VL  - 57
AB  - Aeromonas hydrophila is a pathogenic bacterium that has been implicated in fish,
AB  - animal, and human disease. Recently, a multi-drug resistance (MDR) plasmid pR148
AB  - was isolated from A. hydrophila obtained from a tilapia (Oreochromis niloticus)
AB  - farm in Thailand. pR148 is a 165,906 bp circular plasmid containing 147 coding
AB  - regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a
AB  - human pathogen. It was also very similar to other IncA/C plasmids isolated from
AB  - humans, animals, food, and fish. pR148 contains a mercuric resistance operon and
AB  - encodes the complete set of genes for the type 4 secretion system. pR148 encodes
AB  - for a Tn21 type transposon. This contains the drug resistance genes qacH,
AB  - bla(OXA-10), aadA1, and sul1 in a class 1 integron; tetA and tetR in a transposon
AB  - Tn1721; and catA2 and a duplicate sul1 in a locus showing 100% similarity to IncU
AB  - plasmids isolated from fish. The bla(OXA-10) and aadA1 genes showed 100%
AB  - similarity with those from the Acinetobacter baumannii AYE chromosomal genome.
AB  - The similarity of pR148 to a human pathogen-derived plasmid indicates that the
AB  - plasmids were either transferred between them or that they are derived from a
AB  - common origin. Previous studies have shown that IncA/C plasmids retain a
AB  - conserved backbone, while the accessory region points to lateral gene transfer.
AB  - These observations point out the dangers of indiscriminate use of antibiotics in
AB  - humans and in animals and the necessity of understanding how drug resistance
AB  - determinants are disseminated and transferred.
ER  -

TY  - JOUR
AU  - Del Cerro, C.
AU  - Felpeto-Santero, C.
AU  - Rojas, A.
AU  - Tortajada, M.
AU  - Ramon, D.
AU  - Garcia, J.L.
TI  - Genome Sequence of the Butanol Hyperproducer Clostridium saccharoperbutylacetonicum N1-4.
JO  - Genome Announcements
PY  - 2013
SP  - e0007013
EP  - e0007013
VL  - 1
AB  - Clostridium saccharoperbutylacetonicum is one of the most important acetone-butanol-ethanol
AB  - (ABE)-generating industrial microorganisms and one of the
AB  - few bacteria containing choline in its cell wall. Here, we report the draft
AB  - genome sequence of C. saccharoperbutylacetonicum strain N1-4 (6.6 Mbp; G+C
AB  - content, 29.4%) and the findings obtained from the annotation of the genome.
ER  -

TY  - JOUR
AU  - Del Cerro, C.
AU  - Garcia, J.M.
AU  - Rojas, A.
AU  - Tortajada, M.
AU  - Ramon, D.
AU  - Galan, B.
AU  - Prieto, M.A.
AU  - Garcia, J.L.
TI  - Genome Sequence of the Methanotrophic Poly-beta-Hydroxybutyrate Producer Methylocystis parvus OBBP.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5709
EP  - 5710
VL  - 194
AB  - Methylocystis parvus OBBP is an obligate methylotroph considered the type species of the genus
AB  - Methylocystis. Two pmoCAB particulate methane monooxygenase operons
AB  - and one additional singleton pmoC paralog were identified in the sequence. No
AB  - evidence of genes encoding soluble methane monooxygenase was found. Comparison of
AB  - M. parvus OBBP and Methylocystis sp. strain Rockwell (ATCC 49242) suggests that
AB  - both species should be taxonomically classified in different genera.
ER  -

TY  - JOUR
AU  - del Gaudio, R.
AU  - Di Giaimo, R.
AU  - Potenza, N.
AU  - Branno, M.
AU  - Aniello, F.
AU  - Geraci, G.
TI  - Characterization of a new variant DNA (cytosine-5)-methyltransferase unable to methylate double stranded DNA isolated from the marine annelid worm Chaetopterus variopedatus.
JO  - FEBS Lett.
PY  - 1999
SP  - 380
EP  - 384
VL  - 460
AB  - The enzyme S-adenosylmethionine-DNA (cytosine-5)-methyltransferase has been identified, first
AB  - time for invertebrates, in embryos of the marine polychaete annelid worm Chaetopterus
AB  - variopedatus. The molecule has been isolated from embryos at 15 h of development. It is a
AB  - single peptide of about 200 kDa molecular weight, cross-reacting with antibodies against sea
AB  - urchin DNA methyltransferase. The enzymatic properties of the molecule are similar to those of
AB  - Dnmt1 methyltransferases isolated from other organisms, but with the peculiarity to be unable
AB  - to make 'de novo' methylation on double stranded DNA.
ER  -

TY  - JOUR
AU  - Del Giudice, L.
TI  - Method for isolating restriction- and modificationless mutants of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1979
SP  - 673
EP  - 676
VL  - 137
AB  - A simple method is described for the selection and isolation of restriction- and
AB  - modificationless mutants in Escherichia coli K-12 by using the following properties: (i) the
AB  - temperature-sensitive repressor activity of phage lambda-cI857; (ii) a mutant of lambda phage
AB  - defective in integration and the establishment of repression (lambda-b2cI); (iii) a virulent
AB  - phage insensitive to the repressor activity.  The final yield of spontaneously arising rK- mK+
AB  - and rK- mK- mutants from stationary-phase cultures was about 5% of the surviving cells.
ER  -

TY  - JOUR
AU  - Del Rio, T.G. et al.
TI  - Complete genome sequence of Intrasporangium calvum type strain (7 KIP).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 294
EP  - 303
VL  - 3
AB  - Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus
AB  - Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae.
AB  - The species is a Gram-positive bacterium that forms a branching mycelium, which
AB  - tends to break into irregular fragments. The mycelium of this strain may bear
AB  - intercalary vesicles but does not contain spores. The strain described in this
AB  - study is an airborne organism that was isolated from a school dining room in
AB  - 1967. One particularly interesting feature of I. calvum is that the type of its
AB  - menaquinone is different from all other representatives of the family
AB  - Intrasporangiaceae. This is the first completed genome sequence from a member of
AB  - the genus Intrasporangium and also the first sequence from the family
AB  - Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding
AB  - and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Delahodde, A.
AU  - Goguel, V.
AU  - Becam, A.M.
AU  - Creusot, F.
AU  - Perea, J.
AU  - Banroques, J.
AU  - Jacq, C.
TI  - Site-specific DNA endonuclease and RNA maturase activities of two homologous intron-encoded proteins from yeast mitochondria.
JO  - Cell
PY  - 1989
SP  - 431
EP  - 444
VL  - 56
AB  - Two introns of the mitochondrial genome 777-3A of S. cerevisiae, bI4 in cob and aI4 in cox1
AB  - genes, contain ORFs that can be translated into two homologous proteins. We changed the UGA,
AB  - AUA, and CUN codons of these ORFs to the universal genetic code, in order to study the
AB  - functions of their translated products in E. coli and in yeast, by retargeting the nuclear
AB  - encoded protein into mitochondria. The p27b14 protein has been shown to be required for the
AB  - splicing of both introns bI4 and aI4. The homologous p28aI4 protein is highly toxic to E.
AB  - coli. It can specifically cleave double-stranded DNA at a sequence representing the junction
AB  - of the two fused flanking exons. We present evidence that this system is a good model for
AB  - studying the role of mitochondrial intron-encoded proteins in the rearrangement of genetic
AB  - information at both the RNA (RNA splicing-bI4 maturase) and DNA levels (intron
AB  - transposition-aI4 transposase).
ER  -

TY  - JOUR
AU  - Delamuta, J.R.
AU  - Gomes, D.F.
AU  - Ribeiro, R.A.
AU  - Chueire, L.M.
AU  - Souza, R.C.
AU  - Almeida, L.G.
AU  - Vasconcelos, A.T.
AU  - Hungria, M.
TI  - Genome Sequence of Bradyrhizobium tropiciagri Strain CNPSo 1112T, Isolated from a Root Nodule of Neonotonia wightii.
JO  - Genome Announcements
PY  - 2015
SP  - e01482
EP  - e01415
VL  - 3
AB  - CNPSo 1112(T) is a nitrogen-fixing symbiont of perennial soybean, a tropical legume forage.
AB  - Its draft genome indicates a large genome with a circular
AB  - chromosome and 9,554 coding sequences (CDSs). Operons of nodulation, nitrogen
AB  - fixation, and uptake hydrogenase were present in the symbiotic island, and the
AB  - genome encompasses several CDSs of stress tolerance.
ER  -

TY  - JOUR
AU  - Delamuta, J.R.
AU  - Ribeiro, R.A.
AU  - Gomes, D.F.
AU  - Souza, R.C.
AU  - Chueire, L.M.
AU  - Hungria, M.
TI  - Genome Sequence of Bradyrhizobium stylosanthis Strain BR 446T, a Nitrogen-Fixing  Symbiont of the Legume Pasture Stylosanthes guianensis.
JO  - Genome Announcements
PY  - 2016
SP  - e00631
EP  - e00616
VL  - 4
AB  - Bradyrhizobium stylosanthis BR 446(T) is a nitrogen-fixing symbiont of the tropical legume
AB  - pasture Stylosanthes guianensis Its draft genome contains 8,801,717 bp and 8,239 coding
AB  - sequences (CDSs). Several putative genes that might confer high competitiveness and
AB  - saprophytic capacity under the stressful conditions of tropical soils were identified in the
AB  - genome.
ER  -

TY  - JOUR
AU  - Delamuta, J.R.M.
AU  - Ribeiro, R.A.
AU  - Gomes, D.F.
AU  - Souza, R.C.
AU  - Chueire, L.M.
AU  - Hungria, M.
TI  - Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48T, a Nitrogen-Fixing Symbiont of Pachyrhizus erosus (L.) Urb.
JO  - Genome Announcements
PY  - 2015
SP  - e01074
EP  - e01015
VL  - 3
AB  - Bradyrhizobium pachyrhizi PAC48(T) has been isolated from a jicama nodule in Costa Rica. The
AB  - draft genome indicates high similarity with that of Bradyrhizobium elkanii. Several coding
AB  - sequences (CDSs) of the stress response might help in survival in the tropics. PAC48(T)
AB  - carries nodD1 and nodK, similar to Bradyrhizobium (Parasponia) ANU 289 and a particular nodD2
AB  - gene.
ER  -

TY  - JOUR
AU  - Delannoy, C.M.
AU  - Zadoks, R.N.
AU  - Lainson, F.A.
AU  - Ferguson, H.W.
AU  - Crumlish, M.
AU  - Turnbull, J.F.
AU  - Fontaine, M.C.
TI  - Draft Genome Sequence of a Nonhemolytic Fish-Pathogenic Streptococcus agalactiae  Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6341
EP  - 6342
VL  - 194
AB  - Streptococcus agalactiae is a significant Gram-positive bacterial pathogen of terrestrial and
AB  - aquatic animals. A subpopulation of nonhemolytic strains which
AB  - appear to be pathogenic only for poikilotherms exists. We report here the first
AB  - draft genome sequence of a nonhemolytic S. agalactiae isolate recovered from a
AB  - diseased fish.
ER  -

TY  - JOUR
AU  - Delannoy, S.
AU  - Mariani-Kurkdjian, P.
AU  - Bonacorsi, S.
AU  - Liguori, S.
AU  - Ison, S.A.
AU  - Fach, P.
TI  - Draft Genome Sequences of Human-Pathogenic Escherichia coli O26:H11 Strains Carrying the stx2 Gene Only and Circulating in France.
JO  - Genome Announcements
PY  - 2015
SP  - e00852
EP  - e00815
VL  - 3
AB  - Shiga toxin-producing Escherichia coli (STEC) O26:H11 is one of the most frequent pathogens
AB  - associated with diarrhea and hemolytic-uremic syndrome (HUS). In this
AB  - report, we present the draft genome sequences of seven strains of STEC O26:H11
AB  - carrying the stx2a or stx2d gene only and isolated in France from HUS patients.
ER  -

TY  - JOUR
AU  - Deleo, F.R.
AU  - Chen, L.
AU  - Porcella, S.F.
AU  - Martens, C.A.
AU  - Kobayashi, S.D.
AU  - Porter, A.R.
AU  - Chavda, K.D.
AU  - Jacobs, M.R.
AU  - Mathema, B.
AU  - Olsen, R.J.
AU  - Bonomo, R.A.
AU  - Musser, J.M.
AU  - Kreiswirth, B.N.
TI  - Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - 4988
EP  - 4993
VL  - 111
AB  - Infections caused by drug-resistant bacteria are a major problem worldwide.
AB  - Carbapenem-resistant Klebsiella pneumoniae, most notably isolates classified as
AB  - multilocus sequence type (ST) 258, have emerged as an important cause of hospital
AB  - deaths. ST258 isolates are predominantly multidrug resistant, and therefore
AB  - infections caused by them are difficult to treat. It is not known why the ST258
AB  - lineage is the most prevalent cause of multidrug-resistant K. pneumoniae
AB  - infections in the United States and other countries. Here we tested the
AB  - hypothesis that carbapenem-resistant ST258 K. pneumoniae is a single genetic
AB  - clone that has disseminated worldwide. We sequenced to closure the genomes of two
AB  - ST258 clinical isolates and used these genomes as references for comparative
AB  - genome sequencing of 83 additional clinical isolates recovered from patients at
AB  - diverse geographic locations worldwide. Phylogenetic analysis of the SNPs in the
AB  - core genome of these isolates revealed that ST258 K. pneumoniae organisms are two
AB  - distinct genetic clades. This unexpected finding disproves the single-clone
AB  - hypothesis. Notably, genetic differentiation between the two clades results from
AB  - an approximately 215-kb region of divergence that includes genes involved in
AB  - capsule polysaccharide biosynthesis. The region of divergence appears to be a
AB  - hotspot for DNA recombination events, and we suggest that this region has
AB  - contributed to the success of ST258 K. pneumoniae. Our findings will accelerate
AB  - research on novel diagnostic, therapeutic, and vaccine strategies designed to
AB  - prevent and/or treat infections caused by multidrug resistant K. pneumoniae.
ER  -

TY  - JOUR
AU  - Delestre, C.
AU  - Laugraud, A.
AU  - Ridgway, H.
AU  - Ronson, C.
AU  - O'Callaghan, M.
AU  - Barrett, B.
AU  - Ballard, R.
AU  - Griffiths, A.
AU  - Young, S.
AU  - Blond, C.
AU  - Gerard, E.
AU  - Wakelin, S.
TI  - Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 121
EP  - 121
VL  - 10
AB  - Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N2-fixing
AB  - microsymbiont of white clover (Trifolium repens L.). The bacterium has
AB  - been widely used in both Australia and New Zealand as a clover seed inoculant
AB  - and, as such, has delivered the equivalent of millions of dollars of nitrogen
AB  - into these pastoral systems. R. leguminosarum strain CC275e is a rod-shaped,
AB  - motile, Gram-negative, non-spore forming bacterium. The genome was sequenced on
AB  - an Illumina MiSeq instrument using a 2 x 150 bp paired end library and assembled
AB  - into 29 scaffolds. The genome size is 7,077,367 nucleotides, with a GC content of
AB  - 60.9 %. The final, high-quality draft genome contains 6693 protein coding genes,
AB  - close to 85 % of which were assigned to COG categories. This Whole Genome Shotgun
AB  - project has been deposited at DDBJ/EMBL/GenBank under the accession JRXL00000000.
AB  - The sequencing of this genome will enable identification of genetic traits
AB  - associated with host compatibility and high N2 fixation characteristics in
AB  - Rhizobium leguminosarum. The sequence will also be useful for development of
AB  - strain-specific markers to assess factors associated with environmental fitness,
AB  - competiveness for host nodule occupancy, and survival on legume seeds (New
AB  - Zealand Ministry of Business, Innovation and Employment program, 'Improving
AB  - forage legume-rhizobia performance' contract C10X1308 and DairyNZ Ltd.).
ER  -

TY  - JOUR
AU  - Delhalle, E.
TI  - Restriction and modification of bacteriophages by Escherichia coli K12 involving a cryptic P1 prophage associated with different plasmids.
JO  - Ann. Microbiol. (Paris)
PY  - 1973
SP  - 173
EP  - 178
VL  - 124A
AB  - By transducing hybrid plasmids with P1, two transductants were found to carry a cryptic P1
AB  - phage closely associated with plasmids R(T), Ton or Col(VI), Trp.  The presence of these
AB  - cryptic P1 phages was manifested by restriction and modification of phages T1 and T7.  Linkage
AB  - on a single genetic structure of the cryptic P1 phage and the other extrachromosomal genes was
AB  - demonstrated by associated transfer by conjugation and P1-transduction.  The two cryptic P1
AB  - phages were not identical.
ER  -

TY  - JOUR
AU  - Deligios, M.
AU  - Bacciu, D.
AU  - Deriu, E.
AU  - Corti, G.
AU  - Bordoni, R.
AU  - De Bellis, G.
AU  - Leori, G.S.
AU  - Rubino, S.
AU  - Uzzau, S.
TI  - Draft Genome Sequence of the Host-Restricted Salmonella enterica Serovar Abortusovis Strain SS44.
JO  - Genome Announcements
PY  - 2014
SP  - e00261
EP  - e00214
VL  - 2
AB  - Salmonella enterica serovar Abortusovis is a pathogen strictly adapted to ovines, in which it
AB  - causes abortion. To enhance our understanding of this pathogen, we assembled the first draft
AB  - sequence of an S. Abortusovis genome (strain SS44). The obtained genomic data might facilitate
AB  - the study of S. enterica evolution and host adaptation.
ER  -

TY  - JOUR
AU  - DeLong, E.F.
AU  - Preston, C.M.
AU  - Mincer, T.
AU  - Rich, V.
AU  - Hallam, S.J.
AU  - Frigaard, N.U.
AU  - Martinez, A.
AU  - Sullivan, M.B.
AU  - Edwards, R.
AU  - Brito, B.R.
AU  - Chisholm, S.W.
AU  - Karl, D.M.
TI  - Community genomics among stratified microbial assemblages in the ocean's interior.
JO  - Science
PY  - 2006
SP  - 496
EP  - 503
VL  - 311
AB  - Microbial life predominates in the ocean, yet little is known about its genomic variability,
AB  - especially along the depth continuum. We report here
AB  - genomic analyses of planktonic microbial communities in the North Pacific
AB  - Subtropical Gyre, from the ocean's surface to near-sea floor depths.
AB  - Sequence variation in microbial community genes reflected vertical
AB  - zonation of taxonomic groups, functional gene repertoires, and metabolic
AB  - potential. The distributional patterns of microbial genes suggested
AB  - depth-variable community trends in carbon and energy metabolism,
AB  - attachment and motility, gene mobility, and host-viral interactions.
AB  - Comparative genomic analyses of stratified microbial communities have the
AB  - potential to provide significant insight into higher-order community
AB  - organization and dynamics.
ER  -

TY  - JOUR
AU  - Delorme, C.
AU  - Bartholini, C.
AU  - Luraschi, M.
AU  - Pons, N.
AU  - Loux, V.
AU  - Almeida, M.
AU  - Guedon, E.
AU  - Gibrat, J.F.
AU  - Renault, P.
TI  - Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5581
EP  - 5582
VL  - 193
AB  - Streptococcus thermophilus is a dairy species commonly used in the manufacture of cheese and
AB  - yogurt. Here, we report the complete sequence of
AB  - S. thermophilus strain JIM8232, isolated from milk and which produces a
AB  - yellow pigment, an atypical trait for this bacterium.
ER  -

TY  - JOUR
AU  - Delorme, C.
AU  - Guedon, E.
AU  - Pons, N.
AU  - Cruaud, C.
AU  - Couloux, A.
AU  - Loux, V.
AU  - Chiapello, H.
AU  - Poyart, C.
AU  - Gautier, C.
AU  - Sanchez, N.
AU  - Almeida, M.
AU  - Kennedy, S.
AU  - Ehrlich, S.D.
AU  - Gibrat, J.F.
AU  - Wincker, P.
AU  - Renault, P.
TI  - Complete Genome Sequence of the clinical Streptococcus salivarius strain CCHSS3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5041
EP  - 5042
VL  - 193
AB  - Streptococcus salivarius is a commensal species commonly found in the human oral cavity and
AB  - digestive tract, although it is also associated with
AB  - human infections such as meningitis, endocarditis and bacteremia. Here, we
AB  - report the complete sequence of S. salivarius strain CCHSS3 isolated from
AB  - human blood.
ER  -

TY  - JOUR
AU  - DelVecchio, V.G. et al.
TI  - The genome sequence of the facultative intracellular pathogen Brucella melitensis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 443
EP  - 448
VL  - 99
AB  - Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in
AB  - goats and sheep and Malta fever in humans. The genome of B. melitensis strain 16M was
AB  - sequenced and found to contain 3,294,935 bp distributed over two circular chromosomes of
AB  - 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the bioinformatics suite ERGO,
AB  - 2,487 (78%) ORFs were assigned functions. The origins of replication of the two chromosomes
AB  - are similar to those of other -proteobacteria. Housekeeping genes, including those involved in
AB  - DNA replication, transcription, translation, core metabolism, and cell wall biosynthesis, are
AB  - distributed on both chromosomes. Type I, II, and III secretion systems are absent, but genes
AB  - encoding sec-dependent, sec-independent, and flagella-specific type III, type IV, and type V
AB  - secretion systems as well as adhesins, invasins, and hemolysins were identified. Several
AB  - features of the B. melitensis genome are similar to those of the symbiotic Sinorhizobium
AB  - meliloti.
ER  -

TY  - JOUR
AU  - Delver, E.P.
AU  - Agofanova, O.V.
AU  - Tupikova, E.E.
AU  - Vorobeva, E.P.
AU  - Belogurov, A.A.
TI  - System controlling expression of antirestriction genes ardA and ardB of IncN transmission plasmid pKM101 (R46).
JO  - Mol. Biol. (Mosk)
PY  - 1998
SP  - 208
EP  - 213
VL  - 32
AB  - A system regulating the expression of antirestriction genes ardA and ardB of transmission
AB  - plasmid pKM101 (R46) was studied.  These phylogenetically distant genes are involved in
AB  - protecting plasmid DNA from cell restriction enzymes and adapting to a new host after conjugal
AB  - transfer.  The regulatory system involves two conserved upstream repeats, which flank the 5'
AB  - end of ard and contain a potent promoter, and regulatory proteins ArdK and ArdR.  At least one
AB  - of the proteins, ArdK, can bind with the promoter and act as a suppressor.  Both proteins
AB  - control the expression of their own genes.  The regulatory system was assumed to trigger the
AB  - coordinated expression of the ard genes and efficient synthesis of the Ard antirestriction
AB  - proteins, which are essential to conjugal transfer of the plasmid and its adaptation to the
AB  - new host.
ER  -

TY  - JOUR
AU  - Delver, E.P.
AU  - Kotova, V.U.
AU  - Zavilgelsky, G.B.
AU  - Belogurov, A.A.
TI  - Nucleotide sequence of the Gene (ard) encoding the antirestriction protein of plasmid colIb-P9.
JO  - J. Bacteriol.
PY  - 1991
SP  - 5887
EP  - 5892
VL  - 173
AB  - The IncI1 plasmid ColIb-P9 was found to encode an antirestriction function.
AB  - The relevant gene, and (alleviation of restriction of DNA), maps about 5 kb
AB  - from the origin of transfer, in the region transferred early during bacterial
AB  - conjugation.  Ard inhibits both restriction and modification by each of the
AB  - four type I systems of Escherichia coli tested, but it had no effect on
AB  - restriction by EcoRI, a type II system, or EcoP1, a type III system.  The
AB  - nucleotide sequence of the ColIb ard gene was determined; the predicted
AB  - molecular weight of the Ard polypeptide is 19,193.  The proposed polypeptide
AB  - chain contains an excess of 25 negatively charged amino acids, suggesting that
AB  - its overall character is very acidic.  Deletion analysis of the gene revealed
AB  - that the Ard protein contained a distinct functional domain located in the
AB  - COOH-terminal half of the polypeptide.  We suggest that the biological role of
AB  - the ColIb Ard protein is associated with overcoming host-controlled restriction
AB  - during bacterial conjugation.
ER  -

TY  - JOUR
AU  - Demarre, G.
AU  - Chattoraj, D.K.
TI  - DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle.
JO  - PLoS Genet.
PY  - 2010
SP  - e1000939
EP  - e1000939
VL  - 6
AB  - DNA adenine methylation is widely used to control many DNA transactions, including
AB  - replication. In Escherichia coli, methylation serves to silence newly
AB  - synthesized (hemimethylated) sister origins. SeqA, a protein that binds to
AB  - hemimethylated DNA, mediates the silencing, and this is necessary to restrict
AB  - replication to once per cell cycle. The methylation, however, is not essential
AB  - for replication initiation per se but appeared so when the origins (oriI and
AB  - oriII) of the two Vibrio cholerae chromosomes were used to drive plasmid
AB  - replication in E. coli. Here we show that, as in the case of E. coli, methylation
AB  - is not essential for oriI when it drives chromosomal replication and is needed
AB  - for once-per-cell-cycle replication in a SeqA-dependent fashion. We found that
AB  - oriII also needs SeqA for once-per-cell-cycle replication and, additionally, full
AB  - methylation for efficient initiator binding. The requirement for initiator
AB  - binding might suffice to make methylation an essential function in V. cholerae.
AB  - The structure of oriII suggests that it originated from a plasmid, but unlike
AB  - plasmids, oriII makes use of methylation for once-per-cell-cycle replication, the
AB  - norm for chromosomal but not plasmid replication.
ER  -

TY  - JOUR
AU  - Dematheis, F.
AU  - Antwerpen, M.H.
AU  - Grass, G.
AU  - Walter, M.C.
AU  - Borgmann, S.
TI  - Genome Sequence of Bacillus safensis Strain Ingolstadt Isolated from the Pectoralis Pouch of a Patient with Defibrillator-Related Surgery.
JO  - Genome Announcements
PY  - 2017
SP  - e01031
EP  - e01017
VL  - 5
AB  - We report the draft genome sequence of clindamycin-resistant Bacillus safensis strain
AB  - Ingolstadt isolated from a patient with bacterial colonization after heart
AB  - surgery. The draft genome comprises 3.75 Mbp and harbors 3,793 predicted
AB  - protein-encoding genes and a small plasmid.
ER  -

TY  - JOUR
AU  - deMayo, J.A.
AU  - Maas, K.R.
AU  - Klassen, J.L.
AU  - Balunas, M.J.
TI  - Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a  Tunicate Collected in Long Island Sound.
JO  - Genome Announcements
PY  - 2016
SP  - e00874
EP  - e00816
VL  - 4
AB  - Streptomyces sp. AVP053U2 is a marine bacterium isolated from Styela clava, a tunicate
AB  - collected in Long Island Sound. Here, we report a draft genome for this
AB  - bacterium, which was found to contain a high capacity for secondary metabolite
AB  - production based on analysis and identification of numerous biosynthetic gene
AB  - clusters.
ER  -

TY  - JOUR
AU  - Demey, L.M.
AU  - Miller, C.R.
AU  - Manzella, M.P.
AU  - Spurbeck, R.R.
AU  - Sandhu, S.K.
AU  - Reguera, G.
AU  - Kashefi, K.
TI  - The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 47
EP  - 47
VL  - 12
AB  - Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples
AB  - collected from the Hulk sulfide mound on the main Endeavour
AB  - Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth
AB  - 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared
AB  - 99.77% similarity with the complete genome of the type strain Su06T, which shares
AB  - with strain Hulk the ability to reduce iron and nitrate for respiration. The
AB  - annotation of the genome of strain Hulk identified genes for the reduction of
AB  - several sulfur-containing electron acceptors, an unsuspected respiratory
AB  - capability in this species that was experimentally confirmed for strain Hulk.
AB  - This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to
AB  - gain energy for growth by reduction of iron, nitrate, and sulfur-containing
AB  - electron acceptors. Here we present the most notable features of the genome of P.
AB  - delaneyi strain Hulk and identify genes encoding proteins critical to its
AB  - respiratory versatility at high temperatures. The description presented here
AB  - corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019
AB  - protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.
ER  -

TY  - JOUR
AU  - Demidova, G.V.
AU  - Goncharov, E.K.
AU  - Tynianova, V.I.
TI  - Comparison of specific recognition sites of adenine and cytosine DNA-methyltransferase of Yersinia pestis EV 76C dam and dcm by Escherichia coli methylases.
JO  - Biokhimiia
PY  - 1984
SP  - 1594
EP  - 1597
VL  - 49
AB  - Using enzymatic modelling of in vitro methylation of chromosome DNAs from Yersinia pestis EV
AB  - 76, E. coli 834 and E. coli C600 RII by DNA methylases of EcoRII and EcoDam as well as of DNA
AB  - hydrolysis of plasmid pBR 322 from the cells of Y. pestis EV 76, E. coli C600 and E. coli 834
AB  - by restrictases of EcoRII and CfuI, it was found that cytosine DNA methylase from plaque
AB  - bacteria does not correspond to the type of RII methylases of E. coli.  Adenine DNA methylase
AB  - is related to E. coli methylases type dam and modified adenine in the nucleotide sequence of
AB  - GATC.
ER  -

TY  - JOUR
AU  - Dempsey, R.M.
AU  - Carroll, D.
AU  - Kong, H.M.
AU  - Higgins, L.
AU  - Keane, C.T.
AU  - Coleman, D.C.
TI  - Sau421, a Bcgl-like restriction-modification system encoded by the Staphylococcus aureus quadruple-converting phage phi 42.
JO  - Microbiology
PY  - 2005
SP  - 1301
EP  - 1311
VL  - 151
AB  - The serotype F phage 042 of Staphylococcus aureus is a triple-converting bacteriophage that
AB  - encodes the staphylokinase gene
AB  - (sak) and the enterotoxin A gene (entA). Lysogeny results in loss of
AB  - expression of the chromosomal beta-haemolysin gene (hlb) (negative
AB  - conversion), the expression of staphylokinase and enterotoxin A
AB  - (positive conversion), and the acquisition of resistance to lysis by
AB  - all 23 phages of the International Basic Set (IBS) of S. aureus typing
AB  - phages. Until this study, the basis of 042 resistance to lysis by
AB  - exogenous phages was unknown. The authors report here that phage 042
AB  - encodes a restriction-modification (R-M) system, termed Sau42I,
AB  - adjacent to and in the same orientation to the phage integrase gene
AB  - int. The genes encoding Sau42I were cloned and sequenced, and found to
AB  - consist of two overlapping reading frames, ORF S (specificity) and ORF
AB  - RM (restriction-modification), in the same orientation. The ORFs share
AB  - a high degree of DNA and amino acid sequence homology with the
AB  - previously characterized BcgI R-M system of Bacillus coagulans.
AB  - Expression of the cloned Sau421 ORF S and ORF RM in S. aureus 80CR3
AB  - transformants from a plasmid vector conferred resistance to lysis by
AB  - all 23 IBS phages. Similarly, transformants of S. aureus RN4220
AB  - harbouring recombinant plasmids containing both ORFs were resistant to
AB  - lysis by the IBS typing phages. However, transformants harbouring
AB  - plasmids encoding either ORF S or ORF RM were susceptible to lysis by
AB  - the IBS phages, and they had the same phage-susceptibility pattern as
AB  - the respective parental isolates. In vitro analysis of crude and
AB  - partially purified extracts of S. aureus transformants harbouring both
AB  - the 042 ORF S and ORF RM genes indicated that Sau421 has endonuclease
AB  - activity and requires co-factors Mg2+ and S-adenosylmethionine in order
AB  - to function, and activity is optimized at pH 8, although the precise
AB  - recognition sequence has yet to be determined. The findings of this
AB  - study confirm that phi 42 is a quadruple-converting phage, believed to
AB  - be the first described for S. aureus, and show that it encodes a novel
AB  - R-M system termed Sau421.
ER  -

TY  - JOUR
AU  - den Bakker, H.C.
AU  - Moreno-Switt, A.I.
AU  - Govoni, G.
AU  - Cummings, C.A.
AU  - Ranieri, M.L.
AU  - Degoricija, L.
AU  - Hoelzer, K.
AU  - Rodriguez-Rivera, L.D.
AU  - Brown, S.
AU  - Bolchacova, E.
AU  - Furtado, M.R.
AU  - Wiedmann, M.
TI  - Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.
JO  - BMC Genomics
PY  - 2011
SP  - 425
EP  - 425
VL  - 12
AB  - BACKGROUND: Divergence of bacterial populations into distinct subpopulations is
AB  - often the result of ecological isolation. While some studies have suggested the
AB  - existence of Salmonella enterica subsp. enterica subclades, evidence for these
AB  - subdivisions has been ambiguous. Here we used a comparative genomics approach to
AB  - define the population structure of Salmonella enterica subsp. enterica, and
AB  - identify clade-specific genes that may be the result of ecological
AB  - specialization. RESULTS: Multi-locus sequence analysis (MLSA) and single
AB  - nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly
AB  - available genomes showed an unambiguous subdivision of S. enterica subsp.
AB  - enterica into at least two subpopulations, which we refer to as clade A and clade
AB  - B. Clade B strains contain several clade-specific genes or operons, including a
AB  - beta-glucuronidase operon, a S-fimbrial operon, and cell surface related genes,
AB  - which strongly suggests niche specialization of this subpopulation. An additional
AB  - set of 123 isolates was assigned to clades A and B by using qPCR assays targeting
AB  - subpopulation-specific SNPs and genes of interest. Among 98 serovars examined,
AB  - approximately 20% belonged to clade B. All clade B isolates contained two
AB  - pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin
AB  - islet; a combination of these two islands was previously thought to be exclusive
AB  - to serovars Typhi and Paratyphi A. Presence of beta-glucuronidase in clade B
AB  - isolates specifically suggests an adaptation of this clade to the vertebrate
AB  - gastrointestinal environment. CONCLUSIONS: S. enterica subsp. enterica consists
AB  - of at least two subpopulations that differ specifically in genes involved in host
AB  - and tissue tropism, utilization of host specific carbon and nitrogen sources and
AB  - are therefore likely to differ in ecology and transmission characteristics.
ER  -

TY  - JOUR
AU  - Denes, T.
AU  - Vongkamjan, K.
AU  - Ackermann, H.W.
AU  - Moreno-Switt, A.I.
AU  - Wiedmann, M.
AU  - den Bakker, H.C.
TI  - Comparative genomic and morphological analysis of Listeria phages isolated from farm environments.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 4616
EP  - 4625
VL  - 80
AB  - The genus Listeria is ubiquitous in the environment and includes the globally
AB  - important foodborne pathogen Listeria monocytogenes. While the genomic diversity
AB  - of Listeria has been well studied, considerably less is known about the genomic
AB  - and morphological diversity of Listeria bacteriophages. In this study, we
AB  - sequenced and analyzed the genomes of 14 Listeria phages mostly isolated from New
AB  - York dairy farm environments, as well as one related Enterococcus faecalis phage,
AB  - to obtain information on genome characteristics and diversity. We also examined
AB  - 12 of the phages by electron microscopy to characterize their morphology. These
AB  - Listeria phages, based on gene orthology and morphology, together with previously
AB  - sequenced Listeria phages could be classified into five orthoclusters, including
AB  - one novel orthocluster. One orthocluster (I) consists of large genome (
AB  - approximately 135 kb) myoviruses belonging to the genus "Twort-like viruses",
AB  - three orthoclusters (II-IV) contain small genome (36-43 kb) siphoviruses with
AB  - icosahedral heads, and the novel orthocluster V contains medium-sized genome (
AB  - approximately 66 kb) siphoviruses with elongated heads. A novel orthocluster (VI)
AB  - of E. faecalis phages, with medium-sized genomes ( approximately 56 kb), was
AB  - identified which grouped together and shares morphological features with the
AB  - novel Listeria phage orthocluster V. This new group of phages (i.e.,
AB  - orthoclusters V and VI) is composed of putative lytic phages that may prove to be
AB  - useful in phage-based applications for biocontrol, detection, and therapeutic
AB  - purposes.
ER  -

TY  - JOUR
AU  - Deng, H.
AU  - Yang, X.
AU  - Yeo, S.P.
AU  - Gao, Z.
TI  - Highly Sensitive Electrochemical Methyltransferase Activity Assay.
JO  - Anal. Chem.
PY  - 2014
SP  - 2117
EP  - 2123
VL  - 86
AB  - A simple and highly sensitive electrochemical DNA methyltransferase (MTase) activity assay is
AB  - presented in this report. The assay employs the electrocatalytic oxidation of ascorbic acid
AB  - (AA) by a threading intercalator (N,N'-bis(3propylimidazole)-1,4,5,8-naphthalene diimide
AB  - (PIND) functionalized with electrocatalytic redox Os(bpy)(2)Cl+ moieties (PIND-Os)). Briefly,
AB  - a double-stranded DNA (ds-DNA) containing the symmetric sequence of 5'-CCGG-3' is first
AB  - immobilized on a gold electrode. The electrode is then incubated with M.SssI CpG
AB  - methyltransferase (M.SssI MTase) which catalyzes the methylation of the specific CpG
AB  - dinucleotides, and the electrode is subsequently treated with a restriction endonuclease HpaII
AB  - which recognizes the 5'-CCGG-3' sequence. Once the CpG site in the 5'-CCGG-3' is
AB  - methylated, HpaII recognition is blocked. Higher M.SssI MTase activity leads to more CpG sites
AB  - being methylated and consequently impedes more the restriction endonuclease HpaII digestion
AB  - process. Thus, a larger amount of ds-DNA remains on the electrode surface after the HpaII.
AB  - treatment. Thereafter, the electrode is incubated with PIND-Os during which PIND-Os
AB  - specifically inserts itself between base pairs of ds-DNA and catalyzes the electrooxidation of
AB  - AA. The methylation event corresponding to the MTase activity can therefore be monitored and
AB  - amplified by the electrocatalytic oxidation of AA. A linear correlation between the catalytic
AB  - oxidation current of AA and the activity of M.SssI MTase ranged from 0 to 120 U/mL with a
AB  - current sensitivity of 0.046 mu A mL U-1 is obtained. The inhibitor screening ability of the
AB  - developed MTase activity assay is also demonstrated.
ER  -

TY  - JOUR
AU  - Deng, J.
AU  - Szyf, M.
TI  - Multiple isoforms of DNA methyltransferase are encoded by the vertebrate cytosine DNA methyltransferase gene.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 22869
EP  - 22872
VL  - 273
AB  - This manuscript tests the hypothesis that multiple forms of cytosine-DNA methyltransferase are
AB  - expressed in vertebrates in vivo.  Vertebrate genomes are distinguished by tissue- and
AB  - gene-specific DNA methylation patterns.  Specific methylation patterns are believed to encode
AB  - epigenetic information.  In distinction from the remarkable diversity of DNA methylation
AB  - patterns, only one functional DNA MeTase cDNA has been identified to date in different
AB  - vertebrate organisms.  Using reverse transcription-polymerase chain reaction and RNase
AB  - protection analyses, we show that the methyltransferase domain of the rat DNA MeTase is
AB  - alternatively spliced in vivo, generating different in-frame variants of DNA MeTase in
AB  - specific tissues.  This process is developmentally regulated and is induced in PC12 cells by a
AB  - known inducer of neuronal differentiation, nerve growth factor.  The data presented here point
AB  - toward a new mechanism for generating diversity of DNA MeTases and possibly diverse DNA
AB  - methylation patterns.
ER  -

TY  - JOUR
AU  - Deng, P.
AU  - Wang, X.
AU  - Baird, S.M.
AU  - Lu, S.E.
TI  - Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 117
EP  - 117
VL  - 10
AB  - Strain UFB2 was isolated from a soybean field soil in Mississippi and identified  as a member
AB  - of Pseudomonas chlororaphis. Strain UFB2 has a broad-spectrum
AB  - antimicrobial activity against common soil-borne pathogens. Plate assays showed
AB  - that strain UFB2 was especially efficient in inhibiting the growth of Clavibacter
AB  - michiganensis 1-07, the causal agent of the devastating bacterial canker of
AB  - tomato. Here, the complete genome sequence of P. chlororaphis strain UFB2 is
AB  - reported and described. The strain UFB2 genome consists of a circular chromosome
AB  - of 6,360,256 bp of which 87.86 % are protein-coding bases. Genome analysis
AB  - revealed multiple gene islands encoding various secondary metabolites such as
AB  - 2,4-diacetylphloroglucinol. Further genome analysis will provide more details
AB  - about strain UFB2 antibacterial activities mechanisms and the use of this strain
AB  - as a potential biocontrol agent.
ER  -

TY  - JOUR
AU  - Deng, W. et al.
TI  - Genome sequence of Yersinia pestis KIM.
JO  - J. Bacteriol.
PY  - 2002
SP  - 4601
EP  - 4611
VL  - 184
AB  - We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic
AB  - and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second
AB  - pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames
AB  - (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to
AB  - those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis
AB  - CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome
AB  - rearrangement for strains so closely related. The differences appear to result from multiple
AB  - inversions of genome segments at insertion sequences, in a manner consistent with present
AB  - knowledge of replication and recombination. There are few differences attributable to
AB  - horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing
AB  - surprising amounts of locally colinear "backbone," or synteny, that is not discernible at the
AB  - nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with
AB  - conserved housekeeping functions. However, a number of E. coli pathways and transport systems
AB  - and at least one global regulator were not found, reflecting differences in lifestyle between
AB  - them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including
AB  - iron transport systems, putative adhesins, toxins, and fimbriae.
ER  -

TY  - JOUR
AU  - Deng, W.
AU  - Liou, S.R.
AU  - Plunkett, I.I.I.G.
AU  - Mayhew, G.F.
AU  - Rose, D.J.
AU  - Burland, V.
AU  - Kodoyianni, V.
AU  - Schwartz, D.C.
AU  - Blattner, F.R.
TI  - Comparative Genomics of Salmonella enterica Serovar Typhi Strains Ty2 and CT18.
JO  - J. Bacteriol.
PY  - 2003
SP  - 2330
EP  - 2337
VL  - 185
AB  - We present the 4.8-Mb complete genome sequence of Salmonella enterica serovar Typhi strain
AB  - Ty2, a human-specific pathogen causing typhoid fever.
AB  - A comparison with the genome sequence of recently isolated S. enterica
AB  - serovar Typhi strain CT18 showed that 29 of the 4,646 predicted genes in
AB  - Ty2 are unique to this strain, while 84 genes are unique to CT18. Both
AB  - genomes contain more than 200 pseudogenes; 9 of these genes in CT18 are
AB  - intact in Ty2, while 11 intact CT18 genes are pseudogenes in Ty2. A
AB  - half-genome interreplichore inversion in Ty2 relative to CT18 was
AB  - confirmed. The two strains exhibit differences in prophages, insertion
AB  - sequences, and island structures. While CT18 carries two plasmids, one
AB  - conferring multiple drug resistance, Ty2 has no plasmids and is sensitive
AB  - to antibiotics.
ER  -

TY  - JOUR
AU  - Deng, X.
AU  - Dohmae, N.
AU  - Nealson, K.H.
AU  - Hashimoto, K.
AU  - Okamoto, A.
TI  - Multi-heme cytochromes provide a pathway for survival in energy-limited environments.
JO  - Sci. Adv.
PY  - 2018
SP  - eaao5682
EP  - eaao5682
VL  - 4
AB  - Bacterial reduction of oxidized sulfur species (OSS) is critical for energy
AB  - production in anaerobic marine subsurfaces. In organic-poor sediments, H2 has
AB  - been considered as a major energy source for bacterial respiration. We identified
AB  - outer-membrane cytochromes (OMCs) that are broadly conserved in sediment
AB  - OSS-respiring bacteria and enable cells to directly use electrons from insoluble
AB  - minerals via extracellular electron transport. Biochemical, transcriptomic, and
AB  - microscopic analyses revealed that the identified OMCs were highly expressed on
AB  - the surface of cells and nanofilaments in response to electron donor limitation.
AB  - This electron uptake mechanism provides sufficient but minimum energy to drive
AB  - the reduction of sulfate and other OSS. These results suggest a widespread
AB  - mechanism for survival of OSS-respiring bacteria via electron uptake from solid
AB  - minerals in energy-poor marine sediments.
ER  -

TY  - JOUR
AU  - Deng, X.
AU  - Salazar, J.K.
AU  - Frezet, S.
AU  - Maccannell, D.
AU  - Ribot, E.M.
AU  - Fields, P.I.
AU  - Fricke, W.F.
AU  - Zhang, W.
TI  - Genome Sequence of Salmonella enterica Serotype Tennessee Strain CDC07-0191, Implicated in the 2006-2007 Multistate Food-Borne Outbreak Linked to Peanut  Butter in the United States.
JO  - Genome Announcements
PY  - 2013
SP  - e00260
EP  - e00213
VL  - 1
AB  - Salmonella enterica serotype Tennessee strain CDC07-0191 was isolated from the 2006-2007
AB  - multistate food-borne outbreak linked to peanut butter in the United
AB  - States. Here we report a high-quality draft assembly of the genome sequence of
AB  - this strain, derived from a patient. This is the first reported high-quality
AB  - draft genome sequence for S. enterica serotype Tennessee, which will enable
AB  - in-depth studies of its transmission and virulence.
ER  -

TY  - JOUR
AU  - Deng, Y.
AU  - Chen, C.
AU  - Zhao, Z.
AU  - Huang, X.
AU  - Yang, Y.
AU  - Ding, X.
TI  - Complete Genome Sequence of Vibrio alginolyticus ZJ-T.
JO  - Genome Announcements
PY  - 2016
SP  - e00912
EP  - e00916
VL  - 4
AB  - Vibrio alginolyticus is a ubiquitous Gram-negative bacterium which is normally distributed in
AB  - the coastal and estuarine environments. It has been suggested to
AB  - be an opportunistic pathogen to both marine animals and humans, Here, the
AB  - completed genome sequence of V. alginolyticus ZJ-T was determined by Illumina
AB  - high-throughput sequencing.
ER  -

TY  - JOUR
AU  - Deng, Y.
AU  - Zhu, Y.
AU  - Wang, P.
AU  - Zhu, L.
AU  - Zheng, J.
AU  - Li, R.
AU  - Ruan, L.
AU  - Peng, D.
AU  - Sun, M.
TI  - Complete Genome Sequence of Bacillus subtilis BSn5, an Endophytic Bacterium of Amorphophallus konjac with Antimicrobial Activity for the  Plant Pathogen Erwinia carotovora subsp. carotovora.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2070
EP  - 2071
VL  - 193
AB  - Here, we present the complete genome sequence of Bacillus subtilis strain BSn5, isolated from
AB  - Amorphophallus konjac calli tissue and showing strong
AB  - inhibitory activity to Erwinia carotovora subsp. carotovora, which causes
AB  - Amorphophallus soft rot disease and affects the industry development of
AB  - this organism.
ER  -

TY  - JOUR
AU  - Deng, Y.M.
AU  - Liu, C.Q.
AU  - Dunn, N.W.
TI  - LldI, a plasmid-encoded type I restriction and modification system in Lactococcus lactis.
JO  - DNA Seq.
PY  - 2000
SP  - 239
EP  - 245
VL  - 11
AB  - A plasmid-encoded type I restriction and modification (R-M) system, designated LldI, was
AB  - identified in Lactococcus lactis biovar diacetylactis LD10-1. LldI consists of three genes
AB  - encoding endonuclease, methylase and specificity subunits, respectively. RT-PCR analysis
AB  - revealed that the three genes are co-transcribed as a polycistronic mRNA in L. lactis. The
AB  - specificity subunit of LldI differs significantly in the target recognition domains from those
AB  - of other type I R-M systems, suggesting that LldI confers a novel specificity in L. lactis.
ER  -

TY  - JOUR
AU  - Denjmuchametov, M.M.
AU  - Ruban, N.M.
AU  - Zakharova, M.V.
AU  - Beletzkaja, I.V.
AU  - Kravetz, A.N.
AU  - Solonin, A.S.
TI  - Eco27kI, a new isoschizomer of AvaI from Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1992
EP  - 1992
VL  - 20
AB  - A small collection (108) of Escherichia coli strains isolated in Kiev was surveyed for type II
AB  - restriction endonucleases. 95 strains produced these enzymes; among them Eco27kI, a new
AB  - isoschizomer of AvaI, recognized the palindromic sequence 5'-C/PyCGPuG-3'.
ER  -

TY  - JOUR
AU  - Denjmukhametov, M.M.
AU  - Brevnov, M.G.
AU  - Zakharova, M.V.
AU  - Repyk, A.V.
AU  - Solonin, A.S.
AU  - Petrauskene, O.V.
AU  - Gromova, E.S.
TI  - The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.
JO  - FEBS Lett.
PY  - 1998
SP  - 233
EP  - 236
VL  - 433
AB  - Ecl18kI is a type II restriction-modification system isolated from Enterobacter cloaceae 18kI
AB  - strain.  Genes encoding Ecl18kI methyltransferase (M.Ecl18kI) and Ecl18kI restriction
AB  - endonuclease (R.Ecl18kI) have been cloned and expressed in Escherichia coli.  These enzymes
AB  - recognize the 5'.../CCNGG...3' sequence in DNA; M.Ecl18kI methylates the C5 carbon atom of
AB  - the inner dC residue and R.Ecl18kI cuts DNA as shown by the arrow.  The restriction
AB  - endonuclease and the methyltransferase were purified from E. coli B834 [p18Ap1] cells to near
AB  - homogeneity.  The restriction endonuclease is present in the solution as a tetramer, while the
AB  - methyltransferase is a monomer.  The interactions of M.Ecl18kI and R.Ecl18kI with
AB  - 1,2-dideoxy-D-ribofuranose containing DNA duplexes were investigated.  The target base
AB  - flipping-out mechanism is applicable in the case of M.Ecl18kI.  Correct cleavage of the abasic
AB  - substrates by R.Ecl18kI is accompanied by non-canonical hydrolysis of the modified strand.
ER  -

TY  - JOUR
AU  - Denjmukhametov, M.M.
AU  - Zakharova, M.V.
AU  - Kravets, A.N.
AU  - Pertsev, A.V.
AU  - Sineva, E.V.
AU  - Repik, A.V.
AU  - Beletskaya, I.V.
AU  - Gromova, E.S.
AU  - Solonin, A.S.
TI  - Characterization of plasmids encoding type II restriction-modification systems, isoschizomers of SsoII.
JO  - Mol. Biol. (Mosk)
PY  - 1997
SP  - 831
EP  - 838
VL  - 31
AB  - Five strains of Enterobacteriaceae family have been revealed that have
AB  - restriction-modification systems of type II, isoschizomers of SsoII.  The genes coding for the
AB  - restriction endonucleases and DNA methyltransferases are located on plasmids of two types. The
AB  - plasmids differ in size, capacity for mobilization by conjugative plasmids, and structure of
AB  - locus cer.  Recombinant two-plasmid strains were obtained containing plasmids with genes for
AB  - Ecl18kI and EcoRII restriction endonucleases in the presence of DNA methyltransferase Ecl18kI.
AB  - The stability of the two-plasmid system with the ecoRIIR and ecl18kIM genes implies similar
AB  - mechanisms of concerted regulation of gene expression in the restriction-modification systems
AB  - Ecl18kI and EcoRI.  Genes for Ecl18kI and SsoII restriction-modification systems have
AB  - essentially the same sequence.
ER  -

TY  - JOUR
AU  - Dennison, N.J.
AU  - Saraiva, R.G.
AU  - Cirimotich, C.M.
AU  - Mlambo, G.
AU  - Mongodin, E.F.
AU  - Dimopoulos, G.
TI  - Functional genomic analyses of Enterobacter, Anopheles and Plasmodium reciprocal interactions that impact vector competence.
JO  - Malar. J.
PY  - 2016
SP  - 425
EP  - 425
VL  - 15
AB  - BACKGROUND: Malaria exerts a tremendous socioeconomic impact worldwide despite
AB  - current control efforts, and novel disease transmission-blocking strategies are
AB  - urgently needed. The Enterobacter bacterium Esp_Z, which is naturally harboured
AB  - in the mosquito midgut, can inhibit the development of Plasmodium parasites prior
AB  - to their invasion of the midgut epithelium through a mechanism that involves
AB  - oxidative stress. Here, a multifaceted approach is used to study the tripartite
AB  - interactions between the mosquito, Esp_Z and Plasmodium, towards addressing the
AB  - feasibility of using sugar-baited exposure of mosquitoes to the Esp_Z bacterium
AB  - for interruption of malaria transmission. METHODS: The ability of Esp_Z to
AB  - colonize Anopheles gambiae midguts harbouring microbiota derived from wild
AB  - mosquitoes was determined by qPCR. Upon introduction of Esp_Z via nectar feeding,
AB  - the permissiveness of colonized mosquitoes to Plasmodium falciparum infection was
AB  - determined, as well as the impact of Esp_Z on mosquito fitness parameters, such
AB  - as longevity, number of eggs laid and number of larvae hatched. The genome of
AB  - Esp_Z was sequenced, and transcriptome analyses were performed to identify
AB  - bacterial genes that are important for colonization of the mosquito midgut, as
AB  - well as for ROS-production. A gene expression analysis of members of the
AB  - oxidative defence pathway of Plasmodium berghei was also conducted to assess the
AB  - parasite's oxidative defence response to Esp_Z exposure. RESULTS: Esp_Z persisted
AB  - for up to 4 days in the An. gambiae midgut after introduction via nectar feeding,
AB  - and was able to significantly inhibit Plasmodium sporogonic development.
AB  - Introduction of this bacterium did not adversely affect mosquito fitness.
AB  - Candidate genes involved in the selection of a better fit Esp_Z to the mosquito
AB  - midgut environment and in its ability to condition oxidative status of its
AB  - surroundings were identified, and parasite expression data indicated that Esp_Z
AB  - is able to induce a partial and temporary shutdown of the ookinetes antioxidant
AB  - response. CONCLUSIONS: Esp_Z is capable of inhibiting sporogonic development of
AB  - Plasmodium in the presence of the mosquito's native microbiota without affecting
AB  - mosquito fitness. Several candidate bacterial genes are likely mediating midgut
AB  - colonization and ROS production, and inhibition of Plasmodium development appears
AB  - to involve a shutdown of the parasite's oxidative defence system. A better
AB  - understanding of the complex reciprocal tripartite interactions can facilitate
AB  - the development and optimization of an Esp_Z-based malaria control strategy.
ER  -

TY  - JOUR
AU  - Denny, A.L.
AU  - Arruda, S.E.
TI  - Draft Genome Sequences of Escherichia coli Strains FP2 and FP3, Isolated from the Canada Goose (Branta canadensis).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01079
EP  - e01018
VL  - 7
AB  - Draft genomes of two strains of Escherichia coli, FP2 and FP3, isolated from the  feces of the
AB  - Canada goose (Branta canadensis), were sequenced. Genome sizes were
AB  - 5.26 Mb with a predicted G+C content of 50.54% (FP2) and 5.07 Mb with a predicted
AB  - G+C content of 50.41% (FP3).
ER  -

TY  - JOUR
AU  - Denou, E.
AU  - Bruttin, A.
AU  - Barretto, C.
AU  - Ngom-Bru, C.
AU  - Brussow, H.
AU  - Zuber, S.
TI  - T4 phages against Escherichia coli diarrhea: potential and problems.
JO  - Virology
PY  - 2009
SP  - 21
EP  - 30
VL  - 388
AB  - A combination of in vitro and in vivo experiments with comparative phage
AB  - genomics was used for the rational design of a phage cocktail against E.
AB  - coli diarrhea. Orally applied T4 coliphages representing three different
AB  - subgroups (T4-, RB49- and JS98-like phages) had no negative impact on the
AB  - murine gut microbiota. T4 phages were found with high titers in the cecum
AB  - and colon and lower titers in the small intestine, but were not detected
AB  - in the blood, liver or spleen. No adverse effects were observed after
AB  - one-month exposure to phage nor were serum anti-T4 antibodies detected. T4
AB  - phages belonging to the same subgroup showed closely related genomes that
AB  - differed by 12 (phage JS10 vs. JS98 reference) to 17 (phage JSE vs. RB49
AB  - reference) insertion/deletions mostly representing single small ORFs.
AB  - Bioinformatic analysis did not reveal undesired genes in the T4 genomes.
AB  - Sequence variability was seen over the tail fibre genes, but the
AB  - variability did not correlate with phage host range. The investigated T4
AB  - phages were not only species- but also strain-specific, necessitating the
AB  - use of phage cocktails consisting of 10 and 16 T4 phage isolates to cover
AB  - half to two thirds of E. coli strains representing the five main
AB  - pathotypes isolated from diarrhea patients.
ER  -

TY  - JOUR
AU  - Denovan-Wright, E.M.
AU  - Nedelcu, A.M.
AU  - Lee, R.W.
TI  - Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos.
JO  - Plant Mol. Biol.
PY  - 1998
SP  - 285
EP  - 295
VL  - 36
AB  - The complete  nucleotide sequence of the Chlamydomonas eugametos mitochondrial genome has been
AB  - determined (22,897 bp, 34.6% G+C).  The genes identified in this circular-mapping genome
AB  - include those for apocytochrome b, subunit 1 of the cytochrome oxidase complex.  Subunits
AB  - 1,2,4,5, and 6 of the N dehydrogenase complex, discontinuous large and small subunit ribosomal
AB  - rRNAs and three tRNAs whose anticodons CAU, CCA and UUG are specific for methionine,
AB  - tryptophan and glutamine, respectively.  The C. eugametos mitochondrial DNA, therefore, shares
AB  - almost the same reduced set of coding functions and similar unusual features of rRNA gene
AB  - organization with the linear 15.8 kb mtDNA of Chlamydomonas reinhardtii, the only other
AB  - completely sequenced chlamydomonadalean mtDNA.  However, sequence analysis of the C. eugametos
AB  - mtDNA has revealed the following distinguishing features relative to those of C. reinhardtii:
AB  - (1) the absence of a reverse transcriptase-like gene homologue, (2) the presence of an
AB  - addition gene for tRNAmet that may be a pseudogene, (3) a completely different gene order, (4)
AB  - transcription of all genes from the same mtDNA strand, (5) a lower G+ C content, (6) less
AB  - pronounced bias in codon usage, and (7) nine group I introns, several of which contain open
AB  - reading frames coding for potential maturases/endonucleases and two have a nucleotide at the
AB  - 5' or 3' splice site of the deduced precursor RNAs that deviates from highly conserved
AB  - nucleotides reported in other group I introns.  The features of mitochondrial genome
AB  - organization and gene content shared by C. eugametos and C. reinhardtii contrast with their
AB  - green algal mtDNAs that have been characterized in detail.  The deep evolutionary divergence
AB  - between these two Chlamydomonas taxa within the Chlamydomonadales suggests that their shared
AB  - features of mitochondrial genome organization evolved prior to the origin of this group.
ER  -

TY  - JOUR
AU  - deOliveira-Cunha, C.
AU  - Goda-Zuleta, L.F.
AU  - Paula-deAlmeida, L.G.
AU  - Prioli-Ciapina, L.
AU  - Lustrino-Borges, W.
AU  - Pitard, R.M.
AU  - Baldani, J.I.
AU  - Straliotto, R.
AU  - deFaria, S.M.
AU  - Hungria, M.
AU  - Sousa-Cavada, B.
AU  - Mercante, F.M.
AU  - Ribeiro-deVasconcelos, A.T.
TI  - Complete Genome Sequence of Burkholderia phenoliruptrix BR3459a (CLA1), a Heat-Tolerant, Nitrogen-Fixing Symbiont of Mimosa flocculosa.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6675
EP  - 6676
VL  - 194
AB  - The genus Burkholderia represents a challenge to the fields of taxonomy and phylogeny and,
AB  - especially, to the understanding of the contrasting roles as
AB  - either opportunistic pathogens or bacteria with biotechnological potential. Few
AB  - genomes of nonpathogenic strains, especially of diazotrophic symbiotic bacteria,
AB  - have been sequenced to improve understanding of the genus. Here, we contribute
AB  - with the complete genome sequence of Burkholderia phenoliruptrix strain BR3459a
AB  - (CLA1), an effective diazotrophic symbiont of the leguminous tree Mimosa
AB  - flocculosa Burkart, which is endemic to South America.
ER  -

TY  - JOUR
AU  - DePaoli-Roach, A.
AU  - Roach, P.J.
AU  - Zucker, K.E.
AU  - Smith, S.S.
TI  - Selective phosphorylation of human DNA methyltransferase by protein kinase C.
JO  - FEBS Lett.
PY  - 1986
SP  - 149
EP  - 153
VL  - 197
AB  - Human DNA methyltransferase, the enzyme thought to be responsible for the somatic inheritance
AB  - of patterns of DNA methylation, is an effective substrate for phosphorylation by protein
AB  - kinase C. This provides a plausible mechanistic link between the action of tumor promoting
AB  - phorbol esters, which stimulate protein kinase C, and abnormal patterns of DNA methylation
AB  - often observed in transformed cells.
ER  -

TY  - JOUR
AU  - Deplus, R.
AU  - Brenner, C.
AU  - Burgers, W.A.
AU  - Putmans, P.
AU  - Kouzarides, T.
AU  - de Launoit, Y.
AU  - Fuks, F.
TI  - Dnmt3L is a transcriptional repressor that recruits histone deacetylase.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3831
EP  - 3838
VL  - 30
AB  - The Dnmt3L protein belongs to the Dnmt3 family of DNA methyltransferases by virtue of its
AB  - sequence homology in the plant homeodomain (PHD)-like motif. Dnmt3L is essential for the
AB  - establishment of maternal genomic imprints and, given its lack of key methyltransferase
AB  - motifs, is more likely to act as a regulator of methylation rather than as an enzyme that
AB  - methylates DNA. Here, we show that Dnmt3L, like Dnmt3a and Dnmt3b, interacts both in vitro and
AB  - in vivo with the histone deacetylase HDAC1. Consistent with the binding to a deacetylase,
AB  - Dnmt3L purifies histone deacetylase activity from nuclear extracts. We find that Dnmt3L can
AB  - repress transcription and that this repression is dependent on HDAC1 and is relieved by
AB  - treatment with the HDAC inhibitor trichostatin A. Binding of Dnmt3L to HDAC1 as well as its
AB  - repressive function require the PHD-like motif. Our results indicate that Dnmt3L plays a role
AB  - in transcriptional regulation and that recruitment of the HDAC repressive machinery is a
AB  - shared and conserved feature of the Dnmt3 family. The fact that, despite the absence of a
AB  - methyltransferase domain, Dnmt3L retains the capacity to contact deacetylase further
AB  - substantiates the notion that the Dnmts can repress transcription independently of their
AB  - methylating activities.
ER  -

TY  - JOUR
AU  - Deppenmeier, U. et al.
TI  - The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea.
JO  - J. Mol. Microbiol. Biotechnol.
PY  - 2002
SP  - 453
EP  - 461
VL  - 4
AB  - The Archaeon Methanosarcina mazei and related species are of great ecological importance as
AB  - they are the only organisms fermenting acetate, methylamines and methanol to methane, carbon
AB  - dioxide and ammonia (in case of methylamines). Since acetate is the precursor of 60% of the
AB  - methane produced on earth these organisms contribute significantly to the production of this
AB  - greenhouse gas, e.g. in rice paddies. The 4,096,345 base pairs circular chromosome of M. mazei
AB  - is more than twice as large as the genomes of the methanogenic Archaea currently completely
AB  - sequenced (Bult et al., 1996; Smith et al., 1997). 3,371 open reading frames (ORFs) were
AB  - identified. Based on currently available sequence data 376 of these ORFs are
AB  - Methanosarcina-specific and 1,043 ORFs find their closest homologue in the bacterial domain.
AB  - 544 of these ORFs reach significant similarity values only in the bacterial domain. They
AB  - include 56 of the 102 transposases, and proteins involved in gluconeogenesis, proline
AB  - biosynthesis, transport processes, DNA-repair, environmental sensing, gene regulation, and
AB  - stress response. Striking examples are the occurrence of the bacterial GroEL/GroES chaperone
AB  - system and the presence of tetrahydrofolate-dependent enzymes. These findings might indicate
AB  - that lateral gene transfer has played an important evolutionary role in forging the physiology
AB  - of this metabolically versatile methanogen.
ER  -

TY  - JOUR
AU  - Deptula, P.
AU  - Laine, P.K.
AU  - Roberts, R.J.
AU  - Smolander, O.P.
AU  - Vihinen, H.
AU  - Piironen, V.
AU  - Paulin, L.
AU  - Jokitalo, E.
AU  - Savijoki, K.
AU  - Auvinen, P.
AU  - Varmanen, P.
TI  - De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii.
JO  - BMC Genomics
PY  - 2017
SP  - 790
EP  - 790
VL  - 18
AB  - BACKGROUND: Propionibacterium freudenreichii is an industrially important bacterium granted
AB  - the Generally Recognized as Safe (the GRAS) status, due to its
AB  - long safe use in food bioprocesses. Despite the recognized role in the food
AB  - industry and in the production of vitamin B12, as well as its documented
AB  - health-promoting potential, P. freudenreichii remained poorly characterised at
AB  - the genomic level. At present, only three complete genome sequences are available
AB  - for the species. RESULTS: We used the PacBio RS II sequencing platform to
AB  - generate complete genomes of 20 P. freudenreichii strains and compared them in
AB  - detail. Comparative analyses revealed both sequence conservation and genome
AB  - organisational diversity among the strains. Assembly from long reads resulted in
AB  - the discovery of additional circular elements: two putative conjugative plasmids
AB  - and three active, lysogenic bacteriophages. It also permitted characterisation of
AB  - the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed
AB  - identification of DNA modifications, which in turn allowed characterisation of
AB  - the restriction-modification systems together with their recognition motifs. The
AB  - observed genomic differences suggested strain variation in surface piliation and
AB  - specific mucus binding, which were validated by experimental studies. The
AB  - phenotypic characterisation displayed large diversity between the strains in
AB  - ability to utilise a range of carbohydrates, to grow at unfavourable conditions
AB  - and to form a biofilm. CONCLUSION: The complete genome sequencing allowed
AB  - detailed characterisation of the industrially important species, P.
AB  - freudenreichii by facilitating the discovery of previously unknown features. The
AB  - results presented here lay a solid foundation for future genetic and functional
AB  - genomic investigations of this actinobacterial species.
ER  -

TY  - JOUR
AU  - Deraspe, M.
AU  - Alexander, D.C.
AU  - Xiong, J.
AU  - Ma, J.H.
AU  - Low, D.E.
AU  - Jamieson, F.B.
AU  - Roy, P.H.
TI  - Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176.
JO  - FEMS Microbiol. Lett.
PY  - 2014
SP  - 212
EP  - 216
VL  - 356
AB  - Pseudomonas aeruginosa PA96 is a clinical isolate from Guangzhou, China, that is
AB  - multiresistant to antibiotics. We previously described the 500-kb IncP-2 plasmid, pOZ176 that
AB  - encodes many resistance genes including the IMP-9 carbapenemase. Whole-genome sequencing of
AB  - PA96 enabled characterization of its genomic islands, virulence factors, and chromosomal
AB  - resistance genes. We filled gaps using PCR and used optical mapping to confirm the correct
AB  - contig order. We automatically annotated the core genome and manually annotated the genomic
AB  - islands. The genome is 6 444 091 bp and encodes 5853 ORFs. From the whole-genome sequence, we
AB  - constructed a physical map and constructed a phylogenetic tree for comparison with sequenced
AB  - P. aeruginosa strains. Analysis of known core genome virulence factors and resistance genes
AB  - revealed few differences with other strains, but the major virulence island is closer to that
AB  - of DK2 than to PA14. PA96 most closely resembles the environmental strain M18, and notably
AB  - shares a common serotype, pyoverdin type, flagellar operon, type IV pilin, and several genomic
AB  - islands with M18.
ER  -

TY  - JOUR
AU  - Derbise, A.
AU  - Chenal-Francisque, V.
AU  - Huon, C.
AU  - Fayolle, C.
AU  - Demeure, C.E.
AU  - Chane-Woon-Ming, B.
AU  - Medigue, C.
AU  - Hinnebusch, B.J.
AU  - Carniel, E.
TI  - Delineation and Analysis of Chromosomal Regions Specifying Yersinia pestis.
JO  - Infect. Immun.
PY  - 2010
SP  - 3930
EP  - 3941
VL  - 78
AB  - Yersinia pestis, the causative agent of plague, has recently diverged from the less virulent
AB  - enteropathogen Yersinia pseudotuberculosis. Its
AB  - emergence has been characterized by massive genetic loss and
AB  - inactivation and limited gene acquisition. The acquired genes include
AB  - two plasmids, a filamentous phage, and a few chromosomal loci. The aim
AB  - of this study was to characterize the chromosomal regions acquired by
AB  - Y. pestis. Following in silico comparative analysis and PCR screening
AB  - of 98 strains of Y. pseudotuberculosis and Y. pestis, we found that
AB  - eight chromosomal loci (six regions [R1(pe) to R6(pe)] and two coding
AB  - sequences [CDS1(pe) and CDS2(pe)]) specified Y. pestis. Signatures of
AB  - integration by site specific or homologous recombination were
AB  - identified for most of them. These acquisitions and the loss of
AB  - ancestral DNA sequences were concentrated in a chromosomal region
AB  - opposite to the origin of replication. The specific regions were
AB  - acquired very early during Y. pestis evolution and were retained during
AB  - its microevolution, suggesting that they might bring some selective
AB  - advantages. Only one region (R3(pe)), predicted to carry a lambdoid
AB  - prophage, is most likely no longer functional because of mutations.
AB  - With the exception of R1(pe) and R2(pe), which have the potential to
AB  - encode a restriction/modification and a sugar transport system,
AB  - respectively, no functions could be predicted for the other Y.
AB  - pestis-specific loci. To determine the role of the eight chromosomal
AB  - loci in the physiology and pathogenicity of the plague bacillus, each
AB  - of them was individually deleted from the bacterial chromosome. None of
AB  - the deletants exhibited defects during growth in vitro. Using the
AB  - Xenopsylla cheopis flea model, all deletants retained the capacity to
AB  - produce a stable and persistent infection and to block fleas.
AB  - Similarly, none of the deletants caused any acute flea toxicity. In the
AB  - mouse model of infection, all deletants were fully virulent upon
AB  - subcutaneous or aerosol infections. Therefore, our results suggest that
AB  - acquisition of new chromosomal materials has not been of major
AB  - importance in the dramatic change of life cycle that has accompanied
AB  - the emergence of Y. pestis.
ER  -

TY  - JOUR
AU  - Derbyshire, V.
AU  - Kowalski, J.C.
AU  - Dansereau, J.T.
AU  - Hauer, C.R.
AU  - Belfort, M.
TI  - Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 494
EP  - 506
VL  - 265
AB  - I-TevI, the T4 td intron-encoded endonuclease, catalyzes the first step in intron homing by
AB  - making a double-strand break in the intronless allele within a sequence designated the homing
AB  - site.  The 28 kDa enzyme, which interacts with the homing site over a span of 37 bp, binds as
AB  - a monomer, contacting two domains of the substrate.  In this study, limited proteolysis
AB  - experiments indicate that I-TevI consists of two domains that behave as discrete physical
AB  - entities as judged by a number of functional and structural criteria.  Overexpression clones
AB  - for each domain were constructed and the proteins were purified.  The carboxy-terminal domain
AB  - has DNA-binding activity coincident with the primary binding region of the homing site and
AB  - binds with the same affinity as the full-length enzyme.  The isolated amino-terminal domain,
AB  - contains the conserved GIY-YIG motif, consistent with its being the catalytic domain.
AB  - Furthermore, site-directed mutagenesis of a conserved arginine residue within the extended
AB  - motif rendered the full-length protein catalytically inactive, although DNA-binding was
AB  - maintained.  This is the first evidence that the GIY-YIG motif is important for catalytic
AB  - activity.  An enzyme with an N-terminal catalytic domain and a C-terminal DNA-binding domain
AB  - connected by a flexible linker is in accord with the bipartite structure of the homing site.
ER  -

TY  - JOUR
AU  - Dertli, E.
AU  - Skory, C.D.
AU  - Simsek, O.
TI  - Genome Sequences of Five Lactobacillus sp. Isolates from Traditional Turkish Sourdough.
JO  - Genome Announcements
PY  - 2018
SP  - e00616
EP  - e00618
VL  - 6
AB  - A high level of variation in microflora can be observed in profiles of lactic acid bacteria
AB  - (LAB) from sourdoughs. Here, we present draft genome sequences of
AB  - Lactobacillus reuteri E81, L. reuteri LR5A, L. rhamnosus LR2, L. plantarum
AB  - PFC-311, and the novel Lactobacillus sp. strain PFC-70, isolated from traditional
AB  - Turkish backslopped wheat sourdoughs.
ER  -

TY  - JOUR
AU  - Desai, D.
AU  - Li, J.H.
AU  - van Zijll-de-Jong, E.
AU  - Braun, R.
AU  - Pitman, A.
AU  - Visnovsky, S.
AU  - Hampton, J.
AU  - Christey, M.
TI  - Draft Genome Sequences of Two New Zealand Xanthomonas campestris pv. campestris Isolates, ICMP 4013 and ICMP 21080.
JO  - Genome Announcements
PY  - 2015
SP  - e01247
EP  - e01215
VL  - 3
AB  - Xanthomonas campestris pv. campestris is a necrotrophic bacterial pathogen of crucifers. We
AB  - report here the draft genome sequences of isolates ICMP 4013 and
AB  - ICMP 21080 from New Zealand. These sequences will facilitate the identification
AB  - of race-specific factors in X. campestris pv. campestris.
ER  -

TY  - JOUR
AU  - Desai, H.P.
AU  - Morrison, S.S.
AU  - Diaz, M.H.
AU  - Benitez, A.J.
AU  - Wolff, B.J.
AU  - Winchell, J.M.
TI  - Complete Genome Sequence of Mycoplasma pneumoniae Type 2 Reference Strain FH Using Single-Molecule Real-Time Sequencing Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e01629
EP  - e01616
VL  - 5
AB  - Mycoplasma pneumoniae type 2 strain FH was previously sequenced with Illumina (FH-Illumina)
AB  - and 454 (FH-454) technologies according to Xiao et al. (2015) and
AB  - Krishnakumar et al. (2010). Comparative analyses revealed differences in genomic
AB  - content between these sequences, including a 6-kb region absent from the FH-454
AB  - submission. Here, we present a complete genome sequence of FH sequenced with the
AB  - Pacific Biosciences RSII platform.
ER  -

TY  - JOUR
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - Long, F.
AU  - Cheng, P.
AU  - Wollam, A.
AU  - Bhonagiri-Palsikar, V.
AU  - Hallsworth-Pepin, K.
AU  - Clifton, S.W.
AU  - Weinstock, G.M.
AU  - McClelland, M.
TI  - Evolutionary Genomics of Salmonella enterica Subspecies.
JO  - MBio
PY  - 2013
SP  - e00198
EP  - e00113
VL  - 4
AB  - Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies
AB  - enterica) is responsible for nearly all infections in humans and warm-blooded animals, while
AB  - five other subspecies are isolated principally from coldblooded animals. We sequenced 21
AB  - phylogenetically diverse strains, including two representatives from each of the previously
AB  - unsequenced five subspecies and 11 diverse new strains from S. enterica subspecies enterica,
AB  - to put this species into an evolutionary perspective. The phylogeny of the subspecies was
AB  - partly obscured by abundant recombination events between lineages and a relatively short
AB  - period of time within which subspeciation took place. Nevertheless, a variety of different
AB  - tree-building methods gave congruent evolutionary tree topologies for subspeciation. A total
AB  - of 285 gene families were identified that were recruited into subspecies enterica, and most of
AB  - these are of unknown function. At least 2,807 gene families were identified in one or more of
AB  - the other subspecies that are not found in subspecies I or Salmonella bongori. Among these
AB  - gene families were 13 new candidate effectors and 7 new candidate fimbrial clusters. A third
AB  - complete type III secretion system not present in subspecies enterica (I) isolates was found
AB  - in both strains of subspecies salamae (II). Some gene families had complex taxonomies, such as
AB  - the type VI secretion systems, which were recruited from four different lineages in five of
AB  - six subspecies. Analysis of nonsynonymous-to-synonymous substitution rates indicated that the
AB  - more-recently acquired regions in S. enterica are undergoing faster fixation rates than the
AB  - rest of the genome. Recently acquired AT-rich regions, which often encode virulence functions,
AB  - are under ongoing selection to maintain their high AT content.
ER  -

TY  - JOUR
AU  - Deschamps, P.
AU  - Zivanovic, Y.
AU  - Moreira, D.
AU  - Rodriguez-Valera, F.
AU  - Lopez-Garcia, P.
TI  - Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 1549
EP  - 1563
VL  - 6
AB  - Horizontal gene transfer (HGT) is an important force in evolution, which may
AB  - lead, among other things, to the adaptation to new environments by the import of
AB  - new metabolic functions. Recent studies based on phylogenetic analyses of a few
AB  - genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from
AB  - deep-sea metagenomic libraries have suggested that marine planktonic archaea
AB  - could be affected by high HGT frequency. Likewise, a composite genome of an
AB  - uncultured marine euryarchaeote showed high levels of gene sequence similarity to
AB  - bacterial genes. In this work, we ask whether HGT is frequent and widespread in
AB  - genomes of these marine archaea, and whether HGT is an ancient and/or recurrent
AB  - phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones
AB  - from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth)
AB  - and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I
AB  - archaea) and Euryarchaeota belonging to the uncultured Groups II and III
AB  - Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference
AB  - genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome
AB  - allowed us to define sets of core, lineage-specific core, and shell gene ortholog
AB  - clusters for the two archaeal lineages. Molecular phylogenetic analyses of all
AB  - gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of
AB  - GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is
AB  - not only extensive and directional but also ongoing, with high HGT levels in
AB  - lineage-specific core (ancient transfers) and shell (recent transfers) genes.
AB  - Many of the acquired genes are related to metabolism and membrane biogenesis,
AB  - suggesting an adaptive value for life in cold, oligotrophic oceans. We
AB  - hypothesize that the acquisition of an important amount of foreign genes by the
AB  - ancestors of these archaeal groups significantly contributed to their divergence
AB  - and ecological success.
ER  -

TY  - JOUR
AU  - Deschavanne, P.
AU  - Radman, M.
TI  - Counterselection of GATC sequences in enterobacteriophages by the components of the methyl-directed mismatch repair system.
JO  - J. Mol. Evol.
PY  - 1991
SP  - 125
EP  - 132
VL  - 33
AB  - Weak to severe deficit of GATC sequences in the DNA of enterobacteriophages appears to be
AB  - correlated with their undermethylation during growth in dam+ (GATC ade-methylase) bacteria.
AB  - This observation is corroborated by the sequence analysis showing no evidence for
AB  - site-specific mutagenicity of 6meAde. The MutH protein of the methyl-directed mismatch repair
AB  - system recognizes and cleaves the undermethylated GATC sequences in the course of mismatch
AB  - repair. To enquire whether the MutH function of the methyl-directed mismatch repair system
AB  - participates in counterselection of GATC sequences in enterobacteriophages, we have studied
AB  - the yield of bacteriophage PhiX174 containing either 0, 1, or 2 GATC sequences, in wild type,
AB  - dam, and mut (H,L,S,U) Escherichia coli. Following transfection with unmethylated DNA
AB  - containing two GATC sequences, a net decrease in the yield of infective particles was observed
AB  - in all bacterial mutH+ dam- strains, whereas no detectable decrease was observed in bacteria
AB  - infected by DNA without GATC sequence. This effect of the MutH function is maximum in wild
AB  - type and mutL and mutS bacteria whereas the effect is not significant in mutU bacteria,
AB  - suggesting an interaction of the helicase II with the MutH protein.
AB  - 
AB  - However, in dam+ bacteria, the presence of GATC sequences leads to an increased yield of
AB  - infective particles. The effect of GATC sequence and its Dam methylation system on phage yield
AB  - in mutH- bacteria reveals that methylated GATC sequences are advantageous to the phage. These
AB  - results suggest that the methyl-directed mismatch repair system, and in particular its MutH
AB  - protein, may have participated in severe counterselection of GATC sequences from
AB  - enterobacteriophages, presumably by DNA cleavage or by interfering with DNA replication or
AB  - packaging when GATC sequences are undermethylated. Coevolution of the Dam and MutH proteins
AB  - could then account for the loss of GATC sequences from DNA of bacteriophages growing in dam+
AB  - hosts.
AB  - 
ER  -

TY  - JOUR
AU  - Descloux, S.
AU  - Rossano, A.
AU  - Perreten, V.
TI  - Characterization of new Staphylococcal Cassette Chromosome mec (SCCmec) and topoisomerase genes in fluoroquinolone and methicillin-resistant Staphylococcus pseudintermedius.
JO  - J. Clin. Microbiol.
PY  - 2008
SP  - 1818
EP  - 1823
VL  - 46
AB  - Fluoroquinolone and methicillin-resistant Staphylococcus pseudintermedius isolates harbor two
AB  - new Staphylococcal Cassette Chromosome (SCCmec) which belong to class A, allotype 3 (SCCmec
AB  - II-III) and to the new allotype 5 (SCCmec VII). Analysis of the complete nucleotide sequence
AB  - of the topoisomerase loci gyrB/A and grlB/A revealed mutations involved in fluoroquinolone
AB  - resistance.
ER  -

TY  - JOUR
AU  - Deshpande, N.P.
AU  - Wong, Y.K.
AU  - Manefield, M.
AU  - Wilkins, M.R.
AU  - Lee, M.
TI  - Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00720
EP  - e00713
VL  - 1
AB  - The chloroform-respiring bacterium Dehalobacter UNSWDHB was isolated from subsurface soil
AB  - contaminated with a mixture of organohalides, including
AB  - chloroform. Here, we present its 3.2-Mb genome.
ER  -

TY  - JOUR
AU  - Deshuillers, P.L.
AU  - Santos, A.P.
AU  - do Nascimento, N.C.
AU  - Hampel, J.A.
AU  - Bergin, I.L.
AU  - Dyson, M.C.
AU  - Messick, J.B.
TI  - Complete Genome Sequence of Mycoplasma ovis Strain Michigan, a Hemoplasma of Sheep with Two Distinct 16S rRNA Genes.
JO  - Genome Announcements
PY  - 2014
SP  - e01235
EP  - e01213
VL  - 2
AB  - We report the complete genome sequence of Mycoplasma ovis strain Michigan. Its single circular
AB  - chromosome has 702,511 bp and contains 2 copies of the 16S rRNA
AB  - gene, one corresponding to M. ovis and the other to 'Candidatus Mycoplasma
AB  - haemovis.' All housekeeping genes and the 5S-23S rRNA genes are present in single
AB  - copies.
ER  -

TY  - JOUR
AU  - Desiere, F.
AU  - McShan, W.M.
AU  - van Sinderen, D.
AU  - Ferretti, J.J.
AU  - Brussow, H.
TI  - Comparative Genomics Reveals Close Genetic Relationships between Phages from Dairy Bacteria and Pathogenic Streptococci: Evolutionary Implications for Prophage-Host Interactions.
JO  - Virology
PY  - 2001
SP  - 325
EP  - 341
VL  - 288
AB  - The genome of the highly pathogenic M1 serotype Streptococcus pyogenes isolate SF370 contains
AB  - eight prophage elements. Only prophage SF370.1 could be induced by mitomycin C treatment.
AB  - Prophage SF370.3 showed a 33.5-kb-long genome that closely resembled the genome organization
AB  - of the cos-site temperate Siphovirus r1t infecting the dairy bacterium Lactococcus lactis. The
AB  - two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA
AB  - packaging, head and tail genes. Analysis of the SF370.3 genome revealed mutations in the
AB  - replisome organizer gene that may prevent the induction of the prophage. The mutated phage
AB  - replication gene was closely related to a virulence marker identified in recently emerged M3
AB  - serotype S. pyogenes strains in Japan. This observation suggests that prophage genes confer
AB  - selective advantage to the lysogenic host. SF370.3 encodes a hyaluronidase and a DNase that
AB  - may facilitate the spreading of S. pyogenes through tissue planes of its human host. Prophage
AB  - SF370.2 showed a 43-kb-long genome that closely resembled the genome organization of pac-site
AB  - temperate Siphoviridae infecting the dairy bacteria S. thermophilus and L. lactis. Over part
AB  - of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205
AB  - extended to the nucleotide sequence level. SF370.2 showed two probable inactivating mutations:
AB  - one in the replisome organizer gene and another in the gene encoding the portal protein.
AB  - Prophage SF370.2 also encodes a hyaluronidase and in addition two very likely virulence
AB  - factors: prophage-encoded toxins acting as superantigens that may contribute to the immune
AB  - deregulation observed during invasive streptococcal infections. The superantigens are encoded
AB  - between the phage lysin and the right attachment site of the prophage genome. The genes were
AB  - nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer.
AB  - The trend for prophage genome inactivation was even more evident for the remaining five
AB  - prophage sequences that showed massive losses of prophage DNA. In these prophage remnants only
AB  - 13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes
AB  - strain SF370 within the framework of Darwinian coevolution of prophages and lysogenic bacteria
AB  - and suggest elements of genetic cooperation and elements of an arms race in this host-parasite
AB  - relationship.
ER  -

TY  - JOUR
AU  - Desiniotis, A.
AU  - Kouvelis, V.N.
AU  - Davenport, K.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, C.
AU  - Goodwin, L.A.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Typas, M.A.
AU  - Pappas, K.M.
TI  - Complete Genome Sequence of the Ethanol-Producing Zymomonas mobilis subsp. mobilis Centrotype ATCC 29191.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5966
EP  - 5967
VL  - 194
AB  - Zymomonas mobilis is an ethanologenic bacterium that has been studied for use in  biofuel
AB  - production. Of the sequenced Zymomonas strains, ATCC 29191 has been
AB  - described as the phenotypic centrotype of Zymomonas mobilis subsp. mobilis, the
AB  - taxon that harbors the highest ethanol-producing Z. mobilis strains. ATCC 29191
AB  - was isolated in Kinshasa, Congo, from palm wine fermentations. This strain is
AB  - reported to be a robust levan producer, while in recent years it has been
AB  - employed in studies addressing Z. mobilis respiration. Here we announce the
AB  - finishing and annotation of the ATCC 29191 genome, which comprises one chromosome
AB  - and three plasmids.
ER  -

TY  - JOUR
AU  - Desirazu, N.R.
AU  - Reddy, Y.V.
TI  - Targetted DNA distortion by EcoP15I DNA methyltransferase.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A309
EP  - A309
VL  - 28
AB  - EcoP15I DNA methyltransferase, a member of the type III restriction-modification system, binds
AB  - to the sequence 5'-CAGCAG-3' transferring a methyl group from S-adenosyl-L-methionine to the
AB  - second adenine.  We have investigated protein-DNA interactions in the methylase-DNA complex by
AB  - three methods.  Determination of equilibrium dissociation constants indicated that the enzyme
AB  - had higher affinity for DNA containing mismatches at the target base within the recognition
AB  - sequence.  Potassium permanganate footprinting studies revealed that there was a
AB  - hyper-reactive cleavage site coincident with adenine that is the target base for methylation.
AB  - More importantly, to detect DNA conformational alterations within the enzyme-DNA complexes, we
AB  - have used a fluorescence-based assay, when the enzyme bound to DNA containing 2-aminopurine
AB  - substitutions within the cognate sequence, an 8-10 fold fluorescence enhancement resulting
AB  - from enzymatic flipping of the target adenine was observed, fluorescence spectroscopy analysis
AB  - showed that the changes attributable to structural distortion were specific for only the bases
AB  - within the recognition sequence.  Interestingly, we observed that both the adenines in the
AB  - recognition site appear to be structurally distorted to the same extent.  While the target
AB  - adenine is probably flipped out of the DNA duplex, our results also suggest that fluorescence
AB  - enhancements could be derived from protein-DNA interactions other than base flipping.  Taken
AB  - together, our results support the proposed base flipping mechanism for adenine
AB  - methyltransferases.
ER  -

TY  - JOUR
AU  - Detich, N.
AU  - Hamm, S.
AU  - Just, G.
AU  - Knox, J.D.
AU  - Szyf, M.
TI  - The methyl donor S-adenosylmethionine inhibits active demethylation of DNA: a candidate novel mechanism for the pharmacological effects of s-adenosylmethionine.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 20812
EP  - 20820
VL  - 278
AB  - S-Adenosylmethionine (AdoMet) is the methyl donor of numerous methylation reactions. The
AB  - current model is that an increased concentration of AdoMet
AB  - stimulates DNA methyltransferase reactions, triggering hypermethylation
AB  - and protecting the genome against global hypomethylation, a hallmark of
AB  - cancer. Using an assay of active demethylation in HEK 293 cells, we show
AB  - that AdoMet inhibits active demethylation and expression of an ectopically
AB  - methylated CMV-GFP (green fluorescent protein) plasmid in a dose-dependent
AB  - manner. The inhibition of GFP expression is specific to methylated GFP;
AB  - AdoMet does not inhibit an identical but unmethylated CMV-GFP plasmid.
AB  - S-Adenosylhomocysteine (AdoHcy), the product of methyltransferase
AB  - reactions utilizing AdoMet does not inhibit demethylation or expression of
AB  - CMV-GFP. In vitro, AdoMet but not AdoHcy inhibits methylated DNA-binding
AB  - protein 2/DNA demethylase as well as endogenous demethylase activity
AB  - extracted from HEK 293, suggesting that AdoMet directly inhibits
AB  - demethylase activity, and that the methyl residue on AdoMet is required
AB  - for its interaction with demethylase. Taken together, our data support an
AB  - alternative mechanism of action for AdoMet as an inhibitor of
AB  - intracellular demethylase activity, which results in hypermethylation of
AB  - DNA.
ER  -

TY  - JOUR
AU  - Detich, N.
AU  - Ramchandani, S.
AU  - Szyf, M.
TI  - A conserved 3'-untranslated element mediates growth regulation of DNA methyltransferase 1 and inhibits its transforming activity.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 24881
EP  - 24890
VL  - 276
AB  - Ectopic expression of DNA methyltransferase 1 (DNMT1) has been proposed to play an important
AB  - role in cancer. dnmt1 mRNA is undetectable in
AB  - growth-arrested cells but is induced upon entrance into the S phase of the cell cycle, and
AB  - until now, the mechanisms responsible for this regulation were unknown. In this report, we
AB  - demonstrate that the 3'-untranslated region (3'-UTR) of the dnmt1 mRNA can confer a
AB  - growth-dependent regulation on its own message as well as a heterologous beta-globin mRNA Our
AB  - results indicate that a 54-nucleotide highly conserved element within the 3'-UTR is necessary
AB  - and sufficient to mediate this regulation. Cell-free mRNA decay experiments demonstrate that
AB  - this element increases mRNA turnover rates and does so to a greater extent in the presence of
AB  - extracts prepared from arrested cells. A specific RNA-protein complex is formed with the
AB  - 3'-UTR only in growth-arrested cells, and a UV cross-linking analysis revealed a 40-kDa
AB  - protein (p40), the binding of which is dramatically increased in growth-arrested cells and is
AB  - inversely correlated with dnmt1 mRNA levels as cells are induced into the cell cycle. Although
AB  - ectopic expression of human DNMT1 lacking the 3'-UTR can transform NIH-3T3 cells, inclusion
AB  - of the 3'-UTR prevents transformation. These
AB  - results support the hypothesis that deregulated expression of DNMT1
AB  - with the cell cycle is important for cellular transformation.
ER  -

TY  - JOUR
AU  - Detich, N.
AU  - Theberge, J.
AU  - Szyf, M.
TI  - Promoter-specific activation and demethylation by MBD2/demethylase.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 35791
EP  - 35794
VL  - 277
AB  - MBD2 is the only member of a family of methyl-CpG-binding proteins that has been reported to
AB  - be both a transcriptional repressor and a DNA
AB  - demethylase (dMTase). To understand the apparently contradictory function
AB  - of MBD2/dMTase, we studied the effects of dMTase overexpression on the
AB  - activity of various in vitro methylated promoters transiently transfected
AB  - into HEK293 cells. We found that forced expression of a MBD2/dMTase
AB  - expression vector (His-dMTase) differentially activated two methylated
AB  - reporters, pSV40-CAT (the SV40 enhancerless promoter adjacent to the
AB  - chloramphenicol acetyltransferase (CAT) reporter gene) and pGL2T+I4xTBRE
AB  - (a region of the p21 promoter next to the luciferase reporter gene), in a
AB  - time- and dose-dependent manner. His-dMTase increased pSV40-CAT expression
AB  - by 3-10-fold after 96 h, while pGL2T+I4xTBRE expression was increased by
AB  - 2-3-fold after only 48 h and did not further increase at 96 h. Gene
AB  - activation was not universal because no effect was seen with the p19-ARF
AB  - promoter. We then assessed whether activation might be due to
AB  - demethylation within the promoter region. Using bisulfite mapping, we
AB  - found that exogenous expression of His-dMTase induced demethylation at 8
AB  - of the 10 CpG sites within the SV40 promoter. The observation that
AB  - His-dMTase increases the demethylase activity in the cells was also
AB  - confirmed using an in vitro CpG demethylase assay with a mC32pG
AB  - oligonucleotide substrate and purified Q-Sepharose fractions from HEK293
AB  - cells transfected with His-dMTase or empty pcDNA3.1His vector. We propose
AB  - that a single protein possessing both repressor and demethylase functions
AB  - has evolved to coordinate a program that requires suppression of some
AB  - methylated genes and activation of others.
ER  -

TY  - JOUR
AU  - Deutsch, J.
AU  - Razin, A.
AU  - Sedat, J.
TI  - Analysis of 5-methylcytosine in DNA.
JO  - Anal. Biochem.
PY  - 1976
SP  - 586
EP  - 592
VL  - 72
AB  - A method is described for the unambiguous rapid identification and quantitation of the minor
AB  - base, 5-methylcytosine, in DNA using high resolution mass spectrometry.  This method can
AB  - detect one 5-methylcytosine residue per 5500 nucleotides in Phi X174 DNA, in a sample of less
AB  - than 10 micrograms and requires less than 1 micrograms of calf thymus DNA in which the molar
AB  - ratio of 5-methylcytosine/cytosine is about 0.05.
ER  -

TY  - JOUR
AU  - Devajyothi, C.
AU  - Brahmachari, V.
TI  - Detection of a CpA methylase in an insect system: Characterization and substrate specificity.
JO  - Mol. Cell. Biochem.
PY  - 1992
SP  - 103
EP  - 111
VL  - 110
AB  - a cytosine-specific DNA methyltransferase (EC 2.1.1.37) has been purified to near homogeneity
AB  - from a mealybug (Planococcus lilacinus). The enzyme can methylate cytosine residues in CpG
AB  - sequences as well as CpA sequences. The apparent molecular weight of the enzymes was estimated
AB  - as 135,000 daltons by FPLC. The enzyme exhibits a processive mode of action and a salt
AB  - dependance similar to mammalian methylases. Mealybug methylase exhibits a preference for
AB  - denatured DNA substrates.
ER  -

TY  - JOUR
AU  - Deveau, A.
AU  - Gross, H.
AU  - Morin, E.
AU  - Karpinets, T.
AU  - Utturkar, S.
AU  - Mehnaz, S.
AU  - Martin, F.
AU  - Frey-Klett, P.
AU  - Labbe, J.
TI  - Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8.
JO  - Genome Announcements
PY  - 2014
SP  - e01152
EP  - e01113
VL  - 2
AB  - We report the draft genome sequence of the mycorrhizal helper bacterium Pseudomonas
AB  - fluorescens strain BBc6R8. This is the first genome of a mycorrhizal
AB  - helper bacterium. The draft genome contains 6,952,353 bp and is predicted to
AB  - encode 6,317 open reading frames. Comparative genomic analyses will help to
AB  - identify helper traits.
ER  -

TY  - JOUR
AU  - Devers-Lamrani, M.
AU  - Spor, A.
AU  - Mounier, A.
AU  - Martin-Laurent, F.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain ADP, a Bacterial Model for Studying the Degradation of the Herbicide Atrazine.
JO  - Genome Announcements
PY  - 2016
SP  - e01733
EP  - e01715
VL  - 4
AB  - We report here the 7,259,392-bp draft genome of Pseudomonas sp. strain ADP. This  is a
AB  - bacterial strain that was first isolated in the 1990s from soil for its
AB  - ability to mineralize the herbicide atrazine. It has extensively been studied as
AB  - a model to understand the atrazine biodegradation pathway. This genome will be
AB  - used as a reference and compared to evolved populations obtained by experimental
AB  - evolution conducted on this strain under atrazine selection pressure.
ER  -

TY  - JOUR
AU  - Devi, S.H.
AU  - Taylor, T.D.
AU  - Avasthi, T.S.
AU  - Kondo, S.
AU  - Suzuki, Y.
AU  - Megraud, F.
AU  - Ahmed, N.
TI  - Genome of Helicobacter pylori Strain 908.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6488
EP  - 6489
VL  - 192
AB  - Helicobacter pylori is a genetically diverse and coevolved pathogen inhabiting human gastric
AB  - niches and leading to a spectrum of gastric
AB  - diseases in susceptible populations. We describe the genome sequence of H.
AB  - pylori 908, which was originally isolated from an African patient living
AB  - in France who suffered with recrudescent duodenal ulcer disease. The
AB  - strain was found to be phylogenetically related to H. pylori J99, and its
AB  - comparative analysis revealed several specific genome features and novel
AB  - insertion-deletion and substitution events. The genome sequence revealed
AB  - several strain-specific deletions and/or gain of genes exclusively present
AB  - in HP908 compared with different sequenced genomes already available in
AB  - the public domain. Comparative and functional genomics of HP908 and its
AB  - subclones will be important in understanding genomic plasticity and the
AB  - capacity to colonize and persist in a changing host environment.
ER  -

TY  - JOUR
AU  - Devi, U.
AU  - Khatri, I.
AU  - Kumar, N.
AU  - Kumar, L.
AU  - Sharma, D.
AU  - Subramanian, S.
AU  - Saini, A.K.
TI  - Draft Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Serratia fonticola Strain AU-P3(3).
JO  - Genome Announcements
PY  - 2013
SP  - e00946
EP  - e00913
VL  - 1
AB  - Plant growth-promoting rhizobacteria (PGPR), found in the rhizospheric region of  plants, not
AB  - only suppress plant disease, but also directly improve plant health
AB  - by improving the availability of nutrients and by providing phytostimulants.
AB  - Herein, we report the high-quality genome sequence of Serratia fonticola strain
AB  - AU-P3(3), a PGPR of the pea plant, which confers phosphate solubilization,
AB  - indole-3-acetic acid production, ammonia production, hydrogen cyanide (HCN)
AB  - production, and siderophore production and also confers activity against
AB  - Rhizoctonia species. The 5.02-Mb genome sequence contains genes related to plant
AB  - growth promotion and biocontrol activities.
ER  -

TY  - JOUR
AU  - Devi, U.
AU  - Khatri, I.
AU  - Kumar, N.
AU  - Sharma, D.
AU  - Subramanian, S.
AU  - Saini, A.K.
TI  - Draft Genome Sequence of Plant-Growth-Promoting Rhizobacterium Serratia fonticola Strain AU-AP2C, Isolated from the Pea Rhizosphere.
JO  - Genome Announcements
PY  - 2013
SP  - e01022
EP  - e01013
VL  - 1
AB  - Plant health can be augmented by plant-growth-promoting rhizobacteria (PGPR) that confer
AB  - biofertilizer, phytostimulation, and biocontrol activities. Herein, we
AB  - provide the high-quality draft genome sequence of Serratia fonticola strain
AB  - AU-AP2C, a Gram-negative motile PGPR of the pea plant, conferring phosphate
AB  - solubilization, ammonia production, and antifungal activity against Fusarium sp.
AB  - The 4.9-Mb genome contains genes related to plant growth promotion and synthesis
AB  - of siderophores.
ER  -

TY  - JOUR
AU  - Devitt, N.P.
AU  - Herman, B.
AU  - Luchterhand, R.A.
AU  - Costa, M.A.
AU  - Jacobi, J.L.
AU  - Davin, L.B.
AU  - Lewis, N.G.
AU  - Bell, C.J.
TI  - Draft Genome Sequence of a Gordonia sp. Isolated from the Soil of a Red Alder Plant.
JO  - Genome Announcements
PY  - 2017
SP  - e01039
EP  - e01017
VL  - 5
AB  - A Gordonia species was cultured from soil of a red alder (Alnus rubra) plant. Here we present
AB  - the assembled and annotated genome sequence to aid investigations
AB  - into the potential of this organism as a symbiont and comparative studies of the
AB  - genus Gordonia.
ER  -

TY  - JOUR
AU  - Devor, E.J.
TI  - The relative efficiency of restriction enzymes:  an update.
JO  - Am. J. Hum. Genet.
PY  - 1988
SP  - 179
EP  - 182
VL  - 42
AB  - The question of which restriction enzymes to use in screening newly cloned
AB  - probes for RFLPs continues to come up.  The importance of this question is
AB  - obvious when it is recognised that, as of this writing, more than 140
AB  - restriction endonucleases are listed as commerically available.  By way of
AB  - aiding the decision process, Wijsman (1984) produced a model with which the
AB  - efficiency of any restriction enzyme relative to that of any other might be
AB  - assessed.  The model involves a calculation of the relative efficiency (RE) of
AB  - the enzyme, which takes into account the recognition sequence of the enzyme,
AB  - the size of the DNA fragment being used to probe the digests, and the minimum
AB  - restriction-fragment size detectable in the usual 0.7%-1.25% agarose gels.  RE
AB  - is thus a unitless value by means of which any two or more enzymes might be
AB  - compared.  All other things being equal, the higher the RE value the more
AB  - efficient the enzyme is in detecting sequence variants.  In this letter this
AB  - model is applied to an expanded and updated list of restriction enzymes, with
AB  - the result that some apparently good screening candidates and a few poor
AB  - candidates are observed.
ER  -

TY  - JOUR
AU  - Dey, R.
AU  - Pal, K.K.
AU  - Sherathia, D.
AU  - Dalsania, T.
AU  - Savsani, K.
AU  - Patel, I.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Thomas, M.
AU  - Ghorai, S.
AU  - Vanpariya, S.
AU  - Rupapara, R.
AU  - Rawal, P.
AU  - Saxena, A.K.
TI  - Draft Genome Sequence of Bacillus sp. Strain NSP2.1, a Nonhalophilic Bacterium Isolated from the Salt Marsh of the Great Rann of Kutch, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00909
EP  - e00913
VL  - 1
AB  - The 5.52-Mbp draft genome sequence of Bacillus sp. strain NSP2.1, a nonhalophilic bacterium
AB  - isolated from the salt marsh of the Great Rann of Kutch, India, is
AB  - reported here. An analysis of the genome of this organism will facilitate the
AB  - understanding of its survival in the salt marsh.
ER  -

TY  - JOUR
AU  - Dey, R.
AU  - Pal, K.K.
AU  - Sherathia, D.
AU  - Dalsania, T.
AU  - Savsani, K.
AU  - Patel, I.
AU  - Thomas, M.
AU  - Ghorai, S.
AU  - Vanpariya, S.
AU  - Rupapara, R.
AU  - Rawal, P.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Saxena, A.K.
TI  - Draft Genome Sequence of Bacillus sp. Strain NSP9.1, a Moderately Halophilic Bacterium Isolated from the Salt Marsh of the Great Rann of Kutch, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00835
EP  - e00813
VL  - 1
AB  - We report the 4.52-Mbp draft genome sequence of Bacillus sp. strain NSP9.1, a moderately
AB  - halophilic bacterium isolated from the salt marsh of the Great Rann of
AB  - Kutch, India. Analysis of the genome of this organism will lead to a better
AB  - understanding of the genes and metabolic pathways involved in imparting
AB  - osmotolerance.
ER  -

TY  - JOUR
AU  - Dey, R.
AU  - Pal, K.K.
AU  - Sherathia, D.
AU  - Sukhadiya, B.
AU  - Dalsania, T.
AU  - Patel, I.
AU  - Savsani, K.
AU  - Thomas, M.
AU  - Vanpariya, S.
AU  - Mandaliya, M.
AU  - Rupapara, R.
AU  - Rawal, P.
AU  - Ghorai, S.
AU  - Bhayani, S.
AU  - Shah, A.
AU  - Saxena, A.K.
TI  - Insight into the First Draft Genome Sequence of the Genus Sediminibacillus, Sediminibacillus halophilus Strain NSP9.3.
JO  - Genome Announcements
PY  - 2014
SP  - e01133
EP  - e01113
VL  - 2
AB  - We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain
AB  - NSP9.3, a moderate halophile isolated from a seasonal salt marsh of the
AB  - Great Rann of Kutch, India. Exploring the genome of this organism will facilitate
AB  - the understanding of the mechanism(s) of osmotolerance and survival in
AB  - differential osmolarity.
ER  -

TY  - JOUR
AU  - Dey, R.
AU  - Pal, K.K.
AU  - Sherathia, D.
AU  - Vanpariya, S.
AU  - Patel, I.
AU  - Dalsania, T.
AU  - Savsani, K.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Thomas, M.
AU  - Ghorai, S.
AU  - Rupapara, R.
AU  - Rawal, P.
TI  - Draft Genome Sequence of the Obligate Halophilic Bacillus sp. Strain NSP22.2, Isolated from a Seasonal Salt Marsh of the Great Rann of Kutch, India.
JO  - Genome Announcements
PY  - 2013
SP  - e01104
EP  - e01113
VL  - 1
AB  - Here, we report the 4.0-Mbp draft genome of an obligate halophile, Bacillus sp. strain
AB  - NSP22.2, isolated from a seasonal salt marsh of the Great Rann of Kutch,
AB  - India. To understand the mechanism(s) of obligate halophilism and to isolate the
AB  - relevant gene(s), the genome of Bacillus sp. NSP22.2 was sequenced.
ER  -

TY  - JOUR
AU  - Dhakal, R.
AU  - Seale, R.
AU  - Brent, D.
AU  - Hilton, C.
AU  - Craven, H.
AU  - Turner, M.S.
TI  - Draft Genome Comparison of Representatives of the Three Dominant Genotype Groups of Dairy Bacillus licheniformis Strains.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 3453
EP  - 3462
VL  - 80
AB  - The spore-forming bacterium Bacillus licheniformis is a common contaminant of milk and milk
AB  - products. Strains of this species isolated from dairy products can be differentiated into
AB  - three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA
AB  - (RAPD) analysis; however, little is known about the genomic differences between these groups
AB  - and the identity of the fragments that make up their RAPD profiles. In this work we obtained
AB  - high-quality draft genomes of representative strains from each of the three RAPD groups
AB  - (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to
AB  - B. licheniformis ATCC 14580 and Bacillus subtilis 168. Whole-genome comparison and multilocus
AB  - sequence typing revealed that strain G-1 contains significant sequence variability and belongs
AB  - to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding
AB  - for a type I restriction modification system, urease production, and bacitracin synthesis, as
AB  - well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In
AB  - agreement with this, all isolates of group G, but no group F isolates, were found to possess
AB  - urease activity and antimicrobial activity against Micrococcus. Identification of RAPD band
AB  - sequences revealed that differences in the RAPD profiles were due to differences in gene
AB  - lengths, 3' ends of predicted primer binding sites, or gene presence or absence. This work
AB  - provides a greater understanding of the phylogenetic and phenotypic differences observed
AB  - within the B. licheniformis species.
ER  -

TY  - JOUR
AU  - Dhakan, D.B.
AU  - Saxena, R.
AU  - Chaudhary, N.
AU  - Sharma, V.K.
TI  - Draft Genome Sequence of Tepidimonas taiwanensis Strain MB2, a Chemolithotrophic  Thermophile Isolated from a Hot Spring in Central India.
JO  - Genome Announcements
PY  - 2016
SP  - e01723
EP  - e01715
VL  - 4
AB  - Tepidimonas taiwanensis strain MB2 is a thermophile isolated from a hot spring located in
AB  - central India. Here, we report a 28,49,160 bp draft genome sequence of
AB  - Tepidimonas taiwanensis MB2. The genome shows properties of sulfur metabolism,
AB  - nitrogen fixation, ammonia metabolism, assimilation of organic acids, and a wide
AB  - variety of proteases.
ER  -

TY  - JOUR
AU  - Dhar, H.
AU  - Swarnkar, M.K.
AU  - Gulati, A.
AU  - Singh, A.K.
AU  - Kasana, R.C.
TI  - Draft Genome Sequence of a Cellulase-Producing Psychrotrophic Paenibacillus Strain, IHB B 3415, Isolated from the Cold Environment of the Western Himalayas,  India.
JO  - Genome Announcements
PY  - 2015
SP  - e01581
EP  - e01514
VL  - 3
AB  - Paenibacillus sp. strain IHB B 3415 is a cellulase-producing psychrotrophic bacterium isolated
AB  - from a soil sample from the cold deserts of Himachal Pradesh,  India. Here, we report an
AB  - 8.44-Mb assembly of its genome sequence with a G+C content of 50.77%. The data presented here
AB  - will provide insights into the mechanisms of cellulose degradation at low temperature.
ER  -

TY  - JOUR
AU  - Dharmalingam, K.
AU  - Goldberg, E.B.
TI  - Restriction in vivo.  IV. Effect of restriction of parental DNA on the expression of restriction alleviation systems in phage T4.
JO  - Virology
PY  - 1979
SP  - 404
EP  - 411
VL  - 96
AB  - Under restricting conditions expression of early T4 genes is determined in part by the
AB  - location of the particular gene relative to the cleavage site.  Some genes are inactivated
AB  - directly by cleavage of the DNA.  Other genes are inactivated by secondary exonucleolytic
AB  - degradation of cleaved DNA.  A third class of genes continues to be expressed from the small
AB  - fragments which remain after the exonucleolytic degradation of the cleaved fragments.
AB  - Expression of phage genes coding for the inhibitors of the restriction endonuclease and
AB  - restriction exonuclease are prevented by endonucleolytic cleavage and exonucleolytic
AB  - degradation, respectively.
ER  -

TY  - JOUR
AU  - Dharmalingam, K.
AU  - Goldberg, E.B.
TI  - Mechanism localisation and control of restriction cleavage of phage T4 and lambda chromosomes in vivo.
JO  - Nature
PY  - 1976
SP  - 406
EP  - 410
VL  - 260
AB  - The primary action of restriction endonuclease, cleaving infecting DNA, has
AB  - been demonstrated in vivo.  This primary cleavage is followed rapidly by
AB  - hydrolysis of the cleaved DNA at its newly exposed termini.  Infecting viruses
AB  - can inactivate cytoplasmic and membrane restriction endonucleases to prevent
AB  - cleavage of unmodified DNA replicas.
ER  -

TY  - JOUR
AU  - Dharmalingam, K.
AU  - Goldberg, E.B.
TI  - Restriction in vivo.  V. Induction of SOS functions in Escherichia coli by restricted T4 phage DNA and alleviation of restriction by SOS functions.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 51
EP  - 58
VL  - 178
AB  - Degradation products of restricted T4 DNA induced filamentation, mutagenesis,
AB  - and to a lesser extent, synthesis of recA protein in wild type cells but not in
AB  - recA, lexA or recBC mutants of Escherichia coli.  We conclude that the
AB  - structural damage to the DNA caused by restriction cleavage and exonuclease V
AB  - degradation can induce SOS functions.  Degradation of restricted
AB  - nonglucosylated T4 DNA by exonuclease V delayed cell division and induced
AB  - filament formation and mutagenesis in lexA+ but not in lexA- cells.  Delay of
AB  - cell division was also dependent upon recA and recBC functions.  Such
AB  - degradation of DNA also dramatically increased mutagenesis in tif- Sfi- cells
AB  - at 42.  The synthesis of recA protein continued in the restricting host after
AB  - infection by the nonglucosylated T4 phage, but enhanced synthesis is not
AB  - induced to the extent seen in SOS induced tif cells grown at 42.  We also found
AB  - that restriction of nonglucosylated T4 was alleviated in UV irradiated cells.
AB  - The UV induced alleviation of rgl and rK restriction depended upon post
AB  - irradiation protein synthesis and was not observed in recA, lexA or recBC
AB  - mutants.
ER  -

TY  - JOUR
AU  - Dharmalingam, K.
AU  - Goldberg, E.B.
TI  - Phage-coded protein prevents restriction of unmodified progeny T4 DNA.
JO  - Nature
PY  - 1976
SP  - 454
EP  - 455
VL  - 260
AB  - None
ER  -

TY  - JOUR
AU  - Dharmalingam, K.
AU  - Revel, H.R.
AU  - Goldberg, E.B.
TI  - Physical mapping and cloning of bacteriophage T4 anti-restriction ednonuclease gene.
JO  - J. Bacteriol.
PY  - 1982
SP  - 694
EP  - 699
VL  - 149
AB  - We have proposed that the ability of T4 to produce non-glucosylated progeny
AB  - after a single cycle of growth on a galU rglA rglB+ mutant of Escherichia coli
AB  - is due to the inhibition of the rglB+ function by a phage-coded,
AB  - anti-restriction endonuclease protein.  Based on this hypothesis, we screened
AB  - T4 deletion mutants for failure to give a burst in this host.  The absence of
AB  - an arn gene in phage mutants secondary infecting non-glucosylated phage from
AB  - rglB-controlled cleavage.  A functional arn gene was cloned on plasmid pBR325,
AB  - and the 0.8-kilobase insert DNA was shown to be homologous to the DNA missing
AB  - in the arn deletion phage.
ER  -

TY  - JOUR
AU  - Dharmaprakash, A.
AU  - Reghunathan, D.
AU  - Sivakumar, K.C.
AU  - Prasannakumar, M.
AU  - Thomas, S.
TI  - Insights into the Genome Sequences of an N-Acyl Homoserine Lactone Molecule Producing Two Pseudomonas spp. Isolated from the Arctic.
JO  - Genome Announcements
PY  - 2016
SP  - e00767
EP  - e00716
VL  - 4
AB  - We report for the first time the draft genome sequence of two psychrotrophic Pseudomonas
AB  - species, Pseudomonas simiae RGCB 73 and Pseudomonas brenneri RGCB
AB  - 108, from the Arctic that produce more than one acyl homoserine lactone molecule
AB  - of varied N-acyl length. The study confirms the presence of a LuxR-LuxI (type)
AB  - mediated quorum-sensing system in both the Pseudomonas species and enables us to
AB  - understand the role of quorum sensing in their survival in extremely cold
AB  - environments.
ER  -

TY  - JOUR
AU  - Dherbecourt, J.
AU  - Falentin, H.
AU  - Canaan, S.
AU  - Thierry, A.
TI  - A genomic search approach to identify esterases in Propionibacterium freudenreichii involved in the formation of flavour in Emmental cheese.
JO  - Microb. Cell Fact.
PY  - 2008
SP  - 16
EP  - 16
VL  - 7
AB  - ABSTRACT: BACKGROUND: Lipolysis is an important process of cheese ripening
AB  - that contributes to the formation of flavour. Propionibacterium
AB  - freudenreichii is the main agent of lipolysis in Emmental cheese; however,
AB  - the enzymes involved produced by this species have not yet been
AB  - identified. Lipolysis is performed by esterases (carboxylic ester
AB  - hydrolases, EC 3.1.1.-) which are able to hydrolyse acylglycerols bearing
AB  - short, medium and long chain fatty acids. The genome sequence of P.
AB  - freudenreichii type strain CIP103027T was recently obtained in our
AB  - laboratory.The aim of this study was to identify as exhaustively as
AB  - possible the potential esterases in P. freudenreichii that could be
AB  - involved in the hydrolysis of acylglycerols in Emmental cheese. The
AB  - proteins identified were produced in a soluble and active form by
AB  - heterologous expression in Escherichia coli for further study of their
AB  - activity and specificity of hydrolysed substrates. RESULTS: The approach
AB  - chosen was a genomic search approach that combined and compared four
AB  - methods based on automatic and manual searches of homology and motifs
AB  - among P. freudenreichii CIP103027T predicted proteins. Twenty-three
AB  - putative esterases were identified in this step. Then a selection step
AB  - permitted to focus the study on the 12 most probable esterases, according
AB  - to the presence of the GXSXG motif of the alpha/beta hydrolase fold
AB  - family. The 12 corresponding coding sequences were cloned in expression
AB  - vectors, containing soluble N-terminal fusion proteins. The best
AB  - conditions to express each protein in a soluble form were found thanks to
AB  - an expression screening, using an incomplete factorial experimental
AB  - design. Eleven out of the 12 proteins were expressed in a soluble form in
AB  - E. coli and six showed esterase activity on 1-naphthyl acetate and/or
AB  - propionate, as demonstrated by a zymographic method. CONCLUSION: We were
AB  - able to demonstrate that our genomic search approach was efficient to
AB  - identify esterases from the genome of a P. freudenreichii strain, more
AB  - exhaustively than classical approaches. This study highlights the interest
AB  - in using the automatic search of motifs, with the manual search of
AB  - homology to previously characterised enzymes as a complementary method.
AB  - Only further characterisations would permit the identification of the
AB  - esterases of P. freudenreichii involved in the lipolysis in Emmental
AB  - cheese.
ER  -

TY  - JOUR
AU  - Dhillon, B.
AU  - Cavaletto, J.R.
AU  - Wood, K.V.
AU  - Goodwin, S.B.
TI  - Accidental Amplification and Inactivation of a Methyltransferase Gene Eliminates Cytosine Methylation in Mycosphaerella graminicola.
JO  - Genetics
PY  - 2010
SP  - 67
EP  - 67
VL  - 186
AB  - A de novo search for repetitive elements in the genome sequence of the wheat pathogen
AB  - Mycosphaerella graminicola identified a family of
AB  - repeats containing a DNA cytosine methyltransferase sequence (MgDNMT).
AB  - All 23 MgDNMT sequences identified carried signatures of repeat induced
AB  - point mutation (RIP). All copies were subtelomeric in location except
AB  - for one on chromosome 6. Synteny with M. fijiensis implied that the
AB  - nontelomeric copy on chromosome 6 served as a template for subsequent
AB  - amplifications. Southern analysis revealed that the MgDNMT sequence
AB  - also was amplified in 15 additional M. graminicola isolates from
AB  - various geographical regions. However, this amplification event was
AB  - specific to M. graminicola; a search for MgDNMT homologs identified
AB  - only a single, unmutated copy in the genomes of 11 other ascomycetes. A
AB  - genome-wide methylation assay revealed that M. graminicola lacks
AB  - cytosine methylation, as expected if its MgDNMT gene is inactivated.
AB  - Methylation was present in several other species tested, including the
AB  - closest known relatives of M. graminicola, species S1 and S2.
AB  - Therefore, the observed changes most likely occurred within the past
AB  - 10,500 years since the divergence between M. graminicola and S1. Our
AB  - data indicate that the recent amplification of a single-copy MgDNMT
AB  - gene made it susceptible to RIP, resulting in complete loss of cytosine
AB  - methylation in M. graminicola.
ER  -

TY  - JOUR
AU  - Di Bonaventura, M.P.
AU  - Desalle, R.
AU  - Pop, M.
AU  - Nagarajan, N.
AU  - Figurski, D.H.
AU  - Fine, D.H.
AU  - Kaplan, J.B.
AU  - Planet, P.J.
TI  - Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.
JO  - J. Bacteriol.
PY  - 2009
SP  - 4693
EP  - 4694
VL  - 191
AB  - We report the finished and annotated genome sequence of Aggregatibacter aphrophilus strain
AB  - NJ8700, a strain isolated from the oral flora of a healthy individual, and discuss
AB  - characteristics that may affect its dual roles in human health and disease. This strain has a
AB  - rough appearance, and its genome contains genes encoding a type VI secretion system and
AB  - several factors that may participate in host colonization.
ER  -

TY  - JOUR
AU  - Di Cagno, R.
AU  - De Angelis, M.
AU  - Cattonaro, F.
AU  - Gobbetti, M.
TI  - Draft Genome Sequence of Lactobacillus rossiae DSM 15814T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5460
EP  - 5461
VL  - 194
AB  - The draft genome sequence of Lactobacillus rossiae DSM 15814(T) (CS1, ATCC BAA-88) was
AB  - determined by a whole-genome shotgun approach. Reads were assembled
AB  - to a 2.9-Mb draft version. RAST genome annotation evidenced 2,723 predicted
AB  - coding sequences. Many carbohydrate, amino acid, and amino acid derivative
AB  - subsystem features were found.
ER  -

TY  - JOUR
AU  - Di Gennaro, P.
AU  - Zampolli, J.
AU  - Presti, I.
AU  - Cappelletti, M.
AU  - D'Ursi, P.
AU  - Orro, A.
AU  - Mezzelani, A.
AU  - Milanesi, L.
TI  - Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2014
SP  - e00827
EP  - e00814
VL  - 2
AB  - Rhodococcus opacus strain R7 (CIP107348) degrades several mono- and polycyclic aromatic
AB  - hydrocarbons. Here, we present the high-quality draft genome sequence of
AB  - strain R7, consisting of 10,118,052 bp, with a G+C content of 67.0%, 9,602
AB  - protein-coding genes, and 62 RNAs genes.
ER  -

TY  - JOUR
AU  - Di Giaimo, R.
AU  - Locascio, A.
AU  - Aniello, F.
AU  - Branno, M.
AU  - del Gaudio, R.
AU  - Potenza, N.
AU  - Geraci, G.
TI  - DNA (cytosine-5) methyltransferase turnover and cellular localization in developing Paracentrotus lividus sea urchin embryo.
JO  - Gene
PY  - 2001
SP  - 199
EP  - 208
VL  - 272
AB  - The turnover and localization of the enzyme DNA (cytosine-5) methyltransferase (Dnmt1) were
AB  - studied during Paracentrotus lividus sea urchin embryo development using antibody preparations
AB  - against the NH(2) and COOH-terminal regions of the molecule. The antibodies reveal, by Western
AB  - blots and whole-mount analyses, that the enzyme is differentially required during embryonic
AB  - development. The changeover point is at blastula stage, where a proteolytic mechanism
AB  - hydrolyses the enzyme present in all embryonic cells by removing a peptide of about 45 kDa
AB  - from the amino terminal region of the 190 kDa enzyme initially synthesized on maternal
AB  - transcripts. The resulting 145 kDa enzyme shows modified catalytic properties, different
AB  - antibody reactivity and is rapidly destroyed in the few hours before gastrulation. At more
AB  - advanced stages of development the enzyme is newly synthesized but only in particular cell
AB  - types, among which are neurons. The data show that Dnmt1 is removed from embryonic cells
AB  - before gastrulation to be synthesized again at different levels in different cell types,
AB  - indicating that the concentration of Dnmt1 is critical for the various differentiated cells of
AB  - the developing sea urchin embryo.
ER  -

TY  - JOUR
AU  - Di Lallo, G.
AU  - Evangelisti, M.
AU  - Mancuso, F.
AU  - Ferrante, P.
AU  - Marcelletti, S.
AU  - Tinari, A.
AU  - Superti, F.
AU  - Migliore, L.
AU  - D'Addabbo, P.
AU  - Frezza, D.
AU  - Scortichini, M.
AU  - Thaller, M.C.
TI  - Isolation and partial characterization of bacteriophages infecting Pseudomonas syringae pv. actinidiae, causal agent of kiwifruit bacterial canker.
JO  - J. Basic Microbiol.
PY  - 2014
SP  - 1
EP  - 12
VL  - 54
AB  - The phytopathogen Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of bacterial
AB  - canker of kiwifruit. In the last years, it has caused severe economic losses to Actinidia spp.
AB  - cultivations, mainly in Italy and New Zealand. Conventional strategies adopted did not provide
AB  - adequate control of infection. Phage therapy may be a realistic and safe answer to the urgent
AB  - need for novel antibacterial agents aiming to control this bacterial pathogen. In this study,
AB  - we described the isolation and characterization of two bacteriophages able to specifically
AB  - infect Psa. phiPSA1, a member of the Siphoviridae family, is a temperate phage with a narrow
AB  - host range, a long latency, and a burst size of 178; phiPSA2 is a lytic phage of Podoviridae
AB  - family with a broader host range, a short latency, a burst size of 92 and a higher
AB  - bactericidal activity as determined by the TOD value. The genomic sequence of phiPSA1 has a
AB  - length of 51,090 bp and a low sequence homology with the other siphophages, whereas phiPSA2
AB  - has a length of 40 472 bp with a 98% homology with Pseudomonas putida bacteriophage gh-1. Of
AB  - the two phages examined, phiPSA2 may be considered as a candidate for phage therapy of
AB  - kiwifruit disease, while phiPSA1 seems specific toward the recent outbreak's isolates and
AB  - could be useful for Psa typing.
ER  -

TY  - JOUR
AU  - Di Pilato, V.
AU  - Chiarelli, A.
AU  - Boinett, C.J.
AU  - Riccobono, E.
AU  - Harris, S.R.
AU  - D'Andrea, M.M.
AU  - Thomson, N.R.
AU  - Rossolini, G.M.
AU  - Giani, T.
TI  - Complete Genome Sequence of the First KPC-Type Carbapenemase-Positive Proteus mirabilis Strain from a Bloodstream Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e00607
EP  - e00616
VL  - 4
AB  - Sequencing of the blaKPC-positive strain Proteus mirabilis AOUC-001 was performed using both
AB  - the MiSeq and PacBio RS II platforms and yielded a single molecule of
AB  - 4,272,433 bp, representing the complete chromosome. Genome analysis showed the
AB  - presence of several acquired resistance determinants, including two copies of
AB  - blaKPC-2 carried on a fragment of a KPC-producing plasmid previously described in
AB  - Klebsiella pneumoniae.
ER  -

TY  - JOUR
AU  - Di Pilato, V.
AU  - Pollini, S.
AU  - Rossolini, G.M.
TI  - Characterization of plasmid pAX22, encoding VIM-1 metallo-beta-lactamase, reveals a new putative mechanism of In70 integron mobilization.
JO  - J. Antimicrob. Chemother.
PY  - 2014
SP  - 67
EP  - 71
VL  - 69
AB  - Objectives: VIM-type enzymes are among the most widespread acquired metallo-b-lactamases among
AB  - Gramnegative pathogens. Integron In70 is a class 1 integron that has emerged as a successful
AB  - genetic support for
AB  - blaVIM-1 (one of themostprevalent blaVIM allelic variants) in
AB  - Gram-negativenon-fermenters,andis usually chromosome borne. The objective of this study was to
AB  - characterize plasmid pAX22 from Achromobacter xylosoxidans
AB  - AX22, which represents the only In70-harbouring plasmid known so far, to gather insights into
AB  - the mechanisms of evolution and dissemination of In70-like elements.
AB  - Methods: The complete sequence of pAX22was obtained by pyrosequencing and assembled with Roche
AB  - Newbler software. The draft sequence, completed using a PCR-based strategy, was annotated via
AB  - the BASys tool and compared with known sequences using BLAST algorithms.
AB  - Results: The backbone of pAX22 showed significant similarity with that of pNOR-2000, a
AB  - blaVIM-2-harbouring plasmid from Pseudomonas aeruginosa, and with the TnCP23 transposon. The
AB  - three elements differed from each other mainly by the class 1 integron cassette arrays and by
AB  - some integron-associated structures. In pAX22, In70was associated with a novel putative
AB  - transposon, Tn7017, composed of a defective Tn402-like transposon
AB  - carrying In70 and the ISPa17 insertion sequence.
AB  - Conclusion: Plasmid pAX22 belongs to a lineage of plasmids circulating among Gram-negative
AB  - non-fermenters. In70 was probably acquired by pAX22 by transposition of Tn7017, revealing a
AB  - novel putative mechanism of In70
AB  - mobilization. Our results highlight the potential role that ISPa17couldhave in mobilizing
AB  - defective Tn402-like transposons carrying class 1 integrons.
ER  -

TY  - JOUR
AU  - Di, D.Y.
AU  - Jang, J.
AU  - Unno, T.
AU  - Hur, H.G.
TI  - Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-beta-lactamase, in an urban river in South Korea.
JO  - J. Antimicrob. Chemother.
PY  - 2017
SP  - 1063
EP  - 1067
VL  - 72
AB  - Objectives: To examine the presence of pathogenic bacteria carrying New Delhi
AB  - metallo-beta-lactamase in the environment and to characterize the genome
AB  - structures of these strains. Methods: Phenotypic screening of antimicrobial
AB  - susceptibility and WGS were conducted on three Klebsiella variicola strains
AB  - possessing NDM-9 isolated from an urban river. Results: Three
AB  - carbapenem-resistant K. variicola isolated from Gwangju tributary were found to
AB  - possess bla NDM-9 genes. Antimicrobial susceptibility testing indicated
AB  - resistance of these strains to aminoglycosides, carbapenems, cephems, folate
AB  - pathway inhibitors, fosfomycin and penicillins, but susceptibility to
AB  - fluoroquinolones, phenicols, tetracyclines and miscellaneous agents. WGS revealed
AB  - that the 108 kb IncFII(Y)-like plasmids carry bla NDM-9 sandwiched between IS 15
AB  - for the GJ1 strain, IS 26 for the GJ2 strain, IS 15D1 for the GJ3 strain and IS
AB  - Vsa3 , and further bracketed by IS 26 and Tn AS3 along with the mercury
AB  - resistance operon upstream and the class 1 integron composed of gene cassettes of
AB  - aadA2 , dfrA12 and sul1 downstream. An aph(3')-Ia gene conferring resistance to
AB  - aminoglycosides is located after the integrons. Chromosomally encoded bla LEN-13
AB  - , fosA , aqxA and oqxB genes, as well as plasmid-mediated bla TEM-1B and bla
AB  - CTX-M-65 encoding ESBL, ant(3')-Ia and mph (A) genes, were also identified.
AB  - Conclusions: The findings of the present study provide us with the information
AB  - that NDM-9 has been spreading into the environment. Dissemination of NDM-9 in the
AB  - environment has raised a health risk alarm as this variant of NDM carries MDR
AB  - genes with highly transferable mobile genetic elements, increasing the
AB  - possibility of resistance gene transfer among microorganisms in the environment.
ER  -

TY  - JOUR
AU  - Diagne, N.
AU  - Swanson, E.
AU  - Pesce, C.
AU  - Fall, F.
AU  - Diouf, F.
AU  - Bakhoum, N.
AU  - Fall, D.
AU  - Faye, M.N.
AU  - Oshone, R.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Moulin, L.
AU  - Diouf, D.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequences for Mesorhizobium sp. Strains LCM 4576, LCM 4577, and ORS3428, Salt-Tolerant, Nitrogen-Fixing Bacteria Isolated from  Senegalese Soils.
JO  - Genome Announcements
PY  - 2017
SP  - e01154
EP  - e01117
VL  - 5
AB  - The genus Mesorhizobium contains many species that are able to form nitrogen-fixing nodules on
AB  - plants of the legume family. Here, we report the draft
AB  - genome sequences for three Mesorhizobium strains. The genome sizes of strains LCM
AB  - 4576, LCM 4577, and ORS3428 were 7.24, 7.02, and 6.55 Mbp, respectively.
ER  -

TY  - JOUR
AU  - Diagne, N.
AU  - Swanson, E.
AU  - Pesce, C.
AU  - Fall, F.
AU  - Diouf, F.
AU  - Bakhoum, N.
AU  - Fall, D.
AU  - Ndigue, F.M.
AU  - Oshone, R.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Moulin, L.
AU  - Diouf, D.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Ensifer sp. Strain LCM 4579, a Salt-Tolerant,  Nitrogen-Fixing Bacterium Isolated from Senegalese Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00117
EP  - e00117
VL  - 5
AB  - The genus Ensifer (formerly Sinorhizobium) contains many species able to form nitrogen-fixing
AB  - nodules on plants of the legume family. Here, we report the
AB  - 6.1-Mb draft genome sequence of Ensifer sp. strain LCM 4579, with a G+C content
AB  - of 62.4% and 5,613 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Diagne, N.
AU  - Swanson, E.
AU  - Pesce, C.
AU  - Fall, F.
AU  - Diouf, F.
AU  - Bakhoum, N.
AU  - Fall, D.
AU  - Ndigue, F.M.
AU  - Oshone, R.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Moulin, L.
AU  - Diouf, D.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Rhizobium sp. Strain LCM 4573, a Salt-Tolerant, Nitrogen-Fixing Bacterium Isolated from Senegalese Soils.
JO  - Genome Announcements
PY  - 2017
SP  - e00285
EP  - e00217
VL  - 5
AB  - The genus Rhizobium contains many species that are able to form nitrogen-fixing nodules on
AB  - plants of the legume family. Here, we report the 5.5-Mb draft genome
AB  - sequence of the salt-tolerant Rhizobium sp. strain LCM 4573, which has a G+C
AB  - content of 61.2% and 5,356 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Dias, G.M.
AU  - Thompson, C.C.
AU  - Fishman, B.
AU  - Naka, H.
AU  - Haygood, M.G.
AU  - Crosa, J.H.
AU  - Thompson, F.L.
TI  - Genome Sequence of the Marine Bacterium Vibrio campbellii DS40M4, Isolated from Open Ocean Water.
JO  - J. Bacteriol.
PY  - 2012
SP  - 904
EP  - 904
VL  - 194
AB  - Vibrio sp. strain DS40M4 is a marine bacterium that was isolated from open ocean water. In
AB  - this work, using genomic taxonomy, we were able to
AB  - classify this bacterium as V. campbellii. Our genomic analysis revealed
AB  - that V. campbellii DS40M4 harbors genes related to iron transport,
AB  - virulence, and environmental fitness, such as those encoding anguibactin
AB  - and vanchrobactin biosynthesis proteins, type II, III, IV, and VI
AB  - secretion systems, and proteorhodopsin.
ER  -

TY  - JOUR
AU  - Dias, L.M.
AU  - Alves, J.T.
AU  - Veras, A.A.
AU  - Barauna, R.A.
AU  - Sa, P.H.
AU  - Spier, S.
AU  - Edman, J.M.
AU  - Guimaraes, L.C.
AU  - Rocha, F.S.
AU  - Ramos, R.T.
AU  - Azevedo, V.
AU  - Silva, A.
AU  - Carneiro, A.R.
TI  - Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated  from the Abscess of a Goat in California.
JO  - Genome Announcements
PY  - 2016
SP  - e00038
EP  - e00016
VL  - 4
AB  - Corynebacterium pseudotuberculosis is the etiological agent of a caseous lymphadenitis
AB  - disease. Herein, we present the first complete genome sequencing of
AB  - C. pseudotuberculosis strain 226, isolated from an abscess of the sub-iliac lymph
AB  - node of a goat from California (USA). The genome contains 2,138 coding sequences
AB  - (CDSs), 12 rRNAs, 49 tRNAs, and 72 pseudogenes.
ER  -

TY  - JOUR
AU  - Diaz, L.A.
AU  - Hardisson, C.
AU  - Rodicio, M.R.
TI  - Isolation and characterization of actinophages infecting Streptomyces species and their interaction with host restriction-modification systems.
JO  - J. Gen. Microbiol.
PY  - 1989
SP  - 1847
EP  - 1856
VL  - 135
AB  - Nine different phages, PhiA1 to PhiA9, were isolated from soil samples on
AB  - Streptomyces antibioticus ATCC 11891, a strain which produces the macrolide
AB  - antibiotic oleandomycin.  Each phage displayed a different host-range which did
AB  - not extend beyond Streptomyces species.  Host-range was mainly limited by
AB  - adsorption specificity and host-controlled restriction-modification systems.
AB  - All the phages except PhiA3 and PhiA9 formed turbid plaques on S. antibioticus,
AB  - but did not lysogenize this host.  However, three of the phages (PhiA5, PhiA7
AB  - and PhiA8) were identified as temperate, since they were able to lysogenize
AB  - other Streptomyces strains.  All of the phages were morphologically similar and
AB  - belonged to group B of Bradley's classification.  They had polyhedral heads and
AB  - long, non-contractile tails.  PhiA5, PhiA6 and PhiA7 had a base plate at the
AB  - terminal end of the tail.  Analysis with restriction endonucleases indicated
AB  - that the nine phages contained double-stranded DNA.  Hybridization studies
AB  - between the phage genomes, together with results on genome structure, allowed
AB  - classification of the phages into five groups: (I) PhiA2, PhiA4 and PhiA9, (II)
AB  - PhiA3 and PhiA8, (III) PhiA7, (IV) PhiA5 and PhiA6, and (V) PhiA1.
ER  -

TY  - JOUR
AU  - Diaz, M.
AU  - Wegmann, U.
AU  - Akinyemi, N.
AU  - Oguntoyinbo, F.A.
AU  - Sayavedra, L.
AU  - Mayer, M.J.
AU  - Narbad, A.
TI  - Complete Genome Sequence of Ochrobactrum haematophilum FI11154, Isolated from Kunu-Zaki, a Nigerian Millet-Based Fermented Food.
JO  - Genome Announcements
PY  - 2018
SP  - e00428
EP  - e00418
VL  - 6
AB  - Ochrobactrum haematophilum FI11154 was isolated from kunu-zaki, a Nigerian traditional
AB  - fermented millet-based food. Here, we present the first complete
AB  - genome sequence of this species. The genome consists of five replicons and
AB  - contains genes related to iron uptake and phosphatase activities.
ER  -

TY  - JOUR
AU  - Diaz, M.H.
AU  - Desai, H.P.
AU  - Morrison, S.S.
AU  - Benitez, A.J.
AU  - Wolff, B.J.
AU  - Caravas, J.
AU  - Read, T.D.
AU  - Dean, D.
AU  - Winchell, J.M.
TI  - Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.
JO  - PLoS ONE
PY  - 2017
SP  - E0174701
EP  - E0174701
VL  - 12
AB  - Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide.
AB  - Despite a minimal and highly conserved genome, genetic diversity within the
AB  - species may impact disease. We performed whole genome sequencing (WGS) analysis
AB  - of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific
AB  - BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic
AB  - analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in
AB  - total, including 520 type-specific SNPs. Population structure analysis supported
AB  - the existence of six distinct subgroups, three within each type. We developed a
AB  - predictive model to classify an isolate based on whole genome SNPs called against
AB  - the reference genome into the identified subtypes, obviating the need for genome
AB  - assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to
AB  - date, underscoring the power of combining complementary sequencing technologies
AB  - to overcome difficult-to-sequence regions and highlighting potential differential
AB  - genomic signatures in M. pneumoniae.
ER  -

TY  - JOUR
AU  - Diaz-Cardenas, C.
AU  - Lopez, G.
AU  - Alzate-Ocampo, J.D.
AU  - Gonzalez, L.N.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Restrepo, S.
AU  - Baena, S.
TI  - Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565(T) an anaerobic,  slightly halophilic bacterium isolated from a Colombian saline spring.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 86
EP  - 86
VL  - 12
AB  - A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in
AB  - 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis
AB  - USBA 82(T) (DSM 21565(T)= KCTC 5659(T)) is a mesophilic, strictly anaerobic,
AB  - slightly halophilic, Gram negative bacterium with a diderm cell envelope. The
AB  - strain ferments peptides, amino acids and a few organic acids. Here we present
AB  - the description of the complete genome sequencing and annotation of the type
AB  - species Dethiosulfovibrio salsuginis USBA 82(T). The genome consisted of 2.68 Mbp
AB  - with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were
AB  - protein coding genes and 66 were RNA genes. We detected in USBA 82(T) genome six
AB  - Synergistetes conserved signature indels (CSIs), specific for Jonquetella,
AB  - Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as
AB  - expected, genes related to amino acid transport, amino acid metabolism and
AB  - thiosulfate reduction. These genes represent the major gene groups of
AB  - Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of
AB  - the genes in the genome belonged to the amino acid fermentation COG category. In
AB  - addition, we identified in the genome some ammonification genes such as nitrate
AB  - reductase genes. The presence of proline operon genes could be related to de novo
AB  - synthesis of proline to protect the cell in response to high osmolarity. Our
AB  - bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to
AB  - identify bacteriocins genes in the genome.
ER  -

TY  - JOUR
AU  - Diaz-Quinonez, J.A.
AU  - Hernandez-Monroy, I.
AU  - Lopez-Martinez, I.
AU  - Ortiz-Alcantara, J.
AU  - Gonzalez-Duran, E.
AU  - Ruiz-Matus, C.
AU  - Kuri-Morales, P.
AU  - Ramirez-Gonzalez, J.E.
TI  - Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013.
JO  - Genome Announcements
PY  - 2014
SP  - e01123
EP  - e01114
VL  - 2
AB  - We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a
AB  - cholera outbreak in Mexico. The genome showed the Vibrio 7th
AB  - pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the
AB  - integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXphi
AB  - and RS1phi.
ER  -

TY  - JOUR
AU  - Diaz-Sanchez, S.
AU  - Hernandez-Jarguin, A.
AU  - Fernandez-de-Mera, I.G.
AU  - Alberdi, P.
AU  - Zweygarth, E.
AU  - Gortazar, C.
AU  - de la Fuente, J.
TI  - Draft Genome Sequences of Anaplasma phagocytophilum, A. marginale, and A. ovis Isolates from Different Hosts.
JO  - Genome Announcements
PY  - 2018
SP  - e01503
EP  - e01517
VL  - 6
AB  - Here, we report the draft genome sequences of isolates of Anaplasma phagocytophilum, Anaplasma
AB  - marginale, and Anaplasma ovis The genomes of A.
AB  - phagocytophilum (human), A. marginale (cattle), and A. ovis (goat) isolates from
AB  - the United States were sequenced and characterized. This is the first report of
AB  - an A. ovis genome sequence.
ER  -

TY  - JOUR
AU  - Dib, J.R.
AU  - Angelov, A.
AU  - Liebl, W.
AU  - Dobber, J.
AU  - Voget, S.
AU  - Schuldes, J.
AU  - Gorriti, M.
AU  - Farias, M.E.
AU  - Meinhardt, F.
AU  - Daniel, R.
TI  - Complete Genome Sequence of the Linear Plasmid pJD12 Hosted by Micrococcus sp. D12, Isolated from a High-Altitude Volcanic Lake in Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e00627
EP  - e00615
VL  - 3
AB  - The linear plasmid pDJ12 from Micrococcus D12, isolated from the high-altitude volcanic
AB  - Diamante Lake in the northwest of Argentina, was completely sequenced
AB  - and annotated. It is noteworthy that the element is probably conjugative and
AB  - harbors genes potentially instrumental in coping with stress conditions that
AB  - prevail in such an extreme environment.
ER  -

TY  - JOUR
AU  - Dichosa, A.E. et al.
TI  - Draft Genome Sequence of Thauera sp. Strain SWB20, Isolated from a Singapore Wastewater Treatment Facility Using Gel Microdroplets.
JO  - Genome Announcements
PY  - 2015
SP  - e00132
EP  - e00115
VL  - 3
AB  - We report here the genome sequence of Thauera sp. strain SWB20, isolated from a Singaporean
AB  - wastewater treatment facility using gel microdroplets (GMDs) and
AB  - single-cell genomics (SCG). This approach provided a single clonal microcolony
AB  - that was sufficient to obtain a 4.9-Mbp genome assembly of an ecologically
AB  - relevant Thauera species.
ER  -

TY  - JOUR
AU  - Dick, G.J.
AU  - Andersson, A.F.
AU  - Baker, B.J.
AU  - Simmons, S.L.
AU  - Thomas, B.C.
AU  - Yelton, A.P.
AU  - Banfield, J.F.
TI  - Community-wide analysis of microbial genome sequence signatures.
JO  - Genome Biology
PY  - 2009
SP  - R85
EP  - R85
VL  - 10
AB  - BACKGROUND: Analyses of DNA sequences from cultivated microorganisms have
AB  - revealed genome-wide, taxa-specific nucleotide compositional characteristics,
AB  - referred to as genome signatures. These signatures have far-reaching implications
AB  - for understanding genome evolution and potential application in classification of
AB  - metagenomic sequence fragments. However, little is known regarding the
AB  - distribution of genome signatures in natural microbial communities or the extent
AB  - to which environmental factors shape them. RESULTS: We analyzed metagenomic
AB  - sequence data from two acidophilic biofilm communities, including composite
AB  - genomes reconstructed for nine archaea, three bacteria, and numerous associated
AB  - viruses, as well as thousands of unassigned fragments from strain variants and
AB  - low-abundance organisms. Genome signatures, in the form of tetranucleotide
AB  - frequencies analyzed by emergent self-organizing maps, segregated sequences from
AB  - all known populations sharing < 50 to 60% average amino acid identity and
AB  - revealed previously unknown genomic clusters corresponding to low-abundance
AB  - organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters
AB  - were resolved because intra-genome differences resulting from translational
AB  - selection or protein adaptation to the intracellular (pH approximately 5) versus
AB  - extracellular (pH approximately 1) environment were small relative to
AB  - inter-genome differences. We found that these genome signatures stem from
AB  - multiple influences but are primarily manifested through codon composition, which
AB  - we propose is the result of genome-specific mutational biases. CONCLUSIONS: An
AB  - important conclusion is that shared environmental pressures and interactions
AB  - among coevolving organisms do not obscure genome signatures in acid mine drainage
AB  - communities. Thus, genome signatures can be used to assign sequence fragments to
AB  - populations, an essential prerequisite if metagenomics is to provide ecological
AB  - and biochemical insights into the functioning of microbial communities.
ER  -

TY  - JOUR
AU  - Dick, G.J.
AU  - Podell, S.
AU  - Johnson, H.A.
AU  - Rivera-Espinoza, Y.
AU  - Bernier-Latmani, R.
AU  - McCarthy, J.K.
AU  - Torpey, J.W.
AU  - Clement, B.G.
AU  - Gaasterland, T.
AU  - Tebo, B.M.
TI  - Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 2646
EP  - 2658
VL  - 74
AB  - Microbial Mn(II) oxidation has important biogeochemical consequences in
AB  - marine, freshwater, and terrestrial environments, but many aspects of the
AB  - physiology and biochemistry of this process remain obscure. Here, we
AB  - report genomic insights into Mn(II) oxidation by the marine
AB  - alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the
AB  - oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors
AB  - the genetic potential for metabolic versatility, with genes for
AB  - organoheterotrophy, methylotrophy, oxidation of sulfur and carbon
AB  - monoxide, the ability to grow over a wide range of O(2) concentrations
AB  - (including microaerobic conditions), and the complete Calvin cycle for
AB  - carbon fixation. Although no growth could be detected under autotrophic
AB  - conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1
AB  - grown on glycerol are dramatically stimulated by addition of Mn(II),
AB  - suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II)
AB  - oxidase is encoded by duplicated multicopper oxidase genes that have a
AB  - complex evolutionary history including multiple gene duplication, loss,
AB  - and ancient horizontal transfer events. The Mn(II) oxidase was most
AB  - abundant in the extracellular fraction, where it cooccurs with a putative
AB  - hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing
AB  - the cellular response to Fe and Mn concentration were identified, and 39
AB  - targets of these regulators were detected. The putative Mn(II) oxidase
AB  - genes were not among the predicted targets, indicating that regulation of
AB  - Mn(II) oxidation is controlled by other factors yet to be identified.
AB  - Overall, our results provide novel insights into the physiology and
AB  - biochemistry of Mn(II) oxidation and reveal a genome specialized for life
AB  - at the oxic/anoxic interface.
ER  -

TY  - JOUR
AU  - Dickerson, R.E.
AU  - Drew, H.R.
TI  - Structure of a B-DNA dodecamer  II.  Influence of base sequence on helix structure.
JO  - J. Mol. Biol.
PY  - 1981
SP  - 761
EP  - 786
VL  - 149
AB  - Detailed examination of the structure of the B-DNA dodecamer
AB  - C-G-C-G-A-A-T-T-C-G-C-G, obtained by single-crystal X-ray analysis (Drew et
AB  - al., 1981), reveals that the local helix parameters, twist, tilt and roll, are
AB  - much more strongly influenced by base sequence than by crystal packing or any
AB  - other external forces.  The central EcoRI restriction endonuclease recognition
AB  - site, G-A-A-T-T-C, is a B helix with an average of 9.8 base-pairs per turn.  It
AB  - is flanked on either side by single base-pair steps having aspects of an A-like
AB  - helix character.  The dodecamer structure suggests several general principles,
AB  - whose validity must be tested by other B-DNA analyses.  (1) When an external
AB  - bending moment is applied to a B-DNA double helix, it bends smoothly, without
AB  - kinks or breaks, and with relatively little effect on local helix parameters.
AB  - (2) Purine-3', 5'-pyrimidine steps open their base planes towards the major
AB  - groove, pyrimidine-purine steps open toward the minor groove, and homopolymer
AB  - (Pur-Pur, Pyr-Pyr) steps resist rolling in either direction.  This behavior is
AB  - related to the preference of pyrimidines for more negative glycosyl torsion
AB  - angles.  (3) CpG steps have smaller helical twist angles than do GpC, as though
AB  - in compensation for their smaller intrinsic base overlap.  Data on A-T steps
AB  - are insufficient for generalization.  (4) G-C base-pairs have smaller propellor
AB  - twist than A-T, and this arises mainly from interstrand base overlap rather
AB  - than the presence of the third hydrogen bond.  (5) DNAase I cuts preferentially
AB  - at positions of high helical twist, perhaps because of increased exposure of
AB  - the backbone to attack.  The correlation of the digestion patterns in solution
AB  - and helical twist in the crystal argues for the essential identity of the helix
AB  - structure in the two environments.  (6) In the two places where the sequence
AB  - TpCpG occurs, the C slips from under T in order to stack more efficiently over
AB  - G.  At the paired bases of this CpG step, the G and C are tilted so the angle
AB  - between base planes is splayed out to the outside of the helix.  This TpC is
AB  - the most favored cutting site for DNAse I by a factor of 4-5 (Lomonossoff et
AB  - al., 1981).  (7) The EcoRI restriction endonuclease and methylase both appear
AB  - to prefer a cutting site of the type purine-purine-A-T-T-pyrimidine, involving
AB  - two adjacent homopolymer triplets, and this may be a consequence of the
AB  - relative stiffness of homopolymer base-stacking observed in the dodecamer.
ER  -

TY  - JOUR
AU  - Dickman, S.
TI  - Lithuanian biochemist builds enzyme empire.
JO  - Science
PY  - 1992
SP  - 1473
EP  - 1474
VL  - 257
AB  - Vilnius -If you like to browse through laboratory catalogs looking for the latest equipment
AB  - and reagents, you might have come across a surprising entry in the most recent offering from
AB  - New England Biolabs.  There, on page 46, you'll find a whole set of new restriction enzymes
AB  - -the enzymes that chop up DNA and are a vital part of every molecular biologist's toolbox.
AB  - The surprise: The enzymes are all labeled "Made in Lithuania".  Lithuania? How could a small
AB  - Baltic state, independent for less than a year, compete with hot shot Western biotech
AB  - companies in supplying enzymes to the United States? Ask Rich Roberts, the former Cold Spring
AB  - Harbor Laboratory molecular biologist who is now director of research for New England Biolabs
AB  - and he will answer in a word: "Janulaitis".  Vidas Janulaitis (pronounced Yanoo-LITEis), he
AB  - will tell you, is professor of biochemistry a the University of Vilnius, head of the Institute
AB  - of Applied Enzymology -and creator of one of the world's largest collections of restriction
AB  - enzymes, with more than 100 on offer.  He also appears to be the first successful
AB  - biotechnology entrepreneur to emerge from the former Soviet Union -and New England Biolabs'
AB  - competitors are well aware of his talents.  "Formidable", is how Jeremy Walker of Amersham
AB  - International describes Janulaitis' contribution to the number of new restriction enzymes
AB  - marketed each year.
ER  -

TY  - JOUR
AU  - Didelot, X.
AU  - Pang, B.
AU  - Zhou, Z.
AU  - McCann, A.
AU  - Ni, P.
AU  - Li, D.
AU  - Achtman, M.
AU  - Kan, B.
TI  - The role of china in the global spread of the current cholera pandemic.
JO  - PLoS Genet.
PY  - 2015
SP  - E1005072
EP  - E1005072
VL  - 11
AB  - Epidemics and pandemics of cholera, a severe diarrheal disease, have occurred
AB  - since the early 19th century and waves of epidemic disease continue today.
AB  - Cholera epidemics are caused by individual, genetically monomorphic lineages of
AB  - Vibrio cholerae: the ongoing seventh pandemic, which has spread globally since
AB  - 1961, is associated with lineage L2 of biotype El Tor. Previous genomic studies
AB  - of the epidemiology of the seventh pandemic identified three successive
AB  - sub-lineages within L2, designated waves 1 to 3, which spread globally from the
AB  - Bay of Bengal on multiple occasions. However, these studies did not include
AB  - samples from China, which also experienced multiple epidemics of cholera in
AB  - recent decades. We sequenced the genomes of 71 strains isolated in China between
AB  - 1961 and 2010, as well as eight from other sources, and compared them with 181
AB  - published genomes. The results indicated that outbreaks in China between 1960 and
AB  - 1990 were associated with wave 1 whereas later outbreaks were associated with
AB  - wave 2. However, the previously defined waves overlapped temporally, and are an
AB  - inadequate representation of the shape of the global genealogy. We therefore
AB  - suggest replacing them by a series of tightly delineated clades. Between 1960 and
AB  - 1990 multiple such clades were imported into China, underwent further
AB  - microevolution there and then spread to other countries. China was thus both a
AB  - sink and source during the pandemic spread of V. cholerae, and needs to be
AB  - included in reconstructions of the global patterns of spread of cholera.
ER  -

TY  - JOUR
AU  - Didier, S.
AU  - Lazzaroni, J.C.
AU  - Portalier, R.
TI  - Cell localization of EcoRI endonuclease in Escherichia coli K-12.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1988
SP  - 468
EP  - 470
VL  - 28
AB  - Cell compartmentation of EcoRI endonuclease was analyzed using either parental
AB  - or tolA excretory strains of Escherichia coli.  Cells were subjected to various
AB  - fractionation procedures such as osmotic shock or spheroplast formation.  Our
AB  - results showed that EcoRI activity was almost entirely recovered into
AB  - cytoplasmic fractions and consequently was not released into the extracellular
AB  - medium by a tolA mutant.  These results did not support previous reports
AB  - suggesting a periplasmic location for the EcoRI enzyme and did not allow to
AB  - develop a simple method for EcoRI purification from culture supernatants of
AB  - excretory mutants.
ER  -

TY  - JOUR
AU  - Didovyk, A.
TI  - The structural basis of DNA recognition and base extrusion by a DNA cytosine-5 methyltransferase M.HaeIII.
JO  - Ph.D. Thesis, Harvard University, USA
PY  - 2010
AB  - The goal of this study is to elucidate the mechanism of sequence specific DNA recognition and
AB  - base extrusion by DNA cytosine-5 methyltransferase from Haemophilus aegyptius M.Haelll. We
AB  - have solved the crystal structure of the C71S mutant of M.Haelll in complex with the substrate
AB  - DNA at 2.4A resolution (InC below for brevity). For the first time an X-ray structure reveals
AB  - a fully intrahelical target cytosine
AB  - poised for extrusion by a cytosine-5 methyltransferase. The target cytosine
AB  - is destabilized, having lost most of its stacking interactions with both neighbouring bases
AB  - and making longer hydrogen bonds with the complementary guanine. In addition the protein
AB  - competes for Watson-Crick hydrogen bonding of the target base pair.  Both the protein and the
AB  - DNA conformations are remarkably different from those in the structure where the target
AB  - cytosine is extrahelical (ExC for brevity) [57]. In the ExC structure the cytosine 3 ' of the
AB  - target base is the one forming a base pair with the guanine of the target base pair, whereas
AB  - in the InC structure the bases within the
AB  - recognition sequence stay correctly paired. The conformation of the DNA backbone 3' to the
AB  - target cytosine changes significantly as well - it shifts further away from the protein. The
AB  - catalytic loop of M.Haelll (residues 71-89) is retracted away from the DNA as well. The
AB  - results suggest that M.Haelll actively participates in base flipping.  It destabilizes the
AB  - target base by altering both stacking and Watson-Crick hydrogen bonding - two fundamental
AB  - interactions that keep DNA bases intrahelical.  In order to elucidate the role of the
AB  - intercalating residue Ile-221 in base extrusion,
AB  - a glycine mutant was constructed. Its structure in complex with the specific DNA has been
AB  - determined using X-ray crystallography. This structure is essentially identical to the ExC,
AB  - suggesting that the extrahelical state, observed in ExC, can be achieved in the absence of the
AB  - DNA helix stabilization provided by Ile-221.
ER  -

TY  - JOUR
AU  - Didovyk, A.
AU  - Verdine, G.L.
TI  - Structural Origins of DNA Target Selection and Nucleobase Extrusion by a DNA Cytosine Methyltransferase.
JO  - J. Biol. Chem.
PY  - 2012
SP  - 40099
EP  - 40105
VL  - 287
AB  - Epigenetic methylation of cytosine residues in DNA is an essential element of genome
AB  - maintenance and function in organisms ranging from
AB  - bacteria to humans. DNA 5-cytosine methyltransferase enzymes (DCMTases)
AB  - catalyze cytosine methylation via reaction intermediates in which the
AB  - DNA is drastically remodeled, with the target cytosine residue extruded
AB  - from the DNA helix and plunged into the active site pocket of the
AB  - enzyme. We have determined a crystal structure of M.HaeIII DCMTase in
AB  - complex with its DNA substrate at a previously unobserved state, prior
AB  - to extrusion of the target cytosine and frameshifting of the DNA
AB  - recognition sequence. The structure reveals that M.HaeIII selects the
AB  - target cytosine and destabilizes its base-pairing through a precise,
AB  - focused, and coordinated assault on the duplex DNA, which isolates the
AB  - target cytosine from its nearest neighbors and thereby facilitates its
AB  - extrusion from DNA.
ER  -

TY  - JOUR
AU  - Dieguez, A.L.
AU  - Romalde, J.L.
TI  - Complete Genome Sequence of Arcobacter sp. Strain LFT 1.7 Isolated from Great Scallop (Pecten maximus) Larvae.
JO  - Genome Announcements
PY  - 2017
SP  - e01617
EP  - e01616
VL  - 5
AB  - Arcobacter sp. strain LFT 1.7 was isolated from great scallop (Pecten maximus) larvae.
AB  - Analysis of the 16S rRNA gene sequence showed that strain LFT 1.7 formed
AB  - an independent lineage in the genus Arcobacter The draft genome of LFT 1.7 was
AB  - sequenced to determine the taxonomic position and ecological function of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Dieguez, A.L.
AU  - Romalde, J.L.
TI  - Draft Genome Sequences of Neptuniibacter sp. Strains LFT 1.8 and ATR 1.1.
JO  - Genome Announcements
PY  - 2017
SP  - e01541
EP  - e01516
VL  - 5
AB  - We present the draft genomes of two strains previously identified as Neptuniibacter sp. LFT
AB  - 1.8 (= CECT 8936 = DSM 100781) and ATR 1.1 (= CECT 8938 =
AB  - DSM 100783) isolated from larvae of great scallops (Pecten maximus) and seawater,
AB  - respectively. Both strains surely constitute two novel species in this genus,
AB  - with putative applications for aromatic compound degradation.
ER  -

TY  - JOUR
AU  - Diekmann, S.
AU  - McLaughlin, L.W.
TI  - DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction.
JO  - J. Mol. Biol.
PY  - 1988
SP  - 823
EP  - 834
VL  - 202
AB  - The ligation of a decadeoxynucleotide containing the EcoRI recognition site
AB  - forms a series of multimers which appear to be curved based on observed
AB  - anomalous gel migration in polyacrylamide gels.  The degree of DNA curvature
AB  - present in the recognition sequence, based upon the observed migration anomaly,
AB  - can be altered by modifications to the purine functional groups at the 2- and
AB  - 6-positions.  Deletion of the guanine 2-amino group, occurring in the minor
AB  - groove of the B-DNA helix, is most effective in increasing the observed DNA
AB  - curvature.  Conversely, the displacement of an amino group from the major
AB  - groove to the minor groove eliminates curvature.  DNA curvature is also
AB  - modulated by the exocyclic group at the purine 6-position with decreasing
AB  - curvature observed when changing the amino group to a carbonyl or proton
AB  - substitute.
ER  -

TY  - JOUR
AU  - Diene, S.M.
AU  - Merhej, V.
AU  - Henry, M.
AU  - El Filali, A.
AU  - Roux, V.
AU  - Robert, C.
AU  - Azza, S.
AU  - Gavory, F.
AU  - Barbe, V.
AU  - La Scola, B.
AU  - Raoult, D.
AU  - Rolain, J.M.
TI  - The Rhizome of the Multidrug-Resistant Enterobacter aerogenes Genome Reveals How New 'Killer Bugs' Are Created because of a Sympatric Lifestyle.
JO  - Mol. Biol. Evol.
PY  - 2013
SP  - 369
EP  - 383
VL  - 30
AB  - Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes
AB  - clinical isolate that killed a patient and was resistant to almost all current
AB  - antibiotics (except gentamicin) commonly used to treat Enterobacterial
AB  - infections, including colistin. Genomic and phylogenetic analyses explain the
AB  - discrepancies of this bacterium and show that its core genome originates from
AB  - another genus, Klebsiella. Atypical characteristics of this bacterium (i.e.,
AB  - motility, presence of ornithine decarboxylase, and lack of urease activity) are
AB  - attributed to genomic mosaicism, by acquisition of additional genes, such as the
AB  - complete 60,582 bp flagellar assembly operon acquired "en bloc" from the genus
AB  - Serratia. The genealogic tree of the 162,202 bp multidrug-resistant conjugative
AB  - plasmid shows that it is a chimera of transposons and integrative conjugative
AB  - elements from various bacterial origins, resembling a rhizome. Moreover, we
AB  - demonstrate biologically that a G53S mutation in the pmrA gene results in
AB  - colistin resistance. E. aerogenes has a large RNA population comprising 8 rRNA
AB  - operons and 87 cognate tRNAs that have the ability to translate transferred genes
AB  - that use different codons, as exemplified by the significantly different codon
AB  - usage between genes from the core genome and the "mobilome." On the basis of our
AB  - findings, the evolution of this bacterium to become a "killer bug" with new
AB  - genomic repertoires was from three criteria that are "opportunity, power, and
AB  - usage" to indicate a sympatric lifestyle: "opportunity" to meet other bacteria
AB  - and exchange foreign sequences since this bacteria was similar to sympatric
AB  - bacteria; "power" to integrate these foreign sequences such as the acquisition of
AB  - several mobile genetic elements (plasmids, integrative conjugative element,
AB  - prophages, transposons, flagellar assembly system, etc.) found in his genome; and
AB  - "usage" to have the ability to translate these sequences including those from
AB  - rare codons to serve as a translator of foreign languages.
ER  -

TY  - JOUR
AU  - Diep, A.L.
AU  - Lang, J.M.
AU  - Darling, A.E.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2013
SP  - e00197
EP  - e00113
VL  - 1
AB  - Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP,
AB  - isolated from a residential toilet handle. The assembly contains
AB  - 3,915,613 bp. The genome sequences of only two other Dietzia species have been
AB  - published, those of Dietzia alimentaria and Dietzia cinnamea.
ER  -

TY  - JOUR
AU  - Diep, B.A.
AU  - Gill, S.R.
AU  - Chang, R.F.
AU  - Phan, T.H.
AU  - Chen, J.H.
AU  - Davidson, M.G.
AU  - Lin, F.
AU  - Lin, J.
AU  - Carleton, H.A.
AU  - Mongodin, E.F.
AU  - Sensabaugh, G.F.
AU  - Perdreau-Remington, F.
TI  - Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus.
JO  - Lancet
PY  - 2006
SP  - 731
EP  - 739
VL  - 367
AB  - BACKGROUND: USA300, a clone of meticillin-resistant Staphylococcus aureus, is a major source
AB  - of community-acquired infections in the USA, Canada, and
AB  - Europe. Our aim was to sequence its genome and compare it with those of
AB  - other strains of S aureus to try to identify genes responsible for its
AB  - distinctive epidemiological and virulence properties. METHODS: We
AB  - ascertained the genome sequence of FPR3757, a multidrug resistant USA300
AB  - strain, by random shotgun sequencing, then compared it with the sequences
AB  - of ten other staphylococcal strains. FINDINGS: Compared with closely
AB  - related S aureus, we noted that almost all of the unique genes in USA300
AB  - clustered in novel allotypes of mobile genetic elements. Some of the
AB  - unique genes are involved in pathogenesis, including Panton-Valentine
AB  - leucocidin and molecular variants of enterotoxin Q and K. The most
AB  - striking feature of the USA300 genome is the horizontal acquisition of a
AB  - novel mobile genetic element that encodes an arginine deiminase pathway
AB  - and an oligopeptide permease system that could contribute to growth and
AB  - survival of USA300. We did not detect this element, termed arginine
AB  - catabolic mobile element (ACME), in other S aureus strains. We noted a
AB  - high prevalence of ACME in S epidermidis, suggesting not only that ACME
AB  - transfers into USA300 from S epidermidis, but also that this element
AB  - confers a selective advantage to this ubiquitous commensal of the human
AB  - skin. INTERPRETATION: USA300 has acquired mobile genetic elements that
AB  - encode resistance and virulence determinants that could enhance fitness
AB  - and pathogenicity.
ER  -

TY  - JOUR
AU  - Dikic, J.
AU  - Menges, C.
AU  - Clarke, S.
AU  - Kokkinidis, M.
AU  - Pingoud, A.
AU  - Wende, W.
AU  - Desbiolles, P.
TI  - The rotation-coupled sliding of EcoRV.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 4064
EP  - 4070
VL  - 40
AB  - It has been proposed that certain type II restriction enzymes (REs), such as EcoRV, track the
AB  - helical pitch of DNA as they diffuse along DNA, a so-called
AB  - rotation-coupled sliding. As of yet, there is no direct experimental observation
AB  - of this phenomenon, but mounting indirect evidence gained from single-molecule
AB  - imaging of RE-DNA complexes support the hypothesis. We address this issue by
AB  - conjugating fluorescent labels of varying size (organic dyes, proteins and
AB  - quantum dots) to EcoRV, and by fusing it to the engineered Rop protein scRM6.
AB  - Single-molecule imaging of these modified EcoRVs sliding along DNA provides us
AB  - with their linear diffusion constant (D(1)), revealing a significant size
AB  - dependency. To account for the dependence of D(1) on the size of the EcoRV label,
AB  - we have developed four theoretical models describing different types of motion
AB  - along DNA and find that our experimental results are best described by
AB  - rotation-coupled sliding of the protein. The similarity of EcoRV to other type II
AB  - REs and DNA binding proteins suggests that this type of motion could be widely
AB  - preserved in other biological contexts.
ER  -

TY  - JOUR
AU  - Dila, D.
AU  - Raleigh, E.A.
TI  - Genetic dissection of the methylcytosine-specific restriction system mcrB of Escherichia coli K-12.
JO  - Gene
PY  - 1988
SP  - 23
EP  - 24
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Dila, D.
AU  - Sutherland, E.
AU  - Moran, L.
AU  - Slatko, B.
AU  - Raleigh, E.A.
TI  - Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1990
SP  - 4888
EP  - 4900
VL  - 172
AB  - The mcrB (rglB) locus of Escherichia coli K-12 mediates sequence-specific restriction of
AB  - cytosine-modified DNA.  Genetic and sequence analysis shows that the locus actually comprises
AB  - two genes, mcrB and mcrC.  We show here that in vivo, McrC modifies the specificity of McrB
AB  - restriction by expanding the range of modified sequences restricted.  That is, the sequences
AB  - sensitive to McrB+-dependent restriction can be divided into two sets:  some modified
AB  - sequences containing 5-methylcytosine are restricted by McrB+McrC+ cells.  The sequences
AB  - restricted only by McrB+C+ include T-even bacteriophage containing 5-hydroxymethylcytosine
AB  - (restriction of this phage is the RglB+ phenotype), some sequences containing
AB  - N4-methylcytosine, and some sequences containing 5-methylcytosine.  The sequence codes for two
AB  - polypeptides of 54 (McrB) and 42 (McrC) kilodaltons, whereas in vitro translation yields four
AB  - products, of ~29 and ~49 (McrB) and of ~38 and ~40 (McrC) kilodaltons.  The McrB polypeptide
AB  - sequence contains a potential GTP-binding motif, so this protein presumably binds the
AB  - nucleotide cofactor.  The deduced McrC polypeptide is somewhat basic and may bind to DNA,
AB  - consistent with its genetic activity as a modulator of the specificity of McrB.  At the
AB  - nucleotide sequence level, the G+C content of mcrBC is very low for E. coli, suggesting that
AB  - the genes may have been acquired recently during the evolution of the species.
ER  -

TY  - JOUR
AU  - Dimitrova, D.
AU  - Engelbrecht, K.C.
AU  - Putonti, C.
AU  - Koenig, D.W.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798).
JO  - Genome Announcements
PY  - 2017
SP  - e00573
EP  - e00517
VL  - 5
AB  - Here, we present the draft genome sequence of Escherichia coli ATCC 10798. E. coli ATCC 10798
AB  - is a K-12 strain, one of the most well-studied model
AB  - microorganisms. The size of the genome was 4,685,496 bp, with a G+C content of
AB  - 50.70%. This assembly consists of 62 contigs and the F plasmid.
ER  -

TY  - JOUR
AU  - Dinakaran, V.
AU  - Shankar, M.
AU  - Jayashree, S.
AU  - Rathinavel, A.
AU  - Gunasekaran, P.
AU  - Rajendhran, J.
TI  - Genome Sequence of Staphylococcus arlettae Strain CVD059, Isolated from the Blood of a Cardiovascular Disease Patient.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6615
EP  - 6616
VL  - 194
AB  - We have isolated a Staphylococcus arlettae strain, strain CVD059, from the blood  of a
AB  - rheumatic mitral stenosis patient. Here, we report the genome sequence and
AB  - potential virulence factors of this clinical isolate. The draft genome of S.
AB  - arlettae CVD059 is 2,565,675 bp long with a G+C content of 33.5%.
ER  -

TY  - JOUR
AU  - Ding, F.
AU  - Chaillet, J.R.
TI  - In vivo stabilization of the Dnmt1 (cytosine-5)-methyltransferase protein.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 14861
EP  - 14866
VL  - 99
AB  - The Dnmt1o form of the Dnmt1 (cytosine-5)-methyltransferase enzyme is synthesized and stored
AB  - in the cytoplasm of the oocyte and is used after fertilization to maintain methylation
AB  - patterns on imprinted genes. After implantation of the blastocyst, Dnmt1o is replaced by the
AB  - Dnmt1 form, which has an additional 118 aa at its amino terminus. To investigate functional
AB  - differences between Dnmt1o and Dnmt1, mice were generated with a mutant allele, Dnmt1(V),
AB  - which synthesized Dnmt1o instead of Dnmt1 in all somatic cells. Homozygous Dnmt1(V) mice were
AB  - phenotypically normal, and had normal levels of genomic methylation, indicating that Dnmt1o
AB  - adopts the maintenance methyltransferase function of Dnmt1. Despite the apparent equivalence
AB  - of Dnmt1o and Dnmt1 maintenance methyltransferase function in somatic cells, the Dnmt1o
AB  - protein was found at high levels (with a corresponding high enzymatic activity) in Dnmt1(V)
AB  - mice. In heterozygous Dnmt1(V)/+ embryonic stem cells and early embryos, equal steady-state
AB  - levels of Dnmt1o and Dnmt1 proteins were produced from the Dnmt1(V) and the WT Dnmt1 alleles,
AB  - respectively. However, in older embryos and adults, the Dnmt1(V) allele produced five times
AB  - the steady-state level of protein of the WT Dnmt1 allele. The difference in Dnmt1o and Dnmt1
AB  - levels is due to a developmentally regulated mechanism that degrades the Dnmt1 protein. The
AB  - intrinsic stability of the Dnmt1o protein is the most likely reason for its use as a
AB  - maternal-effect protein; stable ooplasmic stores of Dnmt1o would be available to traffick into
AB  - the nuclei of the eight-cell stage embryo and maintain methylation patterns on alleles of
AB  - imprinted genes during the fourth embryonic S phase.
ER  -

TY  - JOUR
AU  - Ding, F.
AU  - Patel, C.
AU  - Ratnam, S.
AU  - McCarrey, J.R.
AU  - Chaillet, J.R.
TI  - Conservation of Dnmt1o Cytosine methyltransferase in the marsupial Monodelphis domestica.
JO  - Genesis
PY  - 2003
SP  - 209
EP  - 213
VL  - 36
AB  - Imprinted genes have been identified in both eutherian mammals and in marsupials. In eutherian
AB  - species, there is a conservation of the
AB  - imprinting process, both in terms of the genes imprinted and the
AB  - epigenetic inheritance mechanism. In the mouse, the inheritance of gametic
AB  - methylation patterns depends on an oocyte-derived isoform of the Dnmt1
AB  - (cytosine-5)-methyltransferase protein, Dnmt1o, which functions during
AB  - preimplantation development to maintain methylation patterns on imprinted
AB  - alleles. To determine if this component of genomic imprinting is also
AB  - found in marsupials, Dnmt1 isoforms were examined in somatic cells and
AB  - germ cells of the South American opossum Monodelphis domestica. There is a
AB  - Dnmt1o protein in Monodelphis oocytes that is synthesized, as in the
AB  - mouse, from a different transcript than the somatic Dnmt1 protein. Thus,
AB  - an essential component of imprinting in eutherian mammals is found in a
AB  - marsupial species, suggesting that marsupials and eutherian mammals
AB  - imprint their genes with the same methylation-dependent mechanism.
ER  -

TY  - JOUR
AU  - Ding, H.
AU  - Moksa, M.M.
AU  - Hirst, M.
AU  - Beatty, J.T.
TI  - Draft Genome Sequences of Six Rhodobacter capsulatus Strains, YW1, YW2, B6, Y262, R121, and DE442.
JO  - Genome Announcements
PY  - 2014
SP  - e00050
EP  - e00014
VL  - 2
AB  - Rhodobacter capsulatus is a model organism for studying a novel type of horizontal gene
AB  - transfer mediated by a phage-like gene transfer agent (RcGTA).
AB  - Here we report the draft genome sequences of six R. capsulatus strains that
AB  - exhibit different RcGTA properties, including RcGTA overproducers, RcGTA
AB  - nonproducers, and/or RcGTA nonreceivers.
ER  -

TY  - JOUR
AU  - Ding, H.
AU  - Niu, B.
AU  - Fan, H.
AU  - Li, Y.
AU  - Wang, Q.
TI  - Draft Genome Sequence of Bacillus cereus 905, a Plant Growth-Promoting Rhizobacterium of Wheat.
JO  - Genome Announcements
PY  - 2016
SP  - e00489
EP  - e00416
VL  - 4
AB  - Bacillus cereus 905 is a plant growth-promoting rhizobacterium, isolated from wheat
AB  - rhizosphere. The draft genome sequence of this strain is 5.39 Mb and
AB  - harbors 5,412 coding sequences.
ER  -

TY  - JOUR
AU  - Ding, J.
AU  - Dou, Y.
AU  - Wang, Y.
AU  - Chang, Y.
TI  - Draft Genome Sequence of Vibrio fortis Dalian14 Isolated from Diseased Sea Urchin (Strongylocentrotus intermedius).
JO  - Genome Announcements
PY  - 2014
SP  - e00409
EP  - e00414
VL  - 2
AB  - Here, we report the draft genome sequence of Vibrio fortis Dalian14 isolated from diseased sea
AB  - urchin (Strongylocentrotus intermedius) during disease outbreaks in
AB  - North China. The availability of this genome sequence will facilitate the study
AB  - of the mechanisms of pathogenicity and evolution of Vibrio species.
ER  -

TY  - JOUR
AU  - Ding, J.
AU  - Pan, Y.
AU  - Jiang, H.
AU  - Cheng, J.
AU  - Liu, T.
AU  - Qin, N.
AU  - Yang, Y.
AU  - Cui, B.
AU  - Chen, C.
AU  - Liu, C.
AU  - Mao, K.
AU  - Zhu, B.
TI  - Whole genome sequences of four Brucella strains.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3674
EP  - 3675
VL  - 193
AB  - Brucella melitensis and Brucella suis are intracellular pathogens to livestock and humans.
AB  - Here we report four genome sequences, the virulent strain B. melitensis M28-12 and vaccine
AB  - strains B. melitensis M5, M111 and B. suis S2 that show varied virulence and pathogenicity,
AB  - which will help to design more effective brucellosis vaccine.
ER  -

TY  - JOUR
AU  - Ding, J.-Y.
AU  - Shiu, J.-H.
AU  - Chen, W.-M.
AU  - Chiang, Y.-R.
AU  - Tang, S.-L.
TI  - Genomic Insight into the Host Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host.
JO  - Front. Microbiol.
PY  - 2016
SP  - 251
EP  - 251
VL  - 7
AB  - The bacterial genus Endozoicomonas was commonly detected in healthy corals in many
AB  - coral-associated bacteria studies in the past decade.  Although, it is likely to be a core
AB  - member of coral microbiota, little is known about its ecological roles.  To decipher potential
AB  - interactions between bacteria and their coral hosts, we sequenced and investigated the first
AB  - culturable endozoicomonal bacterium from coral, the E. montiporae CL-33T.  Its genome had
AB  - potential sign of ongoing genome erosion and gene exchange with its host.  Testosterone
AB  - degradation and type III secretion system are commonly present in Endozoicomonas and may have
AB  - roles to recognize and deliver effectors to their hosts.  Moreover, genes of eukaryotic ephrin
AB  - ligand B2 are present in its genome; presumably this bacterium could move into coral cells via
AB  - endocytosis after binding to coral's Eph receptors.  In addition, 7,8-dihydro-8-oxoguanine
AB  - triphosphatase and isocitrate lyase are possible type III secretion effectors that might help
AB  - coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under
AB  - stress conditions.  Based on all these findings, we inferred that E. montiporae was a
AB  - facultative endosymbiont that can recognize, translocate, communicate and modulate its coral
AB  - host.
ER  -

TY  - JOUR
AU  - Ding, J.Y.
AU  - Chiang, P.W.
AU  - Hong, M.J.
AU  - Dyall-Smith, M.
AU  - Tang, S.L.
TI  - Complete Genome Sequence of the Extremely Halophilic Archaeon Haloarcula hispanica Strain N601.
JO  - Genome Announcements
PY  - 2014
SP  - e00178
EP  - e00114
VL  - 2
AB  - Haloarcula hispanica has been widely used in haloarchaeal studies, particularly in the
AB  - isolation of haloviruses. The genome of strain N601, a laboratory
AB  - derivative of the type strain ATCC 33960, was sequenced. Several potentially
AB  - significant differences from the published sequence of the type strain (CGMCC
AB  - 1.2049 = ATCC 33960) were observed.
ER  -

TY  - JOUR
AU  - Ding, R.
AU  - Li, Y.
AU  - Qian, C.
AU  - Wu, X.
TI  - Draft Genome Sequence of Paenibacillus elgii B69, a Strain with Broad Antimicrobial Activity.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4537
EP  - 4537
VL  - 193
AB  - Here, we report the draft genome sequence of Paenibacillus elgii B69, which was isolated from
AB  - soil and with broad-spectrum antimicrobial
AB  - activity. As far as we know, the P. elgii genome is the biggest one among
AB  - Paenibacillus genus with genome sequence available. Multiple sets of genes
AB  - related to antibiotic biosynthetic pathways have been found in the genome.
ER  -

TY  - JOUR
AU  - Dingman, D.W.
TI  - Presence of N6-methyladenine in GATC sequences of Bacillus popilliae and Bacillus lentimorbus KLN2.
JO  - J. Bacteriol.
PY  - 1990
SP  - 6156
EP  - 6159
VL  - 172
AB  - Nine strains of Bacillus popilliae and Bacillus lentimorbus KLN2 contain N6-methyladenine in
AB  - GATC sequences, as determined by using the restriction enzymes MboI and DpnI. Among eight
AB  - other Bacillus species examined, all, except one strain of Bacillus brevis (ATCC 9999), lacked
AB  - adenine methylation in GATC. A methylase with Escherichia coli dcm site specificity was not
AB  - present in any of the Bacillus species studied.
ER  -

TY  - JOUR
AU  - Dingman, D.W.
TI  - Four Complete Paenibacillus larvae Genome Sequences.
JO  - Genome Announcements
PY  - 2017
SP  - e00407
EP  - e00417
VL  - 5
AB  - Four complete genome sequences of genetically distinct Paenibacillus larvae strains have been
AB  - determined. Pacific BioSciences single-molecule real-time
AB  - (SMRT) sequencing technology was used as the sole method of sequence
AB  - determination and assembly. The chromosomes exhibited a G+C content of 44.1 to
AB  - 44.2% and a molecular size range of 4.29 to 4.67 Mbp.
ER  -

TY  - JOUR
AU  - Dinsmore, P.K.
AU  - Klaenhammer, T.R.
TI  - Bacteriophage resistance in Lactococcus.
JO  - Mol. Biotechnol.
PY  - 1995
SP  - 297
EP  - 314
VL  - 4
AB  - Lactic acid bacteria are industrial micoorganisms used in many food fermentations.
AB  - Lactococcus species are susceptible to bacteriophage infections that may result in slowed or
AB  - failed fermentations.  A substantial amount of research has focused on characterizing natural
AB  - mechanisms by which bacterial cells defend themselves against phage.  Numerous natural phage
AB  - defense mechanisms have been identified and studied, and recent efforts have improved phage
AB  - resistance by using molecular techniques.  The study of how phages overcome these resistance
AB  - mechanisms is also an important objective.  New strategies to minimize the presence,
AB  - virulence, and evolution of phage are being developed and are likely to be applied
AB  - industrially.
ER  -

TY  - JOUR
AU  - Diop, A.
AU  - Diop, K.
AU  - Tomei, E.
AU  - Raoult, D.
AU  - Fenollar, F.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus.
JO  - Genome Announcements
PY  - 2018
SP  - e01487
EP  - e01417
VL  - 6
AB  - We report here the draft genome sequence of Ezakiella peruensis strain M6.X2(T) The draft
AB  - genome is 1,672,788 bp long and harbors 1,589 predicted
AB  - protein-encoding genes, including 26 antibiotic resistance genes with 1 gene
AB  - encoding vancomycin resistance. The genome also exhibits 1 clustered regularly
AB  - interspaced short palindromic repeat region and 333 genes acquired by horizontal
AB  - gene transfer.
ER  -

TY  - JOUR
AU  - Divyashri, G.
AU  - Rajagopal, K.
AU  - Prapulla, S.G.
TI  - Draft Genome Sequence of Lactobacillus plantarum Kanjika 2007, Isolated from Kanjika, a South Indian Traditional Food.
JO  - Genome Announcements
PY  - 2016
SP  - e00924
EP  - e00916
VL  - 4
AB  - The draft genome sequence of Lactobacillus plantarum Kanjika 2007, isolated from  the South
AB  - Indian staple, medicinal, and traditional food kanjika, is reported
AB  - here. The whole genome consists of 3.16 Mb with a G+C content of 44.7% and 3,009
AB  - protein-coding genes, 78 tRNAs, and 4rRNAs (5S-23S-16S).
ER  -

TY  - JOUR
AU  - Dix, T.I.
AU  - Kieronska, D.H.
TI  - Errors between sites in restriction site mapping.
JO  - Comput. Appl. Biosci.
PY  - 1988
SP  - 117
EP  - 123
VL  - 4
AB  - Restriction site mapping programs construct maps by generating permutations of
AB  - fragments and checking for consistency.  Unfortunately many consistent maps
AB  - often are obtained within the experimental error bounds, even though there is
AB  - only one actual map.  A particularly efficient algorithm is presented that aims
AB  - to minimize error bounds between restriction sites.  The method is generalized
AB  - for linear and circular maps.  The time complexity is derived and execution
AB  - times are given for multiple enzymes and a range of error bounds.
ER  -

TY  - JOUR
AU  - Djao, O.D. et al.
TI  - Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 268
EP  - 275
VL  - 3
AB  - Syntrophothermus lipocalidus Sekiguchi et al. 2000 is the type species of the genus
AB  - Syntrophothermus. The species is of interest because of its strictly
AB  - anaerobic lifestyle, its participation in the primary step of the degradation of
AB  - organic maters, and for releasing products which serve as substrates for other
AB  - microorganisms. It also contributes significantly to maintain a regular pH in its
AB  - environment by removing the fatty acids through beta-oxidation. The strain is
AB  - able to metabolize isobutyrate and butyrate, which are the substrate and the
AB  - product of degradation of the substrate, respectively. This is the first complete
AB  - genome sequence of a member of the genus Syntrophothermus and the second in the
AB  - family Syntrophomonadaceae. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. The 2,405,559 bp long
AB  - genome with its 2,385 protein-coding and 55 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Djordjevic, G.M.
TI  - Development of a triggered suicide system for bacteriophage defense.
JO  - Diss. Abstr.
PY  - 1997
SP  - 1095B
EP  - 1095B
VL  - 58
AB  - A novel bacteriophage defense mechanism was developed for Lactococcus lactis where an
AB  - inducible phage promoter was used to activate bacterial suicide system after the infection.
AB  - The LlaIR+ restriction endonuclease was exploited as a lethal gene of a phage-inducible
AB  - suicide system.  When expressed from a constitutive promoter, the LlaIR+ endonuclease was
AB  - lethal across a wide range of Gram-positive bacteria, including L. lactis.  Lethality of the
AB  - LlaIR+ was exploited to develop several novel, positive selection cloning vectors for these
AB  - organisms.  A middle, phage-inducible promoter (Phi31P) from lytic lactococcal bacteriophage
AB  - Phi31 was cloned upstream of the LlaIR+ on the high-copy plasmid (pTRK414H).  When L. lactis
AB  - (pTRK414h) was infected with 10^7 pfu/ml phage in broth culture, at multiplicity of infection
AB  - (MOI) of 0.1, no lysis was observed and the culture developed normally.  The efficiency of
AB  - plaquing (EOP) for Phi31 on L. lactis (pTRK414H) was lowered to 10^-4.  Center of infection
AB  - assays revealed that 85% of the infected L. lactis (pTRK414H) cells did not release progeny
AB  - phage.  The burst size of Phi31 in L. lactis (pTRK414H) was 41, four-fold lower than in
AB  - control cells.  The Phi31P/LlaIR+ cassette also inhibited four Phi31-recombinant derivatives,
AB  - at levels at least ten-fold greater than Phi31.  However, mutant phages could be enriched that
AB  - were less sensitive to the Phi31P/LlaIR+-encoded restriction.  These phages were altered in
AB  - the strength and timing of Phi31P induction.  The efficiency of the Phi31P/LlaIR+-based
AB  - suicide system was improved by increasing promoter strength, providing a restriction enhancer
AB  - llaIC, and by combination with other abortive defenses, per31 and abiA.  When either per31 or
AB  - abiA were combined with llaIC and Phi31P/LlaIR+, the EOP was reduced to <10^ -10 and virulent
AB  - phages were eliminated from the infected population.  Broader application of bacterial suicide
AB  - systems depends on the availability of phage-specific promoters.  A rapid method for isolation
AB  - of these promoters, based on the "capping" activity of the vaccinia virus guanylytransferase,
AB  - was developed in this study and used successfully to identify a phage-specific promoter from
AB  - lytic lactococcal bacteriophage sk1.
ER  -

TY  - JOUR
AU  - Djordjevic, G.M.
AU  - Klaenhammer, T.R.
TI  - Positive selection, insertion cloning vectors for lactic acid bacteria based on a restriction endonuclease cassette.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1995
SP  - 527
EP  - 527
VL  - 95
AB  - Lactococcus lactis contains numerous restriction and modification (R/M) systems of different
AB  - specificity.  A novel IIS type R/M system has been characterized from the Lactococcus lactis
AB  - conjugative plasmid pTR2030.  The LlaI operon is composed of six genes; the methylase gene
AB  - llaM is followed by three genes (llaI.1, llaI.2, and llaI.3), all of which are essential for
AB  - restriction activity.  We have successfully subcloned the llaI.1, llaI.2, and llaI.3 genes,
AB  - without llaIM, as a suicide cassette into the E. coli-lactococcal shuttle vectors pTRKL2 and
AB  - pBV5030.  A promoter (P6) from Lactobacillus acidophilus ATCC4356, which is functional in E.
AB  - coli, lactococci, and lactobacilli, was cloned upstream of the three gene cassette.
AB  - Restriction activity (R+) was evaluated in Escherichia coli and various lactic acid bacteria
AB  - (LAB).  The R+ cassette was not functional in E. coli, but was lethal to L. lactis,
AB  - Lactobacillus plantarum, Lactobacillus gasseri, Lactobacillus johnsonii, Enterococcus
AB  - faecalis, and Carnobacterium pisicola.  The R+ suicide vector has several unique restriction
AB  - cloning sites located within the R+ three gene cassette that can facilitate cloning, including
AB  - NdeI, StuI, NarI and EcoRV.  Random genomic fragments from Lb. johnsonii were cloned into the
AB  - NdeI site resulting in complete inactivation of R+ activity and providing unconditional
AB  - selection for recombinant plasmids in surviving transformants.  These positive selection
AB  - cloning vectors are the first for lactic acid bacteria that are based on a restriction
AB  - endonuclease cassette.  Functional activity of the llaI genes in various lactic acid bacteria
AB  - will also enable use of the R+ vector for positive screening of promoter and terminator
AB  - sequences in these genera.
ER  -

TY  - JOUR
AU  - Djordjevic, G.M.
AU  - Klaenhammer, T.R.
TI  - Positive selection, cloning vectors for gram-positive bacteria based on a restriction endonuclease cassette.
JO  - Plasmid
PY  - 1996
SP  - 37
EP  - 45
VL  - 35
AB  - Lactococcus lactis contains numerous restriction and modification (R/M) systems of different
AB  - specificities.  A novel IIS type R/M system encoded by the LlaI operon has previously been
AB  - characterized from the L. lactis conjugative plasmid pTR2030.  The LlaI operon is composed of
AB  - six genes: First, a small regulatory gene IIaIC precedes the methylase gene llaIM.  The
AB  - following three genes, llaI.1, llaI.2, llaI.3, are all essential for restriction endonuclease
AB  - activity and are designated as the restriction cassette llaIR.  The fourth open reading frame
AB  - of unknown function follows the llaIR gene cassette.  We have successfully subcloned the three
AB  - llaIR genes, llaI.1, llaI.2, and llaI.3, without llaIM, as a suicide cassette into the three
AB  - shuttle vectors pTRKL2, pTRKH2, and pBV5030.  A promoter (P6) from Lactobacillus acidophilus
AB  - ATCC4356, which is functional in E. coli, lactococci, and lactobacilli was cloned upstream of
AB  - the three gene cassette.  Restriction activity was evaluated in Escherichia coli and several
AB  - gram-positive bacteria.  The llaIR restriction cassette was not functional in E. coli, but its
AB  - presence was lethal to L. lactis, Lactobacillus gasseri, Lactobacillus plantarum,
AB  - Lactobacillus johnsonii, Lactobacillus acidophilus, Carnobacterium pisicola, Enterococcus
AB  - faecalis, Bacillus subtilis, and Leuconostoc gelidum.  Several novel, positive selection
AB  - cloning vectors were developed that can exploit unique cloning sites within the llaIR
AB  - cassette.  Insertions in llaI.1 resulted in complete inactivation of restriction activity and
AB  - provided unconditional selection for recombinant plasmids in surviving transformants.  These
AB  - positive selection cloning vectors are the first for gram-positive bacteria that are based on
AB  - a restriction endonuclease cassette.  Functional activity of the llaIR genes in various
AB  - gram-positive bacteria would also enable use of these cloning vectors for positive selection
AB  - of promoters, terminators, and regulatory sequences across these genera.
ER  -

TY  - JOUR
AU  - Djordjevic, G.M.
AU  - O'Sullivan, D.J.
AU  - Walker, S.A.
AU  - Conkling, M.A.
AU  - Klaenhammer, T.R.
TI  - A triggered-suicide system designed as a defense against bacteriophages.
JO  - J. Bacteriol.
PY  - 1997
SP  - 6741
EP  - 6748
VL  - 179
AB  - A novel bacteriophage protection system for Lactococcus lactis based on a genetic trap, in
AB  - which a strictly phage-inducible promoter isolated from the lytic phage Phi31 is used to
AB  - activate a bacterial suicide system after infection, was developed.  The lethal gene of the
AB  - suicide system consists of the three-gene restriction cassette LlaIR+, which is lethal across
AB  - a wide range of gram-positive bacteria.  The phage-inducible trigger promoter (Phi31P) and the
AB  - LlaIR+ restriction cassette were cloned in Escherichia coli on a high-copy-number replicon to
AB  - generate pTRK414H.  Restriction activity was not apparent in E. coli or L. lactis prior to
AB  - phage infection.  In phage challenges of L. lactis (pTRK414H) with Phi31, the efficiency of
AB  - plaquing was lowered to a 10^-4 and accompanied by a fourfold reduction in burst size.
AB  - Center-of-infection assays revealed that only 15% of infected cells released progeny phage.
AB  - In addition to phage Phi31, the Phi31P/LlaIR+ suicide cassette also inhibited four
AB  - Phi31-derived recombinant phages at levels at least 10-fold greater than that of Phi31.  The
AB  - Phi31P/LlaIR+-based suicide system is a genetically engineered form of abortive infection that
AB  - traps and eliminates phages potentially evolving in fermentation environments by destroying
AB  - the phage genome and killing the propagation host.  This type of phage-triggered suicide
AB  - system could be designed for any bacterium-phage combination, given a universal lethal gene
AB  - and an inducible promoter which is triggered by the infecting bacteriophage.
ER  -

TY  - JOUR
AU  - Djordjevic, M.
TI  - Modeling bacterial immune systems: Strategies for expression of toxic - but useful - molecules.
JO  - Biosystems
PY  - 2013
SP  - 139
EP  - 144
VL  - 112
AB  - Protection of bacterial cells against virus infection requires expression of molecules that
AB  - are able to destroy the incoming foreign
AB  - DNA. However, these molecules can also be toxic for the host cell. In
AB  - both restriction-modification (R-M), and the recently discovered
AB  - CRISPR/Cas systems, the toxicity is (in part) avoided through rapid
AB  - transition of the expression of the toxic molecules from 'OFF' to 'ON'
AB  - state. In restriction-modification systems the rapid transition is
AB  - achieved through a large binding cooperativity, and low translation
AB  - rate of the control protein. On the other hand, CRISPR array expression
AB  - in CRISPR/Cas systems involves a mechanism where a small decrease of
AB  - unprocessed RNAs leads to a rapid increase of processed small RNAs.
AB  - Surprisingly, this rapid amplification crucially depends on fast
AB  - non-specific degradation of the unprocessed molecules by an
AB  - unidentified nuclease, rather than on large cooperativity in protein
AB  - binding. Furthermore, the major control elements that are responsible
AB  - for fast transition of R-M and CRISPR/Cas systems from 'OFF' to 'ON'
AB  - state, are also directly involved in increased stability of the steady
AB  - states of these systems. We here discuss mechanisms that allow rapid
AB  - transition of toxic molecules from the unproductive to the productive
AB  - state in R-M and CRISPR/Cas systems. The main purpose of this
AB  - discussion is to put relevant theoretical and experimental work in a
AB  - perspective that points to general similarities in otherwise
AB  - mechanistically very different bacterial immune systems.
ER  -

TY  - JOUR
AU  - Djukic, M.
AU  - Becker, D.
AU  - Poehlein, A.
AU  - Voget, S.
AU  - Daniel, R.
TI  - Genome Sequence of Paenibacillus alvei DSM 29, a Secondary Invader during European Foulbrood Outbreaks.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6365
EP  - 6365
VL  - 194
AB  - Paenibacillus alvei is known as a secondary invader during European foulbrood of  honeybees.
AB  - Here, we announce the 6.83-Mb draft genome sequence of P. alvei type
AB  - strain DSM 29. Putative genes encoding an antimicrobial peptide, a binary toxin,
AB  - a mosquitocidal toxin, alveolysin, and different polyketides and nonribosomal
AB  - peptides were identified.
ER  -

TY  - JOUR
AU  - Djukic, M.
AU  - Daniel, R.
AU  - Poehlein, A.
TI  - First Insights into the Genome of Fructobacillus sp. EFB-N1, Isolated from Honey  Bee Larva Infected with European Foulbrood.
JO  - Genome Announcements
PY  - 2015
SP  - e00868
EP  - e00815
VL  - 3
AB  - European foulbrood is a worldwide disease affecting the honey bee brood. Here, we report the
AB  - draft genome sequence of Fructobacillus sp. EFB-N1, which was isolated
AB  - from an infected honey bee larva derived from a Swiss European foulbrood
AB  - outbreak. The genome consists of 68 contigs and harbors 1,629 predicted
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Djukic, M.
AU  - Poehlein, A.
AU  - Strauss, J.
AU  - Tann, F.J.
AU  - Leimbach, A.
AU  - Hoppert, M.
AU  - Daniel, R.
TI  - High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 16
EP  - 16
VL  - 10
AB  - The lactic acid bacterium Lactobacillus kunkeei has been described as an inhabitant of
AB  - fructose-rich niches. Here we report on the genome sequence of L.
AB  - kunkeei EFB6, which has been isolated from a honeybee larva infected with
AB  - European foulbrood. The draft genome comprises 1,566,851 bp and 1,417 predicted
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Djukic, M.
AU  - Poehlein, A.
AU  - Thurmer, A.
AU  - Daniel, R.
TI  - Genome Sequence of Brevibacillus laterosporus LMG 15441, a Pathogen of Invertebrates.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5535
EP  - 5536
VL  - 193
AB  - Here we announce the genome sequence of the bacterium Brevibacillus laterosporus LMG 15441,
AB  - which is a pathogen of invertebrates. The genome
AB  - consists of one chromosome and two circular plasmids. Sequence analysis
AB  - revealed a large potential to produce polyketides, nonribosomal peptides,
AB  - and toxins.
ER  -

TY  - JOUR
AU  - Dmitrenko, O.A.
AU  - Sidorenko, S.V.
AU  - Zhukhovitsky, V.G.
AU  - Terekhova, R.V.
AU  - Karabak, V.I.
AU  - Tarasevich, N.N.
AU  - Vasilyeva, E.I.
AU  - Prokhorov, V.Y.
TI  - Comparative effectiveness of typing Staphylococcus aureus methicillin-resistant strains, isolated in Moscow hospitals, with the use of three collections of bacteriophages.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 2003
SP  - 3
EP  - 9
VL  - 1
AB  - The typing of S. aureus methicillin-resistant strains, isolated in different hospitals of
AB  - Moscow; was carried out with the use of three
AB  - collections of phages: the International Set of Phages; the set of phages
AB  - of the International Center of S. aureus phage typing in London (L); and
AB  - the experimental collection of phages of the Gamaleya Institute of
AB  - Epidemiology and Microbiology in Moscow (M). In this study made with the
AB  - use of both the phages of the International Diagnostic Set and phages L in
AB  - the standard typing dose of 1 TP about 6% of the cultures under study
AB  - proved to be sensitive. When the typing dose was increased to 100 TP the
AB  - phages of the international diagnostic set lyzed 75.5% of the cultures.
AB  - The typed strains were found to belong to phage types 77 (71.7%), 77/84/85
AB  - (19.6%) and 94/96 (6.5%). At a concentration of 100 TP phages L lyzed
AB  - 83.7% of the cultures, but the dominating phage types could not be
AB  - determined due to a great variety of phage markers. In contrast to the two
AB  - preceding collections, the third phage collection M was composed in such a
AB  - way that in the study of the investigated culture the specificity of its
AB  - restriction modification was primarily evaluated and only then the
AB  - presence of antiphage immunity was determined. This latter collection was
AB  - used in the evaluation of 93.1% of the cultures. By the specificity of
AB  - their restriction specification system the majority of them were
AB  - classified with two new groups, heretofore not described. Only this
AB  - collection M made it possible to differentiate epidemic and sporadic
AB  - strains and to evaluate the epidemic situation in all 6 hospitals.
ER  -

TY  - JOUR
AU  - do Nascimento, N.C.
AU  - Dos Santos, A.P.
AU  - Chu, Y.
AU  - Guimaraes, A.M.
AU  - Pagliaro, A.
AU  - Messick, J.B.
TI  - Genome Sequence of Mycoplasma parvum (Formerly Eperythrozoon parvum), a Diminutive Hemoplasma of the Pig.
JO  - Genome Announcements
PY  - 2013
SP  - e00986
EP  - e00913
VL  - 1
AB  - We report the complete genome sequence of Mycoplasma parvum strain Indiana. Its circular
AB  - chromosome is 564,395 bp, which is smaller than that of Mycoplasma
AB  - genitalium, which was previously considered the smallest member of the
AB  - Mollicutes. Comparative analyses of the genomes of M. parvum and Mycoplasma suis
AB  - will provide novel insights into the molecular basis of their virulence.
ER  -

TY  - JOUR
AU  - do Nascimento, N.C.
AU  - Guimaraes, A.M.
AU  - Santos, A.P.
AU  - Sanmiguel, P.J.
AU  - Messick, J.B.
TI  - Complete Genome Sequence of Mycoplasma haemocanis Strain Illinois.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1605
EP  - 1606
VL  - 194
AB  - Mycoplasma haemocanis is a blood pathogen that may cause acute disease in immunosuppressed or
AB  - splenectomized dogs. The genome of the strain Illinois is a
AB  - single circular chromosome with 919,992 bp and a GC content of 35%. Analyses of
AB  - the M. haemocanis genome will provide insights into its biology and in vitro
AB  - cultivation requirements.
ER  -

TY  - JOUR
AU  - Do, J.W.
AU  - Moon, C.H.
AU  - Kim, H.J.
AU  - Ko, M.S.
AU  - Kim, S.B.
AU  - Son, J.H.
AU  - Kim, J.S.
AU  - An, E.J.
AU  - Kim, M.K.
AU  - Lee, S.K.
AU  - Han, M.S.
AU  - Cha, S.J.
AU  - Park, M.S.
AU  - Park, M.A.
AU  - Lee, J.S.
AU  - Kim, Y.C.
AU  - Choi, D.L.
AU  - Kim, J.W.
AU  - Park, J.W.
TI  - Complete genomic DNA sequence of rock bream iridovirus.
JO  - Virology
PY  - 2004
SP  - 351
EP  - 363
VL  - 325
AB  - Iridovirus is a causative agent of epizootics among cultured rock bream
AB  - (Oplegnathus fasciatus) in Korea. Here, we report the complete genomic
AB  - sequence of rock bream iridovirus (RBIV). The genome of RBIV was 112080 bp
AB  - long and contained at least 118 putative open reading frames (ORFs), and
AB  - its genome organization was similar to that of infectious spleen and
AB  - kidney necrosis virus (ISKNV). Of the RBIV's 118 ORFs, 85 ORFs showed
AB  - 60-99% amino acid identity to those of ISKNV. Phylogenetic analysis of
AB  - major capsid protein (MCP), DNA repair protein RAD2, and DNA polymerase
AB  - type-B family indicated that RBIV is closely related to red sea bream
AB  - iridovirus (RSIV), Grouper sleepy disease iridovirus (GSDIV), Dwarf
AB  - gourami iridovirus (DGIV), and ISKNV. The genome sequence provides useful
AB  - information concerning the evolution and divergence of iridoviruses in
AB  - cultured fish.
ER  -

TY  - JOUR
AU  - Doan, D.P.
AU  - Lessor, L.E.
AU  - Hernandez, A.C.
AU  - Kuty, E.G.F.
TI  - Complete Genome Sequence of Enterotoxigenic Escherichia coli Siphophage Seurat.
JO  - Genome Announcements
PY  - 2015
SP  - e00044
EP  - e00015
VL  - 3
AB  - Enterotoxigenic Escherichia coli (ETEC) is one of the leading causes of diarrhea in developing
AB  - countries. Bacteriophage therapy has the potential to aid in the prevention and treatment of
AB  - ETEC-related illness. To that end, we present here the complete genome of ETEC siphophage
AB  - Seurat and describe its major features.
ER  -

TY  - JOUR
AU  - Doberenz, S.
AU  - Eckweiler, D.
AU  - Reichert, O.
AU  - Jensen, V.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Kordes, A.
AU  - Frangipani, E.
AU  - Luong, K.
AU  - Korlach, J.
AU  - Heeb, S.
AU  - Overmann, J.
AU  - Kaever, V.
AU  - Haussler, S.
TI  - Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles.
JO  - MBio
PY  - 2017
SP  - e02312
EP  - e02316
VL  - 8
AB  - DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are
AB  - catalyzed by adenine DNA methyltransferases, which are part of
AB  - restriction-modification (R-M) systems. R-M systems are known for their role in
AB  - the defense against foreign DNA; however, DNA methyltransferases also play
AB  - functional roles in gene regulation. In this study, we used single-molecule
AB  - real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in
AB  - the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved
AB  - sequence motif targeted by an adenine methyltransferase of a type I R-M system
AB  - and quantified the presence of N6-methyladenine using liquid
AB  - chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1
AB  - methylation status were dependent on growth conditions and affected P. aeruginosa
AB  - pathogenicity in a Galleria mellonella infection model. Furthermore, we found
AB  - that methylated motifs in promoter regions led to shifts in sense and antisense
AB  - gene expression, emphasizing the role of enzymatic DNA methylation as an
AB  - epigenetic control of phenotypic traits in P. aeruginosa Since the DNA
AB  - methylation enzymes are not encoded in the core genome, our findings illustrate
AB  - how the acquisition of accessory genes can shape the global P. aeruginosa
AB  - transcriptome and thus may facilitate adaptation to new and challenging
AB  - habitats.IMPORTANCE With the introduction of advanced technologies, epigenetic
AB  - regulation by DNA methyltransferases in bacteria has become a subject of intense
AB  - studies. Here we identified an adenosine DNA methyltransferase in the
AB  - opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA
AB  - methylation of a conserved sequence motif. The methylation level of all target
AB  - sequences throughout the PAO1 genome was approximated to be in the range of 65 to
AB  - 85% and was dependent on growth conditions. Inactivation of the methyltransferase
AB  - revealed an attenuated-virulence phenotype in the Galleria mellonella infection
AB  - model. Furthermore, differential expression of more than 90 genes was detected,
AB  - including the small regulatory RNA prrF1, which contributes to a global
AB  - iron-sparing response via the repression of a set of gene targets. Our finding of
AB  - a methylation-dependent repression of the antisense transcript of the prrF1 small
AB  - regulatory RNA significantly expands our understanding of the regulatory
AB  - mechanisms underlying active DNA methylation in bacteria.
ER  -

TY  - JOUR
AU  - Doberva, M.
AU  - Sanchez-Ferandin, S.
AU  - Ferandin, Y.
AU  - Intertaglia, L.
AU  - Croue, J.
AU  - Suzuki, M.
AU  - Lebaron, P.
AU  - Lami, R.
TI  - Genome Sequence of the Sponge-Associated Ruegeria halocynthiae Strain MOLA R1/13b, a Marine Roseobacter with Two Quorum-Sensing-Based Communication Systems.
JO  - Genome Announcements
PY  - 2014
SP  - e00998
EP  - e00914
VL  - 2
AB  - Ruegeria halocynthiae MOLA R1/13b is an alphaproteobacterium isolated from the Mediterranean
AB  - sea sponge Crambe crambe. We report here the genome sequence and
AB  - its annotation, revealing the presence of quorum-sensing genes. This is the first
AB  - report of the full genome of a Ruegeria halocynthiae strain.
ER  -

TY  - JOUR
AU  - Doberva, M.
AU  - Sanchez-Ferandin, S.
AU  - Ferandin, Y.
AU  - Intertaglia, L.
AU  - Joux, F.
AU  - Lebaron, P.
AU  - Lami, R.
TI  - Genome Sequence of Maribius sp. Strain MOLA 401, a Marine Roseobacter with a Quorum-Sensing Cell-Dependent Physiology.
JO  - Genome Announcements
PY  - 2014
SP  - e00997
EP  - e00914
VL  - 2
AB  - Maribius sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon
AB  - located in New Caledonia, France. We report the genome sequence and its
AB  - annotation which, interestingly, reveals the presence of genes involved in quorum
AB  - sensing. This is the first report of a full genome within the genus Maribius.
ER  -

TY  - JOUR
AU  - Dobkin, C.
AU  - Ferrando, C.
AU  - Brown, W.T.
TI  - PFGE of human DNA: 5-azacytidine improves restriction.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3183
EP  - 3183
VL  - 15
AB  - Pulsed field gel electrophoresis of human DNA and the development of long-range restriction
AB  - maps are frequently hampered by the cytosine methylation that occurs at CG dinucleotides in
AB  - human DNA.  This methylation can interfere with restriction and change the size, number and
AB  - concentration of fragments detected in Southern blots.  We have found that these effects,
AB  - which vary at different loci and in different cell lines, can be partially overcome by growing
AB  - cells in 5-azacytidine prior to DNA isolation.  This treatment increases the number of enzymes
AB  - that can be used to map a locus; it can help distinguish between polymorphic methylation
AB  - patterns and polymorphic restriction patterns; and it can establish distinguishing
AB  - characteristics for particular restriction fragments.
ER  -

TY  - JOUR
AU  - Dobrindt, U.
AU  - Blum-Oehler, G.
AU  - Nagy, G.
AU  - Schneider, G.
AU  - Johann, A.
AU  - Gottschalk, G.
AU  - Hacker, J.
TI  - Genetic structure and distribution of four pathogenicity islands (PAI I(536) to PAI IV(536)) of uropathogenic Escherichia coli strain 536.
JO  - Infect. Immun.
PY  - 2002
SP  - 6365
EP  - 6372
VL  - 70
AB  - For the uropathogenic Escherichia coli strain 536 (O6:K15:H31), the DNA
AB  - sequences of three pathogenicity islands (PAIs) (PAI I(536) to PAI
AB  - III(536)) and their flanking regions (about 270 kb) were determined to
AB  - further characterize the virulence potential of this strain. PAI I(536) to
AB  - PAI III(536) exhibit features typical of PAIs, such as (i) association
AB  - with tRNA-encoding genes; (ii) G+C content differing from that of the host
AB  - genome; (iii) flanking repeat structures; (iv) a mosaic-like structure
AB  - comprising a multitude of functional, truncated, and nonfunctional
AB  - putative open reading frames (ORFs) with known or unknown functions; and
AB  - (v) the presence of many fragments of mobile genetic elements. PAI I(536)
AB  - to PAI III(536) range between 68 and 102 kb in size. Although these
AB  - islands contain several ORFs and known virulence determinants described
AB  - for PAIs of other extraintestinal pathogenic E. coli (ExPEC) isolates,
AB  - they also consist of as-yet-unidentified ORFs encoding putative virulence
AB  - factors. The genetic structure of PAI IV(536), which represents the core
AB  - element of the so-called high-pathogenicity island encoding a siderophore
AB  - system initially identified in pathogenic yersiniae, was further
AB  - characterized by sample sequencing. For the first time, multiple PAI
AB  - sequences (PAI I(536) to PAI IV(536)) in uropathogenic E. coli were
AB  - studied and their presence in several wild-type E. coli isolates was
AB  - extensively investigated. The results obtained suggest that these PAIs or
AB  - at least large fragments thereof are detectable in other pathogenic E.
AB  - coli isolates. These results support our view that the acquisition of
AB  - large DNA regions, such as PAIs, by horizontal gene transfer is an
AB  - important factor for the evolution of bacterial pathogens.
ER  -

TY  - JOUR
AU  - Dobritsa, A.P.
AU  - Dobritsa, S.V.
TI  - DNA protection with the DNA methylase M.BbvI from Bacillus brevis var. GB against cleavage by the restriction endonucleases PstI and PvuII.
JO  - Gene
PY  - 1980
SP  - 105
EP  - 112
VL  - 10
AB  - BamHI fragments of the Bacillus brevis var. GB plasmid pAD1 have been cloned in Escherichia
AB  - coli HB101 using pBR322 plasmid as a vector.  The analysis of the recombinant plasmids showed
AB  - that additional PstI sites had appeared in cloned fragments of pAD1.  Methylation of the
AB  - recombinant plasmids in vitro by enzymes from B. brevis GB cells blocks cleavage at these
AB  - additional PstI sites of cloned pAD1 fragments and at the PstI site of pBR322.  Among DNA
AB  - methylases of B. brevis GB, the cytosine DNA methylase M.BbvI is the most likely agent
AB  - modifying the recognition sequences of PstI.  The methylase can modify cytosine residues in
AB  - PstI or PvuII sites if these recognition sequences are linked to G at 5'- or to C at
AB  - 3'-termini.  In particular, in vitro methylation of the SV40 DNA by B. brevis GB methylases
AB  - protects one of the two PstI sites and two of the three PvuII sites.  The described effect of
AB  - the protection of the specific PstI and PvuII sites may be used for physical mapping of
AB  - genomes and DNA cloning.
ER  -

TY  - JOUR
AU  - Dobritsa, A.P.
AU  - Mikhailov, A.A.
AU  - Vanyushin, B.F.
TI  - Methylation of phage 1P+f DNA of Bacillus brevis var. G-B.
JO  - Biokhimiia
PY  - 1975
SP  - 1269
EP  - 1274
VL  - 40
AB  - The DNA of a virulent mutant of temperate phage 1P+f of Bacillus brevis var.
AB  - G-B belongs to the AT type (GC=34.5 mole %) and contains 5-methylcytosine (0.17
AB  - mole %) and N6-methyl-adenine (0.32 mole %) as minor bases.  The amount of
AB  - these bases in the phage DNA does not depend on the nature of the host (P- and
AB  - S variants of B. brevis var. G-B).  In contrast to the host DNA and
AB  - heterologous DNA of Pseudomonas aeruginosa the DNAs of phages 1P+f (P-) and
AB  - 1P+f (S) do not accept methyl groups during in vitro methylation by enzymes
AB  - from B. brevis var. G-B cells.  Consequently, these phage DNAs are completely
AB  - methylated in vivo.  The nature of the methylation of phage DNA in cells of
AB  - different variants of B. brevis var. G-B is the same, i.e., dissociation of the
AB  - culture is not accompanied by a change in the specificity of the methylation of
AB  - the DNA.  In phage 1P+f DNA 5-methylcytosine is present in all of the
AB  - pyrimidine isopliths; the maximum amount of this base (~27%) is found in the
AB  - dipyrimidine clusters.  In the host DNA all of the 5-methylcytosine is located
AB  - only in mono- and dipyrimidine fragments in a ratio of 1:1.  This means that
AB  - the specificities of the methylation of the cytosine residues in the host and
AB  - phage DNAs are different.  This difference is apparently due to the
AB  - participation of some specific methylase, induced by phage 1P+f, in the
AB  - methylation of the phage DNA.
ER  -

TY  - JOUR
AU  - Dodd, A.
AU  - Swanevelder, D.
AU  - Featherston, J.
AU  - Rumbold, K.
TI  - Draft Genome Sequence of Streptomyces albulus Strain CCRC 11814, an {varepsilon}-Poly-L-Lysine-Producing Actinomycete.
JO  - Genome Announcements
PY  - 2013
SP  - e00696
EP  - e00613
VL  - 1
AB  - Here, we report the draft genome sequence of Streptomyces albulus strain CCRC 11814, a
AB  - soil-dwelling, Gram-positive bacterium. S. albulus produces
AB  - epsilon-poly-l-lysine, which has diverse antimicrobial activity. The genome is
AB  - 9.43 Mb in size, with a G+C content of 72.2%, and contains 9,177 protein-coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Dodge, A.G.
AU  - Wackett, L.P.
AU  - Sadowsky, M.J.
TI  - Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. Strain Mel.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 1397
EP  - 1403
VL  - 78
AB  - Rhodococcus sp. strain Mel was isolated from soil by enrichment and grew in
AB  - minimal medium with melamine as the sole N source with a doubling time of 3.5 h.
AB  - Stoichiometry studies showed that all six nitrogen atoms of melamine were
AB  - assimilated. The genome was sequenced by Roche 454 pyrosequencing to 13x
AB  - coverage, and a 22.3-kb DNA region was found to contain a homolog to the melamine
AB  - deaminase gene trzA. Mutagenesis studies showed that the cyanuric acid hydrolase
AB  - and biuret hydrolase genes were clustered together on a different 17.9-kb contig.
AB  - Curing and gene transfer studies indicated that 4 of 6 genes required for the
AB  - complete degradation of melamine were located on an approximately 265-kb
AB  - self-transmissible linear plasmid (pMel2), but this plasmid was not required for
AB  - ammeline deamination. The Rhodococcus sp. strain Mel melamine metabolic pathway
AB  - genes were located in at least three noncontiguous regions of the genome, and the
AB  - plasmid-borne genes encoding enzymes for melamine metabolism were likely recently
AB  - acquired.
ER  -

TY  - JOUR
AU  - Doerfler, W.
TI  - Patterns of DNA methylation-evolutionary vestiges of foreign DNA inactivation as a host defense mechanism.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1991
SP  - 557
EP  - 564
VL  - 372
AB  - The proposals in this review are based on experimental work on the integration
AB  - of foreign DNA in mammalian cells, on the establishment of specific de novo
AB  - patterns of DNA methylation, and on the inhibition of transcription by the
AB  - sequence-specific methylation of promoter sequences.  It is suggested that
AB  - eukaryotic cells have developed several mechanisms of defense against the
AB  - uptake, integration, and continued expression of foreign DNA.  In the course of
AB  - evolution and continuing at present, cells have been exposed to foreign DNA,
AB  - entire genomes or fragments of them.  A particularly problematic organ system
AB  - in that respect must be the digestive tract in higher organisms.  The defense
AB  - mechanisms are thought to be the folling:  (1) degradation and/or excretion of
AB  - foreign DNA; (ii) excision and loss of previously integrated DNA from the host
AB  - genome; (iii) targeted inactivation of foreign genes by sequence-specific
AB  - methylation.  Genes whose products could be advantageous to the transformed
AB  - cells can somehow be selectively excluded from this silencing mechanism.  In
AB  - part, the specificity of de novo methylation must reside in the DNA
AB  - methyltransferase systems of the host cell.  However, nucleotide sequence,
AB  - structure, and chromatin arrangement in the foreign DNA could also play an
AB  - important role.  Since defense processes must have been activated many times in
AB  - evolution, patterns of DNA methylation as they can be observed today, may
AB  - represent vestiges of evolution, i.e. the sum total of selective de novo
AB  - methylations, possibly demethylations, and mutations.  Could existing patterns
AB  - of DNA methylation be altered during embryogenesis?  One has also to consider
AB  - the possibility that the insertion and progressive methylation of foreign DNA
AB  - can lead to alterations in the methylation of flanking host cell DNA-sequences
AB  - abutting the site of integration.  It will be interesting to investigate to
AB  - what extent these changes can contribute to the oncogenic transformation of
AB  - cells, particularly after the insertion of foreign (viral) genomes in cells
AB  - transformed by oncogenic viruses.
ER  -

TY  - JOUR
AU  - Doggett, N.A.
AU  - Stubben, C.J.
AU  - Chertkov, O.
AU  - Bruce, D.C.
AU  - Detter, J.C.
AU  - Johnson, S.L.
AU  - Han, C.S.
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789.
JO  - Genome Announcements
PY  - 2013
SP  - e01023
EP  - e01013
VL  - 1
AB  - Bacillus thuringiensis is an important microbial insecticide for controlling agricultural
AB  - pests. We report the finished genome sequence of Bacillus
AB  - thuringiensis serovar israelensis strain HD-789, which contains genes encoding 7
AB  - parasporal crystals consisting of Cry4Aa3, Cry4Ba5 (2 genes), Cry10Aa3, Cry11Aa3,
AB  - Cry60Ba3, and Cry60Aa3, plus 3 Cyt toxin genes and 1 hemagglutinin gene.
ER  -

TY  - JOUR
AU  - Dogs, M. et al.
TI  - Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and  emendation of the species description of Phaeobacter inhibens.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 334
EP  - 350
VL  - 9
AB  - Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a
AB  - secondary metabolite producing bacterium affiliated to the
AB  - Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the
AB  - German Wadden Sea, southern North Sea. Here we describe the complete genome
AB  - sequence and annotation of this bacterium with a special focus on the secondary
AB  - metabolism and compare it with the genomes of the Phaeobacter inhibens strains
AB  - DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic
AB  - relationship based on the 16S rRNA gene sequences of these three strains. The
AB  - genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and
AB  - shows high similarities in genetic and genomic characteristics compared to P.
AB  - inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T)
AB  - possesses four plasmids, three of which show a high similarity to the plasmids of
AB  - the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid
AB  - suggested horizontal gene transfer. Most of the genes on this plasmid are not
AB  - present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide
AB  - reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C
AB  - content was calculated from the genome sequence and differs significantly from
AB  - the previously published value, thus warranting an emendation of the species
AB  - description.
ER  -

TY  - JOUR
AU  - Dogs, M. et al.
TI  - Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation  of Phaeobacter daeponensis.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 142
EP  - 159
VL  - 9
AB  - TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a
AB  - facultatively anaerobic Phaeobacter species isolated from tidal flats.
AB  - Here we describe the draft genome sequence and annotation of this bacterium
AB  - together with previously unreported aspects of its phenotype. We analyzed the
AB  - genome for genes involved in secondary metabolite production and its anaerobic
AB  - lifestyle, which have also been described for its closest relative Phaeobacter
AB  - caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310
AB  - protein-coding genes and 78 RNA genes including four rRNA operons and consists of
AB  - five replicons: one chromosome and four extrachromosomal elements with sizes of
AB  - 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses
AB  - all of the genes for indigoidine biosynthesis, and on specific media the strain
AB  - showed a blue pigmentation. We also found genes for dissimilatory nitrate
AB  - reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous
AB  - to the LuxR/I system.
ER  -

TY  - JOUR
AU  - Doherty, J.P.
AU  - Lindeman, R.
AU  - Trent, R.J.
AU  - Graham, M.W.
AU  - Woodcock, D.M.
TI  - Escherichia coli host strains SURE and SRB fail to preserve a palindrome cloned in lambda phage: improved alternate host strains.
JO  - Gene
PY  - 1993
SP  - 29
EP  - 35
VL  - 124
AB  - We have attempted to produce Escherichia coli strains with the optimal combination of host
AB  - mutations required for the construction of genomic libraries in lambda and cosmid vectors. For
AB  - lambda vectors, we defined this as a strain that combined high efficiency of phage plating
AB  - with optimal tolerance to DNA methylation and the ability to propagate recombinants containing
AB  - regions of potential secondary structure. To optimize this latter property, we have tested a
AB  - series of strains for the ability to propagate a lambda phage containing a palindromic
AB  - sequence. These included an mcr- derivative of a strain shown by Ishiura et al. [J. Bacteriol.
AB  - 171 (1989)] 1068-1074] to allow optimal stability of inserts in cosmid clones. All the sbcC
AB  - strains allowed plaque formation of the palindrome-containing lambda phage. However, while the
AB  - palindrome-containing phage plated with reasonable efficiency of SURE (recB sbcC recJ umuC
AB  - uvrC) and SRB (sbcC recJ umuC uvrC), the majority of phage recovered from these strains no
AB  - longer required an sbcC host for subsequent plating. These two strains also gave poorer titres
AB  - with a low-yielding phage clone from the huma Prader-Willi chromosome region. Optimal phage
AB  - hosts appear to be those that are McrA (mcrBC-hse-mrr)combined with mutations in sbcC plus
AB  - recBC or recD and without mutations in additional recombination functions such as recJ or recJ
AB  - umuC uvrC.
ER  -

TY  - JOUR
AU  - Dohra, H.
AU  - Miyake, Y.
AU  - Kodani, S.
TI  - Draft Genome Sequence of Streptomyces olivochromogenes NBRC 3561, a Bioactive Peptide-Producing Actinobacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01048
EP  - e01017
VL  - 5
AB  - Recently, we found that Streptomyces olivochromogenes NBRC 3561 produced a bioactive peptide,
AB  - so we sequenced its genome to clarify its biosynthesis. We
AB  - report here the draft genome sequence of S. olivochromogenes NBRC 3561, in which
AB  - 40 potential secondary metabolite gene clusters were predicted by antiSMASH.
ER  -

TY  - JOUR
AU  - Dohra, H.
AU  - Suzuki, H.
AU  - Suzuki, T.
AU  - Tanaka, K.
AU  - Fujishima, M.
TI  - Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate Paramecium caudatum.
JO  - Genome Announcements
PY  - 2013
SP  - e00664
EP  - e00613
VL  - 1
AB  - Holospora undulata is a micronucleus-specific symbiont of the ciliate Paramecium  caudatum. We
AB  - report here the draft genome sequence of H. undulata strain HU1.
AB  - This genome information will contribute to the study of symbiosis between H.
AB  - undulata and the host P. caudatum.
ER  -

TY  - JOUR
AU  - Dohra, H.
AU  - Suzuki, T.
AU  - Inoue, Y.
AU  - Kodani, S.
TI  - Draft Genome Sequence of Planomonospora sphaerica JCM9374, a Rare Actinomycete.
JO  - Genome Announcements
PY  - 2016
SP  - e00779
EP  - e00716
VL  - 4
AB  - Planomonospora sphaerica is a rare actinomycete that is a potential antibiotic producer. Here,
AB  - we report the draft genome sequence of P. sphaerica strain
AB  - JCM9374. This is the first genome report of a bacterium belonging to the genus
AB  - Planomonospora The genome information of P. sphaerica will contribute to studies
AB  - on the structure and function of antibiotics.
ER  -

TY  - JOUR
AU  - Doi, A.
AU  - Pack, S.P.
AU  - Kodaki, T.
AU  - Makino, K.
TI  - Reinvestigation of the Molecular Influence of Hypoxanthine on the DNA Cleavage Efficiency of Restriction Endonucleases BglII, EcoRI and BamHI.
JO  - J. Biochem. (Tokyo)
PY  - 2009
SP  - 201
EP  - 208
VL  - 146
AB  - Hypoxanthine (Hyp), a deaminated base of adenine (Ade), can be employed as a good probe
AB  - molecule to reveal the significance of the minor groove
AB  - of guanine (Gua) in biomolecular interactions because Hyp possesses a
AB  - similar structure to Gua lacking its 2-amino group. In this study, we
AB  - examined cleavage efficiencies of restriction endonuclease enzymes on
AB  - DNA substrates with Hyp in their recognition sequences. As a substrate
AB  - for BglII, EcoRI and BamHI, 24-mer DNA oligomer with Hyp (in place of
AB  - Gua) was prepared together with its complementary sequences with
AB  - cytosine (Cyt) or thymine (Thy) as the counter base. At 37 degrees C
AB  - incubation for 1h, BglII and EcoRI showed higher DNA cleavage
AB  - reactivity on Hyp-containing DNA substrates than on normal ones,
AB  - whereas BamHI showed lower values on Hyp-containing substrates. Such
AB  - high cleavage performance of BglII and EcoRI on Hyp-containing DNA
AB  - substrates is in contrast to the results obtained 20 years ago, in
AB  - which short DNA substrates (8- or 10-mer) and low reaction temperatures
AB  - (15-20 degrees C) were employed. These new results suggest that the
AB  - lack of the exocyclic 2-amino group of Gua could contribute to enhanced
AB  - recognition access of BglII and EcoRI to DNA substrates.
ER  -

TY  - JOUR
AU  - Doi, K.
AU  - Fujino, Y.
AU  - Nagayoshi, Y.
AU  - Ohshima, T.
AU  - Ogata, S.
TI  - Complete Genome Sequence of Thiostrepton-Producing Streptomyces laurentii ATCC 31255.
JO  - Genome Announcements
PY  - 2016
SP  - e00360
EP  - e00316
VL  - 4
AB  - Streptomyces laurentii ATCC 31255 produces thiostrepton, a thiopeptide class antibiotic. Here,
AB  - we report the complete genome sequence for this strain, which
AB  - contains a total of 8,032,664 bp, 7,452 predicted coding sequences, and a G+C
AB  - content of 72.3%.
ER  -

TY  - JOUR
AU  - Doi, K.
AU  - Mori, K.
AU  - Martono, H.
AU  - Nagayoshi, Y.
AU  - Fujino, Y.
AU  - Tashiro, K.
AU  - Kuhara, S.
AU  - Ohshima, T.
TI  - Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with  Bacteriophage OH2.
JO  - Genome Announcements
PY  - 2013
SP  - e00634
EP  - e00613
VL  - 1
AB  - Geobacillus kaustophilus strain GBlys was isolated along with the bacteriophage OH2, which
AB  - infects G. kaustophilus NBRC 102445(T). Here we present a draft
AB  - sequence of this strain's genome, which consists of 216 contigs for a total of
AB  - 3,541,481 bp, 3,679 predicted coding sequences, and a G+C content of 52.1%.
ER  -

TY  - JOUR
AU  - Doi, K.
AU  - Mori, K.
AU  - Mutaguchi, Y.
AU  - Tashiro, K.
AU  - Fujino, Y.
AU  - Ohmori, T.
AU  - Kuhara, S.
AU  - Ohshima, T.
TI  - Draft Genome Sequence of D-Branched-Chain Amino Acid Producer Lactobacillus otakiensis JCM 15040T, Isolated from a Traditional Japanese Pickle.
JO  - Genome Announcements
PY  - 2013
SP  - e00546
EP  - e00513
VL  - 1
AB  - Lactobacillus otakiensis strain JCM 15040(T) was isolated from an unsalted pickling solution
AB  - used in the production of sunki, a traditional Japanese pickle.
AB  - Here, we prepared a draft genome sequence for this strain consisting of 40
AB  - contigs containing a total of 2,347,132 bp, 2,310 predicted coding sequences, and
AB  - a G+C content of 42.4%.
ER  -

TY  - JOUR
AU  - Doi, K.
AU  - Mori, K.
AU  - Tashiro, K.
AU  - Fujino, Y.
AU  - Nagayoshi, Y.
AU  - Hayashi, Y.
AU  - Kuhara, S.
AU  - Ohshima, T.
TI  - Draft Genome Sequence of Pediococcus lolii NGRI 0510Q(T) Isolated from Ryegrass Silage.
JO  - Genome Announcements
PY  - 2013
SP  - e00156
EP  - e00112
VL  - 1
AB  - Pediococcus lolii NGRI 0510Q(T) was isolated from ryegrass silage produced on Ishigaki Island,
AB  - Okinawa Prefecture, Japan. Here we present a draft genome
AB  - sequence for this strain, consisting of 103 contigs for a total of 2,047,078 bp,
AB  - 2,154 predicted coding sequences, and a G+C content of 42.1%.
ER  -

TY  - JOUR
AU  - Doi, N.
AU  - Kumadaki, S.
AU  - Oishi, Y.
AU  - Matsumura, N.
AU  - Yanagawa, H.
TI  - In vitro selection of restriction endonucleases by in vitro compartmentalization.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - e95
EP  - e95
VL  - 32
AB  - Restriction endonucleases are widely used in laboratory applications from recombinant DNA
AB  - technology to diagnostics, but engineering of restriction
AB  - enzymes by structure-guided design and in vivo directed evolution is at an
AB  - early stage. Here, we report the use of an in vitro compartmentalization
AB  - system for completely in vitro selection of restriction enzymes.
AB  - Compartmentalization of a single gene in a rabbit reticulocyte in vitro
AB  - transcription/translation system serves to isolate individually
AB  - synthesized enzymes from each other. In each compartment, an active enzyme
AB  - cleaves only its own encoding gene, whereas genes encoding inactive
AB  - enzymes remain intact. Affinity selection of the cleaved DNA encoding
AB  - active restriction endonucleases was accomplished by the use of
AB  - streptavidin-immobilized beads and dUTP-biotin, which was efficiently
AB  - incorporated into the cohesive end of the cleaved DNA using a DNA
AB  - polymerase. We confirmed that genes encoding active restriction
AB  - endonuclease FokI could be selected from a randomized library. This method
AB  - overcomes the limitations of current in vivo technologies and should prove
AB  - useful for rapid screening and evolution of novel restriction enzymes from
AB  - diverse mutant libraries, as well as for studies of catalytic and
AB  - evolutionary mechanisms of restriction enzymes.
ER  -

TY  - JOUR
AU  - Doi, N.
AU  - Yanagawa, H.
TI  - In vitro selection of restriction enzyme and receptor ligands by microcapsulated cell free protein synthesis system.
JO  - Baiotekunoroji Janaru
PY  - 2005
SP  - 84
EP  - 86
VL  - 5
ER  -

TY  - JOUR
AU  - Doi, Y.
AU  - Hazen, T.H.
AU  - Boitano, M.
AU  - Tsai, Y.C.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Rasko, D.A.
TI  - Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 5947
EP  - 5953
VL  - 58
AB  - The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01,
AB  - which coproduces NDM-1 and OXA-232 carbapenemases, was determined in
AB  - this study. The use of single-molecule, real-time (SMRT) sequencing provided a
AB  - closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single
AB  - chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2
AB  - (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the
AB  - chromosome were similar to that of the K. pneumoniae reference genome strain MGH
AB  - 78578, with the exception of a large inversion spanning 23.3% of the chromosome.
AB  - In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an
AB  - IncHI1B-like plasmid, carries the blaNDM-1, armA, and qnrB1 genes, along with
AB  - tellurium and mercury resistance operons. blaNDM-1 is carried on a unique
AB  - structure in which Tn125 is further bracketed by IS26 downstream of a class 1
AB  - integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance
AB  - elements, including blaCTX-M-15 and a mercury resistance operon. The ColE-type
AB  - plasmid pPKPN4 carrying blaOXA-232 is identical to a plasmid previously reported
AB  - from France. SMRT sequencing was useful in resolving the complex bacterial
AB  - genomic structures in the de novo assemblies.
ER  -

TY  - JOUR
AU  - Doi, Y.
AU  - Takizawa, N.
TI  - Complete Genome Sequence of Enterococcus faecalis Strain W11 Isolated from an Algal Food Product.
JO  - Genome Announcements
PY  - 2016
SP  - e01037
EP  - e01016
VL  - 4
AB  - Here, we report the complete genome sequence of Enterococcus faecalis strain W11  isolated
AB  - from an algal food product in Japan. This study should facilitate the
AB  - identification of a novel mechanism of glycerol metabolic control in lactic acid
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Doing, G.
AU  - Perron, G.G.
AU  - Jude, B.A.
TI  - Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed.
JO  - Genome Announcements
PY  - 2018
SP  - e01428
EP  - e01417
VL  - 6
AB  - Iodobacter species are among a number of freshwater Gram-negative violacein-producing
AB  - bacteria. Janthinobacterium lividum and Chromobacterium
AB  - violaceum have had their whole genomes sequenced and annotated. This is the first
AB  - report of a draft whole-genome sequence of a violacein-producing Iodobacter
AB  - strain that was isolated from the Hudson Valley watershed.
ER  -

TY  - JOUR
AU  - Doiron, K.M.
AU  - Lavigne-Nicolas, J.
AU  - Cupples, C.G.
TI  - Effect of interaction between 5-azacytidine and DNA (cytosine-5) methyltransferase on C-to-G and C-to-T mutations in Escherichia coli.
JO  - Mutat. Res.
PY  - 1999
SP  - 37
EP  - 44
VL  - 429
AB  - The purpose of this study was to determine the effect of the Dcm
AB  - cytosine methyltransferase on 5-azacytidine (5-azaC) mutagenesis in
AB  - Escherichia coli. We used a Lac reversion assay to measure C-to-G and C-
AB  - to-T mutations at a single, methylatable cytosine in the lacZ gene, in
AB  - the presence and absence of Dcm. C-to-G mutations are stimulated by 5-
AB  - azaC but are largely independent of Dcm. In contrast, C-to-T mutations
AB  - are not stimulated by 5-azaC in either wild type or dcm cells. However,
AB  - in cells which contain Dcm but are defective in very short patch
AB  - repair, the normally high frequency of spontaneous C-to-T mutations is
AB  - decreased by the analog in a dose-dependent manner.
ER  -

TY  - JOUR
AU  - Doiron, K.M.J.
AU  - Viau, S.
AU  - Koutroumanis, M.
AU  - Cupples, C.G.
TI  - Overexpression of vsr in Escherichia coli is mutagenic.
JO  - J. Bacteriol.
PY  - 1996
SP  - 4294
EP  - 4296
VL  - 178
AB  - Overexpression of vsr in Escherichia coli stimulates transition and frameshift mutations.  The
AB  - pattern of mutations suggests that mutagenesis is due to saturation or inactivation of
AB  - dam-directed mismatch repair.
ER  -

TY  - JOUR
AU  - Dolka, B.
AU  - Boyen, F.
AU  - Butaye, P.
AU  - Heidemann, O.R.
AU  - Naundrup, T.I.C.
AU  - Christensen, J.P.
TI  - Draft Genome Sequences of Two Commensal Enterococcus cecorum Strains Isolated from Chickens in Belgium.
JO  - Genome Announcements
PY  - 2015
SP  - e01108
EP  - e01115
VL  - 3
AB  - Here, we report the draft genome sequences of two commensal Enterococcus cecorum  strains
AB  - (1710s23 and 1711s24), cultivated from the ceca of healthy laying hens originating from
AB  - different farms in Belgium.
ER  -

TY  - JOUR
AU  - Dolka, B.
AU  - Heidemann, O.R.
AU  - Naundrup, T.I.C.
AU  - Christensen, J.P.
TI  - Draft Genome Sequences of Five Clinical Enterococcus cecorum Strains Isolated from Different Poultry Species in Poland.
JO  - Genome Announcements
PY  - 2015
SP  - e01082
EP  - e01015
VL  - 3
AB  - Here, we report five draft genome sequences of Enterococcus cecorum strains that  were
AB  - isolated from different bird species of affected poultry flocks (commercial  broilers [CB],
AB  - broiler breeders [BB], commercial layers [CL], ducks [D], and geese [G]) in Poland.
ER  -

TY  - JOUR
AU  - Domann, E.
AU  - Fischer, F.
AU  - Glowatzki, F.
AU  - Fritzenwanker, M.
AU  - Hain, T.
AU  - Zechel-Gran, S.
AU  - Giffhorn-Katz, S.
AU  - Neubauer, B.A.
TI  - Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and  Encephalopathy.
JO  - Genome Announcements
PY  - 2016
SP  - e00747
EP  - e00716
VL  - 4
AB  - d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic
AB  - acid bacteria is a rarely diagnosed neurological complication
AB  - of patients with short bowel syndrome. Here, we report the draft genome sequence
AB  - of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel
AB  - syndrome and previous d-lactic acidosis/encephalopathy.
ER  -

TY  - JOUR
AU  - Dombroski, D.F.
AU  - Morgan, A.R.
TI  - Restriction nuclease digestions driven to completion by Escherichia coli RNA polymerase and T4 gene 32 protein.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 415
EP  - 417
VL  - 260
AB  - Restriction enzyme digestions of large scale DNA preparations often do not go
AB  - to completion.  This is due to product inhibition by the newly generated ends
AB  - of the digested DNA.  The addition of exogenous proteins that bind tightly to
AB  - the free ends of DNA or to single-stranded DNA will relieve this inhibition.
AB  - We show that a considerable savings on restriction nucleases can be attained by
AB  - the addition of RNA polymerase or T4 gene 32 protein in stoichiometric amounts
AB  - to the newly produced DNA ends.
ER  -

TY  - JOUR
AU  - Domingo, M.C.
AU  - Fournier, E.
AU  - Masse, C.
AU  - Charest, H.
AU  - Bernard, K.
AU  - Cote, J.C.
AU  - Tremblay, C.
TI  - Draft Genome Sequences of Two Toxigenic Corynebacterium ulcerans Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e00699
EP  - e00615
VL  - 3
AB  - Here, we present the draft genome sequences of two toxigenic Corynebacterium ulcerans strains
AB  - isolated from two different patients: one from a blood sample
AB  - and the other from a scar exudate following surgery. Although these two strains
AB  - harbor the diphtheria toxin gene tox, no full prophage sequences were found in
AB  - the flanking regions.
ER  -

TY  - JOUR
AU  - Domingos, D.F.
AU  - Dellagnezze, B.M.
AU  - Greenfield, P.
AU  - Reyes, L.R.
AU  - Melo, I.S.
AU  - Midgley, D.J.
AU  - Oliveira, V.M.
TI  - Draft Genome Sequence of Bacillus pumilus CCMA-560, Isolated from an Oil-Contaminated Mangrove Swamp.
JO  - Genome Announcements
PY  - 2013
SP  - e00707
EP  - e00713
VL  - 1
AB  - Bacillus pumilus strain CCMA-560 was isolated from an oil-contaminated mangrove swamp and was
AB  - shown to produce biosurfactants. The strain appears to be capable
AB  - of degrading some plant cell wall-related compounds, including hemicelluose and
AB  - pectin. Genes for biopolymer export and polysaccharide intercellular adhesin
AB  - synthesis were also annotated.
ER  -

TY  - JOUR
AU  - Domingos, D.F.
AU  - Dellagnezze, B.M.
AU  - Greenfield, P.
AU  - Reyes, L.R.
AU  - Melo, I.S.
AU  - Midgley, D.J.
AU  - Oliveira, V.M.
TI  - Draft Genome Sequence of the Biosurfactant-Producing Bacterium Gordonia amicalis  Strain CCMA-559, Isolated from Petroleum-Impacted Sediment.
JO  - Genome Announcements
PY  - 2013
SP  - e00894
EP  - e00813
VL  - 1
AB  - Gordonia amicalis strain CCMA-559 was isolated from an oil-contaminated mangrove  swamp and
AB  - shown to produce biosurfactants. This strain is a strict aerobe that
AB  - readily degrades an array of carbon sources, including N-acetylglucosamine,
AB  - cellobiose, Tween 80, and 4-hydroxybenzoic acid, and, like other G. amicalis
AB  - strains, likely desulfurizes dibenzothiophene.
ER  -

TY  - JOUR
AU  - Dominguez, M.A. Jr.
AU  - Thornton, K.C.
AU  - Melendez, M.G.
AU  - Dupureur, C.M.
TI  - Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease.
JO  - Proteins
PY  - 2001
SP  - 55
EP  - 61
VL  - 45
AB  - Incorporation of fluorine into proteins has long served as a means of probing structure and
AB  - function, yet there are few studies that examine the impact of fluorine substitution,
AB  - particularly at locations distant from the active sites of enzymes. The flexibility of
AB  - isomeric fluorine incorporation at Phe is used to explore subtle substitution effects on
AB  - enzyme activity and conformation. The unnatural amino acids o-, m-, and p-fluorophenylalanines
AB  - were incorporated biosynthetically into the representative PvuII restriction endonuclease.
AB  - Interestingly, m-fluoro-Phe-PvuII endonuclease exhibits very similar conformational stability
AB  - to that of the native enzyme, but it exhibits a reproducible, 2-fold higher average specific
AB  - activity. Given the level of incorporation and the distribution of species, the species of
AB  - modified enzyme responsible for this increase in specific activity is most likely even faster.
AB  - Further, moving the fluorine atom from the meta- to the para-position of Phe results in a
AB  - 4-fold decrease in specific activity and a decrease in conformational stability of 1.5
AB  - kcal/mol. Since none of the Phe residues in PvuII endonuclease lies near the DNA recognition
AB  - or catalytic sites, this differential behavior alludes to the impact of subtle changes in
AB  - enzyme conformation on endonuclease activity and suggests novel ways to influence catalytic
AB  - behavior.
ER  -

TY  - JOUR
AU  - Dominguez-Bello, M.G.
AU  - Maldonado, A.L.
TI  - Population dynamics and Restriction-Modification (RM) systems in Helicobacter pylori.
JO  - Zoonoses Public Health
PY  - 2007
SP  - 114
EP  - 114
VL  - 54
AB  - H. pylori is highly recombinant, but RMs provide a barrier to recombination and preserve
AB  - species identity.  A strain with higher RM numbers is expected to have high barriers to
AB  - recombination.  As human hosts mix, H. pylori strains recombine.  In Latin America we have
AB  - evidence of an increasing dominance of European strains at the expense of Amerindian, and
AB  - African strains.  We hypothesize that European strains of H. pylori have higher number
AB  - methylases than Amerindian strains.  We compared the number of restriction sites (using
AB  - pDRAW32) in 3406 bp DNA sequences from H. pylori strains from different geographic phylotypes.
AB  - We also determined in vitro, the restriction profile of 16 RE to infer the number of active
AB  - methylases.  The number of possible restriction sites for 16 RE on multilocus sequences from
AB  - 102 strains of diverse geographical origin did not vary among strain groups.  All strains had
AB  - cognate sequences for at least 13 of the 16 tested RE.  Average restriction sites were 5.2;
AB  - 5.7; 6.1 and 6.3 for strains hpWAfrica, hpEurope, hspEAsia and hspAmerind respectively.  Only
AB  - Hpy8I, HpyCH4IV, HpyCH4V, had variable number of restriction sites by strain group.  MLST
AB  - sequences do not indicate a substantial variation in the number of RE cognate restriction
AB  - sites between strain phylotypes.  Preliminary results indicate however that the number of
AB  - active methylases is very variable among strains.  So far, based on restriction profiles to 17
AB  - RE, 2 Amerindian strains show 0 and 4 methylases and one European strain shows 5 methylases.
AB  - In conclusion, variations in RE activity in H. pylori populations do not seem to be due to
AB  - differences in the number of restriction sites in the DNA, but rather to the number of active
AB  - methylases.
ER  -

TY  - JOUR
AU  - Dominova, I.N.
AU  - Kublanov, I.V.
AU  - Podosokorskaya, O.A.
AU  - Derbikova, K.S.
AU  - Patrushev, M.V.
AU  - Toshchakov, S.V.
TI  - Complete Genomic Sequence of 'Thermofilum adornatus' Strain 1910bT, a Hyperthermophilic Anaerobic Organotrophic Crenarchaeon.
JO  - Genome Announcements
PY  - 2013
SP  - e00726
EP  - e00713
VL  - 1
AB  - The complete genomic sequence of a novel hyperthermophilic crenarchaeon, strain 1910b(T), was
AB  - determined. The genome comprises a 1,750,259-bp circular chromosome
AB  - containing single copies of 3 rRNA genes, 43 tRNA genes, and 1,896 protein-coding
AB  - sequences. In silico genome-genome hybridization suggests the proposal of a novel
AB  - species, 'Thermofilum adornatus' strain 1910b(T).
ER  -

TY  - JOUR
AU  - Dominova, I.N.
AU  - Sorokin, D.Y.
AU  - Kublanov, I.V.
AU  - Patrushev, M.V.
AU  - Toshchakov, S.V.
TI  - Complete Genome Sequence of Salinarchaeum sp. Strain HArcht-Bsk1T, Isolated from  Hypersaline Lake Baskunchak, Russia.
JO  - Genome Announcements
PY  - 2013
SP  - e00505
EP  - e00513
VL  - 1
AB  - The complete genome sequence of a novel halophilic archaeon, Salinarchaeum sp. strain
AB  - HArcht-Bsk1(T), was determined using next-generation sequencing. The
AB  - genome comprises a 3,255,260-bp circular chromosome with a G+C content of 66.7%.
AB  - Automatic annotation of the genome revealed a single rRNA operon, 45 tRNAs, and
AB  - 3,013 protein-coding gene sequences.
ER  -

TY  - JOUR
AU  - Domotor, D.
AU  - Becsagh, P.
AU  - Rakhely, G.
AU  - Schneider, G.
AU  - Kovacs, T.
TI  - Complete Genomic Sequence of Erwinia amylovora Phage PhiEaH2.
JO  - J. Virol.
PY  - 2012
SP  - 10899
EP  - 10899
VL  - 86
AB  - Erwinia amylovora is the causative agent of fire blight, a serious disease of
AB  - some Rosaceae plants. The newly isolated bacteriophage PhiEaH2 is able to lyse E.
AB  - amylovora in the laboratory and has reduced the occurrence of fire blight cases
AB  - in field experiments. This study presents the sequenced complete genome and
AB  - analysis of phage PhiEaH2.
ER  -

TY  - JOUR
AU  - Donado-Godoy, P.
AU  - Bernal, J.F.
AU  - Rodriguez, F.
AU  - Gomez, Y.
AU  - Agarwala, R.
AU  - Landsman, D.
AU  - Marino-Ramirez, L.
TI  - Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain.
JO  - Genome Announcements
PY  - 2015
SP  - e01265
EP  - e01215
VL  - 3
AB  - Salmonella enterica is a pathogen of significant public health importance that is frequently
AB  - associated with foodborne illness. We report the whole-genome sequences of four
AB  - multidrug-resistant Salmonella enterica serovar Paratyphi B and Heidelberg strains, isolated
AB  - from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance
AB  - genes for aminoglycosides, beta-lactams, fluoroquinolones, sulfonamides, tetracycline, and
AB  - trimethoprim.
ER  -

TY  - JOUR
AU  - Donahue, J.P.
AU  - Israel, D.A.
AU  - Peek, R.M.
AU  - Blaser, M.J.
AU  - Miller, G.G.
TI  - Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 1066
EP  - 1074
VL  - 37
AB  - Helicobacter pylori strains demonstrate substantial variability in the efficiency of
AB  - transformation by plasmids from Escherichia coli, and many strains are completely resistant to
AB  - transformation. Among the barriers to transformation are numerous strain-specific
AB  - restriction-modification systems in H. pylori. We have developed a method to protect plasmid
AB  - DNA from restriction by in vitro site-specific methylation using cell-free extracts of H.
AB  - pylori before transformation. In two cases, plasmid DNA treated with cell-free extracts in
AB  - vitro acquired the restriction pattern characteristic of genomic DNA from the source strain.
AB  - Among three strains examined in detail, the transformation frequency by treated plasmid
AB  - shuttle and suicide vectors was significantly increased compared with mock-treated plasmid
AB  - DNA. The results indicate that the restriction barrier in H. pylori can be largely overcome by
AB  - specific DNA methylation in vitro. The approach described should significantly enhance the
AB  - ability to manipulate gene function in H. pylori and other organisms that have substantial
AB  - restriction barriers to transformation.
ER  -

TY  - JOUR
AU  - Donahue, J.P.
AU  - Israel, D.A.
AU  - Torres, V.J.
AU  - Necheva, A.S.
AU  - Miller, G.G.
TI  - Inactivation of a Helicobacter pylori DNA methyltransferase alters dnaK operon expression following host-cell adherence.
JO  - FEMS Microbiol. Lett.
PY  - 2002
SP  - 295
EP  - 301
VL  - 208
AB  - The Helicobacter pylori hpyIM gene encodes a type II DNA methyltransferase that is highly
AB  - conserved among strains. To investigate the potential role of M.HpyI methyltransferase
AB  - activity in controlling gene expression in H. pylori, we analyzed gene transcription profiles
AB  - in wild-type strain J166 and an isogenic hpyIM mutant strain using gene arrays. This analysis
AB  - showed that the expression of a majority of genes was unaffected by hpyIM mutation, especially
AB  - in exponential phase cultures. However, in stationary phase cultures and in cells adherent to
AB  - AGS gastric epithelial cells in vitro, loss of hpyIM function altered the expression of the
AB  - stress-responsive dnaK operon. Complementation of the hpyIM mutation using a shuttle plasmid
AB  - encoding a wild-type copy of the gene re-established the wild-type pattern of dnaK operon
AB  - expression. These data suggested that hpyIM, encoding a DNA methyltransferase, may have a role
AB  - in H. pylori physiology that supersedes its original function in a type II
AB  - restriction-modification system.
ER  -

TY  - JOUR
AU  - Donahue, J.P.
AU  - Peek, R.M. Jr.
TI  - Restriction and modification systems.
JO  - Helicobacter pylori: Physiology and Genetics
PY  - 2001
SP  - 269
EP  - 276
AB  - Prokaryotic restriction-modification (R-M) systems were first recognized in Escherichia coli
AB  - nearly 50 years ago and are now known to be ubiquitous among bacterial species.  In general,
AB  - R-M systems consist of two distinct enzymatic activities: first, a restriction endonuclease
AB  - that cleaves DNA at a specific recognition sequence, and second, a DNA methyltransferase that
AB  - methylates DNA at the same site and thus prevents cleavage by the cognate restriction enzyme.
AB  - The genomic sequences of Helicobacter pylori strains J99 and 26695 have revealed that this
AB  - bacterium contains an abundance of restriction and modification genes, some of which have been
AB  - subsequently shown to function as authentic R-M systems or as partial systems, composed of the
AB  - DNA methyltransferase component alone.  Interestingly, R-M genes comprise a significant
AB  - percentage of H. pylori strain-specific genes and are more prevalent in H. pylori than in
AB  - other bacterial species whose genomes have been fully sequenced.  R-M systems in H. pylori
AB  - have been identified on the basis of sequence similarity to known restriction enzymes and
AB  - methyltransferases, genetic organization, and specific enzyme isolation and characterization.
AB  - This chapter summarizes the current state of knowledge regarding the structure and function of
AB  - the large number of putative R-M genes and systems that are now recognized to be present in H.
AB  - pylori.
ER  -

TY  - JOUR
AU  - Donati, C. et al.
TI  - Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species.
JO  - Genome Biol.
PY  - 2010
SP  - R107
EP  - R107
VL  - 11
AB  - BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases
AB  - in humans. The genomes of 44 diverse strains of S. pneumoniae
AB  - were analyzed and compared with strains of non-pathogenic streptococci of the
AB  - Mitis group. RESULTS: Despite evidence of extensive recombination, the S.
AB  - pneumoniae phylogenetic tree revealed six major lineages. With the exception of
AB  - serotype 1, the tree correlated poorly with capsular serotype, geographical site
AB  - of isolation and disease outcome. The distribution of dispensable genes--genes
AB  - present in more than one strain but not in all strains--was consistent with
AB  - phylogeny, although horizontal gene transfer events attenuated this correlation
AB  - in the case of ancient lineages. Homologous recombination, involving short
AB  - stretches of DNA, was the dominant evolutionary process of the core genome of S.
AB  - pneumoniae. Genetic exchange occurred both within and across the borders of the
AB  - species, and S. mitis was the main reservoir of genetic diversity of S.
AB  - pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with
AB  - the number of strains and linearly with the number of polymorphic sites of the
AB  - sampled genomes, suggesting that acquired genes accumulate proportionately to the
AB  - age of clones. Most genes associated with pathogenicity were shared by all S.
AB  - pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis,
AB  - indicating that these genes are not sufficient to determine virulence.
AB  - CONCLUSIONS: Genetic exchange with related species sharing the same ecological
AB  - niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome
AB  - guarantees the species a quick and economical response to diverse environments.
ER  -

TY  - JOUR
AU  - Dong, A.
AU  - Yoder, J.A.
AU  - Zhang, X.
AU  - Zhou, L.
AU  - Bestor, T.H.
AU  - Cheng, X.
TI  - Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 439
EP  - 448
VL  - 29
AB  - DNMT2 is a human protein that displays strong sequence similarities to DNA
AB  - (cytosine-5)-methyltransferases (m(5)C MTases) of both prokaryotes and eukaryotes. DNMT2
AB  - contains all 10 sequence motifs that are conserved among m(5)C MTases, including the consensus
AB  - S:-adenosyl-L-methionine-binding motifs and the active site ProCys dipeptide. DNMT2 has close
AB  - homologs in plants, insects and Schizosaccharomyces pombe, but no related sequence can be
AB  - found in the genomes of  Saccharomyces cerevisiae or Caenorhabditis elegans.  The crystal
AB  - structure of a deletion mutant of DNMT2 complexed with S-adenosyl-L-homocysteine (AdoHcy) has
AB  - been determined at 1.8 A resolution. The structure of the large domain that contains the
AB  - sequence motifs involved in catalysis is remarkably similar to that of M.HhaI, a confirmed
AB  - bacterial m(5)C MTase, and the smaller target recognition domains of DNMT2 and M.HhaI are also
AB  - closely related in overall structure. The small domain of DNMT2 contains three short helices
AB  - that are not present in M.HhaI. DNMT2 binds AdoHcy in the same conformation as confirmed m(5)C
AB  - MTases and, while DNMT2 shares all sequence and structural features with m(5)C MTases, it has
AB  - failed to demonstrate detectable transmethylase activity. We show here that homologs of DNMT2,
AB  - which are present in some organisms that are not known to methylate their genomes, contain a
AB  - specific target-recognizing sequence motif including an invariant CysPheThr tripeptide. DNMT2
AB  - binds DNA to form a denaturant-resistant complex in vitro. While the biological function of
AB  - DNMT2 is not yet known, the strong binding to DNA suggests that DNMT2 may mark specific
AB  - sequences in the genome by binding to DNA through the specific target-recognizing motif.
ER  -

TY  - JOUR
AU  - Dong, A.P.
AU  - Zhou, L.
AU  - Zhang, X.
AU  - Stickel, S.
AU  - Roberts, R.J.
AU  - Cheng, X.D.
TI  - Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
JO  - Biol. Chem.
PY  - 2004
SP  - 373
EP  - 379
VL  - 385
AB  - We have determined the structure of a mutant (Q237W) of HhaI DNA methyltransferase, complexed
AB  - with the methyl-donor product AdoHcy. The
AB  - Q237W mutant proteins were crystallized in the monoclinic space group
AB  - C2 with two molecules in the crystallographic asymmetric unit.
AB  - Protein-protein interface calculations in the crystal lattices suggest
AB  - that the dimer interface has the specific characteristics for homodimer
AB  - protein-protein interactions, while the two active sites are spatially
AB  - independent on the outer surface of the dimer. The solution behavior
AB  - suggests the formation of HhaI dimers as well. The same HhaI dimer
AB  - interface is also observed in the previously characterized binary
AB  - (M.HhaI-AdoMet) and ternary (M.HhaI-DNA-AdoHcy) complex structures,
AB  - crystallized in different space groups. The dimer is characterized
AB  - either by a noncrystallographic twofold symmetry or a crystallographic
AB  - symmetry. The dimer interface involves three segments: the
AB  - amino-terminal residues 2-8, the carboxy-terminal residues 313-327, and
AB  - the linker (amino acids 179-184) between the two functional domains the
AB  - catalytic methylation domain and the DNA target recognition domain.
AB  - Both the amino and carboxyterminal segments are part of the methylation
AB  - domain. We also examined protein-protein interactions of other
AB  - structurally characterized DNA MTases, which are often found as a
AB  - 2-fold related dimer with the largest dimer interface area for the
AB  - group-beta MTases. A possible evolutionary link between the Type I and
AB  - Type II restriction-modification systems is discussed.
ER  -

TY  - JOUR
AU  - Dong, C.
AU  - Bai, X.
AU  - Lai, Q.
AU  - Xie, Y.
AU  - Chen, X.
AU  - Shao, Z.
TI  - Draft Genome Sequence of Sphingobium sp. Strain C100, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.
JO  - Genome Announcements
PY  - 2014
SP  - e01210
EP  - e01213
VL  - 2
AB  - Sphingobium sp. strain C100 was isolated from a polycyclic aromatic hydrocarbon
AB  - (PAH)-degrading consortium from the deep-sea sediment of the Arctic Ocean. It can
AB  - degrade two- to four-ring PAHs at 25 degrees C. Here we present the draft genome
AB  - sequence of this strain, which is 4,776,810 bp with a G+C content of 63.9%.
ER  -

TY  - JOUR
AU  - Dong, C.
AU  - Bai, X.
AU  - Lai, Q.
AU  - Xie, Y.
AU  - Chen, X.
AU  - Shao, Z.
TI  - Draft Genome Sequence of Marinomonas sp. Strain D104, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from the Deep-Sea Sediment of the Arctic Ocean.
JO  - Genome Announcements
PY  - 2014
SP  - e01211
EP  - e01213
VL  - 2
AB  - Marinomonas sp. strain D104 was isolated from a polycyclic aromatic hydrocarbon-degrading
AB  - consortium enriched from deep-sea sediment from the Arctic
AB  - Ocean. The draft genome sequence of D104 (approximately 3.83 Mbp) contains 62
AB  - contigs and 3,576 protein-encoding genes, with a G+C content of 44.8%.
ER  -

TY  - JOUR
AU  - Dong, C.
AU  - Chen, X.
AU  - Xie, Y.
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 893
EP  - 901
VL  - 9
AB  - Strain R6-15 belongs to the genus Thalassolituus, in the family Oceanospirillaceae of
AB  - Gammaproteobacteria. Representatives of this genus are
AB  - known to be the obligate hydrocarbonoclastic marine bacteria. Thalassolituus
AB  - oleivorans R6-15 is of special interest due to its dominance in the crude
AB  - oil-degrading consortia enriched from the surface seawater of the Arctic Ocean.
AB  - Here we describe the complete genome sequence and annotation of this strain,
AB  - together with its phenotypic characteristics. The genome with size of 3,764,053
AB  - bp comprises one chromosome without any plasmids, and contains 3,372
AB  - protein-coding and 61 RNA genes, including 12 rRNA genes.
ER  -

TY  - JOUR
AU  - Dong, H.
AU  - Chang, J.
AU  - He, X.
AU  - Hou, Q.
AU  - Long, W.
TI  - Complete Genome Sequence of Bacillus subtilis Strain CGMCC 12426, an Efficient Poly-gamma-Glutamate Producer.
JO  - Genome Announcements
PY  - 2017
SP  - e01163
EP  - e01117
VL  - 5
AB  - Bacillus subtilis CGMCC 12426 is an efficient producer of poly-gamma-glutamate with regular
AB  - stereochemistry. Here, the complete genome sequence of B. subtilis
AB  - CGMCC 12426 is presented, which may facilitate the design of rational strategies
AB  - for further strain improvements with industrial potential.
ER  -

TY  - JOUR
AU  - Dong, H.J. et al.
TI  - Engineering Clostridium Strain to Accept Unmethylated DNA.
JO  - PLoS ONE
PY  - 2010
SP  - e9038
EP  - e9038
VL  - 5
AB  - It is difficult to genetically manipulate the medically and biotechnologically important genus
AB  - Clostridium due to the existence of
AB  - the restriction and modification (RM) systems. We identified and
AB  - engineered the RM system of a model clostridial species, C.
AB  - acetobutylicum, with the aim to allow the host to accept the
AB  - unmethylated DNA efficiently. A gene CAC1502 putatively encoding the
AB  - type II restriction endonuclease Cac8241 was identified from the genome
AB  - of C. acetobutylicum DSM1731, and disrupted using the ClosTron system
AB  - based on group II intron insertion. The resulting strain SMB009 lost
AB  - the type II restriction endonuclease activity, and can be transformed
AB  - with unmethylated DNA as efficiently as with methylated DNA. The
AB  - strategy reported here makes it easy to genetically modify the
AB  - clostridial species using unmethylated DNA, which will help to advance
AB  - the understanding of the clostridial physiology from the molecular
AB  - level.
ER  -

TY  - JOUR
AU  - Dong, N.
AU  - Zhang, R.
AU  - Liu, L.
AU  - Li, R.
AU  - Lin, D.
AU  - Chan, E.W.
AU  - Chen, S.
TI  - Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China.
JO  - Microbial Genomics
PY  - 2018
SP  - e000149
EP  - e000149
VL  - 4
AB  - The increasing prevalence of KPC-producing Klebsiella pneumoniae strains in clinical settings
AB  - has been largely attributed to dissemination of organisms of
AB  - specific multilocus sequence types, such as ST258 and ST11. Compared with the
AB  - ST258 clone, which is prevalent in North America and Europe, ST11 is common in
AB  - China but information regarding its genetic features remains scarce. In this
AB  - study, we performed detailed genetic characterization of ST11 K. pneumoniae
AB  - strains by analyzing whole-genome sequences of 58 clinical strains collected from
AB  - diverse geographic locations in China. The ST11 genomes were found to be highly
AB  - heterogeneous and clustered into at least three major lineages based on the
AB  - patterns of single-nucleotide polymorphisms. Exhibiting five different capsular
AB  - types, these ST11 strains were found to harbor multiple resistance and virulence
AB  - determinants such as the blaKPC-2 gene, which encodes carbapenemase, and the
AB  - yersiniabactin-associated virulence genes irp, ybt and fyu. Moreover, genes
AB  - encoding the virulence factor aerobactin and the regulator of the mucoid
AB  - phenotype (rmpA) were detectable in six genomes, whereas genes encoding
AB  - salmochelin were found in three genomes. In conclusion, our data indicated that
AB  - carriage of a wide range of resistance and virulence genes constitutes the
AB  - underlying basis of the high level of prevalence of ST11 in clinical settings.
AB  - Such findings provide insight into the development of novel strategies for
AB  - prevention, diagnosis and treatment of K. pneumoniae infections.
ER  -

TY  - JOUR
AU  - Dong, Q.
AU  - Cao, X.
AU  - Zou, G.
AU  - Zhu, R.
TI  - A simple and practical quantitative method for measuring the activity of restriction endonucleases.
JO  - Yichuan
PY  - 1987
SP  - 34
EP  - 36
VL  - 9
AB  - None
ER  -

TY  - JOUR
AU  - Dong, Q.
AU  - Ruan, L.
AU  - Shi, H.
TI  - Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 13
EP  - 13
VL  - 12
AB  - Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated
AB  - strain that belongs to the family Flammeovirgaceae of the class
AB  - Cytophagia. The strain was isolated from the intestine of abalone, which produces
AB  - many extracellular agarases and exhibits efficient degradation activities on
AB  - various polysaccharides, especially agarose. Here we present the high-quality
AB  - draft genome of Flammeovirga sp. SJP92, together with its phenotypic
AB  - characteristics. The genome sequence is 8, 534, 834 bp, which comprised with one
AB  - chromosome and no plasmid. It contained 6, 291 protein-coding and 99 RNA genes,
AB  - including 93 tRNA, 5 rRNA and 1 ncRNA genes.
ER  -

TY  - JOUR
AU  - Dong, Q.
AU  - Zou, G.
AU  - Cao, X.
AU  - Zhu, R.
TI  - Chemical modification and inhibition kinetics of restriction endonuclease Bsp63I.
JO  - Wuhan Daxue Xuebao
PY  - 1996
SP  - 237
EP  - 240
VL  - 42
AB  - Restriction endonuclease Bsp63I has been isolated and purified by affinity chromatography.
AB  - The role of specific amino acid residues in Bsp63I was determined by chemical modification.
AB  - Sulfhydryl groups were modified with p-chloromercuribenzoic acid, lysine residues with
AB  - pyridoxal-5'-phosphate (PLP) and arginine residues with 2,3-butanedione.  The results show
AB  - that these residues are related to the activity of Bsp63I.  Dynamic analysis shows that the
AB  - type of PLP inhibition is analogous anticompetitive inhibition. *>
ER  -

TY  - JOUR
AU  - Dong, Q.Q.
AU  - Hu, H.J.
AU  - Luo, X.G.
AU  - Wang, Q.T.
AU  - Gu, X.C.
AU  - Zhou, H.
AU  - Zhou, W.J.
AU  - Ni, X.M.
AU  - Zhang, T.C.
TI  - Complete Genome Sequence of Lactobacillus plantarum CGMCC 8198.
JO  - Genome Announcements
PY  - 2017
SP  - e01559
EP  - e01516
VL  - 5
AB  - We report the complete genome sequence of Lactobacillus plantarum CGMCC 8198, a novel
AB  - probiotic strain isolated from fermented herbage. We have determined the
AB  - complete genome sequence of strain L. plantarum CGMCC 8198, which consists of
AB  - genes that are likely to be involved in dairy fermentation and that have
AB  - probiotic qualities.
ER  -

TY  - JOUR
AU  - Dong, X.
AU  - Bi, D.
AU  - Wang, H.
AU  - Zou, P.
AU  - Xie, G.
AU  - Wan, X.
AU  - Yang, Q.
AU  - Zhu, Y.
AU  - Chen, M.
AU  - Guo, C.
AU  - Liu, Z.
AU  - Wang, W.
AU  - Huang, J.
TI  - pirAB(vp) -Bearing Vibrio parahaemolyticus and Vibrio campbellii Pathogens Isolated from the Same AHPND-Affected Pond Possess Highly Similar Pathogenic Plasmids.
JO  - Front. Microbiol.
PY  - 2017
SP  - 1859
EP  - 1859
VL  - 8
AB  - Acute hepatopancreatic necrosis disease (AHPND) is a severe shrimp disease
AB  - originally shown to be caused by virulent strains of Vibrio parahaemolyticus
AB  - (VPAHPND). Rare cases of AHPND caused by Vibrio species other than V.
AB  - parahaemolyticus were reported. We compared an AHPND-causing V. campbellii
AB  - (VCAHPND) and a VPAHPND isolate from the same AHPND-affected pond. Both strains
AB  - are positive for the virulence genes pirAB(vp) . Immersion challenge test with
AB  - Litopenaeus vannamei indicated the two strains possessed similar pathogenicity.
AB  - Complete genome comparison showed that the pirAB(vp) -bearing plasmids in the two
AB  - strains were highly homologous, and they both shared high homologies with plasmid
AB  - pVA1, the reported pirAB(vp) -bearing plasmid. Conjugation and DNA-uptake genes
AB  - were found on the pVA1-type plasmids and the host chromosomes, respectively,
AB  - which may facilitate the dissemination of pirAB(vp) . Novel variations likely
AB  - driven by ISVal1 in the genetic contexts of the pirAB(vp) genes were found in the
AB  - two strains. Moreover, the VCAHPND isolate additionally contains multiple
AB  - antibiotic resistance genes, which may bring difficulties to control its future
AB  - outbreak. The dissemination of the pirAB(vp) in non-parahaemolyticus Vibrio also
AB  - rises the concern of missing detection in industrial settings since the isolation
AB  - method currently used mainly targeting V. parahaemolyticus. This study provides
AB  - timely information for better understanding of the causes of AHPND and molecular
AB  - epidemiology of pirAB(vp) and also appeals for precautions to encounter the
AB  - dissemination of the hazardous genes.
ER  -

TY  - JOUR
AU  - Dong, X.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Gavory, F.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genomic Comparison of Rickettsia helvetica and Other Rickettsia Species.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2751
EP  - 2751
VL  - 194
AB  - We report the complete and annotated genome sequence of Rickettsia helvetica strain C9P9,
AB  - which was first isolated in 1979 from Ixodes ricinus ticks in
AB  - Switzerland and is considered a human pathogen.
ER  -

TY  - JOUR
AU  - Dong, X.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia australis, the Agent of Queensland Tick Typhus.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5129
EP  - 5129
VL  - 194
AB  - Rickettsia australis strain Phillips(T) was isolated in Queensland, Australia, in 1950. It is
AB  - the tick-borne agent of Queensland tick typhus, a disease endemic in
AB  - Australia. The 1.29-Mb genome sequence of this bacterium is highly similar to
AB  - that of Rickettsia akari but contains two plasmids.
ER  -

TY  - JOUR
AU  - Dong, X.
AU  - El-Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genomic Analysis of Rickettsia japonica Strain YHT.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6992
EP  - 6992
VL  - 194
AB  - Rickettsia japonica strain YH, isolated in 1984 in Japan, is the type strain of R. japonica,
AB  - the tick-borne agent of Japanese spotted fever. Here, we report the
AB  - 1.33-Mb genome of this rickettsial species.
ER  -

TY  - JOUR
AU  - Dong, Y.
AU  - Chang, Y.J.
AU  - Sanford, R.A.
AU  - Fouke, B.W.
TI  - Draft Genome Sequence of Tepidibacillus decaturensis Strain Z9, an Anaerobic, Moderately Thermophilic, and Heterotrophic Bacterium from the Deep Subsurface of   the Illinois Basin, USA.
JO  - Genome Announcements
PY  - 2016
SP  - e00190
EP  - e00116
VL  - 4
AB  - The genome of the moderately thermophilic and halotolerant bacteriumTepidibacillus
AB  - decaturensisstrain Z9 was sequenced. The draft genome
AB  - comprises three scaffolds, for a total of 2.95 Mb. As the first sequenced genome
AB  - within the genusTepidibacillus, 2,895 protein-coding genes, 52 tRNA genes, and 3
AB  - rRNA operons were predicted.
ER  -

TY  - JOUR
AU  - Dong, Z.
AU  - Hsiang, T.
AU  - Luo, M.
AU  - Xiang, M.
TI  - Draft Genome Sequence of an Isolate of Fusarium oxysporum f. sp. melongenae, the  Causal Agent of Fusarium Wilt of Eggplant.
JO  - Genome Announcements
PY  - 2017
SP  - e01597
EP  - e01516
VL  - 5
AB  - Here, we present the genome sequence of an isolate (14004) of Fusarium oxysporum  f. sp.
AB  - melongenae, an eggplant pathogen. The final assembly consists of 1,631
AB  - scaffolds with 53,986,354 bp (G+C content, 46.4%) and 16,485 predicted genes.
ER  -

TY  - JOUR
AU  - Donner, J.
AU  - Bunk, B.
AU  - Schober, I.
AU  - Sproer, C.
AU  - Bergmann, S.
AU  - Jarek, M.
AU  - Overmann, J.
AU  - Wagner-Dobler, I.
TI  - Complete Genome Sequences of Three Multidrug-Resistant Clinical Isolates of Streptococcus pneumoniae Serotype 19A with Different Susceptibilities to the  Myxobacterial Metabolite Carolacton.
JO  - Genome Announcements
PY  - 2017
SP  - e01641
EP  - e01616
VL  - 5
AB  - The full-genome sequences of three drug- and multidrug-resistant Streptococcus pneumoniae
AB  - clinical isolates of serotype 19A were determined by PacBio
AB  - single-molecule real-time sequencing, in combination with Illumina MiSeq
AB  - sequencing. A comparison to the genomes of other pneumococci indicates a high
AB  - nucleotide sequence identity to strains Hungary19A-6 and TCH8431/19A.
ER  -

TY  - JOUR
AU  - Doolitle, M.M.
AU  - Sirotkin, K.
TI  - Bacteriophage T2 and T4, dam+ and damh and Eco dam+ methylation: preference at different sites.
JO  - Biochim. Biophys. Acta
PY  - 1988
SP  - 240
EP  - 246
VL  - 949
AB  - We present a method for determining preference for methylation at minor methylation sites. The
AB  - target DNA sequence is first subjected to computer-assisted analysis to predict which
AB  - restriction endonuclease(s) will generate fragments that will contain only one or two likely
AB  - minor methylation site(s). The target DNA is then methylated in vitro with a radioactive
AB  - methyl-group donor and subjected to digestion by the chosen restriction enzyme(s). The amount
AB  - of radioactivity in the various fragments is determined, after separating them using
AB  - polyacrylamide gel electrophoresis. We documented the effect of nearby bases on the
AB  - methylation preference and the relative preference for methylation at some specific minor
AB  - methylation sites.
ER  -

TY  - JOUR
AU  - Doolittle, R.F.
TI  - The comings and goings of homing endonucleases and mobile introns.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 5379
EP  - 5381
VL  - 90
AB  - In this issue Belfort and coworkers report the isolation and characterization of a
AB  - thermostable endonuclease from the archaebacterium Desulfurococcus mobilis. Remarkably, the
AB  - enzyme is encoded in an intron in the single gene for 23S rRNA and is expressed only after the
AB  - corresponding RNA segment is excised from the newly made rRNA. Archaebacterial introns are
AB  - unique in that their excision is catalyzed by an enzyme. The endonuclease has a number of
AB  - features characteristic of the homing endonucleases found in fungi and their organelles, and
AB  - these have led the authors to wonder whether trans-kingdom gene transfer may have been
AB  - involved. As the authors suggest, all of these topics--introns, archaebacteria, homing
AB  - endonucleases, and horizontal transfers--are lightning rods for debate.
ER  -

TY  - JOUR
AU  - Dopazo, J.
AU  - Mendoza, A.
AU  - Herrero, J.
AU  - Caldara, F.
AU  - Humbert, Y.
AU  - Friedli, L.
AU  - Guerrier, M.
AU  - Grand-Schenk, E.
AU  - Gandin, C.
AU  - DeFrancesco, M.
AU  - Polissi, A.
AU  - Buell, G.
AU  - Feger, G.
AU  - Garcia, E.
AU  - Peitsch, M.
AU  - Garcia-Bustos, J.F.
TI  - Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate.
JO  - Microb. Drug Resist.
PY  - 2001
SP  - 99
EP  - 125
VL  - 7
AB  - The public availability of numerous microbial genomes is enabling the analysis of bacterial
AB  - biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope.
AB  - Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the
AB  - world.  We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA,
AB  - covering more than 90% of the total estimated size of the genome.  The sequenced strain is a
AB  - clinical isolate resistant to macrolides and tetracycline.  It carries a type 19F capsular
AB  - locus, but multilocus sequence typing for several conserved genetic loci suggests that the
AB  - strain sequence belongs to a pneumococcal lineage that most often expresses a serotype 15
AB  - capsular polysaccharide.  A total of 2,046 putative open reading frames longer than 100 amino
AB  - acids were identified (average of 1,009 bp per ORF), including all described two-component
AB  - systems and aminoacyl tRNA synthetases.  Comparisons to other complete, or nearly complete,
AB  - bacterial genomes were made and are presented in a graphical form for all the predicted
AB  - proteins.
ER  -

TY  - JOUR
AU  - Dordet-Frisoni, E. et al.
TI  - Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae.
JO  - Genome Announcements
PY  - 2013
SP  - e00280
EP  - e00213
VL  - 1
AB  - We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii, two
AB  - species commonly isolated from the external ear canal of Caprinae.
ER  -

TY  - JOUR
AU  - Dornberger, U.
AU  - Leijon, M.
AU  - Fritzsche, H.
TI  - High base pair opening rates in tracts of GC base pairs.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 6957
EP  - 6962
VL  - 274
AB  - Sequence-dependent structural features of the DNA double helix have a strong influence on the
AB  - base pair opening dynamics. Here we report a detailed study of the kinetics of base pair
AB  - breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the
AB  - imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of
AB  - infinite exchange catalyst concentration, the exchange times of the guanine imino protons of
AB  - the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for
AB  - isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all
AB  - of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking
AB  - contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The
AB  - implication of these findings for the structural principles governing spontaneous helix
AB  - opening as well as the DNA-binding.
ER  -

TY  - JOUR
AU  - Dorner, L.F.
AU  - Bitinaite, J.
AU  - Whitaker, R.D.
AU  - Schildkraut, I.
TI  - Genetic analysis of the base-specific contacts of BamHI restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1515
EP  - 1523
VL  - 285
AB  - Here, we investigate the highly specific interaction of the BamHI endonuclease with its
AB  - cognate recognition sequence GGATCC by determining which amino acid residues can be
AB  - substituted at the DNA interface while maintaining specificity.  Mutational studies, together
AB  - with the structural determination of the restriction endonuclease BamHI have revealed the
AB  - amino acid residues which are involved in DNA catalysis and those which play a role in the
AB  - specific binding of the enzyme to its cognate DNA recognition sequence.  Amino acid residues
AB  - N116, S118, R122, D154 and R155 are involved in DNA sequence recognition and are located in
AB  - the major groove in close proximity to the nucleotide bases comprising the recognition
AB  - sequence.  Cassette mutagenesis of these amino acids, together with in vivo transcriptional
AB  - interference selection, was used to identify an array of substitutions which maintain
AB  - site-specific binding to the cognate GGATCC sequence.  This approach has demonstrated the
AB  - extent of acceptable variation among amino acid residues which are directly involved in
AB  - site-specific binding.  One variant, double mutant N116H, S118G was found to cleave DNA only
AB  - when the adenine base in the recognition site is methylated.
ER  -

TY  - JOUR
AU  - Dorner, L.F.
AU  - Schildkraut, I.
TI  - Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 1068
EP  - 1074
VL  - 22
AB  - Variants of BamHI endonuclease in which the glutamate 113 residue has been changed to lysine
AB  - or the aspartate 94 to asparagine were shown to behave as repressor molecules in vivo. This
AB  - was demonstrated by placing a BamHI recognition sequence, GGATCC, positioned as an operator
AB  - sequence in an antisense promoter for the aadA gene (spectinomycin resistance). Repression of
AB  - this promoter relieved the inhibition of expression of spectinomycin resistance. This system
AB  - was then used to select new binding proficient/cleavage deficient BamHI variants. The BamHI
AB  - endonuclease gene was mutagenized either by exposure to hydroxylamine or by PCR. The
AB  - mutagenized DNA was reintroduced into E.coli carrying the aadA gene construct, and
AB  - transformants that conferred spectinomycin resistance were selected. Twenty SP'transformants
AB  - were sequenced. Thirteen of these were newly isolated variants of the previously identified
AB  - D94 and E113 residues which are known to be involved in catalysis. The remaining seven
AB  - variants were all located at residue 111 and the glutamate 111 residue was shown to be
AB  - involved with catalysis.
ER  -

TY  - JOUR
AU  - Doroghazi, J.R.
AU  - Ju, K.S.
AU  - Brown, D.W.
AU  - Labeda, D.P.
AU  - Deng, Z.
AU  - Metcalf, W.W.
AU  - Chen, W.
AU  - Price, N.P.
TI  - Genome Sequences of Three Tunicamycin-Producing Streptomyces Strains, S. chartreusis NRRL 12338, S. chartreusis NRRL 3882, and S. lysosuperificus  ATCC 31396.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7021
EP  - 7022
VL  - 193
AB  - We announce the sequencing of Streptomyces chartreusis NRRL 12338 and NRRL 3882 and
AB  - Streptomyces lysosuperificus ATCC 31396. These are producers of
AB  - tunicamycins, chartreusins, cephalosporins, holomycins, and calcimycin.
AB  - The announced genomes, together with the published Streptomyces
AB  - clavuligerus genome, will facilitate data mining of these secondary
AB  - metabolites.
ER  -

TY  - JOUR
AU  - Doron, S.
AU  - Melamed, S.
AU  - Ofir, G.
AU  - Leavitt, A.
AU  - Lopatina, A.
AU  - Keren, M.
AU  - Amitai, G.
AU  - Sorek, R.
TI  - Systematic discovery of antiphage defense systems in the microbial pangenome.
JO  - Science
PY  - 2018
SP  - eaar4120
EP  - eaar4120
VL  - 359
AB  - The arms race between bacteria and phages led to the development of sophisticated antiphage
AB  - defense systems, including CRISPR-Cas and restriction-modification
AB  - systems. Evidence suggests that unknown defense systems are located in 'defense
AB  - islands' in microbial genomes. We comprehensively characterized the bacterial
AB  - defensive arsenal by examining gene families that are clustered next to known
AB  - defense genes in prokaryotic genomes. Candidate defense systems were
AB  - systematically engineered and validated in model bacteria for their antiphage
AB  - activities. We report nine previously unknown antiphage systems and one
AB  - antiplasmid system that are widespread in microbes and strongly protect against
AB  - foreign invaders. These include systems that adopted components of the bacterial
AB  - flagella and condensin complexes. Our data also suggest a common, ancient
AB  - ancestry of innate immunity components shared between animals, plants, and
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Doronina, V.A.
AU  - Murray, N.E.
TI  - Proteolytic control of restriction by the type I restriction enzyme EcoKI.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A177
EP  - A177
VL  - 2000
AB  - Type I restriction systems are sophisticated molecular machines that methylate (modify) or cut
AB  - duplex DNA depending upon the methylation status of their target sequences.  When unmodified
AB  - DNA enters the bacterial cells this DNA is a substrate for restriction, a process in which
AB  - extensive DNA translocation precedes DNA breakage.  An amino acid substitution in EcoKI, which
AB  - changes a motif essential for the active site of the modification activity, leads to an enzyme
AB  - that is unable to modify the DNA but retains the ability to recognize unmodified target
AB  - sequences and make double-stranded breaks in the DNA.  In vivo, breakage of unmodified
AB  - chromosomes is prevented by a posttranslational mechanism that depends on ClpXP-dependent
AB  - proteolysis and leads to the degradation of the subunit within the restriction enzyme that is
AB  - essential for restriction but not modification.  Analysis of mutants that affect different
AB  - stages of the restriction reaction suggests a model in which the degradation occurs after the
AB  - enzyme has recognized unmodified target sequences and initiated the DNA translocation that
AB  - precedes DNA breakage.  The mechanisms that allow cells to distinguish between chromosomal and
AB  - foreign DNA are under investigation.
ER  -

TY  - JOUR
AU  - Doronina, V.A.
AU  - Murray, N.E.
TI  - The proteolytic control of restriction activity in Escherichia coli K-12.
JO  - Mol. Microbiol.
PY  - 2001
SP  - 416
EP  - 428
VL  - 39
AB  - The endonuclease activity of EcoKI is regulated by the ClpXP-dependent degradation of the
AB  - subunit that is essential for restriction, but not modification.  We monitored proteolysis in
AB  - mutants blocked at different steps in the restriction pathway.  Mutations that prevent DNA
AB  - translocation render EcoKI refractory to proteolysis, whereas those that permit DNA
AB  - translocation, but block endonuclease activity, do not.  Although proteolysis alleviates
AB  - restriction in a mutant that lacks modification activity, some restriction activity remains;
AB  - our evidence indicates residual EcoKI associated with the membrane fraction.  ClpXP protects
AB  - the bacterial chromosome, but little effect was detected on unmodified foreign DNA within the
AB  - cytoplasm of a restriction-proficient cell.  The molecular basis for the distinction between
AB  - unmodified resident and foreign DNA remains to be determined.
ER  -

TY  - JOUR
AU  - Dorr-de-Quadros, P.
AU  - Fulthorpe, R.
AU  - Saati, R.
AU  - Cerqueira, V.
AU  - Bento, F.M.
TI  - Draft Genome Sequence of Bacillus sp. Strain UFRGS-B20, a Hydrocarbon Degrader.
JO  - Genome Announcements
PY  - 2018
SP  - e00052
EP  - e00018
VL  - 6
AB  - Bacillus sp. strain UFRGS-B20 was isolated in 2012 from Brazilian land-farming soil
AB  - contaminated with petrochemical oily sludge. This strain was subjected to
AB  - hydrocarbon biodegradation tests, showing degradation rates of up to 60%. Here,
AB  - we present the 6.82-Mb draft genome sequence of the strain, which contains 2,178
AB  - proteins with functional assignments.
ER  -

TY  - JOUR
AU  - Dorscht, J.
AU  - Klumpp, J.
AU  - Bielmann, R.
AU  - Schmelcher, M.
AU  - Born, Y.
AU  - Zimmer, M.
AU  - Calendar, R.
AU  - Loessner, M.J.
TI  - Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7206
EP  - 7215
VL  - 191
AB  - The genomes of six Listeria bacteriophages were sequenced and analyzed.
AB  - Phages A006, A500, B025, P35, and P40 are members of the Siphoviridae and
AB  - contain double-stranded DNA genomes of between 35.6 kb and 42.7 kb. Phage
AB  - B054 is a unique myovirus and features a 48.2-kb genome. Phage B025
AB  - features 3' overlapping single-stranded genome ends, whereas the other
AB  - viruses contain collections of terminally redundant, circularly permuted
AB  - DNA molecules. Phages P35 and P40 have a broad host range and lack
AB  - lysogeny functions, correlating with their virulent lifestyle. Phages
AB  - A500, A006, and B025 integrate into bacterial tRNA genes, whereas B054
AB  - targets the 3' end of translation elongation factor gene tsf. This is the
AB  - first reported case of phage integration into such an evolutionarily
AB  - conserved genetic element. Peptide fingerprinting of viral proteins
AB  - revealed that both A118 and A500 utilize +1 and -1 programmed
AB  - translational frameshifting for generating major capsid and tail shaft
AB  - proteins with C termini of different lengths. In both cases, the unusual
AB  - +1 frameshift at the 3' ends of the tsh coding sequences is induced by
AB  - overlapping proline codons and cis-acting shifty stops. Although Listeria
AB  - phage genomes feature a conserved organization, they also show extensive
AB  - mosaicism within the genome building blocks. Of particular interest is
AB  - B025, which harbors a collection of modules and sequences with relatedness
AB  - not only to other Listeria phages but also to viruses infecting other
AB  - members of the Firmicutes. In conclusion, our results yield insights into
AB  - the composition and diversity of Listeria phages and provide new
AB  - information on their function, genome adaptation, and evolution.
ER  -

TY  - JOUR
AU  - Dortet, L.
AU  - Bonnin, R.A.
AU  - Girlich, D.
AU  - Imanci, D.
AU  - Bernabeu, S.
AU  - Fortineau, N.
AU  - Naas, T.
TI  - Whole-Genome Sequence of a European Clone II and OXA-72-Producing Acinetobacter baumannii Strain from Serbia.
JO  - Genome Announcements
PY  - 2015
SP  - e01390
EP  - e01315
VL  - 3
AB  - We report here the draft genome sequence of a carbapenem-resistant Acinetobacter  baumannii
AB  - strain isolated from a patient, a strain which previously stayed in
AB  - Serbia. This isolate possessed the blaOXA-72 carbapenemase gene. The draft genome
AB  - sequence consists of a total length of 3.91 Mbp, with an average G+C content of
AB  - 38.8%.
ER  -

TY  - JOUR
AU  - Dorvel, B.
AU  - Sigalov, G.
AU  - Zhao, Q.
AU  - Comer, J.
AU  - Dimitrov, V.
AU  - Mirsaidov, U.
AU  - Aksimentiev, A.
AU  - Timp, G.
TI  - Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 4170
EP  - 4179
VL  - 37
AB  - Restriction endonucleases are used prevalently in recombinant DNA technology because they bind
AB  - so stably to a specific target sequence and,
AB  - in the presence of cofactors, cleave double-helical DNA specifically at a
AB  - target sequence at a high rate. Using synthetic nanopores along with
AB  - molecular dynamics (MD), we have analyzed with atomic resolution how a
AB  - prototypical restriction endonuclease, EcoRI, binds to the DNA target
AB  - sequence-GAATTC-in the absence of a Mg(2+) ion cofactor. We have
AB  - previously shown that there is a voltage threshold for permeation of DNA
AB  - bound to restriction enzymes through a nanopore that is associated with a
AB  - nanonewton force required to rupture the complex. By introducing mutations
AB  - in the DNA, we now show that this threshold depends on the recognition
AB  - sequence and scales linearly with the dissociation energy, independent of
AB  - the pore geometry. To predict the effect of mutation in a base pair on the
AB  - free energy of dissociation, MD is used to qualitatively rank the
AB  - stability of bonds in the EcoRI-DNA complex. We find that the second base
AB  - in the target sequence exhibits the strongest binding to the protein,
AB  - followed by the third and first bases, with even the flanking sequence
AB  - affecting the binding, corroborating our experiments.
ER  -

TY  - JOUR
AU  - Dos Santos, A.P.
AU  - Guimaraes, A.M.
AU  - do Nascimento, N.C.
AU  - Sanmiguel, P.J.
AU  - Messick, J.B.
TI  - Complete Genome Sequence of Mycoplasma wenyonii Strain Massachusetts.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5458
EP  - 5459
VL  - 194
AB  - Mycoplasma wenyonii is a hemotrophic mycoplasma that causes acute and chronic infections in
AB  - cattle. Here, we announce the first complete genome sequence of
AB  - this organism. The genome is a single circular chromosome with 650,228 bp and
AB  - G+C% of 33.9. Analyses of M. wenyonii genome will provide insights into its
AB  - biology.
ER  -

TY  - JOUR
AU  - Dos Santos, R.A.
AU  - Berretta, A.A.
AU  - Barud, H.S.
AU  - Ribeiro, S.J.
AU  - Gonzalez-Garcia, L.N.
AU  - Zucchi, T.D.
AU  - Goldman, G.H.
AU  - Riano-Pachon, D.M.
TI  - Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.
JO  - Genome Announcements
PY  - 2014
SP  - e00731
EP  - e00714
VL  - 2
AB  - Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was
AB  - isolated from Kombucha tea and is capable of producing high levels
AB  - of cellulose.
ER  -

TY  - JOUR
AU  - Dos Santos, R.A.
AU  - Berretta, A.A.
AU  - Barud, H.S.
AU  - Ribeiro, S.J.
AU  - Gonzalez-Garcia, L.N.
AU  - Zucchi, T.D.
AU  - Goldman, G.H.
AU  - Riano-Pachon, D.M.
TI  - Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.
JO  - Genome Announcements
PY  - 2015
SP  - e01404
EP  - e01415
VL  - 3
AB  - Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which
AB  - was isolated from Kombucha tea and is capable of producing cellulose,
AB  - although at lower levels compared to another bacterium from the same environment,
AB  - K. rhaeticus strain AF1.
ER  -

TY  - JOUR
AU  - Doskar, J.
TI  - Determination of the restriction-modification system of the polyvalent bacteriophage 821 in the cells of Staphylococcus-aureus strains.
JO  - Scripta Fac. Sci. Nat. Univ. Purk. Brun.
PY  - 1988
SP  - 421
EP  - 421
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Doskar, J.
TI  - Characteristics of restriction-modification system of the polyvalent phage 812 in strains of staphylococcus aureus.
JO  - Scripta Fac. Sci. Nat. Univ. Purk. Brun.
PY  - 1989
SP  - 391
EP  - 401
VL  - 19
AB  - On the basis of the study of restriction-deficient mutants (r-) a
AB  - restriction-modification (RM) system concerning the polyvalent phage 812 has
AB  - been characterized in some strains of S. aureus.  Capability to modify DNA of
AB  - the phage 812 has been evidenced only in one of the total number of twelve r-
AB  - mutant strains under study isolated earlier (Doskar and Rosypal 1986).
AB  - Modification acquired by the polyvalent phage 812 in this mutant strain enables
AB  - this phage to grow not only on the parent restrictive strain r+ but also on
AB  - certain strains insensitive to the non-modified phage.  A similar pattern of
AB  - sensitivity of these strains both to the modified phage and to certain
AB  - host-range mutants of the phage of the phage 812 leads us to the conclusion
AB  - that RM systems in these strains are similar and that the mutations widening
AB  - the host-range of the polyvalent phage concern restriction-modification
AB  - mechanisms.  Our attempt to detect restriction endonucleases of the class II in
AB  - crude extracts from strains insensitive to the polyvalent phage 812 have not
AB  - been successful.  RM system of the polyvalent phage 812 is believed not to be
AB  - of class II because of the fact that most of r-mutants are
AB  - modification-deficient.
ER  -

TY  - JOUR
AU  - Dotson, G.A.
AU  - Dekker, J.P.
AU  - Palmore, T.N.
AU  - Segre, J.A.
AU  - Conlan, S.
TI  - Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence  Type 111 Pseudomonas aeruginosa Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01663
EP  - e01615
VL  - 4
AB  - Here, we report the draft genome sequence of a sequence type 111 Pseudomonas aeruginosa strain
AB  - isolated in 2014 from a patient at the NIH Clinical Center.
AB  - This P. aeruginosa strain exhibits pan-drug resistance and harbors the blaKPC-2
AB  - gene, encoding the Klebsiella pneumoniae carbapenemase enzyme, on a plasmid.
ER  -

TY  - JOUR
AU  - Dou, D.
AU  - Inagaki, K.
AU  - Kita, K.
AU  - Ohshima, A.
AU  - Hiraoka, N.
AU  - Kishimoto, N.
AU  - Sugio, T.
AU  - Tano, T.
TI  - Restriction endonuclease AfaI from Acidiphilium facilis, a new isoschizomer of RsaI: purification and properties.
JO  - Biochim. Biophys. Acta
PY  - 1989
SP  - 83
EP  - 86
VL  - 1009
AB  - We have purified AfaI endonuclease, an isoschizomer of RsaI, from Acidiphilium
AB  - facilis strain 28H.  The enzyme is homogeneous as judged by polyacrylamide gel
AB  - electrophoresis, and composed of a single polypeptide chain with a molecular
AB  - weight of 30,000.  AfaI endonuclease, like RsaI, recognizes the tetranucleotide
AB  - sequence 5'-G-T-A-C-3', and cleaves between the T and A to produce blunt-ended
AB  - fragments.  The yield of the enzyme is 50-100 times that of the RsaI, which is
AB  - from a phototrophic bacterium, Rhodopseudomonas sphaeroides strain 28/5.
ER  -

TY  - JOUR
AU  - Douc-Rasy, S.
AU  - Kolb, A.
AU  - Prunell, A.
TI  - Protein-induced unwinding of DNA:  measurement by gel electrophoresis of complexes with DNA minicircles.  Application to restriction endonuclease EcoRI, catabolite gene activator protein and lac repressor.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 5173
EP  - 5189
VL  - 17
AB  - An electrophoretic procedure for the measurement of the helix unwinding induced
AB  - by a sequence-specific protein is described.  The method, which was applied
AB  - here to EcoRI, CAP and lac repressor, involved the migration of the complexes
AB  - with positively and negatively supercoiled DNA minicircles carrying a single
AB  - protein binding site.  Mobility shifts of complexes relative to naked DNAs
AB  - appeared to be a result of 1) the unwinding; of 2) an increase in the molecular
AB  - frictional coefficient, which led to a retardation; of 3) bending, in the
AB  - particular case of CAP, which induced an acceleration; and of 4) looping, in
AB  - the case of lac repressor, which also resulted in an acceleration.  Under
AB  - conditions where the migration of the naked topoisomers was V-like (topoisomer
AB  - mobility showed the same linear increase with both negative and positive
AB  - supercoilings; Zivanovic et al. (1986) J. Mol. Biol., 192, 645-660), the
AB  - protein unwinding contribution to mobility was assumed to be identical to that
AB  - experimentally observed in the case of a thermal unwinding:  all negatively
AB  - supercoiled topoisomers were retarded and all positively supercoiled
AB  - topoisomers were accelerated to the same extent.  In contrast, the mobility
AB  - contribution of the frictional term, as well as those of bending and looping,
AB  - appeared to vary strongly with the magnitude of the supercoiling, but only
AB  - weakly with its polarity.  As a consequence, these latter contributions may
AB  - approximately cancel when one is measuring the difference between the shifts
AB  - observed for two comigrating, negatively and positively supercoiled,
AB  - topoisomers, allowing the unwinding to be calculated.  While estimates obtained
AB  - for EcoRI, 23 +/- 3, and CAP, about 29, were in good agreement with previous
AB  - measurements using topoisomerase I, the value found for lac repressor, 13 to
AB  - 16, was significantly smaller.
ER  -

TY  - JOUR
AU  - Doughty, B.
AU  - Kazer, S.W.
AU  - Eisenthal, K.B.
TI  - Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 19979
EP  - 19984
VL  - 108
AB  - The binding of EcoR1 to a 90-bp DNA duplex attached to colloidal microparticles and the
AB  - subsequent cleavage by the enzyme was observed in real time and label-free with time-resolved
AB  - second harmonic (SH) spectroscopy. This method provides a unique way to investigate
AB  - biomolecular interactions based on its sensitivity to changes in structure and electrical
AB  - charge on formation of a complex and subsequent dynamics. The binding of EcoR1 to the
AB  - recognition sequence in DNA appears as a rapid increase in the SH signal, which is attributed
AB  - to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape.
AB  - In the presence of the cofactor Mg(2+), the subsequent decay in the SH signal was monitored in
AB  - real time as the following processes occurred: cleavage of DNA, dissociation of the enzyme
AB  - from the DNA, and diffusion of the 74-bp fragment into the bulk solution leaving the 16-bp
AB  - fragment attached to the microparticle. The observed decay was dependent on the concentration
AB  - of Mg(2+), which functions as a cofactor and as an electrolyte. With SH spectroscopy the
AB  - rehybridization dynamics between the rehybridized microparticle bound and free cleaved DNA
AB  - fragments was observed in real time and label-free following the cleavage of DNA.
AB  - Collectively, the experiments reported here establish SH spectroscopy as a powerful method to
AB  - investigate equilibrium and time-dependent biological processes in a noninvasive and
AB  - label-free way.
ER  -

TY  - JOUR
AU  - Downing, M.E.
AU  - Brady, K.L.
AU  - Caprara, M.G.
TI  - A C-terminal fragment of an intron-encoded maturase is sufficient for promoting group I intron splicing.
JO  - RNA
PY  - 2005
SP  - 437
EP  - 446
VL  - 11
AB  - Group I introns often encode proteins that catalyze site-specific DNA hydrolysis. Some of
AB  - these proteins have acquired the ability to promote
AB  - splicing of their cognate intron, but whether these two activities
AB  - reside in different regions of the protein remains obscure. A crystal
AB  - structure of I-AniI, a dual function intron-encoded protein, has shown
AB  - that the protein has two pseudo-symmetric domains of equal size. Each
AB  - domain contacts its DNA substrate on either side of two cleavage sites.
AB  - As a first step to identify the RNA binding surface, the N- and
AB  - C-terminal domains of I-AniI were separately expressed and tested for
AB  - promoting the splicing of the mitochondrial (mt) COB pre-RNA. The
AB  - N-terminal protein showed no splicing activation or RNA binding,
AB  - suggesting that this domain plays a minimal role in activity or is
AB  - improperly folded. Remarkably, the 16-kDa C-terminal half facilitates
AB  - intron splicing with a rate similar to that of the full-length protein.
AB  - Both the C-terminal fragment and full-length proteins bind tightly to
AB  - the COB intron. RNase footprinting shows that the C-terminal and
AB  - full-length proteins bind to the same regions and induce the same
AB  - conformational changes in the COB intron. Together, these results show
AB  - that the C-terminal fragment of I-AniI is necessary and sufficient for
AB  - maturase activity and suggests that I-AniI acquired splicing function
AB  - by utilizing a relatively small protein surface that likely represents
AB  - a novel RNA binding motif. This fragment of I-AniI represents the
AB  - smallest group I intron splicing cofactor described to date.
ER  -

TY  - JOUR
AU  - Doyle, L.E.
AU  - Williams, R.B.H.
AU  - Rice, S.A.
AU  - Marsili, E.
AU  - Lauro, F.M.
TI  - Draft Genome Sequence of Enterobacter sp. Strain EA-1, an Electrochemically Active Microorganism Isolated from Tropical Sediment.
JO  - Genome Announcements
PY  - 2018
SP  - e00111
EP  - e00118
VL  - 6
AB  - Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical
AB  - sediment in Singapore. Here, the annotated draft genome assembly of
AB  - the bacterium is reported. Whole-genome comparison indicates that Enterobacter
AB  - sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia,
AB  - forms a distinct clade within the Enterobacter genus.
ER  -

TY  - JOUR
AU  - Doyon, J.B.
AU  - Pattanayak, V.
AU  - Meyer, C.B.
AU  - Liu, D.R.
TI  - Directed evolution and substrate specificity profile of homing endonuclease I-SceI.
JO  - J. Am. Chem. Soc.
PY  - 2006
SP  - 2477
EP  - 2484
VL  - 128
AB  - The laboratory evolution of enzymes with tailor-made DNA cleavage specificities would
AB  - represent new tools for manipulating genomes and may enhance our understanding of
AB  - sequence-specific DNA recognition by nucleases.  Below we describe the development and
AB  - successful application of an efficient in vivo positive and negative selection system that
AB  - applies evolutionary pressure either to favor the cleavage of a desired target sequence or to
AB  - disfavor the cleavage of nontarget sequences.  We also applied a previously described in vitro
AB  - selection method to reveal the comprehensive substrate specificity profile of I-SceI homing
AB  - endonucleases with altered DNA cleavage specificities.  The most highly evolved enzyme cleaves
AB  - the target mutant DNA sequence with a selectivity that is comparable to wild-type I-SceI's
AB  - preference for its cognate substrate.
ER  -

TY  - JOUR
AU  - Drace, K.
AU  - Giangiuli, S.
AU  - LeSar, C.
AU  - Kiefer, A.M.
TI  - Draft Genome Sequence of Mercury-Resistant Pseudomonas putida Strain DRA525.
JO  - Genome Announcements
PY  - 2018
SP  - e00370
EP  - e00318
VL  - 6
AB  - We report here the draft genome sequence of Pseudomonas putida strain DRA525, isolated from
AB  - mercury-contaminated soil. This strain shows resistance to mercury
AB  - and multiple antibiotics, and its genome sequence contains several gene sets
AB  - known to confer resistance to heavy metals enzymatically and through multidrug
AB  - efflux pumps.
ER  -

TY  - JOUR
AU  - Draghi, W.O.
AU  - Mancini, V.U.M.
AU  - Wall, L.G.
AU  - Zorreguieta, A.
TI  - Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e01238
EP  - e01215
VL  - 3
AB  - Bacteria of the genus Burkholderia are commonly found in diverse ecological niches in nature.
AB  - We report here the draft genome sequence of Burkholderia cordobensis type strain LMG 27620,
AB  - isolated from agricultural soil in Cordoba, Argentina. This strain harbors several genes
AB  - involved in chitin utilization and phenol degradation, which make it an interesting candidate
AB  - for biocontrol purposes and xenobiotic degradation in polluted environments.
ER  -

TY  - JOUR
AU  - Draper, J.L.
AU  - Hansen, L.M.
AU  - Bernick, D.
AU  - Abedrabbo, S.
AU  - Underwood, J.G.
AU  - Kong, N.
AU  - Huang, C.B.
AU  - Weis, A.M.
AU  - Weimer, B.C.
AU  - van Vliet, A.H.M.
AU  - Pourmand, N.
AU  - Solnick, J.V.
AU  - Karplus, K.
TI  - Fallacy of the unique genome: Sequence diversity within single Helicobacter pylori strains.
JO  - MBio
PY  - 2017
SP  - 0
EP  - 0
VL  - 8
ER  -

TY  - JOUR
AU  - Draper, J.L.
AU  - Hansen, L.M.
AU  - Bernick, D.L.
AU  - Abedrabbo, S.
AU  - Underwood, J.G.
AU  - Kong, N.
AU  - Huang, B.C.
AU  - Weis, A.M.
AU  - Weimer, B.C.
AU  - van Vliet, A.H.
AU  - Pourmand, N.
AU  - Solnick, J.V.
AU  - Karplus, K.
AU  - Ottemann, K.M.
TI  - Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains.
JO  - MBio
PY  - 2017
SP  - e02321
EP  - e02316
VL  - 8
AB  - Many bacterial genomes are highly variable but nonetheless are typically published as a single
AB  - assembled genome. Experiments tracking bacterial genome
AB  - evolution have not looked at the variation present at a given point in time.
AB  - Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its
AB  - parent PMSS1 to assess intra- and intergenomic variability. Using high sequence
AB  - coverage depth and experimental validation, we detected extensive genome
AB  - plasticity within these H. pylori isolates, including movement of the
AB  - transposable element IS607, large and small inversions, multiple single
AB  - nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was
AB  - found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1;
AB  - this copy number variation correlated with protein expression. To gain insight
AB  - into the changes that occurred during mouse adaptation, we also compared SS1 and
AB  - PMSS1 and observed 46 differences that were distinct from the within-genome
AB  - variation. The most substantial was an insertion in cagY, which encodes a protein
AB  - required for a type IV secretion system function. We detected modifications in
AB  - genes coding for two proteins known to affect mouse colonization, the HpaA
AB  - neuraminyllactose-binding protein and the FutB alpha-1,3 lipopolysaccharide (LPS)
AB  - fucosyltransferase, as well as genes predicted to modulate diverse properties. In
AB  - sum, our work suggests that data from consensus genome assemblies from single
AB  - colonies may be misleading by failing to represent the variability present.
AB  - Furthermore, we show that high-depth genomic sequencing data of a population can
AB  - be analyzed to gain insight into the normal variation within bacterial
AB  - strains.IMPORTANCE Although it is well known that many bacterial genomes are
AB  - highly variable, it is nonetheless traditional to refer to, analyze, and publish
AB  - 'the genome' of a bacterial strain. Variability is usually reduced ('only
AB  - sequence from a single colony'), ignored ('just publish the consensus'), or
AB  - placed in the 'too-hard' basket ('analysis of raw read data is more robust'). Now
AB  - that whole-genome sequences are regularly used to assess virulence and track
AB  - outbreaks, a better understanding of the baseline genomic variation present
AB  - within single strains is needed. Here, we describe the variability seen in
AB  - typical working stocks and colonies of pathogen Helicobacter pylori model strains
AB  - SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation
AB  - sequencing (NGS) and confirmed by traditional laboratory techniques. This work
AB  - demonstrates that reliance on a consensus assembly as 'the genome' of a bacterial
AB  - strain may be misleading.
ER  -

TY  - JOUR
AU  - Dreier, J.
AU  - Bickle, T.A.
TI  - ATPase activity of the type IC restriction-modification system EcoR124II.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 960
EP  - 969
VL  - 257
AB  - We have investigated the ATPase activity of the type IC restriction-modification
AB  - (R-M) system EcoR124II.  As with all type I R-M systems EcoR124II requires ATP hydrolysis to
AB  - cut DNA.  We determined the KM for ATP to be 10^-5 to 10^-4 M.  By measuring ATP
AB  - hydrolysis under different conditions and by simultaneously monitoring DNA restriction,
AB  - methylation and ATP hydrolysis we propose that the order of events during restriction is: (1)
AB  - binding of EcoR124II to a non-methylated recognition sequence, (2) start of DNA-dependent ATP
AB  - hydrolysis which continues even after restriction is complete, (3) restriction of DNA, (4)
AB  - methylation of the product.  Non-cleavable DNA substrates, such as recognition site containing
AB  - oligonucleotides, also support ATP hydrolysis.  Methylation can also occur prior to ATP
AB  - hydrolysis and prevent DNA degradation.
ER  -

TY  - JOUR
AU  - Dreier, J.
AU  - MacWilliams, M.P.
AU  - Bickle, T.A.
TI  - DNA cleavage by the type IC restriction-modification enzyme EcoR124II.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 722
EP  - 733
VL  - 264
AB  - Type I restriction-modification systems bind to non-palindromic, bipartite recognition
AB  - sequences.  Although these enzymes methylate specific adenine residues within their
AB  - recognition sequences, they cut DNA at sites up to several thousand base-pairs away.  We have
AB  - investigated the mechanism of how EcoR124II, a type IC restriction-modification system,
AB  - selects the cleavage site.  Restriction studies with different DNA constructs revealed that
AB  - circular DNA requires only one non-methylated recognition sequence to be cut, whereas linear
AB  - DNA needs at least two such sites.  Cleavage of linear DNA is independent of site orientation.
AB  - Further investigations of the linear substrates revealed a mechanism whereby the double-strand
AB  - break is introduced between two recognition sequences.  We propose a model for the selection
AB  - of restriction sites by type I enzymes where two EcoR124II complexes bind to two recognition
AB  - sequences.  Lack of methylation at a site stimulates the enzyme to translocate DNA on both
AB  - sides of the recognition sequence.  Thus the two complexes approach each other and, at the
AB  - point where they meet, they interact to introduce a double-strand break in the DNA.
ER  -

TY  - JOUR
AU  - Dreiseikelmann, B.
AU  - Eichenlaub, R.
AU  - Wackernagel, W.
TI  - The effect of differential methylation by Escherichia coli of plasmid DNA and phage T7 and lambda DNA on the cleavage by restriction endonuclease MboI from Moraxella bovis.
JO  - Biochim. Biophys. Acta
PY  - 1979
SP  - 418
EP  - 428
VL  - 562
AB  - The nucleotide sequence recognized and cleaved by the restriction endonuclease MboI is
AB  - 5'^GATC and is identical to the central tetranucleotide of the restriction sites of BamHI and
AB  - BglII. Experiments on the restriction of DNA from Escherichia coli dam and dam+ confirm the
AB  - notion that GATC sequences are adenosyl-methylated by the dam function of E. coli and thereby
AB  - are made refractory to cleavage by MboI. On the basis of this observation the degree of dam
AB  - methylation of various DNAs was examined by cleavage with MboI and other restriction
AB  - endonuclease. In plasmid DNA essentially all of the GATC sequences are methylated by the dam
AB  - function. The DNA of phage lambda is only partially methylated. Extended methylation is
AB  - observed in the DNA of a substitution mutant of lambda, lambda gal8bio256, and in the lambda
AB  - derived plasmid, lambda dv93, which is completely methylated. In contrast, phage T7 DNA is not
AB  - methylated by dam. A suppression of dam methylation of T7 DNA appears to act only in cis since
AB  - plasmid DNA replicated in a T7-infected cell is completely methylated. The results are
AB  - discussed with respect to the participation of the dam methylase in different replication
AB  - systems.
ER  -

TY  - JOUR
AU  - Dreiseikelmann, B.
AU  - Wackernagel, W.
TI  - Absence in Bacillus subtilis and Staphylococcus aureus of the sequence-specific deoxyribonucleic acid methylation that is conferred in Escherichia coli K-12 by the dam and dcm enzymes.
JO  - J. Bacteriol.
PY  - 1981
SP  - 259
EP  - 261
VL  - 147
AB  - Restriction analysis of plasmid pHV14 deoxyribonucleic acid isolated from Escherichia coli
AB  - K-12, Bacillus subtilis, and Staphylococcus aureus with restriction endonucleases MboI,
AB  - Sau3AI, and EcoRII was used to study the methylation of those nucleotide sequences which in E.
AB  - coli contain the major portions of N6-methyladenine and 5-methylcytosine.
ER  -

TY  - JOUR
AU  - Drew, H.R.
AU  - Travers, A.
TI  - Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 4445
EP  - 4467
VL  - 13
AB  - When a protein binds to DNA, the affinity of this protein for its primary site
AB  - of interaction may be influenced by the nature of flanking sequences.  This is
AB  - thought to be a consequence of local cooperativity in the DNA molecule, where
AB  - the conformation at one point along the helix can influence the conformation at
AB  - another, and thereby modulate the free energy of protein-DNA recognition.In
AB  - order to learn more about this procesas, we have carried out experiments of two
AB  - sorts.  First, we have constructed sequences of the type (dA)11(dG)8, where the
AB  - conformational preferences of the DNA molecule switch from one extreme to
AB  - another over just a single base pair, and subjected them to digestion by DNAase
AB  - I and DNAase II.  This is to learn whether the structure changes abruptly at
AB  - the junction point, or more gradually with an influence extending into residues
AB  - on either side.  Secondly, we have subjected long plasmid DNA to digestion by
AB  - restriction enzymes Fnu DII, HaeIII, HhaI and MspI, to look for correlations
AB  - between cutting rate and the identity of nucleotides on either side of the
AB  - restriction site.  The influence of flanking sequence on nuclease digestion
AB  - specificities is clearly evident in both kinds of experiment, but the rules
AB  - governing this seem complex and not easily formulated.  The best that can be
AB  - done at present is to divide the problem into two parts, "analogue" and
AB  - "digital", representing sugar-phosphate and base components of recognition.
ER  -

TY  - JOUR
AU  - Drexler, H.
AU  - Christensen, J.R.
TI  - Genetic crosses between restricted and unrestricted phage T1 in lysogenic and nonlysogenic hosts.
JO  - Virology
PY  - 1961
SP  - 31
EP  - 39
VL  - 13
AB  - When Shigella dysenteriae is lysogenized by the phage P1, it becomes immune to
AB  - infection with "ordinary" T1 phage ("restricted T1" or "rT1").  A
AB  - host-controlled variant of T1 ("unrestricted T1" or "uT1") can multiply in the
AB  - lysogenic S. dysenteriae.  Three-factor crosses were done between suitably
AB  - marked strains of rT1 and uT1 in both lysogenic and nonlysogenic S.
AB  - dysenteriae.  When lysogenic cells are infected with both rT1 and uT1, one
AB  - finds some recombinants among the progeny, but few, if any phage bearing the
AB  - genotype of the restricted parent.  The proportion of recombinants in the total
AB  - yield is about one-eighth to one-twelfth that in control crosses (in
AB  - nonlysogenic hosts) and is independent of the order of addition of either
AB  - parent and of the time elapsing between the addition of each parent.  We infer,
AB  - then, that (1) the genome of rT1 enters the lysogenic cells; (2) it is neither
AB  - replicated nor is it destroyed; and (3) it can "mate" with genomes of uT1 which
AB  - may be present.  The proportions of the various recombinant classes are
AB  - unusual.  Complementary classes are not equal; certain markers may be recovered
AB  - together with a high frequency, whereas certain others, more closely linked,
AB  - are seldom found together.  Certain "double crossover" classes are more
AB  - frequent than certain "single crossover" classes.  These observations can be
AB  - explained in terms of a "copy choice" mechanism of recombination by assuming
AB  - that the rT1 genome contains at least two "bad spots," the location of which
AB  - can be determined approximately and which force a "switch" in replication from
AB  - the restricted genome to the unrestricted genome.
ER  -

TY  - JOUR
AU  - Dreyer, K.
AU  - Schulte-Holthausen, H.
TI  - Casein is a potent enhancer for restriction enzyme activity.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4295
EP  - 4295
VL  - 19
AB  - Restriction enzymes class II are ATP independent and require magnesium ions for
AB  - their activity.  Bovine serum albumin (BSA) and spermidine are added in some
AB  - reaction buffers.  In our experience addition of spermidine sometimes causes
AB  - severe problems with high molecular weight DNA and BSA has only a slight effect
AB  - on enzyme activity.  Here we show that casein, the major protein component of
AB  - milk is a potent stimulator of restriction enzyme activity.
ER  -

TY  - JOUR
AU  - Dreyfus-Fourcade, M.
AU  - Sebald, M.
AU  - Zavadova, M.
TI  - Host-controlled restriction and modification of phage r in Clostridium perfringens NCTC 8798 and some of its sporulation mutants.
JO  - Ann. Inst. Pasteur Microbiol.
PY  - 1972
SP  - 1117
EP  - 1127
VL  - 122
AB  - The development of phage r, a virulent bacteriophage, in a wild type strain of
AB  - C. perfringens and in its sporulation mutants is described.  The phage is fully
AB  - accepted by the wild type strain and most of the Spo mutants (r-m+).  Some
AB  - mutants have altered host-controlled restriction and modification functions,
AB  - i.e., the phage r is restricted and may be partially modified by the mutant
AB  - strains.  Strains of phenotype r+m+/-, r+/-m+, r+/-m- and r-m- are described.
ER  -

TY  - JOUR
AU  - Driscoll, C.B.
AU  - Otten, T.G.
AU  - Brown, N.M.
AU  - Dreher, T.W.
TI  - Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake  co-culture.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 9
EP  - 9
VL  - 12
AB  - Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of
AB  - a co-culture from Upper Klamath Lake, OR. Genome annotations and
AB  - culture conditions indicate these bacteria are dependent on carbon and nitrogen
AB  - fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was
AB  - assembled to draft-quality. Due to their taxonomic novelty relative to previously
AB  - sequenced bacteria, we have temporarily designated these bacteria as incertae
AB  - sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56.12% GC), incertae sedis
AB  - Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and incertae
AB  - sedis Bacteroidetes strain UKL13-3 (3,236,529 bp and 37.33% GC). Each genome
AB  - consists of a single circular chromosome with no identified plasmids. When
AB  - compared with binned Illumina assemblies of the same three genomes, there was ~7%
AB  - discrepancy in total genome length. Gaps where Illumina assemblies broke were
AB  - often due to repetitive elements. Within these missing sequences were essential
AB  - genes and genes associated with a variety of functional categories. Annotated
AB  - gene content reveals that both Proteobacteria are aerobic anoxygenic phototrophs,
AB  - with Betaproteobacterium UKL13-2 potentially capable of phototrophic oxidation of
AB  - sulfur compounds. Both proteobacterial genomes contain transporters suggesting
AB  - they are scavenging fixed nitrogen from A. flos-aquae in the form of ammonium.
AB  - Bacteroidetes UKL13-3 has few completely annotated biosynthetic pathways, and has
AB  - a comparatively higher proportion of unannotated genes. The genomes were detected
AB  - in only a few other freshwater metagenomes, suggesting that these bacteria are
AB  - not ubiquitous in freshwater systems. Our results indicate that long-read
AB  - sequencing is a viable method for sequencing dominant members from low-diversity
AB  - microbial communities, and should be considered for environmental metagenomics
AB  - when conditions meet these requirements.
ER  -

TY  - JOUR
AU  - Drissi, F.
AU  - Labas, N.
AU  - Merhej, V.
AU  - Raoult, D.
TI  - Draft Genome Sequence of the Lactobacillus agilis Strain Marseille.
JO  - Genome Announcements
PY  - 2015
SP  - e00840
EP  - e00815
VL  - 3
AB  - We report the draft genome sequence of Lactobacillus agilis strain Marseille, isolated from
AB  - stool samples of a child suffering from kwashiorkor. This strain
AB  - can use two metabolic pathways allowing the assimilation of glucose and xylose.
AB  - Here, we present the first draft genome of the Lactobacillus agilis species.
ER  -

TY  - JOUR
AU  - Drissi, F.
AU  - Merhej, V.
AU  - Blanc-Tailleur, C.
AU  - Raoult, D.
TI  - Draft Genome Sequence of the Lactobacillus mucosae Strain Marseille.
JO  - Genome Announcements
PY  - 2015
SP  - e00841
EP  - e00815
VL  - 3
AB  - Lactobacillus mucosae strain Marseille, isolated from stool samples of a child suffering from
AB  - a malnutrition disorder called Kwashiorkor, produces bacteriocin
AB  - and seems to have specific carbohydrate and lipid metabolisms different from
AB  - those of other Lactobacillus organisms. The draft genome sequence of this strain
AB  - is presented here.
ER  -

TY  - JOUR
AU  - Droge, M.
AU  - Puhler, A.
AU  - Selbitschka, W.
TI  - Phenotypic and molecular characterization of conjugative antibiotic resistance plasmids isolated from bacterial communities of activated sludge.
JO  - Mol. Gen. Genet.
PY  - 2000
SP  - 471
EP  - 482
VL  - 263
AB  - In order to isolate antibiotic resistance plasmids from bacterial communities found in
AB  - activated sludge, derivatives of the
AB  - 3-chlorobenzoate-degrading strain Pseudomonas sp. B13, tagged with the
AB  - green fluorescent protein as an identification marker, were used as
AB  - recipients in filter crosses. Transconjugants were selected on agar
AB  - plates containing 3-chlorobenzoate as the sole carbon source and the
AB  - antibiotic tetracycline, streptomycin or spectinomycin, and were
AB  - recovered at frequencies in the range of 10(-5) to 10(-8) per
AB  - recipient. A total of 12 distinct plasmids, designated pB1-pB12, was
AB  - identified. Their sizes ranged between 41 to 69 kb and they conferred
AB  - various patterns of antibiotic resistance on their hosts. Two of the
AB  - plasmids, pB10 and pB11, also mediated resistance to inorganic mercury.
AB  - Seven of the 12 plasmids were identified as broad-host-range plasmids
AB  - displaying extremely high transfer frequencies in filter crosses,
AB  - ranging from 10^-1 to 10^-2 per recipient cell. Ten of the 12
AB  - plasmids belonged to the IncP incompatibility group, based on replicon
AB  - typing using IncP group-specific PCR primers. DNA sequencing of PCR
AB  - amplification products further revealed that eight of the 12 plasmids
AB  - belonged to the IncP beta subgroup, whereas two plasmids were
AB  - identified as IncP alpha plasmids. Analysis of the IncP-specific PCR
AB  - products revealed considerable differences among the IncP beta plasmids
AB  - at the DNA sequence level. In order to characterize the gene 'load'
AB  - of the IncP plasmids, restriction fragments were cloned and their DNA
AB  - sequences established. A remarkable diversity of putative proteins
AB  - encoded by these fragments was identified. Besides transposases and
AB  - proteins involved in antibiotic resistance, two putative DNA invertases
AB  - belonging to the Din family, a methyltransferase of a type I
AB  - restriction/modification system, a superoxide dismutase. parts of a
AB  - putative efflux system belonging to the RND family, and proteins of
AB  - unknown function were identified.
ER  -

TY  - JOUR
AU  - Drotschmann, K.
AU  - Aronshtam, A.
AU  - Fritz, H.-J.
AU  - Marinus, M.G.
TI  - The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 948
EP  - 953
VL  - 26
AB  - Vsr DNA mismatch endonuclease is the key enzyme of very short patch (VSP) DNA mismatch repair
AB  - and nicks the T-containing strand at the site of a T-G mismatch in a sequence-dependent
AB  - manner. MutS is part of the mutHLS repair system and binds to diverse mismatches in DNA. The
AB  - function of the mutL gene product is currently unclear but mutations in the gene abolish
AB  - mutHLS-dependent repair. The absence of MutL severely reduces VSP repair but does not abolish
AB  - it. Purified MutL appears to act catalytically to bind Vsr to its substrate; one-hundredth of
AB  - an equivalent of MutL is sufficient to bring about a significant effect. MutL enhances binding
AB  - of MutS to its substrate 6-fold but does so in a stoichiometric manner. Mutational studies
AB  - indicate that the MutL interaction region lies within the N-terminal 330 amino acids and that
AB  - the MutL multimerization region is at the C-terminal end. MutL mutant monomeric forms can
AB  - stimulate MutS binding.
ER  -

TY  - JOUR
AU  - Drouin, M.
AU  - Lucas, P.
AU  - Otis, C.
AU  - Lemieux, C.
AU  - Turmel, M.
TI  - Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 4566
EP  - 4572
VL  - 28
AB  - Endonuclease assays of the H-N-H proteins encoded by two group I introns in the Chlamydomonas
AB  - moewusii chloroplast psbA gene revealed that the CmpsbA.1 intron specifies a site-specific DNA
AB  - endonuclease, designated I-CmoeI. Like most previously reported intron-encoded endonucleases,
AB  - I-CmoeI generates a double-strand break near the insertion site of its encoding intron,
AB  - leaving 3' extensions of 4 nt. This enzyme was purified from Escherichia coli as a fusion
AB  - protein with a His tag at its N-terminus. The recombinant protein (rI-CmoeI) requires a
AB  - divalent alkaline earth cation for DNA cleavage (Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+)).  It also
AB  - requires a metal cofactor for DNA binding, a property shared with H-N-H colicins but not with
AB  - the homing endonucleases characterized to date. rI-CmoeI binds its recognition sequence as a
AB  - monomer, as revealed by gel retardation assays. K:(m) and k(cat) values of 100 +/- 40 pM and
AB  - 0.26 +/- 0.04 min(-1), respectively, were determined. Replacement of the first histidine of
AB  - the H-N-H motif by an alanine residue abolishes both rI-CMOE:I activity and binding to its
AB  - substrate. We propose that this conserved histidine residue plays a role in binding the metal
AB  - cofactor and that such binding induces a structural modification of the enzyme which is
AB  - required for DNA recognition.
ER  -

TY  - JOUR
AU  - Drozdz, M.
AU  - Piekarowicz, A.
AU  - Bujnicki, J.M.
AU  - Radlinska, M.
TI  - Novel non-specific DNA adenine methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 2119
EP  - 2130
VL  - 40
AB  - The mom gene of bacteriophage Mu encodes an enzyme that converts adenine to
AB  - N(6)-(1-acetamido)-adenine in the phage DNA and thereby protects the viral genome from
AB  - cleavage by a wide variety of restriction endonucleases. Mu-like prophage sequences present in
AB  - Haemophilus influenzae Rd (FluMu), Neisseria meningitidis type A strain Z2491 (Pnme1) and H.
AB  - influenzae biotype aegyptius ATCC 11116 do not possess a Mom-encoding gene. Instead, at the
AB  - position occupied by mom in Mu they carry an unrelated gene that encodes a protein with
AB  - homology to DNA adenine N(6)-methyltransferases (hin1523, nma1821, hia5, respectively).
AB  - Products of the hin1523, hia5 and nma1821 genes modify adenine residues to N(6)-methyladenine,
AB  - both in vitro and in vivo. All of these enzymes catalyzed extensive DNA methylation; most
AB  - notably the Hia5 protein caused the methylation of 61% of the adenines in lambda DNA. Kinetic
AB  - analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the
AB  - possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes.
AB  - Their potential 'sequence specificity' could be summarized as AB or BA (where B = C, G or
AB  - T). Plasmid DNA isolated from Escherichia coli cells overexpressing these novel DNA
AB  - methyltransferases was resistant to cleavage by many restriction enzymes sensitive to adenine
AB  - methylation.
ER  -

TY  - JOUR
AU  - Dryden, D.T.
TI  - Reeling in the bases.
JO  - Nat. Struct. Mol. Biol.
PY  - 2004
SP  - 804
EP  - 806
VL  - 11
AB  - EcoR124I is a type I DNA restriction and modification enzyme. The single-molecule magnetic
AB  - tweezers technique reveals that this
AB  - sophisticated molecular machine is capable of moving thousands of base
AB  - pairs of DNA in one binding event.
ER  -

TY  - JOUR
AU  - Dryden, D.T.
AU  - Davies, G.D.
AU  - Martin, I.
AU  - Powell, L.M.
AU  - Murray, N.E.
AU  - Ellis, D.J.
AU  - Berge, T.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA.
JO  - Biochem. Soc. Trans.
PY  - 1999
SP  - 691
EP  - 696
VL  - 27
ER  -

TY  - JOUR
AU  - Dryden, D.T.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule  measurements.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 4525
EP  - 4531
VL  - 39
AB  - Much insight into the interactions of DNA and enzymes has been obtained using a number of
AB  - single-molecule techniques. However, recent results  generated using two of these
AB  - techniques-atomic force microscopy (AFM) and  magnetic tweezers (MT)-have produced apparently
AB  - contradictory results when applied to the action of the ATP-dependent type III restriction
AB  - endonucleases on DNA. The AFM images show extensive looping of the DNA  brought about by the
AB  - existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT
AB  - experiments show no evidence for looping being a requirement for DNA cleavage, but instead
AB  - support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs,
AB  - leading to cleavage. Not only do these two methods appear to disagree, but also the models
AB  - derived from them have difficulty explaining some ensemble biochemical results on DNA
AB  - cleavage. In this 'Survey and Summary', we describe several different models put forward for
AB  - the action of type III restriction enzymes and their inadequacies. We also attempt to
AB  - reconcile the different models and indicate areas for further experimentation to elucidate the
AB  - mechanism of these enzymes.
ER  -

TY  - JOUR
AU  - Dryden, D.T.
AU  - Murray, N.E.
AU  - Rao, D.N.
TI  - Nucleoside triphosphate-dependent restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3728
EP  - 3741
VL  - 29
AB  - The known nucleoside triphosphate-dependent restriction enzymes are hetero-oligomeric proteins
AB  - that behave as molecular machines in response to their target sequences. They translocate DNA
AB  - in a process dependent on the hydrolysis of a nucleoside triphosphate. For the ATP-dependent
AB  - type I and type III restriction and modification systems, the collision of translocating
AB  - complexes triggers hydrolysis of phosphodiester bonds in unmodified DNA to generate
AB  - double-strand breaks. Type I endonucleases break the DNA at unspecified sequences remote from
AB  - the target sequence, type III endonucleases at a fixed position close to the target sequence.
AB  - Type I and type III restriction and modification (R-M) systems are notable for effective
AB  - post-translational control of their endonuclease activity. For some type I enzymes, this
AB  - control is mediated by proteolytic degradation of that subunit of the complex which is
AB  - essential for DNA translocation and breakage. This control, lacking in the well-studied type
AB  - II R-M systems, provides extraordinarily effective protection of resident DNA should it
AB  - acquire unmodified target sequences. The only well-documented GTP-dependent restriction
AB  - enzyme, McrBC, requires methylated target sequences for the initiation of phosphodiester bond
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
TI  - Bacterial DNA methyltransferases.
JO  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
PY  - 1999
SP  - 283
EP  - 340
AB  - There are four entries for DNA MTases in the E.C. database.  Classes 2.1.1.37 and 2.1.1.73
AB  - both methylate carbon 5 of the cytosine base and differ in that the former group contains a
AB  - large regulatory domain and is only found in multicellular eukarotes.  Classes 2.1.1.72 and
AB  - 2.1.1.113 act on the exocyclic amino groups of adenine and cytosine respectively.  Thus, three
AB  - modifications carried out by MTases have now been identified. Cytosine can be modified at
AB  - either the C5 or N4 position, and adenine at the N6 position.  These methylation sites are all
AB  - in the major groove of B-form DNA which is also the region which allows the most effective
AB  - recognition of a DNA sequence via hydrogen bonding and hydrophobic interactions.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
TI  - Structures of the type I DNA restriction enzymes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2017
SP  - E10261
EP  - E10262
VL  - 114
AB  - The article by Liu et al. (1) on the structure of type I
AB  - DNA restriction and modification enzymes purports to
AB  - significantly advance our understanding of these enzymes
AB  - and proposes a model for their operation.
AB  - While the partial structure of one of these enzymes
AB  - is interesting and defines the interface between some
AB  - of the subunits, the article contains many misinterpretations
AB  - of the literature.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
TI  - The Architecture of Restriction Enzymes.
JO  - Structure
PY  - 2013
SP  - 1720
EP  - 1721
VL  - 21
AB  - In this issue of Structure, Lyumkis and colleagues describe a high resolution structure of a
AB  - polymerized form of the SgrAl restriction enzyme, which shows that it forms a helical assembly
AB  - with four enzyme molecules per turn of the helix. The DNA is arranged on the periphery of the
AB  - protein helix pointing away from the helical axis.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
AU  - Cooper, L.P.
AU  - Murray, N.E.
TI  - Purification and characterization of the methyltransferase from the Type I restriction and modification system of Escherichia coli K12.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 13228
EP  - 13236
VL  - 268
AB  - The DNA methyltransferase component of the type I restriction and modification enzyme of
AB  - Escherichia coli K12 has been purified. The active component, a trimer of molecular mass 170
AB  - kDa consisting of one DNA recognition subunit(S) and two modification subunits(M), showed the
AB  - expected preference for modifying a hemimethylated substrate rather than an unmethylated one.
AB  - Small amounts of the dimers M2 and M1S1 were also isolated. Subunit rearrangements of the
AB  - three protein species occurred on ion exchange and heparin-agarose chromatography.
AB  - Denaturation of the trimer gave folding intermediates, and these and the dimer forms isolated
AB  - during purification may reflect the assembly of the protein in vivo. Enzyme activity was
AB  - recovered on refolding the denatured protein by dilution of the denaturant. A comparison of
AB  - the predicted isoelectric points of all known S subunits of type I restriction and
AB  - modification enzymes revealed values that correlated with the arrangement of type I systems in
AB  - several families. Electrostatic interactions may explain the different subunit stoichiometries
AB  - observed during purification of type I enzymes and the differing preferences for
AB  - hemimethylated DNA displayed by the three type I families.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
AU  - Cooper, L.P.
AU  - Murray, N.E.
TI  - Assembly of the multifunctional EcoKI DNA restriction enzyme in vitro.
JO  - Tech. Prot. Chem.
PY  - 1997
SP  - 593
EP  - 601
VL  - 8
AB  - Type I DNA restriction/modification systems have been found in many strains of Escherichia
AB  - coli and Salmonella enterica and several other gram negative and positive bacteria.  They
AB  - maintain the modification of the host chromosome after DNA replication by methylating adenine
AB  - bases on the newly synthesized DNA strand within specific DNA target sequences.  This
AB  - methylation reaction is triggered by the recognition of targets which are methylated on the
AB  - parental DNA stand.  If methylation is not detected on either strand then the restriction
AB  - reaction is triggered.  Unmodified target sequences will exist on foreign DNA, usually of
AB  - viral origin.  A type I system cleaves the foreign DNA thereby preventing (restricting) its
AB  - replication and propagation.  In contrast to the widely used type II restriction/modification
AB  - systems which have separate restriction endonucleases and modification methyltransferases, the
AB  - type I systems combine both activities in one large oligomeric enzyme.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
AU  - Cooper, L.P.
AU  - Thorpe, P.H.
AU  - Byron, O.
TI  - The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications.
JO  - Biochemistry
PY  - 1997
SP  - 1065
EP  - 1076
VL  - 36
AB  - Type I DNA restriction/modification enzymes protect the bacterial cell from viral infection by
AB  - cleaving foreign DNA which lacks N6-adenine methylation within a target sequence and
AB  - maintaining the methylation of the targets on the host chromosome.  It has been noted that the
AB  - genes specifying type I systems can be transferred to a new host lacking the appropriate,
AB  - protective methylation without any adverse effect.  The modification phenotype apparently
AB  - appears before the restriction phenotype, but no evidence for transcriptional or translational
AB  - control of the genes and the resultant phenotypes has been found.  Type I enzymes contain
AB  - three types of subunit, S for sequence recognition, M for DNA modification (methylation), and
AB  - R for DNA restriction (cleavage), and can function solely as an M2S1 methylase or as a R2M2S1
AB  - bifunctional methylase/nuclease.  We show that the methylase is not stable at the
AB  - concentrations expected to exist in vivo, dissociating into free M subunit and M1S1, whereas
AB  - the complete nuclease is a stable structure.  The M1S1 form can bind the R subunit as
AB  - effectively as the M2S1 methylase but possesses no activity; therefore, upon establishment of
AB  - the system in a new host, we propose that most of the R subunit will initially be trapped in
AB  - an inactive complex until the methylase has been able to modify and protect the host
AB  - chromosome.  We believe that the in vitro assembly pathway will reflect the in vivo situation,
AB  - thus allowing the assembly process to at least partially explain the observations that the
AB  - modification phenotype appears before the restriction phenotype upon establishment of a type I
AB  - system in a new host cell.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
AU  - Davies, G.D.
AU  - Powell, L.M.
AU  - Murray, N.E.
AU  - Ellis, D.J.
AU  - Berge, T.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - The assembly of the EcoKI type I DNA restriction/modification enzyme and its interaction with DNA.
JO  - Biochem. Soc. Trans.
PY  - 1999
SP  - A87
EP  - A87
VL  - 27
AB  - Type I DNA restriction-modification enzymes protect the bacterial cell from viral infection by
AB  - cleaving foreign DNA which lacks N6-adenine methylation within a target sequence and
AB  - maintaining the methylation of the targets on the host chromosome.  They comprise three types
AB  - of subunit, S M and R and can function solely as an M2S1 methylase or as an R2M2S1
AB  - bifunctional methylase/nuclease.  The subunits contain domains related to those in other
AB  - smaller methylases, nucleases and helicases.  The nuclease is a stable structure, whereas the
AB  - methylase dissociates into nonfunctional forms M and M1S1 at the concentrations expected to
AB  - exist in vivo.  The restriction reaction relies upon extensive DNA translocation driven by ATP
AB  - hydrolysis prior to endonucleolytic DNA cleavage.  Cleavage occurs between two,
AB  - widely-separated, target sites.  This is consistent with the translocation process causing the
AB  - collision of two enzymes on the DNA.  However, atomic force microscopy has suggested that DNA
AB  - binding induces dimerization of the enzyme prior to the initiation of translocation and that
AB  - cleavage occurs once the DNA loop bound between the two enzymes has been pulled in towards the
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
AU  - Sturrock, S.S.
AU  - Winter, M.
TI  - Structural modelling of a type I DNA methyltransferase.
JO  - Nat. Struct. Biol.
PY  - 1995
SP  - 632
EP  - 635
VL  - 2
AB  - Amino-acid sequence comparison and tertiary structure modelling suggest a structure for type I
AB  - DNA methyltransferases and an evolutionary link to type II methyltransferases.
ER  -

TY  - JOUR
AU  - Dryden, D.T.F.
AU  - Willcock, D.F.
AU  - Murray, N.E.
TI  - Mutational analysis of conserved amino-acid motifs in EcoKI adenine methyltransferase.
JO  - Gene
PY  - 1995
SP  - 123
EP  - 124
VL  - 157
AB  - The EcoKI methyltransferase (M.EcoKI, MTase) contains the amino acid (aa) sequences AAGTA and
AB  - NPPF believed to represent the two sequences that are strongly conserved in adenine MTases.
AB  - We have analysed a mutation in the first sequence that abolishes cofactor binding and enzyme
AB  - activity, and mutations in the second sequence that reduce or abolish activity without
AB  - affecting cofactor and DNA binding.
ER  -

TY  - JOUR
AU  - du Plessis, M. et al.
TI  - Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015.
JO  - Emerg. Infect. Dis.
PY  - 2017
SP  - 1308
EP  - 1315
VL  - 23
AB  - In 2015, a cluster of respiratory diphtheria cases was reported from
AB  - KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we
AB  - characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients
AB  - and contacts during the outbreak (1 patient was infected with 2 variants of C.
AB  - diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis
AB  - isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel
AB  - lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17)
AB  - and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate
AB  - were ST-395, suggesting ongoing circulation of this lineage for >30 years. The
AB  - absence of preexisting molecular sequence data limits drawing conclusions
AB  - pertaining to the origin of these strains; however, these findings provide
AB  - baseline genotypic data for future cases and outbreaks. Neither ST has been
AB  - reported in any other country; this ST appears to be endemic only in South
AB  - Africa.
ER  -

TY  - JOUR
AU  - Du, J.
AU  - Zhong, X.
AU  - Bernatavichute, Y.V.
AU  - Stroud, H.
AU  - Feng, S.
AU  - Caro, E.
AU  - Vashisht, A.A.
AU  - Terragni, J.
AU  - Chin, H.G.
AU  - Tu, A.
AU  - Hetzel, J.
AU  - Wohlschlegel, J.A.
AU  - Pradhan, S.
AU  - Patel, D.J.
AU  - Jacobsen, S.E.
TI  - Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.
JO  - Cell
PY  - 2012
SP  - 167
EP  - 180
VL  - 151
AB  - DNA methylation and histone modification exert epigenetic control over gene expression. CHG
AB  - methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9
AB  - dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly
AB  - understood. Here, we report multiple lines of evidence that CMT3 interacts with
AB  - H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated
AB  - with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes.
AB  - Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides,
AB  - showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo
AB  - domains. The structures reveal an aromatic cage within both BAH and chromo
AB  - domains as interaction interfaces that capture H3K9me2. Mutations that abolish
AB  - either interaction disrupt CMT3 binding to nucleosomes and show a complete loss
AB  - of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks
AB  - by BAH and chromo domains and reveals a distinct mechanism of interplay between
AB  - DNA methylation and histone modification.
ER  -

TY  - JOUR
AU  - Du, L.
AU  - Zhang, M.
AU  - Burton, R.
AU  - Spielberger, K.
AU  - Mollova, E.
AU  - Gilmanshin, R.
TI  - Rapid mapping of large DNA molecules using fluorescent labeled restriction enzyme.
JO  - Biophys. J.
PY  - 2007
SP  - 331A
EP  - 331A
VL  - S
AB  - Rapid DNA mapping at the single molecule level is a powerful tool for research and clinical
AB  - application. We report here a development of new tags for high throughput mapping of large DNA
AB  - based on our Direct Linear Analysis (DLA) technology. Double-stranded DNA molecules were
AB  - stained with two fluorescent tags: a nonspecific intercalator for uniform backbone staining
AB  - and a sequence-specific tag for physical mapping. These DNA molecules were then stretched by
AB  - elongational flow to a linear conformation in a high-throughput microfluidic device, and the
AB  - positions of site-specific tags were detected. We applied restriction enzymes for DNA tagging
AB  - due to their unique features including high binding affinity, sequence specificity, and fast
AB  - target localization. The restriction enzymes selected for tagging retained high binding
AB  - efficiency in the presence of Ca++ after fluorescent-labeling; however, their cleavage
AB  - function was inactivated. We show that DNA fragments ranging from 50-200 kb, or 16-66
AB  - microns-long, can be tagged with fluorescently labeled AgeI or BamHI, intercalated, stretched
AB  - to their contour length in our device, and then interrogated molecule by molecule. More than
AB  - 5,000 molecules could be analyzed through the microfluidic device in 10-15 minutes and
AB  - identity of the DNA fragments revealed by tagging patterns as well as lengths. We analyzed
AB  - multiple genomic DNA fragments from E. coli stains, demonstrating great potential of using
AB  - this method to obtain information regarding DNA structure and to discriminate DNA fragments
AB  - originated from different organisms.
ER  -

TY  - JOUR
AU  - Du, Q.
AU  - Wang, Z.
AU  - Schramm, V.L.
TI  - Human DNMT1 transition state structure.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2016
SP  - 2916
EP  - 2921
VL  - 113
AB  - Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG
AB  - methylation signatures from parent to daughter strands, producing heritable methylation
AB  - patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves
AB  - nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from
AB  - S-adenosyl-l-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG
AB  - in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major
AB  - transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope
AB  - effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl
AB  - transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically
AB  - rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground
AB  - states, providing the electronic basis for interactions between the protein and reactants at
AB  - the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis
AB  - to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.
ER  -

TY  - JOUR
AU  - Du, X.J.
AU  - Jia, S.R.
AU  - Yang, Y.
AU  - Wang, S.
TI  - Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3395
EP  - 3396
VL  - 193
AB  - Gluconacetobacter are prominent bacteria during traditional vinegar fermentation. Here, we
AB  - report a draft genome sequence of Gluconacetobacter
AB  - sp. strain SXCC-1. This strain was isolated from fermentation starter
AB  - (Daqu) that used for commercial production of Shanxi vinegar, the best
AB  - known vinegar of China.
ER  -

TY  - JOUR
AU  - Du, Y.
AU  - Song, L.
AU  - Feng, W.
AU  - Pei, G.
AU  - Zheng, P.
AU  - Yu, Z.
AU  - Sun, J.
AU  - Qiao, J.
TI  - Draft Genome Sequence of Lactococcus lactis subsp. lactis Strain YF11.
JO  - Genome Announcements
PY  - 2013
SP  - e00599
EP  - e00513
VL  - 1
AB  - Lactococcus lactis subsp. lactis strain YF11 is a food preservative bacterium with a high
AB  - capacity to produce nisin. Here, we announce the draft genome
AB  - sequence of Lactococcus lactis subsp. lactis YF11 (2,527,433 bp with a G+C
AB  - content of 34.81%).
ER  -

TY  - JOUR
AU  - Du, Y.
AU  - Yuan, B.
AU  - Zeng, Y.
AU  - Meng, J.
AU  - Li, H.
AU  - Wang, R.
AU  - Li, G.
AU  - Feng, F.
TI  - Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase.
JO  - Genome Announcements
PY  - 2015
SP  - e01304
EP  - e01314
VL  - 3
AB  - Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in
AB  - Inner Mongolia, North China, has a high capability for producing
AB  - cold-active cellulase at low temperatures. Here, we report the draft genome
AB  - sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49
AB  - RNA-coding sequences.
ER  -

TY  - JOUR
AU  - Du, Z.
AU  - Zhang, Z.
AU  - Miao, T.
AU  - Wu, J.
AU  - Lu, G.
AU  - Yu, J.
AU  - Xiao, J.
AU  - Chen, G.
TI  - Draft Genome Sequence of the Novel Agar-Digesting Marine Bacterium HQM9.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4557
EP  - 4557
VL  - 193
AB  - Strain HQM9, an aerobic rod-shaped marine bacterium from red alga, can produce agarases and
AB  - liquefy solid plating medium efficiently when agar
AB  - was used as coagulant. Here we report the draft genome sequence of strain
AB  - HQM9, which should be a novel species of Flavobacteriaceae, and initial
AB  - findings from its preliminary analysis.
ER  -

TY  - JOUR
AU  - Dua, A.
AU  - Sangwan, N.
AU  - Kaur, J.
AU  - Saxena, A.
AU  - Kohli, P.
AU  - Gupta, A.K.
AU  - Lal, R.
TI  - Draft Genome Sequence of Agrobacterium sp. Strain UHFBA-218, Isolated from Rhizosphere Soil of Crown Gall-Infected Cherry Rootstock Colt.
JO  - Genome Announcements
PY  - 2013
SP  - e00302
EP  - e00313
VL  - 1
AB  - We report here the draft genome sequence of the alphaproteobacterium Agrobacterium sp. strain
AB  - UHFBA-218, which was isolated from rhizosphere soil of
AB  - crown gall-infected cherry rootstock Colt. The draft genome of strain UHFBA-218
AB  - consists of 112 contigs (5,425,303 bp) and 5,063 coding sequences with a G+C
AB  - content of 59.8%.
ER  -

TY  - JOUR
AU  - Duan, C.
AU  - Tong, Y.
AU  - Huang, Y.
AU  - Wang, X.
AU  - Xiong, X.
AU  - Wen, B.
TI  - Complete Genome Sequence of Rickettsia heilongjiangensis, an Emerging Tick-Transmitted Human Pathogen.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5564
EP  - 5565
VL  - 193
AB  - Rickettsia heilongjiangensis is an emerging tick-transmitted human pathogen causing
AB  - far-Eastern spotted fever. Here we report the complete
AB  - sequence and the main features of the genome of R. heilongjiangensis
AB  - (strain 054).
ER  -

TY  - JOUR
AU  - Duan, C.G.
AU  - Zhang, H.
AU  - Tang, K.
AU  - Zhu, X.
AU  - Qian, W.
AU  - Hou, Y.J.
AU  - Wang, B.
AU  - Lang, Z.
AU  - Zhao, Y.
AU  - Wang, X.
AU  - Wang, P.
AU  - Zhou, J.
AU  - Liang, G.
AU  - Liu, N.
AU  - Wang, C.
AU  - Zhu, J.K.
TI  - Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation.
JO  - EMBO J.
PY  - 2015
SP  - 581
EP  - 592
VL  - 34
AB  - Argonaute (AGO) family proteins are conserved key components of small RNA-induced silencing
AB  - pathways. In the RNA-directed DNA methylation (RdDM) pathway in
AB  - Arabidopsis, AGO6 is generally considered to be redundant with AGO4. In this
AB  - report, our comprehensive, genomewide analyses of AGO4- and AGO6-dependent DNA
AB  - methylation revealed that redundancy is unexpectedly negligible in the genetic
AB  - interactions between AGO4 and AGO6. Immunofluorescence revealed that AGO4 and
AB  - AGO6 differ in their subnuclear co-localization with RNA polymerases required for
AB  - RdDM. Pol II and AGO6 are absent from perinucleolar foci, where Pol V and AGO4
AB  - are co-localized. In the nucleoplasm, AGO4 displays a strong co-localization with
AB  - Pol II, whereas AGO6 co-localizes with Pol V. These patterns suggest that RdDM is
AB  - mediated by distinct, spatially regulated combinations of AGO proteins and RNA
AB  - polymerases. Consistently, Pol II physically interacts with AGO4 but not AGO6,
AB  - and the levels of Pol V-dependent scaffold RNAs and Pol V chromatin occupancy are
AB  - strongly correlated with AGO6 but not AGO4. Our results suggest that AGO4 and
AB  - AGO6 mainly act sequentially in mediating small RNA-directed DNA methylation.
ER  -

TY  - JOUR
AU  - Duan, X.
AU  - Gimble, F.S.
AU  - Quiocho, F.A.
TI  - Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.
JO  - Cell
PY  - 1997
SP  - 555
EP  - 564
VL  - 89
AB  - PI-SceI is a bifunctional yeast protein that propagates its mobile gene by catalyzing protein
AB  - splicing and site-specific DNA double-strand cleavage.  Here, we report the 2.4 A crystal
AB  - structure of the PI-SceI protein.  The structure is composed of two separate domains (I and
AB  - II) with novel folds and different functions.  Domain I, which is elongated and formed largely
AB  - from seven beta sheets, harbors the N and C termini residues and two His residues that are
AB  - implicated in protein splicing.  Domain II, which is compact and is primarily composed of two
AB  - similar alpha/beta motifs related by local two-fold symmetry, contains the putative nuclease
AB  - active site with a cluster of two acidic residues and one basic residue commonly found in
AB  - restriction endonucleases.  This report presents prototypic structures of domains with single
AB  - endonuclease and protein splicing active sites.
ER  -

TY  - JOUR
AU  - Duan, Y.
AU  - Wilkosz, P.
AU  - Rosenberg, J.M.
TI  - Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 546
EP  - 555
VL  - 264
AB  - Molecular dynamics simulations on DNA-EcoRI and DNA-EcoRV complexes suggest that the DNA
AB  - within these complexes is significantly more ordered than free DNA.  Similarly, both the
AB  - protein and the DNA are more ordered in the specific (cognate) DNA-EcoRV complex than they are
AB  - in the non-cognate DNA-protein complex, consistent with recently proposed analogies between
AB  - protein folding and sequence-specific DNA-protein recognition.  Analysis of the trajectories
AB  - shows that the net entropy gain upon specific binding to be the result of opposing
AB  - contributions.  Solvent release, which increases entropy versus configurational terms (as
AB  - measured by the magnitude of the atomic fluctuations), and collective terms from tight
AB  - coupling between the motions of the protein and the DNA.
ER  -

TY  - JOUR
AU  - Duarte, V.D.S.
AU  - Treu, L.
AU  - Campanaro, S.
AU  - Dias, R.S.
AU  - Silva, C.C.D.
AU  - Giacomini, A.
AU  - Corich, V.
AU  - de Paula, S.O.
TI  - The Complete Genome Sequence of Trueperella pyogenes UFV1 Reveals a Processing System Involved in the Quorum-Sensing Signal Response.
JO  - Genome Announcements
PY  - 2017
SP  - e00639
EP  - e00617
VL  - 5
AB  - We present here the complete genome sequence of Trueperella pyogenes UFV1. The 2.3-Mbp genome
AB  - contains an extremely interesting AI-2 transporter and processing
AB  - system related to the quorum-sensing signal response. This specific feature is
AB  - described in this species for the first time and might be responsible for a new
AB  - pathogenic behavior.
ER  -

TY  - JOUR
AU  - Dubert, J.
AU  - Spinard, E.J.
AU  - Nelson, D.R.
AU  - Gomez-Chiarri, M.
AU  - Romalde, J.L.
AU  - Barja, J.L.
TI  - Draft Genome Sequence of the New Pathogen for Bivalve Larvae Vibrio bivalvicida.
JO  - Genome Announcements
PY  - 2016
SP  - e00216
EP  - e00216
VL  - 4
AB  - Vibrio bivalvicidais a novel pathogen of bivalve larvae responsible for recent vibriosis
AB  - outbreaks affecting shellfish hatcheries. Here, we announce the draft
AB  - genome sequence ofV. bivalvicida605(T)and describe potential virulence factors.
ER  -

TY  - JOUR
AU  - Dubey, A.K.
AU  - Bhattacharya, S.K.
TI  - Angle and locus of the bend induced by the MspI DNA methyltransferase in a sequence-specific complex with DNA.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2025
EP  - 2029
VL  - 25
AB  - Bending of DNA induced by M.MspI, one of the m5C-DNA methyltransferases, has been investigated
AB  - using circular permutation analysis.  The M.MspI Mtase induced sharp bends in DNA containing
AB  - its recognition sequence 5'-CCGG-3' which was estimated to be 142 +/- 4 degrees and 132 +/-
AB  - 4 degrees for circularly permuted DNA fragments of 127 and 1459 bp respectively.  The bend
AB  - center was found to be asymmetric with respect to the CCGG sequence and appeared to exclude
AB  - the 'target cytosine'.  An estimate of -15 kcal/mol was obtained for the free energy
AB  - associated with M.MspI-induced DNA bending.
ER  -

TY  - JOUR
AU  - Dubey, A.K.
AU  - Bisaria, V.S.
AU  - Mukhopadhyay, S.N.
AU  - Ghose, T.K.
TI  - Stabilization of restriction endonuclease BamHI by cross-linking reagents.
JO  - Biotechnol. Bioeng.
PY  - 1989
SP  - 1311
EP  - 1316
VL  - 33
AB  - Bacillus amyloliquefaciens H produces a restriction endonuclease BamHI which is
AB  - heat labile even at low temperatures.  Studies were conducted to enhance
AB  - thermal stability of BamHI using cross-linking reagents, namely,
AB  - glutaraldehyde, dimethyl adipimidate (DMA), dimethyl suberimidate (DMS), and
AB  - dimethyl 3,3'-dithiobispropionimidate (DTBP).  Reaction with glutaraldehyde did
AB  - not result in a preparation with enhanced thermal stability.  However, the
AB  - DMA-, DMS-, and DTBP-cross-linked preparations of BamHI exhibited significant
AB  - improvement in thermal stability.  Studies on thermal denaturation of the
AB  - cross-linked enzyme preparations revealed that these do not follow a true
AB  - first-order kinetics.  A possible deactivation scheme has been proposed in
AB  - which the enzyme has been envisaged to go through a fully active but more
AB  - susceptible transient state which, on prolonged heat exposure, exhibits a
AB  - first-order decay kinetics.  At 35C, which is close to the optimum reaction
AB  - temperature of 37C for BamHI activity, the half-life of DMA-, DMS-, and
AB  - DTBP-cross-linked preparations were 4.0, 5.25, and 5.5 h, respectively, whereas
AB  - the native enzyme exhibited a half-life of 1.2 h only.  The apparent values of
AB  - deactivation rate constants for native, DMA-, DMS-, and DTBP-cross-linked BamHI
AB  - were 1.13, 0.39, 0.29, and 0.26 h-1, respectively, at the same temperature, and
AB  - the apparent values of activation energies for denaturation of native, DMA-,
AB  - DMS-, and DTBP-cross-linked BamHI were 2.63, 5.24, 6.55, and 9.2 kcal/mol,
AB  - respectively.  The DTBP-cross-linked BamHI was, therefore, the best heat-stable
AB  - preparation among those tested.  The unusually low values of activation
AB  - energies for denaturation of BamHI show their highly thermolabile nature
AB  - compared to other commonly encountered enzymes such as trypsin, having
AB  - activation energies of more than 40 kcal/mol for their denaturation.
ER  -

TY  - JOUR
AU  - Dubey, A.K.
AU  - Mollet, B.
AU  - Roberts, R.J.
TI  - Purification and characteriation of the MspI DNA methyltransferase cloned and overexpressed in E. coli.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1579
EP  - 1585
VL  - 20
AB  - The MspI restriction-modification system, which recognizes the sequence 5'-CCGG-3', has been
AB  - previously cloned and sequenced. We subcloned the methyltransfearse gene (M.MspI) downstream
AB  - of the ptac promoter in the multicopy vector pUC119 and overexpressed it in E. coli. Upon
AB  - induction with IPTG, M.MspI constitutes more than 10% of cellular protein. A scheme has been
AB  - devised to purify large amounts of biologically active M.MspI to apparent homogeneity from
AB  - these overexpressing E. coli cells. Approximately 0.8 mg of pure M.MspI per gram of cells (wet
AB  - weight) can be obtained. The apparent molecular weight of M.MspI is 49 kD, by SDS gel
AB  - electrophoresis and 48-54 kD by gel filtration. At low concentrations (less than 0.4 mg/ml),
AB  - the methyltransferase is a monomer in solution but at higher concentrations (greater than 3.0
AB  - mg/ml) it exists predominantly as a dimer. Polyclonal antibodies raised against M.MspI
AB  - cross-react with the DNA-methyltransferases of several other restriction-modification systems.
ER  -

TY  - JOUR
AU  - Dubey, A.K.
AU  - Mukhopadhyay, S.N.
AU  - Bisaria, V.S.
AU  - Ghose, T.K.
TI  - Sources, production, and purification of restriction enzymes.
JO  - Process. Biochem.
PY  - 1987
SP  - 25
EP  - 34
VL  - 22
AB  - At present restriction enzymes are low volume, high value microbial products
AB  - but information on their production, downstream processing, stability
AB  - characteristics and applications have not been discussed from a
AB  - biotechnological view point.  In this article an attempt has been made to bring
AB  - out relevant information on restriction enzymes in collated form.
ER  -

TY  - JOUR
AU  - Dubey, A.K.
AU  - Roberts, R.J.
TI  - Sequence-specific DNA binding by the MspI DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3167
EP  - 3173
VL  - 20
AB  - The MspI methyltransferase (M.MspI) recognizes the sequence CCGG and catalyzes the formation
AB  - of 5-methylcytosine at the first C-residue. We have investigated the sequence-specific
AB  - DNA-binding properties of M.MspI under equilibrium conditions, using gel-mobility shift assays
AB  - and DNaseI footprinting. M.MspI binds to DNA in a sequence-specific manner either alone or in
AB  - the presence of the normal methyl donor S-adenosyl-L-methionine as well as the analogues,
AB  - sinefungin and S-adenosyl-L-homocysteine. In the presence of S-adenosyl-L-homocysteine, M.MspI
AB  - shows the highest binding affinity to DNA containing a hemimethylated recognition sequence
AB  - (Kd=3.6x10-7M), but binds less well to unmethylated DNA (Kd=8.3x10-7M). Surprisingly it shows
AB  - specific, although poor, binding to fully methylated DNA (Kd=4.2x10-6M). M.MspI binds
AB  - approximately 5-fold more tightly to DNA containing its recognition sequence, CCGG, than to
AB  - nonspecific sequences in the absence of cofactors. In the presence of S-adenosyl-L-methionine,
AB  - S-adenosyl-L-homocysteine or sinefungin the discrimination between specific and nonspecific
AB  - sequences increases up to 100-fold. DNaseI footprinting studies indicate that 16 base pairs of
AB  - DNA are covered by M.MspI, with the recognition sequence CCGG located asymmetrically within
AB  - the footprint.
ER  -

TY  - JOUR
AU  - Dubinina, G.
AU  - Grabovich, M.
AU  - Leshcheva, N.
AU  - Rainey, F.A.
AU  - Gavrish, E.
TI  - Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur-  and thiosulfate-reducing spirochaete isolated from a saline spring.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2011
SP  - 110
EP  - 117
VL  - 61
AB  - A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated
AB  - P(T) was isolated from a sulfur 'Thiodendron' mat in a saline spring
AB  - at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain P(T)
AB  - exhibited a helical shape. The spirochaete required sulfide in the growth medium
AB  - and was able to oxidize it non-enzymically to elemental sulfur via the
AB  - interaction of H(2)O(2) with sulfide and deposit it in the periplasmic space.
AB  - Growth occurred at 4-32 degrees C (optimum at 28-30 degrees C), pH 6.0-8.5
AB  - (optimum pH 7.0-7.5), and in 0.1-1 M NaCl (optimum 0.35 M). The isolate used
AB  - several sugars and polysaccharides as carbon or energy sources but did not use
AB  - peptides, amino acids, organic acids or alcohols. The products of glucose
AB  - fermentation were formate, acetate, ethanol, pyruvate, CO(2) and H(2). The
AB  - genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed
AB  - that strain P(T) fell within a group of species in the genus Spirochaeta,
AB  - including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with
AB  - which it shared less then 89 % sequence similarity. On the basis of its
AB  - morphology, physiology and other phenotypic properties, as well as its
AB  - phylogenetic position, the new isolate is considered to represent a novel species
AB  - of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is
AB  - proposed. The type strain is P(T) (=DSM 19205(T) =VKM B-2514(T)).
ER  -

TY  - JOUR
AU  - Duceppe, M.O.
AU  - Carrillo, C.
AU  - Huang, H.
TI  - Draft Genome Sequence of Listeria monocytogenes Strain ATCC 7644.
JO  - Genome Announcements
PY  - 2017
SP  - e00970
EP  - e00917
VL  - 5
AB  - Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an
AB  - important foodborne bacterial pathogen for humans worldwide
AB  - with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence
AB  - of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection).
ER  -

TY  - JOUR
AU  - Duchateau, P.
AU  - Grizot, S.
AU  - Paques, F.
TI  - Meganuclease engineering.
JO  - BIOFUTUR
PY  - 2008
SP  - 38
EP  - 42
VL  - 0
ER  -

TY  - JOUR
AU  - Duchaud, E. et al.
TI  - The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.
JO  - Nat. Biotechnol.
PY  - 2003
SP  - 1307
EP  - 1313
VL  - 21
AB  - Photorhabdus luminescens is a symbiont of nematodes and a broad-spectrum insect pathogen. The
AB  - complete genome sequence of strain TT01 is 5,688,987
AB  - base pairs (bp) long and contains 4,839 predicted protein-coding genes.
AB  - Strikingly, it encodes a large number of adhesins, toxins, hemolysins,
AB  - proteases and lipases, and contains a wide array of antibiotic
AB  - synthesizing genes. These proteins are likely to play a role in the
AB  - elimination of competitors, host colonization, invasion and bioconversion
AB  - of the insect cadaver, making P. luminescens a promising model for the
AB  - study of symbiosis and host-pathogen interactions. Comparison with the
AB  - genomes of related bacteria reveals the acquisition of virulence factors
AB  - by extensive horizontal transfer and provides clues about the evolution of
AB  - an insect pathogen. Moreover, newly identified insecticidal proteins may
AB  - be effective alternatives for the control of insect pests.
ER  -

TY  - JOUR
AU  - Duchaud, E.
AU  - Boussaha, M.
AU  - Loux, V.
AU  - Bernardet, J.F.
AU  - Michel, C.
AU  - Kerouault, B.
AU  - Mondot, S.
AU  - Nicolas, P.
AU  - Bossy, R.
AU  - Caron, C.
AU  - Bessieres, P.
AU  - Gibrat, J.F.
AU  - Claverol, S.
AU  - Dumetz, F.
AU  - Henaff, M.L.
AU  - Benmansour, A.
TI  - Complete genome sequence of the fish pathogen Flavobacterium psychrophilum.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 763
EP  - 769
VL  - 25
AB  - We report here the complete genome sequence of the virulent strain JIP02/86 (ATCC 49511) of
AB  - Flavobacterium psychrophilum, a widely
AB  - distributed pathogen of wild and cultured salmonid fish. The genome
AB  - consists of a 2,861,988-base pair (bp) circular chromosome with 2,432
AB  - predicted protein-coding genes. Among these predicted proteins, stress
AB  - response mediators, gliding motility proteins, adhesins and many putative
AB  - secreted proteases are probably involved in colonization, invasion and
AB  - destruction of the host tissues. The genome sequence provides the basis
AB  - for explaining the relationships of the pathogen to the host and opens new
AB  - perspectives for the development of more efficient disease control
AB  - strategies. It also allows for a better understanding of the physiology
AB  - and evolution of a significant representative of the family
AB  - Flavobacteriaceae, whose members are associated with an interesting
AB  - diversity of lifestyles and habitats.
ER  -

TY  - JOUR
AU  - Duda, E.G.
AU  - Izsvak, Z.
AU  - Orosz, A.
TI  - Isolation and purification of CeqI endonuclease, an isoschizomer of EcoRV.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 1334
EP  - 1334
VL  - 15
AB  - None
ER  -

TY  - JOUR
AU  - Dudnik, A.
AU  - Dudler, R.
TI  - Non contiguous-finished genome sequence of Pseudomonas syringae pathovar syringae strain B64 isolated from wheat.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 420
EP  - 429
VL  - 8
AB  - The Gram-negative gammaproteobacterium Pseudomonas syringae is one of the most wide-spread
AB  - plant pathogens and has been repeatedly reported to cause significant
AB  - damage to crop plantations. Research on this pathogen is very intensive, but most
AB  - of it is done on isolates that are pathogenic to Arabidopsis, tomato, and bean.
AB  - Here, we announce a high-quality draft genome sequence of Pseudomonas syringae
AB  - pv. syringae B64 which is the first published genome of a P. syringae strain
AB  - isolated from wheat up to date. The genome sequence will assist in gaining
AB  - insights into basic virulence mechanisms of this pathogen which has a relatively
AB  - small complement of type III effectors.
ER  -

TY  - JOUR
AU  - Dudnik, A.
AU  - Dudler, R.
TI  - High-Quality Draft Genome Sequence of Pseudomonas syringae pv. Syringae Strain SM, Isolated from Wheat.
JO  - Genome Announcements
PY  - 2013
SP  - e00610
EP  - e00613
VL  - 1
AB  - Pseudomonas syringae is one of the most widespread plant pathogens that can cause significant
AB  - damage to crop plantations. Here, we announce a noncontiguous
AB  - finished genome sequence of Pseudomonas syringae pv. syringae strain SM, isolated
AB  - from hexaploid wheat. The genome sequence revealed the smallest described
AB  - complement of type III effectors.
ER  -

TY  - JOUR
AU  - Dudnik, A.
AU  - Dudler, R.
TI  - Genome and Transcriptome Sequences of Pseudomonas syringae pv. syringae B301D-R.
JO  - Genome Announcements
PY  - 2014
SP  - e00306
EP  - e00314
VL  - 2
AB  - Strains of the plant pathogen Pseudomonas syringae are commonly found in the phylosphere and
AB  - are able to infect a number of agriculturally important crops. Here, we report a high-quality
AB  - draft genome sequence of Pseudomonas syringae pv. syringae B301D-R, isolated from pears, which
AB  - is a model strain for phytotoxin research in P. syringae.
ER  -

TY  - JOUR
AU  - Dueger, E.L.
AU  - House, J.K.
AU  - Heithoff, D.M.
AU  - Mahan, M.J.
TI  - Salmonella DNA adenine methylase mutants prevent colonization of newly hatched chickens by homologous and heterologous serovars.
JO  - Int. J. Food Microbiol.
PY  - 2003
SP  - 153
EP  - 159
VL  - 80
AB  - Salmonella mutants lacking DNA adenine methylase (Dam) are highly attenuated for virulence and
AB  - confer protection against oral challenge with
AB  - homologous and heterologous Salmonella serovars in mice and chicken
AB  - broilers. To determine whether vaccines based on Dam are efficacious in
AB  - preventing early colonization of newly hatched chickens, a Salmonella
AB  - typhimurium Dam(-) vaccine was evaluated for the protection of chicks
AB  - against oral challenge with homologous and heterologous Salmonella
AB  - serovars. Vaccination of chicks elicited protection 2 and 6 days
AB  - post-challenge as evidenced by a significant reduction in colonization of
AB  - the gastrointestinal tract (ileum, cecum and feces) and visceral organs
AB  - (spleen and bursa) when challenged with homologous S. typhimurium.
AB  - Moderate protection was observed following challenge with heterologous S.
AB  - enteritidis and Salmonella O6, 14, 24:e, h-monophasic) serovars. These
AB  - data suggest that Salmonella Dam mutant strains conferred
AB  - cross-protection, presumably via competitive exclusion mechanisms that
AB  - prevent superinfection of chicks by other Salmonella strains. Such
AB  - protection may reduce pre-harvest Salmonella contamination in poultry,
AB  - decreasing the potential for food-borne transmission of this pathogen to
AB  - humans.
ER  -

TY  - JOUR
AU  - Dueger, E.L.
AU  - House, J.K.
AU  - Heithoff, D.M.
AU  - Mahan, M.J.
TI  - Salmonella DNA adenine methylase mutants elicit protective immune responses to homologous and heterologous serovars in chickens.
JO  - Infect. Immun.
PY  - 2001
SP  - 7950
EP  - 7954
VL  - 69
AB  - Salmonella DNA adenine methylase (Dam) mutants that lack or
AB  - overproduce Dam are highly attenuated for virulence in mice and confer
AB  - protection against murine typhoid fever. To determine whether vaccines
AB  - based on Dam are efficacious in poultry, a Salmonella Dam-vaccine was
AB  - evaluated in the protection of chicken broilers against oral challenge
AB  - with homologous and heterologous Salmonella serovars. A Salmonella
AB  - enterica serovar Typhimurium Dam-vaccine strain was
AB  - attenuated for virulence in day-of-hatch chicks more than 100,000-fold.
AB  - Vaccination of chicks elicited cross-protective immune responses, as
AB  - evidenced by reduced colonization (10- to 10,000-fold) of the
AB  - gastrointestinal tract (ileum, cecum, and feces) and visceral organs
AB  - (bursa and spleen) after challenge with homologous (Typhimurium F98)
AB  - and heterologous (Enteritidis 4973 and S. enterica
AB  - O6,14,24: e,h-monophasic) Salmonella serovars that are
AB  - implicated in Salmonella infection of poultry. The
AB  - protection conferred was observed for the organ or the maximum
AB  - CFU/tissue/bird as a unit of analysis, suggesting that Dam mutant
AB  - strains may serve as the basis for the development of efficacious
AB  - poultry vaccines for the containment of Salmonella.
ER  -

TY  - JOUR
AU  - Dueger, E.L.
AU  - House, J.K.
AU  - Heithoff, D.M.
AU  - Mahan, M.J.
TI  - Salmonella DNA adenine methylase mutants elicit early and late onset protective immune responses in calves.
JO  - Vaccine
PY  - 2003
SP  - 3249
EP  - 3258
VL  - 21
AB  - Salmonellosis is an important disease of livestock and Salmonella contamination of
AB  - livestock-derived food products and effluents pose a
AB  - significant risk to human health. Salmonella vaccines currently available
AB  - to prevent salmonellosis in cattle have limited efficacy. Here we
AB  - evaluated a Salmonella enterica serovar Typhimurium vaccine strain lacking
AB  - the DNA adenine methylase (Dam) for safety and efficacy in calves.
AB  - Vaccination was safe in calves, and following challenge with virulent
AB  - Typhimurium 4 weeks post-immunization, vaccinated animals exhibited
AB  - significantly lower mortality, diarrhea, and rectal temperatures, as well
AB  - as reduced colonization of gastrointestinal tract and visceral organs
AB  - compared to non-vaccinated control animals. Additionally, early onset
AB  - protection (competitive exclusion) in vaccinated neonatal calves was
AB  - demonstrated by attenuated clinical disease (as measured by rectal
AB  - temperatures and attitude scores) and reduced mortality when challenged
AB  - with virulent Typhimurium 24h after immunization. Taken together, these
AB  - data suggest that vaccination with Salmonella Dam mutant strains confer
AB  - significant protection against Salmonella infections in cattle via both
AB  - adaptive immunity and competitive exclusion mechanisms.
ER  -

TY  - JOUR
AU  - Dueholm, M.S.
AU  - Albertsen, M.
AU  - D'Imperio, S.
AU  - Tale, V.P.
AU  - Lewis, D.
AU  - Nielsen, P.H.
AU  - Nielsen, J.L.
TI  - Complete Genome of Rhodococcus pyridinivorans SB3094, a Methyl-Ethyl-Ketone-Degrading Bacterium Used for Bioaugmentation.
JO  - Genome Announcements
PY  - 2014
SP  - e00525
EP  - e00514
VL  - 2
AB  - Here, we present the complete genome of Rhodococcus pyridinivorans SB3094, a
AB  - methyl-ethyl-ketone (MEK)-degrading strain used for bioaugmentation relating to
AB  - the treatment of wastewater contamination with petrochemical hydrocarbons. The
AB  - genome highlights important features for bioaugmentation, including the genes
AB  - involved in the degradation of MEK.
ER  -

TY  - JOUR
AU  - Dueholm, M.S.
AU  - Albertsen, M.
AU  - Stokholm-Bjerregaard, M.
AU  - McIlroy, S.J.
AU  - Karst, S.M.
AU  - Nielsen, P.H.
TI  - Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1.
JO  - Genome Announcements
PY  - 2015
SP  - e00624
EP  - e00615
VL  - 3
AB  - Here, we present the complete genome sequence of the candidate phylum SR1 bacterium
AB  - Aalborg_AAW-1. Its 16S rRNA gene is only 85.5% similar to that of the
AB  - closest relative, RAAC1_SR1, and the genome of Aalborg_AAW-1 consequently
AB  - represents the first of a novel family within the candidate phylum SR1.
ER  -

TY  - JOUR
AU  - Dueholm, M.S.
AU  - Danielsen, H.N.
AU  - Nielsen, P.H.
TI  - Complete Genome Sequence of Pseudomonas sp. UK4, a Model Organism for Studies of  Functional Amyloids in Pseudomonas.
JO  - Genome Announcements
PY  - 2014
SP  - e00898
EP  - e00814
VL  - 2
AB  - Here, we present the complete genome of Pseudomonas sp. UK4. This bacterium was the first
AB  - Pseudomonas strain shown to produce functional amyloids, and it
AB  - represents a model organism for studies of functional amyloids in Pseudomonas
AB  - (Fap).
ER  -

TY  - JOUR
AU  - Duff, M.K.
AU  - Davies, J.K.
TI  - DNA enzymes of Neisseria gonorrhoeae.
JO  - Gonococci and Meningococci
PY  - 1988
SP  - 251
EP  - 256
AB  - Two gonococcal strains, the Dam+ strain D109, and the Dam- strain D211, were investigated for
AB  - enzyme content. Enzymes were obtained from surface washes, by sonication and by osmotic shock.
AB  - They were partially purified by precipitation and heparin-sepharose affinity chromatography.
AB  - Endonuclease activity was assayed by using both dam-methylated and nonmethylated
AB  - bacteriophage lambda DNA.  Two endonuclease activities that have not been previously described
AB  - in the gonococcus were discovered.  One, designated R.NgoIX, is an isoschizomer of DpnI. [The
AB  - enzyme named NgoIX has been renamed NgoDXVII. Enzymes with the specificity NgoX are mixtures
AB  - of NgoI and NgoVIII specificities.]
ER  -

TY  - JOUR
AU  - Duff, M.K.
AU  - Davies, J.K.
TI  - Multiple restriction-modification systems in Neisseria gonorrhoeae.
JO  - Gene
PY  - 1988
SP  - 227
EP  - 228
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Dufresne, A. et al.
TI  - Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 10020
EP  - 10025
VL  - 100
AB  - Prochlorococcus marinus, the dominant photosynthetic organism in the ocean, is found in two
AB  - main ecological forms: high-light-adapted genotypes
AB  - in the upper part of the water column and low-light-adapted genotypes at
AB  - the bottom of the illuminated layer. P. marinus SS120, the complete genome
AB  - sequence reported here, is an extremely low-light-adapted form. The genome
AB  - of P. marinus SS120 is composed of a single circular chromosome of
AB  - 1,751,080 bp with an average G+C content of 36.4%. It contains 1,884
AB  - predicted protein-coding genes with an average size of 825 bp, a single
AB  - rRNA operon, and 40 tRNA genes. Together with the 1.66-Mbp genome of P.
AB  - marinus MED4, the genome of P. marinus SS120 is one of the two smallest
AB  - genomes of a photosynthetic organism known to date. It lacks many genes
AB  - that are involved in photosynthesis, DNA repair, solute uptake,
AB  - intermediary metabolism, motility, phototaxis, and other functions that
AB  - are conserved among other cyanobacteria. Systems of signal transduction
AB  - and environmental stress response show a particularly drastic reduction in
AB  - the number of components, even taking into account the small size of the
AB  - SS120 genome. In contrast, housekeeping genes, which encode enzymes of
AB  - amino acid, nucleotide, cofactor, and cell wall biosynthesis, are all
AB  - present. Because of its remarkable compactness, the genome of P. marinus
AB  - SS120 might approximate the minimal gene complement of a photosynthetic
AB  - organism.
ER  -

TY  - JOUR
AU  - Dugaiczyk, A.
AU  - Boyer, H.W.
AU  - Goodman, H.M.
TI  - Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 171
EP  - 184
VL  - 96
AB  - Double-stranded DNA fragments terminated at their 5'-ends by the
AB  - single-stranded sequence pA-A-T-T-, generated by digestion of DNA with EcoRI
AB  - restriction endonuclease, were ligated with Escherichia coli polynucleotide
AB  - ligase under various conditions of temperature, concentration and time.  The
AB  - linear and circular products of ligation were separated by electrophoresis in
AB  - agarose gel and quantitated by densitometry.  The rate of ligation of
AB  - (EcoRI-cleaved) simian virus (SV40) DNA at a concentration of 100 microgram/ml
AB  - increased from 0C to 5C to 10C (6-fold increase overall); raising the
AB  - temperature to 15C did not further increase the rate of ligation.  At the
AB  - appropriate DNA concentrations, the predominant products of ligation are either
AB  - linear concatemers that are integral multimers of the starting DNA fragment, or
AB  - covalently closed circular structures of the monomeric DNA fragment.  Ligating
AB  - a mixture of two different length DNA fragments gives rise to all of the
AB  - possible expected recombinant molecules.  Linear or circular products of
AB  - ligation were predicted by consideration of the total concentration of DNA
AB  - termini, i, and the local concentration of one terminus in the neighborhood of
AB  - the other on the same DNA molecule, j.  The parameter j is a function of the
AB  - length of a DNA molecule, providing this length is greater than the random coil
AB  - segment of DNA.  Experimentally it was found that circular structures are
AB  - formed in significant amounts only under conditions when the value of j is
AB  - several times greater than that of i.  When j = i, equal amounts of linear and
AB  - circular products would be expected, but most of the molecules were ligated
AB  - into linear concatemers.  No circular structure of a DNA fragment whose contour
AB  - length l (6 x 10-2 microm) is smaller than the random coil segment value b
AB  - (7.17 x 10-2 microm) was observed, while circular structures of the dimer of
AB  - the same molecule (12 x 10-2 microm) were detected.
ER  -

TY  - JOUR
AU  - Dugaiczyk, A.
AU  - Hedgpeth, J.
AU  - Boyer, H.W.
AU  - Goodman, H.M.
TI  - Physical identity of the SV40 deoxyribonucleic acid sequence recognized by the EcoRI restriction endonuclease and modification methylase.
JO  - Biochemistry
PY  - 1974
SP  - 503
EP  - 512
VL  - 13
AB  - The EcoRI modification methylase introduces two methyl groups into one SV40 DNA
AB  - molecule.  The only base methylated has been identified as N6-methyladenine.
AB  - Both of the methyl groups are introduced into the same fragment (designated F,
AB  - about 400 base pairs long) of a HindII endonuclease digest of SV40 DNA.  The
AB  - EcoRI endonuclease makes one double-strand cleavage in SV40 DNA.  The site of
AB  - this cleavage is also contained within the F fragment.  Analysis of
AB  - dinucleoside monophosphates, trinucleoside diphosphates, and tetranucleoside
AB  - triphosphates generated by partial digestion of the methylated DNA with
AB  - pancreatic DNase I gives the following sequence of nucleotides at the site of
AB  - methylation by the EcoRI methylase:  GpApm6ApTpTpC.  This sequence (with A in
AB  - place of m6A) is also found at the site of phosphodiester-bond cleavage by the
AB  - EcoRI restriction endonuclease.  Using [c-32P]rATP and polynucleotide kinase,
AB  - SV40 DNA has been labeled in each strand with 32P specifically at the
AB  - phosphodiester bonds cleaved by the EcoRI endonuclease.  The DNA was
AB  - polymerized at 4o by hydrogen bonding of the cohesive termini of the EcoRI
AB  - endonuclease break.  The labeled 5'-monophosphates at the staggered
AB  - single-strand breaks were esterified with the adjacent 3'-hydroxyl groups by
AB  - polynucleotide ligase at low temperature, and the covalently polymerized DNA
AB  - was methylated by the EcoRI modification methylase using
AB  - S-adenosyl-L-[methyl-3H]methionine.  Analysis of the radioactive labels in the
AB  - mono- and dinucleotides from a partial digest of this double-labeled DNA
AB  - identifies physically the same sequence of base pairs in SV40 DNA as the
AB  - substrate site for the EcoRI endonuclease and for the EcoRI modification
AB  - methylase.
ER  -

TY  - JOUR
AU  - Dugaiczyk, A.
AU  - Kimball, M.
AU  - Linn, S.
AU  - Goodman, H.M.
TI  - Location and nucleotide sequence of the site on SV40 DNA methylated by the EcoB modification methylase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1974
SP  - 1133
EP  - 1140
VL  - 61
AB  - The modification methylase from Escherichia coli strain B, EcoB, introduces two
AB  - methyl groups into one SV40 DNA molecule.  The only base methylated has been
AB  - identified as N6-methyladenine.  Digestion of the methylated SV40 DNA with two
AB  - restriction endonucleases, one from Hemophilus influenzae, HindIII, and another
AB  - from Hemophilus aegyptius, Hae, locates the methyl groups in the same DNA
AB  - fragment, about 250 base pairs long, between 0.860 and 0.907 fractional lengths
AB  - of SV40 DNA clockwise from the EcoRI site on the circular SV40 geneome.
AB  - Analysis of dinucleoside monophosphates, trinucleoside diphosphates, and
AB  - tetranucleoside triphosphates, generated by partial digestion of the methylated
AB  - DNA with pancreatic DNaseI gave the following sequences of nucleotides at the
AB  - site(s) of methylation by the EcoB methylase: 5'...C-m6A-G-C-T...3' and
AB  - 5'...T-G-m6A-A...3' These cannot be incorporated into a simple sequence with
AB  - 2-fold rotational symmetry.
ER  -

TY  - JOUR
AU  - Dugat, T.
AU  - Rossignol, M.N.
AU  - Rue, O.
AU  - Loux, V.
AU  - Marthey, S.
AU  - Moroldo, M.
AU  - Silaghi, C.
AU  - Hoper, D.
AU  - Frohlich, J.
AU  - Pfeffer, M.
AU  - Zweygarth, E.
AU  - Lagree, A.C.
AU  - Boulouis, H.J.
AU  - Haddad, N.
TI  - Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and  One Roe Deer Collected in Europe.
JO  - Genome Announcements
PY  - 2016
SP  - e00950
EP  - e00916
VL  - 4
AB  - Anaplasma phagocytophilum is a zoonotic tick-borne intracellular bacterium responsible for
AB  - granulocytic anaplasmosis. As it is difficult to isolate and
AB  - cultivate, only 20 A. phagocytophilum genomes have been sequenced to date. Here,
AB  - we present eight A. phagocytophilum genome sequences obtained using alternative
AB  - approaches based on sequence capture technology.
ER  -

TY  - JOUR
AU  - Dugat-Bony, E.
AU  - Sarthou, A.S.
AU  - Loux, V.
AU  - Vidal, M.
AU  - Bonnarme, P.
AU  - Irlinger, F.
AU  - Layec, S.
TI  - Draft Genome Sequence of Corynebacterium variabile Mu292, Isolated from Munster,  a French Smear-Ripened Cheese.
JO  - Genome Announcements
PY  - 2016
SP  - e00669
EP  - e00616
VL  - 4
AB  - Here, we report the draft genome sequence of Corynebacterium variabile Mu292, which was
AB  - originally isolated from the surface of Munster, a French smear-ripened
AB  - cheese. This genome investigation will improve our knowledge on the molecular
AB  - determinants potentially involved in the adaptation of this strain during the
AB  - Munster-type cheese manufacturing process.
ER  -

TY  - JOUR
AU  - Duggett, N.A.
AU  - Kay, G.L.
AU  - Sergeant, M.J.
AU  - Bedford, M.
AU  - Constantinidou, C.I.
AU  - Penn, C.W.
AU  - Millard, A.D.
AU  - Pallen, M.J.
TI  - Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca.
JO  - Genome Announcements
PY  - 2016
SP  - e00448
EP  - e00416
VL  - 4
AB  - The chicken is the most common domesticated animal and the most abundant bird in  the world.
AB  - However, the chicken gut is home to many previously uncharacterized
AB  - bacterial taxa. Here, we report draft genome sequences from six bacterial
AB  - isolates from chicken ceca, all of which fall outside any named species.
ER  -

TY  - JOUR
AU  - Duhaime, M.B.
AU  - Wichels, A.
AU  - Sullivan, M.B.
TI  - Six Pseudoalteromonas Strains Isolated from Surface Waters of Kabeltonne, Offshore Helgoland, North Sea.
JO  - Genome Announcements
PY  - 2016
SP  - e01697
EP  - e01615
VL  - 4
AB  - Draft genomes are presented for 6 Pseudoalteromonas sp. strains isolated from surface waters
AB  - at Kabeltonne, Helgoland, a long-term ecological research station
AB  - in the North Sea. These strains contribute knowledge of the genomic underpinnings
AB  - of a developing model system to study phage-host dynamics of a
AB  - particle-associated ocean copiotroph.
ER  -

TY  - JOUR
AU  - Duhaime, M.B.
AU  - Wichels, A.
AU  - Waldmann, J.
AU  - Teeling, H.
AU  - Glockner, F.O.
TI  - Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1.
JO  - ISME J.
PY  - 2011
SP  - 107
EP  - 121
VL  - 5
AB  - Marine phages have an astounding global abundance and ecological impact.
AB  - However, little knowledge is derived from phage genomes, as most of the
AB  - open reading frames in their small genomes are unknown, novel proteins. To
AB  - infer potential functional and ecological relevance of sequenced marine
AB  - Pseudoalteromonas phage H105/1, two strategies were used. First,
AB  - similarity searches were extended to include six viral and bacterial
AB  - metagenomes paired with their respective environmental contextual data.
AB  - This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage
AB  - H105/1, such as its estuarine origin. Second, intrinsic genome signatures
AB  - (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies)
AB  - were evaluated on a resolved intra-genomic level to shed light on the
AB  - evolution of phage functional modules. On the basis of differential codon
AB  - adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas
AB  - spp., regions of the phage genome with the most 'host'-adapted proteins
AB  - also have the strongest bacterial tetra signature, whereas the least
AB  - 'host'-adapted proteins have the strongest phage tetra signature. Such a
AB  - pattern may reflect the evolutionary history of the respective phage
AB  - proteins and functional modules. Finally, analysis of the structural
AB  - proteome identified seven proteins that make up the mature virion, four of
AB  - which were previously unknown. This integrated approach combines both
AB  - novel and classical strategies and serves as a model to elucidate
AB  - ecological inferences and evolutionary relationships from phage genomes
AB  - that typically abound with unknown gene content.
ER  -

TY  - JOUR
AU  - Dujardin, G.
AU  - Jacq, C.
AU  - Slonimski, P.P.
TI  - Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene.
JO  - Nature
PY  - 1982
SP  - 628
EP  - 632
VL  - 298
AB  - An extragenic suppressor mutation, mim2-1, which compensates yeast
AB  - mitochondrial mutants deficient in splicing of the cytochrome b gene, has
AB  - been mapped and sequenced. The mutation is due to a single G leads to A
AB  - transition in the long open reading frame of the fourth intron of the
AB  - oxidase subunit one gene. It causes the replacement of a glutamic codon by
AB  - a lysine codon and the expression of a novel mRNA maturase active in
AB  - splicing. Evolution and regulatory connections between homologous introns
AB  - of nonhomologous genes are discussed.
ER  -

TY  - JOUR
AU  - Dujon, B.
TI  - Homing endonucleases and the yeast mitochondrial omega locus - A historical perspective.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 11
EP  - 31
VL  - 16
AB  - It was May 1985.  Outside the laboratory, near Paris, nature was exulting in its colorful
AB  - mid-spring glory.  The last technical details and experimental pitfalls had been fixed in the
AB  - preceding weeks.  Now, the site-specific endonucleolytic activity of the intron-encoded
AB  - protein I that had been carefully engineered to express in Escherichia coli was detectable.
AB  - According to my autoradiogram, it was cleaving the intron-less DNA exactly where I expected.
AB  - This experiment opened the way to a series of yet unexpected developments, but for me it
AB  - concluded a long and rather solitary quest.  Long, because the route that led to the first
AB  - intron-encoded homing endonuclease, I-SceI according to the present nomenclature, had started
AB  - no less than 15 years before, from a peculiarity of mitochondrial inheritance in yeast.
AB  - Solitary, because, over this long period, the phenomenon that led to this discovery had
AB  - remained a unique oddity of nature, limiting its interest for many.  Indeed, after the
AB  - discovery of I-SceI, it took 3 additional years before the next examples of homing
AB  - endonucleases could be identified, suggesting the generality of the phenomenon.  By this time,
AB  - the enzymatic properties of I-SceI and its unusual specificity were already characterized, and
AB  - it was clear that we were in the presence of a novel class of enzymes.
ER  -

TY  - JOUR
AU  - Dujon, B.
TI  - Group I introns as mobile genetic elements: facts and mechanistic speculations--a review.
JO  - Gene
PY  - 1989
SP  - 91
EP  - 114
VL  - 82
AB  - Group I introns form a structural and functional group of introns with widespread but
AB  - irregular distribution among very diverse organisms and genetic systems. Evidence is now
AB  - accumulating that several group I introns are mobile genetic elements with properties similar
AB  - to those originally described for the omega system of Saccharomyces cerevisiae: mobile group I
AB  - introns encode sequence-specific double-strand (ds) endoDNases, which recognize and cleave
AB  - intronless genes to insert a copy of the intron by a ds-break repair mechanism. This mechanism
AB  - results in: the efficient propagation of group I introns into their cognate sites; their
AB  - maintenance at the site against spontaneous loss; and, perhaps, their transposition to
AB  - different sites. The spontaneous loss of group I introns occurs with low frequency by an
AB  - RNA-mediated mechanism. This mechanism eliminates introns defective for mobility and/or for
AB  - RNA splicing. Mechanisms of intron acquisition and intron loss must create an equilibrium,
AB  - which explains the irregular distribution of group I introns in various genetic systems.
AB  - Furthermore, the observed distribution also predicts that horizontal transfer of intron
AB  - sequences must occur between unrelated species, using vectors yet to be discovered.
ER  -

TY  - JOUR
AU  - Dujon, B.
TI  - Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci.
JO  - Cell
PY  - 1980
SP  - 185
EP  - 197
VL  - 20
AB  - The complete nucleotide sequence has been determined for the intron, its junctions and the
AB  - flanking exon regions of the 21S rRNA gene in three genetically characterized strains
AB  - differing by their omega alleles (omega+, omega- and omega n) and by their
AB  - chloramphenicol-resistant mutations at the rib-1 locus. Comparison of these DNA sequences
AB  - shows that:  omega+ differs from omega- and omega n by the presence of the intron (1143bp), as
AB  - well as by a second and unexpected mini-insert (66bp) located 156bp upstream within the exon,
AB  - whose nature and functions are still unknown but whose striking palindromic structure may
AB  - suggest a mitochondrial transposable element. The two mutations CR321 and CR323 correspond to
AB  - two different monosubstitutions, 56bp apart in the omega- and omega n strains but separated by
AB  - the intron in the omega+ strains. In relation to previous genetic results, a model is
AB  - discussed assuming that the interactions of two different regions or genetic loci determine
AB  - the chloramphenicol resistance, one of which contains the omega n mutations. A long
AB  - uninterrupted coding sequence able to specify a 235 amino acid polypeptide exists within the
AB  - intron. This remarkable observation gives new insight into the origin of the mitochondrial
AB  - introns and raises the question of the possible functions of intron-encoded polypeptides.
AB  - Finally, sequence comparisons with evolutionarily distant organisms, showing that different
AB  - rRNA introns are inserted at different positions of an otherwise highly conserved region of
AB  - the gene, suggest a recent insertion of these introns and a mechanism for splicing after the
AB  - assembly of the large ribosomal subunit.
ER  -

TY  - JOUR
AU  - Dujon, B.
AU  - Colleaux, L.
AU  - Jacquier, A.
AU  - Michel, F.
AU  - Monteilhet, C.
TI  - Mitochondrial introns as mobile genetic elements: The role of intron-encoded proteins.
JO  - Extrachromosomal elements in lower eukaryotes
PY  - 1986
SP  - 5
EP  - 27
VL  - 0
AB  - Introns of organelle genes share distinctive RNA secondary structures that allow their
AB  - classification into two known families. These structures are believed to play an essential
AB  - role in splicing, and members of both structural classes have recently been shown to perform
AB  - self-splicing reactions in vitro. In lower eukaryotes, many structured introns also contain
AB  - long internal open reading frames (ORFs), which are able to code for hydrophilic proteins.
AB  - Several properties of self-splicing structured introns suggest that they resemble mobile
AB  - genetic elements, even though no actual transposition event involving these introns has yet
AB  - been found. We report here on the characterization of two intron-encoded proteins that
AB  - strongly support this attractive idea. First, we show that the class I intron of the 21S
AB  - ribosomal RNA (rRNA) gene of Saccharomyces cerevisiae omega+ strains (r1 intron) encodes a
AB  - specific transposase. This protein has been partially purified from Escherichia coli cells
AB  - that overexpress it from an artificial universal code equivalent to the r1 intronic ORF. The
AB  - omega transposase shows double-strand endonuclease activity in vitro. This activity creates a
AB  - 4-bp staggered cut with 3' OH overhangs within a specific sequence of the 21S rRNA gene of
AB  - omega strains. It is precisely within this sequence that the r1 intron inserts by a
AB  - duplicative transposition. Second, we report on the synthesis, in E. coli, of a putative
AB  - reverse transcriptase encoded by the class II intron of the cytochrome b gene of
AB  - Schizosaccharomyces pombe. This synthesis was obtained from E. coli expression vectors, using
AB  - the class I intronic ORF linked to an artificial initiator sequence.
ER  -

TY  - JOUR
AU  - Dujon, B.
AU  - Colleaux, L.
AU  - Jacquier, A.
AU  - Michel, F.
AU  - Monteilhet, C.
TI  - Mitochondrial introns as mobile genetic elements: the role of intron-encoded proteins.
JO  - Basic Life Sci.
PY  - 1986
SP  - 5
EP  - 27
VL  - 40
AB  - Introns of organelle genes share distinctive RNA secondary structures that allow
AB  - their classification into two known families.  These structures are believed to play an
AB  - essential role
AB  - in splicing, and members of both structural classes have recently been shown to perform self-
AB  - splicing reactions in vitro.  In lower eukaryotes, many structured introns also contain long
AB  - internal
AB  - open reading frames (ORFs), which are able to code for hydrophilic proteins.  Several
AB  - properties
AB  - of self-splicing structured introns suggest that they resemble mobile genetic elements, even
AB  - though
AB  - no actual transposition event involving these introns has yet been found.  We report here on
AB  - the
AB  - characterization of two intron-encoded proteins that strongly support this attractive idea.
AB  - First, we
AB  - show that the class I intron of the 21S ribosomal RNA (rRNA) gene of Saccharomyces cerevisiae
AB  - omega+ strains (r1 intron) encodes a specific transposase.  This protein has been partially
AB  - purified
AB  - from Escherichia coli cells that overexpress it from an artificial universal code equivalent
AB  - to the r1
AB  - intronic ORF.  The omega transposase shows a double-strand endonuclease activity in vitro.
AB  - This
AB  - activity creates a 4-bp staggered cut with 3' OH overhangs within a specific sequence of the
AB  - 21S
AB  - rRNA gene of omega- strains.  It is precisely within this sequence that the r1 intron inserts
AB  - by a
AB  - duplicative transposition.  Second, we report on the synthesis, in E. coli, of a putative
AB  - reverse
AB  - transcriptase encoded by the Class II intron of the cytochrome b gene of Schizosaccharomyces
AB  - pombe.  This synthesis was obtained from E. coli expression vectors, using the class II
AB  - intronic
AB  - ORF linked to an artificial initiator sequence.  As further support of the idea that
AB  - structured introns
AB  - are mobile, we show, from a systematic screening of introns in various yeast species, that the
AB  - r1
AB  - intron has transposed into the ATPase subunit 9 gene of Kluyveromyces fragilis.  Structural
AB  - features observed at the new intron homing site may be relevant to the transposition event.
ER  -

TY  - JOUR
AU  - Dujon, B.
AU  - Cottarel, G.
AU  - Colleaux, L.
AU  - Betermier, M.
AU  - Jacquier, A.
AU  - D'Auriol, L.
AU  - Galibert, F.
TI  - Mechanism of integration of an intron within a mitochondrial gene: a double strand break and the transposase function of an intron encoded protein as revealed by in vivo and in vitro assays.
JO  - Achievements and Perspectives of Mitochondrial Research. Volume II: Biogenesis.
PY  - 1985
SP  - 215
EP  - 225
VL  - 0
AB  - The intron of the mitochondrial 21S rRNA gene (rl intron) is optional in the yeast
AB  - Saccharomyces cerevisiae, being found in some strains (omega+) but not in others (omega-) with
AB  - no phenotypic difference related to its presence or absence. Crosses between omega+ strains
AB  - and omega- strains determine a unique phenomenon that results in the integration of that
AB  - intron into the previously intron minus copies of the 21S rRNA gene. This phenomenon resembles
AB  - a duplicative transposition, with the intron itself representing the transposable element,
AB  - except that the recipient site seems unique and that the transposition is accompanied by a
AB  - unidirectional gene conversion affecting the genetic and molecular markers located in flanking
AB  - exon sequences. In addition, the transposition is nearly quantitative, converting almost all
AB  - intron minus copies of the 21S rRNA gene into intron plus copies, hence efficiently spreading
AB  - that intron within the populations of interbreeding yeasts.
ER  -

TY  - JOUR
AU  - Dumigan, C.R.
AU  - Perry, G.E.
AU  - Pauls, K.P.
AU  - Raizada, M.N.
TI  - Draft Genome Sequence of Enterobacter cloacae 3F11 (Phylum Proteobacteria).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00846
EP  - e00818
VL  - 7
AB  - Presented here is the draft genome sequence of Enterobacter cloacae 3F11. This seed endophyte
AB  - solubilizes rock phosphate and was isolated from Zea
AB  - nicaraguensis. The genome contains 4,579,108 bp in 264 contigs.
ER  -

TY  - JOUR
AU  - Dumonceaux, T.J.
AU  - Town, J.
AU  - Links, M.G.
AU  - Boyetchko, S.
TI  - High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests   of Agricultural Significance.
JO  - Genome Announcements
PY  - 2014
SP  - e00995
EP  - e00914
VL  - 2
AB  - Pseudomonas sp. BRG100 inhibits the growth of certain agricultural pests and is a potentially
AB  - useful biopesticide for weeds and plant diseases. We have sequenced
AB  - the 6.25-Mbp genome of this strain and assembled it into 4 scaffolds. Genome
AB  - sequence comparisons revealed that this strain may represent a novel species of
AB  - Pseudomonas.
ER  -

TY  - JOUR
AU  - Duncan, C.H.
AU  - Wilson, G.A.
AU  - Young, F.E.
TI  - Biochemical and genetic properties of site-specific restriction endonucleases in Bacillus globigii.
JO  - J. Bacteriol.
PY  - 1978
SP  - 338
EP  - 344
VL  - 134
AB  - Bacillus globigii contains two site-specific endonucleases, BglI and BglII.  A
AB  - rapid technique for selection of mutants deficient in each of these enzymes was
AB  - developed using sensitivity to infection by bacteriophage SP50 as an indication
AB  - of the levels of enzyme.  Mutants defective in BglI, BglII, and both BglI and
AB  - BglII retained the wild-type modification phenotype.  Genetic and biochemical
AB  - studies have established that these enzymes are involved in restriction in
AB  - vivo.  Simplified purification procedures for BglI and BglII using these
AB  - mutants are described.
ER  -

TY  - JOUR
AU  - Duncan, S.S.
AU  - Bertoli, M.T.
AU  - Kersulyte, D.
AU  - Valk, P.L.
AU  - Tamma, S.
AU  - Segal, I.
AU  - McClain, M.S.
AU  - Cover, T.L.
AU  - Berg, D.E.
TI  - Genome Sequences of Three hpAfrica2 Strains of Helicobacter pylori.
JO  - Genome Announcements
PY  - 2013
SP  - e00729
EP  - e00713
VL  - 1
AB  - We present the genome sequences of three hpAfrica2 strains of Helicobacter pylori, which are
AB  - postulated to have evolved in isolation for many millennia in
AB  - people of San ethnicity. Although previously considered to be ancestral to
AB  - Helicobacter acinonychis, the hpAfrica2 strains differ markedly from H.
AB  - acinonychis in their gene arrangement. These data provide new insights into
AB  - Helicobacter evolution.
ER  -

TY  - JOUR
AU  - Dunin-Horkawicz, S.
AU  - Feder, M.
AU  - Bujnicki, J.M.
TI  - Phylogenomic analysis of the GIY-YIG nuclease superfamily.
JO  - BMC Genomics
PY  - 2006
SP  - 98
EP  - 98
VL  - 7
AB  - BACKGROUND: The GIY-YIG domain was initially identified in homing endonucleases and later in
AB  - other selfish mobile genetic elements
AB  - (including restriction enzymes and non-LTR retrotransposons) and in
AB  - enzymes involved in DNA repair and recombination. However, to date no
AB  - systematic search for novel members of the GIY-YIG superfamily or
AB  - comparative analysis of these enzymes has been reported. RESULTS: We
AB  - carried out database searches to identify all members of known GIY-YIG
AB  - nuclease families. Multiple sequence alignments together with predicted
AB  - secondary structures of identified families were represented as Hidden
AB  - Markov Models (HMM) and compared by the HHsearch method to the
AB  - uncharacterized protein families gathered in the COG, KOG, and PFAM
AB  - databases. This analysis allowed for extending the GIY-YIG superfamily to
AB  - include members of COG3680 and a number of proteins not classified in COGs
AB  - and to predict that these proteins may function as nucleases, potentially
AB  - involved in DNA recombination and/or repair. Finally, all old and new
AB  - members of the GIY-YIG superfamily were compared and analyzed to infer the
AB  - phylogenetic tree. CONCLUSION: An evolutionary classification of the
AB  - GIY-YIG superfamily is presented for the very first time, along with the
AB  - structural annotation of all (sub)families. It provides a comprehensive
AB  - picture of sequence-structure-function relationships in this superfamily
AB  - of nucleases, which will help to design experiments to study the mechanism
AB  - of action of known members (especially the uncharacterized ones) and will
AB  - facilitate the prediction of function for the newly discovered ones.
ER  -

TY  - JOUR
AU  - Dunitz, M.I.
AU  - Coil, D.A.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Adams, J.Y.
TI  - Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients.
JO  - Genome Announcements
PY  - 2014
SP  - e01278
EP  - e01214
VL  - 2
AB  - We present the draft genome sequences of six strains of Escherichia coli isolated from blood
AB  - cultures collected from patients with sepsis. The strains were
AB  - collected from two patient sets, those with a high severity of illness, and those
AB  - with a low severity of illness. Each genome was sequenced by both Illumina and
AB  - PacBio for comparison.
ER  -

TY  - JOUR
AU  - Dunitz, M.I.
AU  - James, P.M.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Coil, D.A.
AU  - Chandler, J.A.
TI  - Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria) Isolated from Drosophila suzukii Larvae.
JO  - Genome Announcements
PY  - 2014
SP  - e00349
EP  - e00314
VL  - 2
AB  - Here we present the draft genome of Tatumella sp. strain UCD-D_suzukii, the first member of
AB  - this genus to be sequenced. The genome contains 3,602,931 bp in 72 scaffolds. This strain was
AB  - isolated from Drosophila suzukii larvae as part of a larger project to study the microbiota of
AB  - D. suzukii.
ER  -

TY  - JOUR
AU  - Dunlap, C.A.
AU  - Bowman, M.J.
AU  - Schisler, D.A.
TI  - Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: a biocontrol antagonist of Fusarium Head Blight.
JO  - Biol. Control
PY  - 2013
SP  - 166
EP  - 175
VL  - 64
AB  - The complete genome of the biocontrol antagonist Bacillus amyloliquefaciens AS 43.3 is
AB  - reported. B. amyloliquefaciens AS 43.3 has previously been shown to be effective in reducing
AB  - Fusarium head blight in wheat. The 3.9Mbp genome was sequenced, assembled, and annotated.
AB  - Genomic analysis of the strain identified 9 biosynthetic gene clusters encoding secondary
AB  - metabolites associated with biocontrol activity. The analysis identified five non-ribosomal
AB  - peptide synthetase clusters encoding three lipopeptides (surfactin, iturin, and fengycin), a
AB  - siderophore (bacillibactin), and the antibiotic dipeptide bacilysin. In addition, three
AB  - polyketide synthetase clusters were identified which encoded for the antibacterials:
AB  - bacillaene, difficidin, and macrolactin. In addition to the non-ribosomal mediated
AB  - biosynthetic clusters discovered, we identified a ribosomally encoded biosynthetic cluster
AB  - that produces the antibiotic plantazolicin. To confirm the gene clusters were functional,
AB  - cell-free culture supernatant was analyzed using LC=96MS/MS. The technique confirmed the
AB  - presence of all nine metabolites or their derivatives. The study suggests the strain is most
AB  - likely a member of the B. amyloliquefaciens subsp. plantarium clade. Comparative genomics of
AB  - eight completed genomes of B. amyloliquefaciensidentify the core and pan-genomes for the
AB  - species, including identifying genes unique to the biocontrol strains. This study demonstrates
AB  - the growing importance of applying genomic-based studies to biocontrol organisms of plant
AB  - pathogens which can enable the rapid identification of bioactive metabolites produced by a
AB  - prospective biological control organism. In addition, this work provides a foundation for a
AB  - mechanistic understanding of the B. amyloliquefaciens AS 43.3/Fusarium head blight biocontrol
AB  - interaction.
ER  -

TY  - JOUR
AU  - Dunn, N.W.
AU  - Holloway, B.W.
TI  - Transduction and host controlled modification.  The role of the phage.
JO  - Informative molecules in biological systems.
PY  - 1971
SP  - 223
EP  - 233
VL  - 0
AB  - Three unrelated general transducing phages of Pseudomonas aeruginosa have been
AB  - studied to determine if the bacterial chromosomal fragments transferred in
AB  - transduction are always susceptible to restriction.  Using restriction and
AB  - modification mutants of the parent donor and recipient strains, to avoid
AB  - effects on recombination resulting from non-homology, two of the phages, B3 and
AB  - G101, were restricted for both their plaque forming and transducing properties.
AB  - However, a third transducing phage, F116, showed no such restriction when
AB  - transducing from a donor strain with a different DNA specificity to that of the
AB  - recipient strain.  This immunity to restriction appears to be associated with
AB  - the F115 phage genome and a variant of F116 has been found which, while immune
AB  - to restriction of plaque forming ability, is not immune to restriction of its
AB  - transducing ability.  The implication from these results is that a phage may be
AB  - able to protect bacterial DNA from inactivation by the restriction mechanisms
AB  - of host controlled modification.  With phage B3 a second type of immunity was
AB  - found, in that not all bacterial markers showed the same reduction of
AB  - transduction frequency caused by restriction and the results suggest an uneven
AB  - distribution of recognition sites on the bacterial chromosome.
ER  -

TY  - JOUR
AU  - Dunny, G.M.
AU  - McKay, L.L.
TI  - Group II introns and expression of conjugative transfer functions in lactic acid bacteria.
JO  - Antonie Van Leeuwenhoek
PY  - 1999
SP  - 77
EP  - 88
VL  - 76
AB  - The homologous lactococcal conjugative elements pRS01 and the sex factor of Lactococcus lactis
AB  - strain 712 both contain a Group II intron within a gene believed to encode a conjugative
AB  - relaxase enzyme. This enzyme is responsible for nicking of DNA at the origin of transfer
AB  - (oriT) sequence of the sex factor DNA to initiate the strand transfer process. Group II
AB  - introns have been studied in eukaryotes, and several of these elements in yeast mitochondrial
AB  - genes have received considerable attention. These introns are relatively large in size and
AB  - generally encode a protein within the intron sequence. In addition to splicing activity. Group
AB  - II introns are mobile genetic elements. The intron-encoded proteins (IEPs) contain
AB  - endonuclease and reverse transcriptase domains believed to play an enzymatic role in genetic
AB  - mobility reactions, while a putative maturase domain is thought to promote splicing by
AB  - stabilizing the folding of the intron RNA into an active ribozyme structure which carries out
AB  - the splicing reaction. The lactococcal introns represent the first examples of Group II
AB  - introns shown to be functional in vivo in prokaryotes. Because of the advantages of a
AB  - bacterial system for genetic and molecular studies, the Ll.ltrB intron from pRS01 has
AB  - attracted the attention of several laboratories interested in Group II intron biology.
AB  - Recently, it has been shown that the system can be adapted to function in Escherichia coli
AB  - (although at somewhat reduced efficiency). In addition, it has been recently proven that the
AB  - best studied form of mobility, the homing of the intron into an intronless allele of the
AB  - cognate exon gene, occurs via an RNA intermediate and does not require DNA homology or
AB  - generalized host recombination functions. Current efforts are analysis of the role Ll.ltrB
AB  - splicing in regulating expression of pRS01 conjugation functions. The lactococcal Group II
AB  - introns represent the first demonstrated genetically mobile prokaryotic retroelements, and
AB  - they also have considerable potential as genetic engineering tools for Lactic Acid Bacteria
AB  - (LAB) and other organisms.
ER  -

TY  - JOUR
AU  - Dunten, P.W.
AU  - Little, E.J.
AU  - Gregory, M.T.
AU  - Manohar, V.M.
AU  - Dalton, M.
AU  - Hough, D.
AU  - Bitinaite, J.
AU  - Horton, N.C.
TI  - The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 5405
EP  - 5416
VL  - 36
AB  - The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction
AB  - endonuclease SgrAI bound to cognate DNA is presented. SgrAI
AB  - forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme
AB  - active site, with one ion at the interface between the protein and DNA,
AB  - and the second bound distal from the DNA. These sites are differentially
AB  - occupied by Mn(2+), with strong binding at the protein-DNA interface, but
AB  - only partial occupancy of the distal site. The DNA remains uncleaved in
AB  - the structures from crystals grown in the presence of either divalent
AB  - cation. The structure of the dimer of SgrAI is similar to those of Cfr10I,
AB  - Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed.
AB  - DNA contacts to the central CCGG base pairs of the SgrAI canonical target
AB  - sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very
AB  - similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC).
AB  - Specificity at the degenerate YR base pairs of the SgrAI sequence may
AB  - occur via indirect readout using DNA distortion. Recognition of the outer
AB  - GC base pairs occurs through a single contact to the G from an arginine
AB  - side chain located in a region unique to SgrAI.
ER  -

TY  - JOUR
AU  - Dunten, P.W.
AU  - Little, E.J.
AU  - Horton, N.C.
TI  - The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2009
SP  - 393
EP  - 398
VL  - 65
AB  - Uninterpretable electron-density maps were obtained using either MIRAS phases or MR phases in
AB  - attempts to determine the structure of the type
AB  - II restriction endonuclease SgrAI bound to DNA. While neither solution
AB  - strategy was particularly promising (map correlation coefficients of
AB  - 0.29 and 0.22 with the final model, respectively, for the MIRAS and MR
AB  - phases and Phaser Z scores of 4.0 and 4.3 for the rotation and
AB  - translation searches), phase combination followed by density
AB  - modification gave a readily interpretable map. MR with a distantly
AB  - related model located a dimer in the asymmetric unit and provided the
AB  - correct transformation to use in averaging electron density between
AB  - SgrAI subunits. MIRAS data sets with low substitution and MR solutions
AB  - from only distantly related models should not be ignored, as
AB  - poor-quality starting phases can be significantly improved. The
AB  - bootstrapping strategy employed to improve the initial MIRAS phases is
AB  - described.
ER  -

TY  - JOUR
AU  - Duong, D.A.
AU  - Stevens, A.M.
AU  - Jensen, R.V.
TI  - Complete Genome Assembly of Pantoea stewartii subsp. stewartii DC283, a Corn Pathogen.
JO  - Genome Announcements
PY  - 2017
SP  - e00435
EP  - e00417
VL  - 5
AB  - The phytopathogen Pantoea stewartii subsp. stewartii DC283 causes Stewart's wilt  disease in
AB  - corn after transmission from the corn flea beetle insect vector. Here,
AB  - we report that the complete annotated genome of P. stewartii DC283 has been fully
AB  - assembled into one circular chromosome, 10 circular plasmids, and one linear
AB  - phage.
ER  -

TY  - JOUR
AU  - Dupuis, M.-E.
AU  - Villion, M.
AU  - Magadan, A.H.
AU  - Moineau, S.
TI  - CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance.
JO  - Nat. Commun.
PY  - 2013
SP  - 2087
EP  - 2087
VL  - 4
AB  - Bacteria have developed a set of barriers to protect themselves against invaders such as phage
AB  - and plasmid nucleic acids. Different prokaryotic defence systems exist and at least two of
AB  - them directly target the incoming DNA: restriction-modification (R-M) and CRISPR-Cas systems.
AB  - On their own, they are imperfect barriers to invasion by foreign DNA. Here, we show that R-M
AB  - and CRISPR-Cas systems are compatible and act together to increase the overall phage
AB  - resistance of a bacterial cell by cleaving their respective target sites. Furthermore, we show
AB  - that the specific methylation of phage DNA does not impair CRISPR-Cas acquisition or
AB  - interference activities. Taken altogether, both mechanisms can be leveraged to decrease phage
AB  - contaminations in processes relying on bacterial growth and/or fermentation.
ER  -

TY  - JOUR
AU  - Dupureur, C.M.
TI  - Unique P-31 spectral response to the formation of a specific restriction enzyme-DNA complex.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2006
SP  - 747
EP  - 764
VL  - 25
AB  - Protein-induced distortion is a dramatic but not universally observed feature of
AB  - sequence-specific DNA interactions. This is illustrated by
AB  - the crystal structures of restriction enzyme-DNA complexes: While some
AB  - of these structures exhibit DNA distortion, others do not. Among the
AB  - latter is PvuII endonuclease, a small enzyme that is also amenable to
AB  - NMR spectroscopic studies. Here P-31 NMR spectroscopy is applied to
AB  - demonstrate the unique spectral response of DNA to sequence-specific
AB  - protein interactions. The P-31 NMR spectrum of a noncognate DNA
AB  - exhibits only spectral broadening upon the addition of enzyme. However,
AB  - when enzyme is added to target DNA, a number of P-31 resonances ship
AB  - dramatically. The magnitudes of the chemical shifts (2-3 ppm) are among
AB  - the largest observed. Site-specific substitution with phosphoramidates
AB  - and phosphorothioates are used analyze these effects. While such
AB  - spectral features have been interpreted as indicative of DNA backbone
AB  - distortions, FRET analysis indicates that this does not occur in
AB  - PvuII-cognate DNA complexes in solution. The distinct P-31 spectral
AB  - signature observed for cognate DNA mirrors that observed for the
AB  - enzyme, underscoring the unique features of cognate complex formation.
ER  -

TY  - JOUR
AU  - Dupureur, C.M.
TI  - Metal ion-dependent DNA-induced conformational changes in PvuII restriction endonucleases.
JO  - SAAS Bulletin: Biochem. and Biotech.
PY  - 1999
SP  - 43
EP  - 47
VL  - 12
AB  - Using 19F NMR spectroscopy as a solution structural probe, important preliminary
AB  - conformational studies of the interactions between 3-fluorotyrosine-PvuII endonuclease and a
AB  - cognate DNA are described.  Even at high microM to mM concentrations of enzyme and DNA, Ca(II)
AB  - is required to observe enzyme conformational changes associated with the binding of a short
AB  - oligonucleotide.  Further, these structural changes are global: The resonances of no fewer
AB  - than 6 of the 10 3-fluorotyrosine residues per PvuII subunit shift by at least 0.1 ppm
AB  - relative to the free enzyme, far more than can be accounted for as local effects of DNA
AB  - binding.  Partial titration experiments are consistent with a slow off-rate for
AB  - oligonucleotide binding and correspondingly slow (ms) exchange between free and DNA-bound
AB  - conformations of enzyme.  These results demonstrate that this system provides a means to
AB  - explore solution conformational aspects of restriction enzyme-DNA interactions.
ER  -

TY  - JOUR
AU  - Dupureur, C.M.
TI  - NMR studies of restriction enzyme-DNA interactions: Role of conformation in sequence specificity.
JO  - Biochemistry
PY  - 2005
SP  - 5065
EP  - 5074
VL  - 44
AB  - Sequence specific DNA binding proteins are thought to adopt distinct conformations when
AB  - binding to target (cognate) and nontarget
AB  - (noncognate) sequences. There is both biochemical and crystallographic
AB  - evidence that this behavior is important in mediating sequence
AB  - recognition by the Mg(II)-dependent Type II restriction enzymes.
AB  - Despite this, there are few systematic comparisons of the structural
AB  - behavior of these enzymes in various complexes. Here, H-1-N-15 HSQC NMR
AB  - spectroscopy is applied to PvuII endonuclease (2 x 18 kDa) in an effort
AB  - to better understand the relationship between sequence recognition and
AB  - enzyme conformational behavior. Spectra of the free enzyme collected in
AB  - the absence and presence of metal ions indicate that while there is a
AB  - modest backbone conformational response upon binding Ca(II), this does
AB  - not occur with Mg(II). Substrate binding itself is accompanied by very
AB  - dramatic spectral changes consistent with a large-scale conformational
AB  - response. HSQC spectra of the enzyme bound to cognate (specific) and
AB  - noncognate (nonspecific) oligonucleotides in the presence of Ca(II) are
AB  - dramatically distinct, revealing for the first time the structural
AB  - uniqueness of a PvuII cognate complex in solution. The strong
AB  - correlation between NMR spectral overlap and crystallographic data
AB  - (C-alpha rmsd) permits characterization of the nonspecific Pvull
AB  - complex as being more similar to the free enzyme than to the specific
AB  - complex. Collectively, these data support the notion that it is the
AB  - DNA, not the metal ion, which promotes a unique conformational response
AB  - by the enzyme. It therefore follows that the principle role of metal
AB  - ions in complex formation is one of driving substrate affinity and
AB  - stability rather than conformationally priming the enzyme for substrate
AB  - binding and sequence recognition. These results not only provide
AB  - valuable insights into the mechanism of protein-DNA interactions but
AB  - also demonstrate the utility of NMR spectroscopy in structure-function
AB  - studies of these representative nucleic acid systems.
ER  -

TY  - JOUR
AU  - Dupureur, C.M.
AU  - Conlan, L.H.
TI  - A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions.
JO  - Biochemistry
PY  - 2000
SP  - 10921
EP  - 10927
VL  - 39
AB  - In efforts to understand the mechanisms of many nucleic acid enzymes, the first site-directed
AB  - mutations are made at conserved acidic active residues. Almost without exception, the low or
AB  - null activities of the resulting variants are attributed to the importance of the acidic
AB  - residue(s) to the ligation of required metal ions. Using Mg^25 NMR spectroscopy as a direct
AB  - probe of metal ion binding and the homodimeric PvuII restriction endonuclease as a model
AB  - system, this interpretation is examined and clarified. Our results indicate that Mg(II) binds
AB  - wild-type PvuII endonuclease in the absence of DNA with a K(d,app) of 1.9 mM. Hill analysis
AB  - yields an n(H) coefficient of 1.4, a value consistent with the binding of more than one Mg(II)
AB  - ion per monomer active site. Variable pH studies indicate that two ionizable groups are
AB  - responsible for Mg(II) binding by wild-type PvuII endonuclease near physiological pH. The
AB  - pK(a,app) for these ionizations is 6.7, a value which is unusual for acidic residues but
AB  - consistent with data obtained for critical groups in MunI endonuclease and a number of other
AB  - hydrolases. To assign residues critical to ligating Mg(II), binding measurements were
AB  - performed on the low activity catalytic site mutants E68A and D58A. As expected, E68A binds
AB  - Mg(II) ions very weakly (K(d,app) approximately 40 mM), implicating Glu68 as critical to
AB  - Mg(II) binding. Interestingly, while D58A has only residual specific activity, it retains an
AB  - affinity for Mg(II) with a K(d,app) of 3.6 mM and exhibits a Hill coefficient of 0.7.
AB  - Moreover, in this variant, multiple ionizable groups with pK(a,app) of 7.2 are involved in
AB  - Mg(II) binding, suggesting a shuffling of Mg(II) ligands in the active site. These data
AB  - indicate that Asp58 is important for the critical positioning of metal ion(s) required for
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Dupureur, C.M.
AU  - Dominguez, M.A.
TI  - The PD ... (D/E)XK motif in restriction enzymes: A link between function and conformation.
JO  - Biochemistry
PY  - 2001
SP  - 387
EP  - 394
VL  - 40
AB  - The active sites of Mg(II)-dependent nucleases feature a cluster of conserved charged residues
AB  - which includes both acidic (Asp and Glu) and
AB  - basic (Lys) side chains. In restriction enzymes, these side chains are
AB  - part of the conserved PD...(D/E)XK functional sequence motif which has
AB  - been implicated as being important in metal ion binding and catalytic
AB  - steps. Recent work revealing the unusual behavior of the active site
AB  - variant D58A of the representative PvuII endonuclease prompted
AB  - speculation that the array of charged groups in the nuclease active
AB  - site may also be linked to conformational behavior [Dupureur, C. M.
AB  - and Conlan, L. H. (2000) Biochemistry 39, 10921-10927]. To address this
AB  - issue, we analyzed the conformational behavior of active site variants
AB  - of PvuII endonuclease using both NMR spectroscopic and thermodynamic
AB  - methods. NMR spectroscopic analysis via F-19 and H-1-N-15 HSQC
AB  - experiments indicates that a number of side chain and backbone amide
AB  - groups are perturbed upon Ala substitution at conserved active site
AB  - residues Asp58, Glu68, and Lys70. Spectral changes are particularly
AB  - pronounced for the lowest-activity mutants (D58A and K70A). These
AB  - changes are accompanied by perturbations in conformational stability.
AB  - Ala substitution at each of these positions results in 2-5 kcal/mol of
AB  - stabilization over the wild-type enzyme at pH 7.7, changes which
AB  - constitute increases in DeltaG(d)(H2O) of 20-50%. The pH dependencies
AB  - of mutant enzyme stabilities are distinct from those of the wild type,
AB  - results which confirm that these ionizable groups strongly influence
AB  - stability. Wild-type enzyme stability is correlated with the ionization
AB  - of groups shown to be important to metal ion binding and orientation.
AB  - Correlations between spectral changes and conformational stability
AB  - indicate that the latter measurements may prove useful in the
AB  - evaluation of site-directed mutant restriction enzymes. More
AB  - importantly, these results indicate that structure-function
AB  - relationships in restriction enzyme active sites can be complex, and
AB  - that the ensemble of conserved charged residues which mediate DNA
AB  - hydrolysis in Mg(II)-dependent nucleases constitutes a critical link
AB  - between function and conformation.
ER  -

TY  - JOUR
AU  - Dupureur, C.M.
AU  - Hallman, L.M.
TI  - Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.
JO  - Eur. J. Biochem.
PY  - 1999
SP  - 261
EP  - 268
VL  - 261
AB  - The activities of restriction enzymes are important examples of Mg(II)-dependent hydrolysis of
AB  - DNA. While a number of crystallographic studies of enzyme-DNA complexes have also involved
AB  - metal ions, there have been no solution studies exploring the relationship between enzyme
AB  - conformation and metal-ion binding in restriction enzymes.  Using PvuII restriction
AB  - endonuclease as a model system, we have successfully developed biosynthetic fluorination and
AB  - NMR spectroscopy as a solution probe of restriction-enzyme conformation.  The utility of this
AB  - method is demonstrated with a study of metal-ion binding by PvuII endonuclease.  Replacement
AB  - of 74% (+-10%) of the Tyr residues in PvuII endonuclease by 3-fluorotyrosine produces an
AB  - enzyme with Mg(II)-supported specific activity and sequence specificity that is
AB  - indistinguishable from that of the native enzyme.  Mn(II) supports residual activity of both
AB  - the native and fluorinated enzymes; Ca(II) does not support activity in either enzyme, a
AB  - result consistent with previous studies.  1H- and 19F-NMR spectroscopic studies reveal that
AB  - while Mg(II) does not alter the enzyme conformation, the paramagnetic Mn(II) produces both
AB  - short-range spectral broadening and longer range changes in chemical shift.  Most
AB  - interestingly, Ca(II) binding perturbs a larger number of different resonances than Mn(II).
AB  - Coupled with earlier mutagenesis studies that place Ca(II) in the active site these data
AB  - suggest that the enzyme makes conformational adjustments to accommodate the distinct geometric
AB  - preferences of Ca(II) and may play a role in the inability of this metal ion to support
AB  - activity in restriction enzymes.
ER  -

TY  - JOUR
AU  - Dupuy, V. et al.
TI  - Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats.
JO  - Genome Announcements
PY  - 2013
SP  - e00354
EP  - e00313
VL  - 1
AB  - Mycoplasma putrefaciens is one of the etiologic agents of contagious agalactia in goats. We
AB  - report herein the complete genome sequence of Mycoplasma putrefaciens
AB  - strain 9231.
ER  -

TY  - JOUR
AU  - Dupuy, V.
AU  - Thiaucourt, F.
TI  - Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain 9231-Abomsa.
JO  - Genome Announcements
PY  - 2014
SP  - e01067
EP  - e01014
VL  - 2
AB  - Mycoplasma capricolum subsp. capripneumoniae is the etiological agent of contagious caprine
AB  - pleuropneumonia. We report here the complete and annotated
AB  - genome sequence of M. capricolum subsp. capripneumoniae strain 9231-Abomsa.
ER  -

TY  - JOUR
AU  - Duquesne, K.
AU  - Prima, V.
AU  - Ji, B.
AU  - Rouy, Z.
AU  - Medigue, C.
AU  - Talla, E.
AU  - Sturgis, J.N.
TI  - Draft Genome Sequence of the Purple Photosynthetic Bacterium Phaeospirillum molischianum DSM120, a Particularly Versatile Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3559
EP  - 3560
VL  - 194
AB  - Here we present the draft genome sequence of the versatile and adaptable purple photosynthetic
AB  - bacterium Phaeospirillum molischianum DSM120. This study advances
AB  - the understanding of the adaptability of this bacterium, as well as the
AB  - differences between the Phaeospirillum and Rhodospirillum genera.
ER  -

TY  - JOUR
AU  - Duquesne, K.
AU  - Sturgis, J.N.
TI  - Shotgun Genome Sequence of the Large Purple Photosynthetic Bacterium Rhodospirillum photometricum DSM122.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2380
EP  - 2380
VL  - 194
AB  - Here, we present the shotgun genome sequence of the purple photosynthetic bacterium
AB  - Rhodospirillum photometricum DSM122. The photosynthetic apparatus of
AB  - this bacterium has been particularly well studied by microscopy. The knowledge of
AB  - the genome of this oversize bacterium will allow us to compare it with the other
AB  - purple bacterial organisms to follow the evolution of the photosynthetic
AB  - apparatus.
ER  -

TY  - JOUR
AU  - Durai, S.
AU  - Mani, M.
AU  - Kandavelou, K.
AU  - Wu, J.
AU  - Porteus, M.H.
AU  - Chandrasegaran, S.
TI  - Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 5978
EP  - 5990
VL  - 33
AB  - Custom-designed zinc finger nucleases (ZFNs), proteins designed to cut at specific DNA
AB  - sequences, are becoming powerful tools in gene targeting--the
AB  - process of replacing a gene within a genome by homologous recombination
AB  - (HR). ZFNs that combine the non-specific cleavage domain (N) of FokI
AB  - endonuclease with zinc finger proteins (ZFPs) offer a general way to
AB  - deliver a site-specific double-strand break (DSB) to the genome. The
AB  - development of ZFN-mediated gene targeting provides molecular biologists
AB  - with the ability to site-specifically and permanently modify plant and
AB  - mammalian genomes including the human genome via homology-directed repair
AB  - of a targeted genomic DSB. The creation of designer ZFNs that cleave DNA
AB  - at a pre-determined site depends on the reliable creation of ZFPs that can
AB  - specifically recognize the chosen target site within a genome. The
AB  - (Cys2His2) ZFPs offer the best framework for developing custom ZFN
AB  - molecules with new sequence-specificities. Here, we explore the different
AB  - approaches for generating the desired custom ZFNs with high
AB  - sequence-specificity and affinity. We also discuss the potential of
AB  - ZFN-mediated gene targeting for 'directed mutagenesis' and targeted 'gene
AB  - editing' of the plant and mammalian genome as well as the potential of
AB  - ZFN-based strategies as a form of gene therapy for human therapeutics in
AB  - the future.
ER  -

TY  - JOUR
AU  - Duran, E.
AU  - Ramsauer, V.P.
AU  - Ballester, M.
AU  - Torrenegra, R.D.
AU  - Rodriguez, O.E.
AU  - Winkle, S.A.
TI  - Qualitative analysis of sequence specific binding of flavones to DNA using restriction endonuclease activity assays.
JO  - Biopolymers
PY  - 2013
SP  - 530
EP  - 537
VL  - 99
AB  - Flavones, found in nature as secondary plant metabolites, have shown efficacy as anti-cancer
AB  - agents. We have examined the binding of two
AB  - flavones, 5,7-dihydroxy-3,6,8-trimethoxy-2-phenyl-4H-chromen-4-one
AB  - (5,7-dihydroxy-3,6,8-trimethoxy flavone; FlavA) and
AB  - 3,5-dihydroxy-6,7,8-trimethoxy-2-phenyl-4H-chromen-4-one
AB  - (3,5-dihydroxy-6,7,8-trimethoxy flavone; FlavB), to phiX174 RF DNA
AB  - using restriction enzyme activity assays employing the restriction
AB  - enzymes Alw44, AvaII, BssHII, DraI, MluI, NarI, NciI, NruI, PstI, and
AB  - XhoI. These enzymes possess differing target and flanking sequences
AB  - allowing for observation of sequence specificity analysis. Using
AB  - restriction enzymes that cleave once with a mixture of supercoiled and
AB  - relaxed DNA substrates provides for observation of topological effects
AB  - on binding. FlavA and FlavB show differing sequence specificities in
AB  - their respective binding to phiX. For example, with relaxed DNA, FlavA
AB  - shows inhibition of cleavage with DraI (reaction site 5TTTAAA) but not
AB  - BssHII (5GCGCGC) while FlavB shows the opposite results. Evidence for
AB  - tolological specificity is also observed, Molecular modeling and
AB  - conformational analysis of the flavones suggests that the phenyl ring
AB  - of FlavB is coplanar with the flavonoid ring while the phenyl ring of
AB  - FlavA is at an angle relative to the flavonoid ring. This may account
AB  - for aspects of the observed sequence and topological specificities in
AB  - the effects on restriction enzyme activity.
ER  -

TY  - JOUR
AU  - Duranti, S.
AU  - Turroni, F.
AU  - Lugli, G.A.
AU  - Milani, C.
AU  - Viappiani, A.
AU  - Mangifesta, M.
AU  - Gioiosa, L.
AU  - Palanza, P.
AU  - van Sinderen, D.
AU  - Ventura, M.
TI  - Genomic Characterization and Transcriptional Studies of the Starch-Utilizing Strain Bifidobacterium adolescentis 22L.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 6080
EP  - 6090
VL  - 80
AB  - Bifidobacteria are members of the gut microbiota but the genetic basis for their adaptation to
AB  - the human gut is poorly understood.  Analysis of the 2,203,222 bp genome of Bifidobacterium
AB  - adolescentis 22L revealed a nutrient-acquisition strategy that targets diet/plant-derived
AB  - glycans, in particular starch and starch-like carbohydrates.  Starch-like carbohydrates were
AB  - shown to support the growth of B. acelescentis 22L.  Transcriptome profiling of 22L cultures
AB  - grown under in vitro conditions or during colonization of the murine gut by RNAseq and qRT-PCR
AB  - assays revealed the expression of a set of chromosomal loci responsible for starch metabolism
AB  - as well as for pili production.  Such extracellular structures include so-called
AB  - sortase-dependent and type IVb pili, which may be involved in gut colonization of 22L through
AB  - adhesion to extracellular matrix proteins.
ER  -

TY  - JOUR
AU  - Durfee, T.
AU  - Nelson, R.
AU  - Baldwin, S.
AU  - Plunkett, G. III
AU  - Burland, V.
AU  - Mau, B.
AU  - Petrosino, J.F.
AU  - Qin, X.
AU  - Muzny, D.M.
AU  - Ayele, M.
AU  - Gibbs, R.A.
AU  - Csorgo, B.
AU  - Posfai, G.
AU  - Weinstock, G.M.
AU  - Blattner, F.R.
TI  - The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.
JO  - J. Bacteriol.
PY  - 2008
SP  - 2597
EP  - 2606
VL  - 190
AB  - Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It
AB  - is used extensively, taking advantage of properties
AB  - such as high DNA transformation efficiency and maintenance of large
AB  - plasmids. The strain was constructed by serial genetic recombination
AB  - steps, but the underlying sequence changes remained unverified. We report
AB  - the complete genomic sequence of DH10B by using reads accumulated from the
AB  - bovine sequencing project at Baylor College of Medicine and assembled with
AB  - DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear
AB  - with that of the wild-type K-12 strain MG1655, although it is
AB  - substantially more complex than previously appreciated, allowing DH10B
AB  - biology to be further explored. The 226 mutated genes in DH10B relative to
AB  - MG1655 are mostly attributable to the extensive genetic manipulations the
AB  - strain has undergone. However, we demonstrate that DH10B has a 13.5-fold
AB  - higher mutation rate than MG1655, resulting from a dramatic increase in
AB  - insertion sequence (IS) transposition, especially IS150. IS elements
AB  - appear to have remodeled genome architecture, providing homologous
AB  - recombination sites for a 113,260-bp tandem duplication and an inversion.
AB  - DH10B requires leucine for growth on minimal medium due to the deletion of
AB  - leuLABCD and harbors both the relA1 and spoT1 alleles causing both
AB  - sensitivity to nutritional downshifts and slightly lower growth rates
AB  - relative to the wild type. Finally, while the sequence confirms most of
AB  - the reported alleles, the sequence of deoR is wild type, necessitating
AB  - reexamination of the assumed basis for the high transformability of DH10B.
ER  -

TY  - JOUR
AU  - Durham, B.P. et al.
TI  - Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade  possessing an unusually small genome.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 632
EP  - 645
VL  - 9
AB  - Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in  Kaneohe Bay,
AB  - Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter
AB  - clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the
AB  - preliminary characteristics of strain HIMB11, including annotation of the draft
AB  - genome sequence and comparative genomic analysis with other members of the
AB  - Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and
AB  - contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA
AB  - gene analyses indicate that HIMB11 represents a unique sublineage within the
AB  - Roseobacter clade. Comparison with other publicly available genome sequences from
AB  - members of the Roseobacter lineage reveals that strain HIMB11 has the genomic
AB  - potential to utilize a wide variety of energy sources (e.g. organic matter,
AB  - reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced
AB  - number of substrate transporters.
ER  -

TY  - JOUR
AU  - Durmaz, E.
AU  - Higgins, D.L.
AU  - Klaenhammer, T.R.
TI  - Molecular characterization of a second abortive phage resistance gene present in Lactococcus lactis subsp. lactis ME2.
JO  - J. Bacteriol.
PY  - 1992
SP  - 7463
EP  - 7469
VL  - 174
AB  - The fifth phage resistance factor from the prototype phage-insensitive strain Lactococcus
AB  - lactis subsp. lactis ME2 has been characterized and sequenced. The genetic determinant for Prf
AB  - (phage resistance five) was subcloned from the conjugative plasmid pTN20, which also encodes a
AB  - restriction and modification system. Typical of other abortive resistance mechanisms, Prf
AB  - reduces the efficiency of plaquing to 10-2 to 10-3 and decreases the plaque size and burst
AB  - size of the small isometric-headed phage p2 in L. lactis subsp. lactis LM0230. However,
AB  - normal-size plaques occurred at a frequency of 10-4 and contained mutant phages that were
AB  - resistant to Prf, even after repeated propagation through a sensitive host. Prf does not
AB  - prevent phage adsorption or promote restriction and modification activities, but 90% of Prf+
AB  - cells infected with phage p2 die. Thus, phage infections in Prf+ cells are aborted. Prf is
AB  - effective in both L. lactis subsp. lactis and L. lactis subsp. cremoris strains against
AB  - several small isometric-headed phages but not against prolate-headed phages. The Prf
AB  - determinant was localized by Tn5 mutagenesis and subcloning. DNA sequencing identified a
AB  - 1,056-nucleotide strutural gene designated abiC, Prf+ expression was obtained when abiC was
AB  - subcloned into the lactococcal expression vector pMG36e, abiC is distinct from two other
AB  - lactococcal abortive phage resistance genes, abiA (Hsp+, from L. lactis subsp. lactis ME2) and
AB  - abi416 (Abi+, from L. lactis subsp. lactis IL416). Unlike abiA, the action of abiC does not
AB  - appear to affect DNA replication. Thus, abiC represents a second abortive system found in ME2
AB  - that acts at a different point of the phage lytic cycle.
ER  -

TY  - JOUR
AU  - Durmaz, E.
AU  - Klaenhammer, T.R.
TI  - Abortive phage resistance mechanism AbiZ speeds the lysis clock to cause premature lysis of phage-infected Lactococcus lactis.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1417
EP  - 1425
VL  - 189
AB  - The conjugative plasmid pTR2030 has been used extensively to confer phage resistance in
AB  - commercial Lactococcus starter cultures. The
AB  - plasmid harbors a 16-kb region, flanked by insertion sequence (IS)
AB  - elements, that encodes the restriction/modification system L1aI and
AB  - carries an abortive infection gene, abiA. The AbiA system inhibits both
AB  - prolate and small isometric phages by interfering with the early stages
AB  - of phage DNA replication. However, abiA alone does not account for the
AB  - full abortive activity reported for pTR2030. In this study, a 7.5-kb
AB  - region positioned within the IS elements and downstream of abiA was
AB  - sequenced to reveal seven additional open reading frames (ORFs). A
AB  - single ORF, designated abiZ, was found to be responsible for a
AB  - significant reduction in plaque size and an efficiency of plaquing
AB  - (EOP) of 10(-6), without affecting phage adsorption. AbiZ causes phage
AB  - phi 31-infected Lactococcus lactis NCK203 to lyse 15 min early,
AB  - reducing the burst size of phi 31 100-fold. Thirteen of 14 phages of
AB  - the P335 group were sensitive to AbiZ, through reduction in either
AB  - plaque size, EOP, or both. The predicted AbiZ protein contains two
AB  - predicted transmembrane helices but shows no significant DNA
AB  - homologies. When the phage phi 31 lysin and holin genes were cloned
AB  - into the nisin-inducible shuttle vector pMSP3545, nisin induction of
AB  - holin and lysin caused partial lysis of NCK203. In the presence of
AB  - AbiZ, lysis occurred 30 min earlier. In holin-induced cells, membrane
AB  - permeability as measured using propidium iodide was greater in the
AB  - presence of AbiZ. These results suggest that AbiZ may interact
AB  - cooperatively with holin to cause premature lysis.
ER  -

TY  - JOUR
AU  - Durmaz, E.
AU  - Klaenhammer, T.R.
TI  - A starter culture rotation strategy incorporating paired restriction/modification and abortive infection bacteriophage defenses in a single lactococcus lactis strain.
JO  - Appl. Environ. Microbiol.
PY  - 1995
SP  - 1266
EP  - 1273
VL  - 61
AB  - Three derivatives of Lactococcus lactis subsp. lactis NCK203, each with a different pair of
AB  - restriction/modification (R/M) and abortive infection (Abi) phage defense systems, were
AB  - constructed and then rotated in repeated cycles of a milk starter culture activity test (SAT).
AB  - The rotation proceeded successfully through nine successive SATs in the presence of phage and
AB  - whey containing phage from previous cycles. Lactococcus cultures were challenged with 2 small
AB  - isometric-headed phages, omega-31 and ul36, in one rotation series and with a composite of 10
AB  - industrial phages in another series. Two native lactococcal R+/M+ plasmids, pTRK68 and pTRK11,
AB  - and one recombinant plasmid, pTRK308, harboring a third distinct R/M system were incorporated
AB  - into three NCK203 derivatives constructed separately for the rotation. The R+/M+ NCK203
AB  - derivatives were transformed with high-copy-number plasmids encoding four Abi genes, abiA,
AB  - abiC, per31, and per50. Various Abi and R/M combinations constructed in NCK203 were evaluated
AB  - for their effects on cell growth, level of phage resistance, and retardation of phage
AB  - development during repeated cycles of the SAT. The three NCK203 derivatives chosen for use in
AB  - the SAT exhibited additive effects of the R/M and Abi phenotypes against sensitive phages. In
AB  - such combinations, phage escaping restriction are prevented from completing their infective
AB  - cycle by an abortive response that kills the host cell. The rotation series successfully
AB  - controlled modified, recombinant, and mutant phages which were resistant to any one of the
AB  - individual defense systems by presenting a different set of R/M and Abi defenses in the next
AB  - test of the rotation.
ER  -

TY  - JOUR
AU  - Durmaz, E.
AU  - Miller, M.J.
AU  - Azcarate-Peril, M.A.
AU  - Toon, S.P.
AU  - Klaenhammer, T.R.
TI  - Genome sequence and characteristics of Lrm1, a prophage from industrial Lactobacillus rhamnosus strain M1.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 4601
EP  - 4609
VL  - 74
AB  - Prophage Lrm1 was induced with mitomycin C from an industrial Lactobacillus rhamnosus starter
AB  - culture, M1. Electron microscopy of the
AB  - lysate revealed relatively few intact bacteriophage particles among
AB  - empty heads and disassociated tails. The defective Siphoviridae phage
AB  - had an isometric bead of approximately 55 nm and noncontractile tail of
AB  - about 275 nm with a small baseplate. In repeated attempts, the prophage
AB  - could not be cured from L. rhamnosus M1, nor could a sensitive host be
AB  - identified. Sequencing of the phage Lrm1 DNA revealed a genome of
AB  - 39,989 bp and a G+C content of 45.5%. A similar genomic organization
AB  - and mosaic pattern of identities align Lrm1 among the closely related
AB  - Lactobacillus casei temperate phages A2, Phi AT3, and LeaI and with L.
AB  - rhamnosus virulent phage Lu-Nu. Of the 54 open reading frames (ORFs)
AB  - identified, all but 8 shared homology with other phages of this group.
AB  - Five unknown ORFs were identified that had no homologies in the
AB  - databases nor predicted functions. Notably, Lrm1 encodes a putative
AB  - endonuclease and a putative DNA methylase with homology to a methylase
AB  - in Lactococcus lactis phage Tuc2009. Possibly, the DNA methylase,
AB  - endonuclease, or other Lrm1 genes provide a function crucial to L.
AB  - rhamnosus M1 survival, resulting in the stability of the defective
AB  - prophage in its lysogenic state. The presence of a defective prophage
AB  - in an industrial strain could provide superinfection immunity to the
AB  - host but could also contribute DNA in recombination events to produce
AB  - new phages potentially infective for the host strain in a large-scale
AB  - fermentation environment.
ER  -

TY  - JOUR
AU  - Durrell, K.
AU  - Prins, A.
AU  - Le Roes-Hill, M.
TI  - Draft Genome Sequence of Gordonia lacunae BS2T.
JO  - Genome Announcements
PY  - 2017
SP  - e00959
EP  - e00917
VL  - 5
AB  - We report here the draft genome sequence of the soil bacterium Gordonia lacunae BS2T (= DSM
AB  - 45085T = JCM 14873T = NRRL B-24551T), isolated from an estuary in
AB  - Plettenberg Bay, South Africa. Analysis of the draft genome revealed that more
AB  - than 40% of the secondary metabolite biosynthetic genes encode new compounds.
ER  -

TY  - JOUR
AU  - Durrenberger, F.
AU  - Rochaix, J.-D.
TI  - Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii.
JO  - Mol. Gen. Genet.
PY  - 1993
SP  - 409
EP  - 414
VL  - 236
AB  - The chloroplast ribosomal intron of Chlamydomonas reinhardtii encodes a sequence-specific DNA
AB  - endonuclease (I-CreI), which is most probably involved in the mobility of this intron. Here we
AB  - show that I-CreI generates a 4 bp staggered cleavage just downstream of the intron insertion
AB  - site. The I-CreI recognition sequence is 19-24 bp in size and is located asymmetrically around
AB  - the intron insertion site. Screening of natural variants of the I-CreI recognition sequence
AB  - indicates that the I-CreI endonuclease tolerates single and even multiple base changes within
AB  - its recognition sequence.
ER  -

TY  - JOUR
AU  - Durrenberger, F.
AU  - Rochaix, J.-D.
TI  - Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self-splicing, DNA endonuclease activity and in vivo mobility.
JO  - EMBO J.
PY  - 1991
SP  - 3495
EP  - 3501
VL  - 10
AB  - All chloroplast 23S ribosomal RNA genes of the unicellular alga Chlamydomonas reinhardtii
AB  - contain an 888 bp group I intron with an internal open reading frame (ORF). A precursor RNA
AB  - encompassing the intron with its 5' and 3' flanking sequences was shown to self-splice both
AB  - during in vitro transcription and upon incubation of the isolated pre-RNA under self-splicing
AB  - conditions. Expression of the internal ORF in Escherichia coli in the presence of a plasmid
AB  - containing a cDNA corresponding to the intronless form of the 23S rRNA gene resulted in
AB  - specific cleavage of the cDNA at or close to the exon junction sequence. To test whether this
AB  - ORF-encoded double-strand DNA endonuclease is involved in intron mobility in vivo, the same
AB  - ribosomal cDNA was stably integrated into the C. reinhardtii chloroplast genome using particle
AB  - gun mediated transformation. All the transformants with the cDNA integrated at the expected
AB  - site in the chloroplast genome had the intron precisely inserted at the artificial exon
AB  - junction site. These experiments demonstrate that the chloroplast ribosomal intron of C.
AB  - reinhardtii behaves as a ribozyme in vitro and also as a mobile genetic element in vivo
AB  - provided a target site is present.
ER  -

TY  - JOUR
AU  - Durrett, R.
AU  - Miras, M.
AU  - Mirouze, N.
AU  - Narechania, A.
AU  - Mandic-Mulec, I.
AU  - Dubnau, D.
TI  - Genome Sequence of the Bacillus subtilis Biofilm-Forming Transformable Strain PS216.
JO  - Genome Announcements
PY  - 2013
SP  - e00288
EP  - e00213
VL  - 1
AB  - Bacillus subtilis PS216, a strain isolated in Slovenia, has been sequenced. PS216 is
AB  - transformable and forms robust biofilms, making it useful for the study of
AB  - competence regulation in an undomesticated bacterium.
ER  -

TY  - JOUR
AU  - Dussoix, D.
AU  - Arber, W.
TI  - Host Specificity of DNA Produced by Escherichia Coli:  II. Control over acceptance of DNA from infecting phage lambda.
JO  - J. Mol. Biol.
PY  - 1962
SP  - 37
EP  - 49
VL  - 5
AB  - DNA of lambda.K (lambdaphage grown on E. coli strain K12) is shown to be
AB  - degraded upon infection of the new host strains E. coli K12(P1) or E. coli B.
AB  - This breakdown begins shortly after phage attachment and successful DNA
AB  - injection.  32P label from the lambda.K DNA submitted to this degradation
AB  - appears partly in acid-soluble components (organic and inorganic) and partly in
AB  - acid-insoluble compounds.  The host cell survives such an infection and permits
AB  - diffusion of a fraction of the degradation products into the medium, while
AB  - probably re-using another fraction.  Genetic markers from lambda.K are rescued
AB  - in K12(P1) host cells infected with both restricted lambda.K and unrestricted
AB  - lambda.K(P1).  Since DNA breakdown competes in time with the rescue, the
AB  - probability of marker rescue is high if the unrestricted phage infects first
AB  - and low if the restricted phage infects first.  Only closely linked markers
AB  - have a good chance to be rescued together.  The host specificity imparted to
AB  - phage DNA by the bacterial strain on which it was produced is thought to be
AB  - responsible for its recognition as incompatible with a new host strain.
AB  - Bacterial mutants are described which, despite the presence of prophage P1,
AB  - accept infecting lambda.K at relatively high rates.
ER  -

TY  - JOUR
AU  - Dussoix, D.
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli IV.  Host specificity of infectious DNA from bacteriophage lambda.
JO  - J. Mol. Biol.
PY  - 1965
SP  - 238
EP  - 246
VL  - 11
AB  - DNA extracted with phenol from bacteriophage lambda gives rise to phage
AB  - production after uptake by helper-infected, competent recipient cells (Kaiser,
AB  - 2962).  Under our experimental conditions, the number of infective centres
AB  - obtained by infection of Escherichia coli K12 is about 10-3 per phage
AB  - equivalent of DNA from lambda.K or from lambda.K(P1).  But on K12(P1) recipient
AB  - cells only lambda-K(P1) DNA infects with an efficiency of 10-3, while lambda.K
AB  - DNA gives about 100 times less infective centres.  The same factor of
AB  - restriction for lambda.K is found in controls done by infection of the
AB  - competent cells with intact phage particles instead of the phage DNA.
AB  - Similarly, restrictions displayed by K12 against phage grown on E. coli B or E.
AB  - coli C and those displayed by B against phage grown on K12 or C are found to
AB  - hold true for DNA preparations.  E. coli C accepts all tested lambda DNA with
AB  - about the same efficiency.  We conclude that the phenol extraction does not
AB  - affect the host specificity of the phage DNA.  One cycle growth of lambda
AB  - initiated by infection of K12 with lambda.K(P1) DNA confirms this result:  the
AB  - parental P1-directed host specificity is transferred into the phage progeny,
AB  - and it is found only in such phage particles that also inherit one strand of
AB  - the infecting DNA molecule.  The stability of the association of DNA with its
AB  - host specificity is further revealed by its resistance to various physical,
AB  - chemical and enzymic treatments of the lambda DNA.  It is significant with
AB  - respect to the understanding of the mechanism of competence of bacteria for
AB  - infection with lambda DNA that only non-restricted phage acts as a good helper.
ER  -

TY  - JOUR
AU  - Dusterhoft, A.
TI  - Cloning of the restriction-modification systems from Herpetosiphon giganteus Hpa1, Hpa2 and Hpg5 in E. coli - Characterization and comparative analysis of the genetic organization and structure.
JO  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany
PY  - 1990
SP  - 1
EP  - 160
AB  - None - but this thesis shows that M.HgiBI, M.HgiDI, M.HgiDII and M.HgiGI are
AB  - m5C-methylases.  Also, because SalI was used to select M.HgiDII gene and SalI
AB  - can cleave when the last cytosine in the recognition sequence (GTCGAC) is m5C,
AB  - M.HgiDII must methylate the first cytosine in the sequence.
ER  -

TY  - JOUR
AU  - Dusterhoft, A.
AU  - Erdmann, D.
AU  - Kroger, M.
TI  - Stepwise cloning and molecular characterization of the HgiDI restriction-modification system from Herpetosiphon giganteus Hpa2.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 1049
EP  - 1056
VL  - 19
AB  - The restriction-modification system HgiDI from Herpetosiphon giganteus strain
AB  - Hpa2 has been cloned in E. coli in a two-step procedure.  Selection of the
AB  - methyltransferase (M.HgiDI) gene in vitro was performed using the heterologous
AB  - restriction endonuclease AhaII, an isoschizomer of AcyI and HgiDI (GRCGYC).
AB  - Cloning of the complete HgiDI endonuclease (R.HgiDI) gene could only be
AB  - achieved in recipient cells harbouring a recombinant plasmid, which was
AB  - expressing the corresponding methyltransferase and could thereby prevent the
AB  - host from self-destruction of its genetic material.  The HgiDI
AB  - restriction-modification system was sequenced and functionally correlated with
AB  - two open reading frames of 309 (M) and 359 (R) codons.  In homology studies
AB  - M.HgiDI showed significant similarities to 20 other m5C-methyltransferases and
AB  - turned out to be the most compact enzyme of this group described so far.
AB  - Initial attempts for overexpression of M.HgiDI and partial purification of
AB  - R.HgiDI have been successful.
ER  -

TY  - JOUR
AU  - Dusterhoft, A.
AU  - Erdmann, D.
AU  - Kroger, M.
TI  - Isolation and genetic structure of the AvaII isoschizomeric restriction-modification system HgiBI from Herpetosiphon giganteus Hpg5:  M.HgiBI reveals high homology to M.BanI.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 3207
EP  - 3211
VL  - 19
AB  - The complete type II restriction-modification system HgiBI of Herpetosiphon
AB  - giganteus strain Hpg5 recognizing the AvaII specific DNA sequence GGWCC has
AB  - been cloned and expressed functionally active in Escherichia coli.  A
AB  - considerable acceleration in cloning could be achieved by preparing a size
AB  - restricted library after application of a related hybridization probe.  Both
AB  - methyltransferase (437 codons) and restriction endonuclease gene (274 codons)
AB  - were found to be encoded on a 3.6 kilobases ClaI/HincII fragment in the same
AB  - transcriptional orientation separated by one triplet only.  Protein sequence
AB  - comparisons revealed a close resemblance of M.HgiBI to the group of
AB  - m5C-methyltransferases, especially to M.BanI from Bacillus aneurinolyticus with
AB  - the related recognition sequence GGYRCC.  In contrast, no significant
AB  - similarities have been observed for the associated endonuclease R.HgiBI with
AB  - any other restriction enzyme described so far, even not with the isoschizomeric
AB  - R.SinI from Salmonella infantis, or with R.BanI.
ER  -

TY  - JOUR
AU  - Dusterhoft, A.
AU  - Kroger, M.
TI  - Site directed mutagenesis on the restriction endonuclease EcoRI using mixed oligonucleotides.
JO  - Nucl. Nucl.
PY  - 1988
SP  - 737
EP  - 740
VL  - 7
AB  - The restriction endonuclease EcoRI could be modified via site directed
AB  - mutagenesis at position Arg200.  Using the thiophosphate system we introduced
AB  - either Lys, Glu or Gly in a one pot procedure.  Although G recognition should
AB  - be affected, Lys200 showed wildtype specificity.
ER  -

TY  - JOUR
AU  - Dusterhoft, A.
AU  - Kroger, M.
TI  - Cloning, sequence and characterization of m5C-methyltransferase-encoding gene, hgiDIIM (GTCGAC), from Herpetosiphon giganteus strain Hpa2.
JO  - Gene
PY  - 1991
SP  - 87
EP  - 92
VL  - 106
AB  - We have cloned the gene (hgiDIIM) encoding the methyltransferase (MTase) of the SalI
AB  - isoschizomeric restriction-modification (R-M) system, HgiDII (GTCGAC), into Escherichia coli.
AB  - The hgiDIIM gene has been isolated from the same plasmid library of Herpetosiphon giganteus
AB  - strain Hpa2, as was the previously cloned R-M system, HgiDI [AcyI/GRCGYC; Dusterhoft et al.,
AB  - Nucl. Acids Res. 19 (1991) 1049-1056]. Sequencing and functional localization of hgiDIIM
AB  - revealed an open reading frame (ORF) of 354 codons (39786 Da) with significant homologies to
AB  - the group of m5C-, rather than the m4C-/m6A-, MTases. Subsequent cloning and analysis of
AB  - adjacent chromosomal segments led to the identification of two additional ORFs upstream
AB  - (ORF15, 139 codons) and downstream (ORF68, 611 codons) from hgiDIIM with the same
AB  - transcriptional orientation as the hgiDIIM gene. However, the expected restriction enzyme
AB  - function was not found in either of these ORFs.
ER  -

TY  - JOUR
AU  - Dutta, V.
AU  - Altermann, E.
AU  - Olson, J.
AU  - Wray, G.A.
AU  - Siletzky, R.M.
AU  - Kathariou, S.
TI  - Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e00833
EP  - e00816
VL  - 4
AB  - We report here the genome sequences of four agricultural, multidrug-resistant Campylobacter
AB  - spp.: C. coli 11601 and C. jejuni 11601MD, isolated from turkey
AB  - cecum and jejunum, respectively, and C. coli 6067 and C. coli 6461, isolated from
AB  - turkey-house water and swine feces, respectively. The genomes provide insights on
AB  - Campylobacter antimicrobial resistance and host adaptations.
ER  -

TY  - JOUR
AU  - Dutta, V.
AU  - Lee, S.
AU  - Ward, T.J.
AU  - Orwig, N.
AU  - Altermann, E.
AU  - Jima, D.
AU  - Parsons, C.
AU  - Kathariou, S.
TI  - Draft Genome Sequences of Two Historical Listeria monocytogenes Strains from Human Listeriosis Cases in 1933.
JO  - Genome Announcements
PY  - 2016
SP  - e01364
EP  - e01316
VL  - 4
AB  - We report here the draft genome sequences of two Listeria monocytogenes strains from some of
AB  - the earliest reported cases of human listeriosis in North America.
AB  - The strains were isolated in 1933 from patients in Massachusetts and Connecticut,
AB  - USA, and belong to the widely disseminated hypervirulent clonal complex 1 (CC1)
AB  - and CC2.
ER  -

TY  - JOUR
AU  - Dutta, V.
AU  - Lee, S.
AU  - Ward, T.J.
AU  - Orwig, N.
AU  - Altermann, E.
AU  - Jima, D.D.
AU  - Parsons, C.
AU  - Kathariou, S.
TI  - Genome Sequences of Listeria monocytogenes Strains with Resistance to Arsenic.
JO  - Genome Announcements
PY  - 2017
SP  - e00327
EP  - e00317
VL  - 5
AB  - Listeria monocytogenes frequently exhibits resistance to arsenic. We report here  the draft
AB  - genome sequences of eight genetically diverse arsenic-resistant L.
AB  - monocytogenes strains from human listeriosis and food-associated environments.
AB  - The availability of these genomes will help elucidate the role of heavy-metal
AB  - resistance in the ecology of L. monocytogenes.
ER  -

TY  - JOUR
AU  - Duvnjak, S.
AU  - Spicic, S.
AU  - Kusar, D.
AU  - Papic, B.
AU  - Reil, I.
AU  - Zdelar-Tuk, M.
AU  - Pavlinec, Z.
AU  - Duras, M.
AU  - Gomercic, T.
AU  - Hendriksen, R.S.
AU  - Cvetnic, Z.
TI  - Whole-Genome Sequence of the First Sequence Type 27 Brucella ceti Strain Isolated from European Waters.
JO  - Genome Announcements
PY  - 2017
SP  - e00988
EP  - e00917
VL  - 5
AB  - Brucella spp. that cause marine brucellosis are becoming more important, as the disease
AB  - appears to be more widespread than originally thought. Here, we report a
AB  - whole and annotated genome sequence of Brucella ceti CRO350, a sequence type 27
AB  - strain isolated from a bottlenose dolphin carcass found in the Croatian part of
AB  - the northern Adriatic Sea.
ER  -

TY  - JOUR
AU  - Duyvesteyn, M.G.C.
AU  - de Waard, A.
TI  - A new sequence-specific endonuclease from a thermophilic cyanobacterium, Mastigocladus laminosus.
JO  - FEBS Lett.
PY  - 1980
SP  - 423
EP  - 426
VL  - 111
AB  - The screening of a number of cyanobacteria (blue-green algae) for new
AB  - sequence-specific deoxyribonucleases has been very rewarding.  We report here
AB  - the purification of a new enzyme of this type from Mastigocladus laminosus
AB  - (named MlaI) which recognizes and cleaves the nucleotide sequence TT^CGAA.
ER  -

TY  - JOUR
AU  - Duyvesteyn, M.G.C.
AU  - de Waard, A.
AU  - van Ormondt, H.
TI  - Two sequence-specific deoxyribonucleases from Rhodospirillum rubrum.
JO  - FEBS Lett.
PY  - 1980
SP  - 241
EP  - 246
VL  - 117
AB  - The usefulness of sequence-specific endonucleases in solving fundamental
AB  - problems in current molecular biology is well established.  The catalog of
AB  - enzymes has increased steadily.  We report here the isolation and partial
AB  - characterization of two enzymes from Rhodospirillum rubrum, endonucleases
AB  - R.RruI and R.RruII.  The first enzyme is unique in that it recognizes and
AB  - cleaves the hexanucleotide sequence AGT^ACT in DNA molecules of various origin.
AB  - The latter enzyme (endo R.RruII) recognizes the nucleotide sequence CC(A/T)GG
AB  - as does endo R.EcoRII; however, it cleaves the DNA within the site like the
AB  - isoschizomer endo R.BstNI (CC^(A/T)GG).
ER  -

TY  - JOUR
AU  - Duyvesteyn, M.G.C.
AU  - Korsuize, J.
AU  - de Waard, A.
TI  - Isolation and characterization of a sequence-specific deoxyriboendonuclease from Calothrix scopulorum.
JO  - Plant Mol. Biol.
PY  - 1981
SP  - 75
EP  - 79
VL  - 1
AB  - Sequence-specific deoxyriboendonucleases have been isolated from bacteria and
AB  - fungi.  Except in a few cases the nucleotide sequences recognized by the
AB  - cyanobacerial enzymes have been shown to be unique.  In this report we describe
AB  - the isolation and characterization of an endonuclease (endo R. CscI) from a
AB  - cyanobacterium, Calothrix scopulorum which cleaves the deoxynucleotide sequence
AB  - CCGC^GG.  Isoschizomers have been found previously in a fungus and in two
AB  - bacterial strains.
ER  -

TY  - JOUR
AU  - Duyvesteyn, M.G.C.
AU  - Korsuize, J.
AU  - de Waard, A.
AU  - Vonshak, A.
AU  - Wolk, C.P.
TI  - Sequence-specific endonucleases in strains of Anabaena and Nostoc.
JO  - Arch. Microbiol.
PY  - 1983
SP  - 276
EP  - 281
VL  - 134
AB  - The complements of restriction endonucleases of 12 strains of cyanobacteria were determined in
AB  - cell-free extracts, and were compared with the complements of restriction activities assessed
AB  - by measuring the relative efficiencies of plating of cyanophages on those cyanobacteria.  The
AB  - hosts which were susceptible to all of the phages contained endo R.AvaI and endo R.AvaII, and
AB  - in several cases probably endo R.AvaIII, or isoschizomers of these enzymes. Three hosts which
AB  - were lysed by only a subset (1 or 3) of the phages contained different restriction
AB  - endonucleases.  Anabaena sp. PCC 7120 showed apparent phenotypic restriction of phage AN-22
AB  - grown in hosts with (isoschizomers of) AvaI, II and III, but no corresponding endonuclease has
AB  - yet been detected in vitro.  Nostoc sp. ATCC 29131 (PCC 6705) was found to contain a
AB  - restriction enzyme, NspBII, with hitherto unknown specificity, C A/C GC T/G G.
ER  -

TY  - JOUR
AU  - Dwivedi, G.R.
AU  - Sharma, E.
AU  - Rao, D.N.
TI  - Helicobacter pylori DprA alleviates restriction barrier for incoming DNA.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 3274
EP  - 3288
VL  - 41
AB  - Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes
AB  - gastric inflammation. The species is naturally competent and displays remarkable diversity.
AB  - The presence of a large number of restriction-modification (R-M) systems in this bacterium
AB  - creates a barrier against natural transformation by foreign DNA. Yet, mechanisms that protect
AB  - incoming double-stranded DNA (dsDNA) from restriction enzymes are not well understood. A
AB  - DNA-binding protein, DNA Processing Protein A (DprA) has been shown to facilitate natural
AB  - transformation of several Gram-positive and Gram-negative bacteria by protecting incoming
AB  - single-stranded DNA (ssDNA) and promoting RecA loading on it. However, in this study, we
AB  - report that H. pylori DprA (HpDprA) binds not only ssDNA but also dsDNA thereby conferring
AB  - protection to both from various exonucleases and Type II restriction enzymes. Here, we
AB  - observed a stimulatory role of HpDprA in DNA methylation through physical interaction with
AB  - methyltransferases. Thus, HpDprA displayed dual functional interaction with H. pylori R-M
AB  - systems by not only inhibiting the restriction enzymes but also stimulating
AB  - methyltransferases. These results indicate that HpDprA could be one of the factors that
AB  - modulate the R-M barrier during inter-strain natural transformation in H. pylori.
ER  -

TY  - JOUR
AU  - Dwivedi, V.
AU  - Sangwan, N.
AU  - Nigam, A.
AU  - Garg, N.
AU  - Niharika, N.
AU  - Khurana, P.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring  Located atop the Himalayan Ranges at Manikaran, India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3534
EP  - 3534
VL  - 194
AB  - Thermus sp. strain RL was isolated from a hot water spring (90 degrees C to 98 degrees C) at
AB  - Manikaran, Himachal Pradesh, India. Here we report the draft genome
AB  - sequence (20,36,600 bp) of this strain. The draft genome sequence consists of 17
AB  - contigs and 1,986 protein-coding sequences and has an average G+C content of
AB  - 68.77%.
ER  -

TY  - JOUR
AU  - Dwyer, P.A.
AU  - Riftina, F.
AU  - Agarwal, K.L.
TI  - Interaction of HpaI endonuclease with chemically synthesized oligonucleotides.
JO  - Fed. Proc.
PY  - 1979
SP  - 294
EP  - 294
VL  - 38
AB  - The octanucleotide dG-G-T-T-A-A-C-C is cleaved by the restriction endonuclease
AB  - HpaI at the phosphodiester bond between thymidine and adenosine.
AB  - Octanucleotides, containing modified nucleosides in the recognition sequence
AB  - for HpaI, were chemically synthesized by our modified triester method.
AB  - Interaction of the enzyme with dG-G-T-U-A-A-C-C, dG-G-T-U(Br)-A-A-C-C, and
AB  - dG-I-T-T-A-A-C-C will be described.  An octanucleotide, in which the
AB  - phosphodiester bond at the site of cleavage is replaced by its methyl
AB  - phosphonate analogue, was also synthesized and is a reversible inhibitor of the
AB  - HpaI endonuclease.
ER  -

TY  - JOUR
AU  - Dwyer-Hallquist, P.
AU  - Kezdy, F.J.
AU  - Agarwal, K.L.
TI  - Interaction of the HpaI endonuclease with synthetic oligonucleotides.
JO  - Biochemistry
PY  - 1982
SP  - 4693
EP  - 4700
VL  - 21
AB  - To determine which functional groups of bases within the grooves of
AB  - double-helical DNA interact with the HpaI endonuclease, we have employed
AB  - chemically synthesized octanucleotides containing base analogues.  The 5-methyl
AB  - group of thymine was probed as a contact between the HpaI endonuclease and its
AB  - recognition sequence by using the ologonucleotides d(G-G-T-T-A-A-C-C),
AB  - d(G-G-T-U-A-A-C-C), and d(G-G-T-B-A-A-C-C).  The 2-amino group of guanine was
AB  - probed as a contact for the HpaI endonuclease by using the octanucleotide
AB  - d(G-I-T-T-A-A-C-C).  The HpaI endonuclease cleaves octanucleotides
AB  - d(G-G-T-T-A-A-C-C) and d(G-G-T-B-A-A-C-C) according to Michaelis-Menten
AB  - kinetics.  However, both the Km and turnover number for d(G-G-T-B-A-A-C-C) were
AB  - severalfold lower than those for cleave of d(G-G-T-T-A-A-C-C).  In addition,
AB  - d(G-G-T-U A-A-C-C) was not cleaved by HpaI endonuclease, suggesting that the
AB  - 5-methyl group of thymine is a contact between the HpaI endonuclease and its
AB  - recognition sequence.  d(G-I-T-T-A-A-C-C) was not cleaved by the HpaI
AB  - endonuclease which may be due in part to the low thermal stability of the
AB  - duplex.  Nevertheless, our results suggest that the 2-amino group of guanine is
AB  - a contact for the HpaI endonuclease.  A phosphate group 5' external to the HpaI
AB  - recognition sequence has been identified as a contact between the HpaI
AB  - endonuclease and DNA.  The HpaI endonuclease cleaved 5'-phosphorylated
AB  - octanucleotide 30-fold faster than unphosphorylated octanucleotide.  In
AB  - addition, the Km of the d(G-G-T-T-A-A-C-C) was 8000-fold higher than the Km of
AB  - the phage f1 RFI DNA, suggesting that the octanucleotide is too short to take
AB  - advantage of the entire DNA binding site of the enzyme.
ER  -

TY  - JOUR
AU  - Dy, L.
AU  - Chalasani, S.
AU  - Essani, K.
TI  - Isolaton of Escherichia coli mutants lacking methylcytosine-dependent restriction systems for cloning extensively methylated frog virus 3 DNA.
JO  - Gene
PY  - 1993
SP  - 87
EP  - 91
VL  - 131
AB  - Many bacterial strains possess methylation-dependent restriction systems (MDRS) that
AB  - demonstrate methylcytosine-dependent restriction endonuclease activity for the dinucleotide
AB  - sequence, dCpdG. This makes these strains unsuitable for cloning methylated DNA. Some
AB  - commercially available bacterial cells are recommended for cloning DNA fragments with
AB  - methylated cytosines and adenines, e.g., Escherichia coli DH5-alphaMCR. Our attempts to clone
AB  - frog virus 3 (FV3) DNA, which has the highest degree of cytosine methylation ever reported,
AB  - using DH5-alphaMCR cells, were not successful. This and other observations suggested the
AB  - existence of additional MDRS that have not yet been eliminated from DH5-alphaMCR cells. In
AB  - order to isolate a mutant from this bacterial strain that is suitable to clone highly
AB  - methylated FV3 DNA, we transformed these cells with a recombinant pUC19 plasmid containing a
AB  - methylated 1.4-kb genomic DNA fragment from FV3, and selected for ampicillin (Ap) resistance.
AB  - Three such attempts yielded only one colony that contained a fully methylated 1.4-kb FV3
AB  - genomic DNA fragment. Furthermore, plasmid-cured Ap-sensitive colonies originating from this
AB  - clone were isolated and have been successfully employed to clone the highly methylated FV3
AB  - genomic DNA fragment.
ER  -

TY  - JOUR
AU  - Dyachenko, O.V.
AU  - Tarlachkov, S.V.
AU  - Marinitch, D.V.
AU  - Shevchuk, T.V.
AU  - Buryanov, Y.I.
TI  - Expression of exogenous DNA methyltransferases: Application in molecular and cell biology.
JO  - Biokhimiia
PY  - 2014
SP  - 77
EP  - 87
VL  - 79
AB  - DNA methyltransferases might be used as powerful tools for studies in molecular and cell
AB  - biology due to their ability to recognize and modify nitrogen bases in specific sequences of
AB  - the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases
AB  - appears to be a promising approach for studies on chromatin structure. Currently, the
AB  - development of new methods for targeted methylation of specific genetic loci using DNA
AB  - methyltransferases fused with DNA-binding proteins is especially interesting. In the present
AB  - review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the
AB  - functional chromatin structure along with investigation of the functional role of DNA
AB  - methylation in cell processes are discussed, as well as future prospects for application of
AB  - DNA methyltransferases in epigenetic therapy and in plant selection.
ER  -

TY  - JOUR
AU  - Dyachkova, M.S.
AU  - Klimina, K.M.
AU  - Kovtun, A.S.
AU  - Zakharevich, N.V.
AU  - Nezametdinova, V.Z.
AU  - Averina, O.V.
AU  - Danilenko, V.N.
TI  - Draft Genome Sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150: Focusing on the Genes Potentially Involved in the Gut-Brain  Axis.
JO  - Genome Announcements
PY  - 2015
SP  - e00709
EP  - e00715
VL  - 3
AB  - The draft genome sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis
AB  - 150 strains isolated from the human intestinal microbiota are
AB  - reported. Both strains are able to produce gamma-aminobutyric acid (GABA).
AB  - Detailed genomes analysis will help to understand the role of GABA in the
AB  - functioning of gut-brain axis.
ER  -

TY  - JOUR
AU  - Dyall-Smith, M.
AU  - Pfeiffer, F.
AU  - Klee, K.
AU  - Palm, P.
AU  - Gross, K.
AU  - Schuster, S.C.
AU  - Rampp, M.
AU  - Oesterhelt, D.
TI  - Haloquadratum walsbyi: limited diversity in a global pond.
JO  - PLoS ONE
PY  - 2011
SP  - e20968
EP  - e20968
VL  - 6
AB  - Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline
AB  - waters. Its cells are extremely fragile squares requiring .14%(w/v) salt for growth,
AB  - properties that should limit its dispersal and promote geographical isolation and divergence.
AB  - To assess this, the genome sequences of two isolates recovered from sites at near maximum
AB  - distance on Earth, were compared.  Principal Findings: Both chromosomes are 3.1 MB in size,
AB  - and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core
AB  - sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic
AB  - orientation and order), without inversion or rearrangement. Strain-specific
AB  - insertions/deletions could be precisely mapped, often allowing the genetic events to be
AB  - inferred. Many inferred deletions were associated with short direct repeats (4- 20 bp).
AB  - Deletion-coupled insertions are frequent, producing different sequences at identical
AB  - positions. In cases where the inserted and deleted sequences are homologous, this leads to
AB  - variant genes in a common synteneic background (as already described by others). Cas/CRISPR
AB  - systems are present in C23T but have been lost in HBSQ001 except for a few spacer remnants.
AB  - Numerous types of mobile genetic elements occur in both strains, most of which appear to be
AB  - active, and with some specifically targetting others. Strain C23T carries two ,6 kb plasmids
AB  - that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters
AB  - commonly found in haloarchaea. Conclusions: Deletion-coupled insertions show that Hqr. walsbyi
AB  - evolves by uptake and precise integration of foreign DNA, probably originating from close
AB  - relatives. Change is also driven by mobile genetic elements but these do not by themselves
AB  - explain the atypically low gene coding density found in this species. The remarkable genome
AB  - conservation despite the presence of active systems for genome rearrangement implies both an
AB  - efficient global dispersal system, and a high selective fitness for this species.
ER  -

TY  - JOUR
AU  - Dyall-Smith, M.L.
AU  - Liu, Y.
AU  - Billman-Jacobe, H.
TI  - Genome Sequence of an Australian Monophasic Salmonella enterica subsp. enterica Typhimurium Isolate (TW-Stm6) Carrying a Large Plasmid with Multiple  Antimicrobial Resistance Genes.
JO  - Genome Announcements
PY  - 2017
SP  - e00793
EP  - e00717
VL  - 5
AB  - We report the genome sequence of a monophasic Salmonella enterica subsp. enterica Typhimurium
AB  - strain (TW-Stm6) isolated in Australia that is similar to epidemic
AB  - multidrug-resistant strains from Europe and elsewhere. This strain carries
AB  - additional antibiotic and heavy-metal resistance genes on a large (275-kb) IncHI2
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Dyall-Smith, M.L.
AU  - Pfeiffer, F.
AU  - Oberwinkler, T.
AU  - Klee, K.
AU  - Rampp, M.
AU  - Palm, P.
AU  - Gross, K.
AU  - Schuster, S.C.
AU  - Oesterhelt, D.
TI  - Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus.
JO  - Genome Announcements
PY  - 2013
SP  - e0009513
EP  - e0009513
VL  - 1
AB  - The genus Natronomonas contains two species, one haloalkaliphile (N. pharaonis) and one
AB  - neutrophile (N. moolapensis). Here, we report the genome sequence of N.
AB  - moolapensis strain 8.8.11. The overall genome properties are similar for the two
AB  - species. Only the neutrophile contains bacteriorhodopsin and a membrane
AB  - glycolipid.
ER  -

TY  - JOUR
AU  - Dybvig, K.
AU  - Cao, Z.
AU  - French, C.T.
AU  - Yu, H.
TI  - Evidence for type III restriction and modification systems in Mycoplasma pulmonis.
JO  - J. Bacteriol.
PY  - 2007
SP  - 2197
EP  - 2202
VL  - 189
AB  - Mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type III
AB  - restriction and modification (R-M) enzymes. Transposon
AB  - disruption of a gene predicted to code for the endonuclease subunit of the
AB  - enzyme resulted in loss of R-M activity. Genomic data indicate that the
AB  - cassette was acquired by horizontal gene transfer and possibly located on
AB  - a mobile element.
ER  -

TY  - JOUR
AU  - Dybvig, K.
AU  - Sitaraman, R.
AU  - French, C.T.
TI  - A family of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangements.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 13923
EP  - 13928
VL  - 95
AB  - The hsd genes of Mycoplasma pulmonis encode restriction and modification enzymes exhibiting a
AB  - high degree of sequence similarity to the type I enzymes of enteric bacteria.  The S subunits
AB  - of type I systems dictate the DNA sequence specificity of the holoenzyme and are required for
AB  - both the restriction and the modification reactions.  The M. pulmonis chromosome has two hsd
AB  - loci, both of which contains two hsdS genes each and are complex, site-specific DNA inversion
AB  - systems.  Embedded within the coding regions of each hsdS gene are a minimum of three sites at
AB  - which DNA inversions occur to generate extensive amino acid sequence variations in the
AB  - predicted S subunits.  We show that the polymorphic hsdS genes produced by gene rearrangement
AB  - encode a family of functional S subunits with differing DNA sequence specificities.  In
AB  - addition to creating polymorphisms in hsdS sequences, DNA inversions regulate the
AB  - phase-variable production of restriction activity because the other genes required for
AB  - restriction activity (hsdR and hsdM) are expressed only from loci that are oriented
AB  - appropriately in the chromosome relative to the hsd promoter.  These data cast doubt on the
AB  - prevailing paradigms that restriction systems are either selfish or function to confer
AB  - protection from invasion by foreign DNA.
ER  -

TY  - JOUR
AU  - Dybvig, K.
AU  - Swinton, D.
AU  - Maniloff, J.
AU  - Hattman, S.
TI  - Cytosine methylation of the sequence GATC in a mycoplasma.
JO  - J. Bacteriol.
PY  - 1982
SP  - 1420
EP  - 1424
VL  - 151
AB  - Mycoplasma virus L2 is subject to host-specific restriction and modification in
AB  - Acholeplasma laidlawii strains JA1 and K2.  We have examined the DNAs from both
AB  - host cells and viruses propagated on these strains with respect to
AB  - susceptibility to cleavage by restriction endonucleases and for DNA base
AB  - modifications.  We show that, in strain K2 and L2 virus grown on K2 cells,
AB  - cytosine in the sequence GATC is methylated to 5-methylcytosine and, although
AB  - strain K2 and L2 viruses grown on K2 contain N6-methyladenine in their DNA,
AB  - adenine in the sequence GATC is not methylated.  In contrast to K2, strain JA1
AB  - and L2 virus grown on JA1 cells contain no detectable methylated bases.  It is
AB  - not known which of the methylated bases in K2 is the basis for the K2
AB  - restriction-modification system operative on L2 virus.
ER  -

TY  - JOUR
AU  - Dybvig, K.
AU  - Voelker, L.L.
TI  - Molecular biology of mycoplasmas.
JO  - Annu. Rev. Microbiol.
PY  - 1996
SP  - 25
EP  - 57
VL  - 50
AB  - Although mycoplasmas lack cell walls, they are in many respects similar to the gram-positive
AB  - bacteria with which they share a common ancestor.  The molecular biology of mycoplasmas is
AB  - intriguing because the chromosome is uniquely small (<600 kb in some species) and extremely
AB  - A-T rich (as high as 75 mol% in some species).  Perhaps to accommodate DNA with a lower G+C
AB  - content, most mycoplasmas do not have the "universal" genetic code.  In these species, TGA is
AB  - not a stop codon; instead it encodes tryptophan at a frequency 10 times greater than TGG, the
AB  - usual codon for this amino acid.  Because of the presence of TGA codons, the translation of
AB  - mycoplasmal proteins terminates prematurely when cloned genes are expressed in other
AB  - eubacteria, such as Escherichia coli.  Many mycoplasmas possess strikingly dynamic chromosomes
AB  - in which high-frequency changes result from errors in DNA repair or replication and from
AB  - highly active recombination systems.  Often, high-frequency changes in the mycoplasmal
AB  - chromosome are associated with antigenic and phase variation, which regulate the production of
AB  - factors critical to disease pathogenesis.
ER  -

TY  - JOUR
AU  - Dybvig, K.
AU  - Yu, H.
TI  - Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis.
JO  - Mol. Microbiol.
PY  - 1994
SP  - 547
EP  - 560
VL  - 12
AB  - An invertible DNA element of 6.8kb, designated the hsd1 locus, was identified in the
AB  - chromosome of Mycoplasma pulmonis. Infection of host cells with mycoplasma virus P1 revealed
AB  - that the organism's restriction and modification (R-M) properties are controlled by inversion
AB  - of hsd1. The nucleotide sequence of hsd1 revealed several genes, the predicted amino acids of
AB  - which bear striking similarity to the subunits of the type I R-M enzymes previously found only
AB  - in enteric bacteria.
ER  -

TY  - JOUR
AU  - Dybwad, M.
AU  - Aarskaug, T.
AU  - Fykse, E.M.
AU  - Henie, M.E.
AU  - Blatny, J.M.
TI  - Complete Genome Sequences of Six Legionella pneumophila Isolates from Two Collocated Outbreaks of Legionnaires' Disease in 2005 and 2008 in  Sarpsborg/Fredrikstad, Norway.
JO  - Genome Announcements
PY  - 2016
SP  - e01367
EP  - e01316
VL  - 4
AB  - Here, we report the complete genome sequences of Legionella pneumophila isolates  from two
AB  - collocated outbreaks of Legionnaires' disease in 2005 and 2008 in
AB  - Sarpsborg/Fredrikstad, Norway. One clinical and two environmental isolates were
AB  - sequenced from each outbreak. The genome of all six isolates consisted of a 3.36
AB  - Mb-chromosome, while the 2005 genomes featured an additional 68 kb-episome
AB  - sharing high sequence similarity with the L. pneumophila Lens plasmid. All six
AB  - genomes contained multiple mobile genetic elements including novel combinations
AB  - of type-IVA secretion systems. A comparative genomics study will be launched to
AB  - resolve the genetic relationship between the L. pneumophila isolates.
ER  -

TY  - JOUR
AU  - Dymova, M.A.
AU  - Alkhovik, O.I.
AU  - Evdokimova, L.S.
AU  - Cherednichenko, A.G.
AU  - Petrenko, T.I.
TI  - Complete Genome Sequence of a Novel Clinical Isolate, Mycobacterium abscessus Strain NOV0213.
JO  - Genome Announcements
PY  - 2016
SP  - e01407
EP  - e01415
VL  - 4
AB  - Mycobacterium abscessus is a rapid-growing species of nontuberculous mycobacteria that is
AB  - frequently associated with opportunistic infections in humans. We determined the complete
AB  - genome sequence of the M. abscessus strain NOV0213, which was isolated from a patient with
AB  - tuberculosis-like disease and with various antibiotic resistances.
ER  -

TY  - JOUR
AU  - Dynan, W.
AU  - Fox, K.
AU  - Stoddard, B.
TI  - Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 1
EP  - 2
VL  - 42
AB  - In this issue, Nucleic Acids Research presents five Survey and Summary articles that describe
AB  - the historical development of studies on restriction endonucleases and summarize much of our
AB  - current understanding of this diverse and complex group of enzymes. The first of these
AB  - articles, entitled 'Highlights of the DNA cutters: a short history of the restriction
AB  - enzymes' (1), describes seminal studies on bacteriophage host restriction, details subsequent
AB  - work on type I and type III enzymes that established the restriction-modification (RM)
AB  - paradigm and summarizes other landmark events that led to restriction enzymes becoming a main
AB  - driving force in the development of modern biotechnology and molecular medicine. Other Survey
AB  - and Summary articles in this issue describe three of the major types of RM systems as they are
AB  - understood today (2-4). The different types of RM systems-of which there are currently four-
AB  - vary in their cofactor dependence, in the spatial relationship of DNA binding and cleavage
AB  - sites and in the way in which endonuclease and modification activities are physically and
AB  - mechanistically coupled to one another. The last of the Survey and Summary articles in this
AB  - issue discusses RM systems in the broader context of toxin-antitoxin genetic systems, which
AB  - exist in great variety throughout the microbial world (5).
ER  -

TY  - JOUR
AU  - Dyson, P.
AU  - Evans, M.
TI  - Novel post-replicative DNA modification in Streptomyces: analysis of the preferred modification site of plasmid pIJ101.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1248
EP  - 1253
VL  - 26
AB  - Both Streptomyces lividans and Streptomyces avermitilis have the ability to site  specifically
AB  - modify their DNA, rendering it susceptible to in vitro
AB  - Tris-dependent double-strand cleavage. We have cloned a 160 bp fragment
AB  - containing the preferred modification site of plasmid pIJ101 and, employing an in
AB  - vitro primer extension assay, determined that the modifications occur at guanine
AB  - residues on either strand separated by 3 bp. These guanines are located within a
AB  - 6 bp palindromic 'core' sequence. A cloned copy of a 35 bp region of the plasmid
AB  - containing this core sequence was not recognized by the modifying activity in
AB  - vivo. To further investigate the nature of the site specificity a set of deletion
AB  - mutants of the 160 bp sequence were analysed. This revealed that a substantial
AB  - portion of this sequence is essential for authentic modification. The essential
AB  - region contains three 13 bp direct repeats, the central one containing the core
AB  - sequence, while the left-hand and right-hand copies overlap two potential
AB  - stem-loop structures. Deletion of either left- or right-hand repeat structures
AB  - abolishes modification within the core sequence, although the left-hand deletion
AB  - resulted in modification at a secondary site within the right-hand direct repeat.
AB  - These data support a post-replicative mechanism of modification, underlined by
AB  - the observation that the modifications are not detected in single-stranded
AB  - plasmid replication intermediates.
ER  -

TY  - JOUR
AU  - Dziewit, L.
AU  - Adamczuk, M.
AU  - Szuplewska, M.
AU  - Bartosik, D.
TI  - DIY series of genetic cassettes useful in construction of versatile = vectors specific for Alphaproteobacteria.
JO  - J. Microbiol. Methods
PY  - 2011
SP  - 166
EP  - 174
VL  - 86
AB  - We have developed a DIY (Do It Yourself) series of genetic casset=
AB  - tes, which facilitate construction of novel versatile vectors for
AB  - Alphaproteobacteria. All the cassettes are based on defined genetic
AB  - modules derived from three natural plasmids of Paracoccus aminophilus JCM
AB  - 7686. We have constructed over 50 DIY cassettes, which differ in structure
AB  - and specific features. All of them are functional in eight strains
AB  - representing three orders of Alphaproteobacteria: Rhodobacterales,
AB  - Rhizobiales and Caulobacterales. Besides various replication and
AB  - stabilization systems, many of the cassettes also contain selective
AB  - markers appropriate for Alphaproteobacteria (40 cassettes) and genetic
AB  - modules responsible for mobilization for conjugal transfer (24 cassettes).
AB  - All the DIY cassettes are bordered by different types of polylinkers,
AB  - which facilitate vector construction. Using these DIY cassettes, we have
AB  - created a set of compatible Escherichia coli-Alphaproteobacteria
AB  - mobilizable shuttle vectors (high or low copy number in E. coli), which
AB  - will greatly assist the genetic manipulation of Alphaproteobacteria.
ER  -

TY  - JOUR
AU  - Dziewit, L.
AU  - Bartosik, D.
TI  - Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments.
JO  - Front. Microbiol.
PY  - 2014
SP  - 596
EP  - 596
VL  - 5
AB  - Extremely cold environments are a challenge for all organisms. They are mostly inhabited by
AB  - psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the
AB  - cold. Such harsh environments are often highly vulnerable to the influence of external factors
AB  - and may undergo frequent dynamic changes. The rapid adjustment of bacteria to changing
AB  - environmental conditions is crucial for their survival. Such 'short-term' evolution is often
AB  - enabled by plasmids-extrachromosomal replicons that represent major players in horizontal gene
AB  - transfer. The genomic sequences of thousands of microorganisms, including those of many
AB  - cold-active bacteria have been obtained over the last decade, but the collected data have yet
AB  - to be thoroughly analyzed. This report describes the results of a meta-analysis of the NCBI
AB  - sequence databases to identify and characterize plasmids of psychrophilic and psychrotolerant
AB  - bacteria. We have performed in-depth analyses of 66 plasmids, almost half of which are cryptic
AB  - replicons not exceeding 10 kb in size. Our analyses of the larger plasmids revealed the
AB  - presence of numerous genes, which may increase the phenotypic flexibility of their host
AB  - strains. These genes encode enzymes possibly involved in (i) protection against cold and
AB  - ultraviolet radiation, (ii) scavenging of reactive oxygen species, (iii) metabolism of amino
AB  - acids, carbohydrates, nucleotides and lipids, (iv) energy production and conversion, (v)
AB  - utilization of toxic organic compounds (e.g., naphthalene), and (vi) resistance to heavy
AB  - metals, metalloids and antibiotics. Some of the plasmids also contain type II
AB  - restriction-modification systems, which are involved in both plasmid stabilization and
AB  - protection against foreign DNA. Moreover, approx. 50% of the analyzed plasmids carry genetic
AB  - modules responsible for conjugal transfer or mobilization for transfer, which may facilitate
AB  - the spread of these replicons among various bacteria, including across species boundaries.
ER  -

TY  - JOUR
AU  - Dziewit, L.
AU  - Cegielski, A.
AU  - Romaniuk, K.
AU  - Uhrynowski, W.
AU  - Szych, A.
AU  - Niesiobedzki, P.
AU  - Zmuda-Baranowska, M.J.
AU  - Zdanowski, M.K.
AU  - Bartosik, D.
TI  - Plasmid diversity in arctic strains of Psychrobacter spp.
JO  - Extremophiles
PY  - 2013
SP  - 433
EP  - 444
VL  - 17
AB  - Six strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen
AB  - island (Arctic) carried nine plasmids that
AB  - were fully sequenced. These replicons (ranging in size from 2917 to
AB  - 14924 bp) contained either repA (ColE2-type) or repB (iteron-type)
AB  - replication systems of a relatively narrow host range, limited to
AB  - Psychrobacter spp. All but one of the plasmids carried predicted
AB  - mobilization for conjugal transfer systems, encoding relaxases of the
AB  - MOBQ, MOBV or MOBP families. The plasmids also contained diverse
AB  - additional genetic load, including a type II restriction-modification
AB  - system and a gene encoding a putative subunit C of alkyl hydroperoxide
AB  - reductase (AhpC)-an antioxidant enzyme and major scavenger of reactive
AB  - oxygen species. Detailed comparative sequence analyses, extended to all
AB  - plasmids identified so far in psychrophilic bacteria, distinguished
AB  - groups of the most ubiquitous replicons, which play a key role in
AB  - horizontal gene transfer in cold environments.
ER  -

TY  - JOUR
AU  - Dziewit, L.
AU  - Kuczkowska, K.
AU  - Adamczuk, M.
AU  - Radlinska, M.
AU  - Bartosik, D.
TI  - Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686.
JO  - FEMS Microbiol. Lett.
PY  - 2011
SP  - 56
EP  - 63
VL  - 324
AB  - Plasmid pAMI7 of the methylotrophic bacterium Paracoccus aminophilus JCM 7686
AB  - (Alphaproteobacteria) encodes a functional type II
AB  - restriction-modification (R-M) system designated PamI. Homologous
AB  - systems were identified in the genomes of distinct taxonomic groups of
AB  - Bacteria and Archaea, which provides evidence that horizontal gene
AB  - transfer has contributed to the wide dissemination of R-M modules -
AB  - even between domains. Analysis of the cleavage specificity of the R.
AB  - PamI endonuclease revealed that this protein is an isoschizomer of
AB  - restriction enzyme NcoI. Interestingly, bioinformatic analyses suggest
AB  - that R. PamI and NcoI are accompanied by methyltransferases of
AB  - different methylation specificities (C5-methylcytosine and
AB  - N4-methylcytosine methyltransferases, respectively), which possibly
AB  - exemplifies recombinational shuffling of genes coding for individual
AB  - components of R-M systems. The PamI system can stabilize plasmid pAMI7
AB  - in a bacterial population, most probably at the postsegregational
AB  - level. Therefore, it functions in an analogous manner to
AB  - plasmid-encoded toxin-antitoxin (TA) systems. Since the TA system of
AB  - pAMI7 is nonfunctional, it is highly probable that this lack is
AB  - compensated by the stabilizing activity of PamI. This indicates the
AB  - crucial role of the analyzed R-M system in the stable maintenance of
AB  - pAMI7, which is, to our knowledge, the first report of 'symbiosis'
AB  - between a R-M system and a plasmid in the Alphaproteobacteria.
ER  -

TY  - JOUR
AU  - Dziewit, L.
AU  - Oscik, K.
AU  - Bartosik, D.
AU  - Radlinska, M.
TI  - Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, Phi LM21, Encoding DNA Methyltransferase with CcrM-Like Specificity.
JO  - J. Virol.
PY  - 2014
SP  - 13111
EP  - 13124
VL  - 88
AB  - Phi LM21 is a temperate phage isolated from Sinorhizobium sp. strain LM21
AB  - (Alphaproteobacteria). Genomic analysis and electron microscopy suggested that Phi LM21 is a
AB  - member of the family Siphoviridae. The phage has an isometric head and a long noncontractile
AB  - tail. The genome of Phi LM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative
AB  - proteins, including proteins responsible for the assembly of the phage particles, DNA
AB  - packaging, transcription, replication, and lysis. Virion proteins were characterized using
AB  - mass spectrometry, leading to the identification of the major capsid and tail components, tape
AB  - measure, and a putative portal protein. We have confirmed the activity of two gene products, a
AB  - lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity
AB  - with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly,
AB  - the genome of Sinorhizobium phage Phi LM21 shows very limited similarity to other known phage
AB  - genome sequences and is thus considered unique.IMPORTANCEProphages are known to play an
AB  - important role in the genomic diversification of bacteria via horizontal gene transfer. The
AB  - influence of prophages on pathogenic bacteria is very well documented. However, our knowledge
AB  - of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial
AB  - hosts is still limited. In particular, information on prophages of the agronomically important
AB  - Sinorhizobium species is scarce. In this study, we describe the isolation and molecular
AB  - characterization of a novel temperate bacteriophage, Phi LM21, of Sinorhizobium sp. LM21.
AB  - Since we have not found any similar sequences, we propose that this bacteriophage is a novel
AB  - species. We conducted a functional analysis of selected proteins. We have demonstrated that
AB  - the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating
AB  - methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host
AB  - regulatory mechanisms by viruses is quite common in bacteriophages.
ER  -

TY  - JOUR
AU  - Earl, A.M.
AU  - Desjardins, C.A.
AU  - Fitzgerald, M.G.
AU  - Arachchi, H.M.
AU  - Zeng, Q.
AU  - Mehta, T.
AU  - Griggs, A.
AU  - Birren, B.W.
AU  - Toney, N.C.
AU  - Carr, J.
AU  - Posey, J.
AU  - Butler, W.R.
TI  - High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 389
EP  - 397
VL  - 5
AB  - Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus
AB  - in the family Segniliparaceae. A unique and interesting feature of
AB  - this family is the presence of extremely long carbon-chain length mycolic acids
AB  - bound in the cell wall. S. rugosus is also a medically important species because
AB  - it is an opportunistic pathogen associated with mammalian lung disease. This
AB  - report represents the second species in the genus to have its genome sequenced.
AB  - The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part
AB  - of the NIH Roadmap for Medical Research, Human Microbiome Project.
ER  -

TY  - JOUR
AU  - Earl, A.M.
AU  - Eppinger, M.
AU  - Fricke, W.F.
AU  - Rosovitz, M.J.
AU  - Rasko, D.A.
AU  - Daugherty, S.
AU  - Losick, R.
AU  - Kolter, R.
AU  - Ravel, J.
TI  - Whole-Genome Sequences of Bacillus subtilis and Close Relatives.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2378
EP  - 2379
VL  - 194
AB  - We sequenced four strains of Bacillus subtilis and the type strains for two closely related
AB  - species, Bacillus vallismortis and Bacillus mojavensis. We report
AB  - the high-quality Sanger genome sequences of B. subtilis subspecies subtilis
AB  - RO-NN-1 and AUSI98, B. subtilis subspecies spizizenii TU-B-10(T) and DV1-B-1,
AB  - Bacillus mojavensis RO-H-1(T), and Bacillus vallismortis DV1-F-3(T).
ER  -

TY  - JOUR
AU  - Eastberg, J.H.
AU  - Eklund, J.
AU  - Monnat, R.
AU  - Stoddard, B.L.
TI  - Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.
JO  - Biochemistry
PY  - 2007
SP  - 7215
EP  - 7225
VL  - 46
AB  - Several unique protein folds that catalyze the hydrolysis of phosphodiester bonds have arisen
AB  - independently in nature, including the
AB  - PD(D/E)XK superfamily (typified by type II restriction endonucleases
AB  - and many recombination and repair enzymes) and the HNH superfamily
AB  - (found in an equally wide array of enzymes, including bacterial
AB  - colicins and homing endonucleases). Whereas the identity and position
AB  - of catalytic residues within the PD(D/E)XK superfamily are highly
AB  - variable, the active sites of HNH nucleases are much more strongly
AB  - conserved. In this study, the ability of an HNH nuclease to tolerate a
AB  - mutation of its most conserved catalytic residue (its histidine general
AB  - base), and the mechanism of the most active enzyme variant, were
AB  - characterized. Conversion of this residue into several altered
AB  - chemistries, glutamine, lysine, or glutamate, resulted in measurable
AB  - activity. The histidine to glutamine mutant displays the highest
AB  - residual activity and a pH profile similar to that of the wild-type
AB  - enzyme. This activity is dependent on the presence of a neighboring
AB  - imidazole ring, which has taken over as a less efficient general base
AB  - for the reaction. This result implies that mutational pathways to
AB  - alternative HNH-derived catalytic sites do exist but are not as
AB  - extensively or successfully diverged or reoptimized in nature as
AB  - variants of the PD(D/E)XK nuclease superfamily. This is possibly due to
AB  - multiple steric constraints placed on the compact HNH motif, which is
AB  - simultaneously involved in protein folding, DNA binding, and catalysis,
AB  - as well as the use of a planar, aromatic imidazole group as a general
AB  - base.
ER  -

TY  - JOUR
AU  - Eastberg, J.H.
AU  - Smith, A.M.
AU  - Zhao, L.
AU  - Ashworth, J.
AU  - Shen, B.W.
AU  - Stoddard, B.L.
TI  - Thermodynamics of DNA target site recognition by homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 7209
EP  - 7221
VL  - 35
AB  - The thermodynamic profiles of target site recognition have been surveyed for homing
AB  - endonucleases from various structural families. Similar to
AB  - DNA-binding proteins that recognize shorter target sites, homing
AB  - endonucleases display a narrow range of binding free energies and
AB  - affinities, mediated by structural interactions that balance the magnitude
AB  - of enthalpic and entropic forces. While the balance of DeltaH and TDeltaS
AB  - are not strongly correlated with the overall extent of DNA bending,
AB  - unfavorable DeltaH(binding) is associated with unstacking of individual
AB  - base steps in the target site. The effects of deleterious basepair
AB  - substitutions in the optimal target sites of two LAGLIDADG homing
AB  - endonucleases, and the subsequent effect of redesigning one of those
AB  - endonucleases to accommodate that DNA sequence change, were also measured.
AB  - The substitution of base-specific hydrogen bonds in a wild-type
AB  - endonuclease/DNA complex with hydrophobic van der Waals contacts in a
AB  - redesigned complex reduced the ability to discriminate between sites, due
AB  - to nonspecific DeltaS(binding).
ER  -

TY  - JOUR
AU  - Eastman, A.W.
AU  - Weselowski, B.
AU  - Nathoo, N.
AU  - Yuan, Z.C.
TI  - Complete Genome Sequence of Paenibacillus polymyxa CR1, a Plant Growth-Promoting  Bacterium Isolated from the Corn Rhizosphere Exhibiting Potential for Biocontrol,  Biomass Degradation, and Biofuel Production.
JO  - Genome Announcements
PY  - 2014
SP  - e01218
EP  - e01213
VL  - 2
AB  - Here we report the complete genome sequence of the bacterium Paenibacillus polymyxa CR1
AB  - (accession no. CP006941), which consists of one circular chromosome
AB  - of 6,024,666 bp with 5,283 coding sequences (CDS), 87 tRNAs, and 12 rRNA operons.
AB  - Data presented will allow for further insights into the mechanisms underpinning
AB  - agriculturally and industrially relevant processes.
ER  -

TY  - JOUR
AU  - Eberhard, J.
AU  - Oza, J.
AU  - Reich, N.O.
TI  - Cloning, sequence analysis and heterologous expression of the DNA adenine-(N-6) methyltransferase from the human pathogen Actinobacillus actinomycetemcomitans.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 223
EP  - 229
VL  - 195
AB  - We cloned and sequenced the DNA adenine-N-6 methyltransferase gene of the human pathogen
AB  - Actinobacillus actinomycetemcomitans (M.AacDAM).
AB  - Restriction digestion shows that the enzyme methylates adenine in the
AB  - sequence GATC. Expression of the enzyme in a DAM(-) background shows in
AB  - vivo activity. A PSI-BLAST search revealed that M.AacDAM is most
AB  - related to M.HindIV. M.EcoDAM, M.StyDAM. and M.Small. The ClustalW
AB  - alignment shows highly conserved regions in the enzyme characteristic
AB  - for type a MTases. Phylogenetic tree analysis shows a cluster of
AB  - enzymes recognizing the sequence GATC, within a branch of orphan MTases
AB  - harboring M.AacDAM, The cloning and sequencing of this first
AB  - methyltransferase gene described for A. actinomycetemcomitans open the
AB  - path for studies on the potential regulatory impact of DNA methylation
AB  - on gene regulation and virulence in this organism.
ER  -

TY  - JOUR
AU  - Eberhart, L.
AU  - Deringer, J.R.
AU  - Brayton, K.A.
AU  - Sawant, A.
AU  - Besser, T.E.
AU  - Call, D.R.
TI  - Characterization of a novel microcin that kills enterohemorrhagic E. coli O157:H7 and O26.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 6592
EP  - 6599
VL  - 78
AB  - A novel phenotype was recently identified whereby specific strains of Escherichia
AB  - coli inhibit competing E. coli via a mechanism that was designated
AB  - "proximity-dependent inhibition" (PDI). PDI-expressing E. coli (PDI(+)) is known
AB  - to inhibit susceptible E. coli strains (PDI(-)), including several
AB  - enterohemorrhagic (EHEC) and enterotoxigenic (ETEC) strains. In this study every
AB  - strain from a genetically diverse panel of E. coli O157:H7 (n=25) and additional
AB  - strains of E. coli serovar O26 were susceptible to the PDI phenotype. Live-dead
AB  - staining was consistent with inhibition by killing of susceptible cells.
AB  - Comparative genome analysis identified the genetic component of PDI, which is
AB  - composed of a plasmid-borne (Incl1) operon encoding a putative microcin and
AB  - associated genes for transport, immunity, and microcin activation. Transfer of
AB  - the plasmid to a PDI(-) strain resulted in transfer of the phenotype and deletion
AB  - of the genes within the operon resulted in loss of the inhibition phenotype.
AB  - Deletion of chromosomally encoded tolC also resulted in loss of the inhibitory
AB  - phenotype and this confirmed that the putative microcin is most likely secreted
AB  - via a type I secretion pathway. Deletion of an unrelated plasmid gene did not
AB  - affect the PDI phenotype. Quantitative RT-PCR demonstrated that microcin
AB  - expression is correlated with logarithmic-phase growth. The ability to inhibit a
AB  - diversity of E. coli strains indicates this microcin may influence gut community
AB  - composition and could be useful for control of important enteric pathogens.
ER  -

TY  - JOUR
AU  - Eby, J.C.
AU  - Turner, L.
AU  - Nguyen, B.
AU  - Kang, J.
AU  - Neville, C.
AU  - Temple, L.
TI  - Complete Genome Sequence of Bordetella pertussis Strain VA-190 Isolated from a Vaccinated 10-Year-Old Patient with Whooping Cough.
JO  - Genome Announcements
PY  - 2016
SP  - e00972
EP  - e00916
VL  - 4
AB  - The number of cases of pertussis has increased in the United States despite vaccination. We
AB  - present the genome of an isolate of Bordetella pertussis from a
AB  - vaccinated patient from Virginia. The genome was sequenced by long-read
AB  - methodology and compared to that of a clinical isolate used for laboratory
AB  - studies, D420.
ER  -

TY  - JOUR
AU  - Eckstein, F.
TI  - Action of restriction endonucleases on phosphorothioate DNA.
JO  - Biochem. Soc. Trans.
PY  - 1986
SP  - 204
EP  - 205
VL  - 14
AB  - Phosphorothioate analogues of nucleotides possess a number of properties which
AB  - make then interesting compounds for biochemists (Eckstein, 1983).  One of these
AB  - is the often slow rate of enzyme-catalysed hydrolysis of these analogues in
AB  - comparson with the natural compounds.  Thus it has been shown that
AB  - phosphorothioate internucleotidic linkages in DNA are either not or only slowly
AB  - hydrolysed by exonuclease III and the 5' - 3' exonuclease activity of
AB  - polymerase I.  An early observation indicated that at least some restriction
AB  - endonucleases might hydrolyse such groups more slowly than the unmodified
AB  - linkages (Vosberg & Eckstein, 1982).  As restriction endonucleases have found
AB  - wide application in the manipulation of DNA and as this observation might offer
AB  - the possibility of blocking specific sites in DNA against hydrolysis by these
AB  - enzymes, it was decided to initiate a more detailed investigation on the
AB  - interaction of restriction endonucleases with phosphorothioate-containing
AB  - oligonucleotides and DNA.
ER  -

TY  - JOUR
AU  - Eckstein, F.
TI  - Interaction of DNA containing phosphorothioate groups with restriction enzymes.
JO  - Ann. NY Acad. Sci.
PY  - 1986
SP  - 217
EP  - 225
VL  - 471
AB  - Phosphorothioate analogues of nucleotides have become very valuable tools in
AB  - enzymology.  The interest in these compounds is based on a variety of
AB  - properties that distinguish them from the naturally occurring nucleotides.
AB  - These are the generally slow rate of enzymatic hydrolysis of phosphorothioates,
AB  - the chirality of the generally slow rate of enzymatic hydrolysis of
AB  - phosphorothioates, the chirality of the phosphorous when the phosphorothioate
AB  - is linked to two nonidentical groups, and the affinity to metal ions.  The
AB  - various applications of phosphorothioate analogues of nucleotides to the study
AB  - of enzyme mechanisms have been reviewed extensively in recent years.  In this
AB  - article the effect of incorporation of phosphorothioate groups into DNA will be
AB  - discussed.
ER  -

TY  - JOUR
AU  - Eckstein, F.
TI  - Phosphorothioation of DNA in bacteria.
JO  - Nat. Chem. Biol.
PY  - 2007
SP  - 689
EP  - 690
VL  - 3
AB  - A phosphorothioate modificaiton of DNA has been identified in bacteria.  This first observed
AB  - alteration of the DNA phosphate backbone opens many questions about themechanism of sulfur
AB  - incoporation and the function of this modification.
ER  -

TY  - JOUR
AU  - Eckstein, F.
AU  - Connolly, B.A.
AU  - Potter, V.V.L.
TI  - Cleavage of phosphorothioate-containing oligonucleotides and DNA by restriction endonucleases.
JO  - Abteil. Chem.
PY  - 1987
SP  - 23
EP  - 27
VL  - 8
AB  - The oligonucleotide d(GGsAATTCC) containing the recognition sequence of the
AB  - EcoRI restriction endonuclease with a phosphorothioate group at the site of
AB  - cleavage was synthesized by two approaches both based on the polymer support
AB  - phophoroamidite method.  Only the Rp-diastereomer was cleaved by EcoRI, at a
AB  - rate approximately 20 times slower than the all-phosphate-containing octamer.
AB  - To study the interaction of restriction endonucleases with phosphorothioate
AB  - internucleotide linkages double stranded M13mp2 DNA was prepared in which the
AB  - (+)strand contained only phosphate groups but the (-)strand contained phosphate
AB  - groups as well as base specifically introduced phosphorothioate groups of the
AB  - Rp-configuration.  This hybrid DNA was cleaved by several restriction enzymes.
AB  - The results obtained allow the classification of these enzymes into three
AB  - groups:  those which produce nicked DNA as an isolatable intermediate, those
AB  - where the nicked DNA is the final product and a third where ony linearised DNA
AB  - can be detected.  Particularly the second class of enzymes should be of
AB  - interest for the manipulation of DNA.
ER  -

TY  - JOUR
AU  - Eckweiler, D.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Overmann, J.
AU  - Haussler, S.
TI  - Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265.
JO  - Genome Announcements
PY  - 2014
SP  - e01232
EP  - e01213
VL  - 2
AB  - The evolution of small-colony variants within Pseudomonas aeruginosa populations  chronically
AB  - infecting the cystic fibrosis lung is one example of the emergence of
AB  - adapted subpopulations. Here, we present the complete genome sequence of the
AB  - autoaggregative and hyperpiliated P. aeruginosa small-colony variant SCV20265,
AB  - which was isolated from a cystic fi brosis (CF) patient.
ER  -

TY  - JOUR
AU  - Eddy, S.R.
AU  - Gold, L.
TI  - The phage T4 nrdB intron: a deletion mutant of a version found in the wild.
JO  - Genes Dev.
PY  - 1991
SP  - 1032
EP  - 1041
VL  - 5
AB  - Bacteriophage T4 possesses three self-splicing group I introns. Two of the three introns are
AB  - mobile elements; the third, in the gene encoding a subunit of the phage nucleotide reductase
AB  - (nrdB), is not mobile. Because intron mobility offers a reasonable explanation for the
AB  - paradoxical occurrence of large intervening sequences in a space-efficient eubacterial phage,
AB  - it is puzzling that the nrdB intron is not mobile like its compatriots. We have discovered a
AB  - larger nrdB intron in a closely related phage, and we infer from comparative sequence data
AB  - that the T4 intron is a deletion mutant derived from this larger intron. This larger nrdB
AB  - intron encodes an open reading frame of 269 codons, which we have cloned and overexpressed.
AB  - The overexpressed protein shows a dsDNA endonuclease activity for the intronless nrdB gene,
AB  - typical of mobile introns. Thus, we believe that all three introns of T4 are or were mobile
AB  - "infectious introns" and that they have entered into and been maintained in the phage
AB  - population by virtue of this efficient mobility.
ER  -

TY  - JOUR
AU  - Eddy, S.R.
AU  - Gold, L.
TI  - Artificial mobile DNA element constructed from the EcoRI endonuclease gene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 1544
EP  - 1547
VL  - 89
AB  - There exist several examples of mobile group I introns.  These introns appear
AB  - to use a straightforward mechanism to achieve highly site-specific and
AB  - efficient insertion into homologous intronless genes.  Because the only
AB  - intron-specific function required by the prevailing model for the mechanism  of
AB  - intron mobility is the introduction of a site-specific double-stranded break in
AB  - the intronless recipient DNA molecule, we reasoned that it should in principle
AB  - be possible to construct an artificially mobile element from the gene for the
AB  - restriction enzyme EcoRI that is capable of site-specific insertion at rates
AB  - near those of authentic mobile introns.  The generality of the mobility
AB  - mechanism may enable high-efficiency targeted gene replacements or disruptions
AB  - in a variety of organisms.
ER  -

TY  - JOUR
AU  - Edgell, D.
AU  - Kleinstiver, B.
AU  - Wolfs, J.M.
AU  - Wang, L.
AU  - Kolaczyk, T.
AU  - McDowell, B.
AU  - Bogdanove, A.
TI  - Genome engineering nucleases derived from GIY-YIG homing endonucleases.
JO  - J. Biomol. Struct. Dyn.
PY  - 2013
SP  - 64
EP  - 65
VL  - 31
AB  - Efficient targeted manipulation of complex genomes requires highly specific endonucleases to
AB  - generate double-strand breaks at defined locations.  The predominantly engineered nucleases,
AB  - zinc-finger nucleases and TAL effector nucleases use the catalytic domain of FokI as the
AB  - nuclease portion.  This domain, however, functions as a dimer to nonspecifically cleave DNA
AB  - meaning that ZFNs and TALENs must be designed in head-to-head pairs to target a desired
AB  - sequence.  To overcome this limitation and expand the toolbox of genome editing reagents, we
AB  - used the N-terminal catalytic domain and interdomain linker of the monomeric GIY-YIG homing
AB  - endonuclease I-TevI to create I-TevI-zinc-fingers, and I-TevI-TAL effectors.  We also made
AB  - I-TevI fusions to LAGLIDADGs homing endonucleases.  All the three fusions showed activity on
AB  - model substates on par with ZFNs and TALENs in yeast-based recombination assays.  These
AB  - proof-of-concept experiments demonstrate that the catalytic domain of GIY-YIG homing
AB  - endonucleases can be targeted to relevant loci by fusing the domain to characterize
AB  - DNA-binding platforms.  Recent efforts have focused on improving the Tev-TAL platform by (1)
AB  - understanding the spacing requirements between the nuclease cleavage site and the DNA binding
AB  - site, (2) probing the DNA binding requirements of the I-TevI linker domain, and (3)
AB  - demonstrating activity in mammalian systems.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
TI  - Free-standing homing endonucleases of T-even phage: Freeloaders or functionaries?
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 147
EP  - 160
VL  - 16
AB  - The ability of group I and II introns, and of inteins, to promote their own mobility to
AB  - cognate genes lacking the intron or intein is a property that is now well documented in the
AB  - scientific literature.  This so-called homing of introns and inteins is mediated by homing
AB  - endonucleases encoded within the genetic elements.  Other chapters within this book have
AB  - detailed the different classes of homing endonucleases, how homing endonuclease specifically
AB  - recognize their target sequences, and the mechanisms of DNA cleavage.  This chapter deals with
AB  - the surprising observation that homing endonucleases are not always found encoded within
AB  - introns or inteins, and are often found inserted between genes.  Such free-standing homing
AB  - endonucleases are particularly abundant in the well-studied Escherichia coli bacteriophage T4.
AB  - In phage T4, the endonucleases themselves are mobile genetic elements, promoting their spread
AB  - to related T-even phage genomes that lack the endonuclease gene by a double-strand break
AB  - repair pathway.  This process is remarkably similar to endonuclease-mediated intron homing,
AB  - and has been termed intronless homing.  Free-standing endonucleases have been identified in
AB  - most sequenced genomes, but it is unlikely that all practice intronless homing, as some have
AB  - been co-opted by cellular genomes to function in pathways unrelated to endonuclease mobility.
AB  - Here, I will focus on free-standing endonucleases of phage genomes, and highlight differences
AB  - in DNA-binding and cleavage strategies of intron-encoded versus free-standing endonucleases as
AB  - it relates to promoting mobility between genomes.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
TI  - Selfish DNA: Homing Endonucleases Find a Home.
JO  - Curr. Biol.
PY  - 2009
SP  - R115
EP  - R117
VL  - 19
AB  - Self-splicing group I introns come in two flavours - those with a homing endonuclease to
AB  - promote mobility of the intron, and those without an endonuclease. How homing endonucleases
AB  - and self-splicing introns associate to form a composite selfish genetic element is a question
AB  - of long-standing interest. Recent work has revealed that a shared characteristic of both
AB  - introns and endonucleases, the targeting of conserved sequences, may provide the impetus for
AB  - the evolution of composite mobile genetic elements.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Belfort, M.
AU  - Shub, D.A.
TI  - Barriers to intron promiscuity in bacteria.
JO  - J. Bacteriol.
PY  - 2000
SP  - 5281
EP  - 5289
VL  - 182
AB  - The first bacterial intron, a self-splicing group I intron, was found to interrupt the
AB  - thymidylate synthase (td) gene of the Escherichia coli phage T4.  The second and third
AB  - bacterial group I introns were found to interrupt the aerobic (nrdB) and anaerobic (nrdD
AB  - [initially named sunY]) ribonucleotide reductases of phage T4, and another group I intron was
AB  - soon discovered in the DNA polymerase gene of SPO1, a Bacillus phage.  From this (admittedly)
AB  - small sampling of phage genomes, one might have naively expected that group I introns would be
AB  - abundant in phage or bacterial genomes, especially since subsequent laboratory experiments
AB  - demonstrated that group I introns could propagate themselves (by a process called homing)
AB  - throughout populations of intron-minus alleles with near 100% efficiency.  That a similar
AB  - homing phenomenon had also been previously demonstrated for a group I intron in the large rRNA
AB  - gene of yeast mitochondrial gave additional support to the notion that group I introns should
AB  - be able to spread efficiently throughout populations.  However, this expected outcome has
AB  - never been realized in natural phage populations; some phage populations harbor many introns,
AB  - while other related phage populations harbor many introns, while other related phage
AB  - populations are strangely lacking in any introns whatsoever.  Why do group I introns have an
AB  - unusual distribution in phage and bacterial genomes, and what potential barriers might exist
AB  - to prevent their spread?
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Derbyshire, V.
AU  - Van Roey, P.
AU  - LaBonne, S.
AU  - Stanger, M.J.
AU  - Li, Z.
AU  - Boyd, T.M.
AU  - Shub, D.A.
AU  - Belfort, M.
TI  - Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.
JO  - Nat. Struct. Mol. Biol.
PY  - 2004
SP  - 936
EP  - 944
VL  - 11
AB  - Customary binding sites of intron-encoded homing endonucleases lie within cognate intronless
AB  - alleles, at the so-called homing sites. Here,
AB  - we describe a novel, high-affinity binding site for I-TevI
AB  - endonuclease, encoded within the group I td intron of phage T4. This
AB  - site is an operator that overlaps the T4 late promoter, which drives
AB  - I-TevI expression from within the td intron. I-TevI binds the operator
AB  - and homing sites with equal affinity, and functions as a
AB  - transcriptional autorepressor. Distinct sequence and spacing
AB  - requirements of the catalytic domain result in reduced cleavage
AB  - activity on operator DNA. Crystallographic studies showed that the
AB  - overall interactions of the DNA-binding domain with the operator and
AB  - homing sites are similar, but have some different hydrogen-bonding
AB  - contacts. We present a model in which the flexibility in protein-DNA
AB  - interactions allows I-TevI to bind variant intronless alleles to
AB  - promote intron mobility while facilitating its function in
AB  - autorepression, and thereby persistence in its host.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Fast, N.M.
AU  - Doolittle, W.F.
TI  - Selfish DNA: The best defense is a good offense.
JO  - Curr. Biol.
PY  - 1996
SP  - 385
EP  - 388
VL  - 6
AB  - The recent discovery of novel biochemical activities of intron-encoded endonucleases
AB  - emphasizes the selfish nature of mobile genetic elements.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Gibb, E.A.
AU  - Belfort, M.
TI  - Mobile DNA elements in T4 and related phages.
JO  - Virol. J.
PY  - 2010
SP  - 290
EP  - 290
VL  - 7
AB  - Mobile genetic elements are common inhabitants of virtually every genome where they can exert
AB  - profound influences on genome structure and function in addition to promoting their own spread
AB  - within and between genomes. Phage T4 and related phage have long served as a model system for
AB  - understanding the molecular mechanisms by which a certain class of mobile DNA, homing
AB  - endonucleases, promote their spread. Homing endonucleases are site-specific DNA endonucleases
AB  - that initiate mobility by introducing double-strand breaks at defined positions in genomes
AB  - lacking the endonuclease gene, stimulating repair and recombination pathways that mobilize the
AB  - endonuclease coding region. In phage T4, homing endonucleases were first discovered as encoded
AB  - within the self-splicing td, nrdB and nrdD introns of T4. Genomic data has revealed that
AB  - homing endonucleases are extremely widespread in T-even-like phage, as evidenced by the
AB  - astounding fact that similar to 11% of the T4 genome encodes homing endonuclease genes, with
AB  - most of them located outside of self-splicing introns. Detailed studies of the mobile td
AB  - intron and its encoded endonuclease, I-TevI, have laid the foundation for genetic, biochemical
AB  - and structural aspects that regulate the mobility process, and more recently have provided
AB  - insights into regulation of homing endonuclease function. Here, we summarize the current state
AB  - of knowledge regarding T4-encoded homing endonucleases, with particular emphasis on the
AB  - td/I-TevI model system. We also discuss recent progress in the biology of free-standing
AB  - endonucleases, and present areas of future research for this fascinating class of mobile
AB  - genetic elements.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Shub, D.A.
TI  - Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 7898
EP  - 7903
VL  - 98
AB  - A typical homing endonuclease initiates mobility of its group I intron by recognizing DNA both
AB  - upstream and downstream of the intron insertion
AB  - site of intronless alleles, preventing the endonuclease from binding
AB  - and cleaving its own intron-containing allele. Here, we describe a
AB  - GIY-YIG family homing endonuclease. I-BmoI, that possesses an unusual
AB  - recognition sequence, encompassing 1 base pair upstream but 38 base
AB  - pairs downstream of the intron insertion site. I-BmoI binds
AB  - intron-containing and intronless substrates with equal affinity but can
AB  - nevertheless discriminate between the two for cleavage. I-BmoI is
AB  - encoded by a group I intron that interrupts the thymidylate synthase
AB  - CTS) gene (thyA) of Bacillus mojavensis s87-18. This intron resembles
AB  - one inserted 21 nucleotides further downstream in a homologous TS gene
AB  - ltd) of Escherichia coli phage T4. I-TevI, the T4 td intron-encoded
AB  - GIY-YIG endonuclease, is very similar to I-BmoI, but each endonuclease
AB  - gene is inserted within a different position of its respective intron.
AB  - Remarkably, I-TevI and I-BmoI bind a homologous stretch of TS-encoding
AB  - DNA and cleave their intronless substrates in very similar positions.
AB  - Our results suggest that each endonuclease has independently evolved
AB  - the ability to distinguish intron-containing from intronless alleles
AB  - while maintaining the same conserved recognition sequence centered on
AB  - DNA-encoding active site residues of TS.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Stanger, M.J.
AU  - Belfort, M.
TI  - Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 1231
EP  - 1241
VL  - 343
AB  - To maximize spread of their host intron or intein, many homing endonucleases recognize
AB  - nucleotides that code for important and
AB  - conserved amino acid residues of the target gene. Here, we examine the
AB  - cleavage requirements for I-TevI, which binds a stretch of thymidylate
AB  - synthase (TS) DNA that codes for functionally critical residues in the
AB  - TS active site. Using an in vitro selection scheme, we identified two
AB  - base-pairs in the I-TevI cleavage site region as important for cleavage
AB  - efficiency. These were confirmed by comparison of I-TevI cleavage
AB  - efficiencies on mutant and on wild-type substrates. We also showed that
AB  - nicking of the bottom strand by I-TevI is not affected by mutation of
AB  - residues surrounding the bottom-strand cleavage site, unlike other
AB  - homing endonucleases. One of these two base-pairs is universally
AB  - conserved in all TS sequences, and is identical with a previously
AB  - identified cleavage determinant of I-BmoI, a related GIY-YIG
AB  - endonuclease that binds a homologous stretch of TS-encoding DNA. The
AB  - other base-pair is conserved only in a subset of TS genes that includes
AB  - the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and
AB  - I-BmoI cleavage site requirements correspond to functionally critical
AB  - residues involved in an extensive hydrogen bond network within the TS
AB  - active site. Remarkably, these cleavage requirements correlate with TS
AB  - phylogeny in bacteria, suggesting that each endonuclease has
AB  - individually adapted to efficiently cleave distinct TS substrates.
ER  -

TY  - JOUR
AU  - Edgell, D.R.
AU  - Stanger, M.J.
AU  - Belfort, M.
TI  - Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-Bmol.
JO  - Curr. Biol.
PY  - 2003
SP  - 973
EP  - 978
VL  - 13
AB  - Homing endonucleases initiate mobility of their host group I introns by binding to and
AB  - cleaving lengthy recognition sequences that are typically
AB  - centered on the intron insertion site (IS) of intronless alleles. Because
AB  - the intron interrupts the endonucleases' recognition sequence,
AB  - intron-containing alleles are immune to cleavage by their own
AB  - endonuclease. I-TevI and I-BmoI are related GIY-YIG endonucleases that
AB  - bind a homologous stretch of thymidylate synthase (TS)-encoding DNA but
AB  - use different strategies to distinguish intronless from intron-containing
AB  - substrates. I-TevI discriminates between substrates at the level of DNA
AB  - binding, as its recognition sequence is centered on the intron IS. I-BmoI,
AB  - in contrast, possesses a very asymmetric recognition sequence with respect
AB  - to the intron IS, binds both intron-containing and intronless TS-encoding
AB  - substrates, but efficiently cleaves only intronless substrate. Here, we
AB  - show that I-BmoI is extremely tolerant of multiple substitutions around
AB  - its cleavage sites and has a low specific activity. However, a single G-C
AB  - base pair, at position -2 of a 39-base pair recognition sequence, is a
AB  - major determinant for cleavage efficiency and distinguishes intronless
AB  - from intron-containing alleles. Strikingly, this G-C base pair is
AB  - universally conserved in phylogenetically diverse TS-coding sequences;
AB  - this finding suggests that I-BmoI has evolved exquisite cleavage
AB  - requirements to maximize the potential to spread to variant intronless
AB  - alleles, while minimizing cleavage at its own intron-containing allele.
ER  -

TY  - JOUR
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
AU  - Sclair, M.
TI  - Specific endonuclease R fragments of bacteriophage PhiX174 deoxyribonucleic acid.
JO  - J. Virol.
PY  - 1972
SP  - 574
EP  - 582
VL  - 9
AB  - The restriction enzyme from Hemophilus influenzae, endonuclease R, cleaves
AB  - PhiX174 replicative-form deoxyribonucleic acid (DNA) into at least 13 specific
AB  - limit fragments.  The molecular weights of 12 of the fragments have been
AB  - estimated by gel electrophoresis and electron microscopy.  Using the genetic
AB  - assay for small fragments of PhiX DNA, we have shown that we can salvage
AB  - markers from the endonuclease R PhiX-RF fragments.
ER  -

TY  - JOUR
AU  - Edlund, A.
AU  - Liu, Q.
AU  - Watling, M.
AU  - To, T.T.
AU  - Bumgarner, R.E.
AU  - He, X.
AU  - Shi, W.
AU  - McLean, J.S.
TI  - High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model.
JO  - Genome Announcements
PY  - 2016
SP  - e01684
EP  - e01615
VL  - 4
AB  - We announce here a draft genome sequence of Veillonella parvula strain SHI-1, obtained from
AB  - healthy human saliva, discovered to be active at low pH using
AB  - metatranscriptomics within an in vitro oral biofilm model. The genome is composed
AB  - of 7 contigs, for a total of 2,200,064 bp.
ER  -

TY  - JOUR
AU  - Edmonds, P.
AU  - Hall, B.M.
AU  - Edwards, W.R.
AU  - Hartline, K.M.
TI  - Presence of methylated adenine in GATC Sequences in chromosomal DNAs from Campylobacter species.
JO  - J. Bacteriol.
PY  - 1992
SP  - 8156
EP  - 8157
VL  - 174
AB  - We digested chromosomal DNAs from 12 Campylobacter strains (C. jejuni, 4 strains; C. coli, 2
AB  - strains; C. fetus subsp. fetus, 2 strains; C. hyointestinalis, 2 strains; and C. upsaliensis,
AB  - 2 strains) and from 4 Helicobacter strains (H. pylori, 2 strains: and H. mustelae, 2 strains)
AB  - with HindIII, SstI, BamHI, DpnI, MboI, and Sau3AI. Restriction fragments were then separated
AB  - by electrophoresis in 1% agarose or 10% polyacrylamide gels. Only DNAs from three
AB  - Campylobacter species (C. jejuni, C. coli, and C. upsaliensis) were digested with DpnI (an
AB  - enzyme that recognizes only methylated adenine in GATC sequences). We used MboI and Sau3AI to
AB  - confirm these findings.
ER  -

TY  - JOUR
AU  - Edouard, S.
AU  - Bibi, F.
AU  - Dhamodharan, R.
AU  - Lagier, J.C.
AU  - Azhar, E.I.
AU  - Robert, C.
AU  - Caputo, A.
AU  - Yasir, M.
AU  - Jiman-Fatani, A.A.
AU  - Alawi, M.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 987
EP  - 1002
VL  - 9
AB  - Corynebacterium jeddahense sp. nov., strain JCB(T), is the type strain of Corynebacterium
AB  - jeddahense sp. nov., a new species within the genus
AB  - Corynebacterium. This strain, whose genome is described here, was isolated from
AB  - fecal flora of a 24-year-old Saudi male suffering from morbid obesity.
AB  - Corynebacterium jeddahense is a Gram-positive, facultative anaerobic,
AB  - nonsporulating bacillus. Here, we describe the features of this bacterium,
AB  - together with the complete genome sequencing and annotation, and compare it to
AB  - other member of the genus Corynebacterium. The 2,472,125 bp-long genome (1
AB  - chromosome but not plasmid) contains 2,359 protein-coding and 53 RNA genes,
AB  - including 1 rRNA operon.
ER  -

TY  - JOUR
AU  - Edouard, S.
AU  - Sankar, S.
AU  - Dangui, N.P.
AU  - Lagier, J.C.
AU  - Michelle, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 866
EP  - 882
VL  - 9
AB  - Nesterenkonia massiliensis sp. nov., strain NP1(T), is the type strain of Nesterenkonia
AB  - massiliensis sp. nov., a new species within the genus
AB  - Nesterenkonia. This strain, whose genome is described here, was isolated from the
AB  - feces of a 32-year-old French woman suffering from AIDS and living in Marseille.
AB  - Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe
AB  - the features of this bacterium, together with the complete genome sequencing and
AB  - annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains
AB  - 2,663 protein-coding and 51 RNA genes, including 1 rRNA operon.
ER  -

TY  - JOUR
AU  - Edwards, C.R.
AU  - Onstott, T.C.
AU  - Miller, J.M.
AU  - Wiggins, J.B.
AU  - Wang, W.
AU  - Lee, C.K.
AU  - Cary, S.C.
AU  - Pointing, S.B.
AU  - Lau, M.C.Y.
TI  - Draft Genome Sequence of Uncultured Upland Soil Cluster Gammaproteobacteria Gives Molecular Insights into High-Affinity Methanotrophy.
JO  - Genome Announcements
PY  - 2017
SP  - e00047
EP  - e00017
VL  - 5
AB  - Aerated soils form the second largest sink for atmospheric CH4 A near-complete genome of
AB  - uncultured upland soil cluster Gammaproteobacteria that oxidize CH4 at
AB  - <2.5 ppmv was obtained from incubated Antarctic mineral cryosols. This first
AB  - genome of high-affinity methanotrophs can help resolve the mysteries about their
AB  - phylogenetic affiliation and metabolic potential.
ER  -

TY  - JOUR
AU  - Edwards, R.A.
AU  - Helm, R.A.
AU  - Maloy, S.R.
TI  - Increasing DNA transfer efficiency by temporary inactivation of host restriction.
JO  - Biotechniques
PY  - 1999
SP  - 892
EP  - 900
VL  - 26
AB  - E. coli and Salmonella typhimurium are widely used bacterial hosts for genetic manipulation of
AB  - DNA from prokaryotes and eukaryotes.  Introduction of foreign DNA by electroporation or
AB  - transduction into E. coli and Salmonella is limited by host restriction of incoming DNA by the
AB  - recipient cells.  Here, we describe a simple method that temporarily inactivates host
AB  - restriction, allowing high-frequency DNA transfer.  This technique might be readily applied to
AB  - a wide range of bacteria to increase DNA transfer between strains and species.
ER  -

TY  - JOUR
AU  - Ee, R.
AU  - Ambrose, M.
AU  - Lazenby, J.
AU  - Williams, P.
AU  - Chan, K.G.
AU  - Roddam, L.
TI  - Genome Sequences of Two Pandoraea pnomenusa Isolates Recovered 11 Months Apart from a Cystic Fibrosis Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e01389
EP  - e01314
VL  - 3
AB  - Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in
AB  - people with cystic fibrosis (CF), but the clinical significance of
AB  - this infection is ambiguous. We have sequenced and annotated the genomes of two
AB  - multidrug-resistant Pandoraea pnomenusa isolates recovered 11 months apart from
AB  - the same CF patient.
ER  -

TY  - JOUR
AU  - Ee, R.
AU  - Lim, Y.-L.
AU  - Yin, W.-F.
AU  - See-Too, W.-S.
AU  - Roberts, R.J.
AU  - Chan, K.-G.
TI  - Novel methyltransferase recognition motif identified in Chania multitudinisentens RB-25T gen. nov., sp. nov.
JO  - Front. Microbiol.
PY  - 2016
SP  - 1362
EP  - 1362
VL  - 7
AB  - DNA methylation, defined by the addition of a methyl group to adenine or cytosine bases in DNA
AB  - catalyzed by DNA methyltransferases, is one of the most studied post-replicative DNA
AB  - modification mechanism in bacteria.  The three forms of nucleotide methylation identified to
AB  - date are: N6-methyladenine (m6A), N4-methylcytosine (m4C), and 5-methylcyosine (m5C).
ER  -

TY  - JOUR
AU  - Ee, R.
AU  - Lim, Y.L.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology.
JO  - Genome Announcements
PY  - 2014
SP  - e00245
EP  - e00214
VL  - 2
AB  - We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to
AB  - possess quorum-sensing properties. To the best of our knowledge, this is the first
AB  - documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea
AB  - species.
ER  -

TY  - JOUR
AU  - Eevers, N.
AU  - Van Hamme, J.D.
AU  - Bottos, E.M.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Enterobacter aerogenes, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo.
JO  - Genome Announcements
PY  - 2015
SP  - e00317
EP  - e00315
VL  - 3
AB  - We report here the draft genome of Enterobacter aerogenes, a Gram-negative bacterium of the
AB  - Enterobacteriaceae isolated from Cucurbita pepo root tissue.
AB  - This bacterium shows 2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading
AB  - potential and plant growth-promoting capacity. An analysis of its 4.5-Mb draft
AB  - genome will enhance the understanding of DDE degradation pathways and
AB  - phytoremediation applications for DDE-contaminated soils.
ER  -

TY  - JOUR
AU  - Eevers, N.
AU  - Van Hamme, J.D.
AU  - Bottos, E.M.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Sphingomonas taxi, Isolated from Cucurbita pepo, Proves to Be a DDE-Degrading and Plant Growth-Promoting Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00489
EP  - e00415
VL  - 3
AB  - The draft genome of Sphingomonas taxi, a strain of the Sphingomonadaceae isolated from
AB  - Cucurbita pepo root tissue, is presented. This Gram-negative bacterium shows
AB  - 2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading potential and plant
AB  - growth-promoting capacities. An analysis of its 3.9-Mb draft genome will enhance
AB  - the understanding of DDE-degradation pathways and phytoremediation applications
AB  - for DDE-contaminated soils.
ER  -

TY  - JOUR
AU  - Eevers, N.
AU  - Van Hamme, J.D.
AU  - Bottos, E.M.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Methylobacterium radiotolerans, a DDE-Degrading and Plant Growth-Promoting Strain Isolated from Cucurbita pepo.
JO  - Genome Announcements
PY  - 2015
SP  - e00488
EP  - e00415
VL  - 3
AB  - We announce the draft genome of Methylobacterium radiotolerans, a Gram-negative bacterium
AB  - isolated from Cucurbita pepo roots. This strain shows
AB  - 2,2-bis(p-chlorophenyl)-1,1-dichloroethylene (DDE)-degrading potential and plant
AB  - growth-promoting capacities. Analyses of its 6.8-Mb genome will improve our
AB  - understanding of DDE-degradation pathways and aid in the deployment of
AB  - phytoremediation technologies to remediate DDE-contaminated soils.
ER  -

TY  - JOUR
AU  - Efendi, Y.S.
AU  - Susanti, D.
AU  - Tritama, E.
AU  - Pasier, M.L.
AU  - Niwan, P.G.N.
AU  - Raharso, S.
AU  - Iskandar, A.P.
AU  - Giri-Rachman, E.A.
AU  - Mukhopadhyay, B.
AU  - Purwantini, E.
TI  - Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine.
JO  - Genome Announcements
PY  - 2017
SP  - e00235
EP  - e00217
VL  - 5
AB  - PT Bio Farma, the sole World Health Organization-approved Indonesian vaccine producer,
AB  - manufactures a whole-cell whooping cough vaccine (wP) that, as part of
AB  - a pentavalent diphtheria-tetanus-pertussis/hepatitis B/Haemophilus influenzae b
AB  - (DTP/HB/Hib) vaccine, is used in Indonesia and many other countries. We report
AB  - here the whole-genome sequence for Bordetella pertussis Pelita III, PT Bio
AB  - Farma's wP production strain.
ER  -

TY  - JOUR
AU  - Efimov, V.
AU  - Danin-Poleg, Y.
AU  - Green, S.J.
AU  - Elgavish, S.
AU  - Kashi, Y.
TI  - Draft Genome Sequence of the Pathogenic Bacterium Vibrio vulnificus V252 Biotype  1, Isolated in Israel.
JO  - Genome Announcements
PY  - 2015
SP  - e01182
EP  - e01115
VL  - 3
AB  - We report the genome sequence of the pathogenic Vibrio vulnificus biotype 1 clade B, which is
AB  - suggested to have a common ancestor with biotype 3. This draft genome of the clinical strain
AB  - V252, isolated in Israel, represents the clonal clade B group that contains both clinical and
AB  - environmental strains.
ER  -

TY  - JOUR
AU  - Efimova, E.P.
AU  - Delver, E.P.
AU  - Belogurov, A.A.
TI  - Alleviation of type I restriction in adenine methylase (dam) mutants of Escherichia coli.
JO  - Mol. Gen. Genet.
PY  - 1988
SP  - 313
EP  - 316
VL  - 214
AB  - The host-controlled EcoKI-restriction of unmodified phage lambda.O is alleviated in dam
AB  - mutants of Escherichia coli by 100- to 300-fold. In addition, the EcoKI modification activity
AB  - is substantially decreased in dam- strains. We show that type I restriction (EcoBI, EcoDI and
AB  - EcoKI) is detectably alleviated in dam mutants. However, no relief of EcoRI restriction (Type
AB  - II) occurs in dam- strains and only a slight effect of dam mutation on EcoPI restriction (Type
AB  - III) is observed. We interpret the alleviation of the type I restriction in dam- strains to be
AB  - a consequence of induction of the function which interferes with type I restriction systems.
ER  -

TY  - JOUR
AU  - Efimova, E.P.
AU  - Delver, E.P.
AU  - Belogurov, A.A.
TI  - 2-aminopurine and 5-bromouracil induce alleviation of type I restriction in Escherichia coli:  Mismatches function as inducing signals?
JO  - Mol. Gen. Genet.
PY  - 1988
SP  - 317
EP  - 320
VL  - 214
AB  - The EcoKI restriction of unmodified phage lambda is 1000-fold alleviated in Escherichia coli
AB  - grown in the presence of base analogs 2-aminopurine (2AP) and 5-bromouracil (5BU). 2AP
AB  - treatment of bacteria affects specifically the type I restriction systems (EcoAI, EcoBI, EcoDI
AB  - and EcoKI) and does not influence type II (EcoRI) and type III (EcoP1) restriction.
AB  - 2AP-induced alleviation of restriction occurs in bacteria which are deficient in the SOS
AB  - response (recA and lexA) and mismatch repair (mutH, mutL and mutS) and can be distinguished
AB  - from the alleviation of restriction observed in dam-strains. We suggest that mismatches
AB  - induced by 2AP and 5BU may function as an inducing signal for the alleviation of restriction
AB  - observed in the presence of base analogs.
ER  -

TY  - JOUR
AU  - Egan, K.
AU  - Kelleher, P.
AU  - Field, D.
AU  - Rea, M.C.
AU  - Ross, R.P.
AU  - Cotter, P.D.
AU  - Hill, C.
TI  - Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet  Factory.
JO  - Genome Announcements
PY  - 2017
SP  - e01172
EP  - e01117
VL  - 5
AB  - This paper reports the full genome sequence of the antimicrobial-producing bacterium
AB  - Geobacillus stearothermophilus DSM 458, isolated in a sugar beet
AB  - factory in Austria. In silico analysis reveals the presence of a number of novel
AB  - bacteriocin biosynthetic genes.
ER  -

TY  - JOUR
AU  - Egas, C.
AU  - Barroso, C.
AU  - Froufe, H.J.
AU  - Pacheco, J.
AU  - Albuquerque, L.
AU  - da Costa, M.S.
TI  - Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1062
EP  - 1075
VL  - 9
AB  - Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the  phylum
AB  - 'Actinobacteria' isolated from a hot spring in Sao Pedro do Sul, Portugal.
AB  - This aerobic and halotolerant bacterium is also extremely resistant to gamma and
AB  - UV radiation, which are the main reasons for the interest in sequencing its
AB  - genome. Here, we present the complete genome sequence of strain RSPS-4 as well as
AB  - its assembly and annotation. We also compare the gene sequence of this organism
AB  - with that of the type strain of the species R. radiotolerans isolated from a hot
AB  - spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of
AB  - 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp,
AB  - 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA
AB  - genes and a single rRNA operon.
ER  -

TY  - JOUR
AU  - Egidi, E.
AU  - Wood, J.L.
AU  - Aracic, S.
AU  - Kannan, R.
AU  - McDonald, L.
AU  - Bell, C.A.
AU  - Fox, E.M.
AU  - Liu, W.
AU  - Franks, A.E.
TI  - Draft Genome Sequence of Enterobacter ludwigii NCR3, a Heavy Metal-Resistant Rhizobacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e01076
EP  - e01016
VL  - 4
AB  - We report here the draft genome of Enterobacter ludwigii NCR3, a Gram-negative bacterium
AB  - isolated from the Carpobrotus rossii (Haw.) Schwantes rhizosphere. The
AB  - analysis of the ~4.8-Mb draft genome shows that this strain harbors several genes
AB  - associated with heavy metal resistance and plant growth-promoting activity,
AB  - suggesting its potential application in microbe-assisted phytoremediation.
ER  -

TY  - JOUR
AU  - Egidi, E.
AU  - Wood, J.L.
AU  - Fox, E.M.
AU  - Liu, W.
AU  - Franks, A.E.
TI  - Draft Genome Sequence of Leifsonia sp. Strain NCR5, a Rhizobacterium Isolated from Cadmium-Contaminated Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00520
EP  - e00517
VL  - 5
AB  - We report here the draft genome sequence of Leifsonia sp. strain NCR5, a Gram-positive
AB  - actinomycete isolated from Carpobrotus rossii (Haw.) Schwantes
AB  - rhizosphere. The de novo genome of Leifsonia sp. strain NCR5 was assembled with
AB  - 69 scaffolds and a G+C content of 69%, was 4.2 Mb in length, and contained 3,952
AB  - coding sequences.
ER  -

TY  - JOUR
AU  - Egidi, E.
AU  - Wood, J.L.
AU  - Fox, E.M.
AU  - Liu, W.
AU  - Franks, A.E.
TI  - Draft Genome Sequence of Rhodococcus erythropolis NSX2, an Actinobacterium Isolated from a Cadmium-Contaminated Environment.
JO  - Genome Announcements
PY  - 2016
SP  - e01147
EP  - e01116
VL  - 4
AB  - Rhodococcus erythropolis NSX2 is a rhizobacterium isolated from a heavy metal-contaminated
AB  - environment. The 6.2-Mb annotated genome sequence shows that
AB  - this strain harbors genes associated with heavy-metal resistance and xenobiotics
AB  - degradation.
ER  -

TY  - JOUR
AU  - Egidi, E.
AU  - Wood, J.L.
AU  - Mathews, E.
AU  - Fox, E.
AU  - Liu, W.
AU  - Franks, A.E.
TI  - Draft Genome Sequence of Bacillus cereus LCR12, a Plant Growth-Promoting Rhizobacterium Isolated from a Heavy Metal-Contaminated Environment.
JO  - Genome Announcements
PY  - 2016
SP  - e01041
EP  - e01016
VL  - 4
AB  - Bacillus cereus LCR12 is a plant growth-promoting rhizobacterium, isolated from a heavy
AB  - metal-contaminated environment. The 6.01-Mb annotated genome sequence
AB  - provides the genetic basis for revealing its potential application to remediate
AB  - contaminated soils in association with plants.
ER  -

TY  - JOUR
AU  - Ehara, A.
AU  - Suzuki, H.
AU  - Amachi, S.
TI  - Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e01478
EP  - e01414
VL  - 3
AB  - Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring
AB  - bacterium isolated from Japanese paddy soil. It contained two
AB  - distinct arsenic islands, one including genes for a respiratory arsenate
AB  - reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB)
AB  - and the second containing only genes for arsenic resistance.
ER  -

TY  - JOUR
AU  - Ehara, A.
AU  - Suzuki, H.
AU  - Kanesaki, Y.
AU  - Yoshikawa, H.
AU  - Amachi, S.
TI  - Draft genome sequence of strain q-1, an iodide-oxidizing alphaproteobacterium isolated from natural gas brine water.
JO  - Genome Announcements
PY  - 2014
SP  - e00659
EP  - e00614
VL  - 2
AB  - Here we report the draft genome sequence of strain Q-1, an iodide (I(-))-oxidizing
AB  - heterotrophic bacterium in the class Alphaproteobacteria
AB  - isolated from natural gas brine water. The genome sequence contained a
AB  - multicopper oxidase gene probably responsible for iodide oxidation. A
AB  - photosynthetic gene cluster was found but genes for carbon-fixation were absent.
ER  -

TY  - JOUR
AU  - Ehbrecht, H.-J.
AU  - Pingoud, A.
AU  - Urbanke, C.
AU  - Maass, G.
AU  - Gualerzi, C.
TI  - Linear diffusion of restriction endonucleases on DNA.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 6160
EP  - 6166
VL  - 260
AB  - We have investigated the dependence of the rate of cleavage of DNA by EcoRI,
AB  - HindIII, and BamHI on the chain length of the substrate.  In order to keep the
AB  - influence of flanking sequences and of nonspecific binding identical for all
AB  - substrates we have carried out all experiments with the same plasmid DNA which
AB  - had been digested previously with a variety of different restriction enzymes to
AB  - give a set of substrates of different lengths.  Our results show that depending
AB  - on the buffer conditions long substrates are cleaved faster than small ones.
AB  - We interpret these findings to mean that under certain conditions a linear
AB  - diffusion of the enzymes on the DNA is involved in localizing the recognition
AB  - sites.  For EcoRI the mean diffusion length is approximately 1000 base pairs at
AB  - 1 mM MgCl2 which can be shown by diffusion theory to correspond to a linear
AB  - diffusion coefficient of 5.10-10 cm2 s-1.  At 10 mM MgCl2 the linear diffusion
AB  - of EcoRI is negligible and does not lead to a significant enhancement of the
AB  - rate of site localization.  In the presence of nonsaturating amounts of one of
AB  - the prokaryotic histone-like protein Hu (NS 2) small and large DNa substrate
AB  - are cleaved with identical rate by EcoRI indicating that other proteins bound
AB  - to the DNA constitute a barrier across wich linear diffusion cannot take place.
AB  - We conclude that linear diffusion, albeit detectable under certain conditions
AB  - in vitro, probably is of little importance for the process of site localization
AB  - in vivo.
ER  -

TY  - JOUR
AU  - Ehrlich, M.
AU  - Ehrlich, K.
AU  - Mayo, J.A.
TI  - Unusual properties of the DNA from Xanthomonas phage XP-12 in which 5-methylcytosine completely replaces cytosine.
JO  - Biochim. Biophys. Acta
PY  - 1975
SP  - 109
EP  - 119
VL  - 395
AB  - Xanthomonas phage XP-12 contains 5-methylcytosine completely replacing
AB  - cytosine.  This substitution confers several unusual properties upon XP-12 DNA.
AB  - The buoyant density of XP-12 DNA in CsCl gradients is 1.710 g/cm3, 0.016 g/cm3
AB  - lower than that expected for a normal DNA with the same percentage of adenine
AB  - plus thymine.  The melting temperature for XP-12 DNA in 0.012 M Na+ is the
AB  - highest reported for any naturally occurring DNA, 83.2C, 6.1C higher than that
AB  - of normal DNAs with the same percentage of adenine plus thymine.  Unlike the
AB  - minor amounts of 5-methylcytosine found in most plant and animal DNAs, the
AB  - 5-methylcytosine residues of XP-12 derive their methyl group from the 3-carbon
AB  - of serine instead of from the thiomethyl carbon of methionine.
ER  -

TY  - JOUR
AU  - Ehrlich, M.
AU  - Gama-Sosa, M.A.
AU  - Carreira, L.H.
AU  - Ljungdahl, L.G.
AU  - Kuo, K.C.
AU  - Gehrke, C.W.
TI  - DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 1399
EP  - 1412
VL  - 13
AB  - While determining the minor and major base composition of the DNA from 17 types of
AB  - thermophilic bacteria by high performance liquid chromatography (HPLC) of enzymatic digests,
AB  - we have discovered a novel base, N4-methylcytosine (m4C). Its structure was proven by
AB  - comparison of the DNA-derived nucleoside to the analogous authentic compound by HPLC, UV
AB  - spectroscopy, and mass spectroscopy. Eight of the bacterial DNAs contained m4C. Only two
AB  - contained the common minor base, 5-methylcytosine (m5C), and neither of these was from an
AB  - extreme thermophile. The other prevalent modified base of bacterial DNA, N6-methyladenine
AB  - (m6A), was found in nine of the DNAs. Restriction analysis revealed that four of the DNAs had
AB  - dam-type (Gm6ATC) methylation patterns. Due to the propensity of m5C residues to be deaminated
AB  - by heat to thymine residues and to inefficient repair of the resulting mismatched base pairs,
AB  - thermophiles with optimal growth temperatures of >60C generally may avoid having m5C in their
AB  - genomes. Instead, some of them have deamination-resistant m4C residues.
ER  -

TY  - JOUR
AU  - Ehrlich, M.
AU  - Norris, K.F.
AU  - Wang, R.Y.
AU  - Kuo, K.C.
AU  - Gehrke, C.W.
TI  - DNA cytosine methylation and heat-induced deamination.
JO  - Biosci. Rep.
PY  - 1986
SP  - 387
EP  - 393
VL  - 6
AB  - The heat-induced conversion of 5-methylcytosine (m5C) residues to thymine residues and of
AB  - cytosine to uracil residues in single-stranded DNA was studied.
AB  - The calculated rates for deamination at 37 degrees C and pH 7.4 were
AB  - approximately 9.5 X 10(-10) and 2.1 X 10(-10) sec-1, respectively.
AB  - N4-Methyldeoxycytidine, which is in the DNA of certain thermophilic bacteria, was
AB  - more heat-resistant than was deoxycytidine and much more than was
AB  - 5-methyldeoxycytidine. Thermophilic bacteria which contain N4-methylcytosine
AB  - rather than m5C in their genomes may thereby largely avoid heat-induced mutation
AB  - due to deamination, which is incurred by the many organisms that contain m5C in
AB  - their DNA.
ER  -

TY  - JOUR
AU  - Ehrlich, M.
AU  - Wang, R.Y.-H.
TI  - 5-Methylcytosine in eukaryotic DNA.
JO  - Science
PY  - 1981
SP  - 1350
EP  - 1357
VL  - 212
AB  - A small portion of the cytosine residues in the DNA of higher eukaryotes as
AB  - well as in that of many lower eukaryotes is methylated.  The resulting
AB  - 5-methylcytosine residues occur in specific sequences in the DNA, usually
AB  - adjacent to guanine residues on the 3' side.  This methylation of eukaryotic
AB  - DNA has been proposed to function in ways, including control of transcription,
AB  - maintenance of chromosome structure, repair of DNA, establishment of preferred
AB  - sites for mutation, oncogenic transformation, and, in certain systems,
AB  - protection of DNA against enzymatic degradation.
ER  -

TY  - JOUR
AU  - Ehrlich, M.
AU  - Wilson, G.G.
AU  - Kenneth, C.K.
AU  - Gehrke, C.W.
TI  - N4-Methylcytosine as a minor base in bacterial DNA.
JO  - J. Bacteriol.
PY  - 1987
SP  - 939
EP  - 943
VL  - 169
AB  - The DNA base composition, including the minor base content, of 26 strains of
AB  - bacteria was determined.  The studied bacteria are sources of widely used
AB  - restriction endonucleases.  Approximately 35% of the bacterial DNAs contained
AB  - N4-methylcytosine, about 60% contained 5-methylcytosine, and about 90% had
AB  - N6-methyladenine.
ER  -

TY  - JOUR
AU  - Ehsani, E.
AU  - Barrantes, I.
AU  - Vandermaesen, J.
AU  - Geffers, R.
AU  - Jarek, M.
AU  - Boon, N.
AU  - Springael, D.
AU  - Pieper, D.H.
AU  - Vilchez-Vargas, R.
TI  - Draft Genome Sequence of Aeromonas sp. Strain EERV15.
JO  - Genome Announcements
PY  - 2016
SP  - e00811
EP  - e00816
VL  - 4
AB  - We report here the draft genome sequence of Aeromonas sp. strain EERV15 isolated  from sand
AB  - filter. The organism most closely related to Aeromonas sp. EERV15 is
AB  - Aeromonas veronii B565, with an average 83% amino acid sequence similarity of
AB  - putatively encoded protein open reading frames.
ER  -

TY  - JOUR
AU  - Ehsani, E.
AU  - Jauregui, R.
AU  - Geffers, R.
AU  - Jareck, M.
AU  - Boon, N.
AU  - Pieper, D.H.
AU  - Vilchez-Vargas, R.
TI  - Draft Genome Sequence of Rhodococcus sp. Strain 311R.
JO  - Genome Announcements
PY  - 2015
SP  - e00378
EP  - e00315
VL  - 3
AB  - Here, we report the draft genome sequence of Rhodococcus sp. strain 311R, which was isolated
AB  - from a site contaminated with alkanes and aromatic compounds. Strain
AB  - 311R shares 90% of the genome of Rhodococcus erythropolis SK121, which is the
AB  - closest related bacteria.
ER  -

TY  - JOUR
AU  - Ehsani, E.
AU  - Jauregui, R.
AU  - Geffers, R.
AU  - Jarek, M.
AU  - Boon, N.
AU  - Pieper, D.H.
AU  - Vilchez-Vargas, R.
TI  - First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608  (DSM 19327).
JO  - Genome Announcements
PY  - 2015
SP  - e01378
EP  - e01315
VL  - 3
AB  - We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was
AB  - isolated from activated sludge of an aerobic-anaerobic wastewater
AB  - treatment plant. The closest strain to Acidovorax caeni strain R-24608 is
AB  - Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading
AB  - frames (ORFs) average similarity.
ER  -

TY  - JOUR
AU  - Eichhorn, I.
AU  - Tedin, K.
AU  - Fulde, M.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Q1.
JO  - Genome Announcements
PY  - 2017
SP  - e01151
EP  - e01117
VL  - 5
AB  - Here, we report the draft genome sequence of Salmonella enterica subsp. enterica  serovar
AB  - Typhimurium strain Q1. The draft genome contains 4,793,493 bp in 149
AB  - contigs.
ER  -

TY  - JOUR
AU  - Eichhorn, I.
AU  - van der Linden, M.
AU  - Jarek, M.
AU  - Fulde, M.
TI  - Draft Genome Sequence of Zoonotic Streptococcus canis Isolate G361.
JO  - Genome Announcements
PY  - 2017
SP  - e00967
EP  - e00917
VL  - 5
AB  - Here, we report the draft genome sequence of an SCM-positive Streptococcus canis  strain,
AB  - G361, isolated from a vaginal swab of a 40-year-old woman. The draft
AB  - genome comprises 2,045,931 bp in 62 contigs.
ER  -

TY  - JOUR
AU  - Eickbush, T.H.
TI  - Mobile introns: Retrohoming by complete reverse splicing.
JO  - Curr. Biol.
PY  - 1999
SP  - R11
EP  - R14
VL  - 9
AB  - A mobile bacterial group II intron can integrate into DNA by the reverse splicing into a
AB  - target site of its RNA transcript, which then acts as a template for DNA synthesis by an
AB  - encoded reverse transcriptase.  Mobility does not require homologous recombination, which has
AB  - important practical and evolutionary implications.
ER  -

TY  - JOUR
AU  - Eidam, C.
AU  - Poehlein, A.
AU  - Brenner, M.G.
AU  - Kadlec, K.
AU  - Liesegang, H.
AU  - Brzuszkiewicz, E.
AU  - Daniel, R.
AU  - Sweeney, M.T.
AU  - Murray, R.W.
AU  - Watts, J.L.
AU  - Schwarz, S.
TI  - Complete Genome Sequence of Mannheimia haemolytica Strain 42548 from a Case of Bovine Respiratory Disease.
JO  - Genome Announcements
PY  - 2013
SP  - e00318
EP  - e00313
VL  - 1
AB  - Mannheimia haemolytica is the major bacterial component in the bovine respiratory disease
AB  - complex, which accounts for considerable economic losses to the cattle
AB  - industry worldwide. The complete genome sequence of M. haemolytica strain 42548
AB  - was determined. It has a size of 2.73 Mb and contains 2,888 genes, including
AB  - several antibiotic resistance genes.
ER  -

TY  - JOUR
AU  - Eigner, J.
AU  - Block, S.
TI  - Host-controlled restriction of T-even bacteriophages:  relation of four bacterial deoxyribonucleases to restriction.
JO  - J. Virol.
PY  - 1968
SP  - 320
EP  - 326
VL  - 2
AB  - Escherichia coli strains B and K-12, which restrict growth of nonglucosylated
AB  - T-even phage (T*phage), and nonrestricting strains (Shigella sonnei and mutants
AB  - of E. coli B) were tested for levels of endonuclease I and exonucleases I,II,
AB  - and III, by means of in vitro assays.  Cell-free extracts freed from
AB  - deoxyribonucleic acid (DNA) were examined with three substrates: E. coli DNA,
AB  - T*2 DNA, and T2 DNA.  Both restricting and nonrestricting strains had
AB  - comparable levels of the four nuclease activities and had similar patterns of
AB  - preference for the three substrates.  In addition, mutants of E. coli B and
AB  - K-12 that lack endonuclease I were as effective as their respective wild types
AB  - in restricting T* phage.
ER  -

TY  - JOUR
AU  - Eijkelkamp, B.A.
AU  - Stroeher, U.H.
AU  - Hassan, K.A.
AU  - Papadimitrious, M.S.
AU  - Paulsen, I.T.
AU  - Brown, M.H.
TI  - Adherence and motility characteristics of clinical Acinetobacter baumannii isolates.
JO  - FEMS Microbiol. Lett.
PY  - 2011
SP  - 44
EP  - 51
VL  - 323
AB  - Acinetobacter baumannii continues to be a major health problem especially in
AB  - hospital settings. Herein, features that may play a role in persistence and
AB  - disease potential were investigated in a collection of clinical A. baumannii
AB  - strains from Australia. Twitching motility was found to be a common trait in A.
AB  - baumannii international clone I strains and in abundant biofilm formers, whereas
AB  - swarming motility was only observed in isolates not classified within the
AB  - international clone lineages. Bioinformatic analysis of the type IV fimbriae
AB  - revealed a correlation between PilA sequence homology and motility. A high level
AB  - of variability in adherence to both abiotic surfaces and epithelial cells was
AB  - found. We report for the first time the motility characteristics of a large
AB  - number of A. baumannii isolates and present a direct comparison of A. baumannii
AB  - binding to nasopharyngeal and lung epithelial cells.
ER  -

TY  - JOUR
AU  - Eikmeyer, F.
AU  - Hadiati, A.
AU  - Szczepanowski, R.
AU  - Wibberg, D.
AU  - Schneiker-Bekel, S.
AU  - Rogers, L.M.
AU  - Brown, C.J.
AU  - Top, E.M.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.
JO  - Plasmid
PY  - 2012
SP  - 13
EP  - 24
VL  - 68
AB  - The dissemination of antibiotic resistance genes among bacteria often occurs by means of
AB  - plasmids. Wastewater treatment plants (WWTP) were previously recognized as hot spots for the
AB  - horizontal transfer of genetic material. One of the plasmid groups that is often associated
AB  - with drug resistance is the incompatibility group IncN. The aim of this study was to gain
AB  - insights into the diversity and evolutionary history of IncN plasmids by determining and
AB  - comparing the complete genome sequences of the four novel multi-drug resistance plasmids
AB  - pRSB201, pRSB203, pRSB205 and pRSB206 that were exogenously isolated from the final effluent
AB  - of a municipal WWTP. Their sizes range between 42,875bp and 56,488bp and they share a common
AB  - set of backbone modules that encode plasmid replication initiation, conjugative transfer, and
AB  - plasmid maintenance and control. All plasmids are transferable at high rates between
AB  - Escherichia coli strains, but did not show a broad host range. Different genes conferring
AB  - resistances to ampicillin, streptomycin, spectinomycin, sulfonamides, tetracycline and
AB  - trimethoprim were identified in accessory modules inserted in these plasmids. Comparative
AB  - analysis of the four WWTP IncN plasmids and IncN plasmids deposited in the NCBI database
AB  - enabled the definition of a core set of backbone genes for this group. Moreover, this approach
AB  - revealed a close phylogenetic relationship between the IncN plasmids isolated from
AB  - environmental and clinical samples. Phylogenetic analysis also suggests the existence of
AB  - host-specific IncN plasmid subgroups. In conclusion, IncN plasmids likely contribute to the
AB  - dissemination of resistance determinants between environmental bacteria and clinical strains.
AB  - This is of particular importance since multi-drug resistance IncN plasmids have been
AB  - previously identified in members of the Enterobacteriaceae that cause severe infections in
AB  - humans.
ER  -

TY  - JOUR
AU  - Einvik, C.
AU  - Decatur, W.A.
AU  - Embley, T.M.
AU  - Vogt, V.M.
AU  - Johansen, S.
TI  - Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing.
JO  - RNA
PY  - 1997
SP  - 710
EP  - 720
VL  - 3
AB  - We have characterized the structural organization and catalytic properties of the large
AB  - nucleolar group I introns (NaSSU1) of different Naegleria species N. jamiesoni, N. andersoni,
AB  - N. italica, and N. gruberi.  NaSSU1 consists of three distinct RNA domains: an open reading
AB  - frame encoding a homing-type endonuclease, and a small group I ribozyme (NaGIR1) inserted into
AB  - the P6 loop of a second group I ribozyme (NaGIR2).  The two ribozymes have different functions
AB  - in RNA splicing and processing.  NaGIR1 is an unusual self-cleaving group I ribozyme
AB  - responsible for intron processing at two internal sites (IPS1 and IPS2), both close to the 5'
AB  - end of the open reading frame.  This processing is hypothesized to lead to formation of a
AB  - messenger RNA for the endonuclease.  Structurally, NaGIR2 is a typical group IC1 ribozyme,
AB  - catalyzing intron excision and exon ligation reactions.  NaGIR2 is responsible for
AB  - circularization of the excised intron, a reaction that generates full-length RNA circles of
AB  - wild-type intron.  Although it is only distantly related in primary sequence, NaSSU1 RNA has a
AB  - predicted organization and function very similar to that of the mobile group I intron DiSSU1
AB  - of Didymium, the only other group I intron known to encode two ribozymes.  We propose that
AB  - these twin-ribozyme introns define a distinct category of group I introns with a conserved
AB  - structural organization and function.
ER  -

TY  - JOUR
AU  - Eisen, J.A. et al.
TI  - The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 9509
EP  - 9514
VL  - 99
AB  - The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to
AB  - be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence
AB  - from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive
AB  - tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are
AB  - highly conserved among photosynthetic species. Many of these have no assigned function and may
AB  - play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely
AB  - duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism
AB  - of sulfur and nitrogen as well as strong similarities between metabolic processes in C.
AB  - tepidum and many Archaeal species.
ER  -

TY  - JOUR
AU  - Eisen, S.
AU  - Poehlein, A.
AU  - Johnson, D.B.
AU  - Daniel, R.
AU  - Schlomann, M.
AU  - Muhling, M.
TI  - Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T.
JO  - Genome Announcements
PY  - 2015
SP  - e00383
EP  - e00315
VL  - 3
AB  - Extremely acidophilic iron-oxidizing bacteria have largely been characterized for the phyla
AB  - Proteobacteria and Nitrospira. Here, we report the draft genome of an
AB  - iron-oxidizing and -reducing heterotrophic mesophile of the Actinobacteria,
AB  - Ferrimicrobium acidiphilum, which was isolated from an abandoned pyrite mine. The
AB  - genome sequence comprises 3.08 Mb.
ER  -

TY  - JOUR
AU  - Eisen, S.
AU  - Poehlein, A.
AU  - Johnson, D.B.
AU  - Daniel, R.
AU  - Schlomann, M.
AU  - Muhling, M.
TI  - Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial   Genus Acidithrix.
JO  - Genome Announcements
PY  - 2015
SP  - e00382
EP  - e00315
VL  - 3
AB  - Extremely acidophilic iron-oxidizing Gram-positive bacteria comprise species within the phyla
AB  - Firmicutes and Actinobacteria. Here, we report the 4.02-Mb draft
AB  - genome of Acidithrix ferrooxidans Py-F3, which was isolated from a stream
AB  - draining an abandoned copper mine and proposed as the type species of a new genus
AB  - of Actinobacteria.
ER  -

TY  - JOUR
AU  - Eisenschmidt, K.
TI  - Development of a programmable restriction enzyme.
JO  - Ph.D. Thesis, Germany
PY  - 2005
SP  - 1
EP  - 116
ER  -

TY  - JOUR
AU  - Eisenschmidt, K.
AU  - Lanio, T.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - A fluorimetric assay for on-line detection of DNA cleavage by restriction endonucleases.
JO  - J. Biotechnol.
PY  - 2002
SP  - 185
EP  - 191
VL  - 96
AB  - We have developed an assay for online detection of DNA cleavage by restriction endonucleases,
AB  - suitable for the high throughput screening of the activity and flanking sequence preference of
AB  - restriction endonuclease variants. For this purpose oligodeoxynucleotides were used, labeled
AB  - with either 6-FAM or TAMRA whose fluorescence is quenched by a neighboring DABCYL group. After
AB  - endonucleolytic cleavage the products are too short to remain double-stranded and the
AB  - fluorophor labeled strand is released with concomitant increase in fluorescence which can be
AB  - easily quantified.
AB  - Employing this method, cleavage reactions can be monitored continuously, allowing for fast
AB  - detection of specific activity as well as determination of kinetic parameters. To demonstrate
AB  - the reliability of our
AB  - assay we measured K(M) and k(cat) values for the restriction endonuclease EcoRV and obtained
AB  - results similar to those obtained with established assays. Moreover, our method makes it
AB  - possible to observe
AB  - the cleavage of two different substrates differing in the sequences flanking the EcoRV site
AB  - and labeled with different fluorophors in competition in a single experiment. This assay can
AB  - be carried out in a
AB  - microplate format, which allows for the analysis of many restriction endonuclease variants in
AB  - parallel.
ER  -

TY  - JOUR
AU  - Eisenschmidt, K.
AU  - Lanio, T.
AU  - Simoncsits, A.
AU  - Jeltsch, A.
AU  - Pingoud, V.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - Developing a programmed restriction endonuclease for highly specific DNA cleavage.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 7039
EP  - 7047
VL  - 33
AB  - Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic
AB  - DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely
AB  - high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4-C8 bp
AB  - are not sufficiently specific for this purpose. In principle, the specificity of REases can be
AB  - extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or
AB  - triple-helix forming oligonucleotides (TFO). We have chosen to extend the specificity of
AB  - REases using TFOs, given the combinatorial flexibility this fusion offers in addressing a
AB  - short, yet precisely recognized restriction site next to a defined triple-helix forming site
AB  - (TFS). We demonstrate here that the single chain variant of PvuII (scPvuII) covalently coupled
AB  - via the bifunctional cross-linker N-(gamma-maleimidobutryloxy) succinimide ester to a TFO
AB  - (5'-NH2-[CH2]6 or 12-MPMPMPMPMPPPPPPT-3', with M being 5-methyl-2'-deoxycytidine and P
AB  - being 5-[1-propynyl]-2'-deoxyuridine), cleaves DNA specifically at the recognition site of
AB  - PvuII (CAGCTG) if located in a distance of approximately one helical turn to a TFS
AB  - (underlined) complementary to the TFO ('addressed' site:
AB  - 5'-TTTTTTTCTCTCTCTCN~10CAGCTG-3'), leaving 'unaddressed' PvuII sites intact. The
AB  - preference for cleavage of an 'addressed' compared to an 'unaddressed' site is >1000-fold,
AB  - if the cleavage reaction is initiated by addition of Mg2+ ions after preincubation of
AB  - scPvuII-TFO and substrate in the absence of Mg2+ ions to allow triple-helix formation before
AB  - DNA cleavage. Single base pair substitutions in the TFS prevent addressed DNA cleavage by
AB  - scPvuII-TFO.
ER  -

TY  - JOUR
AU  - Ekino, K.
AU  - Kwon, I.
AU  - Goto, M.
AU  - Yoshino, S.
AU  - Furukawa, K.
TI  - Functional analysis of HO gene in delayed homothallism in Saccharomyces cerevisiae wy2.
JO  - Yeast
PY  - 1999
SP  - 451
EP  - 458
VL  - 15
AB  - Saccharomyces cerevisiae wy2 exhibits a novel life cycle, with delayed homothallism caused by
AB  - a defective HO gene. In this strain, gradual diploidization occurs during successive
AB  - subcultures. Three amino acids of wy2 HO were different from those of wild-type (wt) HO, which
AB  - included a nonsense mutation (TAG) from Trp-292 and two amino acid changes of His-475 to Leu
AB  - and Glu-530 to Lys. The ho gene of heterothallic strain CG379 was also sequenced in this
AB  - study. Four amino acids of ho were different from those of HO. Among different amino acids in
AB  - wy2 HO and ho, the alteration of His-475 to Leu was common between them. His-475 in HO was
AB  - previously suggested to be involved in the DNA binding. We constructed a variety of chimeric
AB  - HO genes by exchanging the corresponding restriction fragments generated from the wt HO, wy2
AB  - HO and ho genes. These results and the site-directed mutagenesis studies allowed us to draw
AB  - the following conclusions: (a) Gly-223 is essential for HO activity; (b) mutation of His-475
AB  - to Leu significantly reduces the HO activity; (c) amber mutation (TAG) in wy2 HO car be
AB  - suppressed inefficiently.
ER  -

TY  - JOUR
AU  - Eklund, J.L.
TI  - Design and characterization of homing endonuclease I-PpoI variants with novel DNA sequence specificity.
JO  - Ph.D. Thesis, University of Washington, Seattle, USA
PY  - 2005
SP  - 1
EP  - 115
AB  - Homing endonucleases bind and cleave long DNA target sites with high degree of sequence
AB  - specificity.  The homing endonuclease I-PpoI recognizes a 15 bp, semi-palindromic homing site
AB  - sequence in the rDNA of all eukaryotes.  The co-crystal structure indicates taht a b-sheet in
AB  - the major groove is responsible for most of the DNA-protein contacts that determine sequence
AB  - specificity of the enzyme.  Base pair changes in the +/-6 position of the I-PpoI binding site
AB  - disrupt cleavage.  To better understand the specificity at the +/- site, I have explored
AB  - variants with altered specificity for a +6C/-6G change.  Three libraries of I-PpoI variants
AB  - with varying degrees of rationally designed changes in the b-sheet were generated and screened
AB  - for altered DNA sequence specificity to a +6C/-6G basepair change using a yeast one-hybrid
AB  - assay.  A total of thirteen unique variants were isolated and characterized for binding
AB  - affinity and cleavage activity on the WT site and the +6C/-6G site; the other seven variants
AB  - had generally relaxed specificity or a higher affinity for the WT site.  Only one variant
AB  - showed cleavage activity on the WT site and none of the variants cleaves the +6C/-6G site.
AB  - Select variants were further investigated for their binding affinity for 4 other binding site
AB  - sequences.  Five variants with single amino acid changes to the WT protein sequence and three
AB  - variants with single amino acid changes to a protein variant with a specificity shift were
AB  - generated and biochemically characterized for cleavage activity and binding affinity.  I-PpoI
AB  - variant proteins provide insight into how DNA-protein contacts determine DNA sequence
AB  - specificity.  A deeper understanding of homing endonuclease sequence specificity determinants
AB  - and how specificity shifts occur will aid in the design and generation of homing endonuclease
AB  - variants as useful tools for genomic research and therapy.
ER  -

TY  - JOUR
AU  - Eklund, J.L.
AU  - Ulge, U.Y.
AU  - Eastberg, J.
AU  - Monnat, R.J. Jr.
TI  - Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 5839
EP  - 5850
VL  - 35
AB  - We used a yeast one-hybrid assay to isolate and characterize variants of the eukaryotic homing
AB  - endonuclease I-PpoI that were able to bind a mutant,
AB  - cleavage-resistant I-PpoI target or 'homing' site DNA in vivo. Native
AB  - I-PpoI recognizes and cleaves a semi-palindromic 15-bp target site with
AB  - high specificity in vivo and in vitro. This target site is present in the
AB  - 28S or equivalent large subunit rDNA genes of all eukaryotes. I-PpoI
AB  - variants able to bind mutant target site DNA had from 1 to 8 amino acid
AB  - substitutions in the DNA-protein interface. Biochemical characterization
AB  - of these proteins revealed a wide range of site-binding affinities and
AB  - site discrimination. One-third of variants were able to cleave target site
AB  - DNA, but there was no systematic relationship between site-binding
AB  - affinity and site cleavage. Computational modeling of several variants
AB  - provided mechanistic insight into how amino acid substitutions that
AB  - contact, or are adjacent to, specific target site DNA base pairs determine
AB  - I-PpoI site-binding affinity and site discrimination, and may affect
AB  - cleavage efficiency.
ER  -

TY  - JOUR
AU  - El Aamri, F.
AU  - Acosta, F.
AU  - Real, F.
AU  - Padilla, D.
TI  - Whole-Genome Sequence of the Fish Virulent Strain Streptococcus iniae IUSA-1, Isolated from Gilthead Sea Bream (Sparus aurata) and Red Porgy (Pagrus pagrus).
JO  - Genome Announcements
PY  - 2013
SP  - e0002513
EP  - e0002513
VL  - 1
AB  - Streptococcus iniae is a major fish pathogen that produces invasive infections that result in
AB  - economic losses in aquaculture. In this study, the draft genome
AB  - sequence of Streptococcus iniae strain IUSA-1, isolated from a natural outbreak
AB  - affecting gilthead sea bream (Sparus aurata) and red porgy (Pagrus pagrus), is
AB  - presented.
ER  -

TY  - JOUR
AU  - El Halfawy, N.M.
AU  - El-Naggar, M.Y.
AU  - Andrews, S.C.
TI  - Complete Genome Sequence of Lactobacillus plantarum 10CH, a Potential Probiotic Lactic Acid Bacterium with Potent Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e01398
EP  - e01317
VL  - 5
AB  - Lactobacillus plantarum 10CH is a bacteriocin-producing potential probiotic lactic acid
AB  - bacterium (LAB) strain isolated from cheese. Its complete nucleotide
AB  - sequence shows a single circular chromosome of 3.3 Mb, with a G+C content of
AB  - 44.51%, a 25-gene plantaricin bacteriocin gene cluster, and the absence of
AB  - recognized virulence factors.
ER  -

TY  - JOUR
AU  - El Houmami, N.
AU  - Schrenzel, J.
AU  - Yagupsky, P.
AU  - Robert, C.
AU  - Ceroni, D.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Kingella negevensis SW7208426, the First European Strain of K. negevensis Isolated from a Healthy Child in Switzerland.
JO  - Genome Announcements
PY  - 2017
SP  - e00571
EP  - e00517
VL  - 5
AB  - We report here the draft genome of Kingella negevensis strain SW7208426, isolated from the
AB  - oropharynx of a healthy 6-year-old boy in Geneva, Switzerland. To our
AB  - knowledge, this is the first genome report of the newly described K. negevensis
AB  - species from Europe.
ER  -

TY  - JOUR
AU  - El Kafsi, H.
AU  - Binesse, J.
AU  - Loux, V.
AU  - Buratti, J.
AU  - Boudebbouze, S.
AU  - Dervyn, R.
AU  - Hammani, A.
AU  - Maguin, E.
AU  - van de Guchte, M.
TI  - Genome Sequence of Lactobacillus delbrueckii subsp. lactis CNRZ327, a Dairy Bacterium with Anti-Inflammatory Properties.
JO  - Genome Announcements
PY  - 2014
SP  - e00328
EP  - e00314
VL  - 2
AB  - Lactobacillus delbrueckii subsp. lactis CNRZ327 is a dairy bacterium with anti-inflammatory
AB  - properties both in vitro and in vivo. Here, we report the
AB  - genome sequence of this bacterium, which appears to contain no less than 215
AB  - insertion sequence (IS) elements, an exceptionally high number regarding the
AB  - small genome size of the strain.
ER  -

TY  - JOUR
AU  - El Karkouri, K.
AU  - Mediannikov, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of the Tick-Borne Pathogen Rickettsia raoultii.
JO  - Genome Announcements
PY  - 2016
SP  - e00157
EP  - e00116
VL  - 4
AB  - ITALIC! Rickettsia raoultiiis a tick-associated spotted fever group (SFG) organism, causing
AB  - scalp eschar and neck lymphadenopathy after tick bite (SENLAT)
AB  - in humans. We report here the genome sequence of ITALIC! R. raoultiistrain
AB  - Khabarovsk(T)(CSUR R3(T), ATCC VR-1596(T)), which was isolated from a ITALIC!
AB  - Dermacentor silvarumtick collected in Russia.
ER  -

TY  - JOUR
AU  - El-Arabi, T.F.
AU  - Griffiths, M.W.
AU  - She, Y.M.
AU  - Villegas, A.
AU  - Lingohr, E.J.
AU  - Kropinski, A.M.
TI  - Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group.
JO  - Virol. J.
PY  - 2013
SP  - 48
EP  - 48
VL  - 10
AB  - ABSTRACT: BACKGROUND: Comparatively little information is available on members of
AB  - the Myoviridae infecting low G+C content, Gram-positive host bacteria of the
AB  - family Firmicutes. While numerous Bacillus phages have been isolated up till now
AB  - only very few Bacillus cereus phages have been characterized in detail. RESULTS:
AB  - Here we present data on the large, virulent, broad-host-range B. cereus phage
AB  - vB_BceM_Bc431v3 (Bc431v3). Bc431v3 features a 158,618 bp dsDNA genome,
AB  - encompassing 239 putative open reading frames (ORFs) and, 20 tRNA genes encoding
AB  - 17 different amino acids. Since pulsed-field gel electrophoresis indicated that
AB  - the genome of this phage has a mass of 155-158 kb Bc431v3 DNA appears not to
AB  - contain long terminal repeats that are found in the genome of Bacillus phage
AB  - SPO1. CONCLUSIONS: Bc431v3 displays significant sequence similarity, at the
AB  - protein level, to B. cereus phage BCP78, Listeria phage A511 and Enterococcus
AB  - phage [latin capital letter o with stroke]EF24C and other morphologically related
AB  - phages infecting Firmicutes such as Staphylococcus phage K and Lactobacillus
AB  - phage LP65. Based on these data we suggest that Bc431v3 should be included as a
AB  - member of the Spounavirinae; however, because of all the diverse taxonomical
AB  - information has been addressed recently, it is difficult to determine the genus.
AB  - The Bc431v3 phage contains some highly unusual genes such as gp143 encoding
AB  - putative tRNAHis guanylyltransferase. In addition, it carries some genes that
AB  - appear to be related to the host sporulation regulators. These are: gp098, which
AB  - encodes a putative segregation protein related to FstK/SpoIIIE DNA transporters;
AB  - gp105, a putative segregation protein; gp108, RNA polymerase sigma factor F/B;
AB  - and, gp109 encoding RNA polymerase sigma factor G.
ER  -

TY  - JOUR
AU  - El-Deiry, W.S.
AU  - Nelkin, B.D.
AU  - Celano, P.
AU  - Yen, R.-W.C.
AU  - Falco, J.P.
AU  - Hamilton, S.R.
AU  - Baylin, S.B.
TI  - High expression of the DNA methyltransferase gene characterizes human neoplastic cells and progression stages of colon cancer.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1991
SP  - 3470
EP  - 3474
VL  - 88
AB  - DNA methylation abnormalities occur consistently in human neoplasia including widespread
AB  - hypomethylation and more recently recognized local increases in DNA methylation that hold
AB  - potential for gene inactivation events. To study this imbalance further, we have cloned and
AB  - localized to chromosome 19 a portion of the human DNA methyltransferase gene that codes for
AB  - the enzyme catalyzing DNA methylation. Expression of this gene is low in normal human cells,
AB  - significantly increased (30- to 50-fold by PCR analysis) in virally transformed cells, and
AB  - strikingly elevated in human cancer cells (several hundredfold). In comparison to colon mucosa
AB  - from patients without neoplasia, median levels of DNA methyltransferse transcripts are 15-fold
AB  - increased in histologically normal nucosa from patients with cancers of the benign polyps that
AB  - can precede cancers, 60-fold increased in the premalignant polyps, and >200-fold increased in
AB  - the cancers. Thus, increases in DNA methyltansferase gene expression precede development of
AB  - colonic neoplasia and continue during progression of colonic neoplasms. These increases may
AB  - play a role in the genetic instability of cancer and mark early events in cell transformation.
ER  -

TY  - JOUR
AU  - El-Said, M.M.
AU  - Garcia, J.L.
AU  - Martinez, I.
AU  - Del Cerro, C.
AU  - Nogales, J.
AU  - Diaz, E.
TI  - Genome Sequence of Pseudomonas azelaica Strain Aramco J.
JO  - Genome Announcements
PY  - 2015
SP  - e00037
EP  - e00015
VL  - 3
AB  - We report here the draft genome sequence of Pseudomonas azelaica strain Aramco J  (7.3 Mbp; GC
AB  - content, 61.9%), one of the few bacteria that can completely
AB  - mineralize different hydroxybiphenyls, e.g., 2-hydroxybiphenyl,
AB  - 2,2'-dihydroxybiphenyl, and 3-hydroxybiphenyl. The findings obtained from its
AB  - genome annotation suggest that this strain becomes a useful biocatalyst for
AB  - aromatic bioconversions.
ER  -

TY  - JOUR
AU  - El-Sayed, E.S.A.
AU  - El-Didamony, G.
AU  - Mansour, K.
TI  - Isolation and characterization of two types of actinophage infecting Streptomyces scabies.
JO  - Folia Microbiol. (Praha)
PY  - 2001
SP  - 519
EP  - 526
VL  - 46
AB  - Two types of actinophages, phiS and phiL, were isolated from soil samples by using
AB  - Streptomyces scabies, a potato scab pathogen, as
AB  - indicator strain. The phages were partially characterized according to
AB  - their physicochemical properties, plaques and particles morphology, and
AB  - their host range; this varied from narrow (for phiS) to wide (for
AB  - phiL). The adsorption rate constants of the phiS and phiL were 3.44 and
AB  - 3.18 pL/min, and their burst sizes were 1.61 and 3.75 virions per mL,
AB  - respectively. One-step growth indicated that phiS and phiL have a
AB  - latent period of 1/2 h followed by a rise period of 1/2 h. The
AB  - temperate character of these phages was tested in other isolates of
AB  - Streptomyces. Four of the phages ( phiSS3, phiSS12, phiSS13 and
AB  - phiSS17) were identified as temperate phages, since they were able to
AB  - lysogenize SS3, SS12, SS13 and SS17. phiSS3, phiSS12 and, phiSS13 were
AB  - homoimmune, and they were heteroimmune with respect to SS17. The
AB  - restriction barriers of lysogenic isolates (SS12, SS13 and SS17)
AB  - interfered with the blockage of plaque formation by phages ( phiSS12,
AB  - phiSS13 or phiSS17) propagated on them, about 75 % of lysogenic
AB  - isolates had restriction systems. The exposure of the lysogenic
AB  - isolates (SS12, SS13 and SS17) to UV-irradiation prevented the possible
AB  - restriction barriers of these isolates so that these barriers could be
AB  - overcome.
ER  -

TY  - JOUR
AU  - Elbir, H.
AU  - Gimenez, G.
AU  - Robert, C.
AU  - Bergstrom, S.
AU  - Cutler, S.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Complete Genome Sequence of Borrelia crocidurae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3723
EP  - 3724
VL  - 194
AB  - We announce the draft genome sequence of Borrelia crocidurae (strain Achema). The 1,557,560-bp
AB  - genome (27% GC content) comprises one 919,477-bp linear chromosome
AB  - and 638,083-bp plasmids that together carry 1,472 open reading frames, 32 tRNAs,
AB  - and three complete rRNAs, with almost complete colinearity between B. crocidurae
AB  - and Borrelia duttonii chromosomes.
ER  -

TY  - JOUR
AU  - Elbir, H.
AU  - Larsson, P.
AU  - Normark, J.
AU  - Upreti, M.
AU  - Korenberg, E.
AU  - Larsson, C.
AU  - Bergstrom, S.
TI  - Genome Sequence of the Asiatic Species Borrelia persica.
JO  - Genome Announcements
PY  - 2014
SP  - e01127
EP  - e01113
VL  - 2
AB  - We report the complete genome sequence of Borrelia persica, the causative agent of tick-borne
AB  - relapsing fever borreliosis on the Asian continent. Its genome of
AB  - 1,784,979 bp contains 1,850 open reading frames, three ribosomal RNAs, and 32
AB  - tRNAs. One clustered regularly interspaced short palindromic repeat (CRISPR) was
AB  - detected.
ER  -

TY  - JOUR
AU  - Elbir, H.
AU  - Larsson, P.
AU  - Upreti, M.
AU  - Normark, J.
AU  - Bergstrom, S.
TI  - Genome Sequence of the Relapsing Fever Borreliosis Species Borrelia hispanica.
JO  - Genome Announcements
PY  - 2014
SP  - e01171
EP  - e01113
VL  - 2
AB  - Borrelia hispanica is the etiological pathogen of tick-borne relapsing fever, transmitted to
AB  - humans by infected Ornithodoros erraticus ticks. Here we present
AB  - the 1,783,846-bp draft genome sequence, with an average G+C content of 28%. It
AB  - has 2,140 open reading frames, 3 ribosomal RNAs, and 32 transfer RNAs.
ER  -

TY  - JOUR
AU  - Elbir, H.
AU  - Robert, C.
AU  - Nguyen, T.T.
AU  - Gimenez, G.
AU  - El Sanousi, S.M.
AU  - Flock, J.I.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 1
EP  - 13
VL  - 9
AB  - Staphylococcus aureus subsp. anaerobius is responsible for Morel's disease in animals and a
AB  - cause of abscess in humans. It is characterized by a
AB  - microaerophilic growth, contrary to the other strains of S. aureus. The
AB  - 2,604,446-bp genome (32.7% GC content) of S. anaerobius ST1464 comprises one
AB  - chromosome and no plasmids. The chromosome contains 2,660 open reading frames
AB  - (ORFs), 49 tRNAs and three complete rRNAs, forming one complete operon. The size
AB  - of ORFs ranges between 100 to 4,600 bp except for two ORFs of 6,417 and 7,173 bp
AB  - encoding segregation ATPase and non-ribosomal peptide synthase, respectively. The
AB  - chromosome harbors Staphylococcus phage 2638A genome and incomplete
AB  - Staphylococcus phage genome PT1028, but no detectable CRISPRS. The antibiotic
AB  - resistance gene for tetracycline was found although Staphylococcus aureus subsp.
AB  - anaerobius is susceptible to tetracycline in-vitro. Intact oxygen detoxification
AB  - genes encode superoxide dismutase and cytochrome quinol oxidase whereas the
AB  - catalase gene is impaired by a stop codon. Based on the genome, in-silico
AB  - multilocus sequence typing indicates that S. aureus subsp. anaerobius emerged as
AB  - a clone separated from all other S. aureus strains, illustrating host-adaptation
AB  - linked to missing functions. Availability of S. aureus subsp. anaerobius genome
AB  - could prompt the development of post-genomic tools for its rapid discrimination
AB  - from S. aureus.
ER  -

TY  - JOUR
AU  - Elbir, H.
AU  - Sitlani, P.
AU  - Bergstrom, S.
AU  - Barbour, A.G.
TI  - Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus.
JO  - Genome Announcements
PY  - 2017
SP  - e00018
EP  - e00017
VL  - 5
AB  - Sequences of the linear chromosome and plasmids of Borrelia anserina, the cause of avian
AB  - spirochetosis of poultry, revealed a smaller genome than those of other
AB  - Borrelia spp. transmitted by argasid ticks. Missing or disrupted genes included a
AB  - dam methylase and those in the pathway for synthesis of phospholipids from
AB  - glycerol.
ER  -

TY  - JOUR
AU  - Elcheninov, A.G.
AU  - Menzel, P.
AU  - Gudbergsdottir, S.R.
AU  - Slesarev, A.I.
AU  - Kadnikov, V.V.
AU  - Krogh, A.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Peng, X.
AU  - Kublanov, I.V.
TI  - Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches.
JO  - Front. Microbiol.
PY  - 2017
SP  - 2140
EP  - 2140
VL  - 8
AB  - Xanthan gum, a complex polysaccharide comprising glucose, mannose and glucuronic  acid
AB  - residues, is involved in numerous biotechnological applications in
AB  - cosmetics, agriculture, pharmaceuticals, food and petroleum industries.
AB  - Additionally, its oligosaccharides were shown to possess antimicrobial,
AB  - antioxidant, and few other properties. Yet, despite its extensive usage, little
AB  - is known about xanthan gum degradation pathways and mechanisms. Thermogutta
AB  - terrifontis, isolated from a sample of microbial mat developed in a terrestrial
AB  - hot spring of Kunashir island (Far-East of Russia), was described as the first
AB  - thermophilic representative of the Planctomycetes phylum. It grows well on
AB  - xanthan gum either at aerobic or anaerobic conditions. Genomic analysis unraveled
AB  - the pathways of oligo- and polysaccharides utilization, as well as the mechanisms
AB  - of aerobic and anaerobic respiration. The combination of genomic and
AB  - transcriptomic approaches suggested a novel xanthan gum degradation pathway which
AB  - involves novel glycosidase(s) of DUF1080 family, hydrolyzing xanthan gum backbone
AB  - beta-glucosidic linkages and beta-mannosidases instead of xanthan lyases,
AB  - catalyzing cleavage of terminal beta-mannosidic linkages. Surprisingly, the genes
AB  - coding DUF1080 proteins were abundant in T. terrifontis and in many other
AB  - Planctomycetes genomes, which, together with our observation that xanthan gum
AB  - being a selective substrate for many planctomycetes, suggest crucial role of
AB  - DUF1080 in xanthan gum degradation. Our findings shed light on the metabolism of
AB  - the first thermophilic planctomycete, capable to degrade a number of
AB  - polysaccharides, either aerobically or anaerobically, including the
AB  - biotechnologically important bacterial polysaccharide xanthan gum.
ER  -

TY  - JOUR
AU  - Eldarov, M.A.
AU  - Karpichev, I.V.
AU  - Samko, O.T.
AU  - Anikeitcheva, N.V.
AU  - Kalugin, A.A.
AU  - Khoroshoutina, E.B.
AU  - Sokolov, N.N.
TI  - Isolation and characterization of restriction endonuclease BcuAI from Bacillus cereus A.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2898
EP  - 2898
VL  - 20
AB  - Restriction endonuclease BcuAI, an isoschizomer of AvaII (Figure 1), has been purified from
AB  - Bacillus cereus A. The procedure of isolation of BcuAI included the fractionation with
AB  - ammonium sulfate and column chromatography on DEAE-Sepharose (elution buffer 10 mM
AB  - K-phosphate, pH 7.4, 0.1 mM EDTA, 1 mM DTT, 0.0-1.0 M KCl; elution zone of enzyme activity
AB  - 0.2-0.3 M KCl). 1400 u. BcuAI can be obtained from 1 g. of wet cells. BcuAI showed maximal
AB  - activity at 30-37C, pH between 7.6-8.2, MgCl2 concentration in the range of 5-10 mM and at
AB  - high ionic strength.
ER  -

TY  - JOUR
AU  - Eldarov, M.A.
AU  - Karpichev, I.V.
AU  - Samko, O.T.
AU  - Anikeitcheva, N.V.
AU  - Kalugin, A.A.
AU  - Khoroshoutina, E.B.
AU  - Sokolov, N.N.
TI  - Characterization of BciBII, an isoschizomer of BstNI from a strain of Bacillus circulans B.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2896
EP  - 2896
VL  - 20
AB  - BciBII, an isoschizomer of BstNI (figure 1) has been isolated from Bacillus circulans B. The
AB  - enzyme was purified by precipitation with polyethylenimine, ammonium sulfate and subsequent
AB  - column chromatography on DEAE-sepharose, Blue sepharose and phosphocellulose. Restriction
AB  - endonuclease BciBII showed maximal activity at 37C, pH between 7.4-7.8, MgCl2 concentration in
AB  - the range of 8-12 mM and at high ionic strenghth.
ER  -

TY  - JOUR
AU  - Elde, M.
AU  - Haugen, P.
AU  - Willassen, N.P.
AU  - Johansen, S.
TI  - I-NjaI, a nuclear intron-encoded homing endonuclease from Naegleria, generates a pentanucleotide 3' cleavage-overhang within a 19 base-pair partially symmetric DNA recognition site.
JO  - Eur. J. Biochem.
PY  - 1999
SP  - 281
EP  - 288
VL  - 259
AB  - Different species of the amoebo-flagellate Naegleria harbor optional group I introns in the
AB  - nuclear ribosomal DNA that contain open reading frames.  Intron proteins from Naegleria
AB  - jamiesoni, Naegleria andersoni, and Naegleria italica (named I-NjaI, I-NanI and I-NitI,
AB  - respectively) were expressed in Escherichia coli and found to be isoschizomeric homing
AB  - endonucleases that specifically recognize and cleave intron-lacking homologous alleles of
AB  - ribosomal DNA.  The I-NjaI endonuclease was affinity purified, characterized in more detail,
AB  - and found to generate five-nucleotide 3' staggered ends at the intron insertion site which
AB  - differs from the ends generated by all other known homing endonucleases.  The recognition site
AB  - was delimited and found to cover an ~19 base-pair partially symmetric sequence spanning both
AB  - the cleavage site and the intron insertion site.  The palindromic feature was supported by
AB  - mutational analysis of the target DNA.  All single-site substitutions within the recognition
AB  - sequence were cleaved by the purified I-NjaI endonuclease, but at different efficiencies.  The
AB  - center for symmetry and cleavage was found to be completely degenerate in specificity, which
AB  - resembles that of the subclass IIW bacterial restriction enzymes.
ER  -

TY  - JOUR
AU  - Elde, M.
AU  - Willassen, N.P.
AU  - Johansen, S.
TI  - Functional characterization of isoschizomeric His-Cys box homing endonucleases from Naegleria.
JO  - Eur. J. Biochem.
PY  - 2000
SP  - 7257
EP  - 7266
VL  - 267
AB  - Several species within the amoeboflagellate genus Naegleria harbor an optional ORF containing
AB  - group I introns in their nuclear small subunit ribosomal DNA. The different ORFs encode homing
AB  - endonucleases with 65 to 95% identity at the amino-acid level. I-NjaI, I-NanI and I-NitI, from
AB  - introns in Naegleria jamiesoni, N. andersoni and N. italica, respectively, were analyzed in
AB  - more detail and found to be isoschizomeric endonucleases that recognize and cleave an
AB  - approximately 19-bp partially symmetrical sequence, creating a pentanucleotide 3' overhang
AB  - upon
AB  - cleavage. The optimal conditions for cleavage activity with respect to temperature, pH, salt
AB  - and divalent metal ions were investigated. The optimal cleavage temperature for all three
AB  - endonucleases was found to be 37 degrees C and the activity was dependent on the concentration
AB  - of NaCl with an optimum at 200 mM. Divalent metal ions, primarily Mg2+, are essential for
AB  - Naegleria endonuclease activity. Whereas both Mn2+ and Ca2+ could substitute for Mg2+, but
AB  - with a slower cleavage rate, Zn2+ was unable to support cleavage. Interestingly, the pH
AB  - dependence of DNA cleavage was found to vary significantly between the I-NitI and
AB  - I-NjaI/I-NanI endonucleases with optimal pH values at 6.5 and 9, respectively. Site-directed
AB  - mutagenesis of conserved I-NjaI residues strongly supports the hypothesis that Naegleria
AB  - homing endonucleases share a similar zinc-binding structure and active site with the His-Cys
AB  - box homing endonuclease I-PpoI.
ER  -

TY  - JOUR
AU  - Elfadl, A.K.
AU  - Lee, S.W.
AU  - Kim, J.H.
AU  - Lee, K.L.
AU  - Arif-Ullah, H.M.
AU  - Chung, M.J.
AU  - Ghim, S.G.
AU  - Lee, E.J.
AU  - Kim, Y.D.
AU  - Kim, S.M.
AU  - Jeon, S.G.
AU  - Lim, J.H.
AU  - Choi, H.J.
AU  - Park, J.K.
AU  - Jeong, K.S.
TI  - Fatal fibrino-hemorrhagic bronchopneumonia associated with Morganella morganii in a bottlenose dolphin: a case report.
JO  - Dis. Aquat. Org.
PY  - 2017
SP  - 41
EP  - 47
VL  - 127
AB  - A 5 yr old, 184 kg, and 262 cm total length female bottlenose dolphin Tursiops
AB  - truncatus was found dead in a display after bloody discharge from the blowhole
AB  - was observed 3 h prior to death. Pathological examination revealed fibrinous
AB  - bronchopneumonia with prominent areas of necrosis (sequestra) and numerous
AB  - Gram-negative bacilli within alveoli and in blood vessels of the lungs and liver
AB  - and between muscle fibers. The cause of death was attributed to septicemia.
AB  - Often, cases of fibrinous bronchopneumonia are characterized by bacteremia in the
AB  - latter stages of infection, resulting in the death of the animal. Septicemia
AB  - likely accounts for the ecchymoses and petechiae noted on the spleen, pancreas,
AB  - forestomach, lungs, visceral peritoneum, and small intestine. Additional lesions
AB  - included hemothorax, stable red frothy fluid in the trachea, and lymphoid
AB  - depletion in the spleen and lymph nodes. Pure growth of Morganella morganii was
AB  - isolated from the lungs, blood, liver, and blowhole mucosa. Sequencing of 16s
AB  - rRNA of the isolated bacteria showed more than 99.6% identity with M. morganii
AB  - strain FDAARGOS_172. To our knowledge, this is the first report of fatal
AB  - fibrinonecrotizing bronchopneumonia associated with M. morganii infection in a
AB  - cetacean.
ER  -

TY  - JOUR
AU  - Elhai, J.
TI  - Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases.
JO  - Life
PY  - 2015
SP  - 921
EP  - 948
VL  - 5
AB  - The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency
AB  - in cyanobacterial genomes. An important clue to its function may
AB  - be the presence of two orphan DNA methyltransferases that recognize internal
AB  - sequences GATC and CGATCG. An examination of genomes from 97 cyanobacteria, both
AB  - free-living and obligate symbionts, showed that there are exceptional cases in
AB  - which HIP1 is at a low frequency or nearly absent. In some of these cases, it
AB  - appears to have been replaced by a different GC-rich palindromic sequence,
AB  - alternate HIPs. When HIP1 is at a high frequency, GATC- and CGATCG-specific
AB  - methyltransferases are generally present in the genome. When an alternate HIP is
AB  - at high frequency, a methyltransferase specific for that sequence is present. The
AB  - pattern of 1-nt deviations from HIP1 sequences is biased towards the first and
AB  - last nucleotides, i.e., those distinguish CGATCG from HIP1. Taken together, the
AB  - results point to a role of DNA methylation in the creation or functioning of HIP
AB  - sites. A model is presented that postulates the existence of a GmeC-dependent
AB  - mismatch repair system whose activity creates and maintains HIP sequences.
ER  -

TY  - JOUR
AU  - Elhai, J.
TI  - Determination of bias in the relative abundance of oligonucleotides in DNA sequences.
JO  - J. Comput. Biol.
PY  - 2001
SP  - 151
EP  - 175
VL  - 8
AB  - Different statistical measures of bias of oligonucleotide sequences in DNA sequences were
AB  - compared, both by theoretical analysis and according to their abilities to predict the
AB  - relative abundances of oligonucleotides in the genome of Escherichia coli. The expected
AB  - frequency of an oligonucleotide calculated from a maximal order Markov model was shown to be a
AB  - degenerate case of the expected frequency calculated from biases of all subwords arising when
AB  - noncontiguous subwords exhibit no bias. Since (at least in E, coli) noncontiguous sequences
AB  - exhibit significant bias, the total compositional bias
AB  - approach is expected to represent biases in genomic sequences more
AB  - faithfully than Markov approaches. In fact, the efficacy of statistics
AB  - based on Markov analysis even at the highest order were inferior in
AB  - predicting actual frequencies of oligonucleotides to methods that
AB  - factored out biases of internal subwords with gaps. Using total
AB  - compositional bias as a measure of relative abundance, tetranucleotide
AB  - and hexanucleotide palindromes were found to be distributed differently
AB  - from nonpalindromic sequences, with their means shifted somewhat
AB  - towards underrepresentation, A subpopulation of palindromic
AB  - hexanucleotides, however, was highly underrepresented, and this group
AB  - consisted almost entirely of targets for Type II restriction enzymes
AB  - found within strains of E, coli, Sites recognized by Type I
AB  - endonucleases from related strains were not markedly biased, and with
AB  - pentanucleotides, palindromic and nonpalindromic sequences had nearly
AB  - identical distributions. The loss of restriction sites may be explained
AB  - by the free transfer of plasmids encoding restriction enzymes and
AB  - episodic selection for the presence of the enzymes.
ER  -

TY  - JOUR
AU  - Elhai, J.
AU  - Cai, Y.
AU  - Wolk, C.P.
TI  - Conduction of pEC22, a plasmid coding for MR.EcoT22I, mediated by a resident Tn3-like transposon, Tn5396.
JO  - J. Bacteriol.
PY  - 1994
SP  - 5059
EP  - 5067
VL  - 176
AB  - pEC22 is a small plasmid that encodes the restriction-modification system MR.EcoT22I.
AB  - Restriction and functional analysis of the plasmid identified the positions of genes encoding
AB  - that system. The plasmid is able to be conducted by conjugal plasmids, a process mediated by a
AB  - transposon contained within pEC22. This cryptic transposon, called Tn5396, was isolated from
AB  - pEC22 and partially sequenced. The sequence of Tn5396 is for the most part typical of
AB  - transposons of the Tn3 family and is most similar to that of Tn1000. The transposon differs
AB  - from closely related transposons in that it lacks well-conserved sequences in the
AB  - inverted-repeat region and has an unusually long terminal inverted repeat. Consideration of
AB  - regions of internal sequence similarity in this and other transposons in the Tn3 family
AB  - supports a theory of the mechanism by which the ends of Tn3-like transposons may maintain
AB  - substantial identity between their inverted repeats over the course of evolutionary time.
ER  -

TY  - JOUR
AU  - Elhai, J.
AU  - Vepritskiy, A.
AU  - Muro-Pastor, A.M.
AU  - Flores, E.
AU  - Wolk, C.P.
TI  - Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120.
JO  - J. Bacteriol.
PY  - 1997
SP  - 1998
EP  - 2005
VL  - 179
AB  - The efficiency of conjugal transfer of plasmids from Escherichia coli to the cyanobacterium
AB  - Anabaena sp. strain PCC 7120 was quantitated as a function of the number of restriction sites
AB  - for the restriction enzymes carried by the recipient.  In addition to the previously
AB  - recognized isoschizomers of AvaI and AvaII, PCC 7120 was found to possess an isoschizomer of
AB  - AvaIII.  Plasmids modified in E. coli with methylases that protect in vitro against
AB  - restriction by the three enzymes were transferred with high efficiency, nearly independent of
AB  - the number of restriction sites on the plasmid.  Plasmids left unprotected against one of the
AB  - three restriction enzymes were transferred with lower efficiencies.  For low numbers of sites,
AB  - the efficiency of conjugal transfer decreased as an exponential function of the number of
AB  - unprotected sites.  The methods presented may be used to increase the efficiency of conjugal
AB  - transfer into restriction-competent bacteria.
ER  -

TY  - JOUR
AU  - Elkins, J.G. et al.
TI  - Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47T.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6099
EP  - 6100
VL  - 192
AB  - Caldicellulosiruptor obsidiansis OB47(T) (ATCC BAA-2073, JCM 16842) is an extremely
AB  - thermophilic, anaerobic bacterium capable of hydrolyzing
AB  - plant-derived polymers through the expression of
AB  - multidomain/multifunctional hydrolases. The complete genome sequence
AB  - reveals a diverse set of carbohydrate-active enzymes and provides further
AB  - insight into lignocellulosic biomass hydrolysis at high temperatures.
ER  -

TY  - JOUR
AU  - Elkins, J.G. et al.
TI  - A korarchaeal genome reveals insights into the evolution of the Archaea.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 8102
EP  - 8107
VL  - 105
AB  - The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by
AB  - their small subunit rRNA phylogeny, may have
AB  - diverged early from the major archaeal phyla Crenarchaeota and
AB  - Euryarchaeota. Here, we report the initial characterization of a member of
AB  - the Korarchaeota with the proposed name, "Candidatus Korarchaeum
AB  - cryptofilum," which exhibits an ultrathin filamentous morphology. To
AB  - investigate possible ancestral relationships between deep-branching
AB  - Korarchaeota and other phyla, we used whole-genome shotgun sequencing to
AB  - construct a complete composite korarchaeal genome from enriched cells. The
AB  - genome was assembled into a single contig 1.59 Mb in length with a G + C
AB  - content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%)
AB  - could be assigned to a revised set of archaeal Clusters of Orthologous
AB  - Groups (COGs). The predicted gene functions suggest that the organism
AB  - relies on a simple mode of peptide fermentation for carbon and energy and
AB  - lacks the ability to synthesize de novo purines, CoA, and several other
AB  - cofactors. Phylogenetic analyses based on conserved single genes and
AB  - concatenated protein sequences positioned the korarchaeote as a deep
AB  - archaeal lineage with an apparent affinity to the Crenarchaeota. However,
AB  - the predicted gene content revealed that several conserved cellular
AB  - systems, such as cell division, DNA replication, and tRNA maturation,
AB  - resemble the counterparts in the Euryarchaeota. In light of the known
AB  - composition of archaeal genomes, the Korarchaeota might have retained a
AB  - set of cellular features that represents the ancestral archaeal form.
ER  -

TY  - JOUR
AU  - Elkins, J.G. et al.
TI  - Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.
JO  - Genome Announcements
PY  - 2013
SP  - e00162
EP  - e00113
VL  - 1
AB  - Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from
AB  - Obsidian Pool, Yellowstone National Park, and grows optimally at 83 degrees
AB  - C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has
AB  - been deposited for future genomic studies pertaining to microbial processes and
AB  - nutrient cycles in high-temperature environments.
ER  -

TY  - JOUR
AU  - Ellegaard, K.M.
AU  - Klasson, L.
AU  - Naslund, K.
AU  - Bourtzis, K.
AU  - Andersson, S.G.
TI  - Comparative genomics of wolbachia and the bacterial species concept.
JO  - PLoS Genet.
PY  - 2013
SP  - E1003381
EP  - E1003381
VL  - 9
AB  - The importance of host-specialization to speciation processes in obligate
AB  - host-associated bacteria is well known, as is also the ability of recombination
AB  - to generate cohesion in bacterial populations. However, whether divergent strains
AB  - of highly recombining intracellular bacteria, such as Wolbachia, can maintain
AB  - their genetic distinctness when infecting the same host is not known. We first
AB  - developed a protocol for the genome sequencing of uncultivable endosymbionts.
AB  - Using this method, we have sequenced the complete genomes of the Wolbachia
AB  - strains wHa and wNo, which occur as natural double infections in Drosophila
AB  - simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa
AB  - belong to supergroup A and wNo to supergroup B. A comparative genomics study
AB  - including additional strains supported the supergroup classification scheme and
AB  - revealed 24 and 33 group-specific genes, putatively involved in host-adaptation
AB  - processes. Recombination frequencies were high for strains of the same supergroup
AB  - despite different host-preference patterns, leading to genomic cohesion. The
AB  - inferred recombination fragments for strains of different supergroups were of
AB  - short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo
AB  - were not more similar to each other and did not share more genes than other A-
AB  - and B-group strains that infect different hosts. We conclude that Wolbachia
AB  - strains of supergroup A and B represent genetically distinct clades, and that
AB  - strains of different supergroups can co-exist in the same arthropod host without
AB  - converging into the same species. This suggests that the supergroups are
AB  - irreversibly separated and that barriers other than host-specialization are able
AB  - to maintain distinct clades in recombining endosymbiont populations. Acquiring a
AB  - good knowledge of the barriers to genetic exchange in Wolbachia will advance our
AB  - understanding of how endosymbiont communities are constructed from vertically and
AB  - horizontally transmitted genes.
ER  -

TY  - JOUR
AU  - Elliott, A.G.
AU  - Ganesamoorthy, D.
AU  - Coin, L.
AU  - Cooper, M.A.
AU  - Cao, M.D.
TI  - Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain ATCC 700603.
JO  - Genome Announcements
PY  - 2016
SP  - e00438
EP  - e00416
VL  - 4
AB  - Klebsiella quasipneumoniae subsp. similipneumoniae strain ATCC 700603, formerly known as K.
AB  - pneumoniae K6, is known for producing extended-spectrum
AB  - beta-lactamase (ESBL) enzymes that can hydrolyze oxyimino-beta-lactams, resulting
AB  - in resistance to these drugs. We herein report the complete genome of strain ATCC
AB  - 700603 and show that the ESBL genes are plasmid-encoded.
ER  -

TY  - JOUR
AU  - Elliott, S.L.
AU  - Brazier, J.
AU  - Cosstick, R.
AU  - Connolly, B.A.
TI  - Mechanism of the Escherichia coli DNA T:G-mismatch endonuclease (Vsr protein) probed with thiophosphate-containing oligodeoxynucleotides.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 692
EP  - 703
VL  - 353
AB  - The mechanism of the Escherichia coli DNA T:G mismatch endonuclease (Vsr) has been
AB  - investigated using oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric
AB  - phosphorothioates and a 3'-phosphorothiolate. Binding and kinetic data with the
AB  - phosphorothioates/phosphorothiolate indicate that the two magnesium ions, which constitute
AB  - essential co-factors, are required to stabilise the extra negative charge developed on the
AB  - phosphate as the transition state is formed. Additionally one of the magnesium ions serves to
AB  - activate the leaving group (the non-bridging 3'-oxygen atom of the scissile phosphate) during
AB  - the hydrolysis reaction. Stereochemical analysis, using the R(p) phosphorothioate isomer,
AB  - indicates that Vsr carries out a hydrolytic reaction with inversion of stereochemistry at
AB  - phosphorus, compatible with an in-line attack of water and a pentacovalent transition state
AB  - with trigonal bipyramidal geometry. In conjunction with structures of Vsr bound to its
AB  - products, these data allow the reconstruction of the enzyme-substrate complex and a
AB  - comprehensive description of the hydrolysis mechanism.
ER  -

TY  - JOUR
AU  - Elliott, T.
TI  - Cloning, genetic characterization, and nucleotide sequence of the hemA-prfA operon of Salmonella typhimurium.
JO  - J. Bacteriol.
PY  - 1989
SP  - 3948
EP  - 3960
VL  - 171
AB  - The first step in heme biosynthesis is the formation of 5-aminolevulinic acid (ALA). Mutations
AB  - in two genes, hemA and hemL, result in auxotrophy for ALA in Salmonella typhimurium, but the
AB  - roles played by these genes and the mechanism of ALA synthesis are not understood. I have
AB  - cloned and sequenced the S. typhimurium hemA gene. The predicted polypeptide sequence for the
AB  - HemA protein shows no similarity to known ALA synthases, and no ALA synthase activity was
AB  - detected in extracts prepared from strains carrying the cloned hemA gene. Genetic analysis,
AB  - DNA sequencing of amber mutations, and maxicell studies proved that the open reading frame
AB  - identified in the DNA sequence encodes HemA. Another surprising finding of this study is that
AB  - hemA lies directly upstream of prfA, which encodes peptide chain release factor 1 (RF-1). A
AB  - hemA::Kan insertion mutation, constructed in vitro, was transferred to the chromosome and used
AB  - to show that these two genes form an operon. The hemA gene ends with an amber codon,
AB  - recognized by RF-1. I suggest a model for autogenous control of prfA expression by translation
AB  - reinitiation.
ER  -

TY  - JOUR
AU  - Ellis, D.J.
AU  - Dryden, D.T.
AU  - Berge, T.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopy.
JO  - Nat. Struct. Biol.
PY  - 1999
SP  - 15
EP  - 17
VL  - 6
AB  - Type I DNA restriction and modification enzymes such as EcoKI are multimeric enzymes that
AB  - cleave DNA molecules lacking an appropriate pattern of methylation on a target sequence,
AB  - thereby protecting the host bacterium from invasion by foreign DNA.  The reaction involves the
AB  - initial recognition of an unmethylated DNA target sequence with the aid of the cofactor
AB  - S-adenosyl methionine.  Recognition is followed by extensive ATP-dependent translocation of
AB  - the DNA in both directions toward the enzyme, which remains bound at the target sequence.
AB  - Eventually, endonucleolytic cleavage of the DNA occurs.  Recently, protein complexes with
AB  - nucleic acids have been imaged successfully using fluid tapping-mode atomic force microscopy.
AB  - In this study, we have used AFM to explore the type I DNA restriction and modification
AB  - pathway, and specifically to follow the ATP-dependent translocation and cleavage of a single
AB  - plasmid by the EcoKI enzyme complex under near-physiological conditions.
ER  -

TY  - JOUR
AU  - Ellison, D.W.
AU  - Clark, T.R.
AU  - Sturdevant, D.E.
AU  - Virtaneva, K.
AU  - Porcella, S.F.
AU  - Hackstadt, T.
TI  - Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa.
JO  - Infect. Immun.
PY  - 2008
SP  - 542
EP  - 550
VL  - 76
AB  - Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of
AB  - Rocky Mountain spotted fever. To identify genes
AB  - involved in the virulence of R. rickettsii, the genome of an avirulent
AB  - strain, R. rickettsii Iowa, was sequenced and compared to the genome of
AB  - the virulent strain R. rickettsii Sheila Smith. R. rickettsii Iowa is
AB  - avirulent in a guinea pig model of infection and displays altered plaque
AB  - morphology with decreased lysis of infected host cells. Comparison of the
AB  - two genomes revealed that R. rickettsii Iowa and R. rickettsii Sheila
AB  - Smith share a high degree of sequence identity. A whole-genome alignment
AB  - comparing R. rickettsii Iowa to R. rickettsii Sheila Smith revealed a
AB  - total of 143 deletions for the two strains. A subsequent single-nucleotide
AB  - polymorphism (SNP) analysis comparing Iowa to Sheila Smith revealed 492
AB  - SNPs for the two genomes. One of the deletions in R. rickettsii Iowa
AB  - truncates rompA, encoding a major surface antigen (rickettsial outer
AB  - membrane protein A [rOmpA]) and member of the autotransporter family, 660
AB  - bp from the start of translation. Immunoblotting and immunofluorescence
AB  - confirmed the absence of rOmpA from R. rickettsii Iowa. In addition, R.
AB  - rickettsii Iowa is defective in the processing of rOmpB, an
AB  - autotransporter and also a major surface antigen of spotted fever group
AB  - rickettsiae. Disruption of rompA and the defect in rOmpB processing are
AB  - most likely factors that contribute to the avirulence of R. rickettsii
AB  - Iowa. Genomic differences between the two strains do not significantly
AB  - alter gene expression as analysis of microarrays revealed only four
AB  - differences in gene expression between R. rickettsii Iowa and R.
AB  - rickettsii strain R. Although R. rickettsii Iowa does not cause apparent
AB  - disease, infection of guinea pigs with this strain confers protection
AB  - against subsequent challenge with the virulent strain R. rickettsii Sheila
AB  - Smith.
ER  -

TY  - JOUR
AU  - Ellison, E.L.
AU  - Muscarella, D.E.
AU  - Vogt, V.M.
TI  - Characterization of I-PpoI, an intron-encoded endonuclease from Physarum polycephalum.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 177
EP  - 177
VL  - 17C
AB  - The genetic mobility of group I introns is dependent upon the site-specific endonucleases
AB  - which they encode. We have characterized several properties of I-PpoI, the endonuclease that
AB  - mediates "homing" of intron 3 (PpLSU3) in the nuclear ribosomal DNA (rDNA) of the slime mold
AB  - Physarum polycephalum. From deletion analysis, we conclude that the minimum recognition site
AB  - is a sequence of 15 bp, which is partially symmetric. The purified enzyme behaves as a dimer
AB  - in gel filtration and sedimentation. We have studied the interaction of I-PpoI with DNA by
AB  - bandshift analysis, MPE footprinting and DMS protection. The enzyme, which binds in the major
AB  - groove, protects ca. 21bp of DNA surrounding the cleavage site. The I-PpoI recognition site is
AB  - present in the nuclear rDNA of all eucaryotes. In yeast, expression of the enzyme is lethal,
AB  - presumably because of cleavage of rDNA repeats on chromosome XII. By pulse field gel analysis,
AB  - this is the only chromosome cut in vitro. Yeast mutants that survive the lethal effects of the
AB  - endonuclease occur at surprisingly high frequencies, and are of at least two classes. The
AB  - first consists of cells carrying point mutations in the recognition sequence. All ca. 150
AB  - copies of the rDNA are mutant, as evidenced by the inability of I-PpoI to cleave the rDNA in
AB  - vitro. The second class consists of cells in which the intron has become inserted into all
AB  - copies of the rDNA. These cells express active endonuclease.
ER  -

TY  - JOUR
AU  - Ellison, E.L.
AU  - Vogt, V.M.
TI  - Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.
JO  - Mol. Cell. Biol.
PY  - 1993
SP  - 7531
EP  - 7539
VL  - 13
AB  - Endonucleases encoded by mobile group I introns are highly specific DNases that induce a
AB  - double-strand break near the site to which the intron moves. I-PpoI from the acellular slime
AB  - mold Physarum polycephalum mediates the mobility of intron 3 (Pp LSU3) in the extrachromosomal
AB  - nuclear ribosomal DNA of this organism. We showed previously that cleavage by I-PpoI creates a
AB  - four-base staggered cut near the point of intron insertion. We have now characterized several
AB  - further properties of the endonuclease. As determined by deletion analysis, the minimal target
AB  - site recognized by I-PpoI was a sequence of 13 to 15 bp spanning the cleavage site. The
AB  - purified protein behaved as a globular dimer in sedimentation and gel filtration. In gel
AB  - mobility shift assays in the presence of EDTA, I-PpoI formed a stable and specific complex
AB  - with DNA, dissociating with a half-life of 45 minutes. By footprinting and interference assays
AB  - with methidiumpropyl-EDTA-intron(II), I-PpoI contacted a 22-to 24-bp stretch of DNA. The
AB  - endonuclease protected most of the purines found in both the major and minor grooves of the
AB  - DNA helix from modification by dimethylsulfate (DMS). However, the reactivity to DMS was
AB  - enhanced at some purines, suggesting that binding leads to a conformational change in the DNA.
AB  - The pattern of DMS protection differed fundamentally in the two partially symmetrical halves
AB  - of the recognition sequence.
ER  -

TY  - JOUR
AU  - Ellrott, K.P.
AU  - Kasarjian, J.K.A.
AU  - Jiang, T.
AU  - Ryu, J.
TI  - Restriction enzyme recognition sequence search program.
JO  - Biotechniques
PY  - 2002
SP  - 1322
EP  - 1326
VL  - 33
AB  - A critical and difficult part of characterizing restriction enzymes and methylases is the
AB  - identification of recognition sequences.  To simplify this process, we have developed a
AB  - plasmid transformation method along with a computer program named RM search that determines
AB  - the exact recognition sequences for given restriction and modification systems.
ER  -

TY  - JOUR
AU  - Elnahas, M.O.
AU  - De Leon, K.B.
AU  - Amin, M.A.
AU  - Hussein, M.M.D.
AU  - Ali, A.E.
AU  - Wall, J.D.
TI  - Complete Genome Sequencing of Streptomyces sp. Strain MOE7, Which Produces an Extracellular Polysaccharide with Antioxidant and Antitumor Activities.
JO  - Genome Announcements
PY  - 2017
SP  - e00442
EP  - e00417
VL  - 5
AB  - Streptomyces sp. strain MOE7 is a Gram-positive filamentous bacterium isolated from
AB  - agricultural soil in Columbia, Missouri, USA. Strain MOE7 produces an
AB  - extracellular polysaccharide with antioxidant and antitumor activities. Through
AB  - PacBio RSII sequencing, the MOE7 genome was found to be a linear chromosome of
AB  - 8,399,509 bp with 6,782 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Elsawy, H.
AU  - Chahar, S.
TI  - Increasing DNA substrate specificity of the EcoDam DNA-(adenine N-6)-methyltransferase by site-directed mutagenesis.
JO  - Biokhimiia
PY  - 2014
SP  - 1262
EP  - 1266
VL  - 79
AB  - DNA methylation catalyzed by DNA methyltransferases (MTases) is widespread in prokaryotes. In
AB  - an attempt to find EcoDam variants with enhanced preference for hemimethylated DNA, the L122,
AB  - P134, and V133 residues were replaced with other amino acids using site directed mutagenesis,
AB  - and the catalytic activity of all variants on unmethylated and hemimethylated substrates was
AB  - studied. Our results showed that, in addition to L122A, the L122S and L122A/V133L EcoDam
AB  - variants were able to sense the methylation status of the 5'-GATC-3' double-stranded target
AB  - recognition site and methylated only hemimethylated DNA.
ER  -

TY  - JOUR
AU  - Elsawy, H.
AU  - Chahar, S.
TI  - Increasing DNA substrate specificity of the EcoDam DNA-(adenine N-6)-methyltransferase by site-directed mutagenesis.
JO  - Biochemistry
PY  - 2014
SP  - 1262
EP  - 1266
VL  - 79
AB  - DNA methylation catalyzed by DNA methyltransferases (MTases) is widespread in prokaryotes. In
AB  - an attempt to find EcoDam variants with enhanced preference for hemimethylated DNA, the L122,
AB  - P134, and V133 residues were replaced with other amino acids using site directed mutagenesis,
AB  - and the catalytic activity of all variants on unmethylated and hemimethylated substrates was
AB  - studied. Our results showed that, in addition to L122A, the L122S and L122A/V133L EcoDam
AB  - variants were able to sense the methylation status of the 5'-GATC-3' double-stranded target
AB  - recognition site and methylated only hemimethylated DNA.
ER  -

TY  - JOUR
AU  - Elschner, M.C.
AU  - Busch, A.
AU  - Schliephake, A.
AU  - Gaede, W.
AU  - Zuchantke, E.
AU  - Tomaso, H.
TI  - High-Quality Genome Sequence of Bacillus anthracis Strain 14RA5914 Isolated during an Outbreak in Germany in 2014.
JO  - Genome Announcements
PY  - 2017
SP  - e01002
EP  - e01017
VL  - 5
AB  - Bacillus anthracis is a zoonotic agent causing anthrax, a notifiable disease in animals. The
AB  - last anthrax outbreak among cattle in Germany occurred in April 2014
AB  - in Saxony-Anhalt. Here we report a high-quality genome sequence of the Bacillus
AB  - anthracis strain 14RA5914 Dobichau isolated from the spleen of a dead cow.
ER  -

TY  - JOUR
AU  - Elschner, M.C.
AU  - Thomas, P.
AU  - El-Adawy, H.
AU  - Mertens, K.
AU  - Melzer, F.
AU  - Hnizdo, J.
AU  - Stamm, I.
TI  - Complete Genome Sequence of a Burkholderia pseudomallei Strain Isolated from a Pet Green Iguana in Prague, Czech Republic.
JO  - Genome Announcements
PY  - 2017
SP  - e01761
EP  - e01716
VL  - 5
AB  - Burkholderia pseudomallei was isolated from pus from an abscess of a pet iguana living in a
AB  - private household in Prague, Czech Republic. This paper presents the
AB  - complete genome sequence of B. pseudomallei strain VB976100.
ER  -

TY  - JOUR
AU  - Elschner, M.C.
AU  - Thomas, P.
AU  - Melzer, F.
TI  - Complete Genome Sequence of a Burkholderia mallei Isolate Originating from a Glanderous Horse from the Kingdom of Bahrain.
JO  - Genome Announcements
PY  - 2016
SP  - e01296
EP  - e01216
VL  - 4
AB  - Burkholderia mallei is a zoonotic agent causing glanders, a notifiable disease in equines.
AB  - During the past decades glanders emerged, and the Kingdom of Bahrain
AB  - reported outbreaks to the World Organization of Animal Health in 2010 and 2011.
AB  - This paper presents the complete genome sequence of the Burkholderia mallei
AB  - strain 11RR2811 Bahrain1.
ER  -

TY  - JOUR
AU  - Embleton, M.L.
AU  - Siksnys, V.
AU  - Halford, S.E.
TI  - DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 503
EP  - 514
VL  - 311
AB  - Several type II restriction endonucleases interact with two copies of their target sequence
AB  - before they cleave DNA. Three such enzymes,
AB  - NgoMIV, Cfr10I and NaeI, were tested on plasmids with one or two copies
AB  - of their recognition sites, and on catenanes containing two interlinked
AB  - rings of DNA with one site in each ring. The enzymes showed distinct
AB  - patterns of behaviour. NgoMIV and NaeI cleaved the plasmid with two
AB  - sites faster than that with one site and the catenanes at an
AB  - intermediate rate, while Cfr10I gave similar steady-state rates on all
AB  - three substrates. Both Cfr10I and NgoMIV converted the majority of the
AB  - substrates with two sites directly to the products cut at both sites,
AB  - while NaeI cleaved just one site at a time. All three enzymes thus
AB  - synapse two DNA sites through three-dimensional space before cleaving
AB  - DNA. With Cfr10I and NgoMIV, both sites are cleaved in one turnover, in
AB  - a manner consistent with their tetrameric structures, while the
AB  - cleavage of a single site by NaeI indicates that the second site acts
AB  - not as a substrate but as an activator, as reported previously. The
AB  - complexes spanning two sites have longer lifetimes on catenanes with
AB  - one site in each ring than on circular DNA with two sites, which
AB  - indicates that the catenanes have more freedom for site juxtaposition
AB  - than plasmids with sites in cis.
ER  -

TY  - JOUR
AU  - Embleton, M.L.
AU  - Vologodskii, A.V.
AU  - Halford, S.E.
TI  - Dynamics of DNA loop capture by the Sfil restriction endonuclease on supercoiled and relaxed DNA.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 53
EP  - 66
VL  - 339
AB  - The SfiI endonuclease is a prototype for DNA looping. It binds two copies of its recognition
AB  - sequence and, if Mg2+ is present, cuts both
AB  - concertedly. Looping was examined here on supercoiled and relaxed forms
AB  - of a 5.5 kb plasmid with three SfiI sites: sites 1 and 2 were separated
AB  - by 0.4 kb, and sites 2 and 3 by 2.0 kb. SfiI converted this plasmid
AB  - directly to the products cut at all three sites, though DNA species
AB  - cleaved at one or two sites were formed transiently during a burst
AB  - phase. The burst revealed three sets of doubly cut products,
AB  - corresponding to the three possible pairings of sites. The equilibrium
AB  - distribution between the different loops was evaluated from the burst
AB  - phases of reactions initiated by adding MgCl2 to SfiI bound to the
AB  - plasmid. The short loop was favored over the longer loops, particularly
AB  - on supercoiled DNA. The relative rates for loop capture were assessed
AB  - after adding SfiI to solutions containing the plasmid and MgCl2. On
AB  - both supercoiled and relaxed DNA, the rate of loop capture across 0.4
AB  - kb was only marginally faster than over 2.0 kb or 2.4 kb. The relative
AB  - strengths and rates of looping were compared to computer simulations of
AB  - conformational fluctuations in DNA. The simulations concurred broadly
AB  - with the experimental data, though they predicted that increasing site
AB  - separations should cause a shallower decline in the equilibrium
AB  - constants than was observed but a slightly steeper decline in the rates
AB  - for loop capture. Possible reasons for these discrepancies are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Embleton, M.L.
AU  - Williams, S.A.
AU  - Watson, M.A.
AU  - Halford, S.E.
TI  - Specificity from the synapsis of DNA elements by the SfiI endonuclease.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 785
EP  - 797
VL  - 289
AB  - The synapsis of DNA sites is a prerequisite for the reactions of many proteins that act at
AB  - specific DNA sequences. The requirement for synapsis was investigated by analysing the
AB  - reactions of SfiI, a tetrameric restriction enzyme that cleaves DNA only after interacting
AB  - with two recognition sites. In the presence of Mg2+, oligonucleotide duplexes with the cognate
AB  - recognition sequence were cleaved rapidly, with cooperative kinetics, while non-cognate
AB  - duplexes were not cleaved. In the absence of Mg2+, the primary complex formed by SfiI with
AB  - cognate DNA contained two duplexes synapsed by the tetramer: a secondary complex containing
AB  - one duplex was seen only at elevated SfiI concentrations. In contrast, the principal complex
AB  - with non-cognate DNA contained one duplex bound to SfiI. Pairs of non-cognate duplexes, or one
AB  - cognate and one non-cognate duplex, generally failed to form synaptic complexes. On adding
AB  - Mg2+to complexes with cognate DNA, cleavage occurred much more rapidly in the synaptic complex
AB  - than in the secondary complex. DNA synapsis thus acts to enhance the specificity of SfiI for
AB  - its recognition sequence, by demanding two cognate sites for a catalytically active complex
AB  - and by excluding non-cognate sites from the synaptic complex.
ER  -

TY  - JOUR
AU  - Embley, T.M.
AU  - Dyal, P.
AU  - Kilvington, S.
TI  - A group I intron in the small subunit ribosomal RNA gene from Naegleria andersoni ssp. andersoni strain PPMFB-6.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6411
EP  - 6411
VL  - 20
AB  - PCR reactions designed to amplify the entire small subunit (SSU) ribosomal RNA gene from
AB  - Naegleria species for phylogenetic analyses, demonstrated a single band of approximately 2 kb
AB  - in most species but a band of approximately 3.2 kb in strains of Naegleria andersoni,
AB  - Naegleria andersoni ssp. andersoni and Naegleria australiensis ssp. italica.  The extra length
AB  - in N.andersoni spp. andersoni strain PPMFB-6 is due to an insertion of approximately 1277 base
AB  - pairs in the coding sequence of the rRNA gene.  The insertion is sited near the tip of helix
AB  - 19 immediately prior to the conserved SSU rRNA sequence CC-AG.  Extraction and sizing of total
AB  - rRNA by gel electrophoresis revealed that the insertion was removed in vivo to produce a
AB  - mature SSU rRNA of the same size as strains lacking the insertion in their SSU gene.  The
AB  - insertion in N.andersoni ssp. andersoni was amplified and directly sequenced using a linear
AB  - PCR reaction.  Sequence analysis revealed that it contains motifs which identify it as a group
AB  - I intron.  Thus, the short sequences P, Q, R and S, which represent the conserved core
AB  - structure of group I introns, are all present and they occur in that order.  The intron also
AB  - contains a long open reading frame situated between R and S, which codes for a putative
AB  - protein of unknown function and containing 245 amino acids.  Group I introns are rare in
AB  - nuclear SSU rRNA genes and have hitherto only been reported in Ustilago maydis, Pneumocytis
AB  - carini and Ankistrodesmus stipitatus.  The introns in these taxa are all small (394-480
AB  - bases), they do not contain long open reading frames, and they are inserted at different
AB  - positions in the SSU rRNA gene.  Furthermore, Naegleria branches at a point in the eukaryote
AB  - phylogenetic tree which is much deeper than these taxa.  Thus, our observation significantly
AB  - extends the phylogenetic range of group I introns in Eukaryote nuclear SSU genes.
ER  -

TY  - JOUR
AU  - Emond, E.
AU  - Ee, E.L.
AU  - Drolet, G.
AU  - Moineau, S.
AU  - LaPointe, G.
TI  - Molecular characterization of a theta replication plasmid and its use for development of a two-component food-grade cloning system for Lactococcus lactis.
JO  - Appl. Environ. Microbiol.
PY  - 2001
SP  - 1700
EP  - 1709
VL  - 67
AB  - pCD4, a small, highly stable theta-replicating lactococcal plasmid, was
AB  - used to develop a food-grade cloning system. Sequence analysis revealed
AB  - five open reading frames and two putative cis-acting regions. None appears
AB  - to code for undesirable phenotypes with regard to food applications.
AB  - Functional analysis of the replication module showed that only the
AB  - cis-acting ori region and the repB gene coding for the replication
AB  - initiator protein were needed for the stable replication and maintenance
AB  - of pCD4 derivatives in Lactococcus lactis. A two-component food-grade
AB  - cloning system was derived from the pCD4 replicon. The vector pVEC1, which
AB  - carries the functional pCD4 replicon, is entirely made up of L. lactis DNA
AB  - and has no selection marker. The companion pCOM1 is a repB-deficient pCD4
AB  - derivative that carries an erythromycin resistance gene as a dominant
AB  - selection marker. The pCOM1 construct can only replicate in L. lactis if
AB  - trans complemented by the RepB initiator provided by pVEC1. Since only the
AB  - cotransformants that carry both pVEC1 and pCOM1 can survive on plates
AB  - containing erythromycin, pCOM1 can be used transiently to select cells
AB  - that have acquired pVEC1. Due to the intrinsic incompatibility between
AB  - these plasmids, pCOM1 can be readily cured from the cells grown on an
AB  - antibiotic-free medium after the selection step. The system was used to
AB  - introduce a phage resistance mechanism into the laboratory strain MG1363
AB  - of L. lactis and two industrial strains. The introduction of the antiphage
AB  - barrier did not alter the wild-type plasmid profile of the industrial
AB  - strains. The phenotype was stable after 100 generations and conferred an
AB  - effective resistance phenotype against phages of the 936 and c2 species.
ER  -

TY  - JOUR
AU  - Emond, E.
AU  - Holler, B.J.
AU  - Boucher, I.
AU  - Vandenbergh, P.A.
AU  - Vedamuthu, E.R.
AU  - Kondo, J.K.
AU  - Moineau, S.
TI  - Phenotypic and genetic characterization of the bacteriophage abortive infection mechanism AbiK from Lactococcus lactis.
JO  - Appl. Environ. Microbiol.
PY  - 1997
SP  - 1274
EP  - 1283
VL  - 63
AB  - The natural plasmid pSRQ800 isolated from Lactococcus lactis subsp. lactis W1 conferred strong
AB  - phage resistance against small isometric phages of the 936 and P335 species when introduced
AB  - into phage-sensitive L. lactis strains.  It had very limited effect on prolate phages of the
AB  - c2 species.  The phage resistance mechanism encoded on pSRQ800 is a temperature-sensitive
AB  - abortive infection system (Abi).  Plasmid pSRQ800 was mapped, and the Abi genetic determinant
AB  - was localized on a 4.5-kb EcoRI fragment.  Cloning and sequencing of the 4.5-kb fragment
AB  - allowed the identification of two large open reading frames.  Deletion mutants showed that
AB  - only orf1 was needed to produce the Abi phenotype.  orf1 (renamed abiK) coded for a predicted
AB  - protein of 599 amino acids (AbiK) with an estimated molecular size of 71.4 kDa and a pI of
AB  - 7.98.  DNA and protein sequence alignment programs found no significant homology with
AB  - databases.  However, a database query based on amino acid composition suggested that AbiK
AB  - might be in the same protein family as AbiA.  No phage DNA replication nor phage structural
AB  - protein production was detected in infected AbiK+ L. lactis cells.  This system is believed to
AB  - act at or prior to phage DNA replication.  When cloned into a high-copy vector, AbiK
AB  - efficiency increased 100-fold.  AbiK provides another powerful tool that can be used in
AB  - controlling phages during lactococcal fermentations.
ER  -

TY  - JOUR
AU  - Emond-Rheault, J.G.
AU  - Vincent, A.T.
AU  - Trudel, M.V.
AU  - Brochu, F.
AU  - Boyle, B.
AU  - Tanaka, K.H.
AU  - Attere, S.A.
AU  - Jubinville, E.
AU  - Loch, T.P.
AU  - Winters, A.D.
AU  - Faisal, M.
AU  - Frenette, M.
AU  - Derome, N.
AU  - Charette, S.J.
TI  - Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins.
JO  - Vet. Microbiol.
PY  - 2014
SP  - 68
EP  - 76
VL  - 175
AB  - Aeromonas salmonicida subsp. salmonicida is a fish pathogen. Analysis of its
AB  - genomic characteristics is required to determine the worldwide distribution of
AB  - the various populations of this bacterium. Genomic alignments between the 01-B526
AB  - pathogenic strain and the A449 reference strain have revealed a 51-kb chromosomal
AB  - insertion in 01-B526. This insertion (AsaGEI1a) has been identified as a new
AB  - genomic island (GEI) bearing prophage genes. PCR assays were used to detect this
AB  - GEI in a collection of 139 A. salmonicida subsp. salmonicida isolates. Three
AB  - forms of this GEI (AsaGEI1a, AsaGEI1b, AsaGEI2a) are now known based on this
AB  - analysis and the sequencing of the genomes of seven additional isolates. A new
AB  - prophage (prophage 3) associated with AsaGEI2a was also discovered. Each GEI
AB  - appeared to be strongly associated with a specific geographic region. AsaGEI1a
AB  - and AsaGEI2a were exclusively found in North American isolates, except for one
AB  - European isolate bearing AsaGEI2a. The majority of the isolates bearing AsaGEI1b
AB  - or no GEI were from Europe. Prophage 3 has also a particular geographic
AB  - distribution and was found only in North American isolates. We demonstrated that
AB  - A. salmonicida subsp. salmonicida possesses unsuspected elements of genomic
AB  - heterogeneity that could be used as indicators to determine the geographic
AB  - origins of isolates of this bacterium.
ER  -

TY  - JOUR
AU  - Emperle, M.
AU  - Rajavelu, A.
AU  - Kunert, S.
AU  - Arimondo, P.B.
AU  - Reinhardt, R.
AU  - Jurkowska, R.Z.
AU  - Jeltsch, A.
TI  - The DNMT3A R882H mutant displays altered flanking sequence preferences.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 3130
EP  - 3139
VL  - 46
AB  - The DNMT3A R882H mutation is frequently observed in acute myeloid leukemia (AML). It is
AB  - located in the subunit and DNA binding interface of DNMT3A and has been
AB  - reported to cause a reduction in activity and dominant negative effects. We
AB  - investigated the mechanistic consequences of the R882H mutation on DNMT3A showing
AB  - a roughly 40% reduction in overall DNA methylation activity. Biochemical assays
AB  - demonstrated that R882H does not change DNA binding affinity, protein stability
AB  - or subnuclear distribution of DNMT3A. Strikingly, DNA methylation experiments
AB  - revealed pronounced changes in the flanking sequence preference of the
AB  - DNMT3A-R882H mutant. Based on these results, different DNA substrates with
AB  - selected flanking sequences were designed to be favored or disfavored by R882H.
AB  - Kinetic analyses showed that the R882H favored substrate was methylated by R882H
AB  - with 45% increased rate when compared with wildtype DNMT3A, while methylation of
AB  - the disfavored substrate was reduced 7-fold. Our data expand the model of the
AB  - potential carcinogenic effect of the R882H mutation by showing CpG site specific
AB  - activity changes. This result suggests that R882 is involved in the indirect
AB  - readout of flanking sequence preferences of DNMT3A and it may explain the
AB  - particular enrichment of the R882H mutation in cancer patients by revealing
AB  - mutation specific effects.
ER  -

TY  - JOUR
AU  - Encinas, F.
AU  - Marin, M.A.
AU  - Ramos, J.N.
AU  - Vieira, V.V.
AU  - Mattos-Guaraldi, A.L.
AU  - Vicente, A.C.
TI  - Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil.
JO  - Memorias do Instituto Oswaldo Cruz
PY  - 2015
SP  - 817
EP  - 819
VL  - 110
AB  - We report the complete genome sequence and analysis of an invasive
AB  - Corynebacterium diphtheriae strain that caused endocarditis in Rio de Janeiro,
AB  - Brazil. It was selected for sequencing on the basis of the current relevance of
AB  - nontoxigenic strains for public health. The genomic information was explored in
AB  - the context of diversity, plasticity and genetic relatedness with other
AB  - contemporary strains.
ER  -

TY  - JOUR
AU  - Endlich, B.
AU  - Linn, S.
TI  - The DNA restriction endonuclease of Escherichia coli B.  I. Studies of the DNA translocation and the ATPase activities.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 5720
EP  - 5728
VL  - 260
AB  - Electron microscopic examination of DNA intermediates formed by the restriction
AB  - endonuclease of Escherichia coli B revealed supercoiled loops that are
AB  - presumably formed during an ATP-dependent DNA translocation process in which
AB  - the enzyme remains bound to the recognition site while tracking along the DNA
AB  - helix to a cleavage site.  The rate of DNA translocation during this process is
AB  - at least 5000 base pairs/min at 37C.  Even after all cleavages have been
AB  - completed, complexes are seen that contain terminal loops or loop plus tail
AB  - structures.  During this later phase of the reaction, ATP is hydrolyzed at a
AB  - rate which is dependent upon the size of the largest possible loop (or loop
AB  - plus tail); this ATP hydrolysis can be terminated by one double-strand cleavage
AB  - within the loop region between the recognition site and the terminus.  To
AB  - explain these results, it is hypothesized that after cleavage the enzyme cycles
AB  - between a tracking (and possibly backtracking) mode which is fueled by ATP
AB  - hydrolysis and a relatively long static period in which ATP hydrolysis does not
AB  - occur.  While tracking, the enzyme would be bound both to the recognition site
AB  - and to a distal site but, while static, the enzyme would be bound only at the
AB  - recognition site of nonlooped molecules.  This postnuclease phase of the
AB  - reaction is hypothesized to reflect a reaction whereby the enzyme initially
AB  - scans DNA molecules before making a strand cleavage.
ER  -

TY  - JOUR
AU  - Endlich, B.
AU  - Linn, S.
TI  - The DNA restriction endonuclease of Escherichia coli B.  II.  Further studies of the structure of DNA intermediates and products.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 5729
EP  - 5738
VL  - 260
AB  - The DNA intermediates and final products formed by the Type I restriction
AB  - endonuclease, EcoB, were further characterized.  DNA cleaved on only one strand
AB  - (hemi-restricted DNA) contains gaps of approximately 70-100 nucleotides, while
AB  - the fully restricted products contain 3'-single-stranded tails averaging
AB  - approximately 70-100 nucleotides for each strand cleaved.  The gaps and tails
AB  - are formed with the release of an equal number of nucleotides as small
AB  - oligonucleotides that are soluble in acid.  After purification, neither the
AB  - hemi-restricted nor the fully restricted DNAs are cleaved again by EcoB.  There
AB  - is no apparent specificity for which strand of a duplex is initially cleaved by
AB  - EcoB, nor is there specificity with respect to the composition of the
AB  - 3'-terminal nucleotide formed on the DNA or the 3'- or 5'-terminal nucleotides
AB  - of the acid-soluble oligonucleotides released during DNA cleavage.  The
AB  - structure formed at the 5' terminus of the DNA product which blocks
AB  - phosphorylation by T4 polynucleotide kinase remains unknown, but its removal
AB  - with phage lambda exonuclease allows at least some reutilization of recognition
AB  - sites by EcoB as well as phosphorylation of the newly formed 5' termini.  To
AB  - explain the complex mechanism of this enzyme, it is suggested that the
AB  - unidentified 5'-tails prevent wasteful rerestriction from occurring, whereas
AB  - the 3'-single-stranded tails create DNA which, when nonhomologous to
AB  - chromosomal DNA, cannot be rescued because such tails are not a substrate for
AB  - DNA polymerases.  However, when homologous chromosomal DNA exists, the randomly
AB  - cleaved large fragments with these tails can easily be assimilated by
AB  - recA-mediated genetic recombination, thus stimulating DNA exchange between
AB  - related organisms.
ER  -

TY  - JOUR
AU  - Endlich, B.
AU  - Linn, S.
TI  - Type I restriction enzymes.
JO  - The Enzymes
PY  - 1981
SP  - 137
EP  - 156
VL  - 14
AB  - Many bacteria contain enzymatic systems that act to restrict the expression of
AB  - foreign DNA introduced through phage infection, conjugation, or transformation.
AB  - This phenomenon of host-controlled specificity was first described in the
AB  - early 1950s by Luria and Human, who studied T-even phages, and by Bertani and
AB  - Weigle, who investigated the restriction of the host ranges of lambda and P2
AB  - phages.  It was observed that a particular phage could have widely different
AB  - efficiencies of infection on several closely related bacterial strains, but
AB  - when phages that had initially plated with low efficiency were replated on the
AB  - same bacterial strain, the efficiency of infection increased dramatically.
AB  - This modification of host range was not a hereditary genetic adaptation,
AB  - however, since it could be lost by subsequent propagation of the phage in
AB  - another bacterial strain.  It was subsequently shown that the host-specificity
AB  - system described by Luria and Human was unique to the T-even phages, whereas
AB  - the system described by Bertani and Weigle was more widespread.  The type I
AB  - restriction-modification systems described in this review are of the latter,
AB  - more general, class.  Modification of the T-even phages involves the
AB  - glycosylation of hydroxymethylcytosine residues, and has been reviewed
AB  - elsewhere.  Further investigation of lambda phage host specificity by Arber and
AB  - coworkers led to the hypothesis of a molecular mechanism in which special DNA
AB  - sequences are acted upon by appropriate restriction and modification enzymnes.
AB  - Foreign DNA that happens to contain such specific sequences is cleaved by a
AB  - restriction endonuclease upon entering the cell.  When these same sequence
AB  - exist in the bacterium's own DNA, however, they are protected by a modification
AB  - methylase that imparts methylase that imparts methyl groups to bases within the
AB  - sequences, rendering them resistant to endonuclease action.  This hypothesis
AB  - was substantiated in the late 1960s when restriction endonucleases from the E.
AB  - coli strains K and B were discovered and isolated in highly purified form.
AB  - These nucleases were genetically identified as the restriction enzymes and
AB  - observed to be complex in terms of cofactor requirements, subunit composition,
AB  - and interactions with the DNA substrate.  Other restriction enzymes were soon
AB  - isolated from other bacteria such as Haemophilus influenzae.  Many of these
AB  - endonucleases have distinctly different properties from those of the E. coli B
AB  - and K nucleases, and are distinguished as two additional types of restriction
AB  - endonucleases.  Whether all of these latter enzymes function in situ in a
AB  - restriction capacity is not clear.
ER  -

TY  - JOUR
AU  - Endo, M.
AU  - Nakayama, K.
AU  - Majima, T.
TI  - Design and synthesis of photochemically controllable restriction endonuclease BamHI by manipulating the salt-bridge network in the dimer  interface.
JO  - J. Org. Chem.
PY  - 2004
SP  - 4292
EP  - 4298
VL  - 69
AB  - The strategy for the design of photochemically controllable enzymes by manipulating the dimer
AB  - interface is described. Employing a restriction
AB  - endonuclease BamHI, the selective incorporation of amino acids having a
AB  - photoremovable 6-nitroveratryl group into the specific position
AB  - (Lys132) in the dimer interface of the BamHI mutant (H133A) was
AB  - performed. The activity of the photofunctionalized BamHI mutant was
AB  - significantly suppressed, and the following photoirradiation induced
AB  - the recovery of the activity. In addition, uncaging of the
AB  - 6-nitroveratryl group introduced to Lys132 did not seriously reduce the
AB  - catalytic activity and affinity for the substrate. These results
AB  - indicate that the activity of the enzyme can be effectively regulated
AB  - by caging and uncaging of the specific amino acid in the dimer
AB  - interface using the photoremovable group.
ER  -

TY  - JOUR
AU  - Endow, S.A.
TI  - Analysis of Drosophila melanogaster Satellite IV with restriction endonuclease MboII.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 441
EP  - 449
VL  - 114
AB  - The products of digestion of Drosophila melanogaster satellite IV DNA with
AB  - restriction endonuclease MboII have been analysed and found to be consistent
AB  - with a repeating pentamer sequence (A-G-A-A-G)n for satellite IV.  More than
AB  - 95% of the satellite DNA is digested to fragments less than 25 base-pairs in
AB  - length, suggesting that the DNA sequence is highly conserved.
ER  -

TY  - JOUR
AU  - Endow, S.A.
AU  - Roberts, R.J.
TI  - Two restriction-like enzymes from Xanthomonas malvacearum.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 521
EP  - 529
VL  - 112
AB  - Two sequence-specific endonucleases, XmaI and XmaII, have been purified from
AB  - Xanthomonas malvacearum.  XmaI makes cuts in bacteriophage lambda and
AB  - adenovirus-2 DNA identical with those produced by SmaI, a restriction-like
AB  - enzyme previously isolated from Serratia marcescens Sb.XmaI cleaves within the
AB  - sequence 5'-C^-C-C-G-G-G-3' 3'-G-G-G-C-G-^C-5' at the sites indicated by the
AB  - arrows.  XmaII is an isoschizomer of the specific endonuclease PstI previously
AB  - isolated from Providencia stuartii.
ER  -

TY  - JOUR
AU  - Eng, C.
AU  - Blouin, Y.
AU  - Ding, N.
AU  - Larigauderie, G.
AU  - Ramisse, V.
AU  - Pujol, C.
TI  - Draft Genome Sequence of the Biowarfare Simulant Bacillus atrophaeus Strain 930029.
JO  - Genome Announcements
PY  - 2015
SP  - e00491
EP  - e00415
VL  - 3
AB  - We report here the draft genome sequence of Bacillus atrophaeus strain 930029. Strain 930029
AB  - shows evidence of drift, based on a comparison to the corresponding
AB  - source strain publicly available today.
ER  -

TY  - JOUR
AU  - Eng, W.W.
AU  - Gan, H.M.
AU  - Gan, H.Y.
AU  - Hudson, A.O.
AU  - Savka, M.A.
TI  - Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344.
JO  - Genome Announcements
PY  - 2015
SP  - e00463
EP  - e00415
VL  - 3
AB  - Here, we report the whole-genome sequence and annotation of Pseudomonas kilonensis 1855-344
AB  - (previously known as P. fluorescens 1855-344). The genome
AB  - contains an octopine oxidase gene cluster consistent with the ability to utilize
AB  - octopine. A biosynthetic gene cluster was identified for mangotoxin and
AB  - aryl-polyene using the antiSMASH server.
ER  -

TY  - JOUR
AU  - Engel, P.
TI  - Plasmid transformation of Streptomyces tendae after heat attenuation of restriction.
JO  - Appl. Environ. Microbiol.
PY  - 1987
SP  - 1
EP  - 3
VL  - 53
AB  - Streptomyces tendae ATCC 31160 produces nikkomycin, a fungicide and insecticide
AB  - that inhibits chitin synthases.  Exposure of S. tendae protoplasts to 50C for
AB  - 30 min is required for transformation (10-2 thiostrepton-resistant
AB  - transformants per microgram of DNA) with plasmid pIJ702 or pIJ680 from
AB  - Streptomyces lividans.  pIJ702 and pIJ680 DNA isolated from the S. tendae
AB  - transformants is efficient (10-6 to 10-7 transformants per microgram DNA) in
AB  - subsequent transformations of S. tendae protoplasts generated at 30C.  PstI
AB  - fails to cut the single PstI site in pIJ702 and cuts only one of the two PstI
AB  - sites in pIJ680 DNA isolated from S. tendae transformants.  Digests of plasmid
AB  - DNA mixtures showed that plasmid DNA from S. tendae does not inhibit PstI
AB  - activity.  pIJ702 and pIJ680 DNA from S. tendae transformants was used to
AB  - transform S. lividans to show that plasmid DNA remains unchanged, except for
AB  - modification at some PstI sites in S. tendae, as a consequence of passage
AB  - through S. tendae.  The DNA modification is lost when S. lividans is
AB  - transformed with plasmid DNA from S. tendae transformants.  Since S. tendae
AB  - modifies only some PstI sites, it appears the modification (presumably
AB  - restriction activity also) activity in S. tendae recognizes a sequence that
AB  - includes or overlaps the PstI hexanucleotide recognition sequence.
ER  -

TY  - JOUR
AU  - Engel, P.
AU  - Vizcaino, M.I.
AU  - Crawford, J.M.
TI  - Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthetic pathways.
JO  - Appl. Environ. Microbiol.
PY  - 2015
SP  - 1502
EP  - 1512
VL  - 81
AB  - Secondary metabolites produced by nonribosomal peptide synthetase (NRPS) or
AB  - polyketide synthase (PKS) pathways are chemical mediators of microbial
AB  - interactions in diverse environments. However, little is known about their
AB  - distribution, evolution, and functional roles in bacterial symbionts associated
AB  - with animals. A prominent example is "colibactin", a largely unknown family of
AB  - secondary metabolites produced by Escherichia coli via a hybrid NRPS-PKS
AB  - biosynthetic pathway, inflicting DNA damage upon eukaryotic cells and
AB  - contributing to colorectal cancer and tumor formation in the mammalian gut. Thus
AB  - far, homologs of this pathway have only been found in closely related
AB  - Enterobacteriaceae, while a divergent variant of this gene cluster was recently
AB  - discovered in a marine alphaproteobacterial Pseudovibrio strain. Herein, we
AB  - sequenced the genome of Frischella perrara PEB0191, a bacterial gut symbiont of
AB  - honey bees, and identified a homologous colibactin biosynthetic pathway related
AB  - to those found in Enterobacteriaceae. We show that the colibactin genomic island
AB  - (GI) has conserved gene synteny and biosynthetic module architecture across F.
AB  - perrara, Enterobacteriaceae and the Pseudovibrio strain. Comparative metabolomics
AB  - analyses of F. perrara and E. coli further reveal that these two bacteria produce
AB  - related colibactin pathway-dependent metabolites. Finally, we demonstrate that F.
AB  - perrara, like E. coli, causes DNA damage in eukaryotic cells in vitro in a
AB  - colibactin pathway-dependent manner. Together, these results support that
AB  - divergent variants of the colibactin biosynthetic pathway are widely distributed
AB  - among bacterial symbionts, producing related secondary metabolites and likely
AB  - endowing its producer with functional capabilities important for diverse
AB  - symbiotic associations.
ER  -

TY  - JOUR
AU  - Engelbrecht, K.C.
AU  - Putonti, C.
AU  - Koenig, D.W.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence of Escherichia coli K-12 (ATCC 29425).
JO  - Genome Announcements
PY  - 2017
SP  - e00574
EP  - e00517
VL  - 5
AB  - A draft genome sequence for Escherichia coli ATCC 29425 was investigated. The size of the
AB  - genome was 4,608,319 bp, with an observed G+C content of 50.68%. This
AB  - assembly consisted of 80 contigs, with an average coverage of 122.2x, including
AB  - one contig representative of the complete genome for the temperate phage P1.
ER  -

TY  - JOUR
AU  - Engin, D.
AU  - Hascelik, G.
TI  - iceA genotypes may play a role in acquiring metronidazole resistance in Helicobacter pylori.
JO  - Helicobacter
PY  - 2003
SP  - 356
EP  - 356
VL  - 8
AB  - Homologous recombination contributes to the extraordinary genetic diversity of Helicobacter
AB  - pylori.  Recently, evidence of in vivo horizontal gene transfer was detected in the rdxA gene,
AB  - which is involved in metronidazole resistance.  This bacterium possesses a large number of
AB  - restriction - modification systems that afford protection against transforming DNA, apparently
AB  - regulating the natural transformation of H. pylori.  The newly discovered virulence factor
AB  - icaA exists in two variants, iceA1 which encodes an NlaIIIR homologue restriction enzyme and
AB  - iceA2.  In this study, we evaluated the relationship between the metronidazole resistance and
AB  - iceA genotypes in 76 H. pylori strains.  We determined metronidazole MIC values of H. pylori
AB  - strains by agar dilution.  Following DNA purification iceA genotypes of H. pylori strains were
AB  - determined by using PCR.  Thirty-eight (50.0%) out of 76 H. pylori strains were found
AB  - metronidazole resistant.  MIC50 was 8 and MIC90 value was 128 ug/ml.  Forty-eight (63.2%) and
AB  - 19 (25.0%) of the strains were typed as iceA1 and iceA2, respectively.  Whereas, 9 (11.8%)
AB  - strains yielded PCR products of unexpected length and typed as iceA1a/2a.  No significant
AB  - difference was found between metronidazole MIC values of iceA1 and iceA2 strains.
AB  - Metronidazole MIC values of iceA1a/2a strains were marginally lower than iceA2 strains
AB  - (Mann-Whitney p=0.075).  We conclude that, restriction-modification systems may play an
AB  - important role in acquiring metronidazole resistance in H. pylori.  The organization of iceA
AB  - locus in iceA1a/2a strains should be further evaluated.
ER  -

TY  - JOUR
AU  - Engler, L.E.
AU  - Sapienza, P.
AU  - Dorner, L.F.
AU  - Kucera, R.
AU  - Schildkraut, I.
AU  - Jen-Jacobson, L.
TI  - The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 619
EP  - 636
VL  - 307
AB  - The interaction of BamHI endonuclease with DNA has been studied crystallographically, but has
AB  - not been characterized rigorously in solution. The enzyme binds in solution as a homodimer to
AB  - its recognition site GGATCC. Only six base-pairs are directly recognized, but binding affinity
AB  - (in the absence of the catalytic cofactor Mg(2+)) increases 5400-fold as oligonucleotide
AB  - length increases from 10 to 14 bp. Binding is modulated by sequence context outside the
AB  - recognition site, varying about 30-fold from the best (GTG or TAT) to the worst (CGG)
AB  - flanking triplets. BamHI, EcoRI and EcoRV endonucleases all have different context
AB  - preferences, suggesting that context affects binding by influencing the free energy levels of
AB  - the complexes rather than that of the free DNA. Ethylation interference footprinting in the
AB  - absence of divalent metal shows a localized and symmetrical pattern of phosphate contacts,
AB  - with strong contacts at NpNpNpGGApTCC. In the presence of Mg(2+), first-order cleavage rate
AB  - constants are identical in the two GGA half-sites, are the same for the two nicked
AB  - intermediates and are unaffected by substrate length in the range 10-24 bp. DNA binding is
AB  - strongly enhanced by mutations D94N, E111A or E113K, by binding of Ca(2+) at the active site,
AB  - or by deletion of the scissile phosphate GpGATCC, indicating that a cluster of negative
AB  - charges at the catalytic site contributes at least 3-4 kcal/mol of unfavorable binding free
AB  - energy. This electrostatic repulsion destabilizes the enzyme-DNA complex and favors metal ion
AB  - binding and progression to the transition state for cleavage.
ER  -

TY  - JOUR
AU  - Engler, L.E.
AU  - Welch, K.K.
AU  - Jen-Jacobson, L.
TI  - Specific binding by EcoRV endonuclease to its DNA recognition site GATATC.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 82
EP  - 101
VL  - 269
AB  - Restriction endonuclease EcoRV has been reported to be unable to distinguish its specific DNA
AB  - site, GATATC, from non-specific DNA sites in the absence of the catalytic cofactor Mg2+, and
AB  - thus to exercise sequence specificity solely in the catalytic step.  In contrast, we show here
AB  - that under appropriate conditions of pH and salt concentration, specific complexes with
AB  - oligonucleotides containing the GATATC site can be detected by either filter-binding or
AB  - gel-retardation.  Equilibrium binding constants (KA) are easily measured by both direct
AB  - equilibrium and equilibrium-competition methods.  The preference for "specific" over
AB  - "non-specific" binding at pH 7 in the absence of divalent cations is about 1000-fold (per mole
AB  - of oligonucleotide) or 12,000-fold (per mole of binding sites).  Ethylation-interference
AB  - footprinting shows that the "specific" complex includes strong contacts to the phosphate
AB  - groups GpApTpApTC.  Specific DNA binding is strongly pH-dependent, decreasing about 15-fold
AB  - for each increase of one pH unit above pH 6, but non-specific binding is not; thus, binding
AB  - specificity decreases with increasing pH.  Gel retardation and filter-binding at pH values
AB  - less than 7 yielded essentially identical values of KA for specific-site binding, but at pH>7
AB  - gel retardation significantly underestimates KA.  Specific-site binding is stimulated about
AB  - 700-fold by Ca2+ (not a cofactor for cleavage), but with non-cleavable 3'-phosphorothioate
AB  - and 4'-thiodeoxyribose derivatives whose response to Ca2+ is similar to that of the parent
AB  - oligonucleotide, Mg2+ stimulates binding only fourfold and twofold, respectively.  Thus,
AB  - binding specificity is not dramatically enhanced by Mg2+.  Taking into account discrimination
AB  - in binding and in the first-order rate constant for phosphodiester bond scission, the overall
AB  - discrimination exercised against the incorrect site GTTATC is about 10^7-fold.  EcoRV
AB  - endonuclease is thus not a "new paradigm" for site-specific interaction without binding
AB  - specificity, but like other type II restriction endonucleases achieves sequence specificity by
AB  - discriminating both in DNA binding and in catalysis.
ER  -

TY  - JOUR
AU  - Enikeeva, F.N.
AU  - Severinov, K.V.
AU  - Gelfand, M.S.
TI  - Restriction-modification systems and bacteriophage invasion: Who wins?
JO  - J. Theor. Biol.
PY  - 2010
SP  - 550
EP  - 559
VL  - 266
AB  - The success of a phage that infects a bacterial cell possessing a restriction-modification
AB  - (R-M) system depends on the activities of the
AB  - host methyltransferase and restriction endonuclease, and the number of
AB  - susceptible sites in the phage genome. However, there is no model
AB  - describing this dependency and linking it to observable parameters such
AB  - as the fraction of surviving cells under excess phage, or probability
AB  - of plating at low amount of phages. We model the phage infection of a
AB  - cell with a R-M system as a pure birth process with a killing state. We
AB  - calculate the transitional probabilities and the stationary
AB  - distribution for this process. We generalize the model developed for a
AB  - single cell to the case of multiple identical cells invaded by a
AB  - Poisson-distributed number of phages. The R-M enzyme activities are
AB  - assumed to be constant, time-dependent, or random. The obtained results
AB  - are used to estimate the ratio of the methyltransferase and
AB  - endonuclease activities from the observed fraction of surviving cells.
ER  -

TY  - JOUR
AU  - Epinat, J.C.
AU  - Arnould, S.
AU  - Chames, P.
AU  - Rochaix, P.
AU  - Desfontaines, D.
AU  - Puzin, C.
AU  - Patin, A.
AU  - Zanghellini, A.
AU  - Paques, F.
AU  - Lacroix, E.
TI  - A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 2952
EP  - 2962
VL  - 31
AB  - Homologous gene targeting is the ultimate tool for reverse genetics, but its use is often
AB  - limited by low efficiency. In a number of recent studies,
AB  - site- specific DNA double-strand breaks (DSBs) have been used to induce
AB  - efficient gene targeting. Engineering highly specific, dedicated DNA
AB  - endonucleases is the key to a wider usage of this technology. In this
AB  - study, we present two novel, chimeric meganucleases, derived from homing
AB  - endonucleases. The first one is able to induce recombination in yeast and
AB  - mammalian cells, whereas the second cleaves a novel (chosen) DNA target
AB  - site. These results are a first step toward the generation of custom
AB  - endonucleases for the purpose of targeted genome engineering.
ER  -

TY  - JOUR
AU  - Eppinger, M. et al.
TI  - Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4199
EP  - 4213
VL  - 193
AB  - Bacillus megaterium is deep-rooted in the Bacillus phylogeny, making it an evolutionarily key
AB  - species and of particular importance in understanding
AB  - genome evolution, dynamics, and plasticity in the bacilli. B. megaterium
AB  - is a commercially available, nonpathogenic host for the biotechnological
AB  - production of several substances, including vitamin B(12), penicillin
AB  - acylase, and amylases. Here, we report the analysis of the first complete
AB  - genome sequences of two important B. megaterium strains, the plasmidless
AB  - strain DSM319 and QM B1551, which harbors seven indigenous plasmids. The
AB  - 5.1-Mbp chromosome carries approximately 5,300 genes, while QM B1551
AB  - plasmids represent a combined 417 kb and 523 genes, one of the largest
AB  - plasmid arrays sequenced in a single bacterial strain. We have documented
AB  - extensive gene transfer between the plasmids and the chromosome. Each
AB  - strain carries roughly 300 strain-specific chromosomal genes that account
AB  - for differences in their experimentally confirmed phenotypes. B.
AB  - megaterium is able to synthesize vitamin B(12) through an
AB  - oxygen-independent adenosylcobalamin pathway, which together with other
AB  - key energetic and metabolic pathways has now been fully reconstructed.
AB  - Other novel genes include a second ftsZ gene, which may be responsible for
AB  - the large cell size of members of this species, as well as genes for gas
AB  - vesicles, a second beta-galactosidase gene, and most but not all of the
AB  - genes needed for genetic competence. Comprehensive analyses of the global
AB  - Bacillus gene pool showed that only an asymmetric region around the origin
AB  - of replication was syntenic across the genus. This appears to be a
AB  - characteristic feature of the Bacillus spp. genome architecture and may be
AB  - key to their sporulating lifestyle.
ER  -

TY  - JOUR
AU  - Eppinger, M.
AU  - Baar, C.
AU  - Linz, B.
AU  - Raddatz, G.
AU  - Lanz, C.
AU  - Keller, H.
AU  - Morelli, G.
AU  - Gressmann, H.
AU  - Achtman, M.
AU  - Schuster, S.C.
TI  - Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.
JO  - PLoS Genet.
PY  - 2006
SP  - e120
EP  - e120
VL  - 2
AB  - Helicobacter pylori infection of humans is so old that its population genetic structure
AB  - reflects that of ancient human migrations. A closely
AB  - related species, Helicobacter acinonychis, is specific for large felines,
AB  - including cheetahs, lions, and tigers, whereas hosts more closely related
AB  - to humans harbor more distantly related Helicobacter species. This
AB  - observation suggests a jump between host species. But who ate whom and
AB  - when did it happen? In order to resolve this question, we determined the
AB  - genomic sequence of H. acinonychis strain Sheeba and compared it to
AB  - genomes from H. pylori. The conserved core genes between the genomes are
AB  - so similar that the host jump probably occurred within the last 200,000
AB  - (range 50,000-400,000) years. However, the Sheeba genome also possesses
AB  - unique features that indicate the direction of the host jump, namely from
AB  - early humans to cats. Sheeba possesses an unusually large number of highly
AB  - fragmented genes, many encoding outer membrane proteins, which may have
AB  - been destroyed in order to bypass deleterious responses from the feline
AB  - host immune system. In addition, the few Sheeba-specific genes that were
AB  - found include a cluster of genes encoding sialylation of the bacterial
AB  - cell surface carbohydrates, which were imported by horizontal genetic
AB  - exchange and might also help to evade host immune defenses. These results
AB  - provide a genomic basis for elucidating molecular events that allow
AB  - bacteria to adapt to novel animal hosts.
ER  -

TY  - JOUR
AU  - Eppinger, M.
AU  - Daugherty, S.
AU  - Agrawal, S.
AU  - Galens, K.
AU  - Sengamalay, N.
AU  - Sadzewicz, L.
AU  - Tallon, L.
AU  - Cebula, T.A.
AU  - Mammel, M.K.
AU  - Feng, P.
AU  - Soderlund, R.
AU  - Tarr, P.I.
AU  - Debroy, C.
AU  - Dudley, E.G.
AU  - Fraser, C.M.
AU  - Ravel, J.
TI  - Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e0013412
EP  - e0013412
VL  - 1
AB  - First identified in 1982, Escherichia coli O157:H7 is the dominant enterohemorrhagic serotype
AB  - underlying food-borne human infections in North
AB  - America. Here, we report the genomes of twenty-six strains derived from patients
AB  - and the bovine reservoir. These resources enable detailed whole-genome
AB  - comparisons and permit investigations of genotypic and phenotypic plasticity.
ER  -

TY  - JOUR
AU  - Eppinger, M.
AU  - Guo, Z.
AU  - Sebastian, Y.
AU  - Song, Y.
AU  - Lindler, L.E.
AU  - Yang, R.
AU  - Ravel, J.
TI  - Draft Genome Sequences of Yersinia pestis Isolates From Natural Foci of Endemic Plague in China.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7628
EP  - 7629
VL  - 191
AB  - To gain insights into the evolutionary origin, emergence and pathogenicity of the etiologic
AB  - agent of plague, we have sequenced the genomes of four  Yersinia pestis strains isolated from
AB  - the zoonotic rodent reservoir in  endemic plague foci in China (24). These resources enable
AB  - in-depth studies  of Y. pestis sequence variations, and detailed whole genome comparisons of
AB  - very closely related genomes from the supposed site of the origin and emergence of global
AB  - pandemics of plague.
ER  -

TY  - JOUR
AU  - Eppinger, M.
AU  - Mammel, M.K.
AU  - Leclerc, J.E.
AU  - Ravel, J.
AU  - Cebula, T.A.
TI  - Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 2916
EP  - 2925
VL  - 77
AB  - Cattle comprise a main reservoir of Shiga toxin-producing Escherichia coli
AB  - O157:H7 (STEC). The significant differences in host prevalence,
AB  - transmissibility, and virulence phenotypes among strains from bovine and
AB  - human sources are of major interest to the public health community and
AB  - livestock industry. Genomic analysis revealed divergence into three
AB  - lineages: lineage I and lineage I/II strains are commonly associated with
AB  - human disease, while lineage II strains are overrepresented in the
AB  - asymptomatic bovine host reservoir. Growing evidence suggests that
AB  - genotypic differences between these lineages, such as polymorphisms in
AB  - Shiga toxin subtypes and synergistically acting virulence factors, are
AB  - correlated with phenotypic differences in virulence, host ecology, and
AB  - epidemiology. To assess the genomic plasticity on a genome-wide scale, we
AB  - have sequenced the whole genome of strain EC869, a bovine-associated E.
AB  - coli O157:H7 isolate. Comparative phylogenomic analysis of this key
AB  - isolate enabled us to place accurately bovine lineage II strains within
AB  - the genetically homogenous E. coli O157:H7 clade. Identification of
AB  - polymorphic loci that are anchored both in the chromosomal backbone and
AB  - horizontally acquired regions allowed us to associate bovine genotypes
AB  - with altered virulence phenotypes and host prevalence. This study
AB  - catalogued numerous novel lineage II-specific genome signatures, some of
AB  - which appear to be associated intimately with the altered pathogenic
AB  - potential and niche adaptation within the bovine rumen. The presented
AB  - extended list of polymorphic markers is valuable in the development of a
AB  - robust typing system critical for forensic, diagnostic, and
AB  - epidemiological studies of this emerging human pathogen.
ER  -

TY  - JOUR
AU  - Eppinger, M.
AU  - McNair, K.
AU  - Zogaj, X.
AU  - Dinsdale, E.A.
AU  - Edwards, R.A.
AU  - Klose, K.E.
TI  - Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis.
JO  - Genome Announcements
PY  - 2013
SP  - e00926
EP  - e00913
VL  - 1
AB  - Piscirickettsia salmonis is a Gram-negative intracellular fish pathogen that has  a
AB  - significant impact on the salmon industry. Here, we report the genome sequence
AB  - of P. salmonis strain LF-89. This is the first draft genome sequence of P.
AB  - salmonis, and it reveals interesting attributes, including flagellar genes,
AB  - despite this bacterium being considered nonmotile.
ER  -

TY  - JOUR
AU  - Erdmann, D.
TI  - Cloning of restriction-modification systems from Herpetosiphon giganteus Hpg9 and Hpg24 in E. coli - Characterization and comparative analysis of the genetic organization and structure.
JO  - Ph.D. Thesis, Justus-Liebig University, Geissen, W. Germany
PY  - 1991
SP  - 1
EP  - 204
AB  - None
ER  -

TY  - JOUR
AU  - Erdmann, D.
AU  - Dusterhoft, A.
AU  - Kroger, M.
TI  - Cloning and molecular characterization of the HgiCI restriction/modification system from Herpetosiphon giganteus Hpg9 reveals high similarity to BanI.
JO  - Eur. J. Biochem.
PY  - 1991
SP  - 1247
EP  - 1256
VL  - 202
AB  - The genes coding for the GGYRCC specific restriction/modification system HgiCI from
AB  - Herpetosiphon giganteus Hpg9 have been cloned in Escherichia coli in three steps. As an
AB  - initial step, the methyltransferase gene could be obtained after heterologous in vitro
AB  - selection of a plasmid gene bank by cleavage with the isoschizomeric restriction endonuclease
AB  - BanI. The adjacent endonuclease gene was cloned following Southern blot analysis of flanking
AB  - genomic regions. The two genes code for polypeptides of 420 amino acids (M.HgiCI) and 345
AB  - amino acids (R.HgiCI). Establishing a functional endonuclease gene could only be achieved
AB  - using a tightly regulated expression system or by methylation of the genomic DNA prior to
AB  - transformation of the endonuclease gene. The methyltransferase M.HgiCI shows significant
AB  - similarities to the family of 5-methylcytidine methyltransferases. Striking similarities could
AB  - be found with both the isoschizomeric endonuclease and methyltransferase of the BanI
AB  - restriction/modification system from Bacillus aneurinolyticus.
ER  -

TY  - JOUR
AU  - Erdmann, D.
AU  - Horst, G.
AU  - Dusterhoft, A.
AU  - Kroger, M.
TI  - Stepwise cloning and genetic organization of the seemingly unclonable HgiCII restriction-modification system from Herpetosiphon giganteus strain Hpg9, using PCR technique.
JO  - Gene
PY  - 1992
SP  - 15
EP  - 22
VL  - 117
AB  - The genes, hgiCIIR and hgiCIIM, that encode the HgiCII restriction and modification (R-M)
AB  - system from Herpetosiphon giganteus strain Hpg9, an AvaII isoschizomer recognizing the
AB  - sequence, CCA/TCC, were cloned in Escherichia coli. Cloning the respective hgiCIIM gene was
AB  - achieved via in vitro selection both from a Sau3AI- and an NheI-generated plasmid gene library
AB  - using AvaII, a commercially available isoschizomer of HgiCII. However, all attempts to clone
AB  - the closely linked hgiCIIR and M genes in a single step resulted in deletions spanning parts
AB  - of the coding region of hgiCIIR. Therefore, cloning of the missing 3'-terminal part of this
AB  - gene was achieved by applying the inverse polymerase-chain-reaction technique. All attempts to
AB  - construct an enzymatically active R.HgiCII failed; only the inactivated hgiCIIR gene could be
AB  - cloned. Sequencing of the hgiCIIRM region (carrying predesigned small mutations in the R gene)
AB  - disclosed three open reading frames (ORFs):one small ORF preceding the methyltransferase
AB  - (MTase)-encoding gene, plus those encoding M.HgiCII (49620 Da) and R.HgiCII (30891 Da).
AB  - M.HgiCII exhibits the common motif of ten conserved amino-acid blocks typically found within
AB  - the group of m5C-MTases. The R-M system of HgiCII reveals strong homologies to the
AB  - isoschizomeric R-M system of HgiBI from H. giganteus strain Hpg5, which in contrast, could be
AB  - cloned in one step.
ER  -

TY  - JOUR
AU  - Erickson, K.E.
AU  - Madinger, N.E.
AU  - Chatterjee, A.
TI  - Draft Genome Sequence for a Clinical Isolate of Vancomycin-Resistant Enterococcus faecalis.
JO  - Genome Announcements
PY  - 2016
SP  - e00584
EP  - e00516
VL  - 4
AB  - We report here the draft genome sequence of a multidrug-resistant Enterococcus faecalis
AB  - strain, isolated from a patient at the University of Colorado Hospital.
AB  - The genome assembly is 3,040,186 bp in length with 37.6% GC content. This isolate
AB  - encodes eleven resistance genes, including those for glycopeptide,
AB  - aminoglycoside, macrolide-lincosamide-streptogramin, and tetracycline resistance.
ER  -

TY  - JOUR
AU  - Erickson, K.E.
AU  - Madinger, N.E.
AU  - Chatterjee, A.
TI  - Draft Genome Sequences of Clinical Isolates of Multidrug-Resistant Acinetobacter  baumannii.
JO  - Genome Announcements
PY  - 2017
SP  - e01547
EP  - e01516
VL  - 5
AB  - We report here the draft genome sequences of two clinically isolated Acinetobacter baumannii
AB  - strains. These samples were obtained from patients at the
AB  - University of Colorado Hospital in 2007 and 2013 and encode an estimated 20 and
AB  - 13 resistance genes, respectively.
ER  -

TY  - JOUR
AU  - Erikstad, H.A.
AU  - Birkeland, N.K.
TI  - Draft Genome Sequence of 'Candidatus Methylacidiphilum kamchatkense' Strain Kam1, a Thermoacidophilic Methanotrophic Verrucomicrobium.
JO  - Genome Announcements
PY  - 2015
SP  - e00065
EP  - e00015
VL  - 3
AB  - 'Candidatus Methylacidiphilum kamchatkense' strain Kam1 is an aerobic methane-oxidizing
AB  - thermoacidophilic bacterium belonging to the Verrucomicrobia
AB  - phylum. It was recovered from an acidic geothermal site in Uzon Caldera,
AB  - Kamchatka, Russian Federation. Its genome possesses three complete pmoCAB gene
AB  - clusters encoding particulate methane monooxygenase enzymes and a complete
AB  - Calvin-Benson-Bassham cycle for carbon assimilation.
ER  -

TY  - JOUR
AU  - Erill, I.
AU  - Puigvert, M.
AU  - Legrand, L.
AU  - Guarischi-Sousa, R.
AU  - Vandecasteele, C.
AU  - Setubal, J.C.
AU  - Genin, S.
AU  - Guidot, A.
AU  - Valls, M.
TI  - Comparative Analysis of Ralstonia solanacearum Methylomes.
JO  - Front. Plant Sci.
PY  - 2017
SP  - 504
EP  - 504
VL  - 8
AB  - Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical
AB  - distribution and the ability to cause wilt disease in many
AB  - agriculturally important crops. Genome sequencing of multiple R. solanacearum
AB  - strains has identified both unique and shared genetic traits influencing their
AB  - evolution and ability to colonize plant hosts. Previous research has shown that
AB  - DNA methylation can drive speciation and modulate virulence in bacteria, but the
AB  - impact of epigenetic modifications on the diversification and pathogenesis of R.
AB  - solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031
AB  - using Single Molecule Real-Time technology allowed us to perform a comparative
AB  - analysis of R. solanacearum methylomes. Our analysis identified a novel
AB  - methylation motif associated with a DNA methylase that is conserved in all
AB  - complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a
AB  - methylation motif associated to a phage-borne methylase unique to R. solanacearum
AB  - UY031. Comparative analysis of the conserved methylation motif revealed that it
AB  - is most prevalent in gene promoter regions, where it displays a high degree of
AB  - conservation detectable through phylogenetic footprinting. Analysis of hyper- and
AB  - hypo-methylated loci identified several genes involved in global and virulence
AB  - regulatory functions whose expression may be modulated by DNA methylation.
AB  - Analysis of genome-wide modification patterns identified a significant
AB  - correlation between DNA modification and transposase genes in R. solanacearum
AB  - UY031, driven by the presence of a high copy number of ISrso3 insertion sequences
AB  - in this genome and pointing to a novel mechanism for regulation of transposition.
AB  - These results set a firm foundation for experimental investigations into the role
AB  - of DNA methylation in R. solanacearum evolution and its adaptation to different
AB  - plants.
ER  -

TY  - JOUR
AU  - Erkel, C.
AU  - Kube, M.
AU  - Reinhardt, R.
AU  - Liesack, W.
TI  - Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere.
JO  - Science
PY  - 2006
SP  - 370
EP  - 372
VL  - 313
AB  - Rice fields are a global source of the greenhouse gas methane, which is
AB  - produced by methanogenic archaea, and by methanogens of Rice Cluster I
AB  - (RC-I) in particular. RC-I methanogens are not yet available in pure
AB  - culture, and the mechanistic reasons for their prevalence in rice fields
AB  - are unknown. We reconstructed a complete RC-I genome (3.18 megabases)
AB  - using a metagenomic approach. Sequence analysis demonstrated an
AB  - aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for
AB  - carbohydrate metabolism and assimilatory sulfate reduction, hitherto
AB  - unknown among methanogens. These capacities and a unique set of
AB  - antioxidant enzymes and DNA repair mechanisms as well as
AB  - oxygen-insensitive enzymes provide RC-I with a selective advantage over
AB  - other methanogens in its habitats, thereby explaining the prevalence of
AB  - RC-I methanogens in the rice rhizosphere.
ER  -

TY  - JOUR
AU  - Erlanson, D.A.
AU  - Chen, L.
AU  - Verdine, G.L.
TI  - DNA methylation through a locally upaired intermediate.
JO  - J. Am. Chem. Soc.
PY  - 1993
SP  - 12583
EP  - 12584
VL  - 115
AB  - Methylation of DNA serves essential roles in mammalian development and in bacterial resistance
AB  - to viral pathogens. In this process, a DNA (cytosine-5)-methyltransferase (DCMtase) mediates
AB  - delivery of a methyl group from S-adenosyl-L-methionine to the 5-position of cytosine residues
AB  - in DNA. DCMtases operate by conjugate addition of a cysteine thiolate to the 6-carbon (C6) of
AB  - the substrate cytosine followed by transfer of a methyl group to C5. __-Elimination
AB  - regenerates the free enzyme (Figure 1). We have noted that the stereoelectronic attack
AB  - trajectories for thiolate addition and methyl transfer cannot be accommodated in a canonical
AB  - B-form duplex, suggesting that DCMtases cause transient helical disruption during the
AB  - catalytic event. Here we report evidence in favor of DCMtase-induced distortion of DNA and
AB  - propose a structural model for the enzyme-DNA intermediate.
ER  -

TY  - JOUR
AU  - Erlanson, D.A.
AU  - Wolfe, S.A.
AU  - Chen, L.
AU  - Verdine, G.L.
TI  - Selective base-pair destabilization enhances binding of a DNA methyltransferase.
JO  - Tetrahedron
PY  - 1997
SP  - 12041
EP  - 12056
VL  - 53
AB  - Disulfide crosslinks were introduced into the minor groove of DNA using the convertible
AB  - nucleoside approach.  Depending upon the length of the tether, the modified base pairs were
AB  - either stabilized or destabilized.  When the base-pairs were destabilized, the oligonucleotide
AB  - was bound by a unmodified oligonucleotide.  Insights into the mechanism of DCMtases are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Erova, T.
AU  - Sha, J.
AU  - Fadl, A.
AU  - Khajanchi, B.
AU  - Chopra, A.
TI  - Mutations within the catalytic site of DNA methyltransferase (Dam) of Aeromonas hydrophila reverts the virulence of the dam-overproducing strain to that of the wild-type bacterium.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2006
SP  - 76
EP  - 76
VL  - 106
AB  - A. hydrophila is an opportunistic human pathogen. In our recently published studies, we
AB  - demonstrated that DNA adenine methyltransferase (Dam) of A. hydrophila is crucial for
AB  - bacterial viability, and that it affects virulence of the bacterium by altering biological
AB  - activities associated with type 2 and type 3 secreted proteins. Overall, overproduction of Dam
AB  - in A. hydrophila using an arabinose-inducible pBAD vector attenuated bacterial virulence in a
AB  - mouse model of infection. In this study, we demonstrated that the virulence potential of
AB  - Dam-overproducing strain of A. hydrophila was reverted back to that of the wild-type (WT)
AB  - bacterium when the catalytic site of Dam was mutated. Using Altered Sites in vitro Mutagenesis
AB  - System, we mutated aspartic acid (D) and tyrosine (Y) residues to alanine (A) within the
AB  - conserved catalytic motif (DPPY) of Dam. To confirm that the mutated enzyme lost its
AB  - methyltransferase (MTase) activity, we transformed pBAD/dam*D/A, pBAD/dam*Y/A, and
AB  - pBAD/damnative (as a control) recombinant plasmids into E. coli GM33 (Dam-) strain. Genomic
AB  - DNA (gDNA) isolated from either the E. coli GM33 (pBAD/dam*D/A) or the E. coli GM33
AB  - (pBAD/dam*Y/A) strain grown in the presence of arabinose was sensitive to DpnII digestion and
AB  - resistant to DpnI restriction endonuclease cutting. These data verified that the gDNA were not
AB  - methylated as the gDNA from E. coli GM33 strain with pBAD/damnative plasmid which exhibited
AB  - opposite sensitivity to DpnI and resistance to DpnII digestion. Overproduction of mutated Dam
AB  - in A. hydrophila resulted in bacterial motility, T3SS-associated cytotoxicity as well as
AB  - hemolytic and cytotoxic activity associated with the cytotoxic enterotoxin and that of the
AB  - protease activity similar to that of the WT bacterium which harbored the pBAD vector alone. In
AB  - addition, we noted that lactone production, an indicator of quorum sensing, was increased when
AB  - the native dam gene was over-expressed, with its levels returning to that of the WT bacterium
AB  - when the damgene was mutated. Taken together, our data indicated that MTase activity is
AB  - essential for altered virulence of A. hydrophila.
ER  -

TY  - JOUR
AU  - Erova, T.E.
AU  - Fadl, A.A.
AU  - Sha, J.
AU  - Khajanchi, B.K.
AU  - Pillai, L.L.
AU  - Kozlova, E.V.C.A.K.
TI  - Mutations within the catalytic motif of DNA adenine methyltransferase (Dam) of Aeromonas hydrophila cause the virulence of the Dam-overproducing strain to revert to that of the wild-type phenotype - bacterium DNA denine-methyltransferase catalytic.
JO  - Infect. Immun.
PY  - 2006
SP  - 5763
EP  - 5772
VL  - 74
AB  - AUTHOR ABSTRACT - In this study, we demonstrated that the methyltransferase activity
AB  - associated with Dam was essential for
AB  - attenuation of Aeromonas hydrophila virulence. We mutated aspartic acid
AB  - and tyrosine residues to alanine within the conserved DPPY catalytic
AB  - motif of Dam and transformed the pBAD/dam(D/A), pBAD/dam(Y/A), and
AB  - pBAD/damA(AhSSu) (with the native dam gene) recombinant plasmids into
AB  - the Escherichia coli GM33 (dam-deficient) strain. Genomic DNA (gDNA)
AB  - isolated from either of the E. coli GM33 strains harboring the pBAD
AB  - vector with the mutated dam gene was resistant to DpnI digestion and
AB  - sensitive to DpnII restriction endonuclease cutting. These findings
AB  - were contrary to those with the gDNA of E. coli GM33 strain containing
AB  - the pBAD/dam(AhSSU) plasmid, indicating nonmethylation of E. coli gDNA
AB  - with mutated Dam. Overproduction of mutated Dam in A. hydrophild
AB  - resulted in bacterial motility, hemolytic and cytotoxic activities
AB  - associated with the cytotoxic enterotoxin (Act), and protease activity
AB  - similar to that of the wild-type (WT) bacterium, which harbored the
AB  - pBAD vector and served as a control strain. On the contrary,
AB  - overproduction of native Dam resulted in decreased bacterial motility,
AB  - increased Act-associated biological effects, and increased protease
AB  - activity. Lactone production, an indicator of quorum sensing, was
AB  - increased when the native dam gene was overexpressed, with its levels
AB  - returning to that of the control strain when the dam gene was mutated.
AB  - These effects of Dam appeared to be mediated through a regulatory
AB  - glucose-inhibited division A protein. Infection of mice with the
AB  - mutated Dam-overproducing strains resulted in mortality rates similar
AB  - to those for the control strain, with 100% of the animals dying within
AB  - 2 to 3 days with two 50% lethal doses (LD(50)s) of the WT bacterium.
AB  - Importantly, immunization of mice with a native-Dam-overproducing
AB  - strain at the same LD50 did not result in any lethality and provided
AB  - protection to animals after subsequent challenge with a lethal dose of
AB  - the control strain.
ER  -

TY  - JOUR
AU  - Erova, T.E.
AU  - Kosykh, V.G.
AU  - Sha, J.
AU  - Chopra, A.K.
TI  - DNA adenine methyltransferase (Dam) controls the expression of the cytotoxic enterotoxin (act) gene of Aeromonas hydrophila via tRNA modifying enzyme-glucose-inhibited division protein (GidA).
JO  - Gene
PY  - 2012
SP  - 280
EP  - 287
VL  - 498
AB  - Aeromonas hydrophila is both a human and animal pathogen, and the cytotoxic enterotoxin (Act)
AB  - is a crucial virulence factor of this bacterium because of its associated hemolytic,
AB  - cytotoxic, and enterotoxic activities.
AB  - Previously, to define the role of some regulatory genes in modulating Act production, we
AB  - showed that deletion of a glucose-inhibited division gene (gidA) encoding tRNA methylase
AB  - reduced Act levels, while overproduction
AB  - of DNA adenine methyltransferase (Dam) led to a concomitant increase in Act-associated
AB  - biological activities of a diarrheal isolate SSU of A.  hydrophila. Importantly, there are
AB  - multiple GATC binding sites for Dam within an upstream sequence of the gidA gene and one such
AB  - target site in the act gene upstream region.  We showed the dam gene to be essential for the
AB  - viability of A. hydrophila SSU, and, therefore, to better understand
AB  - the interaction of the encoding genes, Dam and GidA, in act gene regulation, we constructed a
AB  - gidA in-frame deletion mutant of Escherichia coli GM28 (dam+) and GM33 (Adam) strains. We then
AB  - tested the expressional activity of the act and gidA genes by using a promoterless pGlow-TOPO
AB  - vector containing a
AB  - reporter green fluorescent protein (GFP). Our data indicated that in GidA+ strains of E. coli,
AB  - constitutive methylation of the GATC site(s) by Dam negatively regulated act and gidA gene
AB  - expression as measured by
AB  - GFP production. However, in the AgidA strains, irrespective of the presence or absence of
AB  - constitutively active Dam, we did not observe any alteration in the expression of the act gene
AB  - signifying the role of GidA in positively
AB  - regulating Act production. To determine the exact mechanism of how Dam and GidA influence Act,
AB  - a real-time quantitative PCR (RT-qPCR) assay was performed. The analysis indicated an increase
AB  - in gidA and act gene expression in the A. hydrophila Dam-overproducing strain, and these data
AB  - matchedwith Act production in the E. coli GM28 strain. Thus, the extent of DNA methylation
AB  - caused by constitutive versus overproduction of Dam, as well as possible conformation of DNA
AB  - influence the expression of act and gidA genes in A. hydrophila SSU.  Our results indicate
AB  - that the act gene is under the control of both Dam and GidA modification methylases, and Dam
AB  - regulates Act production via GidA.
ER  -

TY  - JOUR
AU  - Erova, T.E.
AU  - Pillai, L.
AU  - Fadl, A.A.
AU  - Sha, J.
AU  - Wang, S.F.
AU  - Galindo, C.L.
AU  - Chopra, A.K.
TI  - DNA adenine methyltransferase influences the virulence of Aeromonas hydrophila.
JO  - Infect. Immun.
PY  - 2005
SP  - 410
EP  - 424
VL  - 74
AB  - Among the various virulence factors produced by Aeromonas hydrophila, a type II secretion
AB  - system (T2SS)-secreted cytotoxic enterotoxin (Act) and the T3SS are crucial in the
AB  - pathogenesis of Aeromonas-associated infections. Our laboratory molecularly characterized both
AB  - Act and the T3SS from a diarrheal isolate, SSU of A. hydrophila, and defined the role of some
AB  - regulatory genes in modulating the biological effects of Act. In this study, we cloned,
AB  - sequenced, and expressed the DNA adenine methyltransferase gene of A. hydrophila SSU
AB  - (dam(AhSSU)) in a T7 promoter-based vector system using Escherichia coli ER2566 as a host
AB  - strain, which could alter the virulence potential of A. hydrophila. Recombinant Dam,
AB  - designated as M.AhySSUDam, was produced as a histidine-tagged fusion protein and purified from
AB  - an E. coli cell lysate using nickel affinity chromatography. The purified Dam had
AB  - methyltransferase activity, based on its ability to transfer a methyl group from
AB  - S-adenosyl-l-methionine to N(6)-methyladenine-free lambda DNA and to protect methylated lambda
AB  - DNA from digestion with DpnII but not against the DpnI restriction enzyme. The dam gene was
AB  - essential for the viability of the bacterium, and overproduction of Dam in A. hydrophila SSU,
AB  - using an arabinose-inducible, P(BAD) promoter-based system, reduced the virulence of this
AB  - pathogen. Specifically, overproduction of M.AhySSUDam decreased the motility of the bacterium
AB  - by 58%. Likewise, the T3SS-associated cytotoxicity, as measured by the release of lactate
AB  - dehydrogenase enzyme in murine macrophages infected with the Dam-overproducing strain, was
AB  - diminished by 55% compared to that of a control A. hydrophila SSU strain harboring the pBAD
AB  - vector alone. On the contrary, cytotoxic and hemolytic activities associated with Act as well
AB  - as the protease activity in the culture supernatant of a Dam-overproducing strain were
AB  - increased by 10-, 3-, and 2.4-fold, respectively, compared to those of the control A.
AB  - hydrophila SSU strain. The Dam-overproducing strain was not lethal to mice (100% survival)
AB  - when given by the intraperitoneal route at a dose twice that of the 50% lethal dose, which
AB  - within 2 to 3 days killed 100% of the animals inoculated with the A. hydrophila control
AB  - strain. Taken together, our data indicated alteration of A. hydrophila virulence by
AB  - overproduction of Dam.
ER  -

TY  - JOUR
AU  - Ershova, A.
AU  - Rusinov, I.
AU  - Vasiliev, M.
AU  - Spirin, S.
AU  - Karyagina, A.
TI  - Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes.
JO  - J. Bioinform. Comput. Biol.
PY  - 2016
SP  - 1641003
EP  - 1641003
VL  - 14
AB  - Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see
AB  - text]-GATC-3[Formula: see text] site is a recognition site of
AB  - different Restriction-Modification (R-M) systems, as well as solitary
AB  - methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and
AB  - cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction
AB  - endonucleases cleave methylated GATC. Methylation of GATC by Dam
AB  - methyltransferase is involved in the regulation of different cellular processes.
AB  - The diversity of functions of GATC-recognizing proteins makes GATC sequence a
AB  - good model for studying the reasons of palindrome avoidance in prokaryotic
AB  - genomes. In this work, the influence of R-M systems and solitary proteins on the
AB  - GATC site avoidance is described by a mathematical model. GATC avoidance is
AB  - strongly associated with the presence of alternate (methyl-directed or classical
AB  - Type II R-M system) genes in different strains of the same species, as we have
AB  - shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale,
AB  - and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a
AB  - DNA exchange between strains with different methylation status of GATC site
AB  - within the process of natural transformation. If this hypothesis is correct, the
AB  - GATC avoidance is a sign of a DNA exchange between bacteria with different
AB  - methylation status in a mixed population.
ER  -

TY  - JOUR
AU  - Ershova, A.S.
AU  - Karyagina, A.S.
AU  - Vasiliev, M.O.
AU  - Lyashchuk, A.M.
AU  - Lunin, V.G.
AU  - Spirin, S.A.
AU  - Alexeevski, A.V.
TI  - Solitary restriction endonucleases in prokaryotic genomes.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 10107
EP  - 10115
VL  - 40
AB  - Prokaryotic restriction-modification (R-M) systems defend the host cell from the  invasion of
AB  - a foreign DNA. They comprise two enzymatic activities: specific DNA
AB  - cleavage activity and DNA methylation activity preventing cleavage. Typically,
AB  - these activities are provided by two separate enzymes: a DNA methyltransferase
AB  - (MTase) and a restriction endonuclease (RE). In the absence of a corresponding
AB  - MTase, an RE of Type II R-M system is highly toxic for the cell. Genes of the R-M
AB  - system are linked in the genome in the vast majority of annotated cases. There
AB  - are only a few reported cases in which the genes of MTase and RE from one R-M
AB  - system are not linked. Nevertheless, a few hundreds solitary RE genes are present
AB  - in the Restriction Enzyme Database (http://rebase.neb.com) annotations. Using the
AB  - comparative genomic approach, we analysed 272 solitary RE genes. For 57 solitary
AB  - RE genes we predicted corresponding MTase genes located distantly in a genome. Of
AB  - the 272 solitary RE genes, 99 are likely to be fragments of RE genes. Various
AB  - explanations for the existence of the remaining 116 solitary RE genes are also
AB  - discussed.
ER  -

TY  - JOUR
AU  - Ershova, A.S.
AU  - Rusinov, I.S.
AU  - Spirin, S.A.
AU  - Karyagina, A.S.
AU  - Alexeevski, A.V.
TI  - Role of Restriction-Modification Systems in Prokaryotic Evolution and Ecology.
JO  - Biokhimiia
PY  - 2015
SP  - 1373
EP  - 1386
VL  - 80
AB  - Restriction-modification (R-M) systems are able to methylate or cleave DNA depending on
AB  - methylation status of their recognition site. It allows them to protect bacterial cells from
AB  - invasion by foreign DNA. Comparative analysis of a large number of available bacterial genomes
AB  - and methylomes clearly demonstrates that the role of R-M systems in bacteria is wider than
AB  - only defense. R-M systems maintain heterogeneity of a bacterial population and are involved in
AB  - adaptation of bacteria to change in their environmental conditions. R-M systems can be
AB  - essential for host colonization by pathogenic bacteria. Phase variation and intragenomic
AB  - recombinations are sources of the fast evolution of the specificity of R-M systems. This
AB  - review focuses on the influence of R-M systems on evolution and ecology of prokaryotes.
ER  -

TY  - JOUR
AU  - Erskine, S.G.
AU  - Baldwin, G.S.
AU  - Halford, S.E.
TI  - Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1997
SP  - 7567
EP  - 7576
VL  - 36
AB  - Rapid-reaction methods have been used previously to identify intermediates in the reaction of
AB  - the EcoRV restriction endonuclease on oligonucleotide substrates.  In this study, the pathway
AB  - on macromolecular DNA was elucidated by using the quench-flow method to analyze EcoRV
AB  - reactions on a plasmid with one recognition site.  Some reactions were carried out by first
AB  - allowing the EcoRV enzyme to bind nonspecifically to the DNA and then initiating DNA cleavage
AB  - by adding magnesium ions.  The subsequent transfer of the enzyme from nonspecific to specific
AB  - sites was extremely rapid, at a random walk rate of at least 5 x 10^5 base pairs per second.
AB  - The two strands of the DNA at the EcoRV recognition site were then cleaved sequentially, at
AB  - rates that were faster than the turnover number of the enzyme.  The rates recorded for the
AB  - cleavage steps were direct measurements of phosphodiester hydrolysis, while the turnover is
AB  - limited by the dissociation of the product cleaved in both strands.  Other reactions were
AB  - initiated by adding EcoRV and MgCl2 to the DNA: these are the processes observed in reactions
AB  - starting from DNA-bound enzyme but also the bimolecular association of the protein with the
AB  - plasmid.  The association rate was limited by diffusion but its rate constant, 1.2 x 10^8 M-1
AB  - s-1, was unusually small for the binding of a protein to DNA.  The slowness of this
AB  - diffusion-controlled process may be due to a rapid oscillation of the protein between closed
AB  - and open conformations, with only the open form capable of binding DNA.
ER  -

TY  - JOUR
AU  - Erskine, S.G.
AU  - Halford, S.E.
TI  - Fluorescent substrates for the EcoRV restriction endonuclease.
JO  - Biochem. Soc. Trans.
PY  - 1994
SP  - 299s
EP  - 299s
VL  - 22
AB  - In the presence of Mg2+, the EcoRV restriction endonuclease cleaves DNA specifically at the
AB  - sequence GAT/ATC (where / denotes the point of scission). Even the change of a single base
AB  - pair within this sequence will lead to a million fold reduction of EcoRV activity.
AB  - Paradoxically, gel retardation experiments in the absence of Mg2+ show that, unlike EcoRI and
AB  - many other type II restriction endonucleases, EcoRV binds to DNA without any sequence
AB  - preference. The specificity of EcoRV is in fact dependent on the production of a high affinity
AB  - binding site for Mg2+ between the protein and the cognate DNA. X-ray crystal structures show
AB  - that the cognate DNA adopts a highly distorted, kinked conformation in its complex with EcoRV,
AB  - in contrast to noncognate DNA which retains a B-like conformation. The difference between the
AB  - delta-G0 for the binding of cognate and noncognate sequences is near to zero and hence the
AB  - energy from the additional contacts with the specific DNA appears to be neutralized by the
AB  - unfavorable energy change from the distortion of the DNA. In addition, the crystal structures
AB  - show that the protein itself must undergo a conformation change before it can bind DNA.
AB  - Therefore, during one cycle of DNA cleavage, the EcoRV protein will undergo several
AB  - conformational changes: due first to binding nonspecific DNA and then specific DNA, and later
AB  - by the sequence of events leading to cleavage and product release.
ER  -

TY  - JOUR
AU  - Erskine, S.G.
AU  - Halford, S.E.
TI  - Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 759
EP  - 772
VL  - 275
AB  - The EcoRV restriction endonuclease cleaves DNA specifically at its recognition sequence in the
AB  - presence of magnesium ions, but several studies have indicated that it binds to DNA in the
AB  - absence of Mg2+ without any preference for its recognition site.  However, specific binding to
AB  - the recognition site has also been reported.  To distinguish between these reports,
AB  - oligodeoxynucleotides were tagged with either dansyl or eosin fluorophores at their 5'
AB  - termini and annealed to form duplexes of 12 to 16 base-pairs.  For each length of duplex, one
AB  - derivative had the EcoRV recognition sequence while another lacked this sequence.  For the
AB  - duplexes with the recognition site, the fluorophores had no effect on DNA cleavage rates by
AB  - EcoRV in the presence of Mg2+.  The binding of the specific and non-specific duplexes to EcoRV
AB  - in the absence of Mg2+ was measured by fluorescence resonance energy transfer and by
AB  - fluorescence depolarization.  In both procedures, the signal from the specific complex
AB  - differed from the complex with non-specific DNA, with the depolarization data indicating that
AB  - non-specific DNA bound to EcoRV retains a higher rotational freedom than specific DNA.  Even
AB  - so, the equilibrium constant for the binding of specific DNA was identical, within error
AB  - limits, to that for non-specific DNA.
ER  -

TY  - JOUR
AU  - Erskine, S.G.
AU  - Halford, S.E.
TI  - Interactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides.
JO  - Gene
PY  - 1995
SP  - 153
EP  - 156
VL  - 157
AB  - A self-complementary dodecadeoxyribonucleotide that contains the recognition sequence for the
AB  - R.EcoRV Enase was synthesized with a primary amino group at its 5' terminus.  The 5' amino
AB  - function was labeled with the fluorescent dye 5-[dimethylamino] napthalene-1-sulfonyl
AB  - chloride.  The labeled oligodeoxyribonucleotide in its duplex form was shown to be a suitable
AB  - substrate for kinetic studies on the ENase and that no significant dye-DNA or dye-protein
AB  - interactions occurred.  Finally, the binding of R.EcoRV to the labeled DNA was followed by
AB  - detecting the fluorescence resonance energy transfer between the tryptophans of the protein
AB  - and the fluorescent labels of the DNA.
ER  -

TY  - JOUR
AU  - Eruslanov, B.V.
AU  - Kramarov, V.M.
AU  - Smolyanivov, V.V.
AU  - Borovik, R.V.
TI  - Isolation of the site-specific endonuclease EcoRI with the aid of an immunoabsorbent.
JO  - Bioorg. Khim.
PY  - 1980
SP  - 1361
EP  - 1369
VL  - 6
AB  - A simple and satisfactorily reproducible method of isolating the site-specific endonuclease
AB  - EcoRI which is based on the chromatography of the enzyme on a column filled with antibodies
AB  - immobilized on Sepharose 4B is described.  The binding of the enzyme to the antibodies is
AB  - carried out directly from a cell extract, and after the support has been washed free from
AB  - unbound protein the enzyme is eluted.  The isolation of the homogeneous enzyme (20,000
AB  - activity units per 1g of biomass) takes place in one stage and lasts 3 h.  The preparation
AB  - obtained is stable on storage in 50% glycerol at -15C for more than six months.  The paper
AB  - also describes a method of purifying the endonuclease EcoRI to the homogeneous state in two
AB  - chromatographic stages:  in columns containing phosphocellulose and Sephadex G-150.  The
AB  - enzyme obtained by this method contains no nonspecific nucleases and possesses a specific
AB  - activity of 750,000 activity units/mg of protein (3750 activity units per 1g of biomass).
ER  -

TY  - JOUR
AU  - Erwin, A.L.
AU  - Gotschlich, E.C.
TI  - Cloning of a Neisseria meningitidis gene for L-lactate dehydrogenase (L-LDH): evidence for a second meningococcal L-LDH with different   regulation.
JO  - J. Bacteriol.
PY  - 1996
SP  - 4807
EP  - 4813
VL  - 178
AB  - We report the cloning of lldA, a Neisseria meningitidis gene for L-lactate dehydrogenase
AB  - (L-LDH). Escherichia coli contains a single L-LDH gene
AB  - (lldD) in the lld operon (previously lct). E. coli grown in complex media
AB  - does not have L-LDH activity, but the activity is induced by growth in
AB  - defined medium with L-lactate as the carbon source. In contrast,
AB  - meningococci contain at least one L-LDH in addition to the lldA gene
AB  - product. These enzymes are active in meningococci grown in complex media
AB  - and are not dependent on growth in L-lactate. The predicted amino acid
AB  - sequence of lldA is homologous to that of E. coli lldD and of other
AB  - prokaryotic and eukaryotic flavin mononucleotide-containing enzymes that
AB  - catalyze the oxidation of L-lactate and other small alpha-hydroxy acids. A
AB  - mutant with a deletion in lldA was found to have reduced L-LDH activity.
AB  - However, this mutant was able to grow on L-lactate, indicating that a
AB  - second L-LDH must exist. Activity of the lldA enzyme was affected by
AB  - growth conditions, being increased by growth on a defined medium with
AB  - either L-lactate or pyruvate as the carbon source. For meningococci grown
AB  - on a complex medium, activity of the lldA enzyme was increased by growth
AB  - on plates or in well-aerated broth. A second L-lactate-oxidizing activity
AB  - was seen in bacteria grown in poorly aerated broth. Neisseria gonorrhoeae
AB  - contains a homolog of lldA. As for meningococci, mutation of the
AB  - gonococcal lldA reduced L-LDH activity but did not affect growth on
AB  - L-lactate.
ER  -

TY  - JOUR
AU  - Erwin, A.L.
AU  - Sandstedt, S.A.
AU  - Bonthuis, P.J.
AU  - Geelhood, J.L.
AU  - Nelson, K.L.
AU  - Unrath, W.C.
AU  - Diggle, M.A.
AU  - Theodore, M.J.
AU  - Pleatman, C.R.
AU  - Mothershed, E.A.
AU  - Sacchi, C.T.
AU  - Mayer, L.W.
AU  - Gilsdorf, J.R.
AU  - Smith, A.L.
TI  - Analysis of genetic relatedness of Haemophilus influenzae isolates by multilocus sequence typing.
JO  - J. Bacteriol.
PY  - 2008
SP  - 1473
EP  - 1483
VL  - 190
AB  - The gram-negative bacterium Haemophilus influenzae is a human-restricted
AB  - commensal of the nasopharynx that can also be associated with disease. The
AB  - majority of H. influenzae respiratory isolates lack the genes for capsule
AB  - production and are nontypeable (NTHI). Whereas encapsulated strains are
AB  - known to belong to serotype-specific phylogenetic groups, the structure of
AB  - the NTHI population has not been previously described. A total of 656 H.
AB  - influenzae strains, including 322 NTHI strains, have been typed by
AB  - multilocus sequence typing and found to have 359 sequence types (ST). We
AB  - performed maximum-parsimony analysis of the 359 sequences and calculated
AB  - the majority-rule consensus of 4,545 resulting equally most parsimonious
AB  - trees. Eleven clades were identified, consisting of six or more ST on a
AB  - branch that was present in 100% of trees. Two additional clades were
AB  - defined by branches present in 91% and 82% of trees, respectively. Of
AB  - these 13 clades, 8 consisted predominantly of NTHI strains, three were
AB  - serotype specific, and 2 contained distinct NTHI-specific and
AB  - serotype-specific clusters of strains. Sixty percent of NTHI strains have
AB  - ST within one of the 13 clades, and eBURST analysis identified an
AB  - additional phylogenetic group that contained 20% of NTHI strains. There
AB  - was concordant clustering of certain metabolic reactions and putative
AB  - virulence loci but not of disease source or geographic origin. We conclude
AB  - that well-defined phylogenetic groups of NTHI strains exist and that these
AB  - groups differ in genetic content. These observations will provide a
AB  - framework for further study of the effect of genetic diversity on the
AB  - interaction of NTHI with the host.
ER  -

TY  - JOUR
AU  - Erxleben, A.
AU  - Wunsch-Palasis, J.
AU  - Gruning, B.A.
AU  - Luzhetska, M.
AU  - Bechthold, A.
AU  - Gunther, S.
TI  - Genome Sequence of Streptomyces sp. Strain Tu6071.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4278
EP  - 4279
VL  - 193
AB  - Streptomyces sp. Tu6071 is a soil-dwelling bacterium which has a highly active isoprenoid
AB  - biosynthesis. Isoprenoids are important precursors for
AB  - biopharmaceutical molecules such as antibiotics or anticancer agents,
AB  - e.g., landomycin. Streptomyces sp. Tu6071 produces the industrially
AB  - important terpene glycosides phenalinolactones, which have antibacterial
AB  - activity against several Gram-positive bacteria. The availability of the
AB  - genome sequence of Streptomyces sp. Tu6071 allows for understanding the
AB  - biosynthesis of these pharmaceutical molecules and will facilitate
AB  - rational genome modification to improve industrial use.
ER  -

TY  - JOUR
AU  - Esani, S.
AU  - Constable, J.V.
AU  - Van Laar, T.A.
TI  - Draft Genome Sequence of a Multidrug-Resistant Strain of Enterococcus faecalis, PM01, Isolated from the Nest of an American Bushtit, Psaltriparius minimus.
JO  - Genome Announcements
PY  - 2017
SP  - e00017
EP  - e00017
VL  - 5
AB  - Pathogenic microorganisms associated with avian nests may detrimentally impact parental health
AB  - and nest success for the nest primary users, potentially
AB  - neighboring avian or terrestrial species, including humans. Here, we report the
AB  - genome sequence of Enterococcus faecalis strain PM01, isolated from a failed nest
AB  - of American bushtits, Psaltriparius minimus.
ER  -

TY  - JOUR
AU  - Escano, J.
AU  - Deng, P.
AU  - Lu, S.E.
AU  - Smith, L.
TI  - Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140.
JO  - Genome Announcements
PY  - 2016
SP  - e00472
EP  - e00416
VL  - 4
AB  - Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin
AB  - 1140, and the strain has been genetically engineered to combat dental
AB  - caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome
AB  - provides new insights into the strain's superior colonization properties and its
AB  - utility in replacement therapy.
ER  -

TY  - JOUR
AU  - Eshaghi, A.
AU  - Soares, D.
AU  - Tsang, R.
AU  - Richardson, D.
AU  - Kus, J.V.
AU  - Patel, S.N.
TI  - Draft Genome Sequences of Two 'Haemophilus quentini' Isolates Recovered from Two  Different Patients' Blood Cultures.
JO  - Genome Announcements
PY  - 2016
SP  - e01321
EP  - e01316
VL  - 4
AB  - Here, we present the draft genome sequences of two strains (K068 and C860) of the genospecies
AB  - 'Haemophilus quentini' The isolates were recovered from blood
AB  - cultures of a newborn neonate and an elderly patient with septicemia in Ontario,
AB  - Canada.
ER  -

TY  - JOUR
AU  - Eshraghi, L.
AU  - De Meyer, S.E.
AU  - Tian, R.
AU  - Seshadri, R.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Tiwari, R.
AU  - Yates, R.
AU  - Howieson, J.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 87
EP  - 87
VL  - 10
AB  - Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod
AB  - that can exist as a soil saprophyte or as a legume
AB  - microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered
AB  - from the roots of an Indigofera sp. growing 20 km north of Carnarvon in
AB  - Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth
AB  - at 37 degrees C. Here we describe the features of Bradyrhizobium sp. strain
AB  - WSM1743, together with genome sequence information and its annotation. The
AB  - 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds
AB  - and 167 contigs, contains 7908 protein-coding genes and 75 RNA-only encoding
AB  - genes and was sequenced as part of the Root Nodule Bacteria chapter of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Eskes, R.
AU  - Liu, L.
AU  - Ma, H.
AU  - Chao, M.Y.
AU  - Dickson, L.
AU  - Lambowitz, A.M.
AU  - Perlman, P.S.
TI  - Multiple homing pathways used by yeast mitochondrial group II introns.
JO  - Mol. Cell. Biol.
PY  - 2000
SP  - 8432
EP  - 8446
VL  - 20
AB  - The yeast mitochondrial DNA group II introns aI1 and aI2 are retroelements that insert site
AB  - specifically into intronless alleles by a process called homing. Here, we used patterns of
AB  - flanking marker coconversion in crosses with wild-type and mutant aI2 introns to distinguish
AB  - three coexisting homing pathways: two that were reverse transcriptase (RT) dependent
AB  - (retrohoming) and one that was RT independent. All three pathways are initiated by cleavage of
AB  - the recipient DNA target site by the intron-encoded endonuclease, with the sense strand
AB  - cleaved by partial or complete reverse splicing, and the antisense strand cleaved by the
AB  - intron-encoded protein.  The major retrohoming pathway in standard crosses leads to insertion
AB  - of the intron with unidirectional coconversion of upstream exon sequences. This pattern of
AB  - coconversion suggests that the major retrohoming pathway is initiated by target DNA-primed
AB  - reverse transcription of the reverse-spliced intron RNA and completed by double-strand break
AB  - repair (DSBR) recombination with the donor allele. The RT-independent pathway leads to
AB  - insertion of the intron with bi-directional coconversion and presumably occurs by a
AB  - conventional DSBR recombination mechanism initiated by cleavage of the recipient DNA target
AB  - site by the intron-encoded endonuclease, as for group I intron homing. Finally, some mutant
AB  - DNA target sites shift up to 43% of retrohoming to another pathway not previously detected for
AB  - aI2 in which there is no coconversion of flanking exon sequences. This new pathway presumably
AB  - involves synthesis of a full-length cDNA copy of the inserted intron RNA, with completion by a
AB  - repair process independent of homologous recombination, as found for the Lactococcus lactis
AB  - Ll.LtrB intron. Our results show that group II intron mobility can occur by multiple pathways,
AB  - the ratios of which depend on the characteristics of both the intron and the DNA target site.
AB  - This remarkable flexibility enables group II introns to use different recombination and repair
AB  - enzymes in different host cells.
ER  -

TY  - JOUR
AU  - Eskes, R.
AU  - Yang, J.
AU  - Lambowitz, A.M.
AU  - Perlman, P.S.
TI  - Mobility of yeast mitochondrial group II introns: Engineering a new site specificity and retrohoming via full reverse splicing.
JO  - Cell
PY  - 1997
SP  - 865
EP  - 874
VL  - 88
AB  - The mobile group II introns aI1 and aI2 of yeast mtDNA encode endonuclease activities that
AB  - cleave intronless DNA target sites to initiate mobility by target DNA-primed reverse
AB  - transcription.  For aI2, sense-strand cleavage occurs mainly by a partial reverse splicing
AB  - reaction, whereas for aI1, complete reverse splicing occurs, leading to insertion of the
AB  - linear intron RNA into double-stranded DNA.  Here, we show that aI1 homing and reverse
AB  - splicing depend on the EBS1 (RNA)/IBS1(DNA) pairing and that target specificity can be changed
AB  - by compensatory changes in the target site and the donor intron.  Using well-marked strains to
AB  - follow coconversion of flanking DNA, we show that homing occurs by both RT-dependent and
AB  - -independent pathways.  Remarkably, in most RT-dependent events, the reverse spliced intron is
AB  - the initial template for first-strand cDNA synthesis.
ER  -

TY  - JOUR
AU  - Eskin, B.
TI  - The host-controlled restriction enzyme of Escherichia coli B.
JO  - Ph.D. Thesis, University of California, Berkeley, USA
PY  - 1973
SP  - 1
EP  - 191
AB  - The restriction endonuclease of Escherichia coli B has been
AB  - purified and is free of non-specific endonuclease.  On sucrose gradients it
AB  - sediments in a broad band with an S20,w of 11 through 18.  As judged by
AB  - polyacrylamide gel electrophoresis the enzyme exists in at leas two active
AB  - forms, each of which possesses three nonidentical polypeptides, alpha,
AB  - beta, and gamma, of molecular weights 135,000, 60,000 and 55,000,
AB  - respectively.  The molecular weights of these two forms have been estimated
AB  - to be around 200,000 and 700,000.  Combining this information with
AB  - estimates of the ratios of subunits present in each form suggests that the
AB  - molecular formulae of the two forms are alpha1beta1gamma1 and
AB  - alpha2beta4gamma2, respectively.  The subunits, beta and gamma, are
AB  - indistinguishable by polyacrylamide gel electrophoresis from the two
AB  - subunits found in the modification methylase of Escherichia coli B.
ER  -

TY  - JOUR
AU  - Eskin, B.
AU  - Lautenberger, J.A.
AU  - Linn, S.
TI  - Host-controlled modification and restriction of bacteriophage T7 by Escherichia coli B.
JO  - J. Virol.
PY  - 1973
SP  - 1020
EP  - 1023
VL  - 11
AB  - T7 phage resists Escherichia coli B host-controlled modification and
AB  - restriction in vivo, but its DNA carries roughly five sites which are
AB  - susceptible to the purified enzymes.
ER  -

TY  - JOUR
AU  - Eskin, B.
AU  - Linn, S.
TI  - The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. III.  Studies of the restriction adenosine triphosphatase.
JO  - J. Biol. Chem.
PY  - 1972
SP  - 6192
EP  - 6196
VL  - 247
AB  - The restriction endonuclease of Escherichia coli B catalyzes a massive
AB  - hydrolysis of ATP to ADP and Pi. The ATPase requires S-adenosylmethionine and
AB  - DNA containing unmodified restriction sites.  The apparent Km for fd
AB  - replicative form DNA is 20 microM DNA nucleotide, and ATP is half-saturating at
AB  - 100 microM.  Like the nuclease, the ATPase is inhibited strongly by
AB  - S-adenosylethionine and 5'-methylthioadenosine, but only weakly by
AB  - S-adenosylhomocysteine.  The hydrolysis of ATP continues long after DNA
AB  - degradation has ceased.  Whereas no ATPase is observed when restricted DNA but
AB  - no unmodified DNA is present in a reaction mixture, restricted DNA is required
AB  - for the maintenance of ATPase once initiated.  A hypothetical scheme is
AB  - presented which involves the conversion of the enzyme during DNA hydrolysis
AB  - from a form capable of nuclease activity to one catalyzing the breakdown of
AB  - ATP.
ER  -

TY  - JOUR
AU  - Eskin, B.
AU  - Linn, S.
TI  - The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. II. Purification, subunit structure, and catalytic properties of the restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1972
SP  - 6183
EP  - 6191
VL  - 247
AB  - The restriction endonuclease of Escherichia coli B has been purified and is
AB  - free of nonspecific endonuclease.  On sucrose gradients it sediments in a broad
AB  - band with an S20,w of 11 through 18.  As judged by polyacrylamide gel
AB  - electrophoresis the enzyme exists in at least two active forms, each of which
AB  - possess three nonidentical polypeptides, a, b, and c, of molecular weights
AB  - 135,000, 60,000 and 55,000, respectively.  The subunits, b, and c, are
AB  - indistinguishable by polyacrylamide gel electrophoresis from the two subunits
AB  - found in the modification methylase of E. coli B.  ATP is half-saturating at 80
AB  - to 100 lM, S-adenosylmethionine has an apparent Km of 0.3 to 0.4 microM, and fd
AB  - replicative form DNA is saturating at greater than 10 to 20 microM
AB  - DNA-nucleotide.  S-adenosylethionine and 5'-methylthioadenosine, but not
AB  - S-adenosylhomocysteine are potent inhibitors of the enzyme.  Modified DNA
AB  - inhibits by 50% when added in a 5-fold excess over unmodified substrate.  The
AB  - restriction nuclease activity ceases after 5 or 10 min, and the enzyme does not
AB  - appear to turn over in the nuclease reaction.  The cleaved DNA product is not
AB  - adenylylated, phosphorylated, or methylated during hydrolysis.  It is
AB  - susceptible to lambda-exonuclease, exonuclease III, the recBC nuclease, and,
AB  - after denaturation, exonuclease I.  These results imply that the termini of the
AB  - restricted DNA have hydroxyl and 5'-phosphoryl groups, and that they have a
AB  - duplex structure.  However, restricted DNA cannot be phosphorylated by
AB  - polynucleotide kinase, even after treatment of the DNA with alkaline
AB  - phosphatase.  Finally, in order to make the enzyme more accessible, relatively
AB  - rapid assay procedures are suggested which are based on the ATPase activity of
AB  - the enzyme, or on the rendering of circular DNA to a linear form which is
AB  - susceptible to the recBC nuclease.
ER  -

TY  - JOUR
AU  - Eskridge, R.W.
AU  - Weinfeld, H.
AU  - Paigen, K.
TI  - Susceptibility of different coliphage genomes to host-controlled variation.
JO  - J. Bacteriol.
PY  - 1967
SP  - 835
EP  - 844
VL  - 93
AB  - Twenty-eight coliphages were studied for their susceptibility to four systems
AB  - of host control variation in Escherichia coli.  Both temperate and virulent
AB  - phages were studied, including phages with ribonucleic acid, double- and
AB  - single-stranded deoxyribonucleic acid (DNA) and glucosylated DNA.  The systems
AB  - examined were E. coli C-K, K-B, B-K, and K-K(P1).  The C-K, K-B, and B-K
AB  - systems affected temperate phages and nonlysogenizing mutants derived from
AB  - temperate phages.  In general, these systems did not restrict virulent phages.
AB  - Phage 21e, a variant of phage 21, lost the ability to undergo restriction in
AB  - the C-K and B-K systems, but retained susceptibility to the K-B and K-K(P(1)
AB  - systems.  This suggests that the genetic site(s) on the phage, as well as in
AB  - the host, determines susceptibility to host-controlled variation.  Both
AB  - temperate and dependent virulent phages were susceptible to the host control
AB  - system resulting from the presence of prophage P1.  The autonomous and small
AB  - virulents were not susceptible.  In a given system, the various susceptible
AB  - phages differed widely in their efficiency of plating on the restricting host.
AB  - If the few infections that occur arise in rare special cells, then different
AB  - populations of special cells are available to different phage species.  For
AB  - most phage types, when a susceptible phage infected a nonrestricting host, the
AB  - progeny showed the specificity appropriate to that host. Behavior of T3 was
AB  - exceptional, however,  When T3 obtained from E. coli K infected E. coli C or B,
AB  - some of the progeny phages retained K host specificity, whereas others acquired
AB  - the specificity of the new host.
ER  -

TY  - JOUR
AU  - Esmaeel, Q.
AU  - Sanchez, L.
AU  - Robineau, M.
AU  - Dorey, S.
AU  - Clement, C.
AU  - Jacquard, C.
AU  - Barka, E.A.
TI  - Draft Genome Sequence of Plant Growth-Promoting Burkholderia sp. Strain BE12, Isolated from the Rhizosphere of Maize.
JO  - Genome Announcements
PY  - 2018
SP  - e00299
EP  - e00218
VL  - 6
AB  - Burkholderia sp. strain BE12, isolated from a French agricultural soil, possesses antifungal
AB  - activity against a set of phytopathogenic fungi and has friendly
AB  - interactions with grapevine. Here, we present the draft genome sequence of BE12,
AB  - along with genes related to plant growth-promoting traits and siderophores that
AB  - this strain contains, supporting its plant growth and antifungal activities.
ER  -

TY  - JOUR
AU  - Espada, J.
AU  - Ballestar, E.
AU  - Fraga, M.F.
AU  - Garea, A.V.
AU  - Juarranz, A.
AU  - Stockert, J.C.
AU  - Robertson, K.D.
AU  - Fuks, F.O.
AU  - Esteller, M.
TI  - Human DNA methyltransferase 1 is required for maintenance of the histone H3 modification pattern.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 37175
EP  - 37184
VL  - 279
AB  - DNA methyltransferase 1 (DNMT1) plays an essential role in murine development and is thought
AB  - to be the enzyme primarily responsible for
AB  - maintenance of the global methylation status of genomic DNA. However,
AB  - loss of DNMT1 in human cancer cells affects only the methylation status
AB  - of a limited number of pericentromeric sequences. Here we show that
AB  - human cancer cells lacking DNMT1 display at least two important
AB  - differences with respect to wild type cells: a profound disorganization
AB  - of nuclear architecture, and an altered pattern of histone H3
AB  - modification that results in an increase in the acetylation and a
AB  - decrease in the dimethylation and trimethylation of lysine 9.
AB  - Additionally, this phenotype is associated with a loss of interaction
AB  - of histone deacetylases (HDACs) and HP1 (heterochromatin protein 1)
AB  - with histone H3 and pericentromeric repetitive sequences (satellite 2).
AB  - Our data indicate that DNMT1 activity, via maintenance of the
AB  - appropriate histone H3 modifications, contributes to the preservation
AB  - of the correct organization of large heterochromatic regions.
ER  -

TY  - JOUR
AU  - Espedido, B.A.
AU  - Steen, J.A.
AU  - Barbagiannakos, T.
AU  - Mercer, J.
AU  - Paterson, D.L.
AU  - Grimmond, S.M.
AU  - Cooper, M.A.
AU  - Gosbell, I.B.
AU  - van Hal, S.J.
AU  - Jensen, S.O.
TI  - Carriage of an ACME II Variant may have contributed to MRSA ST239-like Strain Replacement in Liverpool Hospital, Sydney, Australia.
JO  - Antimicrob. Agents Chemother.
PY  - 2012
SP  - 3380
EP  - 3383
VL  - 56
AB  - Approximately 39% of MRSA ST239-like bloodstream isolates from Liverpool Hospital
AB  - (1997-2008) carry an arginine catabolic mobile element (ACME). Whole genome
AB  - sequencing revealed that an ACME II variant is located between orfX and SCCmec
AB  - III, and based on pulsed-field gel electrophoresis patterns and temporal
AB  - relationships of all ST239-like isolates (n=360), ACME carriage may have
AB  - contributed to sub-pulsotype strain replacement.
ER  -

TY  - JOUR
AU  - Esperito-Santo, C.
AU  - Lin, Y.
AU  - Hao, X.
AU  - Wei, G.
AU  - Rensing, C.
AU  - Grass, G.
TI  - Draft Genome Sequence of Pseudomonas psychrotolerans L19, Isolated from Copper Alloy Coins.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1623
EP  - 1624
VL  - 194
AB  - We report the draft genome sequence of Pseudomonas psychrotolerans strain L19, isolated from a
AB  - European 50-cent copper alloy coin. Multiple genes potentially involved in copper resistance
AB  - were identified; however, it is unknown if these copper ion resistance determinants contribute
AB  - to prolonged survival of this strain on dry metallic copper.
ER  -

TY  - JOUR
AU  - Espinosa-Camacho, L.F.
AU  - Delgado, G.
AU  - Miranda-Novales, G.
AU  - Soberon-Chavez, G.
AU  - Alcaraz, L.D.
AU  - Morales-Espinosa, R.
TI  - Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia.
JO  - Genome Announcements
PY  - 2017
SP  - e00927
EP  - e00917
VL  - 5
AB  - Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were
AB  - sequenced using PacBio RS-II single-molecule real-time (SMRT)
AB  - technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high
AB  - content of mobile elements, and variation in the genetic content of class 1
AB  - integron In1409.
ER  -

TY  - JOUR
AU  - Espinosa-Camacho, L.F.
AU  - Delgado, G.
AU  - Soberon-Chavez, G.
AU  - Alcaraz, L.D.
AU  - Castanon, J.
AU  - Morales-Espinosa, R.
TI  - Complete Genome Sequences of Four Extensively Drug-Resistant Pseudomonas aeruginosa Strains, Isolated from Adults with Ventilator-Associated Pneumonia at   a Tertiary Referral Hospital in Mexico City.
JO  - Genome Announcements
PY  - 2017
SP  - e00925
EP  - e00917
VL  - 5
AB  - Four extensively drug-resistant Pseudomonas aeruginosa strains, isolated from patients with
AB  - pneumonia, were sequenced using PacBio RS-II single-molecule
AB  - real-time (SMRT) technology. Genome sequence analysis identified great
AB  - variability among mobile genetic elements, as well as some previously undescribed
AB  - genomic islands and new variants of class 1 integrons (In1402, In1403, In1404,
AB  - and In1408).
ER  -

TY  - JOUR
AU  - Espinoza-Miranda, S.S.
AU  - Gomez-Rodriguez, J.A.
AU  - Huete-Perez, J.A.
TI  - Mining for restriction endonucleases in Nicaragua.
JO  - Encuentro
PY  - 2012
SP  - 49
EP  - 62
VL  - 93
AB  - The Molecular Biology Center at the University of Central America in Nicaragua (CBM-UCA) was
AB  - founded in 1999 to strengthen biotechnology research capacity and education in Nicaragua and
AB  - the Central American region.  One of the first projects launched by the CBM-UCA was
AB  - bio-prospecting for key industrial enzymes.  This ongoing study seeks to discover and
AB  - characterize restriction enzymes (RE) in bacteria, and to create a database of microorganisms
AB  - isolated and identified by 16S rDNA sequencing methodology.  In this paper we highlight the
AB  - importance of studying the extreme environmental conditions for building knowledge of
AB  - Nicaraguan biodiversity through modern molecular biology techniques such as metagenomics.  The
AB  - isolation of prototype enzymes such as EcoRV and ClaI is presented as an update and extension
AB  - of previously undertaken work.
ER  -

TY  - JOUR
AU  - Espinoza-Valles, I.
AU  - Soto-Rodriguez, S.
AU  - Edwards, R.A.
AU  - Wang, Z.
AU  - Vora, G.J.
AU  - Gomez-Gil, B.
TI  - Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2104
EP  - 2104
VL  - 194
AB  - Vibrio harveyi is a Gram-negative bacterium found in tropical and temperate marine
AB  - environments as a free-living organism or in association with aquatic
AB  - animals. We report the first sequenced genome of a Vibrio harveyi strain, CAIM
AB  - 1792, the etiologic agent of the 'bright red' syndrome of the Pacific white
AB  - shrimp Litopenaeus vannamei.
ER  -

TY  - JOUR
AU  - Esposito, D.
AU  - Fitzmaurice, W.P.
AU  - Benjamin, R.C.
AU  - Goodman, S.D.
AU  - Waldman, A.S.
AU  - Socca, J.J.
TI  - The complete nucleotide sequence of bacteriophage HP1 DNA.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2360
EP  - 2368
VL  - 24
AB  - The complete nucleotide sequence of the temperate phage HP1 of Haemophilus influenzae was
AB  - determined. The phage contains a linear, double-stranded genome of 32 355 nt with cohesive
AB  - termini. Statistical methods were used to identify 41 probable protein coding segments
AB  - organized into five plausible transcriptional units. Regions encoding proteins involved in
AB  - recombination, replication, transcriptional control, host cell lysis and phage production were
AB  - identified. The sizes of proteins in the mature HP1 particle were determined to assist in
AB  - identifying genes for structural proteins. Similarities between HP1 coding sequences and those
AB  - in databases, as well as similar gene organizations and control mechanisms, suggest that HP1
AB  - is a member of the P2-like phage family, with strong similarities to coliphages P2 and 186 and
AB  - some similarity to the retronphage Ec67.
ER  -

TY  - JOUR
AU  - Essani, K.
AU  - Goorha, R.
AU  - Granoff, A.
TI  - An animal virus-induced DNA-methyltransferase.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 222
EP  - 222
VL  - 13D
AB  - The DNA genome of frog virus 3 (FV3), an iridovirus, is highly methylated; more
AB  - than 20% of cytosine residues are methylated at the 5-carbon position.
AB  - Methylation of the viral DNA occurs in the cytoplasm of infected cells by an
AB  - FV3-specified DNA-methyltransferase (DNA-mt).  To determine the role of this
AB  - enzyme in virus replication and gene expression we have isolated a number of
AB  - FV3 mutants defective in the expression of DNA-mt activity.  Combined genetic
AB  - and biochemical analyses of one of the mutants have revealed a 26K polypeptide
AB  - associated with DNA-mt activity.  Attempts to purify the 26K polypeptide have
AB  - resulted in co-purification of two other polypeptides.  30K and 18K, along with
AB  - the 26K one.  Additional experiments directed toward identifying DNA-mt
AB  - activity with the individual polypeptides, together with reconstitution
AB  - experiments, have indicated that at least two polypeptides (26K and 18K) are
AB  - required for functional DNA-mt activity.  These data support the conclusion
AB  - that FV3-induced DNA-mt, unlike any known eukaryotic DNA-mt, resides in a
AB  - complex of at least two polypeptides.
ER  -

TY  - JOUR
AU  - Essani, K.
AU  - Goorha, R.
AU  - Granoff, A.
TI  - Mutation in a DNA-binding protein reveals an association between DNA-methyltransferase activity and a 26,000-Da polypeptide in frog virus 3-infected cells.
JO  - Virology
PY  - 1987
SP  - 211
EP  - 217
VL  - 161
AB  - The DNA of frog virus 3, an iridovirus, is highly methylated; more than 20% of the cytosine
AB  - bases are methylated at the 5-carbon position by an FV3-induced DNA methyltransferase.  To
AB  - determine the role of this enzyme in virus replication and regulation of gene expression, we
AB  - have analyzed an FV3 mutant that lacks DNA-mt activity and is resistant to 5-azacytidine (an
AB  - inhibitor of DNA-mt).  Comparative polypeptide analysis using cytoplasmic extracts from the
AB  - wild-type FV3 and mutant-infected cells, revealed that a single protein of 26,000 molecular
AB  - weight was altered in the mutant-infected cells.  The altered polypeptide migrated faster in
AB  - SDS-polyacrylamide gel as compared to the wild-type FV3 26K protein.  Five spontaneous
AB  - revertants derived from the mutant regained the migrational characteristic of the wild-type
AB  - 26K protein, DNA-mt activity, and methylation of their DNA.  We further show that the 26K
AB  - polypeptide is a DNA-binding protein and that 80% of the enzyme activity can be eluted from an
AB  - ssDNA affinity column.  Taken together, these data support the conclusion that the 26K
AB  - polypeptide is associated with DNA-mt activity.
ER  -

TY  - JOUR
AU  - Estabrook, R.A.
AU  - Lipson, R.
AU  - Hopkins, B.
AU  - Reich, N.
TI  - The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 31419
EP  - 31428
VL  - 279
AB  - Val(121) is positioned immediately above the extrahelical cytosine in HhaI DNA C(5)-cytosine
AB  - methyltransferase, and replacement with alanine
AB  - dramatically interferes with base flipping and catalysis. DNA binding and
AB  - k(cat) are decreased 10^5-fold for the Val(121) --> Ala mutant that has a
AB  - normal circular dichroism spectrum and AdoMet affinity. The magnitude of
AB  - this loss of function is comparable with removal of the essential
AB  - catalytic Cys(81). Surprisingly, DNA binding is completely recovered
AB  - (increase of 10^5-fold) with a DNA substrate lacking the target cytosine
AB  - base (abasic). Thus, interfering with the base flipping transition results
AB  - in a dramatic loss of binding energy. Our data support an induced fit
AB  - mechanism in which tight DNA binding is coupled to both base flipping and
AB  - protein loop rearrangement. The importance of the proximal protein segment
AB  - (His(127)-Thr(132)) in maintaining this critical interaction between
AB  - Val(121) and the flipped cytosine was probed with single site alanine
AB  - substitutions. None of these mutants are significantly altered in
AB  - secondary structure, AdoMet or DNA affinity, k(methylation),
AB  - k(inactivation), or k(cat). Although Val(121) plays a critical role in
AB  - both extrahelical base stabilization and catalysis, its position and
AB  - mobility are not influenced by individual residues in the adjacent peptide
AB  - region. Structural comparisons with other DNA methyltransferases and DNA
AB  - repair enzymes that stabilize extrahelical nucleotides reveal a motif that
AB  - includes a positively charged or polar side chain and a hydrophobic
AB  - residue positioned adjacent to the target DNA base and either the 5'- or
AB  - 3'-phosphate.
ER  -

TY  - JOUR
AU  - Estabrook, R.A.
AU  - Reich, N.
TI  - Observing an induced-fit mechanism during sequence-specific DNA methylation.
JO  - J. Biol. Chem.
PY  - 2006
SP  - 37205
EP  - 37214
VL  - 281
AB  - The characterization of conformational changes that drive induced-fit mechanisms and their
AB  - quantitative importance to enzyme specificity are
AB  - essential for a full understanding of enzyme function. Here, we report on
AB  - M.HhaI, a sequence-specific DNA cytosine C(5) methyltransferase that
AB  - reorganizes a flexible loop (residues 80-100) upon binding cognate DNA as
AB  - part of an induced-fit mechanism. To directly observe this approximately
AB  - 26A conformational rearrangement and provide a basis for understanding its
AB  - importance to specificity, we replaced loop residues Lys-91 and Glu-94
AB  - with tryptophans. The double mutants W41F/K91W and W41F/E94W are
AB  - relatively unperturbed in kinetic and thermodynamic properties. W41F/E94W
AB  - shows DNA sequence-dependent changes in fluorescence: significant changes
AB  - in equilibrium and transient state fluorescence that occur when the enzyme
AB  - binds cognate DNA are absent with nonspecific DNA. These real-time,
AB  - solution-based results provide direct evidence that binding to cognate DNA
AB  - induces loop reorganization into the closed conformer, resulting in the
AB  - correct assembly of the active site. We propose that M.HhaI scans
AB  - nonspecific DNA in the loop-open conformer and rearranges to the closed
AB  - form once the cognate site is recognized. The fluorescence data exclude
AB  - mechanisms in which loop motion precedes base flipping, and we show loop
AB  - rearrangements are directly coupled to base flipping, because the
AB  - sequential removal of single hydrogen bonds within the target
AB  - guanosine:cytosine base pair results in corresponding changes in loop
AB  - motion.
ER  -

TY  - JOUR
AU  - Estes, A.M.
AU  - Hearn, D.J.
AU  - Nadendla, S.
AU  - Pierson, E.A.
AU  - Dunning, H.J.C.
TI  - Draft Genome Sequence of Enterobacter sp. Strain OLF, a Colonizer of Olive Flies.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01068
EP  - e01018
VL  - 7
AB  - Enterobacter sp. strain OLF colonizes laboratory-reared and wild individuals of the olive
AB  - fruit fly Bactrocera oleae. The 5.07-kbp genome sequence of
AB  - Enterobacter sp. strain OLF encodes metabolic pathways that allow the bacterium
AB  - to partially supplement the diet of the olive fly when its dominant endosymbiont,
AB  - Erwinia dacicola, is absent.
ER  -

TY  - JOUR
AU  - Estrada-Acosta, M.
AU  - Medrano-Felix, A.
AU  - Jimenez, M.
AU  - Gomez-Gil, B.
AU  - Leon-Felix, J.
AU  - Amarillas, L.
AU  - Chaidez, C.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Saintpaul Strain S-70, Isolated from an Aquatic Environment.
JO  - Genome Announcements
PY  - 2013
SP  - e01016
EP  - e01013
VL  - 1
AB  - Salmonella is a pathogen of worldwide importance, causing disease in a vast range of hosts,
AB  - including humans. We report the genome sequence of Salmonella enterica
AB  - subsp. enterica serotype Saintpaul strain S-70, isolated from an aquatic
AB  - environment.
ER  -

TY  - JOUR
AU  - Etienne-Mesmin, L.
AU  - Chassaing, B.
AU  - Adekunle, O.
AU  - Mattei, L.M.
AU  - Edwards, A.N.
AU  - McBride, S.M.
AU  - Bushman, F.D.
AU  - Gewirtz, A.T.
TI  - Genome Sequence of a Toxin-Positive Clostridium difficile Strain Isolated from Murine Feces.
JO  - Genome Announcements
PY  - 2017
SP  - e00088
EP  - e00017
VL  - 5
AB  - Herein, we report the genome sequence of a Clostridium difficile strain isolated  from the
AB  - feces of antibiotic-treated C57BL/6 mice. We have named this strain,
AB  - which differs considerably from those of the previously sequenced C. difficile
AB  - strains, LEM1.
ER  -

TY  - JOUR
AU  - Etson, C.M.
AU  - Todorov, P.
AU  - Walt, D.R.
TI  - Elucidating Restriction Endonucleases Reaction Mechanisms via Dwell-Time Distribution Analysis.
JO  - Biophys. J.
PY  - 2014
SP  - 22A
EP  - 22A
VL  - 106
AB  - We have developed a Total Internal Reflection Fluorescence microscopy based assay that allows
AB  - us to simultaneously measure the length of the catalytic cycle for hundreds of restriction
AB  - endonuclease molecules in one experiment.  We stably attach thousands of short duplex DNA
AB  - molecules, each labeled with a single quantum dot semiconductor nanocrystal, to a passivated
AB  - glass surface within a flow channel.  The disappearance of a quantum dot indicates that its
AB  - DNA tether has been cleaved.  We introduce restriction endonuclease molecules into the channel
AB  - in the absence of magnesium, which permits binding to, but not cleavage of the surface
AB  - immobilized DNA substrate.  When buffer containing magnesium is introduced into the flow
AB  - channel, DNA cleavage by the pre-bound restriction endonuclease molecules is initiated.  This
AB  - synchronization allows us to measure the lag time between the introduction of magnesium and
AB  - the completion of DNA cleavage for the entire population of enzymes.  Analysis of the
AB  - dwell-time distributions can provide insights into the DNA cleavage mechanism.  Our
AB  - observations suggest that EcoRV, a dimeric Type II restriction endonuclease that cleaves the
AB  - palindromic sequence GAT/ATCF (where / is the cut site), requires two kinetic steps to
AB  - complete duplex cleavage after prebinding.  However, dwell-time distributions suggest that
AB  - BcnI, which is active as a monomer and cleaves the pseudopalindromic sequence 5'-CC/SGG-5'
AB  - (where S stands for C or G), requires more than four kinetic steps to complete duplex
AB  - cleavage.  Furthermore, experiments performed with strand-specific DNA substrates suggest that
AB  - the number of steps indicated by the dwell-time distribution depends on which strand of the
AB  - recognition site must be cleaved to result in quantum dot release.  By designing additional
AB  - substrates that mimic the various intermediate states, we plan to dissect the mechanism by
AB  - which BcnI cleaves each strand of the intact restriction site.
ER  -

TY  - JOUR
AU  - Etson, C.M.
AU  - Wilburn, F.
AU  - Moody, T.
AU  - Fashakin, V.
AU  - Walt, D.R.
TI  - Single-Molecule Studies of Restriction Endonuclease Kinetics.
JO  - Biophys. J.
PY  - 2012
SP  - 486A
EP  - 486A
VL  - 102
AB  - Under optimal conditions, restriction endonucleases are capable of mediating remarkably
AB  - specific DNA cleavage. This quality makes the restriction endonuclease an indispensible tool
AB  - for genetic modification and manipulation.  However, the mechanism by which restriction
AB  - endonucleases effectively discriminate between their cognate site and other DNA sequences is
AB  - not fully understood. Under certain conditions, many restriction endonucleases display 'star
AB  - activity' - relaxed specificity resulting in DNA cleavage at sequences that differ from their
AB  - normal recognition sequence - but the mechanism by which specificity is relaxed is not fully
AB  - understood. Although at least 600 of the almost 4000 restriction endonucleases that have been
AB  - identified are commercially available in purified form, DNA cleavage kinetics of only a few of
AB  - these enzymes have been studied in detail. We have developed a fluorescence-based approach
AB  - with which we can track the progress of the cleavage reaction in real time, and simultaneously
AB  - determine the values of the kinetic constants for a particular restriction endonuclease at a
AB  - specific sequence. Modeling restriction endonuclease-mediated DNA cleavage as a
AB  - Michaelis-Menten-like process, we expected reaction rates to display a hyperbolic dependence
AB  - on substrate concentration, but our measurements deviate from this dependence, especially
AB  - under conditions associated with increased star activity (such as low ionic strength). These
AB  - observations suggest that substrate inhibition may be a part of the reaction mechanism under
AB  - normal conditions, and that star activity may be a result of an increase in the population of
AB  - this pathway. Using high density arrays of femtoliter-sized reaction
AB  - vessels created by selectively etching bundled optical fibers, we can
AB  - observe the cleavage activity of hundreds of individual restriction endonuclease molecules in
AB  - solution. By characterizing the population distribution of single-enzyme turnover rates under
AB  - a variety of conditions, we hope to gain insight into the reaction mechanisms of both specific
AB  - cleavage and star activity.
ER  -

TY  - JOUR
AU  - Ettinger, C.L.
AU  - Mousa, W.M.
AU  - Raizada, M.N.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria).
JO  - Genome Announcements
PY  - 2015
SP  - e01461
EP  - e01414
VL  - 3
AB  - Here, we present the draft genome of Enterobacter sp. strain UCD-UG_FMILLET. This strain is an
AB  - endophyte isolated from the roots of finger millet, an Afro-Indian
AB  - cereal crop. The genome contains 4,801,411 bp in 53 scaffolds.
ER  -

TY  - JOUR
AU  - Ettinger, C.L.
AU  - Shehata, H.R.
AU  - Johnston-Monje, D.
AU  - Raizada, M.N.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria).
JO  - Genome Announcements
PY  - 2015
SP  - e01462
EP  - e01414
VL  - 3
AB  - Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This
AB  - strain is an endophyte isolated from surface sterilized
AB  - seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains
AB  - 8,527,129 bp in 109 scaffolds.
ER  -

TY  - JOUR
AU  - Etzkorn, C.
AU  - Horton, N.C.
TI  - Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 833
EP  - 849
VL  - 343
AB  - The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing
AB  - GTCGAC and Mn2+ or Mg2+, at 2.50 Angstrom and
AB  - 2.95 Angstrom resolution, respectively, are presented. In both
AB  - structures, the DNA is found cleaved, and the positions of the
AB  - active-site groups, cleaved phosphate group, and 3' oxygen atom of the
AB  - leaving group are in very similar positions. Two highly occupied Mn2+
AB  - positions are found in each active site of the four
AB  - crystallographically independent subunit copies in the HincII/DNA/Mn2+
AB  - structure. The manganese ion closest to the previously identified
AB  - single Ca2+ position of HincII is shifted 1.7 Angstrom and has lost
AB  - direct ligation to the active-site aspartate residue, Asp127. A
AB  - Mn2+-ligated water molecule in a position analogous to that seen in the
AB  - HincII/DNA/Ca2+ structure, and proposed to be the attacking
AB  - nucleophile, is beyond hydrogen bonding distance from the active-site
AB  - lysine residue, Lys129, but remains within hydrogen bonding distance
AB  - from the proRp oxygen atom of the phosphate group 3' to the scissile
AB  - phosphate group. In addition, the position of the cleaved phosphate
AB  - group is on the opposite side of the axis connecting the two metal ions
AB  - relative to that found in the BamHI/product DNA/Mn2+ structure.
AB  - Mechanistic implications are discussed, and a model for the
AB  - two-metal-ion mechanism of DNA cleavage by HincII is proposed.
ER  -

TY  - JOUR
AU  - Etzkorn, C.
AU  - Horton, N.C.
TI  - Ca2+ binding in the active site of HincII: implications for the catalytic mechanism.
JO  - Biochemistry
PY  - 2004
SP  - 13256
EP  - 13270
VL  - 43
AB  - The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and
AB  - cognate DNA containing GTCGAC is presented. The DNA is
AB  - uncleaved, and one calcium ion is bound per active site, in a position
AB  - previously described as site I in the related blunt cutting type II
AB  - restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and
AB  - Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494],
AB  - as well as that found in other related enzymes. Unlike the site I metal in
AB  - EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the
AB  - observed calcium cation is directly ligated to the pro-S(p) oxygen of the
AB  - scissile phosphate. A calcium ion-ligated water molecule is well
AB  - positioned to act as the nucleophile in the phosphodiester bond cleavage
AB  - reaction, and is within hydrogen bonding distance of the conserved active
AB  - site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate
AB  - group 3' of the scissile phosphate, suggesting possible roles for these
AB  - groups in the catalytic mechanism. Kinetic data consistent with an
AB  - important role for the 3'-phosphate group in DNA cleavage by HincII are
AB  - presented. The previously observed sodium ion [Horton, N. C., Dorner, L.
AB  - F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the
AB  - active sites of the Ca(2+)-bound structure; however, kinetic data show
AB  - little effect on the single-turnover rate of DNA cleavage in the absence
AB  - of Na(+) ions.
ER  -

TY  - JOUR
AU  - Euler, C.W.
AU  - Ryan, P.A.
AU  - Martin, J.M.
AU  - Fischetti, V.A.
TI  - M.SpyI, a DNA methyltransferase encoded on a mefA chimeric element, modifies the genome of Streptococcus pyogenes.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1044
EP  - 1054
VL  - 189
AB  - While screening the clonality of Streptococcus pyogenes isolates from an outbreak of
AB  - erythromycin-resistant pharyngitis in Pittsburgh, PA, we found
AB  - a correlation between the presence of the chimeric element Phi10394.4
AB  - (carrying the macrolide efflux gene, mefA) and genomic DNA being resistant
AB  - to cleavage by SmaI restriction endonuclease. A search of the open reading
AB  - frames in Phi10394.4 identified a putative type II
AB  - restriction-modification (R-M) cassette containing a cytosine
AB  - methyltransferase gene (spyIM). Heterologous expression of the cloned
AB  - spyIM gene, as well as allelic-replacement experiments, showed that the
AB  - action of this methyltransferase (M.SpyI) was responsible for the
AB  - inhibition of SmaI digestion of genomic DNA in the Phi10394.4-containing
AB  - isolates. Analysis of the methylation patterns of streptococcal genomic
AB  - DNA from spyIM-positive strains, a spyIM deletion mutant, and a
AB  - spyIM-negative strain determined that M.SpyI specifically recognized and
AB  - methylated the DNA sequence to generate 5'-C(m)CNGG. To our knowledge,
AB  - this is the first methyltransferase gene from S. pyogenes to be cloned and
AB  - to have its activity characterized. These results reveal why pulsed field
AB  - gel electrophoresis analysis of SmaI-digested genomic DNA cannot be used
AB  - to analyze the clonality of some streptococci containing Phi10394.4 and
AB  - may explain the inability of previous epidemiological studies to use SmaI
AB  - to analyze DNAs from macrolide-resistant streptococci. The presence of the
AB  - SpyI R-M cassette in Phi10394.4 could impart a selective advantage to host
AB  - strain survival and may provide another explanation for the observed
AB  - increase in macrolide-resistant streptococci.
ER  -

TY  - JOUR
AU  - Eutsey, R.A.
AU  - Powell, E.
AU  - Dordel, J.
AU  - Salter, S.J.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Ehrlich, G.D.
AU  - Hiller, N.L.
TI  - Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.
JO  - MBio
PY  - 2015
SP  - e00173
EP  - e00115
VL  - 6
AB  - The human pathogen Streptococcus pneumoniae (pneumococcus) exhibits a high degree of genomic
AB  - diversity and plasticity. Isolates with high genomic similarity are
AB  - grouped into lineages that undergo homologous recombination at variable rates.
AB  - PMEN1 is a pandemic, multidrug-resistant lineage. Heterologous gene exchange
AB  - between PMEN1 and non-PMEN1 isolates is directional, with extensive gene transfer
AB  - from PMEN1 strains and only modest transfer into PMEN1 strains.
AB  - Restriction-modification (R-M) systems can restrict horizontal gene transfer, yet
AB  - most pneumococcal strains code for either the DpnI or DpnII R-M system and
AB  - neither limits homologous recombination. Our comparative genomic analysis
AB  - revealed that PMEN1 isolates code for DpnIII, a third R-M system syntenic to the
AB  - other Dpn systems. Characterization of DpnIII demonstrated that the endonuclease
AB  - cleaves unmethylated double-stranded DNA at the tetramer sequence 5' GATC 3', and
AB  - the cognate methylase is a C5 cytosine-specific DNA methylase. We show that
AB  - DpnIII decreases the frequency of recombination under in vitro conditions, such
AB  - that the number of transformants is lower for strains transformed with
AB  - unmethylated DNA than in those transformed with cognately methylated DNA.
AB  - Furthermore, we have identified two PMEN1 isolates where the DpnIII endonuclease
AB  - is disrupted, and phylogenetic work by Croucher and colleagues suggests that
AB  - these strains have accumulated genomic differences at a higher rate than other
AB  - PMEN1 strains. We propose that the R-M locus is a major determinant of genetic
AB  - acquisition; the resident R-M system governs the extent of genome plasticity.
AB  - IMPORTANCE: Pneumococcus is one of the most important community-acquired
AB  - bacterial pathogens. Pneumococcal strains can develop resistance to antibiotics
AB  - and to serotype vaccines by acquiring genes from other strains or species. Thus,
AB  - genomic plasticity is associated with strain adaptability and pneumococcal
AB  - success. PMEN1 is a widespread and multidrug-resistant highly pathogenic
AB  - pneumococcal lineage, which has evolved over the past century and displays a
AB  - relatively stable genome. In this study, we characterize DpnIII, a
AB  - restriction-modification (R-M) system that limits recombination. DpnIII is
AB  - encountered in the PMEN1 lineage, where it replaces other R-M systems that do not
AB  - decrease plasticity. Our hypothesis is that this genomic region, where different
AB  - pneumococcal lineages code for variable R-M systems, plays a role in the
AB  - fine-tuning of the extent of genomic plasticity. It is possible that well-adapted
AB  - lineages such as PMEN1 have a mechanism to increase genomic stability, rather
AB  - than foster genomic plasticity.
ER  -

TY  - JOUR
AU  - Evans, D.A.
AU  - Bronowska, A.K.
TI  - Implications of fast-time scale dynamics of human DNA/RNA cytosine methyltransferases (DNMTs) for protein function.
JO  - Theor. Chem. Acc.
PY  - 2010
SP  - 407
EP  - 418
VL  - 125
AB  - The role of protein dynamics in the control of substrate recognition, catalysis, and
AB  - protein-protein interactions is often underestimated. Recently, a number of studies have
AB  - examined the contribution of protein dynamics to the thermodynamics of ligand binding in
AB  - detail,
AB  - mostly using NMR relaxation measurements and molecular dynamics (MD) simulations. The results
AB  - unequivocally demonstrate that conformational dynamics play a pivotal role in the properties
AB  - and functions of proteins, and
AB  - ignoring this contribution is likely to lead to substantial errors when explaining the
AB  - biological function of proteins and in predictions of the binding affinities of their cognate
AB  - ligands. However, the details of the interplay between structure and dynamics and the way it
AB  - affects the biological function of the target protein remain poorly understood. In
AB  - this study, the changes in fast (picosecond-to-nanosecond time scale) dynamics of catalytic
AB  - domains of four human cytosine DNA methyltransferases (DNMTs) were studied using molecular
AB  - dynamics (MD) simulations. The results
AB  - provide insight into the protein dynamics changes that occur upon binding of the cofactor,
AB  - S-adenosylmethionine (SAM). Contrary to expectations, increased amplitude of motions of
AB  - backbone amide (N-H) and terminal heavy
AB  - atom (C-C) bond vectors was observed in all studied DNMTs upon binding of SAM. These results
AB  - imply that the cofactor binding causes a global increase in the extent of protein dynamics in
AB  - the short time scale. This global
AB  - dynamic change constitutes a favourable entropic contribution to the free energy of SAM
AB  - binding. These results suggest that cytosine DNA methyltransferases may exploit changes in
AB  - their fast scale dynamics to reduce the entropic cost of the substrate binding.
ER  -

TY  - JOUR
AU  - Evans, M.
AU  - Kaczmarek, F.S.
AU  - Stutzman-Engwall, K.
AU  - Dyson, P.
TI  - Characterization of the Streptomyces-lividans-type site-specific DNA modification system in the avermectin-producer Streptomyces avermitilis permits investigation of two novel giant linear plasmids, pSA1 and pSA2.
JO  - Microbiology
PY  - 1994
SP  - 1367
EP  - 1371
VL  - 140
AB  - The degradation of Streptomyces avermitilis DNA samples analysed by conventional pulsed-field
AB  - gel electrophoresis was shown to be due to Tris-dependent, double-strand cleavage.  Using
AB  - alternative electrophoretic conditions, separation of intact DNA molecules was achieved,
AB  - permitting the identification of two novel giant linear plasmids: the 100 kb pSA1 and 250 kb
AB  - pSA2.  Use of pSA2 DNA as a probe showed that pSA1 does not cross-hybridize, indicating that
AB  - the plasmids are not closely related.  The site-specificity of the DNA modifications, which
AB  - render the DNA susceptible to Tris-dependent cleavage, was found to be essentially identical
AB  - to that of similar modifications found in the DNA of S. lividans.
ER  -

TY  - JOUR
AU  - Evans, P.S.
AU  - Luo, Y.
AU  - Muruvanda, T.
AU  - Ayers, S.
AU  - Hiatt, B.
AU  - Hoffman, M.
AU  - Zhao, S.
AU  - Allard, M.W.
AU  - Brown, E.W.
TI  - Complete Genome Sequences of Salmonella enterica Serovar Heidelberg Strains Associated with a Multistate Food-Borne Illness Investigation.
JO  - Genome Announcements
PY  - 2014
SP  - e01154
EP  - e01113
VL  - 2
AB  - Next-generation sequencing is being evaluated for use with food-borne illness investigations,
AB  - especially when the outbreak strains produce patterns that cannot
AB  - be discriminated from non-outbreak strains using conventional procedures. Here we
AB  - report complete genome assemblies of two Salmonella enterica serovar Heidelberg
AB  - strains with a common pulsed-field gel electrophoresis pattern isolated during an
AB  - outbreak investigation.
ER  -

TY  - JOUR
AU  - Evans, T.C. Jr.
AU  - Benner, J.
AU  - Xu, M.Q.
TI  - Semisynthesis of cytotoxic proteins using a modified protein splicing element.
JO  - Protein Sci.
PY  - 1998
SP  - 2256
EP  - 2264
VL  - 7
AB  - Two cytotoxic proteins, bovine pancreatic ribonuclease A (RNase A), and a restriction
AB  - endonuclease from Haemophilus parainfluenzae (HpaI), were produced using a novel semisynthetic
AB  - approach that utilizes a protein splicing element, an intein, to generate a reactive thioester
AB  - at the C-terminus of a recombinant protein. Nucleophilic attack on this thioester by the
AB  - N-terminal cysteine of a synthetic peptide ultimately leads to the ligation of the two
AB  - reactants through a native peptide bond. This strategy was used to produce RNase A and HpaI by
AB  - isolating inactive truncated forms of these proteins, the first 109 and 223 amino acids of
AB  - RNase A and HpaI, respectively, as fusion proteins consisting of the target protein, an
AB  - intein, and a chitin binding domain. Thiol-induced cleavage of the precursor led to the
AB  - liberation of the target protein with a C-terminal thioester-tag. Addition of synthetic
AB  - peptides representing the amino acids missing from the truncated forms led to the generation
AB  - of full-length products that displayed catalytic activity indicative of the wild-type enzymes.
AB  - The turnover numbers and Km for ligated and renatured RNase A were 8.2 s(-1) and 1.5 mM, in
AB  - good agreement with reported values of 8.3 s(-1) and 1.2 mM (Hodges & Merrifield, 1975).
AB  - Ligated HpaI had a specific activity of 0.5-1.5 x 10(6) U/mg, which compared favorably with
AB  - the expected value of 1-2 x 10(6) U/mg (J. Benner, unpubl. obs.). Besides assisting in the
AB  - production of cytotoxic proteins, this technique could allow the easy insertion of unnatural
AB  - amino acids into a protein sequence.
ER  -

TY  - JOUR
AU  - Evdokimov, A.A.
AU  - Sclavi, B.
AU  - Zinoviev, V.V.
AU  - Malygin, E.G.
AU  - Hattman, S.
AU  - Buckle, M.
TI  - Study of bacteriophage T4-encoded dam DNA (Adenine-N-6)-methyltransferase binding with substrates by rapid laser  UV cross-linking.
JO  - J. Biol. Chem.
PY  - 2007
SP  - 26067
EP  - 26076
VL  - 282
AB  - DNA methyltransferases of the Dam family ( including bacteriophage T4-encoded Dam DNA
AB  - (adenine- N-6)-methyltransferase ( T4Dam)) catalyze
AB  - methyl group transfer from S-adenosyl-L-methionine ( AdoMet), producing
AB  - S-adenosyl-Lhomocysteine ( AdoHcy) and methylated adenine residues in
AB  - palindromic GATC sequences. In this study, we describe the application
AB  - of direct ( i. e. no exogenous cross-linking reagents) laser UV
AB  - cross-linking as a universal non-perturbing approach for studying the
AB  - characteristics of T4Dam binding with substrates in the equilibrium and
AB  - transient modes of interaction. UV irradiation of the enzyme center dot
AB  - substrate complexes using an Nd3(+): yttrium aluminum garnet laser at
AB  - 266nm resulted in up to 3 and > 15% yields of direct T4Dam
AB  - cross-linking to DNA and AdoMet, respectively. Consequently, we were
AB  - able to measure equilibrium constants and dissociation rates for enzyme
AB  - center dot substrate complexes. In particular, we demonstrate that both
AB  - reaction substrates, specific DNA and AdoMet( or product AdoHcy),
AB  - stabilized the ternary complex. The improved substrate affinity for the
AB  - enzyme in the ternary complex significantly reduced dissociation rates
AB  - ( up to 2 orders of magnitude). Several of the parameters obtained (
AB  - such as dissociation rate constants for the binary T4Dam center dot
AB  - AdoMet complex and for enzyme complexes with a non-fluorescent
AB  - hemimethylated DNA duplex) were previously inaccessible by other means.
AB  - However, where possible, the results of laser UV cross-linking were
AB  - compared with those of fluorescence analysis. Our study suggests that
AB  - rapid laser UV cross-linking efficiently complements standard DNA
AB  - methyltransferase-related tools and is a method of choice to probe
AB  - enzyme-substrate interactions in cases in which data cannot be acquired
AB  - by other means.
ER  -

TY  - JOUR
AU  - Evdokimov, A.A.
AU  - Zinoviev, V.V.
AU  - Kuznetsov, V.V.
AU  - Netesova, N.A.
AU  - Malygin, E.G.
TI  - Design of oligonucleotide inhibitors for human DNA methyltransferase 1.
JO  - Mol. Biol. (Mosk)
PY  - 2009
SP  - 418
EP  - 425
VL  - 43
AB  - Mammalian DNA methyltransferase 1 (Dnmt1) is responsible for copying the DNA methylation
AB  - pattern during cell division. Since Dnmt1 plays an
AB  - important role in carcinogenesis, it is of particular interest to
AB  - search for its specific inhibitors. To design oligonucleotide
AB  - inhibitors of human Dnmt1, a number of singlestranded, double-stranded,
AB  - and hairpin DNA structures containing a canonical or a modified Dnmt1
AB  - recognition site (5'-CG) were constructed on the basis of a 22-nt
AB  - sequence. Structural features such as a C:A mismatch,
AB  - phosphorothioates, and hairpins proved capable of incrementally
AB  - increasing the oligonucleotide affinity for Dnmt1. An improvement of
AB  - inhibitory properties was also achieved by replacing the target
AB  - cytosine with 5,6-dihydro-5-azacytosine, 5-methyl-2-pyrimidinone, or
AB  - 6-methyl-pyrrolo-[2,3-d]-2-pyrimidinone. The concentration that caused
AB  - 50% inhibition of methylation of 1 mu M poly(dI-dC) center dot
AB  - poly(dI-dC), a conventional DNA substrate, was approximately 10(-7) M
AB  - for the most efficient oligonucleotides. Under the same in vitro
AB  - conditions, these oligonucleotide inhibitors demonstrated a
AB  - substantially stronger effect compared to known Dnmt1 inhibitors, which
AB  - were used as controls.
ER  -

TY  - JOUR
AU  - Evdokimov, A.A.
AU  - Zinoviev, V.V.
AU  - Malygin, E.G.
TI  - The Kinetic Mechanism of Phage T4 DNA-[N6-Adenine]-Methyltransferase.
JO  - Mol. Biol. (Mosk)
PY  - 2002
SP  - 849
EP  - 861
VL  - 36
AB  - Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine to the GATC recognition
AB  - site catalyzed by the phage T4 DNA-[N6-adenine]-methyltransferase [EC 2.1.1.72] showed that
AB  - the reverse reaction is at least 500 times lower than the direct one.  The overall pattern of
AB  - product inhibition corresponds to an ordered steady-state mechanism following the sequence
AB  - SAM/DNA/metDNA/SAH/.  Pronounced inhibition was observed at high concentrations of the
AB  - 20-meric substrate duplex, which may be attributed to formation of a dead-end complex
AB  - MTase-SAH-DNA.  In contrast, high SAM concentrations proportionally accelerated the reaction.
AB  - Thus, the reaction may include a stage whereby the binding of SAM and the release of SAH are
AB  - united into one concerted event.  Computer fitting of alternative kinetic schemes to the
AB  - aggregate of experimental data revealed that the most plausible mechanism involves
AB  - isomerization of the enzyme.
ER  -

TY  - JOUR
AU  - Evdokimov, A.A.
AU  - Zinoviev, V.V.
AU  - Malygin, E.G.
TI  - Effect of S-adenosyl-L-methionine and its analogues on site-specific binding of DNA-(adenine-N6)-methyltransferase of T4 phage with the oligonucleotide substrate.
JO  - Bioorg. Khim.
PY  - 2000
SP  - 797
EP  - 800
VL  - 26
AB  - Using fluorescence of 2-aminopurine-substituted oligonucleotide duplexes, "flipping" of the
AB  - target base in the process of interaction of T4 DNA-(adenine-N6)-methyltransferase (EC
AB  - 2.1.1.72) with the substrate double-stranded DNA was revealed.  It was shown that
AB  - S-adenosyl-L-methionine, the methyl group donor, induces the reorientation of the enzyme
AB  - relative to the asymmetrically modified recognition site.
ER  -

TY  - JOUR
AU  - Evdokimov, A.A.
AU  - Zinoviev, V.V.
AU  - Malygin, E.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Bacteriophage T4 Dam DNA-[N6-adenine]Methyltransferase. Kinetic evidence for a catalytically essential conformational change in the ternary complex.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 279
EP  - 286
VL  - 277
AB  - We carried out a steady state kinetic analysis of the bacteriophage T4
AB  - DNA-[N(6)-adenine]methyltransferase (T4 Dam) mediated methyl group transfer reaction from
AB  - S-adenosyl-l-methionine (AdoMet) to Ade in the palindromic recognition sequence, GATC, of a
AB  - 20-mer oligonucleotide duplex. Product inhibition patterns were consistent with a steady
AB  - state-ordered bi-bi mechanism in which the order of substrate binding and product (methylated
AB  - DNA, DNA(Me) and S-adenosyl-l-homocysteine, AdoHcy) release was AdoMet, DNA, DNA(Me), Hcy. A
AB  - strong reduction in the rate of methylation was observed at high concentrations of the
AB  - substrate 20-mer DNA duplex. In contrast, increasing substrate AdoMet concentration led to
AB  - stimulation in the reaction rate with no evidence of saturation. We propose the following
AB  - model. Free T4 Dam (initially in conformational form E) randomly interacts with substrates
AB  - AdoMet and DNA to form a ternary T4 Dam-AdoMet-DNA complex in which T4 Dam has isomerized to
AB  - conformational state F, which is specifically adapted for catalysis. After the chemical step
AB  - of methyl group transfer from AdoMet to DNA, product DNA(Me) dissociates relatively rapidly
AB  - (k(off) = 1.7 s(-1)) from the complex. In contrast, dissociation of product AdoHcy proceeds
AB  - relatively slowly (k(off) = 0.018 s(-1)), indicating that its release is the rate-limiting
AB  - step, consistent with k(cat) = 0.015 s(-1). After AdoHcy release, the enzyme remains in the F
AB  - conformational form and is able to preferentially bind AdoMet (unlike form E, which randomly
AB  - binds AdoMet and DNA), and the AdoMet-F binary complex then binds DNA to start another
AB  - methylation cycle. We also propose an alternative pathway in which the release of AdoHcy is
AB  - coordinated with the binding of AdoMet in a single concerted event, while T4 Dam remains in
AB  - the isomerized form F. The resulting AdoMet-F binary complex then binds DNA, and another
AB  - methylation reaction ensues. This route is preferred at high AdoMet concentrations.
ER  -

TY  - JOUR
AU  - Evdokimova, N.M.
AU  - Aleshkin, G.I.
AU  - Skavronskaya, A.G.
TI  - Inheritance and phenotypic expression of plasmids coding EcoRI restriction endonuclease in Vibrio cholerae cells.
JO  - Biull. Eksp. Biol. Med.
PY  - 1985
SP  - 472
EP  - 474
VL  - 100
AB  - Restriction endonucleases are widely used nowadays to clone DNA fragments of different origin
AB  - with the aid of vector molecules of plasmids and bacteriophages.  The process of DNA
AB  - recombination, in which restriction endonucleases take part, also takes place in vitro.  The
AB  - obtaining of hybrid molecules in vivo, due to the action of restriction endonucleases can in
AB  - many cases facilitate the task of cloning foreign DNA in bacterial cells.  For instance, by
AB  - means of a technique based on completion of a recA-independent recombination process,
AB  - EcoRI-dependent cloning of DNA has been carried out in Escherichia coli cells in vivo, so that
AB  - it was possible to obtain plasmids carrying recB+C+ genes or enterotoxin Ent genes.
AB  - Reproduction of this process in Vibrio cholerae opens up a new approach to the obtaining of
AB  - recombinant plasmids carrying genes of V. cholerae and, in particular, genes responsible for
AB  - the leading pathogenetic sign of V. cholerae, namely toxin formation.  For this purpose it was
AB  - necessary to transfer into V. cholerae cells a plsmid coding restriction endonuclease EcoRI,
AB  - to preserve it in V. cholerae cells, and to express EcoRI activity in them.  The aim of this
AB  - investigaton was to construct such a plasmid and to investigate the phenotypic expression of
AB  - its genetic determinants in V. cholerae cells.
ER  -

TY  - JOUR
AU  - Evenhuis, J.P.
AU  - LaPatra, S.E.
AU  - Graf, J.
TI  - Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain CSF-298-10.
JO  - Genome Announcements
PY  - 2017
SP  - e00173
EP  - e00117
VL  - 5
AB  - We announce here the draft genome assembly of Flavobacterium columnare CSF-298-10, a strain
AB  - isolated from an outbreak of columnaris disease at a
AB  - commercial trout farm in Hagerman Valley, Idaho, USA. The complete genome
AB  - consists of 13 contigs totaling 3,284,579 bp, with an average G+C content of
AB  - 31.5% and 2,933 predicted coding genes.
ER  -

TY  - JOUR
AU  - Everett, E.A.
TI  - Structure-function analysis of the EcoRI DNA Methylase.
JO  - Ph.D. Thesis, Univ. of California, Santa Barbara
PY  - 1990
SP  - 1
EP  - 190
AB  - The structural characteristics of the E. coli EcoRI methylase involved in methyl transfer from
AB  - S-adenosyl-L-methionine to DNA and in binding these moities were analyzed. This study provides
AB  - a "picture" of the methylase structure binding regions, critical residues and catalytic state.
AB  - Not much structure-function information is available about DNA methylases or S-
AB  - adenosyl-L-methionine binding enzymes. For DNA methylases, little is known about
AB  - protein-cofactor interactions or the mechanisms of methyl transfer to DNA. Information about
AB  - the E. coli EcoRI methylase is of interest since S-adenosyl-L-methionine is the methyl group
AB  - donor for a large range of enzymes and the importance of DNA methylation is becoming
AB  - increasingly obvious. Determination of structure-function relationships used traditional and
AB  - innovative protein chemistries. These included proteolytic patterns, photoaffinity labeling
AB  - with [methyl-3H]8-azido-S-adenosyl-L-methionine, chemical modification of cysteine and
AB  - histidine residues, fluorescence spectroscopy and mass spectrometry.
ER  -

TY  - JOUR
AU  - Everett, E.A.
AU  - Falick, A.M.
AU  - Reich, N.O.
TI  - Identification of a critical cysteine in EcoRI DNA methyltransferase by mass spectrometry.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 17713
EP  - 17719
VL  - 265
AB  - EcoRI DNA methyltransferase (MTase) is rapidly inactivated by N-ethylmaleimide
AB  - with concomitant incorporation of 2 mol of N-ethyl[2-3H]maleimide/mol of
AB  - functional monomer.  Preincubation of the enzyme with either
AB  - S-adenosylmethionine or DNA reduces the rate of activity loss, whereas
AB  - preincubation with DNA and the S-adenosylmethionine analog sinefungin
AB  - completely protects the enzyme from inactivation.  An endo proteinase Glu-C
AB  - digest of N-ethyl[2-3H]maleimide-modified enzyme was prepared and separated by
AB  - high pressure liquid chromatography.  Modified and unmodified
AB  - cysteine-containing peptides were located and identified by radioactivity, mass
AB  - spectrometry, and tandem mass spectrometry.  In the absence of any ligands,
AB  - cysteines 25, 116, and 223 are modified by N-ethylmaleimide; in the presence of
AB  - DNA and sinefungin Cys-223 is essentially unmodified.  Thus, N-ethylmaleimide
AB  - modification of Cys-223 in EcoRI DNA MTase is responsible for the loss of
AB  - enzyme activity.  Cys-223 is preceded by Asn, and this (or Cys-Asn) occurs with
AB  - high frequency in adenine and cytosine (N-4) DNA MTases.  Direct involvement of
AB  - cysteine in methyl transfer reactions to adenine N-6 and cytosine N-4 is
AB  - supported by the similarity of the reactions catalyzed by adenine N-6 and
AB  - cytosine N-4 DNA MTases, the frequent presence of Asn-flanking Cys, and the
AB  - importance of Cys-223 to EcoRI MTase function.
ER  -

TY  - JOUR
AU  - Everett, E.A.
AU  - Reich, N.O.
TI  - Determination of the EcoRI methylase Adomet binding region.
JO  - J. Cell Biol.
PY  - 1988
SP  - 854a
EP  - 854a
VL  - 107
AB  - Although S-Adenosylmethionine (Adomet) is a methyl group donor in many
AB  - enzymatic reactions including DNA methylation, structural features of DNA
AB  - methylases necessary for Adomet binding and DNA methylation have not yet been
AB  - determined.  Investigating structural determinants of activity is critical in
AB  - understanding methylation and its role in gene expression, DNA repair,
AB  - restriction-modification and carcinogenesis.  Our research involves the E. coli
AB  - EcoRI methylase which transfers the methyl group from Adomet to the second
AB  - adenine in GAATC DNA sequences.  Methylation protects the site from cleavage by
AB  - the corresponding endonuclease.  We have synthesized an Adomet photoaffinity
AB  - analog, 3H8-AzidoAdomet, which binds specifically to the Adomet site with
AB  - similar binding and catalytic constants.  Covalent modification of the binding
AB  - site with 3H8-AzAdomet and subsequent chromatographic, electrophoretic,
AB  - autoradiographic and sequence analyses of proteolytic digests are being
AB  - employed in isolating the methylase portion critical for Adomet binding.  A
AB  - peptide segment of the Adomet binding site to which 3H8-AzAdomet binds has been
AB  - obtained and is being identified along with the covalently modified amino acid
AB  - residue or residues.
ER  -

TY  - JOUR
AU  - Everett, E.A.
AU  - Reich, N.O.
TI  - Determination of the EcoRI methylase Adomet binding region.
JO  - ACS Abstracts
PY  - 1988
SP  - 94
EP  - 94
VL  - 196
AB  - Although S-Adenosylmethionine (Adomet) is a methyl group donor in many
AB  - enzymatic reactions including DNA methylation, structural features of DNA
AB  - methylases necessary for Adomet binding and DNA methylation have not yet been
AB  - determined.  Investigating structural determinants of activity is critical in
AB  - understanding methylation and its role in gene expression, DNA repair,
AB  - restriction-modification and carcinogenesis.  Our research involves the E. coli
AB  - EcoRI methylase which transfers the methyl group from Adomet to the second
AB  - adenine in GAATTC DNA sequences.  Methylation protects the site from cleavage
AB  - by the corresponding endonuclease.  We have synthesized an Adomet photoaffinity
AB  - analog.  3H8-AzidoAdomet, which binds specifically to the Adomet site with
AB  - similar binding and catalytic constants.  Covalent modification of the binding
AB  - site with 3H8-AzAdomet and subsequent chromatographic, electrophoretic,
AB  - autoradiographic and sequence analyses of proteolytic digests are being
AB  - employed in isolating the methylase portion critical for Adomet binding.  A
AB  - peptide segment of the Adomet binding site to which 3H8-AzAdomet binds has been
AB  - obtained and is being identified along with the covalently modified amino acid
AB  - residue or residues.
ER  -

TY  - JOUR
AU  - Everett, E.A.
AU  - Reich, N.O.
TI  - EcoRI DNA methylase activity is eliminated upon histidine residue modification.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1989
SP  - 233
EP  - 237
VL  - 164
AB  - The E. coli EcoRI DNA methylase activity is completely eliminated in five
AB  - minutes upon incubation with the histidine residue specific reagent diethyl
AB  - pyrocarbonate.  In that two moles of N-ethoxyformylimidazole per mole of
AB  - methylase are detected spectroscopically upon inactivation and activity is not
AB  - restored by hydroxylamine, it is likely that activity loss is due to double
AB  - modification of a single histidine residue.  This information is critical in
AB  - determining the enzymatic mechanism, causes of the pH-activity curve, designing
AB  - protein mutants and interpreting previous structure-function data.
ER  -

TY  - JOUR
AU  - Everett, K.D.
AU  - Kahane, S.
AU  - Bush, R.M.
AU  - Friedman, M.G.
TI  - An unspliced group I intron in 23S rRNA links chlamydiales, chloroplasts, and mitochondria.
JO  - J. Bacteriol.
PY  - 1999
SP  - 4734
EP  - 4740
VL  - 181
AB  - Chlamydia was the only genus in the order Chlamydiales until the
AB  - recent characterization of Simkania negevensis Z(T) and Parachlamydia
AB  - acanthamoebae strains. The present study of Chlamydiales 23S ribosomal
AB  - DNA (rDNA) focuses on a naturally occurring group I intron in the I-
AB  - CpaI target site of 23S rDNA from S. negevensis. The intron, SnLSU. 1,
AB  - belonged to the IB4 structural subgroup and was most closely related to
AB  - large ribosomal subunit introns that express single-motif, LAGLIDADG
AB  - endonucleases in chloroplasts of algae and in mitochondria of amoebae.
AB  - RT-PCR and electrophoresis of in vivo rRNA indicated that the intron
AB  - was not spliced out of the 23S rRNA. The unspliced 658-nt intron is the
AB  - first group I intron to be found in bacterial rDNA or rRNA, and it may
AB  - delay the S. negevensis developmental replication cycle by affecting
AB  - ribosomal function.
ER  -

TY  - JOUR
AU  - Everroad, R.C.
AU  - Stuart, R.K.
AU  - Bebout, B.M.
AU  - Detweiler, A.M.
AU  - Lee, J.Z.
AU  - Woebken, D.
AU  - Prufert-Bebout, L.
AU  - Pett-Ridge, J.
TI  - Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 53
EP  - 53
VL  - 11
AB  - The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member
AB  - of the order Oscillatoriales within the Cyanobacteria. ESFC-1
AB  - has been shown to be a major diazotroph in the intertidal microbial mat system at
AB  - Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene,
AB  - ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome
AB  - sequence of this strain has now been determined. Here we report features of this
AB  - genome as they relate to the ecological functions and capabilities of strain
AB  - ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92
AB  - RNA genes. One striking feature of this cyanobacterium is the apparent lack of
AB  - either uptake or bi-directional hydrogenases typically expected within a
AB  - diazotroph. Additionally, a large genomic island is found that contains numerous
AB  - low GC-content genes and genes related to extracellular polysaccharide production
AB  - and cell wall synthesis and maintenance.
ER  -

TY  - JOUR
AU  - Everroad, R.C.
AU  - Woebken, D.
AU  - Singer, S.W.
AU  - Burow, L.C.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Detweiler, A.
AU  - Prufert-Bebout, L.
AU  - Pett-Ridge, J.
TI  - Draft Genome Sequence of an Oscillatorian Cyanobacterium, Strain ESFC-1.
JO  - Genome Announcements
PY  - 2013
SP  - e00527
EP  - e00513
VL  - 1
AB  - The nonheterocystous filamentous cyanobacterium strain ESFC-1 has recently been isolated from
AB  - a marine microbial mat system, where it was identified as belonging
AB  - to a recently discovered lineage of active nitrogen-fixing microorganisms. Here,
AB  - we report the draft genome sequence of this isolate. The assembly consists of 3
AB  - scaffolds and contains 5,632,035 bp with a GC content of 46.5%.
ER  -

TY  - JOUR
AU  - Evers, C.
AU  - Patel, K.
AU  - Petrosyan, V.
AU  - Morrison, C.
AU  - Varghese, V.
AU  - Chu, R.A.
AU  - Baig, A.
AU  - Thompson, E.J.
AU  - Chase, M.
AU  - Hu, P.C.
AU  - Kalia, A.
TI  - Draft Genome Sequences of Four Genetically Distinct Human Isolates of Streptococcus dysgalactiae subsp. equisimilis.
JO  - Genome Announcements
PY  - 2015
SP  - e01139
EP  - e01115
VL  - 3
AB  - beta-Hemolytic group C and group G streptococci (GCS-GGS; Streptococcus dysgalactiae subsp.
AB  - equisimilis) emerged as human pathogens in the late 1970s. We report here the draft genome
AB  - sequences of four genetically distinct human strains of GCS-GGS isolated between the 1960s and
AB  - 1980s. Comparative analysis of these genomes may provide a deeper understanding of GCS-GGS
AB  - genome and virulence evolution.
ER  -

TY  - JOUR
AU  - Ewens, W.J.
TI  - Inference problems in population genetics:  DNA sequences, restriction endonucleases and ascertainment sampling.
JO  - Proc. R. Soc. Lond. B Biol. Sci.
PY  - 1983
SP  - 223
EP  - 239
VL  - 219
AB  - A major trend of population genetics theory in the 1970s was the increased
AB  - emphasis on inductive arguments, based on observed genetic data, rather than on
AB  - deductive arguments based on theory and models.  This occurred in part because
AB  - the deductive theory had largely fulfilled its role of describing evolution as
AB  - a genetic process, and in part because of the increasing amounts of data
AB  - available on the genetic constitution of natural populations.  Inference
AB  - procedures raise difficulties not present in the deductive theory.  Often
AB  - conditional arguments are necessary since the data often must fulfil some
AB  - condition to be observed.  Different inference procedures, having different
AB  - efficiencies, apply for data from different apparatuses.  Care must be taken in
AB  - deciding what it is the inference concerns.  These problems are illustrated by
AB  - reference to restriction endonuclease techniques and ascertainment sampling.
ER  -

TY  - JOUR
AU  - Ewers, C.
AU  - Gottig, S.
AU  - Bulte, M.
AU  - Fiedler, S.
AU  - Tietgen, M.
AU  - Leidner, U.
AU  - Heydel, C.
AU  - Bauerfeind, R.
AU  - Semmler, T.
TI  - Genome Sequence of Avian Escherichia coli Strain IHIT25637, an Extraintestinal Pathogenic E. coli Strain of ST131 Encoding Colistin Resistance Determinant  MCR-1.
JO  - Genome Announcements
PY  - 2016
SP  - e00863
EP  - e00816
VL  - 4
AB  - Sequence type 131 (ST131) is one of the predominant Escherichia coli lineages among
AB  - extraintestinal pathogenic E. coli (ExPEC) that causes a variety of
AB  - diseases in humans and animals and frequently shows multidrug resistance. Here,
AB  - we report the first genome sequence of an ST131-ExPEC strain from poultry
AB  - carrying the plasmid-encoded colistin resistance gene mcr-1.
ER  -

TY  - JOUR
AU  - Ezekiel, U.R.
AU  - Zassenhaus, P.
TI  - Evidence for a site-specific endonuclease in yeast mitochondria which recognizes the sequence 5'GCCCGGC.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1994
SP  - 208
EP  - 214
VL  - 201
AB  - We have discovered a mitochondrial, site-specific DNase in Saccharomyces cerevisiae with
AB  - properties like that of a type II restriction endonuclease. The enzyme, termed SceIII, cleaves
AB  - the palindromic sequence, 5'GCCGGC, to give 3' ends recessed by 4 bases. SceIII is the first
AB  - restriction-like endonuclease to be described in yeast mitochondria.
ER  -

TY  - JOUR
AU  - Fabbri, M.
AU  - Garzon, R.
AU  - Cimmino, A.
AU  - Liu, Z.
AU  - Zanesi, N.
AU  - Callegari, E.
AU  - Liu, S.
AU  - Alder, H.
AU  - Costinean, S.
AU  - Fernandez-Cymering, C.
AU  - Volinia, S.
AU  - Guler, G.
AU  - Morrison, C.D.
AU  - Chan, K.K.
AU  - Marcucci, G.
AU  - Calin, G.A.
AU  - Huebner, K.
AU  - Croce, C.M.
TI  - MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 15805
EP  - 15810
VL  - 104
AB  - MicroRNAs (miRNAs) are small, noncoding RNAs that regulate expression of many genes. Recent
AB  - studies suggest roles of miRNAs in
AB  - carcinogenesis. We and others have shown that expression profiles of
AB  - miRNAs are different in lung cancer vs. normal lung, although the
AB  - significance of this aberrant expression is poorly understood. Among
AB  - the reported down-regulated miRNAs in lung cancer, the miRNA (miR)-29
AB  - family (29a, 29b, and 29c) has intriguing complementarities to the
AB  - 3'-UTRs of DNA methyltransferase (DNMT)3A and -3B (de novo
AB  - methyltransferases), two key enzymes involved in DNA methylation, that
AB  - are frequently up-regulated in lung cancer and associated with poor
AB  - prognosis. We investigated whether miR-29s could target DNMT3A and -B
AB  - and whether restoration of miR-29s could normalize aberrant patterns of
AB  - methylation in non-small-cell lung cancer. Here we show that expression
AB  - of miR-29s is inversely correlated to DNMT3A and -3B in lung cancer
AB  - tissues, and that miR-29s directly target both DNMT3A and -3B. The
AB  - enforced expression of miR-29s in lung cancer cell lines restores
AB  - normal patterns of DNA methylation, induces reexpression of
AB  - methylation-silenced tumor suppressor genes, such as FHIT and WWOX, and
AB  - inhibits tumorigenicity in vitro and in vivo. These findings support a
AB  - role of miR-29s in epigenetic normalization of NSCLC, providing a
AB  - rationale for the development of miRNA-based strategies for the
AB  - treatment of lung cancer.
ER  -

TY  - JOUR
AU  - Fabian, J.S.
AU  - Mattson, T.
AU  - Bazar, L.S.
AU  - Chirikjian, J.G.
TI  - Characterization of the Bacillus amyloliquefaciens HI methyltransferase.
JO  - FASEB J.
PY  - 1998
SP  - A1446
EP  - A1446
VL  - 12
AB  - Type II DNA methyltransferases are part of bacterial restriction-modification systems.
AB  - Methyltransferases function as monomers, recognize a palindromic DNA sequence and use
AB  - S-adenosyl-methionine as the methyl donor.  The Bacillus amyloliquefaciens methyltransferase
AB  - is a 49 kDa protein which methylates the N4 position of cytosine in the DNA sequence GGATCC.
AB  - Protein sequence alignment shows that M.BamHI has structural homology to M.TaqI.  The
AB  - carboxyl-terminal region of M.BamHI also contains a region showing 72% identity to the
AB  - predicted DNA binding region of M.DpnA.  Here, we report the properties of truncated proteins
AB  - missing either the N or C terminus amino acids.  These truncated proteins have been tested for
AB  - SAM and DNA binding as well as methylation activity.  However, specificity appears to be
AB  - relaxed. In contrast, deletion of the carboxyl-terminus removes both DNA binding and
AB  - methylating activity although SAM binding activity is retained.  The peptide produced from in
AB  - vitro transcription/translation of the carboxyl-terminal region is being tested for DNA
AB  - binding activity.  These results assign the DNA binding activity of M.BamHI to the
AB  - carboxyl-terminal of the protein as predicted from sequence alignment studies.  The N-terminus
AB  - region is necessary for increasing the specificity of the enzyme.
ER  -

TY  - JOUR
AU  - Fabian, J.S.
AU  - Mattson, T.
AU  - Chirikjian, J.G.
TI  - Characterization of the Bacillus amyloliquefaciens HI methyltransferase.
JO  - FASEB J.
PY  - 1997
SP  - A900
EP  - A900
VL  - 11
AB  - Type II DNA methyltransferases are part of bacterial restriction-modification systems.  Most
AB  - of the Mtases function as monomers, recognize a palindromic DNA sequence and use
AB  - S-Adenosyl-Methionine as the methyl donor.  The Bacillus amyloliquefaciens methyltransferase
AB  - is a 49kDa protein which methylates at the N4 position of cytosine in the sequence GGATCC.
AB  - Crystal structures of three DNA Mtases show that they are folded into two domains.  The
AB  - C-terminal domain is responsible for specific recognition and binding of the target DNA
AB  - sequence.  The N-terminal domain contains the catalytic site formed by the conserved motif IV
AB  - (NPPY in M.TaqI and PCQ in M.HhaI and M.HaeIII) and a deep cleft that harbors the cofactor
AB  - SAM.  Crystal structures have also revealed that these enzymes extrude the target base from
AB  - the double helix into the catalytic pocket where the methyl transfer occurs.  Partial
AB  - proteolytic digestion of the BamHI methylase using Proteinase K generates a 38kDa peptide
AB  - fragment that maintains methylase activity in vitro.  N-terminal peptide sequencing indicates
AB  - that the fragment is missing 103 amino acids from the N-terminal end.  Gel shift assays
AB  - indicate that the 38kDa fragment is able to interact with the DNA in a sequence dependent
AB  - manner.  Preliminary kinetic analysis of the proteolytic fragment shows a decreased Km, Kcat
AB  - and Vmax.  We are currently constructing C-terminal deletion mutants and will test them for
AB  - methylase and DNA binding activity.
ER  -

TY  - JOUR
AU  - Fabian, J.S.
AU  - Mattson, T.
AU  - Chirikjian, J.G.
TI  - Comparative study of the biochemical properties of cellular and viral DNA-methyltransferases from Bacillus amyloliquefaciens H1.
JO  - FASEB J.
PY  - 1996
SP  - A1103
EP  - A1103
VL  - 10
AB  - Methyltransferases (Mtases) are a class of enzymes which place methyl groups onto a variety of
AB  - substrates using S-adenosyl-methionine as a cofactor.  In prokaryotes, Mtases are often part
AB  - of a restriction-modification system in which their role is to protect the host DNA from
AB  - cleavage by the restriction enzyme.  Bacillus amyloliquefaciens HI contains two distinct
AB  - methyltransferases (M.BamHI and M.BamHII) which recognize and methylate the same double
AB  - stranded DNA sequence 5'-GGATCC-3'.  Both methylases have been cloned, sequenced, purified and
AB  - characterized.  The two Mtases have little primary amino acid sequence homology, and therefore
AB  - provide an ideal model for a variety of comparative studies.  The cellular enzyme (M.BamHI),
AB  - is active as a 49KD monomer and methylates the exocyclic N4 nitrogen of the internal cytosine.
AB  - M.BamHI, associated with a prophage, is a 31KD monomeric enzyme that also methylates the
AB  - internal cytosine, although it is not yet known if it has an N4 or a C5 methylation activity.
AB  - Time course experiments will be presented indicating that the specific activity of the viral
AB  - methyltransferase (M.BamHII) is significantly greater than that of the cellular methylase
AB  - (M.BamHI).  The nature of this difference in activity is being investigated.  Gel shift
AB  - experiments will be presented that allow a comparison of the dissociation constants.  If the
AB  - activity of either BamHI or BamHII is similar to that for HhaI, which extrudes the target base
AB  - from the double helix, one might expect a bilobal conformation of the enzyme, at least when
AB  - associated with its target sequence.  The results of limited proteolysis experiments designed
AB  - to address this possibility will also be presented.
ER  -

TY  - JOUR
AU  - Facimoto, C.T.
AU  - Chideroli, R.T.
AU  - Goncalves, D.D.
AU  - Carmo, A.O.D.
AU  - Kalaphotakis, E.
AU  - Pereira, U.P.
TI  - Whole-Genome Sequence of Streptococcus agalactiae Strain S13, Isolated from a Fish Eye from a Nile Tilapia Farm in Southern Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00917
EP  - e00917
VL  - 5
AB  - Streptococcus agalactiae is an important pathogen to world aquaculture due to its high
AB  - mortality rates in fish farms and consequent economic losses. Our study
AB  - presents the complete genome sequence of strain S13, isolated from a tilapia farm
AB  - outbreak in southern Brazil.
ER  -

TY  - JOUR
AU  - Fadeev, E.
AU  - De Pascale, F.
AU  - Vezzi, A.
AU  - Hubner, S.
AU  - Aharonovich, D.
AU  - Sher, D.
TI  - Why close a bacterial genome? The plasmid of Alteromonas macleodii HOT1A3 is a vector for inter-specific transfer of a flexible genomic island.
JO  - Front. Microbiol.
PY  - 2016
SP  - 248
EP  - 248
VL  - 7
AB  - Genome sequencing is rapidly becoming a staple technique in environmental and clinical
AB  - microbiology, yet computational challenges still remain, leading to many draft genomes which
AB  - are typically fragmented into many contigs.  We sequenced and completely assembled the genome
AB  - of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full
AB  - genome to several draft genomes obtained using different reference-based and denovo methods.
AB  - In general, the denovo assemblies clearly outperformed the reference-based orhybridones,
AB  - covering >99%of the genes and representing essentially all of the gene functions.  However,
AB  - only the fully closed genome(4.5Mbp) allowed us to identify the presence of a large, 148 kbp
AB  - plasmid, pAM1A3.  While HOT1A3 belongs to A. macleodii, typically found in surface waters
AB  - (surface ecotype), this plasmid consists of an almost complete flexible genomic island(fGI),
AB  - containing many genes involved in metal resistance previously identified in the genomes of
AB  - Alteromonas mediterranea (deep ecotype).  Indeed, similar to A. mediterranea, A. macleodii
AB  - HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A.
AB  - macleodii strains.  The presence of a plasmid encoding almost an entire fGI suggests that
AB  - wholesale genomic exchange between heterotrophic marine bacteria belonging to related but
AB  - ecologically different populations is not uncommon.
ER  -

TY  - JOUR
AU  - Faelker, S.
AU  - Schilling, J.
AU  - Schmidt, M.A.
AU  - Heusipp, G.
TI  - Overproduction of DNA adenine methyltransferase alters motility, invasion, and the lipopolysaccharide O-antigen composition of Yersinia enterocolitica.
JO  - Infect. Immun.
PY  - 2007
SP  - 4990
EP  - 4997
VL  - 75
AB  - DNA adenine methyltransferase not only regulates basic cellular functions but also interferes
AB  - with the proper expression of virulence factors in various pathogens.  We showed previously
AB  - that for the human pathogen Yersinia enterocolitica, overproduction of Dam results in
AB  - increased invasion of epithelial cells.  Since invasion and motility are coordinately
AB  - regulated in Y. enterocolitica, we analyzed the motility of a Dam-overproducting (DamOP)
AB  - strain and found it to be highly motile.  In DamOP strains, the operon encoding the master
AB  - regulator of flagellum biosynthesis, flh DC, is upregulated.  We show that the increased
AB  - invasion is not due to enhanced expression of known and putative Y. enterocolitica invasion
AB  - and adhesion factors, such as Inv, YadA, Ail, Myf fibrils, Pil, or Flp pili.  However,
AB  - overproduction of Dam results in an increased amount of rough lipopolysaccharide molecules
AB  - lacking O-antigen side chains, this implies that reduced steric hindrance by LPS might
AB  - contribute to increased invasion by a Y. enterocolitica DamOP strain.  Our data add an
AB  - important new aspect to the various virulence-associated phenotypes influenced by DNA
AB  - methylation in Y. enterocolitica and indicate that Dam targets regulatory processes modulating
AB  - the composition and function of the bacterial surface.
ER  -

TY  - JOUR
AU  - Faelker, S.
AU  - Schmidt, M.A.
AU  - Heusipp, G.
TI  - DNA methylation in Yersinia enterocolitica: Role of the DNA adenine methyltransferase in mismatch repair and regulation of virulence factors.
JO  - Microbiology
PY  - 2005
SP  - 2291
EP  - 2299
VL  - 151
AB  - DNA adenine methyltransferase plays an important role in physiological processes of
AB  - Gram-negative bacteria such as mismatch repair and replication.  In addition, Dam regulates
AB  - the expression of virulence genes in various species.  The authors cloned the dam gene of
AB  - Yersinia enterocolitica and showed that Dam is essential for viability.  Dam overproduction in
AB  - Y. enterocolitica resulted in an increased frequency of spontaneous mutation and decreased
AB  - resistance to 2-aminopurine; however, these effects were only marginal compared to the effect
AB  - of overproduction of Escherichia coli-derived Dam in Y. enterocolitica, implying different
AB  - roles or activities of Dam in mismatch repair of the two species.  These differences in Dam
AB  - function are not the cause for the essentiality of Dam in Y. enterocalitica, as Dam of E. coli
AB  - can complement a dam defect in Y. enterocolitica.  Instead, Dam seems to interfere with
AB  - expression of essential genes.  Furthermore, Dam mediates virulence of Y. enterocolitica.  Dam
AB  - overproduction results in increased tissue culture invasion of Y. enterocolitica, while the
AB  - expression of specifically in vivo-expressed genes is not altered.
ER  -

TY  - JOUR
AU  - Fagerlund, A.
AU  - Langsrud, S.
AU  - Moen, B.
AU  - Heir, E.
AU  - Moretro, T.
TI  - Complete Genome Sequences of Six Listeria monocytogenes Sequence Type 9 Isolates  from Meat Processing Plants in Norway.
JO  - Genome Announcements
PY  - 2018
SP  - e00016
EP  - e00018
VL  - 6
AB  - Listeria monocytogenes is a foodborne pathogen that causes the often-fatal disease
AB  - listeriosis. We present here the complete genome sequences of six L.
AB  - monocytogenes isolates of sequence type 9 (ST9) collected from two different meat
AB  - processing facilities in Norway. The genomes were assembled using Illumina and
AB  - Nanopore sequencing data.
ER  -

TY  - JOUR
AU  - Fajardo-Sanchez, E.
AU  - Stricher, F.
AU  - Paques, F.
AU  - Isalan, M.
AU  - Serrano, L.
TI  - Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 2163
EP  - 2173
VL  - 36
AB  - Meganucleases cut long (>12 bp) unique sequences in genomes and can be used to induce targeted
AB  - genome engineering by homologous recombination
AB  - in the vicinity of their cleavage site. However, the use of natural
AB  - meganucleases is limited by the repertoire of their target sequences,
AB  - and considerable efforts have been made to engineer redesigned
AB  - meganucleases cleaving chosen targets. Homodimeric meganucleases such
AB  - as I-CreI have provided a scaffold, but can only be modified to
AB  - recognize new quasi-palindromic DNA sequences, limiting their general
AB  - applicability. Other groups have used dimer-interface redesign and
AB  - peptide linkage to control heterodimerization between related
AB  - meganucleases such as I-DmoI and I-CreI, but until now there has been
AB  - no application of this aimed specifically at the scaffolds from
AB  - existing combinatorial libraries of I-CreI. Here, we show that
AB  - engineering meganucleases to form obligate heterodimers results in
AB  - functional endonucleases that cut non-palindromic sequences. The
AB  - protein design algorithm (FoldX v2.7) was used to design specific
AB  - heterodimer interfaces between two meganuclease monomers, which were
AB  - themselves engineered to recognize different DNA sequences. The new
AB  - monomers favour functional heterodimer formation and prevent homodimer
AB  - site recognition. This design massively increases the potential
AB  - repertoire of DNA sequences that can be specifically targeted by
AB  - designed I-CreI meganucleases and opens the way to safer targeted
AB  - genome engineering.
ER  -

TY  - JOUR
AU  - Falb, M.
AU  - Pfeiffer, F.
AU  - Palm, P.
AU  - Rodewald, K.
AU  - Hickmann, V.
AU  - Tittor, J.
AU  - Oesterhelt, D.
TI  - Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis.
JO  - Genome Res.
PY  - 2005
SP  - 1336
EP  - 1343
VL  - 15
AB  - Natronomonas pharaonis is an extremely haloalkaliphilic archaeon that was isolated from
AB  - salt-saturated lakes of pH 11. We sequenced its 2.6-Mb
AB  - GC-rich chromosome and two plasmids (131 and 23 kb). Genome analysis
AB  - suggests that it is adapted to cope with severe ammonia and heavy metal
AB  - deficiencies that arise at high pH values. A high degree of nutritional
AB  - self-sufficiency was predicted and confirmed by growth in a minimal medium
AB  - containing leucine but no other amino acids or vitamins. Genes for a
AB  - complex III analog of the respiratory chain could not be identified in the
AB  - N. pharaonis genome, but respiration and oxidative phosphorylation were
AB  - experimentally proven. These studies identified protons as coupling ion
AB  - between respiratory chain and ATP synthase, in contrast to other
AB  - alkaliphiles using sodium instead. Secretome analysis predicts many
AB  - extracellular proteins with alkaline-resistant lipid anchors, which are
AB  - predominantly exported through the twin-arginine pathway. In addition, a
AB  - variety of glycosylated cell surface proteins probably form a protective
AB  - complex cell envelope. N. pharaonis is fully equipped with archaeal signal
AB  - transduction and motility genes. Several receptors/transducers signaling
AB  - to the flagellar motor display novel domain architectures. Clusters of
AB  - signal transduction genes are rearranged in haloarchaeal genomes, whereas
AB  - those involved in information processing or energy metabolism show a
AB  - highly conserved gene order.
ER  -

TY  - JOUR
AU  - Faldu, P.R.
AU  - Kothari, V.V.
AU  - Kothari, C.R.
AU  - Rawal, C.M.
AU  - Domadia, K.K.
AU  - Patel, P.A.
AU  - Bhimani, H.D.
AU  - Raval, V.H.
AU  - Parmar, N.R.
AU  - Nathani, N.M.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Kothari, R.K.
TI  - Draft Genome Sequence of Textile Azo Dye-Decolorizing and -Degrading Pseudomonas  aeruginosa Strain PFK10, Isolated from the Common Effluent Treatment Plant of the  Ankleshwar Industrial Area of Gujarat, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00019
EP  - e00014
VL  - 2
AB  - Here, we report the draft genome sequence of Pseudomonas aeruginosa strain PFK10, isolated
AB  - from the common effluent treatment plant (CETP) of the Ankleshwar
AB  - industrial area of Gujarat, India. The 6.04-Mb draft genome sequence of strain
AB  - PFK10 provides information about the genes encoding enzymes that enable the
AB  - strain to decolorize and degrade textile azo dye.
ER  -

TY  - JOUR
AU  - Falentin, H.
AU  - Cousin, S.
AU  - Clermont, D.
AU  - Creno, S.
AU  - Ma, L.
AU  - Chuat, V.
AU  - Loux, V.
AU  - Rudiger, P.
AU  - Bizet, C.
AU  - Bouchier, C.
TI  - Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13T, Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated  from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin.
JO  - Genome Announcements
PY  - 2013
SP  - e00658
EP  - e00613
VL  - 1
AB  - Lactobacillus acidophilus is a natural inhabitant of mammalian gastrointestinal systems and is
AB  - used in dairy and pharmaceutical products. Five draft genome
AB  - sequences, covering 1,995,790 nucleotides (nt) on average, are divided into 19 to
AB  - 34 scaffolds covering 1,995 to 2,053 genes. The draft genome sequences were
AB  - compared to the sequence of the L. acidophilus NCFM dairy strain.
ER  -

TY  - JOUR
AU  - Falentin, H.
AU  - Deutsch, S.M.
AU  - Jan, G.
AU  - Loux, V.
AU  - Thierry, A.
AU  - Parayre, S.
AU  - Maillard, M.B.
AU  - Dherbecourt, J.
AU  - Cousin, F.J.
AU  - Jardin, J.
AU  - Siguier, P.
AU  - Couloux, A.
AU  - Barbe, V.
AU  - Vacherie, B.
AU  - Wincker, P.
AU  - Gibrat, J.F.
AU  - Gaillardin, C.
AU  - Lortal, S.
TI  - The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications.
JO  - PLoS ONE
PY  - 2010
SP  - e11748
EP  - e11748
VL  - 5
AB  - BACKGROUND: Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type
AB  - cheeses and is also considered for its probiotic use. This species
AB  - exhibits slow growth, low nutritional requirements, and hardiness in many
AB  - habitats. It belongs to the taxonomic group of dairy propionibacteria, in
AB  - contrast to the cutaneous species P. acnes. The genome of the type strain, P.
AB  - freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an
AB  - 11-fold coverage. METHODOLOGY/PRINCIPAL FINDINGS: The circular chromosome of 2.7
AB  - Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different
AB  - insertion sequences (3.5% of the genome in base pairs). Using a proteomic
AB  - approach, 490 of the 2439 predicted proteins were confirmed. The annotation
AB  - revealed the genetic basis for the hardiness of P. freudenreichii, as the
AB  - bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of
AB  - aminoacids and vitamins (except panthotenate and biotin) as well as sequences
AB  - involved in metabolism of various carbon sources, immunity against phages,
AB  - duplicated chaperone genes and, interestingly, genes involved in the management
AB  - of polyphosphate, glycogen and trehalose storage. The complete biosynthesis
AB  - pathway for a bifidogenic compound is described, as well as a high number of
AB  - surface proteins involved in interactions with the host and present in other
AB  - probiotic bacteria. By comparative genomics, no pathogenicity factors found in P.
AB  - acnes or in other pathogenic microbial species were identified in P.
AB  - freudenreichii, which is consistent with the Generally Recognized As Safe and
AB  - Qualified Presumption of Safety status of P. freudenreichii. Various pathways for
AB  - formation of cheese flavor compounds were identified: the Wood-Werkman cycle for
AB  - propionic acid formation, amino acid degradation pathways resulting in the
AB  - formation of volatile branched chain fatty acids, and esterases involved in the
AB  - formation of free fatty acids and esters. CONCLUSIONS/SIGNIFICANCE: With the
AB  - exception of its ability to degrade lactose, P. freudenreichii seems poorly
AB  - adapted to dairy niches. This genome annotation opens up new prospects for the
AB  - understanding of the P. freudenreichii probiotic activity.
ER  -

TY  - JOUR
AU  - Falentin, H.
AU  - Deutsch, S.M.
AU  - Loux, V.
AU  - Hammani, A.
AU  - Buratti, J.
AU  - Parayre, S.
AU  - Chuat, V.
AU  - Barbe, V.
AU  - Aury, J.M.
AU  - Jan, G.
AU  - Le Loir, Y.
TI  - Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 6
EP  - 6
VL  - 11
AB  - Propionibacterium freudenreichii belongs to the class Actinobacteria (Gram positive with a
AB  - high GC content). This 'Generally Recognized As Safe' (GRAS)
AB  - species is traditionally used as (i) a starter for Swiss-type cheeses where it is
AB  - responsible for holes and aroma production, (ii) a vitamin B12 and propionic acid
AB  - producer in white biotechnologies, and (iii) a probiotic for use in humans and
AB  - animals because of its bifidogenic and anti-inflammatory properties. Until now,
AB  - only strain CIRM-BIA1T had been sequenced, annotated and become publicly
AB  - available. Strain CIRM-BIA129 (commercially available as ITG P20) has
AB  - considerable anti-inflammatory potential. Its gene content was compared to that
AB  - of CIRM-BIA1 T. This strain contains 2384 genes including 1 ribosomal operon, 45
AB  - tRNA and 30 pseudogenes.
ER  -

TY  - JOUR
AU  - Falentin, H.
AU  - Naquin, D.
AU  - Loux, V.
AU  - Barloy-Hubler, F.
AU  - Loubiere, P.
AU  - Nouaille, S.
AU  - Lavenier, D.
AU  - Le Bourgeois, P.
AU  - Francois, P.
AU  - Schrenzel, J.
AU  - Hernandez, D.
AU  - Even, S.
AU  - Le Loir, Y.
TI  - Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis LD61.
JO  - Genome Announcements
PY  - 2014
SP  - e01176
EP  - e01113
VL  - 2
AB  - Lactococcus lactis is widely used in the dairy industry. We report the draft genome sequence
AB  - of L. lactis subsp. lactis bv. diacetylactis LD61, an industrial
AB  - and extensively studied strain. In contrast to the closely related and
AB  - plasmidless strain IL1403, LD61 contains 6 plasmids, and the genome sequence
AB  - provides additional information related to adaptation to the dairy environment.
ER  -

TY  - JOUR
AU  - Falgenhauer, L.
AU  - Yao, Y.
AU  - Fritzenwanker, M.
AU  - Schmiedel, J.
AU  - Imirzalioglu, C.
AU  - Chakraborty, T.
TI  - Complete Genome Sequence of Phage-Like Plasmid pECOH89, Encoding CTX-M-15.
JO  - Genome Announcements
PY  - 2014
SP  - e00356
EP  - e00314
VL  - 2
AB  - A nonconjugative and nontypable plasmid of a clinical Escherichia coli isolate expressing
AB  - resistance to extended-spectrum cephalosporins (ESCs) was isolated and sequenced. The plasmid
AB  - pECOH89 contains a CTX-M-15 resistance cassette and comprises 111,741 bp, with strong homology
AB  - to bacteriophage-like plasmids and to the Salmonella-specific bacteriophage SSU5.
ER  -

TY  - JOUR
AU  - Falkow, S.
AU  - Formal, S.B.
TI  - Restriction in genetic crosses between Escherichia coli and Shigella flexneri.
JO  - J. Bacteriol.
PY  - 1969
SP  - 540
EP  - 541
VL  - 100
AB  - Shigella flexneri restricts Escherichia coli deoxyribonucleic acid (DNA) and
AB  - can modify phage DNA so that it is restricted in E. coli.
ER  -

TY  - JOUR
AU  - Fallico, V.
AU  - Ross, R.P.
AU  - Fitzgerald, G.F.
AU  - McAuliffe, O.
TI  - Novel conjugative plasmids from the natural isolate Lactococcus lactis subspecies cremoris DPC3758: A repository of genes for the potential improvement of dairy starters.
JO  - J. Dairy Sci.
PY  - 2012
SP  - 3593
EP  - 3608
VL  - 95
AB  - A collection of 17 natural lactococcal isolates from raw milk cheeses were studied in terms of
AB  - their plasmid distribution, content, and
AB  - diversity. All strains in the collection harbored an abundance of
AB  - plasmids, including Lactococcus lactis ssp. cremoris DPC3758, whose
AB  - 8-plasmid complement was selected for sequencing. The complete
AB  - sequences of pAF22 (22,388 kb), pAF14 (14,419 kb), pAF12 (12,067 kb),
AB  - pAF07 (7,435 kb), and pAF04 (3,801 kb) were obtained, whereas gene
AB  - functions of technological interest were mapped to pAF65 (65 kb) and
AB  - pAF45 (45 kb) by PCR. The plasmids of L. lactis DPC3758 were found to
AB  - encode many genes with the potential to improve the technological
AB  - properties of dairy starters. These included 3 anti-phage
AB  - restriction/modification (R/M) systems (1 of type I and 2 of type II)
AB  - and genes for immunity/resistance to nisin, lacticin 481, cadmium, and
AB  - copper. Regions encoding conjugative/mobilization functions were
AB  - present in 6 of the 8 plasmids, including those containing the R/M
AB  - systems, thus enabling the food-grade transfer of these mechanisms to
AB  - industrial strains. Using cadmium selection, the sequential stacking of
AB  - the R/M plasmids into a plasmid-free host provided the recipient with
AB  - increased protection against 936- and c2-type phages. The association
AB  - of food-grade selectable markers and mobilization functions on L.
AB  - lactis DPC3758 plasmids will facilitate their exploitation to obtain
AB  - industrial strains with enhanced phage protection and robustness. These
AB  - natural plasmids also provide another example of the major role of
AB  - plasmids in contributing to host fitness and preservation within its
AB  - ecological niche.
ER  -

TY  - JOUR
AU  - Falquet, L.
AU  - Calderon-Copete, S.P.
AU  - Frey, J.
TI  - Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335.
JO  - Genome Announcements
PY  - 2013
SP  - e00593
EP  - e00513
VL  - 1
AB  - Clostridium chauvoei is the etiological agent of blackleg, a disease of cattle and sheep with
AB  - high mortality rates, causing severe economic losses in livestock
AB  - production. Here, we report the draft genome sequence of the virulent C. chauvoei
AB  - strain JF4335 (2.8 Mbp and 28% G+C content) and the annotation of the genome.
ER  -

TY  - JOUR
AU  - Falquet, L.
AU  - Liljander, A.
AU  - Schieck, E.
AU  - Gluecks, I.
AU  - Frey, J.
AU  - Jores, J.
TI  - Complete Genome Sequences of Virulent Mycoplasma capricolum subsp. capripneumoniae Strains F38 and ILRI181.
JO  - Genome Announcements
PY  - 2014
SP  - e01041
EP  - e01014
VL  - 2
AB  - Contagious caprine pleuropneumonia (CCPP) caused by Mycoplasma capricolum subsp.
AB  - capripneumoniae is a severe epidemic affecting mainly domestic Caprinae species
AB  - but also affects wild Caprinae species. M. capricolum subsp. capripneumoniae
AB  - belongs to the 'Mycoplasma mycoides cluster.' The disease features prominently in
AB  - East Africa, in particular Kenya, Tanzania, and Ethiopia. CCPP also endangers
AB  - wildlife and thus affects not only basic nutritional resources of large
AB  - populations but also expensively built-up game resorts in affected countries.
AB  - Here, we report the complete sequences of two M. capricolum subsp.
AB  - capripneumoniae strains: the type strain F38 and strain ILRI181 isolated druing a
AB  - recent outbreak in Kenya. Both genomes have a G+C content of 24% with sizes of
AB  - 1,016,760 bp and 1,017,183 bp for strains F38 and ILRI181, respectively.
ER  -

TY  - JOUR
AU  - Falsafi, S.
AU  - Reich, N.
TI  - Molecular dynamic-based prediction of DNA structure changes in DNA sequence and correlation to substrate specificity in EcoRI DNA methyltransferase.
JO  - FASEB J.
PY  - 1992
SP  - A221
EP  - A221
VL  - 6
AB  - The object of this computational investigation is to determine the structural
AB  - consequences of single base-pair substitutions in the canonical site GAATTC of
AB  - 14 base-pair oligonucleotide duplexes.  The computational schemes reported
AB  - herein are guided by the earlier approaches established by Kollman and
AB  - co-workers and include 100 picoseconds of molecular dynamics.  The atomic
AB  - trajectories are analyzed for temporal variations of the phosphodiester and
AB  - glycosidic torsion angles and the helicoidal parameters using both AMBER (1986)
AB  - AMBER 3.0, UCSF) and Dials and Windows (J. Biomol. Str. Dyn., 6, 669(1989))
AB  - algorithms.  We first performed two computations using the crystal structure of
AB  - the Dickerson dodecamer and the standard Arnott B-DNA structure as the starting
AB  - points.  The average backbone torsion angles alpha, beta, gamma, delta,
AB  - epsilon, chi 1, chi 2 taken over the entire simulation time show 3% difference
AB  - between the two structures, suggesting convergence towards a unique final
AB  - structure.  The degree of agreement is even greater for the average helical
AB  - twist omega.  These results corroborate Kollman's earlier report, therefore
AB  - establishing the validity of our approach.  In view of our ongoing
AB  - investigation with a series of 14 base-pair oligonucleotides (Biochemistry
AB  - (1991) 30, 2933-2939; Nucleic Acids Research, in press), the sequence
AB  - d(GGCGGAATTCGCGG) was subjected to 100 picoseconds of molecular dynamics.  The
AB  - calculated backbone torsion angles show good agreement with the identical
AB  - conformational values obtained from an earlier calculation on the dodecamer.
AB  - In view of these consistencies, we have used the results from this later
AB  - computation to gauge the structural variations that result from single
AB  - base-pair substitutions within the canonical site GAATTC of d(GGCGGAATTCGCGG).
AB  - It is hoped that these structural differences will ultimately help elucidate
AB  - the mechanisms that describe the enzyme-DNA binding and catalysis for EcoRI
AB  - methyltransferase.
ER  -

TY  - JOUR
AU  - Fan, L.
AU  - Bo, S.
AU  - Chen, H.
AU  - Ye, W.
AU  - Kleinschmidt, K.
AU  - Baumann, H.I.
AU  - Imhoff, J.F.
AU  - Kleine, M.
AU  - Cai, D.
TI  - Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b isolated from the Indian Ocean.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1276
EP  - 1276
VL  - 193
AB  - Bacillus subtilis is a model organism of aerobic spore-forming Gram-positive bacteria and is
AB  - of great industrial significance as the source of diverse novel functional molecules. Here we
AB  - present to our knowledge the first genome sequence of a Bacillus subtilis strain gtP20b
AB  - isolated from the marine environment. A subset of candidate genes and gene clusters were
AB  - identified, which are potentially involved in production of diverse functional molecules like
AB  - novel ribosomal and non-ribosomal antimicrobial peptides. The genome sequence described in
AB  - this paper is due to its high strain-specificity of great importance for basic as well as
AB  - applied researches on marine organisms.
ER  -

TY  - JOUR
AU  - Fan, L.
AU  - Liu, Y.
AU  - Li, Z.
AU  - Baumann, H.I.
AU  - Kleinschmidt, K.
AU  - Ye, W.
AU  - Imhoff, J.F.
AU  - Kleine, M.
AU  - Cai, D.
TI  - Draft genome sequence of a marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3691
EP  - 3692
VL  - 193
AB  - Streptomyces, a branch of aerobic Gram-positive bacteria represents the largest genus of
AB  - actinobacteria. The streptomycetes are characterized by a
AB  - complex secondary metabolism and produce over two-thirds of the clinically
AB  - used natural antibiotics today. Here we report the draft genome sequence
AB  - of a Streptomyces strain PP-C42 isolated from the marine environment. A
AB  - subset of unique genes and gene clusters for diverse secondary metabolites
AB  - as well as antimicrobial peptides (AMPs) could be identified from the
AB  - genome, showing great promise as a source for novel bioactive compounds.
ER  -

TY  - JOUR
AU  - Fan, X.
AU  - Tang, J.
AU  - Nie, L.
AU  - Huang, J.
AU  - Wang, G.
TI  - High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30(T).
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 34
EP  - 34
VL  - 13
AB  - Mucilaginibacter pedocola TBZ30(T) (= CCTCC AB 2015301(T) = KCTC 42833(T)) is a Gram-
AB  - negative, rod-shaped, non-motile and non-spore-forming bacterium isolated
AB  - from a heavy metal contaminated paddy field. It shows resistance to multiple
AB  - heavy metals and can adsorb/remove Zn(2+) and Cd(2+) during cultivation. In
AB  - addition, strain TBZ30(T) produces exopolysaccharides (EPS). These features make
AB  - it a great potential to bioremediate heavy metal contamination and biotechnical
AB  - application. Here we describe the genome sequence and annotation of strain
AB  - TBZ30(T). The genome size is 7,035,113 bp, contains 3132 protein-coding genes
AB  - (2736 with predicted functions), 50 tRNA encoding genes and 14 rRNA encoding
AB  - genes. Putative heavy metal resistant genes and EPS associated genes are found in
AB  - the genome.
ER  -

TY  - JOUR
AU  - Fanelli, F.
AU  - Liuzzi, V.C.
AU  - Quintieri, L.
AU  - Mule, G.
AU  - Baruzzi, F.
AU  - Logrieco, A.F.
AU  - Caputo, L.
TI  - Draft Genome Sequence of Pseudomonas fluorescens Strain ITEM 17298, Associated with Cheese Spoilage.
JO  - Genome Announcements
PY  - 2017
SP  - e01141
EP  - e01117
VL  - 5
AB  - Pseudomonas fluorescens is a genetically and phenotypically heterogeneous species that is
AB  - often reported as a spoiler of fresh foods, but it has recently been
AB  - implicated in clinical infection. In this study, we sequenced the genome of P.
AB  - fluorescens strain ITEM 17298, isolated from mozzarella cheese and able to cause
AB  - several alterations under cold storage.
ER  -

TY  - JOUR
AU  - Fang, G. et al.
TI  - Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.  LID - 10.1038/nbt.2432 [doi].
JO  - Nat. Biotechnol.
PY  - 2012
SP  - 1232
EP  - 1232
VL  - 30
AB  - Single-molecule real-time (SMRT) DNA sequencing allows the systematic detection of chemical
AB  - modifications such as methylation but has not previously been applied on a genome-wide scale.
AB  - We used this approach to detect 49,311 putative 6-methyladenine (m6A) residues and 1,407
AB  - putative 5-methylcytosine (m5C) residues in the genome of a pathogenic Escherichia coli
AB  - strain. We obtained strand-specific information for methylation sites and a quantitative
AB  - assessment of the frequency of methylation at each modified position. We deduced the sequence
AB  - motifs recognized by the methyltransferase enzymes present in this strain without prior
AB  - knowledge of their specificity. Furthermore, we found that deletion of a phage-encoded
AB  - methyltransferase-endonuclease (restriction-modification; RM) system induced global
AB  - transcriptional changes and led to gene amplification, suggesting that the role of RM systems
AB  - extends beyond protecting host genomes from foreign DNA.
ER  -

TY  - JOUR
AU  - Fang, X.
AU  - Fang, Z.
AU  - Zhao, J.
AU  - Zou, Y.
AU  - Li, T.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Chang, D.
AU  - Su, L.
AU  - Ni, P.
AU  - Liu, C.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain ATCC 27853.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3755
EP  - 3755
VL  - 194
AB  - Pseudomonas aeruginosa is a common bacterium that can cause disease. The versatility of
AB  - Pseudomonas aeruginosa enables the organism to infect damaged
AB  - tissues or those with reduced immunity which cause inflammation and sepsis. Here
AB  - we report the genome sequence of the strain ATCC 27853.
ER  -

TY  - JOUR
AU  - Fang, Y.
AU  - Huang, Y.
AU  - Li, Q.
AU  - Chen, H.
AU  - Yao, Z.
AU  - Pan, J.
AU  - Gu, J.
AU  - Tang, B.
AU  - Wang, H.G.
AU  - Yu, B.
AU  - Tong, Y.G.
AU  - Zou, Q.M.
AU  - Mao, X.H.
TI  - First Genome Sequence of a Burkholderia pseudomallei Isolate in China, Strain BPC006, Obtained from a Melioidosis Patient in Hainan.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6604
EP  - 6605
VL  - 194
AB  - Melioidosis, caused by Burkholderia pseudomallei, is considered to be endemic to  Northern
AB  - Australia and Southeast Asia, with high mortality and relapse rates,
AB  - regardless of powerful antibiotic therapy. Here we report the first genome
AB  - sequence of Burkholderia pseudomallei strain BPC006, obtained from a melioidosis
AB  - patient in Hainan, China. The genome sizes of the 2 chromosomes were determined
AB  - to be 4,001,777 bp and 3,153,284 bp.
ER  -

TY  - JOUR
AU  - Fanning, T.G.
AU  - Kreutzfeldt, H.-J.
AU  - Davies, R.W.
AU  - Schreier, P.H.
TI  - Detection of restriction endonucleases with a lac repressor-lac operator filter binding assay.
JO  - FEBS Lett.
PY  - 1976
SP  - 237
EP  - 239
VL  - 61
AB  - The use of restriction enzymes as experimental tools has progressed rapidly
AB  - within the last several years.  The purification of these enzymes, however,
AB  - often poses a problem: since acid-soluable material is normally not released a
AB  - convenient assay for enzyme activity does not exist.  Thus, gel electrophoresis
AB  - or viscometry of digested DNA has often been employed to detect restriction
AB  - enzymes during purification.  These methods are, however, time consuming and
AB  - involve large quantities of DNA and/or expensive equipment.  We report here a
AB  - test for restriction enzymes that avoids these complications; the test is
AB  - inexpensive, rapid and can be done with very small quantities of DNA (0.02
AB  - microgram per test is normally sufficient).
ER  -

TY  - JOUR
AU  - Farah, N.
AU  - Mehdi, A.
AU  - Soomro, S.I.
AU  - Soomro, N.I.
AU  - Tareb, R.
AU  - Desmasures, N.
AU  - Vernoux, J.P.
AU  - Bakhtiar, S.M.
AU  - Imran, M.
TI  - Draft Genome Sequence of Enterococcus mundtii QAUEM2808, Isolated from Dahi, a Fermented Milk Product.
JO  - Genome Announcements
PY  - 2016
SP  - e00995
EP  - e00916
VL  - 4
AB  - Enterococcus mundtii QAUEM2808 has been isolated from dahi, an indigenous fermented milk
AB  - product of Pakistan. Here, we report the draft genome sequence for
AB  - this strain, which consists of 160 contigs corresponding to 2,957,514 bp and a
AB  - G+C content of 38.5%.
ER  -

TY  - JOUR
AU  - Farfan, M.
AU  - Spataro, N.
AU  - Sanglas, A.
AU  - Albarral, V.
AU  - Loren, J.G.
AU  - Bosch, E.
AU  - Fuste, M.C.
TI  - Draft Genome Sequence of the Aeromonas diversa Type Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00330
EP  - e00313
VL  - 1
AB  - We present here the first genome sequence of the Aeromonas diversa type strain (CECT 4254(T)).
AB  - This strain was isolated from the leg wound of a patient in New
AB  - Orleans (Louisiana) and was originally described as enteric group 501 and
AB  - distinguished from A. schubertii by DNA-DNA hybridization and phenotypical
AB  - characterization.
ER  -

TY  - JOUR
AU  - Farias, M.E.
AU  - Revale, S.
AU  - Mancini, E.
AU  - Ordonez, O.
AU  - Turjanski, A.
AU  - Cortez, N.
AU  - Vazquez, M.P.
TI  - Genome sequence of Sphingomonas sp. S17, isolated from an alkaline, hyperarsenic and hypersaline volcanic-associated lake at high altitude in the Argentinean Puna.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3686
EP  - 3687
VL  - 193
AB  - The High-Altitude Andean Lakes (HAAL) in the Argentinian Puna-High Andes region represent an
AB  - almost unexplored ecosystem exposed to extreme
AB  - conditions (high UV irradiation, hypersalinity, drastic temperature
AB  - changes, desiccation, high pH). Here we present the first genome sequence
AB  - isolated from this extreme environment, a Sphingomonas sp.
ER  -

TY  - JOUR
AU  - Farlow, J.
AU  - Filippov, A.A.
AU  - Sergueev, K.V.
AU  - Hang, J.
AU  - Kotorashvili, A.
AU  - Nikolich, M.P.
TI  - Comparative whole genome analysis of six diagnostic brucellaphages.
JO  - Gene
PY  - 2014
SP  - 115
EP  - 122
VL  - 541
AB  - Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze
AB  - (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic
AB  - comparisons including recently described genomes of the Tb phage from Mexico
AB  - (TbM) and Pr phage to elucidate genomic diversity and candidate host range
AB  - determinants. Comparative whole genome analysis revealed high sequence
AB  - homogeneity among these brucellaphage genomes and resolved three genetic groups
AB  - consistent with defined host range phenotypes. Group I was composed of Tb and Fz
AB  - phages that are predominantly lytic for Brucella abortus and Brucella neotomae;
AB  - Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus,
AB  - Brucella melitensis and Brucella suis; Group III was composed of Wb and S708
AB  - phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the
AB  - putative phage collar protein is a variable locus with features that may be
AB  - contributing to the host specificities exhibited by different brucellaphage
AB  - groups. The presence of several candidate host range determinants is illustrated
AB  - herein for future dissection of the differential host specificity observed among
AB  - these phages.
ER  -

TY  - JOUR
AU  - Farlow, J.
AU  - Kotorashvili, A.
TI  - Genome Sequence of the Soviet/Russian Bacillus anthracis Vaccine Strain 55-VNIIVViM.
JO  - Genome Announcements
PY  - 2016
SP  - e01401
EP  - e01416
VL  - 4
AB  - Bacillus anthracis strain 55-VNIIVViM is a live-attenuated nonencapsulated Soviet/Russian
AB  - veterinary anthrax vaccine strain. We report here the genome of 55-VNIIVViM and confirm its
AB  - phylogenetic placement in the global population structure of B. anthracis.
ER  -

TY  - JOUR
AU  - Farrance, I.K.
AU  - Eadie, J.S.
AU  - Ivarie, R.
TI  - Improved chemistry for oligodeoxyribonucleotide synthesis substantially improves restriction enzyme cleavage of a synthetic 35-mer.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 1231
EP  - 1245
VL  - 17
AB  - Two DNA duplexes of identical sequence and 35 nt in length were synthesized by
AB  - an original and a highly improved version of phosphoramidite chemistry.  By
AB  - base composition analysis, DNA synthesized by improved chemistry (termed
AB  - DMTS-imp) contained no detectable modified bases while DNA synthesized by the
AB  - original chemistry (termed DMTS-std) had a large number of modifications.
AB  - Under optimal reaction conditions, HhaI and RsaI cleaved the DMTS-std duplex to
AB  - 76-77% completion and the DMTS-imp duplex to 96-99% completion.  Restriction
AB  - analysis and piperidine treatment yielded estimates of approx. 3.0% modified
AB  - nucleotides in DMTS-std and approx. 1.0% in DMTS-imp.  Overall, the
AB  - improvements in chemistry inreased the restriction efficiency of synthetic DNA
AB  - up to 10-fold.
ER  -

TY  - JOUR
AU  - Farrell, S.O.
TI  - A fast restriction enzyme experiment for the undergraduate biochemistry lab.
JO  - J. Chem. Educ.
PY  - 1994
SP  - 1095
EP  - 1096
VL  - 71
AB  - We recently updated out laboratory curriculum to include some popular and important techniques
AB  - of molecular biology. We have designed a rapid experiment using restriction enzymes that can
AB  - be done in one three-hour lab period. This experiment is one of the highlights of the course,
AB  - and almost every student gets positive results.
ER  -

TY  - JOUR
AU  - Farrugia, D.N.
AU  - Elbourne, L.D.H.
AU  - Hassan, K.A.
AU  - Eijkelkamp, B.A.
AU  - Tetu, S.G.
AU  - Brown, M.H.
AU  - Shah, B.S.
AU  - Peleg, A.Y.
AU  - Mabbutt, B.C.
AU  - Paulsen, I.T.
TI  - The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii.
JO  - PLoS ONE
PY  - 2013
SP  - e58628
EP  - e58628
VL  - 8
AB  - Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable
AB  - of resistance to multiple antimicrobials.
AB  - Community-acquired A. baumannii in contrast, comprise a minor
AB  - proportion of all A. baumannii infections and are highly susceptible to
AB  - antimicrobial treatment. However, these infections also present acute
AB  - clinical manifestations associated with high reported rates of
AB  - mortality. We report the complete 3.70 Mbp genome of A. baumannii
AB  - D1279779, previously isolated from the bacteraemic infection of an
AB  - Indigenous Australian; this strain represents the first
AB  - community-acquired A. baumannii to be sequenced. Comparative analysis
AB  - of currently published A. baumannii genomes identified twenty-four
AB  - accessory gene clusters present in D1279779. These accessory elements
AB  - were predicted to encode a range of functions including polysaccharide
AB  - biosynthesis, type I DNA restriction-modification, and the metabolism
AB  - of novel carbonaceous and nitrogenous compounds. Conversely, twenty
AB  - genomic regions present in previously sequenced A. baumannii strains
AB  - were absent in D1279779, including gene clusters involved in the
AB  - catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii
AB  - antibiotic resistance island, known to bestow resistance to multiple
AB  - antimicrobials in nosocomial strains. Phenomic analysis utilising the
AB  - Biolog Phenotype Microarray system indicated that A. baumannii D1279779
AB  - can utilise a broader range of carbon and nitrogen sources than
AB  - international clone I and clone II nosocomial isolates. However,
AB  - D1279779 was more sensitive to antimicrobial compounds, particularly
AB  - beta-lactams, tetracyclines and sulphonamides. The combined genomic and
AB  - phenomic analyses have provided insight into the features
AB  - distinguishing A. baumannii isolated from community-acquired and
AB  - nosocomial infections.
ER  -

TY  - JOUR
AU  - Faruqi, A.F.
AU  - Ahmed, N.
TI  - Isolation and partial purification of a restriction endonuclease from Pseudomonas ovalis.
JO  - Pak. J. Sci. Ind. Res.
PY  - 1987
SP  - 390
EP  - 392
VL  - 30
AB  - A restriction endonuclease, PovI, has been isolated and partially purified from
AB  - Pseudomonas ovalis by high speed centrifugation and fractionation on a column
AB  - of Biogel followed by dialysis and ion exchange chromatography on a
AB  - phosphocellulose column.  The presence of the restriction endonuclease was
AB  - detected by a simple assay procedure using agarose slab gel electrophoresis.
ER  -

TY  - JOUR
AU  - Fasanella, A.
AU  - Braun, P.
AU  - Grass, G.
AU  - Hanczaruk, M.
AU  - Aceti, A.
AU  - Serrecchia, L.
AU  - Leonzio, G.
AU  - Tolve, F.
AU  - Georgi, E.
AU  - Antwerpen, M.
TI  - Genome Sequence of Bacillus anthracis Isolated from an Anthrax Burial Site in Pollino National Park, Basilicata Region (Southern Italy).
JO  - Genome Announcements
PY  - 2015
SP  - e00141
EP  - e00115
VL  - 3
AB  - A Bacillus anthracis strain was isolated from a burial-site in Pollino National Park where a
AB  - bovine died of anthrax and was buried in 2004. We report the first
AB  - genome sequence of B. anthracis isolated in the Basilicata region (southern
AB  - Italy), which is the highest risk area of anthrax infection in Italy.
ER  -

TY  - JOUR
AU  - Fatemi, M.
AU  - Hermann, A.
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA.
JO  - Eur. J. Biochem.
PY  - 2002
SP  - 4981
EP  - 4984
VL  - 269
AB  - Dnmt3a is a de novo DNA methyltransferase that modifies unmethylated DNA. In contrast Dnmt1
AB  - shows high preference for hemimethylated DNA. However, Dnmt1 can be activated for the
AB  - methylation of unmodified DNA. We show here that the Dnmt3a and Dnmt1 DNA methyltransferases
AB  - functionally cooperate in de novo methylation of DNA, because a fivefold stimulation of
AB  - methylation activity is observed if both enzymes are present. Stimulation is observed if
AB  - Dnmt3a is used before Dnmt1, but not if incubation with Dnmt1 precedes Dnmt3a, demonstrating
AB  - that methylation of the DNA by Dnmt3a stimulates Dnmt1 and that no physical interaction of
AB  - Dnmt1 and Dnmt3a is required. If Dnmt1 and Dnmt3a were incubated together a slightly increased
AB  - stimulation is observed that could be due to a direct interaction of these enzymes. In
AB  - addition, we show that Dnmt1 is stimulated for methylation of unmodified DNA if the DNA
AB  - already carries some methyl groups. We conclude that after initiation of de novo methylation
AB  - of DNA by Dnmt3a, Dnmt1 becomes activated by the pre-existing methyl groups and further
AB  - methylates the DNA. Our data suggest that Dnmt1 also has a role in de novo methylation of DNA.
AB  - This model agrees with the biochemical properties of these enzymes and provides a mechanistic
AB  - basis for the functional cooperation of different DNA MTases in de novo methylation of DNA
AB  - that has also been observed in vivo.
ER  -

TY  - JOUR
AU  - Fatemi, M.
AU  - Hermann, A.
AU  - Pradhan, S.
AU  - Jeltsch, A.
TI  - The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 1189
EP  - 1199
VL  - 309
AB  - The mammalian DNA methyltransferase Dnmt1 is responsible for the maintenance of the pattern of
AB  - DNA methylation in vivo. It is a large multidomain enzyme comprising 1620 amino acid residues.
AB  - We have purified and characterized individual domains of Dnmt1 (NLS-containing domain, NlsD,
AB  - amino acid residues: 1-343; replication foci-directing domain, 350-609; Zn-binding domain
AB  - (ZnD), 613-748; polybromo domain, 746-1110; and the catalytic domain (CatD), 1124-1620). CatD,
AB  - ZnD and NlsD bind to DNA, demonstrating the existence of three independent DNA-binding sites
AB  - in Dnmt1. CatD shows a preference for binding to hemimethylated CpG-sites; ZnD prefers
AB  - methylated CpGs; and NlsD specifically binds to CpG-sites, but does not discriminate between
AB  - unmethylated and methylated DNA. These results are not compatible with the suggestion that the
AB  - target recognition domain of Dnmt1 resides in the N terminus of the enzyme. We show by
AB  - protein-protein interaction assays that ZnD and CatD interact with each other. The isolated
AB  - catalytic domain does not methylate DNA, neither alone nor in combination with other domains.
AB  - Full-length Dnmt1 was purified from baculovirus-infected insect cells. Under the experimental
AB  - conditions, Dnmt1 has a strong (50-fold) preference for hemimethylated DNA. Dnmt1 is
AB  - stimulated to methylate unmodified CpG sites by the addition of fully methylated DNA. This
AB  - effect is dependent on Zn, suggesting that binding of methylated DNA to ZnD triggers the
AB  - allosteric activation of the catalytic center of Dnmt1. The allosteric activation model can
AB  - explain kinetic data obtained by others. It suggests that Dnmt1 might be responsible for
AB  - spreading of methylation, a process that is observed during aging and carcinogenesis but may
AB  - be important for de novo methylation of DNA.
ER  -

TY  - JOUR
AU  - Fauman, E.B.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Structure and evolution of AdoMet-dependent methyltransferases.
JO  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
PY  - 1999
SP  - 1
EP  - 38
AB  - A review of many different types of SAM-sependent Mtases, including DNA methyltransferases,
AB  - RNA methyltransferases and many others.
ER  -

TY  - JOUR
AU  - Fauvart, M.
AU  - Sanchez-Rodriguez, A.
AU  - Beullens, S.
AU  - Marchal, K.
AU  - Michiels, J.
TI  - Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3158
EP  - 3159
VL  - 193
AB  - Rhizobium etli is a Gram-negative soil-dwelling alpha-proteobacterium that carries out
AB  - symbiotic biological nitrogen fixation in close association
AB  - with legume hosts. R. etli strains exhibit high sequence divergence and
AB  - are geographically structured, with a potentially dramatic influence on
AB  - the outcome of symbiosis. Here, we present the genome sequence of R. etli
AB  - CNPAF512, a Brazilian isolate from bean nodules. We anticipate that the
AB  - availability of genome sequences of R. etli strains from distinctly
AB  - different areas will provide valuable new insights into the geographic
AB  - mosaic of the R. etli pangenome and the evolutionary dynamics that shape
AB  - it.
ER  -

TY  - JOUR
AU  - Faye, P.
AU  - Bertrand, C.
AU  - Pedron, J.
AU  - Barny, M.A.
TI  - Draft genomes of 'Pectobacterium peruviense' strains isolated from fresh water in France.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 27
EP  - 27
VL  - 13
AB  - Bacteria belonging to the genus Pectobacterium are responsible for soft rot disease on a wide
AB  - range of cultivated crops. The 'Pectobacterium peruviense'
AB  - specie, recently proposed inside the Pectobacterium genus, gathers strains
AB  - isolated from potato tubers cultivated in Peru at high altitude. Here we report
AB  - the draft genome sequence of two strains belonging to 'P. peruviense' isolated
AB  - from river water in France indicating that the geographic distribution of this
AB  - specie is likely to be larger than previously anticipated. We compared these
AB  - genomes with the one published from the 'P. peruviense' specie type strain
AB  - isolated in Peru.
ER  -

TY  - JOUR
AU  - Fazakerley, G.V.
AU  - Gabarro-Arpa, J.
AU  - Lebret, M.
AU  - Guy, A.
AU  - Guschlbauer, W.
TI  - The GTm6AC sequence is overwound and bent.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 2541
EP  - 2556
VL  - 17
AB  - By a combination of distance constraints obtained from NMR spectra and
AB  - molecular mechanics calculations we have determined the three dimensional
AB  - structure of the self-complementary decanucleotide d(CGCGTm6ACGCG).
AB  - Methylation of an adenine at a position 3' to T induces significant
AB  - conformational changes relative to B-DNA.  This arises from the close proximity
AB  - of the four methyl groups in the large groove in the centre of the sequence.
AB  - The helical twist between the two T.m6A base pairs is found to be 45, as for
AB  - D-DNA, and is accompanied by a high negative value of the wedge roll angle
AB  - between these base pairs.  The overall nonzero wedge roll observed shows that
AB  - the helix is bent.  These constraints appear to be material for the absence of
AB  - the sequence T-m6A in natural DNAs.
ER  -

TY  - JOUR
AU  - Fazakerley, G.V.
AU  - Quignard, E.
AU  - Teoule, R.
AU  - Guy, A.
AU  - Guschlbauer, W.
TI  - A two-dimensional H-NMR study of the dam methylase site:  comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence:  The sequence dependence of methylation upon base-pair lifetimes.
JO  - Eur. J. Biochem.
PY  - 1987
SP  - 397
EP  - 404
VL  - 167
AB  - We report two-dimensional NOE (NOESY) spectra on the sequence d(GCGATCATGG) d(CCATGATCGC)
AB  - which contains the unmethylated dam site. As expected the DNA adopts a B-form conformation but
AB  - appears to be distorted at the TG step of the second strand. This distorsion, probably
AB  - bending, is not seen on the opposite strand. When the first strand is methylated on adenine in
AB  - the GATC or CATG sequence the NOESY spectra indicate little or no change in the conformation.
AB  - However the single strand-duplex change is slowed down to the slow-exchange region on a proton
AB  - NMR time scale. We have assigned the exchangeable imino and cytidine amino resonances of the
AB  - three duplexes. From the imino linewidths as a function of temperature, we observe that the
AB  - unmethylated and the hemimethylated Gm6ATC duplexes melt normally from the ends. However, this
AB  - is not so for the hemimethylated Cm6ATG duplex which, apart from the terminal base pairs,
AB  - melts cooperatively and at high temperature. In spectra recorded in H2O a second duplex is
AB  - observed, for the Gm6ATC sequence, which we have not been able to identify. It is however
AB  - unlikely to be a hairpin structure. Ultraviolet-melting curves also indicate the presence of
AB  - two transitions for this duplex. The effect of methylation upon base-pair lifetimes has been
AB  - studied by comparing the above three duplexes. Little effect is observed upon methylation in
AB  - the GATC sequence but a drastic increase in the lifetimes of all base pairs is observed upon
AB  - methylation in the CATG sequence.
ER  -

TY  - JOUR
AU  - Fazal, M.A.
AU  - Alexander, S.
AU  - Burnett, E.
AU  - Deheer-Graham, A.
AU  - Oliver, K.
AU  - Holroyd, N.
AU  - Parkhill, J.
AU  - Russell, J.E.
TI  - Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.
JO  - Genome Announcements
PY  - 2016
SP  - e01219
EP  - e01216
VL  - 4
AB  - Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the
AB  - first complete genome sequence for Salmonella enterica subsp. enterica
AB  - serovar Java strain NCTC5706. This strain is of historical significance, having
AB  - been isolated in the pre-antibiotic era and was deposited into the National
AB  - Collection of Type Cultures in 1939.
ER  -

TY  - JOUR
AU  - Federici, F.
AU  - Manna, L.
AU  - Rizzi, E.
AU  - Galantini, E.
AU  - Marini, U.
TI  - Draft Genome Sequence of Lactobacillus salivarius SGL 03, a Novel Potential Probiotic Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e01340
EP  - e01317
VL  - 5
AB  - In this work, we report the draft genome sequence of Lactobacillus salivarius SGL 03, a novel
AB  - potential probiotic strain isolated from healthy infant stools.
AB  - Antibiotic resistance analysis revealed the presence of a tetracycline resistance
AB  - gene without elements potentially responsible for interspecific horizontal gene
AB  - transfer.
ER  -

TY  - JOUR
AU  - Fedoreyeva, L.I.
AU  - Vanyushin, B.F.
TI  - N6-Adenine DNA-methyltransferase in wheat seedlings.
JO  - FEBS Lett.
PY  - 2002
SP  - 305
EP  - 308
VL  - 514
AB  - The N(6)-adenine DNA-methyltransferase was isolated from the vacuolar vesicle fraction of
AB  - wheat coleoptiles. In the presence of S-adenosyl-L-methionine the enzyme de novo methylates
AB  - the first adenine residue in the TGATCA sequence in the single- or double-stranded DNA
AB  - substrates but it prefers single-stranded structures. Wheat adenine DNA-methyltransferase
AB  - (wadmtase) is a Mg(2+)- or Ca(2+)-dependent enzyme with a maximum activity at pH 7.5-8.0.
AB  - Wadmtase seems to be responsible for mitochondrial DNA modification that might be involved in
AB  - the regulation of replication of mitochondria in plants.
ER  -

TY  - JOUR
AU  - Fedotova, E.A.
AU  - Protsenko, A.S.
AU  - Zakharova, M.V.
AU  - Lavrova, N.V.
AU  - Alekseevsky, A.V.
AU  - Oretskaya, T.S.
AU  - Karyagina, A.S.
AU  - Solonin, A.S.
AU  - Kubareva, E.A.
TI  - SsoII-like DNA-methyltransferase Ecl18kI: Interaction between regulatory and methylating functions.
JO  - Biochemistry
PY  - 2009
SP  - 85
EP  - 91
VL  - 74
AB  - The interaction of DNA-methyltransferase Ecl18kI (M.Ecl18kI) with a fragment of promoter
AB  - region of restriction-modification system SsoII
AB  - was studied. It is shown that dissociation constants of M.Ecl18kI and
AB  - M.SsoII complexes with DNA ligand carrying a regulatory site previously
AB  - characterized for M.SsoII have comparable values. A deletion derivative
AB  - of M.Ecl18kI, Delta(72-379)Ecl18kI, representing the N-terminal protein
AB  - region responsible for regulation, was obtained. It is shown that such
AB  - polypeptide fragment has virtually no interaction with the regulatory
AB  - site. Therefore, the existence of a region responsible for methylation
AB  - is necessary for maintaining M.Ecl18kI regulatory function. The
AB  - properties of methyl-transferase NlaX, which is actually a natural
AB  - deletion derivative of M.Ecl18kI and M.SsoII lacking the first 70 amino
AB  - acid residues and not being able to regulate gene expression of the
AB  - SsoII restriction-modification system, were studied. The ability of
AB  - mutant forms of M.Ecl18kI incorporating single substitutions in regions
AB  - responsible for regulation and methylation to interact with both sites
AB  - of DNA recognition was characterized. The data show a correlation
AB  - between DNA-binding activity of two M.Ecl18kI regions-regulatory and
AB  - methylating.
ER  -

TY  - JOUR
AU  - Feher, Z.
AU  - Kiss, A.
AU  - Venetianer, P.
TI  - Expression of a bacterial modification methylase gene in yeast.
JO  - Nature
PY  - 1983
SP  - 266
EP  - 268
VL  - 302
AB  - Methylation of specific cytosines in the DNA is generally believed to play some
AB  - role in the regulation of gene expression in eukaryotes.  However, some
AB  - eukaryotes, such as Drosophila and yeast (S. Hattman, personal communication)
AB  - seem not to contain 5-methylcytosine in their DNA.  It would be interesting to
AB  - test, how gene expression in such organisms would respond to the methylation of
AB  - specific cytosines in the genome.  As a first step towards this goal, we have
AB  - introduced the gene encoding the Bacillus sphaericus R modification methylase,
AB  - which methylates the internal cytosine within the recognition sequence 5'-GGCC,
AB  - into yeast cells.  Southern-type hybridization to DNAs isolated from the
AB  - transformed yeast clones revealed that the yeast plasmid carrying the
AB  - prokaryotic methylase gene, as well as the two chromosomal genes tested (his3
AB  - and leu2) were methylated, whereas the bulk of the yeast DNA remained largely
AB  - unmethylated.  This indicates that the Bacillus sphaericus modification
AB  - methylase was expressed in yeast but it modified only certain parts of the
AB  - yeast DNA.
ER  -

TY  - JOUR
AU  - Feher, Z.
AU  - Schlagman, S.L.
AU  - Miner, Z.
AU  - Hattman, S.
TI  - In vivo methylation of yeast DNA by prokaryotic DNA methyltransferases.
JO  - Gene
PY  - 1988
SP  - 193
EP  - 195
VL  - 74
AB  - No detectable amounts of methylated bases are present in the DNA of the yeast, Saccharomyces
AB  - cerevisiae.  This feature and the availability of an Escherichia coli-yeast cloning system
AB  - make yeast an excellent host to study the factors affecting de novo DNA methylation, as well
AB  - as their attendant effects in a eukaryotic cell.  Earlier, Feher et al. (1983) observed
AB  - heterologous expression of the Bacillus sphaericus RI DNA-cytosine methyltransferase in yeast.
AB  - Methylation of two known chromosomal genes was detected, while the bulk DNA remained largely
AB  - unmethylated.  Heterologous expression of the E. coli DNA (N6-adenine)methyltransferase gene
AB  - (dam) in yeast was reported by Brooks et al. (1983) and Hoekstra and Malone (1985; 1986).
ER  -

TY  - JOUR
AU  - Feher, Z.
AU  - Schlagman, S.L.
AU  - Miner, Z.
AU  - Hattman, S.
TI  - The UV excision-repair system of Saccharomyces cerevisiae is involved in the removal of methylcytosines formed in vivo by a cloned prokaryotic DNA methyltransferase.
JO  - Curr. Genet.
PY  - 1989
SP  - 461
EP  - 464
VL  - 16
AB  - DNA methyltransferase activity is not normally found in yeast.  To investigate
AB  - the response of Saccharomyces cerevisiae to the presence of methylated bases,
AB  - we introduced the Bacillus subtilis SPR phage DNA-[cytosine-5]
AB  - methyltransferase gene on the shuttle vector, YEp51.  The methyltransferase
AB  - gene was functionally expressed in yeast under the control of the inducible
AB  - yeast GAL10 promoter.  Following induction we observed a time-dependent
AB  - methylation of yeast DNA in RAD+ and rad2 mutant strains; the rad2 mutant is
AB  - defective in excision-repair of UV-induced DNA damage.  Analysis of restriction
AB  - endonuclease digestion patterns revealed that the relative amount of methylated
AB  - DNA was greater in the excision defective rad2 mutant than in the RAD+ strain.
AB  - These data indicate that the yeast excision-repair system is capable of
AB  - recognizing and removing m5C residues.
ER  -

TY  - JOUR
AU  - Feher, Z.
AU  - Schlagman, S.L.
AU  - Miner, Z.
AU  - Hattman, S.
TI  - Expression of prokaryotic DNA methyltransferase genes in yeast.
JO  - Zentralbl. Mikrobiol.
PY  - 1990
SP  - 343
EP  - 343
VL  - 145
AB  - DNA methyltransferase activity is not normally found in yeast. To investigate the response of
AB  - Saccharomyces cerevisiae to the presence of methylated bases, we introduced two phage-encoded
AB  - DNA methyltransferase genes on the shuttle vector, YEp51. The Bacillus subtilis phage SPR
AB  - enzyme methylates cytosine residues in three distinct recognition sequences [GGCC, CCGG, and
AB  - CC(A/T)GG], whereas the Escherichia coli phage T4 Dam enzyme methylates adenines primarily in
AB  - GATC sequences. Both phage-encoded genes were functionally expressed in yeast under the
AB  - control of the inducible yeast GAL10 promoter. DNA methyltransferase activity was assayed by
AB  - determining the susceptibility of yeast DNA to cleavage by restriction endonucleases:
AB  - resistance to HaeIII and sensitivity to DpnI indicate SPR- and T4 Dam-specific in vivo
AB  - methylation, respectively. Following induction of the GAL10 promoter we observed a
AB  - time-dependent methylation of yeast DNA in the RAD+, as well as rad2 and rad3 mutant strains;
AB  - these rad mutant strains are defective in excision-repair. Analysis of the restriction
AB  - endonuclease digestion patterns revealed that the relative amount of high molecular weight
AB  - methylated DNA was greater in the excision-defective rad mutants than in the RAD+ strain.
AB  - Furthermore, after methyltransferase gene expression was turned off (by the addition of
AB  - glucose to previously induced cells), we observed a decrease in methylation in the RAD+, but
AB  - not in the DNA of the rad mutant. These data indicate that the yeast excision-repair system is
AB  - capable of recognizing and removing m5C and m6A residues. All of our plasmid constructions
AB  - contain more than one AUG initiation codon at the 5' end of the mRNA transcript and some of
AB  - the AUGs are followed by an in-frame stop codon. Since we observed expression of the
AB  - methyltransferase genes, it would appear that, in yeast, one or two short ORFs in the leader
AB  - region do not necessarily prevent translation of a downstream gene.
ER  -

TY  - JOUR
AU  - Feil, H. et al.
TI  - Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 11064
EP  - 11069
VL  - 102
AB  - The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been
AB  - determined and is compared with that of P. syringae
AB  - pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically
AB  - important species of plant pathogenic bacteria differ in host range and
AB  - other interactions with plants, with Pss having a more pronounced
AB  - epiphytic stage of growth and higher abiotic stress tolerance and Pst
AB  - DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a
AB  - genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the
AB  - Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome
AB  - and two plasmids. Although a high degree of similarity exists between the
AB  - two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss
AB  - B728a when compared with Pst DC3000, including large genomic islands
AB  - likely to contribute to virulence and host specificity. Over 375
AB  - repetitive extragenic palindromic sequences unique to Pss B728a when
AB  - compared with Pst DC3000 are widely distributed throughout the chromosome
AB  - except in 14 genomic islands, which generally had lower GC content than
AB  - the genome as a whole. Content of the genomic islands varies, with one
AB  - containing a prophage and another the plasmid pKLC102 of Pseudomonas
AB  - aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in
AB  - Pst DC3000 are those encoding for syringopeptin, syringomycin, indole
AB  - acetic acid biosynthesis, arginine degradation, and production of ice
AB  - nuclei. The genomic comparison suggests that several unique genes for Pss
AB  - B728a such as ectoine synthase, DNA repair, and antibiotic production may
AB  - contribute to the epiphytic fitness and stress tolerance of this organism.
ER  -

TY  - JOUR
AU  - Feingersch, R.
AU  - Suzuki, M.T.
AU  - Shmoish, M.
AU  - Sharon, I.
AU  - Sabehi, G.
AU  - Partensky, F.
AU  - Beja, O.
TI  - Microbial community genomics in eastern Mediterranean Sea surface waters.
JO  - ISME J.
PY  - 2010
SP  - 78
EP  - 87
VL  - 4
AB  - Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on
AB  - Earth in which the primary productivity is phosphorus limited. To study the unexplored
AB  - function and physiology of microbes inhabiting this system, we have analyzed a genomic library
AB  - from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000
AB  - clones. Genome recruitment strategies showed that the majority of high-scoring pairs
AB  - corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales),
AB  - Cyanobacteria (Synechococcus and high-light
AB  - adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure
AB  - observed, as evaluated by both protein similarity scores or metabolic potential, was similar
AB  - to that found in the euphotic zone of the ALOHA station off Hawaii but very different from
AB  - that of deep aphotic
AB  - zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment
AB  - toward phosphate and phosphonate uptake and utilization metabolism was also observed.
ER  -

TY  - JOUR
AU  - Fekete, P.Z.
AU  - Brzuszkiewicz, E.
AU  - Blum-Oehler, G.
AU  - Olasz, F.
AU  - Szabo, M.
AU  - Gottschalk, G.
AU  - Hacker, J.
AU  - Nagy, B.
TI  - DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli.
JO  - Int. J. Med. Microbiol.
PY  - 2012
SP  - 4
EP  - 9
VL  - 302
AB  - In this study the plasmid pTC, a 90kb self-conjugative virulence plasmid
AB  - of the porcine enterotoxigenic Escherichia coli (ETEC) strain EC2173
AB  - encoding the STa and STb heat-stable enterotoxins and tetracycline
AB  - resistance, has been sequenced in two steps. As a result we identified
AB  - five main distinct regions of pTC: (i) the maintenance region responsible
AB  - for the extreme stability of the plasmid, (ii) the TSL (toxin-specific
AB  - locus comprising the estA and estB genes) which is unique and
AB  - characteristic for pTC, (iii) a Tn10 transposon, encoding tetracycline
AB  - resistance, (iv) the tra (plasmid transfer) region, and (v) the colE1-like
AB  - origin of replication. It is concluded that pTC is a self-transmissible
AB  - composite plasmid harbouring antibiotic resistance and virulence genes.
AB  - pTC belongs to a group of large conjugative E. coli plasmids represented
AB  - by NR1 with a widespread tra backbone which might have evolved from a
AB  - common ancestor. This is the first report of a completely sequenced animal
AB  - ETEC virulence plasmid containing an antimicrobial resistance locus,
AB  - thereby representing a selection advantage for spread of pathogenicity in
AB  - the presence of antimicrobials leading to increased disease potential.
ER  -

TY  - JOUR
AU  - Fellag, M.
AU  - Levasseur, A.
AU  - Delerce, J.
AU  - Bittar, F.
AU  - Marie, J.L.
AU  - Davoust, B.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of 'Nocardia suismassiliense' Strain S-137 (CSUR P4007).
JO  - Genome Announcements
PY  - 2018
SP  - e00212
EP  - e00218
VL  - 6
AB  - 'Nocardia suismassiliense' strain S-137 isolated from Sus scrofa feces exhibits a 9.4-Mb
AB  - (67.1% GC content) draft genome sequence containing 8,658 protein-coding
AB  - genes, 66 tRNAs, and 9 rRNAs. In silico DNA-DNA hybridization confirmed strain
AB  - S-137 as representative of a new species, 'Nocardia suismassiliense,' closely
AB  - related to N. tenerifensis and N. brasiliensis.
ER  -

TY  - JOUR
AU  - Felle, M.
AU  - Joppien, S.
AU  - Nemeth, A.
AU  - Diermeier, S.
AU  - Thalhammer, V.
AU  - Dobner, T.
AU  - Kremmer, E.
AU  - Kappler, R.
AU  - Langst, G.
TI  - The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 8355
EP  - 8365
VL  - 39
AB  - Aberrant DNA methylation is often associated with cancer and the formation of tumors; however,
AB  - the underlying mechanisms, in particular the
AB  - recruitment and regulation of DNA methyltransferases remain largely
AB  - unknown. In this study, we identified USP7 as an interaction partner of
AB  - Dnmt1 and UHRF1 in vivo. Dnmt1 and USP7 formed a soluble dimer complex
AB  - that associated with UHRF1 as a trimeric complex on chromatin. Complex
AB  - interactions were mediated by the C-terminal domain of USP7 with the
AB  - TS-domain of Dnmt1, whereas the TRAF-domain of USP7 bound to the
AB  - SRA-domain of UHRF1. USP7 was capable of targeting UHRF1 for
AB  - deubiquitination and affects UHRF1 protein stability in vivo. Furthermore,
AB  - Dnmt1, UHRF1 and USP7 co-localized on silenced, methylated genes in vivo.
AB  - Strikingly, when analyzing the impact of UHRF1 and USP7 on Dnmt1-dependent
AB  - DNA methylation, we found that USP7 stimulated both the maintenance and de
AB  - novo DNA methylation activity of Dnmt1 in vitro. Therefore, we propose a
AB  - dual role of USP7, regulating the protein turnover of UHRF1 and
AB  - stimulating the enzymatic activity of Dnmt1 in vitro and in vivo.
ER  -

TY  - JOUR
AU  - Felley-Bosco, E.
AU  - Pourzand, C.
AU  - Zijlstra, J.
AU  - Amstad, P.
AU  - Cerutti, P.
TI  - A genotypic mutation system measuring mutations in restriction recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2913
EP  - 2919
VL  - 19
AB  - The RFLP/PCR approach (restriction fragment length polymorphism/polymerase
AB  - chain reaction) to genotypic mutation analysis described here measures
AB  - mutations in restriction recognition sequences.  Wild-type DNA is restricted
AB  - before the resistant, mutated sequences are amplified by PCR and cloned.  We
AB  - tested the capacity of this experimental design to isolate a few copies of a
AB  - mutated sequence of the human c-Ha-ras1 gene from a large excess of wild-type
AB  - DNA.  For this purpose we constructed a 272 bp fragment with 2 mutations in the
AB  - PvuII recognition sequence 1727-1732 and studied the rescue by RFLP/PCR of a
AB  - few copies of this PvuII mutant standard.  Following amplification with
AB  - Taq-polymerase induced bp changes were quantitated by hybridization with
AB  - specific oligonucleotide probes.  Our results indicate that 10 PvuII mutant
AB  - standard copies can be rescued from 10/8 to 10/9 wild-type sequences.  Taq
AB  - polymerase errors originating from unrestricted, residual wild-type DNA were
AB  - sequence dependent and consisted mostly of transversions originating at G.C bp.
AB  - In contrast to a doubly mutated standard the capacity to rescue single bp
AB  - mutations by RFLP/PCR is limited by Taq-polymerase errors.  Therefore, we
AB  - assessed the capacity of our protocol to isolate a G to T transversion mutation
AB  - at base pair 1698 of the MspI-site 1695-1698 of the c-Ha-ras1 gene from excess
AB  - wild-type ras1 DNA.  We found that 100 copies of the mutated ras1 fragment
AB  - could be readily rescued from 10/8 copies of wild-type DNA.
ER  -

TY  - JOUR
AU  - Fellinger, K.
AU  - Rothbauer, U.
AU  - Felle, M.
AU  - Laengst, G.
AU  - Leonhardt, H.
TI  - Dimerization of DNA methyltransferase 1 is mediated by its regulatory domain.
JO  - J. Cell. Biochem.
PY  - 2009
SP  - 521
EP  - 528
VL  - 106
AB  - DNA methylation is a major epigenetic modification and plays a crucial role in the regulation
AB  - of gene expression. Within the family of DNA
AB  - methyltransferases (Dnmts), Dnmt3a and 3b establish methylation marks during early
AB  - development, while Dnmt1 maintains methylation
AB  - patterns after DNA replication. The maintenance function of Dnmt1 is regulated by its large
AB  - regulatory N-terminal domain that interacts with
AB  - other chromatin factors and is essential for the recognition of hemi-methylated DNA.
AB  - Gelfiltration analysis showed that purified Dnmt1 elutes
AB  - at an apparent molecular weight corresponding to the size of a dimer. With protein interaction
AB  - assays we could show that Dnmt1 interacts with
AB  - itself through its N-terminal regulatory domain. By deletion analysis and
AB  - co-immunoprecipitations we mapped the dimerization domain to
AB  - the targeting sequence TS that is located in the center of the N-terminal domain (amino acids
AB  - 310-629) and was previously shown to mediate
AB  - replication independent association with heterochromatin at chromocenters. Further mutational
AB  - analyses suggested that the dimeric complex
AB  - has a bipartite interaction interface and is formed in a head-to-head orientation. Dnmt1 dimer
AB  - formation could facilitate the discrimination of
AB  - hemi-methylated target sites as has been found for other palindromic DNA sequence recognizing
AB  - enzymes. These results assign an additional
AB  - function to the TS domain and raise the interesting question how these functions are spatially
AB  - and temporarily co-ordinated.
ER  -

TY  - JOUR
AU  - Fellner, L.
AU  - Huptas, C.
AU  - Simon, S.
AU  - Muhlig, A.
AU  - Scherer, S.
AU  - Neuhaus, K.
TI  - Draft Genome Sequences of Three European Laboratory Derivatives from Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933, Including Two Plasmids.
JO  - Genome Announcements
PY  - 2016
SP  - e01331
EP  - e01315
VL  - 4
AB  - Escherichia coliO157:H7 EDL933, isolated in 1982 in the United States, was the first
AB  - enterohemorrhagicE. coli(EHEC) strain sequenced. Unfortunately, European
AB  - labs can no longer receive the original strain. We checked three European EDL933
AB  - derivatives and found major genetic deviations (deletions, inversions) in two
AB  - strains. All EDL933 strains contain the cryptic EHEC-plasmid, not reported
AB  - before.
ER  -

TY  - JOUR
AU  - Felux, A.K.
AU  - Franchini, P.
AU  - Schleheck, D.
TI  - Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 42
EP  - 42
VL  - 10
AB  - Pseudomonas putida SQ1 was isolated for its ability to utilize the plant sugar sulfoquinovose
AB  - (6-deoxy-6-sulfoglucose) for growth, in order to define its
AB  - SQ-degradation pathway and the enzymes and genes involved. Here we describe the
AB  - features of the organism, together with its draft genome sequence and annotation.
AB  - The draft genome comprises 5,328,888 bp and is predicted to encode 5,824
AB  - protein-coding genes; the overall G + C content is 61.58 %. The genome annotation
AB  - is being used for identification of proteins that might be involved in SQ
AB  - degradation by peptide fingerprinting-mass spectrometry.
ER  -

TY  - JOUR
AU  - Feng, H.
AU  - Zhi, Y.
AU  - Sun, Y.
AU  - Wei, X.
AU  - Luo, Y.
AU  - Zhou, P.
TI  - Draft Genome Sequence of a Novel Streptomyces griseorubens Strain, JSD-1, Active  in Carbon and Nitrogen Recycling.
JO  - Genome Announcements
PY  - 2014
SP  - e00650
EP  - e00614
VL  - 2
AB  - Streptomyces griseorubens JSD-1, isolated from compost-treated soil, is able to utilize
AB  - lignocellulose and nitrate as its sole carbon and nitrogen source for
AB  - growth. Here, we announce the draft genome map of this actinomycete. The genes
AB  - participating in lignocellulose and nitrate metabolism were picked out and
AB  - identified.
ER  -

TY  - JOUR
AU  - Feng, K.
AU  - Li, R.
AU  - Chen, Y.
AU  - Zhao, B.
AU  - Yin, T.
TI  - Sequencing and Analysis of the Pseudomonas fluorescens GcM5-1A Genome: A Pathogen Living in the Surface Coat of Bursaphelenchus xylophilus.
JO  - PLoS ONE
PY  - 2015
SP  - E0141515
EP  - E0141515
VL  - 10
AB  - It is known that several bacteria are adherent to the surface coat of pine wood
AB  - nematode (Bursaphelenchus xylophilus), but their function and role in the
AB  - pathogenesis of pine wilt disease remains debatable. The Pseudomonas fluorescens
AB  - GcM5-1A is a bacterium isolated from the surface coat of pine wood nematodes. In
AB  - previous studies, GcM5-1A was evident in connection with the pathogenicity of
AB  - pine wilt disease. In this study, we report the de novo sequencing of the GcM5-1A
AB  - genome. A 600-Mb collection of high-quality reads was obtained and assembled into
AB  - sequence contigs spanning a 6.01-Mb length. Sequence annotation predicted 5,413
AB  - open reading frames, of which 2,988 were homologous to genes in the other four
AB  - sequenced P. fluorescens isolates (SBW25, WH6, Pf0-1 and Pf-5) and 1,137 were
AB  - unique to GcM5-1A. Phylogenetic studies and genome comparison revealed that
AB  - GcM5-1A is more closely related to SBW25 and WH6 isolates than to Pf0-1 and Pf-5
AB  - isolates. Towards study of pathogenesis, we identified 79 candidate virulence
AB  - factors in the genome of GcM5-1A, including the Alg, Fl, Waa gene families, and
AB  - genes coding the major pathogenic protein fliC. In addition, genes for a complete
AB  - T3SS system were identified in the genome of GcM5-1A. Such systems have proved to
AB  - play a critical role in subverting and colonizing the host organisms of many
AB  - gram-negative pathogenic bacteria. Although the functions of the candidate
AB  - virulence factors need yet to be deciphered experimentally, the availability of
AB  - this genome provides a basic platform to obtain informative clues to be addressed
AB  - in future studies by the pine wilt disease research community.
ER  -

TY  - JOUR
AU  - Feng, L.
AU  - Ma, T.
AU  - Zhang, J.
AU  - Xu, F.
AU  - Shi, L.
TI  - Draft Genome Sequence of Bacillus subtilis QH-1, a Chromium-Reducing Bacterial Strain Isolated in Qinghai Province, China.
JO  - Genome Announcements
PY  - 2014
SP  - e00182
EP  - e00114
VL  - 2
AB  - Bacillus subtilis strain QH-1, a chromium-reducing bacterial strain, was isolated from a soil
AB  - sample from a chromium-containing slag heap. The draft genome
AB  - sequence of this bacterium is 4,034,036 bp in length, with a G+C content of
AB  - 43.71%, and it is predicted to contain 4,082 protein-coding genes.
ER  -

TY  - JOUR
AU  - Feng, L.
AU  - Reeves, P.R.
AU  - Lan, R.
AU  - Ren, Y.
AU  - Gao, C.
AU  - Zhou, Z.
AU  - Ren, Y.
AU  - Cheng, J.
AU  - Wang, W.
AU  - Wang, J.
AU  - Qian, W.
AU  - Li, D.
AU  - Wang, L.
TI  - A recalibrated molecular clock and independent origins for the cholera pandemic clones.
JO  - PLoS ONE
PY  - 2008
SP  - E4053
EP  - E4053
VL  - 3
AB  - Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7
AB  - pandemics, but there were also local outbreaks between the 6(th)
AB  - (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype
AB  - O1, whereas environmental or invertebrate isolates are antigenically
AB  - diverse. The pre 7th pandemic isolates mentioned above, and other minor
AB  - pathogenic clones, are related to the 7(th) pandemic clone, while the
AB  - 6(th) pandemic clone is in the same lineage but more distantly related,
AB  - and non-pathogenic isolates show no clonal structure. To understand the
AB  - origins and relationships of the pandemic clones, we sequenced the genomes
AB  - of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared
AB  - them with the published 7(th) pandemic genome. We distinguished mutational
AB  - and recombinational events, and allocated these and other events, to
AB  - specific branches in the evolutionary tree. There were more mutational
AB  - than recombinational events, but more genes, and 44 times more base pairs,
AB  - changed by recombination. We used the mutational single-nucleotide
AB  - polymorphisms and known isolation dates of the prepandemic and 7(th)
AB  - pandemic isolates to estimate the mutation rate, and found it to be 100
AB  - fold higher than usually assumed. We then used this to estimate the
AB  - divergence date of the 6(th) and 7(th) pandemic clones to be about 1880.
AB  - While there is a large margin of error, this is far more realistic than
AB  - the 10,000-50,000 years ago estimated using the usual assumptions. We
AB  - conclude that the 2 pandemic clones gained pandemic potential
AB  - independently, and overall there were 29 insertions or deletions of one or
AB  - more genes. There were also substantial changes in the major integron,
AB  - attributed to gain of individual cassettes including copying from within,
AB  - or loss of blocks of cassettes. The approaches used open up new avenues
AB  - for analysing the origin and history of other important pathogens.
ER  -

TY  - JOUR
AU  - Feng, L.
AU  - Wang, W.
AU  - Cheng, J.
AU  - Ren, Y.
AU  - Zhao, G.
AU  - Gao, C.
AU  - Tang, Y.
AU  - Liu, X.
AU  - Han, W.
AU  - Peng, X.
AU  - Liu, R.
AU  - Wang, L.
TI  - Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 5602
EP  - 5607
VL  - 104
AB  - The complete genome sequence of Geobacillus thermodenitrificans NG80-2, a thermophilic
AB  - bacillus isolated from a deep oil reservoir in Northern
AB  - China, consists of a 3,550,319-bp chromosome and a 57,693-bp plasmid. The
AB  - genome reveals that NG80-2 is well equipped for adaptation into a wide
AB  - variety of environmental niches, including oil reservoirs, by possessing
AB  - genes for utilization of a broad range of energy sources, genes encoding
AB  - various transporters for efficient nutrient uptake and detoxification, and
AB  - genes for a flexible respiration system including an aerobic branch
AB  - comprising five terminal oxidases and an anaerobic branch comprising a
AB  - complete denitrification pathway for quick response to dissolved oxygen
AB  - fluctuation. The identification of a nitrous oxide reductase gene has not
AB  - been previously described in Gram-positive bacteria. The proteome further
AB  - reveals the presence of a long-chain alkane degradation pathway; and the
AB  - function of the key enzyme in the pathway, the long-chain alkane
AB  - monooxygenase LadA, is confirmed by in vivo and in vitro experiments. The
AB  - thermophilic soluble monomeric LadA is an ideal candidate for treatment of
AB  - environmental oil pollutions and biosynthesis of complex molecules.
ER  -

TY  - JOUR
AU  - Feng, Y.
AU  - Xu, H.F.
AU  - Li, Q.H.
AU  - Zhang, S.Y.
AU  - Wang, C.X.
AU  - Zhu, D.L.
AU  - Cao, F.L.
AU  - Li, Y.G.
AU  - Johnston, R.N.
AU  - Zhou, J.
AU  - Liu, G.R.
AU  - Liu, S.L.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Pullorum RKS5078.
JO  - J. Bacteriol.
PY  - 2012
SP  - 744
EP  - 744
VL  - 194
AB  - Salmonella enterica serovar Pullorum is a chicken-adapted pathogen, causing pullorum disease.
AB  - Its strict host adaptation has been suspected to
AB  - result in gene decay. To validate this hypothesis and identify the decayed
AB  - genes, we sequenced the complete genome of S. Pullorum RKS5078. We found
AB  - 263 pseudogenes in this strain and conducted functional analyses of the
AB  - decayed genes.
ER  -

TY  - JOUR
AU  - Feng, Z.
AU  - Fang, G.
AU  - Korlach, J.
AU  - Clark, T.
AU  - Luong, K.
AU  - Zhang, X.
AU  - Wong, W.
AU  - Schadt, E.
TI  - Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.
JO  - PLOS Comp. Biol.
PY  - 2013
SP  - e1002935
EP  - e1002935
VL  - 9
AB  - DNA modifications such as methylation and DNA damage can play critical regulatory roles in
AB  - biological systems. Single molecule, real time (SMRT) sequencing technology generates DNA
AB  - sequences as well as DNA polymerase kinetic information that can be used for the direct
AB  - detection of DNA modifications. We demonstrate that local sequence context has a strong impact
AB  - on DNA polymerase kinetics in the neighborhood of the incorporation site during the DNA
AB  - synthesis reaction, allowing for the possibility of estimating the expected kinetic rate of
AB  - the enzyme at the incorporation site using kinetic rate information collected from existing
AB  - SMRT sequencing data (historical data) covering the same local sequence contexts of interest.
AB  - We develop an Empirical Bayesian hierarchical model for incorporating historical data. Our
AB  - results show that the model could greatly increase DNA modification detection accuracy, and
AB  - reduce requirement of control data coverage. For some DNA modifications that have a strong
AB  - signal, a control sample is not even needed by using historical data as alternative to
AB  - control. Thus, sequencing costs can be greatly reduced by using the model. We implemented the
AB  - model in a R package named seqPatch, which is available at
AB  - https://github.com/zhixingfeng/seqPatch.
ER  -

TY  - JOUR
AU  - Feng, Z.
AU  - Li, J.
AU  - Zhang, J.R.
AU  - Zhang, X.
TI  - qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of  DNA modification from SMRT sequencing data.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 13488
EP  - 13499
VL  - 42
AB  - In an isogenic cell population, phenotypic heterogeneity among individual cells is common and
AB  - critical for survival of the population under different environment conditions. DNA
AB  - modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The
AB  - single molecule real-time (SMRT) sequencing technology provides a unique platform for
AB  - detecting a wide range of DNA modifications, including N6-methyladenine (6-mA),
AB  - N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel
AB  - bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of
AB  - DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic
AB  - haploid cells, in which the same loci of the genome are differentially modified. We tested the
AB  - reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556.
AB  - qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal
AB  - population of ST556. Subsequent biochemical analyses revealed that the recognition sequences
AB  - of two type I restriction-modification (R-M) systems are responsible for the intercellular
AB  - heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a
AB  - valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA
AB  - modification.
ER  -

TY  - JOUR
AU  - Ferat, J.-L.
AU  - Michel, F.
TI  - Group II self-splicing introns in bacteria.
JO  - Nature
PY  - 1993
SP  - 358
EP  - 361
VL  - 364
AB  - Like nuclear premessenger introns, group II self-splicing introns are excised from primary
AB  - transcripts as branched molecules, containing a 2'-5' phosphodiester bond.  For this reason,
AB  - it is widely believed that the ribozyme (catalytic RNA) core of group II introns, or some
AB  - evolutionarily related molecule, gave rise to the RNA components of the spliceosomal splicing
AB  - machinery of the eukaryotic nucleus.  One difficulty with this hypothesis has been the
AB  - restricted distribution of group II introns.  Unlike group I self-splicing introns, which
AB  - interrupt not only organelle primary transcripts, but also some bacterial and nuclear genes,
AB  - group II introns seemed to be confined to mitochondrial and chloroplast genomes.  We now
AB  - report the discovery of group II introns both in cyanobacteria (the ancestors of chloroplasts)
AB  - and the gamma subdivision of purple bacteria, or proteobacteria, whose alpha subdivision
AB  - probably gave rise to mitochondria.  At least one of these introns actually self-splices in
AB  - vitro.
ER  -

TY  - JOUR
AU  - Ferdous, A.
AU  - Akaike, T.
AU  - Maruyama, A.
TI  - Inhibition of sequence-specific protein-DNA interaction and restriction endonuclease cleavage via triplex stabilization by poly(L-lysine)-graft-dextran copolymer.
JO  - Biomacromolecules
PY  - 2000
SP  - 186
EP  - 193
VL  - 1
AB  - Triplex stabilization by poly(L-lysine)-graft-dextran copolymer within a mammalian gene
AB  - promoter inhibits the DNA binding activity of nuclear proteins from HeLa cells as well as
AB  - restriction endonuclease cleavage at physiological pH and ionic conditions in vitro.
AB  - Electrophoretic mobility shift assays using a 30-mer homopurine-homopyrimidine stretch
AB  - (located between -165 and -146 bp) of the promoter is engineered at the BamHI and PstI sites
AB  - of a plasmid DNA, copolymer-mediated triplex stabilization also remarkably competes
AB  - endonuclease activity of BamHI.  Finally, the triplex-stabilizing efficiency of the copolymer
AB  - is remarkably higher than that of spermine and benzo[e]pyridoindole.  Our results indicate
AB  - that the copolymer, regardless of the length of the target duplex, stabilizes triplexes for
AB  - significant inhibition of protein-DNA interaction and endonuclease activity.  Since stable
AB  - triplex formation within a short region out of a long native duplex is a prerequisite to
AB  - confer the therapeutic potential of antigene strategy, triplex stabilization on a long target
AB  - duplex and inhibition of nuclear protein - DNA interaction may open the possible in vivo
AB  - applicability of the copolymer.
ER  -

TY  - JOUR
AU  - Ferenci, T.
AU  - Zhou, Z.
AU  - Betteridge, T.
AU  - Ren, Y.
AU  - Liu, Y.
AU  - Feng, L.
AU  - Reeves, P.R.
AU  - Wang, L.
TI  - Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 2009
SP  - 4025
EP  - 4029
VL  - 191
AB  - The genome of an Escherichia coli MC4100 strain with a lambda placMu50
AB  - fusion revealed numerous regulatory differences from MG1655, including one
AB  - that arose during laboratory storage. The 194 mutational differences
AB  - between MC4100(MuLac) and other K-12 sequences were mostly allocated to
AB  - specific lineages, indicating the considerable mutational divergence
AB  - between K-12 strains.
ER  -

TY  - JOUR
AU  - Fernandez, A.
AU  - Gil, E.
AU  - Cartelle, M.
AU  - Perez, A.
AU  - Beceiro, A.
AU  - Mallo, S.
AU  - Tomas, M.M.
AU  - Perez-Llarena, F.J.
AU  - Villanueva, R.
AU  - Bou, G.
TI  - Interspecies spread of CTX-M-32 extended-spectrum {beta}-lactamase and the role of the insertion sequence IS1 in down-regulating blaCTX-M gene expression.
JO  - J. Antimicrob. Chemother.
PY  - 2007
SP  - 841
EP  - 847
VL  - 59
AB  - OBJECTIVES: To characterize the extended-spectrum beta-lactamases (ESBLs)
AB  - as well as their genetic environment in different isolates of
AB  - Enterobacteriaceae from a patient with repeated urinary tract infections.
AB  - METHODS: Two isolates of Escherichia coli and one Proteus mirabilis, all
AB  - with ESBL phenotypes, were studied. Conjugation experiments and
AB  - restriction fragment length polymorphisms (RFLPs) were performed. Cloning
AB  - of the bla genes was by plasmid restriction and fragments ligation.
AB  - Antibiotic susceptibility testing was by Etest. The genetic environment
AB  - was analysed by direct sequencing of the DNA surrounding the bla gene.
AB  - RT-PCR was performed to study the differences in the bla(CTX-M) gene
AB  - expression. RESULTS: The bla gene was transferred by conjugation from the
AB  - three clinical isolates, which by RFLP showed the same plasmid. The bla
AB  - gene and surrounding sequences were cloned, an approximately 9 kbp AccI
AB  - fragment was sequenced and the bla(CTX-M-32) gene was identified. The MICs
AB  - of ceftazidime for transconjugants and transformants bearing the
AB  - bla(CTX-M-32) gene were lower than those previously reported. Analysis of
AB  - the DNA surrounding the ESBL gene revealed a new genetic structure with
AB  - two insertion sequences, IS5 and IS1, located immediately upstream of the
AB  - bla(CTX-M-32) gene; IS1 was located between the bla gene and IS5, and
AB  - within the -10 and -35 promoter boxes of the bla(CTX-M-32) gene.
AB  - Microbiological and biochemical studies revealed lower bla(CTX-M-32) gene
AB  - expression in bacterial isolates with IS1 between the promoter boxes.
AB  - CONCLUSIONS: Data suggest putative in vivo horizontal bla(CTX-M-32) gene
AB  - transfer between two different genera of Enterobacteriaceae. A new complex
AB  - structure, IS5-IS1, was detected upstream of the bla gene and IS1
AB  - negatively modulated expression of the bla(CTX-M-32) gene because its
AB  - location modified the bla promoter region.
ER  -

TY  - JOUR
AU  - Fernandez, M.
AU  - Olek, A.
AU  - Walter, J.
AU  - Sanchez, J.
TI  - Analysis of DNA methylation processes related to the inhibition of DNA synthesis by 5-azacytidine in Streptomyces antibioticus ETH 7451.
JO  - Biol. Chem.
PY  - 1998
SP  - 559
EP  - 562
VL  - 379
AB  - 5-Azacytidine inhibits DNA synthesis and to a lesser proportion RNA synthesis in S.
AB  - antibioticus.  The biosynthesis of proteins is not affected.  The main inhibitory effect of
AB  - 5-azacytidine on DNA and RNA synthesis is probably caused by its incorporation into newly
AB  - synthesized DNA or RNA and the formation of covalent complexes between cytosine-specific
AB  - methyltransferases and the modified DNA or RNA templates.  To analyze whether such effects
AB  - could occur at the oriC region of S. antibioticus we analyzed the methylation status of this
AB  - region using the bisulphite assisted genomic sequencing method.  One of the cytosine residues
AB  - found to be partially methylated was contained within a unique NaeI sequence (GCCGGC) in oriC.
AB  - Subsequent analysis shows chromosomal DNA from S. antibioticus to be resistant to R.NaeI
AB  - restriction indicating that this strain contains a NaeI-specific cytosine C5-methyltransferase
AB  - activity.  Following 5-azacytidine treatment the NaeI site within the oriC region becomes
AB  - partially demethylated.  Our results suggest that some of the 5-azacytidine effects on DNA and
AB  - RNA synthesis might indeed be related to the complex formation and inhibition of a
AB  - cytosine-specific DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Fernandez, M.
AU  - Soliveri, J.
AU  - Novella, I.S.
AU  - Yebra, M.J.
AU  - Barbes, C.
AU  - Sanchez, J.
TI  - Effect of  5-azacytidine and sinefungin on Streptomyces development.
JO  - Gene
PY  - 1995
SP  - 221
EP  - 223
VL  - 157
AB  - The effect of two DNA-methyltransferase inhibitors, 5-azacytidine (5azaC) and sinefungin (Sf),
AB  - on the development of Streptomyces antibioticus ETH7451 (Sa) was studied. Pulse labeling
AB  - experiments and SDS-PAGE analysis of proteins from cells grown in sporulation synthetic medium
AB  - showed that both inhibitors affect a limited number of systems. Synthesis of the antibiotic
AB  - rhodomycin was increased in the presence of 5azaC. 5azaC also stimulated the production of
AB  - actinorhodin in cultures of S. coelicolor A3(2) grown in minimal medium. The analog did not
AB  - affect the expression of whiB and whiG, two sporulation genes from S. coelicolor A3(2) whose
AB  - homologues are present in Sa. Overall results indicated that 5azaC and Sf affect specific
AB  - events associated with differentiation and secondary metabolism in Streptomyces.
ER  -

TY  - JOUR
AU  - Fernandez-de-Las-Heras, L.
AU  - Alonso, S.
AU  - de la Vega-de-Leon, A.
AU  - Xavier, D.
AU  - Perera, J.
AU  - Navarro-Llorens, J.M.
TI  - Draft Genome Sequence of the Steroid Degrader Rhodococcus ruber Strain Chol-4.
JO  - Genome Announcements
PY  - 2013
SP  - e00215
EP  - e00213
VL  - 1
AB  - The whole-genome shotgun sequence of Rhodococcus ruber strain Chol-4 is presented here. This
AB  - organism was shown to be able to grow using many steroids as the sole carbon and energy
AB  - sources. These sequence data will help us to further explore the metabolic abilities of this
AB  - versatile degrader.
ER  -

TY  - JOUR
AU  - Fernandez-Gonzalez, A.J.
AU  - Lasa, A.V.
AU  - Fernandez-Lopez, M.
TI  - Whole-Genome Sequences of Two Arthrobacter Strains Isolated from a Holm Oak Rhizosphere Affected by Wildfire.
JO  - Genome Announcements
PY  - 2018
SP  - e00071
EP  - e00018
VL  - 6
AB  - We report here the draft genome sequences of two Arthrobacter strains isolated from a holm oak
AB  - forest affected by wildfire. Both strains were shown to act as
AB  - plant growth promoters, with AFG20 being a member of the most abundant group
AB  - found in this soil and AFG7.2 being the strain with the highest indole-3-acetic
AB  - acid production level.
ER  -

TY  - JOUR
AU  - Fernandez-Natal, M.I.
AU  - Soriano, F.
AU  - Acedo, A.
AU  - Hernandez, M.
AU  - Tauch, A.
AU  - Rodriguez-Lazaro, D.
TI  - Draft Genome Sequences of the Two Unrelated Macrolide-Resistant Corynebacterium argentoratense Strains CNM 463/05 and CNM 601/08, Isolated from Patients in the  University Hospital of Leon, Spain.
JO  - Genome Announcements
PY  - 2015
SP  - e00765
EP  - e00715
VL  - 3
AB  - Corynebacterium argentoratense has been associated mainly with infections in the  human
AB  - respiratory tract. Genome sequencing of two unrelated clinical
AB  - macrolide-resistant strains, CNM 463/05 and CNM 601/08, revealed the presence of
AB  - the antibiotic resistance gene erm(X) allocated to a specific genomic region with
AB  - 100% similarity to the widely distributed transposable element Tn5432.
ER  -

TY  - JOUR
AU  - Fernandez-Natal, M.I.
AU  - Soriano, F.
AU  - Ariza-Miguel, J.
AU  - Marrodan-Ciordia, T.
AU  - Acedo, A.
AU  - Hernandez, M.
AU  - Tauch, A.
AU  - Rodriguez-Lazaro, D.
TI  - Draft Genome Sequences of Corynebacterium kroppenstedtii CNM633/14 and CNM632/14, Multidrug-Resistant and Antibiotic-Sensitive Isolates from Nodules of  Granulomatous Mastitis Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e00525
EP  - e00515
VL  - 3
AB  - Corynebacterium kroppenstedtii has been associated with infections of the female  breast.
AB  - Genome sequencing of two strains revealed a specific genomic island in
AB  - the multidrug-resistant isolate CNM633/14 with similarity to the R plasmid
AB  - pJA144188 of Corynebacterium resistens DSM 45100, being indicative of the
AB  - horizontal transfer of antibiotic resistance genes to C. kroppenstedtii.
ER  -

TY  - JOUR
AU  - Fernandez-Orth, D.
AU  - Cosgaya, C.
AU  - Telli, M.
AU  - Mosqueda, N.
AU  - Mari-Almirall, M.
AU  - Roca, I.
AU  - Vila, J.
TI  - Draft Genome Sequence of JVAP01T, the Type Strain of the Novel Species Acinetobacter dijkshoorniae.
JO  - Genome Announcements
PY  - 2017
SP  - e01480
EP  - e01416
VL  - 5
AB  - Here, we report the draft genome sequence of the type strain of Acinetobacter dijkshoorniae, a
AB  - novel human pathogen within the Acinetobacter
AB  - calcoaceticus-Acinetobacter baumannii (ACB) complex. Strain JVAP01T has an
AB  - estimated genome size of 3.9 Mb, exhibits a 38.8% G+C content, and carries a
AB  - plasmid with the blaNDM-1 carbapenemase gene.
ER  -

TY  - JOUR
AU  - Fernandez-Ramirez, M.D.
AU  - Boekhorst, J.
AU  - de Jong, A.
AU  - Kuipers, O.P.
AU  - Abee, T.
AU  - Nierop-Groot, M.N.
TI  - Draft Whole-Genome Sequences of Three Lactobacillus plantarum Food Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e00560
EP  - e00516
VL  - 4
AB  - Lactobacillus plantarum is a widespread member of the Lactobacillus genus and frequently
AB  - isolated from spoiled acidified food products. Here, we report the
AB  - draft genome sequences of three L. plantarum food isolates.
ER  -

TY  - JOUR
AU  - Fernando, D.M.
AU  - Chong, P.
AU  - Singh, M.
AU  - Spicer, V.
AU  - Unger, M.
AU  - Loewen, P.C.
AU  - Westmacott, G.
AU  - Kumar, A.
TI  - Multi-omics approach to study global changes in a triclosan-resistant mutant strain of Acinetobacter baumannii ATCC 17978.
JO  - Int. J. Antimicrob. Agents
PY  - 2017
SP  - 74
EP  - 80
VL  - 49
AB  - Acinetobacter baumannii AB042, a triclosan-resistant mutant strain, was examined
AB  - for modulated gene expression using whole-genome sequencing, transcriptomics and
AB  - proteomics in order to understand the mechanism of triclosan resistance as well
AB  - as its impact on A. baumannii. Data revealed modulated expression of the fatty
AB  - acid metabolism pathway, co-factors known to play a role in the synthesis of
AB  - fatty acids, as well as several transcriptional regulators. The membrane
AB  - composition of the mutant revealed a decrease in C18 with a corresponding
AB  - increase in C16 fatty acids compared with the parent strain A. baumannii ATCC
AB  - 17978. These data indicate that A. baumannii responds to triclosan by altering
AB  - the expression of genes involved in fatty acid metabolism, antibiotic resistance
AB  - and amino acid metabolism.
ER  -

TY  - JOUR
AU  - Fernando, D.M.
AU  - Xu, W.
AU  - Loewen, P.C.
AU  - Zhanel, G.G.
AU  - Kumar, A.
TI  - Triclosan can select for an AdeIJK-overexpressing mutant of Acinetobacter baumannii ATCC 17978 that displays reduced susceptibility to multiple antibiotics.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 6424
EP  - 6431
VL  - 58
AB  - In order to determine if triclosan can select for mutants of Acinetobacter
AB  - baumannii ATCC 17978 that display reduced susceptibilities to antibiotics, we
AB  - isolated a triclosan-resistant mutant, A. baumannii AB042, by serial passaging of
AB  - A. baumannii ATCC 17978 in growth medium supplemented with triclosan. The
AB  - antimicrobial susceptibility of AB042 was analyzed by the 2-fold serial dilution
AB  - method. Expression of five different resistance-nodulation-division (RND)
AB  - pump-encoding genes (adeB, adeG, adeJ, A1S_2818, and A1S_3217), two outer
AB  - membrane porin-encoding genes (carO and oprD), and the MATE family pump-encoding
AB  - gene abeM was analyzed using quantitative reverse transcriptase (qRT) PCR. A.
AB  - baumannii AB042 exhibited elevated resistance to multiple antibiotics, including
AB  - piperacillin-tazobactam, doxycycline, moxifloxacin, ceftriaxone, cefepime,
AB  - meropenem, doripenem, ertapenem, ciprofloxacin, aztreonam, tigecycline, and
AB  - trimethoprim-sulfamethoxazole, in addition to triclosan. Genome sequencing of A.
AB  - baumannii AB042 revealed a (116)G-->V mutation in fabI, the gene encoding the
AB  - target enzyme for triclosan. Expression analysis of efflux pumps showed
AB  - overexpression of the AdeIJK pump, and sequencing of adeN, the gene that encodes
AB  - the repressor of the adeIJK operon, revealed a 73-bp deletion which would cause a
AB  - premature termination of translation, resulting in an inactive truncated AdeN
AB  - protein. This work shows that triclosan can select for mutants of A. baumannii
AB  - that display reduced susceptibilities to multiple antibiotics from chemically
AB  - distinct classes in addition to triclosan resistance. This multidrug resistance
AB  - can be explained by the overexpression of the AdeIJK efflux pump.
ER  -

TY  - JOUR
AU  - Ferreira, A.C.
AU  - Tenreiro, R.
AU  - Correa-de-Sa, M.I.
AU  - Dias, R.
TI  - Complete Genome Sequences of Two Central European Brucella suis bv. 2 Haplotype 2c Strains Isolated from Wild Boars.
JO  - Genome Announcements
PY  - 2014
SP  - e00686
EP  - e00614
VL  - 2
AB  - The Brucella suis haplotype 2c is commonly isolated from wild boars and domestic  pigs across
AB  - Central Europe, though it is rarely described in the Iberian Peninsula. We report here the
AB  - complete and annotated genome sequences of two haplotype 2c strains isolated from wild boars
AB  - in the northeast region of Spain, above the Ebro River.
ER  -

TY  - JOUR
AU  - Ferreira, A.C.
AU  - Tenreiro, R.
AU  - Correa-de-Sa, M.I.
AU  - Dias, R.
TI  - Complete Genome Sequences of Three Iberian Brucella suis Biovar 2 Strains Isolated from Wild Boars.
JO  - Genome Announcements
PY  - 2014
SP  - e00618
EP  - e00614
VL  - 2
AB  - Brucella suis biovar 2 is the most common biovar isolated from wild boars (Sus scrofa)
AB  - associated with transmission to outdoor-reared pigs in Europe. We report here the complete and
AB  - annotated genome sequences of three strains isolated from wild boars in Portugal and Spain and
AB  - belonging to the Iberian clone (haplotypes 2d and 2e).
ER  -

TY  - JOUR
AU  - Ferreira, V.
AU  - Magalhaes, R.
AU  - Almeida, G.
AU  - Cabanes, D.
AU  - Fritzenwanker, M.
AU  - Chakraborty, T.
AU  - Hain, T.
AU  - Teixeira, P.
TI  - Genome Sequence of Listeria monocytogenes 2542, a Serotype 4b Strain from a Cheese-Related Outbreak in Portugal.
JO  - Genome Announcements
PY  - 2018
SP  - e00540
EP  - e00518
VL  - 6
AB  - We report here the draft genome sequence of Listeria monocytogenes 2542, a serotype 4b
AB  - clinical strain recovered from a placental sample during a
AB  - cheese-related listeriosis outbreak in Portugal.
ER  -

TY  - JOUR
AU  - Ferreras, E.R.
AU  - De Maayer, P.
AU  - Makhalanyane, T.P.
AU  - Guerrero, L.D.
AU  - Aislabie, J.M.
AU  - Cowan, D.A.
TI  - Draft Genome Sequence of Microbacterium sp. Strain CH12i, Isolated from Shallow Groundwater in Cape Hallett, Antarctica.
JO  - Genome Announcements
PY  - 2014
SP  - e00789
EP  - e00714
VL  - 2
AB  - The Antarctic continent is largely covered by an expansive ice sheet, but it harbors diverse
AB  - terrestrial and aquatic habitats in the coastal ice-free
AB  - continental margins. Here we present the draft genome of Microbacterium sp.
AB  - CH12i, which was isolated from hypersaline, alkaline, and nutrient-rich
AB  - groundwater from Cape Hallett, northern Victoria Land, Antarctica.
ER  -

TY  - JOUR
AU  - Ferretti, J.J. et al.
TI  - Complete genome sequence of an M1 strain of Streptococcus pyogenes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 4658
EP  - 4663
VL  - 98
AB  - The 1,852,442-bp sequence of an M1 strain of Streptococcus pyogenes, a Gram-positive pathogen,
AB  - has been determined and contains 1,752 predicted protein-encoding genes. Approximately
AB  - one-third of these genes have no identifiable function, with the remainder falling into
AB  - previously characterized categories of known microbial function. Consistent with the
AB  - observation that S. pyogenes is responsible for a wider variety of human disease than any
AB  - other bacterial species, more than 40 putative virulence-associated genes have been
AB  - identified. Additional genes have been identified that encode proteins likely associated with
AB  - microbial "molecular mimicry" of host characteristics and involved in rheumatic fever or acute
AB  - glomerulonephritis. The complete or partial sequence of four different bacteriophage genomes
AB  - is also present, with each containing genes for one or more previously undiscovered
AB  - superantigen-like proteins. These prophage-associated genes encode at least six potential
AB  - virulence factors, emphasizing the importance of bacteriophages in horizontal gene transfer
AB  - and a possible mechanism for generating new strains with increased pathogenic potential.
ER  -

TY  - JOUR
AU  - Ferrin, L.J.
AU  - Camerini-Otero, R.D.
TI  - Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage.
JO  - Science
PY  - 1991
SP  - 1494
EP  - 1497
VL  - 254
AB  - Current methods for sequence-specific cleavage of large segments of DNA are
AB  - severely limited because of the paucity of possible cleavage sites.  A method
AB  - is described whereby any EcoRI site can be targeted for specific cleavage.  The
AB  - technique is based on the ability of RecA protein from Escherichia coli to pair
AB  - an oligonucleotide to its homologous sequence in duplex DNA and to form a
AB  - three-stranded complex.  This complex is protected from EcoRI methylase; after
AB  - methylation and RecA protein removal, EcoRI restriction enzyme cleavage was
AB  - limited to the site previously protected from methylation.  When pairs of
AB  - oligonucleotides are used, a specific fragment can be cleaved out of genomes.
AB  - The method was tested on lambda phage, Escherichia coli, and human DNA.
AB  - Fragments exceeding 500 kilobases in length and yields exceeding 80 percent
AB  - could be obtained.
ER  -

TY  - JOUR
AU  - Ferris, P.J.
AU  - Vogt, V.M.
TI  - Structure of the central spacer region of extrachromosomal ribosomal DNA in Physarum polycephalum.
JO  - J. Mol. Biol.
PY  - 1982
SP  - 359
EP  - 381
VL  - 159
AB  - We have analyzed the sequence organization of the central spacer region of the
AB  - extrachromosomal ribosomal DNA from two strains of the acellular slime mold
AB  - Physarum polycephalum.  It had been inferred previously from electron
AB  - microscopy that this region, which comprises about one third of the 60 kb++
AB  - palindromic rDNA, contains a complex series of inverted repetitious sequences.
AB  - By partial digestion of end-labeled fragments isolated from purified rDNA and
AB  - from rDNA fragments cloned in Escherichia coli, we have constructed a detailed
AB  - restriction map of this region.  The 22 kb of spacer DNA of each half molecule
AB  - of rDNA contains the following elements:  (a) two separate regions, one of 1.1
AB  - kb and one of 2.1 kb, composed of many direct repeats of the same 30 base-pair
AB  - unit; (b) a region of 4.4 kb composed of a complex series of inverted repeats
AB  - of a 310 base-pair unit; (c) another region of 1.6 kb composed of inverted
AB  - repeats of the same 310 base-pair unit located directly adjacent to the center
AB  - of the rDNA; (d) two copies of a unique sequence of 0.85 kb, which probably
AB  - cocntains a replication origin.  Some of the CpG sequences in the spacer resist
AB  - cleavage by certain restriction endonucleases and thus appear to be methylated.
AB  - The lack of perfect symmetry about the central axis and the arrangement of
AB  - inverted repeated sequences explain the complex pattern of branches and forks
AB  - of the fold-back molecules previously observed by electron microscopy.
AB  - Comparison of the rDNA restriction maps from the two strains of Physarum
AB  - suggests that the repeat units in the spacer are undergoing concerted
AB  - evolution.  We propose a model to explain the evolutionary origin of the
AB  - several palindromic axes in the Physarum rDNA spacer.
ER  -

TY  - JOUR
AU  - Ferrucci, L.
AU  - Rossino, R.
AU  - Mezzanotee, R.
TI  - Factors affecting the digestion of restriction endonucleases in situ.
JO  - Cytobios
PY  - 1991
SP  - 45
EP  - 51
VL  - 68
AB  - The influence of incubation buffers and glycerol on the enzyme activity of naked DNA of lambda
AB  - phage and mouse, and of mouse chromosomal DNA was investigated. The results obtained varied in
AB  - part from previously known data, but confirmed the importance of these factors in determining
AB  - the patterns of in situ restriction enzyme digestion so far attributed exclusively to
AB  - endonuclease activity.
ER  -

TY  - JOUR
AU  - Fettweis, J.M.
AU  - Serrano, M.G.
AU  - Huang, B.
AU  - Brooks, J.P.
AU  - Glascock, A.L.
AU  - Sheth, N.U.
AU  - Strauss, J.F. III
AU  - Jefferson, K.K.
AU  - Buck, G.A.
TI  - An emerging Mycoplasma associated with trichomoniasis, vaginal infection and disease.
JO  - PLoS ONE
PY  - 2014
SP  - E110943
EP  - E110943
VL  - 9
AB  - Humans are colonized by thousands of bacterial species, but it is difficult to
AB  - assess the metabolic and pathogenic potential of the majority of these because
AB  - they have yet to be cultured. Here, we characterize an uncultivated vaginal
AB  - mycoplasma tightly associated with trichomoniasis that was previously known by
AB  - its 16S rRNA sequence as "Mnola." In this study, the mycoplasma was found almost
AB  - exclusively in women infected with the sexually transmitted pathogen Trichomonas
AB  - vaginalis, but rarely observed in women with no diagnosed disease. The genomes of
AB  - four strains of this species were reconstructed using metagenome sequencing and
AB  - assembly of DNA from four discrete mid-vaginal samples, one of which was obtained
AB  - from a pregnant woman with trichomoniasis who delivered prematurely. These
AB  - bacteria harbor several putative virulence factors and display unique metabolic
AB  - strategies. Genes encoding proteins with high similarity to potential virulence
AB  - factors include two collagenases, a hemolysin, an O-sialoglycoprotein
AB  - endopeptidase and a feoB-type ferrous iron transport system. We propose the name
AB  - "Candidatus Mycoplasma girerdii" for this potential new pathogen.
ER  -

TY  - JOUR
AU  - Fevre, C.
AU  - Passet, V.
AU  - Deletoile, A.
AU  - Barbe, V.
AU  - Frangeul, L.
AU  - Almeida, A.S.
AU  - Sansonetti, P.
AU  - Tournebize, R.
AU  - Brisse, S.
TI  - PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma.
JO  - PLoS Neglected Trop. Dis.
PY  - 2011
SP  - E1052
EP  - E1052
VL  - 5
AB  - Rhinoscleroma is a chronic granulomatous infection of the upper airways caused by
AB  - the bacterium Klebsiella pneumoniae subsp. rhinoscleromatis. The disease is
AB  - endemic in tropical and subtropical areas, but its diagnosis remains difficult.
AB  - As a consequence, and despite available antibiotherapy, some patients evolve
AB  - advanced stages that can lead to disfiguration, severe respiratory impairment and
AB  - death by anoxia. Because identification of the etiologic agent is crucial for the
AB  - definitive diagnosis of the disease, the aim of this study was to develop two
AB  - simple PCR assays. We took advantage of the fact that all Klebsiella pneumoniae
AB  - subsp. rhinoscleromatis isolates are (i) of capsular serotype K3; and (ii) belong
AB  - to a single clone with diagnostic single nucleotide polymorphisms (SNP). The
AB  - complete sequence of the genomic region comprising the capsular polysaccharide
AB  - synthesis (cps) gene cluster was determined. Putative functions of the 21 genes
AB  - identified were consistent with the structure of the K3 antigen. The K3-specific
AB  - sequence of gene Kr11509 (wzy) was exploited to set up a PCR test, which was
AB  - positive for 40 K3 strains but negative when assayed on the 76 other Klebsiella
AB  - capsular types. Further, to discriminate Klebsiella pneumoniae subsp.
AB  - rhinoscleromatis from other K3 Klebsiella strains, a specific PCR assay was
AB  - developed based on diagnostic SNPs in the phosphate porin gene phoE. This work
AB  - provides rapid and simple molecular tools to confirm the diagnostic of
AB  - rhinoscleroma, which should improve patient care as well as knowledge on the
AB  - prevalence and epidemiology of rhinoscleroma.
ER  -

TY  - JOUR
AU  - Ffrench-Constant, R.H.
AU  - Waterfield, N.
AU  - Burland, V.
AU  - Perna, N.T.
AU  - Daborn, P.J.
AU  - Bowen, D.
AU  - Blattner, F.R.
TI  - A genomic sample sequence of the entomopathogenic bacterium Photorhabdus luminescens W14: Potential implications for virulence.
JO  - Appl. Environ. Microbiol.
PY  - 2000
SP  - 3310
EP  - 3329
VL  - 66
AB  - Photorhabdus luminescens is a pathogenic bacterium that lives in the guts of insect-pathogenic
AB  - nematodes. After invasion of an insect host
AB  - by a nematode, bacteria are released from the nematode gut and help
AB  - kill the insect, in which both the bacteria and the nematodes
AB  - subsequently replicate. However, the bacterial virulence factors
AB  - associated with this 'symbiosis of pathogens' remain largely obscure.
AB  - In order to identify genes encoding potential virulence factors, we
AB  - performed approximately 2,000 random sequencing reads from a P.
AB  - luminescens W14 genomic library. We then compared the sequences
AB  - obtained to sequences in existing gene databases and to the Escherichia
AB  - coli K-12 genome sequence. Here we describe the different classes of
AB  - potential virulence factors found. These factors include genes that
AB  - putatively encode Tc insecticidal toxin complexes, Rbi-like toxins,
AB  - proteases and lipases, colicin and pyocins, and various antibiotics.
AB  - They also include a diverse array of secretion (e.g., type III), iron
AB  - uptake, and lipopolysaccharide production systems. We speculate on the
AB  - potential functions of each of these gene classes in insect infection
AB  - and also examine the extent to which the invertebrate pathogen P,
AB  - luminescens shares potential antivertebrate virulence factors. The
AB  - implications for understanding both the biology of this insect pathogen
AB  - and links between the evolution of vertebrate virulence factors and the
AB  - evolution of invertebrate virulence factors are discussed.
ER  -

TY  - JOUR
AU  - Fiala, E.S.
AU  - Staretz, M.E.
AU  - Pandya, G.
AU  - El-Bayoumy, K.
AU  - Hamilton, S.R.
TI  - Inhibition of DNA (cytosine-5) methyltransferase (Mtase) by selenium compounds, determined by an improved method for Mtase and global DNA methylation.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1998
SP  - 88
EP  - 88
VL  - 39
AB  - Organoselenium compounds such as benzyl selenocyanate and
AB  - 1,4-phenylenebis(methylene)selenocyanate are efficient chemopreventive agents, inhibiting a
AB  - variety of chemically induced tumors in animal models at both the initiation and
AB  - postinitiation stages.  Because several lines of evidence suggest that inhibition of Mtase in
AB  - tumor cells may be a sufficient condition for the suppression or reversion of carcinogenesis,
AB  - we examined the effects of sodium selenite, BSC, p-XSC and benzyl thiocyanate on Mtase
AB  - activity in extracts from human colon carcinomas, and in HCT116 human colon carcinoma cells in
AB  - culture.  For this purpose, we developed an improved assay of the enzyme, in which label
AB  - derived from S-adenosyl[methyl-3H]methionine is specifically determined in
AB  - 5-methyldeoxycytidine by HPLC with radioflow detection.  Selenite, BSC and p-XSC inhibited
AB  - Mtase extracted from a human colon carcinoma with IC50s of 3.8, 8.1, and 5.2 uM, respectively.
AB  - BTC had no effect.  Selenite, BSC and p-XSC also strongly inhibited the growth and Mtase
AB  - activity of HCT116 cells.  We suggest that inhibition of Mtase may be central to the mechanism
AB  - of chemoprevention by selenium compounds at the stage of postinitiation.
ER  -

TY  - JOUR
AU  - Fiala, E.S.
AU  - Staretz, M.E.
AU  - Pandya, G.A.
AU  - El-Bayoumy, K.
AU  - Hamilton, S.R.
TI  - Inhibition of DNA cytosine methyltransferase by chemopreventive selenium compounds, determined by an improved assay for DNA cytosine methyltransferase and DNA cytosine methylation.
JO  - Carcinogenesis
PY  - 1998
SP  - 597
EP  - 604
VL  - 19
AB  - The organoselenium compounds benzyl selenocyanate and 1,4-phenylenebis(methylene)selenocyanate
AB  - as well as sodium selenite, are effective chemopreventive agents for various chemically
AB  - induced tumors in animal models at both the initiation and postinitiation stages.  The
AB  - mechanisms involved at the postinitiation stage are not clear.  Because several lines of
AB  - evidence indicate that inhibition of excess DNA (cytosine-5)-methyltransferase may be a
AB  - sufficient factor for the suppression or reversion of carcinogenesis, we examined the effects
AB  - of sodium selenite, Bsc, p-XSC and benzyl thiocyanate, the sulfur analog of BSC, on Mtase
AB  - activity in nuclear extracts of human colon carcinomas, and of p-XSC on the Mtase activity of
AB  - HCT116 human colon carcinoma cells in culture.  For this purpose, we developed an improved
AB  - Mtase assay, in which the incorporation of the methyl-[3-H] group from
AB  - S-adenosyl[methyl-3H]methionine into deoxycytidine of poly(dI-dC)-poly(dI-dC), is specifically
AB  - determined by HPLC with radioflow detection after enzymatic hydrolysis, enhancing specificity
AB  - and reliability.  In a variation, using SssI methyltransferase and labeled
AB  - S-adenosylmethionine, the overall methylation status of DNA in various tissues can also be
AB  - compared. Selenite, BSC and p-XSC inhibited Mtase extracted from a human colon carcinoma with
AB  - IC50S of 3.8, 8.1 and 5.2 uM, respectively; BTC had no effect.  P-XSC also inhibited the Mtase
AB  - activity and growth of human colon carcinoma HCT116 cells, with an IC50 of ~20 uM.  The
AB  - improved Mtase assay should prove to be a reliable method for screening potential Mtase
AB  - inhibitors, especially using cells in culture.  We suggest that inhibition of Mtase may be a
AB  - major mechanism of chemoprevention by selenium compounds at the postinitiation stage of
AB  - carcinogenesis.
ER  -

TY  - JOUR
AU  - Fiebig, A.
AU  - Pradella, S.
AU  - Petersen, J.
AU  - Michael, V.
AU  - Pauker, O.
AU  - Rohde, M.
AU  - Goker, M.
AU  - Klenk, H.P.
AU  - Wagner-Dobler, I.
TI  - Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 440
EP  - 448
VL  - 7
AB  - Hoeflea phototrophica Biebl et al. 2006 is a member of the family Phyllobacteriaceae in the
AB  - order Rhizobiales, which is thus far only partially
AB  - characterized at the genome level. This marine bacterium contains the
AB  - photosynthesis reaction-center genes pufL and pufM and is of interest because it
AB  - lives in close association with toxic dinoflagellates such as Prorocentrum lima.
AB  - The 4,467,792 bp genome (permanent draft sequence) with its 4,296 protein-coding
AB  - and 69 RNA genes is a part of the Marine Microbial Initiative.
ER  -

TY  - JOUR
AU  - Fiebig, A.
AU  - Pradella, S.
AU  - Petersen, J.
AU  - Pauker, O.
AU  - Michael, V.
AU  - Lunsdorf, H.
AU  - Goker, M.
AU  - Klenk, H.P.
AU  - Wagner-Dobler, I.
TI  - Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 413
EP  - 426
VL  - 7
AB  - Labrenzia alexandrii Biebl et al. 2007 is a marine member of the family Rhodobacteraceae in
AB  - the order Rhodobacterales, which has thus far only partially
AB  - been characterized at the genome level. The bacterium is of interest because it
AB  - lives in close association with the toxic dinoflagellate Alexandrium lusitanicum.
AB  - Ultrastructural analysis reveals R-bodies within the bacterial cells, which are
AB  - primarily known from obligate endosymbionts that trigger 'killing traits' in
AB  - ciliates (Paramecium spp.). Genomic traits of L. alexandrii DFL-11(T) are in
AB  - accordance with these findings, as they include the reb genes putatively involved
AB  - in R-body synthesis. Analysis of the two extrachromosomal elements suggests a
AB  - role in heavy-metal resistance and exopolysaccharide formation, respectively. The
AB  - 5,461,856 bp long genome with its 5,071 protein-coding and 73 RNA genes consists
AB  - of one chromosome and two plasmids, and has been sequenced in the context of the
AB  - Marine Microbial Initiative.
ER  -

TY  - JOUR
AU  - Fiebig, A.
AU  - Riedel, T.
AU  - Gronow, S.
AU  - Petersen, J.
AU  - Klenk, H.P.
AU  - Goker, M.
TI  - Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 480
EP  - 490
VL  - 8
AB  - Rubellimicrobium thermophilum Denner et al. 2006 is the type species of the genus
AB  - Rubellimicrobium, a representative of the Roseobacter clade within the
AB  - Rhodobacteraceae. Members of this clade were shown to be abundant especially in
AB  - coastal and polar waters, but were also found in microbial mats and sediments.
AB  - They are metabolically versatile and form a physiologically heterogeneous group
AB  - within the Alphaproteobacteria. Strain C-Ivk-R2A-2(T) was isolated from colored
AB  - deposits in a pulp dryer; however, its natural habitat is so far unknown. Here we
AB  - describe the features of this organism, together with the draft genome sequence
AB  - and annotation and novel aspects of its phenotype. The 3,161,245 bp long genome
AB  - contains 3,243 protein-coding and 45 RNA genes.
ER  -

TY  - JOUR
AU  - Fiedler, G.
AU  - Brinks, E.
AU  - Bohnlein, C.
AU  - Cho, G.S.
AU  - Koberg, S.
AU  - Kabisch, J.
AU  - Franz, C.M.A.P.
TI  - Draft Genome Sequence of the Intimin-Positive Enteropathogenic Escherichia albertii Strain MBT-EA1, Isolated from Lettuce.
JO  - Genome Announcements
PY  - 2018
SP  - e00255
EP  - e00218
VL  - 6
AB  - The genome of the intimin (eae)-harboring Escherichia albertii strain MBT-EA1, isolated from
AB  - lettuce in Germany, was sequenced. Sequence analysis showed the
AB  - assembled draft genome size to be 4,560,948 bp, containing a predicted total of
AB  - 4,414 protein-encoding genes, 11 rRNAs, and 82 tRNAs. Furthermore, three plasmid
AB  - sequences were found.
ER  -

TY  - JOUR
AU  - Fiedler, S.
AU  - Bender, J.K.
AU  - Klare, I.
AU  - Halbedel, S.
AU  - Grohmann, E.
AU  - Szewzyk, U.
AU  - Werner, G.
TI  - Tigecycline resistance in clinical isolates of Enterococcus faecium is mediated by an upregulation of plasmid-encoded tetracycline determinants tet(L) and tet(M).
JO  - J. Antimicrob. Chemother.
PY  - 2015
SP  - 871
EP  - 881
VL  - 71
AB  - OBJECTIVES: Tigecycline represents one of the last-line therapeutics to combat
AB  - multidrug-resistant bacterial pathogens, including VRE and MRSA. The German National Reference
AB  - Centre for Staphylococci and Enterococci has received 73 tigecycline-resistant Enterococcus
AB  - faecium and Enterococcus faecalis isolates in recent years. The precise mechanism of how
AB  - enterococci become resistant to tigecycline remains undetermined. This study documents an
AB  - analysis of the role of efflux pumps in tigecycline resistance in clinical isolates of
AB  - Enterococcus spp. METHODS: Various tigecycline MICs were found for the different isolates
AB  - analysed. Tigecycline-resistant strains were analysed with respect to genome and transcriptome
AB  - differences by means of WGS and RT-qPCR. Genes of interest were cloned and expressed in
AB  - Listeria monocytogenes for verification of their functionality. RESULTS: Detailed comparative
AB  - whole-genome analyses of three isogenic strains, showing different levels of tigecycline
AB  - resistance, revealed the major facilitator superfamily (MFS) efflux pump TetL and the
AB  - ribosomal protection protein TetM as possible drug resistance proteins. Subsequent RT-qPCR
AB  - confirmed up-regulation of the respective genes. A correlation of gene copy number and level
AB  - of MIC was inferred from further qPCR analyses. Expression of both tet(L) and tet(M) in L.
AB  - monocytogenes unequivocally demonstrated the potential to increase tigecycline MICs upon
AB  - acquisition of either locus. CONCLUSIONS: Our results indicate that increased expression of
AB  - two tetracycline resistance determinants, a tet(L)-encoded MFS pump and a tet(M)-encoded
AB  - ribosomal protection protein, is capable of conferring tigecycline resistance in enterococcal
AB  - clinical isolates.
ER  -

TY  - JOUR
AU  - Fiedoruk, K.
AU  - Daniluk, T.
AU  - Swiecicka, I.
AU  - Murawska, E.
AU  - Sciepuk, M.
AU  - Leszczynska, K.
TI  - First Complete Genome Sequence of Escherichia albertii Strain KF1, a New Potential Human Enteric Pathogen.
JO  - Genome Announcements
PY  - 2014
SP  - e00004
EP  - e00014
VL  - 2
AB  - Escherichia albertii has been recently recognized as an emerging human and bird enteric
AB  - pathogen. Here, we report the first complete chromosome nucleotide
AB  - sequence of a clinical isolate of E. albertii strain KF1, which may provide
AB  - information about the pathogenic potential of this new species and the mechanisms
AB  - of evolution of enteropathogenic Escherichia spp.
ER  -

TY  - JOUR
AU  - Field, D. et al.
TI  - The minimum information about a genome sequence (MIGS) specification.
JO  - Nat. Biotechnol.
PY  - 2008
SP  - 541
EP  - 547
VL  - 26
AB  - With the quantity of genomic data increasing at an exponential rate, it is imperative that
AB  - these data be captured electronically, in a standard
AB  - format. Standardization activities must proceed within the auspices of
AB  - open-access and international working bodies. To tackle the issues
AB  - surrounding the development of better descriptions of genomic
AB  - investigations, we have formed the Genomic Standards Consortium (GSC).
AB  - Here, we introduce the minimum information about a genome sequence (MIGS)
AB  - specification with the intent of promoting participation in its
AB  - development and discussing the resources that will be required to develop
AB  - improved mechanisms of metadata capture and exchange. As part of its wider
AB  - goals, the GSC also supports improving the 'transparency' of the
AB  - information contained in existing genomic databases.
ER  -

TY  - JOUR
AU  - Fierer, N.
AU  - Breitbart, M.
AU  - Nulton, J.
AU  - Salamon, P.
AU  - Lozupone, C.
AU  - Jones, R.
AU  - Robeson, M.
AU  - Edwards, R.A.
AU  - Felts, B.
AU  - Rayhawk, S.
AU  - Knight, R.
AU  - Rohwer, F.
AU  - Jackson, R.B.
TI  - Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 7059
EP  - 7066
VL  - 73
AB  - Recent studies have highlighted the surprising richness of soil bacterial
AB  - communities; however, bacteria are not the only microorganisms found in
AB  - soil. To our knowledge, no study has compared the diversities of the four
AB  - major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an
AB  - individual soil sample. We used metagenomic and small-subunit RNA-based
AB  - sequence analysis techniques to compare the estimated richness and
AB  - evenness of these groups in prairie, desert, and rainforest soils. By
AB  - grouping sequences at the 97% sequence similarity level (an operational
AB  - taxonomic unit [OTU]), we found that the archaeal and fungal communities
AB  - were consistently less even than the bacterial communities. Although total
AB  - richness levels are difficult to estimate with a high degree of certainty,
AB  - the estimated number of unique archaeal or fungal OTUs appears to rival or
AB  - exceed the number of unique bacterial OTUs in each of the collected soils.
AB  - In this first study to comprehensively survey viral communities using a
AB  - metagenomic approach, we found that soil viruses are taxonomically diverse
AB  - and distinct from the communities of viruses found in other environments
AB  - that have been surveyed using a similar approach. Within each of the four
AB  - microbial groups, we observed minimal taxonomic overlap between sites,
AB  - suggesting that soil archaea, bacteria, fungi, and viruses are globally as
AB  - well as locally diverse.
ER  -

TY  - JOUR
AU  - Fierst, J.L.
AU  - Murdock, D.A.
AU  - Thanthiriwatte, C.
AU  - Willis, J.H.
AU  - Phillips, P.C.
TI  - Metagenome-Assembled Draft Genome Sequence of a Novel Microbial Stenotrophomonas  maltophilia Strain Isolated from Caenorhabditisremanei Tissue.
JO  - Genome Announcements
PY  - 2017
SP  - e01646
EP  - e01616
VL  - 5
AB  - Stenotrophomonas maltophilia is a Gram-negative aerobic bacterium and emerging nosocomial
AB  - pathogen. Here, we present a draft genome sequence for an S.
AB  - maltophilia strain assembled from a metagenomic DNA extract isolated from a
AB  - laboratory stock of the nematode worm Caenorhabditis remanei.
ER  -

TY  - JOUR
AU  - Figueiredo, C.
AU  - Quint, W.G.
AU  - Sanna, R.
AU  - Sablon, E.
AU  - Donahue, J.P.
AU  - Xu, Q.
AU  - Miller, G.G.
AU  - Peek, R.M.
AU  - Blaser, M.J.
AU  - van Doorn, L.
TI  - Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori.
JO  - Gene
PY  - 2000
SP  - 59
EP  - 68
VL  - 246
AB  - The genetic organization and sequence heterogeneity of the iceA locus of Helicobacter pylori
AB  - was studied, and the existence of two distinct gene families, iceA1 and iceA2, at this locus
AB  - was confirmed. iceA1 has significant sequence homology to nlaIIIR, encoding an endonuclease in
AB  - Neisseria lactamica, but the similarity at the protein level is limited, due to frameshift
AB  - mutations of iceA1 in most H. pylori strains. In only five of the 19 iceA1 strains studied, a
AB  - full-length open reading frame (ORF), capable of encoding a 228aa protein, with 52% homology
AB  - to NlaIII was observed. The region upstream of iceA2 is highly variable in length, containing
AB  - up to 15 copies of 8bp tandem repeats. iceA2 can encode proteins of 24, 59, 94, or 129 amino
AB  - acids, consisting of 14 and 10aa domains, conserved in all iceA2 strains, flanking 0, 1, 2, or
AB  - 3 copies of a 35aa cassette. This 35aa cassette consists of domains of 13, 16 and 6aa,
AB  - respectively. The 13aa and 6aa domains are highly conserved, but the 16aa domain exists in two
AB  - variants. In total, five distinct iceA2 subtypes were defined. Database searches did not
AB  - reveal any homologous sequences. Recombinant IceA1 and IceA2 proteins were expressed in
AB  - Escherichia coli, confirming the predicted ORFs. Genotype-specific PCR primers permitted iceA
AB  - genotyping in 318 (99.1%) of a worldwide collection of 321 H. pylori strains. The conserved
AB  - sizes of the amplification products confirmed the worldwide distribution of discrete variants
AB  - of iceA1 and iceA2.
ER  -

TY  - JOUR
AU  - Figueiredo, H.C.
AU  - Leal, C.A.
AU  - Dorella, F.A.
AU  - Carvalho, A.F.
AU  - Soares, S.C.
AU  - Pereira, F.L.
AU  - Azevedo, V.A.
TI  - Complete Genome Sequences of Fish Pathogenic Weissella ceti Strains WS74 and WS105.
JO  - Genome Announcements
PY  - 2014
SP  - e01014
EP  - e01014
VL  - 2
AB  - We describe here the genome sequencing and annotation of Weissella ceti strains WS74 and
AB  - WS105, isolated from diseased rainbow trout in Brazil. The two genomes
AB  - were sequenced with an Ion Torrent personal genome machine (PGM) using a fragment
AB  - library. The genomes of strains WS74 and WS105 consist of circular chromosomes
AB  - 1,389,513 bp and 1,390,396 bp long, respectively, both presenting a G+C content
AB  - of 40.75%.
ER  -

TY  - JOUR
AU  - Figueiredo, H.C.
AU  - Leal, C.A.
AU  - Pereira, F.L.
AU  - Soares, S.C.
AU  - Goncalves, L.A.
AU  - Dorella, F.A.
AU  - Carvalho, A.F.
AU  - Azevedo, V.A.
TI  - Whole-Genome Sequence of Francisella noatunensis subsp. orientalis Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01603
EP  - e01615
VL  - 4
AB  - This paper describes the complete genome sequence of Francisella noatunensis subsp. orientalis
AB  - strain FNO01, which was isolated during the first outbreak of
AB  - francisellosis in cultured Nile tilapia in Brazil. The genome is composed of a
AB  - circular chromosome with 1,859,830 bp and a G+C content of ~32%.
ER  -

TY  - JOUR
AU  - Figueiredo, H.C.
AU  - Leal, G.
AU  - Pereira, F.L.
AU  - Soares, S.C.
AU  - Dorella, F.A.
AU  - Carvalho, A.F.
AU  - Pereira, U.P.
AU  - Azevedo, V.A.
TI  - Whole-Genome Sequence of Weissella ceti Strain WS08, Isolated from Diseased Rainbow Trout in Brazil.
JO  - Genome Announcements
PY  - 2014
SP  - e00851
EP  - e00814
VL  - 2
AB  - We report here the complete genome sequence of Weissella ceti strain WS08, an emerging
AB  - pathogen to farm-raised rainbow trout. The genome of strain WS08 is
AB  - composed of a circular chromosome with 1,355,853 bp and a G+C content of 40.78%.
ER  -

TY  - JOUR
AU  - Figueiredo, S.C.
AU  - Neves-Borges, A.C.
AU  - Coelho, A.
TI  - The neuraminidase gene is present in the non-toxigenic Vibrio cholerae Amazonia strain: a different allele in comparison to the pandemic strains.
JO  - Memorias do Instituto Oswaldo Cruz
PY  - 2005
SP  - 563
EP  - 569
VL  - 100
AB  - The neuraminidase gene, nanH, is present in the O1, non-toxigenic Vibrio
AB  - cholerae Amazonia strain. Its location has been assigned to a 150 kb NotI
AB  - DNA fragment, with the use of pulsed-field gel electrophoresis and DNA
AB  - hybridization. This NotI fragment is positioned inside 630 kb SfiI and
AB  - 1900 kb I-CeuI fragments of chromosome 1. Association of the pathogenicity
AB  - island VPI-2, carrying nanH and other genes, with toxigenic strains has
AB  - been described by other authors. The presence of nanH in a non-toxigenic
AB  - strain is an exception to this rule. The Amazonia strain nanH was
AB  - sequenced (Genbank accession No. AY825932) and compared to available V.
AB  - cholerae sequences. The sequence is different from those of pandemic
AB  - strains, with 72 nucleotide substitutions. This is the first description
AB  - of an O1 strain with a different nanH allele. The most variable domain of
AB  - the Amazonia NanH is the second lectin wing, comprising 13 out of 17 amino
AB  - acid substitutions. Based on the presence of nanH in the same region of
AB  - the genome, and similarity of the adjacent sequences to VPI-2 sequences,
AB  - it is proposed that the pathogenicity island VPI-2 is present in this
AB  - strain.
ER  -

TY  - JOUR
AU  - Figueiredo, T.A.
AU  - Aguiar, S.I.
AU  - Melo-Cristino, J.
AU  - Ramirez, M.
TI  - DNA methylase activity as a marker for the presence of a family of phage-like elements conferring efflux-mediated macrolide resistance in  streptococci.
JO  - Antimicrob. Agents Chemother.
PY  - 2006
SP  - 3689
EP  - 3694
VL  - 50
AB  - Recently, two related chimeric genetic elements (Tn1207.3 and Phi10394.4) were shown to carry
AB  - the macrolide efflux gene mef in Streptococcus
AB  - pyogenes (group A streptococci [GAS]). The dissemination of elements
AB  - belonging to the Tn1207.3/Phi10394.4 family in recent isolates of GAS,
AB  - Streptococcus dysgalactiae subsp. equisimilis, Streptococcus pneumoniae,
AB  - and Streptococcus agalactiae recovered in Portugal was surveyed. In total,
AB  - 149 GAS, 18 S. pneumoniae, 4 S. dysgalactiae subsp. equisimilis, and 5 S.
AB  - agalactiae isolates from infections, presenting the M phenotype of
AB  - macrolide resistance and containing the mef gene, were screened for the
AB  - presence of Tn1207.3/Phi10394.4 by PCR targeting open reading frames
AB  - (ORFs) specific for these related elements. All the GAS isolates tested
AB  - and one of the S. dysgalactiae subsp. equisimilis isolates carried
AB  - Tn1207.3. However, neither of these elements was found in the isolates of
AB  - the other streptococcal species. It was also noted that the DNAs of the
AB  - isolates carrying Tn1207.3 were resistant to cleavage by the endonuclease
AB  - SmaI. Cloning and expression of ORF12 of Tn1207.3 in Escherichia coli
AB  - showed that it encoded a methyltransferase that rendered DNA refractory to
AB  - cleavage by SmaI (M.Spy10394I). Using this characteristic as a marker for
AB  - the presence of the Tn1207.3/Phi10394.4 family, we reviewed the literature
AB  - and concluded that these genetic elements are widely distributed among
AB  - tetracycline-susceptible GAS isolates presenting the M phenotype from
AB  - diverse geographic origins and may have played an important role in the
AB  - dissemination of macrolide resistance in this species.
ER  -

TY  - JOUR
AU  - Filippidou, S.
AU  - Jaussi, M.
AU  - Junier, T.
AU  - Wunderlin, T.
AU  - Jeanneret, N.
AU  - Regenspurg, S.
AU  - Li, P.E.
AU  - Lo, C.C.
AU  - Johnson, S.
AU  - McMurry, K.
AU  - Gleasner, C.D.
AU  - Vuyisich, M.
AU  - Chain, P.S.
AU  - Junier, P.
TI  - Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir.
JO  - Genome Announcements
PY  - 2015
SP  - e00981
EP  - e00915
VL  - 3
AB  - The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus.
AB  - This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The
AB  - availability of this genome can contribute  to the clarification of the taxonomy of the
AB  - closely related Anoxybacillus, Geobacillus, and Aeribacillus genera.
ER  -

TY  - JOUR
AU  - Filippidou, S.
AU  - Jaussi, M.
AU  - Junier, T.
AU  - Wunderlin, T.
AU  - Roussel-Delif, L.
AU  - Jeanneret, N.
AU  - Vieth-Hillebrand, A.
AU  - Vetter, A.
AU  - Regenspurg, S.
AU  - Johnson, S.L.
AU  - McMurry, K.
AU  - Gleasner, C.D.
AU  - Lo, C.C.
AU  - Li, P.
AU  - Vuyisich, M.
AU  - Chain, P.S.
AU  - Junier, P.
TI  - Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species.
JO  - Genome Announcements
PY  - 2015
SP  - e00575
EP  - e00515
VL  - 3
AB  - Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium
AB  - isolated from filter deposits in a geothermal site. This novel species
AB  - has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species,
AB  - and it possesses genes that support its phenotypic metabolic characterization and
AB  - suggest an intriguing link to metals.
ER  -

TY  - JOUR
AU  - Filippidou, S.
AU  - Wunderlin, T.
AU  - Junier, T.
AU  - Jeanneret, N.
AU  - Johnson, S.
AU  - McMurry, K.
AU  - Gleasner, C.D.
AU  - Lo, C.C.
AU  - Li, P.E.
AU  - Vuyisich, M.
AU  - Chain, P.S.
AU  - Junier, P.
TI  - Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent.
JO  - Genome Announcements
PY  - 2015
SP  - e00982
EP  - e00915
VL  - 3
AB  - Bacillus alveayuensis strain 24KAM51 was isolated from a marine hydrothermal vent in Milos,
AB  - Greece. Its genome depicts interesting features of halotolerance and resistance to heavy
AB  - metals.
ER  -

TY  - JOUR
AU  - Filippini, M.
AU  - Qi, W.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Smits, T.H.
AU  - Bagheri, H.C.
TI  - Genome Sequence of Fibrella aestuarina BUZ 2T, a Filamentous Marine Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3555
EP  - 3555
VL  - 194
AB  - Fibrella aestuarina BUZ 2(T) is the type strain of the recently characterized genus Fibrella.
AB  - Here we report the draft genome sequence of this strain, which
AB  - consists of a single scaffold representing the chromosome (with 11 gaps) and a
AB  - 161-kb circular plasmid.
ER  -

TY  - JOUR
AU  - Filippini, M.
AU  - Qi, W.
AU  - Jaenicke, S.
AU  - Goesmann, A.
AU  - Smits, T.H.
AU  - Bagheri, H.C.
TI  - Genome Sequence of the Filamentous Bacterium Fibrisoma limi BUZ 3T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4445
EP  - 4445
VL  - 194
AB  - Fibrisoma limi strain BUZ 3(T), a Gram-negative bacterium, was isolated from coastal mud from
AB  - the North Sea (Fedderwardersiel, Germany) and characterized
AB  - using a polyphasic approach in 2011. The genome consists of a chromosome of about
AB  - 7.5 Mb and three plasmids.
ER  -

TY  - JOUR
AU  - Fillo, S.
AU  - Giordani, F.
AU  - Anselmo, A.
AU  - Fortunato, A.
AU  - Palozzi, A.M.
AU  - De Santis, R.
AU  - Ciammaruconi, A.
AU  - Spagnolo, F.
AU  - Anniballi, F.
AU  - Fiore, A.
AU  - Auricchio, B.
AU  - De Medici, D.
AU  - Lista, F.
TI  - Draft Genome Sequence of Clostridium botulinum B2 450 Strain from Wound Botulism  in a Drug User in Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00238
EP  - e00215
VL  - 3
AB  - Here, we report the draft genome sequence of Clostridium botulinum B2 450, responsible for the
AB  - first reported case of wound botulism in a drug user in
AB  - Italy.
ER  -

TY  - JOUR
AU  - Fillo, S.
AU  - Mancini, F.
AU  - Anselmo, A.
AU  - Fortunato, A.
AU  - Rezza, G.
AU  - Lista, F.
AU  - Ciervo, A.
TI  - Draft Genome Sequence of Streptococcus suis Strain SsRC-1, a Human Isolate from a Fatal Case of Toxic Shock Syndrome.
JO  - Genome Announcements
PY  - 2018
SP  - e00447
EP  - e00418
VL  - 6
AB  - Streptococcus suis is an economically important pathogen in the pig industry and  is also an
AB  - emerging zoonotic agent responsible for severe infections in humans.
AB  - Here, we report the genome sequence of S. suis strain SsRC-1. Specifically, this
AB  - strain was a serotype 2 and was isolated from a human fatal case of toxic shock
AB  - syndrome (TSS) in Italy.
ER  -

TY  - JOUR
AU  - Finan, T.M.
AU  - Weidner, S.
AU  - Wong, K.
AU  - Buhrmester, J.
AU  - Chain, P.
AU  - Vorholter, F.J.
AU  - Hernandez-Lucas, I.
AU  - Becker, A.
AU  - Cowie, A.
AU  - Gouzy, J.
AU  - Golding, B.
AU  - Puhler, A.
TI  - The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 9889
EP  - 9894
VL  - 98
AB  - Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing
AB  - bacterium Sinorhizobium meliloti revealed that the
AB  - replicon has a high gene density with a total of 1,570 protein-coding
AB  - regions, with few insertion elements and regions duplicated elsewhere in
AB  - the genome. The only copies of an essential arg-tRNA gene and the minCDE
AB  - genes are located on pSymB. Almost 20% of the pSymB sequence carries genes
AB  - encoding solute uptake systems, most of which were of the ATP-binding
AB  - cassette family. Many previously unsuspected genes involved in
AB  - polysaccharide biosynthesis were identified and these, together with the
AB  - two known distinct exopolysaccharide synthesis gene clusters, show that
AB  - 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other
AB  - recognizable gene clusters include many involved in catabolic activities
AB  - such as protocatechuate utilization and phosphonate degradation. The
AB  - functions of these genes are consistent with the notion that pSymB plays a
AB  - major role in the saprophytic competence of the bacteria in the soil
AB  - environment.
ER  -

TY  - JOUR
AU  - Fineran, P.C.
AU  - Iglesias, C.M.C.
AU  - Ramsay, J.P.
AU  - Wilf, N.M.
AU  - Cossyleon, D.
AU  - McNeil, M.B.
AU  - Williamson, N.R.
AU  - Monson, R.E.
AU  - Becher, S.A.
AU  - Stanton, J.A.
AU  - Brugger, K.
AU  - Brown, S.D.
AU  - Salmond, G.P.
TI  - Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas  Vesicles.
JO  - Genome Announcements
PY  - 2013
SP  - e01039
EP  - e01013
VL  - 1
AB  - Serratia sp. strain ATCC 39006 is a Gram-negative bacterium and a member of the
AB  - Enterobacteriaceae that produces various bioactive secondary metabolites,
AB  - including the tripyrrole red pigment prodigiosin and the beta-lactam antibiotic
AB  - 1-carbapenen-2-em-3-carboxylic acid (a carbapenem). This strain is the only
AB  - member of the Enterobacteriaceae known to naturally produce gas vesicles, as
AB  - flotation organelles. Here we present the genome sequence of this strain, which
AB  - has served as a model for analysis of the biosynthesis and regulation of
AB  - antibiotic production.
ER  -

TY  - JOUR
AU  - Finkbeiner, S.R.
AU  - Allred, A.F.
AU  - Tarr, P.I.
AU  - Klein, E.J.
AU  - Kirkwood, C.D.
AU  - Wang, D.
TI  - Metagenomic analysis of human diarrhea: viral detection and discovery.
JO  - PLoS Pathog.
PY  - 2008
SP  - e1000011
EP  - e1000011
VL  - 4
AB  - Worldwide, approximately 1.8 million children die from diarrhea annually,
AB  - and millions more suffer multiple episodes of nonfatal diarrhea. On
AB  - average, in up to 40% of cases, no etiologic agent can be identified. The
AB  - advent of metagenomic sequencing has enabled systematic and unbiased
AB  - characterization of microbial populations; thus, metagenomic approaches
AB  - have the potential to define the spectrum of viruses, including novel
AB  - viruses, present in stool during episodes of acute diarrhea. The detection
AB  - of novel or unexpected viruses would then enable investigations to assess
AB  - whether these agents play a causal role in human diarrhea. In this study,
AB  - we characterized the eukaryotic viral communities present in diarrhea
AB  - specimens from 12 children by employing a strategy of "micro-mass
AB  - sequencing" that entails minimal starting sample quantity (<100 mg stool),
AB  - minimal sample purification, and limited sequencing (384 reads per
AB  - sample). Using this methodology we detected known enteric viruses as well
AB  - as multiple sequences from putatively novel viruses with only limited
AB  - sequence similarity to viruses in GenBank.
ER  -

TY  - JOUR
AU  - Finnegan, E.J.
AU  - Dennis, E.S.
TI  - Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2383
EP  - 2388
VL  - 21
AB  - A plant cytosine methyltransferase cDNA was isolated using degenerate oligonucleotides, based
AB  - on homology between prokaryote and mouse methyltransferases, and PCR to amplify a short
AB  - fragment of a methyltansferase gene. A fragment of the predicted size was amplified from
AB  - genomic DNA from Arabidopsis thaliana. Overlapping cDNA clones, some with homology to the PCR
AB  - amplifed fragment, were identified and sequenced. The assembled nucleic acid sequence is 4720
AB  - bp and encodes a protein of 1534 amino acids which has significant homology to prokaryote and
AB  - mammalian cytosine methyltransferases. Like mammalian methylases, this enzyme has a C terminal
AB  - methyltransferase domain linked to a second larger domain. The Arabidopsis methylase has eight
AB  - of the ten conserved sequence motifs found in prokaryote cytosine-5 methyltransferases and
AB  - shows 50% homology to the murine enzyme in the methyltransferase domain. The amino terminal
AB  - domain is only 24% homologous to the murine enzyme and lacks the zinc binding region that has
AB  - been found in methyltransferases from both mouse and man. In contrast to mouse where a single
AB  - methyltransferase gene has been identified, a small multigene family with homology to the
AB  - region amplified in PCR has been identified in Arabidopsis thaliana.
ER  -

TY  - JOUR
AU  - Finnegan, E.J.
AU  - Genger, R.K.
AU  - Peacock, W.J.
AU  - Dennis, E.S.
TI  - DNA methylation in plants.
JO  - Annu. Rev. Plant Physiol. Plant Mol. Biol.
PY  - 1998
SP  - 223
EP  - 247
VL  - 49
AB  - Methylation of cytosine residues in DNA provides a mechanism of gene control.  There are two
AB  - classes of methyltransferase in Arabidopsis; one has a carboxy-terminal methyltransferase
AB  - domain fused to an amino-terminal regulatory domain and is similar to mammalian
AB  - methyltransferases.  The second class apparently lacks an amino-terminal domain and is less
AB  - well conserved.  Methylcytosine can occur at any cytosine residue, but it is likely that
AB  - clonal transmission of methylation patterns only occurs for cytosines in strand-symmetrical
AB  - sequences CpG and CpNpG.  In plants, as in mammals, DNA methylation has dual roles in defense
AB  - against invading DNA and transposable elements and in gene regulation.  Although originally
AB  - reported as having no phenotypic consequence, reduced DNA methylation disrupts normal plant
AB  - development.
ER  -

TY  - JOUR
AU  - Finnegan, E.J.
AU  - Kovac, K.A.
TI  - Plant DNA methyltransferases.
JO  - Plant Mol. Biol.
PY  - 2000
SP  - 189
EP  - 201
VL  - 43
AB  - DNA methylation is an important modification of DNA that plays a role in genome management and
AB  - in regulating gene expression during
AB  - development. Methylation is carried out by DNA methyltransferases which
AB  - catalyse the transfer of a methyl group to bases within the DNA helix.
AB  - Plants have at least three classes of cytosine methyltransferase which
AB  - differ in protein structure and function. The METI family, homologues
AB  - of the mouse Dnmt1 methyltransferase, most likely function as
AB  - maintenance methyltransferases, but may also play a role in de novo
AB  - methylation. The chromomethylases, which are unique to plants, may
AB  - preferentially methylate DNA in heterochromatin; the remaining class,
AB  - with similarity to Dnmt3 methyltransferases of mammals, are putative de
AB  - novo methyltransferases. The various classes of methyltransferase may
AB  - show differential activity on cytosines in different sequence contexts.
AB  - Chromomethylases may preferentially methylate cytosines in CpNpG
AB  - sequences while the Arabidopsis METI methyltransferase shows a
AB  - preference for cytosines in CpG sequences. Additional proteins, for
AB  - example DDM1, a member of the SNF2/SWI2 family of chromatin remodelling
AB  - proteins, are also required for methylation of plant DNA.
ER  -

TY  - JOUR
AU  - Finnegan, E.J.
AU  - Peacock, W.J.
AU  - Dennis, E.S.
TI  - Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 8449
EP  - 8454
VL  - 93
AB  - Arabidopsis plants transformed with an antisense construct of an Arabidopsis methyltransferase
AB  - cDNA (METI) have reduced cytosine methylation in CG dinucleotides. Methylation levels in
AB  - progeny of five independent transformants ranged from 10% to 100% of the wild type. Removal of
AB  - the antisense construct by segregation in sexual crosses did not fully restore methylation
AB  - patterns in the progeny, indicating that methylation patterns are subject to meiotic
AB  - inheritance in Arabidopsis. Plants with decreased methylation displayed a number of phenotypic
AB  - and developmental abnormalities, including reduced apical dominance, smaller plant size,
AB  - altered leaf size and shape, decreased fertility, and altered flowering time. Floral organs
AB  - showed homeotic transformations that were associated with ectopic expression of the floral
AB  - homeotic genes AGAMOUS and APETALA3 in leaf tissue. These observations suggest that DNA
AB  - methylation plays an important role in regulating many developmental pathways in plants and
AB  - that the developmental abnormalities seen in the methyltransferase antisense plants may be due
AB  - to dysregulation of gene expression.
ER  -

TY  - JOUR
AU  - Finster, K.W.
AU  - Kjeldsen, K.U.
AU  - Kube, M.
AU  - Reinhardt, R.
AU  - Mussmann, M.
AU  - Amann, R.
AU  - Schreiber, L.
TI  - Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur  compounds.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 58
EP  - 68
VL  - 8
AB  - Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial  family
AB  - Desulfobulbaceae and is one of two validly described members of its genus.
AB  - This strain was selected for genome sequencing, because it is the first marine
AB  - bacterium reported to thrive on the disproportionation of elemental sulfur, a
AB  - process with a unresolved enzymatic pathway in which elemental sulfur serves both
AB  - as electron donor and electron acceptor. Furthermore, in contrast to its
AB  - phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D.
AB  - sulfexigens is unable to grow by sulfate reduction and appears metabolically
AB  - specialized in growing by disproportionating elemental sulfur, sulfite or
AB  - thiosulfate with CO2 as the sole carbon source. The genome of D. sulfexigens
AB  - contains the set of genes that is required for nitrogen fixation. In an acetylene
AB  - assay it could be shown that the strain reduces acetylene to ethylene, which is
AB  - indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1
AB  - comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a
AB  - predicted function based on auto-annotation. The chromosome furthermore encodes
AB  - 46 tRNA genes and 3 rRNA operons.
ER  -

TY  - JOUR
AU  - Finta, C.
AU  - Kiss, A.
TI  - Footprint analysis of the BspRI DNA methyltransferase -- DNA interaction.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2841
EP  - 2846
VL  - 25
AB  - The interaction between the GGCC-specific BspRI DNA methyltransferase (M.BspRI) and substrate
AB  - DNA was studied with footprinting techniques usiung a DNA fragment that was unmodified on both
AB  - strands.  Footprinting with DNase I revealed an ~14 bp protected region.  Footprinting with
AB  - dimethylsulfate detected major groove interactions with the guanine bases of the recognition
AB  - sequence.  Reaction with 1,10-phenanthroline-copper did not show protection, suggesting that
AB  - minor groove interactions play little role in sequence-specific recognition by M.BspRI.
AB  - Hydroxyl radical footprinting revealed a protected stretch of 6 nt.  The hydroxyl radical
AB  - footprint of M.BspRI differs markedly from the footprint reported for the HhaI and SssI
AB  - methyltransferases.  The pattern of protection from dimethylsulfate and hydroxyl radicals
AB  - suggests that the interactions of M.BspRI with DNA are similar to those detected in the
AB  - co-crystal structure of the HaeIII methyltransferase.
ER  -

TY  - JOUR
AU  - Finta, C.
AU  - Sulima, U.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Purification of the KpnI DNA methyltransferase and photolabeling of the enzyme with S-adenosyl-L-methionine.
JO  - Gene
PY  - 1995
SP  - 65
EP  - 69
VL  - 164
AB  - An Escherichia coli strain overproducing the KpnI DNA methyltransferase (M.KpnI) was
AB  - constructed by cloning the kpnIM gene downstream from the inducible T7 phage omega 10
AB  - promoter.  A method involving three chromatographic steps has been developed to purify M.KpnI
AB  - to homogeneity.  The purified enzyme has a pH optimum around 7.3 and is inhibited by salts.
AB  - M.KpnI can be photolabeled by UV-irradiation of the enzyme in the presence of
AB  - S-adenosyl-L-[methyl-3H]methionine ([methyl-3H]AdoMet).  Photolabeling results from a specific
AB  - interaction betweeen M.KpnI and AdoMet, as indicated by the dependence of photolabeling on
AB  - native enzyme conformation and by the inhibitory effect of the AdoMet analogs, sinefungin and
AB  - S-adenosyl-L-homocysteine (AdoHcy).
ER  -

TY  - JOUR
AU  - Fiore, M.F.
AU  - Alvarenga, D.O.
AU  - Varani, A.M.
AU  - Hoff-Risseti, C.
AU  - Crespim, E.
AU  - Ramos, R.T.
AU  - Silva, A.
AU  - Schaker, P.D.
AU  - Heck, K.
AU  - Rigonato, J.
AU  - Schneider, M.P.
AU  - Jeong, H.
AU  - Sim, Y.M.
AU  - Kim, H.J.
AU  - Lee, Y.J.
AU  - Lee, D.W.
AU  - Lim, S.K.
AU  - Lee, S.J.
TI  - Draft Genome Sequence of the Brazilian Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa Strain SPC777.
JO  - Genome Announcements
PY  - 2013
SP  - e00547
EP  - e00513
VL  - 1
AB  - Microcystis aeruginosa strain SPC777 is an important toxin-producing cyanobacterium, isolated
AB  - from a water bloom of the Billings reservoir (Sao Paulo
AB  - State, Brazil). Here, we report the draft genome sequence and initial findings
AB  - from a preliminary analysis of strain SPC777, including several gene clusters
AB  - involved in nonribosomal and ribosomal synthesis of secondary metabolites.
ER  -

TY  - JOUR
AU  - Firczuk, M.
AU  - Wojciechowski, M.
AU  - Czapinska, H.
AU  - Bochtler, M.
TI  - DNA intercalation without flipping in the specific ThaI-DNA complex.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 744
EP  - 754
VL  - 39
AB  - The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt
AB  - ends. Here, we report the 1.3 A resolution
AB  - structure of the enzyme in complex with substrate DNA and a sodium or
AB  - calcium ion taking the place of a catalytic magnesium ion. The structure
AB  - identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees
AB  - with earlier bioinformatic predictions and implies that the PD and (D/E)XK
AB  - motifs in the sequence are incidental. DNA recognition is very unusual:
AB  - the two Met47 residues of the ThaI dimer intercalate symmetrically into
AB  - the CG steps of the target sequence. They approach the DNA from the minor
AB  - groove side and penetrate the base stack entirely. The DNA accommodates
AB  - the intercalating residues without nucleotide flipping by a doubling of
AB  - the CG step rise to twice its usual value, which is accompanied by drastic
AB  - unwinding. Displacement of the Met47 side chains from the base pair
AB  - midlines toward the downstream CG steps leads to large and compensating
AB  - tilts of the first and second CG steps. DNA intercalation by ThaI is
AB  - unlike intercalation by HincII, HinP1I or proteins that bend or repair
AB  - DNA.
ER  -

TY  - JOUR
AU  - Firman, K.
AU  - Creasey, W.A.
AU  - Watson, G.
AU  - Price, C.
AU  - Glover, S.W.
TI  - Genetic and physical studies of restriction-deficient mutants of the Inc FIV plasmids R124 and R124/3.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 145
EP  - 153
VL  - 191
AB  - R124 and R124/3 are R plasmids that carry the genes for two different
AB  - restriction and modification systems.  The phenotype of strains carrying either
AB  - of these plasmids along with the F'lac+ plasmid, is restriction-deficient
AB  - (Res-).  The Res- phenotype is not due to selection of preexisting mutants but
AB  - rather to a complex mutational event caused by the F plasmid.
AB  - Restriction-deficient mutants carry extensive deletions and other DNA
AB  - rearrangements.  Tn7 insertion is used to locate the restriction gene.  Many of
AB  - the Res- mutants are genetically unstable and revert at exceptionally high
AB  - frequencies.  Reversion is accompanied by DNA rearrangements which result in a
AB  - net gain of 9kb of DNA.  F- derivatives of F+ which do not cause
AB  - restriction-deficiency but do cause deletion were used to distinguish between
AB  - the DNA rearrangements associated with restriction-deficiency and those
AB  - associated with deletion.  From Res+ revertants of strains carrying F'lac+ and
AB  - R124 or R124/3 we have isolated F plasmids that now carry the genes for the
AB  - R124 or R124/3 restriction and modification systems.  It is suggested that
AB  - interaction between part of the F plasmid and that segment of the R plasmid
AB  - which controls the switch in Res-Mod specificity which has been observed
AB  - (Glover et al. 1983) is responsible for the production of
AB  - restriction-deficiency.
ER  -

TY  - JOUR
AU  - Firman, K.
AU  - Dutta, C.
AU  - Weiserova, M.
AU  - Janscak, P.
TI  - The role of subunit assembly in the functional control of Type I restriction-modification enzymes.
JO  - Mol. Biol. Today
PY  - 2000
SP  - 35
EP  - 41
VL  - 1
AB  - Type I restriction-modification enzymes are multifunctional, multisubunit enzymes that provide
AB  - their host bacteria with protection
AB  - against invading DNA. This protection is accomplished through a very
AB  - efficient cleavage of foreign DNA using a complex mechanism involving
AB  - hydrolysis of ATP and subsequent translocation of the substrate DNA. In
AB  - addition, the same enzymes provide protection for the host chromosome
AB  - against cleavage by methylating the target recognition sites. However,
AB  - the restriction (cleavage) activity of the enzyme must be carefully
AB  - controlled both in terms of what constitutes substrate DNA ("foreign"
AB  - versus "host") and the timing of the two activities when transferred to
AB  - a new host (modification must precede restriction to allow
AB  - establishment of the R-M system). The mechanism by which the enzyme
AB  - differentiates between "foreign" and "host" DNA is described and we
AB  - discuss recent evidence showing post-translational control as the
AB  - primary mechanism for temporal control of restriction. The importance
AB  - of subunit assembly in these processes is detailed and extended to
AB  - include novel assemblies with unexpected function.
ER  -

TY  - JOUR
AU  - Firman, K.
AU  - Price, C.
AU  - Glover, S.W.
TI  - The EcoR124 and EcoR124/3 restriction and modification systems:  cloning the genes.
JO  - Plasmid
PY  - 1985
SP  - 224
EP  - 234
VL  - 14
AB  - The Escherichia coli plasmid R124 codes for a type I restriction and
AB  - modification system EcoR124 and carries genetic information, most probably in
AB  - the form of a "silent copy", for the expression of a different R-M specificity
AB  - R124/3.  Characteristic DNA rearrangements have been shown to accompany the
AB  - switch in specificity from R124 to R124/3 and vice versa.  We have cloned a
AB  - 14.2-kb HindIII fragment from R124 and shown that it contains the hsdR, hsdM,
AB  - and hsdS genes which code for the EcoR124 R-M system.  An equivalent fragment
AB  - from the plasmid R124/3 following the switch in R-M specificity has also been
AB  - cloned and shown to contain the genes coding for the EcoR124/3 R-M system.
AB  - These fragments, however, lack a component present on the wild-type plasmid
AB  - essential for the switch in specificity.  Restriction fragment maps and
AB  - preliminary heteroduplex analysis indicate the near identity of the genes that
AB  - encode the two different DNA recognition specificities.  Transposon mutagenesis
AB  - was used to locate the positions of the hsdR, hsdM, and hsdS genes on the
AB  - cloned fragments in conjunction with complementation tests for gene function.
AB  - Indirect evidence indicates that hsdR is expressed from its own promoter and
AB  - that hsdM and hsdS are expressed from a single promoter, unidirectionally.
ER  -

TY  - JOUR
AU  - Firman, K.
AU  - Szczelkun, M.D.
TI  - Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement.
JO  - EMBO J.
PY  - 2000
SP  - 2094
EP  - 2102
VL  - 19
AB  - The type I restriction enzyme EcoR124I cleaves DNA following extensive linear translocation
AB  - dependent upon ATP hydrolysis. Using protein-directed displacement of a DNA triplex, we have
AB  - determined the kinetics of one-dimensional motion without the necessity of measuring DNA or
AB  - ATP hydrolysis. The triplex was pre-formed specifically on linear DNA, 4370 bp from an
AB  - EcoR124I site, and then incubated with endonuclease. Upon ATP addition, a distinct lag phase
AB  - was observed before the triplex-forming oligonucleotide was displaced with exponential
AB  - kinetics. As the distance between type I and triplex sites was shortened, the lag time
AB  - decreased whilst the displacement reaction remained exponential. This is indicative of
AB  - processive DNA translocation followed by collision with the triplex and oligonucleotide
AB  - displacement. A linear relationship between lag duration and inter-site distance gives a
AB  - translocation velocity of 400 +/- 32 bp/s at 20 degrees C. Furthermore, the data can only be
AB  - explained by bi-directional translocation. An endonuclease with only one of the two HsdR
AB  - subunits responsible for motion could still catalyse translocation. The reaction is less
AB  - processive, but can 'reset' in either direction whenever the DNA is released.
ER  -

TY  - JOUR
AU  - Firnhaber, C.
AU  - Gerber, M.
AU  - Tooley, K.
AU  - Scoggin, C.
TI  - DNA Contamination in Commercial Restriction Endonucleases.
JO  - Am. J. Hum. Genet.
PY  - 1986
SP  - 145
EP  - 145
VL  - 39
AB  - None
ER  -

TY  - JOUR
AU  - Fisch, K.M.
AU  - Silva, P.C.
AU  - Genilloud, O.
AU  - Almeida, C.
AU  - Schaberle, T.F.
TI  - Draft Genome Sequence of Burkholderia contaminans 293K04B, an Endosymbiont of the Sponge-Derived Fungus Stachylidium bicolor.
JO  - Genome Announcements
PY  - 2017
SP  - e01142
EP  - e01117
VL  - 5
AB  - Here, we present the draft genome of the endofungal symbiotic bacterium Burkholderia
AB  - contaminans 293K04B, isolated from Stachylidium bicolor 293K04
AB  - (Ascomycota). The fungus was originally isolated from the sponge Callyspongia cf.
AB  - C. flammeaS. bicolor 293K04 produces the endolides A-B, bioactive cyclic peptides
AB  - possibly biosynthesized by its endobacterium B. contaminans 293K04B.
ER  -

TY  - JOUR
AU  - Fischer, A.
AU  - Harrison, K.S.
AU  - Ramirez, Y.
AU  - Auer, D.
AU  - Chowdhury, S.R.
AU  - Prusty, B.K.
AU  - Sauer, F.
AU  - Dimond, Z.
AU  - Kisker, C.
AU  - Scott-Hefty, P.
AU  - Rudel, T.
TI  - Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense.
JO  - eLife
PY  - 2017
SP  - e21465
EP  - e21465
VL  - 6
AB  - Obligate intracellular Chlamydia trachomatis replicate in a membrane-bound
AB  - vacuole called inclusion, which serves as a signaling interface with the host
AB  - cell. Here, we show that the chlamydial deubiquitinating enzyme (Cdu) 1 localizes
AB  - in the inclusion membrane and faces the cytosol with the active deubiquitinating
AB  - enzyme domain. The structure of this domain revealed high similarity to mammalian
AB  - deubiquitinases with a unique alpha-helix close to the substrate-binding pocket.
AB  - We identified the apoptosis regulator Mcl-1 as a target that interacts with Cdu1
AB  - and is stabilized by deubiquitination at the chlamydial inclusion. A chlamydial
AB  - transposon insertion mutant in the Cdu1-encoding gene exhibited increased Mcl-1
AB  - and inclusion ubiquitination and reduced Mcl-1 stabilization. Additionally,
AB  - inactivation of Cdu1 led to increased sensitivity of C. trachomatis for IFNgamma
AB  - and impaired infection in mice. Thus, the chlamydial inclusion serves as an
AB  - enriched site for a deubiquitinating activity exerting a function in selective
AB  - stabilization of host proteins and protection from host defense.
ER  -

TY  - JOUR
AU  - Fischer, A.
AU  - Santana-Cruz, I.
AU  - Giglio, M.
AU  - Nadendla, S.
AU  - Drabek, E.
AU  - Vilei, E.M.
AU  - Frey, J.
AU  - Jores, J.
TI  - Genome Sequence of Mycoplasma feriruminatoris sp. nov., a Fast-Growing Mycoplasma Species.
JO  - Genome Announcements
PY  - 2013
SP  - e00216
EP  - e00212
VL  - 1
AB  - Members of the ' cluster' represent important livestock pathogens worldwide. We report the
AB  - genome sequence of sp. nov., the closest relative to the ' cluster'
AB  - and the fastest-growing species described to date.
ER  -

TY  - JOUR
AU  - Fischer, A.
AU  - Santana-Cruz, I.
AU  - Hegerman, J.
AU  - Gourle, H.
AU  - Schieck, E.
AU  - Lambert, M.
AU  - Nadendla, S.
AU  - Wesonga, H.
AU  - Miller, R.A.
AU  - Vashee, S.
AU  - Weber, J.
AU  - Meens, J.
AU  - Frey, J.
AU  - Jores, J.
TI  - High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afade and B237.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 89
EP  - 89
VL  - 10
AB  - Members of the Mycoplasma mycoides cluster' represent important livestock pathogens
AB  - worldwide. Mycoplasma mycoides subsp. mycoides is the etiologic agent
AB  - of contagious bovine pleuropneumonia (CBPP), which is still endemic in many parts
AB  - of Africa. We report the genome sequences and annotation of two frequently used
AB  - challenge strains of Mycoplasma mycoides subsp. mycoides, Afade and B237. The
AB  - information provided will enable downstream 'omics' applications such as
AB  - proteomics, transcriptomics and reverse vaccinology approaches. Despite the
AB  - absence of Mycoplasma pneumoniae like cyto-adhesion encoding genes, the two
AB  - strains showed the presence of protrusions. This phenotype is likely encoded by
AB  - another set of genes.
ER  -

TY  - JOUR
AU  - Fischer, A.
AU  - Santana-Cruz, I.
AU  - Wambua, L.
AU  - Olds, C.
AU  - Midega, C.
AU  - Dickinson, M.
AU  - Kawicha, P.
AU  - Khan, Z.
AU  - Masiga, D.
AU  - Jores, J.
AU  - Schneider, B.
TI  - Draft Genome Sequence of 'Candidatus Phytoplasma oryzae' Strain Mbita1, the Causative Agent of Napier Grass Stunt Disease in Kenya.
JO  - Genome Announcements
PY  - 2016
SP  - e00297
EP  - e00216
VL  - 4
AB  - Phytoplasmas are bacterial plant pathogens with devastating impact on agricultural production
AB  - worldwide. In eastern Africa, Napier grass stunt disease
AB  - causes serious economic losses in the smallholder dairy industry. This draft
AB  - genome sequence of ' ITALIC! CandidatusPhytoplasma oryzae' strain Mbita1 provides
AB  - insight into its genomic organization and the molecular basis of pathogenicity.
ER  -

TY  - JOUR
AU  - Fischer, M.G.
AU  - Allen, M.J.
AU  - Wilson, W.H.
AU  - Suttle, C.A.
TI  - Giant virus with a remarkable complement of genes infects marine zooplankton.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 19508
EP  - 19513
VL  - 107
AB  - As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a
AB  - critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is
AB  - infected by a giant virus, Cafeteria roenbergensis virus (CroV), which has the largest genome
AB  - of any described marine virus (approximately 730 kb of doublestranded DNA). The central 618-kb
AB  - coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early
AB  - and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively,
AB  - and at least 274 genes were expressed during infection. The diverse coding potential of CroV
AB  - includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein
AB  - MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22
AB  - tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2y, and an Elp3- like histone
AB  - acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region
AB  - of putative bacterial origin, which encodes several predicted carbohydrate metabolizing
AB  - enzymes, including an entire pathway for the biosynthesis of 3- deoxy-D-manno-octulosonate, a
AB  - key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates
AB  - that CroV is a nucleocytoplasmic large DNA virus, with Acanthamoeba polyphaga mimivirus as its
AB  - closest relative, although less than one-third of the genes of CroV have homologs in
AB  - Mimivirus. CroV is a highly complex marine virus and the only virus studied in genetic detail
AB  - that infects one of the major groups of predators in the oceans.
ER  -

TY  - JOUR
AU  - Fischer, W.
AU  - Breithaupt, U.
AU  - Kern, B.
AU  - Smith, S.I.
AU  - Spicher, C.
AU  - Haas, R.
TI  - A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity.
JO  - BMC Genomics
PY  - 2014
SP  - 310
EP  - 310
VL  - 15
AB  - BACKGROUND: The human gastric pathogen Helicobacter pylori is a paradigm for
AB  - chronic bacterial infections. Its persistence in the stomach mucosa is
AB  - facilitated by several mechanisms of immune evasion and immune modulation, but
AB  - also by an unusual genetic variability which might account for the capability to
AB  - adapt to changing environmental conditions during long-term colonization. This
AB  - variability is reflected by the fact that almost each infected individual is
AB  - colonized by a genetically unique strain. Strain-specific genes are dispersed
AB  - throughout the genome, but clusters of genes organized as genomic islands may
AB  - also collectively be present or absent. RESULTS: We have comparatively analysed
AB  - such clusters, which are commonly termed plasticity zones, in a high number of H.
AB  - pylori strains of varying geographical origin. We show that these regions contain
AB  - fixed gene sets, rather than being true regions of genome plasticity, but two
AB  - different types and several subtypes with partly diverging gene content can be
AB  - distinguished. Their genetic diversity is incongruent with variations in the rest
AB  - of the genome, suggesting that they are subject to horizontal gene transfer
AB  - within H. pylori populations. We identified 40 distinct integration sites in 45
AB  - genome sequences, with a conserved heptanucleotide motif that seems to be the
AB  - minimal requirement for integration. CONCLUSIONS: The significant number of
AB  - possible integration sites, together with the requirement for a short conserved
AB  - integration motif and the high level of gene conservation, indicates that these
AB  - elements are best described as integrating conjugative elements (ICEs) with an
AB  - intermediate integration site specificity.
ER  -

TY  - JOUR
AU  - Fisher, E.W.
AU  - Yang, M.-T.
AU  - Jeng, S.-T.
AU  - Gardner, J.F.
AU  - Gumport, R.I.
TI  - Selection of mutations altering specificity in restriction-modification enzymes using the bacteriophage P22 challenge-phage system.
JO  - Gene
PY  - 1995
SP  - 119
EP  - 121
VL  - 157
AB  - A method for selecting mutants of site-specific DNA-binding proteins has been applied to the
AB  - study of the EcoRI and RsrI restriction-modification enzymes.  Catalytically inactive variants
AB  - of both endonucleases are shown to function as pseudo-repressors in the bacteriophage P22
AB  - challenge-phage assay, and, upon further mutagenesis of the gene encoding R.EcoRI, a variant
AB  - of that enzyme has been selected which appears to bind EcoRI-methylated GAATTC sequences to
AB  - the exclusion of unmethylated sites: this specificity is the opposite of that belonging to the
AB  - native enzyme.  Variants of the EcoRI methylase have also been found that lack either
AB  - catalytic activity or both binding and catalytic activities.
ER  -

TY  - JOUR
AU  - Fisher, E.W.
AU  - Yang, M.T.
AU  - Gardner, J.F.
AU  - Gumport, R.I.
TI  - Isolation of a mutant EcoRI endonuclease with enhanced affinity for duplex methylated d(GAATTC).
JO  - FASEB J.
PY  - 1993
SP  - A1290
EP  - A1290
VL  - 7
AB  - The EcoRI endonuclease, one of the best characterized type II restriction endonucleases,
AB  - cleaves duplex DNA at the sequence GAATTC with extreme specificity, catalyzing incorrect
AB  - cleavage fewer than once in 10 to the 7th binding events. A companion DNA methyltransferase
AB  - uniquely methylates the inner adenosine residue of the same sequence, inhibiting recognition
AB  - of the site by the endonuclease. We have applied the bacteriophage P22 challenge-phage system
AB  - to the selection of a mutant of the endonuclease which binds the methylated sequence in
AB  - preference to the normal, unmethylated target sequence. The challenge-phage assay links
AB  - survival of the infected cell to the presence of a protein capable of binding a cloned
AB  - recognition sequence of the user's choice, and permits selection of mutant proteins with this
AB  - capability from a randomly mutagenized population. In this case a methylated EcoRI site was
AB  - chosen as the target recognition sequence by including in the host cells a plasmid bearing the
AB  - EcoRI methylase gene. We have isolated a mutant of EcoRI endonuclease, generated by
AB  - hydroxylamine treatment of a plasmid encoding a catalytically inactive form of the enzyme
AB  - (E111Q), which binds the methylated site tightly enough to form a stable lysogen in
AB  - challenge-phage assays. The challenge-phage data suggests that the mutant protein requires the
AB  - methyl group for binding, because cells lacking the EcoRI methylase gene are unable to form
AB  - lysogens. Current efforts are directed toward identifying the mutational change and examining
AB  - by gel mobility shift assays whether the mutant protein discriminates the methylated from the
AB  - unmethylated site in vitro. This work was supported in part by a grant (GM25621) from the
AB  - National Institute of Health to R.I.G.
ER  -

TY  - JOUR
AU  - Fisher, O.
AU  - Siman-Tov, R.
AU  - Ankri, S.
TI  - Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 287
EP  - 297
VL  - 32
AB  - The DNA methylation status of the protozoan parasite Entamoeba histolytica was heretofore
AB  - unknown.  In the present study, we developed a new technique, based on the affinity of
AB  - methylated DNA to 5-methyl-cytosine antibodies, to identify methylated DNA in this parasite.
AB  - Ribosomal. DNA and ribosomal DNA circles were isolated by this method and we confirmed the
AB  - validity of our approach by sodium bisulfite sequencing.  We also report the identification
AB  - and the characterization of a gene, Ehmeth, encoding a DNA methyltransferase strongly
AB  - homologous to the human DNA methyltransferase 2 (Dnmt2).  Immunofluorescence microscopy using
AB  - an antibody raised against a recombinant Ehmeth showed that Ehmeth is concentrated in the
AB  - nuclei of trophozoites.  The recombinant Ehmeth has a weak but significant methyltransferase
AB  - activity when E. histolytica genomic DNA is used as substrate.  5-Azacytidine (5-AzaC), an
AB  - inhibitor of DNA methyltransferase, was used to study in vivo the role of DNA methylation in
AB  - E. histolytica.  Genomic DNA of trophozoites grown with 5-AzaC (23 uM) was undermethylated and
AB  - the ability of 5-AzaC-treated trophozoites to kill mammalian cells or to cause liver abscess
AB  - in hamsters was strongly impaired.
ER  -

TY  - JOUR
AU  - Fisunov, G.Y.
AU  - Alexeev, D.G.
AU  - Bazaleev, N.A.
AU  - Ladygina, V.G.
AU  - Galyamina, M.A.
AU  - Kondratov, I.G.
AU  - Zhukova, N.A.
AU  - Serebryakova, M.V.
AU  - Demina, I.A.
AU  - Govorun, V.M.
TI  - Core proteome of the minimal cell: comparative proteomics of three mollicute species.
JO  - PLoS ONE
PY  - 2011
SP  - E21964
EP  - E21964
VL  - 6
AB  - Mollicutes (mycoplasmas) have been recognized as highly evolved prokaryotes with
AB  - an extremely small genome size and very limited coding capacity. Thus, they may
AB  - serve as a model of a 'minimal cell': a cell with the lowest possible number of
AB  - genes yet capable of autonomous self-replication. We present the results of a
AB  - comparative analysis of proteomes of three mycoplasma species: A. laidlawii, M.
AB  - gallisepticum, and M. mobile. The core proteome components found in the three
AB  - mycoplasma species are involved in fundamental cellular processes which are
AB  - necessary for the free living of cells. They include replication, transcription,
AB  - translation, and minimal metabolism. The members of the proteome core seem to be
AB  - tightly interconnected with a number of interactions forming core interactome
AB  - whether or not additional species-specific proteins are located on the periphery.
AB  - We also obtained a genome core of the respective organisms and compared it with
AB  - the proteome core. It was found that the genome core encodes 73 more proteins
AB  - than the proteome core. Apart of proteins which may not be identified due to
AB  - technical limitations, there are 24 proteins that seem to not be expressed under
AB  - the optimal conditions.
ER  -

TY  - JOUR
AU  - Fittipaldi, N.
AU  - Beres, S.B.
AU  - Olsen, R.J.
AU  - Kapur, V.
AU  - Shea, P.R.
AU  - Watkins, M.E.
AU  - Cantu, C.C.
AU  - Laucirica, D.R.
AU  - Jenkins, L.
AU  - Flores, A.R.
AU  - Lovgren, M.
AU  - Ardanuy, C.
AU  - Linares, J.
AU  - Low, D.E.
AU  - Tyrrell, G.J.
AU  - Musser, J.M.
TI  - Full-Genome Dissection of an Epidemic of Severe Invasive Disease Caused by a Hypervirulent, Recently Emerged Clone of Group A Streptococcus.
JO  - Am. J. Pathol.
PY  - 2012
SP  - 1522
EP  - 1534
VL  - 180
AB  - Group A Streptococcus (GAS) causes an exceptionally broad range of infections in humans, from
AB  - relatively mild pharyngitis and skin infections to life-threatening necrotizing fasciitis and
AB  - toxic shock syndrome. An epidemic of severe invasive human infections caused by type emm59
AB  - GAS, heretofore an exceedingly rare cause of disease, spread west to east across Canada over a
AB  - 3-year period (2006 to 2008). By sequencing the genomes of 601 epidemic, historic, and other
AB  - emm59 organisms, we discovered that a recently emerged, genetically distinct emm59 clone is
AB  - responsible for the Canadian epidemic. Using near-real-time genome sequencing, we were able to
AB  - show spread of the Canadian epidemic clone into the United States. The extensive genome data
AB  - permitted us to identify patterns of geographic dissemination as well as links between emm59
AB  - subclonal lineages that cause infections. Mouse and nonhuman primate models of infection
AB  - demonstrated that the emerged clone is unusually virulent. Transmission of epidemic emm59
AB  - strains may have occurred primarily by skin contact, as suggested by an experimental model of
AB  - skin transmission. In addition, the emm59 strains had a significantly impaired ability to
AB  - persist in human saliva and to colonize the oropharynx of mice, and seldom caused human
AB  - pharyngitis. Our study contributes new information to the rapidly emerging field of molecular
AB  - pathogenomics of bacterial epidemics and illustrates how full-genome data can be used to
AB  - precisely illuminate the landscape of strain dissemination during a bacterial epidemic.
ER  -

TY  - JOUR
AU  - Fitz-Gibbon, S.
AU  - Tomida, S.
AU  - Chiu, B.H.
AU  - Nguyen, L.
AU  - Du, C.
AU  - Liu, M.
AU  - Elashoff, D.
AU  - Erfe, M.C.
AU  - Loncaric, A.
AU  - Kim, J.
AU  - Modlin, R.L.
AU  - Miller, J.F.
AU  - Sodergren, E.
AU  - Craft, N.
AU  - Weinstock, G.M.
AU  - Li, H.
TI  - Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne.
JO  - J. Invest. Dermatol.
PY  - 2013
SP  - 2152
EP  - 2160
VL  - 133
AB  - The human skin microbiome has important roles in skin health and disease.
AB  - However, bacterial population structure and diversity at the strain level is
AB  - poorly understood. We compared the skin microbiome at the strain level and genome
AB  - level of Propionibacterium acnes, a dominant skin commensal, between 49 acne
AB  - patients and 52 healthy individuals by sampling the pilosebaceous units on their
AB  - noses. Metagenomic analysis demonstrated that although the relative abundances of
AB  - P. acnes were similar, the strain population structures were significantly
AB  - different in the two cohorts. Certain strains were highly associated with acne,
AB  - and other strains were enriched in healthy skin. By sequencing 66 previously
AB  - unreported P. acnes strains and comparing 71 P. acnes genomes, we identified
AB  - potential genetic determinants of various P. acnes strains in association with
AB  - acne or health. Our analysis suggests that acquired DNA sequences and bacterial
AB  - immune elements may have roles in determining virulence properties of P. acnes
AB  - strains, and some could be future targets for therapeutic interventions. This
AB  - study demonstrates a previously unreported paradigm of commensal strain
AB  - populations that could explain the pathogenesis of human diseases. It underscores
AB  - the importance of strain-level analysis of the human microbiome to define the
AB  - role of commensals in health and disease.Journal of Investigative Dermatology
AB  - advance online publication, 28 February 2013; doi:10.1038/jid.2013.21.
ER  -

TY  - JOUR
AU  - Fitz-Gibbon, S.T.
AU  - Ladner, H.
AU  - Kim, U.-J.
AU  - Stetter, K.O.
AU  - Simon, M.I.
AU  - Miller, J.H.
TI  - Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 984
EP  - 989
VL  - 99
AB  - We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum
AB  - aerophilum, a facultatively aerobic nitrate-reducing hyperthermophilic (Topt=100 C)
AB  - crenarchaeon.  Clues were found suggesting explanations of the organism's surprising
AB  - intolerance to sulfur, which may aid in the development of methods for genetic studies of the
AB  - organism.  Many interesting features worthy of further genetic studies were revealed.  Whole
AB  - genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps
AB  - all crenarchaea) lack 5' untranslated regions in their mRNAs and thus appear not to use a
AB  - ribosome-binding site (Shine-Delgarno)-based mechanism for translation initiation at the 5'
AB  - end of transcripts.  Inspection of the lengths and distribution of mononucleotide
AB  - repeat-tracts revealed some interesting features.  For instance, it was seen that
AB  - mononucleotide repeat-tracts of Gs (or Cs) are highly unstable, a pattern expected for an
AB  - organism deficient in mismatch repair.  This result, together with an independent study on
AB  - mutation rates, suggests a "mutator" phenotype.
ER  -

TY  - JOUR
AU  - Fitzgerald, G.F.
AU  - Twomey, D.P.
AU  - Daly, C.
AU  - Coffey, A.G.
TI  - Bacteriophage resistance in Lactococcus: Molecular characterization of the ScrFI restriction/modification system from Lactococcus lactis subsp. cremoris UC503.
JO  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
PY  - 1995
SP  - 581
EP  - 590
VL  - 85
AB  - Members of the genus Lactococcus are used as starter cultures in the manufacture of a range of
AB  - ripened and unripened fermented dairy products such as cheese, lactic butter and cottage
AB  - cheese.  In many cases the production of these foods is concentrated in large manufacturing
AB  - units where starter cultures are used on a more or less continuous and intensive basis.  In
AB  - such modern, highly efficient manufacturing regimes, poor starter performance is undesirable.
AB  - Thus, considerable effort has been targeted to successfully eliminate those factors, such as
AB  - poor milk quality, which could have a negative impact on the activity of the starter culture.
AB  - While there has been considerable success in countering the major problem of bacteriophage
AB  - infection in cheese plants, phage still represent a very significant threat to the efficient
AB  - performance of lactococcal starter cultures.  Obvious physical approaches such as careful
AB  - design of manufacturing plants, aseptic handling of cultures and proper separation of whey
AB  - from the culture preparation area have had considerable success but on their own will not
AB  - guarantee a phage-free environment.  A further approach has been to examine the cultures
AB  - themselves and to use isolates which display inherent resistance to phage.  Thus, carefully
AB  - selected strains, exhibiting considerable levels of natural resistance to phage, have been
AB  - included in defined starter culture systems used in many parts of the world, particularly for
AB  - Cheddar cheese production.  These defined systems have proved to be quite successful in
AB  - countering phage, especially when they are combined with good sanitization and asepsis
AB  - regimes.  The quest for lactococcal hosts exhibiting high levels of resistance to phage has
AB  - stimulated the analysis of phage/host interactions at a fundamental level.  One outcome of
AB  - this research has been the recognition that some of these hosts possess one or more specific
AB  - mechanisms which can confer on the host significant levels of resistance to phage.  These are
AB  - usually, although not always, plasmid-encoded and quite often these plasmids are
AB  - self-transmissible.  In general, three distinct types of resistance have been identified:
AB  - adsorption inhibition, abortive infection (Abi) and restriction/modification (R/M).  Since the
AB  - topic of phage resistance in lactococci has been reviewed in considerable depth in a number of
AB  - recent publications, these specific areas will not be discussed in detail.  The major emphasis
AB  - of this paper will be on the molecular analysis of the ScrFI R/M system, which mediates
AB  - insensitivity to phage in vivo and has a number of unusual and interesting features.
ER  -

TY  - JOUR
AU  - Fitzgerald, L.A.
AU  - Graves, M.V.
AU  - Li, X.
AU  - Feldblyum, T.
AU  - Hartigan, J.
AU  - Van Etten, J.L.
TI  - Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi.
JO  - Virology
PY  - 2007
SP  - 459
EP  - 471
VL  - 358
AB  - Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the
AB  - fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp
AB  - genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella
AB  - Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two
AB  - smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding
AB  - and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding
AB  - genes. The protein-encoding genes are almost evenly distributed on both strands, and
AB  - intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in
AB  - public databases, including some that are the first of their kind to be detected in a virus.
AB  - For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion
AB  - transporter protein and an alkyl sulfatase in FR483, and a dTDP-glucose pyrophosphorylase in
AB  - both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype
AB  - chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three
AB  - viruses.
ER  -

TY  - JOUR
AU  - Fitzgerald, L.A.
AU  - Graves, M.V.
AU  - Li, X.
AU  - Feldblyum, T.
AU  - Nierman, W.C.
AU  - Van Etten, J.L.
TI  - Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A.
JO  - Virology
PY  - 2007
SP  - 472
EP  - 484
VL  - 358
AB  - Viruses NY-2A and AR158, members of the family Phycodnaviridae, genus
AB  - Chlorovirus, infect the fresh water, unicellular, eukaryotic,
AB  - chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A
AB  - and the 344,690-bp genome of AR158 are the two largest chlorella virus
AB  - genomes sequenced to date; NY-2A contains 404 putative protein-encoding
AB  - and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding
AB  - and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly
AB  - distributed on both strands, and intergenic space is minimal. Two of the
AB  - NY-2A genes encode inteins, the large subunit of ribonucleotide reductase
AB  - and a superfamily II helicase. These are the first inteins to be detected
AB  - in the chlorella viruses. Approximately 40% of the viral gene products
AB  - resemble entries in the public databases, including some that are
AB  - unexpected for a virus. These include GDP-d-mannose dehydratase, fucose
AB  - synthase, aspartate transcarbamylase, Ca(++) transporting ATPase and
AB  - ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the
AB  - prototype chlorella virus PBCV-1 indicates that 85% of the genes are
AB  - present in all three viruses.
ER  -

TY  - JOUR
AU  - Fitzgerald, M.C.
AU  - Skowron, P.
AU  - Van Etten, J.L.
AU  - Smith, L.M.
AU  - Mead, D.A.
TI  - Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3753
EP  - 3762
VL  - 20
AB  - A new approach has been developed for the rapid fragmentation and fractionation of DNA into a
AB  - size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally
AB  - cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical
AB  - reaction conditions which alter the specificity of this enzyme (CviJI**) yield a quasi-random
AB  - distribution of DNA fragments from the small molecule pUC19 (2686 base pairs). To
AB  - quantitatively evaluate the randomness of this fragmentation strategy, a CviJI** digest of
AB  - pUC19 was size fractionated by a rapid gel filtration method and directly ligated, without end
AB  - repair, to a lacZ minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI**
AB  - restricts PyGCPy and PuCGPu, in addition to PuGCPy sites, and that new sequence data is
AB  - accumulated at a rate consistent with random fragmentation. Advantages of this approach
AB  - compared to sonication and agarose gel fractionation include: smaller amounts of DNA are
AB  - required (0.2-0.5 ug instead of 2-5 ug), fewer steps are involved (no pre-ligation, end
AB  - repair, chemical extraction, or agarose gel electrophoresis and elution are needed), and
AB  - higher cloning efficiencies are obtained (CviJI** digested and column fractionated DNA
AB  - transforms 3-16 times more efficiently than sonicated, end-repaired, and agarose fractionated
AB  - DNA).
ER  -

TY  - JOUR
AU  - Fitzgerald, S.
AU  - Dillon, S.C.
AU  - Chao, T.C.
AU  - Wiencko, H.L.
AU  - Hokamp, K.
AU  - Cameron, A.D.
AU  - Dorman, C.J.
TI  - Re-engineering cellular physiology by rewiring high-level global regulatory genes.
JO  - Sci. Rep.
PY  - 2015
SP  - 17653
EP  - 17653
VL  - 5
AB  - Knowledge of global regulatory networks has been exploited to rewire the gene
AB  - control programmes of the model bacterium Salmonella enterica serovar
AB  - Typhimurium. The product is an organism with competitive fitness that is superior
AB  - to that of the wild type but tuneable under specific growth conditions. The
AB  - paralogous hns and stpA global regulatory genes are located in distinct regions
AB  - of the chromosome and control hundreds of target genes, many of which contribute
AB  - to stress resistance. The locations of the hns and stpA open reading frames were
AB  - exchanged reciprocally, each acquiring the transcription control signals of the
AB  - other. The new strain had none of the compensatory mutations normally associated
AB  - with alterations to hns expression in Salmonella; instead it displayed
AB  - rescheduled expression of the stress and stationary phase sigma factor RpoS and
AB  - its regulon. Thus the expression patterns of global regulators can be adjusted
AB  - artificially to manipulate microbial physiology, creating a new and resilient
AB  - organism.
ER  -

TY  - JOUR
AU  - Fitzgerlad, G.F.
AU  - Daly, C.
AU  - Brown, L.R.
AU  - Gingeras, T.R.
TI  - ScrFI: a new sequence-specific endonuclease from Streptococcus cremoris.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 8171
EP  - 8179
VL  - 10
AB  - A novel sequence-specific endonuclease has been isolated from Streptococcus cremoris F. ScrFI
AB  - recognizes the sequence:5'CC^NGG3'3'GGN^CC5'and cleaves as indicated by the arrow.  It is
AB  - the first enzyme to recognize this sequence and the first endonuclease reported from the
AB  - lactic streptococci used in dairy fermentations.
ER  -

TY  - JOUR
AU  - Fixen, K.R.
AU  - Starkenburg, S.R.
AU  - Hovde, B.T.
AU  - Johnson, S.L.
AU  - Deodato, C.R.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Harwood, C.S.
AU  - Cattolico, R.A.
TI  - Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte Chrysochromulina tobin.
JO  - Genome Announcements
PY  - 2016
SP  - e01162
EP  - e01116
VL  - 4
AB  - The microalgal division Haptophyta uses a range of nutritional sourcing, including mixotrophy.
AB  - The genome of a member of this taxon, Chrysochromulina
AB  - tobin, suggests that interactions with its bacterial cohort are critical for C.
AB  - tobin physiology. Here, we report the genomes of eight bacterial species in
AB  - coculture with C. tobin.
ER  -

TY  - JOUR
AU  - Flanagan, J.C.
AU  - Lang, J.M.
AU  - Darling, A.E.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2013
SP  - e00244
EP  - e00213
VL  - 1
AB  - Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain
AB  - UCD-AKU, isolated from a residential carpet. The genome
AB  - assembly contains 3,692,614 bp in 130 contigs. This is the first member of the
AB  - Curtobacterium genus to be sequenced.
ER  -

TY  - JOUR
AU  - Fleischman, R.A.
AU  - Campbell, J.L.
AU  - Richardson, C.C.
TI  - Modification and restriction of T-even bacteriophages.
JO  - J. Biol. Chem.
PY  - 1976
SP  - 1561
EP  - 1570
VL  - 251
AB  - Using the single-stranded circular DNA of bacteriophage fd as template,
AB  - double-stranded circular DNA has been prepared in vitro with either 5-
AB  - hydroxymethylcytosine ([hmdC]DNA) or cytosine ([dC]DNA) in the product strand.
AB  - Extracts prepared from Escherichia coli cells restrictive to T-even phage containing
AB  - nonglucosylated DNA degrade [hmdC]DNA to acid-soluble material in vitro, but do not
AB  - degrade [dC]DNA.  In contrast, extracts prepared from E. coli K12 rglA- rglB-, a strain
AB  - permissive to T-even phage containing nonglucosylated DNA, do not degrade [hmdC]DNA
AB  - or [dC]DNA.  In addition, glucosylation of the [hmdC]DNA renders it resistant to
AB  - degradation by extracts from restrictive strains.  The conversion of [hmdC]DNA to acid-
AB  - soluble material in vitro consists of an HmCyt-specific endonucleolytic cleavage requiring
AB  - the presence of the RglB gene product to form a linear molecule, followed by a non-
AB  - HmCyt-specific hydrolysis of the linear DNA to acid-soluble fragments, catalyzed in part
AB  - by exonuclease V.  The RglB protein present in extracts of E. coli K12 rglA- rglB+ has
AB  - been purified 200-fold by complementation with extracts from E. coli K12 rglA- rglB-.
AB  - The purified RglB protein does not contain detectable HmCyt-specific endonuclease or
AB  - exonuclease activity.  In vitro endonucleolytic cleavage of [hmdC]DNA thus requires
AB  - additional factors present in cell extracts.
ER  -

TY  - JOUR
AU  - Fleischman, R.A.
AU  - Richardson, C.C.
TI  - Analysis of host range restriction in Escherichia coli treated with toluene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1971
SP  - 2527
EP  - 2531
VL  - 68
AB  - Escherichia coli cells treated with toluene replicate DNA when they are
AB  - provided with deoxyribonucleoside 5'-triphosphates, ATP, Mg++, and K+.
AB  - However, when deoxycytidine 5'-triphosphate is replaced by hydroxymethyl
AB  - deoxycytidine 5'-triphosphate, incorporation of nucleotides into
AB  - acid-precipitable material by toluene-treated strains restrictive to
AB  - nonglucosylated T-even phage is reduced to less than 5% of that normally
AB  - observed.  Even when dCTP is present in the reaction mixture, a similar effect
AB  - of the hydroxymethyl analogue on DNA replication is observed.  In contrast,
AB  - toluene-treated E. coli K12 r6-r2,4-, a strain permissive to the
AB  - nonglucosylated T-even phage, incorporates hydroxymethyl deoxycytosine into its
AB  - DNA, and replication proceeds at only a slightly reduced rate in the presence
AB  - of the hydroxymethyl deoxycytidine 5'-triphosphate.  The presence of the
AB  - hydroxymethyl deoxycytidine 5'-triphosphate in the reaction mixture does not
AB  - lead to degradation of preexisting DNA of the restrictive host, but it does
AB  - lead to an irreversible inhibition of further DNA replication; the inhibition
AB  - is observed only when the hydroxymethyl deoxycytidine 5'-triphosphate is
AB  - present during replication.  Thus phage-specific enzymes are not necessary for
AB  - the incorporation of hydroxymethylcytosine into phage DNA, and the restrictive
AB  - mechanism, present in the host cell before infection, can recognize
AB  - hydroxymethylcytosine residues in its own DNA, as well as the DNA of the T-even
AB  - phage.
ER  -

TY  - JOUR
AU  - Fleischmann, R.D. et al.
TI  - Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
JO  - Science
PY  - 1995
SP  - 496
EP  - 512
VL  - 269
AB  - An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA
AB  - from the whole chromosome has been applied to obtain the complete nucleotide sequence
AB  - (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd.  This
AB  - approach eliminates the need for initial mapping efforts and is therefore applicable to the
AB  - vast array of microbial species for which genome maps are unavailable.  The H. influenzae Rd
AB  - genome sequence (Genome Sequence Database accession number L42023) represents the only
AB  - complete genome sequence from a free-living organism.
ER  -

TY  - JOUR
AU  - Fletcher, B.S.
TI  - Development and validation of an approach to produce large-scale quantities of CpG-methylated plasmid DNA.
JO  - Micro. Biotech.
PY  - 2008
SP  - 62
EP  - 67
VL  - 1
AB  - The prokaryotic CpG-specific DNA methylase from Spiroplasma, SssI methylase, has been
AB  - extensively used to methylate plasmid DNA in vitro
AB  - to investigate the effects of methylation in vertebrate systems.
AB  - Currently available methods to produce CpG-methylated plasmid DNA have
AB  - certain limitations and cannot generate large quantities of methylated
AB  - DNA without cost or problems of purity. Here we describe an approach in
AB  - which the SssI methylase gene has been introduced into the Escherichia
AB  - coli bacterial genome under the control of an inducible promoter.
AB  - Plasmid DNA propagated in this bacterium under conditions which induce
AB  - the methylase gene result in significant (> 90%) CpG methylation.
AB  - Methylated DNA produced by this approach behaves similarly to
AB  - methylated DNA produced in vitro using the purified methylase. The
AB  - approach is scalable allowing for the production of milligram
AB  - quantities of methylated plasmid DNA.
ER  -

TY  - JOUR
AU  - Flett, F.
AU  - Mersinias, V.
AU  - Smith, C.P.
TI  - High efficiency intergeneric conjugal transfer of plasmid DNA from Escherichia coli to methyl DNA-restricting streptomycetes.
JO  - FEMS Microbiol. Lett.
PY  - 1997
SP  - 223
EP  - 229
VL  - 155
AB  - Many streptomycetes, including S. coelicolor A3(2), possess a potent methyl-specific
AB  - restriction which can present an effective barrier to the
AB  - introduction of heterologous DNA. We have compared the efficiency of intergeneric
AB  - conjugal transfer of different types of plasmids to S. coelicolor and S. lividans
AB  - 66 using two E. coli donors: the standard, methylation proficient strain S17-1,
AB  - and the methylation deficient donor, ET12567(pUB307). We demonstrate that the
AB  - methylation deficient donor can yield > 10(4)-fold more S. coelicolor
AB  - exconjugants than the standard donor. In the case of pSET152 derivatives, which
AB  - integrate into the host chromosome by site-specific recombination, up to 10% of
AB  - streptomycete spores in the conjugation mixture inherit the plasmid. The
AB  - conjugation procedure is efficient enough to obtain exconjugants with 'suicide'
AB  - delivery plasmids and therefore provides a simple route for conducting gene
AB  - disruptions in methyl DNA-restricting streptomycetes, and possibly other
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Flett, F.
AU  - Wotton, S.F.
AU  - Kirby, R.
TI  - A common host specificity in the restriction and modification of a bacteriophage by three distinct Streptomyces species.
JO  - J. Gen. Microbiol.
PY  - 1979
SP  - 465
EP  - 467
VL  - 110
AB  - Restriction/modification of bacteriophage is a well characterized phenomenon in many bacterial
AB  - species and has been identified among streptomycetes in Streptomyces albus G, Streptomyces
AB  - griseus Kr. 15 and Streptomyces coelicolor.  Direct correlation between bacterial restriction
AB  - of bacteriophage and a specific endonuclease has only been demonstrated for a few species,
AB  - including one Streptomyces species.  The discovery of extrachromosomal elements in
AB  - Streptomyces opened up the possibility of detecting such an element carrying
AB  - restriction/modification, as has been shown to occur in eubacteria.
ER  -

TY  - JOUR
AU  - Flick, K.E.
AU  - Jurica, M.S.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
JO  - Nature
PY  - 1998
SP  - 96
EP  - 101
VL  - 394
AB  - Homing endonucleases are a diverse collection of proteins that are encoded by genes with
AB  - mobile, self-splicing introns.  They have also been identified in self-splicing inteins
AB  - (protein introns).  These enzymes promote the movement of the DNA sequences that encode them
AB  - from one chromosome location to another; they do this by making a site-specific double-strand
AB  - break at a target site in an allele that lacks the corresponding mobile intron.  The target
AB  - site recognized by these small endonucleases are generally long (14-44 base pairs).  Four
AB  - families of homing endonucleases have been identified, including the LAGLIDADG, the His-Cys
AB  - box, the GIY-YIG and the H-N-H endonucleases.  The first identified His-Cys box homing
AB  - endonuclease was I-PpoI from the slime mould Physarum polycephalum.  Its gene residues in one
AB  - of only a few nuclear introns known to exhibit genetic mobility.  Here we report the structure
AB  - of the I-PpoI homing endonuclease bound to homing-site DNA determined to 1.8 Angstroms
AB  - resolution.  I-PpoI displays an elongated fold of dimensions 25 x 35 x 80 Angstroms, with
AB  - mixed alpha/beta topology.  Each I-PpoI monomer contains three antiparallel beta-sheets
AB  - flanked by two long alpha-helices and a long carboxy-terminal tail, and is stabilized by two
AB  - bound zinc ions 15 Angstroms apart.  The enzyme possesses a new zinc-bound fold and
AB  - endonuclease active site.  The structure has been determined in both uncleaved substrate and
AB  - cleaved product complexes.
ER  -

TY  - JOUR
AU  - Flick, K.E.
AU  - McHugh, D.
AU  - Heath, J.D.
AU  - Stephens, K.M.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease from Physarum polycephalum.
JO  - Protein Sci.
PY  - 1997
SP  - 2677
EP  - 2680
VL  - 6
AB  - The homing endonuclease I-PpoI is encoded by an optional third intron, Pp LSU 3, found in
AB  - nuclear, extrachromosomal copies of the Physarum polycephalum 26S rRNA gene.  This
AB  - endonuclease promotes the lateral transfer or "homing" of its encoding intron by recognizing
AB  - and cleaving a partially symmetric, 15 bp homing site in 26S rDNA alleles that lack the Pp LSU
AB  - 3 intron.  The open reading frame encoding I-PpoI has been subcloned, and the endonuclease has
AB  - been overproduced in E. coli.  Purified recombinant I-PpoI has been co-crystallized with a 21
AB  - bp homing site DNA duplex.  The crystals belong to space group P3I21, with unit cell
AB  - dimensions a=b=114 A, c= 89 A.  The results of initial X-ray diffraction experiments indicate
AB  - that the asymmetric unit contains an enzyme homodimer and one duplex DNA molecule, and that
AB  - the unit cell has a specific volume of 3.4 A3/dalton.  These experiments also provide strong
AB  - evidence that I-PpoI contains several bound zinc ions as part of its structure.
ER  -

TY  - JOUR
AU  - Fliess, A.
AU  - Wolfes, H.
AU  - Rosenthal, A.
AU  - Schwellnus, K.
AU  - Blocker, H.
AU  - Frank, R.
AU  - Pingoud, A.
TI  - Role of thymidine residues in DNA recognition by the EcoRI and EcoRV restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 3463
EP  - 3474
VL  - 14
AB  - We have synthesized a series of oligonucleotides containing the EcoRI (GAATTC)
AB  - or EcoRV (GATATC) recognition site within which or adjacent to which thymidine
AB  - was substituted by uridine or derivatives of uridine.  The effects of these
AB  - substitutions on the rate of the EcoRI and EcoRV catalyzed cleavage reaction
AB  - were investigated.  Our results show that most of the substitutions within the
AB  - site are quite well tolerated by EcoRI, not, however, by EcoRV.  We conclude
AB  - that the thymin residues most likely are not dirctly involved in the
AB  - recognition process of the EcoRI reaction.  In contrast, they are major points
AB  - of contact, between substrate and enzym in the EcoRV reaction.  The effects of
AB  - substitutions in the position adjacent to the recognition site is also markedly
AB  - different for EcoRI and EcoRV.  Here, EcoRI seems to be considerably more
AB  - selective than EcoRV.
ER  -

TY  - JOUR
AU  - Fliess, A.
AU  - Wolfes, H.
AU  - Seela, F.
AU  - Pingoud, A.
TI  - Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 11781
EP  - 11793
VL  - 16
AB  - We have prepared a series of undecadeoxynucleotides that contain changes in the
AB  - functional group pattern present within the EcoRV recognition site - GATATC -.
AB  - Oligonucleotides were synthesized on solid phase using normal and modified
AB  - beta-cyanoethylphosphoramidites and analyzed in steady state cleavage
AB  - experiments with the EcoRV restriction endonuclease.  The following groups
AB  - appear to interact strongly with the enzyme, since their modification or
AB  - substitution renders the oligonucleotides refractory to cleavage:  the
AB  - exocyclic NH2-groups of both A residues, the N7 of the first A residue, the
AB  - exocyclic NH2-group of the C residue and the CH3-groups of both T residues.
AB  - The exocyclic NH-group of the G residue supports effective recognition, since
AB  - its absence lowers the kcat of the cleavage reaction.  The N7 of the second A
AB  - residue and the C5 position of the C residue apparently are not recognized by
AB  - EcoRV; their substitution by -CH- or modification with -Br or -CH3 does not
AB  - considerably change the rate of cleavage.  All oligonucleotides investigated
AB  - compete with the unmodified substrate for binding to the enzyme.  We conclude
AB  - that EcoRV recognizes its substrate presumably through hydrogen bonds to the
AB  - exocyclic NH2-group and the N7 of the first A residue, the exocyclic NH2-groups
AB  - of the second A and the C residue, as well as through hydrophobic interactions
AB  - with both T residues.
ER  -

TY  - JOUR
AU  - Flinspach, K.
AU  - Ruckert, C.
AU  - Kalinowski, J.
AU  - Heide, L.
AU  - Apel, A.K.
TI  - Draft Genome Sequence of Streptomyces niveus NCIMB 11891, Producer of the Aminocoumarin Antibiotic Novobiocin.
JO  - Genome Announcements
PY  - 2014
SP  - e01146
EP  - e01113
VL  - 2
AB  - Streptomyces niveus NCIMB 11891 is the producer of the gyrase inhibitor novobiocin, which
AB  - belongs to the aminocoumarin class of antibiotics. The genome
AB  - sequence of this strain was found to contain, besides the gene cluster for
AB  - novobiocin, a putative gene cluster for the macrolactam antibiotic BE-14106 and
AB  - further secondary metabolite gene clusters.
ER  -

TY  - JOUR
AU  - Flood, B.E.
AU  - Jones, D.S.
AU  - Bailey, J.V.
TI  - Complete Genome Sequence of Sedimenticola thiotaurini Strain SIP-G1, a Polyphosphate- and Polyhydroxyalkanoate-Accumulating Sulfur-Oxidizing  Gammaproteobacterium Isolated from Salt Marsh Sediments.
JO  - Genome Announcements
PY  - 2015
SP  - e00671
EP  - e00615
VL  - 3
AB  - We report the closed genome sequence of Sedimenticola thiotaurini strain SIP-G1 and an unnamed
AB  - plasmid obtained through PacBio sequencing with 100% consensus
AB  - concordance. The genome contained several distinctive features not found in other
AB  - published Sedimenticola genomes, including a complete nitrogen fixation pathway,
AB  - a complete ethanolamine degradation pathway, and an alkane-1-monooxygenase.
ER  -

TY  - JOUR
AU  - Flood, B.E.
AU  - Leprich, D.
AU  - Bailey, J.V.
TI  - Complete Genome Sequence of Celeribacter baekdonensis Strain LH4, a Thiosulfate-Oxidizing Alphaproteobacterial Isolate from Gulf of Mexico  Continental Slope Sediments.
JO  - Genome Announcements
PY  - 2018
SP  - e00434
EP  - e00418
VL  - 6
AB  - We report here the closed genome sequences of Celeribacter baekdonensis strain LH4 and five
AB  - unnamed plasmids obtained through PacBio sequencing with 99.99%
AB  - consensus concordance. The genomes contained several distinctive features not
AB  - found in other published Celeribacter genomes, including the potential to
AB  - aerobically degrade styrene and other phenolic compounds.
ER  -

TY  - JOUR
AU  - Flores, A.R. et al.
TI  - Sequence type 1 group B Streptococcus, an emerging cause of invasive disease in adults, evolves by small genetic changes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2015
SP  - 6431
EP  - 6436
VL  - 112
AB  - The molecular mechanisms underlying pathogen emergence in humans is a critical
AB  - but poorly understood area of microbiologic investigation. Serotype V group B
AB  - Streptococcus (GBS) was first isolated from humans in 1975, and rates of invasive
AB  - serotype V GBS disease significantly increased starting in the early 1990s. We
AB  - found that 210 of 229 serotype V GBS strains (92%) isolated from the bloodstream
AB  - of nonpregnant adults in the United States and Canada between 1992 and 2013 were
AB  - multilocus sequence type (ST) 1. Elucidation of the complete genome of a 1992
AB  - ST-1 strain revealed that this strain had the highest homology with a GBS strain
AB  - causing cow mastitis and that the 1992 ST-1 strain differed from serotype V
AB  - strains isolated in the late 1970s by acquisition of cell surface proteins and
AB  - antimicrobial resistance determinants. Whole-genome comparison of 202 invasive
AB  - ST-1 strains detected significant recombination in only eight strains. The
AB  - remaining 194 strains differed by an average of 97 SNPs. Phylogenetic analysis
AB  - revealed a temporally dependent mode of genetic diversification consistent with
AB  - the emergence in the 1990s of ST-1 GBS as major agents of human disease.
AB  - Thirty-one loci were identified as being under positive selective pressure, and
AB  - mutations at loci encoding polysaccharide capsule production proteins, regulators
AB  - of pilus expression, and two-component gene regulatory systems were shown to
AB  - affect the bacterial phenotype. These data reveal that phenotypic diversity among
AB  - ST-1 GBS is mainly driven by small genetic changes rather than extensive
AB  - recombination, thereby extending knowledge into how pathogens adapt to humans.
ER  -

TY  - JOUR
AU  - Flores, H.
AU  - Osuna, J.
AU  - Heitman, J.
AU  - Soberon, X.
TI  - Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants.
JO  - Gene
PY  - 1995
SP  - 295
EP  - 301
VL  - 157
AB  - EcoRI recognizes and cleaves DNA at GAATTC sites and is one of the best characterized
AB  - sequence-specific restriction endonucleases (ENases).  In previous studies, an EcoRI mutant,
AB  - which exhibited relaxed substrate specificity and cleaved both canonical and EcoRI star sites,
AB  - was isolated.  This mutant enzyme has Tyr instead of His114.  Here, we subjected residue 114
AB  - of the EcoRI ENase to saturation mutagenesis.  The resulting mutant enzymes were characterized
AB  - both in vivo and in vitro, resulting in the identification of mutants with canonical (H114K,
AB  - Q, D, I) or relaxed (H114Y, F, S, T) specificity, as well as one mutant with severely impaired
AB  - activity (H114P).  In the X-ray structure of an EcoRI-substrate complex, His 114 is located
AB  - between the catalytic and recognition regions of EcoRI and may directly contact the DNA
AB  - phosphate backbone.  Based on our genetic and biochemical findings and the X-ray structure, we
AB  - propose that His114 participates in substrate recognition and catalysis, either directly, via
AB  - protein-DNA interactions, or indirectly, by mediating conformational changes that trigger DNA
AB  - cleavage in response to substrate recognition.
ER  -

TY  - JOUR
AU  - Flores, V.
AU  - Lopez-Merino, A.
AU  - Mendoza-Hernandez, G.
AU  - Guarneros, G.
TI  - Comparative genomic analysis of two brucellaphages of distant origins.
JO  - Genomics
PY  - 2012
SP  - 233
EP  - 240
VL  - 99
AB  - Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb)
AB  - and compared it with that of Pr, a broad host-range brucellaphage recently
AB  - isolated in Mexico. The genomes consist of 41,148bp (Tb) and 38,253bp (Pr), they
AB  - differ mainly in the region encoding structural proteins, in which the genome of
AB  - Tb shows two major insertions. Both genomes share 99.87% nucleotide identity, a
AB  - high percentage of identity among phages isolated at so globally distant
AB  - locations and temporally different occasions. Sequence analysis revealed 57
AB  - conserved ORFs, three transcriptional terminators and four putative
AB  - transcriptional promoters. The co-occurrence of an ORF encoding a putative
AB  - DnaA-like protein and a putative oriC-like origin of replication was found in
AB  - both brucellaphages genomes, a feature not described in any other phage genome.
AB  - These elements suggest that DNA replication in brucellaphages differs from other
AB  - phages, and might resemble that of bacterial chromosomes.
ER  -

TY  - JOUR
AU  - Florez, A.B.
AU  - Reimundo, P.
AU  - Delgado, S.
AU  - Fernandez, E.
AU  - Alegria, A.
AU  - Guijarro, J.A.
AU  - Mayo, B.
TI  - Genome Sequence of Lactococcus garvieae IPLA 31405, a Bacteriocin-Producing, Tetracycline-Resistant Strain Isolated from a Raw-Milk Cheese.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5118
EP  - 5119
VL  - 194
AB  - This work describes the draft genome sequence of Lactococcus garvieae IPLA 31405, isolated
AB  - from a traditional Spanish cheese. The genome contains a
AB  - lactose-galactose operon, a bacteriocin locus, two integrated phages, a
AB  - transposon harboring an active tet(M) gene, and two theta-type plasmid replicons.
AB  - Genes encoding virulence factors were not recorded.
ER  -

TY  - JOUR
AU  - Floriano, A.M.
AU  - Castelli, M.
AU  - Krenek, S.
AU  - Berendonk, T.U.
AU  - Bazzocchi, C.
AU  - Petroni, G.
AU  - Sassera, D.
TI  - The Genome Sequence of 'Candidatus Fokinia solitaria': Insights on Reductive Evolution in Rickettsiales.
JO  - Genome Biol. Evol.
PY  - 2018
SP  - 1120
EP  - 1126
VL  - 10
AB  - "Candidatus Fokinia solitaria" is an obligate intracellular endosymbiont of a
AB  - unicellular eukaryote, a ciliate of the genus Paramecium. Here, we present the
AB  - genome sequence of this bacterium and subsequent analysis. Phylogenomic analysis
AB  - confirmed the previously reported positioning of the symbiont within the
AB  - "Candidatus Midichloriaceae" family (order Rickettsiales), as well as its high
AB  - sequence divergence from other members of the family, indicative of fast sequence
AB  - evolution. Consistently with this high evolutionary rate, a comparative genomic
AB  - analysis revealed that the genome of this symbiont is the smallest of the
AB  - Rickettsiales to date. The reduced genome does not present flagellar genes, nor
AB  - the pathway for the biosynthesis of lipopolysaccharides (present in all the other
AB  - so far sequenced members of the family "Candidatus Midichloriaceae") or genes for
AB  - the Krebs cycle (present, although not always complete, in Rickettsiales). These
AB  - results indicate an evolutionary trend toward a stronger dependence on the host,
AB  - in comparison with other members of the family. Two alternative scenarios are
AB  - compatible with our results; "Candidatus Fokinia solitaria" could be either a
AB  - recently evolved, vertically transmitted mutualist, or a parasite with a high
AB  - host-specificity.
ER  -

TY  - JOUR
AU  - Fluchter, S.
AU  - Poehlein, A.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of the Poly-3-Hydroxybutyrate Producer Clostridium acetireducens  DSM 10703.
JO  - Genome Announcements
PY  - 2016
SP  - e01399
EP  - e01316
VL  - 4
AB  - Here, we report the genome sequence of Clostridium acetireducens (DSM 10703T), a  strictly
AB  - anaerobic bacterium capable of fermenting acetate and leucine to
AB  - butyrate, isovalerate, and poly-3-hydroxybutyrate. The draft genome consists of a
AB  - circular chromosome with a size of 2.4 Mb and harbors 2,239 predicted
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Flusberg, B.A.
AU  - Webster, D.R.
AU  - Lee, J.H.
AU  - Travers, K.J.
AU  - Olivares, E.C.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Turner, S.W.
TI  - Direct detection of DNA methylation during single-molecule, real-time sequencing.
JO  - Nat. Methods
PY  - 2010
SP  - 461
EP  - 465
VL  - 7
AB  - We describe the direct detection of DNA methylation, without bisulfite conversion, through
AB  - single-molecule, real-time (SMRT) sequencing. In SMRT sequencing, DNA polymerases catalyze the
AB  - incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands.
AB  - The arrival times and durations of the resulting fluorescence pulses yield information about
AB  - polymerase kinetics and allow direct detection of modified nucleotides in the DNA template,
AB  - including N6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine.  Measurement of
AB  - polymerase kinetics is an intrinsic part of SMRT sequencing and does not adversely affect
AB  - determination of primary DNA sequence. The various modifications affect polymerase kinetics
AB  - differently, allowing discrimination between them. We used these kinetic signatures to
AB  - identify adenine methylation in genomic samples and found that, in combination with circular
AB  - consensus
AB  - sequencing, they can enable single-molecule identification of epigenetic
AB  - modifications with base-pair resolution. This method is amenable to long read
AB  - lengths and will likely enable mapping of methylation patterns in even highly
AB  - repetitive genomic regions.
ER  -

TY  - JOUR
AU  - Flynn, J.
TI  - Murine DNA cytosine C-5 methyltransferase: Insights into epigenetic control. from enzymological studies.
JO  - Diss. Abstr.
PY  - 1998
SP  - 3614B
EP  - 3614B
VL  - 58
AB  - The processes that contribute to mammalian development are numerous.  Genomic methylation
AB  - patterns change dynamically with each differentiating cell division.  The enzyme responsible
AB  - for DNA methylation is essential for normal development.  A precise functional description is
AB  - catalysis and epigenesis. A rigorous DNA binding assay defined how sequences flanking CpG
AB  - dideoxynucleotides affect the stability of the enzyme:DNA complex.  Oligonucleotides form
AB  - reversible 1:1 complexes with the enzyme sequence-specifically.  A guanine/cytosine-rich
AB  - sequence that mimics the GC-box boundthree-fold more tightly than the adenine/thymine rich
AB  - cyclic AMP responsive element.  Binding discrimination between hemi- and unmethylated forms
AB  - was small and single-stranded substrates bound more weakly than double-stranded DNA.  An in
AB  - vitro screening method selected for CpG flanking sequence preferences from a large, divergent
AB  - population.  After five iterative rounds of increasing selective pressure,
AB  - guanosine/cytosine-rich sequences were abundant.  The enzyme uses sequence-dependent
AB  - conformational features over two helical turns for discrimination, rather than specific base
AB  - interactions.  The constants KmDNA, kcat, and kmethylation were determined.  The rate limiting
AB  - step for most substrates was the methylation step itself.  Contrastingly, hemimethylated
AB  - substrates exhibited burst kinetics, consistent with a rapid methylation event followed by a
AB  - slower step which determines kcat.  Large substrates with multiple recognition sites do not
AB  - show burst kinetics and have turnover constants of 30 hr-1.  Maintenance of genomic
AB  - methylation patterns is preferred over de novo establishment of new patterns.  Four types of
AB  - steady-state analyses were used to identify the order of substrate addition and product
AB  - release.  Steady-state initial velocity studies including product and dead-end inhibition
AB  - studies support an ordered Bi-Bi kinetic model in which DNA binds first, followed by
AB  - S-adenosyl methionine and then release of S-adenosyl homocysteine.
ER  -

TY  - JOUR
AU  - Flynn, J.
AU  - Azzam, R.
AU  - Reich, N.
TI  - DNA binding discrimination of the murine DNA cytosine-C5 methyltransferase.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 101
EP  - 116
VL  - 279
AB  - Mammalian DNA cytosine-C5 methyltransferase modifies the CpG dinucleotide in the context of
AB  - many different genomic sequences.  A rigorous DNA binding assay was developed for the murine
AB  - enzyme and used to define how sequences flanking the CpG dinucleotide affect the stability of
AB  - the enzyme:DNA complex.  Oligonucleotides containing a single CpG site form reversible 1:1
AB  - complexes with the enzyme that are sequence-specific.  A guanine/cytosine-rich 30 base-pair
AB  - sequence, a mimic of the GC-box cis-element, bound threefold more tightly than an
AB  - adenine/thymine-rich sequence, a mimic of the cyclic AMP responsive element.  However, the
AB  - binding discrimination between hemi- and unmethylated forms of these DNA substrates was small,
AB  - as we previously observed at the KmDNA level.  Single-stranded substrates are bound much more
AB  - weakly than double-stranded DNA forms.  An in vitro screening method was used to select for
AB  - CpG flanking sequence preferences of the DNA methyltransferase from a large, divergent
AB  - population of DNA substrates.  After five interactive rounds of increasing selective pressure,
AB  - guanosine/cytosine-rich sequences were abundant and contributed to binding stabilization for
AB  - at least 12 base-pairs on either side of a central CpG.  Our results suggest a read-out of
AB  - sequence-dependent conformational features, such as helical flexibility, minor groove
AB  - dimensions and critical phosphate orientation and mobility, rather than interactions with
AB  - specific bases over the course of two complete helical turns.  Thus, both studies reveal a
AB  - preference for guanosine/cytosine deoxynucleotides flanking the cognate CpG.  The enzyme
AB  - specificity for similar sequences in the genome may contribute to the in vivo functions of
AB  - this vital enzyme.
ER  -

TY  - JOUR
AU  - Flynn, J.
AU  - Fang, J.Y.
AU  - Mikovits, J.A.
AU  - Reich, N.O.
TI  - A potent cell-active allosteric inhibitor of murine DNA cytosine C5 methyltransferase.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 8238
EP  - 8243
VL  - 278
AB  - The major DNA cytosine methyltransferase isoform in mouse erythroleukemia cells, Dnmt1,
AB  - exhibits potent dead-end inhibition with a single-stranded
AB  - nucleic acid by binding to an allosteric site on the enzyme. The
AB  - previously reported substrate inhibition with double-stranded substrates
AB  - also involves binding to an allosteric site. Thus, both forms of
AB  - inhibition involve ternary enzyme-DNA-DNA complexes. The inhibition
AB  - potency of the single-stranded nucleic acid is determined by the sequence,
AB  - length, and most appreciably the presence of a single 5-methylcytosine
AB  - residue. A single-stranded phosphorothioate derivative inhibits DNA
AB  - methylation activity in nuclear extracts. Mouse erythroleukemia cells
AB  - treated with the phosphorothioate inhibitor show a significant decrease in
AB  - global genomic methylation levels. Inhibitor treatment of human colon
AB  - cancer cells causes demethylation of the p16 tumor suppressor gene and
AB  - subsequent p16 re-expression. Allosteric inhibitors of mammalian DNA
AB  - cytosine methyltransferases, representing a new class of molecules with
AB  - potential therapeutic applications, may be used to elucidate novel
AB  - epigenetic mechanisms that control development.
ER  -

TY  - JOUR
AU  - Flynn, J.
AU  - Glickman, J.F.
AU  - Reich, N.O.
TI  - Murine DNA cytosine-C5 methyltransferase: pre-steady- and steady-state kinetic analysis with regulatory DNA sequences.
JO  - Biochemistry
PY  - 1996
SP  - 7308
EP  - 7315
VL  - 35
AB  - We present the first description of KmDNA, KdDNA, kcat, and kmethylation for a mammalian DNA
AB  - methyltransferase.  Homogeneous, 190 000 MrDNA (cytosine-5-)-methyltransferase isolated from
AB  - mouse erythroleukemia cells has turnover constants of 0.15-0.59 h-1 with single-stranded and
AB  - unmethylated double-stranded oligonucleotides containing a single CpG dinucleotide.  These
AB  - substrates were designed to mimic DNA transcriptional cis elements previously reported to have
AB  - cytosine C-5-methylated regulation.  The rate-limiting step for these substrates is the
AB  - methylation step itself.  In contrast, hemimethylated double-stranded substrates show burst
AB  - kinetics, consistent with a rapid methylation event (3 h-1) followed by a slower step which
AB  - determines steady-state kcat.  Hemimethylated and unmethylated double-stranded DNA shows
AB  - similar binding affinities; these results reveal the molecular basis for the enzyme's
AB  - preference for hemimethylated DNA to be the methyl transfer step.  Substrates with multiple
AB  - recognition sites do not show burst kinetics and have turnover rate constants of 6 h-1.
AB  - Catalytic turnover for the mammalian enzyme is thus approximately 10-fold slower than that for
AB  - the related bacterial enzymes.  Our combined results show quantitatively that one enzyme is
AB  - certainly capable of both maintenance and de novo methylation and that maintenance of the
AB  - genomic methylation pattern is preferred over the de novo establishment of new patterns.
AB  - Direct comparison of the mammalian enzyme with the bacterial DNA cytosine-C5
AB  - methyltransferase, M.SssI, indicates dramatic differences in preferences for single-stranded,
AB  - double-stranded, and hemimethylated double-stranded substrates.  Moreover, the specificity
AB  - hierarchy shown for the M.SssI is derived from very different changes in Km and catalysis than
AB  - those observed for the mammalian DCMTase.  These results demonstrate that the M.SssI, and
AB  - perhaps other DNA cytosine methyltransferases from bacteria, is functionally dissimilar to the
AB  - mammalian enzyme.
ER  -

TY  - JOUR
AU  - Flynn, J.
AU  - Reich, N.
TI  - Murine DNA (cytosine-5-)-methyltransferase: Steady-state and substrate trapping analyses of the kinetic mechanism.
JO  - Biochemistry
PY  - 1998
SP  - 15162
EP  - 15169
VL  - 37
AB  - DNA (cytosine-5-)-methyltransferase is essential for viable mammalian development and has a
AB  - central function in the determination and maintenance of epigenetic methylation patterns.
AB  - Steady-state and substrate trapping studies were performed to better understand how the enzyme
AB  - functions.  The catalytic efficiency was dependent on substrate DNA length.  A 14-fold
AB  - increase in KmDNA was observed as the length decreased from 5000 to 100 base pairs and kcat
AB  - decreased by a third.  Steady-state analyses were used to identify the order of substrate
AB  - addition onto the enzyme and the order of product release.  Double-reciprocal patterns of
AB  - velocity versus substrate concentration intersected far from the origin and were nearly
AB  - parallel.  The kinetic mechanism does not appear to change when the DNA substrate is either
AB  - 6250 or 100 base pairs in length.  Isotope trapping studies showed that the initial enzyme -
AB  - AdoMet complex was not catalytically competent; however, the initial enzyme-poly(dI.dC-dI.dC)
AB  - complex was observed to be competent for catalysis.  Product inhibition studies also support a
AB  - sequential ordered bi-bi kinetic mechanism in which DNA binds to the enzyme first, followed by
AB  - S-adenosyl-L-methionine, and then the products S-adenosyl-L-homocysteine and methylated DNA
AB  - are released.  The proposed mechanism is similar to the mechanism proposed for M.HhaI, a
AB  - bacterial DNA (cytosine-5-)-methyltransferase.  Evidence for an enzyme - DNA-DNA ternary
AB  - complex is also presented.
ER  -

TY  - JOUR
AU  - Flynn, J.
AU  - Reich, N.O.
TI  - Identification of flanking sequence dependence of DNA recognition for mammalian DNA cytosine methyltransferase.
JO  - FASEB J.
PY  - 1993
SP  - A1219
EP  - A1219
VL  - 7
AB  - Mammalian DNA cytosine 5-methyltransferase (DNA Mtase) is a DNA modification enzyme which has
AB  - been implicated to have an important role in gene regulation. Cytosines in the context of the
AB  - dinucleotide CpG are differentially methylated in the different tissue types of higher
AB  - eukaryotes. The pattern of methylation throughout the genome is believed to be heritable and
AB  - important for the development of differentiated cell types. The aim of our studies are to
AB  - answer to what extent sequences flanking a CpG determine the binding and catalytic activity of
AB  - DNA Mtase. Our procedure uses a random population of oligonucleotide substrates which contain
AB  - a central CpG dinucleotide flanked by 12 base pair degenerate regions on each side. The
AB  - degenerate regions have been made such that no additional CpG's can be introduced into the
AB  - oligos and contain equivalent proportions of all permutations. Partially purified enzyme was
AB  - used to create ternary complexes with cofactors and 32P end labeled DNA. Complexes using the
AB  - cofactors S-Adenosyl methionine, S-adenosyl homocysteine or sinefungin were shown to mobility
AB  - shift the double stranded DNA in polyacrylamide gels. The addition of DNA Mtase specific
AB  - antibodies to the reaction supershifts the DNA to a less mobile complex. The shifted DNA was
AB  - isolated and amplified by the polymerase chain reaction. When subjecting this DNA to further
AB  - rounds of selection preferential DNA flanking sequences survive. Through this application of
AB  - in vitro genetics CpG flanking sequence dependencies are being resolved.
ER  -

TY  - JOUR
AU  - Flynn, J.D. et al.
TI  - Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems.
JO  - Genome Announcements
PY  - 2016
SP  - e01629
EP  - e01615
VL  - 4
AB  - The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and
AB  - Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs
AB  - are typical members of coastal and hydrothermal vent marine ecosystems.
ER  -

TY  - JOUR
AU  - Foerg, E.
AU  - Saporito, L.
AU  - Huang, S.
AU  - Yang, J.
AU  - Allen, M.M.
TI  - Isolation and characterization of two sequence-specific endonucleases from the cyanobacterium Synechocystis sp. PCC 6308.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 105
EP  - 108
VL  - 69
AB  - The first two restriction endonucleases to be characterized in the cyanobacterium
AB  - Synechocystis sp. PCC 6308 are described.  SynI, an AvaII isoschizomer, recognizes the base
AB  - sequence 5'-GG[AT]CC-3'.  SynII, an XmnI isoschizomer, recognizes the sequence
AB  - 5'-GAANNNNTTC-3'.
ER  -

TY  - JOUR
AU  - Folaranmi, T.A. et al.
TI  - Increased Risk for Meningococcal Disease Among Men Who Have Sex With Men in the United States, 2012-2015.
JO  - Clin. Infect. Dis.
PY  - 2017
SP  - 756
EP  - 763
VL  - 65
AB  - Background: Several clusters of serogroup C meningococcal disease among men who
AB  - have sex with men (MSM) have been reported in the United States in recent years.
AB  - The epidemiology and risk of meningococcal disease among MSM is not well
AB  - described. Methods: All meningococcal disease cases among men aged 18-64 years
AB  - reported to the National Notifiable Disease Surveillance System between January
AB  - 2012 and June 2015 were reviewed. Characteristics of meningococcal disease cases
AB  - among MSM and men not known to be MSM (non-MSM) were described. Annualized
AB  - incidence rates among MSM and non-MSM were compared through calculation of the
AB  - relative risk and 95% confidence intervals. Isolates from meningococcal disease
AB  - cases among MSM were characterized using standard microbiological methods and
AB  - whole-genome sequencing. Results: Seventy-four cases of meningococcal disease
AB  - were reported among MSM and 453 among non-MSM. Annualized incidence of
AB  - meningococcal disease among MSM was 0.56 cases per 100000 population, compared to
AB  - 0.14 among non-MSM, for a relative risk of 4.0 (95% confidence interval [CI],
AB  - 3.1-5.1). Among the 64 MSM with known status, 38 (59%) were infected with human
AB  - immunodeficiency virus (HIV). HIV-infected MSM had 10.1 times (95% CI, 6.1-16.6)
AB  - the risk of HIV-uninfected MSM. All isolates from cluster-associated cases were
AB  - serogroup C sequence type 11. Conclusions: MSM are at increased risk for
AB  - meningococcal disease, although the incidence of disease remains low. HIV
AB  - infection may be an important factor for this increased risk. Routine vaccination
AB  - of HIV-infected persons with a quadrivalent meningococcal conjugate vaccine in
AB  - accordance with Advisory Committee on Immunization Practices recommendations
AB  - should be encouraged.
ER  -

TY  - JOUR
AU  - Foley, S.
AU  - Bruttin, A.
AU  - Brussow, H.
TI  - Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of streptococcus thermophilus bacteriophages.
JO  - J. Virol.
PY  - 2000
SP  - 611
EP  - 618
VL  - 74
AB  - Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings,
AB  - half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was
AB  - demonstrated. Five phages possess a variant form of the intron resulting from three distinct
AB  - deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf
AB  - 253 gene sequence showed a significantly lower GC content than the surrounding intron and
AB  - lysin gene sequences, and the predicted protein shared a motif with endonucleases found in
AB  - phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin
AB  - genes revealed a clear division between intron-containing and intron-free alleles, leading to
AB  - the establishment of a 14-bp consensus sequence associated with intron possession. The
AB  - conserved intron was not found elsewhere in the phage or S. thermophilus bacterial genomes.
AB  - Folding of the intron RNA revealed secondary structure elements shared with other phage
AB  - introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two
AB  - stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, a
AB  - conserved P7.2 region (shared with all phage introns); third, the location of the stop codon
AB  - from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns);
AB  - fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease
AB  - genes found in introns from Lactococcus, Lactobacillus, and Bacillus phages.
ER  -

TY  - JOUR
AU  - Follman, H.
AU  - Balzer, H.-J.
AU  - Schleicher, R.
TI  - Biosynthesis and distribution of methylcytosine in wheat DNA.  How different are plant DNA methyltransferases?
JO  - Nucleic Acid Methylation
PY  - 1990
SP  - 199
EP  - 210
VL  - 0
AB  - One reason for the high methylcytosine content of plant DNA may lie in the
AB  - specificity and activity of plant DNA methyltransferases.  We have analyzed the
AB  - properties of the DNA methylase system previously purified from wheat embryo
AB  - and find that it differs markedly enough from the known mammalian enzymes to
AB  - establish a plant-specific type of DNA methyltransferase.  These differences
AB  - reside, inter alia, in molecular weight, specificity towards DNA substrates of
AB  - varying methylation, and insensitivity towards inhibition by 5-azacytidine.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Akimov, V.N.
AU  - Vasilyeva, L.V.
AU  - Andersen, D.T.
AU  - Vincze, T.
AU  - Roberts, R.J.
TI  - Complete Genome and Methylome Analysis of Psychrotrophic Bacterial Isolates from  Lake Untersee in Antarctica.
JO  - Genome Announcements
PY  - 2017
SP  - e01753
EP  - e01716
VL  - 5
AB  - This paper describes the complete genome sequences and methylome analysis of six
AB  - psychrotrophic strains isolated from perennially ice-covered Lake Untersee in
AB  - Antarctica.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Clark, T.
AU  - Spittle, K.
AU  - Anton, B.M.
AU  - Vincze, T.
AU  - Korlach, J.
AU  - Roberts, R.J.
TI  - Molecular dissection of the methylome of Burkholderia cenocepacia J2315.
JO  - FEBS J.
PY  - 2013
SP  - 72
EP  - 73
VL  - 280
AB  - B. cenocepacia is a pathogenic gram-negative bacterium that often causes an opportunistic
AB  - infection in cystic fibrosis patients.  It is highly antibiotic-resistant, transmissible, and
AB  - often lethal.  Although genome sequences of several strains are available, the study of this
AB  - organism, like many pathogens, has been relatively limited, and genetic study is difficult.
AB  - The aim of this work was to analyze the genomic DNA methylation patterns from the sequenced
AB  - strain, J2315, and identify specificities of putative DNA methyltransferases.  This might
AB  - facilitate the development of an efficient transformation system to enhance genetic studies of
AB  - this strain.  We took advantage of the recently developed platform for single-molecule real
AB  - time sequencing by Pacific Biosciences.  This next generation sequencing technology allowed us
AB  - not only to perform high throughput DNA sequencing, but also to identify the epigenetic status
AB  - of the DNA using the polymerase's kinetic signature on the template during the reaction.  The
AB  - kinetic signature analysis of B. cenocepacia J2315 genomic DNA revealed three modified motifs.
AB  - Additionally, a number of ORF's encoding putative DNA methyltransferases were cloned into
AB  - plasmid vectors, and their specificities were determined using SMRT sequecing.  A type III
AB  - restriction-modificaiton system called M.BceJI resulted in m6A modification in the recognition
AB  - sequence CA-CAG.  98.4% of all CACAG sequences in the genome were modified on just one strand
AB  - as indicated, which is typical of a Type III methyltransferase.  Cloning ORF BCAL3494 showed
AB  - it to be the gene responsible.  The genomic motif GTWWAC, containing a symmetrical
AB  - double-stranded m6A modification, was 95.7% modified in the genome and was caused by the
AB  - product of ORF BCAL992 and was called M.BceJIV.  Another modified motif with m4C modification
AB  - was detected at the low rate of 4.8% within the eight base pair motif GCGGCCGC.  This was
AB  - probably caused by the product of ORF BCAL1036, although when this was cloned and expressed at
AB  - high levels the central tetranucleotide GGCC was m4C modified at high levels.  We called this
AB  - methyltransferase M.BceJII.  Surprisingly, we also detected an unusual kinetic signature on
AB  - the G base that is also associated with the four base core of the GCGGCCGC motif.  We still do
AB  - not know which enzyme is responsible for this G modification.  Preliminary results suggest
AB  - that M.BceJORF178P might also lead to G modification on the first base in the sequence GGNNTA
AB  - albeit with a low IPD ratio in vitro.  This enzyme is highly toxic in E. coli, which has so
AB  - far made a determination of its specificity very difficult.  One rather interesting
AB  - methyltransferase is encoded by ORF pBCA072, which is located on a plasmid.  It results in
AB  - single-stranded, non-specific m6A modification, but was only detected on plasmid DNA.  We have
AB  - called this enzyme M.BceJIII.  A similar enzyme has been found on an E. coli plasmid and both
AB  - could possibly play a restricted role during DNA replication.  The M and S subunits of a
AB  - putative Type I restriction-modification system BceJORF418P have been cloned, but no
AB  - modifications were detected either on genomic or plasmid DNA indicating that the system is
AB  - probably inactive in this strain.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Lunnen, K.D.
AU  - Zhu, Z.
AU  - Anton, B.P.
AU  - Wilson, G.G.
AU  - Vincze, T.
AU  - Roberts, R.J.
TI  - Complete genome sequence and methylome analysis of Bacillus strain X1.
JO  - Genome Announcements
PY  - 2015
SP  - e01593
EP  - e01514
VL  - 3
AB  - Bacillus strain X1 is the source strain for the restriction enzyme BstXI. Its complete
AB  - sequence and full methylome was determined using single-molecule real-time (SMRT) sequencing.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Sun, Z.
AU  - Dila, D.K.
AU  - Anton, B.P.
AU  - Roberts, R.J.
AU  - Raleigh, E.A.
TI  - EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage  site determination.
JO  - PLoS ONE
PY  - 2017
SP  - e0179853
EP  - e0179853
VL  - 12
AB  - Here we characterize the modification-dependent restriction enzyme (MDE) EcoBLMcrX in vivo, in
AB  - vitro and in its genomic environment. MDE cleavage of
AB  - modified DNAs protects prokaryote populations from lethal infection by
AB  - bacteriophage with highly modified DNA, and also stabilizes lineages by reducing
AB  - gene import when sparse modification occurs in the wrong context. The function
AB  - and distribution of MDE families are thus important. Here we describe the
AB  - properties of EcoBLMcrX, an enzyme of the E. coli B lineage, in vivo and in
AB  - vitro. Restriction in vivo and the genome location of its gene, ecoBLmcrX, were
AB  - determined during construction and sequencing of a B/K-12 hybrid, ER2566. In
AB  - classical restriction literature, this B system was named r6 or rglAB. Like many
AB  - genome defense functions, ecoBLmcrX is found within a genomic island, where gene
AB  - content is variable among natural E. coli isolates. In vitro, EcoBLMcrX was
AB  - compared with two related enzymes, BceYI and NhoI. All three degrade fully
AB  - cytosine-modified phage DNA, as expected for EcoBLMcrX from classical T4 genetic
AB  - data. A new method of characterizing MDE specificity was developed to better
AB  - understand action on fully-modified targets such as the phage that provide major
AB  - evolutionary pressure for MDE maintenance. These enzymes also cleave plasmids
AB  - with m5C in particular motifs, consistent with a role in lineage-stabilization.
AB  - The recognition sites were characterized using a site-ranking approach that
AB  - allows visualization of preferred cleavage sites when fully-modified substrates
AB  - are digested. A technical constraint on the method is that ligation of
AB  - one-nucleotide 5' extensions favors G:C over A:T approximately five-fold. Taking
AB  - this bias into account, we conclude that EcoBLMcrX can cleave 3' to the modified
AB  - base in the motif Rm5C|. This is compatible with, but less specific than, the
AB  - site reported by others. Highly-modified site contexts, such as those found in
AB  - base-substituted virulent phages, are strongly preferred.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Sun, Z.
AU  - Vincze, T.
AU  - Dubinina, G.
AU  - Orlova, M.
AU  - Tarlachkov, S.V.
AU  - Anton, B.P.
AU  - Grabovich, M.Y.
AU  - Roberts, R.J.
TI  - Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.
JO  - Genome Announcements
PY  - 2018
SP  - e00311
EP  - e00318
VL  - 6
AB  - Here, we report the complete closed genome sequence and methylome analysis of Beggiatoa
AB  - leptomitoformis strain D-401 (DSM 14945, UNIQEMU 779), which is quite
AB  - different from the previously described Beggiatoa leptomitoformis neotype strain
AB  - D-402(T) (DSM 14946, UNIQEM U 779) with regard to morphology and lithotrophic
AB  - growth in the presence of thiosulfate.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Vincze, T.
AU  - Degtyarev, S.K.
AU  - Roberts, R.J.
TI  - Complete Genome Sequence and Methylome Analysis of Acinetobacter calcoaceticus 65.
JO  - Genome Announcements
PY  - 2017
SP  - e00060
EP  - e00017
VL  - 5
AB  - Acinetobacter calcoaceticus 65 is the original source strain for the restriction  enzyme
AB  - Acc65I. Its complete sequence and full methylome were determined using
AB  - single-molecule real-time (SMRT) sequencing.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Vincze, T.
AU  - Grabovich, M.
AU  - Anton, B.P.
AU  - Dubinina, G.
AU  - Orlova, M.
AU  - Belousova, E.
AU  - Roberts, R.J.
TI  - Complete Genome Sequence of a Strain of Azospirillum thiophilum Isolated from a Sulfide Spring.
JO  - Genome Announcements
PY  - 2016
SP  - e01521
EP  - e01515
VL  - 4
AB  - We report the complete, closed genome sequence and complete methylome of Azospirillum
AB  - thiophilum strain BV-S(T).
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Vincze, T.
AU  - Grabovich, M.Y.
AU  - Dubinina, G.
AU  - Orlova, M.
AU  - Belousova, E.
AU  - Roberts, R.J.
TI  - Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitiformis Neotype Strain D-402T.
JO  - Genome Announcements
PY  - 2015
SP  - e01436
EP  - e01415
VL  - 3
AB  - In this report, we announce the availability of a complete closed genome sequence and
AB  - methylome analysis of Beggiatoa leptomitiformis neotype strain D-402(T) (DSM
AB  - 14946, UNIQEM U 779).
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Vincze, T.
AU  - Grabovich, M.Y.
AU  - Dubinina, G.
AU  - Orlova, M.
AU  - Belousova, E.
AU  - Roberts, R.J.
TI  - Whole-Genome Sequence and Methylome Analysis of the Freshwater Colorless Sulfur Bacterium Thioflexothrix psekupsii D3.
JO  - Genome Announcements
PY  - 2017
SP  - e00904
EP  - e00917
VL  - 5
AB  - In this report, we announce the availability of a whole-genome sequence and methylome analysis
AB  - of Thioflexothrix psekupsii strain D3.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Vincze, T.
AU  - Mersha, F.
AU  - Roberts, R.J.
TI  - Complete Genome Sequence and Methylome Analysis of Bacillus caldolyticus NEB414.
JO  - Genome Announcements
PY  - 2018
SP  - e01605
EP  - e01617
VL  - 6
AB  - Bacillus caldolyticus NEB414 is the original source strain for the restriction enzyme BclI.
AB  - Its complete sequence and full methylome were determined using
AB  - single-molecule real-time sequencing.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Xiao, J.-P.
AU  - Dila, D.
AU  - Raleigh, E.
AU  - Xu, S.-Y.
TI  - The 'endo-blue method' for direct cloning of restriction endonuclease genes in E. coli.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 2399
EP  - 2403
VL  - 22
AB  - A new E. coli strain has been constructed that contains the dinD1::LacZ+ fusion and is
AB  - deficient in methylation-dependent restriction systems (McrA-, McrBC-, Mrr-). This strain has
AB  - been used to clone restriction endonuclease genes directly into E. coli. When E. coli cells
AB  - are not fully protected by the cognate methylase, the restriction enzyme damages the DNA in
AB  - vivo and induces the SOS response. The SOS-induced cells form blue colonies on indicator
AB  - plates containing X-gal. Using this method the genes coding for the thermostable restriction
AB  - enzymes TaqI (5'TCGA3') and Tth111I (5'GACNNNGTC3') have been successfully cloned in E.
AB  - coli. The new strain will be useful to clone other genes involved in DNA metabolism.
ER  -

TY  - JOUR
AU  - Fomenkov, A.
AU  - Xu, S.-Y.
TI  - Isolation of temperature-sensitive mutants of the BamHI restriction endonuclease.
JO  - Gene
PY  - 1995
SP  - 303
EP  - 310
VL  - 157
AB  - Two heat-sensitive R.BamHI mutants, T157I and P173L, and one cold-sensitive R.BamHI mutant,
AB  - T114I, were isolated after chemical mutagenesis of the bamhIR gene that codes for the
AB  - restriction endonuclease BamHI (R.BamHI).  The thermosensitivity of T114I, T157I and P173L is
AB  - revealed by the 10/2-10/3 lower plating efficiency at the non-permissive temperature of
AB  - strains bearing these alleles.  The conditional-lethal phenotype can be rescued by
AB  - introduction of the cognate bamhIM gene into the same cell.  The mutant enzymes induce the SOS
AB  - response in vivo and display reduced phage restriction activity.  The P173L protein, when
AB  - expressed at 30oC and purified, shows reduced thermostability at 65oC.  T157I and P173L
AB  - mutants yield different intermediates during partial trypsin digestion.  The
AB  - conditional-lethal BamHI mutants could be used to deliver in vivo DNA cleavage and for further
AB  - isolation of relaxed-specificity mutants.
ER  -

TY  - JOUR
AU  - Fomenkov, A.I.
AU  - Kramarov, V.M.
AU  - Andreev, L.V.
AU  - Mochalov, V.V.
AU  - Smolyaninov, V.V.
AU  - Matvienko, N.I.
TI  - Isolation and properties of a new site specific endonuclease Bme142I from Bacillus megaterium 142.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 10399
EP  - 10399
VL  - 16
AB  - A new type II restriction endonuclease, Bme142I, was partially purified and characterized from
AB  - Bacillus megaterium 142.  It has been seen in a crude extract, because this bacterial strain
AB  - does not have significant amounts of contaminating nucleases.  The enzyme was purified by
AB  - chromatography on phosphocellulose P11 (elution buffer - 10 mM K-phosphate, pH 7.0, 0.1 mM
AB  - EDTA, 2 mM DTT, 0.2 - 1 M NaCl) and hydroxyapatite (elution buffer - 0.01 - 0.5 M K-phosphate,
AB  - pH 7.0, 1 mM EDTA, 2 mM DTT).  Yield of enzyme is 2000 units per gram of wet cells.  The
AB  - enzyme is stable in elution buffer and may be stored at -20C after addition of glycerol to
AB  - 50%.  The recognition site was determined from the cleavage pattern of pBR322 plasmid.  The
AB  - 5'-end nucleotide is G.  This has been shown by incubation of the 5'-end labelled DNA
AB  - fragments with nuclease P1 followed by thin-layer chromatography on a PEI cellulose plate.
AB  - The points of cleavage of the recognition site were determined by the Maxam-Gilbert method.
AB  - In contrast to its isoschizomer, the restriction endonuclease HaeII, which cleaves the same
AB  - recognition site to produce a 4 base 3' extension, the Bme142I produces blunt-ended DNA
AB  - fragments:
AB  - 5' PuGC^GCPy 3'
AB  - 3' PyCG^CGPu 5'.
ER  -

TY  - JOUR
AU  - Fondi, M.
AU  - Orlandini, V.
AU  - Emiliani, G.
AU  - Papaleo, M.C.
AU  - Maida, I.
AU  - Perrin, E.
AU  - Vaneechoutte, M.
AU  - Dijkshoorn, L.
AU  - Fani, R.
TI  - Draft Genome Sequence of the Hydrocarbon-Degrading and Emulsan-Producing Strain Acinetobacter venetianus RAG-1T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4771
EP  - 4772
VL  - 194
AB  - We report the draft genome sequence of Acinetobacter venetianus strain RAG-1(T),  which is
AB  - able to degrade hydrocarbons and to synthesize a powerful biosurfactant
AB  - (emulsan) that can be employed for oil removal and as an adjuvant for vaccine
AB  - delivery. The genome sequence of A. venetianus RAG-1(T) might be useful for
AB  - bioremediation and/or clinical purposes.
ER  -

TY  - JOUR
AU  - Fondi, M.
AU  - Orlandini, V.
AU  - Maida, I.
AU  - Perrin, E.
AU  - Papaleo, M.C.
AU  - Emiliani, G.
AU  - de Pascale, D.
AU  - Parrilli, E.
AU  - Tutino, M.L.
AU  - Michaud, L.
AU  - Lo, G.A.
AU  - Fani, R.
TI  - Draft Genome Sequence of the Volatile Organic Compound-Producing Antarctic Bacterium Arthrobacter sp. Strain TB23, Able To Inhibit Cystic Fibrosis Pathogens  Belonging to the Burkholderia cepacia Complex.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6334
EP  - 6335
VL  - 194
AB  - Arthrobacter sp. strain TB23 was isolated from the Antarctic sponge Lissodendoryx nobilis.
AB  - This bacterium is able to produce antimicrobial compounds and volatile
AB  - organic compounds (VOCs) that inhibit the growth of other Antarctic bacteria and
AB  - of cystic fibrosis opportunistic pathogens, respectively. Here we report the
AB  - draft genome sequence of Arthrobacter sp. TB23.
ER  -

TY  - JOUR
AU  - Fonfara, I.
AU  - Curth, U.
AU  - Pingoud, A.
AU  - Wende, W.
TI  - Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 847
EP  - 860
VL  - 40
AB  - Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding
AB  - module and a non-specific DNA-cleavage module,
AB  - resulting in nucleases able to cleave DNA at a unique sequence. Here a new
AB  - approach for creating highly specific nucleases was pursued by fusing a
AB  - catalytically inactive variant of the homing endonuclease I-SceI, as DNA
AB  - binding-module, to the type IIP restriction enzyme PvuII, as cleavage
AB  - module. The fusion enzymes were designed to recognize a composite site
AB  - comprising the recognition site of PvuII flanked by the recognition site
AB  - of I-SceI. In order to reduce activity on PvuII sites lacking the flanking
AB  - I-SceI sites, the enzymes were optimized so that the binding of I-SceI to
AB  - its sites positions PvuII for cleavage of the composite site. This was
AB  - achieved by optimization of the linker and by introducing amino acid
AB  - substitutions in PvuII which decrease its activity or disturb its dimer
AB  - interface. The most specific variant showed a more than 1000-fold
AB  - preference for the addressed composite site over an unaddressed PvuII
AB  - site. These results indicate that using a specific restriction enzyme,
AB  - such as PvuII, as cleavage module, offers an alternative to the otherwise
AB  - often used catalytic domain of FokI, which by itself does not contribute
AB  - to the specificity of the engineered nuclease.
ER  -

TY  - JOUR
AU  - Fontana, C.A.
AU  - Salazar, S.M.
AU  - Bassi, D.
AU  - Puglisi, E.
AU  - Lovaisa, N.
AU  - Toffoli, L.M.
AU  - Pedraza, R.
AU  - Cocconcelli, P.S.
TI  - Genome Sequence of Azospirillum brasilense REC3, Isolated from Strawberry Plants.
JO  - Genome Announcements
PY  - 2018
SP  - e00089
EP  - e00018
VL  - 6
AB  - The genome sequence of a plant growth-promoting bacterium and biocontrol agent, Azospirillum
AB  - brasilense REC3, isolated from strawberry roots, is reported here.
AB  - The A. brasilense REC3 total genome contains 7,229,924 bp and has a G+C content
AB  - of 68.7 mol%.
ER  -

TY  - JOUR
AU  - Fontana, P.D.
AU  - Fontana, C.A.
AU  - Bassi, D.
AU  - Puglisi, E.
AU  - Salazar, S.M.
AU  - Vignolo, G.M.
AU  - Coccocelli, P.S.
TI  - Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red  Stripe in Argentina.
JO  - Genome Announcements
PY  - 2016
SP  - e01669
EP  - e01615
VL  - 4
AB  - Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax  avenae. The
AB  - genome sequence from the first isolate of this bacterium in Argentina
AB  - is presented here. The draft genome of the A. avenae T10_61 strain contains
AB  - 5,646,552 bp and has a G+C content of 68.6 mol%.
ER  -

TY  - JOUR
AU  - Fontes-Perez, H.
AU  - Olvera-Garcia, M.
AU  - Chavez-Martinez, A.
AU  - Rodriguez-Almeida, F.A.
AU  - Arzola-Alvarez, C.A.
AU  - Sanchez-Flores, A.
AU  - Corral-Luna, A.
TI  - Genome Sequence of Citrobacter sp. CtB7.12, Isolated from the Gut of the Desert Subterranean Termite Heterotermes aureus.
JO  - Genome Announcements
PY  - 2015
SP  - e01290
EP  - e01215
VL  - 3
AB  - The draft genome of Citrobacter sp. CtB7.12, isolated from termite gut, is presented here.
AB  - This organism has been reported as a cellulolytic bacterium,
AB  - which is biotechnologically important because it can be used as a gene donor for
AB  - the ethanol and biofuel industries.
ER  -

TY  - JOUR
AU  - Foo, S.M.
AU  - Eng, W.W.H.
AU  - Lee, Y.P.
AU  - Gui, K.
AU  - Gan, H.M.
TI  - New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing.
JO  - Genome Announcements
PY  - 2017
SP  - e00302
EP  - e00317
VL  - 5
AB  - The acquisition of Photorhabdus insect-related (Pir) toxin-like genes in Vibrio
AB  - parahaemolyticus has been linked to hepatopancreatic necrosis disease in shrimp.
AB  - We report the whole-genome sequences of genetically virulent and avirulent V.
AB  - parahaemolyticus isolated from a Malaysian aquaculture pond and show that they
AB  - represent previously unreported sequence types of V. parahaemolyticus.
ER  -

TY  - JOUR
AU  - Fookes, M.
AU  - Yu, J.
AU  - De Majumdar, S.
AU  - Thomson, N.
AU  - Schneiders, T.
TI  - Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation.
JO  - Genome Announcements
PY  - 2013
SP  - e00027
EP  - e00012
VL  - 1
AB  - We report the genome sequence of Klebsiella pneumoniae subsp. pneumoniae Ecl8, a  spontaneous
AB  - streptomycin-resistant mutant of strain ECL4, derived from NCIB 418.
AB  - K. pneumoniae Ecl8 has been shown to be genetically tractable for targeted gene
AB  - deletion strategies and so provides a platform for in-depth analyses of this
AB  - species.
ER  -

TY  - JOUR
AU  - Foray, V.
AU  - Grigorescu, A.S.
AU  - Sabri, A.
AU  - Haubruge, E.
AU  - Lognay, G.
AU  - Francis, F.
AU  - Fauconnier, M.L.
AU  - Hance, T.
AU  - Thonart, P.
TI  - Whole-Genome Sequence of Serratia symbiotica Strain CWBI-2.3T, a Free-Living Symbiont of the Black Bean Aphid Aphis fabae.
JO  - Genome Announcements
PY  - 2014
SP  - e00767
EP  - e00714
VL  - 2
AB  - The gammaproteobacterium Serratia symbiotica is one of the major secondary symbionts found in
AB  - aphids. Here, we report the draft genome sequence of S.
AB  - symbiotica strain CWBI-2.3(T), previously isolated from the black bean aphid
AB  - Aphis fabae. The 3.58-Mb genome sequence might provide new insights to understand
AB  - the evolution of insect-microbe symbiosis.
ER  -

TY  - JOUR
AU  - Ford, E.
AU  - Boyer, H.W.
TI  - Degradation of enteric bacterial deoxyribonucleic acid by the Escherichia coli B restriction endonuclease.
JO  - J. Bacteriol.
PY  - 1970
SP  - 594
EP  - 595
VL  - 104
AB  - the deoxyribonucleic acid of five different genera of enteric microorganisms
AB  - was shown to be degraded by the Escherichia coli B restriction endonuclease.
ER  -

TY  - JOUR
AU  - Ford, K.
AU  - Taylor, C.
AU  - Connolly, B.
AU  - Hornby, D.P.
TI  - Effects of co-factor and deoxycytidine substituted oligonucleotides upon sequence-specific interations between MspI DNA methyltransferase and DNA.
JO  - J. Mol. Biol.
PY  - 1993
SP  - 779
EP  - 786
VL  - 230
AB  - MspI methyltransferase (M.MspI) catalyses the transfer of a methyl group from
AB  - S-adenosyl-L-methionine to the C-5 position of the outer deoxycytidine base in the DNA
AB  - sequence 5'-CCGG-3'. Recombinant M.MspI when expressed and purified as a translational
AB  - fusion with glutathione-S-transferase, shows all of the properties of the wild-type enzyme. We
AB  - report the kinetic analysis of M.MspI binding to DNA, which suggests a two-stage methylation
AB  - process, whose initial DNA binding rate is governed by the presence of a positively charged
AB  - sulphonium centre of the coafactor. Results are also presented that indicate that M.MspI binds
AB  - preferentially to hemi-methylated DNA and that full methylation of either deoxycytidine on
AB  - both strands significantly impairs sequence-specific protein-DNA interactions. Furthermore,
AB  - the importance of the 4-amino group of the inner deoxycytidine for sequence-specific
AB  - protein-DNA interactions is demonstrated by substituting deoxycytidine with
AB  - 2-pyrimidinone-1-beta-D-2-deoxyriboside. In addition, we detail the intrinsic structural
AB  - elements of a cofactor, required to enhance the binding of M.MspI to its recognition sequence
AB  - by using S-adenosyl-L-methionine and a range of derivatives.
ER  -

TY  - JOUR
AU  - Forde, A.
AU  - Daly, C.
AU  - Fitzgerald, G.F.
TI  - Identification of four phage resistance plasmids from Lactococcus lactis subsp. cremoris HO2.
JO  - Appl. Environ. Microbiol.
PY  - 1999
SP  - 1540
EP  - 1547
VL  - 65
AB  - The bacteriophage-host sensitivity patterns of 16 strains of Lactococcus lactis originally
AB  - isolated from a mixed strain Cheddar cheese starter culture were determined.  Using phages
AB  - obtained from cheese factory whey, four of the strains were found to be highly phage
AB  - resistant.  One of these isolates, Lactococcus lactis subsp. cremoris HO2, was studied in
AB  - detail to determine the mechanisms responsible for the phage insensitivity phenotypes.
AB  - Conjugal transfer of plasmid DNA from strain HO2 allowed a function to be assigned to four of
AB  - its six plasmids.  A 460kb molecule, designated pCI646, was found to harbor the lactose
AB  - utilization genes, while this and plasmids of 58 kb (pCI658), 42 kb (pCI642), and 4.5 kb
AB  - (pCI605) were shown to be responsible for the phage resistance phenotypes observed against the
AB  - small isometric-headed phage omega-712 (936 phage species) and the prolate-headed phage
AB  - omega-c2 (c2 species).  PCI658 was found to mediate an adsorption-blocking mechanism and was
AB  - also responsible for the fluffy pellet phenotype of cells containing the molecule.  PCI642 and
AB  - pCI605 were both shown to be required for the operation of a restriction-modification system.
ER  -

TY  - JOUR
AU  - Forde, A.
AU  - Fitzgerald, G.F.
TI  - Bacteriophage defence systems in lactic acid bacteria.
JO  - Antonie Van Leeuwenhoek
PY  - 1999
SP  - 89
EP  - 113
VL  - 76
AB  - The study of the interactions between lactic acid bacteria and their bacteriophages has been a
AB  - vibrant and rewarding research activity for a considerable number of years. In the more recent
AB  - past, the application of molecular genetics for the analysis of phage-host relationships has
AB  - contributed enormously to the unravelling of specific events which dictate insensitivity to
AB  - bacteriophage infection and has revealed that while they are complex and intricate in nature,
AB  - they are also extremely effective. In addition, the strategy has laid solid foundations for
AB  - the construction of phage resistant strains for use in commercial applications and has
AB  - provided a sound basis for continued investigations into existing, naturally-derived and
AB  - novel, genetically-engineered defence systems. Of course, it has also become clear that phage
AB  - particles are highly dynamic in their response to those defence systems which they do
AB  - encounter and that they can readily adapt to them as a consequence of their genetic
AB  - flexibility and plasticity. This paper reviews the exciting developments that have been
AB  - described in the literature regarding the study of phage-host interactions in lactic acid
AB  - bacteria and the innovative approaches that can be taken to exploit this basic information for
AB  - curtailing phage infection.
ER  -

TY  - JOUR
AU  - Forde, B.M.
AU  - Ben Zakour, N.L.
AU  - Stanton-Cook, M.
AU  - Phan, M.D.
AU  - Totsika, M.
AU  - Peters, K.M.
AU  - Chan, K.G.
AU  - Schembri, M.A.
AU  - Upton, M.
AU  - Beatson, S.A.
TI  - The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.
JO  - PLoS ONE
PY  - 2014
SP  - E104400
EP  - E104400
VL  - 9
AB  - Escherichia coli ST131 is now recognised as a leading contributor to urinary
AB  - tract and bloodstream infections in both community and clinical settings. Here we
AB  - present the complete, annotated genome of E. coli EC958, which was isolated from
AB  - the urine of a patient presenting with a urinary tract infection in the Northwest
AB  - region of England and represents the most well characterised ST131 strain.
AB  - Sequencing was carried out using the Pacific Biosciences platform, which provided
AB  - sufficient depth and read-length to produce a complete genome without the need
AB  - for other technologies. The discovery of spurious contigs within the assembly
AB  - that correspond to site-specific inversions in the tail fibre regions of
AB  - prophages demonstrates the potential for this technology to reveal dynamic
AB  - evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131
AB  - strains that produce the CTX-M-15 extended spectrum beta-lactamase, are
AB  - fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This
AB  - subgroup includes the Indian strain NA114 and the North American strain JJ1886. A
AB  - comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in
AB  - the arrangement of genomic islands, prophages and other repetitive elements in
AB  - the NA114 genome are not biologically relevant and are due to misassembly. The
AB  - availability of a high quality uropathogenic E. coli ST131 genome provides a
AB  - reference for understanding this multidrug resistant pathogen and will facilitate
AB  - novel functional, comparative and clinical studies of the E. coli ST131 clonal
AB  - lineage.
ER  -

TY  - JOUR
AU  - Forde, B.M.
AU  - Neville, B.A.
AU  - O'Donnell, M.M.
AU  - Riboulet-Bisson, E.
AU  - Claesson, M.J.
AU  - Coughlan, A.
AU  - Ross, R.P.
AU  - O'Toole, P.W.
TI  - Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts.
JO  - Microb. Cell Fact.
PY  - 2011
SP  - S13
EP  - S13
VL  - 10
AB  - Background: The genus Lactobacillus is characterized by an extraordinary degree of phenotypic
AB  - and genotypic
AB  - diversity, which recent genomic analyses have further highlighted. However, the choice of
AB  - species for sequencing
AB  - has been non-random and unequal in distribution, with only a single representative genome from
AB  - the L. salivarius
AB  - clade available to date. Furthermore, there is no data to facilitate a functional genomic
AB  - analysis of motility in the
AB  - lactobacilli, a trait that is restricted to the L. salivarius clade.
AB  - Results: The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a
AB  - single circular
AB  - chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding
AB  - sequences, including genes
AB  - for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase
AB  - enzymes, two CRISPR
AB  - loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin
AB  - was identified, and
AB  - shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L.
AB  - ruminis strain, ATCC
AB  - 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a
AB  - high degree of
AB  - synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L.
AB  - salivarius identified a
AB  - lack of long-range synteny between these closely related species. Comparison of the L.
AB  - salivarius clade core
AB  - proteins with those of nine other Lactobacillus species distributed across 4 major
AB  - phylogenetic groups identified
AB  - the set of shared proteins, and proteins unique to each group.
AB  - Conclusions: The genome of L. ruminis provides a comparative tool for directing functional
AB  - analyses of other
AB  - members of the L. salivarius clade, and it increases understanding of the divergence of this
AB  - distinct Lactobacillus
AB  - lineage from other commensal lactobacilli. The genome sequence provides a definitive resource
AB  - to facilitate
AB  - investigation of the genetics, biochemistry and host interactions of these motile intestinal
AB  - lactobacilli.
ER  -

TY  - JOUR
AU  - Forde, B.M.
AU  - Phan, M.D.
AU  - Gawthorne, J.A.
AU  - Ashcroft, M.M.
AU  - Stanton-Cook, M.
AU  - Sarkar, S.
AU  - Peters, K.M.
AU  - Chan, K.G.
AU  - Chong, T.M.
AU  - Yin, W.F.
AU  - Upton, M.
AU  - Schembri, M.A.
AU  - Beatson, S.A.
TI  - Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone.
JO  - MBio
PY  - 2015
SP  - e01602
EP  - e01615
VL  - 6
AB  - Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has
AB  - emerged rapidly and disseminated globally in both clinical and community
AB  - settings. Members of the ST131 lineage from across the globe have been
AB  - comprehensively characterized in terms of antibiotic resistance, virulence
AB  - potential, and pathogenicity, but to date nothing is known about the methylome of
AB  - these important human pathogens. Here we used single-molecule real-time (SMRT)
AB  - PacBio sequencing to determine the methylome of E. coli EC958, the
AB  - most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081
AB  - methylated adenines in the genome of EC958 discovered three m6A methylation
AB  - motifs that have not been described previously. Subsequent SMRT sequencing of
AB  - isogenic knockout mutants identified the two type I methyltransferases (MTases)
AB  - and one type IIG MTase responsible for m6A methylation of novel recognition
AB  - sites. Although both type I sites were rare, the type IIG sites accounted for
AB  - more than 12% of all methylated adenines in EC958. Analysis of the distribution
AB  - of MTase genes across 95 ST131 genomes revealed their prevalence is highly
AB  - conserved within the ST131 lineage, with most variation due to the presence or
AB  - absence of mobile genetic elements on which individual MTase genes are located.
AB  - IMPORTANCE: DNA modification plays a crucial role in bacterial regulation.
AB  - Despite several examples demonstrating the role of methyltransferase (MTase)
AB  - enzymes in bacterial virulence, investigation of this phenomenon on a
AB  - whole-genome scale has remained elusive until now. Here we used single-molecule
AB  - real-time (SMRT) sequencing to determine the first complete methylome of a strain
AB  - from the multidrug-resistant E. coli sequence type 131 (ST131) lineage. By
AB  - interrogating the methylome computationally and with further SMRT sequencing of
AB  - isogenic mutants representing previously uncharacterized MTase genes, we defined
AB  - the target sequences of three novel ST131-specific MTases and determined the
AB  - genomic distribution of all MTase target sequences. Using a large collection of
AB  - 95 previously sequenced ST131 genomes, we identified mobile genetic elements as a
AB  - major factor driving diversity in DNA methylation patterns. Overall, our analysis
AB  - highlights the potential for DNA methylation to dramatically influence gene
AB  - regulation at the transcriptional level within a well-defined E. coli clone.
ER  -

TY  - JOUR
AU  - Forde, G.K.
AU  - Kedzierski, P.
AU  - Sokalski, W.A.
AU  - Forde, A.E.
AU  - Hill, G.A.
AU  - Leszczynski, J.
TI  - Physical nature of interactions within the active site of cytosine-5-methyltransferase.
JO  - J. Phys. Chem. A
PY  - 2006
SP  - 2308
EP  - 2313
VL  - 110
AB  - The physical nature of interactions within the active site of cytosine-5-methyltransferase
AB  - (CMT) was studied using a
AB  - variation-perturbation energy decomposition scheme defining a sequence
AB  - of approximate intermolecular interaction energy models. These models
AB  - have been used to analyze the catalytic activity of residues
AB  - constituting cytosine-5-methyltransferase active site as well their
AB  - role in the binding group of de novo designed inhibitors. Our results
AB  - indicate that Glu119, Arg163, and Arg165 appear to play the dominant
AB  - role in stabilizing the protonated transition state structure and their
AB  - influence can be qualitatively approximated by electrostatic
AB  - interactions alone. The stabilization of neutral structures of the
AB  - alternative reaction pathway is small, which might suggest the
AB  - protonated pathway as preferred by the enzyme. Exchange and
AB  - delocalization terms are negligible in most cases, or they cancel each
AB  - other to some extent. Interactions of inhibitors with the CMT active
AB  - site are dominated by electrostatic multipole contributions in analogy
AB  - with previously studied transition state analogue inhibitors of leucyl
AB  - aminopeptidase.
ER  -

TY  - JOUR
AU  - Foret, S.
AU  - Kucharski, R.
AU  - Pellegrini, M.
AU  - Feng, S.
AU  - Jacobsen, S.E.
AU  - Robinson, G.E.
AU  - Maleszka, R.
TI  - DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 4968
EP  - 4973
VL  - 109
AB  - In honey bees (Apis mellifera), the development of a larva into either a queen or worker
AB  - depends on differential feeding with royal jelly and involves epigenomic
AB  - modifications by DNA methyltransferases. To understand the role of DNA
AB  - methylation in this process we sequenced the larval methylomes in both queens and
AB  - workers. We show that the number of differentially methylated genes (DMGs) in
AB  - larval head is significantly increased relative to adult brain (2,399 vs. 560)
AB  - with more than 80% of DMGs up-methylated in worker larvae. Several highly
AB  - conserved metabolic and signaling pathways are enriched in methylated genes,
AB  - underscoring the connection between dietary intake and metabolic flux. This
AB  - includes genes related to juvenile hormone and insulin, two hormones shown
AB  - previously to regulate caste determination. We also tie methylation data to
AB  - expressional profiling and describe a distinct role for one of the DMGs encoding
AB  - anaplastic lymphoma kinase (ALK), an important regulator of metabolism. We show
AB  - that alk is not only differentially methylated and alternatively spliced in Apis,
AB  - but also seems to be regulated by a cis-acting, anti-sense non-protein-coding
AB  - transcript. The unusually complex regulation of ALK in Apis suggests that this
AB  - protein could represent a previously unknown node in a process that activates
AB  - downstream signaling according to a nutritional context. The correlation between
AB  - methylation and alternative splicing of alk is consistent with the recently
AB  - described mechanism involving RNA polymerase II pausing. Our study offers
AB  - insights into diet-controlled development in Apis.
ER  -

TY  - JOUR
AU  - Formighieri, E.F. et al.
TI  - The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid.
JO  - Mycol. Res.
PY  - 2008
SP  - 1136
EP  - 1152
VL  - 112
AB  - We present here the sequence of the mitochondrial genome of the basidiomycete phytopathogenic
AB  - hemibiotrophic fungus Moniliophthora perniciosa, causal agent of the Witches' Broom Disease
AB  - in Theobroma cacao.
AB  - The DNA is a circular molecule of 109,103 base pairs, with 31.9% GC, and is the largest
AB  - sequenced so far. This size is due essentially to the presence of numerous non-conserved
AB  - hypothetical ORFs. It contains the 14 genes coding for proteins involved in the oxidative
AB  - phosphorylation, the two rRNA genes, one ORF coding for a ribosomal protein (rps3), and a set
AB  - of 26 tRNA genes that recognize codons for all amino acids. Seven homing endonucleases are
AB  - located inside introns. Except atp8, all conserved known genes are in the same orientation.
AB  - Phylogenetic analysis based on the cox genes agrees with the commonly accepted fungal
AB  - taxonomy. An uncommon feature of this mitochondrial genome is the presence of a region that
AB  - contains a set of four, relatively small, nested, inverted repeats enclosing two genes coding
AB  - for polymerases with an invertron-type structure and three conserved hypothetical genes
AB  - interpreted as the stable integration of a mitochondrial linear plasmid. The integration of
AB  - this plasmid seems to be a recent evolutionary event that could have implications in fungal
AB  - biology. This sequence is available under GenBank accession number AY376688.
ER  -

TY  - JOUR
AU  - Formusa, P.A.
AU  - Hsiang, T.
AU  - Habash, M.B.
AU  - Lee, H.
AU  - Trevors, J.T.
TI  - Genome Sequence of Pseudomonas mandelii PD30.
JO  - Genome Announcements
PY  - 2014
SP  - e00713
EP  - e00714
VL  - 2
AB  - The genome sequence of Pseudomonas mandelii PD30 is reported in this announcement. The genes
AB  - for the reduction of nitrate to dinitrogen were
AB  - identified in the genome assembly and subsequently used in gene expression
AB  - research.
ER  -

TY  - JOUR
AU  - Forn-Cuni, G.
AU  - Tomas, J.M.
AU  - Merino, S.
TI  - Whole-Genome Sequence of Aeromonas hydrophila Strain AH-1 (Serotype O11).
JO  - Genome Announcements
PY  - 2016
SP  - e00920
EP  - e00916
VL  - 4
AB  - Aeromonas hydrophila is an emerging pathogen of aquatic and terrestrial animals,  including
AB  - humans. Here, we report the whole-genome sequence of the septicemic A.
AB  - hydrophila AH-1 strain, belonging to the serotype O11, and the first mesophilic
AB  - Aeromonas with surface layer (S-layer) to be sequenced.
ER  -

TY  - JOUR
AU  - Forn-Cuni, G.
AU  - Tomas, J.M.
AU  - Merino, S.
TI  - Genome Sequence of Aeromonas hydrophila Strain AH-3 (Serotype O34).
JO  - Genome Announcements
PY  - 2016
SP  - e00919
EP  - e00916
VL  - 4
AB  - Aeromonas hydrophila is an emerging pathogen of poikilothermic animals, from fish to mammals,
AB  - including humans. Here, we report the whole-genome sequence of the A.
AB  - hydrophila AH-3 strain, isolated from a fish farm goldfish septicemia outbreak in
AB  - Spain, with a characterized polar and lateral flagellum glycosylation pattern.
ER  -

TY  - JOUR
AU  - Forrow, S.
AU  - Lee, M.
AU  - Souhami, R.L.
AU  - Hartley, J.A.
TI  - The effect of AT and GC sequence specific minor groove binding agents on restriction endonuclease activity.
JO  - ACS Abstracts
PY  - 1994
SP  - 97
EP  - 97
VL  - 208
AB  - The naturally occuring DNA minor groove-binders, netropsin and distamycin A, recognize (A/T)4
AB  - and (A/T)5 sequences respectively. These ligands have well-documented effects on proteins such
AB  - as restriction endonucleases and transcription factors whose DNA recognition sequences have
AB  - high A/T content. We have investigated the ability of two synthetic imidazole containing and
AB  - G/C selective oligopeptides to interfere with the catalytic activity of restriction
AB  - endonucleases, and compared this with the effects of netropsin and distamycin. The
AB  - endonucleases were chosen to have either A/T rich (EcoRI, EcoRV) or G/C rich (BalI, NruI,
AB  - Fnu4HI, BanII) recognition sequences. An agarose gel assay was used to measure the degree of
AB  - cleavage of 32P-labelled DNA in the presence or absence of minor groove-binding ligand, and
AB  - ligand-DNA binding data was obtained using methidium-propyl EDTA (MPE) footprinting
AB  - methodology. The results from these studies will be presented.
ER  -

TY  - JOUR
AU  - Forrow, S.M.
AU  - Lee, M.
AU  - Souhami, R.L.
AU  - Hartley, J.A.
TI  - The effect of AT and GC sequence specific minor groove-binding agents on restriction endonuclease activity.
JO  - Chem. Biol. Interact.
PY  - 1995
SP  - 125
EP  - 142
VL  - 96
AB  - The ability of the naturally occurring A/T specific DNA minor groove binders netropsin and
AB  - distamycin A and two synthetic G/C selective oligopeptide analogues (1 and 2), to interfere
AB  - with the catalytic activity of restriction endonucleases has been investigated. Enzymes were
AB  - chosen to have A/T rich (EcoRI, EcoRV) or G/C rich (BalI, NruI) recognition sequences. An
AB  - agarose gel assay was used to measure the cleavage of 32P-labelled DNA and ligand-DNA binding
AB  - data was obtained using methidium-propyl EDTA footprinting. Netropsin and distamycin bind at
AB  - the recognition sites, and dose-dependently inhibited cleavage by, EcoRI and EcoRV, (EcoRI >
AB  - EcoRV). They were also more effective at inhibiting the catalytic activity of BalI than either
AB  - 1 or 2. NruI was inhibited by distamycin and 2, but not by netropsin or 1. DNA footprinting
AB  - revealed that neither 1 or 2 bound to the BalI or NruI recognition sequences under the
AB  - conditions used whereas netropsin and distamycin footprint at adjacent sites. 1 binds to two
AB  - of the three recognition sequences for the enzyme Fnu4HI (GCNGC) in the fragment studied and
AB  - was shown to inhibit DNA cleavage only at these two sites. 2 binds strongly to two GGGCTC
AB  - sequences which are recognition sites for the enzyme BanII. In this case a pronounced
AB  - stimulation of cleavage was observed in the presence of 2 over a wide dose range. The results
AB  - indicate that enzyme inhibition does not necessarily result from simultaneous occupancy of a
AB  - common site, or at nearby flanking sequences, and in some circumstances, a pronounced
AB  - stimulation of enzyme cleavage can occur.
ER  -

TY  - JOUR
AU  - Forsberg, K.J.
AU  - Patel, S.
AU  - Gibson, M.K.
AU  - Lauber, C.L.
AU  - Knight, R.
AU  - Fierer, N.
AU  - Dantas, G.
TI  - Bacterial phylogeny structures soil resistomes across habitats.
JO  - Nature
PY  - 2014
SP  - 612
EP  - 616
VL  - 509
AB  - Ancient and diverse antibiotic resistance genes (ARGs) have previously been
AB  - identified from soil, including genes identical to those in human pathogens.
AB  - Despite the apparent overlap between soil and clinical resistomes, factors
AB  - influencing ARG composition in soil and their movement between genomes and
AB  - habitats remain largely unknown. General metagenome functions often correlate
AB  - with the underlying structure of bacterial communities. However, ARGs are
AB  - proposed to be highly mobile, prompting speculation that resistomes may not
AB  - correlate with phylogenetic signatures or ecological divisions. To investigate
AB  - these relationships, we performed functional metagenomic selections for
AB  - resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895
AB  - ARGs we discovered were mostly new, and represent all major resistance
AB  - mechanisms. We demonstrate that distinct soil types harbour distinct resistomes,
AB  - and that the addition of nitrogen fertilizer strongly influenced soil ARG
AB  - content. Resistome composition also correlated with microbial phylogenetic and
AB  - taxonomic structure, both across and within soil types. Consistent with this
AB  - strong correlation, mobility elements (genes responsible for horizontal gene
AB  - transfer between bacteria such as transposases and integrases) syntenic with ARGs
AB  - were rare in soil by comparison with sequenced pathogens, suggesting that ARGs
AB  - may not transfer between soil bacteria as readily as is observed between human
AB  - pathogens. Together, our results indicate that bacterial community composition is
AB  - the primary determinant of soil ARG content, challenging previous hypotheses that
AB  - horizontal gene transfer effectively decouples resistomes from phylogeny.
ER  -

TY  - JOUR
AU  - Forsblom, S.
AU  - Rigler, R.
AU  - Ehrenberg, M.
AU  - Pettersson, U.
AU  - Philipson, L.
TI  - Kinetic studies on the cleavage of adenovirus DNA by restriction endonuclease EcoRI.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 3255
EP  - 3269
VL  - 3
AB  - The kinetics of cleavage of DNA from Adenovirus Type 1 (Ad1), Type 5 (Ad5) and
AB  - Type 6 (Ad6) by restriction endonuclease EcoRI was investigated by quantitative
AB  - evaluation of the fluorescence from ethidium stained DNA fragments separated on
AB  - agarose gels.  The apparent rate constants of cleavage at different cleavage
AB  - sites have been determined and large differences in the cleavage sites of the
AB  - individual sites within one type of DNA were found.  From the kinetics of
AB  - cleavage information on the sequence of the DNA fragments can be obtained.  The
AB  - order of the fragments A,B,C,D of Ad6 DNA obtained after complete cleavage by
AB  - restriction endonuclease EcoRI was found to be ADCB; the order of the
AB  - corresponding fragments A,B,C of Ad1 and Ad5 DNA was found to be ACB.
ER  -

TY  - JOUR
AU  - Fortuna, A.
AU  - Ramnarine, R.
AU  - Li, A.
AU  - Fittipaldi, N.
AU  - Frantz, C.
AU  - Mallo, G.V.
TI  - Draft Genome Sequences of Four Clinical Legionella pneumophila Isolates from Ontario, Canada.
JO  - Genome Announcements
PY  - 2018
SP  - e00295
EP  - e00218
VL  - 6
AB  - Legionella pneumophila outbreak investigations require the development of reliable typing
AB  - methods to better understand the genetic relationships of the
AB  - isolates involved. Here, we report the draft genome sequences of four clinical
AB  - Legionella pneumophila isolates obtained between 2000 and 2012 in Ontario,
AB  - Canada.
ER  -

TY  - JOUR
AU  - Foss, H.M.
AU  - Roberts, C.J.
AU  - Claeys, K.M.
AU  - Selker, E.U.
TI  - Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation.
JO  - Science
PY  - 1993
SP  - 1737
EP  - 1741
VL  - 262
AB  - The function and regulation of DNA methylation in eukaryotes remain unclear. Genes affecting
AB  - methylation were identified in the fungus Neurospora crassa. A mutation in one gene, dim-2,
AB  - resulted in the loss of all detectable DNA methylation. Abnormal segregation of the
AB  - methylation defects in crosses led to the discovery that the methylation mutants frequently
AB  - generate strains with extra chromosomes or chromosomal parts. Starvation for
AB  - S-adenosylmethionine, the presumed methyl group donor for DNA methylation, also produced
AB  - aneuploidy. These results suggest that DNA methylation plays a role in the normal control of
AB  - chromosome behavior.
ER  -

TY  - JOUR
AU  - Foster, B. et al.
TI  - Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 1
EP  - 8
VL  - 2
AB  - Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of
AB  - the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of
AB  - interest because of its ability to hydrolyze cellulose and xylan. Here we describe the
AB  - features of this organism, together with the complete genome sequence, and annotation. This is
AB  - the first complete genome sequence of a member of the large family Promicromonosporaceae, and
AB  - the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485
AB  - protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Foster, J. et al.
TI  - The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.
JO  - PLoS Biology
PY  - 2005
SP  - E121
EP  - E121
VL  - 3
AB  - Complete genome DNA sequence and analysis is presented for Wolbachia, the
AB  - obligate alpha-proteobacterial endosymbiont required for fertility and survival
AB  - of the human filarial parasitic nematode Brugia malayi. Although, quantitatively,
AB  - the genome is even more degraded than those of closely related Rickettsia
AB  - species, Wolbachia has retained more intact metabolic pathways. The ability to
AB  - provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely
AB  - to be Wolbachia's principal contribution to the mutualistic relationship, whereas
AB  - the host nematode likely supplies amino acids required for Wolbachia growth.
AB  - Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the
AB  - Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share
AB  - similar metabolic trends, although their genomes show a high degree of genome
AB  - shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level
AB  - of repeated DNA. Both Wolbachia have lost a considerable number of membrane
AB  - biogenesis genes that apparently make them unable to synthesize lipid A, the
AB  - usual component of proteobacterial membranes. However, differences in their
AB  - peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast
AB  - to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to
AB  - wMel, may reflect the loss of genes required for infecting host cells and
AB  - avoiding host defense systems. Analysis of this first sequenced endosymbiont
AB  - genome from a filarial nematode provides insight into endosymbiont evolution and
AB  - additionally provides new potential targets for elimination of cutaneous and
AB  - lymphatic human filarial disease.
ER  -

TY  - JOUR
AU  - Foster, P.L.
AU  - Rosche, W.A.
TI  - Levels of the Vsr endonuclease do not regulate stationary-phase reversion of a Lac- frameshift allele in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1998
SP  - 1944
EP  - 1946
VL  - 180
AB  - Vsr endonuclease, which initiates very short patch repair, has been hypothesized to regulate
AB  - mutation in stationary-phase cells.  Overexpression of Vsr does dramatically increase the
AB  - stationary-phase reversion of a Lac- frameshift allele, but the absence of Vsr has no effect.
AB  - Thus, at least in this case, Vsr has no regulatory role in stationary-phase mutation, and the
AB  - effects of Vsr overproduction are likely to be artifactual.
ER  -

TY  - JOUR
AU  - Fotso, F.A.
AU  - Mediannikov, O.
AU  - Padmanabhan, R.
AU  - Robert, C.
AU  - Fournier, P.E.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Genome Sequence of Borrelia crocidurae Strain 03-02, a Clinical Isolate from Senegal.
JO  - Genome Announcements
PY  - 2014
SP  - e01150
EP  - e01114
VL  - 2
AB  - The draft genome sequence of Borrelia crocidurae strain 03-02, a blood isolate from a febrile
AB  - Senegalese patient, comprises a 920,021-bp linear chromosome
AB  - (27.7% G+C content), 32 tRNAs, 818 open reading frames, and one cluster of
AB  - regularly interspaced short palindromic repeats. Its genotype differs from that
AB  - of the Achema reference strain.
ER  -

TY  - JOUR
AU  - Fougy, L.
AU  - Coeuret, G.
AU  - Champomier-Verges, M.C.
AU  - Chaillou, S.
TI  - Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage.
JO  - Genome Announcements
PY  - 2017
SP  - e00491
EP  - e00417
VL  - 5
AB  - In this study, we present a draft genome sequence of Serratia proteamaculans MFPA44A14-05.
AB  - This strain was isolated from a spoiled organic
AB  - modified-atmosphere-packed beef carpaccio. The draft genome sequence will
AB  - contribute to the understanding of the role of the S. proteamaculans species in
AB  - meat and seafood spoilage.
ER  -

TY  - JOUR
AU  - Foulks, J.M.
AU  - Parnell, K.M.
AU  - Chau, S.
AU  - Swierczek, K.
AU  - Saunders, M.
AU  - Wright, K.
AU  - Hendrickson, T.F.
AU  - McCullar, M.V.
AU  - Kanner, S.B.
TI  - Epigenetic Drug Discovery: Targeting DNA Methyltransferases (vol 17, pg 2, 2012).
JO  - J. Biomol. Screen.
PY  - 2012
SP  - 700
EP  - 700
VL  - 17
AB  - Foulks, J.M.; Parnell, K.M.; Nix, R.N.; Chau, S.; Swierczek, K.; Saunders, M.; Wright, K.;
AB  - Hendrickson, T.F.; Ho, K.K.; McCullar, M.V.; Kanner, S.B. Epigenetic Drug Discovery: Targeting
AB  - DNA Methyltransferases. J. Biomol. Screen. 2012, 17, 2-17. (Original doi:
AB  - 10.1177/1087057111421212).
ER  -

TY  - JOUR
AU  - Fournier, P.E.
AU  - El Karkouri, K.
AU  - Leroy, Q.
AU  - Robert, C.
AU  - Giumelli, B.
AU  - Renesto, P.
AU  - Socolovschi, C.
AU  - Parola, P.
AU  - Audic, S.
AU  - Raoult, D.
TI  - Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction.
JO  - BMC Genomics
PY  - 2009
SP  - 166
EP  - 166
VL  - 10
AB  - ABSTRACT: BACKGROUND: The Rickettsia genus includes 25 validated species,
AB  - 17 of which are proven human pathogens. Among these, the pathogenicity
AB  - varies greatly, from the highly virulent R. prowazekii, which causes
AB  - epidemic typhus and kills its arthropod host, to the mild pathogen R.
AB  - africae, the agent of African tick-bite fever, which does not affect the
AB  - fitness of its tick vector. RESULTS: We evaluated the clonality of R.
AB  - africae in 70 patients and 155 ticks, and determined its genome sequence,
AB  - which comprises a circular chromosome of 1,278,540 bp including a tra
AB  - operon and an unstable 12,377-bp plasmid. To study the genetic
AB  - characteristics associated with virulence, we compared this species to R.
AB  - prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii
AB  - have, respectively, the less and most decayed genomes. Eighteen genes are
AB  - present only in R. africae including one with a putative protease domain
AB  - upregulated at 37degreesC. CONCLUSION: Based on these data, we speculate
AB  - that a loss of regulatory genes causes an increase of virulence of
AB  - rickettsial species in ticks and mammals. We also speculate that in
AB  - Rickettsia species virulence is mostly associated with gene loss.
ER  -

TY  - JOUR
AU  - Fournier, P.E.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Medigue, C.
AU  - Raoult, D.
TI  - Complete Genome Sequence of Rickettsia slovaca, the Agent of Tick-Borne Lymphadenitis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1612
EP  - 1612
VL  - 194
AB  - The present study reports the complete and annotated genome sequence of the human pathogen
AB  - Rickettsia slovaca strain 13-B, which was isolated from a Dermacentor
AB  - tick in Slovakia in 1968. The 1.27-Mb genome provides further insights into the
AB  - acquisition of virulence related to genome reduction in Rickettsia species.
ER  -

TY  - JOUR
AU  - Fournier, P.E.
AU  - Rouli, L.
AU  - El Karkouri, K.
AU  - Nguyen, T.T.
AU  - Yagupsky, P.
AU  - Raoult, D.
TI  - Genomic Comparison of Kingella kingae Strains.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5972
EP  - 5972
VL  - 194
AB  - Kingella kingae is a betaproteobacterium from the order Neisseriales, and it is an agent of
AB  - invasive infections in children. We sequenced the genome from the
AB  - septic arthritis strain 11220434. It is composed of a 1,990,794-bp chromosome but
AB  - no plasmid, and it contains 2,042 protein-coding genes and 52 RNA genes,
AB  - including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Fournier, P.E.
AU  - Vallenet, D.
AU  - Barbe, V.
AU  - Audic, S.
AU  - Ogata, H.
AU  - Poirel, L.
AU  - Richet, H.
AU  - Robert, C.
AU  - Mangenot, S.
AU  - Abergel, C.
AU  - Nordmann, P.
AU  - Weissenbach, J.
AU  - Raoult, D.
AU  - Claverie, J.M.
TI  - Comparative genomics of multidrug resistance in Acinetobacter baumannii.
JO  - PLoS Genet.
PY  - 2006
SP  - e7
EP  - e7
VL  - 2
AB  - Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found
AB  - in water and soil. This organism was susceptible
AB  - to most antibiotics in the 1970s. It has now become a major cause of
AB  - hospital-acquired infections worldwide due to its remarkable propensity to
AB  - rapidly acquire resistance determinants to a wide range of antibacterial
AB  - agents. Here we use a comparative genomic approach to identify the
AB  - complete repertoire of resistance genes exhibited by the
AB  - multidrug-resistant A. baumannii strain AYE, which is epidemic in France,
AB  - as well as to investigate the mechanisms of their acquisition by
AB  - comparison with the fully susceptible A. baumannii strain SDF, which is
AB  - associated with human body lice. The assembly of the whole shotgun genome
AB  - sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2
AB  - Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region
AB  - termed a resistance island--the largest identified to date--in which 45
AB  - resistance genes are clustered. At the homologous location, the SDF strain
AB  - exhibits a 20 kb-genomic island flanked by transposases but devoid of
AB  - resistance markers. Such a switching genomic structure might be a hotspot
AB  - that could explain the rapid acquisition of resistance markers under
AB  - antimicrobial pressure. Sequence similarity and phylogenetic analyses
AB  - confirm that most of the resistance genes found in the A. baumannii strain
AB  - AYE have been recently acquired from bacteria of the genera Pseudomonas,
AB  - Salmonella, or Escherichia. This study also resulted in the discovery of
AB  - 19 new putative resistance genes. Whole-genome sequencing appears to be a
AB  - fast and efficient approach to the exhaustive identification of resistance
AB  - genes in epidemic infectious agents of clinical significance.
ER  -

TY  - JOUR
AU  - Foury, F.
AU  - Roganti, T.
AU  - Lecrenier, N.
AU  - Purnelle, B.
TI  - The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae.
JO  - FEBS Lett.
PY  - 1998
SP  - 325
EP  - 331
VL  - 440
AB  - The currently available yeast mitochondrial DNA (mtDNA) sequence is incomplete, contains many
AB  - errors and is derived from several polymorphic
AB  - strains. Here, we report that the mtDNA sequence of the strain used for
AB  - nuclear genome sequencing assembles into a circular map of 85,779 bp which
AB  - includes 10 kb of new sequence. We give a list of seven small hypothetical
AB  - open reading frames (ORFs). Hot spots of point mutations are found in
AB  - exons near the insertion sites of optional mobile group I intron-related
AB  - sequences. Our data suggest that shuffling of mobile elements plays an
AB  - important role in the remodelling of the yeast mitochondrial genome.
ER  -

TY  - JOUR
AU  - Fouteau, S.
AU  - Guerin, T.
AU  - Magdelenat, G.
AU  - Roumagnac, M.
AU  - Bartoli, M.
AU  - Ollivier, B.
AU  - Dolla, A.
AU  - Barbe, V.
AU  - Pradel, N.
TI  - Genome Sequence of Piezophilic Bacterium Desulfovibrio profundus Strain 500-1, Isolated from a Deep Sediment Layer in the Japan Sea.
JO  - Genome Announcements
PY  - 2017
SP  - e01181
EP  - e01117
VL  - 5
AB  - Piezophilic Desulfovibrio profundus strain 500-1 was isolated in the Japan Sea from a sediment
AB  - layer at 500-m depth under a water column of 1,000 m. Here, we
AB  - report the genome sequence of this strain, which includes a 4,168,905-bp circular
AB  - chromosome and two plasmids of 42,836 bp and 6,167 bp.
ER  -

TY  - JOUR
AU  - Fouts, D.E. et al.
TI  - Major structural differences and novel potential virulence mechanisms from the genomes in multiple Campylobacter species.
JO  - PLoS Biology
PY  - 2005
SP  - e15
EP  - e15
VL  - 3
AB  - Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari
AB  - RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences
AB  - that are associated with the insertion of phage- and plasmid-like genomic islands, as well as
AB  - major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in
AB  - number, and show greater variability in C. upsaliensis than in the other species. Many genes
AB  - involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are
AB  - conserved across the species, but variations that appear to be species specific are evident
AB  - for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel
AB  - Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic
AB  - profiles, as well as their resistance profiles to a range of antibiotics. It is evident that
AB  - the newly identified hypothetical and conserved hypothetical proteins, as well as
AB  - uncharacterized two-component regulatory systems and membrane proteins, may hold additional
AB  - significant information on the major differences in virulence among the species, as well as
AB  - the specificity of the strains for particular hosts.
ER  -

TY  - JOUR
AU  - Fouts, D.E.
AU  - Tyler, H.L.
AU  - DeBoy, R.T.
AU  - Daugherty, S.
AU  - Ren, Q.
AU  - Badger, J.H.
AU  - Durkin, A.S.
AU  - Huot, H.
AU  - Shrivastava, S.
AU  - Kothari, S.
AU  - Dodson, R.J.
AU  - Mohamoud, Y.
AU  - Khouri, H.
AU  - Roesch, L.F.
AU  - Krogfelt, K.A.
AU  - Struve, C.
AU  - Triplett, E.W.
AU  - Methe, B.A.
TI  - Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.
JO  - PLoS Genet.
PY  - 2008
SP  - E1000141
EP  - E1000141
VL  - 4
AB  - We report here the sequencing and analysis of the genome of the
AB  - nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K.
AB  - pneumoniae 342 is a member of the enteric bacteria, it serves as a model
AB  - for studies of endophytic, plant-bacterial associations due to its
AB  - efficient colonization of plant tissues (including maize and wheat, two of
AB  - the most important crops in the world), while maintaining a mutualistic
AB  - relationship that encompasses supplying organic nitrogen to the host
AB  - plant. Genomic analysis examined K. pneumoniae 342 for the presence of
AB  - previously identified genes from other bacteria involved in colonization
AB  - of, or growth in, plants. From this set, approximately one-third were
AB  - identified in K. pneumoniae 342, suggesting additional factors most likely
AB  - contribute to its endophytic lifestyle. Comparative genome analyses were
AB  - used to provide new insights into this question. Results included the
AB  - identification of metabolic pathways and other features devoted to
AB  - processing plant-derived cellulosic and aromatic compounds, and a robust
AB  - complement of transport genes (15.4%), one of the highest percentages in
AB  - bacterial genomes sequenced. Although virulence and antibiotic resistance
AB  - genes were predicted, experiments conducted using mouse models showed
AB  - pathogenicity to be attenuated in this strain. Comparative genomic
AB  - analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed
AB  - that MGH78578 apparently cannot fix nitrogen, and the distribution of
AB  - genes essential to surface attachment, secretion, transport, and
AB  - regulation and signaling varied between each genome, which may indicate
AB  - critical divergences between the strains that influence their preferred
AB  - host ranges and lifestyles (endophytic plant associations for K.
AB  - pneumoniae 342 and presumably human pathogenesis for MGH78578). Little
AB  - genome information is available concerning endophytic bacteria. The K.
AB  - pneumoniae 342 genome will drive new research into this less-understood,
AB  - but important category of bacterial-plant host relationships, which could
AB  - ultimately enhance growth and nutrition of important agricultural crops
AB  - and development of plant-derived products and biofuels.
ER  -

TY  - JOUR
AU  - Fox, K.L.
AU  - Dowideit, S.J.
AU  - Erwin, A.L.
AU  - Srikhanta, Y.N.
AU  - Smith, A.L.
AU  - Jennings, M.P.
TI  - Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 5242
EP  - 5252
VL  - 35
AB  - Phase variably expressed (randomly switching) methyltransferases associated with type III
AB  - restriction-modification (R-M) systems have been
AB  - identified in a variety of pathogenic bacteria. We have previously shown
AB  - that a phase variable methyltransferase (Mod) associated with a type III
AB  - R-M system in Haemophilus influenzae strain Rd coordinates the random
AB  - switching of expression of multiple genes, and constitutes a phase
AB  - variable regulon-'phasevarion'. We have now identified the recognition
AB  - site for the Mod methyltransferase in H. influenzae strain Rd as
AB  - 5'-CGAAT-3'. This is the same recognition site as the previously described
AB  - HinfIII system. A survey of 59 H. influenzae strains indicated significant
AB  - sequence heterogeneity in the central, variable region of the mod gene
AB  - associated with target site recognition. Intra- and inter-strain
AB  - transformation experiments using Mod methylated or non-methylated
AB  - plasmids, and a methylation site assay demonstrated that the sequence
AB  - heterogeneity seen in the region encoding target site specificity does
AB  - correlate to distinct target sites. Mutations were identified within the
AB  - res gene in several strains surveyed indicating that Res is not
AB  - functional. These data suggest that evolution of this type III R-M system
AB  - into an epigenetic mechanism for controlling gene expression has, in some
AB  - strains, resulted in loss of the DNA restriction function.
ER  -

TY  - JOUR
AU  - Fox, K.L.
AU  - Srikhanta, Y.N.
AU  - Jennings, M.P.
TI  - Phase variable type III restriction-modification systems of host-adapted bacterial pathogens.
JO  - Mol. Microbiol.
PY  - 2007
SP  - 1375
EP  - 1379
VL  - 65
AB  - Phase variation, the high-frequency on/off switching of gene expression, is a common feature
AB  - of host-adapted bacterial pathogens. Restriction-modification (R-M) systems, which are
AB  - ubiquitous among bacteria, are classically assigned the role of cellular defence against
AB  - invasion of foreign DNA. These enzymes are not obvious candidates for phase variable
AB  - expression, a characteristic usually associated with surface-expressed molecules subject to
AB  - host immune selection. Despite this, numerous type III R-M systems in bacterial pathogens
AB  - contain repetitive DNA motifs that suggest the potential for phase variation. Several roles
AB  - have been proposed for phase variable R-M systems based on DNA restriction function. However,
AB  - there is now evidence in several important human pathogens, including Haemophilus influenzae,
AB  - Neisseria meningitidis and Neisseria gonorrhoeae, that these systems are 'phasevarions'
AB  - (phasevariable regulons) controlling expression of multiple genes via a novel epigenetic
AB  - mechanism.
ER  -

TY  - JOUR
AU  - Fox, K.R.
TI  - DNAse I footprinting of restriction enzymes.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1988
SP  - 779
EP  - 785
VL  - 155
AB  - DNAse I footprint of restriction enzymes has been achieved by using calcium
AB  - containing digestion buffers so that the enzymes bind to but do not cleave DNA.
AB  - EcoRI produces a footprint 17 bases long, overestimating the region of contact
AB  - with DNA by about 7-8 base pairs.  Restriction enzymes HaeIII and HinP1I
AB  - generate smaller footprints of 15 and 13 base pairs respectively.
ER  -

TY  - JOUR
AU  - Fox, K.R.
AU  - Allinson, S.L.
AU  - Sahagun-Krause, H.
AU  - Brown, T.
TI  - Recognition of GT mismatches by Vsr mismatch endonuclease.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 2535
EP  - 2540
VL  - 28
AB  - The Vsr mismatch endonuclease recognises the sequence CTWGG (W=A or T) in which the indicated
AB  - thymine is paired with guanine and nicks the DNA backbone on the 5'-side of the mispaired
AB  - thymine.  By using base analogues of G and T we have explored the functional groups on the
AB  - mismatch pair which are recognized by the enzyme.  Removal of the thymine 5-methyl group
AB  - causes a 60% reduction in activity, while removing the 2-amino group of guanine reduces
AB  - cleavage by 90%.  Placing 2-aminopurine or nebularine opposite T generates mismatches which
AB  - are cut at a much lower rate (0.1%).  When either base is removed, generating a pseudoabasic
AB  - site (1',2'-dideoxyribose), the enzyme still produces site-specific cleavage, but at only 1%
AB  - of the original rate.  Although TT and CT mismatches at this position are cleaved at a low
AB  - rate (~1%), mismatches with other bases (such as GA and AC) and Watson-Crick base pairs are
AB  - not cleaved by the enzyme.  There is also no cleavage when the mismatched T is replaced with
AB  - difluorotoluene.
ER  -

TY  - JOUR
AU  - Fraga, M.F.
AU  - Ballestar, E.
AU  - Montoya, G.
AU  - Taysavang, P.
AU  - Wade, P.A.
AU  - Esteller, M.
TI  - The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 1765
EP  - 1774
VL  - 31
AB  - The methyl-CpG binding domain (MBD) family of proteins was defined based on sequence
AB  - similarity in their DNA binding domains. In light of their
AB  - high degree of conservation, it is of inherent interest to determine the
AB  - genomic distribution of these proteins, and their associated co-repressor
AB  - complexes. One potential determinant of specificity resides in differences
AB  - in the intrinsic DNA binding properties of the various MBD proteins. In
AB  - this report, we use a capillary electrophoretic mobility shift assay
AB  - (CEMSA) with laser-induced fluorescence (LIF) and neutral capillaries to
AB  - calculate MBD-DNA binding affinities. MBD proteins were assayed on pairs
AB  - of methylated and unmethylated duplex oligos corresponding to the promoter
AB  - regions of the BRCA1, MLH1, GSTP1 and p16(INK4a) genes, and binding
AB  - affinities for each case were calculated by Scatchard analyses. With the
AB  - exception of mammalian MBD3 and Xenopus MBD3 LF, all the MBD proteins
AB  - showed higher affinity for methylated DNA (in the nanomolar range) than
AB  - for unmethylated DNA (in the micromolar range). Significant differences
AB  - between MBD proteins in the affinity for methylated DNA were observed,
AB  - ranging within two orders of magnitude. By mutational analysis of MBD3 and
AB  - using CEMSA, we demonstrate the critical role of specific residues within
AB  - the MBD in conferring selectivity for methylated DNA. Interestingly, the
AB  - binding affinity of specific MBD proteins for methylated DNA fragments
AB  - from naturally occurring sequences are affected by local methyl-CpG
AB  - spacing.
ER  -

TY  - JOUR
AU  - Frampton, R.A.
AU  - Thompson, S.M.
AU  - Kalamorz, F.
AU  - David, C.
AU  - Addison, S.M.
AU  - Smith, G.R.
TI  - Draft Genome Sequence of a 'Candidatus Liberibacter europaeus' Strain Assembled from Broom Psyllids (Arytainilla spartiophila) from New Zealand.
JO  - Genome Announcements
PY  - 2018
SP  - e00430
EP  - e00418
VL  - 6
AB  - Here, we report the draft genome sequence of 'Candidatus Liberibacter europaeus'  ASNZ1,
AB  - assembled from broom psyllids (Arytainilla spartiophila) from New Zealand.
AB  - The assembly comprises 15 contigs, with a total length of 1.33 Mb and a G+C
AB  - content of 33.5%.
ER  -

TY  - JOUR
AU  - Franchina, M.
AU  - Hooper, J.
AU  - Kay, P.H.
TI  - Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes.
JO  - Int. J. Biochem. Cell Biol.
PY  - 2001
SP  - 1104
EP  - 1115
VL  - 33
AB  - Alternative splicing of RNA molecules transcribed from DNA (cytosine-5) methyltransferases has
AB  - been proposed as a mechanism by which methylation is able to effect diverse biological
AB  - processes in higher eukaryotes. This study has investigated transcriptional versatility of DNA
AB  - (cytosine-5) methyltransferase 2, which may methylate cytosine residues within 5'-CCTGG-3'
AB  - pentanucleotides in regions of the human genome devoid of 5'-CG-3' methylation. Five novel
AB  - splice variants of DNA (cytosine-5) methyltransferase 2 were identified in the peripheral
AB  - blood leukocytes of healthy subjects following cloning and sequencing of RT-PCR products
AB  - amplified using gene specific oligodeoxyribonucleotide primers. The generation of some of
AB  - these splice variants may be influenced by the formation of secondary structures within
AB  - pre-mRNA due to the repetition of sequences flanking alternatively spliced exons in a reverse
AB  - and complementary orientation on the same strand. These findings enable novel approaches to
AB  - investigate the role of RNA secondary structures in alternative splicing. The DNA (cytosine-5)
AB  - methyltransferase 2 splice variants are generated in all the major cell types of peripheral
AB  - blood, as well as in neoplastic lymphoid cells indicating that they are unlikely to generate
AB  - proteins involved in control of the cell cycle or cellular differentiation. Interestingly, the
AB  - gene products generated by some splice variants completely or partially lack highly conserved
AB  - amino acid motifs shown to be important for the catalysis of cytosine  methylation. The
AB  - possibility cannot be excluded, therefore, that alternative splicing of DNA (cytosine-5)
AB  - methyltransferase 2 pre-mRNA may generate protein isoforms which have different methylating
AB  - capabilities or which are involved in biological processes other than the catalysis of
AB  - cytosine methylation.
ER  -

TY  - JOUR
AU  - Franchina, M.
AU  - Kay, P.H.
TI  - Evidence that cytosine residues within 5'-CCTGG-3' pentanucleotides can be methylated in human DNA independently of the methylating system that modifies 5'-CG-3' dinucleotides.
JO  - DNA Cell Biol.
PY  - 2000
SP  - 521
EP  - 526
VL  - 19
AB  - In contrast to the complex sequence specificities of the prokaryotic DNA methylating systems,
AB  - the mammalian machinery identified thus far methylates cytosine residues within the context of
AB  - a 5'-CG-3' dinucleotide. To explore the possibility that cytosine residues that do not
AB  - precede guanine may be independently methylated in mammalian DNA, we have examined a region of
AB  - the human myogenic gene, Myf-3, which is not targeted by the methylating system that
AB  - methylates 5'-CG-3' dinucleotides. Our investigations have revealed cytosine methylation
AB  - within the 5'-CCTGG-3' pentanucleotides specified by the 0.8-kb Myf-3 probe. We have also
AB  - found that in DNA from neoplastic cells, in which 5'-CG-3' dinucleotides within Myf-3 become
AB  - abnormally hypermethylated, cytosine residues within 5'-CCTGG-3' pentanucleotides are not
AB  - methylated. Moreover, methylation of 5'-CCTGG-3' pentanucleotides was not detected within
AB  - the closely related Myf-4 gene, which is normally 5'-CG-3' hypermethylated. These findings
AB  - indicate the existence of a system that methylates 5'-CCTGG-3' pentanucleotides
AB  - independently of the system that methylates cytosine residues within 5'-CG-3' dinucleotides.
AB  - It is possible that the 5'-CCTGG-3' methylating system influences the fate of foreign
AB  - integrated DNA.
ER  -

TY  - JOUR
AU  - Franchina, M.
AU  - Kay, P.H.
TI  - Allele-specific variation in the gene copy number of human cytosine 5-methyltransferase.
JO  - Hum. Hered.
PY  - 2000
SP  - 112
EP  - 117
VL  - 50
AB  - Previously, we have identified two alternate allelic forms of cytosine 5-methyltransferase,
AB  - 5-MT I and 5-MT II, specified by polymorphic fragments of 1.5 and 1.1 kb, respectively. In the
AB  - presence study, a 0.8-kb genomic probe was prepared which was confirmed to be included within
AB  - the polymorphic fragments. The 0.8-kb probe hybridised with greater intensity to the 1.1-kb
AB  - fragment than the 1.5-kb fragment. Densitometric analysis indicated that there is 1 copy of
AB  - 5-MT associated with 5-MT I, whereas there may be 1-4 copies of the gene associated with the
AB  - 5-MT II allele. Segregation studies demonstrated that the multiple copies of 5-MT II are
AB  - inherited in a Mendelian fashion. These results allow novel approaches to investigating the
AB  - underlying mechanisms of cytosine methylation and gene duplication.
ER  -

TY  - JOUR
AU  - Francisco, M.S.
AU  - Farias, F.M.
AU  - Santos, I.N.S.
AU  - Marques-Bastos, S.L.S.
AU  - Albano, R.M.
AU  - Bastos, M.D.C.F.
TI  - Draft Genome Sequence of Staphylococcus aureus 4185, a Strain That Produces Aureocyclicin 4185.
JO  - Genome Announcements
PY  - 2017
SP  - e01249
EP  - e01217
VL  - 5
AB  - The draft genome sequence of the aureocyclicin 4185-producing strain Staphylococcus aureus
AB  - 4185 is presented. The assembly contains 2,789,721 bp and a
AB  - G+C content of 32.8%. Genome analysis allowed us to determine the complete
AB  - sequence of the bacteriocinogenic plasmid pRJ101 and to find another bacteriocin
AB  - gene cluster encoded on the bacterial chromosome.
ER  -

TY  - JOUR
AU  - Franco, C.M.
AU  - Araujo, R.
AU  - Adetutu, E.
AU  - Tobe, S.S.
AU  - Mallya, S.
AU  - Paul, B.
AU  - Satyamoorthy, K.
TI  - Complete Genome Sequences of the Endophytic Streptomyces Strains EN16, EN23, and  EN27, Isolated from Wheat Plants.
JO  - Genome Announcements
PY  - 2016
SP  - e01342
EP  - e01316
VL  - 4
AB  - The complete genome sequences of three endophytic Streptomyces species were compared. Strains
AB  - EN16, EN23, and EN27 were isolated from surface-sterilized
AB  - roots of wheat plants from South Australia. In field trials, these strains are
AB  - effective in suppressing fungal root diseases of wheat when added as spore
AB  - coatings to wheat seed.
ER  -

TY  - JOUR
AU  - Franco, C.M.M.
AU  - Adetutu, E.M.
AU  - Le, H.X.
AU  - Ballard, R.A.
AU  - Araujo, R.
AU  - Tobe, S.S.
AU  - Paul, B.
AU  - Mallya, S.
AU  - Satyamoorthy, K.
TI  - Complete Genome Sequences of the Endophytic Streptomyces sp. Strains LUP30 and LUP47B, Isolated from Lucerne Plants.
JO  - Genome Announcements
PY  - 2017
SP  - e00556
EP  - e00517
VL  - 5
AB  - The complete genome sequences of two endophytic Streptomyces sp. strains, LUP30 and LUP47B,
AB  - were analyzed. These strains were isolated from surface-sterilized
AB  - roots of lucerne plants from South Australia and were found to promote the growth
AB  - of the rhizobial partner in vitro and significantly increased nodulation and
AB  - nitrogen fixation in lucerne plants.
ER  -

TY  - JOUR
AU  - Franco, J.A.V.
AU  - Collier, R.
AU  - Wang, Y.
AU  - Huo, N.
AU  - Gu, Y.
AU  - Thilmony, R.
AU  - Thomson, J.G.
TI  - Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659.
JO  - Genome Announcements
PY  - 2016
SP  - e00746
EP  - e00716
VL  - 4
AB  - This work reports the draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 (also
AB  - known as strain K599). The assembled genome contains 5,277,347 bp, composed of one circular
AB  - chromosome, the pRi2659 virulence plasmid, and 17 scaffolds pertaining to the linear
AB  - chromosome. The wild-type strain causes hairy root disease in dicots and has been used to make
AB  - transgenic hairy root cultures and composite plants (nontransgenic shoots with transgenic
AB  - roots). Disarmed variants of the strain have been used to produce stable transgenic monocot
AB  - and dicot plants.
ER  -

TY  - JOUR
AU  - Franco, M.E.
AU  - Lopez, S.
AU  - Medina, R.
AU  - Saparrat, M.C.
AU  - Balatti, P.
TI  - Draft Genome Sequence and Gene Annotation of Stemphylium lycopersici Strain CIDEFI-216.
JO  - Genome Announcements
PY  - 2015
SP  - e01069
EP  - e01015
VL  - 3
AB  - Stemphylium lycopersici is a plant-pathogenic fungus that is widely distributed throughout the
AB  - world. In tomatoes, it is one of the etiological agents of gray leaf spot disease. Here, we
AB  - report the first draft genome sequence of S. lycopersici, including its gene structure and
AB  - functional annotation.
ER  -

TY  - JOUR
AU  - Franco, T.
AU  - Califano, G.
AU  - Goncalves, A.C.
AU  - Cucio, C.
AU  - Costa, R.
TI  - Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the  Gorgonian Coral Eunicella verrucosa.
JO  - Genome Announcements
PY  - 2016
SP  - e01729
EP  - e01715
VL  - 4
AB  - To shed light on the associations established between Vibrio species and soft corals in
AB  - coastal ecosystems, we report here the draft genome sequence of Vibrio
AB  - sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral
AB  - Eunicella verrucosa and that shows antagonistic activity against Escherichia
AB  - coli.
ER  -

TY  - JOUR
AU  - Francois, J.-C.
AU  - Saison-Behmoaras, T.
AU  - Barbier, C.
AU  - Chassignol, M.
AU  - Thuong, N.T.
AU  - Helene, C.
TI  - Sequence-specific recognition and cleavage of duplex DNA via triple-helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1989
SP  - 9702
EP  - 9706
VL  - 86
AB  - Homopyrimidine oligodeoxynucleotides recognize the major groove of the DNA double helix at
AB  - homopurine-homopyrimidine sequences by forming local triple helices. Phenanthroline was
AB  - covalently attached to the 5' end of an 11-mer homopyrimidine oligonuceotide of sequence
AB  - d(TTTCCTCCTCT). Simian virus 40 DNA, which contains a single target site for this
AB  - oligonucleotide, was used as a substrate for the phenanthroline-oligonucleotide conjugate. In
AB  - the presence of copper ions and a reducing agent, a single specific double-strand cleavage
AB  - site was observed at 20oC by agarose gel electrophoresis. The efficiency of double-strand
AB  - cleavage was >70% at 20oC and pH 7.4. Secondary cleavage sites were observed when binding of
AB  - the oligonucleotide to mismatched sequences was allowed to take place at low temperature. The
AB  - exact location of the cleavage sites was determined by polyacrylamide gel electrophoresis of
AB  - denatured fragments by using both simian virus 40 DNA and a synthetic DNA fragment containing
AB  - the target sequence. The asymmetric distribution of the cleavage sites on the two strands
AB  - revealed that the cleavage reaction took place in the minor groove even though the
AB  - phenanthroline linker was located in the major groove. Linkers of different lengths were used
AB  - to tether phenanthroline to the oligonucleotide and their relative efficacies of DNA cleavage
AB  - were compared. Based on these comparative studies and on model building, it is proposed that
AB  - the phenanthroline ring carried by the oligonucleotide intercalates from the major groove and
AB  - that copper chelation locks the complex in place from within the minor groove where the
AB  - cleavage reaction occurs.
ER  -

TY  - JOUR
AU  - Francois, J.-C.
AU  - Saison-Behmoaras, T.
AU  - Thuong, N.T.
AU  - Helene, C.
TI  - Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides.
JO  - Biochemistry
PY  - 1989
SP  - 9617
EP  - 9619
VL  - 28
AB  - A 17-mer homopyrimidine oligonucleotide was designed to bind to the major
AB  - groove of SV40 DNA at a 17 base pair homopurine-homopyrimidine sequence via
AB  - Hoogsteen base pairing.  This sequence contains the recognition site for the
AB  - class II-S restriction enzyme Ksp632I.  The oligonucleotide was shown to
AB  - inhibit enzymatic cleavage under conditions that allow for triple helix
AB  - formation.  Inhibition is sequence-specific and occurs in the micromolar
AB  - concentration range.  Triple helix formation by oligonucleotides opens new
AB  - possibilities for sequence-specific regulation of gene expression.
ER  -

TY  - JOUR
AU  - Frank, J.
AU  - Dingemanse, C.
AU  - Schmitz, A.M.
AU  - Vossen, R.H.
AU  - van Ommen, G.J.
AU  - den Dunnen, J.T.
AU  - Robanus-Maandag, E.C.
AU  - Anvar, S.Y.
TI  - The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius.
JO  - Front. Microbiol.
PY  - 2015
SP  - 1549
EP  - 1549
VL  - 6
AB  - BACKGROUND: Immuno-compromised mice infected with Helicobacter typhlonius are used to model
AB  - microbially inducted inflammatory bowel disease (IBD). The specific
AB  - mechanism through which H. typhlonius induces and promotes IBD is not fully
AB  - understood. Access to the genome sequence is essential to examine emergent
AB  - properties of this organism, such as its pathogenicity. To this end, we present
AB  - the complete genome sequence of H. typhlonius MIT 97-6810, obtained through
AB  - single-molecule real-time sequencing. RESULTS: The genome was assembled into a
AB  - single circularized contig measuring 1.92 Mbp with an average GC content of
AB  - 38.8%. In total 2,117 protein-encoding genes and 43 RNA genes were identified.
AB  - Numerous pathogenic features were found, including a putative pathogenicity
AB  - island (PAIs) containing components of type IV secretion system,
AB  - virulence-associated proteins and cag PAI protein. We compared the genome of H.
AB  - typhlonius to those of the murine pathobiont H. hepaticus and human pathobiont H.
AB  - pylori. H. typhlonius resembles H. hepaticus most with 1,594 (75.3%) of its genes
AB  - being orthologous to genes in H. hepaticus. Determination of the global
AB  - methylation state revealed eight distinct recognition motifs for adenine and
AB  - cytosine methylation. H. typhlonius shares four of its recognition motifs with H.
AB  - pylori. CONCLUSION: The complete genome sequence of H. typhlonius MIT 97-6810
AB  - enabled us to identify many pathogenic features suggesting that H. typhlonius can
AB  - act as a pathogen. Follow-up studies are necessary to evaluate the true nature of
AB  - its pathogenic capabilities. We found many methylated sites and a plethora of
AB  - restriction-modification systems. The genome, together with the methylome, will
AB  - provide an essential resource for future studies investigating gene regulation,
AB  - host interaction and pathogenicity of H. typhlonius. In turn, this work can
AB  - contribute to unraveling the role of Helicobacter in enteric disease.
ER  -

TY  - JOUR
AU  - Frank, O.
AU  - Goker, M.
AU  - Pradella, S.
AU  - Petersen, J.
TI  - Ocean's twelve: Flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization.
JO  - Environ. Microbiol.
PY  - 2015
SP  - 4019
EP  - 4034
VL  - 17
AB  - The marine bacterium Marinovum algicola DG898 is a representative of the
AB  - Roseobacter group (Rhodobacteraceae, Alphaproteobacteria) and harbors a for
AB  - Proteobacteria unprecedented wealth of eleven extrachromosomal replicons (ECRs).
AB  - The relevance of ECRs has previously been exemplified by photosynthesis and
AB  - biofilm plasmids, but the evolutionary forces for the emergence of multipartite
AB  - genomes are largely unknown. The newly established genome revealed the
AB  - exceptional metabolic potential of Marinovum and its adaptation to the
AB  - phycosphere. Comparative codon usage analyses allowed the identification of eight
AB  - chromids and three plasmids. Functional gene clustering is documented by the
AB  - 52-kb biofilm chromid that is required for surface attachment. The most
AB  - conspicuous finding is the presence of a highly expressed chromid-encoded
AB  - flagellum gene cluster (FGC, fla2) that is indispensable for swimming motility.
AB  - M. algicola DG898 harbors an additional chromosome-encoded flagellum (fla1) with
AB  - unknown function. Comprehensive phylogenetic analyses revealed the presence of a
AB  - third FGC type (fla3) in Rhodobacteraceae and indicated the transmission of
AB  - complete FGCs via conjugation. The current Marinovum study indicates a functional
AB  - correlation of the intracellular fla2-chromid localization and the subcellular
AB  - positioning of the flagellum. The proposed mechanism might represent - apart from
AB  - horizontal transfer - a novel driving force for the emergence of multipartite
AB  - genomes.
ER  -

TY  - JOUR
AU  - Frank, O.
AU  - Pradella, S.
AU  - Rohde, M.
AU  - Scheuner, C.
AU  - Klenk, H.P.
AU  - Goker, M.
AU  - Petersen, J.
TI  - Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 914
EP  - 932
VL  - 9
AB  - Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the
AB  - species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to
AB  - the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter
AB  - species are effective colonizers of marine surfaces, including frequent
AB  - associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the
AB  - scallop Pecten maximus. Here we describe the features of this organism, together
AB  - with the complete genome sequence, comprising eight circular replicons with a
AB  - total of 4,448 genes. In addition to a high number of extrachromosomal replicons,
AB  - the genome contains six genomic island and three putative prophage regions, as
AB  - well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses
AB  - confirm previous results, which indicated that the originally reported P.
AB  - gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP
AB  - 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P.
AB  - gallaeciensis.
ER  -

TY  - JOUR
AU  - Frank, S.A.
TI  - Polymorphism of bacterial restriction-modification systems: the advantage of diversity.
JO  - Evolution
PY  - 1994
SP  - 1470
EP  - 1477
VL  - 48
AB  - Bacterial restriction-modification systems provide defense against foreign DNA by using a self
AB  - versus nonself recognition mechanism. A great diversity of recognition motifs is maintained in
AB  - natural populations. Circumstantial evidence suggests that defense against bacteriophage
AB  - viruses favors this diversity. (1) Bacterial restriction enzymes can destroy invading phage
AB  - DNA. (2) Phage DNA can mimic the host's self-recognition mechanism. The ability of the virus
AB  - to pose as a mimic favors diversification of the host's recognition motif. Other observations
AB  - suggest that restriction modification (RM) does not provide any significant defensive
AB  - advantages in mature communities. (1) In laboratory experiments, bacteria evolve resistance to
AB  - phage by mutation and selection of the receptors to which phage adsorb. The outcome of these
AB  - experiments is a community dominated by bacteria with receptor-based resistance, with a low
AB  - abundance of phage and susceptible bacteria. (2) Phage are rare and receptor-based resistance
AB  - is common in samples from natural communities. I present a model that shows two factors
AB  - determine community composition: resources and RM diversity. Communities in resource-rich
AB  - habitats are dominated by receptor-based resistance and support few phage; communities in poor
AB  - habitats are dominated by restriction-modification defense and relatively abundant phage. RM
AB  - diversity is itself a direct cause of community composition. As diversity increases from a low
AB  - level, the abundance of phage increases and the relative abundance of receptor-based
AB  - resistance declines. Further increases in diversity cause a crash in phage abundance, yielding
AB  - a stable community of diverse RM types but an absence of the selective pressure--the
AB  - phage--that drove the diversification. Empirical studies must sample a range of resource
AB  - levels and RM diversity to analyze the forces that determine community composition.
ER  -

TY  - JOUR
AU  - Frankel, A.D.
TI  - Sequence-specific recognition of DNA by the HinfI restriction endonuclease.
JO  - Ph.D. Thesis, Johns Hopkins University, USA
PY  - 1983
SP  - 1
EP  - 92
AB  - A method has been developed for measuring association constants of DNA-protein
AB  - complexes using gel chromatography.  It is suitable for the study of a variety
AB  - of systems and can be used over a wide range of concentrations.  This technique
AB  - has been used to study the sequence-specific interaction of the HinfI
AB  - restriction endonuclease with DNA.  HinfI has a monomer molecular weight of
AB  - 31000 daltons and appears to be active as a dimer.  Its turnover number is 25
AB  - sites cleaved min-1 dimer-1 and its Km is less than 1x10-11M.  The protein was
AB  - found to bind to supercoiled plasmid molecules with an observed free energy of
AB  - association of -13.9 kcal mole-1.  The binding decreases at concentrations of
AB  - NaCl above 50mM and this dependence corresponds to the apparent release of 3.4
AB  - ion pairs.  The affinity of the nuclease for its site was found to be
AB  - independent of pH over the range studied and showed a small dependence on
AB  - temperature.  When the degenerate middle position of the HinfI recognition
AB  - site, 5'GANTC, was varied, no change was observed in the binding constant.  The
AB  - salt and pH dependencies of the cleavage reaction are similar to those of the
AB  - binding constants and each of the degenerate sites studied was equally well
AB  - cleaved.  Linear fragments containing the site are bound as tightly as
AB  - supercoiled molecules.  The enzyme binds to non-specific DNA about 6 orders of
AB  - magnitude more weakly than to its site and is unable to bind to DNA methylated
AB  - at the A position of its recognition site.
ER  -

TY  - JOUR
AU  - Frankel, A.D.
AU  - Ackers, G.K.
AU  - Smith, H.O.
TI  - Measurement of DNA-protein equilibria using gel chromatography:  application to the HinfI restriction endonuclease.
JO  - Biochemistry
PY  - 1985
SP  - 3049
EP  - 3054
VL  - 24
AB  - A method is described for measuring equilibrium constants of DNA-protein
AB  - interactions using gel chromatography.  This technique has been used to study
AB  - the sequence-specific interaction of the HinfI restriction endonuclease with
AB  - DNA.  HinfI has a monomeric molecular weight of 31000 and exists as a dimer in
AB  - its active form.  The protein binds to supercoiled DNA molecules containing its
AB  - recognition site with an apparent free energy of -13.9 kcal/mol of sites.  This
AB  - interaction is highly salt sensitive and causes a release of 3.4 ion pairs.
AB  - The affinity of the nuclease for its recognition site is largely independent of
AB  - both pH (6.5-8.5) and temperature (7-35C) and was not affected by variations in
AB  - the degenerate middle position of the site.  Linear DNA fragments containing
AB  - the HinfI recognition site were bound as tightly as supercoiled molecules.
AB  - Binding to nonspecific DNA sites or to methylated DNA sites was approximately 6
AB  - orders of magnitude weaker.  In general, enzyme activity and binding affinity
AB  - parallel each other.
ER  -

TY  - JOUR
AU  - Frankel, A.D.
AU  - Smith, H.O.
TI  - Restriction and modification enzymes detect no allosteric changes in DNA with bound lac repressor or RNA polymerase.
JO  - J. Mol. Biol.
PY  - 1981
SP  - 611
EP  - 619
VL  - 146
AB  - A 203 base-pair fragment containing the lac operator/promoter region of
AB  - Escherichia coli was inserted into the EcoRI site of the plasmid vector pKC7.
AB  - Rates of restriction endonuclease cleavage of the flanking EcoRI sites and of
AB  - several other restriction sites on the DNA molecule were then compared in the
AB  - presence and absence of bound RNA polymerase or lac repressor.  The rates were
AB  - identical whether or not protein had been bound, even for sites as close as 40
AB  - base-pairs from a protein binding site.  No difference was detected using
AB  - supercoiled, nicked circular, or linear DNA substrates.  No apparent change in
AB  - the rates of methylation of EcoRI sites by EcoRI methylase was produced by
AB  - binding the regulatory proteins.
ER  -

TY  - JOUR
AU  - Franklin, N.C.
AU  - Dove, W.F.
TI  - Genetic evidence for restriction targets in the DNA of phages lambda and Phi80.
JO  - Genet. Res.
PY  - 1969
SP  - 151
EP  - 157
VL  - 14
AB  - The phenomenon of restriction, recently reviewed in depth by Arber (1968) and
AB  - by Arber and Linn (1969), is observed as the inactivation of a genome following
AB  - transfer from one host to another.  Thus, phages propagated on one host may
AB  - form plaques on a second host with an efficiency lower than that on the first.
AB  - Those progeny phages which do emerge from the second host generally will have
AB  - become modified so that they are no longer restricted in that host.  This
AB  - modification is not replicated, and is diluted out upon further propagation of
AB  - the phages in the first host.  The ability of a bacterium to restrict or to
AB  - modify depends upon three linked bacterial cistrons:  one required for
AB  - restriction, the second for modification and the third required for both
AB  - functions and determining the specificity of each (Glover, Schell, Symonds &
AB  - Stacey, 1963; Wood, 1966, Boyer & Roulland-Dussoix, 1969; Glover & Colson,
AB  - 1969).  Restriction of a phage by a bacterium was shown some years ago to be
AB  - exerted directly upon the DNA of the phage after it is injected into the
AB  - bacterial cell (Dussoix & Arber, 1962).  Restricting enzymes have now been
AB  - purified and found to act at only a limited number of sites in the target DNA
AB  - molecule, making double-strand breaks (Meselson & Yuan, 1968; Linn & Arber,
AB  - 1968; Roulland-Dussoix & Boyer, 1969).  Subsequent degradation in vivo
AB  - presumably occurs by non-specific nuclease action on these fragments.
AB  - Comparison of the restriction properties of several phages has now led to
AB  - observations of a genetic nature which confirm the conclusion, based on
AB  - biochemical evidence, that restriction is directed at target sites localized
AB  - within the phage genome.  The restriction system of E. coli K12 is far more
AB  - active on phage lambda than on the related phage Phi80.  The restriction
AB  - properties of these phages are unaffected by each other in a trans
AB  - complementation test.  Rather, the restriction properties can be exchanged only
AB  - by genetic recombination, behaving as a small set of mappable restriction
AB  - targets.  Sensitivity of lambda to K restriction can be lost by genetic
AB  - deletion.
ER  -

TY  - JOUR
AU  - Franzon, V.L.
AU  - Barker, A.
AU  - Manning, P.A.
TI  - Nucleotide sequence encoding the mannose-fucose-resistant hemagglutinin of Vibrio cholerae O1 and construction of a mutant.
JO  - Infect. Immun.
PY  - 1993
SP  - 3032
EP  - 3037
VL  - 61
AB  - The region of DNA encoding the mannose-fucose-resistant hemagglutinin (MFRHA) of Vibrio
AB  - cholerae O1 has been localized, and the nucleotide sequence has been determined. The region
AB  - contains a single open reading frame encoding 230 amino acids, corresponding to a protein of
AB  - 26.9 kDa. The N terminus of this protein is atypical for a protein localized in the outer
AB  - membrane. A mutant lacking MFRHA activity has been constructed by allelic exchange after
AB  - inactivation via the insertion of a kanamycin resistance gene cartridge. The MFRHA-negative
AB  - mutant has been assessed for virulence in the infant mouse cholera model. This mutant shows a
AB  - marked defect in its ability to persist in the infant mouse gut and is incapable of competing
AB  - with the wild-type organism, even when given in 25-fold excess. This defect also leads to a >
AB  - 100-fold increase in the 50% lethal dose. These data suggest that the MFRHA is an important
AB  - colonization factor in the infant mouse model.
ER  -

TY  - JOUR
AU  - Fraser, C.M. et al.
TI  - The minimal gene complement of Mycoplasma genitalium.
JO  - Science
PY  - 1995
SP  - 397
EP  - 403
VL  - 270
AB  - The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the
AB  - smallest known genome of any free-living organism, has been determined by whole-genome random
AB  - sequencing and assembly.  A total of only 470 predicted coding regions were identified that
AB  - include genes required for DNA replication, transcription and translation, DNA repair,
AB  - cellular transport, and energy metabolism.  Comparison of this genome to that of Haemophilus
AB  - influenzae suggests that differences in genome content are reflected as profound differences
AB  - in physiology and metabolic capacity between these two organisms.
ER  -

TY  - JOUR
AU  - Fraser, C.M. et al.
TI  - Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.
JO  - Nature
PY  - 1997
SP  - 580
EP  - 586
VL  - 390
AB  - The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease,
AB  - contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular
AB  - plasmids with a combined size of more than 53,000 base pairs.  The chromosome contains 853
AB  - genes encoding a basic set of proteins for DNA replication, transcription, translation, solute
AB  - transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for
AB  - cellular biosynthetic reactions.  Because B. burgdorferi and M. genitalium are distantly
AB  - related eubacteria, we suggest that their limited metabolic capacities reflect convergent
AB  - evolution by gene loss from more metabolically competent progenitors.  Of 430 genes on 11
AB  - plasmids, most have no known biological function; 39% of plasmid genes are paralogues that
AB  - form 47 gene families.  The biological significance of the multiple plasmid-encoded genes is
AB  - not clear, although they may be involved in antigenic variation or immune evasion.
ER  -

TY  - JOUR
AU  - Fraser, C.M. et al.
TI  - Complete genome sequence of Treponema pallidum, the syphilis spirochete.
JO  - Science
PY  - 1998
SP  - 375
EP  - 388
VL  - 281
AB  - The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006
AB  - pairs containing 1041 predicted coding sequences (open reading frames).  Systems for DNA
AB  - replication, transcription, translation, and repair are intact, but catabolic and biosynthetic
AB  - activities are minimized.  The number of identifiable transporters is small, and no
AB  - phosphoenolpyruvate: phosphotransferase carbohydrate transporters were found.  Potential
AB  - virulence factors include a family of 12 potential membrane proteins and several putative
AB  - hemolysins.  Comparison of the T. pallidum genome sequence with that of another pathogenic
AB  - spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common
AB  - genes and substantiates the considerable diversity observed among pathogenic spirochetes.
ER  -

TY  - JOUR
AU  - Frauer, C.
AU  - Leonhardt, H.
TI  - Twists and turns of DNA methylation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 8919
EP  - 8920
VL  - 108
AB  - DNA methylation, the post-replicative transfer of a methyl group to the C5 position of
AB  - cytosine bases, was the first epigenetic modification identified and has been intensively
AB  - studied for more than half a century.  By now it is clear that Dnmt1, the major eukaryotic DNA
AB  - methyltransferase, faithfully maintains genome-wide methylation patterns and plays an
AB  - essential role in the epigenetic network controlling gene expression and genome stability
AB  - during development.  However, the molecular mechanisms that ultimately control DNA methylation
AB  - still remain elusive.  This is, in part, attributable to the remarkable complexity of the DNA
AB  - methylation reaction, the apparent involvement of several inter- and intra-molecular protein
AB  - interactions, and the limited structural information.  The crystal structure of Dnmt1
AB  - presented in PNAS now provides detailed insights into the inner workings and possible
AB  - regulation of one of the most intriguing enzymes.
ER  -

TY  - JOUR
AU  - Frauer, C.
AU  - Leonhardt, H.
TI  - A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - e22
EP  - e22
VL  - 37
AB  - We present a simple, non-radioactive assay for DNA methyltransferase activity and DNA binding.
AB  - As most proteins are studied as GFP fusions in
AB  - living cells, we used a GFP binding nanobody coupled to agarose beads (GFP
AB  - nanotrap) for rapid one-step purification. Immobilized GFP fusion proteins
AB  - were subsequently incubated with different fluorescently labeled DNA
AB  - substrates. The absolute amounts and molar ratios of GFP fusion proteins
AB  - and bound DNA substrates were determined by fluorescence spectroscopy. In
AB  - addition to specific DNA binding of GFP fusion proteins, the enzymatic
AB  - activity of DNA methyltransferases can also be determined by using suicide
AB  - DNA substrates. These substrates contain the mechanism-based inhibitor
AB  - 5-aza-dC and lead to irreversible covalent complex formation. We obtained
AB  - covalent complexes with mammalian DNA methyltransferase 1 (Dnmt1), which
AB  - were resistant to competition with non-labeled canonical DNA substrates,
AB  - allowing differentiation between methyltransferase activity and DNA
AB  - binding. By comparison, the Dnmt1(C1229W) catalytic site mutant showed
AB  - DNA-binding activity, but no irreversible covalent complex formation. With
AB  - this assay, we could also confirm the preference of Dnmt1 for
AB  - hemimethylated CpG sequences. The rapid optical read-out in a multi-well
AB  - format and the possibility to test several different substrates in direct
AB  - competition allow rapid characterization of sequence-specific binding and
AB  - enzymatic activity.
ER  -

TY  - JOUR
AU  - Fraunhofer, M.E.
AU  - Geissler, A.J.
AU  - Jakob, F.
AU  - Vogel, R.F.
TI  - Multiple Genome Sequences of Exopolysaccharide-Producing, Brewery-Associated Lactobacillus brevis Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00585
EP  - e00517
VL  - 5
AB  - Lactobacillus brevis represents one of the most relevant beer-spoiling bacteria.  Besides
AB  - strains causing turbidity and off flavors upon growth and metabolite
AB  - formation, this species also comprises strains that produce exopolysaccharides
AB  - (EPSs), which increase the viscosity of beer. Here, we report the complete genome
AB  - sequences of three EPS-producing, brewery-associated L. brevis strains.
ER  -

TY  - JOUR
AU  - Fraunholz, M.
AU  - Bernhardt, J.
AU  - Schuldes, J.
AU  - Daniel, R.
AU  - Hecker, M.
AU  - Sinha, B.
TI  - Complete Genome Sequence of Staphylococcus aureus 6850, a Highly Cytotoxic and Clinically Virulent Methicillin-Sensitive Strain with Distant Relatedness to  Prototype Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00775
EP  - e00713
VL  - 1
AB  - Staphylococcus aureus is a frequent human commensal bacterium and pathogen. Here  we report
AB  - the complete genome sequence of strain 6850 (spa type t185; sequence
AB  - type 50 [ST50]), a highly cytotoxic and clinically virulent methicillin-sensitive
AB  - strain from a patient with complicated S. aureus bacteremia associated with
AB  - osteomyelitis and septic arthritis.
ER  -

TY  - JOUR
AU  - Frazao, M.R.
AU  - Cao, G.
AU  - Medeiros, M.I.C.
AU  - Duque, S.D.S.
AU  - Leon, M.S.
AU  - Allard, M.W.
AU  - Falcao, J.P.
TI  - Draft Genome Sequences of 116 Campylobacter jejuni Strains Isolated from Humans,  Animals, Food, and the Environment in Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00250
EP  - e00218
VL  - 6
AB  - Campylobacter jejuni is a major zoonotic pathogen that causes foodborne gastroenteritis
AB  - worldwide. However, clinical cases of campylobacteriosis have
AB  - been underreported and underdiagnosed in Brazil. Herein, we describe the draft
AB  - genome sequences of 116 C. jejuni strains isolated from diverse sources in
AB  - Brazil.
ER  -

TY  - JOUR
AU  - Frederick, C.A.
AU  - Grable, J.
AU  - Melia, M.
AU  - Samudzi, C.
AU  - Jen-Jacobson, L.
AU  - Wang, B.-C.
AU  - Greene, P.
AU  - Boyer, H.W.
AU  - Rosenberg, J.M.
TI  - Kinked DNA in crystalline complex with EcoRI endonuclease.
JO  - Nature
PY  - 1984
SP  - 327
EP  - 331
VL  - 309
AB  - The 3 angstrom electron density map of a co-crystalline recognition complex
AB  - between EcoRI endonuclease and the oligonucleotide TCGCGAATTCGCG reveals that a
AB  - tight, complementary interface between the enzyme and the major groove of the
AB  - DNa is the major determinant of sequence specificity.  The DNA contains a
AB  - torsional kink and other departures from the B conformation which unwind the
AB  - DNA and thereby widen the major groove in the recognition site.
ER  -

TY  - JOUR
AU  - Frederick, C.A.
AU  - Quigley, G.J.
AU  - van der Marel, G.A.
AU  - van Boom, J.H.
AU  - Wang, A.H.-J.
AU  - Rich, A.
TI  - Methylation of the EcoRI recognition site does not alter DNA conformation:  The crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution.
JO  - J. Biol. Chem.
PY  - 1988
SP  - 17872
EP  - 17879
VL  - 263
AB  - Methylation of nucleic acid bases is known to prevent the cleavage of DNA by
AB  - restriction endonucleases.  The effect on the conformation of the DNA molecule
AB  - itself and hence its interactions with other DNA binding proteins has been a
AB  - subject of general interest.  To help address this question, we have solved the
AB  - crystal structure at 2.0 A of the methylated dodecamer, d(CGCGAm6ATTCGCG),
AB  - which contains the EcoRI recognition sequence and have compared the
AB  - conformation of the methylated molecule with that of its nonmethylated
AB  - counterpart.  This methylation produces a bulky hydrophobic patch on the floor
AB  - of the major groove of B-DNA which plays an important role in the mechanism of
AB  - inhibition of EcoRI restriction activity.  However, with the exception of small
AB  - perturbations in the immediate vicinity of the methyl groups, the structure is
AB  - virtually unchanged.  Given the lack of a conformational change upon
AB  - methylation, we have extended this thesis of the recognition process to other
AB  - types of restriction systems and found that different restriction enzymes seem
AB  - to have their own characteristic protein-DNA interactions.  The relative
AB  - spatial orientations of methylation sites and cleavage sites must play a major
AB  - role in ordering protein secondary structure elements as well as
AB  - subunit-subunit interactions along the DNA strand.
ER  -

TY  - JOUR
AU  - Free, A.
AU  - Wakefield, R.I.
AU  - Smith, B.O.
AU  - Dryden, D.T.
AU  - Barlow, P.N.
AU  - Bird, A.P.
TI  - DNA recognition by the methyl-CpG binding domain of MeCP2.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 3353
EP  - 3360
VL  - 276
AB  - The methyl-CpG binding domain (MBD) of the transcriptional repressor MeCP2 has been proposed
AB  - to recognize a single symmetrically methylated CpG base pair via hydrophobic patches on an
AB  - otherwise positively charged DNA binding surface. We have tested this binding model by
AB  - analysis of mutant derivatives of the MeCP2 MBD in electrophoretic mobility shift assays
AB  - complemented by NMR structural analysis. Exposed arginine side chains on the binding face, in
AB  - particular Arg-111, were found to be critical for binding. Arg-111 was found to interact with
AB  - the conserved aspartate side chain Asp-121, which is proposed to orientate the arginine side
AB  - chain to allow specific contacts with the DNA. The conformational flexibility of the
AB  - disordered B-C loop region, which forms part of the binding face, was also shown to be
AB  - important. In contrast, mutation of the exposed hydrophobic side chains had a less severe
AB  - effect on DNA binding. This suggests that the Arg-111 side chain may contribute to
AB  - sequence-specific recognition of the CpG site rather than simply making nonspecific contacts
AB  - with the phosphate backbone. The majority of missense mutations within the MBD found in the
AB  - human genetic disorder Rett syndrome were shown or predicted to affect folding of the domain
AB  - rather than the DNA recognition event directly.
ER  -

TY  - JOUR
AU  - Freese, H.M. et al.
TI  - Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 450
EP  - 464
VL  - 8
AB  - Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members
AB  - are phylogenetically and physiologically diverse. In contrast to
AB  - the type species of this genus, Phaeobacter gallaeciensis, which is well
AB  - characterized, relatively little is known about the characteristics of P.
AB  - arcticus. Here, we describe the features of this organism including the annotated
AB  - high-quality draft genome sequence and highlight some particular traits. The
AB  - 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists
AB  - of one chromosome and five extrachromosomal elements. Prophage sequences
AB  - identified via PHAST constitute nearly 5% of the bacterial chromosome and
AB  - included a potential Mu-like phage as well as a gene-transfer agent (GTA). In
AB  - addition, the genome of strain DSM 23566(T) encodes all of the genes necessary
AB  - for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic
AB  - distances indicate that the classification of the species might need to be
AB  - reconsidered.
ER  -

TY  - JOUR
AU  - Freese, H.M.
AU  - Methner, A.
AU  - Overmann, J.
TI  - Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton.
JO  - Front. Microbiol.
PY  - 2017
SP  - 1659
EP  - 1659
VL  - 8
AB  - The marine Roseobacter group encompasses numerous species which occupy a large
AB  - variety of ecological niches. However, members of the genus Phaeobacter are
AB  - specifically adapted to a surface-associated lifestyle and have so far been found
AB  - nearly exclusively in disjunct, man-made environments including shellfish and
AB  - fish aquacultures, as well as harbors. Therefore, the possible natural habitats,
AB  - dispersal and evolution of Phaeobacter spp. have largely remained obscure.
AB  - Applying a high-throughput cultivation strategy along a longitudinal Pacific
AB  - transect, the present study revealed for the first time a widespread natural
AB  - occurrence of Phaeobacter in the marine pelagial. These bacteria were found to be
AB  - specifically associated to mesoplankton where they constitute a small but
AB  - detectable proportion of the bacterial community. The 16S rRNA gene sequences of
AB  - 18 isolated strains were identical to that of Phaeobacter gallaeciensis
AB  - DSM26640(T) but sequences of internal transcribed spacer and selected genomes
AB  - revealed that the strains form a distinct clade within P. gallaeciensis. The
AB  - genomes of the Pacific and the aquaculture strains were highly conserved and had
AB  - a fraction of the core genome of 89.6%, 80 synteny breakpoints, and differed 2.2%
AB  - in their nucleotide sequences. Diversification likely occurred through neutral
AB  - mutations. However, the Pacific strains exclusively contained two active Type I
AB  - restriction modification systems which is commensurate with a reduced acquisition
AB  - of mobile elements in the Pacific clade. The Pacific clade of P. gallaeciensis
AB  - also acquired a second, homolog phosphonate transport system compared to all
AB  - other P. gallaeciensis. Our data indicate that a previously unknown, distinct
AB  - clade of P. gallaeciensis acquired a limited number of clade-specific genes that
AB  - were relevant for its association with mesozooplankton and for colonization of
AB  - the marine pelagial. The divergence of the Pacific clade most likely was driven
AB  - by the adaptation to this novel ecological niche rather than by geographic
AB  - isolation.
ER  -

TY  - JOUR
AU  - Freese, H.M.
AU  - Sikorski, J.
AU  - Bunk, B.
AU  - Scheuner, C.
AU  - Meier-Kolthoff, J.P.
AU  - Sproer, C.
AU  - Gram, L.
AU  - Overmann, J.
TI  - Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 3297
EP  - 3311
VL  - 9
AB  - The extent of genome divergence and the evolutionary events leading to speciation of marine
AB  - bacteria have mostly been studied for (locally) abundant, free-living
AB  - groups. The genus Phaeobacter is found on different marine surfaces, seems to
AB  - occupy geographically disjunct habitats, and is involved in different biotic
AB  - interactions, and was therefore targeted in the present study. The analysis of
AB  - the chromosomes of 32 closely related but geographically spread Phaeobacter
AB  - strains revealed an exceptionally large, highly syntenic core genome. The
AB  - flexible gene pool is constantly but slightly expanding across all Phaeobacter
AB  - lineages. The horizontally transferred genes mostly originated from bacteria of
AB  - the Roseobacter group and horizontal transfer most likely was mediated by gene
AB  - transfer agents. No evidence for geographic isolation and habitat specificity of
AB  - the different phylogenomic Phaeobacter clades was detected based on the sources
AB  - of isolation. In contrast, the functional gene repertoire and physiological
AB  - traits of different phylogenomic Phaeobacter clades were sufficiently distinct to
AB  - suggest an adaptation to an associated lifestyle with algae, to additional
AB  - nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary
AB  - trajectories of surface-associated marine bacteria can differ significantly from
AB  - free-living marine bacteria or marine generalists.
ER  -

TY  - JOUR
AU  - Freitag, M.
AU  - Selker, E.U.
TI  - Controlling DNA methylation: many roads to one modification.
JO  - Curr. Opin. Genet. Dev.
PY  - 2005
SP  - 191
EP  - 199
VL  - 15
AB  - Genetic, biochemical and cytological studies on DNA methylation in several eukaryotic
AB  - organisms have resulted in leaps of understanding in the past three years. Discoveries of
AB  - mechanistic links between DNA methylation and histone methylation, and between these processes
AB  - and RNA interference (RNAi) machineries have reinvigorated the field. The details of the
AB  - connections between DNA methylation, histone modifications and RNA silencing remain to be
AB  - elucidated, but it is already clear that no single pathway accounts for all DNA methylation
AB  - found in eukaryotes. Rather, different taxa use one or more of several general mechanisms to
AB  - control methylation. Despite recent progress, classic questions remain, including: What are
AB  - the signals for DNA methylation? Are 'de novo' and 'maintenance' methylation truly
AB  - separate processes? How is DNA methylation regulated?
ER  -

TY  - JOUR
AU  - Freitag, M.
AU  - Williams, R.L.
AU  - Kothe, G.O.
AU  - Selker, E.U.
TI  - A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 8802
EP  - 8807
VL  - 99
AB  - During sexual development, Neurospora crassa inactivates genes in duplicated DNA segments by a
AB  - hypermutation process, repeat-induced point mutation (RIP). RIP introduces C:G to T:A
AB  - transition mutations and creates targets for subsequent DNA methylation in vegetative tissue.
AB  - The mechanism of RIP and its relationship to DNA methylation are not fully understood.
AB  - Mutations in DIM-2, a DNA methyltransferase (DMT) responsible for all known cytosine
AB  - methylation in Neurospora, does not prevent RIP. We used RIP to disrupt a second putative DMT
AB  - gene in the Neurospora genome and tested mutants for defects in DNA methylation and RIP. No
AB  - effect on DNA methylation was detected in the tissues that could be assayed, but the mutants
AB  - showed recessive defects in RIP. Duplications of the am and mtr genes were completely stable
AB  - in crosses homozygous for the mutated potential DMT gene, which we call rid (RIP defective).
AB  - The same duplications were inactivated normally in heterozygous crosses. Disruption of the rid
AB  - gene did not noticeably affect fertility, growth, or development. In contrast, crosses
AB  - homozygous for a mutation in a related gene in Ascobolus immersus, masc1, reportedly fail to
AB  - develop and heterozygous crosses reduce methylation induced premeiotically .  We isolated
AB  - homologues of rid from Neurospora tetrasperma and Neurospora intermedia to identify conserved
AB  - regions. Homologues possess all motifs characteristic of eukaryotic DMTs and have large
AB  - distinctive C- and N-terminal domains.
ER  -

TY  - JOUR
AU  - Freitas, A.C.
AU  - Hill, J.E.
TI  - Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from  the Human Vaginal Microbiome.
JO  - Genome Announcements
PY  - 2018
SP  - e01433
EP  - e01417
VL  - 6
AB  - We report here the draft genome sequences of Bifidobacterium strains N4G05 and N5G01, isolated
AB  - from the human vaginal microbiome. Genome sequences were obtained
AB  - by de novo assembly from high-quality reads. Both strains were closely related to
AB  - Bifidobacterium kashiwanohense based on barcode marker sequences and average
AB  - nucleotide identity analysis.
ER  -

TY  - JOUR
AU  - French, C.T.
AU  - Sitaraman, R.
AU  - Dybvig, K.
TI  - DNA inversions regulate a family of phase-variable restriction and modification enzymes in Mycoplasma pulmonis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1998
SP  - 274
EP  - 275
VL  - 0
AB  - Mycoplasma pulmonis is a murine pathogen that produces chronic disease in the reproductive and
AB  - respiratory tracts and joints.  The ability to undergo rapid phenotypic changes is probably an
AB  - important pathogenic attribute allowing the organism to quickly adapt to a changing
AB  - environment.  The hsd1 and hsd2 loci of M. pulmonis are highly homologous, site-specific DNA
AB  - inversion systems that encode proteins exhibiting significant amino acid similarity with the
AB  - type I restriction and modification systems of enteric bacteria.  DNA inversions regulate
AB  - transcription of the hsdS genes, acting as an on/off switches controlling which particular
AB  - hsdS genes are expressed in the cell.  The hsdS genes encode the S subunits which dictate the
AB  - sequence specificity of the type I holoenzyme.  We hypothesized that the various hsdS genes
AB  - that can be induced by DNA inversion encode S subunits with different DNA recognition
AB  - specificities, resulting in the production of R-M enzymes with different specificities.  To
AB  - test this possibility, cultures of M. pulmonis was subcloned using filter cloning methods.
AB  - R-M properties were examined by quantitating PFU of mycoplasma virus P1 on lawns of each
AB  - individual subclone.  The R-M properties of over 100 subclones have been examined thus far.
AB  - Subclones have been divided into five groups, each with unique R-M properties.  Group I is R-M
AB  - negative.  Southern blot and hsd mRNA transcription anlayses suggest that R-M systems are
AB  - "off" in these subclones because the hsd1 and hsd2 loci are oriented in the chromosome such
AB  - that the hsdR and hsdM genes (encoding the R and M subunits of the type I holoenzyme) are not
AB  - transcribed.  Groups II, III, IV and V are R-M positive, with the specificity of the R-M
AB  - activity of each group being distinct.  Gene analyses (Southern hybridization, PCR and
AB  - nucleotide sequencing indicate that different hsdS genes are transcribed in the different
AB  - groups, explaining the unique R-M properties of each group.  These results indicate that M.
AB  - pulmonis possesses a novel family of phase-variable R-M enzymes.  Because hsd inversions have
AB  - previously been correlated with other gene rearrangements that regulate the phase-variable
AB  - production of the V-1 surface proteins, it is possible that R-M enzymes in this system have an
AB  - important but undefined role in disease pathogenesis.
ER  -

TY  - JOUR
AU  - Fresco-Taboada, A.
AU  - Del Cerro, C.
AU  - Fernandez-Lucas, J.
AU  - Arroyo, M.
AU  - Acebal, C.
AU  - Garcia, J.L.
AU  - de la Mata, I.
TI  - Genome of the Psychrophilic Bacterium Bacillus psychrosaccharolyticus, a Potential Source of 2'-Deoxyribosyltransferase for Industrial Nucleoside  Synthesis.
JO  - Genome Announcements
PY  - 2013
SP  - e00309
EP  - e00313
VL  - 1
AB  - Here we report the draft genome sequence of Bacillus psychrosaccharolyticus, a cold-adapted
AB  - bacterium with biotechnological interest. The genome contains genes
AB  - related to the ability of this microorganism to grow at low temperatures and
AB  - includes a nucleoside 2'-deoxyribosyltransferase, which can be used in the
AB  - industrial synthesis of modified nucleosides with therapeutic activity.
ER  -

TY  - JOUR
AU  - Frey, B.
AU  - Kahle, C.
AU  - Zolch, C.
AU  - Kaluza, K.
AU  - Herz, G.
AU  - Lechner, M.
AU  - Auer, J.
AU  - Schmitz, G.
TI  - Screening for novel class-II restriction endonucleases.
JO  - Fresenius Z. Anal. Chem.
PY  - 1992
SP  - 123
EP  - 124
VL  - 343
AB  - More than 1500 class-II restriction endonucleases have been isolated from eu- and
AB  - archaebacteria. In addition only a few restriction enzymes were described from eukaryotic
AB  - sources like virus infected chlorella-like green algae. These enzymes represent more than 170
AB  - different sequence specificities. Class-II restriction endonucleases are important tools in
AB  - recombinant DNA technology. In addition restriction enzymes recognizing octa- and
AB  - heptanucleotide sequences are necessary for the mapping of genomes because they produce very
AB  - large fragments that can be resolved by pulse field gel electrophoresis. Our aim was to find
AB  - and characterize new restriction enzymes and determine the specificities with respect to their
AB  - recognition sequence and cleavage position.
ER  -

TY  - JOUR
AU  - Frey, B.
AU  - Kaluza, K.
AU  - Auer, J.
AU  - Stratidakis, I.
AU  - Rina, M.
AU  - Bouriotis, V.
AU  - Schmitz, G.
TI  - AspEI, a novel Eam11051 isoschizomer from Aureobacterium species recognizing 5'-GACnnn/nnGTC-3' .
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3782
EP  - 3782
VL  - 20
AB  - We have isolated AspEI, a novel class II restriction endonuclease from Aureobacterium species
AB  - 3676 recognizing the palindromic sequence 5'-GACnnn/nnGTC-3' generating a 3'-protruding
AB  - mononucleotide. With respect to its isoschizomer from Eam1105I, the novel enzyme can be easily
AB  - isolated in high purity because of its occurrence as a single restriction enzyme in the
AB  - Aureobacterium strain and the presence of high specific activity even in the crude extract. A
AB  - comparison of cleavage patterns experimentally obtained with AspEI on standard lambda,
AB  - phiX174RF, pBR322, T7 and Ad2 DNAs of known nucleotide sequence, with computer-derived mapping
AB  - data predicts the sequence 5'-GACn5GTC-3'. The cut positions within the AspEI recognitin
AB  - site were determined according to the enzymatic sequencing approach.
ER  -

TY  - JOUR
AU  - Frey, K.G.
AU  - Bishop-Lilly, K.A.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Chertkov, O.
AU  - Freitas, T.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Minogue, T.D.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672.
JO  - Genome Announcements
PY  - 2014
SP  - e01082
EP  - e01014
VL  - 2
AB  - A member of the normal human gut microflora, Providencia stuartii is of clinical  interest due
AB  - to its role in nosocomial infections of the urinary tract and
AB  - because it readily acquires antibiotic resistance. Here, we present the complete
AB  - genome of P. stuartii strain ATCC 33672, consisting of a 4.28-Mbp chromosome and
AB  - a 48.9-kbp plasmid.
ER  -

TY  - JOUR
AU  - Freylikhman, O.
AU  - Kiselev, A.
AU  - Kazakov, S.
AU  - Sergushichev, A.
AU  - Panferova, Y.
AU  - Tokarevich, N.
AU  - Kostareva, A.
TI  - Draft Genome Sequence of Coxiella burnetii Historical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia.
JO  - Genome Announcements
PY  - 2018
SP  - e01464
EP  - e01417
VL  - 6
AB  - This is the announcement of a draft genome sequence of Coxiella burnetii strain Leningrad-2,
AB  - phase I. The strain, which is mildly virulent in infected guinea
AB  - pigs, was isolated in 1957 from the blood of a patient with acute Q fever in
AB  - Leningrad (now Saint Petersburg), Russia.
ER  -

TY  - JOUR
AU  - Fricke, W.F.
AU  - Mammel, M.K.
AU  - McDermott, P.F.
AU  - Tartera, C.
AU  - White, D.G.
AU  - Leclerc, J.E.
AU  - Ravel, J.
AU  - Cebula, T.A.
TI  - Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3556
EP  - 3568
VL  - 193
AB  - Despite extensive surveillance, food-borne Salmonella enterica infections
AB  - continue to be a significant burden on public health systems worldwide. As
AB  - the S. enterica species comprises sublineages that differ greatly in
AB  - antigenic representation, virulence, and antimicrobial resistance
AB  - phenotypes, a better understanding of the species' evolution is critical
AB  - for the prediction and prevention of future outbreaks. The roles that
AB  - virulence and resistance phenotype acquisition, exchange, and loss play in
AB  - the evolution of S. enterica sublineages, which to a certain extent are
AB  - represented by serotypes, remains mostly uncharacterized. Here, we compare
AB  - 17 newly sequenced and phenotypically characterized nontyphoidal S.
AB  - enterica strains to 11 previously sequenced S. enterica genomes to carry
AB  - out the most comprehensive comparative analysis of this species so far.
AB  - These phenotypic and genotypic data comparisons in the phylogenetic
AB  - species context suggest that the evolution of known S. enterica
AB  - sublineages is mediated mostly by two mechanisms, (i) the loss of coding
AB  - sequences with known metabolic functions, which leads to functional
AB  - reduction, and (ii) the acquisition of horizontally transferred phage and
AB  - plasmid DNA, which provides virulence and resistance functions and leads
AB  - to increasing specialization. Matches between S. enterica clustered
AB  - regularly interspaced short palindromic repeats (CRISPR), part of a
AB  - defense mechanism against invading plasmid and phage DNA, and plasmid and
AB  - prophage regions suggest that CRISPR-mediated immunity could control
AB  - short-term phenotype changes and mediate long-term sublineage evolution.
AB  - CRISPR analysis could therefore be critical in assessing the evolutionary
AB  - potential of S. enterica sublineages and aid in the prediction and
AB  - prevention of future S. enterica outbreaks.
ER  -

TY  - JOUR
AU  - Fricke, W.F.
AU  - McDermott, P.F.
AU  - Mammel, M.K.
AU  - Zhao, S.
AU  - Johnson, T.J.
AU  - Rasko, D.A.
AU  - Fedorka-Cray, P.J.
AU  - Pedroso, A.
AU  - Whichard, J.M.
AU  - Leclerc, J.E.
AU  - White, D.G.
AU  - Cebula, T.A.
AU  - Ravel, J.
TI  - Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 5963
EP  - 5971
VL  - 75
AB  - Salmonella enterica, a leading cause of food-borne gastroenteritis
AB  - worldwide, may be found in any raw food of animal, vegetable, or fruit
AB  - origin. Salmonella serovars differ in distribution, virulence, and host
AB  - specificity. Salmonella enterica serovar Kentucky, though often found in
AB  - the food supply, is less commonly isolated from ill humans. The
AB  - multidrug-resistant isolate S. Kentucky CVM29188, isolated from a chicken
AB  - breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp,
AB  - and 46,121 bp), two of which carry resistance determinants (pCVM29188_146
AB  - [strAB and tetRA] and pCVM29188_101 [bla(CMY-2) and sugE]). Both
AB  - resistance plasmids were transferable by conjugation, alone or in
AB  - combination, to S. Kentucky, Salmonella enterica serovar Newport, and
AB  - Escherichia coli recipients. pCVM29188_146 shares a highly conserved
AB  - plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence
AB  - plasmids from avian pathogenic Escherichia coli strains (pAPEC-O1-ColBM
AB  - and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence
AB  - factors include iutA iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR
AB  - analyses of recent (1997 to 2005) S. Kentucky isolates from food animal,
AB  - retail meat, and human sources revealed that 172 (60%) contained similar
AB  - APEC-like plasmid backbones. Notably, though rare in human- and
AB  - cattle-derived isolates, this plasmid backbone was found at a high
AB  - frequency (50 to 100%) among S. Kentucky isolates from chickens within the
AB  - same time span. Ninety-four percent of the APEC-positive isolates showed
AB  - resistance to tetracycline and streptomycin. Together, our findings of a
AB  - resistance-conferring APEC virulence plasmid in a poultry-derived S.
AB  - Kentucky isolate and of similar resistance/virulence plasmids in most
AB  - recent S. Kentucky isolates from chickens and, to lesser degree, from
AB  - humans and cattle highlight the need for additional research in order to
AB  - examine the prevalence and spread of combined virulence and resistance
AB  - plasmids in bacteria in agricultural, environmental, and clinical
AB  - settings.
ER  -

TY  - JOUR
AU  - Fricke, W.F.
AU  - Seedorf, H.
AU  - Henne, A.
AU  - Kruer, M.
AU  - Liesegang, H.
AU  - Hedderich, R.
AU  - Gottschalk, G.
AU  - Thauer, R.K.
TI  - The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.
JO  - J. Bacteriol.
PY  - 2006
SP  - 642
EP  - 658
VL  - 188
AB  - Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic
AB  - archaea. This human intestinal inhabitant can generate methane only by reduction of methanol
AB  - with H2 and is dependent on acetate as a carbon source. We report here the genome sequence of
AB  - M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G+C content of
AB  - 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present
AB  - in the genomes of all other methanogens. Among these are the CDS for synthesis of
AB  - molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetyl-coenzyme A
AB  - synthase complex, which explains why M. stadtmanae cannot reduce CO2 to methane or oxidize
AB  - methanol to CO2 and why this archaeon is dependent on acetate for biosynthesis of cell
AB  - components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were
AB  - found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously
AB  - identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS
AB  - not present in the genomes of all other archaea. Seventy-three of these CDS exhibit high
AB  - levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS
AB  - which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS
AB  - which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the
AB  - biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity
AB  - to the subunits of bacterial type I and III restriction-modification systems.
ER  -

TY  - JOUR
AU  - Fridman, O.
AU  - Goldberg, A.
AU  - Ronin, I.
AU  - Shoresh, N.
AU  - Balaban, N.Q.
TI  - Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.
JO  - Nature
PY  - 2014
SP  - 418
EP  - 421
VL  - 513
AB  - The great therapeutic achievements of antibiotics have been dramatically undercut by the
AB  - evolution of bacterial strategies that overcome antibiotic stress. These strategies fall into
AB  - two classes. 'Resistance' makes it possible for a microorganism to grow in the constant
AB  - presence of the antibiotic, provided that the concentration of the antibiotic is not too high.
AB  - 'Tolerance' allows a microorganism to survive antibiotic treatment, even at high antibiotic
AB  - concentrations, as long as the duration of the treatment is limited. Although both resistance
AB  - and tolerance are important reasons for the failure of antibiotic treatments, the evolution of
AB  - resistance is much better understood than that of tolerance. Here we followed the evolution of
AB  - bacterial populations under intermittent exposure to the high concentrations of antibiotics
AB  - used in the clinic and characterized the evolved strains in terms of both resistance and
AB  - tolerance. We found that all strains adapted by specific genetic mutations, which became fixed
AB  - in the evolved populations. By monitoring the phenotypic changes at the population and
AB  - single-cell levels, we found that the first adaptive change to antibiotic stress was the
AB  - development of tolerance through a major adjustment in the single-cell lag-time distribution,
AB  - without a change in resistance. Strikingly, we found that the lag time of bacteria before
AB  - regrowth was optimized to match the duration of the antibiotic-exposure interval. Whole genome
AB  - sequencing of the evolved strains and restoration of the wild-type alleles allowed us to
AB  - identify target genes involved in this antibiotic-driven phenotype: 'tolerance by lag'
AB  - (tbl). Better understanding of lag-time evolution as a key determinant of the survival of
AB  - bacterial populations under high antibiotic concentrations could lead to new approaches to
AB  - impeding the evolution of antibiotic resistance.
ER  -

TY  - JOUR
AU  - Friedhoff, P.
AU  - Franke, I.
AU  - Krause, K.L.
AU  - Pingoud, A.
TI  - Cleavage experiments with deoxythymidine 3',5'-bis-(p-nitrophenyl phosphate) suggest that the homing endonuclease I-PpoI follows the same mechanism of phosphodiester bond hydrolysis as the non-specific Serratia nuclease.
JO  - FEBS Lett.
PY  - 1999
SP  - 209
EP  - 214
VL  - 443
AB  - We show here that two nucleases, Serratia nuclease and I-PpoI, with contrasting specificities,
AB  - i.e. non-specific vs. highly sequence specific, share a structurally similar active site
AB  - region with conservation of the catalytically relevant histidine and asparagine residues.  On
AB  - the basis of a comparison of the available structures and biochemical data for wild type and
AB  - mutant variants of Serratia nuclease and I-PpoI we propose that both enzymes have a catalytic
AB  - mechanism, a proposition that is supported by our finding that both enzymes accept
AB  - deoxythymidine 3',5'-bis-(p-nitrophenyl phosphate) as a substrate and cleave it in an
AB  - identical manner.  According to this mechanism a histidine residue functions as a general base
AB  - and Mg2+ bound to an asparagine residue as a Lewis acid in phosphodiester bond cleavage.
ER  -

TY  - JOUR
AU  - Friedhoff, P.
AU  - Lurz, R.
AU  - Lueder, G.
AU  - Pingoud, A.
TI  - Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 23581
EP  - 23588
VL  - 276
AB  - Here, we report that Sau3AI, an unusually large type II restriction enzyme with sequence
AB  - homology to the mismatch repair protein MutH, is a monomeric enzyme as shown by gel filtration
AB  - and ultracentrifugation. Structural similarities in the N- and C-terminal halves of the
AB  - protein suggest that Sau3AI is a pseudo-dimer, i.e. a polypeptide with two similar domains.
AB  - Since Sau3AI displays a nonlinear dependence of cleavage activity on enzyme concentration and
AB  - a strong preference for substrates with two recognition sites over those with only one, it is
AB  - likely that the functionally active form of Sau3AI is a dimer of a pseudo-dimer. Indeed,
AB  - electron microscopy studies demonstrate that two distant recognition sites are brought
AB  - together through DNA looping induced by the simultaneous binding of two Sau3AI molecules to
AB  - the DNA. We suggest that the dimeric form of Sau3AI supplies two DNA-binding sites, one that
AB  - is associated with the catalytic center and one that serves as an effector site.
ER  -

TY  - JOUR
AU  - Friedman, J.
AU  - Friedmann, A.
AU  - Razin, A.
TI  - Studies on the biological role of DNA methylation:  III.  Role in excision of one-genome long single-stranded Phi X174 DNA.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 3483
EP  - 3496
VL  - 4
AB  - Accumulation of replicative intermediates of the bacteriophage Phi X174 was
AB  - observed in E. coli C infected cells when phage DNA methylation has been
AB  - inhibited by nicotinamide or when cells were infected with a
AB  - temperature-sensitive mutant in gene A.  Analysis of the accumulating
AB  - replicative intermediates by electron microscopy revealed that these molecules
AB  - are composed of double-stranded DNA rings with multiple-genome length
AB  - single-stranded "tails".  These results suggest that the single
AB  - 5-methylcytosine residue present in the phage DNA serves as a recognition site
AB  - for the gene A protein mediating the excision of one-genome long phage DNA.
ER  -

TY  - JOUR
AU  - Friedman, J.
AU  - Razin, A.
TI  - Studies on the biological role of DNA methylation.  II.  Role of Phi X174 DNA methylation in the process of viral progeny DNA synthesis.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 2665
EP  - 2675
VL  - 3
AB  - In vivo inhibition of bacteriophage Phi X174 DNA methylation by nicotinamide resulted in the
AB  - accumulation of replicative intermediates with multiple-genome length single-stranded "tails".
AB  - These abnormal replicative intermediates could not be chased into viral single-stranded
AB  - circular DNA.  The effect of nicotinamide on phage maturation and accumulation of abnormal
AB  - replicative intermediates could be reversed by washing out the inhibitor.  The results suggest
AB  - that the single methyl group present in the viral DNA serves as a recognition site for a
AB  - specific endonuclease, probably the gene A protein product, that is responsible for the
AB  - excision of the single-stranded one-genome long viral DNA, before final maturation of the
AB  - virus occurs.
ER  -

TY  - JOUR
AU  - Friedman, S.
TI  - The irreversible binding of Azacytosine-containing DNA fragments to bacterial DNA (cytosine-5)methyltransferases.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 5698
EP  - 5705
VL  - 260
AB  - DNA containing 5-azacytosine is an irreversible inhibitor of DNA
AB  - (cytosine-5)methyltransferase.  This paper describes the binding of DNA
AB  - methyltransferase to 32P-labeled fragments of DNA containing 5-azacytosine.
AB  - The complexes were identified by gel electrophoresis.The EcoRII
AB  - methyltransferase specified by the R15 plasmid was purified from Escherichia
AB  - coli B(R15).  This enzyme methylates the second C in the sequence CCAGG and has
AB  - a molecular mass of 60,000 Da.  Specific binding of enzyme to DNA fragments
AB  - could be detected if either excess unlabeled DNA or 0.8% sodium dodecyl sulfate
AB  - was added to the reaction mixture prior to electrophoresis.  Binding was
AB  - dependent upon the presence of both the CCAGG sequence and azacytosine in the
AB  - DNA fragment.  S-Adenosylmethionine stimulated the formation of the complex.
AB  - The complex was stable to 6M urea but could be digested with pronase.  These
AB  - DNA fragments could be used to detect the presence of several different
AB  - methyltransferases in crude extracts of E. coli.  No DNA protein complexes
AB  - could be detected in E. coli B extracts, a strain that contains no
AB  - DNA(cytosine-5)methyltransferases.  The chromosomally determined methylase with
AB  - the same specificity as the purified EcoRII methylase could be detected in
AB  - crude extracts of E. coli K12 strains.  The MspI methylase cloned in E. coli
AB  - HB101 could also be detected in crude extracts.  These enzymes are the only
AB  - proteins that bind azacytosine-containing DNA in crude extracts of E. coli.
ER  -

TY  - JOUR
AU  - Friedman, S.
TI  - The effect of 5-azacytidine on E. coli DNA methylase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1979
SP  - 1328
EP  - 1333
VL  - 89
AB  - 5-Azacytidine, when added to growing E. coli K12, causes a decrease in DNA
AB  - methylation assayed in vitro.  This decrease is greater when E. coli DNA is
AB  - used as substrate than when calf thymus DNA is used.  The decrease in activity
AB  - is not due to the inhibition of protein synthesis caused by this drug, since
AB  - neither chloramphenicol nor rifampin causes a decrease in enzyme activity.  The
AB  - effect is specific for the DNA(cytosine-5)methylase; the methylation of adenine
AB  - is not affected.  The concentration of drug that inhibits the DNA methylase by
AB  - 50% is the same concentration that inhibits cell growth by 50%.
ER  -

TY  - JOUR
AU  - Friedman, S.
TI  - The inhibition of DNA(Cytosine-5)methylases by 5-azacytidine:  The effect of azacytosine-containing DNA.
JO  - Mol. Pharmacol.
PY  - 1981
SP  - 314
EP  - 320
VL  - 19
AB  - DNA extracted from Escherichia coli grown in the presence of 5-azacytidine
AB  - (azaC-DNA) inhibits the DNA(cytosine-5)methyltransferase extracted from E. coli
AB  - K12 cells without affecting the DNA(adenine-N6)methyltransferase present in
AB  - these same cells.  The inhibition is time-dependent and the rate of inhibition
AB  - can be decreased by addition of substrate DNA.  The inhibitory capacity of the
AB  - DNA is destroyed by incubation with pancreatic deoxyribonuclease or micrococcal
AB  - nuclease; however, the inhibited enzyme cannot be reactivated by treatment with
AB  - these enzymes.  The cytosine methylases methylate only double-stranded DNA.
AB  - Similarly, the inhibitory DNA loses activity if it is heat-denatured, and
AB  - regains activity upon reannealing.  The DNA will also inhibit the EcoRII and
AB  - HpaII modification methylases which also synthesize 5-methylcytosine in DNA.
AB  - Digestion of the inhibitory DNA with the respective restriction endonuclease
AB  - destroys, in part, the inhibitory activity of the DNA for the respective
AB  - methylase.  Base analysis indicated that 5-azacytidine replaced 8.4% of the
AB  - cytosine in the azaC-DNA.  These results suggest that DNA containing
AB  - 5-azacytidine irreversibly inhibits DNA(cytosine-5)methylases.
ER  -

TY  - JOUR
AU  - Friedman, S.
TI  - Adducts of the EcoRII methylase and 5-fluorocytosine-containing DNA.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - A436
EP  - A436
VL  - 91
AB  - We have investigated the properties of the adduct formed between the EcoRII
AB  - methyltransferase and DNA containing 5-fluorocytosine.  A polymer of CCCA/TGGG
AB  - containing 75% substitution of cytosine by 5-fluorocytosine was synthesized
AB  - labeled with alpha-32P dATP.  Irreversible inhibition of the enzyme by the DNA
AB  - occurred over a 5 h time course.  This inhibition only occurred in the presence
AB  - of AdoMet.  The DNA was methylated by the enzyme when incubated with
AB  - (methyl-3H)AdoMet with a similar time course.  Digestion with DNase I yielded
AB  - an adduct that was stable to boiling in 1% SDS but was unstable to a pH <5 and
AB  - to ultrafiltration.  However, if the adduct were digested with trypsin a
AB  - portion of the DNA remained bound to a peptide as defined by its altered
AB  - mobility.  The adduct was therefore treated with staphylococcal protease and
AB  - the products purified by HPLC.  The radioactive peak containing both 32P was
AB  - further purified by polyacrylamide gel electrophoresis.  The region containing
AB  - 32P was subjected to peptide sequencing for 20 cycles.  A sequence was obtained
AB  - which included a region of the protein that contains cysteine 186, a residue
AB  - that we had previously identified as being susceptible to photolabeling with
AB  - AdoMet and therefore part of the active site.
ER  -

TY  - JOUR
AU  - Friedman, S.
TI  - Binding of the EcoRII methylase to azacytosine-containing DNA.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 4543
EP  - 4556
VL  - 14
AB  - Binding of DNA (cytosine-5) methyltransferases to azacytosine containing DNA is
AB  - stimulated by the presence of S-adenosyl-methionine or its analogs sinefungin
AB  - or S-adenosyl-L-homocysteine.  Methylation of the DNA is therefore not
AB  - necessary for binding to occur.  There is no relationship between the affinity
AB  - of the analog for the EcoRII enzyme and its ability to stimulate binding.  The
AB  - DNA-enzyme complex partially dissociates on incubation in 0.1% sodium dodecyl
AB  - sulfate and 0.5 M ammonium acetate.  Some of this DNA could again form a tight
AB  - complex with enzyme, indicating that DNA-enzyme complex formation is
AB  - reversible.  Binding occurs when the second cytosine in the sequence CCAGG is
AB  - substituted by azacytosine.  This is the cytosine that would normally be
AB  - methylated by the enzyme.  The binding is therefore due to specific interaction
AB  - of the methylase with azacytosine at the site it would normally methylate.
ER  -

TY  - JOUR
AU  - Friedman, S.
AU  - Ansari, N.
TI  - Binding of the EcoRII methyltransferase to 5-fluorocytosine-containing DNA.  Isolation of a bound peptide.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3241
EP  - 3248
VL  - 20
AB  - The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII
AB  - methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a
AB  - 20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the
AB  - process the enzyme formed a tight binding adduct with the DNA that could be identified by
AB  - sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Enzyme activity was inhibited by
AB  - this interaction. The 20-mer could be used to titrate the active site of the enzyme. The DNA
AB  - polymer formed a tight binding complex that could be identified following digestion of the DNA
AB  - with pancreatic deoxyribonuclease or micrococcal nuclease. A peptide-DNA adduct could be
AB  - isolated after digestion of the EcoRII-DNA adduct with staphylococcal protease V8 by high
AB  - pressure liquid chromatography and polyacrylamide gel electrophoresis. Sequencing of the
AB  - peptide indicated the DNA bound to a region of the protein that is conserved in all
AB  - procaryotic DNA(cytosine-5)-methyltransferases. We have previously shown that this region
AB  - contains a cysteine that can be photomethylated with adenosylmethionine. This region, in
AB  - addition to forming part of, or being adjacent to, the AdoMet binding site, also forms part of
AB  - the DNA binding site.
ER  -

TY  - JOUR
AU  - Friedman, S.
AU  - Cheong, L.C.
TI  - Effect of 5-azacytidine on deoxyribonucleic acid methylation in Escherichia coli K12.
JO  - Biochem. Pharmacol.
PY  - 1984
SP  - 2675
EP  - 2679
VL  - 33
AB  - 5-azacytidine inhibits Escherichia coli DNA (cytosine-5) methylase when added to growing
AB  - cells.  The time-course of recovery of methylase activity and the appearance of
AB  - 5-methylcytosine in DNA following removal of the drug was studied.  When E. coli K12 was
AB  - treated with 5-azacytidine for 30 min, DNA (cytosine-5) methylase levels decreased to less
AB  - than 10% of control levels and slowly recovered to control levels for three generations after
AB  - treatment and returned to control levels after six generations of growth.  In contrast,
AB  - beta-galactosidase levels in induced cells, which declined to 66% of control one generation
AB  - after treatment, returned to control by the third generation of growth.  The rate of induction
AB  - of beta-galactosidase had returned to the control rate two generations after growth resumed.
AB  - Since azacytidine-containing DNA inhibits DNA-cytosine methylases in vitro, the prolonged
AB  - inhibition of cytosine methylation in E. coli K12 following treatment with the drug could be
AB  - due to the persistence of the drug in DNA and thus inhibition of newly synthesized enzymes.
ER  -

TY  - JOUR
AU  - Friedman, S.
AU  - Som, S.
TI  - Induction of EcoRII methyltranserase:  Evidence for autogenous control.
JO  - J. Bacteriol.
PY  - 1993
SP  - 6293
EP  - 6298
VL  - 175
AB  - The cytosine analog 5-azacytidline kills Escherichia coli cells that carry plamids expressing
AB  - EcoRII DNA (cytosine 5)methyltransferase under control of its own promoter. We previously
AB  - showed that this enzyme binds tightly to azacytidine-containing DNA in vitro and proposed that
AB  - such binding is lethal in vivo. In support of this proposal, we now show that the enzyme
AB  - sediments with the nucleoid of azabytidine-treated cells. Azacytidine treatment led to an
AB  - increase in the amount of enzyme, and this increase required sequences in the ecoRIIM promoter
AB  - region. Enzyme inducibility correlated with drug sensitivity: plasmids carrying the
AB  - methyltransferase gene but lacking the wild-type promoter did not confer sensitivity. These
AB  - results suggested that the ecoRIIM gene was under autogenous control. Transcriptional
AB  - ecoRIIM' -lacZ fusions in E. coli were, therefore, constructed. They showed that expression
AB  - from the ecoRIIM promoter was reversed by treating the cells with azacytidine. These results
AB  - provide evidence that the expression of the ecoRIIM gene is under autogenous regulation and
AB  - that call death induced by azacytidine is due, in part, to the disruption of autoregulation.
ER  -

TY  - JOUR
AU  - Friedman, S.
AU  - Som, S.
AU  - Yang, L.-F.
TI  - The core element of the EcoRII methylase as defined by protease digestion and deletion analysis.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 5403
EP  - 5408
VL  - 19
AB  - Binding of the EcoRII DNA methyltransferase to azacytosine-containing DNA
AB  - protects the enzyme from digestion by proteases.  The limit digest yields a
AB  - product having a Mr, on SDS-PAGE 20% less than the intact protein.  The N
AB  - terminus of the tryptic digestion product was sequenced and found to be missing
AB  - the N terminal 82 amino acids.  Under the conditions used unbound enzyme was
AB  - digested to small peptides.  Protection of the enzyme undergoes major
AB  - conformational changes when bound to DNA.  The trypsin sensitive region of the
AB  - EcoRII methyltransferase occurs prior to the first constant region shared with
AB  - other procaryotic DNA(cytosine-5)methyltransferases.  To determine if this
AB  - region played a role in substrate binding or specificity, N-terminal deletion
AB  - mutants were studied.  Deletion of 97 amino acids resulted in a decrease of
AB  - enzyme activity.  Further deletions caused a complete loss of activity.  Enzyme
AB  - deleted through amino acid 85 was purified and found to have the same
AB  - specificity as wild type however there was an increase in Km for both
AB  - S-adenosylmethionine (AdoMet) and DNA of 27 and 18 fold respectively.  The
AB  - N-terminus of the EcoRII methylase, although a variable region present in many
AB  - procaryotic DNA(cytosine-5)methylases, plays no role in determining enzyme
AB  - specificity, although it does contribute to the interaction with both AdoMet
AB  - and DNA.
ER  -

TY  - JOUR
AU  - Friedrich, T.
AU  - Fatemi, M.
AU  - Gowhar, H.
AU  - Leismann, O.
AU  - Jeltsch, A.
TI  - Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase.
JO  - Biochim. Biophys. Acta
PY  - 2000
SP  - 145
EP  - 159
VL  - 1480
AB  - The M.FokI adenine-N(6) DNA methyltransferase recognizes the asymmetric DNA sequence
AB  - GGATG/CATCC. It consists of two domains each containing all motifs characteristic for
AB  - adenine-N(6) DNA methyltransferases. We have studied the specificity of DNA-methylation by
AB  - both domains using 27 hemimethylated oligonucleotide substrates containing recognition sites
AB  - which differ in one or two base pairs from GGATG or CATCC. The N-terminal domain of M.FokI
AB  - interacts very specifically with GATG-sequences, because only one of the altered sites is
AB  - modified. In contrast, the C-terminal domain shows lower specificity. It prefers
AB  - CATCC-sequences but only two of the 12 star sites (i.e. sites that differ in 1 bp from the
AB  - recognition site) are not accepted and some star sites are modified with rates reduced only
AB  - 2-3-fold. In addition, GGATGC- and CGATGC-sites are modified which differ at two positions
AB  - from CATCC. DNA binding experiments show that the N-terminal domain preferentially binds to
AB  - hemimethylated GGATG/C(m)ATCC sequences whereas the C-terminal domain binds to DNA with higher
AB  - affinity but without specificity. Protein-protein interaction assays show that both domains of
AB  - M.FokI are in contact with each other. However, several DNA-binding experiments demonstrate
AB  - that DNA-binding of both domains is mutually exclusive in full-length M.FokI and both domains
AB  - do not functionally influence each other. The implications of these results on the molecular
AB  - evolution of type IIS restriction/modification systems are discussed.
ER  -

TY  - JOUR
AU  - Friedrich, T.
AU  - Roth, M.
AU  - Helm-Kruse, S.
AU  - Jeltsch, A.
TI  - Functional mapping of the EcoRV DNA methyltransferase by random mutagenesis and screening for catalytically inactive mutants.
JO  - Biol. Chem.
PY  - 1998
SP  - 475
EP  - 480
VL  - 379
AB  - M.EcoRV is an alpha-adenine DNA methyltransferase.  According to structure predictions, the
AB  - enzyme consists of a catalytic domain, which has a structure similar to all other
AB  - DNA-methyltransferases, and a smaller DNA-recognition domain.  We have investigated this
AB  - enzyme by random mutagenesis, using error-prone PCR, followed by selection for catalytically
AB  - inactive mutants.  20 single mutants were identified that are completely inactive in vivo as
AB  - His6- and GST-fusion proteins.  13 of them could be overexpressed and purified.  All of these
AB  - mutants are also inactive in vitro.  5 of the mutations are located near the putative binding
AB  - site for a flipped adenine residue (C192R, D193G, E212G, W231R, N239H).  All of these variants
AB  - bind to DNA, demonstrating the importance of this region of the protein in catalysis.  Only
AB  - the W231R mutant could be purified with high yields.  It binds to DNA and AdoMet and, thus,
AB  - behaves like a bona fine active site mutant.  According to the structure prediction Trp231
AB  - corresponds to Val121 in M.HhaI, which forms a hydrophobic contact to the flipped target
AB  - cytosine.  4 of the remaining purified variants are located within a small region of the
AB  - putative DNA-recognition domain (F115S, F117L, S121P, C122Y).  F117L, S121P and C122Y are
AB  - unable to bind to DNA, suggesting a critical role of this region in DNA binding.  Taken
AB  - together, these results are in good agreement with the structural model of M.EcoRV.
ER  -

TY  - JOUR
AU  - Friedrich, V.
AU  - Pabinger, S.
AU  - Chen, T.
AU  - Messner, P.
AU  - Dewhirst, F.E.
AU  - Schaffer, C.
TI  - Draft Genome Sequence of Tannerella forsythia Type Strain ATCC 43037.
JO  - Genome Announcements
PY  - 2015
SP  - e00660
EP  - e00615
VL  - 3
AB  - Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here,
AB  - we report the draft genome sequence of the Tannerella
AB  - forsythia strain ATCC 43037. The previously available genome of this designation
AB  - (NCBI reference sequence NC_016610.1) was discovered to be derived from a
AB  - different strain, FDC 92A2 (= ATCC BAA-2717).
ER  -

TY  - JOUR
AU  - Friend, P.L.
TI  - Association of chloramphenicol resistance of group A streptococci with host-controlled restriction and modification of bacteriophages.
JO  - Can. J. Microbiol.
PY  - 1971
SP  - 1573
EP  - 1576
VL  - 17
AB  - Bacteriophages grown on chloramphenicol (CM)-sensitive group A streptococci
AB  - plate efficiently only on other CM-sensitive strains, while phages propagated
AB  - on CM-resistant strains plate well only on CM-resistant hosts.  Data are
AB  - presented showing that the phages are subject to host-controlled modification
AB  - and restriction, and that these processes are related to the CM resistance
AB  - level of the host.
ER  -

TY  - JOUR
AU  - Friis, C.
AU  - Wassenaar, T.M.
AU  - Javed, M.A.
AU  - Snipen, L.
AU  - Lagesen, K.
AU  - Hallin, P.F.
AU  - Newell, D.G.
AU  - Toszeghy, M.
AU  - Ridley, A.
AU  - Manning, G.
AU  - Ussery, D.W.
TI  - Genomic Characterization of Campylobacter jejuni Strain M1.
JO  - PLoS ONE
PY  - 2010
SP  - e12253
EP  - e12253
VL  - 5
AB  - Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely
AB  - documented case of direct transmission of C. jejuni from chicken to a
AB  - person, resulting in enteritis. We have sequenced the genome of C. jejuni
AB  - strain M1, and compared this to 12 other C. jejuni sequenced genomes
AB  - currently publicly available. Compared to these, M1 is closest to strain
AB  - 81116. Based on the 13 genome sequences, we have identified the C. jejuni
AB  - pan-genome, as well as the core genome, the auxiliary genes, and genes
AB  - unique between strains M1 and 81116. The pan-genome contains 2,427 gene
AB  - families, whilst the core genome comprised 1,295 gene families, or about
AB  - two-thirds of the gene content of the average of the sequenced C. jejuni
AB  - genomes. Various comparison and visualization tools were applied to the 13
AB  - C. jejuni genome sequences, including a species pan- and core genome plot,
AB  - a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on
AB  - the total gene families in each genome are presented. The findings are
AB  - discussed in the background of the proven virulence potential of M1.
ER  -

TY  - JOUR
AU  - Frindte, K. et al.
TI  - Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.
JO  - Genome Announcements
PY  - 2017
SP  - e00526
EP  - e00517
VL  - 5
AB  - The genomes of the aerobic methanotrophs 'Methyloterricola oryzae' strain 73aT and
AB  - Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated
AB  - from rice plants. Methyloterricola oryzae strain 73aT represents the first
AB  - isolate of rice paddy cluster I, and strain 175 is the second representative of
AB  - the recently described genus Methylomagnum.
ER  -

TY  - JOUR
AU  - Frink, S.
AU  - Morales, C.
AU  - Kiang, D.
TI  - Draft Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovars Enteritidis, Veneziana, and Salford, Isolated from Herbs.
JO  - Genome Announcements
PY  - 2016
SP  - e00134
EP  - e00116
VL  - 4
AB  - Salmonellais a foodborne pathogen found in a wide variety of sources. Here, we report draft
AB  - genome sequences of threeSalmonella entericasubsp.entericaserovars
AB  - found in herbs: Enteritidis, Veneziana, and Salford, with the latter two being
AB  - extremely rare in California.
ER  -

TY  - JOUR
AU  - Fritsch, A.
AU  - Tiollais, P.
AU  - Buc, H.
TI  - Preparative purification of lambda-DNA fragments obtained after EcoRI digestion.
JO  - FEBS Lett.
PY  - 1975
SP  - 121
EP  - 126
VL  - 52
AB  - The study of the expression, and structure of bacterial or eukaryotic genes, as
AB  - well as the study of the interaction of a particular gene with specific
AB  - proteins, require the isolation of individual genes, or groups of genes.  In
AB  - bacteria, this can be done with specialized transducing phages, whose DNA is
AB  - hydrolysed by restriction enzymes, and the interesting DNA fragment is then
AB  - purified.  In a previous publication, the purification of the E. coli lac gene,
AB  - via the DNA of a lac tranducing lambda bacteriophage has been reported.  In the
AB  - present work, we describe the purification of all the EcoRI digestion products
AB  - of the DNA of two mutants of lambda bacteriophage.  Two methods have been used:
AB  - polyacrylamide gel electrophoresis, and isopycnic centrifugation in cesium
AB  - sulfate gradients in the presence of silver ions.  As will be seen, the proper
AB  - combination of both methods allows the purification of all fragments of lambda
AB  - genomes with either two, or six sites sensitive to EcoRI digestion.
ER  -

TY  - JOUR
AU  - Fritsche, P.
AU  - Alves, J.
TI  - A monomeric mutant of restriction endonuclease EcoRI nicks DNA without sequence specificity.
JO  - Biol. Chem.
PY  - 2004
SP  - 975
EP  - 985
VL  - 385
AB  - We have mutated the monomer-monomer interface of the restriction endonuclease EcoRI in order
AB  - to destabilize the homodimer and to stabilize heterodimers. Mutations of Leu158 to charged
AB  - amino acid
AB  - residues result in strong destabilization of the dimer. The largest
AB  - effect was detected for the L158D mutant which is monomeric even at
AB  - higher concentrations. It unspecifically degrades DNA by cleaving both
AB  - single strands independently every 15 nucleotides on the average.
AB  - Although cleavage is reproducible, it is not determined by nucleotide
AB  - sequence but by general properties like conformation or deformability
AB  - as has been found for other unspecific nucleases.
AB  - Mutations of Ile230, which is in direct contact with Leu158 of the
AB  - other subunit, cause structural changes with the loss of about ten
AB  - percent alpha-helix content, but interfere only marginally with
AB  - homodimerization and double strand cleavage. Again the mutation to
AB  - aspartate shows the strongest effects. Mixtures of single mutants, one
AB  - containing aspartate at one of the two positions and the other lysine
AB  - at the corresponding position, form heterodimers. These are mainly
AB  - stabilized compared to the homodimers by reestablishment of the
AB  - wildtype hydrophobic interaction at the not mutated residues while an
AB  - interaction of aspartate and lysine seems energetically unfavorable in
AB  - this structural context.
ER  -

TY  - JOUR
AU  - Fritz, A.
AU  - Kuster, W.
AU  - Alves, J.
TI  - Asn141 is essential for DNA recognition by EcoRI restriction endonuclease.
JO  - FEBS Lett.
PY  - 1998
SP  - 66
EP  - 70
VL  - 438
AB  - The amino acid residue Asn141 of the restriction endonuclease EcoRI was proposed to make three
AB  - hydrogen bonds to both adenine residues within the recognition sequence GAATTC.  We have
AB  - mutated Asn141 to alanine, aspartate, serine, and tyrosine.  Only the serine mutant is active
AB  - under normal buffer conditions although 1000-fold less than wild-type EcoRI.  The alanine and
AB  - aspartate mutants can be activated by Mn2+.  At acidic pH the latter mutant becomes even more
AB  - active than the wild-type enzyme in the presence of Mn2+.  We conclude that Asn141 is
AB  - essential for DNA recognition and that serine can partly substitute it.
ER  -

TY  - JOUR
AU  - Fritz, E.
AU  - Miller, M.J.
TI  - Draft Genome Sequence of the Murine Bacterial Isolate Lactobacillus murinus EF-1.
JO  - Genome Announcements
PY  - 2017
SP  - e00077
EP  - e00017
VL  - 5
AB  - Screening for lysogenic lactobacilli in rat fecal samples has identified Lactobacillus murinus
AB  - EF-1. Whole-genome sequencing revealed a 2.30-Mb draft
AB  - genome with 39.6% G+C content and 2,196 open reading frames. PHAST analysis
AB  - identified three intact prophages of 26.1 kb, 25.4 kb, and 49.6 kb in size.
ER  -

TY  - JOUR
AU  - Fritzenwanker, M.
AU  - Chakraborty, A.
AU  - Hain, T.
AU  - Zimmermann, K.
AU  - Domann, E.
TI  - Draft Genome Sequences of the Probiotic Enterococcus faecalis Symbioflor 1 Clones DSM16430 and DSM16434.
JO  - Genome Announcements
PY  - 2016
SP  - e01061
EP  - e01016
VL  - 4
AB  - The probiotic Symbioflor 1 is a historical concoction of 10 isolates of Enterococcus faecalis
AB  - Pulsed-field gel electrophoresis revealed two groups: one
AB  - comprising eight identical clones (DSM16430, DSM16432, DSM16433, DSM16435 to
AB  - DSM16439) and a further two isolates (DSM16431, DSM16434) with marginally
AB  - different profiles. Here, we report a comparative analysis of the draft genome
AB  - sequences of representative isolates.
ER  -

TY  - JOUR
AU  - Fritzenwanker, M.
AU  - Hain, T.
AU  - Kesper, D.A.
AU  - Harb, H.
AU  - Renz, H.
AU  - Domann, E.
TI  - Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties.
JO  - Genome Announcements
PY  - 2016
SP  - e00685
EP  - e00616
VL  - 4
AB  - The hygiene hypothesis states that the tremendous increase in atopic diseases correlates
AB  - significantly with less contact to microbes in childhood. Here, we
AB  - report the draft genome sequence of Acinetobacter lwoffii F78, a rural cowshed
AB  - isolate with strong allergy-protective properties that contains an 8,579-bp
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Fritzenwanker, M.
AU  - Kuenne, C.
AU  - Billion, A.
AU  - Hain, T.
AU  - Zimmermann, K.
AU  - Goesmann, A.
AU  - Chakraborty, T.
AU  - Domann, E.
TI  - Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431.
JO  - Genome Announcements
PY  - 2013
SP  - e00165
EP  - e00112
VL  - 1
AB  - Here, we report the complete and annotated genome sequence of the probiotic Enterococcus
AB  - faecalis Symbioflor 1 clone DSM 16431, included in a commercial
AB  - probiotic product used for more than 50 years without any reports of infection.
AB  - This sequence will provide new insights into the biology of this nonpathogenic
AB  - and probiotic microorganism.
ER  -

TY  - JOUR
AU  - Froman, B.E.
AU  - Tait, R.C.
AU  - Kado, C.I.
AU  - Rodriguez, R.L.
TI  - Purification of restriction endonuclease XcyI from Xanthomonas cyanopsidis.
JO  - Gene
PY  - 1984
SP  - 331
EP  - 335
VL  - 28
AB  - A new type II restriction endonuclease XcyI, purified from Xanthomonas cyanopsidis 13D5, is an
AB  - isoschizomer of SmaI and XmaI that cleaves at the nucleotide sequence 5'-C^CCGG-3' of
AB  - double-stranded DNA. The single restriction activity present in this strain permits rapid
AB  - purification of 8000 units of cleavage activity from 10 g of freshly harvested cells. The
AB  - resulting XcyI preparation is free of contaminating nuclease activities that interfere with in
AB  - vitro manipulation of DNA.
ER  -

TY  - JOUR
AU  - Frommer, M.
AU  - McDonald, L.E.
AU  - Millar, D.S.
AU  - Collis, C.M.
AU  - Watt, F.
AU  - Grigg, G.W.
AU  - Molloy, P.L.
AU  - Paul, C.L.
TI  - A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 1827
EP  - 1831
VL  - 89
AB  - The modulation of DNA-protein interactions by methylation of protein-binding
AB  - sites in DNA and the occurrence in genomic imprinting, X chromosome
AB  - inactivation, and fragile X syndrome of different methylation patterns in DNA
AB  - of different chromosomal origin have underlined the need to establish
AB  - methylation patterns in individual strands of particular genomic sequences.  We
AB  - report a genomic sequencing method that provides positive identification of
AB  - 5-methylcytosine residues and yields strand-specific sequences of individual
AB  - molecules in genomic DNA.  The method utilizes bisulfite-induced modification
AB  - of genomic DNA, under conditions whereby cytosine is converted to uracil, but
AB  - 5-methylcytosine remains nonreactive.  The sequence under investigation is then
AB  - amplified by PCR with two sets of strand-specific primers to yield a pair of
AB  - fragments, one from each strand, in which all uracil and thymine residues have
AB  - been amplified as thymine and only 5-methylcytosine residues have been
AB  - amplified as cytosine.  The PCR products can be sequenced directly to provide a
AB  - strand-specific average sequence for the population of molecules or can be
AB  - cloned and sequenced to provide methylation maps of single DNA molecules.  We
AB  - tested the method by defining the methylation status within single DNA strands
AB  - of two closely spaced CpG dinucleotides in the promoter of the human kininogen
AB  - gene.  During the analysis, we encountered in sperm DNA an unusual methylation
AB  - pattern, which suggests that the high methylation level of single-copy
AB  - sequences in sperm may be locally modulated by binding of protein factors in
AB  - germ-line cells.
ER  -

TY  - JOUR
AU  - Froseth, B.R.
AU  - Harlander, S.K.
AU  - McKay, L.L.
TI  - Plasmid-mediated reduced phage sensitivity in Streptococcus lactis KR5.
JO  - J. Dairy Sci.
PY  - 1988
SP  - 275
EP  - 284
VL  - 71
AB  - The phage insensitivity of Streptococcus lactis KR5 was evaluated for its
AB  - possible linkage to plasmid DNA.  This strain possessed plasmids of
AB  - 40,29,26,21,16.5,10.5,7.8, and 1.5 Mdal.  Plasmid curing using novobiocin
AB  - resulted in derivatives with increased sensitivity to prolate-headed phage,
AB  - suggesting the involvement of plasmid DNA in phage insensitivity.
AB  - Transformation of S. lactis LM0230 protoplasts with the KR5 plasmid DNA pool
AB  - produced transformants containing a plasmid of about 27 Mdal.  These
AB  - erythromycin-resistant transformants were lactose-positive phage-sensitive or
AB  - were lactose-negative and exhibited a reduced sensitivity to phage.  Agarose
AB  - gel electrophoresis and restriction endonuclease digestion analysis showed the
AB  - 17-Mdal plasmid band to be composed of two distinct plasmids of 26 Mdal (pBF61)
AB  - and 29 Mdal (pBF62), which coded for reduced phage sensitivity and
AB  - lactose-positive phenotypes, respectively.  The mechanisms of reduced phage
AB  - sensitivity encoded by pBF61 included a restriction/modification system and a
AB  - mechanism that resulted in reduced plaque size independent of incubation
AB  - temperature.  These results further support the involvement of plasmid DNA in
AB  - the mechanisms for reduced phage sensitivity in dairy streptococci.
ER  -

TY  - JOUR
AU  - Frostesjo, L.
AU  - Holm, I.
AU  - Grahn, B.
AU  - Page, A.W.
AU  - Bestor, T.H.
AU  - Heby, O.
TI  - Interference with DNA methyltransferase activity and genome methylation during F9 teratocarcinoma stem cell differentiation induced by polyamine depletion.
JO  - J. Biol. Chem.
PY  - 1997
SP  - 4359
EP  - 4366
VL  - 272
AB  - When ornithine decarboxylase, the initial and highly regulated enzyme in polyamine
AB  - biosynthesis, is irreversibly inactivated by alpha-difluoromethylornithine, F9 teratocarcinoma
AB  - stem cells are depleted of putrescine and spermidine and as a result differentiate into a cell
AB  - type which phenotypically resembles the parietal endoderm cells of the early mouse embryo.
AB  - Simultaneously the level of decarboxylated S-adenosylmethionine (dcAdoMet), the amino propyl
AB  - group donor in spermidine and spermine synthesis, increases dramatically, as the aminopropyl
AB  - group acceptor molecules (putrescine and spermidine) become limiting.  When this excessive
AB  - accumulation of dcAdoMet is prevented by specific inhibition of the AdoMet decarboxylase
AB  - activity, the differentiative effect is counteracted, despite the fact that the extent of
AB  - polyamine depletion remains almost identical.  Therefore, it may be concluded that dcAdoMet
AB  - plays an important role in the induction of differentiation.  Moreover, this key metabolite
AB  - acts as a competitive inhibitor of DNA methyltransferase and is therefore capable of
AB  - interfering with the maintenance methylation of newly replicated DNA.  During the course of F9
AB  - cell differentiation, the highly methylated genome is gradually demethylated, and its pattern
AB  - of gene expression is changed.  Our present findings, that the DNA remains highly methylated
AB  - and that the differentiative process is counteracted when the build-up of dcAdoMet is
AB  - prevented, provide strong evidence for a causative relation between the level of cdAdoMet and
AB  - the state of DNA methylation as well as cell differentiation.
ER  -

TY  - JOUR
AU  - Fry, P.R.
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Hsieh, H.Y.
AU  - Suntrup, D.G.
AU  - Perry, J.
AU  - Stewart, G.C.
AU  - Middleton, J.R.
TI  - Draft Genome Sequence of Staphylococcus chromogenes Strain MU 970, Isolated from  a Case of Chronic Bovine Mastitis.
JO  - Genome Announcements
PY  - 2014
SP  - e00835
EP  - e00814
VL  - 2
AB  - Coagulase-negative staphylococcal species are a common cause of subclinical bovine mastitis,
AB  - with Staphylococcus chromogenes being one of the most frequently
AB  - identified species in these cases. The draft genome sequence of an S. chromogenes
AB  - isolate (MU 970) recovered from the milk of a cow with a chronic intramammary
AB  - infection is reported here.
ER  -

TY  - JOUR
AU  - Fsihi, H.
AU  - Vincent, V.
AU  - Cole, S.T.
TI  - Homing events in the gyrA gene of some mycobacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 3410
EP  - 3415
VL  - 93
AB  - The A subunit of DNA gyrase in Mycobacterium leprae, unlike its
AB  - counterpart in Mycobacterium tuberculosis, is produced by protein splicing as its gene,
AB  - gyrA, harbors a 1260-bp in-frame insertion encoding an intein, a putative homing
AB  - endonuclease.  Analysis of the gyrA locus from different mycobacterial species revealed the
AB  - presence of inteins in Mycobacterium flavescens, Mycobacterium gordonae, and
AB  - Mycobacterium kansasii but not in 10 other pathogenic or saprophytic mycobacteria.  In all
AB  - four cases where intein coding sequences were found, they were localized in the same
AB  - position in gyrA, immediately downstream of the codon for the key active-site residue Tyr-
AB  - 130.  The intein products were similar, but not identical, in sequence and the splice
AB  - junctions displayed all the features found in other polypeptides known to be produced by
AB  - protein splicing from a precursor protein.  Paired motifs, found in homing endonucleases
AB  - encoded by some group I RNA introns, and inteins showing endonuclease activity, were
AB  - present in the gyrA inteins as were other intein-specific signatures.  Some strains of
AB  - M.flavescens, M. gordonae, and M. kansasii were shown by PCR analysis to have
AB  - inteinless gyrA genes, in contrast to the situation in M. leprae where all the isolates
AB  - possessed insertions in gyrA.  Sequencing of the corresponding regions revealed that,
AB  - although the GyrA protein sequence was conserved, the nucleotide sequences differed in
AB  - gyrA genes with and without inteins, suggesting that the homing endonuclease displays
AB  - sequence specificity.
ER  -

TY  - JOUR
AU  - Fu, A.Q.
AU  - Genereux, D.P.
AU  - Stoger, R.
AU  - Burden, A.F.
AU  - Laird, C.D.
AU  - Stephens, M.
TI  - Statistical Inference of In Vivo Properties of Human DNA Methyltransferases from Double-Stranded Methylation Patterns.
JO  - PLoS ONE
PY  - 2012
SP  - e32225
EP  - e32225
VL  - 7
AB  - DNA methyltransferases establish methylation patterns in cells and transmit these patterns
AB  - over cell generations, thereby influencing each
AB  - cell's epigenetic states. Three primary DNA methyltransferases have
AB  - been identified in mammals: DNMT1, DNMT3A and DNMT3B. Extensive in
AB  - vitro studies have investigated key properties of these enzymes, namely
AB  - their substrate specificity and processivity. Here we study these
AB  - properties in vivo, by applying novel statistical analysis methods to
AB  - double-stranded DNA methylation patterns collected using
AB  - hairpin-bisulfite PCR. Our analysis fits a novel Hidden Markov Model
AB  - (HMM) to the observed data, allowing for potential bisulfite conversion
AB  - errors, and yields statistical estimates of parameters that quantify
AB  - enzyme processivity and substrate specificity. We apply this model to
AB  - methylation patterns established in vivo at three loci in humans: two
AB  - densely methylated inactive X (Xi)-linked loci (FMR1 and G6PD), and an
AB  - autosomal locus (LEP), where methylation densities are tissue-specific
AB  - but moderate. We find strong evidence for a high level of processivity
AB  - of DNMT1 at FMR1 and G6PD, with the mean association tract length being
AB  - a few hundred base pairs. Regardless of tissue types, methylation
AB  - patterns at LEP are dominated by DNMT1 maintenance events, similar to
AB  - the two Xi-linked loci, but are insufficiently informative regarding
AB  - processivity to draw any conclusions about processivity at that locus.
AB  - At all three loci we find that DNMT1 shows a strong preference for
AB  - adding methyl groups to hemi-methylated CpG sites over unmethylated
AB  - sites. The data at all three loci also suggest low (possibly 0)
AB  - association of the de novo methyltransferases, the DNMT3s, and are
AB  - consequently uninformative about processivity or preference of these
AB  - enzymes. We also extend our HMM to reanalyze published data on mouse
AB  - DNMT1 activities in vitro. The results suggest shorter association
AB  - tracts (and hence weaker processivity), and much longer non-association
AB  - tracts than human DNMT1 in vivo.
ER  -

TY  - JOUR
AU  - Fu, B.
AU  - Chen, Q.
AU  - Wei, M.
AU  - Zhu, J.
AU  - Zou, L.
AU  - Li, G.
AU  - Wang, L.
TI  - Complete Genome Sequence of Xanthomonas arboricola pv. juglandis Strain DW3F3, Isolated from a Juglans regia L. Bacterial Blighted Fruitlet.
JO  - Genome Announcements
PY  - 2018
SP  - e00023
EP  - e00018
VL  - 6
AB  - Here, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis DW3F3, a
AB  - strong pathogenic strain isolated from blighted walnut
AB  - immature fruit (Juglans regia L. cv. Qingxiang). The genome consists of a single
AB  - chromosome (5,144 kb).
ER  -

TY  - JOUR
AU  - Fu, Y.
AU  - Wang, R.
AU  - Zhang, Z.
AU  - Jiao, N.
TI  - Complete Genome Sequence of the d-Amino Acid Catabolism Bacterium Phaeobacter sp. Strain JL2886, Isolated from Deep Seawater of the South China Sea.
JO  - Genome Announcements
PY  - 2016
SP  - e00913
EP  - e00916
VL  - 4
AB  - Phaeobacter sp. strain JL2886, isolated from deep seawater of the South China Sea, can
AB  - catabolize d-amino acids. Here, we report the complete genome sequence
AB  - of Phaeobacter sp. JL2886. It comprises ~4.06 Mbp, with a G+C content of 61.52%.
AB  - A total of 3,913 protein-coding genes and 10 genes related to d-amino acid
AB  - catabolism were obtained.
ER  -

TY  - JOUR
AU  - Fu, Y.
AU  - Wu, Y.
AU  - Yuan, Y.
AU  - Gao, M.
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar rongseni Reference Strain SCG04-02, a Strain Toxic to Plutella xylostella.
JO  - Genome Announcements
PY  - 2017
SP  - e00691
EP  - e00617
VL  - 5
AB  - Bacillus thuringiensis (Bt) is widely used to control agricultural and forestry pests, though
AB  - there are only a few available complete genome sequences of the Bt
AB  - reference strain. Here, we report the complete genome sequence of B.
AB  - thuringiensis serovar rongseni reference strain SCG04-02, which is toxic to
AB  - Plutella xylostella.
ER  -

TY  - JOUR
AU  - Fu, Z.
AU  - Xiao, R.
AU  - Luo, R.
AU  - Hu, Z.
AU  - Yang, H.
AU  - Guo, Z.
AU  - Lei, P.
AU  - Shan, S.
TI  - Draft Genome Sequence of Bacillus thuringiensis subsp. aizawai HD133.
JO  - Genome Announcements
PY  - 2017
SP  - e00909
EP  - e00917
VL  - 5
AB  - We report here the 6,512,057-bp draft genome sequence of Bacillus thuringiensis subsp. aizawai
AB  - HD133. This strain contains at least 6 cry genes and 13 candidate
AB  - biosynthetic gene clusters.
ER  -

TY  - JOUR
AU  - Fuchs, B.M.
AU  - Spring, S.
AU  - Teeling, H.
AU  - Quast, C.
AU  - Wulf, J.
AU  - Schattenhofer, M.
AU  - Yan, S.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Glockner, F.O.
AU  - Amann, R.
TI  - Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 2891
EP  - 2896
VL  - 104
AB  - Members of the gammaproteobacterial clade NOR5/OM60 regularly form an abundant
AB  - part, up to 11%, of the bacterioplankton community in coastal systems during the
AB  - summer months. Here, we report the nearly complete genome sequence of one
AB  - cultured representative, Congregibacter litoralis strain KT71, isolated from
AB  - North Sea surface water. Unexpectedly, a complete photosynthesis superoperon,
AB  - including genes for accessory pigments, was discovered. It has a high sequence
AB  - similarity to BAC clones from Monterey Bay [Beja O, Suzuki MT, Heidelberg JF,
AB  - Nelson WC, Preston CM, et al. (2002) Nature 415:630-633], which also share a
AB  - nearly identical gene arrangement. Although cultures of KT71 show no obvious
AB  - pigmentation, bacteriochlorophyll a and spirilloxanthin-like carotenoids could be
AB  - detected by HPLC analysis in cell extracts. The presence of two potential BLUF
AB  - (blue light using flavin adenine dinucleotide sensors), one of which was found
AB  - adjacent to the photosynthesis operon in the genome, indicates a light- and
AB  - redox-dependent regulation of gene expression. Like other aerobic anoxygenic
AB  - phototrophs (AAnPs), KT71 is able to grow neither anaerobically nor
AB  - photoautotrophically. Cultivation experiments and genomic evidence show that KT71
AB  - needs organic substrates like carboxylic acids, oligopeptides, or fatty acids for
AB  - growth. The strain grows optimally under microaerobic conditions and actively
AB  - places itself in a zone of approximately 10% oxygen saturation. The genome
AB  - analysis of C. litoralis strain KT71 identifies the gammaproteobacterial marine
AB  - AAnPs, postulated based on BAC sequences, as members of the NOR5/OM60 clade. KT71
AB  - enables future experiments investigating the importance of this group of
AB  - gammaproteobacterial AAnPs in coastal environments.
ER  -

TY  - JOUR
AU  - Fuchs, C.
AU  - Rosenvold, E.
AU  - Honigman, A.
AU  - Szybalski, W.
TI  - Identification of palindromic sequences recognized by restriction endonucleases, as based on the tabularized sequencing data for seven viral and plasmid DNAs.
JO  - Gene
PY  - 1980
SP  - 357
EP  - 370
VL  - 10
AB  - Computer search  of DNA sequences for phages PhiX174, G4, M13 and fd, plasmids
AB  - pBR322 and pA3, and virus SV40, was employed to prepare tables specifying the
AB  - size classes and frequencies of DNA segments located between all possible
AB  - tetra-, penta, and hexanucleotide palindromes.  As described earlier (Fuchs et
AB  - al., 1978), these tables permit identifying sequences recognized by most of the
AB  - restriction endonucleases.  The effect of sequencing errors on the accuracy of
AB  - the present identification method is evaluated.  Only four of the 224 listed
AB  - sequences do not appear in any of the seven DNAs, leading to discussion (see
AB  - Appendix) on the natural sequence distribution.
ER  -

TY  - JOUR
AU  - Fuchs, C.
AU  - Rosenvold, E.C.
AU  - Honigman, A.
AU  - Szybalski, W.
TI  - A simple method for identifying the palindromic sequences recognized by restriction endonucleases: the nucleotide sequence of the AvaII site.
JO  - Gene
PY  - 1978
SP  - 1
EP  - 23
VL  - 4
AB  - Tables specifying the frequencies, distances between and positions of all
AB  - possible tetra-, penta-, and hexanucleotide palindromes*** in PhiX174 and SV40
AB  - viral DNAs were prepared by a computer search of their base sequences.  A
AB  - simple method based on these tables is described for identifying the sequence
AB  - recognized by any specific restriction endonuclease.  The method requires
AB  - experimental determination of the number and approximate sizes of the fragments
AB  - obtained by digestion of PhiX174 RF and SV40 DNAs.  Using this method we
AB  - identified the sequence for the AvaII restriction endonuclease as 5'-GG(AT)CC.
ER  -

TY  - JOUR
AU  - Fuchs, L.Y.
AU  - Covarrubias, L.
AU  - Escalante, L.
AU  - Sanchez, S.
AU  - Bolivar, F.
TI  - Characterization of a site-specific restriction endonuclease SphI from Streptomyces phaeochromogenes.
JO  - Gene
PY  - 1980
SP  - 39
EP  - 46
VL  - 10
AB  - A new type-II restriction endonuclease SphI, has been partially purified from
AB  - Streptomyces phaeochromogenes.  SphI recognizes the hexanucleotide sequence
AB  - 5'-GCATG^C and cleaves it at the postiion marked by the arrow.  This nucleotide
AB  - sequence is present twice in SV40 DNA, four times in lambda DNA and only once
AB  - in the cloning vehicles pBR322, pBR325, pBR327 and PBR328.
ER  -

TY  - JOUR
AU  - Fuchs, R.
AU  - Blakesley, R.
TI  - Guide to the Use of Type II Restriction  Endonucleases.
JO  - Methods Enzymol.
PY  - 1983
SP  - 3
EP  - 38
VL  - 100
AB  - Type II restriction endonucleases are DNases that recognize specific
AB  - oligonucleotide sequences, make double-strand cleavages, and generate unique,
AB  - equal molar fragments of a DNA molecule.  By the nature of their controllable,
AB  - predictable, infrequent, and site-specific cleavage of DNA, restriction
AB  - endonucleases proved to be extremely useful as tools in dissecting, analyzing,
AB  - and reconfiguring genetic information at the molecular level.  Over 350
AB  - different restriction endonucleases have been isolated from a wide variety of
AB  - prokaryotic sources, representing at least 85 different recognition sequences.
AB  - A number of excellent reviews detail the variety of restriction enzymes and
AB  - their sources, their purification and determination of their sequence
AB  - specificity, ad their physical properties, kinetics, and reaction mechanism.
AB  - Here we provide a summary, based on the literature and our experience in this
AB  - laboratory, emphasizing the practical aspects for using restriction
AB  - endonucleases as tools.  This review focuses on the reaction, its components
AB  - and the conditions that affect enzymic activity and sequence fidelity, methods
AB  - for terinating the reaction, some reaction variations, and a troubleshooting
AB  - guide to help identify and solve restriction endonuclease-related problems.
ER  -

TY  - JOUR
AU  - Fuchs, R.
AU  - Kane, J.F.
TI  - Expression of the genes for the Pst restriction-modification enzymes after cloning into a temperature-sensitive replication plasmid.
JO  - Miami BioTechnology Winter Symposium
PY  - 1982
SP  - 523
EP  - 523
VL  - 19
AB  - Our objective was to develop a model system to study the use of an
AB  - overexpression plasmid to increase synthesis of a restriction enzyme in
AB  - Escherichia coli.  We chose the restriction (PstI)-modification system of
AB  - Providencia stuartii that has been cloned into the HindIII site of pBR322
AB  - (Walder, et al., 1981, P.N.A.S. 78:1503).  One hybrid plasmid, designated
AB  - pPst102, contained a 5.9 kb insert with an internal HindIII site, producing 1.9
AB  - and 4.0 kb fragments.  Although both enzymes were specified by the 4.0 kb
AB  - fragment, the genes were poorly expressed in E. coli.  We subcloned the Pst
AB  - genes into a temperature sensitive runaway plasmid (pBEU I) and transformed E.
AB  - coli HB101.  Four independent transformants were isolated and characterized:
AB  - pRF I (1.9 kb insert); pRF 2 (4.0 kb insert); pRF 3 and pRF 4 (4.9 kb insert).
AB  - All four strains were subjected to temperature shifts to allow for
AB  - overexpression of the plasmid.  Crude cell extracts were prepared and examined
AB  - for PstI.  When the PstI activity of E. coli/pPst 102 is assigned a value
AB  - enzymatic activities were estimated in the four strains: pRF I <0.5; pRF 2
AB  - <0.5; pRF3 <0.5; pRF 4-10.0.  These results demonstrate that the overexpression
AB  - plasmid produces a 10-fold increase in the activity of PstI in E. coli.
AB  - Furthermore, this system provides a basis for studying the regulation of the
AB  - PstI gene.
ER  -

TY  - JOUR
AU  - Fuchu, G.
AU  - Ohtsubo, Y.
AU  - Ito, M.
AU  - Miyazaki, R.
AU  - Ono, A.
AU  - Nagata, Y.
AU  - Tsuda, M.
TI  - Insertion sequence-based cassette PCR: cultivation-independent isolation of gamma-hexachlorocyclohexane-degrading genes from soil DNA.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2008
SP  - 627
EP  - 632
VL  - 79
AB  - gamma-Hexachlorocyclohexane (gamma-HCH) is a highly chlorinated pesticide
AB  - that has caused serious environmental problems. Based on the frequently
AB  - observed association of insertion sequence IS6100 with lin genes for
AB  - gamma-HCH degradation in several gamma-HCH-degrading bacterial strains
AB  - isolated to date, DNA fragments flanked by two copies of IS6100 were
AB  - amplified by nested polymerase chain reaction (PCR) technique using a DNA
AB  - sample extracted from soil contaminated with HCH. Four distinct DNA
AB  - fragments with sizes of 6.6, 2.6, 1.6, and 1.3 kb were obtained, three of
AB  - which carried lin genes: the 6.6-kb fragment carried linD and linE as well
AB  - as linR; the 2.6-kb fragment showed a truncated form of linF; and the
AB  - 1.6-kb fragment carried linB. Our approach, named as insertion sequence
AB  - (IS)-based cassette PCR, was successful in the isolation of the lin genes
AB  - from HCH-contaminated soil without cultivation of host cells and is
AB  - applicable for the culture-independent isolation of other functional genes
AB  - bordered by other IS elements.
ER  -

TY  - JOUR
AU  - Fucik, V.
AU  - Grunnerova, H.
AU  - Zadrazil, S.
TI  - Restriction and modification in Bacillus subtilis 168: Regulation of hsrM(nonB) expression in spoOA mutants and effects on permissiveness for Phi15 and Phi105 phages.
JO  - Mol. Gen. Genet.
PY  - 1982
SP  - 118
EP  - 121
VL  - 186
AB  - Gene hsrM (nonB) of Bacillus subtilis 168, causing non-permissiveness to phage
AB  - SP10 (Saito et al. 1979) and reduced plating efficiency of unmodified phage
AB  - Phi105, is responsible for non-permissiveness of B. subtilis 168 for phages
AB  - Phi15 and PZA.  Upon transformation to sporulation deficiency (allele spoOA) B.
AB  - subtilis 168 becomes permissive for Phi15 and PAZ and loses the ability to
AB  - restrict Phi105.  spoOA str-1 double transformants of B. subtilis 168, however,
AB  - retain the restriction 168 and non-permissiveness for Phi15 and PZA phages, in
AB  - spite of their Spo- phenotype.  Therefore it appears that a functional product
AB  - of the spoOA gene is required for expression of gene hsrM in wild-type
AB  - bacteria, but is not essential in streptomycin-resistant bacteria.  Phage
AB  - genomes (PZA) were trapped in spores of the restriction deficient strain with
AB  - much higher efficiency than in the wild-type.
ER  -

TY  - JOUR
AU  - Fuentes-Valdes, J.J.
AU  - Plominsky, A.M.
AU  - Allen, E.E.
AU  - Tamames, J.
AU  - Vasquez, M.
TI  - Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a  Single Extrachromosomal Element.
JO  - Genome Announcements
PY  - 2016
SP  - e00823
EP  - e00816
VL  - 4
AB  - Cylindrospermopsis raciborskii is a freshwater cyanobacterium producing bloom events and
AB  - toxicity in drinking water source reservoirs. We present the first
AB  - genome sequence for C. raciborskii CS505 (Australia), containing one 4.1-Mbp
AB  - chromosome and one 110-Kbp plasmid having G+C contents of 40.3% (3933 genes) and
AB  - 39.3% (111 genes), respectively.
ER  -

TY  - JOUR
AU  - Fuentes-Valdes, J.J.
AU  - Soto-Liebe, K.
AU  - Perez-Pantoja, D.
AU  - Tamames, J.
AU  - Belmar, L.
AU  - Pedros-Alio, C.
AU  - Garrido, D.
AU  - Vasquez, M.
TI  - Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 26
EP  - 26
VL  - 13
AB  - Members of the genus Cylindrospermopsis represent an important environmental and  health
AB  - concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from
AB  - freshwater reservoirs located in Australia and Uruguay, respectively. While
AB  - CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We
AB  - annotated the draft genomes of these C. raciborskii strains using the assembly of
AB  - reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in
AB  - genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508
AB  - (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs). Finally, both the
AB  - average nucleotide identity (ANI) and the similarity of gene content indicate
AB  - that these two genomes should be considered as strains of the C. raciborskii
AB  - species.
ER  -

TY  - JOUR
AU  - Fuerst, C.R.
TI  - Plating efficiencies of modified lambda-bio particles on temperature-sensitive hsd mutants of Escherichia coli K12.
JO  - Virology
PY  - 1985
SP  - 352
EP  - 356
VL  - 143
AB  - Two mutants of Escherichia coli K12 that are temperature sensitive in cell growth and lambda
AB  - phage production are shown to contain at least two mutations.  One of the mutations in each of
AB  - the isolates is in the hsd locus, and modification and restriction of lambda exhibits
AB  - temperature sensitivity. One of the hsd mutations causes plaque formation by modified
AB  - lambda-bio particles that do not contain an intact ral gene to be temperature dependent.
ER  -

TY  - JOUR
AU  - Fuglsang, A.
TI  - Distribution of potential type II restriction sites (palindromes) in prokaryotes.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2003
SP  - 280
EP  - 285
VL  - 310
AB  - Restriction-modification systems are used as a defensive mechanism against inappropriate
AB  - invasion of foreign DNA. The recognition sequences for the
AB  - common type II restriction enzymes and their corresponding methylases are
AB  - usually palindromes. In this study, we identified the most over- and
AB  - underrepresented words in DNA of four bacteria: Escherichia coli, Bacillus
AB  - subtilis, Clostridium perfringens, and Pseudomonas aeruginosa. Using
AB  - maximum order Markov chain analysis, we found that palindromic words were
AB  - most often more underrepresented than their non-palindromic counterparts.
AB  - No strict rule for the intragenic palindrome content could be derived, but
AB  - for three of the bacteria there was a weak correlation between codon usage
AB  - bias and palindrome content. A clear drop in palindrome counts was
AB  - observed in the Shine-Dalgarno region for B. subtilis and C. perfringens,
AB  - but not in E. coli or P. aeruginosa. It was also shown that palindromes in
AB  - eubacteria and archaebacteria seem to occur slightly more infrequently
AB  - than expected on the basis of the genomic GC-content, but some exceptions
AB  - to this principle exist.
ER  -

TY  - JOUR
AU  - Fujihara, H.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Suenaga, H.
AU  - Kimura, N.
AU  - Hirose, J.
AU  - Watanabe, T.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa KF702 (NBRC 110665), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated   Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00517
EP  - e00515
VL  - 3
AB  - Pseudomonas aeruginosa KF702 (NBRC 110665) utilizes biphenyl as a sole source of  carbon and
AB  - degrades polychlorinated biphenyls (PCBs). Here, we report the
AB  - 7,167,540-bp draft genome sequence of KF702, which contains 6,714 coding
AB  - sequences and a 65.8 mol% G+C content. The strain possesses genes for biphenyl
AB  - catabolism and other genes that mediate degradation of various aromatic
AB  - compounds.
ER  -

TY  - JOUR
AU  - Fujihara, H.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Suenaga, H.
AU  - Kimura, N.
AU  - Hirose, J.
AU  - Watanabe, T.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated   Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00473
EP  - e00415
VL  - 3
AB  - Pseudomonas abietaniphila KF701 utilizes biphenyl as a sole source of carbon and  degrades
AB  - polychlorinated biphenyls (PCBs). Here, we report the 6,886,250-bp draft
AB  - genome sequence of KF701, which contains 6,315 coding sequences and 59.4 mol% G+C
AB  - content. The strain possesses genes for biphenyl catabolism and other genes that
AB  - mediate the degradation of benzoate, salicylate, and phenol.
ER  -

TY  - JOUR
AU  - Fujihara, Y.
AU  - Miyasako, H.
AU  - Kato, K.
AU  - Hayashi, T.
AU  - Toraya, T.
TI  - Molecular Cloning, Expression, and Characterization of Starfish DNA (Cytosine-5)-methyltransferases.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2012
SP  - 1661
EP  - 1671
VL  - 76
AB  - To determine whether and if so how a DNA methylation-dependent epigenetic mechanism for
AB  - transcriptional gene silencing functions in
AB  - Echinoderms, we cloned and sequenced dnmt1 and dnmt3 cDNAs of the
AB  - starfish Asterina pectinifera. Since the Strongylocentrotus purpuratus
AB  - genome has only two loci of DNA (cytosine-5)-methyltransferase genes
AB  - encoding Dnmt1 and Dnmt3, they might constitute a sufficient set of
AB  - timid genes in Echinoderms. The starfish Dnmt3 whose cDNA we cloned
AB  - showed highest homology to a mammalian Dnmt3a2 splicing variant.
AB  - Essentially all the characteristic motifs and sequences of the
AB  - mammalian counterparts were found in the starfish Dnmts as well, except
AB  - that a typical PCNA binding domain motif was lacking in the starfish
AB  - Dnmt1. RT-PCR analysis indicated that the dnmt1 mRNA exists in both
AB  - ovary and oocytes, but its levels in other tissues were very low or
AB  - almost negligible. In contrast, the dnmt3 mRNA was detected only in the
AB  - ovary, and not at all in the oocytes. The size of a dnmt1 transcript
AB  - was about 6.5 kb on Northern blot analysis. On heterologous expression,
AB  - the starfish Dnmt1 protein was expressed in insect cells in
AB  - catalytically active form.
ER  -

TY  - JOUR
AU  - Fujii, T.
AU  - Koike, H.
AU  - Sawayama, S.
AU  - Yano, S.
AU  - Inoue, H.
TI  - Draft Genome Sequence of Talaromyces cellulolyticus Strain Y-94, a Source of Lignocellulosic Biomass-Degrading Enzymes.
JO  - Genome Announcements
PY  - 2015
SP  - e00014
EP  - e00015
VL  - 3
AB  - Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) is a promising fungus for
AB  - cellulase production. Here, we present the draft genome sequence of T. cellulolyticus strain
AB  - Y-94. The genome is 36.4 Mbp long and contains genes for several enzymes involved in the
AB  - degradation of lignocellulosic biomass, including cellulases, hemicellulases, pectinases, and
AB  - amylases.
ER  -

TY  - JOUR
AU  - Fujii, T.
AU  - Tomita, Y.
AU  - Ikushima, S.
AU  - Horie, A.
AU  - Fujiwara, D.
TI  - Draft Genome Sequence of Lactococcus lactis subsp. lactis JCM 5805T, a Strain That Induces Plasmacytoid Dendritic Cell Activation.
JO  - Genome Announcements
PY  - 2015
SP  - e00113
EP  - e00115
VL  - 3
AB  - Lactococcus lactis subsp. lactis JCM 5805(T) is a dairy lactic acid bacterium that induces
AB  - plasmacytoid dendritic cell (pDC) activation. Here, we report the
AB  - 2.55-Mb draft genome and annotation of Lactococcus lactis JCM 5805(T). This
AB  - genome information will provide further insights into the mechanisms underlying
AB  - the immunomodulatory function of this strain.
ER  -

TY  - JOUR
AU  - Fujii, Y.
AU  - Toh, H.
AU  - Matsubara, T.
AU  - Tomida, S.
AU  - Nguyen, C.T.
AU  - Mimura, I.
AU  - Nakamura, S.
AU  - Morita, H.
TI  - Draft Genome Sequence of Probiotic Lactobacillus acidophilus Strain L-55 Isolated from a Healthy Human Gut.
JO  - Genome Announcements
PY  - 2016
SP  - e01357
EP  - e01316
VL  - 4
AB  - Probiotic Lactobacillus acidophilus L-55 was isolated from a healthy human gut. Here, we
AB  - report the draft genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Fujimoto, D.
AU  - Srinivasan, P.R.
AU  - Borek, E.
TI  - On the nature of the deoxyribonucleic acid methylases.  Biological evidence for the multiple nature of the enzymes.
JO  - Biochemistry
PY  - 1965
SP  - 2849
EP  - 2855
VL  - 4
AB  - The minor components of DNA of several bacterial species were determined by growing the
AB  - organisms in the presence of [methyl-14C]methionine and analyzing the labeled bases by isotope
AB  - dilution.  The DNA's were found to contain either 6-methylaminopurine or both
AB  - 6-methylaminopurine and 5-methylcytosine.  The interaction of extracts derived from some of
AB  - these organisms with a variety of DNA's was also examined.  The results of these studies
AB  - suggest that the DNA methylases as well as the substrate DNA's possess directive specificity
AB  - regarding the pattern of methylation.  The findings confirm that the DNA methylases are
AB  - species specific and also demonstrate the existence of two types of DNA methylases: one
AB  - capable of methylating adenine and the other cytosine.  Infection by T2 bacteriophage elevates
AB  - the DNA methylase activity of both E. coli B and E. coli K12.  Extracts of E. coli B can
AB  - methylate only adenine of DNA, whereas in E. coli K12 two methylating capacities are normally
AB  - present, producing 5-methylcytosine and 6-methylaminopurine.  However, on phage infection only
AB  - the level of the adenine methylase was elevated.
ER  -

TY  - JOUR
AU  - Fujimoto, K.
AU  - Iida, H.
AU  - Kawakami, M.
AU  - Bando, T.
AU  - Tao, Z.-F.
AU  - Sugiyama, H.
TI  - Sequence-specific protection of plasmid DNA from restriction endonuclease hydrolysis by pyrrole-imidazole-cyclopropapyrroloindole conjugates.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3748
EP  - 3753
VL  - 30
AB  - The pyrrole-imidazole (Py-Im) triamide-cyclopropapyrroloindole (CPI) conjugates ImPyImLDu86
AB  - (7) and ImImPyLDu86 (14) were synthesized and their alkylating activities and inhibitory
AB  - effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis
AB  - demonstrated that conjugates 7 and 14 specifically alkylated DNA at 5'-CGCGCG-3' and
AB  - 5'-PyGGCCPu-3', respectively. Agarose gel electrophoresis indicated that incubation of a
AB  - supercoiled plasmid, pSPORT I (4109 bp), with conjugate 7 effectively inhibited its hydrolysis
AB  - by BssHII (5'-G_CGCGC-3'), whereas conjugate 14 had no effect on this hydrolysis. These
AB  - results suggest that conjugate 7 sequence-specifically inhibits the hydrolysis of DNA by
AB  - BssHII. Sequence-specific alkylation by the Py-Im triamide-CPI conjugates was further
AB  - confirmed by inhibition of the Eco52I (5'-C_GGCCG-3') hydrolysis of conjugate 14-treated
AB  - pQBI PGK (5387 bp). In clear contrast, hydrolysis of pQB1 PGK by DraI (3'-TTT_AAA-3') was
AB  - not inhibited by 5 micro M conjugate 14. That ImImPy did not inhibit the hydrolysis of pQB1
AB  - PGK indicates that covalent bond formation is necessary for inhibition. A similar experiment,
AB  - using linear pQBI PGK, achieved the same extent of protection of the DNA with approximately
AB  - half the concentration of conjugate 14 as was required to protect supercoiled DNA from
AB  - hydrolysis.
ER  -

TY  - JOUR
AU  - Fujimoto, R.
AU  - Sasaki, T.
AU  - Nishio, T.
TI  - Characterization of DNA methyltransferase genes in Brassica rapa.
JO  - Genes Genet. Syst.
PY  - 2006
SP  - 235
EP  - 242
VL  - 81
AB  - DNA methylation is essential for normal development and plays important roles in regulating
AB  - gene expression in plants. Analysis of the key
AB  - enzymes catalyzing DNA methylation is important to understand
AB  - epigenetic phenomena. In this study, three putative methyltransferase
AB  - genes, BrMET1a, BrMET1b, and BrCMT, were isolated from a genome library
AB  - of Brassica rapa. Structural conservation of the amino acid sequence
AB  - between BrMET1a/BrMET1b and AtMET1 and that between BrCMT and AtCMT3
AB  - suggests that they may function as DNA methyltransferase. BrMET1a was
AB  - expressed in vegetative and reproductive organs, while BrMET1b was
AB  - expressed only in pistils, indicating that these two genes have
AB  - different functions. BrCMT was expressed especially in stamens at the
AB  - stage of 2-4 days before anthesis. We isolated three DNA
AB  - methyltransferase genes in Brassica rapa and indicated differences of
AB  - expression patterns of these DNA methyltransferase genes and expression
AB  - levels in different tissues and developmental stages, suggesting that
AB  - these genes might play important roles in epigenetic gene regulation in
AB  - B. rapa.
ER  -

TY  - JOUR
AU  - Fujimoto, R.
AU  - Sasaki, T.
AU  - Nishio, T.
TI  - Characterization of DNA methyltransferase genes in Brassica rapa.
JO  - Plant Cell Physiol.
PY  - 2006
SP  - S238
EP  - S238
VL  - 47
AB  - Cytosine methylation is an epigenetic process that plays a role in regulating gene expression.
AB  - Plants have at least three classes of cytosine methyltransferase, i.e., MET1 class of
AB  - methyltransferase, Chromomethylases, and de novo DNA methyltransferase.  In our study three
AB  - putative methyltransferase genes, BrMET1a, BrMET1b, and BrCMT were isolated from genome
AB  - library of Brassica rapa.  Identities of amino acid sequences between BrMET1a and atMET1 and
AB  - between BrMET1b and AtMET1 were 72.0% and 66.7%, respectively.  Pfam analysis using deduced
AB  - amino acid sequence showed the presence of BAH domain, CHROMO domain, and methyltransferase
AB  - domain in BrCMT.  RT-PCR analysis revealed the expression of BrMET1a, BrMET1b, and BrCMT.
AB  - These results suggested that these three genes function as methyltransferase in B. rapa.
ER  -

TY  - JOUR
AU  - Fujinami, S.
AU  - Oikawa, Y.
AU  - Araki, T.
AU  - Shinmura, Y.
AU  - Midorikawa, R.
AU  - Ishizaka, H.
AU  - Kato, C.
AU  - Horikoshi, K.
AU  - Ito, M.
AU  - Tamegai, H.
TI  - Genome Sequence of the Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench.
JO  - Genome Announcements
PY  - 2014
SP  - e01313
EP  - e01314
VL  - 2
AB  - Pseudomonas sp. strain MT-1 was the first deep-sea denitrifier isolated and characterized from
AB  - mud recovered from a depth of 11,000 m in the Mariana Trench.
AB  - We report here the genome sequence of this bacterium, which contributes to our
AB  - understanding of denitrification and bioenergetics in the deep sea.
ER  -

TY  - JOUR
AU  - Fujinami, S.
AU  - Takarada, H.
AU  - Kasai, H.
AU  - Sekine, M.
AU  - Omata, S.
AU  - Harada, T.
AU  - Fukai, R.
AU  - Hosoyama, A.
AU  - Horikawa, H.
AU  - Kato, Y.
AU  - Nakazawa, H.
AU  - Fujita, N.
TI  - Complete genome sequence of Ilumatobacter coccineum YM16-304(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 430
EP  - 440
VL  - 8
AB  - Ilumatobacter coccineum YM16-304(T) (=NBRC 103263(T)) is a novel marine actinobacterium
AB  - isolated from a sand sample collected at a beach in Shimane
AB  - Prefecture, Japan. Strain YM16-304(T) is the type strain of the species.
AB  - Phylogenetically, strain YM16-304(T) is close to Ilumatobacter nonamiense
AB  - YM16-303(T) (=NBRC 109120(T)), Ilumatobacter fluminis YM22-133(T) and some
AB  - uncultured bacteria including putative marine sponge symbionts. Whole genome
AB  - sequence of these species has not been reported. Here we report the complete
AB  - genome sequence of strain YM16-304(T). The 4,830,181 bp chromosome was predicted
AB  - to encode a total of 4,291 protein-coding genes.
ER  -

TY  - JOUR
AU  - Fujinami, S.
AU  - Takeda, K.
AU  - Onodera, T.
AU  - Satoh, K.
AU  - Sano, M.
AU  - Narumi, I.
AU  - Ito, M.
TI  - Draft Genome Sequence of Potassium-Dependent Alkaliphilic Bacillus sp. Strain TS-2, Isolated from a Jumping Spider.
JO  - Genome Announcements
PY  - 2014
SP  - e00458
EP  - e00414
VL  - 2
AB  - The potassium-dependent alkaliphilic Bacillus sp. strain TS-2 was isolated from the mashed
AB  - extract of a jumping spider, and its draft genome sequence was
AB  - obtained. Comparative genomic analysis with a previously sequenced
AB  - sodium-dependent alkaliphilic Bacillus species may reveal potassium-dependent
AB  - alkaline adaptation mechanisms.
ER  -

TY  - JOUR
AU  - Fujinami, S.
AU  - Takeda, K.
AU  - Onodera, T.
AU  - Satoh, K.
AU  - Sano, M.
AU  - Narumi, I.
AU  - Ito, M.
TI  - Draft Genome Sequence of Sodium-Independent Alkaliphilic Microbacterium sp. Strain TS-1.
JO  - Genome Announcements
PY  - 2013
SP  - e01043
EP  - e01013
VL  - 1
AB  - Alkaliphilic Microbacterium sp. strain TS-1, newly isolated from the jumping spider, showed
AB  - Na(+)-independent growth and motility. Here, we report the draft
AB  - genome sequence of this bacterium, which may provide beneficial information for
AB  - Na(+)-independent alkaline adaptation mechanisms.
ER  -

TY  - JOUR
AU  - Fujinami, S.
AU  - Takeda-Yano, K.
AU  - Onodera, T.
AU  - Satoh, K.
AU  - Sano, M.
AU  - Takahashi, Y.
AU  - Narumi, I.
AU  - Ito, M.
TI  - Draft Genome Sequence of Calcium-Dependent Paenibacillus sp. Strain TCA20, Isolated from a Hot Spring Containing a High Concentration of Calcium Ions.
JO  - Genome Announcements
PY  - 2014
SP  - e00866
EP  - e00814
VL  - 2
AB  - Calcium-dependent Paenibacillus sp. strain TCA20 was isolated from a water sample of a hot
AB  - spring containing a high concentration of calcium ions. Here, we report
AB  - the draft genome sequence of this bacterium, which may be the basis for the
AB  - research of calcium ion homeostasis.
ER  -

TY  - JOUR
AU  - Fujinami, S.
AU  - Takeda-Yano, K.
AU  - Onodera, T.
AU  - Satoh, K.
AU  - Shimizu, T.
AU  - Wakabayashi, Y.
AU  - Narumi, I.
AU  - Nakamura, A.
AU  - Ito, M.
TI  - Draft Genome Sequence of Methylobacterium sp. ME121, Isolated from Soil as a Mixed Single Colony with Kaistia sp. 32K.
JO  - Genome Announcements
PY  - 2015
SP  - e01005
EP  - e01015
VL  - 3
AB  - Methylobacterium sp. ME121 was isolated from soil as a mixed single colony with Kaistia sp.
AB  - 32K, and its growth was enhanced by coculture. Here, we report the draft genome sequence of
AB  - Methylobacterium sp. ME121, which may contribute to the  study of the molecular mechanisms
AB  - underlying this phenomenon.
ER  -

TY  - JOUR
AU  - Fujino, Y.
AU  - Nagayoshi, Y.
AU  - Ohshima, T.
AU  - Ogata, S.
AU  - Doi, K.
TI  - Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal  Power Plant.
JO  - Genome Announcements
PY  - 2017
SP  - e01596
EP  - e01516
VL  - 5
AB  - Thermus thermophilus TMY (JCM 10668) was isolated from silica scale formed at a geothermal
AB  - power plant in Japan. Here, we report the complete genome sequence for
AB  - this strain, which contains a chromosomal DNA of 2,121,526 bp with 2,500
AB  - predicted genes and a pTMY plasmid of 19,139 bp, with 28 predicted genes.
ER  -

TY  - JOUR
AU  - Fujisawa, H.
AU  - Yonesaki, T.
AU  - Minagawa, T.
TI  - Sequence of the T4 recombination gene, uvsX, and its comparison with that of the recA gene of Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 7473
EP  - 7481
VL  - 13
AB  - We have determined the nucleotide sequence of the uvsX gene of
AB  - bacteriophage T4 which is involved in DNA recombination and damage repair,
AB  - and whose product catalyzes in vitro reactions related to recombination
AB  - process in analogous manners to E. coli recA gene product. The coding
AB  - region consisted of 1170 nucleotides directing the synthesis of a
AB  - polypeptide of 390 amino acids in length with a calculated molecular
AB  - weight of 43,760. Amino acid composition, the sequence of seven
AB  - NH2-terminal amino acids and molecular weight of the protein deduced from
AB  - the nucleotide sequence were consistent with the data from the analysis of
AB  - the purified uvsX protein. The nucleotide sequence and the deduced amino
AB  - acid sequence were compared with those of the recA gene. Although a
AB  - significant homology was not found in the nucleotide sequences, the amino
AB  - acid sequences included 23% of identical and 15% of conservatively
AB  - substituted residues.
ER  -

TY  - JOUR
AU  - Fujisawa, T. et al.
TI  - Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39.
JO  - DNA Res.
PY  - 2010
SP  - 85
EP  - 103
VL  - 17
AB  - A filamentous non-N-2-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an
AB  - important organism for industrial applications and as
AB  - a food supply. Almost the complete genome of A. platensis NIES-39 was
AB  - determined in this study. The genome structure of A. platensis is
AB  - estimated to be a single, circular chromosome of 6.8 Mb, based on
AB  - optical mapping. Annotation of this 6.7 Mb sequence yielded 6630
AB  - protein-coding genes as well as two sets of rRNA genes and 40 tRNA
AB  - genes. Of the protein-coding genes, 78% are similar to those of other
AB  - organisms; the remaining 22% are currently unknown. A total 612 kb of
AB  - the genome comprise group II introns, insertion sequences and some
AB  - repetitive elements. Group I introns are located in a protein-coding
AB  - region. Abundant restriction-modification systems were determined.
AB  - Unique features in the gene composition were noted, particularly in a
AB  - large number of genes for adenylate cyclase and haemolysin-like
AB  - Ca2+-binding proteins and in chemotaxis proteins. Filament-specific
AB  - genes were highlighted by comparative genomic analysis.
ER  -

TY  - JOUR
AU  - Fujiwara, Y.
AU  - Takai, K.
AU  - Uematsu, K.
AU  - Tsuchida, S.
AU  - Hunt, J.C.
AU  - Hashimoto, J.
TI  - Phylogenetic characterization of endosymbionts in three hydrothermal vent mussels: influence on host distributions.
JO  - Mar. Ecol. Prog. Ser.
PY  - 2000
SP  - 147
EP  - 155
VL  - 208
ER  -

TY  - JOUR
AU  - Fukano, H.
AU  - Yoshida, M.
AU  - Katayama, Y.
AU  - Omatsu, T.
AU  - Mizutani, T.
AU  - Kurata, O.
AU  - Wada, S.
AU  - Hoshino, Y.
TI  - Complete Genome Sequence of Mycobacterium stephanolepidis.
JO  - Genome Announcements
PY  - 2017
SP  - e00810
EP  - e00817
VL  - 5
AB  - Mycobacterium stephanolepidis is a rapid-growing nonpigmented species isolated from marine
AB  - teleost fish (Stephanolepis cirrhifer) and is closely related to
AB  - Mycobacterium chelonae Here, we report the complete sequence of its genome,
AB  - comprising a 4.9-Mb chromosome. The sequence represents essential data for future
AB  - phylogenetic and comparative genome studies of this fish pathogen.
ER  -

TY  - JOUR
AU  - Fukano, H.
AU  - Yoshida, M.
AU  - Shimizu, A.
AU  - Iwao, H.
AU  - Katayama, Y.
AU  - Omatsu, T.
AU  - Mizutani, T.
AU  - Kurata, O.
AU  - Wada, S.
AU  - Hoshino, Y.
TI  - Draft Genome Sequence of Mycobacterium montefiorense Isolated from Japanese Black Salamander (Hynobius nigrescens).
JO  - Genome Announcements
PY  - 2018
SP  - e00448
EP  - e00418
VL  - 6
AB  - Mycobacterium montefiorense is a member of the Mycobacterium simiae complex, the  largest
AB  - group of nontuberculous mycobacteria. Here, we report the genome sequence
AB  - of M. montefiorense isolate BS, isolated from diseased Japanese black salamander
AB  - (Hynobius nigrescens) reared in an aquarium in Japan. This is the first reported
AB  - case of an M. montefiorense infection in an amphibian.
ER  -

TY  - JOUR
AU  - Fukao, M.
AU  - Oshima, K.
AU  - Morita, H.
AU  - Toh, H.
AU  - Suda, W.
AU  - Kim, S.W.
AU  - Suzuki, S.
AU  - Yakabe, T.
AU  - Hattori, M.
AU  - Yajima, N.
TI  - Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability.
JO  - PLoS ONE
PY  - 2013
SP  - e60521
EP  - e60521
VL  - 8
AB  - We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic
AB  - acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained
AB  - a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that
AB  - together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes,
AB  - and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and
AB  - the stress response were present in L. brevis KB290 but not in the closely related L. brevis
AB  - ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was
AB  - essential for the strain's gastrointestinal tract tolerance and tendency
AB  - to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains
AB  - to detect low frequency variants, we evaluated genome stability. Deep sequencing of four
AB  - periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and
AB  - 37 minority variation sites, indicating long-term stability and providing a useful method for
AB  - assessing the stability of industrial bacteria at the nucleotide level.
ER  -

TY  - JOUR
AU  - Fuks, F.
AU  - Burgers, W.A.
AU  - Brehm, A.
AU  - Hughes-Davies, L.
AU  - Kouzarides, T.
TI  - DNA methyltransferase Dnmt1 associates with histone deacetylase activity.
JO  - Nat. Genet.
PY  - 2000
SP  - 88
EP  - 91
VL  - 24
AB  - The DNA methyltransferase Dnmt1 is responsible for cytosine methylation in mammals and has a
AB  - role in gene silencing. DNA methylation represses genes partly by recruitment of the
AB  - methyl-CpG-binding protein MeCP2, which in turn recruits a histone deacetylase activity. Here
AB  - we show that Dnmt1 is itself associated with histone deacetylase activity in vivo. Consistent
AB  - with this association, we find that one of the known histone deacetylases, HDAC1, has the
AB  - ability to bind Dnmt1 and can purify methyltransferase activity from nuclear extracts. We have
AB  - identified a transcriptional repression domain in Dnmt1 that functions, at least partly, by
AB  - recruiting histone deacetylase activity and shows homology to the repressor domain of the
AB  - trithorax-related protein HRX (also known as MLL and ALL-1). Our data show a more direct
AB  - connection between DNA methylation and histone deacetylation than was previously considered.
AB  - We suggest that the process of DNA methylation, mediated by Dnmt1, may depend on or generate
AB  - an altered chromatin state via histone deacetylase activity.
ER  -

TY  - JOUR
AU  - Fuks, F.
AU  - Burgers, W.A.
AU  - Godin, N.
AU  - Kasai, M.
AU  - Kouzarides, T.
TI  - Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription.
JO  - EMBO J.
PY  - 2001
SP  - 2536
EP  - 2544
VL  - 20
AB  - The Dnmt3a DNA methyltransferase is essential for mammalian development and is responsible for
AB  - the generation of genomic methylation patterns, which lead to transcriptional silencing. Here,
AB  - we show that Dnmt3a associates with RP58, a DNA-binding transcriptional repressor protein
AB  - found at transcriptionally silent heterochromatin. Dnmt3a acts as a co-repressor for RP58 in a
AB  - manner that does not require its de novo methyltransferase activity. Like other characterized
AB  - co-repressors, Dnmt3a associates with the histone deacetylase HDAC1 using its ATRX-homology
AB  - domain. This domain of Dnmt3a represents an independent transcriptional repressor domain whose
AB  - silencing functions require HDAC activity. These results identify Dnmt3a as a co-repressor
AB  - protein carrying deacetylase activity and show that Dnmt3a can be targeted to specific
AB  - regulatory foci via its association with DNA-binding transcription factors.
ER  -

TY  - JOUR
AU  - Fukuda, E.
AU  - Kaminska, K.H.
AU  - Bujnicki, J.M.
AU  - Kobayashi, I.
TI  - Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases.
JO  - Genome Biology
PY  - 2008
SP  - R163
EP  - R163
VL  - 9
AB  - Background Alteration in epigenetic methylation can affect gene expression and
AB  - other processes. In Prokaryota, DNA methyltransferase genes frequently
AB  - move between genomes and present a potential threat. A methyl-specific
AB  - deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated
AB  - DNAs. Here we examined whether McrBC competes with genome methylation
AB  - systems through host killing by chromosome cleavage.
AB  - Results
AB  - McrBC inhibited the establishment of a plasmid carrying a PvuII
AB  - methyltransferase gene but lacking its recognition sites, likely
AB  - through the lethal cleavage of chromosomes that become methylated.
AB  - Indeed, its phage-mediated transfer caused McrBC-dependent chromosome
AB  - cleavage. Its induction led to cell death accompanied by chromosome
AB  - methylation, cleavage and degradation. RecA/RecBCD functions affect the
AB  - chromosome processing and, together with SOS response, reduce the
AB  - lethality. Our evolutionary/genomic analyses of mcrBC homologs revealed
AB  - (i) wide distribution in Prokaryota, (ii) frequent distant horizontal
AB  - transfer and linkage with mobility-related genes, (iii) diversification
AB  - in the DNA binding domain. In these features, McrBCs resemble Type II
AB  - restriction-modification systems, which behave as selfish mobile
AB  - elements maintaining their frequency by host killing. McrBCs are
AB  - frequently found linked with a methyltransferase homolog, which
AB  - suggests a functional association.
AB  - Conclusions
AB  - Our experiments indicate McrBC can respond to genome methylation
AB  - systems by host killing. Combined with our evolutionary/genomic
AB  - analyses, they support our hypothesis McrBCs have evolved as mobile
AB  - elements competing with specific genome methylation systems through
AB  - host killing. To our knowledge, this represents the first report of a
AB  - defense system against epigenetic systems through cell death.
ER  -

TY  - JOUR
AU  - Fukuda, E.
AU  - Kobayashi, I.
TI  - Suicidal defense against an epigenetic system: a role for a Type IV methyl-dependent restriction enzyme.
JO  - Genes Genet. Syst.
PY  - 2006
SP  - 408
EP  - 408
VL  - 81
AB  - Attack on the host cell chromosome by restriction enzymes is a subject of various biological
AB  - interactions. When several Type II restriction-modification gene complexes enter a new host
AB  - cell, they try to avoid chromosome breakage and cell killing by expressing the modification
AB  - enzyme first. Once they establish themselves, they attack the host chromosome when their
AB  - presence is threatened. Through this postsegregational killing strategy, they force their
AB  - maintenance on the host. On the other
AB  - hand, Escherichia coli cells employ a Type IV restriction enzyme McrBC, which recognizes
AB  - methylated DNAs and cleaves DNA between two of these recognition sites. We hypothesize that
AB  - McrBC serves for suicidal defense against invasion of specific DNA methylation systems. In
AB  - this work, we analyze host attack by McrBC. We demonstrate McrBC-mediated abortion of
AB  - establishment of a modification enzyme gene in E. coli. We also demonstrate McrBC-dependent
AB  - cell death and chromosomal DNA degradation following genome methylation by RM systems. These
AB  - results support our hypothesis. To our knowledge, this represents the first example of direct
AB  - suicidal defense against an epigenetic system.
ER  -

TY  - JOUR
AU  - Fukuda, K.
AU  - Hosoyama, A.
AU  - Tsuchikane, K.
AU  - Ohji, S.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Shintani, M.
AU  - Kimbara, K.
TI  - Complete Genome Sequence of Polychlorinated Biphenyl Degrader Comamonas testosteroni TK102 (NBRC 109938).
JO  - Genome Announcements
PY  - 2014
SP  - e00865
EP  - e00814
VL  - 2
AB  - Comamonas testosteroni TK102 (NBRC 109938; JCM 19603) can utilize biphenyl as a sole carbon
AB  - source and degrade polychlorinated biphenyls (PCBs). The complete
AB  - nucleotide sequence of the TK102 genome was determined. TK102 possesses several
AB  - integrative and conjugative element-like regions, and one of them carries
AB  - biphenyl-degradative genes.
ER  -

TY  - JOUR
AU  - Fukuda, S.
AU  - Toh, H.
AU  - Hase, K.
AU  - Oshima, K.
AU  - Nakanishi, Y.
AU  - Yoshimura, K.
AU  - Tobe, T.
AU  - Clarke, J.M.
AU  - Topping, D.L.
AU  - Suzuki, T.
AU  - Taylor, T.D.
AU  - Itoh, K.
AU  - Kikuchi, J.
AU  - Morita, H.
AU  - Hattori, M.
AU  - Ohno, H.
TI  - Bifidobacteria can protect from enteropathogenic infection through production of acetate.
JO  - Nature
PY  - 2011
SP  - 543
EP  - 547
VL  - 469
AB  - The human gut is colonized with a wide variety of microorganisms,
AB  - including species, such as those belonging to the bacterial genus Bifidobacterium, that have
AB  - beneficial effects on human physiology and pathology1-3. Among the most distinctive benefits
AB  - of bifidobacteria are modulation of host defence responses and protection against infectious
AB  - diseases4-6. Nevertheless, the molecular mechanisms underlying these effects have barely been
AB  - elucidated. To investigate these mechanisms, we used mice associated with certain
AB  - bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic
AB  - Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that
AB  - genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain
AB  - bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We
AB  - found that this effect can be attributed, at least in part, to increased production of acetate
AB  - and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was
AB  - inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal
AB  - defence mediated by epithelial cells and thereby protects the host against lethal infection.
ER  -

TY  - JOUR
AU  - Fukuda, T.
AU  - Nogami, S.
AU  - Ohya, Y.
TI  - VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner.
JO  - Genes Cells
PY  - 2003
SP  - 587
EP  - 602
VL  - 8
AB  - BACKGROUND: Inteins and group I introns found in prokaryotic and eukaryotic organisms
AB  - occasionally behave as mobile genetic elements.
AB  - During meiosis of the yeast Saccharomyces cerevisiae, the site-specific
AB  - endonuclease encoded by VMA1 intein, VDE, triggers a single double-strand
AB  - break (DSB) at an inteinless allele, leading to VMA1 intein homing.
AB  - Besides the accumulating information on the in vitro activity of VDE, very
AB  - little has been known about the molecular mechanism of intein homing in
AB  - yeast nucleus. RESULTS: We developed an assay to detect the product of
AB  - VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA
AB  - homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and
AB  - Tid1p, and found that they all play critical roles in intein inheritance.
AB  - The absence of DSB end processing proteins, Sae2p and those in the
AB  - Mre11-Rad50-Xrs2 complex, also causes partial reduction in homing
AB  - efficiency. As with meiotic recombination, crossover events are frequently
AB  - observed during intein homing. We also observed that the absence of
AB  - premeiotic DNA replication caused by hydroxyurea (HU) or clb5delta
AB  - clb6delta mutation reduces VDE-mediated DSBs. CONCLUSION: The repairing
AB  - system working in intein homing shares molecular machinery with meiotic
AB  - recombination induced by Spo11p. Moreover, like Spo11p-induced DNA
AB  - cleavage, premeiotic DNA replication is a prerequisite for a VDE-induced
AB  - DSB. VMA1 intein thus utilizes several host factors involved in meiotic
AB  - and recombinational processes to spread its genetic information and
AB  - guarantee its progeny through establishment of a parasitic relationship
AB  - with the organism.
ER  -

TY  - JOUR
AU  - Fukuda, T.
AU  - Ohta, K.
AU  - Ohya, Y.
TI  - Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure  around the target site.
JO  - Euk. Cell
PY  - 2006
SP  - 981
EP  - 990
VL  - 5
AB  - VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded
AB  - by the mobile intein-coding sequence within the
AB  - nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE
AB  - recognition sequence (VRS) in the VMA1 gene lacking the intein-coding
AB  - sequence during meiosis to insert a copy of the intein-coding sequence
AB  - at the cleaved site. The mechanism underlying the meiosis specificity
AB  - of VMA1 intein-coding sequence homing remains unclear. We studied
AB  - various factors that might influence the cleavage activity in vivo and
AB  - found that VDE binding to the VRS can be detected only when DNA
AB  - cleavage by VDE takes place, implying that meiosis-specific DNA
AB  - cleavage is regulated by the accessibility of VDE to its target site.
AB  - As a possible candidate for the determinant of this accessibility, we
AB  - analyzed chromatin structure around the VRS and revealed that local
AB  - chromatin structure near the VRS is altered during meiosis. Although
AB  - the meiotic chromatin alteration exhibits correlations with DNA binding
AB  - and cleavage by VDE at the VMA1 locus, such a chromatin alteration is
AB  - not necessarily observed when the VRS is embedded in ectopic gene loci.
AB  - This suggests that nucleosome positioning or occupancy around the VRS
AB  - by itself is not the sole mechanism for the regulation of
AB  - meiosis-specific DNA cleavage by VDE and that other mechanisms are
AB  - involved in the regulation.
ER  -

TY  - JOUR
AU  - Fukuda, T.
AU  - Ohta, K.
AU  - Ohya, Y.
TI  - Strategies of VDE for propagation in yeast nuclear genome.
JO  - Genes Genet. Syst.
PY  - 2005
SP  - 438
EP  - 438
VL  - 80
AB  - VDE, a homing endonuclease in Saccharomyces cerevisiae, is encoded by a mobile intein within
AB  - the nuclear gene, VMA1.  VDE causes double-strand  break at the 31-bp VDE-recognition sequence
AB  - in intein-less VMA1 allele during meiosis. The DSB is then repaired using the
AB  - intein-containing allele as a template, leading to the conversion of intein-less allele to
AB  - intein-containing allele. These processes are called "homing", by which VDE spreads throughout
AB  - the population.  The study on DSB repair process of homing revealed that VDE-introduced DSB is
AB  - repaired by homologous recombination system working in meiotic recombination as if it is one
AB  - of the programmed meiotic DSBs.  To elucidate the meiosis-specificity of DSB formation by VDE,
AB  - we examined several possibilities.  We found that none of expression, endonuclease activity,
AB  - and nuclear import necessarily regulates the meiosis-specific DSB by VDE.  On the other hand,
AB  - chromatin structure around VRS alters during meiosis. Chromatin immunoprecipitation revealed
AB  - that VDE loading onto VRS occurs only when chromatin changes around VRS.  These results raise
AB  - the possibility that chromatin configuration, which is modulated by the intrinsic property of
AB  - VRS, reulates the meiosis-specific integration of VDE.  Thus, several host factors are
AB  - involved in homing at meiosis-specific DSB formation and DSB repair processes to increase the
AB  - copy number of VDE.
ER  -

TY  - JOUR
AU  - Fukui, T.
AU  - Atomi, H.
AU  - Kanai, T.
AU  - Matsumi, R.
AU  - Fujiwara, S.
AU  - Imanaka, T.
TI  - Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.
JO  - Genome Res.
PY  - 2005
SP  - 352
EP  - 363
VL  - 15
AB  - The genus Thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the
AB  - order Thermococcales in Euryarchaeota along with
AB  - the closely related genus Pyrococcus. The members of Thermococcus are
AB  - ubiquitously present in natural high-temperature environments, and are
AB  - therefore considered to play a major role in the ecology and metabolic
AB  - activity of microbial consortia within hot-water ecosystems. To obtain
AB  - insight into this important genus, we have determined and annotated the
AB  - complete 2,088,737-base genome of Thermococcus kodakaraensis strain KOD1,
AB  - followed by a comparison with the three complete genomes of Pyrococcus
AB  - spp. A total of 2306 coding DNA sequences (CDSs) have been identified,
AB  - among which half (1165 CDSs) are annotatable, whereas the functions of 41%
AB  - (936 CDSs) cannot be predicted from the primary structures. The genome
AB  - contains seven genes for probable transposases and four virus-related
AB  - regions. Several proteins within these genetic elements show high
AB  - similarities to those in Pyrococcus spp., implying the natural occurrence
AB  - of horizontal gene transfer of such mobile elements among the order
AB  - Thermococcales. Comparative genomics clarified that 1204 proteins,
AB  - including those for information processing and basic metabolisms, are
AB  - shared among T. kodakaraensis and the three Pyrococcus spp. On the other
AB  - hand, among the set of 689 proteins unique to T. kodakaraensis, there are
AB  - several intriguing proteins that might be responsible for the specific
AB  - trait of the genus Thermococcus, such as proteins involved in additional
AB  - pyruvate oxidation, nucleotide metabolisms, unique or additional metal ion
AB  - transporters, improved stress response system, and a distinct restriction
AB  - system.
ER  -

TY  - JOUR
AU  - Fukushima, J.
AU  - Tojo, F.
AU  - Asano, R.
AU  - Kobayashi, Y.
AU  - Shimura, Y.
AU  - Okano, K.
AU  - Miyata, N.
TI  - Complete Genome Sequence of the Unclassified Iron-Oxidizing, Chemolithoautotrophic Burkholderiales Bacterium GJ-E10, Isolated from an Acidic  River.
JO  - Genome Announcements
PY  - 2015
SP  - e01455
EP  - e01414
VL  - 3
AB  - Burkholderiales bacterium GJ-E10, isolated from the Tamagawa River in Akita Prefecture, Japan,
AB  - is an unclassified, iron-oxidizing chemolithoautotrophic
AB  - bacterium. Its single circular genome, consisting of 3,276,549 bp, was sequenced
AB  - by using three types of next-generation sequencers and the sequences were then
AB  - confirmed by PCR-based Sanger sequencing.
ER  -

TY  - JOUR
AU  - Fukuyama, Y.
AU  - Oguro, T.
AU  - Omae, K.
AU  - Yoneda, Y.
AU  - Yoshida, T.
AU  - Sako, Y.
TI  - Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic  Fronts in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e00242
EP  - e00217
VL  - 5
AB  - Hydrogenogenic carboxydotrophs may provide hydrogen as primary energy for the microbial
AB  - community via carbon monoxide oxidation. To investigate the genetics of
AB  - carbon monoxide metabolism, we report here the draft genome sequences of the
AB  - hydrogenogenic carboxydotrophs Carboxydocella sp. strains JDF658 (2.60 Mbp; G+C
AB  - content, 49.2%) and ULO1 (2.70 Mbp; G+C content, 48.8%).
ER  -

TY  - JOUR
AU  - Fukuyama, Y.
AU  - Omae, K.
AU  - Yoneda, Y.
AU  - Yoshida, T.
AU  - Sako, Y.
TI  - Draft Genome Sequences of Carboxydothermus pertinax and C. islandicus, Hydrogenogenic Carboxydotrophic Bacteria.
JO  - Genome Announcements
PY  - 2017
SP  - e01648
EP  - e01616
VL  - 5
AB  - Carboxydothermus spp. are some of the most studied carbon monoxide-oxidizing anaerobic
AB  - thermophiles. For further investigation into the carbon monoxide
AB  - metabolism of Carboxydothermus spp., we report here the draft genome sequences of
AB  - the hydrogenogenic carboxydotrophs Carboxydothermus pertinax (2.47 Mb; G+C
AB  - content, 40.7%) and C. islandicus (2.39 Mb; G+C content, 42.0%).
ER  -

TY  - JOUR
AU  - Fukuyo, M.
AU  - Nakano, T.
AU  - Zhang, Y.
AU  - Furuta, Y.
AU  - Ishikawa, K.
AU  - Watanabe-Matsui, M.
AU  - Yano, H.
AU  - Hamakawa, T.
AU  - Ide, H.
AU  - Kobayashi, I.
TI  - Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 2841
EP  - 2852
VL  - 43
AB  - The restriction-modification systems use epigenetic modification to distinguish between self
AB  - and nonself DNA. A modification enzyme transfers a methyl group to a base in a specific DNA
AB  - sequence while its cognate restriction enzyme introduces breaks in DNA lacking this methyl
AB  - group. So far, all the restriction enzymes hydrolyze phosphodiester bonds linking the monomer
AB  - units of DNA. We recently reported that a restriction enzyme (R.PabI) of the PabI superfamily
AB  - with half-pipe fold has DNA glycosylase activity that excises an adenine base in the
AB  - recognition sequence (5'-GTAC). We now found a second activity in this enzyme: at the
AB  - resulting apurinic/apyrimidinic (AP) (abasic) site (5'-GT#C, # = AP), its AP lyase activity
AB  - generates an atypical strand break. Although the lyase activity is weak and lacks sequence
AB  - specificity, its covalent DNA-R.PabI reaction intermediates can be trapped by NaBH4 reduction.
AB  - The base excision is not coupled with the strand breakage and yet causes restriction because
AB  - the restriction enzyme action can impair transformation ability of unmethylated DNA even in
AB  - the absence of strand breaks in vitro. The base excision of R.PabI is inhibited by methylation
AB  - of the target adenine base. These findings expand our understanding of genetic and epigenetic
AB  - processes linking those in prokaryotes and eukaryotes.
ER  -

TY  - JOUR
AU  - Fuller-Pace, F.V.
AU  - Bullas, L.R.
AU  - Delius, H.
AU  - Murray, N.E.
TI  - Genetic recombination can generate altered restriction specificity.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 6095
EP  - 6099
VL  - 81
AB  - A recombinant strain, isolated following the transduction of an Escherichia
AB  - coli recipient carrying the Salmonella typhimurium (SB) specificity genes with
AB  - DNA from a donor having the Salmonella potsdam (SP) specificity, was shown
AB  - [Bullas, L.R., Colson, C. and Van Pel, A. (1976) J. Gen. Microbiol. 95,
AB  - 166-172] to have neither SB nor SP specificity but to encode a novel
AB  - restriction specificity, SQ.  The heteroduplex analysis of the hsdS
AB  - (specificity) genes of the SB and SP restriction and modification systems
AB  - described here identifies a conserved sequence of around 100 base pairs flanked
AB  - by two nonhomologous regions each of approximately 500 base pairs.  This
AB  - organization parallels that previously deduced from the DNA sequences of the
AB  - hsdS genes of the related E. coli K-12, B, and D restriction systems.  The
AB  - present heteroduplex analyses further show that the hsdS gene conferring the SQ
AB  - specificity deserves one nonhomologous region from the SB gene and the other
AB  - from the SP gene, as predicted from genetic exchange within the conserved
AB  - sequence.  This finding supports the idea that two domains of an hsdS
AB  - polypeptide, which are different for each specificity, may correlate with two
AB  - regions of the DNA sequence recognized.  It has been shown that the recognition
AB  - sequences for E. coli K-12 and B each consist of two short oligonucleotide
AB  - sequences interrupted by a nonspecific sequence.  A similar organization is
AB  - suggested for the Salmonella specificity systems, providing the potential for
AB  - evolutionary diversification of restriction specificities as a result of
AB  - recombination within the conserved sequence of the hsdS gene.
ER  -

TY  - JOUR
AU  - Fuller-Pace, F.V.
AU  - Cowan, G.M.
AU  - Murray, N.E.
TI  - EcoA and EcoE:  Alternatives to the EcoK Family of Type I Restriction and Modification Systems of Escherichia coli.
JO  - J. Mol. Biol.
PY  - 1985
SP  - 65
EP  - 75
VL  - 186
AB  - The genes (hsd A) encoding EcoA, a restriction and modification system first
AB  - identified in Escherichia coli 15T-, behave in genetic crosses as alleles of
AB  - the genes (hsd K) encoding the archetypal type I restriction and modification
AB  - system of E. coli K12.  Nevertheless, molecular experiments have failed to
AB  - detect relatedness between the A and K systems.  We have cloned the hsd A genes
AB  - and have identified, on the basis of DNA homology, related genes (hsd E)
AB  - conferring a new specificity to a natural isolate of E. coli.  We show that the
AB  - overall organization of the genes encoding EcoA and EcoE closely parallels that
AB  - for EcoK.  Each enzyme is encoded by three genes, of which only one, hsdS,
AB  - confers the specificity of DNA interaction.  The three genes are in the same
AB  - order as those encoding EcoK, i.e. hsdR, hsdM and hsdS and, similarly, they
AB  - include a promter between hsdR and hsdM from which the M and S genes can be
AB  - transcribed.  The evidence indicates that EcoA and EcoE are type I restriction
AB  - and modification enzymes, but they appear to identify an alternative family to
AB  - EcoK.  For both families, the hsdR polypeptide is by far the largest, but the
AB  - sizes of the other two polypeptides are reversed, with the smallest polypeptide
AB  - of EcoK being the product of hsdS, and the smallest for the EcoA family being
AB  - the product of hsdM.  Physiologically, the A restriction and modification
AB  - system differs from that of K and its relatives, in that A-specific methylation
AB  - of unmodified DNA is particularly effective.
ER  -

TY  - JOUR
AU  - Fuller-Pace, F.V.
AU  - Murray, N.E.
TI  - Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1986
SP  - 9368
EP  - 9372
VL  - 83
AB  - The hsd genes of Salmonella typhimurium and Salmonella potsdam encode related
AB  - type I restriction and modification systems designated SB and SP, respectively;
AB  - the polypeptide encoded by the hsdS gene dictates the DNA sequence recognized.
AB  - The hsdS genes of the SB and SP systems have a conserved sequence of around 100
AB  - base pairs flanked by two nonhomologous (variable) regions of around 500 base
AB  - pairs.  Recombination between the hsdS genes of SB and SP generated a system
AB  - (SQ) with a different recognition specificity.  We have localized the position
AB  - of the crossover in the central conserved region by analysis of nucleotide
AB  - sequences.  Concomitant with the generation of a new combination of flanking
AB  - variable regions is the recombination of minor differences in the central
AB  - conserved region.  A polypeptide domain encoded on the 5' side of the crossover
AB  - dictates recognition of the trinucleotide component of the target sequence, and
AB  - a second domain encoded on the 3' side of the crossover, similarly governs
AB  - recognition of the tetra- or penta-nucleotide component.  Our analysis
AB  - implicates at least parts of the variable regions in the determination of the
AB  - specificity of interaction between protein and DNA.  Furthermore, the
AB  - trinucleotide components of the recognition sequences of S. typhimurium and
AB  - Escherichia coli K-12 are identical, and the 5' segments of their hsdS genes
AB  - are strikingly homologous rather than variable.
ER  -

TY  - JOUR
AU  - Fullerton, H.
AU  - Hager, K.W.
AU  - Moyer, C.L.
TI  - Draft Genome Sequence of Mariprofundus ferrooxydans Strain JV-1, Isolated from Loihi Seamount, Hawaii.
JO  - Genome Announcements
PY  - 2015
SP  - e01118
EP  - e01115
VL  - 3
AB  - Mariprofundus ferrooxydans strain JV-1 was isolated in 1998 from Loihi Seamount,  Hawaii.
AB  - Here, we present the draft genome of strain JV-1, which shows similarity  to other sequenced
AB  - Mariprofundus isolates, strains PV-1 and M34.
ER  -

TY  - JOUR
AU  - Fung, W.T.
TI  - Functional analysis of the two subunits of DNA methyltransferase EcoHK31I.
JO  - Ph.D. Thesis, Chinese Univ. of Hong Kong, China
PY  - 2006
SP  - 1
EP  - 224
AB  - Methylation of cytosine residues in DNA occurs in diverse organisms from bacteria to humans.
AB  - In higher eukaryotic organisms cytosine-C5 methyltransferase is the only type of DNA MTase and
AB  - it plays an important role in controlling a number of cellular processes including
AB  - transcription, genomic imprinting and DNA repair.  In bacteria, there are three types of
AB  - MTases, mC4-, mC5- and mA6-, classified according to the methylation site of the DNA.  MTase
AB  - and its cognate restriction endonuclease form restriction-modification system.  The role of
AB  - MTase is to protect the host from its own ENase digestion while the ENase acts to degrade the
AB  - invasion of foreign DNA.  Sequence comparison of nearly 50 bacterial mC5-MTases has shown that
AB  - these enzymes share an overall common protein architecture.  Ten conserved motifs (I to X),
AB  - each 10 to 20 amino acids in length, have been identified, five of which are highly conserved
AB  - (I, IV, VI, VIII and X).  In addition, all of these enzymes have a hypervariable region lying
AB  - between motifs VIII and IX.  It is called the target recognition domain, and is responsible
AB  - for the specificity of DNA recognition and the choice of base to be methylated.  All
AB  - mC5-MTases are monomeric enzymes, except M. EcoHK31I and M.AquI which are MTases composed of
AB  - two polypeptides.  M.EcoHK31I is a mC5-MTase which recognizes the sequence 5-YGGCCR-3' and
AB  - consists of polypeptide a and b, with the latter gene encoded in an alternative reading frame
AB  - of the former.  All of the conserved motifs in mC5-MTases can be found in polypeptide a,
AB  - except motif IX, which is located in polypeptide b.  Both polypeptides are required for in
AB  - vitro methylation.  Since both of the polypeptides a and b of M.EcoHK31I are sequenced and
AB  - cloned into the expression vector separately, the role of DNA recognition and subunits
AB  - interaction of individual polypeptides can be studied.  By electromobility shift assay, we
AB  - found that polypeptides a and b complex recognize specific double strand oligos substrate.
AB  - Polypeptide a-DNA formed aggregates and polypeptide b alone did not bind DNA.  Therefore,
AB  - polypeptide b assists the proper binding of polypeptide a to DNA substrate.  Complex of
AB  - polypeptide a and a polypeptide b variant with N-terminal deletion of 41 amino acids showed a
AB  - 16-fold reduction in methylation activity.  Further deletion resulted in an inactive MTase. By
AB  - surface plasmon resonance assay, the dissociation equilibrium constant of polypeptides a and b
AB  - complex was found to be 56.2nM and the KD for polypeptide a and deltaN46-polypeptide b complex
AB  - was increased by about 95 folds, contributing by a drastic decrease in dissociate rate
AB  - constant and an increase in association rate constant.  This indicated that the N-terminal
AB  - region of polypeptide b takes part in subunit interaction.  To pinpoint which amino acid
AB  - residues located at the variable region of polypeptide a are important for DNA binding and
AB  - subunits interaction, "charge-to-alanine scanning mutagenesis" were performed on 16 charge
AB  - residues between Asp213 and Glu271 in the small domain.  It was found that the five charge
AB  - residues upstream of motif X are not required for activity.  For other residues except K225,
AB  - E240 and D245, the protein is active when the same charge is maintained.
ER  -

TY  - JOUR
AU  - Fung, W.T.
AU  - Sze, K.H.
AU  - Lee, K.F.
AU  - Shaw, P.C.
TI  - Functional studies of the small subunit of EcoHK31I DNA methyltransferase.
JO  - Biol. Chem.
PY  - 2006
SP  - 507
EP  - 513
VL  - 387
AB  - EcoHK311 DNA methyltransferase recognizes the sequence 5'-YGGCCR-3' and adds a methyl group
AB  - to the fifth position of the internal cytosine to
AB  - protect the DNA from cleavage by its cognate endonuclease. M.EcoHK311
AB  - is composed of polypeptides alpha and beta. Polypepticle beta only
AB  - contains the conserved IX motif of the C5-MTase family, and provides a
AB  - unique example to show that this motif alone may be dislocated to
AB  - another polypeptide. By electromobility shift assay, we found that the
AB  - alpha/beta complex recognizes specific oligonucleotide substrates.
AB  - Polypeptide alpha formed aggregates with DNA, while polypeptide p alone
AB  - did not bind DNA. Therefore, polypeptide beta assists in the proper
AB  - binding of polypeptide alpha to DNA substrate. The complex of
AB  - polypeptide alpha and a polypeptide beta variant with an N-terminal
AB  - deletion of 41 amino acids showed a 16-fold reduction in methylation
AB  - activity. Further deletion resulted in an inactive methyltransferase.
AB  - The dissociation equilibrium constant (K-d) of the alpha/beta complex
AB  - was 56.4 nM, while the K-d value for the alpha/Delta N46-polypeptide
AB  - beta complex was increased approximately 95-fold, caused by a drastic
AB  - decrease in dissociate rate constant (k(d)) and an increase in the
AB  - association rate constant (k(a)). This indicates that the N-terminal
AB  - region of polypeptide beta takes part in subunit interaction, while the
AB  - C-terminal region is involved in DNA binding.
ER  -

TY  - JOUR
AU  - Funo, K.
AU  - Kitagawa, W.
AU  - Tanaka, M.
AU  - Sone, T.
AU  - Asano, K.
AU  - Kamagata, Y.
TI  - Draft Genome Sequence of Tomitella biformata AHU 1821T, Isolated from a Permafrost Ice Wedge in Alaska.
JO  - Genome Announcements
PY  - 2014
SP  - e00066
EP  - e00014
VL  - 2
AB  - Tomitella biformata AHU 1821(T) was isolated and cultured from a permafrost ice wedge, aged
AB  - presumably about 25,000 years, in the Fox permafrost tunnel (64.952
AB  - degrees N 147.617 degrees W), Alaska. These genome data provide the basis for
AB  - investigating T. biformata AHU 1821(T), identified as a long-term survivor of the
AB  - extremely cold and closed environment.
ER  -

TY  - JOUR
AU  - Furmanczyk, E.M.
AU  - Kaminski, M.A.
AU  - Dziembowski, A.
AU  - Lipinski, L.
AU  - Sobczak, A.
TI  - Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611.
JO  - Genome Announcements
PY  - 2017
SP  - e01038
EP  - e01017
VL  - 5
AB  - Here, we report the draft genome sequence of Pseudomonas umsongensis type strain  DSM 16611.
AB  - The assembly consists of 14 contigs containing 6,701,403 bp with a GC
AB  - content of 59.73%.
ER  -

TY  - JOUR
AU  - Furmanczyk, E.M.
AU  - Kaminski, M.A.
AU  - Dziembowski, A.
AU  - Lipinski, L.
AU  - Sobczak, A.
TI  - Draft Genome Sequence of the Type Strain Pseudomonas jessenii DSM 17150.
JO  - Genome Announcements
PY  - 2017
SP  - e01035
EP  - e01017
VL  - 5
AB  - We present the draft genome sequence of Pseudomonas jessenii type strain DSM 17150. The
AB  - assembly consists of 13 contigs, contains 6,537,206 bp, and has a GC
AB  - content of 59.7%.
ER  -

TY  - JOUR
AU  - Furmanek, B.
AU  - Gromek, K.
AU  - Sektas, M.
AU  - Kaczorowski, T.
TI  - Isolation and characterization of type IIS restriction endonuclease from Neisseria cuniculi ATCC 14688.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 171
EP  - 176
VL  - 196
AB  - Neisseria cuniculi produces the restriction enzyme NcuI which is an isoschizomer of MboII. We
AB  - have demonstrated that NcuI recognizes a
AB  - pentanucleotide sequence (5'-GAAGA-3'/3'-CTTCT-5'), and cleaves the DNA
AB  - 8 and 7 nucleotides downstream from the recognition site leaving a
AB  - single 3'-protruding nucleotide. We have purified this enzyme to
AB  - electrophoretic homogeneity using a four-step chromatographic procedure.
AB  - NcuI endonuclease is a monomeric protein with an Mr = 48,000 +/- 1,000
AB  - under denaturing conditions. The properties of NcuI are consistent with
AB  - those for MboII, the position of the cleavage site being identical and
AB  - the pH profile and divalent cation requirements being similar.
AB  - Moreover, NcuI cross-reacts strongly with anti-MboII serum suggesting
AB  - the presence of similar antigenic determinants. We have determined the
AB  - sequence of 20 N-terminal amino acids for NcuI and concluded that this
AB  - sequence is identical to the N-terminal portion of the MboII enzyme.
ER  -

TY  - JOUR
AU  - Furmanek, B.
AU  - Sektas, M.
AU  - Wons, E.
AU  - Kaczorowski, T.
TI  - Molecular characterization of the DNA methyltransferase M1.NcuI from Neisseria cuniculi ATCC 14688.
JO  - Res. Microbiol.
PY  - 2007
SP  - 164
EP  - 174
VL  - 158
AB  - The methyltransferase M1.NcuI is a member of the restriction-modification system in Neisseria
AB  - cuniculi ATCC14688 and recognizes the asymmetric
AB  - pentanucleotide sequence 5'-GAAGA-3'/3'-CTTCT-5'. We purified M1.NcuI to
AB  - electrophoretic homogeneity using a four-step chromatographic procedure.
AB  - M1.NcuI is a protein with M(r)=32,000+/-1000 under denaturing conditions.
AB  - It modifies the recognition sequence by transferring the methyl group from
AB  - S-adenosyl-l-methionine to the 3' adenine of the pentanucleotide sequence
AB  - 5'-GAAGA-3'. M1.NcuI, like many other methyltransferases, occurs as a
AB  - monomer in solution, as determined by gel filtration. Divalent cations
AB  - inhibit the methylation activity of M1.NcuI. Optimal enzyme activity was
AB  - observed at a pH of 8.0. M1.NcuI cross-reacted with anti-M1.MboII serum
AB  - which reflects the similarity of M1.NcuI with M1.MboII at the amino acid
AB  - level. The gene coding for the enzyme, designated ncuIM1, was cloned,
AB  - sequenced and overexpressed in Escherichia coli. The structural gene is
AB  - 780 nucleotides in length coding for a protein of 259 amino acids (M(r)
AB  - 30,098). The presence and distribution of nine highly conserved amino acid
AB  - sequence motifs and a putative target recognition domain in the enzyme
AB  - structure suggest that M1.NcuI, similar to M1.MboII and M1.HpyAII, belongs
AB  - to N(6)-adenine beta-class DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Furmanek-Blaszk, B.
TI  - Phenotypic and molecular characteristics of an Aeromonas hydrophila strain isolated from the River Nile.
JO  - Microbiol. Res.
PY  - 2014
SP  - 547
EP  - 552
VL  - 169
AB  - Aeromonas hydrophila, an inhabitant of aquatic ecosystems found in most parts of  the world,
AB  - has considerable virulence potential. The polymerase chain reaction
AB  - technique was used to assay for the presence of five virulence factor genes:
AB  - haemolytic toxins aerA and ahh1, elastase ahyB, the enterotoxin act, and the
AB  - polar flagella flaA/flaB in the A. hydrophila strain isolated from the River
AB  - Nile. Drug screening showed high levels of resistance to beta-lactam antibiotics
AB  - and tetracycline. Slime production was determined by the Congo red agar plate
AB  - test. The isolate produced two restriction enzymes named AehI and AehII which are
AB  - isoschizomers of XhoI and StuI respectively. The complete nucleotide sequence of
AB  - the cryptic plasmid pAhy2.5 (2524 bp) from this strain was determined. Sequence
AB  - analysis revealed the presence of two open reading frames (ORFs) encoding
AB  - putative proteins. The protein coded by ORF1 is homologous with Rep proteins of
AB  - plasmids belonging to the pC194 family, which are known to replicate by the
AB  - rolling-circle mechanism. The putative double-strand origin of replication and a
AB  - region with palindromic sequences that could function as a single-strand origin
AB  - were detected in pAhy2.5.
ER  -

TY  - JOUR
AU  - Furmanek-Blaszk, B.
AU  - Boratynski, R.
AU  - Zolcinska, N.
AU  - Sektas, M.
TI  - M1.Mboll and M2.Mboll type IIS methyltransferases: different specificities, the same target.
JO  - Microbiology
PY  - 2009
SP  - 1111
EP  - 1121
VL  - 155
AB  - Methylation of a base in a specific DNA sequence protects the DNA from nucleolytic cleavage by
AB  - restriction enzymes recognizing the same
AB  - sequence. The Mboll restriction-modification (R-M) system of Moraxella
AB  - bovis ATCC 10900 consists of a restriction endonuclease gene and two
AB  - methyltransferase genes. The enzymes encoded by this system recognize
AB  - an asymmetrical sequence 5'-GAAGA-3'/3'-CTTCT-5'. M1.Mboll modifies the
AB  - last adenine in the recognition sequence 5'-GAAGA-3' to
AB  - N-6-methyladenine. A second methylase, M2.Mboll, was cloned and
AB  - purified to electrophoretic homogeneity using a four-step
AB  - chromatographic procedure. It was demonstrated that M2.Mboll modifies
AB  - the internal cytosine in the recognition sequence 3'-CTTCT-5', yielding
AB  - N-4-methylcytosine, and moreover is able to methylate single-stranded
AB  - DNA. The protein exists in solution as a monomer of molecular mass 30
AB  - 000 +/- 1000 Da under denaturing conditions, Divalent cations (Ca2+,
AB  - Mg2+, Mn2+, and Zn2+) inhibit M2.Mboll methylation activity. It was
AB  - found that the isomethylomer M2.Ncul from Neisseria cuniculi ATCC 14688
AB  - behaves in the same manner. Functional analysis showed that the
AB  - complete Mboll R-M system, consisting of two methyltransferases genes
AB  - and the mbollR gene, is the most stable and the least harmful to
AB  - bacterial cells.
ER  -

TY  - JOUR
AU  - Furmanek-Blaszk, B.
AU  - Sektas, M.
TI  - The SfaNI restriction-modification system from Enterococcus faecalis NEB215 is located on a putative mobile genetic element.
JO  - FEMS Microbiol. Lett.
PY  - 2015
SP  - fnv028
EP  - fnv028
VL  - 362
AB  - A type IIS restriction-modification (R-M) system SfaNI from Enterococcus faecalis NEB215 has
AB  - been characterized. The sfaNIM gene was cloned by the methylase
AB  - selection method. Methyltransferase SfaNI, a protein of 695 amino acids, consists
AB  - of two domains responsible for different DNA-strand recognition and modification,
AB  - and a putative DNA-binding HTH domain located in the N-terminal part of the
AB  - protein. The sfaNIR gene, located adjacent to the gene of the cognate
AB  - modification methyltransferases, encodes a protein of 648 amino acids. The enzyme
AB  - has been purified to apparent homogeneity and its biochemical characteristics
AB  - have been described. The R-M system SfaNI is flanked by a transposase gene at its
AB  - 5(') end, and a cassette chromosome recombinase (ccr) gene complex, encoding
AB  - serine recombinases CcrA and CcrB, at the 3(') end. Both proteins are
AB  - specifically involved in genome rearrangement and are widely distributed among
AB  - staphylococcal species. These results suggested that the R-M system SfaNI is
AB  - present on the putative mobile element.
ER  -

TY  - JOUR
AU  - Fursova, K.K.
AU  - Artem'eva, O.A.
AU  - Nikanova, D.A.
AU  - Larin, A.K.
AU  - Zinovieva, N.A.
AU  - Brovko, F.A.
TI  - Draft Genome Sequences of Five Staphylococcus aureus Strains Isolated from Clinically Healthy Cows in the Russian Federation.
JO  - Genome Announcements
PY  - 2018
SP  - e00275
EP  - e00218
VL  - 6
AB  - We present here the draft genome sequences of five Staphylococcus aureus strains  isolated
AB  - from milk samples from clinically healthy cows in the Russian
AB  - Federation. Four of them were determined to be sequence type 97 (ST-97), and one
AB  - was determined to be ST-22. All the strains are characterized by their genome
AB  - possessing genes that code for enterotoxins and cytotoxins.
ER  -

TY  - JOUR
AU  - Furuta, Y.
TI  - [Diversity in genome and epigenome of Helicobacter pylori].
JO  - Nihon Saikingaku Zasshi
PY  - 2015
SP  - 383
EP  - 389
VL  - 70
AB  - Helicobacter pylori infects human stomach and cause various gastric diseases including gastric
AB  - cancer. The species is also known for rapid evolution and wide
AB  - geographical diversity of genome sequence. Our team sequenced whole genome
AB  - sequences of H. pylori strains isolated from Japanese patients and compared with
AB  - whole genome sequences of H. pylori strains with other geographic origin and
AB  - found that not only the gene repertoire but also genome structures and epigenetic
AB  - modifications such as DNA methylations had large diversity with various
AB  - mechanisms. Genome inversion events were geography specific and some of them were
AB  - found to occur with gene duplication at their termini. DNA methylation states of
AB  - H. pylori genomes suggested that they are diversified by both existence/absence
AB  - repertoire of methyltransferase genes and by the movement of target recognition
AB  - domain in the methyltransferase genes. Omics analysis revealed that methylation
AB  - target sequence and transcriptome status are actually diversified by the domain
AB  - sequence movement. We suggested that H. pylori utilizes these genome structure
AB  - and methylome diversity for its adaptive evolution.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Abe, K.
AU  - Kobayashi, I.
TI  - Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 2428
EP  - 2443
VL  - 38
AB  - The mobility of restriction-modification (RM) gene complexes and their association with genome
AB  - rearrangements is a subject of active
AB  - investigation. Here we conducted systematic genome comparisons and genome
AB  - context analysis on fully sequenced prokaryotic genomes to detect
AB  - RM-linked genome rearrangements. RM genes were frequently found to be
AB  - linked to mobility-related genes such as integrase and transposase
AB  - homologs. They were flanked by direct and inverted repeats at a
AB  - significantly high frequency. Insertion by long target duplication was
AB  - observed for I, II, III and IV restriction types. We found several RM
AB  - genes flanked by long inverted repeats, some of which had apparently
AB  - inserted into a genome with a short target duplication. In some cases,
AB  - only a portion of an apparently complete RM system was flanked by inverted
AB  - repeats. We also found a unit composed of RM genes and an integrase
AB  - homolog that integrated into a tRNA gene. An allelic substitution of a
AB  - Type III system with a linked Type I and IV system pair, and allelic
AB  - diversity in the putative target recognition domain of Type IIG systems
AB  - were observed. This study revealed the possible mobility of all types of
AB  - RM systems, and the diversity in their mobility-related organization.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Abe, K.
AU  - Kobayashi, I.
TI  - Search for genomic rearrangements related to restriction-modification systems through genome comparison.
JO  - Genes Genet. Syst.
PY  - 2009
SP  - 441
EP  - 441
VL  - 84
AB  - We are proposing that restriction-modification systems are mobile element and the data which
AB  - supports the hypothesis is accumulating.  For example, Type II restriction modification
AB  - inserted in genome with long target duplication was found by the intra-genomic comparison
AB  - analysis of Helicobacter pylori. First, we searched for more genome rearrangements related to
AB  - restriction-modification systems by comprehensive bacterial intra-genomic comparison analysis
AB  - and found the examples of (i) insertion with long target duplication of another type of
AB  - restriction-modification systems, (ii) alleles consisted of different types of
AB  - restriction-modification systems and (iii) alleles which have diversity in recognition
AB  - domains. Next, we searched for the restriction-modification systems which are flanked by
AB  - repeat sequences and found that restriction-modifiction systems are flanked by repeats much
AB  - frequently than other genes significantly.  By the genome comparison analysis of those repeats
AB  - flanked restriction-modification systems, we found that the transposon like structure of
AB  - restriction-modification, which was flanked by long inverted repeats, was inserted with short
AB  - direct repeats in the genome.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Kawai, M.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Domain Movement within a Gene: A Novel Evolutionary Mechanism for Protein Diversification.
JO  - PLoS ONE
PY  - 2011
SP  - e18819
EP  - e18819
VL  - 6
AB  - A protein function is carried out by a specific domain localized at a specific position. In
AB  - the present study, we report that, within a gene, a
AB  - specific amino acid sequence can move between a certain position and
AB  - another position. This was discovered when the sequences of
AB  - restriction-modification systems within the bacterial species Helicobacter
AB  - pylori were compared. In the specificity subunit of Type I
AB  - restriction-modification systems, DNA sequence recognition is mediated by
AB  - target recognition domain 1 (TRD1) and TRD2. To our surprise, several
AB  - sequences are shared by TRD1 and TRD2 of genes (alleles) at the same locus
AB  - (chromosomal location); these domains appear to have moved between the two
AB  - positions. The gene/protein organization can be represented as
AB  - x-(TRD1)-y-x-(TRD2)-y, where x and y represent repeat sequences. Movement
AB  - probably occurs by recombination at these flanking DNA repeats. In
AB  - accordance with this hypothesis, recombination at these repeats also
AB  - appears to decrease two TRDs into one TRD or increase these two TRDs to
AB  - three TRDs (TRD1-TRD2-TRD2) and to allow TRD movement between genes even
AB  - at different loci. Similar movement of domains between TRD1 and TRD2 was
AB  - observed for the specificity subunit of a Type IIG restriction enzyme.
AB  - Similar movement of domain between TRD1 and TRD2 was observed for Type I
AB  - restriction-modification enzyme specificity genes in two more eubacterial
AB  - species, Streptococcus pyogenes and Mycoplasma agalactiae. Lateral domain
AB  - movements within a protein, which we have designated DOMO (domain
AB  - movement), represent novel routes for the diversification of proteins.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Kobayashi, I.
TI  - Restriction-modification systems as mobile epigenetic elements.
JO  - Bacterial Integrative Mobile Genetic Elements
PY  - 2011
SP  - 85
EP  - 103
AB  - Transfer of mobile genetic elements between prokaryotes is limited by restriction-modification
AB  - systems.  Restriction-modification systems consist of a modification enzyme that
AB  - epigenetically methylates a specific DNA sequence, and a restriction endonuclease (restriction
AB  - enzyme) that cuts DNA lacking this epigenetic mark.  These elements were discovered because
AB  - they attack mobile genetic elements.  However, recent studies have revealed that they are
AB  - themselves mobile.  In some cases, the mobility of restriction-modification systems is through
AB  - symbiosis with other forms of mobile elements.  In other cases, movement is unlinked to other
AB  - mobile elements.  The systems may insert into the genome with long and variable target
AB  - duplication, or into the intergenic region of an operon.  Insertion of
AB  - restriction-modification systems induces other genome rearrangements such as amplification and
AB  - inversion.  Even a domain within a protein can be the unit of mobility: some
AB  - restriction-modification system subunits that recognize a target DNA sequence contain mobile
AB  - amino acid sequences that can apparently move between different domains of a protein through
AB  - recombination of DNA sequences encoding them.  This mobility extends the biological
AB  - significance of restriction-modification systems beyond defense: the systems define, and
AB  - sometimes even force, epigenetic order on a genome.  The multilevel conflicts involving these
AB  - mobile epigenetic elements may drive prokaryotic evolution.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Kobayashi, I.
TI  - Movement of DNA sequence recognition domains between non-orthologous proteins.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 9218
EP  - 9232
VL  - 40
AB  - Comparisons of proteins show that they evolve through the movement of domains. However, in
AB  - many cases, the underlying mechanisms remain
AB  - unclear. Here, we observed the movements of DNA recognition domains
AB  - between non-orthologous proteins within a prokaryote genome.
AB  - Restriction-modification (RM) systems, consisting of a
AB  - sequence-specific DNA methyltransferase and a restriction enzyme,
AB  - contribute to maintenance/evolution of genomes/epigenomes. RM systems
AB  - limit horizontal gene transfer but are themselves mobile. We compared
AB  - Type III RM systems in Helicobacter pylori genomes and found that
AB  - target recognition domain (TRD) sequences are mobile, moving between
AB  - different orthologous groups that occupy unique chromosomal locations.
AB  - Sequence comparisons suggested that a likely underlying mechanism is
AB  - movement through homologous recombination of similar DNA sequences that
AB  - encode amino acid sequence motifs that are conserved among Type III DNA
AB  - methyltransferases. Consistent with this movement, incongruence was
AB  - observed between the phylogenetic trees of TRD regions and other
AB  - regions in proteins. Horizontal acquisition of diverse TRD sequences
AB  - was suggested by detection of homologs in other Helicobacter species
AB  - and distantly related bacterial species. One of these RM systems in H.
AB  - pylori was inactivated by insertion of another RM system that likely
AB  - transferred from an oral bacterium. TRD movement represents a novel
AB  - route for diversification of DNA-interacting proteins.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Kobayashi, I.
TI  - Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution.
JO  - Mobile Genet. Elements
PY  - 2012
SP  - 292
EP  - 296
VL  - 2
AB  - DNA methylation is one of the best studied epigenetic modifications observed in prokaryotes as
AB  - well as eukaryotes. It affects nearby gene expression. Most DNA
AB  - methylation reactions in prokaryotes are catalyzed by a DNA methyltransferase,
AB  - the modification enzyme of a restriction-modification (RM) system. Its target
AB  - recognition domain (TRD) recognizes a specific DNA sequence for methylation. In
AB  - this commentary, we review recent evidence for movement of TRDs between
AB  - non-orthologous genes and movement within a gene. These movements are likely
AB  - mediated by DNA recombination machinery, and are expected to alter the
AB  - methylation status of a genome. Such alterations potentially lead to changes in
AB  - global gene expression pattern and various phenotypes. The targets of natural
AB  - selection in adaptive evolution might be these diverse methylomes rather than
AB  - diverse genome sequences, the target according to the current paradigm in
AB  - biology. This 'epigenetics-driven adaptive evolution' hypothesis can explain
AB  - several observations in the evolution of prokaryotes and eukaryotes.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Konno, M.
AU  - Osaki, T.
AU  - Yonezawa, H.
AU  - Ishige, T.
AU  - Imai, M.
AU  - Shiwa, Y.
AU  - Shibata-Hatta, M.
AU  - Kanesaki, Y.
AU  - Yoshikawa, H.
AU  - Kamiya, S.
AU  - Kobayashi, I.
TI  - Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection.
JO  - PLoS ONE
PY  - 2015
SP  - e0127197
EP  - e0127197
VL  - 10
AB  - Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis,
AB  - ulcers and cancer, is known to have a high degree of genome/epigenome
AB  - diversity as the result of mutation and recombination. The bacteria often infect
AB  - in childhood and persist for the life of the host. One of the reasons of the
AB  - rapid evolution of H. pylori is that it changes its genome drastically for
AB  - adaptation to a new host. To investigate microevolution and adaptation of the H.
AB  - pylori genome, we undertook whole genome sequencing of the same or very similar
AB  - sequence type in multi-locus sequence typing (MLST) with seven genes in members
AB  - of the same family consisting of parents and children in Japan. Detection of
AB  - nucleotide substitutions revealed likely transmission pathways involving
AB  - children. Nonsynonymous (amino acid changing) mutations were found in
AB  - virulence-related genes (cag genes, vacA, hcpDX, tnfalpha, ggt, htrA and the
AB  - collagenase gene), outer membrane protein (OMP) genes and other cell
AB  - surface-related protein genes, signal transduction genes and
AB  - restriction-modification genes. We reconstructed various pathways by which H.
AB  - pylori can adapt to a new human host, and our results raised the possibility that
AB  - the mutational changes in virulence-related genes have a role in adaptation to a
AB  - child host. Changes in restriction-modification genes might remodel the methylome
AB  - and transcriptome to help adaptation. This study has provided insights into H.
AB  - pylori transmission and virulence and has implications for basic research as well
AB  - as clinical practice.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Namba, H.
AU  - Shibata, T.
AU  - Nishiyama, T.
AU  - Shigenobu, S.
AU  - Suzuki, Y.
AU  - Sugano, S.
AU  - Hasebe, M.
AU  - Kobayashi, I.
TI  - Methylome diversification through changes in the sequence specificity of DNA methyltransferases.
JO  - Genes Genet. Syst.
PY  - 2013
SP  - 347
EP  - 347
VL  - 88
AB  - Helicobacter pylori, a human gastric pathogen, have a large number of DNA methyltransferase
AB  - genes with each strain carrying a unique repertoire.  Previous genome comparison works
AB  - suggested that these methyltransferases often change DNA sequence specificity through movement
AB  - of amino-acid sequences in the target recognition domains between genes and within a gene
AB  - (Domain Movement).  By Single-Molecule Real-Time sequencing technology, we detected methylated
AB  - DNA sites throughout several closely related genomes.  We successfully deduced DNA sequence
AB  - motifs for methylation and assigned each of them to a specific amino-acid sequence group of
AB  - target recognition domains in the specificity determinant genes.  Overall, the methylome
AB  - turned out to be quite variable among the closely-related strains, although there are
AB  - hypermethylated loci in all the strains.  As expected from their effects on gene expression,
AB  - knockout of a specificity gene led to changes in the transcriptome.  These results provide
AB  - evidence for proposed mechanisms of sequence-specificity changes in the DNA methyltransferases
AB  - and lend support to the concept of epigenetics-driven adaptive evolution.
ER  -

TY  - JOUR
AU  - Furuta, Y.
AU  - Namba-Fukuyo, H.
AU  - Shibata, T.F.
AU  - Nishiyama, T.
AU  - Shigenobu, S.
AU  - Suzuki, Y.
AU  - Sugano, S.
AU  - Hasebe, M.
AU  - Kobayashi, I.
TI  - Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity.
JO  - PLoS Genet.
PY  - 2014
SP  - e1004272
EP  - e1004272
VL  - 10
AB  - Epigenetic modifications such as DNA methylation have large effects on gene expression and
AB  - genome maintenance. Helicobacter pylori, a human gastric pathogen,
AB  - has a large number of DNA methyltransferase genes, with different strains having
AB  - unique repertoires. Previous genome comparisons suggested that these
AB  - methyltransferases often change DNA sequence specificity through domain
AB  - movement-the movement between and within genes of coding sequences of target
AB  - recognition domains. Using single-molecule real-time sequencing technology, which
AB  - detects N6-methyladenines and N4-methylcytosines with single-base resolution, we
AB  - studied methylated DNA sites throughout the H. pylori genome for several closely
AB  - related strains. Overall, the methylome was highly variable among closely related
AB  - strains. Hypermethylated regions were found, for example, in rpoB gene for RNA
AB  - polymerase. We identified DNA sequence motifs for methylation and then assigned
AB  - each of them to a specific homology group of the target recognition domains in
AB  - the specificity-determining genes for Type I and other restriction-modification
AB  - systems. These results supported proposed mechanisms for sequence-specificity
AB  - changes in DNA methyltransferases. Knocking out one of the Type I specificity
AB  - genes led to transcriptome changes, which suggested its role in gene expression.
AB  - These results are consistent with the concept of evolution driven by DNA
AB  - methylation, in which changes in the methylome lead to changes in the
AB  - transcriptome and potentially to changes in phenotype, providing targets for
AB  - natural or artificial selection.
ER  -

TY  - JOUR
AU  - Futterer, O.
AU  - Angelov, A.
AU  - Liesegang, H.
AU  - Gottschalk, G.
AU  - Schleper, C.
AU  - Schepers, B.
AU  - Dock, C.
AU  - Antranikian, G.
AU  - Liebl, W.
TI  - Genome sequence of Picrophilus torridus and its implications for life around pH 0.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 9091
EP  - 9096
VL  - 101
AB  - The euryarchaea Picrophilus torridus and Picrophilus oshimae are able to grow around pH 0 at
AB  - up to 65 C, thus they represent the most thermoacidophilic organisms known. Several features
AB  - that may contribute to the thermoacidophilic survival strategy of P. torridus were deduced
AB  - from analysis of its 1.55-megabase genome. P. torridus has the smallest genome among
AB  - nonparasitic aerobic microorganisms growing on organic substrates and simultaneously the
AB  - highest coding density among thermoacidophiles. An exceptionally high ratio of secondary over
AB  - ATP-consuming primary transport systems demonstrates that the high proton concentration in the
AB  - surrounding medium is extensively used for transport processes. Certain genes that may be
AB  - particularly supportive for the extreme lifestyle of P. torridus appear to have been
AB  - internalized into the genome of the Picrophilus lineage by horizontal gene transfer from
AB  - crenarchaea and bacteria. Finally, it is noteworthy that the thermoacidophiles from
AB  - phylogenetically distant branches of the Archaea apparently share an unexpectedly large pool
AB  - of genes.
ER  -

TY  - JOUR
AU  - Fuxreiter, M.
AU  - Osman, R.
TI  - Probing the general base catalysis in the first step of BamHI action by computer simulations.
JO  - Biochemistry
PY  - 2001
SP  - 15017
EP  - 15023
VL  - 40
AB  - BamHI is a type II restriction endonuclease that catalyzes the scission of the phoshodiester
AB  - bond in the GAGTCC cognate sequence in the presence of two divalent metal ions. The first step
AB  - of the reaction is the preparation of water for nucleophilic attack by Glu-113, which has been
AB  - proposed to abstract the proton from the attacking water molecule. Alternatively, the
AB  - 3'-phosphate group to the susceptible phosphodiester bond has been suggested to play a role
AB  - as the general base. The two hypotheses have been tested by computer simulations using the
AB  - semiempirical protein dipoles Langevin dipoles (PDLD/S) method. Deprotonation of water by
AB  - Glu-113 has been found to be less favorable by 5.7 kcal/mol than metal-catalyzed deprotonation
AB  - with a concomitant proton transfer to bulk solvent. The preparation of the nucleophile by the
AB  - 3'-phosphate group is less favorable by 12.3 kcal/mol. These results suggest that both the
AB  - general base and the substrate-assisted mechanisms in the first step of BamHI action are less
AB  - likely than the metal-catalyzed reaction. The metal ions in the active site of BamHI make the
AB  - largest contributions to the reduction of the free energy of hydroxide ion formation. On the
AB  - basis of these findings we propose that the first step of endonuclease catalysis does not
AB  - require a general base; rather, the essential attacking nucleophile in BamHI catalytic action
AB  - is stabilized by the metal ions.
ER  -

TY  - JOUR
AU  - Fuxreiter, M.
AU  - Osman, R.
AU  - Simon, I.
TI  - Computational approaches to restriction endonucleases.
JO  - Theochem.
PY  - 2003
SP  - 469
EP  - 479
VL  - 666-7
AB  - Type II restriction endonucleases catalyze phosphodiester bond hydrolysis in bacteria to
AB  - protect the host cell from invading phage DNA.  Due to their exquisite sequence selectivity
AB  - type II restriction endonucleases serve as excellent model systems for studying protein -
AB  - nucleic acid interactions.  Crystal structures of the PD-(D/E)XK superfamily revealed a common
AB  - a/b core motif and similar active site.  In contrast, these enzymes show little sequence
AB  - similarity and use different strategies to interact with their substrate DNA.  Computational
AB  - approaches have been applied to unify the mechanism of restriction endonucleases and
AB  - rationalize their diversity.  The first step of type II restriction endonuclease catalysis has
AB  - been studied on BamHI by semi-microscopic version of the Protein Dipoles Langevin Dipoles
AB  - method.  The substrate-assisted catalysis and the general base mechanism have been concluded
AB  - as less likely than the metal-catalyzed reaction.  A general model for catalysis has been
AB  - proposed based on the group contributions to the reduction of the activation free energy.
AB  - Factors contributing to structural stability of PD-(D/E)XK type II restriction endonucleases
AB  - have been analyzed to elucidate evolutionary relationship between these enzymes.  Residues
AB  - playing role in catalysis and recognition were highly correlated with those participating in
AB  - stabilization centers.  Thus the main functional motifs were concluded to be evolutionary more
AB  - conserved than other parts of the structure.  This observation is consistent with the proposal
AB  - that these enzymes have developed from a common ancestor with divergent evolution.
ER  -

TY  - JOUR
AU  - Fuxreiter, M.
AU  - Simon, I.
TI  - Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
JO  - Protein Sci.
PY  - 2002
SP  - 1978
EP  - 1983
VL  - 11
AB  - Type II restriction endonucleases recognize 4-8 base-pair-long DNA sequences and catalyze
AB  - their cleavage with remarkable specificity.
AB  - Crystal structures of the PD-(DE)XK superfamily revealed a common
AB  - alpha/beta core motif and similar active site. In contrast, these
AB  - enzymes show little sequence similarity and use different strategies to
AB  - interact with their substrate DNA. The intriguing question is whether
AB  - this enzyme family could have evolved from a common origin. In our
AB  - present work, protein structure stability elements were analyzed and
AB  - compared in three parts of PD-(DE)XK type II restriction endonucleases:
AB  - (1) core motif, (2) active-site residues, and (3) residues playing role
AB  - in DNA recognition. High correlation was found between the active-site
AB  - residues and those stabilization factors that contribute to preventing
AB  - structural decay. DNA recognition sites were also observed to
AB  - participate in stabilization centers. It indicates that recognition
AB  - motifs and active sites in PD-(DE)XK type II restriction endonucleases
AB  - should have been evolutionary more conserved than other parts of the
AB  - structure. Based on this observation it is proposed that PD-(DE)XK type
AB  - II restriction endonucleases have developed from a common ancestor with
AB  - divergent evolution.
ER  -

TY  - JOUR
AU  - Gaba, S.
AU  - Singh, R.N.
AU  - Abrol, S.
AU  - Yadav, A.N.
AU  - Saxena, A.K.
AU  - Kaushik, R.
TI  - Draft Genome Sequence of Halolamina pelagica CDK2 Isolated from Natural Salterns  from Rann of Kutch, Gujarat, India.
JO  - Genome Announcements
PY  - 2017
SP  - e01593
EP  - e01516
VL  - 5
AB  - Halolamina pelagica strain CDK2, a halophilic archaeon (growth range 1.36 to 5.12 M NaCl), was
AB  - isolated from rhizosphere of wild grasses of hypersaline soil of the
AB  - Rann of Kutch, Gujarat, India. Its draft genome contains 2,972,542 bp and 3,485
AB  - coding sequences, depicting genes for halophilic serine proteases and trehalose
AB  - synthesis.
ER  -

TY  - JOUR
AU  - Gabbara, S.
AU  - Bhagwat, A.S.
TI  - The mechanism of inhibition of DNA (cytosine-5-)-methyltransferases by 5-azacytosine is likely to involve methyl transfer to the inhibitor.
JO  - Biochem. J.
PY  - 1995
SP  - 87
EP  - 92
VL  - 307
AB  - The mechanism of inhibition of DNA (cytosine-5-)-methyltransferases by the mechanism-based
AB  - inhibitor 5-azacytosine has remained unclear, mainly because of the unavailability of a
AB  - substrate in which the inhibitor, but not normal cytosine, is present at the target site. We
AB  - synthesized an oligonucleotide duplex containing a single target site for the EcoRII
AB  - methyltransferase, in which the target base is 5-azacytosine. This substrate formed a stable
AB  - covalent complex with EcoRII methyltransferase in the absence and in the presence of the
AB  - cofactor S-adenosylmethionine. The complex formed in the presence of the cofactor was
AB  - resistant to SDS and moderate heat treatment, and a methyl group was incorporated into the
AB  - complex. Enzyme titration and kinetic studies of inhibition suggest that methyl transfer to
AB  - the complex occurred only during the first turnover of the reaction. These results suggest
AB  - that, when the enzyme binds to 5-azacytosine in the presence of the cofactor, a methyl group
AB  - is transferred to the N-5 position of the base, resulting in the inactivation of the enzyme.
ER  -

TY  - JOUR
AU  - Gabbara, S.
AU  - Bhagwat, A.S.
TI  - Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites.
JO  - J. Biol. Chem.
PY  - 1992
SP  - 18623
EP  - 18630
VL  - 267
AB  - EcoRII is unusual among type II restriction enzymes in that, while it cleaves substrates such
AB  - as pBR322 and bacteriophage lambda that contain several recognition sites for the enzyme
AB  - efficiently, substrates such as the genomes of bacteriophages T3 and T7 which contain a small
AB  - number of recognition sites are cut poorly by it. Interestingly, pBR322, or a short DNA duplex
AB  - containing a single site for the enzyme, can activate the enzyme to cleave resistant
AB  - substrates. We show here that at low concentrations, activator short duplexes are themselves
AB  - cleaved poorly by the enzyme. Further, the reaction shows substrate cooperativity, and at high
AB  - concentration, the duplexes are both activators and good substrates for the enzyme. This
AB  - supports the model that the activation of EcoRII involves binding of more than one DNA
AB  - molecule and provides a simple system to study the mechanism of activation. Using a gel
AB  - mobility shift assay, we show that the enzyme forms sequence-specific, methylation-sensitive
AB  - complexes with the duplexes in the absence of activating DNA. Therefore, resistance of the
AB  - short duplexes to the enzyme at low concentrations cannot be due to an inability of the enzyme
AB  - to bind the duplexes. Interestingly, these complexes are stable in the presence of Mg2+, the
AB  - cofactor for the enzyme, and the complexes obtained in the presence of Mg2+ do not contain DNA
AB  - that is cleaved by the enzyme. The inefficient step in the action of EcoRII on resistant
AB  - substrates must occur subsequent to initial substrate binding and it is this step that the
AB  - activating DNA must regulate.
ER  -

TY  - JOUR
AU  - Gabbara, S.
AU  - Sheluho, D.
AU  - Bhagwat, A.S.
TI  - Cytosine methyltransferase from Escherichia coli in which active site cysteine is replaced with serine is partially active.
JO  - Biochemistry
PY  - 1995
SP  - 8914
EP  - 8923
VL  - 34
AB  - EcoRII methyltransferase (M.EcoRII) catalyzes the transfer of methyl groups from
AB  - S-adenosyl-L-methionine (SAM) to C-5 position of second cytosine in the DNA sequence
AB  - 5'-CCWGG (W=A or T).  The reaction is initiated by a nucleophilic attack of the C-6 target
AB  - cytosine
AB  - by a cysteine that is conserved among all cytosine methyltransferases.  We have replaced this
AB  - cysteine in M.EcoRII with serine or alanine and purified the proteins to homogeneity.  The
AB  - catalytic
AB  - efficiency (Kcat/Km) of the mutant enzyme with serine (C186S) for methyl transfer is about
AB  - 10,000 times less than that of WT but is substantially higher than the efficiency of the C186A
AB  - mutant.  We show that the WT enzyme and C186S mutant are proficient in exchange of proton at
AB  - C-5 and that this activity is reduced in the mutant to the same extent as the methyl transfer
AB  - activity.
AB  - The C186S mutant is insensitive to a cysteine-specific inhibitor, and it transfers methyl
AB  - groups to
AB  - the same position of cytosine as the WT enzyme.  The ability of serine to act as a nucleophile
AB  - in the
AB  - enzyme reaction suggests that it - and probably the cysteine in the WT enzyme - is activated
AB  - by a
AB  - nearby base.  Like the WT enzyme, C186S forms stable SDS-resistant complexes with DNA
AB  - containing 5-azacytosine; but unlike the WT enzyme, the mutant reacts faster with
AB  - 5-azacytosine
AB  - than with normal cytosine.  Apparently, greater reactivity of 5-azacytosine assists the C186S
AB  - mutant in catalysis.
ER  -

TY  - JOUR
AU  - Gabbara, S.
AU  - Wyszynski, M.
AU  - Bhagwat, A.S.
TI  - A DNA repair process in Escherichia coli corrects U:G and T:G mismatches to C:G at sites of cytosine methylation.
JO  - Mol. Gen. Genet.
PY  - 1994
SP  - 244
EP  - 248
VL  - 243
AB  - Escherichia coli contains a base mismatch correction system called VSP repair that is known to
AB  - correct T:G mismatches to C:G when they occur in certain sequence contexts. The preferred
AB  - sequence context for this process is the site for methylation by the E. coli DNA cytosine
AB  - methylase (Dcm). For this reason, VSP repair is thought to counteract potential mutagenic
AB  - effects of deamination of 5-methylcytosine to thymine. We have developed a genetic reversion
AB  - assay that quantitates the frequency of C to T mutations at Dcm sites and the removal of such
AB  - mutations by DNA repair processes. Using this assay, we have studied the repair of U:G
AB  - mismatches in DNA to C:G and have found that VSP repair is capable of correcting these
AB  - mismatches. Although VSP repair substantially affects the reversion frequency, it may not be
AB  - as efficient at correcting U:G mismatches as the uracil DNA glycosylase-mediated repair
AB  - process.
ER  -

TY  - JOUR
AU  - Gabbara, S.S.
TI  - Molecular mechanism and mutagenic effects of DNA 5-cytosine methyltransferases.
JO  - Diss. Abstr.
PY  - 1994
SP  - 403B
EP  - 404B
VL  - 55
AB  - DNA (C-S)cytosine methyltransferases (C5 methylases) catalyze the transfer of methyl group to
AB  - position 5 of cytosine in DNA. This type of modification occurs in most organisms, from
AB  - bacteria to humans. In prokaryotes C5 methylases function primarily in protecting the cell
AB  - from viral invasions. In eukaryotes C5 methylases play important roles in the regulation of
AB  - gene expression. All known cytosine methylases, including the mouse and the human methylases,
AB  - share a strong sequence conservation, suggesting a common reaction mechanism. I used the
AB  - Escherichia coli EcoRII methylase in this study as a model enzyme to understand the mechanism
AB  - and function of all cytosine methylases. The reaction catalyzed by the methylase is proposed
AB  - to occur in a Michael fashion. My data using cytosine analogs support this mechanism.
AB  - Furthermore, I show that a cysteine conserved among all cytosine methylases is required for
AB  - catalysis. This role is likely to be in the nucleophilic attack at carbon 6 of cytosine, a
AB  - first step in the reaction. In support of this role substitution of the conserved cysteine by
AB  - serine or alanine reduces kcat of methyl transferase activity by 4 and 6 orders of magnitude,
AB  - respectively, but does not appreciably affect Km. While studying the properties of the mutants
AB  - with serine and alanine changes, I found that the hydroxyl group of the serine, replacing the
AB  - conserved cysteine, can covalently link to DNA. Sites of cytosine methylation are hot-spots
AB  - for cytosine (C) to thymine (T) mutations. In humans such mutations are found to be the cause
AB  - of genetic diseases and cancer. Using a genetic system based on the reversion of a mutation in
AB  - a kanamycin-resistance gene, I show that EcoRII methylase can cause cytosine to uracil (U)
AB  - deaminations at a site of cytosine methylation, and that the uracil formed can propagate in
AB  - vivo to cause C:G to T:A transition mutations. Thus the enzyme-mediated C to U deamination is
AB  - one pathway by which cytosine methylases cause C to T mutations. The contribution of the C to
AB  - U to T pathway in C to T mutagenesis was assessed by analyzing the barriers to its occurrence.
ER  -

TY  - JOUR
AU  - Gabed, N.
AU  - Yang, M.
AU  - Bey, B.H.M.
AU  - Drici, H.
AU  - Gross, R.
AU  - Dandekar, T.
AU  - Liang, C.
TI  - Draft Genome Sequence of the Moderately Heat-Tolerant Lactococcus lactis subsp. lactis bv. diacetylactis Strain GL2 from Algerian Dromedary Milk.
JO  - Genome Announcements
PY  - 2015
SP  - e01334
EP  - e01315
VL  - 3
AB  - Lactococcus lactis subsp. lactis bv. diacetylactis GL2 is a moderately thermotolerant lactic
AB  - acid bacterium isolated from dromedary raw milk. Here, we
AB  - present the draft genome sequence of this potential new dairy starter strain,
AB  - which combines thermotolerance and the capacity to metabolize lactose, casein,
AB  - and citrate.
ER  -

TY  - JOUR
AU  - Gaboyer, F.
AU  - Maignien, L.
AU  - Jebbar, M.
AU  - Alain, K.
TI  - Draft Genome of Halomonas lionensis RHS90T, a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments.
JO  - Genome Announcements
PY  - 2017
SP  - e00311
EP  - e00317
VL  - 5
AB  - Members of the genus Halomonas are physiologically versatile and harbor ecological adaptations
AB  - enabling the colonization of contrasted environments. We
AB  - present here the draft genome of Halomonas lionensis RHS90T, isolated from
AB  - Mediterranean Sea sediments. Numerous genes related to stress tolerance, DNA
AB  - repair, or external signal-sensing systems were predicted, which could represent
AB  - selective advantages of this marine bacterium.
ER  -

TY  - JOUR
AU  - Gaboyer, F.
AU  - Maignien, L.
AU  - Jebbar, M.
AU  - Alain, K.
TI  - Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments.
JO  - Genome Announcements
PY  - 2017
SP  - e00312
EP  - e00317
VL  - 5
AB  - Phaeobacter leonis strain 306T is an alphaproteobacterium isolated from Mediterranean Sea
AB  - sediments. It belongs to the genus Phaeobacter, which was
AB  - recently proposed and is still poorly characterized. In an effort to better
AB  - understand the fundamental aspects of the microbiology of this genus, we present
AB  - here the 4.82-Mb draft genome sequence of Phaeobacter leonis strain 306T.
ER  -

TY  - JOUR
AU  - Gabrielsen, C.
AU  - Brede, D.A.
AU  - Hernandez, P.E.
AU  - Nes, I.F.
AU  - Diep, D.B.
TI  - Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6976
EP  - 6977
VL  - 194
AB  - This work describes the draft genome sequence of Lactococcus garvieae DCC43. The  2.2-Mb draft
AB  - genome contains 2,227 predicted protein-coding genes, among which is
AB  - a region encoding the bacteriocin garvicin ML. No antibiotic resistance genes or
AB  - capsule-related virulence genes were identified. Two plasmid replication regions
AB  - indicate that this strain likely contains plasmids. Comparative genomics suggests
AB  - that this strain displays a high degree of sequence variation from the previously
AB  - sequenced L. garvieae strains.
ER  -

TY  - JOUR
AU  - Gabrielsen, C.
AU  - Drablos, F.
AU  - Afset, J.E.
TI  - Genome Sequences of 11 Shiga Toxin-Producing Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e00418
EP  - e00415
VL  - 3
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are a common cause of both  sporadic
AB  - infection and outbreaks of enteric disease in humans. Here, we present
AB  - draft genome sequences of 11 STEC strains of different serotypes (O145, O121,
AB  - O26, O177, and O-type unknown), that have been isolated from patients with
AB  - enteric disease of various degrees of severity, in the years 2001 to 2014 at St.
AB  - Olavs Hospital in Trondheim, Norway.
ER  -

TY  - JOUR
AU  - Gabris, C.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of Enterococcus faecalis Strain CG_E.
JO  - Genome Announcements
PY  - 2017
SP  - e01488
EP  - e01416
VL  - 5
AB  - Enterococcus faecalis CG_E is a Gram-positive, lactic acid-producing coccus. The  draft genome
AB  - of E. faecalis strain CG_E comprises 2,969,881 bp and exhibits a G+C
AB  - content of 37.34%. The genome encodes 2,848 predicted protein-encoding and 97 RNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Gabris, C.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of Lactobacillus sunkii Strain CG_D.
JO  - Genome Announcements
PY  - 2017
SP  - e01487
EP  - e01416
VL  - 5
AB  - Lactobacillus sunkii CG_D is a rod-shaped, Gram-positive, and heterofermentative  lactic acid
AB  - bacterium. The draft genome of L. sunkii strain CG_D comprises
AB  - 2,794,637 bp with an average G+C content of 42.03%. The genome harbors 2,662
AB  - predicted protein-encoding, and 71 RNA genes.
ER  -

TY  - JOUR
AU  - Gabs, S.
AU  - Josephsen, J.
TI  - Improvement of phage defence in Lactococcus lactis by introduction of the plasmid encoded restriction and modification system LlaAI.
JO  - Lett. Appl. Microbiol.
PY  - 2003
SP  - 332
EP  - 336
VL  - 36
AB  - AIMS: To study the ability of the plasmid-encoded restriction and modification (R/M) system
AB  - LlaAI to function as a bacteriophage resistance
AB  - mechanism in Lactococcus lactis during milk fermentations. METHODS AND
AB  - RESULTS: Plasmid pAIcat4, carrying the R/M system LlaAI and a
AB  - chloramphenicol resistance cassette, was introduced into the plasmid-free
AB  - strain L. lactis MG1614 and the industrial strain L. lactis 964. By
AB  - measuring changes in conductivity the influence of different phage on the
AB  - growth was determined. CONCLUSIONS: The plasmid-encoded R/M system LlaAI
AB  - significantly improves the bacteriophage resistance of L. lactis during
AB  - milk fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: It is essential
AB  - to determine the potential of a phage defence mechanism in L. lactis
AB  - starter culture strains during growth in milk before steps are taken to
AB  - improve starter cultures. This study shows that LlaAI is useful for
AB  - improvement of starter cultures.
ER  -

TY  - JOUR
AU  - Gabsalilow, L.
AU  - Schierling, B.
AU  - Friedhoff, P.
AU  - Pingoud, A.
AU  - Wende, W.
TI  - Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - e83
EP  - e83
VL  - 41
AB  - Targeted genome engineering requires nucleases that introduce a highly specific double-strand
AB  - break in the genome that is either processed by homology-directed repair in the presence of a
AB  - homologous repair template or by non-homologous end-joining (NHEJ) that usually results in
AB  - insertions or deletions. The error-prone NHEJ can be efficiently suppressed by 'nickases'
AB  - that produce a single-strand break rather than a double-strand break. Highly specific nickases
AB  - have been produced by engineering of homing endonucleases and more recently by modifying zinc
AB  - finger nucleases (ZFNs) composed of a zinc finger array and the catalytic domain of the
AB  - restriction endonuclease FokI. These ZF-nickases work as heterodimers in which one subunit has
AB  - a catalytically inactive FokI domain. We present two different approaches to engineer highly
AB  - specific nickases; both rely on the sequence-specific nicking activity of the DNA mismatch
AB  - repair endonuclease MutH which we fused to a DNA-binding module, either a catalytically
AB  - inactive variant of the homing endonuclease I-SceI or the DNA-binding domain of the TALE
AB  - protein AvrBs4. The fusion proteins nick strand specifically a bipartite recognition sequence
AB  - consisting of the MutH and the I-SceI or TALE recognition sequences, respectively, with a more
AB  - than 1000-fold preference over a stand-alone MutH site. TALE-MutH is a programmable nickase.
ER  -

TY  - JOUR
AU  - Gachechiladze, K.K.
AU  - Balardshishvili, N.S.
AU  - Adamia, R.S.
AU  - Chanishvili, T.G.
AU  - Kruger, D.H.
TI  - Host-controlled modification and restriction as a criterion of evaluating the therapeutical potential of Pseudomonas phage.
JO  - J. Basic Microbiol.
PY  - 1991
SP  - 101
EP  - 106
VL  - 31
AB  - The recently isolated phages Phi ST3 and Phi ST1 were compared as to their
AB  - lysis behaviour in about 100 different P. aeruginosa strains.  The growth of
AB  - Phi ST3 varies greatly in different host strains.  We demonstrated one case of
AB  - non-classical, host-dependent modification and restriction.  Here the
AB  - capability to adsorb, and consequently to reproduce in a given host strain
AB  - differs, depending on which modification the phage acquired in its former host.
AB  - The DNA-containing phage Phi ST1 displays stable lysis properties in the
AB  - majority of the host strains.  This make Phi ST1 a candidate for therapeutic
AB  - phage preparations.  One of the reasons for stable lysis properties is the
AB  - apparent selection against recognition sites of restriction enzymes in its
AB  - genome.
ER  -

TY  - JOUR
AU  - Gado, I.
AU  - Laszlo, V.G.
AU  - Negy, B.
AU  - Milch, H.
AU  - Drin, I.
AU  - Awad-Masalmeh, M.
AU  - Horvath, J.
TI  - Phage restriction and the presence of small plasmids in Salmonella enteritidis.
JO  - Zentralbl. Bakteriol.
PY  - 1998
SP  - 509
EP  - 519
VL  - 287
AB  - Between 1990-1994, a total of 16,505 S. enteritidis strains of human, animal and food origin
AB  - were phage-typed, using the Hungarian scheme and the changes of incidence of the dominant
AB  - phage types were monitored.  The incidence of PT1 (corresponding to Ward's PT1 was very high
AB  - between 1990 and 1992 (67.9071.0% of the total S. enteritidis isolates), later, it decreased.
AB  - The prevalence of PT6 (corresponding to Ward's PT4) was rare until 1992, then it gradually
AB  - increased.  The phage type and plasmid content of 78 Salmonella enteritidis strains were
AB  - determined.  Small plasmids were present in 59% of the isolates, together with a
AB  - serotype-specific (38 MDa) plasmid.  A correlation was found between the presence of the small
AB  - plasmid and phage restriction to two phages used for subdividing the Hungarian phage types 1
AB  - (PT1) and 6 (PT6) of S. enteritidis (corresponding to PT1 and PT4 in Ward's typing scheme,
AB  - respectively).
ER  -

TY  - JOUR
AU  - Gaechter, T.
AU  - Wunderlin, C.
AU  - Schmidheini, T.
AU  - Solioz, M.
TI  - Genome Sequence of Enterococcus hirae (Streptococcus faecalis) ATCC 9790, a Model Organism for the Study of Ion Transport, Bioenergetics, and Copper Homeostasis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5126
EP  - 5127
VL  - 194
AB  - Enterococcus hirae ATCC 9790 is a Gram-positive lactic acid bacterium that has been used in
AB  - basic research for over 4 decades. Here we report the sequence and
AB  - annotation of the 2.8-Mb genome of E. hirae and its endemic 29-kb plasmid
AB  - pTG9790.
ER  -

TY  - JOUR
AU  - Gagnevin, L.
AU  - Bolot, S.
AU  - Gordon, J.L.
AU  - Pruvost, O.
AU  - Verniere, C.
AU  - Robene, I.
AU  - Arlat, M.
AU  - Noel, L.D.
AU  - Carrere, S.
AU  - Jacques, M.A.
AU  - Koebnik, R.
TI  - Draft Genome Sequence of Xanthomonas axonopodis pv. allii Strain CFBP 6369.
JO  - Genome Announcements
PY  - 2014
SP  - e00727
EP  - e00714
VL  - 2
AB  - We report here the draft genome sequence of Xanthomonas axonopodis pv. allii strain CFBP 6369,
AB  - the causal agent of bacterial blight of onion. The draft genome
AB  - has a size of 5,425,942 bp and a G+C content of 64.4%.
ER  -

TY  - JOUR
AU  - Gai, Z.
AU  - Wang, X.
AU  - Liu, X.
AU  - Tai, C.
AU  - Tang, H.
AU  - He, X.
AU  - Wu, G.
AU  - Deng, Z.
AU  - Xu, P.
TI  - The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5.
JO  - PLoS ONE
PY  - 2010
SP  - E10018
EP  - E10018
VL  - 5
AB  - BACKGROUND: Carbazole is a recalcitrant compound with a dioxin-like
AB  - structure and possesses mutagenic and toxic activities. Bacteria respond
AB  - to a xenobiotic by recruiting exogenous genes to establish a pathway to
AB  - degrade the xenobiotic, which is necessary for their adaptation and
AB  - survival. Usually, this process is mediated by mobile genetic elements
AB  - such as plasmids, transposons, and insertion sequences. FINDINGS: The
AB  - genes encoding the enzymes responsible for the degradation of carbazole to
AB  - catechol via anthranilate were cloned, sequenced, and characterized from a
AB  - carbazole-degrading Sphingomonas sp. strain XLDN2-5. The car gene cluster
AB  - (carRAaBaBbCAc) and fdr gene were accompanied on both sides by two copies
AB  - of IS6100 elements, and organized as
AB  - IS6100::ISSsp1-ORF1-carRAaBaBbCAc-ORF8-IS6100-fdr-IS6100. Carbazole was
AB  - converted by carbazole 1,9a-dioxygenase (CARDO, CarAaAcFdr), meta-cleavage
AB  - enzyme (CarBaBb), and hydrolase (CarC) to anthranilate and
AB  - 2-hydroxypenta-2,4-dienoate. The fdr gene encoded a novel ferredoxin
AB  - reductase whose absence resulted in lower transformation activity of
AB  - carbazole by CarAa and CarAc. The ant gene cluster (antRAcAdAbAa) which
AB  - was involved in the conversion of anthranilate to catechol was also
AB  - sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100.
AB  - Anthranilate 1,2-dioxygenase (ANTDO) was composed of a reductase (AntAa),
AB  - a ferredoxin (AntAb), and a two-subunit terminal oxygenase (AntAcAd).
AB  - Reverse transcription-PCR results suggested that carAaBaBbCAc gene
AB  - cluster, fdr, and antRAcAdAbAa gene cluster were induced when strain
AB  - XLDN2-5 was exposed to carbazole. Expression of both CARDO and ANTDO in
AB  - Escherichia coli required the presence of the natural reductases for full
AB  - enzymatic activity. CONCLUSIONS/SIGNIFICANCE: We predict that IS6100 might
AB  - play an important role in the establishment of carbazole-degrading
AB  - pathway, which endows the host to adapt to novel compounds in the
AB  - environment. The organization of the car and ant genes in strain XLDN2-5
AB  - was unique, which showed strong evolutionary trail of gene recruitment
AB  - mediated by IS6100 and presented a remarkable example of rearrangements
AB  - and pathway establishments.
ER  -

TY  - JOUR
AU  - Gai, Z.
AU  - Wang, X.
AU  - Tang, H.
AU  - Tai, C.
AU  - Tao, F.
AU  - Wu, G.
AU  - Xu, P.
TI  - Genome Sequence of Sphingobium yanoikuyae XLDN2-5, an Efficient Carbazole-Degrading Strain.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6404
EP  - 6405
VL  - 193
AB  - Sphingobium yanoikuyae XLDN2-5 is an efficient carbazole-degrading strain. Carbazole-degrading
AB  - genes are accompanied on both sides by two copies of
AB  - IS6100 elements. Here, we describe the draft genome sequence of strain
AB  - XLDN2-5, which may provide important clues as to how it recruited
AB  - exogenous genes to establish pathways to degrade the xenobiotics.
ER  -

TY  - JOUR
AU  - Gai, Z.
AU  - Wang, X.
AU  - Zhang, X.
AU  - Su, F.
AU  - Wang, X.
AU  - Tang, H.
AU  - Tai, C.
AU  - Tao, F.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Sphingomonas elodea ATCC 31461, a Highly Productive Industrial Strain of Gellan Gum.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7015
EP  - 7016
VL  - 193
AB  - The commercial gelling agent gellan gum is a heteropolysaccharide produced by Sphingomonas
AB  - elodea ATCC 31461. However, the genes involved in the
AB  - biosynthesis, regulation, and modification of gellan gum have not been
AB  - fully characterized. Here we describe the draft genome sequence of stain
AB  - ATCC 31461 and major findings from its annotation.
ER  -

TY  - JOUR
AU  - Gai, Z.
AU  - Zhang, Z.
AU  - Wang, X.
AU  - Tao, F.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of Pseudomonas aeruginosa DQ8, an Efficient Degrader of n-Alkanes and Polycyclic Aromatic Hydrocarbons.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6304
EP  - 6305
VL  - 194
AB  - Pseudomonas aeruginosa DQ8, which was isolated from the crude oil polluted soil in the Daqing
AB  - oilfield of China, can efficiently degrade diesel, crude oil,
AB  - n-alkanes, and polycyclic aromatic hydrocarbons (PAHs). Here, we present a 6.8-Mb
AB  - assembly of its genome sequence. We have annotated 23 coding sequences (CDSs)
AB  - responsible for catabolism of n-alkanes and PAHs.
ER  -

TY  - JOUR
AU  - Gaido, M.L.
TI  - Purification of BsuE methylase to investigate the role of DNA methylation in rat growth hormone gene expression.
JO  - Diss. Abstr.
PY  - 1988
SP  - 2876B
EP  - 2876B
VL  - 48
AB  - DNA methylation at specific cytosine bases is one mechanism believed to be
AB  - involved in determining tissue specific gene expression.  A tissue specific
AB  - methylation pattern has been observed for the rat growth hormone (rGH) gene.
AB  - In rat pituitary tissue which expresses GH a CGCG sequence 144 basepairs
AB  - upstream from the rGH transcription initiation site is unmethylated.  This site
AB  - is methylated in rat liver, spleen and kidney which do not express GH.  We have
AB  - directly tested the effect of site specific methylation at the CGCG site on rGH
AB  - promoter activity.  1.5 kilobasepairs of rGH promoter sequences were inserted
AB  - in front of two bacterial indicator genes Neo and CAT.  A CGCG specific
AB  - methylase was isolated from Bacillus subtilis strain ISE15 by three column
AB  - chromatography steps:  phosphocellulose, heparin-sepharose and DEAE-Sepharose.
AB  - Its molecular weight was 41,000 by gel filtration.  It exhibits optimal
AB  - activity in mM KCl, 50 mM Tris.HCl, pH 7.3-8.3 and 5 mM 2-mercaptoethanol.
AB  - This enzyme was used to methylate the CGCG sequence in GH1 Neo and GH1.CAT.
AB  - Methylated and unmethylated fusion genes were transferred into GH3 rat
AB  - pituitary tissue culture cells by calcium-phosphate coprecipitation or
AB  - electroporation.  Cells transfected with GH1 Neo were harvested after 2 days,
AB  - replated at 5x10/5 cells/100 cm dish in selective media (400 ug/ml G418), and
AB  - counted after 2 weeks.  Cells were harvested 36 hours after transfection with
AB  - GH1.CAT and acetylation of 14C-chloramphenicol measured in whole cell extracts.
AB  - BsuE methylation resulted in a 68% decrease in GH1-Neo fusion gene activity
AB  - and in a lesser 44% decrease in the control RSV-Neo fusion gene activity.  The
AB  - control methylase, HhaI, which has over twice as many sites on the plasmid,
AB  - inhibited RS V-Neo and GH1-Neo activity by 81%-83%.  We conclude that extensive
AB  - methylation can nonspecifically inhibit fusion gene expression.  BsuE
AB  - methylation of GH1-CAT inhibited fusion gene expression by 49% while the
AB  - control HhaI methylase had no inhibitory effect on GH1-CAT activity in
AB  - transient expression assays.  In addition, neither BsuE or HhaI methylation had
AB  - any inhibitory effect on RSV-CAT activity.  Thus, we conclude that methylation
AB  - of the rGH promoter at CGCG sequences does specifically inhibit rGH promoter
AB  - activity.
ER  -

TY  - JOUR
AU  - Gaido, M.L.
AU  - Prostko, C.R.
AU  - Strobl, J.S.
TI  - Isolation and characterization of BsuE methyltransferase, a CGCG specific DNA methyltransferase from Bacillus subtilis.
JO  - J. Biol. Chem.
PY  - 1988
SP  - 4832
EP  - 4836
VL  - 263
AB  - The DNA methyltransferase M.BsuEI that recognizes the sequence 5'-CGCG-3' has
AB  - been isolated from Bacillus subtilis strain ISE15.  A 1600-fold purification of
AB  - M.BsuEI was achieved by column chromatography on phosphocellulose,
AB  - heparin-Sepharose, and DEAE-Sepharose.  DNA methyltransferase activity was
AB  - monitored in the column eluants radiochemically by the transfer of tritiated
AB  - methyl groups from radiolabeled S-adenosylmethionine to poly(dGdC)-poly(dGdC)
AB  - DNA, a sensitive and specific substrate for M.BsuEI activity.  The DNA sequence
AB  - specificity of this methyltransferase activity was confirmed enzymatically by
AB  - demonstrating that M.BsuEI-methylated DNA was selectively protected from
AB  - cleavage by the restriction enzyme isoschizomers, ThaI and FnuDII.  Purified
AB  - M.BsuEI has an apparent molecular size of 41,000-43,000 as determined by gel
AB  - filtration and migrates as a 41-kDa protein in a sodium dodecyl
AB  - sulfate-poly-acrylamide gel.  DNA methylation by M.BsuEI is dependent upon the
AB  - presence of S-adenosylmethionine and 2-mercaptoethanol.  M.BsuEI
AB  - methyltransferase activity is optimal at 37C in the presence of 50 mM Tris-HCl,
AB  - pH 7.8, 25 mM KCl, 6 micromolar S-adenosylmethionine, 5 mM 2-mercaptoethanol,
AB  - and 10 mM EDTA.  M.BsuEI methylates the external cytidine in its recognition
AB  - sequence in both linear and supercoiled DNA.  A unique property of M.BsuEI is
AB  - its ability to methylate 5'-CGCG-3' in Z-DNA.
ER  -

TY  - JOUR
AU  - Gaido, M.L.
AU  - Strobl, J.S.
TI  - Methylation sensitivity of the restriction enzymes FnuDII and AccII.
JO  - Arch. Microbiol.
PY  - 1987
SP  - 338
EP  - 340
VL  - 46
AB  - The restriction enzymes FnuDII and AccII are isoschizomers of the DNA sequence
AB  - 5'-CGCG-3'.  We have determined that 5-methylcytidine at either cytidine
AB  - position in this recognition sequence inhibits DNA cleavage by FnuDII and
AB  - AccII.  A third isoschizomer, ThaI was previously shown to exhibit an identical
AB  - methylation sensitivity.  It is remarkable that 3 restriction enzymes derived
AB  - from diverse microbiological sources exhibit this identical methylation
AB  - sensitivity.
ER  -

TY  - JOUR
AU  - Gaiero, J.R.
AU  - Formusa, P.A.
AU  - Hsiang, T.
AU  - Nicol, R.W.
AU  - Habash, M.
TI  - Draft Genome Sequence of Ureolytic Environmental Isolate Bacillus galactosidilyticus PL133.
JO  - Genome Announcements
PY  - 2016
SP  - e01067
EP  - e01016
VL  - 4
AB  - We report here the 5.19-Mb draft genome sequence of Bacillus galactosidilyticus PL133 isolated
AB  - from poultry litter. The isolate was an important member of the
AB  - cultivable aerobic bacteria identified to have ureolytic activity, which is
AB  - responsible for ammonia generation in poultry litter residue.
ER  -

TY  - JOUR
AU  - Gaiero, J.R.
AU  - Hsiang, T.
AU  - Nicol, R.W.
AU  - Habash, M.
TI  - Draft Genome Sequence of Ureolytic Environmental Isolate Staphylococcus sp. NA309.
JO  - Genome Announcements
PY  - 2016
SP  - e01066
EP  - e01016
VL  - 4
AB  - We report the 2.7 Mb draft genome sequence of Staphylococcus sp. NA309 isolated from poultry
AB  - litter. The isolate was a dominant member of the cultivable aerobic
AB  - bacteria identified to have ureolytic activity, responsible for ammonia
AB  - generation in poultry litter residue.
ER  -

TY  - JOUR
AU  - Gaigalas, M.
AU  - Maneliene, Z.
AU  - Kazlauskiene, R.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - PfoI, a unique type II restriction endonuclease that recognizes the sequence 5'-T/CCNGGA-3'.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - e98
EP  - e98
VL  - 30
AB  - A new type II restriction endonuclease designated PfoI has been partially purified from
AB  - Pseudomonas fluorescens biovar 126.  PfoI recognizes the interrupted hexanucleotide
AB  - palindromic sequence 5'-T/CCNGGA-3' and cleaves DNA to produce protruding pentanucleotide
AB  - 5'-ends.
ER  -

TY  - JOUR
AU  - Gaiser, R.A.
AU  - Medema, M.H.
AU  - Kleerebezem, M.
AU  - van Baarlen, P.
AU  - Wells, J.M.
TI  - Draft Genome Sequence of a Porcine Commensal, Rothia nasimurium, Encoding a Nonribosomal Peptide Synthetase Predicted To Produce the Ionophore Antibiotic  Valinomycin.
JO  - Genome Announcements
PY  - 2017
SP  - e00453
EP  - e00417
VL  - 5
AB  - We report the draft whole-genome sequence of Rothia nasimurium isolated from a porcine tonsil.
AB  - The genome encodes a nonribosomal peptide synthetase predicted to
AB  - produce valinomycin, a cyclic dodecadepsipeptide ionophore. Previously,
AB  - valinomycin was known to be produced only by Streptomyces species and isolates
AB  - belonging to the Bacillus pumilus group.
ER  -

TY  - JOUR
AU  - Gaisin, V.A.
AU  - Ivanov, T.M.
AU  - Kuznetsov, B.B.
AU  - Gorlenko, V.M.
AU  - Grouzdev, D.S.
TI  - Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser,   Iceland.
JO  - Genome Announcements
PY  - 2016
SP  - e00714
EP  - e00716
VL  - 4
AB  - We report here the draft genome sequence of the thermophilic filamentous anoxygenic
AB  - phototrophic bacterium Chloroflexus sp. strain isl-2, which was
AB  - isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C
AB  - content of 59.65%. The annotated genome sequence offers the genetic basis for
AB  - understanding the strain's ecological role as a phototrophic bacterium within the
AB  - bacterial community.
ER  -

TY  - JOUR
AU  - Gal, S.
AU  - Monteith, N.
AU  - Shkalim, S.
AU  - Huang, H.
AU  - Head, T.
TI  - Methylation of dna may be useful as a computational tool: Experimental evidence.
JO  - Current Developments in Mathematical Biology
PY  - 2007
SP  - 1
EP  - 14
VL  - 38
AB  - Previously we have explained the abstract concept we call 'aqueous computing' and
AB  - illustrated it with concrete wet lab results. Here, we
AB  - explore the use of methylase enzymes to 'write' on double-stranded DNA
AB  - molecules at sites where restriction enzymes will cut if, and only if,
AB  - the sites have not previously been methylated. A site represents the
AB  - bit zero (False, F) if the site has been methylated and the bit one
AB  - (True, T) if it has not been methylated. 'Reading' is done by
AB  - attempting a cut at each of the sites. We found 8 commercially
AB  - available methylases and 8 corresponding restriction enzymes that would
AB  - not cut after the action of one of the methylases. We were able to
AB  - confirm that methylation by each of these 8 enzymes individually
AB  - blocked cleavage only by I he restriction enzyme associated with that
AB  - site and not any other enzyme. We I hen used these enzymes to approach
AB  - a 3-variable, 4-clause satisfiability (SAT) problem using either
AB  - plasmid DNA (pBluescript) or PCR product made from the region
AB  - containing the restriction enzyme sites on the plasmid. Pairs of
AB  - methylases were defined to represent each of the states of the
AB  - operators p, q and r, one methylase for p and another for p', etc. We
AB  - methylated the DNA in parallel at the two sites so either the p site
AB  - was methylated (making p false) or the P' site was methylated (making
AB  - p' false). We did that for the other two variables as well to create a
AB  - set of logically consistent DNA fragments. Then we applied the 4
AB  - clauses using restriction enzymes to cut DNA fragments that did riot
AB  - satisfy them. At the end, we found evidence for intact DNA indicating
AB  - an answer satisfying all of the clauses. To confirm the state of each
AB  - of the Boolean operators, we used cleavage by the appropriate
AB  - restriction enzyme. We found in the computation with both the plasmid
AB  - and the PCR product, one site pair to show false in both sites; q and
AB  - q', for instance. This should not be possible. We suspected incomplete
AB  - cutting during the clauses by one of these restriction Enzymes,
AB  - specifically BssHII In summary, we did successfully show the usefulness
AB  - of DNA methylation in a scheme to do a mathematical computation. Thus,
AB  - we have added to our arsenal of potential methods of performing DNA
AB  - computing in the aqueous style.
ER  -

TY  - JOUR
AU  - Galac, M.R.
AU  - Stam, J.
AU  - Maybank, R.
AU  - Hinkle, M.
AU  - Mack, D.
AU  - Rohde, H.
AU  - Roth, A.L.
AU  - Fey, P.D.
TI  - Complete Genome Sequence of Staphylococcus epidermidis 1457.
JO  - Genome Announcements
PY  - 2017
SP  - e00450
EP  - e00417
VL  - 5
AB  - Staphylococcus epidermidis 1457 is a frequently utilized strain that is amenable  to genetic
AB  - manipulation and has been widely used for biofilm-related research. We
AB  - report here the whole-genome sequence of this strain, which encodes 2,277
AB  - protein-coding genes and 81 RNAs within its 2.4-Mb genome and plasmid.
ER  -

TY  - JOUR
AU  - Galagan, J.E. et al.
TI  - The genome sequence of the filamentous fungus Neurospora crassa.
JO  - Nature
PY  - 2003
SP  - 859
EP  - 868
VL  - 422
AB  - Neurospora crassa is a central organism in the history of twentieth-century genetics,
AB  - biochemistry and molecular biology. Here, we
AB  - report a high-quality draft sequence of the N. crassa genome. The
AB  - approximately 40-megabase genome encodes about 10,000 protein-coding
AB  - genes--more than twice as many as in the fission yeast Schizosaccharomyces
AB  - pombe and only about 25% fewer than in the fruitfly Drosophila
AB  - melanogaster. Analysis of the gene set yields insights into unexpected
AB  - aspects of Neurospora biology including the identification of genes
AB  - potentially associated with red light photobiology, genes implicated in
AB  - secondary metabolism, and important differences in Ca2+ signalling as
AB  - compared with plants and animals. Neurospora possesses the widest array of
AB  - genome defence mechanisms known for any eukaryotic organism, including a
AB  - process unique to fungi called repeat-induced point mutation (RIP). Genome
AB  - analysis suggests that RIP has had a profound impact on genome evolution,
AB  - greatly slowing the creation of new genes through genomic duplication and
AB  - resulting in a genome with an unusually low proportion of closely related
AB  - genes.
ER  -

TY  - JOUR
AU  - Galagan, J.E. et al.
TI  - The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity.
JO  - Genome Res.
PY  - 2002
SP  - 532
EP  - 542
VL  - 12
AB  - Methanogenesis, the biological production of methane, plays a pivotal role in the global
AB  - carbon cycle and contributes significantly to global warming. The majority of methane in
AB  - nature is derived from acetate. Here we report the complete genome sequence of an
AB  - acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most
AB  - metabolically diverse methanogens, thrive in a broad range of environments, and are unique
AB  - among the Archaea in forming complex multicellular structures. This diversity is reflected in
AB  - the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal
AB  - genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of
AB  - metabolic and cellular capabilities. The presence of novel methyltransferases indicates the
AB  - likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of
AB  - single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic
AB  - growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene
AB  - cluster and two complete chemotaxis gene clusters were identified. The availability of genetic
AB  - methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a
AB  - powerful model organism for the study of archaeal biology.
ER  -

TY  - JOUR
AU  - Galardini, M. et al.
TI  - Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 325
EP  - 333
VL  - 9
AB  - Ensifer (syn. Sinorhizobium) meliloti is an important symbiotic bacterial species that fixes
AB  - nitrogen. Strains BO21CC and AK58 were previously investigated for
AB  - their substrate utilization and their plant-growth promoting abilities showing
AB  - interesting features. Here, we describe the complete genome sequence and
AB  - annotation of these strains. BO21CC and AK58 genomes are 6,985,065 and 6,974,333
AB  - bp long with 6,746 and 6,992 genes predicted, respectively.
ER  -

TY  - JOUR
AU  - Galarza, M.
AU  - Tarazona, D.
AU  - Borda, V.
AU  - Agapito, J.C.
AU  - Guio, H.
TI  - Evidence of Clonal Expansion in the Genome of a Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate from Peru.
JO  - Genome Announcements
PY  - 2014
SP  - e00089
EP  - e00014
VL  - 2
AB  - We report the genome sequence of Mycobacterium tuberculosis INS-MDR from Peru, a
AB  - multidrug-resistant tuberculosis (MDR-TB) and Latin American-Mediterranean (LAM)
AB  - lineage strain. Our analysis showed mutations related to drug resistance in the
AB  - rpoB (D516V), katG (S315T), kasA (G269S), and pncA (Q10R) genes. Our evidence
AB  - suggests that INS-MDR may be a clonal expansion related to the African strain KZN
AB  - 1435.
ER  -

TY  - JOUR
AU  - Galburt, E.A.
AU  - Chadsey, M.S.
AU  - Jurica, M.S.
AU  - Chevalier, B.S.
AU  - Erho, D.
AU  - Tang, W.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 877
EP  - 887
VL  - 300
AB  - The homing endonuclease I-PpoI severely bends its DNA target, resulting in significant
AB  - deformations of the minor and major groove near the scissile phosphate groups. To study the
AB  - role of conformational changes within the protein catalyst and the DNA substrate, we have
AB  - determined the structure of the enzyme in the absence of bound DNA, performed gel retardation
AB  - analyses of DNA binding and bending, and have mutagenized a leucine residue that contacts an
AB  - adenine nucleotide at the site of cleavage. The structure of the L116A/DNA complex has been
AB  - determined and the effects of the mutation on affinity and catalysis have been measured. The
AB  - wild-type protein displays a rigid-body rotation of its individual subunits upon DNA binding.
AB  - Homing site DNA is not detectably bent in the absence of protein, but is sharply bent in both
AB  - the wild-type and L116A complexes. These results indicate that binding involves a large
AB  - distortion of the DNA and a smaller change in protein conformation. Leucine 116 is critical
AB  - for binding and catalysis: it appears to be important for forming a well-ordered protein-DNA
AB  - complex at the cleavage site, for maximal deformation of the DNA, and for desolvation of the
AB  - nucleotide bases that are partially unstacked in the enzyme complex.
ER  -

TY  - JOUR
AU  - Galburt, E.A.
AU  - Chevalier, B.
AU  - Tang, W.
AU  - Jurica, M.S.
AU  - Flick, K.E.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - A novel endonuclease mechanism directly visualized for I-PpoI.
JO  - Nat. Struct. Biol.
PY  - 1999
SP  - 1096
EP  - 1099
VL  - 6
AB  - A novel mechanism of DNA endonucleolytic cleavage has been visualized for the homing
AB  - endonuclease I-PpoI by trapping the uncleaved enzyme-substrate complex and comparing it to the
AB  - previously visualized product complex. This enzyme employs a unique single metal mechanism. A
AB  - magnesium ion is coordinated by an asparagine residue and two DNA oxygen atoms and stabilizes
AB  - the phosphoanion transition state and the 3'oxygen leaving group. A hydrolytic water molecule
AB  - is activated by a histidine residue for an in-line attack on the scissile phosphate. A
AB  - strained enzyme-substrate-metal complex is formed before cleavage, then relaxed during the
AB  - reaction.
ER  -

TY  - JOUR
AU  - Galburt, E.A.
AU  - Jurica, M.S.
TI  - His-Cys box homing endonuclease.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 85
EP  - 102
VL  - 16
AB  - Homing endonucleases are often grouped into four families based on distinct sequence motifs.
AB  - One of these families is known as the His-Cys box homing endonucleases and contains two
AB  - clusters of conserved histidine and cysteine residues over a central 100 amino acid region.
AB  - At last count, 23 members of this family had been identified.  The open reading frames of
AB  - these proteins are contained within mobile group I introns found in nuclear rDNA genes of
AB  - several protists.  The nuclear location of these introns and ORFs is currently unique among
AB  - the homing endonuclease families and poses an intriguing puzzle regarding their expression
AB  - from non-coding rRNA transcripts.  The best-studied member of the His-Cys box homing
AB  - endonucleases is I-PpoI from the myxomycete Physarum polycephalum.  Following an introduction
AB  - to all of the known members of the His-Cys box endonuclease family, much of the following
AB  - chapter will outline the extensive characterization of  I-PpoI structure and function.
AB  - Although our understanding of how I-PpoI is expressed in cells is still not fully complete,
AB  - the means by which I-PpoI specifically recognizes a single cleavage site in the host genome to
AB  - mediate homing of its host intron is widely accepted.  Details of DNA recognition and the
AB  - catalytic mechanism of nucleolytic cleavage have been ascertained from both in vivo and in
AB  - vitro activity assays as well as from extensive X-ray crystallographic structural analyses of
AB  - the enzyme bound to its DNA substrate.
ER  -

TY  - JOUR
AU  - Galburt, E.A.
AU  - Stoddard, B.L.
TI  - Restriction endonucleases: one of these things is not like the others.
JO  - Nat. Struct. Biol.
PY  - 2000
SP  - 89
EP  - 91
VL  - 7
AB  - The crystal structure of the restriction endonuclease BglII in complex with its DNA target
AB  - site has been determined. The DNA binding mode and chemistry of catalysis are observed to
AB  - differ from BamHI which cleaves a similar target site. These observations indicate that more
AB  - divergence has occurred within this family of proteins than originally thought.
ER  -

TY  - JOUR
AU  - Galburt, E.A.
AU  - Stoddard, B.L.
TI  - Catalytic mechanisms of restriction and homing endonucleases.
JO  - Biochemistry
PY  - 2002
SP  - 13851
EP  - 13860
VL  - 41
AB  - The catalytic mechanisms of type II restriction endonucleases and homing endonucleases are
AB  - discussed and compared. Brief reviews of the
AB  - chemistry of phosphoryl transfers and canonical one-metal and two-metal
AB  - endonucleolytic mechanisms are provided along with possible future
AB  - directions in the study of endonuclease active sites. The discussion of
AB  - type II restriction endonucleases is comprised of a description of the
AB  - general architecture of the canonical active site structural motif
AB  - followed by more in-depth examples of one- and two-metal mechanisms.
AB  - The homing endonuclease section is comprised of four sections
AB  - describing what is known regarding the cleavage mechanisms of the four
AB  - group I intron homing endonuclease families: LAGLIDADG, His-Cys box,
AB  - H-N-H, and GIY-YIG.
ER  -

TY  - JOUR
AU  - Galia, W.
AU  - Mariani-Kurkdjian, P.
AU  - Loukiadis, E.
AU  - Blanquet-Diot, S.
AU  - Leriche, F.
AU  - Brugere, H.
AU  - Shima, A.
AU  - Oswald, E.
AU  - Cournoyer, B.
AU  - Thevenot-Sergentet, D.
TI  - Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak.
JO  - Genome Announcements
PY  - 2015
SP  - e01568
EP  - e01514
VL  - 3
AB  - The consumption of raw milk cheese can expose populations to Shiga toxin-producing Escherichia
AB  - coli (STEC). We report here the genome sequence of an E. coli O26:H11 strain isolated from
AB  - humans during the first raw milk cheese outbreak described in France (2005).
ER  -

TY  - JOUR
AU  - Galibert, F. et al.
TI  - The composite genome of the legume symbiont Sinorhizobium meliloti.
JO  - Science
PY  - 2001
SP  - 668
EP  - 672
VL  - 293
AB  - The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association
AB  - with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of
AB  - dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the
AB  - alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite
AB  - 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB
AB  - megaplasmids. Genome sequence analysis indicates that all three elements contribute, in
AB  - varying degrees, to symbiosis and reveals how this genome may have emerged during evolution.
AB  - The genome sequence will be useful in understanding the dynamics of interkingdom associations
AB  - and of life in soil environments.
ER  -

TY  - JOUR
AU  - Gallagher, L.A.
AU  - McKevitt, M.
AU  - Ramage, E.R.
AU  - Manoil, C.
TI  - Genetic dissection of the Francisella novicida restriction barrier.
JO  - J. Bacteriol.
PY  - 2008
SP  - 7830
EP  - 7837
VL  - 190
AB  - Francisella tularensis is the causative agent of tularemia and is a category A select agent.
AB  - Francisella novicida, considered by some to be one of four subspecies of F. tularensis, is
AB  - used as a model in pathogenesis studies because it causes a disease similar to tularemia in
AB  - rodents but is not harmful to humans. F. novicida exhibits a strong restriction barrier which
AB  - reduces the transformation frequency of foreign DNA up to 10(6)-fold. To identify the genetic
AB  - basis of this barrier, we carried out a mutational analysis of restriction genes identified in
AB  - the F. novicida genome. Strains carrying combinations of insertion mutations in eight
AB  - candidate loci were created and assayed for reduced restriction of unmodified plasmid DNA
AB  - introduced by transformation. Restriction was reduced by mutations in four genes,
AB  - corresponding to two type I, one type II, and one type III restriction system. Restriction was
AB  - almost fully eliminated in a strain in which all four genes were inactive. The strongest
AB  - contributor to the restriction barrier, the type II gene, encodes an enzyme which specifically
AB  - cleaves Dam-methylated DNA. Genome comparisons show that most restriction genes in the F.
AB  - tularensis subspecies are pseudogenes, explaining the unusually strong restriction barrier in
AB  - F. novicida and suggesting that restriction was lost during evolution of the human pathogenic
AB  - subspecies. As part of this study, procedures were developed to introduce unmodified plasmid
AB  - DNA into F. novicida efficiently, to generate defined multiple mutants, and to produce
AB  - chromosomal deletions of multiple adjacent genes.
ER  -

TY  - JOUR
AU  - Gallagher, M.L.
AU  - Burke, W.F.
TI  - Sequence-specific endonuclease from the transformable cyanobacterium Anacystis nidulans R2.
JO  - FEMS Microbiol. Lett.
PY  - 1985
SP  - 317
EP  - 321
VL  - 26
AB  - Extracts of the transformable cyanobacterial strain Anacystis nidulans R2 were
AB  - analyzed for the presence of restriction endonuclease.  One enzyme, AniI, was
AB  - found and determined to be sequence-specific on the basis of its ability to
AB  - cleave several Bacillus plasmids at a limited number of sites.  The activity of
AB  - this enzyme is significantly reduced in extracts prepared from cell cultures
AB  - grown at 38C.
ER  -

TY  - JOUR
AU  - Gallagher, M.L.
AU  - Burke, W.F.
TI  - Unique cyanobacterial recognition sequence for the restriction endonuclease AniI.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1987
SP  - 224
EP  - 224
VL  - 87
AB  - In previous studies, we have shown that the transformable cyanobacterium
AB  - Anacystis nidulans R2 possesses a sequence specific endonuclease AniI.
AB  - Restriction digest patterns of site-specific endonucleases of cyanobacterial
AB  - origin were compared with AniI generated digests to determine if AniI is an
AB  - isoschizomer of any of these enzymes.  We have previously shown that pBR322 is
AB  - not cleaved by AniI.  We determined that only eight characterized
AB  - cyanobacterial restriction-endonucleases are unable to cleave pBR322.  These
AB  - enzymes or isoschizomers of them, if commercially available, were obtained and
AB  - used to digest plasmid DNA substrates.  Although several enzymes were not
AB  - available, we were able to make a comparison based on published data which
AB  - indicated the number of cleavage sities on various substrate DNA's.  None of
AB  - the commercially available endonucleases produced restriction patterns similar
AB  - to AniI digests.  None of the enzymes which were compared indirectly were found
AB  - to have the same number of cleavage sites on PhiX174 substrate DNA.  We
AB  - therefore conclude that the AniI recognition sequence is unique with respect to
AB  - other cyanobacterial restriction endonucleases.
ER  -

TY  - JOUR
AU  - Gallegos-Monterrosa, R.
AU  - Maroti, G.
AU  - Balint, B.
AU  - Kovacs, A.T.
TI  - Draft Genome Sequence of the Soil Isolate Lysinibacillus fusiformis M5, a Potential Hypoxanthine Producer.
JO  - Genome Announcements
PY  - 2016
SP  - e01272
EP  - e01216
VL  - 4
AB  - Lysinibacillus fusiformis strain M5 is a potential hypoxanthine producer that was isolated
AB  - from clay soil. Here, we present the draft genome sequence that was
AB  - annotated in order to facilitate future studies of L. fusiformis M5.
ER  -

TY  - JOUR
AU  - Galli, D.M.
AU  - Kerr, M.S.
AU  - Fair, A.D.
AU  - Permpanich, P.
AU  - LeBlanc, D.J.
TI  - Parameters associated with cloning in Actinobacillus actinomycetemcomitans.
JO  - Plasmid
PY  - 2002
SP  - 138
EP  - 147
VL  - 47
AB  - Characterization of virulence traits in Actinobacillus actinomycetemcomitans requires the
AB  - application of recombinant DNA
AB  - techniques. To develop appropriate genetic tools it is necessary to
AB  - identify suitable host-vector systems. The Current Study assessed
AB  - cloning parameters in A. actinomycetemcomitans for two preciously
AB  - described vectors. pDMG4 and pMMB67. It was determined that the maximum
AB  - size of recombinant molecule that could be transferred to A.
AB  - actinomycetemcomitans strain ATCC29522 via electroporation was 33 kb.
AB  - The size limit for transformation of the same strain with ligation
AB  - mixtures (direct cloning), however, was limited to 23-24 kb. Additional
AB  - experiments included electroporation of various A.
AB  - actinomycetemcomitans strains with plasmid DNA isolated from
AB  - Escherichia coli and different A. actinomycetemcomitans sources.
AB  - Differences in transformation efficiencies, suggested the presence of a
AB  - restriction modification system for pDMG4 in some strains of A. actinomycetemcomitans. Cloning
AB  - of portions of the enterococcal plasmid pJH1 into A. actinomycetemcomitans resulted in the
AB  - insertion of the intact vector
AB  - into the chromosome.
ER  -

TY  - JOUR
AU  - Gallien, S.
AU  - Perrodou, E.
AU  - Carapito, C.
AU  - Deshayes, C.
AU  - Reyrat, J.M.
AU  - Van Dorsselaer, A.
AU  - Poch, O.
AU  - Schaeffer, C.
AU  - Lecompte, O.
TI  - Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.
JO  - Genome Res.
PY  - 2009
SP  - 128
EP  - 135
VL  - 19
AB  - The progress in sequencing technologies irrigates biology with an ever-increasing
AB  - number of genome sequences. In most cases, the gene repertoire is predicted in
AB  - silico and conceptually translated into proteins. As recently highlighted, the
AB  - predicted genes exhibit frequent errors, particularly in start codons, with a
AB  - serious impact on subsequent biological studies. A new "ortho-proteogenomic"
AB  - approach is presented here for the annotation refinement of multiple genomes at
AB  - once. It combines comparative genomics with an original proteomic protocol that
AB  - allows the characterization of both N-terminal and internal peptides in a single
AB  - experiment. This strategy was applied to the Mycobacterium genus with
AB  - Mycobacterium smegmatis as the reference, and identified 946 distinct proteins,
AB  - including 443 characterized N termini. These experimental data allowed the
AB  - correction of 19% of the characterized start codons, the identification of 29
AB  - proteins missed during the annotation process, and the curation, thanks to
AB  - comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.
ER  -

TY  - JOUR
AU  - Gallo, K.A.
AU  - Shao, K.L.
AU  - Phillips, L.R.
AU  - Regan, J.B.
AU  - Koziolkiewicz, M.
AU  - Uznanski, B.
AU  - Stec, W.J.
AU  - Zon, G.
TI  - Alkyl phosphotriester modified oligodeoxyribonucleotides.  V. Synthesis and absolute configuration of Rp and Sp diastereomers of an ethyl phosphotriester (Et) modified EcoRI recognition sequence, d[GGAA(Et)TTCC].
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 7405
EP  - 7420
VL  - 14
AB  - Protected deoxynucleoside 3'-O-ethyl-N, N-diisopropylphosphoramidite reagents
AB  - were prepared for use in the automated synthesis of ethyl phosphotriester (Et)
AB  - modified oligonucleotides.  The title diastereomers were separated by
AB  - reversed-phase HPLC, and chirality at phosphorus was assigned by an improved
AB  - configurational correlation scheme that was verified by NMR spectroscopic
AB  - studies (accompanying paper, Part VI).  This generally applicable correlation
AB  - scheme involved (1.) enzymatic digestions of each diastereomer to give the
AB  - corresponding diastereomer of d[A(Et)T]; (2.) phosphite triester sulfurization
AB  - to obtain diastereomeric 0-ethyl phosphorothioates, d[AS(Et)T], which were
AB  - separated by HPLC for (3.) stereoretentive oxidation with H2O2 to give
AB  - d[A(Et)T], and (4.) stereoretentive de-ethylation with PhSH-Et3N to give
AB  - diastereomeric phosphorothioates, d[AST], whose configurations at phosphorus
AB  - had been assigned previously.  Neither the Rp-Rp nor Sp-Sp duplex,
AB  - {d[GGAA(Et)TTCC]}2, was cleaved by EcoRI endonuclease under conditions that led
AB  - to cleavage of both the unmodified duplex, [d(GGAATTCC)]2, and the mixture of
AB  - diastereomeric phosphorothioate-modified duplexes, [d(GGAASTTCC)]2.  Cleavage
AB  - of the latter substrates was Sp-selective.
ER  -

TY  - JOUR
AU  - Galloway-Pena, J.
AU  - DebRoy, S.
AU  - Brumlow, C.
AU  - Li, X.
AU  - Tran, T.
AU  - Horstmann, N.
AU  - Yao, H.
AU  - Chen, K.
AU  - Wang, F.
AU  - Pan, B.-F.
AU  - Hawke, D.
AU  - Thompson, E.
AU  - Arias, C.
AU  - Fowler, V.G.
AU  - Bhatti, M.
AU  - Kalia, A.
AU  - Flores, A.R.
AU  - Shelburne, S.A.
TI  - Hypervirulent Group A Streptococcus Emergence in an Acaspular Background is Associated with Marked Remodeling of the Bacterial Cell Surface.
JO  - PLoS ONE
PY  - 2019
SP  - e0207897
EP  - e0207897
VL  - 13
AB  - Inactivating mutations in the control of virulence two-component regulatory system (covRS)
AB  - often account for the hypervirulent phenotype in severe, invasive group A streptococcal
AB  - (GAS) infections. As CovR represses production of the anti-phagocytic hyaluronic acid capsule,
AB  - high level capsule production is generally considered critical to the hypervirulent phenotype
AB  - induced by CovRS inactivation. There have recently been large outbreaks of GAS
AB  - strains lacking capsule, but there are currently no data on the virulence of covRS-mutated,
AB  - acapsular strains in vivo. We investigated the impact of CovRS inactivation in acapsular
AB  - serotype M4 strains using a wild-type (M4-SC-1) and a naturally-occurring CovS-inactivated
AB  - strain (M4-LC-1) that contains an 11bp covS insertion. M4-LC-1 was significantly more virulent
AB  - in a mouse bacteremia model but caused smaller lesions in a subcutaneous mouse
AB  - model. Over 10% of the genome showed significantly different transcript levels in M4-LC-1
AB  - vs. M4-SC-1 strain. Notably, the Mga regulon and multiple cell surface protein-encoding
AB  - genes were strongly upregulateda finding not observed for CovS-inactivated, encapsulated
AB  - M1 or M3 GAS strains. Consistent with the transcriptomic data, transmission electron
AB  - microscopy revealed markedly altered cell surface morphology of M4-LC-1 compared to
AB  - M4-SC-1. Insertional inactivation of covS in M4-SC-1 recapitulated the transcriptome and
AB  - cell surface morphology. Analysis of the cell surface following CovS-inactivation revealed
AB  - that the upregulated proteins were part of the Mga regulon. Inactivation of mga in M4-LC-1
AB  - reduced transcript levels of multiple cell surface proteins and reversed the cell surface
AB  - alterations
AB  - consistent with the effect of CovS inactivation on cell surface composition being mediated
AB  - by Mga. CovRS-inactivating mutations were detected in 20% of current invasive
AB  - serotype M4 strains in the United States. Thus, we discovered that hypervirulent M4 GAS
AB  - strains with covRS mutations can arise in an acapsular background and that such hypervirulence
AB  - is associated with profound alteration of the cell surface.
ER  -

TY  - JOUR
AU  - Galvez, E.J.
AU  - Carrillo-Castro, K.
AU  - Zarate, L.
AU  - Guiza, L.
AU  - Pieper, D.H.
AU  - Garcia-Bonilla, E.
AU  - Salazar, M.
AU  - Junca, H.
TI  - Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a  Colombian Caribbean Aquaculture Outbreak.
JO  - Genome Announcements
PY  - 2016
SP  - e00321
EP  - e00316
VL  - 4
AB  - Bacillus licheniformis strain CG-B52 was isolated as the etiological agent producing a
AB  - self-limited outbreak of high mortalities in commercial Litopenaeus
AB  - vannamei culture ponds on the Colombian Caribbean coast in 2005. Here, we report
AB  - its draft genome and three novel extrachromosomal elements that it harbors.
ER  -

TY  - JOUR
AU  - Gamez, R.M.
AU  - Rodriguez, F.
AU  - Bernal, J.F.
AU  - Agarwala, R.
AU  - Landsman, D.
AU  - Marino-Ramirez, L.
TI  - Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006.
JO  - Genome Announcements
PY  - 2015
SP  - e01391
EP  - e01315
VL  - 3
AB  - Bacillus amyloliquefaciens is an important plant growth-promoting rhizobacterium  (PGPR). We
AB  - report the first whole-genome sequence of PGPR Bacillus
AB  - amyloliquefaciens evaluated in Colombian banana plants. The genome sequences
AB  - encode genes involved in plant growth and defense, including bacteriocins,
AB  - ribosomally synthesized antibacterial peptides, in addition to genes that provide
AB  - resistance to toxic compounds.
ER  -

TY  - JOUR
AU  - Gamez, R.M.
AU  - Rodriguez, F.
AU  - Ramirez, S.
AU  - Gomez, Y.
AU  - Agarwala, R.
AU  - Landsman, D.
AU  - Marino-Ramirez, L.
TI  - Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006.
JO  - Genome Announcements
PY  - 2016
SP  - e00329
EP  - e00316
VL  - 4
AB  - Pseudomonas fluorescens is a well-known plant growth-promoting rhizobacterium (PGPR). We
AB  - report here the first whole-genome sequence of PGPR P. fluorescens
AB  - evaluated in Colombian banana plants. The genome sequences contains genes
AB  - involved in plant growth and defense, including bacteriocins,
AB  - 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and genes that provide
AB  - resistance to toxic compounds.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Chew, T.H.
AU  - Hudson, A.O.
AU  - Savka, M.A.
TI  - Genome Sequence of Novosphingobium sp. Strain Rr 2-17, a Nopaline Crown Gall-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5137
EP  - 5138
VL  - 194
AB  - Novosphingobium sp. strain Rr 2-17 is an N-acyl homoserine lactone (AHL)-producing bacterium
AB  - isolated from the crown gall tumor of a grapevine. To
AB  - our knowledge, this is the first draft genome announcement of a plant-associated
AB  - strain from the genus Novosphingobium.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Chew, T.H.
AU  - Hudson, A.O.
AU  - Savka, M.A.
TI  - Genome Sequence of Methylobacterium sp. Strain GXF4, a Xylem-Associated Bacterium Isolated from Vitis vinifera L. Grapevine.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5157
EP  - 5158
VL  - 194
AB  - Methylobacterium sp. strain GXF4 is an isolate from grapevine. Here we present the sequence,
AB  - assembly, and annotation of its genome, which may shed light on its
AB  - role as a grapevine xylem inhabitant. To our knowledge, this is the first genome
AB  - announcement of a plant xylem-associated strain of the genus Methylobacterium.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Chew, T.H.
AU  - Tay, Y.L.
AU  - Lye, S.F.
AU  - Yahya, A.
TI  - Genome Sequence of Hydrogenophaga sp. Strain PBC, a 4-Aminobenzenesulfonate-Degrading Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4759
EP  - 4760
VL  - 194
AB  - Hydrogenophaga sp. strain PBC is an effective degrader of 4-aminobenzenesulfonate isolated
AB  - from textile wastewater. Here we present the assembly and annotation of
AB  - its genome, which may provide further insights into its metabolic potential. This
AB  - is the first announcement of the draft genome sequence of a strain from the genus
AB  - Hydrogenophaga.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Chew, T.H.
AU  - Tay, Y.L.
AU  - Lye, S.F.
AU  - Yahya, A.
TI  - Genome Sequence of Ralstonia sp. Strain PBA, a Bacterium Involved in the Biodegradation of 4-Aminobenzenesulfonate.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5139
EP  - 5140
VL  - 194
AB  - Ralstonia sp. strain PBA was isolated from textile wastewater in a coculture with
AB  - Hydrogenophaga sp. strain PBC. Here we present the assembly and annotation of its
AB  - genome, which may provide further insights into the mechanism of its interaction
AB  - with strain PBC during 4-aminobenzenesulfonate degradation.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Eng, W.W.H.
AU  - Barton, M.K.
AU  - Adams, L.E.
AU  - Samsudin, N.A.
AU  - Bartl, A.J.
AU  - Hudson, A.O.
AU  - Savka, M.A.
AU  - Thomas, J.A.
TI  - Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a  Giant Phage Mutant Collection.
JO  - Genome Announcements
PY  - 2017
SP  - e00857
EP  - e00817
VL  - 5
AB  - We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium
AB  - strains TT6675 and TT9097, which we utilize for genetic
AB  - analyses of giant bacterial viruses. Our analyses identified several genetic
AB  - variations between the two strains, most significantly confirming strain TT6675
AB  - as a serine suppressor and TT9097 as a nonsuppressor.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Lean, S.S.
AU  - Suhaili, Z.
AU  - Thong, K.L.
AU  - Yeo, C.C.
TI  - Genome Sequence of Acinetobacter baumannii AC12, a Polymyxin-Resistant Strain Isolated from Terengganu, Malaysia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5979
EP  - 5980
VL  - 194
AB  - Acinetobacter baumannii is a major cause of nosocomial infection worldwide. We report the
AB  - draft genome sequence of A. baumannii AC12, a multidrug-resistant
AB  - nosocomial strain with additional resistance to carbapenems and polymyxin. The
AB  - genome data will provide insights into the genetic basis of antimicrobial
AB  - resistance and its adaptive mechanism.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Lee, M.V.J.
AU  - Savka, M.A.
TI  - High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01045
EP  - e01018
VL  - 7
AB  - Using Illumina and Nanopore reads, we assembled a high-quality draft genome sequence of
AB  - Allorhizobium vitis K309(T) (= ATCC 49767(T), = NCPPB 3554(T)), a
AB  - phytopathogenic strain isolated from a grapevine in Australia. The hybrid
AB  - approach generated 50% fewer contigs and a 3-fold increase in the N 50 value
AB  - compared with the previous Illumina-only assembly.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - McGroty, S.E.
AU  - Chew, T.H.
AU  - Chan, K.G.
AU  - Buckley, L.J.
AU  - Savka, M.A.
AU  - Hudson, A.O.
TI  - Whole-Genome Sequence of Enterobacter sp. Strain SST3, an Endophyte Isolated from Jamaican Sugarcane (Saccharum sp.) Stalk Tissue.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5981
EP  - 5982
VL  - 194
AB  - Enterobacter sp. strain SST3 is an endophytic bacterium isolated from Saccharum spp. Here we
AB  - present its annotated draft genome that may shed light on its role
AB  - as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome
AB  - announcement of a sugarcane-associated bacterium from the genus Enterobacter.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Rajasekaram, G.
AU  - Eng, W.W.H.
AU  - Kaniappan, P.
AU  - Dhanoa, A.
TI  - Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia.
JO  - Genome Announcements
PY  - 2017
SP  - e00768
EP  - e00717
VL  - 5
AB  - We report the whole-genome sequences of two carbapenem-resistant clinical isolates of
AB  - Klebsiella quasipneumoniae subsp. similipneumoniae obtained from two
AB  - different patients. Both strains contained three different extended-spectrum
AB  - beta-lactamase genes and showed strikingly high pairwise average nucleotide
AB  - identity of 99.99% despite being isolated 3 years apart from the same hospital.
ER  -

TY  - JOUR
AU  - Gan, H.M.
AU  - Triassi, A.J.
AU  - Wheatley, M.S.
AU  - Savka, M.A.
AU  - Hudson, A.O.
TI  - High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam).
JO  - Genome Announcements
PY  - 2014
SP  - e00170
EP  - e00114
VL  - 2
AB  - Here we report the whole-genome sequences of three endophytic bacteria, Enterobacter sp.
AB  - strain DC1, Enterobacter sp. strain DC3, and Enterobacter sp.
AB  - strain DC4, from root tubers of the yellow yam plant, Dioscorea cayenensis.
AB  - Preliminary analyses suggest that the genomes of the three bacteria contain genes
AB  - involved in acetoin and indole-3-acetic acid metabolism.
ER  -

TY  - JOUR
AU  - Gan, H.Y. et al.
TI  - Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (Bird's Eye Chili) and  Capsicum chinense (Yellow Lantern Chili), Respectively.
JO  - Genome Announcements
PY  - 2015
SP  - e00288
EP  - e00215
VL  - 3
AB  - Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas
AB  - oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the
AB  - synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing
AB  - factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in
AB  - Pseudomonas oryzihabitans RIT370.
ER  -

TY  - JOUR
AU  - Gan, H.Y.
AU  - Gan, H.M.
AU  - Savka, M.A.
AU  - Triassi, A.J.
AU  - Wheatley, M.S.
AU  - Smart, L.B.
AU  - Fabio, E.S.
AU  - Hudson, A.O.
TI  - Whole-genome sequences of 13 endophytic bacteria isolated from shrub willow (salix) grown in geneva, new york.
JO  - Genome Announcements
PY  - 2014
SP  - e00288
EP  - e00214
VL  - 2
AB  - Shrub willow, Salix spp. and hybrids, is an important bioenergy crop. Here we report the
AB  - whole-genome sequences and annotation of 13 endophytic bacteria from
AB  - stem tissues of Salix purpurea grown in nature and from commercial cultivars and
AB  - Salix viminalis x Salix miyabeana grown in bioenergy fields in Geneva, New York.
ER  -

TY  - JOUR
AU  - Gan, H.Y.
AU  - Gan, H.M.
AU  - Tarasco, A.M.
AU  - Busairi, N.I.
AU  - Barton, H.A.
AU  - Hudson, A.O.
AU  - Savka, M.A.
TI  - Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico.
JO  - Genome Announcements
PY  - 2014
SP  - e01133
EP  - e01114
VL  - 2
AB  - Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from
AB  - two sites within the Lechuguilla Cave in the Carlsbad Caverns
AB  - National Park, NM. Three of the five genomes contain an acyl-homoserine lactone
AB  - signal synthase ortholog (luxI) that is involved in cell-to-cell communication
AB  - via quorum sensing.
ER  -

TY  - JOUR
AU  - Gan, H.Y.
AU  - Noor, M.E.
AU  - Saari, N.A.
AU  - Musa, N.
AU  - Mustapha, B.
AU  - Usup, G.
AU  - Danish-Daniel, M.
TI  - Genome Sequence of Vibrio campbellii Strain UMTGB204, a Marine Bacterium Isolated from a Green Barrel Tunicate.
JO  - Genome Announcements
PY  - 2015
SP  - e00210
EP  - e00215
VL  - 3
AB  - Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The  genome of
AB  - this strain comprises 5,652,224 bp with 5,014 open reading frames, 9
AB  - rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental
AB  - tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and
AB  - bacteriocin were also identified.
ER  -

TY  - JOUR
AU  - Ganesan, A.T.
TI  - Genetic recombination during transformation in Bacillus subtilis:  appearance of a deoxyribonucleic acid methylase.
JO  - J. Bacteriol.
PY  - 1979
SP  - 270
EP  - 279
VL  - 139
AB  - In Bacillus subtilis the ability to take up deoxyribonucleic acid (DNA) and
AB  - undergo genetic transformation may coincide with the induction of defective
AB  - phage(s) and the expression of possibly related cryptic genes.  A
AB  - restriction-modification enzyme system appears to be expressed.  Targets of the
AB  - restriction activity on the DNA can be blocked by methylation catalyzed by the
AB  - methyl transferase.  It is shown that cellular DNA becomes progressively
AB  - methylated and reaches the maximum level during the peak of competency.
AB  - Deoxycytidine residues of both incoming donor and resident DNA are methylated.
AB  - The possible participation of these enzymes in recombination and the general
AB  - role of crytptic genes in inducible functions are discussed.
ER  -

TY  - JOUR
AU  - Ganesan, A.T.
TI  - Uptake, restriction, modification and recombination of DNA molecules during transformation in B. subtilis.
JO  - Molecular Cloning and Gene Regulation in Bacilli
PY  - 1982
SP  - 261
EP  - 268
VL  - 0
AB  - Bacillus subtilis can be subjected to regimens of growth conditions that would
AB  - permit them to take up single, double and plasmid superhelical DNA molecules.
AB  - We know very little of transport mechanisms the cell has in store to handle
AB  - different types of molecules.
ER  -

TY  - JOUR
AU  - Gangaiah, D.
AU  - Marinov, G.K.
AU  - Roberts, S.A.
AU  - Robson, J.
AU  - Spinola, S.M.
TI  - Draft Whole-Genome Sequence of Haemophilus ducreyi Strain AUSPNG1, Isolated from  a Cutaneous Ulcer of a Child from Papua New Guinea.
JO  - Genome Announcements
PY  - 2016
SP  - e01661
EP  - e01615
VL  - 4
AB  - Haemophilus ducreyi has recently emerged as a leading cause of cutaneous ulcers in the
AB  - yaws-endemic areas of Papua New Guinea and other South Pacific islands.
AB  - Here, we report the draft genome sequence of the H. ducreyi strain AUSPNG1,
AB  - isolated from a cutaneous ulcer of a child from Papua New Guinea.
ER  -

TY  - JOUR
AU  - Gangaiah, D.
AU  - Webb, K.M.
AU  - Humphreys, T.L.
AU  - Fortney, K.R.
AU  - Toh, E.
AU  - Tai, A.
AU  - Katz, S.S.
AU  - Pillay, A.
AU  - Chen, C.Y.
AU  - Roberts, S.A.
AU  - Munson, R.S. Jr.
AU  - Spinola, S.M.
TI  - Haemophilus ducreyi Cutaneous Ulcer Strains Are Nearly Identical to Class I Genital Ulcer Strains.
JO  - PLoS Neglected Trop. Dis.
PY  - 2015
SP  - E0003918
EP  - E0003918
VL  - 9
AB  - BACKGROUND: Although cutaneous ulcers (CU) in the tropics is frequently
AB  - attributed to Treponema pallidum subspecies pertenue, the causative agent of
AB  - yaws, Haemophilus ducreyi has emerged as a major cause of CU in yaws-endemic
AB  - regions of the South Pacific islands and Africa. H. ducreyi is generally
AB  - susceptible to macrolides, but CU strains persist after mass drug administration
AB  - of azithromycin for yaws or trachoma. H. ducreyi also causes genital ulcers (GU)
AB  - and was thought to be exclusively transmitted by microabrasions that occur during
AB  - sex. In human volunteers, the GU strain 35000HP does not infect intact skin;
AB  - wounds are required to initiate infection. These data led to several questions:
AB  - Are CU strains a new variant of H. ducreyi or did they evolve from GU strains? Do
AB  - CU strains contain additional genes that could allow them to infect intact skin?
AB  - Are CU strains susceptible to azithromycin? METHODOLOGY/PRINCIPAL FINDINGS: To
AB  - address these questions, we performed whole-genome sequencing and antibiotic
AB  - susceptibility testing of 5 CU strains obtained from Samoa and Vanuatu and 9
AB  - archived class I and class II GU strains. Except for single nucleotide
AB  - polymorphisms, the CU strains were genetically almost identical to the class I
AB  - strain 35000HP and had no additional genetic content. Phylogenetic analysis
AB  - showed that class I and class II strains formed two separate clusters and CU
AB  - strains evolved from class I strains. Class I strains diverged from class II
AB  - strains ~1.95 million years ago (mya) and CU strains diverged from the class I
AB  - strain 35000HP ~0.18 mya. CU and GU strains evolved under similar selection
AB  - pressures. Like 35000HP, the CU strains were highly susceptible to antibiotics,
AB  - including azithromycin. CONCLUSIONS/SIGNIFICANCE: These data suggest that CU
AB  - strains are derivatives of class I strains that were not recognized until
AB  - recently. These findings require confirmation by analysis of CU strains from
AB  - other regions.
ER  -

TY  - JOUR
AU  - Gangiredla, J.
AU  - Barnaba, T.J.
AU  - Mammel, M.K.
AU  - Lacher, D.W.
AU  - Elkins, C.A.
AU  - Lampel, K.A.
AU  - Whitehouse, C.A.
AU  - Tartera, C.
TI  - Fifty-Six Draft Genome Sequences of 10 Lactobacillus Species from 22 Commercial Dietary Supplements.
JO  - Genome Announcements
PY  - 2018
SP  - e00621
EP  - e00618
VL  - 6
AB  - Here, we present the genome sequences of 56 isolates of 10 species of the genus Lactobacillus
AB  - that are considered beneficial components of the gut microbiota.
AB  - The isolates examined were found in commercially available dietary supplements in
AB  - the U.S. market.
ER  -

TY  - JOUR
AU  - Gangiredla, J.
AU  - Mammel, M.K.
AU  - Barnaba, T.J.
AU  - Tartera, C.
AU  - Gebru, S.T.
AU  - Patel, I.R.
AU  - Leonard, S.R.
AU  - Kotewicz, M.L.
AU  - Lampel, K.A.
AU  - Elkins, C.A.
AU  - Lacher, D.W.
TI  - Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity.
JO  - Genome Announcements
PY  - 2017
SP  - e01321
EP  - e01317
VL  - 5
AB  - Pathogenic and nonpathogenic Escherichia coli strains present a vast genomic diversity. We
AB  - report the genome sequences of 2,244 E. coli isolates from multiple
AB  - animal and environmental sources. Their phylogenetic relationships and potential
AB  - risk to human health were examined.
ER  -

TY  - JOUR
AU  - Gangiredla, J.
AU  - Mammel, M.K.
AU  - Barnaba, T.J.
AU  - Tartera, C.
AU  - Gebru, S.T.
AU  - Patel, I.R.
AU  - Leonard, S.R.
AU  - Kotewicz, M.L.
AU  - Lampel, K.A.
AU  - Elkins, C.A.
AU  - Lacher, D.W.
TI  - Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.
JO  - Genome Announcements
PY  - 2018
SP  - e00271
EP  - e00218
VL  - 6
AB  - We report here the genome sequences of 55 strains belonging to the genus Escherichia from
AB  - multiple animal and environmental sources. These strains include
AB  - representatives of Escherichia albertii, Escherichia fergusonii, and six
AB  - additional genetically distinct lineages of Escherichia spp., one of which is
AB  - newly discovered and is being reported for the first time here.
ER  -

TY  - JOUR
AU  - Gangoiti, J.
AU  - Meng, X.
AU  - Lammerts-van-Bueren, A.
AU  - Dijkhuizen, L.
TI  - Draft Genome Sequence of Lactobacillus reuteri 121, a Source of alpha-Glucan and  beta-Fructan Exopolysaccharides.
JO  - Genome Announcements
PY  - 2017
SP  - e01691
EP  - e01616
VL  - 5
AB  - The probiotic bacterium Lactobacillus reuteri 121 is a well-known producer of diverse
AB  - homoexopolysaccharides (alpha-glucans and beta-fructans) from sucrose and
AB  - maltodextrins/starches of interest for food applications. Here, we report the
AB  - draft genome sequence of this strain, with a focus on carbohydrate-active
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Ganguly, S.
AU  - Jimenez-Galisteo, G.
AU  - Pletzer, D.
AU  - Winterhalter, M.
AU  - Benz, R.
AU  - Vinas, M.
TI  - Draft Genome Sequence of Dietzia maris DSM 43672, a Gram-Positive Bacterium of the Mycolata Group.
JO  - Genome Announcements
PY  - 2016
SP  - e00542
EP  - e00516
VL  - 4
AB  - Here, we report the draft genome sequence of Dietzia maris, known previously as Rhodococcus
AB  - maris It is 3,505,372 bp in size with a G+C content of 73%. The draft
AB  - genome sequence will improve our understanding of Dietzia maris related to other
AB  - mycolata species and constitutes a basic tool for exploring the cell wall
AB  - proteins.
ER  -

TY  - JOUR
AU  - Ganji, R. et al.
TI  - High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1T Isolated from Great Boiling Spring, Nevada.
JO  - Genome Announcements
PY  - 2016
SP  - e01112
EP  - e01116
VL  - 4
AB  - The draft genome of Thermocrinis jamiesonii GBS1T is 1,315,625 bp in 10 contigs and encodes
AB  - 1,463 predicted genes. The presence of sox genes and various
AB  - glycoside hydrolases and the absence of uptake NiFe hydrogenases (hyaB) are
AB  - consistent with a requirement for thiosulfate and suggest the ability to use
AB  - carbohydrate polymers.
ER  -

TY  - JOUR
AU  - Gann, A.A.F.
TI  - Recognition domains of Type I restriction enzymes.
JO  - Ph.D. Thesis
PY  - 1988
AB  - Type I restriction and modification enzymes recognize asymmetric, bipartite target sequences,
AB  - the specificity of which is dictated by a single subunit encoded by the hsdS gene.  Within the
AB  - K-family, the S genes of members with different specificities have been sequenced.
AB  - Comparisons of these reveal two large variable regions, each of ~450 base pairs, separated by
AB  - a highly conserved region of ~100 base pairs.  Recombination between the central conserved
AB  - regions of two S genes, those of StySP and StySB, has produced a new S gene (StySQ) encoding a
AB  - functional polypeptide that confers a novel, hybrid specificity.  In this thesis I describe
AB  - the formation of a second recombinant S gene, StySJ, which is of reciprocal structure to
AB  - StySQ.  StySJ recognizes a target sequence predicted by a model wherein each S polypeptide
AB  - contains two structurally independent DNA recognition domains which act together in defining
AB  - an enzyme's target sequence.  Site directed mutagenesis was then used to demonstrate that the
AB  - variable N-terminal 150 amino acids of an S polypeptide alone constitute one DNA recognition
AB  - domain.  Two S polypeptides, each deleted for a single recognition domain were also produced.
AB  - Though showing no enzymatic activity in vivo, these truncated polypeptides were capable of
AB  - inhibiting the activities of complete restriction and modification enzymes from their own
AB  - family, but not from another.  This is interpreted as being due to the truncated S
AB  - polypeptides binding other enzyme subunits, thereby disrupting the formation of functional
AB  - complexes.
ER  -

TY  - JOUR
AU  - Gann, A.A.F.
TI  - Recognition domains of type I restriction enzymes.
JO  - Diss. Abstr.
PY  - 1990
SP  - 4377B
EP  - 4377B
VL  - 50
AB  - Type I restriction and modification enzymes recognize asymmetric, bipartite target sequences,
AB  - the specificity of which is dictated by a single subunit encoded by the HsdS gene.  Within the
AB  - K-family, the S genes of members with different specificities have been sequenced (Gough and
AB  - Murray, 1983; Gann et al. 1987).  Comparisons of these reveal two large variable regions, each
AB  - of ~450 base pairs, separated by a highly conserved region of ~100 base pairs. Recombination
AB  - between the central conserved regions of two S genes, those of StySP and StySB, has produced a
AB  - new S gene (StySQ) encoding a functional polypeptide that confers a novel, hybrid specificity
AB  - (Fuller-Pace et al., 1984; Nagaraja, et al. 1985).  In this thesis I describe the formation of
AB  - a second recombinant S gene, StySJ, which is of reciprocal structure to StySQ.  StySJ
AB  - recognizes a target sequence predicted by a model wherein each S polypeptide contains two
AB  - structurally independent DNA recognition domains which act together in defining an enzyme's
AB  - target sequence.  Site directed mutagenesis was then used to demonstrate that the variable
AB  - N-terminal 150 amino acids of an S polypeptide alone constitute one DNA recognition domain.
AB  - Two S polypeptides, each deleted for a single recognition domain were also produced.  Though
AB  - showing no enzymatic activity in vivo, these truncated polypeptide were capable of inhibiting
AB  - the activities of complete restriction and modification enzymes from their own family, but not
AB  - from another.  This is interpreted as being due to the truncated S polypeptides binding other
AB  - enzyme subunits, thereby disrupting the formation of function restriction complexes.
ER  -

TY  - JOUR
AU  - Gann, A.A.F.
AU  - Campbell, A.J.B.
AU  - Collins, J.F.
AU  - Coulson, A.F.W.
AU  - Murray, N.E.
TI  - Reassortment of DNA recognition domains and the evolution of new specificities.
JO  - Mol. Microbiol.
PY  - 1987
SP  - 13
EP  - 22
VL  - 1
AB  - TypeI restriction enzymes comprise three subunits only one of which, the S polypeptide,
AB  - dictates the specificity of the DNA sequence recognized. Recombination between two different
AB  - hsdS genes, SP and SB, led to the isolation of a system, SQ, which had a different specificity
AB  - from that of either parent. The finding that the nucleotide sequence recognized by SQ is a
AB  - hybrid containing components from both the SP and SB target sequences suggested that DNA
AB  - recognition is carried out by two separable domains within each specificity polypeptide.  To
AB  - test this we have made the recombinant gene of reciprocal structure and demonstrate that it
AB  - encodes a polypeptide whose recognition sequence, deduced in vivo, is as predicted by this
AB  - model.  We also report the sequence of the SB specificity gene, so that information is now
AB  - available for the five known members of this family of enzymes.  All show a similar
AB  - organization of conserved and variable regions.  Comparisons of the predicted amino acid
AB  - sequences reveal large non-conserved areas which may not even be structurally similar.  This
AB  - is remarkable since these different S subunits are functionally identical, except for the
AB  - specificity with respect to the DNA sequence with which they interact.  We discuss the
AB  - correlation of the variation in polypeptide sequence with recognition specificities.
ER  -

TY  - JOUR
AU  - Gao, C.
AU  - Hu, C.
AU  - Ma, C.
AU  - Su, F.
AU  - Yu, H.
AU  - Jiang, T.
AU  - Dou, P.
AU  - Wang, Y.
AU  - Qin, T.
AU  - Lv, M.
AU  - Xu, P.
TI  - Genome Sequence of the Lactate-Utilizing Pseudomonas aeruginosa Strain XMG.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4751
EP  - 4752
VL  - 194
AB  - Pseudomonas aeruginosa XMG, isolated from soil, utilizes lactate. Here we present a 6.45-Mb
AB  - assembly of its genome sequence. Besides the lactate utilization
AB  - mechanism of the strain, the genome sequence may also provide other useful
AB  - information related to P. aeruginosa, such as identifying genes involved in
AB  - virulence, drug resistance, and aromatic catabolism.
ER  -

TY  - JOUR
AU  - Gao, E.B.
AU  - Gui, J.F.
AU  - Zhang, Q.Y.
TI  - A Novel Cyanophage with a Cyanobacterial Nonbleaching Protein A Gene in the Genome.
JO  - J. Virol.
PY  - 2012
SP  - 236
EP  - 245
VL  - 86
AB  - A cyanophage, PaV-LD, has been isolated from harmful filamentous cyanobacterium
AB  - Planktothrix agardhii in Lake Donghu, a shallow freshwater lake in China. Here,
AB  - we present the cyanophage's genomic organization and major structural proteins.
AB  - The genome is a 95,299-bp-long, linear double-stranded DNA and contains 142
AB  - potential genes. BLAST searches revealed 29 proteins of known function in
AB  - cyanophages, cyanobacteria, or bacteria. Thirteen major structural proteins
AB  - ranging in size from 27 kDa to 172 kDa were identified by SDS-PAGE and
AB  - mass-spectrometric analysis. The genome lacks major genes that are necessary to
AB  - the tail structure, and the tailless PaV-LD has been confirmed by an electron
AB  - microscopy comparison with other tail cyanophages and phages. Phylogenetic
AB  - analysis of the major capsid proteins also reveals an independent branch of
AB  - PaV-LD that is quite different from other known tail cyanophages and phages.
AB  - Moreover, the unique genome carries a nonbleaching protein A (NblA) gene (open
AB  - reading frame [ORF] 022L), which is present in all phycobilisome-containing
AB  - organisms and mediates phycobilisome degradation. Western blot detection
AB  - confirmed that 022L was expressed after PaV-LD infection in the host filamentous
AB  - cyanobacterium. In addition, its appearance was companied by a significant
AB  - decline of phycocyanobilin content and a color change of the cyanobacterial cells
AB  - from blue-green to yellow-green. The biological function of PaV-LD nblA was
AB  - further confirmed by expression in a model cyanobacterium via an integration
AB  - platform, by spectroscopic analysis and electron microscopy observation. The data
AB  - indicate that PaV-LD is an exceptional cyanophage of filamentous cyanobacteria,
AB  - and this novel cyanophage will also provide us with a new vision of the
AB  - cyanophage-host interactions.
ER  -

TY  - JOUR
AU  - Gao, F.
AU  - Wang, Y.
AU  - Liu, Y.J.
AU  - Wu, X.M.
AU  - Lv, X.
AU  - Gan, Y.R.
AU  - Song, S.D.
AU  - Huang, H.
TI  - Genome sequence of Acinetobacter baumannii MDR-TJ.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2365
EP  - 2366
VL  - 193
AB  - Acinetobacter baumannii is a species of pathogenic bacteria, originally included in the
AB  - aerobic gram-negative bacterium, which is resistant to most antibiotics. In this paper, the
AB  - MDR-TJ strain was isolated by the Second Hospital of Tianjin Medical University, China, which
AB  - was found resistant to penicillin, spore class, aminoglycosides, quinolones and also imipenem.
AB  - The genome sequence of Acinetobacter baumannii strain MDR-TJ was determined using a
AB  - combination of 454 pyrosequencing and paired-end sequencing performed by the Roche Genome
AB  - Sequencer FLX Systems to generate a scaffolded assembly.
ER  -

TY  - JOUR
AU  - Gao, G.
AU  - Li, J.
AU  - Li, T.
AU  - Zhang, Z.
AU  - Wang, L.
AU  - Yuan, X.
AU  - Wang, Y.
AU  - Xu, J.
AU  - Ke, Y.
AU  - Huang, L.
AU  - Wang, D.
AU  - Chen, Z.
AU  - Xu, X.
TI  - Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6680
EP  - 6680
VL  - 194
AB  - Brucella canis infects several species of animals, and canine is the preferred host. Genome
AB  - sequences of strains from different hosts are valuable for
AB  - comparative analysis of host adaptation and microevolution. Here, we report the
AB  - genome sequence of Brucella canis strain 118, a strain isolated from canine.
ER  -

TY  - JOUR
AU  - Gao, H.
AU  - Ma, Y.
AU  - Shao, Q.
AU  - Hong, Q.
AU  - Zheng, G.
AU  - Li, Z.
TI  - Genome Sequence of Corynebacterium pseudotuberculosis Strain KM01, Isolated from  the Abscess of a Goat in Kunming, China.
JO  - Genome Announcements
PY  - 2018
SP  - e00013
EP  - e00018
VL  - 6
AB  - Caseous lymphadenitis (CLA) is an acute, pyogenic, and contagious disease of goat that imposes
AB  - considerable economic losses for farmers, and it is caused by
AB  - Corynebacterium pseudotuberculosis Herein, we introduce the genome sequencing of
AB  - C. pseudotuberculosis strain KM01, isolated from an abscess of a Saanen goat from
AB  - Kunming, China. The genome contains 2,198 genes, the total length of the genes
AB  - was 2,337,666 bp, and the GC content was 52.18%. The number of tandem repeat
AB  - sequences was 44, the total length of the tandem repeat sequences was 1,970 bp
AB  - (0.0772% of the genome), the number of minisatellite DNAs was 36, and there were
AB  - 48 tRNAs and 12 rRNAs.
ER  -

TY  - JOUR
AU  - Gao, J.
AU  - Yu, X.
AU  - Xie, Z.
TI  - Draft Genome Sequence of High-Siderophore-Yielding Pseudomonas sp. Strain HYS.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4121
EP  - 4121
VL  - 194
AB  - We sequenced the genome of the high-siderophore-yielding strain Pseudomonas sp. HYS and then
AB  - analyzed its iron acquisition systems. The 5.6-Mb draft genome
AB  - sequence has a special pattern of pyoverdine synthesis clusters and contains an
AB  - hmuRSTUV heme uptake cluster, which has a homolog only in some strains of the
AB  - order Enterobacteriales.
ER  -

TY  - JOUR
AU  - Gao, L.
AU  - Zhou, J.
AU  - Liu, J.
AU  - Du, G.
AU  - Chen, J.
TI  - Draft Genome Sequence of Gluconobacter oxydans WSH-003, a Strain That Is Extremely Tolerant of Saccharides and Alditols.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4455
EP  - 4456
VL  - 194
AB  - Gluconobacter oxydans is known for its incomplete oxidation of a wide range of alcohols,
AB  - sugars, and acids in a bioprocess. The corresponding oxidation products
AB  - are secreted almost completely into the medium. Here, we present the high-quality
AB  - draft genome sequence of G. oxydans WSH-003, an industrial strain with both high
AB  - l-sorbose productivity and extreme tolerance to saccharides and alditols.
ER  -

TY  - JOUR
AU  - Gao, P.
AU  - Tang, Q.
AU  - An, X.M.
AU  - Yan, X.X.
AU  - Liang, D.C.
TI  - Structure of HsdS Subunit from Thermoanaerobacter tengcongensis Sheds Lights on Mechanism of Dynamic Opening and Closing of Type I Methyltransferase.
JO  - PLoS ONE
PY  - 2011
SP  - e17346
EP  - e17346
VL  - 6
AB  - Type I DNA methyltransferases contain one specificity subunit (HsdS) and two modification
AB  - subunits (HsdM). The electron microscopy model of
AB  - M.EcoKI-M2S1 methyltransferase shows a reasonable closed state of this
AB  - clamp-like enzyme, but the structure of the open state is still
AB  - unclear. The 1.95 angstrom crystal structure of the specificity subunit
AB  - from Thermoanaerobacter tengcongensis (TTE-HsdS) shows an unreported
AB  - open form inter-domain orientation of this subunit. Based on the
AB  - crystal structure of TTE-HsdS and the closed state model of
AB  - M.EcoKI-M2S1, we constructed a potential open state model of type I
AB  - methyltransferase. Mutational studies indicated that two alpha-helices
AB  - (aa30-59 and aa466-495) of the TTE-HsdM subunit are important
AB  - inter-subunit interaction sites in the TTE-M2S1 complex. DNA binding
AB  - assays also highlighted the importance of the C-terminal region of
AB  - TTE-HsdM for DNA binding by the TTE-M2S1 complex. On the basis of
AB  - structural analysis, biochemical experiments and previous studies, we
AB  - propose a dynamic opening and closing mechanism for type I
AB  - methyltransferase.
ER  -

TY  - JOUR
AU  - Gao, Q.
AU  - Thorson, J.S.
TI  - The biosynthetic genes encoding for the production of the dynemicin enediyne core in Micromonospora chersina ATCC53710.
JO  - FEMS Microbiol. Lett.
PY  - 2008
SP  - 105
EP  - 114
VL  - 282
AB  - Dynemicin is a novel anthraquinone-fused member of the 10-membered
AB  - enediyne antitumor antibiotic family. The development of a genetic system
AB  - for the dynemicin producer Micromonospora chersina confirmed, for the
AB  - first time, the requirement of the putative enediyne core biosynthetic
AB  - genes (dynE8, U14 and U15) and a tailoring oxidase gene (orf23) for
AB  - dynemicin production. Cloning and sequence analysis of a 76 kb of genomic
AB  - sequence region containing dynE8 revealed a variety of genes conserved
AB  - among known enediyne loci. Surprisingly, this fragment and flanking
AB  - chromosomal DNA lacked any obvious genes encoding for the biosynthesis of
AB  - the anthraquinone, suggesting that the location of genes encoding for the
AB  - biosynthesis of the dynemicin enediyne core and the dynemicin
AB  - anthraquinone are chromosomally distinct. The demonstrated trace
AB  - production of a shunt product from mutant strain QGD23 (Deltaorf23) also
AB  - sets the stage for subsequent studies to delineate the key steps in
AB  - enediyne core biosynthesis and tailoring.
ER  -

TY  - JOUR
AU  - Gao, X.
AU  - Liu, K.
AU  - Qiu, B.-S.
TI  - An investigation on the genetic background of  Nostoc flagelliforme by similarity analysis of its partial genomic DNA and  phylogenetic comparison of deduced related species.
JO  - Acta Physiol. Plant.
PY  - 2011
SP  - 1301
EP  - 1318
VL  - 33
AB  - Nostoc flagelliforme, which is distributed on arid and semi-arid steppes of northwestern parts
AB  - of China, has attracted increasing interest for its stress tolerance. In order to gain more
AB  - insight into the genetic background of N. flagelliforme, we sequenced its partial genomic DNA
AB  - for
AB  - similarity analyses against current public databases, followed
AB  - by phylogenetic comparison of N. flagelliforme and the potentially related species deduced
AB  - from the similarity analyses. Approximately 430 kb genomic sequence (*5% of genome as a rough
AB  - estimate) was determined from 106
AB  - distinct genomic clones. Nucleotide BLAST showed that *23.1% of the partial genomic sequence
AB  - was similar to N. punctiforme genomic DNA and *12.4% to its plasmid DNA. Similar protein
AB  - search by online FASTA-protein program showed 46.2% of the similar proteins had their
AB  - corresponding orthologs in N. punctiforme genome. Furthermore, phylogenetic comparison based
AB  - on 16S rRNA
AB  - sequences showed N. flagelliforme and N. punctiforme clustered closer among the deduced
AB  - related species. These results indicated that N. punctiforme might also be potentially close
AB  - neighbor species of N. flagelliforme, in addition to the formerly regarded close neighbor
AB  - species N. commune
AB  - and N. sphaeroids. In general, these data enriched our recognition of the evolutionary
AB  - relationship between N. flagelliforme and other Nostoc species, especially N. punctiforme.
ER  -

TY  - JOUR
AU  - Gao, X.Y.
AU  - Zhi, X.Y.
AU  - Li, H.W.
AU  - Zhou, Y.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Haynes, M.
AU  - Lobos, E.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Mavromatis, K.
AU  - Tindall, B.J.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Li, W.J.
TI  - Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 1
EP  - 1
VL  - 10
AB  - Species of the genus Halomonas are halophilic and their flexible adaption to changes of
AB  - salinity and temperature brings considerable potential biotechnology
AB  - applications, such as degradation of organic pollutants and enzyme production.
AB  - The type strain Halomonas lutea YIM 91125(T) was isolated from a hypersaline lake
AB  - in China. The genome of strain YIM 91125(T) becomes the twelfth species sequenced
AB  - in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We
AB  - described the features of H. lutea YIM 91125(T), together with the high quality
AB  - draft genome sequence and annotation of its type strain. The 4,533,090 bp long
AB  - genome of strain YIM 91125(T) with its 4,284 protein-coding and 84 RNA genes is a
AB  - part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial
AB  - genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has
AB  - a larger genome size and more specific genes, which indicated acquisition of
AB  - function bringing better adaption to its environment. DDH analysis demonstrated
AB  - that H. lutea is a distinctive species, and halophilic features and nitrogen
AB  - metabolism related genes were discovered in its genome.
ER  -

TY  - JOUR
AU  - Gao, Y.H.
AU  - Guo, R.J.
AU  - Li, S.D.
TI  - Draft Genome Sequence of Bacillus velezensis B6, a Rhizobacterium That Can Control Plant Diseases.
JO  - Genome Announcements
PY  - 2018
SP  - e00182
EP  - e00118
VL  - 6
AB  - The draft genome of Bacillus velezensis strain B6, a rhizobacterium with good biocontrol
AB  - performance isolated from soil in China, was sequenced. The assembly
AB  - comprises 32 scaffolds with a total size of 3.88 Mb. Gene clusters coding either
AB  - ribosomally encoded bacteriocins or nonribosomally encoded antimicrobial
AB  - polyketides and lipopeptides in the genome may contribute to plant disease
AB  - control.
ER  -

TY  - JOUR
AU  - Gao, Y.X.
AU  - Zhou, Y.Y.
AU  - Xie, Y.
AU  - Wang, M.
AU  - Wang, S.J.
AU  - Shen, S.G.
TI  - Complete Genome Sequence of Actinomyces hongkongensis HKU8T Isolated from Human Blood.
JO  - Genome Announcements
PY  - 2017
SP  - e01650
EP  - e01616
VL  - 5
AB  - Members of the genus Actinomyces are strongly associated with human diseases. We  present here
AB  - the complete genome sequence of Actinomyces hongkongensis HKU8T,
AB  - which consists of one circular chromosome. The strain characteristically contains
AB  - various genes encoding for enzymes involved in arylamidase utilization.
ER  -

TY  - JOUR
AU  - Gao, Z.
AU  - Liu, X.
AU  - Ruan, L.
TI  - Genome Sequence of Anaerophaga sp. Strain HS1, a Novel, Moderately Thermophilic, Strictly Anaerobic Bacterium Isolated from Hot Spring  Sediment.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5572
EP  - 5572
VL  - 193
AB  - Anaerophaga sp. strain HS1 was isolated from offshore hot spring sediment in Xiamen, China. It
AB  - was identified as a novel, moderately thermophilic,
AB  - strictly anaerobic bacterium affiliated with the family Marinilabiaceae
AB  - and showed xylanase activity. Here, we describe the 3.88-Mb draft genome
AB  - sequence of Anaerophaga sp. strain HS1 and the annotation analysis of
AB  - related xylanase genes.
ER  -

TY  - JOUR
AU  - Garau, G.
AU  - Terpolilli, J.
AU  - Hill, Y.
AU  - Tian, R.
AU  - Howieson, J.
AU  - Brau, L.
AU  - Goodwin, L.
AU  - Han, J.
AU  - Reddy, T.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of  Medicago murex and M. polymorpha.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 4
EP  - 4
VL  - 9
AB  - Ensifer medicae Di28 is an aerobic, motile, Gram-negative, non-spore-forming rod  that can
AB  - exist as a soil saprophyte or as a legume microsymbiont of Medicago spp.
AB  - Di28 was isolated in 1998 from a nodule recovered from the roots of M. polymorpha
AB  - growing in the south east of Sardinia (Italy). Di28 is an effective microsymbiont
AB  - of the annual forage legumes M. polymorpha and M. murex and is capable of
AB  - establishing a partially effective symbiotic association with the perennial M.
AB  - sativa. Here we describe the features of E. medicae Di28, together with genome
AB  - sequence information and its annotation. The 6,553,624 bp standard draft genome
AB  - is arranged into 104 scaffolds of 104 contigs containing 6,394 protein-coding
AB  - genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100
AB  - sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for
AB  - Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Garbeva, P.
AU  - van Elsas, J.D.
AU  - de Boer, W.
TI  - Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4119
EP  - 4120
VL  - 194
AB  - Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity
AB  - against different plant pathogens. Here we present the
AB  - 5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain
AB  - PRI-2C with the aim of providing insight into the genomic basis of its
AB  - antagonistic activity.
ER  -

TY  - JOUR
AU  - Garcia, B.G.
AU  - Ooka, T.
AU  - Gotoh, Y.
AU  - Vieira, M.A.M.
AU  - Yamamoto, D.
AU  - Ogura, Y.
AU  - Girao, D.M.
AU  - Sampaio, S.C.F.
AU  - Melo, A.B.
AU  - Irino, K.
AU  - Hayashi, T.
AU  - Gomes, T.A.T.
TI  - Genetic relatedness and virulence properties of enteropathogenic Escherichia coli strains of serotype O119:H6 expressing localized adherence or localized and aggregative adherence-like patterns on HeLa cells.
JO  - Int. J. Med. Microbiol.
PY  - 2016
SP  - 152
EP  - 164
VL  - 306
AB  - Enteropathogenic Escherichia coli (EPEC) induce attaching and effacing (A/E) lesions in
AB  - enterocytes and produce the bundle-forming pilus (BFP) contributing to
AB  - the localized adherence (LA) pattern formation on HeLa cells. Enteroaggregative
AB  - E. coli (EAEC) produce aggregative adherence (AA) on HeLa cells and form
AB  - prominent biofilms. The ability to produce LA or AA is an important hallmark to
AB  - classify fecal E. coli isolates as EPEC or EAEC, respectively. E. coli strains of
AB  - serotype O119:H6 exhibit an LA+ phenotype and have been considered as comprising
AB  - a clonal group of EPEC strains. However, we have recently identified O119:H6 EPEC
AB  - strains that produce LA and an AA-like pattern concurrently (LA/AA-like+). In
AB  - this study, we evaluated the relatedness of three LA/AA-like+ and three LA+
AB  - O119:H6 strains by comparing their virulence and genotypic properties. We first
AB  - found that the LA/AA-like+ strains induced actin accumulation in HeLa cells
AB  - (indicative of A/E lesions formation) and formed biofilms on abiotic surfaces
AB  - more efficiently than the LA+ strains. MLST analysis showed that the six strains
AB  - all belong to the ST28 complex. All strains carried multiple plasmids, but as
AB  - plasmid profiles were highly variable, this cannot be used to differentiate
AB  - LA/AA-like+ and LA+ strains. We further obtained their draft genome sequences and
AB  - the complete sequences of four plasmids harbored by one LA/AA-like+ strain.
AB  - Analysis of these sequences and comparison with 37 fully sequenced E. coli
AB  - genomes revealed that both O119:H6 groups belong to the E. coli phylogroup B2 and
AB  - are very closely related with only 58-67 SNPs found between LA/AA-like+ and LA+
AB  - strains. Search of the draft sequences of the six strains for adhesion-related
AB  - genes known in EAEC and other E. coli pathotypes detected no genes specifically
AB  - present in LA/AA-like+ strains. Unexpectedly however, we found that a large
AB  - plasmid distinct from pEAF is responsible for the AA-like phenotype of the
AB  - LA/AA-like+ strains. Although we have not identified any plasmid genes
AB  - specifically present in all LA/AA-like+ strains and absent in the LA+ strains,
AB  - these results suggest the presence of an unknown mechanism to promote the AA-like
AB  - pattern production and biofilm formation by the LA/AA-like+ strains. Because
AB  - their ability to produce A/E lesions and biofilm concomitantly could exacerbate
AB  - the clinical condition of the patient and lead to persistent diarrhea, the
AB  - mechanism underlying the enhanced biofilm formation by the LA/AA-like+ O119:H6
AB  - strains and their spread and involvement in severe diarrheal diseases should be
AB  - more intensively investigated.
ER  -

TY  - JOUR
AU  - Garcia, J.C.
AU  - Urakawa, H.
AU  - Le, V.Q.
AU  - Stein, L.Y.
AU  - Klotz, M.G.
AU  - Nielsen, J.L.
TI  - Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment.
JO  - Genome Announcements
PY  - 2013
SP  - e00930
EP  - e00913
VL  - 1
AB  - Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp.
AB  - strain APG3 is a psychrotolerant betaproteobacterial
AB  - ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft
AB  - genome revealed that it represents a new species of cluster 0 Nitrosospira, which
AB  - is presently not represented by described species.
ER  -

TY  - JOUR
AU  - Garcia, J.L.
AU  - Rozas, D.
AU  - Del Cerro, C.
AU  - Nogales, J.
AU  - El-Said, M.M.
AU  - Diaz, E.
TI  - Genome Sequence of Pseudomonas azelaica HBP1, Which Catabolizes 2-Hydroxybiphenyl Fungicide.
JO  - Genome Announcements
PY  - 2014
SP  - e01248
EP  - e01213
VL  - 2
AB  - Pseudomonas azelaica HBP1 (DSM 8897) is one of the few bacteria able to completely mineralize
AB  - the 2-hydroxybiphenyl biocide. Here, we report the draft
AB  - genome sequence of this strain (7.4 Mbp; G+C content, 63.5%) and the findings
AB  - obtained from its genome annotation.
ER  -

TY  - JOUR
AU  - Garcia, L.R.
AU  - Molineux, I.J.
TI  - Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 12430
EP  - 12435
VL  - 96
AB  - Infection of Escherichia coli containing the type I restriction enzyme EcoKI by bacteriophage
AB  - T7 0.3 mutants leads to restriction during the late stages of genome entry and during DNA
AB  - replication. Patterns of cleavage in vivo suggest that some cutting occurs near the midpoint
AB  - of two recognition sites, consistent with the idea that EcoKI translocates DNA bidirectionally
AB  - through itself and cuts when two enzyme molecules collide. Rapid ejection of a 0.3(+) T7
AB  - genome from a bacteriophage lambda particle results in degradation of the infecting DNA by
AB  - EcoKI, showing that the normal T7 DNA translocation process delays restriction. A unique
AB  - recognition site inserted at the genomic left end allows EcoKI to function as a molecular
AB  - motor and to translocate the remaining 39 kilobases of T7 DNA into the cell.
ER  -

TY  - JOUR
AU  - Garcia, N.S.
AU  - Yung, C.M.
AU  - Davis, K.M.
AU  - Rynearson, T.
AU  - Hunt, D.E.
TI  - Draft Genome Sequences of Three Bacterial Isolates from Cultures of the Marine Diatom Thalassiosira rotula.
JO  - Genome Announcements
PY  - 2017
SP  - e00316
EP  - e00317
VL  - 5
AB  - Phytoplankton often both provision and depend on heterotrophic bacteria. In order to
AB  - investigate these relationships further, we sequenced draft genomes of three
AB  - bacterial isolates from cultures of the marine diatom Thalassiosira rotula to
AB  - identify metabolic functions that may support interactions with T. rotula.
ER  -

TY  - JOUR
AU  - Garcia, P.
AU  - Monjardin, C.
AU  - Martin, R.
AU  - Madera, C.
AU  - Soberon, N.
AU  - Garcia, E.
AU  - Meana, A.
AU  - Suarez, J.E.
TI  - Isolation of new Stenotrophomonas bacteriophages and genomic characterization of temperate phage S1.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 7552
EP  - 7560
VL  - 74
AB  - Twenty-two phages that infect Stenotrophomonas species were isolated
AB  - through sewage enrichment and prophage induction. Of them, S1, S3, and S4
AB  - were selected due to their wide host ranges compared to those of the other
AB  - phages. S1 and S4 are temperate siphoviruses, while S3 is a virulent
AB  - myovirus. The genomes of S3 and S4, about 33 and 200 kb, were resistant to
AB  - restriction digestion. The lytic cycles lasted 30 min for S3 and about 75
AB  - min for S1 and S4. The burst size for S3 was 100 virions/cell, while S1
AB  - and S4 produced about 75 virus particles/cell. The frequency of
AB  - bacteriophage-insensitive host mutants, calculated by dividing the number
AB  - of surviving colonies by the bacterial titer of a parallel, uninfected
AB  - culture, ranged between 10(-5) and 10(-6) for S3 and 10(-3) and 10(-4) for
AB  - S1 and S4. The 40,287-bp genome of S1 contains 48 open reading frames
AB  - (ORFs) and 12-bp 5' protruding cohesive ends. By using a combination of
AB  - bioinformatics and experimental evidence, functions were ascribed to 21
AB  - ORFs. The morphogenetic and lysis modules are well-conserved, but no
AB  - lysis-lysogeny switch or DNA replication gene clusters were recognized.
AB  - Two major clusters of genes with respect to transcriptional orientation
AB  - were observed. Interspersed among them were lysogenic conversion genes
AB  - encoding phosphoadenosine phosphosulfate reductase and GspM, a protein
AB  - involved in the general secretion system II. The attP site of S1 may be
AB  - located within a gene that presents over 75% homology to a
AB  - Stenotrophomonas chromosomal determinant.
ER  -

TY  - JOUR
AU  - Garcia, R.A.
AU  - Bustamante, C.J.
AU  - Reich, N.O.
TI  - Sequence-specific recognition by cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 7618
EP  - 7622
VL  - 93
AB  - DNA methyltransferases modify specific cytosines and adenines within 2-6 bp recognition
AB  - sequences.  We used scanning force microscopy and gel shift analysis to show that M.HhaI, a
AB  - cytosine C5 methyltransferase, causes only a 2 degree bend upon binding its recognition site.
AB  - Our results are consistent with prior crystallographic analysis showing that the enzyme
AB  - stabilizes an extrahelical base while leaving the DNA duplex otherwise unperturbed.  In
AB  - contrast, similar analysis of M.EcoRI, an adenine N6 DNA methyltransferase, shows an average
AB  - bend angle of approximately 52 degrees.  This distortion of DNA conformation by M.EcoRI is
AB  - shown to be important for sequence-specific binding.
ER  -

TY  - JOUR
AU  - Garcia, R.G.
AU  - Brank, A.S.
AU  - Christman, J.K.
AU  - Marquez, V.E.
AU  - Eritja, R.
TI  - Synthesis of oligonucleotide inhibitors of DNA (cytosine-C5) methyltransferase containing 5-azacytosine residues at specific sites.
JO  - Antisense Nucleic Acid Drug Dev.
PY  - 2001
SP  - 369
EP  - 378
VL  - 11
AB  - The incorporation of 5-azacytosine residues into DNA causes potent inhibition of DNA
AB  - (cytosine-C5) methyltransferases.  The synthesis of oligodeoxyribonucleotides incorporating
AB  - single or multiple 5-aza-2'-deoxycytidine residues at precise sites was undertaken to
AB  - generate an array of sequences containing the reactive 5-azacytosine base as specific target
AB  - sites for enzymatic methylation.  Preparation of these modified oligonucleotides requires the
AB  - use of 2-(p-nitrophenyl) ethyloxycarbonyl (NPEOC) groups for the protection of exocyclic amino
AB  - functions.  These groups are removed under mild conditions, thus avoiding conventional
AB  - protocols that are detrimental to the integrity of the 5-azacytosine ring.
ER  -

TY  - JOUR
AU  - Garcia-Alvarez, L. et al.
TI  - Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study.
JO  - Lancet Infect Dis
PY  - 2011
SP  - 595
EP  - 603
VL  - 11
AB  - BACKGROUND: Animals can act as a reservoir and source for the emergence of
AB  - novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human
AB  - beings. Here, we report the discovery of a strain of S aureus (LGA251)
AB  - isolated from bulk milk that was phenotypically resistant to meticillin
AB  - but tested negative for the mecA gene and a preliminary investigation of
AB  - the extent to which such strains are present in bovine and human
AB  - populations. METHODS: Isolates of bovine MRSA were obtained from the
AB  - Veterinary Laboratories Agency in the UK, and isolates of human MRSA were
AB  - obtained from diagnostic or reference laboratories (two in the UK and one
AB  - in Denmark). From these collections, we searched for mecA PCR-negative
AB  - bovine and human S aureus isolates showing phenotypic meticillin
AB  - resistance. We used whole-genome sequencing to establish the genetic basis
AB  - for the observed antibiotic resistance. FINDINGS: A divergent mecA
AB  - homologue (mecA(LGA251)) was discovered in the LGA251 genome located in a
AB  - novel staphylococcal cassette chromosome mec element, designated type-XI
AB  - SCCmec. The mecA(LGA251) was 70% identical to S aureus mecA homologues and
AB  - was initially detected in 15 S aureus isolates from dairy cattle in
AB  - England. These isolates were from three different multilocus sequence type
AB  - lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130)
AB  - was identified in 60% of bovine isolates. When human mecA-negative MRSA
AB  - isolates were tested, the mecA(LGA251) homologue was identified in 12 of
AB  - 16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from
AB  - Denmark. As in cows, t843 was the most common spa type detected in human
AB  - beings. INTERPRETATION: Although routine culture and antimicrobial
AB  - susceptibility testing will identify S aureus isolates with this novel
AB  - mecA homologue as meticillin resistant, present confirmatory methods will
AB  - not identify them as MRSA. New diagnostic guidelines for the detection of
AB  - MRSA should consider the inclusion of tests for mecA(LGA251). FUNDING:
AB  - Department for Environment, Food and Rural Affairs, Higher Education
AB  - Funding Council for England, Isaac Newton Trust (University of Cambridge),
AB  - and the Wellcome Trust.
ER  -

TY  - JOUR
AU  - Garcia-Fernandez, A.
AU  - Villa, L.
AU  - Carta, C.
AU  - Venditti, C.
AU  - Giordano, A.
AU  - Venditti, M.
AU  - Mancini, C.
AU  - Carattoli, A.
TI  - Klebsiella pneumoniae ST258 Producing KPC-3 Identified in Italy Carries Novel Plasmids and OmpK36/OmpK35 Porin Variants.
JO  - Antimicrob. Agents Chemother.
PY  - 2012
SP  - 2143
EP  - 2145
VL  - 56
AB  - A carbapenemase-resistant Klebsiella pneumoniae strain, clone ST258 producing
AB  - KPC-3, was fully characterized. The entire plasmid content was investigated,
AB  - thereby identifying plasmids of the IncFII(k) (two of them similar to pKPQIL and
AB  - pKPN3, respectively), IncX, and ColE types, carrying a formidable set of
AB  - resistance genes against toxic compounds, metals, and antimicrobial drugs and a
AB  - novel iron(III) uptake system.
ER  -

TY  - JOUR
AU  - Garcia-Heredia, I.
AU  - Martin-Cuadrado, A.-B.
AU  - Mojica, F.J.
AU  - Santos, F.
AU  - Mira, A.
AU  - Anton, J.
AU  - Rodriguez-Valera, F.
TI  - Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.
JO  - PLoS ONE
PY  - 2012
SP  - e33802
EP  - e33802
VL  - 7
AB  - Background: Metaviriomes, the viral genomes present in an environment, have been studied by
AB  - direct sequencing of the viral DNA or by cloning in small insert libraries. The short reads
AB  - generated by both approaches make it very difficult to assemble and annotate such flexible
AB  - genomic entities. Many environmental viruses belong to unknown groups or prey on uncultured
AB  - and little known cellular lineages, and hence might not be present in databases.
AB  - Methodology and Principal Findings: Here we have used a different approach, the cloning of
AB  - viral DNA into fosmids before sequencing, to obtain natural contigs that are close to the size
AB  - of a viral genome. We have studied a relatively low diversity extreme environment: saturated
AB  - NaCl brines, which simplifies the analysis and interpretation of the data. Forty-two different
AB  - viral genomes were retrieved, and some of these were almost complete, and could be tentatively
AB  - identified as head-tail phages (Caudovirales).
AB  - Conclusions and Significance: We found a cluster of phage genomes that most likely infect
AB  - Haloquadratum walsbyi, the square archaeon and major component of the community in these
AB  - hypersaline habitats. The identity of the prey could be confirmed by the presence of CRISPR
AB  - spacer sequences shared by the virus and one of the available strain genomes. Other viral
AB  - clusters detected appeared to prey on the Nanohaloarchaea and on the bacterium Salinibacter
AB  - ruber, covering most of the diversity of microbes found in this type of environment. This
AB  - approach appears then as a viable alternative to describe
AB  - metaviriomes in a much more detailed and reliable way than by the more common approaches based
AB  - on direct sequencing. An example of transfer of a CRISPR cluster including repeats and spacers
AB  - was accidentally found supporting the dynamic nature and frequent transfer of this peculiar
AB  - prokaryotic mechanism of cell protection.
ER  -

TY  - JOUR
AU  - Garcia-Ramon, D.C.
AU  - Palma, L.
AU  - Berry, C.
AU  - Osuna, A.
AU  - Vilchez, S.
TI  - Draft Genome Sequence of the Entomopathogenic Bacterium Bacillus pumilus 15.1, a  Strain Highly Toxic to the Mediterranean Fruit Fly Ceratitis capitata.
JO  - Genome Announcements
PY  - 2015
SP  - e01019
EP  - e01015
VL  - 3
AB  - We present the draft whole-genome sequence of the entomopathogenic Bacillus pumilus 15.1
AB  - strain that consists of 3,795,691 bp and 3,776 predicted protein-coding genes. This genome
AB  - sequence provides the basis for understanding the potential mechanism behind the toxicity and
AB  - virulence of B. pumilus 15.1 against the Mediterranean fruit fly.
ER  -

TY  - JOUR
AU  - Garcia-Romero, I.
AU  - Perez-Pulido, A.J.
AU  - Gonzalez-Flores, Y.E.
AU  - Reyes-Ramirez, F.
AU  - Santero, E.
AU  - Floriano, B.
TI  - Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA.
JO  - BMC Genomics
PY  - 2016
SP  - 93
EP  - 93
VL  - 17
AB  - BACKGROUND: Sphingomonads are Alphaproteobacteria that belong to the
AB  - Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are
AB  - physiologically diverse and broadly distributed in nature, playing important
AB  - roles in oligotrophic environments and in the degradation of recalcitrant
AB  - polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one
AB  - representative (S. alaskensis RB2256) has been deeply characterized. In this
AB  - paper we analyze the genomic features of S. granuli strain TFA (formerly
AB  - Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis
AB  - sequenced genomes, to describe common characteristics of this genus and to
AB  - highlight unique characteristics of strain TFA. RESULTS: The TFA genome has been
AB  - assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis
AB  - and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and
AB  - the S. granuli species. Some regions of the TFA genome show high similarity (ca.
AB  - 100 %) to other bacteria and several genomic islands have been detected. Pathways
AB  - for aromatic compound degradation have been predicted but no growth of TFA has
AB  - been detected using these as carbon or nitrogen sources. Genes for nitrate
AB  - respiration have been identified as TFA exclusive. Experimental data on anaerobic
AB  - growth of TFA using nitrate as a terminal electron acceptor are also provided.
AB  - CONCLUSIONS: Sphingopyxis representatives form a compact phylogenetic group (with
AB  - the exception of S. baekryungensis DSM 16222) that share several characteristics,
AB  - such as being naturally resistant to streptomycin, having only one ribosomal
AB  - operon, a low number of prophages and CRISPR sequences, absence of selenoproteins
AB  - and presence of ectoin and other biosynthesis pathways for secondary metabolites.
AB  - Moreover, the TFA genome organization shows evidence of the presence of putative
AB  - integrative and conjugative elements (ICE) responsible for the acquisition of
AB  - several characteristics by horizontal transfer mechanisms. Sphingopyxis
AB  - representatives have been described as strict aerobes but anaerobic growth using
AB  - nitrate as a terminal electron acceptor might confer an environmental advantage
AB  - to the first S. granuli strain characterized at genomic level.
ER  -

TY  - JOUR
AU  - Garcia-Solache, M.
AU  - Rice, L.B.
TI  - Draft Genome Sequence of Vancomycin-Susceptible, Ampicillin-Intermediate Enterococcus faecium Strain D344RRF.
JO  - Genome Announcements
PY  - 2016
SP  - e01720
EP  - e01715
VL  - 4
AB  - Enterococcus faecium is an important nosocomial pathogen, causing a substantial health burden
AB  - due to high resistance to antibiotics and its ability to colonize
AB  - the gastrointestinal tract. Here, we present the draft genome of
AB  - vancomycin-susceptible, ampicillin-intermediate strain D344RRF, a
AB  - rifampicin/fusidic acid-resistant and commonly used laboratory strain, which is
AB  - useful in studying the transfer of antibiotic resistance.
ER  -

TY  - JOUR
AU  - Garcia-Solache, M.
AU  - Rice, L.B.
TI  - Genome Sequence of the Multiantibiotic-Resistant Enterococcus faecium Strain C68  and Insights on the pLRM23 Colonization Plasmid.
JO  - Genome Announcements
PY  - 2016
SP  - e01719
EP  - e01715
VL  - 4
AB  - Enterococcus faecium infections are a rising concern in hospital settings.
AB  - Vancomycin-resistant enterococci colonize the gastrointestinal tract and replace
AB  - nonresistant strains, complicating the treatment of debilitated patients. Here,
AB  - we present a polished genome of the multiantibiotic-resistant strain C68, which
AB  - was obtained as a clinical isolate and is a useful experimental strain.
ER  -

TY  - JOUR
AU  - Garcia-Valdes, E.
AU  - Gomila, M.
AU  - Mulet, M.
AU  - Lalucat, J.
TI  - Draft Genome Sequence of Pseudomonas oceani DSM 100277(T), a Deep-Sea Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00254
EP  - e00218
VL  - 6
AB  - Pseudomonas oceani DSM 100277(T) was isolated from deep seawater in the Okinawa Trough at 1390
AB  - m. P. oceani belongs to the Pseudomonas pertucinogena group. Here,
AB  - we report the draft genome sequence of P. oceani, which has an estimated size of
AB  - 4.1 Mb and exhibits 3,790 coding sequences, with a G+C content of 59.94 mol%.
ER  -

TY  - JOUR
AU  - Gardes, A.
AU  - Kaeppel, E.
AU  - Shehzad, A.
AU  - Seebah, S.
AU  - Teeling, H.
AU  - Yarza, P.
AU  - Glockner, F.O.
AU  - Grossart, H.P.
AU  - Ullrich, M.S.
TI  - Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism.
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 97
EP  - 107
VL  - 3
AB  - Marinobacter adhaerens HP15 is the type strain of a newly identified marine species, which is
AB  - phylogenetically related to M. flavimaris, M. algicola, and M.
AB  - aquaeolei. It is of special interest for research on marine aggregate formation
AB  - because it showed specific attachment to diatom cells. In vitro it led to
AB  - exopolymer formation and aggregation of these algal cells to form marine snow
AB  - particles. M. adhaerens HP15 is a free-living, motile, rod-shaped, Gram-negative
AB  - gammaproteobacterium, which was originally isolated from marine particles sampled
AB  - in the German Wadden Sea. M. adhaerens HP15 grows heterotrophically on various
AB  - media, is easy to access genetically, and serves as a model organism to
AB  - investigate the cellular and molecular interactions with the diatom Thalassiosira
AB  - weissflogii. Here we describe the complete and annotated genome sequence of M.
AB  - adhaerens HP15 as well as some details on flagella-associated genes. M. adhaerens
AB  - HP15 possesses three replicons; the chromosome comprises 4,422,725 bp and codes
AB  - for 4,180 protein-coding genes, 51 tRNAs and three rRNA operons, while the two
AB  - circular plasmids are ~187 kb and ~42 kb in size and contain 178 and 52
AB  - protein-coding genes, respectively.
ER  -

TY  - JOUR
AU  - Gardiner, D.M.
AU  - Stiller, J.
AU  - Covarelli, L.
AU  - Lindeberg, M.
AU  - Shivas, R.G.
AU  - Manners, J.M.
TI  - Genome Sequences of Pseudomonas spp. Isolated from Cereal Crops.
JO  - Genome Announcements
PY  - 2013
SP  - e00209
EP  - e00213
VL  - 1
AB  - Compared to those of dicot-infecting bacteria, the available genome sequences of  bacteria
AB  - that infect wheat and barley are limited. Herein, we report the draft
AB  - genome sequences of four pseudomonads originally isolated from these cereals.
AB  - These genome sequences provide a useful resource for comparative analyses within
AB  - the genus and for cross-kingdom analyses of plant pathogenesis.
ER  -

TY  - JOUR
AU  - Gardiner, D.M.
AU  - Stiller, J.
AU  - Kazan, K.
TI  - Genome Sequence of Fusarium graminearum Isolate CS3005.
JO  - Genome Announcements
PY  - 2014
SP  - e00227
EP  - e00214
VL  - 2
AB  - Fusarium graminearum is one of the most important fungal pathogens of wheat, barley, and maize
AB  - worldwide. This announcement reports the genome sequence of a highly virulent Australian
AB  - isolate of this species to supplement the existing genome of the North American F. graminearum
AB  - isolate Ph1.
ER  -

TY  - JOUR
AU  - Gardner, A.F.
AU  - Kumar, S.
AU  - Perler, F.B.
TI  - Genome Sequence of the Model Hyperthermophilic Archaeon Thermococcus litoralis NS-C.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2375
EP  - 2376
VL  - 194
AB  - The hyperthermophilic archaeon Thermococcus litoralis strain NS-C, first isolated in 1985, has
AB  - been a foundational organism for archaeal research in biocatalysis,
AB  - DNA replication, metabolism, and the discovery of inteins. Here, we present the
AB  - genome sequence of T. litoralis with a focus on the replication machinery and
AB  - inteins.
ER  -

TY  - JOUR
AU  - Gardner, R.C.
AU  - Howarth, A.J.
AU  - Messing, J.
AU  - Shepherd, R.J.
TI  - Cloning and sequencing of restriction fragments generated by EcoRI*.
JO  - DNA
PY  - 1982
SP  - 109
EP  - 115
VL  - 1
AB  - Thirty-four EcoRI* sites have been identified on the nucleotide sequence of
AB  - CaMV, following cloning of EcoRI* fragments in M13mp2.  From this sequencing
AB  - data, we have deduced that EcoRI* recognizes sites at any one of the six
AB  - positions in the recognition site, with the exception of A5T or T5A changes
AB  - within the central tetramer.  The EcoRI* restriction patterns of PhiX174 and
AB  - pBR322 are consistent with these recognition criteria.  Similarly, BamHI*
AB  - cleavage of PhiX174 and SV40 (George et al., 1980) produces restriction
AB  - patterns that are consistent with single-position degeneracy in the canonical
AB  - BamHI recognition site.  Cohesive termini produced by EcoRI* cleavage were
AB  - ligated into the EcoRI site of M13mp2, even when there was a base pair mismatch
AB  - within the four nucleotide overlap.  Mismatches were corrected asymmetrically
AB  - during subsequent replication of M13 in E. coli.
ER  -

TY  - JOUR
AU  - Gardner, S.P.
AU  - Kendall, K.J.
AU  - Taveirne, M.E.
AU  - Olson, J.W.
TI  - Complete Genome Sequence of Campylobacter jejuni subsp. jejuni ATCC 35925.
JO  - Genome Announcements
PY  - 2017
SP  - e00743
EP  - e00717
VL  - 5
AB  - Here, we report the complete genome sequence of Campylobacter jejuni ATCC 35925,  an avian
AB  - isolate from Sweden. The genome gives insight into the ATCC 35925
AB  - strain's remarkable ability to tolerate copper and its permissiveness to plasmid
AB  - transformation.
ER  -

TY  - JOUR
AU  - Gardner, S.P.
AU  - Olson, J.W.
TI  - Barriers to Horizontal Gene Transfer in Campylobacter jejuni.
JO  - Adv. Appl. Microbiol.
PY  - 2012
SP  - 19
EP  - 42
VL  - 79
AB  - Campylobacter jejuni is among the most frequent agent of food-borne gastroenteritis in the
AB  - world, but its physiology and pathogenesis. is
AB  - less well understood than other bacterial enteric pathogens. This is
AB  - due in part to the incompatibility of the molecular tools that have
AB  - enabled advances in the characterization of other bacterial species.
AB  - Most notably, the dearth of plasmid-based complementation, reporter
AB  - assays, and plasmid-based unmarked mutagenesis procedures in many of
AB  - the type strains has hindered research progress. The techniques
AB  - themselves are not inadequate in Cam pylobacter species, but rather the
AB  - barrier to genetic transfer of these genetic constructs from
AB  - non-Campylobacter cloning stains such as Escherichia coli. Here, we
AB  - review the modes of genetic transfer in C. jejuni and review the
AB  - current state of research into the mechanism of each. Also reviewed are
AB  - two systems (CRISPR-Cas and restriction modification) that are common
AB  - to many strains of C. jejuni and are at least partly responsible for
AB  - these barriers.
ER  -

TY  - JOUR
AU  - Garfin, D.E.
AU  - Boyer, H.W.
AU  - Goodman, H.M.
TI  - Sequences spanning the EcoRI substrate site.
JO  - Nucleic Acids Res.
PY  - 1975
SP  - 1851
EP  - 1865
VL  - 2
AB  - Substrate recognition by the EcoRI restriction endonuclease was investigated by
AB  - analysis of the nucleotide sequences at the sites of enzymatic cleavage in
AB  - various DNA molecules.  5'-end labeling and homochromatographic fingerprinting
AB  - led to the determination of a 17-base-pair sequence spanning the EcoRI site of
AB  - simian virus 40 DNA and a 15-base-pair sequence overlapping the EcoRI site of
AB  - ColE1 plasmid DNA.  Three other DNAs were similarly tested, although extended
AB  - sequences were not determined in these cases.  The EcoRI site was shown to be
AB  - the symmetric, double-stranded equivalent of -N-G-A-A-T-T-C-N-.
ER  -

TY  - JOUR
AU  - Garfin, D.E.
AU  - Goodman, H.M.
TI  - Nucleotide sequences at the cleavage sites of two restriction endonucleases from Hemophilus parainfluenzae.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1974
SP  - 108
EP  - 116
VL  - 59
AB  - The nucleotide sequences at the cleavage sites of two restriction endonucleases from
AB  - Hemophilus parainfluenzae, HpaI and HpaII, have been determined.  Terminal labeling at both
AB  - the 3'- and 5'-termini was used to show that the HpaI enzyme cleaves the sequence
AB  - 5'...N-G-T-T^pA-A-C-N...3' 3'...N-C-A-Ap^T-T-G-N...5' and the sequence cleaved by the
AB  - HpaII enzyme is 5'...N-C^pC-G-G-N...3' 3'...N-G-G-Cp^C-N...5' where the arrows indicate
AB  - the points of strand scission.
ER  -

TY  - JOUR
AU  - Garg, R.
AU  - Kumari, R.
AU  - Tiwari, S.
AU  - Goyal, S.
TI  - Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in Legumes.
JO  - PLoS ONE
PY  - 2014
SP  - 14
EP  - 14
VL  - 9
AB  - DNA methylation plays a crucial role in development through inheritable gene silencing. Plants
AB  - possess three types of DNA methyltransferases (MTases), namely Methyltransferase (MET),
AB  - Chromomethylase (CMT) and Domains Rearranged Methyltransferase (DRM), which maintain
AB  - methylation at CG, CHG and CHH sites. DNA MTases have not been studied in legumes so far.
AB  - Here, we report the identification and analysis of putative DNA MTases in five legumes,
AB  - including chickpea, soybean, pigeonpea, Medicago and Lotus. MTases in legumes could be
AB  - classified in known MET, CMT, DRM and DNA nucleotide methyltransferases (DNMT2) subfamilies
AB  - based on their domain organization. First three MTases represent DNA MTases, whereas DNMT2
AB  - represents a transfer RNA (tRNA) MTase. Structural comparison of all the MTases in plants with
AB  - known MTases in mammalian and plant systems have been reported to assign structural features
AB  - in context of biological functions of these proteins. The structure analysis clearly specified
AB  - regions crucial for protein-protein interactions and regions important for nucleosome binding
AB  - in various domains of CMT and MET proteins. In addition, structural model of DRM suggested
AB  - that circular permutation of motifs does not have any effect on overall structure of DNA
AB  - methyltransferase domain. These results provide valuable insights into role of various domains
AB  - in molecular recognition and should facilitate mechanistic understanding of their function in
AB  - mediating specific methylation patterns. Further, the comprehensive gene expression analyses
AB  - of MTases in legumes provided evidence of their role in various developmental processes
AB  - throughout the plant life cycle and response to various abiotic stresses. Overall, our study
AB  - will be very helpful in establishing the specific functions of DNA MTases in legumes.
ER  -

TY  - JOUR
AU  - Garita-Cambronero, J.
AU  - Palacio-Bielsa, A.
AU  - Lopez, M.M.
AU  - Cubero, J.
TI  - Draft Genome Sequence of Two Strains of Xanthomonas arboricola Isolated from Prunus persica Which Are Dissimilar to Strains That Cause Bacterial Spot Disease on Prunus spp.
JO  - Genome Announcements
PY  - 2016
SP  - e00974
EP  - e00916
VL  - 4
AB  - The draft genome sequences of two strains of Xanthomonas arboricola, isolated from
AB  - asymptomatic peach trees in Spain, are reported here. These strains are
AB  - avirulent and do not belong to the same phylogroup as X. arboricola pv. pruni, a
AB  - causal agent of bacterial spot disease of stone fruits and almonds.
ER  -

TY  - JOUR
AU  - Garita-Cambronero, J.
AU  - Palacio-Bielsa, A.
AU  - Lopez, M.M.
AU  - Cubero, J.
TI  - Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 12
EP  - 12
VL  - 11
AB  - Xanthomonas arboricola is a species in genus Xanthomonas which is mainly comprised of plant
AB  - pathogens. Among the members of this taxon, X. arboricola pv.
AB  - pruni, the causal agent of bacterial spot disease of stone fruits and almond, is
AB  - distributed worldwide although it is considered a quarantine pathogen in the
AB  - European Union. Herein, we report the draft genome sequence, the classification,
AB  - the annotation and the sequence analyses of a virulent strain, IVIA 2626.1, and
AB  - an avirulent strain, CITA 44, of X. arboricola associated with Prunus spp. The
AB  - draft genome sequence of IVIA 2626.1 consists of 5,027,671 bp, 4,720 protein
AB  - coding genes and 50 RNA encoding genes. The draft genome sequence of strain CITA
AB  - 44 consists of 4,760,482 bp, 4,250 protein coding genes and 56 RNA coding genes.
AB  - Initial comparative analyses reveals differences in the presence of structural
AB  - and regulatory components of the type IV pilus, the type III secretion system,
AB  - the type III effectors as well as variations in the number of the type IV
AB  - secretion systems. The genome sequence data for these strains will facilitate the
AB  - development of molecular diagnostics protocols that differentiate virulent and
AB  - avirulent strains. In addition, comparative genome analysis will provide insights
AB  - into the plant-pathogen interaction during the bacterial spot disease process.
ER  -

TY  - JOUR
AU  - Garita-Cambronero, J.
AU  - Sena-Velez, M.
AU  - Palacio-Bielsa, A.
AU  - Cubero, J.
TI  - Draft Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xap33, Causal Agent of Bacterial Spot Disease on Almond.
JO  - Genome Announcements
PY  - 2014
SP  - e00440
EP  - e00414
VL  - 2
AB  - We report the annotated genome sequence of Xanthomonas arboricola pv. pruni strain Xap33,
AB  - isolated from almond leaves showing bacterial spot disease symptoms
AB  - in Spain. The availability of this genome sequence will aid our understanding of
AB  - the infection mechanism of this bacterium as well as its relationship to other
AB  - species of the same genus.
ER  -

TY  - JOUR
AU  - Garnett, J.
AU  - Halford, S.E.
TI  - Properties and subunit structure of EcoRV methyltransferase.
JO  - Gene
PY  - 1988
SP  - 73
EP  - 76
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Garnier, F.
AU  - Taourit, S.
AU  - Glaser, P.
AU  - Courvalin, P.
AU  - Galimand, M.
TI  - Characterization of transposon Tn1549, conferring VanB-type resistance in Enterococcus spp.
JO  - Microbiology
PY  - 2000
SP  - 1481
EP  - 1489
VL  - 146
AB  - Transfer of VanB-type resistance to glycopeptides among enterococci has been reported to be
AB  - associated with the movement of large chromosomal
AB  - genetic elements or of plasmids. The authors report the characterization
AB  - of the 34 kb transposon Tn1549 borne by a plasmid related to pAD1 and
AB  - conferring vancomycin resistance in clinical isolates of Enterococcus spp.
AB  - Tn1549 contained 30 ORFs and appeared to be organized like the Tn916
AB  - family of conjugative transposons into three functional regions: (i) the
AB  - right end, implicated in the excision-integration process; (ii) the
AB  - central part, in which the vanB2 operon replaces the tet(M) gene; and
AB  - (iii) the left extremity, in which eight of the 18 ORFs could be
AB  - implicated in the conjugative transfer.
ER  -

TY  - JOUR
AU  - Garnier, T. et al.
TI  - The complete genome sequence of Mycobacterium bovis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 7877
EP  - 7882
VL  - 100
AB  - Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and
AB  - man, with worldwide annual losses to agriculture of $3
AB  - billion. The human burden of tuberculosis caused by the bovine tubercle
AB  - bacillus is still largely unknown. M. bovis was also the progenitor for
AB  - the M. bovis bacillus Calmette-Guerin vaccine strain, the most widely used
AB  - human vaccine. Here we describe the 4,345,492-bp genome sequence of M.
AB  - bovis AF2122/97 and its comparison with the genomes of Mycobacterium
AB  - tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of
AB  - M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of
AB  - genetic information has led to a reduced genome size. Comparison with M.
AB  - leprae reveals a number of common gene losses, suggesting the removal of
AB  - functional redundancy. Cell wall components and secreted proteins show the
AB  - greatest variation, indicating their potential role in host-bacillus
AB  - interactions or immune evasion. Furthermore, there are no genes unique to
AB  - M. bovis, implying that differential gene expression may be the key to the
AB  - host tropisms of human and bovine bacilli. The genome sequence therefore
AB  - offers major insight on the evolution, host preference, and pathobiology
AB  - of M. bovis.
ER  -

TY  - JOUR
AU  - Garofolo, G.
AU  - Foster, J.T.
AU  - Drees, K.
AU  - Zilli, K.
AU  - Platone, I.
AU  - Ancora, M.
AU  - Camma, C.
AU  - De Massis, F.
AU  - Calistri, P.
AU  - Di Giannatale, E.
TI  - Genome Sequences of 11 Brucella abortus Isolates from Persistently Infected Italian Regions.
JO  - Genome Announcements
PY  - 2015
SP  - e01402
EP  - e01415
VL  - 3
AB  - Bovine brucellosis, typically caused by Brucella abortus, has been eradicated from much of the
AB  - developed world. However, the disease remains prevalent in
AB  - southern Italy, persisting as a public and livestock health concern. We report
AB  - here the whole-genome sequences of 11 isolates from cattle (Bos taurus) and water
AB  - buffalo (Bubalus bubalis) that are representative of the current genetic
AB  - diversity of B. abortus lineages circulating in Italy.
ER  -

TY  - JOUR
AU  - Garrett, M.
AU  - Parker, J.
AU  - Stephens, C.M.
TI  - Draft Genome Sequences of Antibiotic-Resistant Commensal Escherichia coli.
JO  - Genome Announcements
PY  - 2014
SP  - e00873
EP  - e00814
VL  - 2
AB  - Antimicrobial resistance is a significant public health issue. We report here the draft genome
AB  - sequences of three drug-resistant strains of commensal Escherichia
AB  - coli isolated from a single healthy college student. Each strain has a distinct
AB  - genome, but two of the three contain an identical large plasmid with multiple
AB  - resistance genes.
ER  -

TY  - JOUR
AU  - Garrett, R.A.
AU  - Prangishvili, D.
AU  - Shah, S.A.
AU  - Reuter, M.
AU  - Stetter, K.O.
AU  - Peng, X.
TI  - Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles.
JO  - Environ. Microbiol.
PY  - 2010
SP  - 2918
EP  - 2930
VL  - 12
AB  - Summary Two novel viral genomes and four plasmids were assembled from an
AB  - environmental sample collected from a hot spring at Yellowstone National
AB  - Park, USA, and maintained anaerobically in a bioreactor at 85 degrees C
AB  - and pH 6. The double-stranded DNA viral genomes are linear (22.7 kb) and
AB  - circular (17.7 kb), and derive apparently from archaeal viruses HAV1 and
AB  - HAV2. Genomic DNA was obtained from samples enriched in filamentous and
AB  - tadpole-shaped virus-like particles respectively. They yielded few
AB  - significant matches in public sequence databases reinforcing, further, the
AB  - wide diversity of archaeal viruses. Several variants of HAV1 exhibit major
AB  - genomic alterations, presumed to arise from viral adaptation to different
AB  - hosts. They include insertions up to 350 bp, deletions up to 1.5 kb, and
AB  - genes with extensively altered sequences. Some result from recombination
AB  - events occurring at low complexity direct repeats distributed along the
AB  - genome. In addition, a 33.8 kb archaeal plasmid pHA1 was characterized,
AB  - encoding a possible conjugative apparatus, as well as three cryptic
AB  - plasmids of thermophilic bacterial origin, pHB1 of 2.1 kb and two closely
AB  - related variants pHB2a and pHB2b, of 5.2 and 4.8 kb respectively.
AB  - Strategies are considered for assembling genomes of smaller genetic
AB  - elements from complex environmental samples, and for establishing possible
AB  - host identities on the basis of sequence similarity to host CRISPR immune
AB  - systems.
ER  -

TY  - JOUR
AU  - Garrido, L.M.
AU  - Alves, J.M.
AU  - Oliveira, L.S.
AU  - Gruber, A.
AU  - Padilla, G.
AU  - Araujo, W.L.
TI  - Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent.
JO  - Genome Announcements
PY  - 2016
SP  - e01264
EP  - e01216
VL  - 4
AB  - Herein, we report a draft genome sequence of the endophytic Curtobacterium sp. strain ER1/6,
AB  - isolated from a surface-sterilized Citrus sinensis branch, and it
AB  - presented the capability to control phytopathogens. Functional annotation of the
AB  - ~3.4-Mb genome revealed 3,100 protein-coding genes, with many products related to
AB  - known ecological and biotechnological aspects of this bacterium.
ER  -

TY  - JOUR
AU  - Garrigues, C.
AU  - Johansen, E.
AU  - Pedersen, M.B.
TI  - Complete genome sequence of Bifidobacterium animalis subsp. lactis BB-12, a widely consumed probiotic strain.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2467
EP  - 2468
VL  - 192
AB  - Bifidobacterium animalis subsp. lactis BB-12 is a commercially available probiotic strain used
AB  - throughout the world in a variety of functional
AB  - foods and dietary supplements. The benefits of BB-12 have been documented
AB  - in a number of independent clinical trials. Determination of the complete
AB  - genome sequence reveals a single circular chromosome of 1,942,198 bp with
AB  - 1,642 predicted protein-encoding genes, 4 rRNA operons, and 52 tRNA genes.
AB  - Knowledge of this sequence will lead to insight into the specific features
AB  - which give this strain its probiotic properties.
ER  -

TY  - JOUR
AU  - Garvey, P.
AU  - van Sinderen, D.
AU  - Twomey, D.P.
AU  - Hill, C.
AU  - Fitzgerald, G.F.
TI  - Molecular genetics of bacteriophage and natural phage defense systems in the genus Lactococcus.
JO  - Int. Dairy Journal
PY  - 1995
SP  - 905
EP  - 947
VL  - 5
AB  - Bacteriophage infection of starter cultures used in a range of milk fermentation processes,
AB  - particularly those involving Lactococcus lactis, poses a significant problem in industrial
AB  - practice.  The application of genetic and molecular technologies to the study of lactococcal
AB  - bacteriophages has proven to be very rewarding in terms of understanding the nature of phage
AB  - with respect to their physical and genetic organisation.  The availability of the full genomic
AB  - sequence of a number of phages provides an unambiguous basis for determining the relationship
AB  - between them, for elucidating their evolutionary progression and will also yield strategies
AB  - for obstructing successful phage proliferation on previously sensitive hosts.  The genetic
AB  - analysis of plage/host interactions has also highlighted the presence of natural defense
AB  - systems (e.g. adsorption blocking, inhibition of phage DNA entry, restriction modification and
AB  - abortive infection) in lactococci.  A number of restriction modification systems and abortive
AB  - infection mechanisms have been characterized at a molecular level and the genes involved have
AB  - been cloned and sequenced.  Plasmid-encoded phage resistance mechanisms can be exploited to
AB  - generate strains which can successfully counter phage proliferation and will provide a basis
AB  - for understanding the complex interactions between phages and their target hosts at a
AB  - molecular level.
ER  -

TY  - JOUR
AU  - Garza-Ramos, U.
AU  - Silva-Sanchez, J.
AU  - Barrios, H.
AU  - Rodriguez-Medina, N.
AU  - Martinez-Barnetche, J.
AU  - Andrade, V.
TI  - Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e01352
EP  - e01314
VL  - 3
AB  - An antibiotic-susceptible and hypermucoviscous clinical isolate of Klebsiella variicola (K.
AB  - variicola 8917) was obtained from the sputum of an adult patient.
AB  - This work reports the complete draft genome sequence of K. variicola 8917 with
AB  - 103 contigs and an annotation that revealed a 5,686,491-bp circular chromosome
AB  - containing a total of 5,621 coding DNA sequences, 65 tRNA genes, and an average
AB  - G+C content of 56.98%.
ER  -

TY  - JOUR
AU  - Garza-Ramos, U.
AU  - Silva-Sanchez, J.
AU  - Catalan-Najera, J.
AU  - Barrios, H.
AU  - Rodriguez-Medina, N.
AU  - Garza-Gonzalez, E.
AU  - Cevallos, M.A.
AU  - Lozano, L.
TI  - Draft Genome Sequence of a Hypermucoviscous Extended-Spectrum-beta-Lactamase-Producing Klebsiella quasipneumoniae subsp.  similipneumoniae Clinical Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00475
EP  - e00416
VL  - 4
AB  - A clinical isolate of extended-spectrum-beta-lactamase-producing Klebsiella quasipneumoniae
AB  - subsp. similipneumoniae 06-219 with hypermucoviscosity phenotypes
AB  - obtained from a urine culture of an adult patient was used for whole-genome
AB  - sequencing. Here, we report the draft genome sequences of this strain, consisting
AB  - of 53 contigs with an ~5.6-Mb genome size and an average G+C content of 57.36%.
AB  - The annotation revealed 6,622 coding DNA sequences and 77 tRNA genes.
ER  -

TY  - JOUR
AU  - Garza-Ramos, U.
AU  - Tamayo-Legorreta, E.
AU  - Arellano-Quintanilla, D.M.
AU  - Rodriguez-Medina, N.
AU  - Silva-Sanchez, J.
AU  - Catalan-Najera, J.
AU  - Rocha-Martinez, M.K.
AU  - Bravo-Diaz, M.A.
AU  - Alpuche-Aranda, C.
TI  - Draft Genome Sequence of a Multidrug- and Colistin-Resistant mcr-1-Producing Escherichia coli Isolate from a Swine Farm in Mexico.
JO  - Genome Announcements
PY  - 2018
SP  - e00102
EP  - e00118
VL  - 6
AB  - A colistin-resistant mcr-1-carrying Escherichia coli strain, RC2-007, was isolated from a
AB  - swine farm in Mexico. This extraintestinal and uropathogenic
AB  - strain of E. coli belongs to serotype O89:H9 and sequence type 744. Assembly and
AB  - annotation resulted in a 4.9-Mb draft genome that revealed the presence of
AB  - plasmid-mediated mcr-1-ISApI1 genes as part of a prophage.
ER  -

TY  - JOUR
AU  - Garzetti, D.
AU  - Brugiroux, S.
AU  - Bunk, B.
AU  - Pukall, R.
AU  - McCoy, K.D.
AU  - Macpherson, A.J.
AU  - Stecher, B.
TI  - High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community.
JO  - Genome Announcements
PY  - 2017
SP  - e00758
EP  - e00717
VL  - 5
AB  - The Oligo-Mouse-Microbiota (Oligo-MM12) is a community of 12 mouse intestinal bacteria to be
AB  - used for microbiome research in gnotobiotic mice. We present here
AB  - the high-quality whole genome sequences of the Oligo-MM12 strains, which were
AB  - obtained by combining the accuracy of the Illumina platforms with the long reads
AB  - of the PacBio technology.
ER  -

TY  - JOUR
AU  - Garzetti, D.
AU  - Eberl, C.
AU  - Stecher, B.
TI  - Complete Genome Sequencing of the Mouse Intestinal Isolate Escherichia coli Mt1B1.
JO  - Genome Announcements
PY  - 2018
SP  - e00426
EP  - e00418
VL  - 6
AB  - Escherichia coli Mt1B1, a mouse isolate, is a facultative anaerobic bacterium which was shown
AB  - to counteract Salmonella enterica serovar Typhimurium infection
AB  - in a mouse model. In the present study, we describe the complete genome sequence
AB  - of E. coli Mt1B1, composed of a 5.1-Mb chromosome and a 62.6-kb plasmid.
ER  -

TY  - JOUR
AU  - Garzetti, D.
AU  - Heesemann, J.
AU  - Rakin, A.
TI  - Genome Sequences of Four Yersinia enterocolitica Bioserotype 4/O:3 Isolates from  Mammals.
JO  - Genome Announcements
PY  - 2013
SP  - e00466
EP  - e00413
VL  - 1
AB  - We report here the complete genome sequences of four European Yersinia enterocolitica
AB  - mammalian isolates of bioserotype 4/O:3. The genomes have an
AB  - average size of 4.50 Mb, a G+C content of 47%, and between 4,231 and 4,330 coding
AB  - sequences (CDSs). No relevant differences were detected by genome comparison
AB  - between mammalian and human isolates.
ER  -

TY  - JOUR
AU  - Gasc, C.
AU  - Richard, J.Y.
AU  - Peyret, P.
TI  - Genome Sequence of Pseudomonas sp. HUK17, Isolated from Hexachlorocyclohexane-Contaminated Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00275
EP  - e00216
VL  - 4
AB  - Pseudomonassp. HUK17 has been isolated from hexachlorocyclohexane (HCH) long-term contaminated
AB  - soil. The genome of strain HUK17 was sequenced to elucidate its
AB  - adaptation toward HCH and to evaluate the presence of pesticide degradation
AB  - pathways. Here, we report the annotated draft genome sequence (~2.6 Mbp) of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Gasc, C.
AU  - Richard, J.Y.
AU  - Peyret, P.
TI  - Genome Sequence of Staphylococcus aureus Strain HUK16, Isolated from Hexachlorocyclohexane-Contaminated Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00274
EP  - e00216
VL  - 4
AB  - Staphylococcus aureusstrain HUK16 has been isolated from hexachlorocyclohexane (HCH)-long-term
AB  - contaminated soil. The genome of strain HUK16 was sequenced to
AB  - understand the genetic basis of its adaptation to HCH and to find the potential
AB  - metabolic pathways allowing it to degrade the pesticide. Here, we report the
AB  - annotated draft genome sequence (~2.7 Mbp) of this strain.
ER  -

TY  - JOUR
AU  - Gasc, C.
AU  - Richard, J.Y.
AU  - Peyret, P.
TI  - Genome Sequence of Bacillus subtilis Strain HUK15, Isolated from Hexachlorocyclohexane-Contaminated Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00273
EP  - e00216
VL  - 4
AB  - Bacillus subtilisstrain HUK15 has been isolated from hexachlorocyclohexane
AB  - (HCH)-long-term-contaminated soil. The genome of strain HUK15 was sequenced to
AB  - investigate its adaptation toward HCH and its potential capability to degrade the
AB  - pesticide. Here, we report the annotated draft genome sequence (~4.3 Mbp) of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Gasiunas, G.
AU  - Sasnaukas, G.
AU  - Tamulaitis, G.
AU  - Siksnys, V.
TI  - Tetrameric restriction enzyme Cfr42I belongs to the GIY-YIG nuclease family.
JO  - FEBS J.
PY  - 2009
SP  - 140
EP  - 141
VL  - 276
AB  - The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes
AB  - involved in DNA repair and recombination.  Despite wide distribution of this domain,
AB  - biochemical and structural studies of GIY-YIG proteins are often hampered by their
AB  - multi-domain organization and complex functional requirements.  Many of the GIY-YIG family
AB  - enzymes are functional as monomers.  We show that the Cfr42I restriction endonuclease which
AB  - belongs to the GIY-YIG family and recognizes the symmetric sequence 5'-CCGC/GG-3' ('/'
AB  - indicates the cleavage site) is a tetramer in solution.  Moreover, biochemical and kinetic
AB  - studies demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous
AB  - binding of two copies of its recognition sequence.  In that respect Cfr42I resembles the
AB  - homotetrameric Type IIF restriction enzymes that belong to the distinct PD-D/E)XK nuclease
AB  - superfamily.  Unlike the PD-(D/E)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an
AB  - extrmely wide selection of metal ion cofactors, including Mg2+, Mn2+, Co2+, Zn2+, Ni2+, Cu2+
AB  - and Ca2+.  To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme.  Similar
AB  - structural arrangement and phenotypes displayed by restriction enzymes belonging to the
AB  - PD-(D/E)XK and GIY-YIG nuclease families point to the functional significance of
AB  - tetramerization.  In order to understand structure-function relationship within Cfr42I
AB  - restriction enzyme we aim to determine its 3D structure by X-ray crystallography.
ER  -

TY  - JOUR
AU  - Gasiunas, G.
AU  - Sasnauskas, G.
AU  - Tamulaitis, G.
AU  - Urbanke, C.
AU  - Razaniene, D.
AU  - Siksnys, V.
TI  - Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 938
EP  - 949
VL  - 36
AB  - The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes
AB  - involved in DNA repair and recombination. Many of the GIY-YIG family enzymes are functional as
AB  - monomers. We show here that the Cfr42I restriction endonuclease which belongs to the GIY-YIG
AB  - family and recognizes the symmetric sequence 5'-CCGC/GG-3' ('/' indicates the cleavage
AB  - site) is a tetramer in solution. Moreover, biochemical and kinetic studies provided here
AB  - demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous binding of
AB  - two copies of its recognition sequence. In that respect Cfr42I resembles the homotetrameric
AB  - Type IIF restriction enzymes that belong to the distinct PD-(E/D)XK nuclease superfamily.
AB  - Unlike the PD-(E/D)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an extremely wide
AB  - selection of metal-ion cofactors, including Mg(2+), Mn(2+), Co(2+), Zn(2+), Ni(2+), Cu(2+) and
AB  - Ca(2+). To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme. Similar
AB  - structural arrangement and phenotypes displayed by restriction enzymes of the PD-(E/D)XK and
AB  - GIY-YIG nuclease families point to the functional significance of tetramerization.
ER  -

TY  - JOUR
AU  - Gasperik, J.
AU  - Godany, A.
AU  - Hostinova, E.
AU  - Zelinka, J.
TI  - Specific endonuclease Sau3239I from Streptomyces aureofaciens CCM 3239.
JO  - Biologia (Bratisl)
PY  - 1983
SP  - 315
EP  - 319
VL  - 38
AB  - In the research of relations of plasmid DNA to antibiotic production in
AB  - Streptomyces aureofaciens also the prototrophic chlortetracycline (CTC)
AB  - producing strain of S. aureofaciens CCM 3239 was studied.  In this strain the
AB  - presence of plasmid DNA was proven (unpublished data).  After elimination of
AB  - the plasmid there were considerations on using this strain as the acceptor of
AB  - DNA transformation.  The possibility of detection of a restriction-modifying
AB  - system on this extrachromosomal element as found in eubacteria, (Arber, 1974)
AB  - remained open.  Detection of restrictase activity in S. aureofaciens CCM 3239
AB  - was interest as restriction endonucleases were isolated from more than 15 types
AB  - of Streptomyces (Roberts, 1982).  Restriction endonuclease, type II, was also
AB  - found in the non-producing mutant of S. aureofaciens IKA 18/4 (Timko, et al.,
AB  - 1978).  The substrate specificity and the cleavage site of this enzyme, SauI,
AB  - is described in the paper by Timko et al., (1981).
ER  -

TY  - JOUR
AU  - Gasperotti, A.F.
AU  - Studdert, C.A.
AU  - Revale, S.
AU  - Herrera, S.M.K.
TI  - Draft Genome Sequence of Halomonas sp. KHS3, a Polyaromatic Hydrocarbon-Chemotactic Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00020
EP  - e00015
VL  - 3
AB  - The draft genome sequence of Halomonas sp. KHS3, isolated from seawater from Mar  del Plata
AB  - harbor, is reported. This strain is able to grow using aromatic
AB  - compounds as a carbon source and shows strong chemotactic response toward these
AB  - substrates. Genes involved in motility, chemotaxis, and degradation of aromatic
AB  - hydrocarbons were identified.
ER  -

TY  - JOUR
AU  - Gassner, C.
AU  - Schneider-Scherzer, E.S.
AU  - Lottspeich, F.
AU  - Schweiger, M.
AU  - Auer, B.
TI  - Escherichia coli bacteriophage T1 DNA methyltransferase appears to interact with Escherichia coli enolase.
JO  - Biol. Chem.
PY  - 1998
SP  - 621
EP  - 623
VL  - 379
AB  - Infection of Escherichia coli cells with bacteriophage T1 induces synthesis of a
AB  - bacteriophage-specific DNA methyltransferase with a specificity for adenine residues in the
AB  - sequence 5'-GATC-3'.  Purification of M.EcoT1 allowed the determination of the coding
AB  - sequence of the gene.  The peptide of the entire coding sequence was over-expressed as a
AB  - histidine-hexapeptide tagged protein in E. coli.  Affinity purification using a Ni2+ chelating
AB  - (Ni-NTA) resin yielded a recombinant enzyme with almost the same enzymatic properties as the
AB  - protein purified from T1 infected E. coli cells.  Interestingly, in both purification
AB  - procedures, a protein with a molecular weight of 50000 was found to copurify with M.EcoT1.
AB  - The N-terminal amino acid sequence identified these proteins in both cases as E. coli enolase.
ER  -

TY  - JOUR
AU  - Gast, F.U.
AU  - Brinkmann, T.
AU  - Pieper, U.
AU  - Kruger, T.
AU  - Noyer-Weidner, M.
AU  - Pingoud, A.
TI  - The recognition of methylated DNA by the GTP-dependent restriction endonuclease McrBC resides in the N-terminal domain of McrB.
JO  - Biol. Chem.
PY  - 1997
SP  - 975
EP  - 982
VL  - 378
AB  - McrBC is a GTP-dependent restriction endonuclease of E. coli K12, selectively directed against
AB  - DNA containing modified cytosine residues.  McrB, one of its components, is responsible for
AB  - the binding and, together with McrC, for the cleavage of DNAs containing two 5'-PumC sites
AB  - separated by 40-80 base pairs.  Gel retardation assays with wild-type and mutant McrB reveal
AB  - that (i) single 5'-PumC sites in DNA can be sufficient to elicit binding by McrB.  Binding to
AB  - such substrates is, however, weak and strongly dependent on the sequence context of PumC
AB  - sites.  (ii) Strong DNA binding (Kass ~ 10^7M-1) is dependent on the presence of at least two
AB  - PumC sites, even if they are separated by less than 40 bp, and is modulated by the sequence
AB  - context (-AmCCGGT->-AmCTc/gAGT->-AGGmCCT->-AAGmCTT-).  (iii) DNA binding by McrB is
AB  - accompanied by formation of distinct multiple complexes whose distribution is modulated by
AB  - GTP. (iv) McrC, which cannot bind DNA by itself, moderately stimulates the DNA binding of McrB
AB  - and converts McrB-DNA complexes to large aggregates.  (v) Deletion of the C-terminal half of
AB  - McrB, which harbors the three consensus sequences characteristic for guanine nucleotide
AB  - binding proteins, leads to protein inactive in GTP binding and/or hydrolysis and in
AB  - McrC-assisted DNA cleavage; the protein, however, remains fully competent in DNA binding.
AB  - (vi) Mutations in McrB which lead to a reduction in GTP binding and/or hydrolysis can affect
AB  - DNA binding, suggesting that the two activities are coupled in the full-length protein.
ER  -

TY  - JOUR
AU  - Gato, E.
AU  - Alvarez-Fraga, L.
AU  - Vallejo, J.A.
AU  - Rumbo-Feal, S.
AU  - Martinez-Guitian, M.
AU  - Beceiro, A.
AU  - Poza, M.
AU  - Bou, G.
AU  - Perez, A.
TI  - Draft Genome Sequences of Two Epidemic OXA-48-Producing Klebsiella pneumoniae Clinical Strains Isolated during a Large Outbreak in Spain.
JO  - Genome Announcements
PY  - 2018
SP  - e00026
EP  - e00018
VL  - 6
AB  - We report here the draft genome sequences of Klebsiella pneumoniae strains Kp1803 and Kp3380
AB  - isolated during a large outbreak at A Coruna Hospital in Spain. The
AB  - final genome assemblies for Kp1803 and Kp3380 comprise approximately 6.6 and 6.1
AB  - Mb, respectively, and both strains have G+C contents of 57.2%.
ER  -

TY  - JOUR
AU  - Gaudet, F.
AU  - Talbot, D.
AU  - Leonhardt, H.
AU  - Jaenisch, R.
TI  - A short DNA methyltransferase isoform restores methylation in vivo.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 32725
EP  - 32729
VL  - 273
AB  - Two murine DNA methyltransferase isoforms (MTases) have been observed, a longer form in
AB  - somatic and embryonic stem cells and a shorter form in oocytes and preimplantation embryos.
AB  - While the longer MTase is associated with maintenance methyltransferase activity in
AB  - replicating cells, little is known about the shorter form.  We present genetic and biochemical
AB  - evidence that both isoforms are expressed from the same Dnmt1 gene by using different
AB  - translation initiation sites in exons 1 and 4.  We further demonstrate that the shorter
AB  - isoform can functionally rescue Dnmt1 null ES cells that have a hypomethylated genome.  These
AB  - rescued ES cells differentiate in vivo into a variety of cell types, unlike the Dnmt1 null ES
AB  - cells that die upon induction of differentiation.  These results show that the shorter isoform
AB  - can substitute for the longer maintenance MTase in ES and differentiated cells.  Our data
AB  - further indicate that the shorter MTase isoform found in oocytes is fully functional in vivo
AB  - and may play an active role in the regulation of DNA methylation and the establishment of
AB  - imprinting patterns.
ER  -

TY  - JOUR
AU  - Gaultier, N.E. et al.
TI  - Complete Genome Sequence of the Bacterium Serratia marcescens SGAir0764, Isolated from Singapore Air.
JO  - Genome Announcements
PY  - 2018
SP  - e00637
EP  - e00618
VL  - 6
AB  - Serratia marcescens strain SGAir0764 was isolated from a tropical air sample collected in
AB  - Singapore. The complete genome, sequenced on the PacBio RS II
AB  - platform, consists of one chromosome with 5.1 Mb and one plasmid with 76.4 kb.
AB  - Genome annotation predicts 4,723 protein-coding genes, 89 tRNAs, and 22 rRNAs.
ER  -

TY  - JOUR
AU  - Gaultier, N.E. et al.
TI  - Genome Sequence of Geobacillus thermoleovorans SGAir0734, Isolated from Singapore Air.
JO  - Genome Announcements
PY  - 2018
SP  - e00636
EP  - e00618
VL  - 6
AB  - The thermophilic bacterium Geobacillus thermoleovorans was isolated from a tropical air sample
AB  - collected in Singapore. The genome was sequenced on the
AB  - PacBio RS II platform and consists of one chromosome with 3.6 Mb and one plasmid
AB  - with 75 kb. The genome comprises 3,509 protein-coding genes, 88 tRNAs, and 27
AB  - rRNAs.
ER  -

TY  - JOUR
AU  - Gaulton, T.
AU  - Misra, R.
AU  - Rose, G.
AU  - Baybayan, P.
AU  - Hall, R.
AU  - Freeman, J.
AU  - Turton, J.
AU  - Picton, S.
AU  - Korlach, J.
AU  - Gharbia, S.
AU  - Shah, H.
TI  - Complete Genome Sequence of the Hypervirulent Bacterium Clostridium difficile Strain G46, Ribotype 027.
JO  - Genome Announcements
PY  - 2015
SP  - e00073
EP  - e00015
VL  - 3
AB  - Clostridium difficile is one of the leading causes of antibiotic-associated diarrhea in health
AB  - care facilities worldwide. Here, we report the genome sequence
AB  - of C. difficile strain G46, ribotype 027, isolated from an outbreak in Glamorgan,
AB  - Wales, in 2006.
ER  -

TY  - JOUR
AU  - Gauntlett, J.C.
AU  - Nilsson, H.-O.
AU  - Fulurija, A.
AU  - Marshall, B.J.
AU  - Benghezal, M.
TI  - Phase-variable restriction/modification systems are required for Helicobacter pylori colonization.
JO  - Gut Pathog.
PY  - 2014
SP  - 35
EP  - 35
VL  - 6
AB  - Background: One mechanism utilized by bacterial pathogens for host adaptation and immune
AB  - evasion is the generation of phenotypic diversity by the phasevarion that results from the
AB  - differential expression of a suite of genes regulated by the activity of a phase-variable
AB  - methyltransferase within a restriction modification (RM) system. Phasevarions are active in
AB  - Helicobacter pylori, however there have been no studies investigating the significance of
AB  - phase-variable RM systems on host colonization.Methods: Two mutant types incapable of phase
AB  - variation were constructed; a clean deletion mutant ('DEL') and a mutant ('ON') where the
AB  - homopolymeric repeat was replaced with a non-repeat synonymous sequence, resulting in
AB  - expression of the full-length protein. The resulting mutants were assessed for their
AB  - colonisation ability in the mouse model.Results: Five phase-variable genes encoding either
AB  - methyltransferases or members of RM systems were found in H. pylori OND79. Our mutants fell
AB  - into three categories; 1, those with little effect on colonization, 2, those where expression
AB  - of the full-length protein was detrimental, 3, those where both mutations were
AB  - detrimental.Conclusions: Our results demonstrated that phase-variable methyltransferases are
AB  - critical to H. pylori colonization, suggesting that genome methylation and generation of
AB  - epigenetic diversity is important for colonization and pathogenesis. The third category of
AB  - mutants suggests that differential genome methylation status of H. pylori cell populations,
AB  - achieved by the phasevarion, is essential for host adaptation. Studies of phase-variable RM
AB  - mutants falling in the two other categories, not strictly required for colonization, represent
AB  - a future perspective to investigate the role of phasevarion in persistence of H. pylori.
ER  -

TY  - JOUR
AU  - Gautam, S.S.
AU  - Mac Aogain, M.
AU  - O'Toole, R.F.
TI  - Draft Genome Sequence of the First Confirmed Isolate of Multidrug-Resistant Mycobacterium tuberculosis in Tasmania.
JO  - Genome Announcements
PY  - 2017
SP  - e01230
EP  - e01217
VL  - 5
AB  - The spread of multidrug-resistant (MDR) tuberculosis (TB) has become a major global challenge.
AB  - In 2016, Tasmania recorded its first known incidence of MDR-TB.
AB  - Here, we report the draft whole-genome sequence of the Mycobacterium tuberculosis
AB  - isolate from this case, TASMDR1, and describe single-nucleotide polymorphisms
AB  - associated with its drug resistance.
ER  -

TY  - JOUR
AU  - Gauthier, A.
AU  - Turmel, M.
AU  - Lemieux, C.
TI  - A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron.
JO  - Curr. Genet.
PY  - 1991
SP  - 43
EP  - 47
VL  - 19
AB  - During interspecific crosses between Chlamydomonas eugametos and Chlamydomonas moewusii, an
AB  - optional group I intron of 955 base pairs (CeLSU 5) in the C. eugametos chloroplast large
AB  - subunit rRNA gene undergoes a duplicative transposition event which is associated with
AB  - frequent co-conversion of flanking cpDNA sequences. In the present study, we show that the
AB  - basic protein of 218 amino acids encoded by CeLSU 5 could mediate the phenomenon of intron
AB  - transposition, also called intron homing. We overexpressed the ORF specifying this protein in
AB  - E. coli using expression vectors that contain a C. moewusii cpDNA sequence encompassing the
AB  - intron homing site. The expression product was found to exhibit a double-strand DNA
AB  - endonuclease activity that is specific for the homing site. This activity was detected in vivo
AB  - by self linearization of the expression plasmids.
ER  -

TY  - JOUR
AU  - Gauthier, J.
AU  - Charette, S.J.
AU  - Derome, N.
TI  - Draft Genome Sequence of Pseudomonas fluorescens ML11A, an Endogenous Strain from Brook Charr with Antagonistic Properties against Aeromonas salmonicida subsp.  salmonicida.
JO  - Genome Announcements
PY  - 2017
SP  - e01716
EP  - e01716
VL  - 5
AB  - Pseudomonas fluorescens ML11A, isolated from brook charr, showed a strong in vitro inhibitory
AB  - effect against Aeromonas salmonicida subsp. salmonicida, a
AB  - bacterial fish pathogen. Its genome harbors gene clusters for siderophore and
AB  - bacteriocin biosynthesis and shares 99% whole-genome identity with P. fluorescens
AB  - A506, a biological control strain used in agriculture.
ER  -

TY  - JOUR
AU  - Gautier, F.
AU  - Bunemann, H.
AU  - Grotjahn, L.
TI  - Analysis of calif-thymus satellite DNA:  evidence for specific methylation of cytosine in C-G sequences.
JO  - Eur. J. Biochem.
PY  - 1977
SP  - 175
EP  - 183
VL  - 80
AB  - Digestion of purified calf thymus satellite I (density = 1.714 g/cm3) with a
AB  - series of restriction enzymes shows that modification in this satellite occurs
AB  - preferentially in the sequence C-G. This was also shown to be the case in the
AB  - other satellites and in bulk chromosomal calf thymus DNA.  Cloning of purified
AB  - satellite I DNA in Escherichia coli makes sites, previously modified, available
AB  - for cutting with certain restriction enzymes.  All these new sites contain the
AB  - sequence C-G.  High-resolution mass spectroscopy establishes that the
AB  - satellites contain a low concentration of 5-methylcytosine.  This infers that
AB  - methylation which inhibits restriction enzyme cutting must occur preferentially
AB  - in the sequence C-G.  Hybridization of cRNA of cloned satellite I DNA with the
AB  - satellites III (density = 1.706 g/cm3) and IV (density = 1.710 g/cm3) shows
AB  - that there is no or little sequence homology between these satellites.
AB  - Digestion of calf thymus satellite I DNA with endoR.EcoRI and subsequent
AB  - hybridization studies with the fragments shows two EcoRI fragments in addition
AB  - to the usual 1400-base-pair EcoRI repeat unit.
ER  -

TY  - JOUR
AU  - Gautier, M.
AU  - Chopin, M.-C.
TI  - Plasmid-determined systems for restriction and modification activity and abortive infection in Streptococcus cremoris.
JO  - Appl. Environ. Microbiol.
PY  - 1987
SP  - 923
EP  - 927
VL  - 53
AB  - Streptococcus cremoris strain IL964 possessed a restriction and modification
AB  - (R/M) activity which resulted in a bacteriophage efficiency of plating 5x10-6.
AB  - Phage sensitivity of protoplast-induced plasmid-cured derivatives indicated
AB  - that two plasmids called pIL103 (5.7 kiobases) and pIL107 (15.2 kilobases) were
AB  - each coding for one R/M system.  Plasmid pIL103-encoded R/M was ascertained by
AB  - transfer into the plasmid-free, R-/M- strain IL1403 of S. lactis, using
AB  - protoplast cotransformation.  This procedure failed for pIL107 because of some
AB  - degree of incompatibility between pIL107 and the indicator plasmid pHV1301 used
AB  - in cotransformation experiments.  We also observed that plasmid pIL105 (8.7
AB  - kilobases) which showed no incidence of phage sensitivity in the parental
AB  - strain IL964, mediated abortive infection in strain IL1403.  In 97% of the
AB  - infected cells, the phage infection was abortive, while in the remaining 3%
AB  - phages were produced with a decreased burst size (50 instead of 180).
ER  -

TY  - JOUR
AU  - Gautier, M.
AU  - Veaux, M.
AU  - Chopin, M.-C.
TI  - Cloning of three plasmid-determined systems for restriction/modification and abortive infection.
JO  - FEMS Microbiol. Rev.
PY  - 1987
SP  - 44
EP  - 44
VL  - 46
AB  - We have previously described three plasmids encoding phage-defense mechanisms in Streptococcus
AB  - lactis and S. cremoris. Plasmids pIL7 (33 kilobases) and pIL103 (5.7 kb) each encodes for a
AB  - restriction/modification (R/M) system and pIL105 (9.5 kb) encodes phage abortive infection. We
AB  - cloned each of these mechanisms into the plasmid-free, S. lactis strain IL1403. The entire
AB  - small pIL103 plasmid was inserted into the single EcoRI site of vector plasmid pIL204.
AB  - Recombinant DNA molecules formed were used in transformation of S. lactis IL1403 protoplasts.
AB  - Transformants selected for the pIL204-conferred erythromycin resistance were checked for
AB  - resistance to phage 66. All the phage-resistant clones harbored pIL103::pIL204 recombinant
AB  - DNA. In some cases deletions occured allowing the isolation of a 3.5 kb fragment carrying
AB  - genes coding for R/M activity. In the same way, the entire pIL105 plasmid together with
AB  - abortive infection activity was cloned into the single XbaI site of plasmid vector pIL252. A
AB  - 6.5 kb fragment carrying genes coding for R/M activity was isolated from the large pIL7
AB  - plasmid following partial digestion with Sau3A and insertion of the fragments into the single
AB  - BamHI site of plasmid vector pIL252. Experiments are currently in progress to bring together
AB  - the 3 cloned fragments on the same vector plasmid in order to stack phage defense mechanisms
AB  - and construct strains improved in their phage resistance.
ER  -

TY  - JOUR
AU  - Gawthorne, J.A.
AU  - Beatson, S.A.
AU  - Srikhanta, Y.N.
AU  - Fox, K.L.
AU  - Jennings, M.P.
TI  - Origin of the Diversity in DNA Recognition Domains in Phasevarion Associated modA Genes of Pathogenic Neisseria and Haemophilus influenzae.
JO  - PLoS ONE
PY  - 2012
SP  - e32337
EP  - e32337
VL  - 7
AB  - Phase variable restriction-modification (R-M) systems have been identified in a range of
AB  - pathogenic bacteria. In some it has been
AB  - demonstrated that the random switching of the mod (DNA
AB  - methyltransferase) gene mediates the coordinated expression of multiple
AB  - genes and constitutes a phasevarion (phase variable regulon). ModA of
AB  - Neisseria and Haemophilus influenzae contain a highly variable, DNA
AB  - recognition domain (DRD) that defines the target sequence that is
AB  - modified by methylation and is used to define modA alleles. 18 distinct
AB  - modA alleles have been identified in H. influenzae and the pathogenic
AB  - Neisseria. To determine the origin of DRD variability, the 18 modA DRDs
AB  - were used to search the available databases for similar sequences.
AB  - Significant matches were identified between several modA alleles and
AB  - mod gene from distinct bacterial species, indicating one source of the
AB  - DRD variability was via horizontal gene transfer. Comparison of DRD
AB  - sequences revealed significant mosaicism, indicating exchange between
AB  - the Neisseria and H. influenzae modA alleles. Regions of high inter-and
AB  - intra-allele similarity indicate that some modA alleles had undergone
AB  - recombination more frequently than others, generating further
AB  - diversity. Furthermore, the DRD from some modA alleles, such as modA12,
AB  - have been transferred en bloc to replace the DRD from different modA
AB  - alleles.
ER  -

TY  - JOUR
AU  - Gay, N.R.
AU  - Fleming, E.
AU  - Oh, J.
TI  - Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater.
JO  - Genome Announcements
PY  - 2016
SP  - e01397
EP  - e01316
VL  - 4
AB  - Cloacibacterium normanense is a Gram-negative bacterium recovered from untreated  human
AB  - wastewater. Given its high abundance in wastewater and its apparent absence
AB  - in human stool, it may contribute to biological phosphate removal. Here, we
AB  - perform a whole-genome sequence of C. normanense NRS-1(T) and examine particular
AB  - features of this draft genome.
ER  -

TY  - JOUR
AU  - Gayle, R.
AU  - Bennett, G.
TI  - Synthesis of a specific sequence of DNA using restriction enzymes.
JO  - Miami BioTechnology Winter Symposium
PY  - 1982
SP  - 526
EP  - 526
VL  - 19
AB  - The restriction enzyme MboII recognizes the DNA sequence GAAGA and cleaves the
AB  - DNA eight bases downstream from this site, leaving a single 3' protruding base.
AB  - There are no apparent sequence requirements in the stretch of DNA between the
AB  - recognition sequence and the point of cleavage.  Using this property, a segment
AB  - of DNA from one fragment can be transferred to another fragment.
ER  -

TY  - JOUR
AU  - Gayle, R.B.
AU  - Auger, E.A.
AU  - Gough, G.R.
AU  - Gilham, P.T.
AU  - Bennett, G.N.
TI  - Formation of MboII vectors and cassettes using asymmetric MboII linkers.
JO  - Gene
PY  - 1987
SP  - 221
EP  - 228
VL  - 54
AB  - Class-IIS restriction endonucleases such as MboII cleave DNA at a specified
AB  - distance away from their recognition sequences.  This feature was exploited to
AB  - cleave DNA at previously inaccessible locations by preparing special asymmetric
AB  - linker/adapters containing the MboII recognition sequence.  These could be
AB  - joined to DNA fragments and subsequently cleaved by MboII.  Attachment of a 3'
AB  - phosphate to one of the two different oligodeoxynucleotides comprising the
AB  - asymmetric duplex prevented ligation at the improper end of the linker.
AB  - Plasmids were contructed containing a unique BamHI or BclI site between the
AB  - recognition and cleavage site of MboII.  These sites were used to introduce a
AB  - foreign fragment into the plasmid at a position permitting MboII to cleave
AB  - within the newly inserted fragment.  Once cleaved at the unique MboII site,
AB  - another DNA fragment was inserted.  DNA was thus inserted at a sequence not
AB  - previously accessible to specific cleavage by a restriction enzyme.  A cassette
AB  - containing an identifiable marker, the lac operator, between two oppositely
AB  - oriented MboII/BamHI linkers was made and tested in a random insertion linker
AB  - mutagenesis experiment.
ER  -

TY  - JOUR
AU  - Gazzola, S.
AU  - Pietta, E.
AU  - Bassi, D.
AU  - Fontana, C.
AU  - Puglisi, E.
AU  - Cappa, F.
AU  - Cocconcelli, P.S.
TI  - Draft Genome Sequence of Vancomycin-Heteroresistant Staphylococcus epidermidis Strain UC7032, Isolated from Food.
JO  - Genome Announcements
PY  - 2013
SP  - e00709
EP  - e00713
VL  - 1
AB  - Staphylococcus epidermidis strain UC7032 was isolated from ready-to-eat cured meat and is
AB  - heteroresistant to glycopeptide antibiotics. The draft whole-genome
AB  - analysis revealed that this strain shows common characteristics typical of
AB  - strains that are involved in nosocomial infections.
ER  -

TY  - JOUR
AU  - Ge, B.
AU  - Liu, Y.
AU  - Liu, B.
AU  - Zhang, K.
TI  - Draft Genome Sequence of Streptomyces ahygroscopicus subsp. wuyiensis CK-15, Isolated from Soil in Fujian Province, China.
JO  - Genome Announcements
PY  - 2015
SP  - e01125
EP  - e01115
VL  - 3
AB  - We report the first high-quality draft genome sequence of an antibiotic (wuyiencin)-producing
AB  - strain, Streptomyces ahygroscopicus subsp. wuyiensis CK-15, isolated from soil samples
AB  - collected from Fujian Province, China. The 9.41-Mb genome comprises 8,311 protein-coding
AB  - sequences, encodes 89 structural RNAs, and  shows a G+C content of 72.25%.
ER  -

TY  - JOUR
AU  - Ge, F.
AU  - Li, W.
AU  - Chen, G.
AU  - Liu, Y.
AU  - Zhang, G.
AU  - Yong, B.
AU  - Wang, Q.
AU  - Wang, N.
AU  - Huang, Z.
AU  - Li, W.
AU  - Wang, J.
AU  - Wu, C.
AU  - Xie, Q.
AU  - Liu, G.
TI  - Draft genome sequence of Gordonia neofelifaecis NRRL B-59395, a cholesterol-degrading actinomycete.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5045
EP  - 5046
VL  - 193
AB  - We report a draft sequence of the genome of Gordonia neofelifaecis NRRL B-59395, a
AB  - cholesterol-degrading actinomycete isolated from fresh faeces
AB  - of a clouded leopard (Neofelis nebulosa). As predicted, the reported
AB  - genome contains several gene clusters for cholesterol degradation. This is
AB  - the second available genome sequence of the family Gordoniaceae.
ER  -

TY  - JOUR
AU  - Ge, S.
AU  - Ai, W.
AU  - Dong, X.
TI  - High-Quality Draft Genome Sequence of Leucobacter sp. Strain G161, a Distinct and Effective Chromium Reducer.
JO  - Genome Announcements
PY  - 2016
SP  - e01760
EP  - e01715
VL  - 4
AB  - Here, we report the genome sequence for Leucobacter sp. strain G161 due to its distinct and
AB  - effective hexavalent chromium reduction under aerobic growth
AB  - conditions, followed by facultative anaerobic incubation. The draft genome
AB  - sequence of Leucobacter sp. G161 comprises 3,554,188 bp, with an average G+C
AB  - content of 65.3%, exhibiting 3,341 protein-coding genes and 55 predicted RNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Ge, X.
AU  - Zhao, Y.
AU  - Hou, W.
AU  - Zhang, W.
AU  - Chen, W.
AU  - Wang, J.
AU  - Zhao, N.
AU  - Lin, J.
AU  - Wang, W.
AU  - Chen, M.
AU  - Wang, Q.
AU  - Jiao, Y.
AU  - Yuan, Z.
AU  - Xiong, X.
TI  - Complete Genome Sequence of the Industrial Strain Gluconobacter oxydans H24.
JO  - Genome Announcements
PY  - 2013
SP  - e00003
EP  - e00013
VL  - 1
AB  - is characterized by its ability to incompletely oxidize carbohydrates and alcohols. The high
AB  - yields of its oxidation products and complete secretion into
AB  - the medium make it important for industrial use. We report the finished genome
AB  - sequence of H24, an industrial strain with high l-sorbose productivity.
ER  -

TY  - JOUR
AU  - Ge, Y.Z.
AU  - Pu, M.T.
AU  - Gowher, H.
AU  - Wu, H.P.
AU  - Ding, J.P.
AU  - Jeltsch, A.
AU  - Xu, G.L.
TI  - Chromatin targeting of de novo DNA methyltransferases by the PWWP domain.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 25447
EP  - 25454
VL  - 279
AB  - DNA methylation patterns of mammalian genomes are generated in gametogenesis and early
AB  - embryonic development. Two de novo DNA
AB  - methyltransferases, Dnmt3a and Dnmt3b, are responsible for the process.
AB  - Both enzymes contain a long N-terminal regulatory region linked to a
AB  - conserved C-terminal domain responsible for the catalytic activity.
AB  - Although a PWWP domain in the N-terminal region has been shown to bind
AB  - DNA in vitro, it is unclear how the DNA methyltransferases access their
AB  - substrate in chromatin in vivo. We show here that the two proteins are
AB  - associated with chromatin including mitotic chromosomes in mammalian
AB  - cells, and the PWWP domain is essential for the chromatin targeting of
AB  - the enzymes. The functional significance of PWWP-mediated chromatin
AB  - targeting is suggested by the fact that a missense mutation in this
AB  - domain of human DNMT3B causes immunodeficiency, centromeric
AB  - heterochromatin instability, facial anomalies (ICF) syndrome, which is
AB  - characterized by loss of methylation in satellite DNA, pericentromeric
AB  - instability, and immunodeficiency. We demonstrate that the mutant
AB  - protein completely loses its chromatin targeting capacity. Our data
AB  - establish the PWWP domain as a novel chromatin/chromosome-targeting
AB  - module and suggest that the PWWP-mediated chromatin association is
AB  - essential for the function of the de novo methyltransferases during
AB  - development.
ER  -

TY  - JOUR
AU  - Ge, Z.
AU  - Taylor, D.E.
TI  - Contributions of genome sequencing to understanding the biology of Helicobacter pylori.
JO  - Annu. Rev. Microbiol.
PY  - 1999
SP  - 353
EP  - 387
VL  - 53
AB  - About half of the world's population carries Helicobacter pylori, a gram-negative, spiral
AB  - bacterium that colonizes the human stomach. The link between H. pylori and, ulceration as well
AB  - as its association with the development of both gastric cancer and mucosa-associated lymphoid
AB  - tissue lymphoma in humans is a serious public health concern. The publication of the genome
AB  - sequences of two stains of H. pylori gives rise to direct evidence on the genetic diversity
AB  - reported previously with respect to gene organization and nucleotide variability from strain
AB  - to strain. The genome size of H. pylori strain 26695 is 1,6697,867 bp and is 1,643,831 bp for
AB  - strain J99. Approximately 89% of the predicted open reading frames are common to both of the
AB  - strains, confirming H. pylori as a single species. A region containing approximately 45% of H.
AB  - pylori strain-specific open reading frames, termed the plasticity zone, is present on the
AB  - chromosomes, verifying that some strain variability exists. Frequent alteration of nucleotides
AB  - in the third position of the triplet codons and various copies of insertion elements on the
AB  - individual chromosomes appear to contribute to distinct polymorphic fingerprints among strains
AB  - analyzed by restriction fragment length polymorphisms, random amplified polymorphic DNA
AB  - method, and repetitive element-polymerase chain reaction. Disordered chromosomal locations of
AB  - some genes seen by pulsed-field gel electrophoresis are likely caused by rearrangement or
AB  - inversion of certain segments in the genomes. Cloning and functional characterization of the
AB  - genes involved in acidic survival, vacuolating toxin, cag-pathogenicity island, motility,
AB  - attachment to epithelial cells, natural transformation, and the biosynthesis of
AB  - lipopolysaccharides have considerably increased our understanding of the molecular genetic
AB  - basis for the pathogenesis of H. pylori. The homopolymeric nucleotide tracts and dinucleotide
AB  - repeats, which potentially regulate the on- and off-status of the target genes by the
AB  - strand-slipped mispairing mechanism, are often found in the genes encoding the outer-membrane
AB  - proteins, in enzymes for lipopolysaccharide synthesis, and within DNA modification/restriction
AB  - systems. Therefore, these genes may be involved in the H. pylori-host interaction.
ER  -

TY  - JOUR
AU  - Geahigan, K.B.
AU  - Meints, G.A.
AU  - Hatcher, M.E.
AU  - Orban, J.
AU  - Drobny, G.P.
TI  - The dynamic impact of CpG methylation in DNA.
JO  - Biochemistry
PY  - 2000
SP  - 4939
EP  - 4946
VL  - 39
AB  - Solid-state deuterium NMR is used to investigate perturbations of the local, internal dynamics
AB  - in the EcoRI restriction binding site, -GAATTC- induced by cytidine methylation. Methylation
AB  - of the cytidine base in this sequence is known to suppress hydrolysis by the EcoRI restriction
AB  - enzyme. Previous solid-state deuterium NMR studies have detected large amplitude motions of
AB  - the phosphate-sugar backbone at the AT-CG junction of the unmethylated DNA sequence. This
AB  - study shows that methylation of the cytidine base in a CpG dinucleotide reduces the amplitudes
AB  - of motions of the phosphate-sugar backbone. These observations suggest a direct link between
AB  - suppression of the amplitudes of localized, internal motions of the sugar-phosphate backbone
AB  - of the DNA and inhibition of restriction enzyme cleavage.
ER  -

TY  - JOUR
AU  - Gebreyesus, K.H.
AU  - Owens, R.A.
TI  - Selective protection of restriction endonuclease sites.
JO  - Biotechniques
PY  - 2003
SP  - 512
EP  - 523
VL  - 34
AB  - A difficulty that is encountered when attempting to insert a PCR-amplified product or DNA
AB  - fragment of interest into a particular vector is the
AB  - presence within the insert of one or more internal restriction
AB  - endonuclease (RE) sites identical to those selected for the flanks of the
AB  - insert. Our method circumvents this problem by partially protecting
AB  - internal RE sites while flanking sites for the same RE are cleaved. The
AB  - amplified product is first heat denatured in the presence of excess
AB  - amounts of perfectly complementary oligonucleotides that can anneal to the
AB  - flanks of the insert. The mixture is allowed to anneal and is subsequently
AB  - digested with the appropriate endonucleases. This results in the cleavage
AB  - of the flanking RE sites while digestion at the internal RE site is not
AB  - efficient. The mixture is subsequently heat denatured and column purified
AB  - to remove the oligonucleotides. The product is then allowed to anneal and
AB  - can be used directly in a ligation reaction with the plasmid vector. This
AB  - method facilitates the construction of recombinant molecules by creating
AB  - desired flanks while preserving internal RE sites.
ER  -

TY  - JOUR
AU  - Geck, P.
AU  - Molnar, A.
AU  - Nasz, I.
TI  - A mathematical method for the identification of the ATGCAT recognition sequence of a Streptococcus mutans restriction endonuclease.
JO  - Acta Microbiol. Hung.
PY  - 1991
SP  - 43
EP  - 46
VL  - 38
AB  - Taking advantage of a mathematical equation applied so far in different fields the calculation
AB  - of ATGCAT recognition sequence of restriction endonuclease from Streptococcus mutans serotype
AB  - C (SmuCI) is reported together with confirming computer and physical mapping data.
ER  -

TY  - JOUR
AU  - Geck, P.
AU  - Molnar, A.
AU  - Nasz, I.
TI  - Identification of ATGCAT sequence at sites of SmuCI restriction endonuclease by computer and physical mapping of Adenovirus Type I DNA.
JO  - Acta Microbiol. Hung.
PY  - 1991
SP  - 47
EP  - 53
VL  - 38
AB  - Physical mapping of adenovirus type I DNA was carried out in order to analyze the recognition
AB  - sequence of a novel Streptococcus restriction endonuclease. In addition to the new map and
AB  - homology data on this poorly analyzed serotype, the result offers the definite evidence for
AB  - the ATGCAT recognition sequence on adenovirus DNA and the physical map of cleavage points.
ER  -

TY  - JOUR
AU  - Geck, P.
AU  - Molnar, A.
AU  - Nasz, J.
TI  - Elimination of non-specific nucleases from restriction endonuclease preparations by different binding on free DNA ligand.
JO  - Acta Microbiol. Hung.
PY  - 1987
SP  - 241
EP  - 245
VL  - 34
AB  - In the purification of a novel restriction endonuclease (an AvaIII
AB  - isoschizomer, isolated in this laboratory) standard methods were insufficient
AB  - to eliminate non-specific nuclease contaminations.  Taking advantage of the
AB  - specific site recognition and binding of the restriction endonuclease on DNAs,
AB  - a method is described for the simple extraction of non-specific nucleases.  DNA
AB  - substrate without recognizable sites do not bind the restriction endonuclease,
AB  - while non-specific nucleases are absorbed to, and eliminated with, the DNA via
AB  - gel filtration chromatography under special conditions.
ER  -

TY  - JOUR
AU  - Gee, J.E.
AU  - Marston, C.K.
AU  - Sammons, S.A.
AU  - Burroughs, M.A.
AU  - Hoffmaster, A.R.
TI  - Draft Genome Sequence of Bacillus cereus Strain BcFL2013, a Clinical Isolate Similar to G9241.
JO  - Genome Announcements
PY  - 2014
SP  - e00469
EP  - e00414
VL  - 2
AB  - Bacillus cereus strains, such as G9241, causing anthrax-like illnesses have recently been
AB  - discovered. We report the genome sequence of a clinical strain, B.
AB  - cereus BcFL2013, which is similar to G9241, recovered from a patient in Florida.
ER  -

TY  - JOUR
AU  - Geese, W.J.
AU  - Kwon, Y.K.
AU  - Wen, X.P.
AU  - Waring, R.B.
TI  - In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI.
JO  - Eur. J. Biochem.
PY  - 2003
SP  - 1543
EP  - 1554
VL  - 270
AB  - The AnCOB group I intron from Aspergillus nidulans encodes a homing DNA endonuclease called
AB  - I-AniI which also functions as a maturase, assisting
AB  - in AnCOB intron RNA splicing. In this investigation we biochemically
AB  - characterized the endonuclease activity of I-AniI in vitro and utilized
AB  - competition assays to probe the relationship between the RNA- and
AB  - DNA-binding sites. Despite functioning as an RNA maturase, I-AniI still
AB  - retains several characteristic properties of homing endonucleases
AB  - including relaxed substrate specificity, DNA cleavage product retention
AB  - and instability in the reaction buffer, which suggest that the protein has
AB  - not undergone dramatic structural adaptations to function as an
AB  - RNA-binding protein. Nitrocellulose filter binding and kinetic burst
AB  - assays showed that both nucleic acids bind I-AniI with the same 1 : 1
AB  - stoichiometry. Furthermore, in vitro competition activity assays revealed
AB  - that the RNA substrate, when prebound to I-AniI, stoichiometrically
AB  - inhibits DNA cleavage activity, yet in reciprocal experiments, saturating
AB  - amounts of prebound DNA substrate fails to inhibit RNA splicing activity.
AB  - The data suggest therefore that both nucleic acids do not bind the same
AB  - single binding site, rather that I-AniI appears to contain two binding
AB  - sites.
ER  -

TY  - JOUR
AU  - Geese, W.J.
AU  - Waring, R.B.
TI  - A comprehensive characterization of a group IB intron and its encoded maturase reveals that protein-assisted splicing requires an almost intact intron RNA.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 609
EP  - 622
VL  - 308
AB  - The group I intron (AnCOB) of the mitochondrial apocytochrome b gene from Aspergillus nidulans
AB  - encodes a bi-functional maturase protein that is also a DNA endonuclease. Although the AnCOB
AB  - intron self-splices, the encoded maturase protein greatly facilitates splicing, in part, by
AB  - stabilizing RNA tertiary structure. To determine their role in self-splicing and in
AB  - protein-assisted splicing, several peripheral RNA sub-domains in the 313 nucleotide intron
AB  - were deleted (P2, P9, P9.1) or truncated (P5ab, P6a). The sequence in two helices (P2 and P9)
AB  - was also inverted. Except for P9, the deleted regions are not highly conserved among group I
AB  - introns and are often dispensable for catalytic activity. Nevertheless, despite the very tight
AB  - binding of AnCOB RNA to the maturase and the high activity of the bimolecular complex (the
AB  - rate of 5' splice-site cleavage was >20 min(-1) with guanosine as the cofactor), the intron
AB  - was surprisingly sensitive to these modifications. Several mutations inactivated splicing
AB  - completely and virtually all impaired splicing to varying degrees. Mutants containing
AB  - comparatively small deletions in various regions of the intron significantly decreased binding
AB  - affinity (generally >10(4)-fold), indicating that none of the domains that remained
AB  - constitutes the primary recognition site of the maturase. The data argue that tight binding
AB  - requires tertiary interactions that can be maintained by only a relatively intact intron RNA,
AB  - and that the binding mechanism of the maturase differs from those of two other
AB  - well-characterized group I intron splicing factors, CYT-18 and Cpb2. A model is proposed in
AB  - which the protein promotes widespread cooperative folding of an RNA lacking extensive initial
AB  - tertiary structure.
ER  -

TY  - JOUR
AU  - Gefter, M.
AU  - Hausmann, R.
AU  - Gold, M.
AU  - Hurwitz, J.
TI  - The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid.
JO  - J. Biol. Chem.
PY  - 1966
SP  - 1995
EP  - 2006
VL  - 241
AB  - An enzyme activity which leads to the degradation of S-adenosylmethionine appears after T3
AB  - phage infection of Escherichia coli B.  The purification and properties of this activity have
AB  - been described.  The enzyme catalyzes the conversion of S-adenosylmethionine to
AB  - thiomethyladenosine and homoserine.  It has been suggested that a gamma-amino-butyrolactone is
AB  - an intermediate in this reaction.  The enzyme appears only after infection with T3 phage.
AB  - Infection with phages T1, T2, T4, T5, T6, T7, or lambda does not result in the appearance of
AB  - any activity.  The rate of enzyme formation and the requirement for protein synthesis de novo
AB  - suggests that this activity is similar to early enzymes formed after infection with the T-even
AB  - phages.  The enzyme has been isolated both from normal phage T3-infected E. coli and from
AB  - ultraviolet light-inactivated phage T3-infected E. coli.  In the later case, the specific
AB  - activity of cell-free extracts was several-fold higher than extracts obtained from normal
AB  - phage T3-infected cells.  Infection of e. coli with ultraviolet light-inactivated phage T3
AB  - does not result in the cessation of host cell deoxyribonucleic or ribonucleic acid synthesis.
AB  - Thus, newly synthesized DNA and RNA formed after infection with phage T3 are devoid of
AB  - methylated bases.  Phage T2, grown in ultraviolet light-inactivated, phage T3-infected E.
AB  - coli, is likewise devoid of methylated bases.  Such methyl-deficient T2 phage appears to be
AB  - normal in its biological properties so far examined.
ER  -

TY  - JOUR
AU  - Gehlot, H.S. et al.
TI  - High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a  nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 43
EP  - 43
VL  - 11
AB  - Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that  was isolated
AB  - from a nitrogen-fixing nodule of the tree legume P. cineraria (L.)
AB  - Druce (Khejri), which is a keystone species that grows in arid and semi-arid
AB  - regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in
AB  - alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid
AB  - conditions and is able to form an effective symbiosis with several annual crop
AB  - legumes as well as species of mimosoid trees and shrubs. Here we describe the
AB  - features of Ensifer sp. PC2, together with genome sequence information and its
AB  - annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into
AB  - 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139
AB  - RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of
AB  - the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
AB  - Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
ER  -

TY  - JOUR
AU  - Geier, G.E.
AU  - Modrich, P.
TI  - Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of DpnI endonuclease.
JO  - J. Biol. Chem.
PY  - 1979
SP  - 1408
EP  - 1413
VL  - 254
AB  - The recognition sequence for the dam methylase of Escherichia coli K12 has been determined
AB  - directly by use of in vivo methylated ColE1 DNA or DNA methylated in vitro with purified
AB  - enzyme. The methylase recognizes the symmetric tetranucleotide d(pG-A-T-C) and introduces two
AB  - methyl groups per site in duplex DNA with the product of methylation being
AB  - 6-methylaminopurine. This work has also demonstrated that DpnI restriction endonuclease
AB  - cleaves on the 3' side of the modified adenine within the methylated sequence to yield DNA
AB  - fragments possessing fully base-paired termini. All sequences in ColE1 DNA methylated by the
AB  - dam enzyme are subject to double strand cleavage by DpnI endonuclease. Therefore, this
AB  - restriction enzyme can be employed for mapping the location of sequences possessing the dam
AB  - modification.
ER  -

TY  - JOUR
AU  - Geiger, R.
AU  - Ruter, T.
AU  - Alves, J.
AU  - Fliess, A.
AU  - Wolfes, H.
AU  - Pingoud, V.
AU  - Urbanke, C.
AU  - Maass, G.
AU  - Pingoud, A.
AU  - Dusterhoft, A.
AU  - Kroger, M.
TI  - Genetic engineering of EcoRI mutants with altered amino acid residues in the DNA binding site:  Physiochemical investigations give evidence for an altered monomer/dimer equilibrium for the Gln144Lys145 and Gln144Lys145Lys200 mutants.
JO  - Biochemistry
PY  - 1989
SP  - 2667
EP  - 2677
VL  - 28
AB  - We have genetically engineered the Arg200 ->Lys mutant, the Glu144Arg145
AB  - ->GlnLys double mutant, and the Glu144Arg145Arg200 ->GlnLysLys triple mutant of
AB  - the EcoRI endonuclease in extension of previously published work on
AB  - site-directed mutagenesis of the EcoRI endonuclease in which Glu144 had been
AB  - exchanged for Gln and Arg145 for Lys [Wolfes et al. (1986) Nucleic Acids Res.
AB  - 14, 9063].  All these mutants carry modifications in the DNA binding site.
AB  - Mutant EcoRI proteins were purified to homogeneity and characterized by
AB  - physiochemical techniques.  All mutants have a very similar secondary structure
AB  - composition.  However, whereas the Lys200 mutant is not impaired in its
AB  - capacity to form a dimer, the Gln144Lys145 and Gln144Lys145Lys200 mutants have
AB  - a very much decreased propensity to form a dimer or tetramer depending on
AB  - concentration as shown by gel filtration and analytical ultracentrifugation.
AB  - This finding may explain the results of isoelectric focusing experiments which
AB  - show that these two mutants have a considerably more basic pI than expected for
AB  - a protein in which an acidic amino acid was replaced by a neutral one.
AB  - Furthermore, while wild-type EcoRI and the Lys200 mutant are denatured in an
AB  - irreversible manner upon heating to 60C, the thermal denaturation process as
AB  - shown by circular dichroism spectroscopy is fully reversible with the
AB  - Gln144Lys145 double mutant and the Gln144Lys145Lys200 triple mutant.  All EcoRI
AB  - endonuclease mutants described here have a residual enzymatic activity with
AB  - wild-type specificity, since Escherichia coli cells overexpressing the mutant
AB  - proteins can only survive in the presence of EcoRI methylase.  The detailed
AB  - analysis of the enzymatic activity and specificity of the purified mutant
AB  - proteins is the subject of the accompanying paper.
ER  -

TY  - JOUR
AU  - Geiman, T.M.
AU  - Sankpal, U.T.
AU  - Robertson, A.K.
AU  - Chen, Y.
AU  - Mazumdar, M.
AU  - Heale, J.
AU  - Schmiesing, J.A.
AU  - Kim, W.
AU  - Yokomori, K.
AU  - Zhao, Y.
AU  - Robertson, K.D.
TI  - Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 2716
EP  - 2729
VL  - 32
AB  - Proper patterns of genome-wide DNA methylation, mediated by DNA methyltransferases DNMT1, -3A
AB  - and -3B, are essential for embryonic development and genomic stability in mammalian cells. The
AB  - de novo DNA methyltransferase DNMT3B is of particular interest because it is frequently
AB  - overexpressed in tumor cells and is mutated in immunodeficiency, centromere instability and
AB  - facial anomalies (ICF) syndrome. In order to gain a better understanding of DNMT3B, in terms
AB  - of the targeting of its methylation activity and its role in genome stability, we
AB  - biochemically purified endogenous DNMT3B from HeLa cells. DNMT3B co-purifies and interacts,
AB  - both in vivo and in vitro, with several components of the condensin complex (hCAP-C, hCAP-E
AB  - and hCAP-G) and KIF4A. Condensin mediates genome-wide chromosome condensation at the onset of
AB  - mitosis and is critical for proper segregation of sister chromatids. KIF4A is proposed to be a
AB  - motor protein carrying DNA as cargo. DNMT3B also interacts with histone deacetylase 1 (HDAC1),
AB  - the co-repressor SIN3A and the ATP-dependent chromatin remodeling enzyme hSNF2H. Further more,
AB  - DNMT3B co-localizes with condensin and KIF4A on condensed chromosomes throughout mitosis.
AB  - These studies therefore reveal the first direct link between the machineries regulating DNA
AB  - methylation and mitotic chromosome condensation in mammalian cells.
ER  -

TY  - JOUR
AU  - Geiman, T.M.
AU  - Sankpal, U.T.
AU  - Robertson, A.K.
AU  - Zhao, Y.X.
AU  - Zhao, Y.M.
AU  - Robertson, K.D.
TI  - DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2004
SP  - 544
EP  - 555
VL  - 318
AB  - The non-random pattern of genome-wide DNA methylation in mammalian cells is established and
AB  - maintained by DNA methyltransferases DNMT1,
AB  - 3A, and 3B. De novo DNA methyltransferase DNMT3B is critical for
AB  - embryonic development and is mutated in ICF syndrome. Despite its
AB  - importance in normal cellular functioning, little is known about how
AB  - DNMT3B operates in the context of chromatin. Here we demonstrate that
AB  - DNMT3B associates with four chromatin-associated enzymatic activities
AB  - common to transcriptionally repressed, heterochromatic regions of the
AB  - genome: DNA methyltransferase, histone deacetylase, ATPase, and histone
AB  - methylase activities. By immunoprecipitation and GST pull-down, we show
AB  - that DNMT3B interacts with HDAC1, HDAC2, HP1 proteins, Suv39h1, and the
AB  - ATP-dependent chromatin remodeling enzyme hSNF2H. Endogenous hSNF2H is
AB  - also associated with DNA methyltransferase activity. These proteins
AB  - co-localize extensively with DNMT3B in heterochromatic regions. Our
AB  - results therefore link DNMT3B to three other components of the
AB  - epigenetic machinery and provide important insights into how DNA
AB  - methylation patterns may be established within the chromatin
AB  - environment.
ER  -

TY  - JOUR
AU  - Geis, A.
AU  - El Demerdash, H.A.
AU  - Heller, K.J.
TI  - Sequence analysis and characterization of plasmids from Streptococcus thermophilus.
JO  - Plasmid
PY  - 2003
SP  - 53
EP  - 69
VL  - 50
AB  - The nucleotide sequences of eight plasmids isolated from seven Streptococcus thermophilus
AB  - strains have been determined. Plasmids pSt04,
AB  - pER1-1, and pJ34 are related and replicate via a rolling circle mechanism.
AB  - Plasmid pJ34 encodes for a replication initiation protein (RepA) and a
AB  - small polypeptide with unknown function. Plasmids pSt04 and pER1-1 carry
AB  - in addition to repA genes coding for small heat shock proteins (sHsp).
AB  - Expression of these proteins is induced at elevated temperatures or low pH
AB  - and increases the thermo- and acid resistance. Plasmids pER1-2 and pSt22-2
AB  - show identical sequences with five putative open reading frames (ORFs).
AB  - The gene products of ORF1 and ORF4 reveal some similarities to transposon
AB  - encoded proteins of Bacillus subtilis and Tn916. ORF1 of plasmid pSt106
AB  - encodes a protein similar to resolvases of different Gram-positive
AB  - bacteria. Integrity of ORF2 and 3, encoding a putative DNA primase and a
AB  - replication protein, is essential for replication. ORF1 to 3 of plasmid
AB  - pSt08, which are organized in a tricistronic operon, encode a RepA
AB  - protein, an adenosine-specific methyltransferase, and a type II
AB  - restriction endonuclease. Another type II restriction-modification (R/M)
AB  - system is encoded on plasmid pSt0 which is highly similar to those encoded
AB  - on lactococcal plasmid pHW393 and B. subtilis plasmid pXH13. Plasmid-free
AB  - derivatives of strains St0 and St08 show increased phage sensitivity,
AB  - indicating that in the wild-type strains the R/M systems are functionally
AB  - expressed. Recombinant plasmids based on the replicons of plasmids pSt04,
AB  - pJ34, pSt106, pSt08, and pSt0, are able to replicate in Lactococcus lactis
AB  - and B. subtilis, respectively, whereas constructs carrying pER1-2 only
AB  - replicate in S. thermophilus.
ER  -

TY  - JOUR
AU  - Geissler, A.J.
AU  - Behr, J.
AU  - Vogel, R.F.
TI  - Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii.
JO  - Genome Announcements
PY  - 2016
SP  - e00826
EP  - e00816
VL  - 4
AB  - Lactobacillus backii is an important beer-spoiling species. Five strains isolated from four
AB  - different breweries were sequenced using single-molecule real-time
AB  - sequencing. Five complete genomes were generated, which will help to understand
AB  - niche adaptation to beer and provide the basis for consecutive analyses.
ER  -

TY  - JOUR
AU  - Geissler, A.J.
AU  - Behr, J.
AU  - Vogel, R.F.
TI  - Multiple Genome Sequences of Important Beer-Spoiling Lactic Acid Bacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e01077
EP  - e01016
VL  - 4
AB  - Seven strains of important beer-spoiling lactic acid bacteria were sequenced using
AB  - single-molecule real-time sequencing. Complete genomes were obtained for
AB  - strains of Lactobacillus paracollinoides, Lactobacillus lindneri, and Pediococcus
AB  - claussenii The analysis of these genomes emphasizes the role of plasmids as the
AB  - genomic foundation of beer-spoiling ability.
ER  -

TY  - JOUR
AU  - Gelfand, M.S.
AU  - Koonin, E.V.
TI  - Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2430
EP  - 2439
VL  - 25
AB  - Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically
AB  - significant level in the genomes of several bacteria, including the completely sequenced
AB  - Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the
AB  - archaeon Methanococcus jannaschii.  In contrast, there is only moderate avoidance of
AB  - palindromes in the small genome of the bacterium Mycoplasma genitalium and no detectable
AB  - avoidance in the genomes of chloroplasts and mitochondria.  The sites for type II
AB  - restriction-modification enzymes detected in the given species tend to be among the most
AB  - avoided palindromes in a particular genome, indicating a direct connection between the
AB  - avoidance of short oligonucleotide words and restriction-modification systems with the
AB  - respective specificity.  Palindromes corresponding to sites for restriction enzymes from other
AB  - species are also avoided, albeit less significantly, suggesting that in the course of
AB  - evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably
AB  - as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and
AB  - prophages.  Palindromic words appear to accumulate in DNA once it becomes isolated from
AB  - restriction-modification systems, as demonstrated by the case of organellar genomes.  By
AB  - combining these observations with protein sequence analysis, we show that the most avoided
AB  - 4-palindrome and the most avoided 6-palindrome in the archaeon M. jannaschii are likely to be
AB  - recognition sites for two novel restriction-modification systems.
ER  -

TY  - JOUR
AU  - Gelinas, R.E.
AU  - Myers, P.A.
AU  - Roberts, R.J.
TI  - Two sequence-specific endonucleases from Moraxella bovis.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 169
EP  - 179
VL  - 114
AB  - Two new sequence-specific endodeoxyribonucleases have been partially purified from Moraxella
AB  - bovis. These restriction-like enzymes, MboI and MboII, each cleave bacteriophage lambda DNA
AB  - and adenovirus-2 DNA at more than 50 sites. MboI recognizes the sequence 5'^G-A-T-C 3' 3'
AB  - C-T-A-T^5' and cleaves at the sites indicated by the arrows. A specific endonuclease, MosI,
AB  - has also been purified from Moraxella osloenis and recognizes the same sequence as MboI.
ER  -

TY  - JOUR
AU  - Gelinas, R.E.
AU  - Myers, P.A.
AU  - Weiss, G.H.
AU  - Roberts, R.J.
AU  - Murray, K.
TI  - A specific endonuclease from Brevibacterium albidum.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 433
EP  - 440
VL  - 114
AB  - A new restriction-like endonuclease, BalI, has been partially purified from
AB  - Brevibacterium albidum.  This enzyme cleaves bacteriophage lambda DNA at least
AB  - 18 times and adenovirus-2 DNA at least 16 times, but does not cleave simian
AB  - virus 40 DNA.  All sites cleaved by BalI are also cut by the specific
AB  - endonuclease HaeIII from Haemophilus aegyptius.  The recognition sequence of
AB  - BalI is 5'-T-G-G ^ C-C-A-3' 3'-A-C-C ^ G-G-T-5' and the cleavage site is
AB  - indicated by the arrows.
ER  -

TY  - JOUR
AU  - Gemmen, G.J.
AU  - Millin, R.
AU  - Smith, D.E.
TI  - Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA.
JO  - Biophys. J.
PY  - 2006
SP  - 4154
EP  - 4165
VL  - 91
AB  - Looping and cleavage of single DNA molecules by the two-site restriction endonuclease Sau3AI
AB  - were measured with optical tweezers. A DNA template
AB  - containing many recognition sites was used, permitting loop sizes from
AB  - approximately 10 to 10,000 basepairs. At high enzyme concentration,
AB  - cleavage events were detected within 5 s and nearly all molecules were
AB  - cleaved within 5 min. Activity decreased approximately 10-fold as the DNA
AB  - tension was increased from 0.03 to 0.7 pN. Substituting Ca(2+) for Mg(2+)
AB  - blocked cleavage, permitting measurement of stable loops. At low tension,
AB  - the initial rates of cleavage and looping were similar (approximately
AB  - 0.025 s(-1) at 0.1 pN), suggesting that looping is rate limiting. Short
AB  - loops formed more rapidly than long loops. The optimum size decreased from
AB  - approximately 250 to 45 basepairs and the average number of loops (in 1
AB  - min) from 4.2 to 0.75 as tension was increased from 0.03 to 0.7 pN. No
AB  - looping was detected at 5 pN. These findings are in qualitative agreement
AB  - with recent theoretical predictions considering only DNA mechanics, but we
AB  - observed weaker suppression with tension and smaller loop sizes. Our
AB  - results suggest that the span and elasticity of the protein complex,
AB  - nesting of loops, and protein-induced DNA bending and wrapping play an
AB  - important role.
ER  -

TY  - JOUR
AU  - Gemmen, G.J.
AU  - Millin, R.
AU  - Smith, D.E.
TI  - DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 2864
EP  - 2877
VL  - 34
AB  - Proteins interacting at multiple sites on DNA via looping play an important role in many
AB  - fundamental biochemical processes. Restriction
AB  - endonucleases that must bind at two recognition sites for efficient
AB  - activity are a useful model system for studying such interactions. Here we
AB  - used single DNA manipulation to study sixteen known or suspected two-site
AB  - endonucleases. In eleven cases (BpmI, BsgI, BspMI, Cfr10I, Eco57I, EcoRII,
AB  - FokI, HpaII, NarI, Sau3AI and SgrAI) we found that substitution of Ca2+
AB  - for Mg2+ blocked cleavage and enabled us to observe stable DNA looping.
AB  - Forced disruption of these loops allowed us to measure the frequency of
AB  - looping and probability distributions for loop size and unbinding force
AB  - for each enzyme. In four cases we observed bimodal unbinding force
AB  - distributions, indicating conformational heterogeneity and/or complex
AB  - binding energy landscapes. Measured unlooping events ranged in size from 7
AB  - to 7500 bp and the most probable size ranged from less than 75 bp to
AB  - nearly 500 bp, depending on the enzyme. In most cases the size
AB  - distributions were in much closer agreement with theoretical models that
AB  - postulate sharp DNA kinking than with classical models of DNA elasticity.
AB  - Our findings indicate that DNA looping is highly variable depending on the
AB  - specific protein and does not depend solely on the mechanical properties
AB  - of DNA.
ER  -

TY  - JOUR
AU  - Gemmen, G.J.
AU  - Millin, R.
AU  - Smith, D.E.
TI  - Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off" at low force.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 11555
EP  - 11560
VL  - 103
AB  - DNA looping occurs in many important protein-DNA interactions, including those regulating
AB  - replication, transcription, and recombination. Recent
AB  - theoretical studies predict that tension of only a few piconewtons acting
AB  - on DNA would almost completely inhibit DNA looping. Here, we study
AB  - restriction endonucleases that require interaction at two separated sites
AB  - for efficient cleavage. Using optical tweezers we measured the dependence
AB  - of cleavage activity on DNA tension with 15 known or suspected two-site
AB  - enzymes (BfiI, BpmI, BsgI, BspMI, Cfr9I, Cfr10I, Eco57I, EcoRII, FokI,
AB  - HpaII, MboII, NarI, SacII, Sau3AI, and SgrAI) and six one-site enzymes
AB  - (BamHI, EcoRI, EcoRV, HaeIII, HindIII, and DNaseI). All of the one-site
AB  - enzymes were virtually unaffected by 5 pN of tension, whereas all of the
AB  - two-site enzymes were completely inhibited. These enzymes thus constitute
AB  - a remarkable example of a tension sensing "molecular switch." A detailed
AB  - study of one enzyme, Sau3AI, indicated that the activity decreased
AB  - exponentially with tension and the decrease was approximately 10-fold at
AB  - 0.7 pN. At higher forces ( approximately 20-40 pN) cleavage by the
AB  - one-site enzymes EcoRV and HaeIII was partly inhibited and cleavage by
AB  - HindIII was enhanced, whereas BamHI, EcoRI, and DNaseI were largely
AB  - unaffected. These findings correlate with structural data showing that
AB  - EcoRV bends DNA sharply, whereas BamHI, EcoRI, and DNaseI do not. Thus,
AB  - DNA-directed enzyme activity involving either DNA looping or bending can
AB  - be modulated by tension, a mechanism that could facilitate mechanosensory
AB  - transduction in vivo.
ER  -

TY  - JOUR
AU  - Gencay, Y.E.
AU  - Sorensen, M.C.H.
AU  - Brondsted, L.
TI  - Whole-Genome Sequence of the Bacteriophage-Sensitive Strain Campylobacter jejuni  NCTC12662.
JO  - Genome Announcements
PY  - 2017
SP  - e00409
EP  - e00417
VL  - 5
AB  - Campylobacter jejuni NCTC12662 has been the choice bacteriophage isolation strain due to its
AB  - susceptibility to C. jejuni bacteriophages. This trait makes it a good
AB  - candidate for studying bacteriophage-host interactions. We report here the
AB  - whole-genome sequence of NCTC12662, allowing future elucidation of the molecular
AB  - mechanisms of phage-host interactions in C. jejuni.
ER  -

TY  - JOUR
AU  - Geng, J.
AU  - Chiu, C.H.
AU  - Tang, P.
AU  - Chen, Y.
AU  - Shieh, H.R.
AU  - Hu, S.
AU  - Chen, Y.Y.
TI  - Complete Genome and Transcriptomes of Streptococcus parasanguinis FW213: Phylogenic Relations and Potential Virulence Mechanisms.
JO  - PLoS ONE
PY  - 2012
SP  - E34769
EP  - E34769
VL  - 7
AB  - Streptococcus parasanguinis, a primary colonizer of the tooth surface, is also an
AB  - opportunistic pathogen for subacute endocarditis. The complete genome of strain
AB  - FW213 was determined using the traditional shotgun sequencing approach and
AB  - further refined by the transcriptomes of cells in early exponential and early
AB  - stationary growth phases in this study. The transcriptomes also discovered 10
AB  - transcripts encoding known hypothetical proteins, one pseudogene, five
AB  - transcripts matched to the Rfam and additional 87 putative small RNAs within the
AB  - intergenic regions defined by the GLIMMER analysis. The genome contains five
AB  - acquired genomic islands (GIs) encoding proteins which potentially contribute to
AB  - the overall pathogenic capacity and fitness of this microbe. The differential
AB  - expression of the GIs and various open reading frames outside the GIs at the two
AB  - growth phases suggested that FW213 possess a range of mechanisms to avoid host
AB  - immune clearance, to colonize host tissues, to survive within oral biofilms and
AB  - to overcome various environmental insults. Furthermore, the comparative genome
AB  - analysis of five S. parasanguinis strains indicates that albeit S. parasanguinis
AB  - strains are highly conserved, variations in the genome content exist. These
AB  - variations may reflect differences in pathogenic potential between the strains.
ER  -

TY  - JOUR
AU  - Geng, J.
AU  - Huang, S.C.
AU  - Li, S.
AU  - Hu, S.
AU  - Chen, Y.Y.
TI  - Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5596
EP  - 5597
VL  - 193
AB  - Streptococcus salivarius 57.I is one of the most abundant and highly ureolytic bacteria in the
AB  - human mouth. It can utilize urea as the sole
AB  - nitrogen source via the activity of urease. Complete genome sequencing of
AB  - S. salivarius 57.I revealed a chromosome and a phage which are absent in
AB  - strain SK126.
ER  -

TY  - JOUR
AU  - Geng, W.
AU  - Cao, M.
AU  - Song, C.
AU  - Xie, H.
AU  - Liu, L.
AU  - Yang, C.
AU  - Feng, J.
AU  - Zhang, W.
AU  - Jin, Y.
AU  - Du, Y.
AU  - Wang, S.
TI  - Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-{gamma}-glutamic acid.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3393
EP  - 3394
VL  - 193
AB  - Bacillus amyloliquefaciens is one of most prevalent Gram-positive aerobic spore-forming
AB  - bacteria with the ability of synthesizing polysaccharides
AB  - and polypeptides. Here, we report the complete genome sequence of B.
AB  - amyloliquefaciens LL3, which was isolated from fermented food and presents
AB  - the glutamic acid-independent production of poly-gamma-glutamic acid.
ER  -

TY  - JOUR
AU  - Genger, R.K.
AU  - Kovac, K.A.
AU  - Dennis, E.S.
AU  - Peacock, W.J.
AU  - Finnegan, E.J.
TI  - Multiple DNA methyltransferase genes in Arabidopsis thaliana.
JO  - Plant Mol. Biol.
PY  - 1999
SP  - 269
EP  - 278
VL  - 41
AB  - Methylation of plant DNA occurs at cytosines in any sequence context, and as the Arabidopsis
AB  - methyltransferase, METI, preferentially methylates cytosines in CG dinucleotides, it is likely
AB  - that Arabidopsis has other methyltransferases with different target specificities. We have
AB  - identified five additional genes encoding putative DNA methyltransferases. Three of these
AB  - genes are very similar to METI throughout the coding region; these genes probably arose by a
AB  - series of gene duplication events, the most recent giving rise to METIIa and METIIb. METIIa
AB  - and b are expressed at low levels in vegetative and floral organs and the level of transcripts
AB  - is not affected by the introduction of a METI antisense transgene, nor do the METII enzymes
AB  - substitute for the reduced activity of METI in methylating CG dinucleotides. METIII is not
AB  - essential as it encodes a truncated protein. Two other genes encode a second class of DNA
AB  - methyltransferase with the conserved motifs characteristic of cytosine methyltransferases, but
AB  - with little homology to the METI-like methyltransferases through the remainder of the protein.
AB  - These two methyltransferases are characterized by the presence of a chromodomain inserted
AB  - within the methyltransferase domain, suggesting that they may be associated with
AB  - heterochromatin. Both these genes are transcribed at low levels in vegetative and reproductive
AB  - tissues.
ER  -

TY  - JOUR
AU  - Gentzbittel, L.
AU  - Nicolas, P.
TI  - A basic program to construct evolutionary trees from restriction endonuclease data.
JO  - J. Hered.
PY  - 1989
SP  - 254
EP  - 254
VL  - 80
AB  - None
ER  -

TY  - JOUR
AU  - Gentzbittel, L.
AU  - Nicolas, P.
TI  - Improvement of "A BASIC program to construct evolutionary trees from restriction endonuclease data" with the use of PASCAL.
JO  - J. Hered.
PY  - 1990
SP  - 491
EP  - 492
VL  - 81
AB  - None
ER  -

TY  - JOUR
AU  - George, J.
AU  - Blakesley, R.W.
AU  - Chirikjian, J.G.
TI  - Sequence-specific endonuclease BamHI.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 6521
EP  - 6524
VL  - 255
AB  - The specificity of cleavage of BamHI is altered in the presence of hydrophobic
AB  - reagents, such as glycerol and M2SO.  The enzyme with altered specificity,
AB  - designated BamHI.1, generated digestion patterns of various DNAs, which were
AB  - distinct from those generated by BamHI.  Cleavage sites recognized in PhiX174
AB  - RF DNA in the presence of these hydrophobic reagents are not related to the
AB  - BamHI palindrome.  BamHI.1 appears to be an endogenous form of BamHI that can
AB  - be expressed by altering the hydrophobicity of the reaction.
ER  -

TY  - JOUR
AU  - George, J.
AU  - Chirikjian, J.G.
TI  - Biospecific fractionation matrices for sequence specific endonucleases.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 2223
EP  - 2232
VL  - 5
AB  - Fractionation of several type II specific restriction endonucleases was
AB  - achieved by separation on two novel biospecific matrices.  The matrices are
AB  - pyran, a copolymer of divinyl ether of maleic anhydride, and Cibacron Blue
AB  - F3Ga, a blue dye commonly used for the calibration of molecular sieves.  Both
AB  - compounds are insolubilized by coupling to sepharose through a cyanogen bromide
AB  - linkage and in their soluable form inhibit the restriction endonucleases which
AB  - we have tested.  These affinity matrices can be used to obtain restriction
AB  - endonucleases from crude extracts after removal of nucleic acids.  They have
AB  - also proven to have a high capacity when used as subsequent step in enzyme
AB  - purification.  Their additional advantage is the rapid development time and
AB  - reusability of columns packed with the two matrices.
ER  -

TY  - JOUR
AU  - George, J.
AU  - Chirikjian, J.G.
TI  - Sequence-specific endonuclease BamHI: Relaxation of sequence recognition.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1982
SP  - 2432
EP  - 2436
VL  - 79
AB  - The effect of glycerol on the specificity of DNA cleavage by the restriction
AB  - endonuclease BamHI has been examined.  In addition to the canonical G ^ G-A-T-C
AB  - site, BamHI cuts DNA at several sites that we have named noncanonical BamHI.1
AB  - sites.  The number of BamHI.1 sites is simian virus 40 and pBR322 was
AB  - determined to be 13 for each DNA.  Cutting sites determined by DNA sequence
AB  - analysis include G ^ G-A-A-C-C, G ^ G-C-T-C-C, G ^ G-G-T-C-C, and G-A-A-T-C-C
AB  - with the complementary strand sequence assignments of G-G-T-T-C-C, G-G-A-G-C-C,
AB  - G-G-A-C-C-C, and G-G-A-T-T-C.  The relaxation in specificity was related to
AB  - hydrogen bond acceptor and donor sites in the recognition sequence, in an
AB  - attempt to generate a model of BamHI recognition of cognate sites in DNA.
ER  -

TY  - JOUR
AU  - George, J.
AU  - Hamada, Y.-Y.T.
AU  - Chirikjian, J.G.
TI  - Chemical modifications as structural probes for the recognition of DNA palindromes by BamHI and BglI.
JO  - Fed. Proc.
PY  - 1981
SP  - 1848
EP  - 1848
VL  - 40
AB  - BamHI and BglI have been previously purified to apparent homogeneity in our
AB  - laboratory.  The catalytically active form of BamHI is a dimer comprised of two
AB  - apparently identical subunits of 23,000 daltons.  In comparison the active form
AB  - of BglI was isolated as a single polypeptide of 34,000 daltons.  Chemical
AB  - modification of the enzyme and both oligonucleotide and plasmid DNA substrates
AB  - have been undertaken.  Enzyme which has been reductively alkylated (lysine
AB  - modification) with formaldehyde is inactivated.  In contrast when such
AB  - modifications are performed in the presence of a DNA substrate enzymatic
AB  - activity is maintained.  Likewise DNAs that contain no recognition sequences
AB  - for BamHI confer little protection against activity losses.  This suggests that
AB  - upon specific binding to DNA, at least one or a group of lysine residues, are
AB  - protected from chemical modification. BamHI recognizes the palindromic sequence
AB  - G^GATCC.  We have evidence to suggest that the information required for
AB  - recognition specificity resides in the major groove of the DNA double helix.
AB  - This recognition may involve the N6 position of adenine and the 04 position of
AB  - thymine.  The involvement of N7 and N2 of guanine and N3 of adenine are under
AB  - curretn investigation by chemical modification procedures.
ER  -

TY  - JOUR
AU  - George, J.
AU  - Nardone, G.
AU  - Chirikjian, J.G.
TI  - Sequence-specific BamHI endonuclease.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 14387
EP  - 14392
VL  - 260
AB  - Arginyl residues in BamHI endonuclease were examined because of their alleged
AB  - role in proteins that contain nucleotide- or phosphate-binding sites.
AB  - Butanedione, an arginine-specific reagent, inhibited the endonuclease in the
AB  - presence of sodium borate.  The inhibition was decreased by preliminary
AB  - incubation of the enzyme with DNA or competitive inhibitors which were the
AB  - 5'-phosphoryl deoxydinucleotide subsets of the BamHI recognition sequence.  The
AB  - dinucleotide pdGpdG protected the enzyme most efficiently against the
AB  - butanedione modification.  Dinucleotides that were unrelated to the recognition
AB  - sequence failed to protect the enzyme from inactivation.  These studies
AB  - indicate that arginine residues may reside in the enzyme's active site and
AB  - might function in the sequence-specific recognition of the BamHI palindrome.
ER  -

TY  - JOUR
AU  - Georgi, E.
AU  - Walter, M.C.
AU  - Pfalzgraf, M.T.
AU  - Northoff, B.H.
AU  - Holdt, L.M.
AU  - Scholz, H.C.
AU  - Zoeller, L.
AU  - Zange, S.
AU  - Antwerpen, M.H.
TI  - Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East.
JO  - PLoS ONE
PY  - 2017
SP  - E0175425
EP  - E0175425
VL  - 12
AB  - Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare
AB  - in Northern and Western Europe. However, since 2014 a significant increase of
AB  - imported infections caused by Brucella (B.) melitensis has been noticed in
AB  - Germany. Patients predominantly originated from Middle East including Turkey and
AB  - Syria. These circumstances afforded an opportunity to gain insights into the
AB  - population structure of Brucella strains. Brucella-isolates from 57 patients were
AB  - recovered between January 2014 and June 2016 with culture confirmed brucellosis
AB  - by the National Consultant Laboratory for Brucella. Their whole genome sequences
AB  - were generated using the Illumina MiSeq platform. A whole genome-based SNP typing
AB  - assay was developed in order to resolve geographically attributed genetic
AB  - clusters. Results were compared to MLVA typing results, the current gold-standard
AB  - of Brucella typing. In addition, sequences were examined for possible genetic
AB  - variation within target regions of molecular diagnostic assays. Phylogenetic
AB  - analyses revealed spatial clustering and distinguished strains from different
AB  - patients in either case, whereas multiple isolates from a single patient or
AB  - technical replicates showed identical SNP and MLVA profiles. By including WGS
AB  - data from the NCBI database, five major genotypes were identified. Notably,
AB  - strains originating from Turkey showed a high diversity and grouped into seven
AB  - subclusters of genotype II. MLVA analysis congruently clustered all isolates and
AB  - predominantly matched the East Mediterranean genetic clade. This study confirms
AB  - whole-genome based SNP-analysis as a powerful tool for accurate typing of B.
AB  - melitensis. Furthermore it allows special allocation and therefore provides
AB  - useful information on the geographic origin for trace-back analysis. However, the
AB  - lack of reliable metadata in public databases often prevents a resolution below
AB  - geographic regions or country levels and corresponding precise trace-back
AB  - analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an
AB  - important method to complement epidemiological surveys during outbreak
AB  - investigations. This is the first report of a detailed genetic investigation of
AB  - an extensive collection of B. melitensis strains isolated from human cases in
AB  - Germany.
ER  -

TY  - JOUR
AU  - Gerasimaite, R.
AU  - Klimasauskas, S.
TI  - Novel approaches to engineering sequence-specificity of DNA cytosine-5 methyltransferases.
JO  - FEBS J.
PY  - 2007
SP  - 259
EP  - 259
VL  - 274
AB  - Bacterial DNA cytosine-5 methyltransferases (C5-MTases) recognize
AB  - 2-8 bp DNA sequences and transfer the methyl group from
AB  - the cofactor S-adenosyl-L-methionine onto the C5 position of a
AB  - cytosine residue in that particular target sequence. Besides their
AB  - utmost biological importance, DNA MTases were shown to be
AB  - useful tools for site-specific DNA labelling [1] and for the construction
AB  - of bionanodevices [2]. Here we describe the conversion of the
AB  - HhaI methyltransferase (M.HhaI), which recognizes the palindromic
AB  - GCGC site, into a GCG-specific or CGC-specific MTases.
AB  - Due to a non-palindromic nature of the new targets, such engineered
AB  - MTases could be used for creating hemimethylated CpG sites
AB  - in DNA, which are desired models for mechanistic studies of the
AB  - maintenance of genomic methylation patterns in higher eukaryotes
AB  - [3]. Numerous crystal structures available for M.HhaI show that
AB  - the recognition of the GCGC target is accomplished by two recognition
AB  - loops. Directed evolution and rational design approaches
AB  - were employed to obtain variants with the novel substrate specificities.
AB  - Interestingly, one of the most efficient MTase variants contains
AB  - a mutation outside the recognition loops, which allows the
AB  - formation of a non-specific contact to the phosphodiester backbone
AB  - of the DNA. Our results thus demonstrate that new asymmetric
AB  - target specificities can be created by alterations of the
AB  - recognition elements in DNA MTases, and that de novo non-specific
AB  - contacts can compensate for the loss of base-specific DNA
AB  - interactions.
AB  - References
AB  - 1. Lukinavicius, G, et al. (2007). J Am Chem Soc, DOI: 10.1021/
AB  - ja0691876.
AB  - 2. Singer, E, et al. (2006). Nano Lett, 6(6): 1184.
AB  - 3. Vilkaitis, G, et al. (2005). J Biol Chem, 280(1): 64.
ER  -

TY  - JOUR
AU  - Gerasimaite, R.
AU  - Merkiene, E.
AU  - Klimasauskas, S.
TI  - Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 3771
EP  - 3780
VL  - 39
AB  - Methylation of the five position of cytosine in DNA plays important roles in epigenetic
AB  - regulation in diverse organisms including humans. The transfer of methyl groups from the
AB  - cofactor S-adenosyl-l-methionine is carried out by methyltransferase enzymes. Using the
AB  - paradigm bacterial methyltransferase M.HhaI we demonstrate, in a chemically unperturbed
AB  - system, the first direct real-time analysis of the key mechanistic events-the flipping of the
AB  - target cytosine base and its covalent activation; these changes were followed by monitoring
AB  - the hyperchromicity in the DNA and the loss of the cytosine chromophore in the target
AB  - nucleotide, respectively. Combined with studies of M.HhaI variants containing redesigned
AB  - tryptophan fluorophores, we find that the target base flipping and the closure of the mobile
AB  - catalytic loop occur simultaneously, and the rate of this concerted motion inversely
AB  - correlates with the stability of the target base pair. Subsequently, the covalent activation
AB  - of the target cytosine is closely followed by but is not coincident with the methyl group
AB  - transfer from the bound cofactor. These findings provide new insights into the temporal
AB  - mechanism of this physiologically important reaction and pave the way to in-depth studies of
AB  - other base-flipping systems.
ER  -

TY  - JOUR
AU  - Gerasimaite, R.
AU  - Vilkaitis, G.
AU  - Klimasauskas, S.
TI  - A directed evolution design of a GCG-specific DNA hemimethylase.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 7332
EP  - 7341
VL  - 37
AB  - DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific
AB  - modification of DNA and are becoming increasingly
AB  - important tools for biotechnology. Here we describe a structure-guided
AB  - rational protein design combined with random mutagenesis and selection to
AB  - change the specificity of the HhaI C5-MTase from GCGC to GCG. The
AB  - specificity change was brought about by a five-residue deletion and
AB  - introduction of two arginine residues within and nearby one of the target
AB  - recognizing loops. DNA protection assays, bisulfite sequencing and enzyme
AB  - kinetics showed that the best selected variant is comparable to wild-type
AB  - M.HhaI in terms of sequence fidelity and methylation efficiency, and
AB  - supersedes the parent enzyme in transalkylation of DNA using synthetic
AB  - cofactor analogs. The designed C5-MTase can be used to produce
AB  - hemimethylated CpG sites in DNA, which are valuable substrates for studies
AB  - of mammalian maintenance MTases.
ER  -

TY  - JOUR
AU  - Gerbore, J.
AU  - Brutel, A.
AU  - Lemainque, A.
AU  - Mairey, B.
AU  - Medigue, C.
AU  - Vallenet, D.
AU  - Lefort, F.
AU  - Grizard, D.
TI  - Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00058
EP  - e00016
VL  - 4
AB  - The complete genome of Bacillus methylotrophicus strain B25, isolated in Switzerland, was
AB  - sequenced. Its size is 3.85 Mb, and several genes that may
AB  - contribute to plant growth-promoting activities were identified in silico.
ER  -

TY  - JOUR
AU  - Germann, M.W.
AU  - Kalisch, B.W.
AU  - Lundberg, P.
AU  - Vogel, H.J.
AU  - van de Sande, J.H.
TI  - Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1489
EP  - 1498
VL  - 18
AB  - We have investigated loop-induced structural perturbation of the stem structure
AB  - in hairpins d(GAATTCXnGAATTC) (X = A, T, and n = 3, 4, 5 and 6) that contain an
AB  - EcoRI restriction site in close proximity to the hairpin loop.
AB  - Oligonucleotides containing either a T3 or an A3 loop were not hydrolyzed by
AB  - the restriction enzyme and also showed only weak binding to EcoRI in the
AB  - absence of the cofactor Mg2+.  In contrast, hairpins with larger loops are
AB  - hydrolyzed by the enzyme at the scission site next to the loop although the
AB  - substrate with a A4 loop is significantly more resistant than the
AB  - oligonucleotide containing a T4 loop.  The hairpin structures with 3 loop
AB  - residues were found to be thermally most stable while larger hairpin loops
AB  - resulted in structures with lower melting temperatures.  The T-loop hairpins
AB  - are thermally more stable than the hairpins containing the same number of A
AB  - residues in the loop.  As judged from proton NMR spectroscopy and the
AB  - thermodynamic data, the base pair closest to the hairpin loop did form in all
AB  - cases studied.  The hairpin loops did, however, affect the conformation of the
AB  - stem structure of the hairpins.  From 31P and 1H NMR spectroscopy we conclude
AB  - that the perturbation of the stem structure is stronger for smaller hairpin
AB  - loops and that the extent of the perturbation is limited to 2 - 3 base pairs
AB  - for hairpins with T3 or A4 loops.  Our results demonstrate that hairpin loops
AB  - modulate the conformation of the stem residues close to the loop and that this
AB  - in turn reduces the substrate activity for DNA sequence specific proteins.
ER  -

TY  - JOUR
AU  - Germann, M.W.
AU  - Kalisch, B.W.
AU  - Varnum, J.M.
AU  - Vogel, H.J.
AU  - van de Sande, J.H.
TI  - NMR spectroscopic and enzymatic studies of DNA hairpins containing mismatches in the EcoRI recognition site.
JO  - Biochem. Cell Biol.
PY  - 1998
SP  - 391
EP  - 402
VL  - 76
AB  - We have correlated the structural perturbations caused by DNA mismatches with the enzymatic
AB  - data of the interaction of the restriction endonuclease EcoRI with DNA. Oligonucleotides
AB  - d(CGAGAATTCTCA5GAXAATTCT) (X = G, A, T) and d(CGCGAATTYGCGT4CGCXAATTCGCG) (Y = C, X = G, T and
AB  - Y = A, X = T) containing single mismatches within the EcoRI recognition site were
AB  - characterized by NMR spectroscopy and by their EcoRI substrate properties. UV melting and gel
AB  - electrophoresis studies confirm that the oligonucleotides form hairpin structures. The
AB  - presence of either a CT or a CA mismatch results in markedly lower Tm and van't Hoff
AB  - enthalpies compared with the fully base paired control. NMR imino proton spectra of these
AB  - hairpins demonstrate that the perturbation caused by the two mispairs or a noncanonical AT
AB  - pair is localized and limited to one or two base pairs on either side of the perturbation. The
AB  - DNA hairpin structures containing single mismatches, and to a lesser extent also sequences
AB  - with a single noncanonical base pair, are substrates for the restriction endonuclease. In
AB  - addition to the strand scission at the nonperturbed GpA phosphodiester bond some cleavage is
AB  - observed at the mismatched position. The interactions of the CA and CT mismatched hairpin with
AB  - the enzyme are characterized by binding constants that are only 33 and 57 times lower,
AB  - respectively, than that for the canonical sequence, corresponding to 8-10 kJ x mol(-1) less
AB  - favorable free binding energy. This, taken together with the NMR data, indicates that the CA
AB  - and CT mismatches have only small effects on the EcoRI recognition of the DNA substrate. We
AB  - conclude that two out of the three hydrogen bonds that characterize the interaction of EcoRI
AB  - with the CG base pair in the canonical sequence can still be formed for either the CT or CA
AB  - mismatched recognition site.
ER  -

TY  - JOUR
AU  - Gerome, P.
AU  - Le Fleche, P.
AU  - Blouin, Y.
AU  - Scholz, H.C.
AU  - Thibault, F.M.
AU  - Raynaud, F.
AU  - Vergnaud, G.
AU  - Pourcel, C.
TI  - Yersinia pseudotuberculosis ST42 (O:1) Strain Misidentified as Yersinia pestis by Mass Spectrometry Analysis.
JO  - Genome Announcements
PY  - 2014
SP  - e00435
EP  - e00414
VL  - 2
AB  - We report here the draft sequence of strain CEB14_0017, alias HIAD_DUP, recovered from a human
AB  - patient and initially identified as Yersinia pestis by mass
AB  - spectrometry analysis. Genotyping based on tandem repeat polymorphism assigned
AB  - the strain to Yersinia pseudotuberculosis sequence type 42 (ST42). The total
AB  - assembly length is 4,894,739 bp.
ER  -

TY  - JOUR
AU  - Gerrish, R.S.
AU  - Gill, A.L.
AU  - Fowler, V.G.
AU  - Gill, S.R.
TI  - Development of pooled suppression subtractive hybridization to analyze the pangenome of Staphylococcus aureus.
JO  - J. Microbiol. Methods
PY  - 2010
SP  - 56
EP  - 60
VL  - 81
AB  - We describe the development and application of a Pooled Suppression
AB  - Subtractive Hybridization (PSSH) method to describe differences between
AB  - the genomic content of a pool of clinical Staphylococcus aureus isolates
AB  - and a sequenced reference strain. In comparative bacterial genomics,
AB  - Suppression Subtractive Hybridization (SSH) is normally utilized to
AB  - compare genomic features or expression profiles of one strain versus
AB  - another, which limits its ability to analyze communities of isolates.
AB  - However, a PSSH approach theoretically enables the user to characterize
AB  - the entirety of gene content unique to a related group of isolates in a
AB  - single reaction. These unique fragments may then be linked to individual
AB  - isolates through standard PCR. This method was applied to examine the
AB  - genomic diversity found in pools of S.aureus isolates associated with
AB  - complicated bacteremia infections leading to endocarditis and
AB  - osteomyelitis. Across four pools of 10 isolates each, four hundred and
AB  - twenty seven fragments not found in or significantly divergent from the S.
AB  - aureus NCTC 8325 reference genome were detected. These fragments could be
AB  - linked to individual strains within its pool by PCR. This is the first use
AB  - of PSSH to examine the S. aureus pangenome. We propose that PSSH is a
AB  - powerful tool for researchers interested in rapidly comparing the genomic
AB  - content of multiple unstudied isolates.
ER  -

TY  - JOUR
AU  - Gerst, M.M.
AU  - Dudley, E.G.
AU  - Xiaoli, L.
AU  - Yousef, A.E.
TI  - Draft Genome Sequence of Bacillus velezensis GF610, a Producer of Potent Anti-Listeria Agents.
JO  - Genome Announcements
PY  - 2017
SP  - e01046
EP  - e01017
VL  - 5
AB  - Bacillus velezensis GF610 was isolated from soil in Illinois, USA, and found to produce
AB  - amyloliquecidin GF610, a potent two-component antimicrobial peptide. We
AB  - report here the GF610 strain draft genome sequence, which contains 4.29 Mb and an
AB  - overall GC content of 45.91%.
ER  -

TY  - JOUR
AU  - Gerst, M.M.
AU  - Yesil, M.
AU  - Yousef, A.E.
TI  - Draft Genome Sequence of Bacillus velezensis OSY-S3, a Producer of Potent Antimicrobial Agents Active against Bacteria and Fungi.
JO  - Genome Announcements
PY  - 2018
SP  - e01465
EP  - e01417
VL  - 6
AB  - Bacillus velezensis OSY-S3 produces anti-Listeria, anti-Escherichia coli, and antifungal
AB  - compounds. Additionally, fermentate of B. velezensis OSY-S3 culture
AB  - removes Staphylococcus aureus biofilms effectively. The draft genome sequence of
AB  - B. velezensis OSY-S3 reported here had a genome size of ~3.90 Mb and a G+C
AB  - content of 46.5%.
ER  -

TY  - JOUR
AU  - Getaz, M.
AU  - Baeyen, S.
AU  - Blom, J.
AU  - Maes, M.
AU  - Cottyn, B.
AU  - Pothier, J.F.
TI  - High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae  Isolates.
JO  - Genome Announcements
PY  - 2018
SP  - e01585
EP  - e01517
VL  - 6
AB  - Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry
AB  - bacterial leaf blight. We report here the first draft whole-genome
AB  - sequences of five X. arboricola pv. fragariae isolates from Italy and France.
ER  -

TY  - JOUR
AU  - Getaz, M.
AU  - van der Wolf, J.M.
AU  - Blom, J.
AU  - Pothier, J.F.
TI  - Complete Genome Sequences of Three Isolates of Xanthomonas fragariae, the Bacterium Responsible for Angular Leaf Spots on Strawberry Plants.
JO  - Genome Announcements
PY  - 2017
SP  - e00642
EP  - e00617
VL  - 5
AB  - Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf
AB  - spots, thus reducing the yield of production for strawberry fruits.
AB  - Three isolates with various geographic and time origins were sequenced with
AB  - long-read technology (PacBio) to generate finished genome sequences of virulent
AB  - strains and observe the variability in their contents.
ER  -

TY  - JOUR
AU  - Geue, L.
AU  - Menge, C.
AU  - Berens, C.
AU  - Barth, S.A.
TI  - Complete Annotated Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains and One Atypical Enteropathogenic E. coli Strain, Isolated from Naturally  Colonized Cattle of German Origin.
JO  - Genome Announcements
PY  - 2017
SP  - e00321
EP  - e00317
VL  - 5
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are important zoonotic enteric pathogens
AB  - with the main reservoir in cattle. Here, we present the genomes
AB  - of two STEC strains and one atypical enteropathogenic E. coli strain from cattle
AB  - origin, obtained during a longitudinal study in German cattle herds.
ER  -

TY  - JOUR
AU  - Gfeller, K.Y.
AU  - Roth, M.
AU  - Melle, L.
AU  - Teuber, M.
TI  - Sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid pLME300 from Lactobacillus fermentum  ROT1.
JO  - Plasmid
PY  - 2003
SP  - 190
EP  - 201
VL  - 50
AB  - Lactobacillus fermentum ROT1 was isolated from a raw milk dairy product. It is resistant to
AB  - novobiocin, tetracycline, erythromycin and
AB  - dalfopristin. A chromosomal tetracycline-resistance determinant was
AB  - identified as tetM. A 19,398-bp plasmid (pLME300), present in several
AB  - erythromycin-resistant strains of Lb. fermentum, was isolated from strain
AB  - ROT1 and completely sequenced. Based on putative open reading frames,
AB  - pLME300 contains at least four different functional regions. In region I,
AB  - ORF1 shows high homologies to replication proteins of different
AB  - theta-replicating plasmids. In addition, a tandem repeat of a 22-bp
AB  - sequence appears 4.5 times. In region II, ORF3 may code for a methylase,
AB  - and ORF4 has homologies to Mrr restriction system proteins of Deinococcus
AB  - radiodurans and Escherichia coli suggesting a restriction-modification
AB  - system. Region III harbours antibiotic-resistance genes, coding for a
AB  - macrolide-lincosamide-streptogramin B (MLS) methylase Erm(LF) and the
AB  - streptogramin A acetyltransferase Vat(E), which is identical to Vat(E)
AB  - from Enterococcus faecium. Furthermore, region III shows a 91% nucleotide
AB  - sequence identity to an erm-vat linkage of E. faecium. Region IV carries
AB  - ORFs that appear to be involved in plasmid mobilization as characterized
AB  - by a putative origin of transfer and a mobilization protein. pLME300 is
AB  - the largest completely sequenced multi-resistance plasmid isolated from
AB  - any Lactobacillus strain so far.
ER  -

TY  - JOUR
AU  - Ghai, R.
AU  - Martin-Cuadrado, A.B.
AU  - Molto, A.G.
AU  - Heredia, I.G.
AU  - Cabrera, R.
AU  - Martin, J.
AU  - Verdu, M.
AU  - Deschamps, P.
AU  - Moreira, D.
AU  - Lopez-Garcia, P.
AU  - Mira, A.
AU  - Rodriguez-Valera, F.
TI  - Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing.
JO  - ISME J.
PY  - 2010
SP  - 1
EP  - 13
VL  - 0
AB  - The deep chlorophyll maximum (DCM) is a zone of maximal photosynthetic activity, generally
AB  - located toward the base of the photic zone in lakes and oceans. In the tropical waters, this
AB  - is a permanent feature, but in the Mediterranean and other temperate waters, the DCM is a
AB  - seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM
AB  - community has been 454 pyrosequenced both directly and after cloning in fosmids. This study is
AB  - the first to be carried out at this sequencing depth (ca. 600 Mb combining direct and fosmid
AB  - sequencing) at any DCM. Our results indicate a microbial community massively dominated by the
AB  - high-light-adapted Prochlorococcus marinus subsp. pastoris, Synechococcus sp., and the
AB  - heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the
AB  - existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we
AB  - found a large number of cyanophages that could prey on this microbe, although sequence
AB  - conservation was much lower. The high abundance of phage sequences in the cellular size
AB  - fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In
AB  - addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and
AB  - recruited many fragments from the total direct DNA sequencing suggesting that this group might
AB  - be quite abundant in this habitat. The comparison between the direct and fosmids sequencing
AB  - revealed a bias in the fosmid libraries against low-GC DNA and specifically against the two
AB  - most dominant members of the community, Candidatus Pelagibacter and P. marinus subsp.
AB  - pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from
AB  - other less prevalent members of this community.
ER  -

TY  - JOUR
AU  - Ghaskadbi, S.
AU  - Bharathi, S.
AU  - Modak, S.P.
TI  - Inhibition of cleavage by restriction endonucleases due to modifications induced in SV40 DNA by methyl methanesulfonate.
JO  - Cell. Mol. Biol. Res.
PY  - 1995
SP  - 59
EP  - 66
VL  - 41
AB  - Methyl methanesulfonate (MMS), a direct mutagen, methylates DNA bases and causes distortions
AB  - in DNA structure.  Supercoiled SV40 DNA was treated in vitro with varying concentrations of
AB  - MMS from 0.001 mM to 10 mM MMS either for 30 min or 3 h and analyzed by electrophoresis in 1%
AB  - neutral and alkaline agarose gels.  The electrophoretic mobility (EPM) of native DNA did not
AB  - change after treatment with the mutagen, while alkaline gels revealed low MW DNA fragments due
AB  - to single strand breaks at alkali-sensitive sites generated by the action of MMS.  By
AB  - two-dimensional electrophoresis, we find that all three native DNA forms contain
AB  - alkali-sensitive sites after treatment with MMS.  To examine the effect of base modification
AB  - by MMS on DNA-protein interactions, we have used as probes, restriction endonucleases.  These
AB  - cleave DNA in a sequence-specific manner, and their activity is dependent upon the methylation
AB  - status of the substrate DNA.  We find that cleavage by these restriction endonucleases is
AB  - inhibited due to methylation by MMS.
ER  -

TY  - JOUR
AU  - Ghazal, S.
AU  - Hurst, S.G.I.V.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Badr, U.M.
AU  - Hussein, M.A.
AU  - Abouzaied, M.A.
AU  - Khalil, K.M.
AU  - Tisa, L.S.
TI  - Draft Genome Sequence of Photorhabdus luminescens Strain BA1, an Entomopathogenic Bacterium Isolated from Nematodes Found in Egypt.
JO  - Genome Announcements
PY  - 2014
SP  - e00396
EP  - e00314
VL  - 2
AB  - Photorhabdus luminescens strain BA1 is an entomopathogenic bacterium that forms a symbiotic
AB  - association with Heterorhabditis nematodes. We report here a 5.0-Mbp
AB  - draft genome sequence for P. luminscens strain BA1, with a G+C content of 42.46%
AB  - and 4,250 candidate protein-coding genes.
ER  -

TY  - JOUR
AU  - Ghazal, S.
AU  - Oshone, R.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Khalil, K.M.
AU  - Tisa, L.S.
TI  - Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.
JO  - Genome Announcements
PY  - 2016
SP  - e00154
EP  - e00116
VL  - 4
AB  - Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a
AB  - symbiotic association with Heterorhabditis nematodes. We report here
AB  - a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a
AB  - G+C content of 42.4% and containing 4,243 candidate protein-coding genes.
ER  -

TY  - JOUR
AU  - Ghazal, S.
AU  - Swanson, E.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Khalil, K.M.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Photorhabdus temperata Strain Hm, an Entomopathogenic Bacterium Isolated from Nematodes.
JO  - Genome Announcements
PY  - 2017
SP  - e00974
EP  - e00917
VL  - 5
AB  - Photorhabdus temperata strain Hm is an entomopathogenic bacterium that forms a symbiotic
AB  - association with Heterorhabditis nematodes. Here, we report a 5.0-Mbp
AB  - draft genome sequence for P. temperata strain Hm with a G+C content of 44.1% and
AB  - containing 4,226 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Ghequire, M.G.
AU  - Rokni-Zadeh, H.
AU  - Zarrineh, P.
AU  - De Mot, R.
TI  - Draft Genome Sequence of Pseudomonas fluorescens LMG 5329, a White Line-Inducing  Principle-Producing Bioindicator for the Mushroom Pathogen Pseudomonas tolaasii.
JO  - Genome Announcements
PY  - 2013
SP  - e00383
EP  - e00313
VL  - 1
AB  - Pseudomonas tolaasii, the causative agent of Agaricus bisporus brown blotch disease, can be
AB  - identified by the white line reaction, occurring upon
AB  - confrontation of the tolaasin-producing mushroom pathogen with 'Pseudomonas
AB  - reactans,' producing the lipopeptide white line-inducing principle (WLIP). The
AB  - draft genome sequence of the WLIP-producing indicator Pseudomonas fluorescens
AB  - strain LMG 5329 is reported here.
ER  -

TY  - JOUR
AU  - Ghequire, M.G.
AU  - Swings, T.
AU  - Michiels, J.
AU  - Gross, H.
AU  - De Mot, R.
TI  - Draft Genome Sequence of Pseudomonas putida BW11M1, a Banana Rhizosphere Isolate  with a Diversified Antimicrobial Armamentarium.
JO  - Genome Announcements
PY  - 2016
SP  - e00251
EP  - e00216
VL  - 4
AB  - In this study, we report the draft genome ofPseudomonas putidaBW11M1, a banana rhizosphere
AB  - isolate producing various antimicrobial compounds, including a
AB  - lectin-like bacteriocin, an R-type tailocin, the cyclic lipopeptide xantholysin,
AB  - and the fatty acid-derived pseudopyronine.
ER  -

TY  - JOUR
AU  - Ghio, S.
AU  - Martinez, C.A.I.
AU  - Talia, P.
AU  - Grasso, D.H.
AU  - Campos, E.
TI  - Draft Genome Sequence of Cellulolytic and Xylanolytic Paenibacillus sp. A59, Isolated from Decaying Forest Soil from Patagonia, Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e01233
EP  - e01215
VL  - 3
AB  - Paenibacillus sp. A59 was isolated from decaying forest soil in Argentina and characterized as
AB  - a xylanolytic strain. We report the draft genome sequence of this isolate, with an estimated
AB  - genome size of 7 Mb which harbor 6,424 coding sequences. Genes coding for hydrolytic enzymes
AB  - involved in lignocellulose deconstruction were predicted.
ER  -

TY  - JOUR
AU  - Ghodhbane-Gtari, F. et al.
TI  - Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca.
JO  - Genome Announcements
PY  - 2016
SP  - e00770
EP  - e00716
VL  - 4
AB  - Nocardia sp. strain BMG111209 is a non-Frankia actinobacterium isolated from root nodules of
AB  - Casuarina glauca in Tunisia. Here, we report the 9.1-Mbp draft genome
AB  - sequence of Nocardia sp. strain BMG111209 with a G + C content of 69.19% and
AB  - 8,122 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Ghodhbane-Gtari, F. et al.
TI  - Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca.
JO  - Genome Announcements
PY  - 2016
SP  - e00799
EP  - e00716
VL  - 4
AB  - Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain
AB  - BMG51109, isolated from Casuarina glauca root nodules. The
AB  - improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90%
AB  - GC content and 7,307 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Ghodhbane-Gtari, F. et al.
TI  - Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod-) Ineffective (Fix-) Isolate from Coriaria nepalensis.
JO  - Genome Announcements
PY  - 2013
SP  - e0008513
EP  - e0008513
VL  - 1
AB  - We report here the genome sequence of Frankia sp. strain CN3, which was isolated  from
AB  - Coriaria nepalensis. This genome sequence is the first from the fourth
AB  - lineage of Frankia, strains of which are unable to reinfect actinorhizal plants.
AB  - At 10 Mb, it represents the largest Frankia genome sequenced to date.
ER  -

TY  - JOUR
AU  - Ghodhbane-Gtari, F.
AU  - Hurst, S.G.I.V.
AU  - Oshone, R.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Ktari, A.
AU  - Salem, K.
AU  - Gtari, M.
AU  - Tisa, L.S.
TI  - Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina  glauca Grown in Tunisia.
JO  - Genome Announcements
PY  - 2014
SP  - e00520
EP  - e00514
VL  - 2
AB  - Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous
AB  - plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia
AB  - sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules
AB  - of Casuarina glauca collected in Tunisia.
ER  -

TY  - JOUR
AU  - Gholizadeh, A.
AU  - Faizi, M.H.
AU  - Kohnehrouz, B.B.
TI  - Induced expression of EcoRI endonuclease as an active maltose-binding fusion protein in Escherichia coli.
JO  - Microbiology
PY  - 2010
SP  - 167
EP  - 172
VL  - 79
AB  - Among the numerous bacterial Type II restriction enzymes, EcoRI endonuclease is the most
AB  - extensively studied and is widely used in
AB  - recombinant DNA technology. Its heterologous overexpression as
AB  - recombinant protein has already been studied. However, very limited
AB  - information concerning its fused product is available thus far. In the
AB  - present study, the EcoRI restriction endonuclease gene was cloned and
AB  - expressed as a part of maltose-binding fusion protein under the control
AB  - of strong inducible tac promoter in TB1 strain of Escherichia coli
AB  - cells. Transformed cells containing pMALc2X-EcoRI recombinant plasmid
AB  - were unable to grow under experimental conditions. However, fused EcoRI
AB  - protein was purified (with the yield of 0.01 mg/l of bacterial culture)
AB  - by affinity chromatography from E. coli cells induced at the late
AB  - exponential phase of growth. Restriction quality test revealed that the
AB  - purified product could restrict a control plasmid DNA in vitro.
ER  -

TY  - JOUR
AU  - Gholizadeh, A.
AU  - Kohnehrouz, B.B.
TI  - Carborundum-dependent entrance of EcoRI restriction enzyme into plant cells and specific cleavage of genomic DNA.
JO  - Indian J. Exp. Biol.
PY  - 2009
SP  - 684
EP  - 689
VL  - 47
AB  - In a basic research to determine the morpho-molecular interactions of plant tissues with EcoRI
AB  - DNA restriction enzyme, it was demonstrated
AB  - that this protein is capable of entering the sunflower and maize leaf
AB  - cells using a plant tissue-abrading material and cleaving the genomic
AB  - DNA at specific sites. This was inferred from the analysis of
AB  - morphological patterns of EcoRI-treated leaf areas as well as using
AB  - some molecular tests, including the cleavage pattern analysis of
AB  - genomic DNA isolated from treated locations followed by ligation of
AB  - cleaved fragments into EcoRI site of a DNA cloning vector system. The
AB  - overall results indicated that the specific restriction of genomic DNA
AB  - may happen following the entrance of EcoRI protein most likely into the
AB  - nucleus of plant cells.
ER  -

TY  - JOUR
AU  - Ghosh, A.
AU  - Chandratre, K.
AU  - Chaudhary, A.
AU  - Chaudhary, S.
AU  - Badani, N.
AU  - Chaudhary, P.S.
AU  - Dhawan, D.
AU  - Vudathala, S.
AU  - Chikara, S.K.
TI  - Whole-Genome Sequencing of Brevundimonas diminuta XGC1, Isolated from a Tuberculosis Patient in Gujarat, India.
JO  - Genome Announcements
PY  - 2015
SP  - e00686
EP  - e00615
VL  - 3
AB  - We report the draft genome of Brevundimonas diminuta strain XGC1, isolated from a
AB  - tuberculosis-infected patient in Gujarat, India. This study also reveals that the
AB  - B. diminuta XGC1 strain has acquired mutation to confer resistance to quinolone
AB  - drugs.
ER  -

TY  - JOUR
AU  - Ghosh, A.
AU  - Chaudhary, S.A.
AU  - Apurva, S.R.
AU  - Tiwari, T.
AU  - Gupta, S.
AU  - Singh, A.K.
AU  - Katudia, K.H.
AU  - Patel, M.P.
AU  - Chikara, S.K.
TI  - Whole-Genome Sequencing of Micrococcus luteus Strain Modasa, of Indian Origin.
JO  - Genome Announcements
PY  - 2013
SP  - e0007613
EP  - e0007613
VL  - 1
AB  - The hydrocarbon-degrading bacterium Micrococcus luteus strain Modasa was isolated from
AB  - contaminated soil from Modasa, North Gujarat, India. Whole-genome sequencing
AB  - and analysis provide an insight into the potentially important genes responsible
AB  - for bioremediation.
ER  -

TY  - JOUR
AU  - Ghosh, A.
AU  - Passaris, I.
AU  - Tesfazgi, M.M.
AU  - Rocha, S.
AU  - Vanoirbeek, K.
AU  - Hofkens, J.
AU  - Aertsen, A.
TI  - Cellular localization and dynamics of the Mrr type IV restriction endonuclease of Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 3908
EP  - 3918
VL  - 42
AB  - In this study, we examined the intracellular whereabouts of Mrr, a cryptic type IV restriction
AB  - endonuclease of Escherichia coli K12, in response to different
AB  - conditions. In absence of stimuli triggering its activity, Mrr was found to be
AB  - strongly associated with the nucleoid as a number of discrete foci, suggesting
AB  - the presence of Mrr hotspots on the chromosome. Previously established elicitors
AB  - of Mrr activity, such as exposure to high (hydrostatic) pressure (HP) or
AB  - expression of the HhaII methyltransferase, both caused nucleoid condensation and
AB  - an unexpected coalescence of Mrr foci. However, although the resulting
AB  - Mrr/nucleoid complex was stable when triggered with HhaII, it tended to be only
AB  - short-lived when elicited with HP. Moreover, HP-mediated activation of Mrr
AB  - typically led to cellular blebbing, suggesting a link between chromosome and
AB  - cellular integrity. Interestingly, Mrr variants could be isolated that were
AB  - specifically compromised in either HhaII- or HP-dependent activation,
AB  - underscoring a mechanistic difference in the way both triggers activate Mrr. In
AB  - general, our results reveal that Mrr can take part in complex spatial
AB  - distributions on the nucleoid and can be engaged in distinct modes of activity.
ER  -

TY  - JOUR
AU  - Ghosh, H.
AU  - Bunk, B.
AU  - Doijad, S.
AU  - Schmiedel, J.
AU  - Falgenhauer, L.
AU  - Sproer, C.
AU  - Imirzalioglu, C.
AU  - Overmann, J.
AU  - Chakraborty, T.
TI  - Complete Genome Sequence of blaCTX-M-27-Encoding Escherichia coli Strain H105 of  Sequence Type 131 Lineage C1/H30R.
JO  - Genome Announcements
PY  - 2017
SP  - e00736
EP  - e00717
VL  - 5
AB  - Escherichia coli sequence type 131 (ST131) is the most frequent antimicrobial-resistant
AB  - lineage of E. coli, propagating extended-spectrum
AB  - beta-lactamases (ESBL) worldwide. Recently, an alarming rate of increase in
AB  - isolates of the sublineage C1/H30R-blaCTX-M-27 of ST131 in geographically distant
AB  - countries was reported. Here, we present the complete genome sequence of the
AB  - ST131 sublineage C1/H30R E. coli isolate harboring blaCTX-M-27 from Germany.
ER  -

TY  - JOUR
AU  - Ghosh, I.
AU  - Sun, L.
AU  - Evans, T.C.
AU  - Xu, M.Q.
TI  - An improved method for utilization of peptide substrates for antibody characterization and enzymatic assays.
JO  - J. Immunol. Methods
PY  - 2004
SP  - 85
EP  - 95
VL  - 293
AB  - Synthetic peptides have become an important tool in antibody production and enzyme
AB  - characterization. The small size of peptides, however, has
AB  - hindered their use in assays systems, such as Western blots, and as
AB  - immunogens. Here, we present a facile method to improve the properties
AB  - of peptides for multiple applications by ligating the peptides to
AB  - intein-generated carrier proteins. The stoichiometric ligation of
AB  - peptide and carrier achieved by intein-mediated protein ligation (IPL)
AB  - results in the ligation product migrating as a single band on a
AB  - SDS-PAGE gel. The carrier proteins, HhaI methylase (M.HhaI) and
AB  - maltose-binding protein (MBP), were ligated to various peptides; the
AB  - ligated carrier-peptide products gave sharp, reproducible bands when
AB  - used as positive controls for antibodies raised against the same
AB  - peptides during Western blot analysis. We further show that ligation of
AB  - the peptide antigens to a different thioester-tagged carrier protein,
AB  - paramyosin, produced immunogens for the production of antisera in
AB  - rabbits or mice. Furthermore, we demonstrate the generation of a
AB  - substrate for enzymatic assays by ligating a peptide containing the
AB  - phosphorylation site for Abl protein tyrosine kinase to a carrier
AB  - protein. This carrier-peptide protein was used as a kinase substrate
AB  - that could easily be tested for phosphorylation using a phosphotyrosine
AB  - antibody in Western blot analysis. These techniques do not require
AB  - sophisticated equipment, reagents, or skills thereby providing a simple
AB  - method for research and development.
ER  -

TY  - JOUR
AU  - Ghosh, S.
AU  - LaPara, T.M.
AU  - Sadowsky, M.J.
TI  - Draft Genome Sequence of Sphingobacterium sp. Strain PM2-P1-29, a Tetracycline-Degrading TetX-Expressing Aerobic Bacterium Isolated from  Agricultural Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e00963
EP  - e00914
VL  - 2
AB  - The genome of Sphingobacterium sp. strain PM2-P1-29 was sequenced. The bacterium  contains a
AB  - physiologically active tet(X) gene, encoding a tetracycline-degrading
AB  - monooxygenase. To our knowledge, this is the only bacterium naturally harboring
AB  - tet(X) for which tetracycline degradation has been demonstrated.
ER  -

TY  - JOUR
AU  - Ghosh, S.S.
AU  - Eis, P.S.
AU  - Blumeyer, K.
AU  - Fearon, K.
AU  - Millar, D.P.
TI  - Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 3155
EP  - 3159
VL  - 22
AB  - The kinetics of PaeR7I endonuclease-catalysed cleavage reactions of fluorophor-labeled
AB  - oligonucleotide substrates have been examined using fluorescence resonance energy transfer
AB  - (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7I
AB  - recognition site and donor (fluorescein) and acceptor (rhodamine) dyes conjugated to the
AB  - opposing 5' termini. The time-dependent increase in donor fluorescence resulting from
AB  - restriction cleavage of these substrates was continuously monitored and the initial rate data
AB  - was fitted to the Michaelis-Menten equation. The steady state kinetic parameters for these
AB  - substrates were in agreement with the rate constants obtained from a gel electrophoresis-based
AB  - fixed time point assay using radiolabeled substrates. The FRET method provides a rapid
AB  - continuous assay as well as high sensitivity and reproducibility. These features should make
AB  - the technique useful for the study of DNA-cleaving enzymes.
ER  -

TY  - JOUR
AU  - Ghosh, S.S.
AU  - Obermiller, P.S.
AU  - Kwoh, T.J.
AU  - Gingeras, T.R.
TI  - Analysis of substrate specificity of the PaeR7I endonuclease: effect of base methylation on the kinetics of cleavage.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 5063
EP  - 5068
VL  - 18
AB  - In murine cells expressing the PaeR7I endonuclease and methylase genes, the
AB  - recognition sites (CTCGAG) of these enzymes can be methylated at the adenine
AB  - residue by the PaeR7I methylase and at the internal cytosine by the mouse DNA
AB  - methyltransferase.  Using nonadecameric duplex deoxyoligonucleotide substrates,
AB  - the specificity of the PaeR7I endonuclease for unmethylated, hemi-methylated,
AB  - and fully methylated N6-methyladenine (m6A) and C5-methylcytosine (m5C)
AB  - versions of these substrates has been studied.  The Km, kcat, and Ki values for
AB  - these model substrates have been measured and suggest that fully or
AB  - hemi-m6A-methylated PaeR7I sites in the murine genome are completely protected.
AB  - However, the reactivity of fully or hemi-m5C-methylated PaeR7I sites is
AB  - depressed 2900- and 100-fold respectively, compared to unmodified PaeR7I sites.
AB  - The implications of the kinetic constants of the PaeR7I endonuclease for these
AB  - methylated recognition sites as they occur in murine cells expressing this
AB  - endonuclease gene are discussed.
ER  -

TY  - JOUR
AU  - Ghosh, W.
AU  - George, A.
AU  - Agarwal, A.
AU  - Raj, P.
AU  - Alam, M.
AU  - Pyne, P.
AU  - Das Gupta, S.K.
TI  - Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5553
EP  - 5554
VL  - 193
AB  - The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the
AB  - family Alcaligenaceae and is phylogenetically closely
AB  - related to pathogens such as Taylorella and Bordetella species. While a
AB  - complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present
AB  - in its genome, pathogenicity islands or genes associated with virulence,
AB  - disease, cellular invasion, and/or intracellular resistance are completely
AB  - absent.
ER  -

TY  - JOUR
AU  - Giacani, L.
AU  - Iverson-Cabral, S.L.
AU  - King, J.C.
AU  - Molini, B.J.
AU  - Lukehart, S.A.
AU  - Centurion-Lara, A.
TI  - Complete Genome Sequence of the Treponema pallidum subsp. pallidum Sea81-4 Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00333
EP  - e00314
VL  - 2
AB  - Using the rabbit model of syphilis, the Sea81-4 strain of Treponema pallidum subsp. pallidum
AB  - has been found to be more likely than other strains to invade the central nervous system
AB  - (CNS). To identify possible explanations for this important phenotype at the genomic level, we
AB  - sequenced the Sea81-4 strain genome.
ER  -

TY  - JOUR
AU  - Giacani, L.
AU  - Jeffrey, B.M.
AU  - Molini, B.J.
AU  - Le, H.T.
AU  - Lukehart, S.A.
AU  - Centurion-Lara, A.
AU  - Rockey, D.D.
TI  - Complete genome sequence and annotation of the Treponema pallidum subsp. pallidum Chicago strain.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2645
EP  - 2646
VL  - 192
AB  - In syphilis research, the Nichols strain of Treponema pallidum, isolated in 1912, has been the
AB  - most widely studied. Recently, important differences
AB  - among T. pallidum strains emerged; therefore, we sequenced and annotated
AB  - the Chicago strain genome to facilitate and encourage the use of this
AB  - strain in studying the pathogenesis of syphilis.
ER  -

TY  - JOUR
AU  - Giacomodonato, M.N.
AU  - Llana, M.N.
AU  - Castaneda, M.R.
AU  - Buzzola, F.
AU  - Garcia, M.D.
AU  - Calderon, M.D.
AU  - Sarnacki, S.H.
AU  - Cerquetti, M.C.
TI  - Dam methylation regulates the expression of SPI-5-encoded sopB gene in Salmonella enterica serovar Typhimurium.
JO  - Microbes Infect.
PY  - 2014
SP  - 615
EP  - 622
VL  - 16
AB  - DNA adenine methylation is an essential factor in Salmonella virulence. Here, we investigate
AB  - the involvement of DNA adenine methylase (Dam) in the expression and translocation of a
AB  - SPI-5-encoded effector of S. Typhimurium. SopB expression and secretion were determined using
AB  - SopB FLAG-tagged wild type and dam strains of S. Typhimurium. Western blot and quantitative
AB  - reverse transcriptase PCR analysis showed that the dam mutant expresses lower levels of SopB
AB  - protein and sopB mRNA than the wild type strain under SPI-1 and SPI-2 inducing conditions in
AB  - vitro. SopB secretion was also considerably impaired in the absence of dam. In agreement with
AB  - in vitro experiments, SopB synthesis in dam mutants recovered from infected epithelial cells
AB  - and from murine mesenteric lymph nodes was reduced by 40% respect to the wild type strain (p <
AB  - 0.05). SopB translocation was neither detected in the cytosol of epithelial cells nor in the
AB  - cytosol of cells isolated from mesenteric lymph nodes infected with the dam mutant. Taken
AB  - together, our results demonstrate that, in S. Typhimurium, Dam methylation modulates the
AB  - expression and translocation of SPI-5-encoded SopB effector.
ER  -

TY  - JOUR
AU  - Giammanco, G.M.
AU  - Grimont, F.
AU  - Grimont, P.A.
TI  - MboII endonuclease heat inactivation before agarose gel electrophoresis to prevent artifactual bands in restriction patterns.
JO  - Biotechniques
PY  - 1999
SP  - 886
EP  - 887
VL  - 27
AB  - MboII restriction enzyme belongs to class-IIS endonucleases group.  Like all of the enzymes
AB  - belonging to this class, MboII cleaves DNA at a specific distance from its recognition
AB  - sequence and still binds to its recognition sequence after DNA has been cleaved, because
AB  - binding and cleaving domains have separate functions.
ER  -

TY  - JOUR
AU  - Giampetruzzi, A.
AU  - Chiumenti, M.
AU  - Saponari, M.
AU  - Donvito, G.
AU  - Italiano, A.
AU  - Loconsole, G.
AU  - Boscia, D.
AU  - Cariddi, C.
AU  - Martelli, G.P.
AU  - Saldarelli, P.
TI  - Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01538
EP  - e01514
VL  - 3
AB  - We determined the draft genome sequence of the Xylella fastidiosa CoDiRO strain,  which has
AB  - been isolated from olive plants in southern Italy (Apulia). It is
AB  - associated with olive quick decline syndrome (OQDS) and characterized by
AB  - extensive scorching and desiccation of leaves and twigs.
ER  -

TY  - JOUR
AU  - Giampetruzzi, A.
AU  - Loconsole, G.
AU  - Boscia, D.
AU  - Calzolari, A.
AU  - Chiumenti, M.
AU  - Martelli, G.P.
AU  - Saldarelli, P.
AU  - Almeida, R.P.
AU  - Saponari, M.
TI  - Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa.
JO  - Genome Announcements
PY  - 2015
SP  - e01472
EP  - e01415
VL  - 3
AB  - The draft genome sequence of Xylella fastidiosa CO33 isolate, retrieved from symptomatic
AB  - leaves of coffee plant intercepted in northern Italy, is reported.
AB  - The CO33 genome size is 2,681,926 bp with a GC content of 51.7%.
ER  -

TY  - JOUR
AU  - Giampetruzzi, A.
AU  - Saponari, M.
AU  - Almeida, R.P.P.
AU  - Essakhi, S.
AU  - Boscia, D.
AU  - Loconsole, G.
AU  - Saldarelli, P.
TI  - Complete Genome Sequence of the Olive-Infecting Strain Xylella fastidiosa subsp.  pauca De Donno.
JO  - Genome Announcements
PY  - 2017
SP  - e00569
EP  - e00517
VL  - 5
AB  - We report here the complete and annotated genome sequence of the plant-pathogenic bacterium
AB  - Xylella fastidiosa subsp. pauca strain De Donno. This strain was
AB  - recovered from an olive tree severely affected by olive quick decline syndrome
AB  - (OQDS), a devastating olive disease associated with X. fastidiosa infections in
AB  - susceptible olive cultivars.
ER  -

TY  - JOUR
AU  - Giannakis, M.
AU  - Chen, S.L.
AU  - Karam, S.M.
AU  - Engstrand, L.
AU  - Gordon, J.I.
TI  - Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 4358
EP  - 4363
VL  - 105
AB  - We have characterized the adaptations of Helicobacter pylori to a rarely
AB  - captured event in the evolution of its impact on host biology-the
AB  - transition from chronic atrophic gastritis (ChAG) to gastric
AB  - adenocarcinoma-and defined the impact of these adaptations on an
AB  - intriguing but poorly characterized interaction between this bacterium and
AB  - gastric epithelial stem cells. Bacterial isolates were obtained from a
AB  - single human host colonized with a single dominant strain before and after
AB  - his progression from ChAG to gastric adenocarcinoma during a 4-year
AB  - interval. Draft genome assemblies were generated from two isolates, one
AB  - ChAG-associated, the other cancer-associated. The cancer-associated strain
AB  - was less fit in a gnotobiotic transgenic mouse model of human ChAG and
AB  - better able to establish itself within a mouse gastric epithelial
AB  - progenitor-derived cell line (mGEP) that supports bacterial attachment.
AB  - GeneChip-based comparisons of the transcriptomes of mGEPs and a control
AB  - mouse gastric epithelial cell line revealed that, upon infection, the
AB  - cancer-associated strain regulates expression of GEP-associated signaling
AB  - and metabolic pathways, and tumor suppressor genes associated with
AB  - development of gastric cancer in humans, in a manner distinct from the
AB  - ChAG-associated isolate. The effects on GEP metabolic pathways, some of
AB  - which were confirmed in gnotobiotic mice, together with observed changes
AB  - in the bacterial transcriptome are predicted to support aspects of an
AB  - endosymbiosis between this microbe and gastric stem cells. These results
AB  - provide insights about how H. pylori may adapt to and influence stem cell
AB  - biology and how its intracellular residency could contribute to gastric
AB  - tumorigenesis.
ER  -

TY  - JOUR
AU  - Giannino, D.
AU  - Mele, G.
AU  - Cozza, R.
AU  - Bruno, L.
AU  - Testone, G.
AU  - Ticconi, C.
AU  - Frugis, G.
AU  - Bitonti, M.B.
AU  - Innocenti, A.M.
AU  - Mariotti, D.
TI  - Isolation and characterization of a maintenance DNA-methyltransferase gene from peach (Prunus persica [L.] Batsch): transcript localization in vegetative and reproductive meristems of triple buds.
JO  - J. Exp. Bot.
PY  - 2003
SP  - 2623
EP  - 2633
VL  - 54
AB  - A cDNA coding for a DNA (cytosine-5)-methyltransferase (METase) was
AB  - isolated from peach (Prunus persica [L.] Batsch) and the corresponding
AB  - gene designated as PpMETI. The latter encoded a predicted polypeptide of
AB  - 1564 amino acid residues and harboured all the functional domains
AB  - conserved in the maintenance METases group type I. PpMETI was a single
AB  - copy in the cultivar Chiripa which was used as a model in the present
AB  - study. Expression analyses revealed that PpMETI transcripts were more
AB  - abundant in tissues with actively proliferating cells such as apical tips,
AB  - uncurled leaves, elongating herbaceous stems, and small immature fruits.
AB  - Peach plants bear bud clusters (triads or triple buds), consisting of two
AB  - lateral and one central bud with floral and vegetative fates,
AB  - respectively. PpMETI in situ hybridization was performed in triple buds
AB  - during their entire developmental cycle. High and low levels of PpMETI
AB  - transcript were related to burst and quiescence of vegetative growth,
AB  - respectively. Message localization distinguished lateral from central buds
AB  - during the meristem switch to the floral phase. In fact, the PpMETI
AB  - message was abundant in the L1 layer of protruding domes, a morphological
AB  - trait marking the beginning of floral transition. The PpMETI transcript
AB  - was also monitored during organ flower formation. Altogether, these data
AB  - suggest a relationship between DNA replication and PpMETI gene expression.
ER  -

TY  - JOUR
AU  - Gias, E.
AU  - Draper, J.
AU  - Brosnahan, C.L.
AU  - Orr, D.
AU  - McFadden, A.
AU  - Jones, B.
TI  - Draft Genome Sequence of a New Zealand Rickettsia-Like Organism Isolated from Farmed Chinook Salmon.
JO  - Genome Announcements
PY  - 2016
SP  - e00503
EP  - e00516
VL  - 4
AB  - We report here the draft genome sequence of a rickettsia-like organism, isolated  from a New
AB  - Zealand Chinook salmon farm experiencing high mortality. The genome is approximately 3 Mb in
AB  - size, has a G+C content of approximately 39.2%, and is predicted to contain 2,870 coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Gibb, E.A.
AU  - Edgell, D.R.
TI  - Better late than early: delayed translation of intron-encoded endonuclease I-TevI is required for efficient splicing of its host group I intron.
JO  - Mol. Microbiol.
PY  - 2010
SP  - 35
EP  - 46
VL  - 78
AB  - The td group I intron interrupting the thymidylate synthase (TS) gene of phage T4 is a mobile
AB  - intron that encodes the homing endonuclease
AB  - I-TevI. Efficient RNA splicing of the intron is required to restore
AB  - function of the TS gene, while expression of I-TevI from within the
AB  - intron is required to initiate intron mobility. Three distinct layers
AB  - of regulation temporally limit I-TevI expression to late in the T4
AB  - infective cycle, yet the biological rationale for stringent regulation
AB  - has not been tested. Here, we deleted key control elements to
AB  - deregulate I-TevI expression at early and middle times post T4
AB  - infection. Strikingly, we found that deregulation of I-TevI, or of a
AB  - catalytically inactive variant, generated a thymidine-dependent
AB  - phenotype that is caused by a reduction in td intron splicing.
AB  - Prematurely terminating I-TevI translation restores td splicing,
AB  - full-length TS synthesis, and rescues the thymidine-dependent
AB  - phenotype. We suggest that stringent translational control of I-TevI
AB  - evolved to prevent the ribosome from disrupting key structural elements
AB  - of the td intron that are required for splicing and TS function at
AB  - early and middle times post T4 infection. Analogous translational
AB  - regulatory mechanisms in unrelated intron-open reading frame
AB  - arrangements may also function to limit deleterious consequences on
AB  - splicing and host gene function.
ER  -

TY  - JOUR
AU  - Gibson, D.G. et al.
TI  - Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.
JO  - Science
PY  - 2008
SP  - 1215
EP  - 1220
VL  - 319
AB  - We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome,
AB  - named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except
AB  - MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for
AB  - selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites
AB  - known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb),
AB  - assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination
AB  - to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb
AB  - ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli.
AB  - Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the
AB  - correct sequence were identified. The complete synthetic genome was assembled by
AB  - transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then
AB  - isolated and sequenced. A clone with the correct sequence was identified. The methods
AB  - described here will be generally useful for constructing large DNA molecules from chemically
AB  - synthesized pieces and also from combinations of natural and synthetic DNA segments.
ER  -

TY  - JOUR
AU  - Gibson, D.G. et al.
TI  - Creation of a bacterial cell controlled by a chemically synthesized genome.
JO  - Science
PY  - 2010
SP  - 52
EP  - 56
VL  - 329
AB  - We report the design, synthesis, and assembly of the 1.08-mega-base pair
AB  - Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome
AB  - sequence information and its transplantation into a M. capricolum
AB  - recipient cell to create new M. mycoides cells that are controlled only by
AB  - the synthetic chromosome. The only DNA in the cells is the designed
AB  - synthetic DNA sequence, including "watermark" sequences and other designed
AB  - gene deletions and polymorphisms, and mutations acquired during the
AB  - building process. The new cells have expected phenotypic properties and
AB  - are capable of continuous self-replication.
ER  -

TY  - JOUR
AU  - Giebel, H.A.
AU  - Klotz, F.
AU  - Voget, S.
AU  - Poehlein, A.
AU  - Grosser, K.
AU  - Teske, A.
AU  - Brinkhoff, T.
TI  - Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 81
EP  - 81
VL  - 11
AB  - The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of
AB  - surface seawater contaminated with weathered oil (slicks) from the
AB  - Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and
AB  - ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we
AB  - present a preliminary set of physiological features of strain O3.65 and a
AB  - description and annotation of its draft genome sequence. Based on our data we
AB  - suggest potential ecological roles of the isolate in the degradation of crude oil
AB  - within the network of the oil-enriched microbial community. The draft genome
AB  - comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain
AB  - O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and
AB  - energy source and is able to grow on several hydroxylated and substituted
AB  - aromatic compounds. Based on 16S rRNA gene comparison the closest described and
AB  - validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is
AB  - lacking several phenotypic and genomic characteristics specific for the genus
AB  - Phaeobacter. Phylogenomic analyses based on the whole genome support extensive
AB  - genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially
AB  - by using the secretion system type IV. Our physiological observations are
AB  - consistent with the genomic and phylogenomic analyses and support that strain
AB  - O3.65 is a novel species of a new genus within the Rhodobacteraceae.
ER  -

TY  - JOUR
AU  - Gil, R.
AU  - Silva, F.J.
AU  - Zientz, E.
AU  - Delmotte, F.
AU  - Gonzalez-Candelas, F.
AU  - Latorre, A.
AU  - Rausell, C.
AU  - Kamerbeek, J.
AU  - Gadau, J.
AU  - Holldobler, B.
AU  - Van Ham, R.C.
AU  - Gross, R.
AU  - Moya, A.
TI  - The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 9388
EP  - 9393
VL  - 100
AB  - Bacterial symbioses are widespread among insects, probably being one of the key factors of
AB  - their evolutionary success. We present the complete
AB  - genome sequence of Blochmannia floridanus, the primary endosymbiont of
AB  - carpenter ants. Although these ants feed on a complex diet, this symbiosis
AB  - very likely has a nutritional basis: Blochmannia is able to supply
AB  - nitrogen and sulfur compounds to the host while it takes advantage of the
AB  - host metabolic machinery. Remarkably, these bacteria lack all known genes
AB  - involved in replication initiation (dnaA, priA, and recA). The
AB  - phylogenetic analysis of a set of conserved protein-coding genes shows
AB  - that Bl. floridanus is phylogenetically related to Buchnera aphidicola and
AB  - Wigglesworthia glossinidia, the other endosymbiotic bacteria whose
AB  - complete genomes have been sequenced so far. Comparative analysis of the
AB  - five known genomes from insect endosymbiotic bacteria reveals they share
AB  - only 313 genes, a number that may be close to the minimum gene set
AB  - necessary to sustain endosymbiotic life.
ER  -

TY  - JOUR
AU  - Gilbert, M.J.
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Blaser, M.J.
AU  - Wagenaar, J.A.
AU  - Duim, B.
TI  - Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 03-427T.
JO  - Genome Announcements
PY  - 2013
SP  - e01002
EP  - e01013
VL  - 1
AB  - Campylobacter fetus subsp. testudinum has been isolated from reptiles and humans. This
AB  - Campylobacter subspecies is genetically distinct from other C. fetus
AB  - subspecies. Here, we present the first whole-genome sequence for this C. fetus
AB  - subspecies.
ER  -

TY  - JOUR
AU  - Gilbert, M.J.
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Kik, M.
AU  - Wagenaar, J.A.
AU  - Duim, B.
TI  - Complete Genome Sequence of Campylobacter iguaniorum Strain 1485ET, Isolated from a Bearded Dragon (Pogona vitticeps).
JO  - Genome Announcements
PY  - 2014
SP  - e00844
EP  - e00814
VL  - 2
AB  - Campylobacter iguaniorum has been isolated from reptiles. This Campylobacter species is
AB  - genetically related to Campylobacter fetus and Campylobacter
AB  - hyointestinalis. Here we present the first whole-genome sequence for this
AB  - species.
ER  -

TY  - JOUR
AU  - Gill, J.J.
AU  - Berry, J.D.
AU  - Russell, W.K.
AU  - Lessor, L.
AU  - Escobar-Garcia, D.A.
AU  - Hernandez, D.
AU  - Kane, A.
AU  - Keene, J.
AU  - Maddox, M.
AU  - Martin, R.
AU  - Mohan, S.
AU  - Thorn, A.M.
AU  - Russell, D.H.
AU  - Young, R.
TI  - The Caulobacter crescentus phage phiCbK: genomics of a canonical phage.
JO  - BMC Genomics
PY  - 2012
SP  - 542
EP  - 542
VL  - 13
AB  - ABSTRACT: BACKGROUND: The bacterium Caulobacter crescentus is a popular model for
AB  - the study of cell cycle regulation and senescence. The large prolate siphophage
AB  - phiCbK has been an important tool in C. crescentus biology, and has been studied
AB  - in its own right as a model for viral morphogenesis. Although a system of some
AB  - interest, to date little genomic information is available on phiCbK or its
AB  - relatives. RESULTS: Five novel phiCbK-like C. crescentus bacteriophages,
AB  - CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the
AB  - environment. The genomes of phage phiCbK and these five environmental phage
AB  - isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range
AB  - in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448
AB  - proteins (CcrColossus), and were found to contain nonpermuted terminal
AB  - redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to
AB  - map genomic termini, which confirmed termini predicted by coverage analysis. This
AB  - suggests that sequence coverage discontinuities may be useable as predictors of
AB  - genomic termini in phage genomes. Genomic modules encoding virion morphogenesis,
AB  - lysis and DNA replication proteins were identified. The phiCbK-like phages were
AB  - also found to encode a number of intriguing proteins; all contain a clearly
AB  - T7-like DNA polymerase, and five of the six encode a possible homolog of the C.
AB  - crescentus cell cycle regulator GcrA, which may allow the phage to alter the host
AB  - cell's replicative state. The structural proteome of phage phiCbK was determined,
AB  - identifying the portal, major and minor capsid proteins, the tail tape measure
AB  - and possible tail fiber proteins. All six phage genomes are clearly related;
AB  - phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the
AB  - DNA level, while CcrColossus is more diverged but retains significant similarity
AB  - at the protein level. CONCLUSIONS: Due to their lack of any apparent relationship
AB  - to other described phages, this group is proposed as the founding cohort of a new
AB  - phage type, the phiCbK-like phages. This work will serve as a foundation for
AB  - future studies on morphogenesis, infection and phage-host interactions in C.
AB  - crescentus.
ER  -

TY  - JOUR
AU  - Gill, S.R. et al.
TI  - Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.
JO  - J. Bacteriol.
PY  - 2005
SP  - 2426
EP  - 2438
VL  - 187
AB  - Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous
AB  - hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a
AB  - causative agent of infections often associated with implanted medical devices. We have
AB  - sequenced the  2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the
AB  - 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative
AB  - analysis of these and other staphylococcal genomes was used to explore the evolution of
AB  - virulence and resistance between these two species. The S. aureus and S. epidermidis genomes
AB  - are syntenic throughout their lengths and share a core set of 1,681 open reading frames.
AB  - Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity
AB  - and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria
AB  - appears to have shaped their virulence and resistance profiles. Integrated plasmids in S.
AB  - epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface
AB  - proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S.
AB  - epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the
AB  - polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic
AB  - differences are likely the result of single nucleotide polymorphisms, which are most numerous
AB  - in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome
AB  - islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not
AB  - found in S. epidermidis.
ER  -

TY  - JOUR
AU  - Gillings, M.R.
AU  - Labbate, M.
AU  - Sajjad, A.
AU  - Giguere, N.J.
AU  - Holley, M.P.
AU  - Stokes, H.W.
TI  - Mobilization of a Tn402-like class 1 integron with a novel cassette array via flanking miniature inverted-repeat transposable element-like structures.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 6002
EP  - 6004
VL  - 75
AB  - A Tn402-like class 1 integron was recovered from a prawn-associated
AB  - bacterium. One of its cassettes included methionine sulfoxide reductase
AB  - genes, the first example of such genes being captured by an integron. The
AB  - integron was flanked by direct repeats that resemble miniature
AB  - inverted-repeat transposable element sequences. Excision of the integron
AB  - by homologous recombination through these sequences was demonstrated.
ER  -

TY  - JOUR
AU  - Gilrane, V.L.
AU  - Lobo, S.
AU  - Huang, W.
AU  - Zhuge, J.
AU  - Yin, C.
AU  - Chen, D.
AU  - Alvarez, K.J.
AU  - Budhai, A.
AU  - Nadelman, I.
AU  - Dimitrova, N.
AU  - Fallon, J.T.
AU  - Wang, G.
TI  - Complete Genome Sequence of a Colistin-Resistant Escherichia coli Strain Harboring mcr-1 on an IncHI2 Plasmid in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e01095
EP  - e01017
VL  - 5
AB  - We report here the incidental detection and complete genome sequence of a urinary Escherichia
AB  - coli strain harboring mcr-1 and resistant to colistin in a New York
AB  - patient returning from Portugal in 2016. This strain, with sequence type 1485
AB  - (ST1485), was a non-extended-spectrum beta-lactamase (ESBL) and non-carbapenemase
AB  - producer and carried the mcr-1 gene on an IncHI2 plasmid.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
TI  - Engineering homing endonucleases to modify complex genomes.
JO  - Gene Ther. Regul.
PY  - 2006
SP  - 33
EP  - 50
VL  - 3
AB  - Gene targeting to selected chromosomal loci is greatly stimulated when free DNA ends are
AB  - created that initiate double-strand break repair.  Gene therapy reagents can be developed by
AB  - engineering DNA endonucleases that cleave genomes at desired target sequences.  Homing
AB  - endonucleases are naturally occurring rare-cutting enzymes that have well understood DNA
AB  - binding and DNA cleavage properties.  Rational design methods as well as directed evolution
AB  - strategies that involve genetic selections and screens using combinatorial libraries generate
AB  - homing endonucleases with altered sequence specificities.  Molecular switches are being
AB  - introduced into these enzymes to regulate their activity.  This article reviews the progress
AB  - that has been made in constructing homing endonucleases for gene therapy and genome
AB  - engineering, and discusses the challenges that remain.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
TI  - Engineering homing endonucleases for genomic applications.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 177
EP  - 192
VL  - 16
AB  - The rapid progress in molecular biology that has occurred over the last three decades is due
AB  - in large part to the availability of sequence-specific nucleases.  These enzymes have been
AB  - indispensable tools in recombinant DNA protocols.  Most notably, the type II bacterial
AB  - restriction enzymes have permitted the rapid and low-cost production of recombinant DNAs for
AB  - cloning and other methods.  One drawback of these enzymes, however, is the small size of their
AB  - recognition sequences, which range in length from 4-8 base pairs.  An enzyme that recognizes a
AB  - 6-bp target sequence cleaves DNA on average approximately once every 4000 bp.  When these
AB  - enzymes digest DNA from a mammalian genome, which is typically >100 megabases in length, many
AB  - thousands of DNA fragments are generated, and purification of individual species from this
AB  - pool is difficult.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
TI  - Invasion of a multitude of genetic niches by mobile endonuclease genes.
JO  - FEMS Microbiol. Lett.
PY  - 2000
SP  - 99
EP  - 107
VL  - 185
AB  - Persistence of a mobile DNA element in a population reflects a balance between the ability of
AB  - the host to eliminate the element and the ability of the element to survive and to disseminate
AB  - to other individuals. In each of the three biological kingdoms, several families of a mobile
AB  - DNA element have been identified which encode a single protein that acts on nucleic acids.
AB  - Collectively termed homing endonuclease genes (HEGs), these elements employ varied strategies
AB  - to ensure their survival. Some members of the HEG families have a minimal impact on host
AB  - fitness because they associate with genes having self-splicing introns or inteins that remove
AB  - the HEGs at the RNA or protein level. The HEG and the intron/intein gene spread throughout the
AB  - population by a gene conversion process initiated by the HEG-encoded endonuclease called
AB  - 'homing' in which the HEG and intron/intein genes are copied to cognate alleles that lack
AB  - them. The endonuclease activity also contributes to a high frequency of lateral transmission
AB  - of HEGs between species as has been documented in plants and other systems. Other HEGs have
AB  - positive selection value because the proteins have evolved activities that benefit their host
AB  - organisms. The success of HEGs in colonizing diverse genetic niches results from the
AB  - flexibility of the encoded endonucleases in adopting new specificities.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
TI  - Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 4215
EP  - 4223
VL  - 29
AB  - Mobile introns and inteins self-propagate by 'homing', a gene conversion process initiated
AB  - by site-specific homing endonucleases. The VMA intein, which encodes the PI-SceI endonuclease
AB  - in Saccharomyces cerevisiae, is present in several different yeast strains. Surprisingly, a
AB  - wild wine yeast (DH1-1A) contains not only the intein(+) allele, but also an inteinless allele
AB  - that has not undergone gene conversion. To elucidate how these two alleles co-exist, we
AB  - characterized the endonuclease encoded by the DH1-1A intein(+) allele and the target site in
AB  - the intein(-) allele. Sequence analysis reveals seven mutations in the 31 bp recognition
AB  - sequence, none of which occurs at positions that are individually critical for activity.
AB  - However, binding and cleavage of the sequence by PI-SceI is reduced 10-fold compared to the S.
AB  - cerevisiae target. The PI-SceI analog encoded by the DH1-1A intein(+) allele contains 11
AB  - mutations at residues in the endonuclease and protein splicing domains. None affects protein
AB  - splicing, but one, a R417Q substitution, accounts for most of the decrease in DNA cleavage and
AB  - DNA binding activity of the DH1-1A protein. Loss of activity in the DH1-1A endonuclease and
AB  - target site provides one explanation for co-existence of the intein(+) and intein(-) alleles.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
TI  - Broken symmetry in homing endonucleases.
JO  - Structure
PY  - 2006
SP  - 804
EP  - 806
VL  - 14
AB  - Homing DNA endonucleases are highly site-specific enzymes that initiate the transfer of mobile
AB  - DNA elements. In this issue of Structure, Spiegel et al. report the structure of the I-CeuI
AB  - homing enzyme and describe how a symmetric homodimeric enzyme acquired specificity for an
AB  - asymmetric substrate.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
AU  - Duan, X.
AU  - Hu, D.
AU  - Quiocho, F.A.
TI  - Identification of lys-403 in the PI-SceI homing endonuclease as part of a symmetric catalytic center.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 30524
EP  - 30529
VL  - 273
AB  - Superposition of the PI-SceI and I-CreI homing endonuclease three-dimensional x-ray structures
AB  - indicates general similarity between the I-CreI homodimer and the PI-SceI endonuclease domain.
AB  - Saddle-shaped structures are present in each protein that are proposed to bind DNA. At the
AB  - putative endonucleolytic active sites, the superposition reveals that two lysine (Lys-301 and
AB  - Lys-403 in PI-SceI and Lys-98 and Lys-98' in I-CreI) and two aspartic acid residues (Asp-218
AB  - and Asp-326 in PI-SceI and Asp-20 and Asp-20' in I-CreI) are related by 2-fold symmetry. The
AB  - critical role of Lys-301, Asp-218, and Asp-326 in the PI-SceI reaction pathway was reported
AB  - previously. Here, we demonstrate the significance of the active-site symmetry by showing that
AB  - alanine substitution at Lys-403 reduces cleavage activity by greater than 50-fold but has
AB  - little effect on the DNA binding activity of the mutant enzyme. Substitution of Lys-403 with
AB  - arginine, which maintains the positive charge, has only a modest effect on activity.
AB  - Interestingly, even though the Lys-301 and Lys-403 residues display pseudosymmetry, PI-SceI
AB  - mutant proteins with substitutions at these positions have different behaviors. The presence
AB  - of similar basic and acidic residues in many LAGLIDADG homing endonucleases suggests that
AB  - these enzymes use a common reaction mechanism to cleave double-stranded DNA.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
AU  - Moure, C.M.
AU  - Posey, K.L.
TI  - Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 993
EP  - 1008
VL  - 334
AB  - The PI-SceI protein from Saccharomyces cerevisiae is a member of the LAGLIDADG family of
AB  - homing endonucleases that have been used in genomic
AB  - engineering. To assess the flexibility of the PI-SceI-binding interaction
AB  - and to make progress towards the directed evolution of homing
AB  - endonucleases that cleave specified DNA targets, we applied a two-hybrid
AB  - method to select PI-SceI variants from a randomized expression library
AB  - that bind to different DNA substrates. In particular, the codon for Arg94,
AB  - which is located in the protein splicing domain and makes essential
AB  - contacts to two adjacent base-pairs, and the codons for four proximal
AB  - residues were randomized. There is little conservation of the wild-type
AB  - amino acid residues at the five randomized positions in the variants that
AB  - were selected to bind to the wild-type site, yet one of the purified
AB  - derivatives displays DNA-binding specificity and DNA endonuclease activity
AB  - that is similar to that of the wild-type enzyme. A spectrum of DNA-binding
AB  - behaviors ranging from partial relaxation of specificity to marked shifts
AB  - in target site recognition are present in variants selected to bind to
AB  - sites containing mutations at the two base-pairs. Our results illustrate
AB  - the inherent plasticity of the PI-SceI/DNA interface and demonstrate that
AB  - selection based on DNA binding is an effective means of altering the DNA
AB  - cleavage specificity of homing endonucleases. Furthermore, it is apparent
AB  - that homing endonuclease target specificity derives, in part, from
AB  - constraints on the flexibility of DNA contacts imposed by hydrogen bonds
AB  - to proximal residues.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
AU  - Stephens, B.W.
TI  - Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI-SceI endonuclease.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 5849
EP  - 5856
VL  - 270
AB  - The PI-SceI endonuclease from yeast belongs to a protein family whose members contain two
AB  - conserved dodecapeptide motifs within their primary sequences. The function of two acidic
AB  - residues within these motifs, Asp218 and Asp326, was examined by substituting alanine,
AB  - asparagine, and glutamic acid residues at these positions. All of the purified mutant proteins
AB  - bind to the PI-SceI recogniton site with the same affinity and specificity as the wild-type
AB  - enzyme. By contrast, substituting alanine or asparagine amino acids at the two positions
AB  - completely eliminates strand cleavage of substrate DNA, whereas substitution with glutamic
AB  - acid markedly reduces the cleavage activity. Experiments using nicked substrates demonstrate
AB  - that the wild-type enzyme shows no strand preference during cleavage. These results are
AB  - consistent with a model in which both acidic residues are part of a single catalytic center
AB  - that cleaves both DNA strands. Furthermore, substrate binding by wild-type PI-SceI stimulates
AB  - hydroxyl radical or hydroxide ion attack at the cleavage site while binding by the
AB  - alanine-substituted proteins either stimulates this attack significantly less or protects the
AB  - DNA at this position. These findings are discussed in terms of possible reaction mechanisms
AB  - for PI-SceI-mediated endonucleolytic cleavage.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
AU  - Thorner, J.
TI  - Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae.
JO  - Nature
PY  - 1992
SP  - 301
EP  - 306
VL  - 357
AB  - An unusual protein splicing reaction joins the N-terminal segment (A) and the C-terminal
AB  - segment (C) of the 119K primary translation product (ABC) of the yeast VMA1 gene to yield a
AB  - 69K vacuolar H+-ATPase subunit (AC) and an internal 50K polypeptide (B). This 50K protein is a
AB  - site-specific DNA endonuclease that shares 34% indentity with the homothallic switching
AB  - endonuclease. The site cleaved by the VMA1-derived endonuclease exists in a VMA1 allele that
AB  - lacks the derived endonuclease segment of the open reading frame. Cleavage at this site only
AB  - occurs during meiosis and initiates 'homing', a gentic event that converts a VMA1 allele
AB  - lacking the endonuclease coding sequence into one that contains it.
ER  -

TY  - JOUR
AU  - Gimble, F.S.
AU  - Thorner, J.
TI  - Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 21844
EP  - 21853
VL  - 268
AB  - The 119-kDa primary translation product of the VMA1 gene of Saccharomyces cerevisiae undergoes
AB  - a self-catalyzed rearrangement (protein splicing) that excises an internal 50-kDa segment of
AB  - the polypeptide and joins the amino-terminal and carboxyl-terminal segments to generate the
AB  - 69-kDa subunit of the vacuolar membrane-associated H+-ATPase. We have shown previously that
AB  - the internal segment is a site-specific endonuclease (Gimble, F.S., and Thorner, J. (1992)
AB  - Nature 357, 301-306). Here we describe methods for the high level expression and purification
AB  - to near homogeneity of both the authentic VMA1-derived endonuclease (or VDE) from yeast (yield
AB  - 18%) and a recombinant form of VDE made in bacteria (yield 29%). Detailed characterization of
AB  - these preparations demonstrated that the yeast-derived and bacterially produced enzymes were
AB  - indistinguishable, as judged by: (a) behavior during purification; (b) apparent native
AB  - molecular mass (50 kDa); (c) immunological reactivity; and (d) catalytic properties (specific
AB  - activity; cleavage site recognition; and optima for pH, temperature, divalent cation and ionic
AB  - strength). The minimal site required for VDE cleavage was delimited to a 30-base pair sequence
AB  - within its specific substrate ( the VMA1 delvde allele).
ER  -

TY  - JOUR
AU  - Gimble, F.S.
AU  - Wang, J.
TI  - Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 163
EP  - 180
VL  - 263
AB  - PI-SceI, a double-stranded DNA endonuclease from Saccharomyces cerevisiae, is generated by
AB  - protein splicing of an intein, which is an internal polypeptide within a larger precursor
AB  - protein.  The enzyme initiates the mobility of the intein by cleaving at inteinless alleles of
AB  - the VMA1 gene.  Genetic and biochemical studies reveal that the enzyme makes numerous
AB  - base-specific and phosphate backbone contacts with its 31 bp asymmetrical recognition site.
AB  - This site can be divided into two regions, both of which contain nucleotides that are
AB  - essential for cleavage by PI-SceI.  Region I contains the PI-SceI cleavage site while Region
AB  - II includes an adjacent sequence that covers two helical turns.  Mutational, interference and
AB  - DNA mobility shift analyses demonstrate that Region II is sufficient for high-affinity PI-SceI
AB  - binding.  Within this region, PI-SceI uses primarily phosphate backbone and some major groove
AB  - interactions to contact the DNA, while within Region I , protein binding involves
AB  - predominantly major groove interactions that overlap and lie proximal to the cleavage site.
AB  - Interestingly, DNA binding by PI-SceI induces DNA conformational changes within Region II that
AB  - are entirely exclusive of Region I sequences.  Furthermore, additional distortion occurs when
AB  - PI-SceI binds to Region I in conjunction with Region II.  The importance of this latter
AB  - distortion in the cleavage pathway is underscored by substrate mutations at or near the
AB  - cleavage site that reduce or eliminate both Region I DNA bending and substrate cleavage.
AB  - Based on these findings, we propose a model in which sequence-specific contacts made by
AB  - PI-SceI contribute to its localization to the cleavage site and to its stabilization of a DNA
AB  - conformation that is required for catalysis.  Finally, we discuss how the recognition
AB  - characteristics of PI-SceI may have allowed the evolution of other endonucleases with altered,
AB  - but similar, specificities.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
TI  - Restriction-modification systems: Genetic sentries and useful systems in the study of molecular genetics.
JO  - Modern Microbial Genetics
PY  - 1991
SP  - 301
EP  - 321
VL  - 0
AB  - This chapter describes two important roles which restriction-modification
AB  - systems have in molecular genetics.  The first of these roles concerns the
AB  - operation of these systems as genetic sentries.  The second role involves the
AB  - part which restriction-modification systems are playing in the study of several
AB  - important topics in molecular genetics.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
TI  - Restriction endonucleases and their recognition sequences.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 397
EP  - 398
VL  - 8
AB  - None
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Blumenthal, R.M.
AU  - Roberts, R.J.
AU  - Brooks, J.E.
TI  - The isolation and characterization of the E. coli dam methylase gene.
JO  - Metabolism and Enzymology of Nucleic Acids
PY  - 1982
SP  - 329
EP  - 340
VL  - 4
AB  - The E. coli dam (DNA adenine methylase) codes for an enzyme which methylates the DNA sequence
AB  - GATC. When DNA has been modified by dam it is no longer susceptible to endonucleolytic
AB  - cleavage by the restriction endonuclease MboI. Several DNA methylases have been shown to be
AB  - part of a restriction-modification system (Roberts, 1981). However, the dam methylase does not
AB  - seem to be part of such a system. Rather, the dam methylase has been implicated as part of a
AB  - post-replicational mismatch repair system in E. coli. In heteroduplex lambda DNA containing
AB  - only one methylated strand, the repair system will correct the unmethylated strand to match
AB  - the methylated strand. (Wagner and Meselson, 1976, Meselson et al., 1980). Fully methylated
AB  - mismatched heteroduplexes are not corrected. In addition, it has been demonstrated that when
AB  - the dam methylase is not produced (dam-) or is over-produced (damS), such E. coli strains are
AB  - hypermutable. (Herman and Modrich, 1980). An additional function for the dam methylase in E.
AB  - coli may involve its role in DNA replication. It has been shown that the sequence methylated
AB  - by the dam methylase, GATC, occurs at a very high frequency (i.e., 11 times within 245 base
AB  - pairs) at the E. coli origin of replication (J. Zyskind, personal communication). Furthermore,
AB  - such sites have been shown to occur near or at the ends of Okazaki fragments (Gomez-Eichelmann
AB  - and Lark, 1977). Because of the possible important roles that the dam methylasae plays in the
AB  - biology of E. coli, as well as sharing an identical recognition sequence with a set of type II
AB  - restriction and modification enzymes (MboI), we have isolated and characterized clones
AB  - containing the dam methylase gene.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Brooks, J.E.
TI  - Cloned restriction/modification system from Pseudomonas aeruginosa.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1983
SP  - 402
EP  - 406
VL  - 80
AB  - DNA fragments from Pseudomonas aeruginosa carrying the PaeR7 restriction/modification genes
AB  - have been cloned in the plasmid vector pBR322 and propagated in Escherichia coli. A subclone
AB  - (pPAORM3.8) has been constructed that contains the complete restriction/modification system on
AB  - a 3.8-kilobase DNA fragment. Digestion of the pPAORM3.8 plasmid with nuclease BAL-31 has
AB  - yielded two types of clones. One type contains an active methylase gene but no active
AB  - endonuclease gene; such clones will modify the DNA but not restrict the growth of incoming
AB  - phage in vivo. The second type contains an active endonuclease gene but no active methylase
AB  - gene, as judged both by in vivo tests and by the activity of the cell extracts in vitro.
AB  - Although extracts of cells containing these plasmids display restriction endonuclease
AB  - activity, these bacteria are unable to restrict the growth of incoming phage. Furthermore,
AB  - chromosomal and phage DNA isolated from these host cells are not protected against cleavage by
AB  - PaeR7 in vitro. The properties of PaeR7 endonuclease and methylase enzymes have also been
AB  - examined. The PaeR7 restriction endonuclease recognizes and cleaves the sequence C^T-C-G-A-G,
AB  - as does XhoI. However, there exists a canonical XhoI site at 26.5% on the adenovirus 2
AB  - genome which is totally refractory to PaeR7 cleavage but is cut by XhoI. Under conditions of
AB  - low salt, high glycerol, and high enzyme concentrations, a "PaeR7*" activity is found that is
AB  - similar to that observed for EcoRI. Finally, evidence is presented that the PaeR7 methylase
AB  - modifies the adenine residue within the recognition sequence. the restriction enzyme, the
AB  - third describes the purification procedure for the methylase and the fourth describes the
AB  - recognition sequence of the methylase. In some cases, several references appear in one of
AB  - these categories when independent groups have reached similar conclusions.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Ghosh, S.
AU  - Blumeyer, K.
AU  - Eis, R.
AU  - Millar, D.
TI  - A spectrofluorometric method for measurement of restriction endonuclease activity based on fluorescence polarization.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 173
EP  - 173
VL  - 17C
AB  - A method is described for monitoring the enzymatic activity of type II restriction
AB  - endonucleases using fluorophore-labeled oligonucleotide substrates. Cleavage of the duplex
AB  - oligonucleotide substrates, in which one strand is covalently labeled with fluorescein,
AB  - results in a time-dependent change of fluorescence polarization due to the formation of short,
AB  - labeled fragments which are single-stranded at the temperature of the assay. This non-isotopic
AB  - homogeneous approach is extremely sensitive and is much simpler than the current radiolabeled
AB  - procedures which require fixed timepoint assays and the use of filter binding or gel
AB  - electrophoresis for kinetic analysis of the cleavage reaction. The PaeR7I endonuclease has
AB  - been used as an example for the applicability of the method. The kinetic parameters for the
AB  - hydrolysis of a fluorescein-modified oligonucleotide substrate of the enzyme have been
AB  - determined by using this approach to follow reaction rates.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Greenough, L.
AU  - Schildkraut, I.
AU  - Roberts, R.J.
TI  - Two new restriction endonucleases from Proteus vulgaris.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 4525
EP  - 4536
VL  - 9
AB  - Two novel sequence-specific endonucleases have been isolated from Proteus
AB  - vulgaris, ATCC 13315.  PvuI recognizes the sequence: 5' CGAT^CG 3' 3' GC^TAGC
AB  - 5' and PvuII recognizes the sequence: 5' CAG^CTG 3' 3' GTC^GAC 5' and cleave as
AB  - indicated by the arrow.  PvuI is an isoschizomer of XorII, RshI, and XniI.  No
AB  - enzyme with the specificity of PvuII has been described previously.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Milazzo, J.P.
AU  - Roberts, R.J.
TI  - A computer assisted method for the determination of restriction enzyme recognition sites.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 4105
EP  - 4127
VL  - 5
AB  - A computer program has been developed which aids in the determination of
AB  - restriction enzyme recognition sequences.  This is achieved by cleaving DNAs of
AB  - known sequence with a restriction endonuclease and comparing the fragmentation
AB  - pattern with a computer-generated set of patterns.  The feasibility of this
AB  - approach has been tested using fragmentation patterns of PhiX174 DNA produced
AB  - by enzymes of both known and unknown specificity.  Recognition sequences are
AB  - predicted for two restriction endonucleases (BbvI and SfaNI) using this method.
AB  - In addition, recognition sequnces are predicted for two other new enzymes
AB  - (PvuI and MstI) using another computer-assisted method.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Myers, P.A.
AU  - Olson, J.A.
AU  - Hanberg, F.A.
AU  - Roberts, R.J.
TI  - A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 113
EP  - 122
VL  - 118
AB  - A new specific endonuclease, XhoI, has been partially purified from Xanthomonas
AB  - holcicola.  This enzyme cleaves adenovirus-2 DNA at five sites, bacteriophage
AB  - DNA at one site, PhiX174 DNA at one site, but does not cleave simian virus DNA.
AB  - It recognizes the sequence 5'-C-^T-C-G-A-G-3' 3'-G-A-G-C-T^-C-5' and cuts at
AB  - the sites indicated by the arrows.  Enzymes with identical specificity have
AB  - also been found in Xanthomonas papavericola and Brevibacterium luteum.
ER  -

TY  - JOUR
AU  - Gingeras, T.R.
AU  - Theriault, G.
AU  - Brooks, J.E.
TI  - Organization and expression of a type II restriction-modification system from Pseudomonas aeruginosa.
JO  - Metabolism and Enzymology of Nucleic Acids
PY  - 1984
SP  - 267
EP  - 275
VL  - 5
AB  - A series of BAL-31 deletion mutants have been generated affecting both the structural and
AB  - regulatory regions of the PaeR7 restriction-modification system. This system is organized as
AB  - an operon with both the genes sharing a common regulatory region. Deletions in this regulatory
AB  - region lead to a gradient of expression levels for both enzymes. Most striking is the
AB  - observation that depressed levels of expression of endonuclease, as exemplified by both
AB  - pPAOR1.9 and pPAOdel1.3, result in clones that do not restrict infecting phage.
AB  - Cotransformation of pPAOR1.9 and pPACYCM2.7 into the same host did not result in recovery of a
AB  - restriction phenotype. Consequently, phage restriction seems to be critically dependent on the
AB  - levels of endonuclease produced, and not on the effect of an active methylase gene. DNA
AB  - sequences of the control region of this system indicate two PaeR7 sites which are located in a
AB  - critical position in the PaeR7 operon to determine if the levels of methylase are sufficient
AB  - to protect both the plasmid and the DNA of the host cell. The effect of methylation on these
AB  - sites during transcription is being studied as another possible means of controlling
AB  - expression in this system.
ER  -

TY  - JOUR
AU  - Ginn, A.
AU  - Ma, Z.
AU  - Galvao, K.N.
AU  - Jeong, K.C.
TI  - Draft Genome Sequence of an Escherichia coli O8:H19 Sequence Type 708 Strain Isolated from a Holstein Dairy Cow with Metritis.
JO  - Genome Announcements
PY  - 2016
SP  - e00261
EP  - e00216
VL  - 4
AB  - We present here the genome sequence ofEscherichia coliO8:H19 strain KCJ852, belonging to
AB  - multilocus sequence type (MLST) 708, isolated from the uterus of a
AB  - cow with a bovine postpartum uterine infection known as metritis. Genomic
AB  - investigation of KCJ852 will help us understand its virulence potential.
ER  -

TY  - JOUR
AU  - Gioia, J. et al.
TI  - Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032.
JO  - PLoS ONE
PY  - 2007
SP  - e928
EP  - e928
VL  - 2
AB  - BACKGROUND: Bacillus spores are notoriously resistant to unfavorable conditions such as UV
AB  - radiation, gamma-radiation, H(2)O(2), desiccation,
AB  - chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives
AB  - standard decontamination procedures of the Jet Propulsion Lab spacecraft
AB  - assembly facility, and both spores and vegetative cells of this strain
AB  - exhibit elevated resistance to UV radiation and H(2)O(2) compared to other
AB  - Bacillus species. PRINCIPAL FINDINGS: The genome of B. pumilus SAFR-032
AB  - was sequenced and annotated. Lists of genes relevant to DNA repair and the
AB  - oxidative stress response were generated and compared to B. subtilis and
AB  - B. licheniformis. Differences in conservation of genes, gene order, and
AB  - protein sequences are highlighted because they potentially explain the
AB  - extreme resistance phenotype of B. pumilus. The B. pumilus genome includes
AB  - genes not found in B. subtilis or B. licheniformis and conserved genes
AB  - with sequence divergence, but paradoxically lacks several genes that
AB  - function in UV or H(2)O(2) resistance in other Bacillus species.
AB  - SIGNIFICANCE: This study identifies several candidate genes for further
AB  - research into UV and H(2)O(2) resistance. These findings will help explain
AB  - the resistance of B. pumilus and are applicable to understanding
AB  - sterilization survival strategies of microbes.
ER  -

TY  - JOUR
AU  - Gioia, J.
AU  - Qin, X.
AU  - Jiang, H.
AU  - Clinkenbeard, K.
AU  - Lo, R.
AU  - Liu, Y.
AU  - Fox, G.E.
AU  - Yerrapragada, S.
AU  - McLeod, M.P.
AU  - McNeill, T.Z.
AU  - Hemphill, L.
AU  - Sodergren, E.
AU  - Wang, Q.
AU  - Muzny, D.M.
AU  - Homsi, F.J.
AU  - Weinstock, G.M.
AU  - Highlander, S.K.
TI  - The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny.
JO  - J. Bacteriol.
PY  - 2006
SP  - 7257
EP  - 7266
VL  - 188
AB  - The draft genome sequence of Mannheimia haemolytica A1, the causative agent of bovine
AB  - respiratory disease complex (BRDC), is presented. Strain
AB  - ATCC BAA-410, isolated from the lung of a calf with BRDC, was the DNA
AB  - source. The annotated genome includes 2,839 coding sequences, 1,966 of
AB  - which were assigned a function and 436 of which are unique to M.
AB  - haemolytica. Through genome annotation many features of interest were
AB  - identified, including bacteriophages and genes related to virulence,
AB  - natural competence, and transcriptional regulation. In addition to
AB  - previously described virulence factors, M. haemolytica encodes adhesins,
AB  - including the filamentous hemagglutinin FhaB and two trimeric
AB  - autotransporter adhesins. Two dual-function
AB  - immunoglobulin-protease/adhesins are also present, as is a third
AB  - immunoglobulin protease. Genes related to iron acquisition and drug
AB  - resistance were identified and are likely important for survival in the
AB  - host and virulence. Analysis of the genome indicates that M. haemolytica
AB  - is naturally competent, as genes for natural competence and DNA uptake
AB  - signal sequences (USS) are present. Comparison of competence loci and USS
AB  - in other species in the family Pasteurellaceae indicates that M.
AB  - haemolytica, Actinobacillus pleuropneumoniae, and Haemophilus ducreyi form
AB  - a lineage distinct from other Pasteurellaceae. This observation was
AB  - supported by a phylogenetic analysis using sequences of predicted
AB  - housekeeping genes.
ER  -

TY  - JOUR
AU  - Giongo, A.
AU  - Tyler, H.L.
AU  - Zipperer, U.N.
AU  - Triplett, E.W.
TI  - Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission.
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 309
EP  - 317
VL  - 2
AB  - Gluconacetobacter diazotrophicus PAl 5 is of agricultural significance due to its ability to
AB  - provide fixed nitrogen to plants. Consequently, its genome sequence
AB  - has been eagerly anticipated to enhance understanding of endophytic nitrogen
AB  - fixation. Two groups have sequenced the PAl 5 genome from the same source (ATCC
AB  - 49037), though the resulting sequences contain a surprisingly high number of
AB  - differences. Therefore, an optical map of PAl 5 was constructed in order to
AB  - determine which genome assembly more closely resembles the chromosomal DNA by
AB  - aligning each sequence against a physical map of the genome. While one sequence
AB  - aligned very well, over 98% of the second sequence contained numerous
AB  - rearrangements. The many differences observed between these two genome sequences
AB  - could be owing to either assembly errors or rapid evolutionary divergence. The
AB  - extent of the differences derived from sequence assembly errors could be assessed
AB  - if the raw sequencing reads were provided by both genome centers at the time of
AB  - genome sequence submission. Hence, a new genome sequence standard is proposed
AB  - whereby the investigator supplies the raw reads along with the closed sequence so
AB  - that the community can make more accurate judgments on whether differences
AB  - observed in a single stain may be of biological origin or are simply caused by
AB  - differences in genome assembly procedures.
ER  -

TY  - JOUR
AU  - Giordani, F.
AU  - Fillo, S.
AU  - Anselmo, A.
AU  - Palozzi, A.M.
AU  - Fortunato, A.
AU  - Gentile, B.
AU  - Pittiglio, V.
AU  - Spagnolo, F.
AU  - Anniballi, F.
AU  - Fiore, A.
AU  - Auricchio, B.
AU  - De Medici, D.
AU  - Lista, F.
TI  - Whole-Genome Sequence of Clostridium botulinum A2B3 87, a Highly Virulent Strain  Involved in a Fatal Case of Foodborne Botulism in Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00237
EP  - e00215
VL  - 3
AB  - Here, we report the genome sequence of a rare bivalent strain of Clostridium botulinum, A2B3
AB  - 87. The strain was isolated from a foodborne botulism case that
AB  - occurred in Italy in 1995. The case was characterized by rapid evolution of the
AB  - illness and failure of conventional treatments.
ER  -

TY  - JOUR
AU  - Giordano, M.
AU  - Mattachini, M.E.
AU  - Cella, R.
AU  - Pedrali-Noy, G.
TI  - Purification and properties of a novel DNA methyltransferase from cultured rice cells.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1991
SP  - 711
EP  - 719
VL  - 177
AB  - DNA methyltransferase activity has been observed in a total crude homogenate of rice cells
AB  - grown in suspension culture using either native plant DNA or, under the conditions used, the
AB  - more responsive hemimethylated poly (dI-MedC).poly(dI-dC).  Using the latter substrate we have
AB  - purified an enzyme fraction 380-fold by salt extraction of chromatin, DEAE cellulose and
AB  - phosphocellulose.  This purified fraction showed enzyme activity only with poly
AB  - (dI-MedC).poly(dI-dC) thus suggesting the occurrence in plants of a DNA methyltransferase
AB  - specific for hemimethylated DNA.  A Mr value of 54,000 was calculated on the basis of the
AB  - sedimentation coefficient which was determined by sucrose density gradient centrifugation.
AB  - Apparent Km values for poly(dI-MedC).poly(dI-dC) and S-adenosyl-L-methionine were found to be
AB  - 17 ug/ml and 2.6 uM, respectively.
ER  -

TY  - JOUR
AU  - Giorello, F.M.
AU  - Romero, V.
AU  - Farias, J.
AU  - Scavone, P.
AU  - Umpierrez, A.
AU  - Zunino, P.
AU  - Sotelo, S.J.R.
TI  - Draft Genome Sequence and Gene Annotation of the Uropathogenic Bacterium Proteus  mirabilis Pr2921.
JO  - Genome Announcements
PY  - 2016
SP  - e00564
EP  - e00516
VL  - 4
AB  - Here, we report the genome sequence of Proteus mirabilis Pr2921, a uropathogenic  bacterium
AB  - that can cause severe complicated urinary tract infections. After gene
AB  - annotation, we identified two additional copies of ucaA, one of the most studied
AB  - fimbrial protein genes, and other fimbriae related-proteins that are not present
AB  - in P. mirabilis HI4320.
ER  -

TY  - JOUR
AU  - Giovannelli, D. et al.
TI  - Complete genome sequence of Thermovibrio ammonificans HB-1(T), a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 82
EP  - 90
VL  - 7
AB  - type strain HB-1 is a thermophilic (T: 75 degrees C), strictly anaerobic,
AB  - chemolithoautotrophic bacterium that was isolated from an active, high
AB  - temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism
AB  - grows on mineral salts medium in the presence of CO/H, using NO or S as electron
AB  - acceptors, which are reduced to ammonium or hydrogen sulfide, respectively. is
AB  - one of only three species within the genus , a member of the family , and it
AB  - forms a deep branch within the phylum . Here we report the main features of the
AB  - genome of strain HB-1 (DSM 15698).
ER  -

TY  - JOUR
AU  - Giovannelli, D.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Kravitz, S.
AU  - Perez-Rodriguez, I.
AU  - Ricci, J.
AU  - O'Brien, C.
AU  - Voordeckers, J.W.
AU  - Bini, E.
AU  - Vetriani, C.
TI  - Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 135
EP  - 143
VL  - 5
AB  - Caminibacter mediatlanticus strain TB-2(T) [1], is a thermophilic, anaerobic,
AB  - chemolithoautotrophic bacterium, isolated from the walls of an active deep-sea
AB  - hydrothermal vent chimney on the Mid-Atlantic Ridge and the type strain of the
AB  - species. C. mediatlanticus is a Gram-negative member of the Epsilonproteobacteria
AB  - (order Nautiliales) that grows chemolithoautotrophically with H(2) as the energy
AB  - source and CO(2) as the carbon source. Nitrate or sulfur is used as the terminal
AB  - electron acceptor, with resulting production of ammonium and hydrogen sulfide,
AB  - respectively. In view of the widespread distribution, importance and
AB  - physiological characteristics of thermophilic Epsilonproteobacteria in deep-sea
AB  - geothermal environments, it is likely that these organisms provide a relevant
AB  - contribution to both primary productivity and the biogeochemical cycling of
AB  - carbon, nitrogen and sulfur at hydrothermal vents. Here we report the main
AB  - features of the genome of C. mediatlanticus strain TB-2(T).
ER  -

TY  - JOUR
AU  - Giovannoni, S.J.
AU  - Tripp, H.J.
AU  - Givan, S.
AU  - Podar, M.
AU  - Vergin, K.L.
AU  - Baptista, D.
AU  - Bibbs, L.
AU  - Eads, J.
AU  - Richardson, T.H.
AU  - Noordewier, M.
AU  - Rappe, M.S.
AU  - Short, J.M.
AU  - Carrington, J.C.
AU  - Mathur, E.J.
TI  - Genome streamlining in a cosmopolitan oceanic bacterium.
JO  - Science
PY  - 2005
SP  - 1242
EP  - 1245
VL  - 309
AB  - The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are
AB  - found throughout the oceans, where they
AB  - account for about 25% of all microbial cells. Pelagibacter ubique, the
AB  - first cultured member of this clade, has the smallest genome and encodes
AB  - the smallest number of predicted open reading frames known for a
AB  - free-living microorganism. In contrast to parasitic bacteria and archaea
AB  - with small genomes, P. ubique has complete biosynthetic pathways for all
AB  - 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes,
AB  - introns, transposons, extrachromosomal elements, or inteins; few paralogs;
AB  - and the shortest intergenic spacers yet observed for any cell.
ER  -

TY  - JOUR
AU  - Giraud, C.
AU  - Hausmann, S.
AU  - Lemeille, S.
AU  - Prados, J.
AU  - Redder, P.
AU  - Linder, P.
TI  - The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus.
JO  - RNA Biol.
PY  - 2015
SP  - 658
EP  - 674
VL  - 12
AB  - Staphylococcus aureus is a versatile opportunistic pathogen that adapts readily to a variety
AB  - of different growth conditions. This adaptation requires a rapid regulation of gene expression
AB  - including the control of mRNA abundance. The CshA DEAD-box RNA helicase was previously shown
AB  - to be required for efficient turnover of the agr quorum sensing mRNA. Here we show by
AB  - transcriptome-wide RNA sequencing and microarray analyses that CshA is required for the
AB  - degradation of bulk mRNA.
AB  - Moreover a subset of mRNAs is significantly stabilised in absence of CshA.
AB  - Deletion of the C-terminal extension affects RNA turnover similar to the full deletion of the
AB  - cshA gene. In accordance with RNA decay data, the C-terminal region of CshA is required for an
AB  - RNA-independent interaction with components of the RNA degradation machinery. The C-terminal
AB  - truncation of CshA reduces its ATPase activity and this reduction cannot be compensated at
AB  - high RNA concentrations. Finally, the deletion of the C-terminal extension does affect growth
AB  - at low temperatures, but to a significantly lesser degree than the full deletion, indicating
AB  - that the core of the helicase can assume a partial function and opening the possibility that
AB  - CshA is involved in different cellular processes.
ER  -

TY  - JOUR
AU  - Girault, G.
AU  - Parisot, N.
AU  - Peyretaillade, E.
AU  - Peyret, P.
AU  - Derzelle, S.
TI  - Draft Genomes of Three Strains Representative of the Bacillus anthracis Diversity Found in France.
JO  - Genome Announcements
PY  - 2014
SP  - e00736
EP  - e00714
VL  - 2
AB  - We report here the draft genomes of three Bacillus anthracis strains isolated in  France:
AB  - 08-8_20 (A.Br.001/002), 99-100 (A.Br.011/009), and 00-82 (B.Br CNEVA).
AB  - The total lengths of assemblies are 5,440,708 bp, 5,446,472 bp, and 5,436,014 bp
AB  - for 08-8_20, 99-100, and 00-82, respectively.
ER  -

TY  - JOUR
AU  - Girault, G.
AU  - Woudstra, C.
AU  - Martin, B.
AU  - Vorimore, F.
AU  - Lucia-de-Assis-Santana, V.
AU  - Fach, P.
AU  - Madani, N.
AU  - Laroucau, K.
TI  - First Draft Genome for a Burkholderia mallei Isolate Originating from a Glanderous Mule from Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00579
EP  - e00517
VL  - 5
AB  - Burkholderia mallei is the etiological agent of glanders. Here, we present the draft genome
AB  - sequence of Burkholderia mallei strain 16-2438_BM#8 that was
AB  - isolated from a mule found dead in Pernambuco, northeast Brazil. It is the first
AB  - available genomic sequence from a strain isolated on the American continent.
ER  -

TY  - JOUR
AU  - Girlich, D.
AU  - Poirel, L.
AU  - Nordmann, P.
TI  - A diversity of clavulanic acid-inhibited extended-spectrum {beta}-lactamases in Aeromonas sp. from the Seine River, Paris, France.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 1256
EP  - 1261
VL  - 55
AB  - Environmental Aeromonas sp. isolates resistant to ceftazidime were
AB  - recovered during an environmental survey performed with water samples from
AB  - the Seine River, in Paris, France, in November 2009. Selected isolates
AB  - were identified by sequencing of the 16S rRNA and rpoB genes. PCR and
AB  - cloning experiments were used to identify
AB  - broad-spectrum-beta-lactamase-encoding genes and their genetic context.
AB  - Clavulanic acid-inhibited extended-spectrum-beta-lactamase (ESBL) genes
AB  - were identified in 71% of the Aeromonas sp. isolates. A variety of ESBL
AB  - genes were detected, including bla(VEB-1a), bla(SHV-12), bla(PER-1),
AB  - bla(PER-6), bla(TLA-2), and bla(GES-7), suggesting an aquatic reservoir of
AB  - those ESBL genes. Moreover, the repeated elements and different insertion
AB  - sequences were identified in association with the bla(PER-6) and the
AB  - bla(VEB-1a) genes, respectively, indicating a wide diversity of
AB  - mobilization events, making Aeromonas spp. a vehicle for ESBL
AB  - dissemination.
ER  -

TY  - JOUR
AU  - Girlich, D.
AU  - Poirel, L.
AU  - Szczepanowski, R.
AU  - Schluter, A.
AU  - Nordmann, P.
TI  - Carbapenem-Hydrolyzing GES-5-Encoding Gene on Different Plasmid Types Recovered from a Bacterial Community in a Sewage Treatment Plant.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 1292
EP  - 1295
VL  - 78
AB  - Plasmids pRSB113 and pRSB115 were recovered from an activated sludge bacterial
AB  - community of a municipal wastewater treatment plant in Germany. Both plasmids
AB  - carry the same bla(GES-5) carbapenemase gene, located within two distinct class 1
AB  - integrons. These plasmids have different backbones, belong to different
AB  - incompatibility groups, and could replicate in both Pseudomonas aeruginosa and
AB  - Escherichia coli.
ER  -

TY  - JOUR
AU  - Gitschier, J.
TI  - A Half-Century of Inspiration: An Interview with Hamilton Smith.
JO  - PLoS Genet.
PY  - 2012
SP  - e1002466
EP  - e1002466
VL  - 8
AB  - In 1962, Hamilton Smith abandoned a career in medicine to follow his passion for the emerging
AB  - field of molecular biology; within six years, he had made the discovery of a lifetime.  As a
AB  - new Johns Hopkins faculty member, Smith, together with his first graduate student, Kent
AB  - Wilcox, geared up to study recombination in vitro but instead discoverd the restriction enzyme
AB  - "R" in Haemophilus influenzae.  By cobbling together crude techniques, Smith, along with
AB  - Wilcox and later Tom Kelly, showed the R cleaves DNA at a specific recognition sequence, a
AB  - palindromic site, yielding blunt-ended DNA fragments.  Now known as HindII, R proved to be the
AB  - first of an enormous class of Type II restriction enzymes, and as such, presaged gene cloning,
AB  - allowed DNA to be reproducibly fragmented and then sequenced, and enabled physical mapping of
AB  - genomes.  Smith went on to discover DNA methylases that constitute the other half of the
AB  - bacterial host restriction and modification systems, as hypothesized by Werner Arber of
AB  - Switzerland.  Together with Arber and his Hopkins colleague Daniel Nathans, who first used the
AB  - enzyme on SV40 DNA and demonstrated discrete bands on a tube gel, Smith shared the Nobel Prize
AB  - for Physiology or Medicine in 1978.
ER  -

TY  - JOUR
AU  - Giufre, M.
AU  - Accogli, M.
AU  - Graziani, C.
AU  - Busani, L.
AU  - Cerquetti, M.
TI  - Whole-Genome Sequences of Multidrug-Resistant Escherichia coli Strains Sharing the Same Sequence Type (ST410) and Isolated from Human and Avian Sources in  Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00757
EP  - e00715
VL  - 3
AB  - Extraintestinal pathogenic Escherichia coli (ExPEC) is involved in a wide spectrum of human
AB  - diseases. Chickens have been suggested as reservoirs for
AB  - fluoroquinolone (FQ)-resistant ExPEC strains. Here, we report the whole-genome
AB  - sequences of 4 E. coli strains sharing the same sequence type (ST) (ST410) and
AB  - that were isolated from human and avian sources in Italy.
ER  -

TY  - JOUR
AU  - Giufre, M.
AU  - Cardines, R.
AU  - Cerquetti, M.
TI  - First Whole-Genome Sequence of a Haemophilus influenzae Type e Strain Isolated from a Patient with Invasive Disease in Italy.
JO  - Genome Announcements
PY  - 2017
SP  - e00059
EP  - e00017
VL  - 5
AB  - In the present era of conjugate vaccines against Haemophilus influenzae type b,
AB  - non-vaccine-preventable strains are of concern. Here, we report the first
AB  - whole-genome sequence of an invasive H. influenzae type e strain. This genomic
AB  - information will enable further investigations on encapsulated non-type b H.
AB  - influenzae strains.
ER  -

TY  - JOUR
AU  - Giufre, M.
AU  - De Chiara, M.
AU  - Censini, S.
AU  - Guidotti, S.
AU  - Torricelli, G.
AU  - De Angelis, G.
AU  - Cardines, R.
AU  - Pizza, M.
AU  - Muzzi, A.
AU  - Cerquetti, M.
AU  - Soriani, M.
TI  - Whole-Genome Sequences of Nonencapsulated Haemophilus influenzae Strains Isolated in Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00110
EP  - e00115
VL  - 3
AB  - Haemophilus influenzae is an important human pathogen involved in invasive disease. Here, we
AB  - report the whole-genome sequences of 11 nonencapsulated H.
AB  - influenzae (ncHi) strains isolated from both invasive disease and healthy
AB  - carriers in Italy. This genomic information will enrich our understanding of the
AB  - molecular basis of ncHi pathogenesis.
ER  -

TY  - JOUR
AU  - Givan, S.A.
AU  - Zhou, M.Y.
AU  - Bromert, K.
AU  - Bivens, N.
AU  - Chapman, L.F.
TI  - Genome Sequences of Pseudoalteromonas Strains ATCC BAA-314, ATCC 70018, and ATCC  70019.
JO  - Genome Announcements
PY  - 2015
SP  - e00390
EP  - e00315
VL  - 3
AB  - The assembly and annotation of the draft genome sequences for Pseudoalteromonas strains ATCC
AB  - BAA314, ATCC 700518, and ATCC 700519 reveal candidates for promoting
AB  - symbiosis between Pseudoalteromonas strains and eukaryotes. Groups of genes
AB  - generally associated with virulence are present in all three strains, suggesting
AB  - that these bacteria may be pathogenic under specific circumstances.
ER  -

TY  - JOUR
AU  - Gizard, Y.
AU  - Zbinden, A.
AU  - Schrenzel, J.
AU  - Francois, P.
TI  - Whole-Genome Sequences of Streptococcus tigurinus Type Strain AZ_3a and S. tigurinus 1366, a Strain Causing Prosthetic Joint Infection.
JO  - Genome Announcements
PY  - 2013
SP  - e00210
EP  - e00212
VL  - 1
AB  - Streptococcus tigurinus, a novel member of the Streptococcus mitis group, was recently
AB  - identified as a causative agent of invasive infections. We report the
AB  - complete genome sequences of the S. tigurinus type strain AZ_3a and S. tigurinus
AB  - strain 1366. The genome sequences assist in the characterization of virulence
AB  - determinants of S. tigurinus.
ER  -

TY  - JOUR
AU  - Gkorezis, P.
AU  - Bottos, E.M.
AU  - Van Hamme, J.D.
AU  - Franzetti, A.
AU  - Abbamondi, G.R.
AU  - Balseiro-Romero, M.
AU  - Weyens, N.
AU  - Rineau, F.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00909
EP  - e00915
VL  - 3
AB  - The 3.94-Mb draft genome of Acinetobacter calcoaceticus GK1, a hydrocarbonoclastic plant
AB  - growth-promoting Gram-negative rhizospheric bacterium,
AB  - is presented here. Isolated at the Ford Motor Company site in Genk, Belgium, from
AB  - poplar trees planted on a diesel-contaminated plume, GK1 is useful for enhancing
AB  - hydrocarbon phytoremediation.
ER  -

TY  - JOUR
AU  - Gkorezis, P.
AU  - Bottos, E.M.
AU  - Van Hamme, J.D.
AU  - Thijs, S.
AU  - Rineau, F.
AU  - Franzetti, A.
AU  - Balseiro-Romero, M.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01517
EP  - e01515
VL  - 3
AB  - We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic
AB  - Gram-positive bacterium belonging to the Actinobacteria,
AB  - isolated from diesel-contaminated soil at the Ford Motor Company site in Genk,
AB  - Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel
AB  - remediation applications based on plant-bacterium associations.
ER  -

TY  - JOUR
AU  - Gkorezis, P.
AU  - Rineau, F.
AU  - Van Hamme, J.
AU  - Franzetti, A.
AU  - Daghio, M.
AU  - Thijs, S.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Acinetobacter oleivorans PF1, a Diesel-Degrading and Plant-Growth-Promoting Endophytic Strain Isolated from Poplar Trees Growing on a   Diesel-Contaminated Plume.
JO  - Genome Announcements
PY  - 2015
SP  - e01430
EP  - e01414
VL  - 3
AB  - We report the 3.7-Mb draft genome of Acinetobacter oleivorans strain PF1, a
AB  - hydrocarbonoclastic Gram-negative bacterium in the class Gammaproteobacteria,
AB  - isolated from poplar trees growing on a diesel-contaminated plume at the Ford
AB  - Motor Company site in Genk, Belgium. Strain PF1 is a potent plant-growth
AB  - promoter, useful for diesel fuel phytoremediation applications.
ER  -

TY  - JOUR
AU  - Gkorezis, P.
AU  - Van Hamme, J.
AU  - Bottos, E.
AU  - Thijs, S.
AU  - Balseiro-Romero, M.
AU  - Monterroso, C.
AU  - Kidd, P.S.
AU  - Rineau, F.
AU  - Weyens, N.
AU  - Sillen, W.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00608
EP  - e00616
VL  - 4
AB  - We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic
AB  - Gram-positive bacterium of the family Bacillaceae, isolated
AB  - from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium.
AB  - Strain GB2 is an effective plant-growth promoter useful for diesel fuel
AB  - remediation applications based on plant-bacterium associations.
ER  -

TY  - JOUR
AU  - Gkorezis, P.
AU  - Van Hamme, J.D.
AU  - Bottos, E.M.
AU  - Thijs, S.
AU  - Balseiro-Romero, M.
AU  - Monterroso, C.
AU  - Kidd, P.S.
AU  - Rineau, F.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation  Site Planted with Populus.
JO  - Genome Announcements
PY  - 2016
SP  - e00028
EP  - e00016
VL  - 4
AB  - We report the 4.76-Mb draft genome of Pantoea ananatis GB1, a Gram-negative bacterium of the
AB  - family Enterobacteriaceae, isolated from the roots of poplars
AB  - planted for phytoremediation of a diesel-contaminated plume at the Ford Motor
AB  - Company site in Genk, Belgium. Strain GB1 promotes plant growth in various hosts
AB  - and metabolizes hydrocarbons.
ER  -

TY  - JOUR
AU  - Gladitz, J.
AU  - Shen, K.
AU  - Antalis, P.
AU  - Hu, F.Z.
AU  - Post, J.C.
AU  - Ehrlich, G.D.
TI  - Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 3644
EP  - 3658
VL  - 33
AB  - A similarity statistic for codon usage was developed and used to compare novel gene sequences
AB  - found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic,
AB  - eukaryotic and viral genomes. These analyses were performed to obtain an indication as to
AB  - whether individual genes were Haemophilus-like in nature, or if they probably had more
AB  - recently entered the H.influenzae gene pool via horizontal gene transfer from other species.
AB  - The average and SD values were calculated for the similarity statistics from a study of the
AB  - set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino
AB  - acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most
AB  - like other Rd genes. Genes displaying codon usage statistics >1 SD above this range were
AB  - either considered part of the highly expressed group of H.influenzae genes, or were considered
AB  - of foreign origin. An alternative determinant for identifying genes of foreign origin was when
AB  - the similarity statistics produced a value that was much closer to a non-H.influenzae
AB  - reference organism than to any of the Haemophilus species contained in the reference set.
AB  - Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates
AB  - displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced
AB  - similarity statistics closer to one of the other reference genomes thereby suggesting that
AB  - these sequences may have entered the H.influenzae gene pool more re
ER  -

TY  - JOUR
AU  - Gladney, L.M.
AU  - Katz, L.S.
AU  - Knipe, K.M.
AU  - Rowe, L.A.
AU  - Conley, A.B.
AU  - Rishishwar, L.
AU  - Marino-Ramirez, L.
AU  - Jordan, I.K.
AU  - Tarr, C.L.
TI  - Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.
JO  - Genome Announcements
PY  - 2014
SP  - e01188
EP  - e01114
VL  - 2
AB  - Vibrio navarrensis is an aquatic bacterium recently shown to be associated with human illness.
AB  - We report the first genome sequences of three V. navarrensis
AB  - strains obtained from clinical and environmental sources. Preliminary analyses of
AB  - the sequences reveal that V. navarrensis contains genes commonly associated with
AB  - virulence in other human pathogens.
ER  -

TY  - JOUR
AU  - Glady-Croue, J.
AU  - Niu, X.-Z.
AU  - Ramsay, J.P.
AU  - Watkin, E.
AU  - Murphy, R.J.T.
AU  - Croue, J.-P.
TI  - Survival of antibiotic resistant bacteria following artificial solar radiation of secondary wastewater effluent.
JO  - Sci. Total Environ.
PY  - 2018
SP  - 1005
EP  - 1011
VL  - 626
AB  - Urban wastewater treatment plant effluents represent one of the major emission sources of
AB  - antibiotic-resistant
AB  - bacteria(ARB)in natural aquatic environments.  In this study,the effect of artificial solar
AB  - radiation on total culturable heterotrophic bacteria and ARB(including
AB  - amoxicillin-resistant,ciprofloxacin-resistant,rifampicin-
AB  - resistant,sulfamethoxazole-resistant,and tetracycline-resistant bacteria)present in secondary
AB  - effluent was investigated.  Artificial solar radiation was effective in inactivating the
AB  - majority of environmental bacteria, however,
AB  - the proportion of strains with ciprofloxacin-resistance and rifampicin-resistance increased in
AB  - the surviving populations. Isolates of Pseudomonas putida, Serratia marcescens, and
AB  - Stenotrophomonas maltophilia nosocomial path-
AB  - ogens were identified as resistant to solar radiation and to atleast three antibiotics. Draft
AB  - genome sequencing and typing revealed isolates carrying multiple resistance genes; where S.
AB  - maltophilia (resistant to all studied antibiotics)sequence type was similar to strains
AB  - isolated in blood infections. Results from this study confirm that
AB  - solar radiation reduces total bacterial load in secondary effluent, but may indirectly
AB  - increase the relative abundance of ARB.
ER  -

TY  - JOUR
AU  - Gladysheva, I.V.
AU  - Cherkasov, S.V.
AU  - Khlopko, Y.A.
AU  - Plotnikov, A.O.
AU  - Gogoleva, N.E.
TI  - Draft Genome Sequence of Corynebacterium amycolatum Strain ICIS 53 Isolated from  a Female Urogenital Tract.
JO  - Genome Announcements
PY  - 2016
SP  - e01267
EP  - e01216
VL  - 4
AB  - This report describes the draft genome sequence of Corynebacterium amycolatum strain ICIS 53,
AB  - isolated from the reproductive tract of a healthy woman. The size
AB  - of the genome was 2,460,257 bp (58.98% G+C content). Annotation revealed 2,173
AB  - coding sequences, including 2,076 proteins, 7 rRNA genes, and 53 tRNA genes.
ER  -

TY  - JOUR
AU  - Gladysheva, I.V.
AU  - Khlopko, Y.A.
AU  - Cherkasov, S.V.
TI  - Draft Genome Sequence of the Vaginal Isolate Corynebacterium amycolatum ICIS 9.
JO  - Genome Announcements
PY  - 2017
SP  - e00975
EP  - e00917
VL  - 5
AB  - Corynebacterium amycolatum ICIS 9 was isolated from a vaginal smear of a healthy  woman. Here,
AB  - we report the draft genome sequence of C. amycolatum ICIS 9, which
AB  - will be useful for further studies of specific genetic features of this strain
AB  - and for understanding its probiotic properties.
ER  -

TY  - JOUR
AU  - Glaser, P. et al.
TI  - Comparative genomics of Listeria species.
JO  - Science
PY  - 2001
SP  - 849
EP  - 852
VL  - 294
AB  - Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also
AB  - emerged as a paradigm for intracellular parasitism. We present and compare the genome
AB  - sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua
AB  - (3,011,209 base pairs). We found a large number of predicted genes encoding surface and
AB  - secreted proteins, transporters, and transcriptional regulators, consistent with the ability
AB  - of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149
AB  - L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that
AB  - virulence in Listeria results from multiple gene acquisition and deletion events.
ER  -

TY  - JOUR
AU  - Glaser, P.
AU  - Rusniok, C.
AU  - Buchrieser, C.
AU  - Chevalier, F.
AU  - Frangeul, L.
AU  - Msadek, T.
AU  - Zouine, M.
AU  - Couve, E.
AU  - Lalioui, L.
AU  - Poyart, C.
AU  - Trieu-Cuot, P.
AU  - Kunst, F.
TI  - Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease.
JO  - Mol. Microbiol.
PY  - 2002
SP  - 1499
EP  - 1513
VL  - 45
AB  - Streptococcus agalactiae is a commensal bacterium colonizing the intestinal tract of a
AB  - significant proportion of the human population.
AB  - However, it is also a pathogen which is the leading cause of invasive
AB  - infections in neonates and causes septicaemia, meningitis and pneumonia.
AB  - We sequenced the genome of the serogroup III strain NEM316, responsible
AB  - for a fatal case of septicaemia. The genome is 2,211,485 base pairs long
AB  - and contains 2118 protein coding genes. Fifty-five per cent of the
AB  - predicted genes have an ortholog in the Streptococcus pyogenes genome,
AB  - representing a conserved backbone between these two streptococci. Among
AB  - the genes in S. agalactiae that lack an ortholog in S. pyogenes, 50% are
AB  - clustered within 14 islands. These islands contain known and putative
AB  - virulence genes, mostly encoding surface proteins as well as a number of
AB  - genes related to mobile elements. Some of these islands could therefore be
AB  - considered as pathogenicity islands. Compared with other pathogenic
AB  - streptococci, S. agalactiae shows the unique feature that pathogenicity
AB  - islands may have an important role in virulence acquisition and in genetic
AB  - diversity.
ER  -

TY  - JOUR
AU  - Glasner, J.D. et al.
TI  - Genome Sequence of the Plant-Pathogenic Bacterium Dickeya dadantii 3937.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2076
EP  - 2077
VL  - 193
AB  - Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of
AB  - many plants of economic importance. We present here
AB  - the sequence of strain 3937, a strain widely used as a model system for
AB  - research on the molecular biology and pathogenicity of this group of
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Glasner, J.D.
AU  - Marquez-Villavicencio, M.
AU  - Kim, H.S.
AU  - Jahn, C.E.
AU  - Ma, B.
AU  - Biehl, B.S.
AU  - Rissman, A.I.
AU  - Mole, B.
AU  - Yi, X.
AU  - Yang, C.H.
AU  - Dangl, J.L.
AU  - Grant, S.R.
AU  - Perna, N.T.
AU  - Charkowski, A.O.
TI  - Niche-specificity and the variable fraction of the Pectobacterium pan-genome.
JO  - Mol. Plant Microbe Interact.
PY  - 2008
SP  - 1549
EP  - 1560
VL  - 21
AB  - We compare genome sequences of three closely related soft-rot pathogens that vary
AB  - in host range and geographical distribution to identify genetic differences that
AB  - could account for lifestyle differences. The isolates compared, Pectobacterium
AB  - atrosepticum SCRI1043, P. carotovorum WPP14, and P. brasiliensis 1692, represent
AB  - diverse lineages of the genus. P. carotovorum and P. brasiliensis genome contigs,
AB  - generated by 454 pyrosequencing ordered by reference to the previously published
AB  - complete circular chromosome of P. atrosepticum genome and each other, account
AB  - for 96% of the predicted genome size. Orthologous proteins encoded by P.
AB  - carotovorum and P. brasiliensis are approximately 95% identical to each other and
AB  - 92% identical to P. atrosepticum. Multiple alignment using Mauve identified a
AB  - core genome of 3.9 Mb conserved among these Pectobacterium spp. Each core genome
AB  - is interrupted at many points by species-specific insertions or deletions
AB  - (indels) that account for approximately 0.9 to 1.1 Mb. We demonstrate that the
AB  - presence of a hrpK-like type III secretion system-dependent effector protein in
AB  - P. carotovorum and P. brasiliensis and its absence from P. atrosepticum is
AB  - insufficient to explain variability in their response to infection in a plant.
AB  - Additional genes that vary among these species include those encoding peptide
AB  - toxin production, enzyme production, secretion proteins, and antibiotic
AB  - production, as well as differences in more general aspects of gene regulation and
AB  - metabolism that may be relevant to pathogenicity.
ER  -

TY  - JOUR
AU  - Glasner, W.
AU  - Hennecke, F.
AU  - Fritz, H.J.
TI  - Enzymatic properties and biological functions of VSR DNA mismatch endonuclease.
JO  - Structural tools for the analysis of protein-nucleic acid complexes advances in life sciences.
PY  - 1992
SP  - 165
EP  - 173
VL  - 0
AB  - The protein encoded by the vsr gene of E. coli K-12 was produced by construction and
AB  - expression of a chimeric gene. The corresponding fusion protein contains b-lactamase as the
AB  - N-terminal and the Vsr gene product as the C-terminal component. Enzymological studies of the
AB  - fusion protein reveal the Vsr gene product as the first known example of a DNA mismatch
AB  - endonuclease. Its substrate recognition properties are characterized by a combination of
AB  - sequence and structure specificity as follows. Vsr endonuclease recognizes T/G mismatches in
AB  - sequence contexts related to the cognate sequence of Dcm DNA cytosine methyltransferase and
AB  - cleaves the phosphodiester bond on the 5' side of the mismatched T residue, forming a
AB  - phosphorylated 5' end (Hennecke et al. 1991, Nature 353: 775-778). Studies concerning the
AB  - influence of individual functional groups of the mismatched bases on substrate recognition and
AB  - the detailed requirements of DNA sequence context are reported. The enzymology of Vsr
AB  - endonuclease is summarized and its biological role is discussed.
ER  -

TY  - JOUR
AU  - Glasner, W.
AU  - Merkl, R.
AU  - Schellenberger, V.
AU  - Fritz, H.J.
TI  - Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 1
EP  - 7
VL  - 245
AB  - The substrate spectrum of Vsr DNA mismatch endonuclease of Escherichia coli K-12 was
AB  - investigated using fluorescence-labelled oligonucleotide substrates and a DNA sequencer for
AB  - detection and quantification of substrates and reaction products. Fourteen substrates were
AB  - found to be processed by the enzyme, which differ in one or two positions from the canonical
AB  - pentanucleotide sequence CTA/TGG (T mismatched to G). Relative second-order rate constants of
AB  - these substrates were determined in groups of four by multiple substrate kinetics and compared
AB  - to the underrepresentation of the corresponding pentanucleotides in the E. coli K-12 genome.
AB  - The high quality of correlation further establishes active mutagenesis by VSP repair as a
AB  - significant driving force of the evolution of the E. coli K-12 genome and provides clues to
AB  - its possible selective value.
ER  -

TY  - JOUR
AU  - Glass, J.I.
AU  - Lefkowitz, E.J.
AU  - Glass, J.S.
AU  - Heiner, C.R.
AU  - Chen, E.Y.
AU  - Cassell, G.H.
TI  - The complete sequence of the mucosal pathogen Ureaplasma urealyticum.
JO  - Nature
PY  - 2000
SP  - 757
EP  - 762
VL  - 407
AB  - The comparison of the genomes of two very closely related human mucosal pathogens, Mycoplasma
AB  - genitalium and Mycoplasma pneumoniae, has helped define the essential functions of a
AB  - self-replicating minimal cell, as well as what constitutes a mycoplasma.  Here we report the
AB  - complete sequence of a more distant phylogenetic relative of those bacteria, Ureaplasma
AB  - urealyticum (parvum biovar), which is also a mucosal pathogen of humans.  It is the third
AB  - mycoplasma to be sequenced, and has the smallest sequenced prokaryotic genome except for M.
AB  - genitalium.  Although the U. urealyticum genome is similar to the two sequenced mycoplasma
AB  - genomes, features make this organism unique among mycoplasmas and all bacteria.  Almost all
AB  - ATP synthesis is the result of urea hydrolysis, which generates an energy-producing
AB  - electrochemical gradient.  Some highly conserved eubacterial enzymes appear not to be encoded
AB  - by U. urealyticum, including the cell-division protein FtsZ, chaperonins GroES and GroEL, and
AB  - ribonucleoside-diphosphate reductase.  U. urealyticum has six closely related iron
AB  - transporters, which apparently arose through gene duplication, suggesting that it has a kind
AB  - of respiration system not present in other small genome bacteria.  The genome is only 25.5%
AB  - G+C in nucleotide content, and the G+C content of individual genes may predict how essential
AB  - those genes are to ureaplasma survival.
ER  -

TY  - JOUR
AU  - Glatman, L.I.
AU  - Iablokova, M.B.
AU  - Kravets, A.I.
AU  - Terekhov, A.A.
AU  - Samoilenko, I.I.
TI  - Identification of the plasmid pLG13 coding for the DNA modification-restriction system EcoRV and properties of strains carrying this plasmid.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1985
SP  - 39
EP  - 42
VL  - 10
ER  -

TY  - JOUR
AU  - Glatman, L.I.
AU  - Kravets, A.N.
TI  - Systems of DNA restriction-modification.
JO  - Antibiot. Khimioter
PY  - 1989
SP  - 932
EP  - 938
VL  - 34
AB  - None
ER  -

TY  - JOUR
AU  - Glatman, L.I.
AU  - Moroz, A.F.
AU  - Iablokova, M.B.
AU  - Rebentish, B.A.
AU  - Kholmina, G.V.
TI  - New DNA modification-restriction plasmid system detected in a clinical strain of Escherichia coli.
JO  - Dokl. Akad. Nauk.
PY  - 1980
SP  - 993
EP  - 995
VL  - 252
ER  -

TY  - JOUR
AU  - Glatman, L.I.
AU  - Moroz, A.F.
AU  - Yablokova, M.B.
AU  - Rebentish, B.A.
AU  - Kcholmina, G.V.
TI  - A novel plasmid-mediated DNA restriction-modification system in E. coli.
JO  - Plasmid
PY  - 1980
SP  - 350
EP  - 351
VL  - 4
AB  - R plasmids from 101 clinical isolates were transferred to E. coli J62 by conjugation and
AB  - tested for the presence of R plasmid-mediated restriction-modification DNA systems.  Thirty R
AB  - plasmids were found to inhibit phage lambda vir development.  Ten plasmids determined
AB  - restriction-modification system; nine of them proved identical with R.M. EcoRII.  One
AB  - transconjugant, E. coli J62 pLG74, was shown to have a restriction-modification system
AB  - different from all the known R plasmid-mediated systems.  Site-specific endonuclease has been
AB  - isolated from E. coli J62 pLG74 which differed from all the known restriction endonucleases in
AB  - the number of cleavage sites on phages lambda, phiX 174, virus SV40, plasmid pBR322 DNA
AB  - molecules.
ER  -

TY  - JOUR
AU  - Glatman, L.I.
AU  - Terekhov, A.A.
AU  - Kalnin, K.V.
AU  - Bolotin, A.P.
AU  - Rebentish, B.A.
TI  - New site-specific endodesoxyribonuclease EcoHI.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1990
SP  - 32
EP  - 32
VL  - 3
AB  - A new Type II site-specific endonuclease, EcoHI, has been isolated from a strain of
AB  - Escherichia coli and characterized.  Restriction endonuclease EcoHI recognizes the nucleotide
AB  - sequence C C (C/G) G'G with the cleavage site between the fourth and fifth nucleotides.  It
AB  - is an isoschizomer of the restriction endonuclease CauII.  The yield of enzyme is 2500 units
AB  - of activity per 1 g of biomass.  The producing strain Escherichia coli HI is nonpathogenic,
AB  - easily grown with the antiobiotic resistance markers allowing the strain to be cultivated
AB  - under selective conditions.
ER  -

TY  - JOUR
AU  - Glaub, A.
AU  - Bomholt, C.
AU  - Gravermann, K.
AU  - Brinkrolf, K.
AU  - Albersmeier, A.
AU  - Ruckert, C.
AU  - Tauch, A.
TI  - Complete Genome Sequence of Corynebacterium falsenii DSM 44353 To Study the Evolution of Corynebacterium Cluster 3 Species.
JO  - Genome Announcements
PY  - 2014
SP  - e00158
EP  - e00114
VL  - 2
AB  - Corynebacterium falsenii is a member of the natural microflora of wild and domesticated birds
AB  - and is rarely detected in human clinical specimens. The
AB  - chromosomal sequence of the type strain C. falsenii DSM 44353 comprises 2,677,607
AB  - bp and provides detailed insights into the evolution of Corynebacterium species
AB  - assigned to the highly diverse cluster 3.
ER  -

TY  - JOUR
AU  - Glavina Del Rio, T. et al.
TI  - Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 87
EP  - 95
VL  - 2
AB  - Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is
AB  - the type species of the rapidly growing genus Chitinophaga in
AB  - the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga
AB  - vary in shape between filaments and spherical bodies without the production of a
AB  - fruiting body, produce myxospores, and are of special interest for their ability
AB  - to degrade chitin. Here we describe the features of this organism, together with
AB  - the complete genome sequence, and annotation. This is the first complete genome
AB  - sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long
AB  - single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of
AB  - the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Glenn, T.C.
AU  - Waller, D.R.
AU  - Braun, M.J.
TI  - Increasing proportions of uracil in DNA substrates increases inhibition of restriction enzyme digests.
JO  - Biotechniques
PY  - 1994
SP  - 1086
EP  - 1090
VL  - 17
AB  - Techniques that rely upon the incorporation of uracil into DNA are being published with
AB  - increasing frequency, especially in PCR protocols. We report here the efficiency of 18 type II
AB  - restriction enzymes to digest PCR amplicons synthesized with varying proportions of TTP to
AB  - dUTP in the PCR mixture. We find that most enzymes with A:T/U bp in their recognition site
AB  - digest the amplicons less efficiently as the percentage of dUTP in the reaction mixture is
AB  - increased. This effect is most dramatic when the proportion of dUTP in the nucleotide mixture
AB  - exceeds 50%. All but one of the enzymes which fail to digest amplicons that are synthesized
AB  - with 100% dUTP digest some amplicons which are synthesized with 90% dUTP.
ER  -

TY  - JOUR
AU  - Glickman, J.F.
TI  - The murine DNA methyltransferase: Purification, heterologous expression, steady-state kinetics and post-translational processing.
JO  - Diss. Abstr.
PY  - 1997
SP  - 1265B
EP  - 1265B
VL  - 58
AB  - The mammalian DNA methyltransferase catalyzes the transfer of methyl groups from S-adenosyl
AB  - methionine to the C5-cytosine within the d(CpG) dinucleotides of double-stranded DNA.  DNA
AB  - methylation is critical for normal embryonic development, and regulates gene expression by
AB  - controlling the binding of proteins to the regulatory regions of DNA.  Despite the biological
AB  - importance of this enzyme, the DNA methyltransferase itself has not been characterized in
AB  - detail, with respect to size, steady-state kinetic parameters, post-translational
AB  - modifications and N-terminal sequence.  This lack of information has been due to the
AB  - difficulty in  the purification of suitable quantities of the protein for enzymological and
AB  - biochemical studies.  The murine erthroleukemia cell-derived DNA methyltransferase (300-800
AB  - micrograms) of 3 x 10^10 cells grown in 10 liter cultures.  The recombinant enzyme was
AB  - expressed as a fusion protein containing a nickel-affinity leader peptide using a baculovirus
AB  - expression system.  Expression was 50-fold higher per cell than in the MEL-cells.  The
AB  - recombinant enzyme (1-2mg) was purified from 5 x 10^8 Sf21 cells using immobilized nickel
AB  - affinity chromatography.  The steady-state kinetic parameters of kcat, Km for the substrate,
AB  - double-stranded poly(dI-dC) and the cofactor, S-adenosylmethionine were determined for both
AB  - the MEL cell-derived and the recombinant DNA methyltransferases, demonstrating that the two
AB  - enzymes were functionally similar.  The DNA methyltransferase was a noticeably slow enzyme
AB  - (kcat, 7/hr); however, based on an estimate of the number of DNA methyltransferase molecules
AB  - per nucleus, there should be enough methyltransferase activity to account for the levels of
AB  - DNA methylation in a vertebrate cell.  Metabolic labeling experiments revealed that the DNA
AB  - methyltransferase was post-translationally phosphorylated on serine/threonine residues, and
AB  - peptide mapping using HPLC-electrospray mass spectrometry resulted in the identification of a
AB  - single, predominant phosphorylation site on the MEL-derived DNA methyltransferase in the
AB  - domain responsible for targeting of the enzyme to the replication foci.  Data demonstrating a
AB  - single start of translation at the first methionine, as revised by a newly reported cDNA, is
AB  - presented.
ER  -

TY  - JOUR
AU  - Glickman, J.F.
AU  - Flynn, J.
AU  - Reich, N.O.
TI  - Purification and characterization of recombinant baculovirus-expressed mouse DNA methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1997
SP  - 280
EP  - 284
VL  - 230
AB  - DNA methylation is essential for normal embryonic development in mice.  An understanding of
AB  - how DNA methylation is controlled is largely dependent upon the isolation and characterization
AB  - of the cellular components of the DNA methylation system.  The enzyme which methylates DNA in
AB  - eukaryotic cells is a C-5 cytosine DNA methyltransferase.  Historically, the characterization
AB  - of this enzyme has been limited by its availability and purity.  Here, we present a
AB  - single-step purification of 4 mg of baculovirus-expressed mouse DNA methyltransferase
AB  - containing a nickel-affinity leader peptide.  The recombinant DNA methyltransferase copurified
AB  - with inhibitory RNA, which was removed by treatment with ribonuclease A.  Like its
AB  - non-recombinant counterpart, the recombinant enzyme is activated by hemi-methylation.  A
AB  - direct steady-state kinetic comparison between the recombinant baculovirus-expressed enzyme
AB  - with its MEL cell-derived counterpart is presented.
ER  -

TY  - JOUR
AU  - Glickman, J.F.
AU  - Pavlovich, J.G.
AU  - Reich, N.O.
TI  - Peptide mapping of the murine DNA methyltransferase reveals a major phosphorylation site and the start of translation.
JO  - J. Biol. Chem.
PY  - 1997
SP  - 17851
EP  - 17857
VL  - 272
AB  - The murine DNA methyltransferase catalyzes the transfer of methyl groups from
AB  - S-adenosylmethionine to cytosines within d(CpG) dinucleotides.  The enzyme is necessary for
AB  - normal embryonic development and is implicated in a number of important processes, including
AB  - the control of gene expression and cancer.  Metabolic labeling and high pressure liquid
AB  - chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) were performed on DNA
AB  - methyltransferase purified from murine erythroleukemia cells.  Serine 514 was identified as a
AB  - major phosphorylation site that lies in a domain required for targeting of the enzyme to the
AB  - replication foci.  These results present a potential mechanism for the regulation of DNA
AB  - methylation.  HPLC-ESI-MS peptide mapping data demonstrated that the purified murine DNA
AB  - methyltransferase protein contains the N-terminal regions predicted by the recently revised
AB  - 5' gene sequences.  The evidence suggests a start of translation at the first predicted
AB  - methionine, with no alternate translational start sites.  Our peptide mapping results provide
AB  - a more detailed structural characterization of the DNA methyltransferase that will facilitate
AB  - future structure/function studies.
ER  -

TY  - JOUR
AU  - Glickman, J.F.
AU  - Reich, N.O.
TI  - Baculovirus-mediated high level expression of a mammalian DNA methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1994
SP  - 1003
EP  - 1008
VL  - 204
AB  - The murine C-5 cytosine DNA methyltransferase (Mtase, E.C.2.1.1.37) containing a hexahistidine
AB  - affinity leader peptide has been expressed at levels which are at least 50-fold higher than
AB  - previously reported.  The recombinant enzyme has activity levels similar to the wild-type
AB  - enzyme.  The recombinant polypeptide binds to and elutes from a nickel affinity resin (IMAC
AB  - resin).  No dramatic differences in post-translational modification between the wild-type and
AB  - recombinant enzyme were observed.  The recombinant system will be useful in performing
AB  - site-directed mutagenesis and will facilitate enzymological and biological investigations of
AB  - this enzyme.
ER  -

TY  - JOUR
AU  - Glickman, J.F.
AU  - Reich, N.O.
TI  - The expression of the murine DNA cytosine methyltransferase in cultured cells from Spodoptera frugiperda using a recombinant Baculovirus.
JO  - FASEB J.
PY  - 1993
SP  - A1291
EP  - A1291
VL  - 7
AB  - The murine DNA methyltransferase (MTase, EC 2.1.1.371) is a 169.6 kD enzyme which transfers
AB  - methyl groups from the S-adenosyl methionine cofactor to the 5' carbon of cytosine in DNA.
AB  - DNA methylation in mammals has been implicated in the regulation of gene expression,
AB  - immunoglobulin gene re-arrangement, X-chromosome inactivation and carcinogenesis. We have
AB  - expressed the MTase in cultured insect cells using a lethal linear baculovirus system. Our
AB  - data indicates 100-fold enhancement in MTase expression over previous methods. This system
AB  - will enable us to perform more precise enzymology on the MTase because prior studies were
AB  - limited by the quantity of purified enzyme available. To our knowledge, this is the largest
AB  - nuclear protein expressed using the baculovirus system. We are currently optimizing the
AB  - expression system and investigating the role of post-translational modification and
AB  - sub-cellular localization in the regulation of function of MTase function.
ER  -

TY  - JOUR
AU  - Gliniewicz, K.
AU  - Wildung, M.
AU  - Orfe, L.H.
AU  - Wiens, G.D.
AU  - Cain, K.D.
AU  - Lahmers, K.K.
AU  - Snekvik, K.R.
AU  - Call, D.R.
TI  - Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum.
JO  - BMC Microbiol.
PY  - 2015
SP  - 179
EP  - 179
VL  - 15
AB  - BACKGROUND: Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease
AB  - in salmonids. Earlier research showed that a
AB  - rifampicin-passaged strain of F. psychrophilum (CSF 259-93B.17) caused no disease
AB  - in rainbow trout (Oncorhynchus mykiss, Walbaum) while inducing a protective
AB  - immune response against challenge with the virulent CSF 259-93 strain. We
AB  - hypothesized that rifampicin passage leads to an accumulation of genomic
AB  - mutations that, by chance, reduce virulence. To assess the pattern of phenotypic
AB  - and genotypic changes associated with passage, we examined proteomic, LPS and
AB  - single-nucleotide polymorphism (SNP) differences for two F. psychrophilum strains
AB  - (CSF 259-93 and THC 02-90) that were passaged with and without rifampicin
AB  - selection. RESULTS: Rifampicin resistance was conveyed by expected mutations in
AB  - rpoB, although affecting different DNA bases depending on the strain. One
AB  - rifampicin-passaged CSF 259-93 strain (CR) was attenuated (4 % mortality) in
AB  - challenged fish, but only accumulated eight nonsynonymous SNPs compared to the
AB  - parent strain. A CSF 259-93 strain passaged without rifampicin (CN) accumulated
AB  - five nonsynonymous SNPs and was partially attenuated (28 % mortality) compared to
AB  - the parent strain (54.5 % mortality). In contrast, there were no significant
AB  - change in fish mortalities among THC 02-90 wild-type and passaged strains,
AB  - despite numerous SNPs accumulated during passage with (n = 174) and without
AB  - rifampicin (n = 126). While only three missense SNPs were associated with
AB  - attenuation, a Ser492Phe rpoB mutation in the CR strain may contribute to further
AB  - attenuation. All strains except CR retained a gliding motility phenotype. Few
AB  - proteomic differences were observed by 2D SDS-PAGE and there were no apparent
AB  - changes in LPS between strains. Comparative methylome analysis of two strains (CR
AB  - and TR) identified no shared methylation motifs for these two strains.
AB  - CONCLUSION: Multiple genomic changes arose during passage experiments with
AB  - rifampicin selection pressure. Consistent with our hypothesis, unique
AB  - strain-specific mutations were detected for the fully attenuated (CR), partially
AB  - attenuated (CN) and another fully attenuated strain (B17).
ER  -

TY  - JOUR
AU  - Glockner, G.
AU  - Lehmann, R.
AU  - Romualdi, A.
AU  - Pradella, S.
AU  - Schulte-Spechtel, U.
AU  - Schilhabel, M.
AU  - Wilske, B.
AU  - Suhnel, J.
AU  - Platzer, M.
TI  - Comparative analysis of the Borrelia garinii genome.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 6038
EP  - 6046
VL  - 32
AB  - Three members of the genus Borrelia (B.burgdorferi, B.garinii, B.afzelii) cause tick-borne
AB  - borreliosis. Depending on the Borrelia species involved,
AB  - the borreliosis differs in its clinical symptoms. Comparative genomics
AB  - opens up a way to elucidate the underlying differences in Borrelia
AB  - species. We analysed a low redundancy whole-genome shotgun (WGS) assembly
AB  - of a B.garinii strain isolated from a patient with neuroborreliosis in
AB  - comparison to the B.burgdorferi genome. This analysis reveals that most of
AB  - the chromosome is conserved (92.7% identity on DNA as well as on amino
AB  - acid level) in the two species, and no chromosomal rearrangement or larger
AB  - insertions/deletions could be observed. Furthermore, two collinear
AB  - plasmids (lp54 and cp26) seem to belong to the basic genome inventory of
AB  - Borrelia species. These three collinear parts of the Borrelia genome
AB  - encode 861 genes, which are orthologous in the two species examined. The
AB  - majority of the genetic information of the other plasmids of
AB  - B.burgdorferii is also present in B.garinii although orthology is not easy
AB  - to define due to a high redundancy of the plasmid fraction. Yet, we did
AB  - not find counterparts of the B.burgdorferi plasmids lp36 and lp38 or their
AB  - respective gene repertoire in the B.garinii genome. Thus, phenotypic
AB  - differences between the two species could be attributable to the presence
AB  - or absence of these two plasmids as well as to the potentially positively
AB  - selected genes.
ER  -

TY  - JOUR
AU  - Gloeckner, F.O.
AU  - Kube, M.
AU  - Bauer, M.
AU  - Teeling, H.
AU  - Lombardot, T.
AU  - Ludwig, W.
AU  - Gade, D.
AU  - Beck, A.
AU  - Borzym, K.
AU  - Heitmann, K.
AU  - Rabus, R.
AU  - Schlesner, H.
AU  - Amann, R.
AU  - Reinhardt, R.
TI  - Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 8298
EP  - 8303
VL  - 100
AB  - Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally
AB  - distributed and environmentally important
AB  - bacterial order Planctomycetales. Here we report the complete genome
AB  - sequence of a member of this independent phylum. With 7.145 megabases,
AB  - Pirellula sp. strain 1 has the largest circular bacterial genome sequenced
AB  - so far. The presence of all genes required for heterolactic acid
AB  - fermentation, key genes for the interconversion of C1 compounds, and 110
AB  - sulfatases were unexpected for this aerobic heterotrophic isolate.
AB  - Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of
AB  - genes for peptidoglycan synthesis were found. Genes for lipid A
AB  - biosynthesis and homologues to the flagellar L- and P-ring protein
AB  - indicate a former Gram-negative type of cell wall. Phylogenetic analysis
AB  - of all relevant markers clearly affiliates the Planctomycetales to the
AB  - domain Bacteria as a distinct phylum, but a deepest branching is not
AB  - supported by our analyses.
ER  -

TY  - JOUR
AU  - Gloeckner, G.
AU  - Schulte-Spechtel, U.
AU  - Schilhabel, M.
AU  - Felder, M.
AU  - Suehnel, J.
AU  - Wilske, B.
AU  - Platzer, M.
TI  - Comparative genome analysis: Selection pressure on the Borrelia vls cassettes is essential for infectivity.
JO  - BMC Genomics
PY  - 2006
SP  - 211
EP  - 211
VL  - 7
AB  - ABSTRACT: BACKGROUND: At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause
AB  - tick-borne Lyme disease. Previous work including the
AB  - genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a
AB  - highly variable plasmid part. The frequent occurrence of duplicated
AB  - sequence stretches, the observed plasmid redundancy, as well as the mainly
AB  - unknown function and variability of plasmid encoded genes rendered the
AB  - relationships between plasmids within and between species largely
AB  - unresolvable. RESULTS: To gain further insight into Borreliae genome
AB  - properties we completed the plasmid sequences of B. garinii PBi, added the
AB  - genome of a further species, B. afzelii PKo, to our analysis, and compared
AB  - for both species the genomes of pathogenic and apathogenic strains. The
AB  - core of all Bbsl genomes consists of the chromosome and two plasmids
AB  - collinear between all species. We also found additional groups of
AB  - plasmids, which share large parts of their sequences. This makes it very
AB  - likely that these plasmids are relatively stable and share common
AB  - ancestors before the diversification of Borrelia species. The analysis of
AB  - the differences between B. garinii PBi and B. afzelii PKo genomes of low
AB  - and high passages revealed that the loss of infectivity is accompanied in
AB  - both species by a loss of similar genetic material. Whereas B. garinii PBi
AB  - suffered only from the break-off of a plasmid end, B. afzelii PKo lost
AB  - more material, probably an entire plasmid. In both cases the vls gene
AB  - locus encoding for variable surface proteins is affected. CONCLUSIONS: The
AB  - complete genome sequences of a B. garinii and a B. afzelii strain
AB  - facilitates further comparative studies within the genus Borrellia. Our
AB  - study shows that loss of infectivity can be traced back to only one single
AB  - event in B. garinii PBi: the loss of the vls cassettes possibly due to
AB  - error prone gene conversion. Similar albeit extended losses in B. afzelii
AB  - PKo support the hypothesis that infectivity of Borrelia species depends
AB  - heavily on the evasion from the host response.
ER  -

TY  - JOUR
AU  - Glover, S.W.
TI  - Genetics of the R-M systems in Haemophilus.
JO  - Heredity
PY  - 1978
SP  - 123
EP  - 123
VL  - 41
AB  - The genus Haemophilus is an extremely rich source of restriction endonucleases of both type I
AB  - and type II.  Altogether 22 such enzymes have been detected and partially characterized.
AB  - About half of these enzymes have been isolated from Haemophilus influenzae and each of the H.
AB  - influenzae serotypes a, b, c, d, e and f are believed to possess restriction and modification
AB  - (R-M) systems.  The R-M systems from serotypes a, b, d, e and f have been analyzed genetically
AB  - and the restriction endonucleases from serotypes a, f (HinaII, HinaIII and HinfIII) have been
AB  - partially characterized.  All of the evidence indicates that the enzymes which form part of
AB  - the H. influenzae R-M systems are type I enzymes and their role appears to be similar to that
AB  - of other restriction endonucleases that can be detected by in vivo tests.  Type II restriction
AB  - endonucleases have been isolated from all of the H. influenzae serotypes other than serotype a
AB  - and characterized using bacteriophage lambda or other well-defined DNA molecules as substrate.
AB  - These enzymes do not appear to form part of recognized R-M systems and they have little or no
AB  - activity on Haemophilus phage DNA.
ER  -

TY  - JOUR
AU  - Glover, S.W.
TI  - Restriction Endonucleases.  Genetics of restriction/modification systems.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 395
EP  - 400
VL  - 8
AB  - Three different types of restriction/modification system are now recognized: type I, type II
AB  - and type III.  The genetics of type-I systems has been investigated by several groups of
AB  - workers and there is common agreement that three genes are involved: hsdS, hsdR and hsdM.  The
AB  - specificity of the system is determined by the product of the hsdS gene.  Mutations in the
AB  - hsdS gene produce an r-m- phenotype; mutations in the hsdR gene produce an r-m+ phenotype and
AB  - mutations in the hsdM gene produce an r-m- phenotype.  Several such systems have been
AB  - recognized and analysed genetically in Escherichia coli and in Salmonella typhimurium.
AB  - Complementation tests employing partial diploids constructed by using F' strains show that
AB  - the E. coli systems K and B and the S. typhimurium system SB are functionally related, and
AB  - mapping experiments show that they are genetically allelic.  It has been shown that
AB  - restriction endonucleases isolated from type-I systems have the three different polypeptide
AB  - subunits that the three-gene model predicts, and that type-I-modification methylases have the
AB  - two subunits expected from the genetic model.  However, unambiguous assignment of polypeptide
AB  - subunit to coding gene is still lacking. No convincing evidence for regulatory-gene functions
AB  - has been obtained so far.
ER  -

TY  - JOUR
AU  - Glover, S.W.
TI  - Functional analysis of host-specificity mutants in Escherichia coli.
JO  - Genet. Res.
PY  - 1970
SP  - 237
EP  - 250
VL  - 15
AB  - Evidence from a functional analysis of host-specificity mutants in merodiploids
AB  - is presented which supports the suggestion that three genes, hss, hsr and hsm,
AB  - are necessary for the expression of host-controlled restriction and
AB  - modification.  The host-specificity phenotype expressed by the merodiploids
AB  - provides evidence that at least two genes, hss and hsr, are concerned in the
AB  - expression of host-specific restriction of DNA and one of these genes, hss, is
AB  - responsible for the strain specificity of the restriction enzyme.  A class of
AB  - modification-deficient mutants isolated from restriction-deficient,
AB  - modification-proficient mutants, was also tested for complementation in
AB  - merodiploids and the phenotype of these merodiploids provides evidence that at
AB  - least two genes, hss and hsm, are concerned in the expression of host-specific
AB  - modification of DNA and one of these genes, hss, is responsible for the strain
AB  - specificity of the modification enzyme.  How these three genes function at the
AB  - molecular level is discussed in terms of models based on the interaction of
AB  - subunits to form oligomeric enzymes.
ER  -

TY  - JOUR
AU  - Glover, S.W.
TI  - Host specificity in F' heterogenotes of Escherichia coli.
JO  - J. Gen. Microbiol.
PY  - 1968
SP  - i
EP  - ii
VL  - 53
AB  - Host-controlled modification of DNA in strains of Escherichia coli has two
AB  - clearly defined characteristics.  First, modification, a process which acts
AB  - directly on DNA and involves the specific alteration of certain base sequences
AB  - by methylation.  As a result, the DNA synthesized in a particular strain may
AB  - carry a characteristic, strain-specific pattern.  Secondly, restriction, a
AB  - process which may lead to the rapid degradation of DNA introduced into a cell
AB  - of different host strain specificity.  The host specificities of E. coli strain
AB  - K12 and E. coli strain B are different such that DNA from K12 may be degraded
AB  - in B and vice versa.  In both strains mutants have been isolated which either
AB  - have lost the ability to restrict but are still able to modify DNA, or have
AB  - lost both the ability to restrict and to modify DNA.  The genetic location of
AB  - both these mutations has been determined in E. coli K and E. coli B.  Both
AB  - mutations map in the thr-leu region.  An F' factor from E. coli K12 carrying
AB  - thr-leu and the genes determining host specificity has been used to examine the
AB  - host-specificity properties of diploids.  Restriction was assayed simply by
AB  - measuring the efficiency of plating of bacteriophage lambda grown on either E.
AB  - coli K or E. coli B and designated lambda.K and lambda.B respectively.
AB  - Modification was assayed again indirectly by growing phage lambda on the
AB  - diploid strains and measuring its efficiency of plating on standard indicator
AB  - strains.  The results obtained so far indicate that:  1) In strain K the
AB  - wild-type alleles are dominant to both of the mutants described above.  2) The
AB  - diploid K/K may plate lambda.B less efficiently than the haploid strain K.  3)
AB  - The diploid K/B restricts both lambda.K and lambda.B.  4) The diploid K/B
AB  - produces lambda particles which are able to plate on both strains K and B.  5)
AB  - The diploid constructed between K and a mutant of B deficient in both
AB  - restriction and modification is indistinguishable from the haploid K strain.
AB  - 6) The diploid constructed between K and a mutant of B deficient in restriction
AB  - only, restricts both lambda.K and lambda.B and produces lambda particles which
AB  - are able to plate on both strains K and B.  These results will be discussed in
AB  - relation to the several models which have been proposed to explain the genetic
AB  - basis of host-controlled modification of DNA.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Colson, C.
TI  - Genetics of host-controlled restriction and modification in Eschericia coli.
JO  - Genet. Res.
PY  - 1969
SP  - 227
EP  - 240
VL  - 13
AB  - In recent years many aspects of the processes of restriction and modification
AB  - which characterize the host controlled modification (CM) of bacteriophages in
AB  - Escherica coli have been clarified (reviewed by Arber (1965a) and Klein
AB  - (1965)).  In this paper we describe:  (i) the results of genetic experiments
AB  - which locate the sites of these mutations close to the serB locus, (ii) the
AB  - results of genetic crosses between different HCM mutants, and (iii) the results
AB  - of experiments designed to elucidate the number of functional units involved in
AB  - the control of HCM and the relationships between them.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Colson, C.
TI  - Stable and unstable alterations of the host-induced modification properties of Escherichia coli B, K and C.
JO  - Genet. Res.
PY  - 1966
SP  - 223
EP  - 234
VL  - 7
AB  - The system of host-induced modification (HIM) in E. coli B, K and C (Arber &
AB  - Dussoix, 1962) has the following properties.  Normal K, which is able to
AB  - restrict phage lambda grown in either B or C and confers a K-specific
AB  - modification to lambda-DNA synthesized in it, can be represented as K r+m+.
AB  - Similarly, normal B can be represented as B r+m+, indicating that it restricts
AB  - phage lambda grown in either K or C and that it confers a B-specific
AB  - modification to lambda-DNA synthesized in it.  Strain C accepts phage lambda
AB  - grown in K, B or C without restriction.  Recently the genes controlling
AB  - restriction and modification have been mapped close to the marker threonine and
AB  - on the opposite side of it to leucine (Colson, Glover, Symonds & Stacey, 1965).
AB  - In the course of this work, strains were isolated which had HIM properties
AB  - unlike those of B, K or C.  These strains display different patterns of HIM.
AB  - One such pattern can be represented as B r-m+, indicating that the ability to
AB  - restrict lambda grown in K or C has been lost while the ability to confer the
AB  - B-specific modification is retained.  Another can be represented as K r-m- or B
AB  - r-m-:  these strains have lost the ability to restrict lambda.C and to confer
AB  - respectively either the K- or the B-specific modificatiton.  Others are more
AB  - complex and comprise strains which on first isolation appear to bear HIM
AB  - properties intermediate between those of B,K and C, but which on further
AB  - analysis turn out to be unstable.  We shall describe the isolation of these
AB  - strains and present some details of their behaviour.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Colson, C.
TI  - The breakdown of the restriction mechanism in zygotes of Escherichia coli.
JO  - Genet. Res.
PY  - 1965
SP  - 153
EP  - 155
VL  - 6
AB  - A few cells in a culture of E. coli K or E. coli B, usually about 1 in 10-4,
AB  - permit the growth of the restricted phage lambda.C (Arber & Dussoix, 1962).
AB  - Such cells may be genetically different from the majority of the cells in the
AB  - culture or they may be temporarily in such a physiological condition that the
AB  - restriction mechanism breaks down or cannot be expressed.  Mutants which are
AB  - genetically unable to restrict the growth of phage normally restricted by
AB  - wild-type cells have been isolated (Glover et al., 1963; Colson et al., 1964;
AB  - Wood, 1964).  But several environmental factors are known which decrease the
AB  - capacity of wild-type bacteria to restrict the growth of unmodified phage
AB  - particles (Luria, 1953; Lederberg, 1957; Uetake et al., 2964).  We shall report
AB  - here observations which suggest that E. coli zygotes are in a special
AB  - physiological condition such that their ability to restrict phage is reduced by
AB  - more than a factor of 100.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Firman, K.
TI  - Genetic control of DNA specificity.
JO  - Genetic Exchange
PY  - 1982
SP  - 331
EP  - 338
VL  - 0
AB  - The plasmid R124 codes for a unique restriction and modification (RM) system and the
AB  - derivative plasmid R124/3 codes for an RM system with a different DNA specificity.  Evidence
AB  - has been obtained that the genes coding for each RM system are carried by both R124 and R124/3
AB  - and that normally only one set of genes is expressed.  The mechanism that ensues that only one
AB  - set of genes is expressed has been investigated in a series of experiments in which a plasmid
AB  - expressing the genes for the R124 RM system and a plasmid expressing the genes for the R124/3
AB  - can be transposed to F plasmids that are compatible with the R factors.  The results of these
AB  - experiments indicate that a trans-acting regulatory mechanism coded for by a resident plasmid
AB  - switches off the expression of RM genes on an introduced plasmid.  Evidence is also presented
AB  - for an additional trans-acting regulatory mechanism which can switch on the expression of the
AB  - alternative set of genes carried by the introduced plasmid.  The regulatory mechanism(s)
AB  - controlling the switch in expression of R124 and R124/3 RM genes involves a physical
AB  - rearrangement of DNA segments, and a possible model for this regulatory mechanism is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Firman, K.
TI  - A novel class of restriction-deficient mutants.
JO  - Heredity
PY  - 1978
SP  - 122
EP  - 123
VL  - 41
AB  - R124 is a unique R factor in compatability group F IV which confers tetracycline resistance
AB  - (Tc) and carries the genes for a restriction-modification (R-M) system.  R124/3 is a
AB  - derivative plasmid which determines a R-M system of different biological specificity to R124.
AB  - During experiments designed to isolate restriction-deficient (r-) mutants of these R factors
AB  - in which F-lac+.0 was transferred to R124 or R124/3 carrying bacteria virtually all of the
AB  - colonies isolated were restriction-deficient.  Restriction-deficient mutants can be isolated
AB  - just as readily following transfer of these R factors to F-lac+ carrying bacteria.  Many of
AB  - the restriction-deficient mutants isolated are also modification-deficient and some
AB  - unexpectedly express the modifications characteristic of both R124 and R124/3.  Evidence is
AB  - presentd to indicate that the restriction-deficient phenotype of these R factors is not
AB  - dependent on the continued presence of F-lac+ which lead to their isolation and that other
AB  - F-prime factors can interact with R124 to produce r- mutants also at very high frequency.
AB  - Many of these r- mutants show high "reversion" frequencies to r+ and evidence is presented to
AB  - indicate that mutation to Tc sensitivity may also arise frequently following transfer to
AB  - F-lac+ to R+ bacteria.  These results are discussed in relation to what is known about the DNA
AB  - of the plasmid molecules from studies conducted by Dr. S.G. Hughes.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Firman, K.
AU  - Watson, G.
AU  - Price, C.
AU  - Donaldson, S.
TI  - The alternate expression of two restriction and modification systems.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 65
EP  - 69
VL  - 190
AB  - Plasmids R124 and R124/3 carry genes coding for two different R-M systems and
AB  - normally only one set of genes is expressed.  These genes can be translocated
AB  - to F plasmids that are compatible with the R factors and in strains carrying
AB  - these F plasmids and an R factor a transacting regulatory mechanism switches
AB  - off the expression of R-M genes on the introduced plasmid.  Additionally the
AB  - unexpressed genes on the introduced plasmid are expressed.  The regulatory
AB  - mechanism controlling the alternative expression of R124 and R124/3 R-M genes
AB  - involves a physical rearrangement of DNA sequences.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Piekarowicz, A.
TI  - Host specificity of DNA in Haemophilus influenzae:  Restriction and modification in strain Rd.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1972
SP  - 1610
EP  - 1617
VL  - 46
AB  - Wild type strains of Haemophilus influenzae Rd consist of two phenotypic
AB  - classes of bacteria which differ in their abilities to restrict and modify
AB  - phage HP1.  Each of these classes r- m- and r+ m+ is unstable and segregates
AB  - several percent of bacteria of the alternative phenotype.  In addition stable
AB  - r- m- bacteria occur spontaneously in r+ m+ cultures and an r- m+ mutant was
AB  - isolated after mutagenesis of an r+ m+ strain.
ER  -

TY  - JOUR
AU  - Glover, S.W.
AU  - Schell, J.
AU  - Symonds, N.
AU  - Stacey, K.A.
TI  - The control of host-induced modification by phage P1.
JO  - Genet. Res.
PY  - 1963
SP  - 480
EP  - 482
VL  - 4
AB  - The phenomenon of host-induced modification has two facets, restriction and
AB  - modification.  Recently these two processes have been clarified by Arber and
AB  - Dussoix in the system where phage lambda multiplies either in Escherichia coli
AB  - K12, or in K12 cells lysogenic for the phage P1.  The phage lambda.K is
AB  - accepted only by 1 in 10-4 recipient K(P1) cells; these produce modified
AB  - lambda.P1 phage particles, which then are able to infect either K or K(P1)
AB  - cells with an efficiency of one.  In a beautiful series of experiments Arber
AB  - and Dussoix showed that modification must be a process which acts directly on
AB  - the DNA of phage lambda, and that where unmodified lambda-DNA enters K(P1)
AB  - cells it is rapidly degraded into small molecular weight fragments.  These
AB  - findings led Arber to the generalization that modification should affect all
AB  - forms of DNA which are synthesized in K(P1) cells, and that restriction would
AB  - apply to all DNA that can be transferred from K to K(P1).  He was able to
AB  - demonstrate that restriction and modification did occur during the transfer of
AB  - the bacterial genome in conjugation, and also during the transfer of DNA by
AB  - transforming principle and by transduction (Arber & Dussoix, 1962, Dussoix &
AB  - Arber, 1962; Arber, 1962).  In this note we shall first present some data
AB  - extending Arber's observations to the transfer of a variety of episomes, and
AB  - then show how these results can be utilized to demonstrate that the roles of
AB  - restriction and modification imposed by P1 are under independent genetic
AB  - control.
ER  -

TY  - JOUR
AU  - Glushka, J.
AU  - Barany, F.
AU  - Cowburn, D.
TI  - Observation of arginyl-deoxyoligonucleotide interactions in TaqI endonuclease by detection of specific 1H NMR signals from 140 kD [Nn1, Nn2, 15N Arg]TaqI/oligomer complexes.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1989
SP  - 88
EP  - 93
VL  - 164
AB  - Proton and nitrogen signals of the guanidinium amines in [Nn1, Nn2 15N Arg]TaqI
AB  - endonuclease were observed using isotope filtered experiments and proton
AB  - detected H{15N} heterocorrelated two dimensional NMR spectroscopy.  These
AB  - rapidly exchanging protons could be detected in the free enzyme only at pH 4.5;
AB  - at pH 8.5, no signals were measured after extensive signal averaging.  Addition
AB  - of deoxyribonucleotide oligomers resulted in the appearance of two groups of
AB  - signals at about 5.8 and 7.5 ppm.  Since these signals are independent of the
AB  - presence of cognate sequence or Mg2+, it is assumed they represent nonspecific
AB  - arginyl-DNA interactions.  This labeling/NMR approach provides a new method for
AB  - investigating the role of arginine in protein-DNA interactions.
ER  -

TY  - JOUR
AU  - Gnaneshan, S.
AU  - Hsueh, Y.C.
AU  - Liang, L.
AU  - Teatero, S.
AU  - Fittipaldi, N.
AU  - Mallo, G.V.
TI  - Genome Sequence of Listeria monocytogenes Strain F6540 (Sequence Type 360) Collected from Food Samples in Ontario, Canada.
JO  - Genome Announcements
PY  - 2016
SP  - e01507
EP  - e01515
VL  - 4
AB  - Comparative genomic analysis between pathogenic and nonpathogenic Listeria monocytogenes
AB  - strains provides a good model for studying the virulence of this
AB  - organism. Here, we report the genome sequence of the nonpathogenic L.
AB  - monocytogenes strain F6540 (sequence type 360) identified specifically in food
AB  - samples in Ontario, Canada, in 2010.
ER  -

TY  - JOUR
AU  - Gochez, A.M.
AU  - Huguet-Tapia, J.C.
AU  - Minsavage, G.V.
AU  - Shantaraj, D.
AU  - Jalan, N.
AU  - Strauss, A.
AU  - Lahaye, T.
AU  - Wang, N.
AU  - Canteros, B.I.
AU  - Jones, J.B.
AU  - Potnis, N.
TI  - Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains.
JO  - BMC Genomics
PY  - 2018
SP  - 16
EP  - 16
VL  - 19
AB  - BACKGROUND: Xanthomonas citri, a causal agent of citrus canker, has been a
AB  - well-studied model system due to recent availability of whole genome sequences of
AB  - multiple strains from different geographical regions. Major limitations in our
AB  - understanding of the evolution of pathogenicity factors in X. citri strains
AB  - sequenced by short-read sequencing methods have been tracking plasmid reshuffling
AB  - among strains due to inability to accurately assign reads to plasmids, and
AB  - analyzing repeat regions among strains. X. citri harbors major pathogenicity
AB  - determinants, including variable DNA-binding repeat region containing
AB  - Transcription Activator-like Effectors (TALEs) on plasmids. The long-read
AB  - sequencing method, PacBio, has allowed the ability to obtain complete and
AB  - accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas
AB  - citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from
AB  - grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed
AB  - plasmid profiles, copy number and location of TALEs in complete genome sequences
AB  - of X. citri strains. RESULTS: We utilized the power of long reads obtained by
AB  - PacBio sequencing to enable assembly of a complete genome sequence of strain
AB  - Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring
AB  - copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The
AB  - pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs.
AB  - Due to the intriguing nature of this pathogenicity plasmid with Tn3-like
AB  - transposon association, repetitive elements and multiple putative sites for
AB  - origins of replication, we might expect alternative structures of this plasmid in
AB  - nature, illustrating the strong adaptive potential of X. citri strains. Analysis
AB  - of the pathogenicity plasmid among completely sequenced X. citri strains, coupled
AB  - with Southern hybridization of the pathogenicity plasmids, revealed clues to
AB  - rearrangements of plasmids and resulting reshuffling of TALEs among strains.
AB  - CONCLUSIONS: We demonstrate in this study the importance of long-read sequencing
AB  - for obtaining intact sequences of TALEs and plasmids, as well as for identifying
AB  - rearrangement events including plasmid reshuffling. Rearrangement events, such as
AB  - the hybrid plasmid in this case, could be a frequent phenomenon in the evolution
AB  - of X. citri strains, although so far it is undetected due to the inability to
AB  - obtain complete plasmid sequences with short-read sequencing methods.
ER  -

TY  - JOUR
AU  - Godany, A.
AU  - Bukovska, G.
AU  - Farkasovska, J.
AU  - Brnakova, Z.
AU  - Dmitriev, A.
AU  - Tkacikova, L.
AU  - Ayele, T.
AU  - Mikula, I.
TI  - Characterization of a complex restriction-modification system detected in Staphylococcus aureus and Streptococcus agalactiae strains isolated  from infections of domestic animals.
JO  - Folia Microbiol. (Praha)
PY  - 2004
SP  - 307
EP  - 314
VL  - 49
AB  - Characterization of classic type II restriction-modification systems (RMS) (restriction
AB  - endonucleases and modification methyltransferases)
AB  - was carried out in isolates of Staphylococcus aureus and Streptococcus
AB  - agalactiae obtained from clinical material. Among the 100 isolates of
AB  - S. aureus two different RMS type II were detected. The first was
AB  - expressed in isolates 32 and 33 (Sau32 I and Sau33 I); the targeting
AB  - sequence was determined as 5'-GGN CC-3' (Sau96 I isoschizomer). The
AB  - second was found in isolates no. 90, 93, 96*, and 98 (Sau90 I, Sau93 I,
AB  - Sau96* I, Sau98 I) and enzymes recognized sequence 5'-CTY RAG-3' (SmlI
AB  - isoschizomer). Analysis of 40 isolates of S. agalactiae revealed only
AB  - one RMS; it was detected in two isolates (no. 16 and 23; Sag16 I and
AB  - Sag23 I). Restriction endonuclease expressed by these isolates cleaved
AB  - DNA in sequence 5'-CTG CA/G-3' (PstI isoschizomer). In RMS-positive S.
AB  - aureus and S. agalactiae isolates plasmid DNA capable of replication in
AB  - Escherichia coli and Bacillus subtilis was also detected and isolated.
ER  -

TY  - JOUR
AU  - Godany, A.
AU  - Farkasovska, J.
AU  - Bukovska, G.
AU  - Timko, J.
TI  - Connection between foreign DNA replication and induced expression of the restriction-modification system in Streptomyces aureofaciens.
JO  - Folia Microbiol. (Praha)
PY  - 2001
SP  - 193
EP  - 196
VL  - 46
AB  - Tetracycline-producing strains of Streptomyces aureofaciens expressed the SauLPI
AB  - restriction-modification system, which recognized the specific DNA sequence 5-GCCGGC-3'
AB  - (isoschizomer NaeI).  The activation of the second R-M system SauLPII (5'-GAGCTC-3',
AB  - isoschizomer of XhoI), which was silent during the growth cycle, after a foreign DNA transfer
AB  - into this strain was observed.  This phenomenon was tentatively explained as a response of the
AB  - cells against the exogenous DNA entering the cells.  The involvement of a SOS-like response in
AB  - induction of R-M system genes in S. aureofaciens strains has been considered.
ER  -

TY  - JOUR
AU  - Godany, A.
AU  - Pristas, P.
AU  - Oktavcova, B.
AU  - Farkosovska, J.
AU  - Ziffova, M.
AU  - Sevcikova, B.
TI  - Characterization of an XhoI isoschizomer in Streptomyces aureofaciens after actinophage infection.
JO  - FEMS Microbiol. Lett.
PY  - 1996
SP  - 123
EP  - 127
VL  - 138
AB  - After infection of tetracycline producing strains of S. aureofaciens with
AB  - actinophages Mu1/6 and B1 some phage resistant colonies were obtained in each experiment.
AB  - These colonies expressed a new restriction-modification (RM) system of type II, which  was
AB  - different from the common RM system (SauLPI) of these strains recognizing the  sequence
AB  - GCCGGC.  This new RM system was not detected before in parental strains.   The new
AB  - endonuclease was purified from a phage resistant strain of S. aureofaciens B96,  using two
AB  - step column chromatography to the grade without non specific nucleolytic  activity.  SauLPII
AB  - endonuclease recognized and cleaved the palindromic hexanucleotide  sequence 5'-C/TCGAG-3',
AB  - thus it was a true isoschizomer of XhoI.
ER  -

TY  - JOUR
AU  - Goddard, M.R.
AU  - Burt, A.
TI  - Recurrent invasion and extinction of a selfish gene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 13880
EP  - 13885
VL  - 96
AB  - Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in
AB  - populations even when they are of no benefit to the host organism. To test the idea that
AB  - regular horizontal transmission is necessary for the long-term persistence of these genes, we
AB  - surveyed 20 species of yeasts for the omega-homing endonuclease gene and associated group I
AB  - intron. The status of omega could be categorized into three states (functional, nonfunctional,
AB  - or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of
AB  - omega differed significantly from that of the host, strong evidence of horizontal
AB  - transmission. Further analyses indicate that horizontal transmission is more common than
AB  - transposition, and that it occurs preferentially between closely related species. Parsimony
AB  - analysis and coalescent theory suggest that there have been 15 horizontal transmission events
AB  - in the ancestry of our yeast species, through simulations indicate that this value is probably
AB  - an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and
AB  - loss, followed by reinvasion, and each of these transitions is estimated to occur about once
AB  - every 2 million years. The data are thus consistent with the idea that frequent horizontal
AB  - transmission is necessary for the long-term persistence of homing endonuclease genes, and
AB  - further, that this requirement limits these genes to organisms with easily accessible germ
AB  - lines. The data also show that mitochondrial DNA sequences are transferred intact between
AB  - yeast species; if other genes do not show such high levels of horizontal transmission, it
AB  - would be due to lack of selection, rather than lack of opportunity.
ER  -

TY  - JOUR
AU  - Godley, L.A.
AU  - Mondragon, A.
TI  - Molecular biology. Preference by exclusion.
JO  - Science
PY  - 2011
SP  - 1017
EP  - 1018
VL  - 331
AB  - DNA methylation is a modification that controls gene expression and contributes to mammalian
AB  - development, aging, and cancer cell biology.  In mice and humans, the addition of a methyl
AB  - group to a cytosine within a cytosine-guanine dinucleotide is catalyzed by DNA
AB  - methyltransferase enzymes DNMT3A, DNMT3B, or DNMT1.  The latter is the main "maintenance
AB  - methylase" because it adds a methyl group primarily to double-strand DNA that is already
AB  - methylated on one strand (hemimethylated).  How DNMT1 prefers hemimethylated over unmethylated
AB  - DNA, in contrast to DNMT3A and DNMT3B, has not been clear.  On page 1036 of this issue, Song
AB  - et al. present the crystal structures of human and mouse DNMT1 in complex with unmethylated
AB  - DNA, providing an explanation for the mechanism of substrate selection by this crucial enzyme.
ER  -

TY  - JOUR
AU  - Godson, G.N.
AU  - Roberts, R.J.
TI  - A catalogue of cleavages of PhiX174, S13, G4, and ST-1 DNA by 26 different restriction endonucleases.
JO  - Virology
PY  - 1976
SP  - 561
EP  - 567
VL  - 73
AB  - The number of cleavages produced in PhiX174, S12, G4, and ST-1 double-stranded
AB  - RFI DNA by 26 different enzymes is given.  Some enzymes, but not all, produce
AB  - similar-sized fragments from PhiX174 and S13 DNA, but all enzymes produce
AB  - completely different-sized fragments from G4 and ST-1 compared with PhiX174.
AB  - PhiX174 RFI is cleaved once to linear RFIII DNA by PstI, AvaI, and XhoI (BluI).
AB  - S13 RFI is cleaved once by PstI, AvaI, and MboI; G4 RF is cleaved once by
AB  - EcoRI, KpnI, PstI, and BglII; and ST-1 RFI DNA is cleaved once by KpnI and BglI
AB  - and BglII.  The sites of these single cleavages have been mapped.  At least
AB  - eight enzymes cleave single-stranded PhiX174 DNA as well as PhiX174
AB  - double-stranded DNA.
ER  -

TY  - JOUR
AU  - Goedecke, K.
AU  - Pignot, M.
AU  - Goody, R.S.
AU  - Scheidig, A.J.
AU  - Weinhold, E.
TI  - Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.
JO  - Nat. Struct. Biol.
PY  - 2001
SP  - 121
EP  - 125
VL  - 8
AB  - The 2.0 angstrom crystal structure of the N6-adenine DNA methyltransferase M.TaqI in complex
AB  - with specific DNA and a non-reactive cofactor analog reveals a previously unrecognized
AB  - stabilization of the extrahelical target base.  To catalyze the transfer of the methyl group
AB  - from the cofactor S-adenosyl-L-methionine to the 6-amino group of adenine within the
AB  - double-stranded DNA sequence 5'-TCGA-3', the target nucleoside is rotated out of the DNA
AB  - helix.  Stabilization of the extrahelical conformation is achieved by DNA compression
AB  - perpendicular to the DNA helix axis at the target base pair position and relocation of the
AB  - partner base thymine in an interstrand Pi-stacked position, where it would sterically overlap
AB  - with an inner-helical target adenine.  The extrahelical target adenine is specifically
AB  - recognized in the active site, and the 6-amino group of adenine donates two hydrogen bonds to
AB  - Asn 105 and Pro 106, which both belong to the conserved catalytic motif IV of N6-adenine DNA
AB  - methyltransferases.  These hydrogen bonds appear to increase the partial negative charge of
AB  - the N6 atom of adenine and activate it for direct nucleophilic attack on the methyl group of
AB  - the cofactor.
ER  -

TY  - JOUR
AU  - Goen, A.E.
AU  - Silverwood, T.
AU  - Underriner, A.
AU  - Trachtenberg, A.M.
AU  - Kelley, C.
AU  - MacLea, K.S.
TI  - Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154(T).
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00841
EP  - e00818
VL  - 7
AB  - The aerobic, Gram-positive, psychrotolerant bacterium Kurthia sibirica was first  isolated
AB  - from the stomach and intestinal contents of the Magadan mammoth
AB  - recovered from the permafrost in eastern Siberia in 1977. K. sibirica was
AB  - sequenced, and the predicted genome size is 3,496,665 bp, with 36.42% G+C
AB  - content.
ER  -

TY  - JOUR
AU  - Goff, S.P.
AU  - Rambach, A.
TI  - SstI: A restriction endonuclease from Streptomyces sp. stanford.
JO  - Gene
PY  - 1978
SP  - 347
EP  - 352
VL  - 3
AB  - A strain of Streptomyces has been isolated which is a convenient source of a
AB  - new restriction endonuclease.  The enzyme has been prepared from extracts of
AB  - these cells and its cleavage sites localized on phage lambda DNA.  The enzyme,
AB  - termed SstI, produces cohesive ends and should be useful for molecular cloning
AB  - experiments.
ER  -

TY  - JOUR
AU  - Goffin, J.
AU  - Eisenhauer, E.
TI  - DNA methyltransferase inhibitors-state of the art.
JO  - Ann. Oncol.
PY  - 2002
SP  - 1699
EP  - 1716
VL  - 13
AB  - Background: DNA methylation is the addition of a methyl group to the 5 position of cytosine.
AB  - It is an epigenetic process with several effects, including chromatin structure modulation,
AB  - transcriptional repression and the suppression of transposable elements.  In malignancy,
AB  - methylation patterns change, resulting in global hypomethylation with regional
AB  - hypermethylation.  This can lead to genetic instability and the repression of tumor suppressor
AB  - genes.
AB  - Design: A review of the DNA methyltransferase inhibitor literature was conducted.
AB  - Results: DNA methylation inhibitors have demonstrated the ability to inhibit hypermethylation,
AB  - restore suppressor gene expression and exert antitumor effects in in vitro and in vivo
AB  - laboratory models.  Four inhibitors, which are analogs of the nucleoside deoxycytidine, have
AB  - been clinically tested: 5-azacytidine, 5-aza-2'-deoxycytidine, 1-beta-D-arabinofuranosyl-5
AB  - -azacytosine and dihydro-5-azacytidine.  The first two have demonstrated encouraging
AB  - antileukemic activity but little activity in solid tumors, while the latter two are no longer
AB  - under study due to lack of efficacy.  A fifth agent, MG98, is an antisense
AB  - oligodeoxynucleotide directed against the 3' untranslated region of the DNA
AB  - methyltransferase-1 enzyme mRNA, and is now under phase II study.
AB  - Conclusions: While some positive clinical results with DNA methyltransferase inhibitors have
AB  - been seen, a definitive clinical role for these agents will most likely require combination
AB  - therapy, and good phase III studies are needed.
ER  -

TY  - JOUR
AU  - Goffin, P.
AU  - Dehottay, P.
TI  - Complete Genome Sequence of Escherichia coli BLR(DE3), a recA-Deficient Derivative of E. coli BL21(DE3).
JO  - Genome Announcements
PY  - 2017
SP  - e00441
EP  - e00417
VL  - 5
AB  - Escherichia coli BLR(DE3) is a commercially available recA-deficient derivative of BL21(DE3),
AB  - one of the most widely used strains for recombinant protein
AB  - expression. Here, we present the full-genome sequence of BLR(DE3) and highlight
AB  - additional differences with its parent strain BL21(DE3) which were previously
AB  - unreported but may affect its physiology.
ER  -

TY  - JOUR
AU  - Gofton, A.W.
AU  - Margos, G.
AU  - Fingerle, V.
AU  - Hepner, S.
AU  - Loh, S.M.
AU  - Ryan, U.
AU  - Irwin, P.
AU  - Oskam, C.L.
TI  - Genome-wide analysis of Borrelia turcica and 'Candidatus Borrelia tachyglossi' shows relapsing fever-like genomes with unique genomic links to Lyme disease Borrelia.
JO  - Infect. Genet. Evol.
PY  - 2018
SP  - 72
EP  - 81
VL  - 66
AB  - Borrelia are tick-borne bacteria that in humans are the aetiological agents of
AB  - Lyme disease and relapsing fever. Here we present the first genomes of B. turcica
AB  - and B. tachyglossi, members of a recently described and rapidly expanding
AB  - Borrelia clade associated with reptile (B. turcica) or echidna (B. tachyglossi)
AB  - hosts, transmitted by hard ticks, and of unknown pathogenicity. Borrelia
AB  - tachyglossi and B. turcica genomes are similar to those of relapsing fever
AB  - Borrelia species, containing a linear ~ 900kb chromosome, a single long (> 70kb)
AB  - linear plasmid, and numerous short (< 40kb) linear and circular plasmids, as well
AB  - as a suite of housekeeping and macronutrient biosynthesis genes which are not
AB  - found in Lyme disease Borrelia. Additionally, both B. tachyglossi and B. turcica
AB  - contain paralogous vsp and vlp proteins homologous to those used in the
AB  - multiphasic antigen-switching system used by relapsing fever Borrelia to evade
AB  - vertebrate immune responses, although their number was greatly reduced compared
AB  - to human-infectious species. However, B. tachyglossi and B. turcica chromosomes
AB  - also contain numerous genes orthologous to Lyme disease Borrelia-specific genes,
AB  - demonstrating a unique evolutionary, and potentially phenotypic link between
AB  - these groups. Borrelia tachyglossi and B. turcica genomes also have unique
AB  - genetic features, including degraded and deleted tRNA modification genes, and an
AB  - expanded range of macronutrient salvage and biosynthesis genes compared to
AB  - relapsing fever and Lyme disease Borrelia. These genomes and genomic comparisons
AB  - provide an insight into the biology and evolutionary origin of these Borrelia,
AB  - and provide a valuable resource for future work.
ER  -

TY  - JOUR
AU  - Gogarten, J.P.
AU  - Hilario, E.
TI  - Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements.
JO  - BMC Evol. Biol.
PY  - 2006
SP  - 94
EP  - 94
VL  - 6
AB  - Self splicing introns and inteins that rely on a homing endonuclease for propagation are
AB  - parasitic genetic elements. Their life-cycle and
AB  - evolutionary fate has been described through the homing cycle.
AB  - According to this model the homing endonuclease is selected for
AB  - function only during the spreading phase of the parasite. This phase
AB  - ends when the parasitic element is fixed in the population. Upon
AB  - fixation the homing endonuclease is no longer under selection, and its
AB  - activity is lost through random processes. Recent analyses of these
AB  - parasitic elements with functional homing endonucleases suggest that
AB  - this model in its most simple form is not always applicable.
AB  - Apparently, functioning homing endonuclease can persist over long
AB  - evolutionary times in populations and species that are thought to be
AB  - asexual or nearly asexual. Here we review these recent findings and
AB  - discuss their implications. Reasons for the long-term persistence of a
AB  - functional homing endonuclease include: More recombination (sexual and
AB  - as a result of gene transfer) than previously assumed for these
AB  - organisms; complex population structures that prevent the element from
AB  - being fixed; a balance between active spreading of the homing
AB  - endonuclease and a decrease in fitness caused by the parasite in the
AB  - host organism; or a function of the homing endonuclease that increases
AB  - the fitness of the host organism and results in purifying selection for
AB  - the homing endonuclease activity, even after fixation in a local
AB  - population. In the future, more detailed studies of the population
AB  - dynamics of the activity and regulation of homing endonucleases are
AB  - needed to decide between these possibilities, and to determine their
AB  - relative contributions to the long term survival of parasitic genes
AB  - within a population. Two outstanding publications on the amoeba
AB  - Naegleria group I intron (Wikmark et al. BMC Evol Biol 2006, 6: 39) and
AB  - the PRP8 inteins in ascomycetes (Butler et al. BMC Evol Biol 2006, 6:
AB  - 42) provide important stepping stones towards integrated studies on how
AB  - these parasitic elements evolve through time together with, or despite,
AB  - their hosts.
ER  -

TY  - JOUR
AU  - Gogarten, J.P.
AU  - Senejani, A.G.
AU  - Zhaxybayeva, O.
AU  - Olendzenski, L.
AU  - Hilario, E.
TI  - Inteins: Structure, function, and evolution.
JO  - Annu. Rev. Microbiol.
PY  - 2002
SP  - 263
EP  - 287
VL  - 56
AB  - Inteins are genetic elements that disrupt the coding sequence of genes. However, in contrast
AB  - to introns, inteins are transcribed and translated
AB  - together with their host protein. Inteins appear most frequently in
AB  - Archaea, but they are found in organisms belonging to all three domains of
AB  - life and in viral and phage proteins. Most inteins consist of two domains:
AB  - One is involved in autocatalytic splicing, and the other is an
AB  - endonuclease that is important in the spread of inteins. This review
AB  - focuses on the evolution and technical application of inteins and only
AB  - briefly summarizes recent advances in the study of the catalytic
AB  - activities and structures of inteins. In particular, this review considers
AB  - inteins as selfish or parasitic genetic elements, a point of view that
AB  - explains many otherwise puzzling aspects of inteins.
ER  -

TY  - JOUR
AU  - Goguel, V.
AU  - Delahodde, A.
AU  - Jacq, C.
TI  - Connections between RNA splicing and DNA intron mobility in yeast mitochondria: RNA maturase and DNA endonuclease switching experiments.
JO  - Mol. Cell. Biol.
PY  - 1992
SP  - 696
EP  - 705
VL  - 12
AB  - The intron-encoded proteins bI4 RNA maturase and aI4 DNA endonuclease can
AB  - be faithfully expressed in yeast cytoplasm from engineered forms of their
AB  - mitochondrial coding sequences. In this work we studied the relationships
AB  - between these two activities associated with two homologous intron-encoded
AB  - proteins: the bI4 RNA maturase encoded in the fourth intron of the
AB  - cytochrome b gene and the aI4 DNA endonuclease (I-SceII) encoded in the
AB  - fourth intron of the gene coding for the subunit I of cytochrome oxidase.
AB  - Taking advantage of both the high recombinogenic properties of yeast and
AB  - the similarities between the two genes, we constructed in vivo a family of
AB  - hybrid genes carrying parts of both RNA maturase and DNA endonuclease
AB  - coding sequences. The presence of a sequence coding for a mitochondrial
AB  - targeting peptide upstream from these hybrid genes allowed us to study the
AB  - properties of their translation products within the mitochondria in vivo.
AB  - We thus could analyze the ability of the recombinant proteins to
AB  - complement RNA maturase deficiencies in different strains. Many
AB  - combinations of the two parental intronic sequences were found in the
AB  - recombinants. Their structural and functional analysis revealed the
AB  - following features. (i) The N-terminal half of the bI4 RNA maturase could
AB  - be replaced in total by its equivalent from the aI4 DNA endonuclease
AB  - without affecting the RNA maturase activity. In contrast, replacing the
AB  - C-terminal half of the bI4 RNA maturase with its equivalent from the aI4
AB  - DNA endonuclease led to a very weak RNA maturase activity, indicating that
AB  - this region is more differentiated and linked to the maturase activity.
AB  - (ii) None of the hybrid proteins carrying an RNA maturase activity kept
AB  - the DNA endonuclease activity, suggesting that the latter requires the
AB  - integrity of the aI4 protein. These observations are interesting because
AB  - the aI4 DNA endonuclease is known to promote the propagation, at the DNA
AB  - level, of the aI4 intron, whereas the bI4 RNA maturase, which is required
AB  - for the splicing of its coding intron, also controls the splicing process
AB  - of the aI4 intron. We propose a scenario for the evolution of these
AB  - intronic proteins that relies on a switch from DNA endonuclease to RNA
AB  - maturase activity.
ER  -

TY  - JOUR
AU  - Goh, K.M.
AU  - Chan, K.G.
AU  - Yaakop, A.S.
AU  - Chan, C.S.
AU  - Ee, R.
AU  - Tan, W.S.
AU  - Gan, H.M.
TI  - Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00512
EP  - e00515
VL  - 3
AB  - Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was
AB  - isolated from a soil sample in Portugal. J. soli constitutes the
AB  - only Jeotgalibacillus species isolated from a non-marine source. Here, the draft
AB  - genome, several interesting glycosyl hydrolases, and its putative N-acyl
AB  - homoserine lactonases are presented.
ER  -

TY  - JOUR
AU  - Goh, S.
AU  - Ong, P.F.
AU  - Song, K.P.
AU  - Riley, T.V.
AU  - Chang, B.J.
TI  - The complete genome sequence of Clostridium difficile phage {phi}C2 and comparisons to {phi}CD119 and inducible prophages of CD630.
JO  - Microbiology
PY  - 2007
SP  - 676
EP  - 685
VL  - 153
AB  - The complete genomic sequence of a previously characterized temperate
AB  - phage of Clostridium difficile, C2, is reported. The genome is 56 538 bp
AB  - and organized into 84 putative ORFs in six functional modules. The head
AB  - and tail structural proteins showed similarities to that of C. difficile
AB  - phage CD119 and Streptococcus pneumoniae phage EJ-1, respectively.
AB  - Homologues of structural and replication proteins were found in prophages
AB  - 1 and 2 of the sequenced C. difficile CD630 genome. A putative holin
AB  - appears unique to the C. difficile phages and was functional when
AB  - expressed in Escherichia coli. Nucleotide sequence comparisons of C2 to
AB  - CD119 and the CD630 prophage sequences showed relatedness between C2 and
AB  - the prophages, but less so to CD119. C2 integrated into a gene encoding a
AB  - putative transcriptional regulator of the gntR family. C2, CD119 and CD630
AB  - prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that
AB  - the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has
AB  - phage origins. The attP sequences of C2, CD119 and CD630 prophages were
AB  - dissimilar. C2-related sequences were found in 84 % of 37 clinical C.
AB  - difficile isolates and typed reference strains.
ER  -

TY  - JOUR
AU  - Gohda, K.
AU  - Matsuo, N.
AU  - Oda, Y.
AU  - Ikehara, M.
AU  - Uesugi, S.
TI  - Effects of 2'-substituents of the first deoxyguanosine residue in the recognition sequence on EcoRI restriction endonuclease activity.
JO  - J. Biochem. (Tokyo)
PY  - 1997
SP  - 219
EP  - 224
VL  - 121
AB  - The effects of 2'-substituents of the first deoxyguanosine on EcoRI activity were examined
AB  - using synthetic octadeoxynucleotides d(GG*AATTCC) containing 2'-substituted derivatives (G*),
AB  - i.e., 2'-fluoro-2'-deoxyguanosine (dGfl), 2'-chloro-2'-deoxyguanosine (dGcl), and
AB  - guanosine (rG).  The overall structures of the octamers were very similar, as shown by CD and
AB  - UV measurements, although their EcoRI reactivities were very different: 100% in 60 min for
AB  - d(GGAATTCC) and d(GGflAATTCC), 5% in 24h for d[G(rG)AATTCC], and no cleavage at all in 24h for
AB  - d(GGclAATTCC).  However, the kinetics showed the octamers exhibit similar binding-affinity to
AB  - the enzyme (10^6-10^7 M).  31P-NMR analysis suggested the modified octamers change the
AB  - phosphate backbone conformation in a duplex, since an unusual downfield-shifted signal in the
AB  - spectra was commonly observed for the modified octamers at low temperature (i.e., a single
AB  - strand state), which was shifted upfield at high temperature (i.e., a single strand state).
AB  - The order of the differences was dGcl>rG>dGfl-containing octamers, coinciding with that of the
AB  - vdW volume of 2'-substituents (Cl>OH>F) and the cleavage reactivities.  These findings
AB  - suggest the steric hindrance by the 2'-substituents causes a conformational change of the
AB  - phosphate backbone close to the scissile bond, and then interferes with the EcoRI reaction.
ER  -

TY  - JOUR
AU  - Gokce, A.
AU  - Cakar, Z.P.
AU  - Yucel, M.
AU  - Ozcan, O.
AU  - Sencan, S.
AU  - Sertdemir, I.
AU  - Erguner, B.
AU  - Yuceturk, B.
AU  - Sarac, A.
AU  - Yuksel, B.
AU  - Ozturk, Y.
TI  - Draft Genome Sequences of Two Heat-Resistant Mutant Strains (A52 and B41) of the  Photosynthetic Hydrogen-Producing Bacterium Rhodobacter capsulatus.
JO  - Genome Announcements
PY  - 2016
SP  - e00531
EP  - e00516
VL  - 4
AB  - The draft genome sequences of two heat-resistant mutant strains, A52 and B41, derived from
AB  - Rhodobacter capsulatus DSM 1710, and with different hydrogen
AB  - production levels, are reported here. These sequences may help understand the
AB  - molecular basis of heat resistance and hydrogen production in R. capsulatus.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 393
EP  - 401
VL  - 4
AB  - Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca,
AB  - which belongs to the family Syntrophaceae in the class
AB  - Deltaproteobacteria. The species was first observed in a study on the competition
AB  - of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D.
AB  - acetoxidans is considered to be the most abundant acetate-degrading sulfate
AB  - reducer in sludge. It is of interest due to its isolated phylogenetic location in
AB  - the 16S rRNA-based tree of life. This is the second completed genome sequence of
AB  - a member of the family Syntrophaceae to be published and only the third genome
AB  - sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long
AB  - genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Complete genome sequence of the termophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA) from a deep-sea hydrothermal vent.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 407
EP  - 415
VL  - 5
AB  - Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the ge-nus
AB  - Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of
AB  - interest because it represents the first thermophilic bacterium that can act as a primary
AB  - pro-ducer in the temperature range of 45-75oC (optimum 70oC) and is incapable of growing
AB  - un-der microaerophilic conditions. Strain BSAT preferentially synthesizes high-melting-point
AB  - fatty acids (C18 and C20) which is hypothesized to be a strategy to ensure the functionality
AB  - of the membrane at high growth temperatures. This is the second completed genome sequence of a
AB  - member of the family Desulfurobacteriaceae and the first sequence from the genus
AB  - Desulfurobacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes
AB  - and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 230
EP  - 239
VL  - 6
AB  - Thermovirga lienii Dahle and Birkeland 2006 is a member of the genus Thermovirga  in the
AB  - genomically moderately well characterized phylum 'Synergistetes'. Members
AB  - of this relatively recently proposed phylum 'Synergistetes' are of interest
AB  - because of their isolated phylogenetic position and their diverse habitats, e.g.
AB  - from humans to oil wells. The genome of T. lienii Cas60314(T) is the fifth genome
AB  - sequence (third completed) from this phylum to be published. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 1,999,646 bp long genome (including one plasmid) with its 1,914
AB  - protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African  solfataric spring.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1105
EP  - 1117
VL  - 9
AB  - Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized
AB  - genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of
AB  - interest for its origin from a continental solfataric spring vs. predominantly
AB  - marine oil reservoirs of other members of the genus. The genome of strain LA3T
AB  - also provides fresh data for the phylogenomic positioning of the
AB  - (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced
AB  - genome of a type strain from the genus Thermotoga, and the sixth in the family
AB  - Thermotogaceae to be formally described in a publication. Phylogenetic analyses
AB  - do not reveal significant discrepancies between the current classification of the
AB  - group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum
AB  - significantly differs from other Thermotoga species regarding its iron-sulfur
AB  - cluster synthesis, as it contains only a minimal set of the necessary proteins.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 2,039,943 bp long chromosome with its 2,015
AB  - protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia  petrolearia and emended descriptions of the genera Methanoplanus and  Methanolacinia.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1076
EP  - 1088
VL  - 9
AB  - Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated
AB  - from a swamp composed of drilling waste near Naples, Italy, shortly
AB  - after the Archaea were recognized as a separate domain of life. Methanoplanus is
AB  - the type genus in the family Methanoplanaceae, a taxon that felt into disuse
AB  - since modern 16S rRNA gene sequences-based taxonomy was established.
AB  - Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so
AB  - far poorly characterized at the genome level. The only other type strain of the
AB  - genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned
AB  - out to be misclassified and required reclassification to Methanolacinia. Both,
AB  - Methanoplanus and Methanolacinia, needed taxonomic emendations due to a
AB  - significant deviation of the G+C content of their genomes from previously
AB  - published (pre-genome-sequence era) values. Until now genome sequences were
AB  - published for only four of the 33 species with validly published names in the
AB  - Methanomicrobiaceae. Here we describe the features of M. limicola, together with
AB  - the improved-high-quality draft genome sequence and annotation of the type
AB  - strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with
AB  - its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia
AB  - of B acteria and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 66
EP  - 75
VL  - 3
AB  - Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus
AB  - Ignisphaera. This archaeal species is characterized by a coccoid-shape and
AB  - is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic
AB  - and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral,
AB  - boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed
AB  - genome sequence of the genus Ignisphaera and the fifth genome (fourth type
AB  - strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome
AB  - with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Complete genome sequence of Olsenella uli type strain (VPI D76D-27C).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 76
EP  - 84
VL  - 3
AB  - Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus
AB  - Olsenella, which belongs to the actinobacterial family Coriobacteriaceae.
AB  - The species is of interest because it is frequently isolated from dental plaque
AB  - in periodontitis patients and can cause primary endodontic infection. The species
AB  - is a Gram-positive, non-motile and non-sporulating bacterium. The strain
AB  - described in this study was isolated from human gingival crevices. This is the
AB  - first completed sequence of the genus Olsenella and the fifth sequence from a
AB  - member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its
AB  - 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Complete genome sequence of Isosphaera pallida type strain (IS1B).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 63
EP  - 71
VL  - 4
AB  - Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the
AB  - genus Isosphaera. The species is of interest because it was the
AB  - first heterotrophic bacterium known to be phototactic, and it occupies an
AB  - isolated phylogenetic position within the Planctomycetaceae. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. This is the first complete genome sequence of a member of the genus
AB  - Isosphaera and the third of a member of the family Planctomycetaceae. The
AB  - 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763
AB  - protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Goker, M. et al.
TI  - Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 200
EP  - 209
VL  - 4
AB  - Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the
AB  - genus Odoribacter, which belongs to the family Porphyromonadaceae
AB  - in the order 'Bacteroidales'. The species is of interest because members of the
AB  - Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the
AB  - first completed genome sequence of a member of the genus Odoribacter and the
AB  - fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome
AB  - with its 3,672 protein-coding and 74 RNA genes and is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Golanowska, M.
AU  - Galardini, M.
AU  - Bazzicalupo, M.
AU  - Hugouvieux-Cotte-Pattat, N.
AU  - Mengoni, A.
AU  - Potrykus, M.
AU  - Slawiak, M.
AU  - Lojkowska, E.
TI  - Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.
JO  - Genome Announcements
PY  - 2015
SP  - e00109
EP  - e00115
VL  - 3
AB  - Dickeya solani is an important bacterial pathogen of potato cultivars in Europe.  Here, we
AB  - present the draft genome of D. solani strain IFB0099 isolated from
AB  - potato in Poland that shows a high level of pectinolytic activity and a high
AB  - virulence. This genome sequence is 5,094,121 bp and contains 4,365 protein-coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Gold, M.
AU  - Hausmann, R.
AU  - Maitra, U.
AU  - Hurwitz, J.
TI  - The enzymatic methylation of RNA and DNA, VIII.  Effects of bacteriophage  infection on the activity of the methylating enzymes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1964
SP  - 292
EP  - 297
VL  - 52
AB  - We, as well as others, have previously reported on the presence in Escherichia coli of several
AB  - enzymes which catalyze the transfer of methyl groups from S-adenosylmethionine to sRNA,
AB  - ribosomal RNA, and DNA.  Although the biological function of the methylated bases which these
AB  - enzymes produce is still obscure, the species and strain specificity of the methylation
AB  - reactions suggest that they provide a basis for a recognition mechanism.  The virulent
AB  - bacteriophage-host cell system is an example of a phenomenon involving recognition by the host
AB  - of a foreign nucleic acid; in some instances, phage DNA is rapidly synthesized while the host
AB  - DNA is rapidly degraded.  If methylated bases are involved in controlling such a recognition
AB  - mechanism, then a study of the methylated base content of DNA's of various bacteriophages
AB  - grown in different hosts might provide a clue as to the biological function of the methylating
AB  - enzymes.  In order to establish a suitable system for further investigation, we have studied
AB  - the effects of phage infection on the activities of the various methylating enzymes in the
AB  - host cell.  This communication summarizes such studies.  It has been found that while the RNA
AB  - methylases are apparently unchanged, DNA methylation activity increases markedly after
AB  - infection with T2.  In contrast, T3 infection induces an enzyme which cleaves
AB  - S-adenosylmethionine to thiomethyladenosine and homoserine.
ER  -

TY  - JOUR
AU  - Gold, M.
AU  - Hurwitz, J.
TI  - The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. V. Purification and properties of the deoxyribonucleic acid-methylating activity of Escherichia coli.
JO  - J. Biol. Chem.
PY  - 1964
SP  - 3858
EP  - 3865
VL  - 239
AB  - The classical investigations of Wyatt, and Dunn and Smith, established the existence of
AB  - 5-methylcytosine and 6-methylaminopurine as constituents of  the deoxyribonucleic acid of
AB  - higher plants and animals, and of bacteria and bacterial viruses, respectively.  Until
AB  - recently, the biochemical pathways for the  incorporation of these "trace bases" into
AB  - deoxyribonucleic acid was unknown although it had been shown that the deoxyribonucleoside
AB  - triphosphate of 5-methylcytosine could quantitatively replace deoxycytidine triphosphate as a
AB  - substrate for the enzyme deoxyribonucleic acid polymerase.  The discovery that the
AB  - glucosylation of A of the T-even bacteriophages and methylation of soluble ribonucleic acid
AB  - occurred at the polynucleotide level suggested that the incorporation of methyl groups might
AB  - also take place after polymerization in the biosynthesis of DNA.  In previous communications
AB  - from this laboratory, the presence of an enzyme activity of Escherichia coli which catalyzes
AB  - the transfer of methyl groups to cytosine and adenine moieties of a variety of DNAs has been
AB  - reported.  This reaction can be presented by the following equation.  DNA +
AB  - S-adenosylmethionine  + DNA methylase  gives methyl-DNA (containing 5-methylcytosine and
AB  - 6-methylaminopurine) + S-adenosylhomocysteine.  In this report the purification and properties
AB  - of this enzyme activity are described.
ER  -

TY  - JOUR
AU  - Gold, M.
AU  - Hurwitz, J.
AU  - Anders, M.
TI  - THE ENZYMATIC METHYLATION OF RNA AND DNA, II. ON THE SPECIES SPECIFICITY OF THE METHYLATION ENZYMES.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1963
SP  - 164
EP  - 169
VL  - 50
AB  - There is evidence that methylated bases in DNA and sRNA are not randomly distributed in
AB  - polynucleotide chains.  In wheat germ DNA, the two 6-aminopyrimidines, cytosine and
AB  - 5-methylcytosine, do not appear to substitute randomly for each other, as determined by
AB  - chemical analysis of oligonucleotides.  This specificity appears to be related to the direct
AB  - methylation of deoxycytidylate of DNA at the polynucleotide level, as has also been found to
AB  - apply to the origin of the base, 6-methylaminopurine.  These observations are in keeping with
AB  - the incorporation studies of Bessman et al. with the DNA polymerase system.  This enzyme
AB  - readily catalyzes the incorporation of dCMP and 5-methyl dCMP into DNA without distinguishing
AB  - between these deoxynucleotides, and therefore does not appear responsible for localization of
AB  - methylated bases.  In RNA, the methylated bases are uniquely localized to soluble RNA as
AB  - indicated by a large body of information.  Here, RNA polymerase, the enzyme which appears to
AB  - synthesize all RNA species from a DNA template of normal cells, lacks specificity in
AB  - differentiating between methylated bases and normal bases.  Thus, for example, ribothymidylate
AB  - is readily incorporated into RNA in place of uridylate with the same nearest neighbor
AB  - frequency.  However, the distribution of methylated bases of sRNA is not random, and analyses
AB  - of purified sRNA molecules, specific for particular amino acids, indicate that they contain
AB  - varied amounts as well as different methylated bases.  As in the case of DNA, this specific
AB  - distribution of methylated bases has been explained by the observation that methylation occurs
AB  - at the polynucleotide level rather than the mononucleotide stage.  While with DNA it appears
AB  - that methylation is catalyzed by a single enzyme, in the case of sRNA many enzymes are
AB  - involved.  To date, 5 different enzymes catalyzing specific methylation reactions with sRNA
AB  - have been isolated.
ER  -

TY  - JOUR
AU  - Gold, M.
AU  - Hurwitz, J.
AU  - Anders, M.
TI  - The enzymatic methylation of RNA and DNA.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1963
SP  - 107
EP  - 114
VL  - 11
AB  - The methionine origin of the methyl group of the "trace bases" of Escherichia coli and ascites
AB  - cells has been demonstrated by Borek et al. and Biswas et al.  Fleissner and Borek have
AB  - recently reported that extracts of E. coli catalyse the transfer of the methyl group from
AB  - C14-methyl-labeled methionine to E. coli soluble RNA provided this S-RNA was isolated from a
AB  - methionine auxotroph which continues to synthesize RNA when deprived of its essential amino
AB  - acid.  Although the DNA dependent RNA polymerase system incorporated ribothymidylate from
AB  - ribothymidine triphosphate into RNA specifically in place of uridylate, no demonstrable
AB  - phosphorylation of ribothymidylate was detected in extracts of E. coli.  These observations,
AB  - and especially the report of Fleissner and Borek, suggest that the trace nucleotide
AB  - ribothymidylate, is synthesized at the polynucleotide level.
ER  -

TY  - JOUR
AU  - Gold, S.E.
AU  - Blacutt, A.A.
AU  - Meinersmann, R.J.
AU  - Bacon, C.W.
TI  - Whole-Genome Shotgun Sequence of Bacillus mojavensis Strain RRC101, an Endophytic Bacterium Antagonistic to the Mycotoxigenic Endophytic Fungus Fusarium  verticillioides.
JO  - Genome Announcements
PY  - 2014
SP  - e01090
EP  - e01014
VL  - 2
AB  - Here, we report the whole-genome shotgun sequence of Bacillus mojavensis strain RRC101,
AB  - isolated from a maize kernel. This strain is antagonistic to the
AB  - mycotoxigenic plant pathogen Fusarium verticillioides and grows within maize
AB  - tissue, suggesting potential as an endophytic biocontrol agent.
ER  -

TY  - JOUR
AU  - Goldfarb, T.
AU  - Sberro, H.
AU  - Weinstock, E.
AU  - Cohen, O.
AU  - Doron, S.
AU  - Charpak-Amikam, Y.
AU  - Afik, S.
AU  - Ofir, G.
AU  - Sorek, R.
TI  - BREX is a novel phage resistance system widespread in microbial genomes.
JO  - EMBO J.
PY  - 2015
SP  - 169
EP  - 183
VL  - 34
AB  - The perpetual arms race between bacteria and phage has resulted in the evolution  of efficient
AB  - resistance systems that protect bacteria from phage infection. Such
AB  - systems, which include the CRISPR-Cas and restriction-modification systems, have
AB  - proven to be invaluable in the biotechnology and dairy industries. Here, we
AB  - report on a six-gene cassette in Bacillus cereus which, when integrated into the
AB  - Bacillus subtilis genome, confers resistance to a broad range of phages,
AB  - including both virulent and temperate ones. This cassette includes a putative
AB  - Lon-like protease, an alkaline phosphatase domain protein, a putative RNA-binding
AB  - protein, a DNA methylase, an ATPase-domain protein, and a protein of unknown
AB  - function. We denote this novel defense system BREX (Bacteriophage Exclusion) and
AB  - show that it allows phage adsorption but blocks phage DNA replication.
AB  - Furthermore, our results suggest that methylation on non-palindromic TAGGAG
AB  - motifs in the bacterial genome guides self/non-self discrimination and is
AB  - essential for the defensive function of the BREX system. However, unlike
AB  - restriction-modification systems, phage DNA does not appear to be cleaved or
AB  - degraded by BREX, suggesting a novel mechanism of defense. Pan genomic analysis
AB  - revealed that BREX and BREX-like systems, including the distantly related Pgl
AB  - system described in Streptomyces coelicolor, are widely distributed in ~10% of
AB  - all sequenced microbial genomes and can be divided into six coherent subtypes in
AB  - which the gene composition and order is conserved. Finally, we detected a phage
AB  - family that evades the BREX defense, implying that anti-BREX mechanisms may have
AB  - evolved in some phages as part of their arms race with bacteria.
ER  -

TY  - JOUR
AU  - Golding, G.R.
AU  - Bryden, L.
AU  - Levett, P.N.
AU  - McDonald, R.R.
AU  - Wong, A.
AU  - Graham, M.R.
AU  - Tyler, S.
AU  - Van Domselaar, G.
AU  - Mabon, P.
AU  - Kent, H.
AU  - Butaye, P.
AU  - Smith, T.C.
AU  - Kadlec, K.
AU  - Schwarz, S.
AU  - Weese, S.J.
AU  - Mulvey, M.R.
TI  - Whole-Genome Sequence of Livestock-Associated ST398 Methicillin-Resistant Staphylococcus aureus Isolated from Humans in Canada.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6627
EP  - 6628
VL  - 194
AB  - Despite reports of high colonization rates of ST398 livestock-associated methicillin-resistant
AB  - Staphylococcus aureus (LA-MRSA) among pigs and pig farmers,
AB  - the incidence of LA-MRSA infection in the general population in Canada appears to
AB  - be rare in comparison to that in some European countries. In this study, the
AB  - complete genome sequence of a Canadian representative LA-MRSA isolate (08BA02176)
AB  - from a human postoperative surgical site infection was acquired and compared to
AB  - the sequenced genome of an LA-MRSA isolate (S0385) from Europe to identify
AB  - genetic traits that may explain differences in the success of these particular
AB  - strains in some locales.
ER  -

TY  - JOUR
AU  - Golding, M.C.
AU  - Westhusin, M.E.
TI  - Analysis of DNA (cytosine 5) methyltransferase mRNA sequence and expression in bovine preimplantation embryos, fetal and adult tissues.
JO  - Gene Expr. Patterns
PY  - 2003
SP  - 551
EP  - 558
VL  - 3
AB  - Mammalian preimplantation development is a critical stage for establishment of the genomic
AB  - methylation pattern and proper function of
AB  - the enzymes responsible for this appear essential for normal development.
AB  - To date, the vast majority of work concerning the developmental expression
AB  - of the DNA cytosine 5-methyltansferases (Dnmts) has been conducted in
AB  - mice. Here we report the sequence and expression of the Dnmt family during
AB  - bovine preimplantation and fetal development. Bovine Dnmt mRNAs display
AB  - strong sequence homology to those of human and mouse and similar to other
AB  - species, exist as multiple isoforms. Two of these splice variants, which
AB  - have been termed Dnmt2gamma and Dnmt3a4, represent previously unreported
AB  - sequence combinations. Work presented here demonstrates early bovine
AB  - embryos express mRNA coding for the somatic form of Dnmt1 and that this
AB  - transcript fractionates with the ribosome. Unlike the murine model, mRNA
AB  - encoding the de novo methyltransferases, Dnmt3a and 3b are present during
AB  - preimplantation development and can also be found in the ribosomal
AB  - subcellular fraction. Further, results of Real Time PCR analysis indicate
AB  - significant differences in Dnmt mRNA expression levels exist among
AB  - different tissue types as well as between fetal and adult stages.
AB  - Recently, it has been postulated that the cause of abnormal methylation
AB  - observed in cloned embryos may be due in part to misexpression of the
AB  - Dnmt1o isoform during preimplantation development. Work presented here
AB  - raises new and significant hypotheses that must be considered both
AB  - regarding the cadre of DNA methyltranferases that direct epigenetic
AB  - programming during normal development and regarding the implication of
AB  - abnormal DNMT expression in cloned embryos.
ER  -

TY  - JOUR
AU  - Goldstone, R.J.
AU  - Amos, M.
AU  - Talbot, R.
AU  - Schuberth, H.J.
AU  - Sandra, O.
AU  - Sheldon, I.M.
AU  - Smith, D.G.
TI  - Draft Genome Sequence of Trueperella pyogenes, Isolated from the Infected Uterus  of a Postpartum Cow with Metritis.
JO  - Genome Announcements
PY  - 2014
SP  - e00194
EP  - e00114
VL  - 2
AB  - Trueperella pyogenes is a common commensal bacterium and an opportunistic pathogen associated
AB  - with chronic purulent disease, particularly in ruminants. We report here the genome sequence
AB  - of a T. pyogenes isolate from a severe case of bovine metritis. This is the first full record
AB  - of a T. pyogenes genome.
ER  -

TY  - JOUR
AU  - Goldstone, R.J.
AU  - Talbot, R.
AU  - Schuberth, H.J.
AU  - Sandra, O.
AU  - Sheldon, I.M.
AU  - Smith, D.G.
TI  - Draft Genome Sequence of Escherichia coli MS499, Isolated from the Infected Uterus of a Postpartum Cow with Metritis.
JO  - Genome Announcements
PY  - 2014
SP  - e00217
EP  - e00214
VL  - 2
AB  - Specific Escherichia coli strains associated with bovine postpartum uterine infection have
AB  - recently been described. Many recognized virulence factors are
AB  - absent in these strains; therefore, to define a prototypic strain, we report here
AB  - the genome sequence of E. coli isolate MS499 from a cow with the postpartum
AB  - disease metritis.
ER  -

TY  - JOUR
AU  - Golemboski, D.
AU  - Eardly, B.D.
TI  - Draft Genome Sequences of Respiratory and Urinary Tract Isolates of Acinetobacter baumannii from the Same Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00692
EP  - e00614
VL  - 2
AB  - Acinetobacter baumannii is a frequent hospital-acquired human pathogen. This report describes
AB  - the draft genome sequences of two distinct A. baumannii clinical
AB  - isolates from the same patient. A comparison of the genomes revealed differences
AB  - in antibiotic resistance and will enable the determination of genomic differences
AB  - responsible for virulence at each body site.
ER  -

TY  - JOUR
AU  - Golikova, L.N.
AU  - Gutorov, V.V.
AU  - Evdokimov, A.A.
AU  - Shchelkunov, S.N.
AU  - Gonchar, D.A.
AU  - Okhapkina, S.S.
AU  - Degtyarev, S.K.
AU  - Netesova, N.A.
TI  - M.BstF5I-4, the fourth DNA-methyltransferase of the BstF5I restriction-modification system from Bacillus stearothermophilus F5.
JO  - Bioorg. Khim.
PY  - 2002
SP  - 84
EP  - 86
VL  - 28
AB  - The fourth DNA-methyltransferase of the BstF5I restriction-modification (RM) system from
AB  - Bacillus stearothermophilus F5 (M.BstF5I-4) was discovered, which modifies the adenine residue
AB  - within the upper strand of the recognition site 5'-GGATG-3'/5'-CATCC-3'. Thus, unlike
AB  - other known RM systems, the BstF5I RM system comprises four genes encoding
AB  - DNA-methyltransferases, three of which possess the same substrate specificity and methylate
AB  - adenine within the 5'-GGATG sequence.
ER  -

TY  - JOUR
AU  - Golikova, L.N.
AU  - Netosova, N.A.
AU  - Gutorov, V.V.
AU  - Belavin, P.A.
AU  - Abdurashitov, M.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Multiplicity of site-specific DNA-methyltransferases of the BstF5I restriction modification system from Bacillus stearothermophilus F5.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 443
EP  - 447
VL  - 34
AB  - A fragment located downstream of the genes for DNA methyltransferases of Bacillus
AB  - stearothermophilus F5 (M.BstF5I-I and M.BstF5I-2) was
AB  - sequenced. The fragment contains a gene for another methylase,
AB  - M.BstF5I-3, structurally and functionally similar to the N-terminal
AB  - domain of M.FokI. Thus, in contrast to other restriction-modification
AB  - systems, the BstF5I system includes three methylases, two being
AB  - homologous to the individual M.FokI domains.
ER  -

TY  - JOUR
AU  - Goll, M.G.
AU  - Bestor, T.H.
TI  - Eukaryotic cytosine methyltransferases.
JO  - Annu. Rev. Biochem.
PY  - 2005
SP  - 481
EP  - 514
VL  - 74
AB  - Large-genome eukaryotes use heritable cytosine methylation to silence promoters, especially
AB  - those associated with transposons and imprinted
AB  - genes. Cytosine methylation does not reinforce or replace ancestral
AB  - gene regulation pathways but instead endows methylated genomes with the
AB  - ability to repress specific promoters in a manner that is buffered
AB  - against changes in the internal and external environment. Recent
AB  - studies have shown that the targeting of de novo methylation depends on
AB  - multiple inputs; these include the interaction of repeated sequences,
AB  - local states of histone lysine methylation, small RNAs and components
AB  - of the RNAi pathway, and divergent and catalytically inert cytosine
AB  - methyltransferase homologues that have acquired regulatory roles. There
AB  - are multiple families of DNA (cytosine-5) methyltransferases in
AB  - eukaryotes, and each family appears to be controlled by different
AB  - regulatory inputs. Sequence-specific DNA-binding proteins, which
AB  - regulate most aspects of gene expression, do not appear to be involved
AB  - in the establishment or maintenance of genomic methylation patterns.
ER  -

TY  - JOUR
AU  - Golneshin, A.
AU  - Adetutu, E.
AU  - Ball, A.S.
AU  - May, B.K.
AU  - Van, T.T.
AU  - Smith, A.T.
TI  - Complete Genome Sequence of Lactobacillus plantarum Strain B21, a Bacteriocin-Producing Strain Isolated from Vietnamese Fermented Sausage Nem Chua.
JO  - Genome Announcements
PY  - 2015
SP  - e00055
EP  - e00015
VL  - 3
AB  - Lactobacillus plantarum strain B21 was isolated from Vietnamese sausage (nem chua) and
AB  - demonstrated broad antimicrobial activity due to the production of
AB  - bacteriocins. Here, we report the complete genome sequence of this strain
AB  - (3,284,260 bp).
ER  -

TY  - JOUR
AU  - Golneshin, A.
AU  - Gor, M.C.
AU  - Van, T.T.H.
AU  - May, B.
AU  - Moore, R.J.
AU  - Smith, A.T.
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain A6, a Strong Acid Producer Isolated from a Vietnamese Fermented Sausage (Nem Chua).
JO  - Genome Announcements
PY  - 2017
SP  - e00987
EP  - e00917
VL  - 5
AB  - Lactobacillus plantarum strain A6, a strong acid producer, was isolated from a Vietnamese
AB  - fermented sausage (nem chua). Here, we report the genome sequence of
AB  - this strain (3,368,579 bp).
ER  -

TY  - JOUR
AU  - Gololobova, N.S.
AU  - Okhapkina, S.S.
AU  - Abdurashitov, M.A.
AU  - Degtyarev, S.K.
TI  - Determination and analysis of the primary structure of NM.BstSEI operon from Bacillus stearothermophilus SE-589 which produces N.BstSEI site-specific nickase.
JO  - Mol. Biol. (Mosk)
PY  - 2005
SP  - 960
EP  - 964
VL  - 39
AB  - Nucleotide sequence of Bacillus stearothermophilus SE-589 DNA fragment which includes an
AB  - operon for site-specific NM-system with a gene for BstSEI nickase has been determined.
AB  - Analysis of the regions adjacent to nickase gene has revealed two genes encoding DNA
AB  - methyltransferases, which belong to different classes. Three genes which form system operon
AB  - are separated with short open reading frames (ORFs). Analysis of these ORFs has shown that
AB  - they encode polypeptides which are homologous to different parts of BstSEI nickase, NatB
AB  - protein and arginase. A difference in GC-content of the beginning and ending regions of the
AB  - cloned DNA fragment as well as presence of short ORFs similar to genes for known proteins may
AB  - indicate that NM.BstSEI system operon has evolved by horizonthal DNA transfer.
ER  -

TY  - JOUR
AU  - Golomidova, A.K.
AU  - Kulikov, E.E.
AU  - Kudryavtseva, A.V.
AU  - Letarov, A.V.
TI  - Complete Genome Sequence of Escherichia coli Bacteriophage PGT2.
JO  - Genome Announcements
PY  - 2018
SP  - e01370
EP  - e01317
VL  - 6
AB  - Bacteriophage PGT2 was isolated from horse feces by using an uncharacterized Escherichia coli
AB  - strain, 7s, isolated from the same sample as the host.
AB  - Bacteriophage PGT2 and a related phage, phiKT, which was previously isolated from
AB  - the same source, are likely to represent a new genus within the Autographivirinae
AB  - subfamily of the Podoviridae family of viruses.
ER  -

TY  - JOUR
AU  - Golovenko, D.
AU  - Manakova, E.
AU  - Tamulaitiene, G.
AU  - Grazulis, S.
AU  - Siksnys, V.
TI  - Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 6613
EP  - 6624
VL  - 37
AB  - EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T);
AB  - however, it shows no activity on a single recognition site. To activate cleavage it requires
AB  - binding of an additional target site as an allosteric effector. EcoRII dimer consists of three
AB  - structural units: a central catalytic core, made from two copies of the C-terminal domain
AB  - (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report
AB  - DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically
AB  - different structural mechanisms to interact with the effector and substrate DNA. The catalytic
AB  - EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the
AB  - CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically
AB  - in a single defined orientation which is determined by specific hydrogen bonding and van der
AB  - Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the
AB  - target site recognition is shared by the large class of higher plant transcription factors of
AB  - the B3 superfamily.
ER  -

TY  - JOUR
AU  - Golovenko, D.
AU  - Manakova, E.
AU  - Zakrys, L.
AU  - Zaremba, M.
AU  - Sasnauskas, G.
AU  - Grazulis, S.
AU  - Siksnys, V.
TI  - Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 4113
EP  - 4122
VL  - 42
AB  - The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and
AB  - BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common
AB  - structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the
AB  - plant TFs recognize a diverse set of target sequences. The only available
AB  - co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence
AB  - 5'-CCTGG-3'). In order to understand the structural and molecular mechanisms of
AB  - specificity of B3 DBDs, we have solved the crystal structure of BfiI-C
AB  - (recognition sequence 5'-ACTGGG-3') complexed with 12-bp cognate oligoduplex.
AB  - Structural comparison of BfiI-C-DNA and EcoRII-N-DNA complexes reveals a
AB  - conserved DNA-binding mode and a conserved pattern of interactions with the
AB  - phosphodiester backbone. The determinants of the target specificity are located
AB  - in the loops that emanate from the conserved structural core. The BfiI-C-DNA
AB  - structure presented here expands a range of templates for modeling of the
AB  - DNA-bound complexes of the B3 family of plant TFs.
ER  -

TY  - JOUR
AU  - Goltsman, D.S.
AU  - Denef, V.J.
AU  - Singer, S.W.
AU  - VerBerkmoes, N.C.
AU  - Lefsrud, M.
AU  - Mueller, R.S.
AU  - Dick, G.J.
AU  - Sun, C.L.
AU  - Wheeler, K.E.
AU  - Zemla, A.
AU  - Baker, B.J.
AU  - Hauser, L.
AU  - Land, M.
AU  - Shah, M.B.
AU  - Thelen, M.P.
AU  - Hettich, R.L.
AU  - Banfield, J.F.
TI  - Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing 'Leptospirillum rubarum' (Group II) and 'Leptospirillum ferrodiazotrophum' (Group III) bacteria in acid mine drainage biofilms.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 4599
EP  - 4615
VL  - 75
AB  - We analyzed near-complete population (composite) genomic sequences for
AB  - coexisting acidophilic iron-oxidizing Leptospirillum group II and III
AB  - bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a
AB  - Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community
AB  - proteomic analysis of the genomically characterized sample and two other
AB  - biofilms identified 64.6% and 44.9% of the predicted proteins of
AB  - Leptospirillum groups II and III, respectively, and 20% of the predicted
AB  - plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity
AB  - and >60% of their genes, including integrated plasmid-like regions. The
AB  - extrachromosomal plasmid carries conjugation genes with detectable
AB  - sequence similarity to genes in the integrated conjugative plasmid, but
AB  - only those on the extrachromosomal element were identified by proteomics.
AB  - Both bacterial groups have genes for community-essential functions,
AB  - including carbon fixation and biosynthesis of vitamins, fatty acids, and
AB  - biopolymers (including cellulose); proteomic analyses reveal these
AB  - activities. Both Leptospirillum types have multiple pathways for osmotic
AB  - protection. Although both are motile, signal transduction and
AB  - methyl-accepting chemotaxis proteins are more abundant in Leptospirillum
AB  - group III, consistent with its distribution in gradients within biofilms.
AB  - Interestingly, Leptospirillum group II uses a methyl-dependent and
AB  - Leptospirillum group III a methyl-independent response pathway. Although
AB  - only Leptospirillum group III can fix nitrogen, these proteins were not
AB  - identified by proteomics. The abundances of core proteins are similar in
AB  - all communities, but the abundance levels of unique and shared proteins of
AB  - unknown function vary. Some proteins unique to one organism were highly
AB  - expressed and may be key to the functional and ecological differentiation
AB  - of Leptospirillum groups II and III.
ER  -

TY  - JOUR
AU  - Golubov, A.
AU  - Neubauer, H.
AU  - Nolting, C.
AU  - Heesemann, J.
AU  - Rakin, A.
TI  - Structural organization of the pFra virulence-associated plasmid of rhamnose-positive Yersinia pestis.
JO  - Infect. Immun.
PY  - 2004
SP  - 5613
EP  - 5621
VL  - 72
AB  - The 137,036-bp plasmid pG8786 from rhamnose-positive Yersinia pestis G8786
AB  - isolated from the high mountainous Caucasian plague focus in Georgia is an
AB  - enlarged form of the pFra virulence-associated plasmid containing genes
AB  - for synthesis of the antigen fraction 1 and phospholipase D. In addition
AB  - to the completely conserved genes of the pFra backbone, pG8786 contains
AB  - two large regions consisting of 4,642 and 32,617 bp, designated regions 1
AB  - and 2, respectively. Region 1 retains a larger part of Salmonella enterica
AB  - serovar Typhi plasmid pHCM2 resembling the backbone of pFra replicons,
AB  - while region 2 contains 25 open reading frames with high levels of
AB  - similarity to the transfer genes of the F-like plasmids. Surprisingly,
AB  - region 1 is also present in the pFra plasmid of avirulent Y. pestis strain
AB  - 91001 isolated in Inner Mongolia, People's Republic of China. Despite the
AB  - fact that some genes typically involved in conjugative transfer of the
AB  - F-like replicons are missing in pG8786, we cannot exclude the possibility
AB  - that pG8786 might be transmissive under certain conditions. pG8786 seems
AB  - to be an ancient form of the pFra group of plasmids that were conserved
AB  - due to the strict geographical isolation of rhamnose-positive Y. pestis
AB  - strains in the high mountainous Caucasian plague locus.
ER  -

TY  - JOUR
AU  - Golyshin, P.N.
AU  - Werner, J.
AU  - Chernikova, T.N.
AU  - Tran, H.
AU  - Ferrer, M.
AU  - Yakimov, M.M.
AU  - Teeling, H.
AU  - Golyshina, O.V.
TI  - Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T).
JO  - Genome Announcements
PY  - 2013
SP  - e00141
EP  - e00113
VL  - 1
AB  - Thalassolituus oleivorans is one of the most prevalent marine gammaproteobacteria in microbial
AB  - communities, emerging after oil spills in coastal, estuarine, and
AB  - surface seawaters. Here, we present the assembled genome of strain T. oleivorans
AB  - MIL-1 (DSM 14913(T)), which is 3,920,328 bp with a G+C content of 46.6%.
ER  -

TY  - JOUR
AU  - Golyshina, O.V.
AU  - Toshchakov, S.V.
AU  - Makarova, K.S.
AU  - Gavrilov, S.N.
AU  - Korzhenkov, A.A.
AU  - La Cono, V.
AU  - Arcadi, E.
AU  - Nechitaylo, T.Y.
AU  - Ferrer, M.
AU  - Kublanov, I.V.
AU  - Wolf, Y.I.
AU  - Yakimov, M.M.
AU  - Golyshin, P.N.
TI  - 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.
JO  - Nat. Commun.
PY  - 2017
SP  - 60
EP  - 60
VL  - 8
AB  - Intriguing, yet uncultured 'ARMAN'-like archaea are metabolically dependent on other members
AB  - of the microbial community. It remains uncertain though which hosts
AB  - they rely upon, and, because of the lack of complete genomes, to what extent.
AB  - Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with
AB  - Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic
AB  - streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in
AB  - the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome
AB  - points at severe voids in central metabolic pathways, indicating dependence on
AB  - the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different
AB  - sites and shotgun sequence data of Parys Mountain samples suggests an extensive
AB  - genetic exchange between Mia14 and hosts in situ. Within the subset of organisms
AB  - with high-quality genomic assemblies representing the 'DPANN' superphylum, the
AB  - Mia14 lineage has had the largest gene flux, with dozens of genes gained that are
AB  - implicated in the host interaction.In the absence of complete genomes, the
AB  - metabolic capabilities of uncultured ARMAN-like archaea have been uncertain.
AB  - Here, Golyshina et al. apply an enrichment culture technique and find that the
AB  - ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways,
AB  - suggesting dependence on the host archaeon Cuniculiplasma divulgatum.
ER  -

TY  - JOUR
AU  - Gomes, L.H.
AU  - Otto, T.D.
AU  - Vasconcellos, E.A.
AU  - Ferrao, P.M.
AU  - Maia, R.M.
AU  - Moreira, A.S.
AU  - Ferreira, M.A.
AU  - Castello-Branco, L.R.
AU  - Degrave, W.M.
AU  - Mendonca-Lima, L.
TI  - Genome Sequence of Mycobacterium bovis BCG Moreau, the Brazilian Vaccine Strain against Tuberculosis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5600
EP  - 5601
VL  - 193
AB  - Mycobacterium bovis bacillus Calmette-Guerin (BCG) is the only vaccine available against
AB  - tuberculosis, and the strains used worldwide represent a
AB  - family of daughter strains with distinct genotypic characteristics. Here
AB  - we report the complete genome sequence of M. bovis BCG Moreau, the strain
AB  - in continuous use in Brazil for vaccine production since the 1920s.
ER  -

TY  - JOUR
AU  - Gomes, L.L.
AU  - Marin, M.A.
AU  - Lasunskaia, E.
AU  - Vasconcellos, S.E.
AU  - Araujo, M.E.
AU  - de Miranda, A.B.
AU  - Suffys, P.N.
TI  - Genome Comparison of an Ancestral Isolate and a Modern Isolate of Mycobacterium tuberculosis of the Beijing Lineage from Sao Paulo, Brazil.
JO  - Genome Announcements
PY  - 2015
SP  - e01129
EP  - e01115
VL  - 3
AB  - Mycobacterium tuberculosis of the Bejing subtype (MtbB) is transmitted efficiently in high
AB  - burden countries for this genotype. A higher virulence was associated with isolates of the
AB  - 'modern' Beijing genotype sub-lineages when compared to 'ancient' ones. Here, we report
AB  - the full genomes of the strain representing these two genotypes from Brazil, a country with a
AB  - low incidence of MtbB.
ER  -

TY  - JOUR
AU  - Gomez, O.M.
AU  - Alvarez, L.C.
AU  - Munoz, J.F.
AU  - Misas, E.
AU  - Gallo, J.E.
AU  - Jimenez, M.D.P.
AU  - Arango, M.
AU  - McEwen, J.G.
AU  - Hernandez, O.
AU  - Clay, O.K.
TI  - Draft Genome Sequences of Two Sporothrix schenckii Clinical Isolates Associated with Human Sporotrichosis in Colombia.
JO  - Genome Announcements
PY  - 2018
SP  - e00495
EP  - e00418
VL  - 6
AB  - Sporothrix schenckii is a thermodimorphic fungal pathogen with a high genetic diversity. In
AB  - this work, we present the assembly and similarity analysis of the
AB  - whole-genome sequences of two clinical isolates from Colombia of S.
AB  - schenckiisensu stricto.
ER  -

TY  - JOUR
AU  - Gomez, P.
AU  - Ribas-Aparicio, R.M.
AU  - Pelaez, A.I.
AU  - Gomez, A.
AU  - Rodicio, M.R.
TI  - Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola.
JO  - Biochim. Biophys. Acta
PY  - 1997
SP  - 261
EP  - 266
VL  - 1351
AB  - The gene (xamIM) encoding the DNA methyltransferase of the XamI restriction-modification
AB  - system from Xanthomonas campestris pv. amaranthicola (M.XamI) has been cloned in Escherichia
AB  - coli and its nucleotide sequence determined.  The sequence predicts a protein of 527 amino
AB  - acids that contains nine conserved motifs characteristic of DNA amino methyltransferases.  In
AB  - fact, M.XamI shows significant similarity with N6-adenine methyltransferases of the gamma
AB  - group of amino methyltransferases, including M.SalI (from the isoschizomeric SalI
AB  - restriction-modification system) and M.TaqI (the only N6-adenine methyltransferase for which a
AB  - three-dimensional structure is available).  M.XamI and M.SalI share two highly conserved
AB  - regions within the C-terminal domain, one of which aligns with one of the DNA recognition
AB  - loops proposed for M.TaqI.  Analysis of the chromosomal DNA adjacent to xamIM led to the
AB  - identification of an additional ORF (275 codons), downstream, in the same transcriptional
AB  - orientation. Although some limited similarities between the SalI restriction enzyme and the
AB  - product deduced from this ORF were found, the clone carrying xamIM did not express the
AB  - expected endonuclease function.
ER  -

TY  - JOUR
AU  - Gomez, P.
AU  - Ribas-Aparicio, R.M.
AU  - Pelaez, A.I.
AU  - Rodicio, M.R.
TI  - Characterization of IS1389, a new member of the IS3 family of insertion sequences isolated from Xanthomonas campestris pv. amaranthicola.
JO  - Arch. Microbiol.
PY  - 1999
SP  - 15
EP  - 21
VL  - 172
AB  - IS1389, a new insertion sequence belonging to the IS3 family, has been identified in
AB  - Xanthomonas campestris pv. amaranthicola. The genome of this bacterium contains at least 11
AB  - copies of the element, whereas no hybridizing sequences were detected in other Xanthomonas
AB  - species [X. axonopodis, X. fragaridae, X. phaseoli, and X. (Stenotrophomonas) maltophila]. Two
AB  - nearly identical copies of the element (IS1389-A and IS1389-B) were characterized. According
AB  - to analysis of sequence alignments and similar structural features, IS1389 belongs to the
AB  - IS407 subgroup of the IS3 family, which duplicates 4 bp of target DNA upon insertion. IS1389-A
AB  - was found in the proximity of the modification gene of the XamI restriction-modification
AB  - system.
ER  -

TY  - JOUR
AU  - Gomez-Alvarez, V.
AU  - Pfaller, S.
AU  - Revetta, R.P.
TI  - Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System  Simulator.
JO  - Genome Announcements
PY  - 2016
SP  - e00183
EP  - e00116
VL  - 4
AB  - We report the draft genomes of twoSphingopyxissp. strains isolated from a chloraminated
AB  - drinking water distribution system simulator. Both strains are
AB  - ubiquitous residents and early colonizers of water distribution systems. Genomic
AB  - annotation identified a class 1 integron (intI1) gene associated with sulfonamide
AB  - (sul1) and puromycin (pac) antibiotic resistance genes.
ER  -

TY  - JOUR
AU  - Gomez-Alvarez, V.
AU  - Revetta, R.P.
TI  - Whole-Genome Sequences of Four Strains Closely Related to Members of the Mycobacterium chelonae Group, Isolated from Biofilms in a Drinking Water  Distribution System Simulator.
JO  - Genome Announcements
PY  - 2016
SP  - e01539
EP  - e01515
VL  - 4
AB  - We report here the draft genome sequences of four Mycobacterium chelonae strains  from
AB  - biofilms subjected to a 'chlorine burn' in a chloraminated drinking water
AB  - distribution system simulator. These opportunistic pathogens have been detected
AB  - in hospital and municipal water distribution systems, in which biofilms have been
AB  - recognized as an important factor for their persistence.
ER  -

TY  - JOUR
AU  - Gomez-Alvarez, V.
AU  - Revetta, R.P.
TI  - Draft Genome Sequences of Six Mycobacterium immunogenum Strains Obtained from a Chloraminated Drinking Water Distribution System Simulator.
JO  - Genome Announcements
PY  - 2016
SP  - e01538
EP  - e01515
VL  - 4
AB  - We report here the draft genome sequences of six Mycobacterium immunogenum strains isolated
AB  - from a chloraminated drinking water distribution system
AB  - simulator subjected to changes in operational parameters. M. immunogenum, a
AB  - rapidly growing mycobacterium previously reported to be the cause of
AB  - hypersensitivity pneumonitis from contaminated metalworking fluid aerosols, is
AB  - becoming a public health concern.
ER  -

TY  - JOUR
AU  - Gomez-Consarnau, L.
AU  - Akram, N.
AU  - Lindell, K.
AU  - Pedersen, A.
AU  - Neutze, R.
AU  - Milton, D.L.
AU  - Gonzalez, J.M.
AU  - Pinhassi, J.
TI  - Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation.
JO  - PLoS Biology
PY  - 2010
SP  - E1000358
EP  - E1000358
VL  - 8
AB  - Proteorhodopsins are globally abundant photoproteins found in bacteria in the
AB  - photic zone of the ocean. Although their function as proton pumps with
AB  - energy-yielding potential has been demonstrated, the ecological role of
AB  - proteorhodopsins remains largely unexplored. Here, we report the presence and
AB  - function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered
AB  - through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio
AB  - strain AND4 obtained proteorhodopsin through lateral gene transfer, which could
AB  - have modified the ecology of this marine bacterium. We demonstrate an increased
AB  - long-term survival of AND4 when starved in seawater exposed to light rather than
AB  - held in darkness. Furthermore, mutational analysis provides the first direct
AB  - evidence, to our knowledge, linking the proteorhodopsin gene and its biological
AB  - function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness
AB  - advantage to marine bacteria, representing a novel mechanism for bacterioplankton
AB  - to endure frequent periods of resource deprivation at the ocean's surface.
ER  -

TY  - JOUR
AU  - Gomez-Consarnau, L.
AU  - Gonzalez, J.M.
AU  - Coll-Llado, M.
AU  - Gourdon, P.
AU  - Pascher, T.
AU  - Neutze, R.
AU  - Pedros-Alio, C.
AU  - Pinhassi, J.
TI  - Light stimulates growth of proteorhodopsin-containing marine Flavobacteria.
JO  - Nature
PY  - 2007
SP  - 210
EP  - 213
VL  - 445
AB  - Proteorhodopsins are bacterial light-dependent proton pumps. Their discovery
AB  - within genomic material from uncultivated marine bacterioplankton caused
AB  - considerable excitement because it indicated a potential phototrophic function
AB  - within these organisms, which had previously been considered strictly
AB  - chemotrophic. Subsequent studies established that sequences encoding
AB  - proteorhodopsin are broadly distributed throughout the world's oceans.
AB  - Nevertheless, the role of proteorhodopsins in native marine bacteria is still
AB  - unknown. Here we show, from an analysis of the complete genomes of three marine
AB  - Flavobacteria, that cultivated bacteria in the phylum Bacteroidetes, one of the
AB  - principal components of marine bacterioplankton, contain proteorhodopsin.
AB  - Moreover, growth experiments in both natural and artificial seawater (low in
AB  - labile organic matter, which is typical of the world's oceans) establish that
AB  - exposure to light results in a marked increase in the cell yield of one such
AB  - bacterium (Dokdonia sp. strain MED134) when compared with cells grown in
AB  - darkness. Thus, our results show that the phototrophy conferred by
AB  - proteorhodopsin can provide critical amounts of energy, not only for respiration
AB  - and maintenance but also for active growth of marine bacterioplankton in their
AB  - natural environment.
ER  -

TY  - JOUR
AU  - Gomez-Eichelmann, M.C.
TI  - Deoxyribonucleic Acid Adenine and Cytosine Methylation in Salmonella typhimurium  and Salmonella typhi.
JO  - J. Bacteriol.
PY  - 1979
SP  - 574
EP  - 579
VL  - 140
AB  - The methylations of adenine in the sequence - GATC - and of the second cytosine in  the
AB  - sequence - [Formula: see text] - were studied in Salmonella typhimurium and
AB  - in Salmonella typhi. The study was carried out by using endonucleases which
AB  - restrict the plasmid pBR322 by cleavage at the sequences - GATC - (DpnI and MboI)
AB  - and - [Formula: see text] - (EcoRII). The restriction patterns obtained for this
AB  - plasmid isolated from transformed S. typhimurium and S. typhi were compared with
AB  - those of pBR322 isolated from Escherichia coli K-12. In E. coli K-12, adenines at
AB  - the sequence - GATC - and the second cytosines at - [Formula: see text] - are met
AB  - hylated by enzymes coded for by the genes dam and dem, respectively. From
AB  - comparison of the restriction patterns obtained, it is concluded that S.
AB  - typhimurium and S. typhi contain genes responsible for deoxyribonucleic acid
AB  - methylation equivalent to E. coli K-12 genes dam and dcm.Images:
ER  -

TY  - JOUR
AU  - Gomez-Eichelmann, M.C.
AU  - Levy-Mustri, A.
AU  - Ramirez-Santos, J.
TI  - Presence of 5-methylcytosine in CC(A/T)GG sequences (Dcm methylation) in DNAs from different bacteria.
JO  - J. Bacteriol.
PY  - 1991
SP  - 7692
EP  - 7694
VL  - 173
AB  - The presence of CC(A/T)GG sequences with methylated internal cytosine (Dcm methylation) was
AB  - determined in DNA from different genera of eubacteria. This methylation was studied by using
AB  - restriction enzymes EcoRII and BstNI, which cleave unmethylated or methylated CC(A/T)GG
AB  - sequences. Dcm methylation was only detected in genera of the family Enterobacteriaceae
AB  - closely related to Escherichia: Shigella, Citrobacter, Salmonella, and Klebsiella.
ER  -

TY  - JOUR
AU  - Gomez-Eichelmann, M.C.
AU  - Ramirez-Santos, J.
TI  - Methylated cytosine at Dcm (CCA/TGG) sites in Escherichia coli:  Possible function and evolutionary implications.
JO  - J. Mol. Evol.
PY  - 1993
SP  - 11
EP  - 24
VL  - 37
AB  - The frequency and distribution of methylated cytosine (5-MeC) at CCA/TGG (Dcm sites) in 49 E.
AB  - coli DNA loci (207,530 bp) were determined. Principal observations of this analysis were: (1)
AB  - Dcm frequency was higher than expected from random occurrence but lower than calculated with
AB  - Markov chain analysis; (2) CCTGG sites were found more frequently in coding than in noncoding
AB  - regions, while the opposite was true for CCAGG sites; (3) Dcm site distribution does not
AB  - exhibit any identifiably regular pattern on the chromosome; (4) Dcm sites at oriC are probably
AB  - not important for accurate initiation of DNA replication; (5) 5-MeC in codons was more
AB  - frequently found in first than in second and third positions; (6) there are probably few genes
AB  - in which the mutation rate is determined mainly be DNA methylation. It is proposed that the
AB  - function of Dcm methylase is to protect chromosomal DNA from restriction-enzyme EcoRII. The
AB  - Dcm methylation contribution to determine frequency of oligonucleotides, mutation rate, and
AB  - recombination level, and thus evolution of the E. coli genome, could be interpreted as a
AB  - consequence of the acquisition of this methylation.
ER  -

TY  - JOUR
AU  - Gomez-Gil, B.
AU  - Soto-Rodriguez, S.
AU  - Lozano, R.
AU  - Betancourt-Lozano, M.
TI  - Draft Genome Sequence of Vibrio parahaemolyticus Strain M0605, Which Causes Severe Mortalities of Shrimps in Mexico.
JO  - Genome Announcements
PY  - 2014
SP  - e00055
EP  - e00014
VL  - 2
AB  - Acute hepatopancreatic necrosis disease (AHPND), also known as early mortality syndrome (EMS),
AB  - causes high mortalities in cultured shrimps in Asia (L. Tran et
AB  - al., Dis. Aquat. Organ. 105:45-55, 2013, http://dx.doi.org/10.3354/dao02621).
AB  - Here, we report the draft genome sequence of one Mexican strain of Vibrio
AB  - parahaemolyticus that causes similar clinical signs in diseased shrimps.
ER  -

TY  - JOUR
AU  - Gomez-Jimenez, S.
AU  - Noriega-Orozco, L.
AU  - Sotelo-Mundo, R.R.
AU  - Cantu-Robles, V.A.
AU  - Cobian-Guemes, A.G.
AU  - Cota-Verdugo, R.G.
AU  - Gamez-Alejo, L.A.
AU  - Del Pozo-Yauner, L.
AU  - Guevara-Hernandez, E.
AU  - Garcia-Orozco, K.D.
AU  - Lopez-Zavala, A.A.
AU  - Ochoa-Leyva, A.
TI  - High-Quality Draft Genomes of Two Vibrio parahaemolyticus Strains Aid in Understanding Acute Hepatopancreatic Necrosis Disease of Cultured Shrimps in  Mexico.
JO  - Genome Announcements
PY  - 2014
SP  - e00800
EP  - e00814
VL  - 2
AB  - The high-quality draft genomes of two Vibrio parahaemolyticus strains, one that causes the
AB  - acute hepatopancreatic necrosis disease (AHPND) in cultured shrimps
AB  - (FIM-S1708(+)), and another that does not (FIM-S1392(-)) are reported. A
AB  - chromosome-scale assembly for the FIM-S1392(-) genome is reported here. The
AB  - analysis of the two genomes gives some clues regarding the genomic differences
AB  - between the strains.
ER  -

TY  - JOUR
AU  - Gomez-Pereira, P.R.
AU  - Schuler, M.
AU  - Fuchs, B.M.
AU  - Bennke, C.
AU  - Teeling, H.
AU  - Waldmann, J.
AU  - Richter, M.
AU  - Barbe, V.
AU  - Bataille, E.
AU  - Glockner, F.O.
AU  - Amann, R.
TI  - Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.
JO  - Environ. Microbiol.
PY  - 2012
SP  - 52
EP  - 66
VL  - 14
AB  - Bacteroidetes are widespread in marine systems where they play a crucial role in
AB  - organic matter degradation. Whole genome analysis of several strains has revealed
AB  - a broad glycolytic and proteolytic potential. In this study, we used a targeted
AB  - metagenomic approach to investigate the degradation capabilities of distinct
AB  - Bacteroidetes clades from two contrasting regions of the North Atlantic Ocean,
AB  - the Polar Biome (BPLR) and the North Atlantic Subtropical (NAST). We present here
AB  - the analysis of 76 Bacteroidetes fosmids, of which 28 encode the 16S rRNA gene as
AB  - phylogenetic marker, and their comparison to complete Bacteroidetes genomes.
AB  - Almost all of the 16S rRNA harbouring fosmids belonged to clades that we
AB  - previously identified in BPLR and NAST. The majority of sequenced fosmids could
AB  - be assigned to Bacteroidetes affiliated with the class Flavobacteria. We also
AB  - present novel genomic information on the classes Cytophagia and Sphingobacteria,
AB  - suggesting a capability of the latter for attachment to algal surfaces. In our
AB  - fosmid set we identified a larger potential for polysaccharide degradation and
AB  - cell surface attachment in the phytoplankton-rich BPLR. Particularly, two
AB  - flavobacterial fosmids, one affiliated with the genus Polaribacter, showed a
AB  - whole armoury of enzymes that likely function in degradation of sulfated
AB  - polysaccharides known to be major constituents of phytoplankton cell walls. Genes
AB  - involved in protein and peptidoglycan degradation, although present in both
AB  - fosmid sets, seemed to have a slight preponderance in NAST. This study provides
AB  - support for the hypothesis of a distinct specialization among marine
AB  - Bacteroidetes for the degradation of certain types of polymers.
ER  -

TY  - JOUR
AU  - Gomez-Rodriguez, J.A.
AU  - Huete-Perez, J.A.
TI  - Bioprospeccion de enzimas de restriccion en bacterias de suelos y ambientes volcanicos de Nicaragua.
JO  - Encuentro
PY  - 2008
SP  - 70
EP  - 87
VL  - 15
ER  -

TY  - JOUR
AU  - Gomila, M.
AU  - Busquets, A.
AU  - Garcia-Valdes, E.
AU  - Michael, E.
AU  - Cahan, R.
AU  - Nitzan, Y.
AU  - Lalucat, J.
TI  - Draft Genome Sequence of the Toluene-Degrading Pseudomonas stutzeri Strain ST-9.
JO  - Genome Announcements
PY  - 2015
SP  - e00567
EP  - e00515
VL  - 3
AB  - Strain ST-9 was isolated from toluene-contaminated soil (Samaria, Israel). The draft genome
AB  - has an estimated size of 4.8 Mb, exhibits an average G+C content of
AB  - 60.37%, and is predicted to encode 4,183 proteins, including a gene cluster for
AB  - aromatic hydrocarbon degradation. It is assigned to genomovar 3 of Pseudomonas
AB  - stutzeri.
ER  -

TY  - JOUR
AU  - Gomila, M.
AU  - Mulet, M.
AU  - Lalucat, J.
AU  - Garcia-Valdes, E.
TI  - Draft Genome Sequence of the Marine Bacterium Pseudomonas aestusnigri VGXO14T.<jour_book>Genome Announc.
JO  - 
PY  - 2017
SP  - e00765
EP  - e00717
VL  - 5
AB  - The type strain of Pseudomonas aestusnigri (VGXO14), isolated from a crude oil-polluted marine
AB  - sand sample, is a member of the P. pertucinogena phylogenetic
AB  - group. Here, we report the genome sequence (3.83 Mb) of P. aestusnigri to gain
AB  - insights into the biology and taxonomy of marine Pseudomonas spp. adapted to
AB  - polluted marine habitats.
ER  -

TY  - JOUR
AU  - Gomila, M.
AU  - Mulet, M.
AU  - Lalucat, J.
AU  - Garcia-Valdes, E.
TI  - Draft Genome Sequence of Pseudomonas pachastrellae Strain CCUG 46540T, a Deep-Sea Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00136
EP  - e00117
VL  - 5
AB  - Pseudomonas pachastrellae strain CCUG 46540T (KMM 330T) was isolated from a deep-sea sponge
AB  - specimen collected in the Philippine Sea at a depth of 750 m. The
AB  - draft genome has an estimated size of 4.0 Mb, exhibits a G+C content of 61.2
AB  - mol%, and is predicted to encode 3,592 proteins, including pathways for the
AB  - degradation of aromatic compounds.
ER  -

TY  - JOUR
AU  - Goncalves, A.C.
AU  - Franco, T.
AU  - Califano, G.
AU  - Dowd, S.E.
AU  - Pohnert, G.
AU  - Costa, R.
TI  - Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus.
JO  - Genome Announcements
PY  - 2015
SP  - e00521
EP  - e00515
VL  - 3
AB  - We report here the draft genome sequence of Vibrio sp. Vb278, a biofilm-producing strain
AB  - isolated from the marine sponge Sarcotragus spinosulus, showing in vitro
AB  - antibacterial activity. The annotated genome displays a range of symbiotic
AB  - factors and the potential for the biosynthesis of several biologically active
AB  - natural products.
ER  -

TY  - JOUR
AU  - Goncalves, L.A.
AU  - de Castro, S.S.
AU  - Pereira, F.L.
AU  - Dorella, F.A.
AU  - de Carvalho, A.F.
AU  - de Freitas, A.G.M.
AU  - Leal, C.A.
AU  - Azevedo, V.
AU  - Figueiredo, H.C.
TI  - Complete genome sequences of Francisella noatunensis subsp. orientalis strains FNO12, FNO24 and FNO190: a fish pathogen with genomic clonal behavior.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 30
EP  - 30
VL  - 11
AB  - The genus Francisella is composed of Gram-negative, pleomorphic, strictly aerobic and
AB  - non-motile bacteria, which are capable of infecting a variety of terrestrial
AB  - and aquatic animals, among which Francisella noatunensis subsp. orientalis stands
AB  - out as the causative agent of pyogranulomatous and granulomatous infections in
AB  - fish. Accordingly, F. noatunensis subsp. orientalis is responsible for high
AB  - mortality rates in freshwater fish, especially Nile Tilapia. In the current
AB  - study, we present the genome sequences of F. noatunensis subsp. orientalis
AB  - strains FNO12, FNO24 and FNO190. The genomes include one circular chromosome of
AB  - 1,859,720 bp, consisting of 32 % GC content, 1538 coded proteins and 363
AB  - pseudogenes for FNO12; one circular chromosome of 1,862,322 bp, consisting of 32
AB  - % GC content, 1537 coded proteins and 365 pseudogenes for FNO24; and one circular
AB  - chromosome of 1,859,595 bp, consisting of 32 % GC content, 1539 coded proteins
AB  - and 362 pseudogenes for FNO190. All genomes have similar genetic content,
AB  - implicating a clonal-like behavior for this species.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Belichenko, O.A.
AU  - Dedkov, V.S.
AU  - Mezentseva, N.V.
AU  - Tomilova, J.E.
AU  - Degtyarev, S.K.
TI  - PspXI, a novel restriction endonuclease that recognizes the unusual  DNA sequence 5'-VC^TCGAGB-3'.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2005
SP  - 18
EP  - 23
VL  - 1
AB  - We have discovered a bacterial strain Pseudomonas species X11 that produces the novel
AB  - restriction endonuclease PspXI. This enzyme recognizes an unusual degenerate octanucleotide
AB  - sequence 5'-VCTCGAGB-3', where V stands for A, C or G and B stands for T, C or G.  The PspXI
AB  - restriction endonuclease preparation with concentration of 10000 units/ml was isolated using
AB  - four chromatographic steps. PspXI cuts its recognition sequence between C and T producing
AB  - cohesive ends compatible with those of produced by XhoI(5'-C^TCGAG-3') and
AB  - SalI(5'-G^TCGAC-3') restriction endonucleases.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Abdurashitov, M.A.
AU  - Okhapkina, S.S.
AU  - Shagin, D.A.
AU  - Kileva, E.V.
AU  - Degtyarev, S.K.
TI  - Sse9I restriction-modification system: Organization of genes and structural comparison of proteins.
JO  - Mol. Biol. (Mosk)
PY  - 2007
SP  - 491
EP  - 498
VL  - 41
AB  - The nucleotide sequence was established for the operon of the Sse9I type II
AB  - restriction-modification system of Sporosarcina species 9D.  The enzymes of the Sse9I system
AB  - recognize the 5'-AATT-3' tetranucleotide.  The operon includes three genes,
AB  - sse9IC-sse9IR-sse9IM, which are transcribed unidirectionally and code, respectively, for the
AB  - controller protein (C.Sse9I), restriction endonuclease (R.Sse9I), and DNA methyltransferase
AB  - (M.Sse9I).  The region immediately upstream of sse9IC was found to contain a conserved
AB  - nucleotide sequence (C box) providing a binding site for C.Sse9I.  The amino acid sequences of
AB  - C.Sse9I and R.Sse9I were compared with those of related proteins.  In the case of R.Sse9I, the
AB  - highest homology was observed with the R.MunI (5'CAATTG-3') and R.EcoRI (5'GAATTC-3')
AB  - regions that harbor the amino acid residues involved in recognizing the AATT inner
AB  - tetranucleotide.  The sse9IR gene was cloned in an expression vector, and recombinant R.Sse9I
AB  - was isolated.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Akishev, A.G.
AU  - Degtyarev, S.K.
TI  - BlsI- and GlaI-PCR assays - a new method of DNA methylation study.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2010
SP  - 5
EP  - 12
VL  - 6
AB  - Regulation of genes activity in mammalians genomes is based on DNA methylation of CG
AB  - dinucleotides with formation of 5-methylcytosine (5mC) in both DNA strands.  Mammalian
AB  - DNA-methyltransferases Dnmt1, Dnmt3a and Dnmt3b catalyze a reaction of DND methylation.  Dnmt1
AB  - maintains DNA methylation pattern in vivo modifying a new strand after replication.  Dnmt3a
AB  - and Dnmt3b are responsible for DNA methylation de novo and, likely, differ in their function
AB  - and preferable region of modification.  Study of Dnmt3a and Dnmnt3b substrate specificity has
AB  - shown that both enzymes methylate CG-dinucleotide4 mostly in DNA sequence PuCGPy.  At present
AB  - time 5mC determination is represented mostly by a chemical treatment of DNA with sodium
AB  - bisulphite, which results in cytosine transformation into uracil, and native DNA allows to
AB  - locate positions of methylated cytosines in studied DNA.  Method of bisulphite conversion is
AB  - quite expensive, time-consuming and often results in obtaining false positive data.  Because
AB  - of substantial DNA degradation this method is used for analysis of only short (100 - 150 bp)
AB  - DNA sequences.  Among enzymatic methods of 5mC determination, so called methyl-sensitive PCR
AB  - assay is the most popular.  This method is based on inability of restriction enzymes, which
AB  - contain CG dinucleotide in the recognition site, to cut this site if 5mC is present in the
AB  - dinucleotide.  A subsequent PCR from primers, which are located around a chosen recognition
AB  - site, produces a corresponding DNA fragment if there is a methylated CG-dinucleotide within
AB  - this site.  On the contrary, DNA fragment is not produced in PCR if there is no methylated
AB  - CG-dinucleotide in a recognition sequence of restriction enzyme.  Application of
AB  - methyl-sensitive PCR assay is limited by a very short list of recognition sequences.  Recently
AB  - we have discovered and characterized absolutely new enzymes BlsI and GlaI, which belong to the
AB  - type of methyl-directed site-specific DNA endonucleases and cleave only methylated DNA.  GlaI
AB  - recognizes DNA sequence 5'-Pu(5mC)GPy-3'/3'-PyG(5mC)Pu-5', whereas BlsI hydrolyzes DNA
AB  - sequence 5'-GCNGC-3' if at least one 5-methylcytosine (N isn't considering) is present in
AB  - each DNA strand of the recognition site.  In this work we have developed a new method of DNA
AB  - methylation determination -
AB  - BlsI- and GlaI-PCR assays, and have applied this method to study a methylation of regulation
AB  - of tumor suppressor genes in DNA from different human cell lines.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Chernukhin, V.A.
AU  - Abdurashitov, M.A.
AU  - Kileva, E.V.
AU  - Dedkov, V.S.
AU  - Mikhnenkova, N.A.
AU  - Lomakovskaya, E.N.
AU  - Udalyeva, S.G.
AU  - Degtyarev, S.K.
TI  - Cloning and characterization of a new site specific methyl-directed DNA endonuclease EcoBLI recognizing 5'-G(5mC)NGC-3'/3'-CGN(5mC)G-5'.
JO  - BTAIJ
PY  - 2016
SP  - 175
EP  - 181
VL  - 12
AB  - A gene coding BisI, site specific 5mC-directed DNA endonuclease recognizing DNA sequence
AB  - 5'-G(5mC)NGC-3'/3'-CGN(5mC)G-5', was recently identified in the sequenced genome of the
AB  - strain-producer Bacillus subtilis T30.  In this work we have undertaken a search of bisI gene
AB  - homologues among the sequenced genomes of enterobacteria.  DNA analysis has revealed a small
AB  - group of highly homologous ORFs with unknown function including one ORF in DNA of well-known
AB  - strain E. coli.  This ORF WP 001276099.1 from E.coli BL21 (DE3) was amplified and cloned.  An
AB  - obtained recombinant strain E.coli PEcoBLI produces MD-endonuclease named EcoBLI.  The new
AB  - enzyme has the same substrate specificity as BisI MD-endonuclease.  Thus, ORF WP 001276099.1
AB  - from E.coli BL21 (DE3) encodes site-specific  5mC-directed DNA-endonuclease EcoBLI recognizing
AB  - and cleaving DNA sequence as indicated by arrows 5'-G(5mC)^NGC-3'/3'-CGN^(5mC)G-5'.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Dedkov, V.S.
AU  - Verkhozina, V.A.
AU  - Kusner, Y.S.
AU  - Shevchenko, A.V.
AU  - Degtyarev, S.K.
TI  - Restriction endonuclease Sse9I from Sporosarcina sp. strain 9D recognizes the 5'-AATT-3' DNA sequence.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1998
SP  - 139
EP  - 141
VL  - 34
AB  - A new restriction endonuclease Sse9I was isolated from the bacterial strain Sporosarcina sp.
AB  - 9D. The enzyme belongs to type II restrictases and recognizes the tetranucleotide sequence
AB  - 5'-AATT-3'.  The enzyme cleaves DNA before the first adenine residue, so it is a true
AB  - isoschizomer of Tsp509I restrictase.  However, unlike the prototype, Sse9I digests DNA at 55oC
AB  - and loses its activity after 20 min storage at 65oC.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Dedkov, V.S.
AU  - Verkhozina, V.A.
AU  - Kusner, Y.S.
AU  - Shevchenko, A.V.
AU  - Degtyarev, S.K.
TI  - Sse9I, a restriction endonuclease from Sporosarcina sp. 9D which recognizes the sequence 5'AATT-3'.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1998
SP  - 32
EP  - 34
VL  - 2
AB  - Sse9I, a type II restriction endonuclease, has been isolated from Sporosarcina species 9D.
AB  - The recognition sequence and cleavage point of restriction endonuclease Sse9I have been
AB  - determined as 5'-/AATT-3'.  The new enzyme is an isoschizomer of Tsp509I, but its optimal
AB  - incubation temperature is 55 C and it is inactivated at 65 C for 20 min.
ER  -

TY  - JOUR
AU  - Gonchar, D.A.
AU  - Wolf, Y.I.
AU  - Degtyarev, S.K.
TI  - Cloning and characterization of Sse9I DNA-methyltransferase recognizing 5'-AATT-3'.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2790
EP  - 2792
VL  - 24
AB  - The gene from Sporosarcina species 9D encoding Sse9I DNA-methyltransferase (M.Sse9I) was
AB  - cloned and expressed in Escherichia coli.  The recombinant plasmid pMSse-1 contains the
AB  - M.Sse9I gene 1086 bp in length, corresponding to a protein of 362 amino acid residues.
AB  - M.Sse9I recognizes the tetranucleotide sequence 5'-AATT-3' and modifies the second adenine
AB  - within the recognition sequence.  The amino acid sequence of M.Sse9I was compared with those
AB  - of other methylases.  According to mutual positions of four conservative domains the new
AB  - enzyme belongs to a subgroup of D12 class.  This subgroup includes Sse9I, CviAII, NlaIII and
AB  - N-terminal domains of LlaI, FokI and StsI DNA-methyltransferases.
ER  -

TY  - JOUR
AU  - Goncharov, A.
AU  - Grigorjev, S.
AU  - Karaseva, A.
AU  - Kolodzhieva, V.
AU  - Azarov, D.
AU  - Akhremenko, Y.
AU  - Tarasova, L.
AU  - Tikhonov, A.
AU  - Masharskiy, A.
AU  - Zueva, L.
AU  - Suvorov, A.
TI  - Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius.
JO  - Genome Announcements
PY  - 2016
SP  - e01706
EP  - e01715
VL  - 4
AB  - Enterococcus faecium 58m is a putative ancient nonpathogenic strain isolated from the
AB  - intestinal content of an adult woolly mammoth (Mammuthus primigenius). Here,
AB  - we report its draft genome sequence, consisting of 60 contigs. In silico genomic
AB  - analysis was performed to determine the genetic features and pathogenic potential
AB  - of this microorganism.
ER  -

TY  - JOUR
AU  - Goncuoglu, M.
AU  - Aydin, N.D.
AU  - Erol, I.
TI  - Antibiotic resistance of Escherichia coli O157:H7 isolated from cattle and sheep.
JO  - Ann. Microbiol. (Paris)
PY  - 2010
SP  - 489
EP  - 494
VL  - 60
AB  - A total of 102 Escherichia coli O157:H7 colonies recovered from 11 cattle and 14 sheep were
AB  - collected and tested for their antibiotic resistance profiles using a disc diffusion method,
AB  - according to the Clinical and Laboratory Standards Institute. Four (36.36 %) of the 11 cattle
AB  - E. coli O157:H7 isolates were resistant to cephalothin, one (9.09 %) isolate was resistant to
AB  - streptomycin, and one (9.09 %) to nalidixic acid. Two (14.28 %) of the 14 sheep E. coli
AB  - O157:H7 isolates were resistant to sulphamethoxazole,
AB  - one (7.14 %) isolate was resistant to sulphonamide compounds, and one (7.14 %) to
AB  - streptomycin. All cattle and sheep isolates were found to be susceptible to
AB  - cephazolin, gentamicin, ciprofloxacin, imipenem, trimethoprim/sulphamethoxazole,
AB  - chloramphenicol, trimethoprim, and ceftiofur. Six cattle isolates were susceptible at a ratio
AB  - of 54.54 %, and 11 (78.57 %) isolates from sheep were susceptible to all 20 antibiotics
AB  - tested. As an overall result, 68 % of the E. coli O157:H7 isolates belonging to cattle and
AB  - sheep were susceptible to all antibiotics tested. On the other hand, most of the E. coli
AB  - O157:H7 isolates were intermediately resistant to streptomycin, cephalothin,
AB  - sulphamethoxazole, ampicillin, and kanamycin.
ER  -

TY  - JOUR
AU  - Gong, H.Y.
AU  - Wu, S.H.
AU  - Chen, C.Y.
AU  - Huang, C.W.
AU  - Lu, J.K.
AU  - Chou, H.Y.
TI  - Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan.
JO  - Genome Announcements
PY  - 2017
SP  - e01524
EP  - e01516
VL  - 5
AB  - Streptococcus iniae 89353 is a virulent strain isolated from diseased tilapia in  Taiwan. The
AB  - full-genome sequence of S. iniae 89353 is 2,098,647 bp. The revealed
AB  - genome information will be beneficial for identification and understanding of
AB  - potential virulence genes of Streptococcus iniae and possible immunogens for
AB  - vaccine development against streptococcosis.
ER  -

TY  - JOUR
AU  - Gong, W.
AU  - Kisiela, M.
AU  - Schilhabel, M.B.
AU  - Xiong, G.
AU  - Maser, E.
TI  - Genome Sequence of Comamonas testosteroni ATCC 11996, a Representative Strain Involved in Steroid Degradation.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1633
EP  - 1634
VL  - 194
AB  - Comamonas testosteroni strains belong to the family of Comamonadaceae and are known for their
AB  - ability to utilize steroid compounds as carbon source. Here, we
AB  - present the draft genome sequence of strain ATCC 11996, with a G+C content of
AB  - 61.48%.
ER  -

TY  - JOUR
AU  - Gong, W.
AU  - O'Gara, M.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2702
EP  - 2715
VL  - 25
AB  - We have determined the structure of PvuII methyltransferase (M.PvuII) complexed with
AB  - S-adenosyl-L-methionine (AdoMet) by multiwavelength anomalous diffraction, using a crystal of
AB  - the selenomethionine-substituted protein.  M.PvuII catalyzes transfer of the methyl group from
AB  - AdoMet to the exocyclic amino (N4) nitrogen of the central cytosine in its recognition
AB  - sequence 5'-CAGCTG-3'.  The protein is dominated by an open alpha/beta-sheet stucture with a
AB  - prominent V-shaped cleft: AdoMet and catalytic amino acids are located at the bottom of this
AB  - cleft.  The size and the basic nature of the cleft are consistent with duplex DNA binding.
AB  - The target (methylatable) cytosine, if flipped out of the double helical DNA as seen for DNA
AB  - methyltransferases that generate 5-methylcytosine, would fit into the concave active site next
AB  - to the AdoMet.  This M.PvuII alpha/beta-sheet structure is very similar to those of M.HhaI (a
AB  - cytosine C5 methyltransferase) and M.TaqI (an adenine N6 methyltransferase), consistent with a
AB  - model predicting that DNA methyltransferases share a common structural fold while having the
AB  - major functional regions permuted into three distinct linear orders.  The main feature of the
AB  - common fold is a seven-stranded beta-sheet (6/7/5/4/1/2/3/) formed by five parallel
AB  - beta-strands and an antiparallel beta-hairpin.  The beta-sheet is flanked by size parallel
AB  - alpha-helices, three on each side.  The AdoMet binding site is located at the C-terminal ends
AB  - of strands beta1 and beta2 and the active site is at the C-terminal ends of strands beta4 and
AB  - beta5 and the N-terminal end of strand beta7.  The AdoMet-protein interactions are almost
AB  - identical among M.PvuII, M.HhaI and M.TaqI, as well as in an RNA methyltransferase and at
AB  - least one small molecule methyltransferase.  The structural similarity among the active sites
AB  - of M.PvuII, M.TaqI and M.HhaI reveals that catalytic amino acids essential for cytosine N4 and
AB  - adenine N6 methylation coincide spatially with those for cytosine C5 methylation, suggesting a
AB  - mechanism for amino methylation.
ER  -

TY  - JOUR
AU  - Gong, X.
AU  - Skrivergaard, S.
AU  - Korsgaard, B.S.
AU  - Schreiber, L.
AU  - Marshall, I.P.
AU  - Finster, K.
AU  - Schramm, A.
TI  - High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 8
EP  - 8
VL  - 12
AB  - Strain S3-2T, isolated from sediment of a frozen freshwater pond, shares 99% 16S  rRNA gene
AB  - sequence identity with strains of the genus Janthinobacterium. Strain
AB  - S3-2T is a facultative anaerobe that lacks the ability to produce violacein but
AB  - shows antibiotic resistance, psychrotolerance, incomplete denitrification, and
AB  - fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and
AB  - contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties
AB  - of the strain, the low in silico DNA-DNA hybridization (DDH) values with related
AB  - genomes (<35%), and the low whole genome-based average nucleotide identity (ANI)
AB  - (<86%) with other strains within the genus Janthinobacterium, we propose that
AB  - strain S3-2T is the type strain (= DSM 102223 = LMG 29653) of a new species
AB  - within this genus. We propose the name Janthinobacterium psychrotolerans sp. nov.
AB  - to emphasize the capability of the strain to grow at low temperatures.
ER  -

TY  - JOUR
AU  - Goni-Urriza, M.
AU  - Gassie, C.
AU  - Bouchez, O.
AU  - Klopp, C.
AU  - Guyoneaud, R.
TI  - Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e01483
EP  - e01416
VL  - 5
AB  - Desulfovibrio BerOc1 is a sulfate-reducing bacterium isolated from the Berre lagoon (French
AB  - Mediterranean coast). BerOc1 is able to methylate and demethylate mercury. The genome size is
AB  - 4,081,579 bp assembled into five contigs. We identified the hgcA and hgcB genes involved in
AB  - mercury methylation, but not those responsible for mercury demethylation.
ER  -

TY  - JOUR
AU  - Gonzaga, A.
AU  - Lopez-Perez, M.
AU  - Martin-Cuadrado, A.B.
AU  - Ghai, R.
AU  - Rodriguez-Valera, F.
TI  - Complete Genome Sequence of the Copiotrophic Marine Bacterium Alteromonas macleodii Strain ATCC 27126T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6998
EP  - 6998
VL  - 194
AB  - The genome of Alteromonas macleodii strain ATCC 27126(T) has been resequenced and closed into
AB  - a single contig. We describe here the genome of this important and
AB  - globally distributed marine bacterium.
ER  -

TY  - JOUR
AU  - Gonzaga, A.
AU  - Martin-Cuadrado, A.B.
AU  - Lopez-Perez, M.
AU  - Megumi-Mizuno, C.
AU  - Garcia-Heredia, I.
AU  - Kimes, N.E.
AU  - Lopez-Garcia, P.
AU  - Moreira, D.
AU  - Ussery, D.
AU  - Zaballos, M.
AU  - Ghai, R.
AU  - Rodriguez-Valera, F.
TI  - Polyclonality of concurrent natural populations of Alteromonas macleodii.
JO  - Genome Biol. Evol.
PY  - 2012
SP  - 1360
EP  - 1374
VL  - 4
AB  - We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a
AB  - single sample of seawater to evaluate the genomic diversity
AB  - present. We performed full genome sequencing of four isolates and 161 metagenomic
AB  - fosmid clones, all of which were assigned to A. macleodii by sequence similarity.
AB  - Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a
AB  - different genome, whereas AltDE2 and AltDE3 were identical to the previously
AB  - described AltDE. Although the core genome (~80%) had an average nucleotide
AB  - identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands
AB  - (fGIs), that is, genomic islands present in both genomes in the same genomic
AB  - context but having different gene content. Some of the fGIs encode cell surface
AB  - receptors known to be phage recognition targets, such as the O-chain of the
AB  - lipopolysaccharide, whereas others have genes involved in physiological traits
AB  - (e.g., nutrient transport, degradation, and metal resistance) denoting microniche
AB  - specialization. The presence in metagenomic fosmids of genomic fragments
AB  - differing from the sequenced strain genomes, together with the presence of new
AB  - fGIs, indicates that there are at least two more A. macleodii clones present. The
AB  - availability of three or more sequences overlapping the same genomic region also
AB  - allowed us to estimate the frequency and distribution of recombination events
AB  - among these different clones, indicating that these clustered near the genomic
AB  - islands. The results indicate that this natural A. macleodii population has
AB  - multiple clones with a potential for different phage susceptibility and
AB  - exploitation of resources, within a seemingly unstructured habitat.
ER  -

TY  - JOUR
AU  - Gonzalez, D.
AU  - Collier, J.
TI  - Genomic Adaptations to the Loss of a Conserved Bacterial DNA Methyltransferase.
JO  - MBio
PY  - 2015
SP  - e00952
EP  - e00915
VL  - 6
AB  - CcrM is an orphan DNA methyltransferase nearly universally conserved in a vast group of
AB  - Alphaproteobacteria. In Caulobacter crescentus, it controls the
AB  - expression of key genes involved in the regulation of the cell cycle and cell
AB  - division. Here, we demonstrate, using an experimental evolution approach, that C.
AB  - crescentus can significantly compensate, through easily accessible genetic
AB  - changes like point mutations, the severe loss in fitness due to the absence of
AB  - CcrM, quickly improving its growth rate and cell morphology in rich medium. By
AB  - analyzing the compensatory mutations genome-wide in 12 clones sampled from
AB  - independent DeltaccrM populations evolved for ~300 generations, we demonstrated
AB  - that each of the twelve clones carried at least one mutation that potentially
AB  - stimulated ftsZ expression, suggesting that the low intracellular levels of FtsZ
AB  - are the major burden of DeltaccrM mutants. In addition, we demonstrate that the
AB  - phosphoenolpyruvate-carbohydrate phosphotransfer system (PTS) actually modulates
AB  - ftsZ and mipZ transcription, uncovering a previously unsuspected link between
AB  - metabolic regulation and cell division in Alphaproteobacteria. We present
AB  - evidence that point mutations found in genes encoding proteins of the PTS provide
AB  - the strongest fitness advantage to DeltaccrM cells cultivated in rich medium
AB  - despite being disadvantageous in minimal medium. This environmental sign
AB  - epistasis might prevent such mutations from getting fixed under changing natural
AB  - conditions, adding a plausible explanation for the broad conservation of CcrM.
AB  - IMPORTANCE: In bacteria, DNA methylation has a variety of functions, including
AB  - the control of DNA replication and/or gene expression. The cell cycle-regulated
AB  - DNA methyltransferase CcrM modulates the transcription of many genes and is
AB  - critical for fitness in Caulobacter crescentus. Here, we used an original
AB  - experimental evolution approach to determine which of its many targets make CcrM
AB  - so important physiologically. We show that populations lacking CcrM evolve
AB  - quickly, accumulating an excess of mutations affecting, directly or indirectly,
AB  - the expression of the ftsZ cell division gene. This finding suggests that the
AB  - most critical function of CcrM in C. crescentus is to promote cell division by
AB  - enhancing FtsZ intracellular levels. During this work, we also discovered an
AB  - unexpected link between metabolic regulation and cell division that might extend
AB  - to other Alphaproteobacteria.
ER  -

TY  - JOUR
AU  - Gonzalez, D.
AU  - Kozdon, J.B.
AU  - McAdams, H.H.
AU  - Shapiro, L.
AU  - Collier, J.
TI  - The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 3720
EP  - 3735
VL  - 42
AB  - DNA methylation is involved in a diversity of processes in bacteria, including maintenance of
AB  - genome integrity and regulation of gene expression. Here, using
AB  - Caulobacter crescentus as a model, we exploit genome-wide experimental methods to
AB  - uncover the functions of CcrM, a DNA methyltransferase conserved in most
AB  - Alphaproteobacteria. Using single molecule sequencing, we provide evidence that
AB  - most CcrM target motifs (GANTC) switch from a fully methylated to a
AB  - hemi-methylated state when they are replicated, and back to a fully methylated
AB  - state at the onset of cell division. We show that DNA methylation by CcrM is not
AB  - required for the control of the initiation of chromosome replication or for DNA
AB  - mismatch repair. By contrast, our transcriptome analysis shows that >10% of the
AB  - genes are misexpressed in cells lacking or constitutively over-expressing CcrM.
AB  - Strikingly, GANTC methylation is needed for the efficient transcription of dozens
AB  - of genes that are essential for cell cycle progression, in particular for DNA
AB  - metabolism and cell division. Many of them are controlled by promoters methylated
AB  - by CcrM and co-regulated by other global cell cycle regulators, demonstrating an
AB  - extensive cross talk between DNA methylation and the complex regulatory network
AB  - that controls the cell cycle of C. crescentus and, presumably, of many other
AB  - Alphaproteobacteria.
ER  -

TY  - JOUR
AU  - Gonzalez, E.
AU  - Padilla, C.
AU  - Saavedra, C.
AU  - Vasquez, C.
TI  - The expression of the bstVIM gene from Bacillus stearothermophilus V is restricted to vegetative cell growth.
JO  - Microbiology
PY  - 1994
SP  - 1337
EP  - 1340
VL  - 140
AB  - The activity of BstVI DNA methyltransferase was monitored during the sporulative cycle of
AB  - Bacillus stearothermophilus V. Significant methylase activity was found only in bacteria
AB  - growing vegetatively. This was confirmed by Northern hybridization, which indicated that the
AB  - bstVIM gene was not transcribed in cells undergoing sporulation. Supporting evidence came from
AB  - experiments which demonstrated that the RNA polymerase holoenzyme from these cells did not
AB  - recognize the promoter elements upstream of the bstVIM gene.
ER  -

TY  - JOUR
AU  - Gonzalez, E.
AU  - Vasquez, C.
TI  - Characterization of the bstVIRM genes encoding the Bacillus stearothermophilus V restriction-modification system.
JO  - Gene
PY  - 1993
SP  - 103
EP  - 106
VL  - 131
AB  - The nucleotide (nt) sequence of a 2.7-kb HindIII-EcoRI DNA fragment encoding the bstVIR and
AB  - bstVIM genes has been determined. The sequence predicts a restriction endonuclease of 224
AB  - amino acids (aa), Mr 25,104, and a methyltransferase of 561 aa, Mr 65,702. Both genes are
AB  - aligned in the same orientation and are separated by a 102-nt intergenic region. No homology
AB  - was found between R-BstVI and M-BstVI when their deduced aa sequences were compared.
AB  - Significant similarity at the aa level was found, however, when both enzymes were compared to
AB  - their equivalents in the paeR71RM system of Pseudomonas aeruginosa PAO303.
ER  -

TY  - JOUR
AU  - Gonzalez, V.
AU  - Santamaria, R.I.
AU  - Bustos, P.
AU  - Hernandez-Gonzalez, I.
AU  - Medrano-Soto, A.
AU  - Moreno-Hagelsieb, G.
AU  - Janga, S.C.
AU  - Ramirez, M.A.
AU  - Jimenez-Jacinto, V.
AU  - Collado-Vides, J.
AU  - Davila, G.
TI  - The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 3834
EP  - 3839
VL  - 103
AB  - We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium
AB  - Rhizobium etli. Six large plasmids comprise
AB  - one-third of the total genome size. The chromosome encodes most functions
AB  - necessary for cell growth, whereas few essential genes or complete
AB  - metabolic pathways are located in plasmids. Chromosomal synteny is
AB  - disrupted by genes related to insertion sequences, phages, plasmids, and
AB  - cell-surface components. Plasmids do not show synteny, and their orthologs
AB  - are mostly shared by accessory replicons of species with multipartite
AB  - genomes. Some nodulation genes are predicted to be functionally related
AB  - with chromosomal loci encoding for the external envelope of the bacterium.
AB  - Several pieces of evidence suggest an exogenous origin for the symbiotic
AB  - plasmid (p42d) and p42a. Additional putative horizontal gene transfer
AB  - events might have contributed to expand the adaptive repertoire of R.
AB  - etli, because they include genes involved in small molecule metabolism,
AB  - transport, and transcriptional regulation. Twenty-three putative sigma
AB  - factors, numerous isozymes, and paralogous families attest to the
AB  - metabolic redundancy and the genomic plasticity necessary to sustain the
AB  - lifestyle of R. etli in symbiosis and in the soil.
ER  -

TY  - JOUR
AU  - Gonzalez-Ceron, G.
AU  - Miranda-Olivares, O.J.
AU  - Servin-Gonzalez, L.
TI  - Characterization of the methyl-specific restriction system of Streptomyces coelicolor A3(2) and of the role played by laterally acquired nucleases.
JO  - FEMS Microbiol. Lett.
PY  - 2009
SP  - 35
EP  - 43
VL  - 301
AB  - The methyl-specific restriction system of Streptomyces coelicolor A3(2) was analyzed by
AB  - carrying out transformations with unmethylated and
AB  - methylated pSET152 DNA. Streptomyces coelicolor was found to strongly
AB  - restrict DNA methylated in vivo by the Dam, Dcm and Hsd modification
AB  - systems of Escherichia coli. Hsd-modified DNA was restricted as
AB  - strongly as Dam-modified DNA, even though there are significantly fewer
AB  - sites on the plasmid; Dcm-modified plasmid was restricted more strongly
AB  - then either Dam-or Hsd-modified DNA. Restriction of plasmid DNA
AB  - modified in vitro by different methylases also showed a greater
AB  - dependence on the methylated sequence than on the number of methylated
AB  - sites. Streptomyces coelicolor mutants were constructed that lacked
AB  - genes identified as the likely candidates for encoding methyl-specific
AB  - restriction nucleases (the products of the SCO4213, SCO4631 and SCO2863
AB  - genes, as well as the SCO3261-SCO3262 operon) that are located in the
AB  - laterally acquired genomic islands of the S. coelicolor chromosome;
AB  - these mutants showed partial alleviation of methylated DNA restriction.
AB  - Cloning of these genes in the close relative Streptomyces lividans
AB  - increased the restriction of methylated DNA by this species, confirming
AB  - their role as part of the methyl-specific restriction system of S.
AB  - coelicolor.
ER  -

TY  - JOUR
AU  - Gonzalez-Escalona, N.
AU  - Haendiges, J.
AU  - Miller, J.D.
AU  - Sharma, S.K.
TI  - Closed Genome Sequences of Two Clostridium botulinum Strains Obtained by Nanopore Sequencing.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01075
EP  - e01018
VL  - 7
AB  - Here we report the genome sequences of two toxin-producing Clostridium botulinum  strains, one
AB  - environmental sample (83F) and one clinical sample (CDC51232). The
AB  - genomes were closed by a combination of long-read and short-read sequencing. The
AB  - strains belong to C. botulinum sequence type 4 (ST4) and ST7, respectively.
ER  -

TY  - JOUR
AU  - Gonzalez-Escalona, N.
AU  - McFarland, M.A.
AU  - Rump, L.V.
AU  - Payne, J.
AU  - Andrzejewski, D.
AU  - Brown, E.W.
AU  - Evans, P.S.
AU  - Croley, T.R.
TI  - Draft Genome Sequences of Two O104:H21 Escherichia coli Isolates Causing Hemorrhagic Colitis during a 1994 Montana Outbreak Provide Insight into Their  Pathogenicity.
JO  - Genome Announcements
PY  - 2013
SP  - e00805
EP  - e00813
VL  - 1
AB  - We sequenced the genomes of two strains of O104:H21 enterohemorrhagic Escherichia coli (EHEC)
AB  - isolated during an outbreak of hemorrhagic colitis in Montana in
AB  - 1994. These strains carried a plasmid that contains several virulence genes not
AB  - present in pO157. The genome sequences will improve phylogenetic analysis of
AB  - other non-O157 E. coli strains in the future.
ER  -

TY  - JOUR
AU  - Gonzalez-Escalona, N.
AU  - Strain, E.A.
AU  - De Jesus, A.J.
AU  - Jones, J.L.
AU  - Depaola, A.
TI  - Genome sequence of the clinical O4:K12 serotype Vibrio parahaemolyticus strain 10329.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3405
EP  - 3406
VL  - 193
AB  - Vibrio parahaemolyticus is the leading cause of foodborne illnesses worldwide. Here we report
AB  - a draft genome of V. parahaemolyticus strain
AB  - Vp10329 of O4:K12 serotype. It belongs to the main U. S. West Coast clonal
AB  - complex of V. parahaemolyticus (ST36) causing oyster-associated human
AB  - illness. It contains the virulence determinants tdh and trh but appears to
AB  - infect at much lower doses than V. parahaemolyticus strains with these
AB  - same determinants from other areas such as the U.S. Gulf and Atlantic
AB  - coasts.
ER  -

TY  - JOUR
AU  - Gonzalez-Escalona, N.
AU  - Thirunavukkarasu, N.
AU  - Singh, A.
AU  - Toro, M.
AU  - Brown, E.W.
AU  - Zink, D.
AU  - Rummel, A.
AU  - Sharma, S.K.
TI  - Draft Genome Sequence of Bivalent Clostridium botulinum Strain IBCA10-7060, Encoding Botulinum Neurotoxin B and a New FA Mosaic Type.
JO  - Genome Announcements
PY  - 2014
SP  - e01275
EP  - e01214
VL  - 2
AB  - Here we report the genome sequence of a Clostridium botulinum strain IBCA10-7060  producing
AB  - botulinum neurotoxin serotype B and a new toxin serotype. Multilocus
AB  - sequence typing analysis revealed that this strain belongs to a new sequence
AB  - type, and whole-genome single nucleotide polymorphism analysis showed that this
AB  - strain clustered with strains in lineage 2 from group I.
ER  -

TY  - JOUR
AU  - Gonzalez-Nicieza, R.
AU  - Turner, D.P.
AU  - Connolly, B.A.
TI  - DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein).
JO  - J. Mol. Biol.
PY  - 2001
SP  - 501
EP  - 508
VL  - 310
AB  - The Escherichia coli vsr endonuclease recognises T:G base-pair mismatches in double-stranded
AB  - DNA and initiates a repair pathway by
AB  - hydrolysing the phosphate group 5' to the incorrectly paired T. The
AB  - gene encoding the vsr endonuclease is next to the gene specifying the
AB  - E. coli dcm DNA-methyltransferase; an enzyme that adds CH3 groups to
AB  - the first dC within its target sequence CC[A/T]GG, giving
AB  - C5MeC[A/T]GG. Deamination of the d(5Me)C results in CT[A/T]GG in
AB  - which the first T is mis-paired with dG and it is believed that the
AB  - endonuclease preferentially recognises T:G mismatches within the dcm
AB  - recognition site. Here, the preference of the vsr endonuclease for
AB  - bases surrounding the T:G mismatch has been evaluated. Determination of
AB  - specificity constant (k(st)/K-D; k(st) = rate constant for single
AB  - turnover, K-D = equilibrium dissociation constant) confirms vsr's
AB  - preference for a T:G mismatch within a dcm sequence i.e. C (T) under
AB  - bar [A/T]GG (the underlined T being mis-paired with dG) is the best
AB  - substrate. However, the enzyme is capable of binding and hydrolysing
AB  - sequences that differ from the dcm target site by a single base-pair
AB  - (dcm star sites). Individual alteration of any of the four bases
AB  - surrounding the mismatched T gives a substrate, albeit with reduced
AB  - binding affinity and slowed turnover rates. The vsr endonuclease has a
AB  - much lower selectivity for the dcm sequence than type II restriction
AB  - endonucleases have for their target sites. The results are discussed in
AB  - the light of the known crystal structure of the vsr protein and its
AB  - possible physiological role.
ER  -

TY  - JOUR
AU  - Gonzalez-Perez, M.
AU  - Murcia, M.I.
AU  - Landsman, D.
AU  - Jordan, I.K.
AU  - Marino-Ramirez, L.
TI  - Genome Sequence of the Mycobacterium colombiense Type Strain, CECT 3035.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5866
EP  - 5867
VL  - 193
AB  - We report the first whole-genome sequence of the Mycobacterium colombiense type strain, CECT
AB  - 3035, which was initially isolated from Colombian
AB  - HIV-positive patients and causes respiratory and disseminated infections.
AB  - Preliminary comparative analyses indicate that the M. colombiense lineage
AB  - has experienced a substantial genome expansion, possibly contributing to
AB  - its distinct pathogenic capacity.
ER  -

TY  - JOUR
AU  - Gonzalez-Perez, M.N.
AU  - Murcia, M.I.
AU  - Parra-Lopez, C.
AU  - Blom, J.
AU  - Tauch, A.
TI  - Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense.
JO  - New Microbes New Infect.
PY  - 2016
SP  - 98
EP  - 105
VL  - 14
AB  - Mycobacterium avium complex (MAC) contains clinically important nontuberculous
AB  - mycobacteria worldwide and is the second largest medical complex in the
AB  - Mycobacterium genus after the Mycobacterium tuberculosis complex. MAC comprises
AB  - several species that are closely phylogenetically related but diverse regarding
AB  - their host preference, course of disease, virulence and immune response. In this
AB  - study we provided immunologic and virulence-related insights into the M.
AB  - colombiense genome as a model of an opportunistic pathogen in the MAC. By using
AB  - bioinformatic tools we found that M. colombiense has deletions in the genes
AB  - involved in p-HBA/PDIM/PGL, PLC, SL-1 and HspX production, and loss of the ESX-1
AB  - locus. This information not only sheds light on our understanding the virulence
AB  - mechanisms used by opportunistic MAC pathogens but also has great potential for
AB  - the designing of species-specific diagnostic tools.
ER  -

TY  - JOUR
AU  - Gonzalez-Torres, P.
AU  - Gabaldon, T.
TI  - Genome variation in the model halophilic bacterium Salinibacter ruber.
JO  - Front. Microbiol.
PY  - 2018
SP  - 1499
EP  - 1499
VL  - 9
ER  -

TY  - JOUR
AU  - Gonzalgo, M.L.
AU  - Jones, P.A.
TI  - Mutagenic and epigenetic effects of DNA methylation.
JO  - Mutat. Res.
PY  - 1997
SP  - 107
EP  - 118
VL  - 386
AB  - Tumorigenesis begins with the disregulated growth of an abnormal cell that has acquired the
AB  - ability to divide more rapidly than its normal counterparts.  Alterations in global levels and
AB  - regional changes in the patterns of DNA methylation are among the earliest and most frequent
AB  - events known to occur in human cancers.  These changes in methylation may impair the proper
AB  - expression and/or function of cell-cycle regulatory genes and thus confer a selective growth
AB  - advantage to affected cells.  Developments in the field of cancer research over the past few
AB  - years have led to an increased understanding of the role DNA methylation may play in
AB  - tumorigenesis.  Many of these studies have investigated two major mechanisms by which DNA
AB  - methylation may lead to aberrant cell cycle control: (1) through the generation of transition
AB  - mutations via deamination-driven events resulting in the inactivation of tumor suppressor
AB  - genes, or (2) by altering levels of gene expression through epigenetic effects at CpG islands.
AB  - The mechanisms by which the normal function of growth regulatory genes may become affected by
AB  - the mutagenic and epigenetic properties of DNA methylation will be discussed in the framework
AB  - of recent discoveries in the field.
ER  -

TY  - JOUR
AU  - Goodgal, S.H.
AU  - Gromkova, R.
TI  - Separation of specific segments of transforming DNA after treatment with endodeoxyribonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1973
SP  - 503
EP  - 506
VL  - 70
AB  - Hemophilus parainfluenzae endodeoxyribonuclease was used to degrade the DNA of
AB  - H. influenzae and to follow the biological activity of 14 markers associated
AB  - with this DNA.  It was found that some H. influenzae markers were completely
AB  - inactivated by endodeoxyribonuclease treatment, while others appeared to retain
AB  - all or almost all of their original activity.  The bulk of the H. influenzae
AB  - DNA was reduced to double-stranded pieces of the order of 0.8 1 Mdaltons.
AB  - Velocity sedimentation of the DNA in sucrose gradients disclosed that markers
AB  - that retained biological activity were present in DNA particles that were of
AB  - the order of 1 Mdaltons or larger, and indicated a close correlation between
AB  - the size of the DNA fragment and the amount of biological activity retained.
AB  - These data suggest that H. parainfluenzae endodeoxyribonuclease breaks DNA at
AB  - specific sites.  The nalr marker was shown to have twice as much biological
AB  - activity after treatment with endodeoxyribonuclease when assayed at saturating
AB  - DNA concentrations.  In the linear portion of the DNA dose-response curve, the
AB  - biological activity of this marker was reduced 3- to 10-fold compared to
AB  - untreated DNA (in accord with the reduced size of its DNA).  These data
AB  - demonstrate a specific enrichment of the nalr marker by about 6- to 20-fold,
AB  - and suggest a technique for the separation and purification of specific
AB  - segments of DNA.
ER  -

TY  - JOUR
AU  - Goodison, S.
AU  - Urquidi, V.
AU  - Kumar, D.
AU  - Reyes, L.
AU  - Rosser, C.J.
TI  - Complete Genome Sequence of Mycoplasma hyorhinis Strain SK76.
JO  - Genome Announcements
PY  - 2013
SP  - e00101
EP  - e00112
VL  - 1
AB  - Mycoplasma hyorhinis is a eubacterium belonging to the Mollicutes class and is responsible for
AB  - porcine respiratory and arthritic diseases. It is also the major
AB  - contaminant of mammalian tissue cultures in laboratories worldwide. Here, we
AB  - report the complete genome sequence of M. hyorhinis strain SK76.
ER  -

TY  - JOUR
AU  - Goodman, H.M.
AU  - Greene, P.J.
AU  - Garfin, D.E.
AU  - Boyer, H.W.
TI  - DNA site recognition by the EcoRI restriction endonuclease and modification methylase.
JO  - Nucleic Acid - Protein Recognition
PY  - 1977
SP  - 239
EP  - 259
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Goodner, B. et al.
TI  - Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58.
JO  - Science
PY  - 2001
SP  - 2323
EP  - 2328
VL  - 294
AB  - Agrobacterium tumefaciens is a plant pathogen capable of transferring a defined segment of DNA
AB  - to a host plant, generating a gall tumor. Replacing the transferred  tumor-inducing genes with
AB  - exogenous DNA allows the introduction of any desired gene into the plant. Thus, A. tumefaciens
AB  - has been critical for the development of modern plant genetics and agricultural biotechnology.
AB  - Here we describe the genome of A. tumefaciens strain C58, which has an unusual structure
AB  - consisting of one circular and one linear chromosome. We discuss genome architecture and
AB  - evolution and additional genes potentially involved in virulence and metabolic parasitism of
AB  - host plants.
ER  -

TY  - JOUR
AU  - Goodrich-Blair, H.
AU  - Scarlato, V.
AU  - Gott, J.M.
AU  - Xu, M.-Q.
AU  - Shub, D.A.
TI  - A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1.
JO  - Cell
PY  - 1990
SP  - 417
EP  - 424
VL  - 63
AB  - We report a self-splicing intron in bacteriophage SPO1, whose host is the gram-positive
AB  - Bacillus subtilis. The intron contains all the conserved features of primary sequence and
AB  - secondary structure previously described for the group IA introns of eukaryotic organelles and
AB  - the gram-negative bacteriophage T4. The SPO1 intron contains an open reading frame of 522
AB  - nucleotides. As in the T4 introns, this open reading frame begins in a region that is looped
AB  - out of the secondary structure, but ends in a highly conserved region of the intron core. The
AB  - exons encode SPO1 DNA polymerase, which is highly similar to E. coli DNA polymerase I. The
AB  - demonstration of self-splicing introns in viruses of both gram-positive and gram-negative
AB  - eubacteria lends further evidence for their early origin in evolution.
ER  -

TY  - JOUR
AU  - Goodrich-Blair, H.
AU  - Shub, D.A.
TI  - A site- and strand-specific intron-endonuclease is required for marker exclusion.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 177
EP  - 177
VL  - 17C
AB  - The virulent Bacillus subtilis bacteriophage SPO1 and SP82 belong to a closely related family
AB  - that contain hydroxymethyluracil (HMU) in place of thymine in their DNA. The DNA polymerase
AB  - gene of these phage is interrupted by a self-splicing group I intron. We have characterized
AB  - two endonucleases, I-HmuI (encoded by SPO1) and I-HmuII (encoded by SP82) that are encoded
AB  - entirely within the DNA polymerase intron. Other intron-endonucleases are initiators of
AB  - "intron homing". They introduce a double-strand cleavage specifically on intron-less alleles
AB  - and repair of this cleavage, using the intron-plus allele as a template, results in two
AB  - intron-plus copies of DNA via unidirectional gene conversion. The HMU-phage
AB  - intron-endonucleases have several unique features. First, they are strand- as well as
AB  - site-specific, introducing a nick in the noncoding strand 4 nucleotides (nt) (I-HmuI) or 54 nt
AB  - (I-HmuII) downstream of the 3' splice site of the intron, within exon II of the DNA
AB  - polymerase gene. Second, the endonucleases cleave intron-plus as well as intron-less DNA.
AB  - Third, the endonucleases show a distinct preference, both in vitro and in vivo, for the DNA of
AB  - the heterologous phage. These differences in the HMU intron-endonucleases could reflect a
AB  - difference in function. Previous reports indicated that in mixed infections genetic markers of
AB  - SP82 are more likely to be carried by progeny than those of SP01. This exclusion occurs over
AB  - 10 kilobases of DNA surrounding the DNA polymerase gene. We have found that expression of
AB  - I-HmuII by SP82 is required for this exclusion process. We hypothesize that the intron homing
AB  - mechanism of I-HmuII has been expanded to confer a selective advantage on its host in
AB  - competition with close relatives.
ER  -

TY  - JOUR
AU  - Goodrich-Blair, H.
AU  - Shub, D.A.
TI  - Beyond homing: Competition between intron endonucleases confers a selective advantage on flanking genetic markers.
JO  - Cell
PY  - 1996
SP  - 211
EP  - 221
VL  - 84
AB  - The closely related B. subtilis bacteriophages SPO1 and SP82 have similar introns inserted
AB  - into a conserved domain of their DNA polymerase genes.  These introns encode endonucleases
AB  - with unique properties.  Other intron-encoded "homing" endonucleases cleave both strands of
AB  - intronless DNA; subsequent repair results in unidirectional gene conversion to the
AB  - intron-containing allele.  In contrast, the enzymes described here cleave one strand on both
AB  - intron-containing and intronless targets at different distances from their common intron
AB  - insertion site.  Most surprisingly, each enzyme prefers DNA of the heterologous phage.  The
AB  - SP82-encoded endonuclease is responsible for exclusion of the SPO1 intron and flanking genetic
AB  - markers from the progeny of mixed infections, a novel selective advantage imparted by an
AB  - intron to the genome in which it resides.
ER  -

TY  - JOUR
AU  - Goodrich-Blair, H.
AU  - Shub, D.A.
TI  - The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 3715
EP  - 3721
VL  - 22
AB  - A previous report described the discovery of a group I, self-splicing intron
AB  - in the DNA
AB  - polymerase gene of the Bacillus subtilis bacteriophage SPO1.  In this study, the DNA
AB  - polymerase genes of
AB  - three close relatives of SPO1: SP82, 2C and Phi e, were also found to be interrupted by an
AB  - intron.  All of these
AB  - introns have group I secondary structures that are extremely similar to one another in
AB  - primary sequence.
AB  - Each is interrupted by an open reading frame that, unlike the intron core or exon sequences,
AB  - are highly
AB  - diverged.  Unlike the relaives of Escherichia coli bacteriophage T4, most of which do not
AB  - have introns, this
AB  - intron seems to be common among the relatives of SPO1.
ER  -

TY  - JOUR
AU  - Goodsell, D.S.
TI  - Recognition in action: flipping pyrimidine dimers.
JO  - J. Mol. Recognit.
PY  - 2005
SP  - 193
EP  - 195
VL  - 18
AB  - DNA bases are normally sheltered within a double helix, but enzymes that modify and repair DNA
AB  - gain access by flipping individual bases out
AB  - of the double helix.
ER  -

TY  - JOUR
AU  - Goodsell, D.S.
TI  - The molecular perspective: Restriction endonucleases.
JO  - Stem Cells
PY  - 2002
SP  - 190
EP  - 191
VL  - 20
AB  - We live in a remarkable age. Physicians now have an unprecedented range of options for helping
AB  - their patients. Surgery and radiology are using advanced technologies to pinpoint treatments.
AB  - Chemotherapeutic approaches are showing ever-greater effectiveness and specificity,
AB  - approaching the goal of a "magic bullet." And we are now entering a time when we can make
AB  - changes at the most basic level, introducing changes directly into the genetic code. Gene
AB  - therapy, the ability to introduce new genes into living cells, holds great promise for the
AB  - treatment of many diseases, including cancer. Restriction endonucleases are the molecules that
AB  - spawned the field of biotechnology, the first of the many molecular tools that make gene
AB  - therapy a reality. Bacteria build restriction endonucleases to protect themselves from attack
AB  - by viruses. These enzymes cleave DNA at a specific sequence of nucleotides: for instance, one
AB  - enzyme from Escherichia coli cuts the sequence GAATTC and another enzyme from Bacillus
AB  - amyloliquefaciens will not cut it, but instead cuts the similar sequence GGATCC. Each species
AB  - of bacterium protects its own DNA at its personal sequence by adding a bulky methyl group on a
AB  - few of the bases, so only invading viral DNA, which does not have the protective methyl
AB  - groups, is chopped up and destroyed. There are hundreds of forms of these restriction enzymes,
AB  - made by different bacteria to cut DNA at different sequences.
ER  -

TY  - JOUR
AU  - Goodsell, D.S.
TI  - The Molecular Perspective: Restriction Endonucleases.
JO  - The Oncologist
PY  - 2002
SP  - 82
EP  - 83
VL  - 7
AB  - We live in a remarkable age. Physicians now have an unprecedented range of options for helping
AB  - their patients. Surgery and radiology are using advanced technologies to pinpoint treatments.
AB  - Chemotherapeutic approaches are showing ever-greater effectiveness and specificity,
AB  - approaching the goal of a "magic bullet." And we are now entering a time when we can make
AB  - changes at the most basic level, introducing changes directly into the genetic code. Gene
AB  - therapy, the ability to introduce new genes into living cells, holds great promise for the
AB  - treatment of many diseases, including cancer. Restriction endonucleases are the molecules that
AB  - spawned the field of biotechnology, the first of the many molecular tools that make gene
AB  - therapy a reality. Bacteria build restriction endonucleases to protect themselves from attack
AB  - by viruses. These enzymes cleave DNA at a specific sequence of nucleotides: for instance, one
AB  - enzyme from Escherichia coli cuts the sequence GAATTC and another enzyme from Bacillus
AB  - amyloliquefaciens will not cut it, but instead cuts the similar sequence GGATCC. Each species
AB  - of bacterium protects its own DNA at its personal sequence by adding a bulky methyl group on a
AB  - few of the bases, so only invading viral DNA, which does not have the protective methyl
AB  - groups, is chopped up and destroyed. There are hundreds of forms of these restriction enzymes,
AB  - made by different bacteria to cut DNA at different sequences.
ER  -

TY  - JOUR
AU  - Goodwin, S.B. et al.
TI  - Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.
JO  - PLoS Genet.
PY  - 2011
SP  - E1002070
EP  - E1002070
VL  - 7
AB  - The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage:
AB  - Septoria tritici) causes septoria tritici blotch, a disease that greatly
AB  - reduces the yield and quality of wheat. This disease is economically
AB  - important in most wheat-growing areas worldwide and threatens global food
AB  - production. Control of the disease has been hampered by a limited
AB  - understanding of the genetic and biochemical bases of pathogenicity,
AB  - including mechanisms of infection and of resistance in the host. Unlike
AB  - most other plant pathogens, M. graminicola has a long latent period during
AB  - which it evades host defenses. Although this type of stealth pathogenicity
AB  - occurs commonly in Mycosphaerella and other Dothideomycetes, the largest
AB  - class of plant-pathogenic fungi, its genetic basis is not known. To
AB  - address this problem, the genome of M. graminicola was sequenced
AB  - completely. The finished genome contains 21 chromosomes, eight of which
AB  - could be lost with no visible effect on the fungus and thus are
AB  - dispensable. This eight-chromosome dispensome is dynamic in field and
AB  - progeny isolates, is different from the core genome in gene and repeat
AB  - content, and appears to have originated by ancient horizontal transfer
AB  - from an unknown donor. Synteny plots of the M. graminicola chromosomes
AB  - versus those of the only other sequenced Dothideomycete, Stagonospora
AB  - nodorum, revealed conservation of gene content but not order or
AB  - orientation, suggesting a high rate of intra-chromosomal rearrangement in
AB  - one or both species. This observed "mesosynteny" is very different from
AB  - synteny seen between other organisms. A surprising feature of the M.
AB  - graminicola genome compared to other sequenced plant pathogens was that it
AB  - contained very few genes for enzymes that break down plant cell walls,
AB  - which was more similar to endophytes than to pathogens. The stealth
AB  - pathogenesis of M. graminicola probably involves degradation of proteins
AB  - rather than carbohydrates to evade host defenses during the biotrophic
AB  - stage of infection and may have evolved from endophytic ancestors.
ER  -

TY  - JOUR
AU  - Goordial, J.
AU  - Raymond-Bouchard, I.
AU  - Ronholm, J.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Whyte, L.
AU  - Bakermans, C.
TI  - Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 61
EP  - 61
VL  - 10
AB  - The actinobacterium Rhodococcus sp. JG-3 is an aerobic, eurypsychrophilic, soil bacterium
AB  - isolated from permafrost in the hyper arid Upper Dry Valleys of Antarctica. It is yellow
AB  - pigmented, gram positive, moderately halotolerant and capable of growth from 30 degrees C down
AB  - to at least -5 degrees C. The 5.28 Mb high-quality-draft genome is arranged into 6 scaffolds,
AB  - containing 9 contigs and  4998 protein coding genes, with 64 % GC content. Increasing the
AB  - availability of genome sequences from cold-adapted species is crucial to gaining a better
AB  - understanding of the molecular traits of cold adaptation in microbes.
ER  -

TY  - JOUR
AU  - Goossens, M.D.
AU  - Dumez, Y.
AU  - Kaplan, L.
AU  - Lupker, M.
AU  - Chabret, C.
AU  - Henrion, R.
AU  - Rosa, J.
TI  - Prenatal Diagnosis of Sickle-Cell anemia in the First Trimester of Pregnancy.
JO  - N. Engl. J. Med.
PY  - 1983
SP  - 831
EP  - 833
VL  - 309
AB  - To investigate the usefulness of chorionic biopsy for prenatal diagnosis of
AB  - sickle-cell anemia by restriction-endonuclease analysis of fetal DNA, we
AB  - studies 30 pregnancies before elective abortion.  When the reproductibility of
AB  - the technique for obtaining adequate DNA samples was established, we
AB  - successfully applied the test to five pregnancies at risk for sickle-cell
AB  - anemia.  In two cases, sickle-cell disease of the fetus led to a decision to
AB  - terminate the pregnancy.  In three other cases, a normal or AS genotype was
AB  - demonstrated.  One normal infant has been born, and one other pregnancy is
AB  - continuing normally.  In one case in which fetal death was observed three weeks
AB  - after ampling, placental abnormalties found on histologic examination were
AB  - compatible with a chromosomal aberration.  Our study shows that chorionic
AB  - biopsy is feasible for the prenatal diagnosis of sickle-cell disease before the
AB  - 10th gestational week.  If subsequent experience demonstrates this technique to
AB  - be safe enough for mother and fetus, the ability to test in early pregnancy may
AB  - make prenatal diagnosis acceptable to more couples at risk for serious genetic
AB  - disorders.
ER  -

TY  - JOUR
AU  - Gootz, T.D.
AU  - Lescoe, M.K.
AU  - Dib-Hajj, F.
AU  - Dougherty, B.A.
AU  - He, W.
AU  - Della-Latta, P.
AU  - Huard, R.C.
TI  - Genetic organization of transposase regions surrounding blaKPC carbapenemase genes on plasmids from Klebsiella strains isolated in a New York City hospital.
JO  - Antimicrob. Agents Chemother.
PY  - 2009
SP  - 1998
EP  - 2004
VL  - 53
AB  - Carbapenem-resistant Klebsiella strains carrying Klebsiella pneumoniae
AB  - carbapenemases (KPC) are endemic to New York City and are spreading across
AB  - the United States and internationally. Recent studies have indicated that
AB  - the KPC structural gene is located on a 10-kb plasmid-borne element
AB  - designated Tn4401. Fourteen Klebsiella pneumoniae strains and one
AB  - Klebsiella oxytoca strain isolated at a New York City hospital in 2005
AB  - carrying either bla(KPC-2) or bla(KPC-3) were examined for isoforms of
AB  - Tn4401. Ten of the Klebsiella strains contained a 100-bp deletion in
AB  - Tn4401, corresponding to the Tn4401a isoform. The presence of this
AB  - deletion adjacent to the upstream promoter region of bla(KPC) in Tn4401a
AB  - resulted in a different -35 promoter sequence of TGGAGA than that of
AB  - CTGATT present in isoform Tn4401b. Complete sequencing of one plasmid
AB  - carrying bla(KPC) from each of three nonclonal isolates indicated the
AB  - presence of genes encoding other types of antibiotic resistance
AB  - determinants. The 70.6-kb plasmid from K. pneumoniae strain S9 carrying
AB  - bla(KPC-2) revealed two identical copies of Tn4401b inserted in an inverse
AB  - fashion, but in this case, one of the elements disrupted a group II
AB  - self-splicing intron. In K. pneumoniae strain S15, the Tn4401a element
AB  - carrying bla(KPC-2) was found on both a large 120-kb plasmid and a smaller
AB  - 24-kb plasmid. Pulsed-field gel electrophoresis results indicate that the
AB  - isolates studied represent a heterogeneous group composed of unrelated as
AB  - well as closely related Klebsiella strains. Our results suggest that
AB  - endemic KPC-positive Klebsiella strains constitute a generally nonclonal
AB  - population comprised of various alleles of bla(KPC) on several distinct
AB  - plasmid genetic backgrounds. This study increases our understanding of the
AB  - genetic composition of the evolving and expanding role of KPC-producing,
AB  - healthcare-associated, gram-negative pathogens.
ER  -

TY  - JOUR
AU  - Gopal, J.
TI  - Molecular cloning and biochemical characterization of DsaV methyltransferase from Dactylococcopsis salina.
JO  - Diss. Abstr.
PY  - 1995
SP  - 121
EP  - 121
VL  - 57
AB  - The methyltransferase (Mtase) in the DsaV restriction-modification system methylates within
AB  - 5'-CCNGG sequences.  I have cloned the gene for this Mtase and characterized it.  The
AB  - predicted sequence of the Mtase protein contains sequence motifs conserved among all
AB  - cytosine-5 Mtases and is most similar to other Mtases that methylate CCNGG sequences -- namely
AB  - M.ScrFI and M.SsoII.  The "variable" region within the three enzymes that methylate CCNGG can
AB  - be aligned with the sequences of two enzymes that methylate CCWGG sequences.  Remarkably, two
AB  - segments within this region contain significant similarity with the region of M.HhaI that is
AB  - known to contact DNA bases.  These aligments suggest that many cytosine-5 Mtases are likely to
AB  - interact with DNA using a similar structural framework.  I have developed a simple new method
AB  - that can identify the base methylated by a sequence-specific DNA methyltransferase and have
AB  - used it to identify the cytosine that is methylated by DsaV methyltransferase (M.DsaV) within
AB  - its recognition sequence 5'-CCNGG.  The method utilizes the fact that exonuclease III of E.
AB  - coli does not degrade DNA ends with 3' overhangs and cannot hydrolyze a phosphorothioate
AB  - linkage.  DNA duplexes containing phosphorothioate linkages at specific positions were
AB  - methylated with M.DsaV in the presence of [methyl-3H] S-adenosylmethionine and were subjected
AB  - to exonuclease III digestion.  The pattern of [methyl-3H] dCMP release from the duplexes was
AB  - consistent with the methylation of the internal cytosine in CCNGG, but not of the outer
AB  - cytosine.  Methylation of CCWGG (W = A or T) sequences at the internal cytosines is native to
AB  - E. coli and is not restricted by the modified cytosine restriction (Mcr) systems.
AB  - Surprisingly, the gene for M.DsaV was significantly restricted by the McrBC system.  I
AB  - interpret this to mean that M.DsaV may occasionally methylate at sequences other than CCNNGG
AB  - or may occasionally methylate the outer cytosine in its recognition sequence.  I have also
AB  - shown for the first time that M.EcoRII methylates at CCSGG sites and other non-canonical sites
AB  - using a plasmid that substantially overproduces M.EcoRII.  This result suggests that C5
AB  - methylates may occasionally methylate cellular DNA at non-canonical sites and that E. coli
AB  - methylation specific restriction system and DNA mismatch correction systems may have evolved
AB  - to accommodate this fact.
ER  -

TY  - JOUR
AU  - Gopal, J.
AU  - Bhagwat, A.S.
TI  - Determination of methylation specificity of DsaV methyltransferase by a simple biochemical method.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 29
EP  - 35
VL  - 23
AB  - We have developed a simple new method that can identify the base methylated by a
AB  - sequence-specific DNA methyltransferase and have used it to identify the cytosine that is
AB  - methylated by DsaV methyltransferase (M.DsaV) within its recognition sequence 5'-CCNGG. The
AB  - method utilizes the fact that exonuclease III of E.coli does not degrade DNA ends with 3'
AB  - overhangs and cannot hydrolyze a phosphorothioate linkage. DNA duplexes containing
AB  - phosphorothioate linkages at specific positions were methylated with M.DsaV in the presence of
AB  - [methyl-3H] S-adenosylmethionine and were subjected to exonuclease III digestion. The pattern
AB  - of [methyl-3H] dCMP release from the duplexes was consistent with the methylation of the
AB  - internal cytosine in CCNGG, but not of the outer cytosine. To establish the accuracy of this
AB  - method, we confirmed the known specificity of EcoRII methyltransferase by the method. We also
AB  - confirmed the specificity of M.DsaV using an established biochemical method that involves the
AB  - use of a type IIS restriction enzyme. Methylation of CCWGG (W=A or T) sequences at the
AB  - internal cytosines is native to E. coli and is not restricted by the modified cytosine
AB  - restriction (Mcr) systems. Surprisingly, the gene for M.DsaV was significantly restricted by
AB  - the McrBC system. We interpret this to mean that M.DsaV may occasionally methylate at
AB  - sequences other than CCNGG or may occasionally methylate the outer cytosine in its recognition
AB  - sequence.
ER  -

TY  - JOUR
AU  - Gopal, J.
AU  - Yebra, M.J.
AU  - Bhagwat, A.S.
TI  - DsaV methyltransferase and its isoschizomers contain a conserved segment that is similar to the segment in HhaI methyltransferase that is in contact with DNA bases.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 4482
EP  - 4488
VL  - 22
AB  - The methyltransferase (MTase) in the DsaV restriction-modification system methylates within
AB  - 5'-CCNGG sequences. We have cloned the gene for this MTase and determined its sequence. The
AB  - predicted sequence of the MTase protein contains sequence motifs conserved among all
AB  - cytosine-5 MTases and is most similar to other MTases that methylate CCNGG sequences, namely
AB  - M.ScrFI and M.SsoII. All three MTases methylate the internal cytosine within their recognition
AB  - sequence. The 'variable' region within the three enzymes that methylate CCNGG can be aligned
AB  - with the sequences of two enzymes that methylate CCWGG sequences. Remarkably, two segments
AB  - within this region contain significant similarity with the region of M.HhaI that is known to
AB  - contact DNA bases. These alignments suggest that many cytosine-5 MTases are likely to interact
AB  - with DNA using a similar structural framework.
ER  -

TY  - JOUR
AU  - Gopal, J.
AU  - Yebra, M.J.
AU  - Bhagwat, A.S.
TI  - Cloning and characterization of the gene encoding the DsaV methyltransferase.
JO  - Gene
PY  - 1995
SP  - 61
EP  - 63
VL  - 157
AB  - A gene encoding the M.DsaV methyltransferase was cloned and characterized.  The enzyme
AB  - methylates the internal cytosines in the 5'-CCTGG recognition sequence, as determined by a
AB  - novel rapid method employing 3H label and exonuclease III.
ER  -

TY  - JOUR
AU  - Gopalakrishnan, S.
TI  - Functional characterization of the de novo DNA methyltransferase DNMT3B.
JO  - Ph.D. Thesis, Univ. of Florida, Gainesville
PY  - 2009
SP  - 1
EP  - 215
AB  - DNA methylation is an epigenetic mark that is required for transcriptional repression in
AB  - mammalian development, imprinting, and in the maintenance of genome stability. Genome-wide
AB  - methylation patterns are established and maintained by three DNA methyltransferases (DNMTs)-
AB  - DNMT1, DNMT3A, and DNMT3B. DNMT3B is specifically involved in silencing the satellite repeats
AB  - at the centromeric and pericentromeric regions. The role of DNMT3B at the centromeric region
AB  - is also emphasized by mitotic defects arising due to chromosome instability observed in ICF
AB  - syndrome, a disease caused by germline mutations in DNMT3B. Although the mechanism of DNA
AB  - methylation is well known, the targeting of DNA methylation and DNMT3B to certain genomic loci
AB  - remains poorly understood. DNMT3B is also regulated by alternative splicing. Several DNMT3B
AB  - splice variants are overexpressed in tumor cells and negatively regulate normal DNMT3B
AB  - mediated DNA methylation. Therefore it is important to understand the significance of DNMT3B
AB  - splice variants in development and tumorigenesis. In the present study, a yeast two-hybrid
AB  - screening was performed and several novel DNMT3B protein interactions were identified. Of the
AB  - several proteins identified, the interaction of DNMT3B with the mammalian chromatin associated
AB  - factor MCAF and the chromodomain helicase DNA binding protein CHD3 were confirmed, and need
AB  - further characterization. The interaction between DNMT3B and the constitutive centromeric
AB  - protein CENP-C was confirmed in mammalian cells. Results from siRNA knock downs, bisulfite
AB  - genomic sequencing and ChIP, demonstrate that CENP-C recruits DNA methylation and DNMT3B to
AB  - both centromeric and pericentromeric satellite repeats. CENP-C and DNMT3B influence the
AB  - histone modifications in satellite repeat regions, including marks characteristic of
AB  - centromeric chromatin and disruption of this interaction causes elevated transcription of
AB  - centromeric repeats. Loss of CENP-C or DNMT3B leads to elevated chromosome misalignment and
AB  - segregation defects during mitosis. Taken together, the interaction between CENP-C and DNMT3B
AB  - suggests a novel mechanism by which DNA methylation is targeted to discrete regions of the
AB  - genome and contributes to chromosomal stability. In another study, a novel alternatively
AB  - spliced form of DNMT3B lacking exon 5 was identified and characterized. This variant was
AB  - termed DNMT3B3"5 because of its close resemblance with the ubiquitously expressed DNMT3B3
AB  - isoform. The novel splice variant lacking exon 5 is highly expressed in pluripotent cells and
AB  - neural tissues, and is conserved in the mouse and is re-expressed on converting differentiated
AB  - mEFs into pluripotent iPS cells. DNMT3B3"5 also displays altered expression in human tumor
AB  - cell lines as well as an altered subcellular localization. Ectopic overexpression of DNMT3B3"5
AB  - resulted in repetitive element hypomethylation. Taken together, these results demonstrate that
AB  - alternative splicing of exon 5 may play an important role in stem cell maintenance or
AB  - differentiation and exon 5 could influence the functional properties of DNMT3B.
ER  -

TY  - JOUR
AU  - Gopinath, G.
AU  - Jean-Gilles, B.J.
AU  - Grim, C.
AU  - Blaylock, M.
AU  - Blackwell, R.
AU  - Merid, S.
AU  - Diallo, A.
AU  - Hanes, D.
TI  - Whole-Genome Sequences of Six Salmonella enterica Serovar Bovismorbificans Isolates Associated with a 2011 Multistate Hummus-Borne Outbreak.
JO  - Genome Announcements
PY  - 2014
SP  - e01239
EP  - e01213
VL  - 2
AB  - We present six draft genome sequences of Salmonella enterica serovar Bovismorbificans from
AB  - isolates associated with the 2011 hummus-borne multistate
AB  - outbreak. All six genome sequences indicate the presence of two plasmids, one of
AB  - which demonstrates similarity to the 93-kb pSLT2 IncF-type plasmid of Salmonella
AB  - enterica serovar Typhimurium.
ER  -

TY  - JOUR
AU  - Gopinath, G.
AU  - Jean-Gilles, B.J.
AU  - Grim, C.
AU  - Hanes, D.
TI  - Draft Genome Sequences of Nine Salmonella enterica Serovar Bovismorbificans Isolates from Various Sources.
JO  - Genome Announcements
PY  - 2014
SP  - e01249
EP  - e01213
VL  - 2
AB  - The sequences of nine genomes of Salmonella enterica serovar Bovismorbificans were compared to
AB  - study the diversity and distribution of this emerging virulent
AB  - serovar. These whole-genome sequences fill some gaps in knowledge of the
AB  - diversity of the isolates used in this investigation.
ER  -

TY  - JOUR
AU  - Gopinath, G.R.
AU  - Grim, C.J.
AU  - Tall, B.D.
AU  - Mammel, M.K.
AU  - Sathyamoorthy, V.
AU  - Trach, L.H.
AU  - Chase, H.R.
AU  - Fanning, S.
AU  - Stephan, R.
TI  - Genome Sequences of Two Enterobacter pulveris Strains, 601/05T (=LMG 24057T =DSM  19144T) and 1160/04 (=LMG 24058 =DSM 19146), Isolated from Fruit Powder.
JO  - Genome Announcements
PY  - 2013
SP  - e00991
EP  - e00913
VL  - 1
AB  - We report the draft genome sequences of the Enterobacter pulveris strains 601/05(T)
AB  - (=LMG24057(T) =DSM19144(T)) and 1160/04 (=LMG24058 =DSM19146), isolated
AB  - from fruit powder. The genome assemblies for the E. pulveris type strain,
AB  - LMG24057, and strain LMG24058 have sizes of 4,708,624 and 4,811,103 bp and G+C
AB  - contents of 56.6% and 56.5%, respectively.
ER  -

TY  - JOUR
AU  - Goppelt, M.
AU  - Langowski, J.
AU  - Pingoud, A.
AU  - Haupt, W.
AU  - Urbanke, C.
AU  - Mayer, H.
TI  - The effect of several nucleic acid binding drugs on the cleavage of d(GGAATTCC) and pBR322 by the EcoRI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 6115
EP  - 6127
VL  - 9
AB  - The endonucleolytic action of the EcoRI restriction enzyme on the
AB  - double-stranded oligonucleotide d(GGAATTCC) and the supercoiled plasmid DNA
AB  - pBR322 is inhibited by actinomycin D, ethidium bromide, proflavin, distamycin A
AB  - and netropsin.  Half-maximal inhibition is observed at around 100 micromolar
AB  - concentrations for the intercalating drugs, and around 0.1 to 1 micromolar
AB  - concentrations for netropsin and distamycin A.  The inhibitory activity of
AB  - these drugs can be correlated with their affinity to the oligonucleotide and
AB  - the plasmid DNA.  Since at high concentrations of the drugs a complete
AB  - inhibition is observed, it is concluded that the effect of the drugs on the
AB  - sterochemistry of the EcoRI site is such that recognition is excluded.
ER  -

TY  - JOUR
AU  - Goppelt, M.
AU  - Pingoud, A.
AU  - Maass, G.
AU  - Mayer, H.
AU  - Koster, H.
AU  - Frank, R.
TI  - The interaction of the EcoRI restriction endonuclease with its substrate:  A physico-chemical study employing natural and synthetic oligonucleotides and polynucleotides.
JO  - Eur. J. Biochem.
PY  - 1980
SP  - 101
EP  - 107
VL  - 104
AB  - The interaction of the EcoRI restriction endodeoxyribonuclease with
AB  - polynucleotides has been studied in a qualitative manner by an affinity
AB  - adsorption technique using polynucleotides immobilized on cellulose.  It is
AB  - shown that EcoRI binds to single-stranded and double-stranded
AB  - polyribonucleotides and polydeoxyribonucleotides.  Mg2+ ions are not required
AB  - for binding.  In order to define differences between specific and non-specific
AB  - binding we have investigated the interaction of EcoRI with d(TAAATG),
AB  - d(TTACAT), d(GAATTC) and d(GGAATTCC).  We have synthesized for this purpose
AB  - d(TAAATG), d(TTACAT) and d(GAATTC) by the diester approach.  d(GAATTC) and
AB  - d(GGAATTCC) are self complementary.  Differential melting experiments show that
AB  - the octanucleotide has a melting point of 28C under ionic conditions where the
AB  - hexanucleotide is single-stranded even below 0C.  Correspondingly, the
AB  - octanucleotide is cleaved by EcoRI, while the hexanucleotide is not.  The
AB  - binding of oligonucleotides to EcoRI can be monitored by the circular dichroism
AB  - of the enzyme.  Titrations show that in the absence of Mg2+ ions all
AB  - oligonucleotides are bound with similar magnitude:  Ka - 10/7 M-1.  Complex
AB  - formation is weakened with increasing temperature, corresponding to a delta Ho
AB  - of -21 kJ/mol and increasing ionic strength, corresponding to an involvement of
AB  - two ion-pair bonds between DNA and enzyme.  Mg2+ ions have no significant
AB  - influence on the binding of d(TAAATG), d(TTACAT) and d(GAATTC) to the enzyme.
AB  - The binding of d(GGAATTCC) to EcoRI is strengthened by a factor of 50 in the
AB  - presence of Mg2+ ions, as measured by cleavage experiments using d(GAATTC) as a
AB  - competing inhibitor in the enzymatic assay.
ER  -

TY  - JOUR
AU  - Gorbalenya, A.E.
TI  - Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family.
JO  - Protein Sci.
PY  - 1994
SP  - 1117
EP  - 1120
VL  - 3
AB  - A new family of protein domains consisting of 50-80 amino acid residues is described.  It is
AB  - composed of nearly 40 members, including domains encoded by plastid and phage group I introns;
AB  - mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and
AB  - phages.  The name "EX1HH-HX3H" was coined for both domain and family.  It is based on 2 most
AB  - prominent amino acid sequene motifs, each encompassing a pair of highly conserved histidine
AB  - residues in a specific arrangement: EX1HH and HX3H.  The "His" motifs often alternate with
AB  - amino- and carboxy-terminal motifs of a new type of Zn-finger-like structure
AB  - CX2,4CX29-54[CH]X2,3[CH].  The EX1HH-HX3H domain in eubacterial E2-type bacteriocins and in
AB  - phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be
AB  - essential for DNA endonuclease activity of these proteins.  In other proteins, the EX1HH-HX3H
AB  - domain is hypothesized to possess DNase activity as well.  Presumably, this activity promotes
AB  - movement (rearrangement) of group I and group II introns encoding the EX1HH-HX3H domain and
AB  - other gene targets.  In the case of Escherichia coli restrictase McrA and possibly several
AB  - related proteins, it appears to mediate the restriction of alien DNA molecules.
ER  -

TY  - JOUR
AU  - Gorbalenya, A.E.
AU  - Koonin, E.V.
TI  - Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain.
JO  - FEBS Lett.
PY  - 1991
SP  - 277
EP  - 281
VL  - 291
AB  - A statistically significant amino acid sequence similarity is demonstrated
AB  - between the endonuclease (R) subunit of the EcoKI restriction-modification
AB  - (R-M) enzyme, and RNA and DNA helicases of the so-called 'DEAD' family.  It is
AB  - further shown that all three known sequences of R subunits of type-I and
AB  - type-III R-M enzymes contain the conserved amino acid sequence motifs typical
AB  - of the previously described helicase superfamily II (1989) Nucl. Acids Res.
AB  - 17,4713-4730.  A hypothesis is proposed that these enzymes may exert helicase
AB  - activity possibly required for local unwinding of DNA in the cleavage sites.
ER  -

TY  - JOUR
AU  - Gorbunov, Y.A.
AU  - Zinovev, V.V.
AU  - Rechkunova, N.I.
AU  - Ovechkina, L.G.
AU  - Popov, S.G.
AU  - Malygin, E.G.
TI  - Chemical synthesis and characteristics of oligonucleotide substrates for restriction endonuclease BamHI and methylase Eco dam.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 1629
EP  - 1637
VL  - 13
AB  - Oligodeoxyribonucleotides which form a number of duplexes, containing the recognition
AB  - sequences for endonuclease BamHI and DNA methylase Eco dam, were synthesized by the
AB  - phosphotriester approach. Furthermore, synthesis of 3'-phosphorylated
AB  - oligodeoxyribonucleotides from corresponding S-methyl phosphorothioate triester oligomers is
AB  - described. The synthetic duplexes are characterized by some defects in the recognition
AB  - sequences for endonuclease BamHI and methylase Eco dam, viz. nick, absence of an
AB  - internucleotide phosphate, modifications (including partial single-strandedness) of the
AB  - recognition site. Interaction of the enzymes with these synthetic substrates was investigated.
ER  -

TY  - JOUR
AU  - Gordon, S.V.
AU  - Brosch, R.
AU  - Billault, A.
AU  - Garnier, T.
AU  - Eiglmeier, K.
AU  - Cole, S.T.
TI  - Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays.
JO  - Mol. Microbiol.
PY  - 1999
SP  - 643
EP  - 655
VL  - 32
AB  - Whole-genome comparisons of the tubercle bacilli were undertaken using ordered bacterial
AB  - artificial chromosome (BAC) libraries of Mycobacterium
AB  - tuberculosis and the vaccine strain, Mycobacterium bovis BCG-Pasteur,
AB  - together with the complete genome sequence of M. tuberculosis H37Rv.
AB  - Restriction-digested BAC arrays of M. tuberculosis H37Rv were used in
AB  - hybridization experiments with radiolabelled M. bovis BCG genomic DNA to
AB  - reveal the presence of 10 deletions (RD1-RD10) relative to M.
AB  - tuberculosis. Seven of these regions, RD4-RD10, were also found to be
AB  - deleted from M. bovis, with the three M. bovis BCG-specific deletions
AB  - being identical to the RD1-RD3 loci described previously. The distribution
AB  - of RD4-RD10 in Mycobacterium africanum resembles that of M. tuberculosis
AB  - more closely than that of M. bovis, whereas an intermediate arrangement
AB  - was found in Mycobacterium microti, suggesting that the corresponding
AB  - genes may affect host range and virulence of the various tubercle bacilli.
AB  - Among the known products encoded by these loci are a copy of the proposed
AB  - mycobacterial invasin Mce, three phospholipases, several PE, PPE and
AB  - ESAT-6 proteins, epoxide hydrolase and an insertion sequence. In a
AB  - complementary approach, direct comparison of BACs uncovered a third class
AB  - of deletions consisting of two M. tuberculosis H37Rv loci, RvD1 and RvD2,
AB  - deleted from the genome relative to M. bovis BCG and M. bovis. These
AB  - deletions affect a further seven genes, including a fourth phospholipase,
AB  - plcD. In summary, the insertions and deletions described here have
AB  - important implications for our understanding of the evolution of the
AB  - tubercle complex.
ER  -

TY  - JOUR
AU  - Gorecki, R.K.
AU  - Bardowski, J.K.
TI  - Molecular mechanisms of bacteriophage resistance of lactic acid bacteria.
JO  - Postepy Mikrobiologii
PY  - 2011
SP  - 265
EP  - 273
VL  - 50
AB  - Lactic acid bacteria (LAB) constitute a heterogeneous group of bacteria, which are found in
AB  - diverse environments, such as the human body or plants, and are traditionally used to produce
AB  - fermented food. Food bio-transformation in industrial processes increases the economical
AB  - importance of LAB. However, conditions that exist in industrial facilities do not seem to be
AB  - an optimal environment for bacteria. During technological processes, which take place in
AB  - enclosed space, the intensity of physical (temperature shift), chemical (acids) or biological
AB  - (phages) stress factors raises dramatically. In the dairy industry, bacteriophage
AB  - contamination is regarded as a serious problem due to the disturbance or arrest of the
AB  - production processes, which results in significant economical losses. It is well documented
AB  - that LAB evolved defense systems against bacteriophages, which allow them to survive in harsh
AB  - conditions. Therefore, bacteria used in food industry are selected for high level of
AB  - bacteriophage resistance. According to the mode of action, natural bacterial defense systems
AB  - against their predators were divided into 5 categories: (i) inhibition of phage adsorption,
AB  - (ii) blocking of phage DNA injection, (iii) phage abortive infection systems, (iv) restriction
AB  - modification systems, (v) CRISPR/Cas systems. Remarkably, the majority of known bacteriophage
AB  - resistance systems are plasmid-encoded. In this context, future studies on phage resistance
AB  - mechanisms as well as plasmid sequencing may have an impact on solving the problem of phage
AB  - infections in the dairy industry.
ER  -

TY  - JOUR
AU  - Gorecki, R.K.
AU  - Koryszewska-Baginska, A.
AU  - Golebiewski, M.
AU  - Zylinska, J.
AU  - Grynberg, M.
AU  - Bardowski, J.K.
TI  - Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids.
JO  - PLoS ONE
PY  - 2011
SP  - e22238
EP  - e22238
VL  - 6
AB  - The extrachromosomal gene pool plays a significant role both in evolution and in the
AB  - environmental adaptation of bacteria.  The L. lactis subsp. lactis IL594 strain contains seven
AB  - plasmids, named pIL1 to pIL7, and is the parental strain of the plasmidfree L. lactis IL1403,
AB  - which is one of the best characterized lactococcal strains of LAB. Complete nucleotide
AB  - sequences of pIL1 (6,382 bp), pIL2 (8,277 bp), pIL3 (19,244 bp), pIL4 (48,979), pIL5 (23,395),
AB  - pIL6 (28,435 bp) and pIL7 (28,546) were
AB  - established and deposited in the generally accessible database (GeneBank). Nine highly
AB  - homologous repB-containing replicons, belonging to the lactococcal theta-type replicons, have
AB  - been identified on the seven plasmids. Moreover, a putative region involved in conjugative
AB  - plasmid mobilization was found on four plasmids, through identification of the
AB  - presence of mob genes and/or oriT sequences. Detailed bioinformatic analysis of the plasmid
AB  - nucleotide sequences provided new insight into the repertoire of plasmid-encoded functions in
AB  - L. lactis, and indicated that plasmid genes from IL594 strain can be important for L. lactis
AB  - adaptation to specific environmental conditions (e.g. genes coding for proteins involved in
AB  - DNA repair or cold shock response) as well as for technological processes (e.g. genes encoding
AB  - citrate and lactose utilization, oligopeptide transport, restriction-modification system).
AB  - Moreover, global gene analysis indicated
AB  - cooperation between plasmid- and chromosome-encoded metabolic pathways.
ER  -

TY  - JOUR
AU  - Goris, T.
AU  - Hornung, B.
AU  - Kruse, T.
AU  - Reinhold, A.
AU  - Westermann, M.
AU  - Schaap, P.J.
AU  - Smidt, H.
AU  - Diekert, G.
TI  - Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 15
EP  - 15
VL  - 10
AB  - This genome report describes the draft genome and the physiological characteristics of
AB  - Desulfitobacterium hafniense PCE-S, a Gram-positive bacterium
AB  - known to dechlorinate tetrachloroethene (PCE) to dichloroethene by a PCE
AB  - reductive dehalogenase. The draft genome has a size of 5,666,696 bp with a G + C
AB  - content of 47.3%. The genome is very similar to the already sequenced
AB  - Desulfitobacterium hafniense Y51 and the type strain DCB-2. We identified two
AB  - complete reductive dehalogenase (rdh) genes in the genome of D. hafniense PCE-S,
AB  - one of which encodes PceA, the PCE reductive dehalogenase, and is located on a
AB  - transposon. Interestingly, this transposon structure differs from the
AB  - PceA-containing transposon of D. hafniense Y51. The second rdh encodes an unknown
AB  - reductive dehalogenase, highly similar to rdhA 7 found in D. hafniense DCB-2, in
AB  - which the corresponding gene is disrupted. This reductive dehalogenase might be
AB  - responsible for the reductive dechlorination of 2,4,5-trichlorophenol and
AB  - pentachlorophenol, which is mediated by D. hafniense PCE-S in addition to the
AB  - reductive dechlorination of PCE.
ER  -

TY  - JOUR
AU  - Gorkiewicz, G.
AU  - Kienesberger, S.
AU  - Schober, C.
AU  - Scheicher, S.R.
AU  - Gully, C.
AU  - Zechner, R.
AU  - Zechner, E.L.
TI  - A genomic island defines subspecies-specific virulence features of the host-adapted pathogen Campylobacter fetus subsp. venerealis.
JO  - J. Bacteriol.
PY  - 2010
SP  - 502
EP  - 517
VL  - 192
AB  - The pathogen Campylobacter fetus comprises two subspecies, C. fetus subsp.
AB  - fetus and C. fetus subsp. venerealis. Although these taxa are highly
AB  - related on the genome level, they are adapted to distinct hosts and
AB  - tissues. C. fetus subsp. fetus infects a diversity of hosts, including
AB  - humans, and colonizes the gastrointestinal tract. In contrast, C. fetus
AB  - subsp. venerealis is largely restricted to the bovine genital tract,
AB  - causing epidemic abortion in these animals. In light of their close
AB  - genetic relatedness, the specific niche preferences make the C. fetus
AB  - subspecies an ideal model system to investigate the molecular basis of
AB  - host adaptation. In this study, a subtractive-hybridization approach was
AB  - applied to the genomes of the subspecies to identify different genes
AB  - potentially underlying this specificity. The comparison revealed a genomic
AB  - island uniquely present in C. fetus subsp. venerealis that harbors several
AB  - genes indicative of horizontal transfer and that encodes the core
AB  - components necessary for bacterial type IV secretion. Macromolecular
AB  - transporters of this type deliver effector molecules to host cells,
AB  - thereby contributing to virulence in various pathogens. Mutational
AB  - inactivation of the putative secretion system confirmed its involvement in
AB  - the pathogenicity of C. fetus subsp. venerealis.
ER  -

TY  - JOUR
AU  - Gorlas, A.
AU  - Gimenez, G.
AU  - Raoult, D.
AU  - Roux, V.
TI  - Draft Genome Sequences of Actinomyces timonensis Strain 7400942T and Its Prophage.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6613
EP  - 6614
VL  - 194
AB  - A draft genome sequence of Actinomyces timonensis, an anaerobic bacterium isolated from a
AB  - human clinical osteoarticular sample, is described here.
AB  - CRISPR-associated proteins, insertion sequence, and toxin-antitoxin loci were
AB  - found on the genome. A new virus or provirus, AT-1, was characterized.
ER  -

TY  - JOUR
AU  - Gorlas, A.
AU  - Robert, C.
AU  - Gimenez, G.
AU  - Drancourt, M.
AU  - Raoult, D.
TI  - Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4745
EP  - 4745
VL  - 194
AB  - The present study describes the complete and annotated genome sequence of
AB  - Methanomassiliicoccus luminyensis strain B10 (DSM 24529(T), CSUR P135), which was
AB  - isolated from human feces. The 2.6-Mb genome represents the largest genome of a
AB  - methanogenic euryarchaeon isolated from humans. The genome data of M. luminyensis
AB  - reveal unique features and horizontal gene transfer events, which might have
AB  - occurred during its adaptation and/or evolution in the human ecosystem.
ER  -

TY  - JOUR
AU  - Gorlatova, N.V.
AU  - Kryuchkova, E.G.
AU  - Koltovaya, N.A.
AU  - Dolgova, I.N.
AU  - Ananyin, V.M.
AU  - Velkov, V.V.
TI  - Synthesis of EcoRV restriction endonuclease in Escherichia coli continuous culture.  II. Effects of cultivation conditions on efficiency of thermoinduction of synthesis of cloned EcoRV restriction endonuclease.
JO  - Biotekhnologiya
PY  - 1991
SP  - 27
EP  - 30
VL  - 0
AB  - Effects of growth rate of recombinant cells of E. coli K802 (plLRV8) and of induction
AB  - conditions on the efficiency of thermoinduction of synthesis of EcoRV restriction endonuclease
AB  - cloned in PILRV8 plasmid controlled by the pR promoter of lambda phage were studied. The
AB  - efficiency of thermoinduction was shown to be 2-2.5 times higher in E. coli cells growing with
AB  - mu=0.35 h-1 than in fast growing cells with mu=0.6 h-1. Introduction of casamino acids did not
AB  - influence the thermoinduction level in slow (mu=0.35 h-1) growing cells, but stimulated
AB  - restrictase synthesis insignificantly in fast growing cells (mu=0.6 h-1). Addition of glucose
AB  - and glucose + casamino acids into EcoRV induction medium resulted in lowering the
AB  - thermoinduction efficiency of the PR promoter by 13-31%, respectively, as compared with
AB  - induction on nutrient-deficient medium for slow growing cells. At the same time, addition of
AB  - glucose while thermoinducing fast growing cells enhanced synthesis of EcoRV restrictase.
AB  - Dynamics of the induced synthesis of EcoRV restriction endonuclease were observed to be
AB  - different in fast and slow growing cultures of recombinant cells.
ER  -

TY  - JOUR
AU  - Gorlatova, N.V.
AU  - Kryukova, E.G.
AU  - Koltovaya, N.A.
AU  - Dolgova, I.N.
AU  - Velkov, V.V.
TI  - Synthesis of EcoRV restriction endonuclease by chemostatic cultivation of an Escherichia coli K 802 recombinant strain.  1. Effects of growth rate on expression of plasmid genes of EcoRV restriction endonuclease and beta-lactamase.
JO  - Biotekhnologiya
PY  - 1991
SP  - 34
EP  - 38
VL  - 3
AB  - Stability and expression of pILRV8 plasmid in E. coli cells growing on minimal
AB  - glucose medium were studied in chemostatic mode within a wide range of dilution
AB  - rates (D=0; V=0.1-0.6 hr-1) and in turbidostatic mode (Vmax=0.7 hr-1).  High
AB  - segregational and structural stability was characteristic for the strain under
AB  - these conditions.  Beta-lactamase and EcoRV restriction endonuclease determined
AB  - by genes of pILRV8 plasmid were synthesized concertedly, activity increasing
AB  - 4-fold with increasing dilution rate in chemostatic mode.
ER  -

TY  - JOUR
AU  - Gormley, N.A.
AU  - Bath, A.J.
AU  - Halford, S.E.
TI  - Reactions of BglI and other Type II restriction endonucleases with discontinuous recognition sites.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 6928
EP  - 6936
VL  - 275
AB  - Type II restriction enzymes generally recognize continuous sequences of 4-8 consecutive base
AB  - pairs on DNA, but some recognize discontinuous
AB  - sites where the specified sequence is interrupted by a defined length
AB  - of nonspecific DNA. To date, a mechanism has been established for only
AB  - one type II endonuclease with a discontinuous site, SfiI at
AB  - GGCCNNNNNGGCC (where N is any base). In contrast to orthodox enzymes
AB  - such as EcoRV, dimeric proteins that act at a single site, SfiI is a
AB  - tetramer that interacts with two sites before cleaving DNA. BglI has a
AB  - similar recognition sequence (GCCNNNNNGGC) to SfiI but a crystal
AB  - structure like EcoRV. BglI and several other endonucleases with
AB  - discontinuous sites were examined to see if they need two sites for
AB  - their DNA cleavage reactions. The enzymes included some with sites
AB  - containing lengthy segments of nonspecific DNA, such as XcmI
AB  - (CCANNNNNNNNNTGG). In all cases, they acted at individual sites.
AB  - Elongated recognition sites do not necessitate unusual reaction
AB  - mechanisms. Other experiments on BglI showed that it bound to and
AB  - cleaved DNA in the same manner as EcoRV, thus further delineating a
AB  - distinct group of restriction enzymes with similar structures and a
AB  - common reaction mechanism.
ER  -

TY  - JOUR
AU  - Gormley, N.A.
AU  - Hillberg, A.L.
AU  - Halford, S.E.
TI  - The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 4034
EP  - 4041
VL  - 277
AB  - Type IIs endonucleases recognize asymmetric DNA sequences and cleave both strands at fixed
AB  - positions downstream of the sequence. Many type IIs enzymes, including BspMI, cleave
AB  - substrates with two sites more rapidly than those with one site. They usually act sequentially
AB  - on DNA with two sites, but BspMI converted such a substrate directly to the final products cut
AB  - at both sites. The BspMI endonuclease was found to be a tetramer, in contrast to the monomeric
AB  - structures for many type IIs enzymes. No change in subunit association occurred during the
AB  - BspMI reaction. Plasmids with two BspMI sites were cleaved in cis, in reactions spanning sites
AB  - in the same DNA, even when the sites were separated by just 38 bp. Plasmids with one BspMI
AB  - site were cleaved in trans, with the enzyme bridging sites in separate DNA molecules: these
AB  - slow reactions could be accelerated by adding a second DNA with the recognition sequence.
AB  - Thus, whereas many type IIs enzymes dimerize before cleaving DNA, a process facilitated by two
AB  - recognition sites in cis, the BspMI tetramer binds two copies of its recognition sequence
AB  - before cleaving the DNA in both strands at both sites.
ER  -

TY  - JOUR
AU  - Gorovsky, M.A.
AU  - Hattman, S.
AU  - Pleger, G.L.
TI  - [6N]Methyl adenine in the nuclear DNA of a eucaryote, Tetrahymena pyriformis.
JO  - J. Cell Biol.
PY  - 1973
SP  - 697
EP  - 701
VL  - 56
AB  - DNA isolated from macronuclei of the ciliate, Tetrahymena pyriformis, has been found to
AB  - contain [6N]methyl adenine (MeAde); this represents the first clear demonstration of
AB  - significant amounts of MeAde in the DNA of a eucaryote. The amounts of macronuclear MeAde
AB  - differed slightly between different strains of Tetrahymena, with approximately 0.65-0.80% of
AB  - the adenine bases being methylated. The MeAde content of macronuclear DNA did not seem to vary
AB  - in different physiological states. The level of MeAde in DNA isolated from micronuclei, on the
AB  - other hand, was quite low (at least tenfold lower than in macronuclear DNA).
ER  -

TY  - JOUR
AU  - Gorrell, R.
AU  - Kwok, T.
TI  - The Helicobacter pylori Methylome: Roles in Gene Regulation and Virulence.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 2017
SP  - 105
EP  - 127
VL  - 400
AB  - The methylome is defined as a map of DNA methylation patterns at single-base resolution. DNA
AB  - methylation in bacteria was first discovered as a function of restriction-modification (R-M)
AB  - systems. R-M systems in Helicobacter pylori, like those in other bacteria, are important
AB  - host-specificity determinants that provide protection against foreign DNA. Moreover, the gene
AB  - regulatory role of the methyltransferase (Mtase) unit of various Helicobacter pylori R-M
AB  - systems is being increasingly recognized. Recent advances in the application of
AB  - single-molecule real-time (SMRT) DNA sequencing to analyse DNA methylation have revealed for
AB  - the first time comprehensive pictures of the genome-wide distribution of methylation sites in
AB  - various strains of H. pylori. The methylomic data published so far have not only confirmed the
AB  - significant inter-strain diversity of H. pylori Mtases and their DNA methylation profiles, but
AB  - also identified numerous novel Mtase target recognition sites. The precise knowledge of the
AB  - nucleotide sequence of Mtase recognition sites and their distribution within the H. pylori
AB  - genome will in turn enable researchers to more readily test hypotheses on how H. pylori Mtases
AB  - function to orchestrate gene regulation and/or modulate virulence. Methylomic studies hold
AB  - promise for providing a deeper understanding into the roles of H. pylori Mtase and R-M systems
AB  - in the physiology, epigenetics and possibly also pathogenesis of this important human
AB  - pathogen. Consequently, the knowledge gained will provide crucial insights into the potential
AB  - application of H. pylori methylomes as novel biomarkers for the prediction of disease outcome
AB  - and/or antibiotic susceptibility.
ER  -

TY  - JOUR
AU  - Gorski, L.
AU  - Huynh, S.
AU  - Cooper, K.K.
AU  - Parker, C.T.
TI  - Complete Genomic Sequences of Two Salmonella enterica subsp. enterica Serogroup C2 (O:6,8) Strains from Central California.
JO  - Genome Announcements
PY  - 2017
SP  - e01234
EP  - e01217
VL  - 5
AB  - Salmonella enterica subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype
AB  - 6,8:-:e,n,z15, were isolated from environmental samples
AB  - collected in central California in 2009. We report the complete genome sequences
AB  - of these two strains. These genomic sequences are distinct and will provide
AB  - additional data to our understanding of S. enterica genomics.
ER  -

TY  - JOUR
AU  - Gosse, J.T.
AU  - Hill, P.
AU  - Dowd, S.E.
AU  - Boddy, C.N.
TI  - Draft Genome Sequence of Streptomyces sp. Strain PBH53, Isolated from an Urban Environment.
JO  - Genome Announcements
PY  - 2015
SP  - e00859
EP  - e00815
VL  - 3
AB  - We report the draft genome sequence of Streptomyces sp. strain PBH53, a strain isolated from
AB  - an urban transit station in Ottawa, Canada. The analysis of the
AB  - genome using the bioinformatics tool antiSMASH showed the presence of many unique
AB  - natural product biosynthetic pathways.
ER  -

TY  - JOUR
AU  - Goto, T.
AU  - Hirakawa, H.
AU  - Morita, Y.
AU  - Tomida, J.
AU  - Sato, J.
AU  - Matsumura, Y.
AU  - Mitani, A.
AU  - Niwano, Y.
AU  - Takeuchi, K.
AU  - Kubota, H.
AU  - Kawamura, Y.
TI  - Complete Genome Sequence of Moraxella osloensis Strain KMC41, a Producer of 4-Methyl-3-Hexenoic Acid, a Major Malodor Compound in Laundry.
JO  - Genome Announcements
PY  - 2016
SP  - e00705
EP  - e00716
VL  - 4
AB  - We report the complete genome sequence of Moraxella osloensis strain KMC41, isolated from
AB  - laundry with malodor. The KMC41 genome comprises a 2,445,556-bp
AB  - chromosome and three plasmids. A fatty acid desaturase and at least four
AB  - beta-oxidation-related genes putatively associated with 4-methyl-3-hexenoic acid
AB  - generation were detected in the KMC41 chromosome.
ER  -

TY  - JOUR
AU  - Goto, T.
AU  - Nagano, K.
AU  - Hirakawa, H.
AU  - Tanaka, K.
AU  - Yoshimura, F.
TI  - Draft Genome Sequence of Porphyromonas gingivalis Strain Ando Expressing a 53-Kilodalton-Type Fimbrilin Variant of Mfa1 Fimbriae.
JO  - Genome Announcements
PY  - 2015
SP  - e01292
EP  - e01215
VL  - 3
AB  - Periodontopathic Porphyromonas gingivalis strain Ando abundantly expresses a 53-kDa-type Mfa1
AB  - fimbria. Here, we report the draft genome sequence of Ando, with
AB  - a size of 2,229,994 bp, average G+C content of 48.4%, and 1,755 predicted
AB  - protein-coding sequences.
ER  -

TY  - JOUR
AU  - Goto, T.
AU  - Ogura, Y.
AU  - Hirakawa, H.
AU  - Tomida, J.
AU  - Morita, Y.
AU  - Akaike, T.
AU  - Hayashi, T.
AU  - Kawamura, Y.
TI  - Complete Genome Sequence of Helicobacter cinaedi Strain PAGU611, Isolated in a Case of Human Bacteremia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3744
EP  - 3745
VL  - 194
AB  - We report the complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a
AB  - case of human bacteremia. The PAGU611 genome comprises a
AB  - 2,078,348-bp chromosome and a 23,054-bp plasmid. The chromosome contains a unique
AB  - genomic island, encoding a type VI secretion system and clustered regularly
AB  - interspaced short palindromic repeat (CRISPR) loci.
ER  -

TY  - JOUR
AU  - Gott, J.M.
TI  - Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside.
JO  - Genes Dev.
PY  - 1988
SP  - 1791
EP  - 1799
VL  - 2
AB  - The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame
AB  - (ORF). These ORFs are preceded by functional T4 late promoters and, in the case of the nrdB
AB  - intron ORF, a functional middle promoter. Expression of phage-encoded intron ORF-lacZ fusions
AB  - indicates that these T4 genes are highly regulated. The lack of translation of these ORFs from
AB  - the early pre-mRAs can be accounted for by the presence of secondary structures that are
AB  - absent from the late RNAs. Because translation of the intron ORFs could disrupt core
AB  - structural elements required for pre-mRNA splicing, such regulation may be necessary to allow
AB  - expression of the genes in which they reside.
ER  -

TY  - JOUR
AU  - Gottschling, D.E.
TI  - Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 4062
EP  - 4065
VL  - 89
AB  - Genes located near telomeres in Saccharomyces cerevisiae undergo position-effect variegation;
AB  - their transcription is subject to reversible but mitotically heritable repression. This
AB  - position effect and the finding that telomeric DNA is late replicating suggest that yeast
AB  - telomeres exist in a heterochromatin-like state. Mutations in genes that suppress the
AB  - telomeric position effect suggest that a special chromatin structure exists near chromosomal
AB  - termini. Thus transcriptional repression may be explained by the inability of DNA binding
AB  - proteins to access the DNA near telomeres. To test this hypothesis, the Escherichia coli Dam
AB  - DNA methyltransferase, which modifies the sequence GATC, was introduced into S. cerevisiae
AB  - cells. DNA sequences near the telomere were highly refractive to Dam methylation but were
AB  - modified when located at positions more internal on the chromosome. Telomeric sequences were
AB  - accessible to methyltransferase activity in strains that contained a mutation that suppressed
AB  - the telomeric position effect. These data support the model that sequence-specific DNA binding
AB  - proteins are excluded from telomere-proximal sequences in vivo and show that expression of DNA
AB  - methyltransferase activity may serve as a useful tool for mapping chromosomal structural
AB  - domains in vivo.
ER  -

TY  - JOUR
AU  - Goudenege, D.
AU  - Labreuche, Y.
AU  - Krin, E.
AU  - Ansquer, D.
AU  - Mangenot, S.
AU  - Calteau, A.
AU  - Medigue, C.
AU  - Mazel, D.
AU  - Polz, M.F.
AU  - Le Roux, F.
TI  - Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits.
JO  - ISME J.
PY  - 2013
SP  - 1985
EP  - 1996
VL  - 7
AB  - Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia
AB  - and other regions in the Indo-Pacific. The molecular determinants of V.
AB  - nigripulchritudo pathogenicity are unknown; however, molecular epidemiological
AB  - studies have suggested that pathogenicity is linked to particular lineages. Here,
AB  - we performed high-throughput sequencing-based comparative genome analysis of 16
AB  - V. nigripulchritudo strains to explore the genomic diversity and evolutionary
AB  - history of pathogen-containing lineages and to identify pathogen-specific genetic
AB  - elements. Our phylogenetic analysis revealed three pathogen-containing V.
AB  - nigripulchritudo clades, including two clades previously identified from New
AB  - Caledonia and one novel clade comprising putatively pathogenic isolates from
AB  - septicemic shrimp in Madagascar. The similar genetic distance between the three
AB  - clades indicates that they have diverged from an ancestral population roughly at
AB  - the same time and recombination analysis indicates that these genomes have, in
AB  - the past, shared a common gene pool and exchanged genes. As each contemporary
AB  - lineage is comprised of nearly identical strains, comparative genomics allowed
AB  - differentiation of genetic elements specific to shrimp pathogenesis of varying
AB  - severity. Notably, only a large plasmid present in all highly pathogenic (HP)
AB  - strains encodes a toxin. Although less/non-pathogenic strains contain related
AB  - plasmids, these are differentiated by a putative toxin locus. Expression of this
AB  - gene by a non-pathogenic V. nigripulchritudo strain resulted in production of
AB  - toxic culture supernatant, normally an exclusive feature of HP strains. Thus,
AB  - this protein, here termed 'nigritoxin', is implicated to an extent that remains
AB  - to be precisely determined in the toxicity of V. nigripulchritudo.
ER  -

TY  - JOUR
AU  - Gough, J.A.
AU  - Murray, N.E.
TI  - Sequence diversity among related genes for recognition of specific targets in DNA molecules.
JO  - J. Mol. Biol.
PY  - 1983
SP  - 1
EP  - 19
VL  - 166
AB  - Escherichia coli strains K12 and B, and a new strain designed D, each encode a
AB  - characteristic restriction and modification enzyme.  These enzymes (EcoK, EcoB
AB  - and presumably EcoD) comprise three subunits of which one, that encoded by the
AB  - so-called specificity gene (hsdS), is responsible for recognition of the DNA
AB  - sequence speific to that system.  The other two subunits, encoded by hsdR and
AB  - hsdM, are interchangeable between systems, and the available molecular evidence
AB  - suggests that the hsdR and hsdM genes are highly conserved.  The DNA sequence
AB  - of a segment of the hsd region that includes the hsdS gene has been determined
AB  - for each of the three strains.  The hsdS gene varies in length from 1335 to
AB  - 1425 base-pairs and the only regions showing obvious homology, one of about 100
AB  - base-pairs and a second of about 250 base-pairs, are highly conserved.  The
AB  - remainder of each hsdS gene shares little, or no, homology with either of the
AB  - other related specificity genes.  Thus, the specificity subunits, though
AB  - components of a family of closely related enzymes with very similar functions,
AB  - have remarkably dissimilar primary structure.
ER  -

TY  - JOUR
AU  - Gough, M.
AU  - Lederberg, S.
TI  - Methylated bases in the host-modified deoxyribonucleic acid of Escherichia coli and bacteriophage lambda.
JO  - J. Bacteriol.
PY  - 1966
SP  - 1460
EP  - 1468
VL  - 91
AB  - The deoxyribonucleic acid (DNA) from strains of Escherichia coli and phage
AB  - lambda was examined to determine whether the types or amounts of
AB  - methionine-derived methylated bases present correlated with the host-specific
AB  - modification of that DNA.  The DNA of strain C600 (which has K-12 modification
AB  - specificity) and of a modificationless mutant of C600 are similar in their
AB  - content of 5-methylcytosine and 6-methylaminopurine.  Strains Bc251 and its
AB  - Pl-lysogen differ in P1-controlled specificity, but they have the same content
AB  - of 6-methylaminopurine, and both lack 5-methylcytosine in their DNA.  Phage
AB  - lambda contains the same methylated bases as its host of origin, but in reduced
AB  - amounts and in different proportions.  Although minor amounts of these
AB  - methylated bases may have importance as a result of their location, the
AB  - presence of the majority of these methylated bases is irrelevant to the
AB  - specificity of host modification of DNA.
ER  -

TY  - JOUR
AU  - Gourgues, G.
AU  - Barre, A.
AU  - Beaudoing, E.
AU  - Weber, J.
AU  - Magdelenat, G.
AU  - Barbe, V.
AU  - Schieck, E.
AU  - Jores, J.
AU  - Vashee, S.
AU  - Blanchard, A.
AU  - Lartigue, C.
AU  - Sirand-Pugnet, P.
TI  - Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine  Strain against Contagious Bovine Pleuropneumonia.
JO  - Genome Announcements
PY  - 2016
SP  - e00263
EP  - e00216
VL  - 4
AB  - Mycoplasma mycoidessubsp.mycoidesis the etiologic agent of contagious bovine pleuropneumonia.
AB  - We report here the complete genome sequence of the strain T1/44,
AB  - which is widely used as a live vaccine in Africa.
ER  -

TY  - JOUR
AU  - Gouvea-Taketani, R.
AU  - Domingues, Z.T.
AU  - Soares-de-Melo, I.
AU  - Mendes, R.
TI  - Whole-Genome Shotgun Sequencing of Rhodococcus erythropolis Strain P27, a Highly  Radiation-Resistant Actinomycete from Antarctica.
JO  - Genome Announcements
PY  - 2013
SP  - e00763
EP  - e00713
VL  - 1
AB  - Here, we report the draft genome sequence of radiation-resistant Rhodococcus erythropolis
AB  - strain P27, isolated from leaves of Deschampsia antarctica Desv. (Poaceae) in the Admiralty
AB  - Bay area, Antarctica.
ER  -

TY  - JOUR
AU  - Govind, R.
AU  - Fralick, J.A.
AU  - Rolfe, R.D.
TI  - Genomic Organization and Molecular Characterization of Clostridium difficile Bacteriophage {Phi}CD119.
JO  - J. Bacteriol.
PY  - 2006
SP  - 2568
EP  - 2577
VL  - 188
AB  - In this study, we have isolated a temperate phage (PhiCD119) from a
AB  - pathogenic Clostridium difficile strain and sequenced and annotated its
AB  - genome. This virus has an icosahedral capsid and a contractile tail
AB  - covered by a sheath and contains a double-stranded DNA genome. It belongs
AB  - to the Myoviridae family of the tailed phages and the order Caudovirales.
AB  - The genome was circularly permuted, with no physical ends detected by
AB  - sequencing or restriction enzyme digestion analysis, and lacked a cos
AB  - site. The DNA sequence of this phage consists of 53,325 bp, which carries
AB  - 79 putative open reading frames (ORFs). A function could be assigned to 23
AB  - putative gene products, based upon bioinformatic analyses. The PhiCD119
AB  - genome is organized in a modular format, which includes modules for
AB  - lysogeny, DNA replication, DNA packaging, structural proteins, and host
AB  - cell lysis. The PhiCD119 attachment site attP lies in a noncoding region
AB  - close to the putative integrase (int) gene. We have identified the phage
AB  - integration site on the C. difficile chromosome (attB) located in a
AB  - noncoding region just upstream of gene gltP, which encodes a carrier
AB  - protein for glutamate and aspartate. This genetic analysis represents the
AB  - first complete DNA sequence and annotation of a C. difficile phage.
ER  -

TY  - JOUR
AU  - Gowers, D.M.
AU  - Bellamy, S.R.W.
AU  - Halford, S.E.
TI  - One recognition sequence, seven restriction enzymes, five reaction mechanisms.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3469
EP  - 3479
VL  - 32
AB  - The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated
AB  - by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI,
AB  - Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence
AB  - 5'-GGCGCC-3'. Their reactions on plasmids with one or two copies of this sequence revealed
AB  - five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and
AB  - the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves
AB  - only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at
AB  - individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its
AB  - recognition sites, but shows full activity only when bound to two sites, which are then
AB  - cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner
AB  - historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute
AB  - requirement for two sites in close physical proximity, which are cleaved concertedly. The
AB  - range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as
AB  - is the number of enzymes needing two recognition sites.
ER  -

TY  - JOUR
AU  - Gowers, D.M.
AU  - Halford, S.E.
TI  - Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling.
JO  - EMBO J.
PY  - 2003
SP  - 1410
EP  - 1418
VL  - 22
AB  - DNA-binding proteins are generally thought to locate their target sites by first associating
AB  - with the DNA at random and then translocating to the
AB  - specific site by one-dimensional (1D) diffusion along the DNA. We report
AB  - here that non-specific DNA conveys proteins to their target sites just as
AB  - well when held near the target by catenation as when co-linear with the
AB  - target. Hence, contrary to the prevalent view, proteins move from random
AB  - to specific sites primarily by three-dimensional (3D) rather than 1D
AB  - pathways, by multiple dissociation/re-association events within a single
AB  - DNA molecule. We also uncover a role for DNA supercoiling in target-site
AB  - location. Proteins find their sites more readily in supercoiled than in
AB  - relaxed DNA, again indicating 3D rather than 1D routes.
ER  -

TY  - JOUR
AU  - Gowers, D.M.
AU  - Wilson, G.G.
AU  - Halford, S.E.
TI  - Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 15883
EP  - 15888
VL  - 102
AB  - Proteins that act at specific DNA sequences bind DNA randomly and then translocate to the
AB  - target site. The translocation is often ascribed to the protein sliding along the DNA while
AB  - maintaining continuous contact with it. Proteins also can move on DNA by multiple cycles of
AB  - dissociation/reassociation within the same chain. To distinguish these pathways, a strategy
AB  - was developed to analyze protein motion between DNA sites. The strategy reveals whether the
AB  - protein maintains contact with the DNA as it transfers from one site to another by sliding or
AB  - whether it loses contact by a dissociation/reassociation step. In reactions at low salt, the
AB  - test protein stayed on the DNA as it traveled between sites, but only when the sites were <50
AB  - bp apart. Transfers of >30 bp at in vivo salt, and over distances of >50 bp at any salt,
AB  - always included at least one dissociation step. Hence, for this enzyme, 1D sliding operates
AB  - only over short distances at low salt, and 3D dissociation/reassociation is its main mode of
AB  - translocation.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Ehrlich, K.C.
AU  - Jeltsch, A.
TI  - DNA from Aspergillus flavus contains 5-methylcytosine.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 151
EP  - 155
VL  - 205
AB  - DNA from Aspergillus sp. has been reported not to contain 5-methylcytosine. However, it has
AB  - been found that Aspergillus nidulans responds to 5-azacytidine, a drug that is a strong
AB  - inhibitor of DNA methyltransferases. Therefore, we have re-examined the occurrence of
AB  - 5-methylcytosine in DNA from Aspergillus flavus by using a highly sensitive and specific
AB  - method for detection of modified bases in genomic DNA comprising high-performance liquid
AB  - chromatography separation of nucleosides, labeling of the nucleoside with deoxynucleoside
AB  - kinase and two-dimensional thin-layer chromatography. Our results show that 5-methylcytosine
AB  - is present in DNA from A. flavus. We estimate the relative amounts of 5-methylcytosine to
AB  - cytosine to be approximately 1/400.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 20409
EP  - 20414
VL  - 277
AB  - The C-terminal domains of the mammalian DNA methyltransferases Dnmt1, Dnmt3a, and Dnmt3b
AB  - harbor all the conserved motifs characteristic for
AB  - cytosine-C5 methyltransferases. Whereas the isolated catalytic domain
AB  - of Dnmt1 is inactive, we show here that the C-terminal domains of
AB  - Dnmt3a and Dnmt3b are catalytically active. Neither Dnmt3a nor Dnmt3b
AB  - shows a significant preference for the satellite 2 sequence, although
AB  - Dnmt3b is required for methylation of these regions in vivo. However,
AB  - the catalytic domain of Dnmt3a methylates DNA in a distributive
AB  - reaction, whereas Dnmt3b is processive, which accelerates methylation
AB  - of macromolecular DNA in vitro. This property could make Dnmt3b a
AB  - preferred enzyme for methylation at satellite 2 repeats, since they are
AB  - highly CG-rich. We have also analyzed the catalytic activities of six
AB  - different mutations found in ICF (immunodeficiency, centromeric
AB  - instability, and facial abnormalities) patients in the catalytic domain
AB  - of Dnmt3b. Five of them display catalytic activities reduced by
AB  - 10-50-fold; one mutant was inactive in our assay (residual activity
AB  - <1%). These results confirm that a reduced catalytic activity of Dnm3b
AB  - causes ICF. However, the mutations in general do not completely
AB  - abrogate catalytic activity. This finding may explain why ICF patients
AB  - are viable, whereas nmt3b knock-out mice die during embryogenesis.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Molecular enzymology of the EcoRV DNA-(Adenine-N6)-methyltransferase: Kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 93
EP  - 110
VL  - 303
AB  - The EcoRV DNA-(adenine-N(6))-methyltransferase recognizes GATATC sequences and modifies the
AB  - first adenine residue within this site. We show here, that the enzyme binds to the DNA and the
AB  - cofactor S-adenosylmethionine (AdoMet) in an ordered bi-bi fashion, with AdoMet being bound
AB  - first. M.EcoRV binds DNA in a non-specific manner and the enzyme searches for its recognition
AB  - site by linear diffusion with a range of approximately 1800 bp. During linear diffusion the
AB  - enzyme continuously scans the DNA for the presence of recognition sites. Upon specific
AB  - M.EcoRV-DNA complex formation a strong increase in the fluorescence of an oligonucleotide
AB  - containing a 2-aminopurine base analogue at the GAT-2AP-TC position is observed which, most
AB  - likely, is correlated with DNA bending. In contrast to the GAT-2AP-TC substrate, a G-2AP-TATC
AB  - substrate in which the target base is replaced by 2-aminopurine does not show an increase in
AB  - fluorescence upon M.EcoRV binding, demonstrating that 2-aminopurine is not a general tool to
AB  - detect base flipping. Stopped-flow experiments show that DNA bending is a fast process with
AB  - rate constants >10 s(-1).  In the presence of cofactor, the specific complex adopts a second
AB  - conformation, in which the target sequence is more tightly contacted by the enzyme. M.EcoRV
AB  - exists in an open and in a closed state that are in slow equilibrium. Closing the open state
AB  - is a slow process (rate constant approximately 0.7 min(-1)) that limits the rate of DNA
AB  - methylation under single turnover conditions. Product release requires opening of the closed
AB  - complex which is very slow (rate constant approximately 0.05-0.1 min(-1)) and limits the rate
AB  - of DNA methylation under multiple turnover conditions. M.EcoRV methylates DNA sequences
AB  - containing more than one recognition site in a distributive manner. Since the dissociation
AB  - rate from non-specific DNA does not depend on the length of the DNA fragment, DNA dissociation
AB  - does not preferentially occur at the ends of the DNA.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG Sites.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 1201
EP  - 1208
VL  - 309
AB  - We present the first in vitro study investigating the catalytic properties of a mammalian de
AB  - novo DNA methyltransferase. Dnmt3a from mouse was cloned and expressed in Escherichia coli. It
AB  - was shown to be catalytically active in E. coli cells in vivo. The methylation activity of the
AB  - purified protein was highest at pH 7.0 and 30 mM KCl. Our data show that recombinant Dnmt3a
AB  - protein is indeed a de novo methyltransferase, as it catalyzes the transfer of methyl groups
AB  - to unmethylated substrates with similar efficiency as to hemimethylated substrates. With
AB  - oligonucleotide substrates, the catalytic activity of Dnmt3a is similar to that of Dnmt1: the
AB  - Km values for the unmethylated and hemimethylated oligonucleotide substrates are 2.5 microM,
AB  - and the k(cat) values are 0.05 h^-1 and 0.07 h^-1, respectively. The enzyme catalyzes the
AB  - methylation of DNA in a distributive manner, suggesting that Dnmt3a and Dnmt1 may cooperate
AB  - during de novo methylation of DNA. Further, we investigated the methylation activity of Dnmt3a
AB  - at non-canonical sites. Even though the enzyme shows maximum activity at CpG sites, with
AB  - oligonucleotide substrates, a high methylation activity was also found at CpA sites, which are
AB  - modified only twofold slower than CpG sites. Therefore, the specificity of Dnmt3a is
AB  - completely different from that of the maintenance methyltransferase Dnmt1, which shows a 40 to
AB  - 50-fold preference for hemimethylated over unmethylated CpG sites and has almost no
AB  - methylation activity at non-CpG sites. Copyright 2001 Academic Press.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Leismann, O.
AU  - Jeltsch, A.
TI  - DNA of Drosophila melanogaster contains 5-methylcytosine.
JO  - EMBO J.
PY  - 2000
SP  - 6918
EP  - 6923
VL  - 19
AB  - It is commonly accepted that the DNA of Drosophila melanogaster does not contain
AB  - 5-methylcytosine, which is essential in the development of most eukaryotes. We have developed
AB  - a new, highly specific and sensitive assay to detect the presence of 5-methylcytosine in
AB  - genomic DNA. The DNA is degraded to nucleosides, 5-methylcytosine purified by HPLC and, for
AB  - detection by 1D- and 2D-TLC, radiolabeled using deoxynucleoside kinase and [-32P]ATP. Using
AB  - this assay, we show here that 5- methylcytosine occurs in the DNA of D. melanogaster at a
AB  - level of 1 in 1000-2000 cytosine residues in adult flies. DNA methylation is detectable in all
AB  - stages of D. melanogaster development.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Liebert, K.
AU  - Hermann, A.
AU  - Xu, G.L.
AU  - Jeltsch, A.
TI  - Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 13341
EP  - 13348
VL  - 280
AB  - Dnmt3L has been identified as a stimulator of the catalytic activity of de novo DNA
AB  - methyltransferases. It is essential in the development of
AB  - germ cells in mammals. We show here that Dnmt3L stimulates the
AB  - catalytic activity of the Dnmt3A and Dnmt3B enzymes by directly binding
AB  - to their respective catalytic domains via its own C-terminal domain.
AB  - The catalytic activity of Dnmt3A and -3B was stimulated similar to
AB  - 15-fold, and Dnmt3L directly binds to DNA but not to
AB  - S-adenosyl-L-methionine (AdoMet). Complex formation between Dnmt3A and
AB  - Dnmt3L accelerates DNA binding by Dnmt3A 20-fold and lowers its Km for
AB  - DNA. Interaction of Dnmt3L with Dnmt3A increases the binding of the
AB  - coenzyme AdoMet to Dnmt3A, and it lowers the Km of Dnmt3A for AdoMet.
AB  - On the basis of our data we propose a model in which the interaction of
AB  - Dnmt3A with Dnmt3L induces a conformational change of Dnmt3A that opens
AB  - the active site of the enzyme and promotes binding of DNA and the
AB  - AdoMet. We demonstrate that the interaction of Dnmt3A and Dnmt3L is
AB  - transient, and after DNA binding to Dnmt3A, Dnmt3L dissociates from the
AB  - complex. Following dissociation of Dnmt3L, Dnmt3A adopts a closed
AB  - conformation leading to slow rates of DNA release. Therefore, Dnmt3L
AB  - acts as a substrate exchange factor that accelerates DNA and AdoMet
AB  - binding to de novo DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Loutchanwoot, P.
AU  - Vorobjeva, G.
AU  - Handa, V.
AU  - Jurkowska, R.Z.
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 928
EP  - 941
VL  - 357
AB  - On the basis of amino acid sequence alignments and structural data of related enzymes, we have
AB  - performed a mutational analysis of 14 amino
AB  - acid residues in the catalytic domain of the murine Dnmt3a
AB  - DNA-(cytosine C5)-methyltransferase. The target residues are located
AB  - within the ten conserved amino acid sequence motifs characteristic for
AB  - cytosine-C5 methyltransferases and in the putative DNA recognition
AB  - domain of the enzyme (TRD). Mutant proteins were purified and tested
AB  - for their catalytic properties and their abilities to bind DNA and
AB  - AdoMet. We prepared a structural model of Dnmt3a. to interpret our
AB  - results. We demonstrate that Phe50 (motif I) and Glu74 (motif II) are
AB  - important for AdoMet binding and catalysis. D96A (motif III) showed
AB  - reduced AdoMet binding but increased activity under conditions of
AB  - saturation with S-adenosyl-L-methionine (AdoMet), indicating that the
AB  - contact of Asp96 to AdoMet is not required for catalysis. R130A
AB  - (following motif IV), R241A and R246A (in the TRD), R292A, and R297A
AB  - (both located in front of motif X) showed reduced DNA binding. R130A
AB  - displayed a strong reduction in catalytic activity and a complete
AB  - change in flanking sequence preferences, indicating that Arg130 has an
AB  - important role in the DNA interaction of Dnmt3a. R292A also displayed
AB  - reduced activity and changes in the flanking sequence preferences,
AB  - indicating a potential role in DNA contacts farther away from the CG
AB  - target site. N167A (motif VI) and R202A (motif VIII) have normal AdoMet
AB  - and DNA binding but reduced catalytic activity. While Asn167 might
AB  - contribute to the positioning of residues from motif VI, according to
AB  - structural data Arg202 has a role in catalysis of cytosine-C5
AB  - methyltransferases. The R295A variant was catalytically inactive most
AB  - likely because of destabilization of the hinge sub-domain of the
AB  - protein.
ER  -

TY  - JOUR
AU  - Gowher, H.
AU  - Stockdale, C.J.
AU  - Goyal, R.
AU  - Ferreira, H.
AU  - Owen-Hughes, T.
AU  - Jeltsch, A.
TI  - De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases.
JO  - Biochemistry
PY  - 2005
SP  - 9899
EP  - 9904
VL  - 44
AB  - In the cell, DNA is wrapped on histone octamers, which reduces its accessibility for DNA
AB  - interacting enzymes. We investigated de novo
AB  - methylation of nucleosomal DNA in vitro and show that the Dnmt3a and
AB  - Dnmt1 DNA methyltransferases efficiently methylate nucleosomal DNA
AB  - without dissociation of the histone octamer from the DNA. In contrast,
AB  - the prokaryotic SssI DNA methyltransferase and the catalytic domain of
AB  - Dnmt3a are strongly inhibited by nucleosomes. We also found that
AB  - full-length Dnmt1 and Dnmt3a bind to nucleosomes much stronger than
AB  - their isolated catalytic domains, demonstrating that the N-terminal
AB  - parts of the MTases are required for the interaction with nucleosomes.
AB  - Variations of the DNA sequence or the histone tails did not
AB  - significantly influence the methylation activity of Dnmt3a. The
AB  - observation that mammalian methyltransferases directly modify
AB  - nucleosomal DNA provides an insight into the mechanisms by which
AB  - histone tail and DNA methylation patterns can influence each other
AB  - because the DNA methylation pattern can be established while histones
AB  - remain associated to the DNA.
ER  -

TY  - JOUR
AU  - Goyal, R.
AU  - Rathert, P.
AU  - Laser, H.
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Phosphorylation of serine-515 activates the mammalian maintenance methyltransferase Dnmt1.
JO  - EPIGENETICS
PY  - 2007
SP  - 155
EP  - 160
VL  - 2
AB  - DNA methyltransferase 1 methylates hemi-methylated CG sites generated during DNA replication.
AB  - Serine 515 of this enzyme has been shown to be
AB  - phosphorylated. To explore the importance of S515 phosphorylation, we
AB  - generated mutants of Dnmt1 which removed the phosphorylation potential
AB  - (S515A) or mimic phosphoserine (S515E), purified the proteins from
AB  - insect cells and analyzed their DNA methylation activity in vitro. The
AB  - S515E mutant was found to be active, while S515A mutant had severe loss
AB  - in activity when compared to the wild type protein. The loss of
AB  - activity of the S515A variant was not due to loss of DNA binding
AB  - capacity. Furthermore, we show that a phosphorylated peptide whose
AB  - sequence mimics the surrounding of Ser515 ((EKIYISKIVVE)-K-P) inhibited
AB  - the activity of wild type Dnmt1 ten-fold more than the
AB  - non-phosphorylated peptide. The inhibition was specific for Dnmt1 and
AB  - for the particular peptide sequence. Our data suggest that
AB  - phosphorylation of Ser515 is important for an interaction between the
AB  - N-terminal domain of Dnmt1 and its catalytic domain that is necessary
AB  - for activity and that this interaction is specifically disrupted by the
AB  - phosphorylated peptide. We conclude that phosphorylation of Dnmt1 at
AB  - Ser515 could be an important regulator of Dnmt1 activity during cell
AB  - cycle and after proliferative stimuli.
ER  -

TY  - JOUR
AU  - Goyal, R.
AU  - Reinhardt, R.
AU  - Jeltsch, A.
TI  - Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 1182
EP  - 1188
VL  - 34
AB  - DNA methyltransferase 1 (Dnmt1) has a central role in copying the pattern of DNA methylation
AB  - after replication which is one manifestation of
AB  - epigenetic inheritance. With oligonculeotide substrates we show that mouse
AB  - Dnmt1 has a 30- to 40-fold preference for hemimethylated DNA that is
AB  - almost lost after addition of fully methylated oligonucleotides. Using
AB  - long hemimethylated DNA substrates that carry defined methylation patterns
AB  - and bisulfite analysis of the methylation reaction products, we show a
AB  - 15-fold preference for hemimethylated CG sites. Dnmt1 moves along the DNA
AB  - in a random walk methylating hemimethylated substrates with high
AB  - processivity (>50 sites are visited on average which corresponds to linear
AB  - diffusion over 6000 bp). The frequency of skipping sites is very low
AB  - (<0.3%) and there is no detectable flanking sequence preference. CGCTC
AB  - sites tend to terminate the processive methylation of DNA by Dnmt1.
AB  - Unmethylated DNA is modified non-processively with a preference for
AB  - methylation at CCGG sites. We simulate the propagation of methylation
AB  - patterns using a stochastic model with the specificity of Dnmt1 observed
AB  - here and conclude that either methylation of several sites is required to
AB  - propagate the methylation information over several cellular generations or
AB  - additional epigenetic information must be used.
ER  -

TY  - JOUR
AU  - Goyon, C.
TI  - Isolation and identification by sequence homology of a second putative C5-DNA-methyltransferase gene from Ascobolus immersus.
JO  - DNA Seq.
PY  - 1998
SP  - 109
EP  - 112
VL  - 9
AB  - I report the cloning of a new Ascobolus gene (masc 2) that potentially encodes a
AB  - C5-DNA-methyltransferase. The putative protein exhibits the two domains characteristic of
AB  - eukaryotic maintenance DNA-methyltransferase: a large N-terminal domain and a C-terminal
AB  - domain containing all ten catalytic motifs arranged in the canonical order. A new type of
AB  - eukaryotic DNA-methylase gene (masc 1) has been recently found in Ascobolus. Masc1 is
AB  - essential for the de novo methylation and dispensable for methylation maintenance. The masc2
AB  - gene could encode the methylase involved in this maintenance.
ER  -

TY  - JOUR
AU  - Goyon, C.
AU  - Nogueira, T.I.V.
AU  - Faugeron, G.
TI  - Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 42
EP  - 51
VL  - 240
AB  - In the ascomycete Ascobolus immersus, duplicated DNA segments are subject to the methylation
AB  - induced premeiotically (MIP) process. Affected sequences are heavily methylated at their
AB  - cytosine residues. We used the bisulphite genomic sequencing method to determine the
AB  - methylation status of every cytosine residue in a gene which had undergone MIP. Several
AB  - individual DNA molecules, all issued from the replication of a single molecule initially
AB  - subject to MIP, were sequenced. In each molecule, methylation extended over almost the whole
AB  - length of the previously duplicated segment. The methylation extent was precisely delimited
AB  - and constant in each of the molecules, leaving unmethylated a nearly 100-nucleotide region
AB  - next to each end. In none of the molecules did methylation resulting from MIP extend beyond
AB  - the ends. Although the DNA molecules were not all methylated with the same intensity, all
AB  - cytosine residues in the methylated portion could be methylated, most of them belonging to
AB  - non-symmetrical sequences. This finding contrasts with the situation in higher eukaryotes in
AB  - which most, if not all, methylation is at short symmetrical sequences such as CpG or CpNpG,
AB  - ensuring perpetuation of methylation. Methylation at non-symmetrical sequences implies that in
AB  - A. immersus maintenance involves a novel sequence-non-specific methyltransferase.
ER  -

TY  - JOUR
AU  - Grable, J.
AU  - Frederick, C.A.
AU  - Samudzi, C.
AU  - Jen-Jacobson, L.
AU  - Lesser, D.
AU  - Greene, P.
AU  - Boyer, H.W.
AU  - Itakura, K.
AU  - Rosenberg, J.M.
TI  - Two-fold symmetry of crystalline DNA-EcoRI endonuclease recognition complexes.
JO  - J. Biomol. Struct. Dyn.
PY  - 1984
SP  - 1149
EP  - 1160
VL  - 1
AB  - Recognition complexes between EcoRI endonuclease and either of two synthetic
AB  - oligonucleotides (sequences CGCGAATTCGCG and TCGCGAATTCGCG) crystallize in
AB  - space Group P321 with unit cell parameters a=128 and c=47 angstroms and a=118.4
AB  - and c=49.7 angstroms, respectively.  Native diffraction data to 3 angstrom
AB  - resolution have been collected from the form containing the tridecameric
AB  - sequence.  Electrophoretic analyses of dissolved crystals demonstrate that this
AB  - form contains DNA and protein in a ratio of one double helix per enzyme dimer.
AB  - The most likely asymmetric unit contents are one 31,000 dalton enzyme subunit
AB  - and one strand of DNA, yielding VM values of 3.1 cubic angstroms/dal and 2.8
AB  - cubic angstroms/dal for the forms containing dodecameric and tridecameric DNA,
AB  - respectively.  This implies that the DNA-protein complex possesses two-fold
AB  - rotational symmetry, which has been incorporated in the crystalline lattice.
ER  -

TY  - JOUR
AU  - Grabowski, G.
AU  - Alves, J.
TI  - Transformation of the EcoRI restriction endonuclease to an enzyme with altered specificity: Development of a positive in vivo selection system.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S102
EP  - S102
VL  - 376
AB  - The EcoRI restriction endonuclease is one of the best studied enzymes so far.  It cleaves the
AB  - DNA sequence G/AATTC with very high specificity.  All attempts to change the sequence
AB  - specificity of this enzyme by using site-directed mutagenesis methods have not been successful
AB  - until today.  This is caused by the redundancy of enzyme-substrate interactions leading to
AB  - specific sequence recognition and cleavage.  Therefore, we have developed a positive in vivo
AB  - selection system that allows screening for an active enzyme with altered specificity.
AB  - Bacterial cells are transformed with a pool of plasmids containing the randomly mutated
AB  - endonuclease gene.  In order to protect the host DNA from cleavage a methyltransferase
AB  - corresponding to the altered specificity is required.  We used the MunI methylase which is
AB  - specific for the cognate sequence CAATTG.  Selection is carried out by infecting the cells
AB  - with a lambda phage, which carried a gene coding for a toxic protein.  The sequence of this
AB  - gene was altered to generate several sites of the desired new specificity.  The transcription
AB  - of the toxic gene is prevented only when a restriction activity with this specificity is
AB  - present.
ER  -

TY  - JOUR
AU  - Grabowski, G.
AU  - Jeltsch, A.
AU  - Wolfes, H.
AU  - Maass, G.
AU  - Alves, J.
TI  - Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI.
JO  - Gene
PY  - 1995
SP  - 113
EP  - 118
VL  - 157
AB  - The catalytic center of the restriction endonuclease (ENase) EcoRI is structurally homologous
AB  - to that of EcoRV, BamHI and PvuII.  Each of these ENases contains a short motif of three to
AB  - four amino acid (aa) residues which are positioned in a similar orientation to the scissile
AB  - phosphodiester bond.  We have mutated these aa (Pro90, Asp91, Glu111 and Lys113) in EcoRI to
AB  - determine their individual roles in catalysis.  The replacement of Asp91 and Lys113,
AB  - respectively, by conservative mutations (Ala91, Asn91, Ala113, Gln113, His113 and Leu113)
AB  - resulted in a reduction of binding affinity and complete loss of cleavage activity.  Only
AB  - Lys113-Arg substitution still allows to cleave DNA, albeit with a rate reduced by at least
AB  - four orders of magnitude.  Lys113 seems to stabilize the structure of the wild-type (wt) ENase
AB  - since all five ENase variants with mutations at this position show a strongly enhanced
AB  - tendency to aggregate.  The Ala and Gln mutants of Glu111 bind the recognition sequence
AB  - slightly stronger than wt EcoRI and cleave it with a low, but detectable rate.  Only the
AB  - Glu111-Lys mutant, in which the charge is reversed, shows neither binding nor cleavage
AB  - activity.  Pro90 is not important for catalysis, because the Ala90 mutant cleaves DNA with an
AB  - only slightly reduced rate.  Under star conditions, however, this mutant is even more active
AB  - than wt EcoRI.  Therefore, the charged aa Asp91, Glu111 and Lys113 are essential for catalytic
AB  - activity of the EcoRI ENase.  Differences in the individual contributions of these aa to
AB  - binding and catalysis, as compared with results obtained with EcoRV and BamHI mutants, show
AB  - that similar catalytic centers are used in a slightly different way by these three ENases.
ER  -

TY  - JOUR
AU  - Grabowski, G.
AU  - Maass, G.
AU  - Alves, J.
TI  - Asp-59 is not important for the catalytic activity of the restriction endonuclease EcoRI.
JO  - FEBS Lett.
PY  - 1996
SP  - 106
EP  - 110
VL  - 381
AB  - The amino acid Asp-59 was proposed to be involved in EcoRI catalyzed DNA cleavage.  We have
AB  - tested this hypothesis by site directed mutagenesis experiments.  The four mutants D59A, D59E,
AB  - D59G, and D59N bind with similar stability to the specific recognition sequence as wild type
AB  - EcoRI.  The D59E mutant cleaves DNA as fast as the wild type enzyme.  Specific activities of
AB  - the other three mutants are five to tenfold lower.  Therefore, we conclude that Asp-59  is not
AB  - involved in catalysis of the EcoRI restriction endonuclease.  Consequences for catalytic
AB  - mechanisms of EcoRI and other restriction enzymes are discussed.
ER  -

TY  - JOUR
AU  - Grachev, S.A.
AU  - Mamaev, S.V.
AU  - Gurevich, A.I.
AU  - Igoshin, A.V.
AU  - Kolosov, M.N.
AU  - Slyusarenko, A.G.
TI  - Restriction endonuclease TaqXI from Thermus aquaticus.
JO  - Bioorg. Khim.
PY  - 1981
SP  - 628
EP  - 630
VL  - 7
AB  - A new restriction endonuclease TaqXI has been isolated from an unidentified
AB  - strain of Thermus aquaticus.  The enzyme recognizes the pentanucleotide
AB  - sequence CC(A/T)GG and cleaves it between C and A or T, the methylation of the
AB  - C residue is not protecting the sequence from the cleavage.
ER  -

TY  - JOUR
AU  - Grad, Y.H. et al.
TI  - Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 3065
EP  - 3070
VL  - 109
AB  - The degree to which molecular epidemiology reveals information about the sources  and
AB  - transmission patterns of an outbreak depends on the resolution of the
AB  - technology used and the samples studied. Isolates of Escherichia coli O104:H4
AB  - from the outbreak centered in Germany in May-July 2011, and the much smaller
AB  - outbreak in southwest France in June 2011, were indistinguishable by standard
AB  - tests. We report a molecular epidemiological analysis using multiplatform
AB  - whole-genome sequencing and analysis of multiple isolates from the German and
AB  - French outbreaks. Isolates from the German outbreak showed remarkably little
AB  - diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates
AB  - from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in
AB  - isolates from seven individuals infected in the French outbreak. The German
AB  - isolates form a clade within the more diverse French outbreak strains. Moreover,
AB  - five isolates derived from a single infected individual from the French outbreak
AB  - had extremely limited diversity. The striking difference in diversity between the
AB  - German and French outbreak samples is consistent with several hypotheses,
AB  - including a bottleneck that purged diversity in the German isolates, variation in
AB  - mutation rates in the two E. coli outbreak populations, or uneven distribution of
AB  - diversity in the seed populations that led to each outbreak.
ER  -

TY  - JOUR
AU  - Gradnigo, J.S.
AU  - Somerville, G.A.
AU  - Huether, M.J.
AU  - Kemmy, R.J.
AU  - Johnson, C.M.
AU  - Oliver, M.G.
AU  - Moriyama, E.N.
TI  - Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762.
JO  - Genome Announcements
PY  - 2016
SP  - e00615
EP  - e00616
VL  - 4
AB  - Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics
AB  - tetracycline and chlortetracycline. Here, we report the assembly and
AB  - initial annotation of the draft genome sequence of S. aureofaciens ATCC strain
AB  - 10762.
ER  -

TY  - JOUR
AU  - Graessmann, M.
AU  - Graessmann, A.
AU  - Wagner, H.
AU  - Werner, E.
AU  - Simon, D.
TI  - Complete DNA methylation does not prevent polyoma and simian virus 40 virus early gene expression.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1983
SP  - 6470
EP  - 6474
VL  - 80
AB  - The effect of DNA methylation on polyoma virus and simian virus 40 gene
AB  - expression was investigated.  For this purpose, the cytosines of all C-G
AB  - dinucleotides of the viral DNAs were methylated by the use of rat liver
AB  - methylase and the completeness of methylation was verified by dinucleotide
AB  - analysis and restriction endonuclease treatment.  The biological activity of
AB  - unmethylated and fully methylated DNAs was tested by microinjecting them into
AB  - tissue culture cells.  The functions analyzed included early and late viral
AB  - gene expression, viral DNA replication, oncogenic transformation efficiency,
AB  - and virus maturation.  No difference in any of these biological functions was
AB  - observed between methylated and unmethylated DNA.  Early gene expression of
AB  - methylated DNA is not the result of demethylation because viral DNA reextracted
AB  - from the injected cells, under nonpermissive conditions, retained the
AB  - methylation pattern of the input DNA.  In contrast, viral DNA extracted from
AB  - transformed cells or from intact virus particles was partially or completely
AB  - demethylated.
ER  -

TY  - JOUR
AU  - Grana-Miraglia, L.
AU  - Lozano, L.
AU  - Castro-Jaimes, S.
AU  - Cevallos, M.A.
AU  - Volkow, P.
AU  - Castillo-Ramirez, S.
TI  - First Genome Sequence of a Mexican Multidrug-Resistant Acinetobacter baumannii Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00156
EP  - e00116
VL  - 4
AB  - Acinetobacter baumanniihas emerged as an important nosocomial pathogen worldwide. Here, we
AB  - present the draft genome of the first multidrug-resistantA.
AB  - baumanniiisolate, sampled from a tertiary hospital in Mexico City. This genome
AB  - will provide a starting point for studying the genomic diversity of this species
AB  - in Mexico.
ER  -

TY  - JOUR
AU  - Grande, L.
AU  - Michelacci, V.
AU  - Tozzoli, R.
AU  - Ranieri, P.
AU  - Maugliani, A.
AU  - Caprioli, A.
AU  - Morabito, S.
TI  - Whole genome sequence comparison of vtx2-converting phages from Enteroaggregative Haemorrhagic Escherichia coli strains.
JO  - BMC Genomics
PY  - 2014
SP  - 574
EP  - 574
VL  - 15
AB  - BACKGROUND: Enteroaggregative Haemorrhagic E. coli (EAHEC) is a new pathogenic
AB  - group of E. coli characterized by the presence of a vtx2-phage integrated in the
AB  - genomic backbone of Enteroaggregative E. coli (EAggEC). So far, four distinct
AB  - EAHEC serotypes have been described that caused, beside the large outbreak of
AB  - infection occurred in Germany in 2011, a small outbreak and six sporadic cases of
AB  - HUS in the time span 1992-2012. In the present work we determined the whole
AB  - genome sequence of the vtx2-phage, termed Phi-191, present in the first described
AB  - EAHEC O111:H2 isolated in France in 1992 and compared it with those of the
AB  - vtx-phages whose sequences were available. RESULTS: The whole genome sequence of
AB  - the Phi-191 phage was identical to that of the vtx2-phage P13374 present in the
AB  - EAHEC O104:H4 strain isolated during the German outbreak 20 years later.
AB  - Moreover, it was also almost identical to those of the other vtx2-phages of EAHEC
AB  - O104:H4 strains described so far. Conversely, the Phi-191 phage appeared to be
AB  - different from the vtx2-phage carried by the EAHEC O111:H21 isolated in the
AB  - Northern Ireland in 2012.The comparison of the vtx2-phages sequences from EAHEC
AB  - strains with those from the vtx-phages of typical Verocytotoxin-producing E. coli
AB  - strains showed the presence of a 900 bp sequence uniquely associated with EAHEC
AB  - phages and encoding a tail fiber. CONCLUSIONS: At least two different
AB  - vtx2-phages, both characterized by the presence of a peculiar tail fiber-coding
AB  - gene, intervened in the emergence of EAHEC. The finding of an identical
AB  - vtx2-phage in two EAggEC strains isolated after 20 years in spite of the high
AB  - variability described for vtx-phages is unexpected and suggests that such
AB  - vtx2-phages are kept under a strong selective pressure.The observation that
AB  - different EAHEC infections have been traced back to countries where EAggEC
AB  - infections are endemic and the treatment of human sewage is often ineffective
AB  - suggests that such countries may represent the cradle for the emergence of the
AB  - EAHEC pathotype. In these regions, EAggEC of human origin can extensively
AB  - contaminate the environment where they can meet free vtx-phages likely spread by
AB  - ruminants excreta.
ER  -

TY  - JOUR
AU  - Grandori, R.
AU  - Sander, C.
TI  - Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2359
EP  - 2362
VL  - 19
AB  - We have performed computer searches in the database of known protein sequences
AB  - for proteins similar in sequence to bacteriophage regulatory proteins of known
AB  - 3-D structure.  The searches are more selective than other methods due to the
AB  - use of a length-dependent threshold in sequence similarity, above which
AB  - structural homology is implied with high certainty.  Two probable DNA binding
AB  - proteins were identified which are predicted to have a three-dimensional
AB  - structure very similar to bacteriophage cro and repressor proteins.
AB  - Approximate three-dimensional model coordinates are available from the authors.
AB  - Both proteins contain the helix-turn-helix sequence motif typical of a wide
AB  - class of DNA binding proteins and their function is deduced by analogy to
AB  - sequence-similar proteins of known function.  We predict that the Y.SmaI
AB  - protein in the restriction-modification enzyme gene locus of the
AB  - enterobacterium serratia marcescens is a regulator of endonuclease expression;
AB  - and, that the vegetative specific gene VSH7 of the slime mold dictyostelium
AB  - discoideum codes for a regulator of gene expression specific for the slime mold
AB  - growth phage before the onset of the developmental program.  Point mutations
AB  - that would have a strong effect on growth regulation phenotype are suggested.
AB  - The VSH7 protein would be the first eukaryotic representative of the cro /
AB  - phage repressor class.
ER  -

TY  - JOUR
AU  - Grant, S.G.
AU  - Jessee, J.
AU  - Bloom, F.R.
AU  - Hanahan, D.
TI  - Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1990
SP  - 4645
EP  - 4649
VL  - 87
AB  - Plasmids comprising transgene insertions in four lines of transgenic mice have been retrieved
AB  - by plasmid rescue into a set of Escherichia coli strains with
AB  - mutations in different members of the methylation-dependent restriction system
AB  - (MDRS). Statistical analysis of plasmid rescue frequencies has revealed that the
AB  - MDRS loci detect differential modifications of the transgene insertions among
AB  - mouse lines that show distinctive patterns of transgene expression. Plasmids in
AB  - mice that express hybrid insulin transgenes during development can be readily
AB  - cloned into E. coli strains carrying mutations in two of the MDRS loci, mcrA and
AB  - mcrB. In mice in which transgene expression is inappropriately delayed into
AB  - adulthood, plasmids can only be cloned into E. coli that carry mutations in all
AB  - known MDRS activities. Differential cloning frequencies in the presence or
AB  - absence of the various methylation-dependent restriction genes represent a
AB  - further way to distinguish regions of mammalian chromosomes. These multiply
AB  - deficient E. coli strains will also facilitate the molecular cloning of modified
AB  - chromosomal DNA.
ER  -

TY  - JOUR
AU  - Grasby, J.A.
AU  - Connolly, B.A.
TI  - Stereochemical outcome of the hydrolysis reaction catalyzed by the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1992
SP  - 7855
EP  - 7861
VL  - 31
AB  - The stereochemical course of the reaction catalyzed by the EcoRV restriction and endonuclesae
AB  - has been determined. This endonuclease recognizes GATATC sequences and cuts between the
AB  - central T and dA bases. The Rp isomer of d(GACGATsATCGTC) (this dodecamer contains a
AB  - phosphorothioate rather than the usual phosphate group between the central T and dA residues,
AB  - indicated by the s) was a substrate for the endonuclease. Performing this reaction in H2[18O]
AB  - gave [18O]dps(ATCGTC)(a pentamer containing an 18 O-labeled 5'-phosphorothioate) which was
AB  - converted to [18O]dAMPS with nuclese P1. This deoxynucleoside 5'-[18O]phosphorothioate was
AB  - sterospecifically converted to [18O]dATPalphaS with adenylate kinase and pyruvate kinase
AB  - [Brody, R.S., & Frey, P.A.(1981) Biochemistry 20, 1245-1251]. Analysis of the position of the
AB  - 18O in this product by 31P NMR spectroscopy showed that it was in a bridging position between
AB  - the alpha- and beta-phosphorus atoms. This indicates that the EcoRV hydrolysis proceeds with
AB  - inversion of configuration at phosphorus. The simplest interpretation is that the mechanism of
AB  - this endonuclease involves a direct in-line attack at phosphorus by H2O with a trigonal
AB  - bipyramidal transition state. A covalent enzyme oligodeoxynucleotide species can be discounted
AB  - as an intermediate. An identical result has been previously observed with the EcoRI
AB  - endonuclease [Connolly,B.A., Eckstein,F., & Pingoud,A.(1984) J. Biol. Chem. 259, 10760-10763].
AB  - X-ray crystallography has shown that both of these endonucleases contain a conserved array of
AB  - amino acids at their active sites. Possible mechanistic roles for these conserved amino acids
AB  - in the light of the stereochemical findings are discussed.
ER  -

TY  - JOUR
AU  - Grass, G.
AU  - Bierbaum, G.
AU  - Molitor, E.
AU  - Gotte, N.
AU  - Antwerpen, M.
TI  - Genome Sequence of Bacillus pumilus Strain Bonn, Isolated from an Anthrax-Like Necrotic Skin Infection Site of a Child.
JO  - Genome Announcements
PY  - 2016
SP  - e01741
EP  - e01715
VL  - 4
AB  - We report the draft genome sequence of Bacillus pumilus strain Bonn associated with human skin
AB  - infection. B. pumilus Bonn was isolated from a carbuncle-like
AB  - necrotic site, resembling cutaneous anthrax, on the back of the hand of a
AB  - 10-year-old child.
ER  -

TY  - JOUR
AU  - Grass, G.
AU  - Hanczaruk, M.
AU  - Antwerpen, M.
TI  - Genome Sequence of Bacillus anthracis Larissa, Associated with a Case of Cutaneous Anthrax in Greece.
JO  - Genome Announcements
PY  - 2015
SP  - e01273
EP  - e01215
VL  - 3
AB  - We report the genome sequence of Bacillus anthracis strain Larissa, isolated from a diseased
AB  - sheep associated with a human case of cutaneous anthrax in Central
AB  - Greece from 2012. Genome sequence analysis of strain Larissa may aid in
AB  - describing phylogenetic relationships of B. anthracis isolates in Southeastern
AB  - European countries.
ER  -

TY  - JOUR
AU  - Grasso, R.J.
AU  - Paigen, K.
TI  - Loss of host-controlled restriction of lambda bacteriophage in Escherichia coli following methionine deprivation.
JO  - J. Virol.
PY  - 1968
SP  - 1368
EP  - 1373
VL  - 2
AB  - Lambda bacteriophages produced in Escherichia coli C (designated as lambda.C)
AB  - are restricted in their ability to grow in E. coli K-12.  The rare successful
AB  - infections that arise in the K-12 population occur in "special" cells which
AB  - have lost their capacity to restrict lambda.C.  These infections yield modified
AB  - progeny phage (designated as lambda.K) which unlike lambda.C, plate equally
AB  - well on E. coli C and E. coli K-12.  When methionine, but no other amino acid,
AB  - was removed from the growth medium of a mutant strain of E. coli K-12, the
AB  - number of special cells rapidly increased 500- to 3,000-fold.  These new
AB  - special cells retain their capacity to produce modified lambda.K progeny.  This
AB  - conversion of restricting cells into special cells does not require the
AB  - synthesis of new protein.  The special cells formed when methionine was removed
AB  - from the culture did not revert into restricting cells when methionine was
AB  - restored.  Such cells have also lost the ability to divide for at least 4 hr
AB  - after methionine supplementation.  When methionine was restored, the remaining
AB  - restricting cells, but not the special cells, immediately resumed growth.
AB  - Removing methionine from cultures of E. coli B caused a similar increase in the
AB  - number of special cells able to support the growth of lambda.C and lambda.K.
AB  - However, when E. coli K-12 (P1) cultures were deprived of methionine, the
AB  - number of special cells increased for lambda.C but not for lambda.K.  Thus,
AB  - retention of the P1-restriction system, unlike the B- and the K-12 systems,
AB  - does not require the presence of methionine.
ER  -

TY  - JOUR
AU  - Grasso, R.J.
AU  - Paigen, K.
TI  - The effect of amino acids on host-controlled restriction of lambda phage.
JO  - Virology
PY  - 1968
SP  - 1
EP  - 8
VL  - 36
AB  - Phage lambda grown in Escherichia coli C (lambda.C) plates with an efficiency
AB  - of approximately 4 X 10-4 on log phage E. coli K12 grown in broth.  These few
AB  - successful infections occur in "special cells" in the K12 population which have
AB  - lost their ability to restrict lambda.C.  E. coli K12 grown in minimal medium
AB  - has 30-50 times as many special cells.  Supplementation of minimal medium with
AB  - an amino acid mixture reduced the frequency of special cells to that observed
AB  - in broth cultures.  When amino acids were tested individually, the addition of
AB  - either alainine or leucine alone to minimal medium reduced the special cell
AB  - population.  This reduction in the frequency of special cells was reversed by
AB  - the futher addition of several other amino acids to the growth medium.  Medium
AB  - shift experiments with alanine and leucine suggest that these amino acids do
AB  - not act at the time of infection; instead they determine the presence of a
AB  - metabolic system involved in the expression of host-controlled restriction.
AB  - Removal of methionine from K12 cultures containing an otherwise complete amino
AB  - acid mixture caused an increase in the number of special cells.  Unlike the
AB  - alanine and leucine effects, this increase was rapid and occurred in the
AB  - presence of chloramphenicol.  Prolonged growth in methionine was required to
AB  - restore the reduced special cell frequency.  It appears that the removal of
AB  - methionine can convert a restricting cell into a special cell which is then
AB  - incapable of undergoing cell division.  The various amino acid effects are
AB  - specific to the K12-restriction system and do not influence the B- or
AB  - P1-restriction systems of E. coli.
ER  -

TY  - JOUR
AU  - Grasso, R.J.
AU  - Paigen, K.
TI  - Loss of host-controlled restriction and modification of phage lambda in Escherichia coli K12 previously infected with UV-irradiated coli-phage T3.
JO  - Virology
PY  - 1969
SP  - 191
EP  - 194
VL  - 38
AB  - Host range properties of bacteriophages are altered not only by genetic
AB  - mutation, but also by the process of host-controlled modification.
ER  -

TY  - JOUR
AU  - Grau, J.
AU  - Reschke, M.
AU  - Erkes, A.
AU  - Streubel, J.
AU  - Morgan, R.D.
AU  - Wilson, G.G.
AU  - Koebnik, R.
AU  - Boch, J.
TI  - AnnoTALE: bioinformatic tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.
JO  - Sci. Rep.
PY  - 2016
SP  - 21077
EP  - 21077
VL  - 6
AB  - Transcription activator-like effectors (TALEs) are virulence factors, produced by the
AB  - bacterial plant pathogen Xanthomonas, that function as gene activators inside plant cells.
AB  - Although the contribution of individual TALEs to infectivity has been shown, the specific
AB  - roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs
AB  - possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence.
AB  - Here, we describe an improved method for characterizing
AB  - TALE genes by the use of PacBio sequencing. We present AnnoTALE, a suite of applications for
AB  - the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar
AB  - TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas
AB  - TALEs that reveals similarities pointing to related functionalities. This new classification
AB  - enables us to compare related TALEs and to identify base substitutions responsible for the
AB  - evolution of TALE specificities.
ER  -

TY  - JOUR
AU  - Graupner, K.
AU  - Lackner, G.
AU  - Hertweck, C.
TI  - Genome Sequence of Mushroom Soft-Rot Pathogen Janthinobacterium agaricidamnosum.
JO  - Genome Announcements
PY  - 2015
SP  - e00277
EP  - e00215
VL  - 3
AB  - Janthinobacterium agaricidamnosum causes soft-rot disease of the cultured button  mushroom
AB  - Agaricus bisporus and is thus responsible for agricultural losses. Here,
AB  - we present the genome sequence of J. agaricidamnosum DSM 9628. The 5.9-Mb genome
AB  - harbors several secondary metabolite biosynthesis gene clusters, which renders
AB  - this neglected bacterium a promising source for genome mining approaches.
ER  -

TY  - JOUR
AU  - Graves, K.L.
AU  - Butler, M.M.
AU  - Hardy, L.W.
TI  - Site-directed mutagenesis of the gene encoding phage T4 dCMP hydroxymethylase.
JO  - FASEB J.
PY  - 1993
SP  - A1197
EP  - A1197
VL  - 7
AB  - The proposed roles of several amino acid residues in deoxycytidylate (dCMP) hydroxymethylase
AB  - (CH) have been tested. CH catalyzes the formation of 5-hydroxymethyl-dCMP, an essential
AB  - component of phage T4 DNA, from dCMP and methylenetetrahydrofolate (CH2THF). CH resemble
AB  - thymidylate synthase (TS), an enzyme of known crystallographic structure, in both amino acid
AB  - sequence and reaction catalyzed. Conversion of Cys148 to Asp, Gly, or Ser decreases CH
AB  - activity at least 10/5-fold, consistent with a nucleophilic role for Cys148 (analogous to the
AB  - catalytic Cys residue in TS). In TS, hydrogen bonds connect O4 and N3 of the substrate dUMP to
AB  - an Asn. Conversion of the corresponding residue in CH, Asp179 to an Asn reverses the substrate
AB  - preference of CH from dCMP to dUMP. Asp179 is proposed to stabilize covalent catalytic
AB  - intermediates, by protonating N3 of the pyrimidine-CH adduct. CH is inactivated by
AB  - 5-fluoro-deoxyuridylate (FdUMP), a mechanism-based inactivator of TS, by formation of a
AB  - ternary complex between enzyme, CH2THF and FdUMP. Replacement of Cys148 prevents formation of
AB  - such a complex. The secondary equilibrium isotope effect upon the formation of the ternary
AB  - complex, HK/TK, was measured using a mixture of 2(14C)-FdUMP and 6[3H]-FdUMP. The observed
AB  - inverse effect is consistent with the formation of a covalent complex where C6 of FdUMP is sp3
AB  - hybridized and covalently linked to the thiol of Cys148. The proposed roles of a number of
AB  - other residues in CH are currently under investigation.
ER  -

TY  - JOUR
AU  - Gray, T.A.
AU  - Palumbo, M.J.
AU  - Derbyshire, K.M.
TI  - Draft Genome Sequence of MKD8, a Conjugal Recipient Mycobacterium smegmatis Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00148
EP  - e00113
VL  - 1
AB  - We report an annotated draft genome sequence of the Mycobacterium smegmatis strain MKD8. This
AB  - strain acts as a recipient during conjugation with the
AB  - reference M. smegmatis strain mc(2)155. While the genomes of the two strains are
AB  - colinear and have similar sizes, extensive genome-wide sequence variation
AB  - suggests rich diversity within the M. smegmatis clade.
ER  -

TY  - JOUR
AU  - Grazulis, S.
AU  - Deibert, M.
AU  - Rimseliene, R.
AU  - Skirgaila, R.
AU  - Sasnauskas, G.
AU  - Lagunavicius, A.
AU  - Repin, V.
AU  - Urbanke, C.
AU  - Huber, R.
AU  - Siksnys, V.
TI  - Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 876
EP  - 885
VL  - 30
AB  - Crystal structures of Type II restriction endonucleases demonstrate a conserved common core
AB  - and active site residues but diverse structural elements involved in DNA sequence
AB  - discrimination. Comparative structural analysis of restriction enzymes recognizing the same
AB  - nucleotide sequence might therefore contribute to our understanding of the structural
AB  - diversity of specificity determinants within restriction enzymes. We have solved the crystal
AB  - structure of the Bacillus stearothermophilus restriction endonuclease Bse634I by the multiple
AB  - isomorphous replacement technique to 2.17 Angstroms resolution. Bse634I is an isoschisomer of
AB  - the Cfr10I restriction enzyme whose crystal structure has been reported previously.
AB  - Comparative structural analysis of the first pair of isoschisomeric enzymes revealed conserved
AB  - structural determinants of sequence recognition and catalysis. However, conformations of the
AB  - N-terminal subdomains differed between Bse634I/Cfr10I, suggesting a rigid body movement that
AB  - might couple DNA recognition and catalysis. Structural similarities extend to the quaternary
AB  - structure level: crystal contacts suggest that Bse634I similarly to Cfr10I is arranged as a
AB  - tetramer. Kinetic analysis reveals that Bse634I is able to interact simultaneously with two
AB  - recognition sites supporting the tetrameric architecture of the protein. Thus, restriction
AB  - enzymes Bse634I, Cfr10I and NgoMIV, recognizing overlapping nucleotide sequences, exhibit a
AB  - conserved tetrameric architecture that is of functional importance.
AB  - * To whom correspondence should be addressed at: Institute of Biotechnolo
ER  -

TY  - JOUR
AU  - Grazulis, S.
AU  - Manakova, E.
AU  - Roessle, M.
AU  - Bochtler, M.
AU  - Tamulaitiene, G.
AU  - Huber, R.
AU  - Siksnys, V.
TI  - Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 15797
EP  - 15802
VL  - 102
AB  - Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the
AB  - absence of metal ions. BfiI represents a different
AB  - evolutionary lineage of restriction enzymes, as shown by its crystal
AB  - structure at 1.9-A resolution. The protein consists of two structural
AB  - domains. The N-terminal catalytic domain is similar to Nuc, an
AB  - EDTA-resistant nuclease from the phospholipase D superfamily. The
AB  - C-terminal DNA-binding domain of BfiI exhibits a beta-barrel-like
AB  - structure very similar to the effector DNA-binding domain of the
AB  - Mg(2+)-dependent restriction enzyme EcoRII and to the B3-like DNA-binding
AB  - domain of plant transcription factors. BfiI presumably evolved through
AB  - domain fusion of a DNA-recognition element to a nonspecific nuclease akin
AB  - to Nuc and elaborated a mechanism to limit DNA cleavage to a single
AB  - double-strand break near the specific recognition sequence. The crystal
AB  - structure suggests that the interdomain linker may act as an autoinhibitor
AB  - controlling BfiI catalytic activity in the absence of a specific DNA
AB  - sequence. A psi-blast search identified a BfiI homologue in a
AB  - Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an
AB  - EDTA-rich environment.
ER  -

TY  - JOUR
AU  - Green, N.M.
AU  - Zhang, S.
AU  - Porcella, S.F.
AU  - Nagiec, M.J.
AU  - Barbian, K.D.
AU  - Beres, S.B.
AU  - Lefebvre, R.B.
AU  - Musser, J.M.
TI  - Genome Sequence of a Serotype M28 Strain of Group A Streptococcus: Potential New Insights into Puerperal Sepsis and Bacterial Disease   Specificity.
JO  - J. Infect. Dis.
PY  - 2005
SP  - 760
EP  - 770
VL  - 192
AB  - Puerperal sepsis, a major cause of death of young women in Europe in the 1800s, was due
AB  - predominantly to the gram-positive pathogen group A
AB  - Streptococcus. Studies conducted during past decades have shown that
AB  - serotype M28 strains are the major group A Streptococcus organisms
AB  - responsible for many of these infections. To begin to increase our
AB  - understanding of their enrichment in puerperal sepsis, we sequenced the
AB  - genome of a genetically representative strain. This strain has genes
AB  - encoding a novel array of prophage virulence factors, cell-surface
AB  - proteins, and other molecules likely to contribute to host-pathogen
AB  - interactions. Importantly, genes for 7 inferred extracellular proteins are
AB  - encoded by a 37.4-kb foreign DNA element that is shared with group B
AB  - Streptococcus and is present in all serotype M28 strains. Proteins encoded
AB  - by the 37.4-kb element were expressed extracellularly and in human
AB  - infections. Acquisition of foreign genes has helped create a
AB  - disease-specialist clone of this pathogen.
ER  -

TY  - JOUR
AU  - Greenaway, P.J.
TI  - The isolation of a restriction enzyme from Bordetella pertussis.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1980
SP  - 1282
EP  - 1287
VL  - 95
AB  - A restriction enzyme was isolated from Bordetella pertussis cells by a
AB  - single-step purification procedure using chromatography on phosphocellulose.
AB  - Different DNA molecules were digested with this enzyme; the fragmentation
AB  - patterns obtained were compared to those obtained after digestion with the
AB  - HindIII enzyme isolated from Haemophilus influenzae strain Rd.  It was
AB  - concluded that the cleavage site specificities of these enzymes were identical.
ER  -

TY  - JOUR
AU  - Greenberg, D.E.
AU  - Porcella, S.F.
AU  - Zelazny, A.M.
AU  - Virtaneva, K.
AU  - Sturdevant, D.E.
AU  - Kupko, J.J.
AU  - Barbian, K.D.
AU  - Babar, A.
AU  - Dorward, D.W.
AU  - Holland, S.M.
TI  - Genome sequence analysis of the emerging human pathogenic acetic acid bacterium Granulibacter bethesdensis.
JO  - J. Bacteriol.
PY  - 2007
SP  - 8727
EP  - 8736
VL  - 189
AB  - Chronic granulomatous disease (CGD) is an inherited immune deficiency characterized by
AB  - increased susceptibility to infection with
AB  - Staphylococcus, certain gram-negative bacteria, and fungi. Granulibacter
AB  - bethesdensis, a newly described genus and species within the family
AB  - Acetobacteraceae, was recently isolated from four CGD patients residing in
AB  - geographically distinct locales who presented with fever and
AB  - lymphadenitis. We sequenced the genome of the reference strain of
AB  - Granulibacter bethesdensis, which was isolated from lymph nodes of the
AB  - original patient. The genome contains 2,708,355 base pairs in a single
AB  - circular chromosome, in which 2,437 putative open reading frames (ORFs)
AB  - were identified, 1,470 of which share sequence similarity with ORFs in the
AB  - nonpathogenic but related Gluconobacter oxydans genome. Included in the
AB  - 967 ORFs that are unique to G. bethesdensis are ORFs potentially important
AB  - for virulence, adherence, DNA uptake, and methanol utilization. GC% values
AB  - and best BLAST analysis suggested that some of these unique ORFs were
AB  - recently acquired. Comparison of G. bethesdensis to other known CGD
AB  - pathogens demonstrated conservation of some putative virulence factors,
AB  - suggesting possible common mechanisms involved in pathogenesis in CGD.
AB  - Genotyping of the four patient isolates by use of a custom microarray
AB  - demonstrated genome-wide variations in regions encoding DNA uptake systems
AB  - and transcriptional regulators and in hypothetical ORFs. G. bethesdensis
AB  - is a genetically diverse emerging human pathogen that may have recently
AB  - acquired virulence factors new to this family of organisms.
ER  -

TY  - JOUR
AU  - Greene, P.
AU  - Reich, N.O.
AU  - McClarin, J.
AU  - Boyer, H.W.
AU  - Rosenberg, J.
TI  - Site-directed mutagenesis of the EcoRI endonuclease.
JO  - J. Cell Biochem. Suppl.
PY  - 1985
SP  - 94
EP  - 94
VL  - 9B
AB  - The EcoRI endonuclease has been crystallized with its substrate and the X-ray
AB  - structure has been solved to 3 angstroms (Nature 309: 327, 1984).  Sequence
AB  - recognition is mediated by a series of hydrogen bonds between complementary
AB  - surfaces of the protein and the major groove of the DNA.  We have used the
AB  - crystallographic analysis to design putative specificity mutations in the
AB  - endonuclease and to predict possible new specificities that might arise.  In
AB  - particular, a glutamic acid residue which is postulated to interact with the N6
AB  - positions of the adjacent adenines in the recognition sequence has been
AB  - replaced with glutamic acid.  The predicted recognition sequence would contain
AB  - a guanine in place of one of the adenines.  This alteration has been introduced
AB  - into the endonuclease gene by means of mismatch primer mutagenesis.  The
AB  - expression and characterization of the mutant protein is underway.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Ballard, B.T.
AU  - Stephenson, F.
AU  - Kohr, W.J.
AU  - Rodriguez, H.
AU  - Rosenberg, J.M.
AU  - Boyer, H.W.
TI  - Purification and characterization of the restriction endonuclease RsrI, an isoschizomer of EcoRI.
JO  - Gene
PY  - 1988
SP  - 43
EP  - 52
VL  - 68
AB  - Rhodobacter sphaeroides strain 630 produces restriction enzyme RsrI which is an
AB  - isoschizoemr of EcoRI.  We have purified this enzyme and initiated a comparison
AB  - with the EcoRI endonuclease.  The properties of RsrI are consistent with a
AB  - reaction mechanism similar to that of EcoRI:  the position of cleavage within
AB  - the -GAATTC- site is identical, the MgCl2 optimum for the cleavage is
AB  - identical, and the pH profile is similar.  Methylation of the substrate
AB  - sequence by the EcoRI methylase protects the site from cleavage by the RsrI
AB  - endonuclease.  RsrI cross-reacts strongly with anti-EcoRI serum indicating
AB  - three-dimensional structural similarities.  We have determined the sequence of
AB  - 34 N-terminal amino acids for RsrI and this sequence possesses significant
AB  - similarity to the EcoRI N terminus.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Betlach, M.C.
AU  - Boyer, H.W.
AU  - Goodman, H.M.
TI  - The EcoRI restriction endonuclease.
JO  - Methods Mol. Biol.
PY  - 1974
SP  - 87
EP  - 105
VL  - 7
AB  - Type II bacterial restriction endonucleases have become increasingly useful in
AB  - the analysis of small DNA genomes, while attempts to use the Type I restriction
AB  - endonucleases have not been satisfactory because they appear to be less
AB  - specific than originally imagined.  The current purification procedure for the
AB  - EcoRI restriction endonuclease and some of its properties, as well as a
AB  - procedure for partial purification of the related EcoRI modification methylase,
AB  - are described.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Boyer, H.W.
TI  - Genetic and molecular analysis of the EcoRI restriction and modification system.
JO  - Fed. Proc.
PY  - 1981
SP  - 293
EP  - 293
VL  - 40
AB  - The structure and function of the EcoRI endonuclease and methylase are being
AB  - studied in order to elucidate how proteins recognize specific DNA sequences.
AB  - We have crystallized the EcoRI endonuclease and measured space group and unit
AB  - cell parameters.  We plan to sequence the endonuclease and methylase by
AB  - sequencing the DNA which encodes them.  The genes are closely linked on a
AB  - multicopy plasmid, pMB1.  The approximate boundaries of the genes have been
AB  - determined by cloning different restriction fragments.  Based on subunit
AB  - molecular weight estimates of 36,000 daltons and 29,000 daltons for the
AB  - methylase and endonuclease respectively, the required length of DNA for both
AB  - structural genes is ~ 1800 base pairs.  A 2300 base pair restriction fragment
AB  - has been shown to contain all of the information necessary for the expression
AB  - of normal levels of both enzymes.  A detailed restriction map of this fragment
AB  - has been prepared using the technique of end labeling followed by partial
AB  - digestion.  DNA sequencing is underway using chain terminating inhibitors.
AB  - Clones have been isolated with this fragment in both orientations relative to
AB  - the lac promoter and operator in pBH20.  The effect of the lac control system
AB  - on the specific activity of EcoRI enzymes suggests that the direction of
AB  - transcription is from the endonuclease to the methylase.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Gupta, M.
AU  - Boyer, H.W.
AU  - Brown, W.E.
AU  - Rosenberg, J.M.
TI  - Sequence Analysis of the DNA Encoding the EcoRI Endonuclease and Methylase.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 2143
EP  - 2153
VL  - 256
AB  - The EcoRI endonuclease and methylase recognize the same hexanucleotide substrate sequence.  We
AB  - have determined the sequence of a fragment of DNA which encodes these enzymes using the
AB  - chain-termination method of Sanger (Sanger, F., Nicklen, S., and Coulson, A.R. (1977) Proc.
AB  - Natl. Acad. Sci. U.S.A. 74, 5463-5467).  The amino acid sequences of both enzymes were derived
AB  - from the DNA sequence.  The coding regions selected include the only open translational frames
AB  - of sufficient length to accommodate the enzymes.  They coincide with previously established
AB  - gene boundaries and orientation.  The predicted amino acid sequences correlate well with
AB  - analyses of the purified protein. Comparison of the nucleotide and protein sequences reveals
AB  - no homology between the endonuclease and methylase which might provide insight into the origin
AB  - of the restriction-modification system or the mechanism of common substrate recognition.
AB  - Based on secondary structure predictions, the two enzymes also have grossly different
AB  - molecular architecture.  The base composition of the sequence is 65% A + T, and the codon
AB  - usage is signficantly different from that observed in several Escherichia coli chromosomal
AB  - genes.  In some cases, frequently selected codons are recognized by minor tRNA species.  A
AB  - spontaneous mutation in the endonuclease gene was isolated.  Serine replaces arginine at
AB  - residue 187.  In crude extracts, EcoRI specific cleavage is ~0.3% wild type.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Heyneker, H.L.
AU  - Bolivar, F.
AU  - Rodriguez, R.L.
AU  - Betlach, M.C.
AU  - Covarrubias, A.A.
AU  - Backman, K.
AU  - Russel, D.J.
AU  - Tait, R.
AU  - Boyer, H.W.
TI  - A general method for the purification of restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 2373
EP  - 2380
VL  - 5
AB  - An abbreviated procedure has been developed for the purification of restriction
AB  - endonucleases.  This procedure uses chromatography on phosphocellulose and
AB  - hydroxylapatite and results in enzymes of sufficient purity to permit their use
AB  - in the sequencing, molecular cloning, and physical mapping of DNA.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Poonian, M.S.
AU  - Nussbaum, A.L.
AU  - Tobias, L.
AU  - Garfin, D.E.
AU  - Boyer, H.W.
AU  - Goodman, H.M.
TI  - Restriction and modification of a self-complementary octanucleotide containing the EcoRI substrate.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 237
EP  - 261
VL  - 99
AB  - In order to study the interactions of the EcoRI restriction endonuclease and
AB  - modification methylase with DNA, we have synthesized the self-complementary
AB  - octanucleotide, pT-G-A-A-T-T-C-A, which contains the nucleotide sequence of the
AB  - EcoRI substrate.  This octamer can act as a substrate for both the endonuclease
AB  - and methylase; the enzymatic alteration of this molecule is the same as that of
AB  - DNA, with cleavage and methylation both occurring at the same positions on
AB  - either substrate.  The optimum temperature for the reaction of the
AB  - octanucleotide with the endonuclease is 15C and that with the methylase is
AB  - 12.5C.  The optimum temperature for the reactions of both of the enzymes with
AB  - DNA is 37C.  The low temperatures for reactions with the octanucleotide reflect
AB  - the conditions under which this molecule can serve as a substrate for the
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Greene, P.J.
AU  - Yanofsky, S.
AU  - Reich, N.
AU  - Day, J.
AU  - Hager, P.
AU  - Boyer, H.W.
TI  - Structure and function of the EcoRI endonuclease.
JO  - Protein Structure, Folding and Design 2
PY  - 1987
SP  - 3
EP  - 7
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Gregoire, S.T.
TI  - The effect of DNA-mediated restriction on conjugation in Neisseria gonorrhoeae.
JO  - M.Sc. Thesis. Univ. Maryland.
PY  - 1986
SP  - 1
EP  - 138
VL  - 0
AB  - A derivative of the gonococcal shuttle-vector pLES2 containing the proAB genes of Neisseria
AB  - gonorrhoeae strain KH45 was mobilized by the gonococcal conjugal plasmid into Escherichia coli
AB  - recipients independent of the host strain restriction-modification phenotype.  Introduction of
AB  - this plasmid into E. coli via conjugation does not result in deletions.  Expression of the
AB  - proline biosynthesis genes was confirmed by cultivation of transconjugants on media devoid of
AB  - proline.  The plasmid was mobilized to various gonococcal strains.  Transfer frequencies of
AB  - 10^-5 were obtained.  When isogenic crosses between the recipient D13 strain, and D13
AB  - containing pLES4, were compared, transfer occurred at 10^-2.  The role of restriction during
AB  - conjugation was investigated as an explanation for the increase in transfer efficiency.  The
AB  - self-mobilizable plasmid pFT6, propagated in an R.NgoII-, M.NgoII- gonococcal strain, was used
AB  - in filter matings with R.NgoII- M.NgoII+, R.NgoII+ M.NgoII+, and R.NgoII- M.NgoII- recipient
AB  - strains.  The results demonstrated that the plasmid mobilized to the gonococcal recipients at
AB  - equal frequencies, indicating that restriction was not a barrier to conjugation.  Introduction
AB  - of pLES4 into commensal species of the Neisseriaceae via conjugation was unsuccessful.  A
AB  - mechanism other than restriction is presented as a possible factor influencing conjugation in
AB  - the gonococcus.
ER  -

TY  - JOUR
AU  - Gregorova, D.
AU  - Pravcova, M.
AU  - Karpiskova, R.
AU  - Rychlik, I.
TI  - Plasmid pC present in Salmonella enterica serovar Enteritidis PT14b strains encodes a restriction modification system.
JO  - FEMS Microbiol. Lett.
PY  - 2002
SP  - 195
EP  - 198
VL  - 214
AB  - Salmonella enterica serovar Enteritidis (S. enteritidis) possesses plasmids of different sizes
AB  - and roles. Besides the serovar-specific
AB  - virulence plasmid present in most field strains, S. enteritidis can
AB  - harbour plasmids of low molecular mass whose biological role is poorly
AB  - understood. We therefore sequenced plasmid pC present in S. enteritidis
AB  - strains belonging to phage type PT14b. The size of plasmid was
AB  - determined to be 5269 bp and it was predicted to encode four open
AB  - reading frames (ORFs). The first two ORFs were found (initial 3230 bp)
AB  - to be highly homologous to rom and mbeA genes of Co1E1 plasmid of
AB  - Escherichia coli. Proteins encoded by the other two ORFs were 99%
AB  - homologous to a restriction methylase and restriction endonuclease
AB  - encoded by plasmid pECO29 of a field strain of E. coli. Using
AB  - insertional mutagenesis we confirmed experimentally that the plasmid
AB  - pC-encoded restriction modification system was functional and could
AB  - explain the high resistance of S. enteritidis PT14b strains to phage
AB  - infection.
ER  -

TY  - JOUR
AU  - Gregory, R.
AU  - Saunders, V.A.
AU  - Saunders, J.R.
TI  - Rule-based simulation of temperate bacteriophage infection: Restriction-modification as a limiter to infection in bacterial populations.
JO  - Biosystems
PY  - 2010
SP  - 166
EP  - 177
VL  - 100
AB  - An individual-based model (IbM) for bacterial adaptation and evolution, COSMIC-Rules, has been
AB  - employed to simulate interactions of virtual
AB  - temperate bacteriophages (phages) and their bacterial hosts. Outcomes
AB  - of infection mimic those of a phage such as lambda, which can enter
AB  - either the lytic or lysogenic cycle, depending on the nutritional
AB  - status of the host. Infection of different hosts possessing differing
AB  - restriction and modification systems is also simulated. Phages
AB  - restricted upon infection of one restricting host can be adapted (by
AB  - host-controlled modification of the phage genome) and subsequently
AB  - propagate with full efficiency on this host. However, such ability is
AB  - lost if the progeny phages are passaged through a new host with a
AB  - different restriction and modification system before attempted
AB  - re-infection of the original restrictive host. The simulations show
AB  - that adaptation and re-adaptation to a particular host-controlled
AB  - restriction and modification system result in lower efficiency and
AB  - delayed lysis of bacterial cells compared with infection of
AB  - non-restricting host bacteria.
AB  - Such biologically realistic simulations validate the use of the IbM
AB  - approach to predicting behaviour of bacteriophages in bacterial
AB  - populations. The applicability of the model for more complex scenarios
AB  - aimed at predictive modelling of bacterial evolution in a changing
AB  - environment and the implications for the spread of viruses in a wider
AB  - context are discussed.
ER  -

TY  - JOUR
AU  - Greif, G.
AU  - Iraola, G.
AU  - Berna, L.
AU  - Coitinho, C.
AU  - Rivas, C.M.
AU  - Naya, H.
AU  - Robello, C.
TI  - Complete Genome Sequence of Mycobacterium tuberculosis Strain MtURU-001, Isolated from a Rapidly Progressing Outbreak in Uruguay.
JO  - Genome Announcements
PY  - 2014
SP  - e01220
EP  - e01213
VL  - 2
AB  - Despite efficient control programs, large clonal outbreaks of tuberculosis (TB) may arise in
AB  - low-risk populations. Recently, an unusual TB outbreak was reported
AB  - in Uruguay, reaching an elevated disease attack rate (53 to 69%). Here, we report
AB  - the genome sequence of the Mycobacterium tuberculosis strain associated with this
AB  - rapidly progressing outbreak, named MtURU-001.
ER  -

TY  - JOUR
AU  - Greil, F.
AU  - Moorman, C.
AU  - van Steensel, B.
TI  - DamID: Mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase.
JO  - Methods Enzymol.
PY  - 2006
SP  - 342
EP  - 359
VL  - 410
AB  - A large variety of proteins bind to specific parts of the genome to regulate gene expression,
AB  - DNA replication, and chromatin structure.
AB  - DamID is a powerful method used to map the genomic interaction sites of
AB  - these proteins in vivo. It is based on fusing a protein of interest to
AB  - Escherichia coli DNA adenine methyltransferase (dam). Expression of
AB  - this fusion protein in vivo leads to preferential methylation of
AB  - adenines in DNA surrounding the native binding sites of the dam fusion
AB  - partner. Because adenine methylation does not occur endogenously in
AB  - most eukaryotes, it provides a unique tag to mark protein interaction
AB  - sites. The adenine-methylated DNA fragments are isolated by selective
AB  - polymerase chain reaction amplification and can be identified by
AB  - microarray hybridization. We and others have successfully applied DamID
AB  - to the genome-wide identification of interaction sites of several
AB  - transcription factors and other chromatin-associated proteins. This
AB  - chapter discusses DamID technology in detail, and a step-by-step
AB  - experimental protocol is provided for use in Drosophila cell lines.
ER  -

TY  - JOUR
AU  - Grenier, F.
AU  - Matteau, D.
AU  - Baby, V.
AU  - Rodrigue, S.
TI  - Complete Genome Sequence of Escherichia coli BW25113.
JO  - Genome Announcements
PY  - 2014
SP  - e01038
EP  - e01014
VL  - 2
AB  - Escherichia coli BW25113 is the parent strain of the Keio collection comprising nearly 4,000
AB  - single-gene deletion mutants. We report the complete 4,631,469-bp
AB  - genome sequence of this strain and the key variations from the type strain E.
AB  - coli MG1655.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Chorny, I.
AU  - Knowles, S.
AU  - Ng, V.L.
AU  - Chaturvedi, V.
TI  - Draft Genome Sequences of Four NDM-1-Producing Klebsiella pneumoniae Strains from a Health Care Facility in Northern California.
JO  - Genome Announcements
PY  - 2015
SP  - e00421
EP  - e00415
VL  - 3
AB  - We report the draft genome sequences of Klebsiella pneumoniae strains from four patients at a
AB  - northern California health care facility. All strains contained the
AB  - New Delhi metallo-beta-lactamase (NDM1) carbapenemase with extended antibiotic
AB  - resistance, including resistance to expanded-spectrum cephalosporins, imipenem,
AB  - ertapenem, and meropenem. NDM gene alignments revealed that the resistance was
AB  - plasmid encoded.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Cunningham, G.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.
JO  - Genome Announcements
PY  - 2015
SP  - e00930
EP  - e00915
VL  - 3
AB  - We report here the draft genome sequence of Mycobacterium heckeshornense strain RLE isolated
AB  - from a sputum sample from a patient with shortness of breath. This is the first draft genome
AB  - sequence of M. heckeshornense.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Cunningham, G.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - Draft Genome Sequence of Mycobacterium heraklionense Strain Davo.
JO  - Genome Announcements
PY  - 2015
SP  - e00807
EP  - e00815
VL  - 3
AB  - We report the draft genome sequence of Mycobacterium heraklionense strain Davo, isolated from
AB  - a fine-needle aspirate of a right-ankle soft-tissue mass. This is
AB  - the first draft genome sequence of Mycobacterium heraklionense, a nonpigmented
AB  - rapidly growing mycobacterium.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Cunningham, G.
AU  - Hsu, E.D.
AU  - Yu, J.M.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient  Sputum.
JO  - Genome Announcements
PY  - 2015
SP  - e00612
EP  - e00615
VL  - 3
AB  - We report the draft genome sequence of Mycobacterium obuense strain UC1 from a patient sputum
AB  - sample. This is the first draft genome sequence of Mycobacterium
AB  - obuense, a rapidly growing scotochromogenic mycobacterium.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Cunningham, G.
AU  - Yu, J.M.
AU  - Hsu, E.D.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.
JO  - Genome Announcements
PY  - 2015
SP  - e00691
EP  - e00615
VL  - 3
AB  - We report the draft genome sequence of Mycobacterium elephantis strain Lipa from  a sputum
AB  - sample of a patient with pulmonary disease. This is the first draft
AB  - genome sequence of M. elephantis, a rapidly growing mycobacterium.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Cunningham, G.
AU  - Yu, J.M.
AU  - Hsu, E.D.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - Draft Genome Sequence of Mycobacterium arupense Strain GUC1.
JO  - Genome Announcements
PY  - 2015
SP  - e00630
EP  - e00615
VL  - 3
AB  - We report the draft genome sequence of Mycobacterium arupense strain GUC1 from a  sputum
AB  - sample of a patient with bronchiectasis. This is the first draft genome
AB  - sequence of Mycobacterium arupense, a rapidly growing nonchromogenic
AB  - mycobacteria.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Kozyreva, V.
AU  - Truong, C.L.
AU  - Graves, M.
AU  - Chaturvedi, V.
TI  - Draft Genome Sequence of Turicella otitidis TD1, Isolated from a Patient with Bacteremia.
JO  - Genome Announcements
PY  - 2015
SP  - e01060
EP  - e01015
VL  - 3
AB  - We report the draft genome sequence of Turicella otitidis strain TD1, isolated from a central
AB  - line catheter sample from a patient with a history of bowel obstruction. It contained several
AB  - genetic determinants of multidrug-resistant phenotypes such as a cfrA 50S methyltransferase,
AB  - two major facilitator superfamily-type drug resistance transporters, and a putative
AB  - beta-lactamase.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Kozyreva, V.
AU  - Truong, C.L.
AU  - Longoria, R.
AU  - Chaturvedi, V.
TI  - Draft Genome Sequence of Kerstersia gyiorum CG1, Isolated from a Leg Ulcer.
JO  - Genome Announcements
PY  - 2015
SP  - e01036
EP  - e01015
VL  - 3
AB  - We report the first draft genome sequence of Kerstersia gyiorum from a leg ulcer  of a patient
AB  - with diabetes and osteomyelitis. The 3.94-Mb genome assembly included 3,428 annotated coding
AB  - sequences with an N50 of 223,310 bp and a plasmid encoding a type IV secretion system gene and
AB  - two antitoxin genes.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Streithorst, J.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.
JO  - Genome Announcements
PY  - 2016
SP  - e01277
EP  - e01216
VL  - 4
AB  - We report the first draft genome sequences of two isolates previously classified  as CDC EF-4b
AB  - species, Neisseria sp. 83E34 and Neisseria sp. 74A18. Both strains
AB  - were isolated from patients with animal bites and likely constitute novel
AB  - genomospecies with average nucleotide identities of <95% to other sequenced
AB  - strains.
ER  -

TY  - JOUR
AU  - Greninger, A.L.
AU  - Streithorst, J.
AU  - Chiu, C.Y.
AU  - Miller, S.
TI  - First Complete Genome Sequence of Corynebacterium riegelii.
JO  - Genome Announcements
PY  - 2017
SP  - e00084
EP  - e00017
VL  - 5
AB  - Here, we report the first complete genome sequence of Corynebacterium riegelii strain
AB  - PUDD_83A45, isolated from the urine of a patient with urinary tract
AB  - infection. The genome measured 2.56 Mb and contained no plasmid.
ER  -

TY  - JOUR
AU  - Grepinet, O.
AU  - Boumart, Z.
AU  - Virlogeux-Payant, I.
AU  - Loux, V.
AU  - Chiapello, H.
AU  - Gendrault, A.
AU  - Gibrat, J.F.
AU  - Chemaly, M.
AU  - Velge, P.
TI  - Genome Sequence of the Persistent Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2385
EP  - 2386
VL  - 194
AB  - Salmonella enterica subsp. enterica serotype Senftenberg is an emerging serotype  in poultry
AB  - production which has been found to persist in animals and the farm
AB  - environment. We report the genome sequence and annotation of the SS209 strain of
AB  - S. Senftenberg, isolated from a hatchery, which was identified as persistent in
AB  - broiler chickens.
ER  -

TY  - JOUR
AU  - Grepinet, O.
AU  - Rossignol, A.
AU  - Loux, V.
AU  - Chiapello, H.
AU  - Gendrault, A.
AU  - Gibrat, J.F.
AU  - Velge, P.
AU  - Virlogeux-Payant, I.
TI  - Genome Sequence of the Invasive Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2387
EP  - 2388
VL  - 194
AB  - Salmonella enterica subsp. enterica serotype Enteritidis is one of the major causes of
AB  - gastroenteritis in humans due to consumption of poultry derivatives.
AB  - Here we report the whole-genome sequence and annotation, including the virulence
AB  - plasmid, of S. Enteritidis LA5, which is a chicken isolate used by numerous
AB  - laboratories in virulence studies.
ER  -

TY  - JOUR
AU  - Gressmann, H.
AU  - Linz, B.
AU  - Ghai, R.
AU  - Pleissner, K.P.
AU  - Schlapbach, R.
AU  - Yamaoka, Y.
AU  - Kraft, C.
AU  - Suerbaum, S.
AU  - Meyer, T.F.
AU  - Achtman, M.
TI  - Gain and loss of multiple genes during the evolution of Helicobacter pylori.
JO  - PLoS Genet.
PY  - 2005
SP  - e43
EP  - e43
VL  - 1
AB  - Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even
AB  - greater sequence differences differentiate distinct populations of H. pylori from different
AB  - continents, but it was not clear whether these populations also differ in gene content. To
AB  - address this question, we tested 56 globally representative strains of H. pylori and four
AB  - strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of
AB  - 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H.
AB  - pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome
AB  - present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and
AB  - possess unusual GC content; many of them have probably been imported by horizontal gene
AB  - transfer. Phylogenetic trees based on the microarray data differ from those based on sequences
AB  - of seven genes from the core genome. These discrepancies are due to homoplasies resulting from
AB  - independent gene loss by deletion or recombination in multiple strains, which distort
AB  - phylogenetic patterns. The patterns of these discrepancies versus population structure allow a
AB  - reconstruction of the timing of the acquisition of variable genes within this species.
AB  - Variable genes that are located within the cag pathogenicity island were apparently first
AB  - acquired en bloc after speciation. In contrast, most other variable genes are of unknown
AB  - function or encode restriction/modification enzymes, transposases, or outer membrane proteins.
AB  - These seem to have been acquired prior to speciation of H. pylori and were subsequently lost
AB  - by convergent evolution within individual strains. Thus, the use of microarrays can reveal
AB  - patterns of gene gain or loss when examined within a phylogenetic context that is based on
AB  - sequences of core genes.
ER  -

TY  - JOUR
AU  - Greub, G.
AU  - Kebbi-Beghdadi, C.
AU  - Bertelli, C.
AU  - Collyn, F.
AU  - Riederer, B.M.
AU  - Yersin, C.
AU  - Croxatto, A.
AU  - Raoult, D.
TI  - High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.
JO  - PLoS ONE
PY  - 2009
SP  - E8423
EP  - E8423
VL  - 4
AB  - BACKGROUND: With the availability of new generation sequencing
AB  - technologies, bacterial genome projects have undergone a major boost.
AB  - Still, chromosome completion needs a costly and time-consuming gap
AB  - closure, especially when containing highly repetitive elements. However,
AB  - incomplete genome data may be sufficiently informative to derive the
AB  - pursued information. For emerging pathogens, i.e. newly identified
AB  - pathogens, lack of release of genome data during gap closure stage is
AB  - clearly medically counterproductive. METHODS/PRINCIPAL FINDINGS: We thus
AB  - investigated the feasibility of a dirty genome approach, i.e. the release
AB  - of unfinished genome sequences to develop serological diagnostic tools. We
AB  - showed that almost the whole genome sequence of the emerging pathogen
AB  - Parachlamydia acanthamoebae was retrieved even with relatively short reads
AB  - from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed
AB  - to select immunogenic proteins, which were then expressed and used to
AB  - elaborate the first steps of an ELISA. CONCLUSIONS/SIGNIFICANCE: This work
AB  - constitutes the proof of principle for a dirty genome approach, i.e. the
AB  - use of unfinished genome sequences of pathogenic bacteria, coupled with
AB  - proteomics to rapidly identify new immunogenic proteins useful to develop
AB  - in the future specific diagnostic tests such as ELISA,
AB  - immunohistochemistry and direct antigen detection. Although applied here
AB  - to an emerging pathogen, this combined dirty genome sequencing/proteomic
AB  - approach may be used for any pathogen for which better diagnostics are
AB  - needed. These genome sequences may also be very useful to develop DNA
AB  - based diagnostic tests. All these diagnostic tools will allow further
AB  - evaluations of the pathogenic potential of this obligate intracellular
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Grewal, S.
AU  - Vakhlu, J.
AU  - Gupta, V.
AU  - Sangwan, N.
AU  - Kohli, P.
AU  - Nayyar, N.
AU  - Rani, P.
AU  - Sance, S.S.
AU  - Lal, R.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain JMM, a Sediment-Hosted Environmental Isolate.
JO  - Genome Announcements
PY  - 2014
SP  - e00879
EP  - e00814
VL  - 2
AB  - Pseudomonas sp. strain JMM was isolated from the sediments of a natural water reservoir (pH, 6
AB  - to 7) located at Chambyal village in Samba district of Jammu and
AB  - Kashmir, India. Here we report the annotated draft genome sequence of strain JMM
AB  - having 52 contigs with 5,884 genes and an average G+C content of 66.5%.
ER  -

TY  - JOUR
AU  - Griffin, S.
AU  - Branch, P.
AU  - Xu, Y.-Z.
AU  - Karran, P.
TI  - DNA mismatch binding and incision at modified guanine bases by extracts of mammalian cells: implications for tolerance to DNA methylation damage.
JO  - Biochemistry
PY  - 1994
SP  - 4787
EP  - 4793
VL  - 33
AB  - Two activities involved in separate pathways for correcting G.T mispairs in DNA have been
AB  - assayed on duplex substrates containing modified guanine bases. The first, the G.T mismatch
AB  - incision activity, is specifically involved in short-patch repair of mispairs arising via
AB  - deamination of 5-methylcytosine. The second activity can be detected by its ability to bind to
AB  - G.T mispairs and may initiate correction by a long-patch mechanism. 6-Thioguanine and
AB  - 06-methylguanine paired with thymine were efficiently incised by cell extracts if the modified
AB  - guanine was in a CpG dinucleotide. Incision was not observed when either purine was paired
AB  - with cytosine. Extracts of cells that are tolerant both to methylation damage and to
AB  - 6-thioguanine in DNA also incised 6-thioguanine.T and O6-methylguanine.T base pairs. The data
AB  - suggest that this activity is unlikely to contribute significantly to the biological effects
AB  - of 06-methylguanine in DNA. A defect in this pathway is therefore unlikely to explain the
AB  - cross-resistance of tolerant cells to the two base analogs in DNA. In binding assays,
AB  - 6-thioguanine-T base pairs were recognized efficiently and to an equivalent extent by the same
AB  - protein complex as G.T mispairs. O6-methylguanine.T base pairs were also recognized but with
AB  - reduced efficiency. No binding was observed to 6-thioguanine.C or O6-methylguanine.C base
AB  - pairs. Recognition by the binding complex was essentially independent of the base immediately
AB  - 5' to the mismatched guanine but was somewhat more efficient if O6-methylguanine was preceded
AB  - by a purine. Extracts of two tolerant lines with a known defect in G.T mismatch binding failed
AB  - to form complexes with substrates containing the modified bases. The ability of the G.T
AB  - binding factor to recognize both O6-methylguanine.T and 6-thioguanine.T pairs indicates that
AB  - the long-patch repair pathway is more likely to be involved in mediating the cytotoxicity of
AB  - the two-base analogs.
ER  -

TY  - JOUR
AU  - Grigaite, R.
AU  - Maneliene, Z.
AU  - Janulaitis, A.
TI  - AarI, a restriction endonuclease from Arthrobacter aurescens SS2-322, which recognizes the novel non-palindromic sequence 5'-CACCTGC(N)4/8-3'.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - e123
EP  - e123
VL  - 30
AB  - A new type II restriction endonuclease AarI has been isolated from Arthrobacter aurescens
AB  - SS2-322. AarI recognizes the non-palindromic heptanucleotide sequence 5'-CACCTGC(N)(4/8)-3'
AB  - and makes a staggered cut at the fourth and eighth bases downstream of the target duplex
AB  - producing a four base 5'-protruding end. AarI activity is stimulated by
AB  - oligodeoxyribonucleotide duplexes containing an enzyme-specific recognition sequence.
ER  -

TY  - JOUR
AU  - Grigorescu, A.
AU  - Horvath, M.
AU  - Wilkosz, P.A.
AU  - Chandrasekhar, K.
AU  - Rosenberg, J.M.
TI  - The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 137
EP  - 177
VL  - 14
AB  - DNA has been selected as the biological information storage molecule for many reasons; one of
AB  - which is its stability.  The rate of spontaneous hydrolysis of DNA (at 24oC and pH 7.4) was
AB  - estimated at 5.7x10-14S-1; more recently, Radzicka and Wolfenden have estimated this value at
AB  - 1.7x10-13 s-1.  This corresponds to an estimated half-life of 130,000 years for a DNA
AB  - phosphodiester bond in solution, placing DNA hydrolysis among the slowest of biochemical
AB  - reactions in the absence of enzymes.
ER  -

TY  - JOUR
AU  - Grigorescu, A.A.
AU  - Rosenberg, J.M.
TI  - A local folding transition coupled to site-specific binding in EcoRI restriction endonuclease.
JO  - Biophys. J.
PY  - 2004
SP  - 591a
EP  - 591a
VL  - 86
AB  - Restriction endonuclease EcoRI is not only an invaluable tool in genetic engineering but also
AB  - a paradigm for understanding the molecular
AB  - mechanisms of protein-DNA recognition. Recent crystallographic data
AB  - demonstrate that a major localized folding transition accompanies
AB  - binding of the EcoRI restriction endonuclease to its cognate DNA site;
AB  - this result is in accordance with previous biophysical studies which
AB  - indicated a large conformational change taking place in the protein
AB  - upon site-specific binding. The three-dimensional structure of the apo
AB  - EcoRI enzyme reveals an unusual molecular architecture: a rigid
AB  - scaffold with a small minidomain on top of it. In the absence of
AB  - stabilizing inter-molecular contacts the minidomain does not adopt a
AB  - well-ordered conformation. A structural analysis indicates that the
AB  - metastability of this region of the protein is dictated by a
AB  - combination of favorable and unfavorable tertiary interactions. The
AB  - conformation of the minidomain observed in the specific protein-DNA
AB  - complex is apparently stabilized by a set of favorable inter-molecular
AB  - contacts. Many of these are highly specific contacts (recognition
AB  - interactions) between the protein and the DNA substrate. All the amino
AB  - acid substitutions that have been shown to alter (i.e. reduce) the DNA
AB  - sequence specificity of the enzyme are localized in regions that
AB  - exhibit low structural stability in the unbound protein. This, and
AB  - other lines of evidence suggest that local native metastability is
AB  - important for the molecular recognition function of the EcoRI
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Grigoryeva, T.V.
AU  - Laikov, A.V.
AU  - Naumova, R.P.
AU  - Manolov, A.I.
AU  - Larin, A.K.
AU  - Karpova, I.Y.
AU  - Semashko, T.A.
AU  - Alexeev, D.G.
AU  - Kostryukova, E.S.
AU  - Muller, R.
AU  - Govorun, V.M.
TI  - Draft Genome of the Nitrogen-Fixing Bacterium Pseudomonas stutzeri Strain KOS6 Isolated from Industrial Hydrocarbon Sludge.
JO  - Genome Announcements
PY  - 2013
SP  - e00072
EP  - e00012
VL  - 1
AB  - Here we present a draft genome of Pseudomonas stutzeri strain KOS6. This strain was isolated
AB  - from industrial hydrocarbon sludge as a diazotrophic microorganism.
AB  - It represents one of the major parts of the culturable community of the waste and
AB  - has potential importance for phytoremediation technology.
ER  -

TY  - JOUR
AU  - Grim, C.J.
AU  - Gopinath, G.R.
AU  - Jarvis, K.G.
AU  - Sathyamoorthy, V.
AU  - Trach, L.H.
AU  - Chase, H.R.
AU  - Tall, B.D.
TI  - Genome Sequence of Cronobacter sakazakii Serogroup O:4, Sequence Type 4 Strain CDC 2009-03746, Isolated from a Fatal Case of Infantile Meningitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00492
EP  - e00415
VL  - 3
AB  - We report the draft genome sequence of a Cronobacter sakazakii serogroup O:4, sequence type 4
AB  - strain, CDC 2009-03746 (=NM1240=2009-06-01), isolated from a
AB  - fatal case of infantile meningitis. The draft genome has a size of 4,492,904 bp
AB  - and a G+C% content of 56.7.
ER  -

TY  - JOUR
AU  - Grim, C.J.
AU  - Gopinath, G.R.
AU  - Mammel, M.K.
AU  - Sathyamoorthy, V.
AU  - Trach, L.H.
AU  - Chase, H.R.
AU  - Tall, B.D.
AU  - Fanning, S.
AU  - Stephan, R.
TI  - Genome Sequence of an Enterobacter helveticus Strain, 1159/04 (LMG 23733), Isolated from Fruit Powder.
JO  - Genome Announcements
PY  - 2013
SP  - e01038
EP  - e01013
VL  - 1
AB  - We report the draft genome sequence of Enterobacter helveticus strain LMG 23733,  isolated
AB  - from fruit powder. The draft genome assembly for E. helveticus strain
AB  - LMG 23733 has a size of 4,635,476 bp and a G+C content of 55.9%.
ER  -

TY  - JOUR
AU  - Grim, C.J.
AU  - Hasan, N.A.
AU  - Taviani, E.
AU  - Haley, B.
AU  - Chun, J.
AU  - Brettin, T.S.
AU  - Bruce, D.C.
AU  - Detter, J.C.
AU  - Han, C.S.
AU  - Chertkov, O.
AU  - Challacombe, J.
AU  - Huq, A.
AU  - Nair, G.B.
AU  - Colwell, R.R.
TI  - Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3524
EP  - 3533
VL  - 192
AB  - The genomes of Vibrio cholerae O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33,
AB  - and altered O1 El Tor CIRS101 were sequenced. All three
AB  - strains were found to belong to the phylocore group 1 clade of V.
AB  - cholerae, which includes the 7th-pandemic O1 El Tor and serogroup O139
AB  - isolates, despite displaying certain characteristics of the classical
AB  - biotype. All three strains were found to harbor a hybrid variant of CTXPhi
AB  - and an integrative conjugative element (ICE), leading to their
AB  - establishment as successful clinical clones and the displacement of
AB  - prototypical O1 El Tor. The absence of strain- and group-specific genomic
AB  - islands, some of which appear to be prophages and phage-like elements,
AB  - seems to be the most likely factor in the recent establishment of
AB  - dominance of V. cholerae CIRS101 over the other two hybrid strains.
ER  -

TY  - JOUR
AU  - Grim, C.J.
AU  - Schreier, H.J.
TI  - Draft Genome Sequence of Vibrio (Listonella) anguillarum ATCC 14181.
JO  - Genome Announcements
PY  - 2016
SP  - e01185
EP  - e01116
VL  - 4
AB  - We report the draft genome sequence of Vibrio anguillarum ATCC 14181, a Gram-negative,
AB  - hemolytic, O2 serotype marine bacterium that causes mortality in
AB  - mariculture species. The availability of this genome sequence will add to our
AB  - knowledge of diversity and virulence mechanisms of Vibrio anguillarum as well as
AB  - other pathogenic Vibrio spp.
ER  -

TY  - JOUR
AU  - Grimaud, R.
AU  - Ghiglione, J.F.
AU  - Cagnon, C.
AU  - Lauga, B.
AU  - Vaysse, P.J.
AU  - Rodriguez-Blanco, A.
AU  - Mangenot, S.
AU  - Cruveiller, S.
AU  - Barbe, V.
AU  - Duran, R.
AU  - Wu, L.F.
AU  - Talla, E.
AU  - Bonin, P.
AU  - Michotey, V.
TI  - Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17,  Which Forms Biofilms on Hydrophobic Organic Compounds.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3539
EP  - 3540
VL  - 194
AB  - Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between
AB  - water and hydrophobic organic compounds (HOCs) that are used as
AB  - carbon and energy sources. Biofilm formation at the HOC-water interface has been
AB  - recognized as a strategy to overcome the low availability of these nearly
AB  - water-insoluble substrates. Here, we present the genome sequence of SP17, which
AB  - could provide further insights into the mechanisms of enhancement of HOCs
AB  - assimilation through biofilm formation.
ER  -

TY  - JOUR
AU  - Grime, S.K.
AU  - Martin, R.L.
AU  - Holaway, B.L.
TI  - Inhibition of restriction enzyme cleavage of DNA modified with 7-deaza-dGTP.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2791
EP  - 2791
VL  - 19
AB  - DNA templates containing G+C rich regions or stable secondary structures can
AB  - potentially pose problems for PCR amplification.  Incorporation of the
AB  - structure destabilizing analogue, 7-deaza-dGTP into the PCR reaction allows
AB  - successful amplification of such template sequences.  It has been reported that
AB  - when 7-deaza-dGTP is substituted for dGTP in a DNA-fragment, the cleavage rate
AB  - by the restriction enzyme EcoRI is reduced.  We find that EcoRI as well as
AB  - other commonly used restriction enzymes will not cut DNA containing
AB  - 7-deaza-dGTP when it is incorporated into PCR product.  Substrates for the
AB  - restriction enzymes were amplified by PCR using pUC19 and bacteriophage lambda
AB  - sequences.  Each 100 microliter reaction contained 200 microM each of dATP,
AB  - dCTP, dTTP, dGTP or 7-deaza-dGTP, 1 microM of each primer, 2.5 units Taq DNA
AB  - Polymerase, 1 ng DNA template, 50 mM KCl, 10 mM Tris-HCl, pH 8.3 @ 37C, 1.5 mM
AB  - MgCl2, 0.01% gelatin.  Five hundred nanograms of the PCR product from reactions
AB  - containing either 7-deaza-dGTP or dGTP were incubated with commonly-used
AB  - restriction enzymes.  Restriction digests were resolved on 1.2% agarose gels
AB  - with ethidium bromide staining.  Table 1 summarizes the results of the
AB  - restriction digests where 7-deaza-dGTP was substituted for dGTP in the PCR
AB  - reaction.  For most enzymes tested, inclusion of 7-deaza-dGTP in the PCR
AB  - product prevented the restriction enzyme from cutting the DNA.  It is not yet
AB  - clear to us how this inhibition occurs.  We assume that the presence of the
AB  - deaza residue in the recognition sequence affects proper binding and/or cutting
AB  - of the DNA substrate.  As yet the details of the spatial interaction between
AB  - the modified G residue and various restriction enzyme active/binding sites is
AB  - unclear.  Inhibition of cutting can occur when the G residues are 5 prime (eg.
AB  - EcoRI), 3 prime (eg. PstI), immediately adjacent (eg. SalI), or two bases away
AB  - from the cut site (eg. AccI).  Three enzymes (XbaI, HindIII, MaeII) are not
AB  - inhibited by the presence of modified G residues in their recognition sequence.
AB  - We have no knowledge of how modified G residues may inhibit cutting from a
AB  - complementary strand of DNA.  7-deaza-dGTP could be beneficial for applications
AB  - such as cDNA cloning where multiple internal restriction sites are protected
AB  - during linker digestion. This would be similar to the strategy of methylating
AB  - cDNA prior to digestion with methyl-sensitive restriction enzymes.  Use of
AB  - 7-deaza-dGTP to this end may allow the use of a greater number of enzymes.
ER  -

TY  - JOUR
AU  - Grimes, E.
AU  - Koob, M.
AU  - Szybalski, W.
TI  - Achilles' heel cleavage: creation of rare restriction sites in lambda phage genomes and evaluation of additional operators, repressors and restriction/modification systems .
JO  - Gene
PY  - 1990
SP  - 1
EP  - 7
VL  - 90
AB  - A novel technique for the creation of rare restriction sites was described by Koob et al.
AB  - [Science 241 (1988) 1084-1086]. This technique, Achilles' heel cleavage (AC), relies on the
AB  - use of a bound repressor molecule to protect only one of many identical restriction sites from
AB  - a modification methyltransferase that inactivates all other restriction sites. The technique
AB  - was applied to a small plasmid and shown to work efficiently with two repressor/operator
AB  - systems: lac repressor/lacO operator and lambda repressor/lambda OL1 operator. Here, we have
AB  - extended these results to a lac operator carried by a much larger vector, namely a 44-kb phage
AB  - lambda construct. In addition, we have evaluated the effect of altering the stability of the
AB  - lac repressor/lac operator complex by varying both the operator and the repressor. We have
AB  - also evaluated several more restriction/modification systems (MboI, Dam, MspI and AluI) in
AB  - addition to HhaI and HaeII used earlier. Finally, we extended the AC technique to a third
AB  - system, that of the phage 434 repressor and a synthetic 434 operator. From our results we
AB  - conclude that the ACT method should be applicable to the mapping of large genomes and to
AB  - measuring the strength of operator-repressor interactions. AC could also be applied to
AB  - identifying and evaluating many different DNA-binding proteins and their sites of action.
ER  -

TY  - JOUR
AU  - Grimm, I.
AU  - Dumke, J.
AU  - Vollmer, T.
AU  - Hinse, D.
AU  - Ruckert, C.
AU  - Kalinowski, J.
AU  - Knabbe, C.
AU  - Dreier, J.
TI  - Complete Genome Sequence of the Streptococcus gallolyticus subsp. gallolyticus Strain DSM 16831.
JO  - Genome Announcements
PY  - 2017
SP  - e00108
EP  - e00117
VL  - 5
AB  - Streptococcus gallolyticus subsp. gallolyticus DSM 16831 is an intriguing strain  because of
AB  - its low virulent phenotype compared to other isolates. We present here
AB  - the complete genome sequence for this strain isolated from koala feces.
ER  -

TY  - JOUR
AU  - Grindl, W.
AU  - Wende, W.
AU  - Pingoud, V.
AU  - Pingoud, A.
TI  - The protein splicing domain of the homing endonuclease PI-SceI is responsible for specific DNA binding.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1857
EP  - 1862
VL  - 26
AB  - The homing endonuclease PI-SceI consists of a protein splicing domain (I) and an
AB  - endonucleolytic domain (II).  To characterize the two domains with respect to their
AB  - contribution to DNA recognition we cloned, purified and characterized the isolated domains.
AB  - Both domains have no detectable endonucleolytic activity.  Domain I binds specifically to the
AB  - PI-SceI recognition sequence, whereas domain II displays only weak non-specific DNA binding.
AB  - In the specific complex with domain I the DNA is bent to a similar extent as observed with the
AB  - initial complex formed between PI-SceI and DNA.  Our results indicate that protein splicing
AB  - domain I is also involved in recognition of the DNA substrate.
ER  -

TY  - JOUR
AU  - Grinkevich, P.
AU  - Sinha, D.
AU  - Iermak, I.
AU  - Guzanova, A.
AU  - Weiserova, M.
AU  - Ludwig, J.
AU  - Mesters, J.R.
AU  - Ettrich, R.H.
TI  - Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.
JO  - J. Biol. Chem.
PY  - 2018
SP  - 15043
EP  - 15054
VL  - 293
AB  - Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it
AB  - still presents many challenges to detailed analyses because of its
AB  - structural and functional complexity and missing structural information. In all
AB  - available structures of its motor subunit HsdR, responsible for DNA translocation
AB  - and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal
AB  - structure of the C terminus of HsdR, obtained with a crystallization chaperone in
AB  - the form of pHluorin fusion and refined to 2.45 A, revealed that this part of the
AB  - protein forms an independent domain with its own hydrophobic core and displays a
AB  - unique alpha-helical fold. The full-length HsdR model, based on the WT structure
AB  - and the C-terminal domain determined here, disclosed a proposed DNA-binding
AB  - groove lined by positively charged residues. In vivo and in vitro assays with a
AB  - C-terminal deletion mutant of HsdR supported the idea that this domain is
AB  - involved in complex assembly and DNA binding. Conserved residues identified
AB  - through sequence analysis of the C-terminal domain may play a key role in
AB  - protein-protein and protein-DNA interactions. We conclude that the motor subunit
AB  - of EcoR124 comprises five structural and functional domains, with the fifth, the
AB  - C-terminal domain, revealing a unique fold characterized by four conserved motifs
AB  - in the IC subfamily of Type I restriction-modification systems. In summary, the
AB  - structural and biochemical results reported here support a model in which the
AB  - C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is
AB  - involved in complex assembly and DNA binding.
ER  -

TY  - JOUR
AU  - Grishin, A.
AU  - Fonfara, I.
AU  - Alexeevski, A.
AU  - Spirin, S.
AU  - Zanegina, O.
AU  - Karyagina, A.
AU  - Alexeyevsky, D.
AU  - Wende, W.
TI  - IDENTIFICATION OF CONSERVED FEATURES OF LAGLIDADG HOMING ENDONUCLEASES.
JO  - J. Bioinform. Comput. Biol.
PY  - 2010
SP  - 453
EP  - 469
VL  - 8
AB  - LAGLIDADG family of homing endonucleases are rare-cutting enzymes which recognize long target
AB  - sequences and are of great interest in genome
AB  - engineering. Despite advances in homing endonuclease engineering,
AB  - effective methods of broadening the range of cleaved sequences are
AB  - still lacking. Here, we present a study of conserved structural
AB  - features of LAGLIDADG homing endonucleases that might aid further
AB  - development of such methods. The protein-DNA interface of LAGLIDADG
AB  - homing endonucleases differs considerably with the particular nuclease,
AB  - and the analysis of conserved protein-DNA interactions could not
AB  - identify any residues crucial for DNA binding and common to most
AB  - nucleases of the family. For the homing endonuclease PI-SceI, a
AB  - comparison of structural and experimental data derived from literature
AB  - helped to identify 23 residues that are likely to be important for DNA
AB  - binding. Analysis of the LAGLIDADG domain dimerization interface
AB  - allowed the choosing of six positions that contribute to dimerization
AB  - specificity most, while comparison of 446 sequences of LAGLIDADG
AB  - endonucleases revealed groups of residues in these positions that
AB  - appear to be most favorable for dimerization.
ER  -

TY  - JOUR
AU  - Gritsenko, O.M.
AU  - Koudan, E.V.
AU  - Mikhailov, S.N.
AU  - Ermolinsky, B.S.
AU  - VanAerschot, A.
AU  - Herdewijn, P.
AU  - Gromova, E.S.
TI  - Affinity modification of EcoRII DNA methyltransferase by the dialdehyde-substituted DNA duplexes: mapping the enzyme region that interacts with DNA.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2002
SP  - 753
EP  - 764
VL  - 21
AB  - Affinity modification of EcoRII DNA methyltransferase (M.EcoRII) by DNA duplexes containing
AB  - oxidized 2'-O-beta-D-ribofuranosylcytidine (Crib*) or 1-(beta-D-galactopyranosyl)thymine
AB  - (Tgal*) residues was performed. Cross-linking yields do not change irrespective of whether
AB  - active Crib* replaces an outer or an inner (target) deoxycytidine within the EcoRII
AB  - recognition site. Chemical hydrolysis of M.EcoRII in the covalent cross-linked complex with
AB  - the Tgal*-substituted DNA indicates the region Gly268-Met391 of the methylase that is likely
AB  - to interact with the DNA sugar-phosphate backbone. Both specific and non-specific DNA interact
AB  - with the same M.EcoRII region. Our results support the theoretically predicted DNA binding
AB  - region of M.EcoRII.
ER  -

TY  - JOUR
AU  - Gritsenko, O.M.
AU  - Mikhailov, S.N.
AU  - Efimtseva, E.V.
AU  - Van Aerschot, A.
AU  - Herdewijn, P.
AU  - Gromova, E.S.
TI  - Probing the MvaI methyltransferase region that interacts with DNA: Affinity labeling with the dialdehyde-containing DNA duplexes.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2000
SP  - 1805
EP  - 1820
VL  - 19
AB  - Affinity labeling of methyltransferase MvaI by DNA duplexes containing oxidized
AB  - 2'-O-beta-D-ribofuranosylcytidine or 1-(beta-D-galactopyranosyl)thymine residues was
AB  - performed. Partial chemical hydrolysis of the covalently bound methylase in the conjugates
AB  - with the dialdehyde-containing DNA allowed us to determine the amino acid region in the C
AB  - terminus of methylase MvaI that interacts with DNA.
ER  -

TY  - JOUR
AU  - Grivell, L.A.
TI  - Homing in on an endosymbiotic endonuclease.
JO  - Curr. Biol.
PY  - 1992
SP  - 450
EP  - 452
VL  - 2
AB  - The "spacer protein" generated by a type of protein splicing in yeast turns out to be an
AB  - endonuclease with the precise DNA-sequence specificity to promote the spread of its own coding
AB  - sequence.
ER  -

TY  - JOUR
AU  - Grivell, L.A.
TI  - Transposition: Mobile introns get into line.
JO  - Curr. Biol.
PY  - 1996
SP  - 48
EP  - 51
VL  - 6
AB  - Group II introns encode highly structured, frequently self-splicing RNAs; they are also mobile
AB  - genetic elements.  This mobility has been found to involve DNA-primed reverse transcription,
AB  - with similarities to retrotransposition and telomere maintenance.
ER  -

TY  - JOUR
AU  - Grizot, S.
AU  - Duclert, A.
AU  - Thomas, S.
AU  - Duchateau, P.
AU  - Paques, F.
TI  - Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 6124
EP  - 6136
VL  - 39
AB  - Homing endonucleases (HE) have emerged as precise tools for achieving gene targeting events.
AB  - Redesigned HEs with tailored specificities can be used to cleave new sequences, thereby
AB  - considerably expanding the number of targetable genes and loci. With HEs, as well as with
AB  - other protein scaffolds, context dependence of DNA/protein interaction patterns remains one of
AB  - the major limitations for rational engineering of new DNA binders. Previous studies have shown
AB  - strong crosstalk between different residues and regions of the DNA binding interface. To
AB  - investigate this phenomenon, we systematically combined mutations from three groups of amino
AB  - acids in the DNA binding regions of the I-CreI HE. Our results confirm that important
AB  - crosstalk occurs throughout this interface in I-CreI. Detailed analysis of success rates
AB  - identified a nearest-neighbour effect, with a more pronounced level of dependence between
AB  - adjacent regions. Taken together, these data suggest that combinatorial engineering does not
AB  - necessarily require the identification of separable functional or structural regions, and that
AB  - groups of amino acids provide acceptable building blocks that can be assembled, overcoming the
AB  - context dependency of the DNA binding interface. Furthermore, the present work describes a
AB  - sequential method to engineer tailored HEs, wherein three contiguous regions are individually
AB  - mutated and assembled to create HEs with engineered specificity.
ER  -

TY  - JOUR
AU  - Grizot, S.
AU  - Epinat, J.C.
AU  - Thomas, S.
AU  - Duclert, A.
AU  - Rolland, S.
AU  - Paques, F.
AU  - Duchateau, P.
TI  - Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 2006
EP  - 2018
VL  - 38
AB  - Homing endonucleases have become valuable tools for genome engineering. Their sequence
AB  - recognition repertoires can be expanded by modifying their
AB  - specificities or by creating chimeric proteins through domain swapping
AB  - between two subdomains of different homing endonucleases. Here, we show
AB  - that these two approaches can be combined to create engineered
AB  - meganucleases with new specificities. We demonstrate the modularity of the
AB  - chimeric DmoCre meganuclease previously described, by successfully
AB  - assembling mutants with locally altered specificities affecting both
AB  - I-DmoI and I-CreI subdomains in order to create active meganucleases with
AB  - altered specificities. Moreover these new engineered DmoCre variants
AB  - appear highly specific and present a low toxicity level, similar to
AB  - I-SceI, and can induce efficient homologous recombination events in
AB  - mammalian cells. The DmoCre based meganucleases can therefore offer new
AB  - possibilities for various genome engineering applications.
ER  -

TY  - JOUR
AU  - Grizot, S.
AU  - Smith, J.
AU  - Daboussi, F.
AU  - Prieto, J.
AU  - Redondo, P.
AU  - Merino, N.
AU  - Villate, M.
AU  - Thomas, S.
AU  - Lemaire, L.
AU  - Montoya, G.
AU  - Blanco, F.J.
AU  - Paques, F.
AU  - Duchateau, P.
TI  - Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5405
EP  - 5419
VL  - 37
AB  - Sequence-specific endonucleases recognizing long target sequences are emerging as powerful
AB  - tools for genome engineering. These endonucleases
AB  - could be used to correct deleterious mutations or to inactivate viruses,
AB  - in a new approach to molecular medicine. However, such applications are
AB  - highly demanding in terms of safety. Mutations in the human RAG1 gene
AB  - cause severe combined immunodeficiency (SCID). Using the I-CreI dimeric
AB  - LAGLIDADG meganuclease as a scaffold, we describe here the engineering of
AB  - a series of endonucleases cleaving the human RAG1 gene, including obligate
AB  - heterodimers and single-chain molecules. We show that a novel single-chain
AB  - design, in which two different monomers are linked to form a single
AB  - molecule, can induce high levels of recombination while safeguarding more
AB  - effectively against potential genotoxicity. We provide here the first
AB  - demonstration that an engineered meganuclease can induce targeted
AB  - recombination at an endogenous locus in up to 6% of transfected human
AB  - cells. These properties rank this new generation of endonucleases among
AB  - the best molecular scissors available for genome surgery strategies,
AB  - potentially avoiding the deleterious effects of previous gene therapy
AB  - approaches.
ER  -

TY  - JOUR
AU  - Grogan, D.W.
TI  - Cytosine methylation by the SuaI restriction-modification system: implications for genetic fidelity in a hyperthermophilic archaeon.
JO  - J. Bacteriol.
PY  - 2003
SP  - 4657
EP  - 4661
VL  - 185
AB  - 5-methylcytosine in chromosomal DNA represents a potential source of frequent spontaneous
AB  - mutation for hyperthermophiles. To determine the
AB  - relevance of this threat for the archaeon Sulfolobus acidocaldarius, the
AB  - mode of GGCC methylation by its restriction-modification system, SuaI, was
AB  - investigated. Distinct isoschizomers of the SuaI endonuclease were used to
AB  - probe the methylation state of GGCC in native S. acidocaldarius DNA. In
AB  - addition, the methylation sensitivity of the SuaI endonuclease was
AB  - determined with synthetic oligonucleotide substrates and modified natural
AB  - DNAs. The results show that the SuaI system uses N(4) methylation to block
AB  - cleavage of its recognition site, thereby avoiding the creation of G. T
AB  - mismatches by spontaneous deamination at extremely high temperature.
ER  -

TY  - JOUR
AU  - Groll, D.H.
AU  - Jeltsch, A.
AU  - Selent, U.
AU  - Pingoud, A.
TI  - Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage?
JO  - Biochemistry
PY  - 1997
SP  - 11389
EP  - 11401
VL  - 36
AB  - Two models for the catalytic mechanism of the restriction endonuclease EcoRV exist which
AB  - differ in the number and function of metal ions proposed to be directly involved in catalysis.
AB  - In one model, two metal ions bound by Glu45, Asp74, and Asp90 are assumed to have a direct
AB  - catalytic function; in the other, only one metal ion bound by Asp74 and Asp90.  We show here
AB  - that in the presence of Mn2+, the catalytic activity of an EcoRV-E45A mutant is only slightly
AB  - reduced (1.8-fold) as compared to wild type EcoRV and that the single-turnover rate constant
AB  - of DNA cleavage by E45A is reduced only 39-fold, whereas the D74A and D90A mutants are
AB  - catalytically inactive under all conditions.  These findings make an important catalytic
AB  - function of Glu45, like binding of an essential divalent metal ion, unlikely.  In addition, we
AB  - have analyzed the dependence of the DNA cleavage rate by EcoRV and EcoRV mutants on the
AB  - concentration of Mg2+ and Mn2+.  We found for the wild type enzyme a sigmoidal dependence of
AB  - the rate of DNA cleavage on the concentration of Mg2+ or Mn2+, indicative of at least two
AB  - metal ions involved in DNA binding and catalysis.  This, however, does not mean that EcoRV
AB  - follows a two-metal-ion mechanism in DNA cleavage, because also for the E45A mutant a
AB  - sigmoidal dependence of the rate of DNA cleavage on the Mg2+ concentration was found, making
AB  - metal ion binding to the E45/D74 site unlikely.  In contrast, the Y219C mutant shows a
AB  - hyperbolic dependence.  In agreement with results obtained earlier, these findings demonstrate
AB  - binding of a Mg2+ ion at a site influenced by Tyr219, an amino acid residue that is far away
AB  - from the active site.  Metal binding at this site does not have a catalytic role but rather
AB  - supports specific DNA binding.  We conclude that on the basis of our data a two-metal-ion
AB  - mechanism of DNA cleavage is unlikely for EcoRV and that the complex metal ion effects
AB  - observed are due to metal ion binding at sites that are not directly involved in catalysis.
ER  -

TY  - JOUR
AU  - Gromek, S.M.
AU  - Sung, A.A.
AU  - Klassen, J.L.
AU  - Balunas, M.J.
TI  - Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.
JO  - Genome Announcements
PY  - 2016
SP  - e00856
EP  - e00816
VL  - 4
AB  - Streptomyces sp. PTY087I2 is a marine bacterium isolated from Styela canopus, a tunicate
AB  - collected in Bocas del Toro, Panama. Here, we report a draft genome
AB  - sequence for this bacterium, found to have 94.7% average nucleotide identity
AB  - (ANI) with Streptomyces roseosporus NRRL 11379, and containing a diverse suite of
AB  - secondary metabolite gene clusters.
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - Bendler, J.
AU  - Goodgal, S.
TI  - Restriction and modification of bacteriophage S2 in Haemophilus influenzae.
JO  - J. Bacteriol.
PY  - 1973
SP  - 1151
EP  - 1157
VL  - 114
AB  - The major conclusion from these studies is that variants of Haemophilus
AB  - influenzae Rd which restrict and modify phage S2 are metastable and capable of
AB  - giving rise to one another with high frequency.  Nonrestrictive RdS cells
AB  - segregate spontaneously to the restricting, modifying phenotype in about 5% of
AB  - the progeny of a single clone.  The restriction cells derived from RdS revert
AB  - to the nonrestrictive phenotype in 15 to 25% of the progeny of a single clone.
AB  - These frequencies are not appreciably affected by treatment with acriflavine or
AB  - ethidium bromide, compounds which affect plasmid stability, or by
AB  - nitrosoguanidine, a powerful mutagen.  The genetic locus for restriction and
AB  - modification of bacteriophage S2 is found to have a chromosomal position
AB  - between the biotin and proline loci.  Restriction-modification of phage S2 has
AB  - been shown to be a function of its deoxyribonucleic acid (DNA) in that
AB  - transfection with S2 phage DNA or prophage DNA is subject to host restriction
AB  - and modification.  An enzyme preparation which contains endodeoxyribonuclease
AB  - but no appreciable exonuclease activity, from mutant H. influenzae com-10 did
AB  - not restrict phage S2.RdS DNA or prophage DNA transfecting activity, indicating
AB  - that this endodeoxyribonuclease is not responsible for phage restriction.  A
AB  - new restriction enzyme isolated from H. influenzae Rd was found to be the major
AB  - enzyme involved in the restriction of bacteriophage S2.  The enzyme inactivated
AB  - the transfecting activity of unmodified phage DNA but did not attack modified
AB  - phage DNA.  Unlike endodeoxyribonuclease R, this enzyme requires adenosine
AB  - triphosphate and S-adenosylmethionine.
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - Goodgal, S.
TI  - On the restriction-modification systems of Haemophilus aegyptius.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1975
SP  - 103
EP  - 103
VL  - 75
AB  - In order to assess the role of type I and type II restriction systems in vivo
AB  - in Haemophilus we have attempted to isolate mutants deficient in restriction
AB  - and modification.  Because no mutants of the type II system were found in H.
AB  - influenze Rd, H. aegyptius was used since it contained different type II
AB  - restriction activities.  Bacteriophage S2 does not form plaques on wild type H.
AB  - aegyptius although it is efficiently absorbed.  Mutants capable of plating S2
AB  - with an efficiency of 10-7 were obtained.  Restriction was completely
AB  - eliminated by three more stepwise mutagenic treatments.  Analysis of these
AB  - mutants suggested that the wild type had at least three independent type I
AB  - systems.  Mutants deficient in restriction-modification were also deficient in
AB  - transforming activity.  The type II restriction systems of H. aegyptius did not
AB  - restrict bacteriophage S2 from H. influenze although its DNA was attacked in
AB  - vitro by purified type II restriction enzymes.  In the same way unmodified S2
AB  - grown on H. aegyptius was not restricted in vivo by the type II restriction
AB  - systems of H. influenzae Rd, but was excluded by its type I restriction system.
AB  - These data support the conclusion that only type I restriction is involved in
AB  - the exclusion of bacteriophage S2 in Haemophilus.  A type I activity was
AB  - isolated from H. aegyptius and appears responsible for restriction of S2.
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - Goodgal, S.H.
TI  - On the role of restriction enzymes in transformation and transfection.
JO  - Mechanisms of recombination
PY  - 1974
SP  - 209
EP  - 215
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - Goodgal, S.H.
TI  - Biological Properties of a Haemophilus influenzae Restriction Enzyme, HindI.
JO  - J. Bacteriol.
PY  - 1976
SP  - 848
EP  - 854
VL  - 127
AB  - A type I restriction enzyme from Haemophilus influenzae, HindI, which requires
AB  - adenosine 5'-triphosphate and 5-adenosyl methionine, was studied for its
AB  - activity on transfecting and transforming deoxyribonucleic acid (DNA).  The
AB  - enzyme reduced the size of unmodified bacteriophage S2 DNA from 37 Mdaltons to
AB  - approximately 10 Mdaltons, but did not affect modified S2 DNA.  Unmodified
AB  - transforming DNA was attacked in vitro by HindI; however, relatively low levels
AB  - of inactivation were obtained for single markers, and linked transformants were
AB  - inactivated as a function of the distance between markers. In contrast,
AB  - unmodified bacterial DNA was not inactivated in vivo for either single or
AB  - linked markers by the HindI restriction system, probably because the segments
AB  - generated by HindI were still capable of being integrated in vivo.  The lack of
AB  - preferential inactivation of markers by the enzyme suggests that it makes
AB  - random breaks in the DNA.
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - Goodgal, S.H.
TI  - On the effect of a restriction modification system on transformation in Haemophilus influenzae.
JO  - Fed. Proc.
PY  - 1975
SP  - 588
EP  - 588
VL  - 34
AB  - Type I restriction enzymes, those that require ATP and S-adenosyl methionine
AB  - for activity, have been isolated and shown to be responsible for restriction of
AB  - bacteriophages S2 and HPlcl in Haemophilus. H. influenzae serotypes Rb and Rd
AB  - have different Type I restriction and modification systems although their type
AB  - II endodeoxyribonucleases have the same specificities.  The H. influenzae Rd
AB  - system has been shown to reversibly segregate, with a high frequency, to a
AB  - restriction modification deficient phenotype, however, the Rb system is stable
AB  - and can be used to study the effect of the type I restriction modification
AB  - system on bacterial transformation.  Mutants with different restriction and
AB  - modification phenotypes were examined for their efficiency of transformation.
AB  - The mutants studied included the first step mutants, r+/-m+, and r-m-; and the
AB  - second step mutants r-m-, r-m+, and r-m+/- obtained by a second round of
AB  - mutation.  A reduction in normal transforming activity ranging from 0.5 to 0.01
AB  - was obtained with all mutants tested with the greatest reductions associated
AB  - with the second step r-m- strains.  Transformation of mutants to the r+m+
AB  - phenotype resulted in recovery of normal transforming efficiency, and,
AB  - conversely transformation of r+m+ wild type recipients to the r-m- phenotype
AB  - resulted in lowered transformability.  The mutants were found to have
AB  - deficiences in their type I restriction and modification enzymes but no changes
AB  - in their levels of type II restriction enzymes.
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - Goodgal, S.H.
TI  - Action of Haemophilus endodeoxyribonuclease on biologically active deoxyribonucleic acid.
JO  - J. Bacteriol.
PY  - 1972
SP  - 987
EP  - 992
VL  - 109
AB  - An enzyme similar to that described by Smith and Wilcox (15) for Haemophilus
AB  - influenzae which attacks foreign deoxyribonucleic acid (DNA) but not its own
AB  - has been isolated and purified from H. parainfluenzae.  The enzyme degrades
AB  - foreign DNA to limited sizes and can destroy the transforming activity of H.
AB  - influenzae and Bacillus subtilis DNA.  The enzyme can also destroy the
AB  - biological activity of H. influenzae phage and prophage DNA.  On the other
AB  - hand, the H. influenzae endodeoxyribonuclease can destroy the transforming
AB  - activity of H. parainfluenzae DNA but not its own DNA.  It also attacks B.
AB  - subtilis DNA and its transforming activity.
ER  -

TY  - JOUR
AU  - Gromkova, R.
AU  - LaPorte, J.
AU  - Goodgal, S.H.
TI  - A restriction enzyme from Haemophilus influenzae requiring adenosine triphosphate and S-adenosyl methionine.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1973
SP  - 72
EP  - 72
VL  - 73
AB  - The endodeoxyribonuclease isolated from H. influenzae does not attack H. influenzae DNA nor H.
AB  - influenzae phage S2 transfecting activity.  Since there is restriction and modification of
AB  - phage S2 in H. influenzae it was clear that another restriction system was present.  A new
AB  - restriction activity (Hd) that destroys the transfecting activity of unmodified DNA from phage
AB  - grown in nonrestrictive recipients and does not inactivate modified DNA has been purified from
AB  - H. influenzae.  Unlike endo-R the enzyme activity which attacks phage DNA requires ATP and
AB  - S-adenosyl methionine.  Transformation by foreign bacterial DNA was also inactivated by the Hd
AB  - system.  This inactivation was stimulated by ATP and SAM.  The enzyme is considerably larger
AB  - than endo-R; it elutes earlier in Bio-Gel fractionation, and sediments further in a glycerol
AB  - sedimentation velocity gradient.  A similar enzyme has been isolated from H. influenzae Reid.
AB  - Since the H. influenzae Reid enzyme can attack the DNA from phage grown in restrictive cells
AB  - of H. influenzae, one can conclude that the H. influenzae and H. influenzae Reid restriction
AB  - systems have different specificities.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Elob, A.A.
AU  - Kubareva, E.A.
AU  - Metelev, V.G.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic fragments of DNA.  IV. DNA duplexes with phosphoamide and pyrophosphate internucleotide bonds -- substrates for the study of single-strand breaks.
JO  - Mol. Biol. (Mosk)
PY  - 1986
SP  - 29
EP  - 40
VL  - 20
AB  - A set of DNA duplexes containing repetitive recognition sites for restriction
AB  - endonucleases EcoRII, EcoRI, and AluI, in which the phosphodiester bonds in the EcoRII
AB  - cleavage sites were replaced by phosphoamide or unbreakable pyrophosphate bonds, was
AB  - synthesized.  It was found that the restriction endonuclease EcoRII does not cleave the
AB  - substrate at the phosphoamide bond.  Using substrates containing modified bonds in the
AB  - EcoRII recognition sites in one of the strands, it was shown that this enzyme is capable of
AB  - catalyzing single-strand breaks both in the dA- and in the dT-containing strand of the
AB  - recognition site.  The restriction endonuclease EcoRII interacts with both strands of the
AB  - recognition site of DNA, whereas cleavage of each of them occurs independently of the
AB  - cleavage of the other.  Restriction endonucleases EcoRI and AluI specifically digest the
AB  - synthesized substrates at the phosphodiester bonds; however, this cleavage is hindered if
AB  - the modified bond is situated in the recognition site (EcoRI) or adjoins it (AluI).  For
AB  - EcoRII and AluI this effect is more pronounced in the case of substrates with
AB  - pyrophosphate bonds than with phosphoamide bonds.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Elob, A.A.
AU  - Kubareva, E.A.
AU  - Metelev, V.G.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic fragments of DNA.
JO  - Mol. Biol. (Mosk)
PY  - 1986
SP  - 22
EP  - 32
VL  - 20
AB  - A set of DNA duplexes containing repetitive recognition sites for restriction endonucleases
AB  - EcoRII, EcoRI, and AluI, in which the phosphodiester bonds in the EcoRII cleavage sites were
AB  - replaced by phosphoamide or unbreakable pyrophosphate bonds, was synthesized.  It was found
AB  - that the restriction endonuclease EcoRII does not cleave the substrate at the phosphoamide
AB  - bond.  Using substrates containing modified bonds in the EcoRII recognition sites in one of
AB  - the strands, it was shown that this enzyme is capable of catalyzing single-strand breaks both
AB  - in the dA- and in the dT-containing strand of the recognition site.  The restriction
AB  - endonuclease EcoRII interacts with both strands of the recognition site of DNA, whereas
AB  - cleavage of each of them occurs independently of the cleavage of the other.  Restriction
AB  - endonucleases EcoRI and AluI specifically digest the synthesized substrates at the
AB  - phosphodiester bonds; however, this cleavage is hindered if the modified bond is situated in
AB  - the recognition site (EcoRI) or adjoins it (AluI).  For EcoRII and AluI this effect is more
AB  - pronounced in the case of substrates with pyrophosphate bonds than with phosphoamide bonds.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Khoroshaev, A.V.
TI  - Prokaryotic DNA methyltransferases: The structure and the mechanism of interaction with DNA.
JO  - Mol. Biol. (Mosk)
PY  - 2003
SP  - 300
EP  - 314
VL  - 37
AB  - The review considers current views on the function of DNA methyltransferases (MTases) that
AB  - belong to prokaryotic type II
AB  - restriction-modification systems. A commonly accepted classification of
AB  - MTases is described along with their primary and tertiary structures and
AB  - molecular mechanisms of their specific interaction with DNA (including
AB  - methylation). MTase inhibitors are also considered. Special emphasis is
AB  - placed on the flipping of the target heterocyclic base out of the double
AB  - helix and on the methods employed in its analysis. Base flipping is a
AB  - fundamentally new type of DNA conformational changes and is also of
AB  - importance in the case of other DNA-operating enzymes. MTases show unique
AB  - sequence homology, and are similar in structure of functional centers and
AB  - in the mechanism of methylation. These data contribute to the
AB  - understanding of the general biological significance of methylation, since
AB  - prokaryotic and eukaryotic MTases are structurally and functionally
AB  - similar.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Kubareva, E.A.
AU  - Vinogradova, M.N.
AU  - Oretskaya, T.S.
AU  - Shabarova, Z.A.
TI  - Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII.
JO  - J. Mol. Recognit.
PY  - 1991
SP  - 133
EP  - 141
VL  - 4
AB  - To elucidate the mechanism of action of restriction endonucleases MvaI and EcoRII a study was
AB  - made of their interaction with a set of synthetic substrates in which the heterocyclic bases
AB  - or the sugar-phosphate backbone has been modified; individual nucleotide residues had been
AB  - removed or replaced with hydrocarbon bridges, and mismatched base pairs had been introduced.
AB  - The groups of atoms in the heterocyclic bases and the phosphates in the recognition site that
AB  - produce the most significant influence on the functioning of endonucleases MvaI and EcoRII
AB  - were discerned. Profound differences were found in the functioning of the MvaI and EcoRII
AB  - neoschizomers. The catalytic activity of EcoRII is significantly affected by any alteration in
AB  - the recognition site structure and conformation, with a modification in one strand of the
AB  - substrate causing the same decrease in the hydrolysis rate of both strands. Endonuclease MvaI
AB  - is tolerant to a number of structural abnormalities; the latter sometimes affect only
AB  - hydrolysis of one strand of the recognition site. The enzyme can preferentially cleave one of
AB  - the substrate strands. Mismatched base pairs retard and sometimes block the hydrolysis. The
AB  - effect depends on the particular enzyme, mismatch and its location.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Kubareva, E.A.
AU  - Yolov, A.A.
AU  - Akatova, E.A.
AU  - Nikolskaya, I.I.
AU  - Shabarova, Z.A.
TI  - Cleavage of concatemeric substrates by restriction endonucleases MvaI and SsoII.
JO  - Biokhimiia
PY  - 1991
SP  - 552
EP  - 559
VL  - 56
AB  - The interaction of enzymes SsoII (^CCNGG) and MvaI (CC^A/TGG) with concatemeric
AB  - duplexes used earlier to study EcoRII (CCA/TGG) was investigated with a view to
AB  - elucidating the general principles of restriction endonuclease function.  A
AB  - pattern common to all three enzymes was observed with DNA duplexes containing
AB  - AA or TT pairs in the central position of the recognition site.  The AA pair
AB  - blocks or substantially hinders the endonuclease action, whereas the TT pair is
AB  - either less inhibitory or altogether inert.  SsoII, like EcoRII was able to
AB  - processively cleave the concatemeric substrates and to interact with (or to be
AB  - close to) the hydrogen in the 5th position of the outer dC residue of the
AB  - recognition site.  MvaI was found to differ from EcoRII in the way they
AB  - recognize and cleave the same nucleotide sequence.  The substrate-bound MvaI
AB  - molecule is incapable of linear diffusion along the DNA.  Effective hydrolysis
AB  - of dU- and m5dC-containing polymers rules out the participation of hydrophobic
AB  - contacts of the enzyme with the methyl group of the dT residue and with the 5th
AB  - hydrogen of the outer dC residue of the recognition site in DNA-protein
AB  - interactions.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Kuchava, E.A.
AU  - Pein, C.-D.
AU  - Oreshkaya, T.S.
AU  - Shabarova, Z.A.
AU  - Check, D.
TI  - Study of the DNA cleavage mechanism of the restriction endonuclease MvaI.
JO  - Dokl. Akad. Nauk.
PY  - 1987
SP  - 1493
EP  - 1497
VL  - 295
AB  - None
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Oretskaya, T.S.
AU  - Eritja, R.
AU  - Guschlbauer, W.
TI  - Kinetic studies of MvaI DNA methyltransferase interaction with modified oligonucleotide duplexes.
JO  - Biochem. Mol. Biol. Int.
PY  - 1995
SP  - 247
EP  - 255
VL  - 36
AB  - We have measured steady-state kinetics of an N4-cytosine methylase, M.MvaI,
AB  - using as substrates modified non-selfcomplementary tetradecanucleotide duplexes containing the
AB  - CCWGG target sequence.  The inner or outer localisation of the dI residue in the MvaI
AB  - recognition
AB  - site seems to be of little importance since the specificity constants kcat/KM are only 2 to 7
AB  - fold
AB  - smaller than that of the canonical substrate.  Replacement of dG residues by dI in both
AB  - strands
AB  - resulted in a 25 to 60-fold decrease of the specificity constant.  Modifications of the
AB  - phosphate
AB  - backbone or opening of the sugar ring of one of the dG residues had only little influence on
AB  - the
AB  - action of M.MvaI.  The enzyme appears to be rather tolerant to different kinds of modification
AB  - in its
AB  - substrate in the minor groove.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Petrauskene, O.V.
AU  - Kubareva, E.A.
TI  - Study of the mechanism of EcoRII endonuclease activation with synthetic substrates.
JO  - Nucleic Acids Symp. Ser.
PY  - 1991
SP  - 217
EP  - 218
VL  - 24
AB  - EcoRII restriction endonuclease is not able to cleave phage DNA with isolated EcoRII
AB  - recognition sites.  However addition of the EcoRII sensitive DNA or short substrates may
AB  - stimulate such a cleavage.  It has been suggested that EcoRII requires at least two
AB  - recognition sites for its activation.  In order to substantiate the mechanism of
AB  - EcoRII-substrate interaction we report a model system convenient for stimulation effect
AB  - studies and the results of testing as activators a wide set of modified and unmodified DNA.
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Shabarova, A.Z.
TI  - DNA-Protein interactions:  The use of synthetic oligo- and polynucleotides for studying single-stranded-DNA-binding proteins and restriction endonucleases.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 1990
SP  - 1
EP  - 47
VL  - 39
AB  - None
ER  -

TY  - JOUR
AU  - Gromova, E.S.
AU  - Vinogradova, M.N.
AU  - Uporova, T.M.
AU  - Gryaznova, O.I.
AU  - Isagulyants, M.G.
AU  - Kosykh, V.G.
AU  - Nikolskaya, I.I.
AU  - Shabarova, Z.A.
TI  - DNA duplexes with phosphoamide bonds:  the interaction with EcoRII and SsoII restriction endonucleases.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 269
EP  - 272
VL  - 13
AB  - We studied the interaction of EcoRII and SsoII restriction endonucleases with
AB  - synthetic DNA duplexes, containing 3'N -> 5'P and 3'P -> 5'N phosphoamide
AB  - internucleotide bonds in one of the cleavage points.  Enzymatic hydrolysis of
AB  - the modified strand of the duplexes is blocked in all cases.  The presence of
AB  - phosphoamide bonds was found to reduce the rate of cleavage of the natural
AB  - strand by EcoRII and to have no influence in case of SsoII.  Properties of the
AB  - EcoRII endonuclease complex with its substrate, containing non-cleavable 3'N ->
AB  - 5'P internucleotide bonds in each cleavage point, were examined.  In the
AB  - presence of Mg2+ ions the equilibrium association constant of the
AB  - enzyme-substrate complex is 3-fold reduced, and the dissociation rate constant
AB  - of the complex is increased by 1.5 times.
ER  -

TY  - JOUR
AU  - Gronenborn, B.
AU  - Messing, J.
TI  - Methylation of single-stranded DNA in vitro introduces new restriction endonuclease cleavage sites.
JO  - Nature
PY  - 1978
SP  - 375
EP  - 377
VL  - 272
AB  - Restriction endonucleases recognise specific sequences in DNA, and these
AB  - endonucleases, especially those which generate cohesive ends, have been widely
AB  - used to clone DNA.  However, many DNAs lack sequences which are recognised by
AB  - endonucleases such as EcoRI, HindIII or BamHI.  A general method of overcoming
AB  - this problem has been described recently. This approach involves the synthesis
AB  - of oligonucleotides sensitive to a specific endonuclease and the blunt end
AB  - ligation of these molecules to the DNA to be cloned.  In contrast, we sought a
AB  - method which avoids the insertion of addtional nucleotides into a DNA sequence,
AB  - but depends on direct modification of DNA.  If a DNA sequence differs in only
AB  - one base pair from the recognition sequence of a restriction endonuclease, a
AB  - particular change of this base pair will generate the proper sequence.  Here we
AB  - describe a way of generating restriction endonuclease cleavage sites by single
AB  - base changes derived after in vitro methylation of single-stranded DNA.
ER  -

TY  - JOUR
AU  - Grones, J.
AU  - Turna, J.
TI  - Some properties of restriction endonucleases from Acetobacter pasteurianus.
JO  - Biologia (Bratisl)
PY  - 1991
SP  - 1103
EP  - 1108
VL  - 46
AB  - Restriction endonucleases ApaBI, ApaCI and ApaDI have been purified from three different
AB  - strains of Acetobacter pasteurianus. The enzyme ApaBI recognized 35 cleavage sites on
AB  - bacteriophage lambda DNA, 20 sites on adeno-virus-2 DNA and 2 sites on plasmid pBR322 DNA.
AB  - The recognition sequence for this enzyme is
AB  - 5'-GCANNNNN/TGC-3'
AB  - 3'-CGT/NNNNNACG-5'
AB  - The ApaCI enzyme is an isoschizomer of the restriction endonuclease BamHI. ApaDI is the
AB  - third enzyme with 6 sites of cleavage on pBR 327 DNA, 7 sites on pAT 153 DNA more than 20
AB  - sites on bacteriophage lambda DNA.
ER  -

TY  - JOUR
AU  - Grones, J.
AU  - Turna, J.
TI  - Some properties of restriction endonuclease ApaBI from Acetobacter pasteurianus.
JO  - Biochim. Biophys. Acta
PY  - 1993
SP  - 323
EP  - 325
VL  - 1162
AB  - A number of restriction endonucleases have been isolated from many species of prokaryotes and
AB  - their specificities documented. Recently, several restriction endonucleases have been isolated
AB  - from Acetobacter genera. Up to date, two restriction endonucleases, ApaI and ApaLI have been
AB  - isolated from Acetobacter pasteurianus cells. The isolation of a new restriction endonuclease,
AB  - type-II ApaBI is described in this article.
ER  -

TY  - JOUR
AU  - Grones, J.
AU  - Turna, J.
TI  - Isolation of a new restriction enzyme, ApaCI, an isoschizomer of BamHI produced by Acetobacter pasteurianus.
JO  - Folia Microbiol. (Praha)
PY  - 1992
SP  - 353
EP  - 356
VL  - 37
AB  - A new Type II restriction endonuclease ApaCI purified from Acetobacter pasteurianus is an
AB  - isoschizomer of BamHI that cleaves at the nucleotide sequence 5'-G/GATCC-3' of
AB  - double-stranded DNA. The single restriction activity present in this strain permits the rapid
AB  - purification of 30,000 units of cleavage activity from 10 g of freshly harvested cells. The
AB  - resulting ApaCI preparation is free of contaminant nuclease activities that might interfere
AB  - with in vitro manipulation of DNA.
ER  -

TY  - JOUR
AU  - Grones, J.
AU  - Turna, J.
TI  - ApaCI, an isoschizomer of BamHI isolated from Acetobacter pasteurianus.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3513
EP  - 3513
VL  - 20
ER  -

TY  - JOUR
AU  - Gronow, S. et al.
TI  - Complete genome sequence of Veillonella parvula type strain (Te3).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 57
EP  - 65
VL  - 2
AB  - Veillonella parvula (Veillon and Zuber 1898) Prevot 1933 is the type species of the genus
AB  - Veillonella in the family Veillonellaceae within the order
AB  - Clostridiales. The species V. parvula is of interest because it is frequently
AB  - isolated from dental plaque in the human oral cavity and can cause opportunistic
AB  - infections. The species is strictly anaerobic and grows as small cocci which
AB  - usually occur in pairs. Veillonellae are characterized by their unusual
AB  - metabolism which is centered on the activity of the enzyme methylmalonyl-CoA
AB  - decarboxylase. Strain Te3(T), the type strain of the species, was isolated from
AB  - the human intestinal tract. Here we describe the features of this organism,
AB  - together with the complete genome sequence, and annotation. This is the first
AB  - complete genome sequence of a member of the large clostridial family
AB  - Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1,859
AB  - protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Gronow, S. et al.
TI  - Complete genome sequence of Paludibacter propionicigenes type strain (WB4).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 36
EP  - 44
VL  - 4
AB  - Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter,
AB  - which belongs to the family Porphyromonadaceae. The species is of
AB  - interest because of the position it occupies in the tree of life where it can be
AB  - found in close proximity to members of the genus Dysgonomonas. This is the first
AB  - completed genome sequence of a member of the genus Paludibacter and the third
AB  - sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with
AB  - its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and
AB  - is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Gronow, S. et al.
TI  - Complete genome sequence of Bacteroides salanitronis type strain (BL78).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 191
EP  - 199
VL  - 4
AB  - Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs
AB  - to the family Bacteroidaceae. The species is of interest because it
AB  - was isolated from the gut of a chicken and the growing awareness that the
AB  - anaerobic microflora of the cecum is of benefit for the host and may impact
AB  - poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome
AB  - and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and
AB  - 101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Groot, M.N.
AU  - Nieboer, F.
AU  - Abee, T.
TI  - Enhanced Transformation Efficiency of Recalcitrant Bacillus cereus and Bacillus weihenstephanensis Isolates upon In Vitro Methylation of Plasmid DNA.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 7817
EP  - 7820
VL  - 74
AB  - Digestion patterns of chromosomal DNAs of Bacillus cereus and Bacillus weihenstephanensis
AB  - strains suggest that Sau3AI-type restriction
AB  - modification systems are widely present among the isolates tested. In
AB  - vitro methylation of plasmid DNA was used to enhance poor plasmid
AB  - transfer upon electroporation to recalcitrant strains that carry Sau3AI
AB  - restriction barriers.
ER  -

TY  - JOUR
AU  - Gros, C.
AU  - Chauvigne, L.
AU  - Poulet, A.
AU  - Menon, Y.
AU  - Ausseil, F.
AU  - Dufau, I.
AU  - Arimondo, P.B.
TI  - Development of a universal radioactive DNA methyltransferase inhibition test for high-throughput screening and mechanistic studies.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 12
EP  - 12
VL  - 41
AB  - DNA methylation is an important epigenetic mark in eukaryotes, and aberrant pattern of this
AB  - modification is involved in numerous diseases such as cancers. Interestingly, DNA methylation
AB  - is reversible and thus is considered a promising therapeutic target. Therefore, there is a
AB  - need for identifying new small inhibitors of C5 DNA methyltransferases (DNMTs). Despite the
AB  - development of numerous in vitro DNMT assays, there is a lack of reliable tests suitable for
AB  - high-throughput screening, which can also  ive insights into inhibitor mechanisms of action.
AB  - We developed a new test based on scintillation proximity assay meeting these requirements.
AB  - After optimizing our assay on human DNMT1 and calibrating it with two known inhibitors, we
AB  - carried out S-Adenosyl-L-Methionine and DNA competition studies on three inhibitors and were
AB  - able to determine each mechanism of action. Finally, we showed that our test was applicable to
AB  - 3 other methyltransferases sources: human DNMT3A, bacterial M. SssI and cellular extracts a s
AB  - well.
ER  -

TY  - JOUR
AU  - Gross, U.
AU  - Brzuszkiewicz, E.
AU  - Gunka, K.
AU  - Starke, J.
AU  - Riedel, T.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Wetzel, D.
AU  - Poehlein, A.
AU  - Chibani, C.
AU  - Bohne, W.
AU  - Overmann, J.
AU  - Zimmermann, O.
AU  - Daniel, R.
AU  - Liesegang, H.
TI  - Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.
JO  - BMC Genomics
PY  - 2018
SP  - 1
EP  - 1
VL  - 19
AB  - BACKGROUND: Clostridioides difficile infections (CDI) have emerged over the past
AB  - decade causing symptoms that range from mild, antibiotic-associated diarrhea
AB  - (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple
AB  - and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM
AB  - 27640 that already initially showed different morphotypes on solid media.
AB  - RESULTS: The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and
AB  - 027 (DSM 27638 and DSM 27640) were phenotypically characterized and high quality
AB  - closed genome sequences were generated. The genomes were compared with seven
AB  - reference strains including three strains of the RT 027, two of the RT 017, and
AB  - one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of
AB  - horizontal gene transfer events revealed gene acquisition incidents that sort the
AB  - strains within the time line of the spread of their RTs within Germany. We could
AB  - show as well that horizontal gene transfer between the members of different RTs
AB  - occurred within this multiple infection. In addition, acquisition and exchange of
AB  - virulence-related features including antibiotic resistance genes were observed.
AB  - Analysis of the two genomes assigned to RT 027 revealed three single nucleotide
AB  - polymorphisms (SNPs) and apparently a regional genome modification within the
AB  - flagellar switch that regulates the fli operon. CONCLUSION: Our findings show
AB  - that (i) evolutionary events based on horizontal gene transfer occur within an
AB  - ongoing CDI and contribute to the adaptation of the species by the introduction
AB  - of new genes into the genomes, (ii) within a multiple infection of a single
AB  - patient the exchange of genetic material was responsible for a much higher genome
AB  - variation than the observed SNPs.
ER  -

TY  - JOUR
AU  - Grosskopf, R.
AU  - Wolf, W.
AU  - Kessler, C.
TI  - Two new restriction endonucleases DraII and DraIII from Deinococcus radiophilus.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 1517
EP  - 1528
VL  - 13
AB  - In addition to recently characterized DraI (1), two new Type II restriction
AB  - endonucleases, DraII and DraIII, with novel site-specificities were isolated
AB  - and purified from Deinococcus radiophilus ATCC 27603.  DraII and DraIII
AB  - recognize the hepta- and nonanucleotide sequences(DraII)5'-Pu G ^ G N C C Py-3'
AB  - 3'-Py C C N G ^ G Pu-5'and(DraIII)5'-C A C N N N ^ G T G-3' 3'-G T G ^ N N N C
AB  - A C-5'The cleavage sites within both strands are indicated by arrows.  The
AB  - recognition sequences were established by mapping of the cleavage sites on
AB  - pBR322 (DraII) and fd109 RF DNA (DraIII).  The sequence specificities were
AB  - confirmed by computer-assisted restriction analyses of the generated fragment
AB  - patterns of the sequenced DNA's of the bacteriophages lambda, PhiX174 RF,
AB  - M13mp8 RF and fd109 RF, the viruses Adeno2 and SV40, and the plasmids pBR322
AB  - and pBR328.  The cleavage positions within the recognition sequences were
AB  - determined by sequencing experiments.
ER  -

TY  - JOUR
AU  - Grote, J. et al.
TI  - Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 269
EP  - 278
VL  - 5
AB  - Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain
AB  - is of interest because it is one of the first known isolates from a globally ubiquitous clade
AB  - of marine bacteria known as SAR116 within the family Rhodospirillaceae. Here we de-scribe
AB  - preliminary features of the organism, together with the draft genome sequence and an-notation.
AB  - This is the second genome sequence of a member of the SAR116 clade. The 2,458,945 bp genome
AB  - contains 2,334 protein-coding and 42 RNA genes.
ER  -

TY  - JOUR
AU  - Grote, J.
AU  - Schott, T.
AU  - Bruckner, C.G.
AU  - Glockner, F.O.
AU  - Jost, G.
AU  - Teeling, H.
AU  - Labrenz, M.
AU  - Jurgens, K.
TI  - Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 506
EP  - 510
VL  - 109
AB  - Eutrophication and global climate change lead to expansion of hypoxia in the ocean, often
AB  - accompanied by the production of hydrogen sulfide, which
AB  - is toxic to higher organisms. Chemoautotrophic bacteria are thought to
AB  - buffer against increased sulfide concentrations by oxidizing hydrogen
AB  - sulfide before its diffusion to oxygenated surface waters. Model organisms
AB  - from such environments have not been readily available, which has
AB  - contributed to a poor understanding of these microbes. We present here a
AB  - detailed study of 'Sulfurimonas gotlandica' str. GD1, an
AB  - Epsilonproteobacterium isolated from the Baltic Sea oxic-anoxic interface,
AB  - where it plays a key role in nitrogen and sulfur cycling. Whole-genome
AB  - analysis and laboratory experiments revealed a high metabolic flexibility,
AB  - suggesting a considerable capacity for adaptation to variable redox
AB  - conditions. S. gotlandica str. GD1 was shown to grow
AB  - chemolithoautotrophically by coupling denitrification with oxidation of
AB  - reduced sulfur compounds and dark CO(2) fixation. Metabolic versatility
AB  - was further suggested by the use of a range of different electron donors
AB  - and acceptors and organic carbon sources. The number of genes involved in
AB  - signal transduction and metabolic pathways exceeds those of other
AB  - Epsilonproteobacteria. Oxygen tolerance and environmental-sensing systems
AB  - combined with chemotactic responses enable this organism to thrive
AB  - successfully in marine oxygen-depletion zones. We propose that S.
AB  - gotlandica str. GD1 will serve as a model organism in investigations that
AB  - will lead to a better understanding how members of the
AB  - Epsilonproteobacteria are able to cope with water column anoxia and the
AB  - role these microorganisms play in the detoxification of sulfidic waters.
ER  -

TY  - JOUR
AU  - Grothusen, H.
AU  - Castillo, A.
AU  - Henriquez, P.
AU  - Navas, E.
AU  - Bohle, H.
AU  - Araya, C.
AU  - Bustamante, F.
AU  - Bustos, P.
AU  - Mancilla, M.
TI  - First Complete Genome Sequence of Tenacibaculum dicentrarchi, an Emerging Bacterial Pathogen of Salmonids.
JO  - Genome Announcements
PY  - 2016
SP  - e01756
EP  - e01715
VL  - 4
AB  - Tenacibaculum-like bacilli have recently been isolated from diseased sea-reared Atlantic
AB  - salmon in outbreaks that took place in the XI region (Region de Aysen)
AB  - of Chile. Molecular typing identified the bacterium as Tenacibaculum
AB  - dicentrarchi. Here, we report the complete genome sequence of the AY7486TD
AB  - isolate recovered during those outbreaks.
ER  -

TY  - JOUR
AU  - Grouzdev, D.S.
AU  - Babich, T.L.
AU  - Tourova, T.P.
AU  - Sokolova, D.S.
AU  - Abdullin, R.R.
AU  - Poltaraus, A.B.
AU  - Schevchenko, M.A.
AU  - Toshchakov, S.V.
AU  - Nazina, T.N.
TI  - Draft Genome Sequence of Roseomonas aestuarii Strain JR1/69-1-13 Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia.
JO  - Genome Announcements
PY  - 2018
SP  - e00583
EP  - e00518
VL  - 6
AB  - The draft genome sequence of Roseomonas aestuarii strain JR1/69-1-13, an aerobic
AB  - chemoorganotrophic bacterium isolated from nitrate- and radionuclide-contaminated
AB  - groundwater in Russia, is presented here. The genome was annotated to elucidate
AB  - the genomic basis for the strain's adaptation to the environment and its
AB  - resistance to nitrate, heavy metals, and metalloids.
ER  -

TY  - JOUR
AU  - Grouzdev, D.S.
AU  - Dziuba, M.V.
AU  - Sukhacheva, M.S.
AU  - Mardanov, A.V.
AU  - Beletskiy, A.V.
AU  - Kuznetsov, B.B.
AU  - Skryabin, K.G.
TI  - Draft Genome Sequence of Magnetospirillum sp. Strain SO-1, a Freshwater Magnetotactic Bacterium Isolated from the Ol'khovka River, Russia.
JO  - Genome Announcements
PY  - 2014
SP  - e00235
EP  - e00214
VL  - 2
AB  - Here, we present the draft genome sequence of Magnetospirillum sp. strain SO-1, a freshwater
AB  - magnetotactic spirillum isolated from the sediments of the Ol'khovka River, Russia.
ER  -

TY  - JOUR
AU  - Grouzdev, D.S.
AU  - Rysina, M.S.
AU  - Bryantseva, I.A.
AU  - Gorlenko, V.M.
AU  - Gaisin, V.A.
TI  - Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order:  phylogenetic and taxonomic implications.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 24
EP  - 24
VL  - 13
AB  - 'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F
AB  - are mesophilic filamentous anoxygenic phototrophic bacteria from
AB  - alkaline aquatic environments. Both bacteria became available in the last few
AB  - years and only in stable enrichment culture. In this study, we report the draft
AB  - genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. Viridilinea
AB  - mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures
AB  - with a fold coverage 86.3x and 163.8x, respectively. The B7-9 (5.8 Mb) and the
AB  - Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding
AB  - genes, respectively. In this article, we analyzed the phylogeny of
AB  - representatives of the Chloroflexineae suborder in view of the appearance of new
AB  - genomic data. These data were used for the revision of earlier published
AB  - group-specific conserved signature indels and for searching for novel signatures
AB  - for taxons in the Chloroflexineae suborder.
ER  -

TY  - JOUR
AU  - Grouzdev, D.S.
AU  - Safonov, A.V.
AU  - Babich, T.L.
AU  - Tourova, T.P.
AU  - Krutkina, M.S.
AU  - Nazina, T.N.
TI  - Draft Genome Sequence of a Dissimilatory U(VI)-Reducing Bacterium, Shewanella xiamenensis Strain DCB2-1, Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia.
JO  - Genome Announcements
PY  - 2018
SP  - e00555
EP  - e00518
VL  - 6
AB  - Here, we describe the draft genome sequence of Shewanella xiamenensis strain DCB2-1, isolated
AB  - from nitrate- and radionuclide-contaminated groundwater. This
AB  - strain is able to reduce nitrate, Tc(VII), Cr(VI), Fe(III), and U(VI), and its
AB  - genome sequence contains several gene sets encoding denitrification, resistance
AB  - to heavy metals, and reduction of metals and metalloids.
ER  -

TY  - JOUR
AU  - Grouzdev, D.S.
AU  - Tikhonova, E.N.
AU  - Krutkina, M.S.
AU  - Kravchenko, I.K.
TI  - Genome Sequence of Methylotrophic Azospirillum sp. Strain B2, Isolated from a Raised Sphagnum Bog.
JO  - Genome Announcements
PY  - 2018
SP  - e00492
EP  - e00418
VL  - 6
AB  - Azospirillum sp. strain B2 is a soil bacterium which was originally isolated from the
AB  - Sosvyatskoe raised Sphagnum bog in Russia. Here, we present the approximately
AB  - 8-Mb draft genome sequence of Azospirillum sp. B2, with the aim of providing
AB  - insight into the genomic basis of its ecological success in peatland settings.
ER  -

TY  - JOUR
AU  - Grover, S.
AU  - Sharma, V.K.
AU  - Mallapa, R.H.
AU  - Batish, V.K.
TI  - Draft Genome Sequence of Lactobacillus fermentum Lf1, an Indian Isolate of Human  Gut Origin.
JO  - Genome Announcements
PY  - 2013
SP  - e00883
EP  - e00813
VL  - 1
AB  - Lactobacillus fermentum is a normal inhabitant of the human gastrointestinal tract. Here, we
AB  - report the draft genome sequence of an Indian isolate of the
AB  - probiotic strain L. fermentum Lf1, isolated from the human gut.
ER  -

TY  - JOUR
AU  - Grover, S.
AU  - Sharma, V.K.
AU  - Mallapa, R.H.
AU  - Batish, V.K.
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain Lp91, a Promising Indian  Probiotic Isolate of Human Gut Origin.
JO  - Genome Announcements
PY  - 2013
SP  - e00976
EP  - e00913
VL  - 1
AB  - Lactobacillus plantarum is a highly versatile species among lactic acid bacteria  that has
AB  - been widely isolated from highly diversified ecological niches,
AB  - including the gastrointestinal tract. Here, we report the first draft genome
AB  - sequence of an Indian isolate of the probiotic strain L. plantarum Lp91, isolated
AB  - from human gut.
ER  -

TY  - JOUR
AU  - Gruber, I.M.
AU  - Nikolskaya, I.I.
AU  - Uporova, T.M.
AU  - Nisilevich, V.F.
TI  - Growth and bioenergetic characteristics of Escherichia coli CK, capable of producing restriction endonuclease, under the conditions of batch cultivation.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1984
SP  - 50
EP  - 55
VL  - 6
AB  - The conditions necessary for the controlled single and multicycle process of
AB  - the batch cultivation of E. coli CK, capable of producing E. coli CK specific
AB  - endonuclease, have been established.  This process can be regulated with
AB  - respect to a number of parameters (temperature, pH, pO2, eH).  The possibility
AB  - of using thermodynamic characteristics, calculated on the basis of the redox
AB  - potential and disclosing the energetics of growth, for evaluating the
AB  - effectiveness of controlled batch cultivation.  The optimum results have been
AB  - obtained during the isolation of E. coli CK restriction endonuclease, active
AB  - and containing no admixture of other endonucleases, at the period from the
AB  - maximum specific growth rate to the end of the exponential growth phase, i.e.
AB  - to the beginning of the stationary phase.
ER  -

TY  - JOUR
AU  - Gruen, M.
AU  - Chang, K.
AU  - Serbanescu, I.
AU  - Liu, D.R.
TI  - An in vivo selection system for homing endonuclease activity.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - e29
EP  - e29
VL  - 30
AB  - Homing endonucleases are enzymes that catalyze the highly sequence-specific cleavage of DNA.
AB  - We have developed an in vivo selection in Escherichia coli that links cell survival with
AB  - homing endonuclease-mediated DNA cleavage activity and sequence specificity. Using this
AB  - selection, wild-type and mutant variants of three homing endonucleases were characterized
AB  - without requiring protein purification and in vitro analysis. This selection system may
AB  - facilitate the study of sequence-specific DNA cleaving enzymes, and selections based on this
AB  - work may enable the evolution of homing endonucleases with novel activities or specificities.
ER  -

TY  - JOUR
AU  - Gruenbaum, Y.
AU  - Cedar, H.
AU  - Razin, A.
TI  - Restriction enzyme digestion of hemimethylated DNA.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 2509
EP  - 2515
VL  - 9
AB  - Hemimethylated duplex DNA of the bacteriophage PhiX174 was synthesized using
AB  - primed repair synthesis in vitro with E. coli DNA polymerase I followed by
AB  - ligation to produce the covalently closed circular duplex (RFI).
AB  - Single-stranded PhiX DNA was used as template, a synthetic oligonucleotide as
AB  - primer and 5-methyldeoxycytidine-5'-triphosphate (5mdCTP) was used in place of
AB  - dCTP.  The hemimethylated product was used as substrate for cleavage by various
AB  - restriction enzymes.  Out of the 17 enzymes tests, only 5 (BstNI, TaqI, HincII,
AB  - HinfI and HpaI) cleaved the hemimethylated DNA.  Two enzymes (MspI and HaeIII)
AB  - were able to produce nicks on the unmethylated strand of the cleavage site.
AB  - MspI, which is known to cleave at CCGG when the internal cytosine residue is
AB  - methylated, does not cleave when both cytosines are methylated.  Another
AB  - enzyme, ApyI, cleaves at the sequence CC(A/T)GG when the internal cytosine is
AB  - methylated, but is inactive on hemimethylated DNA in which both cytosines are
AB  - methylated.  Hemimethylated molecules should be useful for studying DNA
AB  - methylation both in vivo and in vitro.
ER  -

TY  - JOUR
AU  - Grumaz, C.
AU  - Rais, D.
AU  - Kirstahler, P.
AU  - Vainshtein, Y.
AU  - Rupp, S.
AU  - Zibek, S.
AU  - Sohn, K.
TI  - Draft Genome Sequence of Pseudonocardia autotrophica Strain DSM 43083, an Efficient Producer of Peroxidases for Lignin Modification.
JO  - Genome Announcements
PY  - 2017
SP  - e01562
EP  - e01516
VL  - 5
AB  - Pseudonocardia autotrophica strain DSM 43083 is a filamentous actinobacterium and was
AB  - described to degrade or modify lignin. Here, we present its draft genome
AB  - sequence, with a size of 5.8 Mb, to unravel the gene set coding for promising
AB  - monooxygenases, dioxygenases, and DyP-type peroxidases associated with aromatic
AB  - metabolism and lignin modification.
ER  -

TY  - JOUR
AU  - Grumaz, C.
AU  - Vainshtein, Y.
AU  - Kirstahler, P.
AU  - Luetz, S.
AU  - Kittelmann, M.
AU  - Schroer, K.
AU  - Eggimann, F.K.
AU  - Czaja, R.
AU  - Vogel, A.
AU  - Hilberath, T.
AU  - Worsch, A.
AU  - Girhard, M.
AU  - Urlacher, V.B.
AU  - Sandberg, M.
AU  - Sohn, K.
TI  - Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.
JO  - Genome Announcements
PY  - 2017
SP  - e00532
EP  - e00517
VL  - 5
AB  - The three Actinobacteria strains Streptomyces platensis DSM 40041, Pseudonocardia autotrophica
AB  - DSM 535, and Streptomyces fradiae DSM 40063 were described to
AB  - selectively oxyfunctionalize several drugs. Here, we present their draft genomes
AB  - to unravel their gene sets encoding promising cytochrome P450 monooxygenases
AB  - associated with the generation of drug metabolites.
ER  -

TY  - JOUR
AU  - Grunau, C.
AU  - Schattevoy, R.
AU  - Mache, N.
AU  - Rosenthal, A.
TI  - MethTools-a toolbox to visualize and analyze DNA methylation data.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 1053
EP  - 1058
VL  - 28
AB  - The Bisulfite Genomic Sequencing technique has found wide acceptance for the generation of
AB  - DNA-methylation maps with single-base resolution. The method is based on the selective
AB  - deamination of cytosine to uracil (and subsequent conversion to thymine via PCR), whereas
AB  - 5-methylcytosine residues remain unchanged. Methylation maps are created by the comparison of
AB  - bisulfite converted sequences with the untreated genomic sequence. 'MethTools' is a
AB  - collection of software tools that replaces the time-consuming manual comparison process,
AB  - generates graphical outputs of methylation patterns and methylation density, estimates the
AB  - systematic error of the experiment and searches for conserved methylated nucleotide patterns.
AB  - The programs are written in Perl 5 and C, and the source code can be downloaded. All tools run
AB  - independently but the programs are interfaced. Thus, a script can perform the entire analysis
AB  - procedure automatically. In addition, a web-based remote analysis service is offered. Both the
AB  - source code and the remote analysis are available at http://genome.imb-jena.de/methtools/
ER  -

TY  - JOUR
AU  - Gruning, B.A.
AU  - Erxleben, A.
AU  - Hahnlein, A.
AU  - Gunther, S.
TI  - Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of  Avilamycin.
JO  - Genome Announcements
PY  - 2013
SP  - e00384
EP  - e00313
VL  - 1
AB  - Here we present the draft genome sequence of Streptomyces viridochromogenes Tu57. This strain
AB  - is a producer of avilamycin A, an oligosaccharide antibiotic from the
AB  - orthosomycin group, which is active against Gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Grunwald, S.
AU  - Driever, P.H.
AU  - Hoelzer, D.
AU  - Drahovsky, D.
TI  - Reduced methyl group acceptance of 1-beta-D-arabinofuranosylcytosine-containing DNA polymers.
JO  - Biochim. Biophys. Acta
PY  - 1988
SP  - 366
EP  - 373
VL  - 950
AB  - Previous studies have shown that 1-beta-D-arabinofuranosylcytosine (ara-C) can
AB  - induce differentiation of various malignant cells and that DNA methylation
AB  - patterns become altered under ara-C treatment of those cells.  The aim of this
AB  - study was to investigate whether this influence on DNA methylation is caused by
AB  - a direct effect of DNA-incorporated ara-C molecules on nuclear DNA methylase.
AB  - For this reason, we constructed various ara-C-substituted DNA polymers and used
AB  - them as substrates for highly purified eukaryotic DNA methylase isolated from
AB  - murine P815 mastocytoma cells.  The ara-C incorporation into DNA polymers was
AB  - measured by either an ara-C-specific radioimmunoassay or by use of
AB  - radioactive-labelled ara-C during the synthesis of those polymers.  We found an
AB  - inverse correlation between the level of ara-C substitution of the DNA polymers
AB  - and their methyl group acceptance.  Kinetic experiments performed with
AB  - ara-C-modified DNA polymers pointed out that the mode of action of DNA
AB  - methylase remains unaltered.  DNA methylase is neither detached nor fixed at an
AB  - ara-C site, but is somehow hindered in its enzymatic activity, probably by
AB  - slowing down the walking mechanism.  Hence, the previously observed
AB  - hypermethylation of DNA of some eukaryotic cells, propagated in the presence of
AB  - ara-C, is apparently not due to a direct effect of DNA-incorporated ara-C
AB  - molecules on endogenous DNA methylase.
ER  -

TY  - JOUR
AU  - Gu, H.H.
AU  - Xu, J.
AU  - Gallagher, M.
AU  - Dean, G.E.
TI  - Peptide splicing in the vacuolar ATPase subunit A from Candida tropicalis.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 7372
EP  - 7381
VL  - 268
AB  - Subunit A of the vacuolar proton pump appears to be responsible for the ATP hydrolysis which
AB  - is coupled to the pumping of protons into a variety of intracellular acid compartments,
AB  - including the fungal vacuole.  We report here the cloning and sequence determination of the
AB  - gene encoding subunit A from Candida tropicalis.  Southern blot hybridization analysis
AB  - indicates that there is a single gene which encodes this protein.  The gene contains a single
AB  - intron at the extreme 5'-end  of the coding region.  The gene is predicted to encode a
AB  - polypeptide of 1088 residues with a calculated molecular mass of 119,019 daltons, yet the
AB  - mature polypeptide appears to be approximately 67 kDa, indicating that this protein probably
AB  - undergoes the same sort of processing that is evidenced in the homologous protein from
AB  - Saccharomyces cerevisiae in which an approximately 50-kDa polypeptide (the spacer) is spliced
AB  - out of the mature protein.  The Candida gene, with and without this middle portion, has been
AB  - expressed in S. cerevisiae and found to restore a Saccharomyces subunit A deletion mutant
AB  - (tfp1-delta8) to apparently wild-type growth at pH 7.6, and normal vacuolar acidification.
AB  - The peptide sequence of the two predicted mature ends is very similar to the sequences of the
AB  - analogous proteins from Daucus carota, S. cerevisiae, and Neurospora crassa (60.5, 87.4, and
AB  - 72.9% identity, respectively), but the middle portion bears only very limited homology with
AB  - the Saccharomyces protein sequence.  Processing of the gene product occurs in S. cerevisiae,
AB  - Escherichia coli, and in rabbit reticulocyte-mediated in vitro translation, indicating that
AB  - the excision is probably autocatalytic.  The limited sequence identity seen between the
AB  - Saccharomyces and Candida spacer domains may considerably narrow the functionally important
AB  - regions responsible for the excision event.
ER  -

TY  - JOUR
AU  - Gu, J.J.
AU  - Zhou, Y.
AU  - Lu, J.J.
AU  - Ye, B.C.
TI  - Draft Genome Sequence of a Polydroxyalkanoate-Synthesizing Bacterium, Bacillus sp. Strain PJC48, Isolated from Activated Sludge.
JO  - Genome Announcements
PY  - 2017
SP  - e01751
EP  - e01716
VL  - 5
AB  - The genome sequence of a Bacillus strain is capable of synthesizing polyhydroxyalkanoates, and
AB  - Bacillus sp. is considered a platform strain for the
AB  - production of many biodegradable materials. Here, we present the sequence of the
AB  - PJC48 strain genome, which is composed of three chromatin structures, an
AB  - extracellular structure, and a cytoskeleton.
ER  -

TY  - JOUR
AU  - Gu, Y.
AU  - Yang, C.
AU  - Wang, X.
AU  - Geng, W.
AU  - Sun, Y.
AU  - Feng, J.
AU  - Wang, Y.
AU  - Quan, Y.
AU  - Che, Y.
AU  - Zhang, C.
AU  - Gong, T.
AU  - Zhang, W.
AU  - Gao, W.
AU  - Zuo, Z.
AU  - Song, C.
AU  - Wang, S.
TI  - Genome Sequence of the epsilon-Poly-l-Lysine-Producing Strain Streptomyces albulus NK660, Isolated from Soil in Gutian, Fujian Province, China.
JO  - Genome Announcements
PY  - 2014
SP  - e00532
EP  - e00514
VL  - 2
AB  - We determined the complete genome sequence of a soil bacterium, Streptomyces albulus NK660. It
AB  - can produce epsilon-poly-l-lysine, which has antimicrobial
AB  - activity against a spectrum of microorganisms. The genome of S. albulus NK660
AB  - contains a 9,360,281-bp linear chromosome and a 12,120-bp linear plasmid.
ER  -

TY  - JOUR
AU  - Gualtieri, M.
AU  - Ogier, J.C.
AU  - Pages, S.
AU  - Givaudan, A.
AU  - Gaudriault, S.
TI  - Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus szentirmaii Strain DSM16338.
JO  - Genome Announcements
PY  - 2014
SP  - e00190
EP  - e00114
VL  - 2
AB  - We report the genome sequence of Xenorhabdus szentirmaii DSM16338 (4.84 Mb), a symbiont of the
AB  - entomopathogenic nematode Steinernema rarum. This strain produces
AB  - antimicrobial activity.
ER  -

TY  - JOUR
AU  - Guan, P.
AU  - Ai, P.
AU  - Dai, X.
AU  - Zhang, J.
AU  - Xu, L.
AU  - Zhu, J.
AU  - Li, Q.
AU  - Deng, Q.
AU  - Li, S.
AU  - Wang, S.
AU  - Liu, H.
AU  - Wang, L.
AU  - Li, P.
AU  - Zheng, A.
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar Sichuansis Strain MC28.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6975
EP  - 6975
VL  - 194
AB  - Bacillus thuringiensis is an important microbial insecticide used in the control  of
AB  - agricultural pests. Here we report the finished, annotated genome sequence of
AB  - Bacillus thuringiensis serovar Sichuansis strain MC28, which can form parasporal
AB  - crystals consisting of Cry4Cc1, Cry30Fa1, Cry53Ab1, Cry54Aa1, Cry54Ab1, Cry68Aa1,
AB  - Cry69Aa1, Cry69Aa2, Cry70Ba1, Cyt1Da1, and Cyt2Aa3. It is also highly toxic to
AB  - lepidopterous and dipterous insects.
ER  -

TY  - JOUR
AU  - Guan, S.X.
AU  - Blanchard, A.
AU  - Zhang, P.H.
AU  - Zhu, Z.Y.
TI  - Alteration of Sequence Specificity of the Type IIS Restriction Endonuclease BtsI.
JO  - PLoS ONE
PY  - 2010
SP  - e11787
EP  - e11787
VL  - 5
AB  - The Type IIS restriction endonuclease BtsI recognizes and digests at GCAGTG(2/0). It comprises
AB  - two subunits: BtsIA and BtsIB. The BtsIB
AB  - subunit contains the recognition domain, one catalytic domain for
AB  - bottom strand nicking and part of the catalytic domain for the top
AB  - strand nicking. BtsIA has the rest of the catalytic domain that is
AB  - responsible for the DNA top strand nicking. BtsIA alone has no activity
AB  - unless it mixes with BtsIB to reconstitute the BtsI activity. During
AB  - characterization of the enzyme, we identified a BtsIB mutant R119A
AB  - found to have a different digestion pattern from the wild type BtsI.
AB  - After characterization, we found that BtsIB(R119A) is a novel
AB  - restriction enzyme with a previously unreported recognition sequence
AB  - CAGTG(2/0), which is named as BtsI-1. Compared with wild type BtsI,
AB  - BtsI-1 showed different relative activities in NEB restriction enzyme
AB  - reaction buffers NEB1, NEB2, NEB3 and NEB4 and less star activity.
AB  - Similar to the wild type BtsIB subunit, the BtsI-1 B subunit alone can
AB  - act as a bottom nicking enzyme recognizing CAGTG(-/0). This is the
AB  - first successful case of a specificity change among this restriction
AB  - endonuclease type.
ER  -

TY  - JOUR
AU  - Guan, W.
AU  - Shao, J.
AU  - Davis, R.E.
AU  - Zhao, T.
AU  - Huang, Q.
TI  - Genome Sequence of a Xylella fastidiosa Strain Causing Sycamore Leaf Scorch Disease in Virginia.
JO  - Genome Announcements
PY  - 2014
SP  - e00773
EP  - e00714
VL  - 2
AB  - Xylella fastidiosa causes bacterial leaf scorch in landscape trees including sycamore. We
AB  - determined the draft genome of X. fastidiosa strain Sy-Va, isolated
AB  - in Virginia from a sycamore tree displaying leaf scorch symptoms. The Sy-VA
AB  - genome contains 2,477,829 bp, and has a G+C content of 51.64 mol%.
ER  -

TY  - JOUR
AU  - Guan, W.
AU  - Shao, J.
AU  - Zhao, T.
AU  - Huang, Q.
TI  - Genome Sequence of a Xylella fastidiosa Strain Causing Mulberry Leaf Scorch Disease in Maryland.
JO  - Genome Announcements
PY  - 2014
SP  - e00916
EP  - e00913
VL  - 2
AB  - Xylella fastidiosa causes bacterial leaf scorch in landscape trees, including mulberry. We
AB  - determined the draft genome of the mulberry strain Mul-MD in order
AB  - to gain a better understanding of the molecular basis of strain divergence, host
AB  - specificity, nutrient requirements, and pathogenicity, as well as to develop
AB  - genome-based specific detection methods.
ER  -

TY  - JOUR
AU  - Guan, Y.
AU  - Ngugi, D.K.
AU  - Blom, J.
AU  - Ali, S.
AU  - Ferry, J.G.
AU  - Stingl, U.
TI  - Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment.
JO  - Genome Announcements
PY  - 2014
SP  - e01184
EP  - e01114
VL  - 2
AB  - Methanococcoides methylutens, the type species of the genus Methanococcoides, is  a slightly
AB  - halophilic methanogenic archaeon with a methylotrophic metabolism.
AB  - Here, we present the annotated draft genome sequence of M. methylutens, which
AB  - comprises 2,508,511 bp with 2,482 coding sequences, 51 tRNA genes, and a G+C
AB  - content of 42.5%.
ER  -

TY  - JOUR
AU  - Guard, J.
AU  - Cao, G.
AU  - Kastanis, G.J.
AU  - Davison, S.
AU  - McClelland, M.
AU  - Sanchez, L.M.
AU  - Zheng, J.
AU  - Brown, E.
AU  - Allard, M.W.
TI  - Draft Genome Sequences of 64 Salmonella enterica Serotype Enteritidis Isolates Obtained from Wild Mice.
JO  - Genome Announcements
PY  - 2017
SP  - e00953
EP  - e00917
VL  - 5
AB  - Salmonella enterica serotype Enteritidis is a foodborne pathogen of global concern, because it
AB  - is frequently isolated from foods and patients. Draft genome
AB  - sequences are reported here for 64 S Enteritidis strains isolated from the
AB  - intestines and spleens of mice caught live on chicken farms in the U.S.
AB  - Northeast. The availability of these genomes provides baseline information on the
AB  - genomic diversity of S Enteritidis during the 1990s, when foodborne outbreaks
AB  - traced to internal contamination of eggs were prevalent.
ER  -

TY  - JOUR
AU  - Guardiola-Avila, I.
AU  - Acedo-Felix, E.
AU  - Noriega-Orozco, L.
AU  - Yepiz-Plascencia, G.
AU  - Sifuentes-Romero, I.
AU  - Gomez-Gil, B.
TI  - Draft Genome Sequence of Vibrio mimicus Strain CAIM 602T.
JO  - Genome Announcements
PY  - 2013
SP  - e0008413
EP  - e0008413
VL  - 1
AB  - Vibrio mimicus is a Gram-negative bacterium associated with gastrointestinal diseases in
AB  - humans around the world. We report the complete genome sequence of
AB  - the Vibrio mimicus strain CAIM 602(T) (CDC1721-77, LMG 7896(T), ATCC 33653(T)).
ER  -

TY  - JOUR
AU  - Guarischi-Sousa, R.
AU  - Puigvert, M.
AU  - Coll, N.S.
AU  - Siri, M.I.
AU  - Pianzzola, M.J.
AU  - Valls, M.
AU  - Setubal, J.C.
TI  - Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 7
EP  - 7
VL  - 11
AB  - Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia
AB  - solanacearum strain UY031 belongs to the American phylotype IIB,
AB  - sequevar 1, also classified as race 3 biovar 2. Here we report the completely
AB  - sequenced genome of this strain, the first complete genome for phylotype IIB,
AB  - sequevar 1, and the fourth for the R. solanacearum species complex. In addition
AB  - to standard genome annotation, we have carried out a curated annotation of type
AB  - III effector genes, an important pathogenicity-related class of genes for this
AB  - organism. We identified 60 effector genes, and observed that this effector
AB  - repertoire is distinct when compared to those from other phylotype IIB strains.
AB  - Eleven of the effectors appear to be nonfunctional due to disruptive mutations.
AB  - We also report a methylome analysis of this genome, the first for a R.
AB  - solanacearum strain. This analysis helped us note the presence of a toxin gene
AB  - within a region of probable phage origin, raising the hypothesis that this gene
AB  - may play a role in this strain's virulence.
ER  -

TY  - JOUR
AU  - Gubler, M.
AU  - Bickle, T.A.
TI  - Increased protein flexibility leads to promiscuous protein-DNA interactions in type IC restriction-modification systems.
JO  - EMBO J.
PY  - 1991
SP  - 951
EP  - 957
VL  - 10
AB  - We have investigated the role of a four amino acid element that is repeated twice and three
AB  - times, respectively, in the specificity polypeptides of the two allelic
AB  - restriction-modification systems EcoR124 and EcoR124/3. We had earlier shown that this
AB  - difference in amino acid sequence between the two systems is solely responsible for the
AB  - different DNA sequence specificities of the two systems. The effect of single amino acid
AB  - substitutions and small insertion and deletion mutations on restriction activity and
AB  - modification specificity was determined in vivo by phage infection assays and in vitro by
AB  - methylation of DNA with purified modification methylases. Mutant restriction-modification
AB  - systems with changes in the number and the length of the central amino acid repeats exhibited
AB  - decreased restriction activity and in some cases relaxed substrate specificity. Our data
AB  - strongly support the idea that the repetitive amino acid motif in the specificity polypeptides
AB  - forms part of a flexible interdomain linker. It may be responsible for positioning on the DNA
AB  - the two major specificity polypeptide domains which are thought to contact independently the
AB  - half sites of the split recognition sequences typical for all type I restriction-modification
AB  - systems.
ER  -

TY  - JOUR
AU  - Gubler, M.
AU  - Braguglia, D.
AU  - Meyer, J.
AU  - Piekarowicz, A.
AU  - Bickle, T.A.
TI  - Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes.
JO  - EMBO J.
PY  - 1992
SP  - 233
EP  - 240
VL  - 11
AB  - EcoR124I and EcoDXXI are allelic type I restriction-modification (R-M) systems
AB  - whose specificity genes consist of common structural elements: two variable
AB  - regions are separated by a constant, homologous region containing a number of
AB  - repetitive sequence elements.  In vitro recombination of variable and constant
AB  - elements has led to fully active, hybrid R-M systems exhibiting new and
AB  - predictable target site specificities.  Methylation of synthetic DNA sequences
AB  - with purified, hybrid modification methylases was used to confirm the proposed
AB  - recognition sequences.  The results clearly demonstrate the correlation between
AB  - protein domains and target site specificity.  Our data suggest that a bacterial
AB  - population may switch the recognition sequences of its type I R-M system by
AB  - single recombination events and thus is able to maintain a prokaryotic analogue
AB  - of the immune system of variable specificity.
ER  -

TY  - JOUR
AU  - Gueddou, A.
AU  - Swanson, E.
AU  - Ktari, A.
AU  - Nouioui, I.
AU  - Hezbri, K.
AU  - Ghodhbane-Gtari, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Sen, A.
AU  - Gtari, M.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical,  Noninfective, Ineffective Isolates.
JO  - Genome Announcements
PY  - 2017
SP  - e00174
EP  - e00117
VL  - 5
AB  - Here, we present draft genome sequences for three atypical Frankia strains (lineage 4) that
AB  - were isolated from root nodules but are unable to reinfect
AB  - actinorhizal plants. The genome sizes of Frankia sp. strains EUN1h, BMG5.36, and
AB  - NRRL B16386 were 9.91, 11.20, and 9.43 Mbp, respectively.
ER  -

TY  - JOUR
AU  - Guedon, E.
AU  - Delorme, C.
AU  - Pons, N.
AU  - Cruaud, C.
AU  - Loux, V.
AU  - Couloux, A.
AU  - Gautier, C.
AU  - Sanchez, N.
AU  - Layec, S.
AU  - Galleron, N.
AU  - Almeida, M.
AU  - van de Guchte, M.
AU  - Kennedy, S.P.
AU  - Ehrlich, S.D.
AU  - Gibrat, J.F.
AU  - Wincker, P.
AU  - Renault, P.
TI  - Complete Genome Sequence of the commensal Streptococcus salivarius strain JIM8777.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5024
EP  - 5025
VL  - 193
AB  - The commensal bacterium Streptococcus salivarius is a prevalent species of the human
AB  - oropharyngeal tract with an important role in oral ecology.
AB  - Here, we report the complete 2.2-Mb genome sequence and annotation of
AB  - strain JIM8777, which was recently isolated from the oral cavity of a
AB  - healthy, dentate infant.
ER  -

TY  - JOUR
AU  - Gueimonde, M.
AU  - Bottacini, F.
AU  - van Sinderen, D.
AU  - Ventura, M.
AU  - Margolles, A.
AU  - Sanchez, B.
TI  - Genome Sequence of Parascardovia denticolens IPLA 20019, Isolated from Human Breast Milk.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4776
EP  - 4777
VL  - 194
AB  - This work describes the draft genome of Parascardovia denticolens IPLA 20019, isolated from
AB  - human milk. This species, usually isolated from caries lesions, is
AB  - taxonomically related to the genus Bifidobacterium. The genetic information of
AB  - IPLA 20019 enhances our understanding of the adaptation of this P. denticolens
AB  - strain from human breast milk.
ER  -

TY  - JOUR
AU  - Gueimonde, M.
AU  - Ventura, M.
AU  - Margolles, A.
AU  - Sanchez, B.
TI  - Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6997
EP  - 6997
VL  - 194
AB  - In this work, we report the genome sequences of Bifidobacterium bifidum strain LMG13195.
AB  - Results from our research group show that this strain is able to
AB  - interact with human immune cells, generating functional regulatory T cells.
ER  -

TY  - JOUR
AU  - Guellerin, M.
AU  - Passerini, D.
AU  - Fontagne-Faucher, C.
AU  - Robert, H.
AU  - Gabriel, V.
AU  - Loux, V.
AU  - Klopp, C.
AU  - Le Loir, Y.
AU  - Coddeville, M.
AU  - Daveran-Mingot, M.L.
AU  - Ritzenthaler, P.
AU  - Le Bourgeois, P.
TI  - Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough.
JO  - Genome Announcements
PY  - 2016
SP  - e00692
EP  - e00616
VL  - 4
AB  - We report here the complete genome sequence of Lactococcus lactis subsp. lactis strain A12, a
AB  - strain isolated from sourdough. The circular chromosome and the
AB  - four plasmids reveal genes involved in carbohydrate metabolism that are
AB  - potentially required for the persistence of this strain in such a complex
AB  - ecosystem.
ER  -

TY  - JOUR
AU  - Guenthner, C.
AU  - Kim, S.
AU  - Bednarik, D.P.
TI  - Cloning, isolation, and characterization of the human T-cell DNA-cytosine 5-methyltransferase gene.
JO  - J. Cell Biochem. Suppl.
PY  - 1992
SP  - 179
EP  - 179
VL  - 16E
AB  - DNA methylation can affect the latency of HIV and HTLV by effectively silencing
AB  - transcriptional expression. Previous studies have shown that a CpG island in the HIV LTR, when
AB  - methylated by the human DNA-cytosine 5-methyltransferase (MeTase), inactivates HIV
AB  - transcription in cis. Further characterization of the methyltransferase enzyme is therefore of
AB  - obvious interest. A human T-cell cDNA library from the cell line Jurkatt has been screened,
AB  - using a murine DNA methyltransferase cDNA clone as a probe, and a clone of approximately 0.7
AB  - Kb has been isolated (pMET2) and sequenced with 87% homology to an area in the 3' region of
AB  - the murine cDNA. Based on the size of the mature protein (-172 Kdaltons), a gene of at least 5
AB  - Kb is expected. Southern blot analysis of human genomic DNA yielded single fragments of 4.2 Kb
AB  - to over 12 Kb, using the pMET2 fragment as a probe. Northern blot analysis has been employed
AB  - to analyze transcriptional expression, and to determine the size of the methyltranferase
AB  - message. A human genomic library has been screened and four putative clones isolated and shown
AB  - positive by PCR analysis, using primers to pMET2. Southern analysis on phage DNA digested with
AB  - XbaI yields fragments large enough to include a full-length copy of the gene. Sub-cloning into
AB  - an expression vector is underway in order to obtain sequence information, and to further
AB  - characterize this gene.
ER  -

TY  - JOUR
AU  - Guerrero, L.D.
AU  - Makhalanyane, T.P.
AU  - Aislabie, J.M.
AU  - Cowan, D.A.
TI  - Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica.
JO  - Genome Announcements
PY  - 2014
SP  - e01230
EP  - e01213
VL  - 2
AB  - Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first
AB  - draft genome of a member of the genus Williamsia (strain D3) isolated
AB  - from Antarctic soil. The genome of this psychrotolerant bacterium may help to
AB  - elucidate crucial survival mechanisms for organisms inhabiting cold desert soil
AB  - systems.
ER  -

TY  - JOUR
AU  - Guerrero-Araya, E.
AU  - Plaza-Garrido, A.
AU  - Diaz-Yanez, F.
AU  - Pizaro-Guajardo, M.
AU  - Valenzuela, S.L.
AU  - Meneses, C.
AU  - Gil, F.
AU  - Castro-Nallar, E.
AU  - Paredes-Sabja, D.
TI  - Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficile.
JO  - Genome Announcements
PY  - 2016
SP  - e01178
EP  - e01116
VL  - 4
AB  - Clostridium paraputrificum is a gut microbiota member reported in several cases of bacteremia
AB  - and coinfections. So far, only one genome sequence of a C.
AB  - paraputrificum (AGR2156) isolate is available. Here, we present the draft genome
AB  - of C. paraputrificum strain 373-A1, isolated from stools from a patient with C.
AB  - difficile infection.
ER  -

TY  - JOUR
AU  - Guha, S.
TI  - Determination of DNA Sequences Containing Methylcytosine in Bacillus subtilis Marburg.
JO  - J. Bacteriol.
PY  - 1985
SP  - 573
EP  - 579
VL  - 163
AB  - The methylcytosine-containing sequences in the DNA of Bacillus subtilis 168
AB  - Marburg (Restriction-modification Type BSUM) were determined by three different
AB  - methods: (i) examination of in vivo-methylated DNA by restriction enzyme
AB  - digestion and, whenever possible, analysis for methycytosine at the 5' end;
AB  - (ii) methylation in vitro of unmethylated DNA with B. subtilis DNA
AB  - methyltransferase and determination of the methylated sites; and (iii) the
AB  - methylatability of unmethylated DNA by B. subtilis methyltransferase after
AB  - potential sites have been destroyed by digestion with restriction
AB  - endonucleases.  The results obtained by these methods, taken together, show
AB  - that methylcytosine was present only within the sequence 5'-TCGA-3'.  The
AB  - presence of methylcytosine at the 5' end of the DNA fragments generated by
AB  - restriction endonuclease AsuII digestion and the fact that in vivo-methylated
AB  - DNA could not be digested by the enzyme XhoI showed that the recognition
AB  - sequences of these two enzymes contained methylcytosine.  As these two enzymes
AB  - recognized a similar sequence containing a 5' pyrimidine (Py) and a 3' purine
AB  - (pu), 5'-PyTCGAPu'3', the possibility that methylcytosine is present in the
AB  - complementary sequences 5'TTCGAG-3' and 5'CTCGAA-3' was postulated.  This was
AB  - verified by the methylation in vitro, with B. subtilis enzyme, of a
AB  - 2.6-kilobase fragment of lambda DNA containing two such sites and devoid of
AB  - AsuII or XhoI recognition sequences.  By analyzing the methylatable sites, it
AB  - was found that in one of the two PyTCGAPu sequences, cytosine was methylated in
AB  - vitro in both DNA strands.  It is concluded that the sequence 5'-PyTCGAPu'3' is
AB  - methylated by the DNA methyltransferase (of cytosine) of B. subtilis Marburg.
ER  -

TY  - JOUR
AU  - Guha, S.
TI  - DNA methyltransferase of Bacillus subtilis Marburg:  purification, properties and further evidence of specificity.
JO  - Gene
PY  - 1988
SP  - 77
EP  - 81
VL  - 74
AB  - Bacillus subtilis Marburg strain displays DNA methyltransferase activity. This enzyme, M.BsuM,
AB  - methylates cytosine in the sequence 5'-YTCGAR-3' (Y=pyrimidine; R=purine). M.BsuM was
AB  - purified from exponentially growing cells of B. subtilis 168M. This enzyme (45+/- 1 kDa) is
AB  - monomeric and recognizes only double-stranded DNA. It is inhibited partially by Mg2+, Mn2+
AB  - ions and spermidine and almost totally by sodium dodecyl sulfate, urea and agarose. This
AB  - enzyme methylates specifically the three methylatable sites of the plasmid pBM3. Relaxation of
AB  - specificity (star activity) was observed in the presence of organic solvents. A very low
AB  - amount of M.BsuM was obtained in the standard Marburg strain. To obtain sufficient enzyme
AB  - attempts are being made to clone the M.BsuM gene in Escherichia coli by using a constructed
AB  - plasmid (pBM14) vector. Only one transformant containing a 3-kb insert and showing a low level
AB  - of expression, was obtained.
ER  -

TY  - JOUR
AU  - Guha, S.
AU  - Guschlbauer, W.
TI  - Expression of Escherichia coli dam gene in Bacillus subtilis provokes DNA damage response: N6-methyladenine is removed by two repair pathways.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3607
EP  - 3615
VL  - 20
AB  - The dam gene of Excherichia coli encodes a DNA methyltransferase that methylates the N6
AB  - position of adenine in the sequence GATC. It was stably expressed from a shuttle vector in a
AB  - repair- and recombination-proficient strain of Bacillus subtilis. In this strain the majority
AB  - of plasmid DNA molecules was modified at dam sites whereas most chromosomal DNA remained
AB  - unmethylated during exponential growth. During stationary phase the amount of unmethylated DNA
AB  - increased, suggesting that methylated bases were being removed. An ultraviolet damage
AB  - repair-deficient mutant (uvrB) contained highly methylated chromosomal and plasmid DNA. High
AB  - levels of Dam methylation were detrimental to growth and viability of this mutant strain and
AB  - some features of the SOS response were also induced. A mutant defective in the synthesis of
AB  - adaptive DNA alkyltransferases and induction of the adaptive response (ada) also showed high
AB  - methylation and properties similar to that of the dam gene expressing uvrB strain. When
AB  - protein extracts from B. subtilis expressing the Dam methyltransferase or treated with
AB  - N-methyl-N-nitro-N-nitroso-guanidine were incubated with [3H]-labelled Dam methylated DNA, the
AB  - methyl label was bound to two proteins of 14 and 9 kD. Some free N6-methyladenine residues are
AB  - excised by proteins involved in both excision (uvrB) and the adaptive response (ada) DNA
AB  - repair pathways in B. subtilis.
ER  -

TY  - JOUR
AU  - Guha, S.
AU  - Guschlbauer, W.
TI  - Improved plasmids containing the Escherichia coli dam gene under the control of the tac promoter.
JO  - Biochim. Biophys. Acta
PY  - 1992
SP  - 309
EP  - 310
VL  - 1132
AB  - We report the construction of a series of plasmids containing the dam gene under the control
AB  - of the tac promoter. Cells containing these plasmids produce about 8 to 10-fold more Dam
AB  - methyltransferase (Mtase) than the previously used plasmid pTP166 and avoid the use of a high
AB  - temperature step necessary for the expression of Dam Mtase in the plasmid pDOX1 and thus
AB  - allows its use for the study of thermosensitive mutants.
ER  -

TY  - JOUR
AU  - Guhan, N.
AU  - Muniyappa, K.
TI  - The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites: Implications for the dispersal of inteins in natural populations.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 40352
EP  - 40361
VL  - 277
AB  - The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease,
AB  - requires both Mn2+ and ATP for efficient cleavage of the inteinless recA allele. In this
AB  - study, we show that Mg2+ alone was sufficient to stimulate PI-MtuI to cleave double-stranded
AB  - DNA at ectopic sites. In the absence of Mg2+, PI-MtuI formed complexes with topologically
AB  - different forms of DNA containing ectopic recognition sequences with equal affinity but failed
AB  - to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly
AB  - within the ectopic recognition sequence to generate either a blunt end or 1-2 nucleotide
AB  - 3'-hydroxyl overhangs. Mutational analyses of the presumptive metal-ion binding ligands
AB  - (D122, D222 and E220) together with immunoprecipitation assays provided compelling evidence to
AB  - link both the Mg2+- and Mn2+ and ATP-dependent endonuclease activities to PI-MtuI. The kinetic
AB  - mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential
AB  - mechanism with transient accumulation of nicked circular duplex DNA as an intermediate.
AB  - Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA
AB  - transposition and hence its lateral transfer in natural populations.
ER  -

TY  - JOUR
AU  - Guhan, N.
AU  - Muniyappa, K.
TI  - Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn2+ and DNA-dependent ATPase activity.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 4184
EP  - 4191
VL  - 31
AB  - Mycobacterium tuberculosis RecA intein (PI-MtuI), a LAGLIDADG homing endonuclease, displays
AB  - dual target specificity in response to alternative
AB  - cofactors. While both ATP and Mn(2+) were required for optimal cleavage of
AB  - an inteinless recA allele (hereafter referred to as cognate DNA), Mg(2+)
AB  - alone was sufficient for cleavage of ectopic DNA sites. In this study, we
AB  - have explored the ability of PI-MtuI to catalyze ATP hydrolysis in the
AB  - presence of alternative metal ion cofactors and DNA substrates. Our
AB  - results indicate that PI-MtuI displays maximum ATPase activity in the
AB  - presence of cognate but not ectopic DNA. Kinetic analysis revealed that
AB  - Mn(2+) was able to stimulate PI-MtuI catalyzed ATP hydrolysis, whereas
AB  - Mg(2+) failed to do so. Using UV crosslinking, limited proteolysis and
AB  - amino acid sequence analysis, we show that (32)P-labeled ATP was bound to
AB  - a 14 kDa peptide containing the putative Walker A motif. Furthermore, the
AB  - limited proteolysis approach disclosed that cognate DNA was able to induce
AB  - structural changes in PI-MtuI. Mutation of the presumptive metal
AB  - ion-binding ligands (Asp122 and Asp222) in the LAGLIDADG motifs of PI-MtuI
AB  - impaired its affinity for ATP, thus resulting in a reduction in or loss of
AB  - its endonuclease activity. Together, these results suggest that PI-MtuI is
AB  - a (cognate) DNA- and Mn(2+)-dependent ATPase, unique from the LAGLIDADG
AB  - family of homing endonucleases, and implies a possible role for ATP
AB  - hydrolysis in the recognition and/or cleavage of homing site DNA sequence.
ER  -

TY  - JOUR
AU  - Guhan, N.
AU  - Muniyappa, K.
TI  - Mycobacterium tuberculosis RecA intein possesses a novel ATP-dependent site-specific double-stranded DNA endonuclease activity.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 16257
EP  - 16264
VL  - 277
AB  - Mycobacterium tuberculosis recA harbors an intervening sequence in its open reading frame,
AB  - presumed to encode an endonuclease (PI-MtuI) required for intein homing in inteinless recA
AB  - allele. Although the protein-splicing ability of PI-MtuI has been characterized, the
AB  - identification of its putative endonuclease activity has remained elusive. To investigate
AB  - whether PI-MtuI possesses endonuclease activity, recA intervening sequence was cloned,
AB  - overexpressed, and purified to homogeneity. Here we show that PI-MtuI bound both single- and
AB  - double-stranded DNA with similar affinity but failed to cleave DNA in the absence of
AB  - cofactors. Significantly, PI-MtuI nicked supercoiled DNA in the presence of alternative
AB  - cofactors but required both Mn2+ and ATP to generate linear double-stranded DNA. We observed
AB  - that PI-MtuI was able to inflict a staggered double-strand break 24 bp upstream of the
AB  - insertion site in the inteinless recA allele. Similar to a few homing endonucleases, DNA
AB  - cleavage by PI-MtuI was specific with an exceptionally long cleavage site spanning 22 bp. The
AB  - kinetic mechanism of PI-MtuI promoted cleavage supports a sequential rather than concerted
AB  - pathway of strand cleavage with the formation of nicked double-stranded DNA as an
AB  - intermediate. Together, these results reveal that RecA intein is a novel Mn2+-ATP-dependent
AB  - double-strand specific endonuclease, which is likely to be important for homing process in
AB  - vivo.
ER  -

TY  - JOUR
AU  - Guhan, N.
AU  - Muniyappa, K.
TI  - Structural and functional characteristics of homing endonucleases.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 2003
SP  - 199
EP  - 248
VL  - 38
AB  - Mobile genetic elements constitute a remarkably diverse group of nonessential selfish genes
AB  - that provide no apparent function to the host.
AB  - These selfish genes have been implicated in host extinction, speciation
AB  - and architecture of genetic systems. Homing endonucleases, encoded by the
AB  - open reading frames embedded in introns or inteins of mobile genetic
AB  - elements, possess double-stranded DNA-specific endonuclease activity. They
AB  - inflict sequence-specific double-strand breaks at or near the homing site
AB  - in intron- or intein-less allele. Subsequently, through nonreciprocal
AB  - exchange the insertion sequence (intron or intein) is transferred from an
AB  - intein- or intron-containing allele to an intein- or intron-less allele.
AB  - The components of host double-strand break repair pathway are thought to
AB  - finish the "homing" process. Several lines of evidence suggest that homing
AB  - endonucleases are capable of promoting transposition into ectopic sites
AB  - within or across genomes for their survival as well as dispersal in
AB  - natural populations. The occurrence of inteins at high frequencies serves
AB  - as instructive models for understanding the mechanistic aspects of the
AB  - process of homing and its evolution. This review focuses on genetic,
AB  - biochemical, structural, and phylogenetic aspects of homing endonucleases,
AB  - and their comparison with restriction endonucleases.
ER  -

TY  - JOUR
AU  - Guida, B.S.
AU  - Garcia-Pichel, F.
TI  - Draft Genome Assembly of a Filamentous Euendolithic (True Boring) Cyanobacterium, Mastigocoleus testarum Strain BC008.
JO  - Genome Announcements
PY  - 2016
SP  - e01574
EP  - e01515
VL  - 4
AB  - Mastigocoleus testarum strain BC008 is a model organism used to study marine photoautotrophic
AB  - carbonate dissolution. It is a multicellular, filamentous,
AB  - diazotrophic, euendolithic cyanobacterium ubiquitously found in marine benthic
AB  - environments. We present an accurate draft genome assembly of 172 contigs
AB  - spanning 12,700,239 bp with 9,131 annotated genes with an average G+C% of 37.3.
ER  -

TY  - JOUR
AU  - Guild, W.R.
AU  - Smith, M.D.
AU  - Shoemaker, N.B.
TI  - Conjugative transfer of chromosomal R determinants in Streptococcus pneumoniae.
JO  - Microbiology-1982
PY  - 1982
SP  - 88
EP  - 92
VL  - 0
ER  -

TY  - JOUR
AU  - Guilhen, C.
AU  - Iltis, A.
AU  - Forestier, C.
AU  - Balestrino, D.
TI  - Genome Sequence of a Clinical Klebsiella pneumoniae Sequence Type 6 Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01311
EP  - e01315
VL  - 3
AB  - We report here the genome sequence of Klebsiella pneumoniae CH1034, a sequence type 6 (ST6)
AB  - strain isolated in 2012 from a central venous catheter of a
AB  - hospitalized patient.
ER  -

TY  - JOUR
AU  - Guillen, Y.
AU  - Casadella, M.
AU  - Garcia-de-la-Guarda, R.
AU  - Espinoza-Culupu, A.
AU  - Paredes, R.
AU  - Ruiz, J.
AU  - Noguera-Julian, M.
TI  - Whole-Genome Sequencing of Two Bartonella bacilliformis Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e00659
EP  - e00616
VL  - 4
AB  - Bartonella bacilliformis is the causative agent of Carrion's disease, a highly endemic human
AB  - bartonellosis in Peru. We performed a whole-genome assembly of two
AB  - B. bacilliformis strains isolated from the blood of infected patients in the
AB  - acute phase of Carrion's disease from the Cusco and Piura regions in Peru.
ER  -

TY  - JOUR
AU  - Guillen-Nepita, A.L.
AU  - Negrete-Paz, A.M.
AU  - Vazquez-Marrufo, G.
AU  - Cruz-Hernandez, A.
AU  - Fresia, P.
AU  - Naya, H.
AU  - Vazquez-Garciduenas, M.S.
TI  - Sequencing and Annotation of the Genome of Mycobacterium tuberculosis MYC004, a Strain Causing Meningitis in Mexico.
JO  - Genome Announcements
PY  - 2018
SP  - e00523
EP  - e00518
VL  - 6
AB  - Mycobacterium tuberculosis strain MYC004 was isolated from a Mexican patient with tuberculous
AB  - meningitis, the most aggressive form of tuberculosis. The draft
AB  - genome sequence is the first of a meningeal strain of M. tuberculosis reported
AB  - from Latin America and consists of 4,411,530 bp, including 4,251 protein-encoding
AB  - genes.
ER  -

TY  - JOUR
AU  - Guimaraes, A.M.
AU  - Toth, B.
AU  - Santos, A.P.
AU  - do Nascimento, N.C.
AU  - Kritchevsky, J.E.
AU  - Messick, J.B.
TI  - Genome Sequence of 'Candidatus Mycoplasma haemolamae' Strain Purdue, a Red Blood  Cell Pathogen of Alpacas (Vicugna pacos) and Llamas (Lama glama).
JO  - J. Bacteriol.
PY  - 2012
SP  - 6312
EP  - 6313
VL  - 194
AB  - We report the complete genome sequence of 'Candidatus Mycoplasma haemolamae,' an  endemic
AB  - red-cell pathogen of camelids. The single, circular chromosome has
AB  - 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great
AB  - proportion (49.1%) of these CDSs are organized into paralogous gene families,
AB  - which can now be further explored with regard to antigenic variation.
ER  -

TY  - JOUR
AU  - Guimaraes, A.M.
AU  - Zimpel, C.K.
AU  - Ikuta, C.Y.
AU  - do Nascimento, N.C.
AU  - Dos Santos, A.P.
AU  - Messick, J.B.
AU  - Heinemann, M.B.
AU  - Ferreira, N.J.S.
AU  - Brandao, P.E.
TI  - Draft Genome Sequence of Mycobacterium bovis Strain SP38, a Pathogenic Bacterium  Isolated from a Bovine in Brazil.
JO  - Genome Announcements
PY  - 2015
SP  - e00511
EP  - e00515
VL  - 3
AB  - We report a draft genome sequence of Mycobacterium bovis strain SP38, isolated from the lungs
AB  - of a cow in Brazil. The assembly of reads resulted in 36 contigs
AB  - in a total of approximately 4.37 Mb. Comparison of M. bovis strains sequenced to
AB  - date will aid in understanding bovine tuberculosis in Brazil.
ER  -

TY  - JOUR
AU  - Guimaraes, L.C.
AU  - Soares, S.C.
AU  - Albersmeier, A.
AU  - Blom, J.
AU  - Jaenicke, S.
AU  - Azevedo, V.
AU  - Soriano, F.
AU  - Tauch, A.
AU  - Trost, E.
TI  - Complete Genome Sequence of Corynebacterium urealyticum Strain DSM 7111, Isolated from a 9-Year-Old Patient with Alkaline-Encrusted Cystitis.
JO  - Genome Announcements
PY  - 2013
SP  - e00264
EP  - e00213
VL  - 1
AB  - Corynebacterium urealyticum is a common skin colonizer with potent urease activity. It is
AB  - clinically recognized as an opportunistic pathogen causing
AB  - urinary tract infections. The annotated genome sequence of strain DSM 7111,
AB  - isolated from the urine of a young boy with an ectopic kidney, provides new
AB  - insights into the pathomechanisms of this bacterium.
ER  -

TY  - JOUR
AU  - Guimaraes, L.C.
AU  - Viana, M.V.
AU  - Benevides, L.J.
AU  - Mariano, D.C.
AU  - Veras, A.A.
AU  - Sa, P.H.
AU  - Rocha, F.S.
AU  - Vilas, B.P.C.
AU  - Soares, S.C.
AU  - Barbosa, M.S.
AU  - Guiso, N.
AU  - Badell, E.
AU  - Azevedo, V.
AU  - Ramos, R.T.
AU  - Silva, A.
TI  - Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 03-8664 Isolated from a Human Throat.
JO  - Genome Announcements
PY  - 2016
SP  - e00719
EP  - e00716
VL  - 4
AB  - Corynebacterium ulcerans is an emergent pathogen infecting wild and domesticated  animals
AB  - worldwide that may serve as reservoirs for zoonotic infections. In this
AB  - study, we present the draft genome of C. ulcerans strain 03-8664. The draft
AB  - genome has 2,428,683 bp, 2,262 coding sequences, and 12 rRNA genes.
ER  -

TY  - JOUR
AU  - Guimaraes, L.C.
AU  - Viana, M.V.
AU  - Benevides, L.J.
AU  - Mariano, D.C.
AU  - Veras, A.A.
AU  - Sa, P.H.
AU  - Rocha, F.S.
AU  - Vilas, B.P.C.
AU  - Soares, S.C.
AU  - Barbosa, M.S.
AU  - Guiso, N.
AU  - Badell, E.
AU  - Carneiro, A.R.
AU  - Azevedo, V.
AU  - Ramos, R.T.
AU  - Silva, A.
TI  - Draft Genome Sequence of Corynebacterium ulcerans Strain 04-3911, Isolated from Humans.
JO  - Genome Announcements
PY  - 2016
SP  - e00171
EP  - e00116
VL  - 4
AB  - Corynebacterium ulceransis a pathogenic bacterium infecting wild and domesticated animals;
AB  - some infection cases in humans have increased throughout the world. The
AB  - current study describes the draft genome of strain 04-3911, isolated from humans.
AB  - The draft genome has 2,492,680 bp, 2,143 coding sequences, 12 rRNA genes, and 50
AB  - tRNA genes.
ER  -

TY  - JOUR
AU  - Guimaraes, L.C.
AU  - Viana, M.V.
AU  - Benevides, L.J.
AU  - Mariano, D.C.
AU  - Veras, A.A.
AU  - Sa, P.H.
AU  - Rocha, F.S.
AU  - Vilas, B.P.C.
AU  - Soares, S.C.
AU  - Barbosa, M.S.
AU  - Guiso, N.
AU  - Badell, E.
AU  - Carneiro, A.R.
AU  - Azevedo, V.
AU  - Ramos, R.T.
AU  - Silva, A.
TI  - Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France.
JO  - Genome Announcements
PY  - 2016
SP  - e00172
EP  - e00116
VL  - 4
AB  - Here, we present the draft genome of toxigenicCorynebacterium ulceransstrain 04-7514. The
AB  - draft genome has 2,497,845 bp, 2,059 coding sequences, 12 rRNA
AB  - genes, 46 tRNA genes, 150 pseudogenes, 1 clustered regularly interspaced short
AB  - palindromic repeat (CRISPR) array, and a G+C content of 53.50%.
ER  -

TY  - JOUR
AU  - Guimaraes, P.I.
AU  - Leao, T.F.
AU  - de Melo, A.G.
AU  - Ramos, R.T.
AU  - Silva, A.
AU  - Fiore, M.F.
AU  - Schneider, M.P.
TI  - Draft Genome Sequence of the Picocyanobacterium Synechococcus sp. Strain GFB01, Isolated from a Freshwater Lagoon in the Brazilian Amazon.
JO  - Genome Announcements
PY  - 2015
SP  - e00876
EP  - e00815
VL  - 3
AB  - We present the draft genome of the cyanobacterium strain Synechococcus sp. GFB01, the first
AB  - genome sequencing of this genus isolated from South America. This draft
AB  - genome consists of 125 contigs with a total size of 2,339,812 bp. Automatic
AB  - annotation identified several genes involved with heavy metal resistance and
AB  - natural transformation.
ER  -

TY  - JOUR
AU  - Guimont, C.
AU  - Henry, P.
AU  - Linden, G.
TI  - Restriction/modification in Streptococcus thermophilus: isolation and characterization of a type II restriction endonuclease Sth455I.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1993
SP  - 216
EP  - 220
VL  - 39
AB  - Streptococcus thermophilus strain CNRZ 455 produces a type II restriction endonuclease
AB  - designated Sth455I. This enzyme was isolated from cell extracts by anionic and cationic
AB  - exchange chromatography. This yielded an enzyme preparation free of non-specific nucleases.
AB  - The optimal reaction conditions for Sth455I are: MgCl2, 30 mM; pH range, 8-9; incubation
AB  - temperature, 37-40oC; and high NaCl concentration, 100-200 mM. The results of single- and
AB  - double-digestion experiments indicates that Sth455I is an isoschizomer of BstNI and EcoRII
AB  - showing different sensitivity to methylation The enzyme exhibits restriction activity on the
AB  - DNA of three bacteriophages of S. thermophilus and no activity on the phage lytic for strain
AB  - CNRZ 455. The restriction/modification system associated with this strain is discussed.
ER  -

TY  - JOUR
AU  - Guinane, C.M.
AU  - Barrett, E.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
AU  - Ross, R.P.
AU  - Stanton, C.
TI  - Genome Sequence of Bifidobacterium breve DPC 6330, a Strain Isolated from the Human Intestine.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6799
EP  - 6800
VL  - 193
AB  - The draft genome of Bifidobacterium breve DPC 6330, isolated from an elderly patient, was
AB  - determined. B. breve DPC 6330 was previously
AB  - identified to synthesize the beneficial metabolite conjugated linoleic
AB  - acid from free linoleic acid. The sequence will allow identification and
AB  - characterization of the genetic determinants of its putative beneficial
AB  - properties.
ER  -

TY  - JOUR
AU  - Guinane, C.M.
AU  - Kent, R.M.
AU  - Norberg, S.
AU  - Hill, C.
AU  - Fitzgerald, G.F.
AU  - Stanton, C.
AU  - Ross, R.P.
TI  - Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms.
JO  - PLoS ONE
PY  - 2011
SP  - e18740
EP  - e18740
VL  - 6
AB  - Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and
AB  - niche adaptation. We sequenced and annotated
AB  - the genome of Lactobacillus johnsonii DPC6026, a strain isolated from
AB  - the porcine intestinal tract. Although the genome of DPC6026 is similar
AB  - in size (1.97mbp) and GC content (34.8%) to the sequenced human isolate
AB  - L. johnsonii NCC 533, a large symmetrical inversion of approximately
AB  - 750 kb differentiated the two strains. Comparative analysis among 12
AB  - other strains of L. johnsonii including 8 porcine, 3 human and 1
AB  - poultry isolate indicated that the genome architecture found in DPC6026
AB  - is more common within the species than that of NCC 533. Furthermore a
AB  - number of unique features were annotated in DPC6026, some of which are
AB  - likely to have been acquired by horizontal gene transfer (HGT) and
AB  - contribute to protection against phage infection. A putative type III
AB  - restriction-modification system was identified, as were novel Clustered
AB  - Regularly Interspaced Short Palindromic Repeats (CRISPR) elements.
AB  - Interestingly, these particular elements are not widely distributed
AB  - among L. johnsonii strains. Taken together these data suggest
AB  - intra-species genomic rearrangements and significant genetic diversity
AB  - within the L. johnsonii species and indicate towards a host-specific
AB  - divergence of L. johnsonii strains with respect to genome inversion and
AB  - phage exposure.
ER  -

TY  - JOUR
AU  - Guinard, J.
AU  - Vinatzer, B.A.
AU  - Poussier, S.
AU  - Lefeuvre, P.
AU  - Wicker, E.
TI  - Draft Genome Sequences of Nine Strains of Ralstonia solanacearum Differing in Virulence to Eggplant (Solanum melongena).
JO  - Genome Announcements
PY  - 2016
SP  - e01415
EP  - e01415
VL  - 4
AB  - Ralstonia solanacearum displays variability in its virulence to solanaceous crops. We report
AB  - here the draft genome sequences of eight phylotype I strains and
AB  - one phylotype III strain differing in virulence to the resistant eggplant
AB  - genotype AG91-25. These data will allow the identification of virulence- and
AB  - avirulence-related genes.
ER  -

TY  - JOUR
AU  - Guinebretiere, M.H.
AU  - Loux, V.
AU  - Martin, V.
AU  - Nicolas, P.
AU  - Sanchis, V.
AU  - Broussolle, V.
TI  - Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group.
JO  - Genome Announcements
PY  - 2017
SP  - e01568
EP  - e01516
VL  - 5
AB  - Bacteria from the Bacillus cereus group exhibit genetic and physiological diversity through
AB  - different ecotypes. Here, we present the draft genome sequences
AB  - of 20 bacterial strains belonging to the contrasted psychrotolerant and
AB  - thermotolerant ecotypes.
ER  -

TY  - JOUR
AU  - Guio, H.
AU  - Tarazona, D.
AU  - Galarza, M.
AU  - Borda, V.
AU  - Curitomay, R.
TI  - Genome analysis of 17 extensively drug-resistant strains reveals new potential mutations for resistance.
JO  - Genome Announcements
PY  - 2014
SP  - e00759
EP  - e00714
VL  - 2
AB  - We report the whole-genome sequence of an extensively drug-resistant (XDR) tuberculosis (TB)
AB  - strain of Latin American-Mediterranean (LAM) lineage. This
AB  - strain is phenotypically resistant to aminoglycosides, but carries no related
AB  - mutations in rrs, tlyA, and eis. Through genome analysis comparison with 16 XDR
AB  - strains, we found 218 non-synonymous single nucleotide polymorphisms (SNPs)
AB  - shared that could confer resistance.
ER  -

TY  - JOUR
AU  - Guizelini, D.
AU  - Saizaki, P.M.
AU  - Coimbra, N.A.
AU  - Weiss, V.A.
AU  - Faoro, H.
AU  - Sfeir, M.Z.
AU  - Baura, V.A.
AU  - Monteiro, R.A.
AU  - Chubatsu, L.S.
AU  - Souza, E.M.
AU  - Cruz, L.M.
AU  - Pedrosa, F.O.
AU  - Raittz, R.T.
AU  - Marchaukoski, J.N.
AU  - Steffens, M.B.
TI  - Complete Genome Sequence of Herbaspirillum hiltneri N3 (DSM 17495), Isolated from Surface-Sterilized Wheat Roots.
JO  - Genome Announcements
PY  - 2015
SP  - e01288
EP  - e01215
VL  - 3
AB  - We report the complete genome sequence of Herbaspirillum hiltneri N3 (DSM 17495), a member of
AB  - the genus Herbaspirillum of the Betaproteobacteria. The genome is
AB  - contained in a single chromosome, and analysis revealed that N3 lacks the whole
AB  - nitrogen fixation (nif) gene cluster, confirming its inability to fix nitrogen.
ER  -

TY  - JOUR
AU  - Gul, D.
AU  - Potter, R.F.
AU  - Riaz, H.
AU  - Ashraf, S.T.
AU  - Wallace, M.A.
AU  - Munir, T.
AU  - Ali, A.
AU  - Burnham, C.A.
AU  - Dantas, G.
AU  - Andleeb, S.
TI  - Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to  Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics.
JO  - Genome Announcements
PY  - 2017
SP  - e00850
EP  - e00817
VL  - 5
AB  - Typhoid is endemic in developing countries. We report here the first draft genome sequence of
AB  - a Salmonella enterica serovar Typhi clinical isolate from Pakistan
AB  - exhibiting resistance to cefepime (a fourth-generation cephalosporin) and
AB  - fluoroquinolone antibiotics, two of the last-generation therapies against this
AB  - pathogen. The genome is ~4.8 Mb, with two putative plasmids.
ER  -

TY  - JOUR
AU  - Gulati, A.
AU  - Swarnkar, M.K.
AU  - Vyas, P.
AU  - Rahi, P.
AU  - Thakur, R.
AU  - Thakur, N.
AU  - Singh, A.K.
TI  - Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity.
JO  - Genome Announcements
PY  - 2015
SP  - e00943
EP  - e00915
VL  - 3
AB  - The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain
AB  - IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant
AB  - growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate
AB  - solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase
AB  - activity, indole-3-acetic acid  (IAA) production, and stress response.
ER  -

TY  - JOUR
AU  - Gully, D.
AU  - Teulet, A.
AU  - Busset, N.
AU  - Nouwen, N.
AU  - Fardoux, J.
AU  - Rouy, Z.
AU  - Vallenet, D.
AU  - Cruveiller, S.
AU  - Giraud, E.
TI  - Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with  Aeschynomene Legumes.
JO  - Genome Announcements
PY  - 2017
SP  - e00421
EP  - e00417
VL  - 5
AB  - Here, we report the complete genome sequence of Bradyrhizobium sp. strain ORS285, which is
AB  - able to nodulate Aeschynomene legumes using two distinct strategies that
AB  - differ in the requirement of Nod factors. The genome sequence information of this
AB  - strain will help understanding of the different mechanisms of interaction of
AB  - rhizobia with legumes.
ER  -

TY  - JOUR
AU  - Gumerov, V.M.
AU  - Mardanov, A.V.
AU  - Beletsky, A.V.
AU  - Prokofeva, M.I.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Ravin, N.V.
AU  - Skryabin, K.G.
TI  - Complete genome sequence of 'Vulcanisaeta moutnovskia' strain 768-28, a novel member of the hyperthermophilic crenarchaeal genus Vulcanisaeta.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2355
EP  - 2356
VL  - 193
AB  - Strain 768-28 was isolated from a hot spring in Kamchatka, Russia and represents a novel
AB  - member of the Vulcanisaeta genus. The complete genome sequence of this thermoacidophilic
AB  - anaerobic crenarchaeon reveals genes for protein and carbohydrate-active enzymes, the
AB  - Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid
AB  - cycle, beta-oxidation of fatty acids, and sulfate reduction.
ER  -

TY  - JOUR
AU  - Gummadidala, P.M.
AU  - Holder, M.E.
AU  - O'Brien, J.L.
AU  - Ajami, N.J.
AU  - Petrosino, J.F.
AU  - Mitra, C.
AU  - Chen, Y.P.
AU  - Decho, A.W.
AU  - Chanda, A.
TI  - Complete Genome Sequence of Vibrio gazogenes ATCC 43942.
JO  - Genome Announcements
PY  - 2017
SP  - e00733
EP  - e00717
VL  - 5
AB  - Vibrio gazogenes ATCC 43942 has the potential to synthesize a plethora of metabolites which
AB  - are of clinical and agricultural significance in response to
AB  - environmental triggers. The complete genomic sequence of Vibrio gazogenes ATCC
AB  - 43942 is reported herein, contributing to the knowledge base of strains in the
AB  - Vibrio genus.
ER  -

TY  - JOUR
AU  - Gumulak-Smith, J.
AU  - Teachman, A.
AU  - Tu, A.H.
AU  - Simecka, J.W.
AU  - Lindsey, J.R.
AU  - Dybvig, K.
TI  - Variations in the surface proteins and restriction enzyme systems of Mycoplasma pulmonis in the respiratory tract of infected rats.
JO  - Mol. Microbiol.
PY  - 2001
SP  - 1037
EP  - 1044
VL  - 40
AB  - Restriction and modification (R-M) systems are generally thought to protect bacteria from
AB  - invasion by foreign DNA. This paper proposes the existence of an alternative role for the
AB  - phase-variable R-M systems encoded by the hsd loci of Mycoplasma pulmonis. Populations of M.
AB  - pulmonis cells that arose during growth in different environments were compared with respect
AB  - to R-M activity and surface antigen production. When M. pulmonis strain X1048 was propagated
AB  - in laboratory culture medium, > 95% of colony-forming units (cfu) lacked R-M activity and
AB  - produced the variable surface protein VsaA. Mycoplasmas isolated from the nose of
AB  - experimentally infected rats also lacked R-M activity and produced VsaA. In contrast, the cell
AB  - population of mycoplasmas isolated from the lower respiratory tract of the infected rats was
AB  - more complex. The most dramatic results were obtained for mycoplasmas isolated from the
AB  - trachea. At 14 days postinfection, 38% of mycoplasma isolates produced a Vsa protein other
AB  - than VsaA, and 34% of isolates had active restriction systems. These data suggest that
AB  - differences in selection pressures in animal tissues affect the surface proteins and the R-M
AB  - activity of the mycoplasmal cell population. We propose that variations in the production of
AB  - R-M activity and cell surface proteins are important for the survival of the mycoplasma within
AB  - the host.
ER  -

TY  - JOUR
AU  - Gunaletchumy, S.P.
AU  - Teh, X.
AU  - Khosravi, Y.
AU  - Ramli, N.S.
AU  - Chua, E.G.
AU  - Kavitha, T.
AU  - Mason, J.N.
AU  - Lee, H.T.
AU  - Alias, H.
AU  - Zaidan, N.Z.
AU  - Yassin, N.B.
AU  - Tay, L.C.
AU  - Rudd, S.
AU  - Mitchell, H.M.
AU  - Kaakoush, N.O.
AU  - Loke, M.F.
AU  - Goh, K.L.
AU  - Vadivelu, J.
TI  - Draft Genome Sequences of Helicobacter pylori Isolates from Malaysia, Cultured from Patients with Functional Dyspepsia and Gastric Cancer.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5695
EP  - 5696
VL  - 194
AB  - Helicobacter pylori is the main bacterial causative agent of gastroduodenal disorders and a
AB  - risk factor for gastric adenocarcinoma and mucosa-associated
AB  - lymphoid tissue (MALT) lymphoma. The draft genomes of 10 closely related H.
AB  - pylori isolates from the multiracial Malaysian population will provide an insight
AB  - into the genetic diversity of isolates in Southeast Asia. These isolates were
AB  - cultured from gastric biopsy samples from patients with functional dyspepsia and
AB  - gastric cancer. The availability of this genomic information will provide an
AB  - opportunity for examining the evolution and population structure of H. pylori
AB  - isolates from Southeast Asia, where the East meets the West.
ER  -

TY  - JOUR
AU  - Gunn, J.S.
AU  - Piekarowicz, A.
AU  - Chien, R.
AU  - Stein, D.C.
TI  - Cloning and linkage analysis of Neisseria gonorrhoeae DNA methyltransferases.
JO  - J. Bacteriol.
PY  - 1992
SP  - 5654
EP  - 5660
VL  - 174
AB  - We have cloned DNA methyltransferases (MTases) from various strains of Neisseria gonorrhoeae.
AB  - Each of these clones represents a single specificity, indicating that the multiple gonococcal
AB  - MTase specificities are encoded by monospecific MTases. The DNAs of five strains (FA5100, F62,
AB  - MS11, Pgh3-2, and WR302) were digested with NheI, SpeI, or NheI plus SpeI and subjected to
AB  - pulsed-field gel electrophoresis. The DNA MTase clones were used to probe Southern blots of
AB  - these pulsed-field gels to determine whether the MTase genes are linked and whether there are
AB  - stain-to-strain differences. The results indicate that none of these genes are closely linked,
AB  - but variable hybridization patterns indicate that there exist restriction fragment length
AB  - polymorphisms between the strains tested. Most of the chromosomal regions containing these
AB  - restriction fragment length polymorphisms are clustered in regions containing gonococcal genes
AB  - known or suspected to antigenically vary via genetic recombination.
ER  -

TY  - JOUR
AU  - Gunn, J.S.
AU  - Stein, D.C.
TI  - The Neisseria gonorrhoeae S.NgoVIII restriction/modification system: a type IIs system homologous to the Haemophilus parahaemolyticus HphI restriction/modification system.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4147
EP  - 4152
VL  - 25
AB  - Strains of Neisseria gonorrhoeae possess numerous restriction-modification systems.  One of
AB  - these systems, which has been found in all strains tested, encodes the S.NgoVIII specificity
AB  - (5' TCACC 3') R-M system.  We cloned two adjacent methyltransferase genes (dcmH and damH),
AB  - each encoding proteins whose actions protect DNA from digestion by R.HphI or R.NgoBI (%'
AB  - TCACC 3').  The damH gene product is a N6-methyladenine methyltransferase that recognizes
AB  - this sequence.  We constructed a plasmid containing multiple copies of the S.NgoVIII sequence,
AB  - grew it in the presence of damH and used the HPLC to demonstrate the presence of
AB  - N6-methyladenine in the DNA.  A second plasmid, containing overlapping damH and Escherichia
AB  - coli dam recognition sequences in combination with various restriction digests, was used to
AB  - identify which adenine in the recognition sequence was modified by damH.  The predicted dcmH
AB  - gene product is homologous to 5-methylcytosine methyltransferases.  The products of both the
AB  - dcmH and damH genes, as well as an open reading frame downstream of the damH gene are highly
AB  - similar to the Haemophilus parahaemolyticus hphIMC, hphIMA and hphIR gene products, encoding
AB  - the HphI type IIs R-M system.  The S.NgoVIII R-M genes are flanked by a 97 bp direct repeat
AB  - that may be involved in the mobility of this R-M system.
ER  -

TY  - JOUR
AU  - Gunn, J.S.
AU  - Stein, D.C.
TI  - Natural variation of the NgoII restriction-modification of Neisseria gonorrhoeae.
JO  - Gene
PY  - 1993
SP  - 15
EP  - 20
VL  - 132
AB  - The NgoII restriction-modification (R-M) system of Neisseria gonorrhoeae recognizes the
AB  - sequence 5'-GGCC-3'. This system is encoded by two separate genes, dcmB for the
AB  - methyltransferase (MTase) and dcrB for the restriction endonuclease (ENase). Three strains
AB  - that vary in their NgoII phenotype were examined. Strain Pgh3-2 produced detectable levels of
AB  - both enzymes, strain F62 lacked detectable levels of the dcrB gene product, and strain WR302
AB  - failed to produce either gene product. Strains that lacked either enzyme activity still
AB  - possessed the genes that encode them. Transcriptional fusions of dcrB in strains F62 and
AB  - Pgh3-2 indicate that this gene is transcribed at nearly identical levels in each strain. The
AB  - DNA encoding the NgoII R-M system was cloned from the three strains, and the nucleotide
AB  - sequence was determined. The dcrB genes of WR302 and F62 possess the same frameshift mutation
AB  - (base position 1435) which would result in a truncated protein. The WR302 dcmB was found to
AB  - have a point mutation that changed Arg 288 (a residue that is conserved in all prokaryotic and
AB  - phage cytosine MTases sequenced to date) to Trp.
AB  - [ The enzyme called NgoII in this abstract has been renamed NgoCII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Gunn, J.S.
AU  - Stein, D.C.
TI  - Use of a non-selective transformation technique to construct a multiply restriction/modification-deficient mutant of Neisseria gonorrhoeae.
JO  - Mol. Gen. Genet.
PY  - 1996
SP  - 509
EP  - 517
VL  - 251
AB  - A technique that allows for easy identification of transformants of Neisseria gonorrhoeae in
AB  - the absence of selective pressure has been developed.  A suicide vector that contains a
AB  - gonococcal DNA uptake sequence was constructed to aid in DNA uptake.  In this transformation
AB  - procedure, a limiting number of cells is incubated with an excess amount of DNA, and the
AB  - mixture is plated onto a non-selective medium.  At least 20% of the resulting colonies
AB  - contained cells that had been transformed.  This strategy was utilized to construct specific
AB  - deletions of the S.NgoI, II, IV, V, and VII restriction-modification (R/M) genes.  All five
AB  - deletions were successfully incorporated into the chromosome of FA19, producing strain JUG029.
AB  - Strain JUG029 could be transformed with non-methylated plasmid DNA while strain FA19 could not
AB  - be transformed with such DNA.  The development of a simple, non-slective transformation
AB  - technique, coupled with the construction of a strain that is more permissive for DNA-mediated
AB  - transformation, will aid in genetic manipulations of the gonococcus.
ER  -

TY  - JOUR
AU  - Gunsalus, R.P.
AU  - Cook, L.E.
AU  - Crable, B.
AU  - Rohlin, L.
AU  - McDonald, E.
AU  - Mouttaki, H.
AU  - Sieber, J.R.
AU  - Poweleit, N.
AU  - Zhou, H.
AU  - Lapidus, A.L.
AU  - Daligault, H.E.
AU  - Land, M.
AU  - Gilna, P.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Culley, D.E.
AU  - McInerney, M.J.
TI  - Complete genome sequence of Methanospirillum hungatei type strain JF1.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 2
EP  - 2
VL  - 11
AB  - Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type
AB  - species of the genus Methanospirillum, which belongs to the
AB  - family Methanospirillaceae within the order Methanomicrobiales. Its genome was
AB  - selected for sequencing due to its ability to utilize hydrogen and carbon dioxide
AB  - and/or formate as a sole source of energy. Ecologically, M. hungatei functions as
AB  - the hydrogen- and/or formate-using partner with many species of syntrophic
AB  - bacteria. Its morphology is distinct from other methanogens with the ability to
AB  - form long chains of cells (up to 100 mum in length), which are enclosed within a
AB  - sheath-like structure, and terminal cells with polar flagella. The genome of M.
AB  - hungatei strain JF1 is the first completely sequenced genome of the family
AB  - Methanospirillaceae, and it has a circular genome of 3,544,738 bp containing
AB  - 3,239 protein coding and 68 RNA genes. The large genome of M. hungatei JF1
AB  - suggests the presence of unrecognized biochemical/physiological properties that
AB  - likely extend to the other Methanospirillaceae and include the ability to form
AB  - the unusual sheath-like structure and to successfully interact with syntrophic
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Gunther, N.W. IV
AU  - Bono, J.L.
AU  - Needleman, D.S.
TI  - Complete Genome Sequence of Campylobacter jejuni RM1285, a Rod-Shaped Morphological Variant.
JO  - Genome Announcements
PY  - 2015
SP  - e01361
EP  - e01315
VL  - 3
AB  - Campylobacter jejuni is a spiral shaped Gram-negative food-borne bacterial pathogen of humans
AB  - found on poultry products. Strain RM1285 is a rod-shaped variant of this species. The genome
AB  - of RM1285 was determined to be 1,635,803 bp, with a G+C content of 30.5%.
ER  -

TY  - JOUR
AU  - Gunther, N.W. IV
AU  - Reichenberger, E.R.
TI  - Complete Genome Sequence of Campylobacter jejuni RM1246-ERRC, Which Exhibits Resistance to Quaternary Ammonium Compounds.
JO  - Genome Announcements
PY  - 2017
SP  - e00978
EP  - e00917
VL  - 5
AB  - Campylobacter jejuni strain RM1246-ERRC is a clinical isolate. In laboratory experiments,
AB  - RM1246-ERRC exhibited greater resistance to the antimicrobial
AB  - effects of quaternary ammonium compounds than other C. jejuni strains. The
AB  - chromosome of RM1246-ERRC is 1,659,694 bp with a G+C content of 30.56%. The
AB  - strain also possesses a 45,197-bp plasmid.
ER  -

TY  - JOUR
AU  - Gunther, N.W. IV
AU  - Reichenberger, E.R.
AU  - Bono, J.L.
TI  - Complete Genome Sequence of UV-Resistant Campylobacter jejuni RM3194, Including an 81.08-Kilobase Plasmid.
JO  - Genome Announcements
PY  - 2016
SP  - e00305
EP  - e00316
VL  - 4
AB  - Campylobacter jejuni strain RM3194 was originally isolated from a human with enteritis and
AB  - contains a novel 81,079-bp plasmid. RM3194 has exhibited superior
AB  - survival compared to other Campylobacter jejuni strains when challenged with UV
AB  - light. The chromosome of RM3194 was determined to be 1,651,183 bp, with a G+C
AB  - content of 30.5%.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Freund, M.
AU  - Trautner, T.A.
TI  - Restriction and modification in Bacillus subtilis:  Two DNA methyltransferases with BsuRI specificity.  I.  Purification and Physical Properties.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 9340
EP  - 9345
VL  - 256
AB  - Two S-adenosyl-L-methionine: DNA (cytosine 5)-methyltransferases, termed
AB  - M.BsuRIa and M.BsuRIb, were purified 3,000- and 4,000-fold, respectively, from
AB  - Bacillus subtilis strain OG3R (r+m+) by successive column chromatography.  The
AB  - molecular weights determined by gel filtration were 37,000 for M.BsuRIa and
AB  - 40,000 for M.BsuRIb.  The sedimentation coefficients s20,w were 3.55 for both
AB  - enzymes as determined by glycerol gradient centrifugation, corresponding to
AB  - molecular weights of 43,000.  Analysis of the two methyltransferases by agarose
AB  - gel electrophoresis, showed correspondence of the M.BsuRIa activity with one
AB  - protein band at a molecular weight of 41,000, whereas M.BsuRIb activity was
AB  - associated with two protein bands with molecular weights of 42,000 and 39,000,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Jentsch, S.
AU  - Freund, M.
TI  - Restriction and modification in Bacillus subtilis:  Two DNA Methyltransferases with BsuRI specificity.  II.  Catalytic properties, substrate specificity, and mode of action.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 9346
EP  - 9351
VL  - 256
AB  - The properties of two DNA methyltransferases, termed M.BsuRIa and M.BsuRIb,
AB  - whose isolation was described in the preceding paper (Gunthert, U., Freund, M.,
AB  - and Trautner, T.A. (1981) J. Biol. Chem. 256: 9340-9345) were compared.  Both
AB  - enzymes recognize the same target sequence in double-stranded DNA, leading to
AB  - methylation of the internal cytosine:  5'GGC*C  The enzymes have identical
AB  - reaction constants with their substrates, DNA (km = 2.7 nM for the 5'GGCC
AB  - sequence), and S-adenosyl-L-methionine (km = 0.7 microM).  Initial rates of
AB  - methyl group transfer were proportional to enzyme concentration over a range of
AB  - 50-fold, indicating absence of aggregation.  The enzymes are different in their
AB  - ionic strength requirements using Tris-HCl, pH 8.4.  M.BsuRIa is most active at
AB  - 100 mM, M.BsuRIb at 440 mM.  As measured by incorporation kinetics and heat
AB  - inactivation, M.BsuRIa is the more stable enzyme of the two.  Equilibrium
AB  - dialysis was used to study the mode of methyl group transfer to the DNA with
AB  - either enzyme.  The data indicate that initially S-adenosyl-L-methionine binds
AB  - to methyltransferase.  This complex attaches to either modified or nonmodified
AB  - DNA.  The methyl group will then be transfered to a nonmodified target
AB  - sequence, leading to the disociation of enzyme and S-adenosyl-L-homocysteine
AB  - from the DNA.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Lauster, R.
AU  - Reiners, L.
TI  - Multispecific DNA methyltransferases from Bacillus subtilis phages Properties of wild-type and various mutant enzymes with altered DNA affinity.
JO  - Eur. J. Biochem.
PY  - 1986
SP  - 485
EP  - 492
VL  - 159
AB  - Temperate Bacillus subtilis phages SPR, Phi3T, d11 and SPbeta code for DNA
AB  - methyltransferases, each having mutliple sequence specificities.  The SPR
AB  - wild-type and various mutant methyltransferases were overproduced 1000-fold in
AB  - Escherichia coli and were purified by three consecutive chromatographic steps.
AB  - The stable form of these multispecific enzymes in solution are monomers with a
AB  - relative molecular mass (Mr) of about 50,000.  The methyl-transfer kinetics of
AB  - the SPR wild-type and mutant enzymes were determined with DNA substrates
AB  - carrying either none or one of the three recognition sequences (GGCC, CCGG,
AB  - CCA/TGG).  Evaluation of the catalytic properties for DNA and
AB  - S-adenosylmethionine binding suggested that the NH2-terminal part of the
AB  - protein is important for both non-sequence-specific DNA binding and
AB  - S-adenosylmethionine binding as well as transfer of methyl groups.  On the
AB  - other hand, mutations in the COOH-terminal part lead to weaker site-specific
AB  - interactions of the enzyme.  Antibodies raised against the purified SPR enzyme
AB  - specifically immunoprecipitated the Phi3T,d11 and SPbeta methyltransferases,
AB  - but failed to precipitate the chromosomally coded enzymes from B. subtilis
AB  - (BsuRI) and B. sphaericus (BspRI).  Immunoaffinity chromatography is an
AB  - efficient purification step for the related phage methyltransferases.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Pawlek, B.
AU  - Stutz, J.
AU  - Trautner, T.A.
TI  - Restriction and Modification in Bacillus subtilis: Inducibility of a DNA Methylating Activity in Nonmodifying Cells.
JO  - J. Virol.
PY  - 1976
SP  - 188
EP  - 195
VL  - 20
AB  - The nonrestricting/nonmodifying strain Bacillus subtilis 222 (4-m-) can be
AB  - induced to synthesize a DNA-modifying activity upon treatment with either
AB  - mitomycin C (MC) or UV light.  This is shown by the following facts.  (i)
AB  - Infection of MC-pretreated 222 cells with unmodified SPP1 phage yields about 3%
AB  - modified phage that are resistant to restriction in B. subtilis R (r+m+).  The
AB  - induced modifying activity causes the production of a small fraction of fully
AB  - modified phage in a minority class of MC-treated host cells.  (ii) The
AB  - MC-pretreated host cells contain a DNA cytosine methylating activity; both
AB  - bacterial and phage DNAs have elevated levels of 5-methylcytosine.  (iii) The
AB  - MC-induced methylation of SPP1 DNA takes place at the recognition nucleotide
AB  - sequences of restriction endonuclease R from B. subtilis R.  (iv) Crude
AB  - extracts of MC-pretreated 222 cells have enhanced DNA methyltransferase
AB  - activities, with a substrate specificity similar to that found in modification
AB  - enzymes present in (constituitively) modifying strains.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Reiners, L.
TI  - Bacillus subtilis phage SPR codes for a DNA methyltransferase with triple sequence specificity.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3689
EP  - 3701
VL  - 15
AB  - SPR, a temperate Bacillus subtilis phage, codes for a DNA methyltransferase
AB  - that can methylate the sequences GGCC (or GGCC) and CCGG at the cytosines
AB  - indicated.  We show here that it can also methylate the sequence CC(A/T)GG and
AB  - protect it from cleavage with EcoRII and ApyI.  This methylation can be seen in
AB  - vivo as well as in vitro with purified SPR methyltransferase.  SPR19 and SPR83
AB  - are two mutant phages, defective in GGCC or CCGG methylation, respectively.
AB  - These mutants have not lost their ability to methylate CC(A/T)GG sites.
AB  - Mutation SPR26 has lost the ability to methylate all three sites.  Thus the SPR
AB  - methyltransferase codes for three genetically distinguishable methylation
AB  - abilities.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Reiners, L.
AU  - Lauster, R.
TI  - Cloning and expression of Bacillus subtilis phage DNA methyltransferase genes in Escherichia coli and B. subtilis.
JO  - Gene
PY  - 1986
SP  - 261
EP  - 270
VL  - 41
AB  - The DNA methyltransferase (Mtase) genes of the temperate Bacillus subtilis
AB  - phages SPR (wild type and various mutants), Phi3T, p11 and SBb have been cloned
AB  - and expressed in Escherichia coli and B. subtilis host-plasmid vector systems.
AB  - Mtase activity has been quantitated in these clones by performing in vitro
AB  - methylation assays of cell-free extracts.  The four-phage Mtase genes differ in
AB  - the amount of Mtase synthesized when transcribed from their genuine promoters.
AB  - In B. subtilis as well as in E. coli the SPR Mtase is always produced in
AB  - smaller amounts than the other phage Mtases.  Expression levels of the SPR
AB  - Mtase are dependent on the strength of the upstream vector promoter sequences.
AB  - Overproduction of the SPR wild-type and mutant enzymes was achieved in E. coli
AB  - (inducible expression) by fusions to the lambda pL or the tac promoter and in
AB  - B. subtilis (constitutive expression) by means of the phage SP02 promoter.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Storm, K.
AU  - Bald, R.
TI  - Restriction and modification in Bacillus subtilis. Localization of the methylated nucleotide in the BsuRI recognition sequence.
JO  - Eur. J. Biochem.
PY  - 1978
SP  - 581
EP  - 583
VL  - 90
AB  - Calf thymus DNA was methylated in vitro with cell extracts of Bacillus subtilis OG3R (r+m+)
AB  - and S-adenosyl[Me-3H]methionine.  After depurination of the [3H]methylated DNA, the analysis
AB  - of the pyrimidine dinucleotides revealed the following positions of the methylated nucleosides
AB  - (indicated by an asterisk) with the BsuRI recognition sequence:
AB  - 5' dG-dG-dC*-dC
AB  - dC-dC*-dG-dG 5'.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Stutz, J.
AU  - Klotz, G.
TI  - Restriction and modification in B. subtilis.
JO  - Mol. Gen. Genet.
PY  - 1975
SP  - 185
EP  - 191
VL  - 142
AB  - The content of 5-methylcytosine (5MC) and 6-methyladenine (6MA) in modified and
AB  - nonmodified DNAs from B. subtilis and B. subtilis phage SPP1 were determined.
AB  - Non-modified SPP1-O DNA contains about 15 5MC residues/molecule.  Each modified
AB  - SPP1-R DNA molecule carries 190 modification specific methyl groups.  This
AB  - number is sufficient to account for modification of the 80 restriction sites in
AB  - SPP1 DNA (Bron and Murray, 1975) against endo R.BsuR, assuming each modified
AB  - site contains two 5MC residues.  Resistance of SPO1 DNA against endo R.BsuR
AB  - restriction both in vivo and in vitro is probably not due to methylation of
AB  - endo R.BsuR recognition sites.
ER  -

TY  - JOUR
AU  - Gunthert, U.
AU  - Trautner, T.A.
TI  - DNA methyltransferases of Bacillus subtilis and its bacteriophages.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 1984
SP  - 11
EP  - 22
VL  - 108
AB  - Postreplicative DNA methylation occurs with a high incidence in bacteria and may affect
AB  - resident DNA and that of infecting bacteriophages. By far the most widespread role of DNA
AB  - methylation is to provide the DNA with "modification" i.e., protection against the
AB  - endonucleolytic attack of cellular restriction enzymes. Important aspects of this role in
AB  - connection with type-I enzymes are discussed in the review of Suri et al. (this volume).
AB  - Another well-studied physiological function of DNA methylation observed in Escherichia coli is
AB  - its role in strand recognition for proofreading during DNA synthesis, which is covered in the
AB  - review by Radman and Wagner (this volume). Some role of host-mediated DNA methylation is
AB  - implemented in the regulation of gene expression of bacteriophage mu; this work is the subject
AB  - of the review by Kahmann (this volume).
ER  -

TY  - JOUR
AU  - Guo, H.
AU  - Karberg, M.
AU  - Long, M.
AU  - Jones, J.P. III
AU  - Sullenger, B.
AU  - Lambowitz, A.M.
TI  - Group II introns designed to insert into therapeutically relevant DNA target sites in human cells.
JO  - Science
PY  - 2000
SP  - 452
EP  - 457
VL  - 289
AB  - Mobile group II intron RNA's insert directly into DNA target sites and are then
AB  - reverse-transcribed into genomic DNA by the associated intron-encoded protein.  Target site
AB  - recognition involves modifiable base-pairing interactions between the intron RNA and a
AB  - >14-nucleotide region of the DNA target site, as well as fixed interactions between the
AB  - protein and flanking regions.  Here, we developed a highly efficient Escherichia coli genetic
AB  - assay to determine detailed target site recognition rules for the Lactococcus lactis group II
AB  - intron Ll.LtrB and to select introns that insert into desired target sites.  Using human
AB  - immunodeficiency virus-type 1 (HIV-1) proviral DNA and the human CCR5 gene as examples, we
AB  - show that group II introns can be retargeted to insert efficiently into virtually any target
AB  - DNA and that the retargeted introns retain activity in human cells.  This work provides the
AB  - practical basis for potential applications of targeted group II introns in genetic
AB  - engineering, functional genomics, and gene therapy.
ER  -

TY  - JOUR
AU  - Guo, H.
AU  - Zimmerly, S.
AU  - Perlman, P.S.
AU  - Lambowitz, A.M.
TI  - Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA.
JO  - EMBO J.
PY  - 1997
SP  - 6835
EP  - 6848
VL  - 16
AB  - Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease
AB  - activities for site-specific insertion into DNA.  Remarkably, the endonucleases are
AB  - ribonucleoprotein complexes in which the excised intron RNA cleaves the sense strand of the
AB  - recipient DNA by reverse splicing, while the intron-encoded protein cleaves the antisense
AB  - strand.  Here, studies with the yeast group II intron aI2 indicate that both the RNA and
AB  - protein components of the endonuclease contribute to recognition of an ~30 bp DNA target site.
AB  - Our results lead to a model in which the protein component first recognizes specific
AB  - nucleotides in the most distal 5' exon region of the DNA target site (E2-21 to -11).  Binding
AB  - of the protein then leads to DNA unwinding, enabling the intron RNA to base pair to a 13
AB  - nucleotide DNA sequence (E2-12 to E3+1) for reverse splicing.  Antisense-strand cleavage
AB  - requires additional interactions of the protein with the 3' exon DNA (E3 +1 to +10).  Our
AB  - results show how enzymes can use RNA and protein subunits cooperatively to recognize specific
AB  - sequences in double-stranded DNA.
ER  -

TY  - JOUR
AU  - Guo, H.-C.
TI  - Type II restriction endonucleases: Structures and applications.
JO  - Recent Res. Devel. Macromol.
PY  - 2003
SP  - 225
EP  - 245
VL  - 7
AB  - Restriction endonucleases are enzymes that recognize specific double-strand DNA sequences and
AB  - cleave at a defined point within or close to that sequence.  These enzymes have become
AB  - indispensable tools in modern biochemistry, recombinant DNA technology, genome mapping, and
AB  - genetic manipulation.  Diverse recognition strategies and high specificity make restriction
AB  - enzymes an ideal system for structural studies of DNA recognition and cleavage by proteins.
AB  - For various applications such as DNA fingerprinting to study cancer or infectious diseases,
AB  - there have also been long-standing interests in rational design of artificial restriction
AB  - enzymes with desired specificities.  However, restriction enzymes have proven to be a
AB  - difficult case for protein engineering.  In general initial attempts were not successful,
AB  - mainly because the tight coupling of specific binding to catalysis was not fully understood.
AB  - New structures reported reveal that these enzymes are more diverse than expected.  Comparisons
AB  - of twelve available structures of Type II restriction enzyme/DNA complexes indicate that
AB  - structural elements responsible for allosteric coupling of recognition to catalysis, as well
AB  - as dimer structures, correlate well with their cleavage patterns on DNA.  It is thus likely
AB  - that enzymes in the existing pool with different cleavage patterns reflect different control
AB  - mechanisms that couple DNA recognition to DNA cleavage and/or dimer structures.  A systematic
AB  - study of restriction enzymes with unique DNA cleavage patterns may illuminate alternative
AB  - coupling mechanisms suitable for manipulation in order to create tailor-made restriction
AB  - enzymes with desired specificities.
ER  -

TY  - JOUR
AU  - Guo, H.T.
AU  - Xu, X.D.
TI  - Broad host range plasmid-based gene transfer system in the cyanobacterium Gloeobacter violaceus which lacks thylakoids.
JO  - Prog. Nat. Sci.
PY  - 2004
SP  - 31
EP  - 35
VL  - 14
AB  - Gloeobacter violaceus, a cyanobacterium lack of thylakoids, is refractory to genetic
AB  - manipulations because its cells are enveloped by
AB  - a thick gelatinous sheath and in colonial form. In this study, a large
AB  - number of single cells were obtained by repeated pumping with a syringe
AB  - with the gelatinous sheath removed. And an exogenous broad host range
AB  - plasmid pKT210 was conjugatively transferred into G. violaceus.
AB  - Analyses with dot-blot hybridization and restriction mapping showed
AB  - that the exogenous plasmid pKT210 had been introduced into G. violaceus
AB  - and stably maintained with no alteration in its structure. pKT210
AB  - extracted from G. violaceus exconjugants could be transformed into the
AB  - mcr - mrr - E. coli strain DH10B but not the mcr(+) mrr(+) strain
AB  - DH5alpha, which suggests that a methylase system may be present in G.
AB  - violaceus.
ER  -

TY  - JOUR
AU  - Guo, J.
AU  - Gaj, T.
AU  - Barbas, C.F.I.I.I.
TI  - Directed Evolution of an Enhanced and Highly Efficient FokI Cleavage Domain for Zinc Finger Nucleases.
JO  - J. Mol. Biol.
PY  - 2010
SP  - 96
EP  - 107
VL  - 400
AB  - Zinc finger nucleases (ZFNs) are powerful tools for gene therapy and genetic engineering. The
AB  - high specificity and affinity of these chimeric
AB  - enzymes are based on custom-designed zinc finger proteins (ZFPs). To
AB  - improve the performance of existing ZFN technology, we developed an in
AB  - vivo evolution-based approach to improve the efficacy of the FokI cleavage
AB  - domain (FCD). After multiple rounds of cycling mutagenesis and DNA
AB  - shuffling, a more efficient nuclease variant (Sharkey) was generated. In
AB  - vivo analyses indicated that Sharkey is >15-fold more active than
AB  - wild-type FCD on a diverse panel of cleavage sites. Further, a mammalian
AB  - cell-based assay showed a three to sixfold improvement in targeted
AB  - mutagenesis for ZFNs containing derivatives of the Sharkey cleavage
AB  - domain. We also identified mutations that impart sequence specificity to
AB  - the FCD that might be utilized in future studies to further refine ZFNs
AB  - through cooperative specificity. In addition, Sharkey was observed to
AB  - enhance the cleavage profiles of previously published and newly selected
AB  - heterodimer ZFN architectures. This enhanced and highly efficient cleavage
AB  - domain will aid in a variety of ZFN applications in medicine and biology.
ER  -

TY  - JOUR
AU  - Guo, M.
AU  - Han, X.
AU  - Jin, T.
AU  - Zhou, L.
AU  - Yang, J.
AU  - Li, Z.
AU  - Chen, J.
AU  - Geng, B.
AU  - Zou, Y.
AU  - Wan, D.
AU  - Li, D.
AU  - Dai, W.
AU  - Wang, H.
AU  - Chen, Y.
AU  - Ni, P.
AU  - Fang, C.
AU  - Yang, R.
TI  - Genome sequences of three species in the family planctomycetaceae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3740
EP  - 3741
VL  - 194
AB  - Most of the species in the family Planctomycetaceae are of interest for their eukaryotic-like
AB  - cell structures and characteristics of resistance to extreme
AB  - environments. Here, we report draft genome sequences of three aquatic parasitic
AB  - species of this family, Singulisphaera acidiphila (DSM 18658T), Schlesneria
AB  - paludicola (DSM 18645T), and Zavarzinella formosa (DSM 19928T).
ER  -

TY  - JOUR
AU  - Guo, P.
AU  - Cao, B.
AU  - Qiu, X.
AU  - Lin, J.
TI  - Draft Genome Sequence of the Crude Oil-Degrading and Biosurfactant-Producing Strain Cobetia sp. QF-1.
JO  - Genome Announcements
PY  - 2018
SP  - e01456
EP  - e01417
VL  - 6
AB  - We report here the draft genome of Cobetia sp. QF-1, a cold-adapted bacterium isolated from
AB  - crude oil-contaminated seawater of the Yellow Sea, China. This
AB  - genome is approximately 4.1 Mb (G+C content, 57.44%) with 3,513 protein-coding
AB  - sequences. Cobetia sp. QF-1 shows crude oil degradation and biosurfactant
AB  - production activity at low temperature.
ER  -

TY  - JOUR
AU  - Guo, Q.
AU  - Li, S.
AU  - Lu, X.
AU  - Zhang, X.
AU  - Wang, P.
AU  - Ma, P.
TI  - Complete Genome Sequence of Bacillus subtilis BAB-1, a Biocontrol Agent for Suppression of Tomato Gray Mold.
JO  - Genome Announcements
PY  - 2014
SP  - e00744
EP  - e00714
VL  - 2
AB  - Bacillus subtilis BAB-1, isolated from cotton rhizosphere soil, is an excellent biocontrol
AB  - agent for tomato gray mold. The genome of B. subtilis strain BAB-1 was
AB  - fully sequenced and annotated, genes encoding the antifungal active compound were
AB  - identified, and multiple sets of regulatory systems were found in the genome.
ER  -

TY  - JOUR
AU  - Guo, S.
AU  - Mao, Z.
AU  - Wu, Y.
AU  - Hao, K.
AU  - He, P.
AU  - He, Y.
TI  - Genome Sequencing of Bacillus subtilis Strain XF-1 with High Efficiency in the Suppression of Plasmodiophora brassicae.
JO  - Genome Announcements
PY  - 2013
SP  - e0006613
EP  - e0006613
VL  - 1
AB  - The genome of the rhizobacterium Bacillus subtilis XF-1 is 4.06 Mb in size and harbors 3,853
AB  - coding sequences (CDS). Giant gene clusters were dedicated to the
AB  - nonribosomal synthesis of antimicrobial lipopeptides and polyketides. Remarkably,
AB  - XF-1 possesses a gene cluster involved in the synthesis of chitosanase that is
AB  - related to the suppression of the pathogen Plasmodiophora brassicae.
ER  -

TY  - JOUR
AU  - Guo, W.
AU  - Wang, Y.
AU  - Song, C.
AU  - Yang, C.
AU  - Li, Q.
AU  - Li, B.
AU  - Su, W.
AU  - Sun, X.
AU  - Song, D.
AU  - Yang, X.
AU  - Wang, S.
TI  - Complete genome of Pseudomonas mendocina NK-01, which synthesizes medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3413
EP  - 3414
VL  - 193
AB  - Pseudomonas mendocina NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA(MCL))
AB  - and alginate oligosaccharides (AO)
AB  - simultaneously from glucose in the condition of limited nitrogen source.
AB  - Here we report the complete sequence of the 5.4-Mbp genome of Pseudomonas
AB  - mendocina NK-01, that was isolated from farmland soil in Tianjin, China.
ER  -

TY  - JOUR
AU  - Guo, X.
AU  - Liao, Z.
AU  - Holtzapple, M.
AU  - Hu, Q.
AU  - Zhao, B.
TI  - Draft Genome Sequence of Natranaerobius trueperi DSM 18760T, an Anaerobic, Halophilic, Alkaliphilic, Thermotolerant Bacterium Isolated from a Soda Lake.
JO  - Genome Announcements
PY  - 2017
SP  - e00785
EP  - e00717
VL  - 5
AB  - The anaerobic, halophilic, alkaliphilic, thermotolerant bacterium Natranaerobius  trueperi was
AB  - isolated from a soda lake in Wadi An Natrun, Egypt. It grows
AB  - optimally at 3.7 M Na+, pH 9.5, and 43 degrees C. The draft genome consists of
AB  - 2.63 Mb and is composed of 2,681 predicted genes. Genomic analysis showed that
AB  - various genes are potentially involved in the adaptation mechanisms for osmotic
AB  - stress, pH homeostasis, and high temperatures.
ER  -

TY  - JOUR
AU  - Guo, X.
AU  - Liao, Z.
AU  - Yan, Y.
AU  - Holtzapple, M.
AU  - Hu, Q.
AU  - Zhao, B.
TI  - Draft Genome Sequence of Natronolimnobius baerhuensis CGMCC 1.3597T, an Aerobic Haloalkaliphilic Archaeon Isolated from a Soda Lake.
JO  - Genome Announcements
PY  - 2017
SP  - e00710
EP  - e00717
VL  - 5
AB  - The haloalkaliphilic archaeon Natronolimnobius baerhuensis was isolated from a soda lake in
AB  - Inner Mongolia (China), growing optimally at about 20% NaCl and pH
AB  - 9.0. The draft genome consists of approximately 3.91 Mb and contains 3,810
AB  - predicted genes. Some genes that regulate intracellular osmotic stress and pH
AB  - homeostasis were identified, providing insight into specific adaptations to this
AB  - double-extreme environment.
ER  -

TY  - JOUR
AU  - Guo, X.
AU  - Wang, L.
AU  - Li, J.
AU  - Ding, Z.
AU  - Xiao, J.
AU  - Yin, X.
AU  - He, S.
AU  - Shi, P.
AU  - Dong, L.
AU  - Li, G.
AU  - Tian, C.
AU  - Wang, J.
AU  - Cong, Y.
AU  - Xu, Y.
TI  - Structural insight into autoinhibition and histone H3-induced activation of DNMT3A.
JO  - Nature
PY  - 2015
SP  - 640
EP  - 644
VL  - 517
AB  - DNA methylation is an important epigenetic modification that is essential for various
AB  - developmental processes through regulating gene expression, genomic
AB  - imprinting, and epigenetic inheritance. Mammalian genomic DNA methylation is
AB  - established during embryogenesis by de novo DNA methyltransferases, DNMT3A and
AB  - DNMT3B, and the methylation patterns vary with developmental stages and cell
AB  - types. DNA methyltransferase 3-like protein (DNMT3L) is a catalytically inactive
AB  - paralogue of DNMT3 enzymes, which stimulates the enzymatic activity of Dnmt3a.
AB  - Recent studies have established a connection between DNA methylation and histone
AB  - modifications, and revealed a histone-guided mechanism for the establishment of
AB  - DNA methylation. The ATRX-DNMT3-DNMT3L (ADD) domain of Dnmt3a recognizes
AB  - unmethylated histone H3 (H3K4me0). The histone H3 tail stimulates the enzymatic
AB  - activity of Dnmt3a in vitro, whereas the molecular mechanism remains elusive.
AB  - Here we show that DNMT3A exists in an autoinhibitory form and that the histone H3
AB  - tail stimulates its activity in a DNMT3L-independent manner. We determine the
AB  - crystal structures of DNMT3A-DNMT3L (autoinhibitory form) and DNMT3A-DNMT3L-H3
AB  - (active form) complexes at 3.82 and 2.90 A resolution, respectively. Structural
AB  - and biochemical analyses indicate that the ADD domain of DNMT3A interacts with
AB  - and inhibits enzymatic activity of the catalytic domain (CD) through blocking its
AB  - DNA-binding affinity. Histone H3 (but not H3K4me3) disrupts ADD-CD interaction,
AB  - induces a large movement of the ADD domain, and thus releases the autoinhibition
AB  - of DNMT3A. The finding adds another layer of regulation of DNA methylation to
AB  - ensure that the enzyme is mainly activated at proper targeting loci when
AB  - unmethylated H3K4 is present, and strongly supports a negative correlation
AB  - between H3K4me3 and DNA methylation across the mammalian genome. Our study
AB  - provides a new insight into an unexpected autoinhibition and histone H3-induced
AB  - activation of the de novo DNA methyltransferase after its initial genomic
AB  - positioning.
ER  -

TY  - JOUR
AU  - Guo, X.P.
AU  - Ding, D.W.
AU  - Bao, W.Y.
AU  - Yang, J.L.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain ECSMB14103, Isolated from the East China Sea.
JO  - Genome Announcements
PY  - 2015
SP  - e00330
EP  - e00315
VL  - 3
AB  - Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms formed  on the East
AB  - China Sea. The draft genome sequence comprises 4.11 Mp with a G+C
AB  - content of 39.7%. The information from the draft genome will contribute to an
AB  - understanding of bacteria-animal interaction.
ER  -

TY  - JOUR
AU  - Guo, Y.
AU  - Cen, Z.
AU  - Zou, Y.
AU  - Fang, X.
AU  - Li, T.
AU  - Wang, J.
AU  - Chang, D.
AU  - Su, L.
AU  - Liu, Y.
AU  - Chen, Y.
AU  - Yang, R.
AU  - Liu, C.
TI  - Whole-Genome Sequence of Klebsiella pneumonia Strain LCT-KP214.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3281
EP  - 3281
VL  - 194
AB  - Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting,
AB  - facultative anaerobic, rod-shaped bacterium found in the
AB  - normal flora of the mouth, skin, and intestines. Here we present the fine-draft
AB  - genome sequence of K. pneumoniae strain LCT-KP214, which originated from K.
AB  - pneumoniae strain CGMCC 1.1736.
ER  -

TY  - JOUR
AU  - Guo, Y.
AU  - Jiao, Z.
AU  - Li, L.
AU  - Wu, D.
AU  - Crowley, D.E.
AU  - Wang, Y.
AU  - Wu, W.
TI  - Draft Genome Sequence of Rahnella aquatilis Strain HX2, a Plant Growth-Promoting  Rhizobacterium Isolated from Vineyard Soil in Beijing, China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6646
EP  - 6647
VL  - 194
AB  - Rahnella aquatilis strain HX2 is a plant growth-promoting, disease-suppressive rhizobacterium
AB  - that was isolated from a vineyard soil in Beijing, China. Here, we
AB  - report the genome sequence of this strain, which provides a valuable resource for
AB  - future research examining the mechanisms of traits associated with plant growth
AB  - promotion and biocontrol.
ER  -

TY  - JOUR
AU  - Guo, Y.
AU  - Wang, H.
AU  - Li, Y.
AU  - Song, Y.
AU  - Chen, C.
AU  - Liao, Y.
AU  - Ren, L.
AU  - Guo, C.
AU  - Tong, W.
AU  - Shen, W.
AU  - Chen, M.
AU  - Mao, X.
AU  - Guo, G.
AU  - Zou, Q.
TI  - Genome of Helicobacter pylori Strain XZ274, an Isolate from a Tibetan Patient with Gastric Cancer in China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4146
EP  - 4147
VL  - 194
AB  - The infection rate of Helicobacter pylori is high all over the world, especially  in the
AB  - Chinese Tibetan Plateau. Here, we report the genome sequence of
AB  - Helicobacter pylori strain XZ274 isolated from a Tibetan patient with gastric
AB  - cancer. The strain contains 1,634,138 bp with 1,654 coding sequences and a pXZ274
AB  - plasmid of 22,406 bp with 26 coding sequences. This is the first complete genome
AB  - sequence of Helicobacter pylori from the Tibetan Plateau in China.
ER  -

TY  - JOUR
AU  - Guo, Z.
AU  - Chen, P.
AU  - Ren, P.
AU  - Kuang, S.
AU  - Zhou, Z.
AU  - Li, Z.
AU  - Liu, M.
AU  - Shi, D.
AU  - Xiao, Y.
AU  - Wang, X.
AU  - Zhou, R.
AU  - Jin, H.
AU  - Bi, D.
TI  - Genome Sequence of Duck Pathogen Mycoplasma anatis Strain 1340.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5883
EP  - 5884
VL  - 193
AB  - Mycoplasma anatis, a member of the class Mollicutes, is the causative agent of a contagious
AB  - infectious disease of domestic ducklings, wild
AB  - birds, and eggs. Increasing reports show that coinfection of M. anatis
AB  - with Escherichia coli results in substantial economic impacts on the duck
AB  - farms in China. Here, we announce the first genome sequence of M. anatis.
ER  -

TY  - JOUR
AU  - Guo, Z.
AU  - Xu, X.
AU  - Zheng, Q.
AU  - Li, T.
AU  - Kuang, S.
AU  - Zhang, Z.
AU  - Chen, Y.
AU  - Lu, X.
AU  - Zhou, R.
AU  - Bi, D.
AU  - Jin, H.
TI  - Genome Sequence of Mycoplasma columbinum Strain SF7.
JO  - Genome Announcements
PY  - 2013
SP  - e00157
EP  - e00113
VL  - 1
AB  - Mycoplasma columbinum is a member of nonglycolytic Mycoplasma species which can hydrolyze
AB  - arginine. Increasingly research has revealed that M. columbinum is
AB  - associated with respiratory disease of pigeons and that the respiratory disease
AB  - symptoms could be eliminated via the use of mycoplasma treatment medicine. Here
AB  - we report the genome sequence of M. columbinum strain SF7, which is the first
AB  - genome report for M. columbinum.
ER  -

TY  - JOUR
AU  - Guolin, A.
AU  - Shiwen, L.
AU  - Yong, Z.
AU  - Mingyi, Q.
AU  - Tong, Z.
TI  - Effects of organic solvents on the specificity and activity of restriction endonuclease Bsp63I and Bsp78I.
JO  - J. Wuhan Univ.
PY  - 1991
SP  - 135
EP  - 138
VL  - 3
ER  -

TY  - JOUR
AU  - Gupta, H.K.
AU  - Gupta, R.D.
AU  - Singh, A.
AU  - Chauhan, N.S.
AU  - Sharma, R.
TI  - Genome Sequence of Rheinheimera sp. Strain A13L, Isolated from Pangong Lake, India.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5873
EP  - 5874
VL  - 193
AB  - Rheinheimera sp. strain A13L, which has antimicrobial activity, was isolated from alkaline
AB  - brackish water of the high-altitude Pangong Lake of
AB  - Ladakh, India. Here we report the draft genome sequence of Rhienheimera
AB  - sp. strain A13L (4,523,491 bp with a G+C content of 46.23%). The genome is
AB  - predicted to contain genes for marinocine and colicin V production, which
AB  - may be responsible for the antimicrobial activity of the strain.
ER  -

TY  - JOUR
AU  - Gupta, R.
AU  - Capalash, N.
AU  - Sharma, P.
TI  - Restriction endonucleases: natural and directed evolution.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2012
SP  - 583
EP  - 599
VL  - 94
AB  - Type II restriction endonucleases (REs) are highly sequence-specific compared with other
AB  - classes of nucleases. PD-(D/E)XK nucleases,
AB  - initially represented by only type II REs, now comprise a large and
AB  - extremely diverse superfamily of proteins and, although sharing a
AB  - structurally conserved core, typically display little or no detectable
AB  - sequence similarity except for the active site motifs. Sequence
AB  - similarity can only be observed in methylases and few isoschizomers. As
AB  - a consequence, REs are classified according to combinations of
AB  - functional properties rather than on the basis of genetic relatedness.
AB  - New alignment matrices and classification systems based on structural
AB  - core connectivity and cleavage mechanisms have been developed to
AB  - characterize new REs and related proteins. REs recognizing more than
AB  - 300 distinct specificities have been identified in RE database (REBASE:
AB  - http://rebase.neb.com/cgi-bin/statlist) but still the need for newer
AB  - specificities is increasing due to the advancement in molecular biology
AB  - and applications. The enzymes have undergone constant evolution through
AB  - structural changes in protein scaffolds which include random mutations,
AB  - homologous recombinations, insertions, and deletions of coding DNA
AB  - sequences but rational mutagenesis or directed evolution delivers
AB  - protein variants with new functions in accordance with defined
AB  - biochemical or environmental pressures. Redesigning through random
AB  - mutation, addition or deletion of amino acids, methylation-based
AB  - selection, synthetic molecules, combining recognition and cleavage
AB  - domains from different enzymes, or combination with domains of
AB  - additional functions change the cleavage specificity or substrate
AB  - preference and stability. There is a growing number of patents awarded
AB  - for the creation of engineered REs with new and enhanced properties.
ER  -

TY  - JOUR
AU  - Gupta, R.
AU  - Vakhlu, J.
AU  - Agarwal, A.
AU  - Nilawe, P.D.
TI  - Draft Genome Sequence of Plant Growth-Promoting Bacillus amyloliquefaciens Strain W2 Associated with Crocus sativus (Saffron).
JO  - Genome Announcements
PY  - 2014
SP  - e00862
EP  - e00814
VL  - 2
AB  - Bacillus sp. strain W2 is a plant growth-promoting rhizobacterium isolated from saffron fields
AB  - of Kashmir, India. Here, we report the draft genome sequence (3.9
AB  - Mb) of Bacillus amyloliquefaciens strain W2 having 65 contigs (3, 997, 511 bp),
AB  - 4,163 coding sequences, and an average 46.45% GC content. Despite the 99%
AB  - identity of the 16S rRNA gene with that of Bacillus amyloliquefaciens subsp.
AB  - plantarum FZB42, the genome comparison revealed that only 48.7% of the W2 genome
AB  - has homology with that of FZB42.
ER  -

TY  - JOUR
AU  - Gupta, R.
AU  - Xu, S.-Y.
AU  - Sharma, P.
AU  - Capalsh, N.
TI  - Characterization of MspNI (G/GWCC) and MspNII (R/GATCY), novel thermostable Type II restriction endonucleases from Meiothermus sp., isoschizomers of AvaII and BstYI.
JO  - Mol. Biol. Rep.
PY  - 2012
SP  - 5607
EP  - 5614
VL  - 39
AB  - MspNI and MspNII, isoschizomers of prototype Type II restriction endonucleases AvaII and
AB  - BstYI, were extracted from an extreme thermophile bacterium belonging to the genus
AB  - Meiothermus, isolated from the hot sulphur springs in north Himalayan region of India where
AB  - temperature and pH ranged from 60 to 80C and 7.5 to 8.5, respectively. The two enzymes were
AB  - purified to homogeneity using Cibacron-Blue 3GA Agarose, Q-Sepharose and SP-Sepharose
AB  - chromatography and were homodimers with subunit molecular weights of 27 and 45 kDa,
AB  - respectively. Restriction mapping and run-off sequencing of MspNI and MspNII cleaved pBR322
AB  - DNA showed that they recognized and cleaved 5'-G/GWCC-3' and 5'-R/GATCY-3' sites,
AB  - respectively.
AB  - MspNI and MspNII worked optimally at 60 and 70C, 6 and 5 mM MgCl(2), respectively and showed
AB  - no star activity in organic solvents. Both were resistant to sequence methylation and were
AB  - stable up to 25 PCR cycles.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McCleland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Putten Strain CRJJGF_00159 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e00895
EP  - e00816
VL  - 4
AB  - Here, we report a 4.90 Mbp draft genome sequence of Salmonella enterica subsp. enterica
AB  - serovar Putten strain CRJJGF_00159 isolated from food animal in 2004.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Barrett, J.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain CRJJGF_00165 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e01322
EP  - e01316
VL  - 4
AB  - Here, we report a 4.78-Mb draft genome sequence of the Salmonella enterica subsp. diarizonae
AB  - serovar 61:k:1,5,(7) strain CRJJGF_00165 [also called S. enterica
AB  - subsp. IIIb serovar 61:k:1,5,(7) strain CRJJGF_00165], isolated from ground beef
AB  - in 2007.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Bardo Strain CRJJGF_00099 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e00964
EP  - e00916
VL  - 4
AB  - Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella
AB  - enterica subsp. enterica serovar Bardo strain CRJJGF_00099, isolated
AB  - from dairy cattle in 2005.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Widemarsh Strain CRJJGF_00058 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e00604
EP  - e00616
VL  - 4
AB  - Here, we report a 4.73 Mbp draft genome sequence of Salmonella enterica subsp. enterica
AB  - serovar Widemarsh strain CRJJGF_00058, isolated from eggs in 2008.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Lille Strain CRJJGF_000101 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e00603
EP  - e00616
VL  - 4
AB  - Here, we report a 4.98 Mbp draft genome sequence of Salmonella enterica subsp. enterica
AB  - serovar Lille strain CRJJGF_000101, isolated from ground beef in 2007.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Orion Strain CRJJGF_00093 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e01063
EP  - e01016
VL  - 4
AB  - Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica
AB  - serovar Orion strain CRJJGF_00093, isolated from a dog in 2005.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Kiambu Strain CRJJGF_00061 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e00588
EP  - e00516
VL  - 4
AB  - We report a 4.58 Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar
AB  - Kiambu strain CRJJGF_00061 isolated from cattle in 2004.
ER  -

TY  - JOUR
AU  - Gupta, S.K.
AU  - McMillan, E.A.
AU  - Jackson, C.R.
AU  - Desai, P.T.
AU  - Porwollik, S.
AU  - McClelland, M.
AU  - Hiott, L.M.
AU  - Humayoun, S.B.
AU  - Frye, J.G.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Blockley Strain CRJJGF_00147 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e00954
EP  - e00916
VL  - 4
AB  - Here, we report a 4.72-Mbp draft genome sequence of Salmonella enterica subsp. enterica
AB  - serovar Blockley strain CRJJGF_00147, isolated from chicken rinse in
AB  - 2009.
ER  -

TY  - JOUR
AU  - Gupta, Y.K.
AU  - Chan, S.H.
AU  - Xu, S.Y.
AU  - Aggarwal, A.K.
TI  - Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.
JO  - Nat. Commun.
PY  - 2015
SP  - 7363
EP  - 7363
VL  - 6
AB  - Type III R-M enzymes were identified >40 years ago and yet there is no structural information
AB  - on these multisubunit enzymes. Here we report the structure of a Type
AB  - III R-M system, consisting of the entire EcoP15I complex (Mod2Res1) bound to DNA.
AB  - The structure suggests how ATP hydrolysis is coupled to long-range diffusion of a
AB  - helicase on DNA, and how a dimeric methyltransferase functions to methylate only
AB  - one of the two DNA strands. We show that the EcoP15I motor domains are
AB  - specifically adapted to bind double-stranded DNA and to facilitate DNA sliding
AB  - via a novel 'Pin' domain. We also uncover unexpected 'division of labour', where
AB  - one Mod subunit recognizes DNA, while the other Mod subunit methylates the target
AB  - adenine-a mechanism that may extend to adenine N6 RNA methylation in mammalian
AB  - cells. Together the structure sheds new light on the mechanisms of both helicases
AB  - and methyltransferases in DNA and RNA metabolism.
ER  -

TY  - JOUR
AU  - Gupta, Y.K.
AU  - Yang, L.
AU  - Chan, S.H.
AU  - Samuelson, J.C.
AU  - Xu, S.Y.
AU  - Aggarwal, A.K.
TI  - Structural Insights into the Assembly and Shape of Type III Restriction-Modification (R-M) EcoP15I Complex by Small-Angle X-ray Scattering.
JO  - J. Mol. Biol.
PY  - 2012
SP  - 261
EP  - 268
VL  - 420
AB  - EcoP15I is the prototype of the Type III restriction enzyme family, composed of two
AB  - modification (Mod) subunits to which two (or one)
AB  - restriction (Res) subunits are then added. The Mod subunits are
AB  - responsible for DNA recognition and methylation, while the Res subunits
AB  - are responsible for ATP hydrolysis and cleavage. Despite extensive
AB  - biochemical and genetic studies, there is still no structural
AB  - information on Type III restriction enzymes. We present here
AB  - small-angle X-ray scattering (SAXS) and analytical ultracentrifugation
AB  - analysis of the EcoP15I holoenzyme and the Mod(2) subcomplex. We show
AB  - that the Mod(2) subcomplex has a relatively compact shape with a radius
AB  - of gyration (R-G) of similar to 37.4 angstrom and a maximal dimension
AB  - of similar to 110 angstrom. The holoenzyme adopts an elongated crescent
AB  - shape with an R-G of similar to 65.3 angstrom and a maximal dimension
AB  - of similar to 218 angstrom. From reconstructed SAXS envelopes, we
AB  - postulate that Mod(2) is likely docked in the middle of the holoenzyme
AB  - with a Res subunit at each end. We discuss the implications of our
AB  - model for EcoP15I. action, whereby the Res subunits may come together
AB  - and form a 'sliding clamp' around the DNA.
ER  -

TY  - JOUR
AU  - Guray, A.
AU  - Erarslan, A.
AU  - Ozbilen, O.
TI  - A buffer system suitable for most restriction enzymes.
JO  - DOGA TU J. Biol.
PY  - 1989
SP  - 14
EP  - 17
VL  - 13
AB  - For the digestion of DNA samples by several restriction enzymes, the use of a
AB  - single potassium glutamate buffer instead of different buffers recommended by
AB  - the manufacturers was investigated.  Almost all of the restriction enzymes that
AB  - we have tested to digest lambda DNA, showed the same activity with both buffer
AB  - systems.  Thus the convenience of potassium glutamate buffer was clearly
AB  - understood to be used with most restriction enzymes in place of the buffers
AB  - recommended by the vendors.
ER  -

TY  - JOUR
AU  - Guschlbauer, W.
TI  - The DNA and S-adenosylmethionine-binding regions of EcoDam and related methyltransferases.
JO  - Gene
PY  - 1988
SP  - 211
EP  - 214
VL  - 74
AB  - Previous comparison of the amino acid sequences of the GATC-methylating Escherichia coli Dam
AB  - methyltransferase (MTase) with those of other adenine MTases (M.EcoRV, M.DpnII and T4Dam)
AB  - localized four conserved regions. Regions III and IV have similarities with many other MTases.
AB  - The sequence DPPY (or NPPY) is always present in region IV. It was suggested to be the AdoMet
AB  - binding site. Publication of the nucleotide and amino acid sequences of M.CviBIII, M.DpnA and
AB  - MutH give further credence to this assignment: M.DpnA, which also methylates GATC, has strong
AB  - similarities with regions III and IV; M.CviBIII, a cytosine methylase, has a characteristic
AB  - NPPY sequence in region IV, and only limited resemblance in region III; MutH, the
AB  - GATC-specific endonuclease in DNA mismatch repair, has significant similarities uniquely in
AB  - region III. The presently available evidence suggests that region III is the GAT(C) binding
AB  - site and region IV is the AdoMet binding site. This hypothesis is strengthened by recent
AB  - genetic findings.
ER  -

TY  - JOUR
AU  - Guseinov, O.A.
AU  - Bogdarina, I.G.
AU  - Kossykh, V.G.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Sensitivity of chromosomal and plasmid E. coli DNA to restriction endonuclease EcoRII.
JO  - Biokhimiia
PY  - 1978
SP  - 1718
EP  - 1720
VL  - 43
AB  - It was shown that E. coli C, E. coli MRE 600 DNA, and also plasmid DNA of Col E1, RSF 2124
AB  - from E. coli K-12, and plasmid DNA from E. coli MRE 600 were completely resistant against
AB  - restriction endonuclease R. EcoRII.  Plasmid DNA's of Col E1, RSF 2124 amplified for 4 hours
AB  - in the presence of chloramphenicol are sensitive to R.EcoRII but after 16-hour amplification
AB  - in the presence of chloramphenicol these DNA's acquire complete resistance against R.EcoRII.
AB  - These data point to the slower rate of modification of DNA in vivo by DC-methylases of EcoRII
AB  - type in comparison with DNA methylase EcoRII.
ER  -

TY  - JOUR
AU  - Guss, A.M.
AU  - Olson, D.G.
AU  - Caiazza, N.C.
AU  - Lynd, L.R.
TI  - Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum.
JO  - Biotechnol. Biofuels.
PY  - 2012
SP  - 30
EP  - 30
VL  - 5
AB  - Background: Industrial production of biofuels and other products by cellulolytic
AB  - microorganisms is of interest but hindered by the nascent
AB  - state of genetic tools. Although a genetic system for Clostridium
AB  - thermocellum DSM1313 has recently been developed, available methods
AB  - achieve relatively low efficiency and similar plasmids can transform C.
AB  - thermocellum at dramatically different efficiencies.
AB  - Results: We report an increase in transformation efficiency of C.
AB  - thermocellum for a variety of plasmids by using DNA that has been
AB  - methylated by Escherichia coli Dam but not Dcm methylases. When
AB  - isolated from a dam + dcm + E. coli strain, pAMG206 transforms C.
AB  - thermocellum 100-fold better than the similar plasmid pAMG205, which
AB  - contains an additional Dcm methylation site in the pyrF gene. Upon
AB  - removal of Dcm methylation, transformation with pAMG206 showed a four-
AB  - to seven-fold increase in efficiency; however, transformation
AB  - efficiency of pAMG205 increased 500-fold. Removal of the Dcm
AB  - methylation site from the pAMG205 pyrF gene via silent mutation
AB  - resulted in increased transformation efficiencies equivalent to that of
AB  - pAMG206. Upon proper methylation, transformation efficiency of plasmids
AB  - bearing the pMK3 and pB6A origins of replication increased ca. three
AB  - orders of magnitude.
AB  - Conclusions: E. coli Dcm methylation decreases transformation
AB  - efficiency in C. thermocellum DSM1313. The use of properly methylated
AB  - plasmid DNA should facilitate genetic manipulation of this industrially
AB  - relevant bacterium.
ER  -

TY  - JOUR
AU  - Guthrie, E.P.
AU  - Quinton-Jager, T.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Kucera, R.B.
AU  - Benner, J.S.
AU  - Wilson, G.G.
AU  - Brooks, J.E.
TI  - Cloning, expression and sequence analysis of the SphI restriction-modification system.
JO  - Gene
PY  - 1996
SP  - 107
EP  - 112
VL  - 180
AB  - SphI, a type II restriction-modification system from the bacterium Streptomyces
AB  - phaeochromogenes, recognizes the sequence 5'-GCATGC.  The SphI methyltransferase encoding
AB  - gene, sphIM, was cloned into Escherichia coli using Mtase selection to isolate the clone.
AB  - However, none of these clones contained the restriction endonuclease gene.  Repeated attempts
AB  - to clone the complete Enase gene along with sphIM in one step failed, presumably due to
AB  - expression of SphI Enase gene, sphIR, in the presence of inadequate expression of sphIM.  The
AB  - complete sphIR was finally cloned using a two-step process.  PCR was used to isolate the 3'
AB  - end of sphIR from a library.  The intact sphIR, reconstructed under control of an inducible
AB  - promoter, was introduced into an E. coli strain containing a plasmid with the NlaIII
AB  - Mtase-encoding gene (nlaIIIM).  The nucleotide sequence of the SphI system was determined,
AB  - analyzed and compared to previously sequenced R-M systems.  The sequence was also examined for
AB  - features which would help explain why sphIR unlike other actinomycete Enase genes seemed to be
AB  - expressed in E. coli.
ER  -

TY  - JOUR
AU  - Gutierrez, G.
TI  - Draft Genome Sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium Isolated from the Methane Producer Amoeba Pelomyxa palustris.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6967
EP  - 6968
VL  - 194
AB  - Here is reported the draft genome sequence of Methanobacterium formicicum DSM 3637, which was
AB  - isolated from the methane-producing amoeba Pelomyxa palustris.
AB  - This bacterium was determined to be an endosymbiont living in the cytoplasm of P.
AB  - palustris and the source of methane; however, the global characteristics of its
AB  - genome suggest a free-living lifestyle rather than an endosymbiotic one.
ER  -

TY  - JOUR
AU  - Gutierrez, T. et al.
TI  - Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate  Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.
JO  - Genome Announcements
PY  - 2015
SP  - e00672
EP  - e00615
VL  - 3
AB  - Porticoccus hydrocarbonoclasticus strain MCTG13d is a recently discovered bacterium that is
AB  - associated with marine eukaryotic phytoplankton and that almost
AB  - exclusively utilizes polycyclic aromatic hydrocarbons (PAHs) as the sole source
AB  - of carbon and energy. Here, we present the genome sequence of this strain, which
AB  - is 2,474,654 bp with 2,385 genes and has an average G+C content of 53.1%.
ER  -

TY  - JOUR
AU  - Gutierrez, T. et al.
TI  - Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic  Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic  Phytoplankton.
JO  - Genome Announcements
PY  - 2015
SP  - e00207
EP  - e00215
VL  - 3
AB  - Polycyclovorans algicola strain TG408 is a recently discovered bacterium associated with
AB  - marine eukaryotic phytoplankton and exhibits the ability to
AB  - utilize polycyclic aromatic hydrocarbons (PAHs) almost exclusively as sole
AB  - sources of carbon and energy. Here, we present the genome sequence of this
AB  - strain, which is 3,653,213 bp, with 3,477 genes and an average G+C content of
AB  - 63.8%.
ER  -

TY  - JOUR
AU  - Gutierrez, T. et al.
TI  - Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton.
JO  - Genome Announcements
PY  - 2016
SP  - e00765
EP  - e00716
VL  - 4
AB  - Arenibacter algicola strain TG409 was isolated from Skeletonema costatum and exhibits the
AB  - ability to utilize polycyclic aromatic hydrocarbons as sole sources
AB  - of carbon and energy. Here, we present the genome sequence of this strain, which
AB  - is 5,550,230 bp with 4,722 genes and an average G+C content of 39.7%.
ER  -

TY  - JOUR
AU  - Gutierrez, T. et al.
TI  - Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00793
EP  - e00715
VL  - 3
AB  - Halomonas sp. strain MCTG39a was isolated from coastal sea surface water based on its ability
AB  - to utilize n-hexadecane. During growth in marine medium the strain
AB  - produces an amphiphilic exopolymeric substance (EPS) amended with glucose, which
AB  - emulsifies a variety of oil hydrocarbon substrates. Here, we present the genome
AB  - sequence of this strain, which is 4,979,193 bp with 4,614 genes and an average
AB  - G+C content of 55.0%.
ER  -

TY  - JOUR
AU  - Gutierrez, T. et al.
TI  - Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum.
JO  - Genome Announcements
PY  - 2016
SP  - e00937
EP  - e00916
VL  - 4
AB  - Marinobacter sp. strain MCTG268 was isolated from the cosmopolitan marine diatom  Skeletonema
AB  - costatum and can degrade oil hydrocarbons as sole sources of carbon
AB  - and energy. Here, we present the genome sequence of this strain, which is
AB  - 4,449,396 bp with 4,157 genes and an average G+C content of 57.0%.
ER  -

TY  - JOUR
AU  - Gutierrez, T.
AU  - Whitman, W.B.
AU  - Huntemann, M.
AU  - Copeland, A.
AU  - Chen, A.
AU  - Vargese, N.
AU  - Kyrpides, N.C.
AU  - Pillay, M.
AU  - Ivanova, N.
AU  - Mikhailova, N.
AU  - Mukherjee, S.
AU  - Stamatis, D.
AU  - Reddy, T.B.K.
AU  - Ngan, C.Y.
AU  - Chovatia, M.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Woyke, T.
TI  - Genome Sequence of Roseovarius sp. Strain MCTG156(2b) Isolated from a Phytoplankton Net Trawl on the Scottish West Coast.
JO  - Genome Announcements
PY  - 2017
SP  - e00837
EP  - e00817
VL  - 5
AB  - Roseovarius sp. strain MCTG156(2b) was isolated from a phytoplankton net sample collected on
AB  - the west coast of Scotland and was selected based on its ability to
AB  - degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of
AB  - this strain, which is 5,113,782 bp, with 5,142 genes and an average G+C content
AB  - of 60.7%.
ER  -

TY  - JOUR
AU  - Gutierrez, T.
AU  - Whitman, W.B.
AU  - Huntemann, M.
AU  - Copeland, A.
AU  - Chen, A.
AU  - Vargese, N.
AU  - Kyrpides, N.C.
AU  - Pillay, M.
AU  - Ivanova, N.
AU  - Mikhailova, N.
AU  - Mukherjee, S.
AU  - Stamatis, D.
AU  - Reddy, T.B.K.
AU  - Ngan, C.Y.
AU  - Chovatia, M.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Woyke, T.
TI  - Genome Sequence of Oceanicola sp. Strain MCTG156(1a), Isolated from a Scottish Coastal Phytoplankton Net Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e00796
EP  - e00717
VL  - 5
AB  - Oceanicola sp. strain MCTG156(1a) was isolated from a phytoplankton net sample collected on
AB  - the west coast of Scotland and selected based on its ability to
AB  - degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of
AB  - this strain, which comprises 3,881,122 bp with 3,949 genes and an average G+C
AB  - content of 62.7%.
ER  -

TY  - JOUR
AU  - Gutierrez-Escobar, A.J.
AU  - Bayona, R.M.
AU  - Barragan, V.C.
AU  - Trujillo, C.E.
AU  - Bravo, M.M.
TI  - Draft Genome Sequence of a Helicobacter pylori Strain Isolated from a Patient with Diffuse Gastritis from a Region of High Cancer Risk in Colombia.
JO  - Genome Announcements
PY  - 2015
SP  - e00244
EP  - e00215
VL  - 3
AB  - The draft genome sequence of one Colombian Helicobacter pylori strain is presented. This
AB  - strain was isolated from a patient with diffuse gastritis from
AB  - Tibana, Boyaca, a region with high gastric cancer risk.
ER  -

TY  - JOUR
AU  - Gutjahr, A.
AU  - Xu, S.Y.
TI  - Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - e77
EP  - e77
VL  - 42
AB  - N.Gamma is a strand-specific and site-specific DNA nicking enzyme (YCG downward arrowGT or AC
AB  - upward arrowCGR). Here we describe the isolation of single and
AB  - double mutants of N.Gamma with attenuated activity. The nicking domains (NDs) of
AB  - E59A and 11 double mutants were fused to the 5mCG-binding domain of MBD2 and
AB  - generated fusion enzymes that preferentially nick 5mCG-modified DNA. The CG
AB  - dinucleotide can be modified by C5 methyltransferases (MTases) such as M.SssI,
AB  - M.HhaI or M.HpaII to create composite sites AC upward arrowYGG N(8-15) 5mCG. We
AB  - also constructed a fusion enzyme 2xMBD2-ND(N.BceSVIII) targeting more frequent
AB  - composite sites AS upward arrowYS N(5-12) 5mCG in Mn2+ buffer. 5mCG-dependent
AB  - nicking requires special digestion conditions in high salt (0.3 M KCl) or in Ni2+
AB  - buffer. The fusion enzyme can be used to nick and label 5mCG-modified plasmid and
AB  - genomic DNAs with fluorescently labeled Cy3-dUTP and potentially be useful for
AB  - diagnostic applications, DNA sequencing and optical mapping of epigenetic
AB  - markers. The importance of the predicted catalytic residues D89, H90, N106 and
AB  - H115 in N.Gamma was confirmed by mutagenesis. We found that the wild-type enzyme
AB  - N.Gamma prefers to nick 5mCG-modified DNA in Ni2+ buffer even though the nicking
AB  - activity is sub-optimal compared to the activity in Mg2+ buffer.
ER  -

TY  - JOUR
AU  - Guyot, J.-B.
AU  - Caudron, B.
TI  - Statistical significance of amino acid sequence similarity in type II DNA methyltransferases.
JO  - C.R. Acad. Sci. III
PY  - 1994
SP  - 20
EP  - 24
VL  - 317
AB  - The statistical significance of amino acid sequence similarities previously observed in type
AB  - II DNA methyltransferases has been investigated. It is shown: (1) that the intramolecular
AB  - similarities observed among various type II Mtases are not statistically significant and thus
AB  - cannot be used to support a gene duplication model; (2) that the intermolecular similarities
AB  - observed in a peptide in various type II adenine methylases are statistically confirmed; (3)
AB  - that the similarities observed between MutH and these proteins for this peptide are not
AB  - statistically significant and therefore cannot be used to propose a functional role in DNA
AB  - recognition for this peptide.
ER  -

TY  - JOUR
AU  - Guyot, J.B.
AU  - Grassi, J.
AU  - Hahn, U.
AU  - Guschlbauer, W.
TI  - The role of the preserved sequences of Dam methylase.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3183
EP  - 3190
VL  - 21
AB  - We have undertaken a site directed mutational analysis of two of the preserved regions in the
AB  - amino acids sequence of Dam methylase in order to characterize their role. Mutations in region
AB  - IV (sequence DPPY) abolish catalytic activity and greatly affect AdoMet crosslinking. Mutants
AB  - in region III display a lowered specific activity with an unchanged AdoMet crosslinking
AB  - capacity. We have also made a series of deletions both at the N and C terminal parts of the
AB  - protein, which have been found to provide inactive enzyme. We discuss the significance of
AB  - these results for the understanding of the functional properties of the enzyme.
ER  -

TY  - JOUR
AU  - Guzman, M.S.
AU  - McGinley, B.
AU  - Santiago-Merced, N.
AU  - Gupta, D.
AU  - Bose, A.
TI  - Draft Genome Sequences of Three Closely Related Isolates of the Purple Nonsulfur  Bacterium Rhodovulum sulfidophilum.
JO  - Genome Announcements
PY  - 2017
SP  - e00029
EP  - e00017
VL  - 5
AB  - We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a
AB  - single population that will serve as a model system for
AB  - understanding genomic traits that underlie metabolic variation within closely
AB  - related marine purple nonsulfur bacteria in natural microbial communities.
ER  -

TY  - JOUR
AU  - Gwinn, D.D.
AU  - Lawton, W.D.
TI  - Alteration of host specificity in Bacillus subtilis.
JO  - Bacteriol. Rev.
PY  - 1968
SP  - 297
EP  - 301
VL  - 32
AB  - Restriction of bacteriophages in host bacteria has been reported by many investigators, most
AB  - of whom have observed the phenomenon to be associated with host-induced modification.  This
AB  - report describes the restriction of bacteriophage without any apparent host-induced
AB  - modification.  After a period of incubation at 53C, Bacillus subtilis 168 (ind-) cells were
AB  - rendered permissive in their response to infection by phages SP-10 and SP-20.  Because phage
AB  - SP-20 infected heated 168 cells with an efficiency 100 times greater than phage SP-10, most of
AB  - the work described here was done with phage SP-20.
ER  -

TY  - JOUR
AU  - Gyllborg, M.C.
AU  - Sahl, J.W.
AU  - Cronin, D.C.I.I.I.
AU  - Rasko, D.A.
AU  - Mandel, M.J.
TI  - Draft Genome Sequence of Vibrio fischeri SR5, a Strain Isolated from the Light Organ of the Mediterranean Squid Sepiola robusta.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1639
EP  - 1639
VL  - 194
AB  - Here, we describe the draft genome sequence of Vibrio fischeri SR5, a squid symbiotic isolate
AB  - from Sepiola robusta in the Mediterranean Sea. This 4.3-Mbp
AB  - genome sequence represents the first V. fischeri genome from an S. robusta
AB  - symbiont and the first from outside the Pacific Ocean.
ER  -

TY  - JOUR
AU  - Ha, J.-H.
AU  - Spolar, R.S.
AU  - Record, M.T.
TI  - Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 801
EP  - 816
VL  - 209
AB  - The site-specific binding interaction of lac repressor with a symmetric
AB  - operator sequence and of EcoRI endonuclease with its specific recognition site
AB  - both exhibit a characteristic dependence of equilibrium binding constant (Kobs)
AB  - on temperature, in which Kobs attains a relative maximum in the physiologically
AB  - relevant temperature range.  This behavior, which appears to be quite general
AB  - for site-specific protein-DNA interactions, is indicative of a large negative
AB  - standard heat capacity change (DeltaCoP,obs) in the association process.  By
AB  - analogy with model compound transfer studies and protein folding data, we
AB  - propose that this DeltaCoP,obs results primarily from the removal of non-polar
AB  - surface from water in the association process.  From DeltaCoP,obs we obtain
AB  - semiquantitative information regarding the change in water-exposed non-polar
AB  - surface area (DeltaAnp) and the corresponding hydrophobic driving force for
AB  - association (DeltaGohyd):Delta Go hyd~8(+/- 1) x 10/1 DeltaCoP,obs~ -22 (+/-5)
AB  - DeltaAnp.  We propose that removal of non-polar surface from water (the
AB  - hydrophobic effect) and release of cations (the polyelectrolyte effect) drive
AB  - the thermodynamically unfavorable processes (e.g. conformational distortions)
AB  - necessary to achieve mutually complementary recognition surfaces (at a steric
AB  - and functional-group level) in the specific complex.
ER  -

TY  - JOUR
AU  - Haake, S.K.
AU  - Yoder, S.C.
AU  - Attarian, G.
AU  - Podkaminer, K.
TI  - Native plasmids of Fusobacterium nucleatum: Characterization and use in development of genetic systems.
JO  - J. Bacteriol.
PY  - 2000
SP  - 1176
EP  - 1180
VL  - 182
AB  - Three native plasmids of Fusobacterium nucleatum were characterized, including DNA sequence
AB  - analysis of one plasmid, pFN1. A shuttle plasmid, pHS17, capable of transforming Escherichia
AB  - coli and F. nucleatum ATCC 10953 was constructed with pFN1. pHS17 was stably maintained in the
AB  - F. nucleatum transformants, and differences in the transformation efficiencies suggested the
AB  - presence of a restriction-modification system in F. nucleatum.
ER  -

TY  - JOUR
AU  - Haas, D.
AU  - Gerbaud, C.
AU  - Sahin, N.
AU  - Pernodet, J.L.
AU  - Lautru, S.
TI  - Draft Genome Sequence of Streptomyces sp. M1013, a Close Relative of Streptomyces ambofaciens and Streptomyces coelicolor.
JO  - Genome Announcements
PY  - 2017
SP  - e00643
EP  - e00617
VL  - 5
AB  - We report the draft genome sequence of Streptomyces sp. M1013, a strain isolated  from the
AB  - Medicago arborea rhizosphere in Izmir, Turkey. An average nucleotide
AB  - identity (ANI) analysis reveals that this strain belongs to the same species as
AB  - Streptomyces canus ATCC12647 and is closely related to Streptomyces ambofaciens
AB  - and Streptomyces coelicolor.
ER  -

TY  - JOUR
AU  - Habe, H.
AU  - Kobuna, A.
AU  - Hosoda, A.
AU  - Kouzuma, A.
AU  - Yamane, H.
AU  - Nojiri, H.
AU  - Omori, T.
AU  - Watanabe, K.
TI  - Subtractive hybridization and random arbitrarily primed PCR analyses of a benzoate-assimilating bacterium, Desulfotignum balticum.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2008
SP  - 87
EP  - 95
VL  - 79
AB  - Subtractive hybridization (SH) and random arbitrarily primed PCR (RAP-PCR) were used to detect
AB  - genes involved in anaerobic benzoate degradation by
AB  - Desulfotignum balticum. Through SH, we obtained 121 DNA sequences specific
AB  - for D. balticum but not for D. phosphitoxidans (a
AB  - non-benzoate-assimilating species). Furthermore, RAP-PCR analysis showed
AB  - that a 651-bp DNA fragment, having 55% homology with the solute-binding
AB  - protein of the ABC transporter system in Methanosarcina barkeri, was
AB  - expressed when D. balticum was grown on benzoate, but not on pyruvate. By
AB  - shotgun sequencing of the fosmid clone (38,071 bp) containing the DNA
AB  - fragment, 33 open reading frames (ORFs) and two incomplete ORFs were
AB  - annotated, and several genes within this region corresponded to the DNA
AB  - fragments obtained by SH. An 11.3-kb gene cluster (ORF10-17) revealed
AB  - through reverse transcription-PCR showed homology with the ABC transporter
AB  - system and TonB-dependent receptors, both of which are presumably involved
AB  - in the uptake of siderophore/heme/vitamin B(12), and was expressed in
AB  - response to growth on benzoate.
ER  -

TY  - JOUR
AU  - Haber, J.E.
AU  - Wolfe, K.H.
TI  - Function and evolution of HO and VDE endonucleases in fungi.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 161
EP  - 175
VL  - 16
AB  - The site-specific HO and VDE endonucleases are unusual members of a family of so-called group
AB  - I LAGLIDADG homing endonucleases that are generally implicated in the homing of intron and
AB  - intein sequences.  The great majority of these endonucleases are found in mitochondria and
AB  - plastids of eukaryotes, but in budding yeast two members of this family apparently "escaped"
AB  - into the nucleus.  In each case, the endonuclease creates a site-specific double-strand break
AB  - in a target and promotes mobility of DNA sequences by homologous recombination requiring the
AB  - Rad52 and Rad51 group of recombination proteins.  The HO endonuclease has been the subject of
AB  - a great deal of interest, both because of its remarkable evolution and because of its great
AB  - utility in the detailed analysis of DSB-mediated recombination.  Unlike most homing
AB  - endonucleases, the HO endonuclease does not promote its own amplification, but rather
AB  - catalyzes the switching/replacement of yeast's mating-type genes.  In addition, budding
AB  - yeasts harbor the VDE endonuclease, which is found as an intein in the VMA1 gene.  VDE
AB  - promotes its propagation from a VMA1 gene containing the VDE intein into a VMA1 gene lacking
AB  - such a sequence.  VDE is remarkable also in sharing a close sequence and presumably
AB  - evolutionary relationship with HO.
ER  -

TY  - JOUR
AU  - Haber, K.
AU  - Neumark, T.
AU  - Foldes, I.
TI  - Restriction-modification like phenomenon observed in Mycobacterium smegmatis strains are consequences of natural polylysogeny.
JO  - Acta Microbiol. Hung.
PY  - 1988
SP  - 180
EP  - 181
VL  - 35
AB  - Titrating phage butyricum (By) on its original host, Mycobacterium smegmatis
AB  - butyricum, and on M. smegmatis SN2 (SN2), phenomena similar to
AB  - restriction-modification could be observed.  On the contrary, observations
AB  - showing that By phages propagated on SN2 cells have altered morphological
AB  - structure - instead of the icosahedral shape of the head of phage By, the head
AB  - of phage By propagated on SN2 cells is elongated - could not be explained by
AB  - the effect of DNA modification.  It has been assumed that the phenomena
AB  - observed resulted as a consequence of natural lysogeny of the M. smegmatis
AB  - strains.  This hypothesis was proved by biological methods and electron
AB  - microscopic observations.  Phages with non-contractile tails of both types of
AB  - head morphology were found to be present in lysates of M. smegmatis butyricum
AB  - and SN2 cells, showing the polylysogenic property of their strains.
ER  -

TY  - JOUR
AU  - Haberman, A.
TI  - The bacteriophage P1 restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 545
EP  - 563
VL  - 89
AB  - The bacteriophage P1 restriction endonuclease has been purified from
AB  - Escherichia coli lysogenic for P1.  This restriction endonuclease P has a
AB  - sedimentation coefficient of 9.3S.  Unlike the E. coli K restriction
AB  - endonuclease, endonuclease P does not require S-adenosylmethionine for breakage
AB  - of DNA.  S-adenosylmethionine does, however, stimulate the rate of
AB  - double-strand breakage of DNA by endonuclease P.  Hydrolysis of ATP by
AB  - endonuclease P could not be detected under conditions in which the K
AB  - restriction endonuclease massively degrades ATP.  The enzyme makes a limited
AB  - number of double-strand breaks in unmodified or heterologously modified lambda
AB  - DNA.  In the presence of S-adenosylmethionine, it does not cut every DNA
AB  - molecule to the same extent.  Incubation of lambda DNA with excess amounts of
AB  - the enzyme results in less breakage of the DNA than with smaller amounts of
AB  - enzyme.  This effect is not seen in the absence of S-adenosylmethionine appears
AB  - to be greater than the maximum amount of cutting in its presence.  This is most
AB  - likely due to the modification methylase activity of P1 restriction
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Haberman, A.
AU  - Heywood, J.
AU  - Meselson, M.
TI  - DNA modification methylase activity of Escherichia coli restriction endonucleases K and P.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3138
EP  - 3141
VL  - 69
AB  - The highly purified restriction endonucleases of E. coli K and coliphage P1
AB  - transfer methyl groups from S-adenosylmethionine to adenine residues of
AB  - unmodified DNA.  Incubation of unmodified DNA with endonucleases K or P and
AB  - S-adenosylmethionine renders the DNA resistant to restriction.  The enzymes,
AB  - therefore, have both restriction endonuclease and modification methylase
AB  - activities.
ER  -

TY  - JOUR
AU  - Habibi, R.
AU  - Tarighi, S.
AU  - Behravan, J.
AU  - Taheri, P.
AU  - Kjoller, A.H.
AU  - Brejnrod, A.
AU  - Madsen, J.S.
AU  - Sorensen, S.J.
TI  - Whole-Genome Sequence of Pseudomonas fluorescens EK007-RG4, a Promising Biocontrol Agent against a Broad Range of Bacteria, Including the Fire Blight  Bacterium Erwinia amylovora.
JO  - Genome Announcements
PY  - 2017
SP  - e00026
EP  - e00017
VL  - 5
AB  - Here, we report the first draft whole-genome sequence of Pseudomonas fluorescens  strain
AB  - EK007-RG4, which was isolated from the phylloplane of a pear tree. P.
AB  - fluorescens EK007-RG4 displays strong antagonism against Erwinia amylovora, the
AB  - causal agent for fire blight disease, in addition to several other pathogenic and
AB  - non-pathogenic bacteria.
ER  -

TY  - JOUR
AU  - Hadi, S.M.
TI  - A site-specific DNA methylase from Escherichia coli K.
JO  - Indian J. Biochem. Biophys.
PY  - 1981
SP  - 295
EP  - 297
VL  - 18
AB  - A DNA methylase has been partially purified from E. coli K using heparin-agarose and
AB  - DEAE-sephacel chromatography.  Plasmid pBR322 DNA was methylated by the enzyme and cleaved
AB  - with restriction endonuclease HaeIII.  Among the DNA fragments obtained, only a few were
AB  - methylated demonstrating that the enzyme recognizes specific sites on DNA.  Since all the
AB  - EcoRII cleavage sites fall within the methylated fragments, the DNA methylase may be the
AB  - cytosine methylase of E. coli K which is known to render the methylated sites resistant to
AB  - EcoRII cleavage.
ER  -

TY  - JOUR
AU  - Hadi, S.M.
AU  - Bachi, B.
AU  - Iida, S.
AU  - Bickle, T.A.
TI  - DNA restriction-modification enzymes of phage P1 and plasmid p15B.
JO  - J. Mol. Biol.
PY  - 1983
SP  - 19
EP  - 34
VL  - 165
AB  - We have purified the type III restriction enzymes EcoPI and EcoP15 to
AB  - homogeneity from bacteria that contain the structural genes for the enzymes
AB  - cloned on small, multicopy plasmids and which overproduce the enzymes.  Both of
AB  - the enzymes contain two different subunits.  The molecular weights of the
AB  - subunits are the same for both enzymes and antibodies prepared against one
AB  - enzyme cross-react with both subunits of the other.  Bacteria containing a
AB  - plasmid derivative in which a large part of one of the structural genes has
AB  - been deleted have a restriction- modification+ phenotype and contain only the
AB  - smaller of the two subunits.  This subunit therefore must be the one that both
AB  - recognizes the specific DNA sequence and methylates it in the modification
AB  - reaction (the restriction enzyme itself also acts as a modification methylase).
AB  - We have purified the PI and P15 modification subunits from these deletion
AB  - derivatives and have shown that in vitro they have the expected properties:
AB  - they are sequence-specific modification methylases.  In addition, we have
AB  - demonstrated that strains carrying the full restriction/modification system
AB  - also contain a pool of free modification subunits that might be responsible for
AB  - in vivo modification.
ER  -

TY  - JOUR
AU  - Hadi, S.M.
AU  - Bachi, B.
AU  - Shepherd, J.C.W.
AU  - Yuan, R.
AU  - Ineichen, K.
AU  - Bickle, T.A.
TI  - DNA Recognition and Cleavage by the EcoP15 Restriction Endonuclease.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 655
EP  - 666
VL  - 134
AB  - EcoP15 is a restriction-modification enzyme coded by the P15 plasmid of
AB  - Escherichia coli.  We have determined the sites recognized by this enzyme on
AB  - pBR322 and simian virus 40 DNA.  The enzyme recognizes the sequence: 5'
AB  - C-A-G-C-A-G 3'. . . . . . 3' G-T-C-G-T-C 5' for restriction, the enzyme cleaves
AB  - the DNA 25 to 26 base-pairs 3' to this sequence and cleaves single-stranded 5'
AB  - protrusions two bases long.
ER  -

TY  - JOUR
AU  - Hadi, S.M.
AU  - Bickle, T.A.
AU  - Yuan, R.
TI  - The role of S-adenosylmethionine in the cleavage of deoxyribonucleic acid by the restriction endonuclease from Escherichia coli K.
JO  - J. Biol. Chem.
PY  - 1975
SP  - 4159
EP  - 4164
VL  - 250
AB  - The restriction endonuclease from Escherichia coli K specifically cleaves
AB  - foreign DNA in the presence of S-adenosylmethionine, ATP, and Mg++.  The role
AB  - of S-adenosylmethionine in this reaction has been studied by following the
AB  - specific binding of the enzyme to unmodified DNA.  The results indicate that
AB  - S-adenosylmethionine acts as an allosteric effector.  However, the
AB  - rate-limiting step in the activation of the enzyme is not the binding of the
AB  - effector itself, but an event subsequent to it.  The interaction of the
AB  - S-adenosylmethionine with two mutant K restriction endonucleases isolated
AB  - previously has also been investigated.  One of them, which is defective in
AB  - restriction, can be activated in a manner similar to the wild type enzyme,
AB  - while the other one, which lacks both restriction and modification activities
AB  - (due to a mutation in the subunit responsible for DNA recognition), shows no
AB  - such effect.
ER  -

TY  - JOUR
AU  - Hadi, S.M.
AU  - Yuan, R.
TI  - Complementation in vitro by restriction enzymes from mutant strains E. coli K12.
JO  - Experientia
PY  - 1973
SP  - 752
EP  - 752
VL  - 29
AB  - The restriction endonuclease from E. coli K12 has previously been shownw to a)
AB  - bind and then cleave unmodified lambda DNA in the presence of SAM, ATP and
AB  - Mg++, b) hydrolyze the ATP to ADP and inorganic phosphate in the course of the
AB  - restriction reaction, and c) methylate unmodified lambda DNA when only SAM is
AB  - present.  The restriction deficient mutant strains from E. coli K12, gamma
AB  - K-mK+ and gamma K-mK- have been shown to complement in vivo to yield a wild
AB  - type phenotype, gamma K+mK+.  Using a binding assay based on complementation in
AB  - vitro between the two mutant extracts, the restriction endonucleases from the
AB  - two mutant strains were purified extensively.  Complementation in vitro could
AB  - be detected by specific binding and also by cleavage of the unmodified DNA when
AB  - both mutant proteins were present.  Either mutant protein by itself showed no
AB  - activity.  Studies on the methylase and ATPase activities of these mutant
AB  - proteins, either alone or in combination are currently in progress.
ER  -

TY  - JOUR
AU  - Hadi, S.M.
AU  - Yuan, R.
TI  - Complementation in vitro by mutant restriction enzymes from Escherichia coli K.
JO  - J. Biol. Chem.
PY  - 1974
SP  - 4580
EP  - 4586
VL  - 249
AB  - Two mutant strains of Escherichia coli K, K-18 lacking restriction activity
AB  - (endonucleolytic cleavage of foreign DNA), and the other, K-19 lacking both
AB  - restriction and modification activities (specific DNA methylation that protects
AB  - against the homologous restriction activity), complement in vivo to yield a
AB  - wild type phenotype.  Although neither mutant extract alone binds unmodified
AB  - DNA, the wild type extract and the mixture of mutant extracts do.  Retention of
AB  - the DNA-enzyme complex on membrane filters was used as an assay to purify the
AB  - two mutant restriction enzymes.  Both of these sediment like the wild type
AB  - enzyme.  Complementation in vitro by the two mutant enzymes could be
AB  - demonstrated by specific DNA binding, cleavage of the unmodified DNA, and
AB  - restriction-dependent ATP hydrolysis.  All of these activities are absent in
AB  - the individual mutant endonucleases but present in the wild type restriction
AB  - endonuclease from E. coli K.  However, both mutant enzymes show an activity
AB  - that hydrolyzes ATP which is different from that of the wild type enzyme since
AB  - it does not require unmodified DNA, but is dependent on the presence of
AB  - S-adenosylmethionine.
ER  -

TY  - JOUR
AU  - Hadjadj, L.
AU  - Jiyipong, T.
AU  - Bittar, F.
AU  - Morand, S.
AU  - Rolain, J.M.
TI  - First Draft Genome Sequences of Two Bartonella tribocorum Strains from Laos and Cambodia.
JO  - Genome Announcements
PY  - 2018
SP  - e01435
EP  - e01417
VL  - 6
AB  - Bartonella tribocorum is a Gram-negative bacterium known to infect animals, and rodents in
AB  - particular, throughout the world. In this report, we present the draft
AB  - genome sequences of two strains of B. tribocorum isolated from the blood of a
AB  - rodent in Laos and a shrew in Cambodia.
ER  -

TY  - JOUR
AU  - Hadjadj, L.
AU  - Rathored, J.
AU  - Keita, M.B.
AU  - Michelle, C.
AU  - Levasseur, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Rolain, J.M.
AU  - Bittar, F.
TI  - Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 32
EP  - 32
VL  - 11
AB  - Strain G3(T) (CSUR P207 = DSM 26203) was isolated from the fecal sample of a wild gorilla
AB  - (Gorilla gorilla subsp gorilla) from Cameroon. It is a Gram-positive,
AB  - facultative anaerobic short rod. This strain exhibits a 16S rRNA sequence
AB  - similarity of 98.2 % with Microbacterium thalassium, the closest validly
AB  - published Microbacterium species and member of the family Microbacteriaceae.
AB  - Moreover, it shows a low MALDI-TOF-MS score (1.1 to 1.3) that does not allow any
AB  - identification. Thus, it is likely that this strain represents a new species.
AB  - Here we describe the phenotypic features of this organism, the complete genome
AB  - sequence and annotation. The 3,692,770 bp long genome (one chromosome but no
AB  - plasmid) contains 3,505 protein-coding and 61 RNA genes, including 4 rRNA genes.
AB  - In addition, digital DNA-DNA hybridization values for the genome of the strain
AB  - G3(T) against the closest Microbacterium genomes range between 19.7 to 20.5, once
AB  - again confirming its new status as a new species. On the basis of these
AB  - polyphasic data, consisting of phenotypic and genomic analyses, we propose the
AB  - creation of Microbacterium gorillae sp. nov. that contains the strain G3(T).
ER  -

TY  - JOUR
AU  - Hadziabdic, S.
AU  - Borowiak, M.
AU  - Bloch, A.
AU  - Malorny, B.
AU  - Szabo, I.
AU  - Guerra, B.
AU  - Kaesbohrer, A.
AU  - Fischer, J.
TI  - Complete Genome Sequence of an Avian Native NDM-1-Producing Salmonella enterica subsp. enterica Serovar Corvallis Strain.
JO  - Genome Announcements
PY  - 2018
SP  - e00593
EP  - e00518
VL  - 6
AB  - Carbapenems are an important class of beta-lactams and one of the last options for treating
AB  - severe human infections. We present here the complete genome
AB  - sequence of avian native carbapenemase-producing Salmonella enterica subsp.
AB  - enterica serovar Corvallis strain 12-01738, harboring a blaNDM-1-carrying IncA/C2
AB  - plasmid, isolated in 2012 from a wild bird (Milvus migrans) in Germany.
ER  -

TY  - JOUR
AU  - Haendiges, J.
AU  - Blessington, T.
AU  - Zheng, J.
AU  - Davidson, G.
AU  - Miller, J.D.
AU  - Hoffmann, M.
TI  - Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States.
JO  - Genome Announcements
PY  - 2018
SP  - e00630
EP  - e00618
VL  - 6
AB  - A multistate outbreak of 11 Salmonella infections linked to pistachio nuts occurred in 2016.
AB  - In this announcement, we report the complete genome sequences
AB  - of four Salmonella enterica subsp. enterica serovar Senftenberg and S. enterica
AB  - subsp. enterica serovar Montevideo isolates from pistachios collected during the
AB  - 2016 outbreak investigation.
ER  -

TY  - JOUR
AU  - Haendiges, J.
AU  - Timme, R.
AU  - Allard, M.
AU  - Myers, R.A.
AU  - Payne, J.
AU  - Brown, E.W.
AU  - Evans, P.
AU  - Gonzalez-Escalona, N.
TI  - Draft Genome Sequences of Clinical Vibrio parahaemolyticus Strains Isolated in Maryland (2010 to 2013).
JO  - Genome Announcements
PY  - 2014
SP  - e00776
EP  - e00714
VL  - 2
AB  - Vibrio parahaemolyticus is the leading cause of food-borne illnesses associated with the
AB  - consumption of raw shellfish worldwide. Here, we report 45 draft genomes
AB  - of V. parahaemolyticus. Thirty-five of them are strains that were isolated from
AB  - clinical cases in the state of Maryland from 2010 to 2013. The remaining 10
AB  - strains were historical isolates, isolated mostly from the West Coast of the
AB  - United States during the period of 1988 to 2004. The availability of these
AB  - genomes will allow for future phylogenetic analyses with other V.
AB  - parahaemolyticus strains.
ER  -

TY  - JOUR
AU  - Haesendonck, R.
AU  - Van Nieuwerburgh, F.
AU  - Haesebrouck, F.
AU  - Deforce, D.
AU  - Pasmans, F.
AU  - Martel, A.
TI  - Genome Sequence of Devriesea agamarum, Isolated from Agamid Lizards with Dermatitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00949
EP  - e00915
VL  - 3
AB  - We report the genome sequence of Devriesea agamarum strain IMP2, isolated from the liver of a
AB  - female Agama impalearis. This actinobacterium is associated with
AB  - septicemia and dermatitis in agamid lizards. Availability of this genome sequence
AB  - will contribute to the understanding of this pathogen's virulence.
ER  -

TY  - JOUR
AU  - Hafez, M.
AU  - Guha, T.K.
AU  - Hausner, G.
TI  - I-OmiI and I-OmiII: Two intron-encoded homing endonucleases within the Ophiostoma minus rns gene.
JO  - Fungal Biol.
PY  - 2014
SP  - 721
EP  - 731
VL  - 118
AB  - The mitochondrial small subunit ribosomal RNA (rns) gene of the ascomycetous fungus Ophiostoma
AB  - minus [strain WIN(M)371] was found to contain a group IC2 and a group IIB1 intron at positions
AB  - mS569 and mS952 respectively. Both introns have open reading frames (ORFs) embedded that
AB  - encode double motif LAGLIDADG homing endonucleases (I-OmiI and I-OmiII respectively).
AB  - Codon-optimized versions of I-OmiI and I-OmiII were synthesized for overexpression in
AB  - Escherichia coli. The in vitro characterization of I-OmiII showed that it is a functional
AB  - homing endonuclease that cleaves the rns target site two nucleotides upstream (sense strand)
AB  - of the intron insertion site generating 4 nucleotide 3' overhangs. The endonuclease activity
AB  - of I-OmiII was tested using linear and circular substrates and cleavage activity was evaluated
AB  - at various temperatures. The I-OmiI protein was expressed in E. coli, but purification was
AB  - difficult, thus the endonuclease activity of this protein was tested via in vivo assays.
AB  - Overall this study showed that there are many native forms of functional homing endonucleases
AB  - yet to be discovered among fungal mtDNA genomes.
ER  -

TY  - JOUR
AU  - Hafstrom, T.
AU  - Jansson, D.S.
AU  - Segerman, B.
TI  - Complete Genome Sequence of Brachyspira intermedia Reveals Unique Genomic Features in Brachyspira Species and Phage-mediated Horizontal Gene Transfer.
JO  - BMC Genomics
PY  - 2011
SP  - 395
EP  - 395
VL  - 12
AB  - ABSTRACT: BACKGROUND: Brachyspira spp. colonize the intestines of some
AB  - mammalian and avian species and show different degrees of
AB  - enteropathogenicity. Brachyspira intermedia can cause production losses in
AB  - chickens and strain PWS/AT now becomes the fourth genome to be completed
AB  - in the genus Brachyspira. RESULTS: 15 classes of unique and shared genes
AB  - were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B.
AB  - pilosicoli. The largest number of unique genes was found in B. intermedia
AB  - and B. murdochii. This indicates the presence of larger pan-genomes. In
AB  - general, hypothetical protein annotations are overrepresented among the
AB  - unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT.
AB  - The plasmid was also present in the B. murdochii strain but not in nine
AB  - other Brachyspira isolates. Within the Brachyspira genomes, genes had been
AB  - translocated and also frequently switched between leading and lagging
AB  - strands, a process that can be followed by different AT-skews in the third
AB  - positions of synonymous codons. We also found evidence that bacteriophages
AB  - were being remodeled and genes incorporated into them. CONCLUSIONS: The
AB  - accessory gene pool shapes species-specific traits. It is also influenced
AB  - by reductive genome evolution and horizontal gene transfer. Gene-transfer
AB  - events can cross both species and genus boundaries and bacteriophages
AB  - appear to play an important role in this process. A mechanism for
AB  - horizontal gene transfer appears to be gene translocations leading to
AB  - remodeling of bacteriophages in combination with broad tropism.
ER  -

TY  - JOUR
AU  - Hagemann, M.
AU  - Gartner, K.
AU  - Scharnagl, M.
AU  - Bolay, P.
AU  - Lott, S.C.
AU  - Fuss, J.
AU  - Huettel, B.
AU  - Reinhardt, R.
AU  - Klahn, S.
AU  - Hess, W.R.
TI  - Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803.
JO  - DNA Res.
PY  - 2018
SP  - 343
EP  - 352
VL  - 25
AB  - DNA methylation in bacteria is important for defense against foreign DNA, but is  also
AB  - involved in DNA repair, replication, chromosome partitioning, and regulatory
AB  - processes. Thus, characterization of the underlying DNA methyltransferases in
AB  - genetically tractable bacteria is of paramount importance. Here, we characterized
AB  - the methylome and orphan methyltransferases in the model cyanobacterium
AB  - Synechocystis sp. PCC 6803. Single molecule real-time (SMRT) sequencing revealed
AB  - four DNA methylation recognition sequences in addition to the previously known
AB  - motif m5CGATCG, which is recognized by M.Ssp6803I. For three of the new
AB  - recognition sequences, we identified the responsible methyltransferases.
AB  - M.Ssp6803II, encoded by the sll0729 gene, modifies GGm4CC, M.Ssp6803III, encoded
AB  - by slr1803, represents the cyanobacterial dam-like methyltransferase modifying
AB  - Gm6ATC, and M.Ssp6803V, encoded by slr6095 on plasmid pSYSX, transfers methyl
AB  - groups to the bipartite motif GGm6AN7TTGG/CCAm6AN7TCC. The remaining methylation
AB  - recognition sequence GAm6AGGC is probably recognized by methyltransferase
AB  - M.Ssp6803IV encoded by slr6050. M.Ssp6803III and M.Ssp6803IV were essential for
AB  - the viability of Synechocystis, while the strains lacking M.Ssp6803I and
AB  - M.Ssp6803V showed growth similar to the wild type. In contrast, growth was
AB  - strongly diminished of the Deltasll0729 mutant lacking M.Ssp6803II. These data
AB  - provide the basis for systematic studies on the molecular mechanisms impacted by
AB  - these methyltransferases.
ER  -

TY  - JOUR
AU  - Hager, P.W.
AU  - Boyer, H.W.
AU  - Day, J.O.
AU  - Reich, N.O.
AU  - Greene, P.
TI  - Analysis of noncanonical DNA cleavage by EcoRI endonuclease mutants.
JO  - J. Cell Biochem. Suppl.
PY  - 1987
SP  - 206
EP  - 206
VL  - 11C
AB  - It has been proposed that DNA sequence specificity for the EcoRI endonuclease
AB  - results from the formation of twelve hydrogen bonds between bases exposed at
AB  - the major groove of the EcoRI site and six amino acid side chains (3 from each
AB  - subunit) in the enzyme.  (Rosenberg and Greene, DNA 1, 117-124 (1982),
AB  - Rosenberg et al., Science, in press) Conservative replacements in the 3 amino
AB  - acids identified in the x-ray crystallographic structure as responsible for
AB  - specificity were made (Glu 144 to Asp, Arg 145 to Lys, and Arg 200 to Lys).
AB  - These changes failed to alter the site of primary cleavage.  However, all of
AB  - these proteins nick noncanonical DNA sequences in pBR322 lacking the EcoRI
AB  - site.  The location of these single strand cleavage sites is being determined
AB  - for the wild type and mutant enzymes.  The identification of the sequences
AB  - recognized by the different enzymes and the hierarchy of the rates at which
AB  - these sequences are hydrolyzed will contribute to our understanding of how the
AB  - endonuclease discriminates between DNA squences.
ER  -

TY  - JOUR
AU  - Hager, P.W.
AU  - Reich, N.O.
AU  - Day, J.P.
AU  - Coche, T.G.
AU  - Boyer, H.W.
AU  - Rosenberg, J.M.
AU  - Greene, P.J.
TI  - Probing the role of glutamic acid 144 in the EcoRI endonuclease using aspartic acid and glutamine replacements.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 21520
EP  - 21526
VL  - 265
AB  - The x-ray structure of the EcoRI endonuclease-DNA complex suggests that
AB  - hydrogen bonds between amino acids, glutamic acid 144, arginine 145, and
AB  - arginine 200, and major groove base moieties are the molecular determinants of
AB  - specificity.  We have investigated residue 144 using aspartate and glutamine
AB  - substitutions introduced by site-directed mutagenesis.  Substitution with
AB  - glutamine results in a null phenotype (at least a 2000-fold reduction in
AB  - activity).  On the other hand, the aspartic acid mutant (ED144) retained in
AB  - vivo activity.  Substrate binding and catalytic studies were done with purified
AB  - ED144 enzyme.  The affinity of the ED144 enzyme for the canonical sequence
AB  - 5'-GAATTC-3' is about 340-fold less than the wild-type (WT) enzyme, while its
AB  - affinity for nonspecific DNA is about 50 times greater.  The ED144 enzyme
AB  - cleaves one strand in the EcoRI site in plasmid pBR322 with a kcat/Km similar
AB  - to WT.  In contrast to the WT enzyme, the ED144 enzyme dissociates after the
AB  - first strand cleavage.  Partitioning between cleavage and dissociation at the
AB  - first and second cleavage steps for the ED144 enzyme is extremely
AB  - salt-sensitive.  The altered partitioning results largely from a
AB  - destabilization of the enzyme-DNA complex, particularly the enzyme-nicked DNA
AB  - complex, with only small changes in the respective cleavage rates.  The
AB  - hydrogen bonds of Glu-144 are critical, they appear to act cooperatively with
AB  - other specificity contacts to stabilize the enzyme-DNA complex.
ER  -

TY  - JOUR
AU  - Hahn, C.
AU  - Harrison, E.M.
AU  - Parkhill, J.
AU  - Holmes, M.A.
AU  - Paterson, G.K.
TI  - Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66.
JO  - Genome Announcements
PY  - 2015
SP  - e00697
EP  - e00615
VL  - 3
AB  - We have used HiSeq 2000 technology to generate a draft genome sequence of Streptococcus
AB  - pneumoniae strain A66. This is a common study strain used in
AB  - investigations of pneumococcal bacterium-host interactions and was used in the
AB  - seminal genetic studies of Avery et al.
ER  -

TY  - JOUR
AU  - Hahn, D.R.
AU  - McHenney, M.A.
AU  - Baltz, R.H.
TI  - Characterization of FP22, a large streptomycete bacteriophage with DNA insensitive to cleavage by many restriction enzymes.
JO  - J. Gen. Microbiol.
PY  - 1990
SP  - 2395
EP  - 2404
VL  - 136
AB  - Bacteriophage FP22 has a very broad host range within streptomycetes and
AB  - appeared to form lysogens of Streptomyces ambofaciens ATCC 15154.  FP22 shared
AB  - strong cross-immunity and antibody cross-reactivity with bacteriophage P23, but
AB  - not with seven other streptomycete bacteriophages.  FP22 particles had a head
AB  - diameter of 71 nm and a tail length of 307 mm.  The FP22 genome was 131 kb,
AB  - which is the largest bacteriophage genome reported for streptomycetes.  The G+C
AB  - content of the genome was 46 mol% and restriction mapping indicated that FP22
AB  - DNA had discrete ends.  NaCl- and pyrophosphate-resistant deletion mutants were
AB  - readily isolated and the extent of the deletions defined at least 23 kb of
AB  - dispensable DNA in two regions of the genome.  The DNA was not cleaved by most
AB  - restriction endonucleases (or isoschizomers) which have been identified in the
AB  - streptomycetes, including the tetranucleotide cutter MboI (GATC).
ER  -

TY  - JOUR
AU  - Hahnke, R.L. et al.
TI  - High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 46
EP  - 46
VL  - 10
AB  - Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in
AB  - the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly
AB  - published name, and has been isolated from the spring of a hard water rivulet in Northern
AB  - Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA
AB  - gene sequence phylogeny revealed a clustering of members of the genus Myroides as a
AB  - monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its
AB  - next  relatives seem more closely related to the genus Myroides than to the type species of
AB  - the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391
AB  - protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A
AB  - rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active
AB  - enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo
AB  - (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl
AB  - transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase
AB  - families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and
AB  - one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and
AB  - algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting
AB  - candidate for further physiological studies and the role of Bacteroidetes in the decomposition
AB  - of complex polymers in the environment.
ER  -

TY  - JOUR
AU  - Hahnke, S.
AU  - Abendroth, C.
AU  - Langer, T.
AU  - Codoner, F.M.
AU  - Ramm, P.
AU  - Porcar, M.
AU  - Luschnig, O.
AU  - Klocke, M.
TI  - Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.
JO  - Genome Announcements
PY  - 2018
SP  - e00030
EP  - e00018
VL  - 6
AB  - A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of
AB  - grass, was isolated from a mesophilic two-stage laboratory-scale
AB  - leach bed biogas system. The draft annotated genome sequence presented in this
AB  - study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C
AB  - with the family Ruminococcaceae outside recently described genera.
ER  -

TY  - JOUR
AU  - Haigh, R.D.
AU  - Crawford, L.A.
AU  - Ralph, J.D.
AU  - Wanford, J.J.
AU  - Vartoukian, S.R.
AU  - Hijazi, K.
AU  - Wade, W.
AU  - Oggioni, M.R.
TI  - Draft Whole-Genome Sequences of Periodontal Pathobionts Porphyromonas gingivalis, Prevotella intermedia, and Tannerella forsythia Contain Phase-Variable  Restriction-Modification Systems.
JO  - Genome Announcements
PY  - 2017
SP  - e01229
EP  - e01217
VL  - 5
AB  - Periodontal disease comprises mild to severe inflammatory host responses to oral  bacteria
AB  - that can cause destruction of the tooth-supporting tissue. We report
AB  - genome sequences for 18 clinical isolates of Porphyromonas gingivalis, Prevotella
AB  - intermedia, and Tannerella forsythia, Gram-negative obligate anaerobes that play
AB  - a role in the periodontal disease process.
ER  -

TY  - JOUR
AU  - Haim, M.S.
AU  - Mollerach, M.
AU  - Van Domselaar, G.
AU  - Teves, S.A.
AU  - Degrossi, J.
AU  - Cardona, S.T.
TI  - Draft Genome Sequences of Burkholderia contaminans FFI-28, a Strain Isolated from a Contaminated Pharmaceutical Solution.
JO  - Genome Announcements
PY  - 2016
SP  - e01177
EP  - e01116
VL  - 4
AB  - Burkholderia contaminans is a species of the Burkholderia cepacia complex, a group of bacteria
AB  - that can grow in pharmaceutical products and are capable of
AB  - infecting the immunocompromised and people with cystic fibrosis. Here, we report
AB  - draft genome sequences for Burkholderia contaminans FFI-28, a strain isolated
AB  - from a contaminated pharmaceutical solution.
ER  -

TY  - JOUR
AU  - Haima, P.
AU  - Bron, S.
AU  - Venema, G.
TI  - The effect of restriction on shotgun cloning and plasmid stability in Bacillus subtilis Marburg.
JO  - Mol. Gen. Genet.
PY  - 1987
SP  - 335
EP  - 342
VL  - 209
AB  - Using the bifunctional cloning vehicle pHP13, which carries the replication
AB  - functions of the cryptic Bacillus subtilis plasmid pTA1060, the effects of BsuM
AB  - restriction on the efficiency of shotgun cloning of heterologous Escherichia
AB  - coli DNA were studied.  In a restriction-deficient but modification-proficient
AB  - mutant of B. subtilis, clones were obtained at a high frequency, comparable to
AB  - frequencies normally obtained in E. coli (10/4 clones per microgram target
AB  - DNA).  Large inserts were relatively abundant (26% of the clones contained
AB  - inserts in the range of 6 to 15 kb), which resulted in a high average insert
AB  - length (3.6 kb).  In the restriction-proficient B. subtilis strain, the class
AB  - of large inserts was underrepresented.  Transformation of B. subtilis with E.
AB  - coli-derived individual recombinant plasmids was affected by BsuM restriction
AB  - in two ways.  First, the transforming activities of recombinant plasmids
AB  - carrying inserts larger than 4kb, were, in comparison with the vector pHP13,
AB  - reduced to varying degrees in the restricting host.  The levels of the
AB  - reduction increased with insert length, resulting in a 7800-fold reduction for
AB  - the largest plasmid used (pC23; insert length 16 kb).  Second, more than 80% of
AB  - the pC23 transformants in the restricting strain contained a deleted plasmid.
AB  - In the non-restricting strain, the transforming activities of the plasmids were
AB  - fairly constant as a function of insert length (in the range of 0-16 kb), and
AB  - no structural instability was observed.  It is concluded that for shotgun
AB  - cloning in B. subtillis, the use of restriction-deficient strains is highly
AB  - preferable.  Evidence is presented that in addition to XhoI other sequences are
AB  - involved in BsuM restriction.  It is postulated that AsuII sites are additional
AB  - target sites for BsuM restriction.
ER  -

TY  - JOUR
AU  - Hain, T. et al.
TI  - Whole-Genome Sequence of Listeria welshimeri Reveals Common Steps in Genome Reduction with Listeria innocua as Compared to Listeria  monocytogenes.
JO  - J. Bacteriol.
PY  - 2006
SP  - 7405
EP  - 7415
VL  - 188
AB  - We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the
AB  - genus Listeria. Listeria welshimeri harbors a
AB  - circular chromosome of 2,814,130 bp with 2,780 open reading frames.
AB  - Comparative genomic analysis of chromosomal regions between L. welshimeri,
AB  - Listeria innocua, and Listeria monocytogenes shows strong overall
AB  - conservation of synteny, with the exception of the translocation of an
AB  - F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the
AB  - result of deletions in all of the genes involved in virulence and of
AB  - "fitness" genes required for intracellular survival, transcription
AB  - factors, and LPXTG- and LRR-containing proteins as well as 55 genes
AB  - involved in carbohydrate transport and metabolism. In total, 482 genes are
AB  - absent from L. welshimeri relative to L. monocytogenes. Of these, 249
AB  - deletions are commonly absent in both L. welshimeri and L. innocua,
AB  - suggesting similar genome evolutionary paths from an ancestor. We also
AB  - identified 311 genes specific to L. welshimeri that are absent in the
AB  - other two species, indicating gene expansion in L. welshimeri, including
AB  - horizontal gene transfer. The species L. welshimeri appears to have been
AB  - derived from early evolutionary events and an ancestor more compact than
AB  - L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
ER  -

TY  - JOUR
AU  - Haines, A.
AU  - Nebergall, E.
AU  - Besong, E.
AU  - Council, K.
AU  - Lambert, O.
AU  - Gauthier, D.
TI  - Draft Genome Sequences for Seven Streptococcus parauberis Isolates from Wild Fish in the Chesapeake Bay.
JO  - Genome Announcements
PY  - 2016
SP  - e00741
EP  - e00716
VL  - 4
AB  - Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus
AB  - uberis and Streptococcus iniae We report the genomes of seven S.
AB  - parauberis strains recovered from striped bass (Morone saxatilis) in the
AB  - Chesapeake Bay. The availability of these genomes will allow comparative genomic
AB  - analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured
AB  - from other animal hosts and geographic regions.
ER  -

TY  - JOUR
AU  - Halazonetis, T.D.
AU  - Kandil, A.N.
TI  - Predicted structural similarities of the DNA binding domains of c-Myc and endonuclease EcoRI.
JO  - Science
PY  - 1992
SP  - 464
EP  - 466
VL  - 255
AB  - The c-Myc oncoprotein belongs to a family of proteins whose DNA binding domains
AB  - contain a basic region-helix-loop-helix (bHLH) motif.  Systematic mutagenesis
AB  - of c-Myc revealed that dimerized bHLH motifs formed a parallel four-helix
AB  - bundle with the amino termini of helices 1 and 2 directed toward the inner and
AB  - outer nucleotides of the DNA binding site, respectively.  Both the basic region
AB  - and the carboxyl-terminal end of the loop contributed to DNA binding
AB  - specificity.  The DNA binding domain of c-Myc may therefore be structurally
AB  - similar to that of restriction endonuclease EcoRI.
ER  -

TY  - JOUR
AU  - Halden, N.F.
AU  - Wolf, J.B.
AU  - Cross, S.L.
AU  - Leonard, W.J.
TI  - Identification and characterization of a novel restriction enzyme derived from Mycoplasma fermentans.
JO  - Clin. Res.
PY  - 1988
SP  - 404a
EP  - 404a
VL  - 36
AB  - During our studies defining proteins that bind to the 5' regulatory regions of
AB  - the human interleukin-2 receptor alpha chain (IL2Ralpha,p55, Tac antigen) gene,
AB  - we have unexpectedly identified a new restriction enzyme specific for a
AB  - sequence not cleaved by any known restriction enzyme.  Nuclear extracts from
AB  - various cell lines were incubated with 32P-labeled DNA from the IL2Ralpha
AB  - promoter region.  In the absence of any exogenous nuclease, extracts from
AB  - Jurkat and MT-2 cells, but not from HeLa and HUT-102B2 cells, were capable of
AB  - cleaving the DNA.  Subsequent analysis confirmed that only the Jurkat and MT-2
AB  - T cells were infected with mycoplasma.  When extracts were prepared from the
AB  - same Jurkat cell line cured with BM cycline, the activity was not present.  We
AB  - have therefore concluded that the nuclease activity was derived from the
AB  - mycoplasma rather than the T cells.  The mycoplasma strain containing both MT-2
AB  - and Jurkat cells was identified as M. fermentans.  The new enzyme specifically
AB  - recognizes the palindrome CAATTG, is inactivated by 15 min treatment at 65C, by
AB  - proteinase K, and by 20 mM EDTA, and works optimally in low salt (<10mM NaCl)
AB  - restriction enzyme buffer.  In conclusion, this enzyme recognizes a new
AB  - recognition sequence and therefore has potential for general use in molecular
AB  - biology.  In addition, it is possible that a rapid diagnostic test for
AB  - mycoplasma may result from the use of mycoplasma specific restriction
AB  - endonuclease assays on appropriate sequences of DNA.
ER  -

TY  - JOUR
AU  - Halden, N.F.
AU  - Wolf, J.B.
AU  - Leonard, W.J.
TI  - Identification of a novel site specific endonuclease produced by Mycoplasma fermentans:  discovery while characterizing DNA binding proteins in T lymphocyte cell lines.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 3491
EP  - 3499
VL  - 17
AB  - We have discovered a new restriction endonuclease, MfeI, in nuclear extracts
AB  - from T cells contaminated with Mycoplasma fermentans.  This endonuclease was
AB  - identified while studying proteins binding to the interleukin-2 receptor alpha
AB  - chain gene promoter.  MfeI cuts at the recognition sequence C^AATTG generating
AB  - EcoRI compatible cohesive ends.  Potential applications are discussed.
ER  -

TY  - JOUR
AU  - Halder, U.
AU  - Banerjee, A.
AU  - Chaudhry, V.
AU  - Varshney, R.K.
AU  - Mantri, S.
AU  - Bandopadhyay, R.
TI  - Draft Genome Report of Bacillus altitudinis SORB11, Isolated from the Indian Sector of the Southern Ocean.
JO  - Genome Announcements
PY  - 2017
SP  - e00339
EP  - e00317
VL  - 5
AB  - Here, we present the draft genome sequence of Bacillus altitudinis SORB11, which  is tolerant
AB  - to UV radiation. The strain was isolated from the Indian sector of
AB  - the Southern Ocean at a depth of 3.8 km. The genome sequence information reported
AB  - here for B. altitudinis SORB11 gives the basis of its UV resistance mechanism and
AB  - provides data for further comparative studies with other bacteria resistant to UV
AB  - radiation.
ER  -

TY  - JOUR
AU  - Hale, W.B.
AU  - van der Woude, M.W.
AU  - Low, D.A.
TI  - Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli.
JO  - J. Bacteriol.
PY  - 1994
SP  - 3438
EP  - 3441
VL  - 176
AB  - Seven GATC sites that are nonmethylated in logarithmic growth phase cells using glycerol as a
AB  - carbon source were isolated from the Escherichia coli chromosome.  Three of these GATC sites
AB  - are located upstream of the operons gut, mtl, and ppiA, whereas DNA sequences adjacent to
AB  - three other nonmethylated GATC sites are not homologous to previously identified genes.  The
AB  - seventh nonmethylated GATC site is located downstream of uspA.  The protection of this site
AB  - from DNA methylation requires leucine-responsive regulatory protein and is leucine responsive.
AB  - The carbon source and the growth phase influenced the protection of the GATC site 5' of the
AB  - ppiA gene.  The other five sites were protected under all the environmental conditions
AB  - examined.
ER  -

TY  - JOUR
AU  - Haley, B.J.
AU  - Choi, S.Y.
AU  - Hasan, N.A.
AU  - Abdullah, A.S.
AU  - Cebula, T.A.
AU  - Huq, A.
AU  - Colwell, R.R.
TI  - Genome Sequences of Clinical Vibrio cholerae Isolates from an Oyster-Borne Cholera Outbreak in Florida.
JO  - Genome Announcements
PY  - 2013
SP  - e00966
EP  - e00913
VL  - 1
AB  - Between November 2010 and April 2011, 11 cases of cholera were identified and associated with
AB  - the consumption of raw oysters harvested from Apalachicola Bay,
AB  - Florida. The etiological agent was the ctxAB-positive Vibrio cholerae serogroup
AB  - O75. The genome sequences of the isolates provide useful information and are
AB  - deposited in the public genome databases.
ER  -

TY  - JOUR
AU  - Haley, B.J.
AU  - Kim, S.W.
AU  - Liljebjelke, K.
AU  - Guard, J.
AU  - Van Kessel, J.A.
TI  - Genome Sequences of Two Salmonella enterica Serovar Kentucky Isolates Recovered from Poultry Carcasses in the United States.
JO  - Genome Announcements
PY  - 2016
SP  - e01289
EP  - e01216
VL  - 4
AB  - We report here the draft genome sequences of two Salmonella enterica serovar Kentucky
AB  - eBurstGroup 15 isolates collected from poultry carcasses in Georgia
AB  - (USA).
ER  -

TY  - JOUR
AU  - Haley, B.J.
AU  - Kim, S.W.
AU  - Whitehead, T.R.
TI  - Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit.
JO  - Genome Announcements
PY  - 2016
SP  - e00978
EP  - e00916
VL  - 4
AB  - The swine gastrointestinal tract and stored swine manure may serve as reservoirs  of
AB  - antibiotic resistance genes, as well as sources of novel bacteria. Here, we
AB  - report the draft genome sequence of a novel taxon in the Erysipelotrichaceae
AB  - family, isolated from a swine manure storage pit that is resistant to multiple
AB  - antibiotics.
ER  -

TY  - JOUR
AU  - Haley, B.J.
AU  - Luo, Y.
AU  - Wang, C.
AU  - Brown, E.
AU  - Allard, M.
AU  - Karns, J.S.
AU  - Van Kessel, J.A.S.
TI  - Genome Sequences of Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e01119
EP  - e01117
VL  - 5
AB  - Salmonella enterica subsp. enterica serovar Kentucky (S. Kentucky) is frequently  isolated
AB  - from dairy cows in the United States, but is an infrequent cause of
AB  - human salmonellosis. To investigate the genomic features of S Kentucky strains
AB  - isolated from a single dairy farm, the genomes of eight isolates were sequenced
AB  - and added to the public domain.
ER  -

TY  - JOUR
AU  - Haley, B.J.
AU  - Luo, Y.
AU  - Wang, C.
AU  - Pettengill, J.
AU  - Allard, M.
AU  - Brown, E.
AU  - Karns, J.S.
AU  - Van Kessel, J.A.
TI  - Genome Sequences of Eight Salmonella enterica subsp. enterica Serovars Isolated from a Single Dairy Farm.
JO  - Genome Announcements
PY  - 2014
SP  - e00082
EP  - e00014
VL  - 2
AB  - Here, we report draft genome sequences of 26 isolates of Salmonella enterica subsp. enterica,
AB  - representing eight serotypes, which were isolated from cows in a Pennsylvania dairy herd, the
AB  - farm on which they were reared, and the associated off-site heifer-raising facility over an
AB  - 8-year sampling period.
ER  -

TY  - JOUR
AU  - Haley, B.J.
AU  - Pirone, C.
AU  - Muruvanda, T.
AU  - Brown, E.
AU  - Allard, M.
AU  - Karns, J.S.
AU  - Van Kessel, J.A.
TI  - Complete Genome Sequence and Methylome of Salmonella enterica subsp. enterica Cerro, a Frequent Dairy Cow Serovar.
JO  - Genome Announcements
PY  - 2016
SP  - e01350
EP  - e01315
VL  - 4
AB  - Salmonella enterica subsp. enterica serovar Cerro is an infrequent pathogen of humans and
AB  - other mammals but is frequently isolated from the hindgut of
AB  - asymptomatic cattle in the United States. To further understand the genomic
AB  - determinants of S. Cerro specificity for the bovine hindgut, the genome of
AB  - isolate CFSAN001588 was fully sequenced and deposited in the GenBank database.
ER  -

TY  - JOUR
AU  - Halford, S.
TI  - Restriction enzymes in DNA-protein interactions.
JO  - SERC Bulletin
PY  - 1986
SP  - 12
EP  - 13
VL  - 3
AB  - Within any organism from Escherichia coli to man, the genetic information is stored as a
AB  - sequence of bases in the DNA but this constitutes only a blue-print for that organism.  The
AB  - retrieval of the genetic information is absolutely dependent upon proteins that interact with
AB  - the DNA.  The molecular basis of DNA-protein interactions is being studied by a group at the
AB  - Bristol University who have used the EcoRI restriction endonuclease, an enzyme widely used in
AB  - genetic engineering, as the test system.
ER  -

TY  - JOUR
AU  - Halford, S.E.
TI  - Restriction enzymes.
JO  - Encyclopaedia of Molecular Biology
PY  - 1994
SP  - 954
EP  - 956
AB  - Restriction enzymes are endonucleases that cleave DNA in response to a recognition site on the
AB  - DNA.  The recognition site consists of a specific sequence of nucleotides in the DNA duplex,
AB  - typically 4-8 base pairs long.  These endonucleases are found in many species of bacteria,
AB  - where they function in restriction and modification systems.  The bacterial R/M system is
AB  - analogous to an immune system, in that it enables the bacterium to distinguish its own DNA
AB  - from foreign DNA and to eliminate the latter.  The discovery of restriction-modification
AB  - systems followed the observation more than 30 years ago that a single cycle of phage growth in
AB  - a particular bacterial host could alter the host range of the progeny phage; they had become
AB  - 'restricted' in their host range as a result of 'modification' in the original host.
AB  - Restriction-modification is achieved by a combination of two enzyme activities: a modification
AB  - methyltransferase and a restriction endonuclease.  The former transfers methyl groups from
AB  - S-adenosylmethionine to specific bases within the recognition sequence, generally one in each
AB  - strand: if one strand is already methylated, the second strand remains a substrate.  The
AB  - latter cleaves the DNA but only if the recognition site is not methylated in either strand.
AB  - Methylation of just one strand blocks restriction activity, so the bacterial DNA is protected
AB  - from the endonuclease even after its semiconservative replication.  However, DNA that is
AB  - foreign to the cell carrying the R/M system will lack the appropriate methylation and, if such
AB  - DNA enters the cell, it is likely to be cleaved by the restriction enzyme.
ER  -

TY  - JOUR
AU  - Halford, S.E.
TI  - The specificity of the EcoRI restriction endonuclease.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 399
EP  - 400
VL  - 8
AB  - None
ER  -

TY  - JOUR
AU  - Halford, S.E.
TI  - How does EcoRI cleave its recognition site on DNA?
JO  - Trends Biochem. Sci.
PY  - 1983
SP  - 455
EP  - 460
VL  - 8
AB  - The two protein subunits of the EcoRI restriction enzyme interact symmetrically
AB  - with the recognition site on DNA, so that each subunit is in position to cleave
AB  - one strand of the DNA.  But each subunit seems to require a protein
AB  - conformation change before it can cleave DNA.  Depending upon whether one or
AB  - both subunits change conformation during the life-time of the enzyme-DNA
AB  - complex, a single reaction of the EcoRI enzyme cleaves either one or both
AB  - strands of the DNA.  Reaction profiles with other restriction enzymes differ
AB  - from EcoRI, though the underlying mechanisms may be the same.
ER  -

TY  - JOUR
AU  - Halford, S.E.
TI  - Restriction enzymes that act simultaneously at two DNA sites.
JO  - Biochem. Soc. Trans.
PY  - 1999
SP  - A88
EP  - A88
VL  - 27
AB  - The reaction of a type II restriction enzyme commonly results in DNA cleavage at a single
AB  - site.  DNA with multiple recognition sites is cleaved by a succession of separate reactions at
AB  - individual sites.  However, it has been discovered recently that many of the type II
AB  - endonucleases can convert a substrate with two recognition sites directly into the product
AB  - cleaved at both sites, without liberating DNA cut at a single site.  The coupled cleavage of
AB  - two sites can be due to a processive mechanism involving the intramolecular transfer of the
AB  - enzyme from one site to another.  Whilst such transfers have generally been considered to
AB  - occur by "sliding", the linear diffusion of the protein along the DNA, studies on the EcoRV
AB  - endonuclease have excluded "sliding" as a major pathway for intramolecular transfer and have
AB  - indicated instead that the transfer occurs by "hopping", the dissociation of the protein from
AB  - one site on the DNA followed by its reassociation to another site on the same molecule of DNA.
AB  - In other cases, concerted action at two DNA sites is achieved by the restriction enzyme being
AB  - unable to cleave DNA until it has bound to two copies of its recognition sequence, either by
AB  - looping out the DNA between sites on the same DNA molecule or by bridging sites on separate
AB  - molecules.  The SfiI endonuclease provides an illustration of the latter system.
ER  -

TY  - JOUR
AU  - Halford, S.E.
TI  - The (billion dollar) consequences of studying why certain isolates of phage lambda infect only certain strains of E. coli: restriction enzymes.
JO  - Biochemist
PY  - 2009
SP  - 10
EP  - 13
VL  - 31
AB  - In 1953, Bertani and Weigle1 reported that samples of bacteriophage e that had been propagated
AB  - on certain strains of Escherichia coli retained the ability to infect that same strain of E.
AB  - coli but were unable to infect other strains. A contemporary version of their study is shown
AB  - in Figure 1; phage e, obtained by infecting E. coli strain K (eK), is applied to two different
AB  - E. coli strains, K and B. The eK particles infect E. coli K with an efficiency of 1: i.e.,
AB  - every phage produces a plaque in a lawn of E. coli K cells. But the same preparation of eK
AB  - shows a pathetic efficiency of infection on E. coli B, about 10-4: i.e., 10,000 phage
AB  - particles yield just one plaque on the lawn of E. coli B cells. The phage obtained from the
AB  - few productive infections of E. coli B (eB) are then tested against the same two strains, K
AB  - and B. This time, the phage have largely lost the ability to infect E. coli K, as they now
AB  - show an efficiency of 10-4 instead of 1, but they infect E. coli B much more readily than
AB  - before, with an efficiency raised from 10-4 to 1.
ER  -

TY  - JOUR
AU  - Halford, S.E.
TI  - Hopping, jumping and looping by restriction enzymes.
JO  - Biochem. Soc. Trans.
PY  - 2001
SP  - 363
EP  - 373
VL  - 29
AB  - Type II restriction endonucleases recognize specific DNA sequences and cleave both strands of
AB  - the DNA at fixed locations at or near their
AB  - recognition sites. Many of these enzymes are dimeric proteins that
AB  - recognize, in symmetrical fashion, palindromic DNA sequences. They
AB  - generally catalyse independent reactions at each recognition site on
AB  - the DNA, although in some cases they act processively; cutting the DNA
AB  - first at one site, then translocating along the DNA to another site and
AB  - cutting that before leaving the DNA. The way in which the degree of
AB  - processivity varies with the length of DNA between the sites can reveal
AB  - the mechanism of translocation. In contrast with the common view that
AB  - proteins move along DNA by 'sliding', the principal mode of transfer of
AB  - the EcoRV endonuclease is by 'hopping' and 'jumping', i.e. the
AB  - dissociation of the protein from one site followed by its
AB  - re-association with another site in the same DNA molecule, either close
AB  - to or distant from the original site. Other type II restriction enzymes
AB  - require two copies of their recognition sites for their DNA cleavage
AB  - reactions. Many of these enzymes, such as SfiI, are tetramers with two
AB  - DNA-binding surfaces. SfiI has no activity when bound to just one
AB  - recognition site, and instead both DNA-binding surfaces have to be
AB  - filled before it becomes active. Although the two sites can be on
AB  - separate DNA molecules, SfiI acts optimally with two sites on the same
AB  - DNA, where it traps the DNA between the sites in a loop. SfiI thus
AB  - constitutes a test system for the analysis of DNA looping.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Baldwin, G.S.
AU  - Vipond, I.B.
TI  - DNA recognition by EcoRV.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 152
EP  - 152
VL  - 17C
AB  - In the presence of magnesium ions, the EcoRV restriction endonuclease cleaves DNA specifically
AB  - at its recognition sequence, GATATC.  Sequences that differ from the recognition site by one
AB  - base pair are cleaved at least a million times more slowly.  Yet, in binding to DNA in the
AB  - absence of magnesium ions, the EcoRV restriction enzyme shows no sequence specificity.  The
AB  - protein binds all sequences with equal affinity, and it can transfer readily from one site to
AB  - another along the DNA molecule without dissociating from the DNA.  However, the DNA cleavage
AB  - activity that is observed at any particular sequence is a function of the fractional
AB  - saturation of the relevant enzyme-DNA complex with magnesium ions.  The observed difference in
AB  - cleavage rates is due to the fact that the EcoRV enzyme has a high affinity for magnesium when
AB  - it is located at its recognition site on DNA, but it has a low affinity for magnesium when it
AB  - is located on any other DNA sequence.  Once it has bound the metal ion, the intrinsic activity
AB  - of the EcoRV enzyme at noncognate sites is similar to that at the recognition site.  This
AB  - mechanism can be correlated to the crystal structures of the EcoRV endonuclease that have been
AB  - determined by F.K. Winkler.  Three structures were solved: the free enzyme in the absence of
AB  - DNA; the specific complex at its recognition sequence, a nonspecific complex at a different
AB  - DNA sequence.  The specific complex displays a large number of sequence-specific interactions
AB  - between the protein and the DNA.  These are missing in the nonspecific complex.  But the
AB  - additional interactions that are seen in the specific complex contribute nothing to the net
AB  - free energy change for DNA binding.  Instead, all of the energy from the specific interactions
AB  - is used to distort the DNA, and in other conformational changes: the structure of the specific
AB  - DNA bound to EcoRV is extensively distorted while the nonspecific DNA is close to B-form.  The
AB  - distortion results in only the specific complex being able to bind magnesium ions and to
AB  - catalyse the reaction.  The communication between DNA recognition and catalysis thus seems to
AB  - be mediated by the structure of the DNA itself.  This model is currently being tested by
AB  - mutational analyses of EcoRV and by using fluorescence methods to monitor the conformational
AB  - changes in the DNA and in the protein.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Bilcock, D.T.
AU  - Stanford, N.P.
AU  - Williams, S.A.
AU  - Milsom, S.E.
AU  - Gormley, N.A.
AU  - Watson, M.A.
AU  - Bath, A.J.
AU  - Embleton, M.L.
AU  - Gowers, D.M.
AU  - Daniels, L.E.
AU  - Parry, S.H.
AU  - Szczelkun, M.D.
TI  - Restriction endonuclease reactions requiring two recognition sites.
JO  - Biochem. Soc. Trans.
PY  - 1999
SP  - 696
EP  - 699
VL  - 27
AB  - The standard perception of a restriction enzyme is of an endonuclease that recognizes a short
AB  - palindrome of DNA and which cleaves both strands of the DNA at fixed locations in that
AB  - sequence, in a reaction that requires only Mg2+ ions as a cofactor.  The perception thus
AB  - refers to the type II restriction enzymes, as opposed to the type I and the type III systems.
AB  - Many of the type II restriction enzymes conform to this perception.  Their recognition sites
AB  - are often symmetrical palindromes, 4, 6 or occasionally 8 bp long, although in some instances
AB  - the palindrome is interrupted by a fixed length of unspecified sequence.  They are usually
AB  - dimers of identical subunits that interact symmetrically with their recognition sequences,
AB  - even when the recognition site is an interrupted palindrome.  One active site in the dimer
AB  - cleaves one strand of the DNA, while the second active site cleaves the symmetrically
AB  - equivalent position in the other strand of the DNA.  The reactions of these enzymes are thus
AB  - independent events at individual recognition sites, unless the enzyme hops along the DNA from
AB  - one site to another.  The type II enzymes that match the standard perception include several
AB  - well-characterized endonucleases, such as EcoRV, BglI and BamHI.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Catto, L.E.
AU  - Pernstich, C.
AU  - Rusling, D.A.
AU  - Sanders, K.L.
TI  - The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites.
JO  - Biochem. Soc. Trans.
PY  - 2011
SP  - 584
EP  - 588
VL  - 39
AB  - The FokI endonuclease is a monomeric protein with discrete DNA-recognition and catalytic
AB  - domains. The latter has only one active site so, to cut both
AB  - strands, the catalytic domains from two monomers associate to form a
AB  - dimer. The dimer involving a monomer at the recognition site and another
AB  - from free solution is less stable than that from two proteins tethered to
AB  - the same DNA. FokI thus cleaves DNA with two sites better than one-site
AB  - DNA. The two sites can be immediately adjacent, but they can alternatively
AB  - be many hundreds of base pairs apart, in either inverted or repeated
AB  - orientations. The catalytic domain of FokI is often a component of zinc
AB  - finger nucleases. Typically, the zinc finger domains of two such nucleases
AB  - are designed to recognize two neighbouring DNA sequences, with the
AB  - objective of cutting the DNA exclusively between the target sequences.
AB  - However, this strategy fails to take account of the fact that the
AB  - catalytic domains of FokI can dimerize across distant sites or even at a
AB  - solitary site. Additional copies of either target sequence elsewhere in
AB  - the chromosome must elicit off-target cleavages.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Goodall, A.J.
TI  - Modes of DNA cleavage by the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1988
SP  - 1771
EP  - 1777
VL  - 27
AB  - The mechanism of action ofthe EcoRV restriction endonuclease at its single
AB  - recognition site on the plasmid pAT153 was analyzed by kinetic methods.  In
AB  - reactions at pH 7.5, close to the optimum for this enzyme, both strands of the
AB  - DNA were cut in a single concerted reaction:  DNA cut in only one strand of the
AB  - duplex was neither liberated from the enzyme during the catalytic turnover nor
AB  - accumulated as a steady-state intermediate.  In contrast, reactions at pH 6.0
AB  - involved the sequential cutting of the two strands of the DNA.  Under these
AB  - conditions, DNA cut in a single strand was an obligatory intermediate in the
AB  - reaction pathway and a fraction of the nicked DNA dissociated from the enzyme
AB  - during the turnover.  The different reaction profiles are shown to be
AB  - consistent with a single mechanism in which the kinetic activity of each
AB  - subunit of the dimeric protein is governed by its affinity for Mg2+ ions.  At
AB  - pH 7.5, Mg2+ is bound to both subunits of the dimer for virtually the complete
AB  - period of the catalytic turnover, while at pH 6.0 Mg2+ is bound transiently to
AB  - one subunit at a time.  The kinetics of the EcoRV nuclease were unaffected by
AB  - the DNA supercoiling.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Gowers, D.M.
AU  - Sessions, R.B.
TI  - Two are better than one.
JO  - Nat. Struct. Biol.
PY  - 2000
SP  - 705
EP  - 707
VL  - 7
AB  - A crystal structure of a tetrameric restriction enzyme, NgoMIV, bound to two DNA duplexes has
AB  - been determined.  Two subunits contact each duplex in much the same manner as a dimeric
AB  - restriction enzyme recognizing a single site, but the dimeric units are packed back-to-back,
AB  - placing the duplexes on opposite sides of the tetramer.  Interaction with two recognition
AB  - sites, presumably via looping, enhances NgoMIV activity.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Johnson, N.P.
TI  - Single turnovers of the EcoRI restriction endonuclease.
JO  - Biochem. J.
PY  - 1983
SP  - 405
EP  - 415
VL  - 211
AB  - Single turnovers of the EcoRI restriction endonuclease, cleaving its recognition site on the
AB  - covalently closed form of plasmid pMB9, were examined. Two methods were used to monitor the
AB  - progress of the reactions: one involved quenching the reaction at various times followed by
AB  - the electrophoretic separation of the products cleaved in one and in both strands of the
AB  - duplex; the other employed a stopped-flow fluorimeter to measure the amount of ethidium
AB  - bromide bound to the DNA as it changes when the DNA, cleaved in at least one strand,
AB  - dissociates from the enzyme.  Two procedures were used to initiate the reactions.  For some,
AB  - one solution containing the enzyme was mixed with a second containing both DNA and MgCl2: in
AB  - these reactions, the fluorescence changed at the same rate as the cleavage of the first strand
AB  - of the duplex. Other reactions were started by the addition of MgCl2 to a pre-equilibrium of
AB  - enzyme and DNA: here, both strands of the DNA were cleaved faster than before, with the
AB  - fluorescence signal now occurring at the same time as the cleavage of the second strand.  The
AB  - different kinetics from the two assays and the two mixing procedures are consistent with the
AB  - rates of these reactions being controlled by protein conformational changes.  These may affect
AB  - either one subunit alone within the dimeric EcoRI enzyme, allowing the enzyme to cleave only
AB  - one strand of the DNA in each turnover.  Alternatively, both subunits of the dimer may change,
AB  - so that the enzyme then cleaves both strands during the life-time of one enzyme-DNA complex.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Johnson, N.P.
TI  - The EcoRI restriction endonuclease, covalently closed DNA and ethidium bromide.
JO  - Biochem. J.
PY  - 1981
SP  - 767
EP  - 777
VL  - 199
AB  - The reactions of the EcoRI restriction endonuclease on the covalently closed
AB  - DNA of plamid pMB9 were studied in the presence of ethidium bromide.  At the
AB  - concentrations of ethidium bromide tested, which covered the range over which
AB  - the DNA is changed from negatively to positively supercoiled, the dye caused no
AB  - alteration to the rate at which this enzyme cleaved the covalently closed DNA
AB  - to yield the open-circle form, but the rate at which these open circles were
AB  - cleaved to the linear product could be inhibited.  The fluorescence change,
AB  - caused by ethidium bromide binding with different stoichiometries to covalently
AB  - clodsed and open-circle DNA, provided a direct and sensitive signal for
AB  - monitoring the cleavage of DNA by this enzyme.  This method was used for a
AB  - steady-state kinetic analysis of the reaction catalysed by the EcoRI
AB  - restriction enzyme.  Reaction mechanisms where a complex between DNA and Mg2+
AB  - is the substrate for this enzyme were eliminated, and instead DNA and Mg2+ must
AB  - bind to the enzyme in separate stages.  The requisite controls for this
AB  - fluorimetric assay in both steady-state and transient kinetics studies, and its
AB  - application to other enzymes that alter the structure of covalently closed DNA,
AB  - are described.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Johnson, N.P.
TI  - The EcoRI restriction endonuclease with bacteriophage lambda DNA.  Equilibrium binding sites.
JO  - Biochem. J.
PY  - 1980
SP  - 593
EP  - 604
VL  - 191
AB  - The EcoRI restriction endonuclease was found by the filter binding technique to
AB  - form stable complexes, in the absence of Mg2+, with the DNA from derivatives of
AB  - bacteriophage lambda that either contain or lack EcoRI recognition sites.  The
AB  - amount of complex formed at different enzyme concentrations followed a
AB  - hyperbolic equilibrium-binding curve with DNA molecules containing EcoRI
AB  - recognition sites, but a sigmoidal equilibrium-binding curve was obtained with
AB  - a DNA molecule lacking EcoRI recognition sites.  The EcoRI enzyme displayed the
AB  - same affinity for individual recognition sites on lambda DNA, even under
AB  - conditions where it cleaves these sites at different rates.  The binding of the
AB  - enzyme to a DNA molecule lacking EcoRI sites was decreased by Mg2+.  These
AB  - observations indicate that (a) the EcoRI restriction enzyme binds
AB  - preferentially to its recognition site on DNA, and that different reaction
AB  - rates at different recognition sites are due to the rate of breakdown of this
AB  - complex; (b) the enzyme also binds to other DNA sequences, but that two
AB  - molecules of enzyme, in a different protein conformation, are involved in the
AB  - formation of the complex at non-specific sequences; (c) the different
AB  - affinities of the enzyme for the recognition site and for other sequences on
AB  - DNA, coupled with the different protein conformations, account for the
AB  - specificity of this enzyme for the cleavage of DNA at its recognition site; (d)
AB  - the decrease in the affinity of the enzyme for DNA, caused by Mg2+, liberates
AB  - binding energy from the DNA-protein complex that can be used in the catalytic
AB  - reaction.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Johnson, N.P.
AU  - Grinsted, J.
TI  - The EcoRI restriction endonuclease with bacteriophage lambda DNA.  Kinetic studies.
JO  - Biochem. J.
PY  - 1980
SP  - 581
EP  - 592
VL  - 191
AB  - The kinetics of the reactions of the EcoRI restriction endonuclease at
AB  - individual recognition sites on the DNA from bacteriophage lambdawere found to
AB  - differ markedly from site to site.  Under certain conditions of pH and ionic
AB  - strength, the rates for the cleavage of the DNA were the same at each
AB  - recognition site.  But under altered experimental conditions, different
AB  - reaction rates were observed at each recognition site.  These results are
AB  - consistent with a mechanism in which the kinetic stability of the complex
AB  - between the enzyme and the recognition site on the DNA differs among the sites,
AB  - due to the effect of interactions between the enzyme and DNA sequences
AB  - surrounding each recognition site upon the transition state of the reaction.
AB  - Reactions at individual sites on a DNA molecule containing more than one
AB  - recognition site were found to be independent of each other, thus excluding the
AB  - possibility of a processive mechanism for the EcoRI enzyme.  The consequences
AB  - of these observations are discussed with regard to both DNA-protein
AB  - interactions and to the application of restriction enzymes in the study of the
AB  - structure of DNA molecules.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Johnson, N.P.
AU  - Grinsted, J.
TI  - The reactions of the EcoRI and other restriction endonucleases.
JO  - Biochem. J.
PY  - 1979
SP  - 353
EP  - 365
VL  - 179
AB  - The reaction of the EcoRI restriction endonuclease was studied with both the
AB  - plasmid pMB9 and DNA from bacteriophage lambda as the substrates.  With both
AB  - circular and linear DNA molecules, the only reaction catalysed by the EcoRI
AB  - restriction endonuclease was the hydrolysis of the phosphodiester bond within
AB  - one strand of the recognition site on the DNA duplex.  The cleavage of both
AB  - strands of the duplex was achieved only after two independent reactions, each
AB  - involving a single-strand scission.  The reactivity of the enzyme for
AB  - single-strand scissions was the same for both the first and the second cleavage
AB  - within its recognition site.  No differences were observed between the
AB  - mechanism of action on supercoiled and linear DNA substrates.  Other
AB  - restriction endonucleases were tested against plasmid pMB9.  The HindIII
AB  - restriction endonuclease cleaved DNA in the same manner as the EcoRI enzyme.
AB  - However, in contrast with EcoRI, the SalI and the BamHI restriction
AB  - endonucleases appeared to cleave both strands of the DNA duplex almost
AB  - simultaneously.  The function of symmetrical DNA sequences and the conformation
AB  - of the DNA involved in these DNA-protein interactions are discussed in the
AB  - light of these observations.  The fact that the same reactions were observed on
AB  - both supercoiled and linear DNA substrates implies that these interactions do
AB  - not involve the unwinding of the duplex before catalysis.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Lovelady, B.M.
AU  - McCallum, S.
TI  - Altered specificity of the EcoRV restriction endonuclease.
JO  - Biochem. Soc. Trans.
PY  - 1986
SP  - 260
EP  - 261
VL  - 14
AB  - Type II restriction endonucleases recognize specific sequences of nucleotides on DNA and, in
AB  - the presence of Mg2+, cleave both strands of the DNA at fixed locations relative to the
AB  - recognition site.  These enzymes generally show very high specificities: the rates at which
AB  - they cleave their recognition sites can be several orders of magnitude faster than that for
AB  - any cleavage at alternative DNA sequences.  However, in altered environments such as at high
AB  - pH or in the presence of water-miscible organic solvents, many restriction enzymes show
AB  - reduced specificity and cleave DNA at several sites in addition to the recognition site.  This
AB  - phenomena was first observed with the EcoRI restriction enzyme, the altered activity at high
AB  - pH being noted as EcoRI.  We describe here a similar alteration in the specificity of the
AB  - EcoRV restriction enzyme and show that each additional site cleaved by EcoRV differs from the
AB  - canonical EcoRV recognition sequence, 5'-G-A-T-A-T-C-3', by one nucleotide.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Lovelady, B.M.
AU  - McCallum, S.A.
TI  - Relaxed specificity of the EcoRV restriction endonuclease.
JO  - Gene
PY  - 1986
SP  - 173
EP  - 181
VL  - 41
AB  - The EcoRV restriction endonuclease normally shows a high specificity for its recognition site
AB  - on DNA, GATATC. In standard reactions, it cleaves DNA at this site several orders of magnitude
AB  - more readily than at any alternative sequence. But in the presence of dimethyl sulphoxide and
AB  - at high pH, the EcoRV enzyme cleaves DNA at several sites that differ from its recognition
AB  - site by one nucleotide. Of the 18 (3 x 6) possible sequences that differ from GATATC by one
AB  - base, all were cleaved readily except for the following 4 sites: TATATC, CATATC, GATATA and
AB  - GATATG. However, two of the sites that could be cleaved by EcoRV in the presence of dimethyl
AB  - suphoxide, GAGATC and GATCTC, were only cleaved on DNA that lacked dam methylation: both
AB  - contain the sequence GATC, the recognition site for the dam methylase of Escherichia coli.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Marko, J.F.
TI  - How do site-specific DNA-binding proteins find their targets?
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3040
EP  - 3052
VL  - 32
AB  - Essentially all the biological functions of DNA depend on site-specific DNA-binding proteins
AB  - finding their targets, and therefore ?searching? through megabases of non-target DNA. In this
AB  - article, we review current understanding of how this sequence searching is done. We review how
AB  - simple diffusion through solution may be unable to account for the rapid rates of association
AB  - observed in experiments on some model systems, primarily the Lac repressor. We then present a
AB  - simplified version of the ?facilitated diffusion? model of Berg, Winter and von Hippel,
AB  - showing how non-specific DNA?protein interactions may account for accelerated targeting, by
AB  - permitting the protein to sample many binding sites per DNA encounter. We discuss the
AB  - 1-dimensional ?sliding? motion of protein along non-specific DNA, often proposed to be the
AB  - mechanism of this multiple site sampling, and we discuss the role of short-range diffusive
AB  - ?hopping? motions. We then derive the optimal range of sliding for a few physical situations,
AB  - including simple models of chromosomes in vivo, showing that a sliding range of ~100bp before
AB  - dissociation optimizes targeting in vivo. Going beyond first-order binding kinetics, we
AB  - discuss how processivity, the interaction of a protein with two or more targets on the same
AB  - DNA, can reveal the extent of sliding and we review recent experiments studying processivity
AB  - using the restriction enzyme EcoRV. Finally, we discuss how single molecule techniques might
AB  - be used to study the dynamics of DNA site-specific targeting of proteins.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Taylor, J.D.
AU  - Vermote, C.L.M.
AU  - Vipond, I.B.
TI  - Mechanism of action of restriction endonuclease EcoRV.
JO  - Nucl. Acids and Mol. Biol.
PY  - 1993
SP  - 47
EP  - 69
VL  - 7
AB  - Type II restriction/modification (R/M) systems, such as EcoRV, consist of two enzymes that act
AB  - at the same DNA sequence; a modification methyltransferase and a restriction endonuclease
AB  - (Bennett and Halford 1989; Wilson and Murray 1991). For EcoRV, the recognition sequence is
AB  - GATATC (Kholmina et al. 1980). The EcoRV modification enzyme methylates the first adenine
AB  - within this sequence (Nwosu et al. 1988) while, in the presence of Mg2+ ions, the EcoRV
AB  - restriction enzymes cleaves DNA specifically at this site (Schilkdraut et al. 1984). The
AB  - endonuclease cuts both strands at the center of the sequence, to leave blunt-ended DNA
AB  - fragments. However, prior methylation of the recognition site blocks restriction activity. The
AB  - basic tenet of R/M systems is that, in vivo, the restriction enzyme cuts only DNA molecules
AB  - that have not been exposed previously to the methyltransferase. Hence, they enable the cell to
AB  - degrade foreign DNA entering the cell without destroying host DNA. E. coli strains carrying
AB  - the EcoRV system show this phenotype (Bougueleret et al. 1984).
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Taylor, J.D.
AU  - Vermote, C.L.M.
AU  - Vipond, I.B.
TI  - Assays for restriction endonucleases using plasmid substrates.
JO  - Methods Mol. Biol.
PY  - 1994
SP  - 385
EP  - 396
VL  - 30
AB  - A type II restriction enzyme purchased from a commercial supplier comes with a specified
AB  - number of units of enzyme activity. The units of restriction enzyme activity are defined by
AB  - the minimal amount of enzyme needed to complete the digestion of 1 ug of bacteriophage lambda
AB  - DNA in 1 h. These units are usually measured by making serial dilutions of the stock solution
AB  - of the enzyme, adding 1 uL from each dilution to 1 ug of phage lambda DNA in a suitable
AB  - buffer, incubating the reactions for 1 h at 37oC, and then analyzing the DNA by
AB  - electrophoresis through agarose. This is, at best, a semiquantitative assay. It cannot yield
AB  - quantitative data about the rate of the reaction of a restricton enzyme on a DNA substrate.
ER  -

TY  - JOUR
AU  - Halford, S.E.
AU  - Welsh, A.J.
AU  - Szczelkun, M.D.
TI  - Enzyme-mediated DNA looping.
JO  - Annu. Rev. Biophys. Biomol. Struct.
PY  - 2004
SP  - 1
EP  - 24
VL  - 33
AB  - Most reactions on DNA are carried out by multimeric protein complexes that interact with two
AB  - or more sites in the DNA and thus loop out the DNA
AB  - between the sites. The enzymes that catalyze these reactions usually have
AB  - no activity until they interact with both sites. This review examines the
AB  - mechanisms for the assembly of protein complexes spanning two DNA sites
AB  - and the resultant triggering of enzyme activity. There are two main routes
AB  - for bringing together distant DNA sites in an enzyme complex: either the
AB  - proteins bind concurrently to both sites and capture the intervening DNA
AB  - in a loop, or they translocate the DNA between one site and another into
AB  - an expanding loop, by an energy-dependent translocation mechanism. Both
AB  - capture and translocation mechanisms are discussed here, with reference to
AB  - the various types of restriction endonuclease that interact with two
AB  - recognition sites before cleaving DNA.
ER  -

TY  - JOUR
AU  - Halim, M.A.
AU  - Rahman, A.Y.
AU  - Sim, K.S.
AU  - Yam, H.C.
AU  - Rahim, A.A.
AU  - Ghazali, A.H.
AU  - Najimudin, N.
TI  - Genome Sequence of a Gram-Positive Diazotroph, Paenibacillus durus Type Strain ATCC 35681.
JO  - Genome Announcements
PY  - 2016
SP  - e00005
EP  - e00016
VL  - 4
AB  - Here, we report the complete genome sequence of Paenibacillus durus type strain ATCC 35681,
AB  - which can fix atmospheric nitrogen even in the presence of nitrate.
ER  -

TY  - JOUR
AU  - Halim, M.Z.A.
AU  - Jaafar, M.M.
AU  - Teh, L.K.
AU  - Ismail, M.I.
AU  - Lee, L.S.
AU  - Ngeow, Y.F.
AU  - Nor, N.M.
AU  - Zainuddin, Z.F.
AU  - Tang, T.H.
AU  - Najimudin, M.N.
AU  - Salleh, M.Z.
TI  - Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB) PR10 strain.
JO  - Genomics Data
PY  - 2016
SP  - 245
EP  - 246
VL  - 7
AB  - Here, we report the draft genome sequence and annotation of a multidrug resistant
AB  - Mycobacterium tuberculosis strain PR10 (MDR-TB PR10) isolated from a patient diagnosed with
AB  - tuberculosis. The size of the draft genome MDR-TB PR10 is 4.34 Mbp with 65.6% of G + C content
AB  - and consists of 4637 predicted genes. The determinants were categorized by RAST into 400
AB  - subsystems with 4286 coding sequences and 50 RNAs. The whole genome shotgun project has been
AB  - deposited at DDBJ/EMBL/GenBank under the accession number CP010968.
ER  -

TY  - JOUR
AU  - Hall, M.F.
AU  - Noren, C.J.
AU  - Perler, F.B.
AU  - Schildkraut, I.
TI  - Creation of an artificial bifunctional intein by grafting a homing endonuclease into a mini-intein.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 173
EP  - 179
VL  - 323
AB  - The majority of inteins are comprised of a protein splicing domain and a homing endonuclease
AB  - domain. Experimental evidence has demonstrated that the splicing domain and the endonuclease
AB  - domain in a bifunctional intein are largely independent of each other with respect to both
AB  - structure and activity. Here, an artificial bifunctional intein has been created through the
AB  - insertion of an existing homing endonuclease into a mini-intein that is naturally lacking this
AB  - functionality. The gene for I-CreI, an intron-encoded homing endonuclease, was grafted into
AB  - the monofunctional Mycobacterium xenopi GyrA intein at the putative site of the missing
AB  - endonuclease. The resulting fusion protein was found to be capable of protein splicing similar
AB  - to that of the parent intein. In addition, the protein demonstrated site-specific endonuclease
AB  - activity that is characteristic of the I-CreI homing endonuclease. The function of each domain
AB  - therefore remained unaffected by the presence of the other domain. This artificial fusion of
AB  - the two domains is a potential novel mobile genetic element.
ER  -

TY  - JOUR
AU  - Hall, R.K.
AU  - Larcom, L.L.
TI  - Blockage of restriction endonuclease cleavage by thymine dimers.
JO  - Photochem. Photobiol.
PY  - 1982
SP  - 429
EP  - 432
VL  - 36
AB  - Viral DNAs were subjected to 254 nm irradiation and then digested with type II
AB  - restriction endonucleases.  At the fluences used, irradiation inhibited
AB  - cleavage by nucleases which recognize sites containing neighboring thymines.
AB  - Cleavage by endonucleases with other recognition sequences was not affected.
AB  - In viral and plasmid DNAs, this effect could be used to study thymine dimer
AB  - formation at a few specific, mapped sites of defined base sequence.
ER  -

TY  - JOUR
AU  - Hall, R.M.
TI  - The DNA adenine methyltransferase (dam+) gene of bacteriophage T4 reverses the mutator phenotype of an Escherichia coli dam mutant.
JO  - J. Bacteriol.
PY  - 1990
SP  - 2812
EP  - 2813
VL  - 172
AB  - The mutator phenotype of Escherichia coli dam mutants was found to be reversed
AB  - by introduction of the bacteriophage T4 gene for DNA adenine methyltransferase.
AB  - This precludes a direct role for the E. coli DNA adenine methyltransferase in
AB  - mismatch repair, in addition to its role in strand discrimination, as suggested
AB  - by earlier studies.
ER  -

TY  - JOUR
AU  - Hallam, S.J.
AU  - Konstantinidis, K.T.
AU  - Putnam, N.
AU  - Schleper, C.
AU  - Watanabe, Y.
AU  - Sugahara, J.
AU  - Preston, C.
AU  - de la Torre, J.
AU  - Richardson, P.M.
AU  - DeLong, E.F.
TI  - Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 18296
EP  - 18301
VL  - 103
AB  - Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes,
AB  - and ocean waters. To further describe the cosmopolitan
AB  - nonthermophilic Crenarchaeota, we analyzed the genome sequence of one
AB  - representative, the uncultivated sponge symbiont Cenarchaeum symbiosum. C.
AB  - symbiosum genotypes coinhabiting the same host partitioned into two
AB  - dominant populations, corresponding to previously described a- and b-type
AB  - ribosomal RNA variants. Although they were syntenic, overlapping a- and
AB  - b-type ribotype genomes harbored significant variability. A single tiling
AB  - path comprising the dominant a-type genotype was assembled and used to
AB  - explore the genomic properties of C. symbiosum and its planktonic
AB  - relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from
AB  - previously sequenced genomes. The remaining genes partitioned between
AB  - functional RNAs (2.4%) and hypotheticals (42%) with limited homology to
AB  - known functional genes. The latter category included some genes likely
AB  - involved in the archaeal-sponge symbiotic association. Conversely, 525 C.
AB  - symbiosum ORFs were most highly similar to sequences from marine
AB  - environmental genomic surveys, and they apparently represent orthologous
AB  - genes from free-living planktonic Crenarchaeota. In total, the C.
AB  - symbiosum genome was remarkably distinct from those of other known Archaea
AB  - and shared many core metabolic features in common with its free-living
AB  - planktonic relatives.
ER  -

TY  - JOUR
AU  - Hallam, S.J.
AU  - Mincer, T.J.
AU  - Schleper, C.
AU  - Preston, C.M.
AU  - Roberts, K.
AU  - Richardson, P.M.
AU  - DeLong, E.F.
TI  - Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.
JO  - PLoS Biology
PY  - 2006
SP  - e95
EP  - e95
VL  - 4
AB  - Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to
AB  - significantly influence biogeochemical cycling in marine
AB  - ecosystems. Prior studies using specific archaeal lipid biomarkers and
AB  - isotopic analyses indicated that planktonic Crenarchaeota have the
AB  - capacity for autotrophic growth, and more recent cultivation studies
AB  - support an ammonia-based chemolithoautotrophic energy metabolism. We
AB  - report here analysis of fosmid sequences derived from the uncultivated
AB  - marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction
AB  - of carbon and energy metabolism. Genes predicted to encode multiple
AB  - components of a modified 3-hydroxypropionate cycle of autotrophic carbon
AB  - assimilation were identified, consistent with utilization of carbon
AB  - dioxide as a carbon source. Additionally, genes predicted to encode a near
AB  - complete oxidative tricarboxylic acid cycle were also identified,
AB  - consistent with the consumption of organic carbon and in the production of
AB  - intermediates for amino acid and cofactor biosynthesis. Therefore, C.
AB  - symbiosum has the potential to function either as a strict autotroph, or
AB  - as a mixotroph utilizing both carbon dioxide and organic material as
AB  - carbon sources. From the standpoint of energy metabolism, genes predicted
AB  - to encode ammonia monooxygenase subunits, ammonia permease, urease, and
AB  - urea transporters were identified, consistent with the use of reduced
AB  - nitrogen compounds as energy sources fueling autotrophic metabolism.
AB  - Homologues of these genes, recovered from ocean waters worldwide,
AB  - demonstrate the conservation and ubiquity of crenarchaeal pathways for
AB  - carbon assimilation and ammonia oxidation. These findings further
AB  - substantiate the likely global metabolic importance of Crenarchaeota with
AB  - respect to key steps in the biogeochemical transformation of carbon and
AB  - nitrogen in marine ecosystems.
ER  -

TY  - JOUR
AU  - Hallam, S.J.
AU  - Putnam, N.
AU  - Preston, C.M.
AU  - Detter, J.C.
AU  - Rokhsar, D.
AU  - Richardson, P.M.
AU  - DeLong, E.F.
TI  - Reverse methanogenesis: Testing the hypothesis with environmental genomics.
JO  - Science
PY  - 2004
SP  - 1457
EP  - 1462
VL  - 305
AB  - Microbial methane consumption in anoxic sediments significantly impacts the global environment
AB  - by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance,
AB  - the biological mechanisms controlling anaerobic methane oxidation are not well characterized.
AB  - One current model suggests that relatives of methane-producing Archaea developed the capacity
AB  - to reverse methanogenesis and thereby to consume methane to produce cellular carbon and
AB  - energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses
AB  - of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes
AB  - typically associated with methane production are present in one specific group of archaeal
AB  - methanotrophs. These genome-based observations support previous hypotheses and provide an
AB  - informed foundation for metabolic modeling of anaerobic methane oxidation.
ER  -

TY  - JOUR
AU  - Hallenbeck, P.C.
AU  - Grogger, M.
AU  - Mraz, M.
AU  - Veverka, D.
TI  - Draft Genome Sequence of a Thermophilic Cyanobacterium from the Family Oscillatoriales (Strain MTP1) from the Chalk River, Colorado.
JO  - Genome Announcements
PY  - 2016
SP  - e01571
EP  - e01515
VL  - 4
AB  - The draft genome (57.7% GC, 7,647,882 bp) of the novel thermophilic cyanobacterium MTP1 was
AB  - determined by metagenomics of an enrichment culture. The
AB  - genome shows that it is in the family Oscillatoriales and encodes multiple heavy
AB  - metal resistances as well as the capacity to make exopolysaccharides.
ER  -

TY  - JOUR
AU  - Hallenbeck, P.C.
AU  - Grogger, M.
AU  - Mraz, M.
AU  - Veverka, D.
TI  - Draft Genome Sequence of the Photoheterotrophic Chloracidobacterium thermophilum  Strain OC1 Found in a Mat at Ojo Caliente.
JO  - Genome Announcements
PY  - 2016
SP  - e01570
EP  - e01515
VL  - 4
AB  - Metagenomics of an enrichment culture from a New Mexico hot spring allowed the description of
AB  - a draft genome of a Chloracidobacterium thermophilum strain for
AB  - the first time outside Yellowstone National Park with a surprisingly high degree
AB  - of identity with the type strain.
ER  -

TY  - JOUR
AU  - Hallet, B.
TI  - Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteria.
JO  - Curr. Opin. Microbiol.
PY  - 2001
SP  - 570
EP  - 581
VL  - 4
AB  - Phase variation is the adaptive process by which bacteria undergo frequent and reversible
AB  - phenotypic changes resulting from genetic alterations in specific loci
AB  - of their genomes. This process is crucial for the survival of pathogens and
AB  - commensals in hostile and ever-changing host environments. Despite important
AB  - differences in the molecular mechanisms that mediate and regulate phase
AB  - variation, related strategies have evolved to generate high levels of genetic
AB  - diversity through complex and combinatorial reshuffling of genetic information.
AB  - Recent studies, supported by the emergence of global genomic approaches, have
AB  - revealed that bacterial pathogens often use a combination of different mechanisms
AB  - to vary the expression of a variety of biological functions, providing new
AB  - insights into bacterial adaptation and virulence mechanisms. Recent advances in
AB  - the understanding of the molecular mechanisms of phase variation are reviewed,
AB  - and differences in these mechanisms outlined.
ER  -

TY  - JOUR
AU  - Halling, S.M.
AU  - Peterson-Burch, B.D.
AU  - Bricker, B.J.
AU  - Zuerner, R.L.
AU  - Qing, Z.
AU  - Li, L.L.
AU  - Kapur, V.
AU  - Alt, D.P.
AU  - Olsen, S.C.
TI  - Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis.
JO  - J. Bacteriol.
PY  - 2005
SP  - 2715
EP  - 2726
VL  - 187
AB  - Brucellosis is a worldwide disease of humans and livestock that is caused by a number of very
AB  - closely related classical Brucella species in the
AB  - alpha-2 subdivision of the Proteobacteria. We report the complete genome
AB  - sequence of Brucella abortus field isolate 9-941 and compare it to those
AB  - of Brucella suis 1330 and Brucella melitensis 16 M. The genomes of these
AB  - Brucella species are strikingly similar, with nearly identical genetic
AB  - content and gene organization. However, a number of insertion-deletion
AB  - events and several polymorphic regions encoding putative outer membrane
AB  - proteins were identified among the genomes. Several fragments previously
AB  - identified as unique to either B. suis or B. melitensis were present in
AB  - the B. abortus genome. Even though several fragments were shared between
AB  - only B. abortus and B. suis, B. abortus shared more fragments and had
AB  - fewer nucleotide polymorphisms with B. melitensis than B. suis. The
AB  - complete genomic sequence of B. abortus provides an important resource for
AB  - further investigations into determinants of the pathogenicity and
AB  - virulence phenotypes of these bacteria.
ER  -

TY  - JOUR
AU  - Halpin, J.L.
AU  - Hill, K.
AU  - Johnson, S.L.
AU  - Bruce, D.C.
AU  - Shirey, T.B.
AU  - Dykes, J.K.
AU  - Luquez, C.
TI  - Finished Whole-Genome Sequences of Clostridium butyricum Toxin Subtype E4 and Clostridium baratii Toxin Subtype F7 Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00375
EP  - e00317
VL  - 5
AB  - Clostridium butyricum and Clostridium baratii species have been known to produce  botulinum
AB  - toxin types E and F, respectively, which can cause botulism, a rare but
AB  - serious neuroparalytic disease. Here, we present finished genome sequences for
AB  - two of these clinically relevant strains.
ER  -

TY  - JOUR
AU  - Halpin, J.L.
AU  - Hill, K.
AU  - Johnson, S.L.
AU  - Bruce, D.C.
AU  - Shirey, T.B.
AU  - Dykes, J.K.
AU  - Luquez, C.
TI  - Finished Whole-Genome Sequence of Clostridium argentinense Producing Botulinum Neurotoxin Type G.
JO  - Genome Announcements
PY  - 2017
SP  - e00380
EP  - e00317
VL  - 5
AB  - Here, we present a closed genome sequence for Clostridium argentinense strain 89G, the first
AB  - strain identified to produce botulinum neurotoxin type G (BoNT/G).
AB  - Although discovered in 1970, to date, there have been no reference quality
AB  - sequences publicly available for this species.
ER  -

TY  - JOUR
AU  - Halpin, J.L.
AU  - Hill, K.
AU  - Johnson, S.L.
AU  - Bruce, D.C.
AU  - Shirey, T.B.
AU  - Dykes, J.K.
AU  - Luquez, C.
TI  - Finished Whole-Genome Sequences of Two Clostridium botulinum Type A(B) Isolates.
JO  - Genome Announcements
PY  - 2017
SP  - e00381
EP  - e00317
VL  - 5
AB  - Clostridium botulinum secretes a potent neurotoxin that causes devastating effects when
AB  - ingested, including paralysis and death if not treated. In the
AB  - United States, some clinically significant strains produce toxin type A while
AB  - also harboring a silent B gene. These are the first two closed genome sequences
AB  - published for this subset.
ER  -

TY  - JOUR
AU  - Ham, J.S.
AU  - Kim, H.W.
AU  - Seol, K.H.
AU  - Jang, A.
AU  - Jeong, S.G.
AU  - Oh, M.H.
AU  - Kim, D.H.
AU  - Kang, D.K.
AU  - Kim, G.B.
AU  - Cha, C.J.
TI  - Genome Sequence of Lactobacillus salivarius NIAS840, Isolated from Chicken Intestine.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5551
EP  - 5552
VL  - 193
AB  - Lactobacillus salivarius is a well-known lactic acid bacterium to which increasing attention
AB  - has been paid recently for use as probiotics for
AB  - humans and animals. L. salivarius NIAS840 was first isolated from broiler
AB  - chicken feces, displaying antimicrobial activities against
AB  - multidrug-resistant Staphylococcus aureus and Salmonella enterica serovar
AB  - Typhimurium. Here, we report the genome sequence of L. salivarius NIAS840
AB  - (2,046,557 bp) including a small plasmid and two megaplasmids.
ER  -

TY  - JOUR
AU  - Ham, J.S.
AU  - Lee, T.
AU  - Byun, M.J.
AU  - Lee, K.T.
AU  - Kim, M.K.
AU  - Han, G.S.
AU  - Jeong, S.G.
AU  - Oh, M.H.
AU  - Kim, D.H.
AU  - Kim, H.
TI  - Complete Genome Sequence of Bifidobacterium longum subsp. longum KACC 91563.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5044
EP  - 5044
VL  - 193
AB  - Bifidobacterium longum strains predominate the colonic microbiota of breast-fed infants. Here
AB  - we report a complete genome sequence of B. longum
AB  - subsp. longum KACC 91563 isolated from feces of neonates. A single
AB  - circular chromosome of 2,385,301 bp contains 1,980 protein coding genes,
AB  - 56 tRNA genes, and 3 rRNA operons.
ER  -

TY  - JOUR
AU  - Hamablet, L.
AU  - Chen, G.C.
AU  - Brown, A.
AU  - Roberts, R.J.
TI  - LpnI, from Legionella pneumophila, is a neoschiozmer of HaeII.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 6417
EP  - 6417
VL  - 17
AB  - LpnI is a Type II restriction endonuclease that was previously isolated from Legionella
AB  - pneumophila strain 11 EJ and partially purified (1). Further purification by phosphocellulose
AB  - and DNA-agrose chromatography, with an intermediate 50-75% ammonium sulphate
AB  - concentration/fractionation step gave enzyme sufficiently pure for detailed characterization.
AB  - LpnI cleaves pUC19 DNA at three sites. Double digests of pUC19 DNA with LpnI and either AatII,
AB  - EcoRI, PvuI or RsaI mapped the LpnI cleavage site to approximately 230, 690 and 1090
AB  - nucleotides. These sites lie close to those predicted for HaeII. Double digest between HaeII
AB  - and LpnI on bacteriophage lambda DNA confirmed that these enzymes are isoschizomers (Fig 1a).
ER  -

TY  - JOUR
AU  - Hamada, M.
AU  - Ichikawa, N.
AU  - Oguchi, A.
AU  - Fujita, N.
TI  - Draft Genome Sequence of Lysinimicrobium mangrovi NBRC 105856T, Isolated from the Rhizosphere of a Mangrove.
JO  - Genome Announcements
PY  - 2014
SP  - e01131
EP  - e01114
VL  - 2
AB  - Here, we report the draft genome sequence of the only species of the genus Lysinimicrobium,
AB  - Lysinimicrobium mangrovi NBRC 105856(T), isolated from the
AB  - rhizosphere of a mangrove. The first genomic sequence of this genus and species
AB  - presented here will facilitate taxonomical, ecological, and functional studies of
AB  - this rare actinobacterial group.
ER  -

TY  - JOUR
AU  - Hamada, M.
AU  - Ichikawa, N.
AU  - Oguchi, A.
AU  - Komaki, H.
AU  - Tamura, T.
AU  - Fujita, N.
TI  - Draft genome sequences of eight type strains of the genus demequina.
JO  - Genome Announcements
PY  - 2015
SP  - e00281
EP  - e00215
VL  - 3
AB  - Here, we report the draft genome sequences of the type strains of Demequina aestuarii,
AB  - Demequina aurantiaca, Demequina flava, Demequina globuliformis,
AB  - Demequina lutea, Demequina oxidasica, Demequina salsinemoris, and Demequina
AB  - sediminicola. The genome sequences presented here will facilitate taxonomical,
AB  - ecological, and functional studies of members of the genus Demequina.
ER  -

TY  - JOUR
AU  - Hamblin, M.
AU  - Spinard, E.
AU  - Gomez-Chiarri, M.
AU  - Nelson, D.R.
AU  - Rowley, D.C.
TI  - Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95.
JO  - Genome Announcements
PY  - 2015
SP  - e00858
EP  - e00815
VL  - 3
AB  - Bacillus pumilus RI06-95 is a marine bacterium isolated in Narragansett, Rhode Island, which
AB  - has shown probiotic activity against marine pathogens in larval shellfish. We report the
AB  - genome of B. pumilus RI06-95, which provides insight into the microbe's probiotic ability and
AB  - may be used in future studies of the probiotic mechanism.
ER  -

TY  - JOUR
AU  - Hamidian, M.
AU  - Hawkey, J.
AU  - Holt, K.E.
AU  - Hall, R.M.
TI  - Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.
JO  - Genome Announcements
PY  - 2015
SP  - e01478
EP  - e01415
VL  - 3
AB  - Multiply antibiotic-resistant Acinetobacter baumannii isolate D36 was recovered in Australia
AB  - in 2008 and belongs to a distinct lineage of global clone 1 (GC1).
AB  - Here, we present the complete 4.13 Mbp genome sequence (chromosome plus 4
AB  - plasmids), generated via long read sequencing (PacBio).
ER  -

TY  - JOUR
AU  - Hamidian, M.
AU  - Venepally, P.
AU  - Hall, R.M.
AU  - Adams, M.D.
TI  - Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1.
JO  - Genome Announcements
PY  - 2017
SP  - e00836
EP  - e00817
VL  - 5
AB  - Extensively antibiotic-resistant Acinetobacter baumannii isolate AB0057 recovered in the
AB  - United States in 2004 was one of the first global clone 1 isolates to be
AB  - completely sequenced. Here, the complete 4.05-Mb genome sequence (chromosome and
AB  - one plasmid) has been revised using Illumina HiSeq data and targeted sequencing
AB  - of PCR products.
ER  -

TY  - JOUR
AU  - Hamilton, R. et al.
TI  - Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.
JO  - Genome Announcements
PY  - 2015
SP  - e00515
EP  - e00515
VL  - 3
AB  - Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata,
AB  - Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent
AB  - aerobic methanotrophs typically isolated from various terrestrial ecosystems.
ER  -

TY  - JOUR
AU  - Hammer, A.J.
AU  - Walters, A.
AU  - Carroll, C.
AU  - Newell, P.D.
AU  - Chaston, J.M.
TI  - Draft Genome Sequence of Lactobacillus paracasei DmW181, a Bacterium Isolated from Wild Drosophila.
JO  - Genome Announcements
PY  - 2017
SP  - e00545
EP  - e00517
VL  - 5
AB  - The draft genome sequence of Lactobacillus paracasei DmW181, an anaerobic bacterium isolate
AB  - from wild Drosophila flies, is reported here. Strain DmW181
AB  - possesses genes for sialic acid and mannose metabolism. The assembled genome is
AB  - 3,201,429 bp, with 3,454 predicted genes.
ER  -

TY  - JOUR
AU  - Hammerl, J.A.
AU  - Irrgang, A.
AU  - Grobbel, M.
AU  - Tenhagen, B.A.
AU  - Kasbohrer, A.
TI  - Complete Genome Sequence of a blaCTX-M-1-Harboring Escherichia coli Isolate Recovered from Cattle in Germany.
JO  - Genome Announcements
PY  - 2018
SP  - e01476
EP  - e01417
VL  - 6
AB  - We describe here the whole-genome sequence and basic characteristics of Escherichia coli
AB  - isolate 15-AB01393, recovered from German beef within a national
AB  - monitoring program in 2015. This isolate was identified as an
AB  - extended-spectrum-beta-lactamase-producing E. coli strain of multilocus sequence
AB  - type (MLST) ST58 harboring the antimicrobial resistance genes blaCTX-M-1, mph(A),
AB  - sul2, dfrA5, strA, and strB.
ER  -

TY  - JOUR
AU  - Hammerl, J.A.
AU  - Jackel, C.
AU  - Reetz, J.
AU  - Beck, S.
AU  - Alter, T.
AU  - Lurz, R.
AU  - Barretto, C.
AU  - Brussow, H.
AU  - Hertwig, S.
TI  - Campylobacter jejuni Group III Phage CP81 Contains Many T4-Like Genes without Belonging to the T4-Type Phage Group: Implications for the Evolution of T4 Phages.
JO  - J. Virol.
PY  - 2011
SP  - 8597
EP  - 8605
VL  - 85
AB  - CP81 is a virulent Campylobacter group III phage whose linear genome
AB  - comprises 132,454 bp. At the nucleotide level, CP81 differs from other
AB  - phages. However, a number of its structural and replication/recombination
AB  - proteins revealed a relationship to the group II Campylobacter phages
AB  - CP220/CPt10 and to T4-type phages. Unlike the T4-related phages, the CP81
AB  - genome does not contain conserved replication and virion modules. Instead,
AB  - the respective genes are scattered throughout the phage genome. Moreover,
AB  - most genes for metabolic enzymes of CP220/CPt10 are lacking in CP81. On
AB  - the other hand, the CP81 genome contains nine similar genes for homing
AB  - endonucleases which may be involved in the attrition of the conserved gene
AB  - order for the virion core genes of T4-type phages. The phage apparently
AB  - possesses an unusual modification of C or G bases. Efficient cleavage of
AB  - its DNA was only achieved with restriction enzymes recognizing pure A/T
AB  - sites. Uncommonly, phenol extraction leads to a significant loss of CP81
AB  - DNA from the aqueous layer, a property not yet described for other phages
AB  - belonging to the T4 superfamily.
ER  -

TY  - JOUR
AU  - Hammerl, J.A.
AU  - Jackel, C.
AU  - Reetz, J.
AU  - Hertwig, S.
TI  - The Complete Genome Sequence of Bacteriophage CP21 Reveals Modular Shuffling in Campylobacter Group II Phages.
JO  - J. Virol.
PY  - 2012
SP  - 8896
EP  - 8896
VL  - 86
AB  - Campylobacter group II phages described so far share a high degree of sequence
AB  - similarity. We report the 182,833-bp genomic sequence of the closely related
AB  - group II phage CP21 and show that it has a completely different genomic
AB  - organization. As in other group II phages, the CP21 genome is composed of large
AB  - modules separated by long DNA repeat regions which obviously trigger
AB  - recombination and modular shuffling.
ER  -

TY  - JOUR
AU  - Hammerl, J.A.
AU  - Klein, I.
AU  - Lanka, E.
AU  - Appel, B.
AU  - Hertwig, S.
TI  - Genetic and functional properties of the self-transmissible Yersinia enterocolitica plasmid pYE854, which mobilizes the virulence plasmid pYV.
JO  - J. Bacteriol.
PY  - 2008
SP  - 991
EP  - 1010
VL  - 190
AB  - Yersinia strains frequently harbor plasmids, of which the virulence
AB  - plasmid pYV, indigenous in pathogenic strains, has been thoroughly
AB  - characterized during the last decades. Yet, it has been unknown whether
AB  - the nonconjugative pYV can be transferred by helper plasmids naturally
AB  - occurring in this genus. We have isolated the conjugative plasmids pYE854
AB  - (95.5 kb) and pYE966 (70 kb) from a nonpathogenic and a pathogenic
AB  - Yersinia enterocolitica strain, respectively, and demonstrate that both
AB  - plasmids are able to mobilize pYV. The complete sequence of pYE854 has
AB  - been determined. The transfer proteins and oriT of the plasmid reveal
AB  - similarities to the F factor. However, the pYE854 replicon does not belong
AB  - to the IncF group and is more closely related to a plasmid of
AB  - gram-positive bacteria. Plasmid pYE966 is very similar to pYE854 but lacks
AB  - two DNA regions of the larger plasmid that are dispensable for
AB  - conjugation.
ER  -

TY  - JOUR
AU  - Hammerl, J.A.
AU  - Lasch, P.
AU  - Nitsche, A.
AU  - Dabrowski, P.W.
AU  - Hahmann, H.
AU  - Wicke, A.
AU  - Kleta, S.
AU  - Dahouk, S.A.
AU  - Dieckmann, R.
TI  - Draft Genome Sequences of Klebsiella oxytoca Isolates Originating from a Highly Contaminated Liquid Hand Soap Product.
JO  - Genome Announcements
PY  - 2015
SP  - e00820
EP  - e00815
VL  - 3
AB  - In 2013, contaminated liquid soap was detected by routine microbiological monitoring of
AB  - consumer products through state health authorities. Because of its
AB  - high load of Klebsiella oxytoca, the liquid soap was notified via the European
AB  - Union Rapid Alert System for Dangerous Non-Food Products (EU-RAPEX) and recalled.
AB  - Here, we present two draft genome sequences and a summary of their general
AB  - features.
ER  -

TY  - JOUR
AU  - Hammond, A.W.
AU  - Gerard, G.F.
AU  - Campbell, J.H.
AU  - Chatterjee, D.K.
TI  - Characterization of a restriction enzyme from a strain of Neisseria gonorrhoea which recognizes 5'G^CCGGC3', an isoschizomer of NaeI.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 3320
EP  - 3320
VL  - 17
AB  - A type II restriction enzyme, NgoAIV, has been isolated from a strain of Neisseria gonorrhoea.
AB  - NgoAIV recognizes the palindromic sequence, 5'G^CCGGC3', and cleaves between the first G and
AB  - C residues producing a 4- base 5' extension.
ER  -

TY  - JOUR
AU  - Hammond, A.W.
AU  - Gerard, G.F.
AU  - Chatterjee, D.K.
TI  - Characterization of NgoAIII, an isoschizomer of SstII from a strain of Neisseria gonorrhoea.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 6750
EP  - 6750
VL  - 17
AB  - Note that this enzyme has been renamed NgoFIII because the strain it is from is
AB  - FA1090 and not WR220, from which the NgoA series of enzymes have been reported.
ER  -

TY  - JOUR
AU  - Hammond, A.W.
AU  - Gerard, G.F.
AU  - Chatterjee, D.K.
TI  - Cloning the KpnI restriction-modification system in Escherichia coli.
JO  - Gene
PY  - 1991
SP  - 97
EP  - 102
VL  - 97
AB  - The genes encoding the KpnI restriction and modification (R-M) system from
AB  - Klebsiella pneumoniae, recognizing the sequence, 5'-GGTAC^C-3', were cloned and
AB  - expressed in Escherichia coli.  Although the restriction endonuclease (ENase)-
AB  - and methyltransferase (MTase)-encoding genes were closely linked, initial
AB  - attempts to clone both genes as a single DNA fragment in a plasmid vector
AB  - resulted in deletions spanning all or part of the gene coding for the ENase.
AB  - Initial protection of the E. coli host with MTase expressed on a plasmid was
AB  - required to stabilize a compatible plasmid carrying both the ENase- and the
AB  - MTase-encoding genes on a single DNA fragment.  However, once established, the
AB  - MTase activity can be supplied in cis to the kpnIR gene, without an extra copy
AB  - of kpnIM.  A chromosomal map was generated localizing the kpnIR and kpnIM genes
AB  - on 1.7-kb and 3.5-kb fragments, respectively.  A final E. coli strain was
AB  - constructed, AH29, which contained two compatible plasmids: an inducible
AB  - plasmid carrying the kpnIR gene which amplifies copy number at elevated
AB  - temperatures and a pBR322 derivative expressing M.KpnI.  This strain produces
AB  - approx. 10 million units of R.KpnI/g of wet-weight cells, which is several
AB  - 1000-fold higher than the level of R.KpnI produced by K. pneumoniae.  In
AB  - addition, DNA methylated with M.KpnI in vivo does not appear to be restricted
AB  - by the mcrA, mcrB or mrr systems of E. coli.
ER  -

TY  - JOUR
AU  - Han, C. et al.
TI  - Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 54
EP  - 62
VL  - 1
AB  - Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of
AB  - the rapidly growing genus Pedobacter within the family
AB  - Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest,
AB  - because it was the first isolated strain shown to grow with heparin as sole
AB  - carbon and nitrogen source and because it produces several enzymes involved in
AB  - the degradation of mucopolysaccharides. All available data about this species are
AB  - based on a sole strain that was isolated from dry soil. Here we describe the
AB  - features of this organism, together with the complete genome sequence, and
AB  - annotation. This is the first report on a complete genome sequence of a member of
AB  - the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its
AB  - 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Han, C. et al.
TI  - Complete genome sequence of Kangiella koreensis type strain (SW-125).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 226
EP  - 233
VL  - 1
AB  - Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic
AB  - interest because of the very isolated location of the genus
AB  - Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis
AB  - SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated
AB  - from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the
AB  - features of this organism, together with the complete genome sequence, and
AB  - annotation. This is the first completed genome sequence from the genus Kangiella
AB  - and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp
AB  - long single replicon genome with its 2647 protein-coding and 48 RNA genes is part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Han, C. et al.
TI  - Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 94
EP  - 103
VL  - 6
AB  - Sulfuricurvum kujiense Kodama and Watanabe 2004 is the type species of the monotypic genus
AB  - Sulfuricurvum, which belongs to the family Helicobacteraceae in
AB  - the class Epsilonproteobacteria. The species is of interest because it is
AB  - frequently found in crude oil and oil sands where it utilizes various reduced
AB  - sulfur compounds such as elemental sulfur, sulfide and thiosulfate as electron
AB  - donors. Members of the species do not utilize sugars, organic acids or
AB  - hydrocarbons as carbon and energy sources. This genome sequence represents the
AB  - type strain of the only species in the genus Sulfuricurvum. The genome, which
AB  - consists of a circular chromosome of 2,574,824 bp length and four plasmids of
AB  - 118,585 bp, 71,513 bp, 51,014 bp, and 3,421 bp length, respectively, harboring a
AB  - total of 2,879 protein-coding and 61 RNA genes and is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Han, C. et al.
TI  - Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 337
EP  - 345
VL  - 3
AB  - Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus
AB  - Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII.
AB  - The species is of special interest because T. marianensis is an aerobic,
AB  - thermophilic marine bacterium, originally isolated from the deepest part in the
AB  - western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly,
AB  - the taxonomic status of the genus has not been clarified until now. The genus
AB  - Thermaerobacter may represent a very deep group within the Firmicutes or
AB  - potentially a novel phylum. The 2,844,696 bp long genome with its 2,375
AB  - protein-coding and 60 RNA genes consists of one circular chromosome and is a part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Han, C. et al.
TI  - Complete genome sequence of Treponema succinifaciens type strain (6091).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 361
EP  - 370
VL  - 4
AB  - Treponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this  strictly
AB  - anaerobic, apathogenic member of the genus Treponema oxidizes
AB  - carbohydrates and couples the Embden-Meyerhof pathway via activity of a
AB  - pyruvate-formate lyase to the production of acetyl-coenzyme A and formate. This
AB  - feature separates this species from most other anaerobic spirochetes. The genome
AB  - of T. succinifaciens 6091(T) is only the second completed and published type
AB  - strain genome from the genus Treponema in the family Spirochaetaceae. The
AB  - 2,897,425 bp long genome with one plasmid harbors 2,723 protein-coding and 63 RNA
AB  - genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Han, C. et al.
TI  - Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 371
EP  - 380
VL  - 4
AB  - Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus
AB  - Syntrophobotulus within the family Peptococcaceae. The species is of
AB  - interest because of its isolated phylogenetic location in the genome-sequenced
AB  - fraction of tree of life. When grown in pure culture with glyoxylate as carbon
AB  - source the organism utilizes glyoxylate through fermentative oxidation, whereas,
AB  - when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria,
AB  - it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic
AB  - or inorganic carbon source is utilized by S. glycolicus. The subdivision of the
AB  - family Peptococcaceae into genera does not reflect the natural relationships,
AB  - particularly regarding the genera most closely related to Syntrophobotulus. Both
AB  - Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the
AB  - taxonomic classification is in significant conflict with the 16S rRNA data. S.
AB  - glycolicus is already the ninth member of the family Peptococcaceae with a
AB  - completely sequenced and publicly available genome. The 3,406,739 bp long genome
AB  - with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Han, C.S. et al.
TI  - Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis.
JO  - J. Bacteriol.
PY  - 2006
SP  - 3382
EP  - 3390
VL  - 188
AB  - Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related
AB  - gram-positive, spore-forming bacteria of the B. cereus
AB  - sensu lato group. While independently derived strains of B. anthracis
AB  - reveal conspicuous sequence homogeneity, environmental isolates of B.
AB  - cereus and B. thuringiensis exhibit extensive genetic diversity. Here we
AB  - report the sequencing and comparative analysis of the genomes of two
AB  - members of the B. cereus group, B. thuringiensis 97-27 subsp. konkukian
AB  - serotype H34, isolated from a necrotic human wound, and B. cereus E33L,
AB  - which was isolated from a swab of a zebra carcass in Namibia. These two
AB  - strains, when analyzed by amplified fragment length polymorphism within a
AB  - collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis
AB  - isolates, appear closely related to B. anthracis. The B. cereus E33L
AB  - isolate appears to be the nearest relative to B. anthracis identified thus
AB  - far. Whole-genome sequencing of B. thuringiensis 97-27and B. cereus E33L
AB  - was undertaken to identify shared and unique genes among these isolates in
AB  - comparison to the genomes of pathogenic strains B. anthracis Ames and B.
AB  - cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus
AB  - ATCC 14579. Comparison of these genomes revealed differences in terms of
AB  - virulence, metabolic competence, structural components, and regulatory
AB  - mechanisms.
ER  -

TY  - JOUR
AU  - Han, G.H.
AU  - Kim, W.
AU  - Chun, J.
AU  - Kim, S.W.
TI  - Draft Genome Sequence of Methylophaga aminisulfidivorans MPT.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4265
EP  - 4265
VL  - 193
AB  - Methylophaga aminisulfidivorans MP(T) is a restricted facultatively marine methylotrophic
AB  - bacterium that grows on methanol, methylated amines,
AB  - dimethyl sulfide, and dimethyl sulfoxide. Here we present the high-quality
AB  - draft genome sequence of M. aminisulfidivorans MP(T) (KCTC 12909(T) = JCM
AB  - 14647(T)), consisting of a chromosome (3,092,085 bp) and a plasmid (16,875
AB  - bp).
ER  -

TY  - JOUR
AU  - Han, J.
AU  - Park, B.S.
AU  - Shin, D.J.
AU  - Song, S.Y.
AU  - Jeong, Y.J.
AU  - Lee, N.
TI  - Complete Genome Sequence of Mycoplasma hyopneumoniae Strain KM014, a Clinical Isolate from South Korea.
JO  - Genome Announcements
PY  - 2017
SP  - e01012
EP  - e01017
VL  - 5
AB  - Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia, resulting in
AB  - considerable economic losses in the swine industry. A few genome
AB  - sequences of M. hyopneumoniae have been reported to date, implying that
AB  - additional genome data are needed for further genetic studies. Here, we present
AB  - the annotated genome sequence of M. hyopneumoniae strain KM014.
ER  -

TY  - JOUR
AU  - Han, J.
AU  - Zhang, F.
AU  - Hou, J.
AU  - Liu, X.
AU  - Li, M.
AU  - Liu, H.
AU  - Cai, L.
AU  - Zhang, B.
AU  - Chen, Y.
AU  - Zhou, J.
AU  - Hu, S.
AU  - Xiang, H.
TI  - Complete Genome Sequence of the Metabolically Versatile Halophilic Archaeon Haloferax mediterranei, a Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Producer.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4463
EP  - 4464
VL  - 194
AB  - Haloferax mediterranei, an extremely halophilic archaeon, has shown promise for production of
AB  - poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from unrelated
AB  - cheap carbon sources. Here we report the complete genome (3,904,707 bp) of H.
AB  - mediterranei CGMCC 1.2087, consisting of one chromosome and three megaplasmids.
ER  -

TY  - JOUR
AU  - Han, J.E.
AU  - Hwang, S.Y.
AU  - Kim, J.H.
AU  - Shin, S.P.
AU  - Jun, J.W.
AU  - Chai, J.Y.
AU  - Park, Y.H.
AU  - Park, S.C.
TI  - CPRMethicillin resistant coagulase-negative staphylococci isolated from South Korean ducks exhibiting tremor.
JO  - Acta Vet. Scand.
PY  - 2013
SP  - 88
EP  - 88
VL  - 55
AB  - BACKGROUND: We describe coagulase-negative staphylococci (CoNS) isolates
AB  - collected from ducklings exhibiting tremor in South Korea over the period of 2010
AB  - to 2011. Screening of antimicrobial susceptibility and analysis of SCCmec
AB  - elements of CoNS were also investigated. RESULTS: Staphylococcus cohnii was the
AB  - most frequent staphylococcus (9 isolates) and S. sciuri (4 isolates), S. lentus
AB  - (3 isolate), S. simulans (1 isolate) and S. epidermidis (1 isolate) were also
AB  - detected. Among the 15 antimicrobials tested in this study, resistance against
AB  - oxacillin (15 isolates, 83.3%) was most frequently observed, but only one isolate
AB  - (SNUDS-1) possessed mecA. This isolate was shown to possess SCCmec type III; the
AB  - type 3 ccr complex and the class A mec complex. CONCLUSIONS: Based on these
AB  - results, isolate SNUDS-1 was shown to possess SCCmec type III; the type 3 ccr
AB  - complex and the class A mec complex. Although the SCCmec type III is not
AB  - predominant in human, MR-CoNS (Methicillin resistance Coagulase-negative
AB  - staphylococci) in food animals should be monitored to prevent the dissemination
AB  - of antimicrobial resistance genes and resistant pathogens to the community.
ER  -

TY  - JOUR
AU  - Han, J.E.
AU  - Kim, J.H.
AU  - Choresca, C.
AU  - Shin, S.P.
AU  - Jun, J.W.
AU  - Park, S.C.
TI  - Draft Genome Sequence of a Clinical Isolate, Aeromonas hydrophila SNUFPC-A8, from a Moribund Cherry Salmon (Oncorhynchus masou masou).
JO  - Genome Announcements
PY  - 2013
SP  - e00133
EP  - e00112
VL  - 1
AB  - We present the genome of a clinical isolate, Aeromonas hydrophila SNUFPC-A8, from a moribund
AB  - cherry salmon. The completed draft genome of this strain shows high
AB  - sequence homology to the reference strain A. hydrophila ATCC 7966 (NC008570.1)
AB  - and known plasmids pAsa2 and pAAk1 from other Aeromonas species (NC004925.1 and
AB  - NC019014.1).
ER  -

TY  - JOUR
AU  - Han, J.E.
AU  - Kim, J.H.
AU  - Shin, S.P.
AU  - Jun, J.W.
AU  - Chai, J.Y.
AU  - Park, S.C.
TI  - Draft Genome Sequence of Aeromonas salmonicida subsp. achromogenes AS03, an Atypical Strain Isolated from Crucian Carp (Carassius carassius) in the Republic   of Korea.
JO  - Genome Announcements
PY  - 2013
SP  - e00791
EP  - e00713
VL  - 1
AB  - We present the draft genome sequence of Aeromonas salmonicida subsp. achromogenes strain AS03,
AB  - an atypical A. salmonicida strain that causes erythrodermatitis in
AB  - crucian carp (Carassius carassius). This is the first genome sequence report of
AB  - A. salmonicida subsp. achromogenes, one of the four subspecies of atypical A.
AB  - salmonicida.
ER  -

TY  - JOUR
AU  - Han, J.I.
AU  - Choi, H.K.
AU  - Lee, S.W.
AU  - Orwin, P.M.
AU  - Kim, J.
AU  - Laroe, S.L.
AU  - Kim, T.G.
AU  - O'Neil, J.
AU  - Leadbetter, J.R.
AU  - Lee, S.Y.
AU  - Hur, C.G.
AU  - Spain, J.C.
AU  - Ovchinnikova, G.
AU  - Goodwin, L.
AU  - Han, C.
TI  - Complete genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1183
EP  - 1190
VL  - 193
AB  - Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic
AB  - capabilities, including the biodegradation of both
AB  - biogenic compounds and anthropogenic contaminants. V. paradoxus also
AB  - engages in mutually beneficial interactions with both bacteria and plants.
AB  - The complete genome sequence of V. paradoxus S110 is composed of 6,754,997
AB  - base pairs with 6,279 predicted protein-coding sequences within two
AB  - circular chromosomes. The genomic analysis has revealed multiple metabolic
AB  - features for autotrophic and heterotrophic lifestyles. These metabolic
AB  - diversities enable independent survival as well as a symbiotic lifestyle.
AB  - Consequently, S110 appears to have evolved into a superbly adaptable
AB  - microorganism, able to survive in ever-changing environmental conditions.
AB  - Based on our findings, we suggest V. paradoxus S110 as a potential
AB  - candidate for agrobiotechnological applications, such as biofertilizer and
AB  - biopesticide. Because it has many associations with other biota, it is
AB  - also suited to serve as an additional model system for studies of
AB  - microbe-plant and microbe-microbe interactions.
ER  -

TY  - JOUR
AU  - Han, J.I.
AU  - Spain, J.C.
AU  - Leadbetter, J.R.
AU  - Ovchinnikova, G.
AU  - Goodwin, L.A.
AU  - Han, C.S.
AU  - Woyke, T.
AU  - Davenport, K.W.
AU  - Orwin, P.M.
TI  - Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS.
JO  - Genome Announcements
PY  - 2013
SP  - e00843
EP  - e00813
VL  - 1
AB  - Variovorax paradoxus is a ubiquitous betaproteobacterium involved in plant growth promotion,
AB  - the degradation of xenobiotics, and quorum-quenching activity. The
AB  - genome of V. paradoxus strain EPS consists of a single circular chromosome of
AB  - 6,550,056 bp, with a 66.48% G+C content.
ER  -

TY  - JOUR
AU  - Han, J.W.
AU  - Oh, M.
AU  - Choi, G.J.
AU  - Kim, H.
TI  - Genome Sequence of Delftia acidovorans HK171, a Nematicidal Bacterium Isolated from Tomato Roots.
JO  - Genome Announcements
PY  - 2017
SP  - e01746
EP  - e01716
VL  - 5
AB  - Delftia acidovorans strain HK171, isolated from tomato roots, exhibited nematicidal activity
AB  - against Meloidogyne incognita Here, we present the genome
AB  - sequence of D. acidovorans strain HK171, which consists of one circular
AB  - chromosome of 6,430,384 bp, with 66.9% G+C content.
ER  -

TY  - JOUR
AU  - Han, K.
AU  - Li, Z.F.
AU  - Peng, R.
AU  - Zhu, L.P.
AU  - Zhou, T.
AU  - Wang, L.G.
AU  - Li, S.G.
AU  - Zhang, X.B.
AU  - Hu, W.
AU  - Wu, Z.H.
AU  - Qin, N.
AU  - Li, Y.Z.
TI  - Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu.
JO  - Sci. Rep.
PY  - 2013
SP  - 2101
EP  - 2101
VL  - 3
AB  - Complex environmental conditions can significantly affect bacterial genome size
AB  - by unknown mechanisms. The So0157-2 strain of Sorangium cellulosum is an
AB  - alkaline-adaptive epothilone producer that grows across a wide pH range. Here, we
AB  - show that the genome of this strain is 14,782,125 base pairs, 1.75-megabases
AB  - larger than the largest bacterial genome from S. cellulosum reported previously.
AB  - The total 11,599 coding sequences (CDSs) include massive duplications and
AB  - horizontally transferred genes, regulated by lots of protein kinases, sigma
AB  - factors and related transcriptional regulation co-factors, providing the So0157-2
AB  - strain abundant resources and flexibility for ecological adaptation. The
AB  - comparative transcriptomics approach, which detected 90.7% of the total CDSs, not
AB  - only demonstrates complex expression patterns under varying environmental
AB  - conditions but also suggests an alkaline-improved pathway of the insertion and
AB  - duplication, which has been genetically testified, in this strain. These results
AB  - provide insights into and a paradigm for how environmental conditions can affect
AB  - bacterial genome expansion.
ER  -

TY  - JOUR
AU  - Han, S.J.
AU  - Song, T.
AU  - Cho, Y.J.
AU  - Kim, J.S.
AU  - Choi, S.Y.
AU  - Bang, H.E.
AU  - Chun, J.
AU  - Bai, G.H.
AU  - Cho, S.N.
AU  - Shin, S.J.
TI  - Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 78
EP  - 78
VL  - 10
AB  - Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as
AB  - the most prevalent genotype in South Korea among clinical
AB  - isolates of M. tuberculosis from high school outbreaks. M. tuberculosis K is an
AB  - aerobic, non-motile, Gram-positive, and non-spore-forming rod-shaped bacillus. A
AB  - transmission electron microscopy analysis displayed an abundance of lipid bodies
AB  - in the cytosol. The genome of the M. tuberculosis K strain was sequenced using
AB  - two independent sequencing methods (Sanger and Illumina). Here, we present the
AB  - genomic features of the 4,385,518-bp-long complete genome sequence of M.
AB  - tuberculosis K (one chromosome, no plasmid, and 65.59 % G + C content) and its
AB  - annotation, which consists of 4194 genes (3447 genes with predicted functions),
AB  - 48 RNA genes (3 rRNA and 45 tRNA) and 261 genes with peptide signals.
ER  -

TY  - JOUR
AU  - Han, T.
AU  - Yamada-Mabuchi, M.
AU  - Zhao, G.
AU  - Li, L.
AU  - Liu, G.
AU  - Ou, H.Y.
AU  - Deng, Z.
AU  - Zheng, Y.
AU  - He, X.
TI  - Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 1147
EP  - 1159
VL  - 43
AB  - SET and RING-finger-associated (SRA) domain is involved in establishment and maintenance of
AB  - DNA methylation in eukaryotes. Proteins containing SRA domains
AB  - exist in mammals, plants, even microorganisms. It has been established that
AB  - mammalian SRA domain recognizes 5-methylcytosine (5mC) through a base-flipping
AB  - mechanism. Here, we identified and characterized two SRA domain-containing
AB  - proteins with the common domain architecture of N-terminal SRA domain and
AB  - C-terminal HNH nuclease domain, Sco5333 from Streptomyces coelicolor and Tbis1
AB  - from Thermobispora bispora. Both sco5333 and tbis1 cannot establish in methylated
AB  - Escherichia coli hosts (dcm(+)), and this in vivo toxicity requires both SRA and
AB  - HNH domain. Purified Sco5333 and Tbis1 displayed weak DNA cleavage activity in
AB  - the presence of Mg(2+), Mn(2+) and Co(2+) and the cleavage activity was
AB  - suppressed by Zn(2+). Both Sco5333 and Tbis1 bind to 5mC-containing DNA in all
AB  - sequence contexts and have at least a preference of 100 folds in binding affinity
AB  - for methylated DNA over non-methylated one. We suggest that linkage of
AB  - methyl-specific SRA domain and weakly active HNH domain may represent a universal
AB  - mechanism in competing alien methylated DNA but to maximum extent minimizing
AB  - damage to its own chromosome.
ER  -

TY  - JOUR
AU  - Han, X.
AU  - Li, M.
AU  - Ding, Z.
AU  - Zhao, J.
AU  - Ji, K.
AU  - Wen, M.
AU  - Lu, T.
TI  - Genome Sequence of Streptomyces auratus Strain AGR0001, a Phoslactomycin-Producing Actinomycete.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5472
EP  - 5473
VL  - 194
AB  - Streptomyces auratus strain AGR0001 produces neophoslactomycin A, a novel analog  of
AB  - phoslactomycin that possesses potent activity against some phytopathogenic
AB  - fungi. Here, the draft genome sequence of S. auratus strain AGR0001 is presented,
AB  - which would provide insight into the biosynthetic mechanism of neophoslactomycin
AB  - A.
ER  -

TY  - JOUR
AU  - Han, X.Y.
AU  - Mistry, N.A.
AU  - Thompson, E.J.
AU  - Tang, H.L.
AU  - Khanna, K.
AU  - Zhang, L.
TI  - Draft Genome Sequence of New Leprosy Agent Mycobacterium lepromatosis.
JO  - Genome Announcements
PY  - 2015
SP  - e00513
EP  - e00515
VL  - 3
AB  - Mycobacterium lepromatosis is a newly discovered cause of leprosy. Here, we present a
AB  - near-complete genome of M. lepromatosis from strain FJ924 obtained from
AB  - a patient who died of leprosy. The genome contained 3,215,823 nucleotides and
AB  - matched ~87% with the Mycobacterium leprae genome. This genome is likely the
AB  - smallest of all mycobacterial genomes known to date.
ER  -

TY  - JOUR
AU  - Han, Y.
AU  - Dai, B.
AU  - Zhou, Y.
AU  - Wu, Z.
AU  - Ye, B.C.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. SCPG-7, Isolated from Saline Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00702
EP  - e00717
VL  - 5
AB  - Pseudomonas sp. SCPG-7 was isolated from saline soil. The strain can increase the germination
AB  - rate of cotton seeds and promote the growth of cotton seedlings under
AB  - salt stress conditions. The genome is 6,256,198 bp long, containing 5,672
AB  - predicted open reading frames.
ER  -

TY  - JOUR
AU  - Hanahan, D.
TI  - Mechanisms of DNA Transformation:  Restrictionlike effects in Transformation in Escherichia coli and Salmonella typhimurium.
JO  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
PY  - 1986
SP  - 1
EP  - 7
VL  - 0
AB  - The introduction of naked DNA into Escherichia coli was first demonstrated by
AB  - Mandel and Higa, who observed that incubation of a suspension of E. coli  cells
AB  - and bacteriophage lambda DNA in a solution of CaCl2 at 0C resulted in the
AB  - subsequent appearance of infectious centers.  They further showed that a heat
AB  - pulse, in which the mixture of cells and DNA was briefly incubated at 42C,
AB  - chilled on ice, and then diluted into growth medium, improved the frequency of
AB  - transfection.  The general applicability of these conditions to DNA transfer
AB  - was demonstrated by their use to effect plasmid transformation, in which
AB  - circular plasmids carrying antibiotic resistance genes were stably established
AB  - as replicating episomes; genetic transformation, in which linear E. coli DNA
AB  - was transformed into auxotrophic strains to restore the mutant alleles; and
AB  - transfection of other bacteriophages.  These observations proved to be
AB  - applicable to DNA transformation of Salmonella typhimurium, suggesting that
AB  - induction of the artificial or natural ability to take up DNA reflected general
AB  - strutural or physiological features of these two closely related organisms.
AB  - Most subsequent studies of DNA transformation have employed plasmids carrying
AB  - antibiotic resistance genes, scoring transformation by the appearance of
AB  - drug-resistant colonies under selective conditions.  Primary attention has been
AB  - focused on E. coli, but it appears the observations are, in general, applicable
AB  - to S. typhimurium as well.  Transformation with linear DNAs generally shows the
AB  - same response to conditions, given the genetic distinction that linear DNA
AB  - (chromosomal or bacteriophage) will most efficiently transform strains
AB  - deficient in recBC nuclease, due to its degradative activity on the ends of DNA
AB  - molecules.
ER  -

TY  - JOUR
AU  - Hanak, A.M.
AU  - Nagler, M.
AU  - Weinmaier, T.
AU  - Sun, X.
AU  - Fragner, L.
AU  - Schwab, C.
AU  - Rattei, T.
AU  - Ulrich, K.
AU  - Ewald, D.
AU  - Engel, M.
AU  - Schloter, M.
AU  - Bittner, R.
AU  - Schleper, C.
AU  - Weckwerth, W.
TI  - Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus.
JO  - Genome Announcements
PY  - 2014
SP  - e00276
EP  - e00214
VL  - 2
AB  - Paenibacillus sp. P22 is a Gram-negative facultative anaerobic endospore-forming  bacterium
AB  - isolated from poplar hybrid 741 (female symbol[Populus alba x (P. davidiana + P. simonii) x P.
AB  - tomentosa]). This bacterium shows strong similarities to Paenibacillus humicus, and important
AB  - growth-promoting effects on in vitro grown explants of poplar hybrid 741 have been described.
ER  -

TY  - JOUR
AU  - Hanawa, F.
AU  - Okamoto, M.
AU  - Towers, G.H.N.
TI  - Inhibition of restriction enzyme's DNA sequence recognition by PUVA treatment.
JO  - Photochem. Photobiol.
PY  - 2001
SP  - 269
EP  - 273
VL  - 74
AB  - Applying various restriction enzymes on a specially designed 1.5 kb DNA fragment revealed that
AB  - the inhibitory effects of psoralens + UVA
AB  - irradiation (PUVA) treatment on restriction endonuclease activities are
AB  - caused by recognition inhibition. In this study restriction enzymes
AB  - that have a 5'-TpA sequence at the cleaving site (KpnI, XbaI, PmeI and
AB  - DraI), and the noncleaving site (PacI) in recognition sites, or have
AB  - two 5'-TpA sequences at the recognition site, and a nonspecific
AB  - sequence between the recognition and the cleaving sites (BciVI), were
AB  - inhibited by PUVA treatment. Most of the other restriction enzymes used
AB  - in this study, which do not have a 5'-TpA sequence at their restriction
AB  - site, were not inhibited by PUVA treatment, although a 5'-TpA sequence
AB  - is located adjacent (SmaI) or very close (BamHI, SacI and PstI) to the
AB  - recognition and cleaving sites for these enzymes. Because SphI, which
AB  - does not have 5'-TpA at its restriction site, was strongly inhibited by
AB  - PUVA treatment, the 5'-CpA sequence is suggested to be a new binding
AB  - site of psoralens after UVA irradiation.
ER  -

TY  - JOUR
AU  - Hanck, T.
AU  - Gerwin, N.
AU  - Fritz, H.-J.
TI  - Nucleotide sequence of the dcm locus of Escherichia coli K12.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 5844
EP  - 5844
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Hanck, T.
AU  - Schmidt, S.
AU  - Fritz, H.J.
TI  - Sequence-specific and mechanism-based crosslinking of Dcm DNA cytosine-C5 methyltransferase of E.coli K-12 to synthetic oligonucleotides containing 5-fluoro-2'-deoxycytidine.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 303
EP  - 309
VL  - 21
AB  - The product of the dcm gene is the only DNA cytosine-C5 methyltransferase of Escherichia coli
AB  - K-12; it catalyses transfer of a methyl group from S-adenosyl methionine (SAM) to the C-5
AB  - position of the inner cytosine residue of the cognate sequence CCA/TGG. Sequence-specific,
AB  - covalent crosslinking of the enzyme to synthetic oligonucleotides containing
AB  - 5-fluoro-2'-deoxycytidine is demonstrated. This reaction is abolished if serine replaces the
AB  - cysteine at residue #177 of the enzyme. These results lend strong support to a catalytic
AB  - mechanism in which an enzyme sulfhydryl group undergoes Michael addition to the C5-C6 double
AB  - bond, thus activating position C-5 of the substrate DNA cytosine residue for electrophilic
AB  - attack by the methyl donor SAM. The enzyme is capable of self-methylation in a DNA-independent
AB  - reaction requiring SAM and the presence of cysteine at position #177.
ER  -

TY  - JOUR
AU  - Hancox, E.L.
AU  - Connolly, B.A.
AU  - Walker, R.T.
TI  - Synthesis and properties of oligodeoxynucleotides containing the analogue 2'-deoxy-4'-thiothymidine.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3485
EP  - 3491
VL  - 21
AB  - The 2'-deoxythymidine analogue 2'-deoxy-4'thiothymidine has been incorporated, using
AB  - standard methodology, into a series of dodecadeoxynucleotides containing the EcoRV restriction
AB  - endonuclease recognition site (GATATC). The stability of these oligodeoxynucleotides and their
AB  - ability to act as substrates for the restriction endonuclease and associated methylase have
AB  - been compared with a normal unmodified oligodeoxynucleotide. No problems were encountered in
AB  - the synthesis despite the presence of a potentially oxidisable sulfur atom in the sugar ring.
AB  - The analogue had very little effect on the melting temperature of the self-complementary
AB  - oligodeoxynucleotides so synthesised and all had a CD spectrum compatible with a B-DNA
AB  - structure. The oligodeoxynucleotide containing one analogue in each strand within the
AB  - recognition site, adjacent to the bond to be cleaved (i.e. GAXATC, where X is
AB  - 2'-deoxy-4'-thiothymidine), was neither a substrate for the endonuclease nor was recognized
AB  - by the associated methylase. When still within the recognition hexanucleotide but two further
AB  - residues removed from the site of cleavage (i.e. GATAXC), the oligodeoxynucleotide was a poor
AB  - substrate for both the endonuclease and methylase. Binding of the oligodeoxynucleotide to the
AB  - endonuclease was unaffected but the kcat value was only 0.03% of the value obtained for the
AB  - parent oligodeoxynucleotide. These results show that the incorporation of
AB  - 2'-deoxy-4'-thionucleosides into synthetic oligodeoxynucleotides may shed light on subtle
AB  - interations between proteins and their normal substrates and may also show why
AB  - 2'-deoxy-4'-thiothymidine itself is so toxic in cell culture.
ER  -

TY  - JOUR
AU  - Hancox, E.L.
AU  - Halford, S.E.
TI  - Kinetic analysis of a mutational hot spot in the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1997
SP  - 7577
EP  - 7585
VL  - 36
AB  - The EcoRV endonuclease contacts the minor groove of DNA through a peptide loop encompassing
AB  - residues 67-72.  This loop adapts to distorted DNA in the specific complex and to regular DNA
AB  - in the nonspecific complex.  Random mutagenesis had previously identified glutamine 69 as the
AB  - key component of the loop and this study reports on mutants with glutamate (Q69E), lysine
AB  - (Q69K), or leucine (Q69L) at this position.  The mutants bound DNA specifically at the EcoRV
AB  - recognition site in the presence of Ca2+, in the same manner as wild-type EcoRV.  In the
AB  - absence of divalent metals, Q69K and Q69L showed the same nonspecific binding as native EcoRV
AB  - while Q69E failed to bind DNA.  Glutamate at position 69 presumably repels nonspecific DNA
AB  - whilst allowing the adaptations to specific DNA.  Both Q69E and Q69K had severely impaired DNA
AB  - cleavage activities, while Q69L had a steady-state kcat within an order of magnitude of
AB  - wild-type EcoRV though its primary product was nicked DNA, in contrast to double strand breaks
AB  - by wild-type EcoRV.  The activity of Q69L required higher concentrations of Mg2+ than the
AB  - wild-type and showed a sigmoidal dependence upon the Mg2+ concentration, indicating two metal
AB  - ions per strand scission.  Transient kinetics on Q69L gave lower rate constants for
AB  - phosphodiester hydrolysis than wild-type EcoRV and its reaction also involved a slow
AB  - conformational change preceding DNA cleavage that had no equivalent with the wild-type.  Gln69
AB  - in EcoRV thus plays key roles in the adjustments of the protein to varied DNA structures and
AB  - in the alignment of the catalytic functions for DNA cleavage.
ER  -

TY  - JOUR
AU  - Handa, N.
AU  - Ichige, A.
AU  - Kobayashi, I.
TI  - Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex.
JO  - Microbiology
PY  - 2009
SP  - 2320
EP  - 2332
VL  - 155
AB  - Loss of a type II restriction-modification gene complex, such as EcoRI, from a bacterial cell
AB  - leads to death of its descendant cells through
AB  - attack by residual restriction enzyme molecules on under-methylated target
AB  - sites of newly synthesized chromosomes. Through such post-segregational
AB  - host killing, these gene complexes force their maintenance on their host
AB  - cells. This finding led to re-discovery of type II
AB  - restriction-modification systems as selfish mobile elements. The host
AB  - prokaryote cells were found to cope with such attacks through a variety of
AB  - means. RecBCD pathway of homologous recombination in Escherichia coli
AB  - repairs the lethal lesions on the chromosome while it destroys restricted
AB  - non-self DNA. The recBCD homologs, however, appears very limited in
AB  - distribution among bacterial genomes, while homologs of RecFOR proteins
AB  - responsible for another pathway are widespread in eubacteria, just as the
AB  - restriction-modification systems are. In the present work, therefore, we
AB  - examined possible contribution of RecFOR pathway in cell survival after
AB  - loss of a restriction-modification gene complex. A recF mutation reduced
AB  - the survival in otherwise rec-positive background and, more severely, in a
AB  - recBC sbcBC background. We also found that its effect is prominent in the
AB  - presence of specific non-null mutant forms of RecBCD enzyme: the
AB  - resistance to killing seen with recC1002, recC1004, recC2145 and recB2154
AB  - is much reduced to the level of a null recBC allele when combined with a
AB  - recF, recO or recR mutant allele. Such resistance was also dependent on
AB  - RecJ and RecQ functions. UV resistance of these non-null recBCD mutants is
AB  - also decreased by recF, recJ or recQ mutation. These results demonstrate
AB  - that RecFOR pathway of recombination can greatly contribute to resistance
AB  - to restriction-modification-mediated host killing depending on genetic
AB  - backgrounds.
ER  -

TY  - JOUR
AU  - Handa, N.
AU  - Ichige, A.
AU  - Kusano, K.
AU  - Kobayashi, I.
TI  - Cellular responses to postsegregational killing by restriction-modification genes.
JO  - J. Bacteriol.
PY  - 2000
SP  - 2218
EP  - 2229
VL  - 182
AB  - Plasmids that carry one of several type II restriction modification gene complexes are known
AB  - to show increased stability. The underlying mechanism was proposed to be the lethal attack by
AB  - a restriction enzyme at chromosomal recognition sites in cells that had lost the restriction
AB  - modification gene complex. In order to examine bacterial responses to this postsegregational
AB  - cell killing, we analyzed the cellular processes following loss of the EcoRI restriction
AB  - modification gene complex carried by a temperature-sensitive plasmid in an Escherichia coli
AB  - strain that is wild type with respect to DNA repair. A shift to the nonpermissive temperature
AB  - blocked plasmid replication, reduced the increase in viable cell counts and resulted in loss
AB  - of cell viability. Many cells formed long filaments, some of which were multinucleated and
AB  - others anucleated. In a mutant defective in RecBCD exonuclease/recombinase, these cell death
AB  - symptoms were more severe and cleaved chromosomes accumulated. Growth inhibition was also more
AB  - severe in recA, ruvAB, ruvC, recG, and recN mutants. The cells induced the SOS response in a
AB  - RecBC-dependent manner. These observations strongly suggest that bacterial cells die as a
AB  - result of chromosome cleavage after loss of a restriction modification gene complex and that
AB  - the bacterial RecBCD/RecA machinery helps the cells to survive, at least to some extent, by
AB  - repairing the cleaved chromosomes. These and previous results have led us to hypothesize that
AB  - the RecBCD/Chi/RecA system serves to destroy restricted "nonself" DNA and repair restricted
AB  - "self" DNA.
ER  -

TY  - JOUR
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Post-segregational killing by restriction modification gene complexes: Observations of individual cell deaths.
JO  - Biochimie
PY  - 1999
SP  - 931
EP  - 938
VL  - 81
AB  - Through a mechanism known as post-segregational killing, several plasmids mediate their stable
AB  - maintenance by carrying genes that kill plasmid-free segregant cells. We demonstrated earlier
AB  - that loss of plasmids carrying type II restriction modification (RM) gene complexes inhibits
AB  - the propagation of a cell population and causes chromosome breakage. We now show the
AB  - morphology of individual cells changes following loss of thermosensitive plasmids carrying
AB  - EcoRI RM or PaeR7I RM after a shift to a non-permissive temperature. After a lag, many cells
AB  - formed long filaments containing multiple nuclei as detected by DAPI staining. Several hours
AB  - after the shift, many of these long filaments lacked nuclei. Fragmentation of chromosomal DNA
AB  - down to 5 kb was detected by electrophoresis. These observations lend strong support to the
AB  - concept of post-segregational cell killing by type II restriction modification gene complexes.
ER  -

TY  - JOUR
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function.
JO  - J. Bacteriol.
PY  - 2005
SP  - 7362
EP  - 7373
VL  - 187
AB  - Previous works have demonstrated that DNA breaks generated by restriction enzymes stimulate,
AB  - and are repaired by, homologous recombination with an intact, homologous DNA region through
AB  - the function of lambdoid bacteriophages lambda and Rac. In the present work, we examined the
AB  - effect of bacteriophage functions, expressed in bacterial cells, on restriction of an
AB  - infecting tester phage in a simple plaque formation assay. The efficiency of plaque formation
AB  - on an Escherichia coli host carrying EcoRI, a type II restriction system, is not increased by
AB  - the presence of Rac prophage-presumably because, under the single-infection conditions of the
AB  - plaque assay, a broken phage DNA cannot find a homologue with which to recombine. To our
AB  - surprise, however, we found that the efficiency of plaque formation in the presence of a type
AB  - III restriction system, EcoP1 or EcoP15, is increased by the bacteriophage-mediated homologous
AB  - recombination functions recE and recT of Rac prophage. This type III restriction alleviation
AB  - does not depend on lar on Rac, unlike type I restriction alleviation. On the other hand,
AB  - bacterial RecBCD-homologous recombination function enhances type III restriction. These
AB  - results led us to hypothesize that the action of type III restriction enzymes takes place on
AB  - replicated or replicating DNA in vivo and leaves daughter DNAs with breaks at nonallelic
AB  - sites, that bacteriophage-mediated homologous recombination reconstitutes an intact DNA from
AB  - them, and that RecBCD exonuclease blocks this repair by degradation from the restriction
AB  - breaks.
ER  -

TY  - JOUR
AU  - Handa, N.
AU  - Naito, Y.
AU  - Kobayashi, I.
TI  - Experimental genome evolution: Large-scale genome rearrangements associated with resistance of a chromosomal restriction-modification gene complex to replacement.
JO  - Genes Genet. Syst.
PY  - 2000
SP  - 381
EP  - 381
VL  - 75
AB  - Type II restriction enzymes are paired with modification enzymes that protect type II
AB  - restriction sites from cleavage by methylating them.  A plasmid carrying a type II restriction
AB  - modification gene complex is not easily replaced by an incompatible plasmid because loss of
AB  - the former leads to cell death through chromosome cleavage.  In the present work, we looked to
AB  - see if a chromosomally located restriction modification gene complex could be replaced by a
AB  - homologous stretch of DNA.  We tried to replace the PaeR7I gene complex on the Escherichia
AB  - coli chromosome by transducing a homologous stretch of PaeR7I-modified DNA.  The replacement
AB  - efficiency of the restriction modification complex was lower than expected.  Some of the
AB  - resulting recombinant clones retained the recipient restriction modification gene complex as
AB  - well as the homologous DNA (donor allele), and slowly lost the donor allele in the absence of
AB  - selection.  Analysis of their genome-wide rearrangements by Southern hybridization, inverse
AB  - PCR, and sequence determination demonstrated the occurrence of unequal homologous
AB  - recombination between copies of the transposon IS3.  It was strongly suggested that multiple
AB  - rounds of unequal IS3-IS3 recombination caused large-scale duplication and inversion of the
AB  - chromosome, and that only one of the duplicated copies of the recipient PaeR7I was replaced.
ER  -

TY  - JOUR
AU  - Handa, N.
AU  - Nakayama, Y.
AU  - Sadykov, M.
AU  - Kobayashi, I.
TI  - Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex.
JO  - Mol. Microbiol.
PY  - 2001
SP  - 932
EP  - 940
VL  - 40
AB  - Type II restriction enzymes are paired with modification enzymes that protect type II
AB  - restriction sites from cleavage by methylating them. A plasmid carrying a type II
AB  - restriction-modification gene complex is not easily replaced by an incompatible plasmid
AB  - because loss of the former leads to cell death through chromosome cleavage. In the present
AB  - work, we looked to see whether a chromosomally located restriction-modification gene complex
AB  - could be replaced by a homologous stretch of DNA. We tried to replace the PaeR7I gene complex
AB  - on the Escherichia coli chromosome by transducing a homologous stretch of PaeR7I-modified DNA.
AB  - The replacement efficiency of the restriction-modification complex was lower than expected.
AB  - Some of the resulting recombinant clones retained the recipient restriction-modification gene
AB  - complex as well as the homologous DNA (donor allele), and slowly lost the donor allele in the
AB  - absence of selection. Analysis of their genome-wide rearrangements by Southern hybridization,
AB  - inverse polymerase chain reaction (iPCR) and sequence determination demonstrated the
AB  - occurrence of unequal homologous recombination between copies of the transposon IS3. It was
AB  - strongly suggested that multiple rounds of unequal IS3-IS3 recombination caused large-scale
AB  - duplication and inversion of the chromosome, and that only one of the duplicated copies of the
AB  - recipient PaeR7I was replaced.
ER  -

TY  - JOUR
AU  - Handa, V.
AU  - Jeltsch, A.
TI  - Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 1103
EP  - 1112
VL  - 348
AB  - Mammalian DNA methyltransferases methylate cytosine residues within CG dinucleotides. By
AB  - statistical analysis of published data of the Human
AB  - Epigenome Project we have determined flanking sequences of up to
AB  - +/- four base-pairs surrounding the central CG site that are
AB  - characteristic of high (5'-CTTGCGCAAG-3') and low (5'-TGTTCGGTGG-3')
AB  - levels of methylation in human genomic DNA. We have investigated the
AB  - influence of flanking sequence on the catalytic activity of the Dnmt3a
AB  - and Dnmt3b de novo DNA methyltransferases using a set of synthetic
AB  - oligonucleotide substrates that covers all possible +/- 1 flanks
AB  - in quantitative terms. Methylation kinetics experiments revealed a >13-fold difference between
AB  - the preferred (RCGY) and disfavored +/-
AB  - 1 flanking base-pairs (YCGR). In addition, AT-rich flanks are preferred
AB  - over GC-rich ones. These experimental preferences coincide with the
AB  - genomic methylation patterns. Therefore, we have expanded our
AB  - experimental analysis and found a >500-fold difference in the
AB  - methylation rates of the consensus sequences for high and low levels of
AB  - methylation in the genome. This result demonstrates a very pronounced
AB  - flanking sequence preference of Dnmt3a and Dnmt3b. It suggests that the
AB  - methylation pattern of human DNA is due, in part, to the flanking
AB  - sequence preferences of the de novo DNA MTases and that flanking
AB  - sequence preferences could be involved in the origin of CG islands.
AB  - Furthermore, similar flanking sequence preferences have been found for
AB  - the stimulation of the immune system by unmethylated CGs, suggesting a
AB  - co-evolution of DNA MTases and the immune system.
ER  -

TY  - JOUR
AU  - Handayani, I.
AU  - Ratnakomala, S.
AU  - Lisdiyanti, P.
AU  - Fahrurrozi, A.M.
AU  - Wohlleben, W.
AU  - Mast, Y.
TI  - Complete Genome Sequence of Streptomyces sp. Strain BSE7F, a Bali Mangrove Sediment Actinobacterium with Antimicrobial Activities.
JO  - Genome Announcements
PY  - 2018
SP  - e00618
EP  - e00618
VL  - 6
AB  - The strain Streptomyces sp. BSE7F, a novel Streptomyces strain isolated from Indonesian
AB  - mangrove sediment, displays antimicrobial activities against
AB  - Gram-positive bacteria, Gram-negative bacteria, and yeast. Bioinformatic analysis
AB  - of the genome sequence revealed the occurrence of 22 biosynthetic gene clusters
AB  - disclosing the secondary metabolite capacity of strain BSE7F.
ER  -

TY  - JOUR
AU  - Handique, A.K.
TI  - New technique for thermostability of restriction and modifying enzymes.
JO  - Curr. Sci.
PY  - 1994
SP  - 103
EP  - 104
VL  - 66
AB  - Commentary on the use of trehalose to stabilize restriction enzymes
ER  -

TY  - JOUR
AU  - Handley, K.M.
AU  - Upton, M.
AU  - Beatson, S.A.
AU  - Hery, M.
AU  - Lloyd, J.R.
TI  - Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1T.
JO  - Genome Announcements
PY  - 2013
SP  - E00231
EP  - E00213
VL  - 1
AB  - Marinobacter santoriniensis NKSG1(T) originates from metalliferous marine
AB  - sediment. It can respire and redox cycle arsenic species and perform mixotrophic,
AB  - nitrate-dependent Fe(II) oxidation. The genome sequence, reported here, will help
AB  - further elucidate the genetic mechanisms underlying these and other potential
AB  - biogeochemically relevant functions, such as arsenic and mercury resistance and
AB  - hydrocarbon degradation.
ER  -

TY  - JOUR
AU  - Handtke, S.
AU  - Volland, S.
AU  - Methling, K.
AU  - Albrecht, D.
AU  - Becher, D.
AU  - Nehls, J.
AU  - Bongaerts, J.
AU  - Maurer, K.-H.
AU  - Lalk, M.
AU  - Liesegang, H.
AU  - Voigt, B.
AU  - Daniel, R.
AU  - Hecker, M.
TI  - Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-An omics-based approach.
JO  - J. Biotechnol.
PY  - 2014
SP  - 204
EP  - 214
VL  - 192
AB  - Members of the species Bacillus pumilus get more and more in focus of the biotechnological
AB  - industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain
AB  - Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The
AB  - proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was
AB  - analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182
AB  - cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for
AB  - about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS,
AB  - IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed
AB  - metabolic pathways. In the genome sequence a functional secretion system including the
AB  - components of the Sec-and Tat-secretion machinery was found. Analysis of the exoproteome
AB  - revealed secretion of about 70 proteins with predicted secretion signals. In addition,
AB  - selected production-relevant genome features such as restriction modification systems and NRPS
AB  - clusters of B. pumilus Jo2 are discussed. (C) 2014 Elsevier B.V. All rights reserved.
ER  -

TY  - JOUR
AU  - Hang, J.
AU  - Mullins, K.E.
AU  - Clifford, R.J.
AU  - Onmus-Leone, F.
AU  - Yang, Y.
AU  - Jiang, J.
AU  - Leguia, M.
AU  - Kasper, M.R.
AU  - Maguina, C.
AU  - Lesho, E.P.
AU  - Jarman, R.G.
AU  - Richards, A.L.
AU  - Blazes, D.
TI  - Complete Genome Sequence of Bartonella ancashensis Strain 20.00, Isolated from the Blood of a Patient with Verruga Peruana.
JO  - Genome Announcements
PY  - 2015
SP  - e01217
EP  - e01215
VL  - 3
AB  - Here we present the complete genome sequence of Bartonella ancashensis strain 20.00, isolated
AB  - from the blood of a Peruvian patient with verruga peruana, known
AB  - as Carrion's disease. Bartonella ancashensis is a Gram-negative bacillus,
AB  - phylogenetically most similar to Bartonella bacilliformis, the causative agent of
AB  - Oroya fever and verruga peruana.
ER  -

TY  - JOUR
AU  - Hanish, J.
AU  - McClelland, M.
TI  - Controlled partial restriction digestions of DNA by competition with modification methyltransferases.
JO  - Anal. Biochem.
PY  - 1989
SP  - 357
EP  - 360
VL  - 179
AB  - Competitive reactions, using defined ratios of DNA restriction
AB  - methyltransferase to endonuclease, are shown to result in reliable partial
AB  - restriction digests of DNA.  This method is suitable over a wide range of DNA
AB  - concentrations and works on DNA in liquid or embedded in agarose.  Simultaneous
AB  - methylase/endonuclease reactions using endonucleases that cleave human DNA very
AB  - infrequently, such as ClaI or NotI, should generate very large discrete DNA
AB  - fragments suitable for physical mapping in the million base-pair range.
AB  - Another possible application of methylase/endonuclease competitive reactions is
AB  - the production of defined partial digests for making cosmid, lambda, or other
AB  - genomic libraries.
ER  -

TY  - JOUR
AU  - Hanish, J.
AU  - McClelland, M.
TI  - Methylase-limited partial NotI cleavage for physical mapping of genomic DNA.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3287
EP  - 3291
VL  - 18
AB  - Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an
AB  - important technique for genomic mapping. However, partial genomic cleavage with this enzyme is
AB  - impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we
AB  - have purified the blocking methylase M.BspRI (5'...GGmCC...3') for competititon digests with
AB  - NotI. The resulting methylase-limited partial DNA cleavage is shown to be superior to standard
AB  - techniques on bacterial genomic DNA.
ER  -

TY  - JOUR
AU  - Hanish, J.
AU  - McClelland, M.
TI  - Activity of DNA modification and restriction enzymes in KGB, a potassium glutamate buffer.
JO  - Gene Anal. Tech.
PY  - 1988
SP  - 105
EP  - 107
VL  - 5
AB  - The most abundant intracellular cation in bacteria is potassium, and the most abundant anion
AB  - is glutamate. However, most recommended restriction endonuclease buffers contain Na+ and Cl-.
AB  - Restriction endonucleases retain their ability to cleave DNA over a much broader range of
AB  - potassium glutamate (KGlu) concentrations than NaCl concentrations. These facts encouraged us
AB  - to investigate the possibility that we could use KGlu in an NaCl-free buffer and achieve
AB  - normal levels of activity for all restriction endonuclease. In this paper we present data
AB  - comparing the activity of 85 restriction endonucleases and 11 DNA methylases in a series of
AB  - KGlu buffers (KGC) against that found under optimal conditions recommended by the vendors (New
AB  - England Biolabs, Boehringer Mannheim Biochem., and International Biotech Inc.).
ER  -

TY  - JOUR
AU  - Hanish, J.
AU  - McClelland, M.
TI  - Enzymatic cleavage of a bacterial chromosome at a transposon-inserted rare site.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 829
EP  - 832
VL  - 19
AB  - The sequential use of the methylase M.XbaI (5'-TCTAGm6A) and the methylation-dependent
AB  - endonuclease DpnI (5'-Gm6A/TC) results in cleavage at 5'-TCTAGA/TCTAGA. This recognition
AB  - sequence was introduced into a transposon derived from the Mu bacteriophage and transposed
AB  - into the genome of the bacterium Salmonella typhimurium. M.XbaI methylation was provided in
AB  - vivo by a plasmid containing the M.XbaI gene and the S. typhimurium genome was cleaved to
AB  - completion by DpnI at one or more sites, depending on the number of transposon insertions. The
AB  - resulting genomic fragments were resolved by pulsed-field electrophoresis. The potential use
AB  - of single M.XbaI/DpnI cleavage sites as reference positions to map rare restriction sites is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Hanish, J.
AU  - Rebelsky, M.
AU  - McClelland, M.
AU  - Westbrook, C.
TI  - Application of methylase-limited partial NotI cleavage for a long-range restriction map of the human ABL locus.
JO  - Genomics
PY  - 1991
SP  - 681
EP  - 685
VL  - 10
AB  - The use of partial restriction digests for mapping complex genomes by
AB  - pulsed-field gel electrophoresis has been limited by the difficulty of
AB  - consistently obtaining these digests in agarose, which is a necessary matrix
AB  - for high-molecular-weight DNA.  Enzyme cleavage in agarose is faster then
AB  - diffusion for most of the enzymes which cleave infrequently.  We have developed
AB  - a method for the production of partial digests in agarose for the endonuclease
AB  - NotI (5' ...GC/GGCCGC...3') which circumvents the diffusion problem by using
AB  - the blocking methylase M.BspRI (5' ...GGmCC...3'), which competes for the same
AB  - sites.  Using various ratios of the methylase and endonuclease results in
AB  - partial digests in any size range desired.  We report the successful
AB  - application of this technique to the production of NotI partial digests of
AB  - human genomic DNA for the mapping of the ABL locus of human chromosome 9.
ER  -

TY  - JOUR
AU  - Hanley, A.B.
AU  - Furniss, C.S.M.
AU  - Kwiatkowska, C.A.
AU  - Mackie, A.R.
TI  - The manipulation of DNA with restriction enzymes in low water systems.
JO  - Biochim. Biophys. Acta
PY  - 1991
SP  - 40
EP  - 44
VL  - 1074
AB  - The cleavage of phage lambda DNA by the restriction enzyme HindIII in low water
AB  - systems has been investigated.  Two types of low water systems have been
AB  - studied - those which contain a surfactant in a reverse micelle environment and
AB  - a surfactant-free system in which a solid support (celite) is used.  The effect
AB  - of the surfactants themselves in a normal aqueous environment has also been
AB  - studied.  Charged surfactants were found to greatly inhibit HindIII activity in
AB  - aqueous buffer, while non-ionic surfactants did not affect either the activity
AB  - or the specificity of the restriction enzyme.  The rate of cleavage by HindIII
AB  - in a reverse micelle system consisting of sodium dioctylsulphosuccinate is very
AB  - slow, however, in a Triton B system the expected fragments are observed.  In a
AB  - surfactant-free low water environment, cleavage occurs at the expected sites
AB  - but in a different order to that observed in normal aqueous systems.  These
AB  - results sugest that DNA tertiary structure in low water systems is different to
AB  - that in aqueous solution and that this influences cleavage by the restriction
AB  - enzyme HindIII.
ER  -

TY  - JOUR
AU  - Hanley, A.B.
AU  - Grinfeld, E.
AU  - Baxter, R.L.
TI  - The cleavage of nucleic acids in reversed micelles using site specific endonucleases.
JO  - Biocatalysis
PY  - 1990
SP  - 253
EP  - 258
VL  - 3
AB  - Plasmid and lambda DNA molecules of between 2.2 and 48.5 kb pairs can be
AB  - solubilised in n-hexane containing the surfactant sodium dioctyl sulfosuccinate
AB  - (AOT) and aqueous buffers.  Linear lambda phage DNA fragments (2.2-23.1 kb
AB  - pairs) and intact lambda bio 1 DNA (48.5 kb pairs) are efficiently cleaved by
AB  - BamHI and EcoRI in systems containing 100 mM AOT.  Under these conditions,
AB  - lambda bio 1 DNA undergoes regioselective restriction by HindIII at only one
AB  - site but is completely cleaved when the surfactant concentration is lowered to
AB  - 50 mM.  Covalent closed circular plasmid DNA (pUC8, 2.73 kb pairs) is only
AB  - partially linearised by EcoRI and BamHI in reversed micelles; HaeII cleavage
AB  - affords both complete and partial restriction fragments.  The results suggest
AB  - that the tertiary structures adopted by substrate DNA in reversed micelles
AB  - influence the availability of restriction sites.
ER  -

TY  - JOUR
AU  - Hansen, C.M.
AU  - Choi, S.C.
AU  - Parker, J.
AU  - Hueffer, K.
AU  - Chen, J.
TI  - Draft Genome Sequence of a Taxonomically Unique Neisseria Strain Isolated from a  Greater White-Fronted Goose (Anser albifrons) Egg on the North Slope of Alaska.
JO  - Genome Announcements
PY  - 2015
SP  - e00772
EP  - e00715
VL  - 3
AB  - We report here the draft genome sequence of a unique Neisseria strain that was isolated from a
AB  - greater white-fronted goose (Anser albifrons) egg. The sequencing
AB  - was performed with an Illumina MiSeq system, and the sequence consists of 275
AB  - contigs. The total genome is 2,397,978 bp long and has a G+C content of 46.4%.
ER  -

TY  - JOUR
AU  - Hansen, R.S.
AU  - Wijmenga, C.
AU  - D'Esposito, M.
AU  - Weemaes, C.M.R.
AU  - Gartier, S.M.
TI  - Mutations in the DNMT3B DNA methyltransferase gene cause the ICF syndrome.
JO  - Am. J. Hum. Genet.
PY  - 2000
SP  - 1724
EP  - 1724
VL  - 66
AB  - Immunodeficiency, Centromeric instability and Facial anomalies are characteristics of a rare
AB  - genetic disorder termed the ICF syndrome.  The centromeric instability of chromosomes 1, 9,
AB  - and 16 is associated with the abnormal hypomethylation of their pericentromeric satellite
AB  - regions.  Hypomethylation has also been reported for other types of heterochromatin, including
AB  - the inactive X chromosome.  We examined these phenomena further at the molecular level and
AB  - report here examples of extensive hypomethylation of these regions in ICF cells that are
AB  - associated with nuclease hypersensitivity, advanced replication time and a variable escape
AB  - from silencing for genes on the inactive X and Y chromosomes.  The ICF locus has been mapped
AB  - to a 9 c-M region of chromosome 20 by homozygosity mapping.  By searching for homologies to
AB  - known DNA methyltransferases, we identified a genomic sequence located in the ICF region that
AB  - contains a full length homologue of the mouse DNMT3B methyltransferase gene.  The human
AB  - sequence was used to screen ICF kindreds and we discovered mutations in 4 patients from 3
AB  - families.  Restriction enzyme and bisulfite methylation analyses revealed extensive
AB  - hypomethylation of 5' CpG islands at all 10 genes examined on the inactive X and 1 gene on
AB  - the Y in two ICF females and 3 ICF males.  Abnormal hypomethylation in ICF was also associated
AB  - with advanced replication time for several loci examined, including satellite II sequences.
AB  - Consistent with these data, we discovered novel examples of escape from inactivation in
AB  - untreated diploid fibroblasts and lymphoblasts from ICF patients for G5PD, MPP1, and SYBL1.
AB  - This escape is variable, and appears to correlate with the degree of advanced replication time
AB  - for these loci.  The ICF phenotype, therefore, is likely to involve abnormalities in gene
AB  - silencing at multiple loci that arise from defects in methylation and late replication.  We
AB  - found that the satellite hypomethylation defect in ICF cells can be complemented by somatic
AB  - cell fusion to CHO cells.  We presume that this de novo methylation results from
AB  - complementation of the defective human ICF gene with a functional hamster homologue and we
AB  - sought to identify and localize DNA methyltransferases with de novo activity.  Dnmt3a and
AB  - Dnmt3b are two very homologous DNA methyltransferases with de novo activity that were recently
AB  - identified in the mouse.  Because the ICF locus maps to the proximal long arm of chromosome
AB  - 20, we searched the unfinished chromosome 20 sequence data at the Sanger Centre for homology
AB  - to these genes and identified a PAC sequence containing a full length coding sequence that is
AB  - highly homologous to the murine Dnmt3b gene.  The predicted DNMT38 sequence was verified by
AB  - sequencing RT-PCR and PCR products amplified with derived primers.  We examined the DNMT3B
AB  - gene in ICF patients for mutations and found three ICF-specific mutations: a T to G
AB  - transversion resulting in a V726G missense substitution that is homozygous in the two affected
AB  - brothers of Family 1, a CpG to CpA missense transition (A603T) that is heterozygous in the P4
AB  - ICF female of Family 3, and an intronic CpG to CpA splice mutation resulting in an STP
AB  - insertion before codon 897 that is homozygous in the P3 patient of Family 2 and heterozygous
AB  - in the P4 patient of Family 3.  None of the mutations were present in over 200 normal
AB  - chromosomes examined from unrelated individuals.  All three DNMT3B mutations are predicted to
AB  - be in all major splice forms and occur in regions that are invariant among the DNMT3-like
AB  - methyltransferases that have been identified in zebra-fish, mouse and man and are in or near
AB  - regions of homology to certain bacteriophage methyltransferases.  These mutations all appear
AB  - to be in the catalytic domain of the enzyme as they are within or near motifs present in
AB  - nearly all m5C-methyltransferases.  Our observations of escape from X inactivation,
AB  - complementation for the ICF methylation defect in somatic cells, and of DNMT3B mutations in
AB  - ICF patients provide a useful model for examining the role of this enzyme in the establishment
AB  - and maintenance of somatic methylation patterns.  This is the first example of a mutation in a
AB  - human gene that alters DNA methylation patterns.
ER  -

TY  - JOUR
AU  - Hansen, R.S.
AU  - Wijmenga, C.
AU  - Luo, P.
AU  - Stanek, A.M.
AU  - Canfield, T.K.
AU  - Weemaes, C.M.
AU  - Gartler, S.M.
TI  - The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 14412
EP  - 14417
VL  - 96
AB  - DNA methylation is an important regulator of genetic information in species ranging from
AB  - bacteria to humans. DNA methylation appears to be critical for mammalian development because
AB  - mice nullizygous for a targeted disruption of the DNMT1 DNA methyltransferase die at an early
AB  - embryonic stage. No DNA methyltransferase mutations have been reported in humans until now. We
AB  - describe here the first example of naturally occurring mutations in a mammalian DNA
AB  - methyltransferase gene. These mutations occur in patients with a rare autosomal recessive
AB  - disorder, which is termed the ICF syndrome, for immunodeficiency, centromeric instability, and
AB  - facial anomalies. Centromeric instability of chromosomes 1, 9, and 16 is associated with
AB  - abnormal hypomethylation of CpG sites in their pericentromeric satellite regions. We are able
AB  - to complement this hypomethylation defect by somatic cell fusion to Chinese hamster ovary
AB  - cells, suggesting that the ICF gene is conserved in the hamster and promotes de novo
AB  - methylation. ICF has been localized to a 9-centimorgan region of chromosome 20 by homozygosity
AB  - mapping. By searching for homologies to known DNA methyltransferases, we identified a genomic
AB  - sequence in the ICF region that contains the homologue of the mouse Dnmt3b methyltransferase
AB  - gene. Using the human sequence to screen ICF kindreds, we discovered mutations in four
AB  - patients from three families. Mutations include two missense substitutions and a 3-aa
AB  - insertion resulting from the creation of a novel 3' splice acceptor. None of the mutations
AB  - were found in over 200 normal chromosomes. We conclude that mutations in the DNMT3B are
AB  - responsible for the ICF syndrome.
ER  -

TY  - JOUR
AU  - Hanson, D.K.
AU  - Lamb, M.R.
AU  - Mahler, H.R.
AU  - Perlman, P.S.
TI  - Evidence for translated intervening sequences in the mitochondrial genome of Saccharomyces cerevisiae.
JO  - J. Biol. Chem.
PY  - 1982
SP  - 3218
EP  - 3224
VL  - 257
AB  - In yeast, the mitochondrial genes for subunit I of cytochrome oxidase (oxi3) and for
AB  - apocytochrome b (cob) are known to be split. In some strains, the latter contains five
AB  - intervening sequences, three of which coincide with clusters of mutational sites referred to
AB  - in their order of transcription as the loci box3, 10, and 7, respectively. Mutations at the
AB  - first of these result in the accumulation of novel, large polypeptides (apparent Mr = about
AB  - 43,000) believed to originate from a fusion of sequences found in the NH2-terminal segment of
AB  - apocytochrome b to others encoded in the intervening sequence itself. We now provide evidence
AB  - for close similarities of at least a part of translated intron sequences between (a) mutants
AB  - in box7 in "long" form and "short" form strains (which lack the first three introns including
AB  - the one for the box3 locus); (b) mutants in a subset of box7 mutants and those in box3, and
AB  - (c) between intron sequences in box7 and a sequence presumably encoded in oxi3. These
AB  - structural homologies presumably encoded in oxi3. These structural homologies have been
AB  - analyzed and shown to be referable to sequence homologies in two proteins, one derived from
AB  - the second intron (box3) in cob and the other from oxi3. The accumulation in certain cob
AB  - mutants of proteins and of a transcript containing a sequence specified by oxi3 provides
AB  - additional strong evidence for the previously suggested regulation of oxi3 by the penultimate,
AB  - box7-containing intron of cob.
ER  -

TY  - JOUR
AU  - Hanson-Drury, S.
AU  - To, T.T.
AU  - Liu, Q.
AU  - Vo, A.T.
AU  - Kim, M.
AU  - Watling, M.
AU  - Bumgarner, R.S.
AU  - McLean, J.S.
TI  - Draft Genome Sequence of Tannerella forsythia Clinical Isolate 9610.
JO  - Genome Announcements
PY  - 2017
SP  - e00024
EP  - e00017
VL  - 5
AB  - We present here the draft genome sequence of Tannerella forsythia 9610, a clinical isolate
AB  - obtained from a periodontitis patient. The genome is composed of
AB  - 79 scaffolds with 82 contigs, for a length of 3,201,941 bp and a G+C of 47.3%.
ER  -

TY  - JOUR
AU  - Hanvey, J.C.
AU  - Shimizu, M.
AU  - Wells, R.D.
TI  - Site-specific inhibition of EcoRI restriction/modification enzymes by a DNA triple helix.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 157
EP  - 161
VL  - 18
AB  - The abilility of oligopyrimidines to inhibit, through triple helix formation,
AB  - the specific protein-DNA interactions of the EcoRI restriction and modification
AB  - enzymes (EcoRI and M.EcoRI) with their recognition sequence (GAATTC) was
AB  - studied.  The oligonucleotides (CTT)4 and (CTT)8 formed triplexes in plasmids
AB  - at (GAA)n repeats containing EcoRI sites.  Cleavage and methylation of EcoRI
AB  - sites within these sequences were specifically inhibited by the
AB  - oligonucleotides, whereas an EcoRI site adjacent to a (GAA)n sequence was
AB  - inhibited much less.  Also, other EcoRI sites within the plasmid, or in
AB  - exogenously added lambda DNA, were not inhibited.  These results demonstrate
AB  - the potential of using triplex-forming oligonucleotides to block protein-DNA
AB  - interactions at specific sites, and thus this technique may be useful in
AB  - chromosome mapping and in the modulation of gene expression.
ER  -

TY  - JOUR
AU  - Hao, H.
AU  - Chen, S.
AU  - Li, Y.
AU  - Sun, H.
AU  - Zhao, P.
AU  - Jian, Y.
AU  - Gao, Y.
AU  - Wu, C.
AU  - Liu, Y.
AU  - Chu, Y.
TI  - Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain zly1309F, Isolated from Endangered Tibetan Antelope.
JO  - Genome Announcements
PY  - 2017
SP  - e00496
EP  - e00417
VL  - 5
AB  - Mycoplasma capricolum subsp. capripneumoniae is an important pathogen of goats that causes
AB  - contagious caprine pleuropneumonia. Here, we report the complete
AB  - genome sequence of M. capricolum subsp. capripneumoniae strain zly1309F, isolated
AB  - from a Tibetan antelope (Pantholops hodgsonii) in China.
ER  -

TY  - JOUR
AU  - Hao, K.
AU  - He, P.
AU  - Blom, J.
AU  - Rueckert, C.
AU  - Mao, Z.
AU  - Wu, Y.
AU  - He, Y.
AU  - Borriss, R.
TI  - The Genome of Plant Growth-Promoting Bacillus amyloliquefaciens subsp. plantarum  Strain YAU B9601-Y2 Contains a Gene Cluster for Mersacidin Synthesis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3264
EP  - 3265
VL  - 194
AB  - The genome of rhizobacterium Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2 was 4.24
AB  - Mb in size and harbored 3,991 coding sequences (CDS). Giant
AB  - gene clusters were dedicated to nonribosomal synthesis of antimicrobial
AB  - lipopeptides and polyketides. Remarkably, CAU B946 possessed a gene cluster
AB  - involved in synthesis of mersacidin.
ER  -

TY  - JOUR
AU  - Hao, K.
AU  - Li, H.
AU  - Li, F.
AU  - Guo, P.
TI  - Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China.
JO  - Genome Announcements
PY  - 2016
SP  - e01079
EP  - e01016
VL  - 4
AB  - Bacillus pumilus strain PDSLzg-1, an efficient hydrocarbon-degrading bacterium, was isolated
AB  - from oil-contaminated soil. Here, we present the complete sequence
AB  - of its circular chromosome and circular plasmid. The genomic information is
AB  - essential for the study of degradation of oil by B. pumilus PDSLzg-1.
ER  -

TY  - JOUR
AU  - Hao, P.
AU  - Zheng, H.
AU  - Yu, Y.
AU  - Ding, G.
AU  - Gu, W.
AU  - Chen, S.
AU  - Yu, Z.
AU  - Ren, S.
AU  - Oda, M.
AU  - Konno, T.
AU  - Wang, S.
AU  - Li, X.
AU  - Ji, Z.-S.
AU  - Zhao, G.
TI  - Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production.
JO  - PLoS ONE
PY  - 2011
SP  - e15964
EP  - e15964
VL  - 6
AB  - Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic
AB  - Acid Bacteria (LAB) used for cheese and
AB  - yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial
AB  - strain mainly used for yogurt production, was completely sequenced and
AB  - compared against the other two ATCC collection strains of the same
AB  - subspecies. Specific physiological properties of strain 2038, such as
AB  - lysine biosynthesis, formate production, aspartate-related
AB  - carbon-skeleton intermediate metabolism, unique EPS synthesis and
AB  - efficient DNA restriction/modification systems, are all different from
AB  - those of the collection strains that might benefit the industrial
AB  - production of yogurt. Other common features shared by Lb. bulgaricus
AB  - strains, such as efficient protocooperation with Streptococcus
AB  - thermophilus and lactate production as well as well-equipped stress
AB  - tolerance mechanisms may account for it being selected originally for
AB  - yogurt fermentation industry. Multiple lines of evidence suggested that
AB  - Lb. bulgaricus 2038 was genetically closer to the common ancestor of
AB  - the subspecies than the other two sequenced collection strains,
AB  - probably due to a strict industrial maintenance process for strain 2038
AB  - that might have halted its genome decay and sustained a gene network
AB  - suitable for large scale yogurt production.
ER  -

TY  - JOUR
AU  - Hao, X.
AU  - Lin, Y.
AU  - Johnstone, L.
AU  - Baltrus, D.A.
AU  - Miller, S.J.
AU  - Wei, G.
AU  - Rensing, C.
TI  - Draft Genome Sequence of Plant Growth-Promoting Rhizobium Mesorhizobium amorphae, Isolated from Zinc-Lead Mine Tailings.
JO  - J. Bacteriol.
PY  - 2012
SP  - 736
EP  - 737
VL  - 194
AB  - Here, we describe the draft genome sequence of Mesorhizobium amorphae strain CCNWGS0123,
AB  - isolated from nodules of Robinia pseudoacacia growing
AB  - on zinc-lead mine tailings. A large number of metal(loid) resistance
AB  - genes, as well as genes reported to promote plant growth, were identified,
AB  - presenting a great future potential for aiding phytoremediation in
AB  - metal(loid)-contaminated soil.
ER  -

TY  - JOUR
AU  - Hao, X.
AU  - Lin, Y.
AU  - Johnstone, L.
AU  - Liu, G.
AU  - Wang, G.
AU  - Wei, G.
AU  - McDermott, T.
AU  - Rensing, C.
TI  - Genome Sequence of the Arsenite-Oxidizing Strain Agrobacterium tumefaciens 5A.
JO  - J. Bacteriol.
PY  - 2012
SP  - 903
EP  - 903
VL  - 194
AB  - Microbial transformations of arsenic influence its mobility and toxicity. We report the draft
AB  - genome sequence of the arsenite-oxidizing strain
AB  - Agrobacterium tumefaciens 5A isolated from an As-contaminated soil in the
AB  - Madison River Valley, MT. A large number of metal (or metalloid)
AB  - resistance genes, especially contributing to arsenite oxidation, were
AB  - identified.
ER  -

TY  - JOUR
AU  - Hao, Y.
AU  - Huang, D.
AU  - Guo, H.
AU  - Xiao, M.
AU  - An, H.
AU  - Zhao, L.
AU  - Zuo, F.
AU  - Zhang, B.
AU  - Hu, S.
AU  - Song, S.
AU  - Chen, S.
AU  - Ren, F.
TI  - Complete Genome Sequence of Bifidobacterium longum subsp. longum BBMN68, a New Strain from Healthy Chinese Centenarian.
JO  - J. Bacteriol.
PY  - 2010
SP  - 787
EP  - 788
VL  - 193
AB  - Bifidobacterium longum subsp. longum BBMN68 was isolated from the fecal of healthy centenarian
AB  - living in longevity area of BaMa, Guangxi, China.
AB  - Here, we reported the main genome features of B. longum BBMN68 strain and
AB  - the identification of several predicted proteins that tailored to the
AB  - ecological niche of longevity.
ER  -

TY  - JOUR
AU  - Hao, Z.
AU  - Li, L.
AU  - Liu, J.
AU  - Ren, Y.
AU  - Wang, L.
AU  - Bartlam, M.
AU  - Egli, T.
AU  - Wang, Y.
TI  - Genome Sequence of a Freshwater Low-Nucleic-Acid-Content Bacterium, Betaproteobacterium Strain CB.
JO  - Genome Announcements
PY  - 2013
SP  - e00135
EP  - e00113
VL  - 1
AB  - Betaproteobacterium strain CB is a typical minute freshwater bacterium, representing the
AB  - small-cell bacteria that are numerically dominant in most
AB  - freshwater environments. The genome of betaproteobacterium CB consists of a
AB  - circular 2,045,720-bp chromosome, and the information we report will provide
AB  - insights into the mechanisms underlying its survival and ecological function.
ER  -

TY  - JOUR
AU  - Haq, I.
AU  - O'Brien, R.
AU  - Lagunavicius, A.
AU  - Siksnys, V.
AU  - Ladbury, J.E.
TI  - Specific DNA Recognition by the Type II Restriction Endonuclease MunI: The Effect of pH.
JO  - Biochemistry
PY  - 2001
SP  - 14960
EP  - 14967
VL  - 40
AB  - To investigate the effect of pH on sequence-specific binding, a thermodynamic characterization
AB  - of the interaction of the protein MunI with a specific, and a nonspecific, oligonucleotide was
AB  - performed. MunI is a type II restriction endonuclease which is able to bind specifically, but
AB  - loses its enzymatic activity in the absence of magnesium ions. Comparison of the specific and
AB  - nonspecific interactions at 10 and 25 degrees C shows that the latter is accompanied by a
AB  - small change in enthalpy, and a negligible change in constant pressure heat capacity. On going
AB  - through the pH range 5.75-9.0 at 25 degrees C, the affinity of specific complex formation is
AB  - reduced by 20-fold. The interaction is accompanied by the protonation of groups assumed to be
AB  - on the protein. Based on the simplest model that will fit the data, two distinct protonation
AB  - events are observed. At low pH, two groups per protein molecule undergo protonation with a
AB  - pK(a) of 6.0 and 6.9 in the free and bound forms, respectively. At high pH, a further
AB  - independent protonation occurs involving two groups with pK(a) values of 8.9 and approximately
AB  - 10.7 in the free and bound forms, respectively. The change in heat capacity ranges from -2.7
AB  - to -1.7 kJ mol(-)(1) K(-)(1) in going from pH 6.5 to 8.5. This range of variation of change in
AB  - heat capacity can be accounted for by the effects of protonation of the interacting molecules.
AB  - The change in heat capacity, calculated from surface area burial using a previously
AB  - established relationship (1.15 kJ mol(-)(1) K(-)(1)), does not correlate well with the
AB  - experimentally determined values.
ER  -

TY  - JOUR
AU  - Haqqi, T.M.
AU  - Ahmad, S.
AU  - Ahmad, N.S.
AU  - Ahmad, M.
AU  - Hasnain, A.
AU  - Siddiqi, M.
AU  - Hadi, S.M.
TI  - Cloning and expression of EcoRI specific restriction modification system.
JO  - Indian J. Biochem. Biophys.
PY  - 1985
SP  - 252
EP  - 254
VL  - 22
AB  - RI-specific restriction-modification genes have been cloned in the multicopy
AB  - plasmid pBR322.  Plasmid DNA, isolated from E. coli RY13, was cleaved with
AB  - restriction enzyme BamHI and inserted at the BamHI site in pBR322 and cloned in
AB  - E. coli HB101.  The recombinant DNA transnformants were selected by their
AB  - resistance to ampicillin and sensitivity to tetracycline.  EcoRI-specific
AB  - clones were identified by determining the efficiency of plating on
AB  - transformants of modified and unmodified lambda phage.  Crude enzyme prepared
AB  - from several of the transformants by dextran polyethylene glycol phase
AB  - partition procedure yielded the same restriction pattern as the parental strain
AB  - and purified EcoRI.
ER  -

TY  - JOUR
AU  - Harada, J.
AU  - Yamada, T.
AU  - Giri, S.
AU  - Hamada, M.
AU  - Nobu, M.K.
AU  - Narihiro, T.
AU  - Tsuji, H.
AU  - Daimon, H.
TI  - Draft Genome Sequence of Moorella sp. Strain Hama-1, a Novel Acetogenic Bacterium Isolated from a Thermophilic Digestion Reactor.
JO  - Genome Announcements
PY  - 2018
SP  - e00517
EP  - e00518
VL  - 6
AB  - Moorella sp. strain Hama-1 was isolated from a thermophilic anaerobic digestion reactor
AB  - treating poly(l-lactic acid). The strain is a thermophilic acetogen
AB  - capable of lactate oxidation under anaerobic conditions. Here, we report the
AB  - draft genome sequence of strain Hama-1, comprising 3.27 Mb in 48 contigs, with a
AB  - G+C content of 56.6%.
ER  -

TY  - JOUR
AU  - Harden, L.K.
AU  - Morales, K.M.
AU  - Hughey, J.R.
TI  - Complete Genome Sequence of Nonhemolytic Streptococcus agalactiae Serotype V Strain 1, Isolated from the Buccal Cavity of a Canine.
JO  - Genome Announcements
PY  - 2016
SP  - e01612
EP  - e01615
VL  - 4
AB  - The complete genome sequence from a nonhemolytic strain of Streptococcus agalactiae from the
AB  - oral cavity of a canine was assembled. The genome is
AB  - 2,165,968 bp, contains 2,055 genes, and is classified as group B streptococcus
AB  - (GBS) serotype V, strain 1. A comparison to other S. agalactiae sequences shows
AB  - high gene synteny with human and bovine strains.
ER  -

TY  - JOUR
AU  - Hardwick, J.M.
AU  - von Sprecken, R.S.
AU  - Yielding, K.L.
AU  - Yielding, L.W.
TI  - Ethidium binding sites on plasmid DNA determined by photoaffinity labeling.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 11090
EP  - 11097
VL  - 259
AB  - Photoaffinity labeling of pBR322 with ethidium monoazide
AB  - (8-azido-3-amino-5-ethyl-6-phenylphenanthridinium chloride) was used to provide evidence for
AB  - the sequence specifity of ethidium binding to native DNA. DNA-drug interactions were examined
AB  - at concentrations of eight covalently bound ethidium drugs per molecule of pBR322 (4363 base
AB  - pairs). Restriction enzyme cutting was blocked by the covalent binding of a drug molecule at
AB  - (or near) the enzyme recognition sequence. This phenomenon was observed with all restriction
AB  - enzymes tested and was not limited to specific regions of the pBR322 molecule.
AB  - Double-digestion experiments indicated that a drug molecule may bind 2 to 3 base pairs outside
AB  - the recognition sequence and still block restriction enzyme digestion. Intact plasmid was
AB  - treated with [3H] ethidium monoazide and digested with restriction enzymes. The amount of
AB  - covalently-linked ethidium analog was quantitated for different restriction fragments and the
AB  - G-C content of each fragment was determined from the DNA sequence. In approximately half of
AB  - the fragments the drug appeared to preferentially bind at a G-C base pair. However, a
AB  - preference for specific sequences such as 5'-C-G-3' was detected, as had been suggested by
AB  - previous modeling studies with ethidium bromide. The other fragments were located in specific
AB  - map regions of the plasmid and did not bind drug with a strict dependence on GC content
AB  - suggesting that binding specificity may depend on more than one structural feature of the DNA.
ER  -

TY  - JOUR
AU  - Hargrove, E.C.
AU  - Lopez, M.S.
AU  - Hernandez, A.C.
AU  - Kuty, E.G.F.
TI  - Complete Genome Sequence of Bacillus megaterium Podophage Palmer.
JO  - Genome Announcements
PY  - 2015
SP  - e00358
EP  - e00315
VL  - 3
AB  - Bacillus megaterium has been widely used as a research tool for decades. Its use  is on the
AB  - rise as a recombinant protein production host and as a bioremediation
AB  - bacterium. Bacteriophages against this bacterium may have biotechnological
AB  - applications. Here, we describe the novel podophage Palmer, which infects B.
AB  - megaterium.
ER  -

TY  - JOUR
AU  - Harhay, D.M.
AU  - Bono, J.L.
AU  - Smith, T.P.
AU  - Fields, P.I.
AU  - Dinsmore, B.A.
AU  - Santovenia, M.
AU  - Kelley, C.M.
AU  - Wang, R.
AU  - Harhay, G.P.
TI  - Complete Closed Genome Sequences of Salmonella enterica subsp. enterica Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and  Humans.
JO  - Genome Announcements
PY  - 2016
SP  - e01683
EP  - e01615
VL  - 4
AB  - Salmonella enterica spp. are a diverse group of bacteria with a wide range of virulence
AB  - potential. To facilitate genome comparisons across this virulence
AB  - spectrum, we present eight complete closed genome sequences of four S. enterica
AB  - serotypes (Anatum, Montevideo, Typhimurium, and Newport), isolated from various
AB  - cattle samples and from humans.
ER  -

TY  - JOUR
AU  - Harhay, G.P.
AU  - Harhay, D.M.
AU  - Bono, J.L.
AU  - Smith, T.P.L.
AU  - Capik, S.F.
AU  - DeDonder, K.D.
AU  - Apley, M.D.
AU  - Lubbers, B.V.
AU  - White, B.J.
AU  - Larson, R.L.
TI  - Closed Genome Sequences of Seven Histophilus somni Isolates from Beef Calves with Bovine Respiratory Disease Complex.
JO  - Genome Announcements
PY  - 2017
SP  - e01099
EP  - e01017
VL  - 5
AB  - Histophilus somni is a fastidious Gram-negative opportunistic pathogenic Pasteurellaceae that
AB  - affects multiple organ systems and is one of the principal
AB  - bacterial species contributing to bovine respiratory disease complex (BRDC) in
AB  - feed yard cattle. Here, we present seven closed genome sequences isolated from
AB  - three beef calves showing sign of BRDC.
ER  -

TY  - JOUR
AU  - Harhay, G.P.
AU  - Koren, S.
AU  - Phillippy, A.M.
AU  - McVey, D.S.
AU  - Kuszak, J.
AU  - Clawson, M.L.
AU  - Harhay, D.M.
AU  - Heaton, M.P.
AU  - Chitko-McKown, C.G.
AU  - Smith, T.P.
TI  - Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle.
JO  - Genome Announcements
PY  - 2013
SP  - e00188
EP  - e00113
VL  - 1
AB  - Mannheimia haemolytica is a respiratory pathogen affecting cattle and related ruminants
AB  - worldwide. M. haemolytica is commonly associated with bovine
AB  - respiratory disease complex (BRDC), a polymicrobial multifactorial disease. We
AB  - present the first two complete closed genome sequences of this species,
AB  - determined using an automated assembly pipeline requiring no manual finishing.
ER  -

TY  - JOUR
AU  - Harhay, G.P.
AU  - McVey, D.S.
AU  - Koren, S.
AU  - Phillippy, A.M.
AU  - Bono, J.
AU  - Harhay, D.M.
AU  - Clawson, M.L.
AU  - Heaton, M.P.
AU  - Chitko-McKown, C.G.
AU  - Korlach, J.
AU  - Smith, T.P.
TI  - Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever.
JO  - Genome Announcements
PY  - 2014
SP  - e00084
EP  - e00014
VL  - 2
AB  - Bibersteinia trehalosi is a respiratory pathogen affecting cattle and related ruminants
AB  - worldwide. B. trehalosi is closely related to Mannheimia haemolytica
AB  - and is often associated with bovine respiratory disease complex (BRDC), a
AB  - polymicrobial multifactorial disease. We present three complete closed genome
AB  - sequences of this species generated using an automated assembly pipeline.
ER  -

TY  - JOUR
AU  - Harhay, G.P.
AU  - Murray, R.W.
AU  - Lubbers, B.
AU  - Griffin, D.
AU  - Koren, S.
AU  - Phillippy, A.M.
AU  - Harhay, D.M.
AU  - Bono, J.
AU  - Clawson, M.L.
AU  - Heaton, M.P.
AU  - Chitko-McKown, C.G.
AU  - Smith, T.P.
TI  - Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever.
JO  - Genome Announcements
PY  - 2014
SP  - e00088
EP  - e00014
VL  - 2
AB  - Mannheimia varigena is an occasional respiratory pathogen of cattle and pigs. We  present the
AB  - first four complete closed genome sequences of this species.
ER  -

TY  - JOUR
AU  - Harish, S.M.
AU  - Sim, K.S.
AU  - Najimudin, N.
AU  - Aziah, I.
TI  - Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi Isolate PM016/13 from Untreated Well Water Associated with a Typhoid Outbreak in Pasir  Mas, Kelantan, Malaysia.
JO  - Genome Announcements
PY  - 2015
SP  - e01261
EP  - e01215
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Typhi is a human-restricted pathogen  that causes
AB  - typhoid fever. Even though it is a human-restricted pathogen, the bacterium is also isolated
AB  - from environments such as groundwater and pond water. Here, we describe the genome sequence of
AB  - the Salmonella enterica subsp. enterica serovar Typhi PM016/13 which was isolated from well
AB  - water during a typhoid outbreak in Kelantan, Malaysia, in 2013.
ER  -

TY  - JOUR
AU  - Harish, S.M.
AU  - Sim, K.S.
AU  - Nor, F.M.
AU  - Hussin, H.M.
AU  - Hamzah, W.M.
AU  - Najimudin, N.
AU  - Aziah, I.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi Isolate B/SF/13/03/195 Associated with a Typhoid Carrier in Pasir Mas, Kelantan,   Malaysia.
JO  - Genome Announcements
PY  - 2015
SP  - e01285
EP  - e01215
VL  - 3
AB  - We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar
AB  - Typhi B/SF/13/03/195 obtained from a typhoid carrier, who is a food handler in Pasir Mas,
AB  - Kelantan.
ER  -

TY  - JOUR
AU  - Harjes, J.
AU  - Ryu, T.
AU  - Abdelmohsen, U.R.
AU  - Moitinho-Silva, L.
AU  - Horn, H.
AU  - Ravasi, T.
AU  - Hentschel, U.
TI  - Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49.
JO  - Genome Announcements
PY  - 2014
SP  - e00160
EP  - e00114
VL  - 2
AB  - The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces  the
AB  - antitrypanosomal angucycline-like compound actinosporin A. The draft genome
AB  - of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of
AB  - 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996
AB  - genes residing in 36 secondary metabolite gene clusters.
ER  -

TY  - JOUR
AU  - Harmon-Smith, M. et al.
TI  - Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 220
EP  - 227
VL  - 2
AB  - Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus
AB  - Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole
AB  - and type strain of the species was first isolated about 50 years ago from
AB  - intestinal content of Mediterranean termites. The species is of interest for its
AB  - very isolated phylogenetic position within the phylum Fusobacteria in the tree of
AB  - life, with no other species sharing more than 90% 16S rRNA sequence similarity.
AB  - The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Harms, A.
AU  - Segers, F.H.
AU  - Quebatte, M.
AU  - Mistl, C.
AU  - Manfredi, P.
AU  - Korner, J.
AU  - Chomel, B.B.
AU  - Kosoy, M.
AU  - Maruyama, S.
AU  - Engel, P.
AU  - Dehio, C.
TI  - Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 761
EP  - 776
VL  - 9
AB  - The alpha-proteobacterial genus Bartonella comprises a group of ubiquitous
AB  - mammalian pathogens that are studied as a model for the evolution of bacterial
AB  - pathogenesis. Vast abundance of two particular phylogenetic lineages of
AB  - Bartonella had been linked to enhanced host adaptability enabled by
AB  - lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and
AB  - parallel evolution of complex effector repertoires. However, the limited
AB  - availability of genome sequences from one of those lineages as well as other,
AB  - remote branches of Bartonella has so far hampered comprehensive understanding of
AB  - how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella
AB  - evolution. Here, we report the discovery of a third repertoire of Beps associated
AB  - with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any
AB  - signs of host adaptability and is only distantly related to the two species-rich
AB  - lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella
AB  - isolates from under-sampled lineages enabled combined in silico analyses and wet
AB  - lab experiments that suggest several parallel layers of functional
AB  - diversification during evolution of the three Bep repertoires from a single
AB  - ancestral effector. Our analyses show that the Beps of B. ancashensis share many
AB  - features with the two other repertoires, but may represent a more ancestral state
AB  - that has not yet unleashed the adaptive potential of such an effector set. We
AB  - anticipate that the effectors of B. ancashensis will enable future studies to
AB  - dissect the evolutionary history of Bartonella effectors and help unraveling the
AB  - evolutionary forces underlying bacterial host adaptation.
ER  -

TY  - JOUR
AU  - Harms, H.
AU  - Poehlein, A.
AU  - Thurmer, A.
AU  - Konig, G.M.
AU  - Schaberle, T.F.
TI  - Draft Genome Sequence of Zobellia sp. Strain OII3, Isolated from the Coastal Zone of the Baltic Sea.
JO  - Genome Announcements
PY  - 2017
SP  - e00737
EP  - e00717
VL  - 5
AB  - Zobellia sp. strain OII3 was isolated from a marine environmental sample due to its
AB  - heterotrophic lifestyle, i.e., using Escherichia coli cells as prey. It shows
AB  - strong agar-lytic activity. The genome was assembled into 41 contigs with a total
AB  - size of 5.4 Mb, revealing the genetic basis for natural product biosynthesis.
ER  -

TY  - JOUR
AU  - Haroon, M.F.
AU  - Thompson, L.R.
AU  - Stingl, U.
TI  - Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome.
JO  - Genome Announcements
PY  - 2016
SP  - e01711
EP  - e01715
VL  - 4
AB  - A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface
AB  - water sample from the Red Sea, Saudi Arabia. The genome is more
AB  - complete and has a higher G+C content than that of previously sequenced SAR324
AB  - representatives. Its genomic information shows a versatile metabolism that
AB  - confers an advantage to SAR324, which is reflected in its distribution throughout
AB  - different depths of the marine water column.
ER  -

TY  - JOUR
AU  - Harper, S.H.
AU  - Firman, K.
AU  - Glover, S.W.
TI  - The interactions of mini-F with the plasmids R124 and R124/3.
JO  - Plasmids in Bacteria
PY  - 1984
SP  - 920
EP  - 920
VL  - 0
AB  - The Inc FIV plasmid R124 encodes a unique restriction and modification (R-M) system.  R124/3
AB  - is a derivative plasmid which encodes an R-M system of different specificity.  When R124 or
AB  - R124/3 are present in the same cell as the sex Factor F a restriction deficient (r-) phenotype
AB  - results.  This r- phenotype reverts back to r+ with a frequency dependent upon the particular
AB  - isolate.  When the F plasmids are isolated from these reverted strains they are found to
AB  - encode the R-M system of the donor R124 or R124/3 plasmid.  The R-M system is translocated
AB  - into the region of EcoRI fragments 5 and 7 of F, which encodes the Phi and Ori VI functions of
AB  - F.  During this transfer of DNA some F DNA is lost.  Recent work with mini-F (cloned EcoRI
AB  - fragments 5 and 7 of F) have shown that they alone do not result in the translocation of R-M
AB  - genes from R124 or R124/3.  EcoRI fragments 5 and 7 of F when present in the same cell as R124
AB  - or R124/3 result in a fraction of the cells expressing a r- phenotype which reverts back to a
AB  - r+ phenotype.  This reversion process is not accompanied by any DNA transfer or rearrangement
AB  - between F, R124, or R124/3 plasmids.  This strongly suggests that some other region of F is
AB  - involved in the DNA rearrangement.  Studies with mini-F have also shown that under certain
AB  - circumstances the rearrangement results in R124 expressing incF1 incompatability instead of
AB  - the normal Inc FIV.
ER  -

TY  - JOUR
AU  - Harrell, E.A.
AU  - Miller, E.S.
TI  - Genome Sequence of Aeromicrobium erythreum NRRL B-3381, an Erythromycin-Producing Bacterium of the Nocardioidaceae.
JO  - Genome Announcements
PY  - 2016
SP  - e00300
EP  - e00316
VL  - 4
AB  - ITALIC! Aeromicrobium erythreumNRRL B-3381 has a 3,629,239-bp circular genome that has 72% G+C
AB  - content. There are at least 3,121 coding sequences (CDSs), two
AB  - rRNA gene operons, and 47 tRNAs. The genome and erythromycin ( ITALIC! ery)
AB  - biosynthetic gene sequences provide resources for metabolic and combinatorial
AB  - engineering of polyketides.
ER  -

TY  - JOUR
AU  - Harrington, A.
AU  - Hill, C.
TI  - Plasmid involvement in the formation of a spontaneous bacteriophage insensitive mutant of Lactococcus lactis.
JO  - FEMS Microbiol. Lett.
PY  - 1992
SP  - 135
EP  - 141
VL  - 96
AB  - Lactococcus lactis subsp. lactis biovar. diacetylactis DPC721 is a spontaneous bacteriophage
AB  - insensitive mutant of stain DPC220, isolated after challenge with an industrial bacteriophage,
AB  - phiD1. Plasmid analysis demonstrated that the bacteriophage insensitivity was associated with
AB  - the absence of two native DPC220 plasmids (pAH82 and pAH33), and the presence of a novel
AB  - plasmid (pAH90) in DPC721. The plasmids were transferred by conjugative mobilization to a
AB  - plasmid free background where it was confirmed by restriction mapping that pAH90 is a
AB  - co-integrate formed by the precise recombination of pAH82 and pAH33. The resistance phenotype
AB  - encoded by pAH90 was also active against two bacteriophages homologous for the plasmid-free
AB  - strain. Plasmid pAH90 was shown to encode at least two independent resistance mechanisms,
AB  - including an adsorption-inhibition mechanism and a restriction and modification system. The
AB  - adsorption-inhibition mechanism encoded by the co-integrate plasmid was specific for one of
AB  - the phage used in this study.
ER  -

TY  - JOUR
AU  - Harrington, R.
AU  - Ondov, B.D.
AU  - Radune, D.
AU  - Friss, M.B.
AU  - Klubnik, J.
AU  - Diviak, L.
AU  - Hnath, J.
AU  - Cendrowski, S.R.
AU  - Blank, T.E.
AU  - Karaolis, D.
AU  - Friedlander, A.M.
AU  - Burans, J.P.
AU  - Rosovitz, M.J.
AU  - Treangen, T.
AU  - Phillippy, A.M.
AU  - Bergman, N.H.
TI  - Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.
JO  - Genome Announcements
PY  - 2013
SP  - e00067
EP  - e00012
VL  - 1
AB  - The Bacillus anthracis Carbosap genome, which includes the pXO1 and pXO2 plasmids, has been
AB  - shown to encode the major B. anthracis virulence factors, yet this strain's attenuation has
AB  - not yet been explained. Here we report the draft genome sequence of this strain, and a
AB  - comparison to fully virulent B. anthracis.
ER  -

TY  - JOUR
AU  - Harris, A.P.
AU  - Techtmann, S.M.
AU  - Stelling, S.C.
AU  - Utturkar, S.M.
AU  - Alshibli, N.K.
AU  - Brown, S.D.
AU  - Hazen, T.C.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain ND6B, an Oil-Degrading Isolate from Eastern Mediterranean Sea Water Collected at a Depth of 1,210  Meters.
JO  - Genome Announcements
PY  - 2014
SP  - e01212
EP  - e01214
VL  - 2
AB  - Here, we report the draft genome of Pseudoalteromonas sp. strain ND6B, which is able to grow
AB  - with crude oil as a carbon source. Strain ND6B was isolated from
AB  - eastern Mediterranean Sea deep water at a depth of 1,210 m. The genome of strain
AB  - ND6B provides insight into the oil-degrading ability of the Pseudoalteromonas
AB  - species.
ER  -

TY  - JOUR
AU  - Harris, V.H.
AU  - Hamilton, A.
AU  - Williams, D.M.
AU  - Hornby, D.P.
TI  - Studying the function of methyltransferases using nucleotide analogue based random mutagenesis.
JO  - Collection Symposium Series
PY  - 1999
SP  - 209
EP  - 212
VL  - 2
AB  - The function of two methyltransferases M.SPR and M.HhaI have been investigated using a PCR
AB  - based random mutagenesis procedure using nucleotide analogues with ambiguous base pairing
AB  - properties.  The mutagenesis procedure was compared with traditional protocols in which
AB  - manganese ions are introduced to decrease the fidelity of the DNA polymerase.
ER  -

TY  - JOUR
AU  - Harris-Warrick, R.M.
AU  - Elkana, Y.
AU  - Ehrlich, S.D.
AU  - Lederberg, J.
TI  - Electrophoretic separation of Bacillus subtilis genes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1975
SP  - 2207
EP  - 2211
VL  - 72
AB  - The cleavage of Bacillus subtilis DNA by EcoRI restriction endonuclease
AB  - produces segments which retain various degrees of genetic transforming
AB  - activity.  The active segments analyzed thus far, range in size from 23 to 3
AB  - kilobases and can be partially separated by agarose gel electrophoresis.
AB  - Various markers can thus be enriched from 30- to 60-fold.
ER  -

TY  - JOUR
AU  - Harrison, A.
AU  - Dyer, D.W.
AU  - Gillaspy, A.
AU  - Ray, W.C.
AU  - Mungur, R.
AU  - Carson, M.B.
AU  - Zhong, H.
AU  - Gipson, J.
AU  - Gipson, M.
AU  - Johnson, L.S.
AU  - Lewis, L.
AU  - Bakaletz, L.O.
AU  - Munson, R.S. Jr.
TI  - Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: Comparative study with H. influenzae serotype d, strain KW20.
JO  - J. Bacteriol.
PY  - 2005
SP  - 4627
EP  - 4636
VL  - 187
AB  - In 1995, the Institute for Genomic Research completed the genome sequence of a rough
AB  - derivative of Haemophilus influenzae serotype d, strain KW20. Although extremely useful in
AB  - understanding the basic biology of H. influenzae, these data have not provided significant
AB  - insight into disease caused by nontypeable H. influenzae, as serotype d strains are not
AB  - pathogens. In contrast, strains of nontypeable H. influenzae are the primary pathogens of
AB  - chronic and recurrent otitis media in children. In addition, these organisms have an important
AB  - role in acute otitis media in children as well as other respiratory diseases. Such strains
AB  - must therefore contain a gene repertoire that differs from that of strain Rd. Elucidation of
AB  - the differences between these genomes will thus provide insight into the pathogenic mechanisms
AB  - of nontypeable H. influenzae. The genome of a representative nontypeable H. influenzae strain,
AB  - 86-028NP, isolated from a patient with chronic otitis media was therefore sequenced and
AB  - annotated. Despite large regions of synteny with the strain Rd genome, there are large
AB  - rearrangements in strain 86-028NP's genome architecture relative to the strain Rd genome. A
AB  - genomic island similar to an island originally identified in H. influenzae type b is present
AB  - in the strain 86-028NP genome, while the mu-like phage present in the strain Rd genome is
AB  - absent from the strain 86-028NP genome. Two hundred eighty open reading frames were identified
AB  - in the strain 86-028NP genome that were absent from the strain Rd genome. These data provide
AB  - new insight that complements and extends the ongoing analysis of nontypeable H. influenzae
AB  - virulence determinants.
ER  -

TY  - JOUR
AU  - Harrison, J.
AU  - Dornbusch, M.R.
AU  - Samac, D.
AU  - Studholme, D.J.
TI  - Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa.
JO  - Genome Announcements
PY  - 2016
SP  - e01722
EP  - e01715
VL  - 4
AB  - We report here the annotated draft genome sequence of Pseudomonas syringae pv. syringae strain
AB  - ALF3, isolated in Wyoming. A comparison of this genome sequence
AB  - with those of closely related strains of P. syringae adapted to other hosts will
AB  - facilitate research into interactions between this pathogen and alfalfa.
ER  -

TY  - JOUR
AU  - Harrison, J.
AU  - Grant, M.R.
AU  - Studholme, D.J.
TI  - Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants.
JO  - Genome Announcements
PY  - 2016
SP  - e01705
EP  - e01715
VL  - 4
AB  - We report here the annotated draft genome sequences of strains Xanthomonas arboricola pv.
AB  - celebensis NCPPB 1832 and NCPPB 1630 (NCPPB, National Collection
AB  - of Plant Pathogenic Bacteria), both isolated from Musa species in New Zealand.
AB  - This will allow the comparison of genomes between phylogenetically distant
AB  - xanthomonads that have independently converged with the ability to colonize
AB  - banana plants.
ER  -

TY  - JOUR
AU  - Harrison, L.B.
AU  - Hanson, N.D.
TI  - Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34.
JO  - Genome Announcements
PY  - 2017
SP  - e01307
EP  - e01317
VL  - 5
AB  - Pseudomonas aeruginosa is a serious threat to patients suffering from cystic fibrosis. These
AB  - organisms are exposed to a unique set of selective pressures
AB  - within the lung. Here, we report the draft genome sequence of a mucoid P.
AB  - aeruginosa clinical isolate obtained from a cystic fibrosis patient colonized
AB  - with P. aeruginosa.
ER  -

TY  - JOUR
AU  - Harro, J.M.
AU  - Daugherty, S.
AU  - Bruno, V.M.
AU  - Jabra-Rizk, M.A.
AU  - Rasko, D.A.
AU  - Shirtliff, M.E.
TI  - Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate  MRSA-M2.
JO  - Genome Announcements
PY  - 2013
SP  - e00037
EP  - e00012
VL  - 1
AB  - We report the draft genome sequence of a methicillin-resistant strain of Staphylococcus
AB  - aureus, designated MRSA-M2. This clinical isolate was obtained
AB  - from an osteomyelitis patient undergoing treatment at the University of Texas
AB  - Medical Branch (Galveston, TX). This strain is an ST30, spa type T019, agr III
AB  - strain and has been utilized as a model S. aureus strain in a number of
AB  - proteomic, transcriptomic, and animal model studies.
ER  -

TY  - JOUR
AU  - Hartke, A.
AU  - Benachour, A.
AU  - Boutibonnes, P.
AU  - Auffray, Y.
TI  - Characterization of a complex restriction/modification system detected in a Bifidobacterium longum strain.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1996
SP  - 132
EP  - 136
VL  - 45
AB  - Two type-II restriction endonucleases, BloI and BloII, have been detected in a
AB  - Bifidobacterium longum strain.  BloI is influenced by dam methylation: it cleaves dam- but not
AB  - dam+ DNA.  It shows a temperature and pH optimum of 45oC and pH 7.5.  Restriction analysis
AB  - and cloning experiments showed that the recognition sequence is RGATCY and that the enzyme
AB  - cuts 5' to the guanine residue.  It is an isoschizomer of commercial enzymes, BstYI and XhoII.
AB  - The second activity is not inhibited by dam methylation.  It has a temperature optimum between
AB  - 25oC and 30oC and shows a broad pH optimum between 4.5 and 7.0.  The activity is thermolabile
AB  - and can be heat-killed by a 5 min incubation at 60oC.  Cloning and sequencing experiments
AB  - revealed that its recognition sequence is CTGCAG and that it cuts 5' to the second guanine
AB  - residue
AB  - in the sequence.  This enzyme is the first described isoschizomer of PstI.
ER  -

TY  - JOUR
AU  - Hartman, A.L.
AU  - Norais, C.
AU  - Badger, J.H.
AU  - Delmas, S.
AU  - Haldenby, S.
AU  - Madupu, R.
AU  - Robinson, J.
AU  - Khouri, H.
AU  - Ren, Q.
AU  - Lowe, T.M.
AU  - Maupin-Furlow, J.
AU  - Pohlschroder, M.
AU  - Daniels, C.
AU  - Pfeiffer, F.
AU  - Allers, T.
AU  - Eisen, J.A.
TI  - The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.
JO  - PLoS ONE
PY  - 2010
SP  - E9605
EP  - E9605
VL  - 5
AB  - BACKGROUND: Haloferax volcanii is an easily culturable moderate halophile
AB  - that grows on simple defined media, is readily transformable, and has a
AB  - relatively stable genome. This, in combination with its biochemical and
AB  - genetic tractability, has made Hfx. volcanii a key model organism, not
AB  - only for the study of halophilicity, but also for archaeal biology in
AB  - general. METHODOLOGY/PRINCIPAL FINDINGS: We report here the sequencing and
AB  - analysis of the genome of Hfx. volcanii DS2, the type strain of this
AB  - species. The genome contains a main 2.848 Mb chromosome, three smaller
AB  - chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2
AB  - plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE: The completed genome sequence,
AB  - presented here, provides an invaluable tool for further in vivo and in
AB  - vitro studies of Hfx. volcanii.
ER  -

TY  - JOUR
AU  - Hartman, N.
AU  - Zinder, N.D.
TI  - The effect of B specific restriction and modification of DNA on linkage relationships in f1 bacteriophage II.  Evidence for a heteroduplex intermediate in f1 recombination.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 357
EP  - 369
VL  - 85
AB  - We have analyzed the results of three gene II amber x gene II amber f1 phage
AB  - crosses.  Each was done in a non-restricting (K) host, and in a restricting (B)
AB  - host.  In each cross, only one parent was sensitive to B restriction.  The
AB  - other parent was protected from B restriction, either because of a combination
AB  - of genetic mutation at one site governing sensitivity to B restriction, and B
AB  - specific modification at the other, or because of genetic mutation at both
AB  - sites.  In all cases, B restriction resulted in the disruption of linkage
AB  - relationships between the gene II region and the unselected sensitivity site
AB  - markers.  Previously we have shown that when such crosses involve a protected
AB  - parent which is B modified at both sensitivity sites, linkage relationships
AB  - remain the same under restricting and non-restricting conditions.  Hence, the
AB  - SB protection is conferred by mutation rather than modification.  Taken
AB  - together, these results imply that, in a restricted cross, the B host
AB  - specificity system can distinguish a protected parent which is B modified from
AB  - one which is a sensitivity site mutant.  Since such a distinction could be made
AB  - most easily on an intermediate structure containing hybrid DNA, we interpret
AB  - these results in terms of a recombination mechanism mediated by an asymmetric
AB  - heteroduplex.
ER  -

TY  - JOUR
AU  - Hartman, N.
AU  - Zinder, N.D.
TI  - The effect of B specific restriction and modification of DNA on linkage relationships in f1 bacteriophage.  I.  Studies on the mechanism of B restriction in vivo.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 345
EP  - 356
VL  - 85
AB  - We have examined the effect of B specific restriction and modification of DNA
AB  - on bacteriophage f1 recombination, using a procedure which enabled us to
AB  - isolate the products of individual recombination events.  We have analyzed the
AB  - results of a series of recombination experiments, each consisting of a cross
AB  - between two gene II amber mutants, carried out both under conditions in which
AB  - neither parent was restricted, and under conditions in which one parent was
AB  - restricted while the other was protected from restriction because of B specific
AB  - modification of its genome.  At least half of the recombination events under
AB  - both restricting and nonrestricting conditions generated one parent and one
AB  - recombinant.  By considering the ratio of recombinant types emerging wiwth each
AB  - parent, linkage relationships between selected and unselected markers were
AB  - established.  These linkage relationships remained the same under restricting
AB  - and non-restricting conditions, except that under restricting conditions,
AB  - neither the sensitive parent nor the class of recombinants normally associated
AB  - with that parent was found.  We interpret this result as evidence that
AB  - restriction cleavage does not occur at the sites governing sensitivity to B
AB  - restriction, and perhaps is random.
ER  -

TY  - JOUR
AU  - Hartmann, H.
AU  - Goebel, W.
TI  - A new restriction enzyme from Enterobacter cloacae (EclI).
JO  - FEBS Lett.
PY  - 1977
SP  - 285
EP  - 287
VL  - 80
AB  - Deoxyribonucleases, which recognize specific nucleotide sequences in a duplex
AB  - deoxypolynucleotide chain, are designated as restriction enzymes.  These
AB  - enzymes, which may be partially involved in the phenomenon of genetic
AB  - restriction, have been isolated from many bacterial species.  Among them are
AB  - relatively few members of the large family of enterobacteriaceae.  We wish to
AB  - report here the isolation of a restriction enzyme of type II from an
AB  - Enterobacter cloacae strain.  As judged from the lambdacleavage pattern
AB  - obtained with this enzyme, which is designated EclI, it recognizes a sequence
AB  - different from that of a large variety of other type II restriction enzymes.
ER  -

TY  - JOUR
AU  - Harunari, E.
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Kimura, A.
AU  - Hamada, M.
AU  - Igarashi, Y.
TI  - Draft genome sequence of Streptomyces hyaluromycini MB-PO13(T), a hyaluromycin producer.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 2
EP  - 2
VL  - 13
AB  - Streptomyces hyaluromycini MB-PO13(T) (=NBRC 110483(T) = DSM 100105(T)) is type strain of the
AB  - species, which produces a hyaluronidase inhibitor, hyaluromycin.
AB  - Here, we report the draft genome sequence of this strain together with features
AB  - of the organism and generation, annotation and analysis of the genome sequence.
AB  - The 11.5 Mb genome of Streptomyces hyaluromycini MB-PO13(T) encoded 10,098
AB  - putative ORFs, of which 5317 were assigned with COG categories. The genome
AB  - harbored at least six type I PKS clusters, three type II PKS gene clusters, two
AB  - type III PKS gene clusters, six NRPS gene clusters, and one hybrid PKS/NRPS gene
AB  - cluster. The type II PKS gene cluster including
AB  - 2-amino-3-hydroxycyclopent-2-enone synthetic genes was identified to be
AB  - responsible for hyaluromycin synthesis. We propose the biosynthetic pathway based
AB  - on bioinformatic analysis.
ER  -

TY  - JOUR
AU  - Harvey, Z.H.
AU  - Snider, M.J.
TI  - Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923.
JO  - Genome Announcements
PY  - 2014
SP  - e01251
EP  - e01214
VL  - 2
AB  - Bacillus niacini is a member of a small yet diverse group of bacteria able to catabolize
AB  - nicotinic acid. We report here the availability of a draft genome for
AB  - B. niacini, which we will use to understand the evolution of its namesake
AB  - phenotype, which appears to be unique among the species in its phylogenetic
AB  - neighborhood.
ER  -

TY  - JOUR
AU  - Harvill, E.T.
AU  - Goodfield, L.L.
AU  - Ivanov, Y.
AU  - Meyer, J.A.
AU  - Newth, C.
AU  - Cassiday, P.
AU  - Tondella, M.L.
AU  - Liao, P.
AU  - Zimmerman, J.
AU  - Meert, K.
AU  - Wessel, D.
AU  - Berger, J.
AU  - Dean, J.M.
AU  - Holubkov, R.
AU  - Burr, J.
AU  - Liu, T.
AU  - Brinkac, L.
AU  - Kim, M.
AU  - Losada, L.
TI  - Genome Sequences of 28 Bordetella pertussis U.S. Outbreak Strains Dating from 2010 to 2012.
JO  - Genome Announcements
PY  - 2013
SP  - e01075
EP  - e01013
VL  - 1
AB  - Despite the availability of highly effective vaccines, Bordetella pertussis incidence has been
AB  - rapidly rising in highly vaccinated populations. Recent
AB  - outbreaks have received media attention, feeding concerns about the emergence of
AB  - dangerous new strains with increased virulence or that escape vaccine-induced
AB  - immunity. To accelerate the study of this reemerging pathogen, we sequenced the
AB  - genomes of 28 B. pertussis strains isolated during outbreaks from 2010 through
AB  - 2012, making both strains and sequence data available to the scientific
AB  - community.
ER  -

TY  - JOUR
AU  - Harvill, E.T.
AU  - Goodfield, L.L.
AU  - Ivanov, Y.
AU  - Smallridge, W.E.
AU  - Meyer, J.A.
AU  - Cassiday, P.K.
AU  - Tondella, M.L.
AU  - Brinkac, L.
AU  - Sanka, R.
AU  - Kim, M.
AU  - Losada, L.
TI  - Genome Sequences of Nine Bordetella holmesii Strains Isolated in the United States.
JO  - Genome Announcements
PY  - 2014
SP  - e00438
EP  - e00414
VL  - 2
AB  - An increasing number of pertussis-like cases are attributed to the emergent pathogen
AB  - Bordetella holmesii. The genomes of 9 clinical isolates show that they
AB  - are clonal, lack the virulence factors encoded by B. pertussis, and are more
AB  - similar to nonpertussis bordetellae. New markers for B. holmesii can be developed
AB  - using these sequences.
ER  -

TY  - JOUR
AU  - Harwich, M.D. Jr.
AU  - Alves, J.M.
AU  - Buck, G.A.
AU  - Strauss, J.F. III
AU  - Patterson, J.L.
AU  - Oki, A.T.
AU  - Girerd, P.H.
AU  - Jefferson, K.K.
TI  - Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies.
JO  - BMC Genomics
PY  - 2010
SP  - 375
EP  - 375
VL  - 11
AB  - BACKGROUND: Worldwide, bacterial vaginosis (BV) is the most common vaginal
AB  - disorder. It is associated with risk for preterm birth and HIV infection. The
AB  - etiology of the condition has been debated for nearly half a century and the lack
AB  - of knowledge about its cause and progression has stymied efforts to improve
AB  - therapy and prevention. Gardnerella vaginalis was originally identified as the
AB  - causative agent, but subsequent findings that it is commonly isolated from
AB  - seemingly healthy women cast doubt on this claim. Recent studies shedding light
AB  - on the virulence properties of G. vaginalis, however, have drawn the species back
AB  - into the spotlight. RESULTS: In this study, we sequenced the genomes of a strain
AB  - of G. vaginalis from a healthy woman, and one from a woman with bacterial
AB  - vaginosis. Comparative analysis of the genomes revealed significant divergence
AB  - and in vitro studies indicated disparities in the virulence potential of the two
AB  - strains. The commensal isolate exhibited reduced cytotoxicity and yet the
AB  - cytolysin proteins encoded by the two strains were nearly identical, differing at
AB  - a single amino acid, and were transcribed at similar levels. The BV-associated
AB  - strain encoded a different variant of a biofilm associated protein gene and
AB  - demonstrated greater adherence, aggregation, and biofilm formation. Using filters
AB  - with different pore sizes, we found that direct contact between the bacteria and
AB  - epithelial cells is required for cytotoxicity. CONCLUSIONS: The results indicated
AB  - that contact is required for cytotoxicity and suggested that reduced cytotoxicity
AB  - in the commensal isolate could be due to impaired adherence. This study outlines
AB  - two distinct genotypic variants of G. vaginalis, one apparently commensal and one
AB  - pathogenic, and presents evidence for disparate virulence potentials.
ER  -

TY  - JOUR
AU  - Harwich, M.D. Jr.
AU  - Serrano, M.G.
AU  - Fettweis, J.M.
AU  - Alves, J.M.
AU  - Reimers, M.A.
AU  - Buck, G.A.
AU  - Jefferson, K.K.
TI  - Genomic sequence analysis and characterization of Sneathia amnii sp. nov.
JO  - BMC Genomics
PY  - 2012
SP  - S4
EP  - S4
VL  - 13
AB  - BACKGROUND: Bacteria of the genus Sneathia are emerging as potential pathogens of the female
AB  - reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be
AB  - part of the normal microbiota of the genitourinary tracts of men and women, but they are also
AB  - associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia,
AB  - preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections.
AB  - Sneathia species also exhibit a significant correlation with sexually transmitted diseases and
AB  - cervical cancer. Because Sneathia species are fastidious and rarely cultured successfully in
AB  - vitro; and the genomes of members of the genus had until now not been characterized, very
AB  - little is known about the physiology or the virulence of these organisms. RESULTS: Here, we
AB  - describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously
AB  - designated "Leptotrichia amnionii". As part of the Vaginal Human Microbiome Project at VCU, a
AB  - vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and
AB  - bacteriologically cloned. The biochemical characteristics and virulence properties of the
AB  - organism were examined in vitro, and the genome of the organism was sequenced, annotated and
AB  - analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282
AB  - protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical
AB  - phenotype, and several genes potentially associated with pathogenicity were identified.
AB  - CONCLUSIONS:
AB  - Bacteria with complex growth requirements frequently remain poorly characterized and, as a
AB  - consequence, their roles in health and disease are unclear. Elucidation of the physiology and
AB  - identification of genes putatively involved in the metabolism and virulence of S. amnii may
AB  - lead to a better understanding of the role of this potential pathogen in bacterial vaginosis,
AB  - preterm birth, and other issues associated with vaginal and reproductive health.
ER  -

TY  - JOUR
AU  - Haryono, M.
AU  - Lo, W.S.
AU  - Gasparich, G.E.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma sp. NBRC 100390.
JO  - Genome Announcements
PY  - 2017
SP  - e00008
EP  - e00017
VL  - 5
AB  - Spiroplasma sp. NBRC 100390 was initially described as a duplicate of S. atrichopogonis
AB  - GNAT3597T (=ATCC BAA-520T) but later found to be different in the
AB  - 16S rDNA sequences. Here, we report the complete genome sequence of this
AB  - bacterium to establish its identity and to facilitate future investigation.
ER  -

TY  - JOUR
AU  - Hasan, N.
AU  - Kim, S.C.
AU  - Podhajska, A.J.
AU  - Szybalski, W.
TI  - A novel multistep method for generating precise unidirectional deletions using BspMI, a class-IIS restriction enzyme.
JO  - Gene
PY  - 1986
SP  - 55
EP  - 62
VL  - 50
AB  - A novel approach is described that permits the introduction of unidirectional
AB  - deletions into a cloned DNA fragment, in a precisely controlled manner.  The
AB  - method is based on the use of a special vector and a class-IIS restriction
AB  - endonuclease, BspMI, which produces staggered cuts 4 and 8 nucleotides (nt) to
AB  - the 3' from its recognition site 5' -ACCTGC-3'.  The DNA fragment is inserted
AB  - into the pUC19-based plasmid, which contains a unique BspMI recognition site,
AB  - and the appropriate number of cleavage-and-deletion cycles is performed, each
AB  - cycle removing 4 bp.  Since the recognition site is not affected by the BspMI
AB  - cleavage, no recloning of the DNA fragment is necessary.  Each cycle consists
AB  - of (i) BspMI cleavage, (ii) removal of the 4-nt single-stranded cohesive ends
AB  - with mung bean nuclease (MB), and (iii) blunt-end ligation to recircularize the
AB  - plasmid.  The shortened plasmid is reintroduced into the host, after one or
AB  - after several such 4-bp deletion cycles.  When DNA is inserted into the
AB  - multiple cloning site in the lacZ-alpha gene, the progress of 4-bp removal can
AB  - be followed by determining the Lac phenotype, since removal of multiples of 3
AB  - bp retains the reading frame while other kinds of deletions distort (or
AB  - restore) the reading frame.  Loss of pre-existing restriction sites or creation
AB  - of new ones also permits monitoring the progress of the deletion process.  The
AB  - partial fill-in of the cohesive ends with less than four deoxyribonucleotide
AB  - triphosphates, as mediated by Klenow fragment of E. coli DNA polymerase I
AB  - (PolIk), would result in 1,2 or 3-bp deletions or additions in a given cleavage
AB  - cycle, which permits one to create precise deletions.  An analogous series of
AB  - cycles of BspMI cleavage employing a PolIk-mediated fill-in reaction instead of
AB  - the MB digestion step, and followed by ligation, would permit one to synthesize
AB  - various 4-bp direct-repeat sequences and desired variants of them.
ER  -

TY  - JOUR
AU  - Hasan, N.A.
AU  - Davidson, R.M.
AU  - de Moura, V.C.
AU  - Garcia, B.J.
AU  - Reynolds, P.R.
AU  - Epperson, L.E.
AU  - Farias-Hesson, E.
AU  - DeGroote, M.A.
AU  - Jackson, M.
AU  - Strong, M.
TI  - Draft Genome Sequence of Mycobacterium chelonae Type Strain ATCC 35752.
JO  - Genome Announcements
PY  - 2015
SP  - e00536
EP  - e00515
VL  - 3
AB  - Mycobacterium chelonae is a rapidly growing opportunistic nontuberculous mycobacterial (NTM)
AB  - species that causes infections in humans and other hosts.
AB  - Here, we report the draft genome sequence of Mycobacterium chelonae type strain
AB  - ATCC 35752, consisting of 4.89 Mbp, 63.96% G+C content, 4,489 protein-coding
AB  - genes, 48 tRNAs, and 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Hasan, N.A.
AU  - Grim, C.J.
AU  - Haley, B.J.
AU  - Chun, J.
AU  - Alam, M.
AU  - Taviani, E.
AU  - Hoq, M.
AU  - Munk, A.C.
AU  - Saunders, E.
AU  - Brettin, T.S.
AU  - Bruce, D.C.
AU  - Challacombe, J.F.
AU  - Detter, J.C.
AU  - Han, C.S.
AU  - Xie, G.
AU  - Nair, G.B.
AU  - Huq, A.
AU  - Colwell, R.R.
TI  - Comparative genomics of clinical and environmental Vibrio mimicus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 21134
EP  - 21139
VL  - 107
AB  - Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has
AB  - been the subject of taxonomic controversy. A genomic analysis was undertaken to
AB  - resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and
AB  - VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and
AB  - encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I
AB  - (C-I) predominantly contains genes necessary for growth and viability, whereas
AB  - chromosome II (C-II) bears genes for adaptation to environmental change. C-I
AB  - harbors many virulence genes, including some not previously reported in V.
AB  - mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic
AB  - hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2
AB  - (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes.
AB  - Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution
AB  - and genesis of speciation for the genus Vibrio. The number of virulence regions
AB  - discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron
AB  - integrase, IntI4) with no notable difference in potential virulence genes between
AB  - clinical and environmental strains suggests these genes also may play a role in
AB  - the environment and that pathogenic strains may arise in the environment.
AB  - Significant genome synteny with prototypic pre-seventh pandemic strains of V.
AB  - cholerae was observed, and the results of phylogenetic analysis support the
AB  - hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged
AB  - from a common ancestor with a prototypic sixth pandemic genomic backbone.
ER  -

TY  - JOUR
AU  - Hasan, N.A.
AU  - Honda, J.R.
AU  - Davidson, R.M.
AU  - Epperson, L.E.
AU  - Bankowski, M.J.
AU  - Chan, E.D.
AU  - Strong, M.
TI  - Complete Genome Sequence of Mycobacterium chimaera Strain AH16.
JO  - Genome Announcements
PY  - 2016
SP  - e01276
EP  - e01216
VL  - 4
AB  - Mycobacterium chimaera is a nontuberculous mycobacterial species that causes cardiovascular,
AB  - pulmonary, and postsurgical infections. Here, we report the first
AB  - complete genome sequence of M. chimaera This genome is 6.33 Mbp, with a G+C
AB  - content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs,
AB  - one ncRNA, and three rRNA genes.
ER  -

TY  - JOUR
AU  - Hasan, N.A.
AU  - Lawsin, A.
AU  - Perry, K.A.
AU  - Alyanak, E.
AU  - Toney, N.C.
AU  - Malecha, A.
AU  - Rowe, L.A.
AU  - Batra, D.
AU  - Moulton-Meissner, H.
AU  - Miller, J.R.
AU  - Strong, M.
AU  - Laufer, H.A.
TI  - Complete Genome Sequence of Mycobacteriumchimaera Strain CDC2015-22-71.
JO  - Genome Announcements
PY  - 2017
SP  - e00693
EP  - e00617
VL  - 5
AB  - Mycobacterium chimaera is a nontuberculous mycobacterium species commonly found in the
AB  - environment. Here, we report the first complete genome sequence of a
AB  - strain from the investigation of invasive infections following open-heart
AB  - surgeries that used contaminated LivaNova Sorin Stockert 3T heater-cooler
AB  - devices.
ER  -

TY  - JOUR
AU  - Hasan, N.A.
AU  - Warren, R.L.
AU  - Epperson, L.E.
AU  - Malecha, A.
AU  - Alexander, D.C.
AU  - Turenne, C.Y.
AU  - MacMillan, D.
AU  - Birol, I.
AU  - Pleasance, S.
AU  - Coope, R.
AU  - Jones, S.J.M.
AU  - Romney, M.G.
AU  - Ng, M.
AU  - Chan, T.
AU  - Rodrigues, M.
AU  - Tang, P.
AU  - Gardy, J.L.
AU  - Strong, M.
TI  - Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e00963
EP  - e00917
VL  - 5
AB  - Mycobacterium chimaera, a nontuberculous mycobacterium (NTM) belonging to the Mycobacterium
AB  - avium complex (MAC), is an opportunistic pathogen that can cause
AB  - respiratory and disseminated disease. We report the complete genome sequence of a
AB  - strain, SJ42, isolated from an immunocompromised male presenting with MAC
AB  - pneumonia, assembled from Illumina and Oxford Nanopore data.
ER  -

TY  - JOUR
AU  - Hasegawa, M.
AU  - Nakajima, Y.
AU  - Wong, S.K.
AU  - Nakamura, K.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Kogure, K.
AU  - Yoshizawa, S.
TI  - Draft Genome Sequence of Saccharospirillum sp. Strain MSK14-1, Isolated from Surface Seawater Collected at Aburatsubo Inlet in Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00469
EP  - e00418
VL  - 6
AB  - Here, we report the draft genome sequence of Saccharospirillum sp. strain MSK14-1, isolated
AB  - from surface seawater collected at Aburatsubo Inlet in Japan.
AB  - The genome sequence of strain MSK14-1 should contribute to our understanding of
AB  - the characteristics of the genus Saccharospirillum.
ER  -

TY  - JOUR
AU  - Hasegawa, N.
AU  - Sekizuka, T.
AU  - Sugi, Y.
AU  - Kawakami, N.
AU  - Ogasawara, Y.
AU  - Kato, K.
AU  - Yamashita, A.
AU  - Takeuchi, F.
AU  - Kuroda, M.
TI  - Characterization of the pathogenicity of Streptococcus intermedius TYG1620 isolated from a human brain abscess based on the complete genome sequence with transcriptome analysis and transposon mutagenesis in a murine subcutaneous abscess model.
JO  - Infect. Immun.
PY  - 2017
SP  - e00886
EP  - e00816
VL  - 85
AB  - Streptococcus intermedius is known to cause periodontitis and pyogenic infections
AB  - in the brain and liver. Here we report the complete genome sequence of strain
AB  - TYG1620 (genome size: 2,006,877 bp; GC content: 37.6%; 2,020 predicted ORFs)
AB  - isolated from a brain abscess in an infant. Comparative genome analysis of S.
AB  - intermedius genome sequences suggested that TYG1620 carries a notable type VII
AB  - secretion system (T7SS), two long-repeat regions and 19 ORFs for
AB  - cell-wall-anchored proteins (CWAPs). To elucidate genes responsible for the
AB  - pathogenicity of TYG1620, transcriptome analysis was performed in a murine
AB  - subcutaneous abscess model. The results suggest that the expression of small
AB  - hypothetical proteins similar to phenol-soluble modulin (PSM) beta1, a
AB  - staphylococcal virulence factor, significantly increased in the abscess model. In
AB  - addition, an experiment in a murine subcutaneous abscess model with random
AB  - Tn-mutant attenuation suggested that Tn-mutants in 212 ORFs in the Tn-mutant
AB  - library were attenuated in the murine abscess model (629 ORFs disrupted in
AB  - total); the 212 ORFs are putatively essential for abscess formation.
AB  - Transcriptome analysis identified 37 ORFs, including paralogs of the T7SS and
AB  - putative glucan-binding CWAP in long-repeat regions, as upregulated and
AB  - attenuated in vivo This study provides a comprehensive characterization of S.
AB  - intermedius pathogenicity based on the complete genome sequence and a murine
AB  - subcutaneous abscess model with transcriptome and Tn-mutagenesis, leading to
AB  - identification of pivotal targets for vaccines or antimicrobial agents for the
AB  - control of S. intermedius infections.
ER  -

TY  - JOUR
AU  - Hashimoto, H.
AU  - Shimizu, T.
AU  - Imasaki, T.
AU  - Kato, M.
AU  - Shichijo, N.
AU  - Kita, K.
AU  - Sato, M.
TI  - Crystal structures of type II restriction endonuclease Eco0109I and its complex with cognate DNA.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 5605
EP  - 5610
VL  - 280
AB  - EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY.
AB  - Here we describe the crystal structures of
AB  - EcoO109I and its complex with DNA. A comparison of the two structures
AB  - shows that the catalytic domain moves drastically to capture the DNA.
AB  - One metal ion and two water molecules are observed near the active site
AB  - of the DNA complex. The metal ion is a Lewis acid that stabilizes the
AB  - pentavalent phosphorus atom in the transition state. One water
AB  - molecule, activated by Lys-126, attacks the phosphorus atom in an S(N)2
AB  - mechanism, whereas the other water interacts with the W-leaving oxygen
AB  - to donate a proton to the oxygen. EcoO109I is similar to EcoRI family
AB  - enzymes in terms of its DNA cleavage pattern and folding topology of
AB  - the common motif in the catalytic domain, but it differs in the manner
AB  - of DNA recognition. Our findings propose a novel classification of the
AB  - type II restriction endonucleases and lead to the suggestion that
AB  - EcoO109I represents a new subclass of the EcoRI family.
ER  -

TY  - JOUR
AU  - Hashimoto, H.
AU  - Takahashi, H.
AU  - Nishioka, M.
AU  - Fujiwara, S.
AU  - Takagi, M.
AU  - Imanaka, T.
AU  - Inoue, T.
AU  - Kai, Y.
TI  - Crystallographic study of intein homing endonuclease II encoded in the archaeal DNA polymerase gene.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2000
SP  - 1185
EP  - 1186
VL  - 56
AB  - Intein homing endonucleases are proteins spliced out from a precursor protein and
AB  - site-specific enzymes that make double-strand breaks in inteinless alleles. Crystals of intein
AB  - homing endonuclease II from the hyperthermophilic archaeon Pyrococcus kodakaraensis strain
AB  - KOD1 (PI-PkoII) have been grown at room temperature using ammonium sulfate as a precipitant.
AB  - The diffraction pattern of the crystal extends to 3.0 A resolution at room temperature upon
AB  - exposure to synchrotron X-rays at KEK-PF, Japan. The crystals have symmetry consistent with
AB  - space group C222(1), with unit-cell parameters a = 107.6, b = 150.5, c = 146.8 A. A full set
AB  - of X-ray diffraction data were collected to 3.0 A Bragg spacing from a native crystal with an
AB  - overall R(merge) of 4.8% and a completeness of 96.6%.
ER  -

TY  - JOUR
AU  - Hashimoto-Gotoh, T.
TI  - Quantitative determination of effective nibbling activities contaminating restriction endonuclease preparations.
JO  - Anal. Biochem.
PY  - 1995
SP  - 230
EP  - 236
VL  - 231
AB  - A simple and sensitive procedure with which to detect residual exonucleolytic nibbling
AB  - activities contaminating restriction endonuclease preparations is described.  The procedure
AB  - uses the kyosei-plasmid, pKF4, which confers kanamycin resistance and enforces streptomycin
AB  - sensitivity encoded by the trp promoter/operator-driven rpsL+4amber (POtrp-rpsL+4am) gene onto
AB  - Escherichia coli streptomycin-resistant, amber-suppressive, trp repressor-negative strains
AB  - such as TH5.  When TH5 cells transformed by pKF4 were selected on agar medium containing
AB  - kanamycin plus streptomycin, the efficiency of transformation plating was substantially lower
AB  - than that on agar containing kanamycin alone.  However, when pKF4 DNA was digested by
AB  - restriction enzymes that cut once per molecule within POtrp-rpsL+4am and religated, the
AB  - plating efficiency increased depending on the degree of contamination of exonucleolytic
AB  - nibbling activities in the enzyme preparations, due to deletion mutation at the ligation
AB  - junction.  Plating efficiency was converted to "effective nibbling activity" corresponding to
AB  - Bal31 nuclease-equivalent units.  Using this procedure, effective nibbling activities were
AB  - detected in 17 of 34 commercial samples of restriction enzymes tested.  The method is simple
AB  - and more sensitive than the procedures used by the commercial suppliers and it is applicable
AB  - to the quality control testing of more than 100 restriction enzymes.
ER  -

TY  - JOUR
AU  - Hashimoto-Gotoh, T.
AU  - Tsujimura, A.
AU  - Ogasahara, Y.
TI  - Detection of exonuclease activities in restriction endonuclease preparations using an enforcement plasmid for kanamycin-resistance selection.
JO  - Gene
PY  - 1995
SP  - 41
EP  - 44
VL  - 164
AB  - A new enforcement (kyosei-) cloning plasmid vector, designated pKF4, was constructed which
AB  - confers kanamycin resistance (KmR) and enforces streptomycin sensitivity (SmS).  Since it is
AB  - important to employ restriction endonuclease (ENase) preparations free of exonuclease (Exo)
AB  - activities for effective use of the kyosei-cloning procedure, ENases such as HpaI and SmaI
AB  - purchased from four different suppliers were examined for possible contamination by
AB  - exonucleases using pKF4.  The plasmid DNA was digested with either ENase, ligated and
AB  - transformed into Escherichia coli mutants, rpsL, supE, trpR.  With pKF4 intact DNA (approx. 8
AB  - ng), 2.3 x 10/5 KmR transformant and four KmRsmR transformant colonies were obtained: the
AB  - efficiency of transformation plating (ETP) of the intact DNA was approx. 2 x 10-5.  On the
AB  - other hand, the ETP values were significantly higher by one to three orders of magnitude when
AB  - cut and rejoined DNAs were used under the same conditions in six out of either ENase samples
AB  - examined.  The results indicate that even commercially supplied ENases, that should have
AB  - passed their quality control test, could have been contaminated with Exo sufficient to
AB  - interfere with effective use of the kyosei-cloning method.  Therefore, it is advisable to
AB  - examine ENase samples for possible contamination with Exo activities, in order to choose the
AB  - right preparations for this method at the beginning of the experiments.
ER  -

TY  - JOUR
AU  - Haskett, T.
AU  - Wang, P.
AU  - Ramsay, J.
AU  - O'Hara, G.
AU  - Reeve, W.
AU  - Howieson, J.
AU  - Terpolilli, J.
TI  - Complete Genome Sequence of Mesorhizobium ciceri Strain CC1192, an Efficient Nitrogen-Fixing Microsymbiont of Cicer arietinum.
JO  - Genome Announcements
PY  - 2016
SP  - e00516
EP  - e00516
VL  - 4
AB  - We report the complete genome sequence of Mesorhizobium ciceri strain CC1192, an  efficient
AB  - nitrogen-fixing microsymbiont of Cicer arietinum (chickpea). The genome
AB  - consists of 6.94 Mb distributed between a single chromosome (6.29 Mb) and a
AB  - plasmid (0.65 Mb).
ER  -

TY  - JOUR
AU  - Haskett, T.
AU  - Wang, P.
AU  - Ramsay, J.
AU  - O'Hara, G.
AU  - Reeve, W.
AU  - Howieson, J.
AU  - Terpolilli, J.
TI  - Complete Genome Sequence of Mesorhizobium ciceri bv. biserrulae Strain WSM1284, an Efficient Nitrogen-Fixing Microsymbiont of the Pasture Legume Biserrula  pelecinus.
JO  - Genome Announcements
PY  - 2016
SP  - e00514
EP  - e00516
VL  - 4
AB  - We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284,
AB  - a nitrogen-fixing microsymbiont of the pasture legume Biserrula
AB  - pelecinus The genome consists of 6.88 Mb distributed between a single chromosome
AB  - (6.33 Mb) and a single plasmid (0.55 Mb).
ER  -

TY  - JOUR
AU  - Hasman, H.
AU  - Mevius, D.
AU  - Veldman, K.
AU  - Olesen, I.
AU  - Aarestrup, F.M.
TI  - beta-Lactamases among extended-spectrum beta-lactamase (ESBL)-resistant Salmonella from poultry, poultry products and human patients in The Netherlands.
JO  - J. Antimicrob. Chemother.
PY  - 2005
SP  - 115
EP  - 121
VL  - 56
AB  - OBJECTIVES: The purpose of this work was to study the genetic determinants
AB  - responsible for extended-spectrum beta-lactamase (ESBL) resistance of
AB  - Salmonella isolated from Dutch poultry, poultry meat and hospitalized
AB  - humans. METHODS: Thirty-four ESBL-resistant Salmonella isolates from The
AB  - Netherlands were tested towards 21 antimicrobial agents. PCR and
AB  - sequencing were used to determine the underlying genetic determinants
AB  - responsible for the ESBL phenotypes. The transferability of the ESBL
AB  - phenotypes was tested by conjugation to a susceptible Salmonella enterica
AB  - serovar Dublin and plasmid purification, restriction fragment length
AB  - polymorphism (RFLP) and pulsed-field gel electrophoresis (PFGE) were
AB  - employed to further characterize a subset of the isolates. RESULTS: A
AB  - great genetic diversity was seen among the isolates. The bla(TEM-52) gene
AB  - was most predominant and was found among Salmonella enterica serovars
AB  - Blockley, Thomson, London, Enteritidis phage type 14b, Paratyphi B,
AB  - Virchow and Typhimurium phage types 11 and 507. We also found the
AB  - bla(TEM-20) gene in S. Paratyphi B var. Java and the bla(TEM-63) gene in
AB  - S. Isangi. Furthermore, we detected the bla(CTX-M-28) gene in S. Isangi
AB  - and the bla(CTX-M-3) gene in S. Typhimurium phage type 507. The
AB  - bla(CTX-M-2) gene was identified in S. Virchow, which also contained a
AB  - copy of the bla(SHV-2) gene and a copy of the bla(TEM-1) gene. The
AB  - bla(SHV-12) gene was found alone in S. Concord and together with the
AB  - bla(TEM-52) gene in S. Typhimurium. Finally, the bla(ACC-1) gene was
AB  - cloned from a S. Bareilly isolate and was found to be present on
AB  - indistinguishable plasmids in all S. Bareilly isolates examined as well as
AB  - in a S. Braenderup isolate and a S. Infantis isolate. CONCLUSIONS: Our
AB  - data underscore the diversity of ESBL genes in Salmonella enterica
AB  - isolated from animals, food products and human patients.
ER  -

TY  - JOUR
AU  - Hassan, I.
AU  - Eastman, A.W.
AU  - Weselowski, B.
AU  - Mohamedelhassan, E.
AU  - Yanful, E.K.
AU  - Yuan, Z.C.
TI  - Complete Genome Sequence of Arthrobacter sp. Strain LS16, Isolated from Agricultural Soils with Potential for Applications in Bioremediation and  Bioproducts.
JO  - Genome Announcements
PY  - 2016
SP  - e01586
EP  - e01515
VL  - 4
AB  - Here we report the complete genomic sequence of the bacterium Arthrobacter sp. strain LS16,
AB  - consisting of a single circular chromosome of 3.85 Mb with no
AB  - identified plasmid. Data contained within will facilitate future genetic
AB  - modification and engineering of the Arthrobacter sp. LS16 metabolic network to
AB  - enhance traits relevant to bioremediation and bioproducts.
ER  -

TY  - JOUR
AU  - Hassan, K.A.
AU  - Elbourne, L.D.
AU  - Tetu, S.G.
AU  - Johnson, E.A.
AU  - Paulsen, I.T.
TI  - Genome Sequence of the Neurotoxigenic Clostridium butyricum Strain 5521.
JO  - Genome Announcements
PY  - 2014
SP  - e00632
EP  - e00614
VL  - 2
AB  - Clostridium strains from six phylogenetic groups, C. botulinum groups I to IV, C. baratii, and
AB  - C. butyricum, display the capacity to produce botulinum neurotoxin.
AB  - Here, we present the genome sequence of a C. butyricum isolate, the
AB  - neurotoxigenic strain 5521, which encodes the type E botulinum neurotoxin.
ER  -

TY  - JOUR
AU  - Hassan, K.A.
AU  - Tetu, S.G.
AU  - Elbourne, L.D.
AU  - Johnson, E.A.
AU  - Paulsen, I.T.
TI  - Genome Sequence of the Group III Clostridium botulinum Strain Eklund-C.
JO  - Genome Announcements
PY  - 2013
SP  - e0004413
EP  - e0004413
VL  - 1
AB  - The neurotoxins produced by Clostridium botulinum strains are among the world's most potent
AB  - toxins and are the causative agents of paralytic botulism. Here, we
AB  - present the draft genome sequence of the group III C. botulinum strain Eklund-C,
AB  - including a pseudolysogen-like bacteriophage that harbors the type C neurotoxin
AB  - operon.
ER  -

TY  - JOUR
AU  - Hassan, S.S. et al.
TI  - Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation  sequencing technology.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 189
EP  - 199
VL  - 7
AB  - The Actinobacteria, Corynebacterium pseudotuberculosis strain P54B96, a nonmotile,
AB  - non-sporulating and a mesophile bacterium, was isolated from liver,
AB  - lung and mediastinal lymph node lesions in an antelope from South Africa. This
AB  - strain is interesting in the sense that it has been found together with
AB  - non-tuberculous mycobacteria (NTMs) which could nevertheless play a role in the
AB  - lesion formation. In this work, we describe a set of features of C.
AB  - pseudotuberculosis P54B96, together with the details of the complete genome
AB  - sequence and annotation. The genome comprises of 2.34 Mbp long, single circular
AB  - genome with 2,084 protein-coding genes, 12 rRNA, 49 tRNA and 62 pseudogenes and a
AB  - G+C content of 52.19%. The analysis of the genome sequence provides means to
AB  - better understanding the molecular and genetic basis of virulence of this
AB  - bacterium, enabling a detailed investigation of its pathogenesis.
ER  -

TY  - JOUR
AU  - Hassan, S.S. et al.
TI  - Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5718
EP  - 5719
VL  - 194
AB  - Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic
AB  - importance, since it affects livestock, mainly sheep and goats, worldwide,
AB  - together with reports of its presence in camels in several Arabic, Asiatic, and
AB  - East and West African countries, as well as Australia. In this article, we report
AB  - the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected
AB  - from the external neck abscess of a camel in the United Kingdom.
ER  -

TY  - JOUR
AU  - Hassan, Y.I.
AU  - Lepp, D.
AU  - He, J.
AU  - Zhou, T.
TI  - Draft Genome Sequences of Devosia sp. Strain 17-2-E-8 and Devosia riboflavina Strain IFO13584.
JO  - Genome Announcements
PY  - 2014
SP  - e00994
EP  - e00914
VL  - 2
AB  - Here we report the draft genome of Devosia sp. strain 17-2-E-8, isolated from Ontario
AB  - agricultural soil (Canada) with promising deoxynivalenol
AB  - biotransformation capabilities. In addition, we report the draft genome of
AB  - Devosia riboflavina strain IFO13584, used as a control strain in our studies
AB  - aimed at highlighting unique gene clusters involved in deoxynivalenol
AB  - epimerization.
ER  -

TY  - JOUR
AU  - Hassan, Y.I.
AU  - Lepp, D.
AU  - Li, X.Z.
AU  - Zhou, T.
TI  - Insights into the Hydrocarbon Tolerance of Two Devosia Isolates, D. chinhatensis  Strain IPL18T and D. geojensis Strain BD-c194T, via Whole-Genome Sequence  Analysis.
JO  - Genome Announcements
PY  - 2015
SP  - e00890
EP  - e00815
VL  - 3
AB  - Hexachlorocyclohexane (HCH) was among the most commonly used pesticides after the Second World
AB  - War. The extensive use of this hydrocarbon for almost six decades
AB  - has created a contamination problem on a global scale, and bioremediation methods
AB  - are being extensively explored. The reported ability of some Devosia species to
AB  - grow in the presence of appreciable amounts of hydrocarbons (2,000 mg/kg of
AB  - contaminated soil) is attracting closer attention. Here, we report the de novo
AB  - genome assembly of two hydrocarbon-tolerating Devosia isolates, D. chinhatensis
AB  - strain IPL18(T) and D. geojensis strain BD-c194(T), as a first step toward
AB  - understanding the metabolic pathways involved in their environmental adaptation
AB  - and tolerance toward hydrocarbons.
ER  -

TY  - JOUR
AU  - Hassan, Y.I.
AU  - Lepp, D.
AU  - Zhou, T.
TI  - Genome Assemblies of Three Soil-Associated Devosia species: D. insulae, D. limi,  and D. soli.
JO  - Genome Announcements
PY  - 2015
SP  - e00514
EP  - e00515
VL  - 3
AB  - Agricultural soils constitute highly diverse ecosystems with very rich bacterial  populations.
AB  - Recent studies employing next-generation sequencing techniques have
AB  - begun to explore the dynamics of bacterial species of such soils and utilized
AB  - metagenomics approaches to understand how the diversity in soil microorganisms is
AB  - affected or modified by agricultural practices. Understanding any microorganism's
AB  - environmental adaptability in the genomic era starts by fully appreciating their
AB  - encoding genome. Here, we report the draft genome sequences of three Devosia
AB  - species based on three type strains that originated from soil samples: D. insulae
AB  - strain DS-56, D. limi strain DSM17137, and D. soli strain GH2-10.
ER  -

TY  - JOUR
AU  - Hassani, I.I.
AU  - Robert, C.
AU  - Michelle, C.
AU  - Raoult, D.
AU  - Hacene, H.
AU  - Desnues, C.
TI  - Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 160
EP  - 174
VL  - 9
AB  - Halopiger djelfamassiliensis strain IIH2(T) sp. nov. is the type strain of Halopiger
AB  - djelfamassiliensis sp. nov., a new species within the genus Halopiger.
AB  - This strain, whose genome is described here, was isolated from evaporitic
AB  - sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H.
AB  - Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic
AB  - archaeon. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 3,771,216 bp long genome-contains
AB  - 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Hassaninasab, A.
AU  - Hashimoto, Y.
AU  - Tomita-Yokotani, K.
AU  - Kobayashi, M.
TI  - Discovery of the curcumin metabolic pathway involving a unique enzyme in an intestinal microorganism.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 6615
EP  - 6620
VL  - 108
AB  - Polyphenol curcumin, a yellow pigment, derived from the rhizomes of a plant (Curcuma longa
AB  - Linn) is a natural antioxidant exhibiting a variety of pharmacological activities and
AB  - therapeutic properties. It has long been used as a traditional medicine and as a preservative
AB  - and coloring agent in foods. Here, curcumin-converting microorganisms were isolated from human
AB  - feces, the one exhibiting the highest activity being identified as Escherichia coli. We are
AB  - thus unique in discovering that E. coli was able to act on curcumin. The curcumin-converting
AB  - enzyme was purified from E. coli and characterized. The native enzyme had a molecular mass of
AB  - about 82 kDa and consisted of two identical subunits. The enzyme has a narrow substrate
AB  - spectrum, preferentially acting on curcumin. The microbial metabolism of curcumin by the
AB  - purified enzyme was found to comprise a two-step reduction, curcumin being converted
AB  - NADPH-dependently into an intermediate product, dihydrocurcumin, and then the end product,
AB  - tetrahydrocurcumin. We named this enzyme 'NADPH-dependent curcumin/dihydrocurcumin
AB  - reductase' (CurA). The gene (curA) encoding this enzyme was also identified. A homology
AB  - search with the BLAST program revealed that a unique enzyme involved in curcumin metabolism
AB  - belongs to the medium-chain dehydrogenase/reductase superfamily.
ER  -

TY  - JOUR
AU  - Hassen, W.
AU  - Neifar, M.
AU  - Cherif, H.
AU  - Najjari, A.
AU  - Chouchane, H.
AU  - Driouich, R.C.
AU  - Salah, A.
AU  - Naili, F.
AU  - Mosbah, A.
AU  - Souissi, Y.
AU  - Raddadi, N.
AU  - Ouzari, H.I.
AU  - Fava, F.
AU  - Cherif, A.
TI  - Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation.
JO  - Front. Microbiol.
PY  - 2018
SP  - 34
EP  - 34
VL  - 9
AB  - A number of Pseudomonas strains function as inoculants for biocontrol,
AB  - biofertilization, and phytostimulation, avoiding the use of pesticides and
AB  - chemical fertilizers. Here, we present a new metabolically versatile plant
AB  - growth-promoting rhizobacterium, Pseudomonas rhizophila S211, isolated from a
AB  - pesticide contaminated artichoke field that shows biofertilization, biocontrol
AB  - and bioremediation potentialities. The S211 genome was sequenced, annotated and
AB  - key genomic elements related to plant growth promotion and biosurfactant (BS)
AB  - synthesis were elucidated. S211 genome comprises 5,948,515 bp with 60.4% G+C
AB  - content, 5306 coding genes and 215 RNA genes. The genome sequence analysis
AB  - confirmed the presence of genes involved in plant-growth promoting and
AB  - remediation activities such as the synthesis of ACC deaminase, putative
AB  - dioxygenases, auxin, pyroverdin, exopolysaccharide levan and rhamnolipid BS. BS
AB  - production by P. rhizophila S211 grown on olive mill wastewater based media was
AB  - effectively optimized using a central-composite experimental design and response
AB  - surface methodology (RSM). The optimum conditions for maximum BS production yield
AB  - (720.80 +/- 55.90 mg/L) were: 0.5% (v/v) inoculum size, 15% (v/v) olive oil mill
AB  - wastewater (OMWW) and 40 degrees C incubation temperature at pH 6.0 for 8 days
AB  - incubation period. Biochemical and structural characterization of S211 BS by
AB  - chromatography and spectroscopy studies suggested the glycolipid nature of the
AB  - BS. P. rhizophila rhamnolipid was stable over a wide range of temperature (40-90
AB  - degrees C), pH (6-10), and salt concentration (up to 300 mM NaCl). Due to its
AB  - low-cost production, emulsification activities and high performance in
AB  - solubilization enhancement of chemical pesticides, the indigenous BS-producing
AB  - PGPR S211 could be used as a promising agent for environmental bioremediation of
AB  - pesticide-contaminated agricultural soils.
ER  -

TY  - JOUR
AU  - Hata, E.
TI  - Complete Genome Sequence of Mycoplasma canadense Strain HAZ 360_1 from Bovine Mastitic Milk in Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e00984
EP  - e00914
VL  - 2
AB  - Bovine mycoplasmal mastitis is spreading quickly among cows. Mycoplasma canadense, a causal
AB  - species of bovine mastitis, reduces milk quality and quantity
AB  - via the infiltration of numerous inflammatory cells. Presented here is the
AB  - complete 693,241-bp genome sequence of M. canadense strain HAZ 360_1, which was
AB  - isolated in Japan.
ER  -

TY  - JOUR
AU  - Hata, E.
TI  - Complete Genome Sequence of Mycoplasma arginini Strain HAZ 145_1 from Bovine Mastitic Milk in Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e00265
EP  - e00215
VL  - 3
AB  - Mycoplasma arginini is a species sometimes isolated from bovine specimens, mastitic milk, etc.
AB  - Its pathogenicity against cows, however, is unspecific,
AB  - unlike other bovine mycoplasmas. Its whole-genome sequence is needed to
AB  - comprehend its real image. We present here the 678,592-bp complete genome
AB  - sequence of M. arginini strain HAZ 145_1.
ER  -

TY  - JOUR
AU  - Hata, E.
AU  - Murakami, K.
TI  - Complete Genome Sequence of Mycoplasma californicum Strain HAZ160_1 from Bovine Mastitic Milk in Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e00684
EP  - e00614
VL  - 2
AB  - Bovine mycoplasmal mastitis is spreading quickly among cows. It often leads to clinical
AB  - mastitis outbreaks and often results in huge economic losses. Mycoplasma
AB  - californicum is an important causal species of bovine mastitis. Presented here is
AB  - the 799,088-bp complete genome sequence of M. californicum strain HAZ160_1, which
AB  - was isolated in Japan.
ER  -

TY  - JOUR
AU  - Hata, E.
AU  - Nagai, K.
AU  - Murakami, K.
TI  - Complete Genome Sequence of Mycoplasma bovirhinis Strain HAZ141_2 from Bovine Nasal Discharge in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01000
EP  - e01017
VL  - 5
AB  - Mycoplasma bovirhinis, a mycoplasmal species involved in bovine respiratory diseases, is also
AB  - a commensal microorganism that inhabits the bovine respiratory
AB  - and reproductive organs. We present the complete 948,039-bp genome sequence of M.
AB  - bovirhinis strain HAZ141_2, which was isolated from bovine nasal discharge in
AB  - Japan.
ER  -

TY  - JOUR
AU  - Hata, E.
AU  - Nagai, K.
AU  - Murakami, K.
TI  - Complete Genome Sequence of Mycoplasma bovigenitalium Strain HAZ 596 from a Bovine Vagina in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01554
EP  - e01516
VL  - 5
AB  - Mycoplasma bovigenitalium, a mycoplasmal species involved in various bovine diseases,
AB  - including genital disease and mastitis, is also a commensal
AB  - microorganism that inhabits the bovine genital organs. We present here the
AB  - complete 853,553-bp genome sequence of M. bovigenitalium strain HAZ 596, which
AB  - was isolated from a bovine vagina in Japan.
ER  -

TY  - JOUR
AU  - Hata, K.
AU  - Okano, M.
AU  - Lei, H.
AU  - Li, E.
TI  - Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice.
JO  - Development
PY  - 2002
SP  - 1983
EP  - 1993
VL  - 129
AB  - Genomic imprinting is regulated by differential methylation of the paternal and maternal
AB  - genome. However, it remains unknown how parental imprinting is established during
AB  - gametogenesis. In this study, we demonstrate that Dnmt3L, a protein sharing homology with DNA
AB  - methyltransferases, Dnmt3a and Dnmt3b, but lacking enzymatic activity, is essential for the
AB  - establishment of maternal methylation imprints and appropriate expression of maternally
AB  - imprinted genes. We also show that Dnmt3L interacts with Dnmt3a and Dnmt3b and co-localizes
AB  - with these enzymes in the nuclei of transfected cells, suggesting that Dnmt3L may regulate
AB  - genomic imprinting via the Dnmt3 family enzymes. Consistent with this model, we show that
AB  - [Dnmt3a(-/-), Dnmt3b()] mice also fail to establish maternal methylation imprints. In
AB  - addition, both Dnmt3a and Dnmt3L are required for spermatogenesis. Together, our findings
AB  - suggest that Dnmt3L may cooperate with Dnmt3 family methyltransferases to carry out de novo
AB  - methylation of maternally imprinted genes in oocytes.
ER  -

TY  - JOUR
AU  - Hatch, M.
AU  - Allison, M.J.
AU  - Yu, F.
AU  - Farmerie, W.
TI  - Genome Sequence of Oxalobacter formigenes Strain HC-1.
JO  - Genome Announcements
PY  - 2017
SP  - e00533
EP  - e00517
VL  - 5
AB  - The lack of Oxalobacter formigenes colonization of the human gut has been correlated with the
AB  - formation of calcium oxalate kidney stones and also with the
AB  - number of recurrent kidney stone episodes. Here, we present the genome sequence
AB  - of HC-1, a human strain isolated from an individual residing in Iowa, USA.
ER  -

TY  - JOUR
AU  - Hatch, M.
AU  - Allison, M.J.
AU  - Yu, F.
AU  - Farmerie, W.
TI  - Genome Sequence of Oxalobacter formigenes Strain OXCC13.
JO  - Genome Announcements
PY  - 2017
SP  - e00534
EP  - e00517
VL  - 5
AB  - The lack of Oxalobacter formigenes colonization in the human gut is generally acknowledged as
AB  - a risk factor for kidney stone formation since this microorganism
AB  - can play an important role in oxalate homeostasis. Here, we present the genome
AB  - sequence of OXCC13, a human strain isolated from an individual residing in
AB  - Germany.
ER  -

TY  - JOUR
AU  - Hatfull, G.F.
TI  - Complete Genome Sequences of 138 Mycobacteriophages.
JO  - J. Virol.
PY  - 2012
SP  - 2382
EP  - 2384
VL  - 86
AB  - Bacteriophages are the most numerous biological entities in the biosphere, and
AB  - although their genetic diversity is high, it remains ill defined.
AB  - Mycobacteriophages-the viruses of mycobacterial hosts-provide insights into this
AB  - diversity as well as tools for manipulating Mycobacterium tuberculosis. We report
AB  - here the complete genome sequences of 138 new mycobacteriophages, which-together
AB  - with the 83 mycobacteriophages previously reported-represent the largest
AB  - collection of phages known to infect a single common host, Mycobacterium
AB  - smegmatis mc(2) 155.
ER  -

TY  - JOUR
AU  - Hatfull, G.F. et al.
TI  - Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform.
JO  - PLoS Genet.
PY  - 2006
SP  - e92
EP  - e92
VL  - 2
AB  - Bacteriophages are the most abundant forms of life in the biosphere and carry genomes
AB  - characterized by high genetic diversity and mosaic
AB  - architectures. The complete sequences of 30 mycobacteriophage genomes show
AB  - them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins
AB  - belonging to 1,536 "phamilies" of related sequences, and a statistical
AB  - analysis predicts that these represent approximately 50% of the total
AB  - number of phamilies in the mycobacteriophage population. These phamilies
AB  - contain 2.19 proteins on average; more than half (774) of them contain
AB  - just a single protein sequence. Only six phamilies have representatives in
AB  - more than half of the 30 genomes, and only three-encoding tape-measure
AB  - proteins, lysins, and minor tail proteins-are present in all 30 phages,
AB  - although these phamilies are themselves highly modular, such that no
AB  - single amino acid sequence element is present in all 30 mycobacteriophage
AB  - genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence
AB  - similarity to previously reported proteins, reflecting the enormous
AB  - genetic diversity of the entire phage population. The abundance and
AB  - diversity of phages, the simplicity of phage isolation, and the relatively
AB  - small size of phage genomes support bacteriophage isolation and
AB  - comparative genomic analysis as a highly suitable platform for
AB  - discovery-based education.
ER  -

TY  - JOUR
AU  - Hatmaker, E.A.
AU  - Riley, L.A.
AU  - O'Dell, K.B.
AU  - Papanek, B.
AU  - Graveley, B.R.
AU  - Garrett, S.C.
AU  - Wei, Y.
AU  - Terns, M.P.
AU  - Guss, A.M.
TI  - Complete Genome Sequence of Industrial Dairy Strain Streptococcus thermophilus DGCC 7710.
JO  - Genome Announcements
PY  - 2018
SP  - e01587
EP  - e01517
VL  - 6
AB  - We report here the complete genome sequence of Streptococcus thermophilus DGCC 7710. S.
AB  - thermophilus is widely used in industrial dairy production.
ER  -

TY  - JOUR
AU  - Hatolkar, S.M.
AU  - Misra, R.N.
AU  - Mahato, R.
AU  - Jadhav, S.
TI  - Whole-Genome Sequencing and Annotation of a Drug-Resistant Extrapulmonary Clinical Isolate of Beijing Genotype Mycobacterium tuberculosis from Pune, India.
JO  - Genome Announcements
PY  - 2018
SP  - e00504
EP  - e00518
VL  - 6
AB  - Whole-genome sequencing has emerged as a powerful tool to map genetic diversity among
AB  - Mycobacterium tuberculosis isolates and identify the genomic signatures
AB  - associated with drug resistance, pathogenesis, and disease transmission. Isolate
AB  - LJ319 of the Mycobacterium tuberculosis complex (MTC)-Beijing genotype
AB  - circulating in Maharashtra, India, which was obtained from the cerebrospinal
AB  - fluid (CSF) of an immunocompetent patient, was subjected to whole-genome
AB  - sequencing.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - The functioning of T-even phages with unglucosylated DNA in restricting Escherichia coli host cells.
JO  - Virology
PY  - 1964
SP  - 333
EP  - 348
VL  - 24
AB  - The DNA of the T-even bacteriophages contains glucose bound to the pyrimidine
AB  - base 5-hydroxymethylcytosine.  Modified forms of T-even phage, designated T*
AB  - phage, which contain little or no glucose, are produced by growth in certain
AB  - bacterial mutants blocked at some step in the synthesis of uridine
AB  - diphosphoglucose.  The T* phage is able to grow on some strains of Shigella
AB  - (permissive hosts) but grows poorly or not at all on various strains of
AB  - Escherichia coli (restrictive hosts).  Evidence is presented that the DNA of T*
AB  - phage undergoes extensive degradation to acid-soluble fragments following
AB  - infection of restricting E. coli cells, whereas infection of E. coli with
AB  - wild-type phage, or of Shigella with T* phage, causes very little degradation
AB  - of phage DNA.  T* phage can perform certain functions after infection of
AB  - restricting hosts.  In these respects the T* forms of phages T2,T4, and T6
AB  - differ to some extent.  Also, phage T*2 can undergo extensive growth activation
AB  - in E. coli cells in multiple infection, whereas T*4 and T*6 do not exhibit this
AB  - multiplicity activation.  In mixed infection of E. coli B with the mutant
AB  - T4am122, unable to induce synthesis of the enzyme
AB  - deoxycytidylate-hydroxymethylase, T*2 and T*6 are capable of complementing the
AB  - missing function, whereas T*4 cannot.  Evidence is presented that T* phages can
AB  - in fact direct synthesis of some early enzymes in restricting hosts.  Despite
AB  - the occurrence of some early enzyme synthesis, phage DNA synthesis does not
AB  - occur after infection of restricting bacteria with T* phage except in the cells
AB  - where restriction fails.  The ability of permissive hosts to support
AB  - replication of T* phage is not due to an initial glucosylation of the incoming
AB  - nonglucosylated DNA.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Methylation of adenine residues in bacteriophage T2 DNA.
JO  - Virology
PY  - 1972
SP  - 404
EP  - 412
VL  - 49
AB  - It has been previously shown that uP1 mutants, derived from phage T2 gt rP1, determine an
AB  - altered form of the phage-induced DNA methylase. The uP1 enzyme methylates two- to threefold
AB  - more adenine residues on phage DNA than does the wild-type methylase. The question of whether
AB  - the presence of 5-hydroxymethylcytosine (HMC) in T2 DNA plays a role in determining methylase
AB  - specificity was investigated. A triple amber mutantn was constructed which is defective in the
AB  - synthesis of the enzymes, deoxycytidine triphosphatase (dCTPase) and deoxycytidylate
AB  - hydroxymethylase (dCMP-HMase) as well as in the ability to degrade completely host DNA (genes
AB  - 56,42 and 47, respectively). In host cells lacking an amber suppressor (su-), the mutant is
AB  - shown to synthesize DNA which contains cytosine (C) in place of HMC. This C-containing DNA has
AB  - the same level of N6-methyladenine (MeAde) as observed in the HMC-containing DNA of T2 gt. rP1
AB  - DNAs behaved similarly as substrates for in vitro methylation by extracts of phage-infected
AB  - cells. These data indicate that the 5-hydroxymethyl group on HMC does not interfere with the
AB  - activity of the wilde-type DNA methylase, nor does it enhance the activity of the uP1 enzyme.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Partial purification of the Escherichia coli K-12 mec+ deoxyribonucleic acid-cytosine methylase:  in vitro methylation completely protects bacteriophage lambda deoxyribonucleic acid against cleavage by R.EcoRII.
JO  - J. Bacteriol.
PY  - 1977
SP  - 1330
EP  - 1334
VL  - 129
AB  - A procedure is described for the partial purification of the deoxyribonucleic
AB  - acid (DNA)-cytosine methylases controlled by the RII plasmid and by the
AB  - Escherichia coli mec+ gene.  The two enzymes exhibit similar but distinct
AB  - chromatographic behavior on diethylaminoethyl-cellulose and phosphocellulose.
AB  - Preliminary studies on the two methylases indicate that they are
AB  - indistinguishable with respect to their Km for S-adenosylmethionine and their
AB  - pH [in tris(hydroxymethyl)aminomethane buffer] and NaCl concentration optima.
AB  - In vitro methylation of various phage lambda DNA substrates by the mec+ or RII
AB  - enzyme modifies the DNA to a form that is completely resistant to
AB  - double-stranded cleavage by the RII restriction endonuclease (R.EcoRII).  These
AB  - results are consistent with our earlier proposal that the mec+ methylase
AB  - recognizes RII host specificity sites.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Specificity of the bacteriophage Mu mom+-controlled DNA modification.
JO  - J. Virol.
PY  - 1980
SP  - 277
EP  - 279
VL  - 34
AB  - Bacteriophage Mu DNA was labeled after induction in the presence of
AB  - [8-3H]adenine.  Purified DNA was enzymatically digested, and the 3H-labeled
AB  - dinucleotides were isolated.  Approximately 15 to 20% of the adenine residues
AB  - were modified to a new form, Ax, as observed previously (S. Hattman, J. Virol.
AB  - 32:468-475, 1979) in bulk DNA.  Paper electrophoretic analysis revealed that
AB  - only two dinucleotide species contain Ax, namely, (Ax,C) and (Ax,G).  The
AB  - observation that only C and G are the nearest neighbors of Ax is consistent
AB  - with the proposal of Kahmann and Kamp (R. Kahmann and D. Kamp, J. Mol. Biol.,
AB  - in press) that modification of Mu DNA occurs at the A residue within the
AB  - pentanucleotide sequence 5'...(C/G)-A-(G/C)-N-Py...3'.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Plasmid-controlled variation in the content of methylated bases in bacteriophage lambda deoxyribonucleic acid.
JO  - J. Virol.
PY  - 1972
SP  - 356
EP  - 361
VL  - 10
AB  - The N6-methyladenine (MeAde) and 5-methylcytosine (MeC) contents in deoxyribonucleic acid
AB  - (DNA) of bacteriophage lambda has been analyzed as a function of host specificity. The
AB  - following facts have emerged: (i) lambda grown on strains harboring the P1 prophage contain
AB  - ca. 70 more MeAde residues/DNA molecule than lambda grown either in the P1-sensitive parent,
AB  - or in a P1 immune-defective lysogen which does not confer P1 modification; (ii) lambda grown
AB  - on strains harboring the N-3 drug-resistance factor contain ca. 60 more MeC residues/DNA
AB  - molecule than lambda grown on the parental strain lacking the factor; (iii) lambda grown in
AB  - Escherichia coli B strains is devoid of MeC, whereas lambda grown in a B (N-3) host contains a
AB  - high level of MeC; (iv) the MeAde content in lambda DNA is not affected by the N-3 factor.
AB  - These results suggest that P1 controls an adenine-specific DNA methylase, and that the N-3
AB  - plasmid controls a cytosine-specific DNA methylase. The N-3 factor has been observed
AB  - previously to direct cytosine-specific methylation of phage P22 DNA and E. coli B DNA in vivo;
AB  - in vitro studies presented here demonstrate this activity.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Unusual Modification of Bacteriophage Mu DNA.
JO  - J. Virol.
PY  - 1979
SP  - 468
EP  - 475
VL  - 32
AB  - Bacteriophage mu DNA was labeled after induction in the presence of [2-3H]adenine or
AB  - [8-3H]adenine. Both Mu mom+.dam+ DNA and Mu mom-.dam+ DNA have similar N6 -methyladenine
AB  - (MeAde) contents, as well as similar frequencies of MeAde nearest neighbors. Both DNAs are
AB  - sensitive to in vitro cleavage by R.DpnI but resistant to cleavage by R.DpnI but resistant to
AB  - cleavage by R.DpnII. These results indicate that the mom+ protein does not alter the sequence
AB  - specificity of the host dam+ methylase to produce MeAde at new sites. However, we have
AB  - discovered a new modified base, denoted Ax, in Mu mom+.dam+ DNA; approximately 15% of the
AB  - adenine residues are modified to Ax. Although the precise nature of the modification is not
AB  - yet defined, analysis be electrophoresis and chromatography indicates that the N6-amino group
AB  - is not the site of modification, and that the added moiety contains a free carboxyl group. Ax
AB  - is not present in Mu mom+.dam+ or Mu mom-.dam+ phage DNA or in cellular DNA from unonduced Mu
AB  - mom+.dam+ lysogens. These results suggest that expression of the dam+ and mom+ genes are
AB  - required for the Ax modification and that this modification is responsible for protecting Mu
AB  - DNA against certain restriction nucleases. Mu mom+.dam+ DNA and Mu mom-.dam- DNA contain a
AB  - very low level of MeAde (ca. 1 MeAde per 5,000 adenine residues). Since the only nearest
AB  - neighbor to MeAde appears to be cytosine, we suggest that the methylated sequence is
AB  - 5'...C-A-C...3' and that this methylation is mediated by the EcoK modification enzyme.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Plasmid-controlled variation in the content of methylated bases in single-stranded DNA phages M13 and fd.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 749
EP  - 752
VL  - 74
AB  - The N6-methyladenine and 5-methylcytosine contents in the DNA of bacteriophages
AB  - M13 and fd have been analyzed.  The results are summarized as follows. (1)
AB  - After growth in bacteria harboring the N-3 fi- drug resistance-factor, fd and
AB  - M13 are observed to contain approximately 1 to 2 more 5-methylcytosine residues
AB  - per DNA molecule than after rgrowth in the parental drug-sensitive host; no
AB  - effect on the N6-methyladenine content is produced by the plasmid.  (2) After
AB  - growth in bacteria harboring P1 prophage, fd and M13 are observed to contain
AB  - approximately 2 to 3 more N6-methyladenine residues per DNA molecule than after
AB  - growth in the parental P1-sensitive host; no apparent effect on the
AB  - 5-methylcytosine content was produced by the P1 plasmid.  (3) In agreement with
AB  - others, fd carrying B-host specificity (fd.B) is observed to contain 2 more
AB  - N6-methyladenine residues/DNA molecule than fd.K.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - DNA Modification:  Methylation.
JO  - Bacteriophage T4
PY  - 1983
SP  - 152
EP  - 155
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - DNA methylation of T-even bacteriophages and of their nonglucosylated mutants:  its role in P1-directed restriction.
JO  - Virology
PY  - 1970
SP  - 359
EP  - 367
VL  - 42
AB  - The 6-methylaminopurine (MAP) content of bacteriophages T2,T4,T6 and their nonglucosylated gt
AB  - mutants has been analyzed. Phage T2 contains 25% more MAP than T4; the nonglucosylated forms
AB  - of T2 and T4 contain 30-100% more MAP than their respective wild-type parents; the level of
AB  - MAP is affected by the growth temperature and by the level of glucosylation. T6 and its
AB  - nonglucosylated mutants are devoid of MAP. Support for the hypothesis that methylation has a
AB  - role in P1-directed restriction of gt mutants of T-even phages (Revel and Georgopoulos, 1969)
AB  - is presented: (1) mutants of T2gt and T4gt insensitive to P1-restriction, designated uP1
AB  - (Revel and Georgopoulos, 1969) contain hypermethylated DNA; (2) cells simultaneously infected
AB  - with P1-sensitive T2gt or T6gt (designated rP1) and ultraviolet-irradiated T2gt uP1 yield
AB  - progeny rP1 phage which contain hypermethylated DNA and are partially resistant to P1
AB  - restriction. It is proposed that the uP1 mutations occur in the structural gene for phage DNA
AB  - methylase. Methylation does not appear to be involved in the restriction of T2gt and T4gt by
AB  - certain bacterial hosts that do not restrict T5gt (these bacteria are designated r6-r2,4+)
AB  - because of the findings that (1) a T4gt mutant lacking MAP is still restricted in r6-r2,4+;
AB  - (2) phenotypically methylated T6gt is accepted in r6-r2,4+.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - Variation of 6-methylaminopurine content in bacteriophage P22 deoxyribonucleic acid as a function of host specificity.
JO  - J. Virol.
PY  - 1971
SP  - 690
EP  - 691
VL  - 7
AB  - The 6-methylaminopurine (MAP) content of P22 deoxyribonucleic acid has been
AB  - analyzed as a function of the host specificity it carries.  A 40 to 50%
AB  - reduction in MAP level occurs as a result of growth in host cells defective in
AB  - the ability to confer LT specificity.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - DNA methylation.
JO  - The Enzymes
PY  - 1981
SP  - 517
EP  - 548
VL  - 14
AB  - Almost all biological macromolecules undergo some form of processing event
AB  - subsequent to their biosynthesis.  Polypeptides are specifically folded,
AB  - cleaved, phosphorylated, acetylated, methylated, or covalently bound to other
AB  - polypeptides.  RNA molecules are specifically cleaved, lengthened, spliced,
AB  - methylated, thiolated, or otherwise base-modified.  These processes are
AB  - obligatory events in the establishment of functional expression of these
AB  - molecules.  It has been known for almost three decades that DNA is also subject
AB  - to post-replication modification.  The main topic of this chapter is to
AB  - consider the phenomenon of DNA methylation, its nature, distribution, analysis,
AB  - specificity, and biological function.  In addition, I briefly review other DNA
AB  - modifications known to occur among prokaryotes and eukaryotes.
ER  -

TY  - JOUR
AU  - Hattman, S.
TI  - DNA methyltransferase-dependent transcription of the phage Mu mom gene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1982
SP  - 5518
EP  - 5521
VL  - 79
AB  - The phage Mu mom gene controls an unusual DNA modification. Expression of the mom function
AB  - requires an active host (dam+) DNA adenine methylase [S-adenosyl-L-methionine:DNA
AB  - (6-aminopurine)-methyltranasferase]; in dam- hosts, Mu development is normal except that the
AB  - viral DNA does not undergo the mom modification. The present communication compares
AB  - transcription of the mom gene in dam+ versus dam- cells. 32P-labeled probes were prepared by
AB  - nick-translation of a purified mom gene-containing restriction fragment and of virion DNA,
AB  - respectively. These probes were hybridized with various RNAs blotted onto nitrocellulose
AB  - filters (after fractionation by agarose gel electrophoresis). The salient findings are: (i)
AB  - mom-specific RNA was readily detected in dam+ lysogenic cells, but only after induction of the
AB  - Mu prophage; (ii) the level of mom RNA was decreased at least to 1/20th in induced dam- Mu
AB  - lysogens; and (iii) little difference, if any, was observed between dam+ and dam- cells with
AB  - respect to total Mu transcripts produced after prophage induction. These results are in accord
AB  - with the known pattern of mom gene expression and Mu development. They show that the host
AB  - (dam+) DNA adenine methylase activity is required for transcription of the mom gene. This
AB  - represents a unique example where a DNA methylase exerts a positive regulatory role in mRNA
AB  - transcription; alternative mechanisms for this process will be discussed.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Brooks, J.E.
AU  - Masurekar, M.
TI  - Sequence specificity of the P1 modification methylase (M.EcoP1) and the DNA methylase (M.Ecodam) controlled by the Escherichia coli dam gene.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 367
EP  - 380
VL  - 126
AB  - Labeled oligonucleotides have been fractionated from pancreatic DNase digests of DNA that had
AB  - been methylated in vitro with the P1 modification enzyme (M.EcoP1) or with the DNA-adenine
AB  - methylase (M.Ecodam) controlled by the Escherichia coli dam gene. The sequences of methylated
AB  - oligonucleotides were established for M.Eco dam modification of calf thymus DNA. The results
AB  - show that M.Ecodam methylates adenine residues contained in the twofold symmetrical sequence,
AB  - 5'...G-A-T-C...3'. The sequence for the site methylated by M.EcoP1 has also been deduced; we
AB  - proposed that M.EcoP1 modification produces the following methylated pentameric sequence:
AB  - 5'...A-G-A*-C-Py...3' (where A* = N6 methyladenine and Py is C or T).
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Cousens, L.
TI  - Location of the region controlling host specificity (hsII) with respect to drug resistance markers on the fi- R factor, N-3.
JO  - J. Bacteriol.
PY  - 1972
SP  - 1428
EP  - 1430
VL  - 112
AB  - The region controlling host specificity (hsII) has been mapped, by P22
AB  - transduction, with respect to drug resistance markers carried on the fi- R
AB  - factor, N-3.  The relative linear sequence of contransducible markers is
AB  - Tc-Su-Sm-hsII.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Fukasawa, T.
TI  - Host-induced modification of T-even phages due to defective glucosylation of their DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1963
SP  - 297
EP  - 300
VL  - 50
AB  - None
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Gold, E.
AU  - Plotnik, A.
TI  - Methylation of cytosine residues in DNA controlled by a drug resistance factor.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 187
EP  - 190
VL  - 69
AB  - The proportion of 5-methylcytosine (5MeCyt) and 6-methylaminopurine
AB  - (N6-methyladenine, 6MeAde) in bacteriophage P22 DNA was analyzed as a function
AB  - of the host-specificity the phage carried.  In the DNA of P22 grown in stsrains
AB  - harboring the modifying drug-resistance-transfer-factor N-3, the 5MeCyt content
AB  - was at least twice that after growth in strains lacking the factor.  In
AB  - contrast, the 6MeAde level of P33 DNA was unaffected by the presence or absence
AB  - of the factor.  The 6MeAde and 5MeCyt levels were unaffected by factors 222 and
AB  - N-1, which do not modify phage DNA.  The 5MeCyt/6MeAde ratio was only slightly
AB  - higher int he DNA of Salmonella strains that had received the N-3 factor.
AB  - After transfer of the N-3 factor to Escherichia coli strain B, which normally
AB  - lacks 5MeCyt, a high content of 5MeCyt is observed.  We conclude that the N-3
AB  - factor controls a DNA methylase specific for cytosine residues.  If the N-3
AB  - host specificity is imparted by cytosine methylation, this would be the first
AB  - instance where a biological role for 5MeCyt has been elucidated.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Goradia, M.
AU  - Monaghan, C.
AU  - Bukhari, A.I.
TI  - Regulation of the DNA-modification function of bacteriophage Mu.
JO  - Cold Spring Harb. Symp. Quant. Biol.
PY  - 1983
SP  - 647
EP  - 653
VL  - 47
AB  - The DNA-modification function of bacteriophage Mu, termed the mom function,
AB  - presents very interesting examples of DNA modification and regulation of gene
AB  - expression.  On both counts it sets new precedents.  The modification involved
AB  - is new, and the expression of the mom gene appears to require methylation of
AB  - sequences adjacent to the gene.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Gribbin, C.
AU  - Hutchison, C.A.
TI  - In vivo methylation of bacteriophage PhiX174 DNA.
JO  - J. Virol.
PY  - 1979
SP  - 845
EP  - 851
VL  - 32
AB  - A mutant (designated mec-) has been isolated from Escherichia coli C which has
AB  - lost DNA-cytosine methylase activity and the ability to protect phage lambda
AB  - against in vivo restriction by the RII endonuclease.  This situation is
AB  - analogous to that observed with an E. coli K-12 mec- mutant; thus, the E. coli
AB  - C methylase appears to have overlapping sequence specificity with the K-12 and
AB  - RII enzymes; (the latter methylases have been shown previously to recognize the
AB  - same sequence).  Covalently closed, supertwisted double-stranded DNA (RFI) was
AB  - isolated from C mec+ and C mec- cells infected with bacteriophage PhiX174.
AB  - PhiX.mec- RFI is sensitive to in vitro cleavage by R.EcoRII and is cut twice to
AB  - produce two fragments of almost equal size.  In contrast, PhiX.mec+ RFI is
AB  - relatively resistant to in vitro cleavage by R.EcoRII.  R.BstI, which cleaves
AB  - mec+/RII sites independent of the presence or absence of 5-methylcytosine,
AB  - cleaves both forms of the RFI and produces two fragments similar in size to
AB  - those with R.EcoRII.  These results demonstrate that PhiX.mec+ RFI is
AB  - methylated in vivo by the host mec+ enzyme and that this methylation protects
AB  - the DNA against cleavage by R.EcoRII.  This is consistent with the known
AB  - location of two mec+/RII sequences (viz., 5' ... C-C-A/T-G-G ...3') on the
AB  - PhiX174 map.  Mature single-stranded virion DNA was isolated from PhiX174
AB  - propagated in C mec+ or C mec- in the presence of L-[methyl-3H]methionine.
AB  - Paper chromatographic analyses of acid hydrolysates revealed that PhiX.mec+ DNA
AB  - had a 10-fold-higher ratio of [3H]5-methylcytosine to [3H]cytosine compared to
AB  - PhiX.mec-.  Since PhiX.mec+ contains, on the average, approximately 1
AB  - 5-methylcytosine residue per viral DNA, we conclude that methylation of PhiX174
AB  - is mediated by the host mec+ enzyme only.  These results are not consistent
AB  - with the conclusions of previous reports that PhiX174 methylation is mediated
AB  - by a phage-induced enzyme and that methylation is essential for normal phage
AB  - development.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Keister, T.
AU  - Gottehrer, A.
TI  - Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 701
EP  - 711
VL  - 124
AB  - DNA methylation in Bacillus amyloliquefaciens strain H (Bam) and Bacillus
AB  - brevis (Bbv) has been examined by a variety of techniques.  In vivo labelling
AB  - studies revealed that Bam DNA contains no N6-methyladenine (MeAde), but
AB  - contains 5-methylcytosine (MeCyt); approximately 0.7% of the cytosine residues
AB  - are methylated.  DNA methylase activity was partially purified from both Bam
AB  - and Bbv; the Bam enzyme preparation transferred methyl groups from
AB  - S-adenosyl-L-[methyl-3H]methionine ([3H]AdoMet) to specific DNA cytosine
AB  - residues only; in agreement with Vanyushin & Dobritsa (1975), the Bbv enzyme
AB  - preparation methylated both DNA adenine and cytosine residues.  The (partial)
AB  - sequence specificity of the methylases was determined by analyzing
AB  - [3H]methyl-labelled dinucleotides obtained from enzymatic digests of DNA
AB  - methylated in vitro.  Bam and Bbv each contain a DNA-cytosine methylase with
AB  - overlapping sequence specificity; e.g. both enzymes produce G-C*, C*-A and
AB  - C*-T.  This is consistent with a single, twofold symmetrical methylation
AB  - sequence of 5'...G-C*-(A or T)-G-C...3'; this was observed by Vanyushin &
AB  - Dobritsa (1975) for a different Bbv strain.  Bam contains a second DNA-cytosine
AB  - methylase (not present in Bbv), which produces T-C* and C*-T.  We propose that
AB  - this methylase is the BamI modification enzyme, and that the modified sequence
AB  - is 5'...G-G-A-G-C*-C...3'.  Bbv appears to contain two DNA-adenine methylases
AB  - which produce the (partial) methylated sequences, 5'...G-A*-T...3' and
AB  - 5'...A-A*-G...3', respectively; in the former case, all the G-A-T-C sites on
AB  - Bbv DNA appear to be methylated.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Malygin, E.G.
TI  - Bacteriophage T2Dam and T4Dam DNA-[N6-adenine]-methyltransferases.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 2004
SP  - 67
EP  - 126
VL  - 77
AB  - DNA mewthyltransferases are important enzymes that methylate DNA as a post replicative event.
AB  - DNA MTases, encoded by both cellular and viral genes, catalyze methyl group transfer from
AB  - S-adenosyl-L-methionine, producing S-adenosyl-L-homocysteine and methylated DNA.  The methyl
AB  - group acceptor atom is either an exocyclic amino nitrogen (N6-Ade or N4-Cyt) or a ring carbon
AB  - (C5-Cyt).  The DNA-[amino]-MTases [EC2.1.1.72 and 113]transfer methyl groups directly to the
AB  - exocyclic nitrogen without the formation of a covalent enzyme-DNA intermediate, which occurs
AB  - with the C5-Cyt MTases [EC2.1.73].  While most phokaryote DNA MTases are components of
AB  - restriction-modification systems important in protecting cells from foreign DNAs, certain
AB  - MTases do not have cognate restriction enzymes associated with them.  These include a family
AB  - (Dam) of prokaryotic DNA-adenine MTases that methylate Ade in GATC sequences.  Several
AB  - bacteriophages, such as T2 and T4, also encode Dam MTases.  Generally speaking, the Dam MTases
AB  - are not essential for viability of bacteria or phage; however, they do have a variety of
AB  - functions including regulation of transcription of certain genes, timing of DNA replication
AB  - initiation, and protection against restriction endonucleases, and they play a crucial role in
AB  - pathogenicity of intestinal bacteria.  Because they methylate specific nucleotide sequences,
AB  - they provide excellent objects for studies on protein-DNA interactions.  Valuable insights
AB  - into the organization/function of MTases have come from the identification of common motifs
AB  - discovered by amino acid-seqence alignments.  The solution of a number of MTase crystal
AB  - structures has added key details on the specific protein-DNA and protein-cofactor
AB  - interactions.  However, genetic and biochemical analyses are essential for a more complete
AB  - understanding of the functioning of these enzymes.  Here, we present results from all three
AB  - approaches directed at characterizing the bacteriophage T2/T4 Dam DNA-[N6-adenine]-MTase.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Revel, H.R.
AU  - Luria, S.E.
TI  - Enzyme synthesis directed by nonglucosylated T-even bacteriophages in restriction hosts.
JO  - Virology
PY  - 1966
SP  - 427
EP  - 438
VL  - 30
AB  - Phage T2gt, defective in ability to initiate production of Alpha-glucosyl
AB  - transferase, elicits the synthesis of other phage directed early enzymes in the
AB  - host bacterium Escherichia coli B in which it cannot grow.  This early-enzyme
AB  - synthesis is arrested at about the same time in infection with either T2gt or
AB  - T2, despite the fact that T2gt DNA is apparently not replicated in E. coli B.
AB  - A similar pattern of phage-enzyme synthesis is observed with other T even
AB  - phages with nonglucosylated DNA.  Experiments with UV-irradiated phage and with
AB  - inhibitors of protein synthesis indicate that the arrest of enzyme synthesis in
AB  - infection with nonglucosylated phage is due not to the regulatory process
AB  - operative in infection with normal phage, but to a different mechanism.  The
AB  - evidence suggests that this mechanism is the rapid degradation of the
AB  - nonglucosylated phage DNA.  The experiments also provide estimates for the
AB  - half-life of phage-specific mRNA in the presence or absence of protein
AB  - synthesis.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Schlagman, S.
AU  - Cousens, L.
TI  - Isolation of a mutant of Escherichia coli defective in cytosine-specific deoxyribonucleic acid methylase activity and in partial protection of bacteriophage lambda against restriction by cells containing the N-3 drug-resistance factor.
JO  - J. Bacteriol.
PY  - 1973
SP  - 1103
EP  - 1107
VL  - 115
AB  - A mutant (designated mec-) of Escherichia coli F+ 100 endoI- su+ rk-mk+ has
AB  - been isolated which is defective in cytosine-specific deoxyribonucleic acid
AB  - (DNA) methylase activity.  The DNA of this mutant, as well as the DNA of phage
AB  - lambda and fd propagated in it, is virtually devoid of 5-methyl-cytosine (MeC);
AB  - in contrast, the mutation has no significant effect on the level of
AB  - N6-methyladenine in DNA.  Phage lambda grown on the mec- mutant is more
AB  - strongly restricted by N-3-containing cells than is lambda grown on the mec+
AB  - parent.  These results suggest that methylation of certain cytosine residues by
AB  - the E. coli K-12 enzyme partially protects lambda DNA from either the N-3
AB  - restriction nuclease or against secondary degradation subsequent to
AB  - N-3-specific degradation.  Analysis of the MeC level in viral and cellular DNA
AB  - obtained from mec+, mec+ (mN3+), and mec- (mN3+) strains has led to the
AB  - conclusion that the R-factor controlled DNA-cytosine methylase may be capable
AB  - of methylating a sequence(s) which is a substrate for the K-12 enzyme.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Schlagman, S.
AU  - Goldstein, L.
AU  - Frohlich, M.
TI  - Salmonella typhimurium SA Host Specificity System is based on Deoxyribonucleic Acid-Adenine Methylation.
JO  - J. Bacteriol.
PY  - 1976
SP  - 211
EP  - 217
VL  - 127
AB  - We have determined the nature of the deoxyribonucleic acid (DNA) modification
AB  - governed by the SA host specificity system of Salmonella typhimurium.  Two
AB  - lines of evidence indicate that SA modification is based on methylation of
AB  - DNA-adenine residues.  (i) The SA+ locus of Salmonella was transferred into
AB  - Escherichia coli B, a strain that does not contain 5-methylcytosine in its DNA;
AB  - although the hybrid strain was able to confer SA modification, its DNA still
AB  - did not contain 5-methylcytosine.  (ii) the N6-methyladenine content of phage L
AB  - DNA was measured after growth in various host strains; phage lacking SA
AB  - modification contained fewer N6-methyladenine residues per DNA.  We also
AB  - investigated the possibility, suggested by others, that SA modification
AB  - protects phage DNA against restriction by the RII host specificity system.
AB  - Phages lambda, P3, and L were grown in various SA+ and SA- hosts and tested for
AB  - their relative plating ability on strains containing or lacking RII
AB  - restriction; the presence or absence of SA modification had no effect on RII
AB  - restriction.  In vitro studies revealed, however, that Salmonella DNA is
AB  - protected against cleavage by purified RII restriction endonuclease (R-EcoRII).
AB  - This protection is not dependent on SA modification; rather, it appears to be
AB  - due to methylation by a DNA-cytosine methylase which has overlapping
AB  - specificity with the RII modification enzyme, but which is not involved in any
AB  - other known host specificity system.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - van Ormondt, H.
AU  - de Waard, A.
TI  - Sequence specificity of the wild-type (dam+) and mutant (damh) forms of bacteriophage T2 DNA adenine methylase.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 361
EP  - 376
VL  - 119
AB  - Non-glucosylated, non-methylated phage T2 DNA was methylated in vitro with partially purified
AB  - wild-type (dam+) or mutant (damh) T2 DNA adenine methylase. The radioactively labeled
AB  - methyladenine-containing DNA was enzymatically degraded and the resulting oligonucleotides
AB  - were separated according to chain length by DEAE-cellulose chromatography. Following
AB  - "fingerprinting" by two-dimensional electrophoresis, we determined the sequence for vaious
AB  - di-, tri- and tetranucleotides containing radioactive N6-methyldeoxyadenosine. From this
AB  - analysis we conclude that both T2 dam+ and T2 damh contain the sequence 5'...G-mA-Py...3'.
ER  -

TY  - JOUR
AU  - Hattman, S.
AU  - Wilkinson, J.
AU  - Swinton, D.
AU  - Schlagman, S.
AU  - MacDonald, P.M.
AU  - Mosig, G.
TI  - Common evolutionary origin of the Phage T4 dam and host Escherichia coli dam DNA-adenine methyltransferase genes.
JO  - J. Bacteriol.
PY  - 1985
SP  - 932
EP  - 937
VL  - 164
AB  - We compared the known DNA nucleotide and encoded amino acid sequences of the Escherichia coli
AB  - and bacteriophage T4 dam (DNA-adenine methyltransferase) genes. Despite the absence of any DNA
AB  - sequence homology, there were four regions (11 to 33 residues long) of amino acid sequence
AB  - homology containing 45 to 64% identity. These results suggest that the genes for these two
AB  - enzymes have a common evolutionary origin.
ER  -

TY  - JOUR
AU  - Hattori, M. et al.
TI  - The DNA sequence of human chromosome 21.
JO  - Nature
PY  - 2000
SP  - 311
EP  - 319
VL  - 405
AB  - Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down
AB  - syndrome, the most frequent genetic cause of significant mental retardation, which affects up
AB  - to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions
AB  - for common complex disorders have also been mapped to this chromosome, and loss of
AB  - heterozygosity has been observed in regions associated with solid tumours. Here we report the
AB  - sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361
AB  - base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only
AB  - three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus,
AB  - we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The
AB  - structural features identified include duplications that are probably involved in chromosomal
AB  - abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of
AB  - the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Brockmeier, S.L.
AU  - Frana, T.S.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of Nine Streptococcus suis Strains Isolated in the United  States.
JO  - Genome Announcements
PY  - 2015
SP  - e01301
EP  - e01315
VL  - 3
AB  - Streptococcus suis is a swine pathogen responsible for economic losses to the pig industry
AB  - worldwide. Additionally, it is a zoonotic agent that can cause severe
AB  - infections in those in close contact with infected pigs and/or who consume
AB  - uncooked or undercooked pork products. Here, we report nine draft genome
AB  - sequences of S. suis.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Davies, P.R.
AU  - Haan, J.S.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from Humans with Long-Term Swine  Contact.
JO  - Genome Announcements
PY  - 2017
SP  - e01079
EP  - e01017
VL  - 5
AB  - Humans have been found to harbor livestock-associated methicillin-resistant Staphylococcus
AB  - aureus (LA-MRSA) isolates. LA-MRSA isolates are considered adapted
AB  - to colonizing livestock and less pathogenic in humans than their hospital- and
AB  - community-acquired counterparts. Here, we present nine LA-MRSA sequence type 5
AB  - isolates from veterinarians with long-term swine contact.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Frana, T.S.
AU  - Nicholson, T.L.
TI  - Complete Genome Sequence of a Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolate from the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e00791
EP  - e00717
VL  - 5
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) may be the largest
AB  - MRSA reservoir outside the hospital setting. One concern with LA-MRSA
AB  - is the acquisition of novel mobile genetic elements by these isolates. Here, we
AB  - report the complete genome sequence of a swine LA-MRSA sequence type 5 isolate
AB  - from the United States.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Frana, T.S.
AU  - Nicholson, T.L.
TI  - Complete Genome Sequence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolated from Swine in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e00790
EP  - e00717
VL  - 5
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) colonizes and causes disease in many animal
AB  - species. Livestock-associated MRSA (LA-MRSA) isolates are
AB  - represented by isolates of the sequence type 398 (ST398). These isolates are
AB  - considered to be livestock adapted. This report provides the complete genome
AB  - sequence of one swine-associated LA-MRSA ST398 isolate from the United States.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Frana, T.S.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from Humans after  Short-Term Swine Contact.
JO  - Genome Announcements
PY  - 2017
SP  - e01080
EP  - e01017
VL  - 5
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 5
AB  - (ST5) has raised concerns surrounding the potential for these
AB  - isolates to colonize or cause disease in humans with swine contact. Here, we
AB  - report draft genome sequences for nine LA-MRSA ST5 isolates obtained from humans
AB  - after short term swine contact.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Frana, T.S.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of 14 Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolates from Swine Farms in the United  States.
JO  - Genome Announcements
PY  - 2017
SP  - e01082
EP  - e01017
VL  - 5
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is a bacterium
AB  - carried by or obtained from swine and other livestock. The initial and
AB  - predominant swine-associated LA-MRSA sequence type (ST) identified is ST398.
AB  - Here, we present 14 draft genome sequences from LA-MRSA ST398 isolates found in
AB  - the United States.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Frana, T.S.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of 63 Swine-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e01081
EP  - e01017
VL  - 5
AB  - Methicillin-resistant Staphylococcus aureus colonizes humans and other animals such as swine.
AB  - Livestock-associated methicillin-resistant Staphylococcus aureus
AB  - (LA-MRSA) sequence type 5 (ST5) isolates are a public concern due to their
AB  - pathogenicity and ability to acquire mobile genetic elements. This report
AB  - presents draft genome sequences for 63 LA-MRSA ST5 isolates in the United States.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Nicholson, T.L.
TI  - Complete Genome Sequences of Two Staphylococcus aureus Sequence Type 5 Isolates from California, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e00099
EP  - e00017
VL  - 5
AB  - Staphylococcus aureus causes a variety of human diseases ranging in severity. The
AB  - pathogenicity of S. aureus can be partially attributed to the acquisition of
AB  - mobile genetic elements. In this report, we provide two complete genome sequences
AB  - from human clinical S. aureus isolates.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of 14 Staphylococcus aureus Sequence Type 5 Isolates from  California, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e00098
EP  - e00017
VL  - 5
AB  - Staphylococcus aureus is part of the human epithelial microbiota; however, it is  also a
AB  - pathogen. The acquisition of mobile genetic elements plays a role in the
AB  - virulence of S. aureus isolates and contributes to treatment failures. This
AB  - report details the draft genome sequences of 14 clinical S. aureus isolates.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of One Methicillin-Sensitive and Seven Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained in   California.
JO  - Genome Announcements
PY  - 2017
SP  - e01084
EP  - e01017
VL  - 5
AB  - Staphylococcus aureus is a commensal bacterium of humans that can cause a spectrum of
AB  - diseases. An isolate's capacity to cause disease is partially
AB  - attributed to the acquisition of novel mobile genetic elements. This report
AB  - provides the draft genome sequence of one methicillin-susceptible and seven
AB  - methicillin-resistant clinical human S. aureus isolates.
ER  -

TY  - JOUR
AU  - Hau, S.J.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Nicholson, T.L.
TI  - Draft Genome Sequences of 50 Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from a U.S. Hospital.
JO  - Genome Announcements
PY  - 2017
SP  - e01083
EP  - e01017
VL  - 5
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) can be a commensal or pathogen in humans.
AB  - Pathogenicity and disease are related to the acquisition of mobile
AB  - genetic elements encoding virulence and antimicrobial resistance genes. Here, we
AB  - report draft genome sequences for 50 clinical MRSA isolates from humans with
AB  - MRSA-related disease.
ER  -

TY  - JOUR
AU  - Haugen, P.
AU  - Bhattacharya, D.
TI  - The spread of LAGLIDADG homing endonuclease genes in rDNA.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 2049
EP  - 2057
VL  - 32
AB  - Group I introns that encode homing endonuclease genes (HEGs) are highly invasive genetic
AB  - elements. Their movement into a homologous position in
AB  - an intron-less allele is termed homing. Although the mechanism of
AB  - homing is well understood, the evolutionary relationship between HEGs
AB  - and their intron partners remains unclear. Here we have focused on the
AB  - largest family of HEGs (encoding the protein motif, LAGLIDADG) to
AB  - understand how HEGs and introns move in rDNA. Our analysis shows the
AB  - phylogenetic clustering of HEGs that encode a single copy of the
AB  - LAGLIDADG motif in neighboring, but often evolutionarily distantly
AB  - related, group I introns. These endonucleases appear to have inserted
AB  - into existing introns independent of ribozymes. In contrast, our data
AB  - support a common evolutionary history for a large family of
AB  - heterologous introns that encode HEGs with a duplicated LAGLIDADG
AB  - motif. This finding suggests that intron/double-motif HEG elements can
AB  - move into heterologous sites as a unit. Our data also suggest that a
AB  - subset of the double-motif HEGs in rDNA originated from the duplication
AB  - and fusion of a single-motif HEG encoded by present-day ribozymes in
AB  - LSU rDNA.
ER  -

TY  - JOUR
AU  - Haugen, P.
AU  - De Jonckheere, J.F.
AU  - Johansen, S.
TI  - Characterization of the self-splicing products of two complex Naegleria LSU rDNA group I introns containing homing endonuclease genes.
JO  - Eur. J. Biochem.
PY  - 2002
SP  - 1641
EP  - 1649
VL  - 269
AB  - The two group I introns Nae.L1926 and Nmo.L2563, found at two different sites in nuclear LSU
AB  - rRNA genes of Naegleria amoebo-flagellates, have been characterized in vitro. Their structural
AB  - organization is related to that of the mobile Physarum intron Ppo.L1925 (PpLSU3) with ORFs
AB  - extending the L1-loop of a typical group IC1 ribozyme. Nae.L1926, Nmo.L2563 and Ppo.L1925 RNAs
AB  - all self-splice in vitro, generating ligated exons and full-length intron circles as well as
AB  - internal processed excised intron RNAs. Formation of full-length intron circles is found to be
AB  - a general feature in RNA processing of ORF-containing nuclear group I introns. Both Naegleria
AB  - LSU rDNA introns contain a conserved polyadenylation signal at exactly the same position in
AB  - the 3' end of the ORFs close to the internal processing sites, indicating an RNA polymerase
AB  - II-like expression pathway of intron proteins in vivo. The intron proteins I-NaeI and I-NmoI
AB  - encoded by Nae.L1926 and Nmo.L2563, respectively, correspond to His-Cys homing endonucleases
AB  - of 148 and 175 amino acids. I-NaeI contains an additional sequence motif homologous to the
AB  - unusual DNA binding motif of three antiparallel beta sheets found in the I-PpoI endonuclease,
AB  - the product of the Ppo.L1925 intron ORF.
ER  -

TY  - JOUR
AU  - Haugen, P.
AU  - Huss, V.A.R.
AU  - Nielsen, H.
AU  - Johansen, S.
TI  - Complex group-I introns in nuclear SSU rDNA of red and green algae: Evidence of homing-endonuclease pseudogenes in the Bangiophyceae.
JO  - Curr. Genet.
PY  - 1999
SP  - 345
EP  - 353
VL  - 36
AB  - The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large
AB  - group-IC1 introns in their nuclear small subunit
AB  - ribosomal RNA genes due to the presence of open reading frames at the
AB  - 5' end of the introns. The putative 555 amino-acid Scenedesmus-encoded
AB  - protein harbors a sequence motif resembling the bacterial S9 ribosomal
AB  - proteins. The Porphyra intron self-splices in vitro, and generates both
AB  - ligated exons and a full-length intron RNA circle. The Porphyra intron
AB  - has an unusual structural organization by encoding a potential 149
AB  - amino-acid homing-endonuclease-like protein on the complementary
AB  - strand. A comparison between related group-I introns in the
AB  - Bangiophyceae revealed homing-endonuclease-like pseudogenes due to
AB  - frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and
AB  - Porphyra introns provide new insights into the evolution and possible
AB  - novel functions of nuclear group-I intron proteins.
ER  -

TY  - JOUR
AU  - Haugen, P.
AU  - Simon, D.M.
AU  - Bhattacharya, D.
TI  - The natural history of group I introns.
JO  - Trends Genet.
PY  - 2005
SP  - 111
EP  - 119
VL  - 21
AB  - There are four major classes of introns: self-splicing group I and group II introns, tRNA
AB  - and/or archaeal introns and spliceosomal introns
AB  - in nuclear pre-mRNA. Group I introns are widely distributed in
AB  - protists, bacteria and bacteriophages. Group II introns are found in
AB  - fungal and land plant mitochondria, algal plastids, bacteria and
AB  - Archaea. Group II and spliceosomal introns share a common splicing
AB  - pathway and might be related to each other. The tRNA and/or archaeal
AB  - introns are found in the nuclear tRNA of eukaryotes and in archaeal
AB  - tRNA, rRNA and mRNA. The mechanisms underlying the self-splicing and
AB  - mobility of a few model group I introns are well understood. By
AB  - contrast, the role of these highly distinct processes in the evolution
AB  - of the 1500 group I introns found thus far in nature (e.g. in algae and
AB  - fungi) has only recently been clarified. The explosion of new sequence
AB  - data has facilitated the use of comparative methods to understand group
AB  - I intron evolution in a broader context and to generate hypotheses
AB  - about intron insertion, splicing and spread that can be tested
AB  - experimentally.
ER  -

TY  - JOUR
AU  - Haugen, P.
AU  - Wikmark, O.-G.
AU  - Vader, A.
AU  - Coucheron, D.H.
AU  - Sjottem, E.
AU  - Johansen, S.D.
TI  - The recent transfer of a homing endonuclease gene.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 2734
EP  - 2741
VL  - 33
AB  - The myxomycete Didymium iridis (isolate Panama 2) contains a mobile group I intron named
AB  - Dir.S956-1 after position 956 in the nuclear small subunit (SSU) rRNA gene. The intron is
AB  - efficiently spread through homing by the intron-encoded homing endonuclease I-DirI. Homing
AB  - endonuclease genes (HEGs) usually spread with their associated introns as a unit, but
AB  - infrequently also spread independent of introns (or inteins). Clear examples of HEG mobility
AB  - are however sparse. Here, we provide evidence for the transfer of a HEG into a group I intron
AB  - named Dir.S956-2 that is inserted into the SSU rDNA of the Costa Rica 8 isolate of D.iridis.
AB  - Similarities between intron sequences that flank the HEG and rDNA sequences that flank the
AB  - intron (the homing endonuclease recognition sequence) suggest that the HEG invaded the intron
AB  - during the recent evolution in a homing-like event. Dir.S956-2 is inserted into the same SSU
AB  - site as Dir.S956-1. Remarkably, the two group I introns encode distantly related splicing
AB  - ribozymes with phylogenetically related HEGs inserted on the opposite strands of different
AB  - peripheral loop regions. The HEGs are both interrupted by small spliceosomal introns that must
AB  - be removed during RNA maturation.
ER  -

TY  - JOUR
AU  - Hauglund, M.J.
AU  - Tatum, F.M.
AU  - Bayles, D.O.
AU  - Maheswaran, S.K.
AU  - Briggs, R.E.
TI  - Genome Sequences of Mannheimia haemolytica Serotype A2 Isolates D171 and D35, Recovered from Bovine Pneumonia.
JO  - Genome Announcements
PY  - 2015
SP  - e00093
EP  - e00015
VL  - 3
AB  - Here, we report two genomes, one complete and one draft, from isolates of serotype A2
AB  - Mannheimia haemolytica recovered from pneumonic bovine lung.
ER  -

TY  - JOUR
AU  - Hauglund, M.J.
AU  - Tatum, F.M.
AU  - Bayles, D.O.
AU  - Maheswaran, S.K.
AU  - Briggs, R.E.
TI  - Genome Sequences of Serotype A6 Mannheimia haemolytica Isolates D174 and D38 Recovered from Bovine Pneumonia.
JO  - Genome Announcements
PY  - 2015
SP  - e00086
EP  - e00015
VL  - 3
AB  - Here, we report two genomes, one complete and one draft, from virulent bovine strains of
AB  - Mannheimia haemolytica serotype A6 recovered prior to the field usage
AB  - of modern antimicrobial drugs.
ER  -

TY  - JOUR
AU  - Hauglund, M.J.
AU  - Tatum, F.M.
AU  - Bayles, D.O.
AU  - Maheswaran, S.K.
AU  - Briggs, R.E.
TI  - Genome Sequences of Mannheimia haemolytica Serotype A1 Strains D153 and D193 from Bovine Pneumonia.
JO  - Genome Announcements
PY  - 2013
SP  - e00848
EP  - e00813
VL  - 1
AB  - Here we report two genome sequences, one complete and one draft, from virulent bovine strains
AB  - of Mannheimia haemolytica serotype A1 recovered prior to the field
AB  - usage of modern antimicrobial drugs.
ER  -

TY  - JOUR
AU  - Hauptmann, A.L.
AU  - Glaring, M.A.
AU  - Hallin, P.F.
AU  - Prieme, A.
AU  - Stougaard, P.
TI  - Draft Genome Sequence of the Psychrophilic and Alkaliphilic Rhodonellum psychrophilum Strain GCM71T.
JO  - Genome Announcements
PY  - 2013
SP  - e01014
EP  - e01013
VL  - 1
AB  - Rhodonellum psychrophilum GCM71(T), isolated from the cold and alkaline submarine ikaite
AB  - columns in the Ikka Fjord in Greenland, displays optimal growth at 5 to 10
AB  - degrees C and pH 10. Here, we report the draft genome sequence of this strain,
AB  - which may provide insight into the mechanisms of adaptation to these extreme
AB  - conditions.
ER  -

TY  - JOUR
AU  - Hauser, H.
AU  - Richter, D.C.
AU  - van Tonder, A.
AU  - Clark, L.
AU  - Preston, A.
TI  - Comparative genomic analyses of the Taylorellae.
JO  - Vet. Microbiol.
PY  - 2012
SP  - 195
EP  - 203
VL  - 159
AB  - Contagious equine metritis (CEM) is an important venereal disease of horses that
AB  - is of concern to the thoroughbred industry. Taylorella equigenitalis is a
AB  - causative agent of CEM but very little is known about it or its close relative
AB  - Taylorella asinigenitalis. To reveal novel information about Taylorella biology,
AB  - comparative genomic analyses were undertaken. Whole genome sequencing was
AB  - performed for the T. equigenitalis type strain, NCTC11184. Draft genome sequences
AB  - were produced for a second T. equigenitalis strain and for a strain of T.
AB  - asinigenitalis. These genome sequences were analysed and compared to each other
AB  - and the recently released genome sequence of T. equigenitalis MCE9. These
AB  - analyses revealed that T. equigenitalis strains appear to be very similar to each
AB  - other with relatively little strain-specific DNA content. A number of genes were
AB  - identified that encode putative toxins and adhesins that are possibly involved in
AB  - infection. Analysis of T. asinigenitalis revealed that it has a very similar gene
AB  - repertoire to that of T. equigenitalis but shares surprisingly little DNA
AB  - sequence identity with it. The generation of genome sequence information greatly
AB  - increases knowledge of these poorly characterised bacteria and greatly
AB  - facilitates study of them.
ER  -

TY  - JOUR
AU  - Hausmann, B.
AU  - Pjevac, P.
AU  - Schreck, K.
AU  - Herbold, C.W.
AU  - Daims, H.
AU  - Wagner, M.
AU  - Loy, A.
TI  - Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.
JO  - Genome Announcements
PY  - 2018
SP  - e01524
EP  - e01517
VL  - 6
AB  - The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum
AB  - siberiense 26-4b1 was isolated from a Siberian peatland. We
AB  - report here a 6.20-Mbp near-complete high-quality draft genome sequence of T.
AB  - siberiense that reveals expected and novel metabolic potential for the genus
AB  - Telmatospirillum, including genes for sulfur oxidation.
ER  -

TY  - JOUR
AU  - Hausmann, R.
AU  - Gold, M.
TI  - The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid.
JO  - J. Biol. Chem.
PY  - 1966
SP  - 1985
EP  - 1994
VL  - 241
AB  - Infection of Escherichia coli B with bacteriophages T1, T2, or T4 results in increase in the
AB  - activity of deoxyribonucleic acid methylase assayed in crude extracts of the infected cells.
AB  - The largest increase is observed after infection with T2 phage; T4 and T1 phages lead to
AB  - smaller increases in that order of decreasing magnitude.  After infection with T3, T5, or T6
AB  - phages, a decrease in activity was observed; T7 and lambda phages had no effect.  The kinetics
AB  - of the increase in methylase activity after T2 infection is similar to those found with the
AB  - "early enzymes" induced by T-even phages, and protein synthesis is necessary for the increase
AB  - to occur.  The properties of the methylase activity of phage T2-infected bacteria suggest that
AB  - it is a new phage-directed enzyme.
ER  -

TY  - JOUR
AU  - Hausner, G.
AU  - Iranpour, M.
AU  - Kim, J.-J.
AU  - Breuil, C.
AU  - Davis, C.N.
AU  - Gibb, E.A.
AU  - Reid, J.
AU  - Loewen, P.C.
AU  - Hopkin, A.A.
TI  - Fungi vectored by the introduced bark beetle Tomicus piniperda in Ontario, Canada and comments on the taxonomy of Leptographium lundbergii, L. terebrantis, L. truncatum and L. wingfieldii.
JO  - Can. J. Bot.
PY  - 2005
SP  - 1222
EP  - 1237
VL  - 83
AB  - Fungi isolated from Tomicus piniperda (L.) galleries in infected trap logs, standing trees,
AB  - and directly from insects were identified using morphological features and molecular data
AB  - obtained from the mitochondrial and nuclear DNA region. Identified strains represented
AB  - Leptographium wingfieldii Morelet, Leptographium procerum (Kendr.) Wingf., Leptographium
AB  - lundbergii Lag.
ER  -

TY  - JOUR
AU  - Havelaar, K.J.
AU  - Korsuize, J.
TI  - Differences in susceptibility to restriction by E. coli B between various heteroduplex molecules of bacteriophage FD DNA.
JO  - Mol. Biol. Rep.
PY  - 1974
SP  - 453
EP  - 455
VL  - 1
AB  - Fragments of B-modified bacteriophage fd sB1o sB2 RF DNA were prepared with the help of
AB  - purified endonuclease R from Haemophilus parainfluenzae.  These were hybridized with
AB  - unmodified circular single stranded fd DNA.  The resulting partial heteroduplex molecules were
AB  - assayed for infectivity on competent cells of B-restricting and non-restricting strains of E.
AB  - coli.  Three of such heteroduplexes originating from neighboring fragments on the physical map
AB  - of fd RF DNA were shown to be more resistant to EcoB restriction than six others and the
AB  - unmodified control.  It is suggested that the three corresponding vicinal fragments contain
AB  - essential parts of the EcoB recognition site on this phage DNA.
ER  -

TY  - JOUR
AU  - Havelsrud, O.E.
AU  - Sorum, H.
AU  - Gaustad, P.
TI  - Genome Sequences of Corynebacterium pseudotuberculosis Strains 48252 (Human, Pneumonia), CS_10 (Lab Strain), Ft_2193/67 (Goat, Pus), and CCUG 27541.
JO  - Genome Announcements
PY  - 2014
SP  - e00869
EP  - e00814
VL  - 2
AB  - Here we report the genome sequencess of four Corynebacterium pseudotuberculosis strains. These
AB  - include a strain isolated from a patient with C.
AB  - pseudotuberculosis pneumonia (48252), a strain isolated from pus in goat
AB  - (Ft_2193/67), a laboratory strain originating from strain Ft_2193/67 (CS_10), and
AB  - the draft genome of an equine reference strain, CCUG 27541.
ER  -

TY  - JOUR
AU  - Hawkey, J.
AU  - Edwards, D.J.
AU  - Dimovski, K.
AU  - Hiley, L.
AU  - Billman-Jacobe, H.
AU  - Hogg, G.
AU  - Holt, K.E.
TI  - Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm.
JO  - BMC Genomics
PY  - 2013
SP  - 800
EP  - 800
VL  - 14
AB  - BACKGROUND: The bacterium Salmonella enterica serovar Typhimurium (S.
AB  - Typhimurium) is one of the most frequent causes of foodborne outbreaks of
AB  - gastroenteritis. Between 2005-2008 a series of S. Typhimurium outbreaks occurred
AB  - in Tasmania, Australia, that were all traced to eggs originating from a single
AB  - chicken farm. We sequenced the genomes of 12 isolates linked to these outbreaks,
AB  - in order to investigate the microevolution of a pathogenic S. Typhimurium clone
AB  - in a natural, spatiotemporally restricted population. RESULTS: The isolates,
AB  - which shared a phage type similar to DT135 known locally as 135@ or 135a, formed
AB  - a clade within the S. Typhimurium population with close similarity to the
AB  - reference genome SL1334 (160 single nucleotide polymorphisms, or SNPs). Ten of
AB  - the isolates belonged to a single clone (<23 SNPs between isolate pairs) which
AB  - likely represents the population of S. Typhimurium circulating at the chicken
AB  - farm; the other two were from sporadic cases and were genetically distinct from
AB  - this clone. Divergence dating indicated that all 12 isolates diverged from a
AB  - common ancestor in the mid 1990 s, and the clone began to diversify in 2003-2004.
AB  - This clone spilled out into the human population several times between 2005-2008,
AB  - during which time it continued to accumulate SNPs at a constant rate of 3-5 SNPs
AB  - per year or 1x10-6 substitutions site-1 year-1, faster than the longer-term (~50
AB  - year) rates estimated previously for S. Typhimurium. Our data suggest that
AB  - roughly half of non-synonymous substitutions are rapidly removed from the S.
AB  - Typhimurium population, after which purifying selection is no longer important
AB  - and the remaining substitutions become fixed in the population. The S.
AB  - Typhimurium 135@ isolates were nearly identical to SL1344 in terms of gene
AB  - content and virulence plasmids. Their phage contents were close to SL1344, except
AB  - that they carried a different variant of Gifsy-1, lacked the P2 remnant found in
AB  - SL1344 and carried a novel P2 phage, P2-Hawk, in place SL1344's P2 phage
AB  - SopEvarphi. DT135 lacks P2 prophage. Two additional plasmids were identified in
AB  - the S. Typhimurium 135@ isolates, pSTM2 and pSTM7. Both plasmids were IncI1, but
AB  - phylogenetic analysis of the plasmids and their bacterial hosts shows these
AB  - plasmids are genetically distinct and result from independent plasmid acquisition
AB  - events. CONCLUSIONS: This study provides a high-resolution insight into
AB  - short-term microevolution of the important human pathogen S. Typhimurium. It
AB  - indicates that purifying selection occurs rapidly in this population (</= 6
AB  - years) and then declines, and provides an estimate for the short-term
AB  - substitution rate. The latter is likely to be more relevant for foodborne
AB  - outbreak investigation than previous estimates based on longer time scales.
ER  -

TY  - JOUR
AU  - Hawtrey, A.O.
AU  - Ariatti, M.
TI  - A possible model for the methylation of deoxycytidine in DNA.
JO  - Med. Hypotheses
PY  - 1984
SP  - 125
EP  - 134
VL  - 15
AB  - The modified base 5-methylcytidine has been found in the DNA of a number of
AB  - different eukaryotic cells where it occurs principally in the dinucleotide
AB  - sequence -CmpG- which is present as a palindrome in double-strand nucleic acid
AB  - molecules.  There is considerable evidence to indicate and suggest that
AB  - 5-methylcytosine serves as a regulatory signal in eukaryotic gene expression.
AB  - Replication of DNA containing -CmpG- gives rise to daughter DNA molecules
AB  - containing new -CpG- dinucleotide sequences in which the cytidine residues are
AB  - not methylated.  Methylation of these residues is carried out by a methylase
AB  - enzyme using S-adenosyl-L-methionine as a specific methyl group donor.  This
AB  - model discussed in the present communication tries to explain in chemical and
AB  - biological terms the mechanism of the methylation reaction.  The first
AB  - reactions of the scheme are well known through the work of other investigators.
AB  - However, we introduce a new concept into our reaction mechanism by postulating
AB  - the direct involvement of S-adenosyl-L-methionine in the reaction through its
AB  - covalent attachment to the cytosine ring followed by a specific ring closure
AB  - and methylation involving transfer of a hydride ion.  The model also gives a
AB  - possible explanation of mechanism of interaction of dimethyl sulphoxide with
AB  - the enzyme systems of certain eukaryotic cells, which are altered or changed in
AB  - the regulation of gene expression by this chemical reagent.
ER  -

TY  - JOUR
AU  - Hayakawa, T.
AU  - Ono, A.
AU  - Ueda, T.
TI  - Synthesis of decadeoxyribonucleotides containing 5-modified uracils and their interactions with restriction endonucleases BglII, Sau3AI and MboI (Nucleosides and Nucleotides 82).
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4761
EP  - 4776
VL  - 16
AB  - Decadeoxyribonucleotides containing uracil, 5-bromouracil, 5-cyanouracil and 5-ethyluracil in
AB  - recognition sequences of restriction endonucleases BglII, Sau3AI, MboI were synthesized.
AB  - Decanucleotides containing 5-bromouracil in place of thymine had essentially the same
AB  - susceptibility to all the restriction endonucleases.  Uracil-containing decanucleotides were
AB  - however very resistant to attack.  Decanucleotides containing 5-cyanouracil in the recognition
AB  - sequence were strongly resistant to hydrolysis by Sau3AI, but were hydrolysed by BglII and
AB  - MboI as well as the parent decanucleotide.  Decanucleotides containing 5-ethyluracil were
AB  - strongly resistant to hydrolysis by Sau3AI, but were partially resistant to hydrolysis by
AB  - BglII and MboI.
ER  -

TY  - JOUR
AU  - Hayano-Kanashiro, C.
AU  - Lopez-Arredondo, D.L.
AU  - Cruz-Morales, P.
AU  - Alcaraz, L.D.
AU  - Olmedo, G.
AU  - Barona-Gomez, F.
AU  - Herrera-Estrella, L.
TI  - First draft genome sequence of a strain from the genus citricoccus.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6092
EP  - 6093
VL  - 193
AB  - Bacteria of the genus Citricoccus have been isolated from ecological niches characterized by
AB  - diverse abiotic stress conditions. Here we report
AB  - the first genome draft of a strain of the genus Citricoccus isolated from
AB  - the extremely oligotrophic Churince system in the Cuatro Cienegas Basin
AB  - (CCB) in Coahuila, Mexico.
ER  -

TY  - JOUR
AU  - Hayashi, K.
AU  - Morooka, N.
AU  - Yamamoto, Y.
AU  - Fujita, K.
AU  - Isono, K.
AU  - Choi, S.
AU  - Ohtsubo, E.
AU  - Baba, T.
AU  - Wanner, B.L.
AU  - Mori, H.
AU  - Horiuchi, T.
TI  - Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.
JO  - Mol. Syst. Biol.
PY  - 2006
SP  - 2006.0007
EP  - 2006.0007
VL  - 2
AB  - With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell,
AB  - highly accurate genomes were determined for two closely related K-12 strains, MG1655 and
AB  - W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed
AB  - differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions
AB  - or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13
AB  - sites with an insertion sequence element or defective prophage in only one strain and two
AB  - sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with
AB  - short indel and base disparities revealed that only eight sites are true differences. The
AB  - other 243 discrepancies were due to errors in the original MG1655 sequence, including 79
AB  - frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense,
AB  - and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per
AB  - 13,000 bases) were mostly within portions sequenced with out-dated technology based on
AB  - radioactive chemistry.
ER  -

TY  - JOUR
AU  - Hayashi, T. et al.
TI  - Complete genome sequence of Enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
JO  - DNA Res.
PY  - 2001
SP  - 11
EP  - 22
VL  - 8
AB  - Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea,
AB  - hemorrhagic colitis, and hemolytic uremic syndrome. Here we report the complete chromosome
AB  - sequence of an O157:H7 strain isolated from the Sakai outbreak, and the results of genomic
AB  - comparison with a benign laboratory strain, K-12 MG1655. The chromosome is 5.5 Mb in size, 859
AB  - Kb larger than that of K-12. We identified a 4.1-Mb sequence highly conserved between the two
AB  - strains, which may represent the fundamental backbone of the E. coli chromosome. The remaining
AB  - 1.4-Mb sequence comprises of O157:H7-specific sequences, most of which are horizontally
AB  - transferred foreign DNAs. The predominant roles of bacteriophages in the emergence of O157:H7
AB  - is evident by the presence of 24 prophages and prophage-like elements that occupy more than
AB  - half of the O157:H7-specific sequences. The O157:H7 chromosome encodes 1632 proteins and 20
AB  - tRNAs that are not present in K-12. Among these, at least 131 proteins are assumed to have
AB  - virulence-related functions.  Genome-wide codon usage analysis suggested that the
AB  - O157:H7-specific tRNAs are involved in the efficient expression of the strain-specific genes.
AB  - A complete set of the genes specific to O157:H7 presented here sheds new insight into the
AB  - pathogenicity and the physiology of O157:H7, and will open a way to fully understand the
AB  - molecular mechanisms underlying the O157:H7 infection.
ER  -

TY  - JOUR
AU  - Hayashi, T.
AU  - Kamio, Y.
AU  - Hishinuma, F.
AU  - Usami, Y.
AU  - Titani, K.
AU  - Terawaki, Y.
TI  - Pseudomonas aeruginosa cytotoxin: the nucleotide sequence of the gene and the mechanism of activation of the protoxin.
JO  - Mol. Microbiol.
PY  - 1989
SP  - 861
EP  - 868
VL  - 3
AB  - The gene encoding cytotoxin (ctx) was cloned from Pseudomonas aeruginosa 158 and
AB  - the nucleotide sequence was determined. The structural gene of ctx encodes the
AB  - procytotoxin of 286 amino acid residues with a molecular mass of 31,681 Daltons.
AB  - Procytotoxin was activated by removal of 20 amino acid residues from the C
AB  - terminus with trypsin. The cloned ctx gene was not expressed in either an
AB  - Escherichia coli strain or a cytotoxin non-producing strain of P. aeruginosa. An
AB  - expression system for the ctx gene was constructed by placing the structural gene
AB  - of ctx downstream of tac promoter on a broad host-range vector plasmid.
ER  -

TY  - JOUR
AU  - Hayashimoto, N.
AU  - Morita, H.
AU  - Inoue, T.
AU  - Yasuda, M.
AU  - Yamamoto, M.
AU  - Itoh, T.
TI  - Draft Genome Sequence of Enteropathogenic Escherichia coli, Isolated from the Bloody Stool Sample of a Common Marmoset (Callithrix jacchus).
JO  - Genome Announcements
PY  - 2015
SP  - e01161
EP  - e01115
VL  - 3
AB  - Here, we report the draft genome sequence of Escherichia coli strain R811. This bacterium was
AB  - isolated from the bloody stool sample of a common marmoset, and was categorized as
AB  - enteropathogenic E. coli because it possessed eae.
ER  -

TY  - JOUR
AU  - Hayatsu, M.
AU  - Tago, K.
AU  - Uchiyama, I.
AU  - Toyoda, A.
AU  - Wang, Y.
AU  - Shimomura, Y.
AU  - Okubo, T.
AU  - Kurisu, F.
AU  - Hirono, Y.
AU  - Nonaka, K.
AU  - Akiyama, H.
AU  - Itoh, T.
AU  - Takami, H.
TI  - An acid-tolerant ammonia-oxidizing gamma-proteobacterium from soil.
JO  - ISME J.
PY  - 2017
SP  - 1130
EP  - 1141
VL  - 11
AB  - Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs
AB  - in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB)
AB  - that have been isolated from soil to date are acid-sensitive. Here we report the
AB  - isolation and characterization of an acid-adapted AOB from an acidic agricultural
AB  - soil. The isolated AOB, strain TAO100, is classified within the
AB  - Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the
AB  - pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming
AB  - cell aggregates. Whereas all known gammaproteobacterial AOB (gamma-AOB) species,
AB  - which have been isolated from marine and saline aquatic environments, are
AB  - halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the
AB  - first soil-originated and non-halophilic gamma-AOB. The TAO100 genome is
AB  - considerably smaller than those of other gamma-AOB and lacks several genes
AB  - associated with salt tolerance which are unnecessary for survival in soil. The
AB  - ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in
AB  - abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in
AB  - the strongly acidic soil. These results indicate that TAO100 plays an important
AB  - role in the nitrification of acidic soils. Based on these results, we propose
AB  - TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.The
AB  - ISME Journal advance online publication, 10 January 2017;
AB  - doi:10.1038/ismej.2016.191.
ER  -

TY  - JOUR
AU  - Hayden, H.S.
AU  - Gillett, W.
AU  - Saenphimmachak, C.
AU  - Lim, R.
AU  - Zhou, Y.
AU  - Jacobs, M.A.
AU  - Chang, J.
AU  - Rohmer, L.
AU  - D'Argenio, D.A.
AU  - Palmieri, A.
AU  - Levy, R.
AU  - Haugen, E.
AU  - Wong, G.K.
AU  - Brittnacher, M.J.
AU  - Burns, J.L.
AU  - Miller, S.I.
AU  - Olson, M.V.
AU  - Kaul, R.
TI  - Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.
JO  - Genomics
PY  - 2008
SP  - 530
EP  - 537
VL  - 91
AB  - Large-insert genome analysis (LIGAN) is a broadly applicable,
AB  - high-throughput technology designed to characterize genome-scale
AB  - structural variation. Fosmid paired-end sequences and DNA fingerprints
AB  - from a query genome are compared to a reference sequence using the Genomic
AB  - Variation Analysis (GenVal) suite of software tools to pinpoint locations
AB  - of insertions, deletions, and rearrangements. Fosmids spanning regions
AB  - that contain new structural variants can then be sequenced. Clonal pairs
AB  - of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were
AB  - used to validate the LIGAN technology. Approximately 1.5 Mb of inserted
AB  - sequences were identified, including 743 kb containing 615 ORFs that are
AB  - absent from published P. aeruginosa genomes. Six rearrangement breakpoints
AB  - and 220 kb of deleted sequences were also identified. Our study expands
AB  - the "genome universe" of P. aeruginosa and validates a technology that
AB  - complements emerging, short-read sequencing methods that are better suited
AB  - to characterizing single-nucleotide polymorphisms than structural
AB  - variation.
ER  -

TY  - JOUR
AU  - Hayes, M.M.
AU  - MacIntyre, A.M.
AU  - Allen, C.
TI  - Complete Genome Sequences of the Plant Pathogens Ralstonia solanacearum Type Strain K60 and R. solanacearum Race 3 Biovar 2 Strain UW551.
JO  - Genome Announcements
PY  - 2017
SP  - e01088
EP  - e01017
VL  - 5
AB  - Ralstonia solanacearum is a globally distributed plant pathogen that causes bacterial wilt
AB  - diseases of many crop hosts, threatening both sustenance farming
AB  - and industrial agriculture. Here, we present closed genome sequences for the R.
AB  - solanacearum type strain, K60, and the cool-tolerant potato brown rot strain R.
AB  - solanacearum UW551, a highly regulated U.S. select agent pathogen.
ER  -

TY  - JOUR
AU  - Hayrapetyan, H.
AU  - Boekhorst, J.
AU  - de Jong, A.
AU  - Kuipers, O.P.
AU  - Nierop, G.M.N.
AU  - Abee, T.
TI  - Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e00485
EP  - e00416
VL  - 4
AB  - Bacillus cereus is a foodborne pathogen causing emetic and diarrheal-type syndromes. Here, we
AB  - report the whole-genome sequences of 11 B. cereus food
AB  - isolates.
ER  -

TY  - JOUR
AU  - Hayward, G.S.
AU  - Frenkel, N.
AU  - Roizman, B.
TI  - Anatomy of herpes simplex virus DNA: Strain differences and heterogeneity in the locations of restriction endonuclease cleavage sites.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1975
SP  - 1768
EP  - 1772
VL  - 72
AB  - Digestion of herpes simplex virus DNA by the HindII or EcoRI restriction
AB  - endonucleases yielded 11 to 15 fragments with molecular weights between 2 and
AB  - 28 million.  The electrophoretic profiles obtained in 0.3% agarose gels with
AB  - DNA fragments from nine different strains of herpes simplex virus type 1 could
AB  - be readily differentiated from the patterns exhibited by the corresponding
AB  - fragments from four separate strains of type 2 virus; however, within each
AB  - serotype, the laboratory strains differed significantly among themselves and
AB  - also from isolates passaged a minimum number of times outside the human host.
AB  - Digestion of all DNAs of herpes simplex virus with either enzyme reproducibly
AB  - generated two classes of fragments (major and minor) which differed in molar
AB  - concentration.  Moreover, although the molecular weight of an intact herpes
AB  - simplex 1 (F1) DNA molecule is approximately 98 Md, the summed molecular
AB  - weights of all major and minor HindIII fragments totalled 160 Md, and the seven
AB  - major fragments alone accounted for only 60 Md.  These unusual features
AB  - indicate the existence of limited heterogeneity in the positions of cleavage
AB  - sites along individual molecules.  We have eliminated the possibility that
AB  - minor fragments arose from contamination with the defective DNA of high buoyant
AB  - density which appears on serial undiluted passage of the virus.  In fact, this
AB  - latter type of DNA was resistant to cleavage by HindIII and gave large amounts
AB  - of only two species of EcoRI fragments, suggesting that the defective molecules
AB  - consist of many tandem repeats of a small segment of viral DNA.  The
AB  - heterogeneity in the viral DNA of normal density appears to be related to the
AB  - structural organization of the molecules and does not necessarily imply
AB  - differences in genetic content.
ER  -

TY  - JOUR
AU  - Hazen, T.H.
AU  - Humphrys, M.S.
AU  - Ochieng, J.B.
AU  - Parsons, M.
AU  - Bopp, C.A.
AU  - O'Reilly, C.E.
AU  - Mintz, E.
AU  - Rasko, D.A.
TI  - Draft Genome Sequences of Nine Enteropathogenic Escherichia coli Strains from Kenya.
JO  - Genome Announcements
PY  - 2014
SP  - e00582
EP  - e00514
VL  - 2
AB  - We report here the draft genome sequences of nine enteropathogenic Escherichia coli (EPEC)
AB  - strains isolated from children in Kenya who died during
AB  - hospitalization with diarrhea. Each of the isolates possess the EPEC adherence
AB  - factor (EAF) plasmid encoding the bundle-forming pilus, which is characteristic
AB  - of EPEC. These isolates represent diverse serogroups and EPEC phylogenomic
AB  - lineages.
ER  -

TY  - JOUR
AU  - Hazen, T.H.
AU  - Mettus, R.T.
AU  - McElheny, C.L.
AU  - Bowler, S.L.
AU  - Doi, Y.
AU  - Rasko, D.A.
TI  - Draft Genome Sequences of blaKPC-Containing Enterobacter aerogenes, Citrobacter freundii, and Citrobacter koseri Strains.
JO  - Genome Announcements
PY  - 2018
SP  - e00035
EP  - e00018
VL  - 6
AB  - We report here the draft genome sequences of four blaKPC-containing bacteria identified as
AB  - Klebsiella aerogenes, Citrobacter freundii, and Citrobacter koseri
AB  - Additionally, we report the draft genome sequence of a K. aerogenes strain that
AB  - did not contain a blaKPC gene but was isolated from the patient who had the
AB  - blaKPC-2-containing K. aerogenes strain.
ER  -

TY  - JOUR
AU  - Hazen, T.H.
AU  - Robinson, G.L.
AU  - Harris, A.D.
AU  - Rasko, D.A.
AU  - Johnson, J.K.
TI  - Genome Sequence of Klebsiella oxytoca 11492-1, a Nosocomial Isolate Possessing a  FOX-5 AmpC beta-Lactamase.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3028
EP  - 3029
VL  - 194
AB  - Klebsiella oxytoca strain 11492-1 was isolated from a perianal swab culture from  a patient at
AB  - the University of Maryland Medical Center in 2005. The K. oxytoca 11492-1 draft genome
AB  - contains multiple antibiotic resistance genes, including a FOX-5 AmpC beta-lactamase encoded
AB  - on a large IncA/C plasmid.
ER  -

TY  - JOUR
AU  - Hazen, T.H.
AU  - Sahl, J.W.
AU  - Fraser, C.M.
AU  - Donnenberg, M.S.
AU  - Scheutz, F.
AU  - Rasko, D.A.
TI  - Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates.
JO  - Genome Announcements
PY  - 2013
SP  - e00516
EP  - e00513
VL  - 1
AB  - We report the draft genome sequences of three enteropathogenic Escherichia coli (EPEC)
AB  - isolates that display the O157 serogroup but do not have the Shiga toxin
AB  - genes (stx), which are characteristic of O157 enterohemorrhagic E. coli (EHEC).
AB  - E. coli strain RN587/1 has the O157:H8 serotype and possesses the EAF plasmid
AB  - characteristic of typical EPEC (J. B. Kaper, J. P. Nataro, and H. L. Mobley, Nat.
AB  - Rev. Microbiol. 2:123-140, 2004). The other two isolates, strains C844-97 and
AB  - C639-08, are both O157:H45 and possess the locus of enterocyte effacement (LEE)
AB  - pathogenicity island; however, they do not contain the EAF plasmid or the
AB  - stx-carrying phage.
ER  -

TY  - JOUR
AU  - Hazen, T.H.
AU  - Sahl, J.W.
AU  - Redman, J.C.
AU  - Morris, C.R.
AU  - Daugherty, S.C.
AU  - Chibucos, M.C.
AU  - Sengamalay, N.A.
AU  - Fraser-Liggett, C.M.
AU  - Steinsland, H.
AU  - Whittam, T.S.
AU  - Whittam, B.
AU  - Manning, S.D.
AU  - Rasko, D.A.
TI  - Draft Genome Sequences of the Diarrheagenic Escherichia coli Collection.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3026
EP  - 3027
VL  - 194
AB  - We report the draft genome sequences of the collection referred to as the Escherichia coli
AB  - DECA collection, which was assembled to contain representative isolates of the 15 most common
AB  - diarrheagenic clones in humans
AB  - (http://shigatox.net/new/). These genomes represent a valuable resource to the community of
AB  - researchers who examine these enteric pathogens.
ER  -

TY  - JOUR
AU  - Hazen, T.H.
AU  - Wu, D.
AU  - Eisen, J.A.
AU  - Sobecky, P.A.
TI  - Sequence Characterization and Comparative Analysis of Three Plasmids Isolated from Environmental Vibrio spp.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 7703
EP  - 7710
VL  - 73
AB  - The horizontal transfer of genes by mobile genetic elements such as
AB  - plasmids and phages can accelerate genome diversification of Vibrio spp.,
AB  - affecting their physiology, pathogenicity, and ecological character. In
AB  - this study, sequence analysis of three plasmids from Vibrio spp.
AB  - previously isolated from salt marsh sediment revealed the remarkable
AB  - diversity of these elements. Plasmids p0908 (81.4 kb), p23023 (52.5 kb),
AB  - and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding
AB  - sequences and G+C contents of 49.2%, 44.7%, and 42.4%, respectively. A
AB  - phylogenetic tree based on concatenation of the host 16S rRNA and rpoA
AB  - nucleotide sequences indicated p23023 and p09022 were isolated from
AB  - strains most closely related to V. mediterranei and V. campbellii,
AB  - respectively, while the host of p0908 forms a clade with V. fluvialis and
AB  - V. furnissii. Many predicted proteins had amino acid identities to
AB  - proteins of previously characterized phages and plasmids (24 to 94%).
AB  - Predicted proteins with similarity to chromosomally encoded proteins
AB  - included RecA, a nucleoid-associated protein (NdpA), a type IV helicase
AB  - (UvrD), and multiple hypothetical proteins. Plasmid p0908 had striking
AB  - similarity to enterobacteria phage P1, sharing genetic organization and
AB  - amino acid identity for 23 predicted proteins. This study provides
AB  - evidence of genetic exchange between Vibrio plasmids, phages, and
AB  - chromosomes among diverse Vibrio spp.
ER  -

TY  - JOUR
AU  - He, H.
AU  - Deng, M.
AU  - He, J.
AU  - Weng, S.
TI  - Structure and sequence analysis of cytosine DNA methyltransferase gene form infectious spleen and kidney necrosis virus.
JO  - Bingdu Xuebao
PY  - 2001
SP  - 349
EP  - 355
VL  - 17
AB  - In the infectious spleen and kidney necrosis virus genome, an iridovirus, we have identified
AB  - an open reading frame whose deduced amino acid sequence contains motifs characteristic of
AB  - cytosine DNA methyltransferases.  The ORF consists of 684bp which codes for a protein of 227
AB  - aa with a predicted molecular mass of 25,855 Da. Compared with some MTases found in bacteria,
AB  - ISKNV MTase ORF contains the first four highly conserved  motifs of cytosine MTase, but the
AB  - motif, responsible for DNA binding specificity, is missing.  Compared with 6 vertebrate
AB  - iridoviruses, ISKNV is considered as a new group of Iridoviridae.  Partial sequences of 7
AB  - vertebrate iridovirus MTases are highly conserved, they can be used to design primers to
AB  - identify vertebrate iridovirus by PCR method.
ER  -

TY  - JOUR
AU  - He, J.
AU  - Shao, X.
AU  - Zheng, H.
AU  - Li, M.
AU  - Wang, S.
AU  - Zhang, Q.
AU  - Li, L.
AU  - Liu, Z.
AU  - Sun, M.
AU  - Wang, S.
AU  - Yu, Z.
TI  - The Complete Genome Sequence of Bacillus thuringiensis Mutant Strain BMB171.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4074
EP  - 4075
VL  - 192
AB  - Bacillus thuringiensis is widely used as biopesticide for a long time. Here we report the
AB  - finished and annotated genome sequence of B.
AB  - thuringiensis mutant strain BMB171, a crystalliferous mutant strain
AB  - obtained and stocked in our laboratory, with a high transformation
AB  - frequency.
ER  -

TY  - JOUR
AU  - He, J.
AU  - Sundararajan, A.
AU  - Devitt, N.P.
AU  - Schilkey, F.D.
AU  - Ramaraj, T.
AU  - Melancon, C.E.I.I.I.
TI  - Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology.
JO  - Genome Announcements
PY  - 2016
SP  - e00337
EP  - e00316
VL  - 4
AB  - Here, we report the complete genome sequence of Streptomyces venezuelae ATCC 15439, a producer
AB  - of the methymycin/pikromycin family of macrolide antibiotics
AB  - and a model host for natural product studies, obtained exclusively using PacBio
AB  - sequencing technology. The 9.03-Mbp genome harbors 8,775 genes and 11 polyketide
AB  - and nonribosomal peptide natural product gene clusters.
ER  -

TY  - JOUR
AU  - He, J.
AU  - Wang, J.
AU  - Yin, W.
AU  - Shao, X.
AU  - Zheng, H.
AU  - Li, M.
AU  - Zhao, Y.
AU  - Sun, M.
AU  - Wang, S.
AU  - Yu, Z.
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. chinensis strain CT-43.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3407
EP  - 3408
VL  - 193
AB  - Bacillus thuringiensis is widely used as agricultural biopesticide for a long time. As a
AB  - producing strain, B. thuringiensis subsp. chinensis strain
AB  - CT-43 has high toxin to lepidopterous and dipterous insects. It can form
AB  - various parasporal crystals consisting of Cry1Aa3, Cry1Ba1, Cry1Ia14,
AB  - Cry2Aa9, and Cry2Ab1. During fermentation, it simultaneously generates
AB  - vegetative insecticidal protein Vip3Aa10, as well as insecticidal
AB  - nucleotide analogue thuringiensin. Here we report the finished, annotated
AB  - genome sequence of B. thuringiensis strain CT-43.
ER  -

TY  - JOUR
AU  - He, J.G.
AU  - Deng, M.
AU  - Weng, S.P.
AU  - Li, Z.
AU  - Zhou, S.Y.
AU  - Long, Q.X.
AU  - Wang, X.Z.
AU  - Chan, S.M.
TI  - Complete genome analysis of the mandarin fish infectious spleen and kidney necrosis iridovirus.
JO  - Virology
PY  - 2001
SP  - 126
EP  - 139
VL  - 291
AB  - The nucleotide sequence of the infectious spleen and kidney necrosis virus
AB  - (ISKNV) genome was determined and found to comprise 111,362 bp with a G+C
AB  - content of 54.78%. It contained 124 potential open reading frames (ORFs)
AB  - with coding capacities ranging from 40 to 1208 amino acids. The analysis
AB  - of the amino acid sequences deduced from the individual ORFs revealed that
AB  - 35 of the 124 potential gene products of ISKNV show significant homology
AB  - to functionally characterized proteins of other species. Some of the
AB  - putative gene products of ISKNV showed significant homologies to proteins
AB  - in the GenBank/EMBL/DDBJ databases including enzymes and structural
AB  - proteins involved in virus replication, transcription, protein
AB  - modification, and virus-host interaction. In addition, one major repeated
AB  - sequence showing significant homology to the Red Sea bream iridovirus
AB  - (RSIV) genome was identified. Based on the information obtained from
AB  - biological properties (including histopathology, tissue tropisms, natural
AB  - host range, and geographic distribution), physiochemical and physical
AB  - properties, and genome analysis, we suggest that ISKNV, RSIV, sea bass
AB  - iridovirus, grouper iridovirus, and African lampeye iridovirus may belong
AB  - to a new genus of the Iridoviridae family and are tentatively referred to
AB  - as cell hypertrophy iridoviruses.
ER  -

TY  - JOUR
AU  - He, M. et al.
TI  - Evolutionary dynamics of Clostridium difficile over short and long time scales.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 7527
EP  - 7532
VL  - 107
AB  - Clostridium difficile has rapidly emerged as the leading cause of antibiotic-associated
AB  - diarrheal disease, with the transcontinental spread of
AB  - various PCR ribotypes, including 001, 017, 027 and 078. However, the genetic
AB  - basis for the emergence of C. difficile as a human pathogen is unclear. Whole
AB  - genome sequencing was used to analyze genetic variation and virulence of a
AB  - diverse collection of thirty C. difficile isolates, to determine both macro and
AB  - microevolution of the species. Horizontal gene transfer and large-scale
AB  - recombination of core genes has shaped the C. difficile genome over both short
AB  - and long time scales. Phylogenetic analysis demonstrates C. difficile is a
AB  - genetically diverse species, which has evolved within the last 1.1-85 million
AB  - years. By contrast, the disease-causing isolates have arisen from multiple
AB  - lineages, suggesting that virulence evolved independently in the highly epidemic
AB  - lineages.
ER  -

TY  - JOUR
AU  - He, P.
AU  - Hao, K.
AU  - Blom, J.
AU  - Rueckert, C.
AU  - Vater, J.
AU  - Mao, Z.
AU  - Wu, Y.
AU  - Hou, M.
AU  - He, P.
AU  - He, Y.
AU  - Borriss, R.
TI  - Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites.
JO  - J. Biotechnol.
PY  - 2012
SP  - 281
EP  - 291
VL  - 164
AB  - The plant-associated Bacillus amyloliquefaciens subsp. plantarum strain B9601-Y2, isolated
AB  - from wheat rhizosphere, is a powerful plant
AB  - growth-promoting rhizobacterium. Its relative large genome size of 4.24
AB  - Mbp, exceeding that of other representatives of the B.
AB  - amyloliquefaciens subsp. plantarum taxon, is mainly due to the presence
AB  - of 18 DNA-islands containing remnants of phages, a unique restriction
AB  - modification system, a gene cluster for mersacidin synthesis, and an
AB  - orphan gene cluster devoted to non-ribosomal synthesis of an
AB  - unidentified peptide. Like other members of the taxon, the Y2 genome
AB  - contains giant gene clusters for non-ribosomal synthesis of the
AB  - polyketides macrolactin, difficidin, and bacillaene, the antifungal
AB  - lipopeptides bacillomycin D, and fengycin, the siderophore
AB  - bacillibactin, and the dipeptide bacilysin. A gene cluster encoding
AB  - enzymes for a degradative pathway with 2-keto-3-deoxygluconate and
AB  - 2-keto-3-deoxy-phosphogluconate as intermediates was explored by genome
AB  - mining and found as being a unique feature for representatives of the
AB  - plantarum subspecies. A survey of the Y2 genome against other B.
AB  - amyloliquefaciens genomes revealed 130 genes only occurring in subsp.
AB  - plantarum but not in subsp. amyloliquefaciens. Notably, the surfactin
AB  - gene cluster is not functional due to a large deletion removing parts
AB  - of the Srf synthetases B and C. Expression of polyketides,
AB  - lipopeptides, mersacidin, and of the growth hormone indole-3-acetic
AB  - acid in Y2 was demonstrated by matrix-assisted laser desorption
AB  - ionization-time of flight mass spectroscopy and high-performance liquid
AB  - chromatography, respectively.
ER  -

TY  - JOUR
AU  - He, X.
AU  - Hull, V.
AU  - Thomas, J.A.
AU  - Fu, X.
AU  - Gidwani, S.
AU  - Gupta, Y.K.
AU  - Black, L.W.
AU  - Xu, S.Y.
TI  - Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference.
JO  - Sci. Rep.
PY  - 2015
SP  - 9747
EP  - 9747
VL  - 5
AB  - The first reported Type IV restriction endonuclease (REase) GmrSD consists of GmrS and GmrD
AB  - subunits. In most bacteria, however, the gmrS and gmrD genes are
AB  - fused together to encode a single-chain protein. The fused coding sequence for
AB  - ECSTEC94C_1402 from E. coli strain STEC_94C was expressed in T7 Express. The
AB  - protein designated as Eco94GmrSD displays modification-dependent ATP-stimulated
AB  - REase activity on T4 DNA with glucosyl-5-hydroxymethyl-cytosines (glc-5hmC) and
AB  - T4gt DNA with 5-hydroxymethyl-cytosines (5hmC). A C-terminal 6xHis-tagged protein
AB  - was purified by two-column chromatography. The enzyme is active in Mg(2+) and
AB  - Mn(2+) buffer. It prefers to cleave large glc-5hmC- or 5hmC-modified DNA. In
AB  - phage restriction assays, Eco94GmrSD weakly restricted T4 and T4gt, whereas T4
AB  - IPI*-deficient phage (Deltaip1) were restricted more than 10(6)-fold, consistent
AB  - with IPI* protection of E. coli DH10B from lethal expression of the closely
AB  - homologous E. coli CT596 GmrSD. Eco94GmrSD is proposed to belong to the
AB  - His-Asn-His (HNH)-nuclease family by the identification of a putative C-terminal
AB  - REase catalytic site D507-H508-N522. Supporting this, GmrSD variants D507A,
AB  - H508A, and N522A displayed no endonuclease activity. The presence of a large
AB  - number of fused GmrSD homologs suggests that GmrSD is an effective phage
AB  - exclusion protein that provides a mechanism to thwart T-even phage infection.
ER  -

TY  - JOUR
AU  - He, X.
AU  - Ou, H.Y.
AU  - Yu, Q.
AU  - Zhou, X.
AU  - Wu, J.
AU  - Liang, J.
AU  - Zhang, W.
AU  - Rajakumar, K.
AU  - Deng, Z.
TI  - Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related  bacteria.
JO  - Mol. Microbiol.
PY  - 2007
SP  - 1034
EP  - 1048
VL  - 65
AB  - The complete sequence (92 770 bp) of a genomic island (GI) named SLG from Streptomyces
AB  - lividans 66, encoding a novel DNA S-modification system (dnd), was
AB  - determined. Its overall G+C content was 67.8%, lower than those of three
AB  - sequenced Streptomyces genomes. Among 85 predicted open reading frames (ORFs) in
AB  - SLG, 22 ORFs showed little homology with previously known proteins. SLG displays
AB  - a mosaic structure composed of four modules, indicative of multiple recombination
AB  - events in its formation. Spontaneous excision and circularization of SLG was
AB  - observed, and the excision rate appeared to be induced at least fivefold by MNNG
AB  - exposure. Using constructed mini-islands of SLG, we demonstrated that Slg01, a
AB  - P4-like integrase, was sufficient to promote SLG integration, excision and
AB  - circularization. Eleven counterpart dnd clusters, which also mapped to GIs in 10
AB  - chromosomes and a plasmid, were found in taxonomically unrelated bacterial
AB  - species from various geographic niches. Additionally, c. 10% of actinomycetes
AB  - were found to possess a dnd cluster in a survey involving 74 strains. Comparison
AB  - of dnd clusters in the 12 bacteria strongly suggests that these dnd-bearing
AB  - elements might have evolved from a common ancestor similar to plasmid-originated
AB  - chromosome II of Pseudoalteromonas haloplanktis TAC125.
ER  -

TY  - JOUR
AU  - He, Y.
AU  - Wei, K.
AU  - Si, K.
AU  - Mathieu, J.
AU  - Li, M.
AU  - Alvarez, P.J.J.
TI  - Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06.
JO  - Genome Announcements
PY  - 2017
SP  - e00625
EP  - e00617
VL  - 5
AB  - We report here the complete genome sequence of Mycobacterium dioxanotrophicus PH-06, which is
AB  - capable of using 1,4-dioxane as a sole source of carbon and
AB  - energy. The reported sequence will enable the elucidation of this novel metabolic
AB  - pathway and the development of molecular biomarkers to assess bioremediation
AB  - potential at contaminated sites.
ER  -

TY  - JOUR
AU  - He, Y.
AU  - Yan, X.
AU  - Reed, S.
AU  - Xie, Y.
AU  - Chen, C.Y.
AU  - Irwin, P.
TI  - Complete Genome Sequence of Campylobacter jejuni YH001 from Beef Liver, Which Contains a Novel Plasmid.
JO  - Genome Announcements
PY  - 2015
SP  - e01492
EP  - e01414
VL  - 3
AB  - Campylobacter jejuni, commonly found in poultry and meat products, causes gastroenteritis in
AB  - humans. Here, we report the complete genome sequence of a C.
AB  - jejuni strain, YH001, isolated from retail beef liver. The genome is 1,712,361 bp
AB  - and has a 30.5% G+C content and two plasmids of 46.5 kb and 4.4 kb.
ER  -

TY  - JOUR
AU  - He, Z.
AU  - Crist, M.
AU  - Yen, H.-C.
AU  - Duan, X.
AU  - Quiocho, F.A.
AU  - Gimble, F.S.
TI  - Amino acid residues in both the protein splicing and endonuclease domains of the PI-SceI intein mediate DNA binding.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 4607
EP  - 4615
VL  - 273
AB  - A structure-based model describing the interaction of the two-domain PI-SceI endonuclease with
AB  - its 31-base pair DNA substrate suggests that the endonuclease domain (domain II) contacts the
AB  - cleavage site region of the substrate, while the protein splicing domain (domain I) interacts
AB  - with a distal region that is sufficient for high affinity binding.  To support this model,
AB  - alanine-scanning mutagenesis was used to assemble a set of 49 PI-SceI mutant proteins that
AB  - were purified and assayed for their DNA binding and cleavage properties.  Fourteen mutant
AB  - proteins were 4- to >500-fold less active than wild-type PI-SceI in cleavage assays, and one
AB  - mutant (T225A) was 3-fold more active.  Alanine substitution at two positions in domain I
AB  - reduces overall binding >60-fold by perturbing the interaction of PI-SceI with the minimal
AB  - binding region.  Conversely, mutations in domain II have little effect on binding, reduce
AB  - binding to the cleavage site region only, or affect binding to both regions.  Interestingly,
AB  - substitutions at Lys301, which is part of the endonucleolytic active site, eliminate binding
AB  - to the cleavage site region but permit contact with the minimal binding region.  This
AB  - experimental evidence demonstrates that the protein splicing domain as well as the
AB  - endonuclease domain is involved in binding of a DNA substrate with the requisite length.
ER  -

TY  - JOUR
AU  - He, Z.
AU  - Jiang, X.
AU  - Xue, J.
AU  - Zheng, W.
TI  - Purification of BamHI DNA methylase and protection function of DNA methylation against restriction endonuclease BamHI.
JO  - Weishengwuxue Tongbao
PY  - 1989
SP  - 217
EP  - 220
VL  - 16
AB  - None
ER  -

TY  - JOUR
AU  - Heard, E.
AU  - Fried, M.
TI  - The use of 5-azacytidine to increase cleavage of methylation sensitive rare cutting restriction enzymes sites in amplified DNA.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6147
EP  - 6148
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Heath, P.J.
AU  - Stephens, K.M.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - The structure of I-Crel, a group I intron-encoded homing endonuclease.
JO  - Nat. Struct. Biol.
PY  - 1997
SP  - 468
EP  - 476
VL  - 4
AB  - The structure of I-Crel provides the first view of a protein encoded by a gene within an
AB  - intron. This endonuclease recognizes a long DNA site approximately 20 base pairs in length and
AB  - facilitates the lateral transfer of that intron. The protein exhibits a DNA-binding surface
AB  - consisting of four antiparallel beta-strands that form a 20 A wide groove which is over 70 A
AB  - long. The architecture of this fold is different from that of the TATA binding protein, TBP,
AB  - which also contains an antiparallel beta-saddle. The conserved LAGLIDADG motif, which is found
AB  - in many mobile intron endonucleases, maturases and inteins, forms a novel helical interface
AB  - and contributes essential residues to the active site.
ER  -

TY  - JOUR
AU  - Heather, Z.
AU  - Holden, M.T.
AU  - Steward, K.F.
AU  - Parkhill, J.
AU  - Song, L.
AU  - Challis, G.L.
AU  - Robinson, C.
AU  - Davis-Poynter, N.
AU  - Waller, A.S.
TI  - A novel streptococcal integrative conjugative element involved in iron acquisition.
JO  - Mol. Microbiol.
PY  - 2008
SP  - 1274
EP  - 1292
VL  - 70
AB  - In this study, we determined the function of a novel non-ribosomal peptide
AB  - synthetase (NRPS) system carried by a streptococcal integrative
AB  - conjugative element (ICE), ICESe2. The NRPS shares similarity with the
AB  - yersiniabactin system found in the high-pathogenicity island of Yersinia
AB  - sp. and is the first of its kind to be identified in streptococci. We
AB  - named the NRPS product 'equibactin' and genes of this locus eqbA-N.
AB  - ICESe2, although absolutely conserved in Streptococcus equi, the causative
AB  - agent of equine strangles, was absent from all strains of the closely
AB  - related opportunistic pathogen Streptococcus zooepidemicus. Binding of
AB  - EqbA, a DtxR-like regulator, to the eqbB promoter was increased in the
AB  - presence of cations. Deletion of eqbA resulted in a small-colony
AB  - phenotype. Further deletion of the irp2 homologue eqbE, or the genes eqbH,
AB  - eqbI and eqbJ encoding a putative ABC transporter, or addition of the iron
AB  - chelator nitrilotriacetate, reversed this phenotype, implicating iron
AB  - toxicity. Quantification of (55)Fe accumulation and sensitivity to
AB  - streptonigrin suggested that equibactin is secreted by S. equi and that
AB  - the eqbH, eqbI and eqbJ genes are required for its associated iron import.
AB  - In agreement with a structure-based model of equibactin synthesis,
AB  - supplementation of chemically defined media with salicylate was required
AB  - for equibactin production.
ER  -

TY  - JOUR
AU  - Heaton, M.P.
AU  - Harhay, G.P.
AU  - Smith, T.P.
AU  - Bono, J.L.
AU  - Chitko-McKown, C.G.
TI  - Complete Closed Genome Sequences of a Mannheimia haemolytica Serotype A1 Leukotoxin Deletion Mutant and Its Wild-Type Parent Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00417
EP  - e00415
VL  - 3
AB  - Mannheimia haemolytica is a bacterial pathogen that secretes leukotoxin (LktA) which binds to
AB  - leukocyte membranes via CD18, causing bacterial pneumonia in
AB  - ruminants. We report the complete closed genome sequences of a leukotoxin mutant
AB  - and its parent strain that are frequently used in respiratory disease studies.
ER  -

TY  - JOUR
AU  - Heavens, D.
AU  - Tailford, L.E.
AU  - Crossman, L.
AU  - Jeffers, F.
AU  - Mackenzie, D.A.
AU  - Caccamo, M.
AU  - Juge, N.
TI  - Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4015
EP  - 4016
VL  - 193
AB  - Lactobacillus reuteri inhabiting the gastrointestinal tract of a range of vertebrates is a
AB  - true symbiont with established beneficial effects to the host. Here we describe the draft
AB  - genome of L. reuteri ATCC 53608 strain isolated from pig. The genome sequence provides
AB  - important insights into the evolutionary changes underlying host specialisation.
ER  -

TY  - JOUR
AU  - Hebert, E.M.
AU  - Raya, R.R.
AU  - Brown, L.
AU  - Font-de-Valdez, G.
AU  - Savoy-de-Giori, G.
AU  - Taranto, M.P.
TI  - Genome Sequence of the Cheese-Starter Strain Lactobacillus delbrueckii subsp. lactis CRL 581.
JO  - Genome Announcements
PY  - 2013
SP  - e00602
EP  - e00613
VL  - 1
AB  - We report the genome sequence of Lactobacillus delbrueckii subsp. lactis CRL 581  (1,911,137
AB  - bp, GC 49.7%), a proteolytic strain isolated from a homemade
AB  - Argentinian hard cheese which has a key role in bacterial nutrition and releases
AB  - bioactive health-beneficial peptides from milk proteins.
ER  -

TY  - JOUR
AU  - Hebert, E.M.
AU  - Saavedra, L.
AU  - Taranto, M.P.
AU  - Mozzi, F.
AU  - Magni, C.
AU  - Nader, M.E.
AU  - Font-de-Valdez, G.
AU  - Sesma, F.
AU  - Vignolo, G.
AU  - Raya, R.R.
TI  - Genome Sequence of the Bacteriocin-Producing Lactobacillus curvatus Strain CRL705.
JO  - J. Bacteriol.
PY  - 2012
SP  - 538
EP  - 539
VL  - 194
AB  - Lactobacillus curvatus is one of the most prevalent lactic acid bacteria found in fermented
AB  - meat products. Here, we present the draft genome
AB  - sequence of Lactobacillus curvatus CRL705, a bacteriocin producer strain
AB  - isolated from an Argentinean artisanal fermented sausage, which consists
AB  - of 1,833,251 bp (GC content, 41.9%) and two circular plasmids of 12,342 bp
AB  - (pRC12; GC, 43.9%) and 18,664 bp (pRC18; GC, 34.4%).
ER  -

TY  - JOUR
AU  - Hebert, L.
AU  - Moumen, B.
AU  - Duquesne, F.
AU  - Breuil, M.F.
AU  - Laugier, C.
AU  - Batto, J.M.
AU  - Renault, P.
AU  - Petry, S.
TI  - Genome sequence of Taylorella equigenitalis MCE9, the causative agent of contagious equine metritis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1785
EP  - 1785
VL  - 193
AB  - Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a
AB  - sexually-transmitted infection of horses. We herein report the genome sequence of T.
AB  - equigenitalis strain MCE9, isolated in 2005 from the urethral fossa of a 4-year-old stallion
AB  - in France.
ER  -

TY  - JOUR
AU  - Hebert, L.
AU  - Touzain, F.
AU  - de Boisseson, C.
AU  - Breuil, M.F.
AU  - Duquesne, F.
AU  - Laugier, C.
AU  - Blanchard, Y.
AU  - Petry, S.
TI  - Draft Genome Sequence of Taylorella equigenitalis Strain MCE529, Isolated from a  Belgian Warmblood Horse.
JO  - Genome Announcements
PY  - 2014
SP  - e01214
EP  - e01214
VL  - 2
AB  - Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a
AB  - sexually transmitted infection of horses. We herein report the genome
AB  - sequence of T. equigenitalis strain MCE529, isolated in 2009 from the urethral
AB  - fossa of a 15-year-old Belgian Warmblood horse in France.
ER  -

TY  - JOUR
AU  - Hedges, R.W.
TI  - Phenotypic characterization of fi- R factors determining the restriction and modification hspII specificity.
JO  - Mol. Gen. Genet.
PY  - 1972
SP  - 225
EP  - 233
VL  - 115
AB  - All known determinants of the restriction, modification specificity hspII are
AB  - plasmids of the compatibility class N.  Two I-like R factors, R56 and R64 are
AB  - able to interfere with the lytic cycle of phage lambda (in liberation of phage
AB  - by lysogens or newly infected cells) by a different mechanism.
ER  -

TY  - JOUR
AU  - Hedges, R.W.
AU  - Datta, N.
TI  - R124, an fi+ R factor of a new compatibility class.
JO  - J. Gen. Microbiol.
PY  - 1972
SP  - 403
EP  - 405
VL  - 71
AB  - The plasmids of Gram-negative bacteria can be classified as fi+ or fi-
AB  - (Watanabe et al. 1964).  The former are capable of repressing the fertility
AB  - functions, notably the production of sex pili, determined by the F factor
AB  - (Nishimura, Ishibashi, Meynell & Hirota, 1967).  Most fi+ plasmids carry genes
AB  - determining the production of sex pili similar to those determined by the F
AB  - factor (F-like pili) in antigenic specificity and phage adsorption (Meynell &
AB  - Datta, 1966; Lawn & Meynell, 1970; Dennison & Hedges, 1972).  Among the fi-
AB  - plasmids a number of compatibility classes has been described (Watanabe, 1968;
AB  - Datta & Hedges, 1971; Datta et al. 1971; Hedges & Datta, 1971).  Two plasmids
AB  - belonging to the same compatibility class cannot stably co-exisit in a single
AB  - cell.  Among the fi+ plasmids four compatibility classes have been described,
AB  - three of which we propose to name as follows:  FI, the class including F,
AB  - ColV2, ColV3 (MacFarren & Clowes, 1967) and R386 (Dennison, 1972); FII, the
AB  - class including RI and many other fi+ R factors (Meynell, Meynell & Datta,
AB  - 1968); FIII, the class including ColB-K98 and ColB-K166 (Frydman & Meynell,
AB  - 1969); fourthly, the class including R62 (R62, though fi+, determines I-like
AB  - pili and has the compatibility of a typical I-like plasmid) (lawn, Meynell,
AB  - Meynell & Datta, 1967; N. Datta & R.W. Hedges, unpublished).  R124 is an fi+ R
AB  - factor carrying tetracycline resistance and specifying F-like pili (Meynell &
AB  - Datta, 1966).  It is the only fi+ R factor carrying tetracycline resistance and
AB  - specifying F-like pili (Meynell & Datta, 1966).  It is the only fi+ R factor so
AB  - far tested to determine restriction and modification of a number of DNA phages
AB  - including lambda.  The specificity of this restriction, which is unique, is
AB  - termed hsp I (Bannister & Glover, 1968).  Among the fi- R factors, all those
AB  - capable of restriction or modification fall into a single compatibility group N
AB  - (Hedges, 1972) and it seemed interesting to determine the compatibility
AB  - specificity of R124.  In this paper we show that this plasmid co-exists stably
AB  - with members of all the compatibility groups listed above and is thus the first
AB  - example of a new compatibility group, FIV.
ER  -

TY  - JOUR
AU  - Hedgpeth, J.
AU  - Boyer, H.W.
TI  - Hydrolysis of adenosine triphosphate accompanying interaction between Escherichia coli B restriction endonuclease and unmodified deoxyribonucleic acid.
JO  - Biochim. Biophys. Acta
PY  - 1973
SP  - 310
EP  - 317
VL  - 331
AB  - The Escherichia coli B restriction endonuclease hydrolyzes ATP to ADP and Pi in
AB  - the presence of unmodified, double-strand DNA and Mg2+.  The requirements for
AB  - maximum ATP hydrolysis are essentially the same as those for phosphodiester
AB  - bond cleavage.  However, ATP is hydrolyzed under conditions where
AB  - phosphodiester bond cleavage is prevented, namely, in the absence of
AB  - S-adenosyl-L-methionine and in the presence of DNA which is resistant to the
AB  - endonuclease by virtue of mutations.  ATP is shown to be necessary for the
AB  - formation of the endonuclease-unmodified DNA complex.
ER  -

TY  - JOUR
AU  - Hedgpeth, J.
AU  - Goodman, H.M.
AU  - Boyer, H.W.
TI  - DNA nucleotide sequence restricted by the RI Endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3448
EP  - 3452
VL  - 69
AB  - The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by
AB  - the RI restriction endonuclease in unmodified DNA from coliphage lambda has
AB  - been determined.  The 5'-terminal nucleotide labeled with 32P and
AB  - oligonucleotides up to the heptamer were analyzed from a pancreatic DNase
AB  - digest.  The following sequence of nucleotides adjacent to the RI break made in
AB  - lambda DNA was deduced from these data and from the 3'-dinucleotide sequence
AB  - and nearest-neighbor analysis obtained from repair synthesis with the DNA
AB  - polymerase of Rous sarcoma virus 5'....A/TpG^pApApTpTpCpT/A....3'
AB  - 3'....T/ApCpTpTpApAp^GpA/T....5' The RI endonuclease cleavage of the
AB  - phosphodiester bonds (indicated by arrows) generates 5'-phosphodiester bonds
AB  - (indicated by arrows) generates 5'-phosphoryls and short cohesive termini of
AB  - four nucleotides, pApApTpT.  The most striking feature of the sequence is its
AB  - symmetry.
ER  -

TY  - JOUR
AU  - Hedlund, B.P. et al.
TI  - High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism.
JO  - Genome Announcements
PY  - 2015
SP  - e01410
EP  - e01415
VL  - 3
AB  - The draft genome of Kallotenue papyrolyticum JKG1(T), a member of the order Kallotenuales,
AB  - class Chloroflexia, consists of 4,475,263 bp in 4 contigs and
AB  - encodes 4,010 predicted genes, 49 tRNA-encoding genes, and 3 rRNA operons. The
AB  - genome is consistent with a heterotrophic lifestyle including catabolism of
AB  - polysaccharides and amino acids.
ER  -

TY  - JOUR
AU  - Hegna, I.K.
AU  - Bratland, H.
AU  - Kolsto, A.
TI  - BceS1, a new addition to the type III restriction and modification family.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 189
EP  - 193
VL  - 202
AB  - The nucleotide sequence of an 11-kb chromosomal BglII fragment from Bacillus cereus American
AB  - Type Culture Collection (ATCC) 10987 strain revealed two closely adjacent open reading frames
AB  - organized in an operon, of which the deduced amino acids showed identity to the type III
AB  - restriction and modification (R/M) subunits described in Gram-negative bacteria. An enhanced
AB  - transcription level was revealed when the culture was grown in the presence of foreign DNA. A
AB  - cell-free extract from this culture restricted pUC19, whereas from a plain medium the
AB  - restriction was very weak. The in vitro methylation protected pUC 19 from restriction. The R/M
AB  - system was designated BceS1 as this endonuclease required ATP and Mg(2+) as cofactors like
AB  - other type III endonucleases. BceS1 is the first chromosomal type III R/M system characterized
AB  - in a Gram-positive bacterium.
ER  -

TY  - JOUR
AU  - Hegna, I.K.
AU  - Karlstrom, E.S.
AU  - Lopez, R.
AU  - Kristensen, T.
AU  - Kolsto, A.-B.
TI  - A type-II DNA restriction and modification system in Bacillus cereus?
JO  - Gene
PY  - 1992
SP  - 149
EP  - 150
VL  - 114
AB  - The deduced amino acid (aa) sequence of an open reading frame, present on a fragment of the
AB  - Bacillus cereus ATCC10987 geneome, shows 29.3% identity within a 368-aa segment of the
AB  - type-III EcoPI modification and restriction operon.
ER  -

TY  - JOUR
AU  - Hehlmann, R.
AU  - Hattman, S.
TI  - Mutants of bacteriophage T2 gt with altered DNA methylase activity.
JO  - J. Mol. Biol.
PY  - 1972
SP  - 351
EP  - 360
VL  - 67
AB  - Certain non-glucosylated (gt) T-even bacteriophage mutants are restricted by
AB  - prophage P1 (these are designated rP1).  Unrestricted mutants (uP1) have been
AB  - shown earlier to contain hypermethylated DNA compared to their rP1 parent.  The
AB  - DNA methylating enzyme induced by rP1 and uP1 phage has been partially purified
AB  - by affinity chromatography on DNA cellulose. Both rP1 and uP1 methylase
AB  - methylate adenine exclusively.  The uP1 methylase shows a greater thermal
AB  - lability than the rP1 enzyme; both enzymic forms are stabilized against heat
AB  - inactivation in the presence of substrate S-adenosylmethionine.  In terms of
AB  - their ability to methylate non-viral cytosine-containing DNA's, rP1 and uP1
AB  - methylase exhibit similar Km values and extents of methylation.  However, the
AB  - uP1 methylase shows a higher affinity (lowered Km) and greater site recognition
AB  - (higher extent of methylation) than the rP1 methylase with various T-even phage
AB  - (5-hydroxymethylcytosine-containing) DNA's.  These results are consistent with
AB  - the notion that mutation from rP1 to uP1 produces an alteration in the
AB  - viral-induced DNA methylase.
ER  -

TY  - JOUR
AU  - Heidelberg, J.F. et al.
TI  - DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
JO  - Nature
PY  - 2000
SP  - 477
EP  - 483
VL  - 406
AB  - Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium
AB  - Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two
AB  - circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading
AB  - frames. The vast majority of recognizable genes for essential cell functions (such as DNA
AB  - replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for
AB  - example, toxins, surface antigens and adhesins) are located on the large chromosome. In
AB  - contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared
AB  - with the large chromosome (42%), and also contains many more genes that appear to have origins
AB  - other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system
AB  - (the integron island) and host 'addiction' genes that are typically found on plasmids; thus,
AB  - the small chromosome may have originally been a megaplasmid that was captured by an ancestral
AB  - Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding
AB  - how a free-living, environmental organism emerged to become a significant human bacterial
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Heidelberg, J.F. et al.
TI  - Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
JO  - Nat. Biotechnol.
PY  - 2002
SP  - 1118
EP  - 1123
VL  - 20
AB  - Shewanella oneidensis is an important model organism for bioremediation studies because of its
AB  - diverse respiratory capabilities, conferred in part by multicomponent, branched electron
AB  - transport systems. Here we report the sequencing of the S. oneidensis genome, which consists
AB  - of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open
AB  - reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first
AB  - Shewanella lambda-like phage, providing a potential tool for further genome engineering.
AB  - Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S.
AB  - oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the
AB  - electron transport system. This genome sequence represents a critical step in the elucidation
AB  - of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and
AB  - chromium (Cr), and offers a starting point for defining this organism's complex electron
AB  - transport systems and metal ion-reducing capabilities.
ER  -

TY  - JOUR
AU  - Heidmann, S.
AU  - Seifert, W.
AU  - Kessler, C.
AU  - Domdey, H.
TI  - Cloning, characterization and heterologous expression of the SmaI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9783
EP  - 9796
VL  - 17
AB  - The genes coding for the class-II Serratia marcescens restriction-modification
AB  - system have been cloned and expressed in E. coli.  Recombinant clones
AB  - restricted incoming phage only poorly; the recombinant plasmids, however,
AB  - became fully modified in vivo, i.e. completely resistant against digestion with
AB  - R.SmaI.  The determined nucleotide sequence of the cloned system revealed three
AB  - open reading frames with lengths of 252 bp, 741 bp, and 876 bp.  Through
AB  - various deletion experiments and an insertion-mutation experiment the 876 bp
AB  - open reading frame could be assigned to the SmaI DNA modification enzyme and
AB  - the 741 bp open reading frame to the SmaI restriction endonuclease.  Mapping of
AB  - the transcription start sites of the genes revealed that the SmaI endonuclease
AB  - is transcribed as a polycistronic mRNA together with a 252 bp long preceding
AB  - open reading frame of unknown function.  No homology was found when comparing
AB  - the amino acid sequence of M.SmaI with the published sequences of m5C-specific
AB  - DNA modification methyltransferases.  On the other hand, a stretch of 14 amino
AB  - acids in the C-proximal region of M.SmaI shows a signficant homology to the
AB  - C-proximal amino acid sequences of the N6A-methyltransferases M.HinfI and
AB  - M.DpnIIA and the N4C-methyltransferase M.PvuII.
ER  -

TY  - JOUR
AU  - Heikal, A.
AU  - Samuelsen, O.
AU  - Kristensen, T.
AU  - Okstad, O.A.
TI  - Complete Genome Sequence of a Multidrug-Resistant, blaNDM-1-Expressing Klebsiella pneumoniae K66-45 Clinical Isolate from Norway.
JO  - Genome Announcements
PY  - 2017
SP  - e00601
EP  - e00617
VL  - 5
AB  - Multidrug-resistant Klebsiella pneumoniae is a major cause of hospital-acquired infections.
AB  - Here, we report the complete genome sequence of the
AB  - multidrug-resistant, blaNDM-1-positive strain K. pneumoniae K66-45, isolated from
AB  - a hospitalized Norwegian patient.
ER  -

TY  - JOUR
AU  - Heil, J.R.
AU  - Lynch, M.D.J.
AU  - Cheng, J.
AU  - Matysiakiewicz, O.
AU  - D'Alessio, M.
AU  - Charles, T.C.
TI  - The Completed PacBio Single-Molecule Real-Time Sequence of Methylosinus trichosporium Strain OB3b Reveals the Presence of a Third Large Plasmid.
JO  - Genome Announcements
PY  - 2017
SP  - e01349
EP  - e01317
VL  - 5
AB  - Presented here is the complete genome sequence of the well-studied Rhizobiales methanotroph
AB  - Methylosinus trichosporium strain OB3b. The assembly contains
AB  - 5,183,433 bp, corresponding to a chromosome of 4,508,832 bp and three circular
AB  - plasmids of 285,280 bp, 209,102 bp, and 180,219 bp.
ER  -

TY  - JOUR
AU  - Heininger, K.
AU  - Horz, W.
AU  - Zachau, H.G.
TI  - Specificity of cleavage by a restriction nuclease from Bacillus subtilis.
JO  - Gene
PY  - 1977
SP  - 291
EP  - 303
VL  - 1
AB  - The restriction nuclease from B. subtilis (Bsu) which cleaves in the middle of
AB  - the tetra-nucleotide sequence 5'-GGCC-3'	 3'-CCGG-5' has been found to decrease
AB  - its substrate specificity at high nuclease concentrations.  There are special
AB  - conditions, high pH, low ionic strength, and high glycerol contents, which
AB  - strongly enhance splitting with decreased specificity and also lead to
AB  - splitting of single-stranded DNA.  By sequence analyses it is shown that the
AB  - reduction in specificity of Bsu corresponds to cleavage predominantly at
AB  - 5'-GC-3' 3'-CG-5' sequences.  No comparable change in specificity has been
AB  - observed in a restriction nuclease from Haemophilus aegyptius (HaeIII), an
AB  - isoschizomer of Bsu.
ER  -

TY  - JOUR
AU  - Heinl, S.
AU  - Wibberg, D.
AU  - Eikmeyer, F.
AU  - Szczepanowski, R.
AU  - Blom, J.
AU  - Linke, B.
AU  - Goesmann, A.
AU  - Grabherr, R.
AU  - Schwab, H.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage.
JO  - J. Biotechnol.
PY  - 2012
SP  - 153
EP  - 166
VL  - 161
AB  - Lactobacillus buchneri belongs to the group of heterofermentative lactic acid
AB  - bacteria and is a common member of the silage microbiome. Here we report the
AB  - completely annotated genomic sequence of L. buchneri CD034, a strain isolated
AB  - from stable grass silage. The whole genome of L. buchneri CD034 was sequenced on
AB  - the Roche Genome Sequencer FLX platform. It was found to consist of four
AB  - replicons, a circular chromosome, and three plasmids. The circular chromosome was
AB  - predicted to encode 2319 proteins and contains a genomic island and two prophages
AB  - which significantly differ in G+C-content from the remaining chromosome. It
AB  - possesses all genes for enzymes of a complete phosphoketolase pathway, whereas
AB  - two enzymes necessary for glycolysis are lacking. This confirms the
AB  - classification of L. buchneri CD034 as an obligate heterofermentative lactic acid
AB  - bacterium. A set of genes considered to be involved in the lactate degradation
AB  - pathway and genes putatively involved in the breakdown of plant cell wall
AB  - polymers were identified. Moreover, several genes encoding putative S-layer
AB  - proteins and two CRISPR systems, belonging to the subclasses I-E and II-A, are
AB  - located on the chromosome. The largest plasmid pCD034-3 was predicted to encode
AB  - 57 genes, including a putative polysaccharide synthesis gene cluster, whereas the
AB  - functions of the two smaller plasmids, pCD034-1 and pCD034-2, remain cryptic.
AB  - Phylogenetic analysis based on sequence comparison of the conserved marker gene
AB  - rpoA reveals that L. buchneri CD034 is more closely related to Lactobacillus
AB  - hilgardii strains than to Lactobacillus brevis and Lactobacillus plantarum
AB  - strains. Comparison of the L. buchneri CD034 core genome to other fully sequenced
AB  - and closely related members of the genus Lactobacillus disclosed a high degree of
AB  - conservation between L. buchneri CD034 and the recently sequenced L. buchneri
AB  - strain NRRL B-30929 and a more distant relationship to L. buchneri ATCC 11577 and
AB  - L. brevis ssp. gravesensis ATCC 27305, which cluster together with L. hilgardii
AB  - type strain ATCC 8290. L. buchneri CD034 genome information will certainly
AB  - provide the basis for further postgenome studies with the objective to optimize
AB  - application of the strain in silage production.
ER  -

TY  - JOUR
AU  - Heinle, C.E. et al.
TI  - Complete Genome Sequence of Lelliottia nimipressuralis Type Strain SGAir0187, Isolated from Tropical Air Collected in Singapore.
JO  - Genome Announcements
PY  - 2018
SP  - e00231
EP  - e00218
VL  - 6
AB  - Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples
AB  - collected in Singapore. The genome was assembled with an average coverage
AB  - of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end
AB  - reads. The genome measures 4.8 Mb and contains 4,424 protein-coding genes, 83
AB  - tRNAs, and 25 rRNAs.
ER  -

TY  - JOUR
AU  - Heinsch, S.C.
AU  - Otto-Hanson, L.
AU  - Hsu, S.Y.
AU  - Kinkel, L.
AU  - Smanski, M.J.
TI  - Genome Sequences for Streptomyces spp. Isolated from Disease-Suppressive Soils and Long-Term Ecological Research Sites.
JO  - Genome Announcements
PY  - 2017
SP  - e00493
EP  - e00417
VL  - 5
AB  - We report here the high-quality genome sequences of three Streptomyces spp. isolated as part
AB  - of a long-term study of microbial soil ecology. Streptomyces sp.
AB  - strain GS93-23 was isolated from naturally disease-suppressive soil (DSS) in
AB  - Grand Rapids, MN, and Streptomyces sp. strains S3-4 and 3211-3 were isolated from
AB  - experimental plots in the Cedar Creek Ecosystem Science Reserve (CCESR).
ER  -

TY  - JOUR
AU  - Heintschel von Heinegg, E.
AU  - Nalik, H.P.
AU  - Schmid, E.N.
TI  - Characterisation of a Helicobacter pylori phage (HP1).
JO  - J. Med. Microbiol.
PY  - 1993
SP  - 245
EP  - 249
VL  - 38
AB  - The infection of two Helicobacter pylori strains with a
AB  - phage-containing supernate of the lysogenic H. pylori strain IMMi 290/89
AB  - resulted in a lytic cycle and propagation of phage HP1. In
AB  - negatively-stained preparations, the empty phage heads measured 55-60 nm
AB  - in diameter and mature heads measured 50 nm. The flexible, striated
AB  - phage tail was c. 170 nm in length and 9.5 nm in diameter. The phage
AB  - showed a mean density of 1.40 g/cm3 in sucrose-density gradients and
AB  - contained double-stranded DNA c. 22,000 bp in length.
ER  -

TY  - JOUR
AU  - Heinze, R.J.
AU  - Giron-Monzon, L.
AU  - Solovyova, A.
AU  - Elliot, S.L.
AU  - Geisler, S.
AU  - Cupples, C.G.
AU  - Connolly, B.A.
AU  - Friedhoff, P.
TI  - Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 4453
EP  - 4463
VL  - 37
AB  - DNA mismatch repair (MMR) and very-short patch (VSP) repair are two pathways involved in the
AB  - repair of T:G mismatches. To learn about
AB  - competition and cooperation between these two repair pathways, we analyzed
AB  - the physical and functional interaction between MutL and Vsr using
AB  - biophysical and biochemical methods. Analytical ultracentrifugation
AB  - reveals a nucleotide-dependent interaction between Vsr and the N-terminal
AB  - domain of MutL. Using chemical crosslinking, we mapped the interaction
AB  - site of MutL for Vsr to a region between the N-terminal domains similar to
AB  - that described before for the interaction between MutL and the strand
AB  - discrimination endonuclease MutH of the MMR system. Competition between
AB  - MutH and Vsr for binding to MutL resulted in inhibition of the
AB  - mismatch-provoked MutS- and MutL-dependent activation of MutH, which
AB  - explains the mutagenic effect of Vsr overexpression. Cooperation between
AB  - MMR and VSP repair was demonstrated by the stimulation of the Vsr
AB  - endonuclease in a MutS-, MutL- and ATP-hydrolysis-dependent manner, in
AB  - agreement with the enhancement of VSP repair by MutS and MutL in vivo.
AB  - These data suggest a mobile MutS-MutL complex in MMR signalling, that
AB  - leaves the DNA mismatch prior to, or at the time of, activation of
AB  - downstream effector molecules such as Vsr or MutH.
ER  -

TY  - JOUR
AU  - Heip, J.
AU  - Rolfe, B.
AU  - Schell, J.
TI  - Abolition of host cell restriction by high multiplicity of phage infection.
JO  - Virology
PY  - 1974
SP  - 356
EP  - 370
VL  - 59
AB  - When restricting host cells (Escherichia coli K12 or E. coli B) are infected
AB  - first with a nonmodified lambda phage (called the helper phage) at high
AB  - multiplicity and subsequently superinfected with a second nonmodified lambda
AB  - vir phage (called the test phage), it can be shown that an increased number of
AB  - infected cells produce a successful infection of phage which carry the virulent
AB  - marker of the test phage.  This multiplicity effect has been studied both in
AB  - normal and in recombination defective strains, in the presence or the absence
AB  - of chloramphenicol and mitomycin C and in circumstances where the gene
AB  - expression of the nonmodified helper phage was prevented by immunity.  The
AB  - results indicate that the nonmodified helper-phage causes a temporary
AB  - inactivation of the restricting system and that the multiplicity effect is not
AB  - due to gene complementation or cooperation or to recombination.  Furthermore,
AB  - this multiplicity effect can be observed in different hosts and with various
AB  - nonmodified phages.  When similar experiments were performed with modified
AB  - helper phage no multiplicity effect was observed.
ER  -

TY  - JOUR
AU  - Heiter, D.F.
AU  - Lunnen, K.D.
AU  - Wilson, G.G.
TI  - Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 631
EP  - 640
VL  - 348
AB  - The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric
AB  - recognition sequence, thus: CCTCAGC/GCGAGG -> CC^TCAGC/GC^TGAGG. We show that R.BbvCI
AB  - comprises
AB  - two different subunits, R-1 and R-2; that each subunit contains a
AB  - catalytic site for DNA strand hydrolysis; and that these sites act
AB  - independently and strand-specifically. In turn, each catalytic site was
AB  - inactivated by mutagenesis to form dimeric enzymes in which only one
AB  - bite remained functional. The altered enzymes hydrolyzed just one
AB  - strand of the recognition sequence, nicking the DNA rather than
AB  - cleaving it. Enzymes in which the catalytic site in the R-1 subunit
AB  - remained functional nicked the bottom strand of the sequence, producing
AB  - CCTCAGC/GC^TGAGG, while those in which the catalytic site
AB  - in the R-2 subunit remained functional nicked the top strand, producing
AB  - CC^TCAGC/GCTGAGG. These DNA-nicking enzymes could prove
AB  - useful for investigation of DNA repair, recombination, and replication,
AB  - and for laboratory procedures that initiate from nicks, such as DNA
AB  - degradation, synthesis, and amplification.
ER  -

TY  - JOUR
AU  - Heithoff, D.M.
AU  - Enioutina, E.Y.
AU  - Daynes, R.A.
AU  - Sinsheimer, R.L.
AU  - Low, D.A.
AU  - Mahan, M.J.
TI  - Salmonella DNA adenine methylase mutants confer cross-protective immunity.
JO  - Infect. Immun.
PY  - 2001
SP  - 6725
EP  - 6730
VL  - 69
AB  - Salmonella isolates that lack or overproduce DNA adenine methylase elicited a cross-protective
AB  - immune response to different Salmonella serovars.  The protection afforded by the Salmonella
AB  - enterica serovar Typhimurium Dam vaccine was greater than that elicited in mice that survived
AB  - a virulent infection.  S. enterica serovar Typhimurium Dam mutant strains exhibited enhanced
AB  - sensitivity to mediators of innate immunity such as antimicrobial peptides, bile, salts, and
AB  - hydrogen peroxide.  Also, S. enterica serovar Typhimurium Dam- vaccines were not
AB  - immunosuppressive; unlike wild-type vaccines, they failed to induce increased nitric oxide
AB  - levels and permitted a subsequent robust humoral response to diptheria toxoid antigen in
AB  - infected mice.  Dam mutant strains exhibited a low-grade persistence which, coupled with the
AB  - nonimmunosuppression and the ectopic protein expression caused by altered levels of Dam, may
AB  - provide an expanded source of potential antigens in vaccinated hosts.
ER  -

TY  - JOUR
AU  - Heithoff, D.M.
AU  - House, J.K.
AU  - Thomson, P.C.
AU  - Mahan, M.J.
TI  - Development of a Salmonella cross-protective vaccine for food animal production systems.
JO  - Vaccine
PY  - 2015
SP  - 100
EP  - 107
VL  - 33
AB  - Intensive livestock production is associated with increased Salmonella exposure, transmission,
AB  - animal disease, and contamination of food and water supplies. Modified live Salmonella
AB  - enterica vaccines that lack a functional DNA adenine methylase (Dam) confer cross-protection
AB  - to a diversity of salmonellae in experimental models of murine, avian, ovine, and bovine
AB  - models of salmonellosis. However, the commercial success of any vaccine is dependent upon the
AB  - therapeutic index, the ratio of safety/efficacy. Herein, secondary virulence-attenuating
AB  - mutations targeted to genes involved in intracellular and/or systemic survival were introduced
AB  - into Salmonella dam vaccines to screen for vaccine candidates that were safe in the animal and
AB  - the environment, while maintaining the capacity to confer cross-protective immunity to
AB  - pathogenic salmonellae serotypes. Salmonella dam mgtC, dam sifA, and dam spvB vaccine strains
AB  - exhibited significantly improved vaccine safety as evidenced by the failure to give rise to
AB  - virulent revertants during the infective process, contrary to the parental Salmonella dam
AB  - vaccine. Further, these vaccines exhibited a low grade persistence in host tissues that was
AB  - associated with reduced vaccine shedding, reduced environmental persistence, and induction of
AB  - cross-protective immunity to pathogenic serotypes derived from infected livestock. These data
AB  - indicate that Salmonella dam double mutant vaccines are suitable for commercial applications
AB  - against salmonellosis in livestock production systems. Reducing pre-harvest salmonellae load
AB  - through vaccination will promote the health and productivity of livestock and reduce
AB  - contamination of livestock-derived food products, while enhancing overall food safety. (C)
AB  - 2014 Elsevier Ltd. All rights reserved.
ER  -

TY  - JOUR
AU  - Heithoff, D.M.
AU  - Julio, S.M.
AU  - Mahan, M.J.
TI  - Regulation of bacterial virulence by DNA methylation.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 73
EP  - 73
VL  - 102
AB  - Salmonella that lack or overproduce DNA adenine methylase (Dam) elicited a cross-protective
AB  - immune response to different Salmonella
AB  - serovars. Mice immunized with Dam mutant strains conferred
AB  - significantly more protection than that conferred by mice exposed to a
AB  - sub-lethal challenge with the virulent strain. In contrast to
AB  - Salmonella and E. coli, Dam is essential for viability in Vibrio
AB  - cholerae and Yersinia pseudotuberculosis; however, Dam overproduction
AB  - is not lethal and significantly attenuated the virulence of both
AB  - pathogens. Y. pseudotuberculosis mutants that overproduce Dam conferred
AB  - fully protective immune responses and secreted several Yersinia outer
AB  - proteins (Yops) under conditions that are nonpermissive for secretion
AB  - in wild-type strains. Dam overproduction disrupted both the thermal and
AB  - calcium regulation of the synthesis of the YopE cytotoxin, and relaxed
AB  - the thermal but not the calcium dependence of YopE secretion. Because
AB  - alterations of Dam activity attenuate such a diverse set of pathogenic
AB  - organisms, the role of Dam in virulence may emerge as a general theme
AB  - in bacterial pathogenesis.
ER  -

TY  - JOUR
AU  - Heithoff, D.M.
AU  - Julio, S.M.
AU  - Mahan, M.J.
TI  - The role of DNA adenine methylation in controlling bacterial virulence.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 59
EP  - 59
VL  - 101
AB  - Salmonella DNA adenine methylase (Dam) mutants are avirulent and are effective as live
AB  - vaccines against murine typhoid fever. The role of
AB  - Dam in virulence and in the elicitation of protective immune responses
AB  - may rely on its capacity as a global regulator of gene expression. Dam
AB  - was shown to regulate the expression of many genes that are induced
AB  - during infection, and Dam- and Dam over-producer mutants expressed
AB  - several proteins distinct from each other and from wild-type Salmonella
AB  - grown in vitro. To explore whether Dam mutants were attenuated for
AB  - virulence in pathogens other than Salmonella, we attempted to construct
AB  - Dam-mutations in V. cholerae and Y. pseudotuberculosis. Dam is
AB  - essential for viability in V. cholerae and in Yersinia. However, Dam
AB  - overproduction in both organisms was not lethal and lead to reduced
AB  - virulence in both organisms. Overproduction of Dam in Yersinia resulted
AB  - in the ectopic secretion of Yersinia outer proteins (Yops) and a fully
AB  - protective immune response in vaccinated mice. Since DNA adenine
AB  - methylases are highly conserved in a wide variety of virulent bacteria,
AB  - dysregulation of Dam activity is potentially a general strategy for the
AB  - development of vaccines against varied bacterial pathogens.
ER  -

TY  - JOUR
AU  - Heithoff, D.M.
AU  - Sinsheimer, R.L.
AU  - Low, D.A.
AU  - Mahan, M.J.
TI  - In vivo gene expression and the adaptive response: From pathogenesis to vaccines and antimicrobials.
JO  - Philos. Trans. R. Soc. Lond. B. Biol. Sci.
PY  - 2000
SP  - 633
EP  - 642
VL  - 355
AB  - Microbial pathogens possess a repertoire of virulence determinants that each make unique
AB  - contributions to fitness during infection. Analysis of
AB  - these in vivo-expressed functions reveals the biology of the infection
AB  - process, encompassing the bacterial infection strategies and the host
AB  - ecological and environmental retaliatory strategies designed to combat
AB  - them (e.g. thermal, osmotic, oxygen, nutrient and acid stress). Many of
AB  - the bacterial virulence functions that contribute to a successful
AB  - infection are normally only expressed during infection. A genetic
AB  - approach was used to isolate mutants that ectopically expressed many of
AB  - these functions in a laboratory setting. Lack of DNA adenine methylase
AB  - (Dam) in Salmonella typhimurium abolishes the preferential expression
AB  - of many bacterial virulence genes in host tissues. Dam- Salmonella were
AB  - proficient in colonization of mucosal sites but were defective in
AB  - colonization of deeper tissue sites. Additionally, Dam- mutants were
AB  - totally avirulent and effective as live vaccines against murine typhoid
AB  - fever. Since dam is highly conserved in many pathogenic bacteria that
AB  - cause significant morbidity and mortality worldwide, Dams are
AB  - potentially excellent targets for both vaccines and antimicrobials.
ER  -

TY  - JOUR
AU  - Heithoff, D.M.
AU  - Sinsheimer, R.L.
AU  - Low, D.A.
AU  - Mahan, M.J.
TI  - An essential role for DNA adenine methylation in bacterial virulence.
JO  - Science
PY  - 1999
SP  - 967
EP  - 970
VL  - 284
AB  - Salmonella typhimurium lacking DNA adenine methylase were fully proficient in colonization of
AB  - mucosal sites but showed severe defects in colonization of deeper tissue sites.  These Dam-
AB  - mutants were totally avirulent and were effective as live vaccines against murine typhoid
AB  - fever.  Dam regulated the expression of at least 20 genes known to be induced during
AB  - infection; a subset of these genes are among those activated by the PhoP global virulence
AB  - regulator.  PhoP, in turn, affected Dam methylation at specific genomic sites, as evidenced by
AB  - alterations in DNA methylation patterns.  Dam inhibitors are likely to have broad
AB  - antimicrobial action, and Dam- derivatives of these pathogens may serve as live attenuated
AB  - vaccines.
ER  -

TY  - JOUR
AU  - Heitman, J.
TI  - On the origins, structures and functions of restriction-modification enzymes.
JO  - Genet. Eng. (N Y)
PY  - 1993
SP  - 57
EP  - 108
VL  - 15
AB  - Typically, restriction-modification (RM) systems consist of two enzymes: an endonuclease that
AB  - recognizes and cleaves a specific DNA sequence, and a methyltransferase that modifies the same
AB  - sequence to protect the host chromosome from cleavage. These enzymes also play an important
AB  - role in genetic engineering and provide insight into the basis of sequence-specific
AB  - DNA-protein interactions. A growing number of type II restriction endonucleases and
AB  - methyltransferases are being subjected to biochemical and genetic studies which, when combined
AB  - with ongoing X-ray crystallographic analyses, promise to provide detailed models for
AB  - mechanisms of DNA recognition and catalysis. Studies on anti-restriction systems, the repair
AB  - of DNA-single- and double-strand breaks, and the roles of DNA lesions in recombination
AB  - initiation, suggest RM systems may provoke genome rearrangements and assimilate foreign DNA
AB  - into the host genome and point towards possible evolutionary sources of this interesting group
AB  - of DNA metabolizing enzymes.
ER  -

TY  - JOUR
AU  - Heitman, J.
TI  - How the EcoRI endonuclese recognizes and cleaves DNA.
JO  - Bioessays
PY  - 1992
SP  - 445
EP  - 454
VL  - 14
AB  - One popular recombinant DNA tool is the EcoRI endonuclease, which cleaves DNA at GAATTC sites
AB  - and serves as a paradigm for sequence specific DNA-enzyme interactions. The recently revised
AB  - X-ray crystal structure of an EcoRI-DNA complex reveals EcoRI employs novel DNA recognition
AB  - motifs, a four a-helix bundle and two extended chains, which project into the major groove to
AB  - contact substrate purines and pyrimidines. Interestingly, pyrimidine contacts had been
AB  - predicted based on genetic and biochemical studies. Current work focuses on the EcoRI active
AB  - site structure, enzyme and substrate conformational changes during catalysis, and
AB  - host-restriction system interactions.
ER  -

TY  - JOUR
AU  - Heitman, J.
TI  - On the repair of DNA breaks and the specificity of the EcoRI restriction enzyme.
JO  - Ph.D. Thesis, Rockefeller University, NY, USA
PY  - 1989
SP  - 1
EP  - 209
AB  - We would like to understand how proteins and enzymes interact with DNA.  We
AB  - describe here our studies of the Mrr methylation dependent restriction enzyme,
AB  - DNA single- and double-strand break repair in E. coli, and substrate
AB  - recognition by the EcoRI endonuclease.  Many species of bacteria make
AB  - restriction-modification systems to destroy foreign DNA that enters the cell.
AB  - These systems usually consist of an endonuclease that cleaves a specific DNA
AB  - sequence and a methylase which modifies the DNA to protect the host chromosome.
AB  - We observed that when foreign site-specific methylases are expressed in E.
AB  - coli, the SOS DNA repair response is induced.  This DNA damage is inflicted by
AB  - E. coli restriction enzymes that cleave adenine (Mrr) or cytosine (McrB)
AB  - methylated DNA.  The genes encoding four of the five known E. coli restriction
AB  - systems lie clustered together, perhaps to coordinate or sequester the cellular
AB  - defense system.  Several of these restriction systems differ between E. coli
AB  - species, suggesting that their action may establish species boundaries.  The
AB  - EcoRI endonuclease cleaves DNA molecules at the sequence GAATTC.  This enzyme
AB  - is well characterized biochemically, the sequence of its gene is known, and the
AB  - X-ray crystal structure of an EcoRI-DNA complex has been solved at 3 A
AB  - resolution.  (McClarin, et al., 1986).  EcoRI serves as a paradigm for other
AB  - restriction enzymes and as a model of DNA-protein interactions.  We took a
AB  - genetic approach to study the EcoRI endonuclease.  We first asked if EcoRI DNA
AB  - double-strand breaks are repaired in E. coli.  To this end, a series of
AB  - temperature-sensitive EcoRI endouclease alleles were isolated.  Temperature
AB  - shifts with these alleles revealed that in vivo DNA scission induces the E.
AB  - coli SOS DNA  repair response.  However, neither SOS induction nor
AB  - recombination are required to repair these lesions.  DNA ligase is required and
AB  - may suffice to repair EcoRI breaks in the E. coli chromosome.  An in vivo DNA
AB  - scission assay was devised based on the finding that DNA breaks induce the SOS
AB  - response.  SOS induction was monitored with strains carrying the lactose operon
AB  - fused to an SOS inducible promoter.  After DNA scission, these strains produce
AB  - Beta-galactosidase and form blue colonies on X-Gal medium.  With this blue
AB  - colony phenotype as a screen, two approaches were taken to isolate EcoRI
AB  - mutants altered or disrupted in substrate specificity.  First, amino acids
AB  - (E144, R200) implicated in substrate binding by the crystal structure were
AB  - subjected to site-directed mutagenesis.  Of 50 of the 60 possible
AB  - substitutions, several alleles retain weak endonuclease activity which, in vivo
AB  - and in vitro, is of wild-type specificity.  Therefore the simple hydrogen bond
AB  - model proposed from the crystal structure is insufficient to explain substrate
AB  - recognition and additional interactions must participate in the
AB  - substrate-enzyme complex.  In the second approach, mutants of an EcoRI ts
AB  - allele were isolated which conditionally induce the SOS response and impair
AB  - cell growth in spite of the normally protective methylase.  In vitro, these
AB  - mutant proteins exhibit enhanced cleavage activity at EcoRI* sites, sequences
AB  - which differ by one nucleotide from the normal recognition site and are also
AB  - cleaved by the wild-type enzyme under altered buffer conditions.  Four of the
AB  - five mutations of this type lie at the DNA-protein interface and may directly
AB  - alter or disrupt substrate recognition.  One other (H114Y) lies far from the
AB  - binding and cleavage sites.  This mutation falls three amino acids away from a
AB  - previously described mutation, E111G (King et al., 1986, 1988), which severly
AB  - impairs cleavage activity without altering DNA binding.  These two mutations
AB  - support a model whereby DNA scission by the EcoRI endonuclease is
AB  - allosterically activated upon substrate binding:  we suggest that the E111G
AB  - mutation inhibits this conformational change while the H114Y mutation renders
AB  - it more facile such that additional DNA sequences act as allosteric effectors
AB  - and trigger cleavage.
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Fulford, W.
AU  - Model, P.
TI  - Phage Trojan horses: a conditional expression system for lethal genes.
JO  - Gene
PY  - 1989
SP  - 193
EP  - 197
VL  - 85
AB  - The EcoRI restriction enzyme (ENase) cleaves DNA molecules within the sequence
AB  - GAATTC.  Cells expressing this lethal activity normally make a second enzyme,
AB  - the M.EcoRI methyltransferase (MTase), which protects their chromosomal DNA by
AB  - modifying the EcoRI recognition sites.  To isolate mutants of the EcoRI ENase,
AB  - its gene was cloned into a filamentous phage vector (M13mp18) under control of
AB  - the lac promoter.  Normally, filamentous phages (M13, f1 and their derivatives)
AB  - form turbid plaques by impairing the growth of their host cell without killing
AB  - it.  In contrast, phages expressing the EcoRI ENase kill the host cell, but
AB  - survive long enough to produce plaques which are very clear.  Expression of the
AB  - M.EcoRI MTase rescues the host and restores turbid plaque formation.  EcoRI
AB  - ENase mutants were isolated by screening for mutants that make turbid, instead
AB  - of clear, plaques on an M- host.  This conditional expression system may be
AB  - useful for cloning and mutating genes for other toxic proteins.
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Ivanenko, T.
AU  - Kiss, A.
TI  - DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli.
JO  - Mol. Microbiol.
PY  - 1999
SP  - 1141
EP  - 1151
VL  - 33
AB  - Two mutants of the EcoRI endonuclease (R200K and E144C) predominantly nick only one strand of
AB  - the DNA substrate. Temperature sensitivity of the mutant enzymes allowed us to study the
AB  - consequences of inflicting DNA nicks at EcoRI sites in vivo. Expression of the EcoRI
AB  - endonuclease mutants in the absence of the EcoRI methyltransferase induces the SOS DNA repair
AB  - response and greatly reduces viability of recA56, recB21 and lexA3 mutant strains of
AB  - Escherichia coli. In parallel studies, overexpression of the EcoRV endonuclease in cells also
AB  - expressing the EcoRV methyltransferase was used to introduce nicks at non-cognate EcoRV sites
AB  - in the bacterial genome. EcoRV overproduction was lethal in recA56 and recB21 mutant strains
AB  - and moderately toxic in a lexA3 mutant strain. The toxic effect of EcoRV overproduction could
AB  - be partially alleviated by introduction into the cells of multiple copies of the E. coli DNA
AB  - ligase gene. These observations suggest that an increased number of DNA nicks can overwhelm
AB  - the repair capacity of DNA ligase, resulting in the conversion of a proportion of DNA nicks
AB  - into DNA lesions that require recombination for repair.
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Model, P.
TI  - Site-specific methylases induce the SOS DNA repair response in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1987
SP  - 3243
EP  - 3250
VL  - 169
AB  - Expression of the site-specific adenine methylase HhaII (GmeANTC, where me
AB  - is methyl) or PstI (CTGCmeAG) induced the SOS DNA repair response in Escherichia
AB  - coli. In contrast, expression of methylases indigenous to E. coli either did not induce SOS
AB  - (EcoRI-GAmeATTC) or induced SOS to a lesser extent (dam-GmeATC). Recognition of
AB  - adenine-methylated DNA required the product of a previously undescribed gene, which we
AB  - named mrr (methylated adenine recognition and restriction). We suggest that mrr encodes
AB  - an endonuclease that cleaves DNA containing N6-methyladenine and that DNA double-
AB  - strand breaks induce the SOS response. Cytosine methylases foreign to E. coli (MspI
AB  - [meCCGG], HaeIII [GGmeCC], BamHI [GGATmeCC],HhaI [GmeCGC],
AB  - BsuRI[GGmeCC], and M.SPR) also induced SOS, whereas one indigenous to E. coli
AB  - (EcoRII [CmeCA/TGG]) did not. SOS induction by cytosine methylation required the rglB
AB  - locus, which encodes an endonuclease that cleaves DNA containing 5-hydroxymethyl- or
AB  - 5-methylcytosine (E. A. Raleigh and G. Wilson, Proc. Natl. Acad. Sci. USA 83:9070-
AB  - 9074, 1986).
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Model, P.
TI  - Substrate recognition by the EcoRI endonuclease.
JO  - Proteins
PY  - 1990
SP  - 185
EP  - 197
VL  - 7
AB  - The EcoRI restriction endonuclease is one of the most widely used tools for
AB  - recombinant DNA maniulations.  Because the EcoRI enzyme has been extremely well
AB  - characterized biochemically and its structure is known at 3 angstrom resolution
AB  - as an enzyme-DNA complex, EcoRI also serves as a paradigm for other restriction
AB  - enzymes and as an important model of DNA-protein interactions.  To facilitate a
AB  - genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay
AB  - based on our finding that DNA double-strand breaks induce the Escherichia coli
AB  - SOS response and thereby increase beta-galactosidase expression from SOS::lacZ
AB  - gene fusions.  By site-directed mutagenesis, 50 of 60 possible point mutations
AB  - were generated at three amino acids (E144, R145, and R200) implicated in
AB  - substrate recognition by the crystal structure.  Although several of these
AB  - mutant enzymes retain partial endonuclease activity, none are altered in
AB  - substrate specificity in vivo or in vitro.  These findings argue that, in
AB  - addition to the hydrogen bond interactions revealed by the crystal structure,
AB  - the EcoRI enzyme must make additional contacts to recognize its substrate.
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Model, P.
TI  - Mutants of the EcoRI endonuclease with promiscuous substrate specificity implicate residues involved in substrate recognition.
JO  - EMBO J.
PY  - 1990
SP  - 3369
EP  - 3378
VL  - 9
AB  - The EcoRI restriction endonuclease cleaves DNA molecules at the sequence GAATTC. We devised a
AB  - genetic screen to isolate EcoRI mutants with altered or broadened substrate specificity. In
AB  - vitro, the purified mutant enzymes cleave both the wild-type substrate and sites which differ
AB  - from this by one nucleotide (EcoRI star sites). These mutations identify four residues
AB  - involved in substrate recognition and catalysis that are different from the amino acids
AB  - proposed to recognize the substrate based on the EcoRI-DNA co-crystal structure. In fact,
AB  - these mutations suppress EcoRI mutants altered at some of the proposed substrate binding
AB  - residues (R145, R200). We argue that these mutations permit cleavage of additional DNA
AB  - sequences either by perturbing or removing direct DNA-protein interactions or by facilitating
AB  - conformational changes that allosterically couple substrate binding to DNA scission.
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Model, P.
TI  - SOS induction as an in vivo assay of enzyme-DNA interactions.
JO  - Gene
PY  - 1991
SP  - 1
EP  - 9
VL  - 103
AB  - We have constructed strains which are convenient and sensitive indicators of
AB  - DNA damage and describe their use.  These strains utilize an SOS::lacZ fusion
AB  - constructed by Kenyon and Walker [Proc. Natl. Acad. Sci. USA 77 (1980)
AB  - 2819-2823] and respond to DNA damage by producing Beta-galactosidase.  They can
AB  - be used to characterize restriction systems and screen for restriction
AB  - endonuclease mutants.  Applications include the study of other enzymes involved
AB  - in DNA metabolism, such as DNA methyltransferases, topoisomerases,
AB  - recombinases, and DNA replication and repair enzymes.
ER  -

TY  - JOUR
AU  - Heitman, J.
AU  - Zinder, N.D.
AU  - Model, P.
TI  - Repair of the Escherichia coli chromosome after in vivo scission by the EcoRI endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1989
SP  - 2281
EP  - 2285
VL  - 86
AB  - We prepared a set of temperature-sensitive mutants of the EcoRI endonuclease.
AB  - Under semipermissive conditions, Escherichia coli strains bearing these alleles
AB  - form poorly growing colonies in which intracellular substrates are cleaved at
AB  - EcoRI sites and the SOS DNA repair response is induced.  Strains defective in
AB  - SOS induction (lexA3 mutant) or SOS induction and recombination (recA56 and
AB  - recB21 mutants) are not more sensitive to this in vivo DNA scission, whereas
AB  - strains deficient in DNA ligase (lig4 and lig ts7 mutants) are extremely
AB  - sensitive.  We conclude that although DNA scission induces the SOS response,
AB  - neither this induction nor recombination are required for repair.  DNA ligase
AB  - is necessary and may be sufficient to repair EcoRI-mediated DNA breaks in the
AB  - E. coli chromosome.
ER  -

TY  - JOUR
AU  - Heitman, J.B.
TI  - On the repair of DNA breaks and the specificity of the EcoRI restriction enzyme.
JO  - Diss. Abstr.
PY  - 1990
SP  - 562B
EP  - 562B
VL  - 51
AB  - We took a genetic approach to study the well characterized EcoRI restriction
AB  - enzyme, an endonuclease that cleaves DNA molecules at the sequence GAATTC.
AB  - First, a series of temperature-sensitive EcoRI endonuclease alleles were
AB  - isolated.  Temperature shifts with these alleles revealed that in vivo DNA
AB  - scission induces the E. coli SOS DNA repair response.  However, neither SOS
AB  - induction nor recombination are required to repair these lesions.  DNA ligase
AB  - is required and may suffice to repair EcoRI breaks in the E. coli chromosome.
AB  - To monitor DNA scission in vivo we employed strains carrying the lactose operon
AB  - fused to an SOS inducible promoter.  After DNA scission, these strains produce
AB  - beta-galactosidase and form blue colonies on X-Gal medium.  Using this assay,
AB  - two approaches were taken to isolate EcoRI mutants altered or disrupted in
AB  - substrate specificity.  First, amino acids (E144, R145, R200) implicated in
AB  - substrate binding by the crystal structure were subjected to site-directed
AB  - mutagenesis.  Of 50 of the 60 possible substitutions, several alleles retain
AB  - weak endonuclease activity which is of wild-type specificity.  Therefore the
AB  - simple hydrogen bond model proposed from the crystal structure is insufficient
AB  - to explain substrate recognition and additional interactions must participate
AB  - in the substrate-enzyme complex.  In the second approach, mutants of an EcoRI
AB  - ts allele were isolated which conditionally induce the SOS response in spite of
AB  - the protective methylase.  These mutant proteins exhibit enhanced cleavage
AB  - activity at EcoRI sites.  Four of five isolated mutations lie at the
AB  - DNA-protein interface and may directly alter or disrupt substrate recognition.
AB  - One other (H114Y) lies far from the binding or cleavage sites and falls three
AB  - amino acids away from a previously described mutation, E111G (King et al, 1986,
AB  - 1988), which severely impairs DNA cleavage without altering DNA binding.  These
AB  - mutations support a model whereby DNA scission by the EcoRI endonuclease is
AB  - allosterically activated upon substrate binding: the E111G mutation may inhibit
AB  - this conformational change while the H114Y mutation may render it more facile
AB  - such that additional DNA sequences act as allosteric effectors and trigger
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Hejnova, J.
AU  - Dobrindt, U.
AU  - Nemcova, R.
AU  - Rusniok, C.
AU  - Bomba, A.
AU  - Frangeul, L.
AU  - Hacker, J.
AU  - Glaser, P.
AU  - Sebo, P.
AU  - Buchrieser, C.
TI  - Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31).
JO  - Microbiology
PY  - 2005
SP  - 385
EP  - 398
VL  - 151
AB  - Colonization by the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31) has proved to
AB  - be safe and efficient in the prophylaxis and
AB  - treatment of nosocomial infections and diarrhoea of preterm and newborn
AB  - infants in Czech paediatric clinics over the past three decades. In
AB  - searching for traits contributing to this beneficial effect related to the
AB  - gut colonization capacity of the strain, the authors have analysed its
AB  - genome by DNA-DNA hybridization to E. coli K-12 (MG1655) genomic DNA
AB  - arrays and to 'Pathoarrays', as well as by multiplex PCR, bacterial
AB  - artificial chromosome (BAC) library cloning and shotgun sequencing. Four
AB  - hundred and ten E. coli K-12 ORFs were absent from A0 34/86, while 72 out
AB  - of 456 genes associated with pathogenicity islands of E. coli and Shigella
AB  - were also detected in E. coli A0 34/86. Furthermore, extraintestinal
AB  - pathogenic E. coli-related genes involved in iron uptake and adhesion were
AB  - detected by multiplex PCR, and genes encoding the HlyA and cytotoxic
AB  - necrotizing factor toxins, together with 21 genes of the uropathogenic E.
AB  - coli 536 pathogenicity island II, were identified by analysis of 2304
AB  - shotgun and 1344 BAC clone sequences of A0 34/86 DNA. Multiple sequence
AB  - comparisons identified 31 kb of DNA specific for E. coli A0 34/86; some of
AB  - the genes carried by this DNA may prove to be implicated in the
AB  - colonization capacity of the strain, enabling it to outcompete pathogens.
AB  - Among 100 examined BAC clones roughly covering the A0 34/86 genome, one
AB  - reproducibly conferred on the laboratory strain DH10B an enhanced capacity
AB  - to persist in the intestine of newborn piglets. Sequencing revealed that
AB  - this BAC clone carried gene clusters encoding gluconate and mannonate
AB  - metabolism, adhesion (fim), invasion (ibe) and restriction/modification
AB  - functions. Hence, the genome of this clinically safe and highly efficient
AB  - colonizer strain appears to harbour many 'virulence-associated' genes.
AB  - These results highlight the thin line between bacterial 'virulence' and
AB  - 'fitness' or 'colonization' factors, and question the definition of
AB  - enterobacterial virulence factors.
ER  -

TY  - JOUR
AU  - Helene, C.
TI  - Sequence-selective recognition and cleavage of double-helical DNA.
JO  - Curr. Opin. Biotechnol.
PY  - 1993
SP  - 29
EP  - 36
VL  - 4
AB  - Single sites within long double-helical DNA molecules can be recognized by a variety of
AB  - mechanisms. Different strategies have been used to adapt sequence-specific recognition to
AB  - sequence-specific cleavage of duplex DNA. Any nucleic acid can be converted into an artificial
AB  - nuclease by the attachment of a cleaving reagent. Alternatively, a sequence-specific ligand
AB  - can be used to protect a methylase recognition site from methylation. The protected site may
AB  - then be cleaved selectively by a restriction endonuclease (the so-called 'Achilles heel'
AB  - cleavage technique). Recent developments in this area have shown that it is possible to cleave
AB  - chromosomal DNA at single sites within bacterial and eukaryotic genomes.
ER  -

TY  - JOUR
AU  - Helene, L.C.
AU  - Gomes, D.F.
AU  - Delamuta, J.R.
AU  - Ribeiro, R.A.
AU  - Souza, R.C.
AU  - Almeida, L.G.
AU  - Vasconcelos, A.T.
AU  - Hungria, M.
TI  - Genome Sequence of Bradyrhizobium viridifuturi Strain SEMIA 690T, a Nitrogen-Fixing Symbiont of Centrosema pubescens.
JO  - Genome Announcements
PY  - 2015
SP  - e01481
EP  - e01415
VL  - 3
AB  - SEMIA 690(T) is a nitrogen-fixing symbiont of Centrosema pubescens, and comprises the recently
AB  - described species Bradyrhizobium viridifuturi. Its draft genome
AB  - indicates that it belongs to the Bradyrhizobium elkanii superclade. SEMIA 690(T)
AB  - carries two copies of the regulatory nodD gene, and the nod and nif operons
AB  - resemble those of Bradyrhizobium diazoefficiens.
ER  -

TY  - JOUR
AU  - Helene, L.C.F.
AU  - Ribeiro, R.A.
AU  - Hungria, M.
TI  - Genome Sequence of Rhizobium esperanzae Type Strain CNPSo 668, Isolated from Phaseolus vulgaris Nodules in Mexico.
JO  - Genome Announcements
PY  - 2017
SP  - e00935
EP  - e00917
VL  - 5
AB  - Rhizobium esperanzae CNPSo 668T is a nitrogen-fixing symbiont of Phaseolus vulgaris isolated
AB  - from Mexican soils. Its genome is estimated at 6,294,057 bp,
AB  - with 6,219 coding sequences (CDSs) showing higher similarity (92.9%) with
AB  - Rhizobium etli Three copies of the regulatory nodD, in addition to other
AB  - nodulation genes, should define its host specificity.
ER  -

TY  - JOUR
AU  - Helling, R.B.
AU  - Goodman, H.M.
AU  - Boyer, H.W.
TI  - Analysis of endonuclease R EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis.
JO  - J. Virol.
PY  - 1974
SP  - 1235
EP  - 1243
VL  - 14
AB  - By means of agarose-gel electrophoresis, endonuclease R EcoRI-generated
AB  - fragments of DNA from various viruses were separated, their molecular weights
AB  - were determined, and complete or partial fragment maps for lambda, Phi80, and
AB  - hybrid phages were constructed.
ER  -

TY  - JOUR
AU  - Hemavathy, K.C.
AU  - Nagaraja, V.
TI  - DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences.
JO  - FEMS Immunol Med Microbiol
PY  - 1995
SP  - 291
EP  - 296
VL  - 11
AB  - The presence of 6-methyladenine and 5-methylcytosine at Dam (GATC) and Dcm (CCA/TGG) sites in
AB  - DNA of mycobacterial species was investigated using
AB  - isoschizomer restriction enzymes. In all species examined, Dam and Dcm
AB  - recognition sequences were not methylated indicating the absence of these
AB  - methyltransferases. On the other hand, high performance liquid chromatographic
AB  - analysis of genomic DNA from Mycobacterium smegmatis and Mycobacterium
AB  - tuberculosis showed significant levels of 6-methyladenine and 5-methylcytosine
AB  - suggesting the presence of DNA methyltransferases other than Dam and Dcm.
AB  - Occurrence of methylation was also established by a sensitive genetic assay.
ER  -

TY  - JOUR
AU  - Hemeon, I.
AU  - Gutierrez, J.A.
AU  - Ho, M.-C.
AU  - Schramm, V.L.
TI  - Characterizing DNA methyltransferases with an ultrasensitive luciferase-linked continuous assay.
JO  - Anal. Chem.
PY  - 2011
SP  - 4996
EP  - 5004
VL  - 83
AB  - DNA (cytosine-5)-methyltransferases (DNMTs) catalyze the transfer of a methyl group from
AB  - S-adenosyl-L-methionine (AdoMet) to the 5-position of cytosine residues and thereby silence
AB  - transcription of regulated genes. DNMTs are important epigenetic targets. However, isolated
AB  - DNMTs are weak catalysts and are difficult to assay. We report an ultrasensitive
AB  - luciferase-linked continuous assay that converts the S-adenosyl-L-homocysteine product of DNA
AB  - methylation to a quantifiable luminescent signal. Results with this assay are compared with
AB  - the commonly used DNA labeling from [methyl-3H]AdoMet. A
AB  - 50-methylthioadenosine-adenosylhomocysteine nucleosidase is used to hydrolyze AdoHcy to
AB  - adenine. Adenine phosphoribosyl transferase converts adenine to AMP and pyruvate
AB  - orthophosphate dikinase converts AMP to ATP. Firefly luciferase gives a stable luminescent
AB  - signal that results from continuous AMP recycling to ATP. This assay exhibits a broad dynamic
AB  - range (0.1-1000 pmol of AdoHcy). The rapid response time permits continuous assays of DNA
AB  - methylation detected by light output. The assay is suitable for high-throughput screening of
AB  - chemical libraries for DNMT inhibition activity. The kinetic properties of human and bacterial
AB  - CpG methyltransferases are characterized using this assay. Human catalytic domain DNMT3b
AB  - activation byDNMT3L is shown to involve two distinct kinetic states that alter kcat but not Km
AB  - for AdoMet. The assay is shown to be robust in the presence of high concentrations of the
AB  - pyrimidine analogues 5-azacytidine and 5-azacytosine.
ER  -

TY  - JOUR
AU  - Hemme, C.L. et al.
TI  - Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6494
EP  - 6496
VL  - 192
AB  - Modern methods to develop microbe-based biomass conversion processes require a system-level
AB  - understanding of the microbes involved. Clostridium
AB  - species have long been recognized as ideal candidates for processes
AB  - involving biomass conversion and production of various biofuels and other
AB  - industrial products. To expand the knowledge base for clostridial species
AB  - relevant to current biofuel production efforts, we have sequenced the
AB  - genomes of 20 species spanning multiple genera. The majority of species
AB  - sequenced fall within the class III cellulosome-encoding Clostridium and
AB  - the class V saccharolytic Thermoanaerobacteraceae. Species were chosen
AB  - based on representation in the experimental literature as model organisms,
AB  - ability to degrade cellulosic biomass either by free enzymes or by
AB  - cellulosomes, ability to rapidly ferment hexose and pentose sugars to
AB  - ethanol, and ability to ferment synthesis gas to ethanol. The sequenced
AB  - strains significantly increase the number of noncommensal/nonpathogenic
AB  - clostridial species and provide a key foundation for future studies of
AB  - biomass conversion, cellulosome composition, and clostridial systems
AB  - biology.
ER  -

TY  - JOUR
AU  - Hemp, J.
AU  - Ward, L.M.
AU  - Pace, L.A.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Levilinea saccharolytica KIBI-1, a Member of the Chloroflexi Class Anaerolineae.
JO  - Genome Announcements
PY  - 2015
SP  - e01357
EP  - e01315
VL  - 3
AB  - We report the draft genome sequence of Levilinea saccharolytica KIBI-1, a facultative
AB  - anaerobic member of the Chloroflexi class Anaerolineae. While L.
AB  - saccharolytica was characterized as an obligate anaerobe, genome analysis
AB  - provides evidence for the presence of both aerobic respiration and partial
AB  - denitrification pathways.
ER  -

TY  - JOUR
AU  - Hemp, J.
AU  - Ward, L.M.
AU  - Pace, L.A.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae.
JO  - Genome Announcements
PY  - 2015
SP  - e01353
EP  - e01315
VL  - 3
AB  - We report the draft genome sequence of Ornatilinea apprima P3M-1, a strictly anaerobic member
AB  - of the Chloroflexi class Anaerolineae. This genome provides
AB  - insight into the diversity of metabolism within the Anaerolineae, and the
AB  - evolution of respiration within the Chloroflexi.
ER  -

TY  - JOUR
AU  - Hemp, J.
AU  - Ward, L.M.
AU  - Pace, L.A.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia.
JO  - Genome Announcements
PY  - 2015
SP  - e01347
EP  - e01315
VL  - 3
AB  - We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced
AB  - member of class Ardenticatenia of the phylum Chloroflexi. This
AB  - thermophilic organism is capable of a range of physiologies, including aerobic
AB  - respiration and iron reduction. It also encodes a complete denitrification
AB  - pathway with a novel nitric oxide reductase.
ER  -

TY  - JOUR
AU  - Henaut, A.
AU  - Rouxel, T.
AU  - Gleizes, A.
AU  - Moszer, I.
AU  - Danchin, A.
TI  - Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 574
EP  - 585
VL  - 257
AB  - This work reconsiders the GATC motif distribution in a 1.6 Mb segment of the Escherichia coli
AB  - genome, compared to its distribution in phages and plasmids.  At first sight the distribution
AB  - of GATC words looks random.  But when a realistic model of the chromosome (made of average
AB  - genes having the same codon usage as in the real chromosome), is used as a theoretical
AB  - reference, strong biases are observed.  GATC pairs such as GATCNNGATC are under-represented
AB  - while there is a strong positive selection for motifs separated by 10, 19, 70 and 1100 bp.
AB  - The last class is the only one present in E. coli parasites.  It can be ascribed to the
AB  - triggering sequences of the long-patch mismatch repair system.  The 6 bp class overlaps with
AB  - the consensus of CAP (catabolite activator protein) and FNR (fumarate/nitrate regulator)
AB  - binding sites, thus accounting for counter-selection.  The other classes, which could be
AB  - targets for a nucleic acid binding protein, are almost always present inside protein coding
AB  - sequences, and are members of clusters of GATC motifs.  Analysis of the genes containing these
AB  - motifs suggests that they correspond to a regulatory process monitoring the shift from
AB  - anaerobic to aerobic growth conditions  In particular this regulation, closing down
AB  - transcription of a large number of genes involved in intermediary metabolism would be well
AB  - suited for the cold and oxygen shift from the mammal's gut to the standard environmental
AB  - conditions.  In this process the methylation status of GATC clusters would be very important
AB  - for tuning transcription, and a DNA binding protein, probably a member of the cold-shock
AB  - proteins family would be needed for alleviating the effects mediated by slackening of the pace
AB  - of methylation during the shift.
ER  -

TY  - JOUR
AU  - Henderson, I.R.
AU  - Deleris, A.
AU  - Wong, W.
AU  - Zhong, X.H.
AU  - Chin, H.G.
AU  - Horwitz, G.A.
AU  - Kelly, K.A.
AU  - Pradhan, S.
AU  - Jacobsen, S.E.
TI  - The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA-Directed DNA Methylation in Arabidopsis thaliana.
JO  - PLoS Genet.
PY  - 2010
SP  - e1001182
EP  - e1001182
VL  - 6
AB  - Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive
AB  - sequences, including transposons and retroviruses.
AB  - This silencing is stable between cell generations as cytosine
AB  - methylation is maintained epigenetically through DNA replication. The
AB  - Arabidopsis thaliana Dnmt3 cytosine methyltransferase ortholog DOMAINS
AB  - REARRANGED METHYLTRANSFERASE2 (DRM2) is required for establishment of
AB  - small interfering RNA (siRNA) directed DNA methylation. In mammals PIWI
AB  - proteins and piRNA act in a convergently evolved RNA-directed DNA
AB  - methylation system that is required to repress transposon expression in
AB  - the germ line. De novo methylation may also be independent of RNA
AB  - interference and small RNAs, as in Neurospora crassa. Here we identify
AB  - a clade of catalytically mutated DRM2 paralogs in flowering plant
AB  - genomes, which in A. thaliana we term DOMAINS REARRANGED
AB  - METHYLTRANSFERASE3 (DRM3). Despite being catalytically mutated, DRM3 is
AB  - required for normal maintenance of non-CG DNA methylation,
AB  - establishment of RNA-directed DNA methylation triggered by repeat
AB  - sequences and accumulation of repeat-associated small RNAs. Although
AB  - the mammalian catalytically inactive Dnmt3L paralogs act in an
AB  - analogous manner, phylogenetic analysis indicates that the DRM and
AB  - Dnmt3 protein families diverged independently in plants and animals. We
AB  - also show by site-directed mutagenesis that both the DRM2 N-terminal
AB  - UBA domains and C-terminal methyltransferase domain are required for
AB  - normal RNA-directed DNA methylation, supporting an essential targeting
AB  - function for the UBA domains. These results suggest that plant and
AB  - mammalian RNA-directed DNA methylation systems consist of a combination
AB  - of ancestral and convergent features.
ER  -

TY  - JOUR
AU  - Hendrich, B.
AU  - Bird, A.
TI  - Mammalian methyltransferases and methyl-CpG-binding domains: proteins involved in DNA methylation.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 2000
SP  - 55
EP  - 74
VL  - 249
AB  - The modified base 5-methylcytosine has been known to exist in mammalian DNA since 1950.  It
AB  - wasn't until 1988 that the gene encoding the enzyme reponsible for the maintenance of
AB  - 5-methylcytosine in mammals, DNA-(cytosine-5) methyltransferase 1, was identified.  The
AB  - following year, a protein activity was reported; it was able to bind DNA containing methylated
AB  - cytosine followed by guanosine but, otherwise, it was indifferent to the sequence context.  A
AB  - different protein activity, which was also capable of binding the sequence MeCpG, was
AB  - identified in 1992, and the corresponding gene was cloned.  This provided the first molecular
AB  - handle on MeCpG-binding proteins.  For the following 5 years, however, no further proteins
AB  - were identified that were able to either methylate DNA or to bind specifically to methylated
AB  - DNA.  The past 2 years have seen a flurry of activity in this field, with the reporting of
AB  - three new candidate methyltransferases and four new candidate MeCPs.  Also developing is an
AB  - ever-more-precise molecular picture of exactly how DNA methylation affects transcription. In
AB  - this chapter, we will review that is known about the mammalian proteins involved in both
AB  - methylating DNA and in interpreting the signal that DNA methylation represents.  For an
AB  - evolutionary discussion of the known eukaryotic DNMTs, we refer the reader to a recent review
AB  - by Colot and Rossignol.  In this review, we will only discuss MeCPs that do not require
AB  - additional DNA sequence for specific binding to DNA.  For a summary of MeCPs in general we
AB  - refer the reader to a review by Tate and Bird.
ER  -

TY  - JOUR
AU  - Hendrich, B.
AU  - Bird, A.
TI  - Identification and characterization of a family of mammalian methyl-CpG binding proteins.
JO  - Mol. Cell. Biol.
PY  - 1998
SP  - 6538
EP  - 6547
VL  - 18
AB  - Methylation at the DNA sequence 5'-CpG is required for mouse development. MeCP2 and MBD1
AB  - (formerly PCM1) are two known proteins that bind specifically to methylated DNA via a related
AB  - amino acid motif and that can repress transcription. We describe here three novel human and
AB  - mouse proteins (MBD2, MBD3, and MBD4) that contain the methyl-CpG binding domain. MBD2 and
AB  - MBD4 bind specifically to methylated DNA in vitro. Expression of MBD2 and MBD4 tagged with
AB  - green fluorescent protein in mouse cells shows that both proteins colocalize with foci of
AB  - heavily methylated satellite DNA. Localization is disrupted in cells that have greatly reduced
AB  - levels of CpG methylation. MBD3 does not bind methylated DNA in vivo or in vitro. MBD1, MBD2,
AB  - MBD3, and MBD4 are expressed in somatic tissues, but MBD1 and MBD2 expression is reduced or
AB  - absent in embryonic stem cells which are known to be deficient in MeCP1 activity. The data
AB  - demonstrate that MBD2 and MBD4 bind specifically to methyl-CpG in vitro and in vivo and are
AB  - therefore likely to be mediators of the biological consequences of the
AB  - methylation signal.
ER  -

TY  - JOUR
AU  - Hendrickson, E.L. et al.
TI  - Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.
JO  - J. Bacteriol.
PY  - 2004
SP  - 6956
EP  - 6956
VL  - 186
AB  - The genome sequence of the genetically tractable, mesophilic, hydrogenotrophic methanogen
AB  - Methanococcus maripaludis contains 1,722 protein-coding genes in a single circular chromosome
AB  - of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a
AB  - function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were
AB  - unique to M. maripaludis. Of the unique ORFs, 27 were confirmed to encode proteins by the mass
AB  - spectrometric identification of unique peptides. Genes for most known functions and pathways
AB  - were identified. For example, a full complement of hydrogenases and methanogenesis enzymes was
AB  - identified, including eight selenocysteine-containing proteins, with each being paralogous to
AB  - a cysteine-containing counterpart. At least 59 proteins were predicted to contain iron-sulfur
AB  - centers, including ferredoxins, polyferredoxins, and subunits of enzymes with various redox
AB  - functions. Unusual features included the absence of a Cdc6 homolog, implying a variation in
AB  - replication initiation, and the presence of a bacterial-like RNase HI as well as an RNase HII
AB  - typical of the Archaea. The presence of alanine dehydrogenase and alanine racemase, which are
AB  - uniquely present among the Archaea, explained the ability of the organism to use L- and
AB  - D-alanine as nitrogen sources. Features that contrasted with the related organism
AB  - Methanocaldococcus jannaschii included the absence of inteins, even though close homologs of
AB  - most intein-containing proteins were encoded. Although two-thirds of the ORFs had their
AB  - highest Blastp hits in Methanocaldococcus jannaschii, lateral gene transfer or gene loss has
AB  - apparently resulted in genes, which are often clustered, with top Blastp hits in more
AB  - distantly related groups.
ER  -

TY  - JOUR
AU  - Hendrix, J.
AU  - Read, T.
AU  - Lalonde, J.-F.
AU  - Jensen, P.K.
AU  - Heymann, W.
AU  - Lovelace, E.
AU  - Zimmermann, S.A.
AU  - Brasino, M.
AU  - Rokicki, J.
AU  - Dowell, R.D.
TI  - Engineered Calcium-Precipitable Restriction Enzyme.
JO  - ACS Synth. Biol.
PY  - 2014
SP  - 969
EP  - 971
VL  - 3
AB  - We have developed a simple system for tagging and purifying proteins. Recent experiments have
AB  - demonstrated that RTX (Repeat in Toxin) motifs from the adenylate cyclase toxin gene (CyaA) of
AB  - B. pertussis undergo a conformational change upon binding calcium, resulting in precipitation
AB  - of fused proteins and making this method a viable alternative for bioseparation. We have
AB  - designed an iGEM Biobrick comprised of an RTX tag that can be easily fused to any protein of
AB  - interest. In this paper, we detail the process of creating an RTX tagged version of the
AB  - restriction enzyme EcoRI and describe a method for expression and purification of the
AB  - functional enzyme.
ER  -

TY  - JOUR
AU  - Hendrix, J.D.
AU  - Welker, N.E.
TI  - Isolation of a Bacillus stearothermophilus mutant exhibiting increased thermostability in its restriction endonuclease.
JO  - J. Bacteriol.
PY  - 1985
SP  - 682
EP  - 692
VL  - 162
AB  - A procedure was developed for the selection of spontaneous mutants of Bacillus
AB  - stearothermophilus NUB31 that are more efficient than the wild type in the
AB  - restriction of phage at elevated temperatures.  Inactivation studies revealed
AB  - that two mutants contained a more thermostable restriction enzyme and one
AB  - mutant contained three times more enzyme than the wild type.  The restriction
AB  - endonucleases from the wild type and one of the mutants were purified to
AB  - apparent homogeneity.  The mutant enzyme was more thermostable than the
AB  - wild-type enzyme.  The subunit molecular weight, amino acid composition,
AB  - N-terminal and C-terminal amino acid residues, tryptic peptide map, and
AB  - catalytic properties of the two enzymes were determined.  The two enzymes have
AB  - similar catalytic properties, but the molecular size of the mutant enzyme is
AB  - approximately 6 to 7 kilodaltons larger than that of the wild-type enzyme.  The
AB  - mutant enzyme contains 54 additional amino acid residues, of which 26 to 28 are
AB  - aspartate/asparagine, 8 to 15 are glutamate/glutamine, and 8 to 9 are tyrosine
AB  - residues.  The two enzymes contained similar amounts of the other amino acids,
AB  - identical N-terminal residues, and different C-terminal residues.  Tryptic
AB  - peptide analyses revealed a high degree of homology between the two enzymes.
AB  - The increased thermostability observed in the mutant enzyme appears to have
AB  - been achieved by a mutation that resulted in the addition of amino acid
AB  - residues to the wild-type enzyme.  A number of mechanisms are discussed that
AB  - could account for the observed difference between the mutant and wild-type
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Hendrix, R.W.
AU  - Ko, C.C.
AU  - Jacobs-Sera, D.
AU  - Hatfull, G.F.
AU  - Erhardt, M.
AU  - Hughes, K.T.
AU  - Casjens, S.R.
TI  - Genome Sequence of Salmonella Phage chi.
JO  - Genome Announcements
PY  - 2015
SP  - e01229
EP  - e01214
VL  - 3
AB  - Salmonella bacteriophage chi is a member of the Siphoviridae family that gains entry into its
AB  - host cells by adsorbing to their flagella. We report the complete  59,578-bp sequence of the
AB  - genome of phage chi, which together with its relatives, exemplifies a largely unexplored type
AB  - of tailed bacteriophage.
ER  -

TY  - JOUR
AU  - Hendrix, R.W.
AU  - Smith, M.C.M.
AU  - Burns, R.N.
AU  - Ford, M.E.
AU  - Hatfull, G.F.
TI  - Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 2192
EP  - 2197
VL  - 96
AB  - We report DNA and predicted protein sequence similarities, implying homology, among genes of
AB  - double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range
AB  - of host bacteria. The sequence matches reported here establish genetic connections, not always
AB  - direct, among the lambdoid phages of Escherichia coli, phage phiC31 of Streptomyces, phages of
AB  - Mycobacterium, a previously unrecognized cryptic prophage, phiflu, in the Haemophilus
AB  - influenzae genome, and two small prophage-like elements, phiRv1 and phiRv2, in the genome of
AB  - Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of
AB  - the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure
AB  - and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with
AB  - access, by horizontal exchange, to a large common genetic pool but in which access to the gene
AB  - pool is not uniform for all phage.
ER  -

TY  - JOUR
AU  - Heng, N.C.
AU  - Haji-Ishak, N.S.
AU  - Kalyan, A.
AU  - Wong, A.Y.
AU  - Lovric, M.
AU  - Bridson, J.M.
AU  - Artamonova, J.
AU  - Stanton, J.A.
AU  - Wescombe, P.A.
AU  - Burton, J.P.
AU  - Cullinan, M.P.
AU  - Tagg, J.R.
TI  - Genome Sequence of the Bacteriocin-Producing Oral Probiotic Streptococcus salivarius Strain M18.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6402
EP  - 6403
VL  - 193
AB  - Streptococcus salivarius is a Gram-positive bacterial commensal and pioneer colonizer of the
AB  - human oral cavity. Many strains produce
AB  - ribosomally synthesized proteinaceous antibiotics (bacteriocins), and some
AB  - strains have been developed for use as oral probiotics. Here, we present
AB  - the draft genome sequence of the bacteriocin-producing oral probiotic S.
AB  - salivarius strain M18.
ER  -

TY  - JOUR
AU  - Heng, N.C.
AU  - Yeh, C.W.
AU  - Malik, A.
TI  - Draft Genome Sequence of Weissella confusa MBF8-1, a Glucansucrase- and Bacteriocin-Producing Strain Isolated from a Homemade Soy Product.
JO  - Genome Announcements
PY  - 2017
SP  - e01497
EP  - e01416
VL  - 5
AB  - We report here the draft genome sequence of Weissella confusa MBF8-1, an isolate  from a
AB  - homemade fermented soybean product that produces sucrases and exhibits
AB  - antibacterial (bacteriocin) activity. The draft genome of W. confusa MBF8-1
AB  - comprises a 2.2-Mbp chromosome and a 17.8-kbp bacteriocin-encoding plasmid. Two
AB  - putative glucansucrase genes were also identified.
ER  -

TY  - JOUR
AU  - Henikoff, S.
AU  - Comai, L.
TI  - A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis.
JO  - Genetics
PY  - 1998
SP  - 307
EP  - 318
VL  - 149
AB  - Chromodomains are thought to mediate protein-protein interactions between chromatin
AB  - components.  We have detected a chromodomain embedded within the catalytic region of a
AB  - predicted Arabidopsis DNA methyltransferase that is diverged from other eukaryotic enzymes.
AB  - The 791 residue "chromomethylase" is encoded by a floral transcript that is spliced from 20
AB  - exons and is present at only ~1/10^-7 of total mRNA.  Genomic sequencing reveals an ancient
AB  - haplotype split at CMT1 between Col-0 + Metz and the other ecotypes examined.  In the Col-0 +
AB  - Metz haplotype, alternative mRNA processing at intron 13 truncates the coding region.  In Ler,
AB  - RLD, and No-0, similar truncation is caused by insertion of an intact retrotransposon,
AB  - Evelknievel, which is present as a single copy in Ler and RLD and is currently methylated and
AB  - inactive.  Evelknievel is found at this site on a single branch that connects the Ler, RLD,
AB  - and No-0 ecotypes but is absent from the genomes of all other ecotypes examined.  A stop codon
AB  - within exon 6 of the Metz ecotype confirms that CMT1 is nonessential.  Nevertheless,
AB  - comparison to CMT1 of Cardaminopsis arenosa, an outcrossing relative, indicates conservation
AB  - for DNA methyltransferase function.  We discuss how allelic diversity of CMT1 may reflect
AB  - loosened selective constraints in a self-fertilizing species such as Arabidopsis thaliana.
ER  -

TY  - JOUR
AU  - Henke, R.M.
TI  - Molecular and biochemical studies on a bifunctional group I intron encoded protein of yeast mitochondria.
JO  - Diss. Abstr.
PY  - 2000
SP  - 2899
EP  - 2899
VL  - 61
AB  - Intron 4a (aI4a) of the yeast mitochondrial COXI gene is a mobile group I intron that contains
AB  - a reading frame encoding both the homing endonuclease I-SceII and a latent maturase capable of
AB  - splicing both aI4a and the fourth intron of the cytochrome b (COB) gene (bI4).  The aI4a
AB  - reading frame is a member of a large gene family recognized by the presence of related
AB  - dodecapeptide sequence motifs called P1 and P2.  In this study missense mutations of P1 and P2
AB  - were placed in mtDNA by biolistic transformation and the effects of the mutations on intron
AB  - mobility, I-SceII activity and maturase function were tested.  The mutations of P1 strongly
AB  - affected intron mobility and I-SceII activity but had little or no effect on maturase
AB  - function, while mutations of P2 affected splicing but not mobility or I-SceII activity.
AB  - Surprisingly, the conditional (ts) mutations at P1 and P2 block one or the other function of
AB  - the protein but not both.  This study indicates that the two functions depend on separate
AB  - domains of the intron-encoded protein.  Normally splicing of the aI4a intron requires the bI4
AB  - maturase.  In strains lacking the bI4 maturase, second site-suppressors that activate the aI4a
AB  - maturase have been isolated; some map to the nuclear NAM2 gene (NAM2-1) and another to the
AB  - aI4a ORF (MIM2-1, glu 117) and then transformed into yeast mitochondria.  These changes were
AB  - designed to determine if activation of aI4a maturase results from the loss of a negative
AB  - charge or the gain of a positive charge at the mim2 site.  Substitution of a positively
AB  - charged amino acid (lys or arg) results in an active aI4a maturase, while the substitution of
AB  - either a negatively charged amino acid (wild-type, glu) or a neutral amino acid (gln) was
AB  - insufficient to activate the maturase.  These data show that the presence of a positive charge
AB  - at the mim2 residue is sufficient to activate aI4a's latent maturase activity.  The mim2
AB  - alleles were further characterized by assaying them for intron mobility.  All the mim2 alleles
AB  - retain wild-type levels of intron mobility, indicating that they encode I-SceII activity.  The
AB  - presence of both maturase and I-SceII activity in several alleles, (lys and arg) clearly
AB  - demonstrates that both functions can co-exist within the same poly-peptide.  This study also
AB  - characterizes several new in vitro DNA binding properties of I-SceII and speculates on their
AB  - in vivo significance.
ER  -

TY  - JOUR
AU  - Henke, R.M.
AU  - Butow, R.A.
AU  - Perlman, P.S.
TI  - Maturase and endonuclease functions depend on separate conserved domains of the bifunctional protein encoded by the group I intron aI4a of yeast mitochondrial DNA.
JO  - EMBO J.
PY  - 1995
SP  - 5094
EP  - 5099
VL  - 14
AB  - Intron 4a (aI4a) of the yeast mitochondrial COXI gene is a mobile group I intron that contains
AB  - a reading frame encoding both the homing endonuclease I-SceII and a latent maturase capable
AB  - of splicing both aI4a and the fourth intron of the cytochrome b (COB) gene (bI4).  The aI4a
AB  - reading frame is a member of a large gene family recognized by the presence of related
AB  - dodecapeptide sequence motifs called P1 and P2.  In this study, missense mutations of P1 and
AB  - P2 were placed in mitochondrial DNA by biolistic transformation.  The effects of the mutations
AB  - on intron mobility, endonuclease I-SceII activity and maturase function were tested.  The
AB  - mutations of P1 strongly affected mobility and endonuclease I-SceII activity, but had little
AB  - or no effect on maturase function; mutations of P2 affected splicing but not mobility or
AB  - endonuclease I-SceII activity.  Surprisingly, the conditional (temperature-sensitive)
AB  - mutations at P1 and P2 block one or the other function of the protein but not both.  This
AB  - study indicates that the two functions depend on separate domains of the intron-encoded
AB  - protein.
ER  -

TY  - JOUR
AU  - Henkel, C.V.
AU  - den Dulk-Ras, A.
AU  - Zhang, X.
AU  - Hooykaas, P.J.
TI  - Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5.
JO  - Genome Announcements
PY  - 2014
SP  - e00225
EP  - e00214
VL  - 2
AB  - We have sequenced the complete genome of the plant pathogen Agrobacterium tumefaciens strain
AB  - LBA4213, a derivative of the wild-type strain A. tumefaciens
AB  - Ach5 and the ancestor of A. tumefaciens strain LBA4404 used in genetic
AB  - engineering. The genome consists of a circular chromosome and a linear
AB  - chromosome, as well as a megaplasmid and a tumor-inducing plasmid.
ER  -

TY  - JOUR
AU  - Henkin, T.M.
TI  - Classic spotlight: Bacteria versus phage--the Battle Rages!
JO  - J. Bacteriol.
PY  - 2016
SP  - 1007
EP  - 1007
VL  - 198
AB  - Early studies of bacteriophages and their hosts revealed that
AB  - some host strains were more resistant to certain phage isolates
AB  - than were other closely related bacterial strains. Analysis of this
AB  - phenomenon led to the discovery that many bacterial strains contain
AB  - restriction/modification systems. Systems of this type include
AB  - restriction endonucleases that cleave foreign DNA and modification
AB  - enzymes that protect host DNA from cleavage. These restriction
AB  - endonucleases provided the backbone for the development
AB  - of DNA cloning technologies. Demonstration that bacterial
AB  - hosts affected phage properties (1) and characterization of restriction
AB  - and modification systems in Escherichia coli were provided
AB  - in seminal papers by Luria and Human (1), Herbert
AB  - Boyer (2), and Seymour Lederberg (3) in the Journal of Bacteriology
AB  - (JB), as was demonstration that restriction occurs by
AB  - DNA cleavage (4).
ER  -

TY  - JOUR
AU  - Hennecke, F.
AU  - Kolmar, H.
AU  - Brundl, K.
AU  - Fritz, H.-J.
TI  - The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease.
JO  - Nature
PY  - 1991
SP  - 776
EP  - 778
VL  - 253
AB  - In Escherichia coli K-12, the Dcm methyltransferase catalyses methylation of the inner
AB  - cytosine residue in the sequence CCA/TGG. Hydrolytic deamination of 5-methylcytosine bases in
AB  - DNA leads to thymine residues, and hence to T/G mismatches, pre-mutagenic DNA lesions
AB  - consisting of two natural DNA constituents and thus devoid of an obvious marker of the damaged
AB  - DNA strand. These mismatches are corrected by the VSP repair pathway, which is characterized
AB  - by very short patches of DNA repair synthesis. It depends on genes vsr and polA and is
AB  - strongly stimulated by mutL and mutS. The vsr gene product (Vsr; Mr 18,000) was purified and
AB  - characterized as a DNA mismatch endonuclease, a unique and hitherto unknown type of enzyme.
AB  - Vsr endonuclease nicks double-stranded DNA within the sequence CTA/TGN or NTA/TGG next to the
AB  - underlined thymidine residue, which is mismatched to 2'-deoxyguanosine. The incision is
AB  - mismatch-dependent and strand-specific. These results illustrate how Vsr endonuclease
AB  - initiates VSP mismatch repair.
ER  -

TY  - JOUR
AU  - Hennessy, R.C.
AU  - Glaring, M.A.
AU  - Michelsen, C.F.
AU  - Olsson, S.
AU  - Stougaard, P.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain In5 Isolated from a Greenlandic Disease Suppressive Soil with Potent Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2015
SP  - e01251
EP  - e01215
VL  - 3
AB  - Pseudomonas sp. In5 is an isolate of disease suppressive soil with potent activity against
AB  - pathogens. Its antifungal activity has been linked to a gene
AB  - cluster encoding nonribosomal peptide synthetases producing the peptides
AB  - nunamycin and nunapeptin. The genome sequence will provide insight into the
AB  - genetics behind the antimicrobial activity of this strain.
ER  -

TY  - JOUR
AU  - Henriques, A.C.
AU  - De Marco, P.
TI  - Genome Sequence of Rhodococcus sp. Strain RD6.2 DSM 46800, a Methanesulfonate-Degrading Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00730
EP  - e00715
VL  - 3
AB  - The complete genome sequence of a methanesulfonate-degrading strain, Rhodococcus  sp. strain
AB  - RD6.2 DSM 46800, which was isolated from a brackish marsh sediment
AB  - sample, is described here. This is the first reported genome of a
AB  - nonproteobacterial strain using methanesulfonate (MSA) as a sole source of carbon
AB  - and energy, which does not possess the conventional MSA-monooxygenase (MSAMO).
ER  -

TY  - JOUR
AU  - Henriques, A.C.
AU  - De Marco, P.
TI  - Complete Genome Sequences of Two Strains of 'Candidatus Filomicrobium marinum,' a Methanesulfonate-Degrading Species.
JO  - Genome Announcements
PY  - 2015
SP  - e00160
EP  - e00115
VL  - 3
AB  - Two novel methanesulfonate-degrading bacterial strains of 'Candidatus Filomicrobium marinum'
AB  - (strains Y and W) were isolated from a marine water
AB  - enrichment, and their complete genome sequences are presented here. These are the
AB  - first full genomes reported for the genus Filomicrobium and for methanesulfonate
AB  - (MSA)-degrading bacteria.
ER  -

TY  - JOUR
AU  - Henriques, A.O.
AU  - Beall, B.W.
AU  - Roland, K.
AU  - Moran, C.P. Jr.
TI  - Characterization of cotJ, a sigma E-controlled operon affecting the polypeptide composition of the coat of Bacillus subtilis spores.
JO  - J. Bacteriol.
PY  - 1995
SP  - 3394
EP  - 3406
VL  - 177
AB  - The outermost protective structure found in endospores of Bacillus subtilis is a thick protein
AB  - shell known as the coat, which makes a key
AB  - contribution to the resistance properties of the mature spore and also
AB  - plays a role in its interaction with compounds able to trigger
AB  - germination. The coat is organized as a lamellar inner layer and an
AB  - electron-dense outer layer and has a complex polypeptide composition. Here
AB  - we report the cloning and characterization of an operon, cotJ, located at
AB  - about 62 degrees on the B. subtilis genetic map, whose inactivation
AB  - results in the production of spores with an altered pattern of coat
AB  - polypeptides. The cotJ operon was identified by screening a random library
AB  - of lacZ transcriptional fusions for a conditional (inducer-dependent) Lac+
AB  - phenotype in cells of a strain in which the structural gene (spoIIGB) for
AB  - the early-acting, mother-cell-specific transcriptional factor sigma E was
AB  - placed under the control of the IPTG
AB  - (isopropyl-beta-D-thiogalactopyranoside)-inducible Pspac promoter.
AB  - Sequence analysis of cloned DNA from the cotJ region complemented by
AB  - genetic experiments revealed a tricistronic operon preceded by a strong
AB  - sigma E-like promoter. Expression of an SP beta-borne cotJ-lacZ fusion
AB  - commences at around h 2 of sporulation, as does expression of other sigma
AB  - E-dependent genes, and shows an absolute requirement for sigma E. Studies
AB  - with double-reporter strains bearing a cotJ-gusA fusion and lacZ fusions
AB  - to other cot genes confirmed that expression of cotJ is initiated during
AB  - sporulation prior to activation of genes known to encode coat structural
AB  - proteins (with the sole exception of cotE). An in vitro-constructed
AB  - insertion-deletion mutation in cotJ resulted in the formation of spores
AB  - with no detectable morphological or resistance deficiency. However,
AB  - examination of the profile of electrophoretically separated spore coat
AB  - proteins from the null mutant revealed a pattern that was essentially
AB  - identical to that of a wild-type strain in the range of 12 to 65 kDa,
AB  - except for polypeptides of 17 and 24 kDa, the putative products of the
AB  - second (cotJB) and third (cotJC) cistrons of the operon, that were missing
AB  - or reduced in amount in the coat of the mutant. Polypeptides of the same
AB  - apparent sizes are detected in spores of a cotE null mutant, on which
AB  - basis we infer that the products of the cotJ operon are required for the
AB  - normal formation of the inner layers of the coat or are themselves
AB  - structural components of the coat. Because the onset of cotJ transcription is temporally
AB  - coincident with the appearance of active sigmaE, we speculate that cotJ-encoded products may
AB  - be involved in an early stage of coat assembly.
ER  -

TY  - JOUR
AU  - Henriques, I.
AU  - Juca, R.R.T.
AU  - Barauna, R.A.
AU  - de Sa, P.H.
AU  - Marinho, A.D.
AU  - Carneiro, A.R.
AU  - Barbosa, S.
AU  - Pereira, A.
AU  - Alves, A.
AU  - Saavedra, M.J.
AU  - Egas, C.
AU  - Silva, A.
AU  - Correia, A.
TI  - Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water.
JO  - Genome Announcements
PY  - 2013
SP  - e00970
EP  - e00913
VL  - 1
AB  - Serratia fonticola UTAD54 is an environmental isolate that is resistant to carbapenems due to
AB  - the presence of a class A carbapenemase and a
AB  - metallo-beta-lactamase that are unique to this strain. Its draft genome sequence
AB  - was obtained to clarify the molecular basis of its carbapenem resistance and
AB  - identify the genomic context of its carbapenem resistance determinants.
ER  -

TY  - JOUR
AU  - Henry, P.M.
AU  - Leveau, J.H.
TI  - Finished Genome Sequences of Xanthomonas fragariae, the Cause of Bacterial Angular Leaf Spot of Strawberry.
JO  - Genome Announcements
PY  - 2016
SP  - e01271
EP  - e01216
VL  - 4
AB  - Xanthomonas fragariae is a foliar pathogen of strawberry that is of significant concern to
AB  - nursery production of strawberry transplants and field production of
AB  - strawberry fruit. Long-read sequencing was employed to generate finished genomes
AB  - for two isolates (each with one chromosome and two plasmids) from symptomatic
AB  - plants in northern California.
ER  -

TY  - JOUR
AU  - Hensgens, L.A.M.
AU  - Bonen, L.
AU  - de Haan, M.
AU  - van der Horst, G.
AU  - Grivell, L.A.
TI  - Two intron sequences in yeast mitochondrial COX1 gene:  homology among URF-containing introns and strain-dependent variation in flanking exons.
JO  - Cell
PY  - 1983
SP  - 379
EP  - 389
VL  - 32
AB  - The DNA sequences of two optional introns in the gene for subunit I of cytochome c oxidase in
AB  - yeast mitochondrial DNA have been determined. Both contain long unassigned reading frames
AB  - (URFs). These display regions of amino acid homology with six other URFs, two of which encode
AB  - proteins involved in mitochondrial RNA splicing. Such conserved regions may thus define
AB  - functionally important domains of proteins involved in RNA processing. This homology also
AB  - implies that these URFs had a common ancestral sequence, which has been duplicated and
AB  - sipersed around the genome. Comparison of the flanking exons in the long strain KL14-4A with
AB  - their unsplit counterpart in D273-10B reveals clustered sequence differences, which lead in
AB  - D273-10B to codonas rearely used in exons. These differences may be linked to the loss or
AB  - absence of one of the optional introns.
ER  -

TY  - JOUR
AU  - Hensley, P.
AU  - Nardone, G.
AU  - Chirikjian, J.G.
AU  - Wastney, M.E.
TI  - The time-resolved kinetics of superhelical DNA cleavage by BamHI restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 15300
EP  - 15307
VL  - 265
AB  - The kinetics of the cleavage of superhelical plasmid DNA (pBR322) by the
AB  - restriction endonuclease, BamHI, have been analyzed in terms of a compartmental
AB  - model consistent with the chemistry first proposed by Rubin and Modrich (Rubin,
AB  - R.A., and Modrich, P. (1978) Nucleic Acids Res. 5, 2991-2997) for analysis of
AB  - the kinetics of the restriction endonuclease, EcoRI.  The model was defined in
AB  - terms of two compartments representing DNA substrate (bound and free), two
AB  - compartments representing nicked intermediate (bound and free), one compartment
AB  - representing linear product, and one compartment for free enzyme.  A
AB  - simultaneous analysis of concentration changes over time of the three DNA forms
AB  - (superhelical, nicked, and linear) at six different enzyme concentrations was
AB  - undertaken employing this compartmental model using SAAM (Simulation Analysis
AB  - and Modeling) software.  Results showed that rate constants characterizing the
AB  - association of enzyme with superhelical DNA (6.0 x 10/5M-1S-1) and nicked DNA
AB  - (2.8 x 10/5M-1S-1) were similar in magnitude and rate constants characterizing
AB  - cleavage of the first (1.2 x 10-2S-1) and second phosphodiester bonds (3.1 x
AB  - 10-2S-1) were also similar.  The analysis yields a kinetically determined
AB  - equilibrium constant of 12.9 nM for the dissociation of nicked intermediate
AB  - from the enzyme.  The rate constant describing the release of the nicked
AB  - intermediate from the enzyme has a value of 3.7 x 10-3S-1.  By comparing the
AB  - value of this release rate constant to the value of the constant describing the
AB  - second cleavage event, it can be determined that only 10% of the nicked
AB  - intermediate bound to the enzyme is released as free nicked DNA and that 90% of
AB  - the nicked intermediate is processed to the linear form without being released.
AB  - Hence, most of the DNA is cleaved as the result of a single enzyme-DNA
AB  - recognition event.  No steady state assumptions were made in the analysis.  The
AB  - approach was to directly solve the differential equations which described the
AB  - kinetic processes using an interactive method.  This study demonstrates the
AB  - usefulness of this approach for the analysis of kinetics of protein-DNA
AB  - interactions for the restriction endonucleases.
ER  -

TY  - JOUR
AU  - Hentosh, P.
AU  - McCastlain, J.C.
TI  - Effects of 2-chloroadenine substitution in DNA on restriction endonuclease cleavage reactions.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 3143
EP  - 3148
VL  - 19
AB  - The purine analog, 2-chloro-2'-deoxyadenosine triphosphate (CldATP), was
AB  - incorporated enzymatically in place of dATP into the minus strand of M13mp18
AB  - duplex DNA.  Its effect on protein-DNA interactions was assessed by determining
AB  - the amount of DNA cleavage by type II restriction endonucleases.  Substitution
AB  - of chloroadenine (ClAde) for adenine (Ade) in DNA appreciably decreased the
AB  - amount and rate of DNA cleavage of the minus strand when the analog was
AB  - situated within the appropriate endonuclease recognition site.  ClAde residues
AB  - flanking a restriction site had variable effects.  SmaI cleaved both
AB  - ClAde-containing and control substrates with equal efficiency.  NarI, however,
AB  - was stimulated 1.5-fold by the presence of ClAde outside its recognition site.
AB  - The effects of analog incorporation on restriction enzyme cleavage of an
AB  - opposing unsubstituted strand of duplex DNA was examined by enzymatically
AB  - incorporating CldATP into complementary minus strand of a 36-base
AB  - oligonucleotide.  Endonucleolytic cleavage of both plus and minus strands was
AB  - reduced on 36-mers containing ClAde residues located within only the minus
AB  - strand.  These data suggest that ClAde residues incorporated into a single DNA
AB  - strand may have an appreciable effect of DNA-protein interactions that involve
AB  - one or both strands of duplex DNA.
ER  -

TY  - JOUR
AU  - Hepburn, P.A.
AU  - Margison, G.P.
AU  - Tisdale, M.J.
TI  - Enzymatic methylation of cytosine in DNA is prevented by adjacent 06-methylguanine residues.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 7985
EP  - 7987
VL  - 266
AB  - The effect of 06-alkylation of guanine residues on the enzymatic methylation of
AB  - cytosine has been studied using synthetic oligonucleotides in which all
AB  - guanines in cytosine-guanine sequences at potentially methylatable sites are
AB  - replaced by 06-methylguanine.  In contrast with the unmodified forms, which
AB  - showed high acceptance activity for methyl-3H-labeled groups from
AB  - S-adenosyl-L-[methyl-3H]methionine in the presence of DNA methylase, the
AB  - modified oligonucleotides were not substrates for the enzyme neither in the
AB  - single-stranded or annealed forms.  In view of the importance of cytosine
AB  - methylation in the down-regulation of certain genes, the potential to affect
AB  - gene expression by this mechanism may be a contributory factor in the toxic and
AB  - carcinogenic effects of chemical methylating agents.
ER  -

TY  - JOUR
AU  - Hepburn, P.A.
AU  - Tisdale, M.J.
TI  - Importance of the O6 position of guanine residues in the binding of DNA methylase to DNA.
JO  - Biochim. Biophys. Acta
PY  - 1991
SP  - 341
EP  - 344
VL  - 1088
AB  - Methylation of Micrococcus lysodeikticus DNA by purified DNA methylase isolated
AB  - from L1210 leukaemia cells is potently and specifically inhibited by both
AB  - hetero and homoribo and deoxyribopolynucleotides containing guanine residues.
AB  - The inhibitory effect is unaffected by chain length, but is abolished when the
AB  - O6 residue of guanine is substituted as in poly[d(O6MeG)]20.  Potent inhibition
AB  - is also shown by polyinosinic and polyxanthylic acids, but not by polyadenylic
AB  - acid or by heteropolymers containing adenine and thymine.  These results
AB  - suggest that the 6-position of the purine nucleus is important in binding of
AB  - the DNA methylase to a particular region of the DNA duplex and that the
AB  - hydrogen bonding properties of this group are important in enzyme recognition.
ER  -

TY  - JOUR
AU  - Hepworth, P.J.
AU  - Ashelford, K.E.
AU  - Hinds, J.
AU  - Gould, K.A.
AU  - Witney, A.A.
AU  - Williams, N.J.
AU  - Leatherbarrow, H.
AU  - French, N.P.
AU  - Birtles, R.J.
AU  - Mendonca, C.
AU  - Dorrell, N.
AU  - Wren, B.W.
AU  - Wigley, P.
AU  - Hall, N.
AU  - Winstanley, C.
TI  - Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes.
JO  - Environ. Microbiol.
PY  - 2011
SP  - 1549
EP  - 1560
VL  - 13
AB  - Although the major food-borne pathogen Campylobacter jejuni has been
AB  - isolated from diverse animal, human and environmental sources, our
AB  - knowledge of genomic diversity in C. jejuni is based exclusively on human
AB  - or human food-chain-associated isolates. Studies employing multilocus
AB  - sequence typing have indicated that some clonal complexes are more
AB  - commonly associated with particular sources. Using comparative genomic
AB  - hybridization on a collection of 80 isolates representing diverse sources
AB  - and clonal complexes, we identified a separate clade comprising a group of
AB  - water/wildlife isolates of C. jejuni with multilocus sequence types
AB  - uncharacteristic of human food-chain-associated isolates. By genome
AB  - sequencing one representative of this diverse group (C. jejuni 1336), and
AB  - a representative of the bank-vole niche specialist ST-3704 (C. jejuni
AB  - 414), we identified deletions of genomic regions normally carried by human
AB  - food-chain-associated C. jejuni. Several of the deleted regions included
AB  - genes implicated in chicken colonization or in virulence. Novel genomic
AB  - insertions contributing to the accessory genomes of strains 1336 and 414
AB  - were identified. Comparative analysis using PCR assays indicated that
AB  - novel regions were common but not ubiquitous among the water/wildlife
AB  - group of isolates, indicating further genomic diversity among this group,
AB  - whereas all ST-3704 isolates carried the same novel accessory regions.
AB  - While strain 1336 was able to colonize chicks, strain 414 was not,
AB  - suggesting that regions specifically absent from the genome of strain 414
AB  - may play an important role in this common route of Campylobacter infection
AB  - of humans. We suggest that the genomic divergence observed constitutes
AB  - evidence of adaptation leading to niche specialization.
ER  -

TY  - JOUR
AU  - Herbert, J.A.
AU  - Mitchell, A.M.
AU  - Ritchie, R.
AU  - Ma, J.
AU  - Ross-Hutchinson, K.
AU  - Mitchell, T.J.
TI  - Expression of the lux genes in Streptococcus pneumoniae modulates pilus expression and virulence.
JO  - PLoS ONE
PY  - 2018
SP  - e0189426
EP  - e0189426
VL  - 13
AB  - Bioluminescence has been harnessed for use in bacterial reporter systems and for  in vivo
AB  - imaging of infection in animal models. Strain Xen35, a bioluminescent
AB  - derivative of Streptococcus pneumoniae serotype 4 strain TIGR4 was previously
AB  - constructed for use for in vivo imaging of infections in animal models. We have
AB  - shown that strain Xen35 is less virulent than its parent TIGR4 and that this is
AB  - associated with the expression of the genes for bioluminescence. The expression
AB  - of the luxA-E genes in the pneumococcus reduces virulence and down regulates the
AB  - expression of the pneumococcal pilus.
ER  -

TY  - JOUR
AU  - Herbert, M.
AU  - O'Keeffe, T.A.
AU  - Purdy, D.
AU  - Elmore, M.
AU  - Minton, N.P.
TI  - Gene transfer into Clostridium difficile CD630 and characterisation of its methylase genes.
JO  - FEMS Microbiol. Lett.
PY  - 2003
SP  - 103
EP  - 110
VL  - 229
AB  - Ignorance of pathogenesis in Clostridium difficile may be attributable to a lack of effective
AB  - genetic tools. We have now shown that oriT-based
AB  - shuttle vectors may be conjugated from Escherichia coli donors to the C.
AB  - difficile strain CD630, at frequencies of around 10(-6) transconjugants
AB  - per donor cell. Transfer is unaffected by either sequences present on the
AB  - vector or its methylation status. Whilst the genome of this strain carries
AB  - five methylase genes, there is no in silico or experimental evidence for
AB  - cognate restriction enzymes. It would seem that the identified methylases
AB  - do not participate in restriction-modification, and must, therefore,
AB  - fulfil another role. A similar situation most likely applies to other
AB  - clostridia.
ER  -

TY  - JOUR
AU  - Herd, M.
AU  - Kocks, C.
TI  - Gene fragments distinguishing an epidemic-associated strain from a virulent prototype strain of Listeria monocytogenes belong to a distinct   functional subset of genes and partially cross-hybridize with other   Listeria species.
JO  - Infect. Immun.
PY  - 2001
SP  - 3972
EP  - 3979
VL  - 69
AB  - Most major food-borne outbreaks of listeriosis in Europe and in the United States have been
AB  - caused by genetically closely related Listeria
AB  - monocytogenes strains of serotype 4b. In order to assess whether genomic
AB  - loci exist that could underlie this increased epidemic potential, we
AB  - subtracted the genome of the virulent prototype L. monocytogenes strain
AB  - EGD from a prototype epidemic strain. A total of 39 DNA fragments
AB  - corresponding to 20% of an estimated total of 150 to 190 kb of
AB  - differential genome material were isolated. For 21 of these fragments, no
AB  - function on the basis of homology could be predicted. Of the remaining 18
AB  - fragments, 15 had homologies to bacterial surface proteins, some of which
AB  - have been implicated in virulence mechanisms such as cell invasion,
AB  - adhesion, or immune escape. Southern hybridization of arrays containing
AB  - the epidemic-clone-specific DNA segments with genomic DNA of different L.
AB  - monocytogenes strains was consistent with the current lineage division.
AB  - Surprisingly, however, some of the fragments hybridized in a mosaic-like
AB  - fashion to genomes of two other Listeria species, the animal pathogen L.
AB  - ivanovii and the nonpathogen L. innocua. Taken together, our results
AB  - provide a starting point for the identification of
AB  - epidemic-trait-associated genes.
ER  -

TY  - JOUR
AU  - Herman, G.E.
AU  - Modrich, P.
TI  - Escherichia coli K-12 clones that overproduce dam methylase are hypermutable.
JO  - J. Bacteriol.
PY  - 1981
SP  - 644
EP  - 646
VL  - 145
AB  - A strain of Escherichia coli K-12 that overproduces dam methylase 50-fold was found to be
AB  - hypermutable, and mutations which resulted in loss of excess methylase activity restored
AB  - mutation frequencies to wild-type levels. These results are consistent with involvement of
AB  - this deoxyribonucleic acid methylase in mismatch correction.
ER  -

TY  - JOUR
AU  - Herman, G.E.
AU  - Modrich, P.
TI  - Escherichia coli dam methylase physical and catalytic properties of the homogeneous enzyme.
JO  - J. Biol. Chem.
PY  - 1982
SP  - 2605
EP  - 2612
VL  - 257
AB  - The Escherichia coli dam methylase has been purified 3000-fold to a purity of 95% from a clone
AB  - which overproduces the enzyme 10- to 20-fold. Physical properties of enzyme purified from the
AB  - overproducing clone were identical with those of enzyme previously obtained from a
AB  - non-overproducing E. coli strain (Geier, G.E., and Modrich, P. (1979) J. Biol. Chem. 254,
AB  - 1408-1413). The methylase is comprised of a single polypeptide chain of Mr = 31,000 has an
AB  - S20,W of 2.8 S, a Stokes radius of 24 A, and exists in solution as a monomer. Its aggregation
AB  - state is not affected by the presence of S-adenosyl-L-methionine. The simple kinetic behavior
AB  - of the methylase indicates that it functions as a monomer. Initial rates of methyl transfer
AB  - are first order in enzyme concentration, and Michaelis-Menten behavior is obeyed with respect
AB  - to both substrates. At 37C, in the presence of saturating DNA, the enzyme has a turnover
AB  - number of 19 methyl transfers/min with a KM for S-adenosyl-L-methionine of 12.2 lM. At
AB  - half-saturating S-adenosyl-L-methionine, the apparent KM for d(G-A-T-C) sites in ColE1 DNA is
AB  - 3.6NM. The mechanism of methyl transfer is also consistent with the monomer being the
AB  - functional form of the enzyme. Studies with G4 RFI DNA (two d(G-A-T-C) sites) indicate that
AB  - the methylase transfers 1 methyl group to a recognition site and then dissociates from this
AB  - DNA prior to subsequent catalysis. It appears that kinetic parameters for methyl transfer to
AB  - sites already modified on one DNA strand may be slightly more favorable than those for
AB  - transfer to sites in which both strands are unmethylated.
ER  -

TY  - JOUR
AU  - Herman, J.
AU  - Nelkin, B.
AU  - Mabry, M.
AU  - Wilson, G.
AU  - Baylin, S.
TI  - Introduction and expression of HhaI DNA methyltransferase in eukaryotic cells.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 223
EP  - 223
VL  - 13D
AB  - DNA methylation abnormalities, which include both widespread hypomethylation
AB  - and regional hypermethylation, hve been reported for many malignancies.  In
AB  - culture, tumor cells often have increased DNA methyltransferase activity with
AB  - unknown consequences.  To assess functional consequences of increased cytosine
AB  - methylation in eukaryotic cells, we are using a constitutively expressed
AB  - prokaryotic DNA methyltransferase enzyme in murine fibroblasts.  We inserted
AB  - the cloned DNA sequence for the bacterial DNA methyltransferase M.HhaI
AB  - (methylated sequence G^mCGC) into the retroviral expression vector pZIPneo
AB  - SV(X).  Abundant G418 resistant colonies were produced in PA 317 amphotropic
AB  - packaging cells after infection with either the pZIPneo SV(X) vector alone or
AB  - M.HhaI inserted in the antisense direction.  However, insertion of M.HhaI in
AB  - the sense orientation resulted in a total of two G418 resistant clones in 5
AB  - independent experiments.  Southern and Northern blots probed with M.HhaI
AB  - sequences demonstrated integration and expression.  Each M.HhaI clone in the
AB  - sense orientation was tumorigenic in nude mice, and one of the clones was
AB  - morphologically distinct from control PA 317 cells.  Other data suggest that
AB  - constitutive expression of M.HhaI is often lethal to eukaryotic cells in
AB  - culture, and may cause transformation of surviving cells.
ER  -

TY  - JOUR
AU  - Herman, J.
AU  - Nelkin, B.
AU  - Mabry, M.
AU  - Wilson, G.
AU  - Baylin, S.
TI  - Introduction of prokaryotic HhaI DNA methyltransferase alters the phenotype of 3T3 cells.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1989
SP  - 428
EP  - 428
VL  - 30
AB  - DNA methylation abnormalities are common in cancer.  Recently, we described
AB  - hypermethylation on chromosome 11p (PNAS USA 85:5693-5697, 1988) which could
AB  - result from the fact that tumor cells often have increased DNA
AB  - methyltransferase activity.  To assess the functional consequences of
AB  - increasing cytosine methylation capacity in eukaryotic cells, we have
AB  - constitutively expressed two prokaryotic DNA methyltransferase enzymes in
AB  - murine fibroblasts.  DNA sequences for the bacterial DNA methyltransferases
AB  - M.HhaI (methylated sequence GmCGC), and M.HpaII (CmCGG) were introduced via the
AB  - retroviral expression vector pZIPneo SV(X).  Abundant G418 resistant colonies,
AB  - typically 60/experiment, were produced in PA317 amphotropic packaging cells
AB  - after infection with the pZIPneo SV(X) vector alone, the M.HhaI inserted in the
AB  - antisense direction, and M.HpaII in both directions.  However, insertion of
AB  - M.HhaI in the sense orientation resulted in a total of only two G418 resistant
AB  - clones in 5 independent experiments.  M.HhaI sequences were integrated and
AB  - expressed in each clone.  Both clones were tumorigenic in nude mice, and one of
AB  - the clones was morphologically distinct from control PA317 cells.  We also
AB  - observed a similar discrepancy in the ability to select stably transfected Psi2
AB  - cells used to infect the PA317 cells with the sense M.HhaI construct.  Our data
AB  - suggest that constitutive expression of M.HhaI is most often lethal to 3T3
AB  - cells in culture, and may cause transformation of those cells which survive.
ER  -

TY  - JOUR
AU  - Hermann, A.
AU  - Fatemi, M.
AU  - Jeltsch, A.
TI  - Molecular enzymology of the Dnmt1 DNA methyltransferase explains the mechanism of cis-spreading of DNA methylation.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A248
EP  - A248
VL  - 28
AB  - In mammals, methylation of DNA within CpG-sequences is involved in epigenetic control of gene
AB  - expression, chromatin condensation and genetic imprinting.  So far, three active DNA
AB  - methyltransferases have been identified in mice: Dnmt1 which is responsible for maintenance
AB  - methylation, as well as Dnmt3a and 3b which are required for de novo methylation.  Methylation
AB  - of DNA is essential in mammals because mice deficient in either Dnmt1, Dnmt3a or Dnmt3b die
AB  - during development.  During tumorigenesis or aging, spreading of methylation is observed, i.e.
AB  - starting from one modified CpG-site methylation spreads to neighboring CpGs until one region
AB  - of the DNA is completely methylated.  The Dnmt1 enzyme consists of a catalytic domain (500
AB  - amino acid residues) which closely resembles prokaryotic DNA-(cytosine-C5)-methyltransferases
AB  - and a large regulatory N-terminal domain comprising about 1100 amino acid residues.  By
AB  - cloning and characterizing several fragments of the Dnmt1 enzyme, we demonstrate that the
AB  - N-terminal domain forms a DNA binding site distinct from the active center.  In kinetic assays
AB  - with purified full-length Dnmt1, we show that binding of methylated CpGs to this additional
AB  - DNA binding site allosterically activates the enzyme.  These enzymological properties of Dnmt1
AB  - can explain the phenomenon of spreading of DNA methylation.
ER  -

TY  - JOUR
AU  - Hermann, A.
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Biochemistry and biology of mammalian DNA methyltransferases.
JO  - Cell. Mol. Life Sci.
PY  - 2004
SP  - 2571
EP  - 2587
VL  - 61
AB  - DNA methylation is a stable but not irreversible epigenetic signal that silences gene
AB  - expression. It has a variety of important functions in mammals, including control of gene
AB  - expression, cellular differentiation and development, preservation of chromosomal integrity,
AB  - parental imprinting and X-chromosome inactivation. In addition, it has been implicated in
AB  - brain function and the development of the immune system. Somatic alterations in genomic
AB  - methylation patterns contribute to the etiology of human cancers and ageing. It is tightly
AB  - interwoven with the modification of histone tails and other epigenetic signals. Here we review
AB  - our current understanding of the molecular enzymology of the mammalian DNA methyltransferases
AB  - Dnmt1, Dnmt3a, Dnmt3b and Dnmt2 and the roles of the enzymes in the above-mentioned biological
AB  - processes.
ER  -

TY  - JOUR
AU  - Hermann, A.
AU  - Goyal, R.
AU  - Jeltsch, A.
TI  - The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 48350
EP  - 48359
VL  - 279
AB  - In the cell Dnmt1 is the major enzyme to maintain the pattern of DNA methylation after DNA
AB  - replication. Evidence suggests the protein is
AB  - located at the replication fork where it could directly modify nascent DNA
AB  - immediately after replication. To elucidate the potential mechanism of
AB  - this process, we investigate the processivity of DNA methylation and
AB  - accuracy of copying an existing pattern of methylation in this study using
AB  - purified Dnmt1 and hemimethylated substrate DNA. We demonstrate that Dnmt1
AB  - methylates a hemimethylated 958mer substrate in a highly processive
AB  - reaction. Fully methylated and unmethylated CG sites do not inhibit
AB  - processive methylation of the DNA. Extending previous work, we show that
AB  - unmethylated sites embedded in a hemimethylated context are modified at an
AB  - approx. 24-fold reduced rate which demonstrates that the enzyme accurately
AB  - copies existing patterns of methylation. Completely unmodified DNA is
AB  - methylated even more slowly due to an allosteric activation of Dnmt1 by
AB  - methylcytosine-containing DNA. Interestingly, Dnmt1 is not able to
AB  - methylate hemimethylated CG sites on different strands of the DNA in a
AB  - processive manner indicating that Dnmt1 keeps its orientation with respect
AB  - to the DNA while methylating the CG sites on one strand of the DNA.
ER  -

TY  - JOUR
AU  - Hermann, A.
AU  - Jeltsch, A.
TI  - Methylation sensitivity of restriction enzymes interacting with GATC sites.
JO  - Biotechniques
PY  - 2003
SP  - 924
EP  - 930
VL  - 34
AB  - DNA methylation plays an important role in many species ranging from bacteria to man, by
AB  - controlling the expression of genes and protection of the genome from selfish DNA like
AB  - transposons and viruses.  In E. coli and other gamma-proteobacteria, methylation of adenine
AB  - residues (dam, DNA adenine methylation) occurs at GATC sites.  It serves to discriminate
AB  - between parental and daughter strand during post-replicative mismatch repair, to coordinate
AB  - cell cycle, DNA replication, and to regulate gene expression.  It also controls the
AB  - pathogenicity of different gamma-proteobacteria.  To investigate the methylation state of DNA
AB  - from various bacteria, archaea as well as lower and higher eukaryotes, digestion of the DNA
AB  - with GATC-interacting restriction enzymes is often used.
ER  -

TY  - JOUR
AU  - Hermann, A.
AU  - Schmitt, S.
AU  - Jeltsch, A.
TI  - The human Dnmt2 has residual DNA-(cytosine-C5)-methyltransferase activity.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 31717
EP  - 31721
VL  - 278
AB  - The human Dnmt2 protein is one member of a protein family conserved from Schizosaccharomyces
AB  - pombe and Drosophila melanogaster to Mus musculus and
AB  - Homo sapiens. It contains all of the amino acid motifs characteristic for
AB  - DNA-(Cytosine-C5) methyltransferases, and its structure is very similar to
AB  - prokaryotic DNA methyltransferases. Nevertheless, so far all attempts to
AB  - detect catalytic activity of this protein have failed. We show here by two
AB  - independent assay systems that the purified Dnmt2 protein has weak DNA
AB  - methyltransferase activity. Methylation was observed at CG sites in a
AB  - loose ttnCGga(g/a) consensus sequence, suggesting that Dnmt2 has a more
AB  - specialized role than other mammalian DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Hernandez, D.
AU  - Seidl, K.
AU  - Corvaglia, A.R.
AU  - Bayer, A.S.
AU  - Xiong, Y.Q.
AU  - Francois, P.
TI  - Genome Sequences of Sequence Type 45 (ST45) Persistent Methicillin-Resistant Staphylococcus aureus (MRSA) Bacteremia Strain 300-169 and ST45 Resolving MRSA  Bacteremia Strain 301-188.
JO  - Genome Announcements
PY  - 2014
SP  - e00174
EP  - e00114
VL  - 2
AB  - Persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia (positive blood
AB  - cultures after >/=7 days) represents a challenging subset of
AB  - invasive MRSA infections. The comparison of genome sequences of persistent
AB  - (300-169) and resolving (301-188) MRSA bacteremia isolates with similar genetic
AB  - background (sequence type 45 [ST45]) will help us to better understand underlying
AB  - mechanisms of persistent MRSA bacteremia.
ER  -

TY  - JOUR
AU  - Hernandez, D.
AU  - van der Mee-Marquet, N.
AU  - Kluytmans, J.
AU  - Donnio, P.Y.
AU  - Quentin, R.
AU  - Corvaglia, A.R.
AU  - Francois, P.
TI  - Whole-Genome Sequences of Staphylococcus aureus ST398 Strains of Animal Origin.
JO  - Genome Announcements
PY  - 2013
SP  - e00689
EP  - e00613
VL  - 1
AB  - Staphylococcus aureus sequence type 398 (ST398) was originally associated with animal
AB  - infections. We announce the complete genome sequences of two ST398
AB  - methicillin-susceptible S. aureus strains from the livestock environment. These
AB  - genome sequences assist in the characterization of interesting ST398 features
AB  - relying on host tropism and epidemiological settings.
ER  -

TY  - JOUR
AU  - Hernandez, I.
AU  - Fernandez, C.
TI  - Draft Genome Sequence and Assembly of a Lysobacter enzymogenes Strain with Biological Control Activity against Root Knot Nematodes.
JO  - Genome Announcements
PY  - 2017
SP  - e00271
EP  - e00217
VL  - 5
AB  - Lysobacter enzymogenes strain B25, an isolate from an agricultural field, acts as a biological
AB  - control agent against root knot nematodes in tomato plants. B25 also
AB  - controls several fungal diseases and promotes plant growth under abiotic stress.
AB  - We hereby report on the draft genome sequence and assembly of B25.
ER  -

TY  - JOUR
AU  - Hernandez-Gonzalez, I.L.
AU  - Olmedo-Alvarez, G.
TI  - Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T.
JO  - Genome Announcements
PY  - 2016
SP  - e00640
EP  - e00616
VL  - 4
AB  - Bacillus aquimaris TF12 is a Gram-positive bacteria isolated from a tidal flat of the Yellow
AB  - Sea in South Korea. We report the draft whole-genome sequence of
AB  - Bacillus aquimaris TF12, the type strain of a set of bacteria typically
AB  - associated with marine habitats and with a potentially high biotechnology value.
ER  -

TY  - JOUR
AU  - Hernandez-Gonzalez, I.L.
AU  - Olmedo-Alvarez, G.
TI  - Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719.
JO  - Genome Announcements
PY  - 2016
SP  - e00641
EP  - e00616
VL  - 4
AB  - Members of the Bacillus genus have been extensively studied because of their ability to
AB  - produce enzymes with high biotechnological value. Here, we report the
AB  - draft of the whole-genome sequence of the type strain Bacillus horikoshii DSM
AB  - 8719, an alkali-tolerant strain.
ER  -

TY  - JOUR
AU  - Hernandez-Maldonado, J.
AU  - Stoneburner, B.
AU  - Boren, A.
AU  - Miller, L.
AU  - Rosen, M.
AU  - Oremland, R.S.
AU  - Saltikov, C.W.
TI  - Genome Sequence of the Photoarsenotrophic Bacterium Ectothiorhodospira sp. Strain BSL-9, Isolated from a Hypersaline Alkaline Arsenic-Rich Extreme Environment.
JO  - Genome Announcements
PY  - 2016
SP  - e01139
EP  - e01116
VL  - 4
AB  - The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple
AB  - sulfur bacterium encodes an arxA-type arsenite oxidase within the
AB  - arxB2AB1CD gene island and is capable of carrying out 'photoarsenotrophy'
AB  - anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb
AB  - and has approximately 63% G+C content.
ER  -

TY  - JOUR
AU  - Hernandez-Mendoza, A.
AU  - Lozano-Aguirre, B.L.F.
AU  - Martinez-Ocampo, F.
AU  - Quiroz-Castaneda, R.E.
AU  - Dantan-Gonzalez, E.
TI  - A Newly Sequenced Alcaligenes faecalis Strain: Implications for Novel Temporal Symbiotic Relationships.
JO  - Genome Announcements
PY  - 2014
SP  - e01246
EP  - e01214
VL  - 2
AB  - We report here the draft genome sequence of Alcaligenes faecalis strain MOR02, a  bacterium
AB  - that is able to colonize nematodes in a temporary fashion and kill
AB  - insects for their own benefit. The availability of the genome should enable us to
AB  - explain these phenotypes.
ER  -

TY  - JOUR
AU  - Hernandez-Mendoza, A.
AU  - Martinez-Ocampo, F.
AU  - Lozano-Aguirre, B.L.F.
AU  - Popoca-Ursino, E.C.
AU  - Ortiz-Hernandez, L.
AU  - Sanchez-Salinas, E.
AU  - Dantan-Gonzalez, E.
TI  - Draft Genome Sequence of the Organophosphorus Compound-Degrading Burkholderia zhejiangensis Strain CEIB S4-3.
JO  - Genome Announcements
PY  - 2014
SP  - e01323
EP  - e01314
VL  - 2
AB  - Burkholderia species are widely distributed in the environment. A Burkholderia zhejiangensis
AB  - strain was isolated from pesticide-contaminated soil from an
AB  - agricultural field in Mexico and identified as an organophosphorus
AB  - compound-degrading bacterium. In this study, we report the draft genome sequence
AB  - of Burkholderia zhejiangensis strain CEIB S4-3.
ER  -

TY  - JOUR
AU  - Hernandez-Salmeron, J.E.
AU  - Hernandez-Leon, R.
AU  - Orozco-Mosqueda, M.C.
AU  - Valencia-Cantero, E.
AU  - Moreno-Hagelsieb, G.
AU  - Santoyo, G.
TI  - Draft Genome Sequence of the Biocontrol and Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens strain UM270.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 5
EP  - 5
VL  - 11
AB  - The Pseudomonas fluorescens strain UM270 was isolated form the rhizosphere of wild Medicago
AB  - spp. A previous work has shown that this pseudomonad isolate was
AB  - able to produce diverse diffusible and volatile compounds involved in plant
AB  - protection and growth promotion. Here, we present the draft genome sequence of
AB  - the rhizobacterium P. fluorescens strain UM270. The sequence covers 6,047,974 bp
AB  - of a single chromosome, with 62.66 % G + C content and no plasmids. Genome
AB  - annotations predicted 5,509 genes, 5,396 coding genes, 59 RNA genes and 110
AB  - pseudogenes. Genome sequence analysis revealed the presence of genes involved in
AB  - biological control and plant-growth promoting activities. We anticipate that the
AB  - P. fluorescens strain UM270 genome will contribute insights about bacterial plant
AB  - protection and beneficial properties through genomic comparisons among
AB  - fluorescent pseudomonads.
ER  -

TY  - JOUR
AU  - Hernandez-Santana, A.
AU  - Gomez-Garzon, C.
AU  - Dussan, J.
TI  - Complete Genome Sequence of Lysinibacillus sphaericus WHO Reference Strain 2362.
JO  - Genome Announcements
PY  - 2016
SP  - e00545
EP  - e00516
VL  - 4
AB  - Lysinibacillus sphaericus is a species that contains strains widely used in the biological
AB  - control of mosquitoes. Here, we present the complete 4.67-Mb genome of
AB  - the WHO entomopathogenic reference strain L. sphaericus 2362, which is probably
AB  - one of the most commercialized and studied strains. Genes coding for
AB  - mosquitocidal toxin proteins were detected.
ER  -

TY  - JOUR
AU  - Herren, C.D. et al.
TI  - Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai.
JO  - Genome Announcements
PY  - 2017
SP  - e01233
EP  - e01217
VL  - 5
AB  - Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect
AB  - Mycobacterium smegmatis mc(2)155 were isolated. The four phages are
AB  - closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative
AB  - protein-coding genes, including tyrosine integrases, cro, immunity repressors,
AB  - and excise genes involved in the establishment of lysogeny.
ER  -

TY  - JOUR
AU  - Herrin, D.L.
AU  - Chen, Y.-F.
AU  - Schmidt, G.W.
TI  - RNA splicing in Chlamydomonas chloroplasts.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 21134
EP  - 21140
VL  - 265
AB  - The 23 rRNA gene of the Chlamydomonas reinhardtii chloroplast contains an 888-base pair intron
AB  - with structural features characteristic of Group I introns. The nuclear, chloroplast
AB  - ribosome-deficient mutant of C. reinhardtii, ac20, overaccumulates an approx. 3.6-kilobase
AB  - unspliced 23 S preRNA compared to wild-type cells. We have used [a-32P]GTP labeling of total
AB  - RNA preparations from ac20 to rapidly determine that 23 S preRNA is capable of self-splicing.
AB  - The ability of the 23 S intron (with flanking exon sequences) to correctly catalyze its own
AB  - splicing was confirmed using RNA produced by in vitro transcription of cloned DNA. These
AB  - results identify the first example of a self-splicing RNA of chloroplast origin.
ER  -

TY  - JOUR
AU  - Herschend, J.
AU  - Raghupathi, P.K.
AU  - Roder, H.L.
AU  - Sorensen, S.J.
AU  - Burmolle, M.
TI  - Draft Genome Sequences of Two Kocuria Isolates, K. salsicia G1 and K. rhizophila  G2, Isolated from a Slaughterhouse in Denmark.
JO  - Genome Announcements
PY  - 2016
SP  - e00075
EP  - e00016
VL  - 4
AB  - We report here the draft genome sequences ofKocuria salsiciaG1 andKocuria rhizophilaG2, which
AB  - were isolated from a meat chopper at a small slaughterhouse
AB  - in Denmark. The two annotated genomes are 2.99 Mb and 2.88 Mb in size,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Herschend, J.
AU  - Raghupathi, P.K.
AU  - Roder, H.L.
AU  - Sorensen, S.J.
AU  - Burmolle, M.
TI  - Genome Sequence of Kocuria palustris Strain W4.
JO  - Genome Announcements
PY  - 2016
SP  - e00074
EP  - e00016
VL  - 4
AB  - We report the 3.09 Mb draft genome sequence ofKocuria palustrisW4, isolated from  a
AB  - slaughterhouse in Denmark.
ER  -

TY  - JOUR
AU  - Herschend, J.
AU  - Raghupathi, P.K.
AU  - Roder, H.L.
AU  - Sorensen, S.J.
AU  - Burmolle, M.
TI  - Genome Sequence of Arthrobacter antarcticus Strain W2, Isolated from a Slaughterhouse.
JO  - Genome Announcements
PY  - 2016
SP  - e00073
EP  - e00016
VL  - 4
AB  - We report the draft genome sequence ofArthrobacter antarcticusstrain W2, which was isolated
AB  - from a wall of a small slaughterhouse in Denmark. The 4.43-Mb genome
AB  - sequence was assembled into 170 contigs.
ER  -

TY  - JOUR
AU  - Hersemann, L.
AU  - Wibberg, D.
AU  - Blom, J.
AU  - Widmer, F.
AU  - Kolliker, R.
TI  - Draft Genome Sequence of the Xanthomonas bromi Type Strain LMG 947.
JO  - Genome Announcements
PY  - 2016
SP  - e00961
EP  - e00916
VL  - 4
AB  - Here, we report the draft genome sequence of the Xanthomonas bromi type strain LMG 947, an
AB  - important pathogen of bromegrasses (Bromus spp.). Comparative
AB  - analysis with other Xanthomonas spp. that are pathogenic on forage grasses will
AB  - assist the analysis of host-plant adaptation at the genome level.
ER  -

TY  - JOUR
AU  - Hersemann, L.
AU  - Wibberg, D.
AU  - Widmer, F.
AU  - Vorholter, F.J.
AU  - Kolliker, R.
TI  - Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities  for forage grasses.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 50
EP  - 50
VL  - 11
AB  - As causal agents of bacterial wilt in pastures and meadows, bacteria of the species
AB  - Xanthomonas translucens are a serious issue in forage grass production.
AB  - So far, only little is known about host-pathogen interactions at the molecular
AB  - level and the lack of comprehensive genome data impeded targeted breeding
AB  - strategies towards resistant forage grass cultivars. Here we announce the draft
AB  - genome sequences of three grass-pathogenic Xanthomonas translucens pathotype
AB  - strains, i.e. pv. arrhenatheri LMG 727, pv. poae LMG 728 and pv. phlei LMG 730
AB  - isolated from Arrhenatherum elatius (L.) P. Beauv. ex J. Presl & C. Presl
AB  - (Switzerland), Poa trivialis L. (Switzerland) and Phleum pratense L. (Norway),
AB  - respectively. The genomes of all three strains revealed a non-canonical type III
AB  - secretion system and a set of 22 type III effectors as common virulence-related
AB  - traits. Distinct inter-pathovar differences were observed for the
AB  - lipopolysaccharide biosynthesis gene cluster and the presence of nonribosomal
AB  - peptide synthetases.
ER  -

TY  - JOUR
AU  - Hertwig, S.
AU  - Klein, I.
AU  - Schmidt, V.
AU  - Beck, S.
AU  - Hammerl, J.A.
AU  - Appel, B.
TI  - Sequence analysis of the genome of the temperate Yersinia enterocolitica phage PY54.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 605
EP  - 622
VL  - 331
AB  - The temperate Yersinia phage PY54 belongs to the unusual group of phages that replicate as
AB  - linear plasmids with covalently closed ends. Besides
AB  - Escherichia coli phage N15, PY54 is the only member of this group to be
AB  - identified. We have determined the complete sequence (46,339 bp) of the
AB  - PY54 genome. Bioinformatic analyses revealed 67 open reading frames (ORFs)
AB  - with good coding potential located on both DNA strands. The comparison of
AB  - the deduced PY54 gene products with known proteins encoded by other phages
AB  - and bacteria along with functional studies have enabled us to assign the
AB  - possible functions of 25 ORFs. In the left arm of the PY54 genome, we
AB  - identified a number of ORFs that obviously code for head and tail
AB  - proteins. Furthermore, this part of the phage genome contains genes
AB  - probably involved in plasmid partitioning. Regarding the predicted gene
AB  - functions and gene order, the PY54 and N15 left arms are similar. However,
AB  - there are only weak DNA homologies and, in contrast to N15, the Yersinia
AB  - phage harbours only a few ORFs related to genes found in lambdoid phages.
AB  - The PY54 right arm comprises mainly regulatory genes as well as genes
AB  - important for plasmid replication, DNA methylation, and host cell lysis.
AB  - Out of 36 deduced products of the right arm, 13 revealed strongest
AB  - database homologies to N15 proteins, of which the protelomerase and the
AB  - Rep protein are exclusively homologous to their N15 counterparts. A number
AB  - of PY54 genes essential for the lytic or lysogenic cycle were identified
AB  - by functional analysis and characterization of phage mutants. In order to
AB  - study transcription during the lytic and lysogenic stage, we analysed 34
AB  - PY54 ORFs by reverse transcriptase (RT)-PCR. The phage transcription
AB  - patterns in lysogenic bacteria and at the late lytic stage of infection
AB  - are nearly identical. The reasons for this finding are spontaneous release
AB  - of phages during lysogeny and a high rate of phages that lysogenize their
AB  - Yersinia host upon infection.
ER  -

TY  - JOUR
AU  - Hess, J.F.
AU  - FitzGerald, P.G.
TI  - Protection of a restriction enzyme from heat inactivation by alpha-crystallin.
JO  - Mol. Vis.
PY  - 1998
SP  - 29
EP  - 32
VL  - 4
AB  - To determine whether the chaperone activity of human alpha-crystallin can protect a
AB  - restriction enzyme from heat inactivation.  The restriction enzyme NdeI was heated in the
AB  - presence or absence of purified bovine alpha-crystallin.  Following heat treatment, the
AB  - enzymatic activity of the heat treated samples was assayed by cleavage of plasmid DNA.  The
AB  - extent of digestion was monitored by agarose gel electrophoresis and visualization of DNA
AB  - fragments by ethidium bromide staining.  Heating of NdeI in the absence of alpha-crystallin
AB  - resulted in inactivation.  However, NdeI heated in the presence of alpha-crystallin remained
AB  - active.  Furthermore, an increased amount of alpha-crystallin provided a longer period of
AB  - thermal protection.  The chaperone activity and thermo-protective effect of alpha-crystallin
AB  - extend to protection of enzymatic activity, not merely the protection from thermally induced
AB  - aggregation/denaturation.  In addition, inclusion of alpha-crystallin during some enzymatic
AB  - reactions may be beneficial.
ER  -

TY  - JOUR
AU  - Heuer, H.
AU  - Kopmann, C.
AU  - Binh, C.T.
AU  - Top, E.M.
AU  - Smalla, K.
TI  - Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content.
JO  - Environ. Microbiol.
PY  - 2009
SP  - 937
EP  - 949
VL  - 11
AB  - Bioactive amounts of antibiotics as well as resistant bacteria reach the
AB  - soil through manure fertilization. We investigated plasmids that may
AB  - stimulate the environmental spread and interspecies transfer of antibiotic
AB  - resistance. After treatment of two soils with manure, either with or
AB  - without the sulfonamide antibiotic sulfadiazine, a significant increase in
AB  - copies of the sulfonamide resistance gene sul2 was detected by qPCR. All
AB  - sul2 carrying plasmids, captured in Escherichia coli from soil, belonged
AB  - to a novel class of self-transferable replicons. Manuring and sulfadiazine
AB  - significantly increased the abundance of this replicon type in a
AB  - chemically fertilized but not in an annually manured soil, as determined
AB  - by qPCR targeting a transfer gene. Restriction patterns and antibiograms
AB  - showed a considerable diversity within this novel plasmid group. Analysis
AB  - of three complete plasmid sequences revealed a conserved 30 kbp backbone
AB  - with only 36% G+C content, comprised of transfer and maintenance genes
AB  - with moderate homology to plasmid pIPO2 and a replication module (rep and
AB  - oriV) of other descent. The plasmids differed in composition of the
AB  - 27.0-28.3 kbp accessory region, each of which carried ISCR2 and several
AB  - resistance genes. Acinetobacter spp. was identified as a potential host of
AB  - such LowGC-type plasmids in manure and soil.
ER  -

TY  - JOUR
AU  - Heuer, H.
AU  - Szczepanowski, R.
AU  - Schneiker, S.
AU  - Puhler, A.
AU  - Top, E.M.
AU  - Schluter, A.
TI  - The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1{beta} group without any accessory genes.
JO  - Microbiology
PY  - 2004
SP  - 3591
EP  - 3599
VL  - 150
AB  - The nucleotide sequences of the broad-host-range antibiotic resistance
AB  - plasmids pB2 (61 kb) and pB3 (56 kb), which were isolated from a
AB  - wastewater treatment plant, were determined and analysed. Both have a
AB  - nearly identical IncP-1beta backbone, which diverged early from the
AB  - sequenced IncP-1beta plasmids R751, pB10, pJP4, pADP1 and pUO1. In
AB  - contrast to the latter plasmids, the pB2 and pB3 backbone does not seem to
AB  - have undergone any deletions. The complete partition gene parA is located
AB  - downstream of the mating pair formation (trb) module. A 14.4 kb or 19.0 kb
AB  - mobile genetic element is present between traC and parA of pB3 and pB2,
AB  - respectively. This region is typical for insertions in IncP-1beta
AB  - plasmids, but the insertion site is unique. Both elements differ only by a
AB  - duplication in pB2 of a tetA(C)-tetR-tnpA(IS26) fragment. The 5 bp target
AB  - site duplication and the 26 bp inverted repeats flanking the mobile
AB  - genetic elements are still intact, indicating that the insertion occurred
AB  - recently. The element consists of three nested transposable elements: (i)
AB  - a relict of a Tn402-like transposon with a gene for a new class D
AB  - beta-lactamase (bla(NPS-2)); (ii) within that, another Tn402-like element
AB  - with a class 1 integron harbouring the gene cassettes cmlA1 for a
AB  - chloramphenicol efflux protein and aadA2 encoding a
AB  - streptomycin/spectinomycin adenylyltransferase, and a copy of IS6100;
AB  - (iii) into the integrase gene intI1 a tetracycline resistance module
AB  - tetA(C)-tetR flanked by copies of IS26 is inserted. Interestingly, in
AB  - contrast to all other IncP-1beta plasmids analysed so far, the oriV region
AB  - between trfA and klcA is not interrupted by accessory genes, and there is
AB  - no indication that previously inserted accessory genes have subsequently
AB  - been deleted. The genes kluAB are also missing in that region and should
AB  - thus be considered acquired genes. These findings, together with the fact
AB  - that IncP-1beta plasmids acquired accessory elements at various positions
AB  - in the backbone, suggest that IncP-1beta plasmids without any accessory
AB  - genes exist in microbial communities. They must occasionally acquire
AB  - accessory genes by transposition events, resulting in those plasmids that
AB  - have been found based on selectable phenotypic traits.
ER  -

TY  - JOUR
AU  - Heuermann, D.
AU  - Haas, R.
TI  - A stable shuttle vector system for efficient genetic complementation of Helicobacter pylori strains by transformation and conjugation.
JO  - Mol. Gen. Genet.
PY  - 1998
SP  - 519
EP  - 528
VL  - 257
AB  - A versatile plasmid shuttle vector system was constructed, which is useful for genetic
AB  - complementation of Helicobacter pylori strains or mutants with cloned genes of homologous or
AB  - heterologous origin.  The individual plasmid vectors consist of the minimal essential genetic
AB  - elements, including an origin of replication for Escherichia coli, a H. pylori-specific
AB  - replicon originally identified on a small cryptic H. pylori plasmid, an oriT sequence and a
AB  - multiple cloning site.  Shuttle plasmid pHel2 carries a chloramphenicol resistance cassette
AB  - (catGC) and pHel3 contains a kanamycin resistance gene (aphA-3) as the selectable marker; both
AB  - are functional in E. coli and H. pylori.  The shuttle plasmids were introduced into the H.
AB  - pylori strain P1 by natural transformation.  An efficiency of 7.0 x 10^-7 and 4.7 x 10^-7
AB  - transformants per viable recipient was achieved with pHel2 and pHel3, respectively, and both
AB  - vectors showed stable, autonomous replication of H. pylori.  An approximately 100-fold higher
AB  - H. pylori transformation rate was obtained when the shuttle vectors for transformation were
AB  - isolated from the homologous H. pylori strain, rather than E. coli, indicating that DNA
AB  - restriction and modification mechanisms play a crucial role in plasmid transformation.
AB  - Interestingly, both shuttle vectors could also be mobilized efficiently from E. coli into
AB  - different H. pylori recipients, with pHel2 showing an efficiency of 2.0 x 10^-5
AB  - transconjugants per viable H. pylori P1 recipient.  Thus, DNA restriction seems to be strongly
AB  - reduced or absent during conjugal transfer.  The functional complementation of a
AB  - recA-deficient H. pylori mutant by the cloned H. pylori recA+ gene, and the expression of the
AB  - heterologous green fluorescent protein in H. pylori demonstrate the general usefulness of this
AB  - system, which will significantly facilitate the molecular analysis of H. pylori virulence
AB  - factors in the future.
ER  -

TY  - JOUR
AU  - Heumann, W.
TI  - Rhizobium lupini genetics.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 1979
SP  - 1
EP  - 24
VL  - 88
AB  - The purpose of this article is to review a genetic system that differs in many
AB  - aspects to the well-known Escherichia coli system.  It is not the aim of the
AB  - author to deal directly with the complex issues of Rhizobium symbiosis with
AB  - Legumes nor with the problem of symbiotic nitrogen fixation by the Rhizobia.
AB  - However, genetical investigations of the rhizobial strains involved may
AB  - contribute to some understanding of the genetics of this complex system of
AB  - symbiotic nitrogen fixation.  The mutants used in this study were obtained by
AB  - mutagenesis of Rhizobium lupini strains isolated directly from Lupinus luteus
AB  - root nodules in 1960.  These strains lost certain characteristics of the
AB  - wild-type Rhizobium, especially its capacity to nodulate Lupins.  They are,
AB  - however, characterized by high conjugational fertility, a prerequisite for the
AB  - investigation of their genetics, by star formation, a recognition mechanism;
AB  - and also by their bright yellow colony pigmentation.  This pigmentation arises
AB  - from carotenoids localized in the plasma membrane of the cells which protect
AB  - the cell's cytochromes from photoinactivation.  These three characteristics,
AB  - conjugation, star formation, and carotenoid pigmentation, proved very useful
AB  - for genetic investigation of these Rhizobium mutants.
ER  -

TY  - JOUR
AU  - Heurgue-Hamard, V.
AU  - Champ, S.
AU  - Engstrom, A.
AU  - Ehrenberg, M.
AU  - Buckingham, R.H.
TI  - The hemK gene in Escherichia coli encodes the N5-glutamine methyltransferase that modifies peptide release factors.
JO  - EMBO J.
PY  - 2002
SP  - 769
EP  - 778
VL  - 21
AB  - Class 1 peptide release factors (RFs) in Escherichia coli are N5-methylated on the glutamine
AB  - residue of the universally conserved GGQ motif. One other protein alone has been shown to
AB  - contain N5-methylglutamine: E.coli ribosomal protein L3. We identify the L3 methyltransferase
AB  - as YfcB and show that it methylates ribosomes from a yfcB strain in vitro, but not RF1 or RF2.
AB  - HemK, a close orthologue of YfcB, is shown to methylate RF1 and RF2 in vitro. hemK is
AB  - immediately downstream of and co-expressed with prfA. Its deletion in E.coli K12 leads to very
AB  - poor growth on rich media and abolishes methylation of RF1. The activity of unmethylated RF2
AB  - from K12 strains is extremely low due to the cumulative effects of threonine at position 246,
AB  - in place of alanine or serine present in all other bacterial RFs, and the lack of
AB  - N5-methylation of Gln252. Fast-growing spontaneous revertants in hemK K12 strains contain the
AB  - mutations Thr246Ala or Thr246Ser in RF2. HemK and YfcB are the first identified
AB  - methyltransferases modifying glutamine, and are widely distributed in nature.
ER  -

TY  - JOUR
AU  - Heusipp, G.
AU  - Falker, S.
AU  - Schmidt, M.A.
TI  - DNA adenine methylation and bacterial pathogenesis.
JO  - Int. J. Med. Microbiol.
PY  - 2007
SP  - 1
EP  - 7
VL  - 297
AB  - Methylation of DNA by the DNA adenine methyltransferase (Dam) provides an epigenetic signal
AB  - that influences and regulates numerous physiological processes in the bacterial cell including
AB  - chromosome replication, mismatch repair, transposition, and transcription. A growing number of
AB  - reports describe a role for DNA adenine methylation in regulating the expression of various
AB  - bacterial genes related to virulence in diverse pathogens, suggesting that DNA methylation may
AB  - be a widespread and versatile regulator of virulence gene expression. Here, we summarize the
AB  - current knowledge about the influence of DNA methylation on virulence functions and discuss
AB  - perspectives for future research.
ER  -

TY  - JOUR
AU  - Heylen, K.
AU  - De Vos, P.
AU  - Vekeman, B.
TI  - Draft Genome Sequences of Eight Obligate Methane Oxidizers Occupying Distinct Niches Based on Their Nitrogen Metabolism.
JO  - Genome Announcements
PY  - 2016
SP  - e00421
EP  - e00416
VL  - 4
AB  - The genome sequences of Methylomonas methanica (NCIMB 11130(T), R-45363, and R-45371),
AB  - Methylomonas koyamae (R-45378, R-45383, and R-49807), Methylomonas
AB  - lenta (R-45370), and Methylosinus sp. (R-45379) were obtained. These aerobic
AB  - methanotrophs were isolated from terrestrial ecosystems, and their distinct
AB  - phenotypes related to nitrogen assimilation and dissimilation were previously
AB  - reported.
ER  -

TY  - JOUR
AU  - Heyrman, J.
AU  - Logan, N.A.
AU  - Busse, H.J.
AU  - Balcaen, A.
AU  - Lebbe, L.
AU  - Rodriguez-Diaz, M.
AU  - Swings, J.
AU  - De Vos, P.
TI  - Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2003
SP  - 501
EP  - 511
VL  - 53
AB  - A group of 13 strains was isolated from samples of biofilm formation on the mural
AB  - paintings of the Servilia tomb (necropolis of Carmona, Spain) and the
AB  - Saint-Catherine chapel (castle at Herberstein, Austria). The strains were
AB  - subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA
AB  - sequence analysis, DNA-DNA hybridizations, DNA base ratio determination, analysis
AB  - of fatty acids, polar lipids and menaquinones and morphological and biochemical
AB  - characterization. In a phylogenetic tree based on neighbour-joining of 16S rDNA
AB  - sequences, the strains are divided in two major groups, representing three novel
AB  - species according to DNA-DNA relatedness, that are positioned at approximately
AB  - equal distances from Virgibacillus and Salibacillus. After comparison of the
AB  - novel results with existing data, the transfer of the species of Salibacillus to
AB  - Virgibacillus is proposed, with the resulting new combinations Virgibacillus
AB  - marismortui comb. nov. and Virgibacillus salexigens comb. nov. Additionally,
AB  - three novel species are described, for which the names Virgibacillus carmonensis
AB  - sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov.
AB  - are proposed. The respective type strains are LMG 20964T (=DSM 14868T), LMG
AB  - 19488T (=DSM 14866T) and LMG 19492T (= DSM 14867T). Finally, an emended
AB  - description of the genus Virgibacillus is given.
ER  -

TY  - JOUR
AU  - Hickman, A.B.
AU  - Li, Y.
AU  - Mathew, S.V.
AU  - May, E.W.
AU  - Craig, N.L.
AU  - Dyda, F.
TI  - Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
JO  - Mol. Cell
PY  - 2000
SP  - 1025
EP  - 1034
VL  - 5
AB  - Transposition requires a coordinated series of DNA breakage and joining reactions. The Tn7
AB  - transposase contains two proteins: TnsA, which carries out DNA breakage at the 5' ends of the
AB  - transposon, and TnsB, which carries out breakage and joining at the 3' ends of the
AB  - transposon. TnsB is a member of the retroviral integrase superfamily whose hallmark is a
AB  - conserved DDE motif. We report here the structure of TnsA at 2.4 A resolution. Surprisingly,
AB  - the TnsA fold is that of a type II restriction endonuclease. Thus, Tn7 transposition involves
AB  - a collaboration between polypeptides, one containing a DDE motif and one that does not. This
AB  - result indicates that the range of biological processes that utilize restriction enzyme-like
AB  - folds also includes DNA transposition.
ER  -

TY  - JOUR
AU  - Hicks, M.R.
AU  - Rodger, A.
AU  - Thomas, C.M.
AU  - Batt, S.M.
AU  - Dafforn, T.R.
TI  - Restriction enzyme kinetics monitored by UV linear dichroism.
JO  - Biochemistry
PY  - 2006
SP  - 8912
EP  - 8917
VL  - 45
AB  - The use of linear dichroism (LD) spectroscopy for biological applications has been brought to
AB  - the forefront recently by our
AB  - development of thermostated microvolume Couette cells. We present a
AB  - method for following the digestion of DNA by restriction endonucleases
AB  - in real time without the use of any extrinsic dyes or labels. This is
AB  - accomplished using linear dichroism spectroscopy (the differential
AB  - absorbance of light polarized parallel and perpendicular to the sample
AB  - orientation axis). The differential absorbance signal depends on the
AB  - degree of alignment of the molecules. In this case the DNA is aligned
AB  - by Couette flow (flowing the solution in the annular gap between two
AB  - concentric cylinders), and we monitor the increase in alignment upon
AB  - linearization of a circular DNA molecule. In addition, we observe a
AB  - decrease in alignment upon further digestion and subsequent shortening
AB  - of the DNA. Ten enzymes were investigated: seven enzymes with a single
AB  - cut site (EcoRI, KpnI, NdeI, NotI, NruI, SmaI, XbaI), two enzymes with
AB  - two cut sites (BstZ17I, EagI), and one enzyme with no cut site (ClaI).
AB  - LD, as implemented in this new assay, is broadly applicable across a
AB  - wide range of DNA-modifying enzymes and compounds and, as such, is a
AB  - useful addition to the toolbox of biological characterization.
ER  -

TY  - JOUR
AU  - Hien, L.-T.
AU  - Zatsepin, T.S.
AU  - Schierling, B.
AU  - Volkov, E.M.
AU  - Wende, W.
AU  - Pingoud, A.
AU  - Kubareva, E.A.
AU  - Oretskaya, T.S.
TI  - Restriction Endonuclease SsoII with Photoregulated Activity: A 'Molecular Gate' Approach.
JO  - Bioconjugate Chem.
PY  - 2011
SP  - 1366
EP  - 1373
VL  - 22
AB  - A novel method for regulating the activity of homodimeric
AB  - proteins-"molecular gate" approach-was proposed and its usefulness illustrated for the type II
AB  - restriction endonuclease SsoII (R.SsoII) as a model. The "molecular gate" approach is based on
AB  - the modification of R.SsoII with azobenzene derivatives, which allows regulating DNA binding
AB  - and cleavage via illumination with light. R. SsoII variants with single cysteine residues
AB  - introduced at selected positions were obtained and modified with maleimidoazobenzene
AB  - derivatives. A twofold change in the enzymatic activity after illumination with light of
AB  - wavelengths of 365 and 470 nm, respectively,
AB  - was demonstrated when one or two molecules of azobenzene derivatives were attached to the
AB  - R.SsoII at the entrance of or within the DNA-binding site.
ER  -

TY  - JOUR
AU  - Hiessl, S.
AU  - Schuldes, J.
AU  - Thurmer, A.
AU  - Halbsguth, T.
AU  - Broker, D.
AU  - Angelov, A.
AU  - Liebl, W.
AU  - Daniel, R.
AU  - Steinbuchel, A.
TI  - Involvement of Two Latex-Clearing Proteins during Rubber Degradation and Insights into the Subsequent Degradation Pathway Revealed by the Genome Sequence of Gordonia polyisoprenivorans Strain VH2.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 2874
EP  - 2887
VL  - 78
AB  - The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber
AB  - leads to huge challenges in waste management. Only a few bacteria are known to
AB  - degrade rubber, and little is known about the mechanism of microbial rubber
AB  - degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one
AB  - of the most effective rubber-degrading bacteria, was sequenced and annotated to
AB  - elucidate the degradation pathway and other features of this actinomycete. The
AB  - genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid
AB  - of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It
AB  - contains 5,110 putative protein-coding sequences, including many candidate genes
AB  - responsible for rubber degradation and other biotechnically relevant pathways.
AB  - Furthermore, we detected two homologues of a latex-clearing protein, which is
AB  - supposed to be a key enzyme in rubber degradation. The deletion of these two
AB  - genes for the first time revealed clear evidence that latex-clearing protein is
AB  - essential for the microbial utilization of rubber. Based on the genome sequence,
AB  - we predict a pathway for the microbial degradation of rubber which is supported
AB  - by previous and current data on transposon mutagenesis, deletion mutants, applied
AB  - comparative genomics, and literature search.
ER  -

TY  - JOUR
AU  - Hiett, K.
AU  - Meinersmann, R.
TI  - Isolation of a putative retriction/modification system from Campylobacter jejuni.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 224
EP  - 224
VL  - 94
AB  - Molecular studies of the Campylobacter jejuni genome can often prove difficult; one reason is
AB  - that C. jejuni genomic DNA can be digested with only a small number of restriction
AB  - endonucleases. Our goal was to isolate, characterize, and eventually disrupt a
AB  - restriction/modification system in C. jejuni so that future genetic manipulation might prove
AB  - easier.
AB  - 
AB  - A lambda-zapII library was constructed using C. jejuni A74/O genomic DNA. The library was
AB  - then transfected simultaneously with XL-1 blue and XL-1 Blue/pAN4, a plasmid containing the
AB  - EcoRI loci in pBR322. Primary plaques were counted and compared from both transfection
AB  - conditions; the number of plaques on XL-1 Blue were significantly higher than those on XL-1
AB  - Blue/pAN4. Forty-two primary plaques were then picked from the XL-1 Blue/pAN4 lysates and
AB  - again transfected using both XL-1 Blue and XL-1Blue/pAN4 lysates and again transfected using
AB  - both XL-1 Blue and XL-1 Blue/pAN4. Primary plaques that gave similar lysate numbers when
AB  - transfected into both E. coli were chosen on the hypothesis that they carried a C. jejuni
AB  - restriction/modification system. Six of these secondary plaques were transfected into XL-1
AB  - Blue for phage DNA isolation; isolated DNA was digested using a series of six restriction
AB  - endonucleases. Only one of the six enzymes chosen allowed digestion of the phage DNA's.
AB  - Future studies will include further characterization of the C. jejuni inserts to determine if
AB  - a restriction/modification system is present.
AB  - 
ER  -

TY  - JOUR
AU  - Higashide, M.
AU  - Kuroda, M.
AU  - Omura, C.T.
AU  - Kumano, M.
AU  - Ohkawa, S.
AU  - Ichimura, S.
AU  - Ohta, T.
TI  - Methicillin-resistant Staphylococcus saprophyticus Carrying Staphylococcal Cassette Chromosome mec (SCCmec) Have Emerged in Urogenital Tract  Infections.
JO  - Antimicrob. Agents Chemother.
PY  - 2008
SP  - 2061
EP  - 2068
VL  - 52
AB  - Staphylococcus saprophyticus is a uropathogenic bacterium that causes acute uncomplicated
AB  - urinary tract infections (UTIs), particularly in
AB  - female outpatients. We investigated the dissemination and antimicrobial
AB  - susceptibility of 101 S. saprophyticus isolates from the genitourinary
AB  - tracts of patients in Japan. Eight of these isolates were mecA-positive
AB  - and showed beta-lactam resistance. Pulsed field gel electrophoresis (PFGE)
AB  - showed that only some isolates were isogenic, indicating that the mecA
AB  - gene was apparently acquired independently by mecA-positive isolates
AB  - through staphylococcal cassette chromosome mec (SCCmec). Type
AB  - determination of SCCmec by multiplex PCR showed non-typeable element in
AB  - the 8 mecA-positive isolates. Sequence analysis of the entire SCCmec
AB  - element from a prototype S. saprophyticus strain revealed that it is
AB  - non-typeable with the current SCCmec classification due to the novel
AB  - composition of the class A mec gene complex (IS431-mecA-mecR1-mecI genes)
AB  - and the ccrA1/ccrB3 gene complex. Intriguingly, the attachment sites of
AB  - SCCmec are similar to those of type I SCCmec in S. aureus NCTC 10442.
AB  - Further, the genes around the mec gene complex are similar to those of
AB  - type II/III SCCmec in S. aureus, while those around the ccr gene complex
AB  - are similar to those of SCC15305RM found in S. saprophyticus ATCC 15305.
AB  - In comparison with known SCCmec elements, this S. saprophyticus SCCmec is
AB  - a novel type.
ER  -

TY  - JOUR
AU  - Higashioka, Y.
AU  - Kojima, H.
AU  - Watanabe, T.
AU  - Fukui, M.
TI  - Draft Genome Sequence of Desulfatitalea tepidiphila S28bFT.
JO  - Genome Announcements
PY  - 2015
SP  - e01326
EP  - e01315
VL  - 3
AB  - Desulfatitalea tepidiphila S28bF(T) is a sulfate-reducing bacterium closely related to
AB  - Desulfosarcina species. Here, the draft genome sequence of strain
AB  - S28bF(T) is reported.
ER  -

TY  - JOUR
AU  - Higgins, D.L.
AU  - Sanozky-Dawes, R.
AU  - Klaenhammer, T.R.
TI  - Characterization of a cointegrate conjugal plasmid encoding phage restriction and modification activities in lactic streptococci.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1987
SP  - 154
EP  - 154
VL  - 87
AB  - The conjugal plasmid pTN1060 (Tra+) encodes lactose-fermenting ability (Lac+),
AB  - resistance to nisin (Nisr), and restriction and modification activities (R/M+)
AB  - against phages of lactic streptococci.  Physical characterization of pTN1060
AB  - revealed the plasmid was a cointegrate formed from pTR1040 (Lac+, Nisr) and a
AB  - 30 kb fragment that conferred Tra+ and R/M+ functions.  To identify the origin
AB  - of the 30kb fragment, exconjugants from S. lactis N1 were characterized for
AB  - Tra+ and R/M+ activities.  Exconjugants harboring either 60 Md pTN1060-like
AB  - plasmids, or pTR1040 in combination with a 30 kb plasmid (pTN20) exhibited
AB  - Lac+, Nisr, R/M+ and Tra+.  Phenotypic analysis, curing studies, and genetic
AB  - transfer experiments with derivatives harboring pTN20 demonstrated a direct
AB  - correlation of pTN20 with R/M+ activities and conjugal transfer ability.  pTN20
AB  - probes hybridized with pTN1060 but not with pTR1040.  Restriction mapping
AB  - further confirmed that pTN20 fragments were present in pTN1060.  The data
AB  - demonstrated that pTN1060 was a cointegrate plasmid comprised of pTR1040 and
AB  - pTN20.
ER  -

TY  - JOUR
AU  - Higgins, D.L.
AU  - Sanozky-Dawes, R.B.
AU  - Klaenhammer, T.R.
TI  - Restriction and modification activities from Streptococcus lactis ME2 are encoded by a self-transmissible plasmid, pTN20, that forms cointegrates during mobilization of lactose-fermenting ability.
JO  - J. Bacteriol.
PY  - 1988
SP  - 3435
EP  - 3442
VL  - 170
AB  - A self-transmissible (Tra+) plasmid encoding determinants for restriction and
AB  - modification activities (R+/M+) from Streptococcus lactis ME2 was isolated and
AB  - characterized.  The 28-kilobase (kb) plasmid (pTN20) was detected in
AB  - lactose-fermenting (Lac+) transconjugants generated from matings between S.
AB  - lactis N1, an ME2 variant, and a plasmid-free recipient, S. lactis LM2301.  The
AB  - plaquing efficiencies of prolate- and small isometric-headed phages were
AB  - reduced on transconjugants containing either pTN20 (R+/M+ Tra+) or 100-kb
AB  - plasmids encoding Lac+, R+/M+, and Tra+.  Lac+ transconjugants which harbored
AB  - pTR1040 (Lac+) and pTN20 (R+/M+) were phenotypically R-/M- and transferred Lac+
AB  - at low frequency in subsequent matings to give rise to 100-kb R+/M+ plasmids.
AB  - R+/M+ activities and high-frequency conjugal transfer ability were detected in
AB  - Lac+ transconjugants that contained pTR1041 (Lac+) and pTN20 (R+/M+).  No
AB  - 100-kb R+/M+ plasmids were recovered after these matings, suggesting that
AB  - pTR1041 was mobilized by pTN20 through a process that resembled plasmid
AB  - donation.  pTR1041 was identical to pTR1040 but contained an additional 3.3-kb
AB  - DNA fragment.  These data suggested that phenotypic expression of R+/M+ and
AB  - Tra+ is affected by coresident Lac+ plasmids.  Restriction enzyme analysis and
AB  - hybridization reactions demonstrated that the 100-kb R+/M+ plasmid was formed
AB  - by a cointegration event between pTR1040 (Lac+) and pTN20 (R+/M+Tra+) during
AB  - conjugal transfer via a conductive-type process.  This is the first report that
AB  - defines self-transmissible restriction and modification plasmids in the lactic
AB  - streptococci.
ER  -

TY  - JOUR
AU  - Higgins, L.S.
AU  - Besnier, C.
AU  - Kong, H.
TI  - The nicking endonuclease N.BstNBI is closely related to Type IIs restriction endonucleases MlyI and PleI.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 2492
EP  - 2501
VL  - 29
AB  - N.BstNBI is a nicking endonuclease that recognizes the sequence GAGTC and nicks the top strand
AB  - preferentially. The Type IIs restriction endonucleases PleI and MlyI also recognize GAGTC, but
AB  - cleave both DNA strands. Cloning and sequencing the genes encoding each of these three
AB  - endonucleases discloses significant sequence similarities. Mutagenesis studies reveal a
AB  - conserved set of catalytic residues among the three endonucleases, suggesting that they are
AB  - closely related to each other. Furthermore, PleI and MlyI contain a single active site for DNA
AB  - cleavage. The results from cleavage assays show that the reactions catalyzed by PleI and MlyI
AB  - are sequential two step processes. The double-stranded DNA is first nicked on one DNA strand
AB  - and then further cleaved on the second strand to form linear DNA. Gel filtration analysis
AB  - shows that MlyI dimerizes in the presence of a cognate DNA and Ca(2+) whereas N.BstNBI remains
AB  - a monomer, implicating dimerization as a requisite for the second strand cleavage. We suggest
AB  - that N.BstNBI, MlyI and PleI diverged from a common ancestor and propose that N.BstNBI differs
AB  - from MlyI and PleI in having an extremely limited second strand cleavage activity, resulting
AB  - in a site-specific nicking endonuclease.
ER  -

TY  - JOUR
AU  - Higgins, P.G.
AU  - Chan, J.Z.
AU  - Seifert, H.
AU  - Pallen, M.J.
AU  - Millard, A.D.
TI  - Draft Genome Sequences of 11 Clinical Isolates of Acinetobacter baumannii.
JO  - Genome Announcements
PY  - 2016
SP  - e00269
EP  - e00216
VL  - 4
AB  - The development of multidrug-resistantAcinetobacter baumanniiis of serious concern in the
AB  - hospital setting. Here, we report draft genome sequences of 11A.
AB  - baumanniiisolates that were isolated from a single patient over a 65-day period,
AB  - during which time the isolates exhibited increased antimicrobial resistance.
ER  -

TY  - JOUR
AU  - Higgins, P.G.
AU  - Koehler, D.
AU  - Chan, J.Z.
AU  - Cornely, O.A.
AU  - Fatkenheuer, G.
AU  - Gillis, M.
AU  - Pallen, M.J.
AU  - Tien, J.
AU  - Seifert, H.
AU  - Vehreschild, M.J.
AU  - Millard, A.D.
TI  - Draft Genome Sequences of Nine Clinical Isolates of Vancomycin-Resistant Enterococci.
JO  - Genome Announcements
PY  - 2016
SP  - e00803
EP  - e00816
VL  - 4
AB  - In 2012, there was an increase in vancomycin-resistant enterococci (VRE) isolated from the
AB  - intensive care unit at the University Hospital of Cologne. Using
AB  - whole-genome sequencing it was possible to establish that bloodstream infections
AB  - with VRE were not the result of an outbreak or cross infections.
ER  -

TY  - JOUR
AU  - Highlander, S.K. et al.
TI  - Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus.
JO  - BMC Microbiol.
PY  - 2007
SP  - 99
EP  - 99
VL  - 7
AB  - ABSTRACT: BACKGROUND: Community acquired (CA) methicillin-resistant Staphylococcus aureus
AB  - (MRSA) increasingly causes disease worldwide. USA300
AB  - has emerged as the predominant clone causing superficial and invasive
AB  - infections in children and adults in the USA. Epidemiological studies
AB  - suggest that USA300 is more virulent than other CA-MRSA. The genetic
AB  - determinants that render virulence and dominance to USA300 remain unclear.
AB  - RESULTS: We sequenced the genomes of two pediatric USA300 isolates: one
AB  - CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas
AB  - Children's Hospital in Houston. DNA sequencing was performed by Sanger
AB  - dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing
AB  - strategies. The sequence of the USA300 MRSA strain was rigorously
AB  - annotated. In USA300, MRSA 2685 chromosomal open reading frames were
AB  - predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300
AB  - MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid.
AB  - Two regions found in US300 MRSA were absent in USA300 MSSA. The USA300
AB  - sequence was aligned with other sequenced S. aureus genomes and regions
AB  - unique to USA300 MRSA were identified. CONCLUSIONS: USA300-MRSA is highly
AB  - similar to other MRSA strains based on whole genome alignments and gene
AB  - content, indicating that the differences in pathogenesis are due to subtle
AB  - changes rather than to large-scale acquisition of virulence factor genes.
AB  - The USA300 Houston isolate differs from another sequenced USA300 strain
AB  - isolate, derived from a patient in San Francisco, in plasmid content and a
AB  - number of sequence polymorphisms. Such differences will provide new
AB  - insights into the evolution of pathogens.
ER  -

TY  - JOUR
AU  - Highlander, S.K.
AU  - Garza, O.
TI  - The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymes.
JO  - Gene
PY  - 1996
SP  - 89
EP  - 96
VL  - 178
AB  - Genes encoding the type I restriction-modification (R-M) system of the bovine pathogen,
AB  - Pasteurella haemolytica, have been identified immediately downstream of a locus that encodes a
AB  - transcriptional activator of P. haemolytica leukotoxin expression.  Type I enzymes are encoded
AB  - by three genes called hsdM, hsdS and hsdR, and have fallen into three groups, called Ia, Ib
AB  - and Ic.  HsdS provides a sequence recognition function which in concert with HsdM forms an
AB  - active methyltransferase (Mtase).  Inclusion of the HsdR subunit in the complex creates an
AB  - active restriction endonuclease (Enase) capable of cleaving unmethylated target DNA.  The P.
AB  - haemolytica hsdMSR genes were mapped using transposon Tn10d-Cam insertions, and bacteriophage
AB  - restriction and modification assays in Escherichia coli.  We determined the nucleotide
AB  - sequences of hsdM, hsdS and hsdR, and observed that the deduced amino acid (aa) sequences were
AB  - very similar to predicted R-M subunits in the respiratory pathogen, Haemophilus influenzae.
AB  - Phylogenetic comparisons of all known Hsd aa sequences placed the P. haemolytica and H.
AB  - influenzae proteins into a new group which we labeled the Type Id R-M family.  Expression of
AB  - the P. haemolytica R-M genes in E. coli was inefficient and is likely to be a consequence of
AB  - the unusual codon usage in P. haemolytica genes.
ER  -

TY  - JOUR
AU  - Highlander, S.K.
AU  - Hang, V.T.
TI  - A putative leucine zipper activator of Pasteurella haemolytica leukotoxin transcription and the potential for modulation of its synthesis by slipped-strand  mispairing.
JO  - Infect. Immun.
PY  - 1997
SP  - 3970
EP  - 3975
VL  - 65
AB  - A Pasteurella haemolytica cosmid clone that activates leukotoxin transcription in Escherichia
AB  - coli has been isolated. The activator locus, alxA, is part of a
AB  - continuous open reading frame that includes the type I hsdM methylase gene. AlxA
AB  - and HsdM peptides are processed from a precursor, and translation of the
AB  - polyprotein can be modulated by slipped-strand mispairing across a
AB  - pentanucleotide repeat, ACAGC, within the 5' end of alxA-hsdM. Extracts
AB  - containing AlxA can bind to a leukotoxin promoter fragment.
ER  -

TY  - JOUR
AU  - Higuchi, Y.
AU  - Mori, K.
AU  - Suyama, A.
AU  - Huang, Y.
AU  - Tashiro, K.
AU  - Kuhara, S.
AU  - Takegawa, K.
TI  - Draft Genome Sequence of Bacillus clausii AKU0647, a Strain That Produces Endo-beta-N-Acetylglucosaminidase A.
JO  - Genome Announcements
PY  - 2016
SP  - e00310
EP  - e00316
VL  - 4
AB  - To comprehensively identify glycosyl hydrolase genes in the genome of Bacillus clausii strain
AB  - AKU0647, which produces endo-beta-N-acetylglucosaminidase A
AB  - (Endo-A), we conducted whole-genome shotgun sequencing. We identified several
AB  - other putative glycosyl hydrolase genes apart from the Endo-A gene, and report
AB  - these findings here.
ER  -

TY  - JOUR
AU  - Higuera, G.
AU  - Gonzalez-Escalona, N.
AU  - Veliz, C.
AU  - Vera, F.
AU  - Romero, J.
TI  - Draft Genome Sequences of Four Xanthomonas arboricola pv. juglandis Strains Associated with Walnut Blight in Chile.
JO  - Genome Announcements
PY  - 2015
SP  - e01160
EP  - e01115
VL  - 3
AB  - Xanthomonas arboricola pv. juglandis is an important pathogen responsible for walnut blight
AB  - outbreaks globally. Here, we report four draft genome sequences of  X. arboricola pv.
AB  - juglandis strains isolated from Chilean walnut trees.
ER  -

TY  - JOUR
AU  - Hikida, Y.
AU  - Kimoto, M.
AU  - Hirao, I.
AU  - Yokoyama, S.
TI  - Crystal structure of Deep Vent DNA polymerase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2017
SP  - 52
EP  - 57
VL  - 483
AB  - DNA polymerases are useful tools in various biochemical experiments. We have focused on the
AB  - DNA polymerases involved in DNA replication including the
AB  - unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and
AB  - 2-nitro-4-propynylpyrrole (Px). Many reports have described the different
AB  - combinations between unnatural base pairs and DNA polymerases. As an example, for
AB  - the replication of the Ds-Px pair, Deep Vent DNA polymerase exhibits high
AB  - efficiency and fidelity, but Taq DNA polymerase shows much lower efficiency and
AB  - fidelity. In the present study, we determined the crystal structure of Deep Vent
AB  - DNA polymerase in the apo form at 2.5 A resolution. Using this structure, we
AB  - constructed structural models of Deep Vent DNA polymerase complexes with DNA
AB  - containing an unnatural or natural base in the replication position. The models
AB  - revealed that the unnatural Ds base in the template-strand DNA clashes with the
AB  - side-chain oxygen of Thr664 in Taq DNA polymerase, but not in Deep Vent DNA
AB  - polymerase.
ER  -

TY  - JOUR
AU  - Hikima, J.
AU  - Sakai, M.
AU  - Aoki, T.
AU  - Takeyama, H.
AU  - Hawke, J.
AU  - Mori, K.
AU  - Tashiro, K.
AU  - Kuhara, S.
TI  - Draft Genome Sequence of the Fish Pathogen Mycobacterium pseudoshottsii Strain JCM15466, a Species Closely Related to M. marinum.
JO  - Genome Announcements
PY  - 2016
SP  - e01630
EP  - e01615
VL  - 4
AB  - Mycobacterium pseudoshottsii is a slowly growing photochromogenic mycobacterium and fish
AB  - pathogen isolated from wild marine fishes. M. pseudoshottsii closely
AB  - resembles M. marinum, which is a human and animal pathogen. Here, we report the
AB  - draft genome sequence of M. pseudoshottsii strain JCM15466, originally isolated
AB  - from striped bass, Morone saxatilis.
ER  -

TY  - JOUR
AU  - Hilbert, H.
AU  - Himmelreich, R.
AU  - Plagens, H.
AU  - Herrmann, R.
TI  - Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pneumoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 628
EP  - 639
VL  - 24
AB  - To sequence the entire 800 kilobase pair genome of the bacterium Mycoplasma pneumoniae, a
AB  - plasmid library was established which contained the majority of the EcoRI fragments from M.
AB  - pneumoniae.  The EcoRI fragments were subcloned from an ordered cosmid library comprising the
AB  - complete M. pneumoniae genome.  Individual plasmid clones were sequenced in an ordered fashion
AB  - mainly by primer walking.  We report here the initial results from the sequence analysis of
AB  - about 56 kb comprising the dnaA region as a potential origin of replication, the ATPase operon
AB  - and a region coding for a cluster of ribosomal protein genes.  The data were compared with the
AB  - corresponding genes/operons from Bacillus subtilis, Escherichia coli, Mycoplasma capricolum
AB  - and Mycoplasma gallisepticum.
ER  -

TY  - JOUR
AU  - Hill, A.E.
AU  - Lainson, F.A.
TI  - Survey of restriction-modification systems and transformation in Mannheimia haemolytica and Pasteurella trehalosi.
JO  - Vet. Microbiol.
PY  - 2003
SP  - 103
EP  - 109
VL  - 92
AB  - A significant obstacle to molecular studies of Mannheimia (Pasteurella) haemolytica, has been
AB  - its resistance to genetic transformation. The lack
AB  - of competence of many M. haemolytica strains has been attributed to the
AB  - presence of restriction modification systems. In this study,
AB  - representative strains of 12 M. haemolytica serotypes and four Pasteurella
AB  - trehalosi serotypes were successfully transformed by electroporation using
AB  - a recombinant vector derived from the native M. haemolytica A1 serotype
AB  - plasmid pNSF2176. Transformation was achieved despite PCR-based evidence
AB  - for the presence of genes encoding a type I restriction enzyme, phaI, and
AB  - a type II restriction enzyme hsdM, in each of the M. haemolytica strains.
ER  -

TY  - JOUR
AU  - Hill, C.
TI  - Bacteriophage and bacteriophage resistance in lactic acid bacteria.
JO  - FEMS Microbiol. Rev.
PY  - 1993
SP  - 87
EP  - 108
VL  - 12
AB  - The study of bacteriophage-host interactions has been instrumental in the development of
AB  - genetic systems in many genera, and laid many of the foundations of modern molecular genetics.
AB  - Research into bacteriophage and bacteriophage resistance in the lactic acid bacteria has moved
AB  - into a new and exciting dimension in recent years. Mechanisms such as adsorption inhibition,
AB  - restriction and modification, and abortive infection which have been detected and described
AB  - phenotypically over the past decade are now being subjected to molecular analysis, and this
AB  - has led to a better understanding of the nature and variety of resistance systems employed by
AB  - lactic acid bacteria to combat phage attack. In addition, analysis of different bacteriophage
AB  - has increased our knowledge of these ubiquitous particles to the point where it is possible to
AB  - construct novel phage resistances based on the phage genome itself. This review outlines the
AB  - recent progress in the molecular analysis of bacteriophage, bacteriophage resistance and
AB  - counter resistance, and the construction of novel resistance mechansims.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Garvey, P.
AU  - Fitzgerald, G.F.
TI  - Bacteriophage-host interactions and resistance mechanisms, analysis of the conjugative bacteriophage resistance plasmid pNP40.
JO  - Lait
PY  - 1996
SP  - 67
EP  - 79
VL  - 76
AB  - Research into bacteriophage and bacteriophage resistance in the lactic acid bacteria
AB  - has moved into a new and exciting dimension in recent years.  Mechanisms such as adsorption
AB  - inhibition, restriction and modification, and abortive infection which have been described
AB  - phenotypically over the past decade are now being subjected to molecular analysis, and this
AB  - has led
AB  - to a better understanding of the nature and variety of resistance systems employed by lactic
AB  - acid
AB  - bacteria to combat phage attack.  In addition, analysis of different bacteriophage has
AB  - increased our
AB  - knowlege of these ubiquitous particles to the point where it is possible to construct novel
AB  - phage
AB  - resistances based on the phage genome.  This review will briefly outline the recent progress
AB  - in the
AB  - molecular analysis of bacteriophage-host interactions, bacteriophage resistance and counter
AB  - resistance, and the construction of novel resistance mechanisms.  In particular, recent
AB  - evidence
AB  - regarding the mechanisms of resistance employed by the conjugative plasmid pNP40 will be
AB  - described in some detail.  In addition, an instance will be described in which pNP40 has been
AB  - used
AB  - in the construction of phage resistant starters which have been successfully exploited by the
AB  - dairy
AB  - industry.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Miller, L.
AU  - Klaenhammer, T.
TI  - Molecular characterization of a Type II methylase gene exchanged between pTR2030 and a virulent phage in Lactococci.
JO  - Plasmid
PY  - 1990
SP  - 167
EP  - 168
VL  - 23
AB  - None
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Miller, L.A.
AU  - Klaenhammer, T.R.
TI  - Nucleotide sequence and distribution of the pTR2030 resistance determinant (hsp) which aborts bacteriophage infection in Lactococci.
JO  - Appl. Environ. Microbiol.
PY  - 1990
SP  - 2255
EP  - 2258
VL  - 56
AB  - The lactococcal plasmid pTR2030 encodes resistance to bacteriophage attack via
AB  - two mechanisms, an abortive-infection mechanism, designated Hsp, and a
AB  - restriction and modification system.  We present the complete sequence of the
AB  - hsp structural gene.  The gene is 1,887 base pairs in length and encodes a
AB  - protein with a predicted molecular mass of 73.8 kilodaltons.  The upstream
AB  - region was cloned in a promoter-screening vector and shown to direct the
AB  - constitutive expression of the cat-86 gene.  An internal probe was used to
AB  - determine the distribution of the hsp sequence in industrially significant
AB  - lactococcal strains and to evaluate its relatedness to another lactococcal
AB  - plasmid implicated in an abortive-infection-type mechanism, pNP40.  No homology
AB  - was detected, suggesting that this gene is not widely distributed in
AB  - lactococci.  Therefore, there are at least two independent abortive-infection
AB  - genotypes in lactococci.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Miller, L.A.
AU  - Klaenhammer, T.R.
TI  - Cloning, expression, and sequence determination of a bacteriophage fragment encoding bacteriophage resistance in Lactococcus lactis.
JO  - J. Bacteriol.
PY  - 1990
SP  - 6419
EP  - 6426
VL  - 172
AB  - A number of host-encoded phage resistance mechanisms have been described in
AB  - lactococci.  However, the phage genome has not been exploited as a source of
AB  - additional resistance determinants.  A 4.5-kb BamHI-HindIII fragment of phage
AB  - nck202.50 (Phi50) was subcloned in streptococcus-Escherichia coli shuttle
AB  - plasmid pSA3 and introduced into Lactoccus lactis NCK203 and MG1363 by
AB  - protoplast transformation.  This cloned phage fragment directed a bacteriophage
AB  - resistance phenotype designated Per (phage-encoded resistance).  Both Phi50 and
AB  - a distantly related phage, nck202.48 (Phi48), formed small plaques on strain
AB  - NCK213 at a slightly reduced efficiency of plaquing on the Per+ host.  The per
AB  - locus was further reduced to a 1.4-kb fragment through in vitro deletion
AB  - analysis.  The 1.4-kb fragment was sequenced, and the Per phenotype was found
AB  - to be associated with a ca. 500-bp region rich in direct and inverted repeats.
AB  - We present evidence that the Per region contains a phage origin of replication
AB  - which, in trans, may interfere with phage replication by titration of DNA
AB  - polymerase or other essential replication factors.  It was demonstrated that
AB  - the Per+ activity was not detected against six independent phages which were
AB  - previously shown to be sensitive to the Hsp+ mechanism.  The mutually exclusive
AB  - resistance mechanisms could be combined to confer resistance to both types of
AB  - phages (Hsp resistant and Per resistant) in a single host.  This is the first
AB  - description in lactococci of a phage resistance phenotype, other than
AB  - superinfection immunity, originating from a lactococcal phage genome.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Miller, L.A.
AU  - Klaenhammer, T.R.
TI  - In vivo genetic exchange of a functional domain from a Type II A methylase between lactococcal plasmid pTR2030 and a virulent bacteriophage.
JO  - J. Bacteriol.
PY  - 1991
SP  - 4363
EP  - 4370
VL  - 173
AB  - The conjugative plasmid pTR2030 confers bacteriophage resistance to lactococci by two
AB  - independent mechanisms, an abortive infection mechanism (Hsp+) and a restriction and
AB  - modification system (R+/M+).  pTR2030 transconjugants of lactococcal strains are used in the
AB  - dairy industry to prolong the usefulness of mesophilic starter cultures.  One bacteriophage
AB  - which has emerged against a pTR2030 transconjugant is not susceptible to either of the two
AB  - defense systems encoded by the plasmid.  Phage nck202.50 (Phi50) is completely resistant to
AB  - restriction by pTR2030.  A region of homology between pTR2030 Phi50 was subcloned, physically
AB  - mapped, and sequenced.  A region of 1,273 bp was identical in both plasmid and phage,
AB  - suggesting that the fragment had recently been transferred between the two genomes.  Sequence
AB  - analysis confirmed that the transferred region encoded >55% of the amino domain of the
AB  - structural gene for a type II methylase designated LlaI.  The LlaI gene is 1,869 bp in length
AB  - and shows organizational similarities to the type II A methylase FokI.  In addition to the
AB  - amino domain, upstream sequences, possibly containing the expression signals, were present on
AB  - the phage genome.  The phage Phi50 fragment containing the methylase amino domain, designated
AB  - LlaPI, when cloned onto the shuttle vector pSA3 was capable of modifying another phage genome
AB  - in trans.  This is the first report of the genetic exchange between a bacterium and a phage
AB  - which confers a selective advantage on the phage.  Definition of the LlaI system on pTR2030
AB  - provides the first evidence that type II systems contribute to restriction and modification
AB  - phenotypes during host-dependent replication of phages in lactococci.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Miller, L.A.
AU  - Klaenhammer, T.R.
TI  - The bacteriophage resistance plasmid pTR2030 forms high-molecular-weight multimers in Lactococci.
JO  - Plasmid
PY  - 1991
SP  - 105
EP  - 112
VL  - 25
AB  - Lactococcus lactis ME2 can transfer a 46-kb plasmid, pTR2030, which encodes
AB  - abortive phage infection (Hsp) and restriction/modification (R/M) activities.
AB  - pTR2030 can be detected as a monomeric plasmid in transconjugants at low copy
AB  - number, but not in ME2.  pTR2030-specific probes were cloned and used to
AB  - determine the location of the element in ME2.  No homology was observed between
AB  - these pTR2030-specific probes and the CsCl-purified plasmid content of ME2.
AB  - However, probes specific for pTR2030 hybridized strongly to a
AB  - high-molecular-weight moiety, and not to chromosomal DNA, in total DNA isolated
AB  - by a gentle lysis procedure.  The absence of junction fragments indicates that
AB  - pTR2030 forms high-molecular-weight multimers in lactococci.  A phage-sensitive
AB  - derivative of ME1, L. lactis N1, is cured of pTR2030 and no longer possesses
AB  - the high-molecular-weight species.  When pTR2030 was reintroduced to N1 via
AB  - conjugation, an ME2-like phage-insensitive phenotype was restored.  pTR2030
AB  - could remain as a detectable monomeric plasmid in the N1 transconjugants or
AB  - could revert to the high-molecular-weight structure.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Pierce, K.
AU  - Klaenhammer, T.R.
TI  - The conjugative plasmid pTR2030 encodes two bacteriophage defense mechanisms in Lactococci, restriction modification (R+/M+) and abortive infection (Hsp+).
JO  - Appl. Environ. Microbiol.
PY  - 1989
SP  - 2416
EP  - 2419
VL  - 55
AB  - pTR2030 is a conjugative plasmid which encodes resistance to bacteriophage in
AB  - lactococci by a mechanism that aborts the phage infection (Hsp+).  Subcloning
AB  - and in vivo deletion events showed that two independent mechanisms of
AB  - resistance are located on a 13.6-kilobase BglII fragment cloned in pSA3; one
AB  - mechanism is responsible for the abortive infection, and the other encodes a
AB  - restriction modification system.  The introduction of pTR2030 or the
AB  - recombinant plasmid pTK6 resulted in the loss of a resident restriction
AB  - modification plasmid in Lactococcus lactis NCK202 which was not previously
AB  - identified.
ER  -

TY  - JOUR
AU  - Hill, C.
AU  - Romero, D.A.
AU  - McKenney, D.S.
AU  - Finer, K.R.
AU  - Klaenhammer, T.R.
TI  - Localization, cloning, and expression of genetic determinants for bacteriophage resistance (Hsp) from the conjugative plasmid pTR2030.
JO  - Appl. Environ. Microbiol.
PY  - 1989
SP  - 1684
EP  - 1689
VL  - 55
AB  - Genetic determinants for a bacteriophage resistance mechanism (Hsp+) encoded by plasmid
AB  - pTR2030 (46.2 kilobases [kb]) were localized by mapping an 11.5 -kb deletion that accompanied
AB  - the transition of Lactococcus lactis LMA 12-4 transconjugants (M.E. Sanders, P.J. Leonard,
AB  - W.D. Sing and T.R. Klaenhammer, Appl. Environ. Microbiol. 52:1001-1007, 1986) from phage
AB  - resistance to phage sensitivity. The deleted 34.7-kb replicon (pTR2023, Hsp-) retained its
AB  - conjugative ability, demonstrating that the phage resistance and conjugal transfer
AB  - determinants were genetically distinct. The Hsp region of pTR2030, which was contained within
AB  - a 13.6-kb BglII fragment, was cloned into the BamHI site of bacteriophage lambda EMBL3, and
AB  - Hsp was subcloned into the Escherichia coli-Streptococcus shuttle vector pSa3. The recombinant
AB  - plasmids pTK6 and pTK9 were recovered in E. coli HB101 and contained a 13.6-kb insert in
AB  - opposite orientations. L. lactis MG1363 transformants carrying pTK6 or pTK9 exhibited a
AB  - significant reduction in plaque size, in addition to a slight reduction in the efficiency of
AB  - plaquing for both prolate and small isometric phages. Phenotypic reactions observed for the
AB  - recombinant plasmids suggest that pTR2030-encoded Hsp acts similarly against both prolate and
AB  - small isometric phages. Tn5 mutagenesis was used to define the region essential for the
AB  - expression of the Hsp+ phenotype. Any of four insertions within a 3-kb region resulted in the
AB  - loss of phagge resistance, whereas a further 26 insertions outside this locus had no effect on
AB  - Hsp expression. In vitro deletion analysis confirmed that the 3-kb region contained all the
AB  - information necessary for the observed resistance.
ER  -

TY  - JOUR
AU  - Hill, S.A.
TI  - Cell to cell transmission of donor DNA overcomes differential incorporation of non-homologous and homologous markers in Neisseria gonorrhoeae.
JO  - Gene
PY  - 1999
SP  - 175
EP  - 182
VL  - 240
AB  - The neisseriae are naturally competent for DNA transformation. This genetic study examines
AB  - whether the modification status of chromosomal donor DNA affects transformation of Neisseria
AB  - gonorrhoeae to drug resistance. When a single modification system was inactivated, unmodified
AB  - chromosomal donor DNA was not restricted when used to transform the cognate restriction+ host,
AB  - irrespective of whether the donor DNA carried a point mutation (homologous marker) or a
AB  - drug-resistance gene cassette (non-homologous marker). These observations contrasted
AB  - transformations performed with unmodified plasmid donor DNAs, where the incoming DNA was
AB  - excluded. However, during the study, it became apparent that certain strains of gonococci
AB  - showed differential incorporation of non-homologous markers when compared with the
AB  - incorporation of the homologous marker, even when the donor DNAs were prepared from parental
AB  - strains. Differential incorporation of markers could be rescued either through cell to cell
AB  - transmission of donor DNA, or by performing in vitro transformations with donor DNA
AB  - preparations that were obtained from spent culture supernatants. Overall, the data indicate
AB  - that, in addition to the exclusion of foreign DNA through the requirement for a genus-specific
AB  - uptake sequence, gonococci appear capable of excluding DNA on the basis of homology.
ER  -

TY  - JOUR
AU  - Hiller, D.A.
TI  - Mechanism of DNA bending and its role in the specificity of EcoRV restriction endonuclease.
JO  - Ph.D. Thesis, Univ. of California, Santa Barbara
PY  - 2005
SP  - 1
EP  - 160
AB  - Many DNA binding proteins involved in transcription, packaging and other processes bend their
AB  - target sequences as part of their function.  The mechanism of DNA bending and its role in
AB  - specificity, therefore, are topics of fundamental interest.  The homodimeric EcoRV restriction
AB  - endonuclease, which recognizes the six base pair sequence GATATC, has emerged as one of the
AB  - best studied nucleic acid binding proteins.  EcoRV bends the center TA step by 50 degrees to
AB  - facilitate cleavage of the phosphodiester backbone.  A fluorescence resonance energy transfer
AB  - assay was developed to monitor the DNA bending step, in addition to the binding and cleavage
AB  - steps previously observed.  Bending of cognate DNA is rapid and appears to be simultaneous
AB  - with binding.  Furthermore, no bending was observed in the absence of divalent metal. To
AB  - elucidate the mechanism of DNA bending by EcoRV, electrostatic contacts between the protein
AB  - and DNA were deleted.  This was done by mutating positively charged residues to alanine,
AB  - replacing negatively charged DNA phosphates with uncharged methylphosphonates, and making both
AB  - substitutions simultaneously.  It was found that asymmetric neutralization of the phosphate
AB  - backbone improves DNA binding, bending, and cleavage, which indicates that DNA bending begins
AB  - during the initial association process and has increasing importance throughout the catalytic
AB  - pathway.  DNA bending was also stabilized by the diffuse charge present in the
AB  - carboxy-terminal domain of each monomer, as observed by fluorescence in solution.  The crystal
AB  - structure of a mutant lacking these domains also showed small changes at the active site,
AB  - leading to destabilized binding of the divalent metal needed for catalysis.  To further
AB  - understand how induced fit contributes to specificity, the transient kinetic techniques
AB  - developed were used in partnership with x-ray crystallography to study discrimination against
AB  - a noncognate sequence, GAATTC.  Again, binding and bending were simultaneous; however the bend
AB  - angle decreased in response to a steric block at the center step.  The crystal structure
AB  - showed that metal binding was disrupted, and this was suffient to reduce the cleavage rate
AB  - 105-fold.  Together, these studies demonstrate that specificity is coupled to catalysis by
AB  - induced fit and partially establish the timing and mechanism of DNA bending by a site-specific
AB  - nucleic acid enzyme.
ER  -

TY  - JOUR
AU  - Hiller, D.A.
AU  - Fogg, J.M.
AU  - Martin, A.M.
AU  - Beechem, J.M.
AU  - Reich, N.O.
AU  - Perona, J.J.
TI  - Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.
JO  - Biochemistry
PY  - 2003
SP  - 14375
EP  - 14385
VL  - 42
AB  - The complete catalytic cycle of EcoRV endonuclease has been observed by combining fluorescence
AB  - anisotropy with fluorescence resonance energy
AB  - transfer (FRET) measurements. Binding, bending, and cleavage of substrate
AB  - oligonucleotides were monitored in real time by rhodamine-x anisotropy and
AB  - by FRET between rhodamine and fluorescein dyes attached to opposite ends
AB  - of a 14-mer DNA duplex. For the cognate GATATC site binding and bending
AB  - are found to be nearly simultaneous, with association and bending rate
AB  - constants of (1.45-1.6) x 10(8) M(-1) s(-1). On the basis of the
AB  - measurement of k(off) by a substrate-trapping approach, the equilibrium
AB  - dissociation constant of the enzyme-DNA complex in the presence of
AB  - inhibitory calcium ions was calculated as 3.7 x 10(-12) M from the kinetic
AB  - constants. Further, the entire DNA cleavage reaction can be observed in
AB  - the presence of catalytic Mg(2+) ions. These measurements reveal that the
AB  - binding and bending steps occur at equivalent rates in the presence of
AB  - either Mg(2+) or Ca(2+), while a slow decrease in fluorescence intensity
AB  - following bending corresponds to k(cat), which is limited by the cleavage
AB  - and product dissociation steps. Measurement of k(on) and k(off) in the
AB  - absence of divalent metals shows that the DNA binding affinity is
AB  - decreased by 5000-fold to 1.4 x 10(-8) M, and no bending could be detected
AB  - in this case. Together with crystallographic studies, these data suggest a
AB  - model for the induced-fit conformational change in which the role of
AB  - divalent metal ions is to stabilize the sharply bent DNA in an orientation
AB  - suitable for accessing the catalytic transition state.
ER  -

TY  - JOUR
AU  - Hiller, D.A.
AU  - Perona, J.J.
TI  - Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.
JO  - Biochemistry
PY  - 2006
SP  - 11453
EP  - 11463
VL  - 45
AB  - The carboxy-terminal subdomains of the homodimeric EcoRV restriction endonuclease each bear a
AB  - net charge of +4 and are positioned on the inner
AB  - concave surface of the 50 degree DNA bend that is induced by the enzyme. A
AB  - complete kinetic and structural analysis of a truncated EcoRV mutant
AB  - lacking these domains was performed to assess the importance of this
AB  - diffuse charge in facilitating DNA binding, bending, and cleavage. At the
AB  - level of formation of an enzyme-DNA complex, the association rate for the
AB  - dimeric mutant enzyme was sharply decreased by 10(3)-fold, while the
AB  - equilibrium dissociation constant was weakened by nearly 10(6)-fold
AB  - compared with that of wild-type EcoRV. Thus, the C-terminal subdomains
AB  - strongly stabilize the enzyme-DNA ground-state complex in which the DNA is
AB  - known to be bent. Further, the extent of DNA bending as observed by
AB  - fluorescence resonance energy transfer was also significantly decreased.
AB  - The crystal structure of the truncated enzyme bound to DNA and calcium
AB  - ions at 2.4 A resolution reveals that the global fold is preserved and
AB  - suggests that a divalent metal ion crucial to catalysis is destabilized in
AB  - the active site. This may explain the 100-fold decrease in the rate of
AB  - metal-dependent phosphoryl transfer observed for the mutant. These results
AB  - show that diffuse positive charge associated with the C-terminal
AB  - subdomains of EcoRV plays a key role in DNA association, bending, and
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Hiller, D.A.
AU  - Rodriguez, A.M.
AU  - Perona, J.J.
TI  - Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 121
EP  - 136
VL  - 354
AB  - The crystal structure of EcoRV endonuclease bound to non-cognate DNA at 2.0 angstroms
AB  - resolution shows that very small structural adaptations are sufficient to ensure the extreme
AB  - sequence specificity characteristic of restriction enzymes. EcoRV bends its specific GATATC
AB  - site sharply by 50 degrees into the major groove at the center TA step, generating unusual
AB  - base-base interactions along each individual DNA strand. In the symmetric non-cognate complex
AB  - bound to GAATTC, the center step bend is relaxed to avoid steric hindrance caused by the
AB  - different placement of the exocyclic thymine methyl groups. The decreased base-pair unstacking
AB  - in turn leads to small conformational rearrangements in the sugar-phosphate backbone,
AB  - sufficient to destabilize binding of crucial divalent metal ions in the active site. A second
AB  - crystal structure of EcoRV bound to the base-analog GAAUTC site shows that the 50 degrees
AB  - center-step bend of the DNA is restored. However, while divalent metals bind at high occupancy
AB  - in this structure, one metal ion shifts away from binding at the scissile DNA phosphate to a
AB  - position near the 3'-adjacent phosphate group. This may explain why the 10(4)-fold attenuated
AB  - cleavage efficiency toward GAATTC is reconstituted by less than tenfold toward GAAUTC.
AB  - Examination of DNA binding and bending by equilibrium and stopped-flow florescence quenching
AB  - and fluorescence resonance energy transfer (FRET) methods demonstrates that the capacity of
AB  - EcoRV to bend the GAATTC non-cognate site is severely limited, but that full bending of GAAUTC
AB  - is achieved at only a threefold reduced rate compared with the cognate complex. Together, the
AB  - structural and biochemical data demonstrate the existence of distinct mechanisms for ensuring
AB  - specificity at the bending and catalytic steps, respectively. The limited conformational
AB  - rearrangements observed in the EcoRV non-cognate complex provide a sharp contrast to the
AB  - extensive structural changes found in a non-cognate BamHI-DNA crystal structure, thus
AB  - demonstrating a diversity of mechanisms by which restriction enzymes are able to achieve
AB  - specificity.
ER  -

TY  - JOUR
AU  - Hiller, N.L.
AU  - Janto, B.
AU  - Hogg, J.S.
AU  - Boissy, R.
AU  - Yu, S.
AU  - Powell, E.
AU  - Keefe, R.
AU  - Ehrlich, N.E.
AU  - Shen, K.
AU  - Hayes, J.
AU  - Barbadora, K.
AU  - Klimke, W.
AU  - Dernovoy, D.
AU  - Tatusova, T.
AU  - Parkhill, J.
AU  - Bentley, S.D.
AU  - Post, J.C.
AU  - Ehrlich, G.D.
AU  - Hu, F.Z.
TI  - Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.
JO  - J. Bacteriol.
PY  - 2007
SP  - 8186
EP  - 8195
VL  - 189
AB  - The distributed-genome hypothesis (DGH) states that pathogenic bacteria
AB  - possess a supragenome that is much larger than the genome of any single
AB  - bacterium and that these pathogens utilize genetic recombination and a
AB  - large, noncore set of genes as a means of diversity generation. We
AB  - sequenced the genomes of eight nasopharyngeal strains of Streptococcus
AB  - pneumoniae isolated from pediatric patients with upper respiratory
AB  - symptoms and performed quantitative genomic analyses among these and nine
AB  - publicly available pneumococcal strains. Coding sequences from all strains
AB  - were grouped into 3,170 orthologous gene clusters, of which 1,454 (46%)
AB  - were conserved among all 17 strains. The majority of the gene clusters,
AB  - 1,716 (54%), were not found in all strains. Genic differences per strain
AB  - pair ranged from 35 to 629 orthologous clusters, with each strain's genome
AB  - containing between 21 and 32% noncore genes. The distribution of the
AB  - orthologous clusters per genome for the 17 strains was entered into the
AB  - finite-supragenome model, which predicted that (i) the S. pneumoniae
AB  - supragenome contains more than 5,000 orthologous clusters and (ii) 99% of
AB  - the orthologous clusters ( approximately 3,000) that are represented in
AB  - the S. pneumoniae population at frequencies of >or=0.1 can be identified
AB  - if 33 representative genomes are sequenced. These extensive genic
AB  - diversity data support the DGH and provide a basis for understanding the
AB  - great differences in clinical phenotype associated with various
AB  - pneumococcal strains. When these findings are taken together with previous
AB  - studies that demonstrated the presence of a supragenome for Streptococcus
AB  - agalactiae and Haemophilus influenzae, it appears that the possession of a
AB  - distributed genome is a common host interaction strategy.
ER  -

TY  - JOUR
AU  - Hilt, E.E.
AU  - Price, T.K.
AU  - Diebel, K.
AU  - Putonti, C.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae.
JO  - Genome Announcements
PY  - 2016
SP  - e01248
EP  - e01216
VL  - 4
AB  - A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was
AB  - investigated. The size of the genome was 1,578,043 bp, with an
AB  - observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA
AB  - genes, and 1,532 protein-coding sequences. Genome coverage was 727x and consisted
AB  - of 32 contigs, with an N50 of 109,831 bp.
ER  -

TY  - JOUR
AU  - Hilty, M. et al.
TI  - Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals  a deep-branching classic lineage that is distinct from multiple sporadic lineages.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 3281
EP  - 3294
VL  - 6
AB  - The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence
AB  - factor and is targeted by pneumococcal conjugate vaccines (PCV).
AB  - However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated
AB  - globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve
AB  - sporadically, if they have high antibiotic nonsusceptiblity rates and a unique,
AB  - specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates
AB  - sourced from 17 different locations around the world was performed. Results
AB  - revealed a deep-branching classic lineage that is distinct from multiple sporadic
AB  - lineages. The sporadic lineages clustered with a previously sequenced, global
AB  - collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic
AB  - lineage is comprised mainly of the frequently identified multilocus sequences
AB  - types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates
AB  - had high nonsusceptiblity rates to beta-lactams and other antimicrobials.
AB  - Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an
AB  - increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp.
AB  - Performing adherence assays to human epithelial cells for selected classic and
AB  - sporadic non-Ec-Sp revealed that the presence of a integrative conjugative
AB  - element (ICE) results in increased adherence to human epithelial cells (P =
AB  - 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in
AB  - vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates
AB  - from the classic lineage have evolved separately. They have spread globally, are
AB  - well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due
AB  - to continued use of PCV, non-Ec-Sp may become more prevalent.
ER  -

TY  - JOUR
AU  - Himmelreich, R.
AU  - Hilbert, H.
AU  - Plagens, H.
AU  - Pirkl, E.
AU  - Li, B.-C.
AU  - Herrmann, R.
TI  - Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 4420
EP  - 4449
VL  - 24
AB  - The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced.  It has a
AB  - size of 816,394 base pairs with an average G+C content of 40.0 mol%.  We predict 677 open
AB  - reading frames (ORFs) and 39 genes coding for various RNA species.  Of the predicted ORFs,
AB  - 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did
AB  - not reveal any significant similarity to gene sequences in databases.  This permitted us
AB  - tentatively to assign a functional classification to a large number of ORFs and to deduce the
AB  - biochemical and physiological properties of this bacterium.  The reduction of the genome size
AB  - of M.pneumoniae during its reductive evolution from ancestral bacteria can be explained by the
AB  - loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways.  Therefore,
AB  - M.pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision
AB  - of exogenous essential metabolites.  All the major classes of cellular processes and metabolic
AB  - pathways are briefly described.  For a number of activities/functions present in M.pneumoniae
AB  - according to experimental evidence, the corresponding genes could not be identified by
AB  - similarity search.  For instance we failed to identify genes/proteins involved in motility,
AB  - chemotaxis and management of oxidative stress.
ER  -

TY  - JOUR
AU  - Himmelreich, R.
AU  - Plagens, H.
AU  - Hilbert, H.
AU  - Reiner, B.
AU  - Herrmann, R.
TI  - Comparative anlaysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 701
EP  - 712
VL  - 25
AB  - The sequenced genomes of the two closely related bacteria Mycoplasma genitalium and Mycoplasma
AB  - pneumoniae were compared with emphasis on genome organization and coding capacity.  All the
AB  - 470 proposed open reading frames (ORFs) of the smaller M.genitalium genome (580 kb) were
AB  - contained in the larger genome (816 kb) of M.pneumoniae.  There were some discrepancies in
AB  - annotation, but inspection of the DNA sequences showed that the corresponding DNA was always
AB  - present in M.pneumoniae.  The two genomes could be subdivided into six segments.  The order of
AB  - orthologous genes was well conserved within individual segments but the order of these
AB  - segments in both bacteria was different.  We explain the different organization of the
AB  - segments by translocation via homologous recombination.  The translocations did not disturb
AB  - the continuous bidirectional course of transcription in both genomes, starting at the proposed
AB  - origin of replication.  The additional 236 kb in M.pneumoniae, compared with the M.genitalium
AB  - genome, were coding for 209 proposed ORFs not identified in M.genitalium.  Of these ORFs, 110
AB  - were amplifications of ORFs existing mainly as single copies in M.genitalium.  In addition, 23
AB  - ORFs containing a copy of either one of the three repetitive DNA sequences RepMP2/3, RepMP4
AB  - and RepMP5 were annotated in M.pneumoniae but not in M.genitalium, although similar DNA
AB  - sequences were present.  The M.pneumoniae-specific genes included a restriction-modification
AB  - system, two transport systems for carbohydrates, the complete set of three genes coding for
AB  - the arginine dihydrolase pathway and 14 copies of the repetitive DNA sequence RepMP1 which
AB  - were part of several different translated genes with unknown function.
ER  -

TY  - JOUR
AU  - Hines, J.L.
AU  - Agarwal, K.L.
TI  - Purification and characterization of HpaI and HpaII.
JO  - Fed. Proc.
PY  - 1979
SP  - 294
EP  - 294
VL  - 38
AB  - The restriction endonucleases from Haemophilus parainfluenzae, HpaI and HpaII,
AB  - have been purified to homogeneity.  HpaI has been purified 10,000 fold and has
AB  - a specific activity of 2.2 x 106 units/mg.  (1 unit corresponds to the amount
AB  - of enzyme required to cleave 1 microgram of lambda DNA to completion in 60
AB  - minutes.) HpaI has a monomer molecular weight of 29,000 daltons and exists as a
AB  - 58,000 dalton dimer under native conditions.  A specific volume (V) of 0.72
AB  - cc/g used in the molecular weight determinations was calculated from the amino
AB  - acid composition.  The sedimentation velocity is 3.61 x 10-13 sec.  A ratio of
AB  - frictional coefficients (f/fo) was found to be 1.5 indicating an elongated
AB  - molecule.  HpaII has been purified 8,000 fold and has a specific activity of
AB  - 1.8 x 106 units/mg.  (Same units as above.)  HpaII has a monomer molecular
AB  - weight of 41,000 and exists as an 82,000 dalton dimer under native conditions.
AB  - A specific volume (v) of 0.73 cc/g used in the molecular weight determinations
AB  - was calculated from the amino acid composition.  The sedimentation velocity is
AB  - 4.45 x 10-13 sec.  A ratio of frictional coefficients (f/fo) was found to be
AB  - 1.45 indicating that HpaII is also an elongated molecule.
ER  -

TY  - JOUR
AU  - Hines, J.L.
AU  - Chauncey, T.R.
AU  - Agarwal, K.L.
TI  - Preparation and properties of HpaI and HpaII endonucleases.
JO  - Methods Enzymol.
PY  - 1980
SP  - 153
EP  - 163
VL  - 65
AB  - Two restriction endonuclease activities, HpaI and HpaII, have been isolated
AB  - from Haemophilus parainfluenzae.  Endonuclease HpaI has been isolated in
AB  - homogeneous form, while HpaII has been purified free of contaminating nuclease
AB  - and phosphatase activies.  HpaI recognizes the DNA sequence and cleaves the
AB  - phosphodiester bonds in both strands as indicated.  HpaII recognizes the DNA
AB  - sequence and cleaves the phosphodiester bonds in a staggered fashion as
AB  - indicated.  The reaction products, in both cases, contain 5'-phosphoryl and
AB  - 3'-hydroxyl termini.
ER  -

TY  - JOUR
AU  - Hingorani-Varma, K.
AU  - Bitinaite, J.
TI  - Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 40392
EP  - 40399
VL  - 278
AB  - SgrAI restriction endonuclease cooperatively interacts and cleaves two target sites that
AB  - include both the canonical sites, CPuCCGGPyG, and the
AB  - secondary sites, CPuCCGGPy(A/T/C). It has been observed that the cleaved
AB  - canonical sites stimulate SgrAI cleavage at the secondary sites.
AB  - Equilibrium binding studies show that SgrAI binds to its canonical sites
AB  - with a high affinity (Ka = 4-8 x 10(10) M-1) and that it has a 15-fold
AB  - lower affinity for the cleaved canonical sites and a 30-fold lower
AB  - affinity for the secondary sites. Steady-state kinetics reveals substrate
AB  - cooperativity for SgrAI cleavage on both canonical and secondary sites.
AB  - The specificity of SgrAI for the secondary site CACCGGCT, as measured by
AB  - kcat/K is about 500-fold lower than that for the canonical site CACCGGCG,
AB  - but this difference is reduced to 10-fold in the presence of the cleaved
AB  - canonical sites. The efficiency of canonical site cleavage also increases
AB  - by 3-fold when the cleaved canonical sites are present in the reaction.
AB  - Furthermore, the substrate cooperativity for SgrAI cleavage is abolished
AB  - for both types of sites in the presence of cleaved canonical sites. These
AB  - results indicate that target site cleavage occurs via a coordinated
AB  - interaction of two SgrAI protein subunits, where the subunit bound to the
AB  - cleaved site stimulates the cleavage of the uncut site bound by the other
AB  - subunit. The free subunits of SgrAI have the flexibility to bind different
AB  - target sites and, consequently, assemble into various catalytically active
AB  - complexes, which differ in their catalytic efficiencies.
ER  -

TY  - JOUR
AU  - Hinkle, N.F.
AU  - Miller, R.V.
TI  - pMG7-mediated restriction of Pseudomonas aeruginosa phage DNAs is determined by a class II restriction endonuclease.
JO  - Plasmid
PY  - 1979
SP  - 387
EP  - 393
VL  - 2
AB  - A class II restriction endonuclease, PaeR7, has been isolated from a Pseudomonas aeruginosa
AB  - strain containing the resistance plasmid pMG7. The activity cannot be isolated from an
AB  - isogenic strain which does not contain this resistance plasmid. EndoR-PaeR7 requires Mg2+ for
AB  - activity but does not require ATP or S-adenosyl-L-methionine. Specific digestion patterns are
AB  - produced upon agarose gel electrophoresis of substrate DNAs which have been digested with the
AB  - enzyme. The enzyme is the biochemical basis for the pMG7-mediated phage interference reported
AB  - by Jacoby and Sutton (1977). DNAs isolated from restricted phages act as substrates for the
AB  - enzyme while DNAs isolated from unrestricted phages and phages which have been modified by
AB  - growth on strains containing pMG7 do not act as substrates for the enzyme.
ER  -

TY  - JOUR
AU  - Hinsch, B.
AU  - Kula, M.-R.
TI  - Physical and kinetic properties of the site specific endonuclease BamHI from Bacillus amyloliquefaciens.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 623
EP  - 633
VL  - 8
AB  - The site specific endonuclease BamHI which is composed of subunits of a
AB  - molecular weight of 22,000 can aggregate to complexes of a molecular weight of
AB  - 36,0000.  It is an acidic protein with an iselectric point at pH 5.3.  Optimal
AB  - activity is reached at 13 mM MgCl2.  A very simple method is presented to
AB  - determine kinetic constants of restriction enzymes directly from agarose gel
AB  - photographs without any further equipment applying the integrated Michaelis
AB  - Menten equation.  With pJC 80 DNA as a substrate KM was found to be 3.6 10-10
AB  - M.  The method can be used to redefine the unit activity of site specific
AB  - endonucleases unambiguously.
ER  -

TY  - JOUR
AU  - Hinsch, B.
AU  - Kula, M.-R.
TI  - Reaction kinetics of some important site-specific endonucleases.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 3159
EP  - 3174
VL  - 9
AB  - Reaction kinetics of the site-specific endonucleases BamHI, BglII, ClaI, EcoRI,
AB  - HpaII, PstI, SalI, SmaI, and XorII were investigated employing some frequently
AB  - used substrates.  Six of these enzymes could be analyzed under steady-state
AB  - conditions.  Kinetic data were obtained from progres curves applying an
AB  - integrated Michaelis-Menten equation.  KM ranged from 4 - 10-9M to 4 - 10-11 M.
AB  - Activities also spanned two orders of magnitude.  In the case of ClaI the
AB  - analysis of the pre-steady-state kinetics ("burst reaction") allowed the
AB  - assessment of several rate constants.  The rate-limiting step is the very slow
AB  - dissociation of the enzyme-product complex (0.22 min-1).  This complex is
AB  - formed from the enzyme-bound nicked intermediate at a rate of about 6.  SmaI
AB  - and XorII resembled ClaI in their kinetics.  The burst reaction can be used for
AB  - the easy and unambiguous determination of molar concentrations of site-specific
AB  - endonucleases in any preparation, which is free of non-specific DNases.
ER  -

TY  - JOUR
AU  - Hinsch, B.
AU  - Mayer, H.
AU  - Kula, M.-R.
TI  - Binding of non-substrate nucleotides to a restriction endonuclease: a model for the interaction of Bam HI with its recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 2547
EP  - 2559
VL  - 8
AB  - The kinetic constants of the site-specific endonuclease Bam HI for various
AB  - substrates were determined and binding of non-substrate nucleotides to the
AB  - enzyme was studied.  Agarose gel assays in combination with an integrated
AB  - Michaelis-Menten equation were used for the evaluation of data.  The turnover
AB  - number was 2.2 min-1 at 37C with pJC80 DNA as the substrate.  It depends on the
AB  - conformation and base composition of the substrate.  Michaelis constants also
AB  - depend on substrate conformation.  Non-substrate polynucleotides were found to
AB  - inhibit Bam competitively with KI ranging from 10-6 to >10-3 M depending on
AB  - base composition, base pairing, and helix conformation.  Dinucleotides showed
AB  - sequence-specific, competitive inhibition with KIs ranging from 10-5 to >10-3
AB  - M.  Mononucleotides and -nucleosides acted noncompetitively.  Binding was
AB  - influenced by the extent of phosphorylation, but not by the nature of the base.
AB  - KIs varied between 10-3 and 10-2 M.  The results are discussed with respect to
AB  - the recognition requirements of Bam HI.
ER  -

TY  - JOUR
AU  - Hiom, K.
AU  - Sedgwick, S.G.
TI  - Simple methods for making EcoK and McrA restrictionless mutants.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2502
EP  - 2502
VL  - 19
AB  - Restriction systems present a major obstacle to the cloning and expression of
AB  - heterologous DNAs in bacteria such as E. coli.  Many modern cloning strains
AB  - therefore carry disabling mutations in genes encoding restriction endonucleases
AB  - to prevent degradation of these heterologous DNAs, however many laboratory
AB  - strains of E. coli are not deficient in host restriction activity and are
AB  - therefore inaccessible to foreign DNAs.  Here we describe simple methods for
AB  - genetically eliminating EcoK and McrA restriction from E. coli that are
AB  - generally applicable to strain improvement programs with other bacterial
AB  - species.
ER  -

TY  - JOUR
AU  - Hiom, K.
AU  - Sedgwick, S.G.
TI  - Cloning and structural characterization of the mcrA locus of Escherichia coli.
JO  - J. Bacteriol.
PY  - 1991
SP  - 7368
EP  - 7373
VL  - 173
AB  - Escherichia coli has DNA restriction systems which are able to recognize and
AB  - attack modified cytosine residues in the DNA of incoming bacteriophages and
AB  - plasmids.  The locus for the McrA/RglA system of modified cytosine restriction
AB  - was located near the pin gene of the defective element, e14.  Hence, loss of
AB  - the e14 element through abortive induction after UV irradiation caused a
AB  - permanent loss of McrA restriction activity.  e14 DNA encoding McrA restriction
AB  - was cloned and sequenced to reveal a single open reading frame of 831 bp with a
AB  - predicted gene product of 31 kDa.  Clones expressing the complete open reading
AB  - frame conferred both McrA and RglA phenotypes; however, a deletion derivative
AB  - was found which complemented RglA restriction against nonglucosylated T6gt
AB  - phage but did not complement for McrA restriction of methylated plasmid DNA.
AB  - Possible explanations for this activity and a comparison with the different
AB  - organization of the McrB/RglB restriction system are discussed.
ER  -

TY  - JOUR
AU  - Hiom, K.
AU  - Thomas, S.M.
AU  - Sedgwick, S.G.
TI  - Different mechanisms for SOS induced alleviation of DNA restriction in Escherichia coli.
JO  - Biochimie
PY  - 1991
SP  - 399
EP  - 405
VL  - 73
AB  - The alleviation of DNA restriction during the SOS response in Escherichia coli has been
AB  - further investigated.  With the EcoK DNA restriction system UV irradiated wild-type cells show
AB  - a 10^4-fold increase in ability to plate non-modified lambda phage and a 3-4 fold increase in
AB  - transformation by non-modified plasmid DNA.  A role for the umuDC genes of E. coli in the
AB  - process of SOS-induced restriction alleviation was identified by showing that a umuC122::Tn5
AB  - mutant could alleviate EcoK restriction to only 5% that of wild-type levels.  Although umuDC
AB  - are better characterized for their pivotal role in SOS induced mutagenesis, it is demonstrated
AB  - here that umu-dependent alleviation of EcoK restriction is a transient process in which
AB  - umu-dependent mutagenesis plays little part.  A second form of SOS induced alleviation of DNA
AB  - restriction is described in this paper involving the McrA restriction system.  The mcrA gene
AB  - is shown to be encoded within a defective prophage called e14 situated at the 25 min region on
AB  - the Escherichia coli genetic map.  e14 is known to abortively excise from the chromosome after
AB  - SOS induction and it is demonstrated in this report that mcrA is lost from the genome after
AB  - SOS induction as part of e14.  This results in a co-ordinate decrease in the level of mcrA
AB  - restriction within a population of cells.
ER  -

TY  - JOUR
AU  - Hiom, K.J.
AU  - Sedgwick, S.G.
TI  - Alleviation of EcoK DNA restriction in Escherichia coli and involvement of umuDC activity.
JO  - Mol. Gen. Genet.
PY  - 1992
SP  - 265
EP  - 275
VL  - 231
AB  - The activity of the EcoKI DNA restriction system of Escherichia coli reduces
AB  - both the plating efficiency of unmodified phage lambda and the transforming
AB  - ability of unmodified pBR322 plasmid DNA.  However, restriction can be
AB  - alleviated in wild-type cells, by UV irradiation and expression of the SOS
AB  - response, so that 10/3- to 10/4-fold increases in phage growth and fourfold
AB  - increases in plasmid transformation occurred with unmodified DNA.  Restriction
AB  - alleviation was found to be a transient effect because induced cells, which
AB  - initially failed to restrict unmodified plasmid DNA, later restricted
AB  - unmodified phage lambda.  Although the SOS response was needed for restriction
AB  - alleviation, constitutive SOS induction, elicited genetically with a recA730
AB  - mutation, did not alleviate restriction and UV irradiation was still needed.  A
AB  - hitherto unsuspected involvement of the umuDC operon in this alleviation of
AB  - restriction is characterized and, by differential complementation, was
AB  - separated from the better known role of umuDC in mutagenic DNA repair.  The
AB  - need for cleavage of UmuD for restriction alleviation was shown with plasmids
AB  - encoding cleavable, cleaved, and non-cleavable forms of UmuD.  However, UV
AB  - irradiation was still needed even when cleaved UmuD was provided.  The
AB  - possibility that restriction alleviation occurs by a general inhibition of the
AB  - EcoK restriction/modification complex was tested and discounted because
AB  - modification of lambda was not reduced by UV irradiation.  An alternative idea,
AB  - that restriction activity was competitively reduced by an increase in EcoK
AB  - modification, was also discounted by the lack of any increase in the
AB  - modification of lambda Ral-, a naturally undermodified phage.  Other possible
AB  - mechanisms for restriction alleviation are discussed.
ER  -

TY  - JOUR
AU  - Hiraide, Y.
AU  - Oshima, K.
AU  - Fujisawa, T.
AU  - Uesaka, K.
AU  - Hirose, Y.
AU  - Tsujimoto, R.
AU  - Yamamoto, H.
AU  - Okamoto, S.
AU  - Nakamura, Y.
AU  - Terauchi, K.
AU  - Omata, T.
AU  - Ihara, K.
AU  - Hattori, M.
AU  - Fujita, Y.
TI  - Loss of Cytochrome cM Stimulates Cyanobacterial Heterotrophic Growth in the Dark.
JO  - Plant Cell Physiol.
PY  - 2015
SP  - 334
EP  - 345
VL  - 56
AB  - Although cyanobacteria are photoautotrophs, they have the capability for
AB  - heterotrophic metabolism that enables them to survive in their natural habitat.
AB  - However, cyanobacterial species that grow heterotrophically in the dark are rare.
AB  - It remains largely unknown how cyanobacteria regulate heterotrophic activity. The
AB  - cyanobacterium Leptolyngbya boryana grows heterotrophically with glucose in the
AB  - dark. A dark-adapted variant dg5 isolated from the wild type (WT) exhibits
AB  - enhanced heterotrophic growth in the dark. We sequenced the genomes of dg5 and
AB  - the WT to identify the mutation(s) of dg5. The WT genome consists of a circular
AB  - chromosome (6,176,364 bp), a circular plasmid pLBA (77,793 bp) and two linear
AB  - plasmids pLBX (504,942 bp) and pLBY (44,369 bp). Genome comparison revealed three
AB  - mutation sites. Phenotype analysis of mutants isolated from the WT by introducing
AB  - these mutations individually revealed that the relevant mutation is a single
AB  - adenine insertion causing a frameshift of cytM encoding Cyt cM. The respiratory
AB  - oxygen consumption of the cytM-lacking mutant grown in the dark was significantly
AB  - higher than that of the WT. We isolated a cytM-lacking mutant, DeltacytM, from
AB  - another cyanobacterium Synechocystis sp. PCC 6803, and DeltacytM grew in the dark
AB  - with a doubling time of 33 h in contrast to no growth of the WT. The respiratory
AB  - oxygen consumption of DeltacytM grown in the dark was about 2-fold higher than
AB  - that of the WT. These results suggest a suppressive role(s) for Cyt cM in
AB  - regulation of heterotrophic activity.
ER  -

TY  - JOUR
AU  - Hiramatsu, K.
AU  - Aritaka, N.
AU  - Hanaki, H.
AU  - Kawasaki, S.
AU  - Hosoda, Y.
AU  - Hori, S.
AU  - Fukuchi, Y.
AU  - Kobayashi, I.
TI  - Dissemination in Japanese hospitals of strains of Staphylococcus aureus heterogeneously resistant to vancomycin.
JO  - Lancet
PY  - 1997
SP  - 1670
EP  - 1673
VL  - 350
AB  - BACKGROUND: Since the discovery of the vancomycin-resistant Staphylococcus aureus (VRSA)
AB  - strain Mu50 (minimum inhibitory concentration [MIC] 8 mg/L),
AB  - there has been concern about the potential spread of such strains
AB  - throughout Japanese hospitals. Two important questions need to be
AB  - answered: (1) what is the prevalence of VRSA, and (2) by what mechanism
AB  - does vancomycin resistance occur. METHODS: The vancomycin susceptibilities
AB  - of three methicillin-resistant S aureus (MRSA) strains (Mu50, Mu3, and H1)
AB  - and the methicillin-susceptible S aureus type strain FDA209P were compared
AB  - by MIC determinations and population analysis. Mu3 (MIC 3 mg/L) was
AB  - isolated from the sputum of a patient with pneumonia after surgery who had
AB  - failed vancomycin therapy. H1 (MIC 2 mg/L), which is a representative
AB  - vancomycin-susceptible MRSA strain, was isolated from a patient with
AB  - pneumonia who responded favourably to vancomycin therapy. Subclones of Mu3
AB  - with increased resistance against vancomycin were selected with serial
AB  - concentrations of vancomycin and their MICs were determined. The
AB  - prevalence of VRSA and Mu3-like strains in Japanese hospitals was
AB  - estimated by population analysis from 1149 clinical MRSA isolates obtained
AB  - from 203 hospitals throughout Japan. The genetic traits of the Mu3 and
AB  - Mu50 strains were compared with clonotypes of MRSA from around the world.
AB  - FINDINGS: Mu3 and Mu50 had an identical pulsed-field gel electrophoresis
AB  - banding pattern. When grown in a drug-free medium, Mu3 produced
AB  - subpopulation of cells with varying degrees of vancomycin resistance, thus
AB  - demonstrating natural heterogeneity, or variability, in susceptibility to
AB  - vancomycin. In the presence of vancomycin, Mu3 produced subclones with
AB  - resistance roughly proportional to the concentrations of vancomycin used.
AB  - Selection of Mu3 with 8 mg/L or more of vancomycin gave rise to subclones
AB  - with vancomycin resistance equal to that of Mu50 (MIC 8 mg/L) at a
AB  - frequency of 1/1,000,000. During screening of Japanese MRSA strains, no
AB  - strain of VRSA additional to Mu50 was found. The prevalence of MRSA
AB  - isolates heterogeneously resistant to vancomycin was 20% in Juntendo
AB  - University Hospital, 9.3% in the other seven university hospitals, and
AB  - 1.3% in non-university hospitals or clinics. INTERPRETATION:
AB  - Heterogeneously resistant VRSA is a preliminary stage that allows
AB  - development into VRSA upon exposure to vancomycin. Heterogeneously
AB  - resistant VRSA was found in hospitals throughout Japan. This finding could
AB  - explain, at least partly, the frequent therapeutic failure of MRSA
AB  - infection with vancomycin in Japan.
ER  -

TY  - JOUR
AU  - Hiraoka, N.
AU  - Kita, K.
AU  - Nakajima, H.
AU  - Kimizuka, F.
AU  - Obayashi, A.
TI  - Site-Specific Restriction Endonucleases of Several Non-Pathogenic Bacteria.
JO  - J. Ferment. Technol.
PY  - 1985
SP  - 151
EP  - 157
VL  - 63
AB  - Seventy-one non-pathogenic bacterial strains were surveyed for the presence of Type II
AB  - restriction endonucleases in aerobic culture. Five strains were found to contain specific
AB  - enzymes: CflI from Cellulomonas flavignea, GalI from Gluconobacter albidus, GceI from
AB  - Gluconobacter cerinus, HacI from Halococcus acetoinfaciens, and MflI from Microbacterium
AB  - flavum. These enzymes cleaved respectively the sequences of 5'-CTGCA^G-3', 5'-CCGC^GG-3',
AB  - 5'-CCGC^GG-3', 5'-^GATC-3', and 5'Pu^GATCPy'3' at the positions indicated. HacI and
AB  - MflI digested DNA from the Escherichia coli Dam-strain but not from the Dam+ strain,
AB  - indicating that they react only with unmodified sequences. With NaCl or KCl, the optimal salt
AB  - concentrations were 40-60 mM for CflI and 175-300mM for HacI; GalI and GceI did not require
AB  - either salts. Activity was greatest at pH 7.1-7.5 for CflI and HacI, and pH 7.5-8.0 for GalI
AB  - and GceI.
ER  -

TY  - JOUR
AU  - Hiraoka, N.
AU  - Kita, K.
AU  - Nakajima, H.
AU  - Obayashi, A.
TI  - Purification and characterization of sequence-specific restriction endonuclease MflI.
JO  - J. Ferment. Technol.
PY  - 1984
SP  - 583
EP  - 588
VL  - 62
AB  - Class II restriction endonuclease MflI was purified 790-fold from the crude extract of
AB  - Microbacterium flavum by chromatography on Phosphocellulose, DEAE-cellulose, and
AB  - Heparin-sepharose columns. The purified preparation was free from non-specific nucleases and
AB  - phosphatases. The enzyme required 7 to 20 mM Mg++ ions but not monovalent cations for its
AB  - activity, and the maximum activity was obtained at pH 8.0-8.5 in the Tris-HCl buffer system.
AB  - This enzyme recognized 5'-PuGATCPy-3' in DNA and cleaved between Pu and G in this sequence.
AB  - However, MflI digested DNA from Escherichia coli Dam- strain, but not DNA from its Dam+ (wild
AB  - type) strain, indicating that this enzyme only restricts the unmodified sequence.
ER  -

TY  - JOUR
AU  - Hirata, R.
AU  - Anraku, Y.
TI  - Mutations at the putative junction sites of the yeast Vma1 protein, the catalytic subunit of the vacuolar membrane H+-ATPase, inhibit its processing by protein splicing.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1992
SP  - 40
EP  - 47
VL  - 188
AB  - A single gene, VMA1, encodes the 69-kDa subunit of the vacuolar
AB  - membrane H+-ATPase in the yeast Saccharomyces cerevisiae.  We have proposed that the
AB  - subunit is synthesized as a precursor of 120 kDa (1,071 amino acids) and then converted to
AB  - the 69-kDa form by an unusual processing reaction, which removes the internal domain of
AB  - 454 amino acids (residues 284-737) and joins the N- and C-terminal domains.  Cysteine to
AB  - serine mutations at residues 284 and 738, the residues that bracket the internal domain,
AB  - were introduced into the VMA1 gene by site-directed mutagenesis, and the mutant genes
AB  - were expressed in a null vma1 mutant.  Cells harboring either of the mutant vma1 genes
AB  - accumulate nonfunctional fragments of the subunit.  The mutation of Cys-284 inhibited the
AB  - cleavage of the N-terminal junction site.  Cys-738 -> Ser mutation appeared to block the
AB  - processing at both junction sites although the mutant gene yielded a small fraction of the
AB  - functional 69-kDa subunit.
ER  -

TY  - JOUR
AU  - Hirata, R.
AU  - Ohsumi, Y.
AU  - Nakano, A.
AU  - Kawasaki, H.
AU  - Suzuki, K.
AU  - Anraku, Y.
TI  - Molecular structure of a gene, VMA1, encoding the catalytic subunit of H+-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 6726
EP  - 6733
VL  - 265
AB  - Subunit alpha of the vacuolar membrane H+-translocating adenosine triphosphatase of the yeast
AB  - Saccharomyces cerevisiae contains a catalytic site for ATP hydrolysis. N-terminal sequences of
AB  - six tryptic peptides of the subunit were determined. Based on the peptide sequence
AB  - information, a 39-base oligonucleotide probe was synthesized, and the gene encoding the
AB  - subunit (VMA1) was isolated from a genomic DNA library by hybridization. The nucleotide
AB  - sequence of the gene predicts a polypeptide of 1,071 amino acids with a calculated molecular
AB  - mass of 118,635 daltons, which is much larger than the value 67 kDa estimated on sodium
AB  - dodecyl sulfate-polyacrylamide gels. N- and C-terminal regions of the deduced sequence
AB  - (residues 1-284 and 739-1,071) are very similar to those of the catalytic subunits of carrot
AB  - (69 kDa) and Neurospora crassa (67 kDa) vacuolar membrane H+-ATPases (62 and 73% identity over
AB  - 600 residues, respectively). The homologous regions also show about 25% sequence identity over
AB  - 400 residues with beta-subunits of F0F1-ATPases. In contrast, the internal region containing
AB  - 454 amino acid residues (residues 285-738) shows no detectable sequence similarities to any
AB  - known ATPase subunits and instead is similar to a yeast endonuclease encoded by the HO gene.
AB  - None of the six tryptic peptides is located in this internal region. Northern blotting
AB  - analysis detected a single mRNA of 3.5 kilobases, indicating that the gene has no introns.
AB  - Although the reason for the discrepancy in molecular mass is unclear at present, these results
AB  - suggest that a novel processing mechanism, which might involve a post-translational excision
AB  - of the internal region followed by peptide ligation, operates on the yeast VMA1 product. The
AB  - VMA1 gene has proved to be the same gene as the TFP1 gene whose dominant mutant allele
AB  - (TFP1-408) confers a dominant trifluoperazine resistance and Ca2+-sensitive growth. This and
AB  - our findings suggest that the vacuolar membrane H+-ATPase participates in maintenance of
AB  - cytoplasmic Ca2+ homeostasis.
ER  -

TY  - JOUR
AU  - Hirayama, N.
TI  - Molecules controlling genetic information, Part 4, Restriction endonucleases.
JO  - Gendai Kagaku
PY  - 2001
SP  - 52
EP  - 54
VL  - 368
ER  -

TY  - JOUR
AU  - Hirk, S.
AU  - Lepuschitz, S.
AU  - Cabal, R.A.
AU  - Huhulescu, S.
AU  - Blaschitz, M.
AU  - Stoger, A.
AU  - Stadlbauer, S.
AU  - Hasenberger, P.
AU  - Indra, A.
AU  - Schmid, D.
AU  - Ruppitsch, W.
AU  - Allerberger, F.
TI  - Draft Genome Sequences of Interpatient and Intrapatient Epidemiologically Linked  Neisseria gonorrhoeae Isolates.
JO  - Genome Announcements
PY  - 2018
SP  - e00319
EP  - e00318
VL  - 6
AB  - Neisseria gonorrhoeae is the causative agent of gonorrhea and was identified by the World
AB  - Health Organization as an urgent public health threat due to emerging
AB  - antibiotic resistance. Here, we report 13 draft genome sequences of N.
AB  - gonorrhoeae isolates derived from two epidemiologically linked cases from
AB  - Austria.
ER  -

TY  - JOUR
AU  - Hirose, J.
AU  - Tsuda, N.
AU  - Miyatake, M.
AU  - Yokoi, H.
AU  - Shimodaira, J.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain LLC-1 (NBRC 111237), Capable of Metabolizing Lignin-Derived Low-Molecular-Weight Compounds.
JO  - Genome Announcements
PY  - 2018
SP  - e00308
EP  - e00318
VL  - 6
AB  - Pseudomonas sp. strain LLC-1 (NBRC 111237), isolated from soil, metabolizes lignin-derived
AB  - low-molecular-weight compounds and utilizes vanillin and vanillic
AB  - acid as its sole sources of carbon. Here, we report the draft genome sequence of
AB  - Pseudomonas sp. strain LLC-1.
ER  -

TY  - JOUR
AU  - Hirose, J.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Kimura, N.
AU  - Suenaga, H.
AU  - Watanabe, T.
AU  - Fujihara, H.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas stutzeri KF716 (NBRC 110668).
JO  - Genome Announcements
PY  - 2015
SP  - e01215
EP  - e01215
VL  - 3
AB  - Pseudomonas stutzeri KF716 (NBRC 110668) utilizes biphenyl as a sole source of carbon and
AB  - energy and degrades polychlorinated biphenyls. Here, we report the first draft genome sequence
AB  - of a biphenyl-degrading strain of the species P. stutzeri.
ER  -

TY  - JOUR
AU  - Hirose, J.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Kimura, N.
AU  - Suenaga, H.
AU  - Watanabe, T.
AU  - Fujihara, H.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Comamonas testosteroni KF712 (NBRC 110673).
JO  - Genome Announcements
PY  - 2015
SP  - e01214
EP  - e01215
VL  - 3
AB  - We present a 5.89-Mb draft genome sequence of Comamonas testosteroni KF712 (NBRC  110673), a
AB  - polychlorinated biphenyl degrader. The genome sequence clarified that  KF712 harbors the gene
AB  - clusters coding for the catabolism of biphenyl and at least seven other aromatic compounds.
ER  -

TY  - JOUR
AU  - Hirose, Y.
AU  - Fujisawa, T.
AU  - Ohtsubo, Y.
AU  - Katayama, M.
AU  - Misawa, N.
AU  - Wakazuki, S.
AU  - Shimura, Y.
AU  - Nakamura, Y.
AU  - Kawachi, M.
AU  - Yoshikawa, H.
AU  - Eki, T.
AU  - Kanesaki, Y.
TI  - Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755.
JO  - Genome Announcements
PY  - 2016
SP  - e00090
EP  - e00016
VL  - 4
AB  - Cyanobacterial genus Leptolyngbya comprises genetically diverse species, but the  availability
AB  - of their complete genome information is limited. Here, we isolated
AB  - Leptolyngbya sp. strain NIES-3755 from soil at the Toyohashi University of
AB  - Technology, Japan. We determined the complete genome sequence of the NIES-3755
AB  - strain, which is composed of one chromosome and three plasmids.
ER  -

TY  - JOUR
AU  - Hirose, Y.
AU  - Katayama, M.
AU  - Ohtsubo, Y.
AU  - Misawa, N.
AU  - Iioka, E.
AU  - Suda, W.
AU  - Oshima, K.
AU  - Hanaoka, M.
AU  - Tanaka, K.
AU  - Eki, T.
AU  - Ikeuchi, M.
AU  - Kikuchi, Y.
AU  - Ishida, M.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3709, Which Harbors a Phycoerythrin-Rich Phycobilisome.
JO  - Genome Announcements
PY  - 2015
SP  - e00385
EP  - e00315
VL  - 3
AB  - The cyanobacterium Geminocystis sp. strain NIES-3709 accumulates a larger amount  of
AB  - phycoerythrin than the related NIES-3708 strain does. Here, we determined the
AB  - complete genome sequence of the NIES-3709 strain. Our genome data suggest that
AB  - the different copy number of rod linker genes for phycoerythrin leads to the
AB  - different phycoerythrin contents between the two strains.
ER  -

TY  - JOUR
AU  - Hirose, Y.
AU  - Katayama, M.
AU  - Ohtsubo, Y.
AU  - Misawa, N.
AU  - Iioka, E.
AU  - Suda, W.
AU  - Oshima, K.
AU  - Hanaoka, M.
AU  - Tanaka, K.
AU  - Eki, T.
AU  - Ikeuchi, M.
AU  - Kikuchi, Y.
AU  - Ishida, M.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Cyanobacterium Geminocystis sp. Strain NIES-3708, Which Performs Type II Complementary Chromatic Acclimation.
JO  - Genome Announcements
PY  - 2015
SP  - e00357
EP  - e00315
VL  - 3
AB  - To explore the variation of the light-regulated genes during complementary chromatic
AB  - acclimation (CCA), we determined the complete genome sequence of the
AB  - cyanobacterium Geminocystis sp. strain NIES-3708. Within the light-regulated
AB  - operon for CCA, we found genes for phycoerythrin but not phycocyanin, suggesting
AB  - that this cyanobacterium modulates phycoerythrin composition only (type II CCA).
ER  -

TY  - JOUR
AU  - Hirsch, A.M. et al.
TI  - Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina  equisetifolia Root Nodules.
JO  - Genome Announcements
PY  - 2013
SP  - e00759
EP  - e00713
VL  - 1
AB  - Micromonospora species live in diverse environments and exhibit a broad range of  functions,
AB  - including antibiotic production, biocontrol, and degradation of
AB  - complex polysaccharides. To learn more about these versatile actinomycetes, we
AB  - sequenced the genome of strain L5, originally isolated from root nodules of an
AB  - actinorhizal plant growing in Mexico.
ER  -

TY  - JOUR
AU  - Hirsch, J.A.
AU  - Wah, D.A.
AU  - Dorner, L.F.
AU  - Shildkraut, I.
AU  - Aggarwal, A.K.
TI  - Crystallization and preliminary X-ray analysis of restriction endonuclease FokI bound to DNA.
JO  - FEBS Lett.
PY  - 1997
SP  - 136
EP  - 138
VL  - 403
AB  - FokI is a type IIs restriction endonuclease which recognizes an asymmetric DNA sequence and
AB  - cleaves DNA a short distance away from the sequence.  The enzyme is bipartite in nature with
AB  - its DNA recognition and cleavage functions located on distinct domains.  We report here
AB  - cocrystals of the complete FokI enzyme (579 amino acids) bound to a 20-bp DNA fragment
AB  - containing its recognition sequence.  The complex is amongst the largest protein-DNA complexes
AB  - to be crystallized, and required macroseeding techniques for optimal crystal growth.  The
AB  - cocrystals diffract to at least 2.8 Angstroms in resolution and belong to space group P21 with
AB  - unit cell dimensions of a=67.9, b=119.8, c=69.1 Angstroms, b=96.6 degrees.  Using specific
AB  - amino acid analysis we show that asymmetric unit contains a single FokI molecule bound to the
AB  - 20-bp DNA fragment.  This paper reports the first cocrystals of a type IIs restriction
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Hirsch-Kauffmann, M.
AU  - Sauerbier, W.
TI  - Inhibition of modification and restriction for phages lambda and Tl by co-infecting T3.
JO  - Mol. Gen. Genet.
PY  - 1968
SP  - 89
EP  - 94
VL  - 102
AB  - The host controlled modifications of phage lambda DNA by Escherichia coli B,K, and C(P1) can
AB  - be suppressed by preinfecting the bacteria with UV-irradiated phage T3.  Since UV-irradiated
AB  - T3 induces an enzyme which cleaves S-adenosylmethionine into homoserine and thiomethyl
AB  - adenosine, and since S-adenosylmethionine is the only methyl group donor for DNA methylation,
AB  - we conclude that methylation is a required step in the host controlled modification of
AB  - lambda-DNA.  T3 itself successfully infects E. coli K and B with its nonmethylated DNA.  Also,
AB  - restricted phage lambda or Tl will be accepted by the restrictive hosts E. coli B,K, and C(P1)
AB  - if these are preinfected with UV-T3.  It thus appears that T3 is capable of blocking the
AB  - restriction mechanisms in these hosts.  The inability of T3 to grow on C(P1) is not
AB  - understood.  Since T3-DNA is restricted but not degraded into nucleotides by E. coli C(P1) we
AB  - presume that degradation is not the initial step in restriction.
ER  -

TY  - JOUR
AU  - Hisata, K.
AU  - Ito, T.
AU  - Matsunaga, N.
AU  - Komatsu, M.
AU  - Jin, J.
AU  - Li, S.
AU  - Watanabe, S.
AU  - Shimizu, T.
AU  - Hiramatsu, K.
TI  - Dissemination of multiple MRSA clones among community-associated methicillin-resistant Staphylococcus aureus infections from Japanese children with impetigo.
JO  - J. Infect. Chemother.
PY  - 2011
SP  - 609
EP  - 621
VL  - 17
AB  - The proportion of MRSA strains that cause skin
AB  - and soft infections has recently increased. In 3 months we
AB  - have characterized 17 MRSA strains isolated from children
AB  - with impetigo at a Japanese hospital. Seventeen MRSA
AB  - strains belonged to 7 clones defined by clonal complex
AB  - (CC) in MLST genotype and type of SCCmec, which were
AB  - rarely identified among healthcare-associated MRSA: CC
AB  - 91-SCCmecIIb (4 strains); CC91-SCCmecIIn (2 strains);
AB  - CC91-SCCmecIVa (2 strains); CC91-SCCmecV (4 strains);
AB  - CC88-SCCmecIVg (3 strains); CC1-SCCmecIVc (1 strain);
AB  - and CC5-SCCmecIVn (1 strain). Although one strain
AB  - belonged to CC5, which has been commonly identified in
AB  - healthcare-associated MRSA, it did not carry type II
AB  - SCCmec, but carried type IV SCCmec. Fourteen of the 17
AB  - strains carried exfoliative toxin a or b gene, and none
AB  - carried Panton-Valentine leukocidine gene. Furthermore,
AB  - we determined the entire nucleotide sequences of two type
AB  - V SCCmec elements carried by strains JCSC5952, a CC91
AB  - strain, and TSGH17, a Taiwanese CC59 strain. The structure
AB  - of SCCmecJCSC5952 was more than 99% homologous
AB  - in nucleotide identity with those of Taiwanese
AB  - PVL-positive ST59 MRSA strains TSGH17 and PM1,
AB  - which were designated as type V
ER  -

TY  - JOUR
AU  - Hisatsune, J.
AU  - Hagiya, H.
AU  - Shiota, S.
AU  - Sugai, M.
TI  - Complete Genome Sequence of Systemically Disseminated Sequence Type 8 Staphylococcal Cassette Chromosome mec Type IVl Community-Acquired  Methicillin-Resistant Staphylococcus aureus.
JO  - Genome Announcements
PY  - 2017
SP  - e00852
EP  - e00817
VL  - 5
AB  - Staphylococcus aureus JH4899, a community-acquired methicillin-resistant Staphylococcus aureus
AB  - (CA-MRSA) isolate collected from a patient with
AB  - systematically disseminated infection, is classified as sequence type 8 and
AB  - carries the staphylococcal cassette chromosome mec type IVl (SCCmecIVl). It
AB  - produces TSST-1, SEC, a newly discovered enterotoxin (SE1), and epidermal cell
AB  - differentiation inhibitor A (EDIN-A). Here, we present the complete genome
AB  - sequence of the chromosome and a plasmid harboring the se1 and ednA genes.
ER  -

TY  - JOUR
AU  - Hishinuma, T.
AU  - Katayama, Y.
AU  - Matsuo, M.
AU  - Sasaki, T.
AU  - Hiramatsu, K.
TI  - Complete Genome Sequence of Vancomycin-Intermediate Staphylococcus aureus Strain  MI (HIP5827).
JO  - Genome Announcements
PY  - 2016
SP  - e00123
EP  - e00116
VL  - 4
AB  - We report the complete genome sequence of vancomycin-intermediate Staphylococcus  aureus
AB  - (VISA) strain MI (HIP5827).
ER  -

TY  - JOUR
AU  - Hjerde, E.
AU  - Pierechod, M.M.
AU  - Williamson, A.K.
AU  - Bjerga, G.E.
AU  - Willassen, N.P.
AU  - Smalas, A.O.
AU  - Altermark, B.
TI  - Draft Genome Sequence of the Actinomycete Rhodococcus sp. Strain AW25M09, Isolated from the Hadsel Fjord, Northern Norway.
JO  - Genome Announcements
PY  - 2013
SP  - e0005513
EP  - e0005513
VL  - 1
AB  - The cold-adapted Rhodococcus sp. strain AW25M09 was isolated from an Atlantic hagfish caught
AB  - off the shore of northern Norway as part of an ongoing
AB  - bioprospecting project that aims to identify novel bacteria with biotechnological
AB  - potential. Here, we present the 5.8-Mb draft genome sequence, together with
AB  - details regarding the origin of the strain and its sequence assembly.
ER  -

TY  - JOUR
AU  - Hjorleifsdottir, S.
AU  - Pelursdottir, S.
AU  - Kristjansson, J.K.
AU  - Korpela, J.
AU  - Torsti, A.-M.
AU  - Mattila, P.
TI  - Screening of Rhodothermus marinus for restriction endonucleases.
JO  - Thermophiles Sci. Technol.
PY  - 1992
SP  - 17
EP  - 17
VL  - 20
AB  - A screening of 43 Rhodothermus marinus strains for restriction endonucleases was done.  Two
AB  - types of DNA substrates were used in the screening assay.  They were T7 DNA and lambda DNA.  A
AB  - total of 27 strains (63%) showed cleavage of one or both substrates.  Restriction
AB  - endonuclease positive strains were compared with a dendrogram based on a number of
AB  - characteristics of the Rhodothermus marinus group genus.  The comparison revealed that
AB  - restriction endonucleases exist in certain groups of strains.  Characterization of the
AB  - restriction endonucleases indicate that all positive strains contain RmaI, an isoschizomer of
AB  - MaeI and 3 strains contain a second restriction endonuclease, an isoschizomer of EcoRV as
AB  - well.  RmaI, a type II restriction endonuclease, has been put on the market.
ER  -

TY  - JOUR
AU  - Hjorleifsdottir, S.
AU  - Petursdottir, S.K.
AU  - Korpela, J.
AU  - Torsti, A.-M.
AU  - Mattila, P.
AU  - Kristjansson, J.K.
TI  - Screening for restriction endonucleases in aerobic, thermophilic eubacteria.
JO  - Biotechnol. Tech.
PY  - 1996
SP  - 13
EP  - 18
VL  - 10
AB  - A total of 216 Icelandic aerobic, heterotrophic, thermophiles belonging to three different
AB  - genera were screened for type II restriction endonucleases.  The frequency of positive strains
AB  - was 44% for both Thermus and Bacillus but 63% for Rhodothermus.  Approximately half of the
AB  - enzymes from each group were characterised and a total of 14 different restriction enzymes
AB  - were found.  In all cases they were isoschizomers of known enzymes.  Thermus contained 9
AB  - different types, Bacillus 6 and Rhodothermus had 3.  This is the first time that isoschizomers
AB  - of BspEI, BglI, EagI and EcoRV are found in Thermus and BstBI and EcoRV are found in
AB  - Rhodothermus.
ER  -

TY  - JOUR
AU  - Hlavaty, J.J.
AU  - Benner, J.S.
AU  - Hornstra, L.J.
AU  - Schildkraut, I.
TI  - Identification of the metal-binding sites of restriction endonucleases by Fe(2+)-mediated oxidative cleavage.
JO  - Biochemistry
PY  - 2000
SP  - 3097
EP  - 3105
VL  - 39
AB  - Fenton chemistry [Fenton (1894) J. Chem. Soc. 65, 899-910] techniques were employed to
AB  - identify the residues involved in metal binding located at the active sites of restriction
AB  - endonucleases. This process uses transition metals to catalytically oxidize the peptide
AB  - linkage that is in close proximity to the amino acid residues involved in metal ligation.
AB  - Fe(2+) was used as the redox-active transition metal. It was expected that Fe(2+) would bind
AB  - to the endonucleases at the Mg(2+)-binding site [Liaw et al. (1993) Biochemistry 32,
AB  - 7999-4003; Ermacora et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 6383-6387; Soundar and
AB  - Colman (1993) J. Biol. Chem. 268, 5264-5271; Wei et al. (1994) Biochemistry 33, 7931-7936;
AB  - Ettner et al. (1995) Biochemistry 34, 22-31; Hlavaty and Nowak (1997) Biochemistry 36,
AB  - 15515-15525). Fe(2+)-mediated oxidation was successfully performed on TaqI endonuclease,
AB  - suggesting that this approach could be applied to a wide array of endonucleases [Cao and
AB  - Barany (1998) J. Biol. Chem. 273, 33002-33010]. The restriction endonucleases BamHI, FokI,
AB  - BglI, BglII, PvuII, SfiI, BssSI, BsoBI, EcoRI, EcoRV, MspI, and HinP1I were subjected to
AB  - oxidizing conditions in the presence of Fe(2+) and ascorbate. All proteins were inactivated
AB  - upon treatment with Fe(2+) and ascorbate. BamHI, FokI, BglI, BglII, PvuII, SfiI, BssSI, and
AB  - BsoBI were specifically cleaved upon treatment with Fe(2+)/ascorbate. The site of
AB  - Fe(2+)/ascorbate-induced protein cleavage for each enzyme was determined. The Fe(2+)-mediated
AB  - oxidative cleavage of BamHI occurs between residues Glu77 and Lys78. Glu77 has been shown by
AB  - structural and mutational studies to be involved in both metal ligation and catalysis [Newman
AB  - et al. (1995) Science 269, 656-663; Viadiu and Aggarwal (1998) Nat. Struct. Biol. 5, 910-916;
AB  - Xu and Schildkraut (1991) J. Biol. Chem. 266, 4425-4429]. The sites of
AB  - Fe(2+)/ascorbate-induced cleavage for PvuII, FokI, BglI, and BsoBI agree with the
AB  - metal-binding sites identified in their corresponding three-dimensional structures or from
AB  - mutational studies [Cheng et al. (1994) EMBO J. 13, 3297-3935; Wah et al. (1997) Nature 388,
AB  - 97-100; Newman et al. (1998) EMBO J. 17, 5466-5476; Ruan et al. (1997) Gene 188, 35-39]. The
AB  - metal-binding residues of BglII, SfiI, and BssSI are proposed based on amino acid sequencing
AB  - of their Fe(2+)/ascorbate-generated cleavage fragments. These results suggest that Fenton
AB  - chemistry may be a useful methodology in identifying amino acids involved in metal binding in
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Ho, A.Y.
AU  - Chow, K.H.
AU  - Law, P.Y.
AU  - Tse, H.
AU  - Ho, P.L.
TI  - Draft Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains of Sequence Type ST92 and ST96.
JO  - Genome Announcements
PY  - 2013
SP  - e00296
EP  - e00213
VL  - 1
AB  - The global epidemiology of multidrug-resistant Acinetobacter baumannii is dominated by a
AB  - limited number of clones. Here, we announce the draft genome
AB  - sequences of two multidrug-resistant A. baumannii strains, 1H8 and 4A3,
AB  - representing the major epidemic clones, sequence type 92 (ST92) and ST96,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Ho, D.K.
AU  - Wu, J.C.
AU  - Santi, D.V.
AU  - Floss, H.G.
TI  - Stereochemical studies of the C-methylation of deoxycytidine catalyzed by HhaI methylase and the N-methylation of deoxyadenosine catalyzed by EcoRI methylase.
JO  - Arch. Biochem. Biophys.
PY  - 1991
SP  - 264
EP  - 269
VL  - 284
AB  - The steric course of methyl group transfer catalyzed by two DNA methylases, HhaI methylase,
AB  - HhaI methylase, a DNA (cytosine-5) methyltransferase, and EcoRI methylase, which methylates at
AB  - N6 of adenosine, has been studied with (methyl-R)- and (methyl-S)-[methyl-2H1,3H]
AB  - adenosylmethionine as the methyl donor, using as substrates poly-d(GC) (HhaI) and the
AB  - dodecamer oligonucleotide duplex d(CGCGAATTCGCG) (EcoRI), respectively. The methylated
AB  - nucleotides were degraded to convert the chiral methyl groups into acetic acid for
AB  - configurational analysis. It was found that both enzymatic reactions proceed with inversion of
AB  - configuration of the methyl group.
ER  -

TY  - JOUR
AU  - Ho, M.T.
AU  - Weselowski, B.
AU  - Yuan, Z.C.
TI  - Complete Genome Sequence of Acinetobacter calcoaceticus CA16, a Bacterium Capable of Degrading Diesel and Lignin.
JO  - Genome Announcements
PY  - 2017
SP  - e00494
EP  - e00417
VL  - 5
AB  - We report here the complete assembled genome sequence of Acinetobacter calcoaceticus CA16,
AB  - which is capable of utilizing diesel and lignin as a sole
AB  - carbon source. CA16 contains a 4,110,074-bp chromosome and a 5,920-bp plasmid.
AB  - The assembled sequences will help elucidate potential metabolic pathways and
AB  - mechanisms responsible for CA16's hydrocarbon degradation ability.
ER  -

TY  - JOUR
AU  - Ho, N.
AU  - Lingohr, E.J.
AU  - Villegas, A.
AU  - Cole, L.
AU  - Kropinski, A.M.
TI  - Genomic characterization of two new Salmonella bacteriophages: vB_SosS_Oslo and vB_SemP_Emek.
JO  - Ann. Agrar. Sci.
PY  - 2012
SP  - 18
EP  - 23
VL  - 10
AB  - Salmonella are classified on the basis of their surface antigens of which the O-antigen, which
AB  - is the immunodominant portion of the lipopolysaccharide molecule, is highly variable among
AB  - different strains.  Enzymes modifying O-antigenes are often encoded by prophages which
AB  - represent the genomes of integrated temperate phages.  The expression of certain prophage
AB  - genes by the lysogen can often result in the change in serotype of the host.  It was
AB  - hypothesized that O-antigenes 14 and 20 of Salmonella strains might be encoded on prophages.
AB  - This report outlines the isolation and sequencing of two novel bacteriophages,one from each fo
AB  - Salmonella enterica serovars Oslo and Emek thought to have given rise to O-antigens 14 and 20,
AB  - respectively.  Further analysis through lysogen isolation and serotyping has proven otherwise.
ER  -

TY  - JOUR
AU  - Ho, P.L.
AU  - Liu, M.C.
AU  - Chow, K.H.
AU  - Tse, C.W.
AU  - Lo, W.U.
AU  - Mak, S.K.
AU  - Lo, W.K.
TI  - Emergence of ileS2-Carrying, Multidrug-Resistant Plasmids in Staphylococcus lugdunensis.
JO  - Antimicrob. Agents Chemother.
PY  - 2016
SP  - 6411
EP  - 6414
VL  - 60
AB  - Of 137 Staphylococcus lugdunensis isolates collected from two nephrology centers
AB  - in Hong Kong, 10 (7.3%) and 3 (2.2%) isolates had high-level and low-level
AB  - mupirocin resistance, respectively. Isolates with high-level resistance contained
AB  - the plasmid-mediated ileS2 gene, while isolates with low-level resistance
AB  - contained the mutation V588F within the chromosomal ileS gene. All but one of the
AB  - ileS2-positive isolates belong to the predominating clone HKU1. Plasmids carrying
AB  - the ileS2 gene were mosaic and also cocarry multiple other resistance
AB  - determinants.
ER  -

TY  - JOUR
AU  - Ho, P.L.
AU  - Lo, W.U.
AU  - Chan, J.
AU  - Cheung, Y.Y.
AU  - Chow, K.H.
AU  - Yam, W.C.
AU  - Lin, C.H.
AU  - Que, T.L.
TI  - pIMP-PH114 Carrying bla IMP-4 in a Klebsiella pneumoniae Strain is Closely Related to Other Multidrug-Resistant IncA/C2 Plasmids.
JO  - Curr. Microbiol.
PY  - 2014
SP  - 227
EP  - 232
VL  - 68
AB  - The IncA/C plasmids are broad host-range vehicles which have been associated with
AB  - wide dissemination of CMY-2 among Enterobacteriaceae of human and animal origins.
AB  - Acquired metallo-beta-lactamases (MBLs) such as the IMP-type enzymes are
AB  - increasingly reported in multidrug-resistant Gram-negative bacteria worldwide,
AB  - particularly in Enterobacteriaceae. We described the complete sequence of the
AB  - first IMP-4-encoding IncA/C2 plasmid, pIMP-PH114 (151,885 bp), from a sequence
AB  - type 1 Klebsiella pneumoniae strain that was recovered from a patient who was
AB  - hospitalized in the Philippines. pIMP-PH114 consists of a backbone from the
AB  - IncA/C2 plasmids, with the insertion of a novel Tn21-like class 1 integron
AB  - composite structure (containing the cassette array bla IMP-4-qacG-aacA4-catB3,
AB  - followed by a class C beta-lactamase bla DHA-1 and the mercury resistance operon,
AB  - merRTPCADE) and a sul2-floR encoding region. Phylogenetic analysis of the IncA/C
AB  - repA sequences showed that pIMP-PH114 formed a subgroup with other IncA/C
AB  - plasmids involved in the international spread of CMY-2, TEM-24 and NDM-1.
AB  - Identical bla IMP-4 arrays have been described among different Enterobacteriaceae
AB  - and Acinetobacter spp. in China, Singapore and Australia but the genetic context
AB  - is different. The broad host range of IncA/C plasmids may have facilitated
AB  - dissemination of the bla IMP-4 arrays among different diverse groups of bacteria.
ER  -

TY  - JOUR
AU  - Ho, P.L.
AU  - Poon, W.W.
AU  - Loke, S.L.
AU  - Leung, M.S.
AU  - Chow, K.H.
AU  - Wong, R.C.
AU  - Yip, K.S.
AU  - Lai, E.L.
AU  - Tsang, K.W.
TI  - Community emergence of CTX-M type extended-spectrum beta-lactamases among urinary Escherichia coli from women.
JO  - J. Antimicrob. Chemother.
PY  - 2007
SP  - 140
EP  - 144
VL  - 60
AB  - OBJECTIVES: To conduct a territory-wide study of extended-spectrum
AB  - beta-lactamases (ESBLs) among community isolates of urinary Escherichia
AB  - coli from women in Hong Kong. METHODS: Up to 50 consecutive single-patient
AB  - E. coli isolates, collected from 13 laboratories in 2004, were studied.
AB  - The ESBLs were characterized by PCR sequencing using specific primers. The
AB  - epidemiological relationship of the isolates was studied by PFGE and
AB  - phylogenetic group PCRs. RESULTS: Forty-two ESBL producers were found
AB  - among 600 consecutive isolates tested. The ESBL prevalence was 7.3%
AB  - (15/205) for women aged 18-35 years, 5% (11/219) for women aged 36-50
AB  - years, 6.3% (4/63) for women aged 51-64 years and 10.6% (12/113) for women
AB  - aged >or=65 years (P=0.3). The ESBL-producing isolates were often
AB  - multidrug-resistant and CTX-M-14 was found in 37 isolates, CTX-M-15 in 3
AB  - isolates and CTX-M-3 in 2 isolates. PFGE revealed no significant clusters
AB  - among the ESBL producers. Overall, CTX-M-14 producers were significantly
AB  - more likely to belong to group D than non-ESBL producers [18/37 (48.6%)
AB  - versus 13/57 (22.8%), P=0.009]. However, 7 of 13 (53.8%) CTX-M-14
AB  - producers from women aged 18-35 years represented phylogenetic group B2,
AB  - compared with 7 of 24 (29.2%) for women of all other ages (P=0.1).
AB  - CONCLUSIONS: The study documented the community emergence of CTX-M as the
AB  - predominant ESBL type among urinary isolates from women. The spread of
AB  - CTX-M enzymes among isolates from young women is concerning and deserves
AB  - close monitoring.
ER  -

TY  - JOUR
AU  - Ho, W.S.
AU  - Gan, H.M.
AU  - Yap, K.P.
AU  - Balan, G.
AU  - Yeo, C.C.
AU  - Thong, K.L.
TI  - Genome Sequence of Multidrug-Resistant Escherichia coli EC302/04, Isolated from a Human Tracheal Aspirate.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6691
EP  - 6692
VL  - 194
AB  - Escherichia coli is an important etiologic agent of lower respiratory tract infections (LRTI).
AB  - Multidrug-resistant E. coli EC302/04 was isolated from a
AB  - tracheal aspirate, and its genome sequence is expected to provide insights into
AB  - antimicrobial resistance as well as adaptive and virulence mechanisms of E. coli
AB  - involved in LRTI.
ER  -

TY  - JOUR
AU  - Ho, W.S.
AU  - Ou, H.Y.
AU  - Yeo, C.C.
AU  - Thong, K.L.
TI  - The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.
JO  - BMC Genomics
PY  - 2015
SP  - 199
EP  - 199
VL  - 16
AB  - Background: Strains of Escherichia coli that are non-typeable by pulsed-field gel
AB  - electrophoresis (PFGE) due to in-gel degradation can influence their molecular
AB  - epidemiological data. The DNA degradation phenotype (Dnd+) is mediated by the dnd
AB  - operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering
AB  - the modified DNA susceptible to oxidative cleavage during a PFGE run. In this
AB  - study, a PCR assay was developed to detect the presence of the dnd operon in
AB  - Dnd+E. coli strains and to improve their typeability. Investigations into the
AB  - genetic environments of the dnd operon in various E. coli strains led to the
AB  - discovery that the dnd operon is harboured in various diverse genomic islands.
AB  - Results: The dndBCDE genes (dnd operon) were detected in all Dnd+E. coli strains
AB  - by PCR. The addition of thiourea improved the typeability of Dnd+E. coli strains
AB  - to 100% using PFGE and the Dnd+ phenotype can be observed in both clonal and
AB  - genetically diverse E. coli strains.Genomic analysis of 101 dnd operons from
AB  - genome sequences of Enterobacteriaceae revealed that the dnd operons of the same
AB  - bacterial species were generally clustered together in the phylogenetic tree.
AB  - Further analysis of dnd operons of 52 E. coli genomes together with their
AB  - respective immediate genetic environments revealed a total of 7 types of genetic
AB  - organizations, all of which were found to be associated with genomic islands
AB  - designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and
AB  - the genomic context of the 7 islands (with 1 representative genome from each type
AB  - of genetic organization) were also highly variable, suggesting multiple
AB  - recombination events. This is also the first report where two dnd operons were
AB  - found within a strain although the biological implication is unknown.
AB  - Surprisingly, dnd operons were frequently found in pathogenic E. coli although
AB  - their link with virulence has not been explored. Conclusion: Genomic islands
AB  - likely play an important role in facilitating the horizontal gene transfer of the
AB  - dnd operons in E. coli with 7 different types of islands discovered so far.
AB  - Electronic supplementary material: The online version of this article
AB  - (doi:10.1186/s12864-015-1421-8) contains supplementary material, which is
AB  - available to authorized users.
ER  -

TY  - JOUR
AU  - Ho, W.S.
AU  - Yap, K.P.
AU  - Yeo, C.C.
AU  - Rajasekaram, G.
AU  - Thong, K.L.
TI  - The Complete Sequence and Comparative Analysis of a Multidrug-Resistance and Virulence Multireplicon IncFII Plasmid pEC302/04 from an Extraintestinal Pathogenic Escherichia coli EC302/04 Indicate Extensive Diversity of IncFII Plasmids.
JO  - Front. Microbiol.
PY  - 2016
SP  - 1547
EP  - 1547
VL  - 6
AB  - Extraintestinal pathogenic Escherichia coli (ExPEC) that causes extraintestinal
AB  - infections often harbor plasmids encoding fitness traits such as resistance and
AB  - virulence determinants that are of clinical importance. We determined the
AB  - complete nucleotide sequence of plasmid pEC302/04 from a multidrug-resistant E.
AB  - coli EC302/04 which was isolated from the tracheal aspirate of a patient in
AB  - Malaysia. In addition, we also performed comparative sequence analyses of 18
AB  - related IncFIIA plasmids to determine the phylogenetic relationship and diversity
AB  - of these plasmids. The 140,232 bp pEC302/04 is a multireplicon plasmid that bears
AB  - three replication systems (FII, FIA, and FIB) with subtype of F2:A1:B1. The
AB  - plasmid is self-transmissible with a complete transfer region. pEC302/04 also
AB  - carries antibiotic resistance genes such as bla TEM-1 and a class I integron
AB  - containing sul1, cml and aadA resistance genes, conferring multidrug resistance
AB  - (MDR) to its host, E. coli EC302/04. Besides, two iron acquisition systems
AB  - (SitABCD and IutA-IucABCD) which are the conserved virulence determinants of
AB  - ExPEC-colicin V or B and M (ColV/ColBM)-producing plasmids were identified in
AB  - pEC302/04. Multiple toxin-antitoxin (TA)-based addiction systems (i.e.,
AB  - PemI/PemK, VagC/VagD, CcdA/CcdB, and Hok/Sok) and a plasmid partitioning system,
AB  - ParAB, and PsiAB, which are important for plasmid maintenance were also found.
AB  - Comparative plasmid analysis revealed only one conserved gene, the repA1 as the
AB  - core genome, showing that there is an extensive diversity among the IncFIIA
AB  - plasmids. The phylogenetic relationship of 18 IncF plasmids based on the core
AB  - regions revealed that ColV/ColBM-plasmids and non-ColV/ColBM plasmids were
AB  - separated into two distinct groups. These plasmids, which carry highly diverse
AB  - genetic contents, are also mosaic in nature. The atypical combination of genetic
AB  - materials, i.e., the MDR- and ColV/ColBM-plasmid-virulence encoding regions in a
AB  - single ExPEC plasmid is rare but of clinical importance. Such phenomenon is
AB  - bothersome when the plasmids are transmissible, facilitating the spread of
AB  - virulence and resistance plasmids among pathogenic bacteria. Notably, certain TA
AB  - systems are more commonly found in particular ExPEC plasmid types, indicating the
AB  - possible relationships between certain TA systems and ExPEC pathogenesis.
ER  -

TY  - JOUR
AU  - Ho, Y.
AU  - Kim, S.-J.
AU  - Waring, R.B.
TI  - A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 8994
EP  - 8999
VL  - 94
AB  - Some group I introns self-splice in vitro, but almost all are thought to be assisted by
AB  - proteins in vivo.  Mutational analysis has shown that the splicing of certain group I introns
AB  - depends upon a maturase protein encoded by the intron itself.  However the effect of a protein
AB  - on splicing can be indirect.  We now provide evidence that a mitochondrial intron-encoded
AB  - protein from Aspergillus nidulans directly facilitates splicing in vitro.  This demonstrates
AB  - that a maturase is an RNA splicing protein.  The protein-assisted reaction is as fast as that
AB  - of any other known group I intron.  Interestingly the protein is also a DNA endonuclease, an
AB  - activity required for intron mobilization.  Mobile elements frequently encode proteins that
AB  - promote their propagation.  Intron-encoded proteins that also assist RNA splicing would
AB  - facilitate both the transposition and horizontal transmission of introns.
ER  -

TY  - JOUR
AU  - Ho, Y.
AU  - Waring, R.B.
TI  - The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 987
EP  - 1001
VL  - 292
AB  - The AnCOB group I intron from Aspergillus nidulans self-splices, providing the
AB  - Mg(2+)concentration is >/=15 mM. The splicing reaction is greatly stimulated by a maturase
AB  - protein encoded within the intron itself. An initial structural and biochemical analysis of
AB  - the splicing reaction has now been performed. The maturase bound rapidly to the precursor RNA
AB  - (kon approximately 3x10^9 M^-1 min^-1) and remained tightly bound (koff</=0.04 min^-1). The
AB  - catalytic step of 5' splice-site cleavage occurred at a rate of up to 11 min^-1 under single
AB  - turnover conditions. The maturase- assisted reaction of heat-denatured RNA proceeded at a rate
AB  - of about 1 min^-1, arguing that there are early steps of folding that cannot be readily
AB  - facilitated by the protein. pH analysis revealed a biphasic profile with a pKa of 7.0. The
AB  - rate of the maturase-assisted reaction was independent of the Mg(2+)concentration down to 3
AB  - mM. Self-splicing in optimal Mg(2+)(>/=150 mM) was tenfold slower, in part because of the
AB  - existence of an equilibrium between folded and partially folded RNA. In contrast, the maturase
AB  - very effectively stabilized tertiary structure in 5 mM Mg(2+), a noticeable example being an
AB  - interaction between the P8 helix and a GNRA sequence that constitutes the L2 terminal loop of
AB  - the P2 helix. Formation of the 5' splice-site recognition helix was assisted by either the
AB  - maturase or high concentrations of Mg(2+). The maturase was required during splicing so it is
AB  - not a true chaperone. However, RNase protection assays and kinetic studies suggest that the
AB  - maturase recognizes and facilitates folding of an intron with limited tertiary structure and
AB  - even incomplete secondary structure.
ER  -

TY  - JOUR
AU  - Ho, Y.N.
AU  - Huang, C.C.
TI  - Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01327
EP  - e01315
VL  - 3
AB  - An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has
AB  - shown its abilities for both in planta biocontrol and plant growth
AB  - promotion. Its draft genome sequence was determined to provide insights into
AB  - those metabolic pathways involved in plant-beneficial activity. This is the first
AB  - genome report for endophytic B. cenocepacia.
ER  -

TY  - JOUR
AU  - Ho, Y.S.
AU  - Adroub, S.A.
AU  - Abadi, M.
AU  - Al, A.B.
AU  - Alkhateeb, R.
AU  - Gao, G.
AU  - Ragab, A.
AU  - Ali, S.
AU  - van Soolingen, D.
AU  - Bitter, W.
AU  - Pain, A.
AU  - Abdallah, A.M.
TI  - Complete Genome Sequence of Mycobacterium vaccae Type Strain ATCC 25954.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6339
EP  - 6340
VL  - 194
AB  - Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is
AB  - generally not considered a human pathogen and is of major pharmaceutical
AB  - interest as an immunotherapeutic agent. We report here the annotated genome
AB  - sequence of the M. vaccae type strain, ATCC 25954.
ER  -

TY  - JOUR
AU  - Ho, Y.S.
AU  - Adroub, S.A.
AU  - Aleisa, F.
AU  - Mahmood, H.
AU  - Othoum, G.
AU  - Rashid, F.
AU  - Zaher, M.
AU  - Ali, S.
AU  - Bitter, W.
AU  - Pain, A.
AU  - Abdallah, A.M.
TI  - Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain  DSM46621.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6337
EP  - 6338
VL  - 194
AB  - Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM).
AB  - It is ubiquitous in water and soil habitats, including
AB  - hospital environments. M. fortuitum is increasingly recognized as an
AB  - opportunistic nosocomial pathogen causing disseminated infection. Here we report
AB  - the genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.
ER  -

TY  - JOUR
AU  - Hoang, V.A.
AU  - Kim, Y.J.
AU  - Nguyen, N.L.
AU  - Yang, D.C.
TI  - Brachybacterium ginsengisoli sp. nov., isolated from soil of a ginseng field.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 3063
EP  - 3068
VL  - 64
AB  - A novel Gram-staining-positive, aerobic bacterium, designed DCY80(T), was
AB  - isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene
AB  - sequence analysis revealed that strain DCY80(T) belonged to the genus
AB  - Brachybacterium (95.8-98.2 % similarity) and was most closely related to
AB  - Brachybacterium faecium DSM 4810(T) (98.2 %). Colonies were circular, entire,
AB  - low-convex, opaque and 0.5-1.0 mm in diameter after growth for 2 days on TSA at
AB  - 30 degrees C. Growth occurred at 4-34 degrees C (optimum, 25 degrees C), at pH
AB  - 5.0-10.0 (optimum, pH 6.5-7.0) and in the presence of 0-7.0 % NaCl. Strain
AB  - DCY80(T) produced siderophores and was sensitive to penicillin G, erythromycin,
AB  - cefazolin, oleandomycin, ceftazidime, vancomycin, tetracycline, novobiocin,
AB  - carbamicillin, rifampicin and neomycin. The DNA G+C content was 71.0 mol%. Levels
AB  - of DNA-DNA relatedness between strain DCY80(T) and B. faecium DSM 4810(T), B.
AB  - paraconglomeratum KCTC 9916(T), B. saurashtrense DSM 23186(T) and B.
AB  - conglomeratum KCTC 9915(T) were 46.9+/-0.5, 28.9+/-0.6, 20.4+/-0.9 and 17.3+/-0.4
AB  - %, respectively. The cell-wall peptidoglycan of strain DCY80(T) contained
AB  - meso-diaminopimelic acid as the diagnostic diamino acid. The menaquinones were
AB  - MK-7 (85.8 %) and MK-8 (14.2 %). The major cellular fatty acids were anteiso-C15
AB  - : 0 (69.1 %) and anteiso-C17 : 0 (12.2 %). Phosphatidylglycerol,
AB  - diphosphatidylglycerol, an unidentified glycolipid, two unidentified
AB  - phospholipids and five unidentified polar lipids were found. On the basis of our
AB  - phenotypic and genotypic analyses, strain DCY80(T) represents a novel species of
AB  - the genus Brachybacterium, for which the name Brachybacterium ginsengisoli sp.
AB  - nov. is proposed (type strain DCY80(T) = KCTC 29226(T) = JCM 19356(T)).
ER  -

TY  - JOUR
AU  - Hobley, G.
AU  - McKelvie, J.C.
AU  - Harmer, J.E.
AU  - Howe, J.
AU  - Oyston, P.C.F.
AU  - Roach, P.L.
TI  - Development of rationally designed DNA N6 adenine methyltransferase inhibitors.
JO  - Bioorg. Med. Chem. Lett.
PY  - 2012
SP  - 3079
EP  - 3082
VL  - 22
AB  - A series of bisubstrate inhibitors for DNA N6 adenine methyltransferase (Dam) have been
AB  - synthesized by linking an amine analogue of
AB  - S-adenosylmethionine to an aryl moiety designed to probe the binding
AB  - pocket of the DNA adenine base. An initial structure-activity
AB  - relationship study has identified substituents that increase inhibitor
AB  - potency to the similar to 10 mu M range and improve selectivity against
AB  - the human cytosine methyltransferase Dnmt1.
ER  -

TY  - JOUR
AU  - Hobom, G.
AU  - Schwarz, E.
AU  - Melzer, M.
AU  - Mayer, H.
TI  - Restriction endonuclease EcaI from Enterobacter cloacae.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 4823
EP  - 4832
VL  - 9
AB  - Restriction endonuclease EcaI obtained from Enterobacter cloacae DSM30056
AB  - recognizes the group of heptanucleotide palindromes 5'-G-^G-T-N-A-C-C-3', and
AB  - on cleavage (arrow) produces fragments with 5' - terminal pentanucleotide
AB  - extensions.  It is identical in specificity with restriction endonuclease
AB  - BstEII from Bacillus stearothermophiulus ET.
ER  -

TY  - JOUR
AU  - Hobson, N.
AU  - Price, N.L.
AU  - Ward, J.D.
AU  - Raivio, T.L.
TI  - Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.
JO  - BMC Microbiol.
PY  - 2008
SP  - 13
EP  - 13
VL  - 8
AB  - Background: Many microbes possess restriction-modification systems that protect them from
AB  - parasitic DNA molecules. Unfortunately, the presence of a restriction-modification system in a
AB  - given microbe also hampers genetic analysis. Although plasmids can be successfully conjugated
AB  - into the enteropathogenic Escherichia coli strain E2348/69 and optimized protocols for
AB  - competent cell preparation have been developed, we found that a large, low copy (similar to
AB  - 15) bioluminescent reporter plasmid, pJW15, that we modified for use in EPEC, was exceedingly
AB  - difficult to transform into E2348/69. We reasoned that a restriction-modification system could
AB  - be responsible for the low transformation efficiency of E2348/69 and sought to identify and
AB  - inactivate the responsible gene(s), with the goal of creating an easily transformable strain
AB  - of EPEC that could complement existing protocols for genetic manipulation of this important
AB  - pathogen.Results: Using bioinformatics, we identified genes in the unfinished enteropathogenic
AB  - Escherichia coli (EPEC) strain E2348/69 genome whose predicted products bear homology to the
AB  - HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type
AB  - I restriction-modification systems. We constructed a strain carrying a deletion of the
AB  - conserved enzymatic domain of the EPEC HsdR homologue, NH4, and showed that its transformation
AB  - efficiency was up to four orders of magnitude higher than that of the parent strain. Further,
AB  - the modification capacity of NH4 remained intact, since plasmids that were normally
AB  - recalcitrant to transformation into E2348/69 could be transformed upon passage through NH4.
AB  - NH4 was unaffected in virulence factor production, since bundle forming pilus (BFP) subunits
AB  - and type III secreted (T3S) proteins were present at equivalent levels to those seen in
AB  - E2348/69. Further, NH4 was indistinguishable from E2348/69 in tissue culture infection model
AB  - assays of localized adherence and T3S.Conclusion: We have shown that EPEC strain E2348/69
AB  - utilizes a type 1 restriction- modification system to limit entry of new DNA. This
AB  - restriction- modification system does not appear to be involved in virulence determinant
AB  - expression or infection phenotypes. The hsdR mutant strain should prove useful in genetic
AB  - analysis of the important diarrheal pathogen EPEC.
ER  -

TY  - JOUR
AU  - Hobson, S.D.
AU  - Falick, A.M.
AU  - Reich, N.O.
TI  - Identification of a critical histidine in EcoRI DNA methyltransferase using protein modification and tandem mass spectrometry.
JO  - FASEB J.
PY  - 1993
SP  - A1275
EP  - A1275
VL  - 7
AB  - Diethyl pyrocarbonate (DEPC) is a known histidine specific reagent. Reaction of DEPC with
AB  - EcoRI DNA methyltransferase causes a time-dependent loss of activity due to modification of a
AB  - critical histidine(s) in the enzyme. The second order rate constant of the inactivation of the
AB  - enzyme is 570 M-1s-1. A kinetic analysis of the inactivation by DEPC has been used to
AB  - determine that only one of the seven histidines in the enzyme is critical. The number of
AB  - critical histidines has also been determined spectrophotometrically. This analysis revealed
AB  - that approximately 1.75 histidines are modified by DEPC-mediated inactivation suggests that
AB  - the residue has a pKa of about 6.0. The modified histidines are being identified via tandem
AB  - mass spectrometry methods in a novel LC-m.s. setup.
ER  -

TY  - JOUR
AU  - Hochhut, B.
AU  - Wilde, C.
AU  - Balling, G.
AU  - Middendorf, B.
AU  - Dobrindt, U.
AU  - Brzuszkiewicz, E.
AU  - Gottschalk, G.
AU  - Carniel, E.
AU  - Hacker, J.
TI  - Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536.
JO  - Mol. Microbiol.
PY  - 2006
SP  - 584
EP  - 595
VL  - 61
AB  - The genome of uropathogenic Escherichia coli isolate 536 contains five well-characterized
AB  - pathogenicity islands (PAIs) encoding key virulence
AB  - factors of this strain. Except PAI IV(536), the four other PAIs of strain
AB  - 536 are flanked by direct repeats (DRs), carry intact integrase genes and
AB  - are able to excise site-specifically from the chromosome. Genome screening
AB  - of strain 536 identified a sixth putative asnW-associated PAI. Despite the
AB  - presence of DRs and an intact integrase gene, excision of this island was
AB  - not detected. To investigate the role of PAI-encoded integrases for the
AB  - recombination process the int genes of each unstable island of strain 536
AB  - were inactivated. For PAI I(536) and PAI II(536), their respective P4-like
AB  - integrase was required for their excision. PAI III(536) carries two
AB  - integrase genes, intA, encoding an SfX-like integrase, and intB, coding
AB  - for an integrase with weak similarity to P4-like integrases. Only intB was
AB  - required for site-specific excision of this island. For PAI V(536),
AB  - excision could not be abolished after deleting its P4-like integrase gene
AB  - but additional deletion of the PAI II(536)-specific integrase gene was
AB  - required. Therefore, although all mediated by P4-like integrases, the
AB  - activity of the PAI excision machinery is most often restricted to its
AB  - cognate island. This work also demonstrates for the first time the
AB  - existence of a cross-talk between integrases of different PAIs and shows
AB  - that this cross-talk is unidirectional.
ER  -

TY  - JOUR
AU  - Hochwind, K.
AU  - Weinmaier, T.
AU  - Schmid, M.
AU  - van Hemert, S.
AU  - Hartmann, A.
AU  - Rattei, T.
AU  - Rothballer, M.
TI  - Draft Genome Sequence of Lactobacillus casei W56.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6638
EP  - 6638
VL  - 194
AB  - We announce the draft genome sequence of Lactobacillus casei W56 in one contig. This strain
AB  - shows immunomodulatory and probiotic properties. The strain is also
AB  - an ingredient of commercially available probiotic products.
ER  -

TY  - JOUR
AU  - Hodges, R.A.
AU  - Perler, F.B.
AU  - Noren, C.J.
AU  - Jack, W.E.
TI  - Protein splicing removes intervening sequences in an archaea DNA polymerase.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6153
EP  - 6157
VL  - 20
AB  - The Vent DNA polymerase gene from Thermococcus litoralis contains two in-frame insertions that
AB  - must be spliced out to form the mature polymerase. Primer extension and cDNA PCR revealed no
AB  - evidence of spliced RNA to account for this editing. In contrast, pulse-chase analysis
AB  - indicated that expression constructs lacking the first insertion produced a protein precursor
AB  - in Escherichia coli that was processed post-translationally to form polymerase and I-TliI, the
AB  - endonuclease protein that is the product of the second insertion. At least one intermediate,
AB  - which migrated more slowly than the precursor and may be branched, was also detected. Amino
AB  - acid substitutions at the splice junction slowed or blocked the protein splicing reaction.
AB  - Processing occurs in several heterologous systems, indicating either self-splicing or
AB  - ubiquitous splicing factors. Processing occurs in a mutant lacking I-TliI endonuclease
AB  - activity, establishing the independence of splicing and endonuclease activities.
ER  -

TY  - JOUR
AU  - Hodges-Garcia, Y.
AU  - Hagerman, P.J.
TI  - Cytosine methylation can induce local distortion in the structure of duplex DNA.
JO  - Biochemistry
PY  - 1992
SP  - 7595
EP  - 7599
VL  - 31
AB  - Methyl groups at the C5 position of pyrimidines located within oligopurine-oligopyrimidine
AB  - tracts in DNA have been shown previously to modulate curvature generated by those tracts.
AB  - However, it was not known whether the influence of such methyl groups is consequent to the
AB  - altered helical structure within the tracts themselves. In the current study, it is
AB  - demonstrated that methylation of cytosines up to three base pairs away from a (dA)5(dT)5 tract
AB  - (A-tract) can still result in alterations of the net curvature of the A-tract-containing DNA,
AB  - as measured by alterations in electrophoretic mobility. This latter effect depends strongly on
AB  - both the sequence of the non-A-tract DNA and the positions of the methylated C residues. The
AB  - current results lend further support to the notion that the biological consequences of
AB  - cytosine methylation may be effected through local alteration in DNA structure as well as
AB  - through direct protein-DNA interactions.
ER  -

TY  - JOUR
AU  - Hodgson, C.P.
TI  - A rapid visual method for the identification of 4- or 6-base restriction endonuclease sites.
JO  - Biotechniques
PY  - 1989
SP  - 148
EP  - 149
VL  - 7
AB  - In this report, we describe a rapid approach to identification of restriction
AB  - endonuclease sites which makes computer searching unnecessary.  Increased speed
AB  - is possible because searching with specific sequences is eliminated,
AB  - substituting a one-time visual identification of palindromes.  These can be
AB  - marked and identified with the aid of a chart at a later time.  In this manner,
AB  - it is possible to identify 10-20 sites per minute with practice.  The technique
AB  - will be especially useful for short pieces of DNA (2 kb or less), for newly
AB  - published sequences, and for cloning experiments involving complex DNA
AB  - constructions which are not readily available on a database.
ER  -

TY  - JOUR
AU  - Hoefler, B.C.
AU  - Konganti, K.
AU  - Straight, P.D.
TI  - De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing.
JO  - Genome Announcements
PY  - 2013
SP  - e00535
EP  - e00513
VL  - 1
AB  - We report a draft genome assembly of Streptomyces sp. strain Mg1, a competitive soil isolate
AB  - with multiple secondary metabolite gene clusters.
ER  -

TY  - JOUR
AU  - Hoekstra, M.F.
AU  - Malone, R.E.
TI  - Expression of the Escherichia coli dam methylase in Saccharomyces cerevisiae:  Effect of in vivo adenine methylation on genetic recombination and mutation.
JO  - Mol. Cell. Biol.
PY  - 1985
SP  - 610
EP  - 618
VL  - 5
AB  - The Escherichia coli DNA adenine methylase (dam) gene has been introduced into Saccharomyces
AB  - cerevisiae on a yeast-E. coli shuttle vector. Sau3AI, MboI, and DpnI restriction enzyme
AB  - digests and Southern hybridization analysis indicated that the dam gene is expressed in yeast
AB  - cells and methylates GATC sequences. Analysis of digests of total genomic DNA indicated that
AB  - some GATC sites are not sensitive to methylation. The failure to methylate may reflect an
AB  - inaccessibility to the methylase due to chromosome structure. The effects of this in vivo
AB  - methylation on the processes of recombination and mutation in mitotic cells were determined. A
AB  - small but definite general increase was found in the frequency of mitotic recombination. A
AB  - similar increase was observed for reversion of some auxotrophic markers; other markers
AB  - demonstrated a small decrease in mutation frequency. The effects on mutation appear to be
AB  - locus (or allele) specific. Recombination in meiotic cells was measured and was not detectably
AB  - altered by the presence of 6-methyladenine in GATC sequences.
ER  -

TY  - JOUR
AU  - Hoekstra, W.P.M.
AU  - DeHaan, P.G.
TI  - The location of the restriction locus for lambda.K in Escherichia coli.
JO  - Mutat. Res.
PY  - 1965
SP  - 204
EP  - 212
VL  - 2
AB  - Analysis of recombinants from E. coli K12 Hfr x E. coli B F- crosses showed
AB  - that one locus on the chromososme of Escherichia coli, controlling restriction
AB  - and probably also the modification of phage lambda, is located between the
AB  - leading point of the Hfr H chromosome and the locus for threonine synthesis.
AB  - The restriction locus also controls the restriction of the fertility factor of
AB  - K12 and the restriction of chromosomal DNA of K12 in E. coli B.  The presence
AB  - of the defective prophage X in E. coli B causes an additional restriction for
AB  - phage lambda and for the fertility factor.
ER  -

TY  - JOUR
AU  - Hoelzer, K.
AU  - Shackelton, L.A.
AU  - Parrish, C.R.
TI  - Presence and role of cytosine methylation in DNA viruses of animals.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 2825
EP  - 2837
VL  - 36
AB  - Nucleotide composition varies greatly among DNA viruses of animals, yet the evolutionary
AB  - pressures and biological mechanisms driving these patterns are unclear. One of the most
AB  - striking discrepancies lies in the frequency of CpG (the dinucleotide CG, linked by a
AB  - phosphate group), which is underrepresented in most small DNA viruses (those with genomes
AB  - below 10 kb) but not in larger DNA viruses. Cytosine methylation might be partially
AB  - responsible, but research on this topic has focused on a few virus groups. For several viruses
AB  - that integrate their genome into the host genome, the methylation status during this stage has
AB  - been studied extensively, and the relationship between methylation and viral-induced tumor
AB  - formation has been examined carefully. However, for actively replicating viruses-particularly
AB  - small DNA viruses-the methylation status of CpG motifs is rarely known and the effects on the
AB  - viral life cycle are obscure. In vertebrate host genomes, most cytosines at CpG sites are
AB  - methylated, which in vertebrates acts to regulate gene expression and facilitates the
AB  - recognition of unmethylated, potentially pathogen-associated DNA. Here we briefly introduce
AB  - cytosine methylation before reviewing what is currently known about CpG methylation in DNA
AB  - viruses.
ER  -

TY  - JOUR
AU  - Hoet, P.P.
AU  - Coene, M.M.
AU  - Cocito, C.G.
TI  - Replication cycle of Bacillus subtilis hydroxymethyluracil-containing phages.
JO  - Annu. Rev. Microbiol.
PY  - 1992
SP  - 95
EP  - 116
VL  - 46
AB  - The present review focuses on phage 2C, a member of a family of virulent phages that multiply
AB  - in Bacillus subtilis. The best known members of this group are SP01, Phie, H1, 2C, SP8, and
AB  - Sp82, the genomes of which are made of double-stranded DNA of about 150 kilobase pairs (kbp).
AB  - The two DNA strands have different buoyant densities. Moreover, thymine (T) is completely
AB  - replaced by hydroxymethyluracil (hmUra). Comparison of the phage DNAs has shown that both base
AB  - substitutions and deletions have contributed to the evolution of their genomes. In addition,
AB  - all of the hmUra-phage genomes contain colinear redundant ends, amounting to 10% of total
AB  - bases. Two lines of evidence suggest that the redundant ends of 2C DNA, in spite of extensive
AB  - homology, contain unique sequences. Further studies focused on DNA replication during the
AB  - lytic cycle. The semiconservative replication of the infecting viral genome is followed by
AB  - extensive recombination. At the level of replication forks, viral DNA synthesis in
AB  - permeabilized infected bacteria, was incorporated in small amounts into phage DNA. The
AB  - putative primary origin of replication has been cloned and localized on the viral genome. Some
AB  - viral promoters have been successfully cloned in Escherichia coli. These sequences, however,
AB  - did not promote transcription in B. subtilis. The abnormal base might be required for promoter
AB  - activity in the natural host.
ER  -

TY  - JOUR
AU  - Hoetzinger, M.
AU  - Schmidt, J.
AU  - Jezberova, J.
AU  - Koll, U.
AU  - Hahn, M.W.
TI  - Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.
JO  - Appl. Environ. Microbiol.
PY  - 2017
SP  - e02266
EP  - e02216
VL  - 83
AB  - Microdiversification of a planktonic freshwater bacterium was studied by comparing 37
AB  - Polynucleobacter asymbioticus strains obtained from three
AB  - geographically separated sites in the Austrian Alps. Genome comparison of nine
AB  - strains revealed a core genome of 1.8 Mb, representing 81% of the average genome
AB  - size. Seventy-five percent of the remaining flexible genome is clustered in
AB  - genomic islands (GIs). Twenty-four genomic positions could be identified where
AB  - GIs are potentially located. These positions are occupied strain specifically
AB  - from a set of 28 GI variants, classified according to similarities in their gene
AB  - content. One variant, present in 62% of the isolates, encodes a pathway for the
AB  - degradation of aromatic compounds, and another, found in 78% of the strains,
AB  - contains an operon for nitrate assimilation. Both variants were shown in
AB  - ecophysiological tests to be functional, thus providing the potential for
AB  - microniche partitioning. In addition, detected interspecific horizontal exchange
AB  - of GIs indicates a large gene pool accessible to Polynucleobacter species. In
AB  - contrast to core genes, GIs are spread more successfully across spatially
AB  - separated freshwater habitats. The mobility and functional diversity of GIs allow
AB  - for rapid evolution, which may be a key aspect for the ubiquitous occurrence of
AB  - Polynucleobacter bacteria. IMPORTANCE: Assessing the ecological relevance of
AB  - bacterial diversity is a key challenge for current microbial ecology. The
AB  - polyphasic approach which was applied in this study, including targeted isolation
AB  - of strains, genome analysis, and ecophysiological tests, is crucial for the
AB  - linkage of genetic and ecological knowledge. Particularly great importance is
AB  - attached to the high number of closely related strains which were investigated,
AB  - represented by genome-wide average nucleotide identities (ANI) larger than 97%.
AB  - The extent of functional diversification found on this narrow phylogenetic scale
AB  - is compelling. Moreover, the transfer of metabolically relevant genomic islands
AB  - between more distant members of the Polynucleobacter community provides important
AB  - insights toward a better understanding of the evolution of these globally
AB  - abundant freshwater bacteria.
ER  -

TY  - JOUR
AU  - Hofer, B.
TI  - The sensitivity of DNA cleavage by SpeI and ApaLI to methylation by M.EcoK.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 5206
EP  - 5206
VL  - 16
AB  - During work on site-directed mutagenesis of the human interleukin-2 gene an
AB  - EcoK site was created which overlapped recognition sequences for SpeI and ApaLI
AB  - (Fig. 1a).  Isolation of the DNA from m+K strain DH1 and m-K strain HB101 and
AB  - subsequent incubation with the two restriction endonucleases revealed that EcoK
AB  - methylation completely or almost completely protected both DNA strands from
AB  - cleavage by SpeI, but did not prevent cleavage of either strand by ApaLI (Fig.
AB  - 1b).  Thus, methylation of only one of the 5'-terminal A's of the SpeI site is
AB  - sufficient to protect it against SpeI, whereas methylation of one of the two
AB  - A's of the ApaLI sequence does not interfere with its cleavage by ApaLI.
ER  -

TY  - JOUR
AU  - Hofer, B.
AU  - Koster, H.
TI  - On the influence of thymidine analogues on the activity of phage fd promoters in vitro.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 6143
EP  - 6162
VL  - 8
AB  - RF I DNA of phage fd containing 5-bromo-deoxyuridine (br5Ud) or deoxyuridine
AB  - (Ud) instead of deoxythymidine (Td) in the codogenic strand was synthesized in
AB  - vitro.  The modified genomes could be cleaved by restriction endonuclease
AB  - HpaII.  Although the recognition site of HpaII is CCGG, the cleavage rate was
AB  - significantly reduced with Ud-containing DNA.  Both base substitutions altered
AB  - the mobilities of several DNA fragments under the conditions of polyacrylamide
AB  - gel electrophoresis.  The fragments containing binding sites for RNA polymerase
AB  - were assayed for the rates of stable complex formation.  The substitution of Td
AB  - for both, Ud and br5Ud, strongly influenced this parameter.  Thus the methyl
AB  - group of Td has to be regarded as one of the sites in DNA which determine the
AB  - rate of stable RNA polymerase binding and thereby possibly mediate promoter
AB  - activity in vitro.  In most cases the rate of complex formation was decreased
AB  - by Ud, but increased by br5Ud.
ER  -

TY  - JOUR
AU  - Hofer, B.
AU  - Kuhlein, B.
TI  - The sensitivity of DNA cleavage by SnoI to methylation by M.EcoK.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8009
EP  - 8009
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Hofer, B.
AU  - Ruhe, G.
AU  - Koch, A.
AU  - Koster, H.
TI  - Primary and secondary structure specificity of the cleavage of single-stranded DNA by endonuclease HinfI.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 2763
EP  - 2773
VL  - 10
AB  - The interaction of endonuclease HinfI with single-stranded fd DNA was examined.
AB  - The sizes of the cleavage products indicate that the enzyme cuts this
AB  - substrate at the same sequences as double-stranded DNA (GANTC).  To determine
AB  - whether or not the recognition sites in a single-stranded DNA have to be
AB  - present in double-stranded form in order to be cleaved, DNA fragments
AB  - containing complementary or non-complementary HinfI sequences were prepared and
AB  - tested as substrates.  The results suggest that completely base-paired
AB  - recognition sites are necessary for cleavage.  Sequences surrounding the HinfI
AB  - pentanucleotides significantly modulate the reaction rates.
ER  -

TY  - JOUR
AU  - Hoffmann, L.
AU  - Ramos, R.J.T.
AU  - Guedes, I.A.
AU  - Costa, P.F.
AU  - Miguel, C.R.D.
AU  - Azevedo, S.M.F.O.E.
AU  - Silva, R.
TI  - Draft Genome Sequences of Two Brazilian Cyanobacterial Strains of Cylindrospermopsis raciborskii: Differences in Membrane Transporters, Saxitoxin  Production, and Antioxidant Activities.
JO  - Genome Announcements
PY  - 2017
SP  - e00879
EP  - e00817
VL  - 5
AB  - We report here the draft genome sequences of two Brazilian strains of Cylindrospermopsis
AB  - raciborskii, a saxitoxin-producer (CYRF) and a non-saxitoxin
AB  - producer (CYLP), with each strain comprising one assembled scaffold. We revealed
AB  - differences in the compositions of gene members coding for membrane transporters
AB  - and antioxidant activities between the strains.
ER  -

TY  - JOUR
AU  - Hoffmann, M.
AU  - Luo, Y.
AU  - Lafon, P.C.
AU  - Timme, R.
AU  - Allard, M.W.
AU  - McDermott, P.F.
AU  - Brown, E.W.
AU  - Zhao, S.
TI  - Genome Sequences of Salmonella enterica Serovar Heidelberg Isolates Isolated in the United States from a Multistate Outbreak of Human Salmonella Infections.
JO  - Genome Announcements
PY  - 2013
SP  - e00004
EP  - e00012
VL  - 1
AB  - Salmonella enterica is recognized as one of the most common bacterial agents of foodborne
AB  - illness. We report draft genomes of four Salmonella serovar Heidelberg isolates associated
AB  - with the recent multistate outbreak of human Salmonella Heidelberg infections linked to kosher
AB  - broiled chicken livers in the United States in 2011. Isolates 2011K-1259 and 2011K-1232 were
AB  - recovered from humans, whereas 2011K-1724 and 2011K-1726 were isolated from chicken liver.
AB  - Whole genome sequence analysis of these isolates provides a tool for studying the short-term
AB  - evolution of these epidemic clones and can be used for characterizing potentially new
AB  - virulence factors.
ER  -

TY  - JOUR
AU  - Hoffmann, M.
AU  - Muruvanda, T.
AU  - Allard, M.W.
AU  - Korlach, J.
AU  - Roberts, R.J.
AU  - Timme, R.
AU  - Payne, J.
AU  - McDermott, P.F.
AU  - Evans, P.
AU  - Meng, J.
AU  - Brown, E.W.
AU  - Zhao, S.
TI  - Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.
JO  - Genome Announcements
PY  - 2014
SP  - e00294
EP  - e00214
VL  - 2
AB  - Volume 1, no. 6, e01068-13, 2013.  Page 2: The following should be added to the
AB  - Acknowledgments.  "Research reported in this publication was supported by the Small Business
AB  - Innovation Research Program (NIGMS) of the National Institutes of Health under award number
AB  - R44GM105125 to R.J.R.  The content is solely the responsibility of the authors and does not
AB  - necessarily represent the official views of the National Institutes of Health."
ER  -

TY  - JOUR
AU  - Hoffmann, M.
AU  - Muruvanda, T.
AU  - Allard, M.W.
AU  - Korlach, J.
AU  - Roberts, R.J.
AU  - Timme, R.
AU  - Payne, J.
AU  - McDermott, P.F.
AU  - Evans, P.
AU  - Meng, J.
AU  - Brown, E.W.
AU  - Zhao, S.
TI  - Complete Genome Sequence of a Multidrug-Resistant Salmonella enterica Serovar Typhimurium var. 5- Strain Isolated from Chicken Breast.
JO  - Genome Announcements
PY  - 2013
SP  - e01068
EP  - e01013
VL  - 1
AB  - Salmonella enterica subsp. enterica serovar Typhimurium is a leading cause of salmonellosis.
AB  - Here, we report a closed genome sequence, including sequences of 3
AB  - plasmids, of Salmonella serovar Typhimurium var. 5- CFSAN001921 (National
AB  - Antimicrobial Resistance Monitoring System [NARMS] strain ID N30688), which was
AB  - isolated from chicken breast meat and shows resistance to 10 different
AB  - antimicrobials. Whole-genome and plasmid sequence analyses of this isolate will
AB  - help enhance our understanding of this pathogenic multidrug-resistant serovar.
ER  -

TY  - JOUR
AU  - Hoffmann, M.
AU  - Muruvanda, T.
AU  - Pirone, C.
AU  - Korlach, J.
AU  - Timme, R.
AU  - Payne, J.
AU  - Evans, P.
AU  - Meng, J.
AU  - Brown, E.W.
AU  - Allard, M.W.
TI  - First Fully Closed Genome Sequence of Salmonella enterica subsp. enterica Serovar Cubana Associated with a Food-Borne Outbreak.
JO  - Genome Announcements
PY  - 2014
SP  - e01112
EP  - e01114
VL  - 2
AB  - Salmonella enterica subsp. enterica serovar Cubana (Salmonella serovar Cubana) is associated
AB  - with human and animal disease. Here, we used third-generation,
AB  - single-molecule, real-time DNA sequencing to determine the first complete genome
AB  - sequence of Salmonella serovar Cubana CFSAN002050, which was isolated from fresh
AB  - alfalfa sprouts during a multistate outbreak in 2012.
ER  -

TY  - JOUR
AU  - Hoffmann, M.
AU  - Payne, J.
AU  - Roberts, R.J.
AU  - Allard, M.W.
AU  - Brown, E.W.
AU  - Pettengill, J.B.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Agona 460004 2-1, Associated with a Multistate Outbreak in the United States.
JO  - Genome Announcements
PY  - 2015
SP  - e00690
EP  - e00615
VL  - 3
AB  - Within the last several years, Salmonella enterica subsp. enterica serovar Agona  has been
AB  - among the 20 most frequently isolated serovars in clinical cases of
AB  - salmonellosis. In this report, the complete genome sequence of S. Agona strain
AB  - 460004 2-1 isolated from unsweetened puffed-rice cereal during a multistate
AB  - outbreak in 2008 was sequenced using single-molecule real-time DNA sequencing.
ER  -

TY  - JOUR
AU  - Hoffmann, M.
AU  - Zhao, S.
AU  - Luo, Y.
AU  - Li, C.
AU  - Folster, J.P.
AU  - Whichard, J.
AU  - Allard, M.W.
AU  - Brown, E.W.
AU  - McDermott, P.F.
TI  - Genome Sequences of Five Salmonella enterica Serovar Heidelberg Isolates Associated with a 2011 Multistate Outbreak in the United States.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3274
EP  - 3275
VL  - 194
AB  - Salmonella enterica serovar Heidelberg has caused numerous outbreaks in humans. Here, we
AB  - report draft genomes of five isolates of serovar Heidelberg associated
AB  - with the recent (2011) multistate outbreak linked to ground turkey in the United
AB  - States. Isolates 2011K-1110 and 2011K-1132 were recovered from humans, while
AB  - isolates 2011K-1138, 2011K-1224, and 2011K-1225 were recovered from ground
AB  - turkey. Whole-genome sequence analysis of these isolates provides a tool for
AB  - studying the short-term evolution of these epidemic clones.
ER  -

TY  - JOUR
AU  - Hofreuter, D.
AU  - Tsai, J.
AU  - Watson, R.O.
AU  - Novik, V.
AU  - Altman, B.
AU  - Benitez, M.
AU  - Clark, C.
AU  - Perbost, C.
AU  - Jarvie, T.
AU  - Du, L.
AU  - Galan, J.E.
TI  - Unique features of a highly pathogenic Campylobacter jejuni strain.
JO  - Infect. Immun.
PY  - 2006
SP  - 4694
EP  - 4707
VL  - 74
AB  - Campylobacter jejuni, a major human enteric pathogen, exhibits significant strain-to-strain
AB  - differences which result in differences in pathogenic potential.  C. jejuni 81-176 is a highly
AB  - virulent strain that exhibits unique pathogenic features and is used by many research
AB  - laboratories.  We have determined the nucleotide sequence of its genome and compared it to the
AB  - genomes of other sequenced C. jejuni strains.  We identified a number of unique genetic
AB  - features which may confer specific metabolic and pathogenic properties on this strain.  We
AB  - have also identified regions of the C. jejuni genome that are hot spots for the integration of
AB  - horizontally acquired genetic material.  This information should help the understanding of the
AB  - pathogenesis of C. jejuni and, in particular, the unique features of this highly pathogenic
AB  - strain.
ER  -

TY  - JOUR
AU  - Hogg, G.
AU  - Dimovski, K.
AU  - Hiley, L.
AU  - Holt, K.E.
TI  - Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants.
JO  - Genome Announcements
PY  - 2013
SP  - e00293
EP  - e00213
VL  - 1
AB  - Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common cause of gastroenteritis
AB  - in humans. Here, we report the draft genome sequences of 10
AB  - isolates of an S. Typhimurium phage type 135 variant that is linked to
AB  - egg-associated outbreaks in Tasmania, Australia.
ER  -

TY  - JOUR
AU  - Hogg, J.S.
AU  - Hu, F.Z.
AU  - Janto, B.
AU  - Boissy, R.
AU  - Hayes, J.
AU  - Keefe, R.
AU  - Post, J.C.
AU  - Ehrlich, G.D.
TI  - Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.
JO  - Genome Biology
PY  - 2007
SP  - R103
EP  - R103
VL  - 8
AB  - BACKGROUND: The distributed genome hypothesis (DGH) posits that chronic
AB  - bacterial pathogens utilize polyclonal infection and reassortment of genic
AB  - characters to ensure persistence in the face of adaptive host defenses.
AB  - Studies based on random sequencing of multiple strain libraries suggested
AB  - that free-living bacterial species possess a supragenome that is much
AB  - larger than the genome of any single bacterium. RESULTS: We derived high
AB  - depth genomic coverage of nine nontypeable Haemophilus influenzae (NTHi)
AB  - clinical isolates, bringing to 13 the number of sequenced NTHi genomes.
AB  - Clustering identified 2,786 genes, of which 1,461 were common to all
AB  - strains, with each of the remaining 1,328 found in a subset of strains;
AB  - the number of clusters ranged from 1,686 to 1,878 per strain. Genic
AB  - differences of between 96 and 585 were identified per strain pair.
AB  - Comparisons of each of the NTHi strains with the Rd strain revealed
AB  - between 107 and 158 insertions and 100 and 213 deletions per genome. The
AB  - mean insertion and deletion sizes were 1,356 and 1,020 base-pairs,
AB  - respectively, with mean maximum insertions and deletions of 26,977 and
AB  - 37,299 base-pairs. This relatively large number of small rearrangements
AB  - among strains is in keeping with what is known about the transformation
AB  - mechanisms in this naturally competent pathogen. CONCLUSION: A finite
AB  - supragenome model was developed to explain the distribution of genes among
AB  - strains. The model predicts that the NTHi supragenome contains between
AB  - 4,425 and 6,052 genes with most uncertainty regarding the number of rare
AB  - genes, those that have a frequency of <0.1 among strains; collectively,
AB  - these results support the DGH.
ER  -

TY  - JOUR
AU  - Hoheisel, J.D.
AU  - Nizetic, D.
AU  - Lehrach, H.
TI  - Control of partial digestion combining the enzymes dam methylase and MboI.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9571
EP  - 9582
VL  - 17
AB  - A method is described which allows the preparation of reproducible partial digests without
AB  - previous establishment of the incubation conditions. It is based on a combined application of
AB  - dam methylase and the restriction endonuclease MboI, both recognizing the sequence
AB  - 5'-GATC-3' but MboI unable to cut the methylated site. Due to their competition for the same
AB  - substrate the DNA is partially digested with the size of the resulting fragments strongly
AB  - dependent on the ratio of enzymes. The Km of the dam methylase was determined to be 115 ng
AB  - DNA/microliter indicating a variance in fragment sizes generated at low DNA-concentrations.
AB  - This effect is minimized above 150 ng/microliter. Any influence of digestion time is avoided,
AB  - because the reaction runs until complete modification of all sites. The dependence on enzyme
AB  - concentration and presence of agarose was checked. Knowledge of these parameters allows an
AB  - accurate prediction of fragment sizes generated at different conditions. The technique was
AB  - successfully used to construct libraries from different sources, in particular
AB  - chromosome-specific libraries from small amounts of flow-sorted material.
ER  -

TY  - JOUR
AU  - Holden, M.T. et al.
TI  - The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.
JO  - J. Bacteriol.
PY  - 2009
SP  - 261
EP  - 277
VL  - 191
AB  - Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications
AB  - in the treatment of this common genetic disease. Burkholderia
AB  - cenocepacia infection is particularly problematic since this organism has high
AB  - levels of antibiotic resistance, making it difficult to eradicate; the resulting
AB  - chronic infections are associated with severe declines in lung function and
AB  - increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF
AB  - patient and is a member of the epidemic ET12 lineage that originated in Canada or
AB  - the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly
AB  - transmissible pathogen comprises three circular chromosomes and a plasmid and
AB  - encodes a broad array of functions typical of this metabolically versatile genus,
AB  - as well as numerous virulence and drug resistance functions. Although B.
AB  - cenocepacia strains can be isolated from soil and can be pathogenic to both
AB  - plants and man, J2315 is representative of a lineage of B. cenocepacia rarely
AB  - isolated from the environment and which spreads between CF patients. Comparative
AB  - analysis revealed that ca. 21% of the genome is unique in comparison to other
AB  - strains of B. cenocepacia, highlighting the genomic plasticity of this species.
AB  - Pseudogenes in virulence determinants suggest that the pathogenic response of
AB  - J2315 may have been recently selected to promote persistence in the CF lung. The
AB  - J2315 genome contains evidence that its unique and highly adapted genetic content
AB  - has played a significant role in its success as an epidemic CF pathogen.
ER  -

TY  - JOUR
AU  - Holden, M.T. et al.
TI  - Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1473
EP  - 1477
VL  - 189
AB  - Comparisons of the 1.84-Mb genome of serotype M5 Streptococcus pyogenes strain Manfredo with
AB  - previously sequenced genomes emphasized the role of
AB  - prophages in diversification of S. pyogenes and the close relationship
AB  - between strain Manfredo and MGAS8232, another acute rheumatic
AB  - fever-associated strain.
ER  -

TY  - JOUR
AU  - Holden, M.T.
AU  - Lindsay, J.A.
AU  - Corton, C.
AU  - Quail, M.A.
AU  - Cockfield, J.D.
AU  - Pathak, S.
AU  - Batra, R.
AU  - Parkhill, J.
AU  - Bentley, S.D.
AU  - Edgeworth, J.D.
TI  - Genome Sequence of a Recently Emerged, Highly Transmissible, Multi-Antibiotic- and Antiseptic-Resistant Variant of  Methicillin-Resistant Staphylococcus aureus, Sequence Type 239 (TW).
JO  - J. Bacteriol.
PY  - 2010
SP  - 888
EP  - 892
VL  - 192
AB  - The 3.1-Mb genome of an outbreak methicillin-resistant Staphylococcus aureus (MRSA) strain
AB  - (TW20) contains evidence of recently acquired DNA,
AB  - including two large regions (635 kb and 127 kb). The strain is resistant
AB  - to a wide range of antibiotics, antiseptics, and heavy metals due to
AB  - resistance genes encoded on mobile genetic elements and also mutations in
AB  - housekeeping genes.
ER  -

TY  - JOUR
AU  - Holden, M.T.G. et al.
TI  - Genomic plasticity of the causative agent of melioidosis, Berkholderia pseudomallei.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 14240
EP  - 14245
VL  - 101
AB  - Burkholderia pseudomallei is a recognized biothreat agent and the causative agent of
AB  - melioidosis. This Gram-negative bacterium exists as a soil saprophyte in melioidosis-endemic
AB  - areas of the world and accounts for 20% of community-acquired septicaemias in northeastern
AB  - Thailand where half of those affected die. Here we report the complete genome of B.
AB  - pseudomallei, which is composed of two chromosomes of 4.07 megabase pairs and 3.17 megabase
AB  - pairs, showing significant functional partitioning of genes between them. The large chromosome
AB  - encodes many of the core functions associated with central metabolism and cell growth, whereas
AB  - the small chromosome carries more accessory functions associated with adaptation and survival
AB  - in different niches. Genomic comparisons with closely and more distantly related bacteria
AB  - revealed a greater level of gene order conservation and a greater number of orthologous genes
AB  - on the large chromosome, suggesting that the two replicons have distinct evolutionary origins.
AB  - A striking feature of the genome was the presence of 16 genomic islands (GIs) that together
AB  - made up 6.1% of the genome. Further analysis revealed these islands to be variably present in
AB  - a collection of invasive and soil isolates but entirely absent from the clonally related
AB  - organism B. mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is
AB  - an important feature of recent genetic evolution and that this has resulted in a genetically
AB  - diverse pathogenic species.
ER  -

TY  - JOUR
AU  - Holden, M.T.G. et al.
TI  - Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 9786
EP  - 9791
VL  - 101
AB  - Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic
AB  - plasticity has facilitated the evolution of many virulent and drug-resistant strains,
AB  - presenting a major and constantly changing clinical challenge. We sequenced the ~2.8-Mbp
AB  - genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a
AB  - recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus
AB  - EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a
AB  - representative of an invasive community-acquired methicillin-susceptible S. aureus clone
AB  - (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of
AB  - clinically important S. aureus genomes and to identify regions affecting virulence and drug
AB  - resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but
AB  - differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse
AB  - S. aureus strain sequenced to date: ~6% of the genome is novel compared with other published
AB  - genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible,
AB  - but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated
AB  - SCC476), which is integrated at the same site on the chromosome as SCCmec elements in MRSA
AB  - strains but encodes a putative fusidic acid resistance protein. The crucial role that
AB  - accessory elements play in the rapid evolution of S. aureus is clearly illustrated by
AB  - comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired
AB  - strain; the differential distribution of large mobile elements carrying virulence and
AB  - drug-resistance determinants may be responsible for the clinically important phenotypic
AB  - differences in these strains.
ER  -

TY  - JOUR
AU  - Holden, M.T.G. et al.
TI  - Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis.
JO  - PLoS ONE
PY  - 2009
SP  - e6072
EP  - e6072
VL  - 4
AB  - Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally
AB  - cause serious infections in
AB  - humans. S. suis infections occur sporadically in human Europe and North America, but a recent
AB  - major outbreak has been
AB  - described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in
AB  - humans and pigs are poorly
AB  - understood.
AB  - Methodology/Principal Findings: The sequencing of whole genomes of S. suis isolates provides
AB  - opportunities to
AB  - investigate the genetic basis of infection. Here we describe whole genome sequences of three
AB  - S. suis strains from the same
AB  - lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative
AB  - genomic analysis was
AB  - used to investigate the variability of these strains. S. suis is phylogenetically distinct
AB  - from other Streptococcus species for
AB  - which genome sequences are currently available. Accordingly, ,40% of the ,2 Mb genome is
AB  - unique in comparison to
AB  - other Streptococcus species. Finer genomic comparisons within the species showed a high level
AB  - of sequence conservation;
AB  - virtually all of the genome is common to the S. suis strains. The only exceptions are three
AB  - ,90 kb regions, present in the two
AB  - isolates from humans, composed of integrative conjugative elements and transposons. Carried in
AB  - these regions are coding
AB  - sequences associated with drug resistance. In addition, small-scale sequence variation has
AB  - generated pseudogenes in
AB  - putative virulence and colonization factors.
AB  - Conclusions/Significance: The genomic inventories of genetically related S. suis strains,
AB  - isolated from distinct hosts and
AB  - diseases, exhibit high levels of conservation. However, the genomes provide evidence that
AB  - horizontal gene transfer has
AB  - contributed to the evolution of drug resistance.
ER  -

TY  - JOUR
AU  - Holert, J.
AU  - Alam, I.
AU  - Larsen, M.
AU  - Antunes, A.
AU  - Bajic, V.B.
AU  - Stingl, U.
AU  - Philipp, B.
TI  - Genome Sequence of Pseudomonas sp. Strain Chol1, a Model Organism for the Degradation of Bile Salts and Other Steroid Compounds.
JO  - Genome Announcements
PY  - 2013
SP  - e00014
EP  - e00012
VL  - 1
AB  - Bacterial degradation of steroid compounds is of high ecological and biotechnological
AB  - relevance. Pseudomonas sp. strain Chol1 is a model organism for studying the degradation of
AB  - the steroid compound cholate. Its draft genome sequence is presented and reveals one gene
AB  - cluster responsible for the metabolism of steroid compounds.
ER  -

TY  - JOUR
AU  - Holland-Moritz, H.E.
AU  - Bevans, D.R.
AU  - Lang, J.M.
AU  - Darling, A.E.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2013
SP  - e00325
EP  - e00313
VL  - 1
AB  - Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains
AB  - 3,317,267 bp in 11 scaffolds. This strain was isolated from a
AB  - residential toilet as part of an undergraduate project to sequence reference
AB  - genomes of microbes from the built environment.
ER  -

TY  - JOUR
AU  - Holland-Moritz, H.E.
AU  - Coil, D.A.
AU  - Badger, J.H.
AU  - Dmitrov, G.I.
AU  - Khouri, H.
AU  - Ward, N.L.
AU  - Robb, F.T.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1.
JO  - Genome Announcements
PY  - 2014
SP  - e00833
EP  - e00814
VL  - 2
AB  - Here we present the draft genome of Synergistes jonesii 78-1, ATCC 49833, a member of the
AB  - Synergistes phylum. This organism was isolated from the rumen of a
AB  - Hawaiian goat and ferments pyridinediols. The assembly contains 2,747,397 bp in
AB  - 61 contigs.
ER  -

TY  - JOUR
AU  - Hollander, A.
AU  - Kalily, E.
AU  - Shachar, D.
AU  - Yaron, S.
AU  - Danin-Poleg, Y.
TI  - Draft Genome Sequence of Salmonella enterica Serovar Senftenberg 070885 and Its Linalool-Adapted Mutant.
JO  - Genome Announcements
PY  - 2017
SP  - e01036
EP  - e01017
VL  - 5
AB  - Here we report the genome sequences of both Salmonella Senftenberg 070885, a clinical isolate
AB  - from the 2007 outbreak linked to basil, and its mutant
AB  - linalool-adapted S Senftenberg (LASS). These draft genomes of S Senftenberg may
AB  - enable the identification of bacterial genes responsible for resistance to basil
AB  - oil.
ER  -

TY  - JOUR
AU  - Hollensteiner, J.
AU  - Poehlein, A.
AU  - Daniel, R.
AU  - Liesegang, H.
AU  - Vidal, S.
AU  - Wemheuer, F.
TI  - Draft Genome Sequence of Bacillus pumilus Strain GM3FR, an Endophyte Isolated from Aerial Plant Tissues of Festuca rubra L.
JO  - Genome Announcements
PY  - 2017
SP  - e00085
EP  - e00017
VL  - 5
AB  - Here, we report the draft genome sequence of Bacillus pumilus GM3FR, an endophytic bacterium
AB  - isolated from aerial plant tissues of Festuca rubra L. The
AB  - draft genome consists of 3.5 Mb and harbors 3,551 predicted protein-encoding
AB  - genes. The genome provides insights into the biocontrol potential of B. pumilus
AB  - GM3FR.
ER  -

TY  - JOUR
AU  - Hollensteiner, J.
AU  - Poehlein, A.
AU  - Granzow, S.
AU  - Liesegang, H.
AU  - Daniel, R.
AU  - Vidal, S.
AU  - Wemheuer, F.
TI  - Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM5LP Isolated from Lolium perenne.
JO  - Genome Announcements
PY  - 2018
SP  - e01517
EP  - e01517
VL  - 6
AB  - Bacillus mycoides GM5LP is a Gram-positive endophytic bacterium isolated from aerial plant
AB  - tissues of Lolium perenne L. The 6.0-Mb draft genome harbors 6,132
AB  - protein-coding sequences, some of which might be involved in the biosynthesis of
AB  - antimicrobial substances.
ER  -

TY  - JOUR
AU  - Hollensteiner, J.
AU  - Poehlein, A.
AU  - Sproer, C.
AU  - Bunk, B.
AU  - Sheppard, A.E.
AU  - Rosenstiel, P.
AU  - Schulenburg, H.
AU  - Liesegang, H.
TI  - Complete genome sequence of the nematicidal Bacillus thuringiensis MYBT18247.
JO  - J. Biotechnol.
PY  - 2017
SP  - 48
EP  - 52
VL  - 260
AB  - The Gram-positive spore forming bacterium Bacillus thuringiensis MYBT18247 encodes three cry
AB  - toxin genes, (cry6Ba2, cry6Ba3 and cry21-like) which are active
AB  - against nematodes. For a better understanding of the evolution of virulence and
AB  - cry toxins, we present here the complete genome sequence of Bacillus
AB  - thuringiensis MYBT18247. Various additional virulence factors such as
AB  - bacteriocins, proteases and hemolysins were identified. In addition, the
AB  - methylome and the metabolic potential of the strain were analyzed and the strain
AB  - phylogenetically classified.
ER  -

TY  - JOUR
AU  - Hollensteiner, J.
AU  - Poehlein, A.
AU  - Sproer, C.
AU  - Bunk, B.
AU  - Sheppard, A.E.
AU  - Rosentstiel, P.
AU  - Schulenburg, H.
AU  - Liesegang, H.
TI  - Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 48
EP  - 48
VL  - 12
AB  - 10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of  the genus
AB  - 10.1601/nm.4857. The defining feature of the species is the ability to
AB  - produce parasporal crystal inclusion bodies, consisting of delta-endotoxins,
AB  - encoded by cry-genes. Here we present the complete annotated genome sequence of
AB  - the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one
AB  - 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to
AB  - 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes,
AB  - including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis
AB  - of the genome revealed a large number of mobile elements involved in genome
AB  - plasticity including 11 plasmids and 16 chromosomal prophages. Three different
AB  - nematicidal toxin genes were identified and classified according to the Cry toxin
AB  - naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are
AB  - located on the chromosome in close proximity to three separate prophages.
AB  - Moreover, four putative toxin genes of different toxin classes were identified on
AB  - the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two
AB  - Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with
AB  - three closely related 10.1601/nm.5000 strains enabled determination of the
AB  - pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons,
AB  - mostly represented by phage genes, morons and cryptic genes.
ER  -

TY  - JOUR
AU  - Holloway, S.P.
AU  - Deshpande, N.N.
AU  - Herrin, D.L.
TI  - The catalytic group-I introns of the psbA gene of Chlamydomonas reinhardtii: core structures, ORFs and evolutionary implications.
JO  - Curr. Genet.
PY  - 1999
SP  - 69
EP  - 78
VL  - 36
AB  - The sequences and predicted secondary structures of the four catalytic group-I introns in the
AB  - psbA gene of Chlamydomonas reinhardtii, Cr.psbA-1-Cr.psbA-4, have been determined. Cr.psbA-1
AB  - and Cr.psbA-4 are subgroup-IA1 introns and have similar secondary structures, except at the
AB  - 3' end where Cr.psbA-1 contains a large inverted-repeat domain. Cr.psbA-4 is closely related
AB  - to intron 1 of the Chlamydomonas moewusii psbA gene, with which it shares the same location,
AB  - high nucleotide identity in the core, and an identically placed ORF that shows 58% amino-acid
AB  - identity. Cr.psbA-2 is a subgroup-IA3 intron, and shows similarities to the Chlamydomonas
AB  - eugametos rRNA intron, Ce.LSU-1. Cr.psbA-3 is a subgroup-IA2 intron, and is remarkably similar
AB  - to the T4 phage intron, sunY.  Interestingly, a degenerate version of Cr.psbA-3 is located in
AB  - the intergenic region between the chloroplast petA and petD genes. All four introns contain
AB  - ORFs, which potentially code for basic proteins of 11-38 kDa. The ORFs in introns 2 and 3
AB  - contain variants of the GIY-YIG motif; however, the Cr.psbA-2 ORF is free-standing, whereas
AB  - the Cr.psbA-3 ORF is contiguous and in-frame with the upstream exon. The Cr.psbA-4 ORF
AB  - contains an H-N-H motif, and possibly a GIY-YIG motif. These data indicate that the C.
AB  - reinhardtii psbA introns have multiple origins, and illustrate some of the evolutionary DNA
AB  - dynamics associated with group-I introns in Chlamydomonas.
ER  -

TY  - JOUR
AU  - Holm, K.O.
AU  - Nilsson, K.
AU  - Hjerde, E.
AU  - Willassen, N.P.
AU  - Milton, D.L.
TI  - Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 60
EP  - 60
VL  - 10
AB  - Vibrio anguillarum causes a fatal hemorrhagic septicemia in marine fish that leads to great
AB  - economical losses in aquaculture world-wide. Vibrio anguillarum strain NB10 serotype O1 is a
AB  - Gram-negative, motile, curved rod-shaped bacterium,  isolated from a diseased fish on the
AB  - Swedish coast of the Gulf of Bothnia, and is slightly halophilic. Strain NB10 is a virulent
AB  - isolate that readily colonizes fish skin and intestinal tissues. Here, the features of this
AB  - bacterium are described and the annotation and analysis of its complete genome sequence is
AB  - presented. The genome is 4,373,835 bp in size, consists of two circular chromosomes and one
AB  - plasmid, and contains 3,783 protein-coding genes and 129 RNA  genes.
ER  -

TY  - JOUR
AU  - Holm-Hansen, A.C.
AU  - Paulino-Lima, I.G.
AU  - Fujishima, K.
AU  - Rothschild, L.J.
AU  - Jensen, P.R.
TI  - Draft Genome Sequence of Hymenobacter sp. Strain AT01-02, Isolated from a Surface Soil Sample in the Atacama Desert, Chile.
JO  - Genome Announcements
PY  - 2016
SP  - e01701
EP  - e01715
VL  - 4
AB  - Here, we report the 5.09-Mb draft genome sequence of Hymenobacter sp. strain AT01-02, which
AB  - was isolated from a surface soil sample in the Atacama Desert, Chile. The isolate is extremely
AB  - resistant to UV-C radiation and is able to accumulate high intracellular levels of Mn/Fe.
ER  -

TY  - JOUR
AU  - Holmes, M.L.
AU  - Nuttall, S.D.
AU  - Dyall-Smith, M.L.
TI  - Construction and use of Halobacterial shuttle vectors and further studies on Haloferax DNA gyrase.
JO  - J. Bacteriol.
PY  - 1991
SP  - 3807
EP  - 3813
VL  - 173
AB  - We report here on advances made in the construction of plasmid shuttle vectors suitable for
AB  - genetic manipulations in both Escherichia coli and halobacteria. Starting with a 20.4-kb
AB  - construct, pMDS1, new vectors were engineered which were considerably smaller yet retained
AB  - several alternative cloning sites. A restriction barrier observed when plasmid DNA was
AB  - transferred into Haloferax volcanii cells was found to operate via adenine methylation,
AB  - resulting in a 10^3 drop in transformation efficiency and the loss of most constructs by
AB  - incorporation of the resistance marker into the chromosome. Passing shuttle vectors through E.
AB  - coli dam mutants effectively avoided this barrier. Deletion analysis revealed that the gene(s)
AB  - for autonomous replication of pHK2 (the plasmid endogenous to Haloferax strain Aa2.2 and used
AB  - in the construction of pMDS1) was located within a 4.2-kb SmaI-KpnI fragment. Convenient
AB  - restriction sites were identified near the termini of the novobiocin resistance determinant
AB  - (gyrB), allowing the removal of flanking sequences (including gyrA). These deletions did not
AB  - appear to significantly affect transformation efficiencies or the novobiocin resistance
AB  - phenotype of halobacterial transformants. Northern blot hybridization with strand- and
AB  - gene-specific probes identified a single gyrB-gyrA transcript of 4.7 kb. This is the first
AB  - demonstration in prokaryotes that the two subunits of DNA gyrase may be cotranscribed.
ER  -

TY  - JOUR
AU  - Holmfeldt, K.
AU  - Howard-Varona, C.
AU  - Solonenko, N.
AU  - Sullivan, M.B.
TI  - Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera.
JO  - Environ. Microbiol.
PY  - 2014
SP  - 2501
EP  - 2513
VL  - 16
AB  - Bacterial viruses (phages) are abundant, ecologically important biological
AB  - entities. However, our understanding of their impact is limited by model systems
AB  - that are primarily not well represented in nature, e.g. Enterophages and their
AB  - hosts. Here, we investigate genomic characteristics and infection strategies
AB  - among six aquatic Bacteroidetes phages that represent two genera of exceptionally
AB  - large ( approximately 70-75 kb genome) podoviruses, which were isolated from the
AB  - same seawater sample using Cellulophaga baltica as host. Quantitative host range
AB  - studies reveal that these genera have contrasting narrow (specialist) and broad
AB  - (generalist) host ranges, with one-step growth curves revealing reduced burst
AB  - sizes for the generalist phages. Genomic comparisons suggest candidate genes in
AB  - each genus that might explain this host range variation, as well as provide
AB  - hypotheses about receptors in the hosts. One generalist phage, phi38:1, was more
AB  - deeply characterized, as its infection strategy switched from lytic on its
AB  - original host to either inefficient lytic or lysogenic on an alternative host. If
AB  - lysogenic, this phage was maintained extrachromosomally in the alternative host
AB  - and could not be induced by mitomycin C. This work provides fundamental knowledge
AB  - regarding phage-host ranges and their genomic drivers while also exploring the
AB  - 'host environment' as a driver for switching phage replication mode.
ER  -

TY  - JOUR
AU  - Hols, P.
AU  - Hancy, F.
AU  - Fontaine, L.
AU  - Grossiord, B.
AU  - Prozzi, D.
AU  - Leblond-Bourget, N.
AU  - Decaris, B.
AU  - Bolotin, A.
AU  - Delorme, C.
AU  - Ehrlich, S.D.
AU  - Guedon, E.
AU  - Monnet, W.
AU  - Renault, P.
AU  - Kleerebezem, M.
TI  - New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics.
JO  - FEMS Microbiol. Rev.
PY  - 2005
SP  - 435
EP  - 463
VL  - 29
AB  - Streptoeoccus thermophilus is a major dairy starter used for the manufacture of yoghurt and
AB  - cheese. The access to three genome
AB  - sequences, comparative genomics and multilocus sequencing analyses
AB  - suggests that this species recently emerged and is still undergoing a
AB  - process of regressive evolution towards a specialised bacterium for
AB  - growth in milk. Notably, S. thermophilus has maintained a
AB  - well-developed nitrogen metabolism whereas its sugar catabolism has
AB  - been subjected to a high level of degeneracy due to a paucity of carbon
AB  - sources in milk. Furthermore, while pathogenic streptococci are
AB  - recognised for a high capacity to expose proteins at their cell surface
AB  - in order to achieve cell adhesion or to escape the host immune system,
AB  - S. thermophilus has nearly lost this unique feature as well as many
AB  - virulence-related functions. Although gene decay is obvious in S.
AB  - thermophilus genome evolution, numerous small genomic islands, which
AB  - were probably acquired by horizontal gene transfer, comprise important
AB  - industrial phenotypic traits such as polysaccharide biosynthesis,
AB  - bacteriocin production, restriction-modification systems or oxygen
AB  - tolerance.
ER  -

TY  - JOUR
AU  - Holt, D.C.
AU  - Holden, M.T.
AU  - Tong, S.Y.
AU  - Castillo-Ramirez, S.
AU  - Clarke, L.
AU  - Quail, M.A.
AU  - Currie, B.J.
AU  - Parkhill, J.
AU  - Bentley, S.D.
AU  - Feil, E.J.
AU  - Giffard, P.M.
TI  - A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.
JO  - Genome Biol. Evol.
PY  - 2011
SP  - 881
EP  - 895
VL  - 3
AB  - Here we discuss the evolution of the northern Australian Staphylococcus aureus
AB  - isolate MSHR1132 genome. MSHR1132 belongs to the divergent clonal complex 75
AB  - lineage. The average nucleotide divergence between orthologous genes in MSHR1132
AB  - and typical S. aureus is approximately sevenfold greater than the maximum
AB  - divergence observed in this species to date. MSHR1132 has a small accessory
AB  - genome, which includes the well-characterized genomic islands, nuSAalpha and
AB  - nuSabeta, suggesting that these elements were acquired well before the expansion
AB  - of the typical S. aureus population. Other mobile elements show mosaic structure
AB  - (the prophage varphiSa3) or evidence of recent acquisition from a typical S.
AB  - aureus lineage (SCCmec, ICE6013 and plasmid pMSHR1132). There are two differences
AB  - in gene repertoire compared with typical S. aureus that may be significant clues
AB  - as to the genetic basis underlying the successful emergence of S. aureus as a
AB  - pathogen. First, MSHR1132 lacks the genes for production of staphyloxanthin, the
AB  - carotenoid pigment that confers upon S. aureus its characteristic golden color
AB  - and protects against oxidative stress. The lack of pigment was demonstrated in
AB  - 126 of 126 CC75 isolates. Second, a mobile clustered regularly interspaced short
AB  - palindromic repeat (CRISPR) element is inserted into orfX of MSHR1132. Although
AB  - common in other staphylococcal species, these elements are very rare within S.
AB  - aureus and may impact accessory genome acquisition. The CRISPR spacer sequences
AB  - reveal a history of attempted invasion by known S. aureus mobile elements. There
AB  - is a case for the creation of a new taxon to accommodate this and related
AB  - isolates.
ER  -

TY  - JOUR
AU  - Holt, J.P.
AU  - Grant, A.J.
AU  - Coward, C.
AU  - Maskell, D.J.
AU  - Quinlan, J.J.
TI  - Identification of Cj1051c as a Major Determinant for the Restriction Barrier of Campylobacter jejuni Strain NCTC11168.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 7841
EP  - 7848
VL  - 78
AB  - Campylobacter jejuni is a leading cause of human diarrheal illness in the world, and research
AB  - on it has benefitted greatly by the completion
AB  - of several genome sequences and the development of molecular biology
AB  - tools. However, many hurdles remain for a full understanding of this
AB  - unique bacterial pathogen. One of the most commonly used strains for
AB  - genetic work with C. jejuni is NCTC11168. While this strain is readily
AB  - transformable with DNA for genomic recombination, transformation with
AB  - plasmids is problematic. In this study, we have identified a
AB  - determinant of this to be cj1051c, predicted to encode a
AB  - restriction-modification type IIG enzyme. Knockout mutagenesis of this
AB  - gene resulted in a strain with a 1,000-fold-enhanced transformation
AB  - efficiency with a plasmid purified from a C. jejuni host. Additionally,
AB  - this mutation conferred the ability to be transformed by plasmids
AB  - isolated from an Escherichia coli host. Sequence analysis suggested a
AB  - high level of variability of the specificity domain between strains and
AB  - that this gene may be subject to phase variation. We provide evidence
AB  - that cj1051c is active in NCTC11168 and behaves as expected for a type
AB  - IIG enzyme. The identification of this determinant provides a greater
AB  - understanding of the molecular biology of C. jejuni as well as a tool
AB  - for plasmid work with strain NCTC11168.
ER  -

TY  - JOUR
AU  - Holt, K.E.
AU  - Baker, S.
AU  - Weill, F.X.
AU  - Holmes, E.C.
AU  - Kitchen, A.
AU  - Yu, J.
AU  - Sangal, V.
AU  - Brown, D.J.
AU  - Coia, J.E.
AU  - Kim, D.W.
AU  - Choi, S.Y.
AU  - Kim, S.H.
AU  - da Silveira, W.D.
AU  - Pickard, D.J.
AU  - Farrar, J.J.
AU  - Parkhill, J.
AU  - Dougan, G.
AU  - Thomson, N.R.
TI  - Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.
JO  - Nat. Genet.
PY  - 2012
SP  - 1056
EP  - 1059
VL  - 44
AB  - Shigella are human-adapted Escherichia coli that have gained the ability to invade the human
AB  - gut mucosa and cause dysentery, spreading efficiently via
AB  - low-dose fecal-oral transmission. Historically, S. sonnei has been predominantly
AB  - responsible for dysentery in developed countries but is now emerging as a problem
AB  - in the developing world, seeming to replace the more diverse Shigella flexneri in
AB  - areas undergoing economic development and improvements in water quality.
AB  - Classical approaches have shown that S. sonnei is genetically conserved and
AB  - clonal. We report here whole-genome sequencing of 132 globally distributed
AB  - isolates. Our phylogenetic analysis shows that the current S. sonnei population
AB  - descends from a common ancestor that existed less than 500 years ago and that
AB  - diversified into several distinct lineages with unique characteristics. Our
AB  - analysis suggests that the majority of this diversification occurred in Europe
AB  - and was followed by more recent establishment of local pathogen populations on
AB  - other continents, predominantly due to the pandemic spread of a single, rapidly
AB  - evolving, multidrug-resistant lineage.
ER  -

TY  - JOUR
AU  - Holt, K.E.
AU  - Hamidian, M.
AU  - Kenyon, J.J.
AU  - Wynn, M.T.
AU  - Hawkey, J.
AU  - Pickard, D.
AU  - Hall, R.M.
TI  - Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.
JO  - Genome Announcements
PY  - 2015
SP  - e00032
EP  - e00015
VL  - 3
AB  - Acinetobacter baumannii isolate A1 was recovered in the United Kingdom in 1982 and belongs to
AB  - global clone 1 (GC1). Here, we present its complete 3.91-Mbp
AB  - genome sequence, generated via a combination of short-read sequencing (Illumina),
AB  - long-read sequencing (PacBio), and manual finishing.
ER  -

TY  - JOUR
AU  - Holt, K.E.
AU  - Thomson, N.R.
AU  - Wain, J.
AU  - Phan, M.D.
AU  - Nair, S.
AU  - Hasan, R.
AU  - Bhutta, Z.A.
AU  - Quail, M.A.
AU  - Norbertczak, H.
AU  - Walker, D.
AU  - Dougan, G.
AU  - Parkhill, J.
TI  - Multidrug-Resistant Salmonella enterica Serovar Paratyphi A Harbors IncHI1 Plasmids Similar to Those Found in Serovar Typhi.
JO  - J. Bacteriol.
PY  - 2007
SP  - 4257
EP  - 4264
VL  - 189
AB  - Salmonella enterica serovars Typhi and Paratyphi A cause systemic
AB  - infections in humans which are referred to as enteric fever.
AB  - Multidrug-resistant (MDR) serovar Typhi isolates emerged in the 1980s, and
AB  - in recent years MDR serovar Paratyphi A infections have become established
AB  - as a significant problem across Asia. MDR in serovar Typhi is almost
AB  - invariably associated with IncHI1 plasmids, but the genetic basis of MDR
AB  - in serovar Paratyphi A has remained predominantly undefined. The DNA
AB  - sequence of an IncHI1 plasmid, pAKU_1, encoding MDR in a serovar Paratyphi
AB  - A strain has been determined. Significantly, this plasmid shares a common
AB  - IncHI1-associated DNA backbone with the serovar Typhi plasmid pHCM1 and an
AB  - S. enterica serovar Typhimurium plasmid pR27. Plasmids pAKU_1 and pHCM1
AB  - share 14 antibiotic resistance genes encoded within similar mobile
AB  - elements, which appear to form a 24-kb composite transposon that has
AB  - transferred as a single unit into different positions into their IncHI1
AB  - backbones. Thus, these plasmids have acquired similar antibiotic
AB  - resistance genes independently via the horizontal transfer of mobile DNA
AB  - elements. Furthermore, two IncHI1 plasmids from a Vietnamese isolate of
AB  - serovar Typhi were found to contain features of the backbone sequence of
AB  - pAKU_1 rather than pHCM1, with the composite transposon inserted in the
AB  - same location as in the pAKU_1 sequence. Our data show that these serovar
AB  - Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and
AB  - have acquired similar mobile elements encoding antibiotic resistance genes
AB  - in past decades.
ER  -

TY  - JOUR
AU  - Holtz, J.K.
AU  - Topal, M.D.
TI  - Location of putative binding and catalytic sites of NaeI by random mutagenesis.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 27286
EP  - 27290
VL  - 269
AB  - Endonuclease NaeI is a prototype for an unusual group of type II restriction endonucleases
AB  - that must bind two DNA recognition sequences to cleave DNA. The naeIR gene, expressed from a
AB  - Ptac promoter construct, was toxic to Escherichia coli in the absence of NaeI-sequence
AB  - specific methylases. The naeIR gene was mutagenized with N-methyl-N'-nitrosoguanidine; four
AB  - classes of NaeI variants were isolated in the absence of protecting methylase activity. Class
AB  - I variants (T60I, E70K) lacked detectable cleavage activity, but displayed good
AB  - sequence-specific DNA binding. Class II variants (D95N, G141D) displayed 1-5% of the wild-type
AB  - cleavage activity and normal DNA binding. Class III variants (G131E, G131R/A219T, G236S,
AB  - L241P, G245E, G245R, G250E, G270E) lacked both cleavage and binding activities. These results
AB  - imply two amino acids (Thr-60, Glu-70) essential for catalysis. In addition, two domains are
AB  - indicated in NaeI: one (Thr-60 to Gly-155) mediates substrate binding and catalysis, the other
AB  - (Gly-197 to Gly-270) may mediate binding of the activating DNA sequence. Our results are
AB  - compared with the active site residues of EcoRI, EcoRV, and BamHI.
ER  -

TY  - JOUR
AU  - Holubova, I.
AU  - Vejsadova, I.
AU  - Firman, K.
AU  - Weiserovda, M.
TI  - Cellular localization of type I restriction-modification enzymes is family dependent.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2004
SP  - 375
EP  - 380
VL  - 319
AB  - Cellular localization of Type I restriction-modification enzymes EcoKI, EcoAI, and
AB  - EcoR124I-the most frequently studied representatives of IA,
AB  - 113, and IC families-was analyzed by immunoblotting of subcellular
AB  - fractions isolated from Escherichia coli strains harboring the
AB  - corresponding hsd genes. EcoR124I shows characteristics similar to
AB  - those of EcoKI. The complex enzymes are associated with the cytoplasmic
AB  - membrane via DNA interaction as documented by the release of the Hsd
AB  - subunits from the membrane into the soluble fraction following
AB  - benzonase treatment. HsdR subunits of the membrane-bound enzymes EcoKI
AB  - and EcoR124I are accessible, though to a different extent, at the
AB  - external surface of cytoplasmic membrane as shown by trypsinization of
AB  - intact spheroplasts. EcoAI strongly differs from EcoKI and EcoR124I,
AB  - since neither benzonase nor trypsin affects its association with the
AB  - cytoplasmic membrane. Possible reasons for such a different
AB  - organization are discussed in relation of the control of the
AB  - restriction-modification activities in vivo.
ER  -

TY  - JOUR
AU  - Holubova, I.
AU  - Vejsadova, S.
AU  - Weiserova, M.
AU  - Firman, K.
TI  - Localization of the Type I Restriction-Modification Enzyme EcoKI in the Bacterial Cell.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2000
SP  - 46
EP  - 51
VL  - 270
AB  - To localise the type I restriction-modification (R-M) enzyme EcoKI within the bacterial cell,
AB  - the Hsd subunits present in subcellular fractions were analysed using immunoblotting
AB  - techniques. The endonuclease (ENase) as well as the methylase (MTase) were found to be
AB  - associated with the cytoplasmic membrane. HsdR and HsdM subunits produced individually were
AB  - soluble, cytoplasmic polypeptides and only became membrane-associated when coproduced with the
AB  - insoluble HsdS subunit. The release of enzyme from the membrane fraction following benzonase
AB  - treatment indicated a role for DNA in this interaction. Trypsinization of spheroplasts
AB  - revealed that the HsdR subunit in the assembled ENase was accessible to protease, while HsdM
AB  - and HsdS, in both ENase and MTase complexes, were fully protected against digestion. We
AB  - postulate that the R-M enzyme EcoKI is associated with the cytoplasmic membrane in a manner
AB  - that allows access of HsdR to the periplasmic space, while the MTase components are localised
AB  - on the inner side of the plasma membrane.
ER  -

TY  - JOUR
AU  - Holubova, J.
AU  - Josephsen, J.
TI  - Potential of AbiS as defence mechanism determined by conductivity measurement.
JO  - J. Appl. Microbiol.
PY  - 2007
SP  - 2382
EP  - 2391
VL  - 103
AB  - Aim: To compare pH and conductivity used in the determination of growth in reconstituted skim
AB  - milk (RSM), to determine whether the presence of
AB  - one or two plasmids in Lactococcus lactis had any influence on growth,
AB  - and whether AbiS improved bacteriophages resistance of L. lactis.
AB  - Methods and Results: Conductivity and pH were used to determine
AB  - growth in RSM. A small increase in the generation time was found with
AB  - increasing number of plasmids, while their size was unimportant. The
AB  - introduction of a plasmid-encoding AbiS did only enhance the level of
AB  - phage resistance significant when other plasmids encoding either AbiS1
AB  - or the restriction modification system LlaBIII was present.
AB  - Conclusions: The earliest detection of growth was observed by
AB  - measuring pH, rather than conductance. The plasmid-encoded AbiS system
AB  - has a potential to be used as a phage resistance mechanisms in L.
AB  - lactis during milk fermentations, especially when combined with other
AB  - anti-phage mechanisms.
AB  - Significance and Impact of the Study: This study widened the
AB  - knowledge about the influence of plasmid introduction on the growth
AB  - rate of L. lactis, which is important for the construction of new
AB  - strains. The level of protection against 936 groups of phages was only
AB  - significant when the mechanism was present together with the RM system
AB  - LlaBIII.
ER  -

TY  - JOUR
AU  - Holz, B.
AU  - Dank, N.
AU  - Eickhoff, J.E.
AU  - Lipps, G.
AU  - Krauss, G.
AU  - Weinhold, E.
TI  - Identification of the binding site for the extrahelical target base in N6-adenine DNA methyltransferases by photo-cross-linking with duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 15066
EP  - 15072
VL  - 274
AB  - DNA methyltransferases flip their target bases out of the DNA double helix for catalysis. Base
AB  - flipping of C5-cytosine DNA methyltransferases was directly observed in the protein-DNA
AB  - cocrystal structures of M.HhaI and M.HaeIII. Indirect structural evidence for base flipping of
AB  - N6-adenine and N4-cytosine DNA methyltransferases was obtained by modeling DNA into the
AB  - three-dimensional structures of M.TaqI and M.PvuII in complex with the cofactor. In addition,
AB  - biochemical evidence of base flipping was reported for different N6-adenine DNA
AB  - methyltransferases. As no protein-DNA cocrystal structure for the related N6-adenine and
AB  - N4-cytosine DNA methyltransferases is available, we used light-induced photochemical
AB  - cross-linking to identify the binding site of the extrahelical target bases. The N6-adenine
AB  - DNA methyltransferases M.TaqI and M.CviBIII, which both methylate adenine within the
AB  - double-stranded 5'-TCGA-3' DNA sequence, were photo-cross-linked to duplex
AB  - oligodeoxyribonucleotides containing 5-iodouracil at the target position in 50-60% and almost
AB  - quantitative yield, respectively. Proteolytic fragmentation of the M.CviBIII-DNA complex
AB  - followed by Edman degradation and electrospray ionization mass spectrometry indicates
AB  - photo-cross-linking to tyrosine 122. In addition, the mutant methyltransferases M.TaqI/Y108A
AB  - and M.TaqI/F196A were photo-cross-linked with 6-fold and 2-fold reduced efficiency,
AB  - respectively, which suggests that tyrosine 108 is the primary site of modification in M.TaqI.
AB  - Our results indicate a close proximity between the extrahelical target base and tyrosine 122
AB  - in M.CviBIII or tyrosine 108 in M.TaqI. As both residues belong to the conserved motif IV
AB  - ((N/D/S)(P/I)P(Y/F/W)) found in all N6-adenine and N4-cytosine DNA as well as in N6-adenine
AB  - RNA methyltransferases, a similar spatial relationship between the target bases and the
AB  - aromatic amino acid residue within motif IV is expected for all these methyltransferases.
ER  -

TY  - JOUR
AU  - Holz, B.
AU  - Klimasauskas, S.
AU  - Serva, S.
AU  - Weinhold, E.
TI  - 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1076
EP  - 1083
VL  - 26
AB  - DNA base flipping, which was first observed for the C5-cytosine  methyltransferase M.HhaI,
AB  - results in a complete removal of the stacking interactions between the target base and its
AB  - neighboring bases.  We have investigated whether duplex oligodeoxynucleotides containing the
AB  - fluorescent base analogue 2-aminopurine can be used to sense DNA base flipping.  Using M.HhaI
AB  - as a paradigm for a base flipping enzyme, we find that the fluorescence intensity of duplex
AB  - oligodeoxynucleotides containing 2-aminopurine at the target site is dramatically enhanced
AB  - (54-fold) in the presence of M.HhaI.  Duplex oligodeoxynucleotides containing 2-aminopurine
AB  - adjacent to the target cytosine show little fluorescence increase upon addition of M.HhaI.
AB  - These results clearly demonstrate that duplex oligodeoxynucleotides containing 2-aminopurine
AB  - at the target site can serve as fluorescence probes for base flipping.  Another enzyme
AB  - hypothesized to use a base flipping mechanism is the N6-adenine DNA methyltransferase M.TaqI.
AB  - Addition of M.TaqI to duplex oligodeoxynucleotides bearing 2-aminopurine at the target
AB  - position, also results in a strongly enhanced fluorescence (13-fold), whereas addition to
AB  - duplex oligodeoxynucleotides containing 2-aminopurine at the 3'- or 5'-neighboring position
AB  - leads only to small fluorescence increases.  These results give the first experimental
AB  - evidence that the adenine-specific DNA methyltransferase M.TaqI also flips its target base.
ER  -

TY  - JOUR
AU  - Holz, B.
AU  - Pues, H.
AU  - Wolcke, J.
AU  - Weinhold, E.
TI  - Fluorescence studies on the base flipping mechanism of the DNA methyltransferase M.TaqI.
JO  - FASEB J.
PY  - 1997
SP  - A1151
EP  - A1151
VL  - 11
AB  - The DNA methyltransferase from Thermus aquaticus catalyzes the methyl group transfer from
AB  - S-adenosyl-L-methionine to the N6-position of adenine in the double-stranded DNA sequence
AB  - 5'-TCGA-3'.  A model of the ternary complex built with the crystal structure of M.TaqI-SAM
AB  - complex and DNA duplex shows that the distance between the cofactor and the target adenine is
AB  - too large to allow a direct methyl group transfer.  This distance can be decreased if the
AB  - adenine rotates out of the DNA helix as described for a C5-DNA methyltransferase.  DNA
AB  - containing the adenine analogue 2-aminopurine and intrinsic tryptophan fluorescence were used
AB  - to examine such a base flipping mechanism for M.TaqI.  The fluorescence of 2-Ap is highly
AB  - quenched in duplex DNA due to stacking of the neighboring bases.  Addition of M.TaqI to a DNA
AB  - duplex with 2-Ap at the target site causes a large fluorescence increase which points to an
AB  - extrahelical base in this complex.  In stopped-flow experiments this increase is single
AB  - exponential with a rate constant of 20 s^-1.  Binding of DNA leads to a 30% increase of the
AB  - tryptophan fluorescence intensity of M.TaqI.  This increase was resolved into two steps: a
AB  - rapid first step (k+2 = 20 s-1) and a second step with a k+3 = 2 s-1.  Since both steps are
AB  - not concentration dependent we suggest a very fast formation of an initial complex in a time
AB  - scale not resolved by the stopped-flow method.  These data suggest that DNA binding of M.TaqI
AB  - is at least a three step process, where the second step gives rise not only to a
AB  - conformational change of the DNA methyltransferase but also of the DNA.
ER  -

TY  - JOUR
AU  - Holz, B.
AU  - Weinhold, E.
TI  - Probes for DNA base flipping by DNA methyltransferases.
JO  - Bioorganic Chemistry: Highlights and New Aspects
PY  - 1999
SP  - 337
EP  - 345
AB  - In addition to the normal nucleobases adenine, thymine, guanine, and cytosine, the DNA of most
AB  - organisms contains the methylated bases C5-methylcytosine, N6-methyladenine, or
AB  - N4-methylcytosine.  These methylated bases are formed by DNA methyltransferases which catalyze
AB  - the transfer of the activated methyl group from the cofactor S-adenosyl-L-methionine to the C5
AB  - carbon of cytosine, the N6 nitrogen of adenine, or the N4 nitrogen of cytosine within specific
AB  - DNA sequences.  Most DNA Mtases recognize palindromic DNA sequences, which contain two
AB  - symmetry-related target bases.  After DNA replication, only the parental strand contains
AB  - methylated bases (hemi-methylated DNA), and methylation of the daughter strand restores the
AB  - fully methylated DNA.
ER  -

TY  - JOUR
AU  - Holz-Schietinger, C.
AU  - Reich, N.O.
TI  - The Inherent Processivity of the Human de Novo Methyltransferase 3A (DNMT3A) Is Enhanced by DNMT3L.
JO  - J. Biol. Chem.
PY  - 2010
SP  - 29091
EP  - 29100
VL  - 285
AB  - Human DNMT3A is responsible for de novo DNA cytosine methylation patterning during
AB  - development. Here we show that DNMT3A methylates 5-8
AB  - CpG sites on human promoters before 50% of the initially bound enzyme
AB  - dissociates from the DNA. Processive methylation is enhanced 3-fold in
AB  - the presence of DNMT3L, an inactive homolog of DNMT3A, therefore
AB  - providing a mechanism for the previously described DNMT3L activation of
AB  - DNMT3A. DNMT3A processivity on human promoters is also regulated by DNA
AB  - topology, where a 2-fold decrease in processivity was observed on
AB  - supercoiled DNA in comparison with linear DNA. These results are the
AB  - first observation that DNMT3A utilizes this mechanism of increasing
AB  - catalytic efficiency. Processive de novo DNA methylation provides a
AB  - mechanism that ensures that multiple CpG sites undergo methylation for
AB  - transcriptional regulation and silencing of newly integrated viral DNA.
ER  -

TY  - JOUR
AU  - Holz-Schietinger, C.
AU  - Reich, N.O.
TI  - RNA modulation of the human DNA methyltransferase 3A.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 8550
EP  - 8557
VL  - 40
AB  - DNA methyltransferase 3A (DNMT3A) is one of two human de novo DNA methyltransferases essential
AB  - for transcription regulation during cellular
AB  - development and differentiation. There is increasing evidence that RNA plays a
AB  - role in directing DNA methylation to specific genomic locations within mammalian
AB  - cells. Here, we describe two modes of RNA regulation of DNMT3A in vitro. We show
AB  - a single-stranded RNA molecule that is antisense to the E-cadherin promoter binds
AB  - tightly to the catalytic domain in a structurally dependent fashion causing
AB  - potent inhibition of DNMT3A activity. Two other RNA molecules bind DNMT3A at an
AB  - allosteric site outside the catalytic domain, causing no change in catalysis. Our
AB  - observation of the potent and specific in vitro modulation of DNMT3A activity by
AB  - RNA supports in vivo data that RNA interacts with DNMT3A to regulate
AB  - transcription.
ER  -

TY  - JOUR
AU  - Honda, S.
AU  - Selker, E.U.
TI  - Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa.
JO  - Mol. Cell. Biol.
PY  - 2008
SP  - 6044
EP  - 6055
VL  - 28
AB  - DNA methylation is involved in gene silencing and genomic stability in mammals, plants, and
AB  - fungi. Genetics studies of Neurospora crassa have
AB  - revealed that a DNA methyltransferase (DIM-2), a histone H3K9
AB  - methyltransferase (DIM-5), and heterochromatin protein 1 (HP1) are
AB  - required for DNA methylation. We explored the interrelationships of
AB  - these components of the methylation machinery. A yeast two-hybrid
AB  - screen revealed that HP1 interacts with DIM-2. We confirmed the
AB  - interaction in vivo and demonstrated that it involves a pair of
AB  - PXVXL-related motifs in the N-terminal region of DIM-2 and the chromo
AB  - shadow domain of HP1. Both regions are essential for proper DNA
AB  - methylation. We also determined that DIM-2 and HP1 form a stable
AB  - complex independently of the trimethylation of histone H3K9, although
AB  - the association of DIM-2 with its substrate sequences depends on
AB  - trimethyl-H3K9. The DIM-2/HP1 complex does not include DIM-5. We
AB  - conclude that DNA methylation in Neurospora is largely or exclusively
AB  - the result of a unidirectional pathway in which DIM-5 methylates
AB  - histone H3K9 and then the DIM-2/HP1 complex recognizes the resulting
AB  - trimethyl-H3K9 mark via the chromo domain of HP1.
ER  -

TY  - JOUR
AU  - Honda, T.
AU  - Liang, Y.
AU  - Arai, D.
AU  - Ito, Y.
AU  - Yoshino, T.
AU  - Tanaka, T.
TI  - Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG042902, Which Harbors a Homogeneous Plasmid Available for Metabolic  Engineering.
JO  - Genome Announcements
PY  - 2014
SP  - e00704
EP  - e00714
VL  - 2
AB  - The marine cyanobacterium Synechococcus sp. strain NKBG042902 was isolated from coastal areas
AB  - in Japan. Strain NKBG042902 has four plasmids: pSY8, pSY9, pSY10,
AB  - and pSY11. Moreover, the hybrid plasmid pUSY02 containing pSY11 and Escherichia
AB  - coli plasmid pUC18 was constructed for this strain. The genetic manipulation
AB  - technique using pUSY02 was established for this strain and used in metabolic
AB  - engineering. Here, we report the draft genome sequence of this strain, which has
AB  - 77 contigs comprising a total length of 3,319,479 bp, with a G+C content of
AB  - 49.4%.
ER  -

TY  - JOUR
AU  - Honein, K.
AU  - Jagoda, S.S.
AU  - Arulkanthan, A.
AU  - Ushio, H.
AU  - Asakawa, S.
TI  - Draft Genome Sequences of Citrobacter freundii Strains CF04 and A41 Isolated from Moribund, Septicemic Giant Gourami (Osphronemus goramy) in Sri Lanka.
JO  - Genome Announcements
PY  - 2016
SP  - e00820
EP  - e00816
VL  - 4
AB  - Citrobacter freundii is a Gram-negative opportunistic pathogen associated with many infectious
AB  - conditions including septicemia in humans and animals. Here, we
AB  - announce the draft genome sequences of two multidrug-resistant C. freundii
AB  - strains (CF04 and A41) isolated from septicemic giant gourami (Osphronemus
AB  - goramy) collected from aquaria in Sri Lanka.
ER  -

TY  - JOUR
AU  - Honein, K.
AU  - Jagoda, S.S.S.S.
AU  - Arulkanthan, A.
AU  - Ushio, H.
AU  - Asakawa, S.
TI  - Draft Genome Sequence of Aeromonas hydrophila Strain Ae25, Isolated from a Septicemic Moribund Koi Carp (Cyprinus carpio) in Sri Lanka.
JO  - Genome Announcements
PY  - 2018
SP  - e01523
EP  - e01517
VL  - 6
AB  - Motile aeromonad septicemia caused by mesophilic strains of Aeromonas hydrophila  is a
AB  - widespread problem in cultured freshwater fish. We announce here the draft
AB  - genome sequence of the multidrug-resistant A. hydrophila strain Ae25, isolated
AB  - from a koi carp (Cyprinus carpio) with motile aeromonad septicemia that was
AB  - collected from an ornamental fish-breeding farm in Sri Lanka.
ER  -

TY  - JOUR
AU  - Hong, C.E.
AU  - Jo, S.H.
AU  - Jeong, H.
AU  - Park, J.M.
TI  - Draft Genome Sequence of the Endophytic Strain Rhodococcus kyotonensis KB10, a Potential Biodegrading and Antibacterial Bacterium Isolated from Arabidopsis  thaliana.
JO  - Genome Announcements
PY  - 2016
SP  - e00636
EP  - e00616
VL  - 4
AB  - Rhodococcus kyotonensis KB10 is an endophytic bacterium isolated from Arabidopsis thaliana The
AB  - organism showed mild antibacterial activity against the
AB  - phytopathogen Pseudomonas syringae pv. tomato DC3000. This study reports the
AB  - genome sequence of R. kyotonensis KB10. This bacterium contains an ectoine
AB  - biosynthesis gene cluster and has the potential to degrade nitroaromatic
AB  - compounds. The identified bacterium may be a suitable biocontrol agent and
AB  - degrader of environmental pollutants.
ER  -

TY  - JOUR
AU  - Hong, C.E.
AU  - Jo, S.H.
AU  - Jo, I.H.
AU  - Jeong, H.
AU  - Park, J.M.
TI  - Draft Genome Sequence of the Endophytic Bacterium Variovorax paradoxus KB5, Which Has Antagonistic Activity against a Phytopathogen, Pseudomonas syringae pv.  tomato DC3000.
JO  - Genome Announcements
PY  - 2017
SP  - e00950
EP  - e00917
VL  - 5
AB  - Variovorax paradoxus KB5, isolated from the inside of Arabidopsis thaliana leaves, showed
AB  - antibacterial activity against the phytopathogen Pseudomonas
AB  - syringae pv. tomato DC3000. Here, we report a draft genome sequence of V.
AB  - paradoxus KB5, which contains a delftibactin-like nonribosomal peptide
AB  - biosynthetic gene cluster.
ER  -

TY  - JOUR
AU  - Hong, H.H.
AU  - Choi, H.
AU  - Cheon, S.
AU  - Lee, H.G.
AU  - Park, C.
TI  - Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867).
JO  - Genome Announcements
PY  - 2017
SP  - e00674
EP  - e00617
VL  - 5
AB  - In this study, we sequenced the genomes of two Shewanella spp., newly isolated from the gut of
AB  - the sea cucumber Apostichopus japonicus (Selenka, 1867). The
AB  - whole-genome sequences reported here will expand the repertoire of genomic
AB  - information for the members of the genus Shewanella and will provide important
AB  - insights into their roles within microbial communities.
ER  -

TY  - JOUR
AU  - Hong, J.
AU  - Kim, J.
AU  - Kim, B.Y.
AU  - Park, J.W.
AU  - Ryu, J.G.
AU  - Roh, E.
TI  - Complete Genome Sequence of Biofilm-Forming Strain Staphylococcus haemolyticus S167.
JO  - Genome Announcements
PY  - 2016
SP  - e00567
EP  - e00516
VL  - 4
AB  - Staphylococcus haemolyticus S167 has the ability to produce biofilms in large quantities.
AB  - Genomic analyses revealed information on the biofilm-related genes of
AB  - S. haemolyticus S167. Detailed studies of biofilm formation at the molecular
AB  - level could provide a foundation for biofilm control research.
ER  -

TY  - JOUR
AU  - Hong, K.W.
AU  - Gan, H.M.
AU  - Low, S.M.
AU  - Lee, P.K.
AU  - Chong, Y.M.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Draft Genome Sequence of Pantoea sp. Strain A4, a Rafflesia-Associated Bacterium  That Produces N-Acylhomoserine Lactones as Quorum-Sensing Molecules.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6610
EP  - 6610
VL  - 194
AB  - Pantoea sp. strain A4 is a Gram-negative bacterium isolated from the Rafflesia flower. We
AB  - present here, for the first time, the genome sequence of
AB  - Rafflesia-associated Pantoea sp. strain A4, which exhibited quorum-sensing
AB  - activity.
ER  -

TY  - JOUR
AU  - Hong, K.W.
AU  - Koh, C.L.
AU  - Sam, C.K.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Complete Genome Sequence of Burkholderia sp. Strain GG4, a Betaproteobacterium That Reduces 3-Oxo-N-Acylhomoserine Lactones and Produces Different  N-Acylhomoserine Lactones.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6317
EP  - 6317
VL  - 194
AB  - Burkholderia sp. strain GG4, isolated from the ginger rhizosphere, possesses a unique
AB  - N-acylhomoserine lactone (AHL)-modifying activity that reduces 3-oxo-AHLs
AB  - to 3-hydroxy-AHLs. To the best of our knowledge, this is the first sequenced
AB  - genome from a bacterium of the genus Burkholderia that shows both quorum-sensing
AB  - and signaling confusion activities.
ER  -

TY  - JOUR
AU  - Hong, K.W.
AU  - Koh, C.L.
AU  - Sam, C.K.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Whole-Genome Sequence of N-Acylhomoserine Lactone-Synthesizing and -Degrading Acinetobacter sp. Strain GG2.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6318
EP  - 6318
VL  - 194
AB  - Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from
AB  - the ginger rhizosphere. It degrades a broad range of
AB  - N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain
AB  - GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching
AB  - mechanisms in this bacterium.
ER  -

TY  - JOUR
AU  - Hong, K.W.
AU  - Thinagaran, D.A.
AU  - Gan, H.M.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6324
EP  - 6324
VL  - 194
AB  - Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits  broad
AB  - heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate,
AB  - Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III),
AB  - and Zn(II). Here we present the assembly and annotation of its genome.
ER  -

TY  - JOUR
AU  - Hong, S.H.
AU  - Kim, J.S.
AU  - Lee, S.Y.
AU  - In, Y.H.
AU  - Choi, S.S.
AU  - Rih, J.K.
AU  - Kim, C.H.
AU  - Jeong, H.
AU  - Hur, C.G.
AU  - Kim, J.J.
TI  - The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens.
JO  - Nat. Biotechnol.
PY  - 2004
SP  - 1275
EP  - 1281
VL  - 22
AB  - The rumen represents the first section of a ruminant animal's stomach, where feed is
AB  - collected and mixed with microorganisms for initial
AB  - digestion. The major gas produced in the rumen is CO(2) (65.5 mol%), yet
AB  - the metabolic characteristics of capnophilic (CO(2)-loving) microorganisms
AB  - are not well understood. Here we report the 2,314,078 base pair genome
AB  - sequence of Mannheimia succiniciproducens MBEL55E, a recently isolated
AB  - capnophilic Gram-negative bacterium from bovine rumen, and analyze its
AB  - genome contents and metabolic characteristics. The metabolism of M.
AB  - succiniciproducens was found to be well adapted to the oxygen-free rumen
AB  - by using fumarate as a major electron acceptor. Genome-scale metabolic
AB  - flux analysis indicated that CO(2) is important for the carboxylation of
AB  - phosphoenolpyruvate to oxaloacetate, which is converted to succinic acid
AB  - by the reductive tricarboxylic acid cycle and menaquinone systems. This
AB  - characteristic metabolism allows highly efficient production of succinic
AB  - acid, an important four-carbon industrial chemical.
ER  -

TY  - JOUR
AU  - Hong, S.J.
AU  - Park, G.S.
AU  - Khan, A.R.
AU  - Jung, B.K.
AU  - Park, Y.J.
AU  - Yoo, N.K.
AU  - Lee, C.
AU  - Park, C.K.
AU  - Shin, J.H.
TI  - Draft Genome Sequence of Caprolactam-Degrading Pseudomonas putida Strain SJ3.
JO  - Genome Announcements
PY  - 2015
SP  - e00810
EP  - e00815
VL  - 3
AB  - Pseudomonas putida strain SJ3, which possesses caprolactam-degrading ability, was isolated
AB  - from dyeing industry wastewater in Daegu, Republic of Korea. Here, we
AB  - describe the draft genome sequence and annotation of the strain. The
AB  - 5,596,765-bp-long genome contains 4,293 protein-coding genes and 68 RNA genes
AB  - with 61.70% G+C content.
ER  -

TY  - JOUR
AU  - Hong, S.J.
AU  - Ullah, I.
AU  - Park, G.S.
AU  - Jung, B.K.
AU  - Choi, J.
AU  - Khan, A.R.
AU  - Kim, M.C.
AU  - Shin, J.H.
TI  - Draft Genome Sequence and Annotation of the Insect Pathogenic Bacterium Xenorhabdus nematophila Strain C2-3, Isolated from Nematode Steinernema  carpocapsae in the Republic of Korea.
JO  - Genome Announcements
PY  - 2015
SP  - e01521
EP  - e01514
VL  - 3
AB  - Xenorhabdus nematophila strain C2-3, which belongs to the family Enterobacteriaceae, was
AB  - isolated from entomopathogenic nematodes collected in the
AB  - Republic of Korea. Herein, we report a 4.38-Mbp draft genome sequence of X.
AB  - nematophila strain C2-3, with a 43.6% G+C content. The RAST annotation analysis
AB  - revealed 4,994 protein-coding sequences in the draft genome.
ER  -

TY  - JOUR
AU  - Honger, J.
AU  - Monson, R.E.
AU  - Rawlinson, A.
AU  - Salmond, G.P.C.
TI  - Draft Genome Sequences of Serratia marcescens Strains CAPREx SY13 and CAPREx SY21 Isolated from Yams.
JO  - Genome Announcements
PY  - 2017
SP  - e00191
EP  - e00117
VL  - 5
AB  - Serratia marcescens strains CAPREx SY13 and CAPREx SY21 were isolated from Ghanaian yams from
AB  - a London market. The draft genomes suggest that the strains
AB  - are similar, with genomes of 5,308,004 and 5,157,134 bp and 59.35 and 59.62 G+C%,
AB  - respectively. The genes necessary for prodigiosin biosynthesis were present in
AB  - both strains.
ER  -

TY  - JOUR
AU  - Hongoh, Y.
AU  - Sharma, V.K.
AU  - Prakash, T.
AU  - Noda, S.
AU  - Taylor, T.D.
AU  - Kudo, T.
AU  - Sakaki, Y.
AU  - Toyoda, A.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 5555
EP  - 5560
VL  - 105
AB  - Termites harbor a symbiotic gut microbial community that is responsible for their ability to
AB  - thrive on recalcitrant plant matter. The community comprises diverse microorganisms, most of
AB  - which are as yet uncultivable; the detailed symbiotic mechanism remains unclear. Here, we
AB  - present the first complete genome sequence of a termite gut symbiont-an uncultured bacterium
AB  - named Rs-D17 belonging to the candidate phylum Termite Group 1 (TG1). TG1 is a dominant group
AB  - in termite guts, found as intracellular   symbionts of various cellulolytic protists, without
AB  - any physiological information. To acquire the complete genome sequence, we collected Rs-D17
AB  - cells from only a single host protist cell to minimize their genomic  variation and performed
AB  - isothermal whole-genome amplification. This
AB  - strategy enabled us to reconstruct a circular chromosome (1,125,857 bp)
AB  - encoding 761 putative protein-coding genes. The genome additionally contains 121 pseudogenes
AB  - assigned to categories, such as cell wall biosynthesis, regulators, transporters, and defense
AB  - mechanisms. Despite its apparent reductive evolution, the ability to synthesize 15 amino acids
AB  - and various cofactors is retained, some of these genes having been duplicated. Considering
AB  - that diverse termite-gut protists harbor TG1 bacteria, we suggest that this bacterial group
AB  - plays a key role in the gut symbiotic system by stably supplying essential nitrogenous
AB  - compounds deficient in lignocelluloses to their host protists and the termites. Our results
AB  - provide a breakthrough to clarify the functions of and the interactions among the individual
AB  - members of this multilayered symbiotic complex.
ER  -

TY  - JOUR
AU  - Hongoh, Y.
AU  - Sharma, V.K.
AU  - Prakash, T.
AU  - Noda, S.
AU  - Toh, H.
AU  - Taylor, T.D.
AU  - Kudo, T.
AU  - Sakaki, Y.
AU  - Toyoda, A.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis within Protist Cells in Termite Gut.
JO  - Science
PY  - 2008
SP  - 1108
EP  - 1109
VL  - 322
AB  - Termites harbor diverse symbiotic gut microorganisms, the majority of which are as yet
AB  - uncultivable and their interrelationships unclear.  Here, we present the complete genome
AB  - sequence of the uncultured Bacteroidales endosymbiont of the cellulolytic protest
AB  - Pseudotrichonympha grassii, which accounts for 70% of the bacterial cells in the gut of the
AB  - termite Coptotermes formosanus.  Functional annotation of the chromosome (1,114,206 base
AB  - pairs) unveiled its ability to fix dinitrogen and recycle putative host nitrogen wastes for
AB  - biosynthesis of diverse amino acids and cofactors, and import glucose and xylose as energy and
AB  - carbon sources.  Thus, nitrogen fixation and cellulolysis are coupled within the protist's
AB  - cells.  This highly evolved symbiotic system probably underlies the ability of the worldwide
AB  - pest termites Coptotermes to use wood as their sole food.
ER  -

TY  - JOUR
AU  - Honma, Y.
AU  - Fernandez, R.E.
AU  - Maurelli, A.T.
TI  - A DNA adenine methylase mutant of Shigella flexneri shows no significant attenuation of virulence.
JO  - Microbiology
PY  - 2004
SP  - 1073
EP  - 1078
VL  - 150
AB  - Mutants of Salmonella defective in DNA adenine methylase (dam) have been reported to be
AB  - attenuated for virulence and to provide protective
AB  - immunity when used as vaccine strains. To determine whether these
AB  - observations could be extended to Shigella, a dam mutant of Shigella
AB  - flexneri 2a was characterized and examined for the role of dam in
AB  - pathogenesis. The Shigella dam mutant showed some unique
AB  - characteristics; however, it retained virulence in vivo as well as in
AB  - vitro. The mutant invaded cultured L2 monolayer cells as efficiently as
AB  - the wild-type parent, but its intracellular growth was suppressed up to
AB  - 7 h post-invasion. Furthermore, the invading dam mutant formed smaller
AB  - plaques in cell monolayers compared to the parent strain. However, the
AB  - mutant produced keratoconjunctivitis in the Sereny test in guinea pigs
AB  - only slightly more slowly than the wild-type. While the effect of the
AB  - dam mutation on virulence was modest, the rate of spontaneous mutation
AB  - in the dam mutant was 1000-fold greater compared with the wild-type.
AB  - The virulence and high mutability displayed by the dam mutant of Sh.
AB  - flexneri suggest that a general anti-bacterial pathogen vaccine
AB  - strategy based on mutations in dam needs to be re-evaluated.
ER  -

TY  - JOUR
AU  - Hood, D.W.
AU  - Deadman, M.E.
AU  - Jennings, M.P.
AU  - Bisercic, M.
AU  - Fleischmann, R.D.
AU  - Venter, J.C.
AU  - Moxon, E.R.
TI  - DNA repeats identify novel virulence genes in Hemophilus influenzae.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 11121
EP  - 11125
VL  - 93
AB  - The whole genome sequence (1.83 Mbp) of Haemophilus influenzae strain Rd was searched to
AB  - identify tandem oligonucleotide repeat sequences.  Loss or gain of one or more nucleotide
AB  - repeats through a recombination-independent slippage mechanism is known to mediate phase
AB  - variation of surface molecules of pathogenic bacteria, including H. influenzae.  This
AB  - facilitates evasion of host defenses and adaptation to the varying microenvironments of the
AB  - host.  We reasoned that iterative nucleotides could identify novel genes relevant to
AB  - microbe-host interactions.  Our search of the Rd genome sequence identified 9 novel loci with
AB  - multiple (range 6-36, mean 22) tandem tetranucleotide repeats.  All were found to be located
AB  - within putative open reading frames and included homologues of hemoglobin-binding proteins of
AB  - Neisseria, a glycosyltransferase (lgtC gene product) of Neisseria, and an adhesin of Yersinia.
AB  - These tetranucleotide repeat sequences were also shown to be present in two other
AB  - epidemiologically different H. influenzae type b strains, although the number and distribution
AB  - of repeats was different.  Further characterization of the lgtC gene showed that it was
AB  - involved in phenotypic switching of a lipopolysaccharide epitope and that this variable
AB  - expression was associated with changes in the number of tetranucleotide repeats.  Mutation of
AB  - lgtC resulted in attenuated virulence of H., influenzae in an infant rate model of invasive
AB  - infection.  These data indicate the rapidity, economy, and completeness with which whole
AB  - genome sequences can be used to investigate the biology of pathogenic bacteria.
ER  -

TY  - JOUR
AU  - Hooper, C.
TI  - Molecular Evolution: Sampling the New Synthesis.
JO  - J. NIH Res.
PY  - 1993
SP  - 66
EP  - 70
VL  - 5
AB  - Contains a discussion of the evolution of restriction enzymes.
ER  -

TY  - JOUR
AU  - Hoose, S.A.
AU  - Kladde, M.P.
TI  - DNA methyltransferase probing of DNA-protein interactions.
JO  - Methods Mol. Biol.
PY  - 2006
SP  - 225
EP  - 244
VL  - 338
AB  - Effective methods of probing chromatin structure without disrupting DNA-protein interactions
AB  - and associations are necessary for creating an accurate picture of chromatin and its processes
AB  - in vivo.  Expression of cytidine-5 DNA methyltransferases (C5 DMTases) in Saccharomyces
AB  - cerevisiae provides a powerful noninvasive method for asaying relative DNA accessibility in
AB  - chromatin.  DNA MTases are occluded from protein-associated DNA based on the strength and span
AB  - of the DNA-protein interation.  Ectopic regulation of C5 DMTase expression systems allows for
AB  - minimal disruption of yeast physiology.  Methylated sites are detectd by bisulfite genomic
AB  - sequencing, which leads to a positive signal corresponding to modified cytidine residues.
AB  - High-resolution C5 DMTases with dinucleotide recognition specificity are shown to provide
AB  - sufficient coverage to map interactions spanning a relatively short distance.
ER  -

TY  - JOUR
AU  - Hooton, S.P.
AU  - Timms, A.R.
AU  - Moreton, J.
AU  - Wilson, R.
AU  - Connerton, I.F.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium U288.
JO  - Genome Announcements
PY  - 2013
SP  - e00467
EP  - e00413
VL  - 1
AB  - Salmonella enterica serovar Typhimurium U288 has firmly established itself within the United
AB  - Kingdom pig production industry. The prevalence of this highly
AB  - pathogenic multidrug-resistant serovar at such a critical point in the food chain
AB  - is therefore of great concern. To enhance our understanding of this
AB  - microorganism, whole-genome and plasmid sequencing was performed.
ER  -

TY  - JOUR
AU  - Hooven, T.A.
AU  - Randis, T.M.
AU  - Daugherty, S.C.
AU  - Narechania, A.
AU  - Planet, P.J.
AU  - Tettelin, H.
AU  - Ratner, A.J.
TI  - Complete Genome Sequence of Streptococcus agalactiae CNCTC 10/84, a Hypervirulent Sequence Type 26 Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e01338
EP  - e01314
VL  - 2
AB  - Streptococcus agalactiae (group B Streptococcus [GBS]) is a human pathogen with a propensity
AB  - to cause neonatal infections. We report the complete genome sequence
AB  - of GBS strain CNCTC 10/84, a hypervirulent clinical isolate frequently used to
AB  - study GBS pathogenesis. Comparative analysis of this sequence may shed light on
AB  - novel pathogenic mechanisms.
ER  -

TY  - JOUR
AU  - Hopkins, B.B.
AU  - Reich, N.O.
TI  - Simultaneous DNA binding, bending, and base flipping - Evidence for a novel M. EcoRI methyltransferase-DNA complex.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 37049
EP  - 37060
VL  - 279
AB  - We measured the kinetics of DNA bending by M.EcoRI using DNA labeled at both 5'-ends and
AB  - observed changes in fluorescence resonance energy
AB  - transfer. Although known to bend its cognate DNA site, energy transfer
AB  - is decreased upon enzyme binding. This unanticipated effect is shown to
AB  - be robust because we observe the identical decrease with different dye
AB  - pairs, when the dye pairs are placed on the respective 3'-ends, the
AB  - effect is cofactor- and protein-dependent, and the effect is observed
AB  - with duplexes ranging from 14 through 17 base pairs. The same labeled
AB  - DNA shows the anticipated increased energy transfer with EcoRV
AB  - endonuclease, which also bends this sequence, and no change in energy
AB  - transfer with EcoRI endonuclease, which leaves this sequence unbent. We
AB  - interpret these results as evidence for an increased end-to-end
AB  - distance resulting from M.EcoRI binding, mediated by a mechanism novel
AB  - for DNA methyltransferases, combining DNA bending and an overall
AB  - expansion of the DNA duplex. The M.EcoRI protein sequence is poorly
AB  - accommodated into well defined classes of DNA methyltransferases, both
AB  - at the level of individual motifs and overall alignment. Interestingly,
AB  - M.EcoRI has an intercalation motif observed in the FPG DNA glycosylase
AB  - family of repair enzymes. Enzyme-dependent changes in anisotropy and
AB  - fluorescence resonance energy transfer have similar rate constants,
AB  - which are similar to the previously determined rate constant for base
AB  - flipping; thus, the three processes are nearly coincidental. Similar
AB  - fluorescence resonance energy transfer experiments following
AB  - AdoMet-dependent catalysis show that the unbending transition
AB  - determines the steady state product release kinetics.
ER  -

TY  - JOUR
AU  - Horiuchi, K.
TI  - Studies on restriction endonucleases.
JO  - Tanpakushitsu Kakusan Koso
PY  - 1977
SP  - 981
EP  - 991
VL  - 22
ER  -

TY  - JOUR
AU  - Horiuchi, K.
AU  - Vovis, G.F.
AU  - Enea, V.
AU  - Zinder, N.D.
TI  - Cleavage map of bacteriophage f1: Location of the Escherichia coli B-specific modification sites.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 147
EP  - 165
VL  - 95
AB  - Replicative form DNA of bacteriophage f1 was cleaved into specific fragments by
AB  - two endonucleases isolated from Hemophilus aegyptius and an endonuclease
AB  - isolated fom H. influenzae.  The fragments were ordered so as to construct a
AB  - circular map of the phage f1 genome by: (1) digesting the isolated restriction
AB  - fragments with a second restriction enzyme; and (2) testing in a transfection
AB  - system for the ability of the fragments to rescue amber mutations contained on
AB  - single-stranded viral DNA that was hybridized to a particular fragment.  The
AB  - genome of bacteriophage f1 contains two SB sites, genetic sites which confer
AB  - upon a DNA molecule susceptibility to the restriction-modification system of
AB  - Escherichia coli B.  Each of these sites was located on a specific restriction
AB  - fragment by transfection experiments.  In vitro modification of replicative
AB  - form DNA of f1 and its SB mutants by endonuclease R. EcoB and the subsequent
AB  - cleavage of the DNA by the Hemophilus endonucleases showed that the B-specific
AB  - methylation occurs within at least 200 nucleotide pairs of the SB site.
ER  -

TY  - JOUR
AU  - Horiuchi, K.
AU  - Vovis, G.F.
AU  - Enea, V.
AU  - Zinder, N.D.
TI  - Cleavage mapping of the Escherichia coli B-specific modification sites of bacteriophage fl.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1975
SP  - 225
EP  - 225
VL  - 75
AB  - Replicative form DNA (RF) of bacteriophage fl was cleaved into specific
AB  - fragments by two endonucleases, R.HaeII and R.HaeIII, isolated from Hemophilus
AB  - aegyptius and an endonuclease R.HindII isolated from H. influenzae.  The
AB  - fragments were ordered so as to construct a circular map of the fl genome by:
AB  - 1) digesting the isolated restriction fragments with a second restriction
AB  - enzyme; and 2) testing in a transfection system for the ability of the
AB  - fragments to rescue amber mutations contained on single-strand viral DNA that
AB  - was hybridized to a particular fragment.  Both of two SB sites, genetic sites
AB  - which confer upon a DNA molecule susceptibility to the restriction-modification
AB  - system of E. coli B, of fl were located on specific restriction fragments by
AB  - transfection experiments.  In vitro modification of RF of fl and its SB mutants
AB  - and the subsequent cleavage of the DNA by the Hemophilus endonucleases showed
AB  - that the B-specific methylation occurs at, or very near, the SB site.
ER  -

TY  - JOUR
AU  - Horiuchi, K.
AU  - Vovis, G.F.
AU  - Zinder, N.D.
TI  - Effect of deoxyribonucleic acid length on the adenosine triphosphatase activity of Escherichia coli restriction endonuclease B.
JO  - J. Biol. Chem.
PY  - 1974
SP  - 543
EP  - 552
VL  - 249
AB  - Restriction endonuclease B possesses a DNA-dependent ATPase activity.  The ATP
AB  - hydrolysis can continue for hours after the DNA hydrolysis has stopped and is
AB  - due to a stable DNA-enzyme complex.  RF1 of bacteriophage f1 is much more
AB  - active than its full length linear form (RFIII) in stimulating the ATP
AB  - hydrolysis.  Experiments with lambda phage DNA sheared into various size
AB  - molecules indicate that the ATPase activity is a direct function of the
AB  - molecular weight of linear DNA in a range between 0.9 to 13 Mdaltons.  While
AB  - sonicated, unmodified lambda DNA molecules (0.5 Md) fail to stimulate the
AB  - ATPase activity, they do inhibit the intact DNA-stimulated ATP hydrolysis.  The
AB  - results can be interpreted as follows. (a) Endonuclease R-B recognizes DNA at
AB  - the SB sites; this recognition step is independent of DNA length.  (b) The
AB  - probability that a linear DNA molecule is cleaved by an enzyme molecule bound
AB  - to the DNA depends upon the length of the DNA: the greater the number of
AB  - nucleotide pairs the higher the probability of cleavage.  Circularization of a
AB  - small DNA duplex also increases the probability of cleavage.  One possible
AB  - explanation is that the enzyme travels along the DNA molecule before cleaving
AB  - the DNA.  If the enzyme reaches an end of the DNA molecule before cleavage
AB  - occurs, the enzyme molecule is inactivated. (c) After DNA hydrolysis has
AB  - occurred, the enzyme (or one of its components) remains on the DNA molecule and
AB  - causes the massive ATP hydrolysis.
ER  -

TY  - JOUR
AU  - Horiuchi, K.
AU  - Zinder, N.
TI  - Cleavage of bacteriophage f1 DNA by the restriction enzyme of Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3220
EP  - 3224
VL  - 69
AB  - We studied the cleavage of the replicative form DNA (RFI) of bacteriophage f1
AB  - and its SB mutants by purified restriction endonuclease of E. coli B.  The
AB  - results indicate that: (i) Circular replicative forms are broken once to yield
AB  - full-length linear molecules (RFIII).  Such linear molecules are less
AB  - susceptible than RFI to endonuclease R-B.  (ii) The genetic sites (SB sites)
AB  - that confer on the DNA susceptibility to B-restriction are not the actual sites
AB  - of cleavage.  The number of possible cleavage sites is larger than the number
AB  - of SB sites.  We conclude this because an RFIII molecule produced by
AB  - endonuclease R-B from RFI of a mutant that has only one SB site can be
AB  - circularized by denaturation and renaturation.  (iii) The SB site is not
AB  - modified when the DNA is cleaved, since an SB site can be used repeatedly by
AB  - endonuclease R-B; the RF III described in ii can be cleaved by the same enzyme
AB  - after denaturation and renaturation.
ER  -

TY  - JOUR
AU  - Horiuchi, K.
AU  - Zinder, N.D.
TI  - Site-specific cleavage of single-stranded DNA by a Hemophilus restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1975
SP  - 2555
EP  - 2558
VL  - 72
AB  - Single-stranded viral DNA of bacteriophage f1 is cleaved into specific
AB  - fragments by endo R.HaeIII, a restriction endonuclease isolated from Hemophilus
AB  - aegyptius.  The sites of the single strand cleavage correspond to those of the
AB  - double strand cleavage.  A single-stranded DNA fragment containing only one
AB  - HaeIII site is also cleaved by this enzyme.  This observation suggests that the
AB  - reaction of single-stranded DNA cleavage does not require the formation of a
AB  - symmetrical double-stranded structure that would result from the intramolecular
AB  - base-pairing between two different HaeIII sites.  Other restriction
AB  - endonucleases may also cleave single-stranded DNA.
ER  -

TY  - JOUR
AU  - Horn, F.
AU  - Schroeckh, V.
AU  - Netzker, T.
AU  - Guthke, R.
AU  - Brakhage, A.A.
AU  - Linde, J.
TI  - Draft Genome Sequence of Streptomyces iranensis.
JO  - Genome Announcements
PY  - 2014
SP  - e00616
EP  - e00614
VL  - 2
AB  - Streptomyces iranensis HM 35 has been shown to exhibit 72.7% DNA-DNA similarity to the
AB  - important drug rapamycin (sirolimus)-producing Streptomyces rapamycinicus
AB  - NRRL5491. Here, we report the genome sequence of HM 35, which represents a
AB  - partially overlapping repertoire of secondary metabolite gene clusters with S.
AB  - rapamycinicus, including the gene cluster for rapamycin biosynthesis.
ER  -

TY  - JOUR
AU  - Horn, G.
AU  - Taubeneck, U.
TI  - Comparative experiments with DNA restriction factors Escherichia coli and Shigella sonnei.
JO  - Z. Allg. Mikrobiol.
PY  - 1970
SP  - 103
EP  - 119
VL  - 10
AB  - None
ER  -

TY  - JOUR
AU  - Horn, H.
AU  - Hentschel, U.
AU  - Abdelmohsen, U.R.
TI  - Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism.
JO  - Genome Announcements
PY  - 2015
SP  - e01106
EP  - e01115
VL  - 3
AB  - Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora
AB  - sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated
AB  - from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters
AB  - indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings
AB  - demonstrated the chemical  richness of sponge-associated actinomycetes and the efficacy of
AB  - genome mining in  exploring the genomic potential of sponge-derived actinomycetes.
ER  -

TY  - JOUR
AU  - Horn, H.
AU  - Keller, A.
AU  - Hildebrandt, U.
AU  - Kampfer, P.
AU  - Riederer, M.
AU  - Hentschel, U.
TI  - Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 8
EP  - 8
VL  - 11
AB  - The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the
AB  - Arabidopsis thaliana phyllosphere. Here we describe the general physiological
AB  - features of this microorganism together with the draft genome sequence and
AB  - annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and
AB  - 70 RNA genes. To our knowledge, this is only the second reported genome from the
AB  - genus Williamsia and the first sequenced strain from the phyllosphere. The
AB  - presented genomic information is interpreted in the context of an adaptation to
AB  - the phyllosphere habitat.
ER  -

TY  - JOUR
AU  - Hornby, D.P.
TI  - DNA Methyltransferases (EC 2.1.1.72 and EC 2.1.1.73).
JO  - Methods Mol. Biol.
PY  - 1993
SP  - 201
EP  - 211
VL  - 16
AB  - DNA methyltransferases (Mtases) catalyze the transfer of the S-methyl group of
AB  - S-adenosylmethionine (SAM) to deoxycytosine (dC) or deoxyadenine (dA) bases within defined DNA
AB  - sequences. Individual enzymes are specific for one or the other base, and modify at the 6-NH2
AB  - of dA(EC 2.1.1.72) or at the N4 or 5-C position of dC (EC 2.1.1.73) depending on the
AB  - particular enzyme. The reaction is predominantly irreversible. Enzymes, such as
AB  - O6-methylguanine DNA Mtase, that participate in DNA repair processes are not discussed.
ER  -

TY  - JOUR
AU  - Hornby, D.P.
AU  - Bickle, T.A.
TI  - Characterization of EcoPI DNA adenine methylase.
JO  - Biochem. Soc. Trans.
PY  - 1987
SP  - 1039
EP  - 1039
VL  - 15
AB  - Three categories of restriction and modification systems have been documented in bacteria and
AB  - their phage.  Type I enzymes are complex multifunctional assemblies which catalyze DNA
AB  - methylation, DNA hydrolysis, ATP hydrolysis and DNA topoisomerization.  Type II restriction
AB  - and modification genes res and mod encode independent restriction endonuclease and DNA
AB  - methylase activities which both recognize a common DNA sequence motif.  The latter enzymes are
AB  - widely used in molecular cloning.  The most recent family to emerge is a functional hybrid
AB  - between the previous types.  Thus EcoPI, a type III enzyme produced by phage PI is a tetramer
AB  - of subunit stoichiometry (mod)2(res)2.  The methylase subunit recognizes and methylates the
AB  - sequence AGACC at the central adenine, while the endonuclease subunit hydrolyses the DNA
AB  - simultaneously some 25 base pairs downstream.  We are presently investigating the behavior of
AB  - the enzyme on gels in the presence and absence of oligonucleotide duplexes and co-factors to
AB  - elucidate the detailed mechanism of catalysis.
ER  -

TY  - JOUR
AU  - Hornby, D.P.
AU  - Ford, G.C.
TI  - Protein-mediated base flipping.
JO  - Curr. Opin. Biotechnol.
PY  - 1998
SP  - 354
EP  - 358
VL  - 9
AB  - Since the discovery that the DNA methyltransferase M.HhaI utilizes a base flipping mechanism
AB  - to expose its target cytosine during catalysis, this phenomenon has been observed in other
AB  - nucleic acid modifying enzymes.  The crystallographic analyses of such enzyme-DNA complexes
AB  - have revealed the molecular features of extrahelical base stabilization, but have been less
AB  - informative about the flipping process itself.
ER  -

TY  - JOUR
AU  - Hornby, D.P.
AU  - Muller, M.
AU  - Bickle, T.A.
TI  - High level expression of the EcoPI modification methylase gene and characterization of the gene product.
JO  - Gene
PY  - 1987
SP  - 239
EP  - 245
VL  - 54
AB  - We have cloned the gene coding for the EcoPI modification methylase in an
AB  - expression system based on the phage lambda pL promoter and the cI857-coded
AB  - thermoinducible repressor.  We have used this system to purify the enzyme on
AB  - the 20-30 mg scale and have examined some of its enzymatic properties.  The
AB  - enzyme is a tetramer of Mr 72000 subunits and is approximately 40%
AB  - alpha-helical.  Experiments with the methyl donor, S-adenosyl methionine,
AB  - radioactively labelled in different positions indicate that a methyl group is
AB  - transferred to the enzyme during the reaction in what is most likely a covalent
AB  - bond.
ER  -

TY  - JOUR
AU  - Hornby, D.P.
AU  - Whitmarsh, A.
AU  - Pinarbasi, H.
AU  - Kelly, S.M.
AU  - Price, N.C.
AU  - Shore, P.
AU  - Baldwin, G.S.
AU  - Waltho, J.
TI  - The DNA recognition subunit of a DNA methyltransferase is predominantly a molten globule in the absence of DNA.
JO  - FEBS Lett.
PY  - 1994
SP  - 57
EP  - 60
VL  - 355
AB  - Enzyme-catalysed DNA methylation provides an opportunity for the modulation of protein-DNA
AB  - recognition in biological systems. Recently we have demonstrated that the smaller of the two
AB  - subunits of the heterodimeric, cytosine-specific DNA methyltransferase, M.AquI, is largely
AB  - responsible for sequence-specific DNA recognition. Here we present evidence from a series of
AB  - NMR, fluorescence and circular dichroism spectroscopy experiments that the DNA binding subunit
AB  - of M.AquI has the characteristics of a molten globule in the absence of the catalytic
AB  - machinery. In this metastable state this subunit retains its ability to bind DNA in a
AB  - sequence-specific manner. We believe this finding offers an insight into the structural
AB  - flexibility which underpins the mechanism of action of these enzymes, and may provide a
AB  - possible biological role for molten globules in protein function.
ER  -

TY  - JOUR
AU  - Horst, J.-P.
AU  - Fritz, H.-J.
TI  - Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF.
JO  - EMBO J.
PY  - 1996
SP  - 5459
EP  - 5469
VL  - 15
AB  - Spontaneous hydrolytic deamination of DNA 5-methyl-cytosine residues gives rise to T/G
AB  - mismatches which are pre-mutagenic lesions requiring DNA repair.  For fundamental reasons, the
AB  - significance of this and other processes lowering genetic fidelity must be accentuated at
AB  - elevated temperatures, making thermophilic organisms attractive objects for studying how cells
AB  - cope with thermal noise threatening the integrity of their genetic information.  Gene mig of
AB  - Methanobacterium thermoautotrophicum THF, an anaerobic archaeon with an optimal growth
AB  - temperature of 65oC, was isolated and is product (Mig.Mth; EC3.2.2-) shown to be a
AB  - T/G-selective DNA thymine N-glycosylase with the properties required for counteracting the
AB  - mutagenic effect of hydrolytic 5-meC deamination.  The enzyme acts on T/G and U/G oppositions
AB  - with similar efficiency; G/G, A/G, T/C and U/C are minor substrates; no other opposition of
AB  - common nucleobases is attacked and no removal of U from single-stranded DNA is observed.
AB  - Substrate preferences are modulated by sequence context.  Together with the results presented
AB  - here, one example of an enzyme directed against the hydrolytic deamination damage of 5-meC is
AB  - known from each of the three phylogenetic kingdoms; entry into the repair pathway is
AB  - glycosylytic in the eukaryotic and the archaeal case, whereas the eubacterial repair starts
AB  - with an endonucleolytic DNA incision.
ER  -

TY  - JOUR
AU  - Horta-Valerdi, G.
AU  - Sanchez-Alonso, M.P.
AU  - Perez-Marquez, V.M.
AU  - Negrete-Abascal, E.
AU  - Vaca-Pacheco, S.
AU  - Hernandez-Gonzalez, I.
AU  - Gomez-Lunar, Z.
AU  - Olmedo-Alvarez, G.
AU  - Vazquez-Cruz, C.
TI  - The Genome Sequence of Avibacterium paragallinarum Strain CL Has a Large Repertoire of Insertion Sequence Elements.
JO  - Genome Announcements
PY  - 2017
SP  - e00152
EP  - e00117
VL  - 5
AB  - The draft genome sequence of Avibacterium paragallinarum strain CL serovar C is reported here.
AB  - The genome comprises 154 contigs corresponding to 2.4 Mb with 41%
AB  - G+C content and many insertion sequence (IS) elements, a characteristic not
AB  - previously reported in A. paragallinarum.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Restriction endonucleases: Structure of the conserved catalytic core and the role of metal ions in DNA cleavage.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 361
EP  - 392
VL  - 14
AB  - Type II restriction endonucleases are a fascinating group of proteins.  With the REBase
AB  - database currently listing ~3500 Type II REases having nearly 240 distinct DNA sequence
AB  - specificities, they constitute one of the larger known families of enzymes.  These
AB  - DNA-cleaving enzymes combine very high catalytic efficiencies (kcat/kuncat=~1016) with
AB  - exquisite DNA sequence selectivity.  Restriction enzymes that are classified Type II cleave
AB  - specifically within or close to their recognition sites, and do not require ATP hydrolysis for
AB  - their nucleolytic activity.  DNA cleavage by these enzymes can result in DNA with either 5'
AB  - or 3' overhangs or blunt ends.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Bonventre, J.
AU  - Cheng, X.
TI  - How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
JO  - Biol. Chem.
PY  - 1998
SP  - 451
EP  - 458
VL  - 379
AB  - In restriction-modification systems, cleavage of substrate sites in cellular DNA by the
AB  - restriction endonuclease is prevented by the action of a cognate methyltransferase that acts
AB  - on the same substrate sites.  The PvuII restriction endonuclease has been structurally
AB  - characterized in a complex with substrate DNA and as an apoenzyme.  We report here a
AB  - structure, determined to 1.9 A resolution by crystallography, of a complex between R.PvuII and
AB  - iodinated DNA.  The presence of an iodine at the 5-carbon of the methylatable cytosine results
AB  - in the following changes in the protein: His84 moved away from the modified base; this
AB  - movement was amplified in His85 and disrupts an intersubunit hydrogen bond; and the base
AB  - modification disturbs the distribution of water molecules that associate with these histidine
AB  - residues and the area of the scissile bond.  Considering these observations, hypotheses are
AB  - given as to why a similar oligonucleotide, where a methyl group resides on the 5-carbon of the
AB  - methylatable cytosine, is slowly cleaved by R.PvuII.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Borgaro, J.G.
AU  - Griggs, R.M.
AU  - Quimby, A.
AU  - Guan, S.
AU  - Zhang, X.
AU  - Wilson, G.G.
AU  - Zheng, Y.
AU  - Zhu, Z.
AU  - Cheng, X.
TI  - Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 7947
EP  - 7959
VL  - 42
AB  - AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases,
AB  - cleaves deoxyribonucleic acid (DNA) containing
AB  - 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA
AB  - containing unmodified cytosine. AbaSI has been used as a tool for mapping the
AB  - genomic locations of 5hmC, an important epigenetic modification in the DNA of
AB  - higher organisms. Here we report the crystal structures of AbaSI in the presence
AB  - and absence of DNA. These structures provide considerable, although incomplete,
AB  - insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in
AB  - solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI
AB  - subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single
AB  - catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal
AB  - helices mediate most of the homodimer interface. Dimerization brings together the
AB  - two catalytic sites required for double-strand cleavage, and separates the 5hmC
AB  - binding-domains by approximately 70 A, consistent with the known activity of
AB  - AbaSI which cleaves DNA optimally between symmetrically modified cytosines
AB  - approximately 22 bp apart. The eukaryotic SET and RING-associated (SRA) domains
AB  - bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG
AB  - sequence. They make contacts in both the major and minor DNA grooves, and flip
AB  - the modified cytosine out of the helix into a conserved binding pocket. In
AB  - contrast, the SRA-like domain of AbaSI, which has no sequence specificity,
AB  - contacts only the minor DNA groove, and in our current structures the 5hmC
AB  - remains intra-helical. A conserved, binding pocket is nevertheless present in
AB  - this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely,
AB  - therefore, that base-flipping is part of the recognition and cleavage mechanism
AB  - of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior
AB  - to actual recognition.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Cheng, X.
TI  - PvuII endonuclease contains two calcium ions in active sites.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 1049
EP  - 1056
VL  - 300
AB  - Restriction endonucleases differ in their use of metal cofactors despite having remarkably
AB  - similar folds for their catalytic regions. To explore this, we have characterized the
AB  - interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The
AB  - structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex,
AB  - determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal
AB  - mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all
AB  - structurally examined endonucleases, while the second position is similar to that of EcoRV but
AB  - is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike
AB  - that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen
AB  - leaving group. However, the interactions between the DNA scissile phosphate and the metals,
AB  - the first metal and the attacking water, and the attacking water and DNA are the same in PvuII
AB  - as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed
AB  - three-metal or the two-metal models of EcoRV.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Liebert, K.
AU  - Bekes, M.
AU  - Jeltsch, A.
AU  - Cheng, X.D.
TI  - Structure and Substrate Recognition of the Escherichia coli DNA Adenine Methyltransferase.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 559
EP  - 570
VL  - 358
AB  - The structure of the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase in complex with
AB  - cognate DNA was determined at 1.89 (A) over circle resolution in the presence of
AB  - S-adenosyl-L-homocysteine. DNA recognition and the dynamics of base-flipping were studied by
AB  - site-directed mutagenesis, DNA methylation kinetics and fluorescence stopped-flow experiments.
AB  - Our data illustrate the mechanism of coupling of DNA recognition and base-flipping. Contacts
AB  - to the non-target strand in the second (3') half of the GATC site are established by R124 to
AB  - the fourth base-pair, and by L122 and P134 to the third base-pair. The aromatic ring of Y119
AB  - intercalates into the DNA between the second and third base-pairs, which is essential for
AB  - base-flipping to occur. Compared to previous published structures of bacteriophage T4 Dam,
AB  - three major new observations are made in E. coli Dam. (1) The first Gua is recognized by K9,
AB  - removal of which abrogates the first base-pair recognition. (2) The flipped target Ade binds
AB  - to the surface of EcoDam in the absence of S-adenoSyl-L-methionine, which illustrates a
AB  - possible intermediate in the base-flipping pathway. (3) The orphaned Thy residue displays
AB  - structural flexibility by adopting an extrahelical or intrahelical position where it is in
AB  - contact to N120.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Liebert, K.
AU  - Hattman, S.
AU  - Jeltsch, A.
AU  - Cheng, X.
TI  - Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of Dam methyltransferase.
JO  - Cell
PY  - 2005
SP  - 349
EP  - 361
VL  - 121
AB  - DNA methyltransferases methylate target bases within specific nucleotide sequences. Three
AB  - structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary
AB  - complexes with partially and fully specific DNA and a methyl-donor analog. We also report the
AB  - effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam),
AB  - altering residues corresponding to those involved in specific interaction with the canonical
AB  - GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions:
AB  - discriminatory contacts, which stabilize the transition state and accelerate methylation of
AB  - the cognate site, and antidiscriminatory contacts, which do not significantly affect
AB  - methylation of the cognate site but disfavor activity at noncognate sites. These structures
AB  - illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction,
AB  - suggesting that there is a temporal order for formation of specific contacts.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Mabuchi, M.Y.
AU  - Cohen-Karni, D.
AU  - Zhang, X.
AU  - Griggs, R.M.
AU  - Samaranayake, M.
AU  - Roberts, R.J.
AU  - Zheng, Y.
AU  - Cheng, X.
TI  - Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 9763
EP  - 9773
VL  - 40
AB  - The MspJI modification-dependent restriction endonuclease recognizes 5-methylcytosine or
AB  - 5-hydroxymethylcytosine in the context of CNN(G/A) and cleaves both strands at fixed distances
AB  - (N(12)/N(16)) away from the modified cytosine at the 3'-side. We determined the crystal
AB  - structure of MspJI of Mycobacterium sp. JLS at 2.05-A resolution. Each protein monomer harbors
AB  - two domains: an N-terminal DNA-binding domain and a C-terminal endonuclease. The N-terminal
AB  - domain is structurally similar to that of the eukaryotic SET and RING-associated domain, which
AB  - is known to bind to a hemi-methylated CpG dinucleotide. Four protein monomers are found in the
AB  - crystallographic asymmetric unit. Analytical gel-filtration and ultracentrifugation
AB  - measurements confirm that the protein exists as a tetramer in solution. Two monomers form a
AB  - back-to-back dimer mediated by their C-terminal endonuclease domains. Two back-to-back dimers
AB  - interact to generate a tetramer with two double-stranded DNA cleavage modules. Each cleavage
AB  - module contains two active sites facing each other, enabling double-strand DNA cuts.
AB  - Biochemical, mutagenesis and structural characterization suggest three different monomers of
AB  - the tetramer may be involved respectively in binding the modified cytosine, making the first
AB  - proximal N(12) cleavage in the same strand and then the second distal N(16) cleavage in the
AB  - opposite strand. Both cleavage events require binding of at least a second recognition site
AB  - either in cis or in trans.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Nastri, H.G.
AU  - Riggs, P.D.
AU  - Cheng, X.
TI  - Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 1491
EP  - 1504
VL  - 284
AB  - The PvuII restriction endonuclease is a homodimer that recognizes and cleaves the DNA sequence
AB  - 5'-CAGCTG-3' in double-stranded DNA, and the structure of this enzyme has been reported.  In
AB  - the wild-type enzyme, Asp34 interacts with the internal guanine of the recognition sequence on
AB  - the minor groove side.  The Asp34 codon was altered to specify Gly (D34G), and in vitro
AB  - studies have revealed that the D34G protein has lost binding specificity for the central G.C
AB  - base-pairs, and that it cuts the canonical sequence with 10^-4-fold reduced activity as
AB  - compared to the wild-type enzyme.  We have now determined the structure at 1.59 angstroms
AB  - resolution of the D34G PvuII endonuclease complexed with a 12 bp duplex deoxyoligonucleotide
AB  - containing the cognate sequence.  The D34G alteration results in several structural changes
AB  - relative to wild-type protein/DNA complexes.  First, the sugar moiety of the internal guanine
AB  - changes from a C2'-endo to C3'-endo pucker while that of the 3' guanine changes from
AB  - C3'-endo to C2'-endo pucker.  Second, the axial rise between the internal G.C base-pairs is
AB  - reduced while that between the G.C and flanking base-pairs is expanded.  Third, two distinct
AB  - monomeric active sites are observed that we refer to as being "primed" and "unprimed" for
AB  - phosphodiester bond cleavage.  The primed and unprimed sites differ in the conformation of the
AB  - Asp58 side-chain, and in the absence from unprimed sites of four networked water molecules.
AB  - These water molecules, present in the primed site, have been implicated in the catalytic
AB  - mechanism of this and other endonucleases; some of them can be replaced by the Mg2+ necessary
AB  - for cleavage.  Taken together, these structural changes imply that the Asp34 side-chains from
AB  - the two subunits maintain a distinct conformation of its DNA substrate, properly situating the
AB  - target backbone phosphates and indirectly manipulating the active sites.  This provides some
AB  - insight into how recognition of the specific DNA sequence is linked to catalysis by the highly
AB  - specific restriction endonucleases, and reveals one way in which the structural conformation
AB  - of the DNA is modulated coordinately with that of the PvuII protein.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Nugent, R.L.
AU  - Li, A.
AU  - Mabuchi, M.Y.
AU  - Fomenkov, A.
AU  - Cohen-Karni, D.
AU  - Griggs, R.M.
AU  - Zhang, X.
AU  - Wilson, G.G.
AU  - Zheng, Y.
AU  - Xu, S.-Y.
AU  - Cheng, X.
TI  - Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.
JO  - Sci. Rep.
PY  - 2014
SP  - 9
EP  - 9
VL  - 4
AB  - The modification-dependent restriction endonuclease AspBHI recognizes 5-methylcytosine (5mC)
AB  - in the double-strand DNA sequence context of (C/T)(C/G)(5mC) N(C/G) (N = any nucleotide) and
AB  - cleaves the two strands a fixed distance (N-12/N-16) 3' to the modified cytosine. We
AB  - determined the crystal structure of the homo-tetrameric AspBHI. Each subunit of the protein
AB  - comprises two domains: an N-terminal DNA-recognition domain and a C-terminal DNA cleavage
AB  - domain. The N-terminal domain is structurally similar to the eukaryotic SET and
AB  - RING-associated (SRA) domain, which is known to bind to a hemi-methylated CpG dinucleotide.
AB  - The C-terminal domain is structurally similar to classic Type II restriction enzymes and
AB  - contains the endonuclease catalytic-site motif of DX(20)EAK. To understand how specific amino
AB  - acids affect AspBHI recognition preference, we generated a homology model of the AspBHI-DNA
AB  - complex, and probed the importance of individual amino acids by mutagenesis. Ser41 and Arg42
AB  - are predicted to be located in the DNA minor groove 5' to the modified cytosine. Substitution
AB  - of Ser41 with alanine (S41A) and cysteine (S41C) resulted in mutants with altered cleavage
AB  - activity. All 19 Arg42 variants resulted in loss of endonuclease activity.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Ratner, G.
AU  - Banavali, N.K.
AU  - Huang, N.
AU  - Choi, Y.
AU  - Maier, M.A.
AU  - Marquez, V.E.
AU  - MacKerell, A.D. Jr.
AU  - Cheng, X.
TI  - Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3877
EP  - 3886
VL  - 32
AB  - Rotation of a DNA or RNA nucleotide out of the double helix and
AB  - into a protein pocket ('base flipping') is a mechanistic feature common to
AB  - some DNA/RNA-binding proteins. Here, we report the structure of HhaI
AB  - methyltransferase in complex with DNA containing a south-constrained abasic
AB  - carbocyclic sugar at the target site in the presence of the methyl donor
AB  - byproduct AdoHcy. Unexpectedly, the locked south pseudosugar appears to be
AB  - trapped in the middle of the flipping pathway via the DNA major groove,
AB  - held in place primarily through Van der Waals contacts with a set of
AB  - invariant amino acids. Molecular dynamics simulations indicate that the
AB  - structural stabilization observed with the south-constrained pseudosugar
AB  - will not occur with a north-constrained pseudosugar, which explains its
AB  - lowered binding affinity. Moreover, comparison of structural transitions of
AB  - the sugar and phosphodiester backbone observed during computational studies
AB  - of base flipping in the M.HhaIM-DNA-AdoHcy ternary  complex indicate that the
AB  - south-constrained pseudosugar induces a conformation on the phosphodiester
AB  - backbone that corresponds to that of a discrete intermediate of the
AB  - base-flipping pathway. As previous crystal structures of M.HhaI ternary
AB  - complex with DNA displayed the flipped sugar moiety in the antipodal north
AB  - conformation, we suggest that conversion of the sugar pucker from south to
AB  - north beyond the middle of the pathway is an essential part of the
AB  - mechanism through which flipping must proceed to reach its final
AB  - destination. We also discuss the possibility of the south-constrained
AB  - pseudosugar mimicking a transition state in the phosphodiester and sugar
AB  - moieties that occurs during DNA base flipping in the presence of M.HhaI.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Wang, H.
AU  - Mabuchi, M.Y.
AU  - Zhang, X.
AU  - Roberts, R.J.
AU  - Zheng, Y.
AU  - Wilson, G.G.
AU  - Cheng, X.
TI  - Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 12092
EP  - 12101
VL  - 42
AB  - MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine
AB  - (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A
AB  - and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the
AB  - crystal structure of MspJI without DNA and proposed how it might recognize this sequence and
AB  - catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide
AB  - containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the
AB  - modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected
AB  - the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with
AB  - the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this
AB  - organization, however. We found that each DNA molecule interacted with two adjacent tetramers,
AB  - binding one specifically and the other non-specifically. The latter interaction, which
AB  - prevented cleavage-site engagement, also involved base flipping and might represent the
AB  - sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA
AB  - molecules are recognized and cleaved by different subunits. Such interchange of function might
AB  - explain how other complex multimeric restriction enzymes act.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Zhang, X.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent  transcriptional repression.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 4296
EP  - 4308
VL  - 43
AB  - DNA adenine methyltransferase (Dam) is widespread and conserved among the
AB  - gamma-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse
AB  - bacterial cell functions, including gene expression, mismatch repair and
AB  - chromosome replication. Dam also controls virulence in many pathogenic
AB  - Gram-negative bacteria. An unexplained and perplexing observation about
AB  - Escherichia coli Dam (EcoDam) is that there is no obvious relationship between
AB  - the genes that are transcriptionally responsive to Dam and the promoter-proximal
AB  - presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a
AB  - 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a
AB  - non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC
AB  - (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some
AB  - Dam-regulated promoters, including the Pap operon which specifies
AB  - pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC
AB  - sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that
AB  - Dam, in addition to being responsible for GATC methylation, could also function
AB  - as a methylation-independent transcriptional repressor.
ER  -

TY  - JOUR
AU  - Horton, J.R.
AU  - Zhang, X.
AU  - Maunus, R.
AU  - Yang, Z.
AU  - Wilson, G.G.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 939
EP  - 948
VL  - 34
AB  - HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in
AB  - DNA. We report three structures of HinP1I-DNA
AB  - complexes: in the presence of Ca(2+) (pre-reactive complex), in the
AB  - absence of metal ion (binary complex) and in the presence of Mg(2+)
AB  - (post-reactive complex). HinP1I forms a back-to-back dimer with two active
AB  - sites and two DNA duplexes bound on the outer surfaces of the dimer facing
AB  - away from each other. The 10 bp DNA duplexes undergo protein-induced
AB  - distortions exhibiting features of A-, B- and Z-conformations: bending on
AB  - one side (by intercalation of a phenylalanine side chain into the major
AB  - groove), base flipping on the other side of the recognition site (by
AB  - expanding the step rise distance of the local base pair to Z-form) and a
AB  - local A-form conformation between the two central C:G base pairs of the
AB  - recognition site (by binding of the N-terminal helix in the minor groove).
AB  - In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are
AB  - found in the active site. The enzyme appears to cleave DNA sequentially,
AB  - hydrolyzing first one DNA strand, as seen in the post-reactive complex in
AB  - the crystalline state, and then the other, as supported by the observation
AB  - that, in solution, a nicked DNA intermediate accumulates before
AB  - linearization.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Connolly, B.A.
AU  - Perona, J.J.
TI  - Inhibition of EcoRV endonuclease by deoxyribo-3'-S-phosphorothiolates: A high-resolution X-ray crystallographic study.
JO  - J. Am. Chem. Soc.
PY  - 2000
SP  - 3314
EP  - 3324
VL  - 122
AB  - Three high-resolution structures of the restriction endonuclease EcoRV bound to a duplex DNA
AB  - substrate analogue with deoxyribo-3'-S-phosphorothiolate linkages at both scissile phosphates
AB  - are presented.  In each of these structures cocrystallized with Mg2+, Mn2+, or Ca2+ ions, the
AB  - nonesterified pro-S oxygen of the scissile phosphate no longer directly ligates a divalent
AB  - cation, as is observed for the unmodified complex.  Instead, one metal ion in all three
AB  - structures is shifted toward the adjacent 3'-phosphate of the DNA, to occupy a position
AB  - nearly identical to that previously observed in an EcoRV T93A/DNA/Ca2+ complex (N.C. Horton et
AB  - al., Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 13489).  A second divalent metal ion in each
AB  - structure bridges the carboxylate groups of Asp74 and Glu45 (74/45 site), as also seen in both
AB  - wild-type and T93A cocrystals.  The uncleaved 3'-S-phosphorothiolate DNAs in these complexes
AB  - are only slightly distorted from the conformation of the unmodified duplex.  Kinetic
AB  - measurements show that the rate of the chemical step for analogue cleavage is severely reduced
AB  - for each of the active metals Mg2+, Mn2+, and Co2+, and that the thiophilic Mn2+, Cd2+, and
AB  - Zn2+ cations do not provide a measurable reconstitution of activity.  The inability of
AB  - thiophilic metals to improve activity is consistent with models for catalysis derived from
AB  - previous crystal structures, which indicate that ligation of a metal ion to the 3'-oxygen is
AB  - mediated through an inner-sphere water molecule rather than by direct interaction.  The
AB  - structures suggest that 3'-S-phosphorothiolate analogues resist cleavage because the bridging
AB  - sulfur excludes inner-sphere ligation of divalent metal ions to any position on the scissile
AB  - phosphate.  This distinguishes the inhibitory mechanism in EcoRV from that operative in the
AB  - 3'-5' exonuclease active site of DNA polymerase I (C.A. Brautigam et al., Biochemistry,
AB  - 1999, 38, 696), and likely as well from other enzymes which also catalyze phosphoryl transfer
AB  - via direct metal ligation to the 3'-oxygen leaving group.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Dorner, L.F.
AU  - Perona, J.J.
TI  - Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
JO  - Nat. Struct. Biol.
PY  - 2002
SP  - 42
EP  - 47
VL  - 9
AB  - The crystal structure of the HincII restriction endonuclease-DNA complex shows that degenerate
AB  - specificity for blunt-ended cleavage at GTPyPuAC sequences arises from indirect readout of
AB  - conformational preferences at the center pyrimidine-purine step. Protein-induced distortion of
AB  - the DNA is accomplished by intercalation of glutamine side chains into the major groove on
AB  - either side of the recognition site, generating bending by either tilt or roll at three
AB  - distinct loci. The intercalated side chains propagate a concerted shift of all six target-site
AB  - base pairs toward the minor groove, producing an unusual cross-strand purine stacking at the
AB  - center pyrimidine-purine step. Comparison of the HincII and EcoRV cocrystal structures
AB  - suggests that sequence-dependent differences in base-stacking free energies are a crucial
AB  - underlying factor mediating protein recognition by indirect readout.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Dorner, L.F.
AU  - Schildkraut, I.
AU  - Perona, J.J.
TI  - Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 1999
SP  - 1943
EP  - 1945
VL  - 55
AB  - Crystals of the 60 kDa dimeric HincII restriction enzyme bound to a 12 base-pair
AB  - dyad-symmetric duplex DNA carrying the specific 5'-GTCGAC recognition site have been
AB  - obtained. Crystals grew by hanging-drop vapor diffusion from solutions containing polyethylene
AB  - glycol 4000 as precipitating agent. The rod-shaped crystals belong to space group I222 (or
AB  - I2(1)2(1)2(1)), with unit-cell dimensions a = 66.9, b = 176.7, c = 256.0 A. There are most
AB  - likely to be two dimeric complexes in the asymmetric unit. A complete native data set has been
AB  - collected from a high-energy synchrotron source to a resolution of 2.5 A at 100 K, with an
AB  - R(merge) of 4.8%.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Newberry, K.J.
AU  - Perona, J.J.
TI  - Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 13489
EP  - 13494
VL  - 95
AB  - The 2.15-Angstrom resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed
AB  - with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites.  One of
AB  - these metals is ligated through an inner-sphere water molecule to the phosphate group located
AB  - 3' to the scissile phosphate.  A second inner-sphere water on this metal is positioned
AB  - approximately in-line for attack on the scissile phosphate.  This structure corroborates the
AB  - observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified
AB  - without severe loss of catalytic efficiency.  The structural equivalence of key groups,
AB  - conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that
AB  - ligation of a catalytic divalent metal ion to this phosphate may occur in many type II
AB  - restriction enzymes.  Together with previous  cocrystal structures, these data allow
AB  - construction of a detailed model for the pretransition state configuration in EcoRV.  This
AB  - model features three divalent metal ions per active site and invokes assistance in the
AB  - bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion
AB  - nucleophile.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Otey, C.
AU  - Lusetti, S.
AU  - Sam, M.D.
AU  - Kohn, J.
AU  - Martin, A.M.
AU  - Ananthnarayan, V.
AU  - Perona, J.J.
TI  - Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.
JO  - Biochemistry
PY  - 2002
SP  - 10754
EP  - 10763
VL  - 41
AB  - Mutational analysis of amino acids at the periphery of the EcoRV endonuclease active site
AB  - suggests that moderate-range electrostatic effects play a significant role in modulating the
AB  - efficiency of phosphoryl transfer. Asp36 and Lys38 located on minor-groove binding surface
AB  - loops approach within 7-9 angstroms of the scissile phosphates of the DNA. While the rates of
AB  - single-site mutations removing the carboxylate or amine moieties at these positions are
AB  - decreased 10^3-10^5-fold compared to that of wild-type EcoRV, we find that double mutants
AB  - which rebalance the charge improve catalysis by up to 500-fold. Mutational analysis also
AB  - suggests that catalytic efficiency is influenced by Lys173, which is buried at the base of a
AB  - deep depression penetrating from a distal surface of the enzyme. The Lys173 amine group lies
AB  - just 6 angstroms from the amine group of the conserved essential Lys92 side chain in the
AB  - active site. Kinetic and crystallographic analyses of the EcoRV E45A mutant enzyme further
AB  - show that the Glu45 carboxylate group facilitates an extensive set of conformational
AB  - transitions which occur upon DNA binding. The crystal structure of E45A bound to DNA and Mn2+
AB  - ions reveals significant conformational alterations in a small alpha-helical portion of the
AB  - dimer interface located adjacent to the DNA minor groove. This leads to a tertiary
AB  - reorientation of the two monomers as well as shifting of the key major-groove binding
AB  - recognition loops. Because the Glu45 side chain does not appear to play a direct structural
AB  - role in maintaining the active site, these rearrangements may instead originate in an altered
AB  - electrostatic potential caused by removal of the negative charge. A Mn2+ binding site on the
AB  - scissile phosphate is also disrupted in the E45A structure such that inner-sphere metal
AB  - interactions made by the scissile DNA phosphate and conserved Asp90 carboxylate are each
AB  - replaced with water molecules in the mutant. These findings argue against a proposed role for
AB  - Asp36 as the general base in EcoRV catalysis, and reveal that the induced-fit conformational
AB  - changes necessary for active site assembly and metal binding are significantly modulated by
AB  - the electrostatic potential in this region.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Perona, J.J.
TI  - Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexes with d(AAAGAT) + d(ATCTT).
JO  - J. Mol. Biol.
PY  - 1998
SP  - 779
EP  - 787
VL  - 277
AB  - The crystal structure of EcoRV endonuclease has been determined at 2.1 A resolution complexed
AB  - to two five-base-pair DNA duplexes each containing the cognate recognition half-site.  The
AB  - highly localized 50o bend into the major groove seen at the center TA-step of the continuous
AB  - GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates.
AB  - Thus, this crystal structure provides evidence that covalent constraints associated with a
AB  - continuous target site are not essential to enzyme-induced DNA bending, even when these
AB  - constraints are removed directly at the locus of the bend.  The scissile phosphates are also
AB  - absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a
AB  - straight B-like conformation.  We conclude that DNA bending by EcoRV is governed only by the
AB  - sequence and is not influenced by the continuity of the phosphodiester backbone.  Together
AB  - with other data showing that cleavable non-cognate sites different by one or two base-pairs
AB  - from GATATC, but does not bend non-specific sites that are less similar.  Structural and
AB  - thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is
AB  - likely to play an important role in determining the specificity of EcoRV.  This differential
AB  - cost is manifested at the binding step for bent non-cognate sequences and at the catalytic
AB  - step for unbent non-specific sequences.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Perona, J.J.
TI  - Making the most of metal ions.
JO  - Nat. Struct. Biol.
PY  - 2001
SP  - 290
EP  - 293
VL  - 8
AB  - Crystal structures of the homing endonuclease I-Crel bound to substrate DNA and divalent
AB  - metals show that one metal ion is shared between the
AB  - two active sites of the enzyme. This arrangement appears uniquely
AB  - suited to the formation of double-stranded DNA breaks via a concerted
AB  - reaction.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Perona, J.J.
TI  - DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites.
JO  - Biochemistry
PY  - 2004
SP  - 6841
EP  - 6857
VL  - 43
AB  - Four crystal structures of EcoRV endonuclease mutants K92A and K38A provide new insight into
AB  - the mechanism of DNA bending and the structural basis for metal-dependent phosphodiester bond
AB  - cleavage. The removal of a key active site positive charge in the uncleaved K92A-DNA-M(2+)
AB  - substrate complex results in binding of a sodium ion in the position of the amine nitrogen,
AB  - suggesting a key role for a positive charge at this position in stabilizing the sharp DNA bend
AB  - prior to cleavage. By contrast, two structures of K38A cocrystallized with DNA and Mn(2+) ions
AB  - in different lattice environments reveal cleaved product complexes featuring a common, novel
AB  - conformation of the scissile phosphate group as compared to all previous EcoRV structures. In
AB  - these structures, the released 5'-phosphate and 3'-OH groups remain in close juxtaposition
AB  - with each other and with two Mn(2+) ions that bridge the conserved active site carboxylates.
AB  - The scissile phosphates are found midway between their positions in the prereactive substrate
AB  - and postreactive product complexes of the wild-type enzyme. Mn(2+) ions occupy two of the
AB  - three sites previously described in the prereactive complexes and are plausibly positioned to
AB  - generate the nucleophilic hydroxide ion, to compensate for the incipient additional negative
AB  - charge in the transition state, and to ionize a second water for protonation of the
AB  - 3'-oxyanion. Reconciliation of these findings with earlier X-ray and fluorescence studies
AB  - suggests a novel mechanism in which a single initially bound metal ion in a third distinct
AB  - site undergoes a shift in position together with movement of the scissile phosphate deeper
AB  - into the active site cleft. This reconfigures the local environment to permit binding of the
AB  - second metal ion followed by movement toward the pentacovalent transition state. The new
AB  - mechanism suggested here embodies key features of previously proposed two- and three-metal
AB  - catalytic models, and offers a view of the stereochemical pathway that integrates much of the
AB  - copious structural and functional data that are available from exhaustive studies in many
AB  - laboratories.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Perona, J.J.
TI  - Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 21721
EP  - 21729
VL  - 273
AB  - The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal
AB  - lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined,
AB  - shows novel base recognition in the major groove of the DNA flanking the GATATC target site.
AB  - Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of
AB  - flanking cytosines.  Steric exclusion of water molecule-binding sites by the 5'methyl group
AB  - of thymine drives the adoption of alternative water-mediated contacts with AT versus GC
AB  - flanks.  This structure provides a rare example of structural adaptability in the recognition
AB  - of different DNA sequences by a protein and suggests preferred strategies for the expansion of
AB  - target site specificity by EcoRV.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Perona, J.J.
TI  - Crystallographic snapshots along a protein-induced DNA-bending pathway.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 5729
EP  - 5734
VL  - 97
AB  - Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a
AB  - large variation in DNA-bending angles is sampled in the ground state binary complex. Together
AB  - with previous structures, these data reveal a contiguous series of protein conformational
AB  - states delineating a specific trajectory for the induced-fit pathway. Rotation of the
AB  - DNA-binding domains, together with movements of two symmetry-related helices binding in the
AB  - minor groove, causes base unstacking at a key base-pair step and propagates structural changes
AB  - that assemble the active sites. These structures suggest a complex mechanism for DNA bending
AB  - that depends on forces generated by interacting protein segments, and on selective
AB  - neutralization of phosphate charges along the inner face of the bent double helix.
ER  -

TY  - JOUR
AU  - Horton, N.C.
AU  - Sam, M.D.
AU  - Connolly, B.A.
AU  - Perona, J.J.
TI  - Structural mechanism of phosphoryl transfer in EcoRV restriction endonuclease.
JO  - Biophys. J.
PY  - 2000
SP  - 417A
EP  - 417A
VL  - 78
AB  - The structural mechanism of phosphoryl transfer in the type II restriction endonuclease EcoRV
AB  - has been investigated using thermodynamic, kinetic, and crystallographic methods on modified
AB  - substrates and site directed mutants.  A three metal ion mechanism has been proposed based on
AB  - the observation of divalent cation binding sites in the enzyme active site.  pH rate profiles
AB  - using Mg2+ and Mn2+ as the catalytic cofactor support the role of the metal ion in increasing
AB  - the electrophilicity of the scissile phosphorus by direct ligation to the proS oxygen of the
AB  - scissile phosphate.  Thio substitution at the 3'O position, in conjunction with metal
AB  - substitution experiments, support the lack of direct metal ligation at this position.
AB  - Structures of 3'S phosphorothiolate DNA containing the EcoRV cognate sequence, bound to
AB  - EcoRV, and the divalent cations Ca2+, Mg2+ and Mn2+ show loss of direct ligation by the metal
AB  - ion to the proS oxygen of the scissile phosphate, explaining the inability of EcoRV to cleave
AB  - this modified substrate.  A structure of the mutant K38A bound to cognate DNA nd Mn2+ shows a
AB  - new conformation of the scissile phosphate which is pulled deep into the active site, and
AB  - suggests the conformation of an intermediate in the phosphoryl transfer reaction pathway.
ER  -

TY  - JOUR
AU  - Horvath, B.
AU  - Hunyadkurti, J.
AU  - Voros, A.
AU  - Fekete, C.
AU  - Urban, E.
AU  - Kemeny, L.
AU  - Nagy, I.
TI  - Genome sequence of Propionibacterium acnes Type II strain ATCC 11828.
JO  - J. Bacteriol.
PY  - 2011
SP  - 202
EP  - 203
VL  - 194
AB  - Propionibacterium acnes is an anaerobic Gram-positive bacterium that forms part of the normal
AB  - human cutaneous microbiota and is occasionally associated with inflammatory diseases (I.
AB  - Kurokawa et al., Exp. Dermatol. 18:821- 832, 2009). Here we present the complete genome
AB  - sequence for the commercially available P. acnes type II reference strain ATCC 11828 (I. Nagy
AB  - et al., Microbes Infect. 8:2195-2205, 2006) recovered from a subcutaneous abscess.
ER  -

TY  - JOUR
AU  - Horvath, P.
AU  - Barrangou, R.
TI  - Protection against Foreign DNA.
JO  - Bacterial Stress Responses, 2nd Edition
PY  - 2011
SP  - 333
EP  - 348
VL  - 0
AB  - Bacteria rely on several defense systems that allow them to survive exposure to invading
AB  - nucleic acids. Predatory exposure to abundant and ubiquitous viruses, combined with
AB  - competition from a vast array of microbes, has lead to exogenous DNA exposure via
AB  - transduction, conjugation, and transformation. Consequently, bacterial immune systems have
AB  - been developed that allow the cell to recognize and distinguish incoming exogenous 'foreign'
AB  - DNA, from endogenous 'self' DNA. These systems maintain genetic integrity, species identity,
AB  - and genetic uniqueness, yet allow occasional exogenous DNA uptake and conservation of
AB  - advantageous genetic material for adaptation to the environment. In addition to defense
AB  - strategies such as prevention of adsorption, blocking of injection, and abortive infection,
AB  - which are effective against phage, the chapter briefly addresses the well-characterized
AB  - restriction-modification system (R-M), non-sugar-specific nucleases, and histone-like nucleoid
AB  - structuring (H-NS). The chapter more specifically elaborates on clustered regularly
AB  - interspaced short palindromic repeats (CRISPR). CRISPR/Cas, a recently described microbial
AB  - system, provides acquired immunity against phages and plasmids by targeting nucleic acids in a
AB  - sequence-specific manner. CRISPR features may be exploited for typing purposes, ecological and
AB  - epidemiological studies, and also for enhancing phage resistance in bacteria.
ER  -

TY  - JOUR
AU  - Hosford, C.J.
AU  - Chappie, J.S.
TI  - The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding.
JO  - J. Biol. Chem.
PY  - 2018
SP  - 11758
EP  - 11771
VL  - 293
AB  - Restriction modification systems consist of an endonuclease that cleaves foreign  DNA
AB  - site-specifically and an associated methyltransferase that protects the
AB  - corresponding target site in the host genome. Modification-dependent restriction
AB  - systems, in contrast, specifically recognize and cleave methylated and/or
AB  - glucosylated DNA. The LlaJI restriction system contains two 5-methylcytosine
AB  - (5mC) methyltransferases (LlaJI.M1 and LlaJI.M2) and two restriction proteins
AB  - (LlaJI.R1 and LlaJI.R2). LlaJI.R1 and LlaJI.R2 are homologs of McrB and McrC,
AB  - respectively, which in Escherichia coli function together as a
AB  - modification-dependent restriction complex specific for 5mC-containing DNA.
AB  - Lactococcus lactis LlaJI.R1 binds DNA site-specifically, suggesting that the
AB  - LlaJI system uses a different mode of substrate recognition. Here we present the
AB  - structure of the N-terminal DNA-binding domain of Helicobacter pylori LlaJI.R1 at
AB  - 1.97-A resolution, which adopts a B3 domain fold. Structural comparison to B3
AB  - domains in plant transcription factors and other restriction enzymes identifies
AB  - key recognition motifs responsible for site-specific DNA binding. Moreover,
AB  - biochemistry and structural modeling provide a rationale for how H. pylori
AB  - LlaJI.R1 may bind a target site that differs from the 5-bp sequence recognized by
AB  - other LlaJI homologs and identify residues critical for this recognition
AB  - activity. These findings underscore the inherent structural plasticity of B3
AB  - domains, allowing recognition of a variety of substrates using the same
AB  - structural core.
ER  -

TY  - JOUR
AU  - Hoshino, T.
AU  - Uozumi, T.
AU  - Horinouchi, S.
AU  - Ozaki, A.
AU  - Beppu, T.
AU  - Arima, K.
TI  - Purification of cohesive-end-producing restriction endonuclease from Bacillus subtilis G.
JO  - Biochim. Biophys. Acta
PY  - 1977
SP  - 367
EP  - 369
VL  - 479
AB  - A new restriction endonuclease was partially purified from Bacillus subtilis G
AB  - (IAM1247).  This restriction endonuclease (endonuclease RBsuG) seems to produce
AB  - cohesive ends at its cleavage site.
ER  -

TY  - JOUR
AU  - Hoskins, I.C.
AU  - Lax, A.J.
TI  - Identification of restriction barriers in Pasteurella multocida.
JO  - FEMS Microbiol. Lett.
PY  - 1997
SP  - 223
EP  - 226
VL  - 156
AB  - Several naturally occurring antibiotic resistance plasmids were isolated from Pasteurella
AB  - multocida type D strains.  One plasmid, pPM1, was used to study transfer of DNA among P.
AB  - multocida strains, and could be transferred into Escherichia coli and some P. multocida
AB  - isolates.  However, pPM1 could only be transferred into the toxigenic P. multocida LFB3 at
AB  - very low frequency.  Plasmid recovered from the electrotransformants could be transferred to
AB  - LFB3 at high frequency.  These plasmid DNAs were resistant to PstI, and sensitive to DpnI
AB  - digestion.  Sensitivity to DpnI was common to all the P. multocida DNAs, but resistance to
AB  - PstI was confined to LFB3.  Plasmid pPM1 treated with PstI methylase was able to transform
AB  - LFB3 at an increased frequency compared to unmethylated DNA, suggesting that LFB3 has a
AB  - restriction system which cleaves at or near PstI sites.
ER  -

TY  - JOUR
AU  - Hoskins, J. et al.
TI  - Genome of the bacterium Streptococcus pneumoniae strain R6.
JO  - J. Bacteriol.
PY  - 2001
SP  - 5709
EP  - 5717
VL  - 183
AB  - Streptococcus pneumoniae is among the most significant causes of bacterial disease in humans.
AB  - Here we report the 2,038,615-bp genomic sequence of the gram-positive bacterium S. pneumoniae
AB  - R6. Because the R6 strain is avirulent and, more importantly, because it is readily
AB  - transformed with DNA from homologous species and many heterologous species, it is the
AB  - principal platform for investigation of the biology of this important pathogen. It is also
AB  - used as a primary vehicle for genomics-based development of antibiotics for gram-positive
AB  - bacteria. In our analysis of the genome, we identified a large number of new uncharacterized
AB  - genes predicted to encode proteins that either reside on the surface of the cell or are
AB  - secreted. Among those proteins there may be new targets for vaccine and antibiotic
AB  - development.
ER  -

TY  - JOUR
AU  - Hoskisson, P.A.
AU  - Smith, M.C.M.
TI  - Hypervariation and phase variation in the bacteriophage resistome.
JO  - Curr. Opin. Microbiol.
PY  - 2007
SP  - 396
EP  - 400
VL  - 10
AB  - Most bacteria encode proteins for defence against infection by bacteriophages. The mechanisms
AB  - that bring about phage defence are
AB  - extremely diverse, suggesting frequent independent evolution of novel
AB  - processes. Phage defence determinants are often plasmid or
AB  - phage-encoded and many that are chromosomal show evidence of lateral
AB  - transfer. Recent studies on restriction-modification (R-M) systems show
AB  - that these genes are amongst the most rapidly evolving. Some bacteria
AB  - have contingency genes that encode alternative target specificity
AB  - determinants for Type I or Type III R-M systems, thus expanding the
AB  - range of phages against which the host population is immune. The most
AB  - counter-intuitive observation, however, is the prevalence of phase
AB  - variation in many restriction systems, but recent arguments suggest
AB  - that switching off expression of R-M systems can aid phage defence.
ER  -

TY  - JOUR
AU  - Hoskisson, P.A.
AU  - Sumby, P.
AU  - Smith, M.C.
TI  - The phage growth limitation system in Streptomyces coelicolor A(3)2 is a toxin/antitoxin system, comprising enzymes with DNA methyltransferase, protein  kinase and ATPase activity.
JO  - Virology
PY  - 2015
SP  - 100
EP  - 109
VL  - 477
AB  - The phage growth limitation system of Streptomyces coelicolor A3(2) is an unusual
AB  - bacteriophage defence mechanism. Progeny varphiC31 phage from an initial
AB  - infection are thought to be modified such that subsequent infections are
AB  - attenuated in a Pgl(+) host but normal in a Pgl(-) strain. Earlier work
AB  - identified four genes required for phage resistance by Pgl. Here we demonstrate
AB  - that Pgl is an elaborate and novel phage restriction system that, in part,
AB  - comprises a toxin/antitoxin system where PglX, a DNA methyltransferase is toxic
AB  - in the absence of a functional PglZ. In addition, the ATPase activity of PglY and
AB  - a protein kinase activity in PglW are shown to be essential for phage resistance
AB  - by Pgl. We conclude that on infection of a Pgl(+) cell by bacteriophage
AB  - varphiC31, PglW transduces a signal, probably via phosphorylation, to other Pgl
AB  - proteins resulting in the activation of the DNA methyltransferase, PglX and this
AB  - leads to phage restriction.
ER  -

TY  - JOUR
AU  - Hossain, M.
AU  - Alam, M.
AU  - Khaleque, A.
AU  - Islam, S.
AU  - Sadique, A.
AU  - Khan, N.
AU  - Halim, Z.
AU  - Sarker, M.
AU  - El-Sayed, N.M.
AU  - Huq, A.
AU  - Ahsan, G.U.
AU  - Colwell, R.R.
TI  - Virulence-Related Genes Identified from the Genome Sequence of the Non-O1/Non-O139 Vibrio cholerae Strain VcN1, Isolated from Dhaka, Bangladesh.
JO  - Genome Announcements
PY  - 2018
SP  - e01513
EP  - e01517
VL  - 6
AB  - We report here the first draft genome sequence of the non-O1/non-O139 Vibrio cholerae strain
AB  - VcN1, isolated from Dhaka, Bangladesh. The data submitted to
AB  - GenBank for this strain will contribute to advancing our understanding of this
AB  - environmentally disseminated bacterium, including its virulence and its evolution
AB  - as an important pathogen.
ER  -

TY  - JOUR
AU  - Hossain, M.J.
AU  - Beaz-Hidalgo, R.
AU  - Figueras, M.J.
AU  - Liles, M.R.
TI  - Draft Genome Sequences of Two Novel Aeromonas Species Recovered in Association with Cyanobacterial Blooms.
JO  - Genome Announcements
PY  - 2014
SP  - e01181
EP  - e01114
VL  - 2
AB  - Aeromonas aquatica and Aeromonas lacus are two new species that have been found in association
AB  - with cyanobacterial blooms from recreational Finnish lakes where
AB  - adverse human health effects have been recorded. Here, we present the draft
AB  - genome sequences of their type strains.
ER  -

TY  - JOUR
AU  - Hossain, M.S.
AU  - Akhter, M.Z.
AU  - Hossain, M.M.
AU  - Shishir, M.A.
AU  - Khan, S.N.
AU  - Hoq, M.M.
TI  - Complete Genome Sequence of Bacillus subtilis Strain MH1, Which Has a High Level  of Bacteriocin-Like Activity, Isolated from Soil in Bangladesh.
JO  - Genome Announcements
PY  - 2018
SP  - e00516
EP  - e00518
VL  - 6
AB  - Bacillus subtilis MH1 demonstrates a high level of bacteriocin activity against several
AB  - pathogenic bacteria. We announce here the full-genome sequence of strain
AB  - MH1, isolated from soil in Bangladesh. This genome length is 4,094,053 bp, with
AB  - 43.5% GC content, 4,217 coding sequences (CDS), 10 rRNA, 84 tRNA, and 1
AB  - transfer-messenger RNA (tmRNA).
ER  -

TY  - JOUR
AU  - Hosseinkhani, F.
AU  - Emaneini, M.
AU  - van Leeuwen, W.
TI  - High-Quality Genome Sequence of the Highly Resistant Bacterium Staphylococcus haemolyticus, Isolated from a Neonatal Bloodstream Infection.
JO  - Genome Announcements
PY  - 2017
SP  - e00683
EP  - e00617
VL  - 5
AB  - Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the
AB  - multidrug-resistant bacterium Staphylococcus haemolyticus, originating from a
AB  - bloodstream infection in a neonate. The sequence data can be used as an accurate
AB  - reference sequence.
ER  -

TY  - JOUR
AU  - Hotchkiss, R.D.
TI  - The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography.
JO  - J. Biol. Chem.
PY  - 1948
SP  - 315
EP  - 332
VL  - 175
AB  - The separation of amino acid mixtures by migration with
AB  - organic solvents in filter paper has been successfully accomplished by
AB  - many workers since it was first described by Consden, Gordon, and
AB  - Martin.  Each amino acid travels in a more or less well defined spot in
AB  - the body of uniformly migrating solvent and can be visualized in the
AB  - dried paper as a local spot giving a color reaction with ninhydrin.  The
AB  - present paper reports the separation of the purines and pyrimidines
AB  - contained in nucleic acids, and several related compounds, by the
AB  - movement of a boundary of n-butyl alcohol along paper strips.  Vischer
AB  - and Chargaff have described the principal steps of a procedure for
AB  - separating the two bases, guanine and adenine, from nucleic acid in a
AB  - moving body of a quinoline-collidine mixture.  These purines were
AB  - located in the paper by precipitation of mercury sulfide after formation
AB  - of the insoluble mercury salts and washing in dilute acid.  After
AB  - complete removal of the quinoline and collidine it was possible to
AB  - identify the guanine and adenine by their absorption maxima in the
AB  - ultraviolet range.
ER  -

TY  - JOUR
AU  - Hotz, H.R.
AU  - Peters, A.H.
TI  - Protein demethylation required for DNA methylation.
JO  - Nat. Genet.
PY  - 2009
SP  - 10
EP  - 11
VL  - 41
AB  - DNA methylation and histone modifications have essential roles in the transcriptional
AB  - regulation of gene expression. Lysine-specific demethylase-1 (Lsd1), also called KDM1, is an
AB  - enzyme with specificity toward the di and monomethylation states of lysine 4 and lysine 9 of
AB  - histone H3 (H3K4 and H3K9), and of lysine 370 of p53 (ref. 1). Lsd1 serves transcriptional
AB  - co-activator and co-repressor functions during development. On page 125 of this issue, En Li,
AB  - Taiping Chen and colleagues3 identify DNA methyltransferase-1 (Dnmt1) as a novel substrate for
AB  - Lsd1 and show that demethylation of Dnmt1 is required for the maintenance of global DNA
AB  - methylation.
ER  -

TY  - JOUR
AU  - Hou, L.
AU  - Jiang, J.
AU  - Xu, Z.
AU  - Zhou, Y.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of Pseudoxanthomonas suwonensis Strain J1, a Cellulose-Degrading Bacterium Isolated from Leaf- and Wood-Enriched Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00614
EP  - e00615
VL  - 3
AB  - We report here the complete genome sequence of the cellulose-degrading bacterium
AB  - Pseudoxanthomonas suwonensis strain J1, isolated from soil enriched with rotten
AB  - leaves and wood from the Zhong Mountain Scenic Area in Nanjing, China. This
AB  - complete genome may contribute to further investigation of plant biomass
AB  - degradation.
ER  -

TY  - JOUR
AU  - Hou, L.
AU  - Sun, J.
AU  - Xie, X.
AU  - Jiao, N.
AU  - Zhang, Y.
TI  - Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 91
EP  - 91
VL  - 12
AB  - Acuticoccus yangtzensis JL1095(T) is a proteobacterium from a genus belonging to  the family
AB  - Rhodobacteraceae; it was isolated from surface waters of the Yangtze
AB  - Estuary, China. This strain displays the capability to utilize aromatic and
AB  - simple carbon compounds. Here, we present the genome sequence, annotations, and
AB  - features of A. yangtzensis JL1095(T). This strain has a genome size of 5,043,263
AB  - bp with a G + C content of 68.63%. The genome contains 4286 protein-coding genes,
AB  - 56 RNA genes, and 83 pseudo genes. Many of the protein-coding genes were
AB  - predicted to encode proteins involved in carbon metabolism pathways, such as
AB  - aromatic degradation and methane metabolism. Notably, a total of 31 genes were
AB  - predicted to encode form II carbon monoxide dehydrogenases, suggesting potential
AB  - for carbon monoxide oxidation. The genome analysis helps better understand the
AB  - major carbon metabolic pathways of this strain and its role in carbon cycling in
AB  - coastal marine ecosystems.
ER  -

TY  - JOUR
AU  - Hou, P.
AU  - Ji, M.
AU  - He, N.
AU  - Lu, Z.
TI  - A microarray method to evaluate the effect of CA mispairs on the accuracy of BstUI restriction endonuclease.
JO  - Anal. Biochem.
PY  - 2003
SP  - 276
EP  - 279
VL  - 317
AB  - Protein-DNA interaction is an essential event in many biological processes, such as
AB  - transcription, replication, restriction, and modification.  The sequence selectivity of
AB  - DNA-binding proteins plays an important role in controlling these processes in the cell.
AB  - Understanding how DNA-binding proteins select the correct DNA sequence from the nonspecific
AB  - sequences has attracted more and more interest in recent years.  Among DNA-binding proteins,
AB  - restriction endonucleases are perhaps the most extreme in their DNA selectivity.  Research on
AB  - the effects of sequence variations of the canonical recognition sites on the cleavage
AB  - efficiency of restriction endonucleases is important for understanding its specificity.  These
AB  - sequence variations include both a single base pair change and mispairs within the recognition
AB  - site.  The former can result in over a million-fold decrease in activity, and the latter can
AB  - impart a local destabilization on a double helix and affect the deformability and dynamic
AB  - properties of the DNA at the mismatched site.
ER  -

TY  - JOUR
AU  - Hou, P.
AU  - Ji, M.J.
AU  - He, N.Y.
AU  - Lu, Z.H.
TI  - Microarray-based method to evaluate the accuracy of restriction endonucleases HpaII and MspI.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2004
SP  - 110
EP  - 117
VL  - 314
AB  - A double-strand DNA (ds DNA) microarray was fabricated to analyze the structural perturbations
AB  - caused by methylation and the different base
AB  - mismatches in the interaction of the restriction endonucleases HpaII
AB  - and MspI with DNA. First, a series of synthesized oligonucleotides were
AB  - arrayed on the aldehyde-coated glass slides. Second, these
AB  - oligonucleotides were hybridized with target sequences to obtain a ds DNA
AB  - microarray, which includes several types of double strands with-the
AB  - fully methylated, semi-methylated, and unmethylated canonical
AB  - recognition sequences, semi-methylated and unmethylated base mismatches
AB  - within the recognition sequences. The cleavage experiments were carried
AB  - out under normal buffer conditions. The results indicated that MspI
AB  - could partially cleave methylated and semi-methylated canonical
AB  - recognition sequences. In contrast, HpaII could not cleave methylated
AB  - and semi-methylated canonical recognition sequences. HpaII and MspI
AB  - could both cleave the unmethylated canonical recognition sequence.
AB  - However, HpaII could partially cleave the sequence containing one GG
AB  - mismatch and not cleave other base mismatches in the corresponding
AB  - recognition site. In contrast, MspI could not recognize the base
AB  - mismatches within the recognition sequence. A good reproducibility was
AB  - observed in several parallel experiments. The experiment indicates that
AB  - the microarray technology has great potentials in high-throughput
AB  - identifying important interactions between protein and DNA.
ER  -

TY  - JOUR
AU  - Hou, Q.
AU  - Wang, C.
AU  - Guo, H.
AU  - Xia, Z.
AU  - Ye, J.
AU  - Liu, K.
AU  - Yang, Y.
AU  - Hou, X.
AU  - Liu, H.
AU  - Wang, J.
AU  - Du, B.
AU  - Ding, Y.
TI  - Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2015
SP  - e00822
EP  - e00815
VL  - 3
AB  - Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from
AB  - tobacco rhizosphere. Here, we report the draft genome sequence of
AB  - D. tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity
AB  - and environment adaption have been found in the genome. This is the first genome
AB  - sequence of D. tsuruhatensis related to PGPR.
ER  -

TY  - JOUR
AU  - Hou, Q.
AU  - Wang, C.
AU  - Hou, X.
AU  - Xia, Z.
AU  - Ye, J.
AU  - Liu, K.
AU  - Liu, H.
AU  - Wang, J.
AU  - Guo, H.
AU  - Yu, X.
AU  - Yang, Y.
AU  - Du, B.
AU  - Ding, Y.
TI  - Draft Genome Sequence of Brevibacillus brevis DZQ7, a Plant Growth-Promoting Rhizobacterium with Broad-Spectrum Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2015
SP  - e00831
EP  - e00815
VL  - 3
AB  - Brevibacillus brevis DZQ7 is a plant growth-promoting rhizobacterium (PGPR) isolated from
AB  - tobacco rhizosphere. Here, we report the draft genome sequence of
AB  - B. brevis DZQ7. Several functional genes related to antimicrobial activity were
AB  - identified in the genome.
ER  -

TY  - JOUR
AU  - Hou, S. et al.
TI  - Genome sequence of the deep-sea {gamma}-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and   energy.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 18036
EP  - 18041
VL  - 101
AB  - We report the complete genome sequence of the deep-sea gamma-proteobacterium, Idiomarina
AB  - loihiensis, isolated recently from a
AB  - hydrothermal vent at 1,300-m depth on the Loihi submarine volcano, Hawaii.
AB  - The I. loihiensis genome comprises a single chromosome of 2,839,318 base
AB  - pairs, encoding 2,640 proteins, four rRNA operons, and 56 tRNA genes. A
AB  - comparison of I. loihiensis to the genomes of other gamma-proteobacteria
AB  - reveals abundance of amino acid transport and degradation enzymes, but a
AB  - loss of sugar transport systems and certain enzymes of sugar metabolism.
AB  - This finding suggests that I. loihiensis relies primarily on amino acid
AB  - catabolism, rather than on sugar fermentation, for carbon and energy.
AB  - Enzymes for biosynthesis of purines, pyrimidines, the majority of amino
AB  - acids, and coenzymes are encoded in the genome, but biosynthetic pathways
AB  - for Leu, Ile, Val, Thr, and Met are incomplete. Auxotrophy for Val and Thr
AB  - was confirmed by in vivo experiments. The I. loihiensis genome contains a
AB  - cluster of 32 genes encoding enzymes for exopolysaccharide and capsular
AB  - polysaccharide synthesis. It also encodes diverse peptidases, a variety of
AB  - peptide and amino acid uptake systems, and versatile signal transduction
AB  - machinery. We propose that the source of amino acids for I. loihiensis
AB  - growth are the proteinaceous particles present in the deep sea
AB  - hydrothermal vent waters. I. loihiensis would colonize these particles by
AB  - using the secreted exopolysaccharide, digest these proteins, and
AB  - metabolize the resulting peptides and amino acids. In summary, the I.
AB  - loihiensis genome reveals an integrated mechanism of metabolic adaptation
AB  - to the constantly changing deep-sea hydrothermal ecosystem.
ER  -

TY  - JOUR
AU  - Hou, S.P.
AU  - He, P.
AU  - Zhou, Y.
AU  - Wu, X.W.
TI  - Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 772, Isolated from Ascites of a Patient with Chronic Kidney Disease.
JO  - Genome Announcements
PY  - 2018
SP  - e00432
EP  - e00418
VL  - 6
AB  - Campylobacter fetus subsp. testudinum originating in reptiles can cause invasive  infections
AB  - in humans. Here, we present the whole-genome sequence of C. fetus
AB  - subsp. testudinum strain 772, isolated from a human patient in China.
ER  -

TY  - JOUR
AU  - Houlston, C.E.
AU  - Lindsay, H.
AU  - Pradhan, S.
AU  - Adams, R.L.P.
TI  - DNA substrate specificity of pea DNA methylase.
JO  - Biochem. J.
PY  - 1993
SP  - 617
EP  - 624
VL  - 293
AB  - DNA methylase, present in low-salt extracts of nuclei prepared from Pisum sativum shoot tips,
AB  - methylates model DNA substrates containing CNG trinucleotides or CI dinucleotides only. The
AB  - binding to the hemimethylated trinucleotide substrates is very much stronger and more
AB  - persistent than the binding to the unmethylated substrates or to the hemimethylated
AB  - dinucleotide substrate. When the DNA concentration is limiting, the rate of methyl-group
AB  - transfer with the hemimethylated CNG substrate is much greater than that with the unmethylated
AB  - CNG. However, the Vmax. is similar for the two CNG substrates. On fractionation using
AB  - Q-Sepharose, two peaks of activity are seen with different relative activities using the di-
AB  - and trinucleotide substrates. The relative activity with these substrates changes during
AB  - purification, during plant growth and on heating at 35oC as well, indicating that more than
AB  - one enzyme or more than one form of the enzyme may be present.
ER  -

TY  - JOUR
AU  - Howard, K.A.
AU  - Card, C.
AU  - Benner, J.S.
AU  - Callahan, H.L.
AU  - Maunus, R.
AU  - Silber, K.
AU  - Wilson, G.
AU  - Brooks, J.E.
TI  - Cloning the DdeI restriction-modification system using a two-step method.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 7939
EP  - 7951
VL  - 14
AB  - DdeI, a Type II restriction-modification system from the gram-negative
AB  - anaerobic bacterium Desulfovibrio desulfuricans, recognizes the sequence CTNAG.
AB  - The system has been cloned into E. coli in two steps.  First the methylase
AB  - gene was cloned into pBR322 and a derivative expressing higher levels was
AB  - constructed.  Then the endonuclease gene was located by Southern blot analyses;
AB  - BamHI fragments large enough to contain the gene were cloned into pACYC184,
AB  - introduced into a host containing the methylase gene, and screened for
AB  - endonuclease activity.  Both genes are stably maintained in E. coli on separate
AB  - but compatible plasmids.  The DdeI methylase is shown to be a cytosine
AB  - methylase.  DdeI methylase clones decrease in viability as methylation activity
AB  - increases in E. coli RR1 (our original cloning strain).  Therefore the DdeI
AB  - system has been cloned and maintained in ER1467, a new E. coli cloning strain
AB  - engineered to accept cytosine methylases.  Finally, it has been demonstrated
AB  - that a very high level of methylation was necessary in the DdeI system for
AB  - successful introduction of the active endonuclease gene into E. coli.
ER  -

TY  - JOUR
AU  - Howden, B.P.
AU  - Seemann, T.
AU  - Harrison, P.F.
AU  - McEvoy, C.R.
AU  - Stanton, J.A.
AU  - Rand, C.J.
AU  - Mason, C.W.
AU  - Jensen, S.O.
AU  - Firth, N.
AU  - Davies, J.K.
AU  - Johnson, P.D.
AU  - Stinear, T.P.
TI  - Complete Genome Sequence of Staphylococcus aureus Strain JKD6008, an ST239 Clone of Methicillin-Resistant Staphylococcus aureus with  Intermediate-Level Vancomycin Resistance.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5848
EP  - 5849
VL  - 192
AB  - We report here the complete 2.92-Mb genome sequence of a clinical isolate of
AB  - methicillin-resistant Staphylococcus aureus subsp. aureus that
AB  - demonstrates intermediate-level vancomycin resistance. The strain, named
AB  - JKD6008, belongs to multilocus sequence type 239 and was isolated from the
AB  - bloodstream of a patient in New Zealand in 2003.
ER  -

TY  - JOUR
AU  - Hoyos-Mallecot, Y.
AU  - Rojo-Martin, M.D.
AU  - Bonnin, R.A.
AU  - Creton, E.
AU  - Navarro, M.J.M.
AU  - Naas, T.
TI  - Draft Genome Sequence of NDM-1-Producing Leclercia adecarboxylata.
JO  - Genome Announcements
PY  - 2017
SP  - e00135
EP  - e00117
VL  - 5
AB  - Here, we provide the first draft genome sequence of NDM-1-producing Leclercia adecarboxylata,
AB  - a human-opportunistic pathogen. The draft genome sequence
AB  - consists of a total length of 5.13 Mbp, with an average G+C content of 55.2%.
ER  -

TY  - JOUR
AU  - Hsieh, C.-L.
TI  - In vivo activity of murine de novo methyltransferases, Dnmt3a and Dnmt3b.
JO  - Mol. Cell. Biol.
PY  - 1999
SP  - 8211
EP  - 8218
VL  - 19
AB  - The putative de novo methyltransferases, Dnmt3a and Dnmt3b, were reported to have weak
AB  - methyltransferase activity in methylating the 3' long terminal repeat of Moloney murine
AB  - leukemia virus in vitro. The activity of these enzymes was evaluated in vivo, using a stable
AB  - episomal system that employs plasmids as targets for DNA methylation in human cells. De novo
AB  - methylation of a subset of the CpG sites on the stable episomes is detected in human cells
AB  - overexpressing the murine Dnmt3a or Dnmt3b1 protein.  This de novo methylation activity is
AB  - abolished when the cysteine in the P-C motif, which is the catalytic site of cytosine
AB  - methyltransferases, is replaced by a serine. The pattern of methylation on the episome is
AB  - nonrandom, and different regions of the episome are methylated to different extents.
AB  - Furthermore, Dnmt3a also methylates the sequence methylated by Dnmt3a on the stable episome in
AB  - the corresponding chromosomal target. Overexpression of human DNMT1 or murine Dnmt3b does not
AB  - lead to the same pattern or degree of de novo methylation on the episome as overexpression of
AB  - murine Dnmt3a. This finding suggests that these three enzymes may have different targets or
AB  - requirements, despite the fact that weak de novo methyltransferase activity has been
AB  - demonstrated in vitro for all three enzymes. It is also noteworthy that both Dnmt3a and Dnmt3b
AB  - proteins coat the metaphase chromosomes while displaying a more uniform pattern in the
AB  - nucleus. This is the first evidence that Dnmt3a and Dnmt3b have de novo methyltransferase
AB  - function in vivo and the first indication that the Dnmt3a and Dnmt3b proteins may have
AB  - preferred target sites.
ER  -

TY  - JOUR
AU  - Hsieh, P.-C.
AU  - Xiao, J.-P.
AU  - O'Loane, D.
AU  - Xu, S.-Y.
TI  - Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
JO  - J. Bacteriol.
PY  - 2000
SP  - 949
EP  - 955
VL  - 182
AB  - BslI is a thermostable type II restriction endonuclease with interrupted recognition sequence
AB  - CCNNNNN/NNGG (/, cleavage position).  The BslI restriction-modification system from Bacillus
AB  - species was cloned and expressed in Escherichia coli.  The system is encoded by three genes:
AB  - the 2,739-bp BslI methylase gene (bslIM), the bslIRalpha gene, and the bslIRbeta gene.  The
AB  - alpha and beta subunits of BslI can be expressed independently in E. coli in the absence of
AB  - BslI methylase (M.BslI) protection.  BslI endonuclease activity can be reconstituted in vitro
AB  - by mixing the two subunits together.  Gel filtration chromatography and native polyacrylamide
AB  - gel electrophoresis indicated that BslI forms heterodimers (alphabeta), heterotetramers
AB  - (alpha2beta2), and possibly oligomers in solution.  Two beta subunits can be cross-linked by a
AB  - chemical cross-linking agent, indicating formation of heterotetramer BslI complex
AB  - (alpha2beta2).  In DNA mobility shift assays, neither subunit alone can bind DNA.  DNA
AB  - mobility shift activity was detected after mixing the two subunits together.  Because of the
AB  - symmetric recognition sequence of the BslI endonuclease, we propose that its active form is
AB  - alpha2beta2.  M.BslI contains nine conserved motifs of N-4 cytosine DNA methylases within the
AB  - beta group of aminomethyltransferases.  Synthetic duplex deoxyoligonucleotides containing
AB  - cytosine hemimethylated or fully methylated at N-4 in BslI sites in the first or second
AB  - cytosine are resistant to BslI digestion.  C-5 methylation of the second cytosine on both
AB  - strands within the recognition sequence also renders the site refractory to BslI digestion.
AB  - Two putative zinc fingers are found in the alpha subunit of BslI endonuclease.
ER  -

TY  - JOUR
AU  - Hsu, D.W.
AU  - Lin, M.J.
AU  - Lee, T.L.
AU  - Wen, S.C.
AU  - Chen, X.
AU  - Shen, C.J.
TI  - Two major forms of DNA (cytosine-5) methyltransferase in human somatic tissues.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 9751
EP  - 9756
VL  - 96
AB  - Thus far, only one major form of vertebrate DNA (cytosine-5) methyltransferase (CpG MTase, EC
AB  - 2.1.1.37) has been identified, cloned,
AB  - and extensively studied. This enzyme, dnmt1, has been hypothesized to
AB  - be responsible for most of the maintenance as well as the de novo
AB  - methylation activities occurring in the somatic cells of vertebrates.
AB  - We now report the discovery of another abundant species of CpG MTase in
AB  - various types of human cell lines and somatic tissues. Interestingly,
AB  - the mRNA encoding this CpG MTase results from alternative splicing of
AB  - the primary transcript from the Dnmt1 gene, which incorporates in-frame
AB  - an additional 48 nt. between exons 4 and 5. Furthermore, this 48-nt exon
AB  - sequence is derived from the first, or the most upstream, copy of a set
AB  - of seven different Alu repeats located in intron 4. The ratios of
AB  - expression of this mRNA to the expression of the previously known,
AB  - shorter Dnmt1 mRNA species, as estimated by semiquantitative reverse
AB  - transcription-PCR analysis, range from two-thirds to three-sevenths.
AB  - This alternative splicing scheme of the Dnmt1 transcript seems to be
AB  - conserved in the higher primates. We suggest that the originally
AB  - described and the recently discovered forms of CpG MTase be named dnmt1-
AB  - a and dnmt1-b, respectively. The evolutionary and biological
AB  - implications of this finding are discussed in relation to the cellular
AB  - functions of the CpG residues and the CpG MTases.
ER  -

TY  - JOUR
AU  - Hsu, M.
AU  - Berg, P.
TI  - Altering the specificity of restriction endonuclease:  effect of replacing Mg2+ with Mn2+.
JO  - Biochemistry
PY  - 1978
SP  - 131
EP  - 138
VL  - 17
AB  - In the presence of 100 mM Tris buffer (pH 7.5) and 1-10 mM Mg2+ EcoRI
AB  - endonuclease cleaves DNA at a specific nucleotide sequence and in a
AB  - characteristic way: -G^AATTC-.  But if Mg2+ is replaced by Mn2+, the
AB  - specificity of the cleavage is relaxed and cleavages occur at many other sites;
AB  - moreover, there appears to be a hierarchy of cleavage rates at the pseudo-EcoRI
AB  - restriction sites.  For example, SV40 DNA is cleaved only once in the usual
AB  - digestion conditions, but with Mn2+ more than ten cleavages are made; the five
AB  - most rapidly cleaved SV40 DNA map locations are 0/1.0>0.93>0.33 ~0.49>0.25.
AB  - Mn2+ also alters the restriction specificity of HindIII but not HpaII
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Hsu, M.-Y.
AU  - Inouye, M.
AU  - Inouye, S.
TI  - Retron for the 67-base multicopy single-stranded DNA from Escherichia coli: A potential transposable element encoding both reverse transcriptase and Dam methylase functions.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1990
SP  - 9454
EP  - 9458
VL  - 87
AB  - The region (retron-Ec67) required for the biosynthesis of a branched-RNA linked multicopy
AB  - single-stranded DNA (msDNA-Ec67) from a clinical isolate of Escherichia coli was mapped at a
AB  - position equivalent to 19 min on the K-12 chromosome. The element containing the retron
AB  - consisted of a unique 34-kilobase sequence that was flanked by direct repeats of a
AB  - 26-base-pair sequence found in the K-12 chromosomal DNA. This suggests that the 34-kilobase
AB  - element was probably integrated into the E. coli genome by a mechanism related to
AB  - transposition or phage integration. In the 34-kilobase sequence an open reading frame of 285
AB  - residues was found, which displays 44% sequence identity with the E. coli Dam methylase.
AB  - Interestingly, there are three GATC sequences, the site of Dam methylation, in the promoter
AB  - region of the gene for reverse transcriptase.
ER  -

TY  - JOUR
AU  - Hsueh, P.T.
AU  - Chen, Y.S.
AU  - Lin, H.H.
AU  - Liu, P.J.
AU  - Ni, W.F.
AU  - Liu, M.C.
AU  - Chen, Y.L.
TI  - Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei.
JO  - Genome Announcements
PY  - 2015
SP  - e01194
EP  - e01115
VL  - 3
AB  - The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei
AB  - were sequenced. A comparison of the sequences from both strains indicates that they show
AB  - 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have
AB  - 199 single-base variants.
ER  -

TY  - JOUR
AU  - Hsueh, P.T.
AU  - Liu, J.K.
AU  - Chen, Y.L.
AU  - Liu, P.J.
AU  - Ni, W.F.
AU  - Chen, Y.S.
AU  - Wu, K.M.
AU  - Lin, H.H.
TI  - Genomic Sequence of Burkholderia multivorans NKI379, a Soil Bacterium That Inhibits the Growth of Burkholderia pseudomallei.
JO  - Genome Announcements
PY  - 2015
SP  - e01294
EP  - e01215
VL  - 3
AB  - Burkholderia multivorans NKI379 is a soil bacterium that exhibits an antagonistic effect
AB  - against the growth of Burkholderia pseudomallei, the causative agent of
AB  - the infectious disease melioidosis. We report the draft genomic sequence of B.
AB  - multivorans NKI379, which has a G+C content of 67% and 5,203 candidate
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Hu, A.
AU  - He, J.
AU  - Chu, K.H.
AU  - Yu, C.P.
TI  - Genome Sequence of the 17{beta}-Estradiol-Utilizing Bacterium Sphingomonas Strain KC8.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4266
EP  - 4267
VL  - 193
AB  - Sphingomonas strain KC8 is known for its ability to utilize 17beta-estradiol, a natural
AB  - estrogen and an environmental
AB  - endocrine-disrupting compound, as the sole carbon and energy source. Here,
AB  - we report the draft genome sequence of the strain KC8 (4,074,265 bp, with
AB  - a GC content of 63.7%) and major findings from its annotation.
ER  -

TY  - JOUR
AU  - Hu, A.
AU  - Lv, M.
AU  - Yu, C.P.
TI  - Draft Genome Sequence of the Bisphenol A-Degrading Bacterium Sphingobium sp. Strain YL23.
JO  - Genome Announcements
PY  - 2013
SP  - e00549
EP  - e00513
VL  - 1
AB  - Sphingobium sp. strain YL23, a novel bacterium isolated from sewage sludge of a domestic
AB  - wastewater treatment plant, has been shown to completely degrade
AB  - bisphenol A under aerobic conditions. Here, we describe a 3.8-Mb assembly of its
AB  - genome sequence and major findings from its annotation.
ER  -

TY  - JOUR
AU  - Hu, A.-L.W.
TI  - NgoAIV--a new restriction endonuclease compared to its commercially available isoschizomers.
JO  - BRL Focus
PY  - 1994
SP  - 42
EP  - 43
VL  - 15
AB  - The restriction endonuclease NaeI recognizes the sequence GCC^GGC and generates blunt-ended
AB  - DNA fragments. However, NaeI demonstrates a strong site preference in its cleavage rate that
AB  - may result in incomplete cleavage in some DNA. Therefore, there is a need to search for an
AB  - isoschizomer to circumvent the problem. NgoAIV is an isoschizomer of NaeI that was purified
AB  - from a strain of E. coli bearing the cloned NgoAIV gene from Neisseria gonorrhoea. NgoAIV
AB  - cleaves between the first G and C residues, providing cohesive ends for more effective
AB  - ligation. The enzyme has an apparent molecular weight of 31,000 Da on an SDS-PAGE gel.
ER  -

TY  - JOUR
AU  - Hu, A.W.
AU  - Marschel, A.H.
TI  - Endonuclease NciI generates atypical termini.
JO  - Fed. Proc.
PY  - 1982
SP  - 1119
EP  - 1119
VL  - 41
AB  - Cleavage of DNA by the type II restriction endonuclease, NciI, produces termini
AB  - that differ from those produced by most other type II enzymes.  This difference
AB  - is manifested by the inability of T4 DNA ligase to ligate NciI generated
AB  - termini, even under conditions that normally enhance ligation.  Tests for
AB  - contaminating enzymes present in NciI preparations showed negligible levels of
AB  - 3' or 5' single or double strand specific exonucleases.  Similarly, no other
AB  - endonuclease was detected in these preparations.  The presence of a ligation
AB  - inhibitor in NciI preparations was eliminated by mixing DNA fragments produced
AB  - by HpaII or TaqI with NciI fragments and measuring ligation.  Only the NciI
AB  - generated fragments remained resistant to the ligation reaction precluding the
AB  - presence of a nonspecific ligation inhibitor.  A successful ligation procedure
AB  - was designed and included a two step incubation with T4 polynucleotide kinase
AB  - and NciI formed fragments.  Step one utilized conditions that enhanced the
AB  - inherent 3' phosphatase activity of T4 polynucleotide kinase.  The 2nd
AB  - incubation step optimized the phosphorylation of the 5' hydroxyl terminus.  DNA
AB  - fragments treated in this manner were ligated with more than a 50% efficiency
AB  - under normal conditions.  The above result suggests that NciI cleaves DNA
AB  - leaving a 3' phosphate and 5' hydroxyl, and explains the inability of T4 DNA
AB  - ligase to ligate NciI generated fragments.
ER  -

TY  - JOUR
AU  - Hu, D.
AU  - Crist, M.
AU  - Duan, X.
AU  - Gimble, F.S.
TI  - Mapping of a DNA binding region of the PI-SceI homing endonuclease by affinity cleavage and alanine-scanning mutagenesis.
JO  - Biochemistry
PY  - 1999
SP  - 12621
EP  - 12628
VL  - 38
AB  - The PI-SceI protein is a member of the LAGLIDADG family of homing endonucleases that is
AB  - generated by a protein splicing reaction. PI-SceI has a bipartite domain structure, and the
AB  - protein splicing and endonucleolytic reactions are catalyzed by residues in domains I and II,
AB  - respectively. Structural and mutational evidence indicates that both domains mediate DNA
AB  - binding. Treatment of the protein with trypsin breaks a peptide bond within a disordered
AB  - region of the endonuclease domain situated between residues Val-270 and Leu-280 and interferes
AB  - with the ability of this domain to bind DNA. To identify specific residues in this region that
AB  - are involved in DNA binding and/or catalysis, alanine-scanning mutagenesis was used to create
AB  - a set of PI-SceI mutant proteins that were assayed for activity. One of these mutants, N281A,
AB  - was >300-fold less active than wild-type PI-SceI, and two other proteins, R277A and N284A,
AB  - were completely inactive. These decreases in cleavage activity parallel similar decreases in
AB  - substrate binding by the endonuclease domains of these mutant proteins. We mapped the
AB  - approximate position of the disordered region to one of the ends of the 31 base pair PI-SceI
AB  - recognition sequence using mutant proteins that were substituted with cysteine at residues
AB  - Asn-274 and Glu-283 and tethered to the chemical nuclease FeBABE. These mutational and
AB  - affinity cleavage data strongly support a model of PI-SceI docked to its DNA substrate that
AB  - suggests that one or more residues identified here are responsible for contacting base pair
AB  - A/T(-)(9), which is essential for substrate binding.
ER  -

TY  - JOUR
AU  - Hu, D.
AU  - Crist, M.
AU  - Duan, X.
AU  - Quiocho, F.A.
AU  - Gimble, F.S.
TI  - Probing the Structure of the PI-SceI-DNA Complex by Affinity Cleavage and Affinity Photocross-linking.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 2705
EP  - 2712
VL  - 275
AB  - The PI-SceI protein is an intein-encoded homing endonuclease that initiates the mobility of
AB  - its gene by making a double strand break at a single site in the yeast genome. The PI-SceI
AB  - protein splicing and endonucleolytic active sites are separately located in each of two
AB  - domains in the PI-SceI structure. To determine the spatial relationship between bases in the
AB  - PI-SceI recognition sequence and selected PI-SceI amino acids, the PI-SceI-DNA complex was
AB  - probed by photocross-linking and affinity cleavage methods. Unique solvent-accessible cysteine
AB  - residues were introduced into the two PI-SceI domains at positions 91, 97, 170, 230, 376, and
AB  - 378, and the mutant proteins were modified with either 4-azidophenacyl bromide or iron
AB  - (S)-1-(p-bromoacetamidobenzyl)-ethylenediaminetetraacetate (FeBABE). The phenyl azide-coupled
AB  - proteins cross-linked to the PI-SceI target sequence, and the FeBABE-modified proteins cleaved
AB  - the DNA proximal to the derivatized amino acid. The results suggest that an extended
AB  - beta-hairpin loop in the endonuclease domain that contains residues 376 and 378 contacts the
AB  - major groove near the PI-SceI cleavage site. Conversely, residues 91, 97, and 170 in the
AB  - protein splicing domain are in close proximity to a distant region of the substrate. To
AB  - interpret our results, we used a new PI-SceI structure that is ordered in regions of the
AB  - protein that bind DNA. The data strongly support a model of the PI-SceI-DNA complex derived
AB  - from this structure.
ER  -

TY  - JOUR
AU  - Hu, D.
AU  - Li, X.
AU  - Chang, Y.
AU  - He, H.
AU  - Zhang, C.
AU  - Jia, N.
AU  - Li, H.
AU  - Wang, Z.
TI  - Genome Sequence of Streptomyces sp. Strain TOR3209, a Rhizosphere Microecology Regulator Isolated from Tomato Rhizosphere.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1627
EP  - 1627
VL  - 194
AB  - Streptomyces sp. strain TOR3209, isolated from tomato rhizosphere, can regulate the
AB  - rhizosphere microecology of a variety of crops. Strain TOR3209 could improve
AB  - plant systemic resistance and promote plant growth. Here, the genome sequence of
AB  - strain TOR3209 is reported, providing the molecular biological basis of the
AB  - regulation mechanism of rhizosphere microecology.
ER  -

TY  - JOUR
AU  - Hu, D.
AU  - Liu, B.
AU  - Feng, L.
AU  - Ding, P.
AU  - Guo, X.
AU  - Wang, M.
AU  - Cao, B.
AU  - Reeves, P.R.
AU  - Wang, L.
TI  - Origins of the current seventh cholera pandemic.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2016
SP  - E7730
EP  - E7739
VL  - 113
AB  - Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on
AB  - much of the world, but bacterial strains are currently only available for the
AB  - sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in
AB  - Indonesia, but did not originate directly from the classical biotype
AB  - sixth-pandemic strain. Previous studies focused mainly on the spread of the
AB  - seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin,
AB  - evolution, and transition to pandemicity of the seventh-pandemic strain. We used
AB  - high-resolution comparative genomic analysis of strains collected from 1930 to
AB  - 1964, covering the evolution from the first available El Tor biotype strain to
AB  - the start of the seventh pandemic. We define six stages leading to the pandemic
AB  - strain and reveal all key events. The seventh pandemic originated from a
AB  - nonpathogenic strain in the Middle East, first observed in 1897. It subsequently
AB  - underwent explosive diversification, including the spawning of the pandemic
AB  - lineage. This rapid diversification suggests that, when first observed, the
AB  - strain had only recently arrived in the Middle East, possibly from the Asian
AB  - homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained
AB  - the important virulence-associated elements Vibrio seventh pandemic island I
AB  - (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then
AB  - became pandemic in 1961 after only 12 additional mutations. Our data indicate
AB  - that specific niches in the Middle East and Makassar were important in generating
AB  - the pandemic strain by providing gene sources and the driving forces for genetic
AB  - events.
ER  -

TY  - JOUR
AU  - Hu, K.-Y.
AU  - Wuu, J.-A.
AU  - Kao, M.-C.
AU  - Liu, Y.-T.
AU  - Pai, S.-H.
TI  - Isolation and characterization of a newly identified type II restriction endonuclease from a local Streptomyces sp. in Taiwan.
JO  - Appl. Biochem. Biotechnol.
PY  - 1998
SP  - 231
EP  - 241
VL  - 73
AB  - Streptomyces chusanensis ZS-2, isolated from a soil sample in Chusan in Taiwan, was found to
AB  - produce a new Type II restriction endonuclease. This restriction enzyme was designated as
AB  - SchI. The purified enzyme was characterized as having a subunit mol wt of 28 kDa, and was
AB  - apparently free from exonuclease activities. It cleaves the phosphodiester bond between the
AB  - fourth C and the fifth G on the 5'-CCGCGG-3' sequence of DNAs, leaving a 2-nucleotide
AB  - protruding end at its 3' site. This data suggests that SchI is an isoschizomer of SacII. In
AB  - addition, based on the comparison between SchI and SacII regarding reaction parameters, it
AB  - seems that SchI is a better choice of restriction enzyme for genetic analysis and mapping.
ER  -

TY  - JOUR
AU  - Hu, L.
AU  - Li, N.
AU  - Xu, C.
AU  - Zhong, S.
AU  - Lin, X.
AU  - Yang, J.
AU  - Zhou, T.
AU  - Yuliang, A.
AU  - Wu, Y.
AU  - Chen, Y.R.
AU  - Cao, X.
AU  - Zemach, A.
AU  - Rustgi, S.
AU  - von Wettstein, D.
AU  - Liu, B.
TI  - Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - 10642
EP  - 10647
VL  - 111
AB  - Cytosine methylation at CG sites (mCG) plays critical roles in development, epigenetic
AB  - inheritance, and genome stability in mammals and plants. In the dicot
AB  - model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal CG
AB  - methylase, functions to maintain mCG during DNA replication, with its null
AB  - mutation resulting in global hypomethylation and pleiotropic developmental
AB  - defects. Null mutation of a critical CG methylase has not been characterized at a
AB  - whole-genome level in other higher eukaryotes, leaving the generality of the
AB  - Arabidopsis findings largely speculative. Rice is a model plant of monocots, to
AB  - which many of our important crops belong. Here we have characterized a null
AB  - mutant of OsMet1-2, the major CG methylase in rice. We found that seeds
AB  - homozygous for OsMet1-2 gene mutation (OsMET1-2-/-), which directly segregated
AB  - from normal heterozygote plants (OsMET1-2+/-), were seriously maldeveloped, and
AB  - all germinated seedlings underwent swift necrotic death. Compared with wild type,
AB  - genome-wide loss of mCG occurred in the mutant methylome, which was accompanied
AB  - by a plethora of quantitative molecular phenotypes including dysregulated
AB  - expression of diverse protein-coding genes, activation and repression of
AB  - transposable elements, and altered small RNA profiles. Our results have revealed
AB  - conservation but also distinct functional differences in CG methylases between
AB  - rice and Arabidopsis.
ER  -

TY  - JOUR
AU  - Hu, L.
AU  - Zhang, G.
AU  - Allard, M.W.
AU  - Yao, K.
AU  - Stones, R.
AU  - Hoffmann, M.
AU  - Brown, E.W.
TI  - Complete Genome Sequences of Two Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Egg Products in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e00614
EP  - e00617
VL  - 5
AB  - Egg-associated salmonellosis is an important public health problem in many countries. Here, we
AB  - report the genome sequences, including plasmids, of two
AB  - strains of Salmonella enterica subsp. enterica serovar Enteritidis isolated from
AB  - egg products in 2012 and 2013 in the United States. This will provide more
AB  - information and insight into the research about egg-associated salmonellosis.
ER  -

TY  - JOUR
AU  - Hu, P.
AU  - Elliott, J.
AU  - McCready, P.
AU  - Skowronski, E.
AU  - Garnes, J.
AU  - Kobayashi, A.
AU  - Brubaker, R.R.
AU  - Garcia, E.
TI  - Structural organization of virulence-associated plasmids of Yersinia pestis.
JO  - J. Bacteriol.
PY  - 1998
SP  - 5192
EP  - 5202
VL  - 180
AB  - The complete nucleotide sequence and gene organization of the three virulence plasmids from
AB  - Yersinia pestis KIM5 were determined. Plasmid
AB  - pPCP1 (9,610 bp) has a GC content of 45.3% and encodes two previously
AB  - known virulence factors, an associated protein, and a single copy of
AB  - IS100. Plasmid pCD1 (70,504 bp) has a GC content of 44.8%. It is known to
AB  - encode a number of essential virulence determinants, regulatory functions,
AB  - and a multiprotein secretory system comprising the low-calcium response
AB  - stimulation that is shared with the other two Yersinia species pathogenic
AB  - for humans (Y. pseudotuberculosis and Y. enterocolitica). A new
AB  - pseudogene, which occurs as an intact gene in the Y. enterocolitica and Y.
AB  - pseudotuberculosis-derived analogues, was found in pCD1. It corresponds to
AB  - that encoding the lipoprotein YlpA. Several intact and partial insertion
AB  - sequences and/or transposons were also found in pCD1, as well as six
AB  - putative structural genes with high homology to proteins of unknown
AB  - function in other yersiniae. The sequences of the genes involved in the
AB  - replication of pCD1 are highly homologous to those of the cognate plasmids
AB  - in Y. pseudotuberculosis and Y. enterocolitica, but their localization
AB  - within the plasmid differs markedly from those of the latter. Plasmid pMT1
AB  - (100,984 bp) has a GC content of 50.2%. It possesses two copies of IS100,
AB  - which are located 25 kb apart and in opposite orientations. Adjacent to
AB  - one of these IS100 inserts is a partial copy of IS285. A single copy of an
AB  - IS200-like element (recently named IS1541) was also located in pMT1. In
AB  - addition to 5 previously described genes, such as murine toxin, capsule
AB  - antigen, capsule anchoring protein, etc., 30 homologues to genes of
AB  - several bacterial species were found in this plasmid, and another 44 open
AB  - reading frames without homology to any known or hypothetical protein in
AB  - the databases were predicted.
ER  -

TY  - JOUR
AU  - Hu, P.
AU  - Lang, J.
AU  - Wawrousek, K.
AU  - Yu, J.
AU  - Maness, P.C.
AU  - Chen, J.
TI  - Draft Genome Sequence of Rubrivivax gelatinosus CBS.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3262
EP  - 3262
VL  - 194
AB  - Rubrivivax gelatinosus CBS, a purple nonsulfur photosynthetic bacterium, can grow
AB  - photosynthetically using CO and N(2) as the sole carbon and nitrogen nutrients,
AB  - respectively. R. gelatinosus CBS is of particular interest due to its ability to
AB  - metabolize CO and yield H(2). We present the 5-Mb draft genome sequence of R.
AB  - gelatinosus CBS with the goal of providing genetic insight into the metabolic
AB  - properties of this bacterium.
ER  -

TY  - JOUR
AU  - Hu, P.
AU  - Yang, M.
AU  - Zhang, A.
AU  - Wu, J.
AU  - Chen, B.
AU  - Hua, Y.
AU  - Yu, J.
AU  - Chen, H.
AU  - Xiao, J.
AU  - Jin, M.
TI  - Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3428
EP  - 3429
VL  - 193
AB  - Streptococcus suis is a zoonotic pathogen, causing economic loss in swine industry, and is
AB  - also a threat to human health. To date, the mechanism of
AB  - pathogenisis is not fully understood. Here, we report the complete genome
AB  - sequence of S. suis strain ST3 of serotype 3, which provides opportunities
AB  - to reveal genetic basis of infection of S. suis non-serotype 2 strains.
ER  -

TY  - JOUR
AU  - Hu, P.
AU  - Yang, M.
AU  - Zhang, A.
AU  - Wu, J.
AU  - Chen, B.
AU  - Hua, Y.
AU  - Yu, J.
AU  - Xiao, J.
AU  - Jin, M.
TI  - Complete Genome Sequence of Streptococcus suis Serotype 14 Strain JS14.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2375
EP  - 2376
VL  - 193
AB  - Streptococcus suis is an important zoonotic agent leading to a variety of diseases in swine
AB  - and can be transmitted to human being upon close contact. Here, we report the complete genome
AB  - sequence of S. suis serotype 14 strain JS14 which was isolated from a diseased pig in Jiangsu
AB  - Province, China.
ER  -

TY  - JOUR
AU  - Hu, Q.
AU  - Qi, J.
AU  - Bo, H.
AU  - Liu, G.
AU  - Tao, M.
AU  - Ding, Y.
AU  - Xue, Y.
TI  - Complete Genome Sequence of Riemerella anatipestifer Serotype 10 Strain HXb2.
JO  - Genome Announcements
PY  - 2017
SP  - e00278
EP  - e00217
VL  - 5
AB  - The complete genome sequence of highly virulent Riemerella anatipestifer strain HXb2 was
AB  - determined. The genome consisted of a single circular chromosome of
AB  - 2,425,237 bp containing 2,383 putative open reading frames (ORFs), 9 rRNA
AB  - operons, and 40 tRNA genes.
ER  -

TY  - JOUR
AU  - Hu, S.
AU  - Yuan, S.
AU  - Qu, H.
AU  - Jiang, T.
AU  - Zhou, Y.
AU  - Wang, M.
AU  - Ming, D.
TI  - Antibiotic resistance mechanisms of Myroides sp.
JO  - J. Zhejiang Univ. Sci. B
PY  - 2016
SP  - 188
EP  - 199
VL  - 17
AB  - Bacteria of the genus Myroides (Myroides spp.) are rare opportunistic pathogens. Myroides sp.
AB  - infections have been reported mainly in China. Myroides sp. is highly resistant to most
AB  - available antibiotics, but the resistance mechanisms are not fully elucidated. Current strain
AB  - identification methods based on biochemical traits are unable to identify strains accurately
AB  - at the species level. While 16S ribosomal RNA (rRNA) gene sequencing can accurately achieve
AB  - this, it fails to give information on the status and mechanisms of antibiotic resistance,
AB  - because the 16S rRNA sequence contains no information on resistance genes, resistance islands
AB  - or enzymes. We hypothesized that obtaining the whole genome sequence of Myroides sp., using
AB  - next generation sequencing methods, would help to clarify the mechanisms of pathogenesis and
AB  - antibiotic resistance, and guide antibiotic selection to treat Myroides sp. infections.  As
AB  - Myroides sp. can survive in hospitals and the environment, there is a risk of nosocomial
AB  - infections and
AB  - pandemics. For better management of Myroides sp. infections, it is imperative to apply next
AB  - generation sequencing technologies to clarify the antibiotic resistance mechanisms in these
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Hu, S.
AU  - Zheng, H.
AU  - Gu, Y.
AU  - Zhao, J.
AU  - Zhang, W.
AU  - Yang, Y.
AU  - Wang, S.
AU  - Zhao, G.
AU  - Yang, S.
AU  - Jiang, W.
TI  - Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018.
JO  - BMC Genomics
PY  - 2011
SP  - 93
EP  - 93
VL  - 12
AB  - ABSTRACT: BACKGROUND: Clostridium acetobutylicum, a gram-positive and
AB  - spore-forming anaerobe, is a major strain for the fermentative production
AB  - of acetone, butanol and ethanol. But a previously isolated hyper-butanol
AB  - producing strain C. acetobutylicum EA 2018 does not produce spores and has
AB  - greater capability of solvent production, especially for butanol, than the
AB  - type strain C. acetobutylicum ATCC 824. RESULTS: Complete genome of C.
AB  - acetobutylicum EA 2018 was sequenced using Roche 454 pyrosequencing.
AB  - Genomic comparison with ATCC 824 identified many variations which may
AB  - contribute to the hyper-butanol producing characteristics in the EA 2018
AB  - strain, including a total of 46 deletion sites and 26 insertion sites. In
AB  - addition, transcriptomic profiling of gene expression in EA 2018 relative
AB  - to that of ATCC824 revealed expression-level changes of several key genes
AB  - related to solvent formation. For example, spo0A and adhEII have higher
AB  - expression level, and most of the acid formation related genes have lower
AB  - expression level in EA 2018. Interestingly, the results also showed that
AB  - the variation in CEA_G2622 (CAC2613 in ATCC 824), a putative
AB  - transcriptional regulator involved in xylose utilization, might accelerate
AB  - utilization of substrate xylose. CONCLUSIONS: Comparative analysis of C.
AB  - acetobutylicum hyper-butanol producing strain EA 2018 and type strain ATCC
AB  - 824 at both genomic and transcriptomic levels, for the first time,
AB  - provides molecular-level understanding of non-sporulation, higher solvent
AB  - production and enhanced xylose utilization in the mutant EA 2018. The
AB  - information could be valuable for further genetic modification of C.
AB  - acetobutylicum for more effective butanol production.
ER  -

TY  - JOUR
AU  - Hu, W.
AU  - Wang, C.
AU  - Liang, J.
AU  - Zhang, T.
AU  - Hu, Z.
AU  - Wang, Z.
AU  - Lan, W.
AU  - Li, F.
AU  - Wu, H.
AU  - Ding, J.
AU  - Wu, G.
AU  - Deng, Z.
AU  - Cao, C.
TI  - Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification.
JO  - Cell Res.
PY  - 2012
SP  - 1203
EP  - 1206
VL  - 22
AB  - DNA phosphorothioate modification, originally developed as an artificial tool to stabilize
AB  - oligodeoxynucleotides against nuclease degradation, was recently found to be incorporated with
AB  - sulfur into DNA backbone as a novel physiological variation by the five-gene dnd cluster
AB  - (dndA-dndE) products in a sequence- and stereo-specific manner.  This PT modification causes
AB  - the DNA degradation (Dnd) phenotype and is widespread and quantized in bacterial genomes,
AB  - working as a part of a restriction modification system.  This modification can be specifically
AB  - cleaved in vitro by type IV restriction endonuclease.  DndA works as a cysteine desulfurase
AB  - and assembles DndC as a 4Fe-4S cluster protein.  DndC possesses ATP pyrophosphatase activity
AB  - and is predicted to have 3'-phosphoadenosine-5'-phosphosulfate reductase activity, whereas
AB  - DndB has homology to a group of transcriptional regulators.  DndD, known as SpfD in
AB  - Pseudomonas fluorescens Pf0-1, has ATPase activity possibly related to DNA structure
AB  - alteration of nicking during PT incorporation.  Sequence identity (46%) and similarity (61%)
AB  - to phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) from Anabaena variabilis
AB  - suggest that DndE could be an NCAIR synthase analogue.  However, DndE may also act as a
AB  - sulfotransferase due to a specific PAPS binding sequence AAVGK-TLLIHLHR contained in the
AB  - C-terminus of DndE from Streptomyces lividans.  Therefore, the exact function of DndE remains
AB  - unknown.
ER  -

TY  - JOUR
AU  - Hu, W.P.
AU  - Yu, H.S.
AU  - Hsieh, M.C.
AU  - Chen, Y.C.
AU  - Wang, J.J.
TI  - Evaluation of DNA-binding ability of antibiotic DC-81 - indole conjugates by restriction endonuclease BamHI and molecular modeling studies.
JO  - Chin. Pharm. J.
PY  - 2002
SP  - 465
EP  - 470
VL  - 54
AB  - DC-81, an antitumor antibiotic produced by Streptomyces species, belongs to the
AB  - pyrrolo-{2,1-c}{1,4}benzodiazepines which are potent inhibitors of nucleic acid synthesis
AB  - because of their ability to recognize and bind to specific sequence of DNA to form a labile
AB  - covalent adduct.  The hybrid agents comprised of DC-81 and indole carboxylate moiety 2 through
AB  - carbon chain linkers (comprised of zero and two to four carbons) have been designed and
AB  - synthesized by our group.  These compounds with DNA binding ability were determined by
AB  - restriction endonuclease BamHI and molecular modeling studies.  The results demonstrated that
AB  - DC-81 - IC hybrid 3c (with a three carbon chain linker) showed a higher DNA-binding affinity
AB  - and gave rise to a maximal stabilization of the complex with DNA at the minor groove as
AB  - compared to the other complexes formed with 3a, 3b and 3d.
ER  -

TY  - JOUR
AU  - Hu, X.
AU  - Fan, W.
AU  - Han, B.
AU  - Liu, H.
AU  - Zheng, D.
AU  - Li, Q.
AU  - Dong, W.
AU  - Yan, J.
AU  - Gao, M.
AU  - Berry, C.
AU  - Yuan, Z.
TI  - Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus  species.
JO  - J. Bacteriol.
PY  - 2008
SP  - 2892
EP  - 2902
VL  - 190
AB  - Bacillus sphaericus strain C3-41 is an aerobic, mesophilic, spore-forming bacterium that has
AB  - been used with great success in mosquito control
AB  - programs worldwide. Genome sequencing revealed that the complete genome of
AB  - this entomopathogenic bacterium is composed of a chromosomal replicon of
AB  - 4,639,821 bp and a plasmid replicon of 177,642 bp, containing 4,786 and
AB  - 186 potential protein-coding sequences, respectively. Comparison of the
AB  - genome with other published sequences indicated that the B. sphaericus
AB  - C3-41 chromosome is most similar to that of Bacillus sp. strain NRRL
AB  - B-14905, a marine species that, like B. sphaericus, is unable to
AB  - metabolize polysaccharides. The lack of key enzymes and sugar transport
AB  - systems in the two bacteria appears to be the main reason for this
AB  - inability, and the abundance of proteolytic enzymes and transport systems
AB  - may endow these bacteria with exclusive metabolic pathways for a wide
AB  - variety of organic compounds and amino acids. The genes shared between B.
AB  - sphaericus C3-41 and Bacillus sp. strain NRRL B-14905, including mobile
AB  - genetic elements, membrane-associated proteins, and transport systems,
AB  - demonstrated that these two species are a biologically and
AB  - phylogenetically divergent group. Knowledge of the genome sequence of B.
AB  - sphaericus C3-41 thus increases our understanding of the bacilli and may
AB  - also offer prospects for future genetic improvement of this important
AB  - biological control agent.
ER  -

TY  - JOUR
AU  - Hu, X.
AU  - Li, A.
AU  - Lv, L.
AU  - Yuan, C.
AU  - Guo, L.
AU  - Jiang, X.
AU  - Jiang, H.
AU  - Qian, G.
AU  - Zheng, B.
AU  - Guo, J.
AU  - Li, L.
TI  - High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain  hu-01.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 755
EP  - 762
VL  - 9
AB  - Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order
AB  - Bacillales, class Bacilli and phylum Firmicutes. The increasing
AB  - relevance of S. cohnii to human health prompted us to determine the genomic
AB  - sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a
AB  - multidrug-resistant isolate from a hospital in China. Here we describe the
AB  - features of S. cohnii subsp. cohnii strain hu-01, together with the genome
AB  - sequence and its annotation. This is the first genome sequence of the species
AB  - Staphylococcus cohnii.
ER  -

TY  - JOUR
AU  - Hu, X.
AU  - Shang, Y.
AU  - Guo, J.
AU  - Zhang, H.
AU  - Liang, Y.
AU  - Sun, J.
AU  - Yue, F.
TI  - Draft Genome Sequence of Staphylococcus microti DSM 22147, Isolated from the Common Vole.
JO  - Genome Announcements
PY  - 2018
SP  - e00420
EP  - e00418
VL  - 6
AB  - Staphylococcus microti DSM 22147 was isolated from viscera of common voles (Microtus arvalis
AB  - Pallas) with generalized Brucella microti infection in the
AB  - Czech Republic. To the best of our knowledge, the genome sequence of the species
AB  - S. microti has not been previously studied. The complete genome sequence of
AB  - strain DSM 22147 includes a genome of 2,381,859 bp (38.0% GC content) without any
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Hu, X.
AU  - Wang, J.
AU  - Wang, F.
AU  - Chen, Q.
AU  - Huang, Y.
AU  - Cui, Z.
TI  - Complete Genome Sequence of the p-Nitrophenol-Degrading Bacterium Pseudomonas putida DLL-E4.
JO  - Genome Announcements
PY  - 2014
SP  - e00596
EP  - e00514
VL  - 2
AB  - The first complete genome sequence of a p-nitrophenol (PNP)-degrading bacterium is reported
AB  - here. Pseudomonas putida DLL-E4, a Gram-negative bacterium isolated
AB  - from methyl-parathion-polluted soil, can utilize PNP as the sole carbon and
AB  - nitrogen source. P. putida DLL-E4 has a 6,484,062 bp circular chromosome that
AB  - contains 5,894 genes, with a G+C content of 62.46%.
ER  -

TY  - JOUR
AU  - Hu, X.
AU  - Zheng, B.
AU  - Jiang, H.
AU  - Kang, Y.
AU  - Cao, Q.
AU  - Ning, H.
AU  - Shang, J.
TI  - Draft Genome Sequence of Staphylococcus sciuri subsp. sciuri Strain Z8, Isolated  from Human Skin.
JO  - Genome Announcements
PY  - 2015
SP  - e00714
EP  - e00715
VL  - 3
AB  - Staphylococcus sciuri subsp. sciuri strain Z8 was isolated from a skin wound infection of a
AB  - patient with infective endocarditis. To the best of our knowledge,
AB  - the genome sequence of the species S. sciuri has not been previously studied. The
AB  - complete genome sequence of strain Z8 includes a genome of 2,620,868 bp (32.43%
AB  - GC content) without any plasmids.
ER  -

TY  - JOUR
AU  - Hu, Y.
AU  - Feng, Y.
AU  - Qin, J.
AU  - Radolfova-Krizova, L.
AU  - Maixnerova, M.
AU  - Zhang, X.
AU  - Nemec, A.
AU  - Zong, Z.
TI  - Acinetobacter wuhouensis sp. nov., isolated from hospital sewage.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2018
SP  - 3212
EP  - 3216
VL  - 68
AB  - We recovered eight strains of the genus Acinetobacter from hospital sewage at
AB  - West China Hospital in Chengdu, China. Based on the comparative analysis of the
AB  - rpoB sequence, these strains formed a strongly supported and internally coherent
AB  - cluster (intra-cluster identity of >/=98.0 %), which was clearly separated from
AB  - all known Acinetobacter species (</=91.1 %). The eight strains also formed a
AB  - tight and distinct cluster based on the genus-wide comparison of whole-cell mass
AB  - fingerprints generated by matrix-assisted laser desorption/ionization
AB  - time-of-flight mass spectrometry. In addition, the combination of their ability
AB  - to assimilate 2,3-butanediol and phenylacetate, but not 4-hydroxybenzoate, and
AB  - the inability to grow at 37 degrees C could distinguish these eight strains from
AB  - all known Acinetobacter species. Whole-genomic sequencing has been performed for
AB  - two selected strains, WCHA60(T) and WCHA62. There were 96.65 % average nucleotide
AB  - identity (ANI) and 72 % in silico DNA-DNA hybridization (isDDH) values between
AB  - WCHA60(T) and WCHA62, suggesting that the two strains indeed belonged to the same
AB  - species. In contrast, the ANI and isDDH values between the two strains and the
AB  - known Acinetobacter species were <83 and <30 %, respectively; both of which were
AB  - far below the cut-off to define a bacterial species. Therefore, the eight strains
AB  - should be considered to represent a novel species of the genus Acinetobacter, for
AB  - which the name Acinetobacterwuhouensis sp. nov. is proposed. The type strain is
AB  - WCHA60(T) (=CCTCC AB 2016204(T)=GDMCC 1.1100(T)=KCTC 52505(T)).
ER  -

TY  - JOUR
AU  - Hu, Y.
AU  - Li, T.
AU  - Yang, Z.
AU  - Zhang, B.
AU  - Li, Y.
TI  - Phage resistance of Corynebacterium crenatum conferred by the restriction and modification system cglI.
JO  - Sheng Wu Gong Cheng Xue Bao
PY  - 2008
SP  - 760
EP  - 765
VL  - 24
ER  -

TY  - JOUR
AU  - Hu, Y.
AU  - Wu, W.
AU  - Feng, Y.
AU  - Zhang, X.
AU  - Zong, Z.
TI  - Draft Genome Sequence of a Pseudomonas sp. Strain Carrying blaIMP-25 and blaVIM-2 Carbapenemase Genes from Hospital Sewage.
JO  - Genome Announcements
PY  - 2016
SP  - e01027
EP  - e01016
VL  - 4
AB  - Pseudomonas strain WCHP16 recovered from hospital sewage in West China Hospital,  Chengdu,
AB  - China was found to carry two carbapenemase genes blaIMP-25 and blaVIM-2
AB  - Here, we report its 5.7-Mb draft genome sequence, comprising 141 contigs and an
AB  - average 59.53% G+C content. The genome contained 5,504 coding sequences and 67
AB  - tRNA genes.
ER  -

TY  - JOUR
AU  - Hu, Y.
AU  - Xu, X.
AU  - Song, P.
AU  - Jiang, L.
AU  - Zhang, Z.
AU  - Huang, H.
TI  - Draft Genome Sequence of Deinococcus xibeiensis R13, a New Carotenoid-Producing Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00987
EP  - e00913
VL  - 1
AB  - Deinococcus xibeiensis strain R13, isolated from radiation-contaminated soils, synthesizes a
AB  - unique ketocarotenoid, deinoxanthin. Here, we present a 3.49-Mb
AB  - assembly of its genome sequence, which can help us find the key genes of the
AB  - deinoxanthin biosynthesis pathways and modify genes obtaining a high yield of the
AB  - new carotenoid.
ER  -

TY  - JOUR
AU  - Hu, Y.
AU  - Zhang, W.
AU  - Liang, H.
AU  - Liu, L.
AU  - Peng, G.
AU  - Pan, Y.
AU  - Yang, X.
AU  - Zheng, B.
AU  - Gao, G.F.
AU  - Zhu, B.
AU  - Hu, H.
TI  - Whole-Genome Sequence of a Multidrug-Resistant Clinical Isolate of Acinetobacter lwoffii.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5549
EP  - 5550
VL  - 193
AB  - Acinetobacter lwoffii has been considered an opportunistic pathogen that can cause nosocomial
AB  - infections in humans. Here, we present the genome
AB  - sequence of A. lwoffii WJ10621, a multidrug-resistant clinical isolate
AB  - that carries a plasmid with the NDM-1 resistance gene.
ER  -

TY  - JOUR
AU  - Hu, Z.Y.
AU  - Wang, Y.Z.
AU  - Im, W.T.
AU  - Wang, S.Y.
AU  - Zhao, G.P.
AU  - Zheng, H.J.
AU  - Quan, Z.X.
TI  - The first complete genome sequence of the class fimbriimonadia in the phylum armatimonadetes.
JO  - PLoS ONE
PY  - 2014
SP  - E100794
EP  - E100794
VL  - 9
AB  - In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil
AB  - 348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes,
AB  - formerly called as candidate phylum OP10. The complete genome contains a single
AB  - circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open
AB  - reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of
AB  - Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil
AB  - 348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew
AB  - inversion which was usually observed in archaea was found. The predicted gene
AB  - functions suggest that the organism lacks the ability to synthesize histidine,
AB  - and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal
AB  - proteins indicated that strain Gsoil 348T represents a deeply branching lineage
AB  - of sufficient divergence with other phyla, but also strongly involved in
AB  - superphylum Terrabacteria.
ER  -

TY  - JOUR
AU  - Hua, N.M.
AU  - Karska-Wysocki, B.
AU  - Szatmari, G.
AU  - Mamet-Bratley, M.D.
TI  - Purification and characterization of the LlaGI restriction  enodnuclease from Lactococcus lactis subsp. cremoris G2.
JO  - Life Sc. Confer. Ottawa
PY  - 1998
SP  - P001
EP  - P001
VL  - 0
AB  - In the dairy industry, Lactococcus lactis are widely used as starter cultures in the
AB  - manufacture of the dairy products.  Bacteriophage infection is a serious problem for the dairy
AB  - industry.  To date, four categories of natural phage defense mechanisms have been identified
AB  - in lactococci based on the mode of action: adsorption inhibition, penetration blocking,
AB  - abortive infection, and restriction-modification system.  L. lactis subsp. cremoris G2 has
AB  - previously been isolated and purified in our laboratory.  Strain G2, which encodes a type-II
AB  - R-M endonuclease, designated LlaGI, contains at least five plasmids.  When L. lactis strain G2
AB  - was cured from most of its plasmids, the specific nuclease activity was lost.  These results
AB  - strongly indicate that the R-M system is plasmid-encoded.  LlaGI, an isoschizomer of NheI,
AB  - which recognizes the palindromic DNA sequence 5'_GCTAGC_3' has been purified to homogeneity
AB  - by a two-step procedure using ion-exchange and affinity chromatography.  The enzyme yield was
AB  - in excess of 1000 units/g of wet cells.  The purified enzyme was free of nonspecific nuclease
AB  - and requires only magnesium ion for its activity.  Physical properties indicate that LlaGI is
AB  - present in solution as monomer of about 40kDa.
ER  -

TY  - JOUR
AU  - Hua, X.
AU  - Chen, Q.
AU  - Li, X.
AU  - Feng, Y.
AU  - Ruan, Z.
AU  - Yu, Y.
TI  - Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment.
JO  - Genome Announcements
PY  - 2014
SP  - e01337
EP  - e01314
VL  - 2
AB  - Klbesiella pneumoniae is one of the most important human pathogens and frequently causes many
AB  - diseases. To facilitate the comparative genome analysis in
AB  - tigecycline resistance mechanism, we report the complete chromosomal sequence of
AB  - a multidrug-resistance K. pneumoniae strain before tigecycline treatment for
AB  - reference genome.
ER  -

TY  - JOUR
AU  - Hua, X.
AU  - Hua, Y.
TI  - Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing.
JO  - Genome Announcements
PY  - 2016
SP  - e00886
EP  - e00816
VL  - 4
AB  - The genome sequence of Deinococcus radiodurans R1 was published in 1999. We resequenced D.
AB  - radiodurans R1 using PacBio and compared the sequence with the
AB  - published one. Large insertions and single nucleotide polymorphisms (SNPs) were
AB  - observed among the genome sequences. A more accurate genome sequence will be
AB  - helpful to studies of D. radiodurans.
ER  -

TY  - JOUR
AU  - Hua, X.
AU  - Zhou, H.
AU  - Jiang, Y.
AU  - Feng, Y.
AU  - Chen, Q.
AU  - Ruan, Z.
AU  - Yu, Y.
TI  - Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Patient before and after Treatment with Tigecycline.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6979
EP  - 6980
VL  - 194
AB  - Acinetobacter baumannii is a Gram-negative bacterium which emerged as a significant nosocomial
AB  - pathogen worldwide. To investigate the molecular basis of
AB  - the tigecycline-resistant mechanism, we determined the genome sequences of two
AB  - multidrug-resistant A. baumannii strains isolated from a patient before and after
AB  - treatment with tigecycline.
ER  -

TY  - JOUR
AU  - Huai, Q.
AU  - Colandene, J.D.
AU  - Chen, Y.
AU  - Luo, F.
AU  - Zhao, Y.
AU  - Topal, M.D.
AU  - Ke, H.
TI  - Crystal structure of NaeI - an evolutionary bridge between DNA endonuclease and topoisomerase.
JO  - EMBO J.
PY  - 2000
SP  - 3110
EP  - 3118
VL  - 19
AB  - NaeI is transformed from DNA endonuclease to DNA topoisomerase and recombinase by a single
AB  - amino acid substitution. The crystal structure of NaeI was solved at 2.3 A resolution and
AB  - shows that NaeI is a dimeric molecule with two domains per monomer. Each domain contains one
AB  - potential DNA recognition motif corresponding to either endonuclease or topoisomerase
AB  - activity. The N-terminal domain core folds like the other type II restriction endonucleases as
AB  - well as lambda-exonuclease and the DNA repair enzymes MutH and Vsr, implying a common
AB  - evolutionary origin and catalytic mechanism. The C-terminal domain contains a catabolite
AB  - activator protein (CAP) motif present in many DNA-binding proteins, including the type IA and
AB  - type II topoisomerases. Thus, the NaeI structure implies that DNA processing enzymes evolved
AB  - from a few common ancestors. NaeI may be an evolutionary bridge between endonuclease and DNA
AB  - processing enzymes.
ER  -

TY  - JOUR
AU  - Huai, Q.
AU  - Colandene, J.D.
AU  - Topal, M.D.
AU  - Ke, H.
TI  - Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement.
JO  - Nat. Struct. Biol.
PY  - 2001
SP  - 665
EP  - 669
VL  - 8
AB  - NaeI, a novel DNA endonuclease, shows topoisomerase and recombinase activities when a Lys
AB  - residue is substituted for Leu 43. The NaeI-DNA structure demonstrates that each of the two
AB  - domains of NaeI recognizes one molecule of DNA duplex. DNA recognition induces dramatic
AB  - rearrangements: narrowing the binding site of the Topo domain 16 angstroms to grip DNA,
AB  - widening that
AB  - of the Endo domain 8 angstroms to encircle and bend DNA 45 degrees for cleavage, and
AB  - completely
AB  - rebuilding the homodimer interface. The NaeI-DNA structure presents the first example of novel
AB  - recognition of two copies of one DNA sequence by two different amino acid sequences and two
AB  - different structural motifs in one polypeptide.
ER  -

TY  - JOUR
AU  - Huang, B.
AU  - Schaeffer, C.J.
AU  - Li, Q.
AU  - Tsai, M.-D.
TI  - Splase: A new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites.
JO  - J. Protein Chem.
PY  - 1996
SP  - 481
EP  - 489
VL  - 15
AB  - A new restriction endonuclease, named Sp1ase, was constructed by genetically fusing the
AB  - DNA-cleavage domain of the restriction endonuclease FokI with the zinc-finger DNA-binding
AB  - domain of the transcription factor Sp1.  The resulting protein was expressed in Escherichia
AB  - coli, partially purified, and shown to selectively digest plasmid DNA harboring consensus Sp1
AB  - sites.  Sp1ase was also shown to selectively digest the long terminal repeat of the HIV-1 DNA
AB  - at Sp1 sites.  Sp1ase recognizes a 10-bp DNA sequence and hydrolyzes phosphodiester bonds
AB  - upstream of the binding sequence.  The binding specificity of Sp1ase makes this a "rare
AB  - cutter" restriction enzyme which could be valuable in creating large DNA fragments for genome
AB  - sequencing projects.  The result also presents the opportunity to create other restriction
AB  - enzymes by altering the binding specificity of the zing-finger recognition helix.
ER  -

TY  - JOUR
AU  - Huang, B.F.
AU  - Kropinski, A.M.
AU  - Bujold, A.R.
AU  - MacInnes, J.I.
TI  - Complete genome sequence of Actinobacillus equuli subspecies equuli ATCC 19392(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 32
EP  - 32
VL  - 10
AB  - Actinobacillus equuli subsp. equuli is a member of the family Pasteurellaceae that is a common
AB  - resident of the oral cavity and alimentary tract of healthy
AB  - horses. At the same time, it can also cause a fatal septicemia in foals, commonly
AB  - known as sleepy foal disease or joint ill disease. In addition, A. equuli subsp.
AB  - equuli has recently been reported to act as a primary pathogen in breeding sows
AB  - and piglets. To better understand how A. equuli subsp. equuli can cause disease,
AB  - the genome of the type strain of A. equuli subsp. equuli, ATCC 19392(T), was
AB  - sequenced using the PacBio RSII sequencing system. Its genome is comprised of
AB  - 2,431,533 bp and is predicted to encode 2,264 proteins and 82 RNAs.
ER  -

TY  - JOUR
AU  - Huang, C.H.
AU  - Liou, J.S.
AU  - Wang, C.L.
AU  - Huang, L.
TI  - Draft Genome Sequence of Clostridium sp. Strain chh4-2 Isolated from Human Feces.
JO  - Genome Announcements
PY  - 2018
SP  - e00070
EP  - e00018
VL  - 6
AB  - Here, we report the draft genome sequence of a Clostridium sp. strain isolated from a fecal
AB  - sample of a 34-year-old adult male in Taiwan. This strain may
AB  - represent a new bacterium, as suggested by a comparison based on whole-genome
AB  - sequencing. The genome assembly comprised 6,089,737 bp, with a 45.63% G+C
AB  - content.
ER  -

TY  - JOUR
AU  - Huang, C.J.
AU  - Zheng, P.X.
AU  - Ou, J.Y.
AU  - Lin, Y.C.
AU  - Chen, C.Y.
TI  - Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan.
JO  - Genome Announcements
PY  - 2017
SP  - e01290
EP  - e01217
VL  - 5
AB  - Bacillus cereus C1L, a plant growth-promoting rhizobacterium, provides protection against
AB  - fungal pathogens in monocot plants. To gain new insights into the
AB  - biocontrol mechanisms used by this rhizobacterium, we determined the complete
AB  - genome sequence of B. cereus C1L. One chromosome and three plasmids were
AB  - identified with a total size of ~6.0 Mb.
ER  -

TY  - JOUR
AU  - Huang, E.
AU  - Guo, Y.
AU  - Yousef, A.E.
TI  - Draft Genome Sequence of Paenibacillus sp. Strain OSY-SE, a Bacterium Producing the Novel Broad-Spectrum Lipopeptide Antibiotic Paenibacterin.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6306
EP  - 6306
VL  - 194
AB  - A strain of Paenibacillus sp., OSY-SE, was isolated from soil and found to produce a novel
AB  - lipopeptide antibiotic. The antibiotic, paenibacterin, is active
AB  - against Gram-negative and Gram-positive bacterial pathogens. Paenibacterin is
AB  - biosynthesized by a nonribosomal peptide synthetase pathway. Here we report the
AB  - draft genome sequence of Paenibacillus sp. OSY-SE.
ER  -

TY  - JOUR
AU  - Huang, E.
AU  - Yousef, A.E.
TI  - Draft Genome Sequence of Paenibacillus polymyxa OSY-DF, Which Coproduces a Lantibiotic, Paenibacillin, and Polymyxin E1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4739
EP  - 4740
VL  - 194
AB  - Paenibacillus polymyxa OSY-DF is a Gram-positive rod-shaped bacterium isolated from a
AB  - fermented vegetable food. This bacterial strain displays potent
AB  - antimicrobial activities against Gram-positive and Gram-negative pathogenic
AB  - bacteria, attributed to the production of the lantibiotic paenibacillin and the
AB  - colistin peptide polymyxin E1. Here we report the draft genome sequence of
AB  - Paenibacillus polymyxa OSY-DF.
ER  -

TY  - JOUR
AU  - Huang, E.-S.
AU  - Newbold, J.E.
AU  - Pagano, J.S.
TI  - Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z.
JO  - J. Virol.
PY  - 1973
SP  - 508
EP  - 514
VL  - 11
AB  - Limited digestion of simian virus 40 (SV40) DNA from both small- and
AB  - large-plaque strains with the restriction endonuclease Z from Haemophilus
AB  - aegyptius yielded 10 specific fragments.  The number of nucleotide pairs for
AB  - each fragment, determined by co-electrophoresis with PhiX174 RF fragments
AB  - produced by endonuclease Z, ranges from 2,050 to 80.  The difference in the
AB  - pattern between the large- and small-plaque strains is the disappearance of one
AB  - fragment containing approximately 255 nucleotide pairs and the appearance of a
AB  - new fragment with 145 nucleotide pairs.  This finding can be explained either
AB  - by deletions or insertions totaling 110 nucleotide pairs.  Complementary RNA
AB  - synthesized in vitro from the adeno-SV40 hybrid virus, strain ND-1, hybridized
AB  - preferentially to four of the fragments of SV40 DNA.
ER  -

TY  - JOUR
AU  - Huang, H.
AU  - Duceppe, M.O.
AU  - Phipps-Todd, B.
TI  - Draft Genome Sequence of Raoultella ornithinolytica Strain HH3.
JO  - Genome Announcements
PY  - 2018
SP  - e00270
EP  - e00218
VL  - 6
AB  - Raoultella ornithinolytica is a Gram-negative, nonmotile, encapsulated, and aerobic bacillus
AB  - and an emerging hospital-related bacterial pathogen of humans.
AB  - Here, we report a 5,977,517-bp draft genome sequence for Raoultella
AB  - ornithinolytica strain HH3, isolated from a pretreatment sample collected at a
AB  - Canadian wastewater treatment facility.
ER  -

TY  - JOUR
AU  - Huang, H.R.
AU  - Chao, M.Y.
AU  - Armstrong, B.
AU  - Wang, Y.
AU  - Lambowitz, A.M.
AU  - Perlman, P.S.
TI  - The DIVa maturase binding site in the yeast group II intron aI2 is essential for intron homing but not for in vivo splicing.
JO  - Mol. Cell. Biol.
PY  - 2003
SP  - 8809
EP  - 8819
VL  - 23
AB  - Splicing of the Saccharomyces cerevisiae mitochondrial DNA group II intron aI2 depends on the
AB  - intron-encoded 62-kDa reverse transcriptase-maturase
AB  - protein (p62). In wild-type strains, p62 remains associated with the
AB  - excised intron lariat RNA in ribonucleoprotein (RNP) particles that are
AB  - essential for intron homing. Studies of a bacterial group II intron showed
AB  - that the DIVa substructure of intron domain IV is a high-affinity binding
AB  - site for its maturase. Here we first present in vitro evidence extending
AB  - that conclusion to aI2. Then, experiments with aI2 DIVa mutant strains
AB  - show that the binding of p62 to DIVa is not essential for aI2 splicing in
AB  - vivo but is essential for homing. Because aI2 splicing in the DIVa mutant
AB  - strains remains maturase dependent, splicing must rely on other
AB  - RNA-protein contacts. The p62 that accumulates in the mutant strains has
AB  - reverse transcriptase activity, but fractionation experiments at high and
AB  - low salt concentrations show that it associates more weakly than the
AB  - wild-type protein with endogenous mitochondrial RNAs, and that phenotype
AB  - probably explains the homing defect. Replacing the DIVa of aI2 with that
AB  - of the closely related intron aI1 improves in vivo splicing but not
AB  - homing, indicating that DIVa contributes to the specificity of the
AB  - maturase-RNA interaction needed for homing.
ER  -

TY  - JOUR
AU  - Huang, J.
AU  - Qiao, Z.X.
AU  - Tang, J.W.
AU  - Wang, G.
TI  - High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 93
EP  - 93
VL  - 10
AB  - Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming,
AB  - and moderately halophilic bacterium isolated from a salt
AB  - field. In this study, we describe the features of P. yanchengensis strain Y32(T)
AB  - together with a comparison with other four Pontibacillus genomes. The 4,281,464
AB  - bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs
AB  - containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of
AB  - strain Y32(T) possesses many genes related to its halophilic character, flagellar
AB  - assembly and chemotaxis to support its survival in a salt-rich environment.
ER  -

TY  - JOUR
AU  - Huang, J.
AU  - Wang, H.
AU  - Liang, W.
AU  - Xie, X.
AU  - Guo, G.
TI  - Developmental expression of Arabidopsis methyltransferase genes MET1, DRM2, and CMT3.
JO  - Mol. Biol. (Mosk)
PY  - 2014
SP  - 681
EP  - 687
VL  - 48
AB  - Cytosine methylation is an epigenetic mark found in the genome of fungi, plants, and animals.
AB  - DNA methylation is catalyzed by DNA methyltransferases. The function of DNA methyltransferases
AB  - was shown to be highly conserved, but the biological role of these enzymes has not been
AB  - clearly defined. We generated transgenic plants expressing METHYLTRANSFERASES::GUS reporter
AB  - genes for three major DNA methyltransferases (MET1, DRM2 and CMT3) to gain insight into the
AB  - potential physiological relevance of the individual members of the DNA methyltransferase
AB  - family in Arabidopsis thaliana, and to investigate their expression patterns in detail. We
AB  - found that METHYLTRANSFERASE::GUS genes display unique tissue, cell-type, and temporal
AB  - patterns of expression throughout normal development, particularly in the flower. Our findings
AB  - are supported by semi-quantitative reverse-transcription PCR, as well as by analyses of
AB  - microarray databases. These data suggest that DNA methyltransferases may contribute to
AB  - morphogenesis at every developmental stage and in every plant organ.
ER  -

TY  - JOUR
AU  - Huang, J.J.
AU  - Wang, H.H.
AU  - Xie, X.J.
AU  - Zhang, D.
AU  - Liu, Y.
AU  - Guo, G.Q.
TI  - Roles of DNA methyltransferases in Arabidopsis development.
JO  - Afr. J. Biotechnol.
PY  - 2010
SP  - 8506
EP  - 8514
VL  - 9
AB  - DNA methylation plays a vital role during development in gene expression and chromatin
AB  - organization. DNA methyl transferases catalyze the transfer of a methyl group to bases within
AB  - the DNA helix. Plants differ from animals in having methylation at the sites of CHG and CHH.
AB  - In plant, there are at least four classes of cytosine methyltransferase: MET1, CMT3, DRM and
AB  - DNMT2. They show distinct expression patterns and levels in tissues and developmental stages
AB  - and differential activity on cytosines in different sequence contexts. Mutations that cause
AB  - severe loss of DNA methylation often leads to abnormal development. In the present review, we
AB  - summarized recent findings of the three major DNA methyltransferases mutants playing vital
AB  - role in development of Arabidopsis thaliana.
ER  -

TY  - JOUR
AU  - Huang, K.
AU  - Ni, J.
AU  - Xu, K.
AU  - Tang, H.
AU  - Tao, F.
AU  - Xu, P.
TI  - Genome Sequence of Sporolactobacillus terrae DSM 11697, the Type Strain of the Species.
JO  - Genome Announcements
PY  - 2014
SP  - e00465
EP  - e00414
VL  - 2
AB  - Sporolactobacillus terrae DSM 11697 is the type strain of S. terrae. Here, we present a 3.2-Mb
AB  - assembly of its genome sequence. As S. terrae is one of the
AB  - important lactic acid bacteria, the genome sequence may provide insights into the
AB  - molecular mechanism for its further microbial investigation.
ER  -

TY  - JOUR
AU  - Huang, L.
AU  - Zhao, L.
AU  - Su, Y.
AU  - Yan, Q.
TI  - Genome Sequence of Pseudomonas plecoglossicida Strain NZBD9.
JO  - Genome Announcements
PY  - 2018
SP  - e01412
EP  - e01417
VL  - 6
AB  - Pseudomonas plecoglossicida NZBD9 is the causative agent of white nodules in cultured large
AB  - yellow croaker in Fujian Province, China. We sequenced the genome
AB  - of NZBD9 to gain a better understanding of the etiological agent. The genome
AB  - sequence of the bacterium consists of 5.44 million bp, with a G+C content of
AB  - 61.9%.
ER  -

TY  - JOUR
AU  - Huang, L.-H.
AU  - Farnet, C.M.
AU  - Ehrlich, K.C.
AU  - Ehrlich, M.
TI  - Digestion of highly modified bacteriophage DNA by restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 1579
EP  - 1591
VL  - 10
AB  - The ability of thirty Type II restriction endonucleases to cleave five
AB  - different types of highly modified DNA has been examined.  The DNA substrates
AB  - were derived from relatively large bacteriophage genomes which contain all or
AB  - most of the cytosine or thymine residues substitutes at the 5-position.  These
AB  - substituents were a proton (PBS1 DNA), a hydroxymethyl group (SP01 DNA), a
AB  - methyl group (XP12 DNA), a glucosylated 4,5-dihydroxypentyl group (SP15 DNA).
AB  - Although PBS1 DNA and SP01 DNA were digested by most of the enzymes, they were
AB  - cleaved much more slowly than was normal DNA by many of them.
AB  - 5-Methyl-cytosine-rich XP12 DNA and the multiply modified T4 and SP15 DNAs were
AB  - resistant to most of these endonucleases.  The only enzyme that cleaved all
AB  - five of these DNAs was TaqI, which fragmented them extensively.
ER  -

TY  - JOUR
AU  - Huang, L.H.
AU  - Farnet, C.
AU  - Ehrlich, K.C.
AU  - Ehrlich, M.
TI  - Digestion of highly modified phage DNA by restriction endonucleases.
JO  - Fed. Proc.
PY  - 1982
SP  - 1199
EP  - 1199
VL  - 41
AB  - The ability of thirty TypeII restriction endonucleases to cleave five different
AB  - types of highly modified DNA has been examined.  The substrate DNAs were
AB  - derived from relatively large bacteriophage genomes which contain all or most
AB  - of the cytosine or thymine residues substituted at the 5-position.  These
AB  - substituents were a proton (PBS1 DNA), a hydroxymethyl group (SP01 DNA), a
AB  - methyl group (XP12 DNA), a glucosylated hydroxymethyl group (T4 DNA) or a
AB  - phosphoglucuronated, glucosylated 4,5-dihydroxypentyl group (SP15 DNA).  While
AB  - PBSI DNA and SP01 DNA were cleaved many times by most of the enzymes, they were
AB  - cleaved much more slowly than was normal DNA by many of them.
AB  - 5-Methylcytosine-rich XP12 DNA and the multiply modified T4 and SP15 DNAs were
AB  - resistant to most of the enzymes.  The only enzyme which cleaved all of these
AB  - DNAs was TaqI; TaqI fragmented the five highly modified DNAs extensively.  The
AB  - TaqI fragments from XP12 DNA were susceptible to ligation catalyzed by T4 DNA
AB  - ligase.
ER  -

TY  - JOUR
AU  - Huang, N.
AU  - Banavali, N.K.
AU  - MacKerell, A.D. Jr.
TI  - Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 68
EP  - 73
VL  - 100
AB  - DNA methylation, various DNA repair mechanisms, and possibly early events in the opening of
AB  - DNA as required for transcription and replication are
AB  - initiated by flipping of a DNA base out of the DNA double helix. The
AB  - energetics and structural mechanism of base flipping in the presence of
AB  - the DNA-processing enzyme, cytosine 5-methyltransferase from HhaI
AB  - (M.HhaI), were obtained through molecular dynamics based upon free-energy
AB  - calculations. Free-energy profiles for base flipping show that, when in
AB  - the closed conformation, M.HhaI lowers the free-energy barrier to flipping
AB  - by 17 kcalmol and stabilizes the fully flipped state. Flipping is shown to
AB  - occur via the major groove of the DNA. Structural analysis indicates that
AB  - flipping is facilitated by destabilization of the DNA double-helical
AB  - structure and substitution of DNA base-pairing and base-stacking
AB  - interactions with DNA-protein interactions. The fully flipped state is
AB  - stabilized by DNA-protein interactions that are enhanced upon binding of
AB  - coenzyme. This study represents an atomic detail description of the
AB  - mechanism by which a protein facilitates specific structural distortion in
AB  - DNA.
ER  -

TY  - JOUR
AU  - Huang, N.
AU  - MacKerell, A.D.
TI  - Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 265
EP  - 274
VL  - 345
AB  - Sequence-specific interactions between proteins and DNA are essential for a variety of
AB  - biological functions. The
AB  - (cytosine-C5)-methyltransferase from HhaI (M.HhaI) specifically
AB  - modifies the second base in GCGC sequences, employing a
AB  - base flipping mechanism to access the target base being chemically
AB  - modified. The mechanism of sequence-specific recognition of M.HhaI is
AB  - not evident based on crystallographic structures, leading to the
AB  - suggestion that recognition is linked to the flipping event itself, a
AB  - process that may be referred to as energetic recognition. Using
AB  - computational methods, it is shown that the free energy barriers to
AB  - flipping are significantly higher in non-cognate versus the cognate
AB  - sequence, supporting the energetic recognition mechanism. Energetic
AB  - recognition is imparted by two protein "selectivity filters" that
AB  - function via a "web" of protein-DNA interactions in short-lived, high
AB  - energy states present along the base flipping pathway. Other
AB  - sequence-specific DNA binding proteins whose function involves
AB  - significant distortion of DNA's conformation may use a similar
AB  - recognition mechanism.
ER  -

TY  - JOUR
AU  - Huang, N.
AU  - Zou, G.
AU  - Cao, X.
AU  - Zhu, R.
TI  - Studies on chemical modification and kinetics of restriction endonuclease Bsp78I.
JO  - Wuhan Daxue Xuebao
PY  - 1996
SP  - 233
EP  - 236
VL  - 42
AB  - Restriction endonuclease Bsp78I from Bacillus sphaericus 78 has been isolated and purified.
AB  - The purified enzyme was found to be homogeneous.  Michaelis constant of the enzyme is 2.67 x
AB  - 10^-8mol /L (substrate is pBR322 DNA).  The role of specific amino acid residues in Bsp78I was
AB  - assayed by chemical modifications.  Sulfhydryl groups were modified with
AB  - p-chloromercuribenzoic acid, lysine residues with pyridoxal-5'-phosphate and arginine
AB  - residues with 2,3-butanedione.  The results show that these residues are related to the
AB  - activity of Bsp78I.
ER  -

TY  - JOUR
AU  - Huang, S.
AU  - Qian, Y.
AU  - Wei, T.
AU  - Jia, C.
AU  - Yang, P.
AU  - Mao, D.
TI  - Draft Genome Sequence of Novosphingobium sp. Strain HII-3, a Bacterium Capable of Degrading the Cembranoid alpha(beta)-2,7,11-Cembratriene-4,6-Diol to Farnesal.
JO  - Genome Announcements
PY  - 2018
SP  - e00136
EP  - e00118
VL  - 6
AB  - Novosphingobium sp. HII-3, the first bacterium confirmed to degrade the cembranoid
AB  - alpha(beta)-2,7,11-cembratriene-4,6-diol to farnesal, was isolated
AB  - from cured tobacco leaf in Henan, China. Here, we report the annotated draft
AB  - genome sequence of strain HII-3, which has an estimated size of 4.45 Mb and
AB  - comprises 4,072 coding sequences.
ER  -

TY  - JOUR
AU  - Huang, S.
AU  - Vieira, S.
AU  - Bunk, B.
AU  - Riedel, T.
AU  - Sproer, C.
AU  - Overmann, J.
TI  - First Complete Genome Sequence of a Subdivision 6 Acidobacterium Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00469
EP  - e00416
VL  - 4
AB  - Although ubiquitous and abundant in soils, acidobacteria have mostly escaped isolation and
AB  - remain poorly investigated. Only a few cultured representatives and
AB  - just eight genomes of subdivisions 1, 3, and 4 are available to date. Here, we
AB  - determined the complete genome sequence of strain HEG_-6_39, the first genome of
AB  - Acidobacterium subdivision 6.
ER  -

TY  - JOUR
AU  - Huang, S.L.
AU  - Chen, H.
AU  - Hu, A.
AU  - Tuan, N.N.
AU  - Yu, C.P.
TI  - Draft Genome Sequence of Pseudomonas nitroreducens Strain TX1, Which Degrades Nonionic Surfactants and Estrogen-Like Alkylphenols.
JO  - Genome Announcements
PY  - 2014
SP  - e01262
EP  - e01213
VL  - 2
AB  - Pseudomonas nitroreducens TX1 ATCC PTA-6168 was isolated from rice field drainage in Taiwan.
AB  - The bacterium is of special interest because of its capability to use
AB  - nonionic surfactants (alkylphenol polyethoxylates) and estrogen-like compounds
AB  - (4-t-octylphenol and 4-nonylphenol) as a sole carbon source. This is the first
AB  - report on the genome sequence of P. nitroreducens.
ER  -

TY  - JOUR
AU  - Huang, T.W.
AU  - Chen, F.J.
AU  - Miu, W.C.
AU  - Liao, T.L.
AU  - Lin, A.C.
AU  - Huang, I.W.
AU  - Wu, K.M.
AU  - Tsai, S.F.
AU  - Chen, Y.T.
AU  - Lauderdale, T.L.
TI  - Complete Genome Sequence of Staphylococcus aureus M013, a pvl-Positive, ST59-SCCmec Type V Strain Isolated in Taiwan.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1256
EP  - 1257
VL  - 194
AB  - We report the complete genome sequence of M013, a representative strain of a pvl-positive,
AB  - sequence type 59-staphylococcal cassette chromosome mec type V
AB  - (ST59-SCCmec type V) community-associated methicillin-resistant Staphylococcus
AB  - aureus (CA-MRSA) clone in Taiwan. Comparison of M013 with the genomes of two
AB  - CA-MRSA strains in the United States revealed major differences in the regions
AB  - covering several genomic islands and prophages.
ER  -

TY  - JOUR
AU  - Huang, T.W.
AU  - Chen, T.L.
AU  - Chen, Y.T.
AU  - Lauderdale, T.L.
AU  - Liao, T.L.
AU  - Lee, Y.T.
AU  - Chen, C.P.
AU  - Liu, Y.M.
AU  - Lin, A.C.
AU  - Chang, Y.H.
AU  - Wu, K.M.
AU  - Kirby, R.
AU  - Lai, J.F.
AU  - Tan, M.C.
AU  - Siu, L.K.
AU  - Chang, C.M.
AU  - Fung, C.P.
AU  - Tsai, S.F.
TI  - Copy Number Change of the NDM-1 Sequence in a Multidrug-Resistant Klebsiella pneumoniae Clinical Isolate.
JO  - PLoS ONE
PY  - 2013
SP  - e62774
EP  - e62774
VL  - 8
AB  - The genetic features of the antimicrobial resistance of a multidrug resistant Klebsiella
AB  - pneumoniae strain harboring blaNDM-1
AB  - were investigated to increase our understanding of the evolution of NDM-1. The strain, KPX,
AB  - came from a Taiwanese patient with a hospitalization history in New Delhi. Complete DNA
AB  - sequencing was performed; and the genes responsible for antimicrobial resistance were
AB  - systematically examined and isolated by library screening. KPX harbored two resistance
AB  - plasmids, pKPX-1 and pKPX-2, which are 250-kb and 141-kb in size, respectively, with blaNDM-1
AB  - present on pKPX-1. The plasmid pKPX-1 contained genes associated with the IncR and IncF
AB  - groups, while pKPX-2 belonged to the IncF family. Each
AB  - plasmid carried multiple antimicrobial resistance genetic determinants. The gene responsible
AB  - for resistance to carbapenems was found on pKPX-1 and that for resistance to aztreonam was
AB  - found on pKPX-2. To our surprise, we discovered that blaNDM-1 exists on pKPX-1 as multiple
AB  - copies in the form of tandem repeats. Amplification of blaNDM-1 was found to occur by
AB  - duplication of an 8.6-kb unit, with the copy number of the repeat varying from colony to
AB  - colony. This repeat sequence is identical to that of the pNDM-MAR except for two base
AB  - substitutions. The copy number of blaNDM-1 of colonies under
AB  - different conditions was assessed by Southern blotting and quantitative PCR. The blaNDM-1
AB  - sequence was maintained in the presence of the antimicrobial selection; however, removal of
AB  - antimicrobial selection led to the emergence of susceptible bacterial populations with a
AB  - reduced copy number or even the complete loss of the blaNDM-1 sequence. The dynamic nature of
AB  - the NDM-1 sequence provides a strong argument for judicious use of the broad-spectrum
AB  - antimicrobials in order to reduce the development and spread of antimicrobial resistance among
AB  - pathogens.
ER  -

TY  - JOUR
AU  - Huang, W.
AU  - Ojaimi, C.
AU  - Fallon, J.T.
AU  - Travisany, D.
AU  - Maass, A.
AU  - Ivanova, L.
AU  - Tomova, A.
AU  - Gonzalez-Acuna, D.
AU  - Godfrey, H.P.
AU  - Cabello, F.C.
TI  - Genome Sequence of Borrelia chilensis VA1, a South American Member of the Lyme Borreliosis Group.
JO  - Genome Announcements
PY  - 2015
SP  - e01535
EP  - e01514
VL  - 3
AB  - Borrelia chilensis strain VA1 is a recently described South American member of the Borrelia
AB  - burgdorferi sensu lato complex from Chile. Whole-genome sequencing
AB  - analysis determined its linear chromosome and plasmids lp54 and cp26, confirmed
AB  - its membership in the Lyme borreliosis group, and will open new research avenues
AB  - regarding its pathogenic potential.
ER  -

TY  - JOUR
AU  - Huang, X.
AU  - Jiang, W.
AU  - Zhang, F.
AU  - Liang, Z.
TI  - A simplified method for preparation of restriction endonuclease BamHI.
JO  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao
PY  - 1982
SP  - 60
EP  - 62
VL  - 4
AB  - A simplified method for preparation of restriction endonuclease BamHI was described.  With P11
AB  - cellulose column chromatography, the exonuclease and nonspecific endonuclease activity in the
AB  - crude extract could be removed and the activity of BamHI enriched by 10^5 fold.  The enzyme
AB  - preparation thus made might be used for genetic manipulation.
ER  -

TY  - JOUR
AU  - Huang, X.
AU  - Palmer, S.
AU  - Ahn, S.J.
AU  - Richards, V.P.
AU  - Williams, M.L.
AU  - Nascimento, M.M.
AU  - Burne, R.A.
TI  - Characterization of a highly arginolytic Streptococcus species that potently antagonizes Streptococcus mutans.
JO  - Appl. Environ. Microbiol.
PY  - 2016
SP  - 2187
EP  - 2187
VL  - 82
AB  - The ability of certain oral biofilm bacteria to moderate pH through arginine metabolism by the
AB  - arginine deiminase system (ADS) is a deterrent to the development of dental caries. Here, we
AB  - characterize a novel Streptococcus strain, designated strain A12, isolated from supragingival
AB  - dental plaque of a caries-free individual. A12 not only expressed the ADS pathway at high
AB  - levels under a variety of conditions but also effectively inhibited growth and two
AB  - intercellular signaling pathways of the dental caries pathogen Streptococcus mutans. A12
AB  - produced copious amounts of H2O2 via the pyruvate oxidase enzyme that were sufficient to
AB  - arrest the growth of S. mutans. A12 also produced a protease similar to challisin (Sgc) of
AB  - Streptococcus gordonii that was able to block the competence-stimulating peptide (CSP)-ComDE
AB  - signaling system, which is essential for bacteriocin production by S. mutans. Wild-type A12,
AB  - but not an sgc mutant derivative, could protect the sensitive indicator strain Streptococcus
AB  - sanguinis SK150 from killing by the bacteriocins of S. mutans. A12, but not S. gordonii, could
AB  - also block the XIP (comX-inducing peptide) signaling pathway, which is the proximal regulator
AB  - of genetic competence in S. mutans, but Sgc was not required for this activity. The complete
AB  - genome sequence of A12 was determined, and phylogenomic analyses compared A12 to streptococcal
AB  - reference genomes. A12 was most similar to Streptococcus australis and Streptococcus
AB  - parasanguinis but sufficiently different that it may represent a new species. A12-like
AB  - organisms may play crucial roles in the promotion of stable, health-associated oral biofilm
AB  - communities by moderating plaque pH and interfering with the growth and virulence of caries
AB  - pathogens.
ER  -

TY  - JOUR
AU  - Huang, X.
AU  - Wang, Z.
AU  - Liu, Y.
AU  - Zhang, X.
TI  - Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth-Promoting Rhizobacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00233
EP  - e00217
VL  - 5
AB  - The plant growth-promoting rhizobacterium Pseudomonas protegens H78, which was isolated from
AB  - the rhizosphere of oilseed rape in Shanghai, can produce a large
AB  - array of antibiotics with a broad spectrum of activities. Here, we report the
AB  - annotated complete genome sequence of P. protegens H78.
ER  -

TY  - JOUR
AU  - Huang, X.J.
AU  - Lu, H.L.
AU  - Wang, J.W.
AU  - Xu, L.Q.
AU  - Liu, S.Y.
AU  - Sun, J.H.
AU  - Gao, F.
TI  - High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI.
JO  - BMC Genet.
PY  - 2013
SP  - 56
EP  - 56
VL  - 14
AB  - Background: As a well-known epigenomic modification, DNA methylation is found to be common in
AB  - plants and plays an important role in many
AB  - biological processes. Relying on the unique feature of
AB  - methylation-dependent digestion, the family of methylation-requiring
AB  - restriction-like endonuclease, such as MspJI and its homologs, was
AB  - suggested for a potential usage in methylation detection.
AB  - Results: In this study, we combine MspJI digestion and
AB  - electrophoretic band selection with next generation high-throughput
AB  - sequencing technology to detect 5-methylcytosines in Arabidopsis
AB  - genome. By developing a bioinformatics workflow to attribute the CNNR
AB  - sites recognized by MspJI to the reference genome, we fulfilled the
AB  - systematic assessment of this method.
AB  - Conclusions: According to the assessment, here we provide the
AB  - method for generating a detailed map of plant methylome that could be
AB  - feasible, reliable and economical in methylation investigation.
ER  -

TY  - JOUR
AU  - Huang, Y.
AU  - Fang, T.
AU  - Wang, H.
AU  - Zhou, H.
TI  - Draft Genome Sequence of Oleiagrimonas soli 3.5XT, a Type Species in a Newly Identified Genus, Isolated from an Oil Field in China.
JO  - Genome Announcements
PY  - 2015
SP  - e00469
EP  - e00415
VL  - 3
AB  - Oleiagrimonas gudaosoli 3.5X(T) was isolated from an oil field and identified as  a new member
AB  - of a novel genus. The draft genome sequence of this strain, which
AB  - comprises 3,379,958 bp encoding 3,010 open reading frames (ORFs), can provide
AB  - insight into the life style of this newly identified genus in
AB  - petroleum-contaminated soil.
ER  -

TY  - JOUR
AU  - Huang, Y.
AU  - Friedman, S.
TI  - The inhibition of RecA-mediated strand exchange by adducts of azacytosine-containing DNA and EcoRII methylase.
JO  - FASEB J.
PY  - 1990
SP  - A2294
EP  - A2294
VL  - 4
AB  - Recovery of cells from treatment with 5-azacytidine is dependent on the recA,
AB  - recBC pathway.  Cells containing DNA (cytosine-5) methylases which form tight
AB  - binding complexes with azacytosine containing DNA (azaC-DNA) are more sensitive
AB  - to the drug than cells lacking them.  We therefore studied the effect of these
AB  - complexes on recA mediated strand exchange in vitro.  32P labelled 422 bp DNA
AB  - fragment containing three binding sites for the EcoRII methylase and
AB  - azacytosine in the (-) strand was prepared.  We investigated the effect of the
AB  - EcoRII methylase on recA mediated strand exchange of the fragment with
AB  - homologous M13 DNA by electrophoresis on agarose gels.  In the absence of the
AB  - methylase, azaC-DNA has the same rate and extent of strand exchange as control
AB  - DNA.  But in the presence of the methylase incorporation of duplexes into
AB  - recA-ssDNA complexes is decreased from 80-90% to 10%, and strand exchange is
AB  - completely inhibited.  Since there is no incorporation of duplexes with
AB  - heterologous acceptor ssDNA, or in the absence of ATP, the incoporation of
AB  - azaC-DNA duplexes in the presence of methylase is believed to occur by partial
AB  - pairing of duplexes with homologous ssDNA leading to the formation of an
AB  - inactive complex composed of the methylase, dsDNA and recA-ssDNA complexes.
ER  -

TY  - JOUR
AU  - Huang, Y.
AU  - Friedman, S.
TI  - Inhibition of recA-mediated strand exchange by adducts of Azacytosine-containing DNA and the EcoRII methylase.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 17424
EP  - 17429
VL  - 266
AB  - Wild type Escherichia coli cells containing elevated levels of DNA (cytosine-5)
AB  - methyltransferases have increased sensitivity to the toxic effects of
AB  - 5-azacytidine.  The methyltransferases form tight binding complexes with
AB  - azacytosine in DNA which could interfere with the recA recBCD repair pathway
AB  - which is largely responsible for cell survival after treatment with the drug.
AB  - We therefore determined if these complexes interfered with recA-mediated strand
AB  - exchange in vitro, 32P-labeled DNA fragments containing a single EcoRII site,
AB  - with cytosine in the (-) strand replaced by 5-azacytosine, were prepared.  We
AB  - investigated the effect of the EcoRII methyltransferase on recA-mediated strand
AB  - exchange with homologous M13 DNA by electrophoresis in agarose gels.  In the
AB  - absence of the methylase the rate and extent of strand exchange of
AB  - azacytosine-containing DNA is the same as control DNA.  In the presence of the
AB  - methyltransferase strand exchange is inhibited, but some incorporation of
AB  - duplexes into recA-single-stranded DNA (ssDNA) complexes still occurs.  The
AB  - formation of these complexes is dependent on the length of the fragment 3' to
AB  - the methylase binding site on the strand complementary to the ssDNA.  The
AB  - greater the length the greater the number of complexes that form.
AB  - S-Adenosyl-L-methionine, which enhances binding of the methyltransferase to
AB  - azacytosine-containing DNA, causes an increase in the inhibition of strand
AB  - exchange and an increase in the number of inactive complexes formed.  The
AB  - complexes can be dissociated with guanidinium chloride which denatures the
AB  - methyltransferase and leads to release of the (+) strand.  The (-) strand
AB  - remains associated with the ssDNA.  This result implies that a plectonemic
AB  - joint is formed between recA-ssDNA complexes and azacytosine-containing
AB  - DNA-methyltransferase complexes.  However, branch migration in these complexes
AB  - is inhibited.  Denaturation of the methyltransferase allows branch migration to
AB  - proceed to completion, releasing the (+) strand.
ER  -

TY  - JOUR
AU  - Huang, Y.
AU  - Higuchi, Y.
AU  - Mori, K.
AU  - Yamashita, R.
AU  - Okino, N.
AU  - Tashiro, K.
AU  - Takegawa, K.
TI  - Draft Genome Sequence of Sphingobacterium sp. Strain HMA12, Which Encodes Endo-beta-N-Acetylglucosaminidases and Can Specifically Hydrolyze  Fucose-Containing Oligosaccharides.
JO  - Genome Announcements
PY  - 2018
SP  - e01525
EP  - e01517
VL  - 6
AB  - The genome sequence of the soil bacterium Sphingobacterium sp. strain HMA12, the  culture
AB  - supernatant of which exhibited endo-beta-N-acetylglucosaminidase (ENGase)
AB  - activity, was examined for ENGase-encoding genes. Here, we report the
AB  - characterization of new genes of ENGases, obtained by whole-genome shotgun
AB  - sequencing, that are capable of specifically hydrolyzing fucose-containing
AB  - oligosaccharides.
ER  -

TY  - JOUR
AU  - Huang, Y.
AU  - Jian, J.
AU  - Lu, Y.
AU  - Cai, S.
AU  - Wang, B.
AU  - Tang, J.
AU  - Pang, H.
AU  - Ding, Y.
AU  - Wu, Z.
TI  - Draft Genome Sequence of the Fish Pathogen Vibrio harveyi Strain ZJ0603.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6644
EP  - 6645
VL  - 194
AB  - Vibrio harveyi is an important pathogen that causes vibriosis in various aquatic  organisms.
AB  - Here, we announce the draft genome sequence of V. harveyi strain
AB  - ZJ0603, which was isolated from diseased Orange-spotted grouper (Epinephelus
AB  - coioides) in Guangdong, China.
ER  -

TY  - JOUR
AU  - Huang, Y.
AU  - Li, H.
AU  - Rensing, C.
AU  - Zhao, K.
AU  - Johnstone, L.
AU  - Wang, G.
TI  - Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1635
EP  - 1636
VL  - 194
AB  - Acidovorax sp. strain NO1, isolated from gold mine soil, was shown to be a facultative
AB  - anaerobic arsenite-oxidizing and nitrate-reducing bacterium. The
AB  - reported draft genome predicts the presence of genes involved in arsenic
AB  - metabolism, nitrate reduction, phosphate transport, and multiple metal
AB  - resistances and indicates putative horizontal gene transfer events.
ER  -

TY  - JOUR
AU  - Huang, Y.H.
AU  - Chou, S.H.
AU  - Liang, S.W.
AU  - Ni, C.E.
AU  - Lin, Y.T.
AU  - Huang, Y.W.
AU  - Yang, T.C.
TI  - Emergence of an XDR and carbapenemase-producing hypervirulent Klebsiella pneumoniae strain in Taiwan.
JO  - J. Antimicrob. Chemother.
PY  - 2018
SP  - 20392046
EP  - 20392046
VL  - 73
AB  - Background: Carbapenemase-producing Klebsiella pneumoniae causes high mortality
AB  - owing to the limited therapeutic options available. Here, we investigated an
AB  - emergent carbapenem-resistant K. pneumoniae strain with hypervirulence found
AB  - among KPC-2-producing strains in Taiwan. Methods: KPC-producing K. pneumoniae
AB  - strains were collected consecutively from clinical specimens at the Taipei
AB  - Veterans General Hospital between January 2012 and December 2014. Capsular types
AB  - and the presence of rmpA/rmpA2 were analysed, and PFGE and MLST performed using
AB  - these strains. The strain positive for rmpA/rmpA2 was tested in an in vivo mouse
AB  - lethality study to verify its virulence and subjected to WGS to delineate its
AB  - genomic features. Results: A total of 62 KPC-2-producing K. pneumoniae strains
AB  - were identified; all of these belonged to ST11 and capsular genotype K47. One
AB  - strain isolated from a fatal case with intra-abdominal abscess (TVGHCRE225)
AB  - harboured rmpA and rmpA2 genes. This strain was resistant to tigecycline and
AB  - colistin, in addition to carbapenems, and did not belong to the major cluster in
AB  - PFGE. TVGHCRE225 exhibited high in vivo virulence in the mouse lethality
AB  - experiment. WGS showed that TVGHCRE225 acquired a novel hybrid virulence plasmid
AB  - harbouring a set of virulence genes (iroBCDN, iucABCD, rmpA and rmpA2, and iutA)
AB  - compared with the classic ST11 KPC-2-producing strain. Conclusions: We identified
AB  - an XDR ST11 KPC-2-producing K. pneumoniae strain carrying a hybrid virulent
AB  - plasmid in Taiwan. Active surveillance focusing on carbapenem-resistant
AB  - hypervirulent K. pneumoniae strains is necessary, as the threat to human health
AB  - is imminent.
ER  -

TY  - JOUR
AU  - Huang, Y.J.
AU  - Parker, M.M.
AU  - Belfort, M.
TI  - Role of exonucleolytic degradation in group I intron homing in phage T4.
JO  - Genetics
PY  - 1999
SP  - 1501
EP  - 1512
VL  - 153
AB  - Homing of the phage T4 td intron is initiated by the intron-encoded endonuclease I-TevI, which
AB  - cleaves the intronless allele 23 and 25 nucleotides upstream of the intron insertion site
AB  - (IS). The distance between the I-TevI cleavage site (CS) and IS implicates endo- and/or
AB  - exonuclease activities to resect the DNA segment between the IS and CS. Furthermore, 3' tails
AB  - must presumably be generated for strand invasion by 5'-3' exonuclease activity. Three
AB  - experimental approaches were used to probe for phage nucleases involved in homing: a
AB  - comparative analysis of in vivo homing levels of nuclease-deficient phage, an in vitro assay
AB  - of nuclease activity and specificity, and a coconversion analysis of flanking exon markers. It
AB  - was thereby demonstrated that T4 RNase H, a 5'-3' exonuclease, T4 DNA exonuclease A (DexA)
AB  - and the exonuclease activity of T4 DNA polymerase (43Exo), 3'-5' exonucleases, play a role
AB  - in intron homing. The absence of these functions impacts not only homing efficiency but also
AB  - the extent of degradation and flanking marker coconversion. These results underscore the
AB  - critical importance of the 3' tail in intron homing, and they provide the first direct
AB  - evidence of a role for 3' single-stranded DNA ends as intermediates in T4 recombination.
AB  - Also, the involvement of RNase H, DexA, and 43Exo in homing provides a clear example of the
AB  - harnessing of functions variously involved in phage nucleic acid metabolism for intron
AB  - propagation.
ER  -

TY  - JOUR
AU  - Huang, Y.Y.
AU  - Cho, S.T.
AU  - Lo, W.S.
AU  - Wang, Y.C.
AU  - Lai, E.M.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Agrobacterium tumefaciens Ach5.
JO  - Genome Announcements
PY  - 2015
SP  - e00570
EP  - e00515
VL  - 3
AB  - Agrobacterium tumefaciens is a phytopathogenic bacterium that causes crown gall disease. The
AB  - strain Ach5 was isolated from yarrow (Achillea ptarmica L.) and is
AB  - the wild-type progenitor of other derived strains widely used for plant
AB  - transformation. Here, we report the complete genome sequence of this bacterium.
ER  -

TY  - JOUR
AU  - Hubacek, J.
TI  - Biological function of DNA methylation.
JO  - Folia Microbiol. (Praha)
PY  - 1992
SP  - 323
EP  - 329
VL  - 37
AB  - Structural and functional properties of prokaryotic DNA methyltransferases are summarized. The
AB  - different aspects of the role of DNA methylation which influences DNA-protein interaction in
AB  - restriction and modification of DNA and in mismatch repair, DNA replication and gene
AB  - expression are discussed.
ER  -

TY  - JOUR
AU  - Hubacek, J.
TI  - Functional analysis of second-step host specificity mutations in unstable escherichia coli heterozygotes.
JO  - J. Gen. Microbiol.
PY  - 1973
SP  - 257
EP  - 264
VL  - 79
AB  - From an Escherichia coli strain K12 carrying a temperature-sensitive host-specific
AB  - modification (hsm) mutation, second-step mutants have been isolated that are completely
AB  - deficient in modification and restriction. Complementation analysis has revealed that one
AB  - group of these mutants is impaired in the specificity gene hss, while in the other group of
AB  - mutant strains both mutations, i.e. the first-step temperature-sensitive and the second-step
AB  - which impairs restriction and modification completely, are located in hsm. Analysis of the
AB  - heterozygotes used in the complementation experiments suggested a cis- and tandem arrangement
AB  - of the hs and leu genes in haploid, segregating exconjugants; however, the attachement of
AB  - these genes to a cryptic plasmid was not excluded.
ER  -

TY  - JOUR
AU  - Hubacek, J.
AU  - Glover, S.W.
TI  - Complementation analysis of temperature-sensitive host specificity mutations in Escherichia coli.
JO  - J. Mol. Biol.
PY  - 1970
SP  - 111
EP  - 127
VL  - 50
AB  - A selection procedure was devised for the isolation of temperature-sensitive
AB  - mutants of Escherichia coli K12 unable to restrict foreign DNA.  Many of the
AB  - non-restricting mutants isolated also displayed temperature sensitivity in the
AB  - modification of DNA.  The mutations were shown to map in the hs cluster of
AB  - genes which determine the host specificity of DNA in E. coli.  The kinetics of
AB  - inactivation of restriction showed that a short exposure to high temperature
AB  - was sufficient to impair restriction of phage lambda DNA and that after shift
AB  - to low temperature restriction did not return to the wild-type level until a
AB  - period of growth had occurred.  One of the mutants was used as a starting
AB  - strain from which further mutants were then selected for their inability to
AB  - host-modify DNA.  Many of the mutants thus isolated, in addition to being
AB  - impaired in modification, were found to be non-restricting at both high and low
AB  - temperatures.  A complementation analysis of the mutants was carried out using
AB  - an F' donor strain derived from E. coli B and carrying the host-specificity
AB  - genes hssB+ hsr- hsm+.  In all but one of the F' merodiploids constructed
AB  - between this F' and the temperature-sensitive host specificity mutants of E.
AB  - coli K the temperature-sensitivity of the mutant phenotype was complemented and
AB  - the merodiploids displayed K-and B-specific restriction and K- and B-specific
AB  - modification.  From these results it is concluded that all of the
AB  - temperature-sensitive mutants carry mutations in the hsm gene, and are hssK+
AB  - hsr+ hsmts.  In addition it is argued that an hsm-directed polypeptide is
AB  - required for restriction in addition to polypeptides directed by hssK and hsr.
AB  - These results are discussed in terms of models based on the interaction of
AB  - subunits to form oligomeric enzymes.
ER  -

TY  - JOUR
AU  - Hubacek, J.
AU  - Holubova, I.
AU  - Weiserova, M.
TI  - The effect of recA mutation on the expression of EcoKI and EcoR124I hsd genes cloned in a multicopy plasmid.
JO  - Folia Microbiol. (Praha)
PY  - 1998
SP  - 353
EP  - 359
VL  - 43
AB  - Type I restriction-modification endonucleases are composed of three subunits - HsdR, required
AB  - for restriction, and HsdM and HsdS which can produce a separate DNA methyltransferase.  The
AB  - HsdS subunit is required for DNA recognition.  In this paper we describe the effect of cloned
AB  - EcoKI and EcoR124I hsd genes on the resulting R-M phenotype.  The variability in the
AB  - expression of the wild type restriction phenotype after cloning of the wt hsd genes in a
AB  - multicopy plasmid in Escherichia coli recA+ background suggests that the increased production
AB  - of the restriction endonuclease from pBR322 is detrimental to the cell and this leads to the
AB  - deletion of the cloned hsd genes from the hybrid plasmid and/or inactivation of the enzyme.
AB  - The effect of a mutation in the E. coli recA gene on the expression of the R-M phenotype is
AB  - described and discussed in relation to the role of the cell surface and the localization of
AB  - the restriction endonuclease in the cell.
ER  -

TY  - JOUR
AU  - Hubacek, J.
AU  - Weiserova, M.
TI  - Biological function of type I restriction enzymes.
JO  - Gene Manipulation and Expression
PY  - 1985
SP  - 95
EP  - 109
VL  - 0
AB  - Type I restriction enzymes are structurally and functionally so complicated that it was often
AB  - argued that they must perform some vital functions other than restriction and modification of
AB  - DNA. Using a genetic approach that was found to be so fruitful in the past we analyzed
AB  - temperature-sensitive (ts) mutations affecting restriction and modification. The concept of a
AB  - gene, designated hsd.X, which seems to be located outside the hsd operon, was formulated and
AB  - the role of its product in the regulation of expression of restriction and modification and in
AB  - the initiation of DNA replication is discussed. Further, we tried to establish if the
AB  - individual subunits of the type I restriction enzyme from E. coli K12 play some role in
AB  - mini-Mu and Tn9 transposition mechanisms.
ER  -

TY  - JOUR
AU  - Hubacek, J.
AU  - Weiserova, M.
TI  - DNA restriction and modification in Escherichia coli: Functional analysis of the role of the dnaC(D) gene product.
JO  - J. Gen. Microbiol.
PY  - 1980
SP  - 231
EP  - 238
VL  - 119
AB  - Escherichia coli strain PC-7 carries two independent temperature-sensitive mutations, one
AB  - affecting the restriction and modification (R-M) phenotype and the other the DNAC(D)
AB  - phenotype. The results of complementation and P1 transduction analysis of the mutation
AB  - affecting the R-M phenotype implicate a fourth gene, designated hsdX, located close to the hsd
AB  - three-gene complex. The properties of merodiploids constructed between appropriate recipients
AB  - and F' elements with different mutations in hsdS, hsdR and hsdM genes might indicate that in
AB  - strain PC-7 the temperature-sensitive products, determined by hsdR and hsdDK cistrons, are
AB  - synthesized. The role of the temperature-sensitive dnaC(D) gene product in the formation of
AB  - the restriction endonuclease was studied and no direct relation was found between the DnaC(D)
AB  - and R-M phenotypes.
ER  -

TY  - JOUR
AU  - Hubacek, J.
AU  - Weiserova, M.
AU  - Janscak, P.
AU  - Firman, K.
TI  - Restriction endonucleases R.EcoKI and R.EcoR124I are probably located in different environments within the bacterial cell.
JO  - Folia Microbiol. (Praha)
PY  - 1994
SP  - 162
EP  - 165
VL  - 39
AB  - We describe the phenomenon of a transient state of R124I restriction deficiency after
AB  - long-term storage of the E. coli [pCP1005] strain at 4oC, or after growth of the culture in
AB  - synthetic M9 medium with the nonmutagenic solvent dimethyl sulfoxide. The unusual high
AB  - reversion from the R+124 to the R-124 phenotype was observed only in E. coli strain
AB  - transformed with the high-copy number plasmid pCP1005 carrying EcoR124I hsdR, M and S genes
AB  - cloned, but not with strains carrying the natural conjugative plasmid R124. The effect of both
AB  - treatments on the expression of EcoR124I phenotype in relation to the possible location of
AB  - R.EcoR124I restriction endonuclease in E. coli is discussed.
ER  -

TY  - JOUR
AU  - Hubacek, J.
AU  - Zinkevich, V.E.
AU  - Weiserova, M.
TI  - The location of a temperature-sensitive trans-dominant mutation and its effect on restriction and modification in Escherichia coli K12.
JO  - J. Gen. Microbiol.
PY  - 1989
SP  - 3057
EP  - 3065
VL  - 135
AB  - An Escherichia coli K12 chromosomal EcoRI-BamHI fragment containing a mutant
AB  - hsdS locus was cloned into plasmid pBR322.  The mcrB gene, closely linked to
AB  - hsdS, was used for selection of clones with the inserted fragment using T4alpha
AB  - gt57beta gt14 and lambda vir PvuII phages; the phage DNAs contain methylated
AB  - cytosines and hence can be used to demonstrate McrB restriction.  For the
AB  - efficient expression of the hsdS gene, a BglII fragment of phage lambda
AB  - carrying the pR promoter was inserted into the BamHI site of the hybrid
AB  - plasmid.  Under these conditions a trans-dominant effect of the hsdXts+d
AB  - mutation on restriction and modification was detected.  Inactivation of the
AB  - hsdS gene by the insertion of the lambda phage BglII fragment into the BglII
AB  - site within this gene resulted in the disappearance of the trans-dominant
AB  - effect.  When the cloned BamHI-EcoRI fragment was shortened by HpaI and EcoRI
AB  - restriction enzymes, the trans-dominant effect was fully expressed.  The
AB  - results indicate that the Xts+d mutation is located in the hsdS gene.  The
AB  - effect of gene dosage of the HsdS subunit on the expression of Xts+d mutation
AB  - was studied.  The results of complementation experiments, using F'-merodiploids
AB  - or plasmid pBR322 with an inserted Xts+d mutation, support the idea that the
AB  - HsdSts+d product competes with the wild-type HsdS product, and has a
AB  - quantitatively different effect on restriction and modification.
ER  -

TY  - JOUR
AU  - Hubbard, A.T.
AU  - Davies, S.E.
AU  - Baxter, L.
AU  - Thompson, S.
AU  - Collery, M.M.
AU  - Hand, D.C.
AU  - Fink, C.G.
AU  - Thomas, D.J.
TI  - Draft Whole-Genome Sequence of a Haemophilus quentini Strain Isolated from an Infant in the United Kingdom.
JO  - Genome Announcements
PY  - 2016
SP  - e01075
EP  - e01016
VL  - 4
AB  - Haemophilus quentini is a rare and distinct genospecies of Haemophilus that has been suggested
AB  - as a cause of neonatal bacteremia and urinary tract infections in
AB  - men. We present the draft whole-genome sequence of H. quentini MP1 isolated from
AB  - an infant in the United Kingdom, aiding future identification and detection of
AB  - this pathogen.
ER  -

TY  - JOUR
AU  - Hubscher, U.
AU  - Pedrali-Noy, G.
AU  - Knust-Kron, B.
AU  - Doerfler, W.
AU  - Spadari, S.
TI  - DNA methyltransferases: Activity minigel analysis and determination with DNA covalently bound to a solid matrix.
JO  - Anal. Biochem.
PY  - 1985
SP  - 442
EP  - 448
VL  - 150
AB  - We describe two methods that facilitate detection and characterization of DNA
AB  - methyltransferases: activity gel analysis and the use of DNA-cellulose or DNA-Sepharose in DNA
AB  - methylation reactions.  The first permits identification of catalytic subunits, determination
AB  - of the influence of proteolysis, and evolutionary or developmental studies.  The second allows
AB  - accurate and fast determination of DNA methyltransferase activities in crude extracts and
AB  - during purification.
ER  -

TY  - JOUR
AU  - Hudson, C.M.
AU  - Bent, Z.W.
AU  - Meagher, R.J.
AU  - Williams, K.P.
TI  - Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain.
JO  - PLoS ONE
PY  - 2014
SP  - E99209
EP  - E99209
VL  - 9
AB  - Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious
AB  - disease challenge. These strains can accumulate many antibiotic resistance genes
AB  - though horizontal transfer of genetic elements, those for beta-lactamases being
AB  - of particular concern. Some beta-lactamases are active on a broad spectrum of
AB  - beta-lactams including the last-resort carbapenems. The gene for the
AB  - broad-spectrum and carbapenem-active metallo-beta-lactamase NDM-1 is rapidly
AB  - spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146,
AB  - the first U.S. isolate found to encode NDM-1, and describe its repertoire of
AB  - antibiotic-resistance genes and mutations, including genes for eight
AB  - beta-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the
AB  - evolution of this rich repertoire, the mobile elements of the genome were
AB  - characterized, including four plasmids with varying degrees of conservation and
AB  - mosaicism and eleven chromosomal genomic islands. One island was identified by a
AB  - novel phylogenomic approach, that further indicated the cps-lps polysaccharide
AB  - synthesis locus, where operon translocation and fusion was noted. Unique plasmid
AB  - segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was
AB  - transposed recently to the chromosome by ISEcp1. None of the eleven full copies
AB  - of IS26, the most frequent IS element in the genome, had the expected 8-bp direct
AB  - repeat of the integration target sequence, suggesting that each copy underwent
AB  - homologous recombination subsequent to its last transposition event. Comparative
AB  - analysis likewise indicates IS26 as a frequent recombinational junction between
AB  - plasmid ancestors, and also indicates a resolvase site. In one novel use of
AB  - high-throughput sequencing, homologously recombinant subpopulations of the
AB  - bacterial culture were detected. In a second novel use, circular transposition
AB  - intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY
AB  - family, suggesting that it uses the two-step transposition mechanism of IS3.
AB  - Robust genome-based phylogeny showed that a unified Klebsiella cluster contains
AB  - Enterobacter aerogenes and Raoultella, suggesting the latter genus should be
AB  - abandoned.
ER  -

TY  - JOUR
AU  - Hue, F.
AU  - Ghalyanchi, L.A.
AU  - Barbour, A.G.
TI  - Chromosome Sequence of Borrelia miyamotoi, an Uncultivable Tick-Borne Agent of Human Infection.
JO  - Genome Announcements
PY  - 2013
SP  - e00713
EP  - e00713
VL  - 1
AB  - Borrelia miyamotoi is a newly recognized agent of human disease. B. miyamotoi strain LB-2001,
AB  - an isolate from the tick Ixodes scapularis, was propagated in
AB  - mice. The sequence of the chromosome was determined by next-generation sequencing
AB  - of DNA isolated from whole blood. The sequence established that B. miyamotoi is a
AB  - relapsing fever group species.
ER  -

TY  - JOUR
AU  - Huedo, P.
AU  - Conchillo-Sole, O.
AU  - Yero, D.
AU  - Martinez-Servat, S.
AU  - Daura, X.
AU  - Gibert, I.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00576
EP  - e00514
VL  - 2
AB  - Stenotrophomonas maltophilia is an emerging opportunistic pathogen with an increasing
AB  - prevalence of multidrug-resistant strains. Here, we report the draft
AB  - genome sequence of S. maltophilia strain M30, isolated from a pressure ulcer in
AB  - an elderly patient.
ER  -

TY  - JOUR
AU  - Huedo, P.
AU  - Gori, M.
AU  - Scaltriti, E.
AU  - Morganti, M.
AU  - Casadei, G.
AU  - Amato, E.
AU  - Pontello, M.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Napoli Strain SN310, Cause of a Multischool Outbreak in Milan, Italy, in 2014.
JO  - Genome Announcements
PY  - 2015
SP  - e01044
EP  - e01015
VL  - 3
AB  - We report the draft genome sequence of Salmonella enterica subsp. enterica serovar Napoli
AB  - strain SN310, isolated from a stool sample of an affected pupil during a multischool outbreak
AB  - in 2014 in Milan, Italy. This represents the first  reported draft genome sequence of the
AB  - emerging serovar Napoli.
ER  -

TY  - JOUR
AU  - Huggett, M.J.
AU  - Hayakawa, D.H.
AU  - Rappe, M.S.
TI  - Genome sequence of strain HIMB624, a cultured representative from the OM43 clade  of marine Betaproteobacteria.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 11
EP  - 20
VL  - 6
AB  - Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the
AB  - class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii. This strain is of
AB  - interest because it is one of few known isolates from an abundant clade of Betaproteobacteria
AB  - found in cultivation-independent studies of coastal seawater and freshwater environments
AB  - around the globe, known as OM43. Here we describe some preliminary features of the organism,
AB  - draft genome sequence and annotation, and comparative genomic analysis with one other
AB  - sequenced member of this clade (strain HTCC2181). The 1,333,209 bp genome of strain HIMB624 is
AB  - arranged in a single scaffold containing four contigs, and contains 1,381 protein encoding
AB  - genes and 39 RNA genes.
ER  -

TY  - JOUR
AU  - Hughes, C.A.N.
AU  - Johnson, R.C.
TI  - Methylated DNA in Borrelia species.
JO  - J. Bacteriol.
PY  - 1990
SP  - 6602
EP  - 6604
VL  - 172
AB  - The DNA of Borrelia species was examined for the presence of methylated GATC
AB  - sequences.  The relapsing-fever Borrelia sp., B. coriaceae, and only 3 of 22
AB  - strains of B. burgdorferi contained adenine methylation systems.  B. anserina
AB  - lacked an adenine methylation system.  Fundamental differences in DNA
AB  - methylation exist among members of the genus Borrelia.
ER  -

TY  - JOUR
AU  - Hughes, G.L.
AU  - Raygoza, G.J.A.
AU  - Koundal, V.
AU  - Rasgon, J.L.
AU  - Mwangi, M.M.
TI  - Genome Sequence of Stenotrophomonas maltophilia Strain SmAs1, Isolated From the Asian Malaria Mosquito Anopheles stephensi.
JO  - Genome Announcements
PY  - 2016
SP  - e00086
EP  - e00016
VL  - 4
AB  - An isolate of Stenotrophomonas maltophilia was cultured from the Asian malaria vector
AB  - Anopheles stephensi. Here, we present the annotated draft genome sequence
AB  - of this S. maltophilia strain. This genomic resource will facilitate further
AB  - characterization of bacteria associated with mosquitoes.
ER  -

TY  - JOUR
AU  - Hughes, G.L.
AU  - Raygoza, G.J.A.
AU  - Koundal, V.
AU  - Rasgon, J.L.
AU  - Mwangi, M.M.
TI  - Genome Sequences of Staphylococcus hominis Strains ShAs1, ShAs2, and ShAs3, Isolated from the Asian Malaria Mosquito Anopheles stephensi.
JO  - Genome Announcements
PY  - 2016
SP  - e00085
EP  - e00016
VL  - 4
AB  - Staphylococcus hominis is a culturable component of the bacterial microbiome of Anopheles
AB  - stephensi. Here, we present the annotated draft genome sequences of
AB  - three S. hominis isolates from A. stephensi. These genomic resources will
AB  - facilitate experiments to further our understanding of the role of bacteria in
AB  - mosquito biology.
ER  -

TY  - JOUR
AU  - Hughes, H.Y.
AU  - Conlan, S.P.
AU  - Lau, A.F.
AU  - Dekker, J.P.
AU  - Michelin, A.V.
AU  - Youn, J.H.
AU  - Henderson, D.K.
AU  - Frank, K.M.
AU  - Segre, J.A.
AU  - Palmore, T.N.
TI  - Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture.
JO  - J. Clin. Microbiol.
PY  - 2016
SP  - 1167
EP  - 1170
VL  - 54
AB  - Perirectal surveillance cultures and a stool culture grewAeromonasspecies from
AB  - three patients over a 6-week period and were without epidemiological links.
AB  - Detection of theblaKPC-2gene in one isolate prompted inclusion of
AB  - non-Enterobacteriaceaein our surveillance culture workup. Whole-genome sequencing
AB  - confirmed that the isolates were unrelated and provided data
AB  - forAeromonasreference genomes.
ER  -

TY  - JOUR
AU  - Hughes, S.G.
TI  - Studies of plasmid encoded restriction and modification systems.
JO  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
PY  - 1977
SP  - 1
EP  - 70
AB  - Within the general context of the distribution, role, and origin, of restriction and
AB  - modification systems among plasmids, two plasmid encoded systems have been studied.  The
AB  - EcoRII (hspII) system.  The sensitivity of the DNA of bacteriophage lambda to endo R.EcoRII in
AB  - vitro was found to depend on the presence or absence of methylation introduced by the cytosine
AB  - specific DNA methylase of E. coli K.  Subsequently, a revised minimum estimate for the number
AB  - of cleavage sites for endo R.EcoRII and a map of these sites close to the ends of the lambda
AB  - chromosome were made.  The EcoR124 (hspI) system.  The restriction and modification system
AB  - carried by the plasmid R124 was shown to be different from the EcoRI system carried by plasmid
AB  - RY5 (subsequently NTP13) with which it had previously been assumed to be identical.  Endo
AB  - R.EcoR124 was isolated and found to be dependent on ATP and S-adenosylmethionine (it is a
AB  - class I restriction endonuclease).  A derivative of R124 was isolated, by chance, which has
AB  - acquired a restriction and modification system of novel specificity.  The derivative, R124/3,
AB  - also has new cleavage sites for endo R.EcoRI and endo R.SalI in its DNA.  It is proposed that
AB  - the new system, EcoR124/3 arose by recombination between the determinants of EcoK and EcoR124.
ER  -

TY  - JOUR
AU  - Hughes, S.G.
TI  - A map of the cleavage sites for endonuclease AvaI in the chromosome of bacteriophage lambda.
JO  - Biochem. J.
PY  - 1977
SP  - 503
EP  - 509
VL  - 163
AB  - The linear order of nine fragments generated by the action of endonuclease AvaI
AB  - on the DNA of bacteriophage lambda was determined from the altered
AB  - fragmentation patterns of bacteriophages containing known deletions and of
AB  - hybrids of bacteriophages lambdaand U80.  Digestion of 5'-terminally
AB  - 32P-labelled bacteriophage-lambda DNA was used to identify the terminal
AB  - fragments.  Measurement of relative fragment lengths permitted rough mapping of
AB  - the endonuclease-AvaI cleavage sites relative to the ends of the
AB  - bacteriophage-lambda chromosome.  The fragment order was confirmed and the map
AB  - refined by analysis of the fragmentation of derivative phages containing single
AB  - cleavage sites for endonuclease EcoRI.
ER  -

TY  - JOUR
AU  - Hughes, S.G.
AU  - Bruce, T.
AU  - Murray, K.
TI  - The Isolation and Characterization of a Sequence-Specific Endonuclease from Anabaena subcylindrica.
JO  - Biochem. J.
PY  - 1980
SP  - 59
EP  - 63
VL  - 185
AB  - An endonuclease, AsuI, was isolated from extracts of Anabaena subcylindrica on
AB  - the basis of gel-electrophoretic analysis of digests of bacteriophage-lambda
AB  - DNA with the partially purified extracts.  The enzyme requires Mg2+, but no
AB  - other cofactors.  Endonuclease AsuI recognizes the interrupted tetranucleotide
AB  - sequence: 5'-G-^G-N-C-C-3'   -C-C-N-G^-G- and breaks the phosphodiester bonds
AB  - indicated by the arrows to leave single-stranded trinucleotide projections at
AB  - the 5'-termini of the DNA fragments.
ER  -

TY  - JOUR
AU  - Hughes, S.G.
AU  - Hattman, S.
TI  - The sensitivity of bacteriophage lambda DNA to restriction endonuclease RII.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 645
EP  - 647
VL  - 98
AB  - Analysis of fragments of bacteriophage DNA produced by digestion with purified restriction
AB  - endonuclease RII shows that DNA propagated in the presence of the cytosine-specific DNA
AB  - methylase of Escherichia coli K is partially protected.  It is concluded that a fraction of
AB  - the recognition sequences for EcoRII are methylated by this methylase which shares an element
AB  - of sequence specificity with the RII restriction and modification enzymes.
ER  -

TY  - JOUR
AU  - Hughes, S.G.
AU  - Murray, K.
TI  - The Nucleotide Sequences Recognized by Endonucleases AvaI and AvaII from Anabaena variabilis.
JO  - Biochem. J.
PY  - 1980
SP  - 65
EP  - 75
VL  - 185
AB  - Determination of the 5'-terminal sequences flanking all the individual cleavage
AB  - sites for endonuclease AvaI in bacteriophage-lambda DNA has shown that this
AB  - enzyme recognizes the hexanucleotide sequence: 5'-C-^Y-C-G-R-G-3'
AB  - G-R-G-C-Y-^C This sequence is cut as shown by the arrows to give
AB  - single-stranded 5'-tetranucleotide protrusions (cohesive ends).  Endonucleases
AB  - SmaI, XhoI and XmaI recognize different symmetrical subsets of this sequence
AB  - and provide independent evidence for the occurrence of these subsets at
AB  - particular endonuclease-AvaI cleavage sites in the bacteriophage-lambda genome.
AB  - Further evidence for this structure came from the demonstration that DNA
AB  - fragments generated by endonuclease AvaI can be ligated to form a discrete set
AB  - of larger molecules and from nearest-neighbour analysis which showed that
AB  - cytosine residues occurred at the 3'-side of cleavage points.  The observation
AB  - that endonuclease AvaII recognized a subset of the sites recognized by AsuI
AB  - [Hughes, Bruce & Murray (1979) Biochem. J. 185, 59-63] led to the deduction
AB  - that AvaII recognizes the pentanucleotide sequence: 5'-G-^G-A-C-C-3'
AB  - C-C-T-G-^G and breaks internucleotide bonds at the positions indicated by the
AB  - arrows.
ER  -

TY  - JOUR
AU  - Hugon, P.
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Nguyen, T.T.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 1
EP  - 14
VL  - 8
AB  - Brevibacillus massiliensis strain phR(T) sp. nov. is the type strain of B. massiliensis sp.
AB  - nov., a new species within the genus Brevibacillus. This strain
AB  - was isolated from the fecal flora of a woman suffering from morbid obesity. B.
AB  - massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains
AB  - 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%.
ER  -

TY  - JOUR
AU  - Hugon, P.
AU  - Mishra, A.K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Anaerococcus vaginalis.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 356
EP  - 365
VL  - 6
AB  - We report the properties of a draft genome sequence of the bacterium Anaerococcus vaginalis
AB  - strain PH9, a species within the Anaerococcus genus. This strain, whose
AB  - genome is described here, was isolated from the fecal flora of a 26-year-old
AB  - woman suffering from morbid obesity. A. vaginalis is an obligate anaerobic
AB  - coccus. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 2,048,125-bp long (one chromosome
AB  - but no plasmid) and contains 2,095 protein-coding and 38 RNA genes, including
AB  - three rRNA genes.
ER  -

TY  - JOUR
AU  - Hugon, P.
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Rivet, R.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 427
EP  - 439
VL  - 7
AB  - Alistipes obesi sp. nov. strain ph8(T) is the type strain of A. obesi, a new species within
AB  - the genus Alistipes. This strain, whose genome is described here,
AB  - was isolated from the fecal flora of a 26-year-old woman suffering from morbid
AB  - obesity. A. obesi is an obligately anaerobic rod. Here we describe the features
AB  - of this organism, together with the complete genome sequence and annotation. The
AB  - 3,162,233 bp long genome (1 chromosome but no plasmid) contains 2,623
AB  - protein-coding and 49 RNA genes, including three rRNA genes.
ER  -

TY  - JOUR
AU  - Hugon, P.
AU  - Ramasamy, D.
AU  - Robert, C.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 500
EP  - 515
VL  - 8
AB  - Kallipyga massiliensis strain ph2(T) is the type strain of Kallipyga massiliensis gen. nov.,
AB  - sp. nov., the type species of the new genus Kallipyga within the
AB  - family Clostridiales Incertae Sedis XI. This strain, whose genome is described
AB  - here, was isolated from the fecal flora of a 26-year-old woman suffering from
AB  - morbid obesity. K. massiliensis is an obligate anaerobic coccus. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 1,770,679 bp long genome (1 chromosome but no plasmid) contains
AB  - 1,575 protein-coding and 50 RNA genes, including 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Huguet-Tapia, J.C.
AU  - Loria, R.
TI  - Draft Genome Sequence of Streptomyces acidiscabies 84-104, an Emergent Plant Pathogen.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1847
EP  - 1847
VL  - 194
AB  - A draft genome sequence of the plant pathogen Streptomyces acidiscabies 84-104, an emergent
AB  - plant pathogen, is presented here. The genome is among the largest of
AB  - streptomycetes, at more than 11 Mb, and encodes a 100-kb pathogenicity island
AB  - (PAI) shared with other plant-pathogenic streptomycetes. The presence of this
AB  - conserved PAI, and the remnants of a conserved integrase/recombinase at its 3'
AB  - end, supports the hypothesis that S. acidiscabies emerged as a plant pathogen as
AB  - a result of this acquisition.
ER  -

TY  - JOUR
AU  - Huguet-Tapia, J.C.
AU  - Peng, Z.
AU  - Yang, B.
AU  - Yin, Z.
AU  - Liu, S.
AU  - White, F.F.
TI  - Complete Genome Sequence of the African Strain AXO1947 of Xanthomonas oryzae pv.  oryzae.
JO  - Genome Announcements
PY  - 2016
SP  - e01730
EP  - e01715
VL  - 4
AB  - Xanthomonas oryzae pv. oryzae is the etiological agent of bacterial rice blight.  Three
AB  - distinct clades of X. oryzae pv. oryzae are known. We present the complete
AB  - annotated genome of the African clade strain AXO194 using long-read
AB  - single-molecule PacBio sequencing technology. The genome comprises a single
AB  - chromosome of 4,674,975 bp and encodes for nine transcriptional activator-like
AB  - (TAL) effectors. The approach and data presented in this announcement provide
AB  - information for complex bacterial genome organization and the discovery of new
AB  - virulence effectors, and they facilitate target characterization of TAL
AB  - effectors.
ER  -

TY  - JOUR
AU  - Hui, R.K.
AU  - Chen, J.W.
AU  - Chan, K.G.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e01164
EP  - e01114
VL  - 2
AB  - We previously identified and presented the draft genome of a Xanthomonadaceae bacterial strain
AB  - Dyella japonica A8 which shows quorum-quenching activity. Here,
AB  - we report the complete, closed genome sequence of this bacterium. This complete
AB  - genome may help to further investigate the comparative quorum-quenching activity
AB  - among D. japonica strains.
ER  -

TY  - JOUR
AU  - Huja, S.
AU  - Oren, Y.
AU  - Trost, E.
AU  - Brzuszkiewicz, E.
AU  - Biran, D.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Gottschalk, G.
AU  - Hacker, J.
AU  - Ron, E.Z.
AU  - Dobrindt, U.
TI  - Genomic Avenue to Avian Colisepticemia.
JO  - MBio
PY  - 2015
SP  - e01681
EP  - e01614
VL  - 6
AB  - Here we present an extensive genomic and genetic analysis of Escherichia coli strains of
AB  - serotype O78 that represent
AB  - the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic
AB  - Escherichia coli (APEC) strains. It is
AB  - associated with high mortality and morbidity, resulting in significant economic consequences
AB  - for the poultry industry. To understand
AB  - the genetic basis of the virulence of avian septicemic E. coli, we sequenced the entire genome
AB  - of a clinical isolate of serotype
AB  - O78-O78:H19 ST88 isolate 789 (O78-9)-and compared it with three publicly available APEC O78
AB  - sequences and one
AB  - complete genome of APEC serotype O1 strain. Although there was a large variability in genome
AB  - content between the APEC
AB  - strains, several genes were conserved, which are potentially critical for colisepticemia. Some
AB  - of these genes are present in multiple
AB  - copies per genome or code for gene products with overlapping function, signifying their
AB  - importance. A systematic deletion of
AB  - each of these virulence-related genes identified three systems that are conserved in all
AB  - septicemic strains examined and are critical
AB  - for serum survival, a prerequisite for septicemia. These are the plasmid-encoded protein, the
AB  - defective ETT2 (E. coli type 3
AB  - secretion system 2) type 3 secretion system ETT2sepsis, and iron uptake systems. Strain O78-9
AB  - is the only APEC O78 strain that
AB  - also carried the regulon coding for yersiniabactin, the iron binding system of the Yersinia
AB  - high-pathogenicity island. Interestingly,
AB  - this system is the only one that cannot be complemented by other iron uptake systems under
AB  - iron limitation and in serum.
ER  -

TY  - JOUR
AU  - Hulsmann, K.-H.
AU  - Quaas, R.
AU  - Georgalis, Y.
AU  - Saenger, W.
AU  - Hahn, U.
TI  - High-level expression of a semisynthetic dam gene in Escherichia coli.
JO  - Gene
PY  - 1991
SP  - 83
EP  - 88
VL  - 98
AB  - We constructed a semisynthetic gene encoding a DNA-adenine-methyltransferase (Dam) that codes
AB  - for the same amino acid sequence as the wild type (wt) Escherichia coli dam gene. Since for
AB  - unknown reasons the entire wt sequence, from the start codon to the end of the gene, could not
AB  - be cloned, a gene was constructed consisting of a chemically synthesized 5' portion and a 3'
AB  - portion from the E. coli chromosome. Introduction of this semisynthetic gene into a suitable
AB  - vector allows overproduction of E. coli Dam in mg amounts per liter E. coli culture, with
AB  - optimum expression of the gene in the vector pJLA503. This plasmid places the target gene
AB  - under control of the strong, tandemly arranged PR PL promoters from bacteriophage lambda,
AB  - regulated by a temperature-sensitive lambda repressor. A rapid, two-column purification
AB  - protocol is described that allows for very fast purification of the protein. The 32-kDa
AB  - recombinant protein methylates the sequence GATC.
ER  -

TY  - JOUR
AU  - Humann, J.L.
AU  - Wildung, M.
AU  - Cheng, C.-H.
AU  - Lee, T.
AU  - Drew, J.C.
AU  - Triplett, E.W.
AU  - Main, D.
AU  - Schroeder, B.K.
TI  - Complete genome of the onion pathogen Enterobacter cloacae EcWSU1.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 279
EP  - 286
VL  - 5
ER  -

TY  - JOUR
AU  - Humann, J.L.
AU  - Wildung, M.
AU  - Pouchnik, D.
AU  - Bates, A.A.
AU  - Drew, J.C.
AU  - Zipperer, U.N.
AU  - Triplett, E.W.
AU  - Main, D.
AU  - Schroeder, B.K.
TI  - Complete genome of the switchgrass endophyte Enterobacter clocace P101.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 726
EP  - 734
VL  - 9
AB  - The Enterobacter cloacae complex is genetically very diverse. The increasing number of
AB  - complete genomic sequences of E. cloacae is helping to determine the
AB  - exact relationship among members of the complex. E. cloacae P101 is an endophyte
AB  - of switchgrass (Panicum virgatum) and is closely related to other E. cloacae
AB  - strains isolated from plants. The P101 genome consists of a 5,369,929 bp
AB  - chromosome. The chromosome has 5,164 protein-coding regions, 100 tRNA sequences,
AB  - and 8 rRNA operons.
ER  -

TY  - JOUR
AU  - Humbelin, M.
AU  - Suri, B.
AU  - Rao, D.N.
AU  - Hornby, D.P.
AU  - Eberle, H.
AU  - Pripfl, T.
AU  - Kenel, S.
AU  - Bickle, T.A.
TI  - Type III DNA restriction and modification systems EcoP1 and EcoP15.
JO  - J. Mol. Biol.
PY  - 1988
SP  - 23
EP  - 29
VL  - 200
AB  - This paper presents the nucleotide sequence of the mod-res operon of phage P1,
AB  - which encodes the two structural genes for the EcoP1 type III restriction and
AB  - modification system.  We have also sequenced the mod gene of the allelic EcoP15
AB  - system.  The mod gene product is responsible for binding the system-specific
AB  - DNA recognition sequences in both restriction and modification:   it also
AB  - catalyses the modification reaction.  A comparison of the two mod gene product
AB  - sequences shows that they have conserved amino and carboxyl ends but have
AB  - completely different sequences in the middle of the molecules.  Two alleles of
AB  - the EcoP1 mod gene that are defective in modification but not in restriction
AB  - were also sequenced.  The mutations in both alleles lie within the
AB  - non-conserved regions.
ER  -

TY  - JOUR
AU  - Humbert, O.
AU  - Dorer, M.S.
AU  - Salama, N.R.
TI  - Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA  recombination.
JO  - Mol. Microbiol.
PY  - 2011
SP  - 387
EP  - 401
VL  - 79
AB  - P>Helicobacter pylori is a genetically diverse bacterial species, owing in part to its natural
AB  - competence for DNA uptake that facilitates
AB  - recombination between strains. Inter-strain DNA recombination occurs
AB  - during human infection and the H. pylori genome is in linkage
AB  - equilibrium worldwide. Despite this high propensity for DNA exchange,
AB  - little is known about the factors that limit the extent of
AB  - recombination during natural transformation. Here, we identify
AB  - restriction-modification (R-M) systems as a barrier to transformation
AB  - with homeologous DNA and find that R-M systems and several components
AB  - of the recombination machinery control integration length. Type II R-M
AB  - systems, the nuclease nucT and resolvase ruvC reduced integration
AB  - length whereas the helicase recG increased it. In addition, we
AB  - characterized a new factor that promotes natural transformation in H.
AB  - pylori, dprB. Although free recombination has been widely observed in
AB  - H. pylori, our study suggests that this bacterium uses multiple systems
AB  - to limit inter-strain recombination.
ER  -

TY  - JOUR
AU  - Humbert, O.
AU  - Salama, N.R.
TI  - Functional characterization of HP0503: An adenine methyltransferase required for the virulence of Helicobacter pylori.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2007
SP  - 39
EP  - 39
VL  - 107
AB  - Restriction-modification systems have traditionally been implicated in the protection of the
AB  - bacterial genome from invading DNAs, but accumulating evidence suggests that they have other
AB  - cellular functions. Helicobacter pylori contains a large number of these systems with at least
AB  - 23 identified. In silico genome analysis reveals that in many of these systems, the
AB  - restriction-endonuclease component is inactive but the cognate methyltransferase retains full
AB  - activity, implying that it confers a selective advantage to its host. In an effort to identify
AB  - H. pylori factors required for the colonization of the mouse stomach, we identified HP0503, a
AB  - protein of unknown function. Structure prediction algorithms revealed that HP0503 has a
AB  - similar folding pattern to the adenine methyltransferase M.TaqI from Thermus aquaticus,
AB  - leading us to hypothesize that HP0503 is a DNA methyltransferase required for the virulence of
AB  - H. pylori. The methyltransferase activity of HP0503 was demonstrated using an engineered
AB  - strain of E. coli defective in DNA methylation. Upon expression of HP0503 in this E. coli
AB  - strain, genomic DNA methylation could be detected using antibodies recognizing methylated
AB  - adenine. In addition, a point mutation in the predicted catalytic site of HP0503 completely
AB  - abolished adenine methylation, further advocating its function as an adenine
AB  - methyltransferase. To clarify the role of HP0503 in virulence, its DNA recognition site was
AB  - determined. The restriction endonuclease Rsa I could digest genomic DNA from a HP0503 mutant
AB  - strain but not WT, indicating that HP0503 acts on the same sequence as Rsa I, GTAC. This
AB  - finding was confirmed by expressing HP0503 cognate endonuclease, HP0505, in E. coli, which
AB  - cleaved DNA at GTAC sites. Interestingly, while GTAC sites are strongly avoided in the H.
AB  - pylori genome (only 115 to 184 sites/genome), 16 of these sites are found within the 2 copies
AB  - of the 3kbp DNA fragment encoding the 23S rRNA. We are currently testing the methylation
AB  - status of HP0503 cognate sites and examining their impact on gene activity to probe the
AB  - mechanism by which HP0503 confers a fitness advantage during stomach colonization.
ER  -

TY  - JOUR
AU  - Humbert, O.
AU  - Salama, N.R.
TI  - The Helicobacter pylori HpyAXII restriction-modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric  conservation of the DNA methyltransferase and restriction endonuclease  components.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 6893
EP  - 6906
VL  - 36
AB  - The naturally competent organism Helicobacter pylori encodes a large number of
AB  - restriction-modification (R-M) systems that consist of a
AB  - restriction endonuclease and a DNA methyltransferase. R-M systems are not
AB  - only believed to limit DNA exchange among bacteria but may also have other
AB  - cellular functions. We report a previously uncharacterized H. pylori type
AB  - II R-M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC
AB  - sites, which are rare in the H. pylori chromosome but numerous in
AB  - ribosomal RNA genes. As predicted, this type II R-M system showed
AB  - attributes of a selfish element. Deletion of the methyltransferase
AB  - M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII
AB  - unless compensated by adaptive mutation or gene amplification. R.HpyAXII
AB  - effectively restricted both unmethylated plasmid and chromosomal DNA
AB  - during natural transformation and was predicted to belong to the novel
AB  - 'half pipe' structural family of endonucleases. Analysis of a panel of
AB  - clinical isolates revealed that R.HpyAXII was functional in a small number
AB  - of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII
AB  - was highly conserved (92%, n = 50), suggesting that GTAC methylation
AB  - confers a selective advantage to H. pylori. However, M.HpyAXII activity
AB  - did not enhance H. pylori fitness during stomach colonization of a mouse
AB  - infection model.
ER  -

TY  - JOUR
AU  - Humbert, O.M.
TI  - Restriction-modification systems and the regulation of genetic exchange in Helicobacter pylori.
JO  - Ph.D. Thesis, University of Washington, Seattle, USA
PY  - 2010
SP  - 1
EP  - 127
AB  - Helicobacter pylori is a gram negative bacterial pathogen that colonizes the stomach of over
AB  - half of the world population. Various pathologies are associated with H. pylori infection and
AB  - include gastritis, peptic ulcers, gastric cancer and MALT lymphoma. H pylori is one of the
AB  - most genetically diverse bacterial species known, a likely consequence of DNA recombination
AB  - between H. pylori strains facilitated by their natural competence for DNA uptake. Inter-strain
AB  - DNA recombination occurs in patients infected with multiple genetically distinct H. pylori
AB  - isolates but the barriers that limit DNA exchange is this organism are not understood.
AB  - Restriction-Modification (R-M) systems are made of a restriction endonuclease and a DNA
AB  - methyltransferase, both of which target the same DNA sequence. These systems are generally
AB  - believed to protect bacteria from bacteriophages invasion but their role in limiting
AB  - inter-strain recombination remains unexplored. Over the course of my Thesis work, I first
AB  - identified and characterized a novel H. pylori R-M system. I showed that this system targets
AB  - the sequence GTAC and that it effectively restricts unmethylated DNA during natural
AB  - transformation. After designing a novel genetic assay to quickly assess restriction
AB  - endonuclease activity, I made the intriguing observation that the DNA methyltransferase
AB  - activity is highly conserved as compared to the endonuclease activity in H. pylori, and
AB  - suggested that DNA methylation has alternate roles in this organism. In the following chapter,
AB  - I quantified the size of DNA exchanged during H. pylori inter-strain recombination and found
AB  - that R-M systems reduce both recombination frequency and size. Several components of the DNA
AB  - transformation and recombination pathways were also identified as regulators of transformation
AB  - frequency and integration size during both homologous and homeologous DNA transformation. In
AB  - the last chapter, I investigated whether DNA methylation controls gene transcription in H.
AB  - pylori. Global transcriptional profiles of H. pylori bacteria were analyzed by microarrays in
AB  - response to adenine methylation of the recognition sequences GTAC and TCGA. Transcriptional
AB  - changes were observed in response to DNA methylation, but no correlation could be established
AB  - with the distribution of methylation sites. Possible mechanisms of regulation by DNA
AB  - methylation were considered.
ER  -

TY  - JOUR
AU  - Humeny, A.
AU  - Beck, C.
AU  - Becker, C.M.
AU  - Jeltsch, A.
TI  - Detection and analysis of enzymatic DNA methylation of oligonucleotide substrates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
JO  - Anal. Biochem.
PY  - 2003
SP  - 160
EP  - 166
VL  - 313
AB  - Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) mass
AB  - spectrometry was employed to analyze DNA
AB  - methylation carried out by the Escherichia coli dam DNA methyltransferase
AB  - using oligonucleotide substrates with molecular masses of 5000-10,000 Da
AB  - per strand. The mass spectrometry assay offers several advantages: (i) it
AB  - directly shows the methylation as the increase in the mass of the
AB  - substrate DNA, (ii) it is nonradioactive, (iii) it is quantitative, and
AB  - (iv) it can be automated for high-throughput applications. Since
AB  - unmethylated and methylated DNA are detected, the ratio of methylation can
AB  - be determined directly and accurately. Furthermore, the assay allows
AB  - detection individually of the methylation of several substrates in
AB  - competition, offering an ideal setup to analyze the specificity of DNA
AB  - interacting with enzymes. We could not identify methylation at any
AB  - noncanonical site, indicating that the dam MTase is a very specific
AB  - enzyme. Finally, MALDI-TOF mass spectrometry permitted assessment of the
AB  - number of methyl groups incorporated into each DNA strand, thereby,
AB  - allowing study of mechanistic details such as the processivity of the
AB  - methylation reaction. We provide evidence that the dam MTase modifies DNA
AB  - in a processive reaction, confirming earlier findings.
ER  -

TY  - JOUR
AU  - Humphreys, C.M. et al.
TI  - Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.
JO  - BMC Genomics
PY  - 2015
SP  - 1085
EP  - 1085
VL  - 16
AB  - BACKGROUND: Clostridium autoethanogenum is an acetogenic bacterium capable of
AB  - producing high value commodity chemicals and biofuels from the C1 gases present
AB  - in synthesis gas. This common industrial waste gas can act as the sole energy and
AB  - carbon source for the bacterium that converts the low value gaseous components
AB  - into cellular building blocks and industrially relevant products via the action
AB  - of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts
AB  - are focused on the enhancement and extension of product formation in this
AB  - organism via synthetic biology approaches. However, crucial to metabolic
AB  - modelling and directed pathway engineering is a reliable and comprehensively
AB  - annotated genome sequence. RESULTS: We performed next generation sequencing using
AB  - Illumina MiSeq technology on the DSM10061 strain of Clostridium autoethanogenum
AB  - and observed 243 single nucleotide discrepancies when compared to the published
AB  - finished sequence (NCBI: GCA_000484505.1), with 59.1 % present in coding regions.
AB  - These variations were confirmed by Sanger sequencing and subsequent analysis
AB  - suggested that the discrepancies were sequencing errors in the published genome
AB  - not true single nucleotide polymorphisms. This was corroborated by the
AB  - observation that over 90 % occurred within homopolymer regions of greater than 4
AB  - nucleotides in length. It was also observed that many genes containing these
AB  - sequencing errors were annotated in the published closed genome as encoding
AB  - proteins containing frameshift mutations (18 instances) or were annotated despite
AB  - the coding frame containing stop codons, which if genuine, would severely hinder
AB  - the organism's ability to survive. Furthermore, we have completed a comprehensive
AB  - manual curation to reduce errors in the annotation that occur through serial use
AB  - of automated annotation pipelines in related species. As a result, different
AB  - functions were assigned to gene products or previous functional annotations
AB  - rejected because of missing evidence in various occasions. CONCLUSIONS: We
AB  - present a revised manually curated full genome sequence for Clostridium
AB  - autoethanogenum DSM10061, which provides reliable information for genome-scale
AB  - models that rely heavily on the accuracy of annotation, and represents an
AB  - important step towards the manipulation and metabolic modelling of this
AB  - industrially relevant acetogen.
ER  -

TY  - JOUR
AU  - Humphreys, J.R.
AU  - Daniel, R.
AU  - Poehlein, A.
TI  - Insights into the Genome of the Anaerobic Acetogen Sporomusa silvacetica DSM 10669.
JO  - Genome Announcements
PY  - 2017
SP  - e00983
EP  - e00917
VL  - 5
AB  - Sporomusa silvacetica is a spore-forming, anaerobic acetogen isolated from soil derived from
AB  - east central Germany. The genome contains genes of the
AB  - Wood-Ljungdahl pathway required for carbon fixation and genes involved in the
AB  - biosynthesis of the amino acid pyrrolysine. The genome (5.92 Mb) harbors 4,355
AB  - predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Humphreys, J.R.
AU  - Daniel, R.
AU  - Poehlein, A.
TI  - Genome Sequence of the Homoacetogenic, Gram-Negative, Endospore-Forming Bacterium Sporomusa acidovorans DSM 3132.
JO  - Genome Announcements
PY  - 2017
SP  - e00981
EP  - e00917
VL  - 5
AB  - Sporomusa acidovorans DSM 3132 is a strictly anaerobic, spore-forming and acetogenic
AB  - bacterium, which was isolated from effluent of an alcohol distillation
AB  - fermenter. The genome harbors genes involved in the Wood-Ljungdahl pathway for
AB  - carbon fixation and several genes for glycerol metabolism. The genome (6.06 Mb)
AB  - contains 4,506 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Humphries, P.
AU  - Gordon, R.L.
AU  - McConnell, D.J.
AU  - Connolly, P.
TI  - Endonuclease R. Hind fragments of T7 DNA.
JO  - Virology
PY  - 1974
SP  - 25
EP  - 31
VL  - 58
AB  - Restriction enzyme endonuclease R. Hind of Haemophilus influenzae strain Rd,
AB  - prepared by a rapid new method, was used to cleave bacteriophage T7 DNA into a
AB  - minimum of 49 unique fragments which were separated on polyacrylamide gels.
AB  - The fragments were estimated to fall within the size range of 100-200
AB  - nucleotide pairs.
ER  -

TY  - JOUR
AU  - Hung, J.E.
AU  - Mill, C.P.
AU  - Clifton, S.W.
AU  - Magrini, V.
AU  - Bhide, K.
AU  - Francois, J.A.
AU  - Ransome, A.E.
AU  - Fulton, L.
AU  - Thimmapuram, J.
AU  - Wilson, R.K.
AU  - Kappock, T.J.
TI  - Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate.
JO  - Genome Announcements
PY  - 2014
SP  - e00550
EP  - e00514
VL  - 2
AB  - The genome sequence of Acetobacter aceti 1023, an acetic acid bacterium adapted to traditional
AB  - vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids).
AB  - A. aceti 1023 is closely related to the cocoa fermenter Acetobacter pasteurianus
AB  - 386B but possesses many additional insertion sequence elements.
ER  -

TY  - JOUR
AU  - Hung, M.S.
AU  - Karthikeyan, N.
AU  - Huang, B.
AU  - Koo, H.C.
AU  - Kiger, J.
AU  - Shen, C.J.
TI  - Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 11940
EP  - 11945
VL  - 96
AB  - DNA methylation at CpG residues is closely associated with a number of biological processes
AB  - during vertebrate development. Unlike the vertebrates, however, several invertebrate species,
AB  - including the Drosophila, do not have apparent DNA methylation in their genomes. Nor have
AB  - there been reports on a DNA (5-cytosine) methyltransferase (CpG MTase) found in these
AB  - invertebrates. We now present evidence for two CpG MTase-like proteins expressed in Drosophila
AB  - cells. One of these, DmMTR1, is a protein containing peptide epitopes immunologically related
AB  - to the conserved motifs I and IV in the catalytic domain of the mammalian dnmt1. DmMTR1 has an
AB  - apparent molecular mass of 220 kDa and, similar to mammalian dnmt1, it also interacts in vivo
AB  - with the proliferating cell nuclear antigen. During interphase of the syncytial Drosophila
AB  - embryos, the DmMTR1 molecules are located outside the nuclei, as is dnmt1 in the mouse
AB  - blastocyst. However, DmMTR1 appears to be rapidly transported into, and then out of the nuclei
AB  - again, as the embryos undergo mitotic waves. Immunofluorescent data indicate that DmMTR1
AB  - molecules "paint" the whole set of condensed Drosophila chromosomes throughout the mitotic
AB  - phase, suggesting they may play an essential function in the cell-cycle regulated condensation
AB  - of the Drosophila chromosomes. Through search in the genomic database, we also have identified
AB  - a Drosophila polypeptide, DmMT2, that exhibits high sequence homology to the mammalian dnmt2
AB  - and the yeast CpG MTase homolog pmt1. The expression of DmMT2 appears to be developmentally
AB  - regulated. We discuss the evolutionary and functional implications of the discovery of these
AB  - two Drosophila proteins related to mammalian CpG MTases.
ER  -

TY  - JOUR
AU  - Hungria, M.
AU  - Ribeiro, R.A.
AU  - Nogueira, M.A.
TI  - Draft Genome Sequences of Azospirillum brasilense Strains Ab-V5 and Ab-V6, Commercially Used in Inoculants for Grasses and Legumes in Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00393
EP  - e00318
VL  - 6
AB  - Azospirillum brasilense strains Ab-V5 and Ab-V6 are largely used in commercial inoculants for
AB  - grasses and legumes in Brazil. Their genomes were estimated at
AB  - 6,934,595 and 7,197,196 bp, respectively, and encompass genes related to nitrogen
AB  - fixation, synthesis of phytohormones, and environmental adaptation. Although the
AB  - strains differ in phenotypic properties, their genomes are highly similar.
ER  -

TY  - JOUR
AU  - Huntemann, M. et al.
TI  - Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 185
EP  - 193
VL  - 6
AB  - Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which
AB  - belongs to the family Flavobacteriaceae in the phylum
AB  - Bacteroidetes. The species is of interest because of its isolated position in the
AB  - genomically unexplored genus Muricauda, which is located in a part of the tree of
AB  - life containing not many organisms with sequenced genomes. The genome, which
AB  - consists of a circular chromosome of 3,842,422 bp length with a total of 3,478
AB  - protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Huntemann, M. et al.
TI  - Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 177
EP  - 187
VL  - 8
AB  - Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family
AB  - Leptospiraceae, phylum Spirochaetes. Organisms of this family have a
AB  - Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an
AB  - outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather
AB  - than the outer membrane. The two flagella of members of Leptospiraceae extend
AB  - from the cytoplasmic membrane at the ends of the bacteria into the periplasmic
AB  - space and are necessary for their motility. Here we describe the features of the
AB  - L. illini type strain, together with the complete genome sequence, and
AB  - annotation. This is the first genome sequence (finished at the level of Improved
AB  - High Quality Draft) to be reported from of a member of the genus Leptonema and a
AB  - representative of the third genus of the family Leptospiraceae for which complete
AB  - or draft genome sequences are now available. The three scaffolds of the 4,522,760
AB  - bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA
AB  - genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Huntemann, M. et al.
TI  - Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type  strain (MH(2)).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 303
EP  - 311
VL  - 4
AB  - Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which
AB  - belongs to the family Desulfurellaceae within the class
AB  - Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer
AB  - was first isolated from shallow-water hot vents in Matipur Harbor, Papua New
AB  - Guinea. H. maritima was of interest for genome sequencing because of its isolated
AB  - phylogenetic location, as a distant next neighbor of the genus Desulfurella.
AB  - Strain MH(2) (T) is the first type strain from the order Desulfurellales with a
AB  - completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723
AB  - protein-coding and 57 RNA genes consists of one circular chromosome and is a part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Hunter, S.S.
AU  - Yano, H.
AU  - Loftie-Eaton, W.
AU  - Hughes, J.
AU  - De Gelder, L.
AU  - Stragier, P.
AU  - De Vos, P.
AU  - Settles, M.L.
AU  - Top, E.M.
TI  - Draft Genome Sequence of Pseudomonas moraviensis R28-S.
JO  - Genome Announcements
PY  - 2014
SP  - e00035
EP  - e00014
VL  - 2
AB  - We report the draft genome sequence of Pseudomonas moraviensis R28-S, isolated from the
AB  - municipal wastewater treatment plant of Moscow, ID. The strain carries a
AB  - native mercury resistance plasmid, poorly maintains introduced IncP-1 antibiotic
AB  - resistance plasmids, and has been useful for studying the evolution of plasmid
AB  - host range and stability.
ER  -

TY  - JOUR
AU  - Huntley, S.
AU  - Kneip, S.
AU  - Treuner-Lange, A.
AU  - Sogaard-Andersen, L.
TI  - Complete Genome Sequence of Myxococcus stipitatus Strain DSM 14675, a Fruiting Myxobacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e0010013
EP  - e0010013
VL  - 1
AB  - Hallmarks of the myxobacteria include the formation of spore-filled fruiting bodies in
AB  - response to starvation and synthesis of secondary metabolites.
AB  - Myxococcus stipitatus forms morphologically highly distinct fruiting bodies and
AB  - produces secondary metabolites with antibiotic or cytotoxic activities. Here, we
AB  - present the 10.35-Mb genome sequence of M. stipitatus strain DSM 14675.
ER  -

TY  - JOUR
AU  - Huntley, S.
AU  - Zhang, Y.
AU  - Treuner-Lange, A.
AU  - Kneip, S.
AU  - Sensen, C.W.
AU  - Sogaard-Andersen, L.
TI  - Complete Genome Sequence of the Fruiting Myxobacterium Corallococcus coralloides  DSM 2259.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3012
EP  - 3013
VL  - 194
AB  - Corallococcus coralloides, like most other myxobacteria, undergoes a developmental program
AB  - culminating in the formation of fruiting bodies. C.
AB  - coralloides fruiting bodies are morphologically distinct from those of other
AB  - fruiting myxobacteria for which full-length genome sequences are available. The
AB  - genome sequence of the 10.0-Mb C. coralloides genome is presented herein.
ER  -

TY  - JOUR
AU  - Hunyadkurti, J.
AU  - Feltoti, Z.
AU  - Horvath, B.
AU  - Nagymihaly, M.
AU  - Voros, A.
AU  - McDowell, A.
AU  - Patrick, S.
AU  - Urban, E.
AU  - Nagy, I.
TI  - Complete Genome Sequence of Propionibacterium acnes Type IB strain 6609.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4561
EP  - 4562
VL  - 193
AB  - Propionibacterium acnes (P. acnes) is an anaerobic Gram-positive bacterium that forms part of
AB  - the normal human cutaneous microbiota and is thought to
AB  - play central role in acne vulgaris, a chronic inflammatory disease of the
AB  - pilosebaceous unit (8). Here we present the whole genome sequence for the
AB  - P. acnes Type IB strain 6609 isolated from a patient with inflammatory
AB  - acne (15).
ER  -

TY  - JOUR
AU  - Huo, W.
TI  - Enterococcus faecalis genome defense systems and their impact on conjugative antibiotic resistance plasmid transfer.
JO  - Ph.D. Thesis
PY  - 2017
AB  - Enterococcus faecalis is a Gram-positive bacterium that naturally colonizes humans and
AB  - opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis
AB  - strains
AB  - have emerged that are replete with mobile genetic elements (MGEs). Considering that bacteria
AB  - commonly possess two genome defense mechanisms to prevent MGE acquisition,
AB  - restrictionmodification
AB  - (R-M, analogous to an innate immune system) and CRISPR-Cas (adaptive immune
AB  - system), we hypothesize that these barriers may have been compromised in MDR E. faecalis
AB  - strains. However, little was known about the activities of E. faecalis R-M and CRISPR-Cas
AB  - systems. In my dissertation, a functional E. faecalis OG1RF encoded R-M system was identified
AB  - and its activity against MGEs was confirmed using both conjugation and transformation assays.
AB  - This work was the first to demonstrate that R-M provides E. faecalis with significant defense
AB  - capability against antibiotic resistance plasmids. Subsequently, the distribution of R-M
AB  - systems
AB  - in a larger collection of E. faecalis strains was studied. To predict the novel R-M systems, I
AB  - developed an R-M prediction algorithm based on amino acid sequence homology, and
AB  - successfully predicted new R-M systems in 75 E. faecalis genomes. Remarkably, some lineagevi
AB  - i
AB  - specific R-M systems were detected. Especially, hospital-adapted lineages were found to be
AB  - enriched for certain R-M systems, suggesting that these bacteria can readily exchange DNA with
AB  - each other. Another active form of genome defense in E. faecalis, namely CRISPR-Cas, has also
AB  - been investigated. In experimental in vitro evolution studies, we observed that
AB  - chromosomallyencoded
AB  - CRISPR-Cas systems tend to be compromised upon enforced maintenance of antibiotic
AB  - resistance plasmids possessing sequences targeted by CRISPR-Cas. Using deep sequencing, we
AB  - found that CRISPR array alleles are naturally heterogeneous, which provides an evolutionary
AB  - basis for compromised CRISPR-Cas under selection pressure. This work demonstrates that
AB  - antibiotic use can inadvertently select for E. faecalis with enhanced abilities to acquire
AB  - mobile
AB  - genetic elements. Finally, I studied lytic enterococcal phages for their interactions with E.
AB  - faecalis hosts. This work was undertaken because phage therapy is increasingly of interest as
AB  - an
AB  - alternative to antibiotics for infection treatment. The genome modification status of one
AB  - novel
AB  - enterococcal phage was characterized, and the phage was found to be modified at most cytosine
AB  - residues. This phage evades E. faecalis R-M defense, most likely due to this ubiquitous genome
AB  - modification. That the phage encodes an anti-R-M strategy is beneficial for phage therapy
AB  - applications.
ER  -

TY  - JOUR
AU  - Huo, W.
AU  - Adams, H.M.
AU  - Zhang, M.Q.
AU  - Palmer, K.L.
TI  - Genome modification in Enterococcus faecalis OG1RF assessed by bisulfite sequencing and single molecule real time sequencing.
JO  - J. Bacteriol.
PY  - 2015
SP  - 1939
EP  - 1951
VL  - 197
AB  - Enterococcus faecalis is a gram-positive bacterium that natively colonizes the human
AB  - gastrointestinal tract and opportunistically causes life-threatening
AB  - infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing
AB  - treatment options for these infections. MDR E. faecalis have large genomes
AB  - containing mobile genetic elements (MGEs) encoding antibiotic resistance and
AB  - virulence determinants. Bacteria commonly possess genome defense mechanisms to
AB  - block MGE acquisition, and we hypothesize that these mechanisms have been
AB  - compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the
AB  - bacterial genome is methylated at cytosine (C) or adenine (A) residues by a
AB  - methyltransferase (MTase) such that non-self DNA can be distinguished from self
AB  - DNA. A cognate restriction endonuclease digests improperly modified non-self DNA.
AB  - Little is known about R-M in E. faecalis. Here, we use genome resequencing to
AB  - identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of
AB  - the smallest E. faecalis genomes sequenced to date, and possesses few MGEs.
AB  - Single Molecule Real Time (SMRT) and bisulfite sequencing revealed that OG1RF has
AB  - global 5-methylcytosine (m5C) methylation at 5' -GCWGC-3' motifs. A Type II R-M
AB  - system confers the m5C modification, and disruption of this system impacts OG1RF
AB  - electrotransformability and conjugative transfer of an antibiotic resistance
AB  - plasmid. A second DNA MTase was poorly expressed in laboratory conditions but
AB  - conferred global N4-methylcytosine (m4C) methylation at 5' -CCGG-'3 motifs when
AB  - expressed in Escherichia coli. Based on our results, we conclude that R-M can act
AB  - as a barrier to MGE acquisition and likely influences antibiotic resistance gene
AB  - dissemination in the faecalis species. IMPORTANCE: The horizontal transfer of
AB  - antibiotic resistance genes among bacteria is a critical public health concern.
AB  - Enterococcus faecalis is an opportunistic pathogen causing life-threatening
AB  - infections in humans. Multidrug resistance acquired by horizontal gene transfer
AB  - limits treatment options for these infections. In this study, we use innovative
AB  - DNA sequencing methodologies to investigate how a model strain of E. faecalis
AB  - discriminates its own DNA from foreign DNA - i.e., self versus non-self
AB  - discrimination. We also assess the role of an E. faecalis genome modification
AB  - system in modulating conjugative transfer of an antibiotic resistance plasmid.
AB  - These results are significant because they demonstrate that differential genome
AB  - modification impacts horizontal gene transfer frequencies in E. faecalis.
ER  -

TY  - JOUR
AU  - Huo, Y.
AU  - Li, P.
TI  - Separation and purification of restriction endonuclease MspI.
JO  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan
PY  - 1989
SP  - 235
EP  - 236
VL  - 16
AB  - None
ER  -

TY  - JOUR
AU  - Huo, Y.-Y.
AU  - Cheng, H.
AU  - Han, X.-F.
AU  - Jiang, X.-W.
AU  - Sun, C.
AU  - Zhang, X.-Q.
AU  - Zhu, X.-F.
AU  - Liu, Y.-F.
AU  - Li, P.-F.
AU  - Ni, P.-X.
AU  - Wu, M.
TI  - Complete genome sequence of Pelagibacterium halotolerans B2T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 197
EP  - 198
VL  - 194
AB  - Pelagibacterium halotolerans B2T is a marine halotolerant bacterium that was isolated from a
AB  - seawater sample collected from the East China Sea. Here, we present the complete genome
AB  - sequence of the type strain P. halotolerans B2T, which consists of one chromosome (3,944,837
AB  - bp; 61.4% G_C content) and one plasmid (4,050 bp; 56.1% G_C content). This is the first
AB  - complete genome of a member of the Pelagibacterium genus.
ER  -

TY  - JOUR
AU  - Huo, Y.Y.
AU  - Li, Z.Y.
AU  - Cheng, H.
AU  - Wang, C.S.
AU  - Xu, X.W.
TI  - High quality draft genome sequence of the heavy metal resistant bacterium Halomonas zincidurans type strain B6(T).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 30
EP  - 30
VL  - 9
AB  - Halomonas zincidurans strain B6(T) was isolated from a deep-sea heavy metal rich  sediment
AB  - from the South Atlantic Mid-Ocean Ridge. The strain showed significant
AB  - resistance to heavy metals, especially to zinc. Here we describe the genome
AB  - sequence and annotation, as well as the features, of the organism. The genome
AB  - contains 3,325 protein-coding genes (2,848 with predicted functions), 61 tRNA
AB  - genes and 6 rRNA genes. H. zincidurans strain B6(T) encodes 31 genes related to
AB  - heavy metal resistance. And HGT may play an important role in its adaption to the
AB  - heavy metal rich environment. H. zincidurans strain B6(T) may have potential
AB  - applications in the bioremediation of heavy metal-contaminated environments.
ER  -

TY  - JOUR
AU  - Hupfeld, M.
AU  - Fouts, D.E.
AU  - Loessner, M.J.
AU  - Klumpp, J.
TI  - Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01440
EP  - e01414
VL  - 3
AB  - We present the complete genomes of Listeria ivanovii subsp. ivanovii WSLC 3010 (ATCC
AB  - 19119(T)), Listeria ivanovii subsp. londoniensis WSLC 30151 (SLCC 8854),
AB  - and Listeria ivanovii subsp. londoniensis WSLC 30167 (SLCC 6032), representing
AB  - the type strain of the species and two strains of the same serovar but different
AB  - properties, respectively.
ER  -

TY  - JOUR
AU  - Hupkes, M.
AU  - Azevedo, R.
AU  - Jansen, H.
AU  - van Zoelen, E.J.
AU  - Dechering, K.J.
TI  - Identification of Novel Bacterial M.SssI DNA Methyltransferase Inhibitors.
JO  - J. Biomol. Screen.
PY  - 2013
SP  - 348
EP  - 355
VL  - 18
AB  - DNA methylation is an important epigenetic regulator of gene expression. Abnormalities in DNA
AB  - methylation patterns have been
AB  - associated with various developmental and proliferative diseases,
AB  - particularly cancer. Targeting DNA methyltransferases (DNMTs)
AB  - represents a promising strategy for the treatment of such diseases.
AB  - Current DNMT inhibitors suffer important drawbacks with respect to
AB  - their efficacy, specificity, and toxicity. In this study, we have set
AB  - up a robust in vitro bacterial M.SssI DNMT activity assay to
AB  - systematically screen a collection of 26 240 compounds that were
AB  - predicted to compete with the S-adenosyl-L-methionine (SAM) substrate
AB  - of DNMT. This resulted in the identification of a novel set of
AB  - structurally distinct inhibitors of M.SssI DNMT activity. Although
AB  - molecular docking studies using an M.SssI homology model suggest that
AB  - these compounds might compete with SAM binding, mode of activity (MoA)
AB  - assays are still needed to confirm this hypothesis. Our set of novel
AB  - M.SssI DNMT inhibitors, once confirmed in an orthogonal DNMT assay, may
AB  - thus serve as a starting point to identify and characterize suitable
AB  - lead candidates for further drug optimization.
ER  -

TY  - JOUR
AU  - Hurd, P.J.
AU  - Whitmarsh, A.J.
AU  - Baldwin, G.S.
AU  - Kelly, S.M.
AU  - Waltho, J.P.
AU  - Price, N.C.
AU  - Connolly, B.A.
AU  - Hornby, D.P.
TI  - Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 389
EP  - 401
VL  - 286
AB  - DNA duplexes in which the target cytosine base is replaced by 2-H pyrimidinone have previously
AB  - been shown to bind with a significantly greater affinity to C5-cytosine DNA methyltransferases
AB  - than unmodified DNA.  Here, it is shown that 2-H pyrimidinone, when incorporated into DNA
AB  - duplexes containing the recognition sites for M.HgaI-2 and M.MspI, elicits the formation of
AB  - inhibitory covalent nucleoprotein complexes.  We have found that although covalent complexes
AB  - are formed between 2-H pyrimidinone-modified DNA and both M.HgaI-2 and M.MspI, the kinetics of
AB  - complex formation are quite distinct in each case.  Moreover, the formation of a covalent
AB  - complex is still observed between 2-H pyrimidinone DNA and M.MspI in which the active-site
AB  - cysteine residue is replaced by serine or threonine.  Covalent complex formation between
AB  - M.MspI and 2-H pyrimidinone occurs as a direct result of nucleophilic attack by the residue at
AB  - the catalytic position, which is enhanced by the absence of the 4-amino function in the base.
AB  - The substitution of the catalytic cysteine residue by tyrosine or chemical modification of the
AB  - wild-type enzyme with N-ethylmaleimide, abolishes covalent interaction.  Nevertheless the 2-H
AB  - pyrimidinone-substituted duplex still binds to M.MspI with a greater affinity than a standard
AB  - cognate duplex, since the 2-H pyrimidinone base is mis-paired with guanine.
ER  -

TY  - JOUR
AU  - Hurst, M.R.
AU  - Beattie, A.
AU  - Altermann, E.
AU  - Moraga, R.M.
AU  - Harper, L.A.
AU  - Calder, J.
AU  - Laugraud, A.
TI  - The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T.
JO  - Toxins (Basel)
PY  - 2016
SP  - 143
EP  - 143
VL  - 8
AB  - Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows
AB  - 93.8% nucleotide sequence identity to that of Yersinia nurmii type
AB  - strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp.
AB  - In silico analysis identified that, in addition to the previously documented Y.
AB  - entomophaga Yen-TC gene cluster, the genome encodes a diverse array of toxins,
AB  - including two type III secretion systems, and five rhs-associated gene clusters.
AB  - As well as these multicomponent systems, several orthologs of known insect
AB  - toxins, such as VIP2 toxin and the binary toxin PirAB, and distant orthologs of
AB  - some mammalian toxins, including repeats-in-toxin, a cytolethal distending toxin,
AB  - hemolysin-like genes and an adenylate cyclase were identified. The genome also
AB  - contains a large number of hypothetical proteins and orthologs of known effector
AB  - proteins, such as LopT, as well as genes encoding a wide range of proteolytic
AB  - determinants, including metalloproteases and pathogen fitness determinants, such
AB  - as genes involved in iron metabolism. The bioinformatic data derived from the
AB  - current in silico analysis, along with previous information on the pathobiology
AB  - of Y. entomophaga against its insect hosts, suggests that a number of these
AB  - virulence systems are required for survival in the hemocoel and incapacitation of
AB  - the insect host.
ER  -

TY  - JOUR
AU  - Hurst, M.R.
AU  - Glare, T.R.
AU  - Jackson, T.A.
TI  - Cloning Serratia entomophila antifeeding genes--a putative defective prophage active against the grass grub Costelytra zealandica.
JO  - J. Bacteriol.
PY  - 2004
SP  - 5116
EP  - 5128
VL  - 186
AB  - Serratia entomophila and Serratia proteamaculans (Enterobacteriaceae)
AB  - cause amber disease in the grass grub Costelytra zealandica (Coleoptera:
AB  - Scarabaeidae), an important pasture pest in New Zealand. Larval disease
AB  - symptoms include cessation of feeding, clearance of the gut, amber
AB  - coloration, and eventual death. A 155-kb plasmid, pADAP, carries the genes
AB  - sepA, sepB, and sepC, which are essential for production of amber disease
AB  - symptoms. Transposon insertions in any of the sep genes in pADAP abolish
AB  - gut clearance but not cessation of feeding, indicating the presence of an
AB  - antifeeding gene(s) elsewhere on pADAP. Based on deletion analysis of
AB  - pADAP and subsequent sequence data, a 47-kb clone was constructed, which
AB  - when placed in either an Escherichia coli or a Serratia background exerted
AB  - strong antifeeding activity and often led to rapid death of the infected
AB  - grass grub larvae. Sequence data show that the antifeeding component is
AB  - part of a large gene cluster that may form a defective prophage and that
AB  - six potential members of this prophage are present in Photorhabdus
AB  - luminescens subsp. laumondii TTO1, a species which also has sep gene
AB  - homologues.
ER  -

TY  - JOUR
AU  - Hurst, S.G. IV
AU  - Ghazal, S.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Badr, U.M.
AU  - Hussein, M.A.
AU  - AbouZaied, M.A.
AU  - Khalil, K.M.
AU  - Tisa, L.S.
TI  - Draft Genome Sequence of Photorhabdus temperata Strain Meg1, an Entomopathogenic  Bacterium Isolated from Heterorhabditis megidis Nematodes.
JO  - Genome Announcements
PY  - 2014
SP  - e01273
EP  - e01214
VL  - 2
AB  - Photorhabdus temperata strain Meg1 is an entomopathogenic bacterium that forms a  symbiotic
AB  - association with Heterorhabditis nematodes. We report here a 4.9-Mbp
AB  - draft genome sequence for P. temperata strain Meg1, with a G+C content of 43.18%
AB  - and containing 4,340 candidate protein-coding genes.
ER  -

TY  - JOUR
AU  - Hurst, S.G.I.V.
AU  - Oshone, R.
AU  - Ghodhbane-Gtari, F.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Ktari, A.
AU  - Salem, K.
AU  - Mansour, S.
AU  - Gtari, M.
AU  - Tisa, L.S.
TI  - Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown   in Egypt.
JO  - Genome Announcements
PY  - 2014
SP  - e00493
EP  - e00414
VL  - 2
AB  - Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous
AB  - plants termed actinorhizal plants. We report here a 5.3-Mbp draft
AB  - genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium
AB  - isolated from root nodules of Casuarina cunninghamiana collected in Egypt.
ER  -

TY  - JOUR
AU  - Hurtado, U.A.
AU  - Solano, J.S.
AU  - Rodriguez, A.
AU  - Robledo, J.
AU  - Rouzaud, F.
TI  - Draft Genome Sequence of a Mycobacterium africanum Clinical Isolate from Antioquia, Colombia.
JO  - Genome Announcements
PY  - 2016
SP  - e00486
EP  - e00416
VL  - 4
AB  - Mycobacterium africanum is a member of the Mycobacterium tuberculosis complex. Most commonly
AB  - found in West African countries, it has scarcely been described in
AB  - South America. Here, we report the first genome sequence of a Colombian M.
AB  - africanum clinical isolate. It is composed of 4,493,502 bp, with 4,069 genes.
ER  -

TY  - JOUR
AU  - Hussain, M.
AU  - Suliman, M.
AU  - Ahmed, A.
AU  - Altayb, H.
AU  - Elneima, E.
TI  - Draft Genome Sequence of a Multidrug-Resistant Pseudomonas aeruginosa Strain Isolated from a Patient with a Urinary Tract Infection in Khartoum, Sudan.
JO  - Genome Announcements
PY  - 2017
SP  - e00203
EP  - e00217
VL  - 5
AB  - Pseudomonas aeruginosa infection is difficult to treat due to the presence of antibiotic
AB  - resistance determinants. Here, we report the genome sequence of a
AB  - multidrug-resistant P. aeruginosa strain isolated from a patient with a urinary
AB  - tract infection in 2015.
ER  -

TY  - JOUR
AU  - Hutchison, C.A. III
AU  - Peterson, S.N.
AU  - Gill, S.R.
AU  - Cline, R.T.
AU  - White, O.
AU  - Fraser, C.M.
AU  - Smith, H.O.
AU  - Venter, J.C.
TI  - Global transposon mutagenesis and a minimal mycoplasma genome.
JO  - Science
PY  - 1999
SP  - 2165
EP  - 2165
VL  - 286
AB  - Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently
AB  - replicating cell so far identified.  Global transposon mutagenesis was used to identify
AB  - nonessential genes in an effort to learn whether the naturally occurring gene complement is a
AB  - true minimal genome under laboratory growth conditions. The positions of 2209 transposon
AB  - insertions in the completely sequenced genomes of M. genitalium and its close relative M.
AB  - pneumoniae were determined by sequencing across the junction of the transposon and the genomic
AB  - DNA. These junctions defined 1354 distinct sites of insertion that were not lethal.  The
AB  - analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are
AB  - essential under laboratory growth conditions, including about 100 genes of unknown function.
ER  -

TY  - JOUR
AU  - Hutt, L.P.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Palaniappan, K.
AU  - Varghese, N.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Boden, R.
TI  - Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 10
EP  - 10
VL  - 12
AB  - Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic
AB  - sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost
AB  - 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T)
AB  - isolated by Starkey in 1934 from agricultural soil at Rutgers University, New
AB  - Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the
AB  - oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway
AB  - and uses it to fix carbon dioxide It is not capable of heterotrophic or
AB  - mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report
AB  - the genome sequence, annotation and characteristics. The genome contains 3,135
AB  - protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant
AB  - of the Calvin-Benson-Bassham cycle were also identified and an operon encoding
AB  - carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle
AB  - sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase
AB  - (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial
AB  - sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that
AB  - contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302
AB  - gene previously noted in the sox operon of other members of the 'Proteobacteria'
AB  - that can use trithionate as an energy source. In spite of apparently not growing
AB  - anaerobically with denitrification, the nar, nir, nor and nos operons encoding
AB  - enzymes of denitrification are found in the T. thioparus genome, in the same
AB  - arrangements as in the true denitrifier T. denitrificans.
ER  -

TY  - JOUR
AU  - Hwang, C. et al.
TI  - Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated  Leachate Ponds.
JO  - Genome Announcements
PY  - 2016
SP  - e01226
EP  - e01216
VL  - 4
AB  - Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing
AB  - bacterium associated with phylum Firmicutes QYMF was isolated from
AB  - alkaline borax leachate ponds. The genome sequence will help elucidate the role
AB  - of metal-reducing microorganisms under alkaline environments, a capability that
AB  - is not commonly observed in metal respiring-microorganisms.
ER  -

TY  - JOUR
AU  - Hwang, C. et al.
TI  - Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.
JO  - Genome Announcements
PY  - 2015
SP  - e01449
EP  - e01414
VL  - 3
AB  - We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and
AB  - uranium-contaminated subsurface sediment of the Oak Ridge Integrated
AB  - Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN.
AB  - The bacterium's genome sequence will elucidate its physiological potential in
AB  - subsurface sediments undergoing in situ uranium bioremediation and natural
AB  - attenuation.
ER  -

TY  - JOUR
AU  - Hwang, D.K.
AU  - Cho, J.Y.
AU  - Chae, Y.K.
TI  - Recombinant expression and purification of functional XorII, a restriction endonuclease from Xanthomonas oryzae pv. oryzae.
JO  - J. Microbiol.
PY  - 2007
SP  - 175
EP  - 178
VL  - 45
AB  - An endonuclease from Xanthomonas oryzae pathovar oryzae KACC 10331, XorII, was recombinantly
AB  - produced in Escherichia coli using a T7
AB  - system. XorII was purified using a combination of ion exchange and
AB  - immobilized metal affinity chromatography (IMAC). An optimized washing
AB  - protocol was carried out on an IMAC in order to obtain a high purity
AB  - product. The final amount of purified XorII was approximately 2.5 mg/L
AB  - of LB medium. The purified recombinant XorII was functional and showed
AB  - the same cleavage pattern as PvuI. The enzyme activity tested the
AB  - highest at 25 degrees C in 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, and
AB  - 1 mM dithiothreitol at a pH of 7.9.
ER  -

TY  - JOUR
AU  - Hwang, H.-Y.
AU  - Yim, J.
TI  - SolI, a novel isoschizomer of BamHI isolated from Streptoverticillium olivoverticillatum.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 2197
EP  - 2197
VL  - 22
AB  - SolI, a new type II restriction endonuclease has been purified from Streptoverticillium
AB  - olivoverticillatum by chromatography on heparin-agarose and affigel-blue. The enzyme
AB  - recognizes the palindromic hexanucleotide sequence of 5'-GGATCC-3' and cleaves after the
AB  - first G to produce a 4 base 5'-extension.
ER  -

TY  - JOUR
AU  - Hwang, H.Y.
AU  - Yim, J.
TI  - Characterization of a new type II restriction endonuclease isolated from Streptoverticillium olivoverticillatum.
JO  - Korean J. Microbiol.
PY  - 1994
SP  - 208
EP  - 214
VL  - 32
AB  - We screened many species from a wide variety of bacterial genera for a new type II restriction
AB  - endonuclease.  The purification and characterization of SolI from a soil isolate,
AB  - Streptoverticillum olivoverticillatum are described here.  The enzyme turned out to be an
AB  - isoschizomer of BamHI.  It recognized the hexanucleotide sequence 5'-G/GATCC-3' and cleaved
AB  - as shown by the arrow, generating a 4 base 5' extension.  Unlike its isoschizomer, BamHI, the
AB  - activity was sensitive to dam methylation within the recognition sequence.  Following
AB  - ammonium sulfate fractionation of the crude extract, heparin-agarose and Affi-gel Blue column
AB  - chromatography were employed to purify the enzyme.  SolI required at least 0.2 mM of MgCl2 for
AB  - the cleavage to occur.  The enzyme exhibited its maximal activity in the absence of NaCl, but
AB  - was inhibited completely in the presence of 120mM NaCl.  The pH and temperature optima for
AB  - activity were pH 8.6 and 40oC, respectively.  The molecular weight of SolI was estimated to be
AB  - 43,000 Da by Superose-12 gel filtration chromatography.
ER  -

TY  - JOUR
AU  - Hwang, J.Y.
AU  - Kim, S.H.
AU  - Oh, H.R.
AU  - Cho, Y.J.
AU  - Chun, J.
AU  - Chung, Y.R.
AU  - Nam, D.H.
TI  - Draft Genome Sequence of Kitasatospora cheerisanensis KCTC 2395, Which Produces Plecomacrolide against Phytopathogenic Fungi.
JO  - Genome Announcements
PY  - 2014
SP  - e00604
EP  - e00614
VL  - 2
AB  - Kitasatospora cheerisanensis KCTC 2395, which produces antifungal metabolites with bafilomycin
AB  - derivatives, including bafilomycin C1-amide, was isolated from a
AB  - soil sample at Mt. Jiri, South Korea. Here, we report its draft genome sequence,
AB  - which contains 8.04 Mb with 73.6% G+C content and 7,810 protein-coding genes.
ER  -

TY  - JOUR
AU  - Hwang, S.
AU  - Song, Y.
AU  - Cho, B.K.
TI  - Draft Genome Sequence of Acetobacterium bakii DSM 8239, a Potential Psychrophilic Chemical Producer through Syngas Fermentation.
JO  - Genome Announcements
PY  - 2015
SP  - e01070
EP  - e01015
VL  - 3
AB  - Acetobacterium bakii DSM 8239 is an anaerobic, psychrophilic, and chemolithoautotrophic
AB  - bacterium that is a potential platform for producing commodity chemicals from syngas
AB  - fermentation. We report here the draft genome sequence of A. bakii DSM 8239 (4.14 Mb) to
AB  - elucidate its physiological and metabolic properties related to syngas fermentation.
ER  -

TY  - JOUR
AU  - Hwang, S.B.
AU  - Lee, S.H.
TI  - Character and function of restriction enzyme, EcoRI inhibiting substance extracted from spinach chloroplast and Chlamydomonas.
JO  - Singmul Hakhoe Chi
PY  - 1990
SP  - 217
EP  - 223
VL  - 33
AB  - Restriction enzyme inhibiting substance (REIS) extracted from spinach
AB  - chloroplast and Chlamydomonas seems not to be proteinaceous, because its
AB  - inhibiting activity was not lost by heat or trypsin treatment.  And it seems
AB  - not to be lipid or polysaccharide, because its inhibiting activity was not lost
AB  - by lipase or alpha-amylase treatment, respectively.  In Chlamydomonas,
AB  - putrescine, spermidine and spermine were present.  The amount of putrescine was
AB  - the smallest and that of spermine was the greatest.  But only spermine was
AB  - contained in REIS and the activity of REIS.  It was proportional to the amount
AB  - of spermine in REIS and it was hindered by Na+ ion.  So, the inhibiting
AB  - activity of REIS seems to be deeply related to spermine contained in REIS.  But
AB  - restriction enzyme inhibiting activity remained to the same extent although
AB  - salts and spermine were eliminated by dialysis.
ER  -

TY  - JOUR
AU  - Hwangbo, K.
AU  - Um, Y.
AU  - Chung, H.
AU  - Yoo, J.
AU  - Kim, K.Y.
AU  - Madhaiyan, M.
AU  - Sa, T.M.
AU  - Lee, Y.
TI  - Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e00573
EP  - e00516
VL  - 4
AB  - Dyella thiooxydans ATSB10 (KACC 12756(T) = LMG 24673(T)) is a thiosulfate-oxidizing bacterium
AB  - isolated from rhizosphere soils of sunflower
AB  - plants. In this study, we completely sequenced the genome of D. thiooxydans
AB  - ATSB10 and identified the genes involved in thiosulfate oxidation and the
AB  - metabolism of aromatic intermediates.
ER  -

TY  - JOUR
AU  - Hwangbo, K.
AU  - Um, Y.
AU  - Kim, K.Y.
AU  - Madhaiyan, M.
AU  - Sa, T.M.
AU  - Lee, Y.
TI  - Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e00654
EP  - e00616
VL  - 4
AB  - Bacillus velezensis CBMB205 (= KACC 13105(T) = NCCB 100236(T)) was isolated from  the
AB  - rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous
AB  - studies, this bacterium has several genes that can promote plant growth, such as
AB  - the phosphorus-solubilizing protein-coding gene. Here, we present the first
AB  - complete genome of B. velezensis CBMB205.
ER  -

TY  - JOUR
AU  - Hyden, P.
AU  - Pietzka, A.
AU  - Allerberger, F.
AU  - Springer, B.
AU  - Sensen, C.
AU  - Ruppitsch, W.
TI  - Draft Genome Sequence of a 94-Year-Old Listeria monocytogenes Isolate, SLCC208.
JO  - Genome Announcements
PY  - 2016
SP  - e01572
EP  - e01515
VL  - 4
AB  - We report here the draft genome sequence of Listeria monocytogenes strain SLCC208 from
AB  - Seeliger's historical Special Listeria Culture Collection, initially
AB  - cultured from a human case in France in 1921. This is, to our knowledge, the
AB  - oldest L. monocytogenes isolate available and may be useful for comparative
AB  - genomic studies of L. monocytogenes.
ER  -

TY  - JOUR
AU  - Hyman, P.
AU  - Abedon, S.T.
TI  - Bacteriophage Host Range and Bacterial Resistance.
JO  - Adv. Appl. Microbiol.
PY  - 2010
SP  - 217
EP  - 248
VL  - 70
AB  - Host range describes the breadth of organisms a parasite is capable of infecting, with limits
AB  - on host range stemming from parasite, host, or environmental characteristics. Parasites can
AB  - adapt to overcome host or environmental limitations, while hosts can adapt to control the
AB  - negative impact of parasites. We consider these adaptations as they occur among bacteriophages
AB  - (phages) and their bacterial hosts, since they are significant to phage use as antibacterials
AB  - (phage therapy) or to protection of industrial ferments from phage attack. Initially, we
AB  - address how phage host range can (and should) be defined plus summarize claims of host ranges
AB  - spanning multiple bacterial genera. Subsequently, we review bacterial mechanisms of phage
AB  - resistance. These include adsorption resistance, which results in reduced interaction between
AB  - phage and bacterium; what we describe as 'restriction,' where bacteria live but phages die;
AB  - and abortive infections, where both phage and bacterium die. Adsorption resistance includes
AB  - loss of phage receptor molecules on hosts as welt as physical barriers hiding receptor
AB  - molecules (e.g., capsules). Restriction mechanisms include phage-genome uptake blocks,
AB  - superinfection immunity, restriction modification, and CRISPR, all of which function postphage
AB  - adsorption but prior to terminal phage takeover of host metabolism. Standard laboratory
AB  - selection methods, involving exposure of planktonic bacteria to high phage densities, tend to
AB  - directly select for these prehost-takeover resistance mechanisms. Alternatively, resistance
AB  - mechanisms that do not prevent bacterium death are less readily artificially selected.
AB  - Contrasting especially bacteria mutation to adsorption resistance, these latter mechanisms
AB  - likely are an underappreciated avenue of bacterial resistance to phage attack.
ER  -

TY  - JOUR
AU  - Hyman, R.W.
AU  - St-Onge, R.P.
AU  - Allen, E.A.
AU  - Miranda, M.
AU  - Aparicio, A.M.
AU  - Fukushima, M.
AU  - Davis, R.W.
TI  - Multiplex identification of microbes.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 3904
EP  - 3910
VL  - 76
AB  - We have adapted molecular inversion probe technology to identify
AB  - microbes in a highly multiplexed procedure. This procedure does not
AB  - require growth of the microbes. Rather, the technology employs DNA
AB  - homology twice: once for the molecular probe to hybridize to its
AB  - homologous DNA and again for the 20-mer oligonucleotide barcode on the
AB  - molecular probe to hybridize to a commercially available molecular
AB  - barcode array. As proof of concept, we have designed, tested, and
AB  - employed 192 molecular probes for 40 microbes. While these particular
AB  - molecular probes are aimed at our interest in the microbes in the human
AB  - vagina, this molecular probe method could be employed to identify the
AB  - microbes in any ecological niche.
ER  -

TY  - JOUR
AU  - Hynes, R.K.
AU  - Dumonceaux, T.J.
AU  - Kangsopa, J.
AU  - Town, J.R.
TI  - Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Pseudomonas sp. Strain 31-12.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00947
EP  - e00918
VL  - 7
AB  - We present here a draft genome sequence of Pseudomonas sp. strain 31-12, a plant
AB  - growth-promoting rhizobacterium of several crop plants that was isolated from the
AB  - rhizosphere of corn in southern Ontario, Canada.
ER  -

TY  - JOUR
AU  - Hyson, P.
AU  - Shapiro, J.A.
AU  - Wien, M.W.
TI  - Draft Genome Sequence of Exiguobacterium sp. Strain BMC-KP, an Environmental Isolate from Bryn Mawr, Pennsylvania.
JO  - Genome Announcements
PY  - 2015
SP  - e01164
EP  - e01115
VL  - 3
AB  - Exiguobacterium sp. strain BMC-KP was isolated as part of a student environmental sampling
AB  - project at Bryn Mawr College, PA. Sequencing of bacterial DNA assembled  a 3.32-Mb draft
AB  - genome. Analysis suggests the presence of genes for tolerance to  cold and toxic metals, broad
AB  - carbohydrate metabolism, and genes derived from phage.
ER  -

TY  - JOUR
AU  - Hyun, D.W.
AU  - Whon, T.W.
AU  - Cho, Y.J.
AU  - Chun, J.
AU  - Kim, M.S.
AU  - Jung, M.J.
AU  - Shin, N.R.
AU  - Kim, J.Y.
AU  - Kim, P.S.
AU  - Yun, J.H.
AU  - Lee, J.
AU  - Oh, S.J.
AU  - Bae, J.W.
TI  - Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 255
EP  - 263
VL  - 8
AB  - Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family
AB  - Staphylococcaceae. Members of the Salinicoccus are moderately
AB  - halophilic and originate from various salty environments. The halophilic features
AB  - of the Salinicoccus suggest their possible uses in biotechnological applications,
AB  - such as biodegradation and fermented food production. However, the genus
AB  - Salinicoccus is poorly characterized at the genome level, despite its potential
AB  - importance. This study presents the draft genome sequence of S. carnicancri
AB  - strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700
AB  - protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%.
AB  - It was notable that the strain carried 72 predicted genes associated with
AB  - osmoregulation, which suggests the presence of beneficial functions that
AB  - facilitate growth in high-salt environments.
ER  -

TY  - JOUR
AU  - Iartchouk, O.
AU  - Kozyavkin, S.
AU  - Karamychev, V.
AU  - Slesarev, A.
TI  - Complete Genome Sequence of Lactobacillus acidophilus FSI4, Isolated from Yogurt.
JO  - Genome Announcements
PY  - 2015
SP  - e00166
EP  - e00115
VL  - 3
AB  - A new Lactobacillus acidophilus strain, FSI4, isolated from yogurt, was isolated  and
AB  - sequenced in our laboratory. Our data, although supportive of previous
AB  - conclusions regarding the remarkable stability of L. acidophilus species,
AB  - indicate accumulating mutations in commercial L. acidophilus strains that warrant
AB  - further study of the effect of damaged genes on the competitiveness of these
AB  - bacteria in gut microbiota.
ER  -

TY  - JOUR
AU  - Iatsenko, I.
AU  - Corton, C.
AU  - Pickard, D.J.
AU  - Dougan, G.
AU  - Sommer, R.J.
TI  - Draft Genome Sequence of Highly Nematicidal Bacillus thuringiensis DB27.
JO  - Genome Announcements
PY  - 2014
SP  - e00101
EP  - e00114
VL  - 2
AB  - Here, we report the genome sequence of nematicidal Bacillus thuringiensis DB27, which provides
AB  - first insights into the genetic determinants of its pathogenicity
AB  - to nematodes. The genome consists of a 5.7-Mb chromosome and seven plasmids,
AB  - three of which contain genes encoding nematicidal proteins.
ER  -

TY  - JOUR
AU  - Ibacache-Quiroga, C.
AU  - Canales, C.
AU  - Charifeh, M.
AU  - Dinamarca, M.A.
TI  - Genome Sequence of Cobetia sp. Strain MM1IDA2H-1, a Hydrocarbon-Degrading and Biosurfactant-Producing Marine Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00132
EP  - e00117
VL  - 5
AB  - Cobetia sp. strain MM1IDA2H-1 is a marine bacterium isolated from seawater samples that uses
AB  - the heterocyclic aromatic hydrocarbon dibenzothiophene as the
AB  - sole carbon source and produces a biosurfactant that inhibits bacterial quorum
AB  - sensing. The Cobetia sp. MM1IDA2H-1 genome was sequenced, processed, assembled,
AB  - and annotated for basic and applied studies.
ER  -

TY  - JOUR
AU  - Ibanez, M.
AU  - Alvarez, I.
AU  - Rodriguez-Pena, J.M.
AU  - Rotger, R.
TI  - A ColE1-type plasmid from Salmonella enteritidis encodes a DNA cytosine methyltransferase.
JO  - Gene
PY  - 1997
SP  - 145
EP  - 158
VL  - 196
AB  - The multicopy plasmid pFM366 was isolated from a virulent Salmonella enteritidis strain and
AB  - was found to code for DNA methylase activity (Ibanez and Rotger, 1993). The present work was
AB  - aimed at characterizing the genetic organization and functional of this 5.6 kb plasmid. We
AB  - found pFM366 almost identical to the plasmid P4 isolated from Shigella sonnei, that encodes
AB  - the SsoII restriction-modification system (Karyagina et al., 1993), and related to other
AB  - ColE1-type plasmids. Examination of these plasmids revealed a common organization which
AB  - suggests they were the result of similar recombinational events. The cytosine methylase of
AB  - pFM366 is nearly identical to M. SsoII, whereas the gene encoding the restrictase homologous
AB  - to R. SsoII is truncated and its product is inactive. The expression of the cytosine methylase
AB  - encoded by pFM366 is strongly affected by deletion of regions located upstream and downstream
AB  - of its ORF, and is negatively controlled by the rpoS gene in Escherichia coli. The methylase
AB  - activity encoded by pFM366 induces the SOS response, which could be responsible for the
AB  - observed delay in the growth of E. coli.
ER  -

TY  - JOUR
AU  - Ibanez, M.
AU  - Rotger, R.
TI  - Characterization of small cryptic plasmid from Salmonella enteritidis that affects the growth of Escherichia coli.
JO  - FEMS Microbiol. Lett.
PY  - 1993
SP  - 225
EP  - 230
VL  - 109
AB  - We examined the plasmid content of 25 clinical isolates of Salmonella enteritidis, and
AB  - detected the presence of small plasmids (3-5.3 kb) in 9 of them, alone, or in addition to the
AB  - large, so-called virulence plasmid.  A 5.3-kb plasmid isolated as unique extrachromosomal DNA
AB  - from a strain responsible for a high-mortality outbreak was characterized by restriction
AB  - mapping and cloning.  The plasmid replicon was localized in a 1.7-kb fragment, that hybridized
AB  - with three of the small plasmids detected in S. enteritidis, and with another small plasmid
AB  - from Salmonella typhimurium.  A strain of Escherichia coli carrying this plasmid, or a cloned
AB  - 3.7-kb PvuII restriction fragment, showed a slower growth rate, especially in minimal medium,
AB  - as well as a noticeable increase in DNA methyltransferase activity.
ER  -

TY  - JOUR
AU  - Ibarra-Caballero, J.
AU  - Zerillo, M.M.
AU  - Snelling, J.
AU  - Cranshaw, W.
AU  - Boucher, C.
AU  - Tisserat, N.
TI  - Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp. quercina.
JO  - Genome Announcements
PY  - 2014
SP  - e00584
EP  - e00514
VL  - 2
AB  - Two bacteria identified as Lonsdalea quercina subsp. quercina were isolated from  oak trees
AB  - showing symptoms of drippy blight. Here, we present their draft genome assemblies, as well as
AB  - that of the type strain of this species. To our knowledge, these are the first published
AB  - genome sequences of this subspecies of Lonsdalea quercina.
ER  -

TY  - JOUR
AU  - Ibrahim, M.H.
AU  - Cress, B.F.
AU  - Linhardt, R.J.
AU  - Koffas, M.A.
AU  - Gross, R.A.
TI  - Draft Genome Sequence of Bacillus subtilis Ia1a, a New Strain for Poly-gamma-Glutamic Acid and Exopolysaccharide Production.
JO  - Genome Announcements
PY  - 2016
SP  - e01361
EP  - e01316
VL  - 4
AB  - We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated
AB  - poly-gamma-glutamic acid-producing strain, Bacillus subtilis Ia1a. The
AB  - genome sequence is considered a critical tool to facilitate the engineering of
AB  - improved production strains. Exopolysaccharides and many industrially important
AB  - enzymes can be produced by this new strain utilizing different carbon sources.
ER  -

TY  - JOUR
AU  - Ibryashkina, E.M.
AU  - Sasnauskas, G.
AU  - Solonin, A.S.
AU  - Zakharova, M.V.
AU  - Siksnys, V.
TI  - Oligomeric structure diversity within the GIY-YIG nuclease family.
JO  - J. Mol. Biol.
PY  - 2009
SP  - 10
EP  - 16
VL  - 387
AB  - The GIY-YIG nuclease domain has been identified in homing endonucleases, DNA repair and
AB  - recombination enzymes, and restriction endonucleases.  The Type II restriction enzyme Eco29kI
AB  - belongs to the GIY-YIG nuclease superfamily and, like most of other family members, including
AB  - the homing endonuclease I-TevI, is a monomer. It recognizes the palindromic sequence
AB  - 5'-CCGC/GG-3' ('/' marks the cleavage position) and cuts it to generate 3'-staggered
AB  - ends. The Eco29kI monomer, which contains a single active site, either has to nick
AB  - sequentially individual DNA strands or has to form dimers or even higher-order oligomers upon
AB  - DNA binding to make a double-strand break at its target site. Here, we provide experimental
AB  - evidence that Eco29kI monomers dimerize on a single cognate DNA molecule forming the
AB  - catalytically active complex. The mechanism described here for Eco29kI differs from that of
AB  - Cfr42I isoschisomer, which also belongs to the GIY-YIG family but is functional as a tetramer.
AB  - This novel mechanism may have implications for the function of homing endonucleases and other
AB  - enzymes of the GIY-YIG family.
ER  -

TY  - JOUR
AU  - Ibryashkina, E.M.
AU  - Zakharova, M.V.
AU  - Baskunov, V.B.
AU  - Bogdanova, E.S.
AU  - Nagornykh, M.O.
AU  - Den'mukhamedov, M.M.
AU  - Melnik, B.S.
AU  - Kolinski, A.
AU  - Gront, D.
AU  - Feder, M.
AU  - Solonin, A.S.
AU  - Bujnicki, J.M.
TI  - Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.
JO  - BMC Struct. Biol.
PY  - 2007
SP  - 48
EP  - 48
VL  - 7
AB  - The majority of experimentally determined crystal structures of type II restriction
AB  - endonucleases exhibit a common PD-(D/E)XK fold.  Crystal structures have been also determined
AB  - for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI), and
AB  - bioinformatics analyses supported by mutagenesis suggested that some REases belong to the HNH
AB  - fold.  Our previous bioinformatic analysis suggested that REase R.Eco29kl shares sequence
AB  - similarities with one more unrelated nuclease superfamily.  GIY-YIG, however so far no
AB  - experimental data were available to support this prediction.  The determination of a crystal
AB  - structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling
AB  - of R.Eco29kl and prompted us to validate the model experimentally. Using protein
AB  - fold-recognition methods we generated a new alignment between R.Eco29kl and I-TevI, which
AB  - suggested a reassignment of one of the putative catalytic residues.  A theoretical model of
AB  - R.Eco29kl was constructed to illustrate its predicted three-dimensional fold and organization
AB  - of the active site, comprising amino acid residues Y49, Y76, R104, H108, E142, and N154.  A
AB  - series of mutants was constructed to generate amino acid substitutions of selected residues
AB  - (Y49A, R104A, H108F, E142A and N154L) and the mutant proteins were examined for their ability
AB  - to bind the DNA containing the Eco29kl site 5'-CCGCGG-3' and to catalyze the cleavage
AB  - reaction.  Experimental data reveal that residues Y49, R104, E142, H108, and N154 are
AB  - important for the nuclease activity of R.Eco29kl, while H108 and N154 are also important for
AB  - specific DNA binding by this enzyme.
ER  -

TY  - JOUR
AU  - Ichida, H.
AU  - Maeda, K.
AU  - Ichise, H.
AU  - Matsuyama, T.
AU  - Abe, T.
AU  - Yoneyama, K.
AU  - Koba, T.
TI  - In silco irestiriction landmairk genome scanning analysis of Xanthomonas oryzae pathovair oryzae MAFF 311018.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2007
SP  - 852
EP  - 856
VL  - 363
AB  - We have developed a restriction landmark genome scanning (RLGS) system in silico, involving
AB  - two-dimensional electrophoretic analysis of DNA by
AB  - computer simulation that is based on the availability of whole-genome
AB  - sequences for specific organisms. We applied the technique to the
AB  - analysis of the Xanthomonas oryzae pathovar oryzae (Xoo) MAFF 311018,
AB  - which causes bacterial blight in rice. The coverage that was found to
AB  - be achievable using RLGS in silico, as a percentage of the genomic
AB  - regions that could be detected, ranged from 44.5% to 72.7% per image.
AB  - However, this reached a value of 96.7% using four images that were
AB  - obtained with different combinations of landmark restriction enzymes.
AB  - Interestingly, the signal intensity of some of the specific spots
AB  - obtained was significantly lower than that of other surrounding spots
AB  - when Mbol, which cleaves unmethylated 5'-GATC-3' sites, was used. DNA
AB  - gel blot analysis with both DNA adenine methylase (Dam)-sensitive and
AB  - -insensitive isoschizomers (Mbol and Sau3AI) revealed that Dam-mediated
AB  - DNA adenine methylation had indeed occurred at these particular sites.
AB  - These results suggest that a significant portion of the 5'-GATC-3'
AB  - sites within the Xoo genome is stably methylated by Dam.
ER  -

TY  - JOUR
AU  - Ichida, H.
AU  - Matsuyama, T.
AU  - Abe, T.
AU  - Koba, T.
TI  - DNA adenine methylation changes dramatically during establishment of symbiosis.
JO  - FEBS J.
PY  - 2007
SP  - 951
EP  - 962
VL  - 274
AB  - The DNA adenine methylation status on specific 5'-GANTC-3' sites and its
AB  - change during the establishment of plant-microbe interactions was
AB  - demonstrated in several species of alpha-proteobacteria. Restriction
AB  - landmark genome scanning (RLGS), which is a high-resolution two
AB  - dimensional DNA electrophoresis method, was used to monitor the genomewide
AB  - change in methylation. In the case of Mesorhizobium loti MAFF303099, real
AB  - RLGS images obtained with the restriction enzyme MboI, which digests at
AB  - GATC sites, almost perfectly matched the virtual RLGS images generated
AB  - based on genome sequences. However, only a few spots were observed when
AB  - the restriction enzyme HinfI was used, suggesting that most GANTC (HinfI)
AB  - sites were tightly methylated and specific sites were unmethylated. DNA
AB  - gel blot analysis with the cloned specifically unmethylated regions (SUMs)
AB  - showed that some SUMs were methylated differentially in bacteroids
AB  - compared to free-living bacteria. SUMs have also been identified in other
AB  - symbiotic and parasitic bacteria. These results suggest that DNA adenine
AB  - methylation may contribute to the establishment and/or maintenance of
AB  - symbiotic and parasitic relationships.
ER  -

TY  - JOUR
AU  - Ichige, A.
AU  - Kobayashi, I.
TI  - Stability of EcoRI Restriction-Modification Enzymes In Vivo Differentiates the EcoRI Restriction-Modification System from Other Postsegregational   Cell Killing Systems.
JO  - J. Bacteriol.
PY  - 2005
SP  - 6612
EP  - 6621
VL  - 187
AB  - Certain type II restriction modification gene systems can kill host cells when these gene
AB  - systems are eliminated from the host cells. Such ability
AB  - to cause postsegregational killing of host cells is the feature of
AB  - bacterial addiction modules, each of which consists of toxin and antitoxin
AB  - genes. With these addiction modules, the differential stability of toxin
AB  - and antitoxin molecules in cells plays an essential role in the execution
AB  - of postsegregational killing. We here examined in vivo stability of the
AB  - EcoRI restriction enzyme (toxin) and modification enzyme (antitoxin), the
AB  - gene system of which has previously been shown to cause postsegregational
AB  - host killing in Escherichia coli. Using two different methods, namely,
AB  - quantitative Western blot analysis and pulse-chase immunoprecipitation
AB  - analysis, we demonstrated that both the EcoRI restriction enzyme and
AB  - modification enzyme are as stable as bulk cellular proteins and that there
AB  - is no marked difference in their stability. The numbers of EcoRI
AB  - restriction and modification enzyme molecules present in a host cell
AB  - during the steady-state growth were estimated. We monitored changes in
AB  - cellular levels of the EcoRI restriction and modification enzymes during
AB  - the postsegregational killing. Results from these analyses together
AB  - suggest that the EcoRI gene system does not rely on differential stability
AB  - between the toxin and the antitoxin molecules for execution of
AB  - postsegregational cell killing. Our results provide insights into the
AB  - mechanism of postsegregational killing by restriction-modification
AB  - systems, which seems to be distinct from mechanisms of postsegregational
AB  - killing by other bacterial addiction modules.
ER  -

TY  - JOUR
AU  - Ichige, A.
AU  - Kobayashi, I.
TI  - Stability of EcoRI restriction modification enzymes in vivo differentiates EcoRI restriction-modification system from other postsegregational cell killing systems.
JO  - Genes Genet. Syst.
PY  - 2005
SP  - 454
EP  - 454
VL  - 80
AB  - Certain Type II restriction modification gene systems can kill host cells when these gene
AB  - systems are eliminated from the host cells.  Such ability to cause prostsegregational killing
AB  - of host cells is the feature of bacterial addiction modules, each of which consists of toxin
AB  - and antitoxin genes.  With these addiction modules, differential stability of toxin and
AB  - antitoxin molecules in cells plays an essential role in execution of postsegregational
AB  - killing.  We here examined in vivo stability of the EcoRI restriction enzyme (toxin) and
AB  - modification enzyme (antitoxin) in Escherichia coli.  Using Western blot analysis and
AB  - pulse-chase immunoprecipitation analysis, we demonstrated that both the EcoRI restriction
AB  - enzyme and modification enzyme are as stable as bulk cellular proteins and that there is no
AB  - marked difference in their stability.  We also monitored changes in cellular levels of the
AB  - EcoRI restriction and modification enzyme during postsegregational killing.  Results from
AB  - these analyses together suggest that the EcoRI gene system does not rely on differential
AB  - stability between the toxin and the antitoxin molecules for execution of postsegregational
AB  - cell killing.
ER  -

TY  - JOUR
AU  - Ichikawa, N. et al.
TI  - Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae.
JO  - DNA Res.
PY  - 2010
SP  - 393
EP  - 406
VL  - 17
AB  - Kitasatospora setae NBRC 14216T (5KM-6054T) is known to produce setamycin (bafilomycin B1)
AB  - possessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the
AB  - genus Streptomyces, although they are distinguishable from each other on the basis of cell
AB  - wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of
AB  - K. setae NBRC 14216T as the first Streptomycetaceae genome other than Streptomyces. The genome
AB  - is a single linear chromosome of 8 783 278 bp with terminal inverted repeats of 127 148 bp,
AB  - predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes.
AB  - Although these features resemble those of Streptomyces, genome-wide comparison of orthologous
AB  - genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus
AB  - phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the
AB  - Streptomyces genus. Although many of the genes related to morphological differentiation
AB  - identified in Streptomyces were highly conserved in K. setae, there were some differences such
AB  - as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the
AB  - copy number and variation of paralogous components involved in cell wall synthesis.
ER  -

TY  - JOUR
AU  - Ichise, Y.K.
AU  - Kosuge, T.
AU  - Uwate, M.
AU  - Nakae, T.
AU  - Maseda, H.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Strain 8380, Isolated from the Human Gut.
JO  - Genome Announcements
PY  - 2015
SP  - e00520
EP  - e00515
VL  - 3
AB  - Pseudomonas aeruginosa shows multidrug resistance, which is mainly attributable to its
AB  - expression of xenobiotic efflux pumps. However, it is unclear how silent
AB  - pumps are expressed in clinical isolates. Here, we sequenced the complete genome
AB  - of P. aeruginosa strain 8380, which was isolated from a human gut.
ER  -

TY  - JOUR
AU  - Ichiwaki, S.
AU  - Costa, A.C.M.M.
AU  - Silva, E.G.
AU  - Rada, L.R.M.
AU  - Lima, F.R.
AU  - Ortiz-Vera, M.P.
AU  - Garrido, L.M.
AU  - Sato, M.I.Z.
AU  - Araujo, W.L.
AU  - Padilla, G.
TI  - Genome Sequence of Micromonospora sp. NBS 11-29, an Antibiotic and Hydrolytic Enzyme Producer, Isolated from River Sediment in Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00552
EP  - e00517
VL  - 5
AB  - The genus Micromonospora comprises actinomycetes with high biotechnological potential, due to
AB  - their ability to produce secondary metabolites and enzymes. In
AB  - this study, we report the draft genome sequence of Micromonospora sp. NBS 11-29,
AB  - which showed antibacterial, cellulolytic, and xylanolytic activities under in
AB  - vitro conditions.
ER  -

TY  - JOUR
AU  - Ichiyanagi, K.
TI  - Inhibition of MspI cleavage activity by hydroxymethylation of the CpG site A concern for DNA modification studies using restriction endonucleases.
JO  - EPIGENETICS
PY  - 2012
SP  - 131
EP  - 136
VL  - 7
AB  - In mammalian genomic DNA, cytosine methylation predominantly occurs at CpG dinucleotides and
AB  - provides epigenetic information. In some cells,
AB  - 5-methyl-cytosine (5-mC) can be further converted to
AB  - 5-hydroxymethyl-cytosine (5-hmC) by the ten-eleven translocation family
AB  - of proteins. MspI restriction endonuclease has been used to analyze
AB  - these modified cytosines. However, the kinetic analysis in this study
AB  - revealed that MspI activity is dramatically decreased by symmetrical
AB  - hydroxymethylation of its recognition sequence and partly inhibited by
AB  - hemi-hydroxymethylation, whereas TaqI and HaeIII are relatively
AB  - resistant to hydroxymethylation. Therefore, DNA modification studies
AB  - that use MspI, for example, reduced representation bisulfite shotgun
AB  - sequencing, quantitative analysis of 5-hmC and cleavage-sensitivity
AB  - analysis, should be carefully interpreted.
ER  -

TY  - JOUR
AU  - Ichiyanagi, K.
AU  - Ishino, Y.
AU  - Ariyoshi, M.
AU  - Komori, K.
AU  - Morikawa, K.
TI  - Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 889
EP  - 901
VL  - 300
AB  - Inteins possess two different enzymatic activities, self-catalyzed protein splicing and
AB  - site-specific DNA cleavage. These endonucleases, which are classified as part of the homing
AB  - endonuclease family, initiate the mobility of their genetic elements into homologous alleles.
AB  - They recognize long asymmetric nucleotide sequences and cleave both DNA strands in a monomer
AB  - form. We present here the 2.1 A crystal structure of the archaeal PI-PfuI intein from
AB  - Pyrococcus furiosus. The structure reveals a unique domain, designated here as the Stirrup
AB  - domain, which is inserted between the Hint domain and an endonuclease domain. The
AB  - horseshoe-shaped Hint domain contains a catalytic center for protein splicing, which involves
AB  - both N and C-terminal residues. The endonuclease domain, which is inserted into the Hint
AB  - domain, consists of two copies of substructure related by an internal pseudo 2-fold axis. In
AB  - contrast with the I-CreI homing endonuclease, PI-PfuI possibly has two asymmetric catalytic
AB  - sites at the center of a putative DNA-binding cleft formed by a pair of four-stranded
AB  - beta-sheets. DNase I footprinting experiments showed that PI-PfuI covers more than 30 bp of
AB  - the substrate asymmetrically across the cleavage site. A docking model of the DNA-enzyme
AB  - complex suggests that the endonuclease domain covers the 20 bp DNA duplex encompassing the
AB  - cleavage site, whereas the Stirrup domain could make an additional contact with another
AB  - upstream 10 bp region. For the double-strand break, the two strands in the DNA duplex were
AB  - cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is
AB  - catalyzed by each of the two non-equivalent active sites.
ER  -

TY  - JOUR
AU  - Igbinosa, E.O.
AU  - Rathje, J.
AU  - Habermann, D.
AU  - Brinks, E.
AU  - Cho, G.S.
AU  - Franz, C.M.A.P.
TI  - Draft Genome Sequence of Multidrug-Resistant Strain Citrobacter portucalensis MBTC-1222, Isolated from Uziza (Piper guineense) Leaves in Nigeria.
JO  - Genome Announcements
PY  - 2018
SP  - e00123
EP  - e00118
VL  - 6
AB  - In this work, we report the draft whole-genome sequence of the multiply antibiotic-resistant
AB  - Citrobacter portucalensis strain MBTC-1222 isolated from the
AB  - uziza leafy vegetable in Nigeria. Sequence analysis showed the assembled genome
AB  - size to be 4,881,935 bp, containing 4,603 protein-coding genes, 131 pseudogenes,
AB  - 7 rRNAs, 74 tRNAs, and 9 noncoding RNAs (ncRNAs).
ER  -

TY  - JOUR
AU  - Iglesias, N.G.
AU  - Valdes, La.H.D.
AU  - Olguin, N.T.
AU  - Bravo-Ferrada, B.M.
AU  - Brizuela, N.S.
AU  - Tymczyszyn, E.E.
AU  - Bibiloni, H.
AU  - Caballero, A.C.
AU  - Delfederico, L.
AU  - Semorile, L.
TI  - Genome Sequence of Oenococcus oeni UNQOe19, the First Fully Assembled Genome Sequence of a Patagonian Psychrotrophic Oenological Strain.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00889
EP  - e00818
VL  - 7
AB  - Oenococcus oeni UNQOe19 is a native strain isolated from a Patagonian pinot noir  wine
AB  - undergoing spontaneous malolactic fermentation. Here, we present the 1.83-Mb
AB  - genome sequence of O. oeni UNQOe19, the first fully assembled genome sequence of
AB  - a psychrotrophic strain from an Argentinean wine.
ER  -

TY  - JOUR
AU  - Ignatov, A.N.
AU  - Kyrova, E.I.
AU  - Vinogradova, S.V.
AU  - Kamionskaya, A.M.
AU  - Schaad, N.W.
AU  - Luster, D.G.
TI  - Draft Genome Sequence of Xanthomonas arboricola Strain 3004, a Causal Agent of Bacterial Disease on Barley.
JO  - Genome Announcements
PY  - 2015
SP  - e01572
EP  - e01514
VL  - 3
AB  - We report here the annotated genome sequence of Xanthomonas arboricola strain 3004, isolated
AB  - from barley leaves with symptoms of streak and capable of infecting other plant species. We
AB  - sequenced the genome of X. arboricola strain 3004 to improve the understanding of molecular
AB  - mechanisms of the pathogenesis and evolution of the genus Xanthomonas.
ER  -

TY  - JOUR
AU  - Iida, S.
AU  - Meyer, J.
AU  - Bachi, B.
AU  - Stalhammar-Carlemalm, M.
AU  - Schrickel, S.
AU  - Bickle, T.A.
AU  - Arber, W.
TI  - DNA Restriction-Modification Genes of Phage P1 and Plasmid p15B.
JO  - J. Mol. Biol.
PY  - 1983
SP  - 1
EP  - 18
VL  - 165
AB  - The EcoP1 and EcoP15 DNA restriction-modification systems are coded by the related P1 prophage
AB  - and p15B plasmid.  We have examined the organization of the genes for these systems using P1
AB  - itself, "P1-P15" hybrid phages expressing the EcoP15 restriction specificity of p15B and
AB  - cloned restriction fragments derived from these phage DNAs.  The results of transposon
AB  - mutagenesis, restriction cleavage analysis, DNA heteroduplex analysis and in vitro
AB  - transcription mapping allow the following conclusions to be drawn concerning the structural
AB  - genes. (1) All of the genetic information necessary to specify either system is contained
AB  - within a contiguous DNA segment of 5000 bases which encodes two genes.  One of them, necessary
AB  - for both restriction and modification, we call mod and the other, required only for
AB  - restriction (together with mod), we call res.  (2) The res gene is about 2800 bases long and
AB  - at the heteroduplex level is largely identical for P1 and P15:  it shows a small region of
AB  - partial nonhomology and some restriction cleavage site differences.  The mod gene is about
AB  - 2200 bases long and contains a 1200 base long region of non-homology between P1 and P15 toward
AB  - the N-terminus of the gene.  The rest of the gene at this level of analysis is identical for
AB  - the two systems.  (3) Each of the genes is transcribed in vitro from its own promoter.  It is
AB  - possible that the res gene is also transcribed by readthrough from the mod promoter.
ER  -

TY  - JOUR
AU  - Iida, S.
AU  - Streiff, M.B.
AU  - Bickle, T.A.
AU  - Arber, W.
TI  - Two DNA antirestriction systems of bacteriophage P1, darA, and darB:  characterization of darA- phages.
JO  - Virology
PY  - 1987
SP  - 156
EP  - 166
VL  - 157
AB  - Bacteriophage P1 is only weakly restricted when it infects cells carrying type
AB  - I restriction and modification systems even though DNA purified from P1 phage
AB  - particles is a good substrate for type I restriction enzymes in vitro.  Here we
AB  - show that this protection against restriction is due to the products of two
AB  - phage genes which we call darA and darB (dar for defense against restriction).
AB  - Each of the dar gene products provides protection against a different subset of
AB  - type I restriction systems.  The darA and darB gene products are found in the
AB  - phage head and protect any DNA packaged into a phage head, including transduced
AB  - chromosomal markers, from restriction.  The proteins must, therefore, be
AB  - injected into recipient cells along with the DNA.  The proteins act strictly in
AB  - cis.  For example, upon double infection of restricting cells with dar+ and
AB  - dar- P1 phages, the dar+ genomes are protected from restriction while the
AB  - dar-genomes are efficiently restricted.
ER  -

TY  - JOUR
AU  - Iida, T.
AU  - Suetake, I.
AU  - Tajima, S.
AU  - Morioka, H.
AU  - Ohta, S.
AU  - Obuse, C.
AU  - Tsurimoto, T.
TI  - PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA.
JO  - Genes Cells
PY  - 2002
SP  - 997
EP  - 1008
VL  - 7
AB  - Proliferating cell nuclear antigen (PCNA) is a ring-shaped protein known as a processivity
AB  - factor of DNA polymerase delta.  In addition to this role, PCNA interacts with a number of
AB  - other proteins to increase their local concentration at replicated DNA sites.  DNA cytosine
AB  - methyltransferase 1 (Dnmt1), which preserves epigenetic signals by completing the methylation
AB  - of hemimethylated DNA aftr DNA replication, has been indicated as one of these PCNA binding
AB  - proteins by a previous work.  However, the molecular mechanisms and functional significance of
AB  - their association have not yet been studied.  Results: Dnmt1 can be readily isolated from
AB  - nuclear extracts by PCNA affinity chromatography.  Studies of the interactions between the two
AB  - proteins demonstrate that the N-terminal region of Dnmt1, which contains a typical PCNA
AB  - binding
AB  - motif, has core PCNA binding activity, and that the remaining portion of the protein exerts a
AB  - negative influence on the interaction of Dnmt1 with PCNA.  The affinity of Dnmt1 for DNA is
AB  - much higher for DNA bound by PCNA than for free DNA.  Furthermore, DNA methylation assays with
AB  - hemimethylated DNA as a substrate revealed that PCNA clamp-bound DNA is methylated more
AB  - efficiently by Dnmt1 than is free DNA.  Conclusion: These results provide the first
AB  - biochemical evidence that physical interactions between PCNA and Dnmt1 facilitate the
AB  - methylation of newly replicated DNA, on which PCNA remains associated as a functional clamp.
ER  -

TY  - JOUR
AU  - Iida, Y.
AU  - Fujiwara, K.
AU  - Someya, N.
AU  - Shinohara, M.
TI  - Draft Genome Sequence of Rhizobium sp. Strain TBD182, an Antagonist of the Plant-Pathogenic Fungus Fusarium oxysporum, Isolated from a Novel Hydroponics  System Using Organic Fertilizer.
JO  - Genome Announcements
PY  - 2017
SP  - e00007
EP  - e00017
VL  - 5
AB  - Rhizobium sp. strain TBD182, isolated from a novel hydroponics system, is an antagonistic
AB  - bacterium that inhibits the mycelial growth of Fusarium oxysporum
AB  - but does not eliminate the pathogen. We report the draft genome sequence of
AB  - TBD182, which may contribute to elucidation of the molecular mechanisms of its
AB  - fungistatic activity.
ER  -

TY  - JOUR
AU  - Ikawa, S.
AU  - Shibata, T.
AU  - Ando, T.
TI  - Recognition sequence of endonuclease R. BamNx from Bacillus amyloliquefaciens N.
JO  - Agric. Biol. Chem.
PY  - 1979
SP  - 873
EP  - 875
VL  - 43
AB  - Recently, many site-specific deoxyribonucleases including restriction
AB  - endonucleases which cleave DNA strands at unique sites have been isolated from
AB  - various kinds of microorganisms.  Recognition nucleotide sequences on DNA have
AB  - been determined for a number of them.  We have reported that Bacillus
AB  - amyloliquefaciens N and many other Bacillus strains possess site-specific
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Ikawa, S.
AU  - Shibata, T.
AU  - Ando, T.
TI  - Host-Controlled modification and restriction in Bacillus subtilis.  Bsu168-System and BsuR-System in B. subtilis 168.
JO  - Mol. Gen. Genet.
PY  - 1979
SP  - 123
EP  - 127
VL  - 170
AB  - A Bsu168-specific restriction deficient (r-1)6)8) mutant of Bacillus subtilis
AB  - Marburg 168 was transformed to be BsuR-specific restriction proficient (r+R)
AB  - with B. subtilis R DNA as efficiently as the Bsu168-specific restriction
AB  - proficient (r+1)6)8) parental strain (hsrM+, hsdR-). We constructed
AB  - r+Rm+Rr+1m6m8mm+1868 strain (ISMR4), r+Rm+Rr-1m6m8mm+1868 strain (ISR11) and
AB  - r+Rm+Rr-1m6m8mm-1868 strain (ISR6) from strain 101 (r+1868m+1868), strain 1012
AB  - (r-1868m+1868) and strain RM125 (r-1868m-1868), respectively by transformation
AB  - with B. subtilis R DNA, and tested their restriction and modification
AB  - activities on phage Phi105C.  The results show that the sites recognized by
AB  - Bsu168-specific restriction and modification enzymes and the sites recognized
AB  - by BsuR-specific ones are not overlapping. We conclude that the
AB  - Bsu168-modification and restriction system and the BsuR-modification and
AB  - restriction system are controlled independently by two distinct sets of genes
AB  - in the r_Rm+R transformant of r+1868m+1868 strain B. subtilis 168.
ER  -

TY  - JOUR
AU  - Ikawa, S.
AU  - Shibata, T.
AU  - Ando, T.
TI  - The Site-specific Deoxyribonuclease from Bacillus pumilus (Endonuclease R.Bpu1387).
JO  - J. Biochem. (Tokyo)
PY  - 1976
SP  - 1457
EP  - 1460
VL  - 80
AB  - A new site-specific endonuclease (DNase) was isolated from the cells of
AB  - Bacillus pumilus AHU 1387 strain.  This enzyme (endonuclease R.Bpu 1387)
AB  - introduced double-stranded scissions at unique sites on DNA's of coli phage
AB  - lambda, lambda dvl, coli phage T7, Bacillus phage Phi105C, Bacillus phage SP10,
AB  - and Simian Virus 40, in the presence of magnesium ion.  The activity was
AB  - stimulated by the presence of NaCl.
ER  -

TY  - JOUR
AU  - Ikawa, S.
AU  - Shibata, T.
AU  - Ando, T.
AU  - Saito, H.
TI  - Genetic studies on site-specific endodeoxyribonucleases in Bacillus subtilis:  Multiple modification and restriction systems in transformants of Bacillus subtilis 168.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 359
EP  - 368
VL  - 177
AB  - We transformed B. subtilis 168 with DNA from B. subtilis IAM1231, IAM1192 and
AB  - ATCC6633.  When we examined the restriction activities of the transformants in
AB  - vivo and in vitro using phage Phi105C we found the following: (1) Cells of
AB  - either IAM1231 or IAM1192 have two modification and restriction systems
AB  - (Bsu1231(1)-system and Bsu1231(II)-system in IAM1231, and Bsu1192(I)-system and
AB  - Bsu1192(II)-systems in IAM1192), and cells of ATCC6633 have only one system
AB  - (Bsu6633-system).  (2) The restriction enzymes of all of these five systems are
AB  - site-specific endonucleases.  (3) The nucleotide sequence specifities of the
AB  - enzymes involved in Bsu1231(I)-system, Bsu1192(I)-system and Bsu6633-system are
AB  - the same; and those of Bsu1231(II)-system and Bsu1192(II)-system are the same.
AB  - The sequence specificities of these two groups are different from each other
AB  - and also different from those of the Bsu168-system of B. subtilis 168, the
AB  - BsuR-system of B. subtilis R and the Bsu1247(I)-and Bsu1247(II)-systems which
AB  - are systems of B. subtilis IAM1247.  (4) Transformants possessing four
AB  - different modification and restriction systems (Bsu1231(I)-, Bsu1247(I)-, BsuR-
AB  - and Bsu168-systems) were constructed.  (5) Transformation of two derivatives of
AB  - 168 that were mR+rR+ by DNA from IAM1231 produced 16 transformants that had the
AB  - Bsu1231(II) restriction system, but had lost the BsuR system.  Transformation
AB  - of a derivative of 168 that was m+1247(II)r+1247(II) by DNA from
AB  - m+1231(II)r+1231(II)- or mR+rR+-derivative of 168 produced about 100 each of
AB  - transformants that had the Bsu1231(II)-restriction system or the
AB  - BsuR-restriction system.  But all these transformants lost the
AB  - Bsu1247(II)-system.
ER  -

TY  - JOUR
AU  - Ikawa, S.
AU  - Shibata, T.
AU  - Matsumoto, K.
AU  - Iijima, T.
AU  - Saito, H.
AU  - Ando, T.
TI  - Chromosomal loci of genes controlling site-specific restriction endonucleases of Bacillus subtilis.
JO  - Mol. Gen. Genet.
PY  - 1981
SP  - 1
EP  - 6
VL  - 183
AB  - We constructed transformants of B. subtilis 168 which acquired genes for
AB  - site-specific restriction endonucleases.  These endonucleases originated from
AB  - various strains of B. subtilis and were classified into five groups based on
AB  - the specificity of the sequences recognized by the enzymes.  We examined the
AB  - loci of genes for site-specific restriction endonucleases belonging to
AB  - different groups:  hsrE determined Endo.R.Bsu1231(I), hsrB Endo.R.Bsu1247(I),
AB  - hsrR Endo.R.BsuR and hsrC Endo.R.Bsu-1247(II).  One gene, hsrE, was located
AB  - between sacA and purA by transduction crosses with phage PBS1, and another
AB  - gene, hsrB, between hsrE and purA.  Genes hsrR and hsrC had been suggested to
AB  - be allelic or closely linked by previous studies with transformation.  We
AB  - located hsrR and hsrC between purB and tre.  Our previous observation and this
AB  - study show that B. subtilis 168 has at least three independent loci on the
AB  - chromosome for four genes for site-specific restriction endonucleases in
AB  - addition to the locus for the original restriction activity (Bsu168-specific
AB  - restriction) of strain 168.
ER  -

TY  - JOUR
AU  - Ikeda, H.
AU  - Ishikawa, J.
AU  - Hanamoto, A.
AU  - Shinose, M.
AU  - Kikuchi, H.
AU  - Shiba, T.
AU  - Sakaki, Y.
AU  - Hattori, M.
AU  - Omura, S.
TI  - Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
JO  - Nat. Biotechnol.
PY  - 2003
SP  - 526
EP  - 531
VL  - 21
AB  - Species of the genus Streptomyces are of major pharmaceutical interest
AB  - because they synthesize a variety of bioactive secondary metabolites. We
AB  - have determined the complete nucleotide sequence of the linear chromosome
AB  - of Streptomyces avermitilis. S. avermitilis produces avermectins, a group
AB  - of antiparasitic agents used in human and veterinary medicine. The genome
AB  - contains 9,025,608 bases (average GC content, 70.7%) and encodes at least
AB  - 7,574 potential open reading frames (ORFs). Thirty-five percent of the
AB  - ORFs (2,664) constitute 721 paralogous families. Thirty gene clusters
AB  - related to secondary metabolite biosynthesis were identified,
AB  - corresponding to 6.6% of the genome. Comparison with Streptomyces
AB  - coelicolor A3(2) revealed that an internal 6.5-Mb region in the S.
AB  - avermitilis genome was highly conserved with respect to gene order and
AB  - content, and contained all known essential genes but showed perfectly
AB  - asymmetric structure at the oriC center. In contrast, the terminal regions
AB  - were not conserved and preferentially contained nonessential genes.
ER  -

TY  - JOUR
AU  - Ikeda, M.
AU  - Nakagawa, S.
TI  - The Corynebacterium glutamicum genome: Features and impacts on biotechnological processes.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2003
SP  - 99
EP  - 109
VL  - 62
AB  - Corynebacterium glutamicum has played a principal role in the progress of the amino acid
AB  - fermentation industry. The complete genome sequence of the representative wild-type strain of
AB  - C. glutamicum, ATCC 13032, has been determined and analyzed to improve our understanding of
AB  - the molecular biology and physiology of this organism, and to advance the development of more
AB  - efficient production strains. Genome annotation has helped in elucidation of the gene
AB  - repertoire defining a desired pathway, which is accelerating pathway engineering. Post genome
AB  - technologies such as DNA arrays and proteomics are currently undergoing rapid development in
AB  - C. glutamicum. Such progress has already exposed new regulatory networks and functions that
AB  - had so far been unidentified in this microbe. The next goal of these studies is to integrate
AB  - the fruits of genomics into strain development technology. A novel methodology that merges
AB  - genomics with classical strain improvement has been developed and applied for the
AB  - reconstruction of classically derived production strains. How can traditional fermentation
AB  - benefit from the C. glutamicum genomic data? The path from genomics to biotechnological
AB  - processes is presented.
ER  -

TY  - JOUR
AU  - Ikegami, K.
AU  - Aita, Y.
AU  - Shiroma, A.
AU  - Shimoji, M.
AU  - Tamotsu, H.
AU  - Ashimine, N.
AU  - Shinzato, M.
AU  - Ohki, S.
AU  - Nakano, K.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Hirano, T.
AU  - Yohda, M.
TI  - Complete Genome Sequence of Petrimonas sp. Strain IBARAKI, Assembled from the Metagenome Data of a Culture Containing Dehalococcoides spp.
JO  - Genome Announcements
PY  - 2018
SP  - e00384
EP  - e00318
VL  - 6
AB  - The complete genome sequence of Petrimonas sp. strain IBARAKI in a Dehalococcoides-containing
AB  - culture was determined using the PacBio RS II
AB  - platform. The genome is a single circular chromosome of 3,693,233 nucleotides
AB  - (nt), with a GC content of 44%. This is the first genome sequence of a Petrimonas
AB  - species.
ER  -

TY  - JOUR
AU  - Ikram, H.I.
AU  - Catherine, R.
AU  - Caroline, M.
AU  - Didier, R.
AU  - Hocine, H.
AU  - Christelle, D.
TI  - Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 956
EP  - 959
VL  - 9
AB  - Halopiger goleamassiliensis strain IIH3(T) sp. nov. is a novel, extremely halophilic archaeon
AB  - within the genus Halopiger. This strain was isolated from an
AB  - evaporitic sediment in El Golea Lake, Ghardaia region (Algeria). The type strain
AB  - is strain IIH3(T). H. goleamassiliensis is moderately thermophilic, neutrophilic,
AB  - non-motile and coccus-shaped. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. The 3,906,923 bp long
AB  - genome contains 3,854 protein-encoding genes and 49 RNA genes (1 gene is 16S
AB  - rRNA, 1 gene is 23S rRNA, 3 genes are 5S rRNA, and 44 are tRNA genes).
ER  -

TY  - JOUR
AU  - Ilagan-Cruzada, M.F.C.
AU  - Rosana, A.R.R.
AU  - Montecillo, A.D.
AU  - Sabino, N.G.
AU  - Dalmacio, I.F.
TI  - Complete Genome Sequence of Lactobacillus plantarum subsp. plantarum Strain LB1-2, Isolated from the Hindgut of European Honeybees, Apis mellifera L., from  the Philippines.
JO  - Genome Announcements
PY  - 2018
SP  - e00209
EP  - e00218
VL  - 6
AB  - Lactobacillus plantarum subsp. plantarum strain LB1-2, isolated from the hindgut  of European
AB  - honeybees in the Philippines, is active against Paenibacillus larvae
AB  - and has broad activity against several Gram-positive and Gram-negative bacteria.
AB  - The complete genome sequence reported herein contains gene clusters for multiple
AB  - bacteriocins and extensive gene inventories for carbohydrate metabolism.
ER  -

TY  - JOUR
AU  - Ilin, A.I.
AU  - Kulmanov, M.E.
AU  - Korotetskiy, I.S.
AU  - Akhmetova, G.K.
AU  - Lankina, M.V.
AU  - Shvidko, S.V.
AU  - Reva, O.N.
TI  - Complete Genome Sequence of Multidrug-Resistant Clinical Isolate Mycobacterium tuberculosis 187.0, Used To Study the Effect of Drug Susceptibility Reversion by   the New Medicinal Drug FS-1.
JO  - Genome Announcements
PY  - 2015
SP  - e01272
EP  - e01215
VL  - 3
AB  - Complete genome sequence of the multidrug-resistant clinical isolate Mycobacterium
AB  - tuberculosis SCAID 187.0 containing several drug-resistance
AB  - mutations is presented. This strain is used in experiments to study genomic and
AB  - population changes leading to reversion of susceptibility to the 1st line
AB  - anti-tuberculosis (TB) drugs under the influence of a new medicinal drug FS-1.
ER  -

TY  - JOUR
AU  - Illikoud, N.
AU  - Klopp, C.
AU  - Roulet, A.
AU  - Bouchez, O.
AU  - Marsaud, N.
AU  - Jaffres, E.
AU  - Zagorec, M.
TI  - One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 22
EP  - 22
VL  - 13
AB  - Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of
AB  - chilled meat and seafood products through the production of
AB  - various metabolites responsible for off-odors. However, metabolic pathways
AB  - leading to meat and seafood spoilage are not all well known. The production of
AB  - spoiling molecules seems to depend both on strains and on food matrix. Several B.
AB  - thermosphacta genome sequences have been reported, all issued from meat isolates.
AB  - Here, we report four genome sequences, one complete and three as drafts. The four
AB  - B. thermosphacta strains CD 337, TAP 175, BSAS1 3, and EBP 3070 were isolated
AB  - from different ecological niches (seafood or meat products either spoiled or not
AB  - and bovine slaughterhouse). These strains known as phenotypically and genetically
AB  - different were selected to represent intraspecies diversity. CD 337 genome is
AB  - 2,594,337 bp long, complete and circular, containing 2593 protein coding
AB  - sequences and 28 RNA genes. TAP 175, BSAS1 3, and EBP 3070 genomes are arranged
AB  - in 57, 83, and 71 contigs, containing 2515, 2668, and 2611 protein-coding
AB  - sequences, respectively. These genomes were compared with two other B.
AB  - thermosphacta complete genome sequences. The main genome content differences
AB  - between strains are phages, plasmids, restriction/modification systems, and cell
AB  - surface functions, suggesting a similar metabolic potential but a different niche
AB  - adaptation capacity.
ER  -

TY  - JOUR
AU  - Imachi, H.
AU  - Sakai, S.
AU  - Lipp, J.S.
AU  - Miyazaki, M.
AU  - Saito, Y.
AU  - Yamanaka, Y.
AU  - Hinrichs, K.U.
AU  - Inagaki, F.
AU  - Takai, K.
TI  - Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 812
EP  - 818
VL  - 64
AB  - A novel, anaerobic filamentous bacterium, strain MO-CFX1(T), was isolated from a
AB  - methanogenic community, which was originally established from subseafloor
AB  - sediments collected from off the Shimokita Peninsula, Japan. Cells were
AB  - non-spore-forming, non-motile, Gram-stain-negative and filamentous. The filaments
AB  - were longer than 10 microm and 130-150 nm in width. Growth of the strain was
AB  - observed at 10-37 degrees C (optimum 25-30 degrees C), at pH 5.5-8.5 (optimum pH
AB  - 7.0) and in 0-50 g NaCl l(-1) (optimum 15 g NaCl l(-1)). The strain was able to
AB  - grow with a number of carbohydrates in the presence of yeast extract. The major
AB  - cellular fatty acids were monounsaturated C18 : 1omega9, C16 : 1omega7 and
AB  - saturated C18 : 0 and C16 : 0. The intact polar lipids of the strain were
AB  - dominated by diacylglyceride and sphingolipid core lipid structures with
AB  - monoglycosidic, mixed phosphomonoglycosidic and fatty-acid-modified
AB  - monoglycosidic polar head groups. The G+C content of the genomic DNA was 52.4
AB  - mol%. Based on the comparative 16S rRNA gene sequence analysis, strain MO-CFX1(T)
AB  - was affiliated with the class Anaerolineae within the phylum Chloroflexi and was
AB  - most closely related to Leptolinea tardivitalis YMTK-2(T) (sequence identity of
AB  - 91.0 %). Based on phenotypic and genetic properties of the novel isolate, we
AB  - propose a novel species representing a new genus Pelolinea submarina gen. nov.,
AB  - sp. nov., for strain MO-CFX1(T) ( = JCM 17238(T), = KCTC 5975(T)). This is the
AB  - first formal description, to our knowledge, of an isolate of the phylum
AB  - Chloroflexi from the deep-sea sedimentary environment.
ER  -

TY  - JOUR
AU  - Imagawa, T.
AU  - Nakayama, H.
AU  - Katunuma, N.
AU  - Sakuraba, H.
AU  - Ohshima, T.
AU  - Itoh, T.
AU  - Sako, Y.
AU  - Nomura, N.
AU  - Tsuge, H.
TI  - Crystallization and preliminary X-ray diffraction analysis of homing endonuclease I-Tsp061I.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2004
SP  - 2006
EP  - 2008
VL  - 60
AB  - Two crystal forms, rhombohedral and hexagonal, of a homing endonuclease from Thermoproteus sp.
AB  - IC-061 (I-Tsp0611) were obtained by the
AB  - hanging-drop and sitting-drop method, respectively. The hexagonal
AB  - crystals belong to space group P6(3)22, with unit-cell parameters a = b
AB  - = 111.4, c = 97.6 Angstrom, and diffract to 3.2 Angstrom resolution on
AB  - beamline BL44 at SPring-8 (Harima, Japan). The rhombohedral crystals
AB  - belong to space group R32, with unit-cell parameters a = b = 95.4, c =
AB  - 192.9 Angstrom, and diffract to 2.7 Angstrom resolution using a Cu
AB  - Kalpha rotating-anode generator with an R-AXIS VII detector. The
AB  - crystal asymmetric unit contained one protein molecule and the solvent
AB  - contents of the two crystal forms were estimated to be 68.3 and 67.6%
AB  - by volume, respectively.
ER  -

TY  - JOUR
AU  - Imajoh, M.
AU  - Fukumoto, Y.
AU  - Yamane, J.
AU  - Sukeda, M.
AU  - Shimizu, M.
AU  - Ohnishi, K.
AU  - Oshima, S.
TI  - Draft Genome Sequence of Nocardia seriolae Strain N-2927 (NBRC 110360), Isolated  as the Causal Agent of Nocardiosis of Yellowtail (Seriola quinqueradiata) in  Kochi Prefecture, Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e00082
EP  - e00015
VL  - 3
AB  - We report the draft genome sequence of Nocardia seriolae strain N-2927 (NBRC 110360), isolated
AB  - from cultured yellowtail Seriola quinqueradiata. RAST
AB  - annotation of the genome revealed 117 genes involved in the virulence, disease,
AB  - and defense subsystem. Eleven of these genes were predicted as antibiotic
AB  - resistance genes.
ER  -

TY  - JOUR
AU  - Imajoh, M.
AU  - Sukeda, M.
AU  - Shimizu, M.
AU  - Yamane, J.
AU  - Ohnishi, K.
AU  - Oshima, S.
TI  - Draft Genome Sequence of Erythromycin- and Oxytetracycline-Sensitive Nocardia seriolae Strain U-1 (NBRC 110359).
JO  - Genome Announcements
PY  - 2016
SP  - e01606
EP  - e01615
VL  - 4
AB  - In Japan, the emergence of macrolide- and oxytetracycline-resistant strains of Nocardia
AB  - seriolae has previously been reported. Here, we describe the draft
AB  - genome sequence of N. seriolae strain U-1, isolated in 2011 from a diseased
AB  - yellowtail in Kagoshima Prefecture. The draft genome does not have any genes
AB  - responsible for macrolide and tetracycline resistance.
ER  -

TY  - JOUR
AU  - Imajoh, M.
AU  - Tsuji, Y.
AU  - Yamashita, H.
AU  - Ohgi, M.
AU  - Monno, S.
AU  - Ohnishi, K.
AU  - Horioka, K.
TI  - Draft Genome Sequence of Flavobacteriumpsychrophilum Strain SSADA-1411, Isolated  from an Ayu (Plecoglossus altivelis altivelis) Migrating Downriver To Spawn in  the Shimanto River, Kochi, Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e00735
EP  - e00717
VL  - 5
AB  - Here, we report the draft genome sequence and annotation of Flavobacterium psychrophilum
AB  - strain SSADA-1411. This strain was isolated from the skin ulcer of
AB  - an ayu (Plecoglossus altivelis altivelis) migrating downriver to spawn in the
AB  - lower Shimanto River, in western Kochi Prefecture on Shikoku Island in Japan.
ER  -

TY  - JOUR
AU  - Imamovic, L.
AU  - Misiakou, M.A.
AU  - van der Helm, E.
AU  - Panagiotou, G.
AU  - Muniesa, M.
AU  - Sommer, M.O.A.
TI  - Complete Genome Sequence of Escherichia coli Strain WG5.
JO  - Genome Announcements
PY  - 2018
SP  - e01403
EP  - e01417
VL  - 6
AB  - Escherichia coli strain WG5 is a widely used host for phage detection, including  somatic
AB  - coliphages employed as standard ISO method 10705-1 (2000). Here, we
AB  - present the complete genome sequence of a commercial E. coli WG5 strain.
ER  -

TY  - JOUR
AU  - Imber, R.
AU  - Bickle, T.A.
TI  - Purification and properties of the restriction endonuclease BglII from Bacillus globigii.
JO  - Eur. J. Biochem.
PY  - 1981
SP  - 395
EP  - 399
VL  - 117
AB  - The restriction endonuclease BglII from Bacillus globigii has been purified to
AB  - homogeneity.  The enzyme is a dimer of two subunits of Mr = 27000.  The
AB  - reaction mechanism does not involve the accumulation of a DNA intermediate
AB  - nicked in one strand and the enzyme is not affected by superhelical twists in
AB  - the substrate DNA, indicating that DNA binding does not involve either winding
AB  - or unwinding of the double helix.  Antibodies were prepared against BglII.
AB  - These antibodies did not cross react with any other restriction endonucleases
AB  - tested, including other enzymes from B. globigii or from closely related
AB  - strains.  It is thus unlikely that type II restriction enzymes represent a
AB  - closely related group of proteins.
ER  -

TY  - JOUR
AU  - Imhof, P.
AU  - Fischer, S.
AU  - Smith, J.C.
TI  - Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis.
JO  - Biochemistry
PY  - 2009
SP  - 9061
EP  - 9075
VL  - 48
AB  - Endonucleases, Such as the restriction enzyme EcoRV, cleave the DNA backbone at a specific
AB  - recognition sequence. We have investigated the
AB  - catalytic mechanism of backbone phosphodiester hydrolysis by the
AB  - restriction enzyme EcoRV by means of hybrid quantum
AB  - mechanical/molecular mechanical calculations. An exhaustive computation
AB  - of different reaction pathways is performed, thus generating a network
AB  - of pathways. Comparison of the computed (AM1d/MM) enzymatic reaction
AB  - pathways with an analogous mechanism for small-molecule model systems
AB  - [AM1/d and B3LYP/6-31 + +G(d,p)] reveals that the transition barriers
AB  - for associative hydrolysis, which is more probable in the model
AB  - systems, are not lowered by the enzyme. Instead, a reaction mechanism
AB  - which has mostly dissociative character is more likely. The protein
AB  - environment is tuned to significantly electrostatically stabilize the
AB  - transition state structures, The direct catalytic impact of essential
AB  - residues is determined: The magnesium metal Ion activates a water
AB  - molecule, thus facilitating protonation of the leaving group. A
AB  - reduction of the coordination number of the magnesium metal ion from
AB  - six to four upon the positioning of the attacking water molecule
AB  - explains why larger metal ions, such as calcium, are not catalytically
AB  - active. The nucleophile is generated by the transfer of a proton from
AB  - the attacking water molecule to a carboxylic oxygen atom of aspartate
AB  - 90. The catalytic effect of lysine 92 involves proper positioning of
AB  - the scissile phosphate group and, more importantly, stabilization of
AB  - the metaphosphate intermediate in an orientation optimal for attack of
AB  - the nucleophile.
ER  -

TY  - JOUR
AU  - Imori, P.F.M.
AU  - Campioni, F.
AU  - Cao, G.
AU  - Kastanis, G.
AU  - Leon, M.S.
AU  - Allard, M.W.
AU  - Falcao, J.P.
TI  - Draft Genome Sequences of Yersinia frederiksenii, Yersinia intermedia, and Yersinia kristensenii Strains from Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00780
EP  - e00717
VL  - 5
AB  - Yersinia enterocolitica-like strains are usually understudied. In this work, we reported the
AB  - draft genome sequences of two Yersinia frederiksenii, two Yersinia
AB  - intermedia, and two Yersinia kristensenii strains isolated from humans, animals,
AB  - food, and the environment in Brazil. These draft genomes will provide better
AB  - molecular characterizations of these species.
ER  -

TY  - JOUR
AU  - Inaba, T.
AU  - Sato, Y.
AU  - Koike, H.
AU  - Hori, T.
AU  - Kanno, M.
AU  - Kimura, N.
AU  - Kirimura, K.
AU  - Habe, H.
TI  - Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00906
EP  - e00918
VL  - 7
AB  - Pseudomonas citronellolis LA18T catabolizes levulinic acid (LA) from cellulosic biomass
AB  - hydrolysate via acetyl-coenzyme A (acetyl-CoA) and propionyl-CoA. This
AB  - study reports the 7.22-Mbp draft genome sequence of P. citronellolis LA18T. The
AB  - draft genome sequence will aid the study of the LA catabolic pathway, which will
AB  - allow for more applications of LA-utilizing bacteria.
ER  -

TY  - JOUR
AU  - Inada, S.
AU  - Watanabe, K.
TI  - Draft Genome Sequence of Meiothermus ruber H328, Which Degrades Chicken Feathers, and Identification of Proteases and Peptidases Responsible for Degradation.
JO  - Genome Announcements
PY  - 2013
SP  - e00176
EP  - e00113
VL  - 1
AB  - Meiothermus ruber H328 was isolated from Arima Hot Springs, Kobe, Japan, as a moderate
AB  - thermophile. It has a strong ability to degrade intact chicken feathers.
AB  - The enzymatic mechanism of the strain for feather degradation is unclear. The
AB  - draft genome suggests potent enzyme candidates for degradation of keratin, a
AB  - hard-to-degrade protein found in feathers.
ER  -

TY  - JOUR
AU  - Inagaki, K.
AU  - Dou, D.
AU  - Kita, K.
AU  - Hiraoka, N.
AU  - Kishimoto, N.
AU  - Sugio, T.
AU  - Tano, T.
TI  - Isolation and characterization of restriction endonucleases from Acidiphilium sp. 16R and 22M.
JO  - J. Ferment. Bioeng.
PY  - 1990
SP  - 60
EP  - 62
VL  - 69
AB  - Restriction endonucleases (Asp16RI and Asp22MI) have been identified from the acidophilic
AB  - bacteria Acidiphilium sp. 16R and 22M. The cleavage patterns with various DNAs show that both
AB  - enzymes recognize the same sequence as the PvuI restriction endonuclease (5'-CGAT^CG-3'),
AB  - which is from Proteus vulgaris ATCC 13315. Most of the catalytic properties observed for
AB  - Asp16RI and Asp22MI were similar to those observed for PvuI. However, unlike PvuI both enzymes
AB  - efficiently cleaved DNA in the absence of NaCl or KCl. The purification yield of Asp22MI is 60
AB  - times that of PvuI.
ER  -

TY  - JOUR
AU  - Inagaki, K.
AU  - Hikita, T.
AU  - Yanagidani, S.
AU  - Nomura, Y.
AU  - Kishimoto, N.
AU  - Tano, T.
AU  - Tanaka, H.
TI  - Restriction endonuclease Aor13HI from Acidiphilium organovorum 13H, a new isoschizomer of BspMII: Purification and characterization.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1993
SP  - 1716
EP  - 1721
VL  - 57
AB  - A restriction endonuclease, Aor13HI, an isoschizomer of BspMII, was purified to homogeneity
AB  - from cell extracts of Acidiphilium organovorum strain 13H. The enzyme has a molecular mass of
AB  - 60,000 daltons and consists of two subunits identical in molecular mass of 30,000 daltons.
AB  - Aor13HI endonuclease, like BspMII, recognizes the palindromic six-base sequence
AB  - 5'-TCCGGA-3', and cleaves between the T and C to produce a four-base 5' extension. Aor13HI
AB  - is not inhibited by dam-dependent methylation. The isoelectric point of the enzyme is 5.7.
AB  - Aor13HI activity was maximum at pH 7.5, 100 mM KCI, 7.5-10mM MgC12 and 55 degrees C. The
AB  - enzyme was stable up to 60 degrees C. The N-terminal amino acid sequence (30 residues) of
AB  - Aor13HI did not show similarity with the sequence of other restriction endonuclease reported.
ER  -

TY  - JOUR
AU  - Inagaki, K.
AU  - Ito, T.
AU  - Sagawa, H.
AU  - Kotani, H.
AU  - Kishimoto, N.
AU  - Sugio, T.
AU  - Tano, T.
AU  - Tanaka, H.
TI  - AcpI, a novel isoschizomer of AsuII from Acidiphilium cryptum 25H, recognizes the sequence 5'TT^CGAA3'.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6335
EP  - 6335
VL  - 19
AB  - AcpI, a type II restriction endonuclease, has been isolated from Acidiphilium
AB  - cryptum 25H.  AcpI, an isoschizomer of AsuII, recognizes the six base sequence
AB  - 5'TTCGAA3', and cleaves between the T and the C residues to produce a two base
AB  - 5' extension.
ER  -

TY  - JOUR
AU  - Inagaki, K.
AU  - Kobayashi, F.
AU  - Dou, D.
AU  - Nomura, Y.
AU  - Kotani, H.
AU  - Kishimoto, N.
AU  - Sugio, T.
AU  - Tano, T.
TI  - Isolation and identification of restriction endonuclease Asp35HI from Acidiphilium species 35H.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6155
EP  - 6155
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Inano, K.
AU  - Suetake, I.
AU  - Ueda, T.
AU  - Miyake, Y.
AU  - Nakamura, M.
AU  - Okada, M.
AU  - Tajima, S.
TI  - Maintenance-type DNA methyltransferase is highly expressed in post-mitotic neurons and localized in the cytoplasmic compartment.
JO  - J. Biochem. (Tokyo)
PY  - 2000
SP  - 315
EP  - 321
VL  - 128
AB  - Maintenance-type DNA methyltransferase (Dnmt1) is usually down-regulated in nonproliferating
AB  - cells, In the present study, we
AB  - detected significant expression of Dnmt1 protein in adult mouse brain
AB  - where the majority of the cells are in a post-mitotic state. A
AB  - significant amount of Dnmt1 protein was fractionated into the
AB  - post-nuclear fraction for both cerebrum and cerebellum. The Dnmt1 in
AB  - this fraction was enzymatically active. An immunofluorescence study
AB  - revealed that Dnmt1 protein was mainly expressed in neurons and seemed
AB  - to be localized in the cytoplasmic compartment, Primary culturing of
AB  - neurons confirmed the expression and localization of Dnmt1 in the
AB  - cytoplasmic compartment, The findings that the Dnmt1 transcript in the
AB  - brain utilized the somatic-type exon and that the apparent size of the
AB  - Dnmt1 protein in the cytoplasm was identical to that in proliferating
AB  - culture cells indicate that the cytoplasmic Dnmt1 in neurons was of the
AB  - somatic-type.
ER  -

TY  - JOUR
AU  - Indiana, A.
AU  - Briand, M.
AU  - Arlat, M.
AU  - Gagnevin, L.
AU  - Koebnik, R.
AU  - Noel, L.D.
AU  - Portier, P.
AU  - Darrasse, A.
AU  - Jacques, M.A.
TI  - Draft Genome Sequence of the Flagellated Xanthomonas fuscans subsp. fuscans Strain CFBP 4884.
JO  - Genome Announcements
PY  - 2014
SP  - e00966
EP  - e00914
VL  - 2
AB  - We report the draft genome sequence of the flagellated strain CFBP 4884 of Xanthomonas fuscans
AB  - subsp. fuscans, which was isolated in an outbreak of common
AB  - bacterial blight of beans along with non-flagellated strains. Comparative
AB  - genomics will allow one to decipher the genomic diversity of strains cohabiting
AB  - in epidemics.
ER  -

TY  - JOUR
AU  - Inglin, R.C.
AU  - Meile, L.
AU  - Klumpp, J.
AU  - Stevens, M.J.A.
TI  - Complete and Assembled Genome Sequence of Lactobacillus plantarum RI-113 Isolated from Salami.
JO  - Genome Announcements
PY  - 2017
SP  - e00183
EP  - e00117
VL  - 5
AB  - We present here the complete genome sequence of Lactobacillus plantarum RI-113, a strain
AB  - isolated from salami, which was determined using single-molecule real-time
AB  - sequencing.
ER  -

TY  - JOUR
AU  - Inglin, R.C.
AU  - Meile, L.
AU  - Stevens, M.J.A.
TI  - Draft Genome Sequences of 43 Lactobacillus Strains from the Species L. curvatus,  L. fermentum, L. paracasei, L. plantarum, L. rhamnosus, and L. sakei, Isolated  from Food Products.
JO  - Genome Announcements
PY  - 2017
SP  - e00632
EP  - e00617
VL  - 5
AB  - The genome sequences of 43 Lactobacillus strains from the species L. curvatus, L. fermentum,
AB  - L. paracasei, L. plantarum, L. rhamnosus, and L. sakei were determined
AB  - using Illumina MiSeq.
ER  -

TY  - JOUR
AU  - Inocencio, T.
AU  - Vital, J.
AU  - Vitor, J.
AU  - Falcao, A.O.
TI  - Genome inspector: A web tool for exploring bacterial genomes.
JO  - Proc. InForum 2013
PY  - 2013
SP  - 5
EP  - 16
VL  - 0
AB  - Genome Inspector (GIN) is a new interactive web-based application for exploring bacterial
AB  - genomes designed to provide users with a wide choice of options to facilitate the process of
AB  - designing DNA primers for isolating genes from similar bacterial species and strains.  GIN
AB  - employs a project-based approach in which users can select any given set of available genomes
AB  - and perform a comprehensive bioinformatics analysis.  Currently, it encompasses the full set
AB  - of annotated bacterial genomes available on GenBank, a total of 4300 files corresponding to
AB  - over 740,000 annotated genes.  GIN allows new data to be added directly from GenBank as it is
AB  - being generated, as well as new genome uploading for personal analysis.  The application
AB  - interfaces were designed with potential users in mind to assist with their most common
AB  - research goals.  Users can visually explore full circular genomes, search for similar regions
AB  - in other species and strains, and visualize amplified genomic regions for several strains
AB  - simultaneously.  This interactive tool allows for dynamic graphical exploration and refinement
AB  - of search and exploration criteria.  Furthermore, it includes a multiple alignment algorithm
AB  - (MUSCLE) to help researchers in the process of designing primers.  GIN is free and publicly
AB  - available at http://gin.ul.pt/GIN2/index.php.
ER  -

TY  - JOUR
AU  - Inoue, K.
AU  - Ogura, Y.
AU  - Kawano, Y.
AU  - Hayashi, T.
TI  - Complete Genome Sequence of Geobacter sulfurreducens Strain YM18, Isolated from River Sediment in Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00352
EP  - e00318
VL  - 6
AB  - Geobacter sulfurreducens is known to be a dominant species in the anode biofilms  of microbial
AB  - fuel cells. Here, we report the complete genome sequence of G.
AB  - sulfurreducens strain YM18. Strain YM18 was isolated from a biofilm formed on an
AB  - anode poised at -400 mV (versus an Ag/AgCl electrode) in a bioelectrochemical
AB  - system.
ER  -

TY  - JOUR
AU  - Inselburg, J.
TI  - Phage P1 modification of bacterial DNA studied by generalized transduction.
JO  - Virology
PY  - 1966
SP  - 257
EP  - 265
VL  - 30
AB  - Mutants of P1 that either fail to cause restriction, r-m, or neither cause
AB  - restriction nor modification, r-m-, were used to study the phage-induced
AB  - modification of the bacterial chromosome of Escherichia coli K12 and the
AB  - effects of modification on P1 generalized transduction.  The findings made were
AB  - that: (1) the bacterial chromosomal markers transduced by P1 are not sensitive
AB  - to restriction whereas the bacterial chromosomal markers transduced by P1 r-m-
AB  - are sensitive to restriction; (2) the sensitivity to restriction differed for
AB  - different markers; (3) all the regions of the bacterial chromosome tested
AB  - appear to be modified; (4) modification can interfere with the transduction of
AB  - certain markers in a way not associated with protection against restriction;
AB  - (5) the modification of bacterial DNA can probably occur without DNA
AB  - replication; (6) the sensitivity of lambda DNA to restriction is much greater
AB  - than that of bacterial DNA when both are transferred by P1 transducing
AB  - particles.  The implications of the results and limitations in interpreting
AB  - them are discussed.
ER  -

TY  - JOUR
AU  - Inturri, R.
AU  - Ventura, M.
AU  - Ruas-Madiedo, P.
AU  - Lugli, G.A.
AU  - Blandino, G.
TI  - Complete Genome Sequence of Bifidobacterium longum W11 (LMG P-21586), Used as a Probiotic Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e01659
EP  - e01616
VL  - 5
AB  - We report the complete genome sequence of Bifidobacterium longum W11 (LMG P-21586) isolated
AB  - from the intestinal microbiota of a healthy man. The analysis
AB  - of the sequence may provide insights into the microbiological characteristics and
AB  - the functional activity of this probiotic strain.
ER  -

TY  - JOUR
AU  - Ioerger, T.R.
AU  - Feng, Y.
AU  - Chen, X.
AU  - Dobos, K.M.
AU  - Victor, T.C.
AU  - Streicher, E.M.
AU  - Warren, R.M.
AU  - Gey-van-Pittius, N.C.
AU  - Van Helden, P.D.
AU  - Sacchettini, J.C.
TI  - The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa.
JO  - BMC Genomics
PY  - 2010
SP  - 670
EP  - 670
VL  - 11
AB  - BACKGROUND: The Beijing genotype of M. tuberculosis is a virulent strain that is
AB  - disseminating worldwide and has a strong association with drug resistance. In the
AB  - Western Cape of South Africa, epidemiological studies have identified the R220
AB  - cluster of the Beijing genotype as a major contributor to a recent outbreak of
AB  - drug-resistant tuberculosis. Although the outbreak is considered to be due to
AB  - clonal transmission, the relationship among drug resistant isolates has not yet
AB  - been established. RESULTS: To better understand the evolution of drug resistance
AB  - among these strains, 14 drug-resistant clinical isolates of the Beijing genotype
AB  - were sequenced by whole-genome sequencing, including eight from R220 and six from
AB  - a more ancestral Beijing cluster, R86, for comparison. While each cluster shares
AB  - a distinct resistance mutation for isoniazid, mapping of other drug-resistance
AB  - mutations onto a phylogenetic tree constructed from single nucleotide
AB  - polymorphisms shows that resistance mutations to many drugs have arisen multiple
AB  - times independently within each cluster of isolates. Thus, drug resistance among
AB  - these isolates appears to be acquired, not clonally derived. This observation
AB  - suggests that, although the Beijing genotype as a whole might have selective
AB  - advantages enabling its rapid dissemination, the XDR isolates are relatively less
AB  - fit and do not propagate well. Although it has been hypothesized that the
AB  - increased frequency of drug resistance in some Beijing lineages might be caused
AB  - by a mutator phenotype, no significant shift in synonymous substitution patterns
AB  - is observed in the genomes. CONCLUSION: While MDR-TB is spreading by transmission
AB  - in the Western Cape, our data suggests that further drug resistance (i.e. XDR-TB)
AB  - at this stage is acquired.
ER  -

TY  - JOUR
AU  - Iordanescu, S.
AU  - Surdeanu, M.
TI  - Two restriction and modification systems in Staphylococcus aureus NCTC8325.
JO  - J. Gen. Microbiol.
PY  - 1976
SP  - 277
EP  - 281
VL  - 96
AB  - The presence of two distinct host specificities in Staphylococcus aureus strain NCTC8325 was
AB  - revealed by the isolation of restriction- and modification-deficient mutants.  The two host
AB  - specificity systems, designated S1 and S2, are both active on phage 80 Mu Alpha but are not
AB  - additive in their restricting activity.  Restriction-deficient, modification-proficient
AB  - mutants were invariably affected in both restriction systems.  The functional relationship
AB  - between these two systems is discussed.
ER  -

TY  - JOUR
AU  - Ip, M.
AU  - Ma, H.
AU  - Li, C.
AU  - Tsui, S.
AU  - Zhou, H.
TI  - Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19F Sequence Type 271 Clinical Isolates with Low- and High-Level Cefotaxime Resistance.
JO  - Genome Announcements
PY  - 2015
SP  - e00605
EP  - e00615
VL  - 3
AB  - We report here the draft genomes of two pneumococcal isolates in Hong Kong, CU_SPNE1_05 and
AB  - CU_SPNE32_06. Strain CU_SPNE1_05 had a cefotaxime MIC of 1
AB  - microg/ml, and CU_SPNE32_06 had an MIC of 32 microg/ml. Both strains belong to
AB  - the multidrug-resistant serogroup 19, sequence type 271 (clonal complex
AB  - 3200/271).
ER  -

TY  - JOUR
AU  - Ip, M.
AU  - Wang, Z.
AU  - Lam, W.Y.
AU  - Zhou, H.
AU  - Tsui, S.
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus CUHK_188 (ST188), a Health Care-Associated Bacteremic Isolate from Hong Kong.
JO  - Genome Announcements
PY  - 2014
SP  - e00255
EP  - e00214
VL  - 2
AB  - We report the draft genome sequence of a methicillin-resistant Staphylococcus aureus strain
AB  - designated CUHK_188, isolated from a bacteremic patient undergoing treatment at a university
AB  - teaching hospital in Hong Kong. This strain belongs to sequence type 188 (ST188), with spa
AB  - type t189 and staphylococcal cassette chromosome mec type V.
ER  -

TY  - JOUR
AU  - Iraola, G.
AU  - Perez, R.
AU  - Naya, H.
AU  - Paolicchi, F.
AU  - Harris, D.
AU  - Lawley, T.D.
AU  - Rego, N.
AU  - Hernandez, M.
AU  - Calleros, L.
AU  - Carretto, L.
AU  - Velilla, A.
AU  - Morsella, C.
AU  - Mendez, A.
AU  - Gioffre, A.
TI  - Complete Genome Sequence of Campylobacter fetus subsp. venerealis Biovar Intermedius, Isolated from the Prepuce of a Bull.
JO  - Genome Announcements
PY  - 2013
SP  - e00526
EP  - e00513
VL  - 1
AB  - Campylobacter fetus subsp. venerealis is the causative agent of bovine genital
AB  - campylobacteriosis, a sexually transmitted disease distributed worldwide. Campylobacter fetus
AB  - subsp. venerealis biovar Intermedius strains differ in their biochemical behavior and are
AB  - prevalent in some countries. We report the first genome sequence for this biovar, isolated
AB  - from bull prepuce.
ER  -

TY  - JOUR
AU  - Iriarte, A.
AU  - Giner-Lamia, J.
AU  - Silva, C.
AU  - Betancor, L.
AU  - Astocondor, L.
AU  - Cestero, J.J.
AU  - Ochoa, T.
AU  - Garcia, C.
AU  - Puente, J.L.
AU  - Chabalgoity, J.A.
AU  - Garcia-Del Portillo, F.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Infantis Strain SPE101, Isolated from a Chronic Human Infection.
JO  - Genome Announcements
PY  - 2017
SP  - e00679
EP  - e00617
VL  - 5
AB  - We report a 4.99-Mb draft genome sequence of Salmonella enterica subsp. enterica  serovar
AB  - Infantis strain SPE101, isolated from feces of a 5-month-old breast-fed
AB  - female showing diarrhea associated with severe dehydration and malnutrition. The
AB  - infection prolonged for 6 months despite antibiotic treatment.
ER  -

TY  - JOUR
AU  - Irisawa, T.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kitahara, M.
AU  - Sakamoto, M.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Lactobacillus sucicola JCM 15457T, a Motile Lactic Acid  Bacterium Isolated from Oak Sap.
JO  - Genome Announcements
PY  - 2014
SP  - e00403
EP  - e00414
VL  - 2
AB  - Here, we report the draft genome sequence of a motile lactic acid bacterium, Lactobacillus
AB  - sucicola JCM 15457(T), isolated from oak sap. Motility-related
AB  - genes and their organization in the annotated genome were broadly similar to
AB  - those in the sequenced genomes of related lactobacilli.
ER  -

TY  - JOUR
AU  - Irlinger, F.
AU  - Loux, V.
AU  - Bento, P.
AU  - Gibrat, J.F.
AU  - Straub, C.
AU  - Bonnarme, P.
AU  - Landaud, S.
AU  - Monnet, C.
TI  - Genome Sequence of Staphylococcus equorum subsp. equorum Mu2, Isolated from a French Smear-Ripened Cheese.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5141
EP  - 5142
VL  - 194
AB  - Staphylococcus equorum subsp. equorum is a member of the coagulase-negative staphylococcus
AB  - group and is frequently isolated from fermented food products and
AB  - from food-processing environments. It contributes to the formation of aroma
AB  - compounds during the ripening of fermented foods, especially cheeses and
AB  - sausages. Here, we report the draft genome sequence of Staphylococcus equorum
AB  - subsp. equorum Mu2 to provide insights into its physiology and compare it with
AB  - other Staphylococcus species.
ER  -

TY  - JOUR
AU  - Irma-Syakina, M.Z.
AU  - Teh, L.K.
AU  - Salleh, M.Z.
TI  - Draft Genome Sequence of Streptococcus agalactiae PR06.
JO  - Genome Announcements
PY  - 2013
SP  - e00351
EP  - e00313
VL  - 1
AB  - Streptococcus agalactiae (group B streptococcus [GBS]) is a Gram-positive bacterium that was
AB  - first recognized as a causative agent of bovine mastitis. S. agalactiae has subsequently
AB  - emerged as a significant cause of human diseases. Here, we report the draft genome sequence of
AB  - S. agalactiae PR06, which was isolated from a septicemic patient in a local hospital in
AB  - Malaysia.
ER  -

TY  - JOUR
AU  - Irschik, H.
AU  - Kopp, M.
AU  - Weissman, K.J.
AU  - Buntin, K.
AU  - Piel, J.
AU  - Muller, R.
TI  - Analysis of the sorangicin gene cluster reinforces the utility of a combined phylogenetic/retrobiosynthetic analysis for deciphering natural product assembly by trans-AT PKS.
JO  - Chembiochem
PY  - 2010
SP  - 1840
EP  - 1849
VL  - 11
AB  - The sorangicins are a group of polyketide antibiotics produced by several strains of the
AB  - myxobacterium Sorangium cellulosum, whose activity is derived from inhibition of eubacterial
AB  - RNA polymerase.  The core structure of sorangicins A and B, the metabolites of highest
AB  - abundance, comprises a 31-membered lactone that exhibits many unusual features, including a
AB  - tetra-substituted terahydropyran, a trisubstituted dihydropyran, and a signature C31-C36
AB  - bicyclic ether moiety; sorangicin B lacks a hydroxyl group at C22 relative to sorangicin A.
AB  - The sorangicins are the most potent myxobacterial antibiotics identified to date, exhibiting
AB  - activity against both Gram-positive and Gram-negative species.  The corresponding glycosides
AB  - are only poorly active, however, suggesting that this modification might serve to protect S.
AB  - cellulosum from its own antibiotics.
ER  -

TY  - JOUR
AU  - Isakovic, L.
AU  - Saavedra, O.M.
AU  - Llewellyn, D.B.
AU  - Claridge, S.
AU  - Zhan, L.J.
AU  - Bernstein, N.
AU  - Vaisburg, A.
AU  - Elowe, N.
AU  - Petschner, A.J.
AU  - Rahil, J.
AU  - Beaulieu, N.
AU  - Gauthier, F.
AU  - MacLeod, A.R.
AU  - Delorme, D.
AU  - Besterman, J.M.
AU  - Wahhab, A.
TI  - Constrained (L-)-S-adenosyl-L-homocysteine (SAH) analogues as DNA methyltransferase inhibitors.
JO  - Bioorg. Med. Chem. Lett.
PY  - 2009
SP  - 2742
EP  - 2746
VL  - 19
AB  - Potent SAH analogues with constrained homocysteine units have been designed and synthesized as
AB  - inhibitors of human DNMT enzymes. The five
AB  - membered (2S,4S)-4-mercaptopyrrolidine-2-carboxylic acid, in 1a, was a
AB  - good replacement for homocysteine, while the corresponding six-member
AB  - counterpart was less active. Further optimization of 1a, changed the
AB  - selectivity pro. le of these inhibitors. A Chloro substituent at the
AB  - 2-position of 1a, compound 1d, retained potency against DNMT1, while
AB  - N-6 alkylation, compound 7a, conserved DNMT3b2 activity. The
AB  - concomitant substitutions of 1a at both 2- and N-6 positions reduced
AB  - activity against both enzymes.
ER  -

TY  - JOUR
AU  - Isalan, M.
AU  - Choo, Y.
TI  - Engineered Zinc Finger Proteins that Respond to DNA Modification by HaeIII and HhaI Methyltransferase Enzymes.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 471
EP  - 477
VL  - 295
AB  - Zinc finger modules are capable of specifically interacting with DNA that contains
AB  - 5-methylcytosine (5-mC) in place of cytosine, suggesting that zinc finger-DNA binding could be
AB  - regulated by extrinsic methylation of DNA. Here, we have used phage display to engineer zinc
AB  - finger proteins that detect and discriminate DNA methylation by the prokaryotic enzymes HaeIII
AB  - and HhaI. In these systems, zinc finger-DNA complexes are induced by DNA modification using
AB  - the appropriate enzyme, which can therefore act as a switch. To further develop the
AB  - specificity of the switch, zinc finger discrimination between 5-mC and thymine in DNA
AB  - sequences is demonstrated despite the presence of the characteristic major groove methyl group
AB  - that is common to both bases. Specificity was achieved using a DNA-binding strategy involving
AB  - synergy between adjacent zinc fingers. We propose that engineered zinc fingers that recognise
AB  - particular DNA modifications, such as sequence-specific DNA methylation, could be integrated
AB  - into artificial regulatory circuits for the control of gene expression and other biological
AB  - processes.
ER  -

TY  - JOUR
AU  - Isanapong, J. et al.
TI  - High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2744
EP  - 2745
VL  - 194
AB  - Microbial communities in the termite hindgut are essential for degrading plant material. We
AB  - present the high-quality draft genome sequence of the Opitutaceae
AB  - bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be
AB  - isolated from wood-feeding termites. The genomic analysis reveals genes coding
AB  - for lignocellulosic degradation and nitrogen fixation.
ER  -

TY  - JOUR
AU  - Ishaq, M.
AU  - Kaji, A.
TI  - Mechanism of T4 phage restriction by plasmid Rts 1. Cleavage of T4 phage DNA by Rts 1-specific enzyme.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 4040
EP  - 4047
VL  - 255
AB  - Rts 1 is a plasmid which confers upon host bacteria the capacity to restrict T4 phage growth
AB  - at 32oC but not at 42oC. This restriction was not dependent on cellular adenyl cyclase, while
AB  - other phenotypes of Rts 1, such as the temperature-sensitive effect on host growth, were
AB  - dependent on this enzyme. At 32"C, in Escherichia coli 2OSO/Rts 1 cells, 55 to 60% of the
AB  - parental T4 phage DNA became acid-soluble within 5 to 10 min after infection,
AB  - while in E. coli JC7623/Rts 1 cells, which lack exonuclease I and V, very little T4 DNA became
AB  - acidsoluble.  The capacity of E. coli 2OSO/Rts 1 to degrade infecting T, DNA decreased 70%
AB  - within 15 min after shifting the temperature to 42oC. Temperature shift up and down
AB  - experiments in the presence of chloramphenicol showed that the protein responsible for T, DNA
AB  - cleavage is thermosensitive, and once it is denatured it cannot regain its activity by
AB  - lowering the temperature to 32oC in vivo. Alkaline sucrose gradient centrifugation revealed
AB  - that the infecting Tq DNA was nicked in the presence of Rts 1 at 32"C, but not at 42oC in E.
AB  - coli JC7623. The cell-free extract of E. coli JC7623/Rts 1 grown at 32oC contained an enzyme
AB  - which converted Tq DNA to smaller but acid-insoluble fragments. This enzyme could not be
AB  - detected in E. coli JC7623o r E. coli JC7623/Rts 1 grown at 42oC. The enzyme was rapidly
AB  - inactivated when incubated at 42oC in vitro. Analysis of the reaction product by gel
AB  - electrophoresis and alkaline and sodium dodecyl sulfate-neutral sucrose density gradient
AB  - centrifugation, showed marked heterogeneity of the in vitro reaction product. This enzyme did
AB  - not cleave either T7 DNA or nonglucosylated T4 DNA under the same experimental conditions.
AB  - Only M$+ was required for its activity. These experiments suggest that the plasmid Rts 1 codes
AB  - for a thermosensitive enzyme which specifically degrades glucosylated T, DNA, resulting in the
AB  - restriction of T, phage growth at 32oC but not at 42oC. This enzyme, named Rts 1 endonuclease,
AB  - was purified approximately 500-fold.
ER  -

TY  - JOUR
AU  - Ishida, C.
AU  - Ura, K.
AU  - Hirao, A.
AU  - Sasaki, H.
AU  - Toyoda, A.
AU  - Sakaki, Y.
AU  - Niwa, H.
AU  - Li, E.
AU  - Kaneda, Y.
TI  - Genomic organization and promoter analysis of the Dnmt3b gene.
JO  - Gene
PY  - 2003
SP  - 151
EP  - 159
VL  - 310
AB  - The Dnmt3b gene encodes a de novo DNA methyltransferase that is essential for normal mouse
AB  - development. It is highly expressed in early embryos and
AB  - embryonic stem (ES) cells but downregulated in most adult somatic tissues.
AB  - To gain insight into the regulation of Dnmt3b, we have isolated a mouse
AB  - genomic bacterial artificial chromosome clone that contains the Dnmt3b
AB  - gene. Complete sequence analysis of the clone demonstrated that Dnmt3b
AB  - consists of at least 24 exons and spans 38 kilobases. S1 nuclease analysis
AB  - identified two adjacent transcriptional start sites located downstream of
AB  - a unique TATA-like element in a CpG island. There was an unknown gene
AB  - which we named mU(3) 17 kb upstream of the Dnmt3b locus, and it was
AB  - transcribed ubiquitously and in the opposite direction of Dnmt3b.
AB  - Transfection analysis revealed that the minimal promoter region containing
AB  - an Sp1 site was active even in somatic cells, and that there were several
AB  - repressor elements within 7.9 kb upstream of Dnmt3b downregulated this
AB  - gene specifically in somatic cells but not in ES cells. These findings
AB  - provide a basis for future detailed studies of the mechanisms controlling
AB  - Dnmt3b expression.
ER  -

TY  - JOUR
AU  - Ishii, S.
AU  - Amarasiri, M.
AU  - Hashiba, S.
AU  - Yang, P.
AU  - Okabe, S.
AU  - Sano, D.
TI  - Genome Sequence of Enterobacter cloacae Strain SENG-6, a Bacterium Producing Histo-Blood Group Antigen-Like Substances That Can Bind with Human Noroviruses.
JO  - Genome Announcements
PY  - 2016
SP  - e00893
EP  - e00816
VL  - 4
AB  - Enterobacter sp. strain SENG-6, isolated from healthy human feces, produces histo-blood group
AB  - antigen (HBGA)-like substances that can bind with human
AB  - noroviruses. Based on the genome sequence analysis, strain SENG-6 belongs to the
AB  - species Enterobacter cloacae The genome sequence of this strain should help
AB  - identify genes associated with the production of HBGA-like substances.
ER  -

TY  - JOUR
AU  - Ishii, S.
AU  - Tago, K.
AU  - Nishizawa, T.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Senoo, K.
TI  - Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Pseudogulbenkiania sp. Strain NH8B.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6395
EP  - 6396
VL  - 193
AB  - Pseudogulbenkiania sp. strain NH8B is a Neisseriales bacterium isolated from an agricultural
AB  - field. This strain has strong denitrification and
AB  - N(2)O reduction activities. Here, we report the finished and annotated
AB  - genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Ishikawa, J.
AU  - Yamashita, A.
AU  - Mikami, Y.
AU  - Hoshino, Y.
AU  - Kurita, H.
AU  - Hotta, K.
AU  - Shiba, T.
AU  - Hattori, M.
TI  - The complete genomic sequence of Nocardia farcinica IFM 10152.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 14925
EP  - 14930
VL  - 101
AB  - We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and
AB  - revealed the molecular basis of its versatility.  The genome consists of a single circular
AB  - chromosome of 6,021,225 bp with an average G+C content of 70.8% and two plasmids of 184,027
AB  - (pNF1) and 87,093 (pNF2) bp with average G+C contents of 67.2% and 68.4%, respectively.  The
AB  - chromosome encoded 5,674, putative protein-coding sequences, including many candidate genes
AB  - for virulence and multidrug resistance as well as secondary metabolism.  Analyses of
AB  - paralogous protein families suggest that gene duplications have resulted in a bacterium that
AB  - can survive not only in soil environments but also in animal tissues, resulting in disease.
ER  -

TY  - JOUR
AU  - Ishikawa, K.
AU  - Fukuda, E.
AU  - Kobayashi, I.
TI  - Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems.
JO  - DNA Res.
PY  - 2010
SP  - 325
EP  - 342
VL  - 17
AB  - Epigenetic modification of genomic DNA by methylation is important for defining the epigenome
AB  - and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA
AB  - methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction
AB  - enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the
AB  - partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA
AB  - methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within
AB  - the genome. Although restriction enzymes were originally discovered for their ability to
AB  - attack invading DNAs, it may be understood because such DNAs show deviation from this
AB  - epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked
AB  - with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia
AB  - coli, which was discovered because of its methyl-specific restriction. McrBC responds to
AB  - specific genome methylation systems by killing the host bacterial cell through chromosome
AB  - cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and
AB  - wide distribution in prokaryotes similar to restriction-modification systems. These findings
AB  - support the hypothesis that this family of methyl-specific DNases evolved as mobile elements
AB  - competing with specific genome methylation systems through host killing. These restriction
AB  - systems clearly demonstrate the presence of conflicts between epigenetic systems.
ER  -

TY  - JOUR
AU  - Ishikawa, K.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Cleavage of a model DNA replication fork by a Type I restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3531
EP  - 3544
VL  - 37
AB  - Cleavage of a DNA replication fork leads to fork restoration by recombination repair. In
AB  - prokaryote cells carrying
AB  - restriction-modification systems, fork passage reduces genome methylation
AB  - by the modification enzyme and exposes the chromosome to attack by the
AB  - restriction enzyme. Various observations have suggested a relationship
AB  - between the fork and Type I restriction enzymes, which cleave DNA at a
AB  - distance from a recognition sequence. Here, we demonstrate that a Type I
AB  - restriction enzyme preparation cleaves a model replication fork at its
AB  - branch. The enzyme probably tracks along the DNA from an unmethylated
AB  - recognition site on the daughter DNA and cuts the fork upon encountering
AB  - the branch point. Our finding suggests that these restriction-modification
AB  - systems contribute to genome maintenance through cell death and indicates
AB  - that DNA replication fork cleavage represents a critical point in genome
AB  - maintenance to choose between the restoration pathway and the destruction
AB  - pathway.
ER  -

TY  - JOUR
AU  - Ishikawa, K.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Coupling of DNA replication and restriction: A type I restriction enzyme cleaves branched DNAs mimicing replication forks, in vitro.
JO  - Genes Genet. Syst.
PY  - 2008
SP  - 510
EP  - 510
VL  - 83
AB  - Coupling of DNA replication and restriction: A type I restriction enzyme cleaves branched DNAs
AB  - mimicing replication forks, in vitro.  DNA cleavage by a restriction enzyme is prevented by
AB  - methylation on the recognition sequence.  It has been imagined that DNA replication and
AB  - restriction cleavage are coupled because unmethylated site will appear through replication
AB  - fork passage.  In fact, we previously observed an example suggesting such a coupling between
AB  - phage DNA replication and restriction, in vivo.  In the present study, we show that a purified
AB  - type I restriction endonuclease cleaves DNAs with long branch mimicking replication forks, in
AB  - the vicinity of the branch point dependent on an unmethylated recognition sequence.
AB  - Relationship between type I restriction enzymnes and other enzymes known that they cleave
AB  - branched DNA will be discussed.
ER  -

TY  - JOUR
AU  - Ishikawa, K.
AU  - Handa, N.
AU  - Sears, L.
AU  - Raleigh, E.A.
AU  - Kobayashi, I.
TI  - Cleavage of a model DNA replication fork by a methyl-specific endonuclease.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 5489
EP  - 5498
VL  - 39
AB  - Epigenetic DNA methylation is involved in many biological processes. An epigenetic status can
AB  - be altered by gain or loss of a DNA methyltransferase gene or its activity. Repair of DNA
AB  - damage can also remove DNA methylation. In response to such alterations, DNA endonucleases
AB  - that sense DNA methylation can act and may cause cell death. Here, we explored the possibility
AB  - that McrBC, a methylation-dependent DNase of Escherichia coli, cleaves DNA at a replication
AB  - fork. First, we found that in vivo restriction by McrBC of bacteriophage carrying a foreign
AB  - DNA methyltransferase gene is increased in the absence of homologous recombination. This
AB  - suggests that some cleavage events are repaired by recombination and must take place during or
AB  - after replication. Next, we demonstrated that the enzyme can cleave a model DNA replication
AB  - fork in vitro. Cleavage of a fork required methylation on both arms and removed one, the other
AB  - or both of the arms. Most cleavage events removed the methylated sites from the fork. This
AB  - result suggests that acquisition of even rarely occurring modification patterns will be
AB  - recognized and rejected efficiently by modification-dependent restriction systems that
AB  - recognize two sites. This process might serve to maintain an epigenetic status along the
AB  - genome through programmed cell death.
ER  -

TY  - JOUR
AU  - Ishikawa, K.
AU  - Watanabe, M.
AU  - Kuroita, T.
AU  - Uchiyama, I.
AU  - Bujnicki, J.
AU  - Kawakami, B.
AU  - Tanokura, M.
AU  - Kobayashi, I.
TI  - Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.
JO  - Genes Genet. Syst.
PY  - 2005
SP  - 454
EP  - 454
VL  - 80
AB  - To search for restriction endonucleasees, we used a novel plant-based cell-free translation
AB  - procedure that bypasses the toxicity of these enzymes. To identify candidate genes, the
AB  - related genomes of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii
AB  - were compared. In line with the selfish mobile gene hypothesis for restriction-modification
AB  - systems, apparent genome rearrangement around putative restriction genes serve as a selecting
AB  - criterion.  Several candidate restriction genes were identified and expressed with a wheat
AB  - germ-based cell-free protein synthesis system.  The resulting solution could be directly
AB  - assayed for restriction activity.  We identified two deoxyribonucleases.  The novel enzymes
AB  - was denoted as PabI, purified and found to recognize 5'GTAC and leave a 3TA overhang
AB  - (5'GTA/C), a novel restriction enzyme-generated terminus.  PabI is active up to 90oC and
AB  - optimally active at a pH of around 6 and in NaCl concentrations ranging from 100 to 200 mM.
AB  - We predict that it has a novel three-dimensional structure.
ER  -

TY  - JOUR
AU  - Ishikawa, K.
AU  - Watanabe, M.
AU  - Kuroita, T.
AU  - Uchiyama, I.
AU  - Bujnicki, J.M.
AU  - Kawakami, B.
AU  - Tanokura, M.
AU  - Kobayashi, I.
TI  - Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI   (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - e112
EP  - e112
VL  - 33
AB  - To search for restriction endonucleases, we used a novel plant-based cell-free translation
AB  - procedure that bypasses the toxicity of these
AB  - enzymes. To identify candidate genes, the related genomes of the
AB  - hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii were
AB  - compared. In line with the selfish mobile gene hypothesis for
AB  - restriction-modification systems, apparent genome rearrangement around
AB  - putative restriction genes served as a selecting criterion. Several
AB  - candidate restriction genes were identified and then amplified in such a
AB  - way that they were removed from their own translation signal. During their
AB  - cloning into a plasmid, the genes became connected with a plant
AB  - translation signal. After in vitro transcription by T7 RNA polymerase, the
AB  - mRNAs were separated from the template DNA and translated in a
AB  - wheat-germ-based cell-free protein synthesis system. The resulting
AB  - solution could be directly assayed for restriction activity. We identified
AB  - two deoxyribonucleases. The novel enzyme was denoted as PabI, purified and
AB  - found to recognize 5'-GTAC and leave a 3'-TA overhang (5'-GTA/C), a novel
AB  - restriction enzyme-generated terminus. PabI is active up to 90 degrees C
AB  - and optimally active at a pH of around 6 and in NaCl concentrations
AB  - ranging from 100 to 200 mM. We predict that it has a novel 3D structure.
ER  -

TY  - JOUR
AU  - Ishikawa, T.
AU  - Yamada, Y.
TI  - Purification of restriction endonuclease from Acetobacter pasteurianus IFO 13752 (ApaORI) and its properties.
JO  - J. Gen. Appl. Microbiol.
PY  - 1990
SP  - 127
EP  - 135
VL  - 36
AB  - A restriction endonuclease, designated ApaORI, was purified from cell-free
AB  - extracts of A. pasteurianus IFO 13752 by streptomycin treatment, ammonium
AB  - sulfate fractionation, phosphocellulose treatment, hydroxylapatite and
AB  - heparin-Sepharose CL-6B column chromatography, and gel filtration using a
AB  - Superose 12 (HR10/30) column.  The purified enzyme was homogeneous on
AB  - polyacrylamide gel disc electrophoresis.  The molecular weight of the purified
AB  - enzyme was found by gel filtration to be 21,000 daltons.  The isoelectric point
AB  - of the purified enzyme was neutral.  The purified enzyme cleaved lambda,
AB  - PhiX174 RF I, M13mp7 RF I, and pBR322 DNAs at 18 or more, 2, 4 or more, and 4
AB  - or more sites respectively.  The purified enzyme worked best at 37C and pH 7.5
AB  - in a reaction mixture (50 micro liters) containing 1.0 microgram lambda DNA, 10
AB  - mM Tris-HCl, 7 mM 2-mercaptoethanol, 7 mM MgCl2, and 50 mM NaCl.  However, the
AB  - purified enzyme did not require NaCl for its reaction.  The purified enzyme
AB  - recognizes the palindromic pentanucleotides 5'-CC (A or T)GG-3' and cuts
AB  - between C and A (orT), producing 5'-cohesive mononucleotide extensions
AB  - (isoschizomer of BstNI).
ER  -

TY  - JOUR
AU  - Ishino, Y.
AU  - Nomura, Y.
AU  - Kato, I.
TI  - Sse8647I, a new type II restriction endonuclease from a Streptomyces species cutting at 5'-AG/GWCCT-3'.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 742
EP  - 744
VL  - 23
AB  - We isolated and characterized a new type II restriction endonuclease which recognizes the
AB  - palindromic heptanucleotide sequence 5'-AGGWCCT-3' and cleaves double-stranded DNA after the
AB  - first G in the sequence from a microorganism belonging to Streptomyces species. This enzyme
AB  - cleaves adenovirus 2 DNA at eight sites, but does not cleave lambda phage, pBR322, pUC18 and
AB  - 19, M13mp18 and 19, SV40, ColE1 and omega-X174 DNAs.
ER  -

TY  - JOUR
AU  - Ishiwata, N.
AU  - Tanimura, A.
AU  - Miyahara, M.
AU  - Mise, K.
TI  - Studies on restriction endonucleases of bacteria causing peroral infectious diseases.  I. Characterization of Hsd plasmid in Salmonella typhi.
JO  - Shokuhin Eiseigaku Zasshi
PY  - 1995
SP  - 404
EP  - 408
VL  - 36
AB  - An Hsd (host specificity for DNA) plasmid designated pSTd4 was found in Salmonella Typhi D4,
AB  - one of the standard phage typing strains.  The plasmid was introduced into E. coli K-12, and
AB  - the restriction map of this plasmid was constructed.  The efficiency of plating of lambda-O
AB  - phage was drastically reduced with pSTd4 as well as other small Hsd plasmids of
AB  - Enterobacteriaceae origin.  The results clearly indicate that pSTd4 is a type-determining
AB  - plasmid in S. Typhi D4.  We propose that rare phage types such as D4 carrying type-determining
AB  - plasmids or lysogenic phages should be eliminated from the collection of standard phage
AB  - typing strains of S. Typhi.
ER  -

TY  - JOUR
AU  - Ishiyama, S. et al.
TI  - Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance.
JO  - Mol. Cell
PY  - 2017
SP  - 350
EP  - 360.e7
VL  - 68
AB  - The proper location and timing of Dnmt1 activation are essential for DNA methylation
AB  - maintenance. We demonstrate here that Dnmt1 utilizes
AB  - two-mono-ubiquitylated histone H3 as a unique ubiquitin mark for its recruitment
AB  - to and activation at DNA methylation sites. The crystal structure of the
AB  - replication foci targeting sequence (RFTS) of Dnmt1 in complex with H3-K18Ub/23Ub
AB  - reveals striking differences to the known ubiquitin-recognition structures. The
AB  - two ubiquitins are simultaneously bound to the RFTS with a combination of
AB  - canonical hydrophobic and atypical hydrophilic interactions. The C-lobe of RFTS,
AB  - together with the K23Ub surface, also recognizes the N-terminal tail of H3. The
AB  - binding of H3-K18Ub/23Ub results in spatial rearrangement of two lobes in the
AB  - RFTS, suggesting the opening of its active site. Actually, incubation of Dnmt1
AB  - with H3-K18Ub/23Ub increases its catalytic activity in vitro. Our results
AB  - therefore shed light on the essential role of a unique ubiquitin-binding module
AB  - in DNA methylation maintenance.
ER  -

TY  - JOUR
AU  - Ishizawa, H.
AU  - Kuroda, M.
AU  - Ike, M.
TI  - Draft Genome Sequence of Aquitalea magnusonii Strain H3, a Plant Growth-Promoting Bacterium of Duckweed (Lemna minor).
JO  - Genome Announcements
PY  - 2017
SP  - e00812
EP  - e00817
VL  - 5
AB  - Aquitalea magnusonii strain H3 is a promising plant growth-promoting bacterium for duckweed.
AB  - Here, we report the draft genome sequence of strain H3 comprising
AB  - 4,750,601 bp in 73 contigs. Several genes associated with plant root colonization
AB  - were identified.
ER  -

TY  - JOUR
AU  - Ishizawa, H.
AU  - Kuroda, M.
AU  - Morikawa, M.
AU  - Ike, M.
TI  - Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor.
JO  - Biotechnol. Biofuels.
PY  - 2017
SP  - 0
EP  - 0
VL  - 10
ER  -

TY  - JOUR
AU  - Iskander, M.
AU  - Hayden, K.
AU  - Van Domselaar, G.
AU  - Tsang, R.
TI  - First Complete Genome Sequence of Haemophilus influenzae Serotype a.
JO  - Genome Announcements
PY  - 2017
SP  - e01506
EP  - e01516
VL  - 5
AB  - Haemophilus influenzae is an important human pathogen that primarily infects small children.
AB  - In recent years, H. influenzae serotype a has emerged as a
AB  - significant cause of invasive disease among indigenous populations. Here, we
AB  - present the first complete whole-genome sequence of H. influenzae serotype a.
ER  -

TY  - JOUR
AU  - Ismail, A.
AU  - Teh, L.K.
AU  - Ngeow, Y.F.
AU  - Norazmi, M.N.
AU  - Zainul, Z.F.
AU  - Tang, T.H.
AU  - Najimudin, N.
AU  - Salleh, M.Z.
TI  - Draft Genome Sequence of a Clinical Isolate of Mycobacterium tuberculosis Strain  PR05.
JO  - Genome Announcements
PY  - 2013
SP  - e00397
EP  - e00313
VL  - 1
AB  - We report the annotated genome sequence of a clinical isolate, Mycobacterium tuberculosis
AB  - strain PR05, which was isolated from the human cerebrospinal fluid
AB  - of a patient diagnosed with tuberculosis.
ER  -

TY  - JOUR
AU  - Isojarvi, J.
AU  - Shunmugam, S.
AU  - Sivonen, K.
AU  - Allahverdiyeva, Y.
AU  - Aro, E.M.
AU  - Battchikova, N.
TI  - Draft genome sequence of calothrix strain 336/3, a novel h2-producing cyanobacterium isolated from a finnish lake.
JO  - Genome Announcements
PY  - 2015
SP  - e01474
EP  - e01414
VL  - 3
AB  - We announce the draft genome sequence of Calothrix strain 336/3, an N2-fixing heterocystous
AB  - filamentous cyanobacterium isolated from a natural habitat.
AB  - Calothrix 336/3 produces higher levels of hydrogen than Nostoc punctiforme PCC
AB  - 73102 and Anabaena strain PCC 7120 and, therefore, is of interest for potential
AB  - technological applications.
ER  -

TY  - JOUR
AU  - Isokpehi, R.D.
AU  - Coker, A.O.
TI  - Possible stepwise evolution of type II restriction-modification genes in Helicobacter pylori genome.
JO  - Int. J. Med. Microbiol.
PY  - 2001
SP  - 94
EP  - 94
VL  - 291S
AB  - Helicobacter pylori is a gram-negative bacteria associated with peptic ulcer disease.  The
AB  - complete genome sequences of strains 26695 and J99 of the organism have been published and
AB  - compared.  Analyses of these genomes have identified a high number of genes with homology to
AB  - restriction and modification enzymes, many of which are strain specific and may have been
AB  - acquired by horizontal gene transfer.  Restriction-Modification (R-M) genes are widely
AB  - distributed in bacteria and function in defense against invasion by foreign DNA.  Recent
AB  - evidence also suggests their involvement in genomic rearrangement and evolution.  In H.
AB  - pylori, the modification genes may also regulate gene expression.  Variation in base
AB  - composition of genes can provide evidence of the order of introduction of genes into a genome.
AB  - Thus, in order to gain insight into the evolution of R-M genes in H. pylori genome, this study
AB  - examined guanine and cytosine (G+C) content of the type II restriction genes (5 in 26695, 4 in
AB  - J99) and modification genes (17 in 26695, 20 in J99).  In both strains, 4 pairs of R-M genes
AB  - exist, two of which are unique to each strain.  All the type II R-M genes were retrieved from
AB  - their respective databases and compositional features of the codon position were determined
AB  - using a computer program CODONTREE.  In all the paired R-M genes, the overall G+C content of
AB  - the modification gene is greater than its associated restriction gene, suggesting a possible
AB  - stepwise evolutionary process.  Further studies such as time of introgression and amelioration
AB  - of R-M genes in the genome could confirm their stepwise evolution.
ER  -

TY  - JOUR
AU  - Isokpehi, R.D.
AU  - Coker, A.O.
TI  - In silico evidence for horizontal gene transfer of type II restriction-modification genes in Helicobacter pylori.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A185
EP  - A185
VL  - 28
AB  - Helicobacter pylori is a gram-negative bacteria associated with peptic ulcer disease and a
AB  - risk factor for gastric cancer.  The organism is the first for which the complete genome
AB  - sequences of two unrelated strains, 26695 and J99, has been published.  Analyses of these
AB  - genomes have identified a high number of genes with homology to restriction and modification
AB  - enzymes, many of which are strain specific.  Restriction-modification genes are widely
AB  - distributed in bacteria and function in defense against invasion by foreign DNA.  Recent
AB  - evidence also suggests their involvement in genomic rearrangement and evolution.  In order to
AB  - gain insight into the role of R-M genes in H. pylori evolution, this study examined G+C
AB  - content and codon bias of type II R-M genes in J99.  This strain consists of 4 paired type II
AB  - R-M systems as well as 1 unpaired restriction enzyme and 15 unpaired modification enzymes.
AB  - Compositional features of the codon positions for all 24 genes were determined with the
AB  - program CODONTREE.  Overall G+C content in paired genes is higher for modification genes than
AB  - restriction genes, suggesting a possible stepwise evolutionary process.  Three restriction and
AB  - 2 modification genes significantly deviate (P<0.05) in G+C content relative to the mean G+C
AB  - content of the H. pylori genome.  Lastly, a distance matrix based on codon usage in paired R-M
AB  - system genes was generated to test the hypothesis that a restriction gene is more closely
AB  - related to its associated modification gene than to the modification genes of other paired R-M
AB  - systems.  A UPGMA distance tree generated by the program NEIGHBOUR supports this hypothesis.
AB  - These results provide in silico evidence that type II R-M genes in H. pylori J99, may have
AB  - been acquired through horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Issa, R.
AU  - Seradja, V.H.
AU  - Abdullah, M.K.
TI  - Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTB221/11 Isolated from a Cerebrospinal Fluid Sample in Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00376
EP  - e00316
VL  - 4
AB  - Here, we report of the annotated genome sequence of Mycobacterium tuberculosis MTB221/11. The
AB  - organism was isolated from the cerebrospinal fluid of a patient in Malaysia.
ER  -

TY  - JOUR
AU  - Issa, R.
AU  - Seradja, V.H.
AU  - Abdullah, M.K.
AU  - Abdul, H.
TI  - Annotated Sequence of Mycobacterium tuberculosis MTBR3/09 Isolated from a Sputum  Sample in Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00517
EP  - e00516
VL  - 4
AB  - This is a report of the annotated genome sequence of Mycobacterium tuberculosis MTBR3/09. The
AB  - organism was isolated from a sputum sample in Malaysia.
ER  -

TY  - JOUR
AU  - Issa, R.
AU  - Seradja, V.H.
AU  - Abdullah, M.K.
AU  - Abdul, H.
TI  - Annotated Whole-Genome Shotgun Sequence of Mycobacterium tuberculosis MTBR2/09 Isolated from a Sputum Sample in Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00515
EP  - e00516
VL  - 4
AB  - Mycobacterium tuberculosis MTBR2/09 was isolated from a sputum sample from a male patient in
AB  - Malaysia. This is a report of an annotated genome sequence of M.
AB  - tuberculosis MTBR2/09.
ER  -

TY  - JOUR
AU  - Issa, R.
AU  - Seradja, V.H.
AU  - Abdullah, M.K.
AU  - Abdul, H.
TI  - Whole-Genome Shotgun Sequencing and Annotation of Mycobacterium tuberculosis MTBR1/09 Isolated from a Sputum Sample in Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00513
EP  - e00516
VL  - 4
AB  - This is a report of an annotated genome sequence of Mycobacterium tuberculosis MTBR1/09. The
AB  - organism was isolated from a sputum sample from a male patient in
AB  - Malaysia.
ER  -

TY  - JOUR
AU  - Issotta, F.
AU  - Galleguillos, P.A.
AU  - Moya-Beltran, A.
AU  - Davis-Belmar, C.S.
AU  - Rautenbach, G.
AU  - Covarrubias, P.C.
AU  - Acosta, M.
AU  - Ossandon, F.J.
AU  - Contador, Y.
AU  - Holmes, D.S.
AU  - Marin-Eliantonio, S.
AU  - Quatrini, R.
AU  - Demergasso, C.
TI  - Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from  industrial bioleaching operations in northern Chile.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 19
EP  - 19
VL  - 11
AB  - Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped
AB  - bacterium, isolated from an industrial bioleaching operation in
AB  - northern Chile, where chalcocite is the major copper mineral and copper
AB  - hydroxychloride atacamite is present in variable proportions in the ore. This
AB  - strain has unique features as compared to the other members of the species,
AB  - namely resistance to elevated concentrations of chloride, sulfate and metals.
AB  - Basic microbiological features and genomic properties of this biotechnologically
AB  - relevant strain are described in this work. The 2,475,669 bp draft genome is
AB  - arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834
AB  - protein coding genes were predicted from its annotation; 55 % of these were
AB  - assigned a putative function. Release of the genome sequence of this strain will
AB  - provide further understanding of the mechanisms used by acidophilic bacteria to
AB  - endure high osmotic stress and high chloride levels and of the role of
AB  - chloride-tolerant iron-oxidizers in industrial bioleaching operations.
ER  -

TY  - JOUR
AU  - Ito, H.
AU  - Sadaoka, A.
AU  - Kotani, H.
AU  - Hiraoka, N.
AU  - Nakamura, T.
TI  - Cloning, nucleotide sequence, and expression of the HincII restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3903
EP  - 3911
VL  - 18
AB  - Two genes, coding for the HincII from Haemophilus influenzae Rc
AB  - restriction-modification system, were cloned and expressed in Escherichia coli
AB  - RR1.  Their DNA sequences were determined.  The HincII methylase (M.HincII)
AB  - gene was 1,506 base pairs (bp) long, corresponding to a protein of 502 amino
AB  - acid residues (Mr=55,330).  The HincII endonuclease (R.HincII) gene was 774 bp
AB  - long, corresponding to a protein of 258 amino acid residues (Mr=28,490).  The
AB  - amino acid residues predicted from the R.HincII and the N-terminal amino acid
AB  - sequence of the enzyme found by analysis were identical.  These methylase and
AB  - endonuclease genes overlapped by 1 bp on the H. influenzae Rc chromosomal DNA.
AB  - The clone, named E. coli RR1-Hinc, overproduced R.HincII.  The R.HincII
AB  - activity of this clone was 1,000-fold that from H. influenzae Rc.  The amino
AB  - acid sequence of M.HincII was compared with the sequences of four other
AB  - adenine-specific type II methylases.  Important homology was found between the
AB  - M.HincII and these other methylases.
ER  -

TY  - JOUR
AU  - Ito, H.
AU  - Shimato, H.
AU  - Sadaoka, A.
AU  - Kotani, H.
AU  - Kimizuka, F.
AU  - Kato, I.
TI  - Cloning and expression of the HpaI restriction-modification genes.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 705
EP  - 709
VL  - 20
AB  - The genes from Haemophilus parainfluenzae encoding the HpaI
AB  - restriction-modification system were cloned and expressed in Escherichia coli.
AB  - From the DNA sequence, we predicted the HpaI endonuclease (R.HpaI) to have 254
AB  - amino acid residues (Mr 29,630) and the HpaI methyltransferase (M.HpaI) to have
AB  - 314 amino acid residues (37,390).  The R.HpaI and M.HpaI genes overlapped by 16
AB  - base pairs on the chromosomal DNA.  The genes had the same orientation.  The
AB  - clone, named E. coli HB101-HPA2, overproduced R.HpaI.  R.HpaI activity from the
AB  - clone was 100-fold that from H. parainfluenzae.  The amino acid sequence of
AB  - M.HpaI was compared with those of other type II methyltransferases.
ER  -

TY  - JOUR
AU  - Ito, J.
AU  - Kawamura, F.
AU  - Duffy, J.J.
TI  - Susceptibility of non-thymine containing DNA to four bacterial restriction endonucleases.
JO  - FEBS Lett.
PY  - 1975
SP  - 278
EP  - 281
VL  - 55
AB  - None
ER  -

TY  - JOUR
AU  - Ito, J.
AU  - Roberts, R.J.
TI  - Unusual base sequence arrangement in phage Phi29 DNA.
JO  - Gene
PY  - 1979
SP  - 1
EP  - 7
VL  - 5
AB  - Susceptibility of Bacillus subtilis phage Phi29 DNA to 34 different restriction
AB  - endonucleases was determined.  Three enzymes, BglI, XbaI and BstEII, were found
AB  - to cleave Phi29 DNA only once at specific sites.  The sites of these single
AB  - cleavages have been mapped.  Thirteen enzymes did not cut Phi29 DNA.  Phi29
AB  - HindIII DNA fragments inserted into pBR313 plasmid and propagated in
AB  - Escherichia coli, were resistant to these restriction endonucleases.  This
AB  - result suggests that the insusceptibility is due to the absence of the
AB  - nucleotide sequences on Phi29 recognized by the enzymes, and not to the
AB  - presence of modified nucleotides.
ER  -

TY  - JOUR
AU  - Ito, K.
AU  - Nakajima, N.
AU  - Yamamura, S.
AU  - Tomita, M.
AU  - Suzuki, H.
AU  - Amachi, S.
TI  - Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment.
JO  - Genome Announcements
PY  - 2016
SP  - e01155
EP  - e01116
VL  - 4
AB  - Arenibacter sp. strain C-21, isolated from surface marine sediment of Japan, accumulates
AB  - iodine in the presence of glucose and iodide (I-). We report here the
AB  - draft genome sequence of this strain to provide insight into the molecular
AB  - mechanism underlying its iodine-accumulating ability.
ER  -

TY  - JOUR
AU  - Ito, S.
AU  - Shen, L.
AU  - Dai, Q.
AU  - Wu, S.C.
AU  - Collins, L.B.
AU  - Swenberg, J.A.
AU  - He, C.
AU  - Zhang, Y.
TI  - Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine.
JO  - Science
PY  - 2011
SP  - 1300
EP  - 1303
VL  - 333
AB  - 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting,
AB  - and suppression of transposable elements. 5mC can be converted to
AB  - 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins.
AB  - Here, we show that, in addition to 5hmC, the Tet proteins can generate
AB  - 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic
AB  - activity-dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in
AB  - genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content
AB  - of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or
AB  - depletion of Tet proteins. Thus, we identify two previously unknown cytosine
AB  - derivatives in genomic DNA as the products of Tet proteins. Our study raises the
AB  - possibility that DNA demethylation may occur through Tet-catalyzed oxidation
AB  - followed by decarboxylation.
ER  -

TY  - JOUR
AU  - Ito, T.
AU  - Katayama, Y.
AU  - Asada, K.
AU  - Mori, N.
AU  - Tsutsumimoto, K.
AU  - Tiensasitorn, C.
AU  - Hiramatsu, K.
TI  - Structural comparison of three types of Staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus.
JO  - Antimicrob. Agents Chemother.
PY  - 2001
SP  - 1323
EP  - 1336
VL  - 45
AB  - The beta-lactam resistance gene mecA of Staphylococcus aureus is carried by a novel mobile
AB  - genetic element, designated staphylococcal cassette chromosome mec (SCCmec), identified in the
AB  - chromosome of a Japanese methicillin-resistant S. aureus (MRSA) strain.  We now report
AB  - identification of two additional types of mecA-carrying genetic elements found in the MRSA
AB  - strains isolated in other countries of the world.  There were substantial differences in the
AB  - size and nucleotide sequences between the elements and the SCCmec.  However, new elements
AB  - shared the chromosomal integration site with the SCCmec.  Structural analysis of the new
AB  - elements revealed that they possessed all of the salient features of the SCCmec: conserved
AB  - terminal inverted repeats and direct repeats at the integration junction points, conserved
AB  - genetic organization around the mecA gene, and the presence of cassette chromosome recombinase
AB  - genes responsible for the movements of SCCmec.  The elements, therefore, were considered to
AB  - comprise the SCCmeg family of staphylococcal mobile genetic elements together with the
AB  - previously identified SCCmec.  Among 38 epidemic MRSA strains isolated in 20 countries, 34
AB  - were shown to possess one of the three typical SCCmec elements on the chromosome.  Our
AB  - findings indicated that there are at least three distinct MRSA clones in the world with
AB  - different types of SCCmec in their chromosome.
ER  -

TY  - JOUR
AU  - Ito, T.
AU  - Ma, X.X.
AU  - Takeuchi, F.
AU  - Okuma, K.
AU  - Yuzawa, H.
AU  - Hiramatsu, K.
TI  - Novel Type V Staphylococcal Cassette Chromosome mec Driven by a Novel Cassette Chromosome Recombinase, ccrC.
JO  - Antimicrob. Agents Chemother.
PY  - 2004
SP  - 2637
EP  - 2651
VL  - 48
AB  - Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic
AB  - element composed of the mec gene complex, which encodes methicillin
AB  - resistance, and the ccr gene complex, which encodes the recombinases
AB  - responsible for its mobility. The mec gene complex has been classified
AB  - into four classes, and the ccr gene complex has been classified into three
AB  - allotypes. Different combinations of mec gene complex classes and ccr gene
AB  - complex types have so far defined four types of SCCmec elements. Now we
AB  - introduce the fifth allotype of SCCmec, which was found on the chromosome
AB  - of a community-acquired methicillin-resistant Staphylococcus aureus strain
AB  - (strain WIS [WBG8318]) isolated in Australia. The element shared the same
AB  - chromosomal integration site with the four extant types of SCCmec and the
AB  - characteristic nucleotide sequences at the chromosome-SCCmec junction
AB  - regions. The novel SCCmec carried mecA bracketed by IS431
AB  - (IS431-mecA-DeltamecR1-IS431), which is designated the class C2 mec gene
AB  - complex; and instead of ccrA and ccrB genes, it carried a single copy of a
AB  - gene homologue that encoded cassette chromosome recombinase. Since the
AB  - open reading frame (ORF) was found to encode an enzyme which catalyzes the
AB  - precise excision as well as site- and orientation-specific integration of
AB  - the element, we designated the ORF cassette chromosome recombinase C
AB  - (ccrC), and we designated the element type V SCCmec. Type V SCCmec is a
AB  - small SCCmec element (28 kb) and does not carry any antibiotic resistance
AB  - genes besides mecA. Unlike the extant SCCmec types, it carries a set of
AB  - foreign genes encoding a restriction-modification system that might play a
AB  - role in the stabilization of the element on the chromosome.
ER  -

TY  - JOUR
AU  - Ito, T.
AU  - Maruyama, F.
AU  - Sawai, K.
AU  - Nozaki, K.
AU  - Otsu, K.
AU  - Ohya, K.
TI  - Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00362
EP  - e00318
VL  - 6
AB  - Mycobacterium virginiense, a newly described species of the Mycobacterium terrae  complex, is
AB  - a cause of tenosynovitis and osteomyelitis in the United States.
AB  - Here, we report the 4,849,424-bp draft genome sequence of M. virginiense strain
AB  - GF75, isolated from a mud sample taken from a Japanese swine farm.
ER  -

TY  - JOUR
AU  - Ito, Y.
AU  - Azuma, T.
AU  - Ito, S.
AU  - Suto, H.
AU  - Miyaji, H.
AU  - Yamazaki, Y.
AU  - Kato, T.
AU  - Kohli, Y.
AU  - Keida, Y.
AU  - Kuriyama, M.
TI  - Sequence analysis and clinical significance of the iceA gene from Helicobacter pylori strains in Japan.
JO  - J. Clin. Microbiol.
PY  - 2000
SP  - 483
EP  - 488
VL  - 38
AB  - The Helicobacter pylori iceA gene was recently identified as a genetic marker for the
AB  - development of peptic ulcer in a Western population.  To assess the significance of iceA
AB  - subtypes of H. pylori in relation to peptic ulcer, 140 Japanese clinical isolates (88 from
AB  - Fukui and 52 from Okinawa) were characterized.  Sequence analysis of the iceA1 gene from 25
AB  - representative Japanese strains was also carried out to identify the differences in iceA
AB  - between the ulcer group and the gastritis group.  The iceA1 genotype was not correlated with
AB  - the presence of peptide ulceration in either area.  In addition, sequence analysis led to
AB  - identification of five deletions and five point mutations (a nonsense mutation or a 1-bp
AB  - insertion) within the iceA1 open reading frame corresponding to previously published
AB  - sequences.  These mutations were identified in both clinical groups (ulcer and gastritis
AB  - groups) in each area.  Local DNA sequence analysis revealed that the endpoints of all five
AB  - deletions coincided with direct repeats.  We also found four strains that carried longer iceA1
AB  - open reading frames compared with that for strain 60190.  In conclusion, carriage of an iceA1
AB  - strain does not seem to be a risk factor for peptic ulcer in Japanese subjects.  The critical
AB  - mutations in the iceA1 gene in some isolates from patients with peptic ulcers suggested that
AB  - IceA does not participate in the pathogenesis of peptic ulcer in Japan.  We also found
AB  - deletion hot spots that were associated with direct repeats in iceA1 and that favored a
AB  - small-deletion model of slipped mispairing events during replication.  We showed that iceA1
AB  - sequence variations may be useful tools for analysis of the population genetics of H. pylori.
ER  -

TY  - JOUR
AU  - Itoh, T. et al.
TI  - A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map.
JO  - DNA Res.
PY  - 1996
SP  - 379
EP  - 392
VL  - 3
AB  - The 465,813 base pair sequence corresponding to the 40.1-50.0 min region on the genetic map of
AB  - Escherichia coli K-12 (W3110) was determined. Analysis of the sequence revealed that this
AB  - region contained at least 466 potential open reading frames, of which 187 (40%) were
AB  - previously reported, 105 (23%) were homologous to other known genes, 103 (22%) were identical
AB  - or similar to hypothetical genes registered in databases, and the remaining 71 (15%) did not
AB  - show a significant similarity to any other gene. At the 45.2-46.0 min region, we found a very
AB  - large cluster of about 30 genes, whose functions are involved in the biosynthesis of
AB  - polysaccharides as the components of outer membranes. In addition, we identified a new
AB  - asn-tRNA gene, designated asnW, between the asnT and asnU genes and a new lysogenic phage
AB  - attachment site as the cis-element.
ER  -

TY  - JOUR
AU  - Ivancic-Bace, I.
AU  - Vlasic, I.
AU  - Cogelja-Cajo, G.
AU  - Brcic-Kostic, K.
AU  - Salaj-Smic, E.
TI  - Roles of PriA protein and double-strand DNA break repair functions in UV-induced restriction alleviation in Escherichia coli.
JO  - Genetics
PY  - 2006
SP  - 2137
EP  - 2149
VL  - 174
AB  - It has been widely considered that. DNA modification protects the chromosome of bacteria E.
AB  - coli K-12 against their own
AB  - restriction-modification systems. Chromosomal DNA is protected from
AB  - degradation by methylation of target sequences. However, when
AB  - unmethylated target sequences are generated in the host chromosome, the
AB  - endonuclease activity of the EcoKI restriction-modification enzyme is
AB  - inactivated by the ClpXP protease and DNA is protected. This process is
AB  - known as restriction alleviation (RA) and it can be induced by UV
AB  - irradiation (UV-induced RA). It has been proposed that chromosomal
AB  - Unmethylated target sequences, a signal for the cell to protect its own
AB  - DNA, can be generated by homologous recombination during the repair of
AB  - damaged DNA. In this study, we wanted to further investigate the
AB  - genetic requirements for recombination proteins involved in the
AB  - generation Of unmethylated target sequences. For this purpose, we
AB  - monitored the alleviation of EcoKI restriction by measuring the
AB  - survival of unmodified X in UV-irradiated cells. Our genetic analysis
AB  - showed that UV-induced RA is dependent on the excision repair protein
AB  - UvrA, the RecA-loading activity of the RecBCD enzyme, and the primosome
AB  - assembly activity of the PriA helicase and is partially dependent on
AB  - RecFOR proteins. On the basis of our results, we propose that
AB  - Unmethylated target sequences are generated at the D-loop by the strand
AB  - exchange of two hemi-methylated duplex DNAs and subsequent initiation
AB  - of DNA replication.
ER  -

TY  - JOUR
AU  - Ivancic-Jelecki, J.
AU  - Baricevic, M.
AU  - Santak, M.
AU  - Forcic, D.
TI  - Restriction enzyme cleavage of fluorescently labeled DNA fragments - Analysis of the method and its usage in examination of digestion  completeness.
JO  - Anal. Biochem.
PY  - 2006
SP  - 277
EP  - 284
VL  - 349
AB  - Restriction enzymes have proven to be among the most valuable tools in molecular biology.  In
AB  - this work, we demonstrate that the cleavage of fluorescently labeled, PCR-amplified DNA can be
AB  - used as a simple and highly sensitive technique for detection of sequences present in a
AB  - percentage as low as 0.6% in a DNA pool.  Due to the fact that fluorescent labeling of DNA
AB  - fragments enables such sensitive detection and quantification of restriction enzyme cleavage,
AB  - the method was further exploited in monitoring of the enzymatic digestion completeness and in
AB  - determination of factors that influence restriction enzyme effectiveness.  We analyzed the
AB  - activity of six restriction endonucleases; the percentage of uncleaved DNA fragments
AB  - predominantly ranged between 2.0 and 2.5 and the highest value was 8.00%.  We conclude that,
AB  - since the enzymatic digestion completeness may not always be assured, each assay based on
AB  - restriction enzyme cleavage that is intended to be used in investigations of heterogeneity in
AB  - a DNA pool should be constructed so that the presence of cleaved sequences is the indication
AB  - of pool nonuniformity.  When the presence of uncleaved sequences indicates pool heterogeneity,
AB  - the results could be misleading due to possible incompleteness of enzymatic cleavage.
ER  -

TY  - JOUR
AU  - Ivanenko, T.
AU  - Heitman, J.
AU  - Kiss, A.
TI  - Mutational analysis of the function of Met137 and Ile197, two amino acids implicated in sequence-specific DNA recognition by the EcoRI endonuclease.
JO  - Biol. Chem.
PY  - 1998
SP  - 459
EP  - 465
VL  - 379
AB  - The gene encoding the EcoRI endonuclease was altered by site-directed mutagenesis to introduce
AB  - multiple substitutions of M137 and I197, two amino acids which were suggested by the revised
AB  - crystal structure to mediate recognition of the cytosines in the 5'-GAATTC-3' target
AB  - sequence.  Eight substitutions of M137 and ten substitutions of I197 were isolated.  With the
AB  - exception of M137W, M137P and M137K, all mutant enzymes retained enough activity to damage
AB  - cellular DNA in the absence of the EcoRI methyltransferase.  All M137 replacements abolished
AB  - the ability of the enzyme to restrict phage growth.  Conservative replacements at I197 (L, V)
AB  - did not impair phage restriction, whereas non-conservative changes reduced (G, W) or abolished
AB  - (D, P) restriction.  In general, substitutions at M137 were more deleterious than
AB  - substitutions at I197.  Double mutants with combinations of M137G/A and I197G/A mutations
AB  - exhibited a phenotype characteristic for the respective single M137 mutant.  Double mutants
AB  - carrying combinations of the M137G/A replacements and substitutions at R200 were viable even
AB  - in the absence of the methyltransferase, suggesting that disrupting contacts to both bases of
AB  - the GC base pair inactivates the enzyme.  None of the replacements resulted in relaxed
AB  - recognition specificity.  In summary, our findings are consistent with a role for M137 but do
AB  - not support such a role for I197 in substrate recognition by the EcoRI endonuclease.
ER  -

TY  - JOUR
AU  - Ivanova, A.A.
AU  - Naumoff, D.G.
AU  - Miroshnikov, K.K.
AU  - Liesack, W.
AU  - Dedysh, S.N.
TI  - Comparative genomics of four Isosphaeraceae Planctomycetes: a common pool of plasmids and glycoside hydrolase genes shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and strain SH-PL62.
JO  - Front. Microbiol.
PY  - 2017
SP  - 412
EP  - 412
VL  - 8
ER  -

TY  - JOUR
AU  - Ivanova, E.P.
AU  - Ng, H.J.
AU  - Webb, H.K.
AU  - Feng, G.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Ohkuma, M.
AU  - Sergeev, A.F.
AU  - Mikhailov, V.V.
AU  - Crawford, R.J.
AU  - Sawabe, T.
TI  - Draft Genome Sequences of Marinobacter similis A3d10T and Marinobacter salarius R9SW1T.
JO  - Genome Announcements
PY  - 2014
SP  - e00442
EP  - e00414
VL  - 2
AB  - Here, we present the draft genomes of Marinobacter similis A3d10(T), a potential  plastic
AB  - biodegrader, and Marinobacter salarius R9SW1(T), isolated from
AB  - radioactive waters. This genomic information will contribute information on the
AB  - genetic basis of the metabolic pathways for the degradation of both plastic and
AB  - radionuclides.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of Sanguibacter keddieii type strain (ST-74).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 110
EP  - 118
VL  - 1
AB  - Sanguibacter keddieii is the type species of the genus Sanguibacter, the only genus within the
AB  - family of Sanguibacteraceae. Phylogenetically, this family is
AB  - located in the neighborhood of the genus Oerskovia and the family
AB  - Cellulomonadaceae within the actinobacterial suborder Micrococcineae. The strain
AB  - described in this report was isolated from blood of apparently healthy cows. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence, and annotation. This is the first complete genome sequence of a member
AB  - of the family Sanguibacteraceae, and the 4,253,413 bp long single replicon genome
AB  - with its 3735 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 126
EP  - 132
VL  - 1
AB  - Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of
AB  - phylogenetic interest because of its isolated location in the
AB  - sparsely populated and neither taxonomically nor genomically adequately accessed
AB  - family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of
AB  - Leptotrichia are large, fusiform, non-motile, non-sporulating rods, which often
AB  - populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and
AB  - saccharolytic. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. This is the first complete genome
AB  - sequence of the order 'Fusobacteriales' and no more than the second sequence from
AB  - the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its
AB  - 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of Gordonia bronchialis type strain (3410).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 19
EP  - 28
VL  - 2
AB  - Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a
AB  - human-pathogenic organism that has been isolated from a large
AB  - variety of human tissues. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is the first
AB  - completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long
AB  - genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of Haliangium ochraceum type strain (SMP-2).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 96
EP  - 106
VL  - 2
AB  - Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the
AB  - myxococcal family 'Haliangiaceae'. Members of the genus
AB  - Haliangium are the first halophilic myxobacterial taxa described. The cells of
AB  - the species follow a multicellular lifestyle in highly organized biofilms, called
AB  - swarms, they decompose bacterial and yeast cells as most myxobacteria do. The
AB  - fruiting bodies contain particularly small coccoid myxospores. H. ochraceum
AB  - encodes the first actin homologue identified in a bacterial genome. Here we
AB  - describe the features of this organism, together with the complete genome
AB  - sequence, and annotation. This is the first complete genome sequence of a member
AB  - of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single
AB  - replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of Geodermatophilus obscurus type strain (G-20).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 158
EP  - 167
VL  - 2
AB  - Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which  is the type
AB  - genus of the family Geodermatophilaceae. G. obscurus is of interest
AB  - as it has frequently been isolated from stressful environments such as rock
AB  - varnish in deserts, and as it exhibits interesting phenotypes such as lytic
AB  - capability of yeast cell walls, UV-C resistance, strong production of
AB  - extracellular functional amyloid (FuBA) and manganese oxidation. This is the
AB  - first completed genome sequence of the family Geodermatophilaceae. The 5,322,497
AB  - bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.
JO  - Nature
PY  - 2003
SP  - 87
EP  - 91
VL  - 423
AB  - Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal
AB  - or emetic syndromes. It is closely related to the
AB  - animal and human pathogen Bacillus anthracis and the insect pathogen
AB  - Bacillus thuringiensis, the former being used as a biological weapon and
AB  - the latter as a pesticide. B. anthracis and B. thuringiensis are readily
AB  - distinguished from B. cereus by the presence of plasmid-borne specific
AB  - toxins (B. anthracis and B. thuringiensis) and capsule (B. anthracis). But
AB  - phylogenetic studies based on the analysis of chromosomal genes bring
AB  - controversial results, and it is unclear whether B. cereus, B. anthracis
AB  - and B. thuringiensis are varieties of the same species or different
AB  - species. Here we report the sequencing and analysis of the type strain B.
AB  - cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579
AB  - together with the gapped genome of B. anthracis A2012 enables us to
AB  - perform comparative analysis, and hence to identify the genes that are
AB  - conserved between B. cereus and B. anthracis, and the genes that are
AB  - unique for each species. We use the former to clarify the phylogeny of the
AB  - cereus group, and the latter to determine plasmid-independent
AB  - species-specific markers.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of Truepera radiovictrix type strain (RQ-24).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 91
EP  - 99
VL  - 4
AB  - Truepera radiovictrix Albuquerque et al. 2005 is the type species of the genus Truepera within
AB  - the phylum 'Deinococcus/Thermus'. T. radiovictrix is of special
AB  - interest not only because of its isolated phylogenetic location in the order
AB  - Deinococcales, but also because of its ability to grow under multiple extreme
AB  - conditions in alkaline, moderately saline, and high temperature habitats. Of
AB  - particular interest is the fact that, T. radiovictrix is also remarkably
AB  - resistant to ionizing radiation, a feature it shares with members of the genus
AB  - Deinococcus. This is the first completed genome sequence of a member of the
AB  - family Trueperaceae and the fourth type strain genome sequence from a member of
AB  - the order Deinococcales. The 3,260,398 bp long genome with its 2,994
AB  - protein-coding and 52 RNA genes consists of one circular chromosome and is a part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ivanova, N. et al.
TI  - Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 312
EP  - 321
VL  - 4
AB  - Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium,
AB  - which in turn is the type genus of the family Halanaerobiaceae.
AB  - The species is of interest because it is able to reduce a variety of
AB  - nitro-substituted aromatic compounds at a high rate, and because of its ability
AB  - to degrade organic pollutants. The strain is also of interest because it
AB  - functions as a hydrolytic bacterium, fermenting complex organic matter and
AB  - producing intermediary metabolites for other trophic groups such as
AB  - sulfate-reducing and methanogenic bacteria. It is further reported as being
AB  - involved in carbon removal in the Great Salt Lake, its source of isolation. This
AB  - is the first completed genome sequence of a representative of the genus
AB  - Halanaerobium and the second genome sequence from a type strain of the family
AB  - Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and
AB  - 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Ivanovsky, R.N.
AU  - Keppen, O.I.
AU  - Lebedeva, N.N.
AU  - Beletsky, A.V.
AU  - Mardanov, A.V.
AU  - Grouzdev, D.S.
TI  - Draft Genome Sequence of the Anoxygenic Phototrophic Bacterium Phaeospirillum fulvum MGU-K5.
JO  - Genome Announcements
PY  - 2017
SP  - e00895
EP  - e00817
VL  - 5
AB  - Phaeospirillum fulvum MGU-K5 is an anoxygenic, purple, photoheterotrophic, nonsulfur
AB  - alphaproteobacterium. Unlike most purple nonsulfur bacteria, MGU-K5 is
AB  - unable to grow aerobically under chemoorganotrophic conditions. Here, we present
AB  - the draft genome sequence of P. fulvum to provide insights into its physiology.
ER  -

TY  - JOUR
AU  - Ivarie, R.
TI  - Thymine methyls and DNA-protein interactions.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 9975
EP  - 9983
VL  - 15
AB  - Evidence is summarized showing that thymine methyls are as important in the
AB  - recognition of specific sequences by proteins as are the more widely recognized
AB  - hydrogen bonding sites of bases in the major groove.  Strongest evidence has
AB  - come from experiments using functional group mutagenesis in which thymines in a
AB  - specific recognition sequence (e.g., promoters, operators and restriction
AB  - sites) are replaced by oligonucleotide synthesis with methyl-free uracil or
AB  - cytosine and 5-methylcytosine.  Such experiments have shown that thymine
AB  - methyls can provide contact points via van der Waals interactions with amino
AB  - acid side chains of specific DNA binding proteins.  Actual contact between a
AB  - thymine methyl and carbons of a glutamine side chain has been observed in a
AB  - cocrystal of the phage 434 repressor and its operator by X-ray analysis.  The
AB  - issue of why thymine occurs in DNA is discussed in light of these findings.
ER  -

TY  - JOUR
AU  - Ives, C.L.
AU  - Nathan, P.D.
AU  - Brooks, J.E.
TI  - Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis.
JO  - J. Bacteriol.
PY  - 1992
SP  - 7194
EP  - 7201
VL  - 174
AB  - BamHI from Bacillus amyloliquefaciens H, is a type II restriction-modification system
AB  - recognizing and cleaving the sequence G^GATCC. The BamHI restriction-modification system
AB  - contains divergently transcribed endonuclease and methylase genes along with a small open
AB  - reading frame oriented in the direction of the endonuclease gene. The small open reading frame
AB  - has been designated bamHIC (for BamHI controlling element). It acts as both a positive
AB  - activator of endonuclease expression and a negative repressor of methylase expression of BamHI
AB  - clones in Escherichia coli. Methylase activity increased 15-fold and endonuclease activity
AB  - decreased 100-fold when bamHIC was inactivated. The normal levels of activity for both
AB  - methylase and endonuclease were restored by supplying bamHIC in trans. The BamHI
AB  - restriction-modification system was transferred into Bacillus subtilis, where bamHIC also
AB  - regulated endonuclease expression when present on multicopy plasmid vectors or integrated into
AB  - the chromosome. In B. subtilis, disruption of bamHIC caused at least a 1,000-fold decrease in
AB  - endonuclease activity; activity was partially restored by supplying bamHIC in trans.
ER  -

TY  - JOUR
AU  - Ives, C.L.
AU  - Sohail, A.
AU  - Brooks, J.E.
TI  - The regulatory C proteins from different restriction-modification systems can cross-complement.
JO  - J. Bacteriol.
PY  - 1995
SP  - 6313
EP  - 6315
VL  - 177
AB  - The BamHI restriction-modification system contains a third gene, bamHIC, which positively
AB  - regulates bamHIR.  Similar small genes from other systems were tested in vivo for their
AB  - ability to cross-complement.  C.BamHI protein was identified, purified, and used to raise
AB  - polyclonal antibodies.  Attempts to detect other C proteins in cell extracts by
AB  - cross-reactivity with C.BamHI antibodies proved unsuccessful.
ER  -

TY  - JOUR
AU  - Ivic, A.
AU  - Jakeman, K.J.
AU  - Penn, C.W.
AU  - Brown, N.L.
TI  - Type II restriction endonucleases from Helicobacter pylori include an enzyme with a novel recognition sequence.
JO  - FEMS Microbiol. Lett.
PY  - 1999
SP  - 175
EP  - 180
VL  - 179
AB  - Type II restriction endonuclease activities of Helicobacter pylori strain Roberts and of the
AB  - type strain H. pylori NCTC 11637 were detected and analysed by conventional techniques. The
AB  - endonucleases were partially purified, their optima for activity and their recognition and
AB  - cleavage sites were determined. H. pylori (Roberts) contained at least two enzymes: HpyBI was
AB  - an isoschizomer of RsaI (GT/AC) and HpyBII was of a novel specificity (GTN/NAC). H. pylori
AB  - NCTC 11637 was found to contain an isoschizomer of EcoRV (HpyCI: GAT/ATC) and at least one
AB  - other enzyme which was too unstable to characterise.
ER  -

TY  - JOUR
AU  - Ivshina, I.B.
AU  - Kuyukina, M.S.
AU  - Krivoruchko, A.V.
AU  - Barbe, V.
AU  - Fischer, C.
TI  - Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231.
JO  - Genome Announcements
PY  - 2014
SP  - e01297
EP  - e01214
VL  - 2
AB  - We report a draft genome sequence of Rhodococcus ruber IEGM 231, isolated from a  water spring
AB  - near an oil-extracting enterprise (Perm region, Russian Federation).
AB  - This sequence provides important insights into the genetic mechanisms of propane
AB  - and n-butane metabolism, organic sulfide and beta-sitosterol biotransformation,
AB  - glycolipid biosurfactant production, and heavy metal resistance in
AB  - actinobacteria.
ER  -

TY  - JOUR
AU  - Iwabuchi, M.
AU  - Tajima, S.
AU  - Inoue, T.
AU  - Shibata, T.
AU  - Ando, T.
TI  - A restriction enzyme, BpuI is an isoschizomer of BanII.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5850
EP  - 5850
VL  - 20
AB  - We previously identified a type II restriction enzyme in extracts of Bacillus pumilus AHU1387
AB  - and designated it BpuI (1,2), which recognizes the sequence GRGCYC and therefore may be an
AB  - isoschizomer of HgiJII or BanII (3). In the present study, we examined the cleavage site of
AB  - BpuI as well as the effect of methylation on the cleavage reaction in order to show that BpuI
AB  - is an isoschizomer of BanII.
ER  -

TY  - JOUR
AU  - Iwai, M.
AU  - Katoh, H.
AU  - Katayama, M.
AU  - Ikeuchi, M.
TI  - Improved genetic transformation of the thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1.
JO  - Plant Cell Physiol.
PY  - 2004
SP  - 171
EP  - 175
VL  - 45
AB  - We improved genetic transformation of the thermophilic cyanobacterium, Thermosynechococcus
AB  - elongatus BP-1, by combining electroporation with a
AB  - top agar method. Transformation was also improved when a disruptant of a
AB  - putative type I restriction endonuclease (tll2230) was used as recipient
AB  - cells. In particular, some constructs, with which wild type has never been
AB  - transformed, were successfully integrated into the tll2230-disruptant.
AB  - Single-crossover recombination was detected more frequently than the
AB  - double-crossover recombination. In accordance with the presence of all the
AB  - homologs of pil genes in Synechocystis sp. PCC 6803, we found that T.
AB  - elongatus is naturally transformable with exogenous DNA.
ER  -

TY  - JOUR
AU  - Iwamoto, M.
AU  - Hishiki, A.
AU  - Shimada, T.
AU  - Imasaki, T.
AU  - Tsuda, J.
AU  - Kita, K.
AU  - Shimizu, T.
AU  - Sato, M.
AU  - Hashimoto, H.
TI  - Crystallization and X-ray diffraction studies of DNA-free and DNA-bound forms of EcoO109I DNA methyltransferase.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2010
SP  - 1528
EP  - 1530
VL  - 66
AB  - EcoO109I DNA methyltransferase (M.EcoO109I) is a type II modification enzyme from the EcoO109I
AB  - restriction-modification system identified in
AB  - Escherichia coli strain H709c. M.EcoO109I recognizes double-stranded
AB  - RGGNCCY (where R = A or G, Y = T or C and N is any base) and transfers
AB  - a methyl group to the C5 of the inner cytosines from
AB  - S-adenosylmethionine. To reveal the mechanism of substrate recognition
AB  - by M.EcoO109I, DNA-free and DNA-bound forms of M.EcoO109I were
AB  - successfully crystallized. Crystals of the DNA-free and DNA-bound forms
AB  - belonged to space groups P4(2)2(1)2, with unit-cell parameters a = b =
AB  - 120.5, c = 79.8 A, and P2(1), with unit-cell parameters a = 55.8, b =
AB  - 77.4, c = 117.4 A, beta = 93.5 degrees, respectively.
ER  -

TY  - JOUR
AU  - Iwaniec, L.M.
AU  - Kroll, J.J.
AU  - Roethel, W.M.
AU  - Maybaum, J.
TI  - Selective inhibition of sequence-specific protein-DNA interactions by incorporation of 6-thioguanine:  Cleavage by restriction endonucleases.
JO  - Mol. Pharmacol.
PY  - 1991
SP  - 299
EP  - 306
VL  - 39
AB  - Incorporation of the antileukemic agent 6-thioguanine (TG) into cellular DNA
AB  - has been demonstrated to be a major determinant of its cytotoxicity.  We have
AB  - previously shown that complete replacement of G by TG within one DNA strand of
AB  - the SV40 origin of replication can completely inhibit sequence-specific binding
AB  - of the viral replication protein T antigen.  The aim of the present study was
AB  - to determine the effect of more selective TG substitutions on DNA-protein
AB  - interactions, by utilizing the simpler base recognition sequence motifs of
AB  - restriction endonucleases.  In the first part of our study, we replaced G with
AB  - TG in one or two of four possible sites within the duplex hexameric recognition
AB  - sequence of BamHI (5'-G^GATCC-3'), by enzymatic extension of primed
AB  - oligonucleotides.  This extension was stalled, but not completely inhibited, at
AB  - locations where insertion of consecutive TG moieties was required.  Both
AB  - strands of molecules containing a single substitution were cleaved by BamHI at
AB  - reduced rates, with the substituted strand inhibited to a greater degree.  In
AB  - molecules containing two substitutions, neither strand was cut by BamHI.  In
AB  - contrast, we found that scission of these same mono- and disubstituted
AB  - substrates by the less stringent isoschizomer MboI (5'-N^GATCN-3') was
AB  - inhibited only slightly.  In the second part of our study, we investigated the
AB  - effect of analog subsitution on scission by the type II-S enzymes AlwI and
AB  - FokI, in order to separately determine the effects of restriction site
AB  - modification versus scission site modification.  We found that the reactivity
AB  - of these enzymes was completely abolished by TG substitution within the
AB  - recognition site, whereas substitution at the scission site had no effect.  Our
AB  - results demonstrate that infrequent TG substitutions within symmetric DNA
AB  - sequences can inhibit sequence-specific interactions in an asymmetric fashion.
AB  - In addition, although previous reports have shown that TG forms a relatively
AB  - weak base pair with cytosine, it appears that the inhibition of restriction
AB  - endonuclease-mediated cleavage resulting from TG incorporation is a function of
AB  - the sequence requirements of the protein and not a general consequence of
AB  - distrupted base-pairing at the recognition locus.  These data support the idea
AB  - that the cytotoxic consequences of TG incorporation may be due to inhibition of
AB  - sequence-specific protein-DNA interactions.
ER  -

TY  - JOUR
AU  - Iwase, T.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Mizunoe, Y.
TI  - Complete Genome Sequence of Klebsiella oxytoca Strain JKo3.
JO  - Genome Announcements
PY  - 2016
SP  - e01221
EP  - e01216
VL  - 4
AB  - Klebsiella oxytoca can be either pathogenic or beneficial, depending on conditions. These
AB  - opposing characteristics have not been fully elucidated. Here,
AB  - we report the complete sequence of the K. oxytoca JKo3 genome, consisting of a
AB  - single circular chromosome of 5,943,791 bp and four plasmids.
ER  -

TY  - JOUR
AU  - Iwase, T.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Mizunoe, Y.
TI  - Complete Genome Sequence of Klebsiella pneumoniae YH43.
JO  - Genome Announcements
PY  - 2016
SP  - e00242
EP  - e00216
VL  - 4
AB  - We report here the complete genome sequence ofKlebsiella pneumoniaestrain YH43, isolated from
AB  - sweet potato. The genome consists of a single circular chromosome
AB  - of 5,520,319 bp in length. It carries 8 copies of rRNA operons, 86 tRNA genes,
AB  - 5,154 protein-coding genes, and thenifgene cluster for nitrogen fixation.
ER  -

TY  - JOUR
AU  - Iyer, L.M.
AU  - Abhiman, S.
AU  - Aravind, L.
TI  - MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.
JO  - Biol. Direct
PY  - 2008
SP  - 8
EP  - 8
VL  - 3
AB  - The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly
AB  - understood since the discovery of their prototype
AB  - MORCI, which is required for meiotic nuclear division in animals. The
AB  - MORC family contains a combination of a gyrase, histidine kinase, and
AB  - MutL (GHKL) and S5 domains that together constitute a catalytically
AB  - active ATPase module. We identify the prokaryotic MORCs and establish
AB  - that the MORC family belongs to a larger radiation of several families
AB  - of GHKL proteins (paraMORCs) in prokaryotes. Using contextual
AB  - information from conserved gene neighborhoods we show that these
AB  - proteins primarily function in restriction-modification systems, in
AB  - conjunction with diverse superfamily II DNA helicases and
AB  - endonucleases. The common ancestor of these GHKL proteins, MutL and
AB  - topoisomerase ATPase modules appears to have catalyzed structural
AB  - reorganization of protein complexes and concomitant DNA-superstructure
AB  - manipulations along with fused or standalone nuclease domains.
AB  - Furthermore, contextual associations of the prokaryotic MORCs and their
AB  - relatives suggest that their eukaryotic counterparts are likely to
AB  - carry out chromatin remodeling by DNA superstructure manipulation in
AB  - response to epigenetic signals such as histone and DNA methylation.
AB  - Reviewers: This article was reviewed by Arcady Mushegian and Gaspar
AB  - Jekely.
ER  -

TY  - JOUR
AU  - Iyer, L.M.
AU  - Abhiman, S.
AU  - Aravind, L.
TI  - Natural History of Eukaryotic DNA Methylation Systems.
JO  - Prog. Mol. Biol. Transl. Sci.
PY  - 2011
SP  - 25
EP  - 104
VL  - 101
AB  - Methylation of cytosines and adenines in DNA is a widespread epigenetic mark in both
AB  - prokaryotes and eukaryotes. In eukaryotes, it has a profound influence on chromatin structure
AB  - and dynamics. Recent advances in genomics and biochemistry have considerably elucidated the
AB  - functions and provenance of these DNA modifications. DNA methylases appear to have emerged
AB  - first in bacterial restriction-modification (R-M) systems from ancient RNA-modifying enzymes,
AB  - in transitions that involved acquisition of novel catalytic residues and DNA-recognition
AB  - features. DNA adenine methylases appear to have been acquired by ciliates, heterolobosean
AB  - amoeboflagellates, and certain chlorophyte algae. Six distinct clades of cytosine methylases,
AB  - including the DNMT1, DNMT2, and DNMT3 clades, were acquired by eukaryotes through independent
AB  - lateral transfer of their precursors from bacteria or bacteriophages. In addition to these,
AB  - multiple adenine and cytosine methylases were acquired by several families of eukaryotic
AB  - transposons. In eukaryotes, the DNA-methylase module was often combined with distinct modified
AB  - and unmodified peptide recognition domains and other modules mediating specialized
AB  - interactions, for example, the RFD module of DNMT1 which contains a permuted Sm domain linked
AB  - to a helix-turn-helix domain. In eukaryotes, the evolution of DNA methylases appears to have
AB  - proceeded in parallel to the elaboration of histone-modifying enzymes and the RNAi system,
AB  - with functions related to counter-viral and counter-transposon defense, and regulation of DNA
AB  - repair and differential gene expression being their primary ancestral functions. Diverse DNA
AB  - demethylation systems that utilize base-excision repair via DNA glycosylases and cytosine
AB  - deaminases appear to have emerged in multiple eukaryotic lineages. Comparative genomics
AB  - suggests that the link between cytosine methylation and DNA glycosylases probably emerged
AB  - first in a novel R M system in bacteria. Recent studies suggest that the 5mC is not a terminal
AB  - DNA modification, with enzymes of the Tet/JBP family of 2-oxoglutarate- and iron-dependent
AB  - dioxygenases further hydroxylating it to form 5-hydroxy-methylcytosine (5hmC). These enzymes
AB  - emerged first in bacteriophages and appear to have been transferred to eukaryotes on one or
AB  - more occasions. Eukaryotes appear to have recruited three major types of DNA-binding domains
AB  - (SRA/SAD, TAM/MBD, and CXXC) in discriminating DNA with methylated or unmethylated cytosines.
AB  - Analysis of the domain architectures of these domains and the DNA methylases suggests that
AB  - early in eukaryotic evolution they developed a close functional link with SET-domain
AB  - methylases and Jumonji-related demethylases that operate on peptides in chromatin proteins. In
AB  - several eukaryotes, other functional connections were elaborated in the form of various
AB  - combinations between domains related to DNA methylation and those involved in ATP-dependent
AB  - chromatin remodeling and RNAi. In certain eukaryotes, such as mammals and angiosperms, novel
AB  - dependencies on the DNA methylation system emerged, which resulted in it affecting unexpected
AB  - aspects of the biology of these organisms such as parent offspring interactions. In genomic
AB  - terms, this was reflected in the emergence of new proteins related to methylation, such as
AB  - Stella. The well-developed methylation systems of certain heteroloboseans, stramenopiles,
AB  - chlorophytes, and haptophyte indicate that these might be new model systems to explore the
AB  - relevance of DNA modifications in eukaryotes.
ER  -

TY  - JOUR
AU  - Iyer, L.M.
AU  - Tahiliani, M.
AU  - Rao, A.
AU  - Aravind, L.
TI  - Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.
JO  - Cell Cycle
PY  - 2009
SP  - 1698
EP  - 1710
VL  - 8
AB  - Modified bases in nucleic acids present a layer of information that directs biological
AB  - function over and beyond the coding capacity of the
AB  - conventional bases. While a large number of modified bases have been
AB  - identified, many of the enzymes generating them still remain to be
AB  - discovered. Recently, members of the 2-oxoglutarate- and
AB  - iron(II)-dependent dioxygenase super-family, which modify diverse
AB  - substrates from small molecules to biopolymers, were predicted and
AB  - subsequently confirmed to catalyze oxidative modification of bases in
AB  - nucleic acids. Of these, two distinct families, namely the AlkB and the
AB  - kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation
AB  - of bases in nucleic acids. Using sensitive computational analysis of
AB  - sequences, structures and contextual information from genomic structure
AB  - and protein domain architectures, we report five distinct families of
AB  - 2-oxoglutarate- and iron(II)-dependent dioxygenase that we predict to be
AB  - involved in nucleic acid modifications. Among the DNA-modifying families,
AB  - we show that the dioxygenase domains of the kinetoplastid base J-binding
AB  - proteins belong to a larger family that includes the Tet proteins,
AB  - prototyped by the human oncogene Tet1, and proteins from basidiomycete
AB  - fungi, chlorophyte algae, heterolobosean amoeboflagellates and
AB  - bacteriophages. We present evidence that some of these proteins are likely
AB  - to be involved in oxidative modification of the 5-methyl group of cytosine
AB  - leading to the formation of 5-hydroxymethylcytosine. The Tet/JBP homologs
AB  - from basidiomycete fungi such as Laccaria and Coprinopsis show large
AB  - lineage-specific expansions and a tight linkage with genes encoding a
AB  - novel and distinct family of predicted transposases, and a member of the
AB  - Maelstrom-like HMG family. We propose that these fungal members are part
AB  - of a mobile transposon. To the best of our knowledge, this is the first
AB  - report of a eukaryotic transposable element that encodes its own
AB  - DNA-modification enzyme with a potential regulatory role. Through a wider
AB  - analysis of other poorly characterized DNA-modifying enzymes we also show
AB  - that the phage Mu Mom-like proteins, which catalyze the
AB  - N6-carbamoylmethylation of adenines, are also linked to diverse families
AB  - of bacterial transposases, suggesting that DNA modification by
AB  - transposable elements might have a more general presence than previously
AB  - appreciated. Among the other families of 2-oxoglutarate- and
AB  - iron(II)-dependent dioxygenases identified in this study, one which is
AB  - found in algae, is predicted to mainly comprise of RNA-modifying enzymes
AB  - and shows a striking diversity in protein domain architectures suggesting
AB  - the presence of RNA modifications with possibly unique adaptive roles. The
AB  - results presented here are likely to provide the means for future
AB  - investigation of unexpected epigenetic modifications, such as
AB  - hydroxymethyl cytosine, that could profoundly impact our understanding of
AB  - gene regulation and processes such as DNA demethylation.
ER  -

TY  - JOUR
AU  - Iyer, L.M.
AU  - Zhang, D.
AU  - Maxwell, B.A.
AU  - Aravind, L.
TI  - Computational identification of novel biochemical systems involved in oxidation,  glycosylation and other complex modifications of bases in DNA.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 7635
EP  - 7655
VL  - 41
AB  - Discovery of the TET/JBP family of dioxygenases that modify bases in DNA has sparked
AB  - considerable interest in novel DNA base modifications and their
AB  - biological roles. Using sensitive sequence and structure analyses combined with
AB  - contextual information from comparative genomics, we computationally characterize
AB  - over 12 novel biochemical systems for DNA modifications. We predict previously
AB  - unidentified enzymes, such as the kinetoplastid J-base generating
AB  - glycosyltransferase (and its homolog GREB1), the catalytic specificity of
AB  - bacteriophage TET/JBP proteins and their role in complex DNA base modifications.
AB  - We also predict the enzymes involved in synthesis of hypermodified bases such as
AB  - alpha-glutamylthymine and alpha-putrescinylthymine that have remained enigmatic
AB  - for several decades. Moreover, the current analysis suggests that bacteriophages
AB  - and certain nucleo-cytoplasmic large DNA viruses contain an unexpectedly diverse
AB  - range of DNA modification systems, in addition to those using previously
AB  - characterized enzymes such as Dam, Dcm, TET/JBP, pyrimidine hydroxymethylases,
AB  - Mom and glycosyltransferases. These include enzymes generating modified bases
AB  - such as deazaguanines related to queuine and archaeosine, pyrimidines comparable
AB  - with lysidine, those derived using modified S-adenosyl methionine derivatives and
AB  - those using TET/JBP-generated hydroxymethyl pyrimidines as biosynthetic starting
AB  - points. We present evidence that some of these modification systems are also
AB  - widely dispersed across prokaryotes and certain eukaryotes such as
AB  - basidiomycetes, chlorophyte and stramenopile alga, where they could serve as
AB  - novel epigenetic marks for regulation or discrimination of self from non-self
AB  - DNA. Our study extends the role of the PUA-like fold domains in recognition of
AB  - modified nucleic acids and predicts versions of the ASCH and EVE domains to be
AB  - novel 'readers' of modified bases in DNA. These results open opportunities for
AB  - the investigation of the biology of these systems and their use in biotechnology.
ER  -

TY  - JOUR
AU  - Iyer, P.R.
AU  - Geib, S.M.
AU  - Catchmark, J.
AU  - Kao, T.H.
AU  - Tien, M.
TI  - Genome Sequence of a Cellulose Producing Bacterium, Gluconacetobacter hansenii ATCC 23769.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4256
EP  - 4257
VL  - 192
AB  - The Gram-negative bacterium Gluconacetobacter hansenii is considered a model organism for
AB  - studying cellulose synthesis. We have determined the
AB  - genome sequence of the strain ATCC 23769.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas.
JO  - Genome Announcements
PY  - 2016
SP  - e00682
EP  - e00616
VL  - 4
AB  - Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from
AB  - farmland soil in Pecan Grove, Texas, USA. In addition to a capacity
AB  - for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium
AB  - spp., including heavy metal resistance and transport genes that may have
AB  - significant agricultural biotechnology applications.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Exiguobacterium sp. KKBO11, Isolated Downstream of a Wastewater Treatment Plant in Houston, Texas.
JO  - Genome Announcements
PY  - 2016
SP  - e00681
EP  - e00616
VL  - 4
AB  - Exiguobacterium sp. KKBO11, isolated near a wastewater treatment plant in Houston, Texas, USA,
AB  - possesses a large number of genes involved in stress
AB  - response and transport critical to survival in adverse environmental conditions.
AB  - An unusually high copy number of RNA genes also possibly contributes to this
AB  - microorganism's versatility by promoting nutrient uptake.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Pseudomonas putida CBF10-2, a Soil Isolate with Bioremediation Potential in Agricultural and Industrial Environmental Settings.
JO  - Genome Announcements
PY  - 2016
SP  - e00670
EP  - e00616
VL  - 4
AB  - Pseudomonas putida CBF10-2 is a microorganism isolated from farmland soil in Fairchild, TX,
AB  - found to degrade high-impact xenobiotics, including
AB  - organophosphate insecticides, petroleum hydrocarbons, and both monocyclic and
AB  - polycyclic aromatics. The versatility of CBF10-2 makes it useful for multipurpose
AB  - bioremediation of contaminated sites in agricultural and industrial environments.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Pseudomonas stutzeri ODKF13, Isolated from Farmland Soil in Alvin, Texas.
JO  - Genome Announcements
PY  - 2016
SP  - e00293
EP  - e00216
VL  - 4
AB  - Pseudomonas stutzeriODKF13 is a bacterial microorganism isolated from farmland soil in Alvin,
AB  - Texas. This strain is notable for its naphthalene degradation and
AB  - nitrogen fixation pathways and for its characterization as an organophosphate
AB  - degrader of phosphotriester and phosphorothioate insecticides.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Alkane-Degrading Acinetobacter venetianus JKSF02, Isolated from Contaminated Sediment of the San Jacinto River in Houston, Texas.
JO  - Genome Announcements
PY  - 2016
SP  - e00286
EP  - e00216
VL  - 4
AB  - Acinetobacter venetianusJKSF02 was isolated from contaminated sediment in eastern Houston,
AB  - Texas along the San Jacinto River. This microorganism specializes in
AB  - n-alkane degradation and is well suited for bioremediation of the petroleum
AB  - hydrocarbon deposited throughout the region by shipping and industrial activity
AB  - from the Houston Ship Channel.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of the Broad-Spectrum Xenobiotic Degrader Achromobacter xylosoxidans ADAF13.
JO  - Genome Announcements
PY  - 2016
SP  - e00203
EP  - e00216
VL  - 4
AB  - Achromobacter xylosoxidansADAF13, isolated from farmland soil, possesses a large  number of
AB  - putative degradation genes and pathways that break down a wide variety
AB  - of aromatic hydrocarbons, pesticides, endocrine disruptors, and other high-impact
AB  - xenobiotics. These properties make this strain an excellent candidate for further
AB  - development as a broad-spectrum bioremediation agent.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia CBF10-1, an Organophosphate-Degrading Bacterium Isolated from Ranch Soil in Fairchilds,  Texas.
JO  - Genome Announcements
PY  - 2016
SP  - e00378
EP  - e00316
VL  - 4
AB  - Stenotrophomonas maltophilia CBF10-1 was isolated from a ranch in Fairchilds, Texas, USA. Its
AB  - genome reveals a highly adaptable microorganism with a large
AB  - complement of antibiotic and heavy metal resistance genes, efflux pumps,
AB  - multidrug transporters, and xenobiotic degradation pathways.
ER  -

TY  - JOUR
AU  - Iyer, R.
AU  - Damania, A.
TI  - Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13.
JO  - Genome Announcements
PY  - 2016
SP  - e00295
EP  - e00216
VL  - 4
AB  - ITALIC! Ochrobactrum anthropiFRAF13 was isolated from farmland soil in Jersey Village, Texas.
AB  - FRAF13 is a bacterial microorganism with broad antibiotic
AB  - resistance that possesses a number of metal-dependent beta-lactam enzymes with
AB  - secondary phosphotriesterase activity that can initiate the breakdown of
AB  - organophosphate compounds.
ER  -

TY  - JOUR
AU  - Izawa, K.
AU  - Kuwahara, H.
AU  - Kihara, K.
AU  - Yuki, M.
AU  - Lo, N.
AU  - Ito, T.
AU  - Ohkuma, M.
AU  - Hongoh, Y.
TI  - Comparison of intracellular 'Ca. Endomicrobium trichonymphae' genomovars illuminates the requirement and decay of defense systems against foreign DNA.
JO  - Genome Biol. Evol.
PY  - 2016
SP  - 3099
EP  - 3107
VL  - 8
AB  - "Candidatus Endomicrobium trichonymphae" (Bacteria; Elusimicrobia) is an obligate
AB  - intracellular symbiont of the cellulolytic protist genus Trichonympha in the
AB  - termite gut. A previous genome analysis of "Ca Endomicrobium trichonymphae"
AB  - phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in
AB  - the gut of the termite Reticulitermes speratus, revealed that its genome is small
AB  - (1.1 Mb) and contains many pseudogenes; it is in the course of reductive genome
AB  - evolution. Here we report the complete genome sequence of another Rs-D17
AB  - genomovar, Ti2015, obtained from a different T. agilis cell present in an R.
AB  - speratus gut. These two genomovars share most intact protein-coding genes and
AB  - pseudogenes, showing 98.6% chromosome sequence similarity. However,
AB  - characteristic differences were found in their defense systems, which comprised
AB  - restriction-modification and CRISPR/Cas systems. The repertoire of intact
AB  - restriction-modification systems differed between the genomovars, and two of the
AB  - three CRISPR/Cas loci in genomovar Ri2008 are pseudogenized or missing in
AB  - genomovar Ti2015. These results suggest relaxed selection pressure for
AB  - maintaining these defense systems. Nevertheless, the remaining CRISPR/Cas system
AB  - in each genomovar appears to be active; none of the "spacer" sequences (112 in
AB  - Ri2008 and 128 in Ti2015) were shared whereas the "repeat" sequences were
AB  - identical. Furthermore, we obtained draft genomes of three additional
AB  - endosymbiotic Endomicrobium phylotypes from different host protist species, and
AB  - discovered multiple, intact CRISPR/Cas systems in each genome. Collectively,
AB  - unlike bacteriome endosymbionts in insects, the Endomicrobium endosymbionts of
AB  - termite-gut protists appear to require defense against foreign DNA, although the
AB  - required level of defense has likely been reduced during their intracellular
AB  - lives.
ER  -

TY  - JOUR
AU  - Izquierdo, J.A. et al.
TI  - Complete Genome Sequence of Clostridium clariflavum DSM 19732.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 104
EP  - 115
VL  - 6
AB  - Clostridium clariflavum is a Cluster III Clostridium within the family Clostridiaceae isolated
AB  - from thermophilic anaerobic sludge (Shiratori et al,
AB  - 2009). This species is of interest because of its similarity to the model
AB  - cellulolytic organism Clostridium thermocellum and for the ability of
AB  - environmental isolates to break down cellulose and hemicellulose. Here we
AB  - describe features of the 4,897,678 bp long genome and its annotation, consisting
AB  - of 4,131 protein-coding and 98 RNA genes, for the type strain DSM 19732.
ER  -

TY  - JOUR
AU  - Izsvak, Z.
AU  - Duda, E.
TI  - Star activity and complete loss of specificity of CeqI endonuclease.
JO  - Biochem. J.
PY  - 1989
SP  - 301
EP  - 303
VL  - 258
AB  - Restriction endonuclease CeqI, an isoschizomer of EcoRV, exhibits star activity, a relaxation
AB  - of specificity in the presence of Mn2+, dimethyl sulphoxide or glycerol. The enzyme cleaves a
AB  - set of sequences that differ from the canonical GATATC by only one nucleotide in positions
AB  - 2,3,4 or 5. Two of these sequences are not cleaved if modified by dam methylase. A further
AB  - loss of specificity can be observed in circumstances less favourable for the enzyme, namely
AB  - low-ionic-strength buffers of pH values below 6.0 or above 9.4. This activity seems to cleave
AB  - DNA at any sequence, producing a smear of well-defined bands. Partial renaturation of the
AB  - denatured enzyme gives rise to a similar non-specific nuclease activity.
ER  -

TY  - JOUR
AU  - Izsvak, Z.
AU  - Jobbagy, Z.
AU  - Duda, E.
TI  - Purification and characterization of CeqI restriction endonuclease.
JO  - Z. Naturforsch. C
PY  - 1992
SP  - 830
EP  - 834
VL  - 47
AB  - CeqI, a type II restriction endonuclease, an isoschizomer of EcoRV was purified to apparent
AB  - homogeneity by a combination of salt precipitation, ion exchange, dye affinity and hydrophobic
AB  - interaction chromatographies. The crude enzyme was present in the form of large aggregates
AB  - that could be pelleted by high speed centrifugation. The enzyme was not associated with
AB  - cellular membranes, though non-ionic detergents lowered the apparent size of the aggregates.
AB  - The purified enzymes also showed a tendency to form large molecular mass (66-600 kDa)
AB  - complexes under physiological conditions, in the absence of cleavable DNA. The enzyme formed
AB  - smaller complexes in the presence of DNA and non-ionic detergents and dissociated into
AB  - subunits (and undergoes reversible loss of activity) in the presence of high concentrations of
AB  - salts. According to SDS gel electrophoresis and sedimentation analysis the molecular mass of
AB  - the monomer is 32+-2 kDa. The enzyme has a rather broad pH optimum, extending into the
AB  - alkaline range and lost specifcity and activity in buffers below pH6.
ER  -

TY  - JOUR
AU  - Izsvak, Z.
AU  - Jobbagy, Z.
AU  - Takacs, I.
AU  - Duda, E.
TI  - Cloning and characterization of the genes of the CeqI restriction-modification system.
JO  - Int. J. Biochem. Cell Biol.
PY  - 1997
SP  - 895
EP  - 900
VL  - 29
AB  - Two genes from Corynebacterium equii, a Gram-positive producing the CeqI
AB  - restriction-modification enzymes were cloned and sequenced.  In vivo restriction experiments,
AB  - DNA and amino acid sequence data suggest that the two genes code for the endonuclease and the
AB  - methyltransferase enzymes.  However, when the two genes are expressed in E. coli, practically
AB  - no enzyme activity can be detected in the supernatants of sonicated cells.  Based on the DNA
AB  - sequence data CeqI restriction enodnuclease (an EcoRV isoschizomer) consists of 270 amino acid
AB  - residues with a predicted molecular mass of 31.6 kDa, in good agreement with the previously
AB  - measured 32+/- 2kDa.  The methyltansferase is 517 residues long (approx. 60 kDa).  The two
AB  - genes are in opposite orientation and overlap by 37 base pairs on the chromosome.  The deduced
AB  - amino acid sequence of the putative endonuclease gene revealed long stretches of hydrophobic
AB  - amino acids, that may form the structural basis of the unusual aggregation properties of the
AB  - restriction endonuclease.  The amino acid sequence of the methylase shows homologies with
AB  - other type II methyltransferases.
ER  -

TY  - JOUR
AU  - Izumiya, H.
AU  - Sekizuka, T.
AU  - Nakaya, H.
AU  - Taguchi, M.
AU  - Oguchi, A.
AU  - Ichikawa, N.
AU  - Nishiko, R.
AU  - Yamazaki, S.
AU  - Fujita, N.
AU  - Watanabe, H.
AU  - Ohnishi, M.
AU  - Kuroda, M.
TI  - Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 623
EP  - 630
VL  - 55
AB  - Salmonella enterica serovar Typhimurium is frequently associated with
AB  - life-threatening systemic infections, and the recent global emergence of
AB  - multidrug resistance in S. enterica isolates from agricultural and clinical
AB  - settings has raised concerns. In this study, we determined the whole-genome
AB  - sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240
AB  - strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome
AB  - analysis revealed that T000240 displays high sequence similarity to strain LT2,
AB  - which was originally isolated in 1940, indicating that progeny of LT2 might be
AB  - reemerging. T000240 possesses a unique 82-kb genomic island, designated as
AB  - GI-DT12, which is composed of multidrug resistance determinants, including a
AB  - Tn2670-like composite transposon (class 1 integron [intI1, bla(oxa-30), aadA1,
AB  - qacEDelta1, and sul1], mercury resistance proteins, and chloramphenicol
AB  - acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the
AB  - aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron
AB  - transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated
AB  - recombination likely played a role in the acquisition of this genomic island
AB  - through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase
AB  - (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette
AB  - responsible for gentamicin and trimethoprim resistance, respectively, were
AB  - identified on plasmid pSTMDT12_L and appeared to have been acquired through
AB  - homologous recombination with IS26. This study represents the first
AB  - characterization of the unique genomic island GI-DT12 that appears to be
AB  - associated with possible IS1-mediated recombination in S. enterica serovar
AB  - Typhimurium. It is expected that future whole-genome studies will aid in the
AB  - characterization of the horizontal gene transfer events for the emerging S.
AB  - enterica serovar Typhimurium strains.
ER  -

TY  - JOUR
AU  - Izvolsky, K.I.
AU  - Demidov, V.V.
AU  - Nielsen, P.E.
AU  - Frank-Kamenetskii, M.D.
TI  - Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs.
JO  - Biochemistry
PY  - 2000
SP  - 10908
EP  - 10913
VL  - 39
AB  - A new generation of PNAs, so-called pseudocomplementary PNAs (pcPNAs) which are able to target
AB  - the designated sites on duplex DNA with mixed
AB  - sequence of purines and pyrimidines via double-duplex invasion mode,
AB  - has recently been introduced. It has been demonstrated that appropriate
AB  - pairs of decameric pcPNAs block an access of RNA polymerase to the
AB  - corresponding promoter. Here, we show that this type of PNAs protects
AB  - selected DNA sites containing all four nucleobases from the action of
AB  - restriction enzymes and DNA methyltransferases. We have found that
AB  - pcPNAs as short as octamers form stable and sequence-specific complexes
AB  - with duplex DNA in a very salt-dependent manner. In accord with a
AB  - strand-invasion mode of complex formation, the pcPNA binding proceeds
AB  - much faster with supercoiled than with linear plasmids. The
AB  - double-duplex invasion complexes selectively shield specific DNA sites
AB  - from BclI restriction endonuclease and dam methylase. The
AB  - pcPNA-assisted protection against enzymatic methylation is more
AB  - efficient when the PNA-binding site embodies the methylase-recognition
AB  - site rather than overlaps it. We conclude that pcPNAs may provide the
AB  - robust tools allowing to sequence-specifically manipulate DNA duplexes
AB  - in a virtually sequence-unrestricted manner.
ER  -

TY  - JOUR
AU  - Jabbar, M.A.
AU  - Snyder, L.
TI  - Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4.
JO  - J. Virol.
PY  - 1984
SP  - 522
EP  - 529
VL  - 51
AB  - The RNA ligase and polynucleotide kinase of bacteriophage T4 are nonessential
AB  - enzymes in most laboratory Escherichia coli strains.  However, T4 mutants which
AB  - do not induce the enzymes are severely restricted in E. coli CTr5X, a strain
AB  - derived from a clinical E. coli isolate.  We have mapped the restricting locus
AB  - in E. coli CTr5X and have transduced it into other E. coli strains.  The
AB  - restrictive locus seems to be a gene, or genes, unique to CTr5X or to be an
AB  - altered form of a nonessential gene, since deleting the locus seems to cause
AB  - loss of the phenotypes.  In addition to restricting RNA ligase- and
AB  - polynucleotide kinase-deficient T4, the locus also restricts bacteriophages
AB  - lambda and T4 with cytosine DNA.  When lambda or T4 with cytosine DNA infect
AB  - strains with the prr locus, the phage DNA is injected, but phage genes are not
AB  - expressed and the host cells survive.  These phenotypes are unlike anything yet
AB  - described for a phage-host interaction.
ER  -

TY  - JOUR
AU  - Jabbari, N.
AU  - Glusman, G.
AU  - Joesch-Cohen, L.M.
AU  - Reddy, P.J.
AU  - Moritz, R.L.
AU  - Hood, L.
AU  - Lausted, C.G.
TI  - Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1.
JO  - PLoS ONE
PY  - 2018
SP  - e0198135
EP  - e0198135
VL  - 13
AB  - Lyme disease is caused by spirochaetes of the Borrelia burgdorferi sensu lato
AB  - genospecies. Complete genome assemblies are available for fewer than ten strains
AB  - of Borrelia burgdorferi sensu stricto, the primary cause of Lyme disease in North
AB  - America. MM1 is a sensu stricto strain originally isolated in the midwestern
AB  - United States. Aside from a small number of genes, the complete genome sequence
AB  - of this strain has not been reported. Here we present the complete genome
AB  - sequence of MM1 in relation to other sensu stricto strains and in terms of its
AB  - Multi Locus Sequence Typing. Our results indicate that MM1 is a new sequence type
AB  - which contains a conserved main chromosome and 15 plasmids. Our results include
AB  - the first contiguous 28.5 kb assembly of lp28-8, a linear plasmid carrying the
AB  - vls antigenic variation system, from a Borrelia burgdorferi sensu stricto strain.
ER  -

TY  - JOUR
AU  - Jabeen, S.
AU  - Yong, Y.H.
AU  - Abdullah, F.J.F.
AU  - Zakaria, Z.
AU  - Mat, I.N.
AU  - Tan, Y.C.
AU  - Yee, W.Y.
AU  - Omar, A.R.
TI  - Complete Genome Sequence of Pasteurella multocida Serotype A Strain PMTB2.1 Isolated from Buffaloes That Died of Septicemia in Malaysia.
JO  - Genome Announcements
PY  - 2017
SP  - e01190
EP  - e01117
VL  - 5
AB  - Pasteurella multocida causes pneumonic pasteurellosis and hemorrhagic septicemia  (HS) in
AB  - large ruminants. In this study, we determined the complete genome
AB  - sequence of P. multocida strain PMTB2.1 capsular serotype A isolated from
AB  - buffaloes that died of septicemia.
ER  -

TY  - JOUR
AU  - Jack, W.E.
TI  - Participation of outside DNA sequences in the EcoRI endonuclease reaction pathway.
JO  - Ph.D. Thesis
PY  - 1983
SP  - 1
EP  - 153
AB  - I have examined the kinetics of the interaction between EcoRI endonuclease and DNA as a model
AB  - system for the study of recognition site location by sequence-specific DNA binding proteins.
AB  - When the kinetics of interaction of nine linear DNA fragments derived from pBR322 and
AB  - containing the EcoRI site in a central position were examined, the kinetic parameters
AB  - governing both formation and decay of specific endonuclease-DNA complexes was found to
AB  - increase 8-fold with increasing DNA chain length.  In contrast, equilibrium competition
AB  - experiments demonstrated the intrinsic affinity for the recognition site was independent of
AB  - DNA chain length for these molecules.  Thus, sequences outside the EcoRI site enhance the rate
AB  - at which EcoRI endonuclease locates and leaves its recognition site without altering the
AB  - intrinsic affinity of the enzyme for that site.  These results are in accord with a
AB  - facilitated diffusion mechanism for site location, and indicate outside DNA sequences lie on
AB  - the major kinetic pathway by which EcoRI endonuclease locates and leaves its recognition site.
AB  - Competition cleavage experiments demonstrated that longer DNA molecules are preferentially
AB  - cleaved by the endonuclease, suggesting outside DNA sequences also facilitate catalysis by the
AB  - enzyme.  In accord with the view that DNHA sequences outside the EcoRI site are involved in
AB  - the reaction pathway, the enzyme processively cleaves EcoRI sites separated by short distances
AB  - on the same DNA chain.  The rate limiting step in EcoRI endonuclease catalysis has been
AB  - examined by pre-steady state measurements.  Addition of endonuclease to saturating DNA
AB  - resulted in a rapid initial burst of product formation.  This burst was stoichiometric with
AB  - the amount of enzyme added and proves that steps up to and including double strand cleavage
AB  - cannot be rate limiting in catalysis.  A similar burst was observed when EcoRI endonuclease
AB  - was incubated with DNA in the absence of Mg2+, and cleavage  initiated by Mg2+ addition.  This
AB  - latter burst quantitatively reflects the amount of site-specific enzyme-DNA complexes present
AB  - at the time of Mg2+ addition, and has been utilized to assay site-specific binding.
ER  -

TY  - JOUR
AU  - Jack, W.E.
AU  - Greenough, L.
AU  - Dorner, L.F.
AU  - Xu, S.-Y.
AU  - Strzelecka, T.
AU  - Aggarwal, A.K.
AU  - Schildkraut, I.
TI  - Overexpression, purification and crystallization of BamHI endonuclease.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 1825
EP  - 1829
VL  - 19
AB  - The type II restriction endonuclease BamHI has been expressed in E. coli,
AB  - producing 100-fold more enzyme than the wild type Bacillus amyloliquefaciens H
AB  - strain.  This high yield has facilitated purification to homogeneity of large
AB  - amounts of the enzyme, along with its crystallization in a form which diffracts
AB  - to at least 1.9 angstrom in X-ray analysis.
ER  -

TY  - JOUR
AU  - Jack, W.E.
AU  - Rubin, R.A.
AU  - Newman, A.
AU  - Modrich, P.
TI  - Structures and mechanisms of EcoRI DNA restriction and modification enzymes.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 165
EP  - 179
VL  - 1
AB  - *
AB  -   I. Structural properties
AB  -  II. Catalytic properties
AB  - III. Enzyme-substrate interactions
AB  -  IV. Cloning and the structural genes
AB  - 
ER  -

TY  - JOUR
AU  - Jack, W.E.
AU  - Terry, B.J.
AU  - Modrich, P.
TI  - Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1982
SP  - 4010
EP  - 4014
VL  - 79
AB  - We have examined the kinetics of the interaction between endodeoxyribonuclease
AB  - EcoRI (EC 3.1.23.13) and nine linear DNA fragments that range in size between
AB  - 34 and 6,200 base pairs and contain the EcoRI site of plasmid pBR322 in a
AB  - central location.  The kinetic parameters governing both formation and decay of
AB  - specific endonuclease DNA complexes increase 8-fold with increasing chain
AB  - length over this size range.  In contrast, equilibrium competition experiments
AB  - demonstrated that the intrinsic affinity of endonuclease for this recognition
AB  - sequence is independent of DNA chain length over this size range.  In contrast,
AB  - equilibrium competition experiments demonstrated that the intrinsic affinity of
AB  - endonuclease for its recognition sequence is independent of DNA chain length
AB  - over this range.  Thus, DNA sequences outside the recognition site enhance the
AB  - rate at which EcoRI endonuclease locates or leaves its recognition site without
AB  - affecting the intrinsic thermodynamic parameters of site-specific interaction.
AB  - These results are consistent with a facilitated diffusion mechanism for
AB  - specific DNA site location by this enzyme.
ER  -

TY  - JOUR
AU  - Jackson, A.
AU  - Humbert, M.V.
AU  - Pandey, A.
AU  - Bratcher, H.
AU  - Christodoulides, M.
TI  - Draft Genome Sequence of Dichelobacter nodosus ATCC 25549, Strain VPI 2340 [11342], a Bacterium Causing Footrot in Sheep.
JO  - Genome Announcements
PY  - 2015
SP  - e01002
EP  - e01015
VL  - 3
AB  - We report a draft genome sequence for Dichelobacter nodosus ATCC 25549, strain VPI 2340
AB  - [11342], a causative agent of ovine footrot. The draft genome shares ~98% gene similarity with
AB  - the available genome of D. nodosus strain VCS1703A but  is differentiated by extensive gene
AB  - duplication and the absence of 13 particular  genes.
ER  -

TY  - JOUR
AU  - Jackson, D.A.
AU  - Symons, R.H.
AU  - Berg, P.
TI  - Biochemical method for inserting new genetic information into DNA of simian virus 40:  circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 2904
EP  - 2909
VL  - 69
AB  - We have developed methods for covalently joining duplex DNA molecules to one
AB  - another and have used these techniques to construct circular dimers of SV40 DNA
AB  - and to insert a DNA segment containing lambda phage genes and the galactose
AB  - operon of E. coli into SV40 DNA.  The method involves:   (a) converting
AB  - circular SV40 DNA to a linear form, (b) adding single-stranded
AB  - homodeoxypolymeric extensions of defined composition and length to the 3' ends
AB  - of one of the DNA strands with the enzyme terminal deoxynucleotidyl transferase
AB  - (c) adding complementary homodeoxypolymeric extensions to the other DNA strand,
AB  - (d) annealing the two DNA molecules to form a circular duplex structure, and
AB  - (e) filling the gaps and sealing nicks in this structure with E. coli DNA
AB  - polymerase and DNA ligase to form a covalently closed-circular DNA molecule.
ER  -

TY  - JOUR
AU  - Jackson, E.E.
AU  - Ogrodzki, P.
AU  - Pascoe, B.
AU  - Sheppard, S.K.
AU  - Forsythe, S.J.
TI  - Draft Genome Sequence of an Enterobacter Species Associated with Illnesses and Powdered Infant Formula.
JO  - Genome Announcements
PY  - 2016
SP  - e01479
EP  - e01415
VL  - 4
AB  - This is the first report of the draft genome sequence of an Enterobacter species  that may
AB  - have been transmitted from powdered infant formula (PIF) to infants,
AB  - resulting in illness. Enterobacter spp. are currently permitted in PIF, but the
AB  - transmission of this strain indicates that the microbiological criteria for PIF
AB  - may need revision.
ER  -

TY  - JOUR
AU  - Jackson, S.E.
AU  - Koyama, M.
AU  - Ryu, J.
TI  - A novel use of bacterial transformation to discover new restriction enzymes in clinical E. coli strains.
JO  - J. Invest. Med.
PY  - 2001
SP  - 11A
EP  - 11A
VL  - 49
AB  - Recent bacterial genome projects have revealed many new DNA sequences that encode restriction
AB  - endonucleases and their corresponding methylases.  These findings suggest that many
AB  - restriction enzymes have yet to be discovered.  Traditionally, restriction enzymes have been
AB  - discovered by either the classical restriction and modification phenomena of bacteriophages or
AB  - by direct enzyme assay.  To avoid the limitations of these traditional methods, we established
AB  - a simple, quantitative R-M test based on plasmid transformation efficiency (plasmid R-M test)
AB  - using DNA fragments derived from the E. coli phage Lambda.  This new plasmid R-M test works
AB  - similarly to a traditional phage efficiency of plating assay, but is defined as efficiency of
AB  - transformation.  A plasmid kit (p1-p6) was created by combining fragments of Lambda with the
AB  - vector plasmid pMECA, which confers ampicillin resistance.  We used this new EOT method to
AB  - test 250 E. coli strains obtained from 2 local hospitals.  Out of the 250 samples, 58 strains
AB  - were ampicillin sensitive and were used for further study.  The plasmid pMECA and plasmids
AB  - p1-p6 from the kit were transformed into these 58 strains.  Among those, 15 strains had a high
AB  - rate of transformability and a suspected restriction-modification system.  The restriction
AB  - results for these 15 strains were tabulated for p1-p6 by assigning a value of either (+) or
AB  - (-).  Restriction (+) indicates the presence of a DNA recognition site, and thus no bacterial
AB  - growth.  Restriction (-) indicates the absence of a recognition site, and presence of
AB  - bacterial growth.  After comparing the restriction patterns of the 15 clinical strains with
AB  - the restriction patterns of all known E. coli strains (173 listed in REBASE), we found one new
AB  - restriction sequence pattern.  This novel pattern suggests a new DNA recognition sequence.  In
AB  - order to identify this recognition sequence, we, in collaboration with UC Riverside engineers,
AB  - developed a computer program designed to analyze the +/- restriction patterns.  This series of
AB  - experiments indicates that the EOT test can be used to find new restriction enzymes in
AB  - clinical E. coli samples.  We believe that this new method can be expanded to find new
AB  - restriction enzymes and their recognition sequence in many types of bacteria.
ER  -

TY  - JOUR
AU  - Jacob, K.M.
AU  - Spilker, T.
AU  - LiPuma, J.J.
AU  - Dawid, S.R.
AU  - Watson, M.E. Jr.
TI  - Complete Genome Sequence of emm4 Streptococcus pyogenes MEW427, a Throat Isolate  from a Child Meeting Clinical Criteria for Pediatric Autoimmune Neuropsychiatric   Disorders Associated with Streptococcus (PANDAS).
JO  - Genome Announcements
PY  - 2016
SP  - e00127
EP  - e00116
VL  - 4
AB  - We report the complete genome assembly of the Streptococcus pyogenes type emm4 strain MEW427
AB  - (also referred to as strain UM001 in the Pediatric Acute-Onset
AB  - Neuropsychiatric Syndrome [PANS] Research Consortium), a throat isolate from a
AB  - child with acute-onset neuropsychiatric symptoms meeting clinical criteria for
AB  - PANDAS (pediatric autoimmune neuropsychiatric disorders associated with
AB  - streptococcus). The genome length is 1,814,455 bp with 38.51% G+C%.
ER  -

TY  - JOUR
AU  - Jacobs, D.
TI  - Type II restriction-modification systems in Enterobacter aerogenes and Herpetosiphon giganteus.
JO  - Diss. Abstr.
PY  - 1988
SP  - 730B
EP  - 730B
VL  - 49
AB  - The Type II modification methylase M.EaeI corresponding to the restriction
AB  - endonuclease EaeI was partially purified from Enterobacter aerogenes PW201.
AB  - The methylase converts the innermost cytosine residue in each strand of the
AB  - family of related sequences recognised by EaeI (5'-PyGGCCPu-3') to
AB  - 5-methylcytosine.  M.EaeI protects these sites against cleavage by HaeIII and
AB  - also protects overlapping 5'-CCGG-3 sites against cleavage by HpaII and MspI.
AB  - Such protection may be useful in genetic manipulations.  Despite using a
AB  - variety of cloning strategies, attempts to clone the EaeI
AB  - restriction-modification system in Escherichia coli were unsuccessful.  It is
AB  - now apparent that many of the problems encountered during these attempts can be
AB  - explained by the existence in most E. coli strains of restriction systems which
AB  - specifically restrict methylated DNA.  Possible evolutionary relationships
AB  - between Type II restriction-modification systems were investigated in
AB  - Herpetosiphon giganteus.  HgiJI from H. giganteus HFS101 has the recognition
AB  - specificity 5'-GG(A/T)CC-3' and is the fifth isoschizomer of AvaII to have been
AB  - identified in this genus.  The recognition specificities of HgiJII
AB  - (5'-GPuGCPyC-3') and HgiAI (5'-G(A/T)GC(A/T)C-3') from H. giganteus strains
AB  - HFS101 and HP1023 respectively are very similar and the DNAs from these strains
AB  - are resistant to cleavage by both restriction endonucleases.  HgiAI and HgiJII
AB  - may therefore be closely-related enzymes.  The potential role of Type II
AB  - restriction-modification systems in limiting gene transfer between strains in
AB  - this genus is also discussed.
ER  -

TY  - JOUR
AU  - Jacobs, D.
AU  - Brown, N.L.
TI  - Isolation and characterization of the M.EaeI modification methylase.
JO  - Biochem. J.
PY  - 1986
SP  - 613
EP  - 616
VL  - 238
AB  - Restriction endonucleases have found wide use in the analysis and restructuring of DNA
AB  - molecules and as model systems for studying the interactions of proteins and DNA.  Many such
AB  - activities have been characterized from a large number of bacterial genera (Roberts, 1985),
AB  - and in virtually all cases examined a corresponding methylase is present that protects the
AB  - bacterial DNA from cleavage (McClelland & Nelson, 1985).  These modification methylases have
AB  - been less well-studied, presumably because they are of less importance as tools in the
AB  - manipulation of DNA in vitro.  However, such methylases can be used to protect specific sites
AB  - against cleavage by the cognate endonuclease, and they have been used to alter the number of
AB  - target sites for non-cognate restriction endonucleases on DNA to generate novel specificities
AB  - of cleavage (McClelland et al., 1984).We now report the specificity of the methylase M.EaeI
AB  - corresponding to the endonuclease EaeI from Enterobacter aerogenes PW201 (Whitehead & Brown,
AB  - 1983).  We show that the methylase can be used to protect a subset of HaeIII recognition
AB  - sequences from HaeIII cleavage and HpaII/MspI sites from HpaII or MspI cleavage.  Such
AB  - protection may be useful in genetic manipulations.
ER  -

TY  - JOUR
AU  - Jacobs, M.B.
AU  - Norris, S.J.
AU  - Phillippi-Falkenstein, K.M.
AU  - Philipp, M.T.
TI  - Infectivity of the highly transformable BBE02(-) lp56(-) mutant of Borrelia burgdorferi, the Lyme disease spirochete, via ticks.
JO  - Infect. Immun.
PY  - 2006
SP  - 3678
EP  - 3681
VL  - 74
AB  - Infectious Borrelia burgdorferi strains that have increased transformability with the shuttle
AB  - vector pBSV2 were recently
AB  - constructed by inactivating the gene encoding BBE02, a putative
AB  - restriction-modification gene product expressed by the linear plasmid
AB  - 1p25 (Kawabata et al., Infect. Immun. 72:7147-7154, 2004). The absence
AB  - of the linear plasmid 1p56, which carries another putative
AB  - restriction-modification gene, further enhanced transformation rates.
AB  - The infectivity of these mutants was assessed previously in mice that
AB  - were inoculated with needle and syringe and was found to be equivalent
AB  - to that of wild-type spirochetes. Here we examined the infectivity of
AB  - spirochetes to ticks after capillary inoculation of Ixodes scapularis
AB  - nymphs and the subsequent spirochetal infectivity to mice via ticks by
AB  - using B. burgdorferi B31 clonal isolates lacking 1p56 and/or BBE02. The
AB  - absence of 1p56 (but not BBE02) correlated with a lower number of
AB  - spirochetes in ticks after feeding on mice; this plasmid thus may play
AB  - a role, albeit not an essential one, in supporting spirochetal survival
AB  - in the feeding tick. Importantly, however, the absence of 1p56 and
AB  - BBE02 did not detectably influence infectivity to mice via ticks.
ER  -

TY  - JOUR
AU  - Jacoby, G.A.
AU  - Sutton, L.
TI  - Restriction and modification determined by a Pseudomonas R plasmid.
JO  - Plasmid
PY  - 1977
SP  - 115
EP  - 116
VL  - 1
AB  - Pseudomonas plasmid pMG7 interferes with the propagation of bacteriophages B3, D3, F116, and
AB  - G101 by determining a restriction and modification system.  This system also acts on plasmids
AB  - RP-1 and RP8 to limit transfer into a pMG7+ recipient.
ER  -

TY  - JOUR
AU  - Jacoby, G.A.
AU  - Sutton, L.
TI  - Restriction-modification systems determined by Pseudomonas plasmids.
JO  - Plasmid
PY  - 1982
SP  - 141
EP  - 147
VL  - 8
AB  - Four additional Pseudomonas R plasmids determining the PaeR7
AB  - restriction-modification system have been detected.  All are transfer deficient
AB  - and appear to belong to the same incompatibility group.  The Pseudomonas
AB  - fertility plasmid FP110 determines a different restriction-modification system
AB  - and also inhibits the propagation of phage B39 by a separate mechanism.
AB  - Pseudomonas R plasmid pMG73 has a third distinct restriction-modification
AB  - specificity.  PaeFP110 and PaeR73 are proposed as designations for these new
AB  - plasmid-determined systems for restriction and modification.
ER  -

TY  - JOUR
AU  - Jacoby, K.
AU  - Metzger, M.
AU  - Shen, B.W.
AU  - Certo, M.T.
AU  - Jarjour, J.
AU  - Stoddard, B.L.
AU  - Scharenberg, A.M.
TI  - Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 4954
EP  - 4964
VL  - 40
AB  - LAGLIDADG homing endonucleases (LHEs) are a family of highly specific DNA endonucleases
AB  - capable of recognizing target sequences approximately 20 bp in
AB  - length, thus drawing intense interest for their potential academic,
AB  - biotechnological and clinical applications. Methods for rational design of LHEs
AB  - to cleave desired target sites are presently limited by a small number of
AB  - high-quality native LHEs to serve as scaffolds for protein engineering-many are
AB  - unsatisfactory for gene targeting applications. One strategy to address such
AB  - limitations is to identify close homologs of existing LHEs possessing superior
AB  - biophysical or catalytic properties. To test this concept, we searched public
AB  - sequence databases to identify putative LHE open reading frames homologous to the
AB  - LHE I-AniI and used a DNA binding and cleavage assay using yeast surface display
AB  - to rapidly survey a subset of the predicted proteins. These proteins exhibited a
AB  - range of capacities for surface expression and also displayed locally altered
AB  - binding and cleavage specificities with a range of in vivo cleavage activities.
AB  - Of these enzymes, I-HjeMI demonstrated the greatest activity in vivo and was
AB  - readily crystallizable, allowing a comparative structural analysis. Taken
AB  - together, our results suggest that even highly homologous LHEs offer a readily
AB  - accessible resource of related scaffolds that display diverse biochemical
AB  - properties for biotechnological applications.
ER  -

TY  - JOUR
AU  - Jacques, M.A.
AU  - Bolot, S.
AU  - Charbit, E.
AU  - Darrasse, A.
AU  - Briand, M.
AU  - Arlat, M.
AU  - Gagnevin, L.
AU  - Koebnik, R.
AU  - Noel, L.D.
AU  - Portier, P.
AU  - Carrere, S.
AU  - Boureau, T.
TI  - High-Quality Draft Genome Sequence of Xanthomonas alfalfae subsp. alfalfae Strain CFBP 3836.
JO  - Genome Announcements
PY  - 2013
SP  - e01035
EP  - e01013
VL  - 1
AB  - We report the high-quality draft genome sequence of Xanthomonas alfalfae subsp. alfalfae
AB  - strain CFBP 3836, the causal agent of bacterial leaf and stem spot in
AB  - lucerne (Medicago sativa). Comparative genomics will help to decipher the
AB  - mechanisms provoking disease and triggering the defense responses of this
AB  - pathogen of the model legume Medicago truncatula.
ER  -

TY  - JOUR
AU  - Jacquier, A.
AU  - Dujon, B.
TI  - An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene.
JO  - Cell
PY  - 1985
SP  - 383
EP  - 394
VL  - 41
AB  - The intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae possesses a long
AB  - internal reading frame (ORF) that is conserved in various yeast species. In crosses between
AB  - intron-plus and intron-minus variants, this intron determines a specific gene conversion
AB  - phenomenon, which results in the integration of the intron sequence within all previously
AB  - intron-minus copies of the gene. We show, from a frameshift mutant within the intron this ORF
AB  - and from the need of mitochondrial protein synthesis, that ORF encodes a protein active in the
AB  - gene conversion that spreads the intron within populations of interbreeding strains. This new
AB  - intron function is reminiscent of the transposase encoded by mobile genetic elements and is
AB  - discussed in relation to other intron functions.
ER  -

TY  - JOUR
AU  - Jacquier, A.
AU  - Dujon, B.
TI  - The intron of the mitochondrial 21S rRNA gene:  distribution in different yeast species and sequence comparison between Kluyveromyces thermotolerans and Saccharomyces cerevisiae.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 487
EP  - 499
VL  - 192
AB  - We have screened numerous different yeast species for the presence of sequences homologous to
AB  - the intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae (intron r1) and
AB  - found them in all Kluyveromyces species, some of the Saccharomyces species and none of the
AB  - other yeasts tested. We have determined the nucleotide sequence of the r1-intron in K.
AB  - thermotolerans and compared it with that of S. cerevisiae. The two introns are inserted at the
AB  - same position within the 21S rRNA gene. They contain homologous internal open reading frames
AB  - (ORFs) initiated at the same AUG codon which can be aligned over their entire length. Several
AB  - silent multi-substitutions indicate that these intronic ORFs represent selectively conserved
AB  - functional genes. Other intron segments, on the contrary, reveal short blocks of extensive
AB  - homology separated by non-homologous stretches and/or additions-deletions. Comparison of our
AB  - two yeast r1-introns with equivalent introns of N. crassa and A. nidulans mitochondria reveals
AB  - that introns with very similar RNA secondary structures can accommodate different types of
AB  - ORFs.
ER  -

TY  - JOUR
AU  - Jadhav, V.R.
AU  - Ganesh, K.N.
TI  - Design of a combinatorial oligonucleotide library containing all possible hexamer palindromes: PCR synthesis and application for identifying restriction cleavage sites.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1998
SP  - 297
EP  - 302
VL  - 242
AB  - An algorithm for designing a combinatorial library comprehensively representing all hexamer
AB  - palindrome sequences at uniquely defined sites is described.  The expected size for such a
AB  - library of 64 possible hexamer palindromes is 384 bases, which is reduced to 266 bases spread
AB  - over 8 oligonucleotides through a linear overlap of rationally selected hexamer palindromes.
AB  - The single stranded oligonucleotides of the designed sets were chemically synthesized and
AB  - converted into corresponding duplex dimers using PCR primer-dimer method.  The utility of
AB  - these duplex oligomers for identifying cleavage sites of restriction enzymes recognizing
AB  - hexamer palindromes has been demonstrated using some representative enzymes.  The library is
AB  - also useful for screening restriction enzymes with tetramer cleavage sites and identifying the
AB  - "star" sites of restriction enzymes.  The sets of oligonucleotides with high information
AB  - content, though designed for direct and unambiguous characterization of cleavage sites of
AB  - isolated restriction enzymes, have potential applications as templates for characterizing
AB  - sequence selective binding and interaction of small molecules nucleic acid.
ER  -

TY  - JOUR
AU  - Jaen-Luchoro, D.
AU  - Salva-Serra, F.
AU  - Aliaga-Lozano, F.
AU  - Segui, C.
AU  - Busquets, A.
AU  - Ramirez, A.
AU  - Ruiz, M.
AU  - Gomila, M.
AU  - Lalucat, J.
AU  - Bennasar-Figueras, A.
TI  - Complete Genome Sequence of Mycobacterium chelonae Type Strain CCUG 47445, a Rapidly Growing Species of Nontuberculous Mycobacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00550
EP  - e00516
VL  - 4
AB  - Mycobacterium chelonae strains are ubiquitous rapidly growing mycobacteria associated with
AB  - skin and soft tissue infections, cellulitis, abscesses,
AB  - osteomyelitis, catheter infections, disseminated diseases, and postsurgical
AB  - infections after implants with prostheses, transplants, and even hemodialysis
AB  - procedures. Here, we report the complete genome sequence of M. chelonae type
AB  - strain CCUG 47445.
ER  -

TY  - JOUR
AU  - Jaen-Luchoro, D.
AU  - Segui, C.
AU  - Aliaga-Lozano, F.
AU  - Salva-Serra, F.
AU  - Busquets, A.
AU  - Gomila, M.
AU  - Ramirez, A.
AU  - Ruiz, M.
AU  - Moore, E.R.
AU  - Lalucat, J.
AU  - Bennasar-Figueras, A.
TI  - Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286.
JO  - Genome Announcements
PY  - 2016
SP  - e00401
EP  - e00416
VL  - 4
AB  - Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG
AB  - 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781
AB  - bp and covers as many as 5,484 predicted genes. This genome contributes to the
AB  - task of closing the still-existing gap of genomes of rapidly growing
AB  - mycobacterial type strains.
ER  -

TY  - JOUR
AU  - Jaenicke, S.
AU  - Bunk, B.
AU  - Wibberg, D.
AU  - Sproer, C.
AU  - Hersemann, L.
AU  - Blom, J.
AU  - Winkler, A.
AU  - Schatschneider, S.
AU  - Albaum, S.P.
AU  - Kolliker, R.
AU  - Goesmann, A.
AU  - Puhler, A.
AU  - Overmann, J.
AU  - Vorholter, F.J.
TI  - Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).
JO  - Genome Announcements
PY  - 2016
SP  - e01334
EP  - e01316
VL  - 4
AB  - We report here the complete 4.7-Mb genome sequence of Xanthomonas translucens pv. translucens
AB  - DSM 18974T, which causes black chaff disease on barley (Hordeum
AB  - vulgare). Genome data of this X. translucens type strain will improve our
AB  - understanding of this bacterial species.
ER  -

TY  - JOUR
AU  - Jaffe, B.
AU  - Kovacs, K.
AU  - Andras, C.
AU  - Bodi, Z.
AU  - Liu, Z.
AU  - Fray, R.G.
TI  - Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment.
JO  - Plant Cell
PY  - 2008
SP  - 1377
EP  - 1384
VL  - 27
AB  - We report the integration of a type II restriction-methylase, mFokI, into the tobacco
AB  - chloroplast genome and we demonstrate that the
AB  - introduced enzyme effectively directs the methylation of its target
AB  - sequence in vivo and does not affect maternal inheritance. We further
AB  - report the transformation of tobacco with an E. coli dcm methylase
AB  - targeted to plastids and we demonstrate efficient cytosine methylation
AB  - of the plastid genome. Both adenosine methylation of FokI sites and
AB  - cytosine methylation of dcm sites appeared phenotypically neutral. The
AB  - ability to tolerate such plastid genome methylation is a pre-requisite
AB  - for a proposed plant transgene containment system. In such a system, a
AB  - chloroplast located, maternally inherited restriction methylase would
AB  - provide protection from a nuclear-encoded, plastid targeted restriction
AB  - endonuclease. As plastids are not paternally inherited in most crop
AB  - species, pollen from such plants would carry the endonuclease transgene
AB  - but not the corresponding methylase; the consequence of this should be
AB  - containment of all nuclear transgenes, as pollination will only be
AB  - viable in crosses to the appropriate transplastomic maternal
AB  - background.
ER  -

TY  - JOUR
AU  - Jag, V.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA-19 (DSM 43852T).
JO  - Genome Announcements
PY  - 2016
SP  - e00973
EP  - e00916
VL  - 4
AB  - Here, we report the draft genome sequence of Oerskovia enterophila DFA-19 (DSM 43852(T)), a
AB  - facultative anaerobe soil bacterium, which was originally isolated
AB  - from millipede feces and first described as Promicromonospora enterophila The
AB  - genome consists of a circular chromosome comprising approximately 4.65 Mb and
AB  - 4,044 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Jag, V.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 30
EP  - 30
VL  - 12
AB  - A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was
AB  - isolated from soil samples from the botanical garden of Ulm University,
AB  - Ulm, Germany. Here, the isolation procedure, identification, genome sequencing
AB  - and metabolic features of the strain are described. Phylogenetic analysis allowed
AB  - to identify the isolated strain as Oerskovia enterophila. The genus Oerskovia
AB  - belongs to the family Cellulomonadaceae within the order Actinomycetales. The
AB  - length of cells of O. enterophila ranges from 1 mum to 15 mum, depending on the
AB  - growth phase. In the exponential growth phase, cells show an elongated and
AB  - branching shape, whereas cells break up to round or coccoid elements in the
AB  - stationary growth phase. The 4,535,074 bp long genome consists of 85 contigs with
AB  - 3918 protein-coding genes and 57 RNA genes. The isolated strain was shown to
AB  - degrade numerous complex carbon sources such as cellulose, chitin, and starch,
AB  - which can be found ubiquitously in nature. Moreover, analysis of the genomic
AB  - sequence revealed the genetic potential to degrade these compounds.
ER  -

TY  - JOUR
AU  - Jager, K.
AU  - Potts, M.
TI  - Distinct fractions of genomic DNA from cyanobacterium Nostoc commune that differ in the degree of methylation.
JO  - Gene
PY  - 1988
SP  - 197
EP  - 201
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Jaglarz, A.
AU  - Gurgul, A.
AU  - Leigh, W.J.
AU  - Costa, J.Z.
AU  - Thompson, K.D.
TI  - Complete Genome Sequences of Three Streptococcus agalactiae Serotype Ia Isolates  Obtained from Disease Outbreaks in Nile Tilapia (Oreochromis niloticus).
JO  - Genome Announcements
PY  - 2018
SP  - e01432
EP  - e01417
VL  - 6
AB  - This paper describes the whole-genome sequences for three Streptococcus agalactiae serotype Ia
AB  - isolates. The isolates were recovered from the brains of
AB  - clinically sick tilapia, Oreochromis niloticus, that were suffering from
AB  - streptococcosis. One isolate was from tilapia in the United States and the other
AB  - two from fish in China.
ER  -

TY  - JOUR
AU  - Jaglarz, A.
AU  - Gurgul, A.
AU  - Leigh, W.J.
AU  - Costa, J.Z.
AU  - Thompson, K.D.
TI  - Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates.
JO  - Genome Announcements
PY  - 2018
SP  - e00025
EP  - e00018
VL  - 6
AB  - The whole-genome sequences are described here for three group B Streptococcus (GBS) (S.
AB  - agalactiae) serotype Ib isolates obtained from tilapia (Oreochromis
AB  - niloticus) farmed at sites in Honduras, Costa Rica, and the United States. The
AB  - bacteria were isolated from the brains of fish displaying signs of
AB  - streptococcosis.
ER  -

TY  - JOUR
AU  - Jagoda, S.S.
AU  - Tan, E.
AU  - Arulkanthan, A.
AU  - Kinoshita, S.
AU  - Watabe, S.
AU  - Asakawa, S.
TI  - Draft Genome Sequence of Aeromonas hydrophila Strain Ae34, Isolated from a Septicemic and Moribund Koi Carp (Cyprinus carpio koi), a Freshwater Aquarium  Fish.
JO  - Genome Announcements
PY  - 2014
SP  - e00572
EP  - e00514
VL  - 2
AB  - Aeromonas hydrophila is an important opportunistic pathogen that infects a variety of aquatic
AB  - and terrestrial animals, including humans. We report here the
AB  - draft genome sequence of A. hydrophila Ae34, a multidrug-resistant isolate from
AB  - the kidney of a moribund koi carp (Ciprinus carpio koi) with signs of hemorrhagic
AB  - septicemia.
ER  -

TY  - JOUR
AU  - Jair, K.
AU  - Yen, R.-W.C.
AU  - Toyota, M.
AU  - Ho, C.
AU  - Baylin, S.B.
AU  - Issa, J.-P.J.
TI  - De novo DNA methyltransferase activity in a lung cancer cell line.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1998
SP  - 95
EP  - 95
VL  - 39
AB  - In mammalian cells genomic methylation patterns are important for normal embryonic development
AB  - and cell growth.  It has been proposed that distinct DNA methyltransferases are responsible
AB  - for de novo and maintenance methylation, however, only one DNA methyltransferase with
AB  - predominant maintenance activity has been identified in vertebrates so far.  In addition, the
AB  - role of DNA methyltransferases in establishing aberrant patterns of DNA methylation in cancer
AB  - remain poorly defined.  We have now tested both de novo and maintenance methylation activities
AB  - in different cancer cell lines by using a DNA methyltransferase assay with polydldC
AB  - (maintenance) and Drosophila genomic DNA (de novo) as substrates.  One lung cancer cell line,
AB  - H249, had an abnormally high de novo methyltransferase activity.  Interestingly, treatment
AB  - with 5-azadeoxycytidine reduced maintenance methylation activity in this cell, but did not
AB  - affect de novo methylation activity.  Using gel filtration chromatography, we found that the
AB  - peak activities of both maintenance and de novo methylation were detected in the same eluted
AB  - fraction, suggesting that enzymes with similar molecular size, or the same enzyme, are
AB  - responsible for maintenance and de novo methylation activities in this cell line.  Despite
AB  - this in vitro de novo methyltransferase activity, several CpG islands which are commonly
AB  - methylated in cancer remain methylation-free in this  cell line.  Thus, further investigation
AB  - of this cancer cell line H249 may provide us further insights into the mechanisms of
AB  - maintenance and de novo methylation, and their relation to aberrant methylation in cancer.
ER  -

TY  - JOUR
AU  - Jaishankar, J.
AU  - Singh, P.
AU  - Srivastava, P.
TI  - Draft Genome Sequence of a Biodesulfurizing Bacterium, Gordonia sp. Strain IITR100.
JO  - Genome Announcements
PY  - 2017
SP  - e00230
EP  - e00217
VL  - 5
AB  - We report here the whole-genome sequence of a biodesulfurizing bacterium, Gordonia sp. strain
AB  - IITR100. The bacterium has the unique ability to desulfurize
AB  - both aliphatic and aromatic organosulfurs. The draft genome sequence will provide
AB  - insights into the various genes and regulators involved in biodesulfurization and
AB  - other catabolic pathways.
ER  -

TY  - JOUR
AU  - Jaiswal, D.
AU  - Sengupta, A.
AU  - Sohoni, S.
AU  - Sengupta, S.
AU  - Phadnavis, A.G.
AU  - Pakrasi, H.B.
AU  - Wangikar, P.P.
TI  - Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India.
JO  - Sci. Rep.
PY  - 2018
SP  - 16632
EP  - 16632
VL  - 8
AB  - Cyanobacteria provide an interesting platform for biotechnological applications
AB  - due to their efficient photoautotrophic growth, amenability to genetic
AB  - engineering and the ability to grow on non-arable land. An ideal industrial
AB  - strain of cyanobacteria would need to be fast growing and tolerant to high levels
AB  - of temperature, light, carbon dioxide, salt and be naturally transformable. In
AB  - this study, we report Synechococcus elongatus PCC 11801, a strain isolated from
AB  - India that fulfills these requirements. The physiological and biochemical
AB  - characteristics of PCC 11801 under carbon and light-limiting conditions were
AB  - investigated. PCC 11801 shows a doubling time of 2.3 h, that is the fastest
AB  - growth for any cyanobacteria reported so far under ambient CO2 conditions. Genome
AB  - sequence of PCC 11801 shows genome identity of ~83% with its closest neighbors
AB  - Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973. The
AB  - unique attributes of PCC 11801 genome are discussed in light of the physiological
AB  - characteristics that are needed in an industrial strain. The genome of PCC 11801
AB  - shows several genes that do not have homologs in neighbor strains PCC 7942 and
AB  - UTEX 2973, some of which may be responsible for adaptation to various abiotic
AB  - stresses. The remarkably fast growth rate of PCC 11801 coupled with its
AB  - robustness and ease of genetic transformation makes it an ideal candidate for the
AB  - photosynthetic production of fuels and chemicals.
ER  -

TY  - JOUR
AU  - Jaiswal, S.K.
AU  - Saxena, R.
AU  - Mittal, P.
AU  - Gupta, A.
AU  - Sharma, V.K.
TI  - Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman   Islands, India.
JO  - Genome Announcements
PY  - 2017
SP  - e01527
EP  - e01516
VL  - 5
AB  - The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric  region of
AB  - mangroves in the Andaman Islands, is comprised of 3,644,788 bp and
AB  - 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an
AB  - aerobic bacterium capable of performing assimilatory sulfate reduction,
AB  - dissimilatory nitrate reduction, and denitrification.
ER  -

TY  - JOUR
AU  - Jakobsson, H.E.
AU  - Salva-Serra, F.
AU  - Thorell, K.
AU  - Gonzales-Siles, L.
AU  - Boulund, F.
AU  - Karlsson, R.
AU  - Sikora, P.
AU  - Engstrand, L.
AU  - Kristiansson, E.
AU  - Moore, E.R.
TI  - Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.
JO  - Genome Announcements
PY  - 2016
SP  - e00552
EP  - e00516
VL  - 4
AB  - Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human
AB  - respiratory tract. It is associated with otitis media and
AB  - respiratory tract infections. Here, we report the draft genome sequence of M.
AB  - catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of
AB  - 1.89 Mb.
ER  -

TY  - JOUR
AU  - Jakobsson, H.E.
AU  - Salva-Serra, F.
AU  - Thorell, K.
AU  - Karlsson, R.
AU  - Gonzales-Siles, L.
AU  - Boulund, F.
AU  - Engstrand, L.
AU  - Kristiansson, E.
AU  - Moore, E.R.
TI  - Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes  5, 6A, 6B, 18C, 19A, and 23F.
JO  - Genome Announcements
PY  - 2017
SP  - e00125
EP  - e00117
VL  - 5
AB  - Streptococcus pneumoniae is a pathogenic bacterium found most commonly in the respiratory
AB  - tract of humans and is a common cause of pneumonia and bacterial
AB  - meningitis. Here, we report the draft genome sequences of six S. pneumoniae
AB  - strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG
AB  - 35272.
ER  -

TY  - JOUR
AU  - Jakubauskas, A.
TI  - Domain organization analysis of Type II restriction endonucleases.
JO  - Ph.D. Thesis, Vilnius University
PY  - 2007
SP  - 1
EP  - 42
AB  - CONCLUSIONS 1. Two-domain organization of Type IIS REases R.Eco31I and R.Hin4II and Type IIP
AB  - REase R.SdaI was identified by limited proteolysis. 2. The isolated N-domain of R.Eco31I was
AB  - found to be responsible for the specific interaction with DNA. 3. The single HNH nuclease-like
AB  - active site was identified in the C-domain of R.Eco31I. 4. Two R-M systems were cloned in E.
AB  - coli: Hin4II of novel DNA specificity 5'-CCTTC(6/5) and SdaI that recognizes and cleave eight
AB  - base DNA target, 5'-CCTGCA^GG. 5. The HNH nuclease-like active site was identified in the
AB  - C-domain of R.Hin4II by bioinformatic methods.
ER  -

TY  - JOUR
AU  - Jakubauskas, A.
AU  - Dauksaite, V.
TI  - Construction and analysis of chimeric enzymes between type IIs restriction endonucleases Alw26I, Eco31I and Esp3I.
JO  - Biologija
PY  - 1997
SP  - 26
EP  - 30
VL  - 1
AB  - Conserved regions I, III and IV were swapped between restriction endonucleases Alw26I, Eco31I
AB  - and Esp3I, and 16 chimeric enzymes were constructed.  Only the hybrid enzyme
AB  - Eco31I-(N-esp-Mva1269I) containing the N-terminus and conserved region I from Esp3I and the
AB  - remaining part from Eco31I revealed the enzymatic activity of Eco31I specificity in crude
AB  - lysate.  This indicates that the conserved region I belongs to the structural elements of
AB  - Eco31I.  The four hybrid enzymes with swapped intermediate sequences between conserved regions
AB  - III and IV and/or conserved region IV induce an SOS response in E. coli ER1992, which can be
AB  - blocked with M.Alw26I methylase.  These results suggest that DNA lesions incurred by hybrid
AB  - enzymes are site specific.
ER  -

TY  - JOUR
AU  - Jakubauskas, A.
AU  - Giedriene, J.
AU  - Bujnicki, J.M.
AU  - Janulaitis, A.
TI  - Identification of a Single HNH Active Site in Type IIS Restriction Endonuclease Eco31I.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 157
EP  - 169
VL  - 370
AB  - Type IIS restriction endonuclease Eco31I is a "short-distance cutter", which cleaves DNA
AB  - strands close to its recognition sequence, 5'-GGTCTC(1/5). Previously, it has been proposed
AB  - that related endonucleases recognizing a common sequence core GTCTC possess two active sites
AB  - for cleavage of both strands in the DNA substrate. Here, we present bioinformatic
AB  - identification and experimental evidence for a single nuclease active site. We identified a
AB  - short region of homology between Eco31I and HNH nucleases, constructed a three-dimensional
AB  - model of the putative catalytic domain and validated our predictions by random and
AB  - site-specific mutagenesis. The restriction mechanism of Eco31I is suggested by analogy to the
AB  - mechanisms of phage T4 endonuclease VII and homing endonuclease I-PpoI. We propose that
AB  - residues D311 and N334 coordinate the cofactor. H312 acts as a general base-activating water
AB  - molecule for the nucleophilic attack. K337 together with R340 and D345 are located in close
AB  - proximity to the active center and are essential for correct folding of catalytic motif, while
AB  - D345 together with R264 and D273 could be directly involved in DNA binding. We also predict
AB  - that the Eco31I catalytic domain contains a putative Zn-binding site, which is essential for
AB  - its structural integrity. Our results suggest that the HNH-like active site is involved in the
AB  - cleavage of both strands in the DNA substrate. On the other hand, analysis of site-specific
AB  - mutants in the region, previously suggested to harbor the second active site, revealed its
AB  - irrelevance to the nuclease activity. Thus, our data argue against the earlier prediction and
AB  - indicate the presence of a single conserved active site in type IIS restriction endonucleases
AB  - that recognize common sequence core GTCTC.
ER  -

TY  - JOUR
AU  - Jakubauskas, A.
AU  - Kriukiene, E.
AU  - Trinkunaite, L.
AU  - Sapranauskas, R.
AU  - Jurenaite-Urbanaviciene, S.
AU  - Lubys, A.
TI  - Bioinformatic and partial functional analysis of pEspA and pEspB, two plasmids from Exiguobacterium arabatum sp nov RFL1109.
JO  - Plasmid
PY  - 2009
SP  - 52
EP  - 64
VL  - 61
AB  - The complete nucleotide sequences of two plasmids from Exiguobacterium arabatum sp. nov.
AB  - RFL1109, pEspA (4563 bp) and pEspB (.38,945 bp), have
AB  - been determined. Five ORFs were identified in the pEspA plasmid, and
AB  - putative functions were assigned to two of them. Using deletion mapping
AB  - approach, the Rep-independent replication region of pEspA, which
AB  - functions in Bacillus subtilis, was localized within a 0.6 kb DNA
AB  - region. Analysis of the pEspB sequence revealed 42 ORFs. From these,
AB  - function of two genes encoding enzymes of the Lsp11091
AB  - restriction-modification system was confirmed experimentally, while
AB  - putative functions of another 18 ORFs were suggested based on
AB  - comparative analysis. Three functional regions have been proposed for
AB  - the pEspB plasmid: the putative conjugative transfer region, the region
AB  - involved in plasmid replication and maintenance, and the region
AB  - responsible for transposition of the IS21 family-like transposable
AB  - elements.
ER  -

TY  - JOUR
AU  - Jakubauskas, A.
AU  - Sasnauskas, G.
AU  - Giedriene, J.
AU  - Janulaitis, A.
TI  - Domain organization and functional analysis of type IIS restriction endonuclease Eco31I.
JO  - Biochemistry
PY  - 2008
SP  - 8546
EP  - 8556
VL  - 47
AB  - Type IIS restriction endonuclease Eco31I harbors a single HNH active site and cleaves both DNA
AB  - strands close to its recognition sequence,
AB  - 5'-GGTCTC(1/5). A two-domain organization of Eco31I was determined by
AB  - limited proteolysis. Analysis of proteolytic fragments revealed that
AB  - the N-terminal domain of Eco31I is responsible for the specific DNA
AB  - binding, while the C-terminal domain contains the HNH nuclease-like
AB  - active site. Gel-shift and gel-filtration experiments revealed that a
AB  - monomer of the N-terminal domain of Eco31I is able to bind a single
AB  - copy of cognate DNA. However, in contrast to other studied type IIS
AB  - enzymes, the isolated catalytic domain of Eco31I was inactive.
AB  - Steady-state and transient kinetic analysis of Eco31I reactions was
AB  - inconsistent with dimerization of Eco31I on DNA. Thus, we propose that
AB  - Eco31I interacts with individual copies of its recognition sequence in
AB  - its monomeric form and presumably remains a monomer as it cleaves both
AB  - strands of double-stranded DNA. The domain organization and reaction
AB  - mechanism established for Eco31I should be common for a group of
AB  - evolutionary related type IIS restriction endonucleases Alw26I, BsaI,
AB  - BsmAI, BsmBI and Esp3I that recognize DNA sequences bearing the common
AB  - pentanucleotide 5'-GTCTC.
ER  -

TY  - JOUR
AU  - Jalan, N.
AU  - Aritua, V.
AU  - Kumar, D.
AU  - Yu, F.
AU  - Jones, J.B.
AU  - Graham, J.H.
AU  - Setubal, J.C.
AU  - Wang, N.
TI  - Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1 causing citrus bacterial spot and related strains provides insights into  virulence and host-specificity.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6342
EP  - 6357
VL  - 193
AB  - Xanthomonas axonopodis pv. citrumelo (Xacm) is a citrus pathogen causing citrus bacterial spot
AB  - disease that is geographically restricted within the
AB  - state of Florida. Illumina, 454 sequencing and optical mapping were used
AB  - to obtain a complete genome sequence of Xacm strain F1, 4.9Mb in size. The
AB  - strain lacks plasmids as compared to other citrus pathogens. Phylogenetic
AB  - analysis revealed that this pathogen is very close to the tomato bacterial
AB  - spot pathogen Xcv 85-10 with a completely different host range. We also
AB  - compared Xacm to the genome of citrus canker pathogen Xac 306. Comparative
AB  - genomic analysis showed differences in several gene clusters like Type 3
AB  - effectors, Type 4 secretion system, lipopolysaccharide synthesis and
AB  - others. In addition to pthA, effectors such as xopE3, xopAI and hrpW were
AB  - absent in Xacm while present in Xac. These effectors might be responsible
AB  - for survival and reduced virulence of this pathogen on citrus compared to
AB  - Xac. We also identified unique effectors in Xacm that may be related to
AB  - the different host range as compared to Xac. Xacm also lacks various genes
AB  - such as syrE1, syrE2 and RTX toxin family genes, which were present in
AB  - Xac. These may be associated with distinct virulence of Xacm and Xac.
AB  - Comparison of the complete genome sequence of Xacm to Xac and Xcv provides
AB  - valuable insights into the mechanism of bacterial virulence and
AB  - host-specificity.
ER  -

TY  - JOUR
AU  - Jalan, N.
AU  - Kumar, D.
AU  - Yu, F.
AU  - Jones, J.B.
AU  - Graham, J.H.
AU  - Wang, N.
TI  - Complete Genome Sequence of Xanthomonas citri subsp. citri Strain Aw12879, a Restricted-Host-Range Citrus Canker-Causing Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00235
EP  - e00213
VL  - 1
AB  - Xanthomonas citri subsp. citri causes citrus canker. The Asiatic strain has a broad host
AB  - range, whereas the Wellington variant has a restricted host range.
AB  - Here, we present the complete genome of X. citri subsp. citri strain A(W)12879.
AB  - This study lays the foundation to further characterize the mechanisms for
AB  - virulence and host range of X. citri.
ER  -

TY  - JOUR
AU  - Jamoussi, K.
AU  - Lazowska, J.
TI  - Intragenic suppressors that restore the splicing and homing activities of the protein encoded by the second intron of the Saccharomyces capensis cyt b gene.
JO  - Curr. Genet.
PY  - 2000
SP  - 276
EP  - 282
VL  - 38
AB  - The second (bi2) intron of the mitochondrial cyt b gene from Saccharomyces capensis encodes a
AB  - bifunctional protein which acts both
AB  - as a maturase, promoting intron splicing, and as a homing-endonuclease,
AB  - I-ScaI, promoting intron mobility. In this work we isolated and
AB  - characterized revertants from a respiratory-deficient mutant in which
AB  - both functions of the protein have been lost. Intragenic revertants
AB  - resulted mainly from monosubstitutions in the mutated codon and in one
AB  - case from a distant second site mutation. All novel variants of the S.
AB  - capensis bi2 intron-encoded protein are competent for the maturase
AB  - activity but only two of them can partially complement the homing
AB  - function.
ER  -

TY  - JOUR
AU  - Jana, G.A.
AU  - Al-Yahyai, R.
AU  - Yaish, M.W.
TI  - Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity.
JO  - Genome Announcements
PY  - 2017
SP  - e01247
EP  - e01217
VL  - 5
AB  - Microbacterium sp. strain Yaish 1 is a rhizospheric bacterium isolated from date  palm
AB  - orchards with high soil salinity. The genome was sequenced, and genes coding
AB  - for growth-promoting 1-aminocyclopropane-1-carboxylate (ACC) deaminase,
AB  - siderophore-producing proteins, and tryptophan biosynthesis proteins were
AB  - identified. Here, we report the draft whole-genome sequencing of the strain.
ER  -

TY  - JOUR
AU  - Jancovich, J.K.
AU  - Bremont, M.
AU  - Touchman, J.W.
AU  - Jacobs, B.L.
TI  - Evidence for Multiple Recent Host Species Shifts among the Ranaviruses (Family Iridoviridae).
JO  - J. Virol.
PY  - 2010
SP  - 2636
EP  - 2647
VL  - 84
AB  - Members of the genus Ranavirus (family Iridoviridae) have been recognized
AB  - as major viral pathogens of cold-blooded vertebrates. Ranaviruses have
AB  - been associated with amphibians, fish, and reptiles. At this time, the
AB  - relationships between ranavirus species are still unclear. Previous
AB  - studies suggested that ranaviruses from salamanders are more closely
AB  - related to ranaviruses from fish than they are to ranaviruses from other
AB  - amphibians, such as frogs. Therefore, to gain a better understanding of
AB  - the relationships among ranavirus isolates, the genome of epizootic
AB  - hematopoietic necrosis virus (EHNV), an Australian fish pathogen, was
AB  - sequenced. Our findings suggest that the ancestral ranavirus was a fish
AB  - virus and that several recent host shifts have taken place, with
AB  - subsequent speciation of viruses in their new hosts. The data suggesting
AB  - several recent host shifts among ranavirus species increase concern that
AB  - these pathogens of cold-blooded vertebrates may have the capacity to cross
AB  - numerous poikilothermic species barriers and the potential to cause
AB  - devastating disease in their new hosts.
ER  -

TY  - JOUR
AU  - Jancovich, J.K.
AU  - Mao, J.
AU  - Chinchar, V.G.
AU  - Wyatt, C.
AU  - Case, S.T.
AU  - Kumar, S.
AU  - Valente, G.
AU  - Subramanian, S.
AU  - Davidson, E.W.
AU  - Collins, J.P.
AU  - Jacobs, B.L.
TI  - Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America.
JO  - Virology
PY  - 2003
SP  - 90
EP  - 103
VL  - 316
AB  - Disease is among the suspected causes of amphibian population declines, and an iridovirus and
AB  - a chytrid fungus are the primary pathogens
AB  - associated with amphibian mortalities. Ambystoma tigrinum virus (ATV) and
AB  - a closely related strain, Regina ranavirus (RRV), are implicated in
AB  - salamander die-offs in Arizona and Canada, respectively. We report the
AB  - complete sequence of the ATV genome and partial sequence of the RRV
AB  - genome. Sequence analysis of the ATV/RRV genomes showed marked similarity
AB  - to other ranaviruses, including tiger frog virus (TFV) and frog virus 3
AB  - (FV3), the type virus of the genus Ranavirus (family Iridoviridae), as
AB  - well as more distant relationships to lymphocystis disease virus, Chilo
AB  - iridescent virus, and infectious spleen and kidney necrosis virus.
AB  - Putative open reading frames (ORFs) in the ATV sequence identified 24
AB  - genes that appear to control virus replication and block antiviral
AB  - responses. In addition, >50 other putative genes, homologous to ORFs in
AB  - other iridoviral genomes but of unknown function, were also identified.
AB  - Sequence comparison performed by dot plot analysis between ATV and itself
AB  - revealed a conserved 14-bp palindromic repeat within most intragenic
AB  - regions. Dot plot analysis of ATV vs RRV sequences identified several
AB  - polymorphisms between the two isolates. Finally, a comparison of ATV and
AB  - TFV genomic sequences identified genomic rearrangements consistent with
AB  - the high recombination frequency of iridoviruses. Given the adverse
AB  - effects that ranavirus infections have on amphibian and fish populations,
AB  - ATV/RRV sequence information will allow the design of better diagnostic
AB  - probes for identifying ranavirus infections and extend our understanding
AB  - of molecular events in ranavirus-infected cells.
ER  -

TY  - JOUR
AU  - Jang, H. et al.
TI  - Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 35
EP  - 35
VL  - 13
AB  - Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening
AB  - infantile infections, such as meningitis, septicemia, and necrotizing
AB  - enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound
AB  - infections in adults. Here, we report 26 draft genome sequences of C. sakazakii,
AB  - which were obtained from dried spices from the USA, the Middle East, China, and
AB  - the Republic of Korea. The average genome size of the C. sakazakii genomes was
AB  - 4393 kb, with an average of 4055 protein coding genes, and an average genome G +
AB  - C content of 56.9%. The genomes contained genes related to carbohydrate transport
AB  - and metabolism, amino acid transport and metabolism, and cell wall/membrane
AB  - biogenesis. In addition, we identified genes encoding proteins involved in
AB  - osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as
AB  - virulence-related and heat shock-related proteins. Interestingly, a metabolic
AB  - island comprised of a variably-sized xylose utilization operon was found within
AB  - the spice-associated C. sakazakii genomes, which supports the hypothesis that
AB  - plants may serve as transmission vectors or alternative hosts for Cronobacter
AB  - species. The presence of the genes identified in this study can support the
AB  - remarkable phenotypic traits of C. sakazakii such as the organism's capabilities
AB  - of adaptation and survival in response to adverse growth environmental conditions
AB  - (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses
AB  - provided insights into many aspects of physiology and evolutionary history of
AB  - this important foodborne pathogen.
ER  -

TY  - JOUR
AU  - Jang, H.
AU  - Addy, N.
AU  - Ewing, L.
AU  - Jean-Gilles, B.J.
AU  - Lee, Y.
AU  - Woo, J.
AU  - Negrete, F.
AU  - Finkelstein, S.
AU  - Tall, B.D.
AU  - Lehner, A.
AU  - Eshwar, A.
AU  - Gopinath, G.R.
TI  - Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments.
JO  - Genome Announcements
PY  - 2018
SP  - e00223
EP  - e00218
VL  - 6
AB  - Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from
AB  - foods of plant origin and dried-food manufacturing facilities.
AB  - Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb
AB  - and 3,977 to 4,256 gene-coding sequences with G+C contents of approximately
AB  - 57.0%.
ER  -

TY  - JOUR
AU  - Jang, J.Y.
AU  - Lim, H.I.
AU  - Park, H.W.
AU  - Choi, H.J.
AU  - Kim, T.W.
AU  - Kang, M.
AU  - Lee, J.H.
TI  - Draft Genome Sequence of Lactobacillus plantarum wikim18, Isolated from Korean Kimchi.
JO  - Genome Announcements
PY  - 2014
SP  - e00467
EP  - e00414
VL  - 2
AB  - This report describes the draft genome sequence of Lactobacillus plantarum strain wikim18,
AB  - isolated from the traditional Korean food kimchi. The reads generated by
AB  - Ion Torrent PGM were assembled into 327 contigs. RAST annotation of the genome
AB  - revealed 12 tRNAs and 3,316 protein-coding gene sequences.
ER  -

TY  - JOUR
AU  - Jang, K.H.
AU  - Britz, M.L.
TI  - Improved electrotransformation frequencies of Corynebacterium glutamicum using cell-surface mutantstransformation via electroporation using plasmid DNA.
JO  - Biotechnol. Lett.
PY  - 2000
SP  - 539
EP  - 545
VL  - 22
AB  - 6 Strains of Corynebacterium glutamicum were examined for electrotransformation using
AB  - heterologous or homologous DNA. These were:
AB  - AS019, a spontaneous rifampicin-resistant strain of ATCC 13059; MLB133
AB  - and MLB194, auxotrophic cell surface mutants derived from ATCC 13059 by
AB  - exposure to ethylmethane sulfonate; ATCC 13032; and RM3 and RM4,
AB  - restriction modification mutants of ATCC 13032. Heterologous DNA was
AB  - plasmid pCSL17 purified from Escherichia coli LE392. Homologous DNA was
AB  - pCSL17 from C. glutamicum AS019. Transformation by electroporation
AB  - involved a single pulse (2.5 kV, 25 uF) using a Gene-Pulser system,
AB  - with subsequent culture on LBG medium containing glycine and
AB  - isonicotinic acid hydrazide (INH). Transformation efficiency of MLB133
AB  - was up to 100-fold higher than for AS019 and, when using heterologous
AB  - derived DNA, MLB133 showed efficiencies comparable to, or better than,
AB  - RM3 and RM4, demonstrating the importance of cell surface structures in
AB  - impeding DNA uptake. MLB133 had a thinner cell wall than AS019, and
AB  - growth in glycine or INH further diminished its thickness. The impact
AB  - of glycine and INH on the mycolic composition of the strains is
AB  - discussed. (20 ref)
ER  -

TY  - JOUR
AU  - Jang, K.H.
AU  - Chambers, P.
AU  - Britz, M.L.
TI  - Analysis of nucleotide methylation in DNA from Corynebacterium glutamicum and related species.
JO  - FEMS Microbiol. Lett.
PY  - 1996
SP  - 309
EP  - 315
VL  - 136
AB  - Plasmid DNA (pCSL17) isolated from Corynebacterium glutamicum transformed recipient McrBC+
AB  - strains of Escherichia coli with lower efficiency than McrBC- strains, confirming a previous
AB  - report by Tauch et al. which inferred that C. glutamicum DNA contains methylcytidine.
AB  - Analysis of nucleotides in C. glutamicum-derived chromosomal and plasmid DNA failed to detect
AB  - significant levels of methylated adenosine, but methylated cytidine was readily detected.
AB  - Restriction enzymes which are inhibited by the presence of methylcytidine in their recognition
AB  - sequence failed to cut pCSL17 from C. glutamicum, whereas enzymes which require methylation at
AB  - adenosine in GATC sequences failed to cut.  Failure of HaeIII to cut two specific sites of C.
AB  - glutamicum-derived pCSL17 identified the first cytidine in the sequence GGCCGC as one target
AB  - of methylation in this species, which contains the methyltransferase recognition sequence.
AB  - Although Brevibacterium lactofermentum-derived DNA showed a similar methylation pattern by
AB  - HPLC analysis, HaeIII cleaved these GGCCGC sites, suggesting differences in the specificity of
AB  - methylation between these two species.  Results for all analyses of B. flavum DNA were
AB  - identical to those for C. glutamicum.
ER  -

TY  - JOUR
AU  - Jang, K.H.
AU  - Chambers, P.J.
AU  - Britz, M.L.
TI  - Identification of a sequence containing methylated cytidine in Corynebacterium glutamicum and Brevibacterium flavum using bisulfite DNA derivatization and sequencing.
JO  - J. Microbiol. Biotechnol.
PY  - 2001
SP  - 819
EP  - 824
VL  - 11
AB  - The principal DNA modification systems of the amino-acid-producing bacteria Corynebacterium
AB  - glutamicum AS019, Brevibacterium flavum BF4,
AB  - and B. lactofermentum BL1 was investigated using two approaches;
AB  - digestion of plasmid DNA isolated from these species using TseI and
AB  - Fnu4HI, and sequence analysis of the putative methyltransferase target
AB  - sites following the derivatization of DNA using metabisulfite
AB  - treatment. The C. glutamicum and B. flavum strains showed similar
AB  - digestion patterns to the two enzymes, indicating that the target for
AB  - cytidine methyltransferase recognizes 5'-GCSGC-3' (where S is either G
AB  - or C). Mapping the methylated cytidine sites by bisulfite
AB  - derivatization, followed by PCR amplification and sequencing, was only
AB  - possible when the protocol included an additional step eliminating any
AB  - underivatized DNA after PCR amplification, thereby indicating that the
AB  - derivatization was not 100% efficient. This may have been due to the
AB  - high G-C content of this genus. It was confirmed that C. glutamicum
AB  - AS019 and B. flavum BF4 methylated the cytidine in the Gm(5)CCGC
AB  - sequences, yet there were no similar patterns of methylation in B.
AB  - lactofermentum, which was consistent with the distinctive degradation
AB  - pattern seen for the above enzymes. These findings demonstrate the
AB  - successful application of a modified bisulfite derivatization method
AB  - with the Corynebacterium species for determining methylation patterns,
AB  - and showed that different species in the genus contain distinctive
AB  - restriction and modification systems.
ER  -

TY  - JOUR
AU  - Jang, K.J.
AU  - Lee, H.
AU  - Jin, H.L.
AU  - Park, Y.
AU  - Nam, J.M.
TI  - Restriction-Enzyme-Coded Gold-Nanoparticle Probes for Multiplexed DNA Detection.
JO  - Small
PY  - 2009
SP  - 2665
EP  - 2668
VL  - 5
AB  - The development of a multiplexed DNA detection assay has been of great interest in
AB  - gene-expression profiling, drug screening, clinical diagnostics, and the detection of
AB  - pathogens. However, it is still a challenging task to detect many different targets in one
AB  - sample while retaining high target sensitivity. Restriction enzymes that can recognize and
AB  - cleave specific double-stranded DNA (dsDNA) sequences have been widely used in molecular
AB  - biology and genetic engineering.  Over 2000 site-specific endonucleases have been identified
AB  - so far. Restriction enzymes have been used with DNA-modified gold nanoparticles (AuNPs) in
AB  - various applications, such as release of the particle from the surface, conformational effects
AB  - of nanoparticles on bioactivity, nanoparticle assembly and disassembly, and optimal conditions
AB  - of efficient biomanipulation. The availability of numerous enzymatic restriction DNA sequences
AB  - as well as the high specificity of restriction enzymes could be very useful aspects in a
AB  - multiplexed DNA detection assay.
ER  -

TY  - JOUR
AU  - Jang, S.H.
AU  - Kim, J.
AU  - Kim, J.
AU  - Hong, S.
AU  - Lee, C.
TI  - Genome Sequence of Cold-Adapted Pseudomonas mandelii Strain JR-1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3263
EP  - 3263
VL  - 194
AB  - Pseudomonas mandelii is a cold-adapted bacterium that can grow at 4 degrees C but not at 37
AB  - degrees C. Here we report the draft genome sequence of P. mandelii
AB  - strain JR-1.
ER  -

TY  - JOUR
AU  - Jang, S.H.
AU  - Yoon, B.H.
AU  - Chang, H.I.
TI  - Complete nucleotide sequence of the temperate bacteriophage LBR48, a new member of the family Myoviridae.
JO  - Arch. Virol.
PY  - 2011
SP  - 319
EP  - 322
VL  - 156
AB  - The complete genomic sequence of LBR48, a temperate bacteriophage induced
AB  - from a lysogenic strain of Lactobacillus brevis, was found to be 48,211
AB  - nucleotides long and to contain 90 putative open reading frames. Based on
AB  - structural characteristics obtained from microscopic analysis and nucleic
AB  - acid sequence determination, phage LBR48 can be classified as a member of
AB  - the family Myoviridae. Analysis of the genome showed the conserved gene
AB  - order of previously reported phages of the family Siphoviridae from lactic
AB  - acid bacteria, despite low nucleotide sequence similarity. Analysis of the
AB  - attachment sites revealed 15-nucleotide-long core sequences.
ER  -

TY  - JOUR
AU  - Jang, Y.
AU  - Oh, H.M.
AU  - Kang, I.
AU  - Lee, K.
AU  - Yang, S.J.
AU  - Cho, J.C.
TI  - Genome sequence of strain IMCC3088, a proteorhodopsin-containing marine bacterium belonging to the OM60/NOR5 clade.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3415
EP  - 3416
VL  - 193
AB  - Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5
AB  - clade and is closely related to clone OM241,
AB  - Congregibacter litoralis, and strain HTCC2080. Here the genome sequence of
AB  - strain IMCC3088 is presented, showing the absence of photosynthetic gene
AB  - clusters and the presence of proteorhodopsin.
ER  -

TY  - JOUR
AU  - Jang, Y.
AU  - Oh, H.M.
AU  - Kim, H.
AU  - Kang, I.
AU  - Cho, J.C.
TI  - Genome Sequence of Strain IMCC1989, a Novel Member of the Marine Gammaproteobacteria.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3672
EP  - 3673
VL  - 193
AB  - Strain IMCC1989 is a novel member of the oligotrophic marine Gammaproteobateria (OMG) group,
AB  - and is closely related with a symbiont
AB  - group of genera Teredinibacter and 'Candidatus Endobugula'. Here we
AB  - present the genome sequence of strain IMCC1989 that was isolated from the
AB  - Yellow Sea by using dilution-to-extinction culturing.
ER  -

TY  - JOUR
AU  - Jangam, A.K.
AU  - Bhuvaneswari, T.
AU  - Krishnan, A.N.
AU  - Katneni, V.K.
AU  - Avunje, S.
AU  - Grover, M.
AU  - Kumar, S.
AU  - Alavandi, S.V.
AU  - Vijayan, K.K.
TI  - Draft Genome Sequence of Vibrio parahaemolyticus Strain VP14, Isolated from a Penaeus vannamei Culture Farm.
JO  - Genome Announcements
PY  - 2018
SP  - e00149
EP  - e00118
VL  - 6
AB  - Here, we report the draft genome sequence of an isolate of Vibrio parahaemolyticus, VP14,
AB  - recovered from the gut of Penaeus vannamei shrimp farmed
AB  - in southern India. The genome of VP14 comprised 5,224,046 bp with a GC content of
AB  - 45.3% and contained 5,326 genes, including 4,972 coding sequences.
ER  -

TY  - JOUR
AU  - Jangir, P.K.
AU  - Singh, A.
AU  - Shivaji, S.
AU  - Sharma, R.
TI  - Genome Sequence of the Alkaliphilic Bacterium Nitritalea halalkaliphila Type Strain LW7, Isolated from Lonar Lake, India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5688
EP  - 5689
VL  - 194
AB  - An alkaliphilic bacterium, Nitritalea halalkaliphila LW7, which belongs to the family
AB  - Cyclobacteriacae in the phylum Bacteroidetes, was isolated from Lonar Lake
AB  - in Maharastra, India. Here we announce the draft genome sequence of the type
AB  - strain LW7, which contains 3,633,701 bp with a G+C content of 48.58%.
ER  -

TY  - JOUR
AU  - Jankowitsch, F.
AU  - Schwarz, J.
AU  - Ruckert, C.
AU  - Gust, B.
AU  - Szczepanowski, R.
AU  - Blom, J.
AU  - Pelzer, S.
AU  - Kalinowski, J.
AU  - Mack, M.
TI  - The genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6818
EP  - 6827
VL  - 194
AB  - Streptoymces davawensis JCM 4913 synthesizes the antibiotic roseoflavin, a structural
AB  - riboflavin (vitamin B(2)) analog. Here we report the 9,466,619 base
AB  - pair linear chromosome of S. davawensis JCM 4913 and a 89,331 base pair linear
AB  - plasmid. The sequence has an average G + C content of 70.58% and contains six
AB  - rRNA operons (16S-23S-5S) and 69 tRNA genes. The 8,616 predicted protein-coding
AB  - sequences include 32 clusters coding for secondary metabolites several of which
AB  - are unique to S. davawensis. The chromosome contains long terminal inverted
AB  - repeats of 33,255 bp each and atypical telomeres. Sequence analysis with regard
AB  - to riboflavin biosynthesis revealed three different patterns of gene organization
AB  - in Streptomyces species. Heterologous expression of a set of genes present on a
AB  - subgenomic fragment of S. davawensis resulted in the production of roseoflavin by
AB  - the host Streptomyces coelicolor M1152. Phylogenetic analysis revealed that S.
AB  - davawensis is a close relative to Streptomyces cinnabarinus and, much to our
AB  - surprise, we found that the latter bacterium is a roseoflavin producer as well.
ER  -

TY  - JOUR
AU  - Janosi, L.
AU  - Kaji, A.
TI  - Molecular cloning and expression of T-even phage specific restriction enzyme coded by drug resistance plasmid Rts1.
JO  - FASEB J.
PY  - 1992
SP  - A216
EP  - A216
VL  - 6
AB  - Rts1 is a drug resistance factor which restricts the growth of T-even phages at
AB  - 32C but not at 42C (Ishaq & Kaji, 1980, J. Biol. Chem. 255:4040).  Using
AB  - ampicillin and E. coli bacteriophage T4 double selection, a 2.4 kilobase (kb)
AB  - EcoRI fragment of Rts1 DNA was cloned into pUC19 and pBluescript SK+ plasmids.
AB  - The determinant carried by the insert codes for restriction of multiplication
AB  - of T-even phages in E. coli 20SO.  The restriction phenomenon appeared
AB  - independently from the orientation of the insert relative to the lac promoter
AB  - of the carrier plasmids suggesting that the expression of the responsible
AB  - determinant was controlled by its own promoter.  Nucleotide squence
AB  - determination of the entire insert revealed the presence of two larger open
AB  - reading frames (ORFs), both on the same DNA strand.  One, coding for 294 amino
AB  - acids, proved to be related to phage restriction because deletions within this
AB  - ORF by various restriction endonucleases inactivated the activity.  Unusaul
AB  - feature of this ORF is that the distance between the most likely S.D. sequence
AB  - and the ATG codon spans only two nucleotides.
ER  -

TY  - JOUR
AU  - Janosi, L.
AU  - Yonemitsu, H.
AU  - Hong, H.
AU  - Kaji, A.
TI  - Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 45
EP  - 61
VL  - 242
AB  - The kanamycin resistance plasmid Rts1 restricts the growth of bacteriophage T2, T4 and T6. The
AB  - DNA of these phage contains hydroxymethylcytosine (HMC) in place of regular cytosine and is
AB  - modified by glycosylation. When HMC is not glucosylated, as in the DNA of glucosyl
AB  - transferase-deficient T4 phage, this restriction becomes less apparent, a phenomenon not
AB  - observed with any other known restriction systems. On the other hand, glucosylation of HMC to
AB  - T6 phage leads to a less efficient restriction, while restriction of bacteriophage T2 remains
AB  - unchanged. The modulating effect of glucose cannot be seen when cells contain a large amount
AB  - of this enzyme, as in the case when multiple copies of its determinant are present in the
AB  - cells. T-odd phage and bacteriophage lambda are not restricted by Rts1 suggesting that the
AB  - restriction is specific to DNA containing HMC. The restriction phenotype is due to a single
AB  - gene coding for a polypeptide of 293 amino acids. This enzyme has been named PvuRts1I. A gene
AB  - with the sequence motifs similar to modification enzymes was found upstream of the gene coding
AB  - for PvuRts1I. This gene, however, neither modifies the restriction phenotype of PvuRts1I, nor
AB  - codes for detectable modification enzyme. T4 mutants with increased resistance to PvuRts1I
AB  - appear to have deficiency in their beta-glucosyl transferase enzyme.
ER  -

TY  - JOUR
AU  - Jans, C.
AU  - Lacroix, C.
AU  - Follador, R.
AU  - Stevens, M.J.
TI  - Complete Genome Sequence of the Probiotic Bifidobacterium thermophilum Strain RBL67.
JO  - Genome Announcements
PY  - 2013
SP  - e00191
EP  - e00113
VL  - 1
AB  - Bifidobacterium thermophilum RBL67, an isolate from infant feces, exhibits bacteriocin-like
AB  - antimicrobial activity against Listeria spp. and Salmonella spp.
AB  - and protects HT29-MTX cells against Salmonella infection. Here, the complete
AB  - genome sequence of the probiotic B. thermophilum strain RBL67 is presented.
ER  -

TY  - JOUR
AU  - Jans, C.
AU  - Lagler, S.
AU  - Lacroix, C.
AU  - Meile, L.
AU  - Stevens, M.J.A.
TI  - Complete Genome Sequences of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311, Isolated from Fermented Meat Products.
JO  - Genome Announcements
PY  - 2017
SP  - e00915
EP  - e00917
VL  - 5
AB  - The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311
AB  - were sequenced and assembled using PacBio single-molecule
AB  - real-time (SMRT) technology. The strains were isolated from Swiss fermented meat
AB  - products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95
AB  - Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Abadjieva, A.
AU  - Firman, K.
TI  - The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 977
EP  - 991
VL  - 257
AB  - In this paper we describe a two-plasmid system which allows over-production of
AB  - the R.EcoR124I restriction endonuclease.  The endonuclease has been purified to homogeneity in
AB  - milligram amounts and has been shown to be fully active for both restriction and modification.
AB  - Unexpectedly, the enzyme was found to require only ATP and Mg2+ for ATPase activity and
AB  - DNA cleavage; S-adenosyl methionine (SAM), which has been described as a cofactor of type I
AB  - restriction enzymes, is not required by R.EcoR124I.  However, SAM was found to stimulate the
AB  - rate of ATPase activity and DNA cleavage.  This may occur through an increase in specific DNA
AB  - binding by R.EcoR124I in the presence of SAM, as indicated by our surface plasmon resonance
AB  - experiments.  These functional differences from the well described R.EcoKI restriction
AB  - endonuclease are reflected in a possible structural difference between the two enzymes, namely
AB  - that
AB  - the stoichiometry of R.EcoR124I appears to be R1M2S1 while that of R.EcoKI is R2M2S1.
AB  - Supercoiled DNA with one or two SR124I recognition sites is cleaved by the same mechanism
AB  - inferring cooperation between specifically bound and excess enzymes.  Nicked-circle DNA is an
AB  - intermediate of cleavage reaction.  Cleavage of DNA was inhibited by an increased degree of
AB  - negative supercoiling, which may reflect an increased difficulty for the enzyme to translocate
AB  - the
AB  - DNA.  Hemi-methylated DNA was the preferred substrate for methylation.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Bickle, T.A.
TI  - DNA supercoiling during ATP-dependent DNA translocation by the type I restriction enzyme EcoAI.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 1089
EP  - 1099
VL  - 295
AB  - Type I restriction enzymes cleave DNA at non-specific sites far from their recognition
AB  - sequence as a consequence of ATP-dependent DNA translocation past the
AB  - enzyme. During this reaction, the enzyme remains bound to the recognition sequence and
AB  - translocates DNA towards itself simultaneously from both directions, generating
AB  - DNA loops, which appear to be supercoiled when visualised by electron microscopy. To further
AB  - investigate the mechanism of DNA translocation by type I restriction
AB  - enzymes, we have probed the reaction intermediates with DNA topoisomerases. A DNA
AB  - cleavage-deficient mutant of EcoAI, which has normal DNA translocation and
AB  - ATPase activities, was used in these DNA supercoiling assays. In the presence of eubacterial
AB  - DNA topoisomerase I, which specifically removes negative supercoils, the
AB  - EcoAI mutant introduced positive supercoils into relaxed plasmid DNA substrate in a reaction
AB  - dependent on ATP hydrolysis. The same DNA supercoiling activity followed by
AB  - DNA cleavage was observed with the wild-type EcoAI endonuclease. Positive supercoils were not
AB  - seen when eubacterial DNA topoisomerase I was replaced by eukaryotic
AB  - DNA topoisomerase I, which removes both positive and negative supercoils. Furthermore,
AB  - addition of eukaryotic DNA topoisomerase I to the product of the supercoiling
AB  - reaction resulted in its rapid relaxation. These results are consistent with a model in which
AB  - EcoAI translocation along the helical path of closed circular DNA duplex
AB  - simultaneously generates positive supercoils ahead and negative supercoils behind the moving
AB  - complex in the contracting and expanding DNA loops, respectively. In addition,
AB  - we show that the highly positively supercoiled DNA generated by the EcoAI mutant is cleaved by
AB  - EcoAI wild-type endonuclease much more slowly than relaxed DNA. This
AB  - suggests that the topological changes in the DNA substrate associated with DNA translocation
AB  - by type I restriction enzymes do not appear to be the trigger for DNA
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Bickle, T.A.
TI  - The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutations of its polypeptide chain.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 937
EP  - 948
VL  - 284
AB  - The DNA specificity subunit (HsdS) of type I restriction-modification enzymes is composed of
AB  - two independent target recognition domains and several regions whose amino acid sequence is
AB  - conserved within an enzyme family.  The conserved regions participate in intersubunit
AB  - interactions with two modification subunits (HsdM) and two restriction subunits (HsdR) to form
AB  - the complete endonuclease.  It has been proposed that the domains of the HsdS subunit have a
AB  - circular organization providing the required symmetry for their interaction with the other
AB  - subunits and with the bipartite DNA target.  To test this model, we circularly permuted the
AB  - HsdS subunit of the type IB R-M enzyme EcoAI at the DNA level by direct linkage of codons for
AB  - original termini and introduction of new termini elsewhere along the N-terminal and central
AB  - conserved regions.  By analysing the activity of mutant enzymes, two circularly permuted
AB  - variants of HsdS that had termini located at equivalent positions in the N-terminal and
AB  - central repeats, respectively, were found to fold into a functional DNA recognition subunit
AB  - with wild-type specificity, suggesting a close proximity of the N and C termini in the native
AB  - protein.  The wild-type HsdS subunit was purified to homogeneity and shown to form a stable
AB  - trimeric complex with HsdM, M2S1, which was fully active as a DNA methyltransferase.  Gel
AB  - electrophoretic mobility shift assays revealed that the HsdS protein alone was not able to
AB  - form a specific complex with a 30-mer oligoduplex containing a single EcoAI recognition site.
AB  - However, addition of stoichiometric amounts of hsdM to HsdS led to efficient specific DNA
AB  - binding.  Our data provide evidence for the circular organization of domains of the HsdS
AB  - subunit.  In addition, they suggest a possible role of hsdM subunits in the formation of this
AB  - structure.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Dryden, D.T.F.
AU  - Firman, K.
TI  - Analysis of the subunit assembly of the type IC restriction-modification enzyme EcoR124I.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 4439
EP  - 4445
VL  - 26
AB  - Type I restriction-modification enzymes are composed of three different subunits, of which
AB  - HsdS determines DNA specificity, HsdM is responsible for DNA methylation and HsdR is required
AB  - for restriction.  The HsdM and hsdS subunits can also form an independent DNA
AB  - methyltransferase with a subunit stoichiometry of M2S1.  We found that the purified EcoR124I
AB  - R-M enzyme was a mixture of two species as detected by the presence of two differently
AB  - migrating specific DNA-protein complexes in a gel retardation assay.  An analysis of protein
AB  - subunits isolated from the complexes indicated that the larger species had a stoichiometry of
AB  - R2M2S1 and the smaller species had a stoichiometry of R1M2S1.  In vitro analysis of subunit
AB  - assembly revealed that while binding of the first HsdR subunit to the M2S1 complex with an
AB  - apparent Kd of ~2.4 x 10^-7M.  Functional assays have shown that only the R2M2S1 complex is
AB  - capable of DNA cleavage, however, the R1M2S1 complex retains ATPase activity.  The relevance
AB  - of this situation is discussed in terms of the regulation of restriction activity in vivo upon
AB  - conjugative transfer of a plasmid-born R-M system into an unmodified host cell.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - MacWilliams, M.P.
AU  - Sandmeier, U.
AU  - Nagaraja, V.
AU  - Bickle, T.A.
TI  - DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes.
JO  - EMBO J.
PY  - 1999
SP  - 2638
EP  - 2647
VL  - 18
AB  - Type I restriction enzymes bind to a specific DNA sequence and subsequently translocate DNA
AB  - past the complex to reach a non-specific cleavage site.  We have examined several potential
AB  - blocks to DNA translocation, such as positive supercoiling or a Holliday junction, for their
AB  - ability to trigger DNA cleavage by type I restriction enzymes.  Introduction of positive
AB  - supercoiling into plasmid DNA did not have a significant effect on the rate of DNA cleavage by
AB  - EcoAI endonuclease nor on the enzyme's ability to select cleavage sites randomly throughout
AB  - the DNA molecule.  Thus, positive supercoiling does not prevent DNA translocation.  EcoR124II
AB  - endonuclease cleaved DNA at Holliday junctions present on both linear and negatively
AB  - supercoiled substrates.  The latter substrate was cleaved by a single enzyme molecule at two
AB  - sites, one on either side of the junction, consistent with a bi-directional translocation
AB  - model.  Linear DNA molecules with two recognition sites for endonucleases from different type
AB  - I families were cut between the sites when both enzymes were added simultaneously but not when
AB  - a single enzyme was added.  We propose that type I restriction enzymes can track along a DNA
AB  - substrate irrespective of its topology and cleave DNA at any barrier that is able to halt the
AB  - translocation process.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Sandmeier, U.
AU  - Bickle, T.A.
TI  - Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 2638
EP  - 2643
VL  - 27
AB  - Type I restriction enzymes bind to specific DNA sequences but subsequently translocate
AB  - non-specific DNA past the complex in a reaction coupled to ATP hydrolysis and cleave DNA at
AB  - any barrier that can halt the translocation process. The restriction subunit of these enzymes,
AB  - HsdR, contains a cluster of seven amino acid sequence motifs typical of helicase superfamily
AB  - II, that are believed to be relevant to the ATP-dependent DNA translocation. Alignment of all
AB  - available HsdR sequences reveals an additional conserved region at the protein N-terminus with
AB  - a consensus sequence reminiscent of the P-D...(D/E)-X-K catalytic motif of many type II
AB  - restriction enzymes. To investigate the role of these conserved residues, we have produced
AB  - mutants of the type IB restriction enzyme EcoAI. We have found that single alanine
AB  - substitutions at Asp-61, Glu-76 and Lys-78 residues of the HsdR subunit abolished the
AB  - enzyme's restriction activity but had no effect on its ATPase and DNA translocation
AB  - activities, suggesting that these residues are part of the active site for DNA cleavage.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Sandmeier, U.
AU  - Szczelkun, M.D.
AU  - Bickle, T.A.
TI  - Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 417
EP  - 431
VL  - 306
AB  - DNA cleavage by type III restriction endonucleases requires two inversely oriented asymmetric
AB  - recognition sequences and results from
AB  - ATP-dependent DNA translocation and collision of two enzyme molecules.
AB  - Here, we characterized the structure and mode of action of the related
AB  - EcoP1I and EcoP15I enzymes. Analytical ultracentrifugation and gel
AB  - quantification revealed a common Res(2)Mod(2) subunit stoichiometry.
AB  - Single alanine substitutions in the putative nuclease active site of
AB  - ResP1 and ResP15 abolished DNA but not ATP hydrolysis, whilst a
AB  - substitution in helicase motif VI abolished both activities. Positively
AB  - supercoiled DNA substrates containing a pair of inversely oriented
AB  - recognition sites were cleaved inefficiently, whereas the corresponding
AB  - relaxed and negatively supercoiled substrates were cleaved efficiently,
AB  - suggesting that DNA overtwisting impedes the convergence of the
AB  - translocating enzymes. EcoP1I and EcoP15I could co-operate in DNA
AB  - cleavage on a circular substrate containing several EcoP1I sites
AB  - inversely oriented to a single EcoP15I site; cleavage occurred
AB  - predominantly at the EcoP15I site. EcoP15I alone showed nicking
AB  - activity on these molecules, cutting exclusively the top DNA strand at
AB  - its recognition site. This activity was dependent on enzyme
AB  - concentration and local DNA sequence. The EcoP1I nuclease mutant
AB  - greatly stimulated the EcoP15I nicking activity, while the EcoP1I motif
AB  - VI mutant did not. Moreover, combining an EcoP15I nuclease mutant with
AB  - wild-type EcoP1I resulted in cutting the bottom DNA strand at the
AB  - EcoP15I site. These data suggest that double-strand breaks result from
AB  - top strand cleavage by a Res subunit proximal to the site of cleavage,
AB  - whilst bottom strand cleavage is catalysed by a Res subunit supplied in
AB  - trans by the distal endonuclease in the collision complex.
ER  -

TY  - JOUR
AU  - Janscak, P.
AU  - Weiserova, M.
AU  - Hubacek, J.
AU  - Holubova, I.
AU  - Dutta, C.F.
AU  - Firman, K.
TI  - Two temperature-sensitive mutations in the DNA binding subunit of EcoKI with differing properties.
JO  - FEMS Microbiol. Lett.
PY  - 2000
SP  - 99
EP  - 104
VL  - 182
AB  - Two temperature-sensitive mutations in the hsdS gene, which encodes the DNA specificity
AB  - subunit of the type IA restriction-modification system EcoKI, designated Sts1 (Ser(340)Phe)
AB  - and Sts2 (Ala(204)Thr) had a different impact on restriction-modification functions in vitro
AB  - and in vivo. The enzyme activities of the Sts1 mutant were temperature-sensitive in vitro and
AB  - were reduced even at 30 degrees C (permissive temperature). Gel retardation assays revealed
AB  - that the Sts1 mutant had significantly decreased DNA binding, which was temperature-sensitive.
AB  - In contrast the Sts2 mutant did not show differences from the wild-type enzyme even at 42
AB  - degrees C. Unlike the HsdSts1 subunit, the HsdSts2 subunit was not able to compete with the
AB  - wild-type subunit in assembly of the restriction enzyme in vivo, suggesting that the Sts2
AB  - mutation affects subunit assembly. Thus, it appears that these two mutations map two important
AB  - regions in HsdS subunit responsible for DNA-protein and protein-protein interactions,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Janssen, P.J.
AU  - Morin, N.
AU  - Mergeay, M.
AU  - Leroy, B.
AU  - Wattiez, R.
AU  - Vallaeys, T.
AU  - Waleron, K.
AU  - Waleron, M.
AU  - Wilmotte, A.
AU  - Quillardet, P.
AU  - de Marsac, N.T.
AU  - Talla, E.
AU  - Zhang, C.C.
AU  - Leys, N.
TI  - Genome sequence of the edible cyanobacterium Arthrospira sp. PCC 8005.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2465
EP  - 2466
VL  - 192
AB  - We determined the genome sequence of Arthrospira sp. PCC 8005, a cyanobacterial strain of
AB  - great interest to the European Space Agency for
AB  - its nutritive value and oxygenic properties in the Micro-Ecological Life
AB  - Support System Alternative (MELiSSA) biological life support system for
AB  - long-term manned missions into space.
ER  -

TY  - JOUR
AU  - Janssens, T.K.S.
AU  - de Boer, T.E.
AU  - Agamennone, V.
AU  - Zaagman, N.
AU  - van Straalen, N.M.
AU  - Roelofs, D.
TI  - Draft Genome Sequence of Bacillus toyonensis VU-DES13, Isolated from Folsomia candida (Collembola: Entomobryidae).
JO  - Genome Announcements
PY  - 2017
SP  - e00287
EP  - e00217
VL  - 5
AB  - We present here the draft genome of Bacillus toyonensis VU-DES13, which was isolated from the
AB  - midgut of the soil-living springtail Folsomia candida Previous
AB  - research revealed the presence of gene clusters for the biosynthesis of various
AB  - secondary metabolites, including beta-lactam antibiotics, in the host's genome.
AB  - The genome data are discussed in the light of the antimicrobial properties
AB  - against fungi and oomycetes and a high level of beta-lactam resistance of the
AB  - isolate.
ER  -

TY  - JOUR
AU  - Janto, B. et al.
TI  - Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4.
JO  - Environ. Microbiol.
PY  - 2011
SP  - 3289
EP  - 3309
VL  - 13
AB  - Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows
AB  - non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large
AB  - sudden increases in external pH. It is a model organism for studies of
AB  - bioenergetics at high pH, at which energy demands are higher than at neutral pH
AB  - because both cytoplasmic pH homeostasis and ATP synthesis require more energy.
AB  - The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at
AB  - which the pH homeostasis capacity is exceeded, and manages other stresses that
AB  - are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses.
AB  - The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some
AB  - mutants without viability loss. The plasmids may provide a reservoir of mobile
AB  - elements that promote adaptive chromosomal rearrangements under particular
AB  - environmental conditions. The genome also reveals a more acidic pI profile for
AB  - proteins exposed on the outer surface than found in neutralophiles. A large array
AB  - of transporters and regulatory genes are predicted to protect the alkaliphile
AB  - from its overlapping stresses. In addition, unanticipated metabolic versatility
AB  - was observed, which could ensure requisite energy for alkaliphily under diverse
AB  - conditions.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
TI  - Restriction Enzymes and their Applications.
JO  - Trends in Science and Technology. Biotechnology series.
PY  - 1989
SP  - 1
EP  - 204
VL  - 17
ER  -

TY  - JOUR
AU  - Janulaitis, A.
TI  - Restriction endonucleases.
JO  - Zh. Vses. Khim.
PY  - 1984
SP  - 133
EP  - 138
VL  - 29
ER  -

TY  - JOUR
AU  - Janulaitis, A.
TI  - A novel approach to the study of DNA-protein interactions using related restriction endonucleases that recognize overlapping nucleotide sequences.
JO  - Biologija
PY  - 1996
SP  - 28
EP  - 31
VL  - 0
AB  - Multiple attempts to change the specificity of restriction enzymes by substituting amino acids
AB  - predicted by crystallographic analysis to be involved in substrate recognition have so far
AB  - been unsuccessful.  In general, the results argue that the potential of this approach in study
AB  - of RE is limited.  A novel approach to the analysis of such structure-function relationships
AB  - is therefore suggested, which is based on the investigation of structurally related RE which
AB  - recognize overlapping (but not identical) nucleotide sequences.  In an attempt to identify
AB  - such RE, 22 genes encoding RE were cloned, sequenced, and their deduced amino acid sequences
AB  - compared with those of previously described RE by computer analysis.  For the first time a
AB  - group of 18 RE is demonstrated, which can be arranged in pairs (9 pairs) on the basis of
AB  - significant overlap in recognition sequences, and some aa sequence similarity.  Indirect
AB  - evidence is given to support the contention that members of each pair are structurally related
AB  - to provide, in turn, the basis of a new model system for investigation of the role of
AB  - structural changes in the development of changes in specificity.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Bitinaite, J.
AU  - Jaskeleviciene, B.
TI  - A new sequence-specific endonuclease from Gluconobacter suboxydans.
JO  - FEBS Lett.
PY  - 1983
SP  - 243
EP  - 247
VL  - 151
AB  - The isolation of sequence-specific endonucleases from Gluconobacter
AB  - dioxyacetonicus (IAM 1814 and IAM 1840) and Gluconobacter oxydans sub.
AB  - melanogenes (IAM 1836) has been reported.  We have examined six Gluconobacter
AB  - suboxydans strains for the presence of the enzymes of this type and discovered
AB  - in two of them restriction endonucleases of identical specificity (named GsuI
AB  - and GsbI).Here, we describe the isolation procedure of the new site-specific
AB  - endonuclease GsuI, which recognizes a hexanucleotide sequence 5' ...CTCCAG.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Kazlauskiene, R.
AU  - Lazareviciute, L.
AU  - Gilvonauskaite, R.
AU  - Steponaviciene, D.
AU  - Jagelavicius, M.
AU  - Petrusyte, M.
AU  - Bitinaite, J.
AU  - Vezeviciute, Z.
AU  - Kiuduliene, E.
AU  - Butkus, V.
TI  - Taxonomic specificity of restriction-modification enzymes.
JO  - Gene
PY  - 1988
SP  - 229
EP  - 232
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Klimasauskas, S.
AU  - Petrusyte, M.
AU  - Butkus, V.
TI  - Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine.
JO  - FEBS Lett.
PY  - 1983
SP  - 131
EP  - 134
VL  - 161
AB  - The means by which bacteria protect their own DNA from their restriction
AB  - enzymes have not been fully investigated.  In all systems that have been
AB  - studied, cells produce a modification methylase in addition to the retriction
AB  - endonuclease.  Both enzymes recognize the same specific DNA sequence.  Not many
AB  - DNA methylases were studied in detail, but all of those studied methylate
AB  - either adenine to N6-methyladenine (m6A) or cytosine to 5-methylcytosine
AB  - (m5C).Recently a site-specific endonuclease and methylase BcnI, both of which
AB  - recognize the sequence 5'CC(C/G)GG, have been isolated from Bacillus
AB  - centrosporus strain RFLI.  We here describe the property of MBcnI to methylate
AB  - cytosine residues in DNA in vitro at the N4 position yielding N4-methylcytosine
AB  - (m4C).  The same minor base in DNA isolated from B. centrosporus was detected.
AB  - Such an unusual DNA modification is described for the first time.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Marcinkeviciene, L.
AU  - Petrusyte, M.
AU  - Mironov, A.
TI  - A new sequence-specific endonuclease from Streptococcus durans.
JO  - FEBS Lett.
PY  - 1981
SP  - 172
EP  - 174
VL  - 134
AB  - Although a relatively large number of sequence-specific deoxyribonucleases
AB  - (class II restriction endonucleases) is now available, new endonucleases with
AB  - unique recognition sites are desirable, as they increase the flexibility of DNA
AB  - analysis and recombinant techniques.  We report here the isolation from
AB  - Streptococcus durans RFL 3 strain of a new enzyme (SduI) of this type, which
AB  - recognizes hexanucleotide palindromic sequence 5'-G(G/A/T)-GC(C/A/T)C
AB  - degenerated at two positions and consequently should cleave at the level of
AB  - nine possible sites.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Marcinkeviciene, L.Y.
AU  - Petrusyte, M.P.
TI  - A specific endonuclease from Caulobacter fusiformis that cleaves only methylated DNA.
JO  - Dokl. Akad. Nauk.
PY  - 1982
SP  - 241
EP  - 244
VL  - 262
AB  - None
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Petrusyte, M.
AU  - Butkus, V.
TI  - Three sequence-specific endonucleases from Escherichia coli RFL47.
JO  - FEBS Lett.
PY  - 1983
SP  - 213
EP  - 216
VL  - 161
AB  - The characterization of the new restriction enzyme Eco47III recognizing a
AB  - hexanucleotide palindromic sequence 5'AGC^GCT and cleaving, as indicated by the
AB  - arrow, is reported.  It was isolated from Escherichia coli strain RFL47.
AB  - Another two specific endonuclease Eco471 (isoschizomer of AvaII and Ecoz4711
AB  - (isoschizomer of AsuI) were also found in this strain.  There are two Eco47III
AB  - recognition sites on lambda DNA at 20997 and 37060 basepairs.  The central
AB  - Eco47III fragment can be replaced by a cloned fragment in lambda vector mutant
AB  - tR2 gene; i.e. lambda gt.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Petrusyte, M.
AU  - Maneliene, Z.
AU  - Klimasauskas, S.
AU  - Butkus, V.
TI  - Purification and properties of the Eco57I restriction endonuclease and methylase-prototypes of a new class (type IV).
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6043
EP  - 6049
VL  - 20
AB  - The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli
AB  - RR1 strain carrying the Eco57IRM genes on a recombinant plasmid. The molecular weight of the
AB  - denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with
AB  - an apparent molecular weight of 104-108 kDa. R.Eco57I also possesses methylase activity. The
AB  - methylation activities of both enzymes modify the outer A residue in the target sequence
AB  - 5'CTGAAG yielding N6-methyladenine. M.Eco57I modifies both strands of the substrate while
AB  - R.Eco57I modifies only one. Only the methylase enzyme is stimulated by Ca2+. The restriction
AB  - endonuclease shows an absolute requirement for Mg2+ and is stimulated by AdoMet. ATP has no
AB  - influence on either activity of the enzymes. The subunit structure and enzymatic properties of
AB  - the Eco57I enzymes distinguish them from all other restriction-modification enzymes that have
AB  - been described previously. Therefore, RM.Eco57I may be regarded as a representative of a novel
AB  - class of restriction-modification systems, and we propose to classify it as type IV.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Petrusyte, M.A.
AU  - Jaskeleviciene, B.P.
AU  - Krayev, A.S.
AU  - Skryabin, K.G.
AU  - Bayev, A.A.
TI  - A new restriction endonuclease BcnI from Bacillus centrosporus RFL 1.
JO  - FEBS Lett.
PY  - 1982
SP  - 178
EP  - 180
VL  - 137
AB  - Type II restriction endonucleases have proved to be an indispensable tool in
AB  - DNA cloning and sequencing studies.  Over 200 individual enzymes with >60
AB  - different specificities have been already described.  Here, we describe the
AB  - purification and the determination of cleavage specificity of a novel type II
AB  - restriction endonuclease from Bacillus centrosporus RFL 1.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Petrusyte, M.P.
AU  - Jaskeleviciene, B.P.
AU  - Krayev, A.S.
AU  - Skryabin, K.G.
AU  - Bayev, A.A.
TI  - A new restriction endonuclease BcnI from Bacillus centrosporus RFL1.
JO  - Dokl. Akad. Nauk.
PY  - 1981
SP  - 749
EP  - 750
VL  - 257
AB  - Restriction endonucleases are finding wide use in the study of the structure
AB  - and function of genomes and the production of recombinant DNA molecules.  At
AB  - the present time, more than 50 restriction endonucleases with various substrate
AB  - specificities are known; however, the search for new restriction enzymes, as
AB  - before, is an urgent problem, since the detection of new restriction enzymes
AB  - expands the experimenter's possibilities in solving the indicated problems.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Povilionis, P.
AU  - Sasnauskas, K.
TI  - Cloning of the modification methylase gene of Bacillus centrosporus in Escherichia coli.
JO  - Gene
PY  - 1982
SP  - 197
EP  - 204
VL  - 20
AB  - The gene specifying a sequence-specific modification methylase of Bacillus centrosporus has
AB  - been cloned in Escherichia coli using the restriction endonuclease HindIII and the plasmid
AB  - pBR322.  The selection was based on detection of new methylation properties rendering
AB  - recombinant plasmids carrying the methylase gene nonsusceptible to BcnI endonuclease cleavage.
AB  - The presence of a 3.2-kb HindIII fragment in either orientation conferred BcnI resistance on
AB  - the recombinant plasmids.  These results suggest that the BcnI methylase gene is expressed in
AB  - E. coli under the control of a promoter located on the cloned fragment.  The relative level of
AB  - BcnI methylase enzyme in E. coli was similar to that in B. centrosporus.  The recombinant
AB  - clones do not exhibit any BcnI restriction-endonuclease activity.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Stakenas, P.
AU  - Jaskeleviciene, B.
AU  - Lebedenko, E.N.
AU  - Berlin, Y.A.
TI  - A new restriction endonuclease, CfrI from Citrobacter freundii.
JO  - Bioorg. Khim.
PY  - 1980
SP  - 1746
EP  - 1748
VL  - 6
AB  - CfrI, a new site-specific restriction endonuclease, has been isolated from a
AB  - Citrobacter freundii strain.  The enzyme recognizes the sequence 5'
AB  - Py^G-G-C-C-Pu 3' Pu-C-C-G-G^Py in double-stranded DNA and cuts it between Py
AB  - and G residues to give 5'-protruding tetranucleotide ends G-G-C-C.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Stakenas, P.S.
AU  - Berlin, Y.A.
TI  - A new site-specific endodeoxyribonuclease from Citrobacter freundii.
JO  - FEBS Lett.
PY  - 1983
SP  - 210
EP  - 212
VL  - 161
AB  - Cfr10I, a site-specific endonuclease from Citrobacter freundii strain RFL10, was isolated. It
AB  - recognizes and cleaves the family of related sequences: 5'Pu^CCGGPy to generate DNA fragments
AB  - with 5' tetranucleotide extensions. Cfr10I may be useful in molecular cloning experiments,
AB  - especially in conjunction with other enzymes which generate the same terminal extensions. ion
AB  - have led to the detection of specific endodeoxyribonucleases (class II restriction
AB  - endonucleases), distinguished by an exceptionally high substrate specificity, which served as
AB  - the prerequisite for their use in molecular genetic and structural investigations of DNA.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Stakenas, P.S.
AU  - Bitinaite, J.B.
AU  - Jaskeleviciene, B.P.
TI  - Distribution of specific endodeoxyribonucleases in various strains of Citrobacter freundii.
JO  - Dokl. Akad. Nauk.
PY  - 1983
SP  - 483
EP  - 485
VL  - 271
AB  - The discovery of the phenomenon of host specificity at the beginning of the
AB  - fifties and the investigation of its essence, realized in the discovery of
AB  - enzymes of the restriction-modification systems, have made a large contribution
AB  - to the development of modern molecular biology, genetics, and enzymology.  The
AB  - search for and study of enzymes of restriction and modification have led to the
AB  - detection of specific endodeoxyribonucleases (class II restriction
AB  - endonucleases), distinguished by an exceptionally high substrate specificity,
AB  - which served as the prerequisite for their use in molecular genetic and
AB  - structural investigations of DNA.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Stakenas, P.S.
AU  - Lebedenko, E.N.
AU  - Berlin, Y.A.
TI  - A new restriction endonuclease from Citrobacter freundii.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 6521
EP  - 6530
VL  - 10
AB  - CfrI, a new restriction endonuclease of unique substrate specificity, has been
AB  - isolated from a Citrobacter freundii strain.  The enzyme recognizes a
AB  - degenerated sequence PyGGCCPu in double-strand DNA and cleaves it between Py
AB  - and G residues to yield 5'-protruding tetranucleotide ends GGCC.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Stakenas, P.S.
AU  - Petrusyte, M.P.
AU  - Bitinaite, J.B.
AU  - Klimasauskas, S.I.
AU  - Butkus, V.V.
TI  - Specificity of new restrictases and methylases.  Unusual modification of cytosine in position 4.
JO  - Mol. Biol. (Mosk)
PY  - 1983
SP  - 115
EP  - 129
VL  - 18
AB  - Fourteen restrictases and four methylases were extracted and purified from 14 strains of
AB  - independent origin of the species Citrobacter freundii and Escherichia coli. The nucleotide
AB  - sequences recognized by the restrictases were determined by means of a comparison of the
AB  - character of DNA cleavage by the investigated and known enzymes, by study of the cleavage
AB  - frequency of substrates with a known primary structure, and by the mapping method. It was
AB  - established that Cfr10I is a new prototype recognizing the sequence 5'PuCCGGPy. The other
AB  - enzymes proved to be isoschizomers of known restrictases: Cfr5*, Cfr11I, Eco60I, and Eco61I
AB  - are isoschizomers of EcoRII; Cfr4I, Cfr8I, and Cfr12T, Sau96I; Cfr6I, PvuII; Crf9I, SmaI;
AB  - Eco6I, HgiJII; Eco32I, EcoRV; Eco52I, XmaIII; and Eco56I, NaeI. Several of these enzymes were
AB  - demonstrated for the first time in E. coli and C. freundii. A study of the specificity of the
AB  - methylases M.CfrI, M.Cfr6I, M.Cfr9I, and M.Cfr10I showed that these enzymes recognize the same
AB  - nucleotide sequence as does the restrictase extracted from the same strain. Modification of
AB  - DNA in vitro using M.CfrI and M.Cfr10I results in the production of 5-methylcytosine, and in
AB  - the case of M.Cfr6I and M.Cfr9I, N4-methylcytosine. G, where M.HpaII methylates the inner,
AB  - M.BsuFI/M.MspI the outer cytosine. Also the CCGG recognizing TRD of the multispecific B.
AB  - subtilis phage SPR Mtase is distinct from that of the host enzyme, possibly indicating
AB  - different requirements for TRDs operative in mono- and multispecific enzymes.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Vaisvila, R.
AU  - Timinskas, A.
AU  - Klimasauskas, S.
AU  - Butkus, V.
TI  - Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6051
EP  - 6056
VL  - 20
AB  - A 6.3 kb fragment of E.coli RFL57 DNA coding for the type IV restriction-modification system
AB  - Eco57I was cloned and expressed in E.coli RR1. A 5775 bp region of the cloned fragment was
AB  - sequenced which contains three open reading frames (ORF). The methylase gene is 1623 bp long,
AB  - corresponding to a protein of 543 amino acids (62 kDa); the endonuclease gene is 2991 bp in
AB  - length (997 amino acids, 117 kDa). The two genes are transcribed convergently from different
AB  - strands with their 3'-ends separated by 69 bp. The third short open reading frame (186 bp, 62
AB  - amino acids) has been indentified, that precedes and overlaps by 7 nucleotides the ORF
AB  - encoding the methylase. Comparison of the deduced Eco57I endonuclease and methylase amino acid
AB  - sequences revealed three regions of significant similarity. Two of them resemble the conserved
AB  - sequence motifs characteristic of the DNA [adenine-N6] methylases. The third one shares
AB  - similarity with corresponding regions of the PaeR71, TaqI, CviBIII, PstI, BamHI and HincII.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Vaitkevicius, D.P.
TI  - A spectrophotometric procedure for the determination of activity of restriction.
JO  - Anal. Biochem.
PY  - 1981
SP  - 116
EP  - 122
VL  - 116
AB  - A simple procedure basically applicable for the quantitative determination of
AB  - activity of all restriction endonucleases is described.  Native DNA immobilized
AB  - on cellulose is used as a substrate; after the treatment by restriction
AB  - endonucleases this DNA is released to the solution.  Changes of the optical
AB  - density of the solution containing solubilized DNA permit quantitative
AB  - determination of the restriction endonuclease activity.
ER  -

TY  - JOUR
AU  - Janulaitis, A.
AU  - Vaitkevicius, D.P.
TI  - New methodical approach to development of technology for production of restriction endonucleases.  Development of scheme for isolation of homogeneous preparation of restrictase MvaI.
JO  - Biotekhnologiya
PY  - 1985
SP  - 39
EP  - 51
VL  - 1
AB  - Using restrictase MvaI isolated from Microccus varians RJL 19 cells a
AB  - possibility has been investigated for selection of purification schemes of
AB  - restrictases by means of study of binding of a specific enzyme with various
AB  - sorbents (DEAE-cellulose, phosphocellulose, heparinsepharose, blue sepharose,
AB  - Biorex 70 and SP-sephadex) under static conditions.  It has been illustrated
AB  - that the character of interaction of the restrictase under the static
AB  - conditions with various sorbents permits to predict its behavior under
AB  - conditions of the column chromatography and select the effective sorbents,
AB  - sequence of their application and conditions of conducting the column
AB  - chromatography.  A highly effective scheme for purification of MvaI restrictase
AB  - has been created which makes possible to produce electrophoretically
AB  - homogeneous preparation of a specific enzyme as a result of just two stages of
AB  - purification of the cell-free extract of M. varians RJL19 on phosphocellulose
AB  - and blue sepharose.  The prospects of application of the recommended methodical
AB  - approach for rapid development of a process for production on restrictases are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Jaomanjaka, F.
AU  - Ballestra, P.
AU  - Dols-Lafargue, M.
AU  - Le Marrec, C.
TI  - Expanding the diversity of oenococcal bacteriophages: Insights into a novel group based on the integrase sequence.
JO  - Int. J. Food Microbiol.
PY  - 2013
SP  - 331
EP  - 340
VL  - 166
AB  - Temperate bacteriophages are a contributor of the genetic diversity in the lactic
AB  - acid bacterium Oenococcus oeni. We used a classification scheme for oenococcal
AB  - prophages based on integrase gene polymorphism, to analyze a collection of
AB  - Oenococcus strains mostly isolated in the area of Bordeaux, which represented the
AB  - major lineages identified through MLST schemes in the species. Genome sequences
AB  - of oenococcal prophages were clustered into four integrase groups (A to D) which
AB  - were related to the chromosomal integration site. The prevalence of each group
AB  - was determined and we could show that members of the intB- and intC-prophage
AB  - groups were rare in our panel of strains. Our study focused on the so far
AB  - uncharacterized members of the intD-group. Various intD viruses could be easily
AB  - isolated from wine samples, while intD lysogens could be induced to produce
AB  - phages active against two permissive O. oeni isolates. These data support the
AB  - role of this prophage group in the biology of O. oeni. Global alignment of three
AB  - relevant intD-prophages revealed significant conservation and highlighted a
AB  - number of unique ORFs that may contribute to phage and lysogen fitness.
ER  -

TY  - JOUR
AU  - Jaomanjaka, F.
AU  - Claisse, O.
AU  - Philippe, C.
AU  - Le Marrec, C.
TI  - Complete Genome Sequence of Lytic Oenococcus oeni Bacteriophage OE33PA.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00818
EP  - e00818
VL  - 7
AB  - Oenococcus oeni is the most common species of lactic acid bacteria associated with malolactic
AB  - fermentation in wine. Here, we report the genome sequence of the
AB  - lytic phage OE33PA (vB_OeS_OE33PA). It has a morphotype similar to that of
AB  - members of the Siphoviridae family, a linear 39,866-bp double-stranded genome
AB  - with cohesive ends, and 57 predicted open reading frames.
ER  -

TY  - JOUR
AU  - Jara, C.
AU  - Romero, J.
TI  - Genome Sequences of Three Oenococcus oeni Strains Isolated from Maipo Valley, Chile.
JO  - Genome Announcements
PY  - 2015
SP  - e00866
EP  - e00815
VL  - 3
AB  - Oenococcus oeni is part of the microbial terroir involved in wine production. Here, we present
AB  - three genome sequences of O. oeni strains isolated from
AB  - spontaneous malolactic fermentation of cultivar Cabernet Sauvignon Maipo Valley,
AB  - Chile.
ER  -

TY  - JOUR
AU  - Jarjour, J.
AU  - West-Foyle, H.
AU  - Certo, M.T.
AU  - Hubert, C.G.
AU  - Doyle, L.
AU  - Getz, M.M.
AU  - Stoddard, B.L.
AU  - Scharenberg, A.M.
TI  - High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 6871
EP  - 6880
VL  - 37
AB  - Experimental analysis and manipulation of protein-DNA interactions pose unique biophysical
AB  - challenges arising from the structural and chemical
AB  - homogeneity of DNA polymers. We report the use of yeast surface display
AB  - for analytical and selection-based applications for the interaction
AB  - between a LAGLIDADG homing endonuclease and its DNA target. Quantitative
AB  - flow cytometry using oligonucleotide substrates facilitated a complete
AB  - profiling of specificity, both for DNA-binding and catalysis, with single
AB  - base pair resolution. These analyses revealed a comprehensive segregation
AB  - of binding specificity and affinity to one half of the pseudo-dimeric
AB  - interaction, while the entire interface contributed specificity at the
AB  - level of catalysis. A single round of targeted mutagenesis with tandem
AB  - affinity and catalytic selection steps provided mechanistic insights to
AB  - the origins of binding and catalytic specificity. These methods represent
AB  - a dynamic new approach for interrogating specificity in protein-DNA
AB  - interactions.
ER  -

TY  - JOUR
AU  - Jarman, S.N.
TI  - Cleaver: software for identifying taxon specific restriction endonuclease recognition sites.
JO  - Bioinformatics
PY  - 2006
SP  - 2160
EP  - 2161
VL  - 22
AB  - Cleaver is an application for identifying restriction endonuclease recognition sites that
AB  - occur in some taxa, but not in others.
AB  - Differences in DNA fragment restriction patterns among taxa are the
AB  - basis for many diagnostic assays for taxonomic identification and are
AB  - used in procedures for removing the DNA of some taxa from pools of DNA
AB  - from mixed sources. Cleaver analyses restriction digestion of groups of
AB  - orthologous DNA sequences simultaneously to allow identification of
AB  - differences in restriction pattern among the fragments derived from
AB  - different taxa.
ER  -

TY  - JOUR
AU  - Jarrell, K.F.
AU  - Julseth, C.
AU  - Pearson, B.
AU  - Kuzio, J.
TI  - Paucity of the Sau3AI recognition sequence (GATC) in the genome of Methanococcus voltae.
JO  - Mol. Gen. Genet.
PY  - 1987
SP  - 191
EP  - 194
VL  - 208
AB  - High molecular weight genomic DNA isolated from the archaebacterium
AB  - Methanococcus voltae by alkaline-SDS lysis was not effectively digested with
AB  - the restriction enzyme Sau3AI, which recognizes the base sequence GATC.  M.
AB  - voltae DNA was also resistant to digestion by MboI and BamHI which recognize
AB  - sites containing the same GATC sequence.  Examination of a M. voltae genomic
AB  - library prepared in Escherichia coli JM83 with a pUC vector revealed that the
AB  - 5-10 kb inserts were still resistant to Sau3AI digestion, indicating a likely
AB  - lack of the GATC sequence in M. voltae DNA.
ER  -

TY  - JOUR
AU  - Jarvik, T.
AU  - Smillie, C.
AU  - Groisman, E.A.
AU  - Ochman, H.
TI  - Short-term Signatures of Evolutionary Change in the Salmonella enterica serovar Typhimurium 14028 Genome.
JO  - J. Bacteriol.
PY  - 2010
SP  - 560
EP  - 567
VL  - 192
AB  - Salmonella enterica serovar Typhimurium is a Gram-negative pathogen that causes
AB  - gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for
AB  - the disease promoted by the human-adapted S. enterica serovar Typhi. Despite its health
AB  - importance, the only S. Typhimurium strain for which the complete genomic sequence has been
AB  - determined is the avirulent LT2 strain, which is extensively used in genetic and physiologic
AB  - studies. Here, we report the complete genomic sequence of the S. Typhimurium strain 14028s, as
AB  - well as those of its progenitor and two additional derivatives. Comparison of these S.
AB  - Typhimurium genomes revealed differences in the patterns of sequence evolution and the
AB  - complete inventory of genetic alterations incurred in virulent and avirulent strains, as well
AB  - as the sequence changes accumulated during laboratory passage of pathogenic organisms.
ER  -

TY  - JOUR
AU  - Jarvis, A.W.
TI  - Analysis of phage resistance mechanisms encoded by lactococcal plasmid pAJ2074.
JO  - Can. J. Microbiol.
PY  - 1993
SP  - 252
EP  - 258
VL  - 39
AB  - Lactococcal plasmid pAJ2074 is a 74-kb plasmid that confers phage resistance at 30oC against
AB  - all lactococcal phages with prolate heads (referred to as prolate phage), and most small
AB  - lactococcal phages with isometric heads (referred to as small isometric phage) that have been
AB  - tested. The presence of pAJ2074 had no effect on phage adsorption or injection of phage DNA.
AB  - Replication of prolate phage c2 DNA could not be detected in bacterial cells containing the
AB  - plasmid up to 60 minutes after phage infection, whereas phage c2 DNA replication could be
AB  - demonstrated at 20 minutes in the control strain. With pAJ2074 present there was no detectable
AB  - growth of phage c2 and an 87% reduction in burst size for the small isometric phage sk1.
AB  - Infective centres were reduced in the presence of pAJ2074 by 99% for phage c2 and by 93% for
AB  - phage sk1. Plasmid pAJ2074 differed from pTR2030, in that the major effect of pAJ2074 was on
AB  - prolate phage c2, rather than on the small isometric phage sk1, and no restriction and
AB  - modification system could be detected. In addition, no DNA homology was detected between
AB  - pAJ2074 and pTRK67 (derived from pTR2030). A recombinant plasmid pAJ88 containing an 8.4kb
AB  - insert from pAJ2074 conferred an intermediate level of phage resistance. The DNA region that
AB  - encoded reduced phage sensitivity was further defined by the subcloning of a 5.6kb EcoRV
AB  - fragment that conferred resistance similar to pAJ88. The possibility of two phage-resistance
AB  - mechanisms being encoded by pAJ2074 is discussed.
ER  -

TY  - JOUR
AU  - Jarvis, A.W.
AU  - Klaenhammer, T.R.
TI  - Bacteriophage resistance conferred on lactic Streptococci by the conjugative plasmid pTR2030: Effects on small isometric-, large Isometric-,and prolate-headed Phages.
JO  - Appl. Environ. Microbiol.
PY  - 1986
SP  - 1272
EP  - 1277
VL  - 51
AB  - A series of reactions between phages, sensitive hosts, and transconjugants where the
AB  - sensitivity of small isometric-, large isometric-, and prolate-headed phages to
AB  - pTR2030-induced phage resistance was evaluated in Streptococcus lactis and Streptococcus
AB  - cremoris strains. Phage-resistant transconjugants were constructed in the desired hosts by
AB  - conjugal transfer of lactose-fermenting ability (Lac+,pTR1040) and phage resistance (Hsp+
AB  - pTR2030) from S. lactis TEK1. S. lactis and S. cremoris transconjugants harboring pTR2030 were
AB  - resistant to all small isometric-headed phages examined. In contrast, prolate- and large
AB  - isometric-headed phages were either not inhibited in the pTR2030 transconjugants or exhibited
AB  - a reduction in plaque size without a reduction in the efficiency of plaquing. Small
AB  - isometric-headed phages subject to pTR2030 induced inhibition shared no significant DNA
AB  - homology with pTR2030, suggesting that phage immunity genes are not harbored on the plasmid or
AB  - responsible for resistance. The general effectiveness of pTR2030 against small
AB  - isometric-headed phages was highly significant since these are the phages which have been
AB  - isolated most commonly from dairy fermentation plants.
ER  -

TY  - JOUR
AU  - Jaubert, C.
AU  - Danioux, C.
AU  - Oberto, J.
AU  - Cortez, D.
AU  - Bize, A.
AU  - Krupovic, M.
AU  - She, Q.
AU  - Forterre, P.
AU  - Prangishvili, D.
AU  - Sezonov, G.
TI  - Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon.
JO  - Open Biol.
PY  - 2013
SP  - 130010
EP  - 130010
VL  - 3
AB  - The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2,
AB  - was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine
AB  - other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA
AB  - revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic
AB  - region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched
AB  - in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats),
AB  - glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature invertedrepeat
AB  - transposable elements). The tRNAgenes ofLAL14/1 are preferential targets for the integration
AB  - of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the
AB  - genome. LAL14/1 carries five CRISPR loci with 10 per
AB  - cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids
AB  - found in the Icelandic hot springs. Strikingly, theCRISPR_2 region of LAL14/1 carries an
AB  - unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high
AB  - similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for
AB  - S. islandicus LAL14/1 and created DpyrEF and DCRISPR_1 mutants using double cross-over and
AB  - pop-in/pop-out approaches, respectively. Thus,LAL14/1 is a promisingmodel to study virus-host
AB  - interactions and the CRISPR/Cas defence mechanism in Archaea.
ER  -

TY  - JOUR
AU  - Jauregui, R.
AU  - Rodelas, B.
AU  - Geffers, R.
AU  - Boon, N.
AU  - Pieper, D.H.
AU  - Vilchez-Vargas, R.
TI  - Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423.
JO  - Genome Announcements
PY  - 2014
SP  - e00188
EP  - e00114
VL  - 2
AB  - Herbaspirillum sp. strain RV1423 was isolated from a site contaminated with alkanes and
AB  - aromatic compounds and harbors the complete pathway for naphthalene
AB  - degradation. The new features found in RV1423 increase considerably the
AB  - versatility and the catabolic potential of a genus of bacteria previously
AB  - considered mainly to be diazotrophic endophytes to plants.
ER  -

TY  - JOUR
AU  - Javorsky, P.
AU  - Pravdova, M.
AU  - Vanat, I.
AU  - Pristas, P.
AU  - Styriak, I.
TI  - Gene manipulation of Streptococcus bovis: progress and problems.
JO  - Can. J. Anim. Sci.
PY  - 1995
SP  - 654
EP  - 655
VL  - 75
AB  - In general, realization of the goals to control the digestive processes of
AB  - ruminants via genetic manipulation of rumen bacteria, is limited mainly by little information
AB  - about the genome of important rumen bacteria, development of suitable cloning system,
AB  - stability of cloned DNA in rumen bacteria and in the whole rumen ecosystem as well.  In
AB  - our cloning study, the Sau 3A fragments of chromosomal DNA of S. bovis AO 24/85 were
AB  - ligated into BamHI site of shuttle vector pMX 39, as a host was used B. subtilis amy E-.
AB  - The restriction analyses of the recombinant plasmid pJK 108 isolated from B. subtilis alpha-
AB  - amylase positive clone showed that alpha-amylase gene was located within a 2.8 kb fragment of
AB  - the S. bovis chromosomal DNA.  Looking for a suitable transformation system, we have
AB  - transformed S. bovis AO 24/85 with plasmid pNZ12 by electroporation with  transformation
AB  - efficiency 1.1 x 103 ug-1 DNA.  In our laboratory we tested more S. bovis  strains for their
AB  - restriction activities.  We have developed a very simple, rapid and effective  method for
AB  - testing of RE activity of rumen bacteria.  By this method we detected and then  isolated and
AB  - characterized the restriction endonuclease SbvI, an isoschizomer of HaeIII,  from rumen
AB  - amylolytic bacterium S. bovis III/1.  Enzyme SbvI recognizes the 4-bp  palindrome,
AB  - 5'-GGCC-3' and cleaves DNA after the second G in the sequence, producing blunt ends.
ER  -

TY  - JOUR
AU  - Jay, E.
AU  - Wu, R.
TI  - Arthrobacter luteus restriction endonuclease recognition sequence and its cleavage map of SV40 DNA.
JO  - Biochemistry
PY  - 1976
SP  - 3612
EP  - 3620
VL  - 15
AB  - The nucleotide sequence at the cleavage site of the restriction endonuclease
AB  - isolated from Arthrobacter luteus (Alu) has been determined.  The endonuclease
AB  - cleaves at the center of a palindromic tetranucleotide sequence to give
AB  - even-ended duplex DNA fragments phosphorylated at the 5'-end.  The endonuclease
AB  - cleaves SV40 form I DNA into 32 fragments.  The order and sizes of these
AB  - fragments have been determined to provide an Alu cleavage map of the SV40
AB  - genome.
ER  -

TY  - JOUR
AU  - Jay, Z.J.
AU  - Beam, J.P.
AU  - Dohnalkova, A.
AU  - Lohmayer, R.
AU  - Bodle, B.
AU  - Planer-Friedrich, B.
AU  - Romine, M.
AU  - Inskeep, W.P.
TI  - Pyrobaculum yellowstonensis str. WP30 respires on elemental sulfur and/or arsenate in circumneutral sulfidic geothermal sediments of Yellowstone National Park.
JO  - Appl. Environ. Microbiol.
PY  - 2015
SP  - 5907
EP  - 5916
VL  - 81
AB  - Thermoproteales populations (phylum Crenarchaeota) are abundant in
AB  - high-temperature (>70 degrees C) environments of Yellowstone National Park (YNP)
AB  - and are important in mediating biogeochemical cycles of sulfur, arsenic, and
AB  - carbon. The objectives of this study were to determine specific physiological
AB  - attributes of the isolate Pyrobaculum yellowstonensis strain WP30, which was
AB  - obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS] 80
AB  - degrees C; pH 6.1, 135 muM As), and relate this organism to geochemical processes
AB  - occurring in situ. Strain WP30 is a chemoorganoheterotroph and requires elemental
AB  - sulfur and/or arsenate as electron acceptors. Growth in the presence of elemental
AB  - sulfur and arsenate resulted in the formation of thioarsenates and polysulfides.
AB  - The complete genome of this organism was sequenced (1.99 Mb, 58 % G+C), which
AB  - revealed numerous metabolic pathways for the degradation of carbohydrates, amino
AB  - acids, and lipids. Multiple dimethylsulfoxide molybdopterin (DMSO-MPT)
AB  - oxidoreductase genes were identified, which are implicated in the reduction of
AB  - sulfur and arsenic. Pathways for the de novo synthesis of nearly all required
AB  - cofactors and metabolites were identified. Comparative genomics of P.
AB  - yellowstonensis versus assembled metagenome sequence from JCHS showed that this
AB  - organism is highly-related ( approximately 95 % average nucleotide identity) to
AB  - in situ populations. The physiological attributes and metabolic capabilities of
AB  - P. yellowstonensis provide an important foundation for developing an
AB  - understanding of the distribution and function of these populations in YNP.
ER  -

TY  - JOUR
AU  - Jayal, A.
AU  - Johns, B.E.
AU  - Purdy, K.J.
AU  - Maddocks, S.E.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027, Originally Isolated from an Outer Ear Infection.
JO  - Genome Announcements
PY  - 2017
SP  - e01397
EP  - e01317
VL  - 5
AB  - Pseudomonas aeruginosa ATCC 9027 was isolated in 1943 from a case of otitis externa and is
AB  - commonly employed as a quality control strain for sterility,
AB  - assessment of antibiofilm agents, and in vitro study of wound infection. Here, we
AB  - present the 6.34-Mb draft genome sequence and highlight some pertinent genes that
AB  - are associated with virulence.
ER  -

TY  - JOUR
AU  - Jayapal, K.P.
AU  - Lian, W.
AU  - Glod, F.
AU  - Sherman, D.H.
AU  - Hu, W.S.
TI  - Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans.
JO  - BMC Genomics
PY  - 2007
SP  - 229
EP  - 229
VL  - 8
AB  - BACKGROUND: The genomes of Streptomyces coelicolor and Streptomyces lividans bear a
AB  - considerable degree of synteny. While S. coelicolor is the
AB  - model streptomycete for studying antibiotic synthesis and differentiation,
AB  - S. lividans is almost exclusively considered as the preferred host, among
AB  - actinomycetes, for cloning and expression of exogenous DNA. We used whole
AB  - genome microarrays as a comparative genomics tool for identifying the
AB  - subtle differences between these two chromosomes. RESULTS: We identified
AB  - five large S. coelicolor genomic islands (larger than 25 kb) and 18
AB  - smaller islets absent in S. lividans chromosome. Many of these regions
AB  - show anomalous GC bias and codon usage patterns. Six of them are in close
AB  - vicinity of tRNA genes while nine are flanked with near perfect repeat
AB  - sequences indicating that these are probable recent evolutionary
AB  - acquisitions into S. coelicolor. Embedded within these segments are at
AB  - least four DNA methylases and two probable methyl-sensing restriction
AB  - endonucleases. Comparison with S. coelicolor transcriptome and proteome
AB  - data revealed that some of the missing genes are active during the course
AB  - of growth and differentiation in S. coelicolor. In particular, a pair of
AB  - methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor
AB  - biosynthesis, an acyl-CoA dehydrogenase implicated in timing of
AB  - actinorhodin synthesis and bldB, a developmentally significant regulator
AB  - whose mutation causes complete abrogation of antibiotic synthesis belong
AB  - to this category. CONCLUSION: Our findings provide tangible hints for
AB  - elucidating the genetic basis of important phenotypic differences between
AB  - these two streptomycetes. Importantly, absence of certain genes in S.
AB  - lividans identified here could potentially explain the relative ease of
AB  - DNA transformations and the conditional lack of actinorhodin synthesis in
AB  - S. lividans.
ER  -

TY  - JOUR
AU  - Jayaraman, K.S.
TI  - Restriction venture.
JO  - Nature
PY  - 1989
SP  - 272
EP  - 272
VL  - 341
AB  - India has launched its first venture capital company to make restriction enzymes.  Bangalore
AB  - Genei Private Ltd has been set up by Dr. P.S. Babu, a theoretical physicist-turned-molecular
AB  - biologist, and Dr. K. Prasad, an immunologist, both of whom have been associated with the
AB  - Indian Institute of Science, Bangalore.  A large part of the funding for the company comes
AB  - from the Technology Development and Information Company of India.  The new company will obtain
AB  - the know-how for the manufacture of the enzymes from Astra Research Centre, Bangalore, which
AB  - carries out research in medical biotechnology and is developing diagnostic kits for a variety
AB  - of tropical diseases.  The Centre for Genetic Engineering will also assist the new company.
AB  - Restriction enzymes are currently being imported by individual laboratories and in bulk
AB  - quantities by the CSIR Centre for Biochemicals, New Delhi.  The new company will initially
AB  - make the more important and commonly used restriction enzymes.
ER  -

TY  - JOUR
AU  - Jayaraman, R.
TI  - Phase variation and adaptation in bacteria: A 'Red Queen's Race'.
JO  - Curr. Sci.
PY  - 2011
SP  - 1163
EP  - 1171
VL  - 100
AB  - In nature, bacteria are constantly exposed to many stressful conditions of life. This is
AB  - particularly true of pathogens. Survival and
AB  - adaptation under stressful conditions demand multiple strategies,
AB  - genetic as well as phenotypic. Bacteria have many, pre-programmed,
AB  - phenotypic stress response systems which can handle a limited number of
AB  - stresses. Genetically, heritable as well as transient hypermutability
AB  - mechanisms have been found to facilitate bacterial adaptation to varied
AB  - and unpredictable stresses; these processes are not reviewed here.
AB  - Instead, this article will focus on processes which do not increase
AB  - global mutation rates but cause localized hypermutability in specific
AB  - loci called contingency genes which have been identified particularly
AB  - in pathogenic bacteria. These processes are collectively called phase
AB  - and antigenic variations. Most of the contingency genes are involved in
AB  - the synthesis or modification of surface-associated structures and
AB  - enzymes. Phase variation in these genes involves high frequency,
AB  - reversible, switching of their expression (on to off and off to on).
AB  - The mechanisms of this switching are reviewed. However, some phase
AB  - variable genes are not involved in the synthesis or modification of
AB  - surface structures but are components of type I and type III
AB  - restriction-modification (RM) systems. The on/off switching of these
AB  - genes (type III RM genes) leads to regulation of expression of many
AB  - unlinked genes, impacting several properties of cells. This novel type
AB  - of control of multiple gene expression by phase variation has been
AB  - named 'phasevarion'. The adaptive advantages of phase variation in
AB  - contingency genes and phasevarions in the evasion of host immunity,
AB  - virulence, niche adaptation and other phenomena are reviewed with some
AB  - illustrative examples. Phase variation and bacterial adaptation have
AB  - been likened to the 'Red Queen's Race' in Lewis Carrol's classic
AB  - Through the Looking Glass.
ER  -

TY  - JOUR
AU  - Jayashree, S.
AU  - Pooja, S.
AU  - Pushpanathan, M.
AU  - Vishnu, U.
AU  - Sankarasubramanian, J.
AU  - Rajendhran, J.
AU  - Gunasekaran, P.
TI  - Genome Sequence of Lactobacillus fermentum Strain MTCC 8711, a Probiotic Bacterium Isolated from Yogurt.
JO  - Genome Announcements
PY  - 2013
SP  - e00770
EP  - e00713
VL  - 1
AB  - Lactobacillus fermentum strain MTCC 8711 is a lactic acid bacterium isolated from yogurt.
AB  - Here, we describe the draft genome sequence and annotation of this
AB  - strain. The 2,566,297-bp-long genome consisted of a single chromosome and seven
AB  - plasmids. The genome contains 2,609 protein-coding and 74 RNA genes.
ER  -

TY  - JOUR
AU  - Jeddeloh, J.A.
AU  - Stokes, T.L.
AU  - Richards, E.J.
TI  - Maintenance of genomic methylation requires a SW12/SNF2-like protein.
JO  - Nat. Genet.
PY  - 1999
SP  - 94
EP  - 97
VL  - 22
AB  - Altering cytosine methylation by genetic means leads to a variety of developmental defects in
AB  - mice, plants and fungi. Deregulation of cytosine methylation also has a role in human
AB  - carcinogenesis. In some cases, these defects have been tied to the inheritance of epigenetic
AB  - alterations (such as chromatin imprints and DNA methylation patterns) that do not involve
AB  - changes in DNA sequence.  Using a forward genetic screen, we identified a gene (DDM1, decrease
AB  - in DNA methylation) from the flowering plant Arabidopsis thaliana required to maintain normal
AB  - cytosine methylation patterns. Additional ddm1 alleles (som4, 5, 6, 7, 8) were isolated in a
AB  - selection for mutations that relieved transgene silencing (E.J.R., unpublished data). Loss of
AB  - DDM1 function causes a 70% reduction of genomic cytosine methylation, with most of the
AB  - immediate hypomethylation occurring in repeated sequences. In contrast, many low-copy
AB  - sequences initially retain their methylation in ddm1 homozygotes, but lose methylation over
AB  - time as the mutants are propagated through multiple generations by self-pollination. The
AB  - progressive effect of ddm1 mutations on low-copy sequence methylation suggests that ddm1
AB  - mutations compromise the efficiency of methylation of newly incorporated cytosines after DNA
AB  - replication. In parallel with the slow decay of methylation during inbreeding, ddm1 mutants
AB  - accumulate heritable alterations (mutations or stable epialleles) at dispersed sites in the
AB  - genome that lead to morphological abnormalities. Here we report that DDM1 encodes a
AB  - SWI2/SNF2-like protein, implicating chromatin remodelling as an important process for
AB  - maintenance of DNA methylation and genome integrity.
ER  -

TY  - JOUR
AU  - Jeffery, C.J.
TI  - Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins.
JO  - Curr. Opin. Struct. Biol.
PY  - 2004
SP  - 663
EP  - 668
VL  - 14
AB  - Recently determined X-ray crystal structures of moonlighting proteins are helping to elucidate
AB  - how a protein can evolve two different
AB  - functions and, in some cases, switch between its two functions in
AB  - response to cellular conditions. X-ray crystal structures of the I-Anil
AB  - homing endonuclease/maturase and the PutA proline
AB  - dehydrogenase/transcription factor have provided evidence that these
AB  - proteins utilize separate protein surfaces for their multiple
AB  - functions. Also, the structure of the DegP (HtrA) protease/chaperone
AB  - has revealed information about the mechanism of its chaperone activity
AB  - and suggests how the protein regulates its protease activity. Comparing
AB  - the structure of eta-crystallin/retinal dehydrogenase with structures
AB  - of its single-function enzyme homologs provides clues to changes in the
AB  - protein structure that may have improved its ability to serve as a
AB  - crystallin, but at the same time may have adversely affected its
AB  - catalytic activity.
ER  -

TY  - JOUR
AU  - Jeganathan, L.P.
AU  - Prakash, L.
AU  - Sivakumar, N.
AU  - Antony, A.
AU  - Alqarawi, S.
AU  - Prajna, L.
AU  - Devarajan, B.
AU  - Mohankumar, V.
TI  - Draft Genome Sequence of an Invasive Multidrug-Resistant Strain, Pseudomonas aeruginosa BK1, Isolated from a Keratitis Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00153
EP  - e00114
VL  - 2
AB  - Pseudomonas aeruginosa infections are difficult to treat due to the presence of a multitude of
AB  - virulence factors and antibiotic resistance. Here, we report the
AB  - draft genome sequence of P. aeruginosa BK1, an invasive and multidrug-resistant
AB  - strain, isolated from a bacterial keratitis patient in southern India.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
TI  - Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?
JO  - Gene
PY  - 2003
SP  - 13
EP  - 16
VL  - 317
AB  - Bacteria frequently exchange DNA among each other by horizontal gene transfer. However,
AB  - maintenance of species identity and in particular
AB  - speciation requires a certain barrier against an unregulated uptake of
AB  - foreign DNA. Here it is suggested that formation of such a barrier is one
AB  - important biological function of restriction/modification systems, in
AB  - addition to the classical function of protection of bacteria against
AB  - bacteriophage infection. This model explains the extreme variability and
AB  - wide distribution of restriction/modification systems among prokaryotes,
AB  - the prevalence of RM-systems in pathogenic bacteria and the existence of
AB  - several RM-systems in single bacterial strains.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
TI  - Molecular enzymology of mammalian DNA methyltransferases.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 2006
SP  - 203
EP  - 225
VL  - 301
AB  - DNA methylation is an essential modification of DNA in mammals that is involved in gene
AB  - regulation, development, genome defence and disease.
AB  - In mammals 3 families of DNA methyltransferases (MTases) comprising (so
AB  - far) 4 members have been found: Dnmt1, Dnmt2, Dnmt3A and Dnmt3B. In
AB  - addition, Dnmt3L has been identified as a stimulator of the Dnmt3A and
AB  - Dnmt3B enzymes. In this review the enzymology of the mammalian DNA
AB  - MTases is described, starting with a depiction of the catalytic
AB  - mechanism that involves covalent catalysis and base flipping.
AB  - Subsequently, important mechanistic features of the mammalian enzyme
AB  - are discussed including the specificity of Dnmt1 for hemimethylated
AB  - target sites, the target sequence specificity of Dnmt3A, Dnmt3B and
AB  - Dnmt2 and the flanking sequence preferences of Dnmt3A and Dnmt3B. In
AB  - addition, the processivity of the methylation reaction by Dnmt1, Dnmt3A
AB  - and Dnmt3B is reviewed. Finally, the control of the catalytic activity
AB  - of mammalian MTases is described that includes the regulation of the
AB  - activity of Dnmt1 by its N-terminal domain and the interaction of
AB  - Dnmt3A and Dnmt3B with Dnmt3L. The allosteric activation of Dnmt1 for
AB  - methylation at unmodified sites is described. Wherever possible,
AB  - correlations between the biochemical properties of the enzymes and
AB  - their physiological functions in the cell are indicated.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
TI  - The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
JO  - Biol. Chem.
PY  - 2001
SP  - 707
EP  - 710
VL  - 382
AB  - Methylation of DNA occurs at the C5 and N4 positions of cytosine and N6 of adenine. The
AB  - chemistry of methylation is similar among methyltransferases specific for cytosine-N4 and
AB  - adenine-N6. Moreover these enzymes have similar structures and active sites. Previously it has
AB  - been demonstrated that the DNA-(adenine-N6)-methyltransferases M.EcoRV, M.EcoRI, E. coli dam
AB  - and both domains of M.FokI also modify cytosine residues at the N4 position [Jeltsch et al.,
AB  - J. Biol. Chem. 274 (1999), 19538-19544]. Here we show that the cytosine-N4 methyltransferase
AB  - M.PvuII, which modifies the second cytosine in CAGCTG sequences, also methylates adenine
AB  - residues in CAGATG/CAGCTG substrates in which the target cytosine is replaced by adenine in
AB  - one strand of the recognition sequence. Therefore, adenine-N6 and cytosine-N4
AB  - methyltransferases have overlapping target base specificities. These results demonstrate that
AB  - the target base recognition by N-specific DNA methyltransferases is relaxed in many cases.
AB  - Furthermore, it shows that the catalytic mechanisms of adenine-N6 and cytosine-N4
AB  - methyltransferases are very similar.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
TI  - Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.
JO  - Chembiochem
PY  - 2002
SP  - 274
EP  - 293
VL  - 3
AB  - DNA methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to
AB  - cytosine or adenine bases in DNA. These
AB  - enzymes challenge the Watson/Crick dogma in two instances: 1) They
AB  - attach inheritable information to the DNA that is not encoded in the
AB  - nucleotide sequence. This so-called epigenetic information has many
AB  - important biological functions. In prokaryotes, DNA methylation is used
AB  - to coordinate DNA replication and the cell cycle, to direct
AB  - postreplicative mismatch repair, and to distinguish self and nonself
AB  - DNA. In eukaryotes, DNA methylation contributes to the control of gene
AB  - expression, the protection of the genome against selfish DNA,
AB  - maintenance of genome integrity, parental imprinting, X-chromosome
AB  - inactivation in mammals, and regulation of development, 2) The
AB  - enzymatic mechanism of DNA methyltransferases is unusual, because these
AB  - enzymes flip their target base out of the DNA helix and, thereby,
AB  - locally disrupt the B-DNA helix. This review describes the biological
AB  - functions of DNA methylation in bacteria, fungi, plants, and mammals.
AB  - In addition, the structures and mechanisms of the DNA
AB  - methyltransferases, which enable them to specifically recognize their
AB  - DNA targets and to induce such large conformational changes of the DNA,
AB  - are discussed.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
TI  - Circular permutations in the molecular evolution of DNA methyltransferase.
JO  - J. Mol. Evol.
PY  - 1999
SP  - 161
EP  - 164
VL  - 49
AB  - Circular permutations of genes during molecular evolution often are regarded as elusive,
AB  - although a simple model can explain these rearrangements. The model assumes that first a gene
AB  - duplication of the precursor gene occurs in such a way that both genes become fused in frame,
AB  - leading to a tandem protein. After generation of a new start codon within the 5' part of the
AB  - tandem gene and a stop at an equivalent position in the 3' part of the gene, a protein is
AB  - encoded that represents a perfect circular permutation of the precursor gene product. The
AB  - model is illustrated here by the molecular evolution of adenine-N6 DNA methyltransferases.
AB  - Beta- and gamma-type enzymes of this family can be interconverted by a single circular
AB  - permutation event. Interestingly, tandem proteins, proposed as evolutionary intermediates
AB  - during circular permutation, can be directly observed in the case of adenine
AB  - methyltransferases, because some enzymes belonging to type IIS, like the FokI
AB  - methyltransferase, are built up by two fused enzymes, both of which are active independently
AB  - of each other. The mechanism for circular permutation illustrated here is very easy and
AB  - applicable to every protein. Thus, circular permutation can be regarded as a normal process in
AB  - molecular evolution and a changed order of conserved amino acid motifs should not be
AB  - interpreted to argue against divergent evolution.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Alves, J.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - On the catalytic mechanism of EcoRI and EcoRV.  A detailed proposal based on biochemical results, structural data and molecular modelling.
JO  - FEBS Lett.
PY  - 1992
SP  - 4
EP  - 8
VL  - 304
AB  - EcoRI and EcoRV have a very similar active site, as is apparent from a comparison of the
AB  - structures of their respective protein-DNA complexes.  Based on structural and mechanistic
AB  - data, as well as detailed molecular modelling presented here, a mechanism for the DNA cleavage
AB  - by these enzymes is suggested in which the attacking water molecule is activated by the
AB  - phosphate group 3' to the scissile phosphodiester bond, and in which the leaving group is
AB  - protonated by a water molecule associated with the essential cofactor, Mg2+.  The mechanism
AB  - proposed may also apply to other nucleases.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Alves, J.
AU  - Oelgeschlager, T.
AU  - Wolfes, H.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence -GAATTC-and for coupling specific DNA binding to catalysis.
JO  - J. Mol. Biol.
PY  - 1993
SP  - 221
EP  - 234
VL  - 229
AB  - The Gln115 residue of the EcoRI restriction endonuclease has been proposed to form a
AB  - hydrophobic contact to the methyl group of the inner thymidine of the EcoRI recognition
AB  - sequence -GAATTC- and to be involved in intramolecular hydrogen bonds to the mainchain at
AB  - positions 140 and 143 as well as to the side-chain of Asn173. We have exchanged Gln115 for Ala
AB  - and Glu by site-directed mutagenesis and analysed the purified mutant protein (Q115A and
AB  - Q115E) biochemically and physico-chemically. Q115A and Q115E have the same secondary structure
AB  - composition as wild-type EcoRI but are less stable towards thermal denaturation than the
AB  - wild-type enzyme. In contrast to wild-type EcoRI the mutant proteins show a biphasic
AB  - denaturation profile under alkaline pH, presumably because the amino acid exchange labilizes
AB  - one part of the molecule, which unfolds before the rest of the protein is denatured. Q115A is
AB  - catalytically inactive under normal buffer conditions, in part due to a diminished affinity
AB  - towards DNA. At low ionic strength and alkaline pH, as well as in the presence of Mn2+, i.e.
AB  - under conditions where wild-type EcoRI shows a relaxed specificity, Q115A is active, however
AB  - not as much as wild-type EcoRI. Under these conditions it cleaves the canonical sequence
AB  - -GAATTC- with the same kcat/km value as the sequence -GAAUTC-, which differs from the former
AB  - sequence by a single methyl group, while wild-type EcoRI shows a tenfold lower kcat/Km for
AB  - cleavage of -GAAUTC- than for -GAATTC-. Binding experiments, carried out in the absence of
AB  - Mg2+, demonstrate that Q115A has a similar affinity toward -GAATTC- as to -GAAUTC-, while
AB  - wild-type EcoRI binds to -GAATTC- with a tenfold preference over -GAAUTC-. On the basis of
AB  - these thermodynamic and kinetic results it can be concluded that the hydrophobic contact
AB  - between the gamma-methylene group of Gln115 and the methyl group of the inner thymidine
AB  - contributes about 3 kJ/mol (0.7 kcal/mol) to the energy of interaction, both in the ground and
AB  - the transition state, Q115E is catalytically inactive under normal buffer conditions, but
AB  - becomes active at low ionic strength or in the presence of Mn2+. Different from Q15A, Q115E is
AB  - inactive at alkaline pH and its DNA binding affinity is highest at acidic pH. The dependence
AB  - of its DNA cleavage activity on pH, which is governed by a pKa of 7.35, can be attributed to
AB  - the protonation of the newly introduced glutamic acid residue, if it is assumed that the
AB  - carboxyl group is located in a non-polar environment and/or involved in a hydrogen bond as the
AB  - donor. Taken together, these results demonstrate that Gln115, as suggested on the basis of the
AB  - revised EcoRI-DNA co-crystal structure, interacts with the inner thymidine of the EcoRI
AB  - recognition sequence and has a structure stabilizing role. In addition, our results suggest
AB  - that Gln115 is crucial for coupling specific DNA binding to catalysis under normal buffer
AB  - conditions and we suggest that this coupling is achieved because direct and indirect
AB  - involvement of Gln115 in base recognition induces local conformational alterations of the
AB  - C-terminal region of beta-strand beta3, which contains Lys113 and Glu111 that are constituents
AB  - of the catalytic centre of EcoRI. Activation of the catalytic centre, therefore, could be
AB  - triggered by Gln115.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Alves, J.
AU  - Urbanke, C.
AU  - Maass, G.
AU  - Eickstein, H.
AU  - Lianshan, Z.
AU  - Bayer, E.
AU  - Pingoud, A.
TI  - A dodecapeptide comprising the extended chain-alpha-4 region of the restriction endonuclease EcoRI specifically binds to the EcoRI recognition site.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 5122
EP  - 5129
VL  - 270
AB  - The restriction endonuclease EcoRI binds and cleaves DNA containing GAATTC sequences with high
AB  - specificity. According to the crystal structure, most of the specific contacts of the enzyme
AB  - to the DNA are formed by the extended chain region and the first turn of alpha-helix alpha-4
AB  - (amino acids 137-145). Here, we demonstrate that a dodecapeptide (WDGMAAGNAIER), which is
AB  - identical in the underlined parts (M-R) of its sequence to EcoRI amino acids 137-145,
AB  - specifically binds to GAATTC sequences. The peptide inhibits DNA cleavage by EcoRI but not by
AB  - BamHI, BclI, EcoRV, HindIII, PacI, and XbaI. DNA cleavage by XbaI is slowed down at sites that
AB  - partially overlap with EcoRI sites. The peptide inhibits cleavage of GAATTC sites by ApoI,
AB  - which recognizes the sequence RAATTY. It interferes with DNA methylation by the EcoRI
AB  - methyltransferase but not by the BamHI methyltransferase. It competes with EcoRI for DNA
AB  - binding. Based on these results, the DNA binding constant of the peptide to GAATTC sequences
AB  - was calculated to be 3 x 10/4 M-1. DNA binding is not temperature-dependent, suggesting that
AB  - binding of the peptide is entropy-driven. As the peptide does not show any nonspecific binding
AB  - to DNA, its DNA binding specificity is similar to that of EcoRI, in spite of the fact that the
AB  - affinity is much smaller. These results suggest that contacts to the phosphate groups in EcoRI
AB  - mainly provide binding affinity, whereas the specificity of EcoRI is based to a large extent
AB  - on sequence-specific base contacts.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Alves, J.
AU  - Wolfes, H.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 8499
EP  - 8503
VL  - 90
AB  - The crystal structure analyses of the EcoRI-DNA and EcoRV-DNA complexes do not provide clear
AB  - suggestions as to which amino acid residues are responsible for the activation of water to
AB  - carry out the DNA cleavage. Based on molecular modeling, we have proposed recently that the
AB  - attacking water molecule is activated by the negatively charged pro-Rp phosphoryl oxygen of
AB  - the phosphate group 3' to the scissile phosphodiester bond. We now present experimental
AB  - evidence to support this proposal. (i) Oligodeoxynucleotide substrates lacking this phosphate
AB  - group in one strand are cleaved only in the other strand. (ii) Oligodeoxynucleotide substrates
AB  - carrying an H-phosphonate substitution at this position in both strands and, therefore,
AB  - lacking a negatively charged oxygen at this position are cleaved at least four orders of
AB  - magnitude more slowly than the unmodified substrate. These results are supported by other
AB  - modification studies: oligodeoxynucleotide substrates with a phosphorothioate substitution at
AB  - this position in both strands are cleaved only if the negatively charged sulfur is in the Rp
AB  - configuration as shown for EcoRI [Koziolkiewics, M. and Stec, W.J. (1992) Biochemistry 31,
AB  - 9460-9466] and EcoRV (B.A. Connolly, personal communication). As the phosphate residue 3' to
AB  - the scissile phosphodiester bond is not needed for strong DNA binding by both enzymes, these
AB  - findings strongly suggest that this phosphate group plays an active role during catalysis.
AB  - This proposal furthermore, give a straightforward explanation of why in the EcoRI-DNA and
AB  - EcoRV-DNA complexes the DNA is distorted differently, but in each case the 3' phosphate group
AB  - closely approaches the phosphate group that is attacked. Finally, an alternative mechanism for
AB  - DNA cleavage involving two metal ions is unlikely in the light of our findings that both EcoRI
AB  - and EcoRV and need only one Mg2+ per active site for cleavage.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Alves, J.
AU  - Wolfes, H.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA.
JO  - Biochemistry
PY  - 1994
SP  - 10215
EP  - 10219
VL  - 33
AB  - Linear diffusion is a mechanism to accelerate association rates beyond their three-dimensional
AB  - diffusional limit. It is employed by the restriction endonuclease EcoRI as well as many other
AB  - proteins interacting with specific DNA sequences to locate their target sites on the
AB  - macromolecular substrate. In order to investigate biochemical and biophysical details of the
AB  - linear diffusion process, we have developed a competitive cleavage assay which allows us to
AB  - assess with great accuracy the influence of sequence, sequence context, and other structural
AB  - features on the linear diffusion of EcoRI on DNA. We show here that linear diffusion is not a
AB  - hopping but a sliding movement in which EcoRI follows the helical pitch of the DNA, because it
AB  - does not "overlook" any cleavage site. Linear diffusion is slowed when EcoRI encounters sites
AB  - on the DNA which resemble its recognition site ("star" sites). Pauses of up to 20 s are
AB  - induced, depending on sequence and orientation of the star site. These data suggest that EcoRI
AB  - can bind to DNA in two binding modes: one tight, specific, and immobile, leading to DNA
AB  - cleavage, and another one loose and nonspecific, allowing for linear diffusion. Depending on
AB  - the similarity between the recognition sequence and the DNA sequence being encountered by
AB  - EcoRI, there will be a continuous transition between these binding modes. Other proteins bound
AB  - to the DNA and irregular DNA structures such as bent DNA or a triple helix constitute a
AB  - barrier than cannot easily be passed by EcoRI.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Christ, F.
AU  - Fatemi, M.
AU  - Roth, M.
TI  - On the substrate specificity of DNA methyltransferases.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 19538
EP  - 19544
VL  - 274
AB  - Methylation of DNA is important in many organisms and essential in mammals. Nucleobases can be
AB  - methylated at the adenine-N6, cytosine-N4, or cytosine-C5 atoms by specific DNA
AB  - methyltransferases. We show here that the M.EcoRV, M.EcoRI, and Escherichia coli dam
AB  - methyltransferases as well as the N- and C-terminal domains of the M. FokI enzyme, which were
AB  - formerly all classified as adenine-N6 DNA methyltransferases, also methylate cytosine residues
AB  - at position N4. Kinetic analyses demonstrate that the rate of methylation of cytosine residues
AB  - by M.EcoRV and the M.FokI enzymes is reduced by only 1-2 orders of magnitude in relation to
AB  - methylation of adenines. This result shows that although these enzymes methylate DNA in a
AB  - sequence specific manner, they have a low substrate specificity with respect to the target
AB  - base. This unexpected finding has implications on the mechanism of adenine-N6 DNA
AB  - methyltransferases. Sequence comparisons suggest that adenine-N6 and cytosine-N4
AB  - methyltransferases have changed their reaction specificity at least twice during evolution, a
AB  - model that becomes much more likely given the partial functional overlap of both enzyme types.
AB  - In contrast, methylation of adenine residues by the cytosine-N4 methyltransferase M.BamHI was
AB  - not detectable. On the basis of our results, we suggest that adenine-N6 and cytosine-N4
AB  - methyltransferases should be grouped into one enzyme family.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Friedrich, T.
AU  - Roth, M.
TI  - Kinetics of methylation and binding of DNA by the EcoRV adenine-N6 methyltransferase.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 747
EP  - 758
VL  - 275
AB  - The EcoRV DNA methyltransferase specifically methylates the first adenine within its
AB  - recognition sequence GATATC.  Methylation rates of DNA by this enzyme are strongly influenced
AB  - by the length of oligonucleotide substrates employed.  In substrates >20 bp compared to a
AB  - 12mer substrate, the kcat/Km increases 100-fold, although the enzyme does not contact more
AB  - than 12 base-pairs on the DNA.  Single-turnover rates are higher than kcat values.  M.EcoRV
AB  - binding to DNA is fast but dissociation from the DNA is slow, demonstrating that the
AB  - multiple-turnover rate is limited by the rate of product release.  The kinetics of DNA binding
AB  - by M.EcoRV are not in accordance with the thermodynamic binding constant, suggesting that the
AB  - M.EcoRV-DNA complex is involved in a slow conformational change.  The salt dependence of DNA
AB  - binding is different for non-specific substrates (d ln(KAss)/d ln(cNaCl) = -2, indicative of
AB  - electrostatic interactions) and specific substrates (d ln(KAss)/d ln(cNaCl)=+1, indicative of
AB  - hydrophobic interactions).  This result demonstrates that the M.EcoRV-DNA complex has a
AB  - different conformation in both binding modes.  M.EcoRV does not discriminate between
AB  - hemimethylated and unmethylated substrates.  Using the 20mer we have analyzed the temperature
AB  - and pH dependence of the single-turnover rate constant of M.EcoRV-DNA methylation by M.EcoRV
AB  - which has an activation energy of 40 kJ/mol and its rate increases with increasing pH.  The pH
AB  - dependence reveals the presence of an ionizable residue with a pKa of 7.9, which must be
AB  - unprotonated for catalysis.  The rates of DNA methylation remain unchanged if an abasic site
AB  - is introduced instead of the thymidine residue that is base-paired to the target adenine,
AB  - demonstrating that flipping out the target adenine cannot contribute to the rate-limiting step
AB  - of the enzymatic reaction.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Fritz, A.
AU  - Alves, J.
AU  - Wolfes, H.
AU  - Pingoud, A.
TI  - A fast and accurate enzyme-linked immunosorbent assay for the determination of the DNA cleavage activity of restriction endonucleases.
JO  - Anal. Biochem.
PY  - 1993
SP  - 234
EP  - 240
VL  - 213
AB  - We have developed an assay procedure to monitor the cleavage of DNA substrates by restriction
AB  - endonucleases. This procedures uses DNA substrates that are labeled with biotin on one 5' end
AB  - and with an antigenic group, e.g., flourescein or digoxigenin, on the other 5' end. After
AB  - incubation with the restriction enzyme, the reaction is stopped with EDTA and an aliquot is
AB  - pipetted into the well of an avidin-coated microtiter plate. This imobilizes the unreacted
AB  - substrate and the biotinylated cleavage product, whereas the other cleavage product labeled
AB  - with the antigenic group is subsequently washed off. The unreacted substrate is detected by an
AB  - enzyme-linked immunosorbent assay with an appropriate enzyme-linked anitbody. To test our
AB  - assay we have measured the steady-state rate constants for cleavage of DNA by EcoRI yielding a
AB  - kcat of 8.6 min and a Km of 150 nM, which are close to values measured with other assays. The
AB  - advantage of this assay is that it is not only fast and accurate, but also very sensitive. It
AB  - allows for many samples to be analyzed in parallel and lends itself to automation.
AB  - Furthermore, this assay can be designed as a competitive assay, when two substrates carrying
AB  - different antigenic groups are used. The usefulness of such a competitive assay is
AB  - demonstrated by determining the influence of sequence context on the rate of DNA cleavage by
AB  - EcoRI.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Gowhar, H.
TI  - Molecular enzymology of the DNA-(adenine-N6)-methyltransferase M.EcoRV: Kinetic mechanism, kinetics of DNA binding and bending, and linear diffusion.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A312
EP  - A312
VL  - 28
AB  - Methylation of DNA is important in many organisms and essential in mammals.  Nucleobases can
AB  - be methylated at the adenine-N6, cytosine-N4 or cytosine-C5 atoms by specific DNA
AB  - methyltransferases.  The M.EcoRV adenine-N6 DNA methyltransferase specifically transfers a
AB  - methyl group from AdoMet to the first adenine within GATATC sequences.  We show here that
AB  - substrate binding to the enzyme follows an ordered bi-bi mechanism with AdoMet binding before
AB  - DNA.  After DNA binding a non-specific enzyme-DNA complex is formed that slides along the DNA
AB  - for more than 1800 bps by linear diffusion.  Upon specific complex formation the DNA is bent
AB  - in a fast process with rate constants >10s^-1.  The cofactor of the methylation reaction,
AB  - S-adenosylmethionine, but not the product of the reaction, S-adenosylhomocysteine, promotes
AB  - specific complex formation.  In the presence of cofactor, the specific complex can change into
AB  - a second conformation, in which the target sequence is more tightly contacted by the enzyme.
AB  - M.EcoRV exists in a slow equilibrium between an open and a closed conformation.  Cofactor
AB  - binding to the apoenzyme shifts the conformational equilibrium to the open conformation
AB  - thereby promoting DNA binding.  Formation of a closed enzyme-DNA complex is a slow process
AB  - (rate constant < 0.7 min^-1), that limits the rate of DNA methylation under single turnover
AB  - conditions.  Product release requires opening of the closed complex which is very slow (rate
AB  - constant < 0.05-0.1 min^-1) and limits the multiple turnover rate constant.  Slow DNA release
AB  - from the closed complex also explains the high efficiency of linear diffusion of M.EcoRV on
AB  - DNA.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Gumport, R.I.
TI  - DNA Methyltransferases, Bacterial.
JO  - Encyclopedia of Biological Chemistry
PY  - 2004
SP  - 644
EP  - 651
AB  - DNA methylation has a number of important roles in bacteria including the control of gene
AB  - expression, DNA replication, and the cell cycle.  In addition, it is involved in mismatch
AB  - repair and protection of bacteria from foreign DNA in restriction modification systems.  DNA
AB  - methyltransferases are the enzymes that methylate DNA.  They deposit methyl groups on DNA at
AB  - the N6-position of adenine, or the N4- or C5-positions of cytosine in a sequence-specific
AB  - reaction using S-adenosyl-L-methionine as the methyl group donor.  Their reaction mechanism
AB  - includes rotating the target base completely out of the DNA helix in a biphasic process, where
AB  - fast flipping of the base out of the double helix is followed by a slower binding of the
AB  - flipped base into a hydrophobic pocket of the enzyme.  DNA MTases comprise two structural
AB  - domains: the larger domain contains the cofactor-binding site and the binding pocket for the
AB  - flipped base and the smaller domain is responsible for most of the sequence-specific contacts
AB  - of the enzyme to the target site.  The structures of large domains from all known DNA MTases
AB  - are similar, whereas the small domains are more heterogeneous in sequence and structure.  DNA
AB  - MTases are an attractive model system to study how proteins recognize specific sequences of
AB  - DNA and how the specificity of DNA recognition changes during molecular evolution.  In
AB  - addition, they illustrate how the biochemical properties of the enzymes are related to their
AB  - biological functions.  In this article, we shall describe the biological roles of DNA
AB  - methylation in prokaryotes, discuss the chemistry of the enzymatic methylation reaction
AB  - performed by the DNA methyltransferases (the focus of the review), and finally discuss aspects
AB  - of the enzymology of this fascinating family of enzymes that reveal how these molecular
AB  - machines perform their complicated biochemical tasks.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Jurkowska, R.Z.
TI  - Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 8556
EP  - 8575
VL  - 44
AB  - In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases,
AB  - which are all large multi-domain proteins containing a catalytic C-terminal domain and an
AB  - N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs
AB  - were uncovered. It was shown that their catalytic activity is under allosteric control of
AB  - N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD
AB  - domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a
AB  - concerted manner by interactors and posttranslational modifications (PTMs). In this review, we
AB  - describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA
AB  - binding, catalytic mechanism, multimerization and the processes controlling their stability in
AB  - cells with a focus on their regulation and chromatin targeting by PTMs, interactors and
AB  - chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory
AB  - domains acts as a general switch for the modulation of the function of DNMTs, providing
AB  - numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT
AB  - activity and targeting. The combined regulation of DNMT targeting and catalytic activity
AB  - contributes to the precise spatiotemporal control of DNMT function and genome methylation in
AB  - cells.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Jurkowska, R.Z.
TI  - Multimerization of the Dnmt3a DNA Methyltransferase and Its Functional Implications.
JO  - Prog. Mol. Biol. Transl. Sci.
PY  - 2013
SP  - 445
EP  - 464
VL  - 117
AB  - The Dnmt3a DNA cytosine-C5 methyltransferase has been recently shown to exhibit a complex
AB  - oligomerization and multimerization potential, the
AB  - structural basis and functional implications of which will be the
AB  - subject of this contribution. The enzyme forms a linear heterotetramer
AB  - with Dnmt3L, in which the interaction of Dnmt3a and 3L stimulates the
AB  - catalytic activity of Dnmt3a. Isolated Dnmt3a forms protein filaments
AB  - that bind to several DNA molecules oriented in parallel, which plays an
AB  - essential role in the location of the enzyme to heterochromatin. Dnmt3L
AB  - disrupts Dnmt3a protein filaments and leads to a redistribution of the
AB  - enzyme in cells toward euchromatin. Finally, Dnmt3a complexes and
AB  - Dnmt3a/3L heterotetramers cooperatively multimerize on DNA forming
AB  - protein DNA filaments. This leads to a preference of the enzyme for
AB  - periodic methylation of DNA and supports its heterochromatic
AB  - localization.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Jurkowska, R.Z.
AU  - Jurkowski, T.P.
AU  - Liebert, K.
AU  - Rathert, P.
AU  - Schlickenrieder, M.
TI  - Application of DNA methyltransferases in targeted DNA methylation.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2007
SP  - 1233
EP  - 1240
VL  - 75
AB  - DNA methylation is an essential epigenetic modification. In bacteria, it is involved in gene
AB  - regulation, DNA repair, and control of cell cycle. In eukaryotes, it acts in concert with
AB  - other epigenetic modifications to regulate gene expression and chromatin structure. In
AB  - addition to these biological roles, DNA methyltransferases have several interesting
AB  - applications in biotechnology, which are the main focus of this review, namely, (1) in vivo
AB  - footprinting: as several bacterial DNA methyltransferases cannot methylate DNA bound to
AB  - histone proteins, the pattern of DNA methylation after expression of DNA methyltransferases in
AB  - the cell allows determining nucleosome positioning; (2) mapping the binding specificity of DNA
AB  - binding proteins: after fusion of a DNA methyltransferase to a DNA-binding protein and
AB  - expression of the fusion protein in a cell, the DNA methylation pattern reflects the
AB  - DNA-binding specificity of the DNA-binding protein; and (3) targeted gene silencing: after
AB  - fusion of a DNA methyltransferase to a suitable DNA-binding domain, DNA methylation can be
AB  - directed to promoter regions of target genes. Thereby, gene expression can be switched off
AB  - specifically, efficiently, and stably, which has a number of potential medical applications.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Kroger, M.
AU  - Pingoud, A.
TI  - Evidence for an evolutionary relationship among type-II restriction endonucleases.
JO  - Gene
PY  - 1995
SP  - 7
EP  - 16
VL  - 160
AB  - Type-II restriction-modification (R-M) systems comprise two enzymes, a DNA methyltransferase
AB  - (MTase) and a restriction endonuclease (ENase), each of which specifically interact with the
AB  - same 4-8-bp sequence.  All type-II MTases share several amino acid (aa) sequence motifs, which
AB  - makes an evolutionary relatedness among these enzymes probable.  The type-II ENases, in
AB  - contrast, except for some homologous isoschizomers, do not share significant aa sequence
AB  - similarity.  Therefore, ENases in general have been considered unrelated.  Here we show that
AB  - in addition to the analysis of the genotype (aa sequence), a comparison of the phenotype
AB  - (recognition sequence) of these enzymes can provide independent information regarding
AB  - evolutionary relationships, and thereby, help to analyze the significance of weak aa sequence
AB  - similarities.  Multistep Monte-Carlo analyses were employed to demonstrate that the
AB  - recognition sequences of those ENases, which were found to be related by a progressive
AB  - multiple aa sequence alignment, are more similar to each other than would be expected by
AB  - chance.  This analysis supports the notion that not only type-II MTases, but also type-II
AB  - ENases did not arise independently in evolution, but rather evolved from one or a few
AB  - primordial DNA-modifying and DNA-cleaving enzymes, respectively.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Maschke, H.
AU  - Selent, U.
AU  - Wenz, C.
AU  - Kohler, E.
AU  - Connolly, B.A.
AU  - Thorogood, H.
AU  - Pingoud, A.
TI  - DNA binding specificity of the EcoRV restriction endonuclease is increased by Mg2+ binding to a metal ion binding site distinct from the catalytic center of the enzyme.
JO  - Biochemistry
PY  - 1995
SP  - 6239
EP  - 6246
VL  - 34
AB  - In contrast to many other type II restriction endonucleases, EcoRV binds specifically to DNA
AB  - only in the presence of Mg2+. According to the co-crystal structure of an EcoRV--DNA complex,
AB  - Mg2+ ion(s) bind to the active site of EcoRV liganded by Glu45, Asp74, and Asp90. Here we
AB  - present experimental evidence suggesting that the EcoRV--DNA complex also interacts with Mg2+
AB  - ions at other sites: (i) We have prepared an EcoRV triple mutant, in which all acidic amino
AB  - acids in the catalytic center are replaced by alanine. This mutant is catalytically inactive.
AB  - It binds nonspecifically to DNA in the absence of Mg2+, whereas it binds specifically to DNA
AB  - in the presence of Mg2+. This means that Mg2+ induces specific DNA binding in this mutant,
AB  - although all Mg2+ ligands in the catalytic center are removed. Therefore, additional
AB  - interactions between Mg2+ and the EcoRV--DNA complex probably occur at sites distinct from the
AB  - catalytic center. (ii) We have measured the specific and nonspecific DNA binding constants of
AB  - EcoRV and of the triple mutant in the presence and absence of Mg2+. Mg2+ reduces nonspecific
AB  - binding by 3-4 orders of magnitude, presumably because Mg2+ ions bound to the DNA have to be
AB  - released upon complex formation. In contrast, the specific binding of the wild-type enzyme and
AB  - the triple mutant is increased in the presence of Mg2+. This result can only be explained if a
AB  - Mg2+ ion binds to the specific EcoRV--DNA complex probably at a site distinct from the
AB  - catalytic center. (iii) To locate additional metal ion binding sites in the EcoRV--DNA
AB  - complex, we have determined the cleavage rates of several undecadeoxynucleotides which contain
AB  - single phosphorothioate linkages in the presence of Mg2+ and Mn2+. It turned out that an
AB  - oligodeoxynucleotide in which the first phosphate group within the GpATATC sequence (p3) is
AB  - replaced by an Rp phosphorothioate is cleaved by a factor of 50 more readily in the presence
AB  - of Mn2+ than with Mg2+. This result is interpreted to mean that p3, which is far away from the
AB  - active site of EcoRV, interacts with a Mg2+ ion. (iv) We have produced the EcoRV Y219C mutant
AB  - whose DNA cleavage activity compared to wild-type EcoRV is reduced by 3 orders of magnitude.
AB  - It binds nonspecifically to DNA in the absence of Mg2+ but not detectably in the presence of
AB  - Mg2+. Although the distinct role of Tyr219 is unclear at present, it must be pointed out that
AB  - this amino acid is far away from the active site of EcoRV but located in close proximity to
AB  - amino acid residues vis a vis p3. Hence, the behavior of this mutant also supports the
AB  - conclusion that an important interaction between Mg2+ and the EcoRV--DNA complex occurs at a
AB  - site distinct from the catalytic center.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Nellen, W.
AU  - Lyko, F.
TI  - Two substrates are better than one: dual specificities for Dnmt2 methyltransferases.
JO  - Trends Biochem. Sci.
PY  - 2006
SP  - 306
EP  - 308
VL  - 31
AB  - Dnmt2 enzymes have been widely conserved during evolution and contain all of the signature
AB  - motifs of DNA (cytosine-5)-methyltransferases;
AB  - however, the DNA methyltransferase activity of these proteins is
AB  - comparatively weak and their biochemical and functional properties
AB  - remain enigmatic. Recent evidence now shows that Dnmt2 has a novel tRNA
AB  - methyltransferase activity, raising the possibility that the biological
AB  - roles of these proteins might be broader than previously thought. This
AB  - finding has important implications for understanding the evolutionary
AB  - relationships among these enzymes.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA.
JO  - Biochemistry
PY  - 1998
SP  - 2160
EP  - 2169
VL  - 37
AB  - We have examined the kinetic parameters of linear diffusion of EcoRV on DNA.  The data were
AB  - analyzed by Monte Carlo simulations in which the efficiency of recognition of EcoRV sites
AB  - during linear diffusion, the efficiency of linear diffusion, and the behavior of enzymes at
AB  - the ends of linear DNA is explicitly treated.  The analysis of the dependence of linear
AB  - diffusion on the concentrations of NaCl and MgCl2 shows that linear diffusion is maximal at 50
AB  - mM NaCl under all concentrations of MgCl2 tested and increases with increasing concentrations
AB  - of Mg2+ up to 10 mM, the highest concentration used in the test.  Under these conditions,
AB  - EcoRV scans 2 x 10^6 bp during one binding event with a velocity of about 1.7 x 10^6 bp s-1.
AB  - The enzyme tends to overlook cleavage sites at 1 mM but not at 10 mM MgCl2.  This result
AB  - confirms the thermodynamic finding that EcoRV does not bind very specifically to DNA in the
AB  - absence of Mg2+.  It demonstrates that there is a Mg2+-dependent continuous transition between
AB  - a nonspecific and a specific binding mode of EcoRV to DNA.  By comparing cleavage rates of
AB  - linear DNA whose ends are free or blocked, we have shown that EcoRV has a very low probability
AB  - to fall off at the ends of linear DNA.  The enzyme rather is "reflected" and continues linear
AB  - diffusion.  EcoRV does not cleave oligonucleotides containing two EcoRV sites processively.
AB  - Consequently, dissociation of the enzyme from the cleavage products is not preceded by a
AB  - transfer to nonspecific DNA, and linear diffusion is not involved in product dissociation in
AB  - EcoRV.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.
JO  - J. Mol. Evol.
PY  - 1996
SP  - 91
EP  - 96
VL  - 42
AB  - Restriction modification (RM) systems serve to protect bacteria against
AB  - bacteriophages.  They comprise a restriction endonuclease activity that specifically cleaves
AB  - DNA
AB  - and a corresponding methyltransferase activity that specifically methylates the DNA, thereby
AB  - protecting it from cleavage.  Such systems are very common in bacteria.  To find out whether
AB  - the
AB  - widespread distribution of RM systems is due to horizontal gene transfer, we have compared the
AB  - codon usages of 29 type II RM systems with the average codon usage of their respective
AB  - bacterial
AB  - hosts.  Pronounced deviations in codon usage were found in six cases: EcoRI, EcoRV, KpnI,
AB  - SinI, SmaI, and TthHB81.  They are interpreted as evidence for horizontal gene transfer in
AB  - these
AB  - cases.  As the methodology is expected to detect only one-fourth to one-third of all
AB  - horizontal gene
AB  - transfer events, this result implies that horizontal gene transfer had a considerable
AB  - influence on the
AB  - distribution and evolution of RM systems.  In all of these six cases the codon usage
AB  - deviations of
AB  - the restriction enzyme genes are much more pronounced than those of the methyltransferase
AB  - genes.
AB  - This result suggests that in these cases horizontal gene transfer had occurred sequentially
AB  - with the
AB  - gene for the methyltransferase being first acquired by the cell.  This can be explained by the
AB  - fact
AB  - that an active restriction endonuclease is highly toxic in cells whose DNA is not protected
AB  - from
AB  - cleavage by a corresponding methyltransferase.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Pingoud, A.M.
TI  - Methods for determining activity and specificity of DNA binding and DNA cleavage by class II restriction endonucleases.
JO  - Methods Mol. Biol.
PY  - 2001
SP  - 287
EP  - 308
VL  - 160
AB  - Restriction endonucleases coupled with DNA methyltransferases form the
AB  - restriction-modification systems that occur ubiquitously among bacteria.  They protect
AB  - bacterial cells against bacteriophage infection by cleaving incoming foreign DNA highly
AB  - specifically if it contains the recognition sequence.  Cellular DNA is protected from cleavage
AB  - by a specific methylation within the recognition sequence, which is introduced by the
AB  - methyltransferase.  Restriction endonucleases recognize palindromic recognition sites, 4-8
AB  - base pairs in length.  These enzymes are indispensable tools for genetic engineering.  The
AB  - biology and biochemistry of type II restriction endonucleases has been reviewed recently and
AB  - will be summarized only briefly here.  Type IIS restriction enzymes differ from type II
AB  - enzymes in that they recognize an asymmetric recognition sequence.  Monomeric in solution,
AB  - these enzymes consist of a DNA recognition domain and a catalytic domain.  Restriction
AB  - endonucleases initiate DNA cleavage by binding nonspecifically to DNA.  Association of the
AB  - enzymes to DNA is diffusion controlled, with rate constants in the order of 10^7-10^8
AB  - M^-1s^-1.  In a series of dissociation and association steps and/or sliding along the DNA, the
AB  - enzyme scans the DNA and searches for the recognition site in a one-dimensional diffusion
AB  - process.  This process permits much faster target site location than would be possible via a
AB  - three-dimensional search.  During recognition, conformational changes in the enzyme-DNA
AB  - complex lead to the activation of the catalytic centers and cleavage of the DNA.
AB  - Subsequently, the products are released, allowing for a new reaction cycle to take place.
AB  - Often product release is the rate limiting step for multiple turnover cleavage reactions.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Pleckaityte, M.
AU  - Selent, U.
AU  - Wolfes, H.
AU  - Siksnys, V.
AU  - Pingoud, A.
TI  - Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases.
JO  - Gene
PY  - 1995
SP  - 157
EP  - 162
VL  - 157
AB  - Substrate-assisted catalysis was suggested to be involved in the DNA cleavage reaction of the
AB  - restriction endonucleases (ENases) EcoRI and EcoRV, because experimental evidence exists that
AB  - the phosphate group 3' to the scissile bond serves to deprotonate the attacking water.  Here,
AB  - we have addressed the question whether this is a general mechanistic feature of the reactions
AB  - catalyzed by ENases.  For this purpose, the cleavage rates of modified and unmodified
AB  - oligodeoxyribonucleotides (oligos), in which the phosphate group 3' to the scissile bond is
AB  - substituted by a methyl phosphonate, where measured for 17 enzymes.  Only five turned out not
AB  - to be inhibited by this modification (BglII, BstI, BstYI, Cfr10I and MunI); all others cleave
AB  - the modified substrate at a strongly reduced rate or not at all.  By employing a
AB  - hemisubstituted oligo substrate we were able to further investigate the mechanism of
AB  - inhibition of the latter group of ENases.  Some of them cleave the unmodified strand of the
AB  - modified substrate with a nearly unaltered rate, whereas the modified strand is cleaved very
AB  - slowly or not at all (BamHI, Bsp143I, Eco72I, MflI, NdeII, Sau3AI, XhoII).  The others (AluI,
AB  - Cfr9I, DpnII, MboI, PvuII) cleave the modified strand of the modified substrate with a largely
AB  - reduced rate or not at all.  These ENases, however, cleave the unmodified strand with a
AB  - reduced rate, too.  Based on these results we conclude that BamHI, Bsp143I, Cfr9I, DpnII,
AB  - Eco72I, MboI, MflI, NdeII, PvuII, Sau3AI and XhoII may possibly employ substrate assistance in
AB  - catalysis.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Roth, M.
AU  - Friedrich, T.
TI  - Mutational analysis of target base flipping by the EcoRV adenine-N6 DNA methyltransferase.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1121
EP  - 1130
VL  - 285
AB  - DNA methyltransferases flip their target base out of the DNA helix.  Here, we have
AB  - investigated base flipping by wild-type EcoRV DNA methyltransferase and five M.EcoRV variants
AB  - (D193A, Y196A, S229A, W231R and Y258A).  These variants bind to DNA and S-adenosyl-methionine
AB  - but have a severely reduced catalytic efficiency or are catalytically inactive.  To measure
AB  - base flipping three different assays were used, viz. analysis of the yields of
AB  - photocrosslinking reactions between the enzymes and a substrate in which the target base is
AB  - replaced by 5-iodouracil, analysis of the binding constants to substrates containing a
AB  - mismatch base-pair at the target position and analysis of the salt dependence of specific
AB  - complex formation.  Our data show that the Y196A, W231R and Y258A variants are not able to
AB  - stabilize a flipped target base, suggesting that the aromatic amino acid residues (Tyr196,
AB  - Trp231 and Tyr258) are involved in hydrophobic interactions with the flipped base.  The D193A
AB  - variant behaves like wild-type M.EcoRV with respect to base flipping.  The fact that this
AB  - variant is catalytically inactive indicates that Asp193 has a function in chemical catalysis.
AB  - The S229A variant can better flip modified bases but does not tightly lock the flipped base
AB  - into the adenine-binding pocket, suggesting that Ser229 could form a contact to the flipped
AB  - adenine.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Sobotta, T.
AU  - Pingoud, A.
TI  - Structure prediction of the EcoRV DNA methyltransferase based on mutant profiling, secondary structure analysis, comparison with known structures of methyltransferases and isolation of catalytically inactive single mutants.
JO  - Protein Eng.
PY  - 1996
SP  - 413
EP  - 423
VL  - 9
AB  - The EcoRV DNA methyltransferase (M.EcoRV) is an alpha-adenine methyltransferase.  We have used
AB  - two different programs to predict the secondary structure of M.EcoRV.  The resulting consensus
AB  - prediction was tested by a mutant profiling analysis.  29 neutral mutations of M.EcoRV were
AB  - generated by five cycles of random mutagenesis and selection for active variants to increase
AB  - the reliability of the prediction and to get a secondary structure prediction for some
AB  - ambiguously predicted regions.  The predicted consensus secondary structure elements could be
AB  - aligned to the common topology of the structures of the catalytic domains of M.HhaI and
AB  - M.TaqI.  In a complementary approach we have isolated nine catalytically inactive single
AB  - mutants.  Five of these mutants contain an amino acid exchange within the catalytic domain of
AB  - M.EcoRV (Val20-Ala, Lys81Arg, Cys192Arg, Asp193Gly, Trp231Arg).  The Trp231Arg mutant binds
AB  - DNA similarly to wild-type M.EcoRV, but is catalytically inactive.  Hence this mutant behaves
AB  - like a bona fide active site mutant.  According to the structure prediction, Trp231 is located
AB  - in a loop at the putative active site of M.EcoRV.  The other inactive mutants were insoluble.
AB  - They contain amino acid exchanges within the conserved amino acid motifs X, III or IV in
AB  - M.EcoRV confirming the importance of these regions.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Urbanke, C.
TI  - Sliding or hopping?  How restriction enzymes find their way on DNA.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 95
EP  - 110
VL  - 14
AB  - In this contribution, we discuss target site location of restriction endonucleases, which are
AB  - extremely common among prokaryotes occurring in almost every species.  These enzymes
AB  - specifically recognize and cleave short, often palindromic, sequences on bacteriophage or
AB  - other kinds of foreign DNA.  By cleaving incoming DNA, they protect bacteria against
AB  - bacteriophage infections acting like an immune system.  In addition, restriction endonucleases
AB  - have an important role in the control of horizontal gene transfer and bacterial evolution.
AB  - The cellular DNA is protected against nucleolytic attack by an accompanying DNA
AB  - methyltransferase which recognizes the same nucleotide sequence and methylates one adenine or
AB  - cytosine residue within the site.  Since restriction endonucleases and DNA methyltransferases
AB  - are present at the same time in the cell, there is kinetic competition between them, which
AB  - necessitates that the restriction enzyme finds its target site on an invading DNA faster than
AB  - the methyltransferase.  In addition, fast target site location is also important, because the
AB  - invading bacteriophage DNA has to be degraded before it gains control over the cellular
AB  - metabolism.  Therefore, restriction enzymes were among the earliest examples where facilitated
AB  - diffusion has been shown to be effective in target site location.  However, the actual
AB  - mechanism of this process is still under debate; whereas most authors had proposed a sliding
AB  - mechanism, this has recently been disputed by Halford and colleagues who favored a hopping
AB  - process.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Wenz, C.
AU  - Stahl, F.
AU  - Pingoud, A.
TI  - Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme.
JO  - EMBO J.
PY  - 1996
SP  - 5104
EP  - 5111
VL  - 15
AB  - Linear diffusion along DNA is a mechanism of enhancing the association rates of proteins to
AB  - their specific recognition sites on DNA.  It has been demonstrated for several proteins in
AB  - vitro, but to date in no case in vivo.  Here we show that the restriction endonuclease EcoRV
AB  - slides along the DNA, scanning ~1000 bp in one binding event.  This process is critically
AB  - dependent on contacts between amino acid residues of the protein and the backbone of the DNA.
AB  - The disruption of single hydrogen bonds and, in particular, the alteration of electrostatic
AB  - interactions between amino acid side chains of the protein and phosphate groups of the DNA
AB  - interfere with or abolish effective sliding.  The efficiency of linear diffusion is dependent
AB  - on salt concentration, having a maximum at 50mM NaCl.  These results suggest that a
AB  - nonspecific and mobile binding mode capable of linear diffusion is dependent on a subtle
AB  - balance of forces governing the interaction of the enzyme and the DNA.  A strong correlation
AB  - between the ability of EcoRV mutants to slide along the DNA in vitro and to protect
AB  - Escherichia coli cells from phage infection demonstrates that linear diffusion occurs in vivo
AB  - and is essential for effective phage restriction.
ER  -

TY  - JOUR
AU  - Jeltsch, A.
AU  - Wenz, C.
AU  - Wende, W.
AU  - Selent, U.
AU  - Pingoud, A.
TI  - Engineering novel restriction endonucleases: principles and applications.
JO  - Trends Biotechnol.
PY  - 1996
SP  - 235
EP  - 238
VL  - 14
AB  - Restriction endonucleases cleave DNA with remarkable sequence specificity.  In this review, we
AB  - summarize the status of, and prospects for, engineering restriction endonucleases with new
AB  - specificities.  Such variants could be of considerable commercial value because restriction
AB  - enzymes are among the most frequently used enzymes in molecular biology, and not all the
AB  - desirable specificities are available.  While it has not yet been possible to effect
AB  - specificity changes, mutants have been described that (1) exhibit relaxed specificity, (2)
AB  - favor modified substrates over their natural substrates, (3) discriminate between cleavage
AB  - sites located in different sequences, (4) prefer metal ions other than Mg2+ as cofactors for
AB  - cleavage, or (5) possess site-specific DNA-nicking activity.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
TI  - Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions.
JO  - Methods Enzymol.
PY  - 1995
SP  - 305
EP  - 345
VL  - 259
AB  - The solution of a large (and rapidly growing) number of crystal structures of site-specific
AB  - protein-DNA complexes has given us extremely detailed views of the positional relationships at
AB  - the interfaces between proteins and their "correct" DNA recognition sites.  This structural
AB  - information identifies interactions between particular functional groups on the protein and
AB  - particular functional groups on the DNA.  It is important to ask if the same proximity
AB  - relationships and interactions pertain in solution.  Furthermore, structural information alone
AB  - informs us about neither the quantitative contribution of each contact to the overall
AB  - stability of the complex nor the role of the contacts, singly or in combination, in enabling
AB  - the protein to discriminate between correct and incorrect DNA-binding sites.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
TI  - Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
JO  - Biopolymers
PY  - 1997
SP  - 153
EP  - 180
VL  - 44
AB  - This paper considers how enzymes that catalyze reactions at specific DNA sites have been
AB  - engineered to overcome the problem of competitive inhibition by excess nonspecific binding
AB  - sites on DNA.  The formation of a specific protein-DNA recognition complex is discussed from
AB  - both structural and thermodynamic perspectives, and contrasted with formation of nonspecific
AB  - complexes.  Evidence (from EcoRI and BamHI endonucleases) is presented that a wide variety of
AB  - perturbations of the DNA substrate alter binding free energy but do not affect the free energy
AB  - of activation for the chemical step; that is, many energetic factors contribute equally to the
AB  - recognition complex and the transition-state complex.  This implies that the specific
AB  - recognition complex bears a close resemblance to the transition-state complex, such that very
AB  - tight binding to the recognition site on the DNA substrate does not inhibit catalysis, but
AB  - instead provides energy that is efficiently utilized along the path to the transition state.
AB  - It is suggested that this view can be usefully extended to "noncatalytic" site-specific
AB  - DNA-binding proteins like transcriptional activators and general transcription factors.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
AU  - Engler, L.E.
AU  - Ames, J.T.
AU  - Kurpiewski, M.R.
AU  - Grigorescu, A.
TI  - Thermodynamic parameters of specific and nonspecific protein-DNA binding.
JO  - Supramol. Chem.
PY  - 2000
SP  - 143
EP  - 160
VL  - 12
AB  - Proteins that bind preferentially to specific recognition sites on DNA also bind more weakly
AB  - to nonspecific DNA.  We have studied both specific and non-specific binding of the EcoRI and
AB  - BamHI restriction endonucleases, and determined enthalpic and entropic contributions to
AB  - binding free energy (delta G^o bind) using both the van't Hoff method and isothermal
AB  - titration calorimetry.  Specific binding is characterized by a strongly negative delta C^o p
AB  - and can be either enthalpy-driven or entropy-driven, depending on temperature.  Nonspecific
AB  - binding has delta C^o = 0 and is enthalpy-driven.  A strongly negative delta C^o p is the
AB  - "thermodynamic signature" of site-specific binding, because it reflects the characteristics of
AB  - a tight complementary recognition interface: the burial of previously hydrated nonpolar
AB  - surface and restriction of configurational-vibrational freedoms of protein, DNA, and water
AB  - molecules trapped at the protein-DNA interface.  These factors are absent in nonspecific
AB  - complexes.  We probed the contributions to delta C^o p by varying the sequence context
AB  - surrounding the recognition site.  As delta G^o bind improves, delta C^o p, delta H^o and
AB  - delta S^o all become more negative, and there is a linear correlation between delta H^o and
AB  - delta S^o (enthalpy-entropy compensation).  Because these context variations do not change the
AB  - protein-base or protein-phosphate contacts, the hydrophobic contribution or the number of
AB  - trapped water molecules at the interface, we conclude that a better sequence context improves
AB  - the "goodness of fit" in the interface and thus increases the magnitude of the negative
AB  - configurational-vibrational contribution to delta C^o p.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
AU  - Engler, L.E.
AU  - Jacobson, L.A.
TI  - Structural and thermodynamic strategies for site-specific DNA binding proteins.
JO  - Structure
PY  - 2000
SP  - 1015
EP  - 1023
VL  - 8
AB  - BACKGROUND: Site-specific protein-DNA complexes vary greatly in structural properties and in
AB  - the thermodynamic strategy for achieving an appropriate binding free energy. A better
AB  - understanding of the structural and energetic engineering principles might lead to rational
AB  - methods for modification or design of such proteins.
AB  - RESULTS: A novel analysis of ten site-specific protein-DNA complexes reveals a striking
AB  - correspondence between the degree of imposed DNA distortion and the thermodynamic parameters
AB  - of each system. For complexes with relatively undistorted DNA, favorable enthalpy change
AB  - drives unfavorable entropy change, whereas for complexes with highly distorted DNA,
AB  - unfavorable DeltaH^o is driven by favorable DeltaS^o. We show for the first time that
AB  - protein-DNA associations have isothermal enthalpy-entropy compensation, distinct from
AB  - temperature-dependent compensation, so DeltaH^o and DeltaS^o do not vary independently. All
AB  - complexes have favorable DeltaH^o from direct protein-DNA recognition interactions and
AB  - favorable DeltaS^o from water release.  Systems that strongly distort the DNA nevertheless
AB  - have net unfavorable DeltaH^o as the result of molecular strain, primarily associated with the
AB  - base pair destacking. These systems have little coupled protein folding and the strained
AB  - interface suffers less immobilization, so DeltaS^o is net favorable. By contrast, systems with
AB  - little DNA distortion have net favorable DeltaH^o, which must be counterbalanced by net
AB  - unfavorable DeltaS^o, derived from loss of vibrational entropy (a result of isothermal
AB  - enthalpy-entropy compensation) and from coupling between DNA binding and protein folding.
AB  - CONCLUSIONS: Isothermal enthalpy-entropy compensation implies that a structurally optimal,
AB  - unstrained fit is achieved only at the cost of entropically unfavorable immobilization,
AB  - whereas an enthalpically weaker, strained interface entails smaller entropic penalties.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
AU  - Engler, L.E.
AU  - Lesser, D.R.
AU  - Kurpiewski, M.R.
AU  - Yee, C.
AU  - McVerry, B.
TI  - Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites.
JO  - EMBO J.
PY  - 1996
SP  - 2870
EP  - 2882
VL  - 15
AB  - We have studied the interaction of EcoRI endonuclease with oligonucleotides
AB  - containing GAATTC sites bearing one or two adenine-N6-methyl groups, which would be in steric
AB  - conflict with key protein side chains involved in recognition and/or catalysis in the
AB  - canonical
AB  - complex.  Single-strand methylation of either adenine produces small penalties in binding free
AB  - energy (delta delta Gs ~ +1.4 kcal/mol), but elicits asymmetric structural adaptations in the
AB  - complex, such that cleavage rate constants are strongly inhibited and unequal in the two DNA
AB  - strands.  The dependences of cleavage rate constants on the concentration of the Mg2+ cofactor
AB  - are
AB  - unaltered.  When either adenine is methylated on both DNA strands, delta delta Gs
AB  - (~+4kcal/mol)
AB  - is larger than the expected sum of the delta delta Gs values for the single-strand
AB  - methylations,
AB  - because the asymmetric adaptations cannot occur.  Cleavage rate constants are reduced by
AB  - 600,000-fold for the biologically relevant GAmATTC/CTTmAAG site, but the
AB  - GmAATTC/CTTAmAG site forms only a non-specific complex that cannot be cleaved.  These
AB  - observations provide a detailed thermodynamic and kinetic explanation of how single-strand and
AB  - double-strand methylation protect against endonuclease cleavage in vivo.  We propose that non-
AB  - additive effects on binding and structural 'adaptations' are important in understanding how
AB  - DNA
AB  - methylation modulates the biological activities of non-catalytic DNA binding proteins.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
AU  - Kurpiewski, M.
AU  - Lesser, D.
AU  - Grable, J.
AU  - Boyer, H.W.
AU  - Rosenberg, J.M.
AU  - Greene, P.J.
TI  - Coordinate ion pair formation between EcoRI endonuclease and DNA.
JO  - J. Biol. Chem.
PY  - 1983
SP  - 14638
EP  - 14646
VL  - 258
AB  - The free energy of the binding reaction between EcoRI restriction endonuclease
AB  - and a specific cognate dodecadeoxynucleotide (d(CGCGAATTCGCG)) has
AB  - contributions from both electrostatic and nonelectrostatic components.  These
AB  - contributions were dissected by measuring the effects of varying salt
AB  - concentration on the equilibrium binding constant and applying the
AB  - thermodynamic analyses of Record et al. (Record, M.T., Jr., Lohman, T.M., and
AB  - deHaseth, P.L. (1976) J. Mol. Biol. 107: 145-158).  Endonuclease mutation S187
AB  - (Arg 187 to Ser) (Greene, P.J., Gupta, M., Boyer, H.W., Brown, W.E., and
AB  - Rosenberg, J.M. (1981) J. Biol. Chem. 256: 2143-2153) did not significantly
AB  - affect the nonelectrostatic component but did perturb the electrostatic
AB  - contribution to the binding energy (we are numbering the amino acid residues
AB  - according to the DNA sequence).  The former was determined by extrapolating the
AB  - linear portion of the salt dependence curve (0.125 to 0.25M KCl) to 1M ionic
AB  - strength, with the same result for both wild type and S187 endonucleases at
AB  - both pH 6.0 and 7.4 (-8.5 +- 1.5 kcal/mol or greater than 50% of the total
AB  - binding free energy).  The slopes of these same curves yield estimates of eight
AB  - ionic interactions between wild type endonuclease and the DNA at both pH
AB  - values.  By contrast, binding of EcoRI-S187 to dodecanucleotide involves six
AB  - charge-charge interactions at pH 6.0.  Only two ionic interactions are observed
AB  - at pH 7.4.  This was unexpected since gel permeation chromatography
AB  - demonstrated that the recognition complex for both wild type and S187 proteins
AB  - contains an enzyme dimer and a DNA duplex.  EcoRI-S187 endonuclease retains
AB  - wild type DNA sequence specificity, and the rate of the phosphodiester
AB  - hydrolysis step is also unchanged.  Thus, electrostatic interactions are
AB  - functionally separable from sequence recognition and strand cleavage.  Our
AB  - results also establish that arginine 187 plays a key role in the electrostatic
AB  - function and suggest that it might be located at the DNA-protein interface.
AB  - The disproportionate loss of ion pairs at pH 7.4 can be rationalized by a model
AB  - which suggests that six conformationally mobile ionic groups on the protein act
AB  - in a coordinated manner during the interaction with DNA.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
AU  - Lesser, D.
AU  - Kurpiewski, M.
TI  - The enfolding arms of the EcoRI Endonuclease: role in DNA binding and cleavage.
JO  - Cell
PY  - 1986
SP  - 619
EP  - 629
VL  - 45
AB  - The N-terminal segments of the EcoRI endonuclease dimer form part of mobile
AB  - "arms" that encircle DNA in the recognition complex.  By treating
AB  - endonuclease-TCGCGAATTCGCG complexes with proteases, we have prepared a series
AB  - of deletion derivatives lacking defined segments of the N-terminal region.  The
AB  - 5-12 segment is essential for DNA cleavage and forms one electrostatic
AB  - interaction (per subunit) with DNA phosphate.  These ionic contacts are
AB  - directly across the double helix from the scissile phosphodiester bonds; they
AB  - thus may permit the enfolding arms to immobilize DNA in apposition to the
AB  - catalytic cleft and/or contribute to the unusual "kinked" conformation of DNA
AB  - in the complex.  Sequence specificity is fully retained when 28 residues are
AB  - deleted from the N-terminus, but the complexes dissociate more rapidly.
ER  -

TY  - JOUR
AU  - Jen-Jacobson, L.
AU  - Lesser, D.R.
AU  - Kurpiewski, M.R.
TI  - DNA sequence discrimination by EcoRI endonuclease.
JO  - Nucleic Acids and Molecular Biology
PY  - 1991
SP  - 141
EP  - 170
VL  - 5
AB  - The EcoRI restriction endonuclease presents an especially informative case of specificity in
AB  - protein-DNA interactions, because it exhibits extremely high sequence selectivity between its
AB  - canonical recognition site GAATTC and related DNA sites that differ by as little as one base
AB  - pair.  A gene-regulatory protein (the lac repressor) also shows stringent discrimination
AB  - against single base-pair changes in Oc mutant sites.  By contrast, some bacteriophage
AB  - repressors bind to a series of related operator DNA sites in a graduated fashion ("permissive
AB  - discrimination"), yet discriminate stringently between operator and nonoperator DNA.
ER  -

TY  - JOUR
AU  - Jenkinson, E.
AU  - Crickmore, N.
TI  - Identification of a novel DNA methyltransferase activity from Bacillus thuringiensis.
JO  - Curr. Microbiol.
PY  - 2003
SP  - 144
EP  - 145
VL  - 47
AB  - A DNA methyltransferase activity was identified in a strain of Bacillus thuringiensis that was
AB  - found to protect DNA from cleavage by the
AB  - restriction endonuclease HaeIII at overlapping sites. Site-directed
AB  - mutagenesis was used to confirm therecognition sequence of the
AB  - methyltransferase as ACGGC.
ER  -

TY  - JOUR
AU  - Jennert, K.C.
AU  - Tardif, C.
AU  - Young, D.I.
AU  - Young, M.
TI  - Gene transfer to clostridium cellulolyticum ATCC 35319.
JO  - Microbiology
PY  - 2000
SP  - 3071
EP  - 3080
VL  - 146
AB  - Although much is known about the bacterial cellulosome and its various protein components,
AB  - their contributions to bacterial growth on cellulose and the process of cellulolysis in vivo
AB  - cannot currently be assessed. To remedy this, the authors have developed gene transfer
AB  - techniques for Clostridium cellulolyticum ATCC 35319. Firstly, transfer of Tn1545 has been
AB  - obtained using an Enterococcus faecalis donor. Secondly, IncP-mediated conjugative
AB  - mobilization of plasmids from Escherichia coli donors has also been achieved. The yield of
AB  - transconjugants in both cases was low and was probably limited by the suboptimal growth
AB  - conditions that must of necessity be employed for the co-culture of oligotrophic C.
AB  - cellulolyticum with copiotrophic donors. A restriction endonuclease was detected in crude
AB  - extracts of C. cellulolyticum. This enzyme, named CCE:I, is an isoschizomer of MSP:I (HPA:II).
AB  - Electro-transformation was employed to establish plasmids containing the replication functions
AB  - of pAMss1 (En. faecalis), pIM13 (Bacillus subtilis), pCB102 (Clostridium butyricum), pIP404
AB  - (Clostridium perfringens) and pWV01 (Lactococcus lactis subsp. cremoris) in C. cellulolyticum.
AB  - Transformants were only obtained if the DNA was appropriately methylated on the external C of
AB  - the sequence 5'-CCGG-3' using either BSU:FI methylase in vivo or MSP:I methylase in vitro.
AB  - Plasmids based on the pAMss1 and pIM13 replicons were more stably maintained than one based on
AB  - the pCB102 replicon. Selection of transformants on solid medium led to low apparent
AB  - transformation efficiencies (approx. 10(2) transformants per &mgr;g DNA) which might, in part,
AB  - reflect the low plating efficiency of the organism. Selection of transformants in liquid
AB  - medium led to a higher apparent yield of transformants (between 10(5) and 10(7) transformants
AB  - per &mgr;g DNA). The methods developed here will pave the way for functional analysis of the
AB  - various cellulosome components in vivo.
ER  -

TY  - JOUR
AU  - Jennings, M.E.
AU  - Chia, N.
AU  - Boardman, L.A.
AU  - Metcalf, W.W.
TI  - Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e01055
EP  - e01017
VL  - 5
AB  - Methanobrevibacter smithii is a common inhabitant of the human gut. Here, we present a draft
AB  - genome sequence of M. smithii isolate WWM1085, obtained from a
AB  - human stool sample. This sequence will improve our understanding of the genetic
AB  - diversity of this human-associated methanogen.
ER  -

TY  - JOUR
AU  - Jensen, R.V.
AU  - Depasquale, S.M.
AU  - Harbolick, E.A.
AU  - Hong, T.
AU  - Kernell, A.L.
AU  - Kruchko, D.H.
AU  - Modise, T.
AU  - Smith, C.E.
AU  - McCarter, L.L.
AU  - Stevens, A.M.
TI  - Complete Genome Sequence of Prepandemic Vibrio parahaemolyticus BB22OP.
JO  - Genome Announcements
PY  - 2013
SP  - e00002
EP  - e00012
VL  - 1
AB  - The number of inflammatory gastroenteritis outbreaks due to the food-borne pathogen is rising
AB  - sharply worldwide and in the United States in particular. Here
AB  - we report the complete, annotated genome sequence of the prepandemic strain
AB  - BB22OP and make some initial comparisons to the complete genome sequence for
AB  - pandemic strain RIMD2210633.
ER  -

TY  - JOUR
AU  - Jensen, T.O.
AU  - Kvist, T.
AU  - Mikkelsen, M.J.
AU  - Westermann, P.
TI  - Rapid and reliable method for identification of associated endonuclease cleavage and recognition sites.
JO  - Lett. Appl. Microbiol.
PY  - 2014
SP  - 576
EP  - 581
VL  - 58
AB  - One barrier to cross during genetic engineering is the restriction-modification system found
AB  - in many bacteria. In this study, we developed a fast and reliable method for mapping the
AB  - recognition and cleavage site of the restriction endonucleases. Clostridium pasteurianum, a
AB  - model organism for the study of nitrogen fixation, has been found to harbour at least two
AB  - restriction-modification systems including the restriction endonucleases CpaPI, which is an
AB  - isoschizomer of MboI and CpaAI. Dam-methylated DNA was used to isolate the activity of CpaAI.
AB  - Exposing freshly prepared cell lysate to known nucleotide fragments and directly sequencing
AB  - the pool of digested nucleotide fragments enabled identification of the cleavage sites in the
AB  - fragments. By aligning the sequences adjacent to the cleavage site, it was possible to
AB  - identify the recognition sequence. Using this method, we successfully located all CpaAI
AB  - recognition and cleavage sites within the template sequence. By modifying DNA with both Dam
AB  - and CpG methylases (M.SssI) and thereby preventing digestion by CpaPI and CpaAI, no further
AB  - endonuclease activity was detected.Significance and Impact of the
AB  - StudyRestriction-modification systems are important barriers to successful genetic
AB  - modification in many bacterial species. In this study, we demonstrate an efficient and general
AB  - applicable method for identifying endonuclease recognition and cleavage sites. For the study
AB  - and the trails, the model organism for nitrogen fixation Clostridium pasteurianum was used.
AB  - The method was proven to be reliable, and by modifying DNA at the identified sites, it is
AB  - possible to prevent digestion.
ER  -

TY  - JOUR
AU  - Jentsch, S.
TI  - Restriction and modification in Bacillus subtilis:  Sequence specificities of restriction/modification systems BsuM, BsuE, and BsuF.
JO  - J. Bacteriol.
PY  - 1983
SP  - 800
EP  - 808
VL  - 156
AB  - The sequence specificies of three Bacillus subtilis restriction/modification
AB  - systems were established: (i) BsuM (CTCGAG), an isoschizomer to XhoI; (ii) BsuE
AB  - (CGCG), an isoschizomer to FnuDII; and (iii) BsuF (CCGG), an isoschizomer to
AB  - MspI, HpaII.  The BsuM modification enzyme methylates the 3' cytosine of the
AB  - recognition sequence.  The BsuF modification enzyme methylates the 5' cytosine
AB  - of the sequence, rendering such sites resistant to MspI degradation and leaving
AB  - the majority of sites sensitive to HpaII degradation.
ER  -

TY  - JOUR
AU  - Jentsch, S.
AU  - Gunthert, U.
AU  - Trautner, T.A.
TI  - DNA methyltransferases affecting the sequence 5'CCGG.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 2753
EP  - 2759
VL  - 9
AB  - B. subtilis phage SPbeta and Moraxella sp. code for DNA methyl-transferases
AB  - which methylate both cytosines of the sequence 5'CCGG.  Experiments using a B.
AB  - subtilis strain whose DNA is sensitive to HpaII and resistant to MspI
AB  - degradation, indicated that methylation of the outer C of this sequence
AB  - provides protection against the restriction enzyme MspI.
ER  -

TY  - JOUR
AU  - Jentsch, S.
AU  - Pawlek, B.
AU  - Noyer-Weidner, M.
AU  - Gunthert, U.
AU  - Trautner, T.A.
TI  - Restriction and modification in B. subtilis:  Temperate phages SPbeta and Phi3T for BsuR specific methyltransferases.
JO  - Transformation 1980:  Proceedings of the Fifth European Meeting on Bacterial Transformation and Transfection
PY  - 1980
SP  - 363
EP  - 369
VL  - 0
AB  - Genes for BsuR specific methyltransferases have been identified in the genomes
AB  - of SPbeta and Phi3T.  Such genes are interchangeable between these two phages.
AB  - Phages SPbeta and possibly also Phi3T code for additional methyltransferase(s)
AB  - with different sequence specificities.
ER  -

TY  - JOUR
AU  - Jeon, S.J.
AU  - Cunha, F.
AU  - Ginn, A.
AU  - Jeong, K.C.
AU  - Galvao, K.N.
TI  - Draft Genome Sequences of Escherichia coli Strains Isolated at Calving from the Uterus, Vagina, Vulva, and Rectoanal Junction of a Dairy Cow That Later Developed  Metritis.
JO  - Genome Announcements
PY  - 2017
SP  - e01511
EP  - e01516
VL  - 5
AB  - Escherichia coli is involved in the pathogenicity of metritis in cows. We report  here the
AB  - genome sequences of E. coli strains isolated at calving from the uterus,
AB  - vagina, vulva, and rectoanal junction of a dairy cow that later developed
AB  - metritis. The genomic similarities will give an insight into phylogenetic
AB  - relationships among strains.
ER  -

TY  - JOUR
AU  - Jeon, T.J.
TI  - DNA Adenine Methylation of sams1 Gene in Symbiont-Bearing Amoeba proteus.
JO  - J. Microbiol.
PY  - 2008
SP  - 564
EP  - 570
VL  - 46
AB  - The expression of amoeba sams genes is switched from sams1 to sams2 when amoebae are infected
AB  - with Legionella jeonii. To elucidate the
AB  - mechanism for the inactivation of host sams1 gene by endosymbiotic
AB  - bacteria, methylation states of the sams1 gene of D and xD amoebae was
AB  - compared in this study. The sams1 gene of amoebae was methylated at an
AB  - internal adenine residue of GATC site in symbiont-bearing xD amoebae
AB  - but not in symbiont-free D amoebae, suggesting that the modification
AB  - might have caused the inactivation of sams1 in xD amoebae. The sams1
AB  - gene of xD amoebae was inactivated at the transcriptional level.
AB  - Analysis of DNA showed that adenine residues in L. jeonii sams were
AB  - also methylated, implying that L. jeonii bacteria belong to a Dam
AB  - methylase-positive strain. In addition, both SAM and Met appeared to
AB  - act as negative regulators for the expression of sams1 whereas the
AB  - expression of sams2 was not affected in amoebae.
ER  -

TY  - JOUR
AU  - Jeon, W.
AU  - Priscilla, L.
AU  - Park, G.
AU  - Lee, H.
AU  - Lee, N.
AU  - Lee, D.
AU  - Kwon, H.
AU  - Ahn, I.
AU  - Lee, C.
AU  - Lee, H.
AU  - Ahn, J.
TI  - Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 54
EP  - 54
VL  - 12
AB  - A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKTT, isolated
AB  - from hydrothermal sediments in Okinawa, Japan, has been used
AB  - industrially for CO2 bio-mitigation owing to its ability to convert CO2 into
AB  - C5H8NO4- at a high rate of specific mitigation (0.42 g CO2/cell/h). The genome of
AB  - S. lithotrophicum 42BKTT comprised of a single chromosome of 2217,891 bp with
AB  - 2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we
AB  - present its complete genome-sequence information, including information about the
AB  - genes encoding enzymes involved in CO2 fixation and sulfur oxidation.
ER  -

TY  - JOUR
AU  - Jeong, D.W.
AU  - Lee, J.H.
TI  - Complete Genome Sequence of Staphylococcus succinus 14BME20 Isolated from a Traditional Korean Fermented Soybean Food.
JO  - Genome Announcements
PY  - 2017
SP  - e01731
EP  - e01716
VL  - 5
AB  - The complete genome sequence of Staphylococcus succinus 14BME20, isolated from a  Korean
AB  - fermented soybean food and selected as a possible starter culture
AB  - candidate, was determined. Comparative genome analysis with S. succinus CSM-77
AB  - from a Triassic salt mine revealed the presence of strain-specific genes for
AB  - lipid degradation in strain 14BME20.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Barbe, V.
AU  - Lee, C.H.
AU  - Vallenet, D.
AU  - Yu, D.S.
AU  - Choi, S.H.
AU  - Couloux, A.
AU  - Lee, S.W.
AU  - Yoon, S.H.
AU  - Cattolico, L.
AU  - Hur, C.G.
AU  - Park, H.S.
AU  - Segurens, B.
AU  - Kim, S.C.
AU  - Oh, T.K.
AU  - Lenski, R.E.
AU  - Studier, F.W.
AU  - Daegelen, P.
AU  - Kim, J.F.
TI  - Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3).
JO  - J. Mol. Biol.
PY  - 2009
SP  - 644
EP  - 652
VL  - 394
AB  - Escherichia coli K-12 and B have been the subjects of classical experiments from which much of
AB  - our understanding of molecular genetics has
AB  - emerged. We present here complete genome sequences of two E. coli B
AB  - strains, REL606, used in a long-term evolution experiment, and BL21(DE3),
AB  - widely used to express recombinant proteins. The two genomes differ in
AB  - length by 72,304 bp and have 426 single base pair differences, a seemingly
AB  - large difference for laboratory strains having a common ancestor within
AB  - the last 67 years. Transpositions by IS1 and IS150 have occurred in both
AB  - lineages. Integration of the DE3 prophage in BL21(DE3) apparently
AB  - displaced a defective prophage in the lambda attachment site of B. As
AB  - might have been anticipated from the many genetic and biochemical
AB  - experiments comparing B and K-12 over the years, the B genomes are similar
AB  - in size and organization to the genome of E. coli K-12 MG1655 and have
AB  - >99% sequence identity over approximately 92% of their genomes. E. coli B
AB  - and K-12 differ considerably in distribution of IS elements and in
AB  - location and composition of larger mobile elements. An unexpected
AB  - difference is the absence of a large cluster of flagella genes in B, due
AB  - to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS
AB  - core, O antigen, and restriction enzymes differ substantially, presumably
AB  - because of horizontal transfer. Comparative analysis of 32 independently
AB  - isolated E. coli and Shigella genomes, both commensals and pathogenic
AB  - strains, identifies a minimal set of genes in common plus many
AB  - strain-specific genes that constitute a large E. coli pan-genome.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Choi, S.K.
AU  - Kloepper, J.W.
AU  - Ryu, C.M.
TI  - Genome Sequence of the Plant Endophyte Bacillus pumilus INR7, Triggering Induced  Systemic Resistance in Field Crops.
JO  - Genome Announcements
PY  - 2014
SP  - e01093
EP  - e01014
VL  - 2
AB  - Bacillus pumilus INR7 is an endophytic bacterium that has been commercialized as  a biological
AB  - control product against soilborne pathogens as well as foliar
AB  - pathogens by direct antagonism and induction of systemic resistance. In the
AB  - current study, we provide the genome sequence and a possible explanation of the
AB  - function of strain INR7.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Choi, S.K.
AU  - Park, S.H.
TI  - Genome Sequences of Bacillus thuringiensis Serovar kurstaki Strain BP865 and B. thuringiensis Serovar aizawai Strain HD-133.
JO  - Genome Announcements
PY  - 2017
SP  - e01544
EP  - e01516
VL  - 5
AB  - We report the draft genome sequences of two insecticidal strains against lepidopteran pests,
AB  - Bacillus thuringiensis serovar kurstaki strain BP865, an
AB  - isolate from the South Korean phylloplane, and strain HD-133, a reference strain
AB  - of B. thuringiensis serovar aizawai.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Choi, S.K.
AU  - Park, S.Y.
AU  - Kim, S.H.
AU  - Park, S.H.
TI  - Draft Genome Sequence of Paenibacillus peoriae Strain KCTC 3763T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1237
EP  - 1238
VL  - 194
AB  - Paenibacillus peoriae is a potentially plant-beneficial soil bacterium and is a close relative
AB  - to Paenibacillus polymyxa, the type species of the genus
AB  - Paenibacillus. Herein, we present the 5.77-Mb draft genome sequence of the P.
AB  - peoriae type strain with the aim of providing insight into the genomic basis of
AB  - plant growth-promoting Paenibacillus species.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Chun, S.J.
AU  - Srivastava, A.
AU  - Cui, Y.
AU  - Ko, S.R.
AU  - Oh, H.M.
AU  - Ahn, C.Y.
TI  - Genome Sequences of Two Cyanobacterial Strains, Toxic Green Microcystis aeruginosa KW (KCTC 18162P) and Nontoxic Brown Microcystis sp. Strain MC19, under  Xenic Culture Conditions.
JO  - Genome Announcements
PY  - 2018
SP  - e00378
EP  - e00318
VL  - 6
AB  - Bloom-forming cyanobacteria pose concerns for the environment and the health of humans and
AB  - animals by producing toxins and thus lowering water quality. Here, we
AB  - report near-complete genome sequences of two Microcystis strains under xenic
AB  - culture conditions, which were originally isolated from two separate freshwater
AB  - reservoirs from the Republic of Korea.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Jeong, D.E.
AU  - Kim, S.H.
AU  - Song, G.C.
AU  - Park, S.Y.
AU  - Ryu, C.M.
AU  - Park, S.H.
AU  - Choi, S.K.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Bacterium Bacillus siamensis  KCTC 13613T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4148
EP  - 4149
VL  - 194
AB  - Bacillus siamensis KCTC 13613(T), a novel halophilic Bacillus species isolated from a salted
AB  - Thai food, produced antimicrobial compounds against plant pathogens
AB  - and promoted plant growth by volatile emission. We determined the 3.8-Mb genome
AB  - sequence of B. siamensis KCTC 13613(T) to reveal the plant-beneficial effect at
AB  - the genomic level.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Jeong, D.E.
AU  - Sim, Y.M.
AU  - Park, S.H.
AU  - Choi, S.K.
TI  - Genome Sequence of Lysinibacillus sphaericus Strain KCTC 3346T.
JO  - Genome Announcements
PY  - 2013
SP  - e00625
EP  - e00613
VL  - 1
AB  - Lysinibacillus sphaericus is a heterogeneous species that includes strains that produce
AB  - mosquitocidal toxin proteins. Herein, we report the 4.56-Mb draft genome
AB  - sequence of the nonpathogenic L. sphaericus strain KCTC 3346(T), which provides
AB  - clues for the phylogenetic reassessment of L. sphaericus species and an
AB  - understanding of its physiological properties.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Jo, S.H.
AU  - Hong, C.E.
AU  - Park, J.M.
TI  - Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a  Potential Biocontrol Agent against Phytopathogens.
JO  - Genome Announcements
PY  - 2016
SP  - e00279
EP  - e00216
VL  - 4
AB  - ITALIC! Bacillus thuringiensisis the most widely known microbial pesticide used in
AB  - agricultural applications. Herein, we report a draft genome sequence of the
AB  - endophytic bacterium ITALIC! Bacillus thuringiensisstrain KB1, which exhibits
AB  - antagonism against phytopathogens.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Kim, H.J.
AU  - Lee, S.J.
TI  - Complete Genome Sequence of Escherichia coli Strain BL21.
JO  - Genome Announcements
PY  - 2015
SP  - e00134
EP  - e00115
VL  - 3
AB  - Escherichia coli strain BL21 is one of the widely used bacterial hosts for high-level
AB  - recombinant protein production and for other applications. Here, we
AB  - present the complete genome sequence of a commercial version of the Escherichia
AB  - coli BL21 strain.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Kloepper, J.W.
AU  - Ryu, C.M.
TI  - Genome Sequences of Pseudomonas amygdali pv. tabaci Strain ATCC 11528 and pv. lachrymans Strain 98A-744.
JO  - Genome Announcements
PY  - 2015
SP  - e00683
EP  - e00615
VL  - 3
AB  - Certain pathovars of Pseudomonas amygdali, which is newly reclassified from Pseudomonas
AB  - syringae by DNA-DNA hybridization and ribotyping, cause many serious
AB  - diseases of major crop plants. Herein, we present draft genome sequences of P.
AB  - amygdali pv. tabaci strain ATCC 11528 and P. amygdali pv. lachrymans strain
AB  - 98A-744.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Kloepper, J.W.
AU  - Ryu, C.M.
TI  - Genome Sequence of Rhizobacterium Serratia marcescens Strain 90-166, Which Triggers Induced Systemic Resistance and Plant Growth Promotion.
JO  - Genome Announcements
PY  - 2015
SP  - e00667
EP  - e00615
VL  - 3
AB  - The rhizobacterium Serratia marcescens strain 90-166 elicits induced systemic resistance
AB  - against plant pathogens and herbivores and promotes plant growth under
AB  - greenhouse and field conditions. Strain 90-166 secretes volatile compounds,
AB  - siderophores, salicylic acid, and quorum-sensing autoinducers as bacterial
AB  - determinants toward plant health. Herein, we present its draft genome sequence.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Park, S.H.
AU  - Choi, S.K.
TI  - Genome Sequence of Antibiotic-Producing Bacillus amyloliquefaciens Strain KCTC 13012.
JO  - Genome Announcements
PY  - 2015
SP  - e01121
EP  - e01115
VL  - 3
AB  - We report the 4.0-Mb draft genome sequence of Bacillus amyloliquefaciens (syn. Bacillus
AB  - velezensis) KCTC 13012, which exhibits a broad spectrum of antagonistic  activity against
AB  - bacteria and fungi and promotes plant growth as well. The genome contains an array of
AB  - biosynthetic gene clusters for secondary metabolites that are comparable to those in Bacillus
AB  - amyloliquefaciens subsp. plantarum FZB42(T).
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Park, S.H.
AU  - Choi, S.K.
TI  - Genome Sequence of the Acrystalliferous Bacillus thuringiensis Serovar Israelensis Strain 4Q7, Widely Used as a Recombination Host.
JO  - Genome Announcements
PY  - 2014
SP  - e00231
EP  - e00214
VL  - 2
AB  - Bacillus thuringiensis serovar israelensis is well known for its mosquitocidal activity and
AB  - has long been used as a biopesticide. Herein, we present the genome sequence of B.
AB  - thuringiensis serovar israelensis strain 4Q7, a plasmid-cured derivative with higher
AB  - transformation efficiency than wild types.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Park, S.H.
AU  - Choi, S.K.
TI  - Draft Genome Sequences of Four Plant Probiotic Bacillus Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e00358
EP  - e00316
VL  - 4
AB  - Here, we report the whole-genome sequences of four Bacillus strains that exhibit  plant
AB  - probiotic activities. Three of them are the type strains of Bacillus
AB  - endophyticus, 'Bacillus gaemokensis,' and Bacillus trypoxylicola, and the other,
AB  - Bacillus sp. strain KCTC 13219, should be reclassified into a species belonging
AB  - to the genus Lysinibacillus.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Park, S.Y.
AU  - Chung, W.H.
AU  - Kim, S.H.
AU  - Kim, N.
AU  - Park, S.H.
AU  - Kim, J.F.
TI  - Draft Genome Sequence of Paenibacillus polymyxa Type Strain (ATCC 842T), a Plant Growth-Promoting Bacterium.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5026
EP  - 5027
VL  - 193
AB  - Paenibacillus polymyxa is an endospore-forming Gram-positive soil bacterium that is well-known
AB  - for its ability to promote plant growth. Here
AB  - we report the draft genome sequence of P. polymyxa ATCC 842(T), the type
AB  - strain of the species P. polymyxa, and the family Paenibacillaceae. A
AB  - repertoire of biosynthetic genes for antibiotics and hydrolytic enzymes
AB  - accounts for its beneficial effects in rhizosphere to host plants it
AB  - associates with.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Sim, Y.M.
AU  - Kim, H.J.
AU  - Lee, D.W.
AU  - Lim, S.K.
AU  - Lee, S.J.
TI  - Genome Sequence of the Vancomycin-Producing Amycolatopsis orientalis subsp. orientalis Strain KCTC 9412T.
JO  - Genome Announcements
PY  - 2013
SP  - e00408
EP  - e00413
VL  - 1
AB  - Amycolatopsis orientalis is the producer of vancomycin, a glycopeptide antibiotic that is used
AB  - for the treatment of serious infections with Gram-positive bacteria.
AB  - Here we present the next-generation sequencing (NGS)-based 9.06-Mb draft genome
AB  - sequence of the type strain Amycolatopsis orientalis subsp. orientalis KCTC 9412
AB  - (DSM 40040; ATCC 19795).
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Sim, Y.M.
AU  - Kim, H.J.
AU  - Lee, Y.J.
AU  - Lee, D.W.
AU  - Lim, S.K.
AU  - Lee, S.J.
TI  - Genome Sequences of Amycolatopsis orientalis subsp. orientalis Strains DSM 43388  and DSM 46075.
JO  - Genome Announcements
PY  - 2013
SP  - e00545
EP  - e00513
VL  - 1
AB  - Strains of Amycolatopsis orientalis produce vancomycin or other related glycopeptide
AB  - antibiotic compounds. Here we report the draft genome sequences of
AB  - glycopeptide nonproducers Amycolatopsis orientalis subsp. orientalis DSM 43388
AB  - and DSM 46075. Their genome information will provide insights into the
AB  - acquisition and regulation of glycopeptide antibiotic resistance genes.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Sim, Y.M.
AU  - Park, S.H.
AU  - Choi, S.K.
TI  - Complete Genome Sequence of Bacillus subtilis Strain ATCC 6051a, a Potential Host for High-Level Secretion of Industrial Enzymes.
JO  - Genome Announcements
PY  - 2015
SP  - e00532
EP  - e00515
VL  - 3
AB  - Bacillus subtilis ATCC 6051a (=KCTC 1028), which is less domesticated than strain 168, is
AB  - widely used for the secretory expression of industrial enzymes. Herein,
AB  - we present the complete genome sequence of the Bacillus subtilis strain ATCC
AB  - 6051a.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Yim, J.H.
AU  - Lee, C.
AU  - Choi, S.H.
AU  - Park, Y.K.
AU  - Yoon, S.H.
AU  - Hur, C.G.
AU  - Kang, H.Y.
AU  - Kim, D.
AU  - Lee, H.H.
AU  - Park, K.H.
AU  - Park, S.H.
AU  - Park, H.S.
AU  - Lee, H.K.
AU  - Oh, T.K.
AU  - Kim, J.F.
TI  - Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 7066
EP  - 7073
VL  - 33
AB  - Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the
AB  - ocean, pose considerable impacts on marine environments,
AB  - aquatic industries and even public health. Here, we present the
AB  - 7.2-megabase genome of the marine bacterium Hahella chejuensis including
AB  - genes responsible for the biosynthesis of a pigment which has the lytic
AB  - activity against a red-tide dinoflagellate. H.chejuensis is the first
AB  - sequenced species in the Oceanospiralles clade, and sequence analysis
AB  - revealed its distant relationship to the Pseudomonas group. The genome was
AB  - well equipped with genes for basic metabolic capabilities and contained a
AB  - large number of genes involved in regulation or transport as well as with
AB  - characteristics as a marine heterotroph. Sequence analysis also revealed a
AB  - multitude of genes of functional equivalence or of possible foreign
AB  - origin. Functions encoded in the genomic islands include biosynthesis of
AB  - exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron
AB  - utilization, motility, type III protein secretion and pigmentation.
AB  - Molecular structure of the algicidal pigment, which was determined through
AB  - LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In
AB  - conclusion, our work provides new insights into mitigating algal blooms in
AB  - addition to genetic make-up, physiology, biotic interactions and
AB  - biological roles in the community of a marine bacterium.
ER  -

TY  - JOUR
AU  - Jeong, H.
AU  - Zhao, F.
AU  - Igori, D.
AU  - Oh, K.H.
AU  - Kim, S.Y.
AU  - Kang, S.G.
AU  - Kim, B.K.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Song, J.Y.
AU  - Yu, D.S.
AU  - Park, M.S.
AU  - Cho, S.H.
AU  - Kim, J.F.
TI  - Genome Sequence of the Hemolytic-Uremic Syndrome-Causing Strain Escherichia coli  NCCP15647.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3747
EP  - 3748
VL  - 194
AB  - Enterohemorrhagic Escherichia coli (EHEC) causes a disease involving diarrhea, hemorrhagic
AB  - colitis, and hemolytic-uremic syndrome (HUS). Here we present the
AB  - draft genome sequence of NCCP15647, an EHEC isolate from an HUS patient. Its
AB  - genome exhibits features of EHEC, such as genes for verotoxins, a type III
AB  - secretion system, and prophages.
ER  -

TY  - JOUR
AU  - Jeong, H.W.
AU  - Bang, M.S.
AU  - Lee, Y.J.
AU  - Lee, S.J.
AU  - Lee, S.C.
AU  - Shin, J.I.
AU  - Oh, C.H.
TI  - Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_03, Isolated from a Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Nattokinase Activity.
JO  - Genome Announcements
PY  - 2018
SP  - e00526
EP  - e00518
VL  - 6
AB  - We present here the complete genome sequence of Bacillus subtilis strain DKU_NT_03 isolated
AB  - from the traditional Korean food chung-gook-jang, which is
AB  - made from soybeans. This strain was chosen to identify genetic factors with
AB  - high-quality nattokinase activity.
ER  -

TY  - JOUR
AU  - Jeong, J.J.
AU  - Lee, Y.J.
AU  - Pathiraja, D.
AU  - Park, B.
AU  - Choi, I.G.
AU  - Kim, K.D.
TI  - Draft Genome Sequences of Chryseobacterium lactis NCTC11390(T) Isolated from Milk, Chryseobacterium oncorhynchi 701B-08(T) from Rainbow Trout, and Chryseobacterium viscerum 687B-08(T) from Diseased Fish.
JO  - Genome Announcements
PY  - 2018
SP  - e00628
EP  - e00618
VL  - 6
AB  - The genus Chryseobacterium, belonging to the family Flavobacteriaceae, contains Gram-negative,
AB  - yellow-pigmented, rod-shaped, and non-spore-forming bacterial
AB  - species, which may be free living or parasitic. Here, we report draft genome
AB  - sequences of type strains of three species of Chryseobacterium containing genes
AB  - related to biological control and plant growth promotion.
ER  -

TY  - JOUR
AU  - Jeong, J.J.
AU  - Moon, H.J.
AU  - Pathiraja, D.
AU  - Park, B.
AU  - Choi, I.G.
AU  - Kim, K.D.
TI  - Draft Genome Sequences of Bacillus megaterium KU143, Microbacterium testaceum KU313, and Pseudomonas protegens AS15, Isolated from Stored Rice Grains.
JO  - Genome Announcements
PY  - 2018
SP  - e00468
EP  - e00418
VL  - 6
AB  - Bacillus megaterium KU143, Microbacterium testaceum KU313, and Pseudomonas protegens AS15 from
AB  - stored rice grains exhibited antifungal activity against
AB  - Aspergillus and Penicillium spp. predominant in stored rice. Here, we report
AB  - their bacterial draft genomes, which contain genes related to biotic and abiotic
AB  - stress management, as well as antimicrobial and insecticidal traits.
ER  -

TY  - JOUR
AU  - Jeong, J.J.
AU  - Park, B.
AU  - Oh, J.Y.
AU  - Mannaa, M.
AU  - Kim, Y.J.
AU  - Hong, J.K.
AU  - Choi, I.G.
AU  - Kim, K.D.
TI  - Draft Genome Sequences of Chryseobacterium artocarpi UTM-3T and Chryseobacterium  contaminans C26T, Isolated from Rhizospheres, and Chryseobacterium arthrosphaerae  CC-VM-7T, Isolated from the Feces of a Pill Millipede.
JO  - Genome Announcements
PY  - 2016
SP  - e01168
EP  - e01116
VL  - 4
AB  - Species of the genus Chryseobacterium belonging to the family Flavobacteriaceae are nonmotile,
AB  - yellow-pigmented, and rod-shaped bacteria, some of which were
AB  - frequently isolated from soil or plant-related materials. Here, we present draft
AB  - genome sequences of three type strains of Chryseobacterium, which contain genes
AB  - related to plant growth promotion, colonization, or stress adaptation.
ER  -

TY  - JOUR
AU  - Jeong, J.J.
AU  - Park, B.H.
AU  - Park, H.
AU  - Choi, I.G.
AU  - Kim, K.D.
TI  - Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus).
JO  - Genome Announcements
PY  - 2016
SP  - e00577
EP  - e00516
VL  - 4
AB  - Chryseobacterium sp. strain GSE06 is a biocontrol endophytic bacterium against the destructive
AB  - soilborne oomycete Phytophthora capsici, which causes
AB  - Phytophthora blight of pepper. Here, we present its draft genome sequence, which
AB  - contains genes related to biocontrol traits, such as colonization, antimicrobial
AB  - activity, plant growth promotion, and abiotic or biotic stress adaptation.
ER  -

TY  - JOUR
AU  - Jeong, J.J.
AU  - Park, H.
AU  - Park, B.H.
AU  - Mannaa, M.
AU  - Sang, M.K.
AU  - Choi, I.G.
AU  - Kim, K.D.
TI  - Draft Genome Sequence of a Biocontrol Rhizobacterium, Chryseobacterium kwangjuense Strain KJ1R5, Isolated from Pepper (Capsicum annuum).
JO  - Genome Announcements
PY  - 2016
SP  - e00301
EP  - e00316
VL  - 4
AB  - Strain KJ1R5 of the rhizobacterium ITALIC! Chryseobacterium kwangjuenseis an effective
AB  - biocontrol agent against Phytophthora blight of pepper caused by a
AB  - destructive soilborne oomycete, ITALIC! Phytophthora capsici Here, we present the
AB  - draft genome sequence of strain KJ1R5, which contains genes related to
AB  - biocontrol, plant growth promotion, and environmental stress adaptation.
ER  -

TY  - JOUR
AU  - Jeong, J.J.
AU  - Sang, M.K.
AU  - Pathiraja, D.
AU  - Park, B.
AU  - Choi, I.G.
AU  - Kim, K.D.
TI  - Draft Genome Sequence of Phosphate-Solubilizing Chryseobacterium sp. Strain ISE14, a Biocontrol and Plant Growth-Promoting Rhizobacterium Isolated from Cucumber.
JO  - Genome Announcements
PY  - 2018
SP  - e00612
EP  - e00618
VL  - 6
AB  - Chryseobacterium sp. strain ISE14 is a phosphate-solubilizing endophytic bacterium that
AB  - exhibits plant growth promotion and biocontrol activities against
AB  - Phytophthora blight and anthracnose on pepper. Here, we report the draft genome
AB  - sequence of strain ISE14, which contains genes relating to phosphate
AB  - solubilization, plant growth promotion, and biocontrol traits.
ER  -

TY  - JOUR
AU  - Jeong, S.
AU  - Liang, G.N.
AU  - Sharma, S.
AU  - Lin, J.C.
AU  - Choi, S.H.
AU  - Han, H.
AU  - Yoo, C.B.
AU  - Egger, G.
AU  - Yang, A.S.
AU  - Jones, P.A.
TI  - Selective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA.
JO  - Mol. Cell. Biol.
PY  - 2009
SP  - 5366
EP  - 5376
VL  - 29
AB  - Proper DNA methylation patterns are essential for mammalian development and differentiation.
AB  - DNA methyltransferases (DNMTs) primarily establish
AB  - and maintain global DNA methylation patterns; however, the molecular
AB  - mechanisms for the generation and inheritance of methylation patterns
AB  - are still poorly understood. We used sucrose density gradients of
AB  - nucleosomes prepared by partial and maximum micrococcal nuclease
AB  - digestion, coupled with Western blot analysis to probe for the
AB  - interactions between DNMTs and native nucleosomes. This method allows
AB  - for analysis of the in vivo interactions between the chromatin
AB  - modification enzymes and their actual nucleosomal substrates in the
AB  - native state. We show that little free DNA methyltransferase 3A and 3B
AB  - (DNMT3A/3B) exist in the nucleus and that almost all of the cellular
AB  - contents of DNMT3A/3B, but not DNMT1, are strongly anchored to a subset
AB  - of nucleosomes. This binding of DNMT3A/3B does not require the presence
AB  - of other well-known chromatin-modifying enzymes or proteins, such as
AB  - proliferating cell nuclear antigen, heterochromatin protein 1,
AB  - methyl-CpG binding protein 2, Enhancer of Zeste homolog 2, histone
AB  - deacetylase 1, and UHRF1, but it does require an intact nucleosomal
AB  - structure. We also show that nucleosomes containing methylated SINE and
AB  - LINE elements and CpG islands are the main sites of DNMT3A/3B binding.
AB  - These data suggest that inheritance of DNA methylation requires cues
AB  - from the chromatin component in addition to hemimethylation.
ER  -

TY  - JOUR
AU  - Jeong, Y.
AU  - Song, Y.
AU  - Shin, H.S.
AU  - Cho, B.K.
TI  - Draft Genome Sequence of Acid-Tolerant Clostridium drakei SL1T, a Potential Chemical Producer through Syngas Fermentation.
JO  - Genome Announcements
PY  - 2014
SP  - e00387
EP  - e00314
VL  - 2
AB  - Clostridium drakei SL1(T) is a strictly anaerobic, H2-utilizing, and acid-tolerant acetogen
AB  - isolated from an acidic sediment that is a potential
AB  - platform for commodity chemical production from syngas fermentation. The draft
AB  - genome sequence of this strain will enable determination of the acid resistance
AB  - and autotrophic pathway of the acetogen.
ER  -

TY  - JOUR
AU  - Jeong, Y.S.
AU  - Oh, K.B.
AU  - Park, J.S.
AU  - Kim, J.S.
AU  - Kang, Y.K.
TI  - Cytoplasmic Localization of Oocyte-Specific Variant of Porcine DNA Methyltransferase-1 During Early Development.
JO  - Dev. Dyn.
PY  - 2009
SP  - 1666
EP  - 1673
VL  - 238
AB  - DNA methyltransferase-1 (Dnmt1) is involved in the maintenance of genomic methylation
AB  - patterns. Rather than full-length Dnmt1, mouse
AB  - oocytes have a truncated variant called Dnmt1o. Immunofluorescence data
AB  - showed that Dnmt1o localized to the cytoplasm, but this has not been
AB  - confirmed using more direct methods. The cytoplasmic localization of
AB  - Dnmt1o has been assigned to the main cause of global DNA demethylation
AB  - in early mouse embryos. We studied localization of Dnmt1o in mouse and
AB  - pig embryos. We identified pig Dnmt1o protein and its transcript with
AB  - unique 5'-end sequence. Physically separating mouse and pig 2-cell
AB  - embryos into their nuclear and cytoplasmic components demonstrated that
AB  - Dnmt1o of both species localized to the cytoplasm. Cloned pig embryos
AB  - had Dnmt1o as the main form, with no indication of somatic Dnmt1. These
AB  - findings indicate that Dnmt1o is cytoplasmic during early development;
AB  - its presence in both pig and mouse embryos further suggests that Dnmt1o
AB  - is conserved in mammals. Developmental Dynamics 238:1666-1673, 2009.
ER  -

TY  - JOUR
AU  - Jeraldo, P.
AU  - Cunningham, S.A.
AU  - Quest, D.
AU  - Sikkink, R.A.
AU  - O'Brien, D.
AU  - Eckloff, B.W.
AU  - Patel, R.
AU  - Chia, N.
TI  - Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates.
JO  - Genome Announcements
PY  - 2015
SP  - e01154
EP  - e01115
VL  - 3
AB  - We report on nine draft genomes of Pseudomonas aeruginosa isolates, assembled using a hybrid
AB  - paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is
AB  - the ATCC 27853 strain. We also report their multilocus sequence types.
ER  -

TY  - JOUR
AU  - Jeraldo, P.
AU  - Hernandez, A.
AU  - White, B.A.
AU  - O'Brien, D.
AU  - Ahlquist, D.
AU  - Boardman, L.
AU  - Chia, N.
TI  - Draft genome sequences of 24 microbial strains assembled from direct sequencing from 4 stool samples.
JO  - Genome Announcements
PY  - 2015
SP  - e00526
EP  - e00515
VL  - 3
AB  - The ability to assemble genomes from metagenomic sequencing avoids the need for culture and
AB  - any associated culture biases. We assembled 24 essentially complete
AB  - draft genomes from metagenomic pair-end and size-selected mate pair sequencing
AB  - from 4 stool samples, 2 from subjects diagnosed with colorectal cancer and 2 from
AB  - healthy controls.
ER  -

TY  - JOUR
AU  - Jerke, K.
AU  - Nakatsu, C.H.
AU  - Beasley, F.
AU  - Konopka, A.
TI  - Comparative analysis of eight Arthrobacter plasmids.
JO  - Plasmid
PY  - 2008
SP  - 73
EP  - 85
VL  - 59
AB  - Despite the prevalence of Arthrobacter in the environment little is known
AB  - about their plasmids, or the capacity of Arthrobacter plasmids to mediate
AB  - horizontal gene transfer. In this study, we compared eight plasmids from
AB  - five Arthrobacter strains in order to identify putative core maintenance
AB  - genes for replication, segregation, and conjugation. Iteron like sequences
AB  - were identified on some of the plasmids; however, no genes with obvious
AB  - similarity to known replication sequences such as an origin of
AB  - replication, or rep genes were identified. All eight plasmids contained a
AB  - putative conjugation system. Genes with similarity to a relaxase, coupling
AB  - protein, and various components of a type IV secretion system were
AB  - identified on each plasmid; it appears that three different systems may be
AB  - present. Putative parA partitioning genes were found in all of the
AB  - plasmids. Each of the Arthrobacter strains examined contained a putative
AB  - parB gene; however, of the three plasmids in Arthrobacter strain FB24 only
AB  - one plasmid had a putative parB gene. Cluster analysis of many of the
AB  - Arthrobacter genes suggested that they often formed branches within
AB  - existing families of plasmid maintenance genes. Comparison of a
AB  - concatenation of all the maintenance genes from each plasmid suggests that
AB  - the eight Arthrobacter plasmids represent multiple evolutionary pathways.
ER  -

TY  - JOUR
AU  - Jermyn, W.S.
AU  - Boyd, E.F.
TI  - Characterization of a novel Vibrio pathogenicity island (VPI-2) encoding neuraminidase (nanH) among toxigenic Vibrio cholerae isolates.
JO  - Microbiology
PY  - 2002
SP  - 3681
EP  - 3693
VL  - 148
AB  - Acquisition of virulence genes encoded on mobile genetic elements has played an important role
AB  - in the emergence of pathogenic isolates of
AB  - Vibrio cholerae, the causative agent of the diarrhoeal disease cholera.
AB  - The genes encoding cholera toxin (ctxAB) the main cause of profuse
AB  - secretory diarrhoea in cholera, are encoded on a filamentous
AB  - bacteriophage CTXphi. The toxin coregulated pilus (TCP), an essential
AB  - intestinal colonization factor, was originally designated as part of a
AB  - pathogenicity island named the Vibrio pathogenicity island (VPI), but
AB  - this island has more recently been proposed to be the genome of a
AB  - filamentous phage, VPIphi. In this study, it is shown that nanH, which
AB  - encodes neuraminidase, maps within a novel pathogenicity island
AB  - designated VP1-2. The 57-3 kb VP1-2 has all of the characteristic
AB  - features of a pathogenicity island, including the presence of a
AB  - bacteriophage-like integrase (int), insertion in a tRNA gene (serine)
AB  - and the presence of direct repeats at the chromosomal integration
AB  - sites. Additionally, the G+C content of VP1-2 (42 mol%) is considerably
AB  - lower than that of the entire genome (47 mol%). VPI-2 encodes several
AB  - gene clusters, such as a restriction modification system (hsdR and
AB  - hsdM) and genes required for the utilization of amino sugars (nan-nag
AB  - region) as well as neuraminidase. To determine the distribution of
AB  - VPI-2 among V. cholerae, 78 natural isolates were examined using PCR
AB  - and Southern hybridization analysis for the presence of this region.
AB  - All toxigenic V. cholerae 01 serogroup isolates examined contained
AB  - VPI-2, whereas non-toxigenic isolates lacked the island. Of 14 V.
AB  - cholerae 0139 serogroup isolates examined, only one strain, MO2,
AB  - contained the entire 57-3 kb island, whereas 13 0139 isolates contained
AB  - only a 20-0 kb region with most of the 5' region of VPI-2 which
AB  - included nanH deleted in these strains.
ER  -

TY  - JOUR
AU  - Jerome, J.P.
AU  - Klahn, B.D.
AU  - Bell, J.A.
AU  - Barrick, J.E.
AU  - Brown, C.T.
AU  - Mansfield, L.S.
TI  - Draft Genome Sequences of Two Campylobacter jejuni Clinical Isolates, NW and D2600.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5707
EP  - 5708
VL  - 194
AB  - The Campylobacter jejuni human clinical isolates NW and D2600 colonized C57BL/6
AB  - interleukin-10-deficient (IL-10(-/-)) mice without inducing a robust inflammatory
AB  - response (J. A. Bell et al., BMC Microbiol. 9:57, 2009). We announce draft genome
AB  - sequences of NW and D2600 to facilitate comparisons with strains that induce
AB  - gastrointestinal inflammation in this mouse model.
ER  -

TY  - JOUR
AU  - Jessen, W.J.
AU  - Dhasarathy, A.
AU  - Hoose, S.A.
AU  - Carvin, C.D.
AU  - Risinger, A.L.
AU  - Kladde, M.P.
TI  - Mapping chromatin structure in vivo using DNA methyltransferases.
JO  - Methods
PY  - 2004
SP  - 68
EP  - 80
VL  - 33
AB  - Cytosine-5 DNA methyltransferases (C5 DMTases) are effective reagents for analyzing chromatin
AB  - and footprinting DNA-bound factors in vivo.
AB  - Cytosine methylation in accessible regions is assayed positively by the
AB  - PCR-based technique of bisulfite sequencing. In this article, we
AB  - outline two complementary uses for the DNA methyltransferase CviPI
AB  - (M.CviPI, GC specificity) in probing chromatin organization. First, we
AB  - describe the use of the naturally occurring, free enzyme as a
AB  - diffusible probe to map changes in nucleosome structure and to
AB  - footprint factor interactions at cis-regulatory sequences. In a second
AB  - application, termed targeted gene methylation (TAGM), the DMTase is
AB  - targeted via in-frame fusion to a DNA-binding factor. The rapid
AB  - accumulation of DNA methylation enables highly sensitive detection of
AB  - factor binding. Both strategies can be applied with any C5 DMTase, such
AB  - as M.SssI, which also possesses a short-recognition specificity (CG). A
AB  - description of methods for constructing C5 DMTase-expressing strains of
AB  - Saccharomyces cerevisiae and analyzing chromatin regions is provided.
AB  - We also include comprehensive protocols for the isolation and bisulfite
AB  - treatment of genomic DNA as well as the subsequent bisulfite sequencing
AB  - steps. Data demonstrating the efficacy of both DMTase probing
AB  - techniques, theoretical considerations, and experimental analyses are
AB  - presented at GAL1 and PHO5.
ER  -

TY  - JOUR
AU  - Jett, S.D.
AU  - Bear, D.G.
TI  - Snapshot blotting: transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to grids for electron microscopy.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 6870
EP  - 6874
VL  - 91
AB  - We present a technique, "snapshot blotting", for the electrophoretic transfer of nucleic acids
AB  - and nucleoprotein complexes in gel electrophoresis bands onto highly stable carbon film-coated
AB  - grids for imaging by electron microscopy.  The method permits structural analysis of
AB  - macromolecular species that have been resolved by a gel mobility-shift assay.  To demonstrate
AB  - the efficiency and integrity of the transfer process for a multiprotein-DNA assembly, we have
AB  - imaged various species of prokaryotic transcription complex, using the cleavage-defective
AB  - EcoRI(Q111) protein as an orientation marker and as a blockade of transcription elongation.
AB  - Snapshot blotting should be of great utility in the structural characterization of nucleic
AB  - acids and protein-nucleic acid interactions.
ER  -

TY  - JOUR
AU  - Jeukens, J.
AU  - Boyle, B.
AU  - Bianconi, I.
AU  - Kukavica-Ibrulj, I.
AU  - Tummler, B.
AU  - Bragonzi, A.
AU  - Levesque, R.C.
TI  - Complete Genome Sequence of Persistent Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain RP73.
JO  - Genome Announcements
PY  - 2013
SP  - e00568
EP  - e00513
VL  - 1
AB  - Pseudomonas aeruginosa can establish lifelong chronic airway infections in cystic fibrosis
AB  - (CF) patients. However, the genetic features associated with long-term
AB  - persistence in the lung are not understood. We sequenced the genome of P.
AB  - aeruginosa strain RP73, which was isolated after 16.9 years of chronic lung
AB  - infection in a CF patient.
ER  -

TY  - JOUR
AU  - Jeukens, J.
AU  - Freschi, L.
AU  - Kukavica-Ibrulj, I.
AU  - Nguyen, D.
AU  - Levesque, R.C.
TI  - Draft Genome Sequence of Triclosan-Resistant Cystic Fibrosis Isolate Achromobacter xylosoxidans CF304.
JO  - Genome Announcements
PY  - 2015
SP  - e00865
EP  - e00815
VL  - 3
AB  - Achromobacter xylosoxidans is an emerging opportunistic pathogen. Here, we present the genome
AB  - sequence of cystic fibrosis isolate CF304. Assembly resulted
AB  - in 29 contigs adding up to 6.3 Mbp. This is the second genome sequence for a
AB  - cystic fibrosis isolate, and little is known about the genetic basis of
AB  - pathogenicity in this organism.
ER  -

TY  - JOUR
AU  - Jeukens, J.
AU  - Kukavica-Ibrulj, I.
AU  - Freschi, L.
AU  - Jabaji, S.
AU  - Levesque, R.C.
TI  - Draft Genome Sequences of Two Lipopeptide-Producing Strains of Bacillus methylotrophicus.
JO  - Genome Announcements
PY  - 2015
SP  - e01176
EP  - e01115
VL  - 3
AB  - Bacillus methylotrophicus is implicated in phytostimulation and disease suppression of
AB  - agricultural and bioenergy crops. Here, we present the genome sequences of B. methylotrophicus
AB  - strains B26 and OB9. Their assembly resulted in  26 and 24 contigs, respectively. These
AB  - strains are well suited for comparative genomics studies and the evaluation of commercially
AB  - valuable biomolecular compounds.
ER  -

TY  - JOUR
AU  - Jezewska-Frackowiak, J.
AU  - Lubys, A.
AU  - Vitkute, J.
AU  - Zakareviciene, L.
AU  - Zebrowska, J.
AU  - Krefft, D.
AU  - Skowron, M.A.
AU  - Zylicz-Stachula, A.
AU  - Skowron, P.M.
TI  - A new prototype IIS/IIC/IIG endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus, recognising 5 '-TARCCA(N-11/9)-3 ' sequences.
JO  - J. Biotechnol.
PY  - 2015
SP  - 19
EP  - 26
VL  - 194
AB  - The Thermus sp. family of IIS/IIG/IIC enzymes includes the thermostable, bifunctional, fused
AB  - restriction endonuclease (REase)-methyltransferases (MTase): TaqII, Tth111II/TthHB27I, TspGWI,
AB  - TspDTI and TsoI. The enzymes are large proteins (approximately 120 kDa), their enzymatic
AB  - activities are affected by S-adenosylmethionine (SAM), they recognise similar asymmetric
AB  - cognate sites and cleave at a distance of 11/9 nucleotides (nt). The enzymes exhibit
AB  - similarities of their amino acid (aa) sequences and DNA catalytic motifs. Thermus sp. enzymes
AB  - are an example of functional aa sequence homologies among REases recognising different, yet
AB  - related DNA sequences. The family consists of TspGWI- and TspDTI-subfamilies. TsoI appears to
AB  - be a non-identical 'triplet', related to TspDTI and Tth11 1II/TthHB27I. The discovery of
AB  - TsoI, purified from Thermus scotoductus, is described. This prototype, displaying a novel
AB  - specificity, which was determined by: (i) cleavage of a reference plasmid and bacteriophage
AB  - DNA, (ii) cleavage of custom PCR DNA substrates, (iii) run-off sequencing of cleavage products
AB  - and (iv) shotgun cloning and sequencing of bacteriophage lambda (X) DNA digested with TsoI.
AB  - The enzyme recognises a degenerated 5'-TARCCA-3' sequence, whereas DNA strands are cut 11/9
AB  - nt downstream. The discovery of the TsoI prototype is of practical importance in
AB  - biotechnology, as it extends the palette of cleavage specificities for gene cloning.
ER  -

TY  - JOUR
AU  - Jha, G.
AU  - Tyagi, I.
AU  - Kumar, R.
AU  - Ghosh, S.
TI  - Draft Genome Sequence of Broad-Spectrum Antifungal Bacterium Burkholderia gladioli Strain NGJ1, Isolated from Healthy Rice Seeds.
JO  - Genome Announcements
PY  - 2015
SP  - e00803
EP  - e00815
VL  - 3
AB  - We report here the draft genome sequence of Burkholderia gladioli strain NGJ1. The strain was
AB  - isolated from healthy rice seeds and exhibits broad-spectrum
AB  - antifungal activity against several agriculturally important pathogens, including
AB  - Rhizoctonia solani, Magnaporthe oryzae, Venturia inaequalis, and Fusarium
AB  - oxysporum.
ER  -

TY  - JOUR
AU  - Jhon, N.-I.
AU  - Casas-Finet, J.R.
AU  - Maki, A.H.
AU  - Modrich, P.
TI  - Investigation of the complexes of EcoRI endonuclease with decanucleotides containing canonical and modified recognition sequences using fluorescence and optical detection of magnetic resonance spectroscopy.
JO  - Biochim. Biophys. Acta
PY  - 1988
SP  - 189
EP  - 194
VL  - 949
AB  - The binding of EcoRI endonuclease to the oligonucleotides d(GCGAATTCGC) and
AB  - d(GCGAA) (5BrdU) (5BrdU) d(CGC) has been investigated to determine whether
AB  - stacking interactions occur between tryptophan residues and the DNA bases.
AB  - Fluorescence binding isotherms show that the decamer containing the canonical
AB  - and that containing the modified recognition sequence bind with comparable
AB  - affinity.  Optically detected magnetic resonance spectra show limited
AB  - perturbations of the Trp zero-field splitting parameters, which are assigned to
AB  - electrical field effects.  No evidence for Trp stacking interactions has been
AB  - found.
ER  -

TY  - JOUR
AU  - Ji, B.
AU  - Gimenez, G.
AU  - Barbe, V.
AU  - Vacherie, B.
AU  - Rouy, Z.
AU  - Amrani, A.
AU  - Fardeau, M.L.
AU  - Bertin, P.
AU  - Alazard, D.
AU  - Leroy, S.
AU  - Talla, E.
AU  - Ollivier, B.
AU  - Dolla, A.
AU  - Pradel, N.
TI  - Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.).
JO  - Genome Announcements
PY  - 2013
SP  - e00226
EP  - e00212
VL  - 1
AB  - AM13 is a piezophilic, mesophilic, hydrogenotrophic sulfate-reducing bacterium collected from
AB  - a deep-sea hydrothermal chimney on the East Pacific Rise (2,600 m
AB  - depth, 13 degrees N). We report the genome sequence of this bacterium, which
AB  - includes a 3,702,934-bp chromosome and a circular plasmid of 5,328 bp.
ER  -

TY  - JOUR
AU  - Ji, K.
AU  - Wang, W.
AU  - Zeng, B.
AU  - Chen, S.
AU  - Zhao, Q.
AU  - Chen, Y.
AU  - Li, G.
AU  - Ma, T.
TI  - Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07.
JO  - Sci. Rep.
PY  - 2016
SP  - 21863
EP  - 21863
VL  - 6
AB  - Enterobacter sp. FY-07 can produce bacterial cellulose (BC) under aerobic and
AB  - anaerobic conditions. Three potential BC synthesis gene clusters (bcsI, bcsII and
AB  - bcsIII) of Enterobacter sp. FY-07 have been predicted using genome sequencing and
AB  - comparative genome analysis, in which bcsIII was confirmed as the main
AB  - contributor to BC synthesis by gene knockout and functional reconstitution
AB  - methods. Protein homology, gene arrangement and gene constitution analysis
AB  - indicated that bcsIII had high identity to the bcsI operon of Enterobacter sp.
AB  - 638; however, its arrangement and composition were same as those of BC
AB  - synthesizing operon of G. xylinum ATCC53582 except for the flanking sequences.
AB  - According to the BC biosynthesizing process, oxygen is not directly involved in
AB  - the reactions of BC synthesis, however, energy is required to activate
AB  - intermediate metabolites and synthesize the activator, c-di-GMP. Comparative
AB  - transcriptome and metabolite quantitative analysis demonstrated that under
AB  - anaerobic conditions genes involved in the TCA cycle were downregulated, however,
AB  - genes in the nitrate reduction and gluconeogenesis pathways were upregulated,
AB  - especially, genes in three pyruvate metabolism pathways. These results suggested
AB  - that Enterobacter sp. FY-07 could produce energy efficiently under anaerobic
AB  - conditions to meet the requirement of BC biosynthesis.
ER  -

TY  - JOUR
AU  - Jia, B.
AU  - Jin, H.M.
AU  - Lee, H.J.
AU  - Jeon, C.O.
TI  - Draft Genome Sequence of Zhouia amylolytica AD3, Isolated from Tidal Flat Sediment.
JO  - Genome Announcements
PY  - 2016
SP  - e00327
EP  - e00316
VL  - 4
AB  - Zhouia amylolytica AD3 was isolated from tidal flat sediment at Taean, South Korea. We report
AB  - here the draft genome sequence of Z. amylolytica AD3, which is
AB  - the first report of a genome sequence of the genus Zhouia The genomic information
AB  - will provide a better understanding of the physiology, adaptation, and evolution
AB  - of Zhouia species.
ER  -

TY  - JOUR
AU  - Jia, D.
TI  - Crystallographic and biochemical studies of mammalian de novo DNA methyltransferase Dnmt3.
JO  - Ph.D. Thesis, Emory Univ., Atlanta, GA, USA
PY  - 2007
SP  - 1
EP  - 206
AB  - The mammalian DNA methyltransferase 3 (Dnmt3) family is responsible for de novo genomic
AB  - methylation and consists of two active methyltransferases, Dnmt3a and Dnmt3b, and their
AB  - homolog Dnmt3L. Structural and biochemical characterization have identified F261 of human
AB  - DNMT3L as a key residue important for its homo-dimerization and its hetero-dimerization with
AB  - Dnmt3a. This study provides a functional assessment for the tail-to-tail interface and key
AB  - residues observed in the crystal structure of DNMT3L. A structure of the C-terminal domain of
AB  - Dnmt3L in complex with the catalytic domain of active Dnmt3a has been determined in the
AB  - presence of methyl donor analog AdoHcy. The complex structure showed that the heterodimer of
AB  - Dnm3a-3L further dimerizes through Dnmt3a-3a interaction, forming a tetrameric enzyme complex
AB  - with two active sites. Substitution of key residues from Dnmt3a-3a or Dnmt3a-3L interfaces
AB  - eliminated the enzymatic activity of Dnmt3a. The functional implication of the molecular
AB  - architecture of the Dnmt3a-Dnmt3L tetramer with two active sites is being proposed. This
AB  - structure is the first of a genuine mammalian DNA methyltransferase as well as the first of
AB  - any methyltransferase in complex with a regulator protein. This study indicates the complexity
AB  - of mammalian Dnmt in comparison with bacterial enzymes in term of oligomeric state, substrate
AB  - recognition and functional regulation.
ER  -

TY  - JOUR
AU  - Jia, D.
AU  - Jurkowska, R.Z.
AU  - Zhang, X.
AU  - Jeltsch, A.
AU  - Cheng, X.
TI  - Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.
JO  - Nature
PY  - 2007
SP  - 248
EP  - 251
VL  - 449
AB  - Genetic imprinting, found in flowering plants and placental mammals, uses DNA methylation to
AB  - yield gene expression that is dependent on the parent of origin. DNA methyltransferase 3a
AB  - (Dnmt3a) and its regulatory factor, DNA methyltransferase 3-like protein (Dnmt3L), are both
AB  - required for the de novo DNA methylation of imprinted genes in mammalian germ cells. Dnmt3L
AB  - interacts specifically with unmethylated lysine 4 of histone H3 through its amino-terminal PHD
AB  - (plant homeodomain)-like domain. Here we show, with the use of crystallography, that the
AB  - carboxy-terminal domain of human Dnmt3L interacts with the catalytic domain of Dnmt3a,
AB  - demonstrating that Dnmt3L has dual functions of binding the unmethylated histone tail and
AB  - activating DNA methyltransferase. The complexed C-terminal domains of
AB  - Dnmt3a and Dnmt3L showed further dimerization through Dnmt3a-Dnmt3a
AB  - interaction, forming a tetrameric complex with two active sites.
AB  - Substitution of key non-catalytic residues at the Dnmt3a-Dnmt3L interface
AB  - or the Dnmt3a-Dnmt3a interface eliminated enzymatic activity. Molecular
AB  - modelling of a DNA-Dnmt3a dimer indicated that the two active sites are
AB  - separated by about one DNA helical turn. The C-terminal domain of Dnmt3a
AB  - oligomerizes on DNA to form a nucleoprotein filament. A periodicity in the
AB  - activity of Dnmt3a on long DNA revealed a correlation of methylated CpG
AB  - sites at distances of eight to ten base pairs, indicating that
AB  - oligomerization leads Dnmt3a to methylate DNA in a periodic pattern. A
AB  - similar periodicity is observed for the frequency of CpG sites in the
AB  - differentially methylated regions of 12 maternally imprinted mouse genes.
AB  - These results suggest a basis for the recognition and methylation of
AB  - differentially methylated regions in imprinted genes, involving the
AB  - detection of both nucleosome modification and CpG spacing.
ER  -

TY  - JOUR
AU  - Jia, F.
TI  - Genome Sequence of the Oral Probiotic Streptococcus salivarius JF.
JO  - Genome Announcements
PY  - 2016
SP  - e00971
EP  - e00916
VL  - 4
AB  - Streptococcus salivarius is a nonpathogenic Gram-positive bacterium and the predominant
AB  - colonizer of the oral microbiota. It finds a wide application in the
AB  - prevention of upper respiratory tract infections, also reducing the frequency of
AB  - other main pathogens. Here, we present the complete genome sequence of the oral
AB  - probiotic S. salivarius JF.
ER  -

TY  - JOUR
AU  - Jia, F.
TI  - Complete Genome Sequence of Lactobacillus oris J-1, a Potential Probiotic Isolated from the Human Oral Microbiome.
JO  - Genome Announcements
PY  - 2016
SP  - e00970
EP  - e00916
VL  - 4
AB  - Lactobacilli can exert health-promoting effects in the human oral microbiome through many
AB  - mechanisms, including pathogen inhibition, maintenance of microbial
AB  - balance, immunomodulation, and enhancement of the epithelial barrier function.
AB  - Here, we present the complete genome sequence of a potential probiotic,
AB  - Lactobacillus oris J-1, that was isolated from the oral cavity of a health child.
ER  -

TY  - JOUR
AU  - Jia, N.
AU  - Ding, M.Z.
AU  - Du, Y.Z.
AU  - Feng, S.
AU  - Gao, F.
AU  - Yuan, Y.J.
TI  - Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV.
JO  - Genome Announcements
PY  - 2016
SP  - e01426
EP  - e01416
VL  - 4
AB  - Ketogulonicigenium vulgare has been widely used in vitamin C two-step fermentation, which
AB  - converts l-sorbose to 2-keto-l-gluonic acid. Here, the
AB  - complete genome of K. vulgare SKV, which performs better fermentation production
AB  - than K. vulgare Hbe602, is deciphered to understand the key differences in
AB  - metabolism between K. vulgare strains SKV and Hbe602.
ER  -

TY  - JOUR
AU  - Jia, N.
AU  - Du, J.
AU  - Ding, M.Z.
AU  - Gao, F.
AU  - Yuan, Y.J.
TI  - Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium.
JO  - PLoS ONE
PY  - 2015
SP  - E0135104
EP  - E0135104
VL  - 10
AB  - Bacillus strains have been widely used as the companion strain of
AB  - Ketogulonigenium vulgare in the process of vitamin C fermentation. Different
AB  - Bacillus strains generate different effects on the growth of K. vulgare and
AB  - ultimately influence the productivity. First, we identified that Bacillus
AB  - endophyticus Hbe603 was an appropriate strain to cooperate with K. vulgare and
AB  - the product conversion rate exceeded 90% in industrial vitamin C fermentation.
AB  - Here, we report the genome sequencing of the B. endophyticus Hbe603 industrial
AB  - companion strain and speculate its possible advantage in the consortium. The
AB  - circular chromosome of B. endophyticus Hbe603 has a size of 4.87 Mb with GC
AB  - content of 36.64% and has the highest similarity with that of Bacillus megaterium
AB  - among all the bacteria with complete genomes. By comparing the distribution of
AB  - COGs with that of Bacillus thuringiensis, Bacillus cereus and B. megaterium, B.
AB  - endophyticus has less genes related to cell envelope biogenesis and signal
AB  - transduction mechanisms, and more genes related to carbohydrate transport and
AB  - metabolism, energy production and conversion, as well as lipid transport and
AB  - metabolism. Genome-based functional studies revealed the specific capability of
AB  - B. endophyticus in sporulation, transcription regulation, environmental
AB  - resistance, membrane transportation, extracellular proteins and nutrients
AB  - synthesis, which would be beneficial for K. vulgare. In particular, B.
AB  - endophyticus lacks the Rap-Phr signal cascade system and, in part, spore coat
AB  - related proteins. In addition, it has specific pathways for vitamin B12 synthesis
AB  - and sorbitol metabolism. The genome analysis of the industrial B. endophyticus
AB  - will help us understand its cooperative mechanism in the K. vulgare-Bacillus
AB  - strain consortium to improve the fermentation of vitamin C.
ER  -

TY  - JOUR
AU  - Jia, Z.
AU  - Jin, W.
AU  - Huang, Y.
AU  - Song, S.
TI  - Complete Genome Sequence of Bacillus subtilis J-5, a Potential Biocontrol Agent.
JO  - Genome Announcements
PY  - 2017
SP  - e00275
EP  - e00217
VL  - 5
AB  - Bacillus subtilis J-5 was isolated from tomato rhizosphere soil and exhibited strong
AB  - inhibitory activity against Botrytis cinerea To shed light on the
AB  - molecular mechanism underlying the biological control on phytopathogens, the
AB  - whole genome of this strain was sequenced. Genes encoding antimicrobial compounds
AB  - and the regulatory systems were identified in the genome.
ER  -

TY  - JOUR
AU  - Jiang, B.
AU  - Cui, D.
AU  - Li, A.
AU  - Gai, Z.
AU  - Ma, F.
AU  - Yang, J.
AU  - Ren, N.
TI  - Genome Sequence of a Cold-Adaptable Sulfamethoxazole-Degrading Bacterium, Pseudomonas psychrophila HA-4.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5721
EP  - 5721
VL  - 194
AB  - Pseudomonas psychrophila HA-4 is a cold-adaptable, sulfamethoxazole-degrading bacterium. The
AB  - genes related to its cold adaptation mechanism and
AB  - sulfamethoxazole metabolism were unknown. We present the draft genome of strain
AB  - HA-4. It could provide further insight into the sulfamethoxazole-degrading
AB  - mechanism of strain HA-4.
ER  -

TY  - JOUR
AU  - Jiang, B.
AU  - Yao, H.
AU  - Tong, Y.
AU  - Yang, X.
AU  - Huang, Y.
AU  - Jiang, J.
AU  - Cao, W.
TI  - Genome Sequence of Borrelia garinii Strain NMJW1, Isolated from China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6660
EP  - 6661
VL  - 194
AB  - We announce the draft genome sequence of Borrelia garinii strain NMJW1, isolated  from Ixodes
AB  - persulcatus in northeastern China. The 902,789-bp linear chromosome
AB  - (28.4% GC content) contains 813 open reading frames, 33 tRNAs, and 4 complete
AB  - rRNAs.
ER  -

TY  - JOUR
AU  - Jiang, B.H.
AU  - Liu, J.L.
AU  - Hu, X.M.
TI  - Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9.
JO  - Genome Announcements
PY  - 2013
SP  - e00131
EP  - e00113
VL  - 1
AB  - Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a
AB  - soil sample, and is pale pink-pigmented, aerobic, and
AB  - Gram-positive. Here, we report the draft genome sequence and the initial findings
AB  - from a preliminary analysis of strain A9, which is a novel species of
AB  - Paenibacillus.
ER  -

TY  - JOUR
AU  - Jiang, C.
AU  - Yan, C.Y.
AU  - Huang, C.
AU  - Jiang, J.H.
AU  - Yu, R.Q.
TI  - A bioluminescence assay for DNA methyltransferase activity based on methylation-resistant cleavage.
JO  - Anal. Biochem.
PY  - 2012
SP  - 224
EP  - 228
VL  - 423
AB  - DNA methyltransferase (MTase) is a kind of important regulatory factor in various biological
AB  - processes. Current methods to investigate DNA
AB  - MTase activity are still limited in the sensitivity and/or generality.
AB  - Therefore, developing methods with high sensitivity and improved
AB  - generality is needed. Here, we develop a new bioluminescence strategy
AB  - based on methylation-resistant cleavage and protein expression in vitro
AB  - to detect DNA MTase activity. In the strategy, Dam MTase was used as a
AB  - model enzyme and Mbol as the methylation-resistant endonuclease, and
AB  - luciferase reporter DNA (LR-DNA) was used as their action target.
AB  - Because the completely methylated LR-DNA could be expressed as
AB  - detectable luciferase, Dam MTase activity was quantified by measuring
AB  - the luminescence intensity of the expressed luciferase. The assay
AB  - provides a very low detection limit (0.08 U/ml) as well as a wide
AB  - linear range (0.2-100 U/ml). Besides, the analysis mode has improved
AB  - generality and could be extended to the detection of other DNA MTases
AB  - and the corresponding inhibitor screening.
ER  -

TY  - JOUR
AU  - Jiang, C.H.
AU  - Chen, Y.
AU  - Yan, F.
AU  - Fan, Z.H.
AU  - Guo, J.H.
TI  - Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion.
JO  - Genome Announcements
PY  - 2017
SP  - e00886
EP  - e00817
VL  - 5
AB  - Bacillus cereus AR156 was originally isolated from the forest soil of Zhenjiang,  a city in
AB  - China. To shed new light on the molecular mechanisms underlying the
AB  - biological control of soilborne pathogens, the whole genome of this strain was
AB  - sequenced. Here, we report the draft genome sequence of this strain, consisting
AB  - of a single circularized contig measuring 5.66 Mb, with an average GC content of
AB  - 35.5% and 5,367 open reading frames.
ER  -

TY  - JOUR
AU  - Jiang, H.
AU  - Fan, H.J.
AU  - Lu, C.P.
TI  - Identification and distribution of putative virulent genes in strains of Streptococcus suis serotype 2.
JO  - Vet. Microbiol.
PY  - 2009
SP  - 309
EP  - 316
VL  - 133
AB  - In order to identify gene sequences unique to the virulent strains,
AB  - suppression subtractive hybridization (SSH) was conducted using virulent
AB  - Streptococcus suis type 2 (SS2) strain HA9801 and avirulent S. suis type 2
AB  - strain T15. Thirty genomic regions were absent in T15, and the DNA
AB  - sequences of these regions in HA9801 were determined. These DNA fragments,
AB  - containing putative virulence genes, encoded 28 proteins that were
AB  - homologous to proteins involved in various aspects of cellular surface
AB  - structure, molecular synthesis, energy metabolism, regulation, transport
AB  - systems and others of unknown function. According to the published SS2
AB  - genomic sequence of the Chinese strain 98HAH33, PCR primers for 14
AB  - significant DNA fragments were designed and used for detection of the
AB  - distribution of these fragments in S. suis strains from different sources,
AB  - serotypes, regions, groups and times. The results showed that these 14 DNA
AB  - fragments were widely distributed in 37 detected SS2 strains, yet were
AB  - absent among the avirulent strain T15. Moreover, these fragments could be
AB  - detected in other serotypes of S. suis, but each serotype had a different
AB  - distribution of the fragments.
ER  -

TY  - JOUR
AU  - Jiang, H.
AU  - Zou, G.
AU  - Huang, L.
AU  - Zhu, R.
TI  - Purification of restriction endonuclease Bsp63I by two step affinity chromatography.
JO  - Xinan Shifan Daxue Xuebao, Ziran Kexueban
PY  - 2000
SP  - 74
EP  - 77
VL  - 25
AB  - Restriction endonuclease Bsp63I has been isolated and purified by affinity chromatography on
AB  - self-made DNA Sepharose4B and Cibacron Blue F3GA Sepharose 4B from Bacillus sphaericus 63.
AB  - The purified enzyme was found to be homogenous as judged by polyacrylamide gel
AB  - electrophoresis.  The specific activity of the enzyme is greater than 61400 units per mg
AB  - protein and the yield of the purified enzyme is greater than 130 units per gram wet cells.
ER  -

TY  - JOUR
AU  - Jiang, J.
AU  - Alvarez, C.
AU  - Kukutla, P.
AU  - Yu, W.
AU  - Xu, J.
TI  - Draft Genome Sequences of Enterobacter sp. Isolate Ag1 from the Midgut of the Malaria Mosquito Anopheles gambiae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5481
EP  - 5481
VL  - 194
AB  - An isolate of Enterobacter sp. was obtained from the microbial community within the gut of the
AB  - Anopheles gambiae mosquito, a major malaria vector in Africa. This
AB  - genome was sequenced and annotated. The genome sequences will facilitate
AB  - subsequent efforts to characterize the mosquito gut microbiome.
ER  -

TY  - JOUR
AU  - Jiang, K. et al.
TI  - Complete genome sequence of Thauera aminoaromatica strain MZ1T.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 325
EP  - 335
VL  - 6
AB  - Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family
AB  - Rhodocyclaceae and the class the Betaproteobacteria, has been
AB  - characterized for its ability to produce abundant exopolysaccharide and degrade
AB  - various aromatic compounds with nitrate as an electron acceptor. These
AB  - properties, if fully understood at the genome-sequence level, can aid in
AB  - environmental processing of organic matter in anaerobic cycles by
AB  - short-circuiting a central anaerobic metabolite, acetate, from microbiological
AB  - conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain
AB  - from the genus Thauera with a completely sequenced genome. The 4,496,212 bp
AB  - chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes,
AB  - and were sequenced as part of the DOE Community Sequencing Program CSP_776774.
ER  -

TY  - JOUR
AU  - Jiang, K.
AU  - Xue, Y.
AU  - Ma, Y.
TI  - Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 116
EP  - 116
VL  - 10
AB  - Salinicoccus halodurans H3B36 is a moderately halophilic bacterium isolated from  a sediment
AB  - sample of Qaidam Basin at 3.2 m vertical depth. Strain H3B36
AB  - accumulate N (alpha)-acetyl-alpha-lysine as compatible solute against salinity
AB  - and heat stresses and may have potential applications in industrial
AB  - biotechnology. In this study, we sequenced the genome of strain H3B36 using
AB  - single molecule, real-time sequencing technology on a PacBio RS II instrument.
AB  - The complete genome of strain H3B36 was 2,778,379 bp and contained 2,853
AB  - protein-coding genes, 12 rRNA genes, and 61 tRNA genes with 58 tandem repeats,
AB  - six minisatellite DNA sequences, 11 genome islands, and no CRISPR repeat region.
AB  - Further analysis of epigenetic modifications revealed the presence of 11,000
AB  - m4C-type modified bases, 7,545 m6A-type modified bases, and 89,064 other modified
AB  - bases. The data on the genome of this strain may provide an insight into the
AB  - metabolism of N (alpha)-acetyl-alpha-lysine.
ER  -

TY  - JOUR
AU  - Jiang, K.
AU  - Zheng, J.
AU  - Higgins, S.B.
TI  - A generic algorithm for finding restriction sites within DNA sequences.
JO  - Comput. Appl. Biosci.
PY  - 1991
SP  - 249
EP  - 256
VL  - 7
AB  - This paper describes a generic algorithm for finding restriction sites within
AB  - DNA sequences.  The generality of the algorithm is made possible through the
AB  - use of set theory.  Basic elements of DNA sequences, i.e. nucleotides (bases),
AB  - are represented in sets, and DNA sequences, whether specific, ambiguous or even
AB  - protein-coding, are represented as sequences of those sets.  The set
AB  - intersection operation demonstrates its ability to perform pattern-matching
AB  - correctly on various DNA sequences.  The performance analysis showed that the
AB  - degree of complexity of the pattern matching is reduced from exponential to
AB  - linear.  An example is given to show the actual and potential restriction
AB  - sites, derived by the generic algorithm, in the DNA sequence template coding
AB  - for a synthetic calmodulin.
ER  -

TY  - JOUR
AU  - Jiang, L.
AU  - L'Haridon, S.
AU  - Jebbar, M.
AU  - Xu, H.
AU  - Alain, K.
AU  - Shao, Z.
TI  - Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 3
EP  - 3
VL  - 12
AB  - Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium
AB  - isolated from a deep-sea hydrothermal sediment. It belongs to the
AB  - physiologically homogeneous Thermotogaceae family. Here, we describe the
AB  - phenotypic features of K. pacifica together with its genome sequence and
AB  - annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of
AB  - 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S
AB  - rRNA gene sequence of this strain is distantly related to sequences of some
AB  - relatives classified in the same genus (K. olearia 7.02% and K. shengliensis
AB  - 7.83%), with dissimilarity percentages close to the threshold generally described
AB  - for genus delineation. Nevertheless, the percentage of conserved proteins (POCP),
AB  - which is much higher than 50% (around 70%), together with phenotypic features of
AB  - the isolates, confirm the affiliation all Kosmotoga species described so far to
AB  - the same genus.
ER  -

TY  - JOUR
AU  - Jiang, L.
AU  - Lin, M.
AU  - Li, X.
AU  - Cui, H.
AU  - Xu, X.
AU  - Li, S.
AU  - Huang, H.
TI  - Genome Sequence of Thermus thermophilus ATCC 33923, a Thermostable Trehalose-Producing Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00493
EP  - e00413
VL  - 1
AB  - Thermus thermophilus ATCC 33923 contains a thermostable enzyme that can efficiently catalyze
AB  - the conversion of maltose into trehalose. Here we report a
AB  - 2.15-Mb assembly of its genome sequence and other useful information, including
AB  - the coding sequences (CDS) responsible for biological processes such as DNA
AB  - replication, DNA repair, and RNA maturation.
ER  -

TY  - JOUR
AU  - Jiang, L.
AU  - Long, M.
AU  - Shao, Z.
TI  - Draft Genome Sequence of Defluviimonas indica Strain 20V17T, Isolated from a Deep-Sea Hydrothermal Vent Environment in the Southwest Indian Ocean.
JO  - Genome Announcements
PY  - 2014
SP  - e00479
EP  - e00414
VL  - 2
AB  - Here, we present the draft genome sequence of Defluviimonas indica 20V17(T), which was
AB  - isolated from a deep-sea hydrothermal vent chimney sample in the
AB  - southwest Indian Ocean. The draft genome sequence contains 4,268,338 bp, with a
AB  - G+C content of 66.33%.
ER  -

TY  - JOUR
AU  - Jiang, L.
AU  - Zhu, L.
AU  - Xu, X.
AU  - Li, Y.
AU  - Li, S.
AU  - Huang, H.
TI  - Genome Sequence of Clostridium tyrobutyricum ATCC 25755, a Butyric Acid-Overproducing Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00308
EP  - e00313
VL  - 1
AB  - Clostridium tyrobutyricum ATCC 25755 is an efficient producer of butyric acid. Here we report
AB  - a 3.01-Mb assembly of its genome sequence and other useful
AB  - information, including the coding sequences (CDSs) responsible for an alternative
AB  - pathway leading to acetate synthesis as well as a series of membrane transport
AB  - systems.
ER  -

TY  - JOUR
AU  - Jiang, S.
AU  - Zheng, B.
AU  - Ding, W.
AU  - Lv, L.
AU  - Ji, J.
AU  - Zhang, H.
AU  - Xiao, Y.
AU  - Li, L.
TI  - Whole-Genome Sequence of Staphylococcus hominis, an Opportunistic Pathogen.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4761
EP  - 4762
VL  - 194
AB  - Staphylococcus hominis is a commensal coagulase-negative species of staphylococci. It has been
AB  - considered a presumptive and opportunistic pathogen
AB  - that causes nosocomial infections in humans. Here we present the draft genome
AB  - sequence of S. hominis ZBW5, a multidrug-resistant strain isolated from a human
AB  - skin sample, which provides opportunities to understand the mechanism and genetic
AB  - basis of its pathogenesis.
ER  -

TY  - JOUR
AU  - Jiang, S.F.
AU  - Liu, Y.
AU  - Xiao, M.Y.
AU  - Ruan, C.J.
AU  - Lu, Z.J.
TI  - Draft Genome Sequence of Klebsiella variicola Strain KV321 Isolated from Rhizosphere Soil of Pisolithus tinctorius-Eucalyptus Mycorrhiza.
JO  - Genome Announcements
PY  - 2016
SP  - e00676
EP  - e00616
VL  - 4
AB  - The draft genome sequences of Klebsiella variicola strain KV321, which was isolated from
AB  - rhizosphere soil of Pisolithus tinctorius-Eucalyptus mycorrhiza,
AB  - are reported here. The genome sequences contain genes involved in ABC transporter
AB  - function in multiple-antibiotic drug resistance and colonization. This genomic
AB  - analysis will help understand the genomic basis of K. variicola virulence genes
AB  - and how the genes play a part in its interaction with other living organisms.
ER  -

TY  - JOUR
AU  - Jiang, T.
AU  - Gao, C.
AU  - Su, F.
AU  - Zhang, W.
AU  - Hu, C.
AU  - Dou, P.
AU  - Zheng, Z.
AU  - Tao, F.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Pseudomonas stutzeri SDM-LAC, a Typical Strain for Studying the Molecular Mechanism of Lactate Utilization.
JO  - J. Bacteriol.
PY  - 2012
SP  - 894
EP  - 895
VL  - 194
AB  - Pseudomonas stutzeri SDM-LAC is an efficient lactate utilizer with various applications in
AB  - biocatalysis. Here we present a 4.2-Mb assembly of its
AB  - genome. The annotated four adjacent genes form a lactate utilization
AB  - operon, which could provide further insights into the molecular mechanism
AB  - of lactate utilization.
ER  -

TY  - JOUR
AU  - Jiang, X.
AU  - Wang, S.
AU  - Cheng, H.
AU  - Huo, Y.
AU  - Zhang, X.
AU  - Zhu, X.
AU  - Han, X.
AU  - Ni, P.
AU  - Wu, M.
TI  - Genome Sequence of Halobiforma lacisalsi AJ5, an Extremely Halophilic Archaeon Which Harbors a bop Gene.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7023
EP  - 7024
VL  - 193
AB  - The draft genome sequence (4,398,155 bp, with 65.35% G+C content) of Halobiforma lacisalsi
AB  - AJ5, an extremely halophilic archaeon isolated from
AB  - a salt lake, is reported here. This is the first genome report for a
AB  - species of the Halobiforma genus.
ER  -

TY  - JOUR
AU  - Jiang, X.
AU  - Xue, Y.
AU  - Wang, L.
AU  - Yu, B.
AU  - Ma, Y.
TI  - Genome Sequence of a Novel Polymer-Grade L-Lactate-Producing Alkaliphile, Exiguobacterium sp. Strain 8-11-1.
JO  - Genome Announcements
PY  - 2013
SP  - e00616
EP  - e00613
VL  - 1
AB  - Exiguobacterium sp. strain 8-11-1 is a newly isolated alkaliphile, which was reported to
AB  - efficiently produce l-lactate using NaOH as the neutralizing agent.
AB  - Here, we present the first 2.9-Mb assembly of its genome sequence, which may
AB  - provide useful information related to its efficient lactate production and sodium
AB  - ion tolerance capacities.
ER  -

TY  - JOUR
AU  - Jiang, Y.
AU  - Huang, Y.H.
AU  - Long, Z.E.
TI  - De Novo Whole-Genome Sequence of Micromonospora carbonacea JXNU-1 with Broad-Spectrum Antimicrobial Activity, Isolated from Soil Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e00174
EP  - e00115
VL  - 3
AB  - Micromonospora carbonacea JXNU-1 is an actinomycete with broad-spectrum antimicrobial
AB  - activity, isolated from soil samples from the farmland in the area
AB  - of Yaohu Lake in Nanchang, China. Here, we report the whole-genome sequence of M.
AB  - carbonacea JXNU-1.
ER  -

TY  - JOUR
AU  - Jiang, Y.
AU  - Qu, Y.
AU  - Xu, P.
AU  - Tang, H.
TI  - Genome Sequence of a Versatile Aromatic Hydrocarbon-Degrading Bacterium, Arthrobacter sp. W1.
JO  - Genome Announcements
PY  - 2015
SP  - e00387
EP  - e00315
VL  - 3
AB  - Arthrobacter sp. W1 is a versatile aromatic-degrading strain which can directly or
AB  - cometabolically degrade various organic pollutants, such as phenol,
AB  - naphthalene, carbazole, dibenzofuran, and dibenzothiophene. Here, we present a
AB  - 3.8-Mb draft genome sequence of strain W1, which may provide comprehensive
AB  - genetic information for the application in environmental pollution remediation.
ER  -

TY  - JOUR
AU  - Jiang, Y.
AU  - Xiao, P.
AU  - Yu, G.
AU  - Sano, T.
AU  - Pan, Q.
AU  - Li, R.
TI  - Molecular Basis and Phylogenetic Implications of Deoxycylindrospermopsin Biosynthesis in the Cyanobacterium Raphidiopsis curvata.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 2256
EP  - 2263
VL  - 78
AB  - New insights into the distribution and biochemistry of the cyanotoxin
AB  - cylindrospermopsin (CYN) have been provided by the recent determination of its
AB  - biosynthesis gene cluster (cyr) in several cyanobacterial species. Raphidiopsis
AB  - curvata CHAB1150 isolated from China was analyzed for CYN analogues. Only
AB  - 7-deoxy-CYN was detected in the cell extracts. The cyr gene cluster of R. curvata
AB  - CHAB1150 was sequenced, and the cyr genes of this strain were found to have
AB  - extremely high similarities (96% to 100%) to those from other nostocalean
AB  - species. These species include Cylindrospermopsis raciborskii AWT205,
AB  - Aphanizomenon sp. strain 10E6, and Aphanizomenon ovalisporum ILC-146. Insertion
AB  - mutation was identified within the cyrI gene, and transcripts of cyrI and another
AB  - functional gene cyrJ were detected in R. curvata CHAB1150. General congruence
AB  - between the phylogenetic trees based on both cyr and 16S rrn was displayed.
AB  - Neutral evolution was found on the whole sequences of the cyr genes, and 0 to 89
AB  - negative selected codons were detected in each gene. Therefore, the function of
AB  - CyrI is to catalyze the oxygenation of 7-deoxy-CYN in CYN biosynthesis. The
AB  - transcripts of the mutated cyrI gene may result from polycistronic transcription.
AB  - The high conservation of the cyr genes may be ascribed to purifying selection and
AB  - horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Jiang, Y.
AU  - Xu, H.
AU  - Li, Y.
AU  - Liu, H.
AU  - Yu, L.
AU  - Qiao, M.
AU  - Liu, G.
TI  - Draft Genome Sequence of Bacillus subtilis Strain NKYL29, an Antimicrobial-Peptide-Producing Strain from Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e01140
EP  - e01114
VL  - 2
AB  - Bacillus subtilis strain NKYL29 is an antimicrobial-peptide-producing strain isolated from the
AB  - soil of Ranzhuang Tunnel in Hebei Province, China. Here, we
AB  - present the draft genome of this strain, which provides the genetic basis for
AB  - application of the antimicrobial peptide.
ER  -

TY  - JOUR
AU  - Jiang, Y.
AU  - Yang, F.
AU  - Zhang, X.
AU  - Yang, J.
AU  - Chen, L.
AU  - Yan, Y.
AU  - Nie, H.
AU  - Xiong, Z.
AU  - Wang, J.
AU  - Dong, J.
AU  - Xue, Y.
AU  - Xu, X.
AU  - Zhu, Y.
AU  - Chen, S.
AU  - Jin, Q.
TI  - The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei.
JO  - Plasmid
PY  - 2005
SP  - 149
EP  - 159
VL  - 54
AB  - The complete sequence of pSS, which is the large virulence plasmid of Shigella sonnei, was
AB  - determined. The 214-kb plasmid is composed of
AB  - segments of virulence-associated genes, the O-antigen gene clusters, a
AB  - range of replication and maintenance genes, and large numbers of insertion
AB  - sequence (IS) elements. Two hundred and forty-one open reading frames
AB  - (ORFs) were identified, of which 117 are highly homologous to IS elements
AB  - or transposases, 57 are homologous to known pathogenesis-associated
AB  - proteins, and 30 are related to replication, plasmid maintenance, or other
AB  - metabolic functions. Thirty-seven ORFs have no similarity to proteins with
AB  - a known function, including two with no significant similarity to any
AB  - hypothetical proteins. Interestingly, 10 ORFs encoding O-antigen gene
AB  - clusters were identified on the plasmid and this is markedly different
AB  - from most other Shigella spp. virulent plasmids. A novel toxin-antitoxin
AB  - system, a series of stbDE homologs, was found on the plasmid immediately
AB  - downstream of the replication region; the sole segregation stability
AB  - system may be responsible for the instability of pSS. The pSS plasmid is a
AB  - mixture of genes with different origins and functions. The sequence
AB  - suggests a remarkable history of IS-mediated recombination and acquisition
AB  - of DNA across a range of bacterial species.
ER  -

TY  - JOUR
AU  - Jiang, Y.
AU  - Yu, D.L.
AU  - Wei, Z.Q.
AU  - Shen, P.
AU  - Zhou, Z.H.
AU  - Yu, Y.S.
TI  - Complete Nucleotide Sequence of Klebsiella pneumoniae Multidrug Resistance Plasmid pKP048, Carrying bla(KPC-2), bla(DHA-1), qnrB4, and armA.
JO  - Antimicrob. Agents Chemother.
PY  - 2010
SP  - 3967
EP  - 3969
VL  - 54
AB  - The Klebsiella pneumoniae multidrug resistance plasmid pKP048 was completely sequenced. This
AB  - plasmid carries several important resistance
AB  - determinants, such as bla(KPC-2), bla(DHA-1), qnrB4, and armA, which
AB  - confer resistance to carbapenems, cephalosporins, fluoroquinolones, and
AB  - aminoglycosides, respectively. Analysis of the finished 151,188-bp
AB  - sequence data revealed 163 putative genes, 108 of which were assigned
AB  - functions such as replication, stable inheritance, antibiotic
AB  - resistance, a mobile element, conjugal transfer, and a
AB  - restriction-modification system, showing the strong phylogenetic
AB  - mosaicism and plasticity of the plasmid.
ER  -

TY  - JOUR
AU  - Jiang, Y.L.
AU  - Zhang, M.
AU  - Jing, H.L.
AU  - Gao, L.Y.
TI  - [Isolation and characterization of an iridovirus from sick giant salamander (Andrias davidianus)].
JO  - Bing Du Xue Bao
PY  - 2011
SP  - 274
EP  - 282
VL  - 27
AB  - A virus was isolated from cultured sick giant salmander (Andrias davidianus ) in
AB  - a farm, Shanxi Province, China. Skin ulceration and necrosis of the distal limbs
AB  - are main clinical symptoms. Virus propagated and caused CPE at 10 degrees C to 30
AB  - degrees C in BF-2, CO, CHSE, FHM cells. The optimum condition of replication was
AB  - in BF-2 cells at 25 degrees C. The virus was proved to be senstive to chloroform,
AB  - heat, pH3 and pH10 treatment. Viral replication was inhibited by
AB  - 5-Fluoro-2-deoxyuridine (FUDR). These results indicated that the virus possessed
AB  - an envelope and DNA as the genome. Electron-microscopic observation of
AB  - thin-section showed numerous hexagonal viral particles measuring 130 nm to 150 nm
AB  - in diameter orderly arranged in a lattice form in cytoplasm of BF-2 cells. The
AB  - particles showed typical iridovirus morphology. A 413 bp fragment was amplified
AB  - from the viral main capsid protein gene by PCR. The fragments was sequenced and
AB  - analysed. The results showed the isolate shared more than 96% nucleotide identity
AB  - with some Ranaviruses. We suggested that this virus was named as Andrias
AB  - davidianus iridovirus (ADIV) tentatively.
ER  -

TY  - JOUR
AU  - Jiang, Z.F.
AU  - Xia, F.
AU  - Johnson, K.W.
AU  - Bartom, E.
AU  - Tuteja, J.H.
AU  - Stevens, R.
AU  - Grossman, R.L.
AU  - Brumin, M.
AU  - White, K.P.
AU  - Ghanim, M.
TI  - Genome Sequences of the Primary Endosymbiont 'Candidatus Portiera aleyrodidarum'  in the Whitefly Bemisia tabaci B and Q Biotypes.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6678
EP  - 6679
VL  - 194
AB  - 'Candidatus Portiera aleyrodidarum' is the obligate primary endosymbiotic bacterium of
AB  - whiteflies, including the sweet potato whitefly Bemisia tabaci, and
AB  - provides essential nutrients to its host. Here we report two complete genome
AB  - sequences of this bacterium from the B and Q biotypes of B. tabaci.
ER  -

TY  - JOUR
AU  - Jiao, J.
AU  - Paterson, J.
AU  - Busche, T.
AU  - Ruckert, C.
AU  - Kalinowski, J.
AU  - Harwani, D.
AU  - Gross, H.
TI  - Draft Genome Sequence of Streptomyces sp. Strain DH-12, a Soilborne Isolate from  the Thar Desert with Broad-Spectrum Antibacterial Activity.
JO  - Genome Announcements
PY  - 2018
SP  - e00108
EP  - e00118
VL  - 6
AB  - Strain DH-12 exhibits broad-spectrum antibacterial activity toward Gram-positive  and
AB  - Gram-negative pathogens. The 7.6-Mb draft genome sequence gives insight into
AB  - the complete secondary metabolite production capacity and reveals genes
AB  - putatively responsible for its antibacterial activity, as well as genes which
AB  - enable the survival of the organism in an extreme arid environment.
ER  -

TY  - JOUR
AU  - Jiao, J.Y.
AU  - Carro, L.
AU  - Liu, L.
AU  - Gao, X.Y.
AU  - Zhang, X.T.
AU  - Hozzein, W.N.
AU  - Lapidus, A.
AU  - Huntemann, M.
AU  - Reddy, T.B.
AU  - Varghese, N.
AU  - Hadjithomas, M.
AU  - Ivanova, N.N.
AU  - Goker, M.
AU  - Pillay, M.
AU  - Eisen, J.A.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Li, W.J.
TI  - Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 21
EP  - 21
VL  - 12
AB  - Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus
AB  - Jiangella, which is at the present time composed of five species, and
AB  - was isolated from desert soil sample in Gansu Province (China). The five strains
AB  - of this genus are clustered in a monophyletic group when closer actinobacterial
AB  - genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this
AB  - genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here
AB  - we describe the complete genome sequence and annotation of this taxon. The genome
AB  - of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp,
AB  - which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes,
AB  - including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of
AB  - genome sizes of Jiangella species, J. gansuensis shows a smaller size, which
AB  - indicates this strain might have discarded too much genetic information to adapt
AB  - to desert environment. Seven new compounds from this bacterium have recently been
AB  - described; however, its potential should be higher, as secondary metabolite gene
AB  - cluster analysis predicted 60 gene clusters, including the potential to produce
AB  - the pristinamycin.
ER  -

TY  - JOUR
AU  - Jiao, J.Y.
AU  - Liu, L.
AU  - Park, D.J.
AU  - Kim, C.J.
AU  - Xiao, M.
AU  - Chen, J.
AU  - Li, L.
AU  - Zhong, J.M.
AU  - Zhao, J.
AU  - Li, W.J.
TI  - Draft Genome Sequence of Jiangella alkaliphila KCTC 19222T, Isolated from Cave Soil in Jeju, Republic of Korea.
JO  - Genome Announcements
PY  - 2015
SP  - e00721
EP  - e00715
VL  - 3
AB  - We report the draft genome sequence of Jiangella alkaliphila KCTC 19222(T), isolated from cave
AB  - soil in Jeju, Republic of Korea. This genome sequence,
AB  - together with the previously sequenced J. gansuensis strain DSM 44835(T),
AB  - identified from a desert environmental source, will give us a better
AB  - understanding of the school of 'evolutionary taxonomy.'
ER  -

TY  - JOUR
AU  - Jiao, J.Y.
AU  - Liu, L.
AU  - Zhou, E.M.
AU  - Wei, D.Q.
AU  - Ming, H.
AU  - Xian, W.D.
AU  - Yuan, C.G.
AU  - Zhong, J.M.
AU  - Li, W.J.
TI  - Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.
JO  - Antonie Van Leeuwenhoek
PY  - 2015
SP  - 75
EP  - 83
VL  - 108
AB  - Two aerobic, Gram-positive actinomycetes, designated YIM 77502(T) and YIM
AB  - 77510(T), were isolated from geothermally heated soil of Tengchong county, Yunnan
AB  - province, south-west China. The taxonomic position of strains YIM 77502(T) and
AB  - YIM 77510(T) were investigated by a polyphasic approach. Phylogenetic analyses
AB  - based on 16S rRNA gene sequences showed that strains YIM 77502(T) and YIM
AB  - 77510(T) belong to the genus Actinomadura. Both strains form extensively-branched
AB  - substrate and aerial mycelia which differentiated into short spore chains. The
AB  - cell wall of the two strains contained meso-diaminopimelic acid, while the
AB  - whole-cell sugars detected were glucose, madurose, mannose and rhamnose. The
AB  - polar lipid profile of strain YIM 77502(T) was found to consist of
AB  - diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, two
AB  - unidentified phospholipids and an unidentified polar lipid, while strain YIM
AB  - 77510(T) consisted of diphosphatidylglycerol, phosphatidylinositol mannoside and
AB  - phosphatidylinositol. The respiratory quinones of strains YIM 77502(T) and YIM
AB  - 77510(T) were MK-9(H6) and MK-9(H8). The major fatty acids (>10 %) of strain YIM
AB  - 77502(T) were C17:0, iso-C16:0, C17:010-methyl and iso-C18:0, and those of strain
AB  - YIM 77510(T) were iso-C16:0, C17:010-methyl and iso-C18:0. The G+C contents of
AB  - strains YIM 77502(T) and YIM 77510(T) were determined to be 71.3 and 70.2 mol%,
AB  - respectively. The DNA-DNA hybridization values of strains YIM 77502(T), YIM
AB  - 77510(T) and their closest phylogenetic neighbours Actinomadura echinospora BCRC
AB  - 12547(T) and Actinomadura umbrina KCTC 9343(T) were less than 70 %. Based on the
AB  - morphological and physiological properties, and phylogenetic analyses, strains
AB  - YIM 77502(T) and YIM 77510(T) are considered to represent two novel species of
AB  - the genus Actinomadura, for which the names Actinomadura amylolytica sp. nov.
AB  - (type strain YIM 77502(T) = DSM 45822(T) = CCTCC AA 2012024(T)) and Actinomadura
AB  - cellulosilytica sp. nov. (type strain YIM 77510(T) = DSM 45823(T) = CCTCC AA
AB  - 2012023(T)) are proposed.
ER  -

TY  - JOUR
AU  - Jima, D.D.
AU  - Luce-Fedrow, A.
AU  - Yang, Y.
AU  - Maina, A.N.
AU  - Snesrud, E.C.
AU  - Otiang, E.
AU  - Njenga, K.
AU  - Jarman, R.G.
AU  - Richards, A.L.
AU  - Hang, J.
TI  - Whole-Genome Sequence of 'Candidatus Rickettsia asemboensis' Strain NMRCii, Isolated from Fleas of Western Kenya.
JO  - Genome Announcements
PY  - 2015
SP  - e00018
EP  - e00015
VL  - 3
AB  - Herein we present the draft genome sequence and annotation of 'Candidatus Rickettsia
AB  - asemboensis' strain NMRCii. 'Ca. Rickettsia asemboensis' is
AB  - phylogenetically related to but distinct from the flea-borne spotted fever
AB  - pathogen Rickettsia felis. 'Ca. Rickettsia asemboensis' was initially identified
AB  - in and subsequently isolated from Ctenocephalides cat and dog fleas from Kenya.
ER  -

TY  - JOUR
AU  - Jimenez, E.
AU  - Langa, S.
AU  - Martin, V.
AU  - Arroyo, R.
AU  - Martin, R.
AU  - Fernandez, L.
AU  - Rodriguez, J.M.
TI  - Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4800
EP  - 4800
VL  - 192
AB  - Lactobacillus fermentum is a heterofermentative lactic acid bacterium and is frequently
AB  - isolated from mucosal surfaces of healthy humans.
AB  - Lactobacillus fermentum CECT 5716 is a well-characterized probiotic strain
AB  - isolated from human milk and, at present, is used in commercial infant
AB  - formulas. Here, we report the complete and annotated genome sequence of
AB  - this strain.
ER  -

TY  - JOUR
AU  - Jimenez, E.
AU  - Martin, R.
AU  - Maldonado, A.
AU  - Martin, V.
AU  - Gomez-de-Segura, A.
AU  - Fernandez, L.
AU  - Rodriguez, J.M.
TI  - Complete genome sequence of Lactobacillus salivarius CECT 5713, a probiotic strain isolated from human milk and infant feces.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5266
EP  - 5267
VL  - 192
AB  - Lactobacillus salivarius is a homofermentative lactic acid bacterium and is frequently
AB  - isolated from mucosal surfaces of healthy humans. L. salivarius CECT 5713, a strain isolated
AB  - simultaneously from breast milk and infant feces of a healthy mother-infant pair, has
AB  - immunomodulatory, anti-inflammatory, and anti-infectious properties, as revealed by several in
AB  - vitro and in vivo assays. Here, we report its complete and annotated genome sequence.
ER  -

TY  - JOUR
AU  - Jimenez, E.
AU  - Villar-Tajadura, M.A.
AU  - Marin, M.
AU  - Fontecha, J.
AU  - Requena, T.
AU  - Arroyo, R.
AU  - Fernandez, L.
AU  - Rodriguez, J.M.
TI  - Complete Genome Sequence of Bifidobacterium breve CECT 7263, a Strain Isolated from Human Milk.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3762
EP  - 3763
VL  - 194
AB  - Bifidobacterium breve is an actinobacterium frequently isolated from colonic microbiota of
AB  - breastfeeding babies. Here, we report the complete and annotated
AB  - genome sequence of a B. breve strain isolated from human milk, B. breve CECT
AB  - 7263. The genome sequence will provide new insights into the biology of this
AB  - potential probiotic organism and will allow the characterization of genes related
AB  - to beneficial properties.
ER  -

TY  - JOUR
AU  - Jimenez, G.
AU  - Blanch, A.R.
AU  - Tamames, J.
AU  - Rossello-Mora, R.
TI  - Complete Genome Sequence of Bacillus toyonensis BCT-7112T, the Active Ingredient  of the Feed Additive Preparation Toyocerin.
JO  - Genome Announcements
PY  - 2013
SP  - e01080
EP  - e01013
VL  - 1
AB  - Strain BCT-7112, previously identified as Bacillus cereus var. toyoi, is the type strain of
AB  - the species Bacillus toyonensis, a novel species of the B. cereus
AB  - group. The complete genome of this strain, which is the active ingredient of the
AB  - feed additive preparation Toyocerin, has been sequenced and annotated to reveal
AB  - the genetic properties of this probiotic organism with a long history of safe use
AB  - in animal nutrition.
ER  -

TY  - JOUR
AU  - Jimenez-Galisteo, G.
AU  - Villa, T.G.
AU  - Vinuesa, T.
AU  - Vinas, M.
AU  - Dominguez, A.
AU  - Munoz, E.
TI  - Draft Genome Sequence of the Bacterium Gordonia jacobaea, a New Member of the Gordonia Genus.
JO  - Genome Announcements
PY  - 2015
SP  - e00995
EP  - e00915
VL  - 3
AB  - Gordonia jacobaea was isolated and characterized in the Department of Microbiology, University
AB  - of Santiago de Compostela, in 2000. Here we present the  draft genome sequence of this
AB  - species, which will improve our understanding of the diversity and the relation of the cell
AB  - wall proteins of G. jacobaea with other mycolata.
ER  -

TY  - JOUR
AU  - Jin, A.
AU  - Zhang, Y.
AU  - Xia, Y.
AU  - Traylor, E.
AU  - Nelson, M.
AU  - Van Etten, J.L.
TI  - New restriction endonuclease CviRI cleaves DNA at TG^CA sequences.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 3928
EP  - 3929
VL  - 22
AB  - A new type II restriction endonuclease, CviRI, was isolated from virus XZ-6E infected
AB  - chlorella cells. CviRI is the first restriction endonuclease to recognize the sequence
AB  - 5'-TGCA-3' and cleaves DNA between the G and C residues to produce blunt-end termini.
AB  - Methylation of the adenine or cytosine in 5'-TGCA-3' sequences prevents CviRI cleavage. Due
AB  - to its sequence specificity, CviRI may be especially useful for detecting mutant alleles of
AB  - many heritable human genetic diseases.
ER  -

TY  - JOUR
AU  - Jin, B.
AU  - Robertson, K.D.
TI  - DNA Methyltransferases, DNA Damage Repair, and Cancer.
JO  - Adv. Exp. Med. Biol.
PY  - 2013
SP  - 3
EP  - 29
VL  - 754
AB  - The maintenance DNA methyltransferase (DNMT) 1 and the de novo methyltransferases DNMT3A and
AB  - DNMT3B are all essential for mammalian development. DNA methylation, catalyzed by the DNMTs,
AB  - plays an important role in maintaining genome stability. Aberrant expression of DNMTs and
AB  - disruption of DNA methylation patterns are closely associated with many forms of cancer,
AB  - although the exact mechanisms underlying this link remain elusive. DNA damage repair systems
AB  - have evolved to act as a genome-wide surveillance mechanism to maintain chromosome integrity
AB  - by recognizing and repairing both exogenous and endogenous DNA insults. Impairment of these
AB  - systems gives rise to mutations and directly contributes to tumorigenesis. Evidence is
AB  - mounting for a direct link between DNMTs, DNA methylation, and DNA damage repair systems,
AB  - which provide new insight into the development of cancer. Like tumor suppressor genes, an
AB  - array of DNA repair genes frequently sustain promoter hypermethylation in a variety of tumors.
AB  - In addition, DNMT1, but not the DNMT3s, appear to function coordinately with DNA damage repair
AB  - pathways to protect cells from sustaining mutagenic events, which is very likely through a DNA
AB  - methylation-independent mechanism. This chapter is focused on reviewing the links between DNA
AB  - methylation and the DNA damage response.
ER  -

TY  - JOUR
AU  - Jin, D.
AU  - Chen, C.
AU  - Li, L.
AU  - Lu, S.
AU  - Li, Z.
AU  - Zhou, Z.
AU  - Jing, H.
AU  - Xu, Y.
AU  - Du, P.
AU  - Wang, H.
AU  - Xiong, Y.
AU  - Zheng, H.
AU  - Bai, X.
AU  - Sun, H.
AU  - Wang, L.
AU  - Ye, C.
AU  - Gottschalk, M.
AU  - Xu, J.
TI  - Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis.
JO  - BMC Microbiol.
PY  - 2013
SP  - 141
EP  - 141
VL  - 13
AB  - BACKGROUND: The sequences of the 16S rRNA genes extracted from fecal samples
AB  - provide insights into the dynamics of fecal microflora. This potentially gives
AB  - valuable etiological information for patients whose conditions have been ascribed
AB  - to unknown pathogens, which cannot be accomplished using routine culture methods.
AB  - We studied 33 children with diarrhea who were admitted to the Children's Hospital
AB  - in Shanxi Province during 2006. RESULTS: Nineteen of 33 children with diarrhea
AB  - could not be etiologically diagnosed by routine culture and polymerase chain
AB  - reaction methods. Eleven of 19 children with diarrhea of unknown etiology had
AB  - Streptococcus as the most dominant fecal bacterial genus at admission. Eight of
AB  - nine children whom three consecutive fecal samples were collected had
AB  - Streptococcus as the dominant fecal bacterial genus, including three in the
AB  - Streptococcus bovis group and three Streptococcus sp., which was reduced during
AB  - and after recovery. We isolated strains that were possibly from the S. bovis
AB  - group from feces sampled at admission, which were then identified as
AB  - Streptococcus lutetiensis from one child and Streptococcus gallolyticus subsp.
AB  - pasteurianus from two children. We sequenced the genome of S. lutetiensis and
AB  - identified five antibiotic islands, two pathogenicity islands, and five unique
AB  - genomic islands. The identified virulence genes included hemolytic toxin cylZ of
AB  - Streptococcus agalactiae and sortase associated with colonization of pathogenic
AB  - streptococci. CONCLUSIONS: We identified S. lutetiensis and S. gallolyticus
AB  - subsp. pasteurianus from children with diarrhea of unknown etiology, and found
AB  - pathogenic islands and virulence genes in the genome of S. lutetiensis.
ER  -

TY  - JOUR
AU  - Jin, D.
AU  - Zhu, Y.
AU  - Wang, X.
AU  - Kong, X.
AU  - Liu, H.
AU  - Wang, Y.
AU  - Deng, Y.
AU  - Jia, M.
TI  - Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00569
EP  - e00516
VL  - 4
AB  - Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated
AB  - from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we
AB  - report the 5.1-Mb draft genome sequence of this strain, which will provide
AB  - insights into the diversity of Sphingobium spp. and the mechanism of phthalate
AB  - ester degradation in the estuary.
ER  -

TY  - JOUR
AU  - Jin, H.
AU  - Nishizawa, T.
AU  - Guo, Y.
AU  - Nishizawa, A.
AU  - Park, H.D.
AU  - Kato, H.
AU  - Tsuji, K.
AU  - Harada, K.I.
TI  - Complete Genome Sequence of a Microcystin-Degrading Bacterium, Sphingosinicella microcystinivorans Strain B-9.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00898
EP  - e00818
VL  - 7
AB  - Sphingosinicella microcystinivorans strain B-9 has the ability to degrade cyanobacterial
AB  - hepatotoxic cyclic peptides, microcystins, and nodularins. This is
AB  - the first report of the complete genome sequence of the microcystin-degrading
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Jin, H.M.
AU  - Jeong, H.
AU  - Moon, E.J.
AU  - Math, R.K.
AU  - Lee, K.
AU  - Kim, H.J.
AU  - Jeon, C.O.
AU  - Oh, T.K.
AU  - Kim, J.F.
TI  - Complete Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Alteromonas sp. Strain SN2.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4292
EP  - 4293
VL  - 193
AB  - Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated
AB  - from a crude oil-contaminated sea-tidal flat.
AB  - Here we report the complete 4.97-Mb genome sequence and annotation of
AB  - strain SN2. These will advance the understanding of strain SN2's
AB  - adaptation to the sea-tidal flat ecosystem and its pollutant metabolic
AB  - versatility.
ER  -

TY  - JOUR
AU  - Jin, Lu.
AU  - Ye, F.
AU  - Zhao, D.
AU  - Chen, S.
AU  - Zhu, K.
AU  - Zheng, M.
AU  - Jiang, R.-W.
AU  - Jiang, H.
AU  - Luo, C.
TI  - Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis.
JO  - Biomed Res. Int.
PY  - 2014
SP  - 304563
EP  - 304563
VL  - 2014
AB  - DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation,
AB  - which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical
AB  - stack and into the active site of protein provides DNA methyltransferases with an opportunity
AB  - to access and modify the genetic information hidden in DNA. To investigate the conversion
AB  - process of base flipping in the HhaI methyltransferase (M. HhaI), we performed different
AB  - molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The
AB  - results demonstrate that the nonspecific binding of DNA to M. HhaI is initially induced by
AB  - electrostatic interactions. Differences in chemical environment between the major and minor
AB  - grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the
AB  - GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop
AB  - motion is a key factor during this process. Our study indicates that base flipping is likely
AB  - to be an 'induced-fit' process. This study provides a solid foundation for future studies on
AB  - the discovery and development of mechanism-based DNA methyltransferases regulators.
ER  -

TY  - JOUR
AU  - Jin, Q. et al.
TI  - Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 4432
EP  - 4441
VL  - 30
AB  - We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and
AB  - serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed
AB  - of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the
AB  - plasmid shows minor divergence from that sequenced in serotype 5a, striking characteristics of
AB  - the chromosome have been revealed. The S.flexneri chromosome has, astonishingly, 314 IS
AB  - elements, more than 7-fold over those possessed by its close relatives, the non-pathogenic K12
AB  - strain and enterohemorrhagic O157:H7 strain of Escherichia coli. There are 13 translocations
AB  - and inversions compared with the E.coli sequences, all involve a segment larger than 5 kb, and
AB  - most are associated with deletions or acquired DNA sequences, of which several are likely to
AB  - be bacteriophage-transmitted pathogenicity islands. Furthermore, S.flexneri, resembling
AB  - another human-restricted enteric pathogen, Salmonella typhi, also has hundreds of pseudogenes
AB  - compared with the E.coli strains. All of these could be subjected to investigations towards
AB  - novel preventative and treatment strategies against shigellosis.
ER  -

TY  - JOUR
AU  - Jin, S.G.
AU  - Kadam, S.
AU  - Pfeifer, G.P.
TI  - Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - e125
EP  - e125
VL  - 38
AB  - DNA cytosine-5 methylation is a well-studied epigenetic pathway implicated in gene expression
AB  - control and disease pathogenesis. Different
AB  - technologies have been developed to examine the distribution of
AB  - 5-methylcytosine (5mC) in specific sequences of the genome. Recently,
AB  - substantial amounts of 5-hydroxymethylcytosine (5hmC), most likely derived
AB  - from enzymatic oxidation of 5mC by TET1, have been detected in certain
AB  - mammalian tissues. Here, we have examined the ability of several commonly
AB  - used DNA methylation profiling methods to distinguish between 5mC and
AB  - 5hmC. We show that techniques based on sodium bisulfite treatment of DNA
AB  - are incapable of distinguishing between the two modified bases. In
AB  - contrast, techniques based on immunoprecipitation with anti-5mC antibody
AB  - (methylated DNA immunoprecipitation, MeDIP) or those based on proteins
AB  - that bind to methylated CpG sequences (e.g. methylated-CpG island recovery
AB  - assay, MIRA) do not detect 5hmC and are specific for 5mC unless both
AB  - modified bases occur in the same DNA fragment. We also report that several
AB  - methyl-CpG binding proteins including MBD1, MBD2 and MBD4 do not bind to
AB  - sequences containing 5hmC. Selective mapping of 5hmC will require the
AB  - development of unique tools for the detection of this modified base.
ER  -

TY  - JOUR
AU  - Jin, Y.
AU  - Binkowski, G.
AU  - Simon, L.D.
AU  - Norris, D.
TI  - HO endonuclease cleaves MAT DNA in vitro by an inefficient stoichiometric reaction mechanism.
JO  - J. Biol. Chem.
PY  - 1997
SP  - 7352
EP  - 7359
VL  - 272
AB  - Mating type switching in Saccharomyces cerevisiae initiates when HO endonuclease makes a
AB  - double-stranded DNA break at the yeast MAT locus.  In this report, we characterize the
AB  - fundamental biochemical properties of HO.  Using an assay that monitors cleavage of a MAT
AB  - plasmid, we define an optimal in vitro reaction, showing in particular that the enzyme has a
AB  - stringent requirement for zinc ions.  This suggests that zinc finger motifs present in HO are
AB  - important for cleavage.  The most unexpected feature of HO, however, is its extreme
AB  - inefficiency.  Maximal cleavage occurs when HO is present at a concentration of 1 molecule/3
AB  - base pairs of substrate DNA.  Even under these conditions, complete digestion requires >2h.
AB  - This inefficiency results from two characteristics of HO.  First, HO recycles slowly from
AB  - cleaved product to new substrate, in part because the enzyme has an affinity for one end of
AB  - its double strand break product.  Second, high levels of cleavage in the in vitro reaction
AB  - correlate with the appearance of large protein-DNA aggregates.  At optimal HO concentrations,
AB  - these latter aggregates, referred to as "florettes," have an ordered structure consisting of a
AB  - densely staining central region and loops of radiating DNA.  These unusual properties may
AB  - indicate that HO plays a role in other aspects of mating type switching subsequent to double
AB  - strand break formation.
ER  -

TY  - JOUR
AU  - Jindrova, E.
AU  - Schmid-Nuoffer, S.
AU  - Hamburger, F.
AU  - Janscak, P.
AU  - Bickle, T.A.
TI  - On the DNA cleavage mechanism of Type I restriction enzymes.
JO  - FEBS J.
PY  - 2005
SP  - 552
EP  - 552
VL  - 272
AB  - Although the DNA-cleavage mechanism of Type I restriction-modification enzymes has been
AB  - extensively studied, the mode of how these enzymes introduce DNA double-strand breaks still
AB  - remains elusive. In this work, DNA ends produced by EcoKI, EcoAI and EcoR124I, members of the
AB  - Type IA, IB and IC families, respectively, have been characterized by cloning and sequencing
AB  - of restriction products from reactions with a plasmid DNA substrate containing a single
AB  - recognition site for each enzyme. We show that all three enzymes cut this DNA randomly with no
AB  - preference for a particular base composition surrounding the cleavage site, producing both 5'-
AB  - and 3'-overhangs of varying lengths. EcoAI preferentially generated 3''-overhangs of 2-3
AB  - nucleotides, whereas EcoKI and EcoR124I displayed some preference for formation of
AB  - 5'-overhangs in a length of about 6-7 and 3-5 nucleotides, respectively. A mutant EcoAI
AB  - endonuclease assembled from wild-type and nuclease-deficient restriction subunits generated a
AB  - high proportion of nicked circular DNA, whereas the wild-type enzyme catalyzed efficient
AB  - cleavage of both DNA strands. We conclude that Type I restriction enzymes require two
AB  - restriction subunits to introduce DNA double-strand breaks, each providing one catalytic
AB  - center for phosphodiester bond hydrolysis. Possible models for DNA cleavage are further
AB  - studied and discussed.
ER  -

TY  - JOUR
AU  - Jindrova, E.
AU  - Schmid-Nuoffer, S.
AU  - Hamburger, F.
AU  - Janscak, P.
AU  - Bickle, T.A.
TI  - On the DNA cleavage mechanism of Type I restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 1760
EP  - 1766
VL  - 33
AB  - Although the DNA cleavage mechanism of Type I restriction-modification enzymes has been
AB  - extensively studied, the mode of cleavage remains
AB  - elusive. In this work, DNA ends produced by EcoKI, EcoAI and EcoR124I,
AB  - members of the Type IA, IB and IC families, respectively, have been
AB  - characterized by cloning and sequencing restriction products from the
AB  - reactions with a plasmid DNA substrate containing a single recognition
AB  - site for each enzyme. Here, we show that all three enzymes cut this
AB  - substrate randomly with no preference for a particular base composition
AB  - surrounding the cleavage site, producing both 5'- and 3'-overhangs of
AB  - varying lengths. EcoAI preferentially generated 3'-overhangs of 2-3 nt,
AB  - whereas EcoKI and EcoR124I displayed some preference for the formation of
AB  - 5'-overhangs of a length of approximately 6-7 and 3-5 nt, respectively. A
AB  - mutant EcoAI endonuclease assembled from wild-type and nuclease-deficient
AB  - restriction subunits generated a high proportion of nicked circular DNA,
AB  - whereas the wild-type enzyme catalyzed efficient cleavage of both DNA
AB  - strands. We conclude that Type I restriction enzymes require two
AB  - restriction subunits to introduce DNA double-strand breaks, each providing
AB  - one catalytic center for phosphodiester bond hydrolysis. Possible models
AB  - for DNA cleavage are discussed.
ER  -

TY  - JOUR
AU  - Jing, X.
AU  - Cao, X.
AU  - Wang, Li.
AU  - Lan, T.
AU  - Li, Y.
AU  - Xie, G.
TI  - DNA-AuNPs based signal amplification for highly sensitive detection of DNA methylation, methyltransferase activity and inhibitor screening.
JO  - Biosensors and Bioelectronics
PY  - 2014
SP  - 40
EP  - 47
VL  - 58
AB  - A sensitive and selective electrochemical method was developed for the detection of DNA
AB  - methylation, determination of DNA methyltransferase (MTase) activity and screening of MTase
AB  - inhibitor. Methylene blue (MB) was employed as electrochemical indicator and DNA-modified gold
AB  - nanoparticles (AuNPs) were used as signal amplification unit because the DNA strands in this
AB  - composite have strong adsorption ability for MB. First, the thiolated single-stranded DNA S1
AB  - was self-assembled on gold electrode, hybridization between the lower portion of DNA S1 and
AB  - its complementary DNA S2 formed an identical double-stranded tetranucleotide target sequence
AB  - for both DNA adenine methylation (Dam) MTase and methylation-resistant endonuclease Mbo I,
AB  - then the upper portion of DNA S1 was hybridized with its complementary DNA S3 modified on
AB  - AuNPs to bring the DNA S3-AuNPs amplification units onto the electrode. The DNA S1
AB  - /S2/S3-AuNPs bioconjugate has lots of DNA strands, and they can adsorb abundant MB. Mbo I
AB  - endounuclease could not cleave the identical target sequence after it was methylated by Dam
AB  - MTase. On the contrary, the sequence without methylation could be cleaved, which would
AB  - decrease the amount of adsorbed MB. The presence of redox-active MB was detected
AB  - electrochemically by differential pulse voltammetry (DPV). Thus, the activity of Dam MTase and
AB  - methylation status were sensitively converted to the DNA S3-AuNPs amplified DPV signals. The
AB  - DPV signal demonstrated a linear relationship with logarithm of Dam concentration ranging from
AB  - 0.075 to 30 U/mL, achieving a detection limit of 0.02 U/mL (SIN=D3). Also, screening of Dam
AB  - MTase inhibitor 5-fluorouracil was successfully investigated using this fabricated sensor.
ER  -

TY  - JOUR
AU  - Jiricny, J.
AU  - Martin, D.
TI  - Restriction endonucleases HindII and TaqI cleave DNA with mismatched nucleotides within their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 1943
EP  - 1949
VL  - 14
AB  - Restriction endonucleases HindII and TaqI, but not SalI, were found to
AB  - efficiently cleave synthetic hexdecanucleotide duplexes which contained either
AB  - an A/C or a G/T mismatch within their respective restriction sites.
AB  - Double-stranded M13 DNAs with identical mismatches were also cleaved under the
AB  - assay conditions.  These results suggest that the distortion of the DNA duplex,
AB  - caused by these purine/pyrimidine mismatches is not sufficiently large so as to
AB  - interfere with the recognition and the subsequent cleavage of the DNA by these
AB  - two enzymes.  HindII and SalI, but not TaqI, were furthermore shown to
AB  - hydrolyze the two strands of the duplex with different rates.  The differences
AB  - between the mode of recognition of their respective restriction sites by these
AB  - three enzymes are discussed.
ER  -

TY  - JOUR
AU  - Jiricny, J.
AU  - Wood, S.G.
AU  - Martin, D.
AU  - Ubasawa, A.
TI  - Oligonucleotide duplexes containing inosine, 7-deazainosine, tubercidin, nebularine and 7-deazanebularine as substrates for restriction endonucleases HindII, SalI and TaqI.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 6579
EP  - 6590
VL  - 14
AB  - Synthetic hexadecanucleotide duplexes containing a single purine nucleotide
AB  - analogue in the recognition sites of the restriction endonucleases HindII, SalI
AB  - and TaqI were used to investigate the restriction site determinants required by
AB  - these enzymes for sequence recognition and phosphodiester bond cleavage.  The
AB  - enzymes were, in general, unaffected by changes introduced into the minor
AB  - groove of the helix.  SalI was found to be inhibited by the major groove
AB  - modifications introduced into the fourth position of its recognition sequence
AB  - GTCGAC.  HindII and TaqI were, by contrast, able to cleave the sites containing
AB  - the analogues at this position.  TaqI and, to a lesser extent, HindII could
AB  - also be shown to tolerate "mismatch analogues" at this site.
ER  -

TY  - JOUR
AU  - Jneid, J.
AU  - Benamar, S.
AU  - Pagnier, I.
AU  - Levy, P.Y.
AU  - Lavigne, J.P.
AU  - La Scola, B.
TI  - Draft Genome Sequence of Providencia heimbachae, Isolated from a Diabetic Foot Ulcer.
JO  - Genome Announcements
PY  - 2016
SP  - e00276
EP  - e00216
VL  - 4
AB  - Providenciaspp. are ubiquitous Gram-negative bacteria of the familyEnterobacteriaceaethat are
AB  - common opportunistic pathogens. In the present
AB  - work, we have sequenced, annotated, and compared the draft genome ofProvidencia
AB  - heimbachae, which was recovered from a diabetic foot ulcer. It is composed of
AB  - 4.22 Mb and encodes 3,843 protein-coding genes and 79 RNA genes, including 11
AB  - rRNA genes.
ER  -

TY  - JOUR
AU  - Jo, J.
AU  - Choi, H.
AU  - Lee, S.G.
AU  - Oh, J.
AU  - Lee, H.G.
AU  - Park, C.
TI  - Draft Genome Sequences of Pseudoalteromonas tetraodonis CSB01KR and Pseudoalteromonas lipolytica CSB02KR, Isolated from the Gut of the Sea Cucumber Apostichopus japonicus.
JO  - Genome Announcements
PY  - 2017
SP  - e00627
EP  - e00617
VL  - 5
AB  - We present here the complete genome sequences of two newly isolated Pseudoalteromonas
AB  - tetraodonis and Pseudoalteromonas lipolytica strains, isolated
AB  - from the gut of the sea cucumber Apostichopus japonicus, to provide a useful
AB  - means for facilitating the study of antibacterial, bacteriolytic, agarolytic, and
AB  - algicidal activities of marine Pseudoalteromonas species.
ER  -

TY  - JOUR
AU  - Jo, K.
TI  - Evolutionary relationship of NaeI restriction endonuclease with DNA topisomerases.
JO  - Diss. Abstr.
PY  - 1996
SP  - 889
EP  - 889
VL  - 57
AB  - NaeI endonuclease must bind two DNA recognition sequences for cleavage
AB  - to occur.  Therefore, DNAs containing NaeI recognition sequences without sufficient
AB  - affinity to occupy one or the other DNA-binding sites are resistant to cleavage.  Tethering
AB  - resistant and cleavable recognition sequences together caused a switch in their relative
AB  - cleavabilities.  This switching implies that DNA cleavage occurs at the DNA-binding site
AB  - with higher affinity for the resistant sequence.  The other DNA-binding site, with higher
AB  - affinity for the cleavable sequence, acts as the effector DNA-binding site with little to no
AB  - catalytic function.  Examination of the amino acid sequence of NaeI uncovered similarity to
AB  - the active site of human ligase I, except for leucine 43 in NaeI instead of lysine essential
AB  - for
AB  - ligase activity.  Changing leucine 43 to lysine 43 (L43K) changed NaeI activity: NaeI-
AB  - L43K relaxed supercoiled DNA to yield DNA topoisomers and recombined DNA to give
AB  - dimeric molecule.  Interruption of the reactions of NaeI and NaeI-L43K with DNA
AB  - demonstrated transient protein-DNA covalent complexes.  These findings imply coupled
AB  - endonuclease and ligase domains and link NaeI endonuclease to the topoisomerase and
AB  - recombinase protein families.  Glycerol gradient sedimentation of NaeI-L43K showed that
AB  - the active conformation of NaeI-LA3K is a dimer.  The topoisomerase activity of NaeI-
AB  - LA3K changed from processive to distributive with increasing cation concentration.  NaeI-
AB  - L43K decatenated k-DNA and bonded the 5' end of the cleaved DNA.  These
AB  - characteristics mimic those of the classic type II topoisomerases.  Also, the effects of
AB  - topoisomerase drugs on NaeI-LA3K were determined.  NaeI-LA3K activity was
AB  - specifically inhibited by eukaryotic topoisomerase II drugs daunorubicin, ellipticine, and
AB  - m-AMSA.  Especially, the cleavage step of DNA relaxation by NaeI-LA3K was sensitively
AB  - inhibited by these drugs, but the cleavage activity of wild-type NaeI was not.  Therefore,
AB  - L43K amino acid change increased the sensitivity of NaeI protein to the drugs.  The
AB  - increased sensitivity implies that protein-drug interaction is enhanced by the amino acid
AB  - change and that the ligase-like active site, containing LA3K, provides a part of the drug
AB  - binding pocket.
ER  -

TY  - JOUR
AU  - Jo, K.
AU  - Topal, M.D.
TI  - Step-wise DNA relaxation and decatenation by NaeI-43K.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 2380
EP  - 2384
VL  - 26
AB  - NaeI protein was originally isolated for its restriction endonuclease properties.  NaeI was
AB  - later discovered to either relax or cleave supercoiled DNA, depending upon whether NaeI
AB  - position 43 contains a lysine (43K) or leucine (43L) respectively.  NaeI-43K DNA relaxation
AB  - activity appears to be the product of coupling separate endonuclease and ligase domains within
AB  - the same polypeptide.  Whereas NaeI relaxes supercoiled DNA like a topoisomerase, even forming
AB  - a transient covalent intermediate with the substrate DNA, NaeI shows no obvious sequence
AB  - similarity to the topoisomerases.  To further characterize the topoisomerase activity of NaeI,
AB  - we report here that NaeI-43K changes the linking number of a single negatively supercoiled
AB  - topoisomer of pBR322 by units of one and therefore is a type I topoisomerase.  Positively
AB  - supercoiled pBR322 was resistant to NaeI-43K.  At low salt concentration NaeI-43K was
AB  - processive; non-saturating amounts of enzyme relaxed a fraction of the DNA. At high salt
AB  - concentration the same non-saturating amounts of NaeI-43K partially relaxed all the DNA in a
AB  - step-wise fashion to give a Gaussian distribution of topoisomers, demonstrating a switch from
AB  - a processive to a distributive mode of action.  NaeI-43K decatenated kinetoplast DNA
AB  - containing nicked circles, implying that NaeI-43K can cleave opposite a nick.  The products of
AB  - the reaction are decatenated nicked circles under both processive and distributive conditions.
AB  - The behavior of NaeI-43K is consistent with that of a prokaryotic type I topoisomerase.
ER  -

TY  - JOUR
AU  - Jo, K.
AU  - Topal, M.D.
TI  - Effects on NaeI-DNA recognition of the leucine to lysine substitution that transforms restriction endonuclease NaeI to a topoisomerase: a model for restriction endonuclease evolution.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 4171
EP  - 4175
VL  - 24
AB  - Substituting lysine for leucine at position 43 (L43K) transforms NaeI from restriction
AB  - endonuclease to topoisomerase and makes NaeI hypersensitive to intercalative anticancer drugs.
AB  - Here we investigated DNA recognition by NaeI-L43K.  Using DNA competition and gel retardation
AB  - assays, NaeI-L43K showed reduced affinity for DNA substrate and the ability to bind both
AB  - single- and double-stranded DNA with a definite preference for the former.  Sedimentation
AB  - studies showed that under native conditions NaeI-L43K, like NaeI, is a dimer.  Introduction of
AB  - mismatched bases into double-stranded DNA significantly increased that DNA's ability to
AB  - inhibit NaeI-L43K.  Wild-type NaeI showed no detectable binding of either single-stranded DNA
AB  - or mismatched DNA over the concentration range studied.  These results demonstrate that the
AB  - L43K substitution caused a significant change in recognition specificity by NaeI and imply
AB  - that NaeI-L43K's topoisomerase activity is related to its ability to bind single-stranded and
AB  - distorted regions in DNA.  A mechanism is proposed for the evolution of the NaeI
AB  - restriction-modification system from a topoisomerase/ligase by a mutation that abolished
AB  - religation activity and provided a needed change in DNA recognition.
ER  -

TY  - JOUR
AU  - Jo, K.
AU  - Topal, M.D.
TI  - DNA topoisomerase and recombinase activities in NaeI restriction endonuclease.
JO  - Science
PY  - 1995
SP  - 1817
EP  - 1820
VL  - 267
AB  - NaeI endonuclease must bind to two DNA sequences for cleavage. Examination of the amino acid
AB  - sequence of NaeI uncovered similarity to the active site of human DNA ligase I, except for
AB  - leucine 43 in NaeI instead of the lysine essential for ligase activity. Changing leucine 43 to
AB  - lysine 43 (L43K) changed NaeI activity: NaeI-L43K relaxed supercoiled DNA to yield DNA
AB  - topisomers and recombined DNA to give dimeric molecules. Interruption of the reactions of NaeI
AB  - and NaeI-L43K with DNA demonstrated transient protein-DNA covalent complexes. These findings
AB  - imply coupled endonuclease and ligase domains and link NaeI endonuclease to the topoisomerase
AB  - and recombinase protein families.
ER  -

TY  - JOUR
AU  - Jo, K.
AU  - Topal, M.D.
TI  - Changing a leucine to a lysine residue makes NaeI endonuclease hypersensitive to DNA intercalative drugs.
JO  - Biochemistry
PY  - 1996
SP  - 10014
EP  - 10018
VL  - 35
AB  - A single amino acid change transforms restriction enzyme NaeI to a topoisomerase and
AB  - recombinase (NaeI-L43K) that shows no sequence similarity to these protein families.  This
AB  - transformation appears to result from coupled endonuclease and ligase domains.  To further
AB  - elucidate the relationship between NaeI-L43K and the topoisomerase protein family, we studied
AB  - the effect of the topoisomerase inhibitors on NaeI-L43K activity.  The intercalative drugs
AB  - amsacrine, ellipticine, and daunorubicin inhibited NaeI-L43K, whereas the nonintercalating
AB  - drugs camptothecin, VP-16, and oxolinic acid did not.  Ethidium bromide also inhibited
AB  - NaeI-L43K, implying that intercalation is responsible for its inhibition.  The effects of the
AB  - intercalative drugs on the DNA cleavage steps of NaeI and NaeI-L43K were compared.  The drugs
AB  - hardly inhibited DNA cleavage by wild type NaeI but completely inhibited DNA cleavage by
AB  - NaeI-L43K.  This difference in inhibition demonstrates that the L43K amino acid change
AB  - sensitized NaeI to these drugs.  Low concentrations of the intercalative drugs, except for
AB  - ethidium bromide, enhance production of topoisomerase--DNA covalent intermediates but
AB  - inhibited production of the NaeI-L43K-DNA covalent intermediate.  These results imply some
AB  - unique differences between DNA relaxation by NaeI-L43K and DNA topoisomerase.  Concomitant
AB  - with studying inhibition of the cleavage intermediate, NaeI-L53K was found to covalently bond
AB  - with the 5' end of the cleaved DNA strand.
ER  -

TY  - JOUR
AU  - Joardar, V. et al.
TI  - Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.
JO  - J. Bacteriol.
PY  - 2005
SP  - 6488
EP  - 6488
VL  - 187
AB  - Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal
AB  - agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae
AB  - pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular
AB  - chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses
AB  - with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong
AB  - degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as
AB  - putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs
AB  - present in conserved, syntenic blocks. Although these two pathovars are highly similar at the
AB  - physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000
AB  - is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding
AB  - virulence, fitness, and survival factors revealed a substantial, but not complete, overlap
AB  - between these two pathovars. Another distinguishing feature between the two pathovars is their
AB  - distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome
AB  - sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome
AB  - and 365 ORFs that are P. syringae specific.
ER  -

TY  - JOUR
AU  - Jobbagy, Z.
AU  - Izsvak, Z.
AU  - Duda, E.
TI  - Positive co-operative interaction between the subunits of CeqI restriction endonuclease.
JO  - Biochem. J.
PY  - 1992
SP  - 85
EP  - 88
VL  - 286
AB  - CeqI restriction endonuclease, an isoschizomer of EcoRV, forms complexes of 2-20 subunits
AB  - under physiological conditions, in the absence of DNA. These molecules partially dissociate in
AB  - the presence of DNA sequences recognized by CeqI or in the presence of non-ionic detergents.
AB  - In solutions containing high concentrations of salts (e.g. 1M NaCl), the enzyme dissociated
AB  - into subunits, concomitantly losing its activity. According to our experiments, it is the
AB  - tetrameric form of the enzyme that binds the DNA and represents the catalytically active
AB  - molecule. Analysis of the enzyme kinetics revealed a positive co-operative interaction between
AB  - the subunits of the enzyme. Computer-assisted analysis of these data yielded a Hill
AB  - coefficient of approx. 1.35, suggesting two binding sites per tetrameric enzyme molecule, two
AB  - subunits per palindromic recognition site.
ER  -

TY  - JOUR
AU  - Jobling, M.G.
AU  - Raleigh, E.A.
AU  - Frank, D.N.
TI  - Complete Genome Sequence of Escherichia coli ER1821R, a Laboratory K-12 Derivative Engineered To Be Deficient in All Methylcytosine and Methyladenine  Restriction Systems.
JO  - Genome Announcements
PY  - 2016
SP  - e00763
EP  - e00716
VL  - 4
AB  - We present here the complete genomic sequence of a rifampin-resistant derivative  of the
AB  - Escherichia coli K-12 laboratory strain ER1821, engineered to be deficient
AB  - in all known restriction systems, making it suitable for generating unbiased
AB  - libraries from organisms with non-K-12 methylation patterns. The ER1821R genome
AB  - is most closely related to that of DH1, another popular cloning strain (both
AB  - derived from MM294), but is deleted for the e14 prophage (McrA(-)) and the
AB  - immigration control (McrBC(-) EcoKI R(-) M(-) Mrr(-)) loci.
ER  -

TY  - JOUR
AU  - Jogler, C.
AU  - Lin, W.
AU  - Meyerdierks, A.
AU  - Kube, M.
AU  - Katzmann, E.
AU  - Flies, C.
AU  - Pan, Y.
AU  - Amann, R.
AU  - Reinhardt, R.
AU  - Schuler, D.
TI  - Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 3972
EP  - 3979
VL  - 75
AB  - In this report, we describe the selective cloning of large DNA fragments
AB  - from magnetotactic metagenomes from various aquatic habitats. This was
AB  - achieved by a two-step magnetic enrichment which allowed the mass
AB  - collection of environmental magnetotactic bacteria (MTB) virtually free of
AB  - nonmagnetic contaminants. Four fosmid libraries were constructed and
AB  - screened by end sequencing and hybridization analysis using heterologous
AB  - magnetosome gene probes. A total of 14 fosmids were fully sequenced. We
AB  - identified and characterized two fosmids, most likely originating from two
AB  - different alphaproteobacterial strains of MTB that contain several
AB  - putative operons with homology to the magnetosome island (MAI) of
AB  - cultivated MTB. This is the first evidence that uncultivated MTB exhibit
AB  - similar yet differing organizations of the MAI, which may account for the
AB  - diversity in biomineralization and magnetotaxis observed in MTB from
AB  - various environments.
ER  -

TY  - JOUR
AU  - Jogler, C.
AU  - Niebler, M.
AU  - Lin, W.
AU  - Kube, M.
AU  - Wanner, G.
AU  - Kolinko, S.
AU  - Stief, P.
AU  - Beck, A.J.
AU  - de Beer, D.
AU  - Petersen, N.
AU  - Pan, Y.
AU  - Amann, R.
AU  - Reinhardt, R.
AU  - Schuler, D.
TI  - Cultivation-independent characterization of 'Candidatus Magnetobacterium bavaricum' via ultrastructural, geochemical, ecological and metagenomic methods.
JO  - Environ. Microbiol.
PY  - 2010
SP  - f2466
EP  - f2478
VL  - 12
AB  - 'Candidatus Magnetobacterium bavaricum' is unusual among magnetotactic bacteria (MTB) in
AB  - terms of cell size (8-10 microm long, 1.5-2 microm in diameter), cell architecture,
AB  - magnetotactic behaviour and its distinct phylogenetic position in the deep-branching
AB  - Nitrospira phylum. In the present study, improved magnetic enrichment techniques permitted
AB  - high-resolution scanning electron microscopy and energy dispersive X-ray analysis, which
AB  - revealed the intracellular organization of the magnetosome chains. Sulfur globule accumulation
AB  - in the cytoplasm point towards a sulfur-oxidizing metabolism of 'Candidatus M. bavaricum'.
AB  - Detailed analysis of 'Candidatus M. bavaricum' microhabitats revealed more complex
AB  - distribution patterns than previously reported, with cells predominantly found in low oxygen
AB  - concentration. No correlation to other geochemical parameters could be observed. In addition,
AB  - the analysis of a metagenomic fosmid library revealed a 34 kb genomic fragment, which contains
AB  - 33 genes, among them the complete rRNA gene operon of 'Candidatus M. bavaricum' as well as a
AB  - gene encoding a putative type IV RubisCO large subunit.
ER  -

TY  - JOUR
AU  - Johannssen, W.
TI  - Electron microscopy studies of DNA complexes with restriction endonuclease SalGI.
JO  - Z. Allg. Mikrobiol.
PY  - 1983
SP  - 197
EP  - 201
VL  - 23
AB  - The binding properties of the type II restriction endonuclease SalGI to the plasmid DNA pGW10
AB  - has been investigated by electron microscopic studies.  Samples were spread by the BAC
AB  - technique.  In the presence of magnesium, SalGI binds as dimers and tetramers to the specific
AB  - recognition site 5'-G-T-C-G-A-C-3' and with lower rate to the sequence 5'-G-T-C-A-A-C-3',
AB  - which represents the recognition site of the restriction endonucleases HindII and HincII.
ER  -

TY  - JOUR
AU  - Johannssen, W.
TI  - Interaction of restriction endonuclease with DNA as revealed by electron microscopy.
JO  - Methods Microbiol.
PY  - 1988
SP  - 325
EP  - 339
VL  - 20
AB  - None
ER  -

TY  - JOUR
AU  - Johannssen, W.
AU  - Schutte, H.
AU  - Mayer, F.
AU  - Mayer, H.
TI  - Quaternary structure of the isolated restriction endonuclease EndoR.BglI from Bacillus globigii as revealed by electron microscopy.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 707
EP  - 726
VL  - 134
AB  - The restriction endonuclease EndoR.BglI was purified nearly to homogeneity.
AB  - BglI samples, when negatively stained with 4% uranyl acetate, show two
AB  - different particle projections in the electron microscope.  Projection A has an
AB  - outer diameter of 22.5+/-0.8 nm and is composed of six intensity maxima
AB  - arranged in a ring; the centre of the ring exhibits slightly visible additional
AB  - substructures.  Projection B is also a ring; its outer diameter is 23.8+/-0.7
AB  - nm; it does not show detailed fine structure, aside from a probable 10-fold
AB  - rotational symmetry.  Variations of the negative staining technique (single
AB  - carbon layer, 2% uranyl acetate; sandwich preparation with 4% uranyl acetate)
AB  - revealed additional fine structural details for both projections.  From the
AB  - electron microscopic observations, a model of the enzyme particle was developed
AB  - containing 20 identical, biologically active monomers of molecular weight
AB  - around 61,000 arranged as a pentagonal dodecahedron.  Tilting experiments
AB  - established this structure decisively by interconversion of the different
AB  - appearances of given particles in the expected way.  By sodium dodecyl
AB  - sulphate/polyacrylamide gel electrophoresis, polyacrylamide gel electrophoresis
AB  - in a continuous molecular sieve gradient and evaluation of negatively stained
AB  - enzyme particles, a molecular weight of the monomer of 61,000 was estimated,
AB  - resulting in a total enzyme particle molecular weight of 1.2x10/6 also
AB  - determined by linear sucrose density-gradient centrifugation.
ER  -

TY  - JOUR
AU  - Johansen, S.
AU  - Embley, T.M.
AU  - Willassen, N.P.
TI  - A family of nuclear homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4405
EP  - 4405
VL  - 21
AB  - Homing endonucleases from archaea introns, protein insertions, and the mobile group I introns
AB  - from organelles share a common motif, the LAGLI-DADG motif. Sequence motifs like the
AB  - zinc-finger and the BIY-YIG have been found in phage homing endonucleases. However, the only
AB  - described nuclear homing endonuclease, the 18 kd I-Ppo protein has none of the above consensus
AB  - sequences. This unclassified I-Ppo endonuclease is encoded by the mobile intron PpLSU3 found
AB  - in the extrachromosomal ribosomal DNA (rDNA) of the myxomycete Physarum polycephalum.
AB  - Recently, we have discovered two new group I intron elements from nuclear extrachromosomal
AB  - rDNA that bears an apparent similarity to PpLSU3. The myxomycete Didymium iridis has a mobile
AB  - group I intron that encodes a putative homing endonuclease I-Dir of 29kd, whereas the
AB  - amoeba-flagellate Naegleria andersoni ssp andersoni contains a similar intron that encodes a
AB  - putative homing endonuclease I-Naa of 28 kd. I-Dir, I-Naa and I-Ppo are all basic proteins
AB  - with a theoretical isoelectric point of 9.5, 9.9 and 8.2, respectively. Furthermore, we could
AB  - not identify any significant sequence similarity between these proteins and proteins in the
AB  - GenBank and EMBL libraries, and they do not contain any of the sequence motifs (eg. LAGLI-DADG
AB  - or GIY-YIG) found in other homing endonucleases. However, we have identified a conserved
AB  - region among the nuclear homing endonucleases which consists of several His and Cys residues.
AB  - Patterns of His and Cys residues have been associated with protein domains involved in
AB  - metal-binding and interaction with nucleic acids, suggesting a similar function of the His-Cys
AB  - Box. Database searches using the His-Cys box consensus sequence as the test sequence failed to
AB  - identify homologous regions in other proteins. Furthermore, no significant sequence similarity
AB  - is seen between I-Dir, I-Naa and I-Ppo outside this His-Cys Box (less than 10% identify). A
AB  - comparison between three homologous intron-endcoded proteins from different species of
AB  - Naegleria (identity between 85-96%;T.M.E., unpublished results) strongly support the His-Cys
AB  - Box as a highly conserved region. Thus, we propose that the nuclear homing endonucleases are
AB  - all members of the same family, identified by the His-Cys Box.
ER  -

TY  - JOUR
AU  - Johansen, S.
AU  - Vogt, V.M.
TI  - An intron in the nuclear ribosomal DNA of Didymium iridis codes for a group I ribozyme and a novel ribozyme that cooperate in self-splicing.
JO  - Cell
PY  - 1994
SP  - 725
EP  - 734
VL  - 76
AB  - We have discovered a unique group I intron-like insertion (DiSSU) in the nuclear small subunit
AB  - ribosomal RNA gene of the myxomycete Didymium iridis.  By sequence, DiSSU consists of a group
AB  - I ribozyme at the 5' end, an open reading frame (ORF) in the middle, and novel element at the
AB  - 3' end.  Intron RNA self-splices in vitro to yield ten major processed RNAs, including a
AB  - full-length circle.  The group I ribozyme can efficiently cleave at an internal processing
AB  - site, which separates the group I ribozyme from the ORF.  Surprisingly, deletions that remove
AB  - the entire group I ribozyme do not impair cleavage at the 3' splice site, implying that the
AB  - 3' element itself is a catalytic RNA.  Deletions that remove portions of the 3' element
AB  - prevent utilization of the 5' splice site, suggesting that this element cooperates with the
AB  - upstream group I ribozyme in splicing.  DiSSU appears to be the first example for the
AB  - cooperative interaction of distinct ribozymes in RNA splicing.
ER  -

TY  - JOUR
AU  - Johnning, A.
AU  - Jakobsson, H.E.
AU  - Boulund, F.
AU  - Salva-Serra, F.
AU  - Moore, E.R.
AU  - Ahren, C.
AU  - Karami, N.
AU  - Kristiansson, E.
TI  - Draft Genome Sequence of Extended-Spectrum-beta-Lactamase-Producing Escherichia coli Strain CCUG 62462, Isolated from a Urine Sample.
JO  - Genome Announcements
PY  - 2016
SP  - e01382
EP  - e01316
VL  - 4
AB  - The draft genome sequence has been determined for an extended-spectrum-beta-lactamase
AB  - (ESBL)-producing (blaCTX-M-15) Escherichia coli
AB  - strain (CCUG 62462), composed of 119 contigs and a total size of 5.27 Mb. This E.
AB  - coli is serotype O25b and sequence type 131, a pandemic clonal group, causing
AB  - worldwide antimicrobial-resistant infections.
ER  -

TY  - JOUR
AU  - Johnson, C.M.
AU  - Grossman, A.D.
TI  - Complete Genome Sequence of Bacillus subtilis Strain CU1050, Which Is Sensitive to Phage SPbeta.
JO  - Genome Announcements
PY  - 2016
SP  - e00262
EP  - e00216
VL  - 4
AB  - The Gram-positive bacteriumBacillus subtilisis used as a model organism to study  cellular and
AB  - molecular processes. Here, we announce the complete genomic sequence
AB  - ofB. subtilisstrain CU1050, derived fromB. subtilisstrain 168. CU1050 has
AB  - historically been used to study suppressor mutations and phage biology,
AB  - especially the lysogenic phage SPbeta.
ER  -

TY  - JOUR
AU  - Johnson, D.L.
AU  - Reid, T.M.
AU  - Lee, M.-S.
AU  - King, C.M.
AU  - Romano, L.J.
TI  - Preparation and characterization of a viral DNA molecule containing a site-specific 2-aminofluorene adduct:  A new probe for mutagenesis by carcinogens.
JO  - Biochemistry
PY  - 1986
SP  - 449
EP  - 456
VL  - 25
AB  - The synthetic oligonucleotide heptamer 5'-ATCCGTC-3' was reacted in vitro with
AB  - N-acetoxy-N-(trifluoroacetyl)-2-aminofluorene and the resulting product
AB  - isolated by reverse-phase high-performance liquid chromatography (HPLC).  This
AB  - purified oligonucleotide, which was shown by chemical and enzymatic analysis to
AB  - be a heptamer containing a single N-(deoxyguanin-8-yl)-2-aminofluorene adduct,
AB  - was then used to situate the putatively mutagenic aminofluorene lesion within
AB  - the genome of M13 mp9 by ligating it into a complementary single-stranded
AB  - region located at a specific site in the negative strand of the duplex M13 mp9
AB  - DNA molecule.  The presence of the adduct at the anticipated location was
AB  - confirmed by taking advantage of the facts that AF adducts inhibit many
AB  - restriction enzymes when located in or near their restriction sites and that
AB  - the AF moiety should be contained within the HincII recognition sequence on M13
AB  - mp9 DNA.  Upon attempted cleavage of the M13 DNA containing the site-specific
AB  - AF adduct with HincII, we find that the large majority of the DNA remained
AB  - circular, demonstrating the incorporation of the AF adduct in high yield into
AB  - the DNA molecule at this location.  This system should prove useful in vivo for
AB  - the study of mutagenesis by chemical carcinogens and in vitro to study the
AB  - interaction of purified DNA metabolizing proteins with a template containing a
AB  - site-specific lesion.
ER  -

TY  - JOUR
AU  - Johnson, J.
AU  - Shah, B.
AU  - Jain, K.
AU  - Parmar, N.
AU  - Hinsu, A.
AU  - Patel, N.
AU  - Joshi, C.G.
AU  - Madamwar, D.
TI  - Draft Genome Sequence of Paenibacillus sp. Strain DMB5, Acclimatized and Enriched for Catabolizing Anthropogenic Compounds.
JO  - Genome Announcements
PY  - 2016
SP  - e00211
EP  - e00216
VL  - 4
AB  - Here, we present the draft genome sequence ofPaenibacillussp. strain DMB5, isolated from
AB  - polluted sediments of the Kharicut Canal, Vatva, India, having a
AB  - genome size of 7.5 Mbp and 7,077 coding sequences. The genome of this
AB  - dye-degrading bacterium provides valuable information on the microbe-mediated
AB  - biodegradation of anthropogenic compounds.
ER  -

TY  - JOUR
AU  - Johnson, J.G.
AU  - Carpentier, S.
AU  - Spurbeck, R.R.
AU  - Sandhu, S.K.
AU  - Dirita, V.J.
TI  - Genome Sequences of Campylobacter jejuni 81-176 Variants with Enhanced Fitness Relative to the Parental Strain in the Chicken Gastrointestinal Tract.
JO  - Genome Announcements
PY  - 2014
SP  - e00006
EP  - e00014
VL  - 2
AB  - Campylobacter jejuni is a major cause of food-borne infections in the United States due to its
AB  - ability to asymptomatically colonize the gastrointestinal
AB  - tracts of chickens. Using competition assays with parental C. jejuni 81-176,
AB  - variants with consistently improved fitness in chicken ceca relative to the
AB  - parental strain were identified and sequenced.
ER  -

TY  - JOUR
AU  - Johnson, J.G.
AU  - Spurbeck, R.R.
AU  - Sandhu, S.K.
AU  - Matson, J.S.
TI  - Genome Sequence of Klebsiella pneumoniae Respiratory Isolate IA565.
JO  - Genome Announcements
PY  - 2014
SP  - e00896
EP  - e00814
VL  - 2
AB  - Klebsiella pneumoniae is a clinically significant opportunistic bacterial pathogen as well as
AB  - a normal member of the human microbiota. K. pneumoniae strain
AB  - IA565 was isolated from a tracheal aspirate at the University of Iowa Hospitals
AB  - and Clinics. Here, we present the genome sequence of K. pneumoniae IA565.
ER  -

TY  - JOUR
AU  - Johnson, J.G.
AU  - Spurbeck, R.R.
AU  - Sandhu, S.K.
AU  - Matson, J.S.
TI  - Genome Sequence of Klebsiella pneumoniae Urinary Tract Isolate Top52.
JO  - Genome Announcements
PY  - 2014
SP  - e00668
EP  - e00614
VL  - 2
AB  - Klebsiella pneumoniae is a significant cause of nosocomial infections, including
AB  - ventilator-associated pneumonias and catheter-associated urinary tract
AB  - infections. K. pneumoniae strain TOP52 #1721 (Top52) was isolated from a woman
AB  - presenting with acute cystitis and subsequently characterized using various
AB  - murine models of infection. Here we present the genome sequence of K. pneumoniae
AB  - Top52.
ER  -

TY  - JOUR
AU  - Johnson, M.
AU  - Scheinbart, L.
AU  - Pike, M.
AU  - Richardson, B.
TI  - Procainamide inhibits DNA methyltransferase.
JO  - Arthritis Rheum.
PY  - 1989
SP  - S143
EP  - S143
VL  - 32
AB  - We have reported that T cells treated with procainamide (Pca) have
AB  - hypomethylated DNA.  Pca can bind DNA, so we tested whether Pca inhibits T cell
AB  - DNA methyltransferase.  DNA methyltransferase was partially purified from
AB  - nuclei isolated from the human T cell leukemia line Jurkat.  Methyltransferase
AB  - activity was measured by incubating the enzyme with Micrococcus luteus DNA and
AB  - 3H-S-adenosylmethionine (3H-SAM), then precipitating DNA onto fiberglass
AB  - filters with ethanol and determining precipitated 3H.  A dose dependent
AB  - inhibition of DNA methylation was observed, with 100 micromolar Pca inhibiting
AB  - 3H incorporation into DNA by 51+/-5% (mean +/1 SEM of three experiments, each
AB  - performed in triplicate) (p<0.05).  Lineweaver-Burk analysis demonstrated
AB  - competitive inhibition with DNA.  To test whether Pca is a nonspecific
AB  - inhibitor of all transmethylation reactions, Jurkat cells were treated with Pca
AB  - for four days, then incubated with 3H-SAM and 3H incorporation into membrane
AB  - phospholipids measured.  No inhibition was observed.  These results demonstrate
AB  - that Pca is a DNA methyltransferase inhibitor, and suggest that Pca inhibits
AB  - Jurkat DNA methylation by selectively inhibiting this enzyme.
ER  -

TY  - JOUR
AU  - Johnson, P.H.
AU  - Lee, A.S.
AU  - Sinsheimer, R.L.
TI  - Production of specific fragments of PhiX174 replicative form DNA by a restriction enzyme from Haemophilus parainfluenzae, endonuclease HP.
JO  - J. Virol.
PY  - 1973
SP  - 596
EP  - 599
VL  - 11
AB  - A restriction endonuclease from Haemophilus parainfluenzae degrades Phi174
AB  - replicative form DNA into eight specific fragments, ranging from 1,700 to 150
AB  - base pairs and terminated specifically by deoxycytidylic acid.
ER  -

TY  - JOUR
AU  - Johnson, S.A.
AU  - Ormsby, M.J.
AU  - Wall, D.M.
TI  - Draft Genome Sequence of the Tumor-Targeting Salmonella enterica Serovar Typhimurium Strain SL7207.
JO  - Genome Announcements
PY  - 2017
SP  - e01591
EP  - e01516
VL  - 5
AB  - Salmonella enterica serovar Typhimurium strain SL7207 is a genetically modified derivative of
AB  - strain SL1344, which preferentially accumulates in tumors and can
AB  - be used as a vehicle for tissue-specific gene delivery in vivo Here, we report
AB  - the draft genome sequence of SL7207, confirming a purported aroA deletion and
AB  - four single-nucleotide polymorphisms compared to SL1344.
ER  -

TY  - JOUR
AU  - Johnson, S.L. et al.
TI  - Complete genome sequences for 59 burkholderia isolates, both pathogenic and near  neighbor.
JO  - Genome Announcements
PY  - 2015
SP  - e00159
EP  - e00115
VL  - 3
AB  - The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and
AB  - Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention
AB  - Category B listed), and nonpathogenic Gram-negative bacilli. Here we present full
AB  - genome sequences for a panel of 59 Burkholderia strains, selected to aid in
AB  - detection assay development.
ER  -

TY  - JOUR
AU  - Johnson, S.L. et al.
TI  - Complete genome sequences for 35 biothreat assay-relevant bacillus species.
JO  - Genome Announcements
PY  - 2015
SP  - e00151
EP  - e00115
VL  - 3
AB  - In 2011, the Association of Analytical Communities (AOAC) International released  a list of
AB  - Bacillus strains relevant to biothreat molecular detection assays. We
AB  - present the complete and annotated genome assemblies for the 15 strains listed on
AB  - the inclusivity panel, as well as the 20 strains listed on the exclusivity panel.
ER  -

TY  - JOUR
AU  - Johnson, S.L. et al.
TI  - Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica.
JO  - Genome Announcements
PY  - 2015
SP  - e00148
EP  - e00115
VL  - 3
AB  - The genus Yersinia includes three human pathogens, of which Yersinia pestis is responsible for
AB  - >2,000 illnesses each year. To aid in the development of
AB  - detection assays and aid further phylogenetic elucidation, we sequenced and
AB  - assembled the complete genomes of 32 strains (across 9 Yersinia species).
ER  -

TY  - JOUR
AU  - Johnson, S.L. et al.
TI  - Genome sequencing of 18 francisella strains to aid in assay development and testing.
JO  - Genome Announcements
PY  - 2015
SP  - e00147
EP  - e00115
VL  - 3
AB  - Francisella tularensis is a highly infectious bacterium with the potential to cause high
AB  - fatality rates if infections are untreated. To aid in the development
AB  - of rapid and accurate detection assays, we have sequenced and annotated the
AB  - genomes of 18 F. tularensis and Francisella philomiragia strains.
ER  -

TY  - JOUR
AU  - Johnson, S.L. et al.
TI  - Correction for Johnson et al., 'Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species'.
JO  - Genome Announcements
PY  - 2018
SP  - e01144
EP  - e01117
VL  - 6
ER  -

TY  - JOUR
AU  - Johnson, S.L.
AU  - Baker, A.L.
AU  - Chain, P.S.
AU  - Currie, B.J.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Davis, C.B.
AU  - Inglis, T.J.
AU  - Kaestli, M.
AU  - Koren, S.
AU  - Mayo, M.
AU  - Merritt, A.J.
AU  - Price, E.P.
AU  - Sarovich, D.S.
AU  - Warner, J.
AU  - Rosovitz, M.J.
TI  - Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia  pseudomallei.
JO  - Genome Announcements
PY  - 2015
SP  - e01282
EP  - e01214
VL  - 3
AB  - Here, we present the draft genome sequences of 80 isolates of Burkholderia pseudomallei. The
AB  - isolates represent clinical cases of melioidosis and
AB  - environmental isolates from regions in Australia and Papua New Guinea where B.
AB  - pseudomallei is endemic. The genomes provide further context for the diversity of
AB  - the pathogen.
ER  -

TY  - JOUR
AU  - Johnson, S.L.
AU  - Khiani, A.
AU  - Bishop-Lilly, K.A.
AU  - Chapman, C.
AU  - Patel, M.
AU  - Verratti, K.
AU  - Teshima, H.
AU  - Munk, A.C.
AU  - Bruce, D.C.
AU  - Han, C.S.
AU  - Xie, G.
AU  - Davenport, K.W.
AU  - Chain, P.
AU  - Sozhamannan, S.
TI  - Complete Genome Assemblies for Two Single-Chromosome Vibrio cholerae Isolates, Strains 1154-74 (Serogroup O49) and 10432-62 (Serogroup O27).
JO  - Genome Announcements
PY  - 2015
SP  - e00462
EP  - e00415
VL  - 3
AB  - Here, we report the completed genome sequences for two non-O1/non-O139 Vibrio cholerae
AB  - isolates. Each isolate has only a single chromosome, as opposed to the
AB  - normal paradigm of two chromosomes found in all other V. cholerae isolates.
ER  -

TY  - JOUR
AU  - Johnson, S.L.
AU  - Minogue, T.D.
AU  - Daligault, H.E.
AU  - Wolcott, M.J.
AU  - Teshima, H.
AU  - Coyne, S.R.
AU  - Davenport, K.W.
AU  - Jaissle, J.G.
AU  - Chain, P.S.
TI  - Finished Genome Assembly of Warm Spring Isolate Francisella novicida DPG 3A-IS.
JO  - Genome Announcements
PY  - 2015
SP  - e01046
EP  - e01015
VL  - 3
AB  - We sequenced the complete genome of Francisella novicida DPG 3A-IS to closed and  finished
AB  - status. This is a warm spring isolate recovered from Hobo Warm Spring (Utah, USA). The final
AB  - assembly is available in NCBI under accession number CP012037.
ER  -

TY  - JOUR
AU  - Johnson, S.L.
AU  - Minogue, T.D.
AU  - Daligault, H.E.
AU  - Wolcott, M.J.
AU  - Teshima, H.
AU  - Coyne, S.R.
AU  - Davenport, K.W.
AU  - Jaissle, J.G.
AU  - Chain, P.S.
TI  - Finished Genome Assembly of Yersinia pestis EV76D and KIM 10v.
JO  - Genome Announcements
PY  - 2015
SP  - e01024
EP  - e01015
VL  - 3
AB  - Here, we sequenced the completed genome of Yersinia pestis EV76D and KIM 10v, two genomes used
AB  - as references in assay development, to improved high-quality draft status.
ER  -

TY  - JOUR
AU  - Johnson, S.L.
AU  - Minogue, T.D.
AU  - Teshima, H.
AU  - Davenport, K.W.
AU  - Shea, A.A.
AU  - Miner, H.L.
AU  - Wolcott, M.J.
AU  - Chain, P.S.
TI  - Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes.
JO  - Genome Announcements
PY  - 2015
SP  - e01446
EP  - e01414
VL  - 3
AB  - Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male
AB  - muller operator with a fatal case of pneumonia in 2003. Here we
AB  - present the finished genome sequence of that pathogen, including a 5.46-Mb
AB  - chromosome and two plasmids (209 and 52 Kb, respectively).
ER  -

TY  - JOUR
AU  - Johnson, T.J.
AU  - Aziz, M.
AU  - Liu, C.M.
AU  - Sokurenko, E.
AU  - Kisiela, D.I.
AU  - Paul, S.
AU  - Andersen, P.
AU  - Johnson, J.R.
AU  - Price, L.B.
TI  - Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Strain from the H30Rx Subclone of Sequence Type 131 from a Patient with Recurrent Urinary Tract  Infections, Closely Related to a Lethal Urosepsis Isolate from the Patient's  Sister.
JO  - Genome Announcements
PY  - 2016
SP  - e00334
EP  - e00316
VL  - 4
AB  - We report here the complete genome sequence, including five plasmid sequences, of Escherichia
AB  - coli sequence type 131 (ST131) strain JJ1887. The strain was isolated
AB  - in 2007 in the United States from a patient with recurrent cystitis, whose
AB  - caregiver sister died from urosepsis caused by a nearly identical strain.
ER  -

TY  - JOUR
AU  - Johnson, T.J.
AU  - Fernandez-Alarcon, C.
AU  - Bojesen, A.M.
AU  - Nolan, L.K.
AU  - Trampel, D.W.
AU  - Seemann, T.
TI  - Complete Genome Sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3676
EP  - 3677
VL  - 193
AB  - Gallibacterium anatis is a member of the normal flora of avian hosts and an important
AB  - causative agent of peritonitis and salpingitis in laying hens. Here we report the availability
AB  - of the first completed G. anatis genome sequence of strain UMN179, isolated from an Iowa
AB  - laying hen with peritonitis.
ER  -

TY  - JOUR
AU  - Johnson, T.J.
AU  - Hargreaves, M.
AU  - Shaw, K.
AU  - Snippes, P.
AU  - Lynfield, R.
AU  - Aziz, M.
AU  - Price, L.B.
TI  - Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131 H30R Subclade.
JO  - Genome Announcements
PY  - 2015
SP  - e00272
EP  - e00215
VL  - 3
AB  - Here, we report the completed genome sequence of a carbapenem-resistant extraintestinal
AB  - pathogenic Escherichia coli sequence type 131 (ST131) isolate,
AB  - MNCRE44. The isolate was obtained in 2012 in Minnesota, USA, from a sputum sample
AB  - from a hospitalized patient with multiple comorbidities, and it belongs to the
AB  - H30R sublineage.
ER  -

TY  - JOUR
AU  - Johnson, T.J.
AU  - Johnson, S.J.
AU  - Nolan, L.K.
TI  - Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids.
JO  - J. Bacteriol.
PY  - 2006
SP  - 5975
EP  - 5983
VL  - 188
AB  - Avian pathogenic Escherichia coli (APEC), an extraintestinal pathogenic E.
AB  - coli causing colibacillosis in birds, is responsible for significant
AB  - economic losses for the poultry industry. Recently, we reported that the
AB  - APEC pathotype was characterized by possession of a set of genes contained
AB  - within a 94-kb cluster linked to a ColV plasmid, pAPEC-O2-ColV. These
AB  - included sitABCD, genes of the aerobactin operon, hlyF, iss, genes of the
AB  - salmochelin operon, and the 5' end of cvaB of the ColV operon. However,
AB  - the results of gene prevalence studies performed among APEC isolates
AB  - revealed that these traits were not always linked to ColV plasmids. Here,
AB  - we present the complete sequence of a 174-kb plasmid, pAPEC-O1-ColBM,
AB  - which contains a putative virulence cluster similar to that of
AB  - pAPEC-O2-ColV. These two F-type plasmids share remarkable similarity,
AB  - except that they encode the production of different colicins;
AB  - pAPEC-O2-ColV contains an intact ColV operon, and pAPEC-O1-ColBM encodes
AB  - the colicins B and M. Interestingly, remnants of the ColV operon exist in
AB  - pAPEC-O1-ColBM, hinting that ColBM-type plasmids may have evolved from
AB  - ColV plasmids. Among APEC isolates, the prevalence of ColBM sequences
AB  - helps account for the previously observed differences in prevalence
AB  - between genes of the "conserved" portion of the putative virulence cluster
AB  - of pAPEC-O2-ColV and those genes within its "variable" portion. These
AB  - results, in conjunction with Southern blotting and probing of
AB  - representative ColBM-positive strains, indicate that this "conserved"
AB  - cluster of putative virulence genes is primarily linked to F-type
AB  - virulence plasmids among the APEC isolates studied.
ER  -

TY  - JOUR
AU  - Johnson, T.J.
AU  - Kariyawasam, S.
AU  - Wannemuehler, Y.
AU  - Mangiamele, P.
AU  - Johnson, S.J.
AU  - Doetkott, C.
AU  - Skyberg, J.A.
AU  - Lynne, A.M.
AU  - Johnson, J.R.
AU  - Nolan, L.K.
TI  - The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli  genomes.
JO  - J. Bacteriol.
PY  - 2007
SP  - 3228
EP  - 3236
VL  - 189
AB  - Escherichia coli strains that cause disease outside the intestine are known as extraintestinal
AB  - pathogenic E. coli (ExPEC) and include human
AB  - uropathogenic E. coli (UPEC) and avian pathogenic E. coli (APEC).
AB  - Regardless of host of origin, ExPEC strains share many traits. It has been
AB  - suggested that these commonalities may enable APEC to cause disease in
AB  - humans. Here, we begin to test the hypothesis that certain APEC strains
AB  - possess potential to cause human urinary tract infection through virulence
AB  - genotyping of 1,000 APEC and UPEC strains, generation of the first
AB  - complete genomic sequence of an APEC (APEC O1:K1:H7) strain, and
AB  - comparison of this genome to all available human ExPEC genomic sequences.
AB  - The genomes of APEC O1 and three human UPEC strains were found to be
AB  - remarkably similar, with only 4.5% of APEC O1's genome not found in other
AB  - sequenced ExPEC genomes. Also, use of multilocus sequence typing showed
AB  - that some of the sequenced human ExPEC strains were more like APEC O1 than
AB  - other human ExPEC strains. This work provides evidence that at least some
AB  - human and avian ExPEC strains are highly similar to one another, and it
AB  - supports the possibility that a food-borne link between some APEC and UPEC
AB  - strains exists. Future studies are necessary to assess the ability of APEC
AB  - to overcome the hurdles necessary for such a food-borne transmission, and
AB  - epidemiological studies are required to confirm that such a phenomenon
AB  - actually occurs.
ER  -

TY  - JOUR
AU  - Johnston, C.
AU  - Martin, B.
AU  - Granadel, C.
AU  - Polard, P.
AU  - Claverys, J.P.
TI  - Programmed Protection of Foreign DNA from Restriction Allows Pathogenicity Island Exchange during Pneumococcal Transformation.
JO  - PLoS Pathog.
PY  - 2013
SP  - e1003178
EP  - e1003178
VL  - 9
AB  - In bacteria, transformation and restriction-modification (R-M) systems play potentially
AB  - antagonistic roles. While the former, proposed as a
AB  - form of sexuality, relies on internalized foreign DNA to create genetic
AB  - diversity, the latter degrade foreign DNA to protect from bacteriophage
AB  - attack. The human pathogen Streptococcus pneumoniae is transformable
AB  - and possesses either of two R-M systems, DpnI and DpnII, which
AB  - respectively restrict methylated or unmethylated double-stranded (ds)
AB  - DNA. S. pneumoniae DpnII strains possess DpnM, which methylates dsDNA
AB  - to protect it from DpnII restriction, and a second methylase, DpnA,
AB  - which is induced during competence for genetic transformation and is
AB  - unusual in that it methylates single-stranded (ss) DNA. DpnA was
AB  - tentatively ascribed the role of protecting internalized plasmids from
AB  - DpnII restriction, but this seems unlikely in light of recent results
AB  - establishing that pneumococcal transformation was not evolved to favor
AB  - plasmid exchange. Here we validate an alternative hypothesis, showing
AB  - that DpnA plays a crucial role in the protection of internalized
AB  - foreign DNA, enabling exchange of pathogenicity islands and more
AB  - generally of variable regions between pneumococcal isolates. We show
AB  - that transformation of a 21.7 kb heterologous region is reduced by more
AB  - than 4 logs in dpnA mutant cells and provide evidence that the specific
AB  - induction of dpnA during competence is critical for full protection. We
AB  - suggest that the integration of a restrictase/ssDNA-methylase couplet
AB  - into the competence regulon maintains protection from bacteriophage
AB  - attack whilst simultaneously enabling exchange of pathogenicicy
AB  - islands. This protective role of DpnA is likely to be of particular
AB  - importance for pneumococcal virulence by allowing free variation of
AB  - capsule serotype in DpnII strains via integration of DpnI capsule loci,
AB  - contributing to the documented escape of pneumococci from capsule-based
AB  - vaccines. Generally, this finding is the first evidence for a mechanism
AB  - that actively promotes genetic diversity of S. pneumoniae through
AB  - programmed protection and incorporation of foreign DNA.
ER  -

TY  - JOUR
AU  - Johnston, C.
AU  - Martin, B.
AU  - Polard, P.
AU  - Claverys, J.-P.
TI  - Postreplication targeting of transformants by bacterial immune systems?
JO  - Trends Microbiol.
PY  - 2013
SP  - 516
EP  - 521
VL  - 21
AB  - Bacteria are constantly challenged by foreign genetic elements such as bacteriophages and
AB  - plasmids. Several defense systems provide immunity against such attackers, including
AB  - restriction modification (R M) systems and clustered, regularly interspaced short palindromic
AB  - repeats (CRISPRs). These systems target attacking DNA and thus antagonize natural
AB  - transformation, which relies on uptake of exogenous DNA to promote acquisition of new genetic
AB  - traits. It is unclear how this antagonization occurs, becau e transforming DNA is single
AB  - stranded, and thus resistant to these immune systems. Here, we propose a simple model whereby
AB  - these systems limit transformation by attack of transformed chromosomes once double
AB  - strandedness is restored by chromosomal replication.
ER  -

TY  - JOUR
AU  - Johnston, C.D.
AU  - Skeete, C.A.
AU  - Fomenkov, A.
AU  - Roberts, R.J.
AU  - Rittling, S.R.
TI  - Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.
JO  - PLoS ONE
PY  - 2017
SP  - e0185234
EP  - e0185234
VL  - 12
AB  - Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human
AB  - respiratory tract and cystic fibrosis lung infections. Nevertheless, the
AB  - specific mechanisms employed by this pathogen remain only partially characterized
AB  - and poorly understood, largely due to its total lack of genetic accessibility.
AB  - Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing,
AB  - bisulfite sequencing, in addition to cloning and restriction analysis, we define
AB  - the specific genetic barriers to exogenous DNA present in two of the most
AB  - widespread laboratory strains, P. intermedia ATCC 25611 and P. intermedia Strain
AB  - 17. We identified and characterized multiple restriction-modification (R-M)
AB  - systems, some of which are considerably divergent between the two strains. We
AB  - propose that these R-M systems are the root cause of the P. intermedia
AB  - transformation barrier. Additionally, we note the presence of conserved Clustered
AB  - Regularly Interspaced Short Palindromic Repeat (CRISPR) systems in both strains,
AB  - which could provide a further barrier to exogenous DNA uptake and incorporation.
AB  - This work will provide a valuable resource during the development of a genetic
AB  - system for P. intermedia, which will be required for fundamental investigation of
AB  - this organism's physiology, metabolism, and pathogenesis in human disease.
ER  -

TY  - JOUR
AU  - Johnston, C.W.
AU  - Li, Y.
AU  - Magarvey, N.A.
TI  - Draft Genome Sequence of Streptomyces silvensis ATCC 53525, a Producer of Novel Hormone Antagonists.
JO  - Genome Announcements
PY  - 2016
SP  - e00001
EP  - e00016
VL  - 4
AB  - Streptomyces silvensis produces nonribosomal peptides that act as antagonists of  the human
AB  - oxytocin and vasopressin receptors. Here, we present the genome
AB  - sequence of S. silvensis ATCC 53525 and demonstrate that this organism possesses
AB  - a number of additional biosynthetic gene clusters and might be a promising source
AB  - for genome-guided drug discovery efforts.
ER  -

TY  - JOUR
AU  - Jois, P.S.
AU  - Madhu, N.
AU  - Rao, D.N.
TI  - Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis.
JO  - Biochem. J.
PY  - 2008
SP  - 543
EP  - 553
VL  - 410
AB  - Towards understanding the catalytic mechanism of M.EcoP15I [EcoP15I MTase (DNA
AB  - methyltransferase); an adenine methyltransferase], we
AB  - investigated the role of histidine residues in catalysis. M.EcoP15I,
AB  - when incubated with DEPC (diethyl pyrocarbonate), a histidine-specific
AB  - reagent, shows a time- and concentration-dependent inactivation of
AB  - methylation of DNA containing its recognition sequence of 5'-CAGCAG-3'.
AB  - The loss of enzyme activity was accompanied by an increase in
AB  - absorbance at 240 nm. A difference spectrum of modified versus native
AB  - enzyme shows the formation of N-carbethoxyhistidine that is diminished
AB  - by hydroxylamine. This, along with other experiments, strongly suggests
AB  - that the inactivation of the enzyme by DEPC was specific for histidine
AB  - residues. Substrate protection experiments show that pre-incubating the
AB  - methylase with DNA was able to protect the enzyme from DEPC
AB  - inactivation. Site-directed mutagenesis experiments in which the 15
AB  - histidine residues in the enzyme were replaced individually with
AB  - alanine corroborated the chemical modification studies and established
AB  - the importance of His-335 in the methylase activity. No gross
AB  - structural differences were detected between the native and H335A
AB  - mutant MTases, as evident from CD spectra, native PAGE pattern or on
AB  - gel filtration chromatography. Replacement of histidine with alanine
AB  - residue at position 335 results in a mutant enzyme that is
AB  - catalytically inactive and binds to DNA more tightly than the wild-type
AB  - enzyme. Thus we have shown in the present study, through a combination
AB  - of chemical modification and site-directed mutagenesis experiments,
AB  - that His-335 plays an essential role in DNA methylation catalysed by
AB  - M.EcoP15I.
ER  -

TY  - JOUR
AU  - Jomova, K.
AU  - Hegedusova, A.
AU  - Vollmannova, A.
TI  - Restriction endonucleases - a tool for DNA cleavage.
JO  - Chem. Rozhlady
PY  - 2004
SP  - 239
EP  - 245
VL  - 4
ER  -

TY  - JOUR
AU  - Jonczyk, P.
AU  - Hines, R.
AU  - Smith, D.W.
TI  - The Escherichia coli dam gene is expressed as a distal gene of a new operon.
JO  - Mol. Gen. Genet.
PY  - 1989
SP  - 85
EP  - 96
VL  - 217
AB  - DNA containing the Escherichia coli dam gene and sequences upstream from this gene were cloned
AB  - from the Clarke-Carbon plasmids pLC29-47 and pLC13-42. Promoter activity was localized using
AB  - pKO expression vectors and galactokinase assays to two regions, one 1650-2100 bp and the other
AB  - beyond 2400 bp upstream of the dam gene. No promoter activity was detected immediately in
AB  - front of this gene; plasmid pDam118, from which the nucleotide sequence of the dam gene was
AB  - determined, is shown to contain the pBR322 promoter for the primer RNA from the pBR322 rep
AB  - region present on a 76 bp Sau3A fragment inserted upstream of the dam gene in the correct
AB  - orientation for dam expression. The nucleotide sequence upstream of dam has been determined.
AB  - An open reading frame (ORF) is present between the nearest promoter region and the dam gene.
AB  - Codon usage and base frequency analysis indicate that this is expressed as a protein of
AB  - predicted size 46 kDa. A protein of size close to 46 kDa is expressed from this region,
AB  - detected using minicell analysis. No function has been determined for this protein, and no
AB  - significant homology exist between it and sequences in the PIR protein or GenBank DNA
AB  - databases. This unidentified reading frame (URF) is termed urf-74.3, since it is an URF
AB  - located at 74.3 min on the E. coli chromosome. Sequence comparisons between the regions
AB  - upstream of urf-74.3 and the aroB gene show that the aroB gene is located immediately upstream
AB  - of urf-74.3, and that the promoter activity nearest to dam is found within the aroB structural
AB  - gene. This activity is relatively weak (about 15% of that of the E. coli gal operon promoter).
AB  - The promoter activity detected beyond 2400 bp upstream of dam is likely to be that of the aroB
AB  - gene, and is 3 to 4 times stronger than that found within the aroB gene. Three potential DnaA
AB  - binding sites, each with homology of 8 of 9 bp, are present, two in the aroB promoter region
AB  - and one just upstream of the dam gene. Expression through the site adjacent to the dam gene is
AB  - enhanced 2- to 4-fold in dnaA mutants at 38C. Restriction site comparisons map these regions
AB  - precisely on the Clarke-Carbon plasmids pLC13-42 and pLC29-47, and show that the E. coli ponA
AB  - (mrcA) gene resides about 6 kb upstream of aroB.
ER  -

TY  - JOUR
AU  - Jones, A.C. et al.
TI  - Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 8815
EP  - 8820
VL  - 108
AB  - Filamentous cyanobacteria of the genus Lyngbya are important contributors
AB  - to coral reef ecosystems, occasionally forming dominant cover and
AB  - impacting the health of many other co-occurring organisms. Moreover, they
AB  - are extraordinarily rich sources of bioactive secondary metabolites, with
AB  - 35% of all reported cyanobacterial natural products deriving from this
AB  - single pantropical genus. However, the true natural product potential and
AB  - life strategies of Lyngbya strains are poorly understood because of
AB  - phylogenetic ambiguity, lack of genomic information, and their close
AB  - associations with heterotrophic bacteria and other cyanobacteria. To gauge
AB  - the natural product potential of Lyngbya and gain insights into potential
AB  - microbial interactions, we sequenced the genome of Lyngbya majuscula 3L, a
AB  - Caribbean strain that produces the tubulin polymerization inhibitor
AB  - curacin A and the molluscicide barbamide, using a combination of Sanger
AB  - and 454 sequencing approaches. Whereas  approximately  293,000 nucleotides
AB  - of the draft genome are putatively dedicated to secondary metabolism, this
AB  - is far too few to encode a large suite of Lyngbya metabolites, suggesting
AB  - Lyngbya metabolites are strain specific and may be useful in species
AB  - delineation. Our analysis revealed a complex gene regulatory network,
AB  - including a large number of sigma factors and other regulatory proteins,
AB  - indicating an enhanced ability for environmental adaptation or microbial
AB  - associations. Although Lyngbya species are reported to fix nitrogen,
AB  - nitrogenase genes were not found in the genome or by PCR of genomic DNA.
AB  - Subsequent growth experiments confirmed that L. majuscula 3L is unable to
AB  - fix atmospheric nitrogen. These unanticipated life history characteristics
AB  - challenge current views of the genus Lyngbya.
ER  -

TY  - JOUR
AU  - Jones, D.S.
AU  - Roepke, E.W.
AU  - Hua, A.A.
AU  - Flood, B.E.
AU  - Bailey, J.V.
TI  - Complete Genome Sequence of Sulfuriferula sp. Strain AH1, a Sulfur-Oxidizing Autotroph Isolated from Weathered Mine Tailings from the Duluth Complex in  Minnesota.
JO  - Genome Announcements
PY  - 2017
SP  - e00673
EP  - e00617
VL  - 5
AB  - We report the closed and annotated genome sequence of Sulfuriferula sp. strain AH1. Strain AH1
AB  - has a 2,877,007-bp chromosome that includes a partial Sox system
AB  - for inorganic sulfur oxidation and a complete nitrogen fixation pathway. It also
AB  - has a single 39,138-bp plasmid with genes for arsenic and mercury resistance.
ER  -

TY  - JOUR
AU  - Jones, K.J.
AU  - Moore, K.
AU  - Sambles, C.
AU  - Love, J.
AU  - Studholme, D.J.
AU  - Aves, S.J.
TI  - Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp.   Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga  Botryococcus br.
JO  - Genome Announcements
PY  - 2016
SP  - e01527
EP  - e01515
VL  - 4
AB  - A variety of bacteria associate with the hydrocarbon-producing microalga Botryococcus braunii,
AB  - some of which may influence its growth. We report here the
AB  - genome sequences for Achromobacter piechaudii GCS2, Agrobacterium sp. strain
AB  - SUL3, Microbacterium sp. strain GCS4, and Shinella sp. strains GWS1 and SUS2,
AB  - isolated from a laboratory culture of B. braunii, race B, strain Guadeloupe.
ER  -

TY  - JOUR
AU  - Jones, L.B.
AU  - Kunz, D.A.
TI  - Complete Genome Sequence of a Cyanotroph, Pseudomonas fluorescens NCIMB 11764, Employing Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e01111
EP  - e01115
VL  - 3
AB  - We report here the application of single-molecule real-time sequencing for determining the
AB  - entire genome structure of the cyanotroph Pseudomonas fluorescens NCIMB 11764.
ER  -

TY  - JOUR
AU  - Jones, M.
AU  - Wagner, R.
AU  - Radman, M.
TI  - Mismatch repair of deaminated 5-methyl-cytosine.
JO  - J. Mol. Biol.
PY  - 1987
SP  - 155
EP  - 159
VL  - 194
AB  - Deamination of 5-methyl-cytosine in double-stranded DNA produces a G.T mismatch.
AB  - Heteroduplexes of bacteriophage lambda DNA containing a G.T mismatch at the site of G.5-meC
AB  - base-pair in one of the parental phages were constructed and used to transfect Escherichia
AB  - coli cells. Genetic analysis of the progeny phages derived from such heteroduplexes suggests
AB  - that, in E. coli, mismatches resulting from the deamination of 5-methyl-cytosine are repaired
AB  - by a system requiring the E. coli dcm methylase and some, but not all, of the functions of the
AB  - E. coli methyl-directed mismatch repair system. The repair appears to act only on the G.T
AB  - mismatch and acts specifically to restore the cytosine methylation sequence.
ER  -

TY  - JOUR
AU  - Jones, P.A.
TI  - DNA methylation errors and cancer.
JO  - Cancer Res.
PY  - 1996
SP  - 2463
EP  - 2467
VL  - 56
AB  - It has become clear over the last few years that DNA methylation is essential for normal
AB  - embryonic development and that alterations in DNA methylation are very common in cancer cells
AB  - and are capable of directly modifying carcinogenesis.  Cytosine methylation is responsible for
AB  - the induction of a surprisingly high percentage of disease-causing point mutations in tumor
AB  - suppressor genes in somatic and germline cells.  This may either be due to the spontaneous
AB  - deamination of 5-methylcytosine or to a more active process involving side reactions during
AB  - the enzymatic modification of cytosine in DNA.  Current interest in the role of methylation
AB  - has focused on the potential for abnormal methylation events to silence tumor suppressor
AB  - genes, thus giving rise to a novel pathway to cause their progressive epigenetic inactivation.
AB  - Random methylation of CpG islands not methylated in normal cells may contribute to the
AB  - progressive inactivation of growth-inhibitory genes resulting in the clonal selection of cells
AB  - with increasingly abnormal methylation patterns.  This model for gene inactivation during
AB  - cancer development has important clinical implications, since it is possible to reactivate
AB  - these dormant genes using inhibitors of DNA methylation and potentially restore growth control
AB  - to cells.
ER  -

TY  - JOUR
AU  - Jones, P.A.
AU  - Gonzalgo, M.L.
TI  - Altered DNA methylation and genome instability: A new pathway to cancer?
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 2103
EP  - 2105
VL  - 94
AB  - DNA methylation is a mechanism for changing the base sequence of DNA without altering its
AB  - coding function.  As a heritable, yet reversible, epigenetic change, it has the potential of
AB  - altering gene expression and has profound developmental and genetic consequences.  The
AB  - methylation reaction itself is mechanistically complex and involves the flipping of the target
AB  - cytosine out of the intact double helix, so that the transfer of the methyl group from
AB  - S-adenosylmethionine can occur in a cleft in the enzyme.  Cytosine methylation is inherently
AB  - mutagenic, which presumably has led to the 80% suppression of the CpG methyl acceptor site in
AB  - eukarytoic organisms, which methylate their genomes.  It contributes strongly to the
AB  - generation of polymorphisms and germ-line mutations, and to transition mutations that
AB  - inactivate tumor-suppressor genes.  Despite a 10- to 40-fold increase in the rate of
AB  - transitions at methylated versus unmethylated cytosines, methylation is not only tolerated in
AB  - several eukaryotes, but is actually required for the embryonic development of mammals.  The
AB  - reasons 5-methylcytosine is essential for development remain obscure, but most probably relate
AB  - to the well-documented ability of methylation, particularly the methylation of CpG-rich
AB  - promoters, to block transcriptional activation.  Indeed, there is growing evidence that
AB  - methylation plays a pivotal role in key developmental processes such as genomic imprinting and
AB  - stabilization of X-chromosome inactivation.  It therefore is not surprising that alterations
AB  - in this essential epigenetic system might play a role in carcinogenesis.
ER  -

TY  - JOUR
AU  - Jones, P.A.
AU  - Takai, D.
TI  - The role of DNA methylation in mammalian epigenetics.
JO  - Science
PY  - 2001
SP  - 1068
EP  - 1070
VL  - 293
AB  - Genes constitute only a small proportion of the total mammalian genome, and the precise
AB  - control of their expression in the presence of an overwhelming background of noncoding DNA
AB  - presents a substantial problem for their regulation. Noncoding DNA, containing introns,
AB  - repetitive elements, and potentially active transposable elements, requires effective
AB  - mechanisms for its long-term silencing.  Mammals appear to have taken advantage of the
AB  - possibilities afforded by cytosine methylation to provide a heritable mechanism for altering
AB  - DNA-protein interactions to assist in such silencing.  Genes can be transcribed from
AB  - methylation-free promoters even though adjacent transcribed and nontranscribed regions are
AB  - extensively methylated. Gene promoters can be used and regulated while keeping noncoding DNA,
AB  - including transposable elements, suppressed. Methylation is also used for long-term epigenetic
AB  - silencing of X-linked and imprinted genes and can either increase or decrease the level of
AB  - transcription, depending on whether the methylation inactivates a positive or negative
AB  - regulatory element.
ER  -

TY  - JOUR
AU  - Jones, P.L.
AU  - Veenstra, G.J.C.
AU  - Wade, P.A.
AU  - Vermaak, D.
AU  - Kass, S.U.
AU  - Landsberger, N.
AU  - Strouboulis, J.
AU  - Wolffe, A.P.
TI  - Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription.
JO  - Nat. Genet.
PY  - 1998
SP  - 187
EP  - 191
VL  - 19
AB  - CpG methylation in vertebrates correlates with alterations in chromatin structure and gene
AB  - silencing.  Differences in DNA-methylation status are associated with imprinting phenomena and
AB  - carcinogenesis.  In Xenopus laevis oocytes, DNA methylation dominantly silences transcription
AB  - through the assembly of a repressive nucleosomal array.  Methylated DNA assembled into
AB  - chromatin binds the transcriptional repressor MeCP2 which cofractionates with Sin3 and histone
AB  - deacetylase.  Silencing conferred by MeCP2 and methylated DNA can be relieved by inhibition of
AB  - histone deacetylase, facilitating the remodelling of chromatin and transcriptional activation.
AB  - These results establish a direct casual relationship between DNA methylation-dependent
AB  - transcription silencing and the modification of chromatin.
ER  -

TY  - JOUR
AU  - Jones, W.D. Jr.
AU  - Greenberg, J.
TI  - Host modification and restriction with a mycobacteriophage isolated from a pseudolysogenic Mycobacterium chelonei.
JO  - J. Gen. Microbiol.
PY  - 1977
SP  - 389
EP  - 395
VL  - 99
AB  - A pseudolysogenic Mycobacterium chelonei and its phage Phi630 are described.  Phage Phi630 is
AB  - the first mycobacteriophage reported to be resistant to the nonpolar solvents chloroform,
AB  - dioxan and diethyl ether.  The phage had a latent period of 75 min, a rise period of 90 min
AB  - and a burst size of 51.  Evidence is presented for host modification and restriction.  Phage
AB  - Phi630A, grown on host strain M. chelonei F-630 Rg, plated on the alternative host M.
AB  - smegmatis ATCC607 with an efficiency of plating of 10^-5 on the alternative host F-630 Rg.
AB  - Phages Phi630A and Phi630B adsorbed equally well on their alternative hosts and on their
AB  - indicator host strains.  The progeny of plaques from initial platings on the alternative host,
AB  - when grown in the alternative host, exhibited a marked reduction in e.o.p. on their original
AB  - host.
ER  -

TY  - JOUR
AU  - Jones-Dias, D.
AU  - Manageiro, V.
AU  - Sampaio, D.A.
AU  - Vieira, L.
AU  - Canica, M.
TI  - Draft Genome Sequence of a Pathogenic O86:H25 Sequence Type 57 Escherichia coli Strain Isolated from Poultry and Carrying 12 Acquired Antibiotic Resistance Genes.
JO  - Genome Announcements
PY  - 2015
SP  - e01107
EP  - e01115
VL  - 3
AB  - Escherichia coli is a commensal bacterium that is frequently associated with
AB  - multidrug-resistant zoonotic and foodborne infections. Here, we report the 5.6-Mbp draft
AB  - genome sequence of an E. coli recovered from poultry, which encodes multiple acquired
AB  - antibiotic resistance determinants, virulence factors, pathogenicity determinants, and mobile
AB  - genetic elements.
ER  -

TY  - JOUR
AU  - Joo, E.J.
AU  - Park, W.S.
AU  - Kim, S.K.
AU  - Bae, Y.S.
AU  - Moon, B.J.
TI  - Restriction endonuclease EcoRV mutants that switch metal ion requirement.
JO  - Bull. Korean Chem. Soc.
PY  - 1999
SP  - 109
EP  - 111
VL  - 20
AB  - Divalent metal ions, normally Mg2+, are essential for both DNA cleavage by the EcoRV
AB  - restriction endonuclease at its recognition sequence, GATATC, and also for the enzyme's
AB  - discrimination between this particular sequence and all other sequences.  In the absence of
AB  - divalent metal ions, EcoRV demonstrates no catalytic activity, though it can still bind to DNA
AB  - in a nonspecific manner with no preference in its recognition sequence.  The complex of EcoRV
AB  - and its cognate DNA, however, has a high affinity for Mg2+ due to the distortion of the bound
AB  - DNA, creating a metal-binding site between the protein and the DNA.
ER  -

TY  - JOUR
AU  - Jordan, I.K. et al.
TI  - Genome Sequences for Five Strains of the Emerging Pathogen Haemophilus haemolyticus.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5879
EP  - 5880
VL  - 193
AB  - We report the first whole-genome sequences for five strains, two carried and three pathogenic,
AB  - of the emerging pathogen Haemophilus haemolyticus.
AB  - Preliminary analyses indicate that these genome sequences encode markers
AB  - that distinguish H. haemolyticus from its closest Haemophilus relatives
AB  - and provide clues to the identity of its virulence factors.
ER  -

TY  - JOUR
AU  - Jore, J.P.M.
AU  - van Luijk, N.
AU  - Luiten, R.G.M.
AU  - van der Werf, M.J.
AU  - Pouwels, P.H.
TI  - Efficient transformation system for Propionibacterium freudenreichii based on a novel vector.
JO  - Appl. Environ. Microbiol.
PY  - 2001
SP  - 499
EP  - 503
VL  - 67
AB  - A 3.6-kb endogenous plasmid was isolated from a Propionibacterium freudenreichii strain and
AB  - sequenced completely. Based on homologies with plasmids from other bacteria, notably a plasmid
AB  - from Mycobacterium, a region harboring putative replicative functions was defined. Outside
AB  - this region two restriction enzyme recognition sites were used for insertion of an Escherichia
AB  - coli-specific replicon and an erythromycin resistance gene for selection in Propionibacterium.
AB  - Hybrid vectors obtained in this way replicated in both E. coli and P. freudenreichii. Whereas
AB  - electroporation of P. freudenreichii with vector DNA isolated from an E. coli transformant
AB  - yielded 10 to 30 colonies per microgram of DNA, use of vector DNA reisolated from a
AB  - Propionibacterium transformant dramatically increased the efficiency of transformation (> or
AB  - =10(8) colonies per microgram of DNA). It could be shown that restriction-modification was
AB  - responsible for this effect. The high efficiency of the system described here permitted
AB  - successful transformation of Propionibacterium with DNA ligation mixtures.
ER  -

TY  - JOUR
AU  - Jorgensen, S.L.
AU  - Kudirkiene, E.
AU  - Li, L.
AU  - Christensen, J.P.
AU  - Olsen, J.E.
AU  - Nolan, L.
AU  - Olsen, R.H.
TI  - Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 33
EP  - 33
VL  - 12
AB  - Escherichia coli causing infection outside the gastrointestinal system are referred to as
AB  - extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a
AB  - subgroup of extra-intestinal pathogenic E. coli and infections due to avian
AB  - pathogenic E. coli have major impact on poultry production economy and welfare
AB  - worldwide. An almost defining characteristic of avian pathogenic E. coli is the
AB  - carriage of plasmids, which may encode virulence factors and antibiotic
AB  - resistance determinates. For the same reason, plasmids of avian pathogenic E.
AB  - coli have been intensively studied. However, genes encoded by the chromosome may
AB  - also be important for disease manifestation and antimicrobial resistance. For the
AB  - E. coli strain APEC_O2 the plasmids have been sequenced and analyzed in several
AB  - studies, and E. coli APEC_O2 may therefore serve as a reference strain in future
AB  - studies. Here we describe the chromosomal features of E. coli APEC_O2. E. coli
AB  - APEC_O2 is a sequence type ST135, has a chromosome of 4,908,820 bp (plasmid
AB  - removed), comprising 4672 protein-coding genes, 110 RNA genes, and 156
AB  - pseudogenes, with an average G + C content of 50.69%. We identified 82 insertion
AB  - sequences as well as 4672 protein coding sequences, 12 predicated genomic
AB  - islands, three prophage-related sequences, and two clustered regularly
AB  - interspaced short palindromic repeats regions on the chromosome, suggesting the
AB  - possible occurrence of horizontal gene transfer in this strain. The wildtype
AB  - strain of E. coli APEC_O2 is resistant towards multiple antimicrobials, however,
AB  - no (complete) antibiotic resistance genes were present on the chromosome, but a
AB  - number of genes associated with extra-intestinal disease were identified.
AB  - Together, the information provided here on E. coli APEC_O2 will assist in future
AB  - studies of avian pathogenic E. coli strains, in particular regarding strain of E.
AB  - coli APEC_O2, and aid in the general understanding of the pathogenesis of avian
AB  - pathogenic E. coli.
ER  -

TY  - JOUR
AU  - Jorgensen, T.S.
AU  - Xu, Z.
AU  - Hansen, M.A.
AU  - Sorensen, S.J.
AU  - Hansen, L.H.
TI  - Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.
JO  - PLoS ONE
PY  - 2014
SP  - E87924
EP  - E87924
VL  - 9
AB  - Metagenomic approaches are widespread in microbiological research, but so far,
AB  - the knowledge on extrachromosomal DNA diversity and composition has largely
AB  - remained dependant on cultivating host organisms. Even with the emergence of
AB  - metagenomics, complete circular sequences are rarely identified, and have
AB  - required manual curation. We propose a robust in silico procedure for identifying
AB  - complete small plasmids in metagenomic datasets from whole genome shotgun
AB  - sequencing. From one very pure and exhaustively sequenced metamobilome from rat
AB  - cecum, we identified a total of 616 circular sequences, 160 of which were
AB  - carrying a gene with plasmid replication domain. Further homology analyses
AB  - indicated that the majority of these plasmid sequences are novel. We confirmed
AB  - the circularity of the complete plasmid candidates using an inverse-type PCR
AB  - approach on a subset of sequences with 95% success, confirming the existence and
AB  - length of discrete sequences. The implication of these findings is a broadened
AB  - understanding of the traits of circular elements in nature and the possibility of
AB  - massive data mining in existing metagenomic datasets to discover novel pools of
AB  - complete plasmids thus vastly expanding the current plasmid database.
ER  -

TY  - JOUR
AU  - Jose, T.J.
AU  - Conlan, L.H.
AU  - Dupureur, C.M.
TI  - Quantitative evaluation of metal ion binding to PvuII restriction endonuclease.
JO  - J. Biol. Inorg. Chem.
PY  - 1999
SP  - 814
EP  - 823
VL  - 4
AB  - Restriction enzymes are important examples of phosphodiester hydrolysis activity and as such
AB  - have been of increasing interest to structural biologists. Much of the architecture of
AB  - endonuclease active sites has been derived from X-ray crystallographic studies. These
AB  - structures implicate conserved active site acidic residues and the scissile bond of the
AB  - substrate as coordination ligands of required metal ions. Central to the development of
AB  - restriction enzyme mechanism is our understanding of the role of metal ion binding in the
AB  - reaction, an important feature of which is identifying the energetic contributions of the
AB  - enzyme and the substrate to metal ion affinity. To begin to address this issue, isothermal
AB  - titration calorimetry (ITC) and 19F NMR spectroscopy have been applied to evaluate metal ion
AB  - binding by the representative PvuII endonuclease in the absence of substrate. In separate
AB  - experiments, ITC data demonstrate that PvuII endonuclease binds 2.16 Mn(II) ions and 2.05
AB  - Ca(II) metal ions in each monomer active site with Kd values of approximately 1 mM. While
AB  - neither calorimetry nor protein NMR spectroscopy is directly sensitive to Mg(II) binding to
AB  - the enzyme, Mn(II) competes with Mg(II) for common sites(s) on PvuII endonuclease.
AB  - Substitution of the conserved active site carboxylate Glu68 with Ala resulted in a loss of
AB  - affinity for both equivalents of both Ca(II) and Mn(II). Interestingly, the active site mutant
AB  - D58A retained an affinity for Mn(II) with Kd approximately 2 mM. Mn(II) paramagnetic
AB  - broadening in 19F spectra of wild-type and mutant 3-fluorotyrosine PvuII endonucleases are
AB  - consistent with ITC results. Chemical shift analysis of 3-fluorotyrosine mutant enzymes is
AB  - consistent with a perturbed conformation for D58A. Therefore, free PvuII endonuclease binds
AB  - metal ions, and metal ion binding can precede DNA binding. Further, while Glu68 is critical to
AB  - metal ion binding, Asp58 does not appear to be critical to the binding of at least one metal
AB  - ion and appears to also have a role in structure. These findings provide impetus for exploring
AB  - the roles of multiple metal ions in the structure and function of this representative
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Joseph, B.
AU  - Schneiker-Bekel, S.
AU  - Schramm-Gluck, A.
AU  - Blom, J.
AU  - Claus, H.
AU  - Linke, B.
AU  - Schwarz, R.F.
AU  - Becker, A.
AU  - Goesmann, A.
AU  - Frosch, M.
AU  - Schoen, C.
TI  - Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5363
EP  - 5377
VL  - 192
AB  - Neisseria meningitidis serogroup B strains are responsible for most
AB  - meningococcal cases in the industrialized countries, and strains belonging
AB  - to the clonal complex ST-41/44 are among the most prevalent serogroup B
AB  - strains in carriage and disease. Here, we report the first genome and
AB  - transcriptome comparison of a serogroup B carriage strain from the clonal
AB  - complex ST-41/44 to the serogroup B disease strain MC58 from the clonal
AB  - complex ST-32. Both genomes are highly colinear, with only three major
AB  - genome rearrangements that are associated with the integration of mobile
AB  - genetic elements. They further differ in about 10% of their gene content,
AB  - with the highest variability in gene presence as well as gene sequence
AB  - found for proteins involved in host cell interactions, including Opc,
AB  - NadA, TonB-dependent receptors, RTX toxin, and two-partner secretion
AB  - system proteins. Whereas housekeeping genes coding for metabolic functions
AB  - were highly conserved, there were considerable differences in their
AB  - expression pattern upon adhesion to human nasopharyngeal cells between
AB  - both strains, including differences in energy metabolism and stress
AB  - response. In line with these genomic and transcriptomic differences, both
AB  - strains also showed marked differences in their in vitro infectivity and
AB  - in serum resistance. Taken together, these data support the concept of a
AB  - polygenic nature of meningococcal virulence comprising differences in the
AB  - repertoire of adhesins as well as in the regulation of metabolic genes and
AB  - suggest a prominent role for immune selection and genetic drift in shaping
AB  - the meningococcal genome.
ER  -

TY  - JOUR
AU  - Joseph, T.C.
AU  - Baby, A.
AU  - Reghunathan, D.
AU  - Varghese, A.M.
AU  - Murugadas, V.
AU  - Lalitha, K.V.
TI  - Draft Genome Sequence of the Halophilic and Highly Halotolerant Gammaproteobacteria Strain MFB021.
JO  - Genome Announcements
PY  - 2014
SP  - e01156
EP  - e01114
VL  - 2
AB  - We report the 4.25-Mbp first draft sequence of Gammaproteobacteria strain MFB021, a moderate
AB  - halophile isolated from petroleum-contaminated soil in Cochin, India.
AB  - The genome of the strain MFB021 was sequenced to understand the mechanism of
AB  - hydrocarbon degradation and the halophilicity of the bacterium.
ER  -

TY  - JOUR
AU  - Joseph, T.C.
AU  - Varghese, A.M.
AU  - Baby, A.
AU  - Reghunathan, D.
AU  - Murugadas, V.
AU  - Lalitha, K.V.
TI  - First Draft Genome Sequence of a Member of the Genus Mangrovibacter, Isolated from an Aquaculture Farm in India.
JO  - Genome Announcements
PY  - 2014
SP  - e01209
EP  - e01214
VL  - 2
AB  - Mangrovibacter sp. MFB070, a Gram-negative, facultatively anaerobic, nitrogen-fixing
AB  - bacterium, was isolated from an aquaculture farm in Cochin,
AB  - India. Here, we report the first draft genome sequence of a member of the genus
AB  - Mangrovibacter, which may help us to elucidate the evolutionary status of this
AB  - genus. The draft genome sequence of the Mangrovibacter sp. consists of 5,361,682
AB  - bp, encoding 4,971 predicted coding sequences in 57 contigs.
ER  -

TY  - JOUR
AU  - Josephsen, J.
AU  - Jorgen-Jensen, B.
AU  - Nyengaard, N.R.
TI  - Determination of the recognition sequence of the type II restriction endonuclease, LlaCI, from Lactococcus lactis W15.
JO  - FEMS Microbiol. Lett.
PY  - 1998
SP  - 25
EP  - 29
VL  - 163
AB  - A new type II restriction endonuclease, called LlaCI, was partially purified from Lactococcus
AB  - lactis subsp. Cremoris W15.  The characterization of the LlaCI endonuclease showed it to be an
AB  - isoschizomer of HindIII, recognizing the sequence 5'-A/AGCTT-3'.  The cleavage site is
AB  - indicated by the arrow.
ER  -

TY  - JOUR
AU  - Josephsen, J.
AU  - Klaenhammer, T.
TI  - Stacking of three different restriction and modification systems in Lactococcus lactis by cotransformation.
JO  - Plasmid
PY  - 1990
SP  - 71
EP  - 75
VL  - 23
AB  - Four plasmids encoding restriction and modification (R/M) systems are described
AB  - that are different in the specificity of their restrictive activity toward the
AB  - small isometric phage p2 and prolate phage c2.  The R/M plasmids were
AB  - cotransformed into Lactococcus lactis MG1363 with pVS2, encoding resistance to
AB  - chloramphenicol and erythromycin, to indicate successful transformation events.
AB  - Analysis of cotransformants showed that three different R/M plasmids could be
AB  - combined in L. lactis MG1363.  The efficiency at which phage plaqued on the
AB  - transformants decreased as the number of R/M plasmids increased.  Some plasmid
AB  - combinations were unstable suggesting replicon incompatibility.
ER  -

TY  - JOUR
AU  - Josephsen, J.
AU  - Vogensen, F.K.
TI  - Identification of three different plasmid-encoded restriction modification systems in Streptococcus-lactis subsp cremoris W56.
JO  - FEMS Microbiol. Lett.
PY  - 1989
SP  - 161
EP  - 166
VL  - 59
AB  - Streptococcus lactis subsp. cremoris W56 (S. cremoris W56) is a strain partially resistant to
AB  - phage attack. Derivatives which had lost either plasmid pJW563 or pJW566 no longer expressed
AB  - the restriction and modification systems encoded by these plasmids. Genetic evidence for the
AB  - correlation between the plasmids and the R/M systems was obtained by transformation. In
AB  - addition, a third R/M system was discovered among the transformants and was shown to be
AB  - encoded by pJW565. Thus, genetic evidence for at least 3 distinct R/M systems encoded by
AB  - plasmids in S. cremoris W56 is presented. One of the R/M-systems showed stronger restriction
AB  - of the isometric phage p2 than of the prolate phage c2. The other two systems restricted both
AB  - classes of phages with equal efficiencies.
ER  -

TY  - JOUR
AU  - Joshi, C.P.
AU  - Chiang, V.L.
TI  - Conserved sequence motifs in plant S-adenosyl-L-methionine-dependent methyltransferases.
JO  - Plant Mol. Biol.
PY  - 1998
SP  - 663
EP  - 674
VL  - 37
AB  - Plant S-adenosyl-L-methionine-dependent methyltransferases are the key enzymes in
AB  - phenylpropanoid, flavonoid and many other metabolic pathways of biotechnological importance.
AB  - Here we compiled the amino acid sequences of 56 SAM-Mtases from different plants and performed
AB  - a computer analysis for the conserved sequence motifs that could possibly act as SAM-binding
AB  - domains.  To date, genes or cDNAs encoding at least ten distinct groups of SAM-Mtases that
AB  - utilize SAM and a variety of substrates have been reported from higher plants.  Three amino
AB  - acid sequence motifs are conserved in most of these SAM-Mtases.  In addition, many conserved
AB  - domains have been discovered in each group of O-methyltransferases that methylate specific
AB  - substrates and may act as sites for substrate specificity in each enzyme.  Finally, a
AB  - diagrammatic representation of the relationship between different OMTs is presented.  These
AB  - SAM-Mtase sequence signatures will be useful in the identification of SAM-Mtase motifs in the
AB  - hitherto unidentified proteins as well as for designing primers in the isolation of new
AB  - SAM-Mtases from plants.
ER  -

TY  - JOUR
AU  - Joshi, H.K.
AU  - Etzkorn, C.
AU  - Chatwell, L.
AU  - Bitinaite, J.
AU  - Horton, N.C.
TI  - Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.
JO  - J. Biol. Chem.
PY  - 2006
SP  - 23852
EP  - 23869
VL  - 281
AB  - The functional and structural consequences of a mutation of the DNA intercalating residue of
AB  - HincII, Q138F, are presented. Modeling has
AB  - suggested that the DNA intercalation by Gln-138 results in DNA
AB  - distortions potentially used by HincII in indirect readout of its
AB  - cognate DNA, GTYRAC ( Y = C or T, R = A or G) ( Horton, N. C., Dorner,
AB  - L. F., and Perona, J. J. ( 2002) Nat. Struct. Biol. 9, 42 - 47).
AB  - Kinetic data presented here indicate that the mutation of glutamine 138
AB  - to phenylalanine ( Q138F) results in a change in sequence specificity
AB  - at the center two base pairs of the cognate recognition site. We show
AB  - that the preference of HincII for cutting, but not binding, the three
AB  - cognate sites differing in the center two base pairs has been altered
AB  - by the mutation Q138F. Five new crystal structures are presented
AB  - including Q138F HincII bound to GTTAAC and GTCGAC both with and without
AB  - Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The
AB  - Q138F HincII/DNA structures show conformational changes in the protein,
AB  - bound DNA, and at the protein-DNA interface, consistent with the
AB  - formation of adaptive complexes. Analysis of these structures and the
AB  - effect of Ca2+ binding on the protein-DNA interface illuminates the
AB  - origin of the altered specificity by the mutation Q138F in the HincII
AB  - enzyme.
ER  -

TY  - JOUR
AU  - Joshi, M.N.
AU  - Pandit, A.S.
AU  - Sharma, A.
AU  - Pandya, R.V.
AU  - Desai, S.M.
AU  - Saxena, A.K.
AU  - Bagatharia, S.B.
TI  - Draft Genome Sequence of Arthrobacter crystallopoietes Strain BAB-32, Revealing Genes for Bioremediation.
JO  - Genome Announcements
PY  - 2013
SP  - e00452
EP  - e00413
VL  - 1
AB  - Arthrobacter crystallopoietes strain BAB-32, a Gram-positive obligate aerobic actinobacterium
AB  - having potential application in bioremediation and bioreduction
AB  - of a few metals, was isolated from rhizosphere soil of Gandhinagar, Gujarat,
AB  - India. The draft genome (4.3 Mb) of the strain revealed a few vital gene clusters
AB  - involved in the metabolism of aromatic compounds, zinc, and sulfur.
ER  -

TY  - JOUR
AU  - Joshi, M.N.
AU  - Pandit, A.S.
AU  - Sharma, A.
AU  - Pandya, R.V.
AU  - Saxena, A.K.
AU  - Bagatharia, S.B.
TI  - Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008.
JO  - Genome Announcements
PY  - 2013
SP  - e00222
EP  - e00212
VL  - 1
AB  - The sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive,
AB  - orange-pigmented, carotenoid-producing bacterium isolated from saline soil near
AB  - Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence
AB  - to provide insights into its functional genomics and potential applications for
AB  - carotenoid and enzyme production.
ER  -

TY  - JOUR
AU  - Joshi, M.N.
AU  - Sharma, A.
AU  - Pandit, A.S.
AU  - Pandya, R.V.
AU  - Saxena, A.K.
AU  - Bagatharia, S.B.
TI  - Draft Genome Sequence of Brevibacillus sp. Strain BAB-2500, a Strain That Might Play an Important Role in Agriculture.
JO  - Genome Announcements
PY  - 2013
SP  - e00021
EP  - e00013
VL  - 1
AB  - A Gram-positive bacterium, sp. strain BAB-2500, was isolated as a lab contaminant in
AB  - Gandhinagar, Gujarat, India. The draft genome (5.3 Mb) of the strain possesses
AB  - genes for the reduction of arsenate and aluminum. These findings might provide
AB  - insights into the utilization of this strain for improving crop production.
ER  -

TY  - JOUR
AU  - Joshi, M.N.
AU  - Sharma, A.C.
AU  - Pandya, R.V.
AU  - Patel, R.P.
AU  - Saiyed, Z.M.
AU  - Saxena, A.K.
AU  - Bagatharia, S.B.
TI  - Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6329
EP  - 6330
VL  - 194
AB  - Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented,
AB  - menaquinone-7-producing bacterium isolated from sediments of a
AB  - drilling well. The draft genome sequence of the strain, consisting of one
AB  - chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin
AB  - biosynthesis and resistance against various metals and antibiotics.
ER  -

TY  - JOUR
AU  - Joshi, R.
AU  - Ho, K.K.
AU  - Tenney, K.
AU  - Chen, J.H.
AU  - Golden, B.L.
AU  - Gimble, F.S.
TI  - Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity.
JO  - J. Mol. Biol.
PY  - 2011
SP  - 185
EP  - 200
VL  - 405
AB  - Elucidating how homing endonucleases undergo changes in recognition site specificity will
AB  - facilitate efforts to engineer proteins for gene therapy
AB  - applications. I-SceI is a monomeric homing endonuclease that recognizes
AB  - and cleaves within an 18-bp target. It tolerates limited degeneracy in its
AB  - target sequence, including substitution of a C:G(+4) base pair for the
AB  - wild-type A:T(+4) base pair. Libraries encoding randomized amino acids at
AB  - I-SceI residue positions that contact or are proximal to A:T(+4) were used
AB  - in conjunction with a bacterial one-hybrid system to select I-SceI
AB  - derivatives that bind to recognition sites containing either the A:T(+4)
AB  - or the C:G(+4) base pairs. As expected, isolates encoding wild-type
AB  - residues at the randomized positions were selected using either target
AB  - sequence. All I-SceI proteins isolated using the C:G(+4) recognition site
AB  - included small side-chain substitutions at G100 and either contained
AB  - (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R
AB  - substitution. Interestingly, the binding affinities of the selected
AB  - variants for the wild-type A:T(+4) target are 4- to 11-fold lower than
AB  - that of wild-type I-SceI, whereas those for the C:G(+4) target are
AB  - similar. The increased specificity of the mutant proteins is also evident
AB  - in binding experiments in vivo. These differences in binding affinities
AB  - account for the observed  approximately 36-fold difference in target
AB  - preference between the K86R/G100T and wild-type proteins in DNA cleavage
AB  - assays. An X-ray crystal structure of the K86R/G100T mutant protein bound
AB  - to a DNA duplex containing the C:G(+4) substitution suggests how sequence
AB  - specificity of a homing enzyme can increase. This biochemical and
AB  - structural analysis defines one pathway by which site specificity is
AB  - augmented for a homing endonuclease.
ER  -

TY  - JOUR
AU  - Jost, B.H.
AU  - Field, A.C.
AU  - Trinh, H.T.
AU  - Songer, J.G.
AU  - Billington, S.J.
TI  - Tylosin Resistance in Arcanobacterium pyogenes Is Encoded by an Erm X Determinant.
JO  - Antimicrob. Agents Chemother.
PY  - 2003
SP  - 3519
EP  - 3524
VL  - 47
AB  - Arcanobacterium pyogenes, a commensal on the mucous membranes of many economically important
AB  - animal species, is also a pathogen, causing
AB  - abscesses of the skin, joints, and visceral organs as well as mastitis and
AB  - abortion. In food animals, A. pyogenes is exposed to antimicrobial agents
AB  - used for growth promotion, prophylaxis, and therapy, notably tylosin, a
AB  - macrolide antibiotic used extensively for the prevention of liver
AB  - abscessation in feedlot cattle in the United States. Of 48 A. pyogenes
AB  - isolates, 11 (22.9%) exhibited inducible or constitutive resistance to
AB  - tylosin (MIC of > or = 128 microg/ml). These isolates also exhibited
AB  - resistance to other macrolide and lincosamide antibiotics, suggesting a
AB  - macrolide-lincosamide resistance phenotype. Of the 11 resistant isolates,
AB  - genomic DNA from nine hybridized to an erm(X)-specific probe. Cloning and
AB  - nucleotide sequencing of the A. pyogenes erm(X) gene indicated that it was
AB  - >95% similar to erm(X) genes from Corynebacterium and Propionibacterium
AB  - spp. Eight of the erm(X)-containing A. pyogenes isolates exhibited
AB  - inducible tylosin resistance, which was consistent with the presence of a
AB  - putative leader peptide upstream of the erm(X) open reading frame. For at
AB  - least one A. pyogenes isolate, 98-4277-2, erm(X) was present on a plasmid,
AB  - pAP2, and was associated with the insertion sequence IS6100. pAP2 also
AB  - carried genes encoding the repressor-regulated tetracycline efflux system
AB  - determinant Tet 33. The repA gene from pAP2 was nonfunctional in
AB  - Escherichia coli and at least one A. pyogenes isolate, suggesting that
AB  - there may be host-encoded factors required for replication of this
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Jost, J.-P.
TI  - Mechanism of DNA demethylation in vertebrates and its biological significance.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 109
EP  - 125
VL  - 0
AB  - The aim of this chapter is to present some general features of site-specific and genome-wide
AB  - demethylation.  Demethylation of DNA is part of the process responsible for the formation of
AB  - specific methylation patterns.  The establishment of a CpG methylation pattern during
AB  - embryonic development involves at least three components: DNA methyltransferase, a
AB  - demethylation system (passive or active), and sequence-specific cis-trans controlling elements
AB  - located on or near the CpG methylation sites.  The cis-trans controlling elements either
AB  - enhance or inhibit the methylation of specific sequences.  Whether a given CpG site is
AB  - methylated or not depends on the mole ratio of activities of the different factors involved
AB  - and of their respective affinities for a specified CpG site on the DNA.  This concept of
AB  - titratable factors is also valid for the cis-acting control elements.  For example, the
AB  - introduction of DNA-binding sites for specific proteins into the cell could possibly titrate
AB  - out protein factors and engender hypermethylation of the DNA.
ER  -

TY  - JOUR
AU  - Jost, J.-P.
TI  - Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 4684
EP  - 4688
VL  - 90
AB  - Here I show that nuclear extracts of chicken embryos can promote the active demethylation of
AB  - DNA.  The evidence shows that in hemimethylated DNA (i.e., methylated on one strand only)
AB  - demethylation of 5mCpG occurs throughout nucleotide excision repair.  The first step of
AB  - demethylation is the formation of specific nicks 5' from 5-methyldeoxycytidine.  Nicks are
AB  - also observed in vitro on symmetrically methylated CpGs (i.e., methylated on both strands) but
AB  - they result in breakage of the oligonucleotide with no repair.  No specific nicks are observed
AB  - on the nonmethylated CpG. Nicks are strictly 5mCpG specific and do not occur on 5mCpC, 5mCpT,
AB  - 5mCpA, or 6mApT.  The effect of nonspecific nuclease(s) has been ruled out.  The nicking of
AB  - mCpG takes place in the presence of 20 mM EDTA irrespective of the nature of the sequence
AB  - surrounding the 5mCpG.  No methylcytosine glycosylase activity could be detected.  The repair
AB  - is aphidicolin and N-ethylmaleimide resistant, suggesting a repair action by DNA polymerase
AB  - beta.  In extracts of chicken embryos, the excision repair of mCpG is highest between the 6th
AB  - and the 12th day of development, whereas it is barely detectable in nuclear extracts from
AB  - different organs of adults.  The possible implications of 5mCpG endonuclease activity in
AB  - active demethylation of DNA during differentiation is discussed.
ER  -

TY  - JOUR
AU  - Jost, J.-P.
AU  - Fremont, M.
AU  - Siegmann, M.
AU  - Hofsteenge, J.
TI  - The RNA moiety of chick embryo 5-methylcytosine-DNA glycosylase targets DNA demethylation.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4545
EP  - 4550
VL  - 25
AB  - We have previously shown that DNA demethylation by chick embryo 5-methylcytosine (5-MeC)-DNA
AB  - glycosylase needs both protein and RNA.  RNA from enzyme purified by SDS-PAGE was isolated and
AB  - cloned.  The clones have an insert ranging from 240 to 670 bp and contained on average one CpG
AB  - per 14 bases.  All six clones tested had different sequences and did not have any sequence
AB  - homology with any other known RNA.  RNase-inactivated 5-MeC-DNA glycosylase regained enzyme
AB  - activity when incubated with recombinant RNA.  However, when recombinant RNA was incubated
AB  - with the DNA substrate alone there was no demethylation activity.  Short sequences
AB  - complementary to the labeled DNA substrate are present in the recombinant RNA.  Small
AB  - synthetic oligoribonucleotides (11 bases long) complementary to the region of methylated CpGs
AB  - of the hemimethylated double-stranded DNA substrate restore the activity of the
AB  - RNase-inactivated 5-MeC-DNA glycosylase.  The corresponding oligodeoxyribonucleotide or the
AB  - oligoribonucleotide complementary to the non-methylated strand of the same DNA substrate are
AB  - inactive when incubated in the complementation test.  A minimum of 4 bases complementary of
AB  - the CpG target sequence are necessary for reactivation of RNase-treated 5-MeC-DNA glycosylase.
AB  - Complementation with double-stranded oligoribonucleotides does not restore 5-MeC-DNA
AB  - glycosylase activity.  An excess of targeting oligoribonucleotides cannot change the
AB  - preferential substrate specificity of the enzyme for hemimethylated double-stranded DNA.
ER  -

TY  - JOUR
AU  - Jost, J.-P.
AU  - Jost, Y.-C.
TI  - Transient DNA demethylation in differentiating mouse myoblasts correlates with higher activity of 5-methyldeoxycytidine excision repair.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 10040
EP  - 10043
VL  - 269
AB  - It has been recently shown that in developing chicken embryonic nuclear extracts there is a
AB  - 5-methyldeoxycytidine excision repair activity.  We show that in differentiating mouse
AB  - myoblasts, a similar enzymatic reaction may be responsible for the genome-wide DNA
AB  - demethylation (up to 50% of all CmCGG) occurring between the 3rd and 5th days of
AB  - differentiation.  Furthermore, in differentiating myoblasts, there is first a 50% transient
AB  - decrease in DNA methyltransferase activity and a 90% drop in the rate of DNA synthesis,
AB  - followed by an increase in 5-methyl-CpG endonuclease and 5-methyldeoxycytidine excision repair
AB  - activities.  As tested in vitro, the maximal activity of the 5-methyldeoxycytidine excision
AB  - repair coincides with the maximal in vivo genome-wide DNA demethylation.  We also find that
AB  - 3-aminobenzamide, a potent inhibitor of ADP-ribosyltransferase, blocks the differentiation of
AB  - myoblasts, the 5-methyldeoxycytidine excision repair activity, and the genome-wide
AB  - demethylation.
ER  -

TY  - JOUR
AU  - Jost, J.-P.
AU  - Siegmann, M.
AU  - Sun, L.
AU  - Leung, R.
TI  - Mechanism of DNA demethylation in chicken embryos.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 9734
EP  - 9739
VL  - 270
AB  - We have previously shown that in developing chicken embryos and differentiating mouse
AB  - myoblasts, the demethylation of 5-metCpGs occurs through the replacement of 5-methylcytosine
AB  - by cytosine.  We have now purified over 30,000-fold a 5-methylcytosine-DNA glycosylase from
AB  - 12-day-old chicken embryos.  The enzyme copurifies with a mismatch-specific thymine-DNA
AB  - glycosylase and an apyrimidic-endonuclease.  The reaction product of the highly purified
AB  - 5-methylcytosine-DNA glycosylase is 5-methylcytosine.  The copurified apyrimidic-endonuclease
AB  - activity cleaves 3' from the apyrimidic sugar.  A 52.5-kDa peptide, isolated as a single band
AB  - from preparative SDS-polyacrylamide gels, has both the 5-methylcytosine-DNA glycosylase and
AB  - the mismatch-specific thymine-DNA glycosylase activities.  5-Methylcytosine-DNA glycosylase
AB  - has an apparent pI of 5.5-7.5 and maximal activity between pH 6.5 and 7.5.  The Km for
AB  - hemimethylated oligonucleotide substrate is 8 x 10^-8 M with a Vmax of 4 x 10^-11 mol/h/ug
AB  - protein.  5-Methylcytosine-DNA glycosylase binds equally well to methylated and non-methylated
AB  - DNA.  The enzyme reacts six times faster with the hemimethylated DNA than with the same
AB  - bifilarly methylated DNA sequence, and single-stranded methylated DNA is not a substrate.  The
AB  - action of the enzyme is distributive.
ER  -

TY  - JOUR
AU  - Jost, J.-P.
AU  - Siegmann, M.
AU  - Thiry, S.
AU  - Jost, Y.-C.
AU  - Benjamin, D.
AU  - Schwarz, S.
TI  - A re-investigation of the ribonuclease sensitivity of a DNA demethylation reaction in chicken embryo and G8 mouse myoblasts.
JO  - FEBS Lett.
PY  - 1999
SP  - 251
EP  - 254
VL  - 449
AB  - Recently published results suggest that the ribonuclease sensitivity of the DNA demethylation
AB  - reaction may be an experimental artifact due to the possible tight binding of the nucleases to
AB  - the methylated DNA substrate. Using an improved protocol we show for two different systems
AB  - that demethylation of hemi-methylated DNA is indeed sensitive to micrococcal nuclease,
AB  - requires RNA and is not an experimental artifact.  The purified 5-MeC-DNA glycosylase from
AB  - chicken embryos and G8 mouse myoblasts was first incubated for 5 min at 37 C with micrococcal
AB  - nuclease in the presence of Ca2+  in the absence of the DNA substrate.  Upon blocking the
AB  - nuclease activity by the addition of 25 mM EGTA, the DNA demethylation reaction was initiated
AB  - by adding the labeled hemimethylated DNA substrate to the reaction mixture.  Under these
AB  - conditions the DNA demethylation reaction was abolished.  In parallel controls, where the
AB  - purified 5-MeC-DNA glycosylase was pre-incubated at 37 C with the nuclease, Ca2+ and EGTA or
AB  - with the nuclease and EGTA, RNA was not degraded and no inhibition of the demethylation
AB  - reaction was obtained.  As had already been shown for chicken embryos, the loss of 5-MeC-DNA
AB  - glycosylase activity from G8 myoblasts following nuclease treatment can also be restored by
AB  - the addition of synthetic RNA complementary to the methylated strand of the substrate DNA.  No
AB  - reactivation of 5-MeC-DNA glycosylase is obtained by complementation with a random RNA
AB  - sequence, the RNA sequence complementary to the non-methylated strand or DNA, thus ruling out
AB  - a non-specific competition of the RNA for the binding of the nuclease to the labeled DNA
AB  - substrate.
ER  -

TY  - JOUR
AU  - Jothikumar, N.
AU  - Kahler, A.
AU  - Strockbine, N.
AU  - Gladney, L.
AU  - Hill, V.R.
TI  - Draft Genome Sequence of Raoultella planticola, Isolated from River Water.
JO  - Genome Announcements
PY  - 2014
SP  - e01061
EP  - e01014
VL  - 2
AB  - We isolated Raoultella planticola from a river water sample, which was phenotypically
AB  - indistinguishable from Escherichia coli on MI agar. The genome
AB  - sequence of R. planticola was determined to gain information about its metabolic
AB  - functions contributing to its false positive appearance of E. coli on MI agar. We
AB  - report the first whole genome sequence of Raoultella planticola.
ER  -

TY  - JOUR
AU  - Jothikumar, N.
AU  - Kahler, A.
AU  - Strockbine, N.
AU  - Gladney, L.
AU  - Hill, V.R.
TI  - Draft Genome Sequence of Buttiauxella agrestis, Isolated from Surface Water.
JO  - Genome Announcements
PY  - 2014
SP  - e01060
EP  - e01014
VL  - 2
AB  - MI agar is routinely used for quantifying Escherichia coli in drinking water. A suspect E.
AB  - coli colony isolated from a water sample was identified as
AB  - Buttiauxella agrestis. The whole genome sequence of B. agrestis was determined to
AB  - understand the genetic basis for its phenotypic resemblance to E. coli on MI
AB  - agar.
ER  -

TY  - JOUR
AU  - Jou, T.-W.
AU  - Chen, C.-S.
TI  - Purification and characterization of restriction endonuclease CstI from Clostridium sticklandii.
JO  - Bot. Bull. Acad. Sinica
PY  - 1988
SP  - 201
EP  - 208
VL  - 29
AB  - A type II restriction endonuclease CstI was purified to homogeneity from
AB  - Clostridium sticklandii by phosphocellulose chromatography and preparative gel
AB  - electrophoresis.  It was found that CstI was an isoschizomer of PstI which is
AB  - widely used in molecular cloning.  Both CstI and PstI recognize and cleave the
AB  - nucleotide sequence 5'-CTGCAG-3' of double stranded DNA.  Nucleotide sequence
AB  - analysis revealed that both enzymes split the phosphodiester bond between A and
AB  - G.  The molecular weight of CstI determined by disc gel electrophoresis was
AB  - apparently 206,000.  The optimal pH, temperature, sodium chloride and magnesium
AB  - ion concentrations of CstI were shown to be 7-9, 37-40C, 50-200 mM and 5 mM,
AB  - respectively.  CstI is heat-labile.  When incubated at temperature higher than
AB  - 40C for 5 minutes, the enzyme lost its activity rapidly.
ER  -

TY  - JOUR
AU  - Joung, S.M.
AU  - Jeon, S.J.
AU  - Lim, Y.J.
AU  - Lim, J.S.
AU  - Choi, B.S.
AU  - Choi, I.Y.
AU  - Yu, J.H.
AU  - Na, K.I.
AU  - Cho, E.H.
AU  - Shin, S.S.
AU  - Park, Y.K.
AU  - Kim, C.K.
AU  - Kim, H.J.
AU  - Ryoo, S.W.
TI  - Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production.
JO  - Genome Announcements
PY  - 2013
SP  - e0006913
EP  - e0006913
VL  - 1
AB  - Mycobacterium bovis bacillus Calmette-Guerin (BCG) is the only vaccine available  against
AB  - tuberculosis, and the strains used worldwide represent a family of
AB  - daughter strains with distinct genotypic characteristics. Here, we report the
AB  - complete genome sequence of M. bovis BCG Korea, the strain that will be actually
AB  - used in Korea for vaccine production.
ER  -

TY  - JOUR
AU  - Jourda, C.
AU  - Santini, S.
AU  - Rocher, C.
AU  - Le Bivic, A.
AU  - Claverie, J.M.
TI  - Draft Genome Sequence of an Alphaproteobacterium Associated with the Mediterranean Sponge Oscarella lobularis.
JO  - Genome Announcements
PY  - 2015
SP  - e00977
EP  - e00915
VL  - 3
AB  - While sequencing DNA purified from the homoscleromorph sponge Oscarella lobularis, we detected
AB  - a large number of reads with strong similarity to available alphaproteobacteria gene sequences
AB  - of family Rhodobacteraceae. Here, we present the genome sequence of this putative sponge
AB  - symbiont that we propose to designate as 'Candidatus Rhodobacter lobularis.'
ER  -

TY  - JOUR
AU  - Jousset, A.
AU  - Schuldes, J.
AU  - Keel, C.
AU  - Maurhofer, M.
AU  - Daniel, R.
AU  - Scheu, S.
AU  - Thuermer, A.
TI  - Full-Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas protegens CHA0.
JO  - Genome Announcements
PY  - 2014
SP  - e00322
EP  - e00314
VL  - 2
AB  - We report the complete genome sequence of the free-living bacterium Pseudomonas protegens
AB  - (formerly Pseudomonas fluorescens) CHA0, a model organism used in plant-microbe interactions,
AB  - biological control of phytopathogens, and bacterial genetics.
ER  -

TY  - JOUR
AU  - Jovanovic, L.
AU  - Delahunt, B.
AU  - McIver, B.
AU  - Eberhardt, N.L.
AU  - Grebe, S.K.G.
TI  - Optimising restriction enzyme cleavage of DNA derived from archival histopathological samples: an improved HUMARA assay.
JO  - Pathology
PY  - 2003
SP  - 70
EP  - 74
VL  - 35
AB  - Aims: Our aim was to evaluate and optimise methylation-sensitive restriction enzyme assays for
AB  - use in formalin-fixed, paraffin-embedded tissue (FFPET) samples, in order to improve the
AB  - application of the HUMARA X-chromosome inactivation assay to FFPET samples.Methods: We
AB  - extracted DNA from normal male colon and thyroid FFPET. Several DNA clean-up procedures and
AB  - restriction enzyme buffer compositions were tested for two methylation-sensitive enzymes, HhaI
AB  - and HpaII and a non-methylation-sensitive isoschizomere, MspI.Results: By including both a
AB  - non-methylation-sensitive control enzyme and DNA from male archival specimens in our
AB  - experiments, we were able to detect even subtle degrees of incomplete digestion. We showed
AB  - that FFPET-derived DNA is a poor substrate for restriction enzymes, especially for
AB  - methylation-sensitive restriction endonucleases. An optimised DNA clean-up protocol and
AB  - restriction enzyme buffer-mix allowed us to achieve complete digestion.Conclusions: The
AB  - combination of multiple, rigorous controls, DNA clean-up and restriction buffer optimisation
AB  - increases the reliability of HUMARA-based X-chromosome inactivation analysis of FFPET samples.
AB  - Analogous approaches are likely to allow optimisation of other restriction enzyme-based assays
AB  - of FFPET samples.
ER  -

TY  - JOUR
AU  - Juboi, H.
AU  - Basik, A.A.
AU  - Shamsul, S.S.
AU  - Arnold, P.
AU  - Schmitt, E.K.
AU  - Sanglier, J.J.
AU  - Yeo, T.C.
TI  - Luteipulveratus halotolerans sp. nov., a novel actinobacterium (Dermacoccaceae) from Sarawak, Malaysia.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2015
SP  - 4113
EP  - 4120
VL  - 65
AB  - The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample
AB  - collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically,
AB  - strain C296001T is closely associated with the genus Luteipulveratus that forms a distinct
AB  - monophyletic clade with the only described species, L. mongoliensis NBRC 105296T. The 16S rRNA
AB  - gene sequence similarity between strain C296001T and L. mongoliensis is 98.7%. DNA-DNA
AB  - hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was
AB  - only 21.5%. The G+C content of strain C296001T DNA is 71.7 mol%. Using a PacBio RS II system
AB  - whole genome sequences for strains C296001T and NBRC 105296T were obtained. The determined
AB  - genome sizes of 4.5 Mbps and 5.4 Mbps are similar to those of other Dermacoccaceae. The
AB  - cell-wall peptidoglycan containing lysine, alanine, aspartic acid, glutamic acid and serine
AB  - represents the peptidoglycan type A4alpha L-Lys-L-Ser-D-Asp. The major menaquinones are
AB  - MK-8(H4), MK-8, and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol,
AB  - diphosphatidylglycerol and phosphoglycolipid are the polar lipids, while the whole-cell sugars
AB  - are glucose, fucose and lower amount of ribose and galactose. The major fatty acids are
AB  - iso-C16:0, anteiso-C17:0, iso-C16:1 H, anteiso-C17:1 omega9c, iso-C18:0, and C17:0 10-methyl.
AB  - Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the
AB  - genus Luteipulveratus, with the main differences occurring in phenotypic characteristics.
AB  - Based on the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be
AB  - classified as a novel species in the genus Luteipulveratus, for which the name Luteipulveratus
AB  - halotolerans sp. nov. is recommended. The type strain is C296001T (=ATCC TSD-4T =JCM 30660T).
ER  -

TY  - JOUR
AU  - Judge, N.A.
AU  - Fields, J.A.
AU  - Pajaniappan, M.
AU  - Newell, D.G.
AU  - Manning, J.
AU  - Burns, C.M.
AU  - Thompson, S.A.
TI  - Mutation of a Campylobacter jejuni DNA methylase affects expression of multiple genes, motility, and epithelial cell adherence and invasion.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2005
SP  - 79
EP  - 79
VL  - 105
AB  - Campylobacter jejuni causes over 2 million cases of severe bacterial gastroenteritis in the
AB  - U.S. every year. Poultry flocks are ubiquitously and asymptomatically colonized with C.
AB  - jejuni, and the most likely cause of human infection is via the consumption of contaminated
AB  - poultry meat products as well as other foods cross contaminated during preparation, and
AB  - contaminated water. C. jejuni is able to thrive at two different temperatures, 42oC (the core
AB  - temperature of chickens) and 37oC (the core temperature of humans), thus there is likely to be
AB  - temperature regulation of Campylobacter proteins for optimization of expression in each
AB  - environment, including virulence factors important for human infection. We identified an
AB  - ortholog of NCTC11168 cj1461 in C. jejuni strain 81-176 as a gene that was more highly
AB  - expressed at 37oC than at 42oC. cj1461 encodes a predicted DNA methylase that is not
AB  - associated with a cognate restriction endonuclease. We purified Cj1461 as a recombinant
AB  - His-tagged protein and showed that Cj1461 can bind DNA and has DNA methyltransferase activity.
AB  - We hypothesize that Cj1461 does not protect C. jejuni DNA from restriction endonucleases and
AB  - may be involved in the regulation of genes important for the virulence of the bacterium. We
AB  - inactivated the cj1461 ortholog in C. jejuni 81-176 to investigate its potential role in gene
AB  - regulation. Proteome and DNA array results comparing 81-176 with its isogenic 81-176cj1461
AB  - mutant indicated the deregulation of numerous genes, including many involved in
AB  - virulence-associated pathways such as motility, flagellar glycosylation, chemotaxis, oxidative
AB  - stress, iron uptake, and transformation competence. The 81-176cj1461 mutant was significantly
AB  - less motile than C. jejuni 81-176, and was 30 times more adherent, but 800 times less invasive
AB  - than wild-type in an in vitro INT407 tissue culture model. These results suggest that the
AB  - regulation of multiple genes in C. jejuni 81-176, including some important for virulence, can
AB  - be mediated in part by the DNA methyltransferase Cj1461.
ER  -

TY  - JOUR
AU  - Jue, K.
AU  - Bestor, T.
AU  - Trasler, J.M.
TI  - Differential expression of DNA methyltransferase in male germ cells.
JO  - Biol. Reprod.
PY  - 1994
SP  - 80
EP  - 80
VL  - 50
AB  - DNA methylation is involved in regulating gene expression and plays a critical role in normal
AB  - development. Patterns of methylation are believed to be established during gametogenesis and
AB  - early embryogenesis. To better understand how methylation patterns are established in the male
AB  - mouse germ line we focused on the expression of the DNA methyltransferase (DNA MTase) which
AB  - catalyzes the transfer of methyl groups from S-adenosyl-methionine to the 5' position of
AB  - cytosine in DNA. Purified populations of premeiotic, meiotic and postmeiotic germ cells were
AB  - isolated from adult and 17 day old mouse testis using cellular sedimentation at unit gravity
AB  - on a Staput apparatus. Western analysis revealed abundant DNA MTase protein in postmitotic
AB  - leptotene/zygotene spermatocyte and haploid round spermatid fractions but low levels in
AB  - pachytene spermatocyte fractions. A 6.2kb DNA MTase transcript is specific to pachytene
AB  - spermatocytes whereas in other cell types, a 5.2kb mRNA is present. These findings are
AB  - supported by immunofluorescence studies where germ cells were stained for DNA MTase.
AB  - Immunofluorescence further revealed DNA MTase staining patterns to vary within one isolated
AB  - germ cell population suggesting differential expression and localization between the
AB  - developmental steps in various cell types. We conclude that DNA MTase expression is regulated
AB  - during spermatogenesis at a time when de novo methylation is known to occur. These studies
AB  - contribute to our understanding of how methylation patterns are established in the male germ
AB  - line and their importance during early development.
ER  -

TY  - JOUR
AU  - Juez, G.
AU  - Rodriguez-Valera, F.
AU  - Herrero, N.
AU  - Mojica, F.J.M.
TI  - Evidence for salt-associated restriction pattern modifications in the Archaeobacterium Haloferax mediterranei.
JO  - J. Bacteriol.
PY  - 1990
SP  - 7278
EP  - 7281
VL  - 172
AB  - DNA restriction pattern modifications were detected when Haloferax mediterranei
AB  - was grown in low (10%) salt concentrations.  After cells were grown again in
AB  - optimal (25%) salt concentrations, the original pattern was recovered.  These
AB  - salt-associated DNA modifications were revealed with 5% of the 160 DNA
AB  - fragments cloned and used as probes in hybridization experiments.  Patterns
AB  - obtained when genomic DNA was digested with different restriction enzymes
AB  - showed that these modifications are related not to insertions or deletions in
AB  - the genome but to modifications of some specific sequences.
ER  -

TY  - JOUR
AU  - Juhala, R.J.
AU  - Ford, M.E.
AU  - Duda, R.L.
AU  - Youlton, A.
AU  - Hatfull, G.F.
AU  - Hendrix, R.W.
TI  - Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 27
EP  - 51
VL  - 299
AB  - We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022
AB  - (40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and
AB  - members of the lambdoid or lambda-like group of phages. We provide a
AB  - comparative analysis of these sequences with each other and with two
AB  - previously determined lambdoid family genome sequences, those of E. coli
AB  - phage lambda and Salmonella typhimurium phage P22. The comparisons confirm
AB  - that these phages are genetic mosaics, with mosaic segments separated by
AB  - sharp transitions in the sequence. The mosaicism provides clear evidence
AB  - that horizontal exchange of genetic material is a major component of
AB  - evolution for these viruses. The data suggest a model for evolution in
AB  - which diversity is generated by a combination of illegitimate and
AB  - homologous recombination and mutational drift, and selection for function
AB  - produces a population in which most of the surviving mosaic boundaries are
AB  - located at gene boundaries or, in some cases, at protein domain boundaries
AB  - within genes. Comparisons of these genomes highlight a number of
AB  - differences that allow plausible inferences of specific evolutionary
AB  - scenarios for some parts of the genome. The comparative analysis also
AB  - allows some inferences about function of genes or other genetic elements.
AB  - We give examples for the generalized recombination genes of HK97, HK022
AB  - and P22, and for a putative headtail adaptor protein of HK97 and HK022. We
AB  - also use the comparative approach to identify a new class of genetic
AB  - elements, the morons, which consist of a protein-coding region flanked by
AB  - a putative delta 70 promoter and a putative factor-independent
AB  - transcription terminator, all located between two genes that may be
AB  - adjacent in a different phage. We argue that morons are autonomous genetic
AB  - modules that are expressed from the repressed prophage. Sequence
AB  - composition of the morons implies that they have entered the phages'
AB  - genomes by horizontal transfer in relatively recent evolutionary time.
ER  -

TY  - JOUR
AU  - Julio, S.M.
AU  - Heithoff, D.M.
AU  - Provenzano, D.
AU  - Klose, K.E.
AU  - Sinsheimer, R.L.
AU  - Low, D.A.
AU  - Mahan, M.J.
TI  - DNA Adenine Methylase Is Essential for Viability and Plays a Role in the Pathogenesis of Yersinia pseudotuberculosis and Vibrio cholerae.
JO  - Infect. Immun.
PY  - 2001
SP  - 7610
EP  - 7615
VL  - 69
AB  - Salmonella strains that lack or overproduce DNA adenine methylase (Dam) elicit a protective
AB  - immune response to different Salmonella species. To generate vaccines against other bacterial
AB  - pathogens, the dam genes of Yersinia pseudotuberculosis and Vibrio cholerae were disrupted but
AB  - found to be essential for viability. Overproduction of Dam significantly attenuated the
AB  - virulence of these two pathogens, leading to, in Yersinia, the ectopic secretion of virulence
AB  - proteins (Yersinia outer proteins) and a fully protective immune response in vaccinated hosts.
AB  - Dysregulation of Dam activity may provide a means for the development of vaccines against
AB  - varied bacterial pathogens.
ER  -

TY  - JOUR
AU  - Julio, S.M.
AU  - Heithoff, D.M.
AU  - Sinsheimer, R.L.
AU  - Low, D.A.
AU  - Mahan, M.J.
TI  - DNA adenine methylase overproduction in Yersinia pseudotuberculosis alters YopE expression and secretion and host immune responses to  infection.
JO  - Infect. Immun.
PY  - 2002
SP  - 1006
EP  - 1009
VL  - 70
AB  - Yersinia pseudotuberculosis mutants that overproduce the DNA adenine methylase (Dam) are
AB  - highly attenuated, confer fully protective immune
AB  - responses, and secrete several Yersinia virulence proteins (Yersinia
AB  - outer proteins [Yops]) under conditions that are nonpermissive for
AB  - secretion in wild-type strains. We examined here the effects of Dam
AB  - overproduction on Yersinia virulence determinant expression and
AB  - secretion, as well as the host immune response to Yersinia antigens.
AB  - Western blot analysis with convalescent antisera identified several
AB  - low-calcium-responsive antigens whose synthesis was affected by Dam
AB  - overproduction. One of these antigens was shown to be the type III
AB  - secretion effector protein, YopE, a cytotoxin involved in
AB  - antiphagocytosis. Dam overproduction disrupted both the thermal and
AB  - calcium regulation of YopE synthesis and relaxed the thermal but not
AB  - the calcium dependence of YopE secretion. Altered expression and/or
AB  - secretion of Yersinia proteins in Dam-overproducing strains may
AB  - contribute to the decreased virulence and heightened immunity observed
AB  - in vaccinated hosts and may provide a means by which to deliver
AB  - heterologous antigens and/or immune modulators of the inflammatory
AB  - response.
ER  -

TY  - JOUR
AU  - Jullien, P.E.
AU  - Susaki, D.
AU  - Yelagandula, R.
AU  - Higashiyama, T.
AU  - Berger, F.
TI  - DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana.
JO  - Curr. Biol.
PY  - 2012
SP  - 1825
EP  - 1830
VL  - 22
AB  - DNA methylation maintains genome stability and regulates gene expression [1]. In  mammals, DNA
AB  - methylation is reprogrammed in the germline from one generation to
AB  - the next [2]. In plants, it was considered that patterns of DNA methylation are
AB  - stably maintained through sexual reproduction [3-6]. However, a recent report
AB  - showed discrete variations of DNA methylation profiles from mother to daughter
AB  - plants [7]. The mechanisms that explain these variations have remained unknown.
AB  - Here, we report that maintenance DNA methyltransferases are barely expressed
AB  - during Arabidopsis female gametogenesis. In contrast, after fertilization both
AB  - maintenance and de novo DNA methyltransferases are expressed strongly in the
AB  - embryo. Embryogenesis is marked by increased de novo DNA methylation, reaching
AB  - levels that are further maintained in the adult plant. The accumulation of these
AB  - epigenetic marks after fertilization silences a methylation-sensitive fluorescent
AB  - reporter. De novo DNA methylation in the embryo provides a mechanism that could
AB  - account for the gradual remethylation of experimentally demethylated genomes [8,
AB  - 9]. In conclusion, we uncover that DNA methylation activity fluctuates during
AB  - sexual reproduction. This cycle likely explains variations of genome-wide
AB  - patterns of DNA methylation across generations in Arabidopsis [7, 10] and enables
AB  - a limited degree of reprogramming of the epigenome.
ER  -

TY  - JOUR
AU  - Jun, H.S.
AU  - Kim, Y.S.
AU  - Choi, K.R.
AU  - Rho, H.M.
TI  - Cloning and expression of the BdiI methylase gene in E. coli.
JO  - Korean J. Microbiol.
PY  - 1987
SP  - 40
EP  - 45
VL  - 25
AB  - The gene for the BdiI modification enzyme, which is one of BdiI
AB  - restriction-modification system, from Brevibacterium divaricatum FERM 5948 was
AB  - cloned and expressed in E. coli.  For cloning of the BdiI methylase gene, we
AB  - have initially used three cloning site (EcoRI, BamHI and SalI) of plasmid
AB  - vector pBR322 and adopted the retransformation method after BdiI restriction
AB  - endonuclease cleavage.  Selection of transformants carrying the gene was based
AB  - on the resistance of the modified plasmid encoding the enzyme to cleavage by
AB  - BdiI restriction enzyme, and the recombinant plasmid pBDIM116 containing 5.6 kb
AB  - EcoRI insert was proved to carry the gene.  Crude cell extracts prepared from
AB  - strains carrying the plasmid pBDIM116 contained an
AB  - S-adenosylmethionine-dependent methyltransferase activity specific for the BdiI
AB  - recognition site, ATCGAT.  The restriction map was constructed with 11
AB  - restriction enzyme, and the BdiI restriction-modification system was also
AB  - discussed.
ER  -

TY  - JOUR
AU  - Jun, J.W.
AU  - Kim, J.H.
AU  - Choresca, C.H.
AU  - Shin, S.P.
AU  - Han, J.E.
AU  - Park, S.C.
TI  - Draft Genome Sequence of Vibrio parahaemolyticus SNUVpS-1 Isolated from Korean Seafood.
JO  - Genome Announcements
PY  - 2013
SP  - e00132
EP  - e00112
VL  - 1
AB  - Vibrio parahaemolyticus is the leading cause of food-borne diseases, and several  pathogenic
AB  - strains cause global gastroenteritis outbreaks. Here, we report a
AB  - draft genome sequence of V. parahaemolyticus SNUVpS-1, which was isolated from
AB  - seafood in a fishery market in the Republic of Korea and contained TL, toxR, and
AB  - toxRS(old) genes. The current draft genome sequence will contribute to the effort
AB  - to monitor the spread of V. parahaemolyticus seafood isolates and clinical
AB  - isolates.
ER  -

TY  - JOUR
AU  - Jun, X.
AU  - Lupeng, L.
AU  - Minjuan, X.
AU  - Oger, P.
AU  - Fengping, W.
AU  - Jebbar, M.
AU  - Xiang, X.
TI  - Complete Genome Sequence of the Obligate Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii CH1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4297
EP  - 4298
VL  - 193
AB  - Pyrococcus yayanosii CH1 is the first obligate piezophilic hyperthermophilic archaeon isolated
AB  - from the deep-sea hydrothermal site
AB  - Ashadze on the mid-Atlantic ridge at a depth of 4,100 m. This organism
AB  - grows within a temperature range of 80 to 108 degrees C and a hydrostatic
AB  - pressure range of 20 to 120 MPa, with optima at 98 degrees C and 52 MPa,
AB  - respectively. Here, we report the complete genome sequence (1,716,817 bp,
AB  - with a G+C content of 51.6%) of the type strain P. yayanosii CH1(T) (= JCM
AB  - 16557). This genomic information reveals a systematic view of the
AB  - piezoadaptation strategy and evolution scenario of metabolic pathways in
AB  - Thermococcales.
ER  -

TY  - JOUR
AU  - Jung, J.
AU  - Baek, J.H.
AU  - Park, W.
TI  - Complete genome sequence of the diesel-degrading Acinetobacter sp. strain DR1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4794
EP  - 4795
VL  - 192
AB  - The genus Acinetobacter is ubiquitous in soil, aquatic, and sediment environments and includes
AB  - pathogenic strains, such as A. baumannii. Many
AB  - Acinetobacter species isolated from various environments have
AB  - biotechnological potential since they are capable of degrading a variety
AB  - of pollutants. Acinetobacter sp. strain DR1 has been identified as a
AB  - diesel degrader. Here we report the complete genome sequence of
AB  - Acinetobacter sp. DR1 isolated from the soil of a rice paddy.
ER  -

TY  - JOUR
AU  - Jung, J.
AU  - Choi, S.
AU  - Chun, J.
AU  - Park, W.
TI  - Genome Sequence of Pectin-Degrading Alishewanella aestuarii Strain B11T, Isolated from Tidal Flat Sediment.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5476
EP  - 5476
VL  - 194
AB  - We present the genome sequence of Alishewanella aestuarii B11(T) (=KCTC 22051(T)=DSM
AB  - 19476(T)). This species, isolated from tidal flat sediment, was
AB  - reported to be a novel species. A. aestuarii is known to degrade pectin, an
AB  - important component of plant cell wall. The presence of the genes related to
AB  - pectin metabolism in this strain indicates its capability to utilize pectin.
ER  -

TY  - JOUR
AU  - Jung, J.
AU  - Chun, J.
AU  - Park, W.
TI  - Genome Sequence of Extracellular-Protease-Producing Alishewanella jeotgali Isolated from Traditional Korean Fermented Seafood.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2097
EP  - 2097
VL  - 194
AB  - Alishewanella jeotgali MS1(T) (= KCTC 22429(T) = JCM 15561(T)) was isolated from  a
AB  - traditional Korean fermented seafood, gajami sikhae (jeotgal), and has been
AB  - reported as a novel species. A. jeotgali was proven to have extracellular
AB  - proteolytic activity, which may play an important role in the fermentation
AB  - environment of food containing fish flesh. Here, we present the genome sequence
AB  - of Alishewanella jeotgali MS1(T) as the first sequenced strain in the genus
AB  - Alishewanella and its taxonomic relatives.
ER  -

TY  - JOUR
AU  - Jung, J.H.
AU  - Holden, J.F.
AU  - Seo, D.H.
AU  - Park, K.H.
AU  - Shin, H.
AU  - Ryu, S.
AU  - Lee, J.H.
AU  - Park, C.S.
TI  - Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain CL1, Isolated from a Paralvinella sp. Polychaete Worm Collected from a  Hydrothermal Vent.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4769
EP  - 4770
VL  - 194
AB  - Thermococcus sp. strain CL1 is a hyperthermophilic, anaerobic, and heterotrophic  archaeon
AB  - isolated from a Paralvinella sp. polychaete worm living on an active
AB  - deep-sea hydrothermal sulfide chimney on the Cleft Segment of the Juan de Fuca
AB  - Ridge. To further understand the distinct characteristics of this archaeon at the
AB  - genome level, its genome was completely sequenced and analyzed. Here, we announce
AB  - the complete genome sequence (1,950,313 bp) of Thermococcus sp. strain CL1, with
AB  - a focus on H(2)- and energy-producing capabilities and its amino acid
AB  - biosynthesis and acquisition in an extreme habitat.
ER  -

TY  - JOUR
AU  - Jung, J.H.
AU  - Joe, M.H.
AU  - Kim, D.H.
AU  - Park, H.
AU  - Choi, J.I.
AU  - Lim, S.
TI  - Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 31
EP  - 31
VL  - 13
AB  - The Planococcus sp. PAMC21323 is a yellow pigment-producing bacterium isolated from King
AB  - George Island in Antarctica; it has a broad growth temperature range of
AB  - 5-40 degrees C. Herein, we describe the complete genome sequence information of
AB  - the genus Planococcus with its annotated sequence, genetic features for
AB  - bioremediation, and oxidative stress capacity. The Planococcus sp. PAMC21323
AB  - possesses chromosomal DNA (3,196,500-bp) with plasmid DNA (3364-bp). The complete
AB  - 3,199,864-bp of the genome consists of 3171 genes including 60 transfer RNAs and
AB  - 24 ribosomal RNAs. Strain PAMC21323 encodes various genes associated with
AB  - detoxification of heavy metal ions and aromatic hydrocarbons. Moreover, it is
AB  - equipped with diverse stress response systems, which can be used to sense the
AB  - internal and oxidative stresses caused by detoxification. This is the first
AB  - report highlighting the genetic potential of Planococcus sp. PAMC21323 in
AB  - bioremediation, suggesting application of this psychrotrophic strain in
AB  - bioremediation in harsh environments.
ER  -

TY  - JOUR
AU  - Jung, J.H.
AU  - Lee, J.H.
AU  - Holden, J.F.
AU  - Seo, D.H.
AU  - Shin, H.
AU  - Kim, H.Y.
AU  - Kim, W.
AU  - Ryu, S.
AU  - Park, C.S.
TI  - Complete Genome Sequence of the Hyperthermophilic Archaeon Pyrococcus sp. Strain  ST04, Isolated from a Deep-Sea Hydrothermal Sulfide Chimney on the Juan de Fuca  Ridge.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4434
EP  - 4435
VL  - 194
AB  - Pyrococcus sp. strain ST04 is a hyperthermophilic, anaerobic, and heterotrophic archaeon
AB  - isolated from a deep-sea hydrothermal sulfide chimney on the Endeavour
AB  - Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. To further
AB  - understand the distinct characteristics of this archaeon at the genome level
AB  - (polysaccharide utilization at high temperature and ATP generation by a Na(+)
AB  - gradient), the genome of strain ST04 was completely sequenced and analyzed. Here,
AB  - we present the complete genome sequence analysis results of Pyrococcus sp. ST04
AB  - and report the major findings from the genome annotation, with a focus on its
AB  - saccharolytic and metabolite production potential.
ER  -

TY  - JOUR
AU  - Jung, J.Y.
AU  - Ahn, Y.
AU  - Kweon, O.
AU  - LiPuma, J.J.
AU  - Hussong, D.
AU  - Marasa, B.S.
AU  - Cerniglia, C.E.
TI  - Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361T.
JO  - Genome Announcements
PY  - 2017
SP  - e00245
EP  - e00217
VL  - 5
AB  - Burkholderia contaminans LMG 23361 is the type strain of the species isolated from the milk of
AB  - a dairy sheep with mastitis. Some pharmaceutical products
AB  - contain disinfectants such as benzalkonium chloride (BZK) and previously we
AB  - reported that B. contaminans LMG 23361T possesses the ability to inactivate BZK
AB  - with high biodegradation rates. Here, we report an improved high-quality draft
AB  - genome sequence of this strain.
ER  -

TY  - JOUR
AU  - Jung, J.Y.
AU  - Lee, S.H.
AU  - Jeon, C.O.
TI  - Complete Genome Sequence of Leuconostoc carnosum Strain JB16, Isolated from Kimchi.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6672
EP  - 6673
VL  - 194
AB  - Leuconostoc carnosum strain JB16 was isolated from kimchi, the traditional Korean fermented
AB  - food. Here, we report the complete genome sequence of L. carnosum
AB  - strain JB16, consisting of a 1,645,096-bp circular chromosome with a G+C content
AB  - of 37.24% and four plasmids.
ER  -

TY  - JOUR
AU  - Jung, J.Y.
AU  - Lee, S.H.
AU  - Jeon, C.O.
TI  - Complete Genome Sequence of Leuconostoc gelidum Strain JB7, Isolated from Kimchi.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6665
EP  - 6665
VL  - 194
AB  - A strain of Leuconostoc gelidum, designated strain JB7, was isolated from kimchi, the
AB  - representative Korean traditional fermented food. Here we announce the
AB  - complete genome sequence of L. gelidum strain JB7, consisting of a 1,893,499-bp
AB  - circular chromosome with a G+C content of 36.68%, and provide a description of
AB  - its annotation.
ER  -

TY  - JOUR
AU  - Jung, J.Y.
AU  - Lee, S.H.
AU  - Lee, S.H.
AU  - Jeon, C.O.
TI  - Complete Genome Sequence of Leuconostoc mesenteroides subsp. mesenteroides Strain J18, Isolated from Kimchi.
JO  - J. Bacteriol.
PY  - 2012
SP  - 730
EP  - 731
VL  - 194
AB  - Leuconostoc mesenteroides subsp. mesenteroides is one of the most predominant lactic acid
AB  - bacterial groups during kimchi fermentation. Here,
AB  - we report the complete genome sequence of L. mesenteroides subsp.
AB  - mesenteroides J18, which was isolated from kimchi. The genome of the
AB  - strain consists of a 1,896,561-bp chromosome and five plasmids.
ER  -

TY  - JOUR
AU  - Jung, M.J.
AU  - Roh, S.W.
AU  - Kim, M.S.
AU  - Whon, T.W.
AU  - Bae, J.W.
TI  - Genome Sequence of Lentibacillus jeotgali GrbiT, Isolated from Traditional Korean Salt-Fermented Seafood.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6414
EP  - 6415
VL  - 193
AB  - Lentibacillus jeotgali Grbi(T), isolated from a traditional Korean salt-fermented seafood, is
AB  - a strictly aerobic, Gram-positive, nonmotile,
AB  - endospore-forming, moderately halophilic bacterium belonging to the family
AB  - Bacillaceae in the phylum Firmicutes. Here, the draft genome sequence of
AB  - L. jeotgali Grbi(T) (3,775,822 bp with a G+C content of 42.5%) is
AB  - reported. This is the first reported genome sequence from a Lentibacillus
AB  - species.
ER  -

TY  - JOUR
AU  - Jung, V.
AU  - Pestka, S.B.
AU  - Pestka, S.
TI  - Efficient cloning of PCR generated DNA containing terminal restriction endonuclease recognition sites.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6156
EP  - 6156
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Jung, V.
AU  - Pestka, S.B.
AU  - Pestka, S.
TI  - Cloning of polymerase chain reaction-generated DNA containing terminal restriction endonuclease recognition sites.
JO  - Methods Enzymol.
PY  - 1993
SP  - 357
EP  - 362
VL  - 218
AB  - Using the polymerase chain reaction (PCR) to generate DNA containing terminal restriction
AB  - endonuclease recognition sites to permit cloning usually relies on the use of unphosphorylated
AB  - primers incorporating a restriction endonuclease recognition site of choice plus three or four
AB  - extra 5' bases flanking that site. Various sites (e.g., NotI, XhoI, and XbaI) incorporated
AB  - into the termini of PCR products have proved difficult to cut with their respective
AB  - restriction endonucleases. There are several possible explanations for this difficulty; first,
AB  - Taq polymersase might be inefficient for certain terminal sequences, producing frayed ends
AB  - that cannot be cleaved by the restriction endonuclease. Alternatively, the "breathing" of
AB  - terminal sequences might prevent the stable association of restriction endonucleases with
AB  - terminal sites. Also, Taq polymerase or other contaminants might bind to the ends of the PCR
AB  - products, blocking restriction endonuclease activity.
ER  -

TY  - JOUR
AU  - Junghare, M.
AU  - Patil, Y.
AU  - Schink, B.
TI  - Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 90
EP  - 90
VL  - 10
AB  - Azoarcus sp. strain PA01(T) belongs to the genus Azoarcus, of the family Rhodocyclaceae within
AB  - the class Betaproteobacteria. It is a facultatively
AB  - anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short
AB  - rod-shaped bacterium that was isolated from a wastewater treatment plant in
AB  - Constance, Germany. It is of interest because of its ability to degrade
AB  - o-phthalate and a wide variety of aromatic compounds with nitrate as an electron
AB  - acceptor. Elucidation of the o-phthalate degradation pathway may help to improve
AB  - the treatment of phthalate-containing wastes in the future. Here, we describe the
AB  - features of this organism, together with the draft genome sequence information
AB  - and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an
AB  - overall G + C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes
AB  - code for proteins and 87 genes for RNAs. The majority of the protein-encoding
AB  - genes (83.51 %) were assigned a putative function while those remaining were
AB  - annotated as hypothetical proteins.
ER  -

TY  - JOUR
AU  - Juranek, S.
AU  - Wieden, H.-J.
AU  - Lipps, H.J.
TI  - De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 1387
EP  - 1391
VL  - 31
AB  - Dramatic DNA reorganization and elimination processes occur during macronuclear
AB  - differentiation in ciliates. In this study we analyzed
AB  - whether cytosine methylation of specific sequences plays a functional role
AB  - during DNA rearrangement. Three classes of sequences,
AB  - macronuclear-destined sequences (MDSs, pCE7), members from a large family
AB  - of transposon-like elements and micronuclear-specific sequences (pLJ01),
AB  - differing in their structure and future destiny during nuclear
AB  - differentiation, were studied in the micronucleus, the developing
AB  - macronucleus and, when present, in the mature macronucleus. While the MDSs
AB  - become processed to a 1.1 and 1.3 kb gene-sized macronuclear DNA molecule,
AB  - the family of transposon-like elements represented by MaA81 becomes
AB  - removed late in the course of polytene chromosome formation. The
AB  - micronuclear-specific sequence pLJ01 is eliminated together with bulk
AB  - micronuclear DNA during degradation of polytene chromosomes. No methylated
AB  - cytosine could be detected in the vegetative macronucleus and no
AB  - difference in methylation pattern was observed either between micronucleus
AB  - and developing macronucleus in MDSs or in a micronuclear-specific
AB  - sequence. However, a significant percentage of the cytosines contained in
AB  - the transposon-like element becomes methylated de novo in the course of
AB  - macronuclear differentiation. This is the first demonstration that
AB  - cytosine methylation in specific sequences occurs during macronuclear
AB  - differentiation and may provide a first step towards understanding
AB  - epigenetic factors involved in DNA processing.
ER  -

TY  - JOUR
AU  - Jurenaite-Urbanaviciene, S.
TI  - Engineering of bifunctional restriction endonucleases with novel specificities.
JO  - Ph.D. Thesis, Vilnius University
PY  - 2008
SP  - 1
EP  - 46
AB  - CONCLUSIONS 1. The BseMII restriction-modification system is composed of two enzymes, a DNA
AB  - methlytransferase and a restriction endonuclease, which are encoded by two convergently
AB  - transcribed genes. The PpiI and TstI R-M systems are each composed of a single enzyme. 2.
AB  - Regions predicted to participate in DNA target hydrolysis, methylation and recognition were
AB  - identified in the polypeptide of BseMII restriction endonuclease. From the viewpoint of the
AB  - structure-function organization, the BseMII REase is a suitable object for experiments aimed
AB  - at changing specificity. 3. The structure-function organization of PpiI and TstI resemble that
AB  - of AloI. Regions responsible for DNA target hydrolysis, methylation and recognition were
AB  - identified in polypeptides of these enzymes. 4. The construction of active hybrids between
AB  - AloI and PpiI has demonstrated that C-terminal regions of type IIB REases are involved in DNA
AB  - target recognition and revealed that proximal target recognition domains are independent
AB  - interchangeable modules. 5. Active hybrids recognizing novel DNA targets GAGN5GTG were
AB  - generated by swapping of proximal and distal target recognition domains between PpiI and TstI.
AB  - These results have demonstrated that novel type IIB REases can be engineered by recombination
AB  - of their TRDs. 6. The increase in the Tst-PpiTRD1 activity resulting from a single amino acid
AB  - substitution Gly1006Leu demonstrates that properties of hybrid REases can be improved by
AB  - rational mutagenesis. 7. Hybrid type IIB enzymes similarly to progenitor restriction
AB  - endonucleases cleave DNA on both sides of recognition sequences and display cleavage site
AB  - variability: at some positions enzymes hydrolyze DNA at two points differing from each other
AB  - by one nucleotide.
ER  -

TY  - JOUR
AU  - Jurenaite-Urbanaviciene, S.
AU  - Kazlauskiene, R.
AU  - Urbelyte, V.
AU  - Maneliene, Z.
AU  - Petrusyte, M.
AU  - Lubys, A.
AU  - Janulaitis, A.
TI  - Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 5'-CTCAG(N)10/8.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 895
EP  - 903
VL  - 29
AB  - We report the properties of the new BseMII restriction and modification enzymes from Bacillus
AB  - stearothermophilus Isl 15-111, which recognize the sequence 5'-CTCAG, and the nucleotide
AB  - sequence of the genes encoding them. The restriction endonuclease R.BseMII makes a staggered
AB  - cut at the tenth base pair downstream of the recognition sequence on the upper strand,
AB  - producing a two base 3'-protruding end.  Magnesium ions and S-adenosyl-L-methionine (AdoMet)
AB  - are required for cleavage.  S-adenosylhomocysteine and sinefungin can replace AdoMet in the
AB  - cleavage reaction. The BseMII methyltransferase modifies unique adenine residues in both
AB  - strands of the target sequence 5'-CTCAG-3'/5'-CTGAG-3'. Monomeric R.BseMII in addition to
AB  - endonucleolytic activity also possesses methyltransferase activity that modifies the A base
AB  - only within the 5'-CTCAG strand of the target duplex. The deduced amino acid sequence of the
AB  - restriction endonuclease contains conserved motifs of DNA N6-adenine methylases involved in
AB  - S-adenosyl-L-methionine binding and catalysis. According to its structure and enzymatic
AB  - properties, R.BseMII may be regarded as a representative of the type IV restriction
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Jurenaite-Urbanaviciene, S.
AU  - Serksnaite, J.
AU  - Kriukiene, E.
AU  - Giedriene, J.
AU  - Venclovas, C.
AU  - Lubys, A.
TI  - Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 10358
EP  - 10363
VL  - 104
AB  - Type II restriction endonucleases (REases) cleave double-stranded DNA at specific sites within
AB  - or close to their recognition sequences. Shortly
AB  - after their discovery in 1970, REases have become one of the primary tools
AB  - in molecular biology. However, the list of available specificities of type
AB  - II REases is relatively short despite the extensive search for them in
AB  - natural sources and multiple attempts to artificially change their
AB  - specificity. In this study, we examined the possibility of generating
AB  - cleavage specificities of REases by swapping putative target recognition
AB  - domains (TRDs) between the type IIB enzymes AloI, PpiI, and TstI. Our
AB  - results demonstrate that individual TRDs recognize distinct parts of the
AB  - bipartite DNA targets of these enzymes and are interchangeable. Based on
AB  - these properties, we engineered a functional type IIB REase having
AB  - previously undescribed DNA specificity. Our study suggests that the
AB  - TRD-swapping approach may be used as a general technique for the
AB  - generation of type II enzymes with predetermined specificities.
ER  -

TY  - JOUR
AU  - Jurgaitis, A.P.
AU  - Butkus, V.V.
AU  - Klimasauskas, S.J.
AU  - Janulaitis, A.
TI  - The effects of N4-methylcytosine and 5-methylcytosine on the thermal stability of DNA double helix.
JO  - Bioorg. Khim.
PY  - 1988
SP  - 158
EP  - 165
VL  - 14
AB  - The thermodynamic parameters (DeltaH, DeltaS) of the helix-coil transition of
AB  - self-complementary oligonucleotides d(CGCGCGCG), d(CG5mCGCGCG), d(CG4mCGCGCG),
AB  - d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC), and d(GGA4mCCCGGGTCC) were determined.  The
AB  - substitution of 4mC for C was found to decrease the melting temperature of the
AB  - oligonucleotides.  The destabilization effect of the two substitutions is
AB  - equivalent to the change of an A.T for a G.C pair.  The free energy decrease of
AB  - helix-coil transition due to the introduction of two 4mC into an octanucleotide
AB  - was estimated to be 1.24 kcal/mol.
ER  -

TY  - JOUR
AU  - Jurica, M.S.
TI  - I. Structures of  intron encoded homing endonucleases and II. Allosteric regulation of pyruvate kinase.
JO  - Ph.D. Thesis, University of Washington
PY  - 1999
SP  - 1
EP  - 146
AB  - I.  Homing is the lateral transfer of an intervening genetic sequence,
AB  - either an intron or an intein, to a cognate allele lacking the element resulting
AB  - in the duplication of the intervening sequence.  The process of homing is
AB  - initiated by site-specific endonucleases that are encoded by open reading frames
AB  - within the mobile elements.  Several features of these proteins make them
AB  - attractive subjects for structural studies.  First, these unique endonucleases
AB  - may be contrasted with a variety of enzymes involved in nucleic acid strand
AB  - breakage and rearrangement, particularly restriction endonucleases.  Second,
AB  - because they are encoded within the intervening sequence, limitations in the
AB  - length of the open reading frames that encode them are also imposed on the
AB  - folded protein structures.  Third, these enzymes display a unique strategy of
AB  - flexible recognition of very long DNA target sites.  This strategy allows the
AB  - enzymes to minimize non-specific cleavage within the host genome, while
AB  - maximizing their ability to cleave closely related variants of the homing
AB  - recognition site.  The structural studies of homing endonucleases presented here
AB  - provide insight to their unique mechanisms of recognition and cleavage of DNA.
AB  - II.  The activation of regulated isozymes of pyruvate kinase (PK) by fructose-
AB  - 1,6-bis-phosphate (FBP) directly influences cytosolic levels of ATP and GTP and
AB  - the flux of glycolytic carbon into fermentation pathways and the Krebs cycle.
AB  - This pattern of regulation may be important to cell proliferation, as
AB  - demonstrated by the re-expression of an allosterically regulated, fetal isozyme
AB  - of PK in tumor cells.  The structure of allosterically regulated pyruvate kinase
AB  - from Saccharomyces cerevisiae complexed with phosphoglycolate (a substrate
AB  - analogue), Mn2+, and K+ in the presence and absence of FBP was solved to
AB  - identify the allosteric binding site.  The location, structure, and interactions
AB  - within the allosteric site are in agreement with the pattern of alternate
AB  - genetic splicing that leads to regulated forms of the enzyme in humans.
AB  - Deregulating the allosteric control of PK in yeast by either site-directed
AB  - mutation or expression of non-regulated isozymes has profound effects on cell
AB  - growth and cell-cycle profiles.
ER  -

TY  - JOUR
AU  - Jurica, M.S.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI.
JO  - Mol. Cell
PY  - 1998
SP  - 469
EP  - 476
VL  - 2
AB  - The structure of the LAGLIDADG intron-encoded homing endonuclease I-CreI bound to homing site
AB  - DNA has been determined. The interface is formed by an extended, concave beta sheet from each
AB  - enzyme monomer that contacts each DNA half-site, resulting in direct side-chain contacts to 18
AB  - of the 24 base pairs across the full-length homing site. The structure indicates that I-CreI
AB  - is optimized to its role in genetic transposition by exhibiting long site-recognition while
AB  - being able to cleave many closely related target sequences. DNA cleavage is mediated by a
AB  - compact pair of active sites in the I-CreI homodimer, each of which contains a separate bound
AB  - divalent cation.
ER  -

TY  - JOUR
AU  - Jurica, M.S.
AU  - Stoddard, B.L.
TI  - Homing endonucleases: structure, function and evolution.
JO  - Cell. Mol. Life Sci.
PY  - 1999
SP  - 1304
EP  - 1326
VL  - 55
AB  - 'Homing' is the lateral transfer of an intervening genetic sequence, either an intron or an
AB  - intein, to a cognate allele that lacks that element. The end result of homing is the
AB  - duplication of the intervening sequence. The process is initiated by site-specific
AB  - endonucleases that are encoded by open reading frames within the mobile elements. Several
AB  - features of these proteins make them attractive subjects for structural and functional
AB  - studies. First, these endonucleases, while unique, may be contrasted with a variety of enzymes
AB  - involved in nucleic acid strand breakage and rearrangement, particularly restriction
AB  - endonucleases. Second, because they are encoded within the intervening sequence, there are
AB  - interesting limitations on the position and length of their open reading frames, and therefore
AB  - on their structures. Third, these enzymes display a unique strategy of flexible recognition of
AB  - very long DNA target sites. This strategy allows these sequences to minimize nonspecific
AB  - cleavage within the host genome, while maximizing the ability of the endonuclease to cleave
AB  - closely related variants of the homing site. Recent studies explain a great deal about the
AB  - biochemical and genetic mechanisms of homing, and also about the structure and function of
AB  - several representative members of the homing endonuclease families.
ER  -

TY  - JOUR
AU  - Jurkowska, R.Z.
AU  - Anspach, N.
AU  - Urbanke, C.
AU  - Jia, D.
AU  - Reinhardt, R.
AU  - Nellen, W.
AU  - Cheng, X.
AU  - Jeltsch, A.
TI  - Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 6656
EP  - 6663
VL  - 36
AB  - The C-terminal domains of Dnmt3a and Dnmt3L form elongated heterotetramers (3L-3a-3a-3L).
AB  - Analytical ultracentrifugation confirmed the Dnmt3a-C/3L-C
AB  - complex exists as a 2:2 heterotetramer in solution. The 3a-3a interface is
AB  - the DNA-binding site, while both interfaces are essential for AdoMet
AB  - binding and catalytic activity. Hairpin bisulfite analysis shows
AB  - correlated methylation of two CG sites in a distance of approximately 8-10
AB  - bp in the opposite DNA strands, which corresponds to the geometry of the
AB  - two active sites in one Dnmt3a-C/3L-C tetramer. Correlated methylation was
AB  - also observed for two CG sites at similar distances in the same DNA
AB  - strand, which can be attributed to the binding of two tetramers next to
AB  - each other. DNA-binding experiments show that Dnmt3a-C/3L-C complexes
AB  - multimerize on the DNA. Scanning force microscopy demonstrates filament
AB  - formation rather than binding of single tetramers and shows that
AB  - protein-DNA filament formation leads to a 1.5-fold shortening of the DNA
AB  - length.
ER  -

TY  - JOUR
AU  - Jurkowska, R.Z.
AU  - Ceccaldi, A.
AU  - Zhang, Y.
AU  - Arimondo, P.B.
AU  - Jeltsch, A.
TI  - DNA Methyltransferase Assays.
JO  - Methods Mol. Biol.
PY  - 2011
SP  - 157
EP  - 177
VL  - 791
AB  - DNA methyltransferases are important enzymes and their inhibition has many potential
AB  - applications. The investigation of DNA methyltransferases as well as screening for potential
AB  - inhibitors requires specialized enzyme assays. In this chapter, we describe three DNA
AB  - methyltransferase assays, each of them based on a different method: (1) An assay using
AB  - radioactively labeled Ado Met and biotinylated DNA substrates that is ideal for enzymatic
AB  - characterization of these enzymes. (2) An assay using bisulfite conversion of in vitro
AB  - methylated DNA that is ideal to determine details of the methylation pattern introduced by
AB  - DNA-(cytosine C5)-methyltransferases. (3) A novel fluorescence-coupled, restriction-based
AB  - assay suitable for high-throughput screening of DNA methyltransferase inhibitors.
ER  -

TY  - JOUR
AU  - Jurkowska, R.Z.
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - Structure and Function of Mammalian DNA Methyltransferases.
JO  - Chembiochem
PY  - 2011
SP  - 206
EP  - 222
VL  - 12
AB  - DNA methylation plays an important role in epigenetic signalling, having an impact on gene
AB  - regulation, chromatin structure, development
AB  - and disease. Here, we review the structures and functions of the
AB  - mammalian DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b, including
AB  - their domain structures, catalytic mechanisms, localisation,
AB  - regulation, post-translational modifications and interaction with
AB  - chromatin and other proteins, summarising data obtained in genetic,
AB  - cell biology and enzymatic studies. We focus on the question of how the
AB  - molecular and enzymatic properties of these enzymes are connected to
AB  - the dynamics of DNA methylation patterns and to the roles the enzymes
AB  - play in the processes of de novo and maintenance DNA methylation.
AB  - Recent enzymatic and genome-wide methylome data have led to a new model
AB  - of genomic DNA methylation patterns based on the preservation of
AB  - average levels of DNA methylation in certain regions, rather than the
AB  - methylation states of individual CG sites.
ER  -

TY  - JOUR
AU  - Jurkowska, R.Z.
AU  - Siddique, A.N.
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - Approaches to Enzyme and Substrate Design of the Murine Dnmt3a DNA Methyltransferase.
JO  - Chembiochem
PY  - 2011
SP  - 1589
EP  - 1594
VL  - 12
ER  -

TY  - JOUR
AU  - Jurkowski, T.P.
AU  - Anspach, N.
AU  - Kulishova, L.
AU  - Nellen, W.
AU  - Jeltsch, A.
TI  - The M.EcoRV DNA-(adenine N-6)-methyltransferase uses DNA bending for recognition of an expanded EcoDam recognition site.
JO  - J. Biol. Chem.
PY  - 2007
SP  - 36942
EP  - 36952
VL  - 282
AB  - The M. EcoRV DNA methyltransferase recognizes GATATC sites. It is related to EcoDam, which
AB  - methylates GATC sites. The DNA binding domain
AB  - of M. EcoRV is similar to that of EcoDam suggesting a similar mechanism
AB  - of DNA recognition. We show that amino acid residue Lys(11) of M. EcoRV
AB  - is involved in recognition of Gua(1) and Arg(128) contacts the Gua in
AB  - base pair 6. These residues correspond to Lys(9) and Arg(124) in
AB  - EcoDam, which recognize the Gua residues in both strands of the Dam
AB  - recognition sequence, indicating that M. EcoRV and EcoDam make similar
AB  - contacts to outermost base pairs of their recognition sequences and M.
AB  - EcoRV recognizes its target site as an expanded GATC site. In contrast
AB  - to EcoDam, M. EcoRV considerably bends the DNA (59 +/- 4 degrees)
AB  - suggesting indirect readout of the AT-rich inner sequence. Recognition
AB  - of an expanded target site by DNA bending is a new principle for
AB  - changing DNA recognition specificity of proteins during molecular
AB  - evolution. R128A is inefficient in DNA bending and binding, whereas
AB  - K11A bends DNA with relaxed sequence specificity. These results suggest
AB  - a temporal order of the formation of protein-DNA contacts in which the
AB  - Gua(6)-Arg(128) contact forms early followed by DNA bending and,
AB  - finally, the formation of the Lys(11)-Gua(1) contact.
ER  -

TY  - JOUR
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - On the Evolutionary Origin of Eukaryotic DNA Methyltransferases and Dnmt2.
JO  - PLoS ONE
PY  - 2011
SP  - e28104
EP  - e28104
VL  - 6
AB  - The Dnmt2 enzymes show strong amino acid sequence similarity with eukaryotic and prokaryotic
AB  - DNA-(cytosine C5)-methyltransferases. Yet,
AB  - Dnmt2 enzymes from several species were shown to methylate tRNA-Asp and
AB  - had been proposed that eukaryotic DNA methyltransferases evolved from a
AB  - Dnmt2-like tRNA methyltransferase ancestor [Goll et al., 2006, Science,
AB  - 311, 395-8]. It was the aim of this study to investigate if this
AB  - hypothesis could be supported by evidence from sequence alignments. We
AB  - present phylogenetic analyses based on sequence alignments of the
AB  - methyltransferase catalytic domains of more than 2300 eukaryotic and
AB  - prokaryotic DNA-(cytosine C5)-methyltransferases and analyzed the
AB  - distribution of DNA methyltransferases in eukaryotic species. The Dnmt2
AB  - homologues were reliably identified by an additional conserved CFT
AB  - motif next to motif IX. All DNA methyltransferases and Dnmt2 enzymes
AB  - were clearly separated from other RNA-(cytosine-C5)-methyltransferases.
AB  - Our sequence alignments and phylogenetic analyses indicate that the
AB  - last universal eukaryotic ancestor contained at least one member of the
AB  - Dnmt1, Dnmt2 and Dnmt3 families of enzymes and additional RNA
AB  - methyltransferases. The similarity of Dnmt2 enzymes with DNA
AB  - methyltransferases and absence of similarity with RNA
AB  - methyltransferases combined with their strong RNA methylation activity
AB  - suggest that the ancestor of Dnmt2 was a DNA methyltransferase and an
AB  - early Dnmt2 enzyme changed its substrate preference to tRNA. There is
AB  - no phylogenetic evidence that Dnmt2 was the precursor of eukaryotic
AB  - Dnmts. Most likely, the eukaryotic Dnmt1 and Dnmt3 families of DNA
AB  - methyltransferases had an independent origin in the prokaryotic DNA
AB  - methyltransferase sequence space.
ER  -

TY  - JOUR
AU  - Juste, A.
AU  - Van Trappen, S.
AU  - Verreth, C.
AU  - Cleenwerck, I.
AU  - De Vos, P.
AU  - Lievens, B.
AU  - Willems, K.A.
TI  - Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, halophilus subsp. nov. and flandriensis subsp. nov.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2012
SP  - 129
EP  - 137
VL  - 62
AB  - Most bacteria recovered so far from sugar thick juice during storage represent
AB  - strains of the species Tetragenococcus halophilus. Recently, several
AB  - Gram-positive, non-motile, non-spore-forming cocci with other physiological and
AB  - genetic traits were isolated from sugar thick juice samples from different
AB  - origins. In this study, representative isolates were investigated using a
AB  - polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between
AB  - these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%.
AB  - The level of DNA-DNA relatedness between isolate T1(T), representing the newly
AB  - found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a
AB  - DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic
AB  - features demonstrated that the isolates represent a novel species, for which the
AB  - name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type
AB  - strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from
AB  - high-salt and high-sugar environments showed clear differences in several
AB  - physiological and genetic characteristics like RAPD fingerprints and 16S rRNA
AB  - gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness
AB  - between osmophilic and halophilic T. halophilus isolates, demonstrating that the
AB  - different strains belong to the same species. Based on the phenotypic and
AB  - genotypic differences observed, as well as the different origins of the strains
AB  - and the industrial relevance of thick juice degradation, two subspecies of T.
AB  - halophilus are described in this manuscript: T. halophilus subsp. halophilus
AB  - subsp. nov. for the strains isolated from salt media and T. halophilus subsp.
AB  - flandriensis subsp. nov. for the strains isolated from sugar-rich environments,
AB  - which were first isolated in Flanders, Belgium. The type strains for the
AB  - subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T)
AB  - =DSM 23766(T)), respectively.
ER  -

TY  - JOUR
AU  - Juttermann, R.
AU  - Li, E.
AU  - Jaenisch, R.
TI  - Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 11797
EP  - 11801
VL  - 91
AB  - The deoxycytidine analog 5-aza-2'-deoxycytidine (5-azadCyd) has been widely used as a DNA
AB  - methylation inhibitor to experimentally induce gene expression and cellular differentiation.
AB  - Prior to the availability of mutant mice with altered DNA methyltransferase levels, treatment
AB  - of cells with drugs has been the only means to experimentally manipulate the level of genomic
AB  - DNA methylation in mammalian cells. Substitution of DNA with 5-azadCyd leads to covalent
AB  - trapping of the enzyme, thereby depleting the cells of enzyme activity and resulting in DNA
AB  - demethylation. 5-AzadCyd or 5-azacytidine treatment causes multiple changes in treated cells,
AB  - including activation of silent genes, decondensation of chromatin, and induction of cellular
AB  - differentiation, all of which are believed to be consequences of drug-induced demethylation.
AB  - 5-AzadCyd is highly toxic in cultured cells and animals and is utilized as a potent antitumor
AB  - agent for treatment of certain human cancers. It has been postulated that the toxicity of the
AB  - drug in mammalian cells is also due to its inhibition of DNA methylation. The chemistry of the
AB  - methylation reaction is consistent, however, with an alternative mechanism: the cyto-toxic
AB  - effect of 5-azadCyd may be directly mediated through the covalent binding of DNA
AB  - methyltransferase to 5-azadCyd-substituted DNA. We have tested this possibility by using
AB  - embryonic stem cells and mice with reduced levels of DNA methyltransferase due to a targeted
AB  - mutation of the gene. When exposed to 5-azadCyd mutant embryonic stem cells or embryos were
AB  - significantly more resistant to the toxic effects of the drug than wild-type cells and
AB  - embryos, respectively. These results strongly suggest that the cellular DNA methyltransferase
AB  - itself, rather than the secondary demethylation of genomic DNA, is the primary mediator of
AB  - 5-azadCyd cytotoxicity. In light of our results, some conclusions from previous studies using
AB  - 5-azad-Cyd in order to experimentally manipulate cellular methylation levels may have to be
AB  - reassessed. Also, our data make clear predictions for cancer treatment: tumor cells with
AB  - elevated DNA methyltransferase levels would be expected to be susceptible to treatment with
AB  - 5-azadCyd, whereas tumors with reduced levels of the enzyme would be resistant.
ER  -

TY  - JOUR
AU  - Jutur, P.P.
AU  - Hoti, S.L.
AU  - Reddy, A.R.
TI  - Bsu2413I and Bfi2411I, two new thermophilic type II restriction endonucleases from Bacillus subtilis and Bacillus firmus: isolation and  partial purification. Thermophilic endonucleases from two Bacillus  species.
JO  - Mol. Biol. Rep.
PY  - 2004
SP  - 139
EP  - 142
VL  - 31
AB  - Two new thermophilic type II restriction endonucleases, which we designated as Bsu2413I and
AB  - Bfi2411I, have been isolated from gram-positive thermophilic bacteria Bacillus subtilis strain
AB  - 2413 and Bacillus firmus strain 2411 respectively and partially purified.  The restriction
AB  - endonucleases were extracted from cell extracts and purified using single step purification
AB  - through phosphocellulose column chromatography, SDS-PAGE profile showed denatured molecular
AB  - weights of 33 and 67 kDa for the Bsu2413I and 39 and 67 kDa for the Bfi2411I.  The partially
AB  - purified Bsu2413I enzyme restricted pBR322 DNA into two fragments of 3250 and 1100 bp whereas
AB  - Bfi2411I enzyme restricted pBR322 DNA into two fragments of 3500 and 800 bp.  The activity of
AB  - both endonucleases was assayed at 55oC and they required Mg+2 as cofactor like other type II
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Jutur, P.P.
AU  - Reddy, A.R.
TI  - Isolation, purification and properties of new restriction endonucleases from Bacillus badius and Bacillus lentus.
JO  - Microbiol. Res.
PY  - 2007
SP  - 378
EP  - 383
VL  - 162
AB  - We tentatively named two enzymes as Bbal and Blel, which were isolated and purified from
AB  - Gram-positive mesophilic bacteria Bacillus badius
AB  - 1458 and Bacillus lentus 1689 respectively, by ammonium sulphate
AB  - precipitation, phosphocellulose and heparin-sepharose column
AB  - chromatography. SDS-PAGE protein profiles for Bbal and Blel showed
AB  - denatured molecular weights of 52 and 48 kDa, respectively. Bbal
AB  - hydrolyzed pUC18 DNA into 1900 and 700 bp, pBR322 DNA into two
AB  - fragments of 2800 and 1500 bp and Phi x 174 DNA into 3800 and 1600 bp.
AB  - Blel hydrolyzed pUC18 DNA into 1800 and 800 bp, pBR322 DNA into two
AB  - fragments of 2700 and 1600 bp and Phi x 174 DNA into 3700 and 1700 bp.
AB  - The effects of temperature, ionic strength, pH and Mg2+ ion
AB  - concentrations were studied to demonstrate some biochemical properties
AB  - of Bbal and Blel. Maximum activities of these enzymes were observed at
AB  - 37 degrees C (pH 8.0) with 100 mM NaCl and 10 mM Mg2+ concentrations.
ER  -

TY  - JOUR
AU  - Jutur, P.P.
AU  - Reddy, A.R.
TI  - BpaI and BpnI: novel type II restriction endonucleases from Bacillus pasteurii and Bacillus pantothenticus.
JO  - Biotechnol. Lett.
PY  - 2004
SP  - 929
EP  - 932
VL  - 26
AB  - Two novel type II restriction endonucleases, designated as BpaI and BpnI, were isolated from
AB  - Bacillus pasteurii strain 1761 and Bacillus
AB  - pantothenticus strain 1639, respectively. They were partially purified
AB  - and SDS-PAGE indicated Mr values of 28 and 67 kDa for BpaI, 28 and 48
AB  - kDa for BpnI. The partially purified endonucleases hydrolyzed DNA into
AB  - discrete fragments: pUC18 (2.6 kb for BpaI; 1.8 and 0.8 kb for BpnI),
AB  - pBR322 (2.5 and 1.8 kb for BpaI; 2.6 and 1.7 kb for BpnI) and Phix174
AB  - DNA (3.2 and 2.1 kb for BpaI; 4 and 1.3 kb for BpnI).
ER  -

TY  - JOUR
AU  - Jutur, P.P.
AU  - Reddy, A.R.
TI  - Isolation and partial purification of a novel type II restriction endonuclease Bsu121 I, from Bacillus subtilis - Bsu121 I, a type II  restriction endonuclease from Bacillus subtilis.
JO  - Mol. Biol. Rep.
PY  - 2002
SP  - 383
EP  - 385
VL  - 29
AB  - A new type II restriction endonuclease which we designated as Bsu121I has been isolated from
AB  - the
AB  - gram-positive bacterium Bacillus subtilis strain
AB  - 121 and partially purified. The restriction endonuclease was isolated
AB  - from cell extracts using step-wise purification through ammonium
AB  - sulfate precipitation, followed by phosphocellulose column
AB  - chromatography. SDS-PAGE profile showed denatured molecular weights (23
AB  - and 67 kDa) of the endonuclease. The partially purified enzyme
AB  - restricted pBR322 DNA into two fragments of 3200 and 1700 bp. The
AB  - endonuclease activity required Mg+2 as cofactor like other type II
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Kaas, R.S.
AU  - Mordhorst, H.
AU  - Leekitcharoenphon, P.
AU  - Dyring, J.J.
AU  - Haagensen, J.A.J.
AU  - Molin, S.
AU  - Pamp, S.J.
TI  - Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions.
JO  - Genome Announcements
PY  - 2017
SP  - e00155
EP  - e00117
VL  - 5
AB  - Acinetobacter johnsonii C6 originates from creosote-polluted groundwater and performs
AB  - ecological and evolutionary interactions with Pseudomonas putida in
AB  - biofilms. The draft genome of A. johnsonii C6 is 3.7 Mbp and was shaped by mobile
AB  - genetic elements. It reveals genes facilitating the biodegradation of aromatic
AB  - hydrocarbons and resistance to antimicrobials and metals.
ER  -

TY  - JOUR
AU  - Kabisch, J.
AU  - Thurmer, A.
AU  - Hubel, T.
AU  - Popper, L.
AU  - Daniel, R.
AU  - Schweder, T.
TI  - Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host.
JO  - J. Biotechnol.
PY  - 2013
SP  - 97
EP  - 104
VL  - 163
AB  - The genome sequence of Bacillus subtilis ATCC 6051 and its suitability as an
AB  - expression host for recombinant protein production was determined. The comparison
AB  - of this undomesticated wild type with the widely used laboratory strain B.
AB  - subtilis 168 reveals a high degree of congruency between the two strains.
AB  - Differences could only be detected on the level of point mutations or small
AB  - insertions. B. subtilis ATCC 6051 shows none of the auxotrophies known for B.
AB  - subtilis 168 and is able to produce polyketides. It exhibits better use of
AB  - complex media and higher genomic stability through reduced natural competence.
AB  - Consequently, B. subtilis ATCC 6051 was genetically modified to yield an
AB  - optimized strain for the production of heterologously expressed proteins under
AB  - control of an acetoin-inducible promoter.
ER  -

TY  - JOUR
AU  - Kachalova, G.S.
AU  - Artyukh, R.I.
AU  - Lavrova, N.V.
AU  - Ryazanova, E.M.
AU  - Karyagina, A.S.
AU  - Kubareva, E.A.
AU  - Bartunik, H.D.
TI  - Crystallization and preliminary crystallographic analysis of the (cytosine-5)-DNA methyltransferase NlaX from Neisseria lactamica.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2005
SP  - 852
EP  - 854
VL  - 61
AB  - Crystals of the (cytosine-5)-DNA methyltransferase NlaX from Neisseria lactamica (molecular
AB  - weight 36.5 kDa) have been grown at 291 K using 2.5 M NaCl as precipitant.  The crystals
AB  - diffract to 3.0 A resolution at 100 K.  The crystals belong to space group P321, with
AB  - unit-cell parameters a = 121.98, b = 121.98, c = 56.71 A.  There is one molecule in the
AB  - asymmetric unit and the solvent content is estimated to be 62.1% by volume.
ER  -

TY  - JOUR
AU  - Kachalova, G.S.
AU  - Rogulin, E.A.
AU  - Artyukh, R.I.
AU  - Perevyazova, T.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
AU  - Bartunik, H.D.
TI  - Crystallization and preliminary crystallographic analysis of the site-specific DNA nickase Nb.BspD6I.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2005
SP  - 332
EP  - 334
VL  - 61
AB  - Crystals of site-specific DNA nickase Nb.BspD6I (of molecular weight 70.8 kDa) have been grown
AB  - at 291 K using PEG 8000 as precipitant. The
AB  - diffraction pattern of the crystal extends to 3.3 A resolution at 100 K.
AB  - The crystal belongs to space group P2(1), with unit-cell parameters a =
AB  - 57.76, b = 90.67, c = 71.71, beta = 110.1 degrees. There is one molecule
AB  - in the asymmetric unit and the solvent content is estimated to be 53% by
AB  - volume.
ER  -

TY  - JOUR
AU  - Kachalova, G.S.
AU  - Rogulin, E.A.
AU  - Yunusova, A.K.
AU  - Artyukh, R.I.
AU  - Perevyazova, T.A.
AU  - Matvienko, N.I.
AU  - Zheleznaya, L.A.
AU  - Bartunik, H.D.
TI  - Structural Analysis of the Heterodimeric Type IIS Restriction Endonuclease R.BspD6I Acting as a Complex between a Monomeric Site-specific Nickase and  a Catalytic Subunit.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 489
EP  - 502
VL  - 384
AB  - The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a
AB  - pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large
AB  - subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The
AB  - isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We
AB  - solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I
AB  - consists of three domains, two of which exhibit structural similarity to the recognition and
AB  - cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of
AB  - Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative
AB  - catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain
AB  - is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and
AB  - cleavage domains in favorable orientations for interactions with DNA. Docking models of
AB  - complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of
AB  - structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle
AB  - forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations
AB  - of the spatially separated domains to match the distance between the recognition and cleavage
AB  - sites accurately.
ER  -

TY  - JOUR
AU  - Kachalova, G.S.
AU  - Yunusova, A.K.
AU  - Artyukh, R.I.
AU  - Rogulin, E.A.
AU  - Perevyazova, T.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
AU  - Bartunik, H.D.
TI  - Crystallization and preliminary x-ray diffraction analysis of the small subunit of the heterodimeric restriction endonuclease R.BspD6I.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2007
SP  - 795
EP  - 797
VL  - 63
AB  - The heterodimeric restriction endonuclease R.BspD6I is composed of a small subunit with a
AB  - cleavage site and a large subunit, containing a recognition domain and a cleavage domain, that
AB  - may function separately as a monomeric nicking endonuclease.  Here, the crystallization of the
AB  - small subunit and diffraction data collection to 1.5 A resolution are reported.
ER  -

TY  - JOUR
AU  - Kaczorowski, T.
AU  - Sektas, M.
AU  - Skowron, P.
AU  - Podhajska, A.J.
TI  - The FokI methyltransferase from Flavobacterium okeanokoites - Purification and characterization of the enzyme and its truncated derivatives.
JO  - Mol. Biotechnol.
PY  - 1999
SP  - 1
EP  - 15
VL  - 13
AB  - The gene encoding the FokI methyltransferase from Flavobacterium okeanokoites was cloned into
AB  - an Escherichia coli vector. The
AB  - transcriptional start sites were mapped as well as putative -10 and -35
AB  - regions of the fokIM promoter. Enzyme overproduction was ensured by
AB  - cloning the fokIM gene under the phi 10 promoter of phage T7. M.FokI
AB  - was purified using a two-step chromatography procedure. M.FokI is a
AB  - monomeric protein with an Mr = 76,000 +/- 1,500 under denaturing
AB  - conditions. It contains 21 Arg residues, at least one of which is
AB  - required for activity as shown by inhibition using 2,3-butanedione.
AB  - Deletion mutants in the N- and C-terminus of M.FokI were isolated and
AB  - characterized. The N-terminal derivative (M.FokIN) methylates the
AB  - adenine residue within the sequence 5'-GGATG-3', whereas the C-terminal
AB  - derivative (M.FokIC) modifies the adenine residue within the sequence
AB  - 5'-CATCC-3'. Substrate-protection studies, utilizing chemical
AB  - modification combined with data on the effect of divalent cations and
AB  - pH on methylation activity, proved the existence of two catalytic
AB  - centers within the FokI methyltransferase molecule. M.FokI and its
AB  - truncated derivatives require S-adenosyl-L-methionine as the
AB  - methyl-group donor, and they are strongly inhibited by divalent cations
AB  - (Mg2+, Ca2+, Ba2+, Mn2+ and Zn2+) and S-adenosyl-L-homocysteine. The
AB  - Km values for the methyl donor, S-adenosyl-L-methionine are 0.6 microM
AB  - (M.FokI), 0.3 microM (M.FokIN), and 0.9 microM (M.FokIC) while the Km
AB  - values for substrate lambda DNA are 1.2 nM (M.FokI): 1.4 nM (M.FokIN),
AB  - and 1.3 nM (M.FokIC).
ER  -

TY  - JOUR
AU  - Kaczorowski, T.
AU  - Skowron, P.
AU  - Podhajska, A.J.
TI  - Purification and characterization of the FokI restriction endonuclease.
JO  - Gene
PY  - 1989
SP  - 209
EP  - 216
VL  - 80
AB  - The restriction endonuclease FokI from Flavobacterium okeanokoites was purified
AB  - to homogeneity.  Based on gel filtration, sedimentation and sodium dodecyl
AB  - sulfate-polyacrylamide-gel electrophoresis, the following properties of the
AB  - enzyme were determined:  FokI exists in one active monomeric form, and has an
AB  - Mr of 64,000-65,400.  FokI is a strongly basic protein with an isoelectric
AB  - point of 9.4.  The enzyme exhibits restriction activity in the pH range 5.0 to
AB  - 10.5 (maximum level at pH 7.0-8.5) and its divalent cation requirement is
AB  - satisfied not only by Mg2+, but also by Co2+, Mn2+, Ni2+, Cd2+, Zn2+ and Fe2+.
ER  -

TY  - JOUR
AU  - Kaddurah-Daouk, R.
AU  - Cho, P.
AU  - Smith, H.O.
TI  - Catalytic properties of the HhaII restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 15345
EP  - 15351
VL  - 260
AB  - The catalytic properties of the HhaII restriction endonuclease were studied
AB  - using plasmid pSK11 DNA containing a single 5'-G-A-N-T-C HhaII cleavage site as
AB  - substrate.  Reactions were followed by two methods: 1) gel electrophoretic
AB  - analysis of nicked circular and linear DNA products, or 2) release of
AB  - 32P-labeled inorganic phosphate from specifically labeled HhaII sites in a
AB  - reaction coupled with bacterial alkaline phosphatase.  The enzyme is optimally
AB  - active at 37C in 10 mM Tris-HCl (pH 9.1) and 4-10 mM MgCl2 without added NaCl.
AB  - Activity is stabilized by the presence of 2-mercaptoethanol and 0.2% Triton
AB  - X-100 or 50 lg/ml bovine serum albumin.  At enzyme concentrations below 10 nM
AB  - and using pSK11 as substrate, initial kinetic rates were dependent on the order
AB  - of mixing of reactants.  A lag of 3-4 min was observed if enzyme or substrate
AB  - was added last.  Preincubation of substrate and enzyme followed by initiation
AB  - of the reaction with MgCl2 or preincubation of the enzyme with nonspecific DNA
AB  - followed by initiation with substrate eliminated or reduced the lag,
AB  - respectively, and speeded up the reactions.  Under a wide range of reaction
AB  - conditions, nicked pSK11 DNA accumulated early, while linear molecules appeared
AB  - later, suggesting that HhaII cleaves one strand at a time in separate binding
AB  - events.  The apparent Km for covalently closed pSK11 DNA molecules was
AB  - approximately 17 nM, and the turnover number for the conversion of covalent to
AB  - nicked sites was 1.1 single strand scissions/min.  Pre-steady state kinetic
AB  - analysis indicated that cleavage of the first phosphodiester bond in a site is
AB  - first order with a rate constant of about 0.8 min-1, while cleavage of the
AB  - second phosphodiester bond is first order with a rate constant of about 0.2
AB  - min-1.
ER  -

TY  - JOUR
AU  - Kaden, R.
AU  - Agren, J.
AU  - Ferrari, S.
AU  - Lindberg, M.
AU  - Backman, S.
AU  - Wahab, T.
TI  - Whole-Genome Sequence of Brucella canis Strain SVA13, Isolated from an Infected Dog.
JO  - Genome Announcements
PY  - 2014
SP  - e00700
EP  - e00714
VL  - 2
AB  - An outbreak of canine brucellosis in Sweden was confirmed by the National Veterinary Institute
AB  - (SVA) in August 2013. The whole genome of the causative
AB  - agent was sequenced, assembled, and analyzed.
ER  -

TY  - JOUR
AU  - Kadyrov, F.A.
AU  - Kaliman, A.V.
AU  - Kriukov, V.M.
TI  - SegE endonuclease from phage T4. I. Cloning, expression and biochemical characteristics of endonuclease activity.
JO  - Mol. Biol. (Mosk)
PY  - 1996
SP  - 1096
EP  - 1106
VL  - 30
ER  -

TY  - JOUR
AU  - Kadyrov, F.A.
AU  - Kriukov, V.M.
AU  - Shliapnikov, M.G.
AU  - Baev, A.A.
TI  - SegE-a new site-specific endodeoxyribonuclease from bacteriophage T4.
JO  - Dokl. Akad. Nauk.
PY  - 1994
SP  - 404
EP  - 406
VL  - 339
ER  -

TY  - JOUR
AU  - Kadyrov, F.A.
AU  - Kryukov, V.M.
AU  - Shlyapnikov, M.G.
AU  - Baev, A.A.
TI  - SegE--a new site-specific endodeoxyribonuclease of bacteriophage T4.
JO  - Dokl. Biochem.
PY  - 1994
SP  - 145
EP  - 147
VL  - 339
AB  - Introns of group I were found in nuclear DNA of Tetrahymena, mitochondrial genomes of fungi,
AB  - genomes of cyanobacteria, archaebacteria and bacteriophages, particularly in the genome of
AB  - bacteriophage T4.  Most of these introns code for specific endonucleases that provide the
AB  - transfer of intron DNA into genes lacking introns by introducing double-strand breaks at the
AB  - sites of intron insertion.  Earlier, we determined the DNA nucleotide sequence of the region
AB  - of phage T4 hoc and uvsW genes containing an open reading frame (ORF205) designated as hoc2
AB  - gene.  The amino acid sequence of the product of this gene was shown to share a high degree of
AB  - homology with a site-specific endodeoxyribonuclease, SegA.  Subsequently, the gene was
AB  - classified with phage T4 genes coding for proteins, similar to endonucleases of group I
AB  - introns (seg), and termed segE.  The five members of the group (segA, segB, segC, segD, and
AB  - segE) are homologous to each other.
ER  -

TY  - JOUR
AU  - Kadyrov, F.A.
AU  - Shlyapnikov, M.G.
AU  - Kryukov, V.M.
TI  - A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages.
JO  - FEBS Lett.
PY  - 1997
SP  - 75
EP  - 80
VL  - 415
AB  - The bacteriophage T4 segE gene encoding site-specific endonuclease lies between the hoc.1 and
AB  - uvsW genes.  The similar region of T-even-related phage RB30 lacks the segE gene.  Here we
AB  - demonstrate that the phage T4 segE gene is inherited preferably by progeny of mixed infection
AB  - with RB30.  The preferred inheritance of the segE gene depends on its own expression and is
AB  - based on a non-reciprocal homologous recombination event providing the transfer of the gene
AB  - from the segE-containing to the segE-lacking allele.  The SegE endonuclease cleaves DNA in a
AB  - site located at the 5' end of the uvsW gene in the RB30 genome.  The T4 DNA is also cleaved
AB  - by the enzyme, but less efficiently.  The cleavage at the RB30 site appears to initiate the
AB  - observed conversion, which is stimulated by DNA homology and accompanied by co-conversion of
AB  - flanking markers.  Our findings provide a novel example of endonuclease-dependent generation
AB  - of genetic variation in prokaryotes.
ER  -

TY  - JOUR
AU  - Kafka, T.A.
AU  - Geissler, A.J.
AU  - Vogel, R.F.
TI  - Multiple Genome Sequences of Lactobacillus plantarum Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00654
EP  - e00617
VL  - 5
AB  - We report here the genome sequences of four Lactobacillus plantarum strains which vary in
AB  - surface hydrophobicity. Bioinformatic analysis, using additional genomes
AB  - of Lactobacillus plantarum strains, revealed a possible correlation between the
AB  - cell wall teichoic acid-type and cell surface hydrophobicity and provide the
AB  - basis for consecutive analyses.
ER  -

TY  - JOUR
AU  - Kafri, T.
AU  - Hershko, A.
AU  - Razin, A.
TI  - Probing CpG methylation at CACGTG with BbrPI restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2950
EP  - 2950
VL  - 21
AB  - The sequence CACGTG is known to be a recognition site for basic helix-loop-helix binding
AB  - proteins such as Max and Myc. This site is a common element which is present in the upstream
AB  - region of a variety of genes that participate in developmental processes. Being a
AB  - CpG-containing sequence, it is prone to methylation in vertebrates. It is therefore of
AB  - importance to probe for the status of methylation of this site since CpG modification
AB  - frequently affects protein binding. The restriction enzyme BbrPI has been shown to be
AB  - sensitive to cytosine methylation at this site. However, since the substrate used for BbrPI
AB  - digestion has been prepared by PCR with 5-methyldCTP replacing dCTP, it was impossible to
AB  - conclude whether methylation of the outer cytosine, the inner cytosine or both is required to
AB  - inhibit digestion by BbrPI. We, therefore, use here lambda DNA methylated in vitro by M.SssI
AB  - as substrate for BbrPI digestion. The Spiroplasma methylase, M.SssI, is known to methylate
AB  - exclusively CpG sequences. Therefore, only the inner cytosine residue in CACGTG is expected to
AB  - be methylated by M.SssI. The results shown in Figure 1 clearly indicate that methylation of
AB  - the inner cytosine residue in CACGTG is sufficient to inhibit digestion by BbrPI. It is
AB  - therefore possible to probe the status of methylation of this site in mammalian genomic DNA by
AB  - BbrPI digestion followed by Southern blotting. Such an analysis with digested DNA from various
AB  - tissues of the mouse revealed that a BbrPI site in the mouse homeobox gene HoxA5 is methylated
AB  - in a tissue-specific manner.
ER  -

TY  - JOUR
AU  - Kahng, L.S.
AU  - Shapiro, L.
TI  - The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated.
JO  - J. Bacteriol.
PY  - 2001
SP  - 3065
EP  - 3075
VL  - 183
AB  - DNA methylation is now recognized as a regulator of multiple bacterial cellular processes.
AB  - CcrM is a DNA adenine methyltransferase found in
AB  - the alpha subdivision of the proteobacteria. Like the Dam enzyme, which
AB  - is found primarily in Escherichia coli and other gamma proteobacteria,
AB  - it does not appear to be part of a DNA restriction-modification system.
AB  - The CcrM homolog of Agrobacterium tumefaciens was found to be essential
AB  - for viability. Overexpression of CcrM is associated with significant
AB  - abnormalities of cell morphology and DNA ploidy. Mapping of the
AB  - transcriptional start site revealed a conserved binding motif for the
AB  - global response regulator CtrA at the -35 position; this motif was
AB  - footprinted by purified Caulobacter crescentus CtrA protein in its
AB  - phosphorylated state. We have succeeded in isolating synchronized
AB  - populations of Agrobacterium cells and analyzing their progression
AB  - through the cell cycle. We demonstrate that DNA replication and cell
AB  - division can be followed in an orderly manner and that flagellin
AB  - expression is cyclic, consistent with our observation that motility
AB  - varies during the cell cycle. Using these synchronized populations, we
AB  - show that CcrM methylation of the chromosome is restricted to the late
AB  - S phase of the cell cycle. Thus, within the alpha subdivision, there is
AB  - a conserved cell cycle dependence and regulatory mechanism controlling
AB  - ccrM expression.
ER  -

TY  - JOUR
AU  - Kahramanoglou, C.
AU  - Prieto, A.I.
AU  - Khedkar, S.
AU  - Haase, B.
AU  - Gupta, A.
AU  - Benes, V.
AU  - Fraser, G.M.
AU  - Luscombe, N.M.
AU  - Seshasayee, A.S.N.
TI  - Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
JO  - Nat. Commun.
PY  - 2012
SP  - 886
EP  - 886
VL  - 3
AB  - DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene
AB  - expression and genome architecture is less
AB  - understood. Here we perform high-throughput sequencing of
AB  - bisulfite-treated genomic DNA from Escherichia coli K12 to describe,
AB  - for the first time, the extent of cytosine methylation of bacterial DNA
AB  - at single-base resolution. Whereas most target sites (C(m)CWGG) are
AB  - fully methylated in stationary phase cells, many sites with an extended
AB  - CC(m)CWGG motif are only partially methylated in exponentially growing
AB  - cells. We speculate that these partially methylated sites may be
AB  - selected, as these are slightly correlated with the risk of
AB  - spontaneous, non-synonymous conversion of methylated cytosines to
AB  - thymines. Microarray analysis in a cytosine methylation-deficient
AB  - mutant of E. coli shows increased expression of the stress response
AB  - sigma factor RpoS and many of its targets in stationary phase. Thus,
AB  - DNA cytosine methylation is a regulator of stationary phase gene
AB  - expression in E. coli.
ER  -

TY  - JOUR
AU  - Kairov, U.
AU  - Kozhamkulov, U.
AU  - Molkenov, A.
AU  - Rakhimova, S.
AU  - Askapuli, A.
AU  - Zhabagin, M.
AU  - Akhmetova, A.
AU  - Yerezhepov, D.
AU  - Abilova, Z.
AU  - Abilmazhinova, A.
AU  - Bismilda, V.
AU  - Chingisova, L.
AU  - Zhumadilov, Z.
AU  - Akilzhanova, A.
TI  - Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e00466
EP  - e00415
VL  - 3
AB  - Here, we report the draft genome sequences of two clinical isolates of Mycobacterium
AB  - tuberculosis (MTB-476 and MTB-489) isolated from sputum of Kazakh
AB  - patients.
ER  -

TY  - JOUR
AU  - Kajala, K.
AU  - Coil, D.A.
AU  - Brady, S.M.
TI  - Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834.
JO  - Genome Announcements
PY  - 2014
SP  - e01108
EP  - e01114
VL  - 2
AB  - Here, we present the draft genome of Rhizobium rhizogenes strain ATCC 15834. The  genome
AB  - contains 7,070,307 bp in 43 scaffolds. R. rhizogenes, also known as
AB  - Agrobacterium rhizogenes, is a plant pathogen that causes hairy root disease.
AB  - This hairy root induction has been used in biotechnology for the generation of
AB  - transgenic root cultures.
ER  -

TY  - JOUR
AU  - Kakinuma, S.
AU  - Ikeda, H.
AU  - Tanaka, H.
AU  - Omura, S.
TI  - Isolation of restriction-reduced mutants from Streptomyces.
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 2611
EP  - 2617
VL  - 54
AB  - Restriction-reduced mutants were isolated from Streptomyces rosa subsp.
AB  - notoensis KA301 and S. tanashiensis strain Kala which produce the
AB  - benzoisochromanequinone antibiotics nanaomycin and kalafungin, respectively.
AB  - The mutants of S. rosa, which can be transformed with a multi-copy plasmid and
AB  - in which the actinophage Pa16 can propagate, were selected.  They were
AB  - transformed with a single-copy plasmid propagated in S. lividans TK24, and with
AB  - its modified plasmid propagated in the mutant at higher efficiency.  The
AB  - mutants of S. tanashiensis were selected by their capability to be transformed
AB  - with a multi-copy plasmid.  The efficiency of transformation with a single-copy
AB  - plasmid propagated in S. lividans TK24 was low, but was much increased by
AB  - heating the protoplasts at 42C for 15 min prior to the transformation.  These
AB  - mutants derived from both strains probably lack at least one of their
AB  - restriction systems.
ER  -

TY  - JOUR
AU  - Kakizawa, S.
AU  - Makino, A.
AU  - Ishii, Y.
AU  - Tamaki, H.
AU  - Kamagata, Y.
TI  - Draft Genome Sequence of 'Candidatus Phytoplasma asteris' Strain OY-V, an Unculturable Plant-Pathogenic Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00944
EP  - e00914
VL  - 2
AB  - Phytoplasmas are unculturable plant-pathogenic bacteria causing devastating damage to
AB  - agricultural production worldwide. Here, we report the draft genome
AB  - sequence of 'Candidatus Phytoplasma asteris' strain OY-V. Most of the known
AB  - virulence factors and host-interacting proteins were conserved in OY-V. This
AB  - genome furthers our understanding of genetic diversity and pathogenicity of
AB  - phytoplasmas.
ER  -

TY  - JOUR
AU  - Kakutani, T.
AU  - Jeddeloh, J.A.
AU  - Richards, E.J.
TI  - Characterization of an Arabidopsis thaliana DNA hypomethylation mutant.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 130
EP  - 137
VL  - 23
AB  - We have recently isolated two Arabidopsis thaliana DNA hypomethylation mutations, identifying
AB  - the DDM1 locus, that cause a 70% reduction in genomic 5-methylcytosine levels. Here we
AB  - describe further phenotypic and biochemical characterization of the ddm1 mutants. ddm1/ddm1
AB  - homozygotes exhibited altered leaf shape, increased cauline leaf number, and a delay in the
AB  - onset of flowering when compared to non-mutant siblings in a segregating population. Our
AB  - biochemical characterization investigated two possible mechanisms for DNA hypomethylation. In
AB  - order to see if ddm1 mutations affect DNA methyltransferase function, we compared DNA
AB  - methyltransferase activities in extracts from wild-type for both the CpI and CpNpG substrates
AB  - suggesting that the DDM1 locus does not encode a DNA methyltransferase. Moreover, the ddm1
AB  - mutations did not affect the intracellular level of S-adenosylmethionine, the methyl group
AB  - donor for DNA methylation. The possibility that the DDM1 gene product functions as a modifier
AB  - of DNA methylation is discussed.
ER  -

TY  - JOUR
AU  - Kalamorz, F. et al.
TI  - Draft Genome Sequence of the Thermoalkaliphilic Caldalkalibacillus thermarum Strain TA2.A1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4290
EP  - 4291
VL  - 193
AB  - The genes and molecular machines that allow for a thermoalkaliphilic lifestyle have not been
AB  - defined. To address this goal, we report on the
AB  - improved high-quality draft genome sequence of Caldalkalibacillus
AB  - thermarum strain TA2.A1, an obligately aerobic bacterium that grows
AB  - optimally at pH 9.5 and 65 to 70 degrees C on a wide variety of carbon and
AB  - energy sources.
ER  -

TY  - JOUR
AU  - Kalburge, S.S.
AU  - Polson, S.W.
AU  - Boyd, C.K.
AU  - Katz, L.
AU  - Turnsek, M.
AU  - Tarr, C.L.
AU  - Martinez-Urtaza, J.
AU  - Boyd, E.F.
TI  - Complete Genome Sequence of Vibrio parahaemolyticus Environmental Strain UCM-V493.
JO  - Genome Announcements
PY  - 2014
SP  - e00159
EP  - e00114
VL  - 2
AB  - Vibrio parahaemolyticus is the leading bacterial cause of seafood-related gastroenteritis in
AB  - the world. Here, we report the complete genome sequence and
AB  - annotation of an environmental strain of V. parahaemolyticus, UCM-V493, with the
AB  - aim of understanding the differences between the clinical and environmental
AB  - isolates of the bacteria. We also make some preliminary sequence comparisons with
AB  - the clinical strain RIMD2210633.
ER  -

TY  - JOUR
AU  - Kaldhone, P.R.
AU  - Khajanchi, B.K.
AU  - Han, J.
AU  - Nayak, R.
AU  - Ricke, S.C.
AU  - Foley, S.L.
TI  - Draft Genome Sequences of Salmonella enterica Isolates Containing Incompatibility Group I1 Plasmids from Swine, Poultry, and Human Sources.
JO  - Genome Announcements
PY  - 2017
SP  - e01056
EP  - e01017
VL  - 5
AB  - The draft genome sequences of eight Salmonella enterica isolates from various sources were
AB  - evaluated for the influence of incompatibility group I1 (IncI1)
AB  - plasmids on virulence. Strains SE142, SE143, SE144, and SE146 originated from
AB  - swine, SE36N and SE89N from poultry-related sources, and SE991 and SE1148 from
AB  - human patients.
ER  -

TY  - JOUR
AU  - Kaleta, P.
AU  - O'Callaghan, J.
AU  - Fitzgerald, G.F.
AU  - Beresford, T.P.
AU  - Ross, R.P.
TI  - Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 212
EP  - 220
VL  - 76
AB  - Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous
AB  - genotypes depending on the ecosystem from which
AB  - it was isolated. The recently published genome sequence showed the
AB  - remarkable flexibility of its structure, demonstrated by a substantial
AB  - level of insertion sequence (IS) element expansion in association with
AB  - massive gene decay. To assess this diversity and examine the level of
AB  - genome plasticity within the L. helveticus species, an array-based
AB  - comparative genome hybridization (aCGH) experiment was designed in
AB  - which 10 strains were analyzed. The aCGH experiment revealed 16
AB  - clusters of open reading frames (ORFs) flanked by IS elements. Four of
AB  - these ORFs are associated with restriction/modification which may have
AB  - played a role in accelerated evolution of strains in a commercially
AB  - intensive ecosystem undoubtedly challenged through successive phage
AB  - attack. Furthermore, analysis of the IS-flanked clusters demonstrated
AB  - that the most frequently encountered ISs were also those most abundant
AB  - in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63).
AB  - These findings contribute to the overall viewpoint of the versatile
AB  - character of IS elements and the role they may play in bacterial genome
AB  - plasticity.
ER  -

TY  - JOUR
AU  - Kalhoefer, D.
AU  - Thole, S.
AU  - Voget, S.
AU  - Lehmann, R.
AU  - Liesegang, H.
AU  - Wollher, A.
AU  - Daniel, R.
AU  - Simon, M.
AU  - Brinkhoff, T.
TI  - Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.
JO  - BMC Genomics
PY  - 2011
SP  - 324
EP  - 324
VL  - 12
AB  - ABSTRACT: BACKGROUND: Roseobacter litoralis OCh149, the type species of
AB  - the genus, and Roseobacter denitrificans OCh114 were the first described
AB  - organisms of the Roseobacter clade, an ecologically important group of
AB  - marine bacteria. Both species were isolated from seaweed and are able to
AB  - perform aerobic anoxygenic photosynthesis. RESULTS: The genome of R.
AB  - litoralis OCh149 contains one circular chromosome of 4,505,211 bp and
AB  - three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and
AB  - 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122
AB  - (24.7%) are not present in the genome of R. denitrificans. Many of the
AB  - unique genes of R. litoralis are located in genomic islands and on
AB  - plasmids. On pRLO149_83 several potential heavy metal resistance genes are
AB  - encoded which are not present in the genome of R. denitrificans. The
AB  - comparison of the heavy metal tolerance of the two organisms showed an
AB  - increased zinc tolerance of R. litoralis. In contrast to R. denitrificans,
AB  - the photosynthesis genes of R. litoralis are plasmid encoded. The activity
AB  - of the photosynthetic apparatus was confirmed by respiration rate
AB  - measurements, indicating a growth-phase dependent response to light.
AB  - Comparative genomics with other members of the Roseobacter clade revealed
AB  - several genomic regions that were only conserved in the two Roseobacter
AB  - species. One of those regions encodes a variety of genes that might play a
AB  - role in host association of the organisms. The catabolism of different
AB  - carbon and nitrogen sources was predicted from the genome and combined
AB  - with experimental data. In several cases, e.g. the degradation of some
AB  - algal osmolytes and sugars, the genome-derived predictions of the
AB  - metabolic pathways in R. litoralis differed from the phenotype.
AB  - CONCLUSIONS: The genomic differences between the two Roseobacter species
AB  - are mainly due to lateral gene transfer and genomic rearrangements.
AB  - Plasmid pRLO149_83 contains predominantly recently acquired genetic
AB  - material whereas pRLO149_94 was probably translocated from the chromosome.
AB  - Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have
AB  - a common ancestor and are important for cell envelope biosynthesis.
AB  - Several new mechanisms of substrate degradation were indicated from the
AB  - combination of experimental and genomic data. The photosynthetic activity
AB  - of R. litoralis is probably regulated by nutrient availability.
ER  -

TY  - JOUR
AU  - Kaliman, A.V.
AU  - Khasanova, M.A.
AU  - Kryukov, V.M.
AU  - Tanyashin, V.I.
AU  - Baev, A.A.
TI  - Cloning and study of the structural organization of the region of inh(lip)-hoc genes of T4 bacteriophage.
JO  - Dokl. Akad. Nauk.
PY  - 1988
SP  - 1486
EP  - 1489
VL  - 303
AB  - The cells infected with T-even bacteriophages have been demonstrated to carry early and late
AB  - phage-specific mRNA.  It has been established that the early genes are transcribed from the
AB  - l-strand of DNA in anticlockwise direction, whereas the late genes are transcribed clockwise
AB  - in the r-strand of DNA in the genetic map of T4 phage.  A major part of late T4 phage genes is
AB  - located between genes 2 and 54, but the chromosomal segment between genes 24 and 25 contains,
AB  - besides the late genes inh and hoc, early (medium) genes uvsY and uvsW(dar).  The inh(lip)
AB  - codes for the inhibitor of proteinase, the product of gene 21.  This inhibitor, either in its
AB  - natural form or after modification with the help of genetic engineering techniques, is
AB  - particularly interesting for studying the mechanism of protein processing and for its possible
AB  - use in biotechnology analogous to the product of pin gene of T4 phage.  Gene hoc is promising
AB  - for making highly antigenic proteinous structures, which would be discussed below.
ER  -

TY  - JOUR
AU  - Kaliman, A.V.
AU  - Khasanova, M.A.
AU  - Kryukov, V.M.
AU  - Tanyashin, V.I.
AU  - Bayev, A.A.
TI  - The  nucleotide sequence of the region of bacteriophage T4 inh(lip)-hoc genes.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4277
EP  - 4277
VL  - 18
ER  -

TY  - JOUR
AU  - Kalimuddin, S.
AU  - Chen, S.L.
AU  - Lim, C.T.K.
AU  - Koh, T.H.
AU  - Tan, T.Y.
AU  - Kam, M.
AU  - Wong, C.W.
AU  - Mehershahi, K.S.
AU  - Chau, M.L.
AU  - Ng, L.C.
AU  - Tang, W.Y.
AU  - Badaruddin, H.
AU  - Teo, J.
AU  - Apisarnthanarak, A.
AU  - Suwantarat, N.
AU  - Ip, M.
AU  - Holden, M.T.G.
AU  - Hsu, L.Y.
AU  - Barkham, T.
TI  - 2015 Epidemic of Severe Streptococcus agalactiae Sequence Type 283 Infections in Singapore Associated With the Consumption of Raw Freshwater Fish: A Detailed Analysis of Clinical, Epidemiological, and Bacterial Sequencing Data.
JO  - Clin. Infect. Dis.
PY  - 2017
SP  - S145
EP  - S152
VL  - 64
AB  - Background: Streptococcus agalactiae (group B Streptococcus [GBS]) has not been
AB  - described as a foodborne pathogen. However, in 2015, a large outbreak of severe
AB  - invasive sequence type (ST) 283 GBS infections in adults epidemiologically linked
AB  - to the consumption of raw freshwater fish occurred in Singapore. We attempted to
AB  - determine the scale of the outbreak, define the clinical spectrum of disease, and
AB  - link the outbreak to contaminated fish. Methods: Time-series analysis was
AB  - performed on microbiology laboratory data. Food handlers and fishmongers were
AB  - screened for enteric carriage of GBS. A retrospective cohort study was conducted
AB  - to assess differences in demographic and clinical characteristics of patients
AB  - with invasive ST283 and non-ST283 infections. Whole-genome sequencing was
AB  - performed on human and fish ST283 isolates from Singapore, Thailand, and Hong
AB  - Kong. Results: The outbreak was estimated to have started in late January 2015.
AB  - Within the study cohort of 408 patients, ST283 accounted for 35.8% of cases.
AB  - Patients with ST283 infection were younger and had fewer comorbidities but were
AB  - more likely to develop meningoencephalitis, septic arthritis, and spinal
AB  - infection. Of 82 food handlers and fishmongers screened, none carried ST283.
AB  - Culture of 43 fish samples yielded 13 ST283-positive samples. Phylogenomic
AB  - analysis of 161 ST283 isolates from humans and fish revealed they formed a tight
AB  - clade distinguished by 93 single-nucleotide polymorphisms. Conclusions: ST283 is
AB  - a zoonotic GBS clone associated with farmed freshwater fish, capable of causing
AB  - severe disease in humans. It caused a large foodborne outbreak in Singapore and
AB  - poses both a regional and potentially more widespread threat.
ER  -

TY  - JOUR
AU  - Kalinin, V.N.
AU  - Lapaeva, I.A.
AU  - Lunin, V.G.
AU  - Skripkin, E.A.
AU  - Smirnov, V.D.
AU  - Tikchonenko, T.I.
TI  - Isolation of HindIII isoschizomeric restriction endonuclease from Bordetella bronchiseptica.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1986
SP  - 16
EP  - 19
VL  - 0
AB  - Site-specific restriction endonuclease BbrI has been found in bacteriophage resistant strain
AB  - B. bronchioseptica 4994.  The technique was elaborated for purification of BbrI to the stage
AB  - free of nuclease and phosphatase contamination.  The yield of purified enzyme is 6000-20,000
AB  - units per 10 g of biomass.  BbrI recognises and cleaves the same DNA sequence as HindIII with
AB  - the formation of four-nucleotide cohesive ends.  The simplicity of cultivation, security for
AB  - human, presence of the single restriction endonuclease and the high level of tis production
AB  - make B. bronchioseptica 4994 a promising producer of BbrI restriction endonuclease,
AB  - isoschizomeric to HindIII, for use in experimental practice and in industry.
ER  -

TY  - JOUR
AU  - Kalinowski, J. et al.
TI  - The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
JO  - J. Biotechnol.
PY  - 2003
SP  - 5
EP  - 25
VL  - 104
AB  - The complete genomic sequence of Corynebacterium glutamicum ATCC 13032, well-known in industry
AB  - for the production of amino acids, e.g. of
AB  - L-glutamate and L-lysine was determined. The C. glutamicum genome was
AB  - found to consist of a single circular chromosome comprising 3282708 base
AB  - pairs. Several DNA regions of unusual composition were identified that
AB  - were potentially acquired by horizontal gene transfer, e.g. a segment of
AB  - DNA from C. diphtheriae and a prophage-containing region. After automated
AB  - and manual annotation, 3002 protein-coding genes have been identified, and
AB  - to 2489 of these, functions were assigned by homologies to known proteins.
AB  - These analyses confirm the taxonomic position of C. glutamicum as related
AB  - to Mycobacteria and show a broad metabolic diversity as expected for a
AB  - bacterium living in the soil. As an example for biotechnological
AB  - application the complete genome sequence was used to reconstruct the
AB  - metabolic flow of carbon into a number of industrially important products
AB  - derived from the amino acid L-aspartate.
ER  -

TY  - JOUR
AU  - Kalischuk, M.
AU  - Hachey, J.
AU  - Kawchuk, L.
TI  - Complete Genome Sequence of Phytopathogenic Pectobacterium atrosepticum Bacteriophage Peat1.
JO  - Genome Announcements
PY  - 2015
SP  - e00760
EP  - e00715
VL  - 3
AB  - Pectobacterium atrosepticum is a common phytopathogen causing significant economic losses
AB  - worldwide. To develop a biocontrol strategy for this blackleg
AB  - pathogen of solanaceous plants, P. atrosepticum bacteriophage Peat1 was isolated
AB  - and its genome completely sequenced. Interestingly, morphological and sequence
AB  - analyses of the 45,633-bp genome revealed that phage Peat1 is a member of the
AB  - family Podoviridae and most closely resembles the Klebsiella pneumoniae
AB  - bacteriophage KP34. This is the first published complete genome sequence of a
AB  - phytopathogenic P. atrosepticum bacteriophage, and details provide important
AB  - information for the development of biocontrol by advancing our understanding of
AB  - phage-phytopathogen interactions.
ER  -

TY  - JOUR
AU  - Kallimanis, A. et al.
TI  - Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 123
EP  - 130
VL  - 4
AB  - Arthrobacter phenanthrenivorans is the type species of the genus, and is able to  metabolize
AB  - phenanthrene as a sole source of carbon and energy. A.
AB  - phenanthrenivorans is an aerobic, non-motile, and Gram-positive bacterium,
AB  - exhibiting a rod-coccus growth cycle which was originally isolated from a
AB  - creosote polluted site in Epirus, Greece. Here we describe the features of this
AB  - organism, together with the complete genome sequence, and annotation.
ER  -

TY  - JOUR
AU  - Kallimanis, A.
AU  - Karabika, E.
AU  - Mavromatis, K.
AU  - Lapidus, A.
AU  - Labutti, K.M.
AU  - Liolios, K.
AU  - Ivanova, N.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Velentzas, A.D.
AU  - Perisynakis, A.
AU  - Ouzounis, C.C.
AU  - Kyrpides, N.C.
AU  - Koukkou, A.I.
AU  - Drainas, C.
TI  - Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 144
EP  - 153
VL  - 5
AB  - Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site
AB  - in Greece. It was isolated by an enrichment method using pyrene
AB  - as sole carbon and energy source and is capable of degrading a wide range of PAH
AB  - substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene.
AB  - Here we describe the genomic features of this organism, together with the
AB  - complete sequence and annotation. The genome consists of a 5,547,747 bp
AB  - chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and
AB  - 23,681 bp, respectively. In total, 5,588 genes were predicted and annotated.
ER  -

TY  - JOUR
AU  - Kalman, S.
AU  - Mitchell, W.
AU  - Marathe, R.
AU  - Lammel, C.
AU  - Fan, J.
AU  - Hyman, R.W.
AU  - Olinger, L.
AU  - Grimwood, J.
AU  - Davis, R.W.
AU  - Stephens, R.S.
TI  - Comparative genomes of Chlamydia pneumoniae and C. trachomatis.
JO  - Nat. Genet.
PY  - 1999
SP  - 385
EP  - 389
VL  - 21
AB  - Chlamydia are obligate intracellular eubacteria that are phylogenetically separated from other
AB  - bacterial divisions. C. trachomatis and C. pneumoniae are both pathogens of humans but differ
AB  - in their tissue tropism and spectrum of diseases. C. pneumoniae is a newly recognized species
AB  - of Chlamydia that is a natural pathogen of humans, and causes pneumonia and bronchitis. In the
AB  - United States, approximately 10% of pneumonia cases and 5% of bronchitis cases are attributed
AB  - to C. pneumoniae infection. Chronic disease may result following respiratory-acquired
AB  - infection, such as reactive airway disease, adult-onset asthma and potentially lung cancer. In
AB  - addition, C. pneumoniae infection has been associated with atherosclerosis. C. trachomatis
AB  - infection causes trachoma, an ocular infection that leads to blindness, and sexually
AB  - transmitted diseases such as pelvic inflammatory disease, chronic pelvic pain, ectopic
AB  - pregnancy and epididymitis.  Although relatively little is known about C. trachomatis biology,
AB  - even less is known concerning C. pneumoniae. Comparison of the C. pneumoniae genome with the
AB  - C. trachomatis genome will provide an understanding of the common biological processes
AB  - required for infection and survival in mammalian cells.  Genomic differences are implicated in
AB  - the unique properties that differentiate the two species in disease spectrum. Analysis of the
AB  - 1,230,230-nt C. pneumoniae genome revealed 214 protein-coding sequences not found in C.
AB  - trachomatis, most without homologues to other known sequences. Prominent comparative findings
AB  - include  expansion of a novel family of 21 sequence-variant outer-membrane proteins,
AB  - conservation of a type-III secretion virulence system, three serine/threonine protein kinases
AB  - and a pair of  parologous phospholipase-D-like proteins, additional purine and biotin
AB  - biosynthetic capability, a homologue for aromatic amino acid (tryptophan) hydroxylase and the
AB  - loss of tryptophan biosynthesis genes.
ER  -

TY  - JOUR
AU  - Kalman, T.I.
TI  - Glutathione-catalyzed hydrogen isotope exchange at position 5 of uridine.  A model for enzymic carbon alkylation reactions of pyrimidines.
JO  - Biochemistry
PY  - 1971
SP  - 2567
EP  - 2573
VL  - 10
AB  - The effect of glutathione on the exchange of hydrogen to deuterium at
AB  - position 5 of uridine
AB  - was studied by using proton magnetic resonance spectroscopy.  It was found that in D2O
AB  - solutions, at
AB  - 80o, the rate of H-isotope exchange was enhanced in the presence of GSH and that the
AB  - enhancement of
AB  - the pseudo-first-order rate of exchange was proportional to the GSH concentration.  The
AB  - results obtained
AB  - with GSH derivatives indicated the requirement of a free SH group for catalysis.  The
AB  - GSH-catalyzed H-
AB  - isotope exchange showed a bell-shaped dependence on the OD- ion concentration,
AB  - suggesting that in
AB  - the rate-determining step the ionized SH group of GSH reacts with the nonionized species
AB  - of Urd.
AB  - Ionization of Urd causes a substantial shielding of the proton at position 6, indicating the
AB  - increased
AB  - electron density of the 5,6-double bond, which may account for the lack of reactivity
AB  - observed at high pD
AB  - values.  The results are consistent with a catalytic mechanism of H-isotope exchange
AB  - involving the
AB  - reversible addition elimination of the SH group of GSH across the 5,6-double bond of
AB  - Urd.  The
AB  - relevance of these findings to the mechanism of enzyme-catalyzed C-alkylation reactions of
AB  - pyrimidine
AB  - nucleotides is discussed.
ER  -

TY  - JOUR
AU  - Kaloss, W.D.
AU  - Connaughton, J.F.
AU  - Vanek, P.G.
AU  - Chirikijan, J.G.
TI  - Characterization of overexpressed BamHII methylase.
JO  - FASEB J.
PY  - 1992
SP  - A217
EP  - A217
VL  - 6
AB  - Both M.BamHI and M.BamHII recognize the palindromic sequence, 5'-GGATCC-3', and
AB  - catalyze the transfer of a methyl group from S-adenosylmethionine to the
AB  - internal cytosine within the recognition sequence.  Both enzymes have been
AB  - cloned, sequenced and expressed in E. coli.  These two methylases utilize an
AB  - unusual UUG initiation codon and are expressed at limited levels.  We wish to
AB  - report increased expression by changing the initiation codon to AUG using the
AB  - site-directed mutagenesis.  Mutants were subcloned into various expression
AB  - vectors (pSP64, pKK223-3, pPL-Lambda and Pet-11) and sequenced via double
AB  - stranded dideoxy sequencing.  These constructs were transformed into the
AB  - appropriate host and protein production was assayed by SDS-PAGE.  Constructs
AB  - yielding the highest amount of intact protein were selected for subsequent
AB  - purification procedures.  M.BamHI (in pSP64) was purified to apparent
AB  - homogeneity from SURE cells by sequential chromatography using
AB  - Phosphocellulose, Phenyl Sepharose and G-150 as previously cited, (Vanek, P.G.,
AB  - Ph.D. Thesis, Georgetown University, 1991).  M.BamHII (in Pet-11) was purified
AB  - to apparent homogeneity from BL21DE3(pLysS) by sequential chromatography using
AB  - Phosphocellulose, Heparin Sepharose, Blue Sepharose and G-50.  The BamHII
AB  - methylase has an approximate Mw of 32 Kd as predicted from sequence analysis
AB  - and confirmed by SDS-PAGE analysis of the purified protein.  This low Mw
AB  - confers a unique advantage for further biochemical and structural studies.  To
AB  - date, the BamHII methylase has been partially characterized and further
AB  - biochemical and biophysical studies, including crystallization, are in
AB  - progress.
ER  -

TY  - JOUR
AU  - Kaloss, W.D.
AU  - Connaughton, J.F.
AU  - Vanek, P.G.
AU  - Chirikjian, J.C.
TI  - Characterization of overexpressed BamHII methylase.
JO  - Biophys. J.
PY  - 1992
SP  - A217
EP  - A217
VL  - 61
AB  - Both M.BamHI and M.BamHII recognize the palindromic sequence, 5'-GGATCC-3', and
AB  - catalyze the transfer of a methyl group from S-adenosylmethionine to the
AB  - internal cytosine within the recognition sequence.  Both enzymes have been
AB  - cloned, sequenced and expressed in E. coli.  These two methylases utilize an
AB  - unusual UUG initiation codon and are expressed at limited levels.  We wish to
AB  - report increased expression by changing the initiation codon to AUG using the
AB  - site-directed mutagenesis.  Mutants were subcloned into various expression
AB  - vectors (pSP64, pKK223-3, pPL-Lambda and Pet-11) and sequenced via double
AB  - stranded dideoxy sequencing.  These constructs were transformed into the
AB  - appropriate host and protein production was assayed by SDS-PAGE.  Constructs
AB  - yielding the highest amount of intact protein were selected for subsequent
AB  - purification procedures.  M.BamHI (in pSP64) was purified to apparent
AB  - homogeneity from SURE cells by sequential chromatography using
AB  - Phosphocellulose, Phenyl Sepharose and G-150 as previously cited, (Vanek, P.G.,
AB  - Ph.D. Thesis, Georgetown University, 1991).  M.BamHII (in Pet-11) was purified
AB  - to apparent homogeneity from BL21DE3(pLysS) by sequential chromatography using
AB  - Phosphocellulose, Heparin Sepharose, Blue Sepharose and G-50.  The BamHII
AB  - methylase has an approximate Mw of 32 kd as predicted from sequence analysis
AB  - and confirmed by SDS-PAGE analysis of the purified protein.  This low Mw
AB  - confers a unique advantage for further biochemical and structural studies.  To
AB  - date, the BamHII methylase has been partially characterized and further
AB  - biochemical and biophysical studies, including crystallization, are in
AB  - progress.
ER  -

TY  - JOUR
AU  - Kalugin, A.A.
AU  - Rina, M.
AU  - Eldarov, M.A.
AU  - Markaki, M.
AU  - Korolev, S.V.
AU  - Samko, O.T.
AU  - Khoroshutina, E.B.
AU  - Sikolov, N.N.
AU  - Bouriotis, V.
TI  - Bsp153AI and BspM39I - New isoschizomers of restriction endonuclease PvuII.
JO  - Bioorg. Khim.
PY  - 1996
SP  - 108
EP  - 110
VL  - 22
AB  - New restriction endonucleases, Bsp153AI and BspM39I, were isolated from
AB  - Bacillus species strains 153A and M39, respectively.  The enzymes recognize and cleave the
AB  - nucleotide sequence (5')CAG|CTG / (3')GTC|GAC and are true isoschizomers of restriction
AB  - endonuclease PvuII.
ER  -

TY  - JOUR
AU  - Kalyuzhnaya, M.G.
AU  - Lamb, A.E.
AU  - McTaggart, T.L.
AU  - Oshkin, I.Y.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Chistoserdova, L.
TI  - Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e00103
EP  - e00115
VL  - 3
AB  - The genomes of Methylosarcina lacus LW14(T) (=ATCC BAA-1047(T) = JCM 13284(T)), Methylobacter
AB  - sp. strain 21/22, Methylobacter sp. strain 31/32, Methylomonas sp.
AB  - strain LW13, Methylomonas sp. strain MK1, and Methylomonas sp. strain 11b were
AB  - sequenced and are reported here. All the strains are obligately methanotrophic
AB  - bacteria isolated from the sediment of Lake Washington.
ER  -

TY  - JOUR
AU  - Kamachi, K.
AU  - Sota, M.
AU  - Tamai, Y.
AU  - Nagata, N.
AU  - Konda, T.
AU  - Inoue, T.
AU  - Top, E.M.
AU  - Arakawa, Y.
TI  - Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1beta plasmids without accessory mobile elements.
JO  - Microbiology
PY  - 2006
SP  - 3477
EP  - 3484
VL  - 152
AB  - The complete 41 268 bp nucleotide sequence of the IncP-1beta plasmid pBP136 from the human
AB  - pathogen Bordetella pertussis, the primary aetiological agent of whooping cough, was
AB  - determined and analysed. This plasmid carried a total of 46 ORFs: 44 ORFs corresponding to the
AB  - genes in the conserved IncP-1beta backbone, and 2 ORFs similar to the XF1596 and XF1597 genes
AB  - with unknown function of the plant pathogen Xylella fastidiosa. Interestingly, pBP136 had no
AB  - accessory genes carrying genetic traits such as antibiotic or mercury resistance and/or
AB  - xenobiotic degradation. Moreover, pBP136 had only two of the kle genes (kleAE) that have been
AB  - reported to be important for the stability of IncP-1 plasmid in Pseudomonas aeruginosa.
AB  - Phylogenetic analysis of the Kle proteins revealed that the KleA and KleE of pBP136 were
AB  - phylogenetically distant from those of the present IncP-1 plasmids. In contrast, IncC1 and
AB  - KorC, encoded upstream and downstream of the kle genes respectively, and the
AB  - replication-initiation protein, TrfA, were closely related to those of the IncP-1beta 'R751
AB  - group'. These results suggest that (i) pBP136 without any apparent accessory genes diverged
AB  - early from an ancestor of the present IncP-1beta plasmids, especially those of the R751 group,
AB  - and (ii) the kle genes might be incorporated independently into the backbone region of the
AB  - IncP-1 plasmids for their stable maintenance in various host cells.
ER  -

TY  - JOUR
AU  - Kambarev, S.
AU  - Cate, C.
AU  - Corvec, S.
AU  - Pecorari, F.
TI  - Draft Genome Sequence of Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus NTS 31106099 Isolated from a Patient with Infective Endocarditis and  Colorectal Cancer.
JO  - Genome Announcements
PY  - 2015
SP  - e00370
EP  - e00315
VL  - 3
AB  - Streptococcus gallolyticus subsp. gallolyticus is known for its close association with
AB  - infective endocarditis and colorectal cancer in humans. Here, we report the
AB  - draft genome sequence of highly erythromycin-resistant strain NTS 31106099
AB  - isolated from a patient with infective endocarditis and colorectal cancer.
ER  -

TY  - JOUR
AU  - Kambarev, S.
AU  - Corvec, S.
AU  - Chauty, A.
AU  - Marion, E.
AU  - Marsollier, L.
AU  - Pecorari, F.
TI  - Draft Genome Sequence of Mycobacterium ulcerans S4018 Isolated from a Patient with an Active Buruli Ulcer in Benin, Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e00248
EP  - e00217
VL  - 5
AB  - Currently, there are only two publicly available genomes of Mycobacterium ulcerans-the
AB  - causative agent of the neglected, but devastating, tropical disease
AB  - Buruli ulcer. Here, we report the draft genome sequence of isolate S4018,
AB  - recovered from an active cutaneous lesion of a patient with Buruli ulcer in
AB  - Benin, Africa.
ER  -

TY  - JOUR
AU  - Kambarev, S.
AU  - Pecorari, F.
AU  - Corvec, S.
TI  - Draft Genome Sequences of Two Highly Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus Isolates Containing a Novel Tn916-Like Element,   Tn6331.
JO  - Genome Announcements
PY  - 2017
SP  - e00226
EP  - e00217
VL  - 5
AB  - Recently, we reported the draft genome sequence of Streptococcus gallolyticus NTS31106099. It
AB  - was found to contain a previously unknown putative Tn916-like
AB  - conjugative transposon, Tn6263 Here, we report the draft genome sequences of two
AB  - other clinical isolates, NTS31301958 and NTS31307655. Both of them contain
AB  - another novel element, Tn6331, which is highly similar to Tn6263.
ER  -

TY  - JOUR
AU  - Kameshita, I.
AU  - Sekiguchi, M.
AU  - Hamasaki, D.
AU  - Sugiyama, Y.
AU  - Hatano, N.
AU  - Suetake, I.
AU  - Tajima, S.
AU  - Sueyoshi, N.
TI  - Cyclin-dependent kinase-like 5 binds and phosphorylates DNA methyltransferase 1.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2008
SP  - 1162
EP  - 1167
VL  - 377
AB  - DNA methyltransferase 1 (Dnmt1) is an enzyme that recognizes and methylates hemimethylated CpG
AB  - after DNA replication to maintain methylation patterns. Although the N-terminal region of
AB  - Dnmt1 isknown to interact with various proteins, such as methyl-CpG-binding protein 2 (MeCP2),
AB  - the associationsof protein kinases with this region have not been reported. In the present
AB  - study, we found that a 110-kDaprotein kinase in mouse brain could bind to the N-terminal
AB  - domain of Dnmt1. This 110-kDa kinase was
AB  - identified as cyclin-dependent kinase-like 5 (CDKL5) by LC-MS/MS analysis. CDKL5 and Dnmt1
AB  - werefound to colocalize in nuclei and appeared to interact with each other. Catalytically
AB  - active CDKL5,CDKL5(1-352), phosphorylated the N-terminal region of Dnmt1 in the presence of
AB  - DNA. Considering thatdefects in the MeCP2 or CDKL5 genes cause Rett syndrome, we propose that
AB  - the interaction betweenDnmt1 and CDKL5 may contribute to the pathogenic processes of Rett
AB  - syndrome.
ER  -

TY  - JOUR
AU  - Kamimura, K.
AU  - Sharmin, S.
AU  - Yoshino, E.
AU  - Tokuhisa, M.
AU  - Kanao, T.
TI  - Draft Genome Sequence of Acidithiobacillus sp. Strain SH, a Marine Acidophilic Sulfur-Oxidizing Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e01603
EP  - e01617
VL  - 6
AB  - We announce here the genome sequence of a marine acidophilic sulfur-oxidizing bacterium,
AB  - Acidithiobacillus sp. strain SH. The bacterium has potential for use
AB  - in bioleaching of sulfide ores from seawater and contains a noble gene for
AB  - thiosulfate quinone oxidoreductase in addition to specific genes for the
AB  - oxidation of reduced inorganic sulfur compounds.
ER  -

TY  - JOUR
AU  - Kaminska, K.H.
AU  - Kawai, M.
AU  - Boniecki, M.
AU  - Kobayashi, I.
AU  - Bujnicki, J.M.
TI  - Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.
JO  - BMC Struct. Biol.
PY  - 2008
SP  - 48
EP  - 48
VL  - 8
AB  - Background: Catalytic domains of Type II restriction endonucleases (REases) belong to a few
AB  - unrelated three-dimensional folds. While the
AB  - PD-(D/E)XK fold is most common among these enzymes, crystal structures
AB  - have been also determined for single representatives of two other
AB  - folds: PLD (R. Bfil) and half-pipe (R. Pabl). Bioinformatics analyses
AB  - supported by mutagenesis experiments suggested that some REases belong
AB  - to the HNH fold (e. g. R. KpnI), and that a small group represented by
AB  - R. Eco29kl belongs to the GIY-YIG fold. However, for a large fraction
AB  - of REases with known sequences, the three-dimensional fold and the
AB  - architecture of the active site remain unknown, mostly due to extreme
AB  - sequence divergence that hampers detection of homology to enzymes with
AB  - known folds.
AB  - Results: R.Hpy188I is a Type II REase with unknown structure.
AB  - PSI-BLAST searches of the non-redundant protein sequence database
AB  - reveal only 1 homolog (R. HpyF17I, with nearly identical amino acid
AB  - sequence and the same DNA sequence specificity). Standard application
AB  - of state-of-the-art protein fold-recognition methods failed to predict
AB  - the relationship of R. Hpy188I to proteins with known structure or to
AB  - other protein families. In order to increase the amount of evolutionary
AB  - information in the multiple sequence alignment, we have expanded our
AB  - sequence database searches to include sequences from metagenomics
AB  - projects. This search resulted in identification of 23 further members
AB  - of R. Hpy188I family, both from metagenomics and the non-redundant
AB  - database. Moreover, fold-recognition analysis of the extended R.
AB  - Hpy188I family revealed its relationship to the GIY-YIG domain and
AB  - allowed for computational modeling of the R. Hpy188I structure.
AB  - Analysis of the R. Hpy188I model in the light of sequence conservation
AB  - among its homologs revealed an unusual variant of the active site, in
AB  - which the typical Tyr residue of the YIG half-motif had been
AB  - substituted by a Lys residue. Moreover, some of its homologs have the
AB  - otherwise invariant Arg residue in a non-homologous position in
AB  - sequence that nonetheless allows for spatial conservation of the
AB  - guanidino group potentially involved in phosphate binding.
AB  - Conclusion: The present study eliminates a significant "white spot"
AB  - on the structural map of REases. It also provides important insight
AB  - into sequence-structure-function relationships in the GIY-YIG nuclease
AB  - superfamily. Our results reveal that in the case of proteins with no or
AB  - few detectable homologs in the standard "non-redundant" database, it is
AB  - useful to expand this database by adding the metagenomic sequences,
AB  - which may provide evolutionary linkage to detect more remote homologs.
ER  -

TY  - JOUR
AU  - Kaminski, M.A.
AU  - Furmanczyk, E.M.
AU  - Dziembowski, A.
AU  - Sobczak, A.
AU  - Lipinski, L.
TI  - Draft Genome Sequence of the Type Strain Sphingopyxis witflariensis DSM 14551.
JO  - Genome Announcements
PY  - 2017
SP  - e00924
EP  - e00917
VL  - 5
AB  - Here, we present the draft genome sequence of Sphingopyxis witflariensis strain DSM 14551. The
AB  - assembly consists of 38 contigs and contains 4,306,761 bp, with a
AB  - GC content of 63.3%.
ER  -

TY  - JOUR
AU  - Kaminski, M.A.
AU  - Furmanczyk, E.M.
AU  - Dziembowski, A.
AU  - Sobczak, A.
AU  - Lipinski, L.
TI  - Draft Genome Sequence of the Type Strain Sphingopyxis bauzanensis DSM 22271.
JO  - Genome Announcements
PY  - 2017
SP  - e01014
EP  - e01017
VL  - 5
AB  - We present here the draft genome sequence of Sphingopyxis bauzanensis DSM 22271.  The assembly
AB  - contains 4,258,005 bp in 28 scaffolds and has a GC content of 63.3%.
AB  - A series of specific genes involved in the catabolism or transport of aromatic
AB  - compounds was identified.
ER  -

TY  - JOUR
AU  - Kamps-Hughes, N.
AU  - Quimby, A.
AU  - Zhu, Z.
AU  - Johnson, E.A.
TI  - Massively parallel characterization of restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - e119
EP  - e119
VL  - 41
AB  - Restriction endonucleases are highly specific in recognizing the particular DNA sequence they
AB  - act on. However, their activity is affected by sequence context, enzyme concentration and
AB  - buffer composition. Changes in these factors may lead to either ineffective cleavage at the
AB  - cognate restriction site or relaxed specificity allowing cleavage of degenerate 'star'
AB  - sites. Additionally, uncharacterized restriction endonucleases and engineered variants present
AB  - novel activities. Traditionally, restriction endonuclease activity is assayed on simple
AB  - substrates such as plasmids and synthesized oligonucleotides. We present and use
AB  - high-throughput Illumina sequencing-based strategies to assay the sequence specificity and
AB  - flanking sequence preference of restriction endonucleases. The techniques use fragmented DNA
AB  - from sequenced genomes to quantify restriction endonuclease cleavage on a complex genomic DNA
AB  - substrate in a single reaction. By mapping millions of restriction site-flanking reads back to
AB  - the Escherichia coli and Drosophila melanogaster genomes we were able to quantitatively
AB  - characterize the cognate and star site activity of EcoRI and MfeI and demonstrate genome-wide
AB  - decreases in star activity with engineered high-fidelity variants EcoRI-HF and MfeI-HF, as
AB  - well as quantify the influence on MfeI cleavage conferred by flanking nucleotides. The methods
AB  - presented are readily applicable to all type II restriction endonucleases that cleave both
AB  - strands of double-stranded DNA.
ER  -

TY  - JOUR
AU  - Kan, N.C.
AU  - Lautenberger, J.A.
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
TI  - The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 191
EP  - 209
VL  - 130
AB  - The sites recognized by the Escherichia coli K1 restriction endonuclease were
AB  - localized to defined regions on the genomes of phage PhiXsK1, PhiXsK2, and G4
AB  - by the marker rescue technique.  Methyl groups placed on the genome of plasmid
AB  - pBR322 by the E.coli K12 modification methylase were mapped in HinfI fragments
AB  - 1 and 3, and HaeIII fragments 1 and 3.  A homology of seven nucleotides in the
AB  - configuration: 5'-A-A-C . . 6N . . G-T-G-C-3', where 6N represents six
AB  - unspecified nucleotides, was found among the DNA sequences containing the five
AB  - EcoK sites of PhiXsK1, PhiXsK2, G4, and pBR322.  Three lines of evidence
AB  - indicate that this sequence constitutes the recognition site of the E.coli K12
AB  - restriction enzyme.  This sequence does not occur on PhiXam3cs70, simian virus
AB  - 40 (SV40), and fd DNAs which do not possess EcoK sites, and occurs only once on
AB  - PhiXsK1, PhiXsK2, and G4 DNAs, and twice on pBR322 DNA.  In order to prove that
AB  - all seven conserved nucleotides are essential for the recognition by the E.coli
AB  - K12 restriction enzyme, the nucleotide sequences of PhiX174, G4, SV40, fd, and
AB  - pBR322 were searched for sequences differing from the sequence 5'-A-A-C . . 6N
AB  - . . G-T-G-C-3' at only one of the specified positions.  It was found that
AB  - sequences differing at each of the specified positions occur on DNA sequences
AB  - that do not contain the EcoK sites.  Thus, the recognition site of the E.coli
AB  - K12 restriction enzyme has the same basic structure as that of the EcoB site
AB  - (Lautenberger et al., 1978).  In each case there are two domains, one
AB  - containing three and the other four specific nucleotides, separated by a
AB  - sequence of unspecified bases.  However, the unspecified sequence in the EcoK
AB  - site must be precisely six bases instead of the eight found in the EcoB site.
AB  - Alignment of the EcoK and EcoB sites suggests that four of the seven specified
AB  - nucleotides are conserved between the sequences recognized by these two allelic
AB  - restriction and modification systems.
ER  -

TY  - JOUR
AU  - Kan, N.C.
AU  - Lautenberger, J.A.
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
TI  - Recognition site of the Escherichia coli K restriction enzyme.
JO  - Fed. Proc.
PY  - 1978
SP  - 1499
EP  - 1499
VL  - 37
AB  - Two mutations of PhiX174 which confer sensitivity to restriction by E. coli K12
AB  - have been localized on the DNA sequence using the marker rescue technique.  The
AB  - sKI site lies between positions 817 and 953 while  sK2 lies between positions
AB  - 1780 and 1900 (as numbered by Sanger et al., 1977).  The sKI mutation results
AB  - in the loss of the HhaI site between fragments 11 and 14, while the sK2
AB  - mutation leads to loss of the HhaI site between fragments 9a and 8a.  Sequence
AB  - analysis of these two mutant DNAs compared with the PhiX174am3cs70 sequence
AB  - verifies this and shows a C5T change at position 874 on the + strand of sK1
AB  - DNA, and a G5A change at position 1867 on the + strand of sK2 DNA.  The
AB  - following alignment gives the most homology between these sites: 5'
AB  - TAAAAAACGTTCTGGTGCTCGC 3' (+ strand of sK1) 3' CGGAAAACGAACAAGTGCAAGA 3' (-
AB  - strand of sK2) Since GTGC occurs 24 times in the sequence of PhiX174am3cs70 RF
AB  - DNA, some other nucleotides must be involved in the recognition site, which is
AB  - most likely to be an interrupted sequence.  The EcoK site on G4 RF DNA is being
AB  - mapped.  Comparison between the G4 DNA sequence in this region and the two
AB  - sites on PhiX174 should further define the sequence recognized by the EcoK
AB  - restriction enzyme.
ER  -

TY  - JOUR
AU  - Kan, T.N.
AU  - Lin, L.
AU  - Chandrasegaran, S.
TI  - Cloning, sequencing, overproduction, and purification of M.CviBI (GANTC) methyltransferase from Chlorella virus NC-1A.
JO  - Gene
PY  - 1992
SP  - 1
EP  - 7
VL  - 121
AB  - We have cloned and sequenced the cvibIM gene from Chlorella virus NC-1A by selecting for the
AB  - modification phenotype. The modification gene was cloned on a 7-kb BamHI fragment inserted
AB  - into the BamHI site of the pUC13 plasmid. The cvibIM gene was localized at the 3' end of this
AB  - fragment. Sequencing of this region revealed a large open reading frame that codes for
AB  - methyltransferase (MTase: symbol M) (predicting 260 amino acids). M.CviBI (GANTC) aa sequence
AB  - is homologous to M.dam (GATC), M.DpnII (GATC) and M.T4 (GATC), and not so to M.HinfI (GANTC),
AB  - M.HhaII (GANTC), and M.DpnA (GATC). We also describe the use of the polymerase chain reaction
AB  - technique to alter transcriptonal and translational signals surrounding this gene so as to
AB  - achieve overexpression in Escherichia coli. This construct yields M.CviBI at 2-3% of the total
AB  - cellular protein. The MTase was purified by phosphocellulose, DEAE, and gel filtration
AB  - chromatography. Its size by SDS-PAGE is approximately 28 kDa, in good agreement with that
AB  - predicted from the nucleotide sequence.
ER  -

TY  - JOUR
AU  - Kanada, K.
AU  - Takeshita, K.
AU  - Suetake, I.
AU  - Tajima, S.
AU  - Nakagawa, A.
TI  - Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1.
JO  - J. Biochem. (Tokyo)
PY  - 2017
SP  - 271
EP  - 278
VL  - 162
AB  - In mammals, DNA methyltransferase 1 (DNMT1) is responsible for propagating the DNA methylation
AB  - pattern into the next generation through selective methylation of hemi-methylated CpG that
AB  - emerges just after replication, a process known as maintenance methylation. The T1505, which
AB  - is conserved among DNMT1s of vertebrates, in the catalytic domain of mouse DNMT1 forms the
AB  - hydrogen bond with the W1512, which is also conserved among vertebrates and one of the
AB  - essential residues in recognition of the 5-methylcytosine in hemi-methylated CpGs. However,
AB  - importance of the hydrogen bond between T1505 and W1512 is unknown. In this study, we
AB  - determined the crystal structure of mouse DNMT1(291-1620) that replaced T1505 with alanine
AB  - (DNMT1(291-1620)T1505A) and examined its DNA methylation activity in vitro. Although the
AB  - mutation lost the hydrogen bond between T1505 and W1512, the overall structure of
AB  - DNMT1(291-1620)T1505A remained almost identical with that of the wild type. Structural
AB  - stability and DNA methylation activity of DNMT1(291-1620)T1505A under physiological
AB  - temperature were lower than those of DNMT1(291-1620). T1505 is crucial on the DNA methylation
AB  - activity of DNMT1 through stabilizing its structure during ongoing round of DNA methylation.
ER  -

TY  - JOUR
AU  - Kanaras, A.G.
AU  - Wang, Z.X.
AU  - Hussain, I.
AU  - Brust, M.
AU  - Cosstick, R.
AU  - Bates, A.D.
TI  - Site-specific ligation of DNA-modified gold nanoparticles activated by the restriction enzyme StyI.
JO  - Small
PY  - 2007
SP  - 67
EP  - 70
VL  - 3
ER  -

TY  - JOUR
AU  - Kanda, K.
AU  - Nakashima, K.
AU  - Nagano, Y.
TI  - Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard.
JO  - Genome Announcements
PY  - 2015
SP  - e00710
EP  - e00715
VL  - 3
AB  - The genome sequence of Bacillus thuringiensis serovar tolworthi strain Pasteur Institute
AB  - Standard was determined. The genome consists of a 5.9-Mb chromosome and
AB  - eight plasmids, one of which is linear. The second largest plasmid (293 kb)
AB  - carries the genes encoding insecticidal proteins.
ER  -

TY  - JOUR
AU  - Kandavelou, K.
AU  - Mani, M.
AU  - Durai, S.
AU  - Chandrasegaran, S.
TI  - Engineering and applications of chimeric nucleases.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 413
EP  - 434
VL  - 14
AB  - Each human cell contains about 3x10^9 base pairs within its genome.  With the first sequence
AB  - of the human genome now available, biologists estimate that there are about 30,000-40,000
AB  - different genes within the genome.  This is fewer than originally anticipated, but still a
AB  - huge number.  These genes code for all of the human body's proteins.  Simple mutations within
AB  - the coding region of critical genes can lead to the formation of abnormal proteins, resulting
AB  - in disease phenotypes, premature death, or failure of an embryo to develop.  Furthermore,
AB  - mutations that affect the regulatory region of genes can result in aberrant gene expression
AB  - within cells, and give rise to cancer phenotypes.  The Holy Grail of the Human Genome Project
AB  - is Gene Therapy, that is, how genes might someday be used, modified, or even changed to
AB  - correct human disease.
ER  -

TY  - JOUR
AU  - Kanduri, C.
TI  - Restriction enzyme BstZ17I is sensitive to cytosine methylation.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 191
EP  - 193
VL  - 200
AB  - The cleavage patterns of a subset of restriction enzymes are blocked or impaired when a
AB  - methylated CpG is overlapped with either the 5' or 3' end of the canonical restriction site.
AB  - BstZ17I restriction endonuclease is a blunt-end cutter, which recognises the hexanucleotide
AB  - sequence GTA^TAC. In this report, I show that the BstZ17I restriction enzyme is sensitive to
AB  - cytosine methylation. Using both in vitro-methylated episomal plasmids and lambda DNA, I
AB  - demonstrate that the BstZ17I restriction enzyme is sensitive to cytosine methylation that
AB  - occurs 3' and/or 5' of the canonical recognition sequence.
ER  -

TY  - JOUR
AU  - Kane, P.M.
AU  - Yamashiro, C.T.
AU  - Wolczyk, D.F.
AU  - Neff, N.
AU  - Goebl, M.
AU  - Stevens, T.H.
TI  - Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase.
JO  - Science
PY  - 1990
SP  - 651
EP  - 657
VL  - 250
AB  - The TFP1 gene of the yeast Saccharomyces cerevisiae encodes two proteins: the 69-kilodalton
AB  - (kD) catalytic subunit of the vacuolar proton-translocating adenosine triphosphatase
AB  - (H+-ATPase) and a 50-kD protein. The 60-kD subunit is encoded by the 5' and 3' thirds of the
AB  - TFP1 coding region, whereas the 50-kD protein is encoded by the central third. Evidence is
AB  - presented that both the 60-kD and 50-kD proteins are obtained from a single translation
AB  - product that is cleaved to release the 50-kD protein and spliced to form the 69-kD subunit.
ER  -

TY  - JOUR
AU  - Kane, S.R.
AU  - Chakicherla, A.Y.
AU  - Chain, P.S.
AU  - Schmidt, R.
AU  - Shin, M.W.
AU  - Legler, T.C.
AU  - Scow, K.M.
AU  - Larimer, F.W.
AU  - Lucas, S.M.
AU  - Richardson, P.M.
AU  - Hristova, K.R.
TI  - Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1.
JO  - J. Bacteriol.
PY  - 2007
SP  - 1931
EP  - 1945
VL  - 189
AB  - Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely
AB  - metabolize the fuel oxygenate methyl tert-butyl
AB  - ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and
AB  - xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in
AB  - petroleum products. Whole-genome analysis of PM1 revealed an approximately
AB  - 4-Mb circular chromosome and an approximately 600-kb megaplasmid,
AB  - containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and
AB  - alkane degradation, metal resistance, and methylotrophy are encoded on the
AB  - chromosome. The megaplasmid contains an unusual t-RNA island, numerous
AB  - insertion sequences, and large repeated elements, including a 40-kb region
AB  - also present on the chromosome and a 29-kb tandem repeat encoding
AB  - phosphonate transport and cobalamin biosynthesis. The megaplasmid also
AB  - codes for alkane degradation and was shown to play an essential role in
AB  - MTBE degradation through plasmid-curing experiments. Discrepancies between
AB  - the insertion sequence element distribution patterns, the distributions of
AB  - best BLASTP hits among major phylogenetic groups, and the G+C contents of
AB  - the chromosome (69.2%) and plasmid (66%), together with comparative genome
AB  - hybridization experiments, suggest that the plasmid was recently acquired
AB  - and apparently carries the genetic information responsible for PM1's
AB  - ability to degrade MTBE. Comparative genomic hybridization analysis with
AB  - two PM1-like MTBE-degrading environmental isolates ( approximately 99%
AB  - identical 16S rRNA gene sequences) showed that the plasmid was highly
AB  - conserved (ca. 99% identical), whereas the chromosomes were too diverse to
AB  - conduct resequencing analysis. PM1's genome sequence provides a foundation
AB  - for investigating MTBE biodegradation and exploring the genetic regulation
AB  - of multiple biodegradation pathways in M. petroleiphilum and other
AB  - MTBE-degrading beta-proteobacteria.
ER  -

TY  - JOUR
AU  - Kaneda, M.
AU  - Okano, M.
AU  - Hata, K.
AU  - Sado, T.
AU  - Tsujimoto, N.
AU  - Li, E.
AU  - Sasaki, H.
TI  - Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting.
JO  - Nature
PY  - 2004
SP  - 900
EP  - 903
VL  - 429
AB  - Imprinted genes are epigenetically marked during gametogenesis so that they are exclusively
AB  - expressed from either the paternal or the maternal
AB  - allele in offspring. Imprinting prevents parthenogenesis in mammals and is
AB  - often disrupted in congenital malformation syndromes, tumours and cloned
AB  - animals. Although de novo DNA methyltransferases of the Dnmt3 family are
AB  - implicated in maternal imprinting, the lethality of Dnmt3a and Dnmt3b
AB  - knockout mice has precluded further studies. We here report the disruption
AB  - of Dnmt3a and Dnmt3b in germ cells, with their preservation in somatic
AB  - cells, by conditional knockout technology. Offspring from Dnmt3a
AB  - conditional mutant females die in utero and lack methylation and
AB  - allele-specific expression at all maternally imprinted loci examined.
AB  - Dnmt3a conditional mutant males show impaired spermatogenesis and lack
AB  - methylation at two of three paternally imprinted loci examined in
AB  - spermatogonia. By contrast, Dnmt3b conditional mutants and their offspring
AB  - show no apparent phenotype. The phenotype of Dnmt3a conditional mutants is
AB  - indistinguishable from that of Dnmt3L knockout mice, except for the
AB  - discrepancy in methylation at one locus. These results indicate that both
AB  - Dnmt3a and Dnmt3L are required for methylation of most imprinted loci in
AB  - germ cells, but also suggest the involvement of other factors.
ER  -

TY  - JOUR
AU  - Kanehara, K.
AU  - Minamisawa, K.
TI  - Complete Genome Sequence of Bradyrhizobium japonicum J5, Isolated from a Soybean  Nodule in Hokkaido, Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01619
EP  - e01616
VL  - 5
AB  - Soybean bradyrhizobia form root nodules on soybean plants and symbiotically fix N2 Strain J5
AB  - is phylogenetically far from well-known representatives within the
AB  - Bradyrhizobium japonicum linage. The complete genome showed the largest single
AB  - chromosomal (10.1 Mb) and symbiosis island (998 kb) among complete genomes of
AB  - soybean bradyrhizobia.
ER  -

TY  - JOUR
AU  - Kanekar, S.P.
AU  - Saxena, N.
AU  - Pore, S.D.
AU  - Arora, P.
AU  - Kanekar, P.P.
AU  - Dhakephalkar, P.K.
TI  - Draft Genome Sequence of Halostagnicola sp. A56, an Extremely Halophilic Archaeon Isolated from the Andaman Islands.
JO  - Genome Announcements
PY  - 2015
SP  - e01332
EP  - e01315
VL  - 3
AB  - The first draft genome of Halostagnicola sp. A56, isolated from the Andaman Islands is
AB  - reported here. The A56 genome comprises 3,178,490 bp in 26 contigs
AB  - with a G+C content of 60.8%. The genome annotation revealed that A56 could have
AB  - potential applications for the production of polyhydroxyalkanoate or bioplastics.
ER  -

TY  - JOUR
AU  - Kaneko, K.J.
AU  - Burke, J.M.
AU  - Kaplan, L.J.
TI  - The action of endonucleases and methylases:  Electrophoretic analysis of DNA restriction fragments.
JO  - J. Chem. Educ.
PY  - 1987
SP  - 274
EP  - 278
VL  - 64
AB  - The restriction endonucleases have played an essential role in the development
AB  - of the field of recombinant DNA technology.  These enzymes catalyze the
AB  - hydrolysis of double-stranded DNA with a high level of specificity to generate
AB  - a well-defined series of polynucleotides called restriction fragments.  The
AB  - sequence specificity has been employed to generate fragments for the
AB  - construction of recombinant DNA molecules and for DNA sequence analysis.  This
AB  - paper presents the procedures used in endonuclease digestion and the
AB  - electrophoretic analysis of the restriction fragments.  In fact, two related
AB  - experiments are outlined.  One involves the use of a restriction endonuclease
AB  - to generate a set of well-defined fragments which then may be used as molecular
AB  - weight standards for gel electrophoresis.  With this as an aid, the cleavage
AB  - pattern of the DNA with other endonucleases can be analyzed.  The second
AB  - experiment employs endonucleases to monitor the protection afforded the DNA
AB  - upon methylation and illustrates the differences obtained upon in vitro and in
AB  - vivo methylation.
ER  -

TY  - JOUR
AU  - Kaneko, R.
AU  - Wong, S.K.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Yoshizawa, S.
AU  - Hamasaki, K.
TI  - Draft Genome Sequences of Two Fabibacter sp. Strains Isolated from Coastal Surface Water of Aburatsubo Inlet, Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e01360
EP  - e01316
VL  - 4
AB  - Here, we report the draft genome sequences of Fabibacter sp. strain 4D4 and F. misakiensis
AB  - strain SK-8T, isolated from surface seawater of a semienclosed inlet.
ER  -

TY  - JOUR
AU  - Kaneko, T. et al.
TI  - Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120.
JO  - DNA Res.
PY  - 2001
SP  - 205
EP  - 213
VL  - 8
AB  - The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp.
AB  - strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome
AB  - (6,413,771 bp) and six plasmids, designated pCC7120alpha (408,101 bp), pCC7120beta (186,614
AB  - bp), pCC7120gamma (101,965 bp), pCC7120delta (55,414 bp), pCC7120epsilon (40,340 bp), and
AB  - pCC7120zeta (5,584 bp). The chromosome bears 5368 potential protein-encoding genes, four sets
AB  - of rRNA genes, 48 tRNA genes representing 42 tRNA species, and 4 genes for small structural
AB  - RNAs. The predicted products of 45% of the potential protein-encoding genes showed sequence
AB  - similarity to known and predicted proteins of known function, and 27% to translated products
AB  - of hypothetical genes. The remaining 28% lacked significant similarity to genes for known and
AB  - predicted proteins in the public DNA databases. More than 60 genes involved in various
AB  - processes of heterocyst formation and nitrogen fixation were assigned to the chromosome based
AB  - on their similarity to the reported genes. One hundred and ninety-five genes coding for
AB  - components of two-component signal transduction systems, nearly 2.5 times as many as those in
AB  - Synechocystis sp. PCC 6803, were identified on the chromosome. Only 37% of the Anabaena genes
AB  - showed significant sequence similarity to those of Synechocystis, indicating a high degree of
AB  - divergence of the gene information between the two cyanobacterial strains.
ER  -

TY  - JOUR
AU  - Kaneko, T. et al.
TI  - Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803.  II.  Sequence determination of the entire genome and assignment of poential protein-coding regions (supplement).
JO  - DNA Res.
PY  - 1996
SP  - 185
EP  - 209
VL  - 3
AB  - none
ER  -

TY  - JOUR
AU  - Kaneko, T. et al.
TI  - Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. Strain PCC6803.  II.  Sequence determination of the entire genome and assignment of potential protein-coding regions.
JO  - DNA Res.
PY  - 1996
SP  - 109
EP  - 136
VL  - 3
AB  - The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was
AB  - completed.  The total length of the genome finally confirmed was 3,573,470 bp, including the
AB  - previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome.  The
AB  - entire sequence was assembled from the sequences of the physical map-based contigs of cosmid
AB  - clones and of lambda clones and long PCR products which were used for gap-filling.  The
AB  - accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire
AB  - genome.  The authenticity of the assembled sequence wqs supported by restriction analysis of
AB  - long PCR products, which were directly amplified from the genomic DNA using the assembled
AB  - sequence data.  To predict the potential protein-coding regions, analysis of open reading
AB  - frames (ORFs), analysis by the GeneMark program and similarity search to databases were
AB  - performed.  As a result, a total of 3,168 potential protein genes were assigned on the genome,
AB  - in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed
AB  - similarity to reported and hypothetical genes, respectively.  The remaining 1,426 (45.0%) had
AB  - no apparent similarity to any genes in databases.  Among the potential protein genes assigned,
AB  - 128 were related to the genes participating in photosynthetic reactions.  The sum of the
AB  - sequences coding for potential protein genes occupies 87% of the genome length.  By adding
AB  - rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and
AB  - RNA-coding regions.  A notable feature on the gene organization of the genome was that 99
AB  - ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were
AB  - found spread all over the genome, and at least 26 of them appeared to remain intact.  The
AB  - result implies that rearrangement of the genome occurred frequently during and after
AB  - establishment of this species.
ER  -

TY  - JOUR
AU  - Kaneko, T. et al.
TI  - Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti.
JO  - DNA Res.
PY  - 2000
SP  - 331
EP  - 338
VL  - 7
AB  - The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti
AB  - strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome
AB  - (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The
AB  - chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA
AB  - genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed
AB  - sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining
AB  - 25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable
AB  - candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24
AB  - genes for nodulation were assigned in this region.  Codon usage analysis suggested that the
AB  - symbiotic island as well as the plasmids originated and were transmitted from other genetic
AB  - systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential
AB  - protein-coding genes, respectively, for a variety of biological functions. These include genes
AB  - for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication
AB  - and conjugation, but only one gene for nodulation was identified.
ER  -

TY  - JOUR
AU  - Kaneko, T. et al.
TI  - Complete genome structure of the Nitrogen-fixing symbiotic bacterium Mesorhizobium loti (Supplement).
JO  - DNA Res.
PY  - 2000
SP  - 381
EP  - 406
VL  - 7
AB  - none
ER  -

TY  - JOUR
AU  - Kaneko, T. et al.
TI  - Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843.
JO  - DNA Res.
PY  - 2007
SP  - 247
EP  - 256
VL  - 14
AB  - The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa
AB  - NIES-843, was determined. The genome of M.
AB  - aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp)
AB  - in length, with an average GC content of 42.3%. The chromosome comprises
AB  - 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA
AB  - genes representing 41 tRNA species, and genes for tmRNA, the B subunit of
AB  - RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative
AB  - protein-encoding sequences showed sequence similarity to genes of known
AB  - function, 32% were similar to hypothetical genes, and the remaining 23%
AB  - had no apparent similarity to reported genes. A total of 688 kb of the
AB  - genome, equivalent to 11.8% of the entire genome, were composed of both
AB  - insertion sequences and miniature inverted-repeat transposable elements.
AB  - This is indicative of a plasticity of the M. aeruginosa genome, through a
AB  - mechanism that involves homologous recombination mediated by repetitive
AB  - DNA elements. In addition to known gene clusters related to the synthesis
AB  - of microcystin and cyanopeptolin, novel gene clusters that may be involved
AB  - in the synthesis and modification of toxic small polypeptides were
AB  - identified. Compared with other cyanobacteria, a relatively small number
AB  - of genes for two component systems and a large number of genes for
AB  - restriction-modification systems were notable characteristics of the M.
AB  - aeruginosa genome.
ER  -

TY  - JOUR
AU  - Kaneko, T.
AU  - Maita, S.
AU  - Hirakawa, H.
AU  - Uchiike, N.
AU  - Minamisawa, K.
AU  - Watanabe, A.
AU  - Sato, S.
TI  - Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T.
JO  - Genes
PY  - 2011
SP  - 763
EP  - 787
VL  - 2
AB  - The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium
AB  - japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome
AB  - of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont,
AB  - B. japonicum USDA110 (9,105,828 bp).  Comparison of the whole-genome sequences of USDA6T and
AB  - USDA110 showed colinearity of major regions in the two genomes, although a large inversion
AB  - exists between them. A significantly high level of sequence conservation was detected in three
AB  - regions on each genome. The gene constitution and nucleotide sequence features in these three
AB  - regions indicate that they may have been derived from a symbiosis island. An ancestral, large
AB  - symbiosis island, approximately 860 kb in total size, appears to have been split into these
AB  - three regions by unknown large-scale genome rearrangements. The two integration events
AB  - responsible for this appear to have taken place independently, but through comparable
AB  - mechanisms, in both genomes.
ER  -

TY  - JOUR
AU  - Kaneko, T.
AU  - Nakamura, Y.
AU  - Sasamoto, S.
AU  - Watanabe, A.
AU  - Kohara, M.
AU  - Matsumoto, M.
AU  - Shimpo, S.
AU  - Yamada, M.
AU  - Tabata, S.
TI  - Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803.
JO  - DNA Res.
PY  - 2003
SP  - 221
EP  - 228
VL  - 10
AB  - The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single
AB  - chromosome and several plasmids of different sizes,
AB  - and the nucleotide sequences of the chromosome and three small plasmids
AB  - (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly
AB  - determined the nucleotide sequences of four large plasmids, which have
AB  - been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103
AB  - kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the
AB  - genetic information carried by these plasmids. A total of 397 potential
AB  - protein-encoding genes were predicted, but little information was obtained
AB  - about the functional relationship of plasmids to host cell, as a large
AB  - portion of the predicted genes (77%) were of unknown function. The
AB  - occurrence of the potential genes on plasmids was divergent, and parA was
AB  - the only gene common to all four large plasmids. The distribution data of
AB  - a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that
AB  - respective plasmids could have originated from different cyanobacterial
AB  - strains.
ER  -

TY  - JOUR
AU  - Kaneko, T.
AU  - Nakamura, Y.
AU  - Sato, S.
AU  - Minamisawa, K.
AU  - Uchiumi, T.
AU  - Sasamoto, S.
AU  - Watanabe, A.
AU  - Idesawa, K.
AU  - Iriguchi, M.
AU  - Kawashima, K.
AU  - Kohara, M.
AU  - Matsumoto, M.
AU  - Shimpo, S.
AU  - Tsuruoka, H.
AU  - Wada, T.
AU  - Yamada, M.
AU  - Tabata, S.
TI  - Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.
JO  - DNA Res.
PY  - 2002
SP  - 189
EP  - 197
VL  - 9
AB  - The complete nucleotide sequence of the genome of a symbiotic bacterium
AB  - Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a
AB  - single circular chromosome 9,105,828 bp in length with an average GC content of
AB  - 64.1%. No plasmid was detected. The chromosome comprises 8317 potential
AB  - protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent
AB  - of the potential protein genes showed sequence similarity to genes of known
AB  - function and 30% to hypothetical genes. The remaining 18% had no apparent
AB  - similarity to reported genes. Thirty-four percent of the B. japonicum genes
AB  - showed significant sequence similarity to those of both Mesorhizobium loti and
AB  - Sinorhizobium meliloti, while 23% were unique to this species. A presumptive
AB  - symbiosis island 681 kb in length, which includes a 410-kb symbiotic region
AB  - previously reported by Gottfert et al., was identified. Six hundred fifty-five
AB  - putative protein-coding genes were assigned in this region, and the functions of
AB  - 301 genes, including those related to symbiotic nitrogen fixation and DNA
AB  - transmission, were deduced. A total of 167 genes for transposases/104 copies of
AB  - insertion sequences were identified in the genome. It was remarkable that 100 out
AB  - of 167 transposase genes are located in the presumptive symbiotic island. DNA
AB  - segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the
AB  - genome, which generates partial duplication of the target tRNA genes. These
AB  - observations suggest plasticity of the B. japonicum genome, which is probably due
AB  - to complex genome rearrangements such as horizontal transfer and insertion of
AB  - various DNA elements, and to homologous recombination.
ER  -

TY  - JOUR
AU  - Kanesaki, Y.
AU  - Hirose, M.
AU  - Hirose, Y.
AU  - Fujisawa, T.
AU  - Nakamura, Y.
AU  - Watanabe, S.
AU  - Matsunaga, S.
AU  - Uchida, H.
AU  - Murakami, A.
TI  - Draft Genome Sequence of the Nitrogen-Fixing and Hormogonia-Inducing Cyanobacterium Nostoc cycadae Strain WK-1, Isolated from the Coralloid Roots of  Cycas revoluta.
JO  - Genome Announcements
PY  - 2018
SP  - e00021
EP  - e00018
VL  - 6
AB  - We report here the whole-genome sequence of Nostoc cycadae strain WK-1, which was isolated
AB  - from cyanobacterial colonies growing in the coralloid roots of the
AB  - gymnosperm Cycas revoluta It can provide valuable resources to study the
AB  - mutualistic relationships and the syntrophic metabolisms between the
AB  - cyanobacterial symbiont and the host plant, C. revoluta.
ER  -

TY  - JOUR
AU  - Kanesaki, Y.
AU  - Ishige, T.
AU  - Sekigawa, Y.
AU  - Kobayashi, T.
AU  - Torii, Y.
AU  - Yokoyama, E.
AU  - Ishiwata, H.
AU  - Hamada, M.
AU  - Tamura, T.
AU  - Azuma, R.
AU  - Murakami, S.
TI  - Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T.
JO  - Genome Announcements
PY  - 2017
SP  - e00126
EP  - e00117
VL  - 5
AB  - Actinomyces sp. strain Chiba101, isolated from an arthritic leg joint of a pig raised in
AB  - Japan, is a bacterium closely related to Actinomyces denticolens Here,
AB  - we deciphered the complete genome sequence of Actinomyces sp. Chiba101 and the
AB  - high-quality draft genome sequence of A. denticolens DSM 20671T.
ER  -

TY  - JOUR
AU  - Kanesaki, Y.
AU  - Kubota, E.
AU  - Ohtake, R.
AU  - Higashi, Y.
AU  - Nagaoka, J.
AU  - Suzuki, T.
AU  - Akuzawa, S.
TI  - Draft Genome Sequence of Bacillus licheniformis Heshi-B2, Isolated from Fermented Rice Bran in a Japanese Fermented Seafood Dish.
JO  - Genome Announcements
PY  - 2018
SP  - e00118
EP  - e00118
VL  - 6
AB  - Bacillus licheniformis Heshi-B2 was isolated from fermented rice bran in Heshiko, a food
AB  - produced by aging salted mackerel with fresh rice bran. Here, we report
AB  - the draft genome sequence of B. licheniformis Heshi-B2, originating from a
AB  - Heshiko sample from Fukui Prefecture, Japan.
ER  -

TY  - JOUR
AU  - Kanesaki, Y.
AU  - Masutani, H.
AU  - Sakanaka, M.
AU  - Shiwa, Y.
AU  - Fujisawa, T.
AU  - Nakamura, Y.
AU  - Yokota, A.
AU  - Fukiya, S.
AU  - Suzuki, T.
AU  - Yoshikawa, H.
TI  - Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency.
JO  - Genome Announcements
PY  - 2014
SP  - e01311
EP  - e01314
VL  - 2
AB  - Bifidobacterium longum 105-A shows high transformation efficiency and allows for  the
AB  - generation of gene knockout mutants through homologous recombination. Here,
AB  - we report the complete genome sequence of strain 105-A. Genes encoding at least
AB  - four putative restriction-modification systems were found in this genome, which
AB  - might contribute to its transformation efficiency.
ER  -

TY  - JOUR
AU  - Kang, C.
AU  - Wu, C.-W.
TI  - Studies on SP6 promoter using a new plasmid vector that allows gene insertion at the transcription initiation site.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 2279
EP  - 2294
VL  - 15
AB  - This paper documents the cleavage by HphI at a site 9 bases away from the
AB  - recognition sequence, with the production of a single base extension.  This is
AB  - in contrast to the usual 8 bases.
ER  -

TY  - JOUR
AU  - Kang, E.S.
AU  - Park, C.W.
AU  - Chung, J.H.
TI  - Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2001
SP  - 862
EP  - 868
VL  - 289
AB  - Dnmt3b, a DNA methyltransferase, is essential for mammalian development potentially through
AB  - its transcription repression activity. To
AB  - comprehend the underlying regulatory mechanism of Dnmt3b, we isolated
AB  - small ubiquitin-like modifier 1 (SUMO-1) and Ubc9 as Dnmt3b-interacting
AB  - proteins using yeast two-hybrid screens. Deletion analysis and
AB  - colocalization experiment demonstrated that Dnmt3b interacts with
AB  - SUMO-1 and Ubc9 at its N-terminal region. We also confirmed the
AB  - modification of Dnmt3b by SUMO-1 in vivo. These results suggest that
AB  - sumoylation may constitute a regulation mechanism of Dnmt3b in vivo.
ER  -

TY  - JOUR
AU  - Kang, H.L.
AU  - Park, Y.H.
AU  - Lee, E.J.
AU  - Kim, M.H.
AU  - Kim, J.S.
AU  - Park, S.G.
AU  - Song, J.Y.
AU  - Park, J.U.
AU  - Baik, S.C.
AU  - Ko, G.H.
AU  - Youn, H.S.
AU  - Lee, W.K.
AU  - Cho, M.J.
TI  - Distribution of Helicobacter pylori 51-specific genes on other Korean isolates of Helicobacter pylori.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2003
SP  - D
EP  - 069
VL  - 103
AB  - Background: Many disease-related genes of H. pylori such as cagA, vacA, ure and sod were
AB  - identified and well-studied. Entire genome of H.
AB  - pylori strain 51, a Korean isolate, has been sequenced. It had 1,454
AB  - orfs. We searched disease-specific genes on Korean H. pylori isolates.
AB  - Method: The nucleotide sequences of open reading frames of three H.
AB  - pylori strains (26685, J99, 51) were compared one another and searched
AB  - the strain-specific orf. Five type strains of H. pylori and 80 Korean
AB  - isolates were screened with strain 51-specific orfs by overgo
AB  - hybridization. Result: Ninteen Korean strain 51-specific orfs were
AB  - identified. They included restriction endonuclease S subunits (hsdD,
AB  - khp538), ATPase involved in conjugal plasmid transfer (traG, khp924),
AB  - ATPase involved in pili and flagella biosynthesis (virB11, khp925),
AB  - VirB10 component of type IV secretion system (virB10, khp926),
AB  - Adenine-specific DNA methylase (khp1073), site-specific
AB  - integrase-resolvase (khp1371), transposase (khp1372), restriction
AB  - endonuclease S subunits (hsdS, khp1385), amino acid transporters (lysP,
AB  - khp1391), site-specific DNA methylase (dcm, khp1406),
AB  - membrane-associated metal-dependent hydrolase (khp1425) and seven
AB  - putative ORFs. To investigate distribution of the genes, four type
AB  - strains and 80 Korean H. pylori isolates that were isolated from
AB  - gastric cancer, gastric ulcer, duodenal ulcer and gastritis were
AB  - screened. Four orfs (khp594, khp900, khp1251, khp1391) were revealed to
AB  - be abundant in most Korean isolates. Conclusion: We found 19 Korean
AB  - strain 51-specific orfs by the comparison of the nucleotide sequence of
AB  - orfs of three sequenced H. pylori strains. But none of them seemed to
AB  - be disease-specific. But at least four orfs seemed to be specific in
AB  - korean isolates. We are expecting that we can find more reasonable
AB  - result by screening more Korean isolates.
ER  -

TY  - JOUR
AU  - Kang, I.
AU  - Kang, D.
AU  - Oh, H.M.
AU  - Kim, H.
AU  - Kim, H.J.
AU  - Kang, T.W.
AU  - Kim, S.Y.
AU  - Cho, J.C.
TI  - Genome sequence of strain IMCC2047, a novel marine member of the Gammaproteobacteria.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3688
EP  - 3689
VL  - 193
AB  - Strain IMCC2047 was isolated from the Yellow Sea using dilution-to-extinction culturing. The
AB  - strain was shown to occupy a
AB  - distinct phylogenetic position within the Gammaproteobacteria. Here we
AB  - present the genome sequence of strain IMCC2047 that harbors genes for
AB  - various metabolic pathways including proteorhodopsin and ribulose
AB  - bisphosphate carboxylase.
ER  -

TY  - JOUR
AU  - Kang, I.
AU  - Kim, S.
AU  - Islam, M.R.
AU  - Cho, J.C.
TI  - The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures.
JO  - Sci. Rep.
PY  - 2017
SP  - 42252
EP  - 42252
VL  - 7
AB  - The acI lineage of the phylum Actinobacteria is the most abundant bacterial group
AB  - in most freshwater lakes. However, due to difficulties in laboratory cultivation,
AB  - only two mixed cultures and some incomplete single-amplified or
AB  - metagenome-derived genomes have been reported for the lineage. Here, we report
AB  - the initial cultivation and complete genome sequences of four novel strains of
AB  - the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains,
AB  - initially isolated by dilution-to-extinction culturing, eventually failed to be
AB  - maintained as axenic cultures. However, the first complete genomes of the acI
AB  - lineage were successfully obtained from these initial cultures through whole
AB  - genome amplification applied to more than hundreds of cultured acI cells. The
AB  - genome sequences exhibited features of genome streamlining and showed that the
AB  - strains are aerobic chemoheterotrophs sharing central metabolic pathways, with
AB  - some differences among tribes that may underlie niche diversification within the
AB  - acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis
AB  - was complete in only A1 and A4 tribes.
ER  -

TY  - JOUR
AU  - Kang, I.
AU  - Lee, K.
AU  - Yang, S.J.
AU  - Choi, A.
AU  - Kang, D.
AU  - Lee, Y.K.
AU  - Cho, J.C.
TI  - Genome Sequence of 'Candidatus Aquiluna' sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3550
EP  - 3551
VL  - 194
AB  - We report the genome sequence of actinobacterial strain IMCC13023, isolated from  arctic fjord
AB  - seawater. Phylogenetic analysis of 16S rRNA gene showed that the
AB  - strain is related to 'Candidatus Aquiluna rubra.' The genome information suggests
AB  - that strain IMCC13023 is a photoheterotroph carrying actinorhodopsin, with the
AB  - smallest genome ever reported for a free-living member of the Actinobacteria.
ER  -

TY  - JOUR
AU  - Kang, I.
AU  - Oh, H.M.
AU  - Lim, S.I.
AU  - Ferriera, S.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene  cluster and Xanthorhodopsin.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4798
EP  - 4799
VL  - 192
AB  - Fulvimarina pelagi is a Mn(II)-oxidizing marine heterotrophic bacterium in the order
AB  - Rhizobiales. Here we announce the draft genome sequence of F.
AB  - pelagi HTCC2506(T), which was isolated from the Sargasso Sea by using
AB  - dilution-to-extinction culturing. The genome sequence contained a
AB  - xanthorhodopsin gene as well as a photosynthetic gene cluster, which
AB  - suggests the coexistence of two different phototrophic mechanisms in a
AB  - single microorganism.
ER  -

TY  - JOUR
AU  - Kang, I.
AU  - Oh, H.M.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Genome Sequence of the Marine Alphaproteobacterium HTCC2150, Assigned to the Roseobacter Clade.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6315
EP  - 6316
VL  - 192
AB  - Here we announce the genome sequence of a marine bacterium, HTCC2150, that was isolated off
AB  - the Oregon coast using dilution-to-extinction culturing
AB  - and that is affiliated with the Roseobacter clade. The 16S rRNA phylogeny
AB  - showed that the strain was closely related to members of the RCA clade.
AB  - The genome sequence suggests that strain HTCC2150 is an organoheterotroph
AB  - carrying diverse metabolic potential, including a close relationship with
AB  - phytoplankton.
ER  -

TY  - JOUR
AU  - Kang, I.
AU  - Vergin, K.L.
AU  - Oh, H.M.
AU  - Choi, A.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Genome Sequence of strain HTCC2083, a Novel Member of the Marine Roseobacter Clade.
JO  - J. Bacteriol.
PY  - 2010
SP  - 319
EP  - 320
VL  - 193
AB  - Strain HTCC2083 was isolated from Oregon seawater using dilution-to-extinction culturing and
AB  - represents a novel member of the Roseobacter clade. The draft genome sequence of HTCC2083 is
AB  - presented here. The genome is predicted to contain genes for aerobic anoxygenic phototrophy,
AB  - sulfite-oxidizing chemolithotrophy, anapleurotic CO2 fixation, carbon monoxide oxidation, and
AB  - dimethylsulphoniopropionate (DMSP) utilization.
ER  -

TY  - JOUR
AU  - Kang, J.
AU  - Chung, W.H.
AU  - Lim, T.J.
AU  - Lim, S.
AU  - Nam, Y.D.
TI  - Complete genome sequence of the Bifidobacterium animalis subspecies lactis BL3, preventive probiotics for acute colitis and colon cancer.
JO  - New Microbes New Infect.
PY  - 2017
SP  - 34
EP  - 37
VL  - 19
AB  - We report the genome sequence of Bifidobacterium animalis subspecies lactis BL3,
AB  - which has preventive properties on acute colitis and colon cancer. The genome of
AB  - BL3, which was isolated from Korean faeces, consisted of a 1 944 323 bp size
AB  - single chromosome, and its G+C content was 60.5%. Genome comparison against the
AB  - closest Bifidobacterium animalis strain revealed that BL3 had particularly
AB  - different regions of four areas encoding flavin-nucleotide-binding protein,
AB  - transposase, multidrug ABC transporter and ATP binding protein.
ER  -

TY  - JOUR
AU  - Kang, J.
AU  - Chung, W.H.
AU  - Lim, T.J.
AU  - Whon, T.W.
AU  - Lim, S.
AU  - Nam, Y.D.
TI  - Complete Genome Sequence of Lactobacillus casei LC5, a Potential Probiotics for Atopic Dermatitis.
JO  - Front. Immunol.
PY  - 2017
SP  - 413
EP  - 413
VL  - 8
ER  -

TY  - JOUR
AU  - Kang, J.J.S.
AU  - Meier, J.L.
AU  - Dervan, P.B.
TI  - Design of Sequence-Specific DNA Binding Molecules for DNA Methyltransferase Inhibition.
JO  - J. Am. Chem. Soc.
PY  - 2014
SP  - 3687
EP  - 3694
VL  - 136
AB  - The CpG dyad, an important genomic feature in DNA methylation and transcriptional regulation,
AB  - is an attractive target for small molecules. To assess the utility of minor groove binding
AB  - oligomers for CpG recognition, we screened a small library of hairpin pyrrole-imidazole
AB  - polyamides targeting the sequence 5'-CGCG-3' and assessed their sequence specificity using
AB  - an unbiased next-generation sequencing assay. Our findings indicate that hairpin polyamide of
AB  - sequence PyIm beta Im-gamma-PyIm beta Im (1), previously identified as a high affinity
AB  - 5'-CGCG-3' binder, favors 5'-GCGC-3' in an unanticipated reverse binding orientation.
AB  - Replacement of one beta alanine with Py to afford PyImPyIm-gamma-PyIm beta Im (3) restores the
AB  - preference for 5'-CGCG-3' binding in a forward orientation. The minor groove binding hairpin
AB  - 3 inhibits DNA methyltransferase activity in the major groove at its target site more
AB  - effectively than 1, providing a molecular basis for design of sequence-specific antagonists of
AB  - CpG methylation.
ER  -

TY  - JOUR
AU  - Kang, M.S.
AU  - Chung, J.
AU  - Kim, S.M.
AU  - Yang, K.H.
AU  - Oh, J.S.
TI  - Effect of Weissella cibaria isolates on the formation of Streptococcus mutans biofilm.
JO  - Caries Res.
PY  - 2006
SP  - 418
EP  - 425
VL  - 40
AB  - The objective of this study was to isolate and identify lactic acid bacteria able
AB  - to inhibit the in vitro formation of Streptococcus mutans biofilm as well as the
AB  - in vivo formation of oral biofilm. Two strains, CMS1 and CMS3, exhibiting
AB  - profound inhibitory effects on the formation of S. mutans biofilm and the
AB  - proliferation of S. mutans, were isolated from children's saliva and identified
AB  - as Weissella cibaria by 16S rDNA sequencing. The water-soluble polymers produced
AB  - from sucrose by the W. cibaria isolates also inhibited the formation of S. mutans
AB  - biofilm. According to the results of thin-layer chromatographic analysis, the
AB  - hydrolysates of water-soluble polymers produced by the isolates were identical to
AB  - those of dextran, forming mostly alpha-(1-6) glucose linkages. In the clinical
AB  - study, the subjects mouthrinsed with a solution containing W. cibaria CMS1
AB  - evidenced plaque index reduction of approximately 20.7% (p < 0.001). These
AB  - results indicate that the W. cibaria isolates possess the ability to inhibit
AB  - biofilm formation, both in vitro and in vivo.
ER  -

TY  - JOUR
AU  - Kang, M.S.
AU  - Yeu, J.E.
AU  - Oh, J.S.
AU  - Shin, B.A.
AU  - Kim, J.H.
TI  - Complete Genome Sequences of Weissella cibaria Strains CMU, CMS1, CMS2, and CMS3  Isolated from Infant Saliva in South Korea.
JO  - Genome Announcements
PY  - 2017
SP  - e01103
EP  - e01117
VL  - 5
AB  - Weissella cibaria strain CMU is used as a commercial oral care probiotic in South Korea. Here,
AB  - we present the complete genome sequences of four W. cibaria strains
AB  - (CMU, CMS1, CMS2, and CMS3) isolated from the saliva of an infant living in
AB  - Gwangju, South Korea.
ER  -

TY  - JOUR
AU  - Kang, S.
AU  - Lee, H.
AU  - Han, J.S.
AU  - Hwang, D.S.
TI  - Interaction of SeqA and Dam methylase on the hemimethylated origin of Escherichia coli chromosomal DNA replication.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 11463
EP  - 11468
VL  - 274
AB  - Preferential binding of SeqA protein to hemimethylated oriC, the origin of Escherichia coli
AB  - chromosomal replication, delays methylation by Dam methylase.  Because the SeqA-oriC
AB  - interaction appears to be essential in timing of chromosomal replication initiation, the
AB  - biochemical functions of SeqA protein and Dam methylase at the 13-mer L, M., and R region
AB  - containing 4 GATC sequences at the left end of oriC were examined.  We found that SeqA protein
AB  - preferentially bound hemimethylated 13-mers but not fully nor unmethylated 13-mers.
AB  - Regardless of strand methylation, the binding of SeqA protein to the hemimethylated GATC
AB  - sequence of 13-mer L was followed by additional binding to other hemimethylated GATC sequences
AB  - of 13-mer M and R.  On the other hand, Dam methylase did not discriminate binding of 13-mers
AB  - in different methylation patterns and was not specific to GATC sequences.  The binding
AB  - specificity and higher affinity of SeqA protein over Dam methylase to the hemimethylated
AB  - 13-mers along with the reported cellular abundance of this protein explains the dominant
AB  - action of SeqA protein over Dam methylase to the newly replicated oriC for the sequestration
AB  - of chromosomal replication.  Furthermore, SeqA protein bound to hemimethylated 13-mers was not
AB  - dissociated by Dam methylase, and most SeqA protein spontaneously dissociated 10 min after
AB  - binding.  Also, SeqA protein delayed the in vitro methylation of hemimethylated 13-mers by Dam
AB  - methylase.  These in vitro results suggest that the intrinsic binding instability of SeqA
AB  - protein results in release of sequestrated hemimethylated oriC.
ER  -

TY  - JOUR
AU  - Kang, S.C.
AU  - Choi, W.S.
AU  - Yoo, O.J.
TI  - The effects of DNA methylation by HhaI methylase on the cleavage reactions by HaeII, AhaII and BanI endonuclease.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1987
SP  - 482
EP  - 487
VL  - 145
AB  - The DNA methylated by HhaI methylase was resistant against cleavage of HaeII or
AB  - AhaII endonuclease indicating that the methyl group of the C5 position of the
AB  - innermost cytosine nucleotide interferes with the interaction between the
AB  - enzyme and hexameric recognition sequence.  Considering that HaeII or AhaII
AB  - methylase has not been isolated yet, the result explained above is a useful
AB  - information for protecting a double stranded DNA from being cleaved by HaeII or
AB  - AhaII endonuclease. In contrast to HaeII or AhaII endonuclease, BanI
AB  - endonuclease which also has HhaI sequence as its tetrameric core was able to
AB  - cleave the same DNA normally.  This result suggests that the C5 position of the
AB  - inmost pyrimidine nucleotide is not an important contact point between BanI
AB  - endonuclease and its hexameric recognition sequence.
ER  -

TY  - JOUR
AU  - Kang, S.C.
AU  - Yoo, O.J.
TI  - Purification and characterization of AccI endonuclease.
JO  - Korean J. Microbiol.
PY  - 1985
SP  - 13
EP  - 19
VL  - 23
AB  - AccI endonuclease has been isolated from 300g (wet weight) cells of
AB  - Acinetobacter calcoaceticus.  The cells were broken by using French press at
AB  - 20,000 p.s.i.  After ammonium sulfate fractionation, the enzyme was further
AB  - purified by heparin agarose, DEAE-sephadex, Affi-gel Blue, phosphocellulose,
AB  - and hydroxylapatite column chromatography.  The purified AccI endonuclease has
AB  - a single polypeptide species and its subunit molecular weight was 45,000 +/-
AB  - 1,000 daltons as judged by 10% SDS-polyacrylamide gel electrophoresis.  The
AB  - isolated enzyme was essentially free of contaminating nucleases as judged by
AB  - homochromatography by using a 32P-labeled oligonucleotide.  The enzyme showed
AB  - maximum activity at pH values between 8.0 and 11.0, and in the presence of
AB  - MgCl2.  AccI endonuclease was maximally active in the absence of NaCl and was
AB  - completely inhibited at 200 mM NaCl.
ER  -

TY  - JOUR
AU  - Kang, S.C.
AU  - Yoon, H.
AU  - Yoo, O.J.
TI  - DNA protection by methylation with AluI methylase against cleavages of HindIII, SstI, PvuII and SacI endonucleases.
JO  - Korean Biochem. J.
PY  - 1986
SP  - 41
EP  - 46
VL  - 19
AB  - The cleavage reactions of HindIII, SstI, PvuII and SacI endonucleases were inhibited by the
AB  - methylation of AluI methylase.  To analyze the cleavage reactions quantitatively, tritium
AB  - labeled pBR322 and pPG3282 plasmid DNAs (pBR322 DNA contains HindIII and PvuII sites, while
AB  - pPG3282 DNA which is a hog gastrin cDNA clone contains SstI and SacI sites) were used, and the
AB  - degree of the inhibition against cleavages by the four kinds of endonucleases was measured.
AB  - The results imply that we can predict the specificities of the related hexameric restriction
AB  - methylases which have not been isolated yet.  And the predictions are the followings:  (1) The
AB  - methylation sites of SstI methylase is not identical with AluI methylase since SstI
AB  - endonuclease slowly cut the sequences methylated by AluI methylase.  (2)  The methylation
AB  - sites of PvuII and SacI methylases could be identical with AluI methylase since PvuII and SacI
AB  - endonucleases could not cut the sequences methylated by AluI methylase.
ER  -

TY  - JOUR
AU  - Kang, W.Y. et al.
TI  - Stationary Phase Expression, Purification, and Characterization of XorKI, a Restriction Endonuclease from Xanthomonas oryzae pv. oryzae.
JO  - Protein Pept. Lett.
PY  - 2010
SP  - 381
EP  - 385
VL  - 17
AB  - An endonuclease from Xanthomonas oryzae pathovar oryzae KACC 10331, XorKI, was heterologously
AB  - produced in Escherichia coli by applying the
AB  - stationary state induction method. The yield was 5.4 mg of XorKI per
AB  - liter of LB medium. XorKI existed in multiple oligomeric forms as
AB  - evidenced by gel filtration chromatography. The specific activity of
AB  - purified XorKI was 323000 units per mg.
ER  -

TY  - JOUR
AU  - Kang, X.
AU  - Ling, N.
AU  - Sun, G.
AU  - Zhou, Q.
AU  - Zhang, L.
AU  - Sheng, Q.
TI  - Complete Genome Sequence of Streptococcus thermophilus Strain MN-ZLW-002.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4428
EP  - 4429
VL  - 194
AB  - Streptococcus thermophilus MN-ZLW-002 was originally isolated from traditionally  fermented
AB  - Chinese dairy products. One of the strain-dependent characteristics of
AB  - this bacterium is its ability to produce exopolysaccharides (EPSs). This study
AB  - determined and analyzed the genome sequence of MN-ZLW-002. Its complete genome
AB  - comprised 2,046 genes and 1,848,520 nucleotides with an average GC content of
AB  - 39%. The EPS cluster of MN-ZLW-002 includes 25 open reading frames (ORFs), and
AB  - some results indicate a horizontal gene transfer between MN-ZLW-002 and other
AB  - lactic acid bacteria (LAB).
ER  -

TY  - JOUR
AU  - Kang, Y.
AU  - Shen, M.
AU  - Wang, H.
AU  - Zhao, Q.
TI  - Complete Genome Sequence of Bacillus pumilus Strain WP8, an Efficient Plant Growth-Promoting Rhizobacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01452
EP  - e01414
VL  - 3
AB  - Bacillus pumilus strain WP8 is an efficient plant growth-promoting rhizobacterium. Here, we
AB  - present the complete genome of WP8 and its genes
AB  - involved in plant growth promotion and biocontrol.
ER  -

TY  - JOUR
AU  - Kang, Y.K.
AU  - Lee, H.B.
AU  - Noh, M.J.
AU  - Cho, N.-Y.
AU  - Yoo, O.J.
TI  - Different effects of base analog substitutions in BamHI restriction site on recognition by BamHI endonuclease and BamHI methylase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1995
SP  - 997
EP  - 1002
VL  - 206
AB  - BamHI endonuclease and BamHI methylase were used to investigate their specific interaction
AB  - with the common recognition sequence, GGATCC. Five derivatives of the oligonucleotide,
AB  - GACGGATCCGTC, containing a variety of single-base analog substitutions within the hexameric
AB  - recognition core were synthesized. Steady-state kinetics for the reaction of the endonuclease
AB  - and the methylase showed that both enzymes recognize the sequences by contacting with
AB  - functional groups exposed in both major and minor grooves of the site but in different ways.
AB  - Removal or substitution of the 5-methyl group in thymidine blocked the endonuclease reaction
AB  - completely but still allowed the methylase reaction with less efficiency. The data also showed
AB  - that the methylase made a critical minor groove contact with the 2-amino group of the first G
AB  - but the endonuclease did with that of the second G.
ER  -

TY  - JOUR
AU  - Kang, Y.K.
AU  - Ryu, J.
AU  - Yoo, O.J.
TI  - Effects of modified bases in sequence recognition by ClaI endonuclease and ClaI methylase.
JO  - Biochem. Mol. Biol. Int.
PY  - 1993
SP  - 859
EP  - 865
VL  - 29
AB  - To understand the functional groups required for sequence recognition, dodecanucleotides
AB  - containing the ClaI sequence with the middle positions containing modified bases were
AB  - synthesized and used as substrates for ClaI endonuclease and ClaI methylase reactions. For the
AB  - modification, dU, 5-bromo-dU, and dI were used. Km values of these two enzymes were determined
AB  - for normal and modified oligonucleotides. Our data showed that 5-CH3 groups of the first and
AB  - second T residues of the hexanucleotide sequence were essential contact points for ClaI
AB  - methylase. However, ClaI endonuclease was still active without either one of those methyl
AB  - groups with elevated Km values. Bromine could compensate significantly for the loss of 5-CH3
AB  - groups at both positions. On the other hand, the 2-amino group of the G residue appeared to be
AB  - an essential contact point for both enzymes. It has been concluded that ClaI enconuclease and
AB  - ClaI methylase recognize the sequence in different ways.
ER  -

TY  - JOUR
AU  - Kania, J.
AU  - Fanning, T.G.
TI  - Use of a Sequence-Specific DNA-Binding Ligand to probe the Environments of EcoRI Restriction Endonuclease Cleavage Sites.
JO  - Eur. J. Biochem.
PY  - 1976
SP  - 367
EP  - 371
VL  - 67
AB  - The DNAs of bacteriophage lambda and adenovirus were incubated with the
AB  - sequence-specific DNA-binding ligand 6,4'-diamidino-2-phenylindole.  Digestion
AB  - of the ligant - DNA complexes with EcoRI nuclease and subsequent agarose gel
AB  - electrophoresis demonstrated that the ligand inhibited nuclease activity at
AB  - some sites, but not at others.  The results suggest that
AB  - diamidino-2-phenylindole can be used to probe the immediate environments of the
AB  - EcoRI cleavage sites.
ER  -

TY  - JOUR
AU  - Kankel, M.W.
AU  - Ramsey, D.E.
AU  - Stokes, T.L.
AU  - Flowers, S.K.
AU  - Haag, J.R.
AU  - Jeddeloh, J.A.
AU  - Riddle, N.C.
AU  - Verbsky, M.L.
AU  - Richards, E.J.
TI  - Arabidopsis MET1 cytosine methyltransferase mutants.
JO  - Genetics
PY  - 2003
SP  - 1109
EP  - 1122
VL  - 163
AB  - We describe the isolation and characterization of two missense mutations in the
AB  - cytosine-DNA-methyltransferase gene, MET1, from the flowering plant
AB  - Arabidopsis thaliana. Both missense mutations, which affect the catalytic
AB  - domain of the protein, led to a global reduction of cytosine methylation
AB  - throughout the genome. Surprisingly, the met1-2 allele, with the weaker
AB  - DNA hypomethylation phenotype, alters a well-conserved residue in
AB  - methyltransferase signature motif I. The stronger met1-1 allele caused
AB  - late flowering and a heterochronic delay in the juvenile-to-adult rosette
AB  - leaf transition. The distribution of late-flowering phenotypes in a
AB  - mapping population segregating met1-1 indicates that the flowering-time
AB  - phenotype is caused by the accumulation of inherited defects at loci
AB  - unlinked to the met1 mutation. The delay in flowering time is due in part
AB  - to the formation and inheritance of hypomethylated fwa epialleles, but
AB  - inherited defects at other loci are likely to contribute as well.
AB  - Centromeric repeat arrays hypomethylated in met1-1 mutants are partially
AB  - remethylated when introduced into a wild-type background, in contrast to
AB  - genomic sequences hypomethylated in ddm1 mutants. ddm1 met1 double mutants
AB  - were constructed to further our understanding of the mechanism of DDM1
AB  - action and the interaction between two major genetic loci affecting global
AB  - cytosine methylation levels in Arabidopsis.
ER  -

TY  - JOUR
AU  - Kankia, B.I.
TI  - A real-time assay for monitoring nucleic acid cleavage by quadruplex formation.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - e141
EP  - e141
VL  - 34
AB  - Direct and straightforward methods to follow nucleic acid cleavage are needed. A
AB  - spectrophotometric quadruplex formation assay (QFA) was
AB  - developed, which allows real-time monitoring of site-specific cleavage of
AB  - nucleic acids. QFA was applied to study both protein and nucleic acid
AB  - restriction enzymes, and was demonstrated to accurately determine
AB  - Michaelis-Menten parameters for the cleavage reaction catalyzed by EcoRI.
AB  - QFA can be used to study the mechanisms of protein-nucleic acid
AB  - recognition. QFA is also a useful tool for dissecting individual nicking
AB  - rates of a double-stranded cleavage.
ER  -

TY  - JOUR
AU  - Kannan, P.
AU  - Cowan, G.M.
AU  - Daniel, A.S.
AU  - Gann, A.A.F.
AU  - Murray, N.E.
TI  - Conservation of organization in the specificity polypeptides of two families of Type I restriction enzymes.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 335
EP  - 344
VL  - 209
AB  - We have identified the recognition sequence for the Citrobacter freundii
AB  - restriction endonuclease CfrA, a member of the A-family of type I R-M enzymes.
AB  - This bipartite target sequence differs in both its components from those of
AB  - other type I enzymes.  We determined the nucleotide sequence of its specificity
AB  - gene (hsdS) and a comparison of this with its relative EcoA identifies two
AB  - extensive variable regions, an organization analogous to that found in the
AB  - K-family of type I R-M enzymes.  The specificity polypeptides of the A-family,
AB  - unlike those of K, have an N-terminal conserved region, and this includes a
AB  - sequence repeated within the central conserved region.  A second repeat
AB  - sequence, identified at the amino acid level, coincides with the only sequence
AB  - similarity common to all type I S polypeptides.  Sequences immediately
AB  - downstream from the hsdS genes of EcoA, CfrA, EcoK, B and D are almost
AB  - identical, consistent with an allelic chromosomal location.
ER  -

TY  - JOUR
AU  - Kannan, P.R.
AU  - Dharmalingam, K.
TI  - Restriction alleviation and enchancement of mutagenesis of the bacteriophage T4 chromosome in recBCsbcA strains of Escherichia coli.
JO  - Mol. Gen. Genet.
PY  - 1987
SP  - 413
EP  - 418
VL  - 208
AB  - The restriction of non glucosylated phage T4 DNA is reduced significantly in
AB  - host bacterial strains carrying recBCsbcA mutations even in the presence of a
AB  - functional rgl gene.  In recBCsbcA hosts a high frequency of phage mutations
AB  - are observed both in the glucosyl transferase genes and in the DNA sequences
AB  - recognised by the rgl restriction enzymes.  This hypermutagenic property of the
AB  - recBCsbcA strains is not dependent on the glucosylation of the phage DNA, and
AB  - the mutagenesis is localized to certain regions of the T4 chromosome.  However,
AB  - alleviation of rgl restriction in recBCsbcA strains is due neither to the
AB  - increased mutagenesis, nor to the absence of a functional rgl system, since
AB  - second site mutations (rra) restore rgl restriction without affecting
AB  - hypermutagenesis.
ER  -

TY  - JOUR
AU  - Kanrar, S.
AU  - Dhar, A.K.
TI  - Complete Genome Sequence of a Novel Mutant Strain of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).
JO  - Genome Announcements
PY  - 2018
SP  - e00497
EP  - e00418
VL  - 6
AB  - The acute hepatopancreatic necrosis disease (AHPND) of Penaeus vannamei shrimp is caused by
AB  - Vibrio parahaemolyticus carrying toxin genes, pirA and pirB We report
AB  - the complete genome sequence of the novel V. parahaemolyticus strain R14, which
AB  - did not display AHPND symptoms in P. vannamei despite containing the binary toxin
AB  - genes.
ER  -

TY  - JOUR
AU  - Kanrar, S.
AU  - Dhar, A.K.
TI  - Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).
JO  - Genome Announcements
PY  - 2018
SP  - e00544
EP  - e00518
VL  - 6
AB  - Vibrio parahaemolyticus carrying the toxin genes pirA and pirB causes acute hepatopancreatic
AB  - necrosis disease in shrimp. A genome sequence of V.
AB  - parahaemolyticus strain R13 was determined that showed deletions of the entire
AB  - pirA gene and the 5' end of the pirB gene and does not cause the disease in
AB  - experimental challenge.
ER  -

TY  - JOUR
AU  - Kant, J.A.
TI  - DNA restriction enzymes and RFLPs in medicine.
JO  - Methods Biochem. Anal.
PY  - 1992
SP  - 129
EP  - 140
VL  - 36
AB  - *
AB  -     1 Restriction Enzymes (Endonucleases)
AB  -   1.1 General information
AB  -   1.2 Restriction enzymes and molecular cloning
AB  -   1.3 Restriction enzymes, chromosomal mapping, and gene expression
AB  -   1.4 Technical notes
AB  -     2 Restriction fragment-length polymorphisms
AB  -   2.1 RFLPs defined
AB  -   2.2 RFLPs and alleles in human genetic disorders
AB  - 2.2.1 Linkage of RFLPs to genetic diseases
AB  - 2.2.2 Restriction enzymes to detect disease-causing mutations
AB  - 2.2.3 Haplotypes and linkage disequilibrium
AB  -   2.3 RFLPs in neoplasia and cancer
AB  - 2.3.1 Loss of RFLP heterozygosity and tumor suppressor genes
AB  - 2.3.2 Clonality analysis of hematolymphoid neoplasms
AB  - 2.3.3 Consistent chromosomal translocations
AB  - 2.3.4 Clonality studies of nonhematolymphoid tumors
AB  -   2.4 Infectious diseases
AB  -     3 Overview
AB  - 
ER  -

TY  - JOUR
AU  - Kant, R. et al.
TI  - Genome Sequence of 'Pedosphaera parvula' Ellin514, an Aerobic Verrucomicrobial Isolate from Pasture Soil.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2900
EP  - 2901
VL  - 193
AB  - "Pedosphaera parvula" Ellin514 is an aerobically grown verrucomicrobial
AB  - isolate from pasture soil. It is one of the few cultured representatives
AB  - of subdivision 3 of the phylum Verrucomicrobia. Members of this group are
AB  - widespread in terrestrial environments.
ER  -

TY  - JOUR
AU  - Kant, R.
AU  - Paulin, L.
AU  - Alatalo, E.
AU  - de Vos, W.M.
AU  - Palva, A.
TI  - Genome sequence of Lactobacillus amylovorus GRL1118, isolated from the pig ileum.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3147
EP  - 3148
VL  - 193
AB  - Lactobacillus amylovorus is a common member of the beneficial microbiota present in the pig
AB  - gastrointestinal tract (GIT). Here, we report the genome sequence of surface layer (S-layer)
AB  - protein carrying, and potential probiotic L. amylovorus GRL1118, that was isolated from
AB  - porcine ileum and showed strong adherence to the pig intestinal epithelial cells.
ER  -

TY  - JOUR
AU  - Kant, R.
AU  - Paulin, L.
AU  - Alatalo, E.
AU  - de Vos, W.M.
AU  - Palva, A.
TI  - Genome Sequence of Lactobacillus amylovorus GRL1112.
JO  - J. Bacteriol.
PY  - 2010
SP  - 789
EP  - 790
VL  - 193
AB  - Lactobacillus amylovorus is a common member of the normal gastrointestinal tract (GIT)
AB  - microbiota in pigs. Here, we report the genome sequence of L.
AB  - amylovorus GRL1112, a porcine faeces isolate displaying strong adherence
AB  - to the pig intestinal epithelial cells. The strain is of interest as it is
AB  - a potential probiotic bacterium.
ER  -

TY  - JOUR
AU  - Kant, R.
AU  - Rasinkangas, P.
AU  - Satokari, R.
AU  - Pietila, T.E.
AU  - Palva, A.
TI  - Genome Sequence of the Butyrate-Producing Anaerobic Bacterium Anaerostipes hadrus PEL 85.
JO  - Genome Announcements
PY  - 2015
SP  - e00224
EP  - e00215
VL  - 3
AB  - Anaerostipes hadrus PEL 85, which was isolated from human feces, is a Gram-positive rod-shaped
AB  - bacterium. The species may play an important role in gut
AB  - health, as it was previously reported to produce butyric acid. Here, we present
AB  - the genome assembly of PEL 85, a novel strain of A. hadrus.
ER  -

TY  - JOUR
AU  - Kant, R.
AU  - Taponen, S.
AU  - Koort, J.
AU  - Paulin, L.
AU  - Avall-Jaaskelainen, S.
AU  - Palva, A.
TI  - Genome Sequences of Four Staphylococcus aureus Strains Isolated from Bovine Mastitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00334
EP  - e00315
VL  - 3
AB  - Staphylococcus aureus is a major causative agent of mastitis in dairy cows. The pathogenicity
AB  - of S. aureus may vary; it is able to cause severe clinical
AB  - mastitis, but most often it is associated with chronic subclinical mastitis.
AB  - Here, we present the genome assemblies of four S. aureus strains from bovine
AB  - mastitis.
ER  -

TY  - JOUR
AU  - Kant, R.
AU  - Uroic, K.
AU  - Hynonen, U.
AU  - Kos, B.
AU  - Suskovic, J.
AU  - Palva, A.
TI  - Genome Sequence of Lactobacillus brevis Strain D6, Isolated from Smoked Fresh Cheese.
JO  - Genome Announcements
PY  - 2016
SP  - e00264
EP  - e00216
VL  - 4
AB  - The autochthonousLactobacillus brevisstrain D6, isolated from smoked fresh cheese, carries a
AB  - 45-kDa S-layer protein. Strain D6 has shown adhesion to
AB  - extracellular matrix proteins and to Caco-2 intestinal epithelial cells, as well
AB  - as immunomodulatory potential and beneficial milk technological properties.
AB  - Hence, it could be used as a potential probiotic starter culture for cheese
AB  - production.
ER  -

TY  - JOUR
AU  - Kanukollu, S.
AU  - Voget, S.
AU  - Pohlner, M.
AU  - Vandieken, V.
AU  - Petersen, J.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Shapiro, N.
AU  - Goker, M.
AU  - Klenk, H.P.
AU  - Cypionka, H.
AU  - Engelen, B.
TI  - Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 25
EP  - 25
VL  - 11
AB  - Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated
AB  - with the Roseobacter group within the family Rhodobacteraceae. The
AB  - strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m
AB  - below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981
AB  - protein-coding genes and 47 RNA genes. It contains one chromosome and no
AB  - extrachromosomal elements. The genome analysis revealed the presence of genes for
AB  - a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine
AB  - methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl
AB  - sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from
AB  - aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic
AB  - sulfur cycling at the seafloor. Among the ability to convert other sulfur
AB  - compounds it has the genetic capacity to produce climatically active dimethyl
AB  - sulfide. Growth on glutamate as a sole carbon source results in formation of
AB  - cell-connecting filaments, a putative phenotypic adaptation of the
AB  - surface-associated strain to the environmental conditions at the seafloor. Genome
AB  - analysis revealed the presence of a flagellum (fla1) and a type IV pilus
AB  - biogenesis, which is speculated to be a prerequisite for biofilm formation. This
AB  - is also related to genes responsible for signalling such as N-acyl homoserine
AB  - lactones, as well as quip-genes responsible for quorum quenching and antibiotic
AB  - biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence
AB  - similarity to the next relative S. haliotis) and the in silico DNA-DNA
AB  - hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str.
AB  - SK013 to be considered as a new species. The genome analysis of Shimia str. SK013
AB  - offered first insights into specific physiological and phenotypic adaptation
AB  - mechanisms of Roseobacter-affiliated bacteria to the benthic environment.
ER  -

TY  - JOUR
AU  - Kao, C.Y.
AU  - Chen, J.W.
AU  - Huang, Y.T.
AU  - Sheu, S.M.
AU  - Sheu, B.S.
AU  - Wu, J.J.
TI  - Genome Sequence and Annotation of Helicobacter pylori Strain Hp238, Isolated from a Taiwanese Patient with Mucosa-Associated Lymphoid Tissue Lymphoma.
JO  - Genome Announcements
PY  - 2015
SP  - e00006
EP  - e00015
VL  - 3
AB  - We present the complete genome sequence of Helicobacter pylori strain Hp238, isolated from a
AB  - Taiwanese patient with gastric mucosa-associated lymphoid tissue  lymphoma. Importantly, H.
AB  - pylori strain Hp238 can multiply in THP-1 cells after internalization through the induction of
AB  - autophagosome formation. These genome data will help to identify genes associated with H.
AB  - pylori intracellular multiplication and pathogenesis.
ER  -

TY  - JOUR
AU  - Kao, C.Y.
AU  - Yan, J.J.
AU  - Lin, Y.C.
AU  - Zheng, P.X.
AU  - Wu, J.J.
TI  - Complete Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae Strain 1756, Isolated from a Pus Specimen.
JO  - Genome Announcements
PY  - 2017
SP  - e00066
EP  - e00017
VL  - 5
AB  - Carbapenem-resistant Klebsiella pneumoniae strain 1756 was isolated from a pus specimen from a
AB  - Taiwanese patient. Here, the complete genome sequence of strain
AB  - 1756 is presented.
ER  -

TY  - JOUR
AU  - Kapatral, V. et al.
TI  - Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586.
JO  - J. Bacteriol.
PY  - 2002
SP  - 2005
EP  - 2018
VL  - 184
AB  - We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium
AB  - Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this
AB  - anaerobe facilitates the aggregation and establishment of several other species including the
AB  - dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain
AB  - ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO
AB  - bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding
AB  - 2,067 open reading frames, organized on a single circular chromosome with 27% GC content.
AB  - Despite its taxonomic position among the gram-negative bacteria, several features of its core
AB  - metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and
AB  - Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of
AB  - organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight
AB  - outer membrane proteins are predicted from the sequence, none of which has been reported in
AB  - the literature. More than 137 transporters for the uptake of a variety of substrates such as
AB  - peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist
AB  - for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids
AB  - are imported as such or as di- or oligopeptides that are subsequently degraded in the
AB  - cytoplasm. A principal source of energy appears to be the fermentation of glutamate to
AB  - butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H2S, methyl
AB  - mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing
AB  - wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of
AB  - F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the
AB  - mouth.
ER  -

TY  - JOUR
AU  - Kapatral, V.
AU  - Ivanova, N.
AU  - Anderson, I.
AU  - Reznik, G.
AU  - Bhattacharyya, A.
AU  - Gardner, W.L.
AU  - Mikhailova, N.
AU  - Lapidus, A.
AU  - Larsen, N.
AU  - D'Souza, M.
AU  - Walunas, T.
AU  - Haselkorn, R.
AU  - Overbeek, R.
AU  - Kyrpides, N.
TI  - Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586.
JO  - Genome Res.
PY  - 2003
SP  - 1180
EP  - 1189
VL  - 13
AB  - We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp.
AB  - vincentii (FNV), and compare that genome with F.
AB  - nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs)
AB  - with no orthologs in FN have been identified. Of these, 118 ORFs have no
AB  - known function and are unique to FNV, whereas 323 ORFs have functional
AB  - orthologs in other organisms. In addition to the excretion of butyrate,
AB  - H2S and ammonia-like FN, FNV has the additional capability to excrete
AB  - lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate
AB  - galactopyranose, galacturonate, and sialic acid into its O-antigen. It
AB  - appears to transport ferrous iron by an anaerobic ferrous transporter.
AB  - Genes for eukaryotic type serine/threonine kinase and phosphatase,
AB  - transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN.
AB  - Unique ABC transporters, cryptic phages, and three types of
AB  - restriction-modification systems have been identified in FNV. ORFs for
AB  - ethanolamine utilization, thermostable carboxypeptidase, gamma
AB  - glutamyl-transpeptidase, and deblocking aminopeptidases are absent from
AB  - FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but
AB  - thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes
AB  - for resistance to antibiotics such as acriflavin, bacitracin, bleomycin,
AB  - daunorubicin, florfenicol, and other general multidrug resistance are
AB  - present. These capabilities allow Fusobacteria to survive in a mixed
AB  - culture in the mouth.
ER  -

TY  - JOUR
AU  - Kapetaniou, E.G.
AU  - Kotsifaki, D.
AU  - Providaki, M.
AU  - Rina, M.
AU  - Bouriotis, V.
AU  - Kokkinidis, M.
TI  - Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2007
SP  - 12
EP  - 14
VL  - 63
AB  - The DNA methyltransferase M. BseCI from Bacillus stearothermophilus (EC 2.1.1.72), a
AB  - 579-amino-acid enzyme, methylates the N6 atom of the 30
AB  - adenine in the sequence 50-ATCGAT-3'. M.BseCI was crystallized in
AB  - complex with its cognate DNA. The crystals were found to belong to the
AB  - hexagonal space group P6, with unit-cell parameters a = b = 87.0, c =
AB  - 156.1 angstrom, beta = 120.0 degrees and one molecule in the asymmetric
AB  - unit. Two complete data sets were collected at wavelengths of 1.1 and
AB  - 2.0 angstrom to 2.5 and 2.8 angstrom resolution, respectively, using
AB  - synchrotron radiation at 100 K.
ER  -

TY  - JOUR
AU  - Kapfer, W.
AU  - Walter, J.
AU  - Trautner, T.A.
TI  - Cloning, characterization and evolution of the BsuFI restriction endonuclease gene of Bacillus subtilis and purification of the enzyme.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6457
EP  - 6463
VL  - 19
AB  - The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence
AB  - 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had
AB  - previously been characterized. Cloning of the R.BsuFI gene in E. coli was only possible with
AB  - the M.BsuFI Mtase gene present on a compatible plasmid. The cloned R.BsuFI gene was expressed
AB  - in E. coli and restriction activity was observed in vivo and in vitro. The R.BsuFI gene
AB  - consists of 1185 bp, coding for a protein of 395 amino acids with a calculated molecular
AB  - weight of 45.6 kD. The R.BsuFI enzyme was purified to homogeneity following overexpression. It
AB  - presumably works as a dimer and cleaves the 5' CCGG target sequence between the two cytosines
AB  - to produce sticky ends with 5' CG overhangs, like the isoschizomers R.MspI and R.HpaII. The
AB  - relatedness between R.BsuFI and R.MspI is reflected by significant similarities of the amino
AB  - acid sequences of both enzymes. This is the first case where such similarities have been
AB  - observed between isoschizomeric restriction endonucleases which belong to 5mC specific R/M
AB  - systems. This observation suggests that R.BsuFI and R.MspI genes derive from a common
AB  - ancestor. In spite of such functional and evolutionary relatedness, the R/M systems differ in
AB  - the arrangement of their R and M genes. In the BsuFI system transcription of the two genes is
AB  - convergent, whereas divergent transcription occurs in the MspI system.
ER  -

TY  - JOUR
AU  - Kapfhammer, D.
AU  - Blass, J.
AU  - Evers, S.
AU  - Reidl, J.
TI  - Vibrio cholerae phage K139: complete genome sequence and comparative genomics of related phages.
JO  - J. Bacteriol.
PY  - 2002
SP  - 6592
EP  - 6601
VL  - 184
AB  - In this report, we characterize the complete genome sequence of the
AB  - temperate phage K139, which morphologically belongs to the Myoviridae
AB  - phage family (P2 and 186). The prophage genome consists of 33,106 bp, and
AB  - the overall GC content is 48.9%. Forty-four open reading frames were
AB  - identified. Homology analysis and motif search were used to assign
AB  - possible functions for the genes, revealing a close relationship to
AB  - P2-like phages. By Southern blot screening of a Vibrio cholerae strain
AB  - collection, two highly K139-related phage sequences were detected in
AB  - non-O1, non-O139 strains. Combinatorial PCR analysis revealed almost
AB  - identical genome organizations. One region of variable gene content was
AB  - identified and sequenced. Additionally, the tail fiber genes were
AB  - analyzed, leading to the identification of putative host-specific sequence
AB  - variations. Furthermore, a K139-encoded Dam methyltransferase was
AB  - characterized.
ER  -

TY  - JOUR
AU  - Kaplan, D.A.
AU  - Nierlich, D.P.
TI  - Cleavage of nonglucosylated bacteriophage T4 deoxyribonucleic acid by restriction endonuclease EcoRI.
JO  - J. Biol. Chem.
PY  - 1975
SP  - 2395
EP  - 2397
VL  - 250
AB  - DNAs lacking the glucosyl modification (Glc-) and additionally lacking the
AB  - 6-methylaminopurine (N6-methyladenine) modification (Glc-, MeAde-) were
AB  - prepared from appropriate T4 mutants.  These DNAs were cleaved by the purified
AB  - restriction endonuclease EcoRI from Escherichia coli.  Normally modified DNA
AB  - (Glc+, MeAde+) was not attacked.  The EcoRII and the Hemophilus enzymes HindII
AB  - and HindIII do not attack Glc-, MeAde- T4 DNA, possibly due to the presence of
AB  - 6-hydroxymethylcytosine.  EcoRI produces approximately 40 specific fragments
AB  - from Glc- DNA ranging in molecular weights from 0.3 to 10.5x10/6.
ER  -

TY  - JOUR
AU  - Kaplan, D.J.
TI  - Variation in the inhibition of restriction enzyme cleavage of lambda phage DNA produced by two covalent binding antitumor agents:  Anthramycin and Mitomycin C.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1982
SP  - 639
EP  - 648
VL  - 109
AB  - DNA-drug complexes containing various levels of covalently bound mitomycin C
AB  - (MC) or anthramycin were subjected to the actions of a number of restriction
AB  - enzymes.  While MC presented only a partial block to the actions of a number of
AB  - these enzymes, anthramycin, at high binding ratios, blocked enzymatic activity
AB  - very well.  The contrast seen in the restriction cleavage of these DNA-drug
AB  - complexes may be related to the different points of attachement in DNA (minor
AB  - groove vs. major groove) for these drugs.  Although similarities in
AB  - electrophoretic band patterns exist for both drug complexes, certain
AB  - differences indicative of preferences in binding sequences do not necessarily
AB  - lie immediately within the restriction cut sites but may effect the cutting of
AB  - these sites from a distance.  The results also further support anthramycin's
AB  - potential usage as a selective/reversible blocking agent for recombinant
AB  - research.
ER  -

TY  - JOUR
AU  - Kaplan, J.B.
AU  - Lo, C.
AU  - Xie, G.
AU  - Johnson, S.L.
AU  - Chain, P.S.
AU  - Donnelly, R.
AU  - Kachlany, S.C.
AU  - Balashova, N.V.
TI  - Genome Sequence of Kingella kingae Septic Arthritis Isolate PYKK081.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3017
EP  - 3017
VL  - 194
AB  - Kingella kingae is a human oral bacterium that can cause infections of the skeletal system in
AB  - children. The bacterium is also a cardiovascular pathogen
AB  - causing infective endocarditis in children and adults. We report herein the draft
AB  - genome sequence of septic arthritis K. kingae strain PYKK081.
ER  -

TY  - JOUR
AU  - Kapley, A.
AU  - Sagarkar, S.
AU  - Tanksale, H.
AU  - Sharma, N.
AU  - Qureshi, A.
AU  - Khardenavis, A.
AU  - Purohit, H.J.
TI  - Genome Sequence of Alcaligenes sp. Strain HPC1271.
JO  - Genome Announcements
PY  - 2013
SP  - e00235
EP  - e00212
VL  - 1
AB  - We report a draft genome sequence of sp. strain HPC1271, which demonstrates antimicrobial
AB  - activity against multidrug-resistant bacteria. Antibiotic
AB  - production by has not been frequently reported, and hence, the availability of
AB  - the genome sequence should enable us to explore new antibiotic-producing gene
AB  - clusters.
ER  -

TY  - JOUR
AU  - Kappelman, J.R.
AU  - Brady, M.
AU  - Knoche, K.
AU  - Murray, E.
AU  - Schoenfeld, T.
AU  - Williams, R.
AU  - Vesselinova, N.
TI  - SgfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-GCGAT/CGC-3'.
JO  - Gene
PY  - 1995
SP  - 55
EP  - 58
VL  - 160
AB  - A new restriction endonuclease (ENase), SgfI, has been isolated from the bacterium
AB  - Streptomyces sp. SgfI recognizes the 8-bp palindrome 5'-GCGATCGC-3' and cleaves
AB  - double-stranded DNA after the T in this sequence, producing a two-base 3' overhang compatible
AB  - with PvuI termini.  SgfI is a rare-cutting ENase and should be useful for megabase mapping
AB  - experiments.
ER  -

TY  - JOUR
AU  - Kappler, U. et al.
TI  - Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 44
EP  - 58
VL  - 7
AB  - (Starkey 1934) Kelly . 2000 is a member of the family in the order , which is thus far poorly
AB  - characterized at the genome level. Cultures from this species are
AB  - most interesting due to their facultatively chemolithoautotrophic lifestyle,
AB  - which allows them to both consume carbon dioxide and to produce it. This feature
AB  - makes an interesting model organism for studying the genomic basis of regulatory
AB  - networks required for the switch between consumption and production of carbon
AB  - dioxide, a key component of the global carbon cycle. In addition, is of interest
AB  - for its ability to grow on various inorganic sulfur compounds and several
AB  - C1-compounds such as methanol. Besides , is only the second species in the family
AB  - with a completely sequenced genome of a type strain. The current taxonomic
AB  - classification of this group is in significant conflict with the 16S rRNA data.
AB  - The genomic data indicate that the physiological capabilities of the organism
AB  - might have been underestimated. The 4,765,023 bp long chromosome with its 4,511
AB  - protein-coding and 52 RNA genes was sequenced as part of the DOE Joint Genome
AB  - Institute Community Sequencing Program (CSP) 2008.
ER  -

TY  - JOUR
AU  - Kappler, U.
AU  - Davenport, K.
AU  - Beatson, S.
AU  - Lapidus, A.
AU  - Pan, C.
AU  - Han, C.
AU  - Montero-Calasanz, M.C.
AU  - Land, M.
AU  - Hauser, L.
AU  - Rohde, M.
AU  - Goker, M.
AU  - Ivanova, N.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
TI  - Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing gamma-proteobacterium  Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 38
EP  - 38
VL  - 11
AB  - Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae
AB  - in the order Thiotrichales. The gamma-proteobacterium belongs
AB  - to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with
AB  - stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington
AB  - State). Strain ALM 1(T) is characterized by its adaptation to life in the
AB  - oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the
AB  - stable stratified alkaline salt lakes. Strain ALM 1(T) is the first
AB  - representative of the genus Thioalkalimicrobium whose genome sequence has been
AB  - deciphered and the fourth genome sequence of a type strain of the
AB  - Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its
AB  - 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint
AB  - Genome Institute Community Sequencing Program (CSP) 2008.
ER  -

TY  - JOUR
AU  - Kappler, U.
AU  - Dhouib, R.
AU  - Nair, R.P.
AU  - McEwan, A.G.
TI  - Draft Genome Sequences of Three Nontypeable Strains of Haemophilus influenzae, C188, R535, and 1200, Isolated from Different Types of Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e00035
EP  - e00017
VL  - 5
AB  - Nontypeable Haemophilus influenzae is a persistent human respiratory pathogen known to be
AB  - involved in a range of acute and chronic respiratory diseases. Here,
AB  - we report the genome sequences of three H. influenzae strains isolated from
AB  - sputum, otitis media, and blood. Comparative analyses revealed significant
AB  - differences in the gene contents including the presence of genes mediating
AB  - antibiotic resistance.
ER  -

TY  - JOUR
AU  - Kapse, N.
AU  - Singh, P.
AU  - Roy, U.
AU  - Singh, S.M.
AU  - Dhakephalkar, P.K.
TI  - Insights into the Psychrophilic and Sea Ice-Specific Lifestyle of Marinobacter sp. Strain AC-23: a Genomic Approach.
JO  - Genome Announcements
PY  - 2017
SP  - e00134
EP  - e00117
VL  - 5
AB  - Marinobacter sp. strain AC-23 was isolated from Kongsfjorden in the Arctic. Here, we report
AB  - the first draft genome sequence of a putative novel species of the
AB  - genus Marinobacter comprising 4,149,715 bp, with a mean G+C content of 54.4%. The
AB  - draft genome sequence will aid in understanding the psychrophilic and sea
AB  - ice-specific lifestyle.
ER  -

TY  - JOUR
AU  - Kaput, J.
AU  - Sneider, T.W.
TI  - Methylation of somatic vs germ cell DNAs analyzed by restriction endonuclease digestions.
JO  - Nucleic Acids Res.
PY  - 1979
SP  - 2303
EP  - 2322
VL  - 7
AB  - Bacterial restriction endonucleases containing the dinucleotide CpG in their
AB  - cleavage sequences were used to compare the methylation patterns of primarily
AB  - repeated DNA sequences in (1) bovine somatic cell native DNAs vs bovine sperm
AB  - cell native DNA and (2) native vs renatured bovine liver and sperm cell DNAs.
AB  - The restriction patterns of sperm native DNA differ markedly from those of
AB  - somatic cell native DNAs when using HpaII, HhaI, and AvaI but not when using
AB  - the enzymes EcoRI and MspI.  Digestion patterns of germ cell renatured DNA
AB  - differed significantly from those of germ cell native DNA when using HpaII but
AB  - not when using MspI or EcoRI.  The results may not be due to artifacts of
AB  - renaturation of the DNAs.  The results are consistent with the concept that
AB  - germ cell DNA may be strand asymmetrically hemimethylated.  The data also
AB  - suggest that methylation of the 5'-cytosine in the sequence CCGG renders this
AB  - site insensitive to cleavage by MspI.
ER  -

TY  - JOUR
AU  - Karabecov, B.P.
AU  - Oganesian, M.G.
AU  - Airumian, B.A.
TI  - Susceptibility of the bacteriophage T5 to host-controlled restriction and modification in the Salmonella derby strain 456.
JO  - Genetika
PY  - 1970
SP  - 121
EP  - 128
VL  - 6
AB  - It was shown that wild type of bacteriophage T5 (T5h+) was not susceptible to
AB  - host-controlled variation in a bacterial host control system, consisting of E.
AB  - coli strains B, K-12 or BB and Salmonella derby 456 strain.  The h-mutants of
AB  - T5 phage, obtained on B/1,5 strain of E. coli, became susceptible to
AB  - restriction and modification on s. derby 456.  The phage T5h, grown on E. coli
AB  - B, K-12 or BB cells showed an efficiency of plating (eop) on S. derby 456 about
AB  - 10/7 - 10/9.  a small number of plaques formed by these mutants on S. derby
AB  - 456, contained only modified phage T5h 456 possessing eop equal to 1.0 when
AB  - grown on E. coli strains or on S. derby 456.  Acquirement of susceptibility to
AB  - host-controlled variation by phage T5 was due to host range mutation, which
AB  - indicates that the susceptibility of the phages to this variation is an
AB  - inheritant character of phage DNA, and is subjected to genetic changes and
AB  - selection.  The data obtained allow a suggestion concerning phage genome
AB  - contribution to the processes of the host controlled restriction and
AB  - modification.  The rate of restriction of phage T5h, observed in S. derby 456
AB  - host, after maintaining on E. coli strains and T5h+ phage non-susceptibility to
AB  - the observed effect, indicate that this system of HCV (host-controlled
AB  - variation) might be used as a new experimental model for investigating
AB  - processes of mutational changes of susceptibility of DNA molecule to the
AB  - restricting and modifying mechanisms of host cells.
ER  -

TY  - JOUR
AU  - Karamov, E.V.
AU  - Naroditsky, B.S.
AU  - Zavizion, B.A.
AU  - Tikhonenko, T.I.
TI  - Transformation of EcoRI restriction endonuclease substrate specificity under the influence of glycerol.
JO  - Biull. Eksp. Biol. Med.
PY  - 1977
SP  - 46
EP  - 48
VL  - 84
AB  - The restriction endonuclease EcoRI hydrolyzes DNA to a greater number of fragments in the
AB  - presence of glycerol than under normal conditions.  This enzyme begins to work by the
AB  - so-called EcoRI*-type of restriction when glycerol concentration reaches 50%.  The EcoRI*
AB  - activity appeared in experiments only when the ionic strength of the solution was decreased
AB  - and pH of the solution was increased.  However, under such extreme conditions the enzyme was
AB  - quickly inactivated and it was difficult to obtain reproducible results especially for
AB  - hydrolysis of the high-molecular DNA.  The suggested conditions for the EcoRI* activity permit
AB  - to obtain reproducible results, this being practically equivalent to discovery of the new
AB  - restriction endonuclease.
ER  -

TY  - JOUR
AU  - Karas, B.J.
AU  - Jablanovic, J.
AU  - Sun, L.
AU  - Ma, L.
AU  - Goldgof, G.M.
AU  - Stam, J.
AU  - Ramon, A.
AU  - Manary, M.J.
AU  - Winzeler, E.A.
AU  - Venter, J.C.
AU  - Weyman, P.D.
AU  - Gibson, D.G.
AU  - Glass, J.I.
AU  - Hutchison, C.A.I.I.I.
AU  - Smith, H.O.
AU  - Suzuki, Y.
TI  - Direct transfer of whole genomes from bacteria to yeast.
JO  - Nat. Methods
PY  - 2013
SP  - 410
EP  - 412
VL  - 10
AB  - Transfer of genomes into yeast facilitates genome engineering for genetically intractable
AB  - organisms, but this process has been hampered by the need for cumbersome isolation of intact
AB  - genomes before transfer. Here we demonstrate direct cell-to-cell transfer of bacterial genomes
AB  - as large as 1.8 megabases (Mb)into yeast under conditions that promote cell fusion. Moreover,
AB  - we discovered that removal of restriction endonucleases from donor bacteria resulted in the
AB  - enhancement of genome transfer.
ER  -

TY  - JOUR
AU  - Karaseva, A.
AU  - Tsapieva, A.
AU  - Pachebat, J.
AU  - Suvorov, A.
TI  - Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3.
JO  - Genome Announcements
PY  - 2016
SP  - e01622
EP  - e01615
VL  - 4
AB  - We report here the draft genome sequence of the bacteriocin producer Enterococcus faecium
AB  - strain L-3, isolated from a probiotic preparation, Laminolact, which is
AB  - widely used in the Russian Federation. The draft genome sequence is composed of
AB  - 74 contigs for a total of 2,643,001 bp, with 2,646 coding genes. Five clusters
AB  - for bacteriocin production were found.
ER  -

TY  - JOUR
AU  - Karched, M.
AU  - Furgang, D.
AU  - Planet, P.J.
AU  - Desalle, R.
AU  - Fine, D.H.
TI  - Genome Sequence of Aggregatibacter actinomycetemcomitans RHAA1, Isolated from a Rhesus Macaque, an Old World Primate.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1275
EP  - 1276
VL  - 194
AB  - Aggregatibacter actinomycetemcomitans is implicated in localized aggressive periodontitis. We
AB  - report the first genome sequence of an A. actinomycetemcomitans
AB  - strain isolated from an Old World primate.
ER  -

TY  - JOUR
AU  - Karczewska-Golec, J.
AU  - Kochanowska-Lyzen, M.
AU  - Olszewski, P.
AU  - Balut, M.
AU  - Moskot, M.
AU  - Piotrowski, A.
AU  - Golec, P.
AU  - Szalewska-Palasz, A.
TI  - Draft Genome Sequence of Flavobacterium sp. 316, a Baltic Sea Isolate Exhibiting  a High Level of Resistance to Marine Stress Conditions.
JO  - Genome Announcements
PY  - 2016
SP  - e00180
EP  - e00116
VL  - 4
AB  - Here, we present the draft genome sequence ofFlavobacteriumsp. 316, isolated from brackish
AB  - water of the Gulf of Gdansk, southern Baltic Sea. The assembly contains
AB  - 3,971,755 bp in 17 scaffolds. The sequence will facilitate postgenomic studies on
AB  - bacterial stress responses in the challenging habitat of the Baltic Sea.
ER  -

TY  - JOUR
AU  - Karczewska-Golec, J.
AU  - Strapagiel, D.
AU  - Sadowska, M.
AU  - Szalewska-Palasz, A.
AU  - Golec, P.
TI  - Draft Genome Sequence of Shewanella baltica M1 Isolated from Brackish Surface Water of the Gulf of Gdansk.
JO  - Genome Announcements
PY  - 2016
SP  - e00611
EP  - e00616
VL  - 4
AB  - Here, we present the 5.168-Mbp draft genome sequence of Shewanella baltica M1, the first
AB  - Shewanella strain from the Gulf of Gdansk to have its genome sequenced
AB  - and annotated. The availability of the genome sequence of strain M1 will promote
AB  - further global analyses of bacterial stress responses in the unique Gulf of
AB  - Gdansk ecosystem.
ER  -

TY  - JOUR
AU  - Karczmarczyk, M.
AU  - Wang, J.
AU  - Leonard, N.
AU  - Fanning, S.
TI  - Complete nucleotide sequence of a conjugative IncF plasmid from an Escherichia coli isolate of equine origin containing blaCMY-2 within a novel genetic context.
JO  - FEMS Microbiol. Lett.
PY  - 2014
SP  - 123
EP  - 127
VL  - 352
AB  - A blaCMY-2 -containing conjugative IncF plasmid denoted as pEQ011, previously
AB  - identified in a multidrug-resistant Escherichia coli isolate of equine origin,
AB  - was characterized. The plasmid consisted of 85 507 bp, with 118 predicted open
AB  - reading frames. This is the first known report demonstrating the association of a
AB  - blaCMY-2 gene with an IncF incompatibility-type plasmid backbone. A novel genetic
AB  - arrangement was identified wherein the blaCMY-2 resistance gene was proximally
AB  - flanked by IS1294 along with a partial blc gene located distally and within a
AB  - yacABC operon.
ER  -

TY  - JOUR
AU  - Karimi, E.
AU  - Goncalves, J.M.
AU  - Reis, M.
AU  - Costa, R.
TI  - Draft Genome Sequence of Microbacterium sp. Strain Alg239_V18, an Actinobacterium Retrieved from the Marine Sponge Spongia sp.
JO  - Genome Announcements
PY  - 2017
SP  - e01457
EP  - e01416
VL  - 5
AB  - Here, we describe the draft genome sequence of Microbacterium sp. strain Alg239_V18, an
AB  - actinobacterium retrieved from the marine sponge Spongia sp.
AB  - Genome annotation revealed a vast gene repertoire involved in antibiotic and
AB  - heavy metal-resistance, and a versatile carbohydrate assimilation metabolism with
AB  - potential for chitin utilization.
ER  -

TY  - JOUR
AU  - Karl, M.M.
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92T Using Nanopore and Illumina Sequencing Data.
JO  - Genome Announcements
PY  - 2017
SP  - e00423
EP  - e00417
VL  - 5
AB  - Here, we report the closed genome sequence of Clostridium formicaceticum, an Rnf- and
AB  - cytochrome-containing autotrophic acetogen that is able to convert carbon
AB  - monoxide to acetate using the Wood-Ljungdahl pathway. The genome consists of a
AB  - circular chromosome (4.59 Mb).
ER  -

TY  - JOUR
AU  - Karlin, S.
AU  - Burge, C.
AU  - Campbell, A.M.
TI  - Statistical analyses of counts and distributions of restriction sites in DNA sequences.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1363
EP  - 1370
VL  - 20
AB  - Counts and spacings of all 4- and 6-bp palindromes in DNA sequences from a
AB  - broad range of organisms were investigated.  Both 4- and 6-bp average
AB  - palindrome counts were significantly low in all bacteriophages except one,
AB  - probably as a means of avoiding restriction enzyme cleavage.  The exception, T4
AB  - of normal 4- and 6-palindrome counts, putatively derives protection from
AB  - modification of cytosine to hydroxymethylcytosine plus glycosylation.  The
AB  - counts and distributions of 4-bp and of 6-bp restriction sites in bacterial
AB  - species are variable.  Bacterial cells with multiple restriction systems for
AB  - 4-bp or 6-bp target specificities are low in aggregate 4- or 6-bp palindrome
AB  - counts/kb, respectively, but bacterial cells lacking exact 4-cutter enzymes
AB  - generally show normal or high counts of 4-bp palindromes when compared with
AB  - random control sequences of comparable nucleotide frequencies.  For example, E.
AB  - coli, apparently without an exact 4-bp target restriction endonuclease (see
AB  - text), contains normal aggregate 4-palindrome counts/kb, while B. subtilis,
AB  - which abounds with 4-bp restriction system, shows a significant
AB  - under-representation of 4-palindrome counts.  Both E. coli and B. subtilis have
AB  - many 6-bp restriction enzymes and concomitantly diminished aggregate
AB  - 6-palindrome counts/kb.  Eukaryote, viral, and organelle sequences generally
AB  - have aggregate 4- and 6-palindromic counts/kb in the normal range.
AB  - Interpretations of these results are given in terms of restriction/methylation
AB  - regimes, recombination and transcription processes, and possible structural and
AB  - regulatory roles of 4- and 6-bp palindromes.
ER  -

TY  - JOUR
AU  - Karlovsky, P.
TI  - Mutual competitive inhibition between target sites during the restriction endonuclease digestion of DNA.
JO  - J. Theor. Biol.
PY  - 1988
SP  - 1
EP  - 6
VL  - 132
AB  - The reaction rate of restriction endonuclease was evaluated theoretically, considering the
AB  - competition between target sites and a nonspecific DNA.  An equation for the initial cleavage
AB  - rate at a single site for a DNA substrate containing more than one recognition site was
AB  - derived.  The consequences for the study of preferential cleavage were discussed.
ER  -

TY  - JOUR
AU  - Karlovsky, P.
TI  - Calculation of individual cleavage rates from partial digests in restriction endonuclease kinetics.
JO  - J. Theor. Biol.
PY  - 1988
SP  - 7
EP  - 14
VL  - 132
AB  - A correction for results obtained by an analysis of DNA molecules partially
AB  - cleaved with restriction endonuclease was suggested.  The correction was proved
AB  - on model data.  Applications to (i) electron-microscopic analysis of singly
AB  - cleaved molecules, (ii) partial digestion of a circular molecule followed by
AB  - complete digestion with a second enzyme, (iii) systems with great cleavage
AB  - differences, and (iv) partial cleavage of end-labelled molecules were
AB  - discussed.
ER  -

TY  - JOUR
AU  - Karlovsky, P.
TI  - Kinetics of circular DNA molecule digestion by restriction endonuclease A: Computation of kinetic constants from time dependence of fragment concentrations.
JO  - Acta Biotheor.
PY  - 1986
SP  - 279
EP  - 292
VL  - 35
AB  - A model for kinetics of circular substrate cleavage by restriction endonuclease
AB  - was formulated.  The aim of the analysis of the model was to extract kinetic
AB  - constants for all target sites from time-dependence of fragment concentration
AB  - in reaction products.  That was proved to be possible for molecules with an odd
AB  - number of fragments only.  A symmetry of the molecules with an even number of
AB  - fragment is the cause.  A solution for molecules witih an odd number of
AB  - fragments was found and methods for dealing with the other moleculars were
AB  - suggested.
ER  -

TY  - JOUR
AU  - Karlovsky, P.
TI  - A re-evaluation of evidence attributing the difference in cleavage rates of restriction endonuclease at different sites in the substrate to differences in KM values.
JO  - Biochem. J.
PY  - 1986
SP  - 611
EP  - 612
VL  - 235
AB  - The only result supporting the hypothesis that the differences in restriction
AB  - endonuclease cleavage rates at various target sites are caused by differences
AB  - in KM values was reported by Forsblom, Rigler, Ehrenberg, Petterson & Philipson
AB  - [(1976) Nucl. Acids Res. 3, 3255-3269].  The present work shows that the
AB  - kinetic analysis in that paper is based on incorrect derivation and in fact
AB  - provides no support for the hypothesis mentioned.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus plantarum 2165.
JO  - Genome Announcements
PY  - 2014
SP  - e01179
EP  - e01113
VL  - 2
AB  - This report describes a draft genome sequence of Lactobacillus plantarum 2165. The data
AB  - demonstrate the presence of a large number of genes responsible for
AB  - sugar metabolism and the fermentation activity of this bacterium. Different cell
AB  - surface proteins, including fibronectin and mucus-binding adhesins, may
AB  - contribute to the beneficial probiotic properties of this strain.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Khlebnikov, V.C.
AU  - Kosarev, I.V.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus plantarum 2025.
JO  - Genome Announcements
PY  - 2016
SP  - e01532
EP  - e01515
VL  - 4
AB  - A draft genome sequence of Lactobacillus plantarum 2025 was derived using Ion Torrent
AB  - sequencing technology. The total size of the assembly (3.33 Mb) was in
AB  - agreement with the genome sizes of other strains of this species. The data will
AB  - assist in revealing the genes responsible for the specific properties of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Kudryashova, E.B.
AU  - Ariskina, E.V.
TI  - Draft Genome Sequence of 'Cohnella kolymensis' B-2846.
JO  - Genome Announcements
PY  - 2016
SP  - e01587
EP  - e01515
VL  - 4
AB  - A draft genome sequence of 'Cohnella kolymensis' strain B-2846 was derived using  IonTorrent
AB  - sequencing technology. The size of the assembly and G+C content were
AB  - in agreement with those of other species of this genus. Characterization of the
AB  - genome of a novel species of Cohnella will assist in bacterial systematics.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Melnikov, V.G.
TI  - Draft Genome Sequence of Corynebacterium pseudodiphtheriticum Strain 090104 'Sokolov'.
JO  - Genome Announcements
PY  - 2013
SP  - e00921
EP  - e00913
VL  - 1
AB  - This report describes the first draft genome sequence of a Corynebacterium
AB  - pseudodiphtheriticum strain. The information on the genome organization and
AB  - putative gene products will assist in better understanding of the molecular
AB  - mechanisms involved in the beneficial probiotic effects of this bacterium.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Melnikov, V.G.
AU  - Chikindas, M.L.
TI  - Draft Genome Sequence of Bacillus subtilis strain KATMIRA1933.
JO  - Genome Announcements
PY  - 2014
SP  - e00619
EP  - e00614
VL  - 2
AB  - In this report, we present a draft sequence of Bacillus subtilis KATMIRA1933. Previous studies
AB  - demonstrated probiotic properties of this strain partially
AB  - attributed to production of an antibacterial compound, subtilosin. Comparative
AB  - analysis of this strain's genome with that of a commercial probiotic strain, B.
AB  - subtilis Natto, is presented.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Melnikov, V.G.
AU  - Chistyakov, V.A.
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens B-1895.
JO  - Genome Announcements
PY  - 2014
SP  - e00633
EP  - e00614
VL  - 2
AB  - In this report, we present a draft genome sequence of Bacillus amyloliquefaciens  strain
AB  - B-1895. Comparison with the genome of a reference strain demonstrated
AB  - similar overall organization, as well as differences involving large gene
AB  - clusters.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Melnikov, V.G.
AU  - Khlebnikov, V.C.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus crispatus 2029.
JO  - Genome Announcements
PY  - 2014
SP  - e01221
EP  - e01213
VL  - 2
AB  - This report describes a draft genome sequence of Lactobacillus crispatus 2029. The reads
AB  - generated by the Ion Torrent PGM were assembled into contigs with a
AB  - total size of 2.2 Mb. The data were annotated using the NCBI GenBank and RAST
AB  - servers. A comparison with the reference strain revealed specific features of the
AB  - genome.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Melnikov, V.G.
AU  - Kosarev, I.V.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus rhamnosus 2166.
JO  - Genome Announcements
PY  - 2014
SP  - e01222
EP  - e01213
VL  - 2
AB  - In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain
AB  - 2166, a potential novel probiotic. Genome annotation and read
AB  - mapping onto a reference genome of L. rhamnosus strain GG allowed for the
AB  - identification of the differences and similarities in the genomic contents and
AB  - gene arrangements of these strains.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Melnikov, V.G.
AU  - Kosarev, I.V.
AU  - Khlebnikov, V.C.
AU  - Sukhikh, G.T.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus gasseri Strain 2016.
JO  - Genome Announcements
PY  - 2013
SP  - e00624
EP  - e00613
VL  - 1
AB  - Different common factors contribute to the antagonistic properties of Lactobacillus gasseri
AB  - toward various pathogens. However, there is
AB  - strain-to-strain variation in the probiotic properties of this bacterium. The
AB  - draft genome sequence of L. gasseri strain 2016 determined in this study will
AB  - assist in understanding the genetic basis for such variation.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Nadarajah, S.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus jensenii Strain MD IIE-70(2).
JO  - Genome Announcements
PY  - 2013
SP  - e01005
EP  - e01013
VL  - 1
AB  - A draft genome sequence of Lactobacillus jensenii strain MD IIE-70(2) was determined using Ion
AB  - PGM technology. The reads were mapped to a reference strain
AB  - and assembled using a combination of tools. The genetic features revealed in this
AB  - study will assist in understanding the probiotic properties of Lactobacillus
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Raju, K.
AU  - Abramov, V.M.
TI  - Draft Genome Sequence of Lactobacillus fermentum Strain 3872.
JO  - Genome Announcements
PY  - 2013
SP  - e01006
EP  - e01013
VL  - 1
AB  - This report describes a draft genome sequence of Lactobacillus fermentum strain 3872. The data
AB  - revealed remarkable similarity to and dissimilarity with the
AB  - published genome sequences of other strains of the species. The absence of and
AB  - variation in structures of some adhesins and the presence of an additional
AB  - adhesin may reflect adaptation of the bacterium to different host systems and may
AB  - contribute to specific properties of this strain as a new probiotic.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Robyn, J.
AU  - Rasschaert, G.
AU  - Heyndrickx, M.
TI  - Draft Genome Sequence of Enterococcus faecalis MB5259.
JO  - Genome Announcements
PY  - 2014
SP  - e00634
EP  - e00614
VL  - 2
AB  - In this study, we present a draft genome sequence of Enterococcus faecalis MB5259, a promising
AB  - probiotic strain. The identified differences and common
AB  - features between this strain and reference strains will assist in better
AB  - understanding the mechanism of antibacterial action and in developing novel
AB  - probiotics.
ER  -

TY  - JOUR
AU  - Karlyshev, A.V.
AU  - Villena, J.
AU  - Gonzalez, C.
AU  - Albarracin, L.
AU  - Barros, J.
AU  - Garcia, A.
TI  - Draft Genome Sequence of a Probiotic Strain, Lactobacillus fermentum UCO-979C.
JO  - Genome Announcements
PY  - 2015
SP  - e01439
EP  - e01415
VL  - 3
AB  - This report describes a draft genome sequence of Lactobacillus fermentum strain UCO-979C. The
AB  - reads generated by a Ion Torrent PGM were assembled into contigs,
AB  - with a total size of 2.01 Mb. The data were annotated using the NCBI GenBank and
AB  - RAST servers. Specific features of the genome are highlighted.
ER  -

TY  - JOUR
AU  - Karna, S.L.
AU  - Chen, T.
AU  - Chen, P.
AU  - Peacock, T.J.
AU  - Abercrombie, J.J.
AU  - Leung, K.P.
TI  - Genome Sequence of a Virulent Pseudomonas aeruginosa Strain, 12-4-4(59), Isolated from the Blood Culture of a Burn Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e00079
EP  - e00016
VL  - 4
AB  - Pseudomonas aeruginosa is an opportunistic pathogen that frequently infects wounds,
AB  - significantly impairs wound healing, and causes morbidity and mortality
AB  - in burn patients. Here, we report the genome sequence of a virulent strain of P.
AB  - aeruginosa, 12-4-4(59), isolated from the blood culture of a burn patient.
ER  -

TY  - JOUR
AU  - Karpova, E.
AU  - Kubareva, E.
AU  - Petrauskene, O.
AU  - Joschimiak, A.
AU  - Van Kley, H.
TI  - Peculiarity of the recognition and cleavage by restriction endonuclease EcoRII.
JO  - FASEB J.
PY  - 1995
SP  - A1400
EP  - A1400
VL  - 9
AB  - The restriction endonuclease EcoRII binds with high affinity to the duplex DNA 5' CC(A/T)GG
AB  - 3' and specifically cleaves it at the 5' end of the site as indicated by the arrow. It has
AB  - been shown that EcoRII requires an auxiliary site for activation, and the formation of a
AB  - four-strand supersite was suggested. To understand the enzymatic mechanism and the interaction
AB  - of EcoRII with two recognition sites, we have studied binding and cleavage of DNA duplexes
AB  - containing canonical or modified EcoRII sites by EcoRII. The reactions were analyzed by
AB  - polyacrylamide gel electrophoresis under non-denaturing conditions. We have shown, that (T to
AB  - 5-fluorodeoxyuridine) or (A to N6-methyldeoxyadenosine) substitutions in the central base pair
AB  - do not affect DNA recognition, but they have a dramatic influence on cleavage. At the same
AB  - time modification or substitution of C or G nucleotides in the recognition sequence affects
AB  - both recognition and rate of cleavage of DNA. These data suggests that specific interaction
AB  - with the central base pair (A/T) contributes to the catalytic activity of the enzyme. Based on
AB  - these data we present a model for four-strand supersite formation of the enzyme-substrate
AB  - complex.
ER  -

TY  - JOUR
AU  - Karpova, E.A.
AU  - Kubareva, E.A.
AU  - Buryanov, Y.I.
AU  - Gromova, E.S.
TI  - Formation of two types of enzyme-substrate complexes at the interaction of EcoRII restriction endonuclese with synthetic DNA duplexes.
JO  - Mol. Biol. (Mosk)
PY  - 1992
SP  - 993
EP  - 998
VL  - 26
AB  - Binding of EcoRII restriction endonuclease to synthetic oligodeoxyribonucleotide substrates of
AB  - 11-30 base pairs long was investigated by polyacrylamide gel electrophoresis under
AB  - nondenaturing conditions in the absence of Mg2+ ions. Irrespective of the length of a
AB  - substrate, two types of specific DNA-protein complexes were shown to be formed. Their mobility
AB  - in gels was close to that of the monomer (45 kDa) and dimer (90 kDa) of marker protein
AB  - ovalbumin. The ratio of these complexes in solution depended on that of the molar
AB  - concentrations of EcoRII restriction endonuclease and DNA duplexes. The possible structure of
AB  - the complexes is discussed.
ER  -

TY  - JOUR
AU  - Karpova, E.A.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Buryanov, Y.I.
TI  - Peculiaritites of the binding of restriction endonuclease EcoRII to synthetic DNA duplexes.
JO  - Biochem. Mol. Biol. Int.
PY  - 1993
SP  - 113
EP  - 121
VL  - 29
AB  - The binding of restriction endonuclease EcoRII to synthetic oligodeoxyribonucleotide
AB  - substrates 11 to 30 bp long was investigated by gradient polyacrylamide gel electrophoresis
AB  - under nondenaturing conditions in the absence of Mg2+ ions. Irrespective of the substrate's
AB  - length, two types of specific DNA-protein complexes were shown to be formed. Their mobility in
AB  - gels was close to that of the monomer and the dimer of the marker ovalbumin. The number of
AB  - such complexes in solution depended on the ratio of the molar concentrations of restriction
AB  - endonuclease EcoRII and the DNA duplex. The possible structure of the complexes is discussed.
ER  -

TY  - JOUR
AU  - Karpova, E.A.
AU  - Kubareva, E.A.
AU  - Shabarova, Z.A.
TI  - A model of EcoRII restriction endonuclease action: The active complex is most likely formed by one protein subunit and one DNA recognition site.
JO  - Life
PY  - 1999
SP  - 91
EP  - 98
VL  - 48
AB  - To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we
AB  - studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic
AB  - DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'.
AB  - All binding substrates or substrate analogues tested could be divided into two major groups:
AB  - (I) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable
AB  - complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type
AB  - of complex, observed both in the presence and absence of Mg2+.  Unlike the latter, duplexes
AB  - under the first group can be hydrolyzed by endonuclease.  Data obtained suggest that the
AB  - active complex is most likely formed by one protein subunit and one DNA recognition sequence.
AB  - A model of EcoRII endonuclease action is presented.
ER  -

TY  - JOUR
AU  - Karpova, E.A.
AU  - Meehan, E.
AU  - Pusey, M.L.
AU  - Chen, L.
TI  - Crystallization and preliminary x-ray diffraction analysis of restriction endonuclease EcoRII.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 1999
SP  - 1604
EP  - 1605
VL  - 55
AB  - Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion
AB  - technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were
AB  - grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x
AB  - 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a
AB  - cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV
AB  - imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with
AB  - unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal
AB  - asymmetric unit contains two protein molecules, and self-rotation function analysis shows a
AB  - pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of
AB  - crystal diffraction and to search for heavy-atom derivatives are under way.
ER  -

TY  - JOUR
AU  - Karreman, C.
TI  - The genes for two procaryotic DNA modification methylases.
JO  - Ph.D. Thesis, State University of Leiden, Holland
PY  - 1988
SP  - 1
EP  - 95
AB  - None
ER  -

TY  - JOUR
AU  - Karreman, C.
AU  - de Waard, A.
TI  - Isolation and characterization of the modification methylase M.SinI.
JO  - J. Bacteriol.
PY  - 1988
SP  - 2533
EP  - 2536
VL  - 170
AB  - A sequence-specific modification methylase (M.SinI) was isolated and purified from Escherichia
AB  - coli harboring a derivative of recombinant plasmid pSI4 (see accompanying manuscript: C.
AB  - Karreman and A. de Waard, J. Bacteriol. 170:2527-2532, 1988), which contains a Salmonella
AB  - infantis DNA insert. The enzyme uniquely methylates the internal deoxycytidylate residue in
AB  - the nucleotide sequence GG(A/T)MeCC, thereby protecting DNA completely against cleavage by
AB  - restriction endonuclease R.SinI or R.AvaII [GG(A/T)CC], and in part against cleavage by
AB  - R.Sau96I (GGNCC).
ER  -

TY  - JOUR
AU  - Karreman, C.
AU  - de Waard, A.
TI  - Agmenellum quadruplicatum M.AquI, a novel modification methylase.
JO  - J. Bacteriol.
PY  - 1990
SP  - 266
EP  - 272
VL  - 172
AB  - The complete type II modification methylase of Agmenellum quadruplicatum was cloned in
AB  - Escherichia coli as an R.Sau3A fragment of approximately 4.5 kilobases. The coding sequence
AB  - was contained in a stretch of 1,156 base pairs which was organized into two parallel, partly
AB  - overlapping open reading frames of 248 and 139 codons. In vivo complementation experiments
AB  - showed that the synthesis of both predicted peptides was required for full methylase activity.
AB  - The amino acid sequences were considerably similar to regions of other deoxycytidylate
AB  - methylases.
ER  -

TY  - JOUR
AU  - Karreman, C.
AU  - de Waard, A.
TI  - Cloning and complete nucleotide sequences of the TypeII restriction-modification genes of Salmonella infantis.
JO  - J. Bacteriol.
PY  - 1988
SP  - 2527
EP  - 2532
VL  - 170
AB  - The complete typeII restriction-modification system of Salmonella infantis was
AB  - cloned in Escherichia coli as an R.Sau3AI fragment of 3,430 base pairs.  The
AB  - clone was shown to express the restriction endonuclease as well as the
AB  - modification methylase.  The nucleotide sequence of the above fragment showed
AB  - two open reading frames of 461 and 230 codons in tail-to-tail orientation.
AB  - These were shown to represent the modification methylase M.SinI and the
AB  - restriction endonuclease R.SinI, respectively.  The methylase M.SinI amino acid
AB  - sequence revealed a considerable similarity to those of other deoxycytidylate
AB  - methylases.  In contrast, endonuclease R.SinI did not exhibit such a similarity
AB  - to other restriction enzymes.
ER  -

TY  - JOUR
AU  - Karreman, C.
AU  - Tandeau de Marsac, N.
AU  - de Waard, A.
TI  - Isolation of a deoxycytidylate methyl transferase capable of protecting DNA uniquely against cleavage by endonuclease R. AquI (isoschizomer of AvaI).
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 5199
EP  - 5205
VL  - 14
AB  - A sequence-specific modification methylase (M.AquI) was isolated and purified
AB  - from Agmenellum quadruplicatum (Synechococcus PCC 7002).  This enzyme uniquely
AB  - methylates the deoxycytidylate residue in the sequence *CYCGRG indicated by the
AB  - asterisk.  It was shown to protect DNA against cleavage by restriction
AB  - endonucleases AvaI, SmaI and XhoI, which recognize the sequences CYCGRG,
AB  - CCCGGG, and CTCGAG, respectively.
ER  -

TY  - JOUR
AU  - Karrer, K.M.
AU  - VanNuland, T.A.
TI  - Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 1364
EP  - 1370
VL  - 30
AB  - There are about 50 copies of each chromosome in the somatic macronucleus of the ciliated
AB  - protozoan Tetrahymena. Approximately 0.8% of the adenine residues in the macronuclear DNA of
AB  - Tetrahymena are methylated to N6-methyladenine. The degree of methylation varies between sites
AB  - from a very low percentage to >90%. In this study a correlation was found between nucleosome
AB  - positioning and DNA methylation. Eight GATC sites with different levels of methylation were
AB  - examined. There was a direct correlation between the degree of methylation and proximity to
AB  - linker DNA at these sites. Although methylation occurs preferentially in linker DNA, the
AB  - patterns and extent of methylation in a histone H1 knockout strain were virtually
AB  - indistinguishable from those in wild-type cells.
ER  -

TY  - JOUR
AU  - Karrer, K.M.
AU  - VanNuland, T.A.
TI  - Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 4566
EP  - 4573
VL  - 26
AB  - Approximately 0.8% of the adenine residues in the macronuclear DNA of the ciliated protozoan
AB  - Tetrahymena thermophila are modified to N6-methyladenine.  DNA methylation is site specific
AB  - and the pattern of methylation is constant between clonal cell lines.  In vivo, modification
AB  - of adenine residues appears to occur exclusively in the sequence 5'-NAT-3', but no consensus
AB  - sequence for modified sites has been found.  In this study, DNA fragments containing a site
AB  - that is uniformly methylated on the 50 copies of the macronuclear chromosome were cloned into
AB  - the extrachromosomal rDNA.  In the novel location on the rDNA minichromosome, the site was
AB  - unmethylated.  The result was the same whether the sequences were introduced in a methylated
AB  - or unmethylated state and regardless of the orientation of the sequence with respect to the
AB  - origin of DNA replication.  The data show that sequence is insufficient to account for
AB  - site-specific methylation in Tetrahymena and argue that other factors determine the pattern of
AB  - DNA methylation.
ER  -

TY  - JOUR
AU  - Karska-Wysocki, B.
AU  - Hua, N.M.
AU  - Vzdornov, D.
AU  - Szatmari, G.
AU  - Mamet-Bratley, M.D.
TI  - Detection and purification of a new restriction endonuclease, LlaMI, from Lactococcus lactis subsp. lactis M19.
JO  - Sixth Symposium on Lactic Acid Bacteria Genetics, Metabolism and Applications
PY  - 1999
SP  - F17
EP  - F17
VL  - 0
AB  - One of the multiple phage defense systems present in bacteria is the Restriction/modification
AB  - system.  Type II restriction endonucleases recognize specific nucleotide sequences in invading
AB  - phage DNA and cleave the DNA at these sites.  We describe a new restriction activity, LlaMI,
AB  - present in cell extracts of Lactococcus lactis subsp. lactis M19, a variant isolated from a
AB  - commercially available industrial starter culture.  We have characterized the strain M19 by
AB  - molecular typing using AP-PCR fingerprinting and plasmid profile analysis.  During the
AB  - purification of LlaMI, non-specific nuclease activity was detected.  The nuclease activity
AB  - could be separated from the LlaMI activity using low-pressure anion exchange and affinity
AB  - chromatography.  Partially-purified cell extracts were tested for restriction activity on the
AB  - following substrates: DNA of phages lambda, PhiX174 and T7 and plasmids pBR322 and Litmus 29.
AB  - The LlaMI DNA cleavage patterns closely resemble those of restriction enzyme ScrFI, produced
AB  - by Lactococcus lactis subsp. cremoris UC503.
ER  -

TY  - JOUR
AU  - Karska-Wysocki, B.
AU  - Szatmari, G.
AU  - Barrette, B.
AU  - Mamet-Bratley, M.D.
TI  - Characterization of a new restriction endonuclease, LlaGI, produced  by Lactococcus lactis subsp. cremoris G2.
JO  - Life Sc. Confer. Ottawa
PY  - 1996
SP  - P088
EP  - P088
VL  - 0
AB  - A new sequence-specific endonuclease from Lactococcus lactis
AB  - subsp. cremoris G2 was identified, by restriction maping, as the first
AB  - reported isoschizomer of NheI.  We have confirmed this identification with
AB  - a cloning test and have named this new Type II restriction endonuclease
AB  - LlaGI.  We have characterized the enzyme-producing strain G2 by molecular
AB  - typing using AP-PCR fingerprinting and plasmid profile analysis.  These
AB  - tests demonstrated the presence of amplicons of 200 to 900 bp and the
AB  - presence of five plasmid bands at appropriate size positions of 7 to 25
AB  - kbp.  Extracts containing LlaGI nuclease did not digest DNA from the
AB  - producing strain, suggesting that a modification activity is also present
AB  - in this strain.  Specific endonuclease digestion of phage DNA was detected
AB  - in diluted crude extracts corresponding to 0.9 ug (wet-weight) G2
AB  - cells/ml.  During purification of LlaGI from crude extracts, non-specific
AB  - nuclease activity was detected in fractions containing the restriction
AB  - enzyme.  This contamination could be effectively separated from LlaGI
AB  - activity using low-pressure anion exchange chromatography and elution with
AB  - a gradient of NaCl or KCl.  We are currently developing a purification
AB  - protocol for potential commercial production of this new restriction
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Karska-Wysocki, B.
AU  - Szatmari, G.
AU  - Beauregard, G.
AU  - Mamet-Bratley, M.D.
TI  - A new restriction endonuclease activity found in Lactococcus  cremoris G2.
JO  - Life Sc. Confer. Ottawa
PY  - 1995
SP  - D2
EP  - D9
VL  - 0
AB  - Only a few strains of Lactococcus species have been demonstrated
AB  - to have type II restriction endonuclease activity.  These enzymes recognize
AB  - specific nucleotide sequence and cleave DNA at these sites.  Here we
AB  - describe a novel restriction enzyme activity present in cell extracts of a
AB  - Lactococcus cremoris G2 strain isolated from a commercial mixed-starter
AB  - culture used in the manufacture of Cheddar cheese.  Cell crude extracts
AB  - were obtained by sonification of stationary phase cultures grown in M17, or
AB  - in whey medium.  The cell extracts were tested for DNA restriction activity
AB  - on lambda, PhiX174 and pBR322 DNA substrates.  Electrophoretic analysis of
AB  - restriction digests revealed the presence of only one cleavage site in
AB  - lambda and pBR322 DNA, and the absence of cleavage of PhiX174 DNA.  The
AB  - enzymatic activity of the extract was shown to be greater than 13,000 units
AB  - per gram (wet weight) of cells.  The electrophoretic patterns of this
AB  - restriction enzyme activity was compared with known restriction
AB  - enzymes.  This analysis clearly demonstrated that this new restriction
AB  - enzyme activity is identical to that of the restriction enzyme
AB  - NheI.  Indicating that the new restriction enzyme activity is the first
AB  - known isoschizomer of NheI.  The determination of the cleavage site of this
AB  - new enzyme is currently in progress.  We propose that this non-pathogenic
AB  - food-grade microorganism will be a better source for the NheI enzyme, which
AB  - is currently isolated from a Neisseria mucosa species originally isolated
AB  - from the human pharynx.
ER  -

TY  - JOUR
AU  - Kartashova, I.M.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Separation of enzymes for modification methylases and restrictases from Shigella sonnei 47.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1985
SP  - 31
EP  - 35
VL  - 4
AB  - Two systems for DNA host specificity have been demonstrated for Shigella sonnei cells, SsoI
AB  - and SsoII.  The aim of the present work was to separate the modifying methylases and
AB  - restriction endonucleases from Shigella sonnei and to study the modifying functions of
AB  - methylases M.SsoI and M.SsoII.  The possibilities to separate the methylation and restriction
AB  - enzymes by column chromatography on affinity, ion exchange and hydrophobic sorbents were
AB  - analyzed.  The scheme for separation of methylases and restriction endonucleases of Shigella
AB  - sonnei was elaborated, consisting of the fractioning of total preparation on phenylsepharose
AB  - and subsequent isoelectrofocusing on ampholines.  The modification functions of M.SsoI and
AB  - M.SsoII methylases obtained by this technique and devoid of concomitant restriction
AB  - endonucleases were studied.  The in vitro experiments have shown the acceptor DNA methylated
AB  - by M.SsoI or M.SsoII to be resistant to R.SsoI or R.SsoII.
ER  -

TY  - JOUR
AU  - Karunakaran, A.C.
AU  - Milton, A.A.P.
AU  - Rajendrakumar, A.M.
AU  - Sahu, A.R.
AU  - Pandey, A.
AU  - Ghatak, S.
AU  - Abhishek, N.V.K.
AU  - Gandham, R.
AU  - Agarwal, R.K.
TI  - Draft Genome Sequences of Escherichia coli Isolates from India.
JO  - Genome Announcements
PY  - 2018
SP  - e00047
EP  - e00018
VL  - 6
AB  - Escherichia coli causes diarrhea and extraintestinal infections in humans and animals. Here,
AB  - we report the draft genome sequences of Escherichia coli strains
AB  - 360/16 and 646, isolated from neonatal calves.
ER  -

TY  - JOUR
AU  - Karuthedath, V.S.
AU  - Vir, S.A.
AU  - Kumar, S.P.
AU  - Garg, P.
AU  - Mohan, K.V.
AU  - Katoch, K.
AU  - Chauhan, D.S.
AU  - Scaria, V.
AU  - Sivasubbu, S.
TI  - Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493.
JO  - Genome Announcements
PY  - 2013
SP  - e00928
EP  - e00913
VL  - 1
AB  - We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium
AB  - tuberculosis belonging to the Ural strain OSDD493 from India.
ER  -

TY  - JOUR
AU  - Karuthedath-Vellarikkal, S.
AU  - Patowary, A.
AU  - Singh, M.
AU  - Periwal, V.
AU  - Singh, A.V.
AU  - Singh, P.K.
AU  - Garg, P.
AU  - Mohan, K.V.
AU  - Katoch, K.
AU  - Jangir, P.K.
AU  - Sharma, R.
AU  - Chauhan, D.S.
AU  - Scaria, V.
AU  - Sivasubbu, S.
TI  - Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium  tuberculosis East African Indian Strain OSDD271.
JO  - Genome Announcements
PY  - 2013
SP  - e00541
EP  - e00513
VL  - 1
AB  - We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium
AB  - tuberculosis East African Indian (EAI) strain OSDD271 from India.
ER  -

TY  - JOUR
AU  - Karyagina, A.
AU  - Shilov, I.
AU  - Tashlitskii, V.
AU  - Khodoun, M.
AU  - Vasilev, S.
AU  - Lau, P.C.K.
AU  - Nikolskaya, I.
TI  - Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2114
EP  - 2120
VL  - 25
AB  - The regulation of the SsoII restriction-modification system from Shigella sonnei was studied
AB  - in vivo and in vitro.  In lacZ fusion experiments, SsoII methyltransferase (M.SsoII) was found
AB  - to repress its own synthesis but stimulate expression of the cognate restriction endonuclease.
AB  - The N-terminal 72 amino acids of M.SsoII, predicted to form a helix-turn-helix motif, was
AB  - found to be responsible for the specific DNA-binding and regulatory function of M.SsoII.
AB  - Similar HTH motifs are predicted in the N-terminus of a number of 5-methylcytosine
AB  - methyltransferases, particularly M.EcoRII, M.dcm and M.MspI, of which the ability to regulate
AB  - autogenously has been proposed.  In vitro, the binding of M.SsoII to its target DNA was
AB  - investigated using a mobility shift assay.  M.SsoII forms a specific and stable complex with a
AB  - 140 bp DNA fragment containing the promoter region of SsoII R-M system.  The dissociation
AB  - constant (Kd) was determined to be 1.5 x 10^-8 M.  DNaseI footprinting experiments
AB  - demonstrated that M.SsoII protects a 48-52 bp region immediately upstream of the M.SsoII
AB  - coding sequence which includes the predicted -10 promoter sequence of M.SsoII and the -10 and
AB  - -35 sequences of R.SsoII.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
TI  - Genetic determinants for the enzymes of bacterial restriction-modification systems.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1990
SP  - 3
EP  - 11
VL  - 7
AB  - Recent data on the molecular arrangement and functioning of the genetic
AB  - determinants for the enzymes of restriction-modification systems are discussed.
AB  - The problems of restriction endonuclease and methylase gene localization, the
AB  - regulation of the activity of the genes for Type II restriction-modification
AB  - systems, the characteristics of the primary structure of the genes and
AB  - phylogeny of restriction endonucleases and methylases are reviewed.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Levchenko, I.Y.
AU  - Nikolskaya, I.I.
TI  - A new method for isolation and purification of restriction endonuclease SsoII.
JO  - Biokhimiia
PY  - 1993
SP  - 908
EP  - 912
VL  - 58
AB  - A new method for isolation and purification of restriction endonuclease SsoII which results in
AB  - a homogeneous preparation suitable for all types of fine physico-chemical assays has been
AB  - elaborated. The procedure includes four chromatographic steps: fractionation on
AB  - butyl-Toyopearl, combined chromatography on SP-Toyopearl and phosphocellulose PII, and
AB  - chromatography on DEAE-Toyopearl and on QAE-Toyopearl. The use of fast flow sorbents
AB  - (Toyopearl) makes it possible to reduce the time needed for the separation of proteins and to
AB  - optimize the fractionation conditions, thus avoiding the dialysis between the chromatographic
AB  - steps which significantly decreased the enzyme activity yields in previous purification
AB  - schemes. The isolation of restriction endonuclease SsoII by the new method usually takes four
AB  - days.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Lunin, V.G.
AU  - Degtyarenko, K.N.
AU  - Uvarov, V.Y.
AU  - Nikolskaya, I.I.
TI  - Analysis of the nucleotide and derived amino acid sequences of the SsoII restriction endonuclease and methyltransferase.
JO  - Gene
PY  - 1993
SP  - 13
EP  - 19
VL  - 124
AB  - A 2648-bp fragment from the P4 plasmid of Shigella sonnei strain 47 coding for the SsoII
AB  - restriction endonuclease (ENase) and methyltransferase (MTase) (recognition sequence
AB  - 5'-CCNGG) was sequenced. Two divergently arranged open reading frames of 905 bp for the SsoII
AB  - ENase (R.SsoII) and 1137 bp for the MTase (M.SsoII were identified. The coding regions are
AB  - separated by 110 bp. The calculated Mr of R.SsoII (35937) and M.SsoII (42887) are in good
AB  - agreement with values previously obtained by in vitro transcription-translation experiments,
AB  - i.e., 35 and 43 kDa for the ENase and MTase, respectively. The M.SsoII amino acid (aa)
AB  - sequence revealed a considerable similarity to m5C-MTases recognizing the related sequences -
AB  - M.EcoRII, M.dcm, M.MspI, M.BsuFI, M.HpaII, and M.HhaI. Surprisingly, the greatest degree of
AB  - homology has been observed between the aa sequences of M.SsoII and M.NlaX, with an
AB  - unidentified recognition sequence. The multiple alignment of aa sequences helps to identify
AB  - the blocks of conserved aa in variable regions of MTases. These conserved aa can play a key
AB  - role in target recognition. Some aspects of evolution of m5C-MTases are discussed.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Lunin, V.G.
AU  - Gruber, I.M.
AU  - Polyachenko, V.M.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Activity of the restriction endonuclease SsoII in Escherichia coli cells transformed by Shigella sonnei 47 plasmids.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1987
SP  - 26
EP  - 29
VL  - 12
AB  - The inverse dependence of activity of restriction endonuclease SsoII
AB  - preparations on the number of low molecular mass plasmids of Shigella sonnei
AB  - transforming Escherichia coli recipient cells producing the enzyme has been
AB  - shown.  An Escherichia coli strain efficiently producing one of two Shigella
AB  - sonnei 47 restriction endonucleases, SsoII, has been isolated.  The producer
AB  - strain harbours two of the nine Shigella sonnei 47 plasmids.  One of them, P4,
AB  - codes for the SsoII+ phenotype while another, P9, determines the plasmids
AB  - conjugation transfer.  Biochemical and physiological characteristics of the
AB  - producer strain XS13 are identical to the ones of the recipient Escherichia
AB  - coli strain PS200.  XS13 is unable to induce keratoconjunctivitis in guinea
AB  - pigs in pathogenicity test.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Lunin, V.G.
AU  - Levtchenko, I.Y.
AU  - Labbe, D.
AU  - Brousseau, R.
AU  - Lau, P.C.K.
AU  - Nikolskaya, I.I.
TI  - The SsoII and NlaX DNA methyltransferases: overproduction and functional analysis.
JO  - Gene
PY  - 1995
SP  - 93
EP  - 96
VL  - 157
AB  - Overproduction of the NlaX DNA methyltransferase (M.NlaX) in an Escherichia coli host
AB  - conferred resistance to SsoII restriction endonuclease (R.SsoII) digestion.  This suggested an
AB  - overlap of sequence specificity between M.NlaX and M.SsoII, the latter of which modifies the
AB  - internal cytosine of the target sequence 5'-CCNGG-3'.  A variant of M.NlaX (M.Sso/Nla),
AB  - containing an N-terminal extension from M.SsoII, was also enzymatically active.  Using
AB  - deletion analysis, the N-terminal 71 amino-acid residues of M.SsoII were shown to be essential
AB  - for modification activity.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Lunin, V.G.
AU  - Nikolskaia, I.I.
AU  - Debov, S.S.
TI  - Functional characteristics of plasmids of Shigella sonnei 47 strains.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1986
SP  - 16
EP  - 21
VL  - 10
AB  - The phenotypic characteristics of Shigella sonnei strain 47 containing 7 plasmids of low
AB  - molecular weight and 2 plasmids 60-100 Md large have been studied.  The strains of Escherichia
AB  - coli containing the single plasmids or plasmid groups from Shigella sonnei have been obtained
AB  - by transformation and conjugation.  The comparison of phenotypes of the strains obtained has
AB  - helped to find the plasmid location of the determinants for streptomycin resistance (P7),
AB  - genes for colicinogenicity abd colicin immunity (P5), the enzymes of host cell specificty
AB  - system Sso47I (P6), Sso47II (P4) and the genes for the conjugative DNA transfer (P9).
AB  - Escherichia coli strains producing individual restriction enzymes SsoI and SsoII have been
AB  - isolated.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Lunin, V.G.
AU  - Nikolskaya, I.I.
TI  - Characterization of the genetic determinants of SsoII-restriction endonuclease and modification methyltransferase.
JO  - Gene
PY  - 1990
SP  - 113
EP  - 118
VL  - 87
AB  - The genes encoding SsoI and SsoII restriction endonuclease (ENase) and
AB  - methyltransferase (MTase) are located on the small plasmids P6 and P4,
AB  - respectively, of Shigella sonnei strain 47.  Functions provided by plasmids P5,
AB  - P7 and P9, which include colicinogenicity and immunity to colicin E1,
AB  - resistance to streptomycin (Sm), and conjugative DNA transfer, respectively,
AB  - have also been identified.  The genes of the SsoII restriction-modification
AB  - (R-M) system have been cloned into Escherichia coli expressing the
AB  - 35-kDa(ENase) and 43-kDa(MTase) products.  A restriction map of the P4 plasmid
AB  - DNA was determined, and the approximate location of the genes encoding SsoII
AB  - ENase and MTase (ssoIIR and ssoIIM) on that have been established.  SsoI is an
AB  - isoschisomer of EcoRI and SsoII cleaves the recognition sequence 5'-CCNGG
AB  - producing 5'-protruding 5-nt long cohesive ends.
ER  -

TY  - JOUR
AU  - Karyagina, A.S.
AU  - Lunin, V.G.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Localization of SsoII restriction endonuclease and methylase genes on the physical map of plasmid P4.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1989
SP  - 16
EP  - 20
VL  - 3
AB  - A restriction map of naturally occuring plasmid P4 from Shigella sonnei 47
AB  - strain coding for the SsoII restriction endonuclease and methylase genes has
AB  - been made.  Using the genetic engineering approach the locations of the SsoII
AB  - host cell specificity system enzyme genes have been determined.
ER  -

TY  - JOUR
AU  - Kas, E.
AU  - Poljak, L.
AU  - Adachi, Y.
AU  - Laemmli, K.
TI  - A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin.
JO  - EMBO J.
PY  - 1993
SP  - 115
EP  - 126
VL  - 12
AB  - Histone H1 preferentially and cooperatively binds scaffold-associated regions (SARS) in vitro
AB  - via specific interactions with the numerous short A+T-rich tracts (A-tracts) contained in
AB  - these sequences. Selective titration of A-tracts by the oligopeptide distamycin abolishes this
AB  - interaction and results in a redistribution of H1. Similarly, treatment of intact cells and
AB  - isolated nuclei with distamycin specifically enhances cleavage of internucleosomal linkers of
AB  - SARs by topoisomerase II and restriction enzymes. The increased accessibility of these linkers
AB  - is thought to result from the unfolding (or opening) of the chromatin fiber and to be due to a
AB  - reduced occupancy by histone H1. Chromatin extraction and H1 assembly experiments support this
AB  - view. We discuss a model whereby open, H1-depleted chromatin regions may be generated by
AB  - titration of A-tracts by putative distamycin analogues; this local opening may spread to
AB  - adjacent regions assuming highly cooperative H1-H1 interactions in chromatin.
ER  -

TY  - JOUR
AU  - Kasahara, Y.
AU  - Nakai, S.
AU  - Ogasawara, N.
AU  - Yata, K.
AU  - Sadaie, Y.
TI  - Sequence analysis of the groESL-cotA region of the Bacillus subtilis genome, containing the restriction/modification system genes.
JO  - DNA Res.
PY  - 1997
SP  - 335
EP  - 339
VL  - 4
AB  - We have determined a 35-kb sequence of the groESL-gutR-cotA (45o-52o) region of the Bacillus
AB  - subtilis genome.  In addition to the groESL, gutRB and cotA genes reported previously, we have
AB  - newly identified 24 ORFs including gutA and fruC genes, encoding glucitol permease and
AB  - fructokinase, respectively.  The inherent restriction/modification system genes, hsdMR and
AB  - hsdMM, were mapped between groESL and gutRB, and we have identified two open reading frames
AB  - (ORFs) encoding 5-methylcytosine forming DNA methyltransferase and an operon probably encoding
AB  - a restriction enzyme complex.  The unusual genome structure of few ORFs and lower GC content
AB  - around the restriction/modification genes strongly suggests that the region originated from a
AB  - bacteriophage integrated during evolution.
ER  -

TY  - JOUR
AU  - Kasarjian, J.
AU  - Kawai, S.
AU  - Ryu, J.
TI  - Use of plasmid transformation to find new restriction enzymes.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2000
SP  - 371
EP  - 371
VL  - 100
AB  - Recent genome projects have revealed many restriction enzymes and their corresponding
AB  - methylases, specifically of type I and III.  Traditionally, restriction enzymes have been
AB  - discovered by classical restriction and modification phenomenon of bacteriophages (type I, II,
AB  - and III) or direct enzyme assay (most type II enzymes).  Once genes are cloned, DNA
AB  - hybridization is also used to discover other enzymes with similar DNA sequences.  To avoid the
AB  - traditional limitation of using bacteriophages or biochemical assays, we have designed a
AB  - feasibility study using plasmid transformation to detect the restriction activities of the
AB  - cell.  Plasmids were made by subcloning six BamHI fragments from bacteriophage lambda DNA into
AB  - a pUC derivative plasmid, pMECA.  These plasmids were transformed into E. coli strains
AB  - representing each type of restriction system (type I: EcoKI, EcoAI, Eco124I; type II: HindIII;
AB  - type III: EcoPI).  As a control, plasmids were also transformed into E. coli C, which does not
AB  - contain a restriction system and efficiency of transformation values were obtained by
AB  - comparison.  Reduction of relative EOT values (10^-1 - 10^-3) were observed in each BamHI
AB  - subclone containing the corresponding recognition sites.  These results suggest that the
AB  - presence of restriction enzymes can be predicted using this plasmid transformation method as
AB  - an alternative to phage experiments or biochemical studies.  Accumulation of DNA sequence data
AB  - also makes it possible to predict the recognition sequence of a restriction enzyme with the
AB  - use of computer analysis.
ER  -

TY  - JOUR
AU  - Kasarjian, J.
AU  - Valinluck, V.
AU  - Ryu, J.
TI  - Determination of the methylation sites of the type I restriction enzymes, KpnAI and KpnBI of Klebsiella species.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 236
EP  - 236
VL  - 102
AB  - Type I restriction endonucleases have been identified widely in bacteria since the completion
AB  - of the first genome sequence project of
AB  - Haemophilus influenzae in 1995. The enzymes recognize non-palindromic
AB  - bipartite DNA sequences made up of a 3-4 base pair (bp) 5' region, a
AB  - 6-8 bp nonspecific spacer, and a 4-5 bp 3' region. The corresponding
AB  - adenine N6-methyltransferase modifies a specific adenine in each strand
AB  - within the recognition sequence to protect DNA from cleavage.
AB  - Traditionally, type I enzymes in enteric bacteria are classified into
AB  - distinguished families: IA, IB, IC and ID. Two type I restriction and
AB  - modification systems, KpnAI (type ID) and KpnBI (new family), have been
AB  - identified in Klebsiella oxytoca M5a1 (originally classified as K.
AB  - pneumoniae), and Klebsiella pneumoniae GM236, respectively. We have
AB  - previously developed a simple transformation method to identify their
AB  - recognition sequence. Using a series of plasmids with known DNA
AB  - sequence and a computer program, the recognition sequence of KpnAI and
AB  - KpnBI were determined to be GAA(N6)TGCC and CAAA(N6) RTCA,
AB  - respectively. In this study the sensitivity of the type II restriction
AB  - endonuclease, HindIII, to site-specific modification at 6-methyladenine
AB  - is used to determine the methylation sites of KpnAI and KpnBI. We
AB  - designed several synthetic DNA oligonucleotides containing a HindIII
AB  - recognition site overlapping with either a KpnAI or KpnBI site. The
AB  - oligonucleotide was then cloned into plasmid pMECA and transferred into
AB  - a KpnAI or KpnBI containing strain, M5a1 or GM236, respectively for
AB  - modification. Methylated plasmids were subjected to HindIII digestion.
AB  - When the methylated adenine (A*) of the synthetic recognition sequence
AB  - overlapped with the methylated adenine in the HindIII sequence
AB  - (A*AGCTT), the plasmids were protected from cleavage HindIII. The
AB  - methylation of the opposite strand KpnBI recognition sequence was
AB  - determined using the in vivo activity of dam+ and dam- strains.
ER  -

TY  - JOUR
AU  - Kasarjian, J.K.A.
AU  - Burnett, A.S.
AU  - Ryu, J.
TI  - Use of plasmid transformation to find new restriction enzymes and their recognition sequences.
JO  - J. Invest. Med.
PY  - 2001
SP  - 12A
EP  - 12A
VL  - 49
AB  - Restriction-modification systems are widespread in bacteria and consist of both a restriction
AB  - endonuclease and a corresponding methylase.  Bacterial genome sequencing projects, however,
AB  - suggest that many restriction enzymes have yet to be discovered.  Restriction enzymes are
AB  - classified into three types (I, II, III) and type II restriction enzymes are useful in genetic
AB  - engineering.  Traditionally, restriction enzymes have been discovered by classical restriction
AB  - and modification tests, requiring bacteriophages or direct enzyme assay.  DNA hybridization
AB  - can find new homologous sequences, but unique DNA sequences will be overlooked and the high
AB  - cost of bacterial genome projects may limit its usefulness.  We have established a new
AB  - quantitative R-M test based on plasmid transformation efficiency using DNA fragments derived
AB  - from E. coli phage lambda.  This test is similar to traditional "efficiency of plating" assays
AB  - but measures "efficiency of transformation".  Plasmids were made by subcloning six BamHI
AB  - fragments from lambda into pMECA, a pUC derivative plasmid.  These six plasmids were each
AB  - transformed into bacterial strains representing each type of restriction system (type I;
AB  - EcoAI, EcoRI, Eco124I; type II: HindIII; type III: EcoPI).  Reduction of relative EOT values
AB  - (10-1-10-3) were observed in each BamHI subclone containing the corresponding recognition
AB  - sites.  These results confirm the effectiveness of this new method.  This method was also used
AB  - to predict the recognition sequence of KpnAI, a type I R-M system from Klebsiella pneumoniae,
AB  - M5a1.  A total of 29 lambda subclones were constructed and transformed into M5a1 to determine
AB  - the presence (+) or absence (-) of a recognition site.  DNA sequence information was then
AB  - compared using the newly developed computer program, Seth Analyzer.  Transformation of a
AB  - synthetic oligonucleotide containing the predicted recognition sequence confirmed the
AB  - recognition sequence of KpnAI to be GAA(6N)TGCC.  Because plasmid transformation methods are
AB  - available for many bacteria, this model system can be extended to many bacterial species to
AB  - search for new restriction enzymes and their recognition sequences.
ER  -

TY  - JOUR
AU  - Kasarjian, J.K.A.
AU  - Burnett, A.S.
AU  - Ryu, J.
TI  - Identification of the recognition sequence of KpnAI, a type ID restriction enzyme, in Klebsiella pneumoniae M5a1.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 403
EP  - 403
VL  - 101
AB  - Type II restriction enzymes have been studied extensively due to their usefulness in genetic
AB  - engineering, while our knowledge of type I and
AB  - III systems remains limited. Recent bacterial genome sequencing
AB  - projects suggest an abundance of all three types of
AB  - restriction-modification (R-M) systems. Finding new type I and III
AB  - restriction systems and identifying their recognition sites is
AB  - difficult, leaving many recognition sites still unknown. KpnAI, an R-M
AB  - system from Klebsiella pneumoniae, has previously been cloned and
AB  - sequenced in our laboratory. Analysis of both DNA and protein sequences
AB  - identified this system as a new member of the type ID family. Here we
AB  - have determined the recognition sequence for KpnAI using a simple in
AB  - vivo plasmid transformation method, specifically developed in our lab,
AB  - which can also be used as a tool to identify new R-M systems. Two sets
AB  - of plasmids were made by subcloning DNA fragments from bacteriophage
AB  - lambda and Escherichia coli. Each set of 30 plasmids was then
AB  - transformed into M5a1 using the restriction-minus mutant, M5a1R as a
AB  - control. Only when the plasmid contained a restriction site, a
AB  - reduction (10-2) in transformation frequency was observed when compared
AB  - to the control. These results identified the presence of a recognition
AB  - site in 24 plasmids and absence of a site in 32 plasmids. A computer
AB  - program was developed to search for a common sequence that exists in
AB  - all positive plasmids but is not found in any negative plasmids. One
AB  - unique recognition sequence was identified and a 19 base synthetic
AB  - oligonucleotide containing this sequence was cloned into pMECA.
AB  - Transformation into strain M5a1 resulted in a significant reduction in
AB  - transformation frequency confirming the recognition sequence of KpnAI
AB  - to be GAA(6N)TGCC. This model system can be extended to many bacterial
AB  - species to search for new restriction enzymes and their recognition
AB  - sequences.
ER  -

TY  - JOUR
AU  - Kasarjian, J.K.A.
AU  - Hidaka, M.
AU  - Horiuchi, T.
AU  - Iida, M.
AU  - Ryu, J.
TI  - The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - e82
EP  - e82
VL  - 32
AB  - Using an in vivo plasmid transformation method, we have determined the DNA sequences
AB  - recognized by the KpnAI, StySEAI, StySENI and StySGI R-M systems from Klebsiella oxytoca
AB  - strain M5a1, Salmonella eastbourne, Salmonella enteritidis and Salmonella gelsenkirchen,
AB  - respectively. These type I restriction-modification systems were originally identified using
AB  - traditional phage assay, and described here is the plasmid transformation test and computer
AB  - program used to determine their DNA recognition sequences. For this test, we constructed two
AB  - sets of plasmids, pL and pE, that contain phage lambda and Escherichia coli K-12 chromosomal
AB  - DNA fragments, respectively. Further, using the methylation sensitivities of various known
AB  - type II restriction enzymes, we identified the target adenines for methylation (listed in bold
AB  - italics below as A or T in case of the complementary strand). The recognition sequence and
AB  - methylation sites are GAA(6N)TGCC (KpnAI), ACA(6N)TYCA (StySEAI), CGA(6N)TACC (StySENI) and
AB  - TAAC(7N)RTCG (StySGI). These DNA recognition sequences all have a typical type I bipartite
AB  - pattern and represent three novel specificities and one isoschizomer (StySENI). For
AB  - confirmation, oligonucleotides containing each of the predicted sequences were synthesized,
AB  - cloned into plasmid pMECA and transformed into each strain, resulting in a large reduction in
AB  - efficiency of transformation (EOT).
ER  -

TY  - JOUR
AU  - Kasarjian, J.K.A.
AU  - Iida, M.
AU  - Ryu, J.
TI  - New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - e22
EP  - e22
VL  - 31
AB  - The presence of restriction enzymes in bacterial cells has been predicted by either classical
AB  - phage restriction-modification (R-M) tests, direct in
AB  - vitro enzyme assays or more recently from bacterial genome sequence
AB  - analysis. We have applied phage R-M test principles to the transformation
AB  - of plasmid DNA and established a plasmid R-M test. To validate this test,
AB  - six plasmids that contain BamHI fragments of phage lambda DNA were
AB  - constructed and transformed into Escherichia coli strains containing known
AB  - R-M systems including: type I (EcoBI, EcoAI, Eco124I), type II (HindIII)
AB  - and type III (EcoP1I). Plasmid DNA with a single recognition site showed a
AB  - reduction of relative efficiency of transformation (EOT = 10(-1)-10(-2)).
AB  - When multiple recognition sites were present, greater reductions in EOT
AB  - values were observed. Once established in the cell, the plasmids were
AB  - subjected to modification (EOT = 1.0). We applied this test to screen
AB  - E.coli clinical strains and detected the presence of restriction enzymes
AB  - in 93% (14/15) of cells. Using additional subclones and the computer
AB  - program, RM Search, we identified four new restriction enzymes, Eco377I,
AB  - Eco585I, Eco646I and Eco777I, along with their recognition sequences,
AB  - GGA(8N)ATGC, GCC(6N)TGCG, CCA(7N)CTTC, and GGA(6N)TATC, respectively.
AB  - Eco1158I, an isoschizomer of EcoBI, was also found in this study.
ER  -

TY  - JOUR
AU  - Kasarjian, J.K.A.
AU  - Kodama, Y.
AU  - Iida, M.
AU  - Matsuda, K.
AU  - Ryu, J.
TI  - Four new type I restriction enzymes identified in Escherichia coli clinical isolates.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - e114
EP  - e114
VL  - 33
AB  - Using a plasmid transformation method and the RM search computer program, four type I
AB  - restriction enzymes with new recognition sites and two isoschizomers (EcoBI and Eco377I) were
AB  - identified in a collection of clinical Escherichia coli isolates. These new enzymes were
AB  - designated Eco394I, Eco826I, Eco851I and Eco912I. Their recognition sequences were determined
AB  - to be GAC(5N)RTAAY, GCA(6N)CTGA, GTCA(6N)TGAY and CAC(5N)TGGC, respectively. A methylation
AB  - sensitivity assay, using various synthetic oligonucleotides, was used to identify the adenines
AB  - that prevent cleavage when methylated (underlined). These results suggest that type I enzymes
AB  - are abundant in E.coli and many other bacteria, as has been inferred from bacterial genome
AB  - sequencing projects.
ER  -

TY  - JOUR
AU  - Kashyap, R.S.
AU  - Bhullar, S.S.
AU  - More, R.P.
AU  - Puranik, S.
AU  - Purohit, H.J.
AU  - Taori, G.M.
AU  - Daginawala, H.F.
TI  - Genome Sequence of Mycobacterium tuberculosis C2, a Cerebrospinal Fluid Clinical  Isolate from Central India.
JO  - Genome Announcements
PY  - 2014
SP  - e00842
EP  - e00814
VL  - 2
AB  - We report the annotated genome sequence of a Mycobacterium tuberculosis clinical  isolate from
AB  - the cerebrospinal fluid of a tuberculous meningitis patient admitted
AB  - to the Central India Institute of Medical Sciences, Nagpur, India.
ER  -

TY  - JOUR
AU  - Kaszubska, W.
TI  - Studies of a DNA modification methyltransferase from Rhodobacter sphaeroides.
JO  - Diss. Abstr.
PY  - 1991
SP  - 1407B
EP  - 1407B
VL  - 52
AB  - The DNA methyltransferases represent an interesting class of enzymes for the
AB  - study of protein-DNA interactions due to their high specificity, structural
AB  - simplicity, and biological importance.  RsrI methyltransferase (M.RsrI) from
AB  - Rhodobacter sphaeroides recognizes duplex d(GAATTC) and deposits methyl groups
AB  - at the N6 position of the central adenine.  M.RsrI was purified to homogeneity
AB  - from R. sphaeroides, and its gene cloned and sequenced.  The purification used
AB  - four chromatography columns, and yielded up to 100 micrograms of enzyme.
AB  - M.RsrI was overexpressed in E. coli and the yield of the purification improved
AB  - by about 100-fold with respect to that from R. sphaeroides.  Several physical
AB  - and biochemical properties of the RsrI methyltransferase were determined:
AB  - molecular weight under denaturing and nondenaturing conditions, isoelectric
AB  - point, optimal reaction conditions, the mode of methyl group transfer, and the
AB  - enzyme-DNA binding.  M.RsrI was compared to a functionally identical enzyme
AB  - from E. coli, EcoRI methyltransferase (M.EcoRI).  M.RsrI and M.EcoRI differ in
AB  - their physical properties, including a striking lack of similarity in their
AB  - deduced amino acid sequences.  The two methyltransferases might recognize the
AB  - cognate DNA sequence differently, because they do not bind to DNA with equal
AB  - efficiencies under the same conditions.  However, M.RsrI and M.EcoRI share
AB  - identical catalytic properties.  Both transfer one methyl group to the
AB  - recognition sequence per binding event.  M.RsrI and M.EcoRI represent an
AB  - opportunity to elucidate the mode of action of two structurally different but
AB  - functionally identical enzymes.  It is possible that these enzymes retain
AB  - functional similarity by having essentially the same three dimensional
AB  - configuration.  Alternatively, they might have dissimilar structures as well as
AB  - mechanistic differences.
ER  -

TY  - JOUR
AU  - Kaszubska, W.
AU  - Aiken, C.
AU  - O'Connor, C.D.
AU  - Gumport, R.I.
TI  - Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 10403
EP  - 10425
VL  - 17
AB  - RsrI DNA methyltransferase (M.RsrI) from Rhodobacter sphaeroides has been
AB  - purified to homogeneity, and its gene cloned and sequenced.  This enzyme
AB  - catalyzes methylation of the same central adenine residue in the duplex
AB  - recognition sequence d(GAATTC) as does M.EcoRI.  The reduced and denatured
AB  - molecular weight of the RsrI methyltransferase (MTase) is 33,600 Da.  A
AB  - fragment of R. sphaeroides chromosomal DNA exhibited M.RsrI activity in E. coli
AB  - and was used to sequence the rsrIM gene.  The deduced amino acid sequence of
AB  - M.RsrI shows partial homology to those of the type II adenine MTases HinfI and
AB  - DpnA and N4-cytosine MTases BamHI and PvuII, and to the type III adenine MTases
AB  - EcoP1 and EcoP15.  In contrast to their corresponding isoschizomeric
AB  - endonucleases, the deduced amino acid sequences of the RsrI and EcoRI MTases
AB  - show very little homology.  Either the EcoRI and RsrI restriction modification
AB  - systems assembled independently from closely related endonuclease and more
AB  - distantly related MTase genes, or the MTase genes diverged more than their
AB  - partner endonuclease genes.  The rsrIM gene sequence has also been determined
AB  - by Stephenson and Greene (Nucl. Acids Res. (1989) 17, this issue).
ER  -

TY  - JOUR
AU  - Kaszubska, W.
AU  - Aiken, C.R.
AU  - Gumport, R.I.
TI  - RsrI restriction-modification enzymes from Rhodobacter sphaeroides.
JO  - Gene
PY  - 1988
SP  - 83
EP  - 84
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Kaszubska, W.
AU  - Webb, H.K.
AU  - Gumport, R.
TI  - Purification and characterization of the M.RsrI DNA methyltransferase from Escherichia coli.
JO  - Gene
PY  - 1992
SP  - 5
EP  - 11
VL  - 118
AB  - The gene (rsrIM) encoding the RsrI DNA methyltransferase (M.RsrI) from Rhodobacter sphaeroides
AB  - was cloned and expressed in Escherichia coli. Under the control of a bacteriophage T7
AB  - promotor, 2% of the total protein in a crude extract was M.RsrI. This level of expression
AB  - represents an approximately 50-fold increase over that present in the natural host.
AB  - Chromatography using DNA cellulose and the S-adenosylmethionine analogue, sinefungin, was
AB  - useful in purifying the enzyme to homogeneity. The purification yielded 100 times more enzyme
AB  - than was obtained from the same quantity of R.sphaeroides cell paste. M.RsrI deposits one
AB  - methyl group per productive DNA-binding event, as does its functional but
AB  - sequence-nonhomologous analogue, M.EcoRI. Unlike M.EcoRI, the R. sphaeroides enzyme is a dimer
AB  - at micromolar concentrations.
ER  -

TY  - JOUR
AU  - Kataeva, I.A.
AU  - Yang, S.J.
AU  - Dam, P.
AU  - Poole, F.L.I.I.
AU  - Yin, Y.
AU  - Zhou, F.
AU  - Chou, W.C.
AU  - Xu, Y.
AU  - Goodwin, L.
AU  - Sims, D.R.
AU  - Detter, J.C.
AU  - Hauser, L.G.
AU  - Westpheling, J.
AU  - Adams, M.W.
TI  - Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725.
JO  - J. Bacteriol.
PY  - 2009
SP  - 3760
EP  - 3761
VL  - 191
AB  - Anaerocellum thermophilum DSM 6725 is a strictly anaerobic bacterium that grows optimally at
AB  - 75 degrees C. It uses a variety of polysaccharides, including crystalline cellulose and
AB  - untreated plant biomass, and has potential utility in biomass conversion. Here we report its
AB  - complete genome sequence of 2.97 Mb, which is contained within one chromosome and two plasmids
AB  - (of 8.3 and 3.6 kb). The genome encodes a broad set of cellulolytic enzymes, transporters and
AB  - pathways for sugar utilization and compared to those of other saccharolytic, anaerobic
AB  - thermophiles is most similar to that of Caldicellulosiruptor saccharolyticus DSM 8903.
ER  -

TY  - JOUR
AU  - Katahira, K.
AU  - Ogura, Y.
AU  - Gotoh, Y.
AU  - Hayashi, T.
TI  - Draft Genome Sequences of Five Rapidly Growing Mycobacterium Species, M. thermoresistibile, M. fortuitum subsp. acetamidolyticum, M. canariasense, M.  brisbanense, and M. novocastrense.
JO  - Genome Announcements
PY  - 2016
SP  - e00322
EP  - e00316
VL  - 4
AB  - We report here the draft genome sequences of five rapidly growing Mycobacterium (RGM) species
AB  - potentially pathogenic to humans, M. thermoresistibile, M.
AB  - fortuitum subsp. acetamidolyticum, M. canariasense, M. brisbanense, and M.
AB  - novocastrense As the clinical importance of RGMs is increasingly being recognized
AB  - worldwide, these sequences would contribute to further advances in RGM research.
ER  -

TY  - JOUR
AU  - Katani, R.
AU  - Cote, R.
AU  - Raygoza, G.J.A.
AU  - Li, L.
AU  - Arthur, T.M.
AU  - DebRoy, C.
AU  - Mwangi, M.M.
AU  - Kapur, V.
TI  - Complete Genome Sequence of SS52, a Strain of Escherichia coli O157:H7 Recovered  from Supershedder Cattle.
JO  - Genome Announcements
PY  - 2015
SP  - e01569
EP  - e01514
VL  - 3
AB  - Shiga toxin-producing Escherichia coli O157:H7 causes foodborne infections, and cattle are the
AB  - primary reservoir. Some animals, known as supershedders, excrete
AB  - orders of magnitude more E. coli O157:H7 in the feces than normal. Here, we
AB  - report the complete genome sequence of the SS52 supershedder strain of E. coli
AB  - O157:H7.
ER  -

TY  - JOUR
AU  - Katano, Y.
AU  - Fujinami, S.
AU  - Kawakoshi, A.
AU  - Nakazawa, H.
AU  - Oji, S.
AU  - Iino, T.
AU  - Oguchi, A.
AU  - Ankai, A.
AU  - Fukui, S.
AU  - Terui, Y.
AU  - Kamata, S.
AU  - Harada, T.
AU  - Tanikawa, S.
AU  - Suzuki, K.
AU  - Fujita, N.
TI  - Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 406
EP  - 414
VL  - 6
AB  - Oscillibacter valericigenes is a mesophilic, strictly anaerobic bacterium belonging to the
AB  - clostridial cluster IV. Strain Sjm18-20(T) (=NBRC 101213(T) =DSM
AB  - 18026(T)) is the type strain of the species and represents the genus
AB  - Oscillibacter Iino et al. 2007. It was isolated from the alimentary canal of a
AB  - Japanese corbicula clam (Corbicula japonica) collected on a seacoast in Shimane
AB  - Prefecture in Japan. Phylogenetically, strain Sjm18-20(T) is closest to
AB  - uncultured bacteria in digestive tracts, including the enriched cells thought to
AB  - represent Oscillospira guilliermondii Chatton and Perard 1913. The isolated
AB  - phylogenetic position and some distinct characteristics prompted us to determine
AB  - the complete genome sequence. The 4,410,036 bp chromosome and the 60,586 bp
AB  - plasmid were predicted to encode a total of 4,723 protein-coding genes.
ER  -

TY  - JOUR
AU  - Katiliene, Z.
AU  - Katilius, E.
AU  - Woodbury, N.W.
TI  - Single molecule detection of DNA looping by NgoMIV restriction endonuclease.
JO  - Biophys. J.
PY  - 2003
SP  - 4053
EP  - 4061
VL  - 84
AB  - Single molecule fluorescence resonance energy transfer (FRET) and fluorescence correlation
AB  - spectroscopy were used to investigate DNA looping
AB  - by NgoMIV restriction endonuclease. Using a linear double-stranded DNA
AB  - (dsDNA) molecule labeled with a fluorescence donor molecule, Cy3, and
AB  - fluorescence acceptor molecule, Cy5, and by varying the concentration of
AB  - NgoMIV endonuclease from 0 to 3 x 10(-6) M, it was possible to detect and
AB  - determine diffusion properties of looped DNA/protein complexes. FRET
AB  - efficiency distributions revealed a subpopulation of complexes with an
AB  - energy transfer efficiency of 30%, which appeared upon addition of enzyme
AB  - in the picomolar to nanomolar concentration range (using 10(-11) M dsDNA).
AB  - The concentration dependence, fluorescence burst size analysis, and
AB  - fluorescence correlation analysis were all consistent with this
AB  - subpopulation arising from a sequence specific interaction between an
AB  - individual enzyme and a DNA molecule. A 30% FRET efficiency corresponds to
AB  - a distance of approximately 65 A, which correlates well with the distance
AB  - between the ends of the dsDNA molecule when bound to NgoMIV according to
AB  - the crystal structure of this complex. Formation of the looped complexes
AB  - was also evident in measurements of the diffusion times of freely
AB  - diffusing DNA molecules with and without NgoMIV. At very high protein
AB  - concentrations compared to the DNA concentration, FRET and fluorescence
AB  - correlation spectroscopy results revealed the formation of larger
AB  - DNA/protein complexes.
ER  -

TY  - JOUR
AU  - Katna, A.
AU  - Boratynski, R.
AU  - Furmanek-Blaszk, B.
AU  - Zolcinska, N.
AU  - Sektas, M.
TI  - Unbalanced Restriction Impairs SOS-induced DNA Repair Effects.
JO  - J. Microbiol. Biotechnol.
PY  - 2010
SP  - 30
EP  - 38
VL  - 20
AB  - The contribution of a type II restriction-modification system (R-M system) to genome integrity
AB  - and cell viability was investigated. We
AB  - established experimental conditions that enabled the achievement of
AB  - hemimethylated and unmethylated states for the specific bases of the
AB  - recognition sequences of the host's DNA. To achieve this, we
AB  - constructed the MboII R-M system containing only one (i.e., M2.MboII)
AB  - out of two functional MboII methyltransferases found in Moraxella
AB  - bovis. Using the incomplete R-M system, we were able to perturb the
AB  - balance between methylation and restriction in an inducible manner. We
AB  - demonstrate that upon the SOS-induced DNA repair in mitomycin C treated
AB  - cells, restriction significantly reduces cell viability. Similar
AB  - results for the well-studied wild-type EcoRI R-M system, expressed
AB  - constitutively in Escherichia coli, were obtained. Our data provide
AB  - further insights into the benefits and disadvantages of maintaining of
AB  - a type II R-M system, highlighting its impact on host cell fitness.
ER  -

TY  - JOUR
AU  - Kato, F.
TI  - Isolation and characterization of restriction endonuclease from amino acid- or nucleic acid-producing bacteria.
JO  - Dojin News
PY  - 1989
SP  - 3
EP  - 9
VL  - 51
AB  - Restriction enzymes are endonucleases that recognize specific nucleotide
AB  - sequences in double stranded DNA and cleave both strands of the duplex.  In the
AB  - cell of origin each restriction enzyme is part of a restriction-modification
AB  - system, consisting of the restriction endonuclease and a matched modification
AB  - enzyme which recognizes and modifies the same nucleotide sequence in the DNA
AB  - strand.  Modification thus protects cellular DNA from restriction, however,
AB  - foreign DNA cleaved by the restriction endonuclease and further degraded by
AB  - other enzymes.  Such restriction modification systems, first detected by phage
AB  - restriction and modification, are widespread in bacteria and are thought to
AB  - play a role in eliminating foreign DNA that gains entrance to the cell via
AB  - viruses or as naked DNA.  The discovery of the first Class II endonuclease was
AB  - reported by Smith and Wilcox (1970).  Since that time, the number of Class II
AB  - restriction endonucleases available in purified form has been increasing at a
AB  - remarkable pace, and it is now very often possible to find one or several
AB  - restriction endonucleases having the specificity one desires.  This review is
AB  - mainly concerned with general properties and applications of Class II
AB  - restriction endonucleases including some properties of the restriction
AB  - endonucleases isolated from amino acid- or nucleic acid-producing bacteria and
AB  - related species in our laboratory.
ER  -

TY  - JOUR
AU  - Kato, H.
AU  - Ogawa, N.
AU  - Ohtsubo, Y.
AU  - Ohshima, K.
AU  - Toyoda, A.
AU  - Yamazoe, A.
AU  - Mori, H.
AU  - Maruyama, F.
AU  - Nagata, Y.
AU  - Hattori, M.
AU  - Fujiyama, A.
AU  - Kurokawa, K.
AU  - Tsuda, M.
TI  - Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45, Isolated from a Phenanthrene-Degrading Consortium.
JO  - Genome Announcements
PY  - 2015
SP  - e00782
EP  - e00715
VL  - 3
AB  - Many polycyclic aromatic hydrocarbons (PAHs) are serious environmental pollutants, and their
AB  - toxicity threatens human and wildlife health (1, 2). Microbial biodegradation of PAHs has thus
AB  - drawn considerable attention, and various PAHdegrading bacterial strains have been isolated
AB  - (3).
ER  -

TY  - JOUR
AU  - Kato, H.
AU  - Shiwa, Y.
AU  - Oshima, K.
AU  - Machii, M.
AU  - Araya-Kojima, T.
AU  - Zendo, T.
AU  - Shimizu-Kadota, M.
AU  - Hattori, M.
AU  - Sonomoto, K.
AU  - Yoshikawa, H.
TI  - Complete Genome Sequence of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of L-Lactic Acid.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2102
EP  - 2103
VL  - 194
AB  - We report the complete genome sequence of Lactococcus lactis IO-1 (= JCM7638). It is a
AB  - nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and
AB  - produces predominantly l-lactic acid at high xylose concentrations. From ortholog
AB  - analysis with other five L. lactis strains, IO-1 was identified as L. lactis
AB  - subsp. lactis.
ER  -

TY  - JOUR
AU  - Kato, J.
AU  - Endo, T.
AU  - Kawamura, H.
AU  - Nakashima, Y.
AU  - Furukoshi, K.
AU  - Oishi, K.
TI  - Inhibition of restriction endonucleases by hot water extracts of spices.
JO  - Bull. Coll. Agr. Vet. Med.
PY  - 1990
SP  - 84
EP  - 87
VL  - 47
AB  - Forty samples of spices were investigated for their inhibitory activities to
AB  - the cleavage of lambda DNA by restriction endonucleases.  Bayberry, clove
AB  - eucalyptus, melissa, nutmeg, oregano, peppermint and savory showed complete
AB  - inhibition to HindIII, under the condition employed.  Hot water extract of
AB  - clove showed marked inhibitory activity (MIC 2 micrograms/ml) and that of
AB  - oregano and peppermint showed potent inhibition (MIC 20 micrograms/ml).  MIC of
AB  - clove extract for five restriction endonucleases were determined.  MIC for
AB  - EcoRI and HindIII was 0.8 micrograms/ml, and 12.5 micrograms/ml for BamHI, 50
AB  - micrograms/ml for BglII and PstI.  Specificity of inhibition for restriction
AB  - endonucleases by hot water extract of clove was found.
ER  -

TY  - JOUR
AU  - Kato, K.
AU  - Toh, H.
AU  - Sakamoto, N.
AU  - Mori, K.
AU  - Tashiro, K.
AU  - Hibi, N.
AU  - Sonomoto, K.
AU  - Nakayama, J.
TI  - Draft Genome Sequence of Lactobacillus namurensis Chizuka 01, Isolated from Nukadoko, a Pickling Bed of Fermented Rice Bran.
JO  - Genome Announcements
PY  - 2014
SP  - e01263
EP  - e01213
VL  - 2
AB  - Lactobacillus namurensis Chizuka 01 was isolated from nukadoko, which is a fermented rice bran
AB  - bed traditionally used in Japan for pickling vegetables.
AB  - Here, we report the first draft of an annotated genome sequence of this organism.
AB  - This paper is the first published report of the genomic sequence of L.
AB  - namurensis.
ER  -

TY  - JOUR
AU  - Kato, S.
AU  - Oikawa, T.
TI  - Genome Sequence of Lactobacillus sakei LK-145 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids.
JO  - Genome Announcements
PY  - 2017
SP  - e00656
EP  - e00617
VL  - 5
AB  - This announcement reports the complete genome sequence of strain LK-145 of Lactobacillus sakei
AB  - isolated from a Japanese sake cellar as a potent strain for
AB  - the production of large amounts of d-amino acids. Three putative genes encoding
AB  - an amino acid racemase were identified.
ER  -

TY  - JOUR
AU  - Kato, S.
AU  - Oikawa, T.
TI  - Whole-Genome Sequence of Leuconostoc mesenteroides LT-38, a Non-Spore-Forming Gram-Positive Lactic Acid Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00670
EP  - e00617
VL  - 5
AB  - The present study reports the complete genome sequence of Leuconostoc mesenteroides strain
AB  - LT-38, which is a non-spore-forming Gram-positive lactic
AB  - acid bacterium. The genome is composed of a 2,022,184-bp circular chromosome and
AB  - contains 2,005 putative protein-coding genes.
ER  -

TY  - JOUR
AU  - Kato, S.
AU  - Oikawa, T.
TI  - Whole-Genome Sequence of Lactobacillus sakei LT-13 Isolated from Moto Starter of  Sake.
JO  - Genome Announcements
PY  - 2017
SP  - e00651
EP  - e00617
VL  - 5
AB  - Lactobacillus sakei strain LT-13 is a lactic acid bacterium isolated from moto starter of
AB  - Japanese sake. This genome analysis revealed that the genome is
AB  - composed of a circular chromosome and one plasmid, which contain 1,938 and 8
AB  - putative protein-coding genes, respectively.
ER  -

TY  - JOUR
AU  - Kato, S.
AU  - Oikawa, T.
TI  - Genome Sequence of Leuconostoc mesenteroides LK-151 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids.
JO  - Genome Announcements
PY  - 2017
SP  - e00661
EP  - e00617
VL  - 5
AB  - Here, we report the complete genome sequence of strain LK-151 of Leuconostoc mesenteroides,
AB  - which was isolated from a Japanese sake cellar and has the
AB  - potential to produce large amounts of d-amino acids, namely, d-Ala and d-Glu. The
AB  - genome contains 4 genes related to d-amino acid production.
ER  -

TY  - JOUR
AU  - Katoh, H.
AU  - Miyata, S.
AU  - Inoue, H.
AU  - Iwanami, T.
TI  - Unique features of a Japanese 'Candidatus Liberibacter asiaticus' strain revealed by whole genome sequencing.
JO  - PLoS ONE
PY  - 2014
SP  - e106109
EP  - e106109
VL  - 9
AB  - Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide.  It is
AB  - spread by citrus psyllids and is associated with phloem-limited bacteria of three species of
AB  - a-Proteobacteria, namely, 'Candidatus Liberibacter asiaticus', 'Ca.  L. americanus', and
AB  - 'Ca. L. africanus'.  Recent findings suggested that some Japanese strains lack the
AB  - bacteriophage-type DNA polymerase region (DNA pol), in contrast to the Floridian psy62 strain.
AB  - The whole genome sequence of the pol-negative 'Ca. L. asiaticus' Japanese isolate lshi-1 was
AB  - determined by metagenomic analysis of DNA extracted from 'Ca. L. asiaticus'-infected
AB  - psyllids and leaf midribs.  The 1.19-Mb genome has an average 36.32% GC content.  Annotation
AB  - revealed 13 operons encoding rRNA and 44 tRNA genes, but no typical bacterial
AB  - pathogenesis-related genes were located within the genome, similar to the Floridian psy62 and
AB  - Chinese gxpsy.  In contrast to other 'Ca. L. asiaticus' strains, the genome of the Japanese
AB  - Ishi-1 strain lacks a prophage-related region.
ER  -

TY  - JOUR
AU  - Katoh, T.
AU  - Maeshibu, T.
AU  - Kikkawa, K.
AU  - Gotoh, A.
AU  - Tomabechi, Y.
AU  - Nakamura, M.
AU  - Liao, W.-H.
AU  - Yamaguchi, M.
AU  - Ashida, H.
AU  - Yamamoto, K.
AU  - Katayama, T.
TI  - Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2017
SP  - 2018
EP  - 2027
VL  - 81
AB  - Human gut symbiont bifidobacteria possess carbohydrate-degrading enzymes that act on the
AB  - O-linked glycans of intestinal mucins to utilize those carbohydrates as carbon sources.
AB  - However, our knowledge about mucin type O-glycan degradation by bifidobacteria remains
AB  - fragmentary, especially regarding how they decompose sulfated glycans, which are abundantly
AB  - found in mucin sugar-chains. Here, we examined the abilities of several Bifidobacterium
AB  - strains to degrade a sulfated glycan substrate and identified a
AB  - 6-sulfo-beta-d-N-acetylglucosaminidase, also termed sulfoglycosidase, encoded by bbhII from
AB  - Bifidobacterium bifidum JCM 7004. A recombinant BbhII protein showed a substrate preference
AB  - toward 6-sulfated and 3,4-disulfated N-acetylglucosamines over non-sulfated and 3-sulfated
AB  - N-acetylglucosamines. The purified BbhII directly released 6-sulfated N-acetylglucosamine from
AB  - porcine gastric mucin and the expression of bbhII was moderately induced in the presence of
AB  - mucin. This de-capping activity may promote utilization of sulfated glycans of mucin by other
AB  - bacteria including bifidobacteria, thereby establishing the symbiotic relationship between
AB  - human and gut microbes.
ER  -

TY  - JOUR
AU  - Katsura, S.
AU  - Harada, N.
AU  - Maeda, Y.
AU  - Komatsu, J.
AU  - Matsuura, S.
AU  - Takashima, K.
AU  - Mizuno, A.
TI  - Activation of restriction enzyme by electrochemically released magnesium ion.
JO  - J. Biosci. Bioeng.
PY  - 2004
SP  - 293
EP  - 297
VL  - 98
AB  - Observation and cutting of DNA molecules at intended positions permit several new experimental
AB  - methods that are completely different from
AB  - conventional molecular biology methods; therefore several cutting
AB  - methods have been proposed and studied. In this paper. a new cutting
AB  - method for a DNA molecule by localizing the activity of a restriction
AB  - enzyme is presented. Since most restriction enzymes require magnesium
AB  - ions for their activation, local restriction enzyme activity can be
AB  - controlled by the local concentration of magnesium ions. Applying a
AB  - direct current (dc) voltage to a needle electrode of metallic magnesium
AB  - made it possible to control the local magnesium ion concentration at
AB  - the tip of the needle. The restriction enzyme was activated only, when
AB  - magnesium ions were electrochemically supplied.
ER  -

TY  - JOUR
AU  - Katuri, K.P.
AU  - Albertsen, M.
AU  - Saikaly, P.E.
TI  - Draft Genome Sequence of Desulfuromonas acetexigens Strain 2873, a Novel Anode-Respiring Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01522
EP  - e01516
VL  - 5
AB  - Here, we report the draft genome sequence of Desulfuromonas acetexigens strain 2873, which was
AB  - originally isolated from digester sludge from a sewage treatment
AB  - plant in Germany. This bacterium is capable of anode respiration with high
AB  - electrochemical activity in microbial electrochemical systems. The draft genome
AB  - contains 3,376 predicted protein-coding genes and putative multiheme c-type
AB  - cytochromes.
ER  -

TY  - JOUR
AU  - Katz, J.E.
AU  - Dlakic, M.
AU  - Clarke, S.
TI  - Automated identification of putative methyltransferases from genomic open reading frames.
JO  - Mol. Cell. Proteomics
PY  - 2003
SP  - 525
EP  - 540
VL  - 2
AB  - We have analyzed existing methodologies and created novel methodologies for the automatic
AB  - assignment of S-adenosylmethionine (AdoMet)-dependent
AB  - methyltransferase functionality to genomic open reading frames based on
AB  - predicted protein sequences. A large class of the AdoMet-dependent
AB  - methyltransferases shares a common binding motif for the AdoMet cofactor
AB  - in the form of a seven-strand twisted beta-sheet; this structural
AB  - similarity is mirrored in a degenerate sequence similarity that we refer
AB  - to as methyltransferase signature motifs. These motifs are the basis of
AB  - our assignments. We find that simple pattern matching based on the motif
AB  - sequence is of limited utility and that a new method of "sensitized
AB  - matrices for scoring methyltransferases" (SM(2)) produced with modified
AB  - versions of the MEME and MAST tools gives greatly improved results for the
AB  - Saccharomyces cerevisiae yeast genome. From our analysis, we conclude that
AB  - this class of methyltransferases makes up approximately 0.6-1.6% of the
AB  - genes in the yeast, human, mouse, Drosophila melanogaster, Caenorhabditis
AB  - elegans, Arabidopsis thaliana, and Escherichia coli genomes. We provide
AB  - lists of unidentified genes that we consider to have a high probability of
AB  - being methyltransferases for future biochemical analyses.
ER  -

TY  - JOUR
AU  - Katz, L.S.
AU  - Turnsek, M.
AU  - Kahler, A.
AU  - Hill, V.R.
AU  - Boyd, E.F.
AU  - Tarr, C.L.
TI  - Draft Genome Sequence of Environmental Vibrio cholerae 2012EL-1759 with Similarities to the V. cholerae O1 Classical Biotype.
JO  - Genome Announcements
PY  - 2014
SP  - e00617
EP  - e00614
VL  - 2
AB  - Vibrio cholerae 2012EL-1759 is an environmental isolate from Haiti that was recovered in 2012
AB  - during a cholera outbreak. The genomic backbone is similar to
AB  - that of the prototypical V. cholerae O1 classical biotype strain O395, and it
AB  - carries the Vibrio pathogenicity islands (VPI-1 and VPI-2) and a cholera toxin
AB  - (CTX) prephage.
ER  -

TY  - JOUR
AU  - Kauc, L.
AU  - Leszczynska, K.
TI  - Identification of a new restriction endonuclease, EagI, from Enterobacter agglomerans.
JO  - Acta Microbiol. Pol.
PY  - 1986
SP  - 317
EP  - 320
VL  - 35
AB  - The preliminary studies presented in this communication indicate that EndoR.
AB  - EagI and the restriction endonuclease EcoRII as well as EndoR. BstNI recognize
AB  - identical palindromic sites on the DNA substrate i.e. they are isoschizomers.
AB  - Since EndoR. EcoRII and EndoR. BstNI recognize the sequence CC(A/T)GG. EndoR.
AB  - EagI should recognize the same nucleotide sequence.
ER  -

TY  - JOUR
AU  - Kauc, L.
AU  - Piekarowicz, A.
TI  - Degradation of Transforming Deoxyribonucleic Acid by the ATP Dependent Restriction Endonuclease Isolated from Haemophilus Influenzae Rf.
JO  - Modern Trends in Bacterial Transformation and Transfection.
PY  - 1976
SP  - 257
EP  - 262
VL  - 0
AB  - The deoxyribonucleic acid of different serological types of Haemophilus
AB  - influenzae was shown to be degraded by the ATP dependent restriction
AB  - endonuclease isolated from H.influenzae Rf.
ER  -

TY  - JOUR
AU  - Kauc, L.
AU  - Piekarowicz, A.
TI  - Purification and properties of a new restriction endonuclease from Haemophilus influenzae Rf.
JO  - Eur. J. Biochem.
PY  - 1978
SP  - 417
EP  - 426
VL  - 92
AB  - Haemophilus influenzae Rf 232, showing the phenomena of restriction and
AB  - modification, contains an endonuclease that inactivates in vitro the biological
AB  - activity of DNAs lacking the strain-specific modification.  This specific
AB  - restriction endonuclease has been purified to near homogeneity by a procedure
AB  - that includes DNA-agarose chromatography.  This highly purified enzyme requires
AB  - ATP and Mg2+ for activity and is stimulated by S-adenosylmethionine.  The
AB  - enzyme seems to cleave DNA at well-defined sites, since it produces a specific
AB  - pattern of bands upon agarose gel electrophoresis.  The enzyme has no ATPase
AB  - activity.  A methylase activity is observed in the course of the
AB  - endonucleolytic reaction, which probably protects some of the DNA sites from
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Kauc, L.
AU  - Piekarowicz, A.
TI  - Degradation of transforming and transfecting DNA by the restriction endonucleases of Type I and Type II isolated from Haemophilus influenzae.
JO  - Acta Microbiol. Pol.
PY  - 1977
SP  - 137
EP  - 148
VL  - 26
AB  - The restriction endonucleases of type I and II from Haemophilus influenzae were studied for
AB  - their activity on transforming and transfecting DNA.  Type I restriction enzyme from
AB  - Haemophilus influenzae Rf, which requires adenosine 5'-triphosphate, reduced the size of
AB  - unmodified bacterial DNA from 66 x 106 daltons to approximately 18 x 106 daltons and did not
AB  - attack modified DNA.  The action of this enzyme gives only a low level of inactivation of
AB  - single and linked markers in the transforming DNA.  In contrast the HP1c1 phage DNA was
AB  - drastically inactivated by this enzyme.  The endoR.Hind III degrades the unmodified bacterial
AB  - DNA but the segments generated by this enzyme are still capable of being integrated in
AB  - transformation.  The enzyme has no activity on HP1c1 phage DNA.
ER  -

TY  - JOUR
AU  - Kaufman, D.L.
AU  - Evans, G.A.
TI  - Restriction endonuclease cleavage at the termini of PCR products.
JO  - Biotechniques
PY  - 1990
SP  - 304
EP  - 305
VL  - 9
AB  - None
ER  -

TY  - JOUR
AU  - Kaufmann, G.
TI  - Anticodon nucleases.
JO  - Trends Biochem. Sci.
PY  - 2000
SP  - 70
EP  - 74
VL  - 25
AB  - A tRNALys-specific anticodon nuclease is kept in a latent form in a rare Escherichia coli
AB  - strain, complexed with a DNA restriction enzyme. A phage T4 inhibitor of DNA restriction
AB  - activates anticodon nuclease, but other T4 proteins restore tRNALys. Detection of a homologous
AB  - system in Neisseria and a different anticodon nuclease in colicin E5 suggest ubiquity and
AB  - diversity of such tRNA toxins. Analysis of these systems could reveal novel RNA recognition
AB  - and cleavage mechanisms.
ER  -

TY  - JOUR
AU  - Kaufmann, G.
AU  - Amitsur, M.
AU  - Chapman-Shimshoni, D.
TI  - In vivo reconstitution of latent anticodon nuclease: A tRNA restriction enzyme masked by hsd restriction-modification proteins.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 174
EP  - 174
VL  - 17C
AB  - E. coli prr+ strains encode a latent form of phage T4-induced, tRNA Lys-specific anticodon
AB  - nuclease. The latent enzyme comprises a core factor encoded by prrC and cognate masking
AB  - elements encoded by flanking, hsd type Ic restriction modification genes. We have
AB  - reconstituted latent anticodon nuclease from separate, core and masking components in vivo by
AB  - complementing a prr cosmid carrying a null prrC mutation with PrrC provided in trans.
AB  - Expression of prrC from a low copy plasmid, insufficient to elicit detectable core activity by
AB  - itself, yielded in the presence of the hsd masking factors a full-fledged latent anticodon
AB  - nuclease phenotype. The data indicate that the Hsd proteins not only mask PrrC's activity but
AB  - also stabilize it maintaining the RNA restriction enzyme as an antiviral contingency.
ER  -

TY  - JOUR
AU  - Kaunietis, A.
AU  - de Jong, A.
AU  - Pranckute, R.
AU  - Buivydas, A.
AU  - Kuipers, O.P.
TI  - Draft Genome Sequences of Two Geobacillus Species Strains, Isolated from Oil Wells and Surface Soil above Oil Pools.
JO  - Genome Announcements
PY  - 2016
SP  - e01129
EP  - e01116
VL  - 4
AB  - Here, we present the draft genome sequences of two Geobacillus species strains isolated from
AB  - oil wells and surface soil above oil pools in Lithuania.
ER  -

TY  - JOUR
AU  - Kaur, C.
AU  - Selvakumar, G.
AU  - Ganeshamurthy, A.N.
TI  - Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate (Punica granatum) Rhizosphere.
JO  - Genome Announcements
PY  - 2016
SP  - e00844
EP  - e00816
VL  - 4
AB  - We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium
AB  - Paraburkholderia tropica strain P-31, isolated from pomegranate (Punica granatum)
AB  - rhizosphere. The draft genome sequence of Paraburkholderia tropica strain P-31
AB  - consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes,
AB  - and 49 RNAs.
ER  -

TY  - JOUR
AU  - Kaur, J.
AU  - Verma, H.
AU  - Tripathi, C.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03T.
JO  - Genome Announcements
PY  - 2013
SP  - e00751
EP  - e00713
VL  - 1
AB  - Sphingobium baderi strain LL03(T) was isolated from hexachlorocyclohexane (HCH)-contaminated
AB  - soil from Spolana, Czech Republic. Strain LL03(T) is a mutant
AB  - that is deficient in linB and linC (genes that encode hexachlorocyclohexane
AB  - haloalkane dehalogenase and dehydrogenase, respectively). The draft genome
AB  - sequence of LL03(T) (~4.85 Mb) consists of 92 contigs and 4,914 coding sequences,
AB  - with a G+C content of 63.5%.
ER  -

TY  - JOUR
AU  - Kaur, K.
AU  - Rohozinski, J.
AU  - Goorha, R.
TI  - Identification and characterization of the frog virus 3 DNA methyltransferase gene.
JO  - J. Gen. Virol.
PY  - 1995
SP  - 1937
EP  - 1943
VL  - 76
AB  - Cytosine DNA methyltransferases (MTases) first recognize specific nucleotide sequences and
AB  - then transfer a methyl group from S-adenosylmethionine to cytosine.  This division of function
AB  - is reflected in five highly conserved motifs shared by cytosine Mtases.  The region containing
AB  - the first four motifs is responsible for the catalytic function whereas the region containing
AB  - the fifth motif V provides specificity of binding to DNA.  In at least one case, two separate
AB  - proteins, one containing the first four motifs and the second containing the last motif
AB  - combine to provide full functional activity.  In the frog virus 3 (FV3) genome we have
AB  - identified an open reading frame (ORF) whose deduced amino acid (aa) sequence contains motifs
AB  - characteristic of prokaryotic as well as eukaryotic MTases.  The ORF consists of 642 bp which
AB  - codes for a protein of 214 aa with a predicted molecular mass of 24.8 kDa.  This ORF contains
AB  - the first four highly conserved motifs of cytosine MTases but the fifth motif, responsible for
AB  - DNA binding specificity, is missing.  Presumably, FV3 MTase is composed of two subunits.
AB  - Northern blot analysis showed that the putative MTase ORF is transcribed into two transcripts
AB  - belonging to the delayed-early class of FV3 messages.  These two transcripts appear to be
AB  - initiated at two different start sites but terminate in the same 3' region of the gene.  The
AB  - transcription start sites are not preceded by any known promoter sequences, but two regions of
AB  - hyphenated dyad symmetry are present at the 3' end of the message.  A protein with a
AB  - molecular mass of ~28 kDa was synthesized by a rabbit reticulocyte lysate programmed with
AB  - capped runoff transcripts from the cloned gene, suggesting that the ORF can be transcribed
AB  - into a message coding for a viral protein.  Overall, our results suggest that we have
AB  - identified a gene for a subunit of MTase in the FV3 genome.
ER  -

TY  - JOUR
AU  - Kaur, N.
AU  - Kumar, S.
AU  - Bala, M.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T.
JO  - Genome Announcements
PY  - 2013
SP  - e0013813
EP  - e0013813
VL  - 1
AB  - We report the 8.5-Mb genome sequence of Amycolatopsis decaplanina strain DSM 44594(T),
AB  - isolated from a soil sample from India. The draft genome of strain DSM
AB  - 44594(T) consists of 8,533,276 bp with a 68.6% G+C content, 7,899 protein-coding
AB  - genes, and 57 RNAs.
ER  -

TY  - JOUR
AU  - Kaus-Drobek, M.
AU  - Czapinska, H.
AU  - Sokolowska, M.
AU  - Tamulaitis, G.
AU  - Szczepanowski, R.H.
AU  - Urbanke, C.
AU  - Siksnys, V.
AU  - Bochtler, M.
TI  - Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2035
EP  - 2046
VL  - 35
AB  - Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/'
AB  - designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The
AB  - enzyme has been noted for its tolerance towards DNA modifications. Here, we report a
AB  - biochemical characterization and crystal structures of MvaI in an apo-form and in a complex
AB  - with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes
AB  - its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The
AB  - catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the
AB  - bases from the minor grove side. The recognition lobe mediates all major grove interactions
AB  - with the bases. The enzyme in the crystal is bound to the strand with T at the center of the
AB  - recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive
AB  - state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG
AB  - and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand
AB  - instead of making a double-strand break.
ER  -

TY  - JOUR
AU  - Kautharapu, K.B.
AU  - Jarboe, L.R.
TI  - Genome Sequence of the Psychrophilic Deep-Sea Bacterium Moritella marina MP-1 (ATCC 15381).
JO  - J. Bacteriol.
PY  - 2012
SP  - 6296
EP  - 6297
VL  - 194
AB  - Moritella marina MP-1 is a bacterial species known for its production of docosahexaenoic acid.
AB  - We present the draft genome sequence of the type strain
AB  - Moritella marina MP-1 (ATCC 15381), having 4,636,778 bp with a G+C content of
AB  - 40.5% and consisting of 83 contigs.
ER  -

TY  - JOUR
AU  - Kavamura, V.N.
AU  - Santos, S.N.
AU  - Taketani, R.G.
AU  - Vasconcellos, R.L.
AU  - Melo, I.S.
TI  - Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome.
JO  - Genome Announcements
PY  - 2017
SP  - e01534
EP  - e01516
VL  - 5
AB  - The strain of Bacillus sp. CMAA 1363 was isolated from the Brazilian Caatinga biome and showed
AB  - plant growth-promoting traits and ability to promote maize
AB  - growth under drought stress. Sequencing revealed genes involved in stress
AB  - response and plant growth promotion. These genomic features might aid in the
AB  - protection of plants against the negative effects imposed by drought.
ER  -

TY  - JOUR
AU  - Kavousi, N.
AU  - Eng, W.W.
AU  - Lee, Y.P.
AU  - Tan, L.H.
AU  - Thuraisingham, R.
AU  - Yule, C.M.
AU  - Gan, H.M.
TI  - First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone.
JO  - Genome Announcements
PY  - 2016
SP  - e00023
EP  - e00016
VL  - 4
AB  - We report here the first high-quality draft genome sequence of Pasteurella multocida sequence
AB  - type 128, which was isolated from the infected finger bone of
AB  - an adult female who was bitten by a domestic dog. The draft genome will be a
AB  - valuable addition to the scarce genomic resources available for P. multocida.
ER  -

TY  - JOUR
AU  - Kaw, M.K.
AU  - Blumenthal, R.M.
TI  - Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.
JO  - BMC Mol. Biol.
PY  - 2010
SP  - 87
EP  - 87
VL  - 11
AB  - Background: Most type II restriction-modification (RM) systems have two independent enzymes
AB  - that act on the same DNA sequence: a modification
AB  - methyltransferase that protects target sites, and a restriction
AB  - endonuclease that cleaves unmethylated target sites. When RM genes
AB  - enter a new cell, methylation must occur before restriction activity
AB  - appears, or the host's chromosome is digested. Transcriptional
AB  - mechanisms that delay endonuclease expression have been identified in
AB  - some RM systems. A substantial subset of those systems is controlled by
AB  - a family of small transcription activators called C proteins. In the
AB  - PvuII system, C. PvuII activates transcription of its own gene, along
AB  - with that of the downstream endonuclease gene. This regulation results
AB  - in very low R. PvuII mRNA levels early after gene entry, followed by
AB  - rapid increase due to positive feedback. However, given the lethal
AB  - consequences of premature REase accumulation, transcriptional control
AB  - alone might be insufficient. In C-controlled RM systems, there is a +/-
AB  - 20 nt overlap between the C termination codon and the R (endonuclease)
AB  - initiation codon, suggesting possible translational coupling, and in
AB  - many cases predicted RNA hairpins could occlude the ribosome binding
AB  - site for the endonuclease gene.Results: Expression levels of lacZ
AB  - translational fusions to pvuIIR or pvuIIC were determined, with the
AB  - native pvuII promoter having been replaced by one not controlled by C.
AB  - PvuII. In-frame pvuIIC insertions did not substantially decrease either
AB  - pvuIIC-lacZ or pvuIIR-lacZ expression (with or without C. PvuII
AB  - provided in trans). In contrast, a frameshift mutation in pvuIIC
AB  - decreased expression markedly in both fusions, but mRNA measurements
AB  - indicated that this decrease could be explained by transcriptional
AB  - polarity. Expression of pvuIIR-lacZ was unaffected when the pvuIIC stop
AB  - codon was moved 21 nt downstream from its WT location, or 25 or 40 bp
AB  - upstream of the pvuIIR initiation codon. Disrupting the putative
AB  - hairpins had no significant effects.Conclusions: The initiation of
AB  - translation of pvuIIR appears to be independent of that for pvuIIC.
AB  - Direct tests failed to detect regulatory rules for either gene overlap
AB  - or the putative hairpins. Thus, at least during balanced growth,
AB  - transcriptional control appears to be sufficiently robust for proper
AB  - regulation of this RM system.
ER  -

TY  - JOUR
AU  - Kawabata, H.
AU  - Norris, S.J.
AU  - Watanabe, H.
TI  - BBE02 disruption mutants of Borrelia burgdorferi B31 have a highly transformable, infectious phenotype.
JO  - Infect. Immun.
PY  - 2004
SP  - 7147
EP  - 7154
VL  - 72
AB  - We constructed highly transformable and infectious Borrelia burgdorferi B31 by inactivating
AB  - BBE02, a putative restriction-modification gene on
AB  - the linear plasmid lp25. The low-passage-number B31 clones 5A4
AB  - (containing all plasmids) and 5A18 (lp28-4(-) lp56(-)) were used for
AB  - this study, and BBE02 was disrupted by homologous recombination. The
AB  - transformation efficiency with the shuttle vector pBSV2C03::gntDeltakan
AB  - was increased from <1 to similar to10 colonies per mug of DNA for 5A4
AB  - and 5A4 BBE02::Kan(r) and from 14 to approximately 600 colonies per mug
AB  - of DNA for 5A18 and 5A18 BBE02::Kanr. lp25, which is required for
AB  - infectivity in mice, was retained in BBE02 mutants transformed with
AB  - pBSV2C03::gntDeltakan, but lp25 was not detected in transformants of
AB  - the parental clones 5A4 and 5A18. BBE02 disruptants and
AB  - pBSV2C03::gntDeltakan transformants of these clones remained infectious
AB  - in C3H/HeN mice, and the 50% infective doses of the BBE02 disruptants
AB  - were <10(2) organisms per mouse. The inactivation of BBE02 thus
AB  - eliminates a transformation barrier for infectious B. burgdorferi B31
AB  - and will provide a valuable tool for studying the virulence factors of
AB  - Lyme disease.
ER  -

TY  - JOUR
AU  - Kawai, M.
AU  - Higashiura, N.
AU  - Hayasaki, K.
AU  - Okamoto, N.
AU  - Takami, A.
AU  - Hirakawa, H.
AU  - Matsushita, K.
AU  - Azuma, Y.
TI  - Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen.
JO  - DNA Res.
PY  - 2015
SP  - 357
EP  - 366
VL  - 22
AB  - Asaia bogorensis, a member of acetic acid bacteria (AAB), is an aerobic bacterium
AB  - isolated from flowers and fruits, as well as an opportunistic pathogen that
AB  - causes human peritonitis and bacteraemia. Here, we determined the complete
AB  - genomic sequence of the As. bogorensis type strain NBRC 16594, and conducted
AB  - comparative analyses of gene expression under different conditions of co-culture
AB  - with mammalian cells and standard AAB culture. The genome of As. bogorensis
AB  - contained 2,758 protein-coding genes within a circular chromosome of 3,198,265
AB  - bp. There were two complete operons encoding cytochrome bo3-type ubiquinol
AB  - terminal oxidases: cyoABCD-1 and cyoABCD-2. The cyoABCD-1 operon was
AB  - phylogenetically common to AAB genomes, whereas the cyoABCD-2 operon belonged to
AB  - a lineage distinctive from the cyoABCD-1 operon. Interestingly, cyoABCD-1 was
AB  - less expressed under co-culture conditions than under the AAB culture conditions,
AB  - whereas the converse was true for cyoABCD-2. Asaia bogorensis shared
AB  - pathogenesis-related genes with another pathogenic AAB, Granulibacter
AB  - bethesdensis, including a gene coding pathogen-specific large bacterial adhesin
AB  - and additional genes for the inhibition of oxidation and antibiotic resistance.
AB  - Expression alteration of the respiratory chain and unique hypothetical genes may
AB  - be key traits that enable the bacterium to survive under the co-culture
AB  - conditions.
ER  -

TY  - JOUR
AU  - Kawaichi, S.
AU  - Yoshida, T.
AU  - Sako, Y.
AU  - Nakamura, R.
TI  - Draft Genome Sequence of a Heterotrophic Facultative Anaerobic Thermophilic Bacterium, Ardenticatena maritima Strain 110ST.
JO  - Genome Announcements
PY  - 2015
SP  - e01145
EP  - e01115
VL  - 3
AB  - Ardenticatena maritima strain 110S(T) is a filamentous bacterium isolated from an iron-rich
AB  - coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or
AB  - nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the
AB  - draft genome sequence comprising 3,569,367 bp, containing 3,355 predicted coding sequences
AB  - (CDSs).
ER  -

TY  - JOUR
AU  - Kawakami, B.
TI  - Application of recombinant DNA technique to the production of N-acetylneuraminate lyase and restriction enzymes.
JO  - Ph.D. Thesis, University of Kyoto University
PY  - 1991
SP  - 1
EP  - 102
AB  - Chapter I. N-Acetylneuraminate lyase Chapter II. 1) Cloning of BamHI RM system in B. subtilis
AB  - 2) Cloning and sequencing of the AccI RM system 3) Cloning and expression of the BanI and
AB  - BanIII RM systems from Bacillus aneurinolyticus 4) Nucleotide sequence of the BanI RM genes 5)
AB  - Nucleotide sequence of the BanIII M gene.
ER  -

TY  - JOUR
AU  - Kawakami, B.
AU  - Hilzheber, C.
AU  - Nagatomo, M.
AU  - Oka, M.
TI  - Cloning and nucleotide sequences of the AccI restriction-modification genes in Acinetobacter calcoaceticus.
JO  - Agric. Biol. Chem.
PY  - 1991
SP  - 1553
EP  - 1559
VL  - 55
AB  - The genes of the AccI restriction-modification system specific for
AB  - GT(A/C)(G/T)AC were cloned from the chromosomal DNA of Acinetobacter
AB  - calcoaceticus, and their nucleotides sequenced.  The restriction and
AB  - modification genes coded for polypeptides with calculated molecular weights of
AB  - 42,494 and 63,078, respectively.  Both the enzymes were coded by the same DNA
AB  - strand and the restriction gene was upstream of the methylase gene, separated
AB  - by 2 bp.  The restriction gene was significantly expressed in E. coli cells, so
AB  - that the AccI restriction endonuclease could be purified to homogeneity.
AB  - Analysis by sodium dodecyl sulfate-polyacrylamide  gel electrophoresis and gel
AB  - filtration indicated that the catalytically active form of the endonuclease was
AB  - tetrameric.  Sequence comparison with related enzymes indicated that AccI
AB  - methylase contained a segment of tetra-amino acids, NPPY, characteristic of
AB  - N6-adenine methylases.  In addition, some homologous regions were found in the
AB  - sequence of HincII methylase specific for GT(C/T) (A/G)AC.
ER  -

TY  - JOUR
AU  - Kawakami, B.
AU  - Katsuragi, N.
AU  - Maekawa, Y.
AU  - Imanaka, T.
TI  - Cloning and expression of the BamHI restriction-modification system in Bacillus subtilis.
JO  - J. Ferment. Bioeng.
PY  - 1990
SP  - 211
EP  - 214
VL  - 70
AB  - The genes of the GGATCC-specific BamHI restriction-modification system of
AB  - Bacillus amyloliquefaciens H have been cloned and expressed in Bacillus
AB  - subtilis MT-2.  B. subtilis MT-2 carrying the recombinant plasmid (pBamHIRM22)
AB  - produced about 10-fold more BamHI restriction endonuclease and BamHI methylase
AB  - than B. amyloliquefaciens H did.  B. subtilis MT-2(pBamHIRM22) restricted
AB  - unmodified phage.  Restriction and modification genes were stably maintained in
AB  - B. subtilis MT-2 on one plasmid and the produced BamHI endonuclease remained
AB  - stable even in the stationary phase of the culture.  BamHI endonuclease from B.
AB  - subtilis MT-2 (pBamHIRM22) had the same molecular weight and N-terminal amino
AB  - acid sequence as that from B. amyloliquefaciens H.
ER  -

TY  - JOUR
AU  - Kawakami, B.
AU  - Sasaki, A.
AU  - Oka, M.
AU  - Maekawa, Y.
TI  - Nucleotide sequence of the gene coding for the BanIII DNA methyltransferase in Bacillus aneurinolyticus.
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 3227
EP  - 3233
VL  - 54
AB  - The gene coding for the ATCGAT specific BanIII DNA methyltransferase (M.BanIII)
AB  - of Bacillus aneurinolyticus was cloned and its nucleotides sequenced.  The
AB  - coding region was assigned on the nucleotide sequence on the basis of the
AB  - N-terminal amino acid sequence and molecular weight of the enzyme.  The
AB  - M.BanIII gene coded for a protein of 580 amino acid residues (MW 66,344).
AB  - Comparison with other methylases indicated that the M.BanIII sequence contained
AB  - a segment of tetra-amino acids, NPPY, characteristic of N6-adenine methylases.
AB  - In addition, some homologous regions were found in the sequences of type II
AB  - adenine methylases PaeR7I(CTCGAG), TaqI(TCGA) and PstI(CTGCAG), containing TCGA
AB  - within the recognition sequences.
ER  -

TY  - JOUR
AU  - Kawalec, M.
AU  - Borsuk, P.
AU  - Piechula, S.
AU  - Stepien, P.P.
TI  - A novel restriction endonuclease UnbI, a neoschizomer of Sau96I from an unidentified psychrofilic bacterium from Antarctica is inhibited by phosphate ions.
JO  - Acta Biochim. Pol.
PY  - 1997
SP  - 849
EP  - 852
VL  - 44
AB  - A novel type II restriction endonuclease UnbI was isolated from an unidentified psychrofilic
AB  - bacterial strain from Antarctica.  UnbI recognizes and cleaves the sequence 5'-GGNCC-3',
AB  - producing 5 nucleotide long sticky ends.  In this respect it differs from its neoschizomer
AB  - Sau96I and all other restriction enzymes recognizing this sequence.  UnbI has a relatively low
AB  - temperature optimum of 15 C to 20 C and its activity is completely inhibited by inorganic
AB  - phosphate.
ER  -

TY  - JOUR
AU  - Kawamura, M.
AU  - Sakakibara, M.
AU  - Watanabe, T.
AU  - Kita, K.
AU  - Hiraoka, N.
AU  - Obayashi, A.
AU  - Takagi, M.
AU  - Yano, K.
TI  - A new restriction endonuclease from Spirulina platensis.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 1985
EP  - 1989
VL  - 14
AB  - Three restriction endonucleases, SplI, SplII and SplIII have been purified partially from
AB  - Spirulina platensis subspecies siamese and named.  SplI cleaves bacteriophage lambda DNA at
AB  - one site, phi X 174 RF DNA at two sites, but does not cleave pBR322 DNA.  This enzyme
AB  - recognizes the sequence 5'CGTACG3'3'GCATCG5'and cuts the site indicated by the arrows.
AB  - SplIII is an isoschizomer of HaeIII.
ER  -

TY  - JOUR
AU  - Kawarabayasi, Y. et al.
TI  - Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3 (Supplement).
JO  - DNA Res.
PY  - 1998
SP  - 147
EP  - 155
VL  - 5
AB  - The circular genome of Pyrococcus horikoshii OT3, (1,738,505 bp long), was opened at the
AB  - junction of Srf I-C and Srf I-E fragments, and is represented by a linear map starting from
AB  - this site.  The nucleotide positions are indicated on the linear map by numerals in kb.  Above
AB  - and below the physical maps, the potential protein-coding regions assigned are indicated by
AB  - boxes with arrowheads, indicating the direction of transcription.  The detailed assignment
AB  - procedures are described in the main article in this issue.  The results of ORF similarity and
AB  - motif searches are shown using the following color codes: red, similarities to reported genes
AB  - with known functions; blue, similarities to hypothetical genes; green, some motifs but without
AB  - significant similarity to the registered sequences; and no color, no apparent similarity to
AB  - any reported genes and no significant protein motifs.  The ORF names defined in the main
AB  - article are given to each ORF, and the positions of the rRNA and tRNA genes are indicated by
AB  - closed box and vertical bars with a "T", respectively.  The sequence data reported here have
AB  - been deposited in DDBJ/Genbank/EMBL databases under accession numbers AP000001 (nucleotide
AB  - positions 1-287,000), AP000002 (287,001-544,000), AP000003 (544,001-777,000), AP000004
AB  - (777,001-994,000), AP000005 (994,001-1,166,000), AP000006 (1,166,001-1,485,000), and AP000007
AB  - (1,485,001-1,738,505).
ER  -

TY  - JOUR
AU  - Kawarabayasi, Y. et al.
TI  - Complete sequence and gene organization of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus horikoshii OT3.
JO  - DNA Res.
PY  - 1998
SP  - 55
EP  - 76
VL  - 5
AB  - The complete sequence of the genome of a hyper-thermophilic Archaebacterium, Pyrococcus
AB  - horikoshii OT3, has been determined by assembling the sequences of the physical map-based
AB  - contigs of fosmid clones and of long polymerase chain reaction products which were used for
AB  - gap-filling.  The entire length of the genome was 1,738,505 bp.  The authenticity of the
AB  - entire genome sequence was supported by restriction analysis of long PCR products, which were
AB  - directly amplified from the genomic DNA.  As the potential protein-coding regions, a total of
AB  - 2061 open reading frames were assigned, and by similarity search against public databases, 406
AB  - (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences
AB  - registered but with unknown function.  The remaining 1202 ORFs (58.3%) did not show any
AB  - significant similarity to the sequences in the databases.  Sequence comparison among the
AB  - assigned ORFs in the genome provided evidence that a considerable number of ORFs were
AB  - generated by sequence duplication.  By similarity search, 11 ORFs were assumed to contain
AB  - intein elements.  The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA
AB  - genes and 46 tRNA genes including two with the intron structure.  All the assigned ORFs and
AB  - RNA coding regions occupied 91.25% of the whole genome.  The data presented in this paper are
AB  - available on the internet at http://www.nite.go.jp.
ER  -

TY  - JOUR
AU  - Kawarabayasi, Y. et al.
TI  - Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7.
JO  - DNA Res.
PY  - 2001
SP  - 123
EP  - 140
VL  - 8
AB  - The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus
AB  - tokodaii strain7 which optimally grows at 80 degrees C, at low pH, and under aerobic
AB  - conditions, has been determined by the whole genome shotgun method with slight modifications.
AB  - The genomic size was 2,694,756 bp long and the G + C content was 32.8%. The following
AB  - RNA-coding genes were identified: a single 16S-23S rRNA cluster, one 5S rRNA gene and 46 tRNA
AB  - genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were
AB  - SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive
AB  - elements. The genome contained 2826 potential protein-coding regions (open reading frames,
AB  - ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to
AB  - functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145
AB  - (5.1%) contained some motifs, and the remaining 849 (30.0%) did not show any significant
AB  - similarity to the registered sequences. The ORFs with functional assignments included the
AB  - candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain.
AB  - Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of
AB  - genomic structure, and duplication of genomic regions that may be responsible for the larger
AB  - genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes
AB  - which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The
AB  - result suggests that this strain is closer to eukaryotes among the archaea strains so far
AB  - sequenced. The data presented in this paper are also available on the internet homepage
AB  - (http://www.bio.nite.go.jp/E-home/genome_list-e.html).
ER  -

TY  - JOUR
AU  - Kawarabayasi, Y. et al.
TI  - Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1.
JO  - DNA Res.
PY  - 1999
SP  - 83
EP  - 101
VL  - 6
AB  - The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum
AB  - pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome
AB  - shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The
AB  - authenticity of the entire sequence was supported by restriction analysis of long PCR
AB  - products, which were directly amplified from the genomic DNA. As the potential protein-coding
AB  - regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search
AB  - against public databases, 633 (23.5%) of the ORFs were related to genes with putative function
AB  - and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the
AB  - TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of
AB  - the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of
AB  - 2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not
AB  - show any significant similarity to the sequences in the databases. Sequence comparison among
AB  - the assigned ORFs suggested that a considerable member of ORFs were generated by sequence
AB  - duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and
AB  - 47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding
AB  - regions occupied 89.12% of the whole genome. The data presented in this paper are available on
AB  - the internet homepage (http://www.mild.nite.go.jp).
ER  -

TY  - JOUR
AU  - Kawasaki, K.
AU  - Shibata, T.
TI  - Mitochondrial HSP70 as a subunit of eukaryotic multi-site-specific endonuclease, Endo.SceI; auto-phosphorylation and heat stability.
JO  - Mol. Biol. Cell
PY  - 1995
SP  - 135a
EP  - 135a
VL  - 6
AB  - A eukaryotic site-specific endonuclease, Endo.SceI, that cuts DNA at multiple sites, is an
AB  - initiator of homologous gene conversion in yeast mitochondria.  The active form of Endo.SceI
AB  - is a heterodimer of a 75 kDa-subunit and a 50 kDa-subunit.  The 75 kDa-subunit is a
AB  - mitochondrial 70 kDa heat shock protein (HSP70) and encoded by a nuclear gene, ENS1 (identical
AB  - to SSC1).  HSP70 protein has ATP-related activities; such as ATP binding, an ATPase, and a
AB  - protein kinase.  We investigated ATP-related activities of HSP70 protein in Endo.SceI.  We
AB  - found that the 75 kDa-subunit of Endo.SceI exhibits a protein kinase activity.  The kinase
AB  - activity specifically phosphorylated the 75 kDa-subunit, but not the 50 kDa-subunit or other
AB  - proteins tested.  The phosphorylating activity requires Ca2+ and an acidic pH, and is greatly
AB  - stimulated by the presence of the 50 kDa-subunit.  Ca2+ increased the electrophoretic mobility
AB  - of Endo.SceI.  The auto-phosphorylation of the 75 kDa-subunit, by itself, does not have a
AB  - direct effect on DNase, but the phosphorylation condition stabilizes DNase activity of
AB  - Endo.SceI against heat-inactivation.  This stabilization was dependent upon Ca2+ and ATP, as
AB  - well as ATP-gamma-S or ADP.  In addition, ATP-gamma-S and ADP inhibited the
AB  - auto-phosphorylation of the 75 kDa-subunit.  These findings suggest that Ca2+ ions induced the
AB  - conformational change of Endo.SceI in which the binding of nucleotides, such as ATP and ADP,
AB  - regulated the heat-stability and autophosphorylation of Endo.SceI.
ER  -

TY  - JOUR
AU  - Kawasaki, K.
AU  - Shibata, T.
AU  - Ito, F.
TI  - Roles of the HSP70-Subunit in a eukaryotic multi-site-specific endonuclease, Endo.SceI: Autophosphorylation and heat stability.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2004
SP  - 2557
EP  - 2564
VL  - 68
AB  - The 70 kDa heat shock proteins (HSP70) are a family of molecular chaperones that bind
AB  - transiently to unfolded proteins in an ATP/ADP
AB  - dependent manner. Endo.SceI comprises a unique example for mitochondria. HSP70, which exists
AB  - in a stable complex with a nucleolytic subunit as a multi-site specific DNase. The
AB  - HSP70-subunit in Endo.SceI was autophosphorylated by ATP in vitro. The
AB  - autophosphorylation was higher in the Endo.SceI complex form than in
AB  - the free form. Although the autophosphorylation had no significant
AB  - effect on the endonucleolytic activity of Endo.SceI, the factors
AB  - favoring autophosphorylation protected the endonucleolytic activity of
AB  - Endo.SceI against heat inactivation. ATP, adenosine
AB  - 5'-O-(3-thiotriphosphate) (ATP-gamma-S), and ADP not only protected the
AB  - endonucleolytic activity against heat inactivation in the presence of
AB  - Ca2+ ions, but also reduced the labeling of the HSP70-subunit by
AB  - [gamma-P-32]ATP in Endo.SceI. These findings suggest that the
AB  - HSP70-subunit shields Endo.SceI from heat inactivation through ATP/ADP
AB  - binding.
ER  -

TY  - JOUR
AU  - Kawasaki, K.
AU  - Takahashi, M.
AU  - Ando, T.
AU  - Shibata, T.
TI  - Sequence-specific complex formation of DNA and a eukaryotic sequence-specific endonuclease, SceI.
JO  - Eur. J. Biochem.
PY  - 1991
SP  - 665
EP  - 671
VL  - 202
AB  - Endo.SceI is a eukaryotic sequence-specific endonuclease of 120 kDa that causes
AB  - sequence-specific double-stranded scission of DNA.  Unlike results with restriction enzymes,
AB  - we found a consensus sequence around the cleavage sites for Endo.SceI instead of a common
AB  - sequence.  We searched for conditions for studying the binding of Endo.SceI to DNA other than
AB  - cutting.  Under optimized conditions including gel mobility shift assay, Endo.SceI exhibited
AB  - sequence-specific binding to a short double-stranded DNA (41 base pairs) containing a cleavage
AB  - site and the DNA reisolated from the protein-DNA complex was not cleaved.  The analysis of the
AB  - complex of Endo.SceI and DNA isolated by the gel mobility shift experiments showed that the
AB  - DNA-binding entity in the Endo.SceI preparation does have Endo.SceI activity and consists of
AB  - an equal amount of 75-kDa and 50-kDa polypeptides.  Based on this observation from previous
AB  - studies, we conclude that Endo.SceI is a heterodimer of the 75-kDa and 50-kDa subunits.  Under
AB  - the present assay conditions, Endo.SceI did not show binding to single-stranded DNA having the
AB  - same sequence of either plus or minus strand of the double-stranded DNA containing the
AB  - cleavage site (the 41-bp DNA).  Endo.SceI showed significantly higher affinity for the
AB  - consensus sequence than the major cleavage site in pBR322 DNA.  Unlike the cleavage of DNA by
AB  - Endo.SceI which requires Mg2+, this sequence-specific binding is independent of but stimulated
AB  - by Mg2+.
ER  -

TY  - JOUR
AU  - Kawasaki, K.
AU  - Takahashi, M.
AU  - Natori, M.
AU  - Shibata, T.
TI  - DNA sequence recognition by a eukaryotic sequence-specific endonuclease, Endo.SceI, from Saccharomyces cerevisiae.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 5342
EP  - 5347
VL  - 266
AB  - A eukaryotic sequence-specific endonuclease, Endo.SceI, causes
AB  - sequence-specific double-stranded scission of double-stranded DNA to produce
AB  - cohesive ends with four bases protruding at the 3' termini.  Unlike the case of
AB  - restriction enzymes, an asymmetric 26-base pair consensus sequence was found
AB  - around the cleavage site for Endo.SceI instead of a common sequence.  We
AB  - analyzed the base pairs that interacted with Endo.SceI on the recognition of
AB  - its cleavage sites.  A region comprising -10 through +16 base pairs from the
AB  - center of the cleavage site was shown to be essential and sufficient for the
AB  - sequence-specific cutting with Endo.SceI by experiments involving synthesized
AB  - DNAs.  Methylation interference experiments indicate that bases in the region
AB  - comprising the +7 through +14 base pairs are involved in close contact with
AB  - Endo.SceI in its recognition of the cleavage site.  This +7 through +14-base
AB  - pair region overlaps the most stringently conserved sequence in the consensus
AB  - sequence for the cleavage site, suggesting that this region constitutes the
AB  - core for the recognition by Endo.SceI.
ER  -

TY  - JOUR
AU  - Kawasaki, M.
AU  - Delamare-Deboutteville, J.
AU  - Bowater, R.O.
AU  - Walker, M.J.
AU  - Beatson, S.
AU  - Ben Zakour, N.L.
AU  - Barnes, A.C.
TI  - Microevolution of aquatic Streptococcus agalactiae ST-261 from Australia indicates dissemination via imported tilapia and ongoing adaptation to marine hosts or environment.
JO  - Appl. Environ. Microbiol.
PY  - 2018
SP  - AEM.00859
EP  - AEM.00818
VL  - 0
AB  - Streptococcus agalactiae (GBS) causes disease in a wide range of animals. The serotype Ib
AB  - lineage is highly adapted to aquatic hosts, exhibiting substantial
AB  - genome reduction compared with terrestrial conspecifics. Here we sequence genomes
AB  - from 40 GBS isolates including 25 from wild fish and captive stingrays in
AB  - Australia, six local veterinary or human clinical isolates, and nine isolates
AB  - from farmed tilapia in Honduras and compare with 42 genomes from public
AB  - databases. Phylogenetic analysis based on non-recombinant core genome SNPs
AB  - indicated that aquatic serotype Ib isolates from Queensland were distantly
AB  - related to local veterinary and human clinical isolates. In contrast, Australian
AB  - aquatic isolates are most closely related to a tilapia isolate from Israel,
AB  - differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on
AB  - core genome SNPs indicates dissemination of ST-261 from an ancestral tilapia
AB  - strain, which is congruent with several introductions of tilapia into Australia
AB  - from Israel during the 1970s and 1980s. Pan-genome analysis identified 1,440
AB  - genes as core with the majority being dispensable or strain-specific with
AB  - non-protein-coding intergenic regions (IGRs) divided amongst core and
AB  - strain-specific genes. Aquatic serotype Ib strains have lost many virulence
AB  - factors during adaptation, but six adhesins were well conserved across the
AB  - aquatic isolates and might be critical for virulence in fish and targets for
AB  - vaccine development. The close relationship amongst recent ST-261 isolates from
AB  - Ghana, USA and China with the Israeli tilapia isolate from 1988 implicates the
AB  - global trade in tilapia seed for aquaculture in the widespread dissemination of
AB  - serotype Ib fish-adapted GBS.ImportanceStreptococcus agalactiae (GBS) is a
AB  - significant pathogen of humans and animals. Some lineages have become adapted to
AB  - particular hosts and serotype Ib is highly specialized to fish. Here we show that
AB  - this lineage is likely to have been distributed widely by the global trade in
AB  - tilapia for aquaculture, with probable introduction into Australia in the 1970s
AB  - and subsequent dissemination in wild fish populations. We report variability in
AB  - the polysaccharide capsule amongst this lineage, but identify a cohort of common
AB  - surface proteins that may be a focus of future vaccine development to reduce the
AB  - biosecurity risk in international fish trade.
ER  -

TY  - JOUR
AU  - Kawasaki, M.
AU  - Makino, S.-I.
AU  - Matsuzawa, H.
AU  - Satow, Y.
AU  - Ohya, Y.
AU  - Anraku, Y.
TI  - Folding-dependent in vitro protein splicing of the Saccharomyces cerevisiae VMA1 protozyme.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1996
SP  - 827
EP  - 832
VL  - 222
AB  - VMA1 translational product undergoes excision of a 50-kDa intervening segment (VDE:
AB  - VMAI-derived endonuclease) and religation of the flanking regions to create a 69-kDa catalytic
AB  - subunit of vacuolar membrane H+-ATPase.  VDEs conjugated with polypeptides at both N- and
AB  - C-terminal ends were expressed in Escherichia coli and examined for their ability to catalyze
AB  - self-splicing.  Processed VDE was found in soluble pools, while unspliced precursors
AB  - accumulated in insoluble pools, forming inclusion bodies.  We demonstrate in vitro protein
AB  - splicing by refolding of the denatured precursor molecules.  The processing reaction
AB  - efficiently occurs with the purified precursor peptide.  VDE bracketed by only 6 proximal and
AB  - 4 distal amino acids is autocatalytically processed.
ER  -

TY  - JOUR
AU  - Kawashima, T.
AU  - Amano, N.
AU  - Koike, H.
AU  - Makino, S.-i.
AU  - Higuchi, S.
AU  - Kawashima-Ohya, Y.
AU  - Watanabe, K.
AU  - Yamazaki, M.
AU  - Kanehori, K.
AU  - Kawamoto, T.
AU  - Nunoshiba, T.
AU  - Yamamoto, Y.
AU  - Aramaki, H.
AU  - Makino, K.
AU  - Suzuki, M.
TI  - Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 14257
EP  - 14262
VL  - 97
AB  - The complete genomic sequence of the archaeon Thermoplasma volcanium, possessing optimum
AB  - growth temperature (OGT) of 60 degrees C, is reported. By systematically comparing this
AB  - genomic sequence with the other known genomic sequences of archaea, all possessing higher OGT,
AB  - a number of strong correlations have been identified between characteristics of genomic
AB  - organization and the OGT. With increasing OGT, in the genomic DNA, frequency of clustering
AB  - purines and pyrimidines into separate dinucleotides rises (e.g., by often forming AA and TT,
AB  - whereas avoiding TA and AT). Proteins coded in a genome are divided into two distinct
AB  - subpopulations possessing isoelectric points in different ranges (i.e., acidic and basic), and
AB  - with increasing OGT the size of the basic subpopulation becomes larger. At the metabolic
AB  - level, genes coding for enzymes mediating pathways for synthesizing some coenzymes, such as
AB  - heme, start missing. These findings provide insights into the design of individual genomic
AB  - components, as well as principles for coordinating changes in these designs for the adaptation
AB  - to new environments. Full author list: Kawashima, T., Amano, N., Koike, H., Makino, S.-i.,
AB  - Higuchi, S., Kawashima-Ohya, Y., Watanabe, K., Yamazaki, M., Kanehori, K., Kawamoto, T.,
AB  - Nunoshiba, T., Yamamoto, Y., Aramaki, H., Makino, K., Suzuki, M.
ER  -

TY  - JOUR
AU  - Kawashima, T.
AU  - Yamamoto, Y.
AU  - Aramaki, H.
AU  - Nunoshiba, T.
AU  - Kawamoto, T.
AU  - Watanabe, K.
AU  - Yamazaki, M.
AU  - Kanehori, K.
AU  - Amano, N.
AU  - Ohya, Y.
AU  - Makino, K.
AU  - Suzuki, M.
TI  - Determination of the complete genomic DNA sequence of Thermoplasma volcanium GSS1.
JO  - Proc. Jpn. Acad.
PY  - 1999
SP  - 213
EP  - 218
VL  - 75
AB  - The complete genomic DNA sequence of the aero/anaero-facultative archaebacterium, Thermoplasma
AB  - volcanium GSS1, has been determined.  A number of DNA fragments were cloned by using the
AB  - phage, cosmid, and BAC systems, and sequenced.  The remaining 30 gaps were bridged by DNA
AB  - fragments constructed using the polymerase chain reaction.  The repetition in sequencing the
AB  - same base positions was 13.1 +/- 7.5 fold.  The alignment of the DNA fragments and the
AB  - completeness of the genomic sequence were confirmed by the consistency of the genomic sequence
AB  - with the lengths and partial sequences of a second set of DNA fragments that altogether
AB  - covered 88% of the genome.  The number of bases found in the genomic sequence is 1,584,799,
AB  - with a G/C content of 39.9%.  The combination of the four types of bases in the new genomic
AB  - sequence is compared with those in known genomic sequences of similar sizes.
ER  -

TY  - JOUR
AU  - Kawata, Y.
AU  - Kawasaki, K.
AU  - Shigeri, Y.
TI  - Draft Genome Sequence of Halomonas sp. Strain KM-1, a Moderately Halophilic Bacterium That Produces the Bioplastic Poly(3-Hydroxybutyrate).
JO  - J. Bacteriol.
PY  - 2012
SP  - 2738
EP  - 2739
VL  - 194
AB  - We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda
AB  - City, Osaka, Japan, and which produces the bioplastic
AB  - poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811
AB  - bp, and 4,220 coding sequences were predicted within the genome. Genes encoding
AB  - proteins that are involved in the production and depolymerization of
AB  - poly(3-hydroxybutyrate) were identified. The identification of these genes might
AB  - be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its
AB  - monomer 3-hydroxybutyrate.
ER  -

TY  - JOUR
AU  - Kawato, S.
AU  - Nozaki, R.
AU  - Kondo, H.
AU  - Hirono, I.
TI  - Draft Genome Sequence of Vibrio penaeicida Strain TUMSAT-NU1, Isolated from Diseased Shrimp in Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00153
EP  - e00118
VL  - 6
AB  - Vibrio penaeicida is a bacterial pathogen of cultured shrimp. The draft genome sequence of V.
AB  - penaeicida strain TUMSAT-NU1 consists of 100 scaffolds with a
AB  - total of 6.41 Mbp. We identified possible virulence factors, and we found that V.
AB  - penaeicida and Vibrio nigripulchritudo are closely related.
ER  -

TY  - JOUR
AU  - Kawato, Y.
AU  - Yasuike, M.
AU  - Nakamura, Y.
AU  - Shigenobu, Y.
AU  - Fujiwara, A.
AU  - Sano, M.
AU  - Nakai, T.
TI  - Complete Genome Sequence Analysis of Two Pseudomonas plecoglossicida Phages, Potential Therapeutic Agents.
JO  - J. Appl. Environ. Microbiol.
PY  - 2015
SP  - 874
EP  - 881
VL  - 81
ER  -

TY  - JOUR
AU  - Kay, E.
AU  - Wren, B.W.
AU  - Parkhill, J.
TI  - Identification of genetic differences between strains of Campylobacter jejuni using differential genomic hybridisation and comparative  genomics.
JO  - Int. J. Med. Microbiol.
PY  - 2003
SP  - 130
EP  - 131
VL  - 293
AB  - Campylobacter jejuni is the most frequently identified bacterial causative agent of diarrhoeal
AB  - disease in humans worldwide.  Strain diversity and variable host response lead to a spectrum
AB  - of outcomes from infection ranging from asymptomatic to severe inflammatory diarrhoea.  The
AB  - mode of transmission to humans is unclear but strains have been isolated from a variety of
AB  - environmental sources including poultry and water.  It is hypothesised that novel genes within
AB  - different strains may relate to different clinical outcomes for ability to survive in varied
AB  - environmental niches.  In order to test this hypothesis DNA from the sequenced strain
AB  - NCTC11168 was hybridised to whole genome macro-arrays of different strains of C. jejuni with
AB  - different characteristics to identify regions of DNA not presnt in the sequenced strain.  The
AB  - strain specific DNA was further characterized by sequencing, analysis and comparison to the
AB  - sequenced 11168 genome.  Preliminary hybridisation results using strain 81-176 show that this
AB  - method of differential hybridisation can be used to detect variable regions of DNA as well as
AB  - strain-specific DNA.  To date, 271 sequences unique to 81-176 have been assembled into 58
AB  - clusters.  These clusters contain predicted coding sequences with similarity to transporters
AB  - and a -glutamyltranspeptidase as well as several with no database similarities.  In addition,
AB  - genes with similarity to proteins that are suface associated, proteins involved in the
AB  - respiratory chain and restriction modification enzymes were shown to differ between 81-176 and
AB  - 11168; these are all known to be highly variable between Campylobacter strains.
ER  -

TY  - JOUR
AU  - Kayansamruaj, P.
AU  - Pirarat, N.
AU  - Kondo, H.
AU  - Hirono, I.
AU  - Rodkhum, C.
TI  - Draft Genome Sequences of Streptococcus agalactiae Strains Isolated from Nile Tilapia (Oreochromis niloticus) Farms in Thailand.
JO  - Genome Announcements
PY  - 2014
SP  - e01300
EP  - e01314
VL  - 2
AB  - During 2009-2011, two clinical and one environmental strains of Streptococcus agalactiae were
AB  - isolated from Nile tilapia (Oreochromis niloticus) farms in
AB  - Thailand. Draft genome sequences of two clinical isolates comprise 2,048,343 and
AB  - 2,105,006 bp, while environmental isolates comprise 2,097,115 bp, having 1,573 to
AB  - 1,578 coding sequences, respectively.
ER  -

TY  - JOUR
AU  - Kazennova, E.V.
AU  - Tarasov, A.P.
AU  - Mileikovskaya, M.M.
AU  - Semina, I.E.
AU  - Tsvetkova, N.V.
TI  - Isolation and purification of Bordetella pertussis restriction endonuclease BpeI.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1982
SP  - 56
EP  - 57
VL  - 0
AB  - New restriction endonuclease has been isolated from Bordetella pertussis
AB  - vaccine strain 305 and purified in 1 stage on Sepharose covalently bound with
AB  - blue dextran.  The isolated restrictase has been found capable of breaking down
AB  - lambda-phage DNA into 7 fragments.  According to its specificity, BpeI is the
AB  - isoschizomer of HindIII obtained from Haemophilus influenzae strain Rd.
ER  -

TY  - JOUR
AU  - Kazlauskiene, R.
AU  - Maneliene, Z.
AU  - Butkus, V.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - A new specific endodeoxyribonuclease from Escherichia coli RFL 72.
JO  - Bioorg. Khim.
PY  - 1986
SP  - 836
EP  - 838
VL  - 12
AB  - A restriction endonuclease Eco72I with a novel substrate specificity has been isolated from
AB  - Escherichia coli strain RFL 72.  The enzyme recognizes 5'CAG^GTG 3' 3'GTG^CAC 5'
AB  - hexanucleotide palindromic sequence and cleaves it, as indicated by the arrows, to produce
AB  - blunt ended fragments.
ER  -

TY  - JOUR
AU  - Kazmierczak, R.A.
AU  - Best, A.A.
AU  - Nguyen, D.
AU  - Eisenstark, A.
TI  - Whole-Genome Shotgun Sequences of Salmonella enterica Serovar Typhimurium Lilleengen Type Strains LT1, LT18, LT19, LT20, LT21, and LT22.
JO  - Genome Announcements
PY  - 2017
SP  - e00720
EP  - e00717
VL  - 5
AB  - The Lilleengen type (LT) collection of Salmonella enterica serovar Typhimurium strains has
AB  - served the scientific community as a group of model organisms for
AB  - basic genetic and biochemical pathway research. Here, we report the whole-genome
AB  - shotgun sequences of Salmonella enterica serovar Typhimurium strains LT1, LT18,
AB  - LT19, LT20, LT21, and LT22.
ER  -

TY  - JOUR
AU  - Kazou, M.
AU  - Alexandraki, V.
AU  - Pot, B.
AU  - Tsakalidou, E.
AU  - Papadimitriou, K.
TI  - Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA-DC 1533.
JO  - Genome Announcements
PY  - 2017
SP  - e01533
EP  - e01516
VL  - 5
AB  - Lactobacillus acidipiscis is a Gram-positive lactic acid bacterium belonging to the
AB  - Lactobacillus salivarius clade. Here, we present the first complete genome
AB  - sequence of L. acidipiscis isolated from traditional Greek Kopanisti cheese.
AB  - Strain ACA-DC 1533 may play a key role in the strong organoleptic characteristics
AB  - of Kopanisti cheese.
ER  -

TY  - JOUR
AU  - Kazou, M.
AU  - Alexandraki, V.
AU  - Pot, B.
AU  - Tsakalidou, E.
AU  - Papadimitriou, K.
TI  - Complete Genome Sequence of the Sourdough Isolate Lactobacillus zymae ACA-DC 3411.
JO  - Genome Announcements
PY  - 2017
SP  - e00699
EP  - e00617
VL  - 5
AB  - Lactobacillus zymae is a Gram-positive lactic acid bacterium belonging to the Lactobacillus
AB  - brevis clade. Here, we report the first complete genome sequence of
AB  - L. zymae ACA-DC 3411, which was isolated from traditional Greek wheat sourdough.
AB  - Whole-genome analysis may reveal adaptive traits of strain ACA-DC 3411 in the
AB  - sourdough ecosystem.
ER  -

TY  - JOUR
AU  - Kazou, M.
AU  - Alexandraki, V.
AU  - Pot, B.
AU  - Tsakalidou, E.
AU  - Papadimitriou, K.
TI  - Whole-Genome Sequence of the Cheese Isolate Lactobacillus rennini ACA-DC 565.
JO  - Genome Announcements
PY  - 2017
SP  - e01579
EP  - e01516
VL  - 5
AB  - In this study, we present the first complete genome sequence of Lactobacillus rennini ACA-DC
AB  - 565, a strain isolated from a traditional Greek overripened
AB  - Kopanisti cheese called Mana. Although the species has been associated with
AB  - cheese spoilage, the strain ACA-DC 565 may contribute to the intense organoleptic
AB  - characteristics of Mana cheese.
ER  -

TY  - JOUR
AU  - Kazrani, A.A.
AU  - Kowalska, M.
AU  - Czapinska, H.
AU  - Bochtler, M.
TI  - Crystal structure of the 5hmC specific endonuclease PvuRts1I.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 5929
EP  - 5936
VL  - 42
AB  - PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA
AB  - containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not
AB  - 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35
AB  - A resolution. Although the protein has been crystallized in the absence of DNA, the structure
AB  - is very informative. It shows that PvuRts1I consists of an N-terminal, atypical PD-(D/E)XK
AB  - catalytic domain and a C-terminal SRA domain that might accommodate a flipped 5hmC or 5ghmC
AB  - base. Changes to predicted catalytic residues of the PD-(D/E)XK domain or to the putative
AB  - pocket for a flipped base abolish catalytic activity. Surprisingly, fluorescence changes
AB  - indicative of base flipping are not observed when PvuRts1I is added to DNA substrates
AB  - containing pyrrolocytosine in place of 5hmC (5ghmC). Despite this caveat, the structure
AB  - suggests a model for PvuRts1I activity and presents opportunities for protein engineering to
AB  - alter the enzyme properties for biotechnological applications.
ER  -

TY  - JOUR
AU  - Ke, L.
AU  - Liu, P.
AU  - Liu, S.
AU  - Gao, M.
TI  - Complete Genome Sequence of Magnetospirillum sp. ME-1, a Novel Magnetotactic Bacterium Isolated from East Lake, Wuhan, China.
JO  - Genome Announcements
PY  - 2017
SP  - e00485
EP  - e00417
VL  - 5
AB  - A novel spiral magnetotactic bacterium, Magnetospirillum sp. ME-1, was isolated from East Lake
AB  - in China. Here we report the complete genome of ME-1, which
AB  - contains a 4,551,873-bp circular chromosome and a 5,222-bp circular plasmid. The
AB  - magnetosome biogenesis-specific genes are located in a 97,664-bp magnetosome
AB  - genomic island.
ER  -

TY  - JOUR
AU  - Ke, Y.
AU  - Wang, Y.
AU  - Yuan, X.
AU  - Xu, J.
AU  - Zhen, Q.
AU  - Wang, Z.
AU  - Li, T.
AU  - Wang, D.
AU  - Huang, L.
AU  - Song, H.
AU  - Chen, Z.
TI  - Complete Genome Sequence of Brucella suis Field Strain BCB025 of Sequence Type ST22.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6959
EP  - 6959
VL  - 194
AB  - Brucella is a genus of relatively conservative pathogenic bacteria. Brucella suis is the most
AB  - diversified Brucella species. Strains of B. suis belong to different
AB  - sequence types. Here, we report the genome sequence of B. suis strain BCB025, one
AB  - isolate of the sequence type 22 epidemic in China.
ER  -

TY  - JOUR
AU  - Ke, Y.
AU  - Yuan, X.
AU  - Wang, Y.
AU  - Bai, Y.
AU  - Xu, J.
AU  - Song, H.
AU  - Huang, L.
AU  - Chen, Z.
TI  - Genome Sequences of Brucella melitensis 16M and Its Two Derivatives 16M1w and 16M13w, Which Evolved In Vivo.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5489
EP  - 5489
VL  - 194
AB  - Brucella melitensis is an intracellular pathogen that induces chronic infection in humans.
AB  - Here, we report the genome sequences of 16M and its two derivatives,
AB  - 16M1w and 16M13w, which were allowed to adapt in vivo for 1 and 13 weeks,
AB  - respectively. Our findings contribute to the investigation of adaptive mutations
AB  - and mechanisms of chronic infection by B. melitensis.
ER  -

TY  - JOUR
AU  - Ke, Y.
AU  - Yuan, X.
AU  - Zhen, Q.
AU  - Wang, Y.
AU  - Li, T.
AU  - Sun, Y.
AU  - Song, H.
AU  - Huang, L.
AU  - Wang, D.
AU  - Cui, B.
AU  - Mao, K.
AU  - Chen, Z.
TI  - Genome Sequence of Brucella melitensis S66, an Isolate of Sequence Type 8, Prevalent in China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5451
EP  - 5451
VL  - 194
AB  - Brucella melitensis is the most-represented Brucella species causing human brucellosis in
AB  - China. Here we report the complete genome sequence of B.
AB  - melitensis strain S66, a representative strain of sequence type 8 (ST8), which is
AB  - prevalent in China, making it possible to compare the genome sequences of
AB  - isolates from different countries.
ER  -

TY  - JOUR
AU  - Ke, Y.
AU  - Zhen, Q.
AU  - Li, T.
AU  - Wang, Y.
AU  - Yuan, X.
AU  - Xu, J.
AU  - Huang, L.
AU  - Wang, D.
AU  - Song, H.
AU  - Chen, Z.
TI  - Complete Genome Sequence of Brucella melitensis 133, an Isolate of Biovar 1 of Sequence Type 32.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6932
EP  - 6932
VL  - 194
AB  - Brucellosis is highly epidemic in China. Of the six classical species, Brucella melitensis and
AB  - biovar 1 are the most represented species and biovar that cause
AB  - human brucellosis in China. Here, we report the genome sequence of Brucella
AB  - melitensis strain 133, a strain of biovar 1 of sequence type 32.
ER  -

TY  - JOUR
AU  - Keatch, S.A.
AU  - Leonard, P.G.
AU  - Ladbury, J.E.
AU  - Dryden, D.T.
TI  - StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 6540
EP  - 6546
VL  - 33
AB  - The nucleoid-associated protein, StpA, of Escherichia coli binds non-specifically to
AB  - double-stranded DNA (dsDNA) and apparently forms
AB  - bridges between adjacent segments of the DNA. Such a coating of protein on
AB  - the DNA would be expected to hinder the action of nucleases. We
AB  - demonstrate that StpA binding hinders dsDNA cleavage by both the
AB  - non-specific endonuclease, DNase I, and by the site-specific type I
AB  - restriction endonuclease, EcoKI. It requires approximately one StpA
AB  - molecule per 250-300 bp of supercoiled DNA and approximately one StpA
AB  - molecule per 60-100 bp on linear DNA for strong inhibition of the
AB  - nucleases. These results support the role of StpA as a
AB  - nucleoid-structuring protein which binds DNA segments together. The
AB  - inhibition of EcoKI, which cleaves DNA at a site remote from its initial
AB  - target sequence after extensive DNA translocation driven by ATP
AB  - hydrolysis, suggests that these enzymes would be unable to function on
AB  - chromosomal DNA even during times of DNA damage when potentially lethal,
AB  - unmodified target sites occur on the chromosome. This supports a role for
AB  - nucleoid-associated proteins in restriction alleviation during times of
AB  - cell stress.
ER  -

TY  - JOUR
AU  - Keatch, S.A.
AU  - Su, T.J.
AU  - Dryden, D.T.
TI  - Alleviation of restriction by DNA condensation and non-specific DNA binding ligands.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 5841
EP  - 5850
VL  - 32
AB  - During conditions of cell stress, the type I restriction and modification enzymes of bacteria
AB  - show reduced, but not zero, levels of restriction of
AB  - unmethylated foreign DNA. In such conditions, chemically identical
AB  - unmethylated recognition sequences also occur on the chromosome of the
AB  - host but restriction alleviation prevents the enzymes from destroying the
AB  - host DNA. How is this distinction between chemically identical DNA
AB  - molecules achieved? For some, but not all, type I restriction enzymes,
AB  - alleviation is partially due to proteolytic degradation of a subunit of
AB  - the enzyme. We identify that the additional alleviation factor is
AB  - attributable to the structural difference between foreign DNA entering the
AB  - cell as a random coil and host DNA, which exists in a condensed nucleoid
AB  - structure coated with many non-specific ligands. The type I restriction
AB  - enzyme is able to destroy the 'naked' DNA using a complex reaction linked
AB  - to DNA translocation, but this essential translocation process is
AB  - inhibited by DNA condensation and the presence of non-specific ligands
AB  - bound along the DNA.
ER  -

TY  - JOUR
AU  - Kee, C. et al.
TI  - Complete Genome Sequence of Pseudomonas stutzeri Type Strain SGAir0442, Isolated  from Singapore Air Samples.
JO  - Genome Announcements
PY  - 2018
SP  - e00424
EP  - e00418
VL  - 6
AB  - Pseudomonas stutzeri strain SGAir0442 was isolated from tropical air samples collected in
AB  - Singapore. It is a Gram-negative denitrifying bacterium and an
AB  - opportunistic human pathogen. Its complete genome consists of one chromosome of
AB  - 4.52 Mb, containing 4,129 protein-coding genes, 12 rRNA subunits, and 62 tRNAs.
ER  -

TY  - JOUR
AU  - Kee, C. et al.
TI  - Complete Genome Sequence of Acinetobacter schindleri SGAir0122 Isolated from Singapore Air.
JO  - Genome Announcements
PY  - 2018
SP  - e00567
EP  - e00518
VL  - 6
AB  - Acinetobacter schindleri strain SGAir0122 was isolated from tropical air samples  collected in
AB  - Singapore. The prevalence of nosocomial infection caused by this
AB  - Gram-negative bacterium indicates its clinical significance as an opportunistic
AB  - human pathogen. Its complete genome consists of one chromosome of 3.105 Mb and a
AB  - plasmid of 181 kb.
ER  -

TY  - JOUR
AU  - Keeble, A.H.
AU  - Mate, M.J.
AU  - Kleanthous, C.
TI  - HNH Endonucleases.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 49
EP  - 65
VL  - 16
AB  - HNH endonucleases cleave phosphodiester bonds in many biological contexts, including intron
AB  - homing, degradation of genomic DNA, repair of genomic DNA, and restriction of viral DNA.  In
AB  - the 10 years since the HNH motif was first reported, around 500 members have been identified,
AB  - which have the following database identifiers: cd00085, SM00507 and pfam01844.  HNH enzymes
AB  - are found in all biological kingdoms, encoded by group I and group II introns, inteins, as
AB  - well as free-standing open reading frames.  In the first part of this chapter, we describe the
AB  - consensus sequence subsets that are associated with HNH enzymes and the proteins that
AB  - accommodate them.  We then present the biochemical properties of HNH enzymes and the proteins
AB  - that accommodate them.  We then present the biochemical properties of HNH enzymes as a group,
AB  - and finally describe recent structural data on HNH enzymes bound to DNA highlighting plausible
AB  - cleavage mechanisms.  Throughout, we describe how HNH enzymes are part of a wider group of
AB  - enzymes generally referred to as beta beta alpha-Me or His-Me endonucleases that also includes
AB  - His-Cys homing endonucleases and the eukaryotic apoptotic enzyme caspase-activated DNase.
ER  -

TY  - JOUR
AU  - Keeling, P.J.
AU  - Roger, A.J.
TI  - The selfish pursuit of sex.
JO  - Nature
PY  - 1995
SP  - 283
EP  - 283
VL  - 375
AB  - A letter arguing that inteins are selfish elements relevant to the evolution of sex.
ER  -

TY  - JOUR
AU  - Keen, E.C.
AU  - Bliskovsky, V.V.
AU  - Adhya, S.L.
AU  - Dantas, G.
TI  - Draft Genome Sequence of the Naturally Competent Bacillus simplex Strain WY10.
JO  - Genome Announcements
PY  - 2017
SP  - e01295
EP  - e01217
VL  - 5
AB  - We sequenced a naturally competent bacterial isolate, WY10, cultured from a Wyoming soil
AB  - sample. Sequence analysis revealed that WY10 is a novel strain of
AB  - Bacillus simplex To our knowledge, WY10 is the first B. simplex strain to be
AB  - characterized as naturally competent for DNA uptake by transformation.
ER  -

TY  - JOUR
AU  - Kehlet-Delgado, H.
AU  - Richards, G.P.
AU  - Hase, C.
AU  - Mueller, R.S.
TI  - Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries.
JO  - Genome Announcements
PY  - 2017
SP  - e01162
EP  - e01117
VL  - 5
AB  - Reported here are the genome sequences of three Vibrio coralliilyticus isolates RE87, AIC-7,
AB  - and 080116A. Each strain was isolated in association with oyster
AB  - larvae in commercial aquaculture systems. These draft genomes will be useful for
AB  - further studies in understanding the genomic features contributing to V.
AB  - coralliilyticus pathogenicity.
ER  -

TY  - JOUR
AU  - Kehrl, J.H.
AU  - Patel, K.B.
AU  - Kahng, L.S.
TI  - Dam methylation is essential in vibrio vulnificus and influences its interactions with host cells.
JO  - Gastroenterology
PY  - 2008
SP  - A713
EP  - A713
VL  - 134
AB  - DNA methylation is an important epigenetic regulator in bacteria, and several pathogens
AB  - display altered virulence when their methylating
AB  - enzymes are knocked out or overexpressed. We hypothesized that
AB  - methylation by the Dam (DNA adenine methylase) enzyme plays key roles
AB  - in Vibrio vulnificus, a leading cause of lethal seafood-borne
AB  - infections. Our arms were to determine the consequences of altered Dam
AB  - levels on V. vulnificus gene expression and its interactions with host
AB  - cells, specifically its effects on infection-induced barrier function
AB  - alteration and inflammation. We sought to knock out Dam, but
AB  - chromosomal dam could only be disrupted in the presence of a
AB  - plasmid-borne copy of the gene. Thus, dam is essential for the survival
AB  - of this pathogen and so we overexpressed it using the arabinose
AB  - promoter. We then performed 2-D gel analysis of lysates and culture
AB  - supernatants, and found that a discrete subset of proteins was indeed
AB  - up- or downregulated under conditions of dam overexpression. To
AB  - determine whether these changes in protein levels resulted in altered
AB  - bacterial interactions with host cells, we assayed epithelial barrier
AB  - function and the inflammatory response. To study barrier function, we
AB  - characterized the effects of V. vulnificus on the transepithelial
AB  - electrical resistance (TER) of Caco-2 cell monolayers. Wild-type V.
AB  - vulnificus were applied to the apical surface of Caco-2 cells grown on
AB  - permeable filters, using plain medium as a negative control. We
AB  - observed a reproducible drop in TER of the infected monolayer, with a
AB  - decline of 53+/-6% after two hours, when lactate dehydrogenase assays
AB  - determined that cytotoxicity was not significantly different from
AB  - control. TER did not drop when supernatants were used or bacteria were
AB  - treated with chloramphenicol; thus, impairment of barrier function by
AB  - V. vulnificus requires new bacterial protein synthesis. We then studied
AB  - the effects of dam-overexpressing and control strains on TER, after
AB  - confirming that they grew at the same rate. The dam-overexpressing
AB  - strain yielded a delayed decrease in TER (decline of 15 +/- 3% at 2 h
AB  - and 52 +/- 5% at four hours) compared to the control strain. To study
AB  - the inflammatory response to V. vulnificus, we assayed secretion of the
AB  - pro-inflammatory cytokine, IL-8, by Caco-2 cells. incubation of
AB  - wild-type bacteria with the cells led to a reproducible, time-dependent
AB  - induction of IL-8 that was not dependent on flagella and was
AB  - consistently increased by 50% under conditions of dam overexpression.
AB  - In summary, we are the first to demonstrate that dam methylation is not
AB  - only essential for the viability of V. vulnificus but may influence its
AB  - interactions with host cells.
ER  -

TY  - JOUR
AU  - Keita, M.B.
AU  - Diene, S.M.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Bittar, F.
TI  - Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 93
EP  - 105
VL  - 9
AB  - Strain G2(T) sp. nov. is the type strain of B. massiliogorillae, a proposed new species within
AB  - the genus Bacillus. This strain, whose genome is described here,
AB  - was isolated in France from the fecal sample of a wild western lowland gorilla
AB  - from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable,
AB  - rod-shaped bacterium. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 5,431,633 bp long genome (1
AB  - chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes,
AB  - including 91 tRNA genes.
ER  -

TY  - JOUR
AU  - Keita, M.B.
AU  - Padhmanabhan, R.
AU  - Caputo, A.
AU  - Robert, C.
AU  - Delaporte, E.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Bittar, F.
TI  - Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 807
EP  - 820
VL  - 9
AB  - Strain G5(T) gen. nov., sp. nov. is the type strain of Gorillibacterium massiliense, a newly
AB  - proposed genus within the family Paenibacillaceae. This
AB  - strain, whose genome is described here, was isolated in France from a stool
AB  - sample of a wild Gorilla gorilla subsp. gorilla from Cameroon. G. massiliense is
AB  - a facultatively anaerobic, Gram negative rod. Here we describe the features of
AB  - this bacterium, together with the complete genome sequence and annotation. The
AB  - 5,546,433 bp long genome (1 chromosome but no plasmid) contains 5,145
AB  - protein-coding and 76 RNA genes, including 69 tRNA genes.
ER  -

TY  - JOUR
AU  - Keita, M.B.
AU  - Padhmananabhan, R.
AU  - Caputo, A.
AU  - Robert, C.
AU  - Delaporte, E.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Bittar, F.
TI  - Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1031
EP  - 1045
VL  - 9
AB  - Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species
AB  - within the genus Paenibacillus. This strain, whose genome is
AB  - described here, was isolated in France from the fecal sample of a wild western
AB  - lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic,
AB  - Gram-negative, rod-shaped bacterium. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856
AB  - protein-coding and 62 RNAs genes, including 60 tRNA genes.
ER  -

TY  - JOUR
AU  - Kejnovsky, E.
AU  - Nejedly, K.
AU  - Kypr, J.
TI  - Factors influencing resistance of UV-irradiated DNA to the restriction endonuclease cleavage.
JO  - Int. J. Biol. Macromol.
PY  - 2004
SP  - 213
EP  - 222
VL  - 34
AB  - DNA molecules of pUC19, pBR322 and PhiX174 were irradiated by various doses of UV light and
AB  - the irradiated molecules were cleaved by about
AB  - two dozen type II restrictases. The irradiation generally blocked the
AB  - cleavage in a dose-dependent way. In accordance with previous studies,
AB  - the (A + T)-richness and the (PyPy) dimer content of the restriction
AB  - site belongs among the factors that on average, cause an increase in
AB  - the resistance of UV damaged DNA to the restrictase cleavage. However,
AB  - we observed strong effects of UV irradiation even with (G + C)-rich and
AB  - (PyPy)-poor sites. In addition, sequences flanking the restriction site
AB  - influenced the protection in some cases (e.g. HindIII), but not in
AB  - others (e.g. SalI), whereas neoschizomer couples SmaI and AvaI, or SacI
AB  - and Ecl136II, cleaved the UV-irradiated DNA similarly. Hence the
AB  - intrastrand thymine dimers located in the recognition site are not the
AB  - only photoproduct blocking the restrictases. UV irradiation of the
AB  - A-form generally made the irradiated DNA less resistant to restrictase
AB  - cleavage than irradiation in the B-form and in some cases, the A-form
AB  - completely protected the UV-irradiated DNA against the damage
AB  - recognized by the restrictases. The present results also demonstrate
AB  - that the UV irradiation approach used to generate partial digests in
AB  - genomic DNA studies, can be extended to the (G + C)-rich and
AB  - (PyPy)-poor restriction sites. The present extensive and quantitative
AB  - data can be used in genomic applications of UV damage probing by
AB  - restrictases.
ER  -

TY  - JOUR
AU  - Kelleher, J.E.
TI  - Defining domains of the EcoK methylase by mutational analyses and DNA sequence comparisons.
JO  - Ph.D. Thesis, University of Edinburgh
PY  - 1990
SP  - 1
EP  - 207
AB  - EcoK is a type I restriction and modification enzyme. It recognizes a defined DNA sequence and
AB  - may methylate specific adenine residues within this target site, on each stand of the DNA.
AB  - EcoK is composed of three different subunits encoded by the hsdR, M and S genes of E. coli
AB  - K-12. The S subunit dictates the recognition specificity and together with M forms the
AB  - methylase. All three enzyme subunits are necessary to form the restriction complex. Although
AB  - this is also capable of DNA modification its activity is selected in reponse to the presence
AB  - or absence of target site methylation. The methylase too is sensitive to the methylation state
AB  - of the target site. Efficient modification requires the imprint of a methyl group in the
AB  - complementary strand of the recognition sequence, whilst unmodified DNA, the normal substrate
AB  - for restriction, is only methylated inefficiently. (Suri et al., 1984). The experiments
AB  - described aim to identify functional domains of the EcoK methylase, from either the
AB  - comparative analyses of polypeptide sequences, or the phenotypes of mutations. Related type I
AB  - enzymes can interchange their subunits; unrelated enzymes cannot, and no general similarities
AB  - are detected when unrelated polypeptides are compared (see Bickle, 1987). Nevertheless, the
AB  - subunits of unrelated enzymes are presumed to be functionally analogous and sequence motifs
AB  - common to all type I enzymes, may identify polypeptide domains involved in common activities.
AB  - Mutational analyses have been limited to mutant derivatives of the EcoK methylase specifically
AB  - defective in only a particular aspect of their activity, and have focused on mutations that
AB  - apparently alter the substrate specificity of EcoK. The phenotypes of the new mutations
AB  - identified are consistent with enzymes that fail to differentiate between hemimethylated and
AB  - unmethylated target sites. These mutations cluster in a region of the hsdM gene, and may
AB  - identify a polypeptide domain responsible for recognition of target site methylation.
ER  -

TY  - JOUR
AU  - Kelleher, J.E.
AU  - Daniel, A.S.
AU  - Murray, N.E.
TI  - Mutations that confer de novo activity upon a maintenance methyltransferase.
JO  - J. Mol. Biol.
PY  - 1991
SP  - 431
EP  - 440
VL  - 221
AB  - DNA methyltransferases are not only sequence specific in their action, but they
AB  - also differentiate between the alternative methylation states of a target site.
AB  - Some methyltransferases are equally active on either unmethylated or
AB  - hemimethylated DNA and consequently function as de novo methyltransferases.
AB  - Others are specific for hemimethylated target sequences, consistent with the
AB  - postulated role of a maintenance methyltransferase in perpetuating a pattern of
AB  - DNA modification.  The molecular basis for the difference between de novo and
AB  - maintenance methyltransferase activity is unknown, yet fundamental to cellular
AB  - activities that are affected by different methylation states of the genome.
AB  - The methyltransferase activity of the type I restriction and modification
AB  - system, EcoK, is the only known prokaryotic methyltransferase shown to be
AB  - specific for hemimethylated target sequences.  We have isolated mutants of
AB  - Escherichia coli K-12 which are able to modify unmethylated target sequences
AB  - efficiently in a manner indicative of de novo methyltransferase activity.
AB  - Consistent with this change in specificity, some mutations shift the balance
AB  - between DNA restriction and modification as if both activities now compete at
AB  - unmethylated targets.  Two genes encode the methyltransferase and all the
AB  - mutations are loosely clustered within one of them.
ER  -

TY  - JOUR
AU  - Kelleher, J.E.
AU  - Raleigh, E.A.
TI  - A novel activity in Escherichia coli K-12 that directs restriction of DNA modified at CG dinucleotides.
JO  - J. Bacteriol.
PY  - 1991
SP  - 5220
EP  - 5223
VL  - 173
AB  - The restriction systems McrA and McrB of Escherichia coli K-12 are known to
AB  - attack DNA containing modified cytosine.  In strains lacking both activities,
AB  - however, we observed that DNA methylated at CG dinucleotides (as is mammalian
AB  - DNA) was still significantly restricted.  We show that this substantial barrier
AB  - to the acceptance of 5-methylcytosine-containing DNA is attributable to a
AB  - hitherto unknown activity of the Mrr restriction system.  Strikingly, the
AB  - multiple systems used by the gut inhabitant to determine the fate of invading
AB  - DNA will all limit genetic exchange with its mammalian host(s), reinforcing the
AB  - idea that one role of DNA methylation is to serve as a molecular passport (E.A.
AB  - Raleigh, R. Trimarchi, and H. Revel, Genetics 122:279-296, 1989).
ER  -

TY  - JOUR
AU  - Kelleher, J.E.
AU  - Raleigh, E.A.
TI  - On the regulation and diversity of restriction in Escherichia coli.
JO  - Gene
PY  - 1995
SP  - 229
EP  - 230
VL  - 157
AB  - The effect of UV irradiation on restriction mediated by four endogenous restriction systems of
AB  - E. coli K-12 was investigated using a uniform testing method.  Restriction by all four
AB  - systems was reduced when treated cells were separately challenged with lambda phage carrying
AB  - modification patterns that elicit restriction by each system.  The response of each system was
AB  - genetically and physiologically distinct.
ER  -

TY  - JOUR
AU  - Kelleher, J.E.
AU  - Raleigh, E.A.
TI  - Response to UV damage by four Escherichia coli K-12 restriction systems.
JO  - J. Bacteriol.
PY  - 1994
SP  - 5888
EP  - 5896
VL  - 176
AB  - To understand the role of restriction in regulating gene flow in bacterial populations, we
AB  - would like to understand the regulation of restriction enzyme activity. Several
AB  - antirestriction (restriction alleviation) systems are known that reduce the activity of type I
AB  - restriction enzymes like EcoKI in vivo. Most of these do not act on type II or type III
AB  - enzymes, but little information is available for the unclassified modification-dependent
AB  - systems, of which there are three in E. coli K-12. Of particular interest are two
AB  - physiological controls on type I enzymes: EcoKI restriction is reduced 2 to 3 orders of
AB  - magnitude following DNA damage, and a similar effect is seen constitutively in Dam- cells. We
AB  - used the behavior of EcoKI as a control for testing the response to UV treatment of the three
AB  - endogenous modification-dependent restriction systems of K-12, McrA, McrBC, and Mrr. Two of
AB  - these were also tested for response to Dam status. We find that all four resident restriction
AB  - systems show reduced activity following UV treatment, but not in a unified fashion; each
AB  - response was genetically and physiologically distinct. Possible mechanisms are discussed.
ER  -

TY  - JOUR
AU  - Kelleher, P.
AU  - Bottacini, F.
AU  - Mahony, J.
AU  - Kilcawley, K.N.
AU  - van Sinderen, D.
TI  - Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.
JO  - BMC Genomics
PY  - 2017
SP  - 267
EP  - 267
VL  - 18
AB  - BACKGROUND: Lactococcus lactis is among the most widely studied lactic acid
AB  - bacterial species due to its long history of safe use and economic importance to
AB  - the dairy industry, where it is exploited as a starter culture in cheese
AB  - production. RESULTS: In the current study, we report on the complete sequencing
AB  - of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The
AB  - chromosomal features of these 16 L. lactis strains in conjunction with 14
AB  - completely sequenced, publicly available lactococcal chromosomes were assessed
AB  - with particular emphasis on discerning the L. lactis subspecies division,
AB  - evolution and niche adaptation. The deduced pan-genome of L. lactis was found to
AB  - be closed, indicating that the representative data sets employed for this
AB  - analysis are sufficient to fully describe the genetic diversity of the taxon.
AB  - CONCLUSIONS: Niche adaptation appears to play a significant role in governing the
AB  - genetic content of each L. lactis subspecies, while (differential) genome decay
AB  - and redundancy in the dairy niche is also highlighted.
ER  -

TY  - JOUR
AU  - Kellenberger, G.
AU  - Symonds, N.
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli.  8.Its acquisition by phage lambda and its persistence through consecutive growth cycles.
JO  - Z. Vererbungsl.
PY  - 1966
SP  - 247
EP  - 256
VL  - 98
AB  - Earlier papers in this series have demonstrated that host-controlled modification of
AB  - bacteriophage lambda consists of the donation of a specific label to the phage DNA by the
AB  - bacterial host cells.  The experiments to be described in this paper were originally designed
AB  - to extend these observations to other types of host specificity, in particular to that
AB  - produced by E. coli B.  Technically, such experiments were facilitated by the availability of
AB  - restrictionless (r-) bacterial mutants which still provide full modification (m+): Density
AB  - labelled lambda K was grown in normal medium for one cycle on a Br-m+ strain and the progeny
AB  - phages analyzes for their parental DNA content by density gradient centrifugation.  The
AB  - density fractions were then tested for both K and B host specificities.  Phage particles with
AB  - fully heavy, hence conserved, DNA molecules had both K- and B-specificity.  The fractions of
AB  - phages with densities corresponding to particles with halfheavy, supposedly semiconserved DNA
AB  - molecules also plated on both K and B indicator.  But a more careful analysis revealed that
AB  - only about half of such phages still grew on K, whereas the other half was degraded upon
AB  - infection of K bacteria.  Repeated consecutive growth cycles were also performed and allowed
AB  - firstly to confirm the findings of Arber, Hattman and Dussoix (1963) that under normal
AB  - conditions both strands of lambda DNA are carrying host specificity, and secondly to conclude
AB  - that the reduced probability of acceptance by strain K of lambda.K.B phage with semiconserved
AB  - DNA cannot find its explanation in the physico-chemical plarity of the K-modified strand.
ER  -

TY  - JOUR
AU  - Keller, K.L.
AU  - Bender, K.S.
AU  - Wall, J.D.
TI  - A New Counterselectable Marker for Desulfovibrio vulgaris, the upp gene, Allowed for the Construction of a Marker less Deletion of a Type 1 Restriction Enzyme that Exhibits Increased Transformation Efficiency.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2009
SP  - 0
EP  - 0
VL  - 109
AB  - In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio
AB  - vulgaris Hildenborough has seen enormous progress; however, the current method of deletion
AB  - construction via marker exchange mutagenesis does not allow for easy selection of multiple
AB  - sequential gene deletions because of the need for multiple selectable markers. To broaden the
AB  - repertoire of genetic tools for manipulation of D. vulgaris, an in-frame markerless deletion
AB  - system has been developed based on the upp-encoded uracil phosphoribosyltransferase as an
AB  - element for a counterselection strategy. In wild-type D. vulgaris, growth is inhibited by the
AB  - toxic pyrimidine analog 5-fluorouracil (5-FU), whereas a mutant bearing a deletion of the upp
AB  - gene, strain JW710, is resistant to 5-FU. The introduction of a plasmid containing the
AB  - wild-type upp gene expressed constitutively from the aph(5')-III promoter (the promoter for
AB  - the kanamycin resistance gene in Tn5) into JW710 restored sensitivity to 5-FU to wild-type
AB  - levels. This observation is the basis for the establishment of a two-step integration and
AB  - excision strategy for deleting genes of interest. Since this in-frame deletion does not leave
AB  - behind an antibiotic cassette, multiple gene deletions can be generated in a single strain.
AB  - With this method, a markerless deletion of the R-subunit (DVU1703) of a type I
AB  - restriction-modification system (hsdR), strain JW7035, was constructed. The transformation
AB  - efficiency of the JW7035 strain is greater (an approximate 2-log increase in transformants)
AB  - compared to wild-type DvH when transforming stable plasmids via electroporation.
ER  -

TY  - JOUR
AU  - Keller, K.L.
AU  - Bender, K.S.
AU  - Wall, J.D.
TI  - Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased  transformation efficiency.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 7682
EP  - 7691
VL  - 75
AB  - In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio
AB  - vulgaris Hildenborough has seen enormous progress.
AB  - In spite of this progress, the current marker exchange deletion method
AB  - does not allow for easy selection of multiple sequential gene deletions in
AB  - a single strain because of the limited number of selectable markers
AB  - available in D. vulgaris. To broaden the repertoire of genetic tools for
AB  - manipulation, an in-frame, markerless deletion system has been developed.
AB  - The counterselectable marker that makes this deletion system possible is
AB  - the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded
AB  - by upp. In wild-type D. vulgaris, growth was shown to be inhibited by the
AB  - toxic pyrimidine analog 5-fluorouracil (5-FU), whereas a mutant bearing a
AB  - deletion of the upp gene was resistant to 5-FU. When a plasmid containing
AB  - the wild-type upp gene expressed constitutively from the aph(3')-II
AB  - promoter (promoter for the kanamycin resistance gene in Tn5) was
AB  - introduced into the upp deletion strain, sensitivity to 5-FU was restored.
AB  - This observation allowed us to develop a two-step integration and excision
AB  - strategy for the deletion of genes of interest. Since this in-frame
AB  - deletion strategy does not retain an antibiotic cassette, multiple
AB  - deletions can be generated in a single strain without the accumulation of
AB  - genes conferring antibiotic resistances. We used this strategy to generate
AB  - a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I
AB  - restriction-modification system that we designated JW7035. The
AB  - transformation efficiency of the JW7035 strain was found to be 100 to
AB  - 1,000 times greater than that of the wild-type strain when stable plasmids
AB  - were introduced via electroporation.
ER  -

TY  - JOUR
AU  - Keller, L.E.
AU  - Thomas, J.C.
AU  - Luo, X.
AU  - Nahm, M.H.
AU  - McDaniel, L.S.
AU  - Robinson, D.A.
TI  - Draft Genome Sequences of Five Multilocus Sequence Types of Nonencapsulated Streptococcus pneumoniae.
JO  - Genome Announcements
PY  - 2013
SP  - e00520
EP  - e00513
VL  - 1
AB  - Nonencapsulated Streptococcus pneumoniae can colonize the human nasopharynx and cause
AB  - conjunctivitis and otitis media. Different deletions in the capsular
AB  - polysaccharide biosynthesis locus and different multilocus sequence types have
AB  - been described for nonencapsulated strains. Draft genome sequences were generated
AB  - to provide insight into the genomic diversity of these strains.
ER  -

TY  - JOUR
AU  - Keller-Costa, T.
AU  - Silva, R.
AU  - Lago-Leston, A.
AU  - Costa, R.
TI  - Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata.
JO  - Genome Announcements
PY  - 2016
SP  - e00855
EP  - e00816
VL  - 4
AB  - To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome
AB  - sequence of Aquimarina sp. strain EL33, a bacterium isolated from the
AB  - gorgonian coral Eunicella labiata This first-described (to our knowledge)
AB  - animal-associated Aquimarina genome possesses a sophisticated repertoire of genes
AB  - involved in drug/antibiotic resistance and biosynthesis.
ER  -

TY  - JOUR
AU  - Kelly, S. et al.
TI  - Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 7
EP  - 7
VL  - 9
AB  - Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a
AB  - Lotus divaricatus root nodule. Compared to most other M. loti
AB  - strains, it has a broad host range and is one of very few M. loti strains able to
AB  - form effective nodules on the agriculturally important legume Lotus pedunculatus.
AB  - NZP2037 is an aerobic, Gram negative, non-spore-forming rod. This report reveals
AB  - that the genome of M. loti strain NZP2037 does not harbor any plasmids and
AB  - contains a single scaffold of size 7,462,792 bp which encodes 7,318
AB  - protein-coding genes and 70 RNA-only encoding genes. This rhizobial genome is one
AB  - of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic
AB  - Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Kelly, S.
AU  - Kaddurah-Daouk, R.
AU  - Smith, H.O.
TI  - Purification of the HhaII restriction endonuclease from an overproducer Escherichia coli clone.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 15339
EP  - 15344
VL  - 260
AB  - An Escherichia coli K12 strain carrying the HhaII methylase and restriction
AB  - genes on two separate compatible plasmids, pSK5 and pSK7, is used to
AB  - overproduce the restriction endonuclease.  Plasmid pSK5 expresses the methylase
AB  - gene constitutively from its chloramphenicol resistance gene promoter, and
AB  - plasmid pSK7 expresses the restriction endonuclease under control of the lacUV5
AB  - promoter.  Induction of the two-plasmid clone with 1 mM
AB  - isopropyl-1-thio-b-D-galactopyranoside results in a 15-fold increase in HhaII
AB  - endonuclease activity.  The enzyme has been purified to apparent homogeneity.
AB  - It migrates as a 23-kilodalton polypeptide on denaturing sodium dodecyl
AB  - sulfate-polyacrylamide electrophoretic gels and as a 51-kilodalton native
AB  - protein dimer on a high pressure liquid chromatogrpahy sizing column.
ER  -

TY  - JOUR
AU  - Kelly, S.
AU  - Sullivan, J.
AU  - Ronson, C.
AU  - Tian, R.
AU  - Brau, L.
AU  - Munk, C.
AU  - Goodwin, L.
AU  - Han, C.
AU  - Woyke, T.
AU  - Reddy, T.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 6
EP  - 6
VL  - 9
AB  - Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a
AB  - Lotus corniculatus root nodule and is a reisolate of the inoculant
AB  - strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative,
AB  - non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb
AB  - integrative and conjugative element known as the symbiosis island or
AB  - ICEMlSym(R7A). M. loti is the microsymbiont of the model legume Lotus japonicus
AB  - and strain R7A has been used extensively in studies of the plant-microbe
AB  - interaction. This report reveals that the genome of M. loti strain R7A does not
AB  - harbor any plasmids and contains a single scaffold of size 6,529,530 bp which
AB  - encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial
AB  - genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010
AB  - Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB)
AB  - project.
ER  -

TY  - JOUR
AU  - Kelly, S.A.
AU  - Megaw, J.
AU  - Gilmore, B.F.
TI  - Draft Genome Sequence of Salinisphaera sp. Strain KSM-18, an Obligately Halophilic Bacterium Isolated from a Triassic Salt Mine.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00897
EP  - e00818
VL  - 7
AB  - Here, we report the draft genome sequence of Salinisphaera sp. strain KSM-18. This obligately
AB  - halophilic bacterium was isolated from a brine sample obtained
AB  - from a Triassic salt mine.
ER  -

TY  - JOUR
AU  - Kelly, T.J. Jr.
AU  - Smith, H.O.
TI  - A restriction enzyme from Hemophilus influenzae II.  Base sequence of the recognition site.
JO  - J. Mol. Biol.
PY  - 1970
SP  - 393
EP  - 409
VL  - 51
AB  - Hemophilus influenzae strain Rd contains an enzyme, endonuclease R, which
AB  - specifically degrades foreign DNA.  With phage T7 DNA as substrate the
AB  - endonuclease introduces a limited number (about 40) double-strand breaks
AB  - (5'-phosphoryl, 3'-hydroxyl).  The limit product has an average length of about
AB  - 1000 nucleotide pairs and contains no single-strand breaks.  We have explored
AB  - the nucleotide sequences at the 5'-ends of the limit product by labeling the
AB  - 5'-phosphoryl groups (using polynucleotide kinase) and characterizing the
AB  - labeled fragments released by various nucleases.  Two classes of 5'-terminal
AB  - sequences were obtained: pApApCpNp...(60%) and pGpApCpNp...(40%), where N
AB  - indicates that the base in the 4th position is not unique.  The dinucleoside
AB  - monophosphates at the 3'-ends were isolated after micrococcal nuclease
AB  - digestion of the limit product and identified as TpT(60%) and TpC(40%).  We
AB  - conclude that endonuclease R of H. influenzae recognizes the following specific
AB  - nucleotide sequence: 5' . . . pGpTpPy^pPupApCp . . . 3' 3' . . .
AB  - pCpApPup^PypTpGp . . . 5' The implications of the twofold rotational symmetry
AB  - of this sequence are discussed.
ER  -

TY  - JOUR
AU  - Kelly, T.J.
AU  - Smith, H.O.
TI  - The nucleotide sequence of the recognition site for a restriction enzyme from H. influenzae.
JO  - Fed. Proc.
PY  - 1970
SP  - 405
EP  - 405
VL  - 29
AB  - H. influenzae strain Rd contains an endonuclease which specifically degrades
AB  - foreign DNA (Smith & Wilcox, Fed. Proc. 28:465, 1969).  With T7 DNA as
AB  - substrate the endonuclease introduces a limited number (about 40) of
AB  - double-strand breaks (5'-phosphoryl, 3'-hydroxyl).  The limit product has an
AB  - average length of about 1000 nucleotide pairs and contains no single-strand
AB  - breaks.  We have explored the nucleotide sequences at the 5'-ends of the limit
AB  - product by labeling the 5'-phosphoryl groups (using polynucleotide kinase) and
AB  - characterising the labeled fragments released by various nucleases.  Two
AB  - classes of 5'-sequences were obtained:  pApApCpXp...(60%) and
AB  - pGpApCpXp...(40%), where X indicates that the base in the 4th position is not
AB  - unique.  The dinucleoside monophosphates at the 3'-ends were isolated after
AB  - micrococcal nuclease digestion of the limit product and identified as TpT (60%)
AB  - and TpC (40%).  We conclude that the H. influenzae endonuclease recognizes the
AB  - following specific nucleotide sequence: 5' ...pGpTpPy^pPupApCp... 3'     ^break
AB  - 3' ...pCpApPup^PypTpGp... 5' The two-fold rotational symmetry of this sequence
AB  - has interesting implications concerning the mechanism of action of the H.
AB  - influenzae endonuclease.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Altermann, E.
AU  - Lambie, S.C.
AU  - Leahy, S.C.
TI  - Interaction between the genomes of Lactococcus lactis and phages of the P335 species.
JO  - Front. Microbiol.
PY  - 2013
SP  - 257
EP  - 257
VL  - 4
AB  - Phages of the P335 species infect Lactococcus lactis and have been particularly
AB  - studied because of their association with strains of L. lactis subsp. cremoris
AB  - used as dairy starter cultures. Unlike other lactococcal phages, those of the
AB  - P335 species may have a temperate or lytic lifestyle, and are believed to
AB  - originate from the starter cultures themselves. We have sequenced the genome of
AB  - L. lactis subsp. cremoris KW2 isolated from fermented corn and found that it
AB  - contains an integrated P335 species prophage. This 41 kb prophage (Phi KW2) has a
AB  - mosaic structure with functional modules that are highly similar to several other
AB  - phages of the P335 species associated with dairy starter cultures. Comparison of
AB  - the genomes of 26 phages of the P335 species, with either a lytic or temperate
AB  - lifestyle, shows that they can be divided into three groups and that the
AB  - morphogenesis gene region is the most conserved. Analysis of these phage genomes
AB  - in conjunction with the genomes of several L. lactis strains shows that prophage
AB  - insertion is site specific and occurs at seven different chromosomal locations.
AB  - Exactly how induced or lytic phages of the P335 species interact with
AB  - carbohydrate cell surface receptors in the host cell envelope remains to be
AB  - determined. Genes for the biosynthesis of a variable cell surface polysaccharide
AB  - and for lipoteichoic acids (LTAs) are found in L. lactis and are the main
AB  - candidates for phage receptors, as the genes for other cell surface carbohydrates
AB  - have been lost from dairy starter strains. Overall, phages of the P335 species
AB  - appear to have had only a minor role in the adaptation of L. lactis subsp.
AB  - cremoris strains to the dairy environment, and instead they appear to be an
AB  - integral part of the L. lactis chromosome. There remains a great deal to be
AB  - discovered about their role, and their contribution to the evolution of the
AB  - bacterial genome.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Henderson, G.
AU  - Pacheco, D.M.
AU  - Li, D.
AU  - Reilly, K.
AU  - Naylor, G.E.
AU  - Janssen, P.H.
AU  - Attwood, G.T.
AU  - Altermann, E.
AU  - Leahy, S.C.
TI  - The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 26
EP  - 26
VL  - 11
AB  - Acetogens are a specialized group of anaerobic bacteria able to produce acetate from CO2 and
AB  - H2 via the Wood-Ljungdahl pathway. In some gut environments
AB  - acetogens can compete with methanogens for H2, and as a result rumen acetogens
AB  - are of interest in the development of microbial approaches for methane
AB  - mitigation. The acetogen Eubacterium limosum SA11 was isolated from the rumen of
AB  - a New Zealand sheep and its genome has been sequenced to examine its potential
AB  - application in methane mitigation strategies, particularly in situations where
AB  - hydrogenotrophic methanogens are inhibited resulting in increased H2 levels in
AB  - the rumen. The 4.15 Mb chromosome of SA11 has an average G + C content of 47 %,
AB  - and encodes 3805 protein-coding genes. There is a single prophage inserted in the
AB  - chromosome, and several other gene clusters appear to have been acquired by
AB  - horizontal transfer. These include genes for cell wall glycopolymers, a type VII
AB  - secretion system, cell surface proteins and chemotaxis. SA11 is able to use a
AB  - variety of organic substrates in addition to H2/CO2, with acetate and butyrate as
AB  - the principal fermentation end-products, and genes involved in these metabolic
AB  - pathways have been identified. An unusual feature is the presence of 39 genes
AB  - encoding trimethylamine methyltransferase family proteins, more than any other
AB  - bacterial genome. Overall, SA11 is a metabolically versatile organism, but its
AB  - ability to grow on such a wide range of substrates suggests it may not be a
AB  - suitable candidate to take the place of hydrogen-utilizing methanogens in the
AB  - rumen.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Leahy, S.C.
AU  - Altermann, E.
AU  - Yeoman, C.J.
AU  - Dunne, J.C.
AU  - Kong, Z.
AU  - Pacheco, D.M.
AU  - Li, D.
AU  - Noel, S.J.
AU  - Moon, C.D.
AU  - Cookson, A.L.
AU  - Attwood, G.T.
TI  - The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316 Highlights Adaptation to a Polysaccharide-Rich Environment.
JO  - PLoS ONE
PY  - 2010
SP  - E11942
EP  - E11942
VL  - 5
AB  - Determining the role of rumen microbes and their enzymes in plant
AB  - polysaccharide breakdown is fundamental to understanding digestion and
AB  - maximising productivity in ruminant animals. Butyrivibrio proteoclasticus
AB  - B316(T) is a Gram-positive, butyrate-forming rumen bacterium with a key
AB  - role in plant polysaccharide degradation. The 4.4Mb genome consists of 4
AB  - replicons; a chromosome, a chromid and two megaplasmids. The chromid is
AB  - the smallest reported for all bacteria, and the first identified from the
AB  - phylum Firmicutes. B316 devotes a large proportion of its genome to the
AB  - breakdown and reassembly of complex polysaccharides and has a highly
AB  - developed glycobiome when compared to other sequenced bacteria. The
AB  - secretion of a range of polysaccharide-degrading enzymes which initiate
AB  - the breakdown of pectin, starch and xylan, a subtilisin family protease
AB  - active against plant proteins, and diverse intracellular enzymes to break
AB  - down oligosaccharides constitute the degradative capability of this
AB  - organism. A prominent feature of the genome is the presence of multiple
AB  - gene clusters predicted to be involved in polysaccharide biosynthesis.
AB  - Metabolic reconstruction reveals the absence of an identifiable gene for
AB  - enolase, a conserved enzyme of the glycolytic pathway. To our knowledge
AB  - this is the first report of an organism lacking an enolase. Our analysis
AB  - of the B316 genome shows how one organism can contribute to the
AB  - multi-organism complex that rapidly breaks down plant material in the
AB  - rumen. It can be concluded that B316, and similar organisms with broad
AB  - polysaccharide-degrading capability, are well suited to being early
AB  - colonizers and degraders of plant polysaccharides in the rumen
AB  - environment.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Leahy, S.C.
AU  - Li, D.
AU  - Perry, R.
AU  - Lambie, S.C.
AU  - Attwood, G.T.
AU  - Altermann, E.
TI  - The complete genome sequence of the rumen methanogen Methanobacterium formicicum  BRM9.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 15
EP  - 15
VL  - 9
AB  - Methanobacterium formicicum BRM9 was isolated from the rumen of a New Zealand Friesan cow
AB  - grazing a ryegrass/clover pasture, and its genome has been sequenced
AB  - to provide information on the phylogenetic diversity of rumen methanogens with a
AB  - view to developing technologies for methane mitigation. The 2.45 Mb BRM9
AB  - chromosome has an average G + C content of 41%, and encodes 2,352 protein-coding
AB  - genes. The genes involved in methanogenesis are comparable to those found in
AB  - other members of the Methanobacteriaceae with the exception that there is no
AB  - [Fe]-hydrogenase dehydrogenase (Hmd) which links the methenyl-H4MPT reduction
AB  - directly with the oxidation of H2. Compared to the rumen Methanobrevibacter
AB  - strains, BRM9 has a much larger complement of genes involved in determining
AB  - oxidative stress response, signal transduction and nitrogen fixation. BRM9 also
AB  - has genes for the biosynthesis of the compatible solute ectoine that has not been
AB  - reported to be produced by methanogens. The BRM9 genome has a prophage and two
AB  - CRISPR repeat regions. Comparison to the genomes of other Methanobacterium
AB  - strains shows a core genome of ~1,350 coding sequences and 190 strain-specific
AB  - genes in BRM9, most of which are hypothetical proteins or prophage related.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Li, D.
AU  - Lambie, S.C.
AU  - Cox, F.
AU  - Attwood, G.T.
AU  - Altermann, E.
AU  - Leahy, S.C.
TI  - Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1.
JO  - Genome Announcements
PY  - 2016
SP  - e00232
EP  - e00216
VL  - 4
AB  - Methanobrevibacter olleyaeYLM1 is a hydrogenotrophic methanogen, isolated from the rumen of a
AB  - lamb. Its genome has been sequenced to provide information on the
AB  - genomic diversity of rumen methanogens and support the development of approaches
AB  - to reduce methane formation by ruminants.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Li, D.
AU  - Lambie, S.C.
AU  - Jeyanathan, J.
AU  - Cox, F.
AU  - Li, Y.
AU  - Attwood, G.T.
AU  - Altermann, E.
AU  - Leahy, S.C.
TI  - Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen.
JO  - Genome Announcements
PY  - 2016
SP  - e00221
EP  - e00216
VL  - 4
AB  - Methanogenic archaeon ISO4-G1 is a methylotrophic methanogen belonging to the
AB  - orderMethanomassiliicoccalesthat was isolated from a sheep rumen. Its genome has
AB  - been sequenced to provide information on the genetic diversity of rumen
AB  - methanogens in order to develop technologies for ruminant methane mitigation.
ER  -

TY  - JOUR
AU  - Kelly, W.J.
AU  - Pacheco, D.M.
AU  - Li, D.
AU  - Attwood, G.T.
AU  - Altermann, E.
AU  - Leahy, S.C.
TI  - The complete genome sequence of the rumen methanogen Methanobrevibacter millerae  SM9.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 49
EP  - 49
VL  - 11
AB  - Methanobrevibacter millerae SM9 was isolated from the rumen of a sheep maintained on a fresh
AB  - forage diet, and its genome has been sequenced to provide information
AB  - on the phylogenetic diversity of rumen methanogens with a view to developing
AB  - technologies for methane mitigation. It is the first rumen isolate from the
AB  - Methanobrevibacter gottschalkii clade to have its genome sequence completed. The
AB  - 2.54 Mb SM9 chromosome has an average G + C content of 31.8 %, encodes 2269
AB  - protein-coding genes, and harbors a single prophage. The overall gene content is
AB  - comparable to that of Methanobrevibacter ruminantium M1 and the type strain of M.
AB  - millerae (ZA-10(T)) suggesting that the basic metabolism of these two
AB  - hydrogenotrophic rumen methanogen species is similar. However, M. millerae has a
AB  - larger complement of genes involved in methanogenesis including genes for methyl
AB  - coenzyme M reductase II (mrtAGDB) which are not found in M1. Unusual features of
AB  - the M. millerae genomes include the presence of a tannase gene which shows high
AB  - sequence similarity with the tannase from Lactobacillus plantarum, and large
AB  - non-ribosomal peptide synthase genes. The M. millerae sequences indicate that
AB  - methane mitigation strategies based on the M. ruminantium M1 genome sequence are
AB  - also likely to be applicable to members of the M. gottschalkii clade.
ER  -

TY  - JOUR
AU  - Kempf, F.
AU  - Loux, V.
AU  - Germon, P.
TI  - Genome Sequences of Two Bovine Mastitis-Causing Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e00259
EP  - e00215
VL  - 3
AB  - Escherichia coli is one of the main pathogenic agents causing inflammatory infections in the
AB  - bovine udder. Here, we report the draft genome sequences of two
AB  - strains isolated from different cases of clinical mastitis.
ER  -

TY  - JOUR
AU  - Kemter, F.S.
AU  - Messerschmidt, S.J.
AU  - Schallopp, N.
AU  - Sobetzko, P.
AU  - Lang, E.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Teschler, J.K.
AU  - Yildiz, F.H.
AU  - Overmann, J.
AU  - Waldminghaus, T.
TI  - Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae.
JO  - PLoS Genet.
PY  - 2018
SP  - e1007251
EP  - e1007251
VL  - 14
AB  - Vibrio cholerae, the causative agent of the cholera disease, is commonly used as
AB  - a model organism for the study of bacteria with multipartite genomes. Its two
AB  - chromosomes of different sizes initiate their DNA replication at distinct time
AB  - points in the cell cycle and terminate in synchrony. In this study, the
AB  - time-delayed start of Chr2 was verified in a synchronized cell population. This
AB  - replication pattern suggests two possible regulation mechanisms for other Vibrio
AB  - species with different sized secondary chromosomes: Either all Chr2 start DNA
AB  - replication with a fixed delay after Chr1 initiation, or the timepoint at which
AB  - Chr2 initiates varies such that termination of chromosomal replication occurs in
AB  - synchrony. We investigated these two models and revealed that the two chromosomes
AB  - of various Vibrionaceae species terminate in synchrony while Chr2-initiation
AB  - timing relative to Chr1 is variable. Moreover, the sequence and function of the
AB  - Chr2-triggering crtS site recently discovered in V. cholerae were found to be
AB  - conserved, explaining the observed timing mechanism. Our results suggest that it
AB  - is beneficial for bacterial cells with multiple chromosomes to synchronize their
AB  - replication termination, potentially to optimize chromosome related processes as
AB  - dimer resolution or segregation.
ER  -

TY  - JOUR
AU  - Keness, Y.
AU  - Bisharat, N.
TI  - Draft Genome Sequences of Streptococcus pneumoniae with High-Level Resistance to  Respiratory Fluoroquinolones.
JO  - Genome Announcements
PY  - 2016
SP  - e00181
EP  - e00116
VL  - 4
AB  - Streptococcus pneumoniaeis the leading cause of community-acquired pneumonia. Levofloxacin is
AB  - a fluoroquinolone used for treatment of severe community-acquired
AB  - pneumonia. Here, we describe the draft genome sequences ofS. pneumoniaewith
AB  - emerging resistance to levofloxacin, resulting in failure of treatment of
AB  - pneumococcal pneumonia.
ER  -

TY  - JOUR
AU  - Kennaway, C.K.
AU  - Obarska-Kosinska, A.
AU  - White, J.H.
AU  - Tuszynska, I.
AU  - Cooper, L.P.
AU  - Bujnicki, J.M.
AU  - Trinick, J.
AU  - Dryden, D.T.
TI  - The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 762
EP  - 770
VL  - 37
AB  - Type-I DNA restriction-modification (R/M) systems are important agents in limiting the
AB  - transmission of mobile genetic elements responsible for
AB  - spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme
AB  - from Escherichia coli, acts by methylation- and sequence-specific
AB  - recognition, leading to either methylation of DNA or translocation and
AB  - cutting at a random site, often hundreds of base pairs away. Consisting of
AB  - one specificity subunit, two modification subunits, and two DNA
AB  - translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage
AB  - antirestriction protein ocr, a DNA mimic. We present a 3D density map
AB  - generated by negative-stain electron microscopy and single particle
AB  - analysis of the central core of the restriction complex, the M.EcoKI
AB  - M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic
AB  - models of M.EcoKI in complex with ocr and its cognate DNA giving a clear
AB  - picture of the overall clamp-like operation of the enzyme. The model is
AB  - consistent with a large body of experimental data on EcoKI published over
AB  - 40 years.
ER  -

TY  - JOUR
AU  - Kennaway, C.K.
AU  - Taylor, J.E.
AU  - Song, C.F.
AU  - Potrzebowski, W.
AU  - Nicholson, W.
AU  - White, J.H.
AU  - Swiderska, A.
AU  - Obarska-Kosinska, A.
AU  - Callow, P.
AU  - Cooper, L.P.
AU  - Roberts, G.A.
AU  - Artero, J.B.
AU  - Bujnicki, J.M.
AU  - Trinick, J.
AU  - Kneale, G.G.
AU  - Dryden, D.T.F.
TI  - Structure and operation of the DNA-translocating type I DNA restriction enzymes.
JO  - Genes Dev.
PY  - 2012
SP  - 92
EP  - 104
VL  - 26
AB  - Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority
AB  - of bacterial species. Their early discovery paved
AB  - the way for the development of genetic engineering. They control
AB  - (restrict) the influx of foreign DNA via horizontal gene transfer into
AB  - the bacterium while maintaining sequence-specific methylation
AB  - (modification) of host DNA. The endonuclease reaction of these enzymes
AB  - on unmethylated DNA is preceded by bidirectional translocation of
AB  - thousands of base pairs of DNA toward the enzyme. We present the
AB  - structures of two type I RM enzymes, EcoKI and EcoR124I, derived using
AB  - electron microscopy (EM), small-angle scattering (neutron and X-ray),
AB  - and detailed molecular modeling. DNA binding triggers a large
AB  - contraction of the open form of the enzyme to a compact form. The path
AB  - followed by DNA through the complexes is revealed by using a DNA mimic
AB  - anti-restriction protein. The structures reveal an evolutionary link
AB  - between type I RM enzymes and type II RM enzymes.
ER  -

TY  - JOUR
AU  - Kennedy, V.
AU  - Van Laar, T.A.
AU  - Aleru, O.
AU  - Thomas, M.
AU  - Ganci, M.
AU  - Rawat, M.
TI  - Genome Sequences of Three Spore-Forming Bacteria Isolated from the Feces of Organically Raised Chickens.
JO  - Genome Announcements
PY  - 2016
SP  - e00880
EP  - e00816
VL  - 4
AB  - Antibiotic feed supplements have been implicated in the rise of multidrug-resistant bacteria.
AB  - An alternative to antibiotics is probiotics. Here,
AB  - we report the genome sequences of two Bacillus and one Solibacillus species, all
AB  - spore-forming, Gram-positive bacteria, isolated from the feces organically raised
AB  - chicken feces, with potential to serve as probiotics.
ER  -

TY  - JOUR
AU  - Kennell, J.C.
AU  - Moran, J.V.
AU  - Perlman, P.S.
AU  - Butow, R.A.
AU  - Lambowitz, A.M.
TI  - Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria.
JO  - Cell
PY  - 1993
SP  - 133
EP  - 146
VL  - 73
AB  - Group II introns ai1 and ai2 of the yeast mtDNA cox1 gene encode reverse transcriptase-like
AB  - proteins that function in RNA splicing and may play a role in intron mobility and excision. We
AB  - find that ribonucleoprotein particles from yeast mitochondria contain a reverse transcriptase
AB  - activity that is likely encoded by ai1 and ai2 and is highly specific for the introns and
AB  - their flanking exons.  Using a mutant strain with elevated activity, we show that the reverse
AB  - transcriptase uses either excised intron RNA or cox1 pre-mRNA as template and initiates cDNA
AB  - synthesis near the 3' end of ai2 and immediately downstream in E3.  Our results suggest that
AB  - introns ai1 and ai2 are retroelements, which encode reverse transcriptases that have adapted
AB  - to function in RNA splicing.
ER  -

TY  - JOUR
AU  - Kenri, T.
AU  - Horino, A.
AU  - Matsui, M.
AU  - Sasaki, Y.
AU  - Suzuki, S.
AU  - Narita, M.
AU  - Ohya, H.
AU  - Okazaki, N.
AU  - Shibayama, K.
TI  - Complete Genome Sequence of Mycoplasma pneumoniae Type 2a Strain 309, Isolated in Japan.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1253
EP  - 1254
VL  - 194
AB  - Mycoplasma pneumoniae strain 309, a type 2a (subtype 2 variant) strain of this bacterium, has
AB  - variations in the P1 protein, which is responsible for attachment
AB  - of the bacterium to host cells. Here, we report the complete genome sequence of
AB  - M. pneumoniae strain 309 isolated from a pneumonia patient in Japan.
ER  -

TY  - JOUR
AU  - Kenri, T.
AU  - Suzuki, M.
AU  - Horino, A.
AU  - Sekizuka, T.
AU  - Kuroda, M.
AU  - Fujii, H.
AU  - Hashimoto, T.
AU  - Nakajima, H.
AU  - Ohya, H.
AU  - Shibayama, K.
TI  - Complete Genome Sequences of the p1 Gene Type 2b and 2c Strains Mycoplasma pneumoniae KCH-402 and KCH-405.
JO  - Genome Announcements
PY  - 2017
SP  - e00513
EP  - e00517
VL  - 5
AB  - Here, we present the complete genome sequences of Mycoplasma pneumoniae KCH-402 and KCH-405,
AB  - which are p1 gene type 2b and 2c strains, respectively. These
AB  - strains harbor variations in the orf6 gene, which encodes the
AB  - cytadherence-related proteins P40 and P90.
ER  -

TY  - JOUR
AU  - Kenyon, L.J.
AU  - Meulia, T.
AU  - Sabree, Z.L.
TI  - Habitat visualization and genomic analysis of 'Candidatus Pantoea carbekii,' the primary symbiont of the brown marmorated stink bug.
JO  - Genome Biol. Evol.
PY  - 2015
SP  - 620
EP  - 635
VL  - 7
AB  - Phytophagous pentatomid insects can negatively impact agricultural productivity
AB  - and the brown marmorated stink bug (Halyomorpha halys) is an emerging invasive
AB  - pest responsible for damage to many fruit crops and ornamental plants in North
AB  - America. Many phytophagous stink bugs, including H. halys, harbor
AB  - gammaproteobacterial symbionts that likely contribute to host development, and
AB  - characterization of symbiont transmission/acquisition and their contribution to
AB  - host fitness may offer alternative strategies for managing pest species.
AB  - "Candidatus Pantoea carbekii" is the primary occupant of gastric ceca lumina
AB  - flanking the distal midgut of H. halys insects and it is acquired each generation
AB  - when nymphs feed on maternal extrachorion secretions following hatching. Insects
AB  - prevented from symbiont uptake exhibit developmental delays and aberrant
AB  - behaviors. To infer contributions of Ca. P. carbekii to H. halys, the complete
AB  - genome was sequenced and annotated from a North American H. halys population.
AB  - Overall, the Ca. P. carbekii genome is nearly one-fourth (1.2 Mb) that of
AB  - free-living congenerics, and retains genes encoding many functions that are
AB  - potentially host-supportive. Gene content reflects patterns of gene
AB  - loss/retention typical of intracellular mutualists of plant-feeding insects.
AB  - Electron and fluorescence in situ microscopic imaging of H. halys egg surfaces
AB  - revealed that maternal extrachorion secretions were populated with Ca. P.
AB  - carbekii cells. The reported findings detail a transgenerational mode of symbiont
AB  - transmission distinct from that observed for intracellular insect mutualists and
AB  - illustrate the potential additive functions contributed by the bacterial symbiont
AB  - to this important agricultural pest.
ER  -

TY  - JOUR
AU  - Kenzaka, T.
AU  - Ishimoto, Y.
AU  - Tani, K.
TI  - Draft Genome Sequence of Multidrug-Resistant Cellulosimicrobium sp. Strain KWT-B, Isolated from Feces of Hirundo rustica.
JO  - Genome Announcements
PY  - 2017
SP  - e00641
EP  - e00617
VL  - 5
AB  - Migratory birds have been postulated as potential spreaders of antibiotic resistance.
AB  - Multidrug-resistant Cellulosimicrobium sp. strain KWT-B was isolated
AB  - from the feces of Hirundo rustica A draft genome sequence indicated that the
AB  - strain harbors multidrug-resistant transporters, multidrug efflux pumps, a
AB  - vancomycin-resistant protein, and metallo-beta-lactamases.
ER  -

TY  - JOUR
AU  - Kenzaka, T.
AU  - Nakahara, M.
AU  - Higuchi, S.
AU  - Maeda, K.
AU  - Tani, K.
TI  - Draft Genome Sequences of Amoeba-Resistant Aeromonas spp. Isolated from Aquatic Environments.
JO  - Genome Announcements
PY  - 2014
SP  - e01115
EP  - e01114
VL  - 2
AB  - Amoeba-resistant Aeromonas veronii ARB3 and Aeromonas media ARB13 and ARB20, which may be
AB  - important intracellular pathogens of eukaryotic hosts, were isolated
AB  - from pond and river waters. The draft genome sequences indicate that the strains
AB  - harbor multiple protein secretion systems and toxins that induce disruption of
AB  - the actin cytoskeleton.
ER  -

TY  - JOUR
AU  - Kenzaka, T.
AU  - Tani, K.
TI  - Draft Genome Sequence of Multidrug-Resistant Stenotrophomonas pavanii BWK1, Isolated from Mareca penelope Feces.
JO  - Genome Announcements
PY  - 2018
SP  - e00187
EP  - e00118
VL  - 6
AB  - Migratory birds serve as vectors by transmitting antibiotic-resistant bacteria across large
AB  - distances. Here, we isolated a multidrug-resistant Stenotrophomonas
AB  - pavanii strain, BWK1, from Mareca penelope feces. Analysis of the draft genome
AB  - sequence of the isolated strain indicated that BWK1 harbors a class A
AB  - beta-lactamase, metallo-beta-lactamase, and several multidrug efflux pumps.
ER  -

TY  - JOUR
AU  - Kenzaka, T.
AU  - Tani, K.
TI  - Draft Genome Sequence of Carbapenem-Resistant Pseudomonas fluorescens Strain BWKM6, Isolated from Feces of Mareca penelope.
JO  - Genome Announcements
PY  - 2018
SP  - e00186
EP  - e00118
VL  - 6
AB  - Migratory birds are potential vehicles of antibiotic-resistant bacteria. Here, we isolated the
AB  - multidrug-resistant Pseudomonas fluorescens strain BWKM6 from the
AB  - feces of Mareca penelope The strain's draft genome sequence indicates that it
AB  - harbors a metallo-beta-lactamase, a class C beta-lactamase, and several multidrug
AB  - efflux pumps.
ER  -

TY  - JOUR
AU  - Kenzaka, T.
AU  - Tani, K.
TI  - Draft Genome Sequence of Extended-Spectrum Beta-Lactamase-Producing Serratia fonticola BWK15 Isolated from Feces of Anas penelope.
JO  - Genome Announcements
PY  - 2017
SP  - e01102
EP  - e01117
VL  - 5
AB  - Migratory birds have been postulated as potential vehicles of antibiotic resistance. Here we
AB  - isolated the extended-spectrum beta-lactamase
AB  - (ESBL)-producing Serratia fonticola strain BWK15 from the feces of Anas penelope
AB  - The strain's draft genome sequence indicated that it harbors class A ESBL, class
AB  - C beta-lactamase, and many multidrug efflux pumps.
ER  -

TY  - JOUR
AU  - Kenzaka, T.
AU  - Yamada, Y.
AU  - Tani, K.
TI  - Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus.
JO  - Genome Announcements
PY  - 2014
SP  - e00424
EP  - e00414
VL  - 2
AB  - Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding
AB  - environment of a stag beetle. The draft genome sequence indicates that
AB  - strain A1 harbors many biosynthesis molecules, which have antimicrobial
AB  - properties, and thus potentially eliminates the fungi by producing antifungal
AB  - compounds, such as siderophores.
ER  -

TY  - JOUR
AU  - Kera, Y.
AU  - Abe, K.
AU  - Kasai, D.
AU  - Fukuda, M.
AU  - Takahashi, S.
TI  - Draft Genome Sequences of Sphingobium sp. Strain TCM1 and Sphingomonas sp. Strain TDK1, Haloalkyl Phosphate Flame Retardant- and Plasticizer-Degrading Bacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00668
EP  - e00616
VL  - 4
AB  - Sphingobium sp. strain TCM1 and Sphingomonas sp. strain TDK1 are haloalkyl phosphate flame
AB  - retardant- and plasticizer-degrading bacteria. We report here the
AB  - draft genome sequences of these strains to provide insights into the molecular
AB  - mechanism underlying their degradation ability.
ER  -

TY  - JOUR
AU  - Kergourlay, G.
AU  - Messaoudi, S.
AU  - Dousset, X.
AU  - Prevost, H.
TI  - Genome Sequence of Lactobacillus salivarius SMXD51, a Potential Probiotic Strain  Isolated from Chicken Cecum, Showing Anti-Campylobacter Activity.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3008
EP  - 3009
VL  - 194
AB  - We report the draft genome sequence of Lactobacillus salivarius SMXD51, isolated  from the
AB  - cecum of healthy chickens showing an activity against Campylobacter-the
AB  - food-borne pathogen that is the most common cause of gastroenteritis in the
AB  - European Union (EU)-and potentially interesting features for a probiotic strain,
AB  - explaining our interest in it.
ER  -

TY  - JOUR
AU  - Kern, T.
AU  - Fischer, M.A.
AU  - Deppenmeier, U.
AU  - Schmitz, R.A.
AU  - Rother, M.
TI  - Methanosarcina flavescens sp. nov., a methanogenic archaeon isolated from a full-scale anaerobic digester.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2016
SP  - 1533
EP  - 1538
VL  - 66
AB  - A novel, strictly anaerobic, methanogenic archaeon, strain E03.2(T), was isolated
AB  - from a full-scale biogas plant in Germany. Cells were non-motile sarcina-like
AB  - cocci, occurring in aggregates. Strain E03.2(T) grew autotrophically on H2 plus
AB  - CO2, and additionally cells could utilize acetate, methanol, moni-, di- and
AB  - trimethylamine as carbon and energy sources; however, growth or methanogenesis on
AB  - formate was not observed. Yeast extract and vitamins stimulated growth but were
AB  - not mandatory. The optimal growth temperature of strain E03.2(T) was
AB  - approximately 45 degrees C; maximal growth rates were obtained at about pH 7.0 in
AB  - the presence of approximately 6.8 mM NaCl. The DNA G+C content of strain E03.2(T)
AB  - was 41.3 mol%. Phylogenetic analyses based on 16S rRNA gene and mcrA sequences
AB  - placed strain E03.2(T) within the genus Methanosarcina. Based on 16S rRNA gene
AB  - sequence similarity strain E03.2(T) was related to seven different species of the
AB  - genus Methanosarcina, but most closely related to Methanosarcina thermophila
AB  - TM-1(T). Phenotypic, physiological and genomic characteristics indicated that
AB  - strain E03.2(T) represents a novel species of the genus Methanosarcina, for which
AB  - the name Methanosarcina flavescens sp. nov. is proposed. The type strain is
AB  - E03.2(T) ( = DSM 100822(T) = JCM 30921(T)).
ER  -

TY  - JOUR
AU  - Kerouanton, A.
AU  - Hirchaud, E.
AU  - Rose, V.
AU  - Esnault, E.
AU  - Naquin, D.
AU  - Denis, M.
TI  - First Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Derby Strain Associated with Pork in France.
JO  - Genome Announcements
PY  - 2015
SP  - e00853
EP  - e00815
VL  - 3
AB  - In France, Salmonella enterica subsp. enterica serovar Derby is one of the most often isolated
AB  - serovars in pigs. Here, we describe the draft genome sequence of a
AB  - strain isolated from a pig. This strain had the most frequent pulsed-field gel
AB  - electrophoresis (PFGE) and antimicrobial patterns (S, SSU, T) usually observed in
AB  - pig production in France. Those patterns have been also highlighted in human
AB  - isolates.
ER  -

TY  - JOUR
AU  - Kerr, A.L.
AU  - Jeon, Y.J.
AU  - Svenson, C.J.
AU  - Rogers, P.L.
AU  - Neilan, B.A.
TI  - DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2011
SP  - 761
EP  - 769
VL  - 89
AB  - To better understand the DNA restriction-modification (R-M) systems for more amenable strain
AB  - development of the alternative industrial
AB  - ethanologen, Zymomonas mobilis, three gene knockout mutants were
AB  - constructed. The gene knockout mutants were tested for their DNA
AB  - restriction activities by the determination of transformation
AB  - efficiency using methylated and unmethylated foreign plasmid DNAs.
AB  - Inactivation of a putative mrr gene encoded by ZMO0028 (zmrr) resulted
AB  - in a 60-fold increase in the transformation efficiency when
AB  - unmethylated plasmid DNA was used. This indicated that the putative mrr
AB  - gene may serve as a type IV restriction-modification system in Z.
AB  - mobilis ZM4. To assign the function of a putative type I DNA
AB  - methyltransferase encoded by ZMO1933 (putative S subunit) and ZMO1934
AB  - (putative M subunit), the putative S subunit was inactivated. The gene
AB  - inactivation of ZMO1933 resulted in a 30-fold increase in the
AB  - transformation efficiency when methylated plasmid DNA was introduced,
AB  - indicating that the putative S subunit possibly serves as a part of
AB  - functional type I R-M system(s). Growth studies performed on the mutant
AB  - strains indicate inactivation of the type I S subunit resulted in a
AB  - lower maximum specific glucose consumption rate and biomass yield,
AB  - while inactivation of the type IV Zmrr had the opposite effect, with an
AB  - increase in the maximum specific growth rate and biomass yield.
ER  -

TY  - JOUR
AU  - Kersulyte, D.
AU  - Bertoli, M.T.
AU  - Tamma, S.
AU  - Keelan, M.
AU  - Munday, R.
AU  - Geary, J.
AU  - Veldhuyzen-van-Zanten, S.
AU  - Goodman, K.J.
AU  - Berg, D.E.
TI  - Complete Genome Sequences of Two Helicobacter pylori Strains from a Canadian Arctic Aboriginal Community.
JO  - Genome Announcements
PY  - 2015
SP  - e00209
EP  - e00215
VL  - 3
AB  - We report here the complete genome sequences of two Amerind Helicobacter pylori strains from
AB  - Aklavik, Northwest Territories, Canada. One strain contains extra
AB  - iron-cofactored urease genes and ~140 rearrangements in its chromosome relative
AB  - to other described strains (typically differing from one another by <10
AB  - rearrangements), suggesting that it represents a novel lineage of H. pylori.
ER  -

TY  - JOUR
AU  - Kersulyte, D.
AU  - Mukhopadhyay, A.K.
AU  - Shirai, M.
AU  - Nakazawa, T.
AU  - Berg, D.E.
TI  - Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori.
JO  - J. Bacteriol.
PY  - 2000
SP  - 5300
EP  - 5308
VL  - 182
AB  - A search by subtractive hybridization for sequences present in only
AB  - certain strains of Helicobacter pylori led to the discovery of a 2-kb
AB  - transposable element to be called IS607, which further PCR and
AB  - hybridization tests indicated was present in about one-fifth of H. pylori
AB  - strains worldwide. IS607 contained two open reading frames (ORFs) of
AB  - possibly different phylogenetic origin. One ORF (orfB) exhibited
AB  - protein-level homology to one of two putative transposase genes found in
AB  - several other chimeric elements including IS605 (also of H. pylori) and
AB  - IS1535 (of Mycobacterium tuberculosis). The second IS607 gene (orfA) was
AB  - unrelated to the second gene of IS605 and might possibly be chimeric
AB  - itself: it exhibited protein-level homology to merR bacterial regulatory
AB  - genes in the first approximately 50 codons and homology to the second gene
AB  - of IS1535 (annotated as "resolvase," apparently due to a weak short
AB  - recombinase motif) in the remaining three-fourths of its length. IS607 was
AB  - found to transpose in Escherichia coli, and analyses of sequences of
AB  - IS607-target DNA junctions in H. pylori and E. coli indicated that it
AB  - inserted either next to or between adjacent GG nucleotides, and generated
AB  - either a 2-bp or a 0-bp target sequence duplication, respectively.
AB  - Mutational tests showed that its transposition in E. coli required orfA
AB  - but not orfB, suggesting that OrfA protein may represent a new, previously
AB  - unrecognized, family of bacterial transposases.
ER  -

TY  - JOUR
AU  - Kerszman, G.
AU  - Glover, S.W.
AU  - Aronovitch, J.
TI  - The restriction of bacteriophage lambda in Escherichia coli strain W.
JO  - J. Gen. Virol.
PY  - 1967
SP  - 333
EP  - 347
VL  - 1
AB  - Escherichia coli strain w adsorbs phage lambda very efficiently but the phage does not form
AB  - plaques on this strain.  In a very small fraction (10^-4) of the infected cells the phage
AB  - grows and produces small bursts of progeny phage also unable to form plaques on strain w.  E.
AB  - coli strain w is lysogenic for a temperate phage, wPhi, related to phage P2.  Non-restricting
AB  - hosts for phage lambda became restricting hosts when made lysogenic for wPhi.  When
AB  - 32P-labelled lambda adsorbed to restricting wPhi lysogenic hosts, >20% of the 32P become
AB  - acid-soluble shortly after infection.  No wPhi specific modification was carried by the small
AB  - number of lambda phages which escaped this restriction process.  It is concluded that wPhi
AB  - controls a host-restriction mechanism but not a host-modification process, and in parallel
AB  - with other examples of host-controlled restriction and modification can be represented as r+m-
AB  - or r+mo.  LambdaW mutants have been isolated which escape this restriction and which form
AB  - plaques on strain w and wPhi lysogenic strains with an efficiency of I.0.  With these mutants
AB  - a w-specific host modification controlled by the genome of strain w was demonstrated.  Mixed
AB  - infection experiments with restricted lambda and unrestricted lambda w showed that that
AB  - restricted phage did not block the growth of the unrestricted mutant nor did the mutant permit
AB  - the restricted phage to grow.  In addition it was shown that lambda obtained from bacteria
AB  - mixedly infected with lambda and lambdaW was still unable to grow in restricting hosts and
AB  - lambda w similarly obtained from mixedly infected bacteria still retained its ability to grow
AB  - on restricting hosts.  It is concluded that there is a nucleotide sequence in the DNA of phage
AB  - lambda which, when lambda infects a restricting host, is specifically recognized by the
AB  - restriction mechanism controlled by the wPhi.  The mutation to lambda w involves an alteration
AB  - to this sequence such that it is no longer recognized by the restriction mechanism of the
AB  - wPhi.  Mutants of wPhi were isolated not restrictive for phage lambda.
ER  -

TY  - JOUR
AU  - Kerzhner, M.A.
AU  - Shiryaev, S.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease from thermophilic Bacillus species MK strain is isoschizomer of SalI.
JO  - Biokhimiia
PY  - 1997
SP  - 1029
EP  - 1036
VL  - 62
AB  - Screening of thermophilic bacterial strains revealed a strain containing site-specific
AB  - endonuclease BspMKI.  Endonuclease was purified to functional homogeneity during sequential
AB  - chromatographic steps.  The enzyme recognizes sequences 5'-G/TCGAC-3' on DNA molecule and
AB  - its isoschizomer of endonuclease SalI.  The molecular mass of BspMKI is about 45 kD.  The
AB  - enzyme is maximally active at 55oC and MRB (50 mM NaCl, 10 mM Tris-HCl, pH 7.4, 10 mM MgCl2, 1
AB  - mM dithiothreitol) is the optimal buffer.  The enzyme is highly stable and retains its
AB  - activity during two weeks at room temperature.
ER  -

TY  - JOUR
AU  - Kesel, S.
AU  - Moormann, F.
AU  - Gumperlein, I.
AU  - Mader, A.
AU  - Morikawa, M.
AU  - Lieleg, O.
AU  - Opitz, M.
TI  - Draft Genome Sequence of the Biofilm-Producing Bacillus subtilis Strain B-1, Isolated from an Oil Field.
JO  - Genome Announcements
PY  - 2014
SP  - e01163
EP  - e01114
VL  - 2
AB  - We report here the draft genome sequence of the Bacillus subtilis strain B-1, a strain known
AB  - to form biofilms. The biofilm matrix mainly consists of the
AB  - biopolymer gamma-polyglutamate (gamma-PGA). The sequence of the genome of this
AB  - strain allows the study of specific genes involved in biofilm formation.
ER  -

TY  - JOUR
AU  - Keshet, E.
AU  - Cedar, H.
TI  - Effect of CpG methylation on MspI.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 3571
EP  - 3580
VL  - 11
AB  - The restriction enzyme MspI is inhibited by the presence of a methyl moiety at
AB  - the external cytosine of the sequence CCGG, but is generally unaffected by
AB  - methylation at the internal cytosine.  At specific subsets of this sequence
AB  - such as the hexanucleotide CCGGCC, however, methylation of the internal
AB  - cytosine strongly inhibits MspI digestion, leading to artifacts in the
AB  - interpretation of DNA methylation analyses.  Our results show, for instance,
AB  - that the CCGG site at the 5' end of the human gamma globin gene, which was
AB  - thought to be methylated at both the internal and external cytosines, is
AB  - actually methylated only at the internal CpG residue.
ER  -

TY  - JOUR
AU  - Kesminiene, A.
AU  - Maneliene, Z.
AU  - Vitkute, J.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - FspAI, a unique type II restriction endonuclease that recognizes the octanucleotide sequence 5'-RTGC^GCAY-3'.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - e120
EP  - e120
VL  - 29
AB  - A new type II restriction endonuclease designated FspAI has been partially purified from a
AB  - Flexibacter species Tv-m21K. FspAI recognizes the octanucleotide sequence
AB  - 5'-RTGCdecreaseGCAY-3' and cleaves it in the center generating blunt-ended DNA fragments.
ER  -

TY  - JOUR
AU  - Kessler, C.
TI  - Class II restriction endonucleases.
JO  - Cytogenetics
PY  - 1987
SP  - 225
EP  - 279
VL  - 0
AB  - The availability of a large variety of class II restriction endonucleases with
AB  - different site specificities is the basis of recombinant DNA technology and
AB  - numerous analytical applications.  The importance of this enzyme class is
AB  - demonstrated by recent findings in the detailed analysis of gene structure and
AB  - the rapid succession of spectacular advances in genetic engineering (Malcolm
AB  - 1981; O'Connor et al. 1984).
ER  -

TY  - JOUR
AU  - Kessler, C.
TI  - Restriction enzymes.
JO  - Chemie in unserer Zeit
PY  - 1988
SP  - 37
EP  - 49
VL  - 22
AB  - None
ER  -

TY  - JOUR
AU  - Kessler, C.
AU  - Bolton, B.J.
AU  - Comer, M.J.
TI  - Screening for novel Type II restriction endonucleases.
JO  - J. Cell Biochem. Suppl.
PY  - 1986
SP  - 101
EP  - 101
VL  - 10D
AB  - Besides various species of lactic acid bacteria (Lactobacillus, Pediococcus and
AB  - Leuconostoc) we have screened 252 different non-pathogenic species of the
AB  - genera Achromobacter, Acinetobacter, Alcaligenes, Brevibacterium, Enterobacter,
AB  - Flavobacterium and Herpetosiphon for the presence of potentially new type II
AB  - restriction endonucleases.  Among the above lactic acid bacteria screened, we
AB  - could not detect any specific activities, whereas in all the other genera we
AB  - found a high number of species producing different type II restriction
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Kessler, C.
AU  - Holtke, H.J.
TI  - Specificity of restriction endonucleases and methylases - a review (Edition 2).
JO  - Gene
PY  - 1986
SP  - 1
EP  - 153
VL  - 47
AB  - The properties and sources of all known restriction endonucleases and
AB  - methylases are listed.  The enzymes are cross-indexed (Table I), classified
AB  - according to their recognition sequence homologies (Table II), and
AB  - characterized within Table II by the cleavage and methylation positions, the
AB  - number of recognition sites on the double-stranded DNA of the bacteriophages
AB  - lambda, phiX174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and
AB  - pBR328, and the microorganisms from which they originate.  Other tabulated
AB  - properties of the restriction endonucleases included relaxed specificities
AB  - (integrated into Table II), the structure of the generated fragment ends (Table
AB  - III), and the sensitivity to different kinds of DNA methylation (Table V).  In
AB  - Table IV the conversion of two-and four-base 5'-protruding ends into new
AB  - recognition sequences is compiled which is obtained by the fill-in reaction
AB  - with Klenow fragment of the Escherichia coli DNA polymerase I or additional
AB  - nuclease S1 treatment followed by ligation of the modified fragment termini.
AB  - Interconversion of restriction sites generates novel cloning sites without the
AB  - need of linkers.  This should improve the flexibility of genetic engineering
AB  - experiments.  Table VI classifies the restriction methylases according to the
AB  - nature of the methylated base(s) within their recognition sequences.  This
AB  - table also comprises restriction endonucleases which are known to be inhibited
AB  - or activated by the modified nucleotides.  The detailed sequences of those
AB  - overlapping restriction sites are also included which become resistant to
AB  - cleavage after the sequential action of corresponding restriction methylases
AB  - and endonuclease.  By this approach large DNA fragments can be generated which
AB  - is helpful in the construction of genomic libraries.  The data given in both
AB  - Table IV and VI allow the design of novel sequence specificities.  These
AB  - procedures complement the creation of universal cleavage specificities applying
AB  - class IIS enzymes and bivalent DNA adapter molecules.
ER  -

TY  - JOUR
AU  - Kessler, C.
AU  - Manta, V.
TI  - Specificity of restriction endonucleases and DNA modification methyltransferases - a review (Edition 3) .
JO  - Gene
PY  - 1990
SP  - 1
EP  - 248
VL  - 92
AB  - The properties and sources of all known class-I, class-II and class-III
AB  - restriction endonucleases (ENases) and DNA modification methyltransferases
AB  - (MTases) are listed and newly subclassified according to their sequence
AB  - specificity.  In addition, the enzymes are distinguished in a novel manner
AB  - according to sequence specificity, cleavage position and methylation
AB  - sensitivity.  Furthermore, new nomenclature rules are proposed for
AB  - unambiguously defined enzyme names.  In the various Tables, the enzymes are
AB  - cross-indexed alphabetically according to their names (Table I), classified
AB  - according to their recognition sequence homologies (Table II), and
AB  - characterized within Table II by the cleavage and methylation positions, the
AB  - number of recognition sites on the DNA of the bacteriophages lambda, PhiX174,
AB  - and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the
AB  - microorganisms from which they originate.  Other tabulated properties of the
AB  - ENases include relaxed specificities (integrated within Table II), the
AB  - structure of the generated fragment ends (Table III), interconversion of
AB  - restriction sites (Table IV) and the sensitivity to different kinds of DNA
AB  - methylation (Table V).  Table VI shows the influence of class-II MTases on the
AB  - activity of class-II ENases with at least partially overlapping recognition
AB  - sequences.  Table VII lists all class-II restriction endonucleases and MTases
AB  - which are commercially available.
ER  -

TY  - JOUR
AU  - Kessler, C.
AU  - Nesch, G.
AU  - Brack, R.
TI  - SphI restriction map of bacteriophage lambda DNA.
JO  - Gene
PY  - 1981
SP  - 321
EP  - 323
VL  - 16
AB  - Upon reinvestigation, the number of cleavage sites for site-specific
AB  - endonuclease SphI on lambda DNA was found to be six.  The SphI restriction map
AB  - of the lambda cI857Sam7 genome was determined.
ER  -

TY  - JOUR
AU  - Kessler, C.
AU  - Neumaier, P.S.
AU  - Wolf, W.
TI  - Recognition sequences of restriction endonucleases and methylases - a review.
JO  - Gene
PY  - 1985
SP  - 1
EP  - 102
VL  - 33
AB  - The properties and sources of all known endonucleases and methylases acting site-specifically
AB  - on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies
AB  - within their recognition sequences (Table II), and characterized within Table II by the
AB  - cleavage and methylation positions, the number of recognition sites on the DNA of the
AB  - bacteriophages lambda, PhiX174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and
AB  - pBR328 and the microorganims from which they originate. Other tabulated properties of the
AB  - restriction endonucleases include relaxed specificites (Table III), the structure of the
AB  - restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA
AB  - methylation (Table V). Table VI classifies the methylases according to the nature of the
AB  - methylated base(s) within their recognition sequences. This table also comprises those
AB  - restriction endonucleases, which are known to be inhibited by the modified nucleotides.
AB  - Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on
AB  - sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the
AB  - length of the generated fragments ordered according to size, and the effects of the
AB  - Escherichia coli dam- and dcm-coded methylases M Eco dam and M Eco dcmI on the particular
AB  - recognition sites.
ER  -

TY  - JOUR
AU  - Kessner, L.
AU  - Spinard, E.
AU  - Gomez-Chiarri, M.
AU  - Rowley, D.C.
AU  - Nelson, D.R.
TI  - Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease).
JO  - Genome Announcements
PY  - 2016
SP  - e00148
EP  - e00116
VL  - 4
AB  - Aliiroseovarius crassostreae CV919-312 is a marine alphaproteobacterium and the causative
AB  - agent of Roseovarius oyster disease. We announce here the draft genome
AB  - sequence of A. crassostreae CV919-312 and identify potential virulence genes
AB  - involved in pathogenicity.
ER  -

TY  - JOUR
AU  - Ketter, P.
AU  - Guentzel, M.N.
AU  - Chambers, J.P.
AU  - Jorgensen, J.
AU  - Murray, C.K.
AU  - Cap, A.P.
AU  - Yu, J.J.
AU  - Eppinger, M.
AU  - Arulanandam, B.P.
TI  - Genome Sequences of Four Acinetobacter baumannii-A. calcoaceticus Complex Isolates from Combat-Related Infections Sustained in the Middle East.
JO  - Genome Announcements
PY  - 2014
SP  - e00026
EP  - e00014
VL  - 2
AB  - Acinetobacter baumannii is among the most prevalent bacterial causes of combat-related
AB  - infections on the battlefield. Antibiotic resistance and a poor
AB  - understanding of the protective host immune responses make treatment difficult.
AB  - Here, we report the genome sequences of four clinical Acinetobacter baumannii-A.
AB  - calcoaceticus complex isolates exhibiting significant differences in virulence in
AB  - a mouse sepsis model.
ER  -

TY  - JOUR
AU  - Kettler, G.C.
AU  - Martiny, A.C.
AU  - Huang, K.
AU  - Zucker, J.
AU  - Coleman, M.L.
AU  - Rodrigue, S.
AU  - Chen, F.
AU  - Lapidus, A.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Steglich, C.
AU  - Church, G.M.
AU  - Richardson, P.
AU  - Chisholm, S.W.
TI  - Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.
JO  - PLoS Genet.
PY  - 2007
SP  - E231
EP  - E231
VL  - 3
AB  - Prochlorococcus is a marine cyanobacterium that numerically dominates the
AB  - mid-latitude oceans and is the smallest known oxygenic phototroph.
AB  - Numerous isolates from diverse areas of the world's oceans have been
AB  - studied and shown to be physiologically and genetically distinct. All
AB  - isolates described thus far can be assigned to either a tightly clustered
AB  - high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted
AB  - group. The 16S rRNA sequences of the entire Prochlorococcus group differ
AB  - by at most 3%, and the four initially published genomes revealed patterns
AB  - of genetic differentiation that help explain physiological differences
AB  - among the isolates. Here we describe the genomes of eight newly sequenced
AB  - isolates and combine them with the first four genomes for a comprehensive
AB  - analysis of the core (shared by all isolates) and flexible genes of the
AB  - Prochlorococcus group, and the patterns of loss and gain of the flexible
AB  - genes over the course of evolution. There are 1,273 genes that represent
AB  - the core shared by all 12 genomes. They are apparently sufficient,
AB  - according to metabolic reconstruction, to encode a functional cell. We
AB  - describe a phylogeny for all 12 isolates by subjecting their complete
AB  - proteomes to three different phylogenetic analyses. For each non-core
AB  - gene, we used a maximum parsimony method to estimate which ancestor likely
AB  - first acquired or lost each gene. Many of the genetic differences among
AB  - isolates, especially for genes involved in outer membrane synthesis and
AB  - nutrient transport, are found within the same clade. Nevertheless, we
AB  - identified some genes defining HL and LL ecotypes, and clades within these
AB  - broad ecotypes, helping to demonstrate the basis of HL and LL adaptations
AB  - in Prochlorococcus. Furthermore, our estimates of gene gain events allow
AB  - us to identify highly variable genomic islands that are not apparent
AB  - through simple pairwise comparisons. These results emphasize the
AB  - functional roles, especially those connected to outer membrane synthesis
AB  - and transport that dominate the flexible genome and set it apart from the
AB  - core. Besides identifying islands and demonstrating their role throughout
AB  - the history of Prochlorococcus, reconstruction of past gene gains and
AB  - losses shows that much of the variability exists at the "leaves of the
AB  - tree," between the most closely related strains. Finally, the
AB  - identification of core and flexible genes from this 12-genome comparison
AB  - is largely consistent with the relative frequency of Prochlorococcus genes
AB  - found in global ocean metagenomic databases, further closing the gap
AB  - between our understanding of these organisms in the lab and the wild.
ER  -

TY  - JOUR
AU  - Kettling, U.
AU  - Koltermann, A.
AU  - Schwille, P.
AU  - Eigen, M.
TI  - Real-time enzyme kinetics monitored by dual-color fluorescence cross-correlation spectroscopy.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 1416
EP  - 1420
VL  - 95
AB  - A method for sensitively monitoring enzyme kinetics and activities by using dual-color
AB  - fluorescence cross-correlation spectroscopy is described.  This universal method enables the
AB  - development of highly sensitive and precise assays for real-time kinetic analyses of any
AB  - catalyzed cleavage or addition reaction, where a chemical linkage is formed or cleaved through
AB  - an enzyme's action between two fluorophores that can be discriminated spectrally.  In this
AB  - work, a homogeneous assay with restriction endonuclease EcoRI and a 66-bp double-stranded DNA
AB  - containing the GAATTC recognition site and fluorophores at each 5' end is described.  The
AB  - enzyme activity can be quantified down to the low picomolar range (>1.6 pM) where the rate
AB  - constants are linearly dependent on the enzyme concentrations over two orders of magnitude.
AB  - Furthermore, the reactions were monitored online at various initial substrate concentrations
AB  - in the nanomolar range, and the reaction rates were clearly represented by the
AB  - Michaelis-Menten equation with a KM of 14+/- 1 nM and a kcat of 4.6 +/- 0.2 min-1.  In
AB  - addition to kinetic studies and activity determinations, it is proposed that enzyme assays
AB  - based on the dual-color fluorescence cross-correlation spectroscopy will be very useful for
AB  - high-throughput screening and evolutionary biotechnology.
ER  -

TY  - JOUR
AU  - Ketyi, J.
AU  - Orskov, F.
TI  - Host-controlled modification and restriction of foreign chromosomal and plasmid DNA in Shigella flexneri strains.
JO  - Acta Path. Microbiol. Scand.
PY  - 1970
SP  - 51
EP  - 58
VL  - 78
AB  - The hsp gene (the genetic determinant for host-controlled restriction and
AB  - modification) was transferred from an E. coli K12 strain into a S. flexneri
AB  - strain, and in reverse the same gene from a Shigella strain was introduced into
AB  - E. coli K12.  The presence of the heterologous hsp gene was tested by phage T5.
AB  - It was demonstrated in interrupted mating experiments with the hybrids as
AB  - recipients that the hsp hybrids had acquired changed recipient characters
AB  - resembling those of the strains from which the hsp originated.
ER  -

TY  - JOUR
AU  - Key, T.A.
AU  - Richmond, D.P.
AU  - Bowman, K.S.
AU  - Cho, Y.J.
AU  - Chun, J.
AU  - da Costa, M.S.
AU  - Rainey, F.A.
AU  - Moe, W.M.
TI  - Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type  strain (IP3-3(T)).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 44
EP  - 44
VL  - 11
AB  - Dehalogenimonas alkenigignens IP3-3(T) is a strictly anaerobic, mesophilic, Gram  negative
AB  - staining bacterium that grows by organohalide respiration, coupling the
AB  - oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes.
AB  - Growth has not been observed with any non-polyhalogenated alkane electron
AB  - acceptors. Here we describe the features of strain IP3-3(T) together with genome
AB  - sequence information and its annotation. The 1,849,792 bp high-quality-draft
AB  - genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single
AB  - large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S)
AB  - locus. The genome contains 29 predicted reductive dehalogenase genes, a large
AB  - majority of which lack cognate genes encoding membrane anchoring proteins.
ER  -

TY  - JOUR
AU  - Khadem, A.F. et al.
TI  - Draft Genome Sequence of the Volcano-Inhabiting Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum Strain SolV.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3729
EP  - 3730
VL  - 194
AB  - The draft genome of Methylacidiphilum fumariolicum SolV, a thermoacidophilic methanotroph of
AB  - the phylum Verrucomicrobia, is presented. Annotation revealed
AB  - pathways for one-carbon, nitrogen, and hydrogen catabolism and respiration
AB  - together with central metabolic pathways. The genome encodes three orthologues of
AB  - particulate methane monooxygenases. Sequencing of this genome will help in the
AB  - understanding of methane cycling in volcanic environments.
ER  -

TY  - JOUR
AU  - Khajanchi, B.K.
AU  - Han, J.
AU  - Gokulan, K.
AU  - Zhao, S.
AU  - Gies, A.
AU  - Foley, S.L.
TI  - Draft Genome Sequences of Four Salmonella enterica Strains Isolated from Turkey-Associated Sources.
JO  - Genome Announcements
PY  - 2016
SP  - e01122
EP  - e01116
VL  - 4
AB  - We report the draft genomes of four Salmonella enterica isolates evaluated for the
AB  - contribution of plasmids to virulence. Strains SE163A, SE696A, and SE710A
AB  - carry plasmids demonstrated to facilitate plasmid-associated virulence, while
AB  - SE819 is less virulent and has been used as a recipient for conjugation
AB  - experiments to assess plasmid-encoded virulence mechanisms.
ER  -

TY  - JOUR
AU  - Khaleque, H.N.
AU  - Ramsay, J.P.
AU  - Murphy, R.J.
AU  - Kaksonen, A.H.
AU  - Boxall, N.J.
AU  - Watkin, E.L.
TI  - Draft Genome Sequence of the Acidophilic, Halotolerant, and Iron/Sulfur-Oxidizing Acidihalobacter prosperus DSM 14174 (Strain V6).
JO  - Genome Announcements
PY  - 2017
SP  - e01469
EP  - e01416
VL  - 5
AB  - The principal genomic features of Acidihalobacter prosperus DSM 14174 (strain V6) are
AB  - presented here. This is a mesophilic, halotolerant, and iron/sulfur-oxidizing
AB  - acidophile that was isolated from seawater at Vulcano, Italy. It has potential
AB  - for use in biomining applications in regions where high salinity exists in the
AB  - source water and ores.
ER  -

TY  - JOUR
AU  - Khaleque, H.N.
AU  - Ramsay, J.P.
AU  - Murphy, R.J.T.
AU  - Kaksonen, A.H.
AU  - Boxall, N.J.
AU  - Watkin, E.L.J.
TI  - Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species.
JO  - Genome Announcements
PY  - 2017
SP  - e00413
EP  - e00417
VL  - 5
AB  - The use of halotolerant acidophiles for bioleaching provides a biotechnical approach for the
AB  - extraction of metals from regions where high salinity exists in
AB  - the ores and source water. Here, we describe the first draft genome of a new
AB  - species of a halotolerant and iron- and sulfur-oxidizing acidophile,
AB  - Acidihalobacter ferrooxidans DSM 14175 (strain V8).
ER  -

TY  - JOUR
AU  - Khalid, M.I.
AU  - Teh, L.K.
AU  - Lee, L.S.
AU  - Zakaria, Z.A.
AU  - Salleh, M.Z.
TI  - Genome Sequence of Proteus mirabilis Strain PR03, Isolated from a Local Hospital  in Malaysia.
JO  - Genome Announcements
PY  - 2013
SP  - e00327
EP  - e00313
VL  - 1
AB  - Proteus mirabilis is one of the pathogenic agents that commonly causes urinary tract
AB  - infections among elderly individuals and long-term catheterized patients.
AB  - Here, we report a draft genome sequence of Proteus mirabilis strain PR03
AB  - (3,932,623 bp, with a G+C content of 38.6%) isolated from a local hospital in
AB  - Malaysia.
ER  -

TY  - JOUR
AU  - Khalil, A.
AU  - Sivakumar, N.
AU  - Qarawi, S.
TI  - Genome Sequence of Anoxybacillus flavithermus Strain AK1, a Thermophile Isolated  from a Hot Spring in Saudi Arabia.
JO  - Genome Announcements
PY  - 2015
SP  - e00604
EP  - e00615
VL  - 3
AB  - Anoxybacillus flavithermus strain AK1 was isolated from Al-Ain Alhara, a thermal  hot spring
AB  - located 50 km southeast of the city of Gazan, Saudi Arabia (16 degrees
AB  - 56'N, 43 degrees 15'E). The sequenced and annotated genome is 2,630,664 bp and
AB  - encodes 2,799 genes.
ER  -

TY  - JOUR
AU  - Khan, A.
AU  - Khan, H.
AU  - Chung, E.J.
AU  - Hossain, M.T.
AU  - Chung, Y.R.
TI  - Complete Genome Sequence of Martelella endophytica YC6887, Which Has Antifungal Activity Associated with a Halophyte.
JO  - Genome Announcements
PY  - 2015
SP  - e00366
EP  - e00315
VL  - 3
AB  - Martelella endophytica YC6887, which produces antifungal compounds against fungal and oomycete
AB  - pathogens, was isolated from the root of a halophyte, Rosa rugosa,
AB  - collected at a tidal flat in South Korea. Its full-genome sequence shows that it
AB  - is a circular DNA, without a plasmid, of about 4.8 Mb in size.
ER  -

TY  - JOUR
AU  - Khan, A.A.
AU  - Khajanchi, B.K.
AU  - Khan, S.A.
AU  - Elkins, C.A.
AU  - Foley, S.L.
TI  - Draft Genome Sequences of Ciprofloxacin-Resistant Salmonella enterica Strains with Multiple-Antibiotic Resistance, Isolated from Imported Foods.
JO  - Genome Announcements
PY  - 2017
SP  - e01222
EP  - e01217
VL  - 5
AB  - We report here the draft genome sequences of 15 ciprofloxacin-resistant Salmonella enterica
AB  - strains with resistance to multiple other antibiotics,
AB  - including aminoglycosides, beta-lactams, sulfonamides, tetracycline, and
AB  - trimethoprim, isolated from different imported foods. Three strains (NCTR75,
AB  - NCTR281, and NCTR350) showed a high level of ciprofloxacin resistance compared to
AB  - that of the other isolates. The whole-genome sequencing data provide a better
AB  - understanding of the antibiotic resistance mechanisms and virulence properties of
AB  - these isolates.
ER  -

TY  - JOUR
AU  - Khan, A.U.
AU  - Beg, A.Z.
AU  - Verma, P.K.
TI  - Draft Genome Sequence of the First NDM-4-Producing Escherichia coli Strain (AK1), Isolated from Sewage Water of a North Indian Hospital.
JO  - Genome Announcements
PY  - 2017
SP  - e01366
EP  - e01317
VL  - 5
AB  - We report here the draft genome sequence of the first isolated NDM-4-producing Escherichia
AB  - coli strain, isolated from sewage water at a North Indian hospital.
AB  - The genome has an assembly size of 5,076,053 bp, arranged in 129 contigs, with
AB  - 5,271 genes and a G+C content of 50.47%.
ER  -

TY  - JOUR
AU  - Khan, F.
AU  - Furuta, Y.
AU  - Kawai, M.
AU  - Kaminska, K.H.
AU  - Ishikawa, K.
AU  - Bujnicki, J.M.
AU  - Kobayashi, I.
TI  - A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 3019
EP  - 3030
VL  - 38
AB  - Genome comparison and genome context analysis were used to find a putative mobile element in
AB  - the genome of Photorhabdus luminescens, an
AB  - entomopathogenic bacterium. The element is composed of 16-bp direct
AB  - repeats in the terminal regions, which are identical to a part of
AB  - insertion sequences (ISs), a DNA methyltransferase gene homolog, two genes
AB  - of unknown functions and an open reading frame (ORF) (plu0599) encoding a
AB  - protein with no detectable sequence similarity to any known protein. The
AB  - ORF (plu0599) product showed DNA endonuclease activity, when expressed in
AB  - a cell-free expression system. Subsequently, the protein, named R.PluTI,
AB  - was expressed in vivo, purified and found to be a novel type IIF
AB  - restriction enzyme that recognizes 5'-GGCGC/C-3' (/ indicates position of
AB  - cleavage). R.PluTI cleaves a two-site supercoiled substrate at both the
AB  - sites faster than a one-site supercoiled substrate. The modification
AB  - enzyme homolog encoded by plu0600, named M.PluTI, was expressed in
AB  - Escherichia coli and shown to protect DNA from R.PluTI cleavage in vitro,
AB  - and to suppress the lethal effects of R.PluTI expression in vivo. These
AB  - results suggested that they constitute a restriction-modification system,
AB  - present on the putative mobile element. Our approach thus allowed
AB  - detection of a previously uncharacterized family of DNA-interacting
AB  - proteins.
ER  -

TY  - JOUR
AU  - Khan, M.A.
AU  - Isaacson, R.E.
TI  - Identification of Escherichia coli genes that are specifically expressed in a murine model of septicemic infection.
JO  - Infect. Immun.
PY  - 2002
SP  - 3404
EP  - 3412
VL  - 70
AB  - Identification and characterization of bacterial genes that are induced during the disease
AB  - process are important in understanding the molecular
AB  - mechanism of disease and can be useful in designing antimicrobial drugs to
AB  - control the disease. The identification of in vivo induced (ivi) genes of
AB  - an Escherichia coli septicemia strain by using antibiotic-based in vivo
AB  - expression technology is described. Bacterial clones resistant to
AB  - chloramphenicol in vivo were recovered from the livers of infected mice.
AB  - Most of the ivi clones were sensitive to chloramphenicol when grown in
AB  - vitro. Using reverse transcription-PCR, it was demonstrated that selected
AB  - ivi clones expressed cat in the livers of infected mice but not during in
AB  - vitro growth. A total of 750 colonies were recovered after three
AB  - successive rounds of in vivo selection, and 168 isolated ivi clones were
AB  - sequenced. The sequence analysis revealed that 37 clones encoded
AB  - hypothetical proteins found in E. coli K-12, whereas 10 clones contained
AB  - genes that had no significant homology to DNA sequences in GenBank. Two
AB  - clones were found to contain transposon-related functions. Other clones
AB  - contained genes required for amino acid metabolism, anaerobic respiration,
AB  - DNA repair, the heat shock response, and the cellular repressor of the SOS
AB  - response. In addition, one clone contained the aerobactin biosynthesis
AB  - gene iucA. Mutations were introduced in to seven of the identified ivi
AB  - genes. An in vivo mouse challenge-competition assay was used to determine
AB  - if the mutants were attenuated. The results suggested that these ivi genes
AB  - were important for survival in vivo, and three of the seven mutant ivi
AB  - clones were required for successful infection of mice.
ER  -

TY  - JOUR
AU  - Khan, M.W.
AU  - Habibi, N.
AU  - Shaheed, F.
AU  - Mustafa, A.S.
TI  - Draft Genome Sequences of Five Clinical Strains of Brucella melitensis Isolated from Patients Residing in Kuwait.
JO  - Genome Announcements
PY  - 2016
SP  - e01144
EP  - e01116
VL  - 4
AB  - Human brucellosis is a neglected and underrecognized infection of widespread geographic
AB  - distribution. Brucellosis is present on all inhabited continents and
AB  - endemic in many areas of the world, including Kuwait and the Middle East. Here,
AB  - we present draft genome assemblies of five Brucella melitensis strains isolated
AB  - from brucellosis patients in Kuwait.
ER  -

TY  - JOUR
AU  - Khan, S.
AU  - Sung, K.
AU  - Iram, S.
AU  - Nawaz, M.
AU  - Xu, J.
AU  - Marasa, B.
TI  - Draft Genome Sequences of Two Methicillin-Resistant Clinical Staphylococcus aureus Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e01396
EP  - e01315
VL  - 4
AB  - Here, we report the draft genome sequences of two methicillin-resistant Staphylococcus aureus
AB  - (MRSA) clinical isolates, hospital-associated perirectal
AB  - isolate 32S (ST 239) from a colitis tracheostomy patient and community-associated
AB  - MRSA isolate 42S (ST 772) from a hepatic-splenomegaly patient in Rawalpindi,
AB  - Pakistan.
ER  -

TY  - JOUR
AU  - Khan, S.
AU  - Sung, K.
AU  - Marasa, B.
AU  - Min, S.
AU  - Kweon, O.
AU  - Nawaz, M.
AU  - Cerniglia, C.
TI  - Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Clinical Isolate VRE3, with a Sequence Type 16 Pattern and Novel Structural Arrangement of  Tn1546.
JO  - Genome Announcements
PY  - 2015
SP  - e00871
EP  - e00815
VL  - 3
AB  - Multidrug-resistant Enterococcus faecium has emerged as a nosocomial pathogen that may infect
AB  - the body at various sites, including the gastrointestinal tract,
AB  - and has serious implications in human health and disease. Here, we present the
AB  - draft genome sequence of clinical strain VRE3, which exhibited a sequence type 16
AB  - (ST16) pattern and carried truncated Tn1546, a mobile genetic element encoding a
AB  - high level of vancomycin resistance.
ER  -

TY  - JOUR
AU  - Khanna, N. et al.
TI  - Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 359
EP  - 369
VL  - 9
AB  - Enterobacter sp. IIT-BT 08 belongs to Phylum: Proteobacteria, Class: Gammaproteobacteria,
AB  - Order: Enterobacteriales, Family: Enterobacteriaceae. The
AB  - organism was isolated from the leaves of a local plant near the Kharagpur railway
AB  - station, Kharagpur, West Bengal, India. It has been extensively studied for
AB  - fermentative hydrogen production because of its high hydrogen yield. For further
AB  - enhancement of hydrogen production by strain development, complete genome
AB  - sequence analysis was carried out. Sequence analysis revealed that the genome was
AB  - linear, 4.67 Mbp long and had a GC content of 56.01%. The genome properties
AB  - encode 4,393 protein-coding and 179 RNA genes. Additionally, a putative pathway
AB  - of hydrogen production was suggested based on the presence of formate hydrogen
AB  - lyase complex and other related genes identified in the genome. Thus, in the
AB  - present study we describe the specific properties of the organism and the
AB  - generation, annotation and analysis of its genome sequence as well as discuss the
AB  - putative pathway of hydrogen production by this organism.
ER  -

TY  - JOUR
AU  - Khatri, I.
AU  - Dureja, C.
AU  - Raychaudhuri, S.
AU  - Subramanian, S.
TI  - Draft Genome Sequence of the Opportunistic Human Pathogen Morganella morganii SC01.
JO  - Genome Announcements
PY  - 2013
SP  - e00051
EP  - e00012
VL  - 1
AB  - We report the 4.1-Mb draft genome sequence of Morganella morganii SC01, a
AB  - gammaproteobacterium, isolated from an Indian human fecal sample.
ER  -

TY  - JOUR
AU  - Khatri, I.
AU  - Kaur, S.
AU  - Devi, U.
AU  - Kumar, N.
AU  - Sharma, D.
AU  - Subramanian, S.
AU  - Saini, A.K.
TI  - Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4.
JO  - Genome Announcements
PY  - 2013
SP  - e00947
EP  - e00913
VL  - 1
AB  - Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities,
AB  - indicating their potential for increasing crop yield. Herein, we
AB  - provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a
AB  - Gram-negative motile plant growth-promoting rhizobacterium isolated from a
AB  - pomegranate plant. The 4.9-Mb genome contains genes related to plant growth
AB  - promotion and the synthesis of siderophores.
ER  -

TY  - JOUR
AU  - Khatri, I.
AU  - Nupur, K.S.
AU  - Subramanian, S.
AU  - Pinnaka, A.K.
TI  - Draft Genome Sequence of Rhodovulum sp. Strain PH10, a Phototrophic Alphaproteobacterium Isolated from a Soil Sample of Mangrove of Namkhana, India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6363
EP  - 6363
VL  - 194
AB  - We report the 4.8-Mb draft genome of Rhodovulum sp. strain PH10, a phototrophic bacterium
AB  - belonging to class Alphaproteobacteria, isolated from a soil sample
AB  - collected from the mangrove forest of Namkhana in India. This genome is the first
AB  - from the genus Rhodovulum and will lead to a better understanding of the
AB  - genes/pathways involved in activities like phototrophic growth and nitrogen
AB  - fixation in this group of bacteria.
ER  -

TY  - JOUR
AU  - Khatri, I.
AU  - Singh, A.
AU  - Korpole, S.
AU  - Pinnaka, A.K.
AU  - Subramanian, S.
TI  - Draft Genome Sequence of an Alphaproteobacterium, Caenispirillum salinarum AK4(T), Isolated from a Solar Saltern.
JO  - Genome Announcements
PY  - 2013
SP  - e00199
EP  - e00112
VL  - 1
AB  - We report the 4.9-Mb genome sequence of Caenispirillum salinarum AK4(T) isolated  from a
AB  - sediment sample collected from a solar saltern at Kakinada, Andhra
AB  - Pradesh, India.
ER  -

TY  - JOUR
AU  - Khayi, S.
AU  - Blin, P.
AU  - Chong, T.M.
AU  - Chan, K.G.
AU  - Faure, D.
TI  - Complete Chromosome and Plasmid Sequences of Two Plant Pathogens, Dickeya solani  Strains D s0432-1 and PPO 9019.
JO  - Genome Announcements
PY  - 2018
SP  - e00233
EP  - e00218
VL  - 6
AB  - Dickeya solani species are emerging bacterial pathogens of Solanum tuberosum Here, we announce
AB  - the complete genome sequences of two strains, Dickeya solani D
AB  - s0432-1 and PPO 9019. Strain PPO 9019 represents the first described member of
AB  - the genus Dickeya with an extrachromosomal genetic element.
ER  -

TY  - JOUR
AU  - Khayi, S.
AU  - Blin, P.
AU  - Chong, T.M.
AU  - Chan, K.G.
AU  - Faure, D.
TI  - Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 87
EP  - 87
VL  - 11
AB  - Several species of the genus Dickeya provoke soft rot and blackleg diseases on a  wide range
AB  - of plants and crops. Dickeya solani has been identified as the
AB  - causative agent of diseases outbreaks on potato culture in Europe for the last
AB  - decade. Here, we report the complete genome of the D. solani IPO 2222T. Using
AB  - PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp
AB  - was assembled. The G + C content reaches 56% and the genomic sequence contains
AB  - 4,059 predicted proteins. The ANI values calculated for D. solani IPO 2222T vs.
AB  - other available D. solani genomes was over 99.9% indicating a high genetic
AB  - homogeneity within D. solani species.
ER  -

TY  - JOUR
AU  - Khayi, S.
AU  - Blin, P.
AU  - Chong, T.M.
AU  - Robic, K.
AU  - Chan, K.G.
AU  - Faure, D.
TI  - Complete Genome Sequences of the Plant Pathogens Dickeya solani RNS 08.23.3.1.A and Dickeya dianthicola RNS04.9.
JO  - Genome Announcements
PY  - 2018
SP  - e01447
EP  - e01417
VL  - 6
AB  - Dickeya spp. are bacterial pathogens causing soft-rot and blackleg diseases on a  wide range
AB  - of ornamental plants and crops. In this paper, we announce the PacBio
AB  - complete genome sequences of the plant pathogens Dickeya solani RNS 08.23.3.1.A
AB  - (PRI3337) and Dickeya dianthicola RNS04.9.
ER  -

TY  - JOUR
AU  - Khayi, S.
AU  - Mondy, S.
AU  - Beury-Cirou, A.
AU  - Moumni, M.
AU  - Helias, V.
AU  - Faure, D.
TI  - Genome Sequence of the Emerging Plant Pathogen Dickeya solani Strain RNS 08.23.3.1A.
JO  - Genome Announcements
PY  - 2014
SP  - e01270
EP  - e01213
VL  - 2
AB  - Here we present the genome sequence of Dickeya solani strain RNS 08.23.3.1A (PRI3337),
AB  - isolated from Solanum tuberosum. Dickeya solani, recently described on
AB  - potato cultures in Europe, is a proposed new taxon closely related to the Dickeya
AB  - dianthicola and Dickeya dadantii species.
ER  -

TY  - JOUR
AU  - Khayi, S.
AU  - Raoul-des-Essarts, Y.
AU  - Mondy, S.
AU  - Moumni, M.
AU  - Helias, V.
AU  - Beury-Cirou, A.
AU  - Faure, D.
TI  - Draft Genome Sequences of the Three Pectobacterium-Antagonistic Bacteria Pseudomonas brassicacearum PP1-210F and PA1G7 and Bacillus simplex BA2H3.
JO  - Genome Announcements
PY  - 2015
SP  - e01497
EP  - e01414
VL  - 3
AB  - Pectobacterium spp. are bacterial pathogens causing soft rot diseases on a wide range of
AB  - plants and crops. We present in this paper the draft genome sequences of
AB  - three bacterial strains, Pseudomonas brassicacearum PP1-210F and PA1G7 and
AB  - Bacillus simplex BA2H3, which exhibit antagonistic activities against the
AB  - Pectobacterium plant pathogens.
ER  -

TY  - JOUR
AU  - Khayi, S.
AU  - Raoul-des-Essarts, Y.
AU  - Quetu-Laurent, A.
AU  - Moumni, M.
AU  - Helias, V.
AU  - Faure, D.
TI  - Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes.
JO  - Genetica
PY  - 2015
SP  - 241
EP  - 252
VL  - 143
AB  - The blackleg and soft-rot diseases caused by pectinolytic enterobacteria such as
AB  - Pectobacterium and Dickeya are major causes of losses affecting potato crop in the field and
AB  - upon storage. In this work, we report the isolation, characterization and genome analysis of
AB  - the Pectobacterium wasabiae (formerly identified as Pectobacterium carotovorum subsp.
AB  - carotovorum) strain RNS 08.42.1A, that has been isolated from a Solanum tuberosum host plant
AB  - in France. Comparative genomics with 3 other P. wasabiae strains isolated from potato plants
AB  - in different areas in North America and Europe, highlighted both a strong similarity at the
AB  - whole genome level (ANI > 99 %) and a conserved synteny of the virulence genes. In addition,
AB  - our analyses evidenced a robust separation between these four P. wasabiae strains and the type
AB  - strain P. wasabiae CFBP 3304(T), isolated from horseradish in Japan. In P. wasabiae RNS
AB  - 08.42.1A, the expI and expR nucleotidic sequences are more related to those of some
AB  - Pectobacterium atrosepticum and P.
AB  - carotovorum strains (90 % of identity) than to those of the other potato P.
AB  - wasabiae strains (70 to 74 % of identity). This could suggest a recruitment of these genes in
AB  - the P. wasabiae strain RNS 08.42.1A by an horizontal transfer between pathogens infecting the
AB  - same potato host plant.
ER  -

TY  - JOUR
AU  - Khedkar, S.
AU  - Prabhakara, S.
AU  - Loganathan, R.M.
AU  - Chandana, S.
AU  - Gowda, M.
AU  - Arakere, G.
AU  - Seshasayee, A.S.N.
TI  - Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6946
EP  - 6947
VL  - 194
AB  - We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA)
AB  - strain ST672, an emerging disease clone in India, from a septicemia
AB  - patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs).
AB  - The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune
AB  - evasion cluster appear to be different from those of strain ST772 on preliminary
AB  - examination.
ER  -

TY  - JOUR
AU  - Khelaifia, S.
AU  - Garibal, M.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from  the Human Intestinal Microbiota.
JO  - Genome Announcements
PY  - 2014
SP  - e00073
EP  - e00014
VL  - 2
AB  - Methanobrevibacter oralis, an anaerobic methanogenic archaeon, has been previously isolated
AB  - from the human oral cavity. Here, sequencing a stool isolate
AB  - (strain JMR01) yielded a 2.065-Mb genome with a 27.78% G+C content containing a
AB  - total of 2,042 open reading frames and 3 clusters of regularly interspaced short
AB  - palindromic repeat (CRISPR) loci with associated Cas proteins.
ER  -

TY  - JOUR
AU  - Khelaifia, S.
AU  - Garibal, M.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of a Human-Associated Isolate of Methanobrevibacter arboriphilicus, the Lowest-G+C-Content Archaeon.
JO  - Genome Announcements
PY  - 2014
SP  - e01181
EP  - e01113
VL  - 2
AB  - We report the draft genome sequence of Methanobrevibacter arboriphilicus strain ANOR1,
AB  - isolated from the human gut. Its 2.21-Mb genome exhibits a 25.46% G+C
AB  - content, the lowest value among archaea. The genome of M. arboriphilicus contains
AB  - a total of 2,111 open reading frames and three clusters of regularly interspaced
AB  - short palindromic repeat (CRISPR) loci with associated Cas proteins.
ER  -

TY  - JOUR
AU  - Khemayan, K.
AU  - Prachumwat, A.
AU  - Sonthayanon, B.
AU  - Intaraprasong, A.
AU  - Sriurairatana, S.
AU  - Flegel, T.W.
TI  - Complete Genome Sequence of Virulence-Enhancing Siphophage VHS1 from Vibrio harveyi.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 2790
EP  - 2796
VL  - 78
AB  - Vibrio harveyi siphophage 1 (VHS1) is a tailed phage with an icosahedral head of
AB  - approximately 66 nm in diameter and an unornamented, flexible tail of
AB  - approximately 153 nm in length. When Vibrio harveyi 1114GL is lysogenized with
AB  - VHS1, its virulence for the black tiger shrimp (Penaeus monodon) increases by
AB  - more than 100 times, and this coincides with production of a toxin(s) associated
AB  - with shrimp hemocyte agglutination. Curiously, the lysogen does not show
AB  - increased virulence for the whiteleg shrimp (Penaeus [Litopenaeus] vannamei).
AB  - Here we present and annotate the complete, circular genome of VHS1 (81,509 kbp;
AB  - GenBank accession number JF713456). By software analysis, the genome contains 125
AB  - putative open reading frames (ORFs), all of which appear to be located on the
AB  - same DNA strand, similar to the case for many other bacteriophages. Most of the
AB  - putative ORFs show no significant homology to known sequences in GenBank. Notable
AB  - exceptions are ORFs for a putative DNA polymerase and putative phage structural
AB  - proteins, including a portal protein, a phage tail tape measure protein, and a
AB  - phage head protein. The last protein was identified as a component of the
AB  - species-specific toxin mixture described above as being associated with
AB  - agglutination of hemocytes from P. monodon.
ER  -

TY  - JOUR
AU  - Khesin, R.B.
AU  - Bogdanova, E.S.
TI  - The specificity of DNA-methylase in T2-phage infected E. coli B cells.
JO  - Biokhimiia
PY  - 1966
SP  - 405
EP  - 415
VL  - 31
AB  - Activity of the enzymatic system responsible for DNA methylation considerably increases after
AB  - infection of E. coli B cells with T2 phage.  The increase is inhibited by chloramphenicol.
AB  - The non-infected cells contain no inhibitor of DNA methylation, and the infected ones - no
AB  - activator of this reaction.  Hence, there is T2 phage induced production of phage DNA
AB  - methylase along with the synthesis of other enzymes.  Enzymatic preparations from the
AB  - non-infected and infected bacteria are capable of methylating heterologous (thymus, M.
AB  - lysodeikticus etc.) DNA but do not react with DNA from non-infected E. coli and from T2 and T4
AB  - phages.  However, both the enzymes methylate DNA of E. coli and T2 phage if it was
AB  - incompletely methylated in intact cells prior to isolation.  Partially methylated DNA loses
AB  - its methyl-acceptor ability with respect to the enzyme of non-infected cells after incubation
AB  - in vitro with the enzymatic system from infected cells.  Hence, the non-infected and the
AB  - infected cell methylases both react with the same combinations of nucleotides in E. coli and
AB  - T2 phage DNA, i.e., have the same specificity.  It is proposed, that methylated nucleotides in
AB  - DNA have something to do with the interaction with RNA-polymerase.  RNA prior to, as well as
AB  - after infection with T2 phage being synthesized with the same RNA-polymerase, bacterial as
AB  - well as phage DNA ought to contain the same sequences of methylated nucleotides.  This
AB  - explains the observed identity of specificities of the T2-phage induced methylase and of that
AB  - existing prior to infection.
ER  -

TY  - JOUR
AU  - Khetrapal, V.
AU  - Mehershahi, K.S.
AU  - Chen, S.L.
TI  - Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86.
JO  - Genome Announcements
PY  - 2017
SP  - e00243
EP  - e00217
VL  - 5
AB  - Escherichia coli is the most well-studied bacterium and a common colonizer of the lower
AB  - mammalian gastrointestinal tract. We report here the complete genome
AB  - sequence of the original Escherichia coli isolate, strain NCTC86, which was
AB  - described by Theodor Escherich, for whom the genus is named.
ER  -

TY  - JOUR
AU  - Khmaladze, E.
AU  - Dzavashvili, G.
AU  - Chanturia, G.
AU  - Nikolich, M.P.
AU  - Chain, P.S.G.
AU  - Johnson, S.L.
AU  - Imnadze, P.
TI  - Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia.
JO  - Genome Announcements
PY  - 2017
SP  - e00256
EP  - e00217
VL  - 5
AB  - Bacillus anthracis causes the acute fatal disease anthrax, is a proven biological weapon, and
AB  - is endemic in Georgia, where human and animal cases are reported
AB  - annually. Here, we present whole-genome sequences of 10 historical B. anthracis
AB  - strains from Georgia.
ER  -

TY  - JOUR
AU  - Khmelenina, V.N. et al.
TI  - Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00053
EP  - e00013
VL  - 1
AB  - Robust growth of the gammaproteobacterium Methylomicrobium buryatense strain 5G on methane
AB  - makes it an attractive system for CH4-based biocatalysis. Here we
AB  - present a draft genome sequence of the strain that will provide a valuable
AB  - framework for metabolic engineering of the core pathways for the production of
AB  - valuable chemicals from methane.
ER  -

TY  - JOUR
AU  - Kho, M.R.
AU  - Baker, D.J.
AU  - Laayoun, A.
AU  - Smith, S.S.
TI  - Stalling of human DNA (cytosine-5) methyltransferase at single-strand conformers from a site of dynamic mutation.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 67
EP  - 79
VL  - 275
AB  - Single-strand conformers from the C-rich strand of the triplet repeat at the FMR-1 locus are
AB  - rapidly and selectively methylated by the human DNA (cytosine-5) methyltransferase.  The
AB  - apparent affinity of the enzyme for the FMR-1 SSC is about tenfold higher than it is for a
AB  - control Watson-Crick paired duplex.  The de novo methylation rate for the SSC is over 150-fold
AB  - higher than the de novo rate for the control duplex.  Methylation of what is generally called
AB  - a hemi-methylated duplex occurs with a rate enhancement of over 100-fold, while methylation of
AB  - what can be viewed as a hemi-methylated FMR-1 SSC is actually slower than the de novo rate.
AB  - The pronounced inhibition of the methyltransferase by the methylated SSC sugggests that the
AB  - enzyme has a higher affinity for the methylated product of its reaction with the SSC than it
AB  - has for the unmethylated SSC substrate.  Gel retardation studies show that the
AB  - methyltransferase binds selectively to SSCs from the C-rich strand of the FMR-1 triplet
AB  - repeat.  This suggests a two-step stalling process in which the human methyltransferase first
AB  - selectively methylates and subsequently stalls at the C-rich strand SSC.  Stalling may reflect
AB  - the inability of the enzyme to release a DNA product that is fixed in a conformation
AB  - resembling its transition state by the unusual structure of the substrate.  In particular, the
AB  - data suggest that DNA methyltransferase may physically participate in biological processes
AB  - that lead to dynamic mutation at FMR-1.  In general, the data raise the possibility that a
AB  - two-step stalling process occurs at secondary structures associated with chromosome
AB  - instability, chromosome remodelling, viral replication or viral integration and may account
AB  - for the local hypermethylation and global hypomethylation associated with viral and non-viral
AB  - tumorigenesis.
ER  -

TY  - JOUR
AU  - Kholmina, G.V.
AU  - Rebentish, B.A.
AU  - Kozlovskii, Y.-E.
AU  - Sorokin, A.V.
AU  - Goldenberg, D.S.
AU  - Prozorov, A.A.
TI  - Purification and properties of two restriction endonucleases from Bacillus subtilis.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1986
SP  - 23
EP  - 25
VL  - 0
AB  - Two restriction endonucleases, Bsu1532I and Bsu1854I, have been isolated from
AB  - Bac. subtilis 1532 and 1854 cells and characterized.  The first of them,
AB  - Bsu1532I, recognizes and digests the tetranucleotide palindrome sequence GC^GC,
AB  - while Bsu1854I recognizes and digests the degenerate hexanucleotide sequence
AB  - GPuGCPy^C.  The optimum conditions were determined for both enzymes, and the
AB  - influence of various cofactors on the reactions catalyzed by them were studied.
ER  -

TY  - JOUR
AU  - Kholmina, G.V.
AU  - Rebentish, B.A.
AU  - Skoblov, Y.S.
AU  - Mironov, A.A.
AU  - Yankovskii, N.K.
AU  - Kozlov, Y.I.
AU  - Glatmann, L.I.
AU  - Moroz, A.F.
AU  - Debabov, V.G.
TI  - Isolation and characterization of a new site-specific endonuclease, EcoRV.
JO  - Dokl. Akad. Nauk.
PY  - 1980
SP  - 495
EP  - 497
VL  - 253
AB  - None
ER  -

TY  - JOUR
AU  - Kholodii, G.
TI  - The shuffling function of resolvases.
JO  - Gene
PY  - 2001
SP  - 121
EP  - 130
VL  - 269
AB  - Redistribution (shuffling) of genetic material between replicons requires
AB  - consecutive recombination at four points, two of which (X, X') are
AB  - involved in the replicon fusion and the other two (Y, Y'), in the
AB  - cointegrate resolution. The fusion of replicons by bacterial resolvases
AB  - makes the second recombination round at sites Y and Y' problematic because
AB  - of the high probability of the reverse reaction. Structural differences of
AB  - the res sites recognized by resolvase could delay the reverse reaction,
AB  - thus enhancing the probability of recombination at sites Y, Y', but the
AB  - direct reaction ensuring it (i.e. the fusion of replicons via different
AB  - res sites) has not been described yet. Here, a genetic system to test
AB  - intermolecular recombination at heterogeneous res sites has been
AB  - developed. The system was based on the res site (RS2) of the novel
AB  - resolution system, cinH-RS2, encoded by pKLH2, pKLH204 and pKLH205. As its
AB  - partner, the res site of RP4 located in the par locus, the res site of
AB  - transposon gammadelta or Tn1721, the incomplete site RS1 consisting only
AB  - of the (crossover) subsite resI also found in pKLH2/204/205 and others
AB  - were used. Except for the pairing of RS2 x gammadelta res, recombination
AB  - was observed in each case even when the homology shared by partners did
AB  - not exceed 35% (as in RS2 x par). In the latter case, the presence in cis
AB  - of an additional, enhancer-like-acting element was required. Pairing of
AB  - crossover subsites during site-specific recombination occurred in either
AB  - orientation, depending on the structure of res partners and the kind of
AB  - resolvase acting on the sites. With the complete res sites, the
AB  - antiparallel alignment resulted in the production of an unusual res having
AB  - the accessory subsites II and III at both sides of I, and a res lacking II
AB  - and III. The wide range of frequencies was observed not only in the fusion
AB  - formation but also in the dissociation of the resulting cointegrates.
AB  - Hence, the resolvase-mediated interreplicon exchange of the DNA segments
AB  - by fusion via an inefficient reaction (at sites X, X') and dissociation
AB  - via an efficient one (at sites Y, Y') become possible.
ER  -

TY  - JOUR
AU  - Khong, W.X. et al.
TI  - Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches.
JO  - J. Antimicrob. Chemother.
PY  - 2016
SP  - 3081
EP  - 3089
VL  - 71
AB  - OBJECTIVES: Owing to gene transposition and plasmid conjugation, New Delhi
AB  - metallo-beta-lactamase (NDM) is typically identified among varied
AB  - Enterobacteriaceae species and STs. We used WGS to characterize the chromosomal
AB  - and plasmid molecular epidemiology of NDM transmission involving four
AB  - institutions in Singapore. METHODS: Thirty-three Enterobacteriaceae isolates
AB  - (collection years 2010-14) were sequenced using short-read
AB  - sequencing-by-synthesis and analysed. Long-read single molecule, real-time
AB  - sequencing (SMRTS) was used to characterize genetically a novel plasmid pSg1-NDM
AB  - carried on Klebsiella pneumoniae ST147. RESULTS: In 20 (61%) isolates, blaNDM was
AB  - located on the pNDM-ECS01 plasmid in the background of multiple bacterial STs,
AB  - including eight K. pneumoniae STs and five Escherichia coli STs. In six (18%)
AB  - isolates, a novel blaNDM-positive plasmid, pSg1-NDM, was found only in K.
AB  - pneumoniae ST147. The pSg1-NDM-K. pneumoniae ST147 clone (Sg1-NDM) was fully
AB  - sequenced using SMRTS. pSg1-NDM, a 90 103 bp IncR plasmid, carried genes
AB  - responsible for resistance to six classes of antimicrobials. A large portion of
AB  - pSg1-NDM had no significant homology to any known plasmids in GenBank. pSg1-NDM
AB  - had no conjugative transfer region. Combined chromosomal-plasmid phylogenetic
AB  - analysis revealed five clusters of clonal bacterial NDM-positive plasmid
AB  - transmission, of which two were inter-institution clusters. The largest
AB  - inter-institution cluster involved six K. pneumoniae ST147-pSg1-NDM isolates.
AB  - Fifteen patients were involved in transmission clusters, of which four had ward
AB  - contact, six had hospital contact and five had an unknown transmission link.
AB  - CONCLUSIONS: A combined sequencing-by-synthesis and SMRTS approach can determine
AB  - effectively the transmission clusters of blaNDM and genetically characterize
AB  - novel plasmids. Plasmid molecular epidemiology is important to understanding NDM
AB  - spread as blaNDM-positive plasmids can conjugate extensively across species and
AB  - STs.
ER  -

TY  - JOUR
AU  - Khosaka, T.
AU  - Kiwaki, M.
TI  - Restriction endonucleases from Bifidobacterium bifidum.
JO  - FEBS Lett.
PY  - 1984
SP  - 57
EP  - 60
VL  - 177
AB  - Three restriction endonucleases, BbiI, BbiII and BbiIII, have been isolated
AB  - from Bifidobacterium bifidum.  The recognition and cleavage specificity of
AB  - BbiII was determined to be 5'-GR^CGYC-3', identical to that of AcyI isolated
AB  - from a cyanobacterium Anabaena cylindrica.  The other two enzymes, BbiI and
AB  - BbiIII, were found to be isoschizomers of PstI and XhoI, respectively.
ER  -

TY  - JOUR
AU  - Khosaka, T.
AU  - Kiwaki, M.
TI  - BinI: A new site-specific endonuclease from Bifidobacterium infantis.
JO  - Gene
PY  - 1984
SP  - 251
EP  - 255
VL  - 31
AB  - A new restriction endonuclease, BinI, from Bifidobacterium infantis 659 has
AB  - been isolated.  By mapping and sequencing of the cleavage sites on SV40 DNA, it
AB  - was deduced that BinI recognizes the asymmetric pentanucleotide sequence
AB  - 5'-GGATCNNNN^-3'3'-CCTAGNNNNN^5'and cleaves at the sites indicated by the
AB  - arrows, generating mononucleotide 5'-terminal extensions.  BinI is a member of
AB  - a unique class of Type-II restriction endonucleases which recognize a specific
AB  - but asymmetric sequence and cleave at a site several bases away.
ER  -

TY  - JOUR
AU  - Khosaka, T.
AU  - Kiwaki, M.
AU  - Rak, B.
TI  - Two site-specific endonucleases BinSI and BinSII from Bifidobacterium infantis.
JO  - FEBS Lett.
PY  - 1983
SP  - 170
EP  - 174
VL  - 163
AB  - Two site-specific endonucleases, BinSI and BinSII, were isolated from
AB  - Bifidobacterium infantis S76e.  BinSI was found to be an isoschizomer of EcoRII, while
AB  - BinSII was shown to have the same sequence and cutting specificity as BbeI, 5'-
AB  - GGCGCC-3'.  Both BinSII- and BbeI-generated DNA fragments could be ligated with
AB  - HaeII-generated DNA fragments.
ER  -

TY  - JOUR
AU  - Khosaka, T.
AU  - Sakurai, T.
AU  - Takahashi, H.
AU  - Saito, H.
TI  - A new site-specific endonuclease BbeI from Bifidobacterium breve.
JO  - Gene
PY  - 1982
SP  - 117
EP  - 122
VL  - 17
AB  - A new site-specific endonuclease, BbeI, has been partially purified from the
AB  - anerobic bacterium, Bifidobacterium breve.  BbeI recognizes the hexanucleotide
AB  - sequence5'-GGCGC^C-3' 3'-C^CGCGG-5'and cleaves it at the sites indicated by the
AB  - arrows, producing 3'-cohesive termini four bases long.
ER  -

TY  - JOUR
AU  - Khosravi, Y.
AU  - Rehvathy, V.
AU  - Wee, W.Y.
AU  - Wang, S.
AU  - Baybayan, P.
AU  - Singh, S.
AU  - Ashby, M.
AU  - Ong, J.
AU  - Amoyo, A.A.
AU  - Seow, S.W.
AU  - Choo, S.W.
AU  - Perkins, T.
AU  - Chua, E.G.
AU  - Tay, A.
AU  - Marshall, B.J.
AU  - Loke, M.F.
AU  - Goh, K.L.
AU  - Pettersson, S.
AU  - Vadivelu, J.
TI  - Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives.
JO  - Gut Pathog.
PY  - 2013
SP  - 25
EP  - 25
VL  - 5
AB  - Background: Helicobacter pylori is a Gram-negative bacterium that persistently infects the
AB  - human stomach inducing chronic inflammation.
AB  - The exact mechanisms of pathogenesis are still not completely
AB  - understood. Although not a natural host for H. pylori, mouse infection
AB  - models play an important role in establishing the immunology and
AB  - pathogenicity of H. pylori. In this study, for the first time, the
AB  - genome sequences of clinical H. pylori strain UM032 and mice-adapted
AB  - derivatives, 298 and 299, were sequenced using the PacBio Single
AB  - Molecule, Real-Time (SMRT) technology.
AB  - Result: Here, we described the single contig which was achieved for
AB  - UM032 (1,599,441 bp), 298 (1,604,216 bp) and 299 (1,601,149 bp).
AB  - Preliminary analysis suggested that methylation of H. pylori genome
AB  - through its restriction modification system may be determinative of its
AB  - host specificity and adaptation.
AB  - Conclusion: Availability of these genomic sequences will aid in
AB  - enhancing our current level of understanding the host specificity of H.
AB  - pylori.
ER  -

TY  - JOUR
AU  - Khudyakov, I.Y.
AU  - Kirnos, M.D.
AU  - Aleksandrushkina, N.I.
AU  - Vanyushin, B.F.
TI  - 2,6-Diaminopurine - a new adenine-replacing base in the DNA of cyanophage S-2.
JO  - Dokl. Akad. Nauk.
PY  - 1977
SP  - 965
EP  - 968
VL  - 232
AB  - By now only some of the physicochemical properties of extremely few viruses of
AB  - blue-green algae-cyanophages-have been studied.  Unfortunately, the information
AB  - on the nucleotide composition of the DNA of cyanophages is based only on a
AB  - determination of the GC content according to the melting point and buoyant
AB  - density.  However, this does not permit a correct determination even of the
AB  - composition, if the DNA contains unusual and minor bases.  Unusual bases, which
AB  - can entirely replace cytosine or thymine residues, have been found in the DNA
AB  - of many bacterial phages.  The DNAs of cyanophages have not been studied at all
AB  - in this respect.  Moreover, it is unknown whether these DNAs contain the
AB  - modified residues of the usual bases, characterisitic of many prokaryotes and
AB  - responsible for host modification and restriction.  It is also unclear whether
AB  - host restriction and modification analogous to that in bacteria exist in
AB  - blue-green algae and cyanophages.  Therefore, a study of the intrinsic nature
AB  - of the bases in the DNA of cyanophages is of special interest.  In this work we
AB  - studied the composition and some physicochemical properties of the DNA of a new
AB  - cyanophage S-2, which lyses the blue-green alga Synechococcus sp. 698 (from the
AB  - collection of the Biological Institute of Leningrad University).  We isolated
AB  - this cyanophage from aquatic samples, taken in the environs of Leningrad.  It
AB  - consists of an icosahedral head 56 nm in diameter and a flexible,
AB  - noncontractile tail process 120 nm long.  The phage was concentrated by
AB  - chromatography on DEAE-cellulose (Whatman DE32) and purified by centrifuging in
AB  - a CsCl gradient.  The cyanophage DNA was isolated by a phenol method.
ER  -

TY  - JOUR
AU  - Khudyakov, I.Y.
AU  - Kirnos, M.D.
AU  - Alexandrushkina, N.I.
AU  - Vanyushin, B.F.
TI  - Cyanophage S-2L contains DNA with 2,6-diaminopurine substituted for adenine.
JO  - Virology
PY  - 1978
SP  - 8
EP  - 18
VL  - 88
AB  - Cyanophage S-2L, which lyses some strains of unicellular cyanobacteria of the
AB  - genus Synechococcus, has a polyhedral head 56 nm in diameter and a flexible
AB  - noncontractile tail 120 nm in length.  In S-2L phage DNA, 2,6-diaminopurine is
AB  - completely substituted for adenine.  This base and the corresponding
AB  - deoxyribonucleoside have been isolated from acid and enzymatic hydrolyzates of
AB  - the phage DNA, respectively, and have been identified according to optical and
AB  - chromatographic behavior.  S-2L phage DNA is linear and double-stranded and has
AB  - a molecular weight of 26 to 28,000000.  The buoyant density of this DNA is CsCl
AB  - is 1.731 g/cm3.  2,6-Diaminopurine stabilizes the secondary structure of phage
AB  - DNA, i.e., the melting temperature of the latter (Tm is 85.6 degrees in
AB  - 0.1xSSC) is 3.6 degrees higher than that of the usual adenine-containing DNA of
AB  - equivalent base composition.
ER  -

TY  - JOUR
AU  - Kiatpapan, P.
AU  - Murooka, Y.
TI  - Genetic manipulation system in propionibacteria.
JO  - J. Biosci. Bioeng.
PY  - 2002
SP  - 1
EP  - 8
VL  - 93
AB  - Members of the genus Propionibacterium are widely used in the production of vitamin B12'
AB  - tetrapyrrole compounds, and propionic acid
AB  - as well as in the probiotic and cheese industries. Shuttle vectors were
AB  - developed in propionibacteria using replicons from endogenous plasmids
AB  - in Propionibacterium and Escherichia coli and an appropriate selection
AB  - marker. Efficient transformation was achieved using the shuttle
AB  - vector prepared from Propionibacterium freudenreichii to overcome the
AB  - high restriction modification system in propionibacteria. Expression
AB  - vectors with native promoters for use in propionibacteria were also
AB  - developed. Using this system, cholesterol oxidase, which is used as a
AB  - diagnostic enzyme, was produced in P freudenreichii. Genes involved in
AB  - 5-aminolevulinic acid (ALA) and vitamin 13, biosynthesis in
AB  - propionibacteria were isolated. ALA in propionibacteria could be
AB  - synthesized via both the C4 pathway (condensation of glycine and
AB  - succinyl CoA) and the C5 pathway (from glutamate). The hemA gene
AB  - encoding ALA synthase from Rhodobacter spheroides, was overexpressed
AB  - and ALA accumulated in P. freudenreichii. Thus, the genetic manipulation
AB  - systems in propionibacteria will facilitate genetic studies of
AB  - probioties and the vitamin B-12 biosynthetic pathway.
ER  -

TY  - JOUR
AU  - Kibret, M.
AU  - Guerrero-Garzon, J.F.
AU  - Urban, E.
AU  - Zehl, M.
AU  - Wronski, V.K.
AU  - Ruckert, C.
AU  - Busche, T.
AU  - Kalinowski, J.
AU  - Rollinger, J.M.
AU  - Abate, D.
AU  - Zotchev, S.B.
TI  - Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry.
JO  - Front. Microbiol.
PY  - 2018
SP  - 1270
EP  - 1270
VL  - 9
AB  - A total of 416 actinomycete cultures were isolated from various unique
AB  - environments in Ethiopia and tested for bioactivity. Six isolates with pronounced
AB  - antimicrobial activity were chosen for taxonomic identification and further
AB  - investigation. Morphological and cultural properties of the isolates were found
AB  - to be consistent with those of the genus Streptomyces, which was further
AB  - confirmed by phylogenetic analysis based on 16S rRNA gene sequences. One of the
AB  - isolates, designated Streptomyces sp. Go-475, which displayed potent activity
AB  - against both pathogenic yeasts and Gram-positive bacteria, was chosen for further
AB  - investigation. Metabolite profiles and bioactivity of Go-475 incubated on wheat
AB  - bran-based solid and soya flour-based liquid media were compared using
AB  - high-resolution LC-MS. This allowed identification of several known compounds,
AB  - and suggested the ability of Go-475 to produce new secondary metabolites. Major
AB  - anti-bacterial compounds were purified from liquid cultures of Go-475, and their
AB  - structures elucidated by NMR and HRMS as 8-O-methyltetrangomycin and
AB  - 8-O-methyltetrangulol. In addition, many potentially novel metabolites were
AB  - detected, the majority of which were produced in solid media-based fermentation.
AB  - The genome sequence of Streptomyces sp. Go-475 was obtained using a hybrid
AB  - assembly approach of high quality Illumina short read and low quality Oxford
AB  - Nanopore long read data. The complete linear chromosome of 8,570,609 bp,
AB  - featuring a G+C content of 71.96%, contains 7,571 predicted coding sequences, 83
AB  - t(m)RNA genes, and six rrn operons. Analysis of the genome for secondary
AB  - metabolite biosynthesis gene clusters further confirmed potential of this isolate
AB  - to synthesize chemically diverse natural products, and allowed to connect certain
AB  - clusters with experimentally confirmed molecules.
ER  -

TY  - JOUR
AU  - Kidane, D.T.
AU  - Arivett, B.A.
AU  - Crigler, J.
AU  - Vick, E.J.
AU  - Farone, A.L.
AU  - Farone, M.B.
TI  - Draft Genome Sequence of Gardnerella vaginalis Strain ATCC 49145 Associated with  Bacterial Vaginosis.
JO  - Genome Announcements
PY  - 2017
SP  - e00286
EP  - e00217
VL  - 5
AB  - Gardnerella vaginalis is a Gram-variable bacterium associated with bacterial vaginosis, a
AB  - common vaginal inflammation in women of reproductive age. This study
AB  - reports the whole-genome sequencing for the clinical isolate strain ATCC 49145.
AB  - The draft genome is composed of 21 contigs containing 1,325 protein-coding
AB  - sequences, 45 tRNAs and a single tmRNA (SsrA).
ER  -

TY  - JOUR
AU  - Kidanemariam, G.A.
AU  - Bihon, W.
AU  - Faranani, R.
AU  - Mafofo, J.
AU  - Rees, J.
AU  - Madoroba, E.
TI  - Complete Genome Sequence of Mannheimia haemolytica Strain Mh10517, Isolated from  Sheep in South Africa.
JO  - Genome Announcements
PY  - 2015
SP  - e00129
EP  - e00115
VL  - 3
AB  - Respiratory disease caused by Mannheimia haemolytica is a major concern in the cattle and
AB  - small stock industry worldwide. This problem arises due to the
AB  - interaction of numerous contributing factors, including physical stresses
AB  - associated with weaning, shipment, inclement weather, and overcrowding coupled
AB  - with viral and bacterial infections. The whole genome of M. haemolytica strain
AB  - Mh10517 was analyzed using an Illumina MiSeq high-throughput sequencing platform.
AB  - The genome size is 2.67 Mb with 2,879 predicted gene sequences. The availability
AB  - of this genome sequence will advance studies on various aspects of the biology of
AB  - M. haemolytica in Africa and the world at large.
ER  -

TY  - JOUR
AU  - Kienesberger, S.
AU  - Sprenger, H.
AU  - Wolfgruber, S.
AU  - Halwachs, B.
AU  - Thallinger, G.G.
AU  - Perez-Perez, G.I.
AU  - Blaser, M.J.
AU  - Zechner, E.L.
AU  - Gorkiewicz, G.
TI  - Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity.
JO  - PLoS ONE
PY  - 2014
SP  - E85491
EP  - E85491
VL  - 9
AB  - Campylobacter fetus are important animal and human pathogens and the two major
AB  - subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is
AB  - highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus
AB  - subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract
AB  - of animals and humans. We report the complete genomic sequence of C. fetus subsp.
AB  - venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40.
AB  - Functional analysis of genes predicted to be involved in C. fetus virulence was
AB  - performed. The two subspecies are highly syntenic with 92% sequence identity but
AB  - C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element.
AB  - Aside from apparent gene transfer agents and hypothetical proteins, the unique
AB  - genes in both subspecies comprise two known functional groups: lipopolysaccharide
AB  - production, and type IV secretion machineries. Analyses of
AB  - lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to
AB  - particular pathotypes, and mutational inactivation demonstrated their roles in
AB  - regulating virulence and host range. The comparative analysis presented here
AB  - broadens knowledge of the genomic basis of C. fetus pathogenesis and host
AB  - specificity. It further highlights the importance of surface-exposed structures
AB  - to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the
AB  - fitness and host-adaptation of these pathogens.
ER  -

TY  - JOUR
AU  - Kieser, T.
AU  - Hopwood, D.A.
TI  - Genetic manipulation of Streptomyces: integrating vectors and gene replacement.
JO  - Methods Enzymol.
PY  - 1991
SP  - 430
EP  - 458
VL  - 204
AB  - The Streptomyces chromosome is a circle of about 72% G + C DNA at
AB  - least 1.5 times the size of the Escherichia coli chromosome.~ Streptomyces
AB  - coelicolor A3(2) is genetically by far the most studied streptomycete, with
AB  - a detailed chromosomal linkage map 2 and a combined physical/genetic
AB  - map based on pulsed-field gel analysis of large fragments generated by
AB  - enzymes that recognize permutations of the sequence A3T3 such as AseI,
AB  - DraI, and SspI. 3 In S. coelicolor fundamental studies of differentiation,
AB  - antibiotic production, and many other aspects of cell and molecular biology are being made by
AB  - a combination of in vivo and in vitro genetics.4,5 As
AB  - well as being amenable to a wide range of in vivo genetic procedures, the
AB  - A3(2) strain is an excellent host for the homologous cloned DNA required
AB  - for many of these studies. However, S. coelicolor shows very strong
AB  - restriction against DNA from E. coli, so the closely related Streptomyces
AB  - lividans 66 has been used for most heterologous cloning. 6-8 Streptomyces
AB  - lividans is largely nonrestricting and has the added advantage that it can
AB  - be used as an intermediate host for cloned DNA manipulated in E. coli
AB  - and destined for S. coelicolor A3(2). [Streptomyces coelicolor A3(2) has a
AB  - methylation-dependent restriction system. Bifunctional plasmids isolated
AB  - from a completely nonmethylating (Dam- Dcm- HsdS-) strain of E. coli
AB  - transform S. coelicolor. 9 This approach first succeeded for Streptomyces
AB  - avermitilis, which has methylation-dependent restriction systems. ~o]
AB  - Whether the recently discovered ability of some E. coli plasmids to promote
AB  - conjugation with Streptomyces, leading to plasmid transfer, u will
AB  - alleviate restriction barriers remains to be seen, but it clearly has some
AB  - other interesting practical implications. Differences between S. coelicolor
AB  - and S. lividans are listed in Table I.
ER  -

TY  - JOUR
AU  - Kilgore, J.A.
AU  - Hoose, S.A.
AU  - Gustafson, T.L.
AU  - Porter, W.
AU  - Kladde, M.P.
TI  - Single-molecule and population probing of chromatin structure using DNA methyltransferases.
JO  - Methods
PY  - 2007
SP  - 320
EP  - 332
VL  - 41
AB  - Probing chromatin structure with DNA methyltransferases offers advantages over more commonly
AB  - used nuclease-based and chromatin
AB  - immunoprecipitation methods for detection of nucleosomes and
AB  - non-histone protein DNA interactions. Here, we describe two related
AB  - methods in which the readout of MTase accessibility is obtained by
AB  - assaying 5-methylcytosine in DNA through the PCR-based technique of
AB  - bisulfite genomic sequencing. The methyltransferase accessibility
AB  - protocol (MAP) determines the relative frequency at which the enzyme
AB  - accesses each of its target sites over an entire population of PCR
AB  - amplified product. While MAP yields much quantitative information about
AB  - relative accessibility of a region of chromatin, a complementary
AB  - single-molecule view of methyltransferase accessibility, termed MAP for
AB  - individual templates (MAP-IT), is provided by analysis of cloned PCR
AB  - products. Absolute rather than relative methylation frequencies in a
AB  - region are obtained by summing the methylation status at each site over
AB  - a cohort of clones. Moreover, as the integrity of individual molecules
AB  - is maintained in MAP-IT, unique information about the distribution of
AB  - multiple footprints along continuous regions is gleaned. In principle,
AB  - the population MAP and single-molecule MAP-IT strategies can be used to
AB  - analyze chromatin structure in a variety of model systems. Here, we
AB  - describe the application of MAP in living Saccharomyces cerevisiae
AB  - cells and MAP-IT in the analysis of a mammalian tumor suppressor gene
AB  - in nuclei. This application of MAP-IT provides the first means to
AB  - simultaneously determine CpG methylation of mammalian genes and their
AB  - overlying chromatin structure in the same single DNA molecule.
ER  -

TY  - JOUR
AU  - Kim, A.
AU  - Nguyen, T.L.
AU  - Kim, D.H.
TI  - Complete Genome Sequence of the Virulent Aeromonas salmonicida subsp. masoucida Strain RFAS1.
JO  - Genome Announcements
PY  - 2018
SP  - e00470
EP  - e00418
VL  - 6
AB  - Here, we report the complete genome sequence of the pathogenic Aeromonas salmonicida subsp.
AB  - masoucida strain RFAS1, isolated from black rockfish and
AB  - showing signs of furunculosis. Sequencing with the PacBio platform yielded a
AB  - circular chromosome of 4,783,004 bp and two plasmids (70,968 bp and 63,563 bp)
AB  - harboring 4,411, 67, and 71 protein-coding genes, respectively.
ER  -

TY  - JOUR
AU  - Kim, B.
AU  - Kim, J.
AU  - Park, H.
AU  - Park, J.
TI  - Draft Genome Sequence of Toluene-Resistant Staphylococcus epidermidis SNUT.
JO  - Genome Announcements
PY  - 2016
SP  - e00057
EP  - e00016
VL  - 4
AB  - Here, we report draft sequence of the Gram-positive toluene-resistant bacterium Staphylococcus
AB  - epidermidis SNUT. The draft genome sequence is 2,511,658 bases,
AB  - with 2,346 protein-coding genes, 57 tRNA-coding genes, and 8 rRNA genes.
ER  -

TY  - JOUR
AU  - Kim, B.-J.
AU  - Choi, B.S.
AU  - Lim, J.S.
AU  - Choi, I.Y.
AU  - Lee, J.H.
AU  - Chun, J.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Complete Genome Sequence of Mycobacterium intracellulare Strain ATCC 13950T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2750
EP  - 2750
VL  - 194
AB  - Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC
AB  - 13950(T), a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a
AB  - valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of
AB  - the disparity between MAC members.
ER  -

TY  - JOUR
AU  - Kim, B.C.
AU  - Jeong, H.
TI  - Complete Genome Sequence of Methanobrevibacter smithii Strain KB11, Isolated from a Korean Fecal Sample.
JO  - Genome Announcements
PY  - 2018
SP  - e00038
EP  - e00018
VL  - 6
AB  - The archaeon Methanobrevibacter smithii is a major colonizer of the human gut.
AB  - Methanobrevibacter smithii strain KB11 was newly isolated from a Korean fecal
AB  - sample. Here, we present the complete genome sequence of strain KB11 and a brief
AB  - comparison with that of M. smithii type strain ATCC 35061(T).
ER  -

TY  - JOUR
AU  - Kim, B.J.
AU  - Choi, B.S.
AU  - Choi, I.Y.
AU  - Lee, J.H.
AU  - Chun, J.
AU  - Hong, S.H.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-36Y, Belonging to the INT5 Genotype.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4141
EP  - 4142
VL  - 194
AB  - Here we report the complete genome sequence of the Mycobacterium intracellulare clinical
AB  - strain MOTT-36Y, previously grouped into the INT5 genotype among the 5
AB  - genotypes of M. intracellulare. This genome sequence will serve as a valuable
AB  - reference for understanding the disparity in virulence and epidemiologic traits
AB  - between M. intracellulare-related strains.
ER  -

TY  - JOUR
AU  - Kim, B.J.
AU  - Choi, B.S.
AU  - Lim, J.S.
AU  - Choi, I.Y.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-64, Belonging to the INT1 Genotype.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3268
EP  - 3268
VL  - 194
AB  - Here, we report the complete genome sequence of the Mycobacterium intracellulare  clinical
AB  - strain MOTT-64, previously grouped into the INT1 genotype among five
AB  - genotypes of M. intracellulare. This genome sequence will serve as a valuable
AB  - reference for understanding the disparity in the virulence and epidemiologic
AB  - traits among M. intracellulare genotypes.
ER  -

TY  - JOUR
AU  - Kim, B.J.
AU  - Choi, B.S.
AU  - Lim, J.S.
AU  - Choi, I.Y.
AU  - Lee, J.H.
AU  - Chun, J.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-02.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2771
EP  - 2771
VL  - 194
AB  - Here, we report the first complete genome sequence of the Mycobacterium intracellulare
AB  - clinical strain MOTT-02, which was previously grouped in the INT2
AB  - genotype of M. intracellulare. This genome sequence will serve as a valuable
AB  - reference for improving the understanding of the disparity in the virulence and
AB  - epidemiologic traits between M. intracellulare genotypes.
ER  -

TY  - JOUR
AU  - Kim, B.J.
AU  - Kim, B.R.
AU  - Hong, S.H.
AU  - Seok, S.H.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Complete Genome Sequence of Mycobacterium massiliense Clinical Strain Asan 50594, Belonging to the Type II Genotype.
JO  - Genome Announcements
PY  - 2013
SP  - e00429
EP  - e00413
VL  - 1
AB  - We report the complete genome sequence of the Mycobacterium massiliense clinical  strain Asan
AB  - 50594, which was grouped into the M. massiliense type II genotype,
AB  - isolated from a Korean patient. This genome sequence will serve as a valuable
AB  - reference for understanding the disparity in virulence and epidemiological traits
AB  - between strains belonging to the Mycobacterium abscessus complex.
ER  -

TY  - JOUR
AU  - Kim, B.J.
AU  - Kim, B.R.
AU  - Lee, S.Y.
AU  - Seok, S.H.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Whole-Genome Sequence of a Novel Species, Mycobacterium yongonense DSM 45126T.
JO  - Genome Announcements
PY  - 2013
SP  - e00604
EP  - e00613
VL  - 1
AB  - Here, we report the complete genome sequence of Mycobacterium yongonense DSM 45126(T),
AB  - genetically closely related to the INT5 genotype of M. intracellulare.
ER  -

TY  - JOUR
AU  - Kim, B.K.
AU  - Chung, J.H.
AU  - Kim, S.Y.
AU  - Jeong, H.
AU  - Kang, S.G.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Song, J.Y.
AU  - Yu, D.S.
AU  - Ryu, C.M.
AU  - Kim, J.F.
TI  - Genome Sequence of the Leaf-Colonizing Bacterium Bacillus sp. Strain 5B6, Isolated from a Cherry Tree.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3758
EP  - 3759
VL  - 194
AB  - Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here,
AB  - we present the high-quality draft genome sequence of Bacillus
AB  - sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb
AB  - genome uncovers its potential for understanding the nature of leaf colonization
AB  - as well as antibiosis against plant pathogens.
ER  -

TY  - JOUR
AU  - Kim, B.K.
AU  - Jung, M.Y.
AU  - Yu, D.S.
AU  - Park, S.J.
AU  - Oh, T.K.
AU  - Rhee, S.K.
AU  - Kim, J.F.
TI  - Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, 'Candidatus Nitrosoarchaeum koreensis' MY1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5539
EP  - 5540
VL  - 193
AB  - Ammonia-oxidizing archaea are ubiquitous microorganisms which play important
AB  - roles in global nitrogen and carbon cycle on earth. Here we present the
AB  - high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus
AB  - Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil
AB  - sample from the rhizosphere. Its genome contains genes for survival in the
AB  - rhizosphere environment as well as those for carbon fixation and ammonium
AB  - oxidation to nitrite.
ER  -

TY  - JOUR
AU  - Kim, B.K.
AU  - Lee, S.H.
AU  - Kim, S.Y.
AU  - Jeong, H.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Song, J.Y.
AU  - Yu, D.S.
AU  - Kang, S.G.
AU  - Kim, J.F.
TI  - Genome Sequence of an Oligohaline Hyperthermophilic Archaeon, Thermococcus zilligii AN1, Isolated from a Terrestrial Geothermal Freshwater Spring.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3765
EP  - 3766
VL  - 194
AB  - Thermococcus zilligii, a thermophilic anaerobe in freshwater, is useful for physiological
AB  - research and biotechnological applications. Here we report the
AB  - high-quality draft genome sequence of T. zilligii AN1(T). The genome contains a
AB  - number of genes for an immune system and adaptation to a microbial biomass-rich
AB  - environment as well as hydrogenase genes.
ER  -

TY  - JOUR
AU  - Kim, B.K.
AU  - Song, G.C.
AU  - Hong, G.H.
AU  - Seong, W.K.
AU  - Kim, S.Y.
AU  - Jeong, H.
AU  - Kang, S.G.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Song, J.Y.
AU  - Yu, D.S.
AU  - Park, M.S.
AU  - Cho, S.H.
AU  - Kim, J.F.
TI  - Genome Sequence of the Shiga Toxin-Producing Escherichia coli Strain NCCP15657.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3751
EP  - 3752
VL  - 194
AB  - Shiga toxin-producing Escherichia coli causes bloody diarrhea and hemolytic-uremic syndrome
AB  - and serious outbreaks worldwide. Here, we report the
AB  - draft genome sequence of E. coli NCCP15657 isolated from a patient. The genome
AB  - has virulence genes, many in the locus of enterocyte effacement (LEE) island,
AB  - encoding a metalloprotease, the Shiga toxin, and constituents of type III
AB  - secretion.
ER  -

TY  - JOUR
AU  - Kim, B.S.
AU  - Kim, C.T.
AU  - Park, B.H.
AU  - Kwon, S.
AU  - Cho, Y.J.
AU  - Kim, N.
AU  - Kim, C.J.
AU  - Chun, J.
AU  - Kwak, J.
AU  - Maeng, J.S.
TI  - Draft Genome Sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1,  Isolated from the Gills of a Korean Rockfish, Sebastes schlegeli Hilgendorf,  after High Hydrostatic Pressure Processing.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4441
EP  - 4442
VL  - 194
AB  - A bacterium designated M1-1 was isolated from the gills of a Korean rockfish, Sebastes
AB  - schlegeli Hilgendorf, after high hydrostatic pressure processing.
AB  - Studies of 16S rRNA phylogeny and comparative genomics demonstrated that the
AB  - isolate belongs to Staphylococcus saprophyticus subsp. saprophyticus. Here, we
AB  - report the draft genome sequence of S. saprophyticus subsp. saprophyticus M1-1
AB  - (KACC 16562).
ER  -

TY  - JOUR
AU  - Kim, B.Y.
AU  - Kwon, O.S.
AU  - Joo, S.A.
AU  - Park, J.A.
AU  - Heo, K.Y.
AU  - Kim, M.S.
AU  - Ahn, J.S.
TI  - A column method for determination of DNA cytosine-C-5-methyltransferase activity.
JO  - Anal. Biochem.
PY  - 2004
SP  - 21
EP  - 24
VL  - 326
AB  - DNA methylation at the 5th position of cytosine has been found to be correlated with
AB  - tumorigenesis. An inhibitor of DNA methylase could,
AB  - therefore, be used as an anticancer drug. However, only a few
AB  - inhibitory compounds have been discovered due to the limitations for
AB  - assaying the DNA methylation. In this study, we describe a modification
AB  - of DNA cytosine-C5-methyltransferase assay system utilizing
AB  - [H-3]-labeled S-adenosyl-methionine (SAM) and Sephadex G-25 column.
AB  - Pre-treatment of either lambda DNA or the promoter region of human
AB  - telomerase (hTERT) with HaeIII methylase greatly reduced the digestion
AB  - of the DNAs with the corresponding restriction enzyme HaeIII
AB  - endonuclease (over 100-fold), and the result was further confirmed by
AB  - agarose gel electrophoresis. Application of this column method to
AB  - another modification/restriction system, EcoRI methylase/endonuclease,
AB  - gave rise to the similar results. Our data suggest that the newly
AB  - developed column method could be effective for rapid screening of large
AB  - number of cytosine methylase inhibitors and could also be applicable to
AB  - other DNA methylases.
ER  -

TY  - JOUR
AU  - Kim, B.Y.
AU  - Lee, S.Y.
AU  - Ahn, J.H.
AU  - Song, J.
AU  - Kim, W.G.
AU  - Weon, H.Y.
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens subsp. plantarum CC178, a  Phyllosphere Bacterium Antagonistic to Plant Pathogenic Fungi.
JO  - Genome Announcements
PY  - 2015
SP  - e01368
EP  - e01314
VL  - 3
AB  - Bacillus amyloliquefaciens subsp. plantarum strain CC178 is a phyllosphere bacterium with
AB  - antagonistic activity against a wide range of plant fungal
AB  - pathogens. The genome of strain CC178 is 3,916,828 bp in size and harbors 3,972
AB  - genes. Six giant gene clusters are dedicated to the nonribosomal synthesis of
AB  - antimicrobial polypeptides and polyketides.
ER  -

TY  - JOUR
AU  - Kim, C.T.
AU  - Kim, B.S.
AU  - Kim, M.J.
AU  - Park, B.H.
AU  - Kwon, S.
AU  - Maeng, H.Y.
AU  - Kwak, J.
AU  - Chun, J.
AU  - Cho, Y.J.
AU  - Kim, N.
AU  - Kim, C.J.
AU  - Maeng, J.S.
TI  - Draft Genome Sequencing of Bacillus sp. Strain M2-6, Isolated from the Roots of Korean Ginseng, Panax ginseng C. A. Meyer, after High-Hydrostatic-Pressure  Processing.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7003
EP  - 7004
VL  - 194
AB  - A bacterium, designated M2-6, was isolated from Korean ginseng, Panax ginseng C.  A. Meyer,
AB  - roots after high-hydrostatic-pressure processing. On the basis of 16
AB  - rRNA gene phylogeny, the isolate was presumptively identified as a Bacillus sp.
AB  - Here we report the draft genome sequence of Bacillus sp. strain M2-6 (= KACC
AB  - 16563).
ER  -

TY  - JOUR
AU  - Kim, D.-S.
AU  - Jung, M.Y.
AU  - Sin, Y.
AU  - Kim, D.W.
AU  - Paek, J.
AU  - Kim, R.N.
AU  - Park, I.S.
AU  - Kook, J.K.
AU  - Nam, S.H.
AU  - Kim, A.
AU  - Kang, A.
AU  - Park, H.S.
AU  - Choi, S.H.
AU  - Chang, Y.H.
TI  - Genome Sequence of the Anaerobic Bacterium Clostridium arbusti SL206T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2758
EP  - 2758
VL  - 194
AB  - A new Clostridium species has been isolated from pear orchard soil in Daejeon, Republic of
AB  - Korea. The isolate, Clostridium arbusti SL206(T) (KCTC 5449(T)), showed a nitrogenase activity
AB  - as well as an organic acid production. Here we first report the draft genome sequence of a
AB  - novel species in the genus Clostridium within the largest Gram-positive group.
ER  -

TY  - JOUR
AU  - Kim, D.H.
AU  - Jiang, S.
AU  - Lee, J.H.
AU  - Cho, Y.J.
AU  - Chun, J.
AU  - Choi, S.H.
AU  - Park, H.S.
AU  - Hur, H.G.
TI  - Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5039
EP  - 5040
VL  - 193
AB  - The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to
AB  - produce novel photoactive As-S nanotubes via reduction
AB  - of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the
AB  - draft genome sequence and annotation of strain HN-41.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Nam, S.H.
AU  - Kang, A.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus cypricasei KCTC 13900.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5053
EP  - 5054
VL  - 193
AB  - Lactobacillus cypricasei KCTC 13900 is important in the generation of particular flavours and
AB  - in other ripening processes associated with
AB  - specific cheeses. Here we announce the draft genome sequence of
AB  - Lactobacillus cypricasei KCTC 13900, isolated from cheeses and describe
AB  - major findings from its annotation.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Nam, S.H.
AU  - Kang, A.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Leuconostoc gelidum KCTC 3527 Isolated from Kimchi.
JO  - J. Bacteriol.
PY  - 2010
SP  - 799
EP  - 800
VL  - 193
AB  - Leuconostoc gelidum KCTC 3527 is found mainly in vegetables and plays an important role in
AB  - vegetable fermentation, including that of Korean traditional kimchi. Here we announce the
AB  - draft genome sequence of Leuconostoc gelidum KCTC 3527, isolated from Korean traditional
AB  - kimchi and describe major findings from its annotation.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Nam, S.H.
AU  - Kang, A.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus versmoldensis KCTC 3814.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5589
EP  - 5590
VL  - 193
AB  - Lactobacillus versmoldensis KCTC 3814 was isolated from raw fermented poultry salami. The
AB  - species was present in high numbers and frequently
AB  - dominated the lactic acid bacteria (LAB) populations of the products.
AB  - Here, we announce the draft genome sequence of Lactobacillus versmoldensis
AB  - KCTC 3814, isolated from poultry salami, and describe major findings from
AB  - its annotation.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Nam, S.H.
AU  - Kang, A.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Leuconostoc inhae KCTC 3774 Isolated from Kimchi.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1278
EP  - 1279
VL  - 193
AB  - The Leuconostoc inhae KCTC 3774 strain is a gram-positive, non-spore-forming,
AB  - heterofermentative, spherical or lenticular lactic acid bacteria. Here we announce the draft
AB  - genome sequence of Leuconostoc inhae KCTC 3774, isolated from traditional Korean kimchi and
AB  - describe major findings from its annotation.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Kim, D.W.
AU  - Nam, S.H.
AU  - Kim, R.N.
AU  - Kang, A.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Weissella cibaria KACC 11862.
JO  - J. Bacteriol.
PY  - 2010
SP  - 797
EP  - 798
VL  - 193
AB  - The Weissella cibaria KACC 11862 is Gram-positive heterofermentative Leuconostoc-like lactic
AB  - acid bacteria and it is widely distributed in
AB  - Korean traditional foods such as kimchi. Here we report the draft genome
AB  - sequence of the type strain Weissella cibaria KACC 11862 (1,599 known
AB  - gene, 80 RNA), which consists of 72 large contigs (>100 bp in size).
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Jung, M.Y.
AU  - Kang, A.
AU  - Cho, J.
AU  - Sin, Y.
AU  - Paek, J.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Nam, S.H.
AU  - Kim, A.
AU  - Park, H.S.
AU  - Choi, S.H.
AU  - Chang, Y.H.
TI  - Genome Sequence of Peptoniphilus rhinitidis 1-13T, an Anaerobic Coccus Strain Isolated from Clinical Specimens.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2405
EP  - 2406
VL  - 194
AB  - A new Peptoniphilus species has been isolated from samples from a patient who was scheduled
AB  - for endoscopic sinus surgery for chronic rhinosinusitis. The isolate,
AB  - Peptoniphilus rhinitidis 1-13(T) (KCTC 5985(T)), can use peptone as a sole carbon
AB  - source and produce butyrate as a metabolic end product. This is the first report
AB  - of the draft genome sequence of a novel species in the genus Peptoniphilus within
AB  - the group of Gram-positive anaerobic cocci.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Kang, Y.K.
AU  - Yoo, O.J.
TI  - Effects of base analog substitutions in the sequence, CCGG, on the cleavage and methylation reactions of HpaII and MspI endonucleases and their cognate methylases.
JO  - Biochem. Mol. Biol. Int.
PY  - 1994
SP  - 507
EP  - 514
VL  - 32
AB  - HpaII endonuclease, HpaII methylase, MspI endonuclease, and MspI methylase were used to
AB  - investigate their specific interactions with the common recognition sequence, CCGG. Six
AB  - derivatives of the oligonucleotide, AGCCCGGGCT, containing a variety of single base analog
AB  - substitutions within the tetrameric recognition core were synthesized. Steady state kinetic
AB  - values for the reactions of all 4 enzymes with these oligonucleotide substrates were obtained.
AB  - Our data suggest that there are close contacts between the C5 positions of both cytosine
AB  - residues and the enzymes except that MspI endonuclease can accommodate a methyl group at the
AB  - C5 position of the second cytosine residue. The data also showed that minor groove
AB  - interactions between the 2-amino group of both G residues and the HpaII or MspI endonuclease
AB  - were essential for activity. However, these interactions were not essential for methylase
AB  - activity except that the oliogonucleotide substituted with inosine nucleotide at the first G
AB  - position did not react with MspI methylase.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Paek, J.
AU  - Shin, J.H.
AU  - Kim, D.W.
AU  - Jung, M.Y.
AU  - Kim, R.N.
AU  - Sin, Y.
AU  - Kook, J.K.
AU  - Nam, S.H.
AU  - Kim, A.
AU  - Kang, A.
AU  - Park, H.S.
AU  - Choi, S.H.
AU  - Chang, Y.H.
TI  - Genome Sequence of Myroides injenensis M09-0166T, Isolated from Clinical Specimens.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2748
EP  - 2749
VL  - 194
AB  - A new Myroides species has been isolated from the urine of a patient with fever in spite of
AB  - multiple antibiotic treatments who had undergone a radical
AB  - hysterectomy for cervical cancer and percutaneous nephrostomies for
AB  - hydronephrosis in the past. The isolate, Myroides injenensis M09-0166(T) (KCTC
AB  - 23367(T)), showed a high level of resistance to multiple antibiotic agents. Here
AB  - we provide the first report of the draft genome sequence of a novel species in
AB  - the genus Myroides within the nonfermenting Gram-negative group.
ER  -

TY  - JOUR
AU  - Kim, D.S.
AU  - Sin, Y.
AU  - Kim, D.W.
AU  - Paek, J.
AU  - Kim, R.N.
AU  - Jung, M.Y.
AU  - Park, I.S.
AU  - Kim, A.
AU  - Kang, A.
AU  - Park, H.S.
AU  - Choi, S.H.
AU  - Chang, Y.H.
TI  - Genome Sequence of the Probiotic Bacterium Sporolactobacillus vineae SL153T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3015
EP  - 3016
VL  - 194
AB  - The novel Sporolactobacillus vineae SL153(T) strain has excellent intestinal adherence and
AB  - growth inhibitory effect on pathogenic microorganisms, including
AB  - Vibrio genus microorganisms, and therefore can be effectively used for the
AB  - prevention and treatment of disease caused by pathogenic microorganisms. Here, we
AB  - first report the draft genome sequence of a novel species in the genus
AB  - Sporolactobacillus.
ER  -

TY  - JOUR
AU  - Kim, D.W.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Nam, S.H.
AU  - Kim, D.S.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Draft Genome Sequence of Lactobacillus mali KCTC 3596.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5037
EP  - 5037
VL  - 193
AB  - We announce the draft genome sequence of the type strain Lactobacillus mali KCTC 3596
AB  - (2,652,969 bp, with a G+C content of 36.0%) that one of the
AB  - most prevalent lactic acid bacteria present during the manufacturing
AB  - process of Apple juice, which consists of 122 large contigs (>100 bp in
AB  - size). All of the contigs were assembled by Newbler Assembler 2.3 (454
AB  - Life Science).
ER  -

TY  - JOUR
AU  - Kim, D.W.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Nam, S.H.
AU  - Kim, D.S.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Draft Genome Sequence of Lactobacillus zeae KCTC 3804.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5023
EP  - 5023
VL  - 193
AB  - We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804
AB  - (3,110,326 bp, with a G+C content of 47.8%), which is one
AB  - of the most prevalent lactic acid bacteria present during the processing
AB  - of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All
AB  - of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).
ER  -

TY  - JOUR
AU  - Kim, D.W.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Nam, S.H.
AU  - Kim, D.S.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Draft Genome Sequence of Lactobacillus malefermentans KCTC 3548.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5537
EP  - 5537
VL  - 193
AB  - We announce the draft genome sequence of the type strain Lactobacillus malefermentans KCTC
AB  - 3548 (2,003,922 bp, with a G+C content of 41.1%),
AB  - which is one of the most prevalent lactic acid bacteria present during the
AB  - manufacturing process of beer; the genome consists of 172 large contigs
AB  - (>100 bp in size). All of the contigs were assembled by using Newbler
AB  - Assembler 2.3 (454 Life Science).
ER  -

TY  - JOUR
AU  - Kim, D.W.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Nam, S.H.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Kim, D.S.
AU  - Park, H.S.
TI  - Genome Sequence of Leuconostoc pseudomesenteroides KCTC 3652.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4299
EP  - 4299
VL  - 193
AB  - We announce the genome sequence of one of the most prevalent lactic acid bacteria present
AB  - during the manufacturing process of cane juice, the type
AB  - strain Leuconostoc pseudomesenteroides KCTC 3652 (3,244,985 bp, with a G+C
AB  - content of 38.3%), which consists of 1,160 large contigs (>100 bp in
AB  - size). All of the contigs were assembled by the Newbler Assembler 2.3
AB  - software program (454 Life Sciences).
ER  -

TY  - JOUR
AU  - Kim, E.
AU  - Kim, J.H.
AU  - Park, S.B.
AU  - Kim, M.J.
AU  - Kim, H.J.
AU  - Kim, C.G.
AU  - Choo, D.W.
AU  - Kim, H.Y.
TI  - Draft Genome Sequence of Pediococcus pentosaceus Strain FBL2, a Probiotic Bacterium Isolated from Jogaejeot, a Salted Fermented Food, in the Republic of  Korea.
JO  - Genome Announcements
PY  - 2017
SP  - e00303
EP  - e00317
VL  - 5
AB  - Pediococcus pentosaceus strain FBL2 is a lactic acid bacterium isolated in the Republic of
AB  - Korea from jogaejeot, a salted fermented food made with shellfish. P.
AB  - pentosaceus strain FBL2 comprised 54 contigs (>/=1 kb) and had a total draft
AB  - genome size of 1,934,229 bp with a G+C content of 37.2%.
ER  -

TY  - JOUR
AU  - Kim, E.
AU  - Kim, J.H.
AU  - Yang, S.M.
AU  - Suh, S.M.
AU  - Kim, H.J.
AU  - Kim, C.G.
AU  - Choo, D.W.
AU  - Kim, H.Y.
TI  - Draft Genome Sequence of Tetragenococcus halophilus Strain FBL3, a Probiotic Bacterium Isolated from Galchijeot, a Salted Fermented Food, in the Republic of  Korea.
JO  - Genome Announcements
PY  - 2017
SP  - e00304
EP  - e00317
VL  - 5
AB  - Tetragenococcus halophilus strain FBL3 is a lactic acid bacterium isolated from galchijeot, a
AB  - fermented food made from the salted guts of the hairtail fish, in
AB  - the Republic of Korea. The draft genome of T. halophilus strain FBL3 comprised 87
AB  - contigs (>/=1 kb) with a total size of 2,420,904 bp and a G+C content of 38.5%.
ER  -

TY  - JOUR
AU  - Kim, E.B.
AU  - Jin, G.D.
AU  - Lee, J.Y.
AU  - Choi, Y.J.
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain SNU.Lp177 from Pig Feces  in South Korea.
JO  - Genome Announcements
PY  - 2015
SP  - e01184
EP  - e01115
VL  - 3
AB  - Herein we report a draft genome sequence for Lactobacillus plantarum SNU.Lp177, which was
AB  - isolated from animal gut pig feces in South Korea. The draft genome of  L. plantarum SNU.Lp177
AB  - contains 3,204,772 bp with a G+C content of 44.98% in 101  contigs (N50 = 116,595 bp).
ER  -

TY  - JOUR
AU  - Kim, E.B.
AU  - Tyler, C.A.
AU  - Kopit, L.M.
AU  - Marco, M.L.
TI  - Draft Genome Sequence of Fructophilic Lactobacillus florum.
JO  - Genome Announcements
PY  - 2013
SP  - e00025
EP  - e00012
VL  - 1
AB  - Herein we report the first genome sequence for Lactobacillus florum. L. florum 2F was isolated
AB  - from Valencia orange leaves and is fructophilic, like other strains of this species. The draft
AB  - genome of L. florum 2F contains 1,261,842 bp with a G+C content of 41.5% in 46 contigs (>/=500
AB  - bp).
ER  -

TY  - JOUR
AU  - Kim, E.K.
AU  - Kim, S.H.
AU  - Nam, H.J.
AU  - Choi, M.K.
AU  - Lee, K.A.
AU  - Choi, S.H.
AU  - Seo, Y.Y.
AU  - You, H.
AU  - Kim, B.
AU  - Lee, W.J.
TI  - Draft Genome Sequence of Gluconobacter morbifer G707T, a Pathogenic Gut Bacterium Isolated from Drosophila melanogaster Intestine.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1245
EP  - 1245
VL  - 194
AB  - Gluconobacter morbifer G707(T), a minor member of gut microbiota, was isolated from fruit fly
AB  - (Drosophila melanogaster). Here, the draft genome sequence of
AB  - Gluconobacter morbifer G707(T) is reported.
ER  -

TY  - JOUR
AU  - Kim, E.K.
AU  - Kim, S.H.
AU  - Nam, H.J.
AU  - Choi, M.K.
AU  - Lee, K.A.
AU  - Choi, S.H.
AU  - Seo, Y.Y.
AU  - You, H.
AU  - Kim, B.
AU  - Lee, W.J.
TI  - Draft Genome Sequence of Commensalibacter intestini A911T, a Symbiotic Bacterium  Isolated from Drosophila melanogaster Intestine.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1246
EP  - 1246
VL  - 194
AB  - Commensalibacter intestini A911(T), a predominant symbiotic bacterium capable of  stably
AB  - colonizing gut epithelia, was isolated from the fruit fly, Drosophila
AB  - melanogaster. Here we report the draft genome sequence of Commensalibacter
AB  - intestini A911(T).
ER  -

TY  - JOUR
AU  - Kim, E.K.
AU  - Park, Y.M.
AU  - Lee, O.Y.
AU  - Lee, W.J.
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain WJL, a Drosophila Gut Symbiont.
JO  - Genome Announcements
PY  - 2013
SP  - e00937
EP  - e00913
VL  - 1
AB  - Lactobacillus plantarum strain WJL, a member of the symbiotic gut bacteria, was isolated from
AB  - the intestine of the fruit fly, Drosophila melanogaster. Here, we
AB  - report the draft genome sequence of L. plantarum WJL.
ER  -

TY  - JOUR
AU  - Kim, E.L.
AU  - Makhovich, O.P.
AU  - Maliuta, S.S.
TI  - Some differences between BamHI and BnaI, the restrictases with the same specificity.
JO  - Biopol. Kletka
PY  - 1989
SP  - 86
EP  - 89
VL  - 5
AB  - The restriction endonuclease BnaI, being a BamHI true isoschizomer, is isolated from B. natto
AB  - B3364 strain. Its molecular weight, stability and optimal reaction conditions are studied.
AB  - Comparative investigations have shown that according to these physicochemical characteristics
AB  - the BamHI and BnaI enzymes differ from each other in spite of their analogous specificity.
ER  -

TY  - JOUR
AU  - Kim, E.L.
AU  - Maliuta, S.S.
TI  - A new isoschizomer, BnaI, of the BamHI restriction endonuclease.
JO  - Gene
PY  - 1989
SP  - 363
EP  - 368
VL  - 80
AB  - By assaying the yield of phage SPO1 we have identified a new
AB  - restriction-modification activity in the Bacillus natto B3364 strain.  A class
AB  - II restriction endonuclease, BnaI, isolated from the crude extract of B3364
AB  - cells was shown to be a true isoschizomer of the BamHI endonuclease.  The Mr,
AB  - stability and optimal conditions required for DNA digestion were determined for
AB  - BnaI.  Although both enzymes show the same specificity, BnaI and BamHI differ
AB  - from each other in all the properties specified above.
ER  -

TY  - JOUR
AU  - Kim, E.L.
AU  - Maliuta, S.S.
TI  - Purification of a DNA methyltransferase from Bacillus natto B3364.
JO  - FEBS Lett.
PY  - 1989
SP  - 361
EP  - 364
VL  - 255
AB  - An S-adenosyl-L-methionine: DNA-methyltransferase, termed M.BnaI, was purified from Bacillus
AB  - natto B3364 strain by successive column chromatography. The molecular weight determined by gel
AB  - filtration was 37 kDa for M.BnaI. Analysis of methyltransferase by sodium dodecyl
AB  - sulfate-polyacrylamide gel electrophoresis showed correspondence of the M.BnaI activity with
AB  - one protein band at a molecular weight of 35 kDa. Sequencing of pUC19 DNA methylated with
AB  - M.BnaI showed the cytosine-5 methylation in the BnaI recognition sequence GGAT^CC at the
AB  - position indicated by the arrow.
ER  -

TY  - JOUR
AU  - Kim, E.L.
AU  - Malyuta, S.S.
TI  - BnaI a new isoshisomer of the restrictase BamHI.
JO  - Biotekhnologiya
PY  - 1986
SP  - 24
EP  - 27
VL  - 4
AB  - Studies of restricted reproduction of phage SPO1 have disclosed a restriction-modification
AB  - system in the strain Bacillus natto B3364. Restriction endonuclease BnaI of class II has been
AB  - isolated and purified. BnaI has been shown to be a true isoschizomer of the restrictase BamHI.
ER  -

TY  - JOUR
AU  - Kim, E.M.
AU  - Hwang, K.H.
AU  - Park, J.S.
TI  - Complete Genome Sequence of Chryseobacterium camelliae Dolsongi-HT1, a Green Tea  Isolate with Keratinolytic Activity.
JO  - Genome Announcements
PY  - 2018
SP  - e01421
EP  - e01417
VL  - 6
AB  - The complete genome sequence of Chryseobacterium camelliae Dolsongi-HT1 is reported here. C.
AB  - camelliae Dolsongi-HT1, having keratinolytic activity, was
AB  - isolated from green tea leaves in the Dolsongi tea garden in Jeju, South Korea.
AB  - The strain Dolsongi-HT1 has 28 candidate protease genes, which may be utilized in
AB  - further studies and industrial applications of keratinase.
ER  -

TY  - JOUR
AU  - Kim, G.-D.
AU  - Ni, J.
AU  - Kelesoglu, N.
AU  - Roberts, R.J.
AU  - Pradhan, S.
TI  - Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases.
JO  - EMBO J.
PY  - 2002
SP  - 4183
EP  - 4195
VL  - 21
AB  - Three different families of DNA (cytosine-5) methyltransferases, DNMT1, DNMT3a and DNMT3b,
AB  - participate in establishing and maintaining genomic methylation patterns during mammalian
AB  - development. These enzymes have a large N-terminal domain fused to a catalytic domain. The
AB  - catalytic domain is homologous to prokaryotic (cytosine-5) methyltransferases and contains the
AB  - catalytic PC dipeptide, while the N-terminus acts as a transcriptional repressor by recruiting
AB  - several chromatin remodeling proteins. Here, we show that the human de novo enzymes hDNMT3a
AB  - and hDNMT3b form complexes with the major maintenance enzyme hDNMT1. Antibodies against hDNMT1
AB  - pull down both the de novo enzymes. Furthermore, the N-termini of the enzymes are involved in
AB  - protein-protein interactions. Immunocytochemical staining revealed mostly nuclear
AB  - co-localization of the fusion proteins, with the exception of hDNMT3a, which is found either
AB  - exclusively in cytoplasm or in both nucleus and cytoplasm. Pre-methylated substrate DNAs
AB  - exhibited differential methylation by de novo and maintenance enzymes. In vivo co-expression
AB  - of hDNMT1 and hDNMT3a or hDNMT3b leads to methylation spreading in the genome, suggesting
AB  - co-operation between de novo and maintenance enzymes during DNA methylation.
ER  -

TY  - JOUR
AU  - Kim, H.
AU  - Jeong, W.
AU  - Jeoung, H.Y.
AU  - Song, J.Y.
AU  - Kim, J.S.
AU  - Beak, J.H.
AU  - Parisutham, V.
AU  - Lee, S.K.
AU  - Kim, J.W.
AU  - Kim, J.Y.
AU  - Jung, S.C.
AU  - Her, M.
AU  - An, D.J.
TI  - Complete Genome Sequence of Brucella abortus A13334, a New Strain Isolated from the Fetal Gastric Fluid of Dairy Cattle.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5444
EP  - 5444
VL  - 194
AB  - Brucella abortus is a major pathogen that infects livestock and humans. A new strain of B.
AB  - abortus (A13334) was isolated from the fetal gastric fluid of a
AB  - dairy cow, with the aim of using it to compare genetic properties, analyze
AB  - virulence factor, and survey the epidemiological relationship to other Brucella
AB  - species. Here, we report the complete and annotated genome sequence of B. abortus
AB  - A13334.
ER  -

TY  - JOUR
AU  - Kim, H.H.
AU  - Corina, L.E.
AU  - Suh, J.K.
AU  - Herrin, D.L.
TI  - Expression, purification, and biochemical characterization of the intron-encoded endonuclease, I-CreII.
JO  - Protein Expr. Purif.
PY  - 2005
SP  - 162
EP  - 172
VL  - 44
AB  - The ORF of the Cr.psbA4 intron of Chlamydomonas reinhardtii mediates efficient intron homing,
AB  - and contains an H-N-H and possibly a GIY-YIG
AB  - motif. The ORF was over-expressed in Escherichia coli without
AB  - non-native amino acids, but was mostly insoluble. However,
AB  - co-over-expression of E coli chaperonins GroEL/GroES solubilized
AB  - similar to 50% of the protein, which was purified by ion-exchange and
AB  - heparin-affinity chromatography. Biochemical characterization showed
AB  - that the protein is a double-strand-specific endonuclease that cleaves
AB  - fused psbA exon 4-exon 5 DNA, and was named I-CreII. I-CreII has a
AB  - relatively relaxed divalent metal ion requirement (Mg2+, Mn2+, Ca2+,
AB  - and Fe2+ supported cleavage), is insensitive to salt < 350 mM, and is
AB  - stabilized by DNA. Cleavage of target DNA occurs close (4 nt on the top
AB  - strand) to the intron-insertion site, and leaves 2-nt 3'-OH overhangs,
AB  - similar to GIY-YIG endonucleases. The boundaries of the recognition
AB  - sequence span similar to 30 bp, and encompass the cleavage and
AB  - intron-insertion sites. Cleavage of heterologous psbA DNAs indicates
AB  - the enzyme can tolerate multiple, but not all, substitutions in the
AB  - recognition site. This work will facilitate further study of this novel
AB  - endonuclease, which may also find use in site-specific manipulation of
AB  - chloroplast DNA.
ER  -

TY  - JOUR
AU  - Kim, H.J.
AU  - Karki, S.
AU  - Kwon, S.Y.
AU  - Park, S.H.
AU  - Nahm, B.H.
AU  - Kim, Y.K.
AU  - Kwon, H.J.
TI  - A single module type I polyketide synthase directs de novo macrolactone biogenesis during galbonolide biosynthesis in Streptomyces galbus.
JO  - J. Biol. Chem.
PY  - 2014
SP  - 34557
EP  - 34568
VL  - 289
AB  - Galbonolide (GAL) A and B are antifungal macrolactone polyketides produced by
AB  - Streptomyces galbus. During their polyketide chain assembly, GAL-A and -B
AB  - incorporate methoxymalonate and methylmalonate, respectively, in the fourth chain
AB  - extension step. The methoxymalonyl-acyl carrier protein biosynthesis locus (galG
AB  - to K) is specifically involved in GAL-A biosynthesis, and this locus is
AB  - neighbored by a gene cluster composed of galA-E. GalA-C constitute a single
AB  - module, highly reducing type I polyketide synthase (PKS). GalD and GalE are
AB  - cytochrome P450 and Rieske domain protein, respectively. Gene knock-out
AB  - experiments verified that galB, -C, and -D are essential for GAL biosynthesis. A
AB  - galD mutant accumulated a GAL-C that lacked two hydroxyl groups and a double bond
AB  - when compared with GAL-B. A [U-(13)C]propionate feeding experiment indicated that
AB  - no rare precursor other than methoxymalonate was incorporated during GAL
AB  - biogenesis. A search of the S. galbus genome for a modular type I PKS system, the
AB  - type that was expected to direct GAL biosynthesis, resulted in the identification
AB  - of only one modular type I PKS gene cluster. Homology analysis indicated that
AB  - this PKS gene cluster is the locus for vicenistatin biosynthesis. This cluster
AB  - was previously reported in Streptomyces halstedii. A gene deletion of the vinP2
AB  - ortholog clearly demonstrated that this modular type I PKS system is not involved
AB  - in GAL biosynthesis. Therefore, we propose that GalA-C direct macrolactone
AB  - polyketide formation for GAL. Our studies provide a glimpse into a novel
AB  - biochemical strategy used for polyketide synthesis; that is, the iterative
AB  - assembly of propionates with highly programmed beta-keto group modifications.
ER  -

TY  - JOUR
AU  - Kim, H.J.
AU  - Kim, J.H.
AU  - Jun, J.W.
AU  - Giri, S.S.
AU  - Chi, C.
AU  - Yun, S.
AU  - Kim, S.G.
AU  - Kim, S.W.
AU  - Kang, J.W.
AU  - Jeong, D.G.
AU  - Park, S.C.
TI  - Complete Genome Sequence of Vibrio coralliilyticus 58, Isolated from Pacific Oyster (Crassostrea gigas) Larvae.
JO  - Genome Announcements
PY  - 2017
SP  - e00437
EP  - e00417
VL  - 5
AB  - We report here the complete genome of Vibrio coralliilyticus strain 58, which was originally
AB  - isolated from inactive Pacific oyster (Crassostrea gigas) larvae in
AB  - Japan. The assembled genome consisted of two chromosomes and one plasmid. These
AB  - data will provide valuable information and important insights into the
AB  - biodiversity of this organism.
ER  -

TY  - JOUR
AU  - Kim, H.J.
AU  - Lee, J.H.
AU  - Kang, B.R.
AU  - Rong, X.
AU  - McSpadden, G.B.B.
AU  - Ji, H.J.
AU  - Park, C.S.
AU  - Kim, Y.C.
TI  - Draft Genome Sequence of Pantoea ananatis B1-9, a Nonpathogenic Plant Growth-Promoting Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 729
EP  - 729
VL  - 194
AB  - Pantoea ananatis B1-9 is an endophytic Gram-negative rhizobacterium that was isolated for its
AB  - ability to promote plant growth and improve crop
AB  - yield in the field. Here we report the draft genome sequence of P.
AB  - ananatis B1-9. Comparison of this sequence to the sequenced genome of a
AB  - plant-pathogenic P. ananatis strain, LMG20103, indicated that the
AB  - pathogenesis-related genes were absent, but a subset of gene functions
AB  - that may be related to its plant growth promotion were present.
ER  -

TY  - JOUR
AU  - Kim, H.J.
AU  - Park, J.Y.
AU  - Han, S.H.
AU  - Lee, J.H.
AU  - Rong, X.
AU  - McSpadden, G.B.B.
AU  - Park, S.K.
AU  - Kim, Y.C.
TI  - Draft Genome Sequence of the Biocontrol Bacterium Chromobacterium sp. Strain C-61.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6803
EP  - 6804
VL  - 193
AB  - Chromobacterium sp. strain C-61 is a plant-associated bacterium with proven capacities to
AB  - suppress plant diseases. Here, we report the draft
AB  - genome sequence and automatic annotation of strain C-61. A comparison of
AB  - this sequence to the sequenced genome of Chromobacterium violaceum ATCC
AB  - 12472 indicates the novelty of C-61 and a subset of gene functions that
AB  - may be related to its biocontrol activities.
ER  -

TY  - JOUR
AU  - Kim, H.J.
AU  - Yano, A.
AU  - Wada, Y.
AU  - Sano, H.
TI  - Properties of a tobacco DNA methyltransferase, NtMET1 and its involvement in chromatin movement during cell division.
JO  - Ann. Bot.
PY  - 2007
SP  - 845
EP  - 856
VL  - 99
AB  - Background and Aims Plants possess three types of DNA methyltransferase, among which
AB  - methyltransferase type 1 (MET1) is
AB  - considered to play a major role by maintaining the CpG methylation
AB  - patterns. However, little information is available as to its enzymatic
AB  - activity, interacting proteins and spatial and temporal behaviours
AB  - during DNA replication. In the present study, one example, NtMET1 from
AB  - tobacco plants, was selected and an analysis was made of its
AB  - biochemical properties and cellular localization.
AB  - Methods NtMET1 was expressed in Sf9 insect cells, and a purified
AB  - sample was subjected to a standard in vitro methylation assay.
AB  - Intramolecular interaction was examined by the yeast two-hybrid and
AB  - pull-down assays. Transgenic tobacco plants (Nicotiana tabacum)
AB  - over-expressing NtMET1 were constructed via Agrobacterium-mediated
AB  - transformation. Cellular localization was examined by fluorescence
AB  - protein fusion, which was expressed in tobacco bright yellow 2 cells.
AB  - Key Results In vitro assays showed no detectable methylation
AB  - activity when both hemimethylated and unmethylated DNA samples were
AB  - used as the substrate. In planta assays with over-expressing transgenic
AB  - lines showed no hypermethylation but rather hypomethylation of genomc
AB  - DNA. The inability of methylation was conceivably due to a tight
AB  - intramolecular interaction between the N- and C-terminal regions with
AB  - the catalytic domain residing on the C-terminus being completely
AB  - masked. Cellular localization analyses indicated that NtMET1 localized
AB  - to the nucleus in the resting stage and migrates to the cytoplasm
AB  - during mitosis, particularly at metaphase. The pattern observed
AB  - resembled that of Ran GTPase, and in vitro pull-down assays showed a
AB  - clear interaction between NtMET1 and AtRAN3, an Arabidopsis orthologue
AB  - of tobacco Ran GTPase, NtRan-A1.
AB  - Conclusions The results suggest that enzymatic activity of NtMET1
AB  - is well adjusted by its own intra/intermolecular interaction and
AB  - perhaps by interactions with other proteins, one of which was found to
AB  - be Ran GTPase. Results also revealed that NtMET1 becomes localized to
AB  - the vicinity of chromatin with the aid of Ran GTPase during cell
AB  - division, and may play an important role in progress through mitosis
AB  - independently of methylation activity.
ER  -

TY  - JOUR
AU  - Kim, H.S.
AU  - Cha, S.H.
AU  - Suk, H.Y.
AU  - Kwon, T.H.
AU  - Woo, J.H.
TI  - Complete Genome Sequence of Indigo-Producing Bacterium Celeribacter sp. Strain TSPH2.
JO  - Genome Announcements
PY  - 2017
SP  - e01124
EP  - e01117
VL  - 5
AB  - Celeribacter sp. strain TSPH2, a novel producer of indigo, was isolated from oil-contaminated
AB  - sediment. We present here its genome sequence consisting of one
AB  - circular chromosome (4 Mb) and one plasmid (0.15 Mb), with an overall G+C content
AB  - of 60.9%. This strain contains oxygenase genes involved in indigo synthesis, such
AB  - as flavin-containing monooxygenase.
ER  -

TY  - JOUR
AU  - Kim, H.S.
AU  - Cha, S.H.
AU  - Suk, H.Y.
AU  - Park, N.H.
AU  - Woo, J.H.
TI  - Complete Genome Sequence of Sphingorhabdus sp. YGSMI21, Exhibiting High Enantioselective Epoxide Hydrolase Activity.
JO  - Genome Announcements
PY  - 2018
SP  - e01441
EP  - e01417
VL  - 6
AB  - Sphingorhabdus sp. YGSMI21 is a novel strain exhibiting high enantioselective hydrolysis
AB  - activity for styrene oxide. Here, we present its complete genome
AB  - sequence, consisting of one circular chromosome (3.86 Mb) and one plasmid (0.196
AB  - Mb).
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Jung, J.
AU  - Sung, J.S.
AU  - Chun, J.
AU  - Park, W.
TI  - Genome Sequence of Pectin-Degrading Alishewanella agri, Isolated from Landfill Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5135
EP  - 5136
VL  - 194
AB  - Alishewanella agri BL06(T) (= KCTC 22400(T) = JCM 15597(T)) was isolated from landfill soil in
AB  - Pohang, South Korea. A. agri showed the ability to degrade
AB  - pectin, a structural heteropolysaccharide present in the cell wall of plants.
AB  - Here we report the genome sequence of Alishewanella agri BL06(T), the second
AB  - sequenced strain in the genus Alishewanella.
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Kim, S.J.
AU  - Kim, S.H.
AU  - Kim, S.I.
AU  - Moon, Y.J.
AU  - Park, S.J.
AU  - Kahng, H.Y.
AU  - Chung, Y.H.
TI  - Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01256
EP  - e01214
VL  - 2
AB  - Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene,
AB  - was isolated from crude oil-contaminated seashore in Tae-an, South
AB  - Korea. Here, we report the draft genome sequence of this strain, which comprises
AB  - 3,118,428 bp with a G+C content of 62.85 mol%.
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Kim, S.J.
AU  - Kim, S.H.
AU  - Moon, Y.J.
AU  - Park, S.J.
AU  - Kim, S.I.
AU  - Kahng, H.Y.
AU  - Chung, Y.H.
TI  - Genome Sequence of Arthrobacter sp. MWB30, Isolated from a Crude Oil-Contaminated Seashore.
JO  - Genome Announcements
PY  - 2015
SP  - e00013
EP  - e00015
VL  - 3
AB  - We report here the draft genome sequence of Arthrobacter sp. MWB30 strain, isolated from a
AB  - crude oil-contaminated seashore in Tae-an, South Korea, which is  able to degrade the crude
AB  - oil and its derivatives. The draft genome sequence of 4,647,008 bp provides a resource for the
AB  - identification of crude oil-degrading mechanisms in strain MWB30.
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Kwon, K.K.
AU  - Kim, B.K.
AU  - Hong, S.G.
AU  - Oh, H.M.
TI  - Genome Sequence of Deinococcus marmoris PAMC 26562 Isolated from Antarctic Lichen.
JO  - Genome Announcements
PY  - 2017
SP  - e00013
EP  - e00017
VL  - 5
AB  - Deinococcus marmoris strain PAMC 26562 was isolated from Usnea sp., a lichen collected from
AB  - King George Island, Antarctica. We report here the draft genome
AB  - sequence of strain PAMC 26562, which has xanthorhodopsin and carbon monoxide
AB  - dehydrogenase genes in addition to major metabolic pathways presented in
AB  - deinococcal genomes.
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Lindsey, R.L.
AU  - Garcia-Toledo, L.
AU  - Loparev, V.N.
AU  - Rowe, L.A.
AU  - Batra, D.
AU  - Juieng, P.
AU  - Stoneburg, D.
AU  - Martin, H.
AU  - Knipe, K.
AU  - Smith, P.
AU  - Strockbine, N.
TI  - High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated  with PacBio Sequencing.
JO  - Genome Announcements
PY  - 2018
SP  - e00282
EP  - e00218
VL  - 6
AB  - Shigella spp. are enteric pathogens that cause shigellosis. We report here the high-quality
AB  - whole-genome sequences of 59 historical Shigella strains that
AB  - represent the four species and a variety of serotypes.
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Roh, S.W.
AU  - Bae, J.W.
TI  - Draft Genome Sequence of Dietzia alimentaria 72T, Belonging to the Family Dietziaceae, Isolated from a Traditional Korean Food.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6791
EP  - 6791
VL  - 193
AB  - Actinobacterial strain 72(T), named Dietzia alimentaria, which belongs to the family
AB  - Dietziaceae, was isolated from a traditional Korean food made
AB  - from clams. The draft genome sequence of D. alimentaria 72(T) contains
AB  - 3,352,817 bp, with a G+C content of 67.34%.
ER  -

TY  - JOUR
AU  - Kim, J.
AU  - Thorp, H.H.
TI  - Footprinting of cytosine-5--methyltransferase by Pt2(pop)44-.
JO  - ACS Abstracts
PY  - 1996
SP  - A290
EP  - A290
VL  - 212
AB  - The photoreagent Pt2(pop)44- (1, pop = P2O5H22-) cleaves DNA upon visible irradiation via
AB  - abstraction of the 4' and 5' hydrogens, which provide a sequence-neutral cleavage ladder.
AB  - The development of 1 for use as an anionic DNA photocleavage agent has prompted us to apply it
AB  - to obtaining the footprint of the M.HhaI (cytosine-5) methyltransferase.  The binding of
AB  - M.HhaI to its DNA substrate causes large conformational changes with an extensive contact with
AB  - DNA around the active site.  A comparison of photocleavage with data from the crystal
AB  - structure of a reaction intermediate between the M.HhaI methyltransferase and a DNA
AB  - oligonucleotide shows a correlation between cleavage by 1 and the effects of electrostatic
AB  - forces in the binding of protein to nucleic acids.  Also underway is an anlaysis of the
AB  - photocleavage products to provide additional quantitation of the cleavage pathways.
ER  -

TY  - JOUR
AU  - Kim, J.-S.
AU  - DeGiovanni, A.
AU  - Jancarik, J.
AU  - Adams, P.D.
AU  - Yokota, H.
AU  - Kim, R.
AU  - Kim, S.-H.
TI  - Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 3248
EP  - 3253
VL  - 102
AB  - Type I restriction-modification enzymes are differentiated from type II and type III enzymes
AB  - by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving
AB  - DNA randomly away from the recognition sites. They are oligomeric proteins formed by three
AB  - subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved
AB  - the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4 Angstroms
AB  - resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a
AB  - coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular
AB  - structures with almost identical topologies and two separate DNA binding clefts with a modeled
AB  - DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil
AB  - CRs act as a molecular ruler for the separation between two recognized DNA sequences.
AB  - Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound
AB  - dsDNA and exposing of target adenines from the recognized DNA sequences.
ER  -

TY  - JOUR
AU  - Kim, J.F.
AU  - Jeong, H.
AU  - Lee, J.S.
AU  - Choi, S.H.
AU  - Ha, M.
AU  - Hur, C.G.
AU  - Kim, J.S.
AU  - Lee, S.
AU  - Park, H.S.
AU  - Park, Y.H.
AU  - Oh, T.K.
TI  - The Complete Genome Sequence of Leuconostoc citreum KM20.
JO  - J. Bacteriol.
PY  - 2008
SP  - 3093
EP  - 3094
VL  - 190
AB  - Leuconostoc citreum is one of the most prevalent lactic acid bacteria during the manufacturing
AB  - process of kimchi, the best-known Korean
AB  - traditional dish. Here we present the complete genome sequence of L.
AB  - citreum KM20. It consists of a 1.80-Mb chromosome and four circular
AB  - plasmids, and reveals genes likely involved in kimchi fermentation and its
AB  - probiotic effects.
ER  -

TY  - JOUR
AU  - Kim, J.F.
AU  - Jeong, H.
AU  - Park, S.Y.
AU  - Kim, S.B.
AU  - Park, Y.K.
AU  - Choi, S.K.
AU  - Ryu, C.M.
AU  - Hur, C.G.
AU  - Ghim, S.Y.
AU  - Oh, T.K.
AU  - Kim, J.J.
AU  - Park, C.S.
AU  - Park, S.H.
TI  - Genome Sequence of the Polymyxin-Producing Plant-Probiotic Rhizobacterium Paenibacillus polymyxa E681.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6103
EP  - 6104
VL  - 192
AB  - Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from
AB  - the rhizosphere of winter barley grown in South
AB  - Korea, has great potential for agricultural applications due to its
AB  - ability to promote plant growth and suppress plant diseases. Here we
AB  - present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb
AB  - genome encodes functions specialized to the plant-associated lifestyle and
AB  - characteristics that are beneficial to plants, such as the production of a
AB  - plant growth hormone, antibiotics, and hydrolytic enzymes.
ER  -

TY  - JOUR
AU  - Kim, J.F.
AU  - Jeong, H.
AU  - Yu, D.S.
AU  - Choi, S.H.
AU  - Hur, C.G.
AU  - Park, M.S.
AU  - Yoon, S.H.
AU  - Kim, D.W.
AU  - Ji, G.E.
AU  - Park, H.S.
AU  - Oh, T.K.
TI  - Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011.
JO  - J. Bacteriol.
PY  - 2009
SP  - 678
EP  - 679
VL  - 191
AB  - Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the
AB  - guts of most mammals, including humans. Here we
AB  - report the complete genome sequence of B. animalis subsp. lactis AD011
AB  - that was isolated from an infant fecal sample. Biological functions
AB  - encoded in a single circular chromosome of 1,933,695 bp, smallest among
AB  - the completely sequenced bifidobacterial genomes, are suggestive of their
AB  - probiotic functions, such as utilization of bifidogenic factors and a
AB  - variety of glycosidic enzymes and biosynthesis of polysaccharides.
ER  -

TY  - JOUR
AU  - Kim, J.H.
AU  - Boo, Y.B.
AU  - Lee, K.Y.
TI  - Preparation of restriction endonuclease-AluI from Arthrobacter Luteus.
JO  - Korean J. Biochem.
PY  - 1985
SP  - 149
EP  - 154
VL  - 17
AB  - Extraction and purification of the restriction endonuclease, Alu-I, were
AB  - performed from Arthrobacter luteus.  The harvested cells were disrupted by the
AB  - treament of lysozyme and sonification, and the uspernant was precipitated with
AB  - 70% saturation of ammonium sulfate.  The protein sediment was dissolved in
AB  - buffer solution and dialysed to the same buffer solution.  This solution was
AB  - successively applied to phosphocellulose, heparin-agarose, and Ultrogel AcA34
AB  - (LKB) column chromatography for the purification procedure.  The purified AluI
AB  - enzyme was revealed the singel band on SDS-polyacrylamide gel electrophoresis
AB  - and the molecular weight was shown 52 Kdal, attaining its specific activity to
AB  - 312.5 units/mg or protein.  No difference was observed between our enzyme
AB  - preparation and commerical AluI (BRL) on agarose gel electropherogram.  The
AB  - enzyme sample after treatment with heparin-agarose also had multiprotein bands,
AB  - indicating the protein contaminant, however, all bands but a single band of
AB  - AluI enzyme disappeared by the subsequent column chromatography of Ultrogel
AB  - AcA34.
ER  -

TY  - JOUR
AU  - Kim, J.H.
AU  - Kang, D.H.
TI  - Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes.
JO  - Genome Announcements
PY  - 2016
SP  - e00984
EP  - e00916
VL  - 4
AB  - Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a
AB  - microalgal culture pond in South Korea. The genome consists of 13
AB  - contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were
AB  - predicted. This genomic information will allow further exploitation of its
AB  - biotechnological potential for alimentary purposes.
ER  -

TY  - JOUR
AU  - Kim, J.H.
AU  - Kang, D.H.
AU  - Park, S.C.
TI  - Draft Genome Sequence of Human-Pathogenic Lactococcus garvieae LG-ilsanpaik-gs201105 That Caused Acute Acalculous Cholecystitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00464
EP  - e00415
VL  - 3
AB  - Lactococcus garvieae, which is generally known as a marine and freshwater fish pathogen, is
AB  - now considered to be an emerging zoonotic pathogen in both human and
AB  - veterinary medicine. In recent years, we have reported the infection of L.
AB  - garvieae LG-ilsanpaik-gs201105 in the gallbladder of an old fisherman. In this
AB  - study, we present the draft genome sequence of L. garvieae LG-ilsanpaik-gs201105,
AB  - with a total genome size of 1,960,261 bp in 53 contigs and a 38.1% average G+C
AB  - content. Interestingly, the capsule gene cluster, which was known as one of the
AB  - crucial virulence factors in L. garvieae, was not detected in our isolate. This
AB  - is the first genome sequence of human-pathogenic L. garvieae, which caused acute
AB  - acalculous cholecystitis.
ER  -

TY  - JOUR
AU  - Kim, J.H.
AU  - Kim, E.
AU  - Kim, C.G.
AU  - Choo, D.W.
AU  - Kim, H.Y.
TI  - Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e00365
EP  - e00316
VL  - 4
AB  - This report describes the 2,032,158-bp draft genome sequence of Lactobacillus sakei (L. sakei)
AB  - strain FBL1, isolated from mukeunji purchased at the Gwangju
AB  - World Kimchi Culture Festival in 2012, South Korea. The total draft genome size
AB  - was 2,032,158 bp with a G+C content of 41.2%.
ER  -

TY  - JOUR
AU  - Kim, J.J.
AU  - Koh, S.
AU  - Kim, J.S.
AU  - Lee, D.-S.
TI  - Mode of action on EcoRI restriction endonuclease: EcoRI and EcoRI variant N199H have active monomeric forms.
JO  - J. Biochem. Mol. Biol.
PY  - 1998
SP  - 149
EP  - 155
VL  - 31
AB  - The N199H variant of the EcoRI endonuclease has about twice the catalytic activity of the
AB  - wild-type.  A comparison of their biochemical characteristics, using synthetic
AB  - oligonucleotides 5'-dAAAACTTAAGAAAAAAAAAAA-3' (KA) and 5'-dTTTTTGAATTCTTTTTTTTTT-3' (KT),
AB  - helps to define the cleavage reaction pathway of these enzymes.  Both EcoRI and EcoRI variant
AB  - N199H were found to cleave single-stranded KA or KT about three times faster than the
AB  - double-stranded forms, although the KT oligonucleotide was more susceptible.  Using the ssDNA
AB  - substrate in kinetic analyses, lower Km values were obtained for the N199H variant than for
AB  - the wild-type at low (50 mM), as well as high (200 mM), sodium chloride concentrations.  This
AB  - difference between the endonucleases is attributed to a greater accessibility for the
AB  - substrate by the variant, and also a higher affinity for the DNA backbone.  It also appears
AB  - that the relative activities of the two enzymes, particularly at high ionic strength, are
AB  - proportional to their populations in the monomeric enzyme form.  That is, according to gel
AB  - filtration data, half of the N199H molecules exist as monomers in 200 mM NaCl, whereas those
AB  - of the wild-type are mainly dimeric.  Consequently, the Asp199 residue of the EcoRI
AB  - endonuclease may be implicated in the protein-protein interaction leading to dimerization, as
AB  - well as in coupling to DNA substrates.  In summary, it is proposed that active monomeric
AB  - endonuclease molecules, derived from the dimeric enzyme, recognize and form a complex with a
AB  - single stranded form of the DNA substrate, which then undergoes nucleophilic substitution and
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Kim, J.J.
AU  - Min, K.T.
AU  - Kim, M.H.
AU  - Augh, S.J.
AU  - Kim, B.-D.
AU  - Lee, D.-S.
TI  - EcoRI variant N199H has enhanced specific activity.
JO  - Gene
PY  - 1996
SP  - 129
EP  - 130
VL  - 171
AB  - The Asn199 residue of the EcoRI restriction endonuclease has been replaced with
AB  - other amino acids to investigate whether it mediates nucleotide recognition or catalytic
AB  - activity.
AB  - Cassette mutagenesis gave variants of EcoRI: N199D, N199H, N199L, N199R, N199S and
AB  - N199V.  Their relative cleavage rates were found to be in the following order: N199H>EcoRI
AB  - (wild type; wt)>N199L>N199V>N199S>N199R>N199D.  In particular, EcoRI variant N199H
AB  - showed about a two-fold higher specific activity than that of the wt enzyme.
ER  -

TY  - JOUR
AU  - Kim, J.K.
AU  - Samaranayake, M.
AU  - Pradhan, S.
TI  - Epigenetic mechanisms in mammals.
JO  - Cell. Mol. Life Sci.
PY  - 2009
SP  - 596
EP  - 612
VL  - 66
AB  - DNA and histone methylation are linked and subjected to mitotic inheritance in mammals. Yet
AB  - how methylation is propagated and maintained between successive cell divisions is not fully
AB  - understood. A series of enzyme families that can add methylation marks to cytosine
AB  - nucleobases, and lysine and arginine amino acid residues has been discovered. Apart from
AB  - methyltransferases, there are also histone modification enzymes and accessory proteins, which
AB  - can facilitate and/or target epigenetic marks. Several lysine and arginine demethylases have
AB  - been discovered recently, and the presence of an active DNA demethylase is speculated in
AB  - mammalian cells. A mammalian methyl DNA binding protein MBD2 and de novo DNA methyltransferase
AB  - DNMT3A and DNMT3B are shown experimentally to possess DNA demethylase activity. Thus, complex
AB  - mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a
AB  - well-choreographed set of events that take place during mammalian development.
ER  -

TY  - JOUR
AU  - Kim, J.S.
AU  - Jeong, W.
AU  - Jeoung, H.Y.
AU  - Song, J.Y.
AU  - Kim, H.
AU  - Beak, J.H.
AU  - Parisutham, V.
AU  - Lee, S.K.
AU  - Kim, J.W.
AU  - Kim, J.Y.
AU  - Jung, S.C.
AU  - Her, M.
AU  - An, D.J.
TI  - Complete Genome Sequence of Brucella canis Strain HSK A52141, Isolated from the Blood of an Infected Dog.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5134
EP  - 5134
VL  - 194
AB  - Brucella canis infection can be clinically inapparent in dogs, and when infection goes
AB  - unnoticed, there is a chance for dog-to-human transmission. A new strain of
AB  - B. canis was isolated from the blood of an infected dog in order to analyze the
AB  - pathogenic mechanism, compare genetic properties, and develop new genetic tools
AB  - for early diagnosis of canine brucellosis. Herein, we report the complete genome
AB  - sequence of the strain B. canis HSK A52141. This is the second complete genome
AB  - sequence and biological annotation available for a member of B. canis.
ER  -

TY  - JOUR
AU  - Kim, J.S.
AU  - Kim, J.
AU  - Jeon, S.-E.
AU  - Kim, S.-J.
AU  - Kim, N.-O.
AU  - Hong, S.
AU  - Kang, Y.-H.
AU  - Han, S.
AU  - Chung, G.T.
TI  - Complete nucleotide sequence of the IncI1 plasmid pSH4469 encoding CTX-M-15 extended-spectrum beta-lactamase in a clinical isolate of Shigella sonnei from an outbreak in the Republic of Korea.
JO  - Int. J. Antimicrob. Agents
PY  - 2014
SP  - 533
EP  - 537
VL  - 44
AB  - An outbreak of extended-spectrum B-lactamase (ESBL)-producing Shigella sonnei infections
AB  - occurred in a school for disabled children in Gyeongbuk Province, Republic of Korea, in 2008.
AB  - Five students were affected. Pulsed-field gel electrophoresis (PFGE) analysis revealed that
AB  - all of the ESBL-producing S. sonnei isolates belonged to the same clone, and nucleotide
AB  - sequence analysis of ESBL genes revealed that they harboured blaCTX-M-15. This is the first
AB  - identification of blaCTX-M-15 in Shigella spp. in South Korea. In this study, a plasmid
AB  - carrying the blaCTX-M-15 gene, designated pSH4469, recovered from a S. sonnei isolate
AB  - responsible for the outbreak was characterised. Replicon typing and plasmid multilocus
AB  - sequence typing (pMLST) analysis of plasmids in the outbreak strain identified that the
AB  - blaCTX-M-15 gene was located on an IncI1 incompatibility group plasmid of sequence type 16
AB  - (ST16). The complete nucleotide sequence of pSH4469 revealed that this plasmid is 91109 bp and
AB  - harbours 119 putative genes, including another antibiotic resistance gene (blaTEM-1b) that is
AB  - often associated with the ISEcp1-blaCTX-M-15-orf477delta transposable unit. The plasmid
AB  - consists of a large backbone with considerable homology to the pEK204 plasmid isolated from
AB  - Escherichia coli in the UK, except for insertion of an IS66 element found in pEK204. These
AB  - data demonstrate that IncI1 plasmids are used as a successful platform for efficient
AB  - horizontal gene transfer, thereby resulting in the dissemination of CTX-M-type B-lactamases
AB  - among Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Kim, J.S.
AU  - Li, J.
AU  - Barnes, I.H.A.
AU  - Thompson, S.A.
TI  - Cj1461 DNA methyltransferase in Campylobacter jejuni 81-176 is involved in the regulation of virulence characteristics and bacterial cellular functions.
JO  - Zoonoses Public Health
PY  - 2007
SP  - 103
EP  - 103
VL  - 54
AB  - DNA methylases such as Dam can regulate transcription of virulence-associated genes in
AB  - bacteria.  Cj1461 is a DNA methyltransferase conserved in Campylobacter species.  A
AB  - cj1461-insertional mutant of C. jejuni 81-176 had significantly reduced motility at 37C, and
AB  - the reduced motility was partially but significantly recovered in a strain complemented with
AB  - native cj1461 (P<0.05).  A Cj1461-overexpression strain of 81-176 was constructed by
AB  - expressing an inducible cj1461 gene on the shuttle vector pRY111.  cj1461 and cj1462 (flgI)
AB  - were about 1.5- and 1.8-fold overexpressed, respectively, in the Cj1461-overexpression strain
AB  - based on real-time PCR analysis.  In addition, the overexpression strain showed significantly
AB  - increased motility (P<0.05) compared to 81-176 containing pRY111 alone.  Proteome analysis of
AB  - the Cj1461-overexpression strain showed the altered expression of more than 20 proteins
AB  - including PEB1a, PEB3, PEB4, major outer membrane protein, gamma-glutamyl transpeptidase,
AB  - thiol peroxidase, alkyl hydroperoxide reductase, trigger factor and several TCA cycle enzymes.
AB  - These data, along with the altered regulation of numerous C. jejuni genes in the cj1461
AB  - mutant, suggest that Cj1461 DNA methyltransferase is involved in regulating virulence
AB  - characteristics such as motility and other bacterial cellular processes in C. jejuni 81-176.
ER  -

TY  - JOUR
AU  - Kim, J.S.
AU  - Li, J.Q.
AU  - Barnes, I.H.A.
AU  - Baltzegar, D.A.
AU  - Pajaniappan, M.
AU  - Cullen, T.W.
AU  - Trent, M.S.
AU  - Burns, C.M.
AU  - Thompson, S.A.
TI  - Role of the Campylobacter jejuni cj1461 DNA methyltransferase in regulating virulence characteristics.
JO  - J. Bacteriol.
PY  - 2008
SP  - 6524
EP  - 6529
VL  - 190
AB  - Mutation of the cj1461 predicted methyltransferase gene reduced the motility of Campylobacter
AB  - jejuni 81-176. Electron microscopy revealed
AB  - that the mutant strain had flagella but with aberrant structure. The
AB  - Delta cj1461 mutant was sevenfold more adherent to but 50-fold less
AB  - invasive of INT-407 human epithelial cells than the wild type.
ER  -

TY  - JOUR
AU  - Kim, J.W.
AU  - Dutta, V.
AU  - Elhanafi, D.
AU  - Lee, S.
AU  - Osborne, J.A.
AU  - Kathariou, S.
TI  - A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 1995
EP  - 2004
VL  - 78
AB  - Listeria monocytogenes epidemic clone II (ECII) strains are unusual in being completely
AB  - resistant to phage when grown at low temperatures (<=
AB  - 30 degrees C). In the current study we constructed and characterized a
AB  - mariner-based mutant (J46C) of the ECII strain H7550-Cd-S that lacked
AB  - temperature-dependent resistance to phage. The transposon was localized
AB  - in LMOh7858 2753 (open reading frame [ORF] 2753), a member of a 12-ORF
AB  - genomic island unique to ECII strains. ORF 2753 and ORF 2754 exhibited
AB  - homologies to restriction endonucleases and methyltransferases
AB  - associated with type II restriction-modification (RM) systems. In
AB  - silico-based predictions of the recognition site for this putative RM
AB  - system were supported by resistance of DNA from ECII strains to
AB  - digestion by BfuI, a type II restriction enzyme specific for GTATCC
AB  - (N6/5). Similarly to J46C, a mutant harboring an in-frame deletion of
AB  - ORF 2753 was susceptible to phage regardless of temperature of growth
AB  - (25 C or 37 degrees C). Genetic complementation restored phage
AB  - resistance in 25 degrees C-grown cells of ORF 2753 mutants. Reverse
AB  - transcription (RT) and quantitative real-time PCR data suggested
AB  - enhanced transcription of ORF 2753 at low temperatures (<= 25 degrees
AB  - C) compared to 37 degrees C. In contrast, available transcriptional
AB  - data suggested that the putative methyltransferase (ORF 2754) was
AB  - constitutively expressed at all tested temperatures (4 to 37 degrees
AB  - C). Thus, temperature-dependent resistance of L. monocytogenes ECII to
AB  - phage is mediated by temperature-dependent expression of the
AB  - restriction endonuclease associated with a novel RM system (LmoH7)
AB  - unique to this epidemic clone.
ER  -

TY  - JOUR
AU  - Kim, J.W.
AU  - Yoo, J.I.
AU  - Kang, G.S.
AU  - Lee, Y.S.
AU  - Yu, J.Y.
AU  - Park, C.
AU  - Kim, I.H.
TI  - Draft Genome Sequences of Vancomycin-Intermediate Staphylococcus aureus Strains in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e00027
EP  - e00016
VL  - 4
AB  - We report here the draft genome sequences of four vancomycin-intermediate Staphylococcus
AB  - aureus (VISA) strains from South Korean hospitals participating in
AB  - a nationwide laboratory surveillance program for vancomycin-intermediate and
AB  - vancomycin-resistant Staphylococcus aureus All strains harbor mutations in the
AB  - walKR, graSR, and/or rpoB genes that are known frequently mutated determinants of
AB  - VISA.
ER  -

TY  - JOUR
AU  - Kim, J.Y.
AU  - Wang, Y.
AU  - Park, M.S.
AU  - Ji, G.E.
TI  - Improvement of Transformation Efficiency Through In Vitro Methylation and SacII Site Mutation of Plasmid Vector in Bifidobacterium longum MG1.
JO  - J. Microbiol. Biotechnol.
PY  - 2010
SP  - 1022
EP  - 1026
VL  - 20
AB  - The different cleavage patterns of pYBamy59 plasmid isolated from E. coli DH5 alpha and B.
AB  - longum MG1 by the cell extract of B. longum MG1
AB  - suggested that the main reason for its low transformation efficiency
AB  - was related to the restriction modification (R-M) system. To confirm
AB  - the correlation between the R-M system and transformation efficiency,
AB  - in vitro methylation and site-directed mutagenesis were performed in
AB  - pYBamy59. Sequence analysis of pYBamy59 fragments digested by the cell
AB  - extract of B. longum MG1 revealed that all fragments were generated by
AB  - restriction of the sequence recognized by SacII endonuclease. When
AB  - pYBamy59 from E. coli was methylated in vitro by CpG or GpC
AB  - methyltransferase, it was protected from SacII digestion. Site-directed
AB  - mutagenesis, which removed SacII sites from pYBamy59, or in vitro
AB  - methylation of pYBamy59 showed 8- to 15-fold increases in the
AB  - transformation efficiency over intact pYBamy59. Modification of the
AB  - Sad-related R-M system in B. longum MG1 and in vitro methylation in
AB  - pYBamy 59 can improve the transformation efficiency in this strain. The
AB  - results showed that the R-M system is a factor to limit introduction of
AB  - exogenous DNA, and in vitro modification is a convenient method to
AB  - overcome the barrier of the R-M system for transformation.
ER  -

TY  - JOUR
AU  - Kim, K.
AU  - Kwon, S.K.
AU  - Yoon, J.H.
AU  - Kim, J.F.
TI  - Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium  Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea  (Sea of Korea).
JO  - Genome Announcements
PY  - 2016
SP  - e00804
EP  - e00816
VL  - 4
AB  - Dokdonia spp. have been used for investigating the lifestyles of proteorhodopsin-containing
AB  - photoheterotrophs and for understanding marine
AB  - photobiology. Here, we report the complete genome sequence of Dokdonia
AB  - donghaensis DSW-1(T) using the PacBio sequencing platform. It should provide a
AB  - valuable resource for comparative genomic studies of marine life harboring
AB  - microbial rhodopsins among others.
ER  -

TY  - JOUR
AU  - Kim, K.K.
AU  - Lee, K.C.
AU  - Jeong, H.
AU  - Stevens, D.A.
AU  - Lee, J.S.
TI  - Draft Genome Sequence of the Human Pathogen Halomonas stevensii S18214T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5143
EP  - 5143
VL  - 194
AB  - Halomonas stevensii is a Gram-negative, moderately halophilic bacterium causing environmental
AB  - contamination and infections in a dialysis center. Here we present
AB  - the 3.7-Mb draft genome sequence of the type strain (S18214(T)) of H. stevensii,
AB  - which will give insight into the pathogenic potential of H. stevensii.
ER  -

TY  - JOUR
AU  - Kim, K.K.
AU  - Lee, K.C.
AU  - Lee, J.S.
TI  - Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6659
EP  - 6659
VL  - 194
AB  - Halogranum salarium is an extremely halophilic archaeon isolated from evaporitic  salt
AB  - crystals and belongs to the family Halobacteriaceae. Here, we present the
AB  - 4.5-Mb draft genome sequence of the type strain (B-1(T)) of H. salarium. This is
AB  - the first report of the draft genome sequence of a haloarchaeon in the genus
AB  - Halogranum.
ER  -

TY  - JOUR
AU  - Kim, M.
AU  - Kim, S.
AU  - Ryu, S.
TI  - Complete Genome Sequence of Bacteriophage SSU5 Specific for Salmonella enterica serovar Typhimurium Rough Strains.
JO  - J. Virol.
PY  - 2012
SP  - 10894
EP  - 10894
VL  - 86
AB  - Salmonella enterica serovar Typhimurium rough strain-specific phage SSU5 was
AB  - isolated, and its whole genome was sequenced. The 103,229-bp-long double-stranded
AB  - DNA genome of SSU5 encodes 130 open reading frames with one tRNA for asparagine.
AB  - Genomic analysis revealed that SSU5 might be the phylogenetic origin of cryptic
AB  - plasmid pHCM2 harbored by Salmonella Typhi CT18.
ER  -

TY  - JOUR
AU  - Kim, M.
AU  - Ryu, S.
TI  - Antirepression System Associated with the Life Cycle Switch in the Temperate Podoviridae Phage SPC32H.
JO  - J. Virol.
PY  - 2013
SP  - 11775
EP  - 11786
VL  - 87
AB  - Prophages switch from lysogenic to lytic mode in response to the host SOS response. The
AB  - primary factor that governs this switch is a phage repressor, which is typically a host
AB  - RecA-dependent autocleavable protein. Here, in an effort to reveal the mechanism underlying
AB  - the phenotypic differences between the Salmonella temperate phages SPC32H and SPC32N, whose
AB  - genome sequences differ by only two nucleotides, we identified a new class of Podoviridae
AB  - phage lytic switch antirepressor that is structurally distinct from the previously reported
AB  - Sipho- and Myoviridae phage antirepressors. The SPC32H repressor (Rep) is not cleaved by the
AB  - SOS response but instead is inactivated by a small antirepressor (Ant), the expression of
AB  - which is negatively controlled by host LexA. A single nucleotide mutation in the consensus
AB  - sequence of the LexA-binding site, which overlaps with the ant promoter, results in
AB  - constitutive Ant synthesis and consequently induces SPC32N to enter the lytic cycle. Numerous
AB  - potential Ant homologues were identified in a variety of putative prophages and temperate
AB  - Podoviridae phages, indicating that antirepressors may be widespread among temperate phages in
AB  - the order Caudovirales to mediate a prudent prophage induction.
ER  -

TY  - JOUR
AU  - Kim, M.
AU  - Yi, H.
AU  - Cho, Y.J.
AU  - Jang, J.
AU  - Hur, H.G.
AU  - Chun, J.
TI  - Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5149
EP  - 5150
VL  - 194
AB  - An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces  from a
AB  - healthy cow in South Korea. Here, we report the draft genome sequence of
AB  - the isolate, which is closely affiliated with commensal strains belonging to E.
AB  - coli phylogroup B1.
ER  -

TY  - JOUR
AU  - Kim, M.J.
AU  - Ku, S.
AU  - Kim, S.Y.
AU  - Lee, H.H.
AU  - Jin, H.
AU  - Kang, S.
AU  - Li, R.
AU  - Johnston, T.V.
AU  - Park, M.S.
AU  - Ji, G.E.
TI  - Safety Evaluations of Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI.
JO  - Int. J. Mol. Sci.
PY  - 2018
SP  - E1422
EP  - E1422
VL  - 19
AB  - Over the past decade, a variety of lactic acid bacteria have been commercially
AB  - available to and steadily used by consumers. However, recent studies have shown
AB  - that some lactic acid bacteria produce toxic substances and display properties of
AB  - virulence. To establish safety guidelines for lactic acid bacteria, the Food and
AB  - Agriculture Organization of the United Nations (FAO)/World Health Organization
AB  - (WHO) has suggested that lactic acid bacteria be characterized and proven safe
AB  - for consumers and rsquo; health via multiple experiments (e.g., antibiotic
AB  - resistance, metabolic activity, toxin production, hemolytic activity, infectivity
AB  - in immune-compromised animal species, human side effects, and adverse-outcome
AB  - analyses). Among the lactic acid bacteria, Bifidobacterium and Lactobacillus
AB  - species are probiotic strains that are most commonly commercially produced and
AB  - actively studied. Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI
AB  - have been used in global functional food markets (e.g., China, Germany, Jordan,
AB  - Korea, Lithuania, New Zealand, Poland, Singapore, Thailand, Turkey, and Vietnam)
AB  - as nutraceutical ingredients for decades, without any adverse events. However,
AB  - given that the safety of some newly screened probiotic species has recently been
AB  - debated, it is crucial that the consumer safety of each commercially utilized
AB  - strain be confirmed. Accordingly, this paper details a safety assessment of B.
AB  - bifidum BGN4 and B. longum BORI via the assessment of ammonia production,
AB  - hemolysis of blood cells, biogenic amine production, antimicrobial susceptibility
AB  - pattern, antibiotic resistance gene transferability, PCR data on antibiotic
AB  - resistance genes, mucin degradation, genome stability, and possession of
AB  - virulence factors. These probiotic strains showed neither hemolytic activity nor
AB  - mucin degradation activity, and they did not produce ammonia or biogenic amines
AB  - (i.e., cadaverine, histamine or tyramine). B. bifidum BGN4 and B. longum BORI
AB  - produced a small amount of putrescine, commonly found in living cells, at levels
AB  - similar to or lower than that found in other foods (e.g., spinach, ketchup, green
AB  - pea, sauerkraut, and sausage). B. bifidum BGN4 showed higher resistance to
AB  - gentamicin than the European Food Safety Authority (EFSA) cut-off. However, this
AB  - paper shows the gentamicin resistance of B. bifidum BGN4 was not transferred via
AB  - conjugation with L. acidophilus ATCC 4356, the latter of which is highly
AB  - susceptible to gentamicin. The entire genomic sequence of B. bifidum BGN4 has
AB  - been published in GenBank (accession no.: CP001361.1), documenting the lack of
AB  - retention of plasmids capable of transferring an antibiotic-resistant gene.
AB  - Moreover, there was little genetic mutation between the first and 25th
AB  - generations of B. bifidum BGN4. Tetracycline-resistant genes are prevalent among
AB  - B. longum strains; B. longum BORI has a tet(W) gene on its chromosome DNA and has
AB  - also shown resistance to tetracycline. However, this research shows that its
AB  - tetracycline resistance was not transferred via conjugation with L. fermentum
AB  - AGBG1, the latter of which is highly sensitive to tetracycline. These findings
AB  - support the continuous use of B. bifidum BGN4 and B. longum BORI as probiotics,
AB  - both of which have been reported as safe by several clinical studies, and have
AB  - been used in food supplements for many years.
ER  -

TY  - JOUR
AU  - Kim, M.S.
AU  - Whon, T.W.
AU  - Roh, S.W.
AU  - Shin, N.R.
AU  - Bae, J.W.
TI  - Draft Genome Sequence of Bacteroides faecis MAJ27T, a Strain Isolated from Human Feces.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6801
EP  - 6802
VL  - 193
AB  - Despite the ecological importance of the dominant gut bacteria Bacteroides, few genomes have
AB  - been defined. The Gram-negative, strictly
AB  - anaerobic intestinal bacterium Bacteroides faecis MAJ27(T) was isolated
AB  - from the feces of a healthy adult. Here, the draft genome sequence of the
AB  - type strain B. faecis MAJ27 (6.11 Mbp) is reported.
ER  -

TY  - JOUR
AU  - Kim, N.
AU  - Jang, Y.
AU  - Kim, J.K.
AU  - Ryoo, S.
AU  - Kwon, K.H.
AU  - Kang, S.S.
AU  - Byeon, H.S.
AU  - Lee, H.S.
AU  - Lim, Y.H.
AU  - Kim, J.M.
TI  - Complete Genome Sequence of Mycobacterium bovis Clinical Strain 1595, Isolated from the Laryngopharyngeal Lymph Node of South Korean Cattle.
JO  - Genome Announcements
PY  - 2015
SP  - e01124
EP  - e01115
VL  - 3
AB  - Mycobacterium bovis strain 1595 was isolated from the lymph node of South Korean  native
AB  - cattle. The complete genome sequence of strain 1595 was determined in 2 contigs and was found
AB  - to be 4,351,712 bp in size, with a 65.64% G+C content and 4,358 predicted protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Kim, N.
AU  - Jang, Y.
AU  - Park, S.Y.
AU  - Song, W.S.
AU  - Kim, J.T.
AU  - Lee, H.S.
AU  - Lim, Y.H.
AU  - Kim, J.M.
TI  - Whole-Genome Sequence of Mycobacterium bovis W-1171, Isolated from the Laryngopharyngeal Lymph Node of a Wild Boar in South Korea.
JO  - Genome Announcements
PY  - 2015
SP  - e01464
EP  - e01415
VL  - 3
AB  - Mycobacterium bovis W-1171 was isolated from a wild boar living in a free-ranging field in
AB  - Gyeonggido, South Korea. The whole-genome sequence of this strain was
AB  - determined in 50 contigs, which was 4,304,865 bp with a 65.57% G+C content. In
AB  - total 3,945 protein-coding genes were predicted from this assembly.
ER  -

TY  - JOUR
AU  - Kim, R.
AU  - Modrich, P.
AU  - Kim, S.-H.
TI  - Interactive recognition in EcoRI restriction enzyme-DNA complex.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 7285
EP  - 7292
VL  - 12
AB  - A solution study of interaction between DNA and EcoRI restriction enzyme shows
AB  - that there is a definite distortion of DNA in the specific recognition
AB  - complexes but no measurable DNA distortion in the non-specific interaction.
ER  -

TY  - JOUR
AU  - Kim, S.C.
AU  - Podhajska, A.J.
AU  - Szybalski, W.
TI  - Cleaving DNA at any predetermined site with adapter-primers and class-IIS restriction enzymes.
JO  - Science
PY  - 1988
SP  - 504
EP  - 506
VL  - 240
AB  - A four-component system has been designed that makes it possible to prepare a
AB  - double-stranded (ds) DNA fragment; one fragment end is predesigned (by the use
AB  - of a class-IIS restriction enzyme and adapter-primer), and the other end
AB  - corresponds to any normal restriction cut.  The system is composed of the phage
AB  - M13mp7 single stranded (ss) target DNA; the Fok I restriction enzyme; an
AB  - oligodeoxynucleotide adapter-primer, which permits one to introduce Fok I cuts
AB  - at any specified site in the target DNA; and DNA polymerase, which converts the
AB  - ss target into a ds form ready for cloning.  In this system, the
AB  - oligodeoxynucleotide adapter-primer serves several purposes.  The 5' hairpin ds
AB  - domain of the adapter-primer  contains a Fok I recognition site.  Its 3' ss
AB  - domain selects a complementary site on the target ss DNA, hybridizes with it to
AB  - form the ds cleavage site, and serves as a primer to convert the ss M13mp7
AB  - target to ds DNA.
ER  -

TY  - JOUR
AU  - Kim, S.C.
AU  - Posfai, G.
AU  - Szybalski, W.
TI  - A novel gene-fusing vector: construction of a 5'-GGmCC-specific chimeric methyltransferase, M.BspRI/M.BsuRI.
JO  - Gene
PY  - 1991
SP  - 45
EP  - 50
VL  - 100
AB  - A vector was designed to allow predetermined and precise fusion between two
AB  - genes by constructing a cassette with two unique class-IIS restriction sites,
AB  - 5'-ACCTGC3' (BspMI) and 5'-CCGGATG-3' (FokI overlapping with MspI), arranged
AB  - back-to-back in a divergent manner and inserted at the HincII site of a
AB  - multiple cloning site (MCS) in plasmid pUC18 or analogous vehicle.  Two DNA
AB  - fragments or genes to be precisely fused are cloned into the MCS parts located
AB  - on each side of the cassette containing the two unique class-IIS restriction
AB  - sites.  The BspMI and MspI/FokI sites are used to generate unidirectional
AB  - deletions of the genes as previously described (Hasan et al., Gene 50(1986)
AB  - 55-62; Posfai and Szybalski, Nucleic Acids Res. 16(1988)6245).  The precisely
AB  - trimmed genes are ligated after the cassette containing the unique class-IIS
AB  - restriction sites are excised with BspMI + FokI and the termini were blunted
AB  - with mung-bean nuclease.  This method was used to construct a hybrid
AB  - methyltransferase (MTase) from the M.BspRI and M.BsuRI MTases, which share a
AB  - high degree of overall homology (about 65%) and have the identical sequence
AB  - specificity (5'-GGmCC-3').  A hybrid MTase composed of the N-terminal part of
AB  - M.BspRI and the C-terminal part of M.BsuRI was constructed and found to be
AB  - fully functional.
ER  -

TY  - JOUR
AU  - Kim, S.C.
AU  - Skowron, P.M.
AU  - Szybalski, W.
TI  - Structural requirements for FokI-DNA interaction and oligodeoxyribonucleotide- instructed cleavage.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 638
EP  - 649
VL  - 258
AB  - The FokI restriction endonuclease recognizes the double-stranded (ds) 5'-GGATG-3'
AB  - site and cuts at the 9th and 13th nucleotides downstream from the 5'-3' and 3'-5'
AB  - strands, respectively.  To elucidate the interaction between FokI and DNA, and the effect of
AB  - Mg2+
AB  - on this interaction, we used FokI with various combinations of dsDNA, single-stranded (ss) DNA
AB  - and oligodeoxyribonucleotides (oligos) containing a double-stranded hairpin carrying the FokI
AB  - recognition site.  Oligo- and dsDNA-FokI interactions showed that for fully effective
AB  - recognition,
AB  - two or more base-pairs were required outside the 5'-GGATG-3' site.  When using FokI with
AB  - ssDNA and oligos, precise cutting with no observable byproducts was observed at the 9th or
AB  - 13th
AB  - nucleotide.  This was independent of whether the region between the recognition and cut sites
AB  - was
AB  - perfectly complementary or whether there were up to four mismatches in this region, or a
AB  - single
AB  - mismatch within the cut site.  Moreover, FokI cleavage, when followed by step-wise filling-in
AB  - of
AB  - FokI cohesive ends in the dsDNA, allowed FokI to recleave such sites when two or more
AB  - nucleotides were added, releasing 2-mer, 3-mer, or 4-mer single-stranded chains.
AB  - Electrophoretic
AB  - mobility shift assays showed that the DNA helix was bent when complexed with FokI (without
AB  - Mg2+).  Such a complex, when formed in the absence of Mg2+, did not accept the subsequently
AB  - added Mg2+ for several minutes.  This suggests a tight, diffusion-resistant contact between
AB  - the
AB  - enzyme and the cognate DNA sequence.  In the presence of Mg2+, the half-life of the complex
AB  - FokI and dsDNA was 12 minutes at 22oC.  In the absence of Mg2+, such a complex, possessing a
AB  - terminally located 5'-GGATG-3' site, had a half-life of 1.5 to 2 minutes.  However, if
AB  - magnesium
AB  - ions were present, this complex had a stability similar to that of a complex formed with dsDNA
AB  - containing a centrally located 5'-GGATG-3' site.
ER  -

TY  - JOUR
AU  - Kim, S.J.
AU  - Park, S.J.
AU  - Kim, J.G.
AU  - Jung, M.Y.
AU  - Gwak, J.H.
AU  - Rhee, S.K.
TI  - Draft Genome Sequence of 'Candidatus Izimaplasma sp.' Strain ZiA1, Obtained from  a Toluene-Degrading and Iron-Reducing Enrichment Culture.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00861
EP  - e00818
VL  - 7
AB  - Here, we report the draft genome sequence of 'Candidatus Izimaplasma sp.' strain  ZiA1 (1.88
AB  - Mb and 29.6% G+C content). Strain ZiA1 was cocultured with
AB  - iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal
AB  - flat sediment. Like the genomes of other strains of 'Ca. Izimaplasma,' the ZiA1
AB  - genome contained genes required for anaerobic fermentation.
ER  -

TY  - JOUR
AU  - Kim, S.J.
AU  - Shin, S.C.
AU  - Hong, S.G.
AU  - Lee, Y.M.
AU  - Choi, I.G.
AU  - Park, H.
TI  - Genome sequence of a novel member of the genus psychrobacter isolated from antarctic soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2403
EP  - 2403
VL  - 194
AB  - Psychrobacter spp. have shown characteristics indicating remarkable capabilities  at subzero
AB  - temperatures that identify them as potential model organisms for the
AB  - study of low-temperature adaptations. Here we present the draft genome sequence
AB  - of Psychrobacter sp. PAMC 21119, which was isolated from permafrost soil of
AB  - Antarctica; this information could provide insight into adaptation and evolution
AB  - strategies under extreme environmental conditions.
ER  -

TY  - JOUR
AU  - Kim, S.J.
AU  - Shin, S.C.
AU  - Hong, S.G.
AU  - Lee, Y.M.
AU  - Lee, H.
AU  - Lee, J.
AU  - Choi, I.G.
AU  - Park, H.
TI  - Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine  Glacier Cryoconite.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2096
EP  - 2096
VL  - 194
AB  - The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing
AB  - psychrotolerant bacterium, was determined. The strain was
AB  - isolated from glacier cryoconite of the Alps mountain permafrost region. The
AB  - sequence will allow identification and characterization of the genetic
AB  - determination of its cold-adaptive properties.
ER  -

TY  - JOUR
AU  - Kim, S.K.
AU  - Chung, W.H.
AU  - Kim, S.H.
AU  - Jung, K.H.
AU  - Kim, N.
AU  - Chai, Y.G.
TI  - Complete Genome Sequence of Bacillus anthracis HYU01, Isolated from Soil Samples  in the Korean Peninsula.
JO  - Genome Announcements
PY  - 2014
SP  - e00769
EP  - e00714
VL  - 2
AB  - Bacillus anthracis is a Gram-positive endospore-forming bacterium that causes the zoonotic
AB  - disease anthrax. We report a complete genome sequence of B. anthracis
AB  - strain HYU01, isolated from Changnyung, which belongs to the B branch (B.Br.)
AB  - 001/002 canonical single nucleotide polymorphism (canSNP) group.
ER  -

TY  - JOUR
AU  - Kim, S.M.
AU  - Cho, S.J.
AU  - Lee, S.B.
TI  - Genome Sequence of the Unclassified Marine Gammaproteobacterium BDW918.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3753
EP  - 3754
VL  - 194
AB  - The unclassified marine gammaproteobacterium BDW918, which utilizes volatile fatty acids but
AB  - not most common carbohydrates and amino acids, was isolated from
AB  - Dokdo seawater in South Korea. Here we present a draft genome of the strain
AB  - BDW918, which encodes many putative genes related to fatty acid metabolism and
AB  - aromatic hydrocarbon degradation.
ER  -

TY  - JOUR
AU  - Kim, S.W.
AU  - Haley, B.J.
AU  - Roberson, D.
AU  - Allard, M.
AU  - Hammack, T.S.
AU  - Brown, E.W.
AU  - Van Kessel, J.A.
TI  - Genome Sequences of Four Nonhuman/Nonclinical Salmonella enterica Serovar Kentucky ST198 Isolates Recovered between 1972 and 1973.
JO  - Genome Announcements
PY  - 2017
SP  - e01699
EP  - e01616
VL  - 5
AB  - Salmonella enterica serovar Kentucky is a polyphyletic member of S. enterica subclade A1 with
AB  - multiple sequence types that often colonize the same hosts but
AB  - in different frequencies on different continents. To evaluate the genomic
AB  - features involved in S Kentucky host specificity, we sequenced the genomes of
AB  - four isolates recovered in the 1970s.
ER  -

TY  - JOUR
AU  - Kim, S.W.
AU  - Karns, J.S.
AU  - Van Kessel, J.A.S.
AU  - Haley, B.J.
TI  - Genome Sequences of 30 Escherichia coli O157:H7 Isolates Recovered from a Single  Dairy Farm and Its Associated Off-Site Heifer-Raising Facility.
JO  - Genome Announcements
PY  - 2017
SP  - e00814
EP  - e00817
VL  - 5
AB  - Cattle are the primary reservoir of Escherichia coli O157:H7, the most frequently isolated
AB  - serotype of enterohemorrhagic E. coli infections among humans in North
AB  - America. To evaluate the diversity of E. coli O157:H7 isolates within a single
AB  - dairy herd, the genomes of 30 isolates collected over a 7-year period were
AB  - sequenced.
ER  -

TY  - JOUR
AU  - Kim, S.W.
AU  - Karns, J.S.
AU  - Van Kessel, J.A.S.
AU  - Haley, B.J.
TI  - Genome Sequences of Five Multidrug-Resistant Escherichia coli Sequence Type 117 Isolates Recovered from Dairy Calves.
JO  - Genome Announcements
PY  - 2017
SP  - e00732
EP  - e00717
VL  - 5
AB  - Escherichia coli sequence type 117 (ST117) strains have been recovered from poultry with
AB  - colibacillosis, as well as from urinary tract infections and fatal
AB  - septic infections in humans. To further investigate ST117 isolates recovered from
AB  - nonpoultry food animals, we sequenced the genomes of five ST117 isolates from
AB  - dairy calves in Pennsylvania.
ER  -

TY  - JOUR
AU  - Kim, S.Y.
AU  - Hwang, S.M.
AU  - Chang, K.S.
TI  - Correlation between Sau1 restriction and modification complex type and coagulase serotype or SCCmec type of Staphylococcus aureus.
JO  - J. Bacteriol. Virol.
PY  - 2010
SP  - 163
EP  - 170
VL  - 40
AB  - Staphylococcus aureus coagulase serotype I to VIII isolated from clinical samples could be
AB  - classified into two groups,
AB  - methicillin-sensitive S. aurues (MSSA) and methicilln-resistant S. aurues (MRSA), by
AB  - antibiotics susceptibility and
AB  - existence of mecA which is a gene related with methicillin resistance. Coagulase serotype I,
AB  - VI, and VIII were MSSA
AB  - which showed different antimicrobial susceptibility. Coagluase serotype II-V and VII are MRSA
AB  - in which mecA and
AB  - SCCmec are detected. To analyze Sau1 restriction and modification (R-M) complex types by
AB  - coagulase type and
AB  - SCCmec type, sau1hsdR, sau1hsdM and sau1hsdS genes involved in Sau1 R-M complex were detected
AB  - by PCR, we
AB  - found five complex types such as M1, R2M2, R2M2, R2M2S1, and R2M2S2. Coagulase serotype I, VI,
AB  - and VIII of
AB  - MSSA were M1, R2M2 and R2M2, respectively. SCCmec type II and coagulase serotype II, SCCmec
AB  - type III and
AB  - coagulase serotype III, SCCmec type IV and coagulase serotype V, and SCCmec type IV and
AB  - coagulase serotype IV,
AB  - VII of MRSA were Sau1 R-M complex type R2M2S1, R2M2, R2M2, and R2M2S2, respectively. Taken
AB  - together,
AB  - correlation between Sau1 R-M complex types and coagulase or SCCmec types of S. aureus was
AB  - found.
ER  -

TY  - JOUR
AU  - Kim, U.Y.
AU  - Jon, S.C.
AU  - Ra, S.R.
TI  - Optimal culture condition of restriction endonuclease Bci528I producing strain by QE method.
JO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
PY  - 2008
SP  - 42
EP  - 43
VL  - 97
AB  - In this paper we determine optimal culture condition of Bacillus circulans 528 on production
AB  - of a new restriction endonuclease Bci528I by QE method.
ER  -

TY  - JOUR
AU  - Kim, W.J.
AU  - Kim, Y.O.
AU  - Kim, D.G.
AU  - Nam, B.H.
AU  - Kong, H.J.
AU  - Jung, H.
AU  - Lee, S.J.
AU  - Kim, D.W.
AU  - Kim, D.S.
AU  - Chae, S.H.
TI  - Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells.
JO  - Genome Announcements
PY  - 2013
SP  - e00772
EP  - e00713
VL  - 1
AB  - Idiomarina sp. strain 28-8 is an aerobic, Gram-negative, flagellar bacterium isolated from the
AB  - bodies of ark shells (Scapharca broughtonii) collected from
AB  - underwater sediments in Gangjin Bay, South Korea. Here, we present the draft
AB  - genome sequence of Idiomarina sp. 28-8 (2,971,606 bp, with a G+C content of
AB  - 46.9%), containing 2,795 putative coding sequences.
ER  -

TY  - JOUR
AU  - Kim, W.J.
AU  - Kim, Y.O.
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Kim, D.W.
AU  - Lee, J.S.
AU  - Kong, H.J.
AU  - Nam, B.H.
AU  - Kim, B.S.
AU  - Lee, S.J.
AU  - Park, H.S.
AU  - Chae, S.H.
TI  - Draft Genome Sequence of Kocuria rhizophila P7-4.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4286
EP  - 4287
VL  - 193
AB  - We report the draft genome sequence of Kocuria rhizophila P7-4, which was isolated from the
AB  - intestine of Siganus doliatus caught in the Pacific
AB  - Ocean. The 2.83-Mb genome sequence consists of 75 large contigs (>100 bp
AB  - in size) and contains 2,462 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Kim, Y.
AU  - Blasche, S.
AU  - Patil, K.R.
TI  - Draft Genome Sequences of Three Novel Low-Abundance Species Strains Isolated from Kefir Grain.
JO  - Genome Announcements
PY  - 2017
SP  - e00869
EP  - e00817
VL  - 5
AB  - We report here the genome sequences of three novel bacterial species strains-Bacillus
AB  - kefirresidentii Opo, Rothia kefirresidentii KRP, and
AB  - Streptococcus kefirresidentii YK-isolated from kefir grains collected in Germany.
AB  - The draft genomes of these isolates were remarkably dissimilar (average
AB  - nucleotide identities, 77.80%, 89.01%, and 92.10%, respectively) to those of the
AB  - previously sequenced strains.
ER  -

TY  - JOUR
AU  - Kim, Y.
AU  - Chandrasegaran, S.
TI  - Chimeric restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 883
EP  - 887
VL  - 91
AB  - Fok I restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide
AB  - 5'-GGATG-3'-5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nt away from the recognition
AB  - site. Recently, we reported the presence of two distinct and separable domains within this
AB  - enzyme: one for the sequence-specific recognition of DNA (the DNA-binding domain) and the
AB  - other for the endonuclease activity (the cleavage domain). Here, we report the construction of
AB  - a chimeric restriction endonuclease by linking the Drosphila Ultrabithorax homeodomain to the
AB  - cleavage domain (F/N) of Fok I restriction endonuclease. The hybrid enzyme, Ubx-F/N, was
AB  - purified, and its cleavage properties were characterized. The hybrid enzyme show the same DNA
AB  - sequence-binding preference as that of Ubx; as expected, it cleaves the DNA away from the
AB  - recognition site. On the 5'-TTAATGGTT-3' strand the hybrid enzyme cleaves 3 nt away from the
AB  - recognition site, whereas it cuts the complementary 5'-AACCATTAA-3' strand 8, 9, or 10 nt
AB  - away from the binding site. Similarly engineered hybrid enzymes could be valuable tools in
AB  - physical mapping and sequencing of large eukaryotic genomes.
ER  -

TY  - JOUR
AU  - Kim, Y.
AU  - Choi, J.
AU  - Grable, J.C.
AU  - Greene, P.
AU  - Hager, P.
AU  - Rosenberg, J.M.
TI  - Studies on the canonical DNA-EcoRI endonuclease complex and the EcoRI kink.
JO  - Structural Biology: The State of the Art.
PY  - 1994
SP  - 225
EP  - 246
VL  - 0
AB  - The crystal structure of the complex between EcoRI endonuclease and the cognate
AB  - oligonucleotide TCGCGAATTCGCG was determined to 2.7 A resolution by multiple isomorphous
AB  - derivatives and refined to an R-factor of 0.21.  The complex includes two protein subunits
AB  - related by a two-fold axis of rotational symmetry; they have alpha/beta architecture with the
AB  - cleavage site at a "switch point" of the beta sheet.  Sequence specificity is mediated by
AB  - eighteen hydrogen bonds and numerous Van der Walls contacts between the protein and the DNA
AB  - bases.  The DNA is distorted in the complex; the "EcoRI kink" is characterized by unusual
AB  - roll, increased rise, underwinding, a "kink" or "jog" in the backbone at the ApA step and
AB  - widening of both the major and minor grooves.
ER  -

TY  - JOUR
AU  - Kim, Y.
AU  - Grable, J.C.
AU  - Love, R.
AU  - Greene, P.J.
AU  - Rosenberg, J.M.
TI  - Refinement of EcoRI endonuclease crystal structure: A revised protein chain tracing.
JO  - Science
PY  - 1990
SP  - 1307
EP  - 1309
VL  - 249
AB  - None
ER  -

TY  - JOUR
AU  - Kim, Y.-G.
AU  - Cha, J.
AU  - Chandrasegaran, S.
TI  - Hybrid restriction enzymes: Zinc finger fusions to FokI cleavage domain.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 1156
EP  - 1160
VL  - 93
AB  - A long-term goal in the field of restriction-modification enzymes has been to generate
AB  - restriction endonucleases with novel sequence specificities by mutating or engineering
AB  - existing enzymes.  This will avoid the increasingly arduous task of extensive screening of
AB  - bacteria and other microorganisms for new enzymes.  Here, we report the deliberate creation of
AB  - novel site-specific endonucleases by linking two different zinc finger proteins to the
AB  - cleavage domain of FokI endonuclease.  Both fusion proteins are active and under optimal
AB  - conditions cleave DNA in a sequence-specific manner.  Thus, the modular structure of FokI
AB  - endonuclease and the zinc finger motifs makes it possible to create "artificial" nucleases
AB  - that will cut DNA near a predetermined site.  This opens the way to generate many new enzymes
AB  - with tailor-made sequence specifities desirable for various applications.
ER  -

TY  - JOUR
AU  - Kim, Y.-G.
AU  - Kim, P.S.
AU  - Herbert, A.
AU  - Rich, A.
TI  - Construction of a Z-DNA-specific restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 12875
EP  - 12879
VL  - 94
AB  - Novel restriction enzymes can be created by fusing the nuclease domain of FokI endonuclease
AB  - with defined DNA binding domains.  Recently, we have characterized a domain (Za) from the
AB  - N-terminal region of human double-stranded RNA adenosine deaminase, which binds the
AB  - Z-conformation with high specificity.  Here we report creation of a conformation-specific
AB  - endonuclease, Za nuclease, which is a chimera of Za and FokI nuclease.  Purified Za nuclease
AB  - cleaves negatively supercoiled plasmids only when they contain a Z-DNA forming insert, such as
AB  - (dC-dG)13.  The precise location of the cleavage sites was determined by primer extension.
AB  - Cutting has been mapped to the edge of the B-Z junction, suggesting that Za nuclease binds
AB  - within the Z-DNA insert, but cleaves in the nearby B-DNA, by using a mechanism similar to type
AB  - IIs restriction enzymes.  These data show that Za binds Z-DNA in an environment similar to
AB  - that in a cell.  Za nuclease, a structure-specific restriction enzyme, may be a useful tool
AB  - for further study of the biological role of Z-DNA.
ER  -

TY  - JOUR
AU  - Kim, Y.-G.
AU  - Li, L.
AU  - Chandrasegaran, S.
TI  - Insertion and deletion mutants of FokI restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 31978
EP  - 31982
VL  - 269
AB  - FokI restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide,
AB  - 5'-GGATG-3':5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nucleotides away from the
AB  - recognition site. We have reported the presence of two distinct and separable protein domains
AB  - within this enzyme: one for the sequence-specific recognition of DNA (the DNA binding domain)
AB  - and the other for the endonuclease's activity (the cleavage domain). Our studies have
AB  - suggested that the two domains are connected by a linker region, which appears to be amenable
AB  - for repositioning of the DNA-sequence recognition domain with respect to the catalytic domain.
AB  - Here, we report the construction of several insertion (4-, 8-, 12-, 18-, 19-, or 23-amino acid
AB  - residues) and deletion (4- or 7-amino acid residues) mutants of the linker region of FokI
AB  - endonuclease. The mutant enzymes were purified, and their cleavage properties were
AB  - characterized. The mutants have the same DNA sequence specificity as the wild-type enzyme.
AB  - However, compared with the wild-type enzyme, the insertion mutants cleave predominantly one
AB  - nucleotide further away from the recognition site on both strands of the DNA substrate. The
AB  - four-codon deletion mutant shows relaxed specificity at the cut site while the seven-codon
AB  - deletion appears to inactivate the enzyme. The DNA binding and cleavage domains of FokI appear
AB  - to be linked by a relatively malleable linker. No simple linear relationship exists between
AB  - the linker length and the distance of the cut site from the recognition site. Furthermore, the
AB  - four-codon insertion mutants cleave DNA substrates containing hemi-methylated FokI sites; they
AB  - do not cleave fully methylated substrates. These results are best explained as a consequence
AB  - of protein-protein interactions between the domains.
ER  -

TY  - JOUR
AU  - Kim, Y.-G.
AU  - Shi, Y.
AU  - Berg, M.
AU  - Chandrasegaran, S.
TI  - Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions.
JO  - Gene
PY  - 1997
SP  - 43
EP  - 49
VL  - 203
AB  - Zinc-finger proteins of the Cys2His2 type bind DNA-RNA hybrids with affinities comparable to
AB  - those for DNA duplexes.  Such zinc-finger proteins were converted into site-specific cleaving
AB  - enzymes by fusing them to the FokI cleavage domain.  The  proteins are active and under
AB  - optimal conditions cleave DNA duplexes in a sequence-specific manner.  These fusions also
AB  - exhibit site-specific cleavage of the DNA strand within DNA-RNA hybrids albeit at a lower
AB  - efficiency (~/-50-fold) compared to the cleavage of the DNA duplexes.  These engineered
AB  - endonucleases represent the first of their kind in terms of their DNA-RNA cleavage properties,
AB  - and they may have important biological applications.
ER  -

TY  - JOUR
AU  - Kim, Y.-G.
AU  - Smith, J.
AU  - Durgesha, M.
AU  - Chandrasegaran, S.
TI  - Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.
JO  - Biol. Chem.
PY  - 1998
SP  - 489
EP  - 495
VL  - 379
AB  - Gal4, a yeast protein, activates transcription of genes required for metabolism of galactose
AB  - and melibiose.  It binds as a dimer to a consensus palindromic 17-base pair DNA sequence.  It
AB  - is a member of the third family of proteins that contain zinc-mediated peptide loops that
AB  - interact specifically with nucleic acids.  Gal4 has a very distinctive zinc coordination
AB  - profile and mode of DNA-binding.  Here, we report the creation of a novel site-specific
AB  - endonuclease by linking the N-terminal 147 amino acids of Gal4 to the cleavage domain of FokI
AB  - endonuclease.  The fusion protein is active and under optimal conditions, binds to a 17 bp
AB  - consensus DNA site and cleaves near this site.  As expected, the cleavage occurs on either
AB  - side of the consensus binding site(s).
ER  -

TY  - JOUR
AU  - Kim, Y.J.
AU  - Sukweenadhi, J.
AU  - Seok, J.W.
AU  - Kang, C.H.
AU  - Choi, E.S.
AU  - Subramaniyam, S.
AU  - Yang, D.C.
TI  - Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 63
EP  - 63
VL  - 12
AB  - This article reports the full genome sequence of Paenibacillus yonginensis DCY84T (KCTC33428,
AB  - JCM19885), which is a Gram-positive rod-shaped bacterium isolated
AB  - from humus soil of Yongin Forest in Gyeonggi Province, South Korea. The genome
AB  - sequence of strain DCY84T provides greater understanding of the Paenibacillus
AB  - species for practical use. This bacterium displays plant growth promotion via
AB  - induced systemic resistance of abiotic stresses.
ER  -

TY  - JOUR
AU  - Kim, Y.O.
AU  - Kim, W.J.
AU  - Choi, S.H.
AU  - Kim, D.S.
AU  - Kim, D.W.
AU  - Lee, J.S.
AU  - Kong, H.J.
AU  - Nam, B.H.
AU  - Kim, B.S.
AU  - Lee, S.J.
AU  - Park, H.S.
AU  - Chae, S.H.
TI  - Genome Sequence of Acinetobacter sp. Strain P8-3-8, Isolated from Fistularia commersonii in Vietnam.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4288
EP  - 4289
VL  - 193
AB  - Acinetobacter sp. strain P8-3-8 is an aerobic, Gram-negative marine bacterium isolated from
AB  - the intestine of the bluespotted cornetfish
AB  - (Fistularia commersonii). Here, we present the draft genome sequence of
AB  - Acinetobacter sp. P8-3-8 (3,905,565 bp, with a G+C content of 37.6%)
AB  - containing 3,621 putative coding sequences. The genome data reveal a high
AB  - density of genes encoding transcriptional regulators involved in anaerobic
AB  - respiration.
ER  -

TY  - JOUR
AU  - Kim, Y.R.
AU  - Park, S.
AU  - Kim, T.S.
AU  - Kim, M.K.
AU  - Han, J.H.
AU  - Joung, Y.
AU  - Kim, S.B.
TI  - Draft Genome Sequence of Streptacidiphilus oryzae TH49T, an Acidophilic Actinobacterium Isolated from Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00703
EP  - e00715
VL  - 3
AB  - The draft genome sequence of Streptacidiphilus oryzae strain TH49(T), an acidophilic
AB  - actinobacterium, was obtained. The draft is composed of six scaffolds
AB  - totaling 7.8 Mbp, and it contains 6,829 protein-coding genes and 91 RNA genes.
AB  - Genes related to respiratory nitrate reduction, siderophore production, and
AB  - biosynthesis of other secondary metabolites were identified.
ER  -

TY  - JOUR
AU  - Kim, Y.S.
AU  - Jeong, J.O.
AU  - Cho, S.H.
AU  - Jeong, D.Y.
AU  - Uhm, T.-B.
TI  - Antimicrobial and Biogenic Amine-Degrading Activity of.
JO  - Misaengmul Hakhoe Chi
PY  - 2012
SP  - 163
EP  - 170
VL  - 48
AB  - In order to inhibit the growth of pathogens and degrade biogenic amines during the
AB  - fermentation of soybean products, an isolate with antimicrobial activity against pathogens and
AB  - biogenic amine-degrading property was obtained from 83 traditionally fermented soybean
AB  - products. The morphological and biochemical tests and the phylogenetic relationship among 16S
AB  - rRNA gene sequences indicated that the isolate named as the strain SCK B11 was most closely
AB  - related to Bacillus licheniformis. The cell-free supernatant of two day cultures was active
AB  - against several pathogens including Enterococcus faecalis, Listeria monocytosis, Micrococcus
AB  - luteus, Pseudomonas aeruginosa, Bacillus cereus, and Staphylococcus aureus. PCR analysis was
AB  - conducted to determine relatedness to antimicrobial lantibiotics and biosurfactants produced
AB  - by Bacillus spp., but showed negative for the genes encoding surfactin, lichenysin, and
AB  - lichenicidine. Electron microscopic observation indicated that the antimicrobial agent seemed
AB  - to attack the membrane of the pathogens, leaving the ghost or shrunken cells. The strain was
AB  - found to degrade histamine by 72% and tyramine by 66% in the cooked soybean containing 5.3% of
AB  - biogenic amine over 10 days of fermentation time. The use of selected strain would be a
AB  - potential control measure in manufacturing traditionally fermented soybean products that are
AB  - difficult to control pathogens and biogenic amine levels.
ER  -

TY  - JOUR
AU  - Kim, Y.S.
AU  - Rho, H.M.
TI  - Characterization of the restriction endonuclease BdiI from Brevibacterium divaricatum.
JO  - Korean J. Microbiol.
PY  - 1986
SP  - 18
EP  - 23
VL  - 24
AB  - A new type II restriction endonuclease, BdiI, has been isolated from Brevibacterium
AB  - divaricatum FERM 5948 by procedures of ammonium sulfate fractionation, DEAE-cellulose
AB  - chromatography and heparin agarose chromatography. The purified BdiI restriction endonuclease
AB  - had the same cleavage patterns as ClaI whose recognition sequence is 5'ATCGAT3'. From the
AB  - result that lambda-ClaI DNA fragment could be cloned in pBR322 digested with BdiI, it has been
AB  - proven that BdiI cuts between T and C (R'AT/CGAT3') within the recognition sequence and
AB  - produces 5'pCG cohesive end. The optimal temperature for the BdiI restriction endonuclease
AB  - activity was 37C, and optimal salt (NaCl) concentration was 50-100 mM.
ER  -

TY  - JOUR
AU  - Kim, Y.S.
AU  - Rho, H.M.
TI  - Purification and Characterization of PstI Methylase from Providencia stuartii 164.
JO  - Korean Biochem. J.
PY  - 1984
SP  - 107
EP  - 119
VL  - 17
AB  - In this report, we described the purification and characterization of PstI
AB  - methylase from Providencia stuartii 164.  PstI methylase was a site-specific
AB  - methylase and has been found to have methylation activity on single-stranded
AB  - PhiX174 DNA.  This purified PstI methylase will be valuable for the study of
AB  - the structure and expression of PstI restriction-modification gene.
ER  -

TY  - JOUR
AU  - Kimball, M.
AU  - Linn, S.
TI  - The release of oligonucleotides by the Escherichia coli B restriction endonuclease.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1976
SP  - 585
EP  - 591
VL  - 68
AB  - The Escherichia coli B (Eco B) restriction endonuclease releases approximately
AB  - 75 nucleotides as acid-soluable oligonucleotides for each single-strand
AB  - endonucleolytic scission that it catalyzes.  This reaction, like the
AB  - endonucleolytic cleavage, requires ATP, Mg++, S-adenosylmethionine, and
AB  - unmodified DNA containing appropriate specificity sites.  Like the endonuclease
AB  - reaction, the release of oligonucleotides terminates after roughly 5 minutes.
AB  - The acid-soluable oligonucleotides have an average chain length of roughly 7,
AB  - and an apparently random base composition.
ER  -

TY  - JOUR
AU  - Kimbrel, J.A.
AU  - Chang, J.
AU  - Arp, D.J.
AU  - Sayavedra-Soto, L.A.
TI  - The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities.
JO  - Genome Announcements
PY  - 2013
SP  - e00439
EP  - e00413
VL  - 1
AB  - Nocardioides sp. strain CF8 was isolated from a soil sample collected at the Hanford
AB  - Department of Energy site, Richland, WA. The strain was identified in
AB  - microcosms based on its ability to grow on butane and has been characterized for
AB  - its potential applications in the biodegradation of halogenated hydrocarbons.
AB  - Here, the draft genome sequence is reported.
ER  -

TY  - JOUR
AU  - Kimelman, A.
AU  - Levy, A.
AU  - Sberro, H.
AU  - Kidron, S.
AU  - Leavitt, A.
AU  - Amitai, G.
AU  - Yoder-Himes, D.
AU  - Wurtzel, O.
AU  - Zhu, Y.
AU  - Rubin, E.
AU  - Sorek, R.
TI  - A vast collection of microbial genes that are toxic to bacteria.
JO  - Genome Res.
PY  - 2012
SP  - 802
EP  - 809
VL  - 22
AB  - In the process of clone-based genome sequencing, initial assemblies frequently
AB  - contain cloning gaps that can be resolved using cloning-independent methods, but
AB  - the reason for their occurrence is largely unknown. By analyzing 9,328,693
AB  - sequencing clones from 393 microbial genomes, we systematically mapped more than
AB  - 15,000 genes residing in cloning gaps and experimentally showed that their
AB  - expression products are toxic to the Escherichia coli host. A subset of these
AB  - toxic sequences was further evaluated through a series of functional assays
AB  - exploring the mechanisms of their toxicity. Among these genes, our assays
AB  - revealed novel toxins and restriction enzymes, and new classes of small,
AB  - non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses
AB  - also revealed abundant, short, toxic DNA fragments that were predicted to
AB  - suppress E. coli growth by interacting with the replication initiator DnaA. Our
AB  - results show that cloning gaps, once considered the result of technical problems,
AB  - actually serve as a rich source for the discovery of biotechnologically valuable
AB  - functions, and suggest new modes of antimicrobial interventions.
ER  -

TY  - JOUR
AU  - Kimura, B.
AU  - Takahashi, H.
AU  - Hokimoto, S.
AU  - Tanaka, Y.
AU  - Fujii, T.
TI  - Induction of the histidine decarboxylase genes of Photobacterium damselae subsp. damselae (formally P. histaminum) at low pH.
JO  - J. Appl. Microbiol.
PY  - 2009
SP  - 485
EP  - 497
VL  - 107
AB  - AIMS: To elucidate the detailed mechanism of histamine production by Photobacterium damselae
AB  - subsp. damselae. METHODS AND RESULTS: Histidine decarboxylase and related genes of P. damselae
AB  - subsp. damselae were cloned, and three open reading frames named as hdcT, hdcA and hisRS were
AB  - identified. The hdcA gene encodes a polypeptide of 377 amino acids and is considered to be the
AB  - pyridoxal-P dependent histidine decarboxylase. The hdcT gene is assumed to be a
AB  - histidine/histamine antiporter, and the hisRS gene is considered to be a histidyl-tRNA
AB  - synthetase. Recombinant Escherichia coli strains harbouring plasmids carrying the P. damselae
AB  - hdc genes were shown to over-excrete histamine extracellularly. Northern blot analysis and
AB  - quantitative RT-PCR revealed high levels of mono- and bi-cistronic transcripts of hdcA, hdcT
AB  - and hisRS genes under conditions of low pH and histidine excess. CONCLUSIONS: The hdcA gene of
AB  - P. damselae was constructed as an operon with putative histidine/histamine antiporter and
AB  - histidyl-tRNA synthetase. Mono- and poly-cistronic transcripts and acid induction were
AB  - detected. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of cloning the
AB  - histidine decarboxylase gene cluster in gram-negative bacteria. Also, these genes were induced
AB  - under acidic conditions and in the presence of excess histidine.
ER  -

TY  - JOUR
AU  - Kimura, H.
AU  - Ishihara, G.
AU  - Tajima, S.
TI  - Isolation and expression of a Xenopus laevis DNA methyltransferase cDNA.
JO  - J. Biochem. (Tokyo)
PY  - 1996
SP  - 1182
EP  - 1189
VL  - 120
AB  - A Xenopus DNA methyltransferase cDNA was isolated from a Xenopus oocyte cDNA library by
AB  - screening with the mouse DNA methyltransferase cDNA as a probe.  The elucidated nucleotide
AB  - sequence gave a 4,470 nucleotide open reading frame, and the predicted protein was composed of
AB  - 1,490 amino acid residues, showing high homology to animal DNA methyltransferases, especially
AB  - in the catalytic domain in the carboxyl-terminal region.  The cysteine-rich region and the
AB  - Lys-Gly repeat which were first found in the mouse sequence were conserved in Xenopus.
AB  - However, 200 amino acid residues at the amino-terminus of Xenopus DNA methyltransferase were
AB  - quite different from those of mouse and human, but showed 70% homology with those of chicken.
AB  - The cloned Xenopus DNA methyltransferase cDNA expressed in COS1 cells showed a significant DNA
AB  - methyltransferase activity.  The size of the translation product of Xenopus DNA
AB  - methyltransferase cDNA expressed in COS1 cells was identical with that of the endogenous DNA
AB  - methyltransferase in Xenopus A6 cells and also with the size of newly synthesized DNA
AB  - methyltransferase in Xenopus oocytes.  However, a slightly larger immunoreactive band of about
AB  - 205 kDa, and a small immunoreactive band of about 100 kDa, which were poorly labeled by short
AB  - incubation with radiolabeled amino acids, were the main bands in stage I-III and stage IV-VI
AB  - oocytes, respectively.
ER  -

TY  - JOUR
AU  - Kimura, H.
AU  - Nakamura, T.
AU  - Ogawa, T.
AU  - Tanaka, S.
AU  - Shiota, K.
TI  - Transcription of mouse DNA methyltransferase 1 (Dnmt1) is regulated by both E2F-Rb-HDAC-dependent and -independent pathways.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 3101
EP  - 3113
VL  - 31
AB  - Abnormal expression of Dnmt1 in vivo induces cellular alterations such as transformation, and
AB  - an increase in Dnmt1 mRNA plays a causal role in
AB  - c-fos-, ras- and SV40 large T antigen-induced transformation of
AB  - fibroblasts in vitro. Here, we have investigated the regulation of Dnmt1
AB  - transcription. We identified the promoter region and major transcription
AB  - start sites of mouse Dnmt1 and found two important cis-elements within the
AB  - core promoter region. One is an E2F binding site, and the other is a
AB  - binding site for an as yet unidentified factor. Point mutations in the two
AB  - cis-elements decreased promoter activity in both non-transformed and
AB  - transformed cells. Thus, both sites play a critical role in regulation of
AB  - Dnmt1 transcription in proliferating cells. Treatment with trichostatin A,
AB  - a specific inhibitor of histone deacetylase, increased Dnmt1 promoter
AB  - activity in G0/G1-arrested NIH 3T3 cells. Furthermore, the decrease in
AB  - promoter activity induced by expression of E2F-1 and Rb was reversed by
AB  - trichostatin A treatment of Saos-2 cells. Taken together, these data
AB  - indicate that transcription of Dnmt1 is regulated in a complex fashion by
AB  - E2F and other transcription factors through E2F-Rb-HDAC-dependent and
AB  - -independent pathways. These findings suggest that Dnmt1 is a target gene
AB  - of these pathways in cell proliferation, cell transformation and
AB  - tumorigenesis.
ER  -

TY  - JOUR
AU  - Kimura, H.
AU  - Shiota, K.
TI  - Methyl-CpG-binding Protein, MeCP2, Is a Target Molecule for Maintenance DNA Methyltransferase, Dnmt1.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 4806
EP  - 4812
VL  - 278
AB  - During mammalian cell division, DNA methylation patterns are transferred accurately to the
AB  - newly synthesized DNA strand. This depends on
AB  - maintenance DNA methyltransferase activity. DNA methylation can affect
AB  - chromatin organization and gene expression by recruitment of histone
AB  - deacetylases (HDACs). Here we show that the methyl-CpG binding protein,
AB  - MeCP2, interacts directly with the maintenance DNA methyltransferase,
AB  - Dnmt1. The region of MeCP2 that interacts with Dnmt1 corresponds to the
AB  - transcription repressor domain which can also recruit HDACs via a
AB  - corepressor, mSin3A. Dnmt1 can form complexes with HDACs as well as MeCP2.
AB  - Surprisingly, the MeCP2-Dnmt1 complex does not contain the histone
AB  - deacetylase, HDAC1. Thus, Dnmt1 takes the place of the mSin3A-HDAC1
AB  - complex, indicating that the MeCP2-interacting Dnmt1 does not bind to
AB  - HDAC1. Further, we demonstrate that MeCP2 can form a complex with
AB  - hemimethylated as well as fully methylated DNA. Immunoprecipitated MeCP2
AB  - complexes show DNA methyltransferase activity to hemimethylated DNA. These
AB  - results suggest that Dnmt1 associates with MeCP2 in order to perform
AB  - maintenance methylation in vivo. We propose that genome-wide and/or
AB  - -specific local DNA methylation may be maintained by the Dnmt1-MeCP2
AB  - complexes, bound to hemimethylated DNA. Dnmt1 may be recruited to targeted
AB  - regions via multiple steps that may or may not involve histone
AB  - deacetylases.
ER  -

TY  - JOUR
AU  - Kimura, H.
AU  - Suetake, I.
AU  - Tajima, S.
TI  - Xenopus maintenance-type DNA methyltransferase is accumulated and translocated into germinal vesicles of oocytes.
JO  - J. Biochem. (Tokyo)
PY  - 1999
SP  - 1175
EP  - 1182
VL  - 125
AB  - In vertebrates, DNA methylation plays an important role in the regulation of gene expression
AB  - and embryogenesis. DNA methyltransferase, which catalyzes the introduction of a methyl group
AB  - at the 5th position of cytosine in the CpG sequence, is highly accumulated in mouse oocytes
AB  - and is excluded from nuclei [Carlson et al. (1992) Genes Dev. 6, 2536-2541]. In this study, we
AB  - examined the expression level and localization of Xenopus DNA methyltransferase in oocytes
AB  - during oogenesis. The DNA methyltransferase protein was detectable in stage III oocytes and
AB  - increased thereafter, until the oocytes had matured. The rate of DNA methyltransferase
AB  - synthesis rapidly increased after stage IV oocytes. Different from in mouse oocytes, DNA
AB  - methyltransferase was equally distributed in the nuclear and post-nuclear fractions, in stage
AB  - VI oocytes. DNA methyltransferase translocated into nuclei was uniformly localized in the
AB  - nuclear matrix, and the accumulated DNA methyltransferase in stage VI nuclei had DNA
AB  - methylation activity.
ER  -

TY  - JOUR
AU  - Kimura, H.
AU  - Takeda, T.
AU  - Tanaka, S.
AU  - Ogawa, T.
AU  - Shiota, K.
TI  - Expression of rat DNA (cytosine-5) methyltransferase (DNA MTase) in rodent trophoblast giant cells: Molecular cloning and characterization of rat DNA MTase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1998
SP  - 495
EP  - 501
VL  - 253
AB  - Methylation of genomic DNA is involved in the basic mechanism of gene inactivation, chromatin
AB  - organization, X chromosome inactivation and genomic imprinting.  A pattern of DNA methylation
AB  - is maintained in mitotic cells by DNA (cytosine-5) methyltransferase (DNA MTase).  The DNA
AB  - MTase has been shown to be also expressed in postmitotic cells such as neurons.  In the
AB  - present report, as an approach to analyzing mechanisms underlying regulation of DNA MTase
AB  - expression, we first isolated rat DNA MTase cDNA.  The isolated cDNA encoded a protein of
AB  - 1,622 amino acid residues showing 88.3% and 64.2% homology with mouse and human DNA MTase,
AB  - respectively.  Northern blot analysis showed that DNA MTase mRNA was highly expressed in
AB  - placenta during mid- to late-pregnancy.  We then analyzed the expression of DNA MTase in
AB  - Rcho-1 cells, a rat choriocarcinoma-derived cell line, which cease cell division but keep
AB  - replicating genomic DNA when differentiated in vitro.  We found that the expression of DNA
AB  - MTase protein was decreased in terminally differentiated Rcho-1 cells whereas DNA MTase mRNA
AB  - was consistently expressed.  This result suggested posttranscriptional regulation of DNA MTase
AB  - activity in Rcho-1 cells.  The Rcho-1 cells would be a valuable model for studying the
AB  - regulation of gene expression and function of DNA MTase in postmitotic, differentiated cells.
ER  -

TY  - JOUR
AU  - Kimura, N.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Hirose, J.
AU  - Watanabe, T.
AU  - Suenaga, H.
AU  - Fujihara, H.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated  from Biphenyl-Contaminated Soil in Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e00059
EP  - e00015
VL  - 3
AB  - Pseudomonas abietaniphila KF717 utilizes biphenyl as a sole source of carbon and  energy and
AB  - degrades polychlorinated biphenyls (PCBs). We report here the
AB  - 6,930,016-bp genome sequence of this strain, which contains 6,323 predicted
AB  - coding sequences (CDSs), including the biphenyl-utilizing bph gene cluster.
ER  -

TY  - JOUR
AU  - Kinch, L.N.
AU  - Ginalski, K.
AU  - Rychlewski, L.
AU  - Grishin, N.V.
TI  - Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 3598
EP  - 3605
VL  - 33
AB  - Restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely
AB  - diverse superfamily that display little sequence similarity despite retaining a common core
AB  - fold responsible for cleavage. The lack of significant sequence similarity between protein
AB  - families makes homology inference a challenging task and hinders new family identification
AB  - with traditional sequence-based approaches. Using the consensus fold recognition method
AB  - Meta-BASIC that combines sequence profiles with predicted protein secondary structure, we
AB  - identify nine new restriction endonuclease-like fold families among previously uncharacterized
AB  - proteins and predict these proteins to cleave nucleic acid substrates. Application of
AB  - transitive searches combined with gene neighborhood analysis allow us to confidently link
AB  - these unknown families to a number of known restriction endonuclease-like structures and thus
AB  - assign folds to the uncharacterized proteins. Finally, our method identifies a novel
AB  - restriction endonuclease-like domain in the C-terminus of RecC that is not detected with
AB  - structure-based searches of the existing PDB database.
ER  -

TY  - JOUR
AU  - Kincheloe, G.N.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2017
SP  - e01599
EP  - e01516
VL  - 5
AB  - Here we present the draft genome of Arthrobacter sp. strain UCD-GKA. The assembly contains
AB  - 4,930,274 bp in 33 contigs. This strain was isolated from the handle of
AB  - a weight bar in the UC Davis Activities and Recreation Center.
ER  -

TY  - JOUR
AU  - Kinder, S.A.
AU  - Badger, J.L.
AU  - Bryant, G.O.
AU  - Pepe, J.C.
AU  - Miller, V.L.
TI  - Cloning of the YenI restriction endonuclease and methyltransferase from Yersinia enterocolitica serotype O8 and construction of a transformable R-M+ mutant.
JO  - Gene
PY  - 1993
SP  - 271
EP  - 275
VL  - 136
AB  - Two different clonal groups of pathogenic Yersinia enterocolitica strains, American and
AB  - non-American, have been recognized. These are distinguished by a number of criteria, including
AB  - their virulence in a murine model of infection. However, genetic analysis of virulence in
AB  - American strains has been hampered due to the severe restriction of transformed of
AB  - electroporated DNA. Thus, we cloned the yenIMR locus from American serotype strain 8081c,
AB  - which encodes YenI, an isoschizomer pf PstI. This clone encodes both the restriction
AB  - endonuclease and methyltransferase. The location of the genes on the clone was determined and
AB  - this information was used to construct a small deletion (400 bp) that results in an R-M+
AB  - phenotype. This mutation was recombined onto the Y. enterocolitica chromosome to give an R-M+
AB  - mutant which showed at least a 1000-fold increase in electroporation frequency compared to the
AB  - wild-type strain. Southern analysis using a probe derived from yenIMR indicated that American
AB  - serotype strains have this locus whereas non-American serotype strains do not.
ER  -

TY  - JOUR
AU  - King, G.
AU  - Murray, N.E.
TI  - Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12.
JO  - Mol. Microbiol.
PY  - 1995
SP  - 769
EP  - 777
VL  - 16
AB  - Bacteriophage lambda encodes an antirestriction function, Ral, which is able to modulate the
AB  - activity of the Escherichia coli K-12 restriction and modification system, EcoKI. Here we
AB  - report the characterization of an analogous function, Lar, expressed by E. coli sbcA mutants
AB  - and the hybrid phage lambda reverse. E. coli sbcA mutants and lambda reverse both express
AB  - genes of the Rac prophage, and we have located the lar gene immediately downstream of recT in
AB  - this element. The lar gene has been cloned in an expression plasmid, and a combination of
AB  - site-directed mutagenesis and labelling of plasmid-encoded proteins has enabled us to identify
AB  - a number of translational products of lar, the smallest of which is sufficient for restriction
AB  - alleviation. Lar, like Ral, is able both to alleviate restriction and to enhance modification
AB  - by EcoKI. Lar, therefore, is functionally similar to Ral and the nucleotide sequences of their
AB  - genes share 47% identity, indicating a common origin. A comparison of the predicted amino acid
AB  - sequences of Lar and Ral shows only a 25% identity, but a few short regions do align and may
AB  - indicate residues important for structure and/or function.
ER  -

TY  - JOUR
AU  - King, G.
AU  - Murray, N.E.
TI  - Modification enhancement and restriction alleviation by bacteriophage lambda.
JO  - Gene
PY  - 1995
SP  - 225
EP  - 225
VL  - 157
AB  - The activity of EcoKI, and related restriction and modification (R-M) systems, is modulated by
AB  - the bacteriophage lambda ral gene product.  We have identified the coding sequence for an
AB  - analogous function in the Rac prophage of E. coli K-12.
ER  -

TY  - JOUR
AU  - King, G.
AU  - Murray, N.E.
TI  - Restriction enzymes in cells, not eppendorfs.
JO  - Trends Microbiol.
PY  - 1994
SP  - 465
EP  - 469
VL  - 2
AB  - Restriction enzymes are essential reagents to molecular biologists, but their relevance to
AB  - bacterial populations is less obvious. Most bacteria encode restriction and modification
AB  - systems and these are commonly considered to be a barrier to phage infection. Current evidence
AB  - also supports a more general role for them in genetic recombination.
ER  -

TY  - JOUR
AU  - King, J.
AU  - Umezu, K.
AU  - Ryu, J.
TI  - Complementation of type ID restriction-modification systems between KpnAI and StySBLI.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2000
SP  - 371
EP  - 371
VL  - 100
AB  - Type I restriction-modification systems are the most complex R-M systems in bacteria and
AB  - consist of three different subunits, encoded by the hsdR (restriction/cleavage of DNA), hsdM
AB  - (modification/methylation of DNA), and hsdS (recognition of DNA sequence) genes.  KpnAI, a
AB  - restriction system from Klebsiella pneumoniae strain M5a1, is a member of the Type ID family.
AB  - The predicted peptide sequences of KpnAI have a high degree of similarity with the StySBLI
AB  - system, a prototype of type ID, from Salmonella blegdam, showing 95% and 98% homology in the
AB  - HsdR and hsdM peptide sequences, respectively.  Differences in the hsdS genes (44% homology)
AB  - however, suggest that each system has its own distinct DNA recognition sequence.  A series of
AB  - complementation tests were conducted to test whether the two systems are functionally
AB  - homologous.  Classical complementation tests were conducted using chromosomal mutants for
AB  - StySBLI and plasmids containing KpnAI, and then conversely chromosomal mutants for KpnAI and
AB  - plasmids containing StySBLI.  A new complementation method was also conducted by transforming
AB  - two plasmids, containing genes from the KpnAI and StySBLI respectively, into E. coli C.  The
AB  - results were obtained using a classical R-M test with lambda and SBS bacteriophages and
AB  - determining the efficiency of plating (EOP).  The degree of restriction for the StySBLI and
AB  - KpnAI mutants was 10-5 and 10-3, respectively, and 10-3 for the two plasmid complementation.
AB  - The results show that the two different systems are functionally homologous and
AB  - complementable.
ER  -

TY  - JOUR
AU  - King, J.B.
AU  - Bowen, L.M.
AU  - Dupureur, C.M.
TI  - Binding and conformational analysis of phosphoramidate restriction enzyme interactions.
JO  - Biochemistry
PY  - 2004
SP  - 8551
EP  - 8559
VL  - 43
AB  - Phosphoramidates are modified deoxyoligonucleotides that feature nitrogen in place of the
AB  - 3'-oxygen of a phosphodiester linkage. Noted
AB  - for stability against nuclease activity, these linkages are of both
AB  - mechanistic and therapeutic interest. While a number of studies
AB  - characterizing the properties of oligonucleotides composed entirely of
AB  - phosphoramidate linkages have been published, little is known about how
AB  - singly substituted phosphoramidate substitutions affect the
AB  - thermodynamics and structure of protein-oligonucleotide interactions.
AB  - We chose to investigate these interactions with PvuII endonuclease, the
AB  - DNA binding behavior of which is well-characterized. Oligonucleotide
AB  - duplexes containing a phosphoramidate substitution at the scissile
AB  - phosphates were resistant to cleavage by the enzyme, even after
AB  - extended incubations. However, the enzyme was able to cleave the native
AB  - strand in a native: phosphoramidate heteroduplex at a rate comparable
AB  - to that observed with the native substrate. Ca(II)-stimulated PvuII
AB  - binding for a phosphoramidate-substituted oligonucleotide is comparable
AB  - to that of the native duplex (K-d approximate to 200 pM). K-d values
AB  - obtained in the presence of Mg(II) are somewhat weaker (K-d approximate
AB  - to 10 nM). Under metal-free conditions, the enzyme exhibited a
AB  - remarkable approximate to50-fold greater affinity for the modified
AB  - oligonucleotide relative to the native substrate (5 vs 240 nM). While
AB  - P-31 NMR spectra indicate increased chemical shift dispersion in the
AB  - free phosphoramidate duplex, the spectrum of the enzyme-bound duplex is
AB  - similar to that of the native duplex. H-1-N-15 HSQC analysis indicates
AB  - that enzyme conformations in the presence of these oligonucleotides are
AB  - also comparable. The tight binding of the phosphoramidate duplex under
AB  - metal-free conditions and its resistance to cleavage are attributed to
AB  - local conformational adjustments propagating from the O-N substitution.
ER  -

TY  - JOUR
AU  - King, J.S.
AU  - Valcarcel, E.R.
AU  - Rufer, J.T.
AU  - Phillps, J.W.
AU  - Morgan, W.F.
TI  - Noncomplementary DNA double-strand-break rejoining in bacterial and human cells.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 1055
EP  - 1059
VL  - 21
AB  - We examined the rejoining of noncomplementary restriction enzyme-produced DNA double-strand
AB  - breaks in Escherichia coli and in cultured human cells. The enzymes used in this study, ClaI,
AB  - BamHI and SalI, produce double-strand breaks with 5' protruding single strands. The joining
AB  - of a ClaI-produced DNA end to a BamHI-produced end or to a SalI-produced end was examined at
AB  - the DNA sequence level. End rejoining in E.coli was studied by transforming cultures with
AB  - linear plasmid DNA that was gel purified from restriction digests, and end rejoining in
AB  - cultured human cells was studied by introducing enzymes into the cells by electroporation. The
AB  - human cells used contain an Epstein-Barr virus (EBV)-based shuttle vector, pHAZE, that was
AB  - recovered and introduced into E.coli for further analysis. The major products of DNA
AB  - end-joining processes observed in linear plasmid-transformed E.coli and in the human cells
AB  - exposed to restriction enzymes were identical. Furthermore, the deletions observed in both
AB  - systems and in the spontaneous mutant plasmid in untreated human cells had a common underlying
AB  - feature: short stretches of directly repeated DNA at the junction sites.
ER  -

TY  - JOUR
AU  - King, K.
AU  - Benkovic, S.J.
AU  - Modrich, P.
TI  - Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 11807
EP  - 11815
VL  - 264
AB  - Gap repair in the presence of 2'-deoxycytosine 5'-O-(1-thiotriphosphate) has
AB  - been utilized to mutagenize the amino-terminal one-half of the structural gene
AB  - for EcoRI endonuclease.  This approach has led to identification of over 200
AB  - mutants defective in endonuclease function.  One mutant protein, which binds to
AB  - the EcoRI sequence but displays greatly reduced cleavage activity, is the
AB  - consequence of a Glu to Gly change at position 111.  This protein has been
AB  - purified to homogeneity and characterized in detail.  Subunit interactions
AB  - governing the tetramer to dimer transition of the mutant endonuclease are near
AB  - normal as are parameters governing its interaction with specific and
AB  - nonspecific DNA sequences.  However, the rate constants for first and second
AB  - strand cleavage steps are reduced by 60,000- and 30,000-fold, respectively, as
AB  - a consequence of the Glu->Gly change.  The defect in chemical cleavage steps
AB  - can be partially overcome by elevating the pH of the reaction buffer from 7.6
AB  - to 8.5, conditions which enhance the rate of EcoRI strand cleavage by wild type
AB  - enzyme to a similar degree.  We suggest that the Glu-111 mutation affects an
AB  - interface between recognition and cleavage functions of the enzyme, an idea
AB  - consistent with the suggestion that the cleavage center of the endonuclease is
AB  - subject to activation upon specific recognition of the EcoRI sequence.
ER  -

TY  - JOUR
AU  - King, K.
AU  - Wright, D.
AU  - Modrich, P.
TI  - Mutationally altered forms of EcoRI endonuclease selectively defective in DNA cleavage.
JO  - Fed. Proc.
PY  - 1986
SP  - 1913
EP  - 1913
VL  - 45
AB  - Gap repair in the presence of dNTP[alpha-S] has been utilized to mutagenize
AB  - regions of the structural gene for EcoRI endonuclease.  This approach has led
AB  - to identification of several mutant enzymes which retain specific affinity for
AB  - the EcoRI sequence, but display greatly reduced cleavage activity.  One such
AB  - protein, involving a Glu to Gly change at position 111 (BG111), has been
AB  - purified to homogeneity and characterized in detail.  Thermodynamic and kinetic
AB  - parameters governing interaction of the mutant protein with the EcoRI sequence
AB  - are comparable to values for the wild type enzyme.  subunit interactions
AB  - governing the tetramer to dimer transition are also normal.  However, the first
AB  - order rate constants for first and second strand cleavage steps are reduced by
AB  - a factor of at least 10,000-fold relative to wild type endonuclease.  We
AB  - suggest that this mutation affects the interface between recognition and
AB  - cleavage domains of the enzyme.
ER  -

TY  - JOUR
AU  - King, K.
AU  - Wright, D.J.
AU  - Modrich, P.
TI  - Glutamate 111 of EcoRI endonuclease is required for DNA cleavage activation.
JO  - Miami BioTechnology Winter Symposium
PY  - 1988
SP  - 79
EP  - 79
VL  - 8
AB  - The EcoRI restriction endonuclease is a well-characterized model system for
AB  - studying the interaction of enzymes with specific DNA sequences.  X-ray
AB  - crystallography has revealed major features of the interaction of this enzyme
AB  - with DNA, but has not answered important questions about the mechanism of DNA
AB  - cleavage.  We have used the cloned EcoRI endonuclease gene as a target for
AB  - site-directed mutagenesis to probe the functional role of various amino acid
AB  - residues in the enzyme.  Our studies demonstrate that glutamate 111 plays a
AB  - critical role in activation of the cleavage function of the enzyme.
ER  -

TY  - JOUR
AU  - King, K.W.
AU  - Dybvig, K.
TI  - Transformation of Mycoplasma capricolum and examination of DNA restriction modification in M. capricolum and Mycroplasma mycoides subsp. mycoides.
JO  - Plasmid
PY  - 1994
SP  - 308
EP  - 311
VL  - 31
AB  - Plasmids pIKD and pIKD-erm have recently been developed as mycoplasmal cloning vectors. In
AB  - this report, we demonstrate that these plasmids can replicate in Mycoplasma capricolum, a
AB  - mycoplasmal species for which transformation had not previously been characterized. Both
AB  - plasmids are stably maintained at a higher copy number than in their parental species,
AB  - Mycoplasma mycoides subsp. mycoides. We have also examined the possibility of one or more
AB  - restriction-modification systems affecting transformation frequencies in both species.
ER  -

TY  - JOUR
AU  - King, R.A. et al.
TI  - Genome Sequences of Subcluster K5 Mycobacteriophages AlleyCat, Edugator, and Guillsminger.
JO  - Genome Announcements
PY  - 2017
SP  - e01122
EP  - e01117
VL  - 5
AB  - Bacteriophages AlleyCat, Edugator, and Guillsminger were isolated on Mycobacterium smegmatis
AB  - mc(2)155 from enriched soil samples. All are members of
AB  - mycobacteriophage subcluster K5, with genomes of 62,112 to 63,344 bp. Each genome
AB  - contains 92 to 99 predicted protein-coding genes and one tRNA. Guillsminger is
AB  - the first mycobacteriophage to carry an IS1380 family transposon.
ER  -

TY  - JOUR
AU  - Kingry, L.C.
AU  - Batra, D.
AU  - Replogle, A.
AU  - Rowe, L.A.
AU  - Pritt, B.S.
AU  - Petersen, J.M.
TI  - Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii.
JO  - PLoS ONE
PY  - 2016
SP  - E0168994
EP  - E0168994
VL  - 11
AB  - Borrelia mayonii, a Borrelia burgdorferi sensu lato (Bbsl) genospecies, was
AB  - recently identified as a cause of Lyme borreliosis (LB) among patients from the
AB  - upper midwestern United States. By microscopy and PCR, spirochete/genome loads in
AB  - infected patients were estimated at 105 to 106 per milliliter of blood. Here, we
AB  - present the full chromosome and plasmid sequences of two B. mayonii isolates,
AB  - MN14-1420 and MN14-1539, cultured from blood of two of these patients. Whole
AB  - genome sequencing and assembly was conducted using PacBio long read sequencing
AB  - (Pacific Biosciences RSII instrument) followed by hierarchical genome-assembly
AB  - process (HGAP). The B. mayonii genome is ~1.31 Mbp in size (26.9% average GC
AB  - content) and is comprised of a linear chromosome, 8 linear and 7 circular
AB  - plasmids. Consistent with its taxonomic designation as a new Bbsl genospecies,
AB  - the B. mayonii linear chromosome shares only 93.83% average nucleotide identity
AB  - with other genospecies. Both B. mayonii genomes contain plasmids similar to B.
AB  - burgdorferi sensu stricto lp54, lp36, lp28-3, lp28-4, lp25, lp17, lp5, 5 cp32s,
AB  - cp26, and cp9. The vls locus present on lp28-10 of B. mayonii MN14-1420 is
AB  - remarkably long, being comprised of 24 silent vls cassettes. Genetic differences
AB  - between the two B. mayonii genomes are limited and include 15 single nucleotide
AB  - variations as well as 7 fewer silent vls cassettes and a lack of the lp5 plasmid
AB  - in MN14-1539. Notably, 68 homologs to proteins present in B. burgdorferi sensu
AB  - stricto appear to be lacking from the B. mayonii genomes. These include the
AB  - complement inhibitor, CspZ (BB_H06), the fibronectin binding protein, BB_K32, as
AB  - well as multiple lipoproteins and proteins of unknown function. This study shows
AB  - the utility of long read sequencing for full genome assembly of Bbsl genomes,
AB  - identifies putative genome regions of B. mayonii that may be linked to clinical
AB  - manifestation or tissue tropism, and provides a valuable resource for
AB  - pathogenicity, diagnostic and vaccine studies.
ER  -

TY  - JOUR
AU  - Kingry, L.C.
AU  - Batra, D.
AU  - Replogle, A.
AU  - Sexton, C.
AU  - Rowe, L.
AU  - Stermole, B.M.
AU  - Christensen, A.M.
AU  - Schriefer, M.E.
TI  - Chromosome and Linear Plasmid Sequences of a 2015 Human Isolate of the Tick-Borne Relapsing Fever Spirochete, Borrelia turicatae.
JO  - Genome Announcements
PY  - 2016
SP  - e00655
EP  - e00616
VL  - 4
AB  - The sequences of the complete linear chromosome and 7 linear plasmids of the relapsing fever
AB  - spirochete Borrelia turicatae are presented in this report. The
AB  - 925,547 bp of chromosome and 380,211 bp of plasmid sequence were predicted to
AB  - contain a total of 1,131 open reading frames, with an average G+C content of
AB  - 29.7%.
ER  -

TY  - JOUR
AU  - Kingry, L.C.
AU  - Replogle, A.
AU  - Batra, D.
AU  - Rowe, L.A.
AU  - Sexton, C.
AU  - Dolan, M.
AU  - Connally, N.
AU  - Petersen, J.M.
AU  - Schriefer, M.E.
TI  - Toward a Complete North American Borrelia miyamotoi Genome.
JO  - Genome Announcements
PY  - 2017
SP  - e01557
EP  - e01516
VL  - 5
AB  - Borrelia miyamotoi, of the relapsing-fever spirochete group, is an emerging tick-borne
AB  - pathogen causing human illness in the northern hemisphere. Here, we
AB  - present the chromosome, eight extrachromosomal linear plasmids, and a draft
AB  - sequence for five circular and one linear plasmid of a Borrelia miyamotoi strain
AB  - isolated from an Ixodes sp. tick from Connecticut, USA.
ER  -

TY  - JOUR
AU  - Kingry, L.C.
AU  - Replogle, A.
AU  - Dolan, M.
AU  - Sexton, C.
AU  - Padgett, K.A.
AU  - Schriefer, M.E.
TI  - Chromosome and Large Linear Plasmid Sequences of a Borrelia miyamotoi Strain Isolated from Ixodes pacificus Ticks from California.
JO  - Genome Announcements
PY  - 2017
SP  - e00960
EP  - e00917
VL  - 5
AB  - Borrelia miyamotoi, a relapsing fever group spirochete, is an emerging tick-borne pathogen. It
AB  - has been identified in ixodid ticks across the Northern Hemisphere,
AB  - including the West Coast of the United States. We describe the chromosome and
AB  - large linear plasmid sequence of a B. miyamotoi isolate cultured from a
AB  - California field-collected Ixodes pacificus tick.
ER  -

TY  - JOUR
AU  - Kingston, I.J.
AU  - Gormley, N.A.
AU  - Halford, S.E.
TI  - DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognize the relative orientation of two DNA sequences.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 5221
EP  - 5228
VL  - 31
AB  - Many proteins can sense the relative orientations of two sequences at distant locations in
AB  - DNA: some require sites in inverted (head-to-head)
AB  - orientation, others in repeat (head-to-tail) orientation. Like many
AB  - restriction enzymes, the BspMI endonuclease binds two copies of its target
AB  - site before cleaving DNA. Its target is an asymmetric sequence so two
AB  - sites in repeat orientation differ from sites in inverted orientation.
AB  - When tested against supercoiled plasmids with two sites 700 bp apart in
AB  - either repeated or inverted orientations, BspMI had a higher affinity for
AB  - the plasmid with repeated sites than the plasmid with inverted sites. In
AB  - contrast, on linear DNA or on supercoiled DNA with sites 1605 bp apart,
AB  - BspMI interacted equally with repeated or inverted sites. The ability of
AB  - BspMI to detect the relative orientation of two DNA sequences thus depends
AB  - on both the topology and the length of the intervening DNA. Supercoiling
AB  - may restrain the juxtaposition of sites 700 bp apart to a particular
AB  - alignment across the superhelical axis, but the juxtaposition of sites in
AB  - linear DNA or far apart in supercoiled DNA may occur without restraint.
AB  - BspMI can therefore act as a sensor of the conformational dynamics of
AB  - supercoiled DNA.
ER  -

TY  - JOUR
AU  - Kinjo, M.
AU  - Nishimura, G.
AU  - Koyama, T.
AU  - Mets, U.
AU  - Rigler, R.
TI  - Single-molecule analysis of restriction DNA fragments using fluorescence correlation spectroscopy.
JO  - Anal. Biochem.
PY  - 1998
SP  - 166
EP  - 172
VL  - 260
AB  - The cleavage of fluorescence-labeled M13DNA (7250 bp) using HaeIII, HgaI, BsmAI, and BspMI was
AB  - analyzed by fluorescence correlation spectroscopy in a small volume (1.5 x 10^-15 liters).
AB  - The digestion process can be monitored by the decrease in amplitude of the fluorescence
AB  - correlation function while the original DNA molecule is divided into several fragments by the
AB  - enzymes.  To analyze this reaction by FCS, we derived a practical equation for estimating the
AB  - number of molecules in the FCS measurements.  Under standard enzymatic conditions, HaeIII and
AB  - BsmAI digested fluorescence-labeled DNA to completion in the range of 8 h, whereas HgaI and
AB  - BspMI digested the DNA after 40 h.  The comparison of recognition sequences suggested that
AB  - some tagged nucleotides could be inserted between the recognition site and the cleavage site
AB  - of the slow enzyme group.  The decrease in amplitude in the fluorescence correlation function
AB  - quantitatively monitors the hydrolysis of DNA during the digestion process.
ER  -

TY  - JOUR
AU  - Kinjo, Y.
AU  - Bourguignon, T.
AU  - Tong, K.J.
AU  - Kuwahara, H.
AU  - Lim, S.J.
AU  - Yoon, K.B.
AU  - Shigenobu, S.
AU  - Park, Y.C.
AU  - Nalepa, C.A.
AU  - Hongoh, Y.
AU  - Ohkuma, M.
AU  - Lo, N.
AU  - Tokuda, G.
TI  - Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches.
JO  - Genome Biol. Evol.
PY  - 2018
SP  - 1622
EP  - 1630
VL  - 10
AB  - Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium
AB  - cuenoti. On the basis of genome content, Blattabacterium has been
AB  - inferred to recycle nitrogen wastes and provide amino acids and cofactors for its
AB  - hosts. Most Blattabacterium strains sequenced to date harbor a genome of
AB  - approximately 630 kbp, with the exception of the termite Mastotermes darwiniensis
AB  - ( approximately 590 kbp) and Cryptocercus punctulatus ( approximately 614 kbp), a
AB  - representative of the sister group of termites. Such genome reduction may have
AB  - led to the ultimate loss of Blattabacterium in all termites other than
AB  - Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from
AB  - three species of Cryptocercus in order to shed light on the genomic evolution of
AB  - Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived
AB  - Blattabacterium genomes were reduced ( approximately 614 kbp), except for that
AB  - associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic
AB  - analysis of these genomes and their content indicates that Blattabacterium
AB  - experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly
AB  - due to similar selective forces. We found evidence of ongoing genome reduction in
AB  - Blattabacterium from three lineages of the C. punctulatus species complex, which
AB  - independently lost one cysteine biosynthetic gene. We also sequenced the genome
AB  - of the Blattabacterium associated with Salganea taiwanensis, a subsocial
AB  - xylophagous cockroach that does not vertically transmit gut symbionts via
AB  - proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial
AB  - cockroaches. Overall, our results show that genome reduction occurred on multiple
AB  - occasions in Blattabacterium, and is still ongoing, possibly because of new
AB  - associations with gut symbionts in some lineages.
ER  -

TY  - JOUR
AU  - Kinney, S.R.M.
AU  - Pradhan, S.
TI  - Regulation of Expression and Activity of DNA (Cytosine-5) Methyltransferases in Mammalian Cells.
JO  - Prog. Mol. Biol. Transl. Sci.
PY  - 2011
SP  - 311
EP  - 333
VL  - 101
AB  - Three active DNA methyltransferases have been identified in mammalian cells, Dnmt1, Dnmt3a,
AB  - and Dnmt3b.  DNMT1 is primarily a maintenance methyltransferase, as it prefers to methylate
AB  - hemi-methylated DNA during DNA replication and in vitro.  DNMT3A and DNMT3B are de novo
AB  - methyltransferases and show similar activity on unmethylated and hemimethylated DNA. DNMT3L,
AB  - which lacks the catalytic domain, binds to DNMT3A and DNMT3B variants and facilitates their
AB  - chromatin targeting, presumably for de novo methylation.  There are several mechanisms by
AB  - which mammalian cells regulate DNMT levels, including varied transcriptional activation of the
AB  - respective genes and posttranslational modifications of the enzymes that can affect catalytic
AB  - activity, targeting, and enzyme degradation.  In addition, binding of miRNAs or RNA-binding
AB  - proteins can also alter the expression of DNMTs.  These regulatory processes can be disrupted
AB  - in disease or by environmental factors, resulting in altered DNMT expression and aberrant DNA
AB  - methylation patterns.
ER  -

TY  - JOUR
AU  - Kinsella, J.M.
AU  - Shalaev, M.V.
AU  - Ivanisevic, A.
TI  - Ligation of Nanoparticle Coated DNA Cleaved with Restriction Enzymes.
JO  - Chem. Mater.
PY  - 2007
SP  - 3586
EP  - 3588
VL  - 19
AB  - Material synthesis at the nanoscale frequently relies on biological molecules for inspiration,
AB  - selectivity, and specificity.  Molecular templates using biomolecules have been used to
AB  - fabricate structures with specific sizes and shapes.  Often times, the biological function of
AB  - the template molecule is utilized to connect nanoscale structures, site-specifically catalyze
AB  - reactions, or enzymatically modify templated segments.  The specificity of these biomolecular
AB  - interactions can often lead to straightforward fabrication methods of materials that are
AB  - difficult to synthesize by conventional means.  One of the simplest and most easily adapted
AB  - forms of such interactions is that involving the hybridization of single-stranded DNA to its
AB  - double-helix form.  This interaction has been used to drive the formation of complex
AB  - structures, nanoparticle conjugates, and DNA-based electronics.  More recently, the
AB  - introduction of DNA-manipulating enzymes has been investigated.  We have previously
AB  - demonstrated the ability of restriction endonucleases, which cut DNA at specific sequences, to
AB  - fragment phage DNA templated with magnetic nanoparticles.  DNA ligases, which oppose the
AB  - function of restriction enzymes by repairing cleaved DNA molecules, have recently been used to
AB  - generate specific connectivity between DNA-modified nanoparticles.
ER  -

TY  - JOUR
AU  - Kiran, S.
AU  - Swarnkar, M.K.
AU  - Pal, M.
AU  - Thakur, R.
AU  - Tewari, R.
AU  - Singh, A.K.
AU  - Gulati, A.
TI  - Complete Genome Sequencing of Protease-Producing Novel Arthrobacter sp. Strain IHBB 11108 Using PacBio Single-Molecule Real-Time Sequencing Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e00346
EP  - e00315
VL  - 3
AB  - A previously uncharacterized species of the genus Arthrobacter, strain IHBB 11108 (MCC 2780),
AB  - is a Gram-positive, strictly aerobic, nonmotile, cold-adapted, and
AB  - protease-producing alkaliphilic actinobacterium, isolated from shallow
AB  - undersurface water from Chandra Tal Lake, Lahaul-Spiti, India. The complete
AB  - genome of the strain is 3.6 Mb in size with an average 58.97% G+C content.
ER  -

TY  - JOUR
AU  - Kirby, R.
AU  - Sangal, V.
AU  - Tucker, N.P.
AU  - Zakrzewska-Czerwinska, J.
AU  - Wierzbicka, K.
AU  - Herron, P.R.
AU  - Chu, C.J.
AU  - Chandra, G.
AU  - Fahal, A.H.
AU  - Goodfellow, M.
AU  - Hoskisson, P.A.
TI  - Draft Genome Sequence of the Human Pathogen Streptomyces somaliensis, a Significant Cause of Actinomycetoma.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3544
EP  - 3545
VL  - 194
AB  - We report the draft genome sequence of the human pathogen Streptomyces somaliensis (DSM
AB  - 40738), a pathogen within a genus of largely saprophytic
AB  - organisms. S. somaliensis causes severe and debilitating deep tissue and bone
AB  - infections. The genome sequence is deposited in DDBJ/EMBL/GenBank with the
AB  - accession number AJJM01000000.
ER  -

TY  - JOUR
AU  - Kirienko, N.V.
AU  - Lepikhov, K.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Significance of codon usage and irregularities of rare codon distribution in genes for expression of BspLU11III methyltransferases.
JO  - Biokhimiia
PY  - 2004
SP  - 647
EP  - 657
VL  - 69
AB  - Genes of adenine-specific DNA-methyltransferase M.BspLU11IIIa and cytosine-specific
AB  - DNA-methyltransferase M.BspLU11IIIb of the type IIG BspLU11III restriction-modification system
AB  - from the thermophilic strain Bacillus sp. LU11 were expressed in E. coli. They contain a large
AB  - number of codons that are rare in E. coli and are characterized by equal values of codon
AB  - adaptation index (CAI) and expression level measure (E(g)). Rare codons are either diffused
AB  - (M.BspLU11IIIa) or located in clusters (M.BspLU11IIIb). The expression level of the
AB  - cytosine-specific DNA-methyltransferase was increased by a factor of 7.3 and that of
AB  - adenine-specific DNA only by a factor of 1.25 after introduction of the plasmid pRARE
AB  - supplying tRNA genes for six rare codons in E. coli. It can be assumed that the plasmid
AB  - supplying minor tRNAs can strongly increase the expression level of only genes with cluster
AB  - distribution of rare codons. Using heparin-Sepharose and phosphocellulose chromatography and
AB  - gel filtration on Sephadex G-75 both DNA-methyltransferases were isolated as
AB  - electrophoretically homogeneous proteins (according to the results of SDS-PAGE).
ER  -

TY  - JOUR
AU  - Kirino, H.
AU  - Kuwahara, R.
AU  - Hamasaki, N.
AU  - Oshima, T.
TI  - Effect of unusual polyamines on cleavage of DNA by restriction enzymes.
JO  - J. Biochem. (Tokyo)
PY  - 1990
SP  - 661
EP  - 665
VL  - 107
AB  - The effect of unusual polyamines, such as thermine, caldopentamine,
AB  - caldohexamine, tris(3-aminopropyl)amine, or tetrakis(3-aminopropyl)ammonium, on
AB  - the activities of various restriction endonucleases was investigated by using
AB  - an Escherichia coli plasmid as a substrate, which contains a high GC content
AB  - fragment from an extreme thermophile.  Restriction enzymes used were SmaI,
AB  - BanII, NaeI, RsaI, and TaqI.  Most of the polyamines tested were inhibitory to
AB  - the enzyme activities.  The larger and more branched a polyamine was, the more
AB  - the activities of nucleases were inhibited.  The inhibition was positively
AB  - correlated with the polyamine concentration.  The sites protected by a
AB  - polyamine were identical to those protected by other polyamines, and also
AB  - identical to those which were less sensitive to the restriction enzyme in the
AB  - absence of polyamines.  No sequence specificity was seen among these sites.
ER  -

TY  - JOUR
AU  - Kirkeleite, I.O.
AU  - Bohlin, J.
AU  - Scheffer, L.
AU  - Weme, E.T.
AU  - Vestrheim, D.F.
TI  - Draft Genome Sequence of a Potentially Novel Streptococcus Species Belonging to the Streptococcus mitis Group.
JO  - Genome Announcements
PY  - 2018
SP  - e00620
EP  - e00618
VL  - 6
AB  - We report here the draft genome sequence of a Streptococcus species belonging to  the S. mitis
AB  - group. While a clear species identification cannot be made for the
AB  - isolate, it appears that its most recent common ancestor is the species S.
AB  - pseudopneumoniae.
ER  -

TY  - JOUR
AU  - Kirsanova, O.V.
AU  - Baskunov, V.B.
AU  - Gromova, E.S.
TI  - Type IIE and IIF restriction endonucleases interacting with two recognition sites on DNA.
JO  - Mol. Biol. (Mosk)
PY  - 2004
SP  - 886
EP  - 900
VL  - 38
AB  - Recent studies have shown that restriction endonucleases (REs), which are broadly used in
AB  - genetic engineering and molecular biology, vary not
AB  - only in nucleotide sequence of the recognition site, but also in the
AB  - mechanism of their interaction with DNA. This review focuses on type
AB  - IIF and HE REs, which require simultaneous interaction with two
AB  - nucleotide sequences for efficient DNA cleavage. Crystal structures of
AB  - these REs and their complexes with DNA, stepwise interactions with DNA,
AB  - catalytic mechanisms of DNA hydrolysis, and DNA looping are considered.
AB  - Type HE REs have provided an example of a new type of DNA-protein
AB  - recognition: two copies of one recognition sequence interact
AB  - specifically with two different amino acid sequences and two different
AB  - structural motifs of one polypeptide chain.
ER  -

TY  - JOUR
AU  - Kirsanova, O.V.
AU  - Cherepanova, N.A.
AU  - Gromova, E.S.
TI  - Inhibition of C5-cytosine-DNA-methyltransferases.
JO  - Biochemistry
PY  - 2009
SP  - 1175
EP  - 1186
VL  - 74
AB  - Changes in the methylation pattern of genomic DNA, particularly hypermethylation of tumor
AB  - suppressor genes, occur at early stages of tumor development. Errors in DNA methylation
AB  - contribute to both initiation and progression of various cancers. This stimulates significant
AB  - interest in searching for inhibitors of C5-DNA-methyltransferases (MTases). Here we review the
AB  - known nucleoside mechanism-based reversible and irreversible inhibitors of the MTases, as well
AB  - as non-nucleoside ones, and discuss their inhibitory mechanisms and application for MTase
AB  - investigations and cancer therapy.
ER  -

TY  - JOUR
AU  - Kirstahler, P.
AU  - Gunther, M.
AU  - Grumaz, C.
AU  - Lindemann, E.
AU  - Rupp, S.
AU  - Zibek, S.
AU  - Sohn, K.
TI  - Draft Genome Sequence of Amantichitinum ursilacus IGB-41, a New Chitin-Degrading  Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01309
EP  - e01315
VL  - 3
AB  - Amantichitinum ursilacus IGB-41 is a new species of chitin-degrading bacterium isolated from
AB  - soil, which secretes potential industrial enzymes. The genome of A.
AB  - ursilacus was sequenced, and the gene set encoding chitinases was identified.
AB  - Here, we present the draft genome of 4.9 Mb, comprising 38 contigs, and the
AB  - corresponding annotation.
ER  -

TY  - JOUR
AU  - Kiseleva, L.
AU  - Garushyants, S.K.
AU  - Briliute, J.
AU  - Simpson, D.J.
AU  - Cohen, M.F.
AU  - Goryanin, I.
TI  - Genome Sequence of the Electrogenic Petroleum-Degrading Thalassospira sp. Strain  HJ.
JO  - Genome Announcements
PY  - 2015
SP  - e00483
EP  - e00415
VL  - 3
AB  - We present the draft genome of the petroleum-degrading Thalassospira sp. strain HJ, isolated
AB  - from tidal marine sediment. Knowledge of this genomic information
AB  - will inform studies on electrogenesis and means to degrade environmental organic
AB  - contaminants, including compounds found in petroleum.
ER  -

TY  - JOUR
AU  - Kishi, L.T.
AU  - Lopes, E.M.
AU  - Fernandes, C.C.
AU  - Fernandes, G.C.
AU  - Sacco, L.P.
AU  - Carareto, A.L.M.
AU  - Lemos, E.G.
TI  - Draft Genome Sequence of a Chitinophaga Strain Isolated from a Lignocellulose Biomass-Degrading Consortium.
JO  - Genome Announcements
PY  - 2017
SP  - e01056
EP  - e01016
VL  - 5
AB  - Chitinophaga comprises microorganisms capable of degrading plant-derived carbohydrates,
AB  - serving as a source of new tools for the characterization and
AB  - degradation of plant biomass. Here, we report the draft genome assembly of a
AB  - Chitinophaga strain with 8.2 Mbp and 7,173 open reading frames (ORFs), isolated
AB  - from a bacterial consortium that is able to degrade lignocellulose.
ER  -

TY  - JOUR
AU  - Kishimoto, N.
AU  - Sakai, H.
AU  - Jackson, J.
AU  - Jacobsen, S.E.
AU  - Meyerowitz, E.M.
AU  - Dennis, E.S.
AU  - Finnegan, E.J.
TI  - Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus.
JO  - Plant Mol. Biol.
PY  - 2001
SP  - 171
EP  - 183
VL  - 46
AB  - Plants with low levels of DNA methylation show a range of developmental abnormalities
AB  - including homeotic transformation of floral organs. Two independent DNA methyltransferase I
AB  - (METI) antisense transformants with low levels of DNA methylation had flowers with increased
AB  - numbers of stamens which resembled flowers seen on the loss-of-function superman (sup) mutant
AB  - plants and on transgenic plants that ectopically express APETALA3 (AP3). These METI antisense
AB  - plants have both increased and decreased methylation in and around the sup gene, compared with
AB  - untransformed controls. DNA from the antisense plants was demethylated at least 4 kb upstream
AB  - of the sup gene, while there was dense methylation around the start of transcription and
AB  - within the coding region of this gene; these regions were unmethylated in control DNA.
AB  - Methylation within the sup gene was correlated with an absence of SUP transcripts. The pattern
AB  - and density of methylation was heterogeneous among different DNA molecules from the same
AB  - plant, with some molecules being completely unmethylated. Methylcytosine occurred in
AB  - asymmetric sites and in symmetric CpA/TpG but rarely in CpG dinucleotides in the antisense
AB  - plants. In contrast, segregants lacking the METI antisense construct and epimutants with a
AB  - hypermethylated allele of sup (clark kent 3), both of which have active METI genes, showed a
AB  - higher frequency of methylation of CpG dinucleotides and of asymmetric cytosines. We conclude
AB  - that METI is the predominant CpG methyltransferase and directly or indirectly affects
AB  - asymmetric methylation.
ER  -

TY  - JOUR
AU  - Kishnani, P.M.
AU  - Tiwari, A.A.
AU  - Gautam, V.
AU  - Sharma, M.
AU  - Barbuddhe, S.B.
AU  - Doijad, S.P.
AU  - Chakraborty, T.
AU  - Nayak, A.R.
AU  - Bhartiya, N.M.
AU  - Daginawala, H.F.
AU  - Singh, L.R.
AU  - Kashyap, R.S.
TI  - Draft Genome Sequence of Listeria monocytogenes Strain CIIMS-PH-1, a Serovar 4b Isolate from Infant Septicemia.
JO  - Genome Announcements
PY  - 2018
SP  - e01320
EP  - e01317
VL  - 6
AB  - We report here the draft genome sequence of Listeria monocytogenes CIIMS-PH-1, an isolate
AB  - obtained from a 16-day-old infant with septicemia. The draft genome of
AB  - CIIMS-PH-1 consisted of 2,939,183 bp and is a member of sequence type 308, clonal
AB  - complex 1, and lineage I.
ER  -

TY  - JOUR
AU  - Kishnani, P.M.
AU  - Tiwari, A.A.
AU  - Mangalgi, S.S.
AU  - Barbuddhe, S.B.
AU  - Daginawala, H.F.
AU  - Singh, L.R.
AU  - Kashyap, R.S.
TI  - Whole-Genome Sequence of Brucella melitensis CIIMS-BH-2, a Biovar 2 Strain Isolated from Human Blood.
JO  - Genome Announcements
PY  - 2018
SP  - e00079
EP  - e00018
VL  - 6
AB  - Brucella species are the etiological agent of brucellosis in humans and animals.  Here, we
AB  - report the whole-genome sequence of Brucella melitensis strain
AB  - CIIMS-BH-2, belonging to biovar 2. The draft assembly of CIIMS-BH-2 is 3.31 Mb in
AB  - size, with 57.2% G+C content.
ER  -

TY  - JOUR
AU  - Kisiala, M.
AU  - Copelas, A.
AU  - Czapinska, H.
AU  - Xu, S.Y.
AU  - Bochtler, M.
TI  - Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 10489
EP  - 10503
VL  - 46
AB  - TagI belongs to the recently characterized SRA-HNH family of modification-dependent
AB  - restriction endonucleases (REases) that also includes
AB  - ScoA3IV (Sco5333) and TbiR51I (Tbis1). Here, we present a crystal structure of
AB  - dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease
AB  - domains, and separate binding sites for modified DNA bases in the two protomers.
AB  - The nuclease domains have characteristic features of HNH/betabetaalpha-Me REases,
AB  - and catalyze nicks or double strand breaks, with preference for /RY and RYN/RY
AB  - sites, respectively. The SRA domains have the canonical fold. Their pockets for
AB  - the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or
AB  - 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC).
AB  - Such preference is in agreement with the biochemical determination of the TagI
AB  - modification dependence and the results of phage restriction assays. The ability
AB  - of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or
AB  - M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to
AB  - different sequence contexts of the modified base.
ER  -

TY  - JOUR
AU  - Kislichkina, A.A.
AU  - Bogun, A.G.
AU  - Kadnikova, L.A.
AU  - Maiskaya, N.V.
AU  - Platonov, M.E.
AU  - Anisimov, N.V.
AU  - Galkina, E.V.
AU  - Dentovskaya, S.V.
AU  - Anisimov, A.P.
TI  - Nineteen Whole-Genome Assemblies of Yersinia pestis subsp. microtus, Including Representatives of Biovars caucasica, talassica, hissarica, altaica,  xilingolensis, and ulegeica.
JO  - Genome Announcements
PY  - 2015
SP  - e01342
EP  - e01315
VL  - 3
AB  - The etiologic agent of plague, Yersinia pestis, includes two subspecies, of which Y. pestis
AB  - subsp. microtus contains the strains that cause only occasional
AB  - diseases in humans that are not accompanied by human-to-human transmission. Here,
AB  - we report the draft genome sequences of 19 Y. pestis strains (across 6 biovars of
AB  - Y. pestis subsp. microtus).
ER  -

TY  - JOUR
AU  - Kislichkina, A.A.
AU  - Bogun, A.G.
AU  - Kadnikova, L.A.
AU  - Maiskaya, N.V.
AU  - Solomentsev, V.I.
AU  - Dentovskaya, S.V.
AU  - Balakhonov, S.V.
AU  - Anisimov, A.P.
TI  - Nine Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. Altaica Strains Isolated from the Altai Mountain Natural Plague Focus (No. 36) in Russia.
JO  - Genome Announcements
PY  - 2018
SP  - e01440
EP  - e01417
VL  - 6
AB  - We report here the draft genome sequences of nine Yersinia pestis subsp. microtus bv. Altaica
AB  - strains isolated from the Altai Mountain plague focus (no. 36), which
AB  - represent the 0.PE4 phylogroup circulating in populations of Mongolian pika
AB  - (Ochotona pallasi).
ER  -

TY  - JOUR
AU  - Kislichkina, A.A.
AU  - Bogun, A.G.
AU  - Kadnikova, L.A.
AU  - Maiskaya, N.V.
AU  - Solomentsev, V.I.
AU  - Platonov, M.E.
AU  - Dentovskaya, S.V.
AU  - Anisimov, A.P.
TI  - Eight Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. caucasica Isolated from the Common Vole (Microtus arvalis) Plague Focus in Dagestan,  Russia.
JO  - Genome Announcements
PY  - 2017
SP  - e00847
EP  - e00817
VL  - 5
AB  - We here report the draft genome sequences of 8 Yersinia pestis subsp. microtus bv. caucasica
AB  - strains isolated from the East Caucasian (previous name, Dagestan)
AB  - mountain focus (no. 39), representing the most ancient branch of the 0.PE2
AB  - phylogroup circulating in populations of common voles (Microtus arvalis).
ER  -

TY  - JOUR
AU  - Kislichkina, A.A.
AU  - Bogun, A.G.
AU  - Kadnikova, L.A.
AU  - Maiskaya, N.V.
AU  - Solomentsev, V.I.
AU  - Sizova, A.A.
AU  - Dentovskaya, S.V.
AU  - Balakhonov, S.V.
AU  - Anisimov, A.P.
TI  - Six Whole-Genome Assemblies of Yersinia pestis subsp. microtus bv. ulegeica (Phylogroup 0.PE5) Strains Isolated from Mongolian Natural Plague Foci.
JO  - Genome Announcements
PY  - 2018
SP  - e00536
EP  - e00518
VL  - 6
AB  - Here, we report the draft genome sequences of six Yersinia pestis subsp. microtus bv. ulegeica
AB  - strains isolated from the territory of Mongolia and representing the
AB  - 0.PE5 phylogroup circulating in populations of voles and picas.
ER  -

TY  - JOUR
AU  - Kiss, A.
AU  - Baldauf, F.
TI  - Molecular cloning and expression in Escherichia coli of two modification methylase genes of Bacillus subtilis.
JO  - Gene
PY  - 1983
SP  - 111
EP  - 119
VL  - 21
AB  - Two modification methylase genes of Bacillus subtilis R were cloned in
AB  - Escherichia coli by using a selection procedure which is based on the
AB  - expression of these genes.  Both genes code for DNA-methyl-transferases which
AB  - render the DNA of the cloning host E. coli HB101 insensitive to the BspRI
AB  - (5'-GGCC) endonuclease of Bacillus sphaericus R.  One of the cloned genes is
AB  - part of the restriction-modification (RM) system BsuRI of B. subtilis R with
AB  - specificity for 5'-GGCC.  The other one is associated with the lysogenizing
AB  - phage SPbeta and produces the methylase M.BsuSPbetaI with specificity for
AB  - 5'-GGCC.  The fragment carrying the SPbeta-derived gene also directs the
AB  - synthesis in E. coli of a third methylase activity (M.BsuSPbetaII), which
AB  - protects the host DNA against HpaII and MspI cleavage within the sequence
AB  - 5'-CCGG.  Indirect evidence suggests that the two SPbeta modification
AB  - activities are encoded by the same gene.  No cross-hybridization was detected
AB  - either between the M.BsuRI and M.BsuSPbeta genes or between these and the
AB  - modification methylase gene of B. sphaericus R, which codes for the enzyme
AB  - M.BspRI with 5'-GGCC specificity.
ER  -

TY  - JOUR
AU  - Kiss, A.
AU  - Finta, C.
AU  - Venetianer, P.
TI  - M.KpnI is an adenine-methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 3460
EP  - 3460
VL  - 19
AB  - The recognition sequence of the KpnI restriction-modification system is GGTACC.
AB  - There are conflicting reports in the literature concerning the nucleotide
AB  - methylated by the KpnI methyltransferase.  In one paper it was suggested that
AB  - M.KpnI produces m4-cytosine.  Other investigators obtained indirect evidence
AB  - suggesting but not proving that it methylates the adenine in the recognition
AB  - sequence.  Here we present direct evidence showing that M.KpnI is an
AB  - adenine-methyltransferase.
ER  -

TY  - JOUR
AU  - Kiss, A.
AU  - Posfai, G.
AU  - Keller, C.C.
AU  - Venetianer, P.
AU  - Roberts, R.J.
TI  - Nucleotide sequence of the BsuRI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 6403
EP  - 6420
VL  - 13
AB  - The genes of the 5'-GGCC specific BsuRI restriction-modification system of
AB  - Bacillus subtillis have been cloned and expressed in E. coli and their
AB  - nucleotide sequence has been determined.  The restriction and modification
AB  - genes code for polypeptides with calculated molecular weights of 66,314 and
AB  - 49,642, respectively.  Both enzymes are coded by the same DNA strand.  The
AB  - restriction gene is upstream of the methylase gene and the coding regions are
AB  - separated by 780 bp.  Analysis of the RNA transcripts by S1-nuclease mapping
AB  - indicates that the restriction and modification genes are transcribed from
AB  - different promoters.  Comparison of the amino acid sequences revealed no
AB  - homology between the BsuRI restriction and modification enzymes.  There are,
AB  - however, regions of homology between the BsuRI methylase and two other GGCC
AB  - specific modification enzymes, the BspRI and SPR methylases.
ER  -

TY  - JOUR
AU  - Kiss, A.
AU  - Posfai, G.
AU  - Zsurka, G.
AU  - Rasko, T.
AU  - Venetianer, P.
TI  - Role of DNA minor groove interactions in substrate recognition by the M.SinI and M.EcoRII DNA (cytosine-5) methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3188
EP  - 3194
VL  - 29
AB  - The SinI and EcoRII DNA methyltransferases recognize sequences (GG(A)/(T)CC and CC(A)/(T)GG,
AB  - respectively), which are characterized by an (A)/(T) ambiguity. Recognition of the A.T and T.A
AB  - base pair was studied by in vitro methyltransferase assays using oligonucleotide substrates
AB  - containing a hypoxanthine.C base pair in the central position of the recognition sequence.
AB  - Both enzymes methylated the substituted oligonucleotide with an efficiency that was comparable
AB  - to methylation of the canonical substrate. These observations indicate that M.SinI and
AB  - M.EcoRII discriminate between their canonical recognition site and the site containing a G.C
AB  - or a C.G base pair in the center of the recognition sequence (GG(G)/(C)CC and CC(G)/(C)GG,
AB  - respectively) by interaction(s) in the DNA minor groove. M.SinI mutants displaying a decreased
AB  - capacity to discriminate between the GG(A)/(T)CC and GG(G)/(C)CC sequences were isolated by
AB  - random mutagenesis and selection for the relaxed specificity phenotype. These mutations led to
AB  - amino acid substitutions outside the variable region, previously thought to be the sole
AB  - determinant of sequence specificity. These observations indicate that (A)/(T) versus (G)/(C)
AB  - discrimination is mediated by interactions between the large domain of the methyltransferase
AB  - and the minor groove surface of the DNA.
ER  -

TY  - JOUR
AU  - Kiss, A.
AU  - Sain, B.
AU  - Csordas-Toth, E.
AU  - Venetianer, P.
TI  - A new sequence-specific endonuclease (Bsp) from Bacillus sphaericus.
JO  - Gene
PY  - 1977
SP  - 323
EP  - 329
VL  - 1
AB  - A new restriction endonuclease has been isolated from Bacillus sphaericus R.
AB  - The purification procedure includes Bio-Gel filtration (NH4)2SO4 fractionation
AB  - and phosphocellulose chromatography.  After the phosphocellulose step the
AB  - enzyme preparation is free of non-specific nucleases.  Bsp cleaves
AB  - double-stranded DNA with the same specificity as Bacillus subtilis (Bsu) and
AB  - Haemophilus aegyptius (HaeIII) restriction endonucleases, as concluded from
AB  - digests and double-digests of PhiX174 replicative form DNA with Bsu and Bsp.
AB  - The 5'-terminal nucleotide of the cleavage products was shown to be C.
AB  - Bacillus sphaericus R produces Bsp in extremely large quantities and the enzyme
AB  - can be easily purified in high yield.
ER  -

TY  - JOUR
AU  - Kiss, A.
AU  - Weinhold, E.
TI  - Functional reassembly of split enzymes on-site: a novel approach for highly sequence-specific targeted DNA methylation.
JO  - Chembiochem
PY  - 2008
SP  - 351
EP  - 353
VL  - 9
AB  - In mammalian genomes, a significant fraction of the cytosine residues is methylated at the
AB  - 5-position, and this modified nucleobase is found in 5'CG-3' sequences.  The methylation
AB  - patterns of the genome changes during ontogenesis, depends on the tissue and can substantially
AB  - differ in several diseases, notably cancer.  We are only at the beginning of understanding the
AB  - biological role of DNA methylation in higher organisms, but the emerging view is that
AB  - methylation of the promoter region of a substantial fraction of genes leads to transcriptional
AB  - inactivation (gene silencing).
ER  -

TY  - JOUR
AU  - Kiss, H. et al.
TI  - Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 153
EP  - 162
VL  - 3
AB  - 'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus
AB  - 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of
AB  - an acid tolerant, extremely thermophilic species belonging to a phylogenetically
AB  - isolated environmental clone group within the phylum Chloroflexi. At present, the
AB  - name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule
AB  - 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly
AB  - acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA).
AB  - Depending on its final taxonomic allocation, this is likely to be the third
AB  - completed genome sequence of a member of the class Thermomicrobia and the seventh
AB  - type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with
AB  - its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Kiss, H. et al.
TI  - Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 356
EP  - 370
VL  - 5
AB  - Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon,
AB  - which in turn is the type genus of the family Herpetosiphonaceae, type family of the order
AB  - Herpe-tosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments
AB  - which can rapidly glide. The species is of interest not only because of its rather isolated
AB  - position in the tree of life, but also because Herpetosiphon ssp. were identified as predators
AB  - capable of facultative pre-dation by a wolf pack strategy and of degrading the prey organisms
AB  - by excreted hydrolytic en-zymes. The genome of H. aurantiacus strain 114-95T is the first
AB  - completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp
AB  - long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577
AB  - protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute
AB  - Program DOEM 2005.
ER  -

TY  - JOUR
AU  - Kiss, H. et al.
TI  - Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 270
EP  - 279
VL  - 2
AB  - Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus
AB  - Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic
AB  - interest because there are only six genera described in the family
AB  - Deferribacteraceae. D. acetiphilus was isolated as a representative of a
AB  - population reducing nitrate to ammonia in a laboratory column simulating the
AB  - conditions in off-shore oil recovery fields. When nitrate was added to this
AB  - column undesirable hydrogen sulfide production was stopped because the sulfate
AB  - reducing populations were superseded by these nitrate reducing bacteria. Here we
AB  - describe the features of this marine, mesophilic, obligately anaerobic organism
AB  - respiring by nitrate reduction, together with the complete genome sequence, and
AB  - annotation. This is the second complete genome sequence of the order
AB  - Deferribacterales and the class Deferribacteres, which is the sole class in the
AB  - phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and
AB  - 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Kita, A.
AU  - Iwasaki, Y.
AU  - Sakai, S.
AU  - Okuto, S.
AU  - Takaoka, K.
AU  - Suzuki, T.
AU  - Yano, S.
AU  - Sawayama, S.
AU  - Tajima, T.
AU  - Kato, J.
AU  - Nishio, N.
AU  - Murakami, K.
AU  - Nakashimada, Y.
TI  - Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica.
JO  - J. Biosci. Bioeng.
PY  - 2013
SP  - 347
EP  - 352
VL  - 115
AB  - To develop a microbial production platform based on hydrogen and carbon dioxide, a genetic
AB  - transformation system for the thermophilic acetogen
AB  - Moorella thermoacetica ATCC39073 was developed. The uracil auxotrophic
AB  - strain dpyrF was constructed by disrupting pyrF for orotate
AB  - monophosphate decarboxylase. The transformation plasmids were
AB  - methylated by restriction methylases of M. thermoacetica to avoid the
AB  - decomposition of introduced plasmids by restriction-modification
AB  - system. Reintroduction of native pyrF into the mutant by homologous
AB  - recombination ensured recovery from uracil auxotrophy. To test
AB  - heterologous gene expression in dpyrF, the lactate dehydrogenase (LDH)
AB  - gene (T-ldh) from Thermoanaerobacter pseudethanolicus ATCC33223 was
AB  - electroporated into dpyrF with a promoter of the
AB  - glyceraldehyde-3-phosphate dehydrogenase (G3PD) gene of M.
AB  - thermoacetica ATCC39073. The resulting transformant (C31) successfully
AB  - transcribed T-ldh and exhibited higher LDH activity than ATCC39073 and
AB  - dpyrF, yielding 6.8 mM of lactate from fructose, whereas ATCC39073 did
AB  - not produce lactate.
ER  -

TY  - JOUR
AU  - Kita, K.
TI  - Molecular evolution of restriction endonucleases.
JO  - Baiosaiensu to Indasutori
PY  - 2009
SP  - 254
EP  - 257
VL  - 67
ER  -

TY  - JOUR
AU  - Kita, K.
TI  - Type II restriction-modification gene coded by the E. coli genome. Vestiges of horizontal transfer via phages.
JO  - Kagaku To Seibutsu
PY  - 2003
SP  - 348
EP  - 350
VL  - 41
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Hiraoka, N.
AU  - Kimizuka, F.
AU  - Obayashi, A.
TI  - Determination of the cleavage site of restriction enzyme, AccII, using synthetic oligonucleotide.
JO  - Agric. Biol. Chem.
PY  - 1984
SP  - 531
EP  - 532
VL  - 48
AB  - None
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Hiraoka, N.
AU  - Kimizuka, F.
AU  - Obayashi, A.
AU  - Kojima, H.
AU  - Takahashi, H.
AU  - Saito, H.
TI  - Interaction of the restriction endonuclease ScaI with its substrates.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 7015
EP  - 7024
VL  - 13
AB  - The kinetic constants of the site-specific endonuclease, ScaI, for various
AB  - substrates were determined.  We estimated Vmax and Km for octa-, deca-,
AB  - dodeca-, and hexadecanucleotides and for plasmid pBR322 DNA.  Vmax for these
AB  - substrates were close, but Km were quite different (in decreasing order, octa-
AB  - > deca-, dodeca-, hexadeca- > pBR322).  The results were discussed with respect
AB  - to the tertiary structure of substrate.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Hiraoka, N.
AU  - Oshima, A.
AU  - Kadonishi, S.
AU  - Obayashi, A.
TI  - AccIII, a new restriction endonuclease from Acinetobacter calcoaceticus.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 8685
EP  - 8694
VL  - 13
AB  - A new site-spectific restriction endonuclease, AccIII, was isolated from Acinetobacter
AB  - calcoaceticus. AccIII recognizes T^CCGGA and cleaves at the position shown by the arrow.
AB  - AccIII activity was inhibited by adenine methylation at the overlapping dam methylase
AB  - recognition sequence.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Kawakami, H.
AU  - Tanaka, H.
TI  - Evidence for horizontal transfer of the EcoT38I restriction-modification gene to chromosomal DNA by the P2 phage and diversity of defective P2 prophages in Escherichia coli TH38 strains.
JO  - J. Bacteriol.
PY  - 2003
SP  - 2296
EP  - 2305
VL  - 185
AB  - A DNA fragment carrying the genes coding for a novel EcoT38I restriction endonuclease
AB  - (R.EcoT38I) and EcoT38I methyltransferase (M.EcoT38I), which
AB  - recognize G(A/G)GC(C/T)C, was cloned from the chromosomal DNA of
AB  - Escherichia coli TH38. The endonuclease and methyltransferase genes were
AB  - in a head-to-head orientation and were separated by a 330-nucleotide
AB  - intergenic region. A third gene, the C.EcoT38I gene, was found in the
AB  - intergenic region, partially overlapping the R.EcoT38I gene. The gene
AB  - product, C.EcoT38I, acted as both a positive regulator of R.EcoT38I gene
AB  - expression and a negative regulator of M.EcoT38I gene expression.
AB  - M.EcoT38I purified from recombinant E. coli cells was shown to be a
AB  - monomeric protein and to methylate the inner cytosines in the recognition
AB  - sequence. R.EcoT38I was purified from E. coli HB101 expressing M.EcoT38I
AB  - and formed a homodimer. The EcoT38I restriction (R)-modification (M)
AB  - system (R-M system) was found to be inserted between the A and Q genes of
AB  - defective bacteriophage P2, which was lysogenized in the chromosome at
AB  - locI, one of the P2 phage attachment sites observed in both E. coli K-12
AB  - MG1655 and TH38 chromosomal DNAs. Ten strains of E. coli TH38 were
AB  - examined for the presence of the EcoT38I R-M gene on the P2 prophage.
AB  - Conventional PCR analysis and assaying of R activity demonstrated that all
AB  - strains carried a single copy of the EcoT38I R-M gene and expressed R
AB  - activity but that diversity of excision in the ogr, D, H, I, and J genes
AB  - in the defective P2 prophage had arisen.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Kotani, H.
AU  - Hiraoka, N.
AU  - Nakamura, T.
AU  - Yonaha, K.
TI  - Overproduction and crystallization of FokI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8741
EP  - 8753
VL  - 17
AB  - To overproduce FokI endonuclease (R. FokI) in an Escherichia coli system, the coding region of
AB  - R.FokI predicted from the nucleotide sequence was generated from the FokI operon and joined to
AB  - the tac promoter of an expression vector, pKK223-3.  By introduction of the plasmid into E.
AB  - coli UT481 cells expressing the FokI methylase gene, the R.FokI activity was overproduced
AB  - about 30-fold, from which R. FokI was purified in amounts sufficient for crystallization.  The
AB  - removal of a stem-loop structure immediately upstream of the R. FokI coding region was
AB  - essential for overproduction.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Kotani, H.
AU  - Ohta, H.
AU  - Yanase, H.
AU  - Kato, N.
TI  - StsI, a new FokI isoschizomer from Streptococcus sanguis 54, cleaves 5' GGATG(N)10/14 3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 618
EP  - 618
VL  - 20
AB  - StsI, an isoschizomer of FokI has been isolated from Streptococcus sanguis 54.
AB  - StsI recognizes the non-palindromic sequence 5'-GGATG-3'.  Unlike its
AB  - isoschizomer, StsI cleaves DNA 10 nucleotides to the right from the noted
AB  - recognition sequence and 14 nucleotides to the right on the opposite strand.
AB  - StsI was purified from the cell extracts by combined chromatographies on
AB  - phosphocellulose, DEAE-cellulose, heparin-Sepharose, hydroxylapatite, and
AB  - Affi-Gel Blue agarose.  The purified enzyme was homogeneous on
AB  - SDS-polyacrylamide gel electrophoresis.  The molecular mass of the enzyme was
AB  - estimated at 70 kDa.  The StsI activity was eluted at 70 kDa from a gel
AB  - filtration column.  These results indicated that the active form of StsI was a
AB  - monomer.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Kotani, H.
AU  - Sugisaki, H.
AU  - Takanami, M.
TI  - The FokI restriction-modification system  I. Organization and nucleotide sequences of the restriction and modification genes.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 5751
EP  - 5756
VL  - 264
AB  - A DNA fragment that carried the genes coding for FokI endonuclease and
AB  - methylase was cloned from the chromosomal DNA of Flavobacterium okeanokoites,
AB  - and the coding regions were assigned to the nucleotide sequence by deletion
AB  - analysis.  The methylase gene was 1941 base pairs (bp) long, corresponding to a
AB  - protein of 647 amino acid residues (Mr=75622), and the endonuclease gene was
AB  - 1749 bp long, corresponding to a protein of 583 amino acid residues (Mr=66216).
AB  - The assignment of the methylase gene was further confirmed by analysis of the
AB  - N-terminal amino acid sequence.  The endonuclease gene was downstream from the
AB  - methylase gene in the same orientation, separated by 69 bp.  The promoter site,
AB  - which could be recognized by Escherichia coli RNA polymerase, was upstream from
AB  - the methylase gene, and the sequences adhering to the ribosome-binding sequence
AB  - were identified in front of the respective genes.  Analysis of the gene
AB  - products expressed in E. coli cells by gel filtration and sodium dodecyl
AB  - sulfate-polyacrylamide gel electrophoresis indicated that the molecular weights
AB  - of both enzymes coincided well with the values estimated from the nucleotide
AB  - sequences, and that the monomeric forms were catalytically active.  No
AB  - significant similarity was found between the sequences of the two enzymes.
AB  - Sequence comparison with other related enzymes indicated that FokI methylase
AB  - contained two copies of a segment of tetra-amino acids which is characteristic
AB  - of adenine-specific methylase.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Suisha, M.
AU  - Kotani, H.
AU  - Yanase, H.
AU  - Kato, N.
TI  - Cloning and sequence analysis of the StsI restriction-modification gene: presence of homology to FokI restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4167
EP  - 4172
VL  - 20
AB  - StsI endonuclease (R.StsI), a type IIs restriction endonuclease found in Streptococcus sanguis
AB  - 54, recognizes the same sequence as FokI but cleaves at different positions. A DNA fragment
AB  - that carried the genes for R.StsI and StsI methylase (M.StsI) was cloned from the chromosomal
AB  - DNA of S. sanguis 54, and its nucleotide sequence was analyzed. The endonuclease gene was
AB  - 1,806 bp long, corresponding to a protein of 602 amino acid residues (Mr=68,388), and the
AB  - methylase gene was 1,959 bp long, corresponding to a protein of 653 amino acids residues (Mr
AB  - =76,064). The assignment of the endonuclease gene was confirmed by analysis of the N-terminal
AB  - amino acid sequence. Genes for the two proteins were in a tail-to-tail orientation, separated
AB  - by a 131-nucleotide intercistronic region. The predicted amino acid sequences between the StsI
AB  - system and the FokI system showed a 49% identity between the methylases and a 30% identity
AB  - between the endonucleases. The sequence comparison of M.StsI with various methylases showed
AB  - that the N-terminal half of M.StsI matches M.NlaII, and the C-terminal half matches adenine
AB  - methylases that recognize GATC and GATATC.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Suisha, M.
AU  - Shintoh, M.
AU  - Yanase, H.
AU  - Kato, N.
TI  - Overproduction and characterization of the StsI restriction endonuclease.
JO  - Gene
PY  - 1996
SP  - 69
EP  - 73
VL  - 169
AB  - The StsI restriction endonuclease (R.StsI), a class-IIS restriction endonuclease, found in
AB  - Streptococcus sanguis 54, is a heteroschizomer of R.FokI, which recognizes 5M-U-GGATG-3M-U.
AB  - To overproduce R.StsI in Escherichia coli, the coding region of R.StsI was joined to the tac
AB  - promoter of an expression vector, pKK223-3.  By introduction of the plasmid into E. coli UT481
AB  - cells expressing the fokIM gene, R.StsI activity was overproduced, from which R.StsI was
AB  - purified homogeneously.  We compared the properties of R.StsI with those of R.FokI.  The
AB  - optimum reaction conditions for R.StsI were quite different from those for R.FokI.  R.StsI is
AB  - an acidic protein (pI 6.3).  Anti-R.StsI serum did not cross-react with R.FokI, indicating
AB  - three-dimensional structural dissimilarity.  The domain structure of R.StsI was elucidated by
AB  - digestion with trypsin.  In the presence of substrate DNA, R.StsI was digested to yield 45-kDa
AB  - N-terminal and 23-kDa C-terminal fragments.  The amino-acid sequences around the trypsin
AB  - cleavage sites of R.StsI and R.FokI were quite homologous.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Takasaki, Y.
TI  - Enzymology of restriction enzymes.
JO  - Seikagaku
PY  - 1994
SP  - 1237
EP  - 1245
VL  - 66
AB  - A review
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Tsuda, J.
AU  - Kato, T.
AU  - Okamoto, K.
AU  - Yanase, H.
AU  - Tanaka, M.
TI  - Evidence of horizontal transfer of the EcoO109I restriction-modification gene to Escherichia coli chromosomal DNA.
JO  - J. Bacteriol.
PY  - 1999
SP  - 6822
EP  - 6827
VL  - 181
AB  - A DNA fragment carrying the genes coding for EcoO109I endonuclease and EcoO109I methylase,
AB  - which recognize the nucleotide sequence 5'-(A/G) GGNCC(C/T)-3', was cloned from the
AB  - chromosomal DNA of Escherichia coli H709c.  The EcoO109I restriction-modification system was
AB  - found to be inserted between the int and psu genes from satellite bacteriophage P4, which were
AB  - lysogenized in the chromosome at the P4 phage attachment site of the corresponding leuX gene
AB  - observed in E. coli K-12 chromosomal DNA.  The sid gene of the prophage was inactivated by
AB  - insertion of one copy of IS21.  These findings may shed light on the horizontal transfer and
AB  - stable maintenance of the R-M system.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Tsuda, J.
AU  - Nakai, S.-y.
TI  - C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3558
EP  - 3565
VL  - 30
AB  - The EcoO109I restriction-modification system, which recognizes 5'-(A/G)GGNCC(C/T)-3', has
AB  - been cloned, and contains convergently transcribed endonuclease and methylase. The role and
AB  - action mechanism of the gene product, C.EcoO109I, of a small open reading frame located
AB  - upstream of ecoO109IR were investigated in vivo and in vitro.  The results of deletion
AB  - analysis suggested that C.EcoO109I acts as a positive regulator of ecoO109IR expression but
AB  - has little effect on ecoO109IM expression. Assaying of promoter activity showed that the
AB  - expression of ecoO109IC was regulated by its own gene product, C.EcoO109I. C.EcoO109I was
AB  - overproduced as a His-tag fusion protein in recombinant Escherichia coli HB101 and purified to
AB  - homogeneity. C.EcoO109I exists as a homodimer, and recognizes and binds to the DNA sequence
AB  - 5'-CTAAG(N)(5)CTTAG-3' upstream of the ecoO109IC translational start site. It was also shown
AB  - that C.EcoO109I bent the target DNA by 54 +/- 4 degrees.
ER  -

TY  - JOUR
AU  - Kita, K.
AU  - Tsuda, J.
AU  - Nishigaki, R.
TI  - Characterization and overproduction of EcoO109I methyltransferase.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2001
SP  - 2512
EP  - 2518
VL  - 65
AB  - In order to characterize EcoO109I methyltransferase, a recombinant Escherichia coli clone that
AB  - overproduces the enzyme was constructed.
AB  - The coding region of M.EcoO109I was joined to the lac promoter of an
AB  - expression vector, pUC118, and the resulting plasmid was introduced
AB  - into E. coli HB101. M.EcoO109I was purified homogeneously from
AB  - IPTG-induced cells, and was found to consist of a monomer subunit.
AB  - M.EcoO109I uniquely methylates the inner deoxycytidylate residue in the
AB  - sequence 5'-(A/G)GGNCC(C/T)-3' to produce 5-methylcytosine. The enzyme
AB  - was most active at pH 8.0-8.5 and 50 C. The enzyme activity was
AB  - not affected by the addition of Mg2+ or EDTA.
ER  -

TY  - JOUR
AU  - Kitagawa, W.
AU  - Hata, M.
AU  - Sekizuka, T.
AU  - Kuroda, M.
AU  - Ishikawa, J.
TI  - Draft Genome Sequence of Rhodococcus erythropolis JCM 6824, an Aurachin RE Antibiotic Producer.
JO  - Genome Announcements
PY  - 2014
SP  - e01026
EP  - e01014
VL  - 2
AB  - Rhodococcus erythropolis JCM 6824 is the producer of the quinoline antibiotic aurachin RE.
AB  - This bacterium also degrades and utilizes some aromatic compounds,
AB  - such as biphenyl and benzoate. Here, we report the draft genome sequence of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Kitajima, M.
AU  - Ishizaki, S.
AU  - Jang, J.
AU  - Ishii, S.
AU  - Okabe, S.
TI  - Complete Genome Sequence of Klebsiella quasipneumoniae Strain S05, a Fouling-Causing Bacterium Isolated from a Membrane Bioreactor.
JO  - Genome Announcements
PY  - 2018
SP  - e00471
EP  - e00418
VL  - 6
AB  - We report here the complete genome sequence of Klebsiella quasipneumoniae strain  S05, a
AB  - bacterium capable of producing membrane fouling-causing soluble substances
AB  - and capable of respiring on oxygen, nitrate, and an anodic electrode. The genomic
AB  - information of strain S05 should help predict metabolic pathways associated with
AB  - these unique biological properties of this bacterium.
ER  -

TY  - JOUR
AU  - Kits, K.D. et al.
TI  - Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.
JO  - Genome Announcements
PY  - 2013
SP  - e00170
EP  - e00113
VL  - 1
AB  - The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing
AB  - gammaproteobacterium isolated from freshwater, is reported.
AB  - Aside from a conserved inventory of genes for growth on single-carbon compounds,
AB  - M. album BG8 carries a range of gene inventories for additional carbon and
AB  - nitrogen transformations but no genes for growth on multicarbon substrates or for
AB  - N fixation.
ER  -

TY  - JOUR
AU  - Kittichotirat, W.
AU  - Good, N.M.
AU  - Hall, R.
AU  - Bringel, F.
AU  - Lajus, A.
AU  - Medigue, C.
AU  - Smalley, N.E.
AU  - Beck, D.
AU  - Bumgarner, R.
AU  - Vuilleumier, S.
AU  - Kalyuzhnaya, M.G.
TI  - Genome Sequence of Methyloversatilis universalis FAM5T, a Methylotrophic Representative of the Order Rhodocyclales.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4541
EP  - 4541
VL  - 193
AB  - Rhodocyclales are representative of versatile bacteria that are able to utilize a wide variety
AB  - of organic compounds for growth, but only few
AB  - strains have been isolated in pure culture thus far. Here we present the
AB  - genome sequence of Methyloversatilis universalis FAM5(T), the first
AB  - cultivable methylotrophic member of the order.
ER  -

TY  - JOUR
AU  - Kittler, L.
AU  - Bell, A.
AU  - Baguley, B.C.
AU  - Lober, G.
TI  - Inhibition of restriction endonucleases by DNA sequence-reading ligands.
JO  - Biochem. Mol. Biol. Int.
PY  - 1996
SP  - 263
EP  - 272
VL  - 40
AB  - DNA sequence-reading bisquaternary ammonium heterocycles SN 6570, SN 6999, SN 6053, SN 6132,
AB  - SN 6131, SN 18071 and the non-specific binders SN 6113, SN 5754, SN 6324, and SN 4094
AB  - influence the enzymatic activity of restriction endonucleases in different manners.  A
AB  - prerequisite for sequence-specific ligand interaction is a dAdT run of at least four base
AB  - pairs.  The sequence-specific binders inhibit the cleavage activity of restriction
AB  - endonucleases EcoRI, SspI, and DraI with four and six dAdT base pairs in their restriction
AB  - sites, while the activity of SalI and BamHI with less than four dAdT base pairs in their
AB  - recognition motifs remains unaffected.  On the contrary, the non-specific binding DNA ligands
AB  - are incapable of suppressing the digestion for restriction nucleases under research.  These
AB  - results are in line with our footprint data.  The inhibitory effect is independent of the
AB  - number of cleavage sites in DNA and of whether the macromolecule exists in the ccc or lds
AB  - conformation.  Sequence specific binding of the ligand SN 6043 in close vicinity to the
AB  - cleavage sites of restriction endonuclease DraI also interferes with enzyme inhibition.
ER  -

TY  - JOUR
AU  - Kittler, L.
AU  - Bell, A.
AU  - Baguley, B.C.
AU  - Loeber, G.
TI  - Sequence specific modulation of DNA restriction enzyme cleavage by minor groove binders.
JO  - Biol. Chem.
PY  - 1998
SP  - 519
EP  - 525
VL  - 379
AB  - The inhibition of restriction endonuclease cleavage by a series of bisquaternary ammonium
AB  - derivatives which bind to the minor groove of DNA has been studied.  The derivatives
AB  - considered included six sequence-selective binders (SN 6570, SN 6999, SN 6050, SN 6132, SN
AB  - 6131 and SN 18071) and four non-specific binders (SN 6113, SN 5754, SN 6324 and SN 4094) and
AB  - can be distinguished by their activity on restriction endonucleases.  Digestion experiments
AB  - with pUC19 DNA were monitored electrophoretically using the transition of the covalently
AB  - closed circular DNA into the linear double stranded one.  Only the sequence-specific binders
AB  - inhibit the cleavage activity of restriction endonucleases EcoRI, SspI and DraI with four and
AB  - six dAdT-base pairs within their restriction sites, while the activity of SalI and BamHI with
AB  - less than four dAdT-sequences was unaffected.  In contrast, the non-specific binding ligands
AB  - were incapable of suppressing enzyme digestion.  The inhibition of the restriction
AB  - endonuclease PvuII indicates that ligand binding in close vicinity to the cleavage sites is
AB  - also involved in the enzyme inhibition.  The dAdT-content in proximity to the palindromic
AB  - sequences of three DraI cutting sites in pUC19DNA explains why the derivative SN 6053 protects
AB  - these sequences in different manners.  Gel shift experiments indicated that BQA-derivatives
AB  - inhibit the DNA-enzyme complex formation if the ligand was added to the DNA before the enzyme.
AB  - In contrast, complex formation between DNA and enzyme remained unchanged when the enzyme was
AB  - added first.
ER  -

TY  - JOUR
AU  - Kivisto, A.
AU  - Larjo, A.
AU  - Ciranna, A.
AU  - Santala, V.
AU  - Roos, C.
AU  - Karp, M.
TI  - Genome Sequence of Halanaerobium saccharolyticum subsp. saccharolyticum Strain DSM 6643T, a Halophilic Hydrogen-Producing Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00187
EP  - e00113
VL  - 1
AB  - Halanaerobium saccharolyticum is a halophilic anaerobic fermentative bacterium capable of
AB  - producing hydrogen, a potential future energy carrier molecule. The
AB  - high-quality draft genome of H. saccharolyticum subsp. saccharolyticum strain DSM
AB  - 6643(T) consists of 24 contigs for 2,873,865 bp with a G+C content of 32.3%.
ER  -

TY  - JOUR
AU  - Kivisto, R.I.
AU  - Kovanen, S.
AU  - Skarp-de-Haan, A.
AU  - Schott, T.
AU  - Rahkio, M.
AU  - Rossi, M.
AU  - Hanninen, M.-L.
TI  - Evolution and Comparative Genomics of Campylobacter jejuni ST-677 Clonal Complex.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 2424
EP  - 2438
VL  - 6
AB  - Campylobacter is the most common bacterial cause of gastroenteritis in the European Union with
AB  - over 200,000 laboratory-confirmed cases reported annually. This is the first study to describe
AB  - findings related to comparative genomics analyses of the sequence type (ST)-677 clonal complex
AB  - (CC), a Campylobacter jejuni lineage associated with bacteremia cases in humans. We performed
AB  - whole-genome sequencing, using Illumina HiSeq sequencing technology, on five related ST-677 CC
AB  - isolates from two chicken farms to identify microevolution taking place at the farms. Our
AB  - further aim was to identify novel putative virulence determinants from the ST-677 CC genomes.
AB  - For this purpose, clinical isolates of the same CC were included in comparative genomic
AB  - analyses against well-known reference strains of C. jejuni. Overall, the ST-677 CC was
AB  - recognized as a highly clonal lineage with relatively small differences between the genomes.
AB  - Among the farm isolates differences were identified mainly in the lengths of the homopolymeric
AB  - tracts in genes related to the capsule, lipo-oligosaccharide, and flagella. We identified
AB  - genomic features shared with C. jejuni subsp. doylei, which has also been shown to be
AB  - associated with bacteremia in humans. These included the degradation of the cytolethal
AB  - distending toxin operon and similarities between the capsular polysaccharide biosynthesis
AB  - loci. The phase-variable GDP-mannose 4,6-dehydratase (EC 4.2.1.47) (wcbK, CAMP1649),
AB  - associated with the capsular polysaccharide biosynthesis locus, may play a central role in
AB  - ST-677 CC conferring acid and serum resistance during different stages of infection.
AB  - Homology-based searches revealed several additional novel features and characteristics,
AB  - including two putative type Vb secretion systems and a novel restriction
AB  - modification/methyltransferase gene cluster, putatively associated with pathogenesis and niche
AB  - adaptation.
ER  -

TY  - JOUR
AU  - Kiwaki, M.
TI  - Restriction enzymes.
JO  - Bifizusukin Yakurutokabu
PY  - 2009
SP  - 118
EP  - 122
VL  - 0
ER  -

TY  - JOUR
AU  - Kjems, J.
AU  - Garrett, R.A.
TI  - An intron in the 23S ribosomal RNA gene of the archaebacterium Desulfurococcus mobilis.
JO  - Nature
PY  - 1985
SP  - 675
EP  - 677
VL  - 318
AB  - The archaebacteria have been defined, at a molecular level, as constituting a third primary
AB  - kingdom consisting of the methanogens, the extreme halophiles, and the sulphur-dependent
AB  - extreme thermophiles. In reaching this conclusion, Woese and colleagues used the 16S ribosomal
AB  - RNA as an approximate chronometer for evolutionary time and demonstrated that, at a nucleotide
AB  - sequence level, the archaebacteria are as different from the eubacteria and eukaryotes as the
AB  - latter kingdoms are from one another. Current research on archaebacteria is yielding valuable
AB  - insights into the evolutionary relationships between archaebacteria, eubacteria and
AB  - eukaryotes, and into the early forms of cellular life. Here, we extend this knowledge by
AB  - providing the first evidence for the occurrence of an intron within any prokaryotic ribosomal
AB  - RNA. The intron was found within the 23S rRNA gene of the sulphur-dependent and anaerobic
AB  - Thermoproteale Desulfurococcus mobilis, which was isolated from hot acidic springs in Iceland
AB  - at temperatures up to 97oC. The intron contains 622 base pairs (bp); it is very A+T-rich (65%)
AB  - compared with the 23S rRNA gene (34%), and it exhibits a large open reading frame. The
AB  - splicing site occurs in domain IV of the 23S RNA at a position close to that of an intron of
AB  - the lower eukaryote Physarum polycephalum; the intron does not readily fall into one of the
AB  - three classes of eukaryotic nuclear introns because it has features in common with those of
AB  - classes I (rRNA) and III (transfer RNA).
ER  -

TY  - JOUR
AU  - Kladde, M.P.
AU  - Simpson, R.T.
TI  - Rapid detection of functional expression of C-5-DNA methytransferases in yeast.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1354
EP  - 1355
VL  - 26
AB  - We have previously employed the cytosine-5-DNA methyltransferase, M.SssI, as a probe for
AB  - chromatin architecture in intact cells.  Although M.SssI offers the highest resolution of any
AB  - currently available MTase, the difficulty in establishing stable, methylation-positive strains
AB  - poses a barrier to its general utility as a chromatin probe.  We describe a single screen for
AB  - M.SssI-expressing strains that eliminates the purification of PCR products amplified from
AB  - bisulfite-treated DNA, use of radioisotopes, polyacrylamide sequencing gel electrophoresis,
AB  - and autoradiography.  The high throughput of the method now makes it feasible to introduce
AB  - M.SssI into a vareity of wild-type and mutant genetic backgrounds.
ER  -

TY  - JOUR
AU  - Kladde, M.P.
AU  - Simpson, R.T.
TI  - Chromatin structure mapping in vivo using methyltransferases.
JO  - Methods Enzymol.
PY  - 1996
SP  - 214
EP  - 233
VL  - 274
AB  - Realization of the role of chromatin structure in the function of RNA polymerases in
AB  - eukaryotic cells has grown rapidly in the past decade.  Effects of the nucleosomal
AB  - organization of DNA on transcriptional initiation have been documented both in vivo and in
AB  - vitro.  Several studies have addressed the mechanical difficulties faced by RNA polymerase
AB  - encountering a nucleosome during transcriptional elongation, offering varying possible
AB  - resolutions to this problem.   Above the local difficulties which polymerases must face in the
AB  - basic nucleosomal organization of chromatin, there are higher order structures, including
AB  - chromatin domains, which have been implicated in more global silencing, such as position
AB  - effect variegation, X-chromosome inactivation, epigenetic inheritance, and centromeric and
AB  - telomeric repression.  All these considerations make methods for assessment of chromatin
AB  - structure of importance to those scientists interested in transcriptional mechanisms in
AB  - eukaryotic cells.  Historically, chromatin structure investigations have relied on enzymatic
AB  - (micrococcal nuclease or DNase I) or chemical (hydroxyl radical, methidium propyl-EDTA-iron,
AB  - cooper-phenanthroline) probes to degrade DNA; proteins, either histones or non-histone
AB  - regulatory proteins, left a footprint on DNA by blocking the access of the reagent to the
AB  - nucleic acid, enabling deductions about potential structures of the nucleoprotein complex.  In
AB  - general, isolation of nuclei is required prior to analysis of chromatin.  This makes the
AB  - detection of the labile chromatin constituents problematic, limiting conclusions about the
AB  - structure of transcribed or repressed genes.
ER  -

TY  - JOUR
AU  - Kladde, M.P.
AU  - Xu, M.
AU  - Simpson, R.T.
TI  - DNA methyltransferases as probes of chromatin structure in vivo.
JO  - Methods Enzymol.
PY  - 1999
SP  - 431
EP  - 447
VL  - 304
AB  - A complementary strategy to conventional methods for probing chromatin organization utilizes
AB  - the expression of foreign DNA methyltransferases in intact Saccharomyces cerevisiae.  At
AB  - current levels of expression of several foreign methyltransferases in yeast, no deleterious
AB  - effects to cellular metabolism have been detected.  The innocuousness of methyltransferase
AB  - expression and the absence of endogenous adenine or cytosine methylation in the yeast genome
AB  - allow detection of de novo DNA modification in DNA that is directly isolated from engineered,
AB  - methylation-proficient cells.  The ability to bypass the isolation of nuclei, thereby avoiding
AB  - loss of labile constituents or possible reorganization of chromosome structure, has provided
AB  - the motivation for developing methyltransferase probing strategies.
ER  -

TY  - JOUR
AU  - Klaenhammer, T.R.
TI  - Development of bacteriophage-resistant strains of lactic acid bacteria.
JO  - Food Biotech.
PY  - 1991
SP  - 675
EP  - 682
VL  - 19
AB  - One exciting area that has emerged through genetic analysis of the lactococci is the
AB  - definition and practical application of gene systems that provide phage resistance to these
AB  - industrially important bacteria.  Naturally occurring phage-insensitive strains have been
AB  - characterized and found to harbor multiple defense systems which can act at different points
AB  - of the lytic cycle to prevent the successful adsorption, infection, or replication of virulent
AB  - phages.  Although phage attack on lactococcal starter cultures is still a major problem for
AB  - the cultured dairy products industries, this can now be successfully addressed using genetic
AB  - approaches to construct strains which are resistant to the phages often encountered in the
AB  - industry.  In this paper I will describe the various phage defense systems that are naturally
AB  - present in lactococci, their individual and combined effects, and the genetic strategies which
AB  - are currently available to construct phage-insensitive strains for dairy fermentations.  In
AB  - addition, I will discuss the molecular responses of virulent phages which have appeared in the
AB  - industry following the introduction and use of specialized starter cultures carrying defined
AB  - mechanisms of phage resistance.  The genetic routes whereby industrial phages elicit
AB  - counter-defenses against lactococcal resistance mechanism provide new and important
AB  - information that will facilitate the development of improved starter culture systems and
AB  - phage-resistant lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Klaenhammer, T.R.
TI  - Plasmid-directed mechanisms for bacteriophage defense in lactic streptococci.
JO  - FEMS Microbiol. Lett.
PY  - 1987
SP  - 313
EP  - 325
VL  - 46
AB  - Genetic studies with lactic streptococci have identified a variety of plasmids
AB  - coding for systems that interfere with phage adsorption, direct restriction and
AB  - modification activities, and disrupt various stages in the phage lytic cycle.
AB  - This review describes mechanisms of phage defense that are plasmid-directed in
AB  - lactic streptococci, examines the physical and genetic properties of the
AB  - plasmids involved, and discusses genetic strategies for construction of
AB  - phage-insensitive starter cultures for dairy fermentations.
ER  -

TY  - JOUR
AU  - Klaenhammer, T.R.
TI  - Genetic characterization of multiple mechanisms of phage defense from a prototype phage-insensitive strain, Lactococcus lactis ME2.
JO  - J. Dairy Sci.
PY  - 1989
SP  - 3429
EP  - 3443
VL  - 72
AB  - Lactococci used as starter cultures in dairy fermentations are highly
AB  - susceptible to attack by bacteriophage.  Genetic studies with Lactococcus
AB  - lactis ME2, a prototype phage-insensitive strain, have identified
AB  - plasmid-encoded defenses, which interfere with phage adsorption, restrict and
AB  - modify phages, or abort lytic phage infection.  Restriction and modification
AB  - and abortion of phage infection were localized on two distinct
AB  - self-transmissible plasmids, pTN20 and pTR2030, respectively, orginating from
AB  - L. lactis ME2.  A comparison of the physical and genetic characteristics of
AB  - these two conjugative plasmids is presented.  Conjugation and cloning
AB  - strategies employed to assemble these complementary mechanisms of phage
AB  - resistance will be discussed.  The collective expression of different defense
AB  - systems provided a greater phage resistance to dairy lactococci.  Starter
AB  - cultures that are recalcitrant to phage attack can be constructed from existing
AB  - strains through application of genetic technologies, which assemble
AB  - complementary mechanisms of phage defense.
ER  -

TY  - JOUR
AU  - Klaenhammer, T.R.
AU  - Fitzgerald, G.F.
TI  - Bacteriophages and bacteriophage resistance.
JO  - Genetics and Biotechnology of Lactic Acid Bacteria.
PY  - 1994
SP  - 106
EP  - 168
VL  - 0
AB  - Food and dairy fermentations rely on the growth and acid
AB  - producing ability of the lactic acid bacteria.  Many of these have
AB  - remained as traditional fermentations, where the process is driven by
AB  - the natural microflora associated with the raw material.  Increasing
AB  - consistency, improved quality and processing efficiencies have followed
AB  - the development of controlled fermentations.  These rely on the activity
AB  - of a starter culture which is intentionally inoculated in order to drive
AB  - the primary fermentation.  However, with the increased control granted
AB  - through the repeated use of a defined starter culture comes the potential
AB  - for disruption of the fermentation by bacteriophage.
ER  -

TY  - JOUR
AU  - Klaenhammer, T.R.
AU  - Romero, D.
AU  - Sing, W.
AU  - Hill, C.
TI  - Molecular analysis of pTR2030 gene systems that confer bacteriophage resistance to Lactococci.
JO  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
PY  - 1991
SP  - 124
EP  - 130
VL  - 8
AB  - None
ER  -

TY  - JOUR
AU  - Klapatch, T.R.
AU  - Demain, A.L.
AU  - Lynd, L.R.
TI  - Restriction endonuclease activity in Clostridium thermocellum and Clostridium thermosaccharolyticum.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1996
SP  - 127
EP  - 131
VL  - 45
AB  - Clostridium thermocellum cell extracts exhibit specific endonuclease activity with
AB  - very little non-specific exonuclease activity at 55oC.  The Dam methylation system of
AB  - Escherichia
AB  - coli offers complete protection from digestion by C. thermocellum ATCC 27405 cell extracts for
AB  - all
AB  - DNA tested (totaling >100kb, insuring that most potential restriction sequences have been
AB  - exposed).  Based on both the Dam recognition sequence and the similarity of cell extract and
AB  - MboI
AB  - DNA digests, the C. thermocellum restriction enzyme recognition sequence appears to be
AB  - 5' GATC 3'.  Cell extracts made from a second thermophile, C. thermosaccarolyticum ATCC
AB  - 31960 do not exhibit specific endonuclease activity under the conditions tested.  Genomic DNA
AB  - from C. thermocellum exhibits a Dam+ phenotype while genomic DNA from C.
AB  - thermosaccarolyticum exhibits a Dam- phenotype.
ER  -

TY  - JOUR
AU  - Klassen, J.L.
AU  - Adams, S.M.
AU  - Bramhacharya, S.
AU  - Giles, S.S.
AU  - Goodwin, L.A.
AU  - Woyke, T.
AU  - Currie, C.R.
TI  - Draft Genome Sequence of Streptomyces sp. Strain Wigar10, Isolated from a Surface-Sterilized Garlic Bulb.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6999
EP  - 7000
VL  - 193
AB  - Streptomyces sp. strain Wigar10 was isolated from a surface-sterilized garlic bulb (Allium
AB  - sativum var. Purple Stripe). Its genome encodes
AB  - several novel secondary metabolite biosynthetic gene clusters and provides
AB  - a genetic basis for further investigation of this strain's chemical
AB  - biology and potential for interaction with its garlic host.
ER  -

TY  - JOUR
AU  - Klassen, J.L.
AU  - Rischer, M.
AU  - Wolf, T.
AU  - Guo, H.
AU  - Shelest, E.
AU  - Clardy, J.
AU  - Beemelmanns, C.
TI  - Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata.
JO  - Genome Announcements
PY  - 2015
SP  - e01380
EP  - e01315
VL  - 3
AB  - The genomes of three Pseudoalteromonas strains (P1-8, P1-11, and P1-30) were sequenced and
AB  - assembled. These genomes will inform future study of the genes
AB  - responsible for the production of biologically active compounds responsible for
AB  - these strains' antimicrobial, biofouling, and algicidal activities.
ER  -

TY  - JOUR
AU  - Klassen, J.L.
AU  - Wolf, T.
AU  - Rischer, M.
AU  - Guo, H.
AU  - Shelest, E.
AU  - Clardy, J.
AU  - Beemelmanns, C.
TI  - Draft Genome Sequences of Six Pseudoalteromonas Strains, P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, Which Induce Larval Settlement and Metamorphosis in  Hydractinia echinata.
JO  - Genome Announcements
PY  - 2015
SP  - e01477
EP  - e01415
VL  - 3
AB  - To gain a broader understanding of the importance of a surface-associated lifestyle and
AB  - morphogenic capability, we have assembled and annotated the genome
AB  - sequences of Pseudoalteromonas strains P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25,
AB  - and P1-26, isolated from Hydractinia echinata. These genomes will allow detailed
AB  - studies on bacterial factors mediating interkingdom communication.
ER  -

TY  - JOUR
AU  - Klasson, L.
AU  - Westberg, J.
AU  - Sapountzis, P.
AU  - Naslund, K.
AU  - Lutnaes, Y.
AU  - Darby, A.C.
AU  - Veneti, Z.
AU  - Chen, L.
AU  - Braig, H.R.
AU  - Garrett, R.
AU  - Bourtzis, K.
AU  - Andersson, S.G.
TI  - The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 5725
EP  - 5730
VL  - 106
AB  - The obligate intracellular bacterium Wolbachia pipientis infects around 20% of all insect
AB  - species. It is maternally inherited and induces
AB  - reproductive alterations of insect populations by male killing,
AB  - feminization, parthenogenesis, or cytoplasmic incompatibility. Here, we
AB  - present the 1,445,873-bp genome of W. pipientis strain wRi that induces
AB  - very strong cytoplasmic incompatibility in its natural host Drosophila
AB  - simulans. A comparison with the previously sequenced genome of W.
AB  - pipientis strain wMel from Drosophila melanogaster identified 35
AB  - breakpoints associated with mobile elements and repeated sequences that
AB  - are stable in Drosophila lines transinfected with wRi. Additionally, 450
AB  - genes with orthologs in wRi and wMel were sequenced from the W. pipientis
AB  - strain wUni, responsible for the induction of parthenogenesis in the
AB  - parasitoid wasp Muscidifurax uniraptor. The comparison of these A-group
AB  - Wolbachia strains uncovered the most highly recombining intracellular
AB  - bacterial genomes known to date. This was manifested in a 500-fold
AB  - variation in sequence divergences at synonymous sites, with different
AB  - genes and gene segments supporting different strain relationships. The
AB  - substitution-frequency profile resembled that of Neisseria meningitidis,
AB  - which is characterized by rampant intraspecies recombination, rather than
AB  - that of Rickettsia, where genes mostly diverge by nucleotide
AB  - substitutions. The data further revealed diversification of ankyrin repeat
AB  - genes by short tandem duplications and provided examples of horizontal
AB  - gene transfer across A- and B-group strains that infect D. simulans. These
AB  - results suggest that the transmission dynamics of Wolbachia and the
AB  - opportunity for coinfections have created a freely recombining
AB  - intracellular bacterial community with mosaic genomes.
ER  -

TY  - JOUR
AU  - Klaus, S.
AU  - Hartmann, M.
AU  - Krugel, H.
AU  - Roth, M.
AU  - Walter, F.
AU  - Rautenstein, Y.I.
AU  - Solovyeva, N.Y.
TI  - Restriction of Streptomyces phage SH5 by endonuclease ShyI from Streptomyces hygroscopicus 0477.
JO  - Mol. Gen. Genet.
PY  - 1981
SP  - 286
EP  - 288
VL  - 184
AB  - DNA of the temperate Streptomyces phage SH5 (DNA molecular weight 27 x 106) is
AB  - subject to restriction-modification mediated by S. hygroscopicus 0477.  S.
AB  - levoris 1331 and 2340.  The restriction endonuclease ShyI (isoschizomeric with
AB  - SacII) isolated from S. hygroscopicus 0477 is involved in restriction of
AB  - SH5-1331 and SH5-2340 DNAs in S. hygroscopicus 0477.
ER  -

TY  - JOUR
AU  - Klee, S.R.
AU  - Nassif, X.
AU  - Kusecek, B.
AU  - Merker, P.
AU  - Beretti, J.L.
AU  - Achtman, M.
AU  - Tinsley, C.R.
TI  - Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen   Neisseria gonorrhoeae.
JO  - Infect. Immun.
PY  - 2000
SP  - 2082
EP  - 2095
VL  - 68
AB  - The pathogenic species Neisseria meningitidis and Neisseria gonorrhoeae cause dramatically
AB  - different diseases despite strong relatedness at the
AB  - genetic and biochemical levels. N. meningitidis can cross the blood-brain
AB  - barrier to cause meningitis and has a propensity for toxic septicemia
AB  - unlike N. gonorrhoeae. We previously used subtractive hybridization to
AB  - identify DNA sequences which might encode functions specific to bacteremia
AB  - and invasion of the meninges because they are specific to N. meningitidis
AB  - and absent from N. gonorrhoeae. In this report we show that these
AB  - sequences mark eight genetic islands that range in size from 1.8 to 40 kb
AB  - and whose chromosomal location is constant. Five of these genetic islands
AB  - were conserved within a representative set of strains and/or carried genes
AB  - with homologies to known virulence factors in other species. These were
AB  - deleted, and the mutants were tested for correlates of virulence in vitro
AB  - and in vivo. This strategy identified one island, region 8, which is
AB  - needed to induce bacteremia in an infant rat model of meningococcal
AB  - infection. Region 8 encodes a putative siderophore receptor and a
AB  - disulfide oxidoreductase. None of the deleted mutants was modified in its
AB  - resistance to the bactericidal effect of serum. Neither were the mutant
AB  - strains altered in their ability to interact with endothelial cells,
AB  - suggesting that such interactions are not encoded by large genetic islands
AB  - in N. meningitidis.
ER  -

TY  - JOUR
AU  - Kleerebezem, M. et al.
TI  - Complete genome sequence of Lactobacillus plantarum WCFS1.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 1990
EP  - 1995
VL  - 100
AB  - The 3,308,274-bp sequence of the chromosome of Lactobacillus plantarum strain WCFS1, a single
AB  - colony isolate of strain NCIMB8826 that was
AB  - originally isolated from human saliva, has been determined, and contains
AB  - 3,052 predicted protein-encoding genes. Putative biological functions
AB  - could be assigned to 2,120 (70%) of the predicted proteins. Consistent
AB  - with the classification of L. plantarum as a facultative
AB  - heterofermentative lactic acid bacterium, the genome encodes all enzymes
AB  - required for the glycolysis and phosphoketolase pathways, all of which
AB  - appear to belong to the class of potentially highly expressed genes in
AB  - this organism, as was evident from the codon-adaptation index of
AB  - individual genes. Moreover, L. plantarum encodes a large
AB  - pyruvate-dissipating potential, leading to various end-products of
AB  - fermentation. L. plantarum is a species that is encountered in many
AB  - different environmental niches, and this flexible and adaptive behavior is
AB  - reflected by the relatively large number of regulatory and transport
AB  - functions, including 25 complete PTS sugar transport systems. Moreover,
AB  - the chromosome encodes >200 extracellular proteins, many of which are
AB  - predicted to be bound to the cell envelope. A large proportion of the
AB  - genes encoding sugar transport and utilization, as well as genes encoding
AB  - extracellular functions, appear to be clustered in a 600-kb region near
AB  - the origin of replication. Many of these genes display deviation of
AB  - nucleotide composition, consistent with a foreign origin. These findings
AB  - suggest that these genes, which provide an important part of the
AB  - interaction of L. plantarum with its environment, form a lifestyle
AB  - adaptation region in the chromosome.
ER  -

TY  - JOUR
AU  - Kleid, D.
AU  - Humayun, Z.
AU  - Jeffrey, A.
AU  - Ptashne, M.
TI  - Novel properties of a restriction endonuclease isolated from Haemophilus parahaemolyticus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1976
SP  - 293
EP  - 297
VL  - 73
AB  - The sequences in lambda DNA in and around six sites cut by HphI, a restriction
AB  - enzyme isolated from Haemophilus parahaemolyticus, are compared.  The enzyme
AB  - produces a staggered cut around an AT or TA base pair, but the sequences
AB  - immediately surrounding the cleavage sites bear no obvious relation to one
AB  - another.  Eight (in some cases nine) base pairs to one side of each cleavage
AB  - site is the common sequence TCACCAGTGC.  Two lines of evidence indicate that
AB  - these bases constitute part or all of the Hph recognition site.  First,
AB  - mutations in this sequence prevent HphI cutting.  Second,
AB  - dimethylsulfate-mediated methylation of Gs and As in this site prevent cutting,
AB  - whereas methylation of purines in the region between this sequence and the
AB  - cleavage sites has no such effect.  There is discernible 2-fold rotational
AB  - symmetry neither in the common sequence nor around the cleavage sites.
ER  -

TY  - JOUR
AU  - Kleid, D.G.
TI  - Purification and properties of the HphI endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 163
EP  - 166
VL  - 65
AB  - 5' CGGTGATACTGAGCA^CATCAG   3' GCCACTATGACTCG^TGTAGTC The nucleotide
AB  - sequence-specific endonuclease from Haemophilus parahaemolyticus has properties
AB  - that differ from the majority of type II restriction endonuclease.  This enzyme
AB  - recognizes an unsymmetric nucleotide sequence and cleaves the DNA at a site
AB  - approximately one turn of the helix from the center of the recognition
AB  - sequence.  The recognition sequence has been demonstrated to be a five base
AB  - pair sequence 5' GGTGA   3' CCACT.
ER  -

TY  - JOUR
AU  - Klein, A.
TI  - Mechanisms of host-controlled modification of phage T1.
JO  - Z. Vererbungsl.
PY  - 1965
SP  - 346
EP  - 363
VL  - 96
AB  - Complementation tests using T1 amber-mutants show that all genes of restricted
AB  - phage so far investigated are able to function in the restricting host.  This
AB  - ability is quickly lost when m-RNA synthesis is blocked.  The ability of
AB  - functioning of restricted phage genes depends on their location on the phage
AB  - genome.  A model is discussed explaining this polarization in terms of directed
AB  - transcription of T1 DNA.  As in host cells lysogenic for P1 restricted T1 DNA
AB  - is destroyed after infection of strains THU or BG43, which also act on T1 by
AB  - HCM.  T1 phages which do not bear P1 specific modification may in rare cases
AB  - escape from restriction in host cells lysogenic for P1 - either by infecting a
AB  - nonrestricting exceptional cell or when they are very quickly protected against
AB  - destruction, probably by rapid modification.  Multiple infection does not
AB  - increase this low probability of survival of the single phage.  T1 DNA contains
AB  - 5-methylcytosine and 6-methylaminopurine.  The amount of these bases in the DNA
AB  - is independent of the host specificity controlled by P1.  However, coinfection
AB  - of P1 lysogenic cells with T1 and T3 simultaneously prevents T1 DNA from being
AB  - methylated and modified.  It may therefore be concluded that the mechanisms of
AB  - modifying T1 in this host strain consists in methylating T1 DNA in a specific
AB  - pattern.  T2gt, a mutant of T2 containing nonglucosylated DNA, is restricted by
AB  - cells lysogenic for P1 while it cannot be modified by the same host.  The
AB  - question is discussed, whether this result has some implication concerning the
AB  - role of 5 MC in the postulated HCM pattern since 5 MC cannot be formed in T2gt
AB  - DNA.
ER  -

TY  - JOUR
AU  - Klein, A.
TI  - Host-controlled modification.
JO  - Z. Vererbungsl.
PY  - 1965
SP  - 324
EP  - 345
VL  - 96
AB  - The phenomena and effects of host-controlled modification (HCM) as described in
AB  - the literature are comprehensively discussed.  The review includes the
AB  - occurrence of HCM, the restriction and modification caused by CM, its influence
AB  - on bacterial and phage crosses, and the function of restricted genes.  Besides,
AB  - genetic control of HCM and mutation effects of HCM and UV-irradiation are
AB  - reviewed.
ER  -

TY  - JOUR
AU  - Klein, A.
AU  - Sauerbier, W.
TI  - Role of methylation in host controlled modification of phage T1.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1965
SP  - 440
EP  - 445
VL  - 18
AB  - Non-mutational changes upon growth on certain bacterial host strains concerning
AB  - host range properties have been found in many bacteriophages.  This phenomenon
AB  - is known as host controlled modification (HCM).  Phage particles thus carry a
AB  - host specificity determined by the bacterial strain on which they were
AB  - produced.  Upon infection of a different bacterial strain the phage may be
AB  - either accepted or rejected on the basis of its specificity.  If accepted, it
AB  - multiplies in the new host cell and acquires a new specificity.  Arber and
AB  - Dussoix (1962) and Dussoix and Arber (1962) showed that host specificity of
AB  - phage lambda is carried by the phage DNA.  The chemical basis of HCM in lambda
AB  - is unknown.  It was suggested by in vitro experiments of Gold and Hurwitz
AB  - (1963) that different methylation of lambda DNA by different host cells might
AB  - confer different host specificity to the phage.  Ledinko (1964), however, found
AB  - equal amounts of 5-methylcytosine (5-MC) in DNA extracted from phage lambda
AB  - carrying the host specificities derived from the strains Escherichia coli
AB  - C,B,K, or K(P1).  Evidence will be presented here that (1) T1-DNA may in some
AB  - cases be methylated to different extents depending on its host specificity and
AB  - (2) that methylation is the chemical basis or at least an absolute requirement
AB  - for HCM of phage T1 by bacterial host cells lysogenic for P1.  In addition a
AB  - new system of HCM acting on T1 will be described which does not overlap with
AB  - the P1 system.
ER  -

TY  - JOUR
AU  - Klein, B.A.
AU  - Lemon, K.P.
AU  - Faller, L.L.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e01040
EP  - e01016
VL  - 4
AB  - Here, we present the draft genome sequence of the actinobacterium Curtobacterium  sp. strain
AB  - UCD-KPL2560, which was isolated from the running surface of an indoor
AB  - track field house in Medford, MA, USA (42.409716 degrees N, -71.115169 degrees
AB  - W). The genome assembly contains 3,480,487 bp in 156 contigs.
ER  -

TY  - JOUR
AU  - Klein, B.A.
AU  - Lemon, K.P.
AU  - Gajare, P.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility.
JO  - Genome Announcements
PY  - 2017
SP  - e01652
EP  - e01616
VL  - 5
AB  - We present here the draft genome sequences of Dermacoccus nishinomiyaensis strains UCD-KPL2534
AB  - and UCD-KPL2528, which were isolated at an indoor track
AB  - facility in Medford, MA, USA (42.409716, -71.115169) from an exit door handle and
AB  - settle dust, respectively. The genome assemblies contain 3,088,111 bp in 58
AB  - contigs and 3,162,381 bp in 100 contigs, respectively.
ER  -

TY  - JOUR
AU  - Klein, E.A.
AU  - Gitai, Z.
TI  - Draft Genome Sequence of Uropathogenic Escherichia coli Strain J96.
JO  - Genome Announcements
PY  - 2013
SP  - e00245
EP  - e00212
VL  - 1
AB  - J96 (O4:K6) was isolated from a human pyelonephritis patient. Here, we report the draft genome
AB  - sequence of J96, which contains virulence genes, including adhesion
AB  - factors, alpha-hemolysins, and cytotoxic necrotizing factor. J96 infects the
AB  - kidney and bladder, making it an important tool for studying pathogenesis.
ER  -

TY  - JOUR
AU  - Klein, J.M.
AU  - Bennett, R.W.
AU  - MacFarland, L.
AU  - Abranches, Da.S.M.E.
AU  - Meza-Turner, B.M.
AU  - Dark, P.M.
AU  - Frey, M.E.
AU  - Wellappili, D.P.
AU  - Beugli, A.D.
AU  - Jue, H.J.
AU  - Mellander, J.M.
AU  - Wei, W.
AU  - Ream, W.
TI  - Draft Genome Sequence of Erwinia billingiae OSU19-1, Isolated from a Pear Tree Canker.
JO  - Genome Announcements
PY  - 2015
SP  - e01119
EP  - e01115
VL  - 3
AB  - Plant-associated Erwinia include pathogenic and nonpathogenic species. We report  the 5.6-Mb
AB  - genome sequence of Erwinia billingiae OSU19-1, isolated from a canker  on a pear tree
AB  - inoculated with Erwinia amylovora. OSU19-1 and a closely related European isolate, E.
AB  - billingiae Eb661(T), share many similarities including 40 kb of plasmid sequence.
ER  -

TY  - JOUR
AU  - Klein, R.
AU  - Baranyi, U.
AU  - Rossler, N.
AU  - Greineder, B.
AU  - Scholz, H.
AU  - Witte, A.
TI  - Natrialba magadii virus phiCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon.
JO  - Mol. Microbiol.
PY  - 2002
SP  - 851
EP  - 863
VL  - 45
AB  - The double-stranded (ds)DNA virus phiCh1 infects the haloalkaliphilic
AB  - archaeon Natrialba magadii. The complete DNA sequence of 58 498 bp of the
AB  - temperate virus was established, and the probable functions of 21 of 98
AB  - phiCh1-encoded open reading frames (ORFs) have been assigned. This
AB  - knowledge has been used to propose functional modules each required for
AB  - specific functions during virus development. The phiCh1 DNA is terminally
AB  - redundant and circularly permuted and therefore appears to be packaged by
AB  - the so-called headful mechanism. The presence of ORFs encoding homologues
AB  - of proteins involved in plasmid replication as well as experimental
AB  - evidence indicate a plasmid-mediated replication strategy of the virus.
AB  - Results from nanosequencing of virion components suggest covalent
AB  - cross-linking of monomers of at least one of the structural proteins
AB  - during virus maturation. A comparison of the phiCh1 genome with the partly
AB  - sequenced genome of Halobacterium salinarum virus phiH revealed a close
AB  - relationship between the two viruses, although their host organisms live
AB  - in distinct environments with respect to the different pH values required
AB  - for growth.
ER  -

TY  - JOUR
AU  - Kleindienst, S.
AU  - Higgins, S.A.
AU  - Tsementzi, D.
AU  - Konstantinidis, K.T.
AU  - Mack, E.E.
AU  - Loffler, F.E.
TI  - Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00037
EP  - e00016
VL  - 4
AB  - An anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was
AB  - maintained in a microbial consortium. The organism originated
AB  - from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto
AB  - Rico, in October 2009 (latitude 18 degrees 21'43.9', longitude -65 degrees
AB  - 46'8.4'). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.
ER  -

TY  - JOUR
AU  - Kleiner, G.R.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Kalinowski, J.
AU  - Wertz, J.E.
AU  - Friehs, K.
TI  - Complete Draft Genome Sequence of Escherichia coli JF733.
JO  - Genome Announcements
PY  - 2016
SP  - e00298
EP  - e00216
VL  - 4
AB  - ITALIC! Escherichia coliJF733 is a strain with a long history in research on membrane proteins
AB  - and processes. However, tracing back the strain development
AB  - raises some questions concerning the correct genotype of JF733. Here, we present
AB  - the complete draft genome of ITALIC! E. coliJF733 in order to resolve any
AB  - remaining uncertainties.
ER  -

TY  - JOUR
AU  - Kleiner-Grote, G.R.M.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Kalinowski, J.
AU  - Friehs, K.
TI  - Complete Draft Genome Sequence of Escherichia coli K802.
JO  - Genome Announcements
PY  - 2017
SP  - e00934
EP  - e00917
VL  - 5
AB  - Escherichia coli K802 is an old strain used for cloning experiments, as well as for the
AB  - production of recombinant proteins. To understand the genomic background
AB  - of E. coli K802 better, we present here its complete draft genome sequence.
ER  -

TY  - JOUR
AU  - Kleinert, F.
AU  - Kallies, R.
AU  - Zweynert, A.
AU  - Bierbaum, G.
TI  - Draft Genome Sequences of Three Northern German Epidemic Staphylococcus aureus (ST247) Strains Containing Multiple Copies of IS256.
JO  - Genome Announcements
PY  - 2016
SP  - e00936
EP  - e00916
VL  - 4
AB  - We report the draft genome sequences of three multiresistant Staphylococcus aureus strains of
AB  - sequence type 247 (ST247). The methicillin-resistant S. aureus
AB  - (MRSA) SA1450/94 is vancomycin susceptible, while the clinical MRSA isolate S.
AB  - aureus SA137/93A and its spontaneous laboratory mutant SA137/93G are
AB  - characterized by intermediate vancomycin susceptibility.
ER  -

TY  - JOUR
AU  - Kleinstiver, B.P.
AU  - Berube-Janzen, W.
AU  - Fernandes, A.D.
AU  - Edgell, D.R.
TI  - Divalent Metal Ion Differentially Regulates the Sequential Nicking Reactions of the GIY-YIG Homing Endonuclease I-BmoI.
JO  - PLoS ONE
PY  - 2011
SP  - e23804
EP  - e23804
VL  - 6
AB  - Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic
AB  - elements by introducing double-strand breaks or nicks
AB  - at defined locations. Of the major families of homing endonucleases,
AB  - the modular GIY-YIG endonucleases are least understood in terms of
AB  - mechanism. The GIY-YIG homing endonuclease I-BmoI generates a
AB  - double-strand break by sequential nicking reactions during which the
AB  - single active site of the GIY-YIG nuclease domain must undergo a
AB  - substantial reorganization. Here, we show that divalent metal ion plays
AB  - a significant role in regulating the two independent nicking reactions
AB  - by I-BmoI. Rate constant determination for each nicking reaction
AB  - revealed that limiting divalent metal ion has a greater impact on the
AB  - second strand than the first strand nicking reaction. We also show that
AB  - substrate mutations within the I-BmoI cleavage site can modulate the
AB  - first strand nicking reaction over a 314-fold range. Additionally,
AB  - in-gel DNA footprinting with mutant substrates and modeling of an
AB  - I-BmoI-substrate complex suggest that amino acid contacts to a critical
AB  - GC-2 base pair are required to induce a bottom-strand distortion that
AB  - likely directs conformational changes for reaction progress.
AB  - Collectively, our data implies mechanistic roles for divalent metal ion
AB  - and substrate bases, suggesting that divalent metal ion facilitates the
AB  - re-positioning of the GIY-YIG nuclease domain between sequential
AB  - nicking reactions.
ER  -

TY  - JOUR
AU  - Kleinstiver, B.P.
AU  - Fernandes, A.D.
AU  - Gloor, G.B.
AU  - Edgell, D.R.
TI  - A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 2411
EP  - 2427
VL  - 38
AB  - Insight into protein structure and function is best obtained through a synthesis of
AB  - experimental, structural and bioinformatic data. Here, we
AB  - outline a framework that we call MUSE (mutual information, unigenic
AB  - evolution and structure-guided elucidation), which facilitated the
AB  - identification of previously unknown residues that are relevant for
AB  - function of the GIY-YIG homing endonuclease I-BmoI. Our approach
AB  - synthesizes three types of data: mutual information analyses that identify
AB  - co-evolving residues within the GIY-YIG catalytic domain; a unigenic
AB  - evolution strategy that identifies hyper- and hypo-mutable residues of
AB  - I-BmoI; and interpretation of the unigenic and co-evolution data using a
AB  - homology model. In particular, we identify novel positions within the
AB  - GIY-YIG domain as functionally important. Proof-of-principle experiments
AB  - implicate the non-conserved I71 as functionally relevant, with an I71N
AB  - mutant accumulating a nicked cleavage intermediate. Moreover, many
AB  - additional positions within the catalytic, linker and C-terminal domains
AB  - of I-BmoI were implicated as important for function. Our results represent
AB  - a platform on which to pursue future studies of I-BmoI and other
AB  - GIY-YIG-containing proteins, and demonstrate that MUSE can successfully
AB  - identify novel functionally critical residues that would be ignored in a
AB  - traditional structure-function analysis within an extensively studied
AB  - small domain of approximately 90 amino acids.
ER  -

TY  - JOUR
AU  - Kleinstiver, B.P.
AU  - Wolfs, J.M.
AU  - Edgell, D.R.
TI  - The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 5413
EP  - 5427
VL  - 41
AB  - The GIY-YIG nuclease domain is found within protein scaffolds that participate in diverse
AB  - cellular pathways and contains a single active site that hydrolyzes DNA
AB  - by a one-metal ion mechanism. GIY-YIG homing endonucleases (GIY-HEs) are
AB  - two-domain proteins with N-terminal GIY-YIG nuclease domains connected to
AB  - C-terminal DNA-binding and they are thought to function as monomers. Using I-BmoI
AB  - as a model GIY-HE, we test mechanisms by which the single active site is used to
AB  - generate a double-strand break. We show that I-BmoI is partially disordered in
AB  - the absence of substrate, and that the GIY-YIG domain alone has weak affinity for
AB  - DNA. Significantly, we show that I-BmoI functions as a monomer at all steps of
AB  - the reaction pathway and does not transiently dimerize or use sequential
AB  - transesterification reactions to cleave substrate. Our results are consistent
AB  - with the I-BmoI DNA-binding domain acting as a molecular anchor to tether the
AB  - GIY-YIG domain to substrate, permitting rotation of the GIY-YIG domain to
AB  - sequentially nick each DNA strand. These data highlight the mechanistic
AB  - differences between monomeric GIY-HEs and dimeric or tetrameric GIY-YIG
AB  - restriction enzymes, and they have implications for the use of the GIY-YIG domain
AB  - in genome-editing applications.
ER  -

TY  - JOUR
AU  - Kleinstiver, B.P.
AU  - Wolfs, J.M.
AU  - Kolaczyk, T.
AU  - Roberts, A.K.
AU  - Hu, S.X.
AU  - Edgell, D.R.
TI  - Monomeric site-specific nucleases for genome editing.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 8061
EP  - 8066
VL  - 109
AB  - Targeted manipulation of complex genomes often requires the introduction of a double-strand
AB  - break at defined locations by
AB  - site-specific DNA endonucleases. Here, we describe a monomeric nuclease
AB  - domain derived from GIY-YIG homing endonucleases for genome-editing
AB  - applications. Fusion of the GIY-YIG nuclease domain to three-member
AB  - zinc-finger DNA binding domains generated chimeric GIY-zinc finger
AB  - endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions
AB  - (Tev-ZFEs) function in vitro as monomers to introduce a double-strand
AB  - break, and discriminate in vitro and in bacterial and yeast assays
AB  - against substrates lacking a preferred 5'-CNNNG-3' cleavage motif. The
AB  - Tev-ZFEs function to induce recombination in a yeast-based assay with
AB  - activity on par with a homodimeric Zif268 zinc-finger nuclease. We also
AB  - fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG
AB  - homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active
AB  - in vivo and similarly discriminate against substrates lacking the
AB  - 5'-CNNNG-3' motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct
AB  - from the FokI-derived zinc-finger nuclease and TAL effector nuclease
AB  - platforms as the GIY-YIG domain alleviates the requirement to design
AB  - two nuclease fusions to target a given sequence, highlighting the
AB  - diversity of nuclease domains with distinctive biochemical properties
AB  - suitable for genome-editing applications.
ER  -

TY  - JOUR
AU  - Kleiveland, C.R.
AU  - Hult, L.T.
AU  - Kuczkowska, K.
AU  - Jacobsen, M.
AU  - Lea, T.
AU  - Pope, P.B.
TI  - Draft Genome Sequence of the Methane-Oxidizing Bacterium Methylococcus capsulatus (Texas).
JO  - J. Bacteriol.
PY  - 2012
SP  - 6626
EP  - 6626
VL  - 194
AB  - Methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic
AB  - activities that enable the oxidation of one-carbon compounds,
AB  - most notably methane. Here we describe the annotated draft genome sequence of the
AB  - aerobic methanotroph Methylococcus capsulatus (Texas), a type strain originally
AB  - isolated from sewer sludge.
ER  -

TY  - JOUR
AU  - Klenk, H.-P. et al.
TI  - The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.
JO  - Nature
PY  - 1997
SP  - 364
EP  - 370
VL  - 390
AB  - Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence
AB  - determined.  Its genome of 2,178,400 base pairs contains 2,436 open reading frames.  The
AB  - information processing systems and the biosynthetic pathways for essential components
AB  - (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in
AB  - the archaeon Methanococcus jannaschii.  The genomes of these two Archaea indicate dramatic
AB  - differences in the way these organisms sense their environment, perform regulatory and
AB  - transport functions, and gain energy.  In contrast to M. jannaschii, A. fulgidus has fewer
AB  - restriction-modification systems, and none of its genes appears to contain inteins.  A quarter
AB  - (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved
AB  - proteins, two-thirds of which are shared with M. jannaschii (428 ORFs).  Another quarter of
AB  - the genome encodes new proteins indicating substantial archaeal gene diversity.
ER  -

TY  - JOUR
AU  - Klenk, H.P. et al.
TI  - Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as  Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da  Costa and Ra.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 121
EP  - 134
VL  - 5
AB  - Bacillus tusciae Bonjour and Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore
AB  - former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene
AB  - sequencing was well established at the time of the initial description of the organism, 16S
AB  - sequence data were not available and the strain was placed into the genus Bacillus based on
AB  - limited chemotaxonomic information. Despite the now obvious misplacement of strain T2 as a
AB  - member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification
AB  - remained uncorrected for many years, which was likely due to the extremely difficult,
AB  - analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide
AB  - a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its
AB  - reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species
AB  - of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family
AB  - Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its
AB  - 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and
AB  - Archaea project.
ER  -

TY  - JOUR
AU  - Klenk, H.P.
AU  - Held, B.
AU  - Lucas, S.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Hammon, N.
AU  - Pitluck, S.
AU  - Goodwin, L.A.
AU  - Han, C.
AU  - Tapia, R.
AU  - Brambilla, E.M.
AU  - Potter, G.
AU  - Land, M.
AU  - Ivanova, N.
AU  - Rohde, M.
AU  - Goker, M.
AU  - Detter, J.C.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
TI  - Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 220
EP  - 229
VL  - 6
AB  - Saccharomonospora azurea Runmao et al. 1987 is a member of the genus Saccharomonospora, which
AB  - is in the family Pseudonocardiaceae and thus far poorly
AB  - characterized genomically. Members of the genus Saccharomonospora are of interest
AB  - because they originate from diverse habitats, such as leaf litter, manure,
AB  - compost, the surface of peat, and moist and over-heated grain, and may play a
AB  - role in the primary degradation of plant material by attacking hemicellulose.
AB  - Next to S. viridis, S. azurea is only the second member in the genus
AB  - Saccharomonospora for which a completely sequenced type strain genome will be
AB  - published. Here we describe the features of this organism, together with the
AB  - complete genome sequence with project status 'Improved high quality draft', and
AB  - the annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding
AB  - and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing
AB  - Program (CSP) 2010 at the Joint Genome Institute (JGI).
ER  -

TY  - JOUR
AU  - Klenk, H.P.
AU  - Lu, M.
AU  - Lucas, S.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Pitluck, S.
AU  - Goodwin, L.A.
AU  - Han, C.
AU  - Tapia, R.
AU  - Brambilla, E.M.
AU  - Potter, G.
AU  - Land, M.
AU  - Ivanova, N.
AU  - Rohde, M.
AU  - Goker, M.
AU  - Detter, J.C.
AU  - Li, W.J.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
TI  - Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 265
EP  - 275
VL  - 6
AB  - Saccharomonospora marina Liu et al. 2010 is a member of the genus Saccharomonospora, in the
AB  - family Pseudonocardiaceae that is poorly characterized
AB  - at the genome level thus far. Members of the genus Saccharomonospora are of
AB  - interest because they originate from diverse habitats, such as leaf litter,
AB  - manure, compost, surface of peat, moist, over-heated grain, and ocean sediment,
AB  - where they might play a role in the primary degradation of plant material by
AB  - attacking hemicellulose. Organisms belonging to the genus are usually
AB  - Gram-positive staining, non-acid fast, and classify among the actinomycetes. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence (permanent draft status), and annotation. The 5,965,593 bp long
AB  - chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part
AB  - of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome
AB  - Institute (JGI).
ER  -

TY  - JOUR
AU  - Klima, C.L.
AU  - Cook, S.R.
AU  - Hahn, K.R.
AU  - Amoako, K.K.
AU  - Alexander, T.W.
AU  - Hendrick, S.
AU  - McAllister, T.A.
TI  - Draft Genome Sequence of a Mannheimia haemolytica Serotype 6 Isolate Collected from the Nasopharynx of a Beef Calf with Bovine Respiratory Disease.
JO  - Genome Announcements
PY  - 2013
SP  - e0005113
EP  - e0005113
VL  - 1
AB  - The draft genome of a Mannheimia haemolytica serotype 6 isolate obtained from the nasopharynx
AB  - of a feedlot calf with bovine respiratory disease is described.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Investigation of specificity of DNA-methylases BcnI, CfrI and Cfr10I.
JO  - Mol. Biol. (Mosk)
PY  - 1987
SP  - 87
EP  - 92
VL  - 21
AB  - The site specificity of three DNA methylases BcnI, CfrI and Cfr10I was
AB  - determined to be 5'Cm4C(C/G)GG, 5'PyGGm5CCPu and 5'Pum5CCGGPy, respectively.
AB  - Using the modification methylases under investigation with known restriction
AB  - endonucleases, fourteen new DNA cleavage specificities can be created.  Some
AB  - aspects of the use of restriction endonucleases in DNA methylation analysis are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Kumar, S.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - Hhal methyltransferase flips its target base out of the DNA helix.
JO  - Cell
PY  - 1994
SP  - 357
EP  - 369
VL  - 76
AB  - The crystal structure has been determined at 2.8 A resolution for a chemically-trapped
AB  - covalent reaction intermediate between the Hhal DNA cytosine-5-methyltransferase,
AB  - S-adenosyl-L-homocysteine, and a duplex 13-mer DNA oligonucleotide containing methylated
AB  - 5-fluorocytosine at its target. The DNA is located in a cleft between the two domains of the
AB  - protein and has the characteristic conformation of B-form DNA, except for a disrupted G-C base
AB  - pair that contains the target cytosine. The cytosine residue has swung completely out of the
AB  - DNA helix and is positioned in the active site, which itself has undergone a large
AB  - conformational change. The DNA is contacted from both the major and the minor grooves, but
AB  - almost all base-specific interactions between the enzyme and the recognition bases occur in
AB  - the major groove, through two glycine-rich loops from the small domain. The structure suggests
AB  - how the active nucleophile reaches its target, directly supports the proposed mechanism for
AB  - cytosine-5 DNA methylation, and illustrates a novel mode of sequence-specific DNA regonition.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Nelson, J.L.
AU  - Roberts, R.J.
TI  - The sequence specificity domain of cytosine-C5 methylases.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6183
EP  - 6190
VL  - 19
AB  - Prokaryotic DNA[cytosine-C5] methyltransferases (m5C-methylases) share a common
AB  - architectural arrangement of ten conserved sequence motifs.  A series of eleven
AB  - hybrids have been constructed between the HpaII (recognition sequence: Cm5CGG)
AB  - and HhaI (recognition sequence: Gm5CGC) DNA-methylases.  The hybrids were
AB  - over-expressed in E. coli and their in vivo methylation phenotypes
AB  - investigated.  Six were inactive by our assay while five of them retained
AB  - partial methylation activity and full specificity.  In all five cases the
AB  - specificity matched that of the parent methylase which contributed the
AB  - so-called variable region, located between conserved motifs VIII and IX.  This
AB  - was the only sequence held in common between the active hybrids and for the
AB  - first time provides unequivocal evidence that the specificity determinants of
AB  - the mono-specific m5C-methylases are located within the variable region.
AB  - Correlation of the hybrid methylase structure with the efficiency of
AB  - methylation suggests that conserved motif IX may interact with the variable
AB  - region whereas motif X most probably interacts with the N-terminal half of the
AB  - molecule.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Roberts, R.J.
TI  - M.HhaI binds tightly to substrates containing mismatches at the target base.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 1388
EP  - 1395
VL  - 23
AB  - The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped
AB  - completely out of the DAN helix upon binding. We have investigated the effects of replacing
AB  - the target cytosine by other, mismatched bases, including adenine, guanine, thymine and
AB  - uracil. We find that M.HhaI binds more tightly to such mismatched substrates and can even
AB  - transfer a methyl group to uracil if a G:U mismatch is present. Other mismatched substrates in
AB  - which the orphan guanine is changed exhibit similar behavior. Overall, the affinity of DNA
AB  - binding correlates inversely with the stability of the target base pair, while the nature of
AB  - the target base appears irrelevant for complex formation. The presence of a cofactor analog,
AB  - S-adenosyl-L-homocysteine, greatly enhances the selectivity of the methyltransferase for
AB  - cytosine at the target site. We propose that the DNA methyltransferases have evolved from
AB  - mismatch binding proteins and that base flipping was, and still is, a key element in many
AB  - DNA-enzyme interactions.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Roberts, R.J.
TI  - Disruption of the target G-C base-pair by the HhaI methyltransferase.
JO  - Gene
PY  - 1995
SP  - 163
EP  - 164
VL  - 157
AB  - HhaI MTase binds DNA duplexes containing mismatches at the target base position with higher
AB  - affinity than that observed for the canonical substrate.  The stability of these MTase-DNA
AB  - complexes inversely correlates with the strength of the base pair that is disrupted upon
AB  - interaction.  This finding may offer a general tool to detect other enzymes that flip bases
AB  - out of the DNA helix.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Steponaviciene, D.
AU  - Maneliene, Z.
AU  - Petrusyte, M.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - M.SmaI is an N4-methylcytosine specific DNA-methylase.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6607
EP  - 6609
VL  - 18
AB  - An enzymatic activity rendering DNA immune to the action of the SmaI restriction endonuclease
AB  - in the presence of S-adenosyl-L-methionine has been detected in Serratia marcescens Sb. This
AB  - methylase, M.SmaI, modifies the second cytosine residue of the substrate sequence CCCGGG
AB  - yielding N4-methylcytosine.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Szyperski, T.
AU  - Serva, S.
AU  - Wuthrich, K.
TI  - Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
JO  - EMBO J.
PY  - 1998
SP  - 317
EP  - 324
VL  - 17
AB  - Flipping of a nucleotide out of a B-DNA helix into the active site of an enzyme has been
AB  - observed for the HhaI and HaeIII cytosine-5 methyltransferases (M.HhaI and M.HaeIII) and for
AB  - numerous DNA repair enzymes.  Here we studied the base flipping motions in the binary
AB  - M.HhaI-DNA and the ternary M.HhaI-DNA-cofactor systems in solution.  Two 5-fluorocytosines
AB  - were introduced into the DNA in the places of the target cytosine and, as an internal control,
AB  - a cytosine positioned two nucleotides upstream of the recognition sequence 5'-GCGC-3'.  The
AB  - 19F NMR spectra combined with gel mobility data show that interaction with the enzyme induces
AB  - partition of the target base among three states, i.e. stacked in the B-DNA, an ensemble of
AB  - flipped-out forms and the flipped-out form locked in the enzyme active site.  Addition of the
AB  - cofactor analogue S-adenosyl-L-homocysteine greatly enhances the trapping of the target
AB  - cytosine in the catalytic site.  Distinct dynamic modes of the target cytosine have thus been
AB  - identified along the reaction pathway, which includes novel base-flipping intermediates that
AB  - were not observed in previous X-ray structures.  The new data indicate that flipping of the
AB  - target base out of the DNA helix is not dependent on binding of the cytosine in the catalytic
AB  - pocket of M.HhaI, and suggest an active role in the enzyme in the opening of the DNA duplex.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Timinskas, A.
AU  - Menkevicius, S.
AU  - Butkiene, D.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Sequence motifs characteristic of DNA[cytosine-N4]methylases:  similarity to adenine and cytosine-C5 DNA-methylases.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9823
EP  - 9832
VL  - 17
AB  - The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from
AB  - Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been
AB  - determined.  The predicted methylases are proteins of 454 and 300 amino acids,
AB  - respectively.  Primary structure comparison of M.Cfr9I and another m4C-forming
AB  - methylase, M.PvuII, revealed extended regions of homology.  The sequence
AB  - comparison of the three DNA[cytosine-N4]-methylases using originally developed
AB  - software revealed two conserved patterns, DPF-GSGT and TSPPY, which were found
AB  - similar also to those of adenine and DNA[cytosine-C5]-methylases.  These data
AB  - provided a basis for global alignment and classification of DNA-methylase
AB  - sequences.  Structural considerations led us to suggest that the first region
AB  - could be the binding site of AdoMet, while the second is thought to be directly
AB  - involved in the modification of the exocyclic amino group.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Timinskas, A.
AU  - Menkevicius, S.
AU  - Butkiene, D.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Sequence motifs characteristic of DNA-cytosine-N4-methyltransferases:  The two domains of global similarity within DNA-methylases.
JO  - Eksp. Biol.
PY  - 1990
SP  - 4
EP  - 12
VL  - 0
AB  - Sequences coding for DNA [cytosine-N4] methyltransferases MvaI (from Micrococcus varians
AB  - RFL19) and Cfr91 (from Citrobacter freundii RFL9) have been determined.  The methylases
AB  - predicted are proteins of 454 and 300 amino acids, respectively.  Primary structure comparison
AB  - to other m4C-forming methylases, M. PvuII and M. SmaI, revealed two conserved patterns
AB  - DPF-GSGTTGV and TSPPY---R; these patterns were found to have analogues within all adenine and
AB  - DNA[cytosine-C5]-methylase sequences known ever since.  The presence of the two homology
AB  - domains in all known DNA-methylases provided a basis for their global alignment and
AB  - classification.  DNA-methylases can be divided into four groups (S,D,N,G) on the basis of
AB  - substrate-structural peculiarities or into two families (S,D and N,G) based on the relative
AB  - positioning of these domains within sequences.  A subset of SD family sequences differing from
AB  - the others in reversed MTase domain configuration 21 (instead of the usual 12) forms a
AB  - structurally very compact subfamily of proteins.
ER  -

TY  - JOUR
AU  - Klimasauskas, S.
AU  - Weinhold, E.
TI  - A new tool for biotechnology: AdoMet-dependent methyltransferases.
JO  - Trends Biotechnol.
PY  - 2007
SP  - 99
EP  - 104
VL  - 25
AB  - AdoMet-dependent methyltransferases catalyze highly specific methyl group transfers from the
AB  - ubiquitous cofactor S-adenosyl-L-methionine to a multitude of biological targets in the cell.
AB  - Recently, DNA methyltransferases have been used for the sequence-specific, covalent attachment
AB  - of larger chemical groups to plasmid and bacteriophage DNA using two classes of synthetic
AB  - Ado-Met analogs.  These synthetic cofactors, in combination with the myriad AdoMet-dependent
AB  - methyltransferases available in nature, provide new molecular tools for precise, targeted
AB  - functionalization and labeling of large natural DNAs and, in all likelihood, RNAs and
AB  - proteins.  This paves the way for numerous novel applications in the functional analysis of
AB  - biological methylation, biotechnology and medical diagnostics.
ER  -

TY  - JOUR
AU  - Klimkait, T.
TI  - 'Restriction-PCR' - a superior replacement for restriction endonucleases in DNA cloning applications.
JO  - J. Biochem. Mol. Biol.
PY  - 2000
SP  - 162
EP  - 165
VL  - 33
AB  - Polymerase chain reaction (PCR) is well established as an indispensable tool of molecular
AB  - biology; and yet a limitation for cloning
AB  - applications continues to be that products often require subsequent
AB  - restriction digests, blunt-end ligation, or the use of special linear
AB  - vectors, Here a rapid, PCR-based system is described for the simple,
AB  - restriction enzyme-free generation of synthetic, 'restriction-like' DNA
AB  - fragments with staggered ends. Any 3'- or 5'-protruding terminus, but
AB  - also non-palindromic overhangs with an unrestricted single strand
AB  - length are specifically created. With longer overhangs,
AB  - 'Restriction-PCR' does not even require a ligation step prior to
AB  - transformation. Thereby the technique presents a powerful tool e.g. for
AB  - a successive, authentic reconstitution of sub-fragments of long genes
AB  - with no need to manipulate the sequence or to introduce restriction
AB  - sites. Since restriction enzyme-free and thereby devoid of the limitations
AB  - of partial DNA digests, 'Restriction-PCR' allows a straight one-step
AB  - generation and cloning of difficult DNA fragments that internally carry
AB  - additional sites for those endonucleases involved in the cloning. Small
AB  - site-specific sequence insertions or deletions can be precisely
AB  - engineered into genes of interest. With these properties
AB  - 'Restriction-PCR' has the potential to add significant speed and
AB  - versatility to a wide variety of DNA cloning applications.
ER  -

TY  - JOUR
AU  - Klimuk, E.
AU  - Bogdanova, E.
AU  - Nagornykh, M.
AU  - Rodic, A.
AU  - Djordjevic, M.
AU  - Medvedeva, S.
AU  - Pavlova, O.
AU  - Severinov, K.
TI  - Controller protein of restriction-modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 10810
EP  - 10826
VL  - 46
AB  - C-proteins control restriction-modification (R-M) systems' genes transcription to ensure
AB  - sufficient levels of restriction endonuclease to allow protection from
AB  - foreign DNA while avoiding its modification by excess methyltransferase. Here, we
AB  - characterize transcription regulation in C-protein dependent R-M system Kpn2I.
AB  - The Kpn2I restriction endonuclease gene is transcribed from a constitutive, weak
AB  - promoter, which, atypically, is C-protein independent. Kpn2I C-protein (C.Kpn2I)
AB  - binds upstream of the strong methyltransferase gene promoter and inhibits it,
AB  - likely by preventing the interaction of the RNA polymerase sigma subunit with the
AB  - -35 consensus element. Diminished transcription from the methyltransferase
AB  - promoter increases transcription from overlapping divergent C-protein gene
AB  - promoters. All known C-proteins affect transcription initiation from R-M genes
AB  - promoters. Uniquely, the C.Kpn2I binding site is located within the coding region
AB  - of its gene. C.Kpn2I acts as a roadblock stalling elongating RNA polymerase and
AB  - decreasing production of full-length C.Kpn2I mRNA. Mathematical modeling shows
AB  - that this unusual mode of regulation leads to the same dynamics of accumulation
AB  - of R-M gene transcripts as observed in systems where C-proteins act at
AB  - transcription initiation stage only. Bioinformatics analyses suggest that
AB  - transcription regulation through binding of C.Kpn2I-like proteins within the
AB  - coding regions of their genes may be widespread.
ER  -

TY  - JOUR
AU  - Klingeman, D.M.
AU  - Utturkar, S.
AU  - Lu, T.Y.
AU  - Schadt, C.W.
AU  - Pelletier, D.A.
AU  - Brown, S.D.
TI  - Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere.
JO  - Genome Announcements
PY  - 2015
SP  - e01344
EP  - e01315
VL  - 3
AB  - Draft genome sequences for four Actinobacteria from the genus Streptomyces are presented.
AB  - Streptomyces is a metabolically diverse genus that is abundant in
AB  - soils and has been reported in association with plants. The strains described in
AB  - this study were isolated from the Populus trichocarpa endosphere and rhizosphere.
ER  -

TY  - JOUR
AU  - Klinzing, D.C.
AU  - Matias, R.R.
AU  - Skowronski, E.
AU  - Alvarez, M.
AU  - Liles, V.
AU  - Dimamay, M.P.
AU  - Natividad, F.F.
TI  - Shotgun Genome Sequence of a Yersinia enterocolitica Isolate from the Philippines.
JO  - J. Bacteriol.
PY  - 2012
SP  - 542
EP  - 543
VL  - 194
AB  - The first shotgun genome sequence of a microbial pathogen from the Philippines is reported.
AB  - Yersinia enterocolitica subsp. palearctica strain
AB  - PhRBD_Ye1 is the first Y. enterocolitica strain sequenced from an animal
AB  - source, swine, which is a natural source of yersiniosis. The closest
AB  - phylogenetic match is a human clinical isolate from Germany.
ER  -

TY  - JOUR
AU  - Klippel, B. et al.
TI  - Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4547
EP  - 4548
VL  - 193
AB  - Glaciecola sp. 4H-3-7+YE-5 was isolated from subseafloor sediments at Suruga Bay in Japan and
AB  - is capable of efficiently hydrolyzing cellulose
AB  - and xylan. The complete genome sequence of Glaciecola sp. 4H-3-7+YE-5
AB  - revealed several genes encoding putatively novel glycoside hydrolases
AB  - offering a high potential for plant biomass degradation.
ER  -

TY  - JOUR
AU  - Klippel, B. et al.
TI  - Complete Genome Sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family  Flavobacteriaceae.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4545
EP  - 4546
VL  - 193
AB  - Two members of the family Flavobacteriaceae were isolated from subseafloor sediments using
AB  - artificial seawater with cellulose, xylan and chitin as
AB  - sole carbon and energy sources. Here, we present the complete genome
AB  - sequences of Krokinobacter sp. 4H-3-7-5 and Lacinutrix sp. 5H-3-7-4 which
AB  - both encode for putatively novel enzymes involved in cellulose,
AB  - hemicellulose and chitin metabolism.
ER  -

TY  - JOUR
AU  - Klockgether, J.
AU  - Reva, O.
AU  - Larbig, K.
AU  - Tummler, B.
TI  - Sequence Analysis of the Mobile Genome Island pKLC102 of Pseudomonas aeruginosa C.
JO  - J. Bacteriol.
PY  - 2004
SP  - 518
EP  - 534
VL  - 186
AB  - The Pseudomonas aeruginosa plasmid pKLC102 coexists as a plasmid and a
AB  - genome island in clone C strains. Whereas the related plasmid pKLK106
AB  - reversibly recombines with P. aeruginosa clone K chromosomes at one of the
AB  - two tRNA(Lys) genes, pKLC102 is incorporated into the tRNA(Lys) gene only
AB  - close to the pilA locus. Targeting of the other tRNA(Lys) copy in the
AB  - chromosome is blocked by a 23,395-bp mosaic of truncated PAO open reading
AB  - frames, transposons, and pKLC102 homologs. Annotation and phylogenetic
AB  - analysis of the large 103,532-bp pKLC102 sequence revealed that pKLC102 is
AB  - a hybrid of plasmid and phage origin. The plasmid lineage conferred oriV
AB  - and genes for replication, partitioning, and conjugation, including a pil
AB  - cluster encoding type IV thin sex pili and an 8,524-bp chvB glucan
AB  - synthetase gene that is known to be a major determinant for host tropism
AB  - and virulence. The phage lineage conferred integrase, att, and a syntenic
AB  - set of conserved hypothetical genes also observed in the
AB  - tRNA(Gly)-associated genome islands of P. aeruginosa clone C chromosomes.
AB  - In subgroup C isolates from patients with cystic fibrosis, pKLC102 was
AB  - irreversibly fixed into the chromosome by the insertion of the large
AB  - 23,061-bp class I transposon TNCP23, which is a composite of plasmid,
AB  - integron, and IS6100 elements. Intramolecular transposition of a copy of
AB  - IS6100 led to chromosomal inversions and disruption of plasmid synteny.
AB  - The case of pKLC102 in P. aeruginosa clone C documents the intraclonal
AB  - evolution of a genome island from a mobile ancestor via a reversibly
AB  - integrated state to irreversible incorporation and dissipation in the
AB  - chromosome.
ER  -

TY  - JOUR
AU  - Klonowska, A.
AU  - Lopez-Lopez, A.
AU  - Moulin, L.
AU  - Ardley, J.
AU  - Gollagher, M.
AU  - Marinova, D.
AU  - Tian, R.
AU  - Huntemann, M.
AU  - Reddy, T.B.
AU  - Varghese, N.
AU  - Woyke, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Seshadri, R.
AU  - Baeshen, M.N.
AU  - Baeshen, N.A.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a  Mimosa pudica microsymbiont from New Caledonia.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 7
EP  - 7
VL  - 12
AB  - Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that can exist as a soil saprophyte or as an
AB  - effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155
AB  - was isolated in 2009 from a nodule of the trap host M. pudica grown in
AB  - nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum
AB  - STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic
AB  - Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome
AB  - sequencing project. Here we describe the symbiotic properties of R.
AB  - mesoamericanum STM6155, together with its genome sequence information and
AB  - annotation. The 6,927,906 bp high-quality draft genome is arranged into 147
AB  - scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only
AB  - encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced
AB  - R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved
AB  - in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the
AB  - STM6155 genome, we have identified a chr chromate efflux gene cluster of six
AB  - genes arranged into two putative operons and we postulate that this cluster is
AB  - important for the survival of STM6155 in ultramafic soils containing high
AB  - concentrations of chromate.
ER  -

TY  - JOUR
AU  - Klump, H.
TI  - Codification and evolution of experimentally observed specific recognition sites for restriction enzymes on DNA.
JO  - Biosystems
PY  - 1987
SP  - 33
EP  - 49
VL  - 21
AB  - The list of published restriction endonucleases along with their substrates
AB  - provides an excellent data base for the evaluation of the evolution and
AB  - codification of the key elements for specific recognition sites on the DNA.  In
AB  - this paper the considerations will be limited to palindromic tetramer-,
AB  - pentamer-, and hexamer-sequences.  It is basically assumed that each base pair
AB  - within these sequences has to be recognized by directionally unique bidentate
AB  - hydrogen bonds either within the plane of the base pair or by bridging the
AB  - appropriate H-bond donor/acceptor groups of the neighbouring bases of the same
AB  - strand.  Thus sequence specificity is mediated by twelve (eight) H-bonds,
AB  - originating from the protein recognition modules.  Besides a pronounced
AB  - preference for GC base pairs expressed by their high frequency in the most
AB  - abundant sequences, serving the need of maximal thermodynamic stability of the
AB  - double helical substrates, it can also be shown that the stacking of
AB  - consecutive bases within the recognition site sequences plays a major role in
AB  - shaping the particular DNA/protein interface.  Finally it will be demonstrated
AB  - that the full set of sequences discussed in this paper can readily be derived
AB  - by stepwise expanding the vocabulary of three simple tetrameric sequences by
AB  - inserting single base pairs into the centre of a minimal sequence, thus
AB  - creating all the published pentameric restriction sites, or by inserting/adding
AB  - two GC base pairs in a palindromic way, thus creating the known multiplicity of
AB  - hexameric sites.
ER  -

TY  - JOUR
AU  - Klumpp, J.
AU  - Staubli, T.
AU  - Schmitter, S.
AU  - Hupfeld, M.
AU  - Fouts, D.E.
AU  - Loessner, M.J.
TI  - Genome Sequences of Three Frequently Used Listeria monocytogenes and Listeria ivanovii Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00404
EP  - e00414
VL  - 2
AB  - We present the complete de novo assembled genome sequences of Listeria monocytogenes strains
AB  - WSLC 1001 (ATCC 19112) and WSLC 1042 (ATCC 23074) and
AB  - Listeria ivanovii WSLC 3009, three strains frequently used for the propagation
AB  - and study of bacteriophages because they are presumed to be free of inducible
AB  - prophages.
ER  -

TY  - JOUR
AU  - Klysik, J.
AU  - Stirdivant, S.M.
AU  - Singleton, C.K.
AU  - Zacharias, W.
AU  - Wells, R.D.
TI  - Effects of 5 cytosine methylation on the B-Z transition in DNA restriction fragments and recombinant plasmids.
JO  - J. Mol. Biol.
PY  - 1983
SP  - 51
EP  - 71
VL  - 168
AB  - Alternating (dC-dG)n regions in DNA restriction fragments and recombinant
AB  - plasmids were methylated at the 5 position of the cytosine residues by the HhaI
AB  - methylase.  Methylation lowers the concentration of NaCl or MgCl2 necessary to
AB  - cause the B-Z conformational transition in these sequences.  Ionic strengths
AB  - higher than physiological conditions are required to form the Z conformation
AB  - when the methylated (dC-dG)n tract is contiguous with regions that do not form
AB  - Z structures, in contrast to the results with the DNA polymer
AB  - poly(m5dC-dG).poly(m5dC-dG).  In supercoiled plasmids containing (dC-dG)n
AB  - sequences, methylation reduces the number of negative supercoils necessary to
AB  - stabilize the Z conformation.  Calculations of the observed free energy
AB  - contributions of the B-Z junction and cytosine methylation suggest that two
AB  - junctions offset the favorable effect of methylation on the Z conformation in
AB  - (dC-dG)n sequences (about 29 base-pairs in length).  Studies with individual
AB  - methylated topoisomers demonstrate that increasing Na+ concentration up to
AB  - approximately 0.2M inhibits the formation of the Z conformation in the
AB  - (m5dC-dG)n region of supercoiled plasmids.  The results suggest that
AB  - methylation may serve as a triggering mechanism for Z DNA formation in
AB  - supercoiled DNAs.
ER  -

TY  - JOUR
AU  - Kneale, G.G.
TI  - A symmetrical model for the domain structure of Type I DNA methyltransferases.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 1
EP  - 5
VL  - 243
AB  - Type I DNA methyltransferases are complex multisubunit enzymes that methylate a specific base
AB  - in each half of an asymmetric bipartite DNA recognition sequence. The specificity (S) subunit
AB  - contains two corresponding DNA sequence recognition domains, plus a number of conserved
AB  - regions which interact with two modification (M) subunits to form a trimeric enzyme of the
AB  - form M2S. The way in which the subunits interact with DNA in a pseudo-symmetric fashion has
AB  - long been unclear. Analysis of internal sequence repeats in the S-subunit shows the occurrence
AB  - of significant homologies between the central conserved domain and sequences near the N and C
AB  - termini. On the basis of this "split repeat", a "circular" organization of the domains of this
AB  - subunit is proposed that provides the required symmetry for interacting with the M-subunits
AB  - and with the target DNA sequence. In the proposed model, one M-subunit interacts with the N-
AB  - and C-terminal conserved regions of the S-subunit, which are thereby brought into close
AB  - proximity. The second M-subunit makes equivalent contacts with repeated sequences in the
AB  - central conserved domain. The model suggests a more general scheme for the imposition of
AB  - pseudo-dyad symmetry on protein subunits that have internal repeats by making equivalent
AB  - contacts with additional subunits.
ER  -

TY  - JOUR
AU  - Knight, A.I.
AU  - Lilley, R.J.
AU  - Buckland, R.M.
AU  - Warner, P.J.
TI  - Plasmid mediated restricted and modification in Acinetobacter sp.
JO  - Heredity
PY  - 1988
SP  - 284
EP  - 285
VL  - 61
AB  - Evidence will be presented for a novel plasmid mediated restriction and
AB  - modification system active on broad host range plasmids in an alkane utilising
AB  - Acinetobacter sp.  Genetic studies using the transmissable R-factor pAV1 have
AB  - demonstrated that this system is distinct from the previously described system
AB  - specified by pAV2 in Acinetobacter sp. EBF65/65.  Evidence will also be
AB  - presented indicating that pAV1 is able to escape plasmid mediated restriction
AB  - by the mobilisation of cryptic plasmids.
ER  -

TY  - JOUR
AU  - Knizewski, L.
AU  - Kinch, L.N.
AU  - Grishin, N.V.
AU  - Rychlewski, L.
AU  - Ginalski, K.
TI  - Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
JO  - BMC Struct. Biol.
PY  - 2007
SP  - 40
EP  - 40
VL  - 7
AB  - BACKGROUND: PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes
AB  - that display little sequence similarity despite
AB  - retaining a common core fold and a few critical active site residues. This
AB  - makes identification of new PD-(D/E)XK nuclease families a challenging
AB  - task as they usually escape detection with standard sequence-based
AB  - methods. We developed a modified transitive meta profile search approach
AB  - and to consider the structural diversity of PD-(D/E)XK nuclease fold more
AB  - thoroughly we analyzed also lower than threshold Meta-BASIC hits to select
AB  - potentially correct predictions placed among unreliable or incorrect ones.
AB  - RESULTS: Application of a modified transitive Meta-BASIC searches on
AB  - updated PFAM families and PDB structures resulted in detection of five new
AB  - PD-(D/E)XK nuclease families encompassing hundreds of so far
AB  - uncharacterized and poorly annotated proteins. These include four families
AB  - catalogued in PFAM database as domains of unknown function (DUF506,
AB  - DUF524, DUF1626 and DUF1703) and YhgA-like family of putative
AB  - transposases. Three of these families represent extremely distant homologs
AB  - (DUF506, DUF524, and YhgA-like), while two are newly defined in updated
AB  - database (DUF1626 and DUF1703). In addition, we also confidently
AB  - identified an extended AAA-ATPase domain in the N-terminal region of
AB  - DUF1703 family proteins. CONCLUSION: Obtained results suggest that
AB  - detailed analysis of below threshold Meta-BASIC hits may push limits
AB  - further for distant homology detection in the 'midnight zone' of homology.
AB  - All identified families conserve the core evolutionary fold, secondary
AB  - structure and hydrophobic patterns common to existing PD-(D/E)XK nucleases
AB  - and maintain critical active site motifs that contribute to nucleic acid
AB  - cleavage. Further experimental investigations should address the predicted
AB  - activity and clarify potential substrates providing further insight into
AB  - detailed biological role of these newly detected nucleases.
ER  -

TY  - JOUR
AU  - Knoblich, I.M.
AU  - Sellmann, E.
AU  - Kaluza, K.
AU  - Frey, B.
AU  - Auer, J.
AU  - Schmitz, G.G.
AU  - Westermann, P.
TI  - Ssp5230I, a novel isoschizomer of AatII from Streptomyces recognizing 5'-GACGT/C-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2378
EP  - 2378
VL  - 20
AB  - We have isolated Ssp5230I, a novel class-II restriction endonuclease from Streptomyces species
AB  - recognizing the palindromic sequence 5'-GACGT/C-3' generating 3'-protruding
AB  - ACGT-tetranucleotides. With respect to its isoschizomer AatII it can be isolated in higher
AB  - purity and stability. From the mapping and sequencing data the specificity of Ssp5230I is
AB  - concluded as 5'-GACGT/C-3' 3'-C/TGCAG-5'.
ER  -

TY  - JOUR
AU  - Knowle, D.
AU  - Lintner, R.E.
AU  - Touma, Y.M.
AU  - Blumenthal, R.M.
TI  - Nature of the Promoter Activated by C.PvuII, an Unusual Regulatory Protein Conserved among Restriction-Modification Systems.
JO  - J. Bacteriol.
PY  - 2005
SP  - 488
EP  - 497
VL  - 187
AB  - A widely distributed family of small regulators, called C proteins, controls a subset of
AB  - restriction-modification systems. The C proteins
AB  - studied to date activate transcription of their own genes and that of
AB  - downstream endonuclease genes; this arrangement appears to delay
AB  - endonuclease expression relative to that of the protective
AB  - methyltransferase when the genes enter a new cell. C proteins bind to
AB  - conserved sequences called C boxes. In the PvuII system, the C boxes have
AB  - been reported to extend from -23 to +3 relative to the transcription start
AB  - for the gene for the C protein, an unexpected starting position relative
AB  - to a bound activator. This study suggests that transcript initiation
AB  - within the C boxes represents initial, C-independent transcription of
AB  - pvuIICR. The major C protein-dependent transcript appears to be a
AB  - leaderless mRNA starting farther downstream, at the initiation codon for
AB  - the pvuIIC gene. This conclusion is based on nuclease S1 transcript
AB  - mapping and the effects of a series of nested deletions in the promoter
AB  - region. Furthermore, replacing the region upstream of the pvuIIC
AB  - initiation codon with a library of random oligonucleotides, followed by
AB  - selection for C-dependent transcription, yielded clones having sequences
AB  - that resemble -10 promoter hexamers. The -35 hexamer of this promoter
AB  - would lie within the C boxes. However, the spacing between C boxes/-35 and
AB  - the apparent -10 hexamer can be varied by +/-4 bp with little effect. This
AB  - suggests that, like some other activator-dependent promoters, PpvuIICR may
AB  - not require a -35 hexamer. Features of this transcription activation
AB  - system suggest explanations for its broad host range.
ER  -

TY  - JOUR
AU  - Knox, J.D.
AU  - Araujo, F.D.
AU  - Bigey, P.
AU  - Slack, A.D.
AU  - Price, G.B.
AU  - Zannis-Hadjopoulos, M.
AU  - Szyf, M.
TI  - Inhibition of DNA methyltransferase inhibits DNA replication.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 17986
EP  - 17990
VL  - 275
AB  - Ectopic expression of DNA methyltransferase transforms vertebrate cells, and inhibition of DNA
AB  - methyltransferase reverses the transformed phenotype by an unknown mechanism. We tested the
AB  - hypothesis that the presence of an active DNA methyltransferase is required for DNA
AB  - replication in human non-small cell lung carcinoma A549 cells. We show that the inhibition of
AB  - DNA methyltransferase by two novel mechanisms negatively affects DNA synthesis and progression
AB  - through the cell cycle. Competitive polymerase chain reaction of newly synthesized DNA shows
AB  - decreased origin activity at three previously characterized origins of replication following
AB  - DNA methyltransferase inhibition. We suggest that the requirement of an active DNA
AB  - methyltransferase for the functioning of the replication machinery has evolved to coordinate
AB  - DNA replication and inheritance of the DNA methylation pattern.
ER  -

TY  - JOUR
AU  - Kobayashi, H.
AU  - Fu, Q.
AU  - Maeda, H.
AU  - Sato, K.
TI  - Draft Genome Sequence of a Novel Coriobacteriaceae sp. Strain, EMTCatB1, Reconstructed from the Metagenome of a Thermophilic Electromethanogenic  Biocathode.
JO  - Genome Announcements
PY  - 2017
SP  - e00022
EP  - e00017
VL  - 5
AB  - A draft genome of Coriobacteriaceae sp. strain EMTCatB1 was determined through taxonomic
AB  - binning of a metagenome of a thermophilic biocathode actively
AB  - catalyzing electromethanogenesis. This genome will provide information about the
AB  - biocathode ecosystem, as well as the natural diversity of the Coriobacteriaceae
AB  - family.
ER  -

TY  - JOUR
AU  - Kobayashi, H.
AU  - Kawasaki, K.
AU  - Takeishi, K.
AU  - Noda, H.
TI  - Symbiont of the stink bug Plautia stali synthesizes rough-type lipopolysaccharide.
JO  - Microbiol. Res.
PY  - 2011
SP  - 48
EP  - 54
VL  - 167
AB  - The structures and biosynthesis of lipopolysaccharide (LPS), a major component of
AB  - the outer membrane of Gram-negative bacteria, have been studied extensively in
AB  - cultured bacteria such as Escherichia coli. In contrast, little is known about
AB  - the structures and biosynthesis of the LPS of unculturable bacteria, including
AB  - insect symbionts, many of which are Gram-negative bacteria. A brown-winged green
AB  - bug, Plautia stali, is known to harbor a single species of gamma-proteobacterium
AB  - in the posterior mid-gut caeca. To characterize the features of its LPS, we
AB  - analyzed the genome sequence of the symbiont, and identified the putative genes
AB  - involved in LPS synthesis. Genes involved in the synthesis of lipid A and the
AB  - core oligosaccharide were found in the genome, but waaL, which encodes the
AB  - O-antigen ligase, was not. Furthermore, we characterized the LPS of this symbiont
AB  - using SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and Toll-like receptor 4
AB  - (TLR4) stimulation assays. Consistent with the genomic analysis, the SDS-PAGE
AB  - analysis suggested that the symbiont had rough-type LPS, which lacked the
AB  - O-antigen. The TLR4 stimulation assay demonstrated that LPS purified from the
AB  - symbionts activated NF-kappaB-dependent reporter expression, indicating the
AB  - existence of a bioactive lipid A portion in the LPS. These results suggest that
AB  - the P. stali symbiont produces rough-type LPS.
ER  -

TY  - JOUR
AU  - Kobayashi, H.
AU  - Sun, X.
AU  - Fu, Q.
AU  - Maeda, H.
AU  - Sato, K.
TI  - Draft Genome Sequence of Methanothermobacter sp. Strain EMTCatA1, Reconstructed from the Metagenome of a Thermophilic Electromethanogenesis-Catalyzing  Biocathode.
JO  - Genome Announcements
PY  - 2017
SP  - e00892
EP  - e00817
VL  - 5
AB  - A draft genome of Methanothermobacter sp. strain EMTCatA1 was reconstructed from  a metagenome
AB  - of a thermophilic electromethanogenic biocathode. This genome will
AB  - provide information about methanogens catalyzing methanogenesis at the
AB  - biocathodes.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - DNA modification and restriction: Selfish behavior of an epigenetic system.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 155
EP  - 172
VL  - 0
AB  - Type II restriction endonucleases are known to make double-strand breaks within or near
AB  - specific recognition sequences on duplex DNA.  Cognate modification enzymes can methylate
AB  - these sequences and protect them from cleavage.  The tight association of a cognate
AB  - restriction enzyme gene with a modification gene has been termed the (type II)
AB  - restriction-modification system.  Although the RM systems that have been described are
AB  - individually highly specific for one or a few recognition sequences, collectively the
AB  - sequences recognized are quite diverse.  Type II RM systems are ubiquitous in prokaryotes and
AB  - in archaebacteria but are absent from eukaryotes.  Type II restriction enzymes cleave foreign
AB  - DNA such as viral and plasmid DNA when this DNA has not been modified by the appropriate
AB  - modification enzyme.  In this way, cells are protected from invasion by foreign DNA.  Thus, it
AB  - has been widely believed that the evolution and maintenance of type II restriction
AB  - modification systems have been driven by the cell's need to protect itself from infection by
AB  - foreign DNA (the cellular defense hypothesis).  However, there are several unresolved issues
AB  - that cannot be explained satisfactorily by this cellular defense hypothesis.  Here, I present
AB  - experimental evidence and theoretical arguments for an alternative hypothesis (the selfish
AB  - gene hypothesis) that the evolution of at least some RM gene pairs is driven by their
AB  - "selfishness" in the genetic and evolutionary sense of the term.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Restriction-modification systems as minimal forms of life.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 19
EP  - 62
VL  - 14
AB  - A restriction endonuclease recognizes a specific DNA sequence and introduces a double-strand
AB  - break.  A cognate modification enzyme methylates the same sequence and thereby protects it
AB  - from cleavage.  Together, these two enzymes form a restriction-modification system.  The genes
AB  - encoding the restriction endonuclease and the cognate modification enzyme are often tightly
AB  - linked and can be termed a restriction-modification gene complex.  Restriction enzymes will
AB  - cleave incoming DNA if it has not been modified by a cognate or another appropriate
AB  - methyltransferase.  Consequently, it is widely believed that restriction-modification systems
AB  - have been maintained by bacteria because they serve to defend the cells from infection by
AB  - viral, plasmid, and other foreign DNAs (cellular defense hypothesis).
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Genetic addiction: A principle of gene symbiosis in a genome.
JO  - Plasmid Biology
PY  - 2004
SP  - 105
EP  - 144
AB  - One of the surprising aspects of the genome that became clear during its decoding is the
AB  - fluidity of the genes.  Genomes are full of mobile symbiotic or parasitic genetic elements.
AB  - Moreover, evolutionary analyses have suggested that many genes have joined genomes relatively
AB  - recently from distantly related organisms.  This is particularly true for the bacterial and
AB  - archaeal genomes, which contain genes that even come from eukaryotes.  In addition,
AB  - comparisons of closely related genome sequences have revealed that genomes experience frequent
AB  - rearrangements during their evolution.  These observations suggest that, rather than being a
AB  - well-designed blueprint, the genome is a community of genes that essentially act selfishly and
AB  - potentially do not have the overall order of the genome as their primary interest.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Homologous recombination and sex as a strategy against selfish genes attacking the genome.
JO  - Molecular Strategies in Biological Evolution
PY  - 1999
SP  - 354
EP  - 356
AB  - An important issue in current biology is our failure to adequately explain the forces
AB  - underlying the evolution and maintenance of sex.  Here we refer to sex broadly as the
AB  - interaction that occurs between homologous chromosomes of often different clonal original
AB  - (outcrossing), an event that leads to recombination, frequently between distantly located
AB  - genes (crossing-over).  We propose that sex is maintained to combat the existence of
AB  - ever-changing molecular parasites that attack the organism's genome.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Restriction modification systems as selfish mobile genetic elements maintaining and rearranging the genome.
JO  - Plasmid
PY  - 2002
SP  - 260
EP  - 261
VL  - 48
AB  - A restriction enzyme gene is often linked to a modification methylase gene whose role is to
AB  - protect the recognition site from breakage by the restriction enzyme.  Attempts to eliminate
AB  - some of these restriction-modification gene complexes from bacterial cells lead to cell death
AB  - through restriction breakage in the genome.  Such post-segregational cell killing was observed
AB  - when a restriction -modification gene complex was challenged by a competitor genetic element
AB  - and likely has competitive advantage.  Comparison of closely related bacterial genomes
AB  - revealed linkage of genome polymorphisms, such as insertion and inversion, with
AB  - restriction-modification gene complexes.  Restriction site avoidance in bacterial genomes and
AB  - other observations provide further support for our hypothesis that some
AB  - restriction-modification gene complexes behave as selfish mobile elements that have attacked
AB  - and shaped the genomes.  Indeed our attempts to eliminate a restriction-modification gene
AB  - complex from a cell led to various genome rearrangements in the laboratory - genome-wide
AB  - duplication and inversion events, intra-genomic movement of a restriction-modification gene
AB  - complex, and tandem amplification of a restriction-modification gene complex.  These genome
AB  - rearrangements are likely caused and selected by the restriction attacks.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3742
EP  - 3756
VL  - 29
AB  - Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme
AB  - and a modification methylase. RM systems sometimes behave as discrete units of life, like
AB  - viruses and transposons. RM complexes attack invading DNA that has not been properly modified
AB  - and thus may serve as a tool of defense for bacterial cells. However, any threat to their
AB  - maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an
AB  - allelic homologous stretch of DNA, for example) can lead to cell death through restriction
AB  - breakage in the genome. This post-segregational or post-disturbance cell killing may provide
AB  - the RM complexes (and any DNA linked with them) with a competitive advantage. There is
AB  - evidence that they have undergone extensive horizontal transfer between genomes, as inferred
AB  - from their sequence homology, codon usage bias and GC content difference. They are often
AB  - linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The
AB  - comparison of closely related bacterial genomes also suggests that, at times, RM genes
AB  - themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial
AB  - genomes that survived post-disturbance attack by an RM gene complex in the laboratory have
AB  - experienced genome rearrangements. The avoidance of some restriction sites by bacterial
AB  - genomes may result from selection by past restriction attacks. Both bacteriophages and
AB  - bacteria also appear to use homologous recombination to cope with the selfish behavior of RM
AB  - systems. RM systems compete with each other in several ways. One is competition for
AB  - recognition sequences in post-segregational killing. Another is super-infection exclusion,
AB  - that is, the killing of the cell carrying an RM system when it is infected with another RM
AB  - system of the same regulatory specificity but of a different sequence specificity. The
AB  - capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure
AB  - and function of RM enzymes.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Genome comparison: involvement of restriction modification genes in genome rearrangements.
JO  - Tanpakushitsu Kakusan Koso
PY  - 2001
SP  - 2393
EP  - 2399
VL  - 46
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Selfish genes for restriction-modification systems.
JO  - Saibo Kogaku
PY  - 1995
SP  - 1015
EP  - 1023
VL  - 14
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Selfishness and death: raison d'etre of restriction, recombination and mitochondria.
JO  - Trends Genet.
PY  - 1998
SP  - 368
EP  - 374
VL  - 14
AB  - Type II restriction-modification gene complexes, such as the EcoRI system, are not easily lost
AB  - from their host cell.  The descendants of cells that lose a restriction-modification gene
AB  - complex are unable to modify a sufficient number of recognition sites in their chromosomes to
AB  - protect them from lethal attack by the remaining molecules of the restriction enzyme.  This
AB  - capacity to act as a selfish genetic element is likely to have contributed to the spread and
AB  - maintenance of restriction-modification systems.  Homologous recombination machineries of
AB  - cells and viruses appear to be well adapted to cope with these elements.  By extrapolation,
AB  - the capacity of mitochondria to kill their host eukaryotic cell might have stabilized their
AB  - initial symbiosis.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Reshaping the genome: DNA restriction-modification systems as mobile genetic elements.
JO  - Saibo Kogaku
PY  - 1999
SP  - 1846
EP  - 1857
VL  - 18
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Life cycle of restriction-modification gene complexes, powers in genome evolution.
JO  - Int. Congr. Ser.
PY  - 2002
SP  - 191
EP  - 200
VL  - 1246
AB  - Increasing lines of evidence suggest that gene complexes encoding restriction modification
AB  - enzymes may behave as selfish mobile genetic elements affecting genome stability and genome
AB  - evolution.  I here compare their hypothetical life cycles with those of temperate
AB  - bacteriophage DNAs and other mobile elements.  The restriciton modification gene complexes may
AB  - establish themselves in a new host avoiding cell killing.  Upon some environmental signals,
AB  - they would be induced to multiply.  The multiplied RM gene complex may be released to the
AB  - environment and taken up by other cells in naturally competent bacteria.  In some aspects,
AB  - they could be regarded as DNA viruses without a capsid, or DNA viroids.  They may play the
AB  - role of power giving order to the community of genes called the genome.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Why are there restriction enzymes and genetic recombination?
JO  - Cell Struct. Funct.
PY  - 1994
SP  - 464
EP  - 464
VL  - 19
AB  - If self-replication of genetic information is the essential feature of life process, why has
AB  - the process of homologous recombination, which generates variation, evolved at all? The
AB  - double-strand break repair model of homologous recombination (for which we have evidence)
AB  - proposes that generation of double-strand break on otherwise intact DNA initiates homologous
AB  - recombination. Might this be too destructive as a means of generating recombinant progeny? We
AB  - obtained several experimental results that suggest a feature of homologous interaction, a
AB  - feature that enabled evolution of homologous recombination, is destruction of genetic
AB  - information.
AB  - 
AB  - Why are there restriction enzymes?
AB  - 
AB  - Double-strand break of DNA plays an important role in homologous recombination in vivo. It
AB  - is believed that restriction/modification system serves for destruction of foreign DNA such as
AB  - viral DNA. But this theory cannot explain easily presence of rare cutters and other phenomena.
AB  - We found that restriction enzyme gene and modification methylase gene on a plasmid stabilize
AB  - it. Our results support the following post-segregational killing mechanism: When a cell that
AB  - has lost the plasmid continues dividing, the modification enzymes become dilute and cannot
AB  - modify all of the thousands of recognition sites on the chromosome. The remaining restriction
AB  - enzymes will cleave the chromosome and kill the host cells. As a result, most viable cells in
AB  - a population carry the plasmid. In brief, turning off of a pair of genes, a killer and an
AB  - anti-killer, will program cell lineage for death. A restriction modification system is a
AB  - parasite or a selfish element such as a transposon. Its benfit to the host is protection
AB  - against foreign DNA. Thus it can be called a symbiont.
AB  - 
ER  -

TY  - JOUR
AU  - Kobayashi, I.
TI  - Evolution and Diversity.
JO  - Plasmid
PY  - 2001
SP  - 162
EP  - 163
VL  - 45
AB  - A type II restriction enzyme gene is often linked to a modification methylase gene whose role
AB  - is to protect the recognition site from breakage in the genome.  This postsegregational
AB  - killing or postdisturbance killing can be very severe.  Block to replication of a ts plasmid
AB  - carrying an EcoRII RM gene complex leads to immediate loss of viability by several orders of
AB  - magnitude.  The cell killing was observed when an RM plasmid was challenged by an incompatible
AB  - plasmid.  Similar resistance was observed when chromosomally located RM was threatened by a
AB  - homologous stretch of DNA in E. coli.  Many of the progeny carried the donor gene as well as
AB  - the recipient gene and lost the donor gene in the absence of its selection.  Each of these
AB  - unstable diploids have experienced megabase-size genome rearrangements that include
AB  - duplication of the RM locus in question and inversion.  Precise homologous recombination at
AB  - ectopic IS3 was shown to be involved in these rearrangements.  Comparisons of closely related
AB  - bacterial genomes revealed that restriction-modification gene complexes are often linked with
AB  - gross genome polymorphism.  One comparison suggests insertion of restriction modification gene
AB  - complexes into a genome with a long (ca. 100 bp) target duplication.  Comparison of two
AB  - complete genome sequences of Pyrococcus suggested transposition of restriction modification
AB  - gene complexes with linked genes.  We hypothesize that the rearrangements in the laboratory
AB  - and in the natural environments have resulted from attack of restriction enzymes on the
AB  - chromosome.  Only those genomes that have incorporated RM genes in question and allowed their
AB  - expression would survive.  Their behavior as selfish mobile elements may explain their
AB  - competition - specificity of sequence recognition and mutual exclusion (superinfection
AB  - exclusion) - and clarify certain aspects of bacterial recombination repair.  The killing is
AB  - severe in mutants defective in XerCD-mediated site-specific recombination at dif site in E.
AB  - coli chromosome.  This result provides support to the hypothesis that this site-specific
AB  - recombination system is important in DNA damage repair.  Strong postdisturbance killing by
AB  - EcoRII RM is suppressed by Dcm, an orphan methylase.  This vaccine effect may explain why Dcm
AB  - is present at all.  The selfish self-maintenance of the restriction modification genes also
AB  - provides a unique opportunity for stable maintenance and table expression of useful genes in
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Kobayashi, I.
AU  - Nobusato, A.
AU  - Kobayashi-Takahashi, N.
AU  - Uchiyama, I.
TI  - Shaping the genome--restriction-modification systems as mobile genetic elements.
JO  - Curr. Opin. Genet. Dev.
PY  - 1999
SP  - 649
EP  - 656
VL  - 9
AB  - A restriction enzyme gene is often linked to a modification methylase gene the role of which
AB  - is to protect a recognition site on DNA from breakage by the former. Loss of some
AB  - restriction-modification gene complexes leads to cell death through restriction breakage in
AB  - the genome. Their behavior as genomic parasites/symbionts may explain the distribution of
AB  - restriction sites and clarify certain aspects of bacterial recombination repair and
AB  - mutagenesis. A comparison of bacterial genomes supports the hypothesis that
AB  - restriction-modification gene complexes are mobile elements involved in various genome
AB  - rearrangements and evolution.
ER  -

TY  - JOUR
AU  - Kobayashi, M.
AU  - Nomura, M.
AU  - Fujita, Y.
AU  - Ohmomo, S.
AU  - Okamoto, T.
TI  - Molecular characterization of a lactococcal plasmid reducing the growth rate of host cells.
JO  - Japan Agricultural Research Quarterly
PY  - 2003
SP  - 53
EP  - 57
VL  - 37
AB  - Lactococcus lactis subsp. lactis biovar. diacetylactis DRC1 carries more than 6 plasmids,
AB  - including a 7.4 kb cryptic plasmid, which was
AB  - designated as pDR1-1. The pDR1-1 plasmid was found to significantly
AB  - affect the maximum specific growth rate (mu(max)) of the host cells
AB  - because of its limiting effect on growth. To investigate the properties
AB  - of the limiting effect, the entire nucleotide sequence of pDR1-1 was
AB  - determined. It consisted of 7412 bp, and 6 open reading frames (ORFs)
AB  - were identified. The first ORF showed a high degree of similarity to a
AB  - family of replication genes (rep) that are commonly found in
AB  - lactococcal strains. The rep gene in pDR1-1 was followed by a second
AB  - ORF of unknown function. Directly downstream of the second ORF, a third
AB  - ORF was found, that showed homology to the S subunit from type I
AB  - restriction/modification systems. No significant similarity to the
AB  - contents of the database was found for the other ORFs. PCR analysis was
AB  - carried out in order to detect pDR1-1 in the other L. lactis strains.
AB  - The mu(max) of the pDR1-1-positive strain was the same as that of DRC1.
AB  - These results suggest that the load of pDR1-1 (or pDR1-1-like plasmid)
AB  - is a major factor influencing the mu(max) of DRC1 because of its
AB  - limiting effect on growth, an effect which is much more pronounced than
AB  - that produced by the overall load of other coexisting plasmids.
ER  -

TY  - JOUR
AU  - Kobayashi, M.
AU  - Nomura, M.
AU  - Fujita, Y.
AU  - Okamoto, T.
AU  - Ohmomo, S.
TI  - Influence of lactococcal plasmid on the specific growth rate of host cells.
JO  - Lett. Appl. Microbiol.
PY  - 2002
SP  - 403
EP  - 408
VL  - 35
AB  - Aims: To investigate a lactococcal plasmid responsible for a reduction in growth rate of its
AB  - host cell.  Methods and Results: Lactococcus lactis subsp. lactis biovar. diacetylactis DRC1
AB  - carries a high number of plasmids.  The DRC1 wild-type strain was found to grow more slowly
AB  - than a plasmid-free derivative of DRC1.  The plasmids extracted from DRC1 together with an
AB  - indicator plasmid were cotransformed into the plasmid-free strain DRC1021.  A 7.4-kb cryptic
AB  - plasmid, designated pDR1-1, was found to significantly affect the maximum specific growth rate
AB  - (umax) of the host cell.  Polymerase chain reaction (PCR) analysis was carried out in order to
AB  - detect the presence of pDR1-1 in the other L. lactis strains.  The umax of the single
AB  - pDR1-1-positive strain was determined to be the same as that of DRC1.  Significance and Impact
AB  - of the Study: These results suggest that pDR1-1 (or a pDR1-1-like plasmid) is a critical
AB  - factor in the reduction of the umax of DRC1, and that its effect on the umax is significantly
AB  - greater than that of any other coexisting plasmid.
ER  -

TY  - JOUR
AU  - Kobayashi, M.
AU  - Nomura, M.
AU  - Kimoto, H.
TI  - Manipulation for Plasmid Elimination by Transforming Synthetic Competitors Diversifies Lactococcus lactis Starters Applicable to Food Products.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2007
SP  - 2647
EP  - 2654
VL  - 71
AB  - This study was designed selectively to eliminate a theta-plasmid from
AB  - Lactococcus lactis strains by transforming synthetic competitors. A
AB  - shuttle vector for Escherichia coli and L. lactis, pDB1, was constructed
AB  - by ligating a partial replicon of pDR1-1B, which is a 7.3 kb theta-plasmid
AB  - in L. lactis DRC1, with an erythromycin resistance gene into pBluescript
AB  - II KS(+). This versatile vector was used to construct competitors to
AB  - common lactococcal theta-plasmids. pDB1 contains the 5' half of the
AB  - replication origin and the 3' region of repB of pDR1-1B, but lacks the
AB  - 1.1-kb region normally found between these two segments. A set of primers,
AB  - Pv3 and Pv4, was designed to amplify the 1.1-kb middle parts of the
AB  - general theta-replicons of lactococcal plasmids. When the PCR products
AB  - were cloned into the Nru I and Xho I sites of pDB1, synthetic replicons
AB  - were constructed and replication activity was restored. A number of
AB  - theta-plasmids in L. lactis ssp. lactis and cremoris were eliminated
AB  - selectively by transforming the synthetic competitors. These competitors
AB  - were easily eliminated by subculture for a short time in the absence of
AB  - selection. The resulting variants contained no exogenous DNA and are
AB  - suitable for food products, since part of the phenotype was altered
AB  - without altering other plasmids indispensable for fermentation.
ER  -

TY  - JOUR
AU  - Koberl, M.
AU  - White, R.A.I.I.I.
AU  - Erschen, S.
AU  - El-Arabi, T.F.
AU  - Jansson, J.K.
AU  - Berg, G.
TI  - Draft Genome Sequence of Paenibacillus polymyxa Strain Mc5Re-14, an Antagonistic  Root Endophyte of Matricaria chamomilla.
JO  - Genome Announcements
PY  - 2015
SP  - e00861
EP  - e00815
VL  - 3
AB  - Paenibacillus polymyxa strain Mc5Re-14 was isolated from the inner root tissue of Matricaria
AB  - chamomilla (German chamomile). Mc5Re-14 revealed promising in vitro
AB  - antagonistic activity against plant and opportunistic human pathogens. The 6.0-Mb
AB  - draft genome reveals genes putatively involved in pathogen suppression and direct
AB  - and indirect plant growth promotion.
ER  -

TY  - JOUR
AU  - Koberl, M.
AU  - White, R.A.I.I.I.
AU  - Erschen, S.
AU  - El-Arabi, T.F.
AU  - Jansson, J.K.
AU  - Berg, G.
TI  - Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens.
JO  - Genome Announcements
PY  - 2015
SP  - e00860
EP  - e00815
VL  - 3
AB  - Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum
AB  - antagonism against plant pathogenic fungi, bacteria, and
AB  - nematodes. The 8.2-Mb draft genome reveals genes putatively responsible for its
AB  - promising biocontrol activity and genes which enable the soil bacterium to
AB  - directly interact beneficially with plants.
ER  -

TY  - JOUR
AU  - Koberl, M.
AU  - White, R.A.I.I.I.
AU  - Erschen, S.
AU  - Spanberger, N.
AU  - El-Arabi, T.F.
AU  - Jansson, J.K.
AU  - Berg, G.
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis.
JO  - Genome Announcements
PY  - 2015
SP  - e00862
EP  - e00815
VL  - 3
AB  - The genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting
AB  - rhizobacterium (PGPR) with broad-spectrum antagonistic activity
AB  - against plant-pathogenic fungi, bacteria, and nematodes, consists of a single
AB  - 3.9-Mb circular chromosome. The genome reveals genes putatively responsible for
AB  - its promising biocontrol and PGP properties.
ER  -

TY  - JOUR
AU  - Koblizek, M.
AU  - Janouskovec, J.
AU  - Obornik, M.
AU  - Johnson, J.H.
AU  - Ferriera, S.
AU  - Falkowski, P.G.
TI  - Genome Sequence of the Marine Photoheterotrophic Bacterium Erythrobacter sp. Strain NAP1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5881
EP  - 5882
VL  - 193
AB  - Here we report the full genome sequence of marine phototrophic bacterium Erythrobacter sp.
AB  - strain NAP1. The 3.3-Mb genome contains a full set of
AB  - photosynthetic genes organized in one 38.9-kb cluster; however, it does
AB  - not contain genes for CO(2) or N(2) fixation, thereby confirming that the
AB  - organism is a photoheterotroph.
ER  -

TY  - JOUR
AU  - Koch, H.
AU  - Lucker, S.
AU  - Albertsen, M.
AU  - Kitzinger, K.
AU  - Herbold, C.
AU  - Spieck, E.
AU  - Nielsen, P.H.
AU  - Wagner, M.
AU  - Daims, H.
TI  - Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2015
SP  - 11371
EP  - 11376
VL  - 112
AB  - Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally
AB  - most widespread nitrifiers. However, they remain scarcely studied
AB  - and mostly uncultured. Based on genomic and experimental data from Nitrospira
AB  - moscoviensis representing the ubiquitous Nitrospira lineage II, we identified
AB  - ecophysiological traits that contribute to the ecological success of Nitrospira.
AB  - Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves
AB  - urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and
AB  - enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia
AB  - from urea, which is fully nitrified by this consortium through reciprocal
AB  - feeding. The presence of highly similar urease genes in Nitrospira lenta from
AB  - activated sludge, in metagenomes from soils and freshwater habitats, and of other
AB  - ureases in marine nitrite oxidizers, suggests a wide distribution of this
AB  - extended interaction between ammonia and nitrite oxidizers, which enables
AB  - nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A
AB  - soluble formate dehydrogenase lends additional ecophysiological flexibility and
AB  - allows N. moscoviensis to use formate, with or without concomitant nitrite
AB  - oxidation, using oxygen, nitrate, or both compounds as terminal electron
AB  - acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis
AB  - shares the Nitrospira core metabolism but shows substantial genomic dissimilarity
AB  - including genes for adaptations to elevated oxygen concentrations. Reciprocal
AB  - feeding and metabolic versatility, including the participation in different
AB  - nitrogen cycling processes, likely are key factors for the niche partitioning,
AB  - the ubiquity, and the high diversity of Nitrospira in natural and engineered
AB  - ecosystems.
ER  -

TY  - JOUR
AU  - Kochanek, S.
AU  - Renz, D.
AU  - Doerfler, W.
TI  - Probing DNA-protein interactions in vitro with the CpG DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2339
EP  - 2342
VL  - 21
AB  - A sensitive method was devised to monitor the in vitro binding of nuclear proteins from HeLa
AB  - cells presumably to the major groove of DNA. Upon the incubation of DNA with nuclear extracts,
AB  - the complexed DNA was incubated with the CpG DNA methyltransferase from Spiroplasma species.
AB  - Subsequently, the DNA was repurified, and the location of the methylated cytidine residues was
AB  - determined by the hydrazine reaction of the DNA sequencing method. By using as DNA substrate
AB  - the VAI (virus associated) region of human adenovirus type 2 (Ad2) DNA or specific Alu
AB  - sequences associated with a number of human genes, it was documented that those segments of
AB  - DNA that were protected by bound proteins against the reaction with DNaseI also escaped in
AB  - vitro methylation by the CpG DNA methyltransferase. This new footprinting method provides a
AB  - sensitive indicator for in vitro DNA-protein interactions which are specific for the major
AB  - groove of DNA.
ER  -

TY  - JOUR
AU  - Kodaira, K.I.
AU  - Oki, M.
AU  - Kakikawa, M.
AU  - Watanabe, N.
AU  - Hirakawa, M.
AU  - Yamada, K.
AU  - Taketo, A.
TI  - Genome structure of the Lactobacillus temperate phage Phi g1e: the whole genome sequence and the putative promoter/repressor system.
JO  - Gene
PY  - 1997
SP  - 45
EP  - 53
VL  - 187
AB  - The complete genome sequence of a Lactobacillus temperate phage phi g1e was established. The
AB  - double-stranded DNA is composed of 42,259 bp, and encodes for sixty-two possible open reading
AB  - frames (ORF) as well as several potential regulatory sequences. Based on comparative analysis
AB  - with other related proteins of the Lactobacillus and Lactococcus phages as well as the
AB  - Escherichia coli phages (such as lambda), functions were putatively assigned to several phi
AB  - g1e ORFs: cng and cpg (encoding for repressors), hel (helicase), ntp (NTPase), and several
AB  - ORFs (e.g., minor capsid proteins). An about 1000-bp DNA region of phi g1e containing cpg and
AB  - cng was inferred to function as a promoter/repressor system for the phi g1e lysogenic and
AB  - lytic pathway.
ER  -

TY  - JOUR
AU  - Koechler, S.
AU  - Plewniak, F.
AU  - Barbe, V.
AU  - Battaglia-Brunet, F.
AU  - Jost, B.
AU  - Joulian, C.
AU  - Philipps, M.
AU  - Vicaire, S.
AU  - Vincent, S.
AU  - Ye, T.
AU  - Bertin, P.N.
TI  - Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments.
JO  - Genome Announcements
PY  - 2013
SP  - e00819
EP  - e00813
VL  - 1
AB  - We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance
AB  - to arsenite, isolated from multicontaminated sediments of the
AB  - l'Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp
AB  - chromosome and a 157,085-bp plasmid.
ER  -

TY  - JOUR
AU  - Koeck, D.E.
AU  - Maus, I.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Zverlov, V.V.
AU  - Liebl, W.
AU  - Puhler, A.
AU  - Schwarz, W.H.
AU  - Schluter, A.
TI  - Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor.
JO  - Genome Announcements
PY  - 2016
SP  - e00687
EP  - e00616
VL  - 4
AB  - A novel cellulolytic bacterial strain was isolated from an industrial-scale biogas plant. The
AB  - 16S rRNA gene sequence of the strain SD1D showed 96.4%
AB  - similarity to Herbinix hemicellulosilytica T3/55(T), indicating a novel species
AB  - within the genus Herbinix (family Lachnospiraceae). Here, the complete genome
AB  - sequence of Herbinix luporum SD1D is reported.
ER  -

TY  - JOUR
AU  - Koeck, D.E.
AU  - Maus, I.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Zverlov, V.V.
AU  - Liebl, W.
AU  - Puhler, A.
AU  - Schwarz, W.H.
AU  - Schluter, A.
TI  - Draft Genome Sequence of Propionispora sp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor.
JO  - Genome Announcements
PY  - 2016
SP  - e00609
EP  - e00616
VL  - 4
AB  - The novel mesophilic bacterial strain Propionispora sp. 2/2-37 was isolated from  an
AB  - industrial-scale biogas plant. Comparative 16S rRNA gene sequencing revealed
AB  - that the isolate constitutes a new subcluster within the order Selenomonadales
AB  - The 2/2-37 draft genome sequence was established and provides the genetic basis
AB  - for application of this microorganism in degradation of biomass for bio-fuel
AB  - production.
ER  -

TY  - JOUR
AU  - Koenigsaecker, T.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria).
JO  - Genome Announcements
PY  - 2016
SP  - e01121
EP  - e01116
VL  - 4
AB  - Here, we present the draft genome of Gordonia sp. strain UCD-TK1. The assembly contains
AB  - 5,470,576 bp in 98 contigs. This strain was isolated from a disinfected
AB  - ambulatory surgery center.
ER  -

TY  - JOUR
AU  - Koesters, R.
AU  - von Knebel-Doeberitz, M.
TI  - Improved blunt-end cloning by replacing EcoRV with Eco32I.
JO  - Biotechniques
PY  - 2002
SP  - 1244
EP  - 1246
VL  - 32
AB  - The restriction endonuclease EcoRV, which recognizes and cleaves DNA containing 5'-GATATC-3'
AB  - sequences, is among the best characterized and most frequently used blunt-end cutting
AB  - restriction enzymes.  Its recognition site is present in many cloning vectors currently in
AB  - use.  Compared with that of cohesive ends, blunt-end ligation is generally more difficult
AB  - because a higher number of background colonies is formed that result from self-ligation of
AB  - vector  molecules.  We (and others) have found that when using EcoRV even "white color"
AB  - selection often fails so that one ends up with a large number of apparently positive (white)
AB  - colonies.  Here we demonstrate that this problem can be reduced if one uses Eco32I, an
AB  - isoschizomer of EcoRV, instead.
ER  -

TY  - JOUR
AU  - Koh, H.Y.
AU  - Jung, W.
AU  - Do, H.
AU  - Lee, J.H.
AU  - Kim, H.J.
TI  - Draft Genome Sequence of Pseudomonas pelagia CL-AP6, a Psychrotolerant Bacterium  Isolated from Culture of Antarctic Green Alga Pyramimonas gelidicola.
JO  - Genome Announcements
PY  - 2013
SP  - e00699
EP  - e00613
VL  - 1
AB  - Pseudomonas pelagia CL-AP6, isolated from a culture of the Antarctic green alga Pyramimonas
AB  - gelidicola, is a psychrotolerant bacterium. Here, we report the draft
AB  - genome sequence of this strain, which may provide insights into the mutualistic
AB  - interaction between microalgae and bacteria in sea ice, as well as the cold
AB  - adaptation mechanisms of bacteria.
ER  -

TY  - JOUR
AU  - Koh, H.Y.
AU  - Lee, S.G.
AU  - Lee, J.H.
AU  - Doyle, S.
AU  - Christner, B.C.
AU  - Kim, H.J.
TI  - Draft Genome Sequence of Paenisporosarcina sp. Strain TG-14, a Psychrophilic Bacterium Isolated from Sediment-Laden Stratified Basal Ice from Taylor Glacier,    McMurdo Dry Valleys, Antarctica.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6656
EP  - 6657
VL  - 194
AB  - The psychrophilic bacterium Paenisporosarcina sp. TG-14 was isolated from sediment-laden
AB  - stratified basal ice from Taylor Glacier, McMurdo Dry Valleys,
AB  - Antarctica. Here we report the draft genome sequence of this strain, which may
AB  - provide useful information on the cold adaptation mechanism in extremely variable
AB  - environments.
ER  -

TY  - JOUR
AU  - Koh, T.H.
AU  - Abdul-Rahman, N.B.
AU  - Teo, J.W.P.
AU  - La, M.V.
AU  - Periaswamy, B.
AU  - Chen, S.L.
TI  - Draft Genome Sequence of Singapore Klebsiella pneumoniae subsp. pneumoniae Isolate DS32358_14, Which Contains the Carbapenemase Gene blaVIM-1.
JO  - Genome Announcements
PY  - 2018
SP  - e01377
EP  - e01317
VL  - 6
AB  - We sequenced the first blaVIM-1-positive Klebsiella pneumoniae strain isolated in Singapore.
AB  - The isolate belongs to multilocus sequence type 2542 (ST2542), and blaVIM-1 was the first gene
AB  - in an integron that also contained aacA4, aphA15, aadA1, catB2, qacEdelta1, and sul1.
ER  -

TY  - JOUR
AU  - Kohli, P.
AU  - Dua, A.
AU  - Sangwan, N.
AU  - Oldach, P.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00956
EP  - e00913
VL  - 1
AB  - Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading
AB  - bacterium Sphingobium ummariense strain RL-3, which was isolated
AB  - from the HCH dumpsite located in Lucknow, India (27 degrees 00'N and 81 degrees
AB  - 09'E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of
AB  - 139 contigs, 4,645 coding sequences, and 65% G+C content.
ER  -

TY  - JOUR
AU  - Kohlman, M.E.
AU  - Carrillo, C.D.
AU  - Wong, A.
TI  - Draft Genome Sequence of Hafnia paralvei Strain GTA-HAF03.
JO  - Genome Announcements
PY  - 2015
SP  - e01592
EP  - e01514
VL  - 3
AB  - Hafnia paralvei is a Gram-negative member of the Enterobacteriaceae family, closely related to
AB  - the opportunistic pathogen Hafnia alvei. We report here the first draft genome sequence of H.
AB  - paralvei, from the beef trim isolate GTA-HAF03, consisting of a 5.0-Mbp assembly encoding
AB  - 4,382 proteins and 90 predicted RNAs.
ER  -

TY  - JOUR
AU  - Kohlmeier, M.G.
AU  - Yudistira, H.
AU  - Zhang, X.L.
AU  - Fristensky, B.
AU  - Levin, D.B.
AU  - Sparling, R.
AU  - Oresnik, I.J.
TI  - Draft Genome Sequence of the Bacteriocin-Producing Bradyrhizobium japonicum Strain FN1.
JO  - Genome Announcements
PY  - 2015
SP  - e00812
EP  - e00815
VL  - 3
AB  - Bradyrhizobium japonicum strain FN1 was found to produce bacteriocin-like zones of clearing
AB  - when tested against other strains of bradyrhizbia. The genome was
AB  - sequenced, and several putative bacteriocin-producing genes, in addition to the
AB  - expected genes involved in nodulation and nitrogen fixation, were identified.
ER  -

TY  - JOUR
AU  - Kohn, T.
AU  - Heuer, A.
AU  - Jogler, M.
AU  - Vollmers, J.
AU  - Boedeker, C.
AU  - Bunk, B.
AU  - Rast, P.
AU  - Borchert, D.
AU  - Glockner, I.
AU  - Freese, H.M.
AU  - Klenk, H.P.
AU  - Overmann, J.
AU  - Kaster, A.K.
AU  - Rohde, M.
AU  - Wiegand, S.
AU  - Jogler, C.
TI  - Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea.
JO  - Front. Microbiol.
PY  - 2016
SP  - 2079
EP  - 2079
VL  - 7
AB  - Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in
AB  - aquatic and terrestrial habitats. While planctomycetal species are important
AB  - players in the global carbon and nitrogen cycle, this phylum is still
AB  - undersampled and only few genome sequences are available. Here we describe strain
AB  - NH11T, a novel planctomycete obtained from a crustacean shell (Wadden Sea,
AB  - Germany). The phylogenetically closest related cultivated species is Gimesia
AB  - maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts
AB  - have mostly yielded members of the genus Rhodopirellula from water of the German
AB  - North Sea. On the other hand, only one axenic culture of the genus Pirellula was
AB  - obtained from a crustacean thus far. However, the 16S rRNA gene sequence of
AB  - strain NH11T shares only 80% sequence identity with the closest relative of both
AB  - genera, Rhodopirellula and Pirellula. Thus, strain NH11T is unique in terms of
AB  - origin and phylogeny. While the pear to ovoid shaped cells of strain NH11T are
AB  - typical planctomycetal, light-, and electron microscopic observations point
AB  - toward an unusual variation of cell division through budding: during the division
AB  - process daughter- and mother cells are connected by an unseen thin tubular-like
AB  - structure. Furthermore, the periplasmic space of strain NH11T was unusually
AB  - enlarged and differed from previously known planctomycetes. The complete genome
AB  - of strain NH11T, with almost 9 Mb in size, is among the largest planctomycetal
AB  - genomes sequenced thus far, but harbors only 6645 protein-coding genes. The
AB  - acquisition of genomic components by horizontal gene transfer is indicated by the
AB  - presence of numerous putative genomic islands. Strikingly, 45 "giant genes" were
AB  - found within the genome of NH11T. Subsequent analysis of all available
AB  - planctomycetal genomes revealed that Planctomycetes as such are especially rich
AB  - in "giant genes". Furthermore, Multilocus Sequence Analysis (MLSA) tree
AB  - reconstruction support the phylogenetic distance of strain NH11T from other
AB  - cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our
AB  - findings, we propose to classify strain NH11T as Fuerstia marisgermanicae gen.
AB  - nov., sp. nov., with the type strain NH11T, within the phylum Planctomycetes.
ER  -

TY  - JOUR
AU  - Kohring, G.W.
AU  - Mayer, F.
TI  - In situ distribution of EcoRI methylase and restriction endonuclease in cells of Escherichia coli Bs5.
JO  - FEBS Lett.
PY  - 1987
SP  - 207
EP  - 210
VL  - 216
AB  - Specific IgG antibodies were raised in rabbits against purified EcoRI methylase
AB  - and restriction endonuclease.  Post embedding labeling experiments, using the
AB  - protein A-gold technique, were made with paraformaldehyde-glutaraldehyde fixed
AB  - cells, embedded in Lowicryl K4M resin at low temperatures.  Labeling with
AB  - methylase-specific antibodies showed 60-70% of gold particles in the cytoplasm
AB  - and 30-40% at the cell envelope, whereas the use of restriction enzyme-specific
AB  - antibodies led to a distribution of 10-30% in the cytoplasm and 70-90% in the
AB  - cell envelope.  The results coincide with the proposed function of the enzymes:
AB  - in the cytoplasm methylase protects the cells' own DNA from self-destruction,
AB  - and the restriction endonuclease cuts foreign DNA when entering the cell.
ER  -

TY  - JOUR
AU  - Kohring, G.W.
AU  - Mayer, F.
TI  - Immunoelectron microscopic localization of the restriction endonuclease EcoRI in Escherichia coli BS5.
JO  - Eur. J. Cell Biol.
PY  - 1985
SP  - 1
EP  - 6
VL  - 37
AB  - Purified restriction endonuclease EcoRI isolated fom Escherichia coli BS5 was
AB  - used for the production of enzyme-specific IgG antibodies in rabbits.  For
AB  - enzyme localization experiments, paraformaldehyde-glutaraldehyde-fixed cells
AB  - were embedded and polymerized by a low-temperature procedure using Lowicryl
AB  - K4M.  the immuno electron microscopic protein A-gold technique and an
AB  - immuno-gold method revealed that 70% of the enzyme-specific labeling were
AB  - located in the cell envelope whereas 30% were found in the cytoplasm.  In
AB  - metal-shadowed preparations, no indications for the presence of the enzme could
AB  - be found on the cell surface; however, on the surface of cell protoplasts
AB  - enzyme specific labeling could be detected.  The results indicate the presence
AB  - of major amount of EcoRI in the periplasmic space of the cell where it might be
AB  - loosely bound or even freely diffusible.
ER  -

TY  - JOUR
AU  - Koike, H.
AU  - Sato, S.
AU  - Morita, T.
AU  - Fukuoka, T.
AU  - Habe, H.
TI  - Draft Genome Sequence of Acetobacter tropicalis Type Strain NBRC16470, a Producer of Optically Pure d-Glyceric Acid.
JO  - Genome Announcements
PY  - 2014
SP  - e01329
EP  - e01314
VL  - 2
AB  - Here we report the 3.7-Mb draft genome sequence of Acetobacter tropicalis NBRC16470(T), which
AB  - can produce optically pure d-glyceric acid (d-GA; 99%
AB  - enantiomeric excess) from raw glycerol feedstock derived from biodiesel fuel
AB  - production processes.
ER  -

TY  - JOUR
AU  - Koike, H.
AU  - Yokoyama, K.
AU  - Kawashima, T.
AU  - Yamasaki, T.
AU  - Makino, S.
AU  - Clowney, L.
AU  - Suzuki, M.
TI  - GATC Methylation by Dam methylase in archaea: its roles and possible transcription regulation by an FFRP.
JO  - Proc. Jpn. Acad., B, Phys. Biol. Sci.
PY  - 2005
SP  - 278
EP  - 290
VL  - 81
AB  - Methylation of pairs of adenines at their N6 positions in GATC sites (GATC methylation) in
AB  - archaeal genomic DNAs has been studied. Genomic DNAs in cells of three archaeal species were
AB  - found as fully methylated, while those of four other archaeal species were free of such
AB  - methylation. Consistently with this pattern of the presence or absence of GATC methylation,
AB  - homologues of E. coli Dam methylase was found present or absent, but various other types of
AB  - DNA methylases were not. A Dam homologue from Pyrococcus sp. OT3 was expressed and its
AB  - expected function of methylating GATC was confirmed. By methylation of each adenine the DNA
AB  - duplex was destabilized by 0.56 +/- 0.10 Kcal/mol, and this effect was additive. For some
AB  - archaea, transcription regulation of Dam methylase gene appears to be needed upon cell
AB  - replication, and in regions upstream of three Dam methylase genes, nucleotide sequences close
AB  - to TTTTCTTTGAAAA were present. This arrangement, five bases each at the ends, which are
AB  - complementary to each other, sandwiching three T bases at the center, fits into a pattern the
AB  - same as those recognized by dimers of transcription factors, feast/famine regulatory proteins
AB  - (FFRPs).
ER  -

TY  - JOUR
AU  - Kojima, K.K.
AU  - Furuta, Y.
AU  - Yahara, K.
AU  - Fukuyo, M.
AU  - Shiwa, Y.
AU  - Nishiumi, S.
AU  - Yoshida, M.
AU  - Azuma, T.
AU  - Yoshikawa, H.
AU  - Kobayashi, I.
TI  - Population Evolution of Helicobacter pylori through Diversification in DNA Methylation and Interstrain Sequence Homogenization.
JO  - Mol. Biol. Evol.
PY  - 2016
SP  - 2848
EP  - 2859
VL  - 33
AB  - Decoding of closely related genomes is now revealing the process of population evolution. In
AB  - bacteria, population divergence appears associated with a unique
AB  - set of sequence-specific epigenetic DNA methylation systems, often within
AB  - restriction-modification (RM) systems. They might define a unique gene expression
AB  - pattern and limit genetic flux between lineages in population divergence. We
AB  - addressed the contribution of methylation systems to population diversification
AB  - in panmictic bacterial species, Helicobacter pylori, which shows an
AB  - interconnected population structure through frequent mutual recombination. We
AB  - analyzed complete genome sequences of 28 strains collected in Fukui, Japan. Their
AB  - nucleotide sequences are closely related although fine-scale analyses revealed
AB  - two subgroups likely reflecting human subpopulations. Their sequences are tightly
AB  - connected by homologous recombination. Our extensive analysis of RM systems
AB  - revealed an extreme variability in DNA methyltransferases, especially in their
AB  - target recognition domains. Their diversity was, however, not immediately related
AB  - to the genome sequence diversity, except for very closely related strains. An
AB  - interesting exception is a hybrid strain, which likely has conserved the
AB  - methylation gene repertoire from one parent but diversified in sequence by
AB  - massive acquisition of fragmentary DNA sequences from the other parent. Our
AB  - results demonstrate how a bacterial population can be extremely divergent in
AB  - epigenetics and yet homogenized in sequence.
ER  -

TY  - JOUR
AU  - Kokcha, S.
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Million, M.
AU  - Leroy, Q.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 346
EP  - 355
VL  - 6
AB  - Bacillus timonensis strain MM10403188(T) sp. nov. is the type strain of a proposed new species
AB  - within the genus Bacillus. This strain, whose genome is
AB  - described here, was isolated from the fecal flora of a healthy patient. B.
AB  - timonensis is an aerobic Gram-negative rod shaped bacterium. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 4,632,049 bp long genome (1 chromosome but no plasmid) contains
AB  - 4,610 protein-coding and 74 RNA genes, including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Kokcha, S.
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 233
EP  - 245
VL  - 7
AB  - Brevibacterium senegalense strain JC43(T) sp. nov. is the type strain of Brevibacterium
AB  - senegalense sp. nov., a new species within the Brevibacterium
AB  - genus. This strain, whose genome is described here, was isolated from the fecal
AB  - flora of a healthy Senegalese patient. B. senegalense is an aerobic rod-shaped
AB  - Gram-positive bacterium. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 3,425,960 bp long genome (1
AB  - chromosome but no plasmid) contains 3,064 protein-coding and 49 RNA genes.
ER  -

TY  - JOUR
AU  - Kolek, J.
AU  - Sedlar, K.
AU  - Provaznik, I.
AU  - Patakova, P.
TI  - Draft Genome Sequence of Clostridium pasteurianum NRRL B-598, a Potential Butanol or Hydrogen Producer.
JO  - Genome Announcements
PY  - 2014
SP  - e00192
EP  - e00114
VL  - 2
AB  - We present a draft genome sequence of Clostridium pasteurianum NRRL B-598. This strain
AB  - ferments saccharides by two-stage acetone-butanol (AB) fermentation, is
AB  - oxygen tolerant, and has high hydrogen yields.
ER  -

TY  - JOUR
AU  - Kolesnikov, V.A.
AU  - Zinovev, V.V.
AU  - Yashina, L.N.
AU  - Karginov, V.A.
AU  - Baclanov, M.M.
AU  - Malygin, E.G.
TI  - Relaxed specificity of endonuclease BamHI as determined by identification of recognition sites in SV40 and pBR322 DNAs.
JO  - FEBS Lett.
PY  - 1981
SP  - 101
EP  - 104
VL  - 132
AB  - The specificity of restriction nucleases, which is very high under conventional
AB  - conditions, may become 'relaxed' in certain media (e.g., at decreased ionic
AB  - strength, in the presence of organic solvents).  The 'condition-relaxed'
AB  - recognition sites usually correspond to shortened or degenerate sequences
AB  - derived from the 'canonic' ones.  The reasons for relaxation are unclear,
AB  - although they are of great interest for understanding the mechanism of
AB  - restriction nuclease action in general.  Up to now, the structure of 'relaxed'
AB  - sites has been determined for only 3 endonucleases: EcoRI, Bsu1, BstI.  This
AB  - communication is concerned with the determination of the structure of 'relaxed'
AB  - restriction sites for the endonuclease BamHI.  These sites in SV40 and pBR322
AB  - DNAs appeared to be GGATC and GPuATCC (cf. canonic site GGATCC).
ER  -

TY  - JOUR
AU  - Kolocheva, T.I.
AU  - Demidov, S.A.
AU  - Maksakova, G.A.
AU  - Nevinskii, G.A.
TI  - Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides.
JO  - Mol. Biol. (Mosk)
PY  - 1998
SP  - 1025
EP  - 1033
VL  - 32
ER  -

TY  - JOUR
AU  - Kolocheva, T.I.
AU  - Maksakova, G.A.
AU  - Bugreev, D.D.
AU  - Nevinsky, G.A.
TI  - Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides.
JO  - Life
PY  - 2001
SP  - 189
EP  - 195
VL  - 51
AB  - The interaction of EcoRI with different oligodeoxyribonucleotides (ODNs) was analyzed using
AB  - the method of the slow step-by-step simplification in their complexity. Orthophosphate (KI =
AB  - 31 mM), 2-deoxyribose 5-phosphate (KI = 4.6 mM) and different dNMPs (KI = 2.1-2.5 mM) were
AB  - shown to be the minimal ligands of the enzyme. The lengthening of a nonspecific d(pN)n (n =
AB  - 1-6) by one nucleotide unit resulted in the increase of their affinity by a factor of
AB  - approximately 2.0. Weak nonspecific electrostatic contacts of EcoRI with internucleotide
AB  - phosphate groups of ODNs can account for about 5 orders of magnitude in the ligand affinity,
AB  - whereas the contribution of specific interactions between EcoRI and d(pN)n is no more than 2
AB  - orders of magnitude of a total ODN's affinity.
ER  -

TY  - JOUR
AU  - Kolton, M.
AU  - Green, S.J.
AU  - Harel, Y.M.
AU  - Sela, N.
AU  - Elad, Y.
AU  - Cytryn, E.
TI  - Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi).
JO  - J. Bacteriol.
PY  - 2012
SP  - 5462
EP  - 5463
VL  - 194
AB  - Here we report the draft genome sequence of Flavobacterium sp. strain F52, isolated from the
AB  - rhizosphere of bell pepper (Capsicum annuum L. cv. Maccabi).
AB  - Flavobacterium spp. are ubiquitous in the rhizospheres of agricultural crops;
AB  - however, little is known about their physiology. To our knowledge, this is the
AB  - first published genome of a root-associated Flavobacterium strain.
ER  -

TY  - JOUR
AU  - Kolykhalov, A.A.
AU  - Repin, V.E.
AU  - Fish, A.M.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
TI  - Determination of substrate specificity of restriction endonuclease Vha464I.
JO  - Sib. Biol. J.
PY  - 1991
SP  - 60
EP  - 61
VL  - 19
AB  - The recognition sequence and cleavage point of restriction endonuclease Vha464I have been
AB  - determined as 5'C^TTAAG.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Hosoyama, A.
AU  - Ichikawa, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Marine-Derived Bacillus subtilis TP-B0611, a Producer of Bacilosarcins and Amicoumacins.
JO  - Genome Announcements
PY  - 2016
SP  - e01134
EP  - e01116
VL  - 4
AB  - Here, we report the draft genome sequence of Bacillus subtilis TP-B0611, which produces the
AB  - isocoumarin-type compounds bacilosarcin and amicoumacin. The genome
AB  - encodes three nonribosomal peptide synthetase (NRPS) gene clusters and one hybrid
AB  - polyketide synthase (PKS)/NRPS gene cluster. The hybrid PKS/NRPS gene cluster was
AB  - identified to be responsible for the biosynthesis of bacilosarcins and
AB  - amicoumacins.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Hosoyama, A.
AU  - Ichikawa, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0874, a Catechoserine Producer.
JO  - Genome Announcements
PY  - 2016
SP  - e01163
EP  - e01116
VL  - 4
AB  - We report the draft genome sequence of Streptomyces sp. TP-A0874 isolated from compost. This
AB  - strain produces catechoserine, a new catecholate-type inhibitor of
AB  - tumor cell invasion. The genome harbors at least six gene clusters for polyketide
AB  - and nonribosomal peptide biosyntheses. The biosynthetic gene cluster for
AB  - catechoserines was identified by bioinformatic analysis.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Hosoyama, A.
AU  - Ichikawa, N.
AU  - Panbangred, W.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Streptomyces sp. SPMA113, a Prajinamide Producer.
JO  - Genome Announcements
PY  - 2016
SP  - e01126
EP  - e01116
VL  - 4
AB  - We report here the draft genome sequence of Streptomyces sp. SPMA113 isolated from soil in
AB  - Thailand. This strain produces a new modified peptide, prajinamide,
AB  - which has adipocyte differentiation activity. The genome harbors at least 30 gene
AB  - clusters for synthases of polyketide and nonribosomal peptide, suggesting its
AB  - potential to produce diverse secondary metabolites.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Hosoyama, A.
AU  - Kimura, A.
AU  - Ichikawa, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of an Anicemycin Producer, Streptomyces sp. TP-A0648.
JO  - Genome Announcements
PY  - 2017
SP  - e01468
EP  - e01416
VL  - 5
AB  - We report the draft genome sequence of Streptomyces sp. TP-A0648 isolated from a  leaf of
AB  - Aucuba japonica This strain produces a new tumor cell growth inhibitor
AB  - designated anicemycin. The genome harbors at least 12 biosynthetic gene clusters
AB  - for polyketides and nonribosomal peptides, suggesting the potential to produce
AB  - diverse secondary metabolites.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Hosoyama, A.
AU  - Yabe, S.
AU  - Yokota, A.
AU  - Uchino, Y.
AU  - Takano, H.
TI  - Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class  Ktedonobacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e01156
EP  - e01116
VL  - 4
AB  - Here, we report the draft genome sequence of Thermogemmatispora onikobensis NBRC  111776T, an
AB  - aerial mycelium- and spore-forming thermophilic bacterium belonging
AB  - to the class Ktedonobacteria The genome contains five biosynthetic gene clusters
AB  - coding for secondary metabolites, such as terpene, thiopeptide, lantipeptide,
AB  - nonribosomal peptide, and lassopeptide, suggesting the potential to produce
AB  - secondary metabolites.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Harunari, E.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of an Anthracimycin Producer, Streptomyces sp. TP-A0875.
JO  - Genome Announcements
PY  - 2015
SP  - e01149
EP  - e01115
VL  - 3
AB  - Here, we report the draft genome sequence of an anthracimycin producer, Streptomyces sp.
AB  - TP-A0875. The genome contains at least two type I polyketide synthase (PKS) gene clusters, two
AB  - type II PKS gene clusters, and three nonribosomal peptide synthetase gene clusters. The gene
AB  - cluster for anthracimycin biosynthesis was identified based on the PKS domain organization.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Marine-Derived Streptomyces sp. TP-A0873, a Producer of a Pyrrolizidine Alkaloid Bohemamine.
JO  - Genome Announcements
PY  - 2015
SP  - e00008
EP  - e00015
VL  - 3
AB  - Streptomyces sp. TP-A0873, isolated from deep-sea water, produces three different classes of
AB  - secondary metabolites: antimycin, bohemamine, and alkylated butenolides. In order to assess
AB  - the biosynthetic potential of this strain, draft  genome sequencing was carried out. The
AB  - genome contained at least 14 gene clusters for polyketide synthase (PKS) and nonribosomal
AB  - peptide synthetase (NRPS).
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft genome sequence of marine-derived Streptomyces sp. TP-A0598, a producer of  anti-MRSA antibiotic lydicamycins.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 58
EP  - 58
VL  - 10
AB  - Streptomyces sp. TP-A0598, isolated from seawater, produces lydicamycin, structurally unique
AB  - type I polyketide bearing two nitrogen-containing five-membered rings, and four congeners
AB  - TPU-0037-A, -B, -C, and -D. We herein report the 8 Mb draft genome sequence of this strain,
AB  - together with classification and features of the organism and generation, annotation and
AB  - analysis of the genome sequence. The genome encodes 7,240 putative ORFs, of which 4,450 ORFs
AB  - were assigned with COG categories. Also, 66 tRNA genes and one rRNA operon were identified.
AB  - The genome contains eight gene clusters involved in the production of polyketides and
AB  - nonribosomal peptides. Among them, a PKS/NRPS gene  cluster was assigned to be responsible for
AB  - lydicamycin biosynthesis and a plausible biosynthetic pathway was proposed on the basis of
AB  - gene function prediction. This genome sequence data will facilitate to probe the potential of
AB  - secondary metabolism in marine-derived Streptomyces.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Marine-Derived Actinomycete Nocardiopsis sp. Strain TP-A0876, a Producer of Polyketide Pyrones.
JO  - Genome Announcements
PY  - 2014
SP  - e00665
EP  - e00614
VL  - 2
AB  - Here we report the draft genome sequence of Nocardiopsis sp. strain TP-A0876, isolated from
AB  - marine sediment, which produces polyketide-derived pyrones called
AB  - nocapyrones. The genome contains three polyketide synthase (PKS) gene clusters,
AB  - one of which was proposed to be responsible for nocapyrone biosynthesis. This
AB  - genome sequence will facilitate the study of the potential for secondary
AB  - metabolism in Nocardiopsis strains.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0356, a Producer of Yatakemycin.
JO  - Genome Announcements
PY  - 2015
SP  - e01446
EP  - e01415
VL  - 3
AB  - Here, we report the draft genome sequence of Streptomyces sp. TP-A0356, a producer of a potent
AB  - antitumor antibiotic, yatakemycin, to evaluate potential for
AB  - secondary metabolite production. The genome sequence data suggest the presence of
AB  - at least nine gene clusters for polyketide synthases and nonribosomal peptide
AB  - synthetases in this strain.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Nonomuraea sp. TP-A0861, a Producer of Myxochelin A.
JO  - Genome Announcements
PY  - 2015
SP  - e01430
EP  - e01415
VL  - 3
AB  - Nonomuraea sp. TP-A0861 produces the nonribosomal peptide myxochelin A, which is  known as a
AB  - microbial siderophore. Here, we report its draft genome sequence. The
AB  - genome contains at least three nonribosomal peptide synthetase gene clusters, one
AB  - of which is proposed to be responsible for the biosynthesis of myxochelin A.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0871, a Producer of Heronamide C.
JO  - Genome Announcements
PY  - 2015
SP  - e01429
EP  - e01415
VL  - 3
AB  - Streptomyces sp. TP-A0871 produces the polyene macrolactam heronamide C. Here, we report its
AB  - draft genome sequence to get insight into heronamide biosynthesis and
AB  - genome-mining for novel secondary metabolites of polyketide and nonribosomal
AB  - peptide classes. The genome encodes over nine orphan gene clusters for polyketide
AB  - and/or nonribosomal peptide syntheses.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Streptomyces sp. TP-A0890, a Producer of FR-900452 and A-74863a.
JO  - Genome Announcements
PY  - 2015
SP  - e01212
EP  - e01215
VL  - 3
AB  - Here, we report the draft genome sequence of Streptomyces sp. TP-A0890, a producer of
AB  - FR-900452 and A-74863a. The genome was found to contain at least eight polyketide synthase and
AB  - nonribosomal peptide synthetase gene clusters. A prediction of gene functions based on the
AB  - sequence similarity allowed us to assign the biosynthetic gene clusters for FR-900452 and
AB  - A-74863a.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Fujita, N.
AU  - Thamchaipenet, A.
AU  - Igarashi, Y.
TI  - Draft Genome Sequence of Linfuranone Producer Microbispora sp. GMKU 363.
JO  - Genome Announcements
PY  - 2015
SP  - e01471
EP  - e01415
VL  - 3
AB  - Here, we report the draft genome sequence of Microbispora sp. GMKU 363, a plant-derived
AB  - actinomycete that produces linfuranone A, a linear polyketide
AB  - modified with a furanone ring possessing adipocyte differentiation inducing
AB  - activity. The biosynthetic gene cluster for linfuranone was identified by
AB  - analyzing polyketide synthase genes in the genome.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Hamada, M.
AU  - Harunari, E.
AU  - Ishikawa, A.
AU  - Igarashi, Y.
TI  - Draft genome sequence of Micromonospora sp. DSW705 and distribution of biosynthetic gene clusters for depsipeptides bearing 4-amino-2,4-pentadienoate in  actinomycetes.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 84
EP  - 84
VL  - 11
AB  - Here, we report the draft genome sequence of Micromonospora sp. DSW705 (=NBRC 110037), a
AB  - producer of antitumor cyclic depsipeptides rakicidins A and B,
AB  - together with the features of this strain and generation, annotation, and
AB  - analysis of the genome sequence. The 6.8 Mb genome of Micromonospora sp. DSW705
AB  - encodes 6,219 putative ORFs, of which 4,846 are assigned with COG categories. The
AB  - genome harbors at least three type I polyketide synthase (PKS) gene clusters, one
AB  - nonribosomal peptide synthetase (NRPS) gene clusters, and three hybrid PKS/NRPS
AB  - gene clusters. A hybrid PKS/NRPS gene cluster encoded in scaffold 2 is
AB  - responsible for rakicidin synthesis. DNA database search indicated that the
AB  - biosynthetic gene clusters for depsipeptides bearing 4-amino-2,4-pentadienoate
AB  - are widely present in taxonomically diverse actinomycetes.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Oguchi, A.
AU  - Hamada, M.
AU  - Harunari, E.
AU  - Kodani, S.
AU  - Fujita, N.
AU  - Igarashi, Y.
TI  - Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 85
EP  - 85
VL  - 11
AB  - Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated
AB  - alchivemycins A and B. Here, we report the draft genome
AB  - sequence of this strain together with features of the organism and assembly,
AB  - annotation, and analysis of the genome sequence. The 9.9 Mb genome of
AB  - Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were
AB  - assigned with COG categories. We successfully identified a hybrid polyketide
AB  - synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be
AB  - responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway.
AB  - The alchivemycin biosynthetic gene cluster is also present in Streptomyces
AB  - rapamycinicus NRRL 5491T, Streptomyces hygroscopicus subsp. hygroscopicus NBRC
AB  - 16556, and Streptomyces ascomycinicus NBRC 13981T, which are taxonomically highly
AB  - close to strain TP-A0867. This study shows a representative example that
AB  - distribution of secondary metabolite genes is correlated with evolution within
AB  - the genus Streptomyces.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Oguchi, A.
AU  - Hamada, M.
AU  - Tamura, T.
AU  - Fujita, N.
TI  - Draft Genome Sequence of Streptomyces albus Strain NBRC 13014T, the Type Species  of the Genus Streptomyces.
JO  - Genome Announcements
PY  - 2015
SP  - e01527
EP  - e01514
VL  - 3
AB  - Streptomyces albus is the type species of the genus Streptomyces. Here, we report the draft
AB  - genome sequence of S. albus strain NBRC 13014(T). The genome contains
AB  - at least seven orphan polyketide synthase and nonribosomal peptide synthetase
AB  - gene clusters. The genome sequence will also serve as a valuable reference for
AB  - Streptomyces taxonomy.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Oguchi, A.
AU  - Hamada, M.
AU  - Tamura, T.
AU  - Fujita, N.
TI  - Draft genome sequences of six type strains of the genus streptacidiphilus.
JO  - Genome Announcements
PY  - 2015
SP  - e01387
EP  - e01314
VL  - 3
AB  - Members of the genus Streptacidiphilus are acidophilic actinomycetes with streptomycete-like
AB  - features. Here, we report the draft genome sequences of the
AB  - type strains of Streptacidiphilus albus, Streptacidiphilus anmyonensis,
AB  - Streptacidiphilus carbonis, Streptacidiphilus jiangxiensis, Streptacidiphilus
AB  - melanogenes, and Streptacidiphilus neutrinimicus. These genome sequences will
AB  - serve as valuable references for understanding their taxonomic relationships,
AB  - genetic characteristics, and potentials for industry.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ichikawa, N.
AU  - Oguchi, A.
AU  - Hamada, M.
AU  - Tamura, T.
AU  - Suzuki, K.
AU  - Fujita, N.
TI  - Draft Genome Sequence of Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556.
JO  - Genome Announcements
PY  - 2016
SP  - e00139
EP  - e00116
VL  - 4
AB  - Here, we report the draft genome sequence of strain NBRC 16556, deposited as Streptomyces
AB  - hygroscopicus subsp. hygroscopicus into the NBRC culture collection.
AB  - An average nucleotide identity analysis confirmed that the taxonomic
AB  - identification is correct. The genome sequence will serve as a valuable reference
AB  - for genome mining to search new secondary metabolites.
ER  -

TY  - JOUR
AU  - Komaki, H.
AU  - Ishikawa, A.
AU  - Ichikawa, N.
AU  - Hosoyama, A.
AU  - Hamada, M.
AU  - Harunari, E.
AU  - Nihira, T.
AU  - Panbangred, W.
AU  - Igarashi, Y.
TI  - Draft genome sequence of Streptomyces sp. MWW064 for elucidating the rakicidin biosynthetic pathway.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 83
EP  - 83
VL  - 11
AB  - Streptomyces sp. MWW064 (=NBRC 110611) produces an antitumor cyclic depsipeptide  rakicidin D.
AB  - Here, we report the draft genome sequence of this strain together
AB  - with features of the organism and generation, annotation and analysis of the
AB  - genome sequence. The 7.9 Mb genome of Streptomyces sp. MWW064 encoded 7,135
AB  - putative ORFs, of which 6,044 were assigned with COG categories. The genome
AB  - harbored at least three type I polyketide synthase (PKS) gene clusters, seven
AB  - nonribosomal peptide synthetase (NRPS) gene clusters, and four hybrid PKS/NRPS
AB  - gene clusters, from which a hybrid PKS/NRPS gene cluster responsible for
AB  - rakicidin synthesis was successfully identified. We propose the biosynthetic
AB  - pathway based on bioinformatic analysis, and experimentally proved that the
AB  - pentadienoyl unit in rakicidins is derived from serine and malonate.
ER  -

TY  - JOUR
AU  - Komisarova, E.V.
AU  - Kislichkina, A.A.
AU  - Krasilnikova, V.M.
AU  - Bogun, A.G.
AU  - Fursova, N.K.
AU  - Volozhantsev, N.V.
TI  - Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477.
JO  - Genome Announcements
PY  - 2017
SP  - e00694
EP  - e00617
VL  - 5
AB  - The double-stranded DNA (dsDNA) bacteriophage vB_KpnM_KpV477, with a broad spectrum of lytic
AB  - activity against Klebsiella pneumoniae, including strains of
AB  - capsular serotypes K1, K2, and K57, was isolated from a clinical sample. The
AB  - phage genome comprises 168,272 bp, with a G+C content of 39.3%, and it contains
AB  - 275 putative coding sequences (CDSs) and 17 tRNAs.
ER  -

TY  - JOUR
AU  - Komori, K.
AU  - Fujita, N.
AU  - Ichiyanagi, K.
AU  - Shinagawa, H.
AU  - Morikawa, K.
AU  - Ishino, Y.
TI  - PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus.  I. Purification and identification of the homing-type endonuclease activities.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 4167
EP  - 4174
VL  - 27
AB  - We screened for proteins with specific binding activity to Holliday junction DNA from the
AB  - hyperthermophilic archaeon Pyrococcus furiosus and found a protein that has specific affinity
AB  - for DNA with a branched structure, like a three-way or four-way junction. The protein was
AB  - identified as one of the two inteins encoded in the gene for ribonucleotide reductase (RNR) by
AB  - gene cloning. These two inteins were spliced out from the precursor protein as polypeptides
AB  - with molecular weights of 53.078 and 43.976 kDa, respectively. The amino acid sequences of
AB  - these inteins have two copies of the LAGLIDADG motif, which is found in the site-specific DNA
AB  - endonucleases. The purified proteins actually cleaved double-stranded DNA with the sequence of
AB  - the intein(-)allele, and, therefore, they were designated PI-PfuI and PI-PfuII. They generate
AB  - a 4 bp 3'-OH overhang with a 5'-phosphate, like other known homing endonucleases originating
AB  - from inteins. The optimal conditions of the DNA cleavage reaction, including temperature, pH,
AB  - and concentrations of KCl and MgCl(2), have been determined. The high affinity for junction
AB  - DNA of PI-PfuI was confirmed using the purified protein.
ER  -

TY  - JOUR
AU  - Komori, K.
AU  - Ichiyanagi, K.
AU  - Morikawa, K.
AU  - Ishino, Y.
TI  - PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus.  II. Characterization of the binding and cleavage abilities by site-directed mutagenesis.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 4175
EP  - 4182
VL  - 27
AB  - PI-PfuI and PI-PfuII from Pyrococcus furiosus are homing endonucleases, as shown in the
AB  - accompanying paper. These two endonucleases are produced by protein splicing from the
AB  - precursor protein including ribonucleotide reductase (RNR).  We show here that both enzymes
AB  - specifically interact with their substrate DNA and distort the DNA strands by 73 degrees and
AB  - 67 degrees, respectively. They have two copies of the amino acid sequence motif LAGLIDADG,
AB  - which is present in the majority of homing endonucleases and provides some of the catalytic
AB  - residues necessary for DNA cleavage activity.  Site-specific mutagenesis studies showed that
AB  - two acidic residues in the motifs, Asp149 and Glu250 in PI-PfuI, and Asp156 and Asp249 in
AB  - PI-PfuII, were critical for catalysis. The third residues of the active site triads, as
AB  - predicted from the structure of PI-SceI, were Asn225 in PI-PfuI and Lys224 in PI-PfuII.
AB  - Substitution of Asn225 in PI-PfuI by Ala did not affect catalysis. The cleavage activity of
AB  - PI-PfuII was 50-fold decreased by the substitution of Ala for Lys224.  The binding affinity of
AB  - the mutant protein for the substrate DNA also decreased 6-fold. The Lys in PI-PfuII may play a
AB  - direct or indirect role in catalysis of the endonuclease activity.
ER  -

TY  - JOUR
AU  - Konarev, P.V.
AU  - Kachalova, G.S.
AU  - Ryazanova, A.Y.
AU  - Kubareva, E.A.
AU  - Karyagina, A.S.
AU  - Bartunik, H.D.
AU  - Svergun, D.I.
TI  - Flexibility of the Linker between the Domains of DNA Methyltransferase SsoII Revealed by Small-Angle X-Ray Scattering: Implications for Transcription Regulation in SsoII Restriction-Modification System.
JO  - PLoS ONE
PY  - 2014
SP  - e93453
EP  - e93453
VL  - 9
AB  - Cytosine-5)-DNA methyltransferase SsoII (M. SsoII) consists of a methyltransferase domain
AB  - (residues 72-379) and an N-terminal region (residues 1-71) which regulates transcription in
AB  - SsoII restriction-modification system. Small-angle X-ray scattering (SAXS) is employed here to
AB  - study the low resolution structure of M.SsoII and its complex with DNA containing the
AB  - methylation site. The shapes reconstructed ab initio from the SAXS data reveal two distinct
AB  - protein domains of unequal size. The larger domain matches the crystallographic structure of a
AB  - homologous DNA methyltransferase HhaI (M.HhaI), and the cleft in this domain is occupied by
AB  - DNA in the model of the complex reconstructed from the SAXS data. This larger domain can thus
AB  - be identified as the methyltransferase domain whereas the other domain represents the
AB  - N-terminal region. Homology modeling of the M.SsoII structure is performed by using the model
AB  - of M.HhaI for the methyltransferase domain and representing the N-terminal region either as a
AB  - flexible chain of dummy residues or as a rigid structure of a homologous protein (phage 434
AB  - repressor) connected to the methyltransferase domain by a short flexible linker. Both models
AB  - are compatible with the SAXS data and demonstrate high mobility of the N-terminal region. The
AB  - linker flexibility might play an important role in the function of M.SsoII as a transcription
AB  - factor.
ER  -

TY  - JOUR
AU  - Koncz, C.
AU  - Kiss, A.
AU  - Venetianer, P.
TI  - Biochemical characterization of the restriction-modification system of Bacillus sphaericus.
JO  - Eur. J. Biochem.
PY  - 1978
SP  - 523
EP  - 529
VL  - 89
AB  - A type II restriction endonuclease (endo R-Bsp) has been purified from Bacillus
AB  - sphaericus to electrophoretic homogeneity.  The enzyme appears to be a single
AB  - polypeptide chain with a molecular weight of 35000.  Its pH optimum is around
AB  - 8.2, it requires 20 mM Mg2+ for optimal activity and it is inhibited by Zn2+.
AB  - The yield of the enzyme is higher than that of any type I restriction
AB  - endonuclease so far reported.  The enzyme also cleaves single-stranded DNA,
AB  - albeit at a slower rate.  It seems likely that single-stranded DNA is cleaved
AB  - at the same sequences as double-stranded DNA.  Bacillus sphaericus also
AB  - contains a modification methylase (meth M-Bsp) which completely protects the
AB  - cell's own DNA against cleavage by its restriction endonuclease.  The methylase
AB  - activity has been partially purified, it copurifies with the nuclease until the
AB  - next to the last step.  The enzyme does not require ATP or Mg2+, it transfers
AB  - the methyl group of S-adenosyl-methionine to cytosine residues of DNA.  As the
AB  - action of this methylase completely protects any DNA from endo R-Bsp cleavage,
AB  - it seems likely that the methylase recognizes and methylates the same sequence
AB  - (dG-dG-dC-dC) as the nuclease.
ER  -

TY  - JOUR
AU  - Kondo, H.
AU  - Tinwongger, S.
AU  - Proespraiwong, P.
AU  - Mavichak, R.
AU  - Unajak, S.
AU  - Nozaki, R.
AU  - Hirono, I.
TI  - Draft Genome Sequences of Six Strains of Vibrio parahaemolyticus Isolated from Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease Shrimp in Thailand.
JO  - Genome Announcements
PY  - 2014
SP  - e00221
EP  - e00214
VL  - 2
AB  - Some strains of Vibrio parahaemolyticus cause acute hepatopancreatic necrosis disease (AHPND)
AB  - in shrimp. We sequenced 3 AHPND and 3 non-AHPND strains and found that all of them lacked the
AB  - pathogenicity island relevant to human infection. A unique sequence encoding a type IV
AB  - pilus/type IV secretion system was found in 3 AHPND strains.
ER  -

TY  - JOUR
AU  - Kondo, H.
AU  - Van, P.T.
AU  - Dang, L.T.
AU  - Hirono, I.
TI  - Draft Genome Sequence of Non-Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease Strain KC13.17.5, Isolated from Diseased Shrimp in Vietnam.
JO  - Genome Announcements
PY  - 2015
SP  - e00978
EP  - e00915
VL  - 3
AB  - A strain of Vibrio (KC13.17.5) causing acute hepatopancreatic necrosis disease (AHPND) in
AB  - shrimp in northern Vietnam was isolated. Normally, AHPND is caused by  Vibrio
AB  - parahaemolyticus, but the genomic sequence of the strain indicated that it belonged to Vibrio
AB  - harveyi. The sequence data included plasmid-like sequences and putative virulence genes.
ER  -

TY  - JOUR
AU  - Kondo, Y.
AU  - Nishimata, H.
AU  - Hidaka, K.
AU  - Hasuwa, T.
AU  - Moriuchi, H.
AU  - Fujiwara, T.
AU  - Hoshino, T.
TI  - Draft Genome Sequence of a Clinical Isolate of Streptococcus mutans Strain HM.
JO  - Genome Announcements
PY  - 2017
SP  - e00826
EP  - e00817
VL  - 5
AB  - We report the draft genome sequence of Streptococcus mutans strain HM isolated from a
AB  - 4-year-old girl with infective endocarditis. The genomics information will
AB  - provide information on the genetic diversity and virulence potential of S. mutans
AB  - strain HM.
ER  -

TY  - JOUR
AU  - Kondo, Y.
AU  - Ogura, Y.
AU  - Sato, K.
AU  - Imamura, K.
AU  - Hoshino, T.
AU  - Nishiguchi, M.
AU  - Hasuwa, T.
AU  - Moriuchi, H.
AU  - Hayashi, T.
AU  - Fujiwara, T.
TI  - Complete Genome Sequence of Streptococcus sp. Strain NPS 308.
JO  - Genome Announcements
PY  - 2016
SP  - e01349
EP  - e01316
VL  - 4
AB  - Streptococcus sp. strain NPS 308, isolated from an 8-year-old girl diagnosed with infective
AB  - endocarditis, likely presents a novel species of Streptococcus Here, we present a complete
AB  - genome sequence of this species, which will contribute to better understanding of the
AB  - pathogenesis of infective endocarditis.
ER  -

TY  - JOUR
AU  - Konforti, B.
TI  - The servant with the scissors.
JO  - Nat. Struct. Biol.
PY  - 2000
SP  - 99
EP  - 100
VL  - 7
AB  - In 1978, Werner Arber, (Biozentrum der Universitat, Basel, Switzerland), Dan Nathans and
AB  - Hamilton Smith (both at Johns Hopkins University School of Medicine, Baltimore, Maryland, USA)
AB  - were awarded the Nobel Prize in Physiology or Medicine for the discovery of "restriction
AB  - enzymes and their application to problems of molecular genetics".  Almost immediately, the
AB  - application of these enzymes to genetics led to "new and far reaching results".  In fact, it
AB  - is hard to imagine what the biological sciences would look like today without restriction
AB  - maps, cloning and the ability to alter genes at will, to name just a few everyday tools of the
AB  - trade.  But how did this crucial discovery come about?
ER  -

TY  - JOUR
AU  - Kong, C.
AU  - Wang, L.
AU  - Li, P.
AU  - Qu, Y.
AU  - Tang, H.
AU  - Wang, J.
AU  - Zhou, H.
AU  - Ma, Q.
AU  - Zhou, J.
AU  - Xu, P.
TI  - Genome Sequence of Dyella ginsengisoli Strain LA-4, an Efficient Degrader of Aromatic Compounds.
JO  - Genome Announcements
PY  - 2013
SP  - e00961
EP  - e00913
VL  - 1
AB  - Dyella ginsengisoli strain LA-4 can efficiently degrade environmental pollutants  such as
AB  - biphenyl and azo dyes. Here, we present a 4.55-Mb draft genome sequence
AB  - of strain LA-4, which may provide further insights into the molecular mechanism
AB  - in environmental pollution remediation.
ER  -

TY  - JOUR
AU  - Kong, H.
TI  - Characterization of a new restriction-modification system, the BcgI system of Bacillus coagulans.
JO  - Ph.D. Thesis, Boston University
PY  - 1998
SP  - 1
EP  - 130
AB  - The BcgI and other BcgI-like restriction endonucleases differ from other types of
AB  - endonucleases in that they cleave double-stranded DNA on both sides of their recognition
AB  - sequences to excise a short fragment in the presence of Mg++ and S-adenosylmethionine.  To
AB  - understand the relationship between BcgI-like enzymes and the classic types of enzymes, the
AB  - functional organization and enzymatic properties of BcgI of Bacillus coagulans were analyzed.
AB  - The BcgI restriction-modification system is a bifunctional protein complex which can cleave or
AB  - methylate DNA.  The dual cleavage/methylation activities are dependent on the methylation
AB  - state of its DNA substrate.  BcgI cleaves unmethylated DNA only; however, it methylates
AB  - hemimethylated DNA preferentially.  The 71.6-kDa A subunit of BcgI contains two conserved
AB  - m6A-methyltransferase motifs, which form a hydrophobic pocket for AdoMet.  AdoMet serves as
AB  - allosteric activator for both cleavage and methylation reactions.  By mutational analysis, the
AB  - endonuclease activity of BcgI has been assigned to the amino-terminal half of the A subunit,
AB  - and a putative endonuclease motif, PE...EXK, has also been identified.  Substitutions in the
AB  - endonuclease motif of conserved charged residues by Ala completely abolish DNA cleavage
AB  - activity of BcgI, but have no effect on DNA methylation activity, suggesting this motif is
AB  - most likely the endonuclease active site of BcgI.  While the A subunit serves as the
AB  - restriction/methylation subunit, the 39.2-kDa B subunit is likely to be the specificity
AB  - subunit.  This suggestion is based on the required participation of the B subunit in the
AB  - methyltransferase and endonuclease reactions and its structural similarity with the S subunit
AB  - of type I R-M systems.  The stoichiometry of BcgI R-M system is one S subunit, which
AB  - determines the recognition sequence of substrate DNA, and two RM subunits which cleave (or
AB  - methylate) its substrate bilaterally.  BcgI forms a hexamer of (RM)4S2 in solution.  The
AB  - hexamer contains two functional trimer units of (RM)2S1, and may be capable of interacting
AB  - with two recognition sequences.  Indeed, the BcgI enzyme cleaves DNA substrates containing two
AB  - recognition sequences much more efficiently than substrates containing a single sequence.
ER  -

TY  - JOUR
AU  - Kong, H.
TI  - Analyzing the functional organization of a novel restriction modification system, the BcgI system.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 823
EP  - 832
VL  - 279
AB  - BcgI is a novel, multi-subunit, restriction-modification system that differs from all the
AB  - other types of R-M system in its genetic and functional organization.  The holoenzyme contains
AB  - two diferent subunits, BcgI A and BcgI B.  Both are required for endonuclease and
AB  - methyltransferase activities.  Here, we show that the endonuclease activity is mediated by the
AB  - N-terminal portion of the A subunit.  We made this assignment by mutational analysis.  The
AB  - analytic strategy involved three steps.  First, the methyltransferase activity was inactivated
AB  - by site-directed mutagenesis of a conserved methyltransferase motif also found in the A
AB  - subunit.  One of the R+M- mutants could not methylate DNA but was still able to cleave it,
AB  - therefore expression of this mutant gene was lethal to the host.  This lethal phenotype
AB  - allowed the selective isolation of cleavage-deficient mutations in a second round of random
AB  - mutagenesis in this mutant background.  The R- mutations were all located in the N-terminal
AB  - portion of the A subunit.  There are five potential endonuclease motifs within this region.
AB  - Conserved acidic residues in each of these motifs were substituted with alanine by
AB  - site-directed mutagenesis of the wild-type A gene.  The results identified one motif,
AB  - P52E53-(X)12-E66D67K68, as the probable endonuclease active-site.  Further support for this
AB  - assignment was obtained by another round of site-directed mutagenesis directed to residues
AB  - surrounding this motif.  The results showed that DNA cleavage activity was mediated by the
AB  - predicted, conserved residues, and not any of the surrounding non-conserved residues.  One
AB  - mutant protein, BcgI-E53A, with a single amino acid substitution decreased the DNA cleavage
AB  - activity at least 700-fold.  Our present model for the functional organization of BcgI locates
AB  - both endonuclease and methyltransferase domains in the A subunit, with the target recognition
AB  - domain located in the B subunit.
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Chen, Z.
TI  - Isolation and identification of restriction endonuclease BstFI.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 7205
EP  - 7205
VL  - 15
AB  - BstFI, an isoschizomer of HindIII, has been purified from Bacillus stearothermophilus FH58
AB  - isolated from the soil of the campus of Fudan University. Sequencing data show that the
AB  - cleavage site of BstFI is A/AGCTT, the same as HindIII. 10,000 units BstFI can be obtained
AB  - from each gram wet w. of cells. BstFI is active over a temperature range from 37C to 65C.  The
AB  - optimal temperature for its action is 55C. The optimal pH and ionic concentration of the assay
AB  - buffer for the optimum activity of BstFI is 7.0 -7.5 and 50-100 mM NaCl, respectively.  BstFI
AB  - is very stable during incubation at 45C for as long as 10 hrs., but loses its activity easily
AB  - at 50C.
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Lin, L.F.
AU  - Porter, N.
AU  - Stickel, S.
AU  - Byrd, D.
AU  - Posfai, J.
AU  - Roberts, R.J.
TI  - Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3216
EP  - 3223
VL  - 28
AB  - Helicobacter pylori is a gram-negative bacterium, which colonizes the gastric mucosa of
AB  - humans and is implicated in a wide range of gastroduodenal diseases. The genomic sequences of
AB  - two H. pylori strains, 26695 and J99, have been published recently. About two dozen potential
AB  - restriction-modification (R-M) systems have been annotated in both genomes, which is far above
AB  - the average number of R-M systems in other sequenced genomes. Here we describe a functional
AB  - analysis of the 16 putative Type II R-M systems in the H. pylori J99 genome. To express
AB  - potentially toxic endonuclease genes, a unique vector was constructed, which features
AB  - repression and antisense transcription as dual control elements. To determine the methylation
AB  - activities of putative DNA methyltransferases, we developed polyclonal antibodies able to
AB  - detect DNA containing N6-methyladenine or N4-methylcytosine. We found that <30% of the
AB  - potential Type II R-M systems in H. pylori J99 strain were fully functional, displaying both
AB  - endonuclease and methyltransferase activities. Helicobacter pylori may maintain a variety of
AB  - functional R-M systems, which are believed to be a primitive bacterial 'immune' system, by
AB  - alternatively turning on/off a subset of numerous R-M systems.
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Morgan, R.D.
AU  - Chen, Z.
TI  - A new type II restriction endonuclease, BsmAI, from Bacillus stearothermophilus.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 686
EP  - 686
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Morgan, R.D.
AU  - Chen, Z.
TI  - Identification of a new type II restriction endonuclease BsaAI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 2832
EP  - 2832
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Morgan, R.D.
AU  - Maunus, R.E.
AU  - Schildkraut, I.
TI  - A unique restriction endonuclease, BcgI, from Bacillus coagulans.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 987
EP  - 991
VL  - 21
AB  - We have purified and characterized a new restriction endonuclease, BcgI, which has properties
AB  - unlike those of the three recognized classes of restriction enzymes. BcgI was isolated from
AB  - Bacillus coagulans, and it recognizes the sequence CGAN6TGC. BcgI cleaves double stranded DNA
AB  - on both strands upstream and downstream of the recognition sequence, so that the recognition
AB  - sequence is released as a 34-base pair fragment with 2-base 3'-extensions. Mg++ and
AB  - S-adenosylmethionine are required for cleavage. Sinefungin, a structural analogue of AdoMet
AB  - which generally inhibits methylase activity, can replace AdoMet in the cleavage reaction. The
AB  - apparent binding constant Kapp for AdoMet is about 100 nM, while the Kapp for sinefungin is
AB  - about 500 nM.
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Roemer, S.E.
AU  - Waite-Rees, P.A.
AU  - Benner, J.S.
AU  - Wilson, G.G.
AU  - Nwankwo, D.O.
TI  - Characterization of BcgI, a new kind of restriction-modification system.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 683
EP  - 690
VL  - 269
AB  - The BcgI restriction enzyme from Bacillus coagulans is unusual in that it cleaves on both
AB  - sides of its recognition site, CGAN6TGC, releasing a fragment that includes the site and
AB  - several bases on each side. We report the organization and nucleotide sequences of the genes
AB  - for the BcgI restriction-modification system and the properties of the proteins that they
AB  - encode. The system comprises two adjacent, similarly oriented genes. The proximal gene, bcgIA,
AB  - codes for a 637-amino acid protein (molecular mass = 71.6 kDa) that resembles certain m6
AB  - A-specific DNA-methyltransferases, particularly those that constitute the modification subunit
AB  - of type I restriction-modification systems. The distal gene bcgIB, codes for a 341-amino acid
AB  - protein (molecular mass = 39.2 kDa) that resembles none of the sequences in the sequence data
AB  - bases. The two genes overlap by several nucleotides. Alone, neither protein restricts or
AB  - modifies DNA, but, together, they form a complex in the proportion A2B that does both. DNA
AB  - binding assays showed that the DNA-protein complex can be formed only in the presence of both
AB  - subunits, suggesting that the association of inactive subunits generates the active BcgI
AB  - enzyme that can bind DNA and then either cleaves or methylates at target site.
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Smith, C.L.
TI  - Does BcgI, a unique restriction endonuclease, require two recognition sites for cleavage?
JO  - Biol. Chem.
PY  - 1998
SP  - 605
EP  - 609
VL  - 379
AB  - BcgI is a multi-subunit restriction-modification complex.  BcgI prefers pBR322 DNA over pUC19
AB  - in a DNA cleavage reaction. Linearized pBR322 contains two BcgI recognition sites and pUC19
AB  - has only one site.  To test whether two target sites are required for BcgI cleavage, one of
AB  - the two sites in pBR322 was deleted, and as a result pBR322-1 became a poor substrate for
AB  - BcgI.  Conversely, adding a BcgI site to pUC19 makes it a much better substrate for BcgI
AB  - cleavage.  In addition, the BcgI (R-M) complex forms a heterohexamer in solution that is
AB  - capable of interacting with two recognition sites.  Our results suggest that BcgI requires two
AB  - recognition sites for cleavage.
ER  -

TY  - JOUR
AU  - Kong, H.
AU  - Smith, C.L.
TI  - Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, BcgI.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3687
EP  - 3692
VL  - 25
AB  - The BcgI restriction-modification system consists of two subunits, A and B.  It is a
AB  - bifunctional protein complex which can cleave or methylate DNA.  The regulation of these
AB  - competing activities is determined by the DNA substrates and cofactors.  BcgI is an active
AB  - endonuclease and a poor methyltransferase on unmodified DNA substrates.  In contrast, BcgI is
AB  - an active methyltransferase and an inactive endonuclease on hemimethylated DNA substrates.
AB  - The cleavage and methylation reactions share cofactors.  While BcgI requires Mg2+ and
AB  - S-adenosyl methionine (AdoMet) for DNA cleavage, its methylation reaction requires only AdoMet
AB  - and yet is significantly stimulated by Mg2+.  Site-directed mutagenesis was carried out to
AB  - investigate the relationship between AdoMet binding and BcgI DNA cleavage/methylation
AB  - activities.  Most substitutions of conserved residues forming the AdoMet binding pocket in the
AB  - A subunit abolished both methylation and cleavage activities, indicating that AdoMet binding
AB  - is an early common step required for both cleavage and methylation.  However, one mutation
AB  - (Y439A) abolished only the methylation activity, not the DNA cleavage activity.  This mutant
AB  - protein was purified and its methylation, cleavage and AdoMet binding activities were tested
AB  - in vitro.  BcgI-Y439A had no detectable methylation activity, but it retained 40% of the
AB  - AdoMet binding and DNA cleavage activities.
ER  -

TY  - JOUR
AU  - Kong, J.
AU  - Gu, X.
AU  - Ma, G.
TI  - The characterization of pJW566 from L. lactis subsp. cremoris W56.
JO  - Wei Sheng Wu Xue Bao
PY  - 2001
SP  - 542
EP  - 547
VL  - 41
AB  - The plasmid pJW566 was isolated from L. lactis subsp. cremoris W56, one strain for Danish
AB  - chadder mixed starter cultures. The strain containing
AB  - plasmid pJW566 showed resistance against three common phages species
AB  - 936, c2 and P335 worldwide. It was found that pJW566 encoded for an
AB  - restriction and modification system, and showed strong resistance to
AB  - phage CHCP412 when it was introduced into the industrial strain L.
AB  - lactis CHCC2281 in milk medium. The endonuclease activity analysis
AB  - indicated that the endonuclease required Mg2+, ATP, and was stimulated
AB  - by AdoMet.
ER  -

TY  - JOUR
AU  - Kong, J.
AU  - Jiang, H.
AU  - Li, B.
AU  - Zhao, W.
AU  - Li, Z.
AU  - Zhu, S.
TI  - Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat.
JO  - Genome Announcements
PY  - 2016
SP  - e00024
EP  - e00016
VL  - 4
AB  - Pseudomonas syringae pv. lapsa is a pathovar of Pseudomonas syringae that can infect wheat.
AB  - The complete genome of P. syringae pv. lapsa strain ATCC 10859
AB  - contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16
AB  - rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome
AB  - revealed several gene clusters that are related to pathogenesis and virulence.
ER  -

TY  - JOUR
AU  - Kong, J.
AU  - Josephsen, J.
TI  - The ability of the plasmid-encoded restriction and modification system LlaBIII to protect Lactococcus lactis against bacteriophages.
JO  - Lett. Appl. Microbiol.
PY  - 2002
SP  - 249
EP  - 253
VL  - 34
AB  - Aims: To investigate the potential of the plasmid-encoded restriction and modification (R/M)
AB  - system LlaBIII to protect Lactococcus lactis
AB  - against bacteriophages during milk fermentations.
AB  - Methods and Results: The R/M system LlaBIII on plasmid pJW566 was
AB  - cloned with a chloramphenicol cassette, resulting in plasmid pJK1. When
AB  - introduced into L. lactis strains, pJK1 conferred increased phage
AB  - resistance against the three most common lactococcal phage species 936,
AB  - c2, and P335 and three unclassified industrial phages. The growth of
AB  - the strains in RSM was not affected by the presence of plasmid pJK1.
AB  - Conclusions: The plasmid-encoded R/M system LlaBIII has great
AB  - ability to protect L. lactis strains against bacteriophages in milk
AB  - fermentations.
AB  - Significance and Impact of the Study: This study evaluates the
AB  - ability of the LlaBIII R/M system to function as a phage defence
AB  - mechanism which is an essential step prior to considering utilizing it
AB  - for improving starter cultures.
ER  -

TY  - JOUR
AU  - Kong, J.
AU  - Josephsen, J.
AU  - Ma, G.-R.
TI  - The resistance conferred by the R/M system LlaBIII against bacteriophages.
JO  - Wei Sheng Wu Xue Bao
PY  - 2002
SP  - 246
EP  - 250
VL  - 42
AB  - LlaBIII, isolated from the naturally occurring plasmid pJW566 from Lactococcus lactis subsp.
AB  - cremoris W56, encoded a restriction and modification (R/M) system. The plasmid pJK1 carrying
AB  - the R/M system LlaBIII was transformed into L. lactis IL1403 with type I R/M system located on
AB  - chromosome and the strain MG1614(pAW601) with AbiS gene on plasmid pAW601, respectively. The
AB  - transformants obtained showed stacking resistance against bacteriophages. The plasmid pJK1 was
AB  - transformed into industrial strains L. lactis SMQ86 and CHCC2281, the transformants showed the
AB  - EOP of the bacteriophages decreased by 10-3 and 10-5, respectively. The results indicated that
AB  - the R/M system LlaBIII could protect strains from bacteriophages in dairy fermentation.
ER  -

TY  - JOUR
AU  - Kong, J.
AU  - Josephsen, J.
AU  - Ma, G.R.
TI  - Cloning and structure analysis of a restriction and modification system, LlaBIII from Lactococcus lactis subsp. cremoris W56.
JO  - Sheng Wu Gong Cheng Xue Bao
PY  - 2001
SP  - 663
EP  - 668
VL  - 17
AB  - A 22.4 kb naturally occurring plasmid pJW566, isolated from L. lactis W56, was found to encode
AB  - an R/M system named LlaBIII. The LlaBIII R/M system was isolated on a chloramphenicol
AB  - resistant derivative of plasmid pJW566, resulting in a plasmid pJK1. Subcloning analysis
AB  - showed that the LlaBIII determinant was located on a 5 kb HindIII-Sph I fragment. The fragment
AB  - was sequenced. It contained a single open reading frame (ORF), corresponding to a protein of
AB  - 1584 or 1576 aa. In the deduced amino acid sequence seven helicase motifs characteristic of
AB  - endonuclease type I and type III and a conserved catalysis motif X in the R subunits of type I
AB  - R/M systems were located in the N-terminus, followed by four conserved motifs found in DNA
AB  - N6-adenine methyltransferases. The C-terminus of the deduced amino acid sequence showed no
AB  - homology to known R/M systems. Therefore, this polypeptide encoded by LlaBIII is a
AB  - multifunctional protein possessing putative DNA recognition, methylation and restriction
AB  - activities.
ER  -

TY  - JOUR
AU  - Kong, N.
AU  - Davis, M.
AU  - Arabyan, N.
AU  - Huang, B.C.
AU  - Weis, A.M.
AU  - Chen, P.
AU  - Thao, K.
AU  - Ng, W.
AU  - Chin, N.
AU  - Foutouhi, S.
AU  - Foutouhi, A.
AU  - Kaufman, J.
AU  - Xie, Y.
AU  - Storey, D.B.
AU  - Weimer, B.C.
TI  - Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome  Project.
JO  - Genome Announcements
PY  - 2017
SP  - e00518
EP  - e00517
VL  - 5
AB  - Salmonella is a common food-associated bacterium that has substantial impact on worldwide
AB  - human health and the global economy. This is the public release of
AB  - 1,183 Salmonella draft genome sequences as part of the 100K Pathogen Genome
AB  - Project. These isolates represent global genomic diversity in the Salmonella
AB  - genus.
ER  -

TY  - JOUR
AU  - Kong, S.L.
AU  - Liu, X.Y.
AU  - Fu, L.W.
AU  - Yu, X.C.
AU  - An, C.C.
TI  - I-PfoP3I: A Novel Nicking HNH Homing Endonuclease Encoded in the Group I Intron of the DNA Polymerase Gene in Phormidium foveolarum Phage Pf-WMP3.
JO  - PLoS ONE
PY  - 2012
SP  - e43738
EP  - e43738
VL  - 7
AB  - Homing endonucleases encoded in a group I self-splicing intron in a protein-coding gene in
AB  - cyanophage genomes have not been reported, apart
AB  - from some free-standing homing edonucleases. In this study, a nicking
AB  - DNA endonuclease, I-PfoP3I, encoded in a group IA2 intron in the DNA
AB  - polymerase gene of a T7-like cyanophage Pf-WMP3, which infects the
AB  - freshwater cyanobacterium Phormidium foveolarum is described. The
AB  - Pf-WMP3 intron splices efficiently in vivo and self-splices in vitro
AB  - simultaneously during transcription. I-PfoP3I belongs to the HNH family
AB  - with an unconventional C-terminal HNH motif. I-PfoP3I nicks the
AB  - intron-minus Pf-WMP3 DNA polymerase gene more efficiently than the
AB  - Pf-WMP4 DNA polymerase gene that lacks any intervening sequence in
AB  - vitro, indicating the variable capacity of I-PfoP3I. I-PfoP3I cleaves 4
AB  - nt upstream of the intron insertion site on the coding strand of EXON 1
AB  - on both intron-minus Pf-WMP3 and Pf-WMP4 DNA polymerase genes. Using an
AB  - in vitro cleavage assay and scanning deletion mutants of the intronless
AB  - target site, the minimal recognition site was determined to be a 14 bp
AB  - region downstream of the cut site. I-PfoP3I requires Mg2+, Ca2+ or Mn2+
AB  - for nicking activity. Phylogenetic analysis suggests that the intron
AB  - and homing endonuclease gene elements might be inserted in Pf-WMP3
AB  - genome individually after differentiation from Pf-WMP4. To our
AB  - knowledge, this is the first report of the presence of a group I
AB  - self-splicing intron encoding a functional homing endonuclease in a
AB  - protein-coding gene in a cyanophage genome.
ER  -

TY  - JOUR
AU  - Kong, W.J.
AU  - Yan, Y.C.
AU  - Li, X.Y.
AU  - Liu, Z.Y.
TI  - Draft Genome Sequence of Bacillus velezensis PEBA20, a Strain with a Plant Growth-Promoting Effect and Biocontrol Potential.
JO  - Genome Announcements
PY  - 2018
SP  - e00286
EP  - e00218
VL  - 6
AB  - Bacillus velezensis PEBA20 is a poplar endophyte with biocontrol activities and plant
AB  - growth-promoting effects. The genome of B. velezensis PEBA20 was sequenced
AB  - and the draft genome assembled, with a length of 4,249,176 bp and 4,487 genes.
ER  -

TY  - JOUR
AU  - Konishi, K.
AU  - Kumagai, T.
AU  - Sakasegawa, S.I.
AU  - Tamura, T.
TI  - Complete Genome Sequence of Burkholderia stabilis FERMP-21014.
JO  - Genome Announcements
PY  - 2017
SP  - e00636
EP  - e00617
VL  - 5
AB  - Cholesterol esterase (EC 3.1.1.13) was identified in a bacterium, Burkholderia stabilis strain
AB  - FERMP-21014. Here, we report the complete genome sequence of B.
AB  - stabilis FERMP-21014, which has been used in the commercial production of
AB  - cholesterol esterase. The genome sequence information may be useful for improving
AB  - production levels of cholesterol esterase.
ER  -

TY  - JOUR
AU  - Konstantinidis, K.T.
AU  - DeLong, E.F.
TI  - Genomic patterns of recombination, clonal divergence and environment in marine microbial populations.
JO  - ISME J.
PY  - 2008
SP  - 1052
EP  - 1065
VL  - 2
AB  - Microorganisms represent the largest reservoir of biodiversity on Earth,
AB  - both in numbers and total genetic diversity, but it remains unclear
AB  - whether this biodiversity is organized in discrete units that correspond
AB  - to ecologically coherent species. To further explore this question, we
AB  - examined patterns of genomic diversity in sympatric microbial populations.
AB  - Analyses of a total of approximately 200 Mb of microbial community genomic
AB  - DNA sequence recovered from 4000 m depth in the Pacific Ocean revealed
AB  - discrete sequence-defined populations of Bacteria and Archaea, with
AB  - intrapopulation genomic sequence divergence ranging from approximately 1%
AB  - to approximately 6%. The populations appeared to be maintained, at least
AB  - in part, by intrapopulation genetic exchange (homologous recombination),
AB  - although the frequency of recombination was estimated to be about three
AB  - times lower than that observed previously in thermoacidophilic archaeal
AB  - biofilm populations. Furthermore, the genotypes of a given population were
AB  - clearly distinguishable from their closest co-occurring relatives based on
AB  - their relative abundance in situ. The genetic distinctiveness and the
AB  - matching sympatric abundances imply that these genotypes share similar
AB  - ecophysiological properties, and therefore may represent fundamental units
AB  - of microbial diversity in the deep sea. Comparisons to surface-dwelling
AB  - relatives of the Sargasso Sea revealed that distinct sequence-based
AB  - clusters were not always detectable, presumably due to environmental
AB  - variations, further underscoring the important relationship between
AB  - environmental contexts and genetic mechanisms, which together shape and
AB  - sustain microbial population structure.
ER  -

TY  - JOUR
AU  - Kontur, W.S.
AU  - Schackwitz, W.S.
AU  - Ivanova, N.
AU  - Martin, J.
AU  - Labutti, K.
AU  - Deshpande, S.
AU  - Tice, H.N.
AU  - Pennacchio, C.
AU  - Sodergren, E.
AU  - Weinstock, G.M.
AU  - Noguera, D.R.
AU  - Donohue, T.J.
TI  - Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7016
EP  - 7017
VL  - 194
AB  - The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been
AB  - revised, and the annotation of the entire genomic sequence, including
AB  - both chromosomes and the five plasmids, has been updated. Errors in the
AB  - originally published sequence have been corrected, and approximately 11% of the
AB  - coding regions in the original sequence have been affected by the revised
AB  - annotation.
ER  -

TY  - JOUR
AU  - Koo, H.
AU  - Basu, M.K.
AU  - Crowley, M.
AU  - Aislabie, J.
AU  - Bej, A.K.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain Ant30-3, a Psychrotolerant Bacterium with Biodegradative Attribute Isolated from Antarctica.
JO  - Genome Announcements
PY  - 2014
SP  - e00522
EP  - e00514
VL  - 2
AB  - Pseudomonas sp. strain Ant30-3, isolated from fuel-contaminated Antarctic soil, exhibited
AB  - distinctive psychrotolerant attributes and the potential for degrading
AB  - aromatic hydrocarbon compounds at cold temperatures. We report here the 6.14-Mb
AB  - draft genome of Ant30-3, which will provide insights into the genomic basis for
AB  - the psychrotolerant and biodegradative properties of this bacterium.
ER  -

TY  - JOUR
AU  - Koo, H.
AU  - Ptacek, T.
AU  - Crowley, M.
AU  - Swain, A.K.
AU  - Osborne, J.D.
AU  - Bej, A.K.
AU  - Andersen, D.T.
TI  - Draft Genome Sequence of Hymenobacter sp. Strain IS2118, Isolated from a Freshwater Lake in Schirmacher Oasis, Antarctica, Reveals Diverse Genes for  Adaptation to Cold Ecosystems.
JO  - Genome Announcements
PY  - 2014
SP  - e00739
EP  - e00714
VL  - 2
AB  - Hymenobacter sp. IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica,
AB  - produces extracellular polymeric substance (EPS) and manifests
AB  - tolerance to cold, UV radiation (UVR), and oxidative stress. We report the
AB  - 5.26-Mb draft genome of strain IS2118, which will help us to understand its
AB  - adaptation and survival mechanisms in Antarctic extreme ecosystems.
ER  -

TY  - JOUR
AU  - Koo, H.
AU  - Strope, B.M.
AU  - Kim, E.H.
AU  - Shabani, A.M.
AU  - Kumar, R.
AU  - Crowley, M.R.
AU  - Andersen, D.T.
AU  - Bej, A.K.
TI  - Draft Genome Sequence of Janthinobacterium sp. Ant5-2-1, Isolated from Proglacial Lake Podprudnoye in the Schirmacher Oasis of East Antarctica.
JO  - Genome Announcements
PY  - 2016
SP  - e01600
EP  - e01615
VL  - 4
AB  - Janthinobacterium sp. Ant5-2-1, isolated from the Schirmacher Oasis of East Antarctica,
AB  - produces a purple-violet pigment, manifests diverse energy metabolism
AB  - abilities, and tolerates cold, ultraviolet radiation, and other environmental
AB  - stressors. We report here the 6.19-Mb draft genome of strain Ant5-2-1, which will
AB  - help understand its survival mechanisms in extreme Antarctic ecosystems.
ER  -

TY  - JOUR
AU  - Koob, M.
TI  - Conferring new cleavage specificities of restriction endonucleses.
JO  - Methods Enzymol.
PY  - 1992
SP  - 321
EP  - 329
VL  - 216
AB  - Detailed protocols for Achilles Heel cleavage are presented.
ER  -

TY  - JOUR
AU  - Koob, M.
AU  - Burkiewicz, A.
AU  - Kur, J.
AU  - Szybalski, W.
TI  - RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5831
EP  - 5836
VL  - 20
AB  - We have developed a novel version of the Achilles' Cleavage (AC) reaction in which virtually
AB  - any restriction site on DNA of any size can be converted to a unique cleavage site. We first
AB  - polymerized RecA protein on a synthetic oligodeoxyribonucleotide (oligo) in the presence of a
AB  - nonhydrolyzable ATP analogue to generate oligo:RecA nucleoprotein filaments. These filaments
AB  - were then incubated with plasmid or intact chromosomal DNA from Saccharomyces cerevisiae to
AB  - form stable complexes in the yeast LEU2 gene at the target sequence identical (or
AB  - complementary) to that of the oligo. When HhaII (HinfI) methyltransferase (M.HhaII) was added,
AB  - all of the recognition sites for HhaII with the exception of the one protected by the RecA
AB  - filament were methylated and thus no longer cleaved by the cognate restriction endonuclease
AB  - (HinfI). After inactivation of the RecA and the M.HhaII, HinfI was used to efficiently cleave
AB  - the plasmid or chromosome specifically at the targeted restriction site. Since oligos specific
AB  - for any sequence can be easily synthesized and the other reagents necessary to perform
AB  - RecA-mediated AC (RecA-AC) reactions on both plasmids and intact chromosomes are readily
AB  - available, this procedure can be applied immediately to the precise dissection and analysis of
AB  - genomic DNA from any source and to any other research problem requiring efficient, highly
AB  - specific cleavage of DNA at predetermined sites.
ER  -

TY  - JOUR
AU  - Koob, M.
AU  - Grimes, E.
AU  - Szybalski, W.
TI  - Conferring operator specificity on restriction endonucleases.
JO  - Science
PY  - 1988
SP  - 1084
EP  - 1086
VL  - 241
AB  - Mapping and manipulation of very large genomes, including the human genome,
AB  - would be facilitated by the availability of a DNA cleavage method with very
AB  - high site specificity.  Therefore, a general method was devised that extends
AB  - the effective recognition sequences well beyond the present 8-base pair limit
AB  - by combining the specificity of the restriction endonuclease with that of
AB  - another sequence-specific protein that binds tightly to DNA.  It was shown that
AB  - the tightly binding lac or lamba repressor protects a restriction site within
AB  - the operator from specific modification methylases, M.HhaI or M.HphI, while all
AB  - other similar sites are methylated and thus rendered uncleavable.  A plasmid
AB  - containing a symmetric lac operator was specifically cleaved by HhaI, only at
AB  - the site within the operator, after M.HhaI methylation in the presence of the
AB  - lac repressor, whereas the remaining 31 HhaI sites on this plasmid were
AB  - methylated and thus not cleaved.  Analogous results were obtained with the
AB  - HaeII site within the lac operator which was similarly protected by the lac
AB  - repressor, and with the HphI site within the phage lambda OL operator, which
AB  - was protected by lambda repressor from M.HphI methylation.
ER  -

TY  - JOUR
AU  - Koob, M.
AU  - Grimes, E.
AU  - Szybalski, W.
TI  - Conferring new specificity upon restriction endonucleases by combining repressor-operator interaction and methylation.
JO  - Gene
PY  - 1988
SP  - 165
EP  - 167
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Koob, M.D.
TI  - Achilles' cleavage:  A general approach for conferring expanded specificities on restriction endonucleases.
JO  - Diss. Abstr.
PY  - 1991
SP  - 5161B
EP  - 5161B
VL  - 51
AB  - Mapping and manipulation of very large genomes would be facilitated by the
AB  - availability of a DNA cleavage method with a very high site specificity.  I
AB  - have devised a general method for efficiently extending the effective
AB  - recognition sequence of a restriction endonuclease well beyond its natural
AB  - limits.  The key to this process, which I call Achilles' Cleavage (AC), is
AB  - methylation of the DNA substrate in the presence of a DNA-binding molecule that
AB  - forms sequence-specific complexes capable of excluding the methyltransferase
AB  - (MTase).  Cleavable restriction sites remain only at those sites where the
AB  - recognition sites for the cognate restriction enzyme and the DNA-binding
AB  - molecule overlap.  The lac repressor and its ideal, symmetric binding site
AB  - (lacOs), which contains the recognition sites for both HaeII (5'-AGCGCT) and
AB  - HhaI (5'-GCGC), were used as a model system for the development of this
AB  - approach.  Plasmid DNA containing lacOs was methylated by HhaI MTase (M-HhaI)
AB  - in the presence of LacI.  After inactivation of M.HhaI and lacI, HhaI and HaeII
AB  - were used to completely and specifically cleave the plasmid at the lacOs
AB  - sequence.  LacI-mediated AC of a lambda genome containing lacOs produced
AB  - similar results.  In order to test this approach on the large genomes for which
AB  - it was designed, protocols were developed for the efficient methylation and
AB  - digestion of intact chromosomal DNA embedded in agarose microbeads.  Model
AB  - genomes were generated by introducing lacOs into the 4.7-Mb circular genome of
AB  - Escherichia coli and into one of the 16 chromosomes in the 15-Mb genome of
AB  - Saccharomyces cerevisiae.  Subsequent treatment with the AC protocol resulted
AB  - in complete cleavage of these genomes exclusively at the inserted lacOs.  These
AB  - experiments demonstrate the feasibility of using the AC approach to efficiently
AB  - extend the specificity of restriction enzymes and create new tools for the
AB  - mapping precise molecular dissection of multimegabase genomes.
ER  -

TY  - JOUR
AU  - Koonin, E.V.
TI  - A protein splice-junction motif in hedgehog family proteins.
JO  - Trends Biochem. Sci.
PY  - 1995
SP  - 141
EP  - 142
VL  - 20
AB  - Protein splicing is a recently discovered, complex post-translational
AB  - modification that includes two concerted proteolytic cleavages and one ligation reaction,
AB  - and produces two distinct, functional proteins from a single polypeptide.  By analogy with
AB  - introns and exons in RNA precursors, the internal protein that is excised from the
AB  - translation product is called an intein, whereas the two terminal portions, when ligated,
AB  - form a fusion protein called extein.  So far, the intein-extein organization has been
AB  - observed in about ten proteins from yeast, bacteria and Archaea; in most of these cases, the
AB  - inteins are inserted within or near nucleotide-binding domains.  Protein splicing is thought
AB  - to be an autocatalytic process, since it can occur in heterologous systems; for example,
AB  - intein-containing proteins from Mycobacterium and Thermococcus have been synthesized
AB  - in Escherichia coli, and protein splicing has been demonstrated with the purified intein-
AB  - containing DNA polymerase from Pyrococcus.
ER  -

TY  - JOUR
AU  - Kopecka, H.
TI  - A rapid purification method of restriction endonucleases from Haemophilus strains.
JO  - Biochim. Biophys. Acta
PY  - 1975
SP  - 109
EP  - 120
VL  - 391
AB  - A simple and rapid method of purification of restriction endonucleases from
AB  - different Haemophilus strains is presented.  By this method highly purified and
AB  - stable enzymes can be obtained.  Separation of different restriction activities
AB  - present in the same strain is possible.  This method was so far successfully
AB  - used with Haemophilus influenzae, Haemophilus parainfluenzae and Haemophilus
AB  - aegyptius strains.  The main advantages over previously published procedures
AB  - reside in the simplification of certain purification steps (for instance the
AB  - BioGel A 0.5 M filtration is replaced by a hydroxyapatite batch step),
AB  - elimination of exonuclease activity by fractionation with (NH4)2SO4, separation
AB  - of different restriction activities by phosphocellulose chromatography,
AB  - application of this method to various strains and high purification degree of
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Kopel, M.
AU  - Helbert, W.
AU  - Henrissat, B.
AU  - Doniger, T.
AU  - Banin, E.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain PLSV, an Ulvan-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01257
EP  - e01214
VL  - 2
AB  - We present the draft genome sequence of Pseudoalteromonas sp. strain PLSV, isolated from the
AB  - feces of an Aplysia sea slug. The addition of the PLSV genome
AB  - to the existing genomes of three other ulvan-degrading bacterial species will
AB  - enhance our understanding of ulvan utilization.
ER  -

TY  - JOUR
AU  - Kopel, M.
AU  - Helbert, W.
AU  - Henrissat, B.
AU  - Doniger, T.
AU  - Banin, E.
TI  - Draft Genome Sequence of Nonlabens ulvanivorans, an Ulvan-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00793
EP  - e00714
VL  - 2
AB  - Here we report the draft genome sequence of the bacterium Nonlabens ulvanivorans, which was
AB  - recently isolated. To our knowledge, this is the first published genome
AB  - of a characterized ulvan-degrading bacterium. Revealing the ulvan utilization
AB  - pathways may provide access to a vast marine biomass source that has yet to be
AB  - exploited.
ER  -

TY  - JOUR
AU  - Kopel, M.
AU  - Helbert, W.
AU  - Henrissat, B.
AU  - Doniger, T.
AU  - Banin, E.
TI  - Draft Genome Sequences of Two Ulvan-Degrading Isolates, Strains LTR and LOR, That Belong to the Alteromonas Genus.
JO  - Genome Announcements
PY  - 2014
SP  - e01081
EP  - e01014
VL  - 2
AB  - Here, we report the draft genome sequence of two ulvan-degrading Alteromonas spp. isolated
AB  - from the feces of the sea slug, Aplysia. These sequenced genomes display
AB  - a unique ulvan degradation machinery compared with ulvanolytic enzymes previously
AB  - identified in Nonlabens ulvanivorans.
ER  -

TY  - JOUR
AU  - Kopf, M.
AU  - Klahn, S.
AU  - Voss, B.
AU  - Stuber, K.
AU  - Huettel, B.
AU  - Reinhardt, R.
AU  - Hess, W.R.
TI  - Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714.
JO  - Genome Announcements
PY  - 2014
SP  - e00757
EP  - e00714
VL  - 2
AB  - Synechocystis sp. strain PCC 6714 is a unicellular cyanobacterium closely related to the
AB  - popular model organism Synechocystis sp. strain PCC 6803. A combination of
AB  - PacBio SMRT and Illumina GAIIx data results in a highly accurate finished genome
AB  - sequence that provides a reliable resource for further comparative analyses.
ER  -

TY  - JOUR
AU  - Kopke, M.
AU  - Held, C.
AU  - Hujer, S.
AU  - Liesegang, H.
AU  - Wiezer, A.
AU  - Wollherr, A.
AU  - Ehrenreich, A.
AU  - Liebl, W.
AU  - Gottschalk, G.
AU  - Durre, P.
TI  - Clostridium ljungdahlii represents a microbial production platform based on syngas.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 13087
EP  - 13092
VL  - 107
AB  - Clostridium ljungdahlii is an anaerobic homoacetogen, able to ferment
AB  - sugars, other organic compounds, or CO(2)/H(2) and synthesis gas
AB  - (CO/H(2)). The latter feature makes it an interesting microbe for the
AB  - biotech industry, as important bulk chemicals and proteins can be produced
AB  - at the expense of CO(2), thus combining industrial needs with sustained
AB  - reduction of CO and CO(2) in the atmosphere. Sequencing the complete
AB  - genome of C. ljungdahlii revealed that it comprises 4,630,065 bp and is
AB  - one of the largest clostridial genomes known to date. Experimental data
AB  - and in silico comparisons revealed a third mode of anaerobic
AB  - homoacetogenic metabolism. Unlike other organisms such as Moorella
AB  - thermoacetica or Acetobacterium woodii, neither cytochromes nor sodium
AB  - ions are involved in energy generation. Instead, an Rnf system is present,
AB  - by which proton translocation can be performed. An electroporation
AB  - procedure has been developed to transform the organism with plasmids
AB  - bearing heterologous genes for butanol production. Successful expression
AB  - of these genes could be demonstrated, leading to formation of the biofuel.
AB  - Thus, C. ljungdahlii can be used as a unique microbial production platform
AB  - based on synthesis gas and carbon dioxide/hydrogen mixtures.
ER  -

TY  - JOUR
AU  - Korba, B.E.
AU  - Hays, J.B.
TI  - Partially deficient methylation of cytosine in DNA at CCA/TGG sites stimulates genetic recombination of bacteriophage lambda.
JO  - Cell
PY  - 1982
SP  - 531
EP  - 541
VL  - 28
AB  - Lambda bacteriophages grown on arl mutants of Escherichia coli display
AB  - intermediate levels
AB  - of cytosine methylation: less 5-methylcytosine than phages grown on wild-type bacteria but
AB  - more than
AB  - phages grown on dcm mutants, and thus lacking the methylated sequences (Cm5CA/TGG)
AB  - characteristic of E.
AB  - coli K-12 bacteria.  Arl- phages are one twelfth as resistant to EcoRII restriction
AB  - (recognition site CCA/TGG)
AB  - as Arl+ phages, but 40-fold more resistant than Dcm- phages.  Chromatographic analyses
AB  - show the 5-
AB  - methylcytosine content of Arl- DNA to be one third that of Arl+ DNA.  Altered cytosine
AB  - methylation
AB  - frequency correlates with two previously described properties of Arl- phages, increased
AB  - genetic
AB  - recombination and unusual sensitivity of phage DNA to endonuclease S1, which are absent
AB  - in phages grown
AB  - on dcm or dcm arl bacteria.  Methylated/unmethylated heteroduplex DNA prepared in vitro
AB  - (one strand from
AB  - Eco RII-modified phages/one from Dcm- phages) is highly recombinogenic but not S1-
AB  - sensitive.  We
AB  - hypothesize that hemimethylated CCA/TGG sites in Arl- DNA are necessary and sufficient
AB  - for enhanced
AB  - recombination, and necessary but not sufficient for S1 sensitivity.
ER  -

TY  - JOUR
AU  - Korch, C.
TI  - Cross index for improving cloning selectivity by partially filling in 5'-extensions of DNA produced by type II restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3199
EP  - 3220
VL  - 15
AB  - A cross index is presented for using the improved selectivity offered by the
AB  - Hung and Wensink (Nucl. Acids Res. 12, 1863-1874, 1984) method of partially
AB  - filling in 5'-extensions produced by type II restriction endonucleases.   After
AB  - this treatment, DNA fragments which normally cannot be ligated to one another,
AB  - can be joined providing that complementary cohesive ends have been generated.
AB  - The uses of this technique, which include the prevention of DNA fragments (both
AB  - vector and insert) auto-annealing, are discussed.
ER  -

TY  - JOUR
AU  - Korch, C.
AU  - Hagblom, P.
TI  - In-vivo-modified gonococcal plasmid pJD1: A model system for analysis of restriction enzyme sensitivity to DNA modifications.
JO  - Eur. J. Biochem.
PY  - 1986
SP  - 519
EP  - 524
VL  - 161
AB  - The 4207-bp cryptic plasmid (pJD1) of Neisseria gonorrhoeae has 5-methylcytosine bases present
AB  - at several positions in the DNA sequence. Fortuitously, these modified bases lie in the
AB  - recognition sequences of many restriction enzymes.  This feature makes the cryptic plasmid a
AB  - model system for assaying the effect of these modified cytosines on the activities of the
AB  - following restriction endonucleases and their isoschizomers: R.AvaII, R.BamHI, R.BglI,
AB  - R.Fnu4HI, R.HaeII, R.HaeIII, R.HhaI, R.HpaII, R.KpnI, R.MspI, R.NaeI, R.NarI, R.NciI, R.NgoI,
AB  - R.NgoII, and R.Sau96I.  Of particular interest was the finding that methylation of one of the
AB  - external cytosines of the palindrome 5'-CCGG-3' prevented its cleavage by R.MspI, but not by
AB  - R.HpaII as had been suggested by Walder et al. [J. Biol. Chem. (1983) 158,1235-1241]. Shows
AB  - HhaI cleaves hemimethylated GCGm5C and BglI cannot cleave 5'GCCNNNNNGGm5C/3'CGGNNNNNCm5CG.
ER  -

TY  - JOUR
AU  - Korch, C.
AU  - Hagblom, P.
AU  - Normark, S.
TI  - Type III 5-methylcytosine modification of DNA in Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1985
SP  - 1236
EP  - 1237
VL  - 161
AB  - We present here the first report of a type III methyltransferase that modifies a cytosine,
AB  - Neisseria gonorrhoeae 82409/55(pJD1) modifies the first cytosine on only one strand from the
AB  - 5' end of the nonpalindromic sequence: 5'-GGTGA-3' 3'-CCACT-5' m.  We have called this
AB  - modifying activity M.NgoVIII.
AB  - [ The enzyme called NgoVIII in this abstract has been renamed NgoHVIII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Korch, C.
AU  - Hagblom, P.
AU  - Normark, S.
TI  - Sequence-specific DNA modification in Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1983
SP  - 1324
EP  - 1332
VL  - 155
AB  - Neisseria gonorrhoaea 82409/55(pJD1) is postulated to possess six DNA sequence-specific
AB  - cytosine methyltransferases and one DNA sequence-specific N6-adenine methyltransferase.  From
AB  - the DNA sequencing of the plasmid pJD1 (manuscript in preparation) by a modification of the
AB  - Maxam and Gilbert chemical cleavage procedure, the cytosine methylation specificities were
AB  - demonstrated. Five of these methylating enzymes and their respective specificities are M.NgoI
AB  - (5'-PuGmCGCPy-3'), M.NgoII (5'-GGmCC-3'), M.NgoIV (5'-GmCCGGC-3'), M.NgoV
AB  - (5'-GGNNmCC-3'), and M.NgoVII (5'-GmC(C/G)GC-3').  M.NgoVI (5'-GATC-3') does not
AB  - methylate the cytosine of its recognition sequence, in agreement with a detected adenine
AB  - modification.  A biological implication of these different DNA methylating activities is
AB  - discussed.
AB  - [ The enzyme called M.NgoI in this abstract has been renamed M.NgoHIP, Jan/1998. ]
AB  - [ The enzyme called M.NgoII in this abstract has been renamed M.NgoHIIP, Jan/1998. ]
AB  - [ The enzyme called M.NgoIV in this abstract has been renamed M.NgoHIVP, Jan/1998. ]
AB  - [ The enzyme called M.NgoV in this abstract has been renamed M.NgoHVP, Jan/1998. ]
AB  - [ The enzyme called M.NgoVI in this abstract has been renamed M.NgoHVIP, Jan/1998. ]
AB  - [ The enzyme called M.NgoVII in this abstract has been renamed M.NgoHVIIP, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Koren, S.
AU  - Harhay, G.P.
AU  - Smith, T.P.
AU  - Bono, J.L.
AU  - Harhay, D.M.
AU  - McVey, S.D.
AU  - Radune, D.
AU  - Bergman, N.H.
AU  - Phillippy, A.M.
TI  - Reducing assembly complexity of microbial genomes with single-molecule sequencing.
JO  - Genome Biol.
PY  - 2013
SP  - R101
EP  - R101
VL  - 14
AB  - BACKGROUND: The short reads output by first- and second-generation DNA sequencing instruments
AB  - cannot completely reconstruct microbial chromosomes. Therefore, most
AB  - genomes have been left unfinished due to the significant resources required to
AB  - manually close gaps in draft assemblies. Third-generation, single-molecule
AB  - sequencing addresses this problem by greatly increasing sequencing read length,
AB  - which simplifies the assembly problem. RESULTS: To measure the benefit of
AB  - single-molecule sequencing on microbial genome assembly, we sequenced and
AB  - assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267
AB  - complete bacteria and archaea. Our results indicate that the majority of known
AB  - bacterial and archaeal genomes can be assembled without gaps, at finished-grade
AB  - quality, using a single PacBio RS sequencing library. These single-library
AB  - assemblies are also more accurate than typical short-read assemblies and hybrid
AB  - assemblies of short and long reads. CONCLUSIONS: Automated assembly of long,
AB  - single-molecule sequencing data reduces the cost of microbial finishing to $1,000
AB  - for most genomes, and future advances in this technology are expected to drive
AB  - the cost lower. This is expected to increase the number of completed genomes,
AB  - improve the quality of microbial genome databases, and enable high-fidelity,
AB  - population-scale studies of pan-genomes and chromosomal organization.
ER  -

TY  - JOUR
AU  - Korlach, J.
AU  - Turner, S.W.
TI  - Going beyond five bases in DNA sequencing.
JO  - Curr. Opin. Struct. Biol.
PY  - 2012
SP  - 251
EP  - 261
VL  - 22
AB  - DNA sequencing has provided a wealth of information about biological systems, but thus far has
AB  - focused on the four canonical bases, and 5-methylcytosine through
AB  - comparison of the genomic DNA sequence to a transformed four-base sequence
AB  - obtained after treatment with bisulfite. However, numerous other chemical
AB  - modifications to the nucleotides are known to control fundamental life functions,
AB  - influence virulence of pathogens, and are associated with many diseases. These
AB  - modifications cannot be accessed with traditional sequencing methods. In this
AB  - opinion, we highlight several emerging single-molecule sequencing techniques that
AB  - have the potential to directly detect many types of DNA modifications as an
AB  - integral part of the sequencing protocol.
ER  -

TY  - JOUR
AU  - Kornspan, J.D.
AU  - Lysnyansky, I.
AU  - Kahan, T.
AU  - Herrmann, R.
AU  - Rottem, S.
AU  - Nir-Paz, R.
TI  - Genome analysis of a Mycoplasma hyorhinis strain derived from a primary human melanoma cell line.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4543
EP  - 4544
VL  - 193
AB  - The complete genome of Mycoplasma hyorhinis strain MCLD has been sequenced and annotated. This
AB  - genome differs by inversion of a 14.4kb and 3.7kb
AB  - fragments and a deletion of a 9.9kb fragment from M. hyorhinis strain
AB  - HUB-1, isolated from swine respiratory tract. The genome revealed 778 CDSs
AB  - with a limited number of vlp genes encoding for variable surface
AB  - lipoproteins.
ER  -

TY  - JOUR
AU  - Korolev, S.V.
AU  - Samko, O.T.
AU  - Eldarov, M.A.
AU  - Kalugin, A.A.
AU  - Khoroshutina, E.B.
AU  - Omelyanyuk, N.M.
AU  - Sokolov, N.N.
AU  - Skryabin, K.G.
TI  - Site-specific endonuclease BcuAI from Bacillus cereus A.
JO  - Bioorg. Khim.
PY  - 1996
SP  - 528
EP  - 531
VL  - 22
AB  - A new restriction endonuclease was isolated from Bacillus cereus BKM B-814 by means of the
AB  - cell disruption with ultrasonication, ammonium sulfate fractionation of the cell-free extract,
AB  - and chromatography on DEAE-Sepharose to give about 1400 U of the enzyme per gram of cells.
AB  - The enzyme revealed the maximum activity at 30-37oC, pH 7.6-8.2, and 5-10 mM MgCl2 under a
AB  - high ionic strength (50mM Tris-HCl, 100mM NaCl).  The site-specific endonuclease BcuAI was
AB  - found to recognize the 5' G/G(A/T)CC sequence in double-stranded DNA and cleave it as shown
AB  - with the arrow, thus being a true isoschisomer of the AvaII restriction endonuclease.
ER  -

TY  - JOUR
AU  - Korolev, S.V.
AU  - Sokolov, N.N.
AU  - Rina, M.
AU  - Eldarov, M.A.
AU  - Omelyanyuk, N.M.
AU  - Markaki, M.
AU  - Skryabin, K.G.
AU  - Bouriotis, V.
TI  - Isolation and characterization of the specificity of new restriction endonucleases Bsp4009I and AsiI - isoschizomers of BamHI.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1998
SP  - 32
EP  - 35
VL  - 0
AB  - New type II restriction endonucleases AsiI and Bsp4009I are detected in Azotobacter species
AB  - N55 and Bacillus species 4009, respectively.  Purified preparations of the restriction enzymes
AB  - free from interfering nucleases and phosphatases were obtained by column chromatography on
AB  - phosphocellulose and heparin-sepharose (AsiI) and phosphocellulose and DEAE-cellulose
AB  - (Bsp4009I).  The yield of purified AsiI and Bsp4009I was 16 x 10^3 and 8 x 10^3 units per g of
AB  - wet cells, respectively.  The above restriction endonucleases recognize the 5'-G/GATCC-3'
AB  - sequence on double-stranded DNA and cleave it as shown, thus being true isoschizomers of BamHI
AB  - restriction endonuclease.
ER  -

TY  - JOUR
AU  - Korona, R.
AU  - Korona, B.
AU  - Levin, B.R.
TI  - Sensitivity of naturally occurring coliphages to type I and type II restriction and modification.
JO  - J. Gen. Microbiol.
PY  - 1993
SP  - 1283
EP  - 1290
VL  - 139
AB  - Protection against lethal infections by bacteriophage may seem the most likely role of
AB  - restriction-modification (R-M) systems in bacteria and the reason for their evolution. There
AB  - are, however, phenomena which question this phage-mediated selection hypothesis for the
AB  - maintenance of extant R-M systems. Most prominent among these are the mechanisms phage have to
AB  - avoid or otherwise limit the effects of the restriction endonucleases produced by their host
AB  - bacteria. To evaluate the importance of these antirestriction mechanisms in Escherichia coli,
AB  - we have examined the sensitivity of coliphage from natural and laboratory sources to a series
AB  - of type I and II R-M systems. The results of our study indicate that, in vivo, restriction
AB  - endonucleases have no effect on a substantial fraction of naturally occurring coliphage. The
AB  - absence of restriction sites appears to be the most common reason why these phage are
AB  - unaffected by type II restriction endonucleases, but other antirestriction mechanisms also
AB  - operate. On the other hand, the frequency of naturally occurring coliphage sensitive to
AB  - restriction appears sufficiently great for phage-mediated selection to be a viable hypothesis
AB  - for the maintenance R-M in E. coli and its accessory elements.
ER  -

TY  - JOUR
AU  - Korona, R.
AU  - Levin, B.R.
TI  - Phage-mediated selection and the evolution and maintenance of restriction-modification.
JO  - Evolution
PY  - 1993
SP  - 556
EP  - 575
VL  - 47
AB  - Restriction-modification (R-M) was discovered because it provides bacteria with immunity to
AB  - phage infection. But, is phage-mediated selection the sole mechanism responsible for the
AB  - evolution and maintenance of these ubiquitous and multiply evolved systems? In an effort to
AB  - answer this question, we have performed experiments with laboratory populations of E. coli and
AB  - phage and computer simulations. We consider two ecological situations whereby phage-mediated
AB  - selection could favor R-M immunity; i) when bacteria with a novel R-M system invade
AB  - communities of phage-sensitive bacteria in which there are one or more species of phage, and
AB  - ii) when bacteria colonize bacterial-free habitats in which phage are present. The results of
AB  - our experiments indicate that in established communities of bacteria and phage, the advantage
AB  - R-M provides an invading population of bacteria is ephemeral. Within short order, mutants
AB  - resistant (refractory) to the phage evolve in the dominant population and subsequently in the
AB  - invading population. The outcome of competition then depends on the relative fitness of the
AB  - resistant states of these bacterial clones, rather than R-M. As a consequence of sequential
AB  - selection for independent mutants, this rapid evolution of resistance occurs even when two and
AB  - three species of phage are present. While in our experiments resistance also evolved when
AB  - bacteria colonized new habitats in which phage were present, a novel R-M system greatly
AB  - augmented the likelihood of their becoming established. We interpret the results of this study
AB  - as support for the hypothesis that the latter, colonization selection, may play an important
AB  - role in the evolution and maintenance of restriction-modification. However, we also see these
AB  - results and other observations we discuss as questioning whether protection against phage is
AB  - the unique biological role of restriction-modification.
ER  -

TY  - JOUR
AU  - Koryszewska-Baginska, A.
AU  - Aleksandrzak-Piekarczyk, T.
AU  - Bardowski, J.
TI  - Complete Genome Sequence of the Probiotic Strain Lactobacillus casei (Formerly Lactobacillus paracasei) LOCK919.
JO  - Genome Announcements
PY  - 2013
SP  - e00758
EP  - e00713
VL  - 1
AB  - Lactobacillus casei is usually regarded as a bacterium that lives naturally in the human
AB  - intestinal tract, where it can contribute to host health and
AB  - well-being. We describe here the complete genome sequence of L. casei LOCK919, a
AB  - strain with probiotic properties isolated from child feces. The genome consists
AB  - of a 3.11-Mb chromosome and a 29,768-bp plasmid.
ER  -

TY  - JOUR
AU  - Koryszewska-Baginska, A.
AU  - Bardowski, J.
AU  - Aleksandrzak-Piekarczyk, T.
TI  - Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK908.
JO  - Genome Announcements
PY  - 2014
SP  - e00120
EP  - e00114
VL  - 2
AB  - Lactobacillus rhamnosus LOCK908, a patented probiotic strain (Polish patent no. 209987), was
AB  - isolated from the feces of a healthy 6-year-old girl. Here, we
AB  - present the complete genome sequence of LOCK908 and identify genes likely to be
AB  - involved in the biosynthesis of exopolysaccharides (EPSs).
ER  -

TY  - JOUR
AU  - Korzun, V.
AU  - Balzer, H.J.
AU  - Balzer, A.
AU  - Baumlein, H.
AU  - Borner, A.
TI  - Chromosomal location of three wheat sequences with homology to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes in wheat and rye.
JO  - Genome
PY  - 1996
SP  - 1213
EP  - 1215
VL  - 39
AB  - Three wheat sequences, shown to be homologous to pollen allergen encoding, DNA replication
AB  - regulating, and DNA (cytosine-5)-methyltransferase genes were localized on chromosomes using
AB  - nullisomic-tetrasomic wheat ('Chinese Spring') and wheat-rye ('Chinese
AB  - Spring'/'Imperial') addition lines.  Whereas the loci for the pollen allergen encoding
AB  - sequence (Tri a III) were shown to be located on homoeologous group 4, the DNA replication
AB  - regulating (Rep) and DNA (cytosine-5)-methyltransferase (Mtase) genes were located to
AB  - homoeologous groups 1 and 7, respectively, of Triticeae.  Chromosomal rearrangements in wheat
AB  - and rye relative to each other are discussed.
ER  -

TY  - JOUR
AU  - Kos, V.N.
AU  - Deraspe, M.
AU  - McLaughlin, R.E.
AU  - Whiteaker, J.D.
AU  - Roy, P.H.
AU  - Alm, R.A.
AU  - Corbeil, J.
AU  - Gardner, H.
TI  - The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 427
EP  - 436
VL  - 59
AB  - Many clinical isolates of Pseudomonas aeruginosa cause infections that are
AB  - difficult to eradicate due to their resistance to a wide variety of antibiotics.
AB  - Key genetic determinants of resistance were identified through genome sequences
AB  - of 390 clinical isolates of P. aeruginosa, obtained from diverse geographic
AB  - locations collected between 2003 and 2012 and were related to microbiological
AB  - susceptibility data for meropenem, levofloxacin, and amikacin. beta-Lactamases
AB  - and integron cassette arrangements were enriched in the established
AB  - multidrug-resistant lineages of sequence types ST111 (predominantly O12) and
AB  - ST235 (O11). This study demonstrates the utility of next-generation sequencing
AB  - (NGS) in defining relevant resistance elements and highlights the diversity of
AB  - resistance determinants within P. aeruginosa. This information is valuable in
AB  - furthering the design of diagnostics and therapeutics for the treatment of P.
AB  - aeruginosa infections.
ER  -

TY  - JOUR
AU  - Kosaka, T.
AU  - Toh, H.
AU  - Toyoda, A.
TI  - Complete Genome Sequence of a Thermophilic Hydrogenotrophic Methanogen, Methanothermobacter sp. Strain CaT2.
JO  - Genome Announcements
PY  - 2013
SP  - e00672
EP  - e00613
VL  - 1
AB  - We isolated a thermophilic hydrogenotrophic methanogen, Methanothermobacter sp. strain CaT2,
AB  - which is able to aggregate and utilize formate. Here, we report the
AB  - complete genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Kosaka, T.
AU  - Uchiyama, T.
AU  - Ishii, S.
AU  - Enoki, M.
AU  - Imachi, H.
AU  - Kamagata, Y.
AU  - Ohashi, A.
AU  - Harada, H.
AU  - Ikenaga, H.
AU  - Watanabe, K.
TI  - Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum  thermopropionicum.
JO  - J. Bacteriol.
PY  - 2006
SP  - 202
EP  - 210
VL  - 188
AB  - Obligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with
AB  - methanogenic archaea share the intermediate bottleneck
AB  - step in organic-matter decomposition. These organisms (called syntrophs)
AB  - are biologically significant in terms of their growth at the thermodynamic
AB  - limit and are considered to be the ideal model to address bioenergetic
AB  - concepts. We conducted genomic and proteomic analyses of the thermophilic
AB  - propionate-oxidizing syntroph Pelotomaculum thermopropionicum to obtain
AB  - the genetic basis for its central catabolic pathway. Draft sequencing and
AB  - subsequent targeted gap closing identified all genes necessary for
AB  - reconstructing its propionate-oxidizing pathway (i.e., methylmalonyl
AB  - coenzyme A pathway). Characteristics of this pathway include the
AB  - following. (i) The initial two steps are linked to later steps via
AB  - transferases. (ii) Each of the last three steps can be catalyzed by two
AB  - different types of enzymes. It was also revealed that many genes for the
AB  - propionate-oxidizing pathway, except for those for propionate coenzyme A
AB  - transferase and succinate dehydrogenase, were present in an operon-like
AB  - cluster and accompanied by multiple promoter sequences and a putative gene
AB  - for a transcriptional regulator. Proteomic analysis showed that enzymes in
AB  - this pathway were up-regulated when grown on propionate; of these enzymes,
AB  - regulation of fumarase was the most stringent. We discuss this tendency of
AB  - expression regulation based on the genetic organization of the open
AB  - reading frame cluster. Results suggest that fumarase is the central
AB  - metabolic switch controlling the metabolic flow and energy conservation in
AB  - this syntroph.
ER  -

TY  - JOUR
AU  - Kosinski, J.
AU  - Kubareva, E.
AU  - Bujnicki, J.M.
TI  - A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering.
JO  - Proteins
PY  - 2007
SP  - 324
EP  - 336
VL  - 68
AB  - R.MvaI is a Type II restriction enzyme (REase), which specifically recognizes the
AB  - pentanucleotide DNA sequence 5'-CCWGG-3' (W indicates A
AB  - or T). It belongs to a family of enzymes, which recognize related
AB  - sequences, including 5'-CCSGG-3'(S indicates G or C) in the case of
AB  - R.BcnI, or 5'-CCNGG-3' (where N indicates any nucleoside) in the case
AB  - of R.ScrFI. REases from this family hydrolyze the phosphodiester bond
AB  - in the DNA between the 2nd and 3rd base in both strands, thereby
AB  - generating a double strand break with 5'-protruding single nucleotides.
AB  - So far, no crystal structures of REases with similar cleavage patterns
AB  - have been solved. Characterization of sequence-structure-function
AB  - relationships in this family would facilitate understanding of
AB  - evolution of sequence specificity among REases and could aid in
AB  - engineering of enzymes with new specificities. However, sequences of
AB  - R.MvaI or its homologs show no significant similarity to any proteins
AB  - with known structures, thus precluding straightforward comparative
AB  - modeling. We used a fold recognition approach to identify a remote
AB  - relationship between R.MvaI and the structure of DNA repair enzyme
AB  - MutH, which belongs to the PD-(D/E)XK superfamily together with many
AB  - other REases. We constructed a homology model of R.MvaI and used it to
AB  - predict functionally important amino acid residues and the mode of
AB  - interaction with the DNA. In particular, we predict that only one
AB  - active site of R.MvaI interacts with the DNA target at a time, and the
AB  - cleavage of both strands (5'-CCAGG-3' and 5'-CCTGG-3') is achieved by
AB  - two independent catalytic events. The model is in good agreement with
AB  - the available experimental data and will serve as a template for
AB  - further analyses of R.MvaI, R.BcnI, R.ScrFI and other related enzymes.
ER  -

TY  - JOUR
AU  - Koskinen, J.P.
AU  - Laine, P.
AU  - Niemi, O.
AU  - Nykyri, J.
AU  - Harjunpaa, H.
AU  - Auvinen, P.
AU  - Paulin, L.
AU  - Pirhonen, M.
AU  - Palva, T.
AU  - Holm, L.
TI  - Genome Sequence of Pectobacterium sp. Strain SCC3193.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6004
EP  - 6004
VL  - 194
AB  - We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium
AB  - Pectobacterium sp. strain SCC3193, a model strain isolated from
AB  - potato in Finland. The Pectobacterium sp. SCC3193 genome consists of a 516,411-bp
AB  - chromosome, with no plasmids.
ER  -

TY  - JOUR
AU  - Koskinen, P.
AU  - Deptula, P.
AU  - Smolander, O.P.
AU  - Tamene, F.
AU  - Kammonen, J.
AU  - Savijoki, K.
AU  - Paulin, L.
AU  - Piironen, V.
AU  - Auvinen, P.
AU  - Varmanen, P.
TI  - Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 83
EP  - 83
VL  - 10
AB  - Propionibacterium freudenreichii subsp. freudenreichii DSM 20271(T) is the type strain of
AB  - species Propionibacterium freudenreichii that has a long history of
AB  - safe use in the production dairy products and B12 vitamin. P. freudenreichii is
AB  - the type species of the genus Propionibacterium which contains Gram-positive,
AB  - non-motile and non-sporeforming bacteria with a high G + C content. We describe
AB  - the genome of P. freudenreichii subsp. freudenreichii DSM 20271(T) consisting of
AB  - a 2,649,166 bp chromosome containing 2320 protein-coding genes and 50 RNA-only
AB  - encoding genes.
ER  -

TY  - JOUR
AU  - Kossykh, V.
AU  - Repyk, A.
AU  - Kaliman, A.
AU  - Buryanov, Y.
TI  - Nucleotide sequence of the EcoRII restriction endonuclease gene.
JO  - Biochim. Biophys. Acta
PY  - 1989
SP  - 290
EP  - 292
VL  - 1009
AB  - The nucleotide sequence of a 1394 basepair (bp) DNA fragment containing the EcoRII restriction
AB  - endonuclease (R.EcoRII) gene was determined.  The endonuclease gene is 1206 bp in length
AB  - (predicted 402 amino acids (aa) and Mr=45,178) and is separated by 33 bp from the EcoRII
AB  - modification methylase (M.EcoRII) gene.  The EcoRII restriction-modification system has a
AB  - tail-to-tail organization of the two genes.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Lloyd, R.S.
TI  - A DNA Adenine Methyltransferase of Escherichia coli That Is Cell Cycle Regulated and Essential for Viability.
JO  - J. Bacteriol.
PY  - 2004
SP  - 2061
EP  - 2067
VL  - 186
AB  - DNA sequence analysis revealed that the putative yhdJ DNA methyltransferase gene of
AB  - Escherichia coli is 55% identical to the Nostoc
AB  - sp. strain PCC7120 gene encoding DNA methyltransferase AvaIII, which
AB  - methylates adenine in the recognition sequence, ATGCAT. The yhdJ gene was
AB  - cloned, and the enzyme was overexpressed and purified. Methylation and
AB  - restriction analysis showed that the DNA methyltransferase methylates the
AB  - first adenine in the sequence ATGCAT. This DNA methylation was found to be
AB  - regulated during the cell cycle, and the DNA adenine methyltransferase was
AB  - designated M.EcoKCcrM (for "cell cycle-regulated methyltransferase"). The
AB  - CcrM DNA adenine methyltransferase is required for viability in E. coli,
AB  - as a strain lacking a functional genomic copy of ccrM can be isolated only
AB  - in the presence of an additional copy of ccrM supplied in trans. The cells
AB  - of such a knockout strain stopped growing when expression of the inducible
AB  - plasmid ccrM gene was shut off. Overexpression of M.EcoKCcrM slowed
AB  - bacterial growth, and the ATGCAT sites became fully methylated throughout
AB  - the cell cycle; a high proportion of cells with an anomalous size
AB  - distribution and DNA content was found in this population. Thus, the
AB  - temporal control of this methyltransferase may contribute to accurate cell
AB  - cycle control of cell division and cellular morphology. Homologs of
AB  - M.EcoKCcrM are present in other bacteria belonging to the gamma
AB  - subdivision of the class Proteobacteria, suggesting that methylation at
AB  - ATGCAT sites may have similar functions in other members of this group.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Repyk, A.V.
AU  - Hattman, S.
TI  - Sequence motifs common to the EcoRII restriction endonuclease and the proposed sequence specificity domain of three DNA-[cytosine-C5] methyltransferases.
JO  - Gene
PY  - 1993
SP  - 65
EP  - 68
VL  - 125
AB  - We have compared the deduced amino acids (aa) sequences of the EcoRII restriction endonuclease
AB  - (R.EcoRII) and the proposed specificity (target recognition) domains of three
AB  - DNA-[cytosine-C5] methyltransferases (MTases). M.EcoRII, M.Dcm, and M.SPR, each of which
AB  - recognizes the same nucleotide sequence, CCWGG (where W is A or T). We have identified a
AB  - region containing sequence motifs that are partially conserved in the MTases and R.EcoRII.
AB  - This may be the first example of aa sequence homology between a MTase specificity (target
AB  - recognition) domain and its cognate restriction endonuclease (ENase). It suggests that this
AB  - region is important for DNA recognition by R.EcoRII and that the EcoRII ENase and MTase genes
AB  - may have evolved from a common progenitor.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Function of Pro-185 in the ProCys of conserved motif IV in the EcoRII [cytosine-C5]-DNA methyltransferase.
JO  - FEBS Lett.
PY  - 1995
SP  - 75
EP  - 77
VL  - 370
AB  - ProCys in the conserved sequence motif IV of [cytosine-C5]-DNA methyltransferases is known to
AB  - be part of the catalytic site.  The Cys residue is directly involved in forming a covalent
AB  - bond with the C6 of the target cytosine.  We have found that substitution of Pro-185 with
AB  - either Ala or Ser resulted in a reduced rate of methyl group transfer by the EcoRII DNA
AB  - methyltransferase.  In addition, we observed an increase in the Km for substrate
AB  - S-adenosyl-L-methionine (AdoMet), but a decrease in the Km for substrate DNA.  This is
AB  - reflected in minor changes in kcat/Km for DNA, but in 10- to 100-fold reductions in kcat/Km
AB  - for AdoMet.  This suggests that Pro-185 is important to properly orient the activated cytosine
AB  - and AdoMet for methyl group transfer by direct interaction with AdoMet and indirectly via the
AB  - Cys interaction with cytosine.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3563
EP  - 3566
VL  - 21
AB  - Comparison of the deduced amino acid sequences of DNA-[N6-adenine]-methyltransferases has
AB  - revealed several conserved regions. All of these enzymes contain a DPPY-motif, or a variant of
AB  - it. By site-directed mutagenesis of a cloned T4 dam gene, we have altered the first proline
AB  - residue in this motif (located in conserved region IV of the T4 Dam-MTase) to alanine or
AB  - threonine. The mutant enzymic forms, P172A and P172T, were overproduced and purified. Kinetic
AB  - studies showed that compared to the wild-type (wt) the two mutant enzymic forms had:(i) an
AB  - increased (6 and 23-fold, respectively) Km for substrate, S-adenosylmethionine (AdoMet) and an
AB  - increased (6 and 23-fold) Ki for product, S-adenosyl-homocysteine (AdoHcy); (ii) a slightly
AB  - reduced (1.5 and 3-fold lower) kcat; (iii) a strongly reduced kcat/Km AdoMet (10 and 80-fold);
AB  - and (iv) the same Km for substrate DNA. Equilibrium dialysis studies showed that the mutant
AB  - enzymes had a reduced (3 and 7-fold lower) Ka for AdoMet; all forms bound two molecules of
AB  - AdoMet. Taken together these data indicate that the P172A and P172T alterations resulted
AB  - primarily in a reduced affinity for AdoMet. This suggests that the DPPY-motif is important for
AB  - AdoMet-binding, and that region IV contains an AdoMet-binding site.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Phage T4 DNA [N6-adenine]Methyltransferase.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 14389
EP  - 14393
VL  - 270
AB  - The bacteriophage T4 dam gene, encoding the Dam DNA [N6-adenine]methyltransferase (MTase), has
AB  - been subcloned into the plasmid expression vector, pJW2. In this construct, designated
AB  - pINT4dam, transcription is from the regulatable phage lambda PR and PL promoters, arranged in
AB  - tandem. A two-step purification scheme using DEAE-cellulose and phosphocellulose columns in
AB  - series, followed by hydroxyapatite chromatography, was developed to purify the enzyme to near
AB  - homogeneity. The yield of purified protein was 2 mg/g of cell paste. The MTase has an s20,w of
AB  - 3.0 S and a Stokes radius of 23 Angstroms and exists in solution as a monomer. The Km for the
AB  - methyl donor, S-adenosylmethionine, is 0.1 x 10-6M, and the Km for substrate nonglucosylated,
AB  - unmethylated T4 gt-dam- DNA is 1.1 x 10/-12M. The products of DNA methylation,
AB  - S-adenosyl-L-homocysteine and methylated DNA, are competitive inhibitors of the reaction; Ki
AB  - values of 2.4 x 10/-6M and 4.6 x 10/-12 M, respectively, were observed. T4 Dam methylates the
AB  - palindromic tetranucleotide, GATC, designated the canonical sequence. However, at high
AB  - MTase:DNA ratios, T4 Dam can methylate some noncanonical sequences belonging to GAY (where Y
AB  - represents cytosine or thymine).
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4659
EP  - 4662
VL  - 21
AB  - Comparison of the deduced amino acid sequences of DNA-[N6-adenine]-methyltransferases has
AB  - revealed several conserved regions. All of these enzymes contain a DPPY [or closely related]
AB  - motif. By site-directed mutagenesis of a cloned T4 dam gene, we have altered the first proline
AB  - residue in this motif [located in conserved region IV of the T4 Dam-MTase] to alanine or
AB  - threonine. The mutant enzymic forms, P172A and P172T, were overproduced and purified. Kinetic
AB  - studies showed that compared to the wild-type [wt] the two mutant enzymic forms had: (i) an
AB  - increased [5 and 20-fold, respectively] Km for substrate, S-adenosyl-methionine [AdoMet]; (ii)
AB  - a slightly reduced [2 and 4-fold lower] kcat; (iii) a strongly reduced kcat/Km AdoMet [10 and
AB  - 100-fold]; and (iv) almost the same Km for substrate DNA. Equilibrium dialysis studies showed
AB  - that the mutant enzymes had a reduced [4 and 9-fold lower] Ka for AdoMet. Taken together these
AB  - data indicate that the p172A and P172T alterations resulted primarily in a reduced affinity
AB  - for AdoMet. This suggests that the DPPY-motif is important for AdoMet-binding, and that region
AB  - IV contains or is part of an AdoMet-binding site.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Studies on the function of conserved sequence motifs in the T4 Dam-[N6-adenine] and EcoRII [C5-cytosine] DNA methyltransferases.
JO  - Gene
PY  - 1995
SP  - 125
EP  - 126
VL  - 157
AB  - We used site-directed oligodeoxyribonucleotide-mediated mutagenesis and kinetic studies with
AB  - purified wild-type (wt) and mutant proteins to evaluate the role of the conserved sequence
AB  - motifs in two prokaryotic DNA MTases.  We suggest that: (i) the main role of Pro in the
AB  - M.EcoRII PC-motif is to restrict the conformational freedom of Cys and orient it in a manner
AB  - essential for catalysis; (ii) in both M.EcoRII and T4 Dam the FXGXG-motif positions AdoMet
AB  - with respect to the catalytic site; (iii) the DPPY-motif in T4 Dam (region IV) is important
AB  - for AdoMet-binding and may be part of the binding site; and (iv) the RXNXKXXFXXPFK-motif in T4
AB  - Dam (region III) is part of the DNA binding/recognition domain.
ER  -

TY  - JOUR
AU  - Kossykh, V.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Comparative studies of the phage T2 and T4 DNA (N6-adenine) methyltransferases: Amino acid changes that affect catalytic activity.
JO  - J. Bacteriol.
PY  - 1997
SP  - 3239
EP  - 3243
VL  - 179
AB  - The bacteriophage T2 and T4 dam genes code for a DNA (N6-adenine) methyltransferase (Mtase).
AB  - Nonglucosylated, hydroxymethylcytosine-containing T2gt- virion DNA has a higher level of
AB  - methylation than T4gt- virion DNA does.  To investigate the basis for this difference, we
AB  - compared the intracellular enzyme levels following phage infection as well as the in vitro
AB  - intrinsic methylation capabilities of purified T2 and T4 Dam Mtases.  Results from Western
AB  - blotting (immunoblotting) showed that the same amounts of MTase protein were produced after
AB  - infection with T2 and T4.  Kinetic analyses with purified homogeneous enzymes showed that the
AB  - two MTases had similar Km values for the methyl donor, S-adenosyl-L-methionine, and for
AB  - substrate DNA.  In contrast, they had different kcat values (two-fold higher for T2 Dam
AB  - MTase).  We suggest that this difference can account for the ability of T2 Dam to methylate
AB  - viral DNA in vivo to a higher level than does T4 Dam.  Since the T2 and T4 MTases differ at
AB  - only three amino acid residues (at positions 20 [T4, Ser; T2, Pro], 26 [T4, Asn; T2, Asp], and
AB  - 188 [T4, Asp; T2, Glu]), we have produced hybrid proteins to determine which residue(s) is
AB  - responsible for increased catalytic activity.  The results of these analyses showed that the
AB  - residues at positions 20 and 26 are responsible for the different kcat values of the two
AB  - MTases for both canonical and noncanonical sites.  Moreover, a single substitution of either
AB  - residue 20 or 26 was sufficient to increase the kcat of T4 Dam.
ER  -

TY  - JOUR
AU  - Kostiuk, G.
AU  - Dikic, J.
AU  - Schwarz, F.W.
AU  - Sasnauskas, G.
AU  - Seidel, R.
AU  - Siksnys, V.
TI  - The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 5968
EP  - 5979
VL  - 45
AB  - Endonucleases that generate DNA double strand breaks often employ two independent subunits
AB  - such that the active site from each subunit cuts either DNA strand.
AB  - Restriction enzyme BcnI is a remarkable exception. It binds to the 5-CC/SGG-3
AB  - (where S = C or G, '/' designates the cleavage position) target as a monomer
AB  - forming an asymmetric complex, where a single catalytic center approaches the
AB  - scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements
AB  - have previously shown that the same BcnI molecule cuts both DNA strands at the
AB  - target site without dissociation from the DNA. Here, we analyse the BcnI DNA
AB  - binding and target recognition steps at the single molecule level. We find, using
AB  - FRET, that BcnI adopts either 'open' or 'closed' conformation in solution. Next,
AB  - we directly demonstrate that BcnI slides over long distances on DNA using 1D
AB  - diffusion and show that sliding is accompanied by occasional jumping events,
AB  - where the enzyme leaves the DNA and rebinds immediately at a distant site.
AB  - Furthermore, we quantify the dynamics of the BcnI interactions with cognate and
AB  - non-cognate DNA, and determine the preferred binding orientation of BcnI to the
AB  - target site. These results provide new insights into the intricate dynamics of
AB  - BcnI-DNA interactions.
ER  -

TY  - JOUR
AU  - Kostiuk, G.
AU  - Sasnauskas, G.
AU  - Tamulaitiene, G.
AU  - Siksnys, V.
TI  - Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 3744
EP  - 3753
VL  - 39
AB  - Unlike orthodox Type II restriction endonucleases that are homodimers and interact with the
AB  - palindromic 4-8-bp DNA sequences, BcnI is a monomer which has a single active site but cuts
AB  - both DNA strands within the 5'-CC downward arrowCGG-3'/3'-GGG downward arrowCC-5' target
AB  - site (' downward arrow' designates the cleavage position). Therefore, after cutting the
AB  - first strand, the BcnI monomer must re-bind to the target site in the opposite orientation;
AB  - but in this case, it runs into a different central base because of the broken symmetry of the
AB  - recognition site. Crystal-structure analysis shows that to accept both the C:G and G:C base
AB  - pairs at the center of its target site, BcnI employs two symmetrically positioned histidines
AB  - H77 and H219 that presumably change their protonation state depending on the binding mode. We
AB  - show here that a single mutation of BcnI H77 or H219 residues restricts the cleavage activity
AB  - of the enzyme to either the 5'-CCCGG-3' or the 5'-CCGGG-3' strand, thereby converting BcnI
AB  - into a strand-specific nicking endonuclease. This is a novel approach for engineering of
AB  - monomeric restriction enzymes into strand-specific nucleases.
ER  -

TY  - JOUR
AU  - Kostka, J.E.
AU  - Green, S.J.
AU  - Rishishwar, L.
AU  - Prakash, O.
AU  - Katz, L.S.
AU  - Marino-Ramirez, L.
AU  - Jordan, I.K.
AU  - Munk, C.
AU  - Ivanova, N.
AU  - Mikhailova, N.
AU  - Watson, D.B.
AU  - Brown, S.D.
AU  - Palumbo, A.V.
AU  - Brooks, S.C.
TI  - Genome sequences for six rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4461
EP  - 4462
VL  - 194
AB  - We report the first genome sequences for six strains of Rhodanobacter species isolated from a
AB  - variety of soil and subsurface environments. Three of these
AB  - strains are capable of complete denitrification and three others are not.
AB  - However, all six strains contain most of the genes required for the respiration
AB  - of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack
AB  - only the gene for nitrate reduction, the first step in the full denitrification
AB  - pathway. The data suggest that the environmental role of bacteria from the genus
AB  - Rhodanobacter should be reevaluated.
ER  -

TY  - JOUR
AU  - Kostrewa, D.
AU  - Winkler, F.K.
TI  - Mg2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Angstrom resolution.
JO  - Biochemistry
PY  - 1995
SP  - 683
EP  - 696
VL  - 34
AB  - The type II restriction endonuclease EcoRV was crystallized as a complex with the substrate
AB  - DNA undecamer AAAGATATCTT. These crystals diffract to much better resolution (2 Angstrom) than
AB  - was the case for the previously reported complex with the decamer GGGATATCCC. The crystal
AB  - structure contains one dimer complex in the asymmetric unit and was solved by molecular
AB  - replacement. The same kinked DNA conformation characteristic for enzyme-bound cognate DNA is
AB  - observed. Crystals, soaked with Mg2+, show the essential cofactor bound at only one active
AB  - site of the dimer, and the DNA is not cleaved. The Mg2+ has one oxygen from the scissile
AB  - phosphodiester group and two carboxylate oxygens, one from Asp74 and one from Asp90, in its
AB  - octahedral ligand sphere. The scissile phosphodiester group is pulled by 1 Angstrom toward the
AB  - Mg2+. After substrate cleavage in solution, isomorphous crystals containing the
AB  - enzyme--product--Mg2+ complex were obtained. In this structure, each of the 5'-phosphate
AB  - groups is bound to two Mg2+. The kinked DNA conformation is essentially maintained, but the
AB  - two central adenines, 3' to the cleavage sites, form an unusual cross-strand base stacking.
AB  - The structures have been refined to R factors of 0.16 at 2.1-2.0 Angstrom resolution
AB  - maintaining very good stereochemistry. On the basis of these structures and inspired by recent
AB  - kinetic data, we have constructed a transition state model with two metals bound to the
AB  - scissile phosphorane group.
ER  -

TY  - JOUR
AU  - Kostriken, R.
AU  - Strathern, J.N.
AU  - Klar, A.J.S.
AU  - Hicks, J.B.
AU  - Heffron, F.
TI  - A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae.
JO  - Cell
PY  - 1983
SP  - 167
EP  - 174
VL  - 35
AB  - We have detected two site-specific endonucleases in strains of Saccharomyces cerevisiae. One
AB  - endonuclease, which we call YZ endo, is present only in yeast strains that are undergoing
AB  - mating-type interconversion. The site at which YZ endo cleaves corresponds to the in vivo
AB  - double-strand break occuring at the mating-type locus in yeast undergoing mating-type
AB  - interconversion. YZ endo generates a site-specific double-strand break having 4-base 3'
AB  - extensions terminating in 3' hydroxyl groups. The site of cleavage occurs in the Z1 region
AB  - near the YZ junction of the mating-type locus. Mutant mating-type loci known to decrease the
AB  - frequency of mating-type interconversion are correspondingly poor substrates for YZ endo in
AB  - vitro. In vitro analysis of a number of such altered recognition sites has delimited the
AB  - sequences required for cleavage. The molecular genetics of mating-type interconversion is
AB  - discussed in the context of this endonucleolytic activity. The second endonuclease, which we
AB  - refer to as SceII, is present in all strains of S. cerevisiae we have examined. The cleavage
AB  - site of SceII has been determined and proves to be unrelated to the cleavage site of YZ endo.
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
TI  - Escherichia coli K-12 plasmid R245 controlling EcoRII restriction and DNA modification.
JO  - Dokl. Akad. Nauk.
PY  - 1978
SP  - 1227
EP  - 1230
VL  - 238
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Cloning the genes of EcoRII restrictase and methylase.
JO  - Dokl. Akad. Nauk.
PY  - 1979
SP  - 1269
EP  - 1271
VL  - 247
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Buryanov, Y.I.
AU  - Bayev, A.A.
TI  - Molecular Cloning of EcoRII Endonuclease and Methylase Genes.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 717
EP  - 718
VL  - 178
AB  - The genes for restriction-modification system EcoRII have been cloned from
AB  - plasmid N3 DNA using RSF2124 as a vector plasmid.  The hybrid plasmids
AB  - designated pFK321 and pFK322 contained a 5.8 megadaltons EcoRI - fragment
AB  - derived from N3 DNA including the genes for restriction-modification system
AB  - EcoRII and a gene for resistance to sulfanilamide.
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Glinskaite, I.V.
AU  - Buryanov, J.I.
AU  - Baev, A.A.
TI  - Mapping the EcoRII restrictase and methylase genes on recombinant plasmids.
JO  - Dokl. Akad. Nauk.
PY  - 1982
SP  - 727
EP  - 730
VL  - 265
AB  - None
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Mantsygin, Y.A.
AU  - Svyatukhina, N.V.
AU  - Vitenene, I.V.
AU  - Buryanov, Y.I.
TI  - Purification of the restriction endonuclease EcoRII using monoclonal antibodies.
JO  - Biokhimiia
PY  - 1988
SP  - 1474
EP  - 1478
VL  - 53
AB  - Hybridomas producing monoclonal antibodies to the restriction endonuclease
AB  - EcoRII were produced after immunization of two BALB/c mice with a preparation
AB  - of the homogeneous enzyme.  The IgG were obtained from ascites fluid, purified,
AB  - and covalently bonded to CNBr-activated Sepharose 4B.  The immunosorbent
AB  - obtained was used for the isolation of the restriction endonuclease EcoRII.
AB  - The isolated restriction endonuclease EcoRII gave one band in polyacrylamide
AB  - gel electrophoresis with sodium sulfate.  The enzyme was obtained in a good
AB  - yield with high specific activity.
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Puntezhis, S.A.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Isolation, purification and properties of restriction endonuclease EcoRII.
JO  - Biokhimiia
PY  - 1982
SP  - 619
EP  - 625
VL  - 47
AB  - The restriction endonuclease EcoRII was isolated and purified to homogeneity.  The isolation
AB  - procedure involved the use of the E. coli strain B834/pSK323, containing the recombinant
AB  - plasmid pSK323 which provides for the overproduction of EcoRII enzymes.  Data from gel
AB  - filtration and SDS electrophoresis suggest that the restriction endonuclease EcoRII is a
AB  - protein made up of two subunits, each with molecular weight of 44000.
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Repik, A.V.
AU  - Kaliman, A.V.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Primary structure of the restriction endonuclease EcoRII gene.
JO  - Dokl. Akad. Nauk.
PY  - 1989
SP  - 1497
EP  - 1499
VL  - 308
AB  - None
ER  -

TY  - JOUR
AU  - Kosykh, V.G.
AU  - Solonin, A.S.
AU  - Buryanov, Y.I.
AU  - Bayev, A.A.
TI  - Overproduction of the EcoRII endonuclease and methylase by Escherichia coli strains carrying recombinant plasmids constructed in vitro.
JO  - Biochim. Biophys. Acta
PY  - 1981
SP  - 102
EP  - 106
VL  - 655
AB  - Recombinant DNA molecules were constructed from the plasmid pIL203 and the
AB  - EcoRI-fragment of N3 plasmid containing EcoRII endonuclease and methylase genes
AB  - and also a gene for resistance to sulfanilamide.  The pIL203 plasmid, used as a
AB  - vector, consisted of the BamHI-EcoRI-fragment of the plasmid pBR322 conferring
AB  - resistance to ampicillin and the BamHI-EcoRI-fragment of lambda phage
AB  - containing promoters, a thermosensitive mutation in the cI gene and a
AB  - suppressible amber mutation in the cro gene.
AB  - Ampicillin-sulfanilamide-resistant clones were selected and tested for their
AB  - restriction and modification phenotype.  The recombinant plasmid DNA, isolated
AB  - from ApRSuR-resistant clones, which restricted and modified phage lambda imm21
AB  - with EcoRII specificity, had the EcoRI-fragment with EcoRII genes in a single
AB  - orientation.  The recombinant plasmid pSK323 was transferred into E. coli
AB  - strains with su-, su1, su2 or su3 phenotypes.  The synthesis of products of
AB  - EcoRII genes by these strains grown at 37C is increased by 10-50-fold.
ER  -

TY  - JOUR
AU  - Kotak, M.
AU  - Isanapong, J.
AU  - Goodwin, L.
AU  - Bruce, D.
AU  - Chen, A.
AU  - Han, C.S.
AU  - Huntemann, M.
AU  - Ivanova, N.
AU  - Land, M.L.
AU  - Nolan, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Rodrigues, J.L.
TI  - Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes.
JO  - Genome Announcements
PY  - 2015
SP  - e00060
EP  - e00015
VL  - 3
AB  - The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated
AB  - from the wood-feeding termite hindgut. We report here its complete
AB  - genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and
AB  - 99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy,
AB  - lignocellulose degradation, and ammonia and sulfate assimilation.
ER  -

TY  - JOUR
AU  - Kotani, H.
AU  - Nomura, Y.
AU  - Kawashima, Y.
AU  - Sagawa, H.
AU  - Takagi, M.
AU  - Kita, A.
AU  - Ito, H.
AU  - Kato, I.
TI  - Sse8387I, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-CCTGCAGG-3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 5637
EP  - 5640
VL  - 18
AB  - A type II restriction endonuclease designated Sse8387I was partially purified
AB  - from Streptomyces sp. 8387.  This enzyme cleaved adenovirus 2 DNA at three
AB  - sites, lambda phage DNA at five sites, and pUC18 and M13mp18 RF DNA at one site
AB  - each, but did not cleave the DNAs from pBR322, SV40, or PhiX174.  Sse8387I
AB  - recognized the octanucleotide sequence 5'-CCTGCA^GG-3', cleaving where shown by
AB  - the arrow.  Sse8387I is the first restriction endonuclease to be reported that
AB  - recognizes an octanucleotide sequence consisting of all four nucleotides,
AB  - G,A,T, and C.  The frequency of occurrence of Sse83787I sites within sequenced
AB  - regions of primate genomes was 2.4 times that of NotI sites.
ER  -

TY  - JOUR
AU  - Kothari, V.V.
AU  - Kothari, R.K.
AU  - Kothari, C.R.
AU  - Bhatt, V.D.
AU  - Nathani, N.M.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Vyas, B.R.
TI  - Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00337
EP  - e00314
VL  - 2
ER  -

TY  - JOUR
AU  - Kothari, V.V.
AU  - Kothari, R.K.
AU  - Kothari, C.R.
AU  - Bhatt, V.D.
AU  - Nathani, N.M.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Vyas, B.R.
TI  - Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00671
EP  - e00613
VL  - 1
AB  - Bacillus safensis strain VK was isolated from the rhizosphere of a cumin plant growing in the
AB  - saline desert of Radhanpar, Gujarat, India. Here, we provide the
AB  - 3.68-Mb draft genome sequence of B. safensis VK, which might provide information
AB  - about the salt tolerance and genes encoding enzymes for the strain's plant
AB  - growth-promoting potential.
ER  -

TY  - JOUR
AU  - Kotoky, R.
AU  - Singha, L.P.
AU  - Pandey, P.
TI  - Draft Genome Sequence of Heavy Metal-Resistant Soil Bacterium Serratia marcescens S2I7, Which Has the Ability To Degrade Polyaromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2017
SP  - e01338
EP  - e01317
VL  - 5
AB  - Serratia marcescens S2I7 is a heavy metal-resistant, polyaromatic hydrocarbon-degrading
AB  - bacterium isolated from petroleum-contaminated sites. The
AB  - genome contains one circular chromosome (5,241,555 bp; GC content 60.1%) with
AB  - 4,533 coding sequences. The draft genome sequence includes specific genetic
AB  - elements for degradation of hydrocarbons and for heavy metal resistance.
ER  -

TY  - JOUR
AU  - Koton, Y.
AU  - Eghbaria, S.
AU  - Gordon, M.
AU  - Chalifa-Caspi, V.
AU  - Bisharat, N.
TI  - Draft Genome Sequence of Fish Pathogenic Vibrio vulnificus Biotype 2.
JO  - Genome Announcements
PY  - 2014
SP  - e01224
EP  - e01214
VL  - 2
AB  - Vibrio vulnificus is a marine pathogen capable of causing severe soft tissue infections and
AB  - septicemia in humans. V. vulnificus biotype 2 is the etiological
AB  - agent of fish vibriosis. We describe here the first draft genome sequence of V.
AB  - vulnificus biotype 2, strain ES-7601, isolated from an infected eel in Japan.
ER  -

TY  - JOUR
AU  - Kotorashvili, A.
AU  - Meparishvili, G.
AU  - Gogoladze, G.
AU  - Kotaria, N.
AU  - Muradashvili, M.
AU  - Zarandia, M.
AU  - Tsaguria, D.
TI  - Three Draft Genome Sequences of the Bacterial Plant Pathogen Ralstonia solanacearum, Isolated in Georgia.
JO  - Genome Announcements
PY  - 2017
SP  - e00480
EP  - e00417
VL  - 5
AB  - Ralstonia solanacearum, the causative agent of bacterial wilt, is a devastating bacterial
AB  - plant pathogen with a wide range of hosts. We report here the first
AB  - draft genome sequences for three strains of Ralstonia solanacearum isolated from
AB  - infected potato, tomato, and pepper plants in Georgia.
ER  -

TY  - JOUR
AU  - Kotova, V.Y.
AU  - Zavilgelskii, G.B.
AU  - Belogurov, A.A.
TI  - Weakening of the type-I restriction in the presence of plasmids of the incI group. General characteristics and molecular cloning of ard gene.
JO  - Mol. Biol. (Mosk)
PY  - 1988
SP  - 270
EP  - 276
VL  - 22
AB  - Plasmids of the incI group possess the ability to weaken the effect of type-I
AB  - restrictases on unmodified DNA.  The ard locus, which is responsible for weakening of
AB  - type I restriction, is located in plasmid ColIb-P9(incIa) in the region of the Sal GI-C
AB  - fragment.  Cloning was conducted of the ard locus in multicopy vector pBR322.  The ard
AB  - gene specifically weakens type-I restriction (EcoK, EcoB, EcoA, EcoD) and does not
AB  - influence restrictase systems of type II (EcoRI) and III (EcoPI).  Activity of the ard gene
AB  - does not depend on bacterial genes recA, lexA, recBC, recF.  Product of the ard gene does
AB  - not influence the process of methylation of DNA by type-I fragments and is not a specific
AB  - methylase.
ER  -

TY  - JOUR
AU  - Koudan, E.V.
AU  - Brevnov, M.G.
AU  - Subach, O.M.
AU  - Rechkoblit, O.A.
AU  - Bujnicki, J.M.
AU  - Gromova, E.S.
TI  - Probing of contacts between EcoRII DNA methyltransferase and DNA with the use of substrate analogs and molecular modeling.
JO  - Mol. Biol. (Mosk)
PY  - 2007
SP  - 806
EP  - 819
VL  - 41
AB  - The molecular mechanisms of DNA recognition and modification by EcoRII DNA methyltransferase
AB  - (M.EcoRII) were studied using 14-mer substrate
AB  - analogs containing 2-aminopurine or 1',2'-dideoxy-D-ribofuranose in the
AB  - M.EcoRII recognition site. The efficiency of DNA binding and
AB  - methylation depended on the position of a modified nucleoside residue
AB  - in the recognition site. A structural model of M.EcoRII in complex with
AB  - substrate DNA and the cofactor analog S-adenosyl-L-homocysteine
AB  - (AdoHcy) was constructed using the available crystal structures of
AB  - M.Hha and M.HaeIII and the recent Frankenstein's monster approach. The
AB  - amino acid residues interacting with DNA were predicted based on the
AB  - model. In addition, theoretical and experimental findings made it
AB  - possible to predict the groups of atoms of the heterocyclic bases of
AB  - the M.EcoRII recognition site that are presumably involved in the
AB  - interactions with the enzyme.
ER  -

TY  - JOUR
AU  - Koudan, E.V.
AU  - Bujnicki, J.M.
AU  - Gromova, E.S.
TI  - Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.
JO  - J. Biomol. Struct. Dyn.
PY  - 2004
SP  - 339
EP  - 345
VL  - 22
AB  - Prokaryotic DNA methyltransferase M.SssI recognizes and methylates C5 position of the cytosine
AB  - residue within the CG dinucleotides in DNA. It
AB  - is an excellent model for studying the mechanism of interaction between
AB  - CG-specific eukaryotic methyltransferases and DNA. We have built a
AB  - structural model of M.SssI in complex with the substrate DNA and its
AB  - analogues as well as the cofactor analogue S-adenosyl-L-homocysteine
AB  - (AdoHcy) using the previously solved structures of M.HhaI and M.HaeIII
AB  - as templates. The model was constructed according to the recently
AB  - developed "FRankenstein's monster" approach. Based on the model, amino
AB  - acid residues taking part in cofactor binding, target recognition and
AB  - catalysis were predicted. We also modeled covalent modification of the
AB  - DNA substrate and studied its influence on protein-DNA interactions.
ER  -

TY  - JOUR
AU  - Koudan, E.V.
AU  - Subach, O.M.
AU  - Korshunova, G.A.
AU  - Romanova, E.A.
AU  - Eritja, R.
AU  - Gromova, E.S.
TI  - DNA duplexes containing photoactive derivatives of 2'-deoxyuridine as photocrosslinking probes for EcoRII DNA methyltransferase-substrate interaction.
JO  - J. Biomol. Struct. Dyn.
PY  - 2002
SP  - 421
EP  - 428
VL  - 20
AB  - EcoRII DNA methyltransferase (M.EcoRII) recognizes the DNA sequence 5'.CC*T/AGG.3' and
AB  - catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the C5 position of
AB  - the inner cytosine residue (C*). We obtained several DNA duplexes containing photoactive
AB  - 5-iodo-2'-deoxyuridine (i(5)dU) or
AB  - 5-[4-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenyl]-2'-deoxyuridine (Tfmdp-dU) to characterize
AB  - regions of M.EcoRII involved in DNA binding and to investigate the DNA double helix
AB  - conformational changes that take place during methylation. The efficiencies of methylation,
AB  - DNA binding affinities and M.EcoRII-DNA photocrosslinking yields strongly depend on the type
AB  - of modification and its location within the EcoRII recognition site. The data obtained agree
AB  - with the flipping of the target cytosine out of the DNA double helix for catalysis. To probe
AB  - regions of M.EcoRII involved in DNA binding, covalent conjugates M.EcoRII-DNA were cleaved by
AB  - cyanogen bromide followed by analysis of the oligonucleotide-peptides obtained. DNA duplexes
AB  - containing i(5)dU or Tfmdp-dU at the central position of the recognition site, or instead of
AB  - the target cytosine were crosslinked to the Gly(268)-Met(391) region of the EcoRII methylase.
AB  - Amino acid residues from this region may take part both in substrate recognition and
AB  - stabilization of the extrahelical target cytosine residue.
ER  -

TY  - JOUR
AU  - Koufopanou, V.
AU  - Burt, A.
TI  - Degeneration and domestication of a selfish gene in yeast: Molecular evolution versus site-directed mutagenesis.
JO  - Mol. Biol. Evol.
PY  - 2005
SP  - 1535
EP  - 1538
VL  - 22
AB  - VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including
AB  - horizontal transmission, degeneration, and domestication into the mating-type switching locus
AB  - HO. We investigate here the effects of these features on its molecular evolution. In addition,
AB  - we correlate rates of evolution with results from site-directed mutagenesis studies.
AB  - Functional elements have lower rates of evolution than degenerate ones and higher conservation
AB  - at functionally important sites. However, functionally important and unimportant sites are
AB  - equally likely to have been involved in the evolution of new function during the domestication
AB  - of VDE into HO. The domestication event also indicates that VDE has been lost in some species
AB  - and that VDE has been present in yeasts for more than 50 Myr.
ER  -

TY  - JOUR
AU  - Koufopanou, V.
AU  - Goddard, M.R.
AU  - Burt, A.
TI  - Adaptation for horizontal transfer in a homing endonuclease.
JO  - Mol. Biol. Evol.
PY  - 2002
SP  - 239
EP  - 246
VL  - 19
AB  - Selfish genes of no function other than self-propagation are susceptible to degeneration if
AB  - they become fixed in a population, and regular transfer to new species may be the only means
AB  - for their long-term persistence. To test this idea we surveyed 24 species of yeast for VDE, a
AB  - nuclear, intein-associated homing endonuclease gene (HEG) originally discovered in
AB  - Saccharomyces cerevisiae. Phylogenetic analyses show that horizontal transmission has been a
AB  - regular occurrence in its evolutionary history. Moreover, VDE appears to be specifically
AB  - adapted for horizontal transmission. Its 31-bp recognition sequence is an unusually
AB  - well-conserved region in an unusually well-conserved gene. In addition, the nine nucleotide
AB  - sites most critical for homing are also unusually well conserved. Such adaptation for
AB  - horizontal transmission presumably arose as a consequence of selection, both among HEGs at
AB  - different locations in the genome and among variants at the same location. The frequency of
AB  - horizontal transmission must therefore be a key feature constraining the distribution and
AB  - abundance of these genes.
ER  -

TY  - JOUR
AU  - Koukalova, B.
AU  - Kuhrova, V.
AU  - Reich, J.
TI  - Protection of nonmodified phage lambda against EcoK restriction mediated by recA protein.
JO  - Folia Microbiol. (Praha)
PY  - 1985
SP  - 17
EP  - 24
VL  - 30
AB  - A study was conducted to establish whether the EcoK-specific restriction, which is alleviated
AB  - in E. coli cells after UV induction of the SOS response (Day 1977), is also alleviated under
AB  - the influence of an increased level of recA protein without induction of other SOS functions.
AB  - The host cells used were E. coli K-12, strain AB2497, and its derivatives; the nonmodified
AB  - phage lambda was a mutant b2b5(vir).  An increase of the recA protein level was induced using
AB  - the plasmid pX02, which is a recombinant of pBR322 carrying the recA gene of E. coli.
AB  - AB2497(pX02) cells were found to exhibit a lower level of restriction than those without
AB  - plasmid.  The results indicate that the recA protein protects phage DNA during the process of
AB  - restriction.  A further factor affecting restriction is the growth phase of the culture of the
AB  - restricting host: cells in the late stationary phase exhibit lower restriction than those in
AB  - the exponential phase of growth.  By a combination of these two factors (presence of plasmid
AB  - pX02 and stationary growth phase) one can reduce the restriction of nonmodified phage about
AB  - 300 times.
ER  -

TY  - JOUR
AU  - Kouvelis, V.N.
AU  - Davenport, K.W.
AU  - Brettin, T.S.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Han, C.
AU  - Nolan, M.
AU  - Tapia, R.
AU  - Damoulaki, A.
AU  - Kyrpides, N.C.
AU  - Typas, M.A.
AU  - Pappas, K.M.
TI  - Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5049
EP  - 5050
VL  - 193
AB  - Zymomonas mobilis is an alphaproteobacterium studied for bioethanol production. Different
AB  - strains of this organism have been hitherto
AB  - sequenced; they all belong to the Z. mobilis subsp. mobilis taxon. Here we
AB  - report the finished and annotated genome sequence of strain ATCC 29192, a
AB  - cider spoiling agent isolated in the United Kingdom. ATCC 29192 is the
AB  - lectotype of the second best characterized subspecies of Z. mobilis, Z.
AB  - mobilis subsp. pomaceae. The nucleotide sequence of ATCC 29192 is more
AB  - deviant from that of mobilis representatives, which justifies its distinct
AB  - taxonomic positioning and proves particularly useful for comparative and
AB  - functional genomics analyses.
ER  -

TY  - JOUR
AU  - Kouvelis, V.N.
AU  - Saunders, E.
AU  - Brettin, T.S.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Han, C.
AU  - Typas, M.A.
AU  - Pappas, K.M.
TI  - Complete genome sequence of ethanol producer Zymomonas mobilis NCIMB 11163.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7140
EP  - 7141
VL  - 191
AB  - Zymomonas mobilis is an ethanol producing alpha-proteobacterium currently considered as major
AB  - candidate organism for bioethanol production. Here we report the finished and annotated genome
AB  - sequence of the Z. mobilis subsp. mobilis strain NCIMB 11163, a British ale infecting isolate.
AB  - This is the first Z. mobilis strain whose genome, chromosomal and plasmid, is presented in its
AB  - entirety.
ER  -

TY  - JOUR
AU  - Kouvelis, V.N.
AU  - Teshima, H.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, C.
AU  - Tampakopoulou, V.O.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Typas, M.A.
AU  - Pappas, K.M.
TI  - Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer.
JO  - Genome Announcements
PY  - 2014
SP  - e00845
EP  - e00813
VL  - 2
AB  - Zymomonas mobilis subsp. mobilis is one of the most rigorous ethanol-producing organisms known
AB  - to date, considered by many to be the prokaryotic alternative to
AB  - yeast. The two most applied Z. mobilis subsp. mobilis strains, ZM4 and CP4,
AB  - derive from Recife, Brazil, and have been isolated from sugarcane fermentations.
AB  - Of these, ZM4 was the first Z. mobilis representative strain to be sequenced and
AB  - analyzed. Here, we report the finishing of the genome sequence of strain CP4,
AB  - which is highly similar but not identical to that of ZM4.
ER  -

TY  - JOUR
AU  - Kouzminova, E.
AU  - Selker, E.U.
TI  - dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora.
JO  - EMBO J.
PY  - 2001
SP  - 4309
EP  - 4323
VL  - 20
AB  - To understand better the control of DNA methylation, we cloned and characterized the dim-2
AB  - gene of Neurospora crassa, the only eukaryotic gene currently known in which mutations appear
AB  - to eliminate DNA methylation. The dim-2 gene is responsible for methylation in both
AB  - symmetrical and asymmetrical sites. We mapped dim-2 between wc-1 and un-10 on linkage group
AB  - (LG) VIIR and identified the gene by RFLP mapping and genetic complementation. Dim-2 encodes a
AB  - 1454 amino acid protein including a C-terminal domain homologous to known DNA
AB  - methyltransferases (MTases) and a novel N-terminal domain. Neither a deletion that removed the
AB  - first 186 amino acids of the protein nor a mutation in a putative nucleotide binding site
AB  - abolished function, but a single amino acid substitution in the predicted catalytic site did.
AB  - Tests for repeat-induced point mutation (RIP) indicated that dim-2 does not play a role in
AB  - this process, i.e. duplicated sequences are mutated in dim-2 strains, as usual, but the
AB  - mutated sequences are not methylated, unlike the situation in dim-2(+) strains. We conclude
AB  - that dim-2 encodes an MTase that is responsible for all DNA methylation in vegetative tissues
AB  - of Neurospora.
ER  -

TY  - JOUR
AU  - Kovalenko, N.A.
AU  - Sokolov, N.N.
TI  - On the restriction endonucleases immobilization.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1988
SP  - 13
EP  - 15
VL  - 0
AB  - The search for optimal variants of restriction endonuclease immobilization was
AB  - begun recently.  For some enzymes immobilization was successful due to the
AB  - presence of covalent bonds on CNBr-sepharose (EcoRI, BamHI, HindIII, TagI,
AB  - PaeI, SalI, PvuII).  For the enzymes EcoRI, BamHI and HindIII it was due to
AB  - hydrophobic interaction with triethyl-agarose (triethyl-triphenylmethane).  The
AB  - high yield (up to 80%) of enzymatic activity has been obtained for small number
AB  - of restriction endonucleases.  In the experiments of several aminoacid residues
AB  - modification and immobilization of restriction endonucleases the participation
AB  - of lysine, arginine, glutamic acid and SH- or S-S-groups in the catalysis and
AB  - (or) binding of these enzymes with DNA has been shown.  The restriction
AB  - endonuclease immobilization experiments and research into the enzyme's active
AB  - centre enrich each other and are very interesting for their use in molecular
AB  - biology and deepening our knowledge of protein-nucleic interactions.
ER  -

TY  - JOUR
AU  - Kovalenko, N.A.
AU  - Sokolov, N.N.
AU  - Chercasova, T.A.
AU  - Vonsky, V.E.
AU  - Leikin, Y.A.
TI  - Immobilization of restriction endonucleases EcoRI, PaeI and LplI.
JO  - Bioorg. Khim.
PY  - 1992
SP  - 210
EP  - 216
VL  - 18
AB  - In search for sorbents (silica gels, styrene-divinylbenzene copolymers),for immobilization of
AB  - some restriction endonucleases, derivatives of trityl-containing silochroms are shown to bind
AB  - EcoRI, Pae I and LplI endonuclease with the retention of 10-20, 60-70 and 40-60% activity,
AB  - respectively. The immobilized restriction endonucleases have unchanged substrate specificity,
AB  - can be used several times and are stable during storage. Tritylaminopropylsilochrom is
AB  - suggested to be the sorbent of choice.
ER  -

TY  - JOUR
AU  - Kovalevskaya, N.P.
AU  - Ivanov, L.Y.
AU  - Zheleznaya, A.
AU  - Matvienko, N.I.
TI  - Isolation and properties of the restriction endonuclease BstBSI from the thermophilic soil bacterium Bacillus stearothermophilus BS.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1993
SP  - 22
EP  - 25
VL  - 3
AB  - The discovery at the beginning of the 1970s of site-specific endodeoxyribonucleases, known
AB  - under the name of "restriction endonucleases", which cleave DNA into strictly determined
AB  - fragments, served as the basis for the creation of a number of fundamentally new approaches to
AB  - the analysis of nucleic acid structure and was one of the decisive prerequisites for the birth
AB  - of genetic engineering. These enzymes, which interact highly specifically with DNA, are also
AB  - of great interest in the study of the mechanisms of DNA-protein interactions. At present,
AB  - despite the large assortment of site-specific endonucleases already available, the search for
AB  - them is continuing. The main stimulus for continuing investigations, as before, is the effort
AB  - to supplement the arsenal with enzymes with various substrate specificities and thereby to
AB  - expand the possibilities for experimenters.  In the course of the study of the distribution of
AB  - restriction-modification enzymes in various taxonomic groups of microorganisms, we discovered
AB  - several thermophilic strains of the genus Bacillus that produce specific endonucleases. In
AB  - particular, we reported on a new site-specific endonuclease BstBSI from a soil isolate of B.
AB  - stearothermophilus BS. This work presents data on the purification and characterization of the
AB  - endonuclease BstBSI.
ER  -

TY  - JOUR
AU  - Kovalevskaya, N.P.
AU  - Ivanov, L.Y.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - BstBSI, a restriction endonuclease from Bacillus stearothermophilus BS which recognizes 5'GTATAC3'.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4296
EP  - 4296
VL  - 19
AB  - BstBSI, a type II restriction endonuclease, has been isolated from Bacillus stearothermophilus
AB  - BS.  BstBSI, an isoschizomer of SnaI, recognizes the six base palindromic sequence and cleaves
AB  - it as indicated by arrows:
AB  - 5'GTA^TAC3'
AB  - 3'CAT^ATG5'.
AB  - BstBSI recognizes three sites on lambda DNA.  Double digestion mapping with BstBSI and EcoRI,
AB  - SmaI, KpnI, MluI and PvuII showed that BstBSI sites were roughly localized to the genome map
AB  - positions 15200, 18900, 19500.  Examination of the sequences of the lambda DNA showed that the
AB  - sequence GTATAC was present in all of these positions.  The cleavage of the T7 DNA results in
AB  - 7 visible fragments of more than 1 kb length (upper band is a doublet) of expected molecular
AB  - weights.  To identify the cleavage site within the recognition sequence, the recombinant phage
AB  - M13tg130 with KpnI-SmaI fragment with coordinates 18556-19397 of lambda DNA was constructed.
AB  - It has the BstBSI recognition site nearby the KpnI site.  The cleavage site was determined by
AB  - cleavage of a primed-synthesis reaction.  Cleavage product resulted in a single band
AB  - comigrated with A in the middle of the recognition sequence.  An addition of T4 DNA polymerase
AB  - did not change the position of the band.  These results indicate that the BstBSI cleaves the
AB  - recognition sequence in the middle and produces blunt end fragments.  The molecular weight of
AB  - the native enzyme determined by gel filtration method is approximately 80000.  The crude
AB  - extract contained more than 50000 units per gram of wet cells.
ER  -

TY  - JOUR
AU  - Kovalevskaya, N.P.
AU  - Zelinskaya, N.V.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Isolation and properties of the site-specific endonuclease BspTS514I from thermophilic bacterium Bacillus species TS514.
JO  - Bioorg. Khim.
PY  - 1993
SP  - 1073
EP  - 1076
VL  - 19
AB  - New site-specific endonucleases BspBS31I, BstBS32I, BspIS4I, BstTS5I, BspTS514I were isolated
AB  - from five thermophilic soil bacteria Bacillus sp. BS31, B. stearothermophilus BS32, Bacillus
AB  - sp. IS4, B. stearothermophilus TS5, Bacillus sp. TS514. The enzymes are isoschizomers of the
AB  - restriction endonuclease BbvII. Endonuclease BspTS514I was obtained pure from interfering
AB  - contaminations by two consecutive chromatographies on blue agarose and hydroxyapatite. The
AB  - enzyme exhibits a maximal activity at 55oC in 10 mM tris-HCl (pH 9.2), 10 mM MgCl2 and 50 mM
AB  - NaCl.
ER  -

TY  - JOUR
AU  - Kovalevskaya, N.P.
AU  - Zhelenznaya, L.A.
AU  - Zelinskaya, N.V.
AU  - Matvienko, N.I.
TI  - A new thermophilic strain Bacillus coagulans, producing the site-specific endonuclease BcoKI.
JO  - Mikrobiologiia
PY  - 1994
SP  - 235
EP  - 238
VL  - 63
AB  - The strain, producing the new site-specific endonuclease BcoKI has been found during the
AB  - screening of thermophilic bacteria isolated from tobacco. A phenotype characteristic of the
AB  - strain is given. It has been identified as a new strain Bacillus coagulans. BcoKI, a class-IIS
AB  - restriction endonuclease has been obtained by three consecutive chromatographies on blue
AB  - agarose, hydroxyapatite and heparin-Sepharose. BcoKI, an isoschizomer of Ksp6321, recognizes
AB  - the six base non-palindromic sequence 5'CTCTTC3' and cleaves one nucleotide 3' of the 3'
AB  - cytosine on this strand and four nucleotides 5' of the 5' guanine on the opposite strand to
AB  - generate a three base 5' overhang.
ER  -

TY  - JOUR
AU  - Kovalevskaya, N.P.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - BspLS21, a new site-specific endonuclease from thermophilic bacterium Bacillus species LS2.
JO  - Bioorg. Khim.
PY  - 1992
SP  - 1473
EP  - 1477
VL  - 18
AB  - A new restriction endonuclease BspLS2I was isolated from the thermophilic bacterium Bacillus
AB  - species LS2 and purified by blue sepharose and hydroxyapatite chromatographies. The enzyme is
AB  - an isoschizomer of SduI from Streptococcus durans. BspLS2I recognizes the sequence
AB  - 5'G(G/A/T)GC(C/T/A)^C3' on double-stranded DNA and cleaves it is indicated by the arrow to
AB  - yield sticky-ended DNA fragments. Maximum catalytic activity of the endonuclease was found in
AB  - 10 mM Tris-HCl (pH7.9) in the presence of 15-30 mM MgCl2 at 50oC. The phage T4 glucosylated
AB  - DNA is not cleaved by the enzyme.
ER  -

TY  - JOUR
AU  - Kovall, R.A.
AU  - Matthews, B.W.
TI  - Type II restriction endonucleases: structural, functional and evolutionary relationships.
JO  - Curr. Opin. Chem. Biol.
PY  - 1999
SP  - 578
EP  - 583
VL  - 3
AB  - Type II restriction endonucleases are a paradigm for site-specific cleavage of DNA. Recent
AB  - structural analyses, in particular in the presence of various divalent metals, have shed new
AB  - insight into the mechanisms of catalysis. In addition, during this past year the crystal
AB  - structure determinations of MutH, lambda-exonuclease and FokI have revealed that these
AB  - proteins are also members of the same family.
ER  -

TY  - JOUR
AU  - Kovall, R.A.
AU  - Matthews, B.W.
TI  - Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 7893
EP  - 7897
VL  - 95
AB  - Lambda-exonuclease participates in DNA recombination and repair.  It binds a free end of
AB  - double-stranded DNA and degrades one stand in the 5' to 3' direction.  The primary sequence
AB  - does not appear to be related to any other protein, but the crystal structure shows part of
AB  - lambda-exonuclease to be similar to the type II restriction endonucleases PvuII and EcoRV.
AB  - There is also a weaker correspondence with EcoRI, BamHI, and Cfr10I.  The structure
AB  - comparisons not only suggest that these enzymes all share a similar catalytic mechanism and a
AB  - common structural ancestor but also provide strong evidence that the toroidal structure of
AB  - lambda-exonuclease encircles its DNA substrate during hydrolysis.
ER  -

TY  - JOUR
AU  - Kovarik, A.
AU  - Koukalova, B.
AU  - Lim, L.Z.
AU  - Matyasek, R.
AU  - Lichtenstein, C.P.
AU  - Leitch, A.R.
AU  - Bezdek, M.
TI  - Inhibition of tobacco DNA methyltransferase in vivo causes unequal hypomethylation of DNA repeated sequences.
JO  - J. Biomol. Struct. Dyn.
PY  - 2000
SP  - 1144
EP  - 1145
VL  - 17
AB  - DNA repetitive sequences are characterized with a high content of methylated cytosine
AB  - (5-methylcytosine, 5-mC).  In tobacco genomic DNA about 30% of all cytosine residues are
AB  - methylated.  However, in our previous study it was found that two families of 5S rDNA
AB  - reiterated sequence have more than 50% of all cytosine residues methylated suggesting that
AB  - differences in DNA methylation levels between DNA repeated sequences may exist.  The aim of
AB  - this study was to compare the methylation patterns in several repetitive DNA sequences of
AB  - Nicotiana tabacum nuclear genome as well as their susceptibility to the effect of a
AB  - hypomethylating drug dihydroxypropyladenine.  This drug is thought to reduce DNA
AB  - methyltransferase activity by increasing S-adenosylhomocysteine levels.  To detect methylation
AB  - state in CG and CCG sites in DNA loci studied, methylation-sensitive restriction enzymes
AB  - (MspI, HapII, Sau3A1 and BamHI) were used.
ER  -

TY  - JOUR
AU  - Kowalski, J.C.
AU  - Belfort, M.
AU  - Stapleton, M.A.
AU  - Holpert, M.
AU  - Dansereau, J.T.
AU  - Pietrokovski, S.
AU  - Baxter, S.M.
AU  - Derbyshire, V.
TI  - Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 2115
EP  - 2125
VL  - 27
AB  - I-TevI is a member of the GIY-YIG family of homing endonucleases.  It is folded into two
AB  - structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding
AB  - domain, separated by a flexible linker.  In this study we have used genetic anlayses,
AB  - computational sequence analysis and NMR spectroscopy to define the configuration of the
AB  - N-terminal domain and its relationship to the flexible linker.  The catalytic domain is an
AB  - alpha/beta structure contained within the first 92 amino acids of the 245-amino acid protein
AB  - followed by an unstructured linker.  Remarkably, this structured domain corresponds precisely
AB  - to the GIY-YIG module defined by sequence comparisons of 57 proteins including more than 30
AB  - newly reported members of the family.  Although much of the unstructured linker is not
AB  - essential for activity, residues 93-116 are required, raising the possibility that this region
AB  - may adopt an alternate conformation upon DNA binding.  Two invariant residues of the GIY-YIG
AB  - module, Arg27 and Glu75, located in alpha-helices, have properties of catalytic residues.
AB  - Furthermore, the GIY-YIG sequence elements for which the module is named form part of a
AB  - three-stranded antiparallel beta-sheet that is important for I-TevI structure and function.
ER  -

TY  - JOUR
AU  - Kowalski, J.C.
AU  - Derbyshire, V.
TI  - Characterization of homing endonucleases.
JO  - Methods
PY  - 2002
SP  - 365
EP  - 373
VL  - 28
AB  - Homing endonucleases are a class of site-specific DNA endonucleases encoded by open reading
AB  - frames within introns and inteins. They initiate the mobility of their host element by
AB  - recognizing intronless or inteinless alleles of their host gene and making a double-strand
AB  - break. The homing endonucleases are notable for their long target sites and a tolerance for
AB  - sequence polymorphisms in their substrates. The methods used to study homing endonucleases are
AB  - similar to those used to study protein-DNA interactions in general. However, some variations
AB  - and specialized techniques are useful in characterizing homing endonucleases and these methods
AB  - are discussed.
ER  -

TY  - JOUR
AU  - Kozak, N.A.
AU  - Buss, M.
AU  - Lucas, C.E.
AU  - Frace, M.
AU  - Govil, D.
AU  - Travis, T.
AU  - Olsen-Rasmussen, M.
AU  - Benson, R.F.
AU  - Fields, B.S.
TI  - Virulence factors encoded by Legionella longbeachae identified on the basis of the genome sequence analysis of clinical isolate D-4968.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1030
EP  - 1044
VL  - 192
AB  - Legionella longbeachae causes most cases of legionellosis in Australia and may be
AB  - underreported worldwide due to the lack of L. longbeachae-specific diagnostic tests. L.
AB  - longbeachae displays distinctive differences in intracellular trafficking, caspase 1
AB  - activation, and infection in mouse models compared to Legionella pneumophila, yet these two
AB  - species have indistinguishable clinical presentations in humans. Unlike other legionellae,
AB  - which inhabit freshwater systems, L. longbeachae is found predominantly in moist soil. In this
AB  - study, we sequenced and annotated the genome of an L. longbeachae clinical isolate from
AB  - Oregon, isolate D-4968, and compared it to the previously published genomes of L.
AB  - pneumophila. The results revealed that the D-4968 genome is larger than the L.
AB  - pneumophila genome and has a gene order that is different from that of the L.
AB  - pneumophila genome. Genes encoding structural components of type II, type IV Lvh, and type IV
AB  - Icm/Dot secretion systems are conserved. In contrast, only 42/140 homologs of genes encoding
AB  - L. pneumophila Icm/Dot substrates have been found in the D-4968 genome. L. longbeachae encodes
AB  - numerous proteins with eukaryotic motifs and eukaryote-like proteins unique to this species,
AB  - including 16 ankyrin repeat-containing proteins and a novel U-box protein. We predict that
AB  - these proteins are secreted by the L. longbeachae Icm/Dot secretion system. In contrast to the
AB  - L. pneumophila genome, the L. longbeachae D-4968 genome does not contain flagellar
AB  - biosynthesis genes, yet it contains a chemotaxis operon. The lack of a flagellum explains the
AB  - failure of L. longbeachae to activate caspase 1 and trigger pyroptosis in murine macrophages.
AB  - These unique features of L. longbeachae may reflect adaptation of this species to life in
AB  - soil.
ER  -

TY  - JOUR
AU  - Kozak-Muiznieks, N.A.
AU  - Morrison, S.S.
AU  - Mercante, J.W.
AU  - Ishaq, M.K.
AU  - Johnson, T.
AU  - Caravas, J.
AU  - Lucas, C.E.
AU  - Brown, E.
AU  - Raphael, B.H.
AU  - Winchell, J.M.
TI  - Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies.
JO  - Infect. Genet. Evol.
PY  - 2018
SP  - 172
EP  - 185
VL  - 59
AB  - The majority of Legionnaires' disease (LD) cases are caused by Legionella
AB  - pneumophila, a genetically heterogeneous species composed of at least 17
AB  - serogroups. Previously, it was demonstrated that L. pneumophila consists of three
AB  - subspecies: pneumophila, fraseri and pascullei. During an LD outbreak
AB  - investigation in 2012, we detected that representatives of both subspecies
AB  - fraseri and pascullei colonized the same water system and that the
AB  - outbreak-causing strain was a new member of the least represented subspecies
AB  - pascullei. We used partial sequence based typing consensus patterns to mine an
AB  - international database for additional representatives of fraseri and pascullei
AB  - subspecies. As a result, we identified 46 sequence types (STs) belonging to
AB  - subspecies fraseri and two STs belonging to subspecies pascullei. Moreover, a
AB  - recent retrospective whole genome sequencing analysis of isolates from New York
AB  - State LD clusters revealed the presence of a fourth L. pneumophila subspecies
AB  - that we have termed raphaeli. This subspecies consists of 15 STs. Comparative
AB  - analysis was conducted using the genomes of multiple members of all four L.
AB  - pneumophila subspecies. Whereas each subspecies forms a distinct phylogenetic
AB  - clade within the L. pneumophila species, they share more average nucleotide
AB  - identity with each other than with other Legionella species. Unique genes for
AB  - each subspecies were identified and could be used for rapid subspecies detection.
AB  - Improved taxonomic classification of L. pneumophila strains may help identify
AB  - environmental niches and virulence attributes associated with these genetically
AB  - distinct subspecies.
ER  -

TY  - JOUR
AU  - Kozak-Muiznieks, N.A.
AU  - Morrison, S.S.
AU  - Sammons, S.
AU  - Rowe, L.A.
AU  - Sheth, M.
AU  - Frace, M.
AU  - Lucas, C.E.
AU  - Loparev, V.N.
AU  - Raphael, B.H.
AU  - Winchell, J.M.
TI  - Three Genome Sequences of Legionella pneumophila subsp. pascullei Associated with Colonization of a Health Care Facility.
JO  - Genome Announcements
PY  - 2016
SP  - e00335
EP  - e00316
VL  - 4
AB  - Here, we report the complete genome sequences of three Legionella pneumophila subsp. pascullei
AB  - strains (including both serogroup 1 and 5 strains) that were
AB  - found in the same health care facility in 1982 and 2012.
ER  -

TY  - JOUR
AU  - Kozbial, P.Z.
AU  - Mushegian, A.R.
TI  - Natural history of S-adenosylmethionine-binding proteins.
JO  - BMC Struct. Biol.
PY  - 2005
SP  - 19
EP  - 19
VL  - 5
AB  - Background.  S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis
AB  - and modification of virtually every class of biomolecules. The most notable reaction requiring
AB  - S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes,
AB  - S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable
AB  - structure-function studies. Evolutionary trajectories of these enzymes, and especially of
AB  - other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly
AB  - understood. We addressed this issue by computational comparison of sequences and structures of
AB  - various S-adenosylmethionine-binding proteins.  Results.  Two widespread folds, Rossmann fold
AB  - and TIM barrel, have been repeatedly used in evolution for diverse types of
AB  - S-adenosylmethionine conversion. There were also cases of recruitment of other relatively
AB  - common folds for S-adenosylmethionine binding. Several classes of proteins have unique
AB  - unrelated folds, specialized for just one type of chemistry and unified by the theme of
AB  - internal domain duplications. In several cases, functional divergence is evident, when
AB  - evolutionarily related enzymes have changed the mode of binding and the type of chemical
AB  - transformation of S-adenosylmethionine. There are also instances of functional convergence,
AB  - when biochemically similar processes are performed by drastically different classes of
AB  - S-adenosylmethionine-binding proteins.  Comparison of remote sequence similarities and
AB  - analysis of phyletic patterns suggests that the last universal common ancestor of cellular
AB  - life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes,
AB  - providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of
AB  - several substrates, including nucleic acids and peptide chain release factor.  Conclusion.  We
AB  - have observed several novel relationships between families that were not known to be related
AB  - before, and defined 15 large superfamilies of SAM-binding proteins, at least 5 of which may
AB  - have been represented in the last common ancestor.
ER  -

TY  - JOUR
AU  - Kozdon, J.B.
AU  - Melfi, M.D.
AU  - Luong, K.
AU  - Clark, T.A.
AU  - Boitano, M.
AU  - Wang, S.
AU  - Zhou, B.
AU  - Gonzalez, D.
AU  - Collier, J.
AU  - Turner, S.W.
AU  - Korlach, J.
AU  - Shapiro, L.
AU  - McAdams, H.H.
TI  - Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2013
SP  - E4658
EP  - E4667
VL  - 110
AB  - The Caulobacter DNA methyltransferase CcrM is one of five master cell-cycle regulators. CcrM
AB  - is transiently present near the end of DNA replication when it
AB  - rapidly methylates the adenine in hemimethylated GANTC sequences. The timing of
AB  - transcription of two master regulator genes and two cell division genes is
AB  - controlled by the methylation state of GANTC sites in their promoters. To explore
AB  - the global extent of this regulatory mechanism, we determined the methylation
AB  - state of the entire chromosome at every base pair at five time points in the cell
AB  - cycle using single-molecule, real-time sequencing. The methylation state of 4,515
AB  - GANTC sites, preferentially positioned in intergenic regions, changed
AB  - progressively from full to hemimethylation as the replication forks advanced.
AB  - However, 27 GANTC sites remained unmethylated throughout the cell cycle,
AB  - suggesting that these protected sites could participate in epigenetic regulatory
AB  - functions. An analysis of the time of activation of every cell-cycle regulatory
AB  - transcription start site, coupled to both the position of a GANTC site in their
AB  - promoter regions and the time in the cell cycle when the GANTC site transitions
AB  - from full to hemimethylation, allowed the identification of 59 genes as
AB  - candidates for epigenetic regulation. In addition, we identified two previously
AB  - unidentified N6-methyladenine motifs and showed that they maintained a constant
AB  - methylation state throughout the cell cycle. The cognate methyltransferase was
AB  - identified for one of these motifs as well as for one of two 5-methylcytosine
AB  - motifs.
ER  -

TY  - JOUR
AU  - Kozhakhmetov, S.S.
AU  - Kushugulova, A.R.
AU  - Saduakhasova, S.A.
AU  - Shakhabayeva, G.S.
AU  - Khassenbekova, Z.R.
AU  - Molkenov, A.B.
AU  - Kairov, U.E.
AU  - Issayeva, R.B.
AU  - Nurgozhin, T.S.
AU  - Zhumadilov, Z.S.
TI  - Draft Genome Sequence of Lactobacillus rhamnosus CLS17.
JO  - Genome Announcements
PY  - 2015
SP  - e00478
EP  - e00415
VL  - 3
AB  - We announce the draft genome sequence of the type strain Lactobacillus rhamnosus  CLS17
AB  - (2,889,314 nt, with a GC content of 46.8%), which is one of the most
AB  - prevalent lactic acid bacteria present during the manufacturing process of dairy
AB  - products; the genome consists of 71 large contigs (>100 bp in size). It contains
AB  - 2,643 protein-coding sequences, single predicted copies of the 5S, 16S, and 23S
AB  - rRNA genes, and 51 predicted tRNAs.
ER  -

TY  - JOUR
AU  - Koziaeva, V.V.
AU  - Dziuba, M.V.
AU  - Ivanov, T.M.
AU  - Kuznetsov, B.B.
AU  - Skryabin, K.G.
AU  - Grouzdev, D.S.
TI  - Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1.
JO  - Genome Announcements
PY  - 2016
SP  - e00814
EP  - e00816
VL  - 4
AB  - We report here the draft genome sequences of two recently isolated magnetotactic  species,
AB  - Magnetospirillum moscoviense BB-1 and Magnetospirillum marisnigri SP-1.
AB  - The genome of M. moscoviense BB-1 has 4,164,497 bp, 65.2% G+C content, and
AB  - comprises 207 contigs. The genome of M. marisnigri SP-1 consists of 131 contigs
AB  - and has a length of 4,619,819 bp and 64.7% G+C content.
ER  -

TY  - JOUR
AU  - Koziel, M.
AU  - Lucid, A.
AU  - Bullman, S.
AU  - Corcoran, G.D.
AU  - Lucey, B.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of Campylobacter corcagiensis Strain CIT045T, a Representative of a Novel Campylobacter Species Isolated from Lion-Tailed Macaques (Macaca silenus).
JO  - Genome Announcements
PY  - 2014
SP  - e00248
EP  - e00214
VL  - 2
AB  - Campylobacter corcagiensis CIT045(T) (=CCUG 64942(T), LMG 27932(T)), a new member of the
AB  - Campylobacter genus, has recently been isolated from lion-tailed macaques in Cork, Ireland. To
AB  - further characterize this new species and its potential pathogenicity, the genome sequence of
AB  - C. corcagiensis was determined and is presented here.
ER  -

TY  - JOUR
AU  - Koziolkiewicz, M.
TI  - Interactions between EcoRI restriction endonuclease and DNA.
JO  - Postepy Biochem.
PY  - 1991
SP  - 23
EP  - 32
VL  - 37
AB  - *
AB  - A review in Polish arranged as:
AB  -    I. Specific interactions between proteins and DNA
AB  -   II. EcoRI endonuclease
AB  - II-1. EcoRI activity
AB  - II-2. Contact-points between EcoRI protein and DNA
AB  - II-3. Application of synthetic oligonucleotides in the studies on the mechanism of EcoRI
AB  -       endonuclease action
AB  - II-4. X-Ray studies on the EcoRI endonuclease - DNA complex
AB  - 
ER  -

TY  - JOUR
AU  - Koziolkiewicz, M.
AU  - Stec, W.J.
TI  - Application of phosphate-backbone-modified oligonucleotides in the studies on EcoRI endonuclease mechanism of action.
JO  - Biochemistry
PY  - 1992
SP  - 9460
EP  - 9466
VL  - 31
AB  - Chemical synthesis of oligodeoxyribonucleotides modified at a preselected internucleotide bond
AB  - by the replacement of one of the two nonbridging oxygens by a sulfur atom or an ethoxy group
AB  - yields model substrates for studies on DNA-protein interactions. Chromatographic (RP-HPLC)
AB  - separaton of the diastereomers of oligonucleotides containing EcoRI canonical sequence
AB  - together with the assignment of the substituent of orientation in the DNA molecule allowed
AB  - study of the stereochemical aspects of DNA-EcoRI endonuclease interaction. The DNA segment
AB  - involved in interactions between EcoRI protein and phosphate groups appeared to be larger than
AB  - its canonical sequence,...GAATTC...,and was extended to the nonamer. The modification of
AB  - certain internucleotide bonds within this nonamer caused significant or complete protection
AB  - against the nucleolytic action of EcoRI and, in some cases, manifested the
AB  - diastereoselectivity of the enzyme. On the basis of the results of EcoRI-catalyzed hydrolysis
AB  - of stereodefined phosphorothioate and phosphotriester substrates, we propose a model to
AB  - explain this phenomenon at the molecular level.
ER  -

TY  - JOUR
AU  - Kozlowski, J.A.
AU  - Kits, K.D.
AU  - Stein, L.Y.
TI  - Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01541
EP  - e01515
VL  - 4
AB  - The complete genome sequence of Nitrosomonas communis strain Nm2, a mesophilic
AB  - betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Corfu,
AB  - Greece, is reported here. This is the first genome to describe a cluster 8
AB  - Nitrosomonas species and represents an ammonia-oxidizing bacterium commonly found
AB  - in terrestrial ecosystems.
ER  -

TY  - JOUR
AU  - Kozlowski, J.A.
AU  - Kits, K.D.
AU  - Stein, L.Y.
TI  - Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad.
JO  - Genome Announcements
PY  - 2016
SP  - e00094
EP  - e00016
VL  - 4
AB  - The complete genome of Nitrosomonas ureae strain Nm10, a mesophilic betaproteobacterial
AB  - ammonia oxidizer isolated from Mediterranean soils in
AB  - Sardinia, Italy, is reported here. This genome represents a cluster 6a
AB  - nitrosomonad.
ER  -

TY  - JOUR
AU  - Krabbe, M.
AU  - Carlson, K.
TI  - Squence and structure of endonuclease II-dependent cleavage sites in bacteriophage T4 DNA.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 23407
EP  - 23415
VL  - 266
AB  - Endonuclease II of bacteriophage T4 is required for in vivo restriction of
AB  - cytosine-containing DNA from its host, Escherichia coli, (as well as from phage
AB  - mutants lacking cytosine modification), normally the first step in the
AB  - reutilization of host DNA nucleotides for synthesis of phage DNA in infected
AB  - cells.  The phage cytosine-DNA is fragmented incompletely to yield genetically
AB  - defined fragments.  This restriction is different from that of type I, II, or
AB  - III restriction enzymes.  We have located seven major endonuclease II-dependent
AB  - restriction sites in the T4 genome, of which three were analyzed in detail; in
AB  - addition, abundant sites were cleaved in <5% of all molecules.  Sites I, II,
AB  - and III shared the sequence 5'-CCGNNTTGGC-3' and were cleaved in about 25% (I
AB  - and III) and 65% (II) of all molecules, predominantly staggered around the
AB  - first or second of the central unspecified base pairs to yield fragments with
AB  - one 5' base.  The less frequently cleaved sites I and III deviated from site II
AB  - in predicted helical structure when viewed from the consensus strand, and in
AB  - sequence when viewed from the opposite strand.  Thus, interaction with a
AB  - particular helical structure as well as recognition of the bases in DNA appears
AB  - important for efficient cleavage.
ER  -

TY  - JOUR
AU  - Kraev, A.S.
AU  - Kravets, A.N.
AU  - Chernov, B.K.
AU  - Skryabin, K.G.
AU  - Baev, A.A.
TI  - The EcoRV restriction-modification system:  genes, enzymes, synthetic substrates.
JO  - Mol. Biol. (Mosk)
PY  - 1985
SP  - 278
EP  - 284
VL  - 19
AB  - By a combination of deletion mutagenesis induced by nuclease, followed by
AB  - determination of the DNA nucleotide sequence, the organization of the genes of
AB  - the EcoRV restriction-modification system, encoded by plasmid, was established.
AB  - The genes of the restriction endonuclease (a protein with a size of 29,000)
AB  - and methylase (a protein with a size of 35,000) are read in opposite directions
AB  - from an intergene region with a size of 310 nucleotides, containing two
AB  - promoter regions.  No homology of the primary structures of the restriction
AB  - endonuclease EcoRV and the restriction endonuclease EcoRI, which recognizes a
AB  - similar nucleotide sequence and is also encoded by a plasmid, was detected.
AB  - The interaction of restriction endonuclease EcoRV with synthetic
AB  - deoxyoligonucleotides containing a phosphoamide bond in the site of the
AB  - presumed action of the restriction endonuclease was investigated.  It was shown
AB  - that this analog, in contrast to the synthetic dodecamer of the same structure,
AB  - but not containing phosphoamide bonds, is not split out by the restriction
AB  - endonuclease; in the control experiment it was found that under the action of
AB  - the restriction endonuclease EcoRV, blunt ends (GAT^ATC), rather than sticky
AB  - ends (GATAT^C) are formed, as was shown earlier.
ER  -

TY  - JOUR
AU  - Kraev, A.S.
AU  - Zimin, A.A.
AU  - Mironova, M.V.
AU  - Janulaitis, A.
AU  - Tanyashin, V.I.
AU  - Skryabin, K.G.
AU  - Bayev, A.A.
TI  - The DNA ligase gene of bacteriophage T4.
JO  - Dokl. Akad. Nauk.
PY  - 1983
SP  - 1495
EP  - 1500
VL  - 270
AB  - note: This paper shows that GAGCT^C is a site for SduI.  This is the missing
AB  - sequence from the earlier paper in FEBS Lett.
ER  -

TY  - JOUR
AU  - Kraft, C.
AU  - Stack, A.
AU  - Josenhans, C.
AU  - Niehus, E.
AU  - Dietrich, G.
AU  - Correa, P.
AU  - Fox, J.G.
AU  - Falush, D.
AU  - Suerbaum, S.
TI  - Genomic Changes during Chronic Helicobacter pylori Infection.
JO  - J. Bacteriol.
PY  - 2006
SP  - 249
EP  - 254
VL  - 188
AB  - The gastric pathogen Helicobacter pylori shows tremendous genetic variability within human
AB  - populations, both in gene content and at the
AB  - sequence level. We investigated how this variability arises by comparing
AB  - the genome content of 21 closely related pairs of isolates taken from the
AB  - same patient at different time points. The comparisons were performed by
AB  - hybridization with whole-genome DNA microarrays. All loci where
AB  - microarrays indicated a genomic change were sequenced to confirm the
AB  - events. The number of genomic changes was compared to the number of
AB  - homologous replacement events without loss or gain of genes that we had
AB  - previously determined by multilocus sequence analysis and mathematical
AB  - modeling based on the sequence data. Our analysis showed that the great
AB  - majority of genetic changes were due to homologous recombination, with
AB  - 1/650 events leading to a net gain or loss of genes. These results suggest
AB  - that adaptation of H. pylori to the host individual may principally occur
AB  - through sequence changes rather than loss or gain of genes.
ER  -

TY  - JOUR
AU  - Krahn, T.
AU  - Wibberg, D.
AU  - Maus, I.
AU  - Winkler, A.
AU  - Nordmann, P.
AU  - Puhler, A.
AU  - Poirel, L.
AU  - Schluter, A.
TI  - Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-beta-Lactamase Gene blaNDM-1.
JO  - Genome Announcements
PY  - 2015
SP  - e01008
EP  - e01015
VL  - 3
AB  - Acinetobacter baumannii is an emerging human pathogen causing nosocomial and
AB  - community-acquired infections. Here, we present the complete genome sequence of the clinical
AB  - A. baumannii strain R2090 carrying the metallo-beta-lactamase gene blaNDM-1 in its chromosome
AB  - within the transposon Tn125.
ER  -

TY  - JOUR
AU  - Krahn, T.
AU  - Wibberg, D.
AU  - Maus, I.
AU  - Winkler, A.
AU  - Puhler, A.
AU  - Poirel, L.
AU  - Schluter, A.
TI  - Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.
JO  - Genome Announcements
PY  - 2015
SP  - e00850
EP  - e00815
VL  - 3
AB  - The complete genome sequence for the reference strain Acinetobacter baumannii CIP 70.10 (ATCC
AB  - 15151) was established. The strain was isolated in France in 1970, is
AB  - susceptible to most antimicrobial compounds, and is therefore of importance for
AB  - comparative genome analyses with clinical multidrug-resistant (MDR) A. baumannii
AB  - strains to study resistance development and acquisition in this emerging human
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Fomenkov, A.I.
AU  - Matvienko, N.I.
TI  - A new type of cleavage of the recognition sequence by a site-specific endonuclease Bst4.4I from Bacillus stearothermophilus 4.4.
JO  - Bioorg. Khim.
PY  - 1988
SP  - 916
EP  - 920
VL  - 14
AB  - A site-specific endonuclease Bst4.4I was isolated from the cell extract of
AB  - Bacillus stearothermophilus 4.4 and partially purified by chromatography on
AB  - Ultragel AcA-44 and heparin-Sepharose.  It was shown that the endonuclease
AB  - cleaves lambda and M13 DNA yielding distinct fragments just as endonucleases of
AB  - Types II and III but, in contrast to them, can produce two two-strand cuts
AB  - separated with 30 to 32 nucleotides in the region of the recognition site.
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Fomenkov, A.I.
AU  - Matvienko, N.I.
AU  - Ubieta, R.H.
AU  - Smolianinov, V.V.
AU  - Gorlenko, V.M.
TI  - A new sequence-specific endonuclease CauB3I from Chloroflexus aurantiacus B3.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 773
EP  - 776
VL  - 13
AB  - A sequence-specific endonuclease CauB3I has been isolated from cell extracts of
AB  - Chloroflexus aurantiacus and partially purified by chromatography on
AB  - heparin-sepharose; the yield was 3000 units per 1 g of cells.  The final
AB  - preparation is free of non-specific nucleases.  It is shown that endonuclease
AB  - CauB3I recognizes 5' T^CCGGA 3' sequence in double-stranded DNA and cleaves it
AB  - as shown.  Methylation of adenine in the recognition sequence makes it
AB  - resistant to CauB3I.
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Mazanov, A.L.
AU  - Pachkunov, D.M.
AU  - Smolyaninov, V.V.
AU  - Matvienko, N.I.
TI  - Another site-specific endonuclease from Rhodopseudomonas sphaeroides.
JO  - Bioorg. Khim.
PY  - 1984
SP  - 46
EP  - 49
VL  - 10
AB  - A site-specific endonuclease RshII has been purified by chromatography on
AB  - Ultro-gel AcA-44, aminohexyl-Sepharose 4B and heparin-Sepharose 6B.  The final
AB  - preparation did not contain nonspecific nucleases or endonuclease RshI.  The
AB  - RshII endonuclease has been shown to recognize in double-stranded DNA the
AB  - following nucleotide sequence:  5'-C'C (C) GG-3'/3'-GG (G) CC-5'.
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Mazanov, A.L.
AU  - Smolyaninov, V.V.
TI  - Isolation of a second site-specific endonuclease from Xanthomonas holcicola and its characterization.
JO  - Bioorg. Khim.
PY  - 1982
SP  - 220
EP  - 223
VL  - 8
AB  - A method is proposed for purifying the site-specific endonuclease XhoII by
AB  - chromatography on phosphocellulose and aminohexyl-Sepharose.  The final product
AB  - contains no nonspecific nucleases as impurities nor the endonuclease XhoI.  It
AB  - has been shown that the endonuclease recognizes and hydrolyzes DNA in the
AB  - nucleotide sequence 5'R-G-A-T-C-Y3'.  According to the results of gel
AB  - filtration, the molecular weight of the endonuclease is 40,000 +/- 2000.  In
AB  - the hydrolysis of DNA by the endonuclease, Mg2+ can be replaced by Mn2+.
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Pachkunov, D.M.
AU  - Matvienko, N.I.
TI  - Site-specific endonucleases BmeI and RshII.
JO  - Nek. Aspekty Fiziol. Mikroorg. Akad. Nauk. SSR.
PY  - 1983
SP  - 22
EP  - 26
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Skrypina, N.A.
AU  - Smolyaninov, V.V.
AU  - Smirnov, V.V.
AU  - Resnik, S.R.
AU  - Sorokulova, I.B.
AU  - Matvienko, N.I.
TI  - New site-specific endonuclease producer strains of Bacillus genera.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1989
SP  - 42
EP  - 45
VL  - 0
AB  - 52 Bacillus strains have been tested for their production of site-specific
AB  - endonucleases.  The sequence recognized by the enzymes was determined for 23
AB  - enzymes, the cleavage site inside the sequence was determined for 5 enzymes.
AB  - All the enzymes under study were found to be isoschizomers of known enzymes.
AB  - The selected strains are unusual for their high level of site-specific
AB  - endonucleases content and may be used as producers of the enzymes.
ER  -

TY  - JOUR
AU  - Kramarov, V.M.
AU  - Smolyaninov, V.V.
TI  - DNA methylase from Arthrobacter luteus screens DNA from the action of site-specific endonuclease AluI.
JO  - Biokhimiia
PY  - 1981
SP  - 1526
EP  - 1529
VL  - 46
AB  - DNA-methylase was isolated from a cell extract of A. luteus and partially
AB  - purified by chromatography on phosphocellulose.  The purified enzyme methylates
AB  - DNA of phage lambda and plasmids pBR322, thus making them resistant to a
AB  - subsequent action of endonuclease AluI.  It has been shown that cytosine is the
AB  - object of methylation within DNA.  This modification does not screen DNA from
AB  - the action of site-specific endonucleases SalI, Bam HI, EcoRI, EcoRII, XhoI and
AB  - XhoII  It has been experimentally demonstrated that the isolated methylase is
AB  - site-specific and identifies in the DNA the nucleotide sequence 5'-AGCT-3', by
AB  - methylating cytosine in the DNA.
ER  -

TY  - JOUR
AU  - Krasilnikova, M.M.
AU  - Izvolskii, K.I.
AU  - Krupnik, O.V.
AU  - Lazurkin, Y.S.
TI  - Use of specific binding of peptide nucleic acids to DNA in the "Achilles heel" method.
JO  - Dokl. Akad. Nauk.
PY  - 1995
SP  - 552
EP  - 555
VL  - 344
ER  -

TY  - JOUR
AU  - Krasnoslobodtsev, A.V.
AU  - Shlyakhtenko, L.S.
AU  - Lyubchenko, Y.L.
TI  - Probing Interactions within the Synaptic DNA-SfiI Complex by AFM Force Spectroscopy.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 1407
EP  - 1416
VL  - 365
AB  - SfiI belongs to a family of restriction enzymes that function as tetramers, binding two
AB  - recognition regions for the DNA cleavage reaction.
AB  - The SfiI protein is an attractive and convenient model for studying
AB  - synaptic complexes between DNA and proteins capable of site-specific
AB  - binding. The enzymatic action of SfiI has been very well characterized.
AB  - However, the properties of the complex before the cleavage reaction are
AB  - not clear. We used single-molecule force spectroscopy to analyze the
AB  - strength of interactions within the SfiI-DNA complex. In these
AB  - experiments, the stability of the synaptic complex formed by the enzyme
AB  - and two DNA duplexes was probed in a series of approach-retraction cycles.
AB  - In order to do this, one duplex was tethered to the surface and the other
AB  - was tethered to the probe. The complex was formed by the protein present
AB  - in the solution. An alternative setup, in which the protein was anchored
AB  - to the surface, allowed us to probe the stability of the complex formed
AB  - with only one duplex in the approach-retraction experiments, with the
AB  - duplex immobilized at the probe tip. Both types of complexes are
AB  - characterized by similar rupture forces. The stability of the complex was
AB  - determined by measuring the dependence of rupture forces on force loading
AB  - rates (dynamic force spectroscopy) and the results suggest that the
AB  - dissociation reaction of the SfiI-DNA complex has a single energy barrier
AB  - along the dissociation path. Dynamic force spectroscopy was instrumental
AB  - in revealing the role of the 5 bp spacer region within the palindromic
AB  - recognition site on DNA-SfiI in the stability of the complex. The data
AB  - show that, although the change of non-specific sequence does not alter the
AB  - position of the activation barrier, it changes values of the off rates
AB  - significantly.
ER  -

TY  - JOUR
AU  - Krause, A. et al.
TI  - Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
JO  - Nat. Biotechnol.
PY  - 2006
SP  - 1385
EP  - 1391
VL  - 24
AB  - Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other
AB  - grasses, is of agrobiotechnological interest because it supplies
AB  - biologically fixed nitrogen to its host and colonizes plants in remarkably
AB  - high numbers without eliciting disease symptoms. The complete genome
AB  - sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding
AB  - sequences. Genome comparison with the Azoarcus-related soil bacterium
AB  - strain EbN1 revealed a surprisingly low degree of synteny. Coding
AB  - sequences involved in the synthesis of surface components potentially
AB  - important for plant-microbe interactions were more closely related to
AB  - those of plant-associated bacteria. Strain BH72 appears to be 'disarmed'
AB  - compared to plant pathogens, having only a few enzymes that degrade plant
AB  - cell walls; it lacks type III and IV secretion systems, related toxins and
AB  - an N-acyl homoserine lactones-based communication system. The genome
AB  - contains remarkably few mobile elements, indicating a low rate of recent
AB  - gene transfer that is presumably due to adaptation to a stable, low-stress
AB  - microenvironment.
ER  -

TY  - JOUR
AU  - Krause, D.O.
AU  - Little, A.C.
AU  - Dowd, S.E.
AU  - Bernstein, C.N.
TI  - Complete genome sequence of adherent invasive Escherichia coli UM146 isolated from ileal Crohn's disease biopsy tissue.
JO  - J. Bacteriol.
PY  - 2010
SP  - 583
EP  - 583
VL  - 193
AB  - Escherichia coli UM146 was isolated from the ileum of a Crohn's disease patient. It adheres
AB  - to and invades enterocytes and can replicate inside
AB  - macrophages. Its complete genome sequence reveals that it is most closely
AB  - related to the human urinary tract pathogen E. coli CFT073, but it has a
AB  - host of genes that are novel and for which function has not been ascribed.
ER  -

TY  - JOUR
AU  - Krause, K.L.
AU  - Miller, M.D.
TI  - A new engine for cleaving nucleic acid.
JO  - ACS Symp. Ser.
PY  - 2002
SP  - 270
EP  - 293
VL  - 827
AB  - Rapid and accurate cleavage of nucleic acid material, such as DNA and RNA, is a fundamentally
AB  - important biochemical process in all living
AB  - organisms carried out by enzymes called nucleases. We present here a
AB  - discussion and comparison of two nucleases of widely disparate
AB  - properties but who share a newly described nuclease active site
AB  - geometry. Serratia marcescens, a pathogenic Gram negative bacterium
AB  - produces an enzyme that presents a new paradigm in nucleases. Its fold
AB  - is new, it is capable of very rapid, and relatively non sequence
AB  - dependent cleavage of several types of DNA and RNA. On the other hand,
AB  - I-PpoI is a homing endonuclease which is encoded by a group I intron in
AB  - the rRNA genes of Physarum polycephalum (1). It also possesses a new
AB  - fold, but it only slowly cleaves DNA at a very specific 15 by site.
AB  - Both enzymes possess the same active site geometry, but no other
AB  - structural homology. The structural basis for their different
AB  - properties is due to two main factors, the nature of their interaction
AB  - with substrate and the presence of a mobile metal in I-Ppol
AB  - endonuclease that must migrate into position prior to catalysis.
ER  -

TY  - JOUR
AU  - Kravets, A.N.
AU  - Pertsev, A.V.
AU  - Tarutina, Z.E.
AU  - Solonin, A.S.
TI  - High homology of plasmids carrying class II restriction modification systems, EcoRV isoschizomers, and their prevalence in natural Escherichia coli strains.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1998
SP  - 20
EP  - 22
VL  - 3
AB  - Screening of 660 clinical Enterobacteriaceae strains from the collection of L.V. Gromashevsky,
AB  - Kiev Institute of Epidemiology and Infectious Diseases, for specific endonuclease activity
AB  - revealed site-specific endonucleases, EcoRV isoschizomers, in 6 E. coli strains.  Genes coding
AB  - for endonucleases and methyltransferases were localized on small (6.2 kb) multicopy Hsd+
AB  - plasmids.  All plasmids were successfully transferred in laboratory strain E. coli K802.
AB  - Restriction analysis and subcloning showed no differences in the structural and functional
AB  - organization of the plasmids studied and a previously revealed pLB1 plasmid, thus reflecting
AB  - their high homology, if not identity.  These data allow us to propose effective horizontal
AB  - transfer of EcoRV plasmids among natural E. coli isolates in the region studied.
ER  -

TY  - JOUR
AU  - Kravets, A.N.
AU  - Pertsev, A.V.
AU  - Tarutina, Z.Y.
AU  - Krendelev, Y.D.
AU  - Zakharova, M.V.
AU  - Beletskaya, I.V.
AU  - Solonin, A.S.
TI  - New isoschizomers of restriction endonucleases in Pseudomonas aeruginosa strains.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1998
SP  - 14
EP  - 17
VL  - 0
AB  - Testing of Pseudomonas aeruginosa strains from the collection of the L.V. Gromashevsky
AB  - Institute of Epidemiology and Infectious Diseases (Kiev) for specific endonucleases resulted
AB  - in the isolation of five class II restriction endonucleases, which were partially purified and
AB  - their recognition targets were determined.  Two of these endonucleases, Pae2kI and Pae18kI,
AB  - are isoschizomers of BglII (5'-AGACTC-3').  Pae5kI and Pae14kI, recognize the
AB  - 5'-CCGC/GG-3' sequence and are therefore true isoschizomers of SacII.  Hence, Pae17kI is an
AB  - isoschizomer of PvuII and cleaves the DNA within the recognition sequence 5'-CAG/CTG-3'.
AB  - BglII and PvuII are for the first time detected in Pseudomonas aeruginosa.
ER  -

TY  - JOUR
AU  - Kravets, A.N.
AU  - Solonin, A.S.
AU  - Zakharova, M.V.
AU  - Tarutina, Z.E.
TI  - Plasmid localization and cloning of restriction-modification genes from Citrobacter freundii 4111 strain.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1992
SP  - 4
EP  - 7
VL  - 7
AB  - Over 60 producing strains of restriction endonucleases type II have been found among 500
AB  - different strains, mostly Enterobacteriaceae. The strain Citrobacter freundii 4111 produces
AB  - restriction endonuclease CfrBI, a new isoschizomer of StyI. The genes of the
AB  - restriction-modification system CfrBI were located on the multicopy plasmid pZE8 containing
AB  - the ColE1-type replicon and cloned into E. coli K802. The deletion variant of 3.2-kb pZE8
AB  - which contains intact restriction-modification and a DNA fragement responsible for autonomous
AB  - plasmid replication was selected among the recombinant plasmids. The strain with higher R.
AB  - CfrBI production (at least 10,000,000 U/g cells, which is 500-fold higher than the wild
AB  - strain) was constructed.
ER  -

TY  - JOUR
AU  - Kravets, A.N.
AU  - Zakharova, M.V.
AU  - Solonin, A.S.
AU  - Kuzmin, N.P.
AU  - Tanyushin, V.I.
AU  - Glatman, L.I.
AU  - Moroz, A.F.
AU  - Baev, A.A.
TI  - Cloning of genes of the EcoRV restriction-modification system and regulation of their expression.
JO  - Mol. Biol. (Mosk)
PY  - 1990
SP  - 438
EP  - 447
VL  - 24
AB  - A number of recombinant plasmids bearing genes of the EcoRV
AB  - restriction-modification system were constructed.  The individual genes were
AB  - inserted into plasmids belonging to different incompatibility groups.  The
AB  - regulatory regions of the genes coding for the methylase and restriction
AB  - endonuclease were cloned and studied.  It was shown using the specialized
AB  - vector pVE8 that the promoter region determining transcription of the
AB  - restriction endonuclease was comparable in terms of efficiency with the early
AB  - promoters of phage lambda and equaled approximately 70% of the efficiency of
AB  - the left-oriented promoter PL.  The promoter region of the methylase gene
AB  - provided about one half as efficient transcription as did the promoter region
AB  - of the restriction-endonuclease gene.  A recombinant plasmid was obtained in
AB  - which the EcoRV restriction-endonuclease gene found itself under the control of
AB  - the complementary regulated promoter of phage lambda, PR, and provided
AB  - 30-40-fold enhancement of biosynthesis of the restriction endonuclease, given
AB  - inactivation of the phage-lambda-c1857 temperature-sensitive repressor.  Under
AB  - inducing conditions, the amount of EcoRV restriction endonuclease in the
AB  - superproducer strain amounted to approximately 10% of the total cell protein.
AB  - The factors conducive to the level of EcoRV restriction endonuclease induction
AB  - attained are discussed.
ER  -

TY  - JOUR
AU  - Kravetz, A.N.
AU  - Tarutina, Z.E.
AU  - Solonin, A.S.
TI  - Two novel restriction endonucleases from Pseudomonas aeruginosa.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4781
EP  - 4781
VL  - 19
AB  - PaePI and PaeHI, type II restriction endonucleases have been isolated from
AB  - clinical strain Pseudomonas aeruginosa 4148.  The enzymes were separated and
AB  - purified by chromatography on DEAE-cellulose DE52, hydroxylapatite and mono Q
AB  - column (FPLC system, Pharmacia Ltd).
ER  -

TY  - JOUR
AU  - Kravetz, A.N.
AU  - Zakharova, M.V.
AU  - Beletskaya, I.V.
AU  - Sineva, E.V.
AU  - Denjmuchametov, M.M.
AU  - Petrov, S.I.
AU  - Glatman, L.I.
AU  - Solonin, A.S.
TI  - The cleavage sites and localization of genes encoding the restriction endonuclease Eco1831I and EcoHI.
JO  - Gene
PY  - 1993
SP  - 153
EP  - 154
VL  - 129
AB  - The restriction endonucleases Eco1831I and EcoHI cleave before the first 5'-cytosine in the
AB  - recognition sequence 5'CCSGG 3'/3' GGSCC 5' (where S=G or C), generate 5-base 5' cohesive
AB  - ends and are encoded by homologous plasmids that are restricted in McrA+ hosts. Thus, they
AB  - differ in their cleavage specificity from that of the BcnI isoschizomer, which cleaves after
AB  - the second 5' cytosine.
ER  -

TY  - JOUR
AU  - Kravetz, A.N.
AU  - Zakharova, M.V.
AU  - Beljetzkaja, I.V.
AU  - Pertzev, A.V.
AU  - Spivak, O.I.
AU  - Solonin, A.S.
TI  - Two novel restriction endonucleases from Klebsiella pneumoniae.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 1501
EP  - 1501
VL  - 21
AB  - Kpn49kI and Kpn49kII, type II restriction endonucleases have been isolated from the clinical
AB  - strain Klebsiella pneumoniae 49k.
ER  -

TY  - JOUR
AU  - Krawczyk, A.O.
AU  - Berendsen, E.M.
AU  - Eijlander, R.T.
AU  - de Jong, A.
AU  - Wells-Bennik, M.H.
AU  - Kuipers, O.P.
TI  - Draft Genome Sequences of Four Bacillus thermoamylovorans Strains Isolated from Milk and Acacia Gum, a Food Ingredient.
JO  - Genome Announcements
PY  - 2015
SP  - e00165
EP  - e00115
VL  - 3
AB  - The thermophilic bacterium Bacillus thermoamylovorans produces highly heat-resistant spores
AB  - that can contaminate food products, leading to their
AB  - spoilage. Here, we present the whole-genome sequences of four B.
AB  - thermoamylovorans strains, isolated from milk and acacia gum.
ER  -

TY  - JOUR
AU  - Krawczyk, A.O.
AU  - de Jong, A.
AU  - Eijlander, R.T.
AU  - Berendsen, E.M.
AU  - Holsappel, S.
AU  - Wells-Bennik, M.H.
AU  - Kuipers, O.P.
TI  - Next-Generation Whole-Genome Sequencing of Eight Strains of Bacillus cereus, Isolated from Food.
JO  - Genome Announcements
PY  - 2015
SP  - e01480
EP  - e01415
VL  - 3
AB  - Bacillus cereus can contaminate food and cause emetic and diarrheal foodborne illness. Here,
AB  - we report whole-genome sequences of eight strains of B. cereus,
AB  - isolated from different food sources.
ER  -

TY  - JOUR
AU  - Krawczyk, A.O.
AU  - de Jong, A.
AU  - Holsappel, S.
AU  - Eijlander, R.T.
AU  - van Heel, A.
AU  - Berendsen, E.M.
AU  - Wells-Bennik, M.H.
AU  - Kuipers, O.P.
TI  - Genome Sequences of 12 Spore-Forming Bacillus Species, Comprising Bacillus coagulans, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus  sporothermodurans, and Bacillus vallismortis, Isolated from Foods.
JO  - Genome Announcements
PY  - 2016
SP  - e00103
EP  - e00116
VL  - 4
AB  - Here, we report the draft genomes of twelve isolates of five different Bacillus species, all
AB  - spore-forming, Gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Krebes, J.
AU  - Morgan, R.D.
AU  - Bunk, B.
AU  - Sproeer, C.
AU  - Luong, K.
AU  - Parusel, R.
AU  - Anton, B.P.
AU  - Koenig, C.
AU  - Josenhans, C.
AU  - Overmann, J.
AU  - Roberts, R.J.
AU  - Korlach, J.
AU  - Suerbaum, S.
TI  - The complex methylome of the human gastric pathogen Helicobacter pylori.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 2415
EP  - 2432
VL  - 42
AB  - The genome of Helicobacter pylori is remarkable for its large number of
AB  - restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been
AB  - suggested to limit natural transformation, the major driving force of genetic diversification
AB  - in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at
AB  - single base resolution, using Single Molecule Real-Time (SMRT) sequencing. For strains 26695
AB  - and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most
AB  - motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel
AB  - methylation patterns corresponding to nine recognition sequences were detected (26695, 3;
AB  - J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and
AB  - expression of candidate methyltransferases (MTases) permitted not only the functional
AB  - characterization of multiple, yet undescribed, MTases, but also revealed novel features of
AB  - both Type I and Type II R-M systems, including frameshift-mediated changes of sequence
AB  - specificity and the interaction of one MTase with two alternative specificity subunits
AB  - resulting in different methylation patterns. The methylomes of these well-characterized H.
AB  - pylori strains will provide a valuable resource for future studies investigating the role of
AB  - H. pylori R-M systems in limiting transformation as well as in gene regulation and host
AB  - interaction.
ER  -

TY  - JOUR
AU  - Krefft, D.
AU  - Zylicz-Stachula, A.
AU  - Mulkiewicz, E.
AU  - Papkov, A.
AU  - Jezewska-Frackowiak, J.
AU  - Skowron, P.M.
TI  - Two-stage gene assembly/cloning of a member of the TspDTI subfamily of bifunctional restriction endonucleases, TthHB27I.
JO  - J. Biotechnol.
PY  - 2015
SP  - 67
EP  - 80
VL  - 194
AB  - The Therms sp. family of bifunctional type IIS/IIG/IIC restriction endonucleases
AB  - (REase)-methyltransferases (MTase) comprises thermo-stable TaqII, TspGWI, TspDTI, TsoI,
AB  - Tth111II/TthHB27I enzymes as well as a number of putative enzymes/open reading frames (ORFs).
AB  - All of the family members share properties including a large protein size (ca. 120 kDa), amino
AB  - acid (aa) sequence homologies, enzymatic activity modulation by S-adenosylmethionine (SAM),
AB  - recognition of similar asymmetric cognate DNA sites and cleavage at a distance of 1119 nt.
AB  - Analysis of the enzyme aa sequences and domain/motif organisation led to further Therms sp.
AB  - family division into the TspDTI and TspGWI subfamilies. The latter exhibits an unprecedented
AB  - phenomenon of DNA recognition change upon substitution of SAM by its analogue, sinefungin
AB  - (SIN), towards a very frequent DNA cleavage. We report cloning in Escherichia coli (E. coli),
AB  - using a two-stage procedure and a putative tthHB27IRM gene, detected by bioinformatics
AB  - analysis of the Therms thermophilus HB27 (T. thermophilus) genome. The functionality of a 3366
AB  - base pair (bp)-/1121 aa-long, high GC content ORF was validated experimentally through the
AB  - expression in E. coli. Protein features corroborated with the reclassification of TthHB27I
AB  - into the TspDTI subfamily, which manifested in terms of aa-sequence/motif homologies and
AB  - insensitivity to SIN-induced specificity shift. However, both SAM and SIN stimulated the REase
AB  - DNA cleavage activity by at least 16-32 times; the highest was observed for the Therms sp.
AB  - family. The availability of TthHB27I and the need to include SAM or SIN in the reaction in
AB  - order to convert the enzyme from 'hibernation' status to efficient DNA cleavage is of
AB  - practical significance in molecular biotechnology, extending the palette of available REase
AB  - specificities.
ER  -

TY  - JOUR
AU  - Kremer, F.S.
AU  - Eslabao, M.R.
AU  - Provisor, M.
AU  - Woloski, R.D.
AU  - Ramires, O.V.
AU  - Moreno, L.Z.
AU  - Moreno, A.M.
AU  - Hamond, C.
AU  - Lilenbaum, W.
AU  - Dellagostin, O.A.
TI  - Draft Genome Sequences of Leptospira santarosai Strains U160, U164, and U233, Isolated from Asymptomatic Cattle.
JO  - Genome Announcements
PY  - 2015
SP  - e00910
EP  - e00915
VL  - 3
AB  - In the present work, we announce the draft genomes for three new strains (U160, U164, and
AB  - U233) of Leptospira santarosai, isolated from urine samples from
AB  - asymptomatic cattle in Rio de Janeiro, Brazil.
ER  -

TY  - JOUR
AU  - Krempl, P.M.
AU  - Mairhofer, J.
AU  - Striedner, G.
AU  - Thallinger, G.G.
TI  - Finished Genome Sequence of the Laboratory Strain Escherichia coli K-12 RV308 (ATCC 31608).
JO  - Genome Announcements
PY  - 2014
SP  - e00971
EP  - e00914
VL  - 2
AB  - Escherichia coli strain K-12 substrain RV308 is an engineered descendant of the K-12 wild-type
AB  - strain. Like its ancestor, it is an important organism in
AB  - biotechnological research and is heavily used for the expression of single-chain
AB  - variable fragments. Here, we report the complete genome sequence of E. coli K-12
AB  - RV308 (ATCC 31608).
ER  -

TY  - JOUR
AU  - Kresge, N.
AU  - Simoni, R.D.
AU  - Hill, R.L.
TI  - The Characterization of Restriction Endonucleases: the Work of Hamilton Smith.
JO  - J. Biol. Chem.
PY  - 2010
SP  - e2
EP  - e3
VL  - 285
AB  - Hamilton Othanel Smith was born in 1931 in New York City.  In 1937, he and his family moved to
AB  - Champaign-Urbana, Illinois, because his father had joined the faculty of the department of
AB  - education at the University of Illinois.  As a boy, Smith was interested in chemistry,
AB  - electricity, and electronics, and he spent many hours with his brother in their basement
AB  - laboratory, which was stocked with supplies purchased from their paper route earnings.  Smith
AB  - attended a small college preparatory school called the University Laboratory High School and
AB  - graduated in 3 years largely tue to this science teacher who allowed him to complete chemistry
AB  - and physics during the summer.
ER  -

TY  - JOUR
AU  - Kretchmar, S.A.
AU  - Chiu, H.S.
AU  - Srinivasan, A.
TI  - Interaction of caffeine with DNA:  an evaluation with restriction endonucleases.
JO  - Microbios Lett.
PY  - 1986
SP  - 31
EP  - 38
VL  - 31
AB  - The endonucleolytic action of several restriction enzymes on the lambda, pBR322
AB  - and PhiX174 (RF I, RF II and single-stranded virion DNA) were tested in the
AB  - presence of caffeine.  No aberrant restriction cleavage pattern was observed by
AB  - adding caffeine directly to the restriction reaction mixture.  DNA pretreated
AB  - with caffeine also exhibited similar results.  Ligation of DNA fragments,
AB  - havaing either protruding single-strand or flush ends, is not affected by
AB  - caffeine.  These results strongly argue against the possible interaction of
AB  - caffeine with DNA.
ER  -

TY  - JOUR
AU  - Kretz, P.L.
AU  - Kohler, S.W.
AU  - Short, J.M.
TI  - Identification and characterization of a gene responsible for inhibiting propagation of methylated DNA sequences in mcrA mcrB1 Escherichia coli strains.
JO  - J. Bacteriol.
PY  - 1991
SP  - 4707
EP  - 4716
VL  - 173
AB  - Identifying and eliminating endogenous bacterial enzyme systems can
AB  - significantly increase the efficiency of propagation of eukaryotic DNA in
AB  - Escherichia coli.  We have recently examined one such system which inhibits the
AB  - propagation of lambda DNA rescued from transgenic mouse tissues.  This rescue
AB  - procedure utilizes lambda packaging extracts for excision of the lambda DNA
AB  - from the transgenic mouse genome, as well as E. coli cells for subsequent
AB  - infection and propagation.  This assay, in combination with conjugal mating, P1
AB  - transduction, and gene cloning, was used to identify and characterize the E.
AB  - coli locus responsible for this difference in efficiency.  It was determined
AB  - that the E. coli K-12 mcrB gene when expressed on a high-copy-number plasmid
AB  - can cause a decrease in rescue efficiency despite the presence of the mcrB1
AB  - mutation, which inactivates the classic McrB restriction activity.  (This
AB  - mutation was verified by sequence analysis.)  However, this McrB1 activity is
AB  - not observed when the cloned mcrB1 gene is inserted into the E. coli genome at
AB  - one copy per chromosome.  A second locus was identified which causes a decrease
AB  - in rescue efficiency both when expressed on a high-copy-number plasmid and when
AB  - inserted into the genome.  The data presented here suggest that this locus is
AB  - mrr and that the mrr gene product can recognize and restrict
AB  - cytosine-methylated sequences.  Removal of this DNA region including the mrr
AB  - gene from E. coli K-12 strains allows high rescue efficiencies equal to those
AB  - of E. coli C strains.  These modified E. coli K-12 plating strains and lambda
AB  - packaging extract strains should also allow a significant improvement in the
AB  - efficiency and representation of eukaryotic genomic and cDNA libraries.
ER  -

TY  - JOUR
AU  - Kretz, P.L.
AU  - Reid, C.H.
AU  - Greener, A.
AU  - Short, J.M.
TI  - Effect of lambda packaging extract mcr restriction activity on DNA cloning.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 5409
EP  - 5409
VL  - 17
AB  - The negative effect of bacterial mcrA and mcrB restriction activity on the cloning of
AB  - methylated DNA has recently been demonstrated. In order to determine the effect of these
AB  - restriction systems on lambda and cosmid packaging, an mcrA-, B-, hsd-, mrr- packaging extract
AB  - strain was constructed by P1 transduction. The extract prepared from this strain, Gigapack II,
AB  - was tested against the restriction positive (mcrA+,B-) extract, Gigapack I, by comparing
AB  - efficiencies in constructing a cosmid library. The results indicate that these restriction
AB  - enzymes are active in lambda packaging extracts and can affect cloning efficiencies. The
AB  - elimination of mcrA,B restriction activity from Gigapack II allowed a 2-3 fold increase in the
AB  - number of cosmid clones obtained. Similar effects have been observed with lambda libraries.
AB  - This effect has also been shown to increase as the extent of DNA methylation increases. The
AB  - results demonstrate the importance of utilizing restriction deficient lambda packaging
AB  - extracts for improved cloning efficiency and possibly genomic representation. Optimal results
AB  - are obtained when both mcrA-,B- packaging extracts and plating strains are used.
ER  -

TY  - JOUR
AU  - Kriebardis, A.
AU  - Guschlbauer, W.
TI  - dam methylase from E. coli: Circular dichroism investigations of the secondary structure and influence of S-adenosylmethionine.
JO  - FEBS Lett.
PY  - 1987
SP  - 297
EP  - 300
VL  - 213
AB  - The enzyme dam methylase which recognizes and methylates the adenine in the palindromic
AB  - sequence GATC in DNA was isolated and the secondary structure was determined by CD
AB  - spectroscopy and various predicting methods from the amino acid sequence. The interaction of
AB  - dam methylase with S-adenosylmethionine was studied by CD spectroscopy indicating a decrease
AB  - of the percentage of alpha-helix as the amount of S-adenosylmethionine bound to the enzyme was
AB  - increased.
ER  -

TY  - JOUR
AU  - Krishnakumar, R.
AU  - Assad-Garcia, N.
AU  - Benders, G.A.
AU  - Phan, Q.
AU  - Montague, M.G.
AU  - Glass, J.I.
TI  - Targeted Chromosomal Knockouts in Mycoplasma pneumoniae.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 5297
EP  - 5299
VL  - 76
AB  - Most gene knockouts in mycoplasmas are achieved through labor-intensive
AB  - transposon mutagenesis. Here, we describe a method for making targeted
AB  - deletions in Mycoplasma pneumoniae by use of homologous recombination. In
AB  - this method, M. pneumoniae is transformed with a plasmid carrying an
AB  - antibiotic resistance marker flanked by 1-kb regions surrounding the
AB  - target gene. Following selection for the antibiotic resistance, colonies
AB  - are screened for double crossovers which indicate complete deletion of the
AB  - target open reading frame.
ER  -

TY  - JOUR
AU  - Krishnamurthy, V.
AU  - Rao, D.N.
TI  - Interaction of EcoPI modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study.
JO  - Biochem. Mol. Biol. Int.
PY  - 1994
SP  - 623
EP  - 632
VL  - 32
AB  - EcoPI modification methylase was radioactively labeled when incubated with
AB  - S-adenosyl-L-[methyl-3H]methionine in the presence of ultraviolet light. Crosslinking of the
AB  - enzyme as detected by electrophoresis on sodium dodecyl sulfate - polyacrylamide gel followed
AB  - by fluorography and autoradiography, was shown to be specific by a number of criteria. More
AB  - importantly, EcoPI modification methylase was also radioactively labeled with
AB  - S-adenosyl-L-[carboxyl-14C]methionine demonstrating that labeling involved binding of the
AB  - entire AdoMet molecule rather than methylation of the protein. Further, c2 EcoPI mutant DNA
AB  - modification methylases which show negligible or very little methylation activity,
AB  - correspondingly formed a weak or no adduct upon crosslinking. These results suggest that
AB  - photolabeling of EcoPI DNA modification methylase occurs at the AdoMet binding site.
ER  -

TY  - JOUR
AU  - Krishnaswamy, T.D.S.
TI  - Structure-based sequence alignment of type-II restriction endonucleases.
JO  - Biochim. Biophys. Acta
PY  - 2001
SP  - 217
EP  - 228
VL  - 1544
AB  - The type-II restriction endonucleases generally do not share appreciable amino acid sequence
AB  - homology. The crystal structures of restriction endonucleases EcoRI and BamHI have shown these
AB  - enzymes to possess striking 3D-structural resemblance, i.e., they have a similar overall fold
AB  - and similar active sites, though they possess <23% sequence identity. Structural
AB  - superimposition of EcoRI, BamHI, EcoRV, and PvuII based on active site residues led to
AB  - sequence alignments which showed nine possible sequence motifs. EcoRV and PvuII show a more
AB  - similar pattern than EcoRI and BamHI suggesting that they belong to a different subgroup. The
AB  - motifs are characterized by charged and/or hydrophobic residues. From other studies on the
AB  - structure of these endonucleases, three of the motifs could be implicated in DNA binding,
AB  - three in forming the active site and one in dimer formation. However, the motifs were not
AB  - identifiable by regular sequence alignment methods. It is found that motif IX in BamHI is
AB  - formed by reverse sequence order and the motif IX in PvuII is formed from the symmetry related
AB  - monomer of the dimer. The inter-motif distance is also quite different in these cases. Of the
AB  - nine motifs, motif III has been earlier identified as containing the PD motif involving one of
AB  - the active site residues. These motifs were used in a modified profile analysis procedure to
AB  - identify similar regions in eight other endonuclease sequences for which structures are not
AB  - known.
ER  -

TY  - JOUR
AU  - Kriss, J.
AU  - Herrin, G.
AU  - Forman, L.
AU  - Cotton, R.
TI  - Digestion conditions resulting in altered cut site specificity for HinfI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3665
EP  - 3665
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Kristiansen, R.
AU  - Dueholm, M.S.
AU  - Bank, S.
AU  - Nielsen, P.H.
AU  - Karst, S.M.
AU  - Cattoir, V.
AU  - Lienhard, R.
AU  - Grisold, A.J.
AU  - Olsen, A.B.
AU  - Reinhard, M.
AU  - Soby, K.M.
AU  - Christensen, J.J.
AU  - Prag, J.
AU  - Thomsen, T.R.
TI  - Complete Genome Sequence of Actinobaculum schaalii Strain CCUG 27420.
JO  - Genome Announcements
PY  - 2014
SP  - e00880
EP  - e00814
VL  - 2
AB  - Complete genome sequencing of the emerging uropathogen Actinobaculum schaalii indicates that
AB  - an important mechanism of its virulence is attachment pili, which
AB  - allow the organism to adhere to the surface of animal cells, greatly enhancing
AB  - the ability of this organism to colonize the urinary tract.
ER  -

TY  - JOUR
AU  - Kriszt, B.
AU  - Tancsics, A.
AU  - Cserhati, M.
AU  - Toth, A.
AU  - Nagy, I.
AU  - Horvath, B.
AU  - Nagy, I.
AU  - Tamura, T.
AU  - Kukolya, J.
AU  - Szoboszlay, S.
TI  - De Novo Genome Project for the Aromatic Degrader Rhodococcus pyridinivorans Strain AK37.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1247
EP  - 1248
VL  - 194
AB  - Here, we present the complete genome sequence of Rhodococcus pyridinivorans AK37  strain NCAIM
AB  - PB1376, which was isolated from an oil-polluted site in Hungary. R.
AB  - pyridinivorans AK37 is an aerobic, nonsporulating, nonmotile, Gram-positive
AB  - bacterium with remarkable aromatic-decomposing activity.
ER  -

TY  - JOUR
AU  - Kriukiene, E.
TI  - Domain organization and metal ion requirement of the Type IIS restriction endonuclease MnlI.
JO  - FEBS Lett.
PY  - 2006
SP  - 6115
EP  - 6122
VL  - 580
AB  - A two-domain structure of the Type US restriction endonuclease Mull has been identified by
AB  - limited proteolysis. An N-terminal domain of the
AB  - enzyme mediates the sequence-specific interaction with DNA, whereas a
AB  - monomeric C-terminal domain resembles bacterial colicin nucleases in
AB  - its requirement for alkaline earth as well as transition metal ions for
AB  - double- and single-stranded DNA cleavage activities. The results
AB  - indicate that the fusion of the non-specific HNH-type nuclease to the
AB  - DNA binding domain had transformed Mull into a Mg2+-, Ni2+-, Co2+-,
AB  - Mn2+-, Zn2+-, Ca2+-dependent sequence-specific enzyme. Nevertheless,
AB  - Mull retains a residual single-stranded DNA cleavage activity
AB  - controlled by its C-terminal colicin-like nuclease domain.
ER  -

TY  - JOUR
AU  - Kriukiene, E.
TI  - Restriction endonuclease MnlI - A member of the HNH family of endonucleases.
JO  - Ph.D. Thesis, Vilnius University
PY  - 2007
SP  - 1
EP  - 45
AB  - CONCLUSIONS
AB  - 1. The Type IIS restriction-modification system MnlI is composed of N6-methyladenine and
AB  - C5-methylcytosine methyltransferases and a restriction enzyme. The methyltransferases modify
AB  - cytosine and adenine on the opposite strands of the recognition sequence, resulting in
AB  - 5'-m5CCTC-3'/5'-Gm6AGG-3'. The MnlI restriction endonuclease cleaves both DNA strands 7/6
AB  - nucleotides downstream of the recognition site.
AB  - 2. The active site of MnlI REase resembles those of the bacterial colicin DNases ColE7 and
AB  - ColE9, which belong to the HNH superfamily of nucleases. The motif 306Rx3ExHHx14Nx8H located
AB  - in the C-terminal part of the protein comprises the active site of MnlI.
AB  - 3. MnlI is a homodimeric protein capable of binding two copies of its recognition sequence.
AB  - Simultaneous binding of two DNA target sites stimulates DNA cleavage by MnlI.
AB  - 4. A two-domain structure of the Type IIS restriction endonuclease MnlI has been identified by
AB  - limited proteolysis. An N-terminal domain of the enzyme mediates the sequence-specific
AB  - interaction with DNA and in part the dimerization of MnlI. It binds the recognition sequence
AB  - as a monomer, though it displays an ability to interact with two copies of the recognition
AB  - sequence as a dimer. A C-terminal domain of MnlI is determined to be monomeric in solution.
AB  - 5. The C-terminal domain of MnlI REase resembles bacterial colicin nucleases in its oligomeric
AB  - state and requirement for alkaline earth as well as transition metal ions for double- and
AB  - single-stranded DNA cleavage activities.
AB  - 6. The fusion of the non-specific HNH-type nuclease to the DNA binding domain had transformed
AB  - MnlI into a Mg2+-, Ni2+-, Co2+-, Mn2+-, Zn2+-, Ca2+-dependent sequence-specific enzyme.
AB  - Nevertheless, MnlI retains a residual single-stranded DNA cleavage activity controlled by its
AB  - C-terminal colicin-like nuclease domain. The cleavage of ds- and ssDNA by MnlI with a wide
AB  - range of divalent metal ions is unparalleled among restriction endonucleases characterized to
AB  - date.
ER  -

TY  - JOUR
AU  - Kriukiene, E.
AU  - Lubiene, J.
AU  - Lagunavicius, A.
AU  - Lubys, A.
TI  - MnlI - The member of H-N-H subtype of Type IIS restriction endonucleases.
JO  - Biochim. Biophys. Acta
PY  - 2005
SP  - 194
EP  - 204
VL  - 1751
AB  - The Type IIS restriction endonuclease MnlI recognizes the non-palindromic nucleotide sequence
AB  - 5'-CCTC(N)7/6 down arrow and
AB  - cleaves DNA strands as indicated by the arrow. The genes encoding MnlI
AB  - restriction-modification system were cloned and sequenced. It comprises
AB  - N6-methyladenine and C5-methylcytosine methyltransferases and the
AB  - restriction endonuclease. Biochemical studies revealed that MnlI
AB  - restriction endonuclease cleaves double- and single-stranded DNA, and
AB  - that it prefers different metal ions for hydrolysis of these
AB  - substrates. Mg2+ ions were shown to be required for the specific
AB  - cleavage of double-stranded DNA, whereas Ni2+ and some other transition
AB  - metal ions were preferred for nonspecific cleavage of single-stranded
AB  - DNA. The C-terminal part of MnlI restriction endonuclease revealed an
AB  - intriguing similarity with the H-N-H type nucleolytic domain of
AB  - bacterial toxins, Colicin E7 and Colicin E9. Alanine replacements in
AB  - the conserved sequence motif 306Rx(3)ExHHx(14)Nx(8)H greatly reduced
AB  - specific activity of MnlI, and some mutations even completely
AB  - inactivated the enzyme. However, none of these mutations had effect on
AB  - MnlI binding to the specific DNA, and on its oligomerisation state as
AB  - well. We interpret the presented experimental evidence as a suggestion
AB  - that the motif 306Rx(3)ExHHx(14)Nx(8)H represents the active site of
AB  - Mnll. Consequentially, MnlI seems to be the member of Type IIS with the
AB  - active site of the H-N-H type.
ER  -

TY  - JOUR
AU  - Kriukiene, E.
AU  - Lubys, A.
TI  - Cloning and analysis of DNA regions adjacent to methyltransferase Lsp1109I of restriction-modification system Lsp1109I, type IIs.
JO  - Biologija
PY  - 1998
SP  - 62
EP  - 65
VL  - 2
AB  - DNA regions flanking genes lsp11091R? were cloned and sequenced.  Two open reading frames
AB  - transcribed in the same polarity as the lsp1109IMR? were found.  One of them, lsp-inv, encodes
AB  - a protein which has 41-46% of amino acids identical with proteins belonging to the family of
AB  - Din invertases.  This suggests that lsp-inv is possibly the gene of invertase Listeria sp.
AB  - Translation product of the second ORF (lsp-tnp), shares 23-26% homology with transposases of
AB  - various mobile DNA elements.  Possible function of these genes is discussed.  Analysis of
AB  - complementary DNA strand revealed four additional ORFs whose products possess no homology with
AB  - any aa sequence from EMBL data bank.
ER  -

TY  - JOUR
AU  - Kriukiene, E.
AU  - Lubys, A.
TI  - Comparison of two restriction-modification systems recognizing the same GGATCC sequence.
JO  - Biologija
PY  - 1998
SP  - 55
EP  - 59
VL  - 1
AB  - Restriction-modification system Bsp98I from Bacillus species RFL98 recognizing the sequence
AB  - GGATCC has been cloned and sequenced.  The determined sequence predicts a methyltransferase of
AB  - 388 amino acids, Mr 45 kDa, and a restriction endonuclease of 199 aa, Mr 22.5 kDa.
AB  - Comparisons of the predicted aa sequences indicated that Bsp98I and isoschizomeric BamHI
AB  - restriction endonucleases share 28% identity, whereas the corresponding methyltransferases
AB  - share 42% identity.  This observation suggests that Bsp98I and BamHI genes derive from a
AB  - common ancestor.  Regardless of such evolutionary relatedness, the Bsp98I R-M system has no
AB  - equivalent of the bamHIC gene which is involved in regulation of expression of BamHI R-M
AB  - genes.  This clearly indicates that the regulation of Bsp98I R-M genes is different.  Despite
AB  - the marginal similarity among R.BamHI and R.Bsp98I, the aa residues of catalytic/Mg2+ binding
AB  - center as well as the ones making the major groove contacts in R.BamHI can be found in
AB  - appropriate positions of the aligned aa sequence of R.Bsp98I.  In contrast, some amino acids
AB  - of R.BamHI that make contacts in the minor groove are absent in R.Bsp98I.
ER  -

TY  - JOUR
AU  - Kroft, B.S.
AU  - Brown, E.W.
AU  - Meng, J.
AU  - Gonzalez-Escalona, N.
TI  - Draft Genome Sequences of Two Salmonella Strains from the SARA Collection, SARA64 (Muenchen) and SARA33 (Heidelberg), Provide Insight into Their Antibiotic  Resistance.
JO  - Genome Announcements
PY  - 2013
SP  - e00806
EP  - e00813
VL  - 1
AB  - The Salmonella enterica strains that are representatives of the S. enterica serovar
AB  - Typhimurium complex in reference collection A (SARA) are closely related
AB  - but exhibit differences in antibiotic resistance, which could have public health
AB  - consequences. To better understand the mechanisms behind these resistances, we
AB  - sequenced the genomes of two multidrug-resistant strains: SARA64 (Muenchen) and
AB  - SARA33 (Heidelberg).
ER  -

TY  - JOUR
AU  - Kroger, M.
AU  - Blum, E.
AU  - Deppe, E.
AU  - Dusterhoft, A.
AU  - Erdmann, D.
AU  - Kilz, S.
AU  - Meyer-Rogge, S.
AU  - Mostl, D.
TI  - Organization and gene expression within restriction-modification systems of Herpetosiphon giganteus.
JO  - Gene
PY  - 1995
SP  - 43
EP  - 47
VL  - 157
AB  - We have characterized a family of related restriction-modification (R-M) systems from the soil
AB  - bacterium Herpetosiphon giganteus (Hgi).  A comparison of their genetic organization reveals
AB  - two types of regulatory proteins, called controlling ORF C.  While one of these small reading
AB  - frames derived from RM.HgiCI seems to be an enhancer of its own promoter, evidence is provided
AB  - for a silencer function of the other ORF C derived from the closely related AvaII-type
AB  - systems RM.HgiBI/CII/EI.  The respective silencer function is detected during our various
AB  - attempts to clone three isoschizomers with unusually high differences in their specific
AB  - activity.  Sequencing and site-directed mutagenesis revealed just two amino acids as being
AB  - responsible for a massive increase in specific activity of these endonucleases.
ER  -

TY  - JOUR
AU  - Kroger, M.
AU  - Hobom, G.
TI  - Restriction enzyme HgiCI characterization of the 6-nucleotide staggered cut sequence and its application in mismatch cloning.
JO  - Methods Enzymol.
PY  - 1987
SP  - 3
EP  - 10
VL  - 155
AB  - The gliding bacterium Herpetosiphon giganteus became one of the most
AB  - intensively screened groups of organisms in the search for new restriction
AB  - enzymes.  Among the 10 strains tested, 17 enzymes could be found with seven
AB  - different but related recognition sequences.  This led to a hypothesis
AB  - regarding the evolutionary relationship among these enzymes and could be a
AB  - basis for a better understanding of the biochemical mechanism of restriction
AB  - enzymes-DNA target interaction.  Among these enzymes HgiCI is remarkably
AB  - different from all other previously described endonucleases, since it produces
AB  - 5'-hexanucleotide protruding ends.  Combined with the fact that HgiCI
AB  - recognizes a degenerate sequence, specific applications of this enzymatic
AB  - activity in gene technology are possible.  Usually, for specific base pairing
AB  - within 5'- or 3'- protruding ends, a match of 2 bp is fair, while four matching
AB  - base pairs lead to highly efficient ligase reactions.  Since a perfect match of
AB  - 6 bp may not be required, we used HgiCI-restricted DNA fragments in order to
AB  - test whether DNA ligase reactions among hexanucleotide protruding ends could
AB  - proceed in spite of some mismatch positions.  Our results presented here allow
AB  - the conclusion that is is possible to obtain mismatched ligase reaction
AB  - products in considerable fractions.  A wider application of this observation
AB  - seems possible, since an isoschizomer of HgiCI BanI, is available commercially
AB  - and is obtained from an unrelated strain Bacillus aneurinolyticus (IAM 1077).
AB  - In contrast to the data given in the literature, we have determined via
AB  - cross-ligation that BanI also produces 5'-hexanucleotide protruding DNA
AB  - fragments.  In this article we intend to focus on the methodology used to
AB  - characterize recognition sequences and on the application of HgiCI (BanI)
AB  - fragment ends in mismatch cloning rather than on enzyme purification
AB  - procedures.
ER  -

TY  - JOUR
AU  - Kroger, M.
AU  - Hobom, G.
TI  - The nucleotide sequence recognized by the Escherichia coli A restriction and modification enzyme.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 887
EP  - 899
VL  - 12
AB  - The nucleotide recognition sequence for the restriction-modification enzyme of
AB  - Escherichia coli A (EcoA) has been determined to be GAG-7N-GTCA.  This sequence
AB  - is fairly similar, but distinctly different from the two other type I
AB  - restriction enzyme recognition sites known for E. coli B and E. coli K12,
AB  - respectively.  N6-adenosine methylation has been observed at nucleotide
AB  - positions 2 and 12 within that sequence after modification by EcoA.  As a
AB  - reference point for mapping the single EcoA site in lambda, the position of
AB  - lambda point mutation Oam29 has been determined also.
ER  -

TY  - JOUR
AU  - Kroger, M.
AU  - Hobom, G.
AU  - Schutte, H.
AU  - Mayer, H.
TI  - Eight new restriction endonucleases from Herpetosiphon giganteus - divergent evolution in a family of enzymes.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 3127
EP  - 3141
VL  - 12
AB  - Characterization of eight restriction endonucleases isolated from five strains
AB  - of Herpetosiphon giganteus is described.  HgiCI from strain Hpg9 recognizes and
AB  - cleaves the degenerate sequence: 7GGPyPuCC, producing 5'-hexanucleotide
AB  - protruding ends.  Endonucleases HgiBI, HgiCII and HgiEI are isoschizomers of
AB  - AvaII; HgiCIII and HgiDII are isoschizomers of SalI; and HgiDI and HgiGI are
AB  - isoschizomers of AcyI.  Based upon their closely related and in part
AB  - overlapping recognition specificities a close evolutionary relationship is
AB  - proposed for all known Hgi restriction endonucleases.
ER  -

TY  - JOUR
AU  - Krogh, T.J.
AU  - Agergaard, C.N.
AU  - Moller-Jensen, J.
AU  - Justesen, U.S.
TI  - Draft Genome Sequence of Parabacteroides goldsteinii with Putative Novel Metallo-beta-Lactamases Isolated from a Blood Culture from a Human Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e00937
EP  - e00915
VL  - 3
AB  - Parabacteroides goldsteinii was isolated from a blood culture. Genomic DNA was sequenced using
AB  - a MiSeq sequencer and assembled using the SPAdes genome
AB  - assembler. The draft genome sequence was 6,851,868 bp, spanning 282 contigs of
AB  - 5,253 coding sequences, 66 tRNAs, and 5 rRNAs. Several putative novel
AB  - metallo-beta-lactamases were discovered.
ER  -

TY  - JOUR
AU  - Kroon, A.M.
AU  - Bakker, H.
AU  - Holtrop, M.
AU  - Terpstra, P.
TI  - The restriction endonuclease cleavage map of rat liver mitochondrial DNA.
JO  - Biochim. Biophys. Acta
PY  - 1977
SP  - 61
EP  - 68
VL  - 474
AB  - Mitochondrial DNA from rat liver contains six sites for cleavage by the
AB  - restriction endonucleases HindIII and EcoRI.  A large stretch of DNA,
AB  - comprising about 40% of the mitochondrial genome is not cleaved by either of
AB  - the enzymes; eight cleavage sites are located on a DNA stretch of 35% of the
AB  - genome length suggestive of an unequal distribution of the A-T basepairs over
AB  - the molecule.  The number of HindIII and EcoRI fragments is much higher than
AB  - reported for other mammalian mitochondrial DNAs up to now.
ER  -

TY  - JOUR
AU  - Kropinski, A.M.
AU  - Arutyunov, D.
AU  - Foss, M.
AU  - Cunningham, A.
AU  - Ding, W.
AU  - Singh, A.
AU  - Pavlov, A.R.
AU  - Henry, M.
AU  - Evoy, S.
AU  - Kelly, J.
AU  - Szymanski, C.M.
TI  - Genome and Proteome of Campylobacter jejuni Bacteriophage NCTC 12673.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 8265
EP  - 8271
VL  - 77
AB  - Campylobacter jejuni continues to be the leading cause of bacterial food-borne illness
AB  - worldwide, so improvements to current methods used
AB  - for bacterial detection and disease prevention are needed. We describe
AB  - here the genome and proteome of C. jejuni bacteriophage NCTC 12673 and
AB  - the exploitation of its receptor-binding protein for specific bacterial
AB  - detection. Remarkably, the 135-kb Myoviridae genome of NCTC 12673
AB  - differs greatly from any other proteobacterial phage genome described
AB  - (including C. jejuni phages CP220 and CPt10) and instead shows closest
AB  - homology to the cyanobacterial T4-related myophages. The phage genome
AB  - contains 172 putative open reading frames, including 12 homing
AB  - endonucleases, no visible means of packaging, and a putative
AB  - trans-splicing intein. The phage DNA appears to be strongly associated
AB  - with a protein that interfered with PCR amplification and estimation of
AB  - the phage genome mass by pulsed-field gel electrophoresis.
AB  - Identification and analyses of the receptor-binding protein (Gp48)
AB  - revealed features common to the Salmonella enterica P22 phage tailspike
AB  - protein, including the ability to specifically recognize a host
AB  - organism. Bacteriophage receptor-binding proteins may offer promising
AB  - alternatives for use in pathogen detection platforms.
ER  -

TY  - JOUR
AU  - Kropinski, A.M.
AU  - Kovalyova, I.V.
AU  - Billington, S.J.
AU  - Patrick, A.N.
AU  - Butts, B.D.
AU  - Guichard, J.A.
AU  - Pitcher, T.J.
AU  - Guthrie, C.C.
AU  - Sydlaske, A.D.
AU  - Barnhill, L.M.
AU  - Havens, K.A.
AU  - Day, K.R.
AU  - Falk, D.R.
AU  - McConnell, M.R.
TI  - The genome of epsilon 15, a serotype-converting, group E1 Salmonella enterica-specific bacteriophage.
JO  - Virology
PY  - 2007
SP  - 234
EP  - 244
VL  - 369
AB  - The genome sequence of the Salmonella enterica serovar Anatum-specific, serotype-converting
AB  - bacteriophage 05 has been completed. The
AB  - nonredundant genome contains 39,671 bp and 51 putative genes. It most
AB  - closely resembles the genome of phi V10, an Escherichia coli O157:H7
AB  - specific temperate phage, with which it shares 36 related genes. More
AB  - distant relatives include the Burkholderia cepacia-specific phage,
AB  - BccpC6B (8 similar genes), the Bordetella bronchiseptica-specific
AB  - phage, BPP-1 (8 similar genes) and the Photobacterium profundum
AB  - prophage, P P phi pr1 (6 similar genes).
AB  - epsilon 15 gene identifications based on homologies with known gene
AB  - families include the terminase small and large subunits, integrase,
AB  - endolysin, two holins, two DNA methylase enzymes (one adenine-specific
AB  - and one cytosine-specific) and a RecT-like enzyme. Genes identified
AB  - experimentally include those coding for the serotype conversion
AB  - proteins, the tail fiber, the major capsid protein and the major
AB  - repressor. epsilon 15's attP site and the Salmonella attB site with
AB  - which it interacts during lysogenization have also been determined.
ER  -

TY  - JOUR
AU  - Kropp, K.A.
AU  - Lucid, A.
AU  - Carroll, J.
AU  - Belgrudov, V.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - O'Driscoll, A.
AU  - Templeton, K.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United  Kingdom.
JO  - Genome Announcements
PY  - 2014
SP  - e00908
EP  - e00914
VL  - 2
AB  - Herein, we report the draft genome sequence for isolate ED-NGS-1015 of Serratia marcescens,
AB  - cultivated from a blood sample obtained from a neonatal sepsis
AB  - patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Kropp, K.A.
AU  - Lucid, A.
AU  - Carroll, J.
AU  - Belgrudov, V.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - O'Driscoll, A.
AU  - Templeton, K.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00907
EP  - e00914
VL  - 2
AB  - Herein, we report the draft genome sequence of Enterococcus faecalis ED-NGS-1009, cultivated
AB  - from a blood sample taken from a neonatal sepsis patient at the Royal
AB  - Infirmary in Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Kropp, K.A.
AU  - Lucid, A.
AU  - Carroll, J.
AU  - Belgrudov, V.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - O'Driscoll, A.
AU  - Templeton, K.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm  Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.
JO  - Genome Announcements
PY  - 2014
SP  - e00877
EP  - e00814
VL  - 2
AB  - Herein, we report the draft genome sequence of Staphylococcus warneri ED-NGS-1001, cultivated
AB  - from a blood sample taken from a preterm neonate blood
AB  - sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Kropp, K.A.
AU  - Lucid, A.
AU  - Carroll, J.
AU  - Belgrudov, V.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - O'Driscoll, A.
AU  - Templeton, K.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland.
JO  - Genome Announcements
PY  - 2014
SP  - e00875
EP  - e00814
VL  - 2
AB  - Herein, we report the draft genome sequence of Streptococcus agalactiae ED-NGS-1000,
AB  - cultivated from a blood sample taken from a preterm neonate blood
AB  - sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Kropp, K.A.
AU  - Lucid, A.
AU  - Carroll, J.
AU  - Belgrudov, V.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Templeton, K.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - O'Driscoll, A.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of  a Preterm Neonatal Blood Sepsis Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00906
EP  - e00914
VL  - 2
AB  - Herein, we report the draft genome sequence of Staphylococcus aureus ED-NGS-1006, cultivated
AB  - from a blood sample taken from a neonatal sepsis patient at the Royal
AB  - Infirmary in Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Kropp, K.A.
AU  - Lucid, A.
AU  - Carroll, J.
AU  - Belgrudov, V.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Templeton, K.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - O'Driscoll, A.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequence of a Pantoea sp. Isolated from a Preterm Neonatal Blood Sepsis Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00904
EP  - e00914
VL  - 2
AB  - Herein, we report the draft genome sequence of Pantoea sp. ED-NGS-1003, cultivated from a
AB  - blood sample taken from a neonatal sepsis patient at the Royal
AB  - Infirmary, Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Kruasuwan, W.
AU  - Hoskisson, P.A.
AU  - Thamchaipenet, A.
TI  - Draft Genome Sequence of Root-Associated Sugarcane Growth-Promoting Microbispora  sp. Strain GKU 823.
JO  - Genome Announcements
PY  - 2017
SP  - e00647
EP  - e00617
VL  - 5
AB  - The endophytic plant growth-promoting Microbispora sp. strain GKU 823 was isolated from the
AB  - roots of sugarcane cultivated in Thailand. It has an estimated
AB  - 9.4-Mbp genome and a G+C content of 71.3%. The genome sequence reveals several
AB  - genes associated with plant growth-promoting traits and extensive specialized
AB  - metabolite biosynthesis.
ER  -

TY  - JOUR
AU  - Kruasuwan, W.
AU  - Salih, T.S.
AU  - Brozio, S.
AU  - Hoskisson, P.A.
AU  - Thamchaipenet, A.
TI  - Draft Genome Sequence of Plant Growth-Promoting Endophytic Streptomyces sp. GKU 895 Isolated from the Roots of Sugarcane.
JO  - Genome Announcements
PY  - 2017
SP  - e00358
EP  - e00317
VL  - 5
AB  - Streptomyces sp. GKU 895 is an endophytic actinomycete isolated from the roots of sugarcane.
AB  - GKU 895 has a genome of 8.3 Mbp and the genome exhibits adaptations
AB  - related to plant growth-promoting activity. It also has extensive specialized
AB  - metabolite biosynthetic gene clusters apparent in its genome.
ER  -

TY  - JOUR
AU  - Krueger, D.H.
AU  - Kupper, D.
AU  - Meisel, A.
AU  - Reuter, M.
AU  - Schroeder, C.
TI  - The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes.
JO  - FEMS Microbiol. Rev.
PY  - 1995
SP  - 177
EP  - 184
VL  - 17
AB  - Studies on phage T3 and T7 have shown that these viruses avoid restriction not only by the
AB  - phage-coded Ocr (and S-adenosylmethionine hydrolase) protein functions or by the complete loss
AB  - of specific recognition sites for certain restriction endonucleases from their genomes, but
AB  - also that there are two additional modes: resistance towards EcoP15 (which recognizes a non-
AB  - symmetrical sequence) is achieved by an identical orientation of all the recognition sites in
AB  - the virus genome (strand bias) and in the case of EcoRII by the extreme reduction in number
AB  - and thereby greater distance between recognition sites in the genome.  These observations led
AB  - to the discovery that certain restriction endonucleases require the simultaneous cooperation
AB  - with two DNA sites for their function, as well as to the ongoing elucidation of the molecular
AB  - modes of action of these enzymes.  Type II and type III enzymes display fundamentally
AB  - different mechanisms of protein- DNA interaction.  For EcoRII we favor a model of simultaneous
AB  - binding of two DNA sites to a dimeric enzyme molecule (neighboring sites of the same, looping,
AB  - DNA molecule or sites located on different DNA molecules), while the action of EcoP15 seems to
AB  - conform with a tracking- collision model of two enzyme molecules bound to inversely oriented
AB  - recognition sites.  In addition to podoviruses T3 and T7, strand bias of recognition sequences
AB  - for different type III DNA modification-restriction enzymes is also observed in the inoviruses
AB  - M13, IKE and PF3.
ER  -

TY  - JOUR
AU  - Krueger, D.H.
AU  - Kupper, D.
AU  - Meisel, A.
AU  - Tierlich, M.
AU  - Reuter, M.
AU  - Schroeder, C.
TI  - Restriction endonucleases functionally interacting with two DNA sites.
JO  - Gene
PY  - 1995
SP  - 165
EP  - 165
VL  - 157
AB  - Simultaneous interaction with two recognition sites was found to be a precondition for DNA
AB  - cleavage by certain type-II and type-III restriction endonucleases.  Nevertheless, the
AB  - molecular mechanisms of the protein-DNA interaction are different between members of both
AB  - classes of enzymes.
ER  -

TY  - JOUR
AU  - Krueger, D.H.
AU  - Presber, W.
AU  - Hansen, S.
AU  - Rosenthal, H.A.
TI  - Biological functions of the bacteriophage T3 SAMase gene.
JO  - J. Virol.
PY  - 1975
SP  - 453
EP  - 455
VL  - 16
AB  - Certain differences between phage T3 on the one hand and T3sam and T7 on the other hand
AB  - indicate that the T3-coded SAMase function is responsible (i) for the development of the
AB  - pseudolysogenic state by preventing T3 DNA methylation, and (ii) for the partial protection of
AB  - the phage DNA against restriction by the P system.
ER  -

TY  - JOUR
AU  - Krueger, D.H.
AU  - Reuter, M.
TI  - Reliable detection of DNA cytosine methylation at CpNpG sites using the engineered restriction enzyme EcoRII-C.
JO  - Biotechniques
PY  - 2005
SP  - 855
EP  - 856
VL  - 38
AB  - Methylation of cytosine to 5-methylcytosine (mC) is the most important epigenetic DNA
AB  - alteration in eukaryotes.  Cytosine methylation is involved in establishing a silenced
AB  - chromatin stage through interaction with DNA-binding proteins and recruitment of histone
AB  - deacetylases and other histone-modifying enzymes leading to chromatin remodeling.  In this
AB  - fashion, DNA methylation is connected with processes of normal and pathological gene
AB  - regulation, DNA replication, virus latency, parental imprinting embryonic development,
AB  - carcinogenesis, and genetic diseases in higher organisms.  Analogous to the terms
AB  - transcriptome and proteome, the neologism methylome has been proposed to describe the complete
AB  - set of DNA methylation in a cell, which carries information in addition to the naked DNA
AB  - sequence.  The methylome changes over time and, depending on its alterations, is linked to
AB  - aging, cancer, and polymorphic variation in populations.
ER  -

TY  - JOUR
AU  - Krueger, M.
AU  - Meyerdierks, A.
AU  - Gloeckner, F.O.
AU  - Amann, R.
AU  - Widdel, F.
AU  - Kube, M.
AU  - Reinhardt, R.
AU  - Kahnt, J.
AU  - Boecher, R.
AU  - Thauer, R.K.
AU  - Shima, S.
TI  - A conspicuous nickel protein in microbial mats that oxidize methane anaerobically.
JO  - Nature
PY  - 2003
SP  - 878
EP  - 881
VL  - 426
AB  - Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in
AB  - the global carbon cycle and in control of greenhouse
AB  - gas emission. The responsible organisms supposedly reverse the reactions
AB  - of methanogenesis, but cultures providing biochemical proof of this have
AB  - not been isolated. Here we searched for AOM-associated cell components in
AB  - microbial mats from anoxic methane seeps in the Black Sea. These mats
AB  - catalyse AOM rather than carry out methanogenesis. We extracted a
AB  - prominent nickel compound displaying the same absorption spectrum as the
AB  - nickel cofactor F430 of methyl-coenzyme M reductase, the terminal enzyme
AB  - of methanogenesis; however, the nickel compound exhibited a higher
AB  - molecular mass than F430. The apparent variant of F(430) was part of an
AB  - abundant protein that was purified from the mat and that consists of three
AB  - different subunits. Determined amino-terminal amino acid sequences matched
AB  - a gene locus cloned from the mat. Sequence analyses revealed similarities
AB  - to methyl-coenzyme M reductase from methanogenic archaea. The abundance of
AB  - the nickel protein (7% of extracted proteins) in the mat suggests an
AB  - important role in AOM.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
TI  - Host-controlled modification and restriction.
JO  - Encyclop. Virol.
PY  - 1994
SP  - 669
EP  - 674
VL  - 0
AB  - The application of restriction endonucleases has revolutionized molecular biological research.
AB  - As so often was the case, studies on bacterial viruses led to the discovery of this class of
AB  - enzyme. At the beginning of the fifties, the observation was noted that phages 'remember'
AB  - the last host strain in which they reproduced. Depending on the host, the virus carries a
AB  - specific modification which usually improves its ability to grow on the same host in
AB  - subsequent rounds of infection, while impairing its growth in others. Host-controlled
AB  - modification results in a reversible phenotype, clearly distinguishable from irreversible
AB  - mutational changes in host range.
AB  - 
AB  - The molecular explanation of these phenomena (first demonstrated for phage lambda and P2)
AB  - was elaborated in the 60s and 70s by groups of W. Arber, H.O. Smith, M. Meselson and others.
AB  - Host-controlled modification consists of a specific DNA methylation at a defined recognition
AB  - sequence of 4-8 bp. Restriction is caused by DNA cleavage occurring at an unmethylated
AB  - recognition site. Pairs of corresponding DNA methylases and restriction endonucleases (i.e.
AB  - recognizing the same site) coded by hsd genes (host specificity of DNA) in bacterial cells are
AB  - responsible for these activities. During DNA replication, recognition sequences in nascent
AB  - daughter strands are transiently unmethylated. Such hemimethylated sites are preferential
AB  - substrates for DNA methylases, while sites unmethylated in both strands are primary targets of
AB  - restriction endonucleases and are very rarely methylated.
AB  - 
AB  - DNA modification consists of a C-5 or N-4 methylation of cytosine or an N-6 methylation of
AB  - adenine in the recognition sequence. S-Adenosylmethionine (AdoMet) functions as the methyl
AB  - donor. DNA restriction results in fragments with cohesive or blunt ends which are further
AB  - degraded intracellularly by other nucleases, in particular by the recBCD=exoV enzyme.
AB  - 
AB  - DNA modification/restriction (M/R) systems ae ubiquitous in the procaryote world but there
AB  - is no unequivocal evidence of their existence in higher eucaryotes.
AB  - 
ER  -

TY  - JOUR
AU  - Kruger, D.H.
TI  - Methylases as regulators of gene activity.
JO  - Wiss. Fortsch.
PY  - 1987
SP  - 268
EP  - 270
VL  - 37
AB  - None
ER  -

TY  - JOUR
AU  - Kruger, D.H.
TI  - Methylation of DNA as a molecular biological regulatory signal.
JO  - Biol. Zentralbl.
PY  - 1988
SP  - 257
EP  - 266
VL  - 107
AB  - Methylation of adenine or cytosine adds information to the DNA double strand
AB  - which can influence the interactions between DNA and proteins.  Besides the
AB  - protection of DNA against corresponding restriction endonucleases in
AB  - prokaryotic cells, a number of new functions of DNA methylation in prokaryotic
AB  - and eukaryotic cells have been demonstrated.  These observations are mainly
AB  - related to the regulation of gene expression.  In gene technology in vitro,
AB  - artificial DNA methylation is exploited to change the number of sensitive
AB  - recognition sites for certain restriction endonucleases.  Finally, the
AB  - properties of the first natural inhibitory protein (Ocr) against DNA
AB  - methylation and the possible significance of cellular effector molecules
AB  - specifically blocking or enhancing DNA methylation are discussed.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Barcak, G.J.
AU  - Reuter, M.
AU  - Smith, H.O.
TI  - EcoRII can be activated to cleave refractory DNA recognition sites.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 3997
EP  - 4008
VL  - 16
AB  - EcoRII restriction sites [5'-CC(A/T)GG] in phage T3 and T7 DNA are refractory
AB  - to cleavage by EcoRII, but become sensitive to cleavage in the presence of DNAs
AB  - which contain an abundance of EcoRII sensitive sites (e.g. pBR322 or lambda
AB  - DNA).  Studies using fragments of pBR322 containing different numbers of EcoRII
AB  - sites show that the susceptibility to EcoRII cleavage is proportional to the
AB  - number of sites in the individual fragment.  We postulate that EcoRII is the
AB  - prototype of restriction endonucleases which require at least 2 simultaneously
AB  - bound substrate sites for their activation.  EcoRII sites are refractory when
AB  - they occur at relatively low frequency in the DNA.  The restriction enzyme can
AB  - be activated by DNA with a higher frequency of sites.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Barcak, G.J.
AU  - Smith, H.O.
TI  - Abolition of DNA recognition site resistance to the restriction endonuclease EcoRII.
JO  - Biomed. Biochim. Acta
PY  - 1988
SP  - K1
EP  - K5
VL  - 47
AB  - The EcoRII recognition sites 5'-CC(A/T)GG-3' which occur three times in T3 DNA
AB  - are refractory to this restriction endonuclease.  However, these sites are
AB  - specifically cleaved by EcoRII when a second, susceptible DNA species (pBR322,
AB  - phage lambda) is present.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Bickle, T.A.
TI  - Bacteriophage Survival:  Multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts.
JO  - Microbiol. Rev.
PY  - 1983
SP  - 345
EP  - 360
VL  - 47
AB  - None
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Bickle, T.A.
AU  - Reuter, M.
AU  - Pein, C.-D.
AU  - Schroeder, C.
TI  - DNA methylation and restriction processes in Escherichia coli: Insights by use of bacterial viruses T3 and T7.
JO  - Nucleic Acid Methylation
PY  - 1990
SP  - 113
EP  - 124
VL  - 0
AB  - DNA modification-restriction enzymes of Escherichia coli cells can be grouped into 3 families,
AB  - called type I, II, and III. The ocr+ gene of T7 encodes the first known inhibitor protein
AB  - specifically blocking a group of methylases and endonucleases which, in particular, belong to
AB  - the type I (EcoB, EcoK) enzymes. The appearance of recognition sites for type II enzymes
AB  - (e.g., EcoRII, methylases EcoDam and EcoDcm) is strongly counterselected in the T7 genome,
AB  - furthermore, there are additional mechanisms preventing the enzymes from acting on the
AB  - remaining sites. For instance, EcoRII is a restriction enzyme which requires the coordinated
AB  - presence of at least 2 recognition sites in the substrate DNA for its activity. Sites which do
AB  - not fulfill this requirement are refractory to EcoRII but can be cleaved by this enzyme in the
AB  - presence of a second, susceptible DNA species or oligonucleotides. The resistance of T7 DNA
AB  - towards the type III enzyme EcoP15 is explained by the absolute strand bias of the
AB  - non-symmetric sites (in which only 1 strand can be methylated) in the DNA molecule. These data
AB  - allow some understanding of how the endogenous DNA in EcoP15-encoding cells could be protected
AB  - against self-restriction during replication. The frequency and polarity of recognition sites
AB  - in the DNA molecula may play a critical role in the function of certain restriction
AB  - endonucleases and methylases.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Bickle, T.A.
AU  - Reuter, M.
AU  - Pein, C.D.
AU  - Schroeder, C.
TI  - Studies on DNA methylation and restriction processes by use of bacterial virus T7.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 200
EP  - 200
VL  - 13D
AB  - DNA modification-restriction enzymes of Escherichia coli cells can be grouped into 3 families,
AB  - called type I,II, and III. The ocr+ gene of T7 encodes the first known inhibitor protein
AB  - specifically blocking a group of methylases and endonucleases which, in particular, belong to
AB  - the type I (EcoB, EcoK) enzymes. The appearance of recognition sites for type II enzymes
AB  - (e.g., EcoRII, methylases EcoDam and EcoDcm) is strongly counterselected in the T7 genome,
AB  - futhermore, there are additional mechanisms preventing the enzymes from acting on the
AB  - remaining sites. For instance, EcoRII is a restriction enzyme which requires the coordinated
AB  - presence of at least 2 recognition sites in the substrate DNA for its activity. Sites which do
AB  - not fulfill this requirement are refractory to EcoRII but can be cleaved by this enzyme in the
AB  - presence of a second, susceptible DNA species or oligonucleotides (CDP et al., submitted). The
AB  - resistance of T7 DNA towards the type III enzyme EcoP15 is explained by the absolute strand
AB  - bias of the non-symmetric sites (in which only one strand can be methylated) in the DNA
AB  - molecule (4; CS et al., in prep.). These data allow some understanding of how the endogenous
AB  - DNA in EcoP15-encoding cells could be protected against self-restriction during replication.
AB  - The frequency and polarity of recognition sites in the DNA molecule may play a critical role
AB  - the function of certain restriction endonucleases and methylases.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Chernin, L.S.
AU  - Hansen, S.
AU  - Rosenthal, H.A.
AU  - Goldfarb, D.M.
TI  - Protection of foreign DNA against host-controlled restriction in bacterial cells.
JO  - Mol. Gen. Genet.
PY  - 1978
SP  - 107
EP  - 110
VL  - 159
AB  - Foreign F'lac plasmid DNA which is introduced into potentially restricting E.
AB  - coli recipient cells can be protected from restriction by preinfecting the
AB  - recipient cells with UV-inactivated T3 or T7 bacteriophages which express the
AB  - ocr gene function.  The recipient cells survive and are able to replicate
AB  - themselves as well as the newly acquired plasmid.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Gola, G.
AU  - Weisshuhn, I.
AU  - Hansen, S.
TI  - The ocr gene function of bacterial viruses T3 and T7 prevents host-controlled modification.
JO  - J. Gen. Virol.
PY  - 1978
SP  - 189
EP  - 192
VL  - 41
AB  - On pre-infection of the host Escherichia coli B with u.v.-inactivated T3 or T7
AB  - phage able to express their early genes (like 0.3), B-specific modification of
AB  - super-infecting, successfully multiplying viruses does not take place.  the ocr
AB  - gene function (gene 0.3) of T3 and T7 not only prevents host-specific DNA
AB  - restriction but also modification, probably by inhibiting the same late step in
AB  - the interaction between the restriction enzyme and DNA.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Hansen, S.
AU  - Presber, W.
TI  - Host-controlled modification and restriction of bacteriophage T7 by various Escherichia coli B strains in vivo.
JO  - Z. Allg. Mikrobiol.
PY  - 1976
SP  - 73
EP  - 76
VL  - 16
AB  - It is known for more than 20 years that phages possess a "memory" for the host strain on which
AB  - they grew last.  For instance, lambda phages grown on E. coli K are restricted in E. coli B
AB  - cells, i.e. their efficiency of plating on E. coli B cells is several orders of magnitude
AB  - below their e.o.p. on E. coli K host cells.  This effect is reversible, phages grown on E.
AB  - coli B are restricted by E. coli K but grow well on E. coli B.  Therefore, the phage DNA is
AB  - not mutated but rather modified or - in absence of the right modification - restricted by the
AB  - host.  For phage lambda the molecular basis of this modification/restriction consists in a
AB  - host-specific methylation or an endonucleolytic DNA degradation at specific recognition sites
AB  - of the phage DNA.  Meanwhile, the M/R of DNA (not only of phage DNA!) has been recognized as a
AB  - general principle in molecular genetics with wide practical applications.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Hansen, S.
AU  - Reuter, M.
TI  - The ocr+ gene function of bacteriophages T3 and T7 counteracts the Salmonella typhimurium DNA restriction systems SA and SB.
JO  - J. Virol.
PY  - 1983
SP  - 1147
EP  - 1149
VL  - 45
AB  - In host cells containing the Salmonella typhimurium DNA
AB  - restriction-modification systems SA+ and SB+, replication of the ocr+
AB  - bacteriophages T3 and T7 is not impaired.  However, ocr(gene 0.3) mutants of
AB  - these phages are susceptible to DNA restriction and modification by the SA+ and
AB  - SB+ systems.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Presber, W.
AU  - Hansen, S.
AU  - Rosenthal, H.A.
TI  - Different restriction of bacteriophages T3 and T7 by P1-lysogenic cells and the role of the T3-coded SAMase.
JO  - Z. Allg. Mikrobiol.
PY  - 1977
SP  - 581
EP  - 591
VL  - 17
AB  - The intracellular growth of the phages T3 and T7 is restricted in the
AB  - presence of the Escherichia coli prophage P1.  Phage T3 has a higher ability to express its
AB  - genome and to damage the host cell than T7.  This partial protection of T3 against P1
AB  - restriction is due to the T3-coded SAMase, an enzyme which degrades S-
AB  - adenosylmethionine, the cofactor of the P1 restriction endonuclease.  Since we did not
AB  - observe DNA cleavage in vivo, we conclude that the in vivo action of the P1 nuclease is
AB  - limited to a SAM-dependent repressor-like binding to T3 and T7 DNA, while further
AB  - reactions with the DNA (modification vs cleavage) are blocked.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Prosch, S.
AU  - Reuter, M.
AU  - Goebel, W.
TI  - Cloning of the resistant EcoRII recognition site of phage T7 into an EcoRII-sensitive plasmid makes the site susceptible to the restriction enzyme.
JO  - J. Basic Microbiol.
PY  - 1990
SP  - 679
EP  - 683
VL  - 9
AB  - The recognition sequence 5'-CC(A/T)GG for EcoRII in the bacteriophage T7 genome
AB  - is refractory to this restriction endonuclease, despite not bearing the
AB  - specific (protective) methylation.  Following the integration of this site as
AB  - part of a 219 bp fragment (in which the recognition sequence is flanked by
AB  - about 100 bp of T7 origin) into the EcoRII-sensitive vector pUC18, the T7 site
AB  - becomes susceptible to cleavage, too.  The same is true of recombinant pBR322
AB  - plasmids containing the T7-derived recognition site.  The results show that the
AB  - flanking sequences are not immediately responsible for the refractory behaviour
AB  - of EcoRII sites and are in agreement with data according to which EcoRII
AB  - requires the coordinated presence of at least two recognition sites in its DNA
AB  - substrate.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Reuter, M.
AU  - Hansen, S.
AU  - Schroeder, C.
TI  - Influence of phage T3 and T7 gene functions on a Type III (EcoP1) DNA restriction-modification system in vivo.
JO  - Mol. Gen. Genet.
PY  - 1982
SP  - 457
EP  - 461
VL  - 185
AB  - The ocr+ gene function (gp 0.3) of bacteriophages T3 and T7 not only
AB  - counteracts type I (EcoB, EcoK) but also type III restriction endonucleases
AB  - (EcoP1).  Despite the presence of recognition sites, phage DNA as well as
AB  - simultaneously introduced plasmid DNA are protected by ocr+ expression against
AB  - both the endonucleolytic and the methylating activities of the EcoP1 enzyme.
AB  - Nevertheless, the EcoP1 protein causes the exclusion of T3 and T7 in
AB  - P1-lysogenic cells, apparently by exerting a repressor-like effect on phage
AB  - gene expression.  T3 which induces an S-adenosylmethionine hydrolase is less
AB  - susceptible to the repressor effect of the SAM-stimulated EcoP1 enzyme.  The
AB  - abundance of EcoP1 recognition sites in the T7 genome is explained by their
AB  - near identity with the T7 DNA primase recognition site.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Reuter, M.
AU  - Schroeder, C.
AU  - Glatman, L.I.
AU  - Chernin, L.S.
TI  - Restriction of bacteriophage T3 and T7 ocr+ strains by the type II restriction endonuclease EcoRV.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 349
EP  - 351
VL  - 190
AB  - When E. coli cells carrying the plasmid pLG13 coding for the newly discovered
AB  - type II restriction endonuclease EcoRV are infected with phage T3 or T7, only
AB  - T7 is able to replicate normally. T3 wild-type as well as its mutants are
AB  - subject to DNA restriction in vivo and in vitro.  The EcoRV enzyme cuts T3 DNA
AB  - at 5 sites.  T7 and its ocr- mutants have no EcoRV sites in their DNA.  In
AB  - contrast to the anti-restriction acitivity of the T3 and T7 ocr+ gene functon
AB  - against type I and III restriction enzymes, the ocr+ protein is unable to
AB  - inactivate the type II restriction endonuclease EcoRV.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Schroeder, C.
AU  - Hansen, S.
AU  - Rosenthal, H.A.
TI  - Active protection by bacteriophages T3 and T7 against E. coli B- and K-specific restriction of their DNA.
JO  - Mol. Gen. Genet.
PY  - 1977
SP  - 99
EP  - 106
VL  - 153
AB  - The bacteriophages T3 and T7 are not modified and restricted by E. coli
AB  - strains with different host specificity (E. coli B, K, 0) in vivo.  The phages code for a gene
AB  - product with the ability to overcome classical restriction (ocr): ocr- mutants are subject to
AB  - modification and restriction via DNA methylation vs cleavage.  The T3 genome possesses
AB  - recognition sites for the restriction endonuclease R.EcoB which, unless the DNA is B-
AB  - specifically modified, trigger 5-7 DNA cleavages.  The ocr gene function of T3 and T7 is
AB  - located within the gene 0.3 region of these phages and is not identical with the sam
AB  - (SAMase) function of T3.  The mechanism of ocr protection remains unclear, while it is
AB  - certain that this protection by the gene 0.3 protein is exerted in the infected cell and not
AB  - through "over-all" modification in the preceding growth cycle of the phage.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Schroeder, C.
AU  - Reuter, M.
AU  - Bickle, T.A.
AU  - Bogdarina, I.G.
AU  - Buryanov, Y.I.
TI  - Use of bacterial virus T7 as a tool for the study of DNA methylation.
JO  - Gene
PY  - 1988
SP  - 85
EP  - 87
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Schroeder, C.
AU  - Reuter, M.
AU  - Bogdarina, I.G.
AU  - Buryanov, Y.I.
AU  - Bickle, T.A.
TI  - DNA methylation of bacterial viruses T3 and T7 by different DNA methylases in Escherichia coli K12 cells.
JO  - Eur. J. Biochem.
PY  - 1985
SP  - 323
EP  - 330
VL  - 150
AB  - We have investigated the susceptibility of the genomes of the related bacteriophages T3 and T7
AB  - to the three major DNA methyltransferases (EcoK, dam, dcm) of their host, Escherichia coli
AB  - K12. In vivo the EcoK host specificity enzyme only methylates the DNA of ocr phages. This is
AB  - due to an inhibition of the enzyme by the phage ocr gene product, which had previously been
AB  - shown to be an inhibitor of the restriction endonuclease. EcoK-specific DNA methylation
AB  - protects the ocr viruses after one growth cycle on these host cells against the action of
AB  - corresponding restriction endonuclease EcoK. Owing to the unique S-adenosyl-L-methionine
AB  - hydrolase (sam) activity of the T3-coded ocr protein, the T3 DNA is absolutely devoid of the
AB  - methylated bases 6-methylaminopurine and 5-methylcytosine. In contrast to this, T7 derivatives
AB  - and sam- derivatives of T3 carry a small number of about 2-4 molecules 6-methylaminopurine and
AB  - 5-methylcytosine per genome. The presence of 6-methylaminopurine is due to dam methylation,
AB  - though the majority of dam sites remain unmethylated. In vivo as well as in vitro the ocr
AB  - protein has no influence on the activities of the dam and dcm methylase. The experiments gave
AB  - some evidence for the existence of a second cytosine methylase in E. coli K12. Besides dam and
AB  - dcm recognition sites being undermethylated, their absolute number in T3 and T7 DNAs is far
AB  - below the expected value. Moreover, one of the two dcm sites present in T7 (Studier strain) is
AB  - missing in our T7 strain owing to a 1300-base-pair deletion in gene 0.7.
ER  -

TY  - JOUR
AU  - Kruger, D.H.
AU  - Schroeder, C.
AU  - Santibanez-Koref, M.
AU  - Reuter, M.
TI  - Avoidance of DNA methylation:  A virus-encoded methylase inhibitor and evidence for counterselection of methylase recognition sites in viral genomes.
JO  - Cell Biophys.
PY  - 1989
SP  - 87
EP  - 95
VL  - 15
AB  - The ocr+ gene of bacterial virus T7 codes for the first protein recognized to
AB  - inhibit a specific group of DNA methylases.  The recognition sequences of
AB  - several other DNA methylases, not susceptible to Ocr inhibition, are
AB  - significantly suppressed in the virus genome.  The bacterial virus T3 encodes
AB  - an Ado-Met hydrolase, destroying the methyl donor and causing T3 DNA to be
AB  - totally unmethylated.  These observations could stimulate analogous
AB  - investigations into the regulation of DNA methylation patterns of eukaryotic
AB  - viruses and cells.  For instance, an underrepresentation of methylation sites
AB  - (5'-CG) is also true for animal DNA viruses.  Moreover, we were able to
AB  - disclose some novel properties of DNA restriction-modification enzymes
AB  - concerning the protection of DNA recognition sequences in which only one strand
AB  - can be methylated (e.g., type III enzyme EcoP15) and the primary resistance of
AB  - (unmethylated) DNA recognition sites towards type II restriction endonuclease
AB  - EcoRII.
ER  -

TY  - JOUR
AU  - Kruger, H.
AU  - Kirch, H.
TI  - A nuclear protein from HeLa cells containing a methyltransferase specific domain binds to an intragenic region of the adenovirus 12 CS-1 E1A oncogene.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1992
SP  - 789
EP  - 789
VL  - 373
AB  - We identified a binding motif (CAGCTGC) for bHLH (basic region Helix Loop Helix) proteins in
AB  - the coding part of the Adenovirus 12 E1a gene. The growth enhanced but transformation
AB  - defective Vero-cell host range mutant CS-1 of Adenovirus 12 has a 69 bp deletion in E1a
AB  - adjacent to this binding site. We examined the intragenic site in the E1a-gene for binding of
AB  - HeLa and Vero nuclear proteins using gel shift assays. We obtained comparable patterns of 3-4
AB  - retarded bands for wild type and mutant E1a sequences using DNA fragments and mutant
AB  - oligonucleotides (Cdel). Oligonucleotides bearing motifs for the transcription factors AP-4
AB  - and/or AP-1 significantly affected the binding of nuclear proteins to the E1a probes, whereas
AB  - motifs for E2F, ATF, fac-b, and NF1 had little or no effect. SDS-PAGE analysis of Cdel binding
AB  - protein, purified by different methods, revealed average molecular weights of 70 kDa and 84
AB  - kDa. Constructs containing the intragenic DNA fragments of Ad12 wild type and CS-1 mutant E1a,
AB  - the SV40 promotor, and the CAT gene did not cause any enhanced or decreased CAT-activity after
AB  - transfection of HeLa cells compared to pCAT-promotor construct alone. Screening of a HeLa
AB  - lambda-gt11 expression library for Cdel-binding proteins resulted in five identical
AB  - cDNA-clones containing a 450 bp open reading frame. We identified a 25 amino acid long domain
AB  - that has 80% homology to the conserved region X of (cytidine-5)-DNA-methyltransferases. We
AB  - currently investigate the function of the purified protein.
ER  -

TY  - JOUR
AU  - Kruger, T.
AU  - Grund, C.
AU  - Wild, C.
AU  - Noyer-Weidner, M.
TI  - Characterization of the mcrBC region of Escherichia coli K-12 wild-type and mutant strains.
JO  - Gene
PY  - 1992
SP  - 1
EP  - 12
VL  - 114
AB  - We have carried out an analysis of the Escherichia coli K-12 mcrBC locus in order to (1)
AB  - elucidate its genetic organization, (2) to identify the proteins encoded by this region, and
AB  - (3) to characterize their involvement in the restriction of DNA containing methylated cytosine
AB  - residues. In vitro expression of recombinant plasmids carrying all or portions of the mcrBC
AB  - region revealed that the mcrB and mcrC genes are organized as an operon. The mcrBC operon
AB  - specifies five proteins, as evident from parallel in vitro and in in vivo expression studies.
AB  - Three proteins of 53,35 and 34 kDa originate from mcrB expression, while two proteins of 37
AB  - and 16 kDa arise from mcrC expression. Products of both the mcrB and mcrC genes are required
AB  - to restrict the methylated substrate DNA used in this study. We also determined the nature of
AB  - mutant mcrBC loci in comparison to the E. coli K-12 wild-type mcrBC locus. A major goal of
AB  - these studies was to clarify the nature of the mcrB-1 mutation, which is carried by some
AB  - strains employed in previous analyses of the E. coli K-12 McrBC system. Based on our analyses
AB  - the mutant strains investigated could be divided into different complementation groups. The
AB  - mcrB-1 mutation is a nonsense or frameshift mutation located within mcrB. It causes premature
AB  - termination of mcrB gene product synthesis and reduces the level of mcrC gene expression. This
AB  - finding helps to understand an existing conflict in the literature. We also describe
AB  - temperature-sensitive McrA activity in some of the strains analysed and its relationship to
AB  - the previously defined differences in the tolerance levels of E. coli K-12 mcrBC mutants to
AB  - cytosine methylation.
ER  -

TY  - JOUR
AU  - Kruger, T.
AU  - Wild, C.
AU  - Noyer-Weidner, M.
TI  - McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues.
JO  - EMBO J.
PY  - 1995
SP  - 2661
EP  - 2669
VL  - 14
AB  - Restriction of DNA by the Escherichia coli K-12 McrBC restriction endonuclease, which consists
AB  - of the two subunits McrB and McrC, depends on the presence of modified cytosine residues in a
AB  - special constellation. From previous work by others it was known that restriction of
AB  - 5-methylcytosine-containing DNA requires two methylated 5'-PuC sites separated by about 40-80
AB  - non-defined base pairs. Here we show that binding of the McrBC nuclease is mediated
AB  - exclusively by the McrB subunit. McrB has a low affinity for non-methylated DNA, with which it
AB  - forms low molecular weight complexes. The affinity for DNA is significantly increased, with
AB  - variations depending on the sequence context, by hemi- or fully methylated 5'-PuC sites.
AB  - Binding to such substrates yields high molecular weight complexes, presumably involving
AB  - several McrB molecules. Methylation at unique 5'-PuC sites can be sufficient to stimulate DNA
AB  - binding by McrB. As such substrates are not cleaved by the nuclease, restriction apparently
AB  - requires the coordinated interaction of molecules bound to neighboring 5'-PumC sites. The
AB  - binding properties of McrB exhibit some similarities to recently identified eukaryotic
AB  - proteins interacting in a non-sequence-specific manner with DNA containing methylated 5'-CpG
AB  - sequences and might point to a common molecular origin of these proteins. In addition to DNA,
AB  - McrB also binds GTP, an essential cofactor in DNA restriction by McrBC. McrC neither binds to
AB  - DNA nor modulates the DNA binding potential of McrB. As McrC is essential for restriction it
AB  - appears to predominantly function in catalysis.
ER  -

TY  - JOUR
AU  - Kruger, V.D.H.
AU  - Reuter, M.
AU  - Chernin, L.S.
AU  - Gachechiladze, K.K.
AU  - Chanishvili, T.G.
AU  - Schroeder, C.
TI  - Biological functions of restriction endonucleases.
JO  - Biol. Zentralbl.
PY  - 1990
SP  - 257
EP  - 266
VL  - 109
AB  - The biological function of restriction endonucleases in bacterial cells is
AB  - reviewed (in german).  A description of the different classes of restriction
AB  - endonucleases is followed by a discussion of their evolutionary significance in
AB  - maintaining the compromise between genetic stabilility and variability of
AB  - microorganisms.  Restriction enzymes have a role in the defence against lethal
AB  - phage infection as well as in genetic recombination.  Two groups of enzymes in
AB  - Salmonella and Escherichia strains are presented as examples of restriction
AB  - enzyme evolution.  Certain bacterial cells express defence systems which attack
AB  - methylated DNA.  These enzymes complicate the cloning of methylated eukaryotic
AB  - DNA.
ER  -

TY  - JOUR
AU  - Krukov, V.M.
AU  - Shlyapnikov, M.G.
AU  - Kadyrov, F.A.
TI  - Endonuclease SegE phage T4.  II. Determination and characterization of recognition site.
JO  - Mol. Biol. (Mosk)
PY  - 1996
SP  - 1307
EP  - 1315
VL  - 30
ER  -

TY  - JOUR
AU  - Kruse, T. et al.
TI  - Complete genome sequence of Dehalobacter restrictus PER-K23(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 375
EP  - 388
VL  - 8
AB  - Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species
AB  - Dehalobacter restrictus. D. restrictus strain PER-K23 grows by
AB  - organohalide respiration, coupling the oxidation of H2 to the reductive
AB  - dechlorination of tetra- or trichloroethene. Growth has not been observed with
AB  - any other electron donor or acceptor, nor has fermentative growth been shown.
AB  - Here we introduce the first full genome of a pure culture within the genus
AB  - Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82
AB  - RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25
AB  - predicted reductive dehalogenase genes, the majority of which appear to be full
AB  - length. The reductive dehalogenase genes are mainly located in two clusters,
AB  - suggesting a much larger potential for organohalide respiration than previously
AB  - anticipated.
ER  -

TY  - JOUR
AU  - Krylov, V.N.
AU  - Karapetian, A.T.
TI  - Discovery of new type of restriction and modification in enterobacteriaceae.
JO  - Genetika
PY  - 1977
SP  - 1079
EP  - 1088
VL  - 13
AB  - The adsorption of 23 new lamboid bacteriophages to 547 strains which were isolated from a
AB  - natural population of Enterobacteriaceae was studied.  The frequency of positive combinations
AB  - of phage-bacterium with adsorption is not more than 2%.  A study of possible causes of limited
AB  - growth of lambdoid phages in the bacterial strains revealed that neither homoimmune prophage
AB  - nor prophage P2 are single factors of the growth limitation.  It is found that in natural
AB  - populations a selection of bacterial strains with the least limitation of phage takes place.
AB  - Three cases of killing bacteria after infection with high multiplicity are found.  The reason
AB  - of the killing effect is manifestation of some functions by infecting phages.  A new
AB  - restriction-modification system is found which differs from restriction-modification system A,
AB  - B, K, 15, P1, EcoRI, EcoRII.  Most strains, which adsorb phages but do not support their
AB  - growth, are supposed to possess several mechanisms of restriction.  Thus, the search for new
AB  - restriction systems in Escherichia coli is worthwhile.
ER  -

TY  - JOUR
AU  - Krynetskaya, N.F.
AU  - Kubareva, E.A.
AU  - Timchenko, M.A.
AU  - Belkov, V.M.
AU  - Shabarova, Z.A.
TI  - Transition-metal complexes as inhibitors of proteins recognizing double-stranded fragments of nucleic acids.
JO  - Biokhimiia
PY  - 1998
SP  - 1251
EP  - 1257
VL  - 63
AB  - A 30-membered DNA duplex containing the recognition site of restriction endonuclease SsoII and
AB  - a 30-membered RNA-DNA hybrid duplex, a substrate of E. coli RNase H, were synthesized.  The
AB  - cleavage of the 30-membered fragments of nucleic acids catalyzed by endonucleases in the
AB  - presence of Co-phthalocyanine complex [CoPc(COONa)8 containing eight carboxyl groups at the
AB  - periphery of the ligand was studied.  It was shown that the efficiency of enzyme catalysis
AB  - decreases in the presence of the metal complex for both endonucleases.  By addition of a
AB  - 100-fold excess of Co-phthalocyanine complex with respect to DNA duplex the initial rate of
AB  - substrate hydrolysis by restriction endonuclease SsoII is observed to decrease twice.  An
AB  - equimolar ratio of the metal complex and hybrid duplex leads to essentially complete
AB  - inhibition of RNA cleavage by RNase H from E. coli.  The inhibition of catalytic activity of
AB  - enzymes recognizing the double-stranded nucleic acids in the presence of Co-phthalocyanine
AB  - complex is assumed to be caused by the ability of the latter to interact with DNA, RNA, and
AB  - DNA-RNA duplexes.
ER  -

TY  - JOUR
AU  - Krzyzanowska, D.M.
AU  - Iwanicki, A.
AU  - Ossowicki, A.
AU  - Obuchowski, M.
AU  - Jafra, S.
TI  - Genome Sequence of Bacillus subtilis MB73/2, a Soil Isolate Inhibiting the Growth of Plant Pathogens Dickeya spp. and Rhizoctonia solani.
JO  - Genome Announcements
PY  - 2013
SP  - e00238
EP  - e00213
VL  - 1
AB  - Bacillus subilis MB73/2 is a Gram-positive bacterium isolated in Poland from a meadow soil
AB  - sample. When tested in vitro, the strain shows strong antagonism
AB  - toward plant pathogens-the soft rot-causing bacteria Dickeya spp. and the crown
AB  - rot fungus Rhizoctonia solani. Here, we present the genome sequence of MB73/2.
ER  -

TY  - JOUR
AU  - Ktari, A.
AU  - Nouioui, I.
AU  - Furnholm, T.
AU  - Swanson, E.
AU  - Ghodhbane-Gtari, F.
AU  - Tisa, L.S.
AU  - Gtari, M.
TI  - Permanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence  of canonical nod genes, which are highly homologous to those detected in  Candidatus Frankia Dg1 genome.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 51
EP  - 51
VL  - 12
AB  - Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the
AB  - rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range
AB  - includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219
AB  - is closely related to 'Frankia discariae' with a 16S rRNA gene similarity of
AB  - 99.78%. Because of the lack of genetic tools for Frankia, our understanding of
AB  - the bacterial signals involved during the plant infection process and the
AB  - development of actinorhizal root nodules is very limited. Since the first three
AB  - Frankia genomes were sequenced, additional genome sequences covering more diverse
AB  - strains have helped provide insight into the depth of the pangenome and attempts
AB  - to identify bacterial signaling molecules like the rhizobial canonical nod genes.
AB  - The genome sequence of Frankia sp. strain NRRL B-16219 was generated and
AB  - assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content.
AB  - Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes,
AB  - 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL
AB  - B-16219 draft genome contained genes homologous to the rhizobial common
AB  - nodulation genes clustered in two areas. The first cluster contains nodACIJH
AB  - genes whereas the second has nodAB and nodH genes in the upstream region.
AB  - Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than
AB  - their sister groups from rhizobia. PCR-sequencing suggested the widespread
AB  - occurrence of highly homologous nodA and nodB genes in microsymbionts of field
AB  - collected Ceanothus americanus.
ER  -

TY  - JOUR
AU  - Ku, C.
AU  - Lo, W.S.
AU  - Chen, L.L.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma apis B31T (ATCC 33834), a Bacterium Associated with May Disease of Honeybees (Apis mellifera).
JO  - Genome Announcements
PY  - 2014
SP  - e01151
EP  - e01113
VL  - 2
AB  - Spiroplasma apis B31(T) (ATCC 33834) is a wall-less bacterium in the class Mollicutes that has
AB  - been linked to May disease of honeybees (Apis mellifera).
AB  - Here, we report the complete genome sequence of this bacterium to facilitate the
AB  - investigation of its virulence factors.
ER  -

TY  - JOUR
AU  - Ku, C.
AU  - Lo, W.S.
AU  - Chen, L.L.
AU  - Kuo, C.H.
TI  - Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in Spiroplasma.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 1151
EP  - 1164
VL  - 5
AB  - Spiroplasma is a genus of wall-less, low-GC, Gram-positive bacteria with helical morphology.
AB  - As commensals or pathogens of plants, insects, ticks, or crustaceans, they are closely related
AB  - with mycoplasmas and form a monophyletic group (Spiroplasma-
AB  - Entomoplasmataceae-Mycoides) with Mycoplasma mycoides and its relatives. In this study, we
AB  - report the complete genome sequences of S. chrysopicola and S. syrphidicola from the
AB  - Chrysopicola clade. These species form the sister group to the Citri clade, which includes
AB  - several well-known pathogenic spiroplasmas. Surprisingly, these two newly available genomes
AB  - from the Chrysopicola clade contain no plectroviral genes, which were found to be
AB  - highly repetitive in the previously sequenced genomes from the Citri clade. Based on the
AB  - genome alignment and patterns of GC-skew, these two Chrysopicola genomes appear to be
AB  - relatively stable, rather than being highly rearranged as those from the Citri clade.
AB  - Phylogenetic analyses suggest that the susceptibility to plectroviral invasion probably
AB  - originated in the common ancestor of the Citri clade or one of its subclades. This
AB  - susceptibility may be attributed to the absence of antiviral systems found in the Chrysopicola
AB  - clade. Using the virus-free genomes of the Chrysopicola clade as references, we inferred the
AB  - putative viral integration sites in the Citri genomes. Comparisons of syntenic regions suggest
AB  - that the extensive viral invasion in the Citri clade promoted genome rearrangements and
AB  - expansions. More importantly, the viral invasion may have facilitated horizontal gene
AB  - transfers that contributed to adaptation in the Citri clade.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Ortskaya, T.S.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  X. Hydrolysis of substrates with structural anomalies.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 1205
EP  - 1211
VL  - 13
AB  - Interaction of the EcoRII restriction endonuclease with a set of 30-membered
AB  - substrates having structural anomalies in the recognition site (^CCT/AGG) and
AB  - in adjacent sequences has been studied.  A nick in the centre of the EcoRII
AB  - recognition site between dC and dA residues slows down hydrolysis of the
AB  - nonmodified strand, whereas the modified one is not cleaved.  Removal of the
AB  - phosphate group from the nick in this substrate does not alter the rate of the
AB  - cleavage.  The absence of one of the phosphate groups in the flanking sequence
AB  - at a twobase-pair distance from the recognition site slows down the enzymatic
AB  - hydrolysis.  Removal of dA or dT out of the EcoRII recognition site blocks the
AB  - enzymatic reaction.  It appears that EcoRII does not interact with the
AB  - phosphate group between dC and dA residues in the recognition site.
AB  - Suggestions are made concerning possible contacts of the EcoRII restriction
AB  - endonuclease with dA- and dT-residues of the recognition site and with the
AB  - sugar-phosphate backbone of the adjacent nucleotide sequences.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Pein, C.-D.
AU  - Krug, A.
AU  - Oretskaya, T.S.
AU  - Cech, D.
AU  - Shabarova, Z.A.
TI  - Oligonucleotide cleavage by restriction endonucleases MvaI and EcoRII: a comprehensive study on the influence of structural parameters on the enzyme-substrate interaction.
JO  - Biochim. Biophys. Acta
PY  - 1991
SP  - 395
EP  - 400
VL  - 1088
AB  - To elucidate the mechanism of action of restriction endonucleases -
AB  - isoschizomers EcoRII and MvaI - a study was made of their interaction with a
AB  - set of synthetic oligonucleotide duplexes containing a single 5'-d(CCA/TGG)-3'
AB  - EcoRII (MvaI) recognition site.  The substrates had varying length and
AB  - structure of the nucleotide sequences flanking the recognition site.  The
AB  - structure of the flanking sequence is important for the cleavage by EcoRII and
AB  - MvaI enzymes; there is a structure which was found to speed up the EcoRII and
AB  - MvaI action.  The cleavage of oligonucleotide duplexes by EcoRII enzyme does
AB  - not go to completion.  EcoRII endonuclease cleaved extended substrates less
AB  - efficiently than short ones.  Extension of the flanking sequences, with the
AB  - same nucleotide surrounding of the recognition site, substantially altered the
AB  - whole kinetic pattern of MvaI hydrolysis.  This was not observed with EcoRII
AB  - enzyme.  The restriction endonuclease MvaI distinguished between dA and dT
AB  - residues in the recognition site, which was reflected in the higher rate of
AB  - hydrolysis of the dA-containing strand of the quasipalindromic DNA duplex.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Romanova, E.A.
AU  - Oretskaya, T.S.
AU  - Shabarova, Z.A.
TI  - Cleavage of substrates containing modified amino groups in heterocyclic bases by MvaI and EcoRII restriction endonucleases.
JO  - Bioorg. Khim.
PY  - 1990
SP  - 501
EP  - 506
VL  - 16
AB  - 14-membered DNA-duplexes containing modified nucleoside residues, viz 4-N-methyldeoxycytidine
AB  - (m4dC), 6-N-methyldeoxyadenosine (m6dA) or deoxyinosine (dI), in only one strand of the
AB  - recognition site (CCA/TGG) of MvaI and EcoRII endonucleases were synthesized.  It was shown
AB  - that MvaI and EcoRII endonucleases interact with the exocyclic amino groups of the external dC
AB  - residues and of the central dA residue of the recognition site exposed into the DNA major
AB  - groove.  These endonucleases which are isoschizomers were found to possess different
AB  - mechanisms of substrate cleavage.  The ability of MvaI endonuclease to hydrolyze only the
AB  - unmodified strand of methylated duplexes allows one to make site-directed single-strand nicks
AB  - in double-stranded DNA. Elimination of the 2-NH2-group located in the minor groove of DNA by
AB  - substituting dI for dG had little, if any, effect on the hydrolytic activity of EcoRII and
AB  - MvaI endonucleases.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Kuznetsova, S.A.
AU  - Kanevsky, I.A.
AU  - Karyagina, A.S.
AU  - Nikolskaya, I.I.
AU  - Shabarova, Z.A.
TI  - DNA dumbbells as substrates for studying restriction-modification and repair enzymes.
JO  - FASEB J.
PY  - 1997
SP  - A1309
EP  - A1309
VL  - 11
AB  - The use of the DNA dumbbells (duplexes covalently closed on both ends by single stranded
AB  - loops) for investigation of restriction-modification and repair enzymes has been demonstrated.
AB  - Their substrate properties in comparison with DNA hairpins have been analysed in the reactions
AB  - with type II restriction endonucleases (R): MvaI, EcoRII, SsoII and
AB  - DNA-(5-methylcytosine)methyltransferase (M): SsoII.  The hairpin and dumbbell, containing dU
AB  - instead of dT in the center of the restriction-modification enzyme's recognition site
AB  - (5'CCWGG3'), have been used to evaluate the uracil removal from ds DNA with high duplex
AB  - stability by uracil-DNA glycosylase.  R.EcoRII, R.MvaI and R.SsoII interact more efficiently
AB  - with more stable hairpin-like substrate than with equivalent linear DNA duplex.  Less
AB  - efficiency is observed for dumbbell cleavage by restriction endonucleases as compared with
AB  - hairpin-like duplex.  The decreased conformational mobility of the strands in the dumbbell
AB  - might affect adversely on the substrate hydrolysis by the restriction endonucleases.  Addition
AB  - of the 14-membered DNA substrate accelerates the cleavage of the dumbbell by R.EcoRII.
AB  - M.SsoII and UDG reveal 1.5-2.5-fold preference for dsDNA duplex over hairpin-like DNA, which
AB  - is 30 C more stable.  The most stable dumbbell is also a poor substrate for M.SsoII and
AB  - especially for UDG.  The M.SsoII or UDG functioning is more effective when the double helix is
AB  - less stable.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Pein, C.-D.
AU  - Gromova, E.S.
AU  - Kuznezova, S.A.
AU  - Tashlitzki, V.N.
AU  - Chech, D.
AU  - Shabarova, Z.A.
TI  - The role of modifications in oligonucleotides in sequence recognition by MvaI restriction endonuclease.
JO  - Eur. J. Biochem.
PY  - 1988
SP  - 615
EP  - 618
VL  - 175
AB  - The interaction of MvaI restriction endonuclease with 14-membered
AB  - deoxyribonucleotide duplexes containing modifications within the recognition
AB  - site (CC[A/T]GG) has been studied.  Substitution of m5dC for the internal dC
AB  - residue, as well as substitution of fl5dU or rU for dT did not influence the
AB  - initial rate of hydrolysis (Vo) of modified strands, whereas the hydrolysis of
AB  - unmodified strands was inhibited in some cases.  Furthermore, the substitution
AB  - of a pyrophosphate bond for a scissile phosphodiester bond in one strand
AB  - completely inhibited digestion in this strand without any decrease of the rate
AB  - of hydrolysis of the unmodified strand.  In contrast to EcoRI endonuclease,
AB  - which recognizes the same DNA sequence, in the case of MvaI endonuclease
AB  - substrate recognition is possible in a wide range of conformational, electronic
AB  - and hydrophobic alterations within the recognition site.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Petrauskene, O.V.
AU  - Karyagina, A.S.
AU  - Nikolskaya, I.I.
AU  - Gromova, E.S.
TI  - DNA duplexes with non-nucleotide inserts: interaction with restriction endonucleases.
JO  - Nucleic Acids Symp. Ser.
PY  - 1991
SP  - 308
EP  - 308
VL  - 24
AB  - Modified DNA duplexes with trimethylene bridges or 1,2-dideoxy-D-ribofuranose instead of one
AB  - of the nucleoside residues are of interest as DNA analogs with the sugar-phosphate backbone
AB  - partially or completely preserved but with the heterocyclic base removed.  Another type of
AB  - non-nucleotide insert - 9[1'-hydroxy-2'- (hydroxymethyl)ethoxy]methylguanine (acyclic dG) -
AB  - leads to distortion of the sugar moiety of nucleoside residue while the base is preserved.
AB  - 14-membered DNA duplexes have been constructed containing single non-nucleotide inserts in the
AB  - recognition sites (5'-CC(A/T)GG-3' and 5'-CCNGG-3') of a number of restriction
AB  - endonucleases (R).dG residues or one of the nucleosides of the central base-pair of the
AB  - recognition site have been modified.  It has been shown by UV spectroscopy and CD that
AB  - non-nucleotide inserts bring about some destabilization of the double helix without essential
AB  - distortion of its geometry.  Substrate properties of DNA duplexes with non-nucleotide inserts
AB  - have been studied.  R. ScrFI and R.SsoII recognize the CCNGG sequence.  R.ScrFI cleaves all
AB  - the modified duplexes, but with reduced efficiency.  Introduction of trimethylene bridge or
AB  - 1,2-dideoxy-D-ribofuranose into the recognition site induces an increase in the cleavage
AB  - efficiency of modified substrates and change of specificity of their hydrolysis by R.SsoII.
AB  - Restoration of R.SsoII specificity is observed in the case of acyclic dG-containing substrate
AB  - when guanine base is returned.  To preserve canonical R.SsoII specificity the enzyme should be
AB  - able to form discrimination contacts with internal and external dG and central nucleoside
AB  - residues of the recognition site.  DNA duplexes with non-nucleotide inserts in the CC(A/T)GG
AB  - recognition sequence (with the exception of acyclic dG insert) are resistant to R.MvaI,
AB  - R.BstNI and R.EcoRII.  Probably, these enzymes interact specifically with each base of the
AB  - central A.T pair and with both dG residues.  A comparative analysis of the functioning of
AB  - restriction enodnucleases - isoschizomers - has been done on the basis of these data.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Petrauskene, O.V.
AU  - Karyagina, A.S.
AU  - Nikolskaya, I.I.
AU  - Gromova, E.S.
TI  - Change of cleavage site of synthetic substrates by SsoII restriction endonuclease due to non-nucleotide inserts into the recognition sequence.
JO  - Bioorg. Khim.
PY  - 1992
SP  - 1131
EP  - 1134
VL  - 18
AB  - The cleavage of synthetic DNA duplexes containing 1,3-propanediol, 1,2-dideoxy-D-ribofuranose
AB  - or 9-[1'-hydroxy-2'-(hydroxymethyl)ethoxy]methylguanine (glG) residues instead of one of the
AB  - dG residues or one of the nucleosides of the central base pair of the recognition site by
AB  - SsoII restriction endonuclease (CCNGG) has been studied. It is found that the non-nucleotide
AB  - insertions (except for glG) result in a change of the SsoII cleavage site and an increase of
AB  - the efficiency of the cleavage. The novel noncanonical cleavage occurs at the phosphodiester
AB  - bond adjoining the non-nucleotide insert from the 5'-end.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Petrauskiene, O.V.
AU  - Karyagina, A.S.
AU  - Tashlitsky, V.N.
AU  - Nikolskaya, I.I.
AU  - Gromova, E.S.
TI  - Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonuclease SsoII.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4533
EP  - 4538
VL  - 20
AB  - A study was made of the interaction between restriction endonucleases recognizing CCNGG (SsoII
AB  - and ScrFI) or CCA/TGG (MvaI and EcoRII) DNA sequences and a set of synthetic substrates
AB  - containing 1,3-propanediol,1,2-dideoxy-D-ribofuranose or
AB  - 9-[1'-hydroxy-2'-(hydroxymethyl)ethoxy] methylguanine (glG) residues replacing either one of
AB  - the central nucleosides or dG residues in the recognition site. The non-nucleotide inserts
AB  - (except for glG) introduced into the recognition site both increase the efficiency of SsoII
AB  - and change its specificity. A cleavage at the noncanonical position takes place, in some cases
AB  - in addition to the correct ones. Noncanonical hydrolysis by SsoII occurs at the phosphodiester
AB  - bond adjacent to the point of modification towards the 5'-end. With the guanine base returned
AB  - (the substrate with glG), the correct cleavage position is restored. ScrFI specifically
AB  - cleaves all the modified substrates. DNA duplexes with non-nucleotide inserts (except for the
AB  - glG-containing duplex) are resistant to hydrolysis by MvaI and EcoRII. Prompted by the data
AB  - obtained we discuss the peculiarities of recognition by restriction endonucleases of
AB  - 5-membered DNA sequences which have completely or partially degenerate central base pairs. It
AB  - is sugegested that SsoII forms a complex with DNA in an "open" form.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Thole, H.
AU  - Karyagina, A.S.
AU  - Oretskaya, T.S.
AU  - Pingoud, A.
AU  - Pingoud, V.
TI  - Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 1085
EP  - 1091
VL  - 28
AB  - A target sequence-specific DNA binding region of the restriction endonuclease Sso II was
AB  - identified by photocross-linking with an oligodeoxynucleotide duplex which was substituted
AB  - with 5-iododeoxyuridine (5-IdU) at the central position of the Sso II recognition site
AB  - (CCNGG). For this purpose the Sso II-DNA complex was irradiated with a helium/cadmium laser
AB  - (325 nm). The cross-linking yield obtained was approximately 50%. In the presence of excess
AB  - unmodified oligodeoxynucleotide or with oligodeoxynucleotides substituted with 5-IdU
AB  - elsewhere, no cross-linking was observed, indicating the specificity of the cross-linking
AB  - reaction. The cross-linked Sso II-oligodeoxynucleotide complex was digested with chymotrypsin,
AB  - a cross-linked peptide- oligodeoxynucleotide complex isolated and the site of cross-linking
AB  - identified by Edman sequencing to be Trp61. In line with this identification is the finding
AB  - that the W61A variant cannot be cross-linked with the IdU-substituted oligodeoxynucleotide,
AB  - shows a decrease in affinity towards DNA and is inactive in cleavage. It is concluded that the
AB  - region around Trp61 is involved in specific binding of Sso II to its DNA substrate.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Walter, J.
AU  - Karyagina, A.S.
AU  - Vorobeva, O.V.
AU  - Lau, P.C.
AU  - Trautner, T.
TI  - Determination of methylation site of DNA-methyltransferase NlaX by a hybrid method.
JO  - Biotechniques
PY  - 2002
SP  - 526
EP  - 531
VL  - 33
AB  - Using a new method based on a combination of bisulfite reaction, the repair enzyme uracil-DNA
AB  - glycosylase, and synthetic oligodeoxyribonucleotides, the methylation site of
AB  - DNA-methyltransferase NlaX (M.NlaX) from Neisseria lactamica was established to be the inner
AB  - cytosine in the double-stranded pentanucleotide recognition sequence 5'-CCNGG-3' (where N =
AB  - any nucleoside). 5-Methylcytosine (m5C) type modification by M-N1aX was confirmed by the use
AB  - of oligonucleotide substrates that contain 5-fluoro-2'-deoxycytidine.
ER  -

TY  - JOUR
AU  - Kubareva, E.A.
AU  - Walter, J.
AU  - Vorobeva, O.V.
AU  - Razumikhin, M.V.
AU  - Karyagina, A.S.
AU  - Lau, P.C.K.
AU  - Trautner, T.
TI  - Determination of a non-methylated deoxycytidine desidue in the decognition site of DNA-methyltransferases.
JO  - Biokhimiia
PY  - 2001
SP  - 1356
EP  - 1360
VL  - 66
AB  - A method for determination of a non-methylated deoxycytidine (dC) residue in the recognition
AB  - site of 5-cytosine DNA-methyltransferases is suggested. The method is based on treatment of
AB  - methylated DNA by sodium bisulfite and successive reaction of the thus modified DNA with a
AB  - repair enzyme, uracil-DNA glycosylase. This method was successfully applied to identify NlaX
AB  - methyltransferase specificity.
ER  -

TY  - JOUR
AU  - Kube, M.
AU  - Beck, A.
AU  - Zinder, S.H.
AU  - Kuhl, H.
AU  - Reinhardt, R.
AU  - Adrian, L.
TI  - Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1.
JO  - Nat. Biotechnol.
PY  - 2005
SP  - 1269
EP  - 1273
VL  - 23
AB  - Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most
AB  - toxic and persistent chlorinated aromatics and aliphatics
AB  - by reductive dechlorination and are used for in situ bioremediation of
AB  - contaminated sites. Our sequencing of the complete 1,395,502 base pair
AB  - genome of Dehalococcoides strain CBDB1 has revealed the presence of 32
AB  - reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the
AB  - bacteria an immense dehalogenating potential. Most rdh genes were
AB  - associated with genes encoding transcription regulators such as
AB  - two-component regulatory systems or transcription regulators of the
AB  - MarR-type. Four new paralog groups of rdh-associated genes without known
AB  - function were detected. Comparison with the recently sequenced genome of
AB  - Dehalococcoides ethenogenes strain 195 reveals a high degree of gene
AB  - context conservation (synteny) but exceptionally high plasticity in all
AB  - regions containing rdh genes, suggesting that these regions are under
AB  - intense evolutionary pressure.
ER  -

TY  - JOUR
AU  - Kube, M.
AU  - Migdoll, A.M.
AU  - Gehring, I.
AU  - Heitmann, K.
AU  - Mayer, Y.
AU  - Kuhl, H.
AU  - Knaust, F.
AU  - Geider, K.
AU  - Reinhardt, R.
TI  - Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae.
JO  - BMC Genomics
PY  - 2010
SP  - 393
EP  - 393
VL  - 11
AB  - ABSTRACT: BACKGROUND: The genus Erwinia includes plant-associated
AB  - pathogenic and non-pathogenic Enterobacteria. Important pathogens such as
AB  - Erwinia amylovora, the causative agent of fire blight and E. pyrifoliae
AB  - causing bacterial shoot blight of pear in Asia belong to this genus. The
AB  - species E. tasmaniensis and E. billingiae are epiphytic bacteria and may
AB  - represent antagonists for biocontrol of fire blight. The presence of genes
AB  - putative involved in virulence in E. amylovora and E. pyrifoliae is of
AB  - special interest for these species in consequence. RESULTS: Here we
AB  - provide the complete genome sequences of the pathogenic E. pyrifoliae
AB  - strain Ep1/96 with a size of 4.1 Mb and of the non-pathogenic species E.
AB  - billingiae strain Eb661 with a size of 5.4 Mb, de novo determined by
AB  - conventional Sanger sequencing and next generation sequencing techniques.
AB  - Genome comparison reveals large inversions resulting from homologous
AB  - recombination events. Furthermore, comparison of deduced proteins
AB  - highlights a relation of E. billingiae strain Eb661 to E. tasmaniensis
AB  - strain Et1/99 and a distance to E. pyrifoliae for the overall gene content
AB  - as well as for the presence of encoded proteins representing virulence
AB  - factors for the pathogenic species. Pathogenicity of E. pyrifoliae is
AB  - supposed to have evolved by accumulation of potential virulence factors.
AB  - E. pyrifoliae carries factors for type III secretion and cell invasion.
AB  - Other genes described as virulence factors for E. amylovora are involved
AB  - in the production of exopolysaccharides, the utilization of plant
AB  - metabolites such as sorbitol and sucrose. Some virulence-associated genes
AB  - of the pathogenic species are present in E. tasmaniensis but mostly absent
AB  - in E. billingiae. CONCLUSION: The data of the genome analyses correspond
AB  - to the pathogenic lifestyle of E. pyrifoliae and underlines the epiphytic
AB  - localization of E. tasmaniensis and E. billingiae as a saprophyte.
ER  -

TY  - JOUR
AU  - Kube, M.
AU  - Schneider, B.
AU  - Kuhl, H.
AU  - Dandekar, T.
AU  - Heitmann, K.
AU  - Migdoll, A.M.
AU  - Reinhardt, R.
AU  - Seemuller, E.
TI  - The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'.
JO  - BMC Genomics
PY  - 2008
SP  - 306
EP  - 306
VL  - 9
AB  - BACKGROUND: Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that
AB  - cause diseases in hundreds of economically important
AB  - plants. They represent a monophyletic group within the class Mollicutes
AB  - (trivial name mycoplasmas) and are characterized by a small genome with a
AB  - low GC content, and the lack of a firm cell wall. All mycoplasmas,
AB  - including strains of 'Candidatus (Ca.) Phytoplasma asteris' and 'Ca. P.
AB  - australiense', examined so far have circular chromosomes, as is the case
AB  - for almost all walled bacteria. RESULTS: Our work has shown that 'Ca.
AB  - Phytoplasma mali', the causative agent of apple proliferation disease, has
AB  - a linear chromosome. Linear chromosomes were also identified in the
AB  - closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'.
AB  - The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a
AB  - GC content of 21.4%. The chromosome is further characterized by large
AB  - terminal inverted repeats and covalently closed hairpin ends. Analysis of
AB  - the protein-coding genes revealed that glycolysis, the major
AB  - energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in
AB  - 'Ca. P. mali'. Due to the apparent lack of other metabolic pathways
AB  - present in mycoplasmas, it is proposed that maltose and malate are
AB  - utilized as carbon and energy sources. However, complete ATP-yielding
AB  - pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P.
AB  - asteris' by a smaller genome, a lower GC content, a lower number of
AB  - paralogous genes, fewer insertions of potential mobile DNA elements, and a
AB  - strongly reduced number of ABC transporters for amino acids. In contrast,
AB  - 'Ca. P. mali' has an extended set of genes for homologous recombination,
AB  - excision repair and SOS response than 'Ca. P. asteris'. CONCLUSION: The
AB  - small linear chromosome with large terminal inverted repeats and
AB  - covalently closed hairpin ends, the extremely low GC content and the
AB  - limited metabolic capabilities reflect unique features of 'Ca. P. mali',
AB  - not only within phytoplasmas, but all mycoplasmas. It is expected that the
AB  - genome information obtained here will contribute to a better understanding
AB  - of the reduced metabolism of phytoplasmas, their fastidious nutrition
AB  - requirements that prevented axenic cultivation, and the mechanisms
AB  - involved in pathogenicity.
ER  -

TY  - JOUR
AU  - Kube, M.
AU  - Siewert, C.
AU  - Migdoll, A.M.
AU  - Duduk, B.
AU  - Holz, S.
AU  - Rabus, R.
AU  - Seemuller, E.
AU  - Mitrovic, J.
AU  - Muller, I.
AU  - Buttner, C.
AU  - Reinhardt, R.
TI  - Analysis of the Complete Genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and Their Comparison to the Obligate Parasites from ' Candidatus Phytoplasma'.
JO  - J. Mol. Microbiol. Biotechnol.
PY  - 2013
SP  - 19
EP  - 36
VL  - 24
AB  - Analysis of the completely determined genomes of the plant-derived Acholeplasma
AB  - brassicae strain O502 and A. palmae strain J233 revealed that the circular
AB  - chromosomes are 1,877,792 and 1,554,229 bp in size, have a G + C content of 36
AB  - and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis
AB  - of these sequences and previously published genomes of A. laidlawii strain PG-8,
AB  - 'Candidatus Phytoplasma asteris' strains, 'Ca. P. australiense' and 'Ca. P. mali'
AB  - show a limited shared basic genetic repertoire. The acholeplasma genomes are
AB  - characterized by a low number of rearrangements, duplication and integration
AB  - events. Exceptions are the unusual duplication of rRNA operons in A. brassicae
AB  - and an independently introduced second gene for a single-stranded binding protein
AB  - in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by
AB  - encoding the cell division protein FtsZ, a wide variety of ABC transporters, the
AB  - F0F1 ATP synthase, the Rnf-complex, SecG of the Sec-dependent secretion system, a
AB  - richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid
AB  - and partial amino acid metabolism. Conserved metabolic proteins encoded in
AB  - phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters
AB  - and proteins involved in host-interaction, and virulence-associated effectors
AB  - were not predicted for the acholeplasmas. (c) 2013 S. Karger AG, Basel.
ER  -

TY  - JOUR
AU  - Kubiak, A.M.
AU  - Poehlein, A.
AU  - Budd, P.
AU  - Kuehne, S.A.
AU  - Winzer, K.
AU  - Theys, J.
AU  - Lambin, P.
AU  - Daniel, R.
AU  - Minton, N.P.
TI  - Complete Genome Sequence of the Nonpathogenic Soil-Dwelling Bacterium Clostridium sporogenes Strain NCIMB 10696.
JO  - Genome Announcements
PY  - 2015
SP  - e00942
EP  - e00915
VL  - 3
AB  - Clostridium sporogenes is a harmless spore-forming anaerobe that is widely distributed in
AB  - soil/water and in the intestines of humans and animals. It is
AB  - extensively used as a safe model to test the suitability of new preservative
AB  - methods by the food industry and has potential to deliver therapeutic agents to
AB  - tumors.
ER  -

TY  - JOUR
AU  - Kubicek-Sutherland, J.Z.
AU  - Heithoff, D.M.
AU  - Ersoy, S.C.
AU  - Shimp, W.R.
AU  - Mahan, M.J.
TI  - Immunization with a DNA adenine methylase over-producing Yersinia pseudotuberculosis vaccine confers robust cross-protection against heterologous pathogenic serotypes.
JO  - Vaccine
PY  - 2014
SP  - 1451
EP  - 1459
VL  - 32
AB  - Yersinia pseudotuberculosis is a foodborne pathogen that can cause serious human illness.
AB  - Although the source and route of transmission often remain obscure, livestock have been
AB  - implicated in some cases. The diversity of yersiniae present on farms and their widespread
AB  - distribution in animal and environmental reservoirs necessitates the use of broad prophylactic
AB  - strategies that are efficacious against many serotypes simultaneously. Herein, immunization of
AB  - mice with a modified, live attenuated Y. pseudotuberculosis vaccine that overproduces the DNA
AB  - adenine methylase (Dam P) conferred robust protection against virulent challenge (150-fold
AB  - LD50) with homologous and heterologous serotypes that have been associated with human disease
AB  - (O:1, O:1a, O:3). Further, the dam gene was shown to be essential for cell viability in all (7
AB  - of 7) Y. pseudotuberculosis strains tested. Direct selection for the inheritance of dam mutant
AB  - alleles in Y. pseudotuberculosis resulted in dam strain variants that contained compensatory
AB  - (second-site suppressor) mutations in genes encoding methyl-directed mismatch repair proteins
AB  - (mutHLS) that are involved in suppression of the non-viable cell phenotype in all (19/19)
AB  - strains tested. Such dam mutH variants exhibited a significant increase in virulence and
AB  - spontaneous mutation frequency relative to that of a Dam P vaccine strain. These studies
AB  - indicate that Y. pseudotuberculosis Dam P strains conferred potent cross-protective efficacy
AB  - as well as decreased virulence and spontaneous mutation frequency relative to those that lack
AB  - Dam, which have compensatory mutations in mutHLS loci. These data suggest that development of
AB  - yersiniae livestock vaccines based on Dam overproduction is a viable mitigation strategy to
AB  - reduce these potential foodborne contaminants. (C) 2014 Elsevier Ltd. All rights reserved.
ER  -

TY  - JOUR
AU  - Kubota, T.
TI  - DNA methylase 3B (DNMT3B).
JO  - Seitai Kagaku
PY  - 2005
SP  - 378
EP  - 379
VL  - 56
ER  -

TY  - JOUR
AU  - Kuch, D.
AU  - Schermelleh, L.
AU  - Manetto, S.
AU  - Leonhardt, H.
AU  - Carell, T.
TI  - Synthesis of DNA dumbbell based inhibitors for the human DNA methyltransferase Dnmt1.
JO  - Angew. Chem. Int. Ed. Engl.
PY  - 2008
SP  - 1515
EP  - 1518
VL  - 47
AB  - DNA methyltransferases convert deoxycytidine nucleobases in DNA into 5-methyldeoxycytidines
AB  - using the cofactor S-adenosylmethionine as the methyl group donor.  Methylation of the
AB  - canonical dC base, particularly in gene promoter regions, induces complex processes, which
AB  - finally lead to the silencing of the corresponding gene.  This epigenetic gene silencing is of
AB  - paramount importance for cellular differentiation.  Altered methylation patterns and
AB  - corresponding changes in gene expression are found in practically all tumor cells.  The major
AB  - DNA methyltransferase Dnmt1 is a 183-kDa-large protein that preferentially methylates dC bases
AB  - in hemimethylated d(cpG) sequences after DNA replication.
ER  -

TY  - JOUR
AU  - Kuck, D.
AU  - Singh, N.
AU  - Lyko, F.
AU  - Medina-Franco, J.L.
TI  - Novel and selective DNA methyltransferase inhibitors: Docking-based virtual screening and experimental evaluation.
JO  - Bioorg. Med. Chem.
PY  - 2010
SP  - 822
EP  - 829
VL  - 18
AB  - The DNA methyltransferase (DNMT) enzyme family consists of four members with diverse functions
AB  - and represents one of the most promising targets
AB  - for the development of novel anticancer drugs. However, the standard
AB  - drugs for DNMT inhibition are non-selective cytosine analogues with
AB  - considerable cytotoxic side-effects that have been developed several
AB  - decades ago. In this work, we conducted a virtual screening of more
AB  - than 65,000 lead-like compounds selected from the National Cancer
AB  - Institute collection using a multistep docking approach with a
AB  - previously validated homology model of the catalytic domain of human
AB  - DNMT1. Experimental evaluation of top-ranked molecules led to the
AB  - discovery of novel small molecule DNMT1 inhibitors. Virtual screening
AB  - hits were further evaluated for DNMT3B inhibition revealing several
AB  - compounds with selectivity towards DNMT1. These are the first small
AB  - molecules reported with biochemical selectivity towards an individual
AB  - DNMT enzyme capable of binding in the same pocket as the native
AB  - substrate cytosine, and are promising candidates for further rational
AB  - optimization and development as anticancer drugs. The availability of
AB  - enzyme-selective inhibitors will also be of great significance for
AB  - understanding the role of individual DNMT enzymes in epigenetic
AB  - regulation.
ER  -

TY  - JOUR
AU  - Kudirkiene, E.
AU  - Christensen, H.
AU  - Bojesen, A.M.
TI  - Draft Genome Sequence of Gallibacterium anatis bv. haemolytica 12656-12 Liver, an Isolate Obtained from the Liver of a Septicemic Chicken.
JO  - Genome Announcements
PY  - 2013
SP  - e00810
EP  - e00813
VL  - 1
AB  - We report the draft genome sequence of Gallibacterium anatis bv. haemolytica strain 12656-12
AB  - Liver. This strain was isolated from the liver of a septicemic
AB  - layer chicken in Denmark in 1981. The strain has been used extensively for
AB  - experimental purposes.
ER  -

TY  - JOUR
AU  - Kudirkiene, E.
AU  - Hansen, M.J.
AU  - Bojesen, A.M.
TI  - Draft Genome Sequence of Chelonobacter oris Strain 1662T, Associated with Respiratory Disease in Hermann's Tortoises.
JO  - Genome Announcements
PY  - 2014
SP  - e01322
EP  - e01314
VL  - 2
AB  - Chelonobacter oris 1662(T) is a type strain of the recently described species of  the
AB  - Pasteurellaceae family. The strain was isolated from the choanae of a captive
AB  - tortoise with signs of respiratory tract infection. The genome reported here is
AB  - approximately 2.6 Mb in size and has a G+C content of 47.1%.
ER  -

TY  - JOUR
AU  - Kudo, T. et al.
TI  - Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902,  and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms.
JO  - Genome Announcements
PY  - 2014
SP  - e00280
EP  - e00214
VL  - 2
AB  - Four Psychrobacter strains, JCM 18900, JCM 18901, JCM 18902, and JCM 18903, related to either
AB  - Psychrobacter nivimaris or Psychrobacter cibarius, were isolated from frozen marine animals.
AB  - The genome information of these four strains will be useful for studies of their physiology
AB  - and adaptation properties to frozen conditions.
ER  -

TY  - JOUR
AU  - Kudo, T.
AU  - Kawauchi, A.
AU  - Nakahara, T.
AU  - Zhang, X.
AU  - Taniyama, S.
AU  - Takatani, T.
AU  - Arakawa, O.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Iino, T.
AU  - Inoue, T.
AU  - Hongoh, Y.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod.
JO  - Genome Announcements
PY  - 2014
SP  - e00623
EP  - e00614
VL  - 2
AB  - Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing
AB  - scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated
AB  - from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their
AB  - comparative genome information is useful for studies of TTX production in
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Kudo, T.
AU  - Nakahara, T.
AU  - Zhang, X.
AU  - Taniyama, S.
AU  - Arakawa, O.
AU  - Murase, S.
AU  - Nakata, H.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Oshida, Y.
AU  - Inoue, T.
AU  - Hongoh, Y.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Geomicrobium sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples.
JO  - Genome Announcements
PY  - 2014
SP  - e00622
EP  - e00614
VL  - 2
AB  - Haloalkaliphilic strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, closely  related to
AB  - Geomicrobium sediminis, were isolated from aquatic samples, and their
AB  - draft genome sequences were determined. The genome information of these four
AB  - strains will be useful for studies of their physiology and ecology.
ER  -

TY  - JOUR
AU  - Kudo, T.
AU  - Sakamoto, K.
AU  - Akinaga, M.
AU  - Kawauchi, A.
AU  - Nakahara, T.
AU  - Zhang, X.
AU  - Yamada, A.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kuwahara, H.
AU  - Nakamura, N.
AU  - Nogi, Y.
AU  - Kitamura, K.
AU  - Yuki, M.
AU  - Iida, T.
AU  - Moriya, S.
AU  - Inoue, T.
AU  - Hongoh, Y.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047.
JO  - Genome Announcements
PY  - 2014
SP  - e00211
EP  - e00214
VL  - 2
AB  - Bacillus strains JCM 19045, JCM 19046, and JCM 19047 are alkaliphiles that produce
AB  - beta-cyclodextrin from starch. They are related to Bacillus xiaoxiensis
AB  - and Bacillus lehensis. The genome information for these three strains will be
AB  - useful for studies of the physiological role of cyclodextrin and cyclodextrin
AB  - production.
ER  -

TY  - JOUR
AU  - Kuebbing, D.
AU  - Blakesley, R.J.
TI  - A New Restriction Endonuclease from Streptomyces Stanford.
JO  - Fed. Proc.
PY  - 1979
SP  - 780
EP  - 780
VL  - 38
AB  - A new site-specific endonuclease activity distinguishable from Sst I, II and
AB  - III was isolated from Streptomyces stanford. This enzyme, designated Sst IV,
AB  - cleaved SV40 DNA once, adeno-virus type-2 DNA four times, and lambda(wt) DNA
AB  - several times (incompletely), but did not cleave PhiX174 RF or pBR322 DNA.  Sst
AB  - IV was active in 15 mM Tris-HCL (pH 7.5, mM MgCl2, 90 mM NaCl and 6mM
AB  - 2-mercaptoethanol at 37C.  The enzyme was purified free of specific and
AB  - non-specific nucleases by column chromatography which included
AB  - phosphocellulose, DEAE cellulose, hydroxylapatite and Blue-CNBr agarose.  The
AB  - amount of Sst IV recovered was about 2% of that for Sst II.  The number and
AB  - sizes of fragments actually generated by co-digestion of pBR322, PhiX174 RF or
AB  - SV40 DNA with Sst IV and other known restriction endonucleases were compared
AB  - with a computer generated table of predicted fragmentation patterns of these
AB  - DNAs (R. Blakesley, BRL FOCUS 1, NO. 4 (1978)) To tentatively identify the
AB  - recognition sequence of SstIV as 5'-TGATCA-3'.  Thus, SstIV has a specificity
AB  - similar to that of AtuCI, BclI and CpeI.  The recognition sequence is being
AB  - confirmed by direct sequence analysis.
ER  -

TY  - JOUR
AU  - Kuehn, J.S.
AU  - Register, K.B.
AU  - Phillips, G.J.
TI  - Draft Genome Sequences for 10 Isolates of the Swine Pathogen Haemophilus parasuis.
JO  - Genome Announcements
PY  - 2013
SP  - e00739
EP  - e00713
VL  - 1
AB  - Haemophilus parasuis colonizes the upper respiratory tract of swine and can cause a severe
AB  - systemic disease known as Glasser's disease. We report here the draft
AB  - genome sequences of 10 isolates from geographically diverse locations
AB  - representing the full virulence spectrum of the microorganism, which will aid in
AB  - understanding the pathobiology of H. parasuis.
ER  -

TY  - JOUR
AU  - Kuester, W.
AU  - Alves, J.
TI  - Mutational analysis of the function of Ile197 in the EcoRI restriction endonuclease.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S122
EP  - S122
VL  - 376
AB  - The endonuclease EcoRI is one of the best studied type II restriction enzymes.  It recognizes
AB  - and cleaves the double stranded DNA sequence GAATTC in both single strands between G and A
AB  - with high specificity.  Based on the X-ray structure Ile197 has been proposed to form a van
AB  - der Waals contact with cytosine of this recognition sequence.  We have exchanged Ile197 for
AB  - Ala, Arg and Met by site directed mutagenesis and analysed the purified mutant proteins
AB  - (I197A, M and R) biochemically and physicochemically.  Secondary structure composition
AB  - measured by CD-spectroscopy was unchanged for all mutants.  They cleave DNA with approximately
AB  - the same specific activity as the wild type enzyme.  For the I197A and the I197M mutants pH
AB  - optimum is shifted to alkaline conditions resulting in a 5-10 fold higher enzymatic activity
AB  - at pH 8.8.  Furthermore, the I197M mutant shows slight changes in its dependence on sequence
AB  - flanking the recognition sequence.  We assume that a hydrophobic contact of Ile197 to cytosine
AB  - is not important for activity of the EcoRI endonuclease.  But changes at this position
AB  - influence the conformation of the enzyme leading to a higher activity at alkaline pH on
AB  - substrates with a specific sequence surrounding.
ER  -

TY  - JOUR
AU  - Kuever, J. et al.
TI  - Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile  Gram-positive sulfate-reducing bacterium.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 821
EP  - 839
VL  - 9
AB  - Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus
AB  - Desulfotomaculum within the family Peptococcaceae. This
AB  - bacterium was isolated from a freshwater ditch and is of interest because it can
AB  - grow with a large variety of organic substrates, in particular several aromatic
AB  - compounds, short-chain and medium-chain fatty acids, which are degraded
AB  - completely to carbon dioxide coupled to the reduction of sulfate. It can grow
AB  - autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 +
AB  - CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It
AB  - does not require any vitamins for growth. Here, we describe the features of D.
AB  - gibsoniae strain Groll(T) together with the genome sequence and annotation. The
AB  - chromosome has 4,855,529 bp organized in one circular contig and is the largest
AB  - genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate
AB  - protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA
AB  - pathway, possibly involved in heterotrophic growth and in CO2 fixation during
AB  - autotrophic growth, are present. The genome contains a large set of genes for the
AB  - anaerobic transformation and degradation of aromatic compounds, which are lacking
AB  - in the other sequenced Desulfotomaculum genomes.
ER  -

TY  - JOUR
AU  - Kugadas, A.
AU  - Humann, J.L.
AU  - Pierle, S.A.
AU  - Srikumaran, S.
AU  - Brayton, K.A.
TI  - Genome Sequence of Bibersteinia trehalosi Strain Y31 Isolated from the Pneumonic  Lung of a Bighorn Sheep.
JO  - Genome Announcements
PY  - 2016
SP  - e00722
EP  - e00716
VL  - 4
AB  - Here, we report the genome sequence for Bibersteinia trehalosi strain Y31, isolated from the
AB  - lungs of a bighorn sheep (Ovis canadensis) that had succumbed
AB  - to pneumonia, which exhibits proximity-dependent inhibition (PDI) of Mannheimia
AB  - haemolytica The sequence will be used to understand the mechanism of PDI for
AB  - these organisms.
ER  -

TY  - JOUR
AU  - Kuhlmann, U.C.
AU  - Moore, G.R.
AU  - James, R.
AU  - Kleanthous, C.
AU  - Hemmings, A.M.
TI  - Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined?
JO  - FEBS Lett.
PY  - 1999
SP  - 1
EP  - 2
VL  - 463
AB  - Homing endonucleases are classified into four families based on active site sequence motifs.
AB  - Through structural comparisons we have found structural similarities between the endonuclease
AB  - domain of colicin E9, an H-N-H motif-containing enzyme, and both the non-specific nuclease
AB  - from Serratia and I-PpoI, a His-Cys box-containing homing endonuclease. Our comparison
AB  - identifies conservation at the heart of all three enzyme active sites and so argues for a
AB  - re-classification of H-N-H and His-Cys box homing endonucleases as a single family. We suggest
AB  - the 'betabetaalpha-Me family' of homing enzymes to reflect the three elements of secondary
AB  - structure and the metal ion that define the motif.
ER  -

TY  - JOUR
AU  - Kuhn, H.
AU  - Frank-Kamenetskii, M.D.
AU  - Demidov, V.V.
TI  - Site-specific nicking of duplex DNA using PNAs and restriction endonucleases.
JO  - J. Biomol. Struct. Dyn.
PY  - 2003
SP  - 916
EP  - 917
VL  - 20
AB  - A variety of research procedures in molecular biology and biochemistry include as a
AB  - fundamental step the selective cleavage of a designated sequence in only one strand of
AB  - double-stranded DNA (DNA nicking).  To achieve the goal, restriction endonuclease-like nicking
AB  - enzymes can be employed.  However, very few nicking enzymes (nickases) are available and they
AB  - recognize short sequences of less than or equal to 7 bp.  It is therefore highly desirable to
AB  - develop new nicking systems with much higher sequence selectivity.  We design such systems
AB  - using homopyrimidine peptide nucleic acids (PNAs).  In our design we take advantage of the
AB  - ability of homopyrimidine PNAs to sequence-specifically invade duplex DNA.  When such PNAs are
AB  - targeted to two short homopurine stretches on the same strand of duplex DNA, the opposite DNA
AB  - strand becomes accessible for hybridization with an oligonucleotide.  We demonstrate that the
AB  - thus formed secondary DNA duplex can serve as a substrate for a restriction endonuclease,
AB  - provided that it contains the recognition sequence of the enzyme.  As a result, only one
AB  - strand of the parent DNA is cleaved leading to nicked duplex DNA after removal of PNAs.  All
AB  - restriction endonucleases tested by us (AluI, BbsI, BglII, KpnI, SbfI, and SphI), have worked
AB  - well in our design leading to quantitative yield of the nicked product.  Together with the
AB  - fact that the typical target site in our protocol spans about 20-25 bp, our results indicate
AB  - that a vast class of semi-synthetic rare-cleaving DNA nickases has been generated.
ER  -

TY  - JOUR
AU  - Kuhn, H.
AU  - Hu, Y.
AU  - Frank-Kamenetskii, M.D.
AU  - Demidov, V.V.
TI  - Artificial site-specific DNA-nicking system based on common restriction enzymes assisted by PNA openers.
JO  - Biochemistry
PY  - 2003
SP  - 4985
EP  - 4992
VL  - 42
AB  - We report on the peptide nucleic acid (PNA)-directed design of a DNA-nicking system that
AB  - enables selective and quantitative cleavage of one
AB  - strand of duplex DNA at a designated site, thus mimicking natural nickases
AB  - and significantly extending their potential. This system exploits the
AB  - ability of pyrimidine PNAs to serve as openers for specific DNA sites by
AB  - invading the DNA duplex and exposing one DNA strand for oligonucleotide
AB  - hybridization. The resultant secondary duplex can act as a substrate for a
AB  - restriction enzyme, which ultimately creates a nick in the parent DNA. We
AB  - demonstrate that several restriction enzymes of different types could be
AB  - successfully used in the PNA-assisted system we developed. Importantly,
AB  - the enzyme cleavage efficiency is basically not impaired on such
AB  - artificially generated substrates, compared with the efficiency on regular
AB  - DNA duplexes. Our design originates a vast class of semisynthetic
AB  - rare-cleaving DNA nickases, which are essentially absent at present. In
AB  - addition, we show that the site-specific PNA-assisted nicking of duplex
AB  - DNA can be engaged in a rolling-circle DNA amplification (RCA) reaction.
AB  - This new RCA format demonstrates the practical potential of the novel
AB  - biomolecular tool we propose for DNA technology and DNA diagnostics.
ER  -

TY  - JOUR
AU  - Kuhn, I.
AU  - Stephenson, F.
AU  - Boyer, H.
AU  - Greene, P.
TI  - Positive-selection vectors utilizing lethality of the EcoRI endonuclease.
JO  - Gene
PY  - 1986
SP  - 253
EP  - 263
VL  - 42
AB  - The construction and use of a series of positive-selection vectors are
AB  - described.  These plasmids encode EcoRI endonuclease, the synthesis of which is
AB  - under the control of the lacUV5 promoter.  The pKG2 plasmid encodes a wild-type
AB  - EcoRI endonuclease.  In the absence of EcoRI methylase, the endonuclease is
AB  - lethal.  Cloning into any of the unique restriction sites within the
AB  - endonuclease-coding gene allows survival of the transformed
AB  - EcoRI-methylase-less host.  The pKGW and pKGS plasmids encode an altered EcoRI
AB  - endonuclease which, when repressed in the lacIQ host, allows survival in the
AB  - absence of the methylase.  Induction with IPTG, however, results in cell death
AB  - as a result of high-level EcoRI synthesis.  Cloning into any of the unique
AB  - restriction sites within the EcoRI gene of pKGW or pKGS allows survival of
AB  - derepressed transformed cells.  These vectors strongly select for cloning
AB  - events which inactivate the endonuclease gene.
ER  -

TY  - JOUR
AU  - Kuhnlein, U.
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli. XV.  The role of nucleotide methylation in in vitro B-specific modification.
JO  - J. Mol. Biol.
PY  - 1972
SP  - 9
EP  - 19
VL  - 63
AB  - It is shown that in vitro Escherichia coli strain B-specific modification of
AB  - the replicative form of bacteriophage fd DNA is accompanied by the methylation
AB  - of certain adenine moieties to form N-6-methyladenine.  The reaction follows
AB  - first order kinetics and saturation is reached when about four adenines are
AB  - methylated per replicative form.  No methyl groups are transferred to
AB  - B-modified DNA.  The replicative form of a one step mutant of fd, which has a
AB  - reduced sensitivity towards B-specific restriction, has lost two of the four
AB  - methyl acceptor sites.  The replicative form of a second step mutant, which is
AB  - not subject to B-specific restriction, is completely refractory to methylation
AB  - by the modification enzyme.  It is therefore concluded that the B-modification
AB  - and the B-restriction enzyme react with the same sites on the substrate DNA and
AB  - that the replicative form of wild type fd has two such sites.  The number of
AB  - N-6-methyladenines per B-specificity site of fully modified double-stranded DNA
AB  - is two.
ER  -

TY  - JOUR
AU  - Kuhnlein, U.
AU  - Linn, S.
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli, XI.  In vitro modification of phage fd replicative form.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1969
SP  - 556
EP  - 562
VL  - 63
AB  - An enzymatic activity, having the properties expected by a B-specific
AB  - host-controlled modification enzyme, has been purified from an extract of
AB  - Escherichia coli strain B.  This activity renders the unmodified replicative
AB  - form of phage fd resistant to B-specific restriction and is only present in
AB  - strains carrying intact genes for type B modification.  In phosphate buffer,
AB  - the enzyme acts optimally at pH 6 and is dependent upon a single cofactor,
AB  - S-adenosylmethionine.
ER  -

TY  - JOUR
AU  - Kuhnlein, U.
AU  - Linn, S.
AU  - Arber, W.
TI  - In vitro modifikation der replikativen form des bakteriophagen fd.
JO  - Pathol. Microbiol. (Basel)
PY  - 1969
SP  - 136
EP  - 136
VL  - 34
AB  - None
ER  -

TY  - JOUR
AU  - Kulakauskas, S.
AU  - Barsomian, J.M.
AU  - Lubys, A.
AU  - Roberts, R.J.
AU  - Wilson, G.G.
TI  - Organization and sequence of the HpaII restriction-modification system and adjacent genes.
JO  - Gene
PY  - 1994
SP  - 9
EP  - 15
VL  - 142
AB  - We report the organization of the HpaII restriction and modification (R-M) system from
AB  - Haemophilus parainfluenzae (recognition sequence: 5'...CCGG...3'), the sequence of the gene
AB  - coding for the HpaII restriction endonuclease, and the sequence of the upstream flanking DNA.
AB  - The HpaII system comprises two genes, hpaIIM, coding for the methyltransferase (MTase; 358
AB  - amino acids (aa), 40.4 kDa: product, Cm5CGG), and hpaIIR, coding for the restriction
AB  - endonuclease (ENase: 358aa, 40.9 kDa: product, C'CGG). The genes are adjacent, they have the
AB  - same orientation, and they occur in the order hpaIIM then hpaIIR. The ENase bears little aa
AB  - sequence similarity to the isoschizomeric R.BsuFI and R.MspI ENases. Upstream of, and partly
AB  - overlapping hpaIIM is the coding sequence for a 141-aa protein that resembles the
AB  - very-short-patch-repair endonuclease (Vsr) of Escherichia coli. Upstream of that is the coding
AB  - sequence for a protein that resembles valyl-tRNA synthetase (ValS).
ER  -

TY  - JOUR
AU  - Kulakauskas, S.
AU  - Lubys, A.
AU  - Ehrlich, S.D.
TI  - DNA restriction-modification systems mediate plasmid maintenance.
JO  - J. Bacteriol.
PY  - 1995
SP  - 3451
EP  - 3454
VL  - 177
AB  - Two plasmid-carried restriction-modification (R-M) systems, EcoRI (from pMB1 of Escherichia
AB  - coli) and Bsp6I (from pXH13 of Bacillus sp. strain RFL6), enhance plasmid segregational
AB  - stability in E. coli and Bacillus subtilis, respectively. Inactivation of the endonuclease or
AB  - the presence of the methylase in trans abolish the stabilizing activity of the R-M systems. We
AB  - propose that R-M systems mediate plasmid segregational stability by postsegregational killing
AB  - of plasmid-free cells. Plasmid-encoded methyltransferase modifies host DNA and thus prevents
AB  - its digestion by the restriction endonuclease. Plasmid loss entails degradation and/or
AB  - dilution of the methylase during cell growth and appearance of unmethylated sites in the
AB  - chromosome. Double-strand breaks, introduced at these sites by the endonuclease, eventually
AB  - cause the death of the plasmid-free cells. Contribution to plasmid stability is a previously
AB  - unrecognized biological role of the R-M systems.
ER  -

TY  - JOUR
AU  - Kulandai, L.T.
AU  - Lakshmipathy, D.
AU  - Ramasubban, G.
AU  - Vetrivel, U.
AU  - Rao, M.H.
AU  - Rathinam, S.
AU  - Narasimhan, M.
TI  - Whole-Genome Sequencing and Mutation Analysis of Two Extensively Drug-Resistant Sputum Isolates of Mycobacterium tuberculosis (VRFCWCF XDRTB 232 and VRFCWCF  XDRTB 1028) from Chennai, India.
JO  - Genome Announcements
PY  - 2014
SP  - e01173
EP  - e01114
VL  - 2
AB  - We announce the draft genome sequence of two extensively drug-resistant Mycobacterium
AB  - tuberculosis strains, VRFCWCF XDRTB 232 and VRFCWCF XDRTB 1028,
AB  - isolated from the sputum samples of a patient clinically suspected to have
AB  - tuberculosis, and we also report novel mutations that confer drug resistance.
ER  -

TY  - JOUR
AU  - Kulasekara, B.R. et al.
TI  - Analysis of the genome of the Escherichia coli O157:H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence.
JO  - Infect. Immun.
PY  - 2009
SP  - 3713
EP  - 3721
VL  - 77
AB  - In addition to causing diarrhea, Escherichia coli O157:H7 infection can
AB  - lead to hemolytic uremic syndrome (HUS), a severe disease characterized by
AB  - hemolysis and renal failure. Differences in HUS frequency among E. coli
AB  - O157:H7 outbreaks have been noted, but there is incomplete understanding
AB  - of bacterial factors that promote HUS. In 2006, an outbreak of E. coli
AB  - O157:H7, caused by consumption of contaminated spinach, occurred with a
AB  - notably high frequency of HUS. We sequenced the genome of this strain
AB  - (TW14359) with the goal of identifying candidate genetic factors that
AB  - contribute to an enhanced ability to cause HUS. The TW14359 genome
AB  - contains 70-kb of DNA segments not present in either of the two reference
AB  - O157:H7 genomes. We identified seven putative virulence determinants,
AB  - including two putative Type III secretion system effector proteins,
AB  - candidate genes that could result in increased pathogenicity or,
AB  - alternatively, adaptation to plants, and an intact anaerobic nitric oxide
AB  - reductase gene, norV. We surveyed one hundred O157:H7 isolates for the
AB  - presence of these putative virulence determinants. A norV deletion was
AB  - found in over half of strains surveyed and correlates strikingly with the
AB  - absence of stx1. The other putative virulence factors were found in eight
AB  - to thirty-five percent of O157:H7 isolates surveyed and their presence
AB  - also correlates with the presence of norV and absence of stx1 indicating
AB  - the presence of norV may serve as a marker of greater propensity for HUS
AB  - similar to the correlation between the absence of stx1 and HUS propensity.
ER  -

TY  - JOUR
AU  - Kulba, A.M.
AU  - Abdel-Sabur, M.S.
AU  - Butkus, V.V.
AU  - Janulaitis, A.
AU  - Fomichev, Y.K.
TI  - New type-II restrictase from cells of Erwinia herbicola.
JO  - Mol. Biol. (Mosk)
PY  - 1987
SP  - 250
EP  - 254
VL  - 21
AB  - Forty strains of the bacterial genus Erwinia were tested for the presence of
AB  - restrictases.  Type-II restrictases identical in properties were isolated and
AB  - partially purified from cells of Erw. herbicola strains 9/5 and 8608.  It was
AB  - established that restrictase EheI recognizes the sequence of nucleotides
AB  - 5'-GGCGCC-3' and is a false isoschizomer of enzymes NarI, NdaI, NunII, and
AB  - BbeI, since EheI cleaves the sequence in the middle, forming blunt ends, as
AB  - opposed to the enzymes listed, which form sticky 5'- or 3'-ends when cleaving
AB  - DNA.  Optimal conditions of cleavage of DNA by EheI restrictase are determined.
ER  -

TY  - JOUR
AU  - Kulba, A.M.
AU  - Elgammudi, A.A.
TI  - Detection of restriction endonucleases in Aeromonas bacteria.
JO  - Vestn. Beloruss. Gos. Univ.
PY  - 1997
SP  - 47
EP  - 49
VL  - 2
ER  -

TY  - JOUR
AU  - Kuleshov, K.V.
AU  - Koetsveld, J.
AU  - Goptar, I.A.
AU  - Markelov, M.L.
AU  - Kolyasnikova, N.M.
AU  - Sarksyan, D.S.
AU  - Toporkova, M.G.
AU  - Kirdyashkina, N.P.
AU  - Shipulin, G.A.
AU  - Hovius, J.W.
AU  - Platonov, A.E.
TI  - Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia.
JO  - Genome Announcements
PY  - 2018
SP  - e01424
EP  - e01417
VL  - 6
AB  - Here, we report the whole-genome sequence of six clinical Borrelia miyamotoi isolates from the
AB  - Russian Federation. Using two independent next-generation
AB  - sequencing platforms, we determined the complete sequence of the chromosome and
AB  - several plasmids. All strains have an Asian genotype with 99.8% chromosome
AB  - nucleotide similarity with B. miyamotoi strain FR64b.
ER  -

TY  - JOUR
AU  - Kuleshov, K.V.
AU  - Vodop'ianov, S.O.
AU  - Dedkov, V.G.
AU  - Markelov, M.L.
AU  - Kermanov, A.V.
AU  - Kruglikov, V.D.
AU  - Vodop'ianov, A.S.
AU  - Pisanov, R.V.
AU  - Chemisova, O.S.
AU  - Mazrukho, A.B.
AU  - Titova, S.V.
AU  - Shipulin, G.A.
TI  - Draft Genome Sequencing of Vibrio cholerae O1 El Tor Isolates Collected in the Russian Federation from Imported Cholera Cases.
JO  - Genome Announcements
PY  - 2014
SP  - e00624
EP  - e00614
VL  - 2
AB  - We report the draft genome sequencing of five Vibrio cholerae O1 El Tor clinical  isolates
AB  - collected in the Russian Federation from imported cholera cases in 2006,
AB  - 2010, and 2012. In the initial phylogenetic analysis, one isolate clustered with
AB  - the Haiti/Nepal-4 group.
ER  -

TY  - JOUR
AU  - Kuleshov, K.V.
AU  - Vodop'ianov, S.O.
AU  - Markelov, M.L.
AU  - Dedkov, V.G.
AU  - Kermanov, A.V.
AU  - Kruglikov, V.D.
AU  - Vodop'ianov, A.S.
AU  - Pisanov, R.V.
AU  - Mazrukho, A.B.
AU  - Shipulin, G.A.
TI  - Draft Genome Sequences of Vibrio cholerae O1 ElTor Strains 2011EL-301 and P-18785, Isolated in Russia.
JO  - Genome Announcements
PY  - 2013
SP  - e00659
EP  - e00613
VL  - 1
AB  - We report the draft whole-genome sequences of two Vibrio cholerae O1 strains, the
AB  - environmental toxigenic strain 2011EL-301 and the clinical nontoxigenic strain
AB  - P-18785, both isolated in Russia. Some basic data comparing the two against the
AB  - GenBank repository are provided.
ER  -

TY  - JOUR
AU  - Kuley, R.
AU  - Kuijt, E.
AU  - Smits, M.A.
AU  - Roest, H.I.J.
AU  - Smith, H.E.
AU  - Bossers, A.
TI  - Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains.
JO  - Front. Microbiol.
PY  - 2017
SP  - 1526
EP  - 1526
VL  - 8
AB  - Coxiella burnetii is an obligate intracellular bacterium and the etiological
AB  - agent of Q fever. During 2007-2010 the largest Q fever outbreak ever reported
AB  - occurred in The Netherlands. It is anticipated that strains from this outbreak
AB  - demonstrated an increased zoonotic potential as more than 40,000 individuals were
AB  - assumed to be infected. The acquisition of novel genetic factors by these C.
AB  - burnetii outbreak strains, such as virulence-related genes, has frequently been
AB  - proposed and discussed, but is not proved yet. In the present study, the whole
AB  - genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few
AB  - additionally selected strains from different geographical locations and publicly
AB  - available genome sequences were used for a comparative bioinformatics approach.
AB  - The study focuses on the identification of specific genetic differences in the
AB  - outbreak related CbNL01 strains compared to other C. burnetii strains. In this
AB  - approach we investigated the phylogenetic relationship and genomic aspects of
AB  - virulence and host-specificity. Phylogenetic clustering of whole genome sequences
AB  - showed a genotype-specific clustering that correlated with the clustering
AB  - observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA).
AB  - Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP)
AB  - analysis of complete genome sequences demonstrated the presence of
AB  - genotype-specific gene contents and SNP variations in C. burnetii strains. It
AB  - also demonstrated that the currently used MLVA genotyping methods are highly
AB  - discriminatory for the investigated outbreak strains. In the fully reconstructed
AB  - genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a
AB  - relatively large number of transposon-linked genes were identified as compared to
AB  - the other published complete genome sequences of C. burnetii. Additionally, large
AB  - numbers of SNPs in its membrane proteins and predicted virulence-associated genes
AB  - were identified in all Dutch outbreak strains compared to the NM reference strain
AB  - and other strains of the CbNL12 genotype. The presence of large numbers of
AB  - transposable elements and mutated genes, thereof most likely resulted in high
AB  - level of genome rearrangements and genotype-specific pathogenicity of outbreak
AB  - strains. Thus, the epidemic potential of Dutch outbreak strains could be linked
AB  - to increased genome plasticity and mutations in critical genes involved in
AB  - virulence and the evasion of the host immune system.
ER  -

TY  - JOUR
AU  - Kulik, E.M.
AU  - Bickle, T.A.
TI  - Regulation of the activity of the type IC EcoR124I restriction enzyme.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 891
EP  - 906
VL  - 264
AB  - Restriction-modification systems must regulate the expression of their genes so that the
AB  - chromosomal genome is modified at all times by the methyltransferase to protect the host cell
AB  - from the potential lethal action of the cognate restriction endonuclease.  Since type I R-M
AB  - systems can be transferred to non-modified Escherichia coli cells by conjugation or
AB  - transformation without killing the recipient, they must have some means to regulate their
AB  - restriction activity upon entering a new host cell to avoid restriction of unprotected host
AB  - DNA and cell death.  This is especially true for EcoR124I, a type IC family member, which is
AB  - coded for by a conjugative plasmid.  Control of EcoR124I restriction activity is most likely
AB  - at the post-translational level as the transfer of the EcoR124I system into a recipient cell
AB  - that already expressed the HsdR subunit of this system was not a lethal event.  Additionally,
AB  - the kinetics of restriction activity upon transfer of the genes coding for the EcoR124I RM
AB  - system to a recipient cell are the same, irrespective of the modification state of the
AB  - recipient cell or the presence or absence of the EcoR124I HsdR subunit in the new host cells.
AB  - The mechanism controlling the restriction activity of a type IC R-M system upon transfer to a
AB  - new host cell is different from that controlling the chromosomally coded type IA and IB R-M
AB  - systems.  The previously discovered hsdC mutant, which affects the establishment of the type
AB  - IA system EcoKI, was shown to affect the establishment of the type IB system EcoAI, but to
AB  - have no influence on EcoR124I.
ER  -

TY  - JOUR
AU  - Kulkarni, M.
AU  - Nirwan, N.
AU  - van Aelst, K.
AU  - Szczelkun, M.D.
AU  - Saikrishnan, K.
TI  - Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 4396
EP  - 4408
VL  - 44
AB  - Engineering restriction enzymes with new sequence specificity has been an unaccomplished
AB  - challenge, presumably because of the complexity of target
AB  - recognition. Here we report detailed analyses of target recognition by Type ISP
AB  - restriction-modification enzymes. We determined the structure of the Type ISP
AB  - enzyme LlaGI bound to its target and compared it with the previously reported
AB  - structure of a close homologue that binds to a distinct target, LlaBIII. The
AB  - comparison revealed that, although the two enzymes use almost a similar set of
AB  - structural elements for target recognition, the residues that read the bases
AB  - vary. Change in specificity resulted not only from appropriate substitution of
AB  - amino acids that contacted the bases but also from new contacts made by
AB  - positionally distinct residues directly or through a water bridge. Sequence
AB  - analyses of 552 Type ISP enzymes showed that the structural elements involved in
AB  - target recognition of LlaGI and LlaBIII were structurally well-conserved but
AB  - sequentially less-conserved. In addition, the residue positions within these
AB  - structural elements were under strong evolutionary constraint, highlighting the
AB  - functional importance of these regions. The comparative study helped decipher a
AB  - partial consensus code for target recognition by Type ISP enzymes.
ER  -

TY  - JOUR
AU  - Kumagai, Y.
AU  - Yoshizawa, S.
AU  - Nakamura, K.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Kogure, K.
TI  - Complete and Draft Genome Sequences of Eight Oceanic Pseudomonas aeruginosa Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e01255
EP  - e01217
VL  - 5
AB  - Pseudomonas aeruginosa is one of the most common model bacterial species, and genomes of
AB  - hundreds of strains of this species have been sequenced to date.
AB  - However, currently there is only one available genome of an oceanic isolate.
AB  - Here, we report two complete and six draft genome sequences of P. aeruginosa
AB  - isolates from the open ocean.
ER  -

TY  - JOUR
AU  - Kumagai, Y.
AU  - Yoshizawa, S.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Iwasaki, W.
AU  - Kogure, K.
TI  - Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00490
EP  - e00414
VL  - 2
AB  - Winogradskyella sp. strain PG-2 is a marine flavobacterium isolated from surface  seawater.
AB  - This organism contains proteorhodopsin, which can convert light energy
AB  - into available forms of biochemical energy. Here, we present its complete genome
AB  - sequence and annotation, which provide further insights into the life strategy of
AB  - proteorhodopsin-mediated phototrophy in the ocean.
ER  -

TY  - JOUR
AU  - Kumano, M.
AU  - Sakakibara, M.
TI  - Recombination of DNA in blue-green algae - restriction enzyme systems and transfection vectors.
JO  - Baiosaiensu to Indasutori
PY  - 1988
SP  - 38
EP  - 41
VL  - 46
AB  - One table describes the presence of a number of new restriction enzymes in
AB  - seven strains of blue-green algae.  It is concluded that African and American
AB  - strains of Spirulina can be clearly distinguished from one another on the basis
AB  - of restriction enzyme content.
ER  -

TY  - JOUR
AU  - Kumar, A.
AU  - Garg, N.
TI  - Restriction endonucleases.
JO  - Genet. Eng. (N Y)
PY  - 2005
SP  - 55
EP  - 74
VL  - 0
AB  - Restriction endonucleases bind specifically to and cleave the sugar phosphate backbone (bond
AB  - between deoxyribose and phosphate groups) in double stranded DNA at specific sites within or
AB  - adjacent to a particular sequence known as recognition sequence.  Restriction endonucleases
AB  - are of three types: Type I, Type II and Type III.  Types I and III restriction endonucleases
AB  - carry modification (like methylation) and ATP dependent cleavage activities in the same
AB  - protein.  Type III restriction endonucleases cleave the DNA at the recognition site and then
AB  - dissociate from the substrate.  However, type I restriction endonucleases bind to the
AB  - recognition sequence but cleave at random sites when the DNA loops back to the bound enzyme.
AB  - Neither type I nor type III restriction endonucleases are widely used in genetic engineering.
AB  - Type II restriction endonucleases are commonly used in genetic engineering.  They are the
AB  - invaluable molecular scissors.  These restriction endonucleases cut both strands of duplex DNA
AB  - with in a stretch of just a few bases.  Therefore, only type II restriction enonucleases are
AB  - described in this chapter.  Nomenclature of the restriction endonucleases is based on the
AB  - source of their isolation from an organism.  In case of restriction endonucleases, enzyme
AB  - activity is described in units considering one unit of the restriction endonuclease as the
AB  - amount of the enzyme required to hydrolyze one microgram of lambda DNA to completion in one
AB  - hour at the optimum temperature in a total volume of 50 ul of the assay mixture.  The lambda
AB  - DNA, due to its large size (approximately 50 Kb), is considered to have recognition sites
AB  - almost for all the restriction endonucleases.
ER  -

TY  - JOUR
AU  - Kumar, A.
AU  - Munjal, V.
AU  - Sheoran, N.
AU  - Prameela, T.P.
AU  - Suseelabhai, R.
AU  - Aggarwal, R.
AU  - Jain, R.K.
AU  - Eapen, S.J.
TI  - Draft Genome Sequence of Highly Virulent Race 4/Biovar 3 of Ralstonia solanacearum CaRs_Mep Causing Bacterial Wilt in Zingiberaceae Plants in India.
JO  - Genome Announcements
PY  - 2017
SP  - e01420
EP  - e01416
VL  - 5
AB  - The genome of Ralstonia solanacearum CaRs_Mep, a race 4/biovar 3/phylotype I bacterium causing
AB  - wilt in small cardamom and other Zingiberaceae plants, was
AB  - sequenced. Analysis of the 5.7-Mb genome sequence will aid in better
AB  - understanding of the genetic determinants of host range, host jump, survival,
AB  - pathogenicity, and virulence of race 4 of R. solanacearum.
ER  -

TY  - JOUR
AU  - Kumar, B.K.
AU  - Deekshit, V.K.
AU  - Rai, P.
AU  - Gurtler, V.
AU  - Karunasagar, I.
AU  - Karunasagar, I.
TI  - Draft Genome Sequence of trh+ Vibrio parahaemolyticus VP-49, Isolated from Seafood Harvested along the Mangalore Coast, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00607
EP  - e00614
VL  - 2
AB  - Vibrio parahaemolyticus is a seafood-borne pathogen autochthonous to the marine and estuarine
AB  - ecosystem, which is responsible for gastroenteritis due to the
AB  - consumption of contaminated raw seafood. Here, we report the draft genome
AB  - sequence of V. parahaemolyticus VP-49, isolated from seafood, to identify the
AB  - different virulence attributes and to study the mechanisms that enhance its
AB  - environmental fitness.
ER  -

TY  - JOUR
AU  - Kumar, M.
AU  - Gazara, R.K.
AU  - Verma, S.
AU  - Kumar, M.
AU  - Verma, P.K.
AU  - Thakur, I.S.
TI  - Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01240
EP  - e01216
VL  - 4
AB  - We report here the genome sequence of Pandoraea sp. ISTKB, a betaproteobacterium  isolated
AB  - from rhizospheric soil in the backwaters of Alappuzha, Kerala, India.
AB  - The strain is alkalotolerant and grows on medium containing lignin as a sole
AB  - carbon source. Genes and pathways related to lignin degradation were complemented
AB  - by genomic analysis.
ER  -

TY  - JOUR
AU  - Kumar, M.
AU  - Gazara, R.K.
AU  - Verma, S.
AU  - Kumar, M.
AU  - Verma, P.K.
AU  - Thakur, I.S.
TI  - Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.
JO  - Genome Announcements
PY  - 2016
SP  - e01141
EP  - e01116
VL  - 4
AB  - The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering
AB  - bacterium isolated from marble mining rocks in the Umra area,
AB  - Rajasthan, India. This strain grows chemolithotrophically on media that contain
AB  - sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome
AB  - sequence of 5.07 Mb Serratia sp. ISTD04.
ER  -

TY  - JOUR
AU  - Kumar, M.
AU  - Khanna, S.
TI  - Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation.
JO  - J. Appl. Microbiol.
PY  - 2010
SP  - 1252
EP  - 1262
VL  - 108
AB  - AIMS: In order to develop effective bioremediation strategies for
AB  - polyaromatic hydrocarbons (PAHs) degradation, the composition and
AB  - metabolic potential of microbial communities need to be better understood,
AB  - especially in highly PAH contaminated sites in which little information on
AB  - the cultivation-independent communities is available. METHODS AND RESULTS:
AB  - Coal-tar-contaminated soil was collected, which consisted of 122.5 mg
AB  - g(-1) total extractable PAH compounds. Biodegradation studies with this
AB  - soil indicated the presence of microbial community that is capable of
AB  - degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene
AB  - at 50 ppm each. PCR clone libraries were established from the DNA of the
AB  - coal-tar-contaminated soil, targeting the 16S rRNA to characterize (i) the
AB  - microbial communities, (ii) partial gene fragment encoding the Rieske iron
AB  - sulfur center (alpha-subunit) common to all PAH dioxygenase enzymes and
AB  - (iii) beta-subunit of dioxygenase. Phylotypes related to Proteobacteria
AB  - (Alpha-, Epsilon- and Gammaproteobacteria), Acidobacteria, Actinobacteria,
AB  - Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA
AB  - derived clone libraries. Many of the gene fragment sequences of
AB  - alpha-subunit and beta-subunit of dioxygenase obtained from the respective
AB  - clone libraries fell into clades that are distinct from the reference
AB  - dioxygenase gene sequences. Presence of consensus sequence of the Rieske
AB  - type [2Fe-2S] cluster binding site suggested that these gene fragments
AB  - encode for alpha-subunit of dioxygenase gene. CONCLUSIONS: Sequencing of
AB  - the cloned libraries representing alpha-subunit gene fragments (Rf1) and
AB  - beta-subunit of dioxygenase showed the presence of hitherto unidentified
AB  - dioxygenase in coal-tar-contaminated soil. SIGNIFICANCE AND IMPACT OF THE
AB  - STUDY: The combination of the Rieske primers and bacterial community
AB  - profiling represents a powerful tool for both assessing bioremediation
AB  - potential and the exploration of novel dioxygenase genes in a contaminated
AB  - environment.
ER  -

TY  - JOUR
AU  - Kumar, M.R.
AU  - Hosur, R.V.
AU  - Roy, K.B.
AU  - Miles, H.T.
AU  - Govil, G.
TI  - Resonance assignment of the 500-MHz proton NMR spectrum of self-complementary dodecanucleotide d-GGATCCGGATCC:  altered conformations at BamHI cleavage sites.
JO  - Biochemistry
PY  - 1985
SP  - 7703
EP  - 7711
VL  - 24
AB  - Resonance assignments of nonexchangeable base and sugar protons of the
AB  - self-complementary dodecanucleotide d-GGATCCGGATCC have been obtained by
AB  - two-dimensional NMR methods and strategies derived from interproton distance
AB  - calculations on different secondary structures of nucleic acids.
AB  - Conformational details about the glycosidic dihedral angle and sugar pucker
AB  - have been derived from the relative intensities of cross peaks in the
AB  - two-dimensional J-correlated and nuclear Overhauser enhancement correlated
AB  - spectra in D2O solution.  It is observed that d-GGATCCGGATCC assumes a
AB  - predominantly B-type conformation with sequence-dependent changes along the
AB  - chain.  The recognition site of BamHI shows a distinctly different geometrical
AB  - environment.  The sugar rings of G1 and G7 assume a C3'-endo geometry while the
AB  - rest of the sugars possess C2'-endo geometry.
ER  -

TY  - JOUR
AU  - Kumar, N.
AU  - Mukhopadhyay, A.K.
AU  - Patra, R.
AU  - De, R.
AU  - Baddam, R.
AU  - Shaik, S.
AU  - Alam, J.
AU  - Tiruvayipati, S.
AU  - Ahmed, N.
TI  - Next-Generation Sequencing and De Novo Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates  from Duodenal Ulcer Patients in India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5963
EP  - 5964
VL  - 194
AB  - The prevalence of different H. pylori genotypes in various geographical regions indicates
AB  - region-specific adaptations during the course of evolution. Complete
AB  - genomes of H. pylori from countries with high infection burdens, such as India,
AB  - have not yet been described. Herein we present genome sequences of two H. pylori
AB  - strains, NAB47 and NAD1, from India. In this report, we briefly mention the
AB  - sequencing and finishing approaches, genome assembly with downstream statistics,
AB  - and important features of the two draft genomes, including their phylogenetic
AB  - status. We believe that these genome sequences and the comparative genomics
AB  - emanating thereupon will help us to clearly understand the ancestry and biology
AB  - of the Indian H. pylori genotypes, and this will be helpful in solving the
AB  - so-called Indian enigma, by which high infection rates do not corroborate the
AB  - minuscule number of serious outcomes observed, including gastric cancer.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Acharya, V.
AU  - Singh, D.
AU  - Kumar, S.
TI  - Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 11
EP  - 11
VL  - 13
AB  - A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim
AB  - Himalaya was affiliated to Janthinobacterium lividum based on 16S
AB  - rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing
AB  - was performed for the strain to confirm its taxonomy as it lacked the typical
AB  - violet pigmentation of the genus and also to decipher its survival strategy at
AB  - the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated
AB  - genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole
AB  - genome-based multilocus sequence analysis clustering, in silico DDH similarity
AB  - value of 95.1% and, the ANI value of 99.25% established the identity of the
AB  - strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome
AB  - comparisons across genus Janthinobacterium revealed an open pan-genome with the
AB  - scope of the addition of new orthologous cluster to complete the genomic
AB  - inventory. The genomic insight provided the genetic basis of freezing and
AB  - frequent freeze-thaw cycle tolerance and, for industrially important enzymes.
AB  - Extended insight into the genome provided clues of crucial genes associated with
AB  - adaptation in the harsh aquatic ecosystem of high altitude.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Chang, C.C.
AU  - Ng, T.H.
AU  - Ding, J.Y.
AU  - Tseng, T.C.
AU  - Lo, C.F.
AU  - Wang, H.C.
TI  - Draft Genome Sequence of Vibrio parahaemolyticus Strain M1-1, Which Causes Acute  Hepatopancreatic Necrosis Disease in Shrimp in Vietnam.
JO  - Genome Announcements
PY  - 2018
SP  - e01468
EP  - e01417
VL  - 6
AB  - We report here the genome sequence of Vibrio parahaemolyticus strain M1-1, which  causes a
AB  - mild form of shrimp acute hepatopancreatic necrosis disease (AHPND).
AB  - Compared to other virulent strains, the M1-1 genome appeared to express several
AB  - additional genes, while some genes were missing. These instabilities may be
AB  - related to the reduced virulence of M1-1.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Dwivedi, V.
AU  - Negi, V.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite.
JO  - Genome Announcements
PY  - 2013
SP  - e00753
EP  - e00713
VL  - 1
AB  - Sphingobium lactosutens DS20(T) has been isolated from the hexachlorocyclohexane  (HCH)
AB  - dumpsite in Lucknow, India, but does not degrade any of the HCH isomers.
AB  - Here, we present the ~5.36-Mb draft genome sequence of strain DS20(T), which
AB  - consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Mukhopadhyay, A.K.
AU  - Ghosh, P.
AU  - Rao, D.N.
TI  - Comparative Transcriptomics of H. pylori Strains AM5, SS1 and Their hpyAVIBM Deletion Mutants: Possible Roles of Cytosine Methylation.
JO  - PLoS ONE
PY  - 2012
SP  - e42303
EP  - e42303
VL  - 7
AB  - Helicobacter pylori is an important human pathogen and one of the most successful chronic
AB  - colonizers of the human body. H. pylori uses diverse
AB  - mechanisms to modulate its interaction with the host in order to
AB  - promote chronic infection and overcome host immune response.
AB  - Restriction-modification genes are a major part of strain-specific
AB  - genes present in H. pylori. The role of N-6 -adenine methylation in
AB  - bacterial gene regulation and virulence is well established but not
AB  - much is known about the effect of C-5 -cytosine methylation on gene
AB  - expression in prokaryotes. In this study, it was observed by microarray
AB  - analysis and RT-PCR, that deletion of an orphan C-5 -cytosine
AB  - methyltransferase, hpyAVIBM in H. pylori strains AM5and SS1 has a
AB  - significant effect on the expression of number of genes belonging to
AB  - motility, adhesion and virulence. AM Delta DhpyAVIBM mutant strain has
AB  - a different LPS profile and is able to induce high IL-8 production
AB  - compared to wild-type. hpyAVIBM from strain 26695 is able to complement
AB  - mutant SS1 and AM5 strains. This study highlights a possible
AB  - significance of cytosine methylation in the physiology of H. pylori.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Mukhopadhyay, A.K.
AU  - Rao, D.N.
TI  - Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand.
JO  - FEBS J.
PY  - 2010
SP  - 1666
EP  - 1683
VL  - 277
AB  - Genomic sequences of Helicobacter pylori strains 26695, J99, HPAGI and G27 have revealed an
AB  - abundance of restriction and modification genes.
AB  - hp0050, which encodes an N6 adenine DNA methyltransferase, was cloned,
AB  - overexpressed and purified to near homogeneity. It recognizes the
AB  - sequence 5'-GRRG-3' (where R is A or G) and, most intriguingly,
AB  - methylates both adenines when R is A (5'-GAAG-3'). Kinetic analysis
AB  - suggests a nonprocessive (repeated-hit) mechanism of methylation in
AB  - which HP0050 methyltransferase methylates one adenine at a time in the
AB  - sequence 5'-GAAG-3'. This is the first report of an N6 adenine DNA
AB  - methyltransferase that methylates two adjacent residues on the same
AB  - strand. Interestingly, HP0050 homologs from two clinical strains of H.
AB  - pylori (PG227 and 128) methylate only 5'-GAGG-3' compared with
AB  - 5'-GRRG-3' in strain 26695. HP0050 methyltransferase is highly
AB  - conserved as it is present in more than 90% of H. pylori strains.
AB  - Inactivation of hp0050 in strain PG227 resulted in poor growth,
AB  - suggesting its role in the biology of H. pylori. Collectively, these
AB  - findings provide impetus for exploring the role(s) of this conserved
AB  - DNA methyltransferase in the cellular processes of H. pylori.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Prasad, Y.
AU  - Rao, D.N.
TI  - Helicobacter pylori Restriction Modification systems: Role beyond genome protection.
JO  - Helicobacter
PY  - 2014
SP  - 0
EP  - 0
VL  - 19
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Rao, D.N.
TI  - A nucleotide insertion between two adjacent methyltransferases in Helicobacter pylori results in a bifunctional DNA methyltransferase.
JO  - Biochem. J.
PY  - 2011
SP  - 487
EP  - 495
VL  - 433
AB  - Helicobacter pylori has a dynamic R-M (restriction-modification) system. It is capable of
AB  - acquiring new R-M systems from the environment
AB  - in the form of DNA released from other bacteria or other H. pylon
AB  - strains. Random mutations in RM genes can result in non-functional R-M
AB  - systems or R-M systems with new properties. hpyAVIAM and hpyAVIBM are
AB  - two solitary DNA MTase (methyltransferase) genes adjacent to each other
AB  - and lacking a cognate restriction enzyme gene in H. pylori strain
AB  - 26695. Interestingly, in an Indian strain D27, hpyAVIAM hpyAVIBM
AB  - encodes a single bifunctional polypeptide clue to insertion of a
AB  - nucleotide just before the stop codon of hpyAVIBM and, when a similar
AB  - mutation was made in hpyAVIAM hpyAVIBM from strain 26695, a functional
AB  - MTase with an N-terminal C-5-cytosine MTase domain and a C-terminal
AB  - N-6-adenine MTase domain was constructed. Mutations in the AdoMet
AB  - (S-adenosylmethionine)-binding motif or in the catalytic motif of
AB  - M.HpyAVIA or M.HpyAVIB selectively abrogated the C-5-cytosine or
AB  - N-6-adenine methylation activity of M.HpyAVIA-M.HpyAVIB fusion protein.
AB  - The present study highlights the ability of H. pylori to evolve genes
AB  - with unique functions and thus generate variability. For organisms such
AB  - as H. pylori, which have a small genome, these adaptations could be
AB  - important for their survival in the hostile host environment.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Rao, D.N.
TI  - Role of DNA methyltransferases in epigenetic regulation in bacteria.
JO  - Subcell. Biochem.
PY  - 2012
SP  - 81
EP  - 102
VL  - 61
AB  - In prokaryotes, alteration in gene expression was observed with the modification  of DNA,
AB  - especially DNA methylation. Such changes are inherited from generation to
AB  - generation with no alterations in the DNA sequence and represent the epigenetic
AB  - signal in prokaryotes. DNA methyltransferases are enzymes involved in DNA
AB  - modification and thus in epigenetic regulation of gene expression. DNA
AB  - methylation not only affects the thermodynamic stability of DNA, but also changes
AB  - its curvature. Methylation of specific residues on DNA can affect the protein-DNA
AB  - interactions. DNA methylation in prokaryotes regulates a number of physiological
AB  - processes in the bacterial cell including transcription, DNA mismatch repair and
AB  - replication initiation. Significantly, many reports have suggested a role of DNA
AB  - methylation in regulating the expression of a number of genes in virulence and
AB  - pathogenesis thus, making DNA methlytransferases novel targets for the designing
AB  - of therapeutics. Here, we summarize the current knowledge about the influence of
AB  - DNA methylation on gene regulation in different bacteria, and on bacterial
AB  - virulence.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Sabareesh, V.
AU  - Mukhopadhyay, A.K.
AU  - Rao, D.N.
TI  - Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity.
JO  - FEBS J.
PY  - 2012
SP  - 1080
EP  - 1092
VL  - 279
AB  - The genome of Helicobacter pylori is rich in restrictionmodification (RM) systems.
AB  - Approximately 4% of the genome codes for components of RM
AB  - systems. hpyAVIBM, which codes for a phase-variable C5 cytosine
AB  - methyltransferase (MTase) from H. pylori, lacks a cognate restriction
AB  - enzyme. Over-expression of M.HpyAVIB in Escherichia coli enhances the
AB  - rate of mutations. However, when the catalytically inactive F9N or C82W
AB  - mutants of M.HpyAVIB were expressed in E. coli, mutations were not
AB  - observed. The M.HpyAVIB gene itself was mutated to give rise to
AB  - different variants of the MTase. M.HpyAVIB variants were purified and
AB  - differences in kinetic properties and specificity were observed.
AB  - Intriguingly, purified MTase variants showed relaxed substrate
AB  - specificity. Homologues of hpyAVIBM homologues amplified and sequenced
AB  - from different clinical isolates showed similar variations in sequence.
AB  - Thus, hpyAVIBM presents an interesting example of allelic variations in
AB  - H. pylori where changes in the nucleotide sequence result in proteins
AB  - with new properties.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Singh, D.
AU  - Swarnkar, M.K.
AU  - Singh, A.K.
AU  - Kumar, S.
TI  - Genome Assembly of Chryseobacterium polytrichastri ERMR1:04, a Psychrotolerant Bacterium with Cold Active Proteases, Isolated from East Rathong Glacier in  India.
JO  - Genome Announcements
PY  - 2015
SP  - e01305
EP  - e01315
VL  - 3
AB  - We report here the genome assembly of a psychrotolerant bacterium, Chryseobacterium
AB  - polytrichastri ERMR1:04, which secretes cold-active proteases.
AB  - The bacterium was isolated from a pristine location, the East Rathong Glacier in
AB  - the Sikkim Himalaya. The 5.53-Mb genome provides insight into the cold-active
AB  - industrial enzyme and adaptation in the cold environment.
ER  -

TY  - JOUR
AU  - Kumar, R.
AU  - Srivastava, R.
AU  - Singh, R.K.
AU  - Surolia, A.
AU  - Rao, D.N.
TI  - Activation and inhibition of DNA methyltransferases by S-adenosyl-L-homocysteine analogues.
JO  - Bioorg. Med. Chem.
PY  - 2008
SP  - 2276
EP  - 2285
VL  - 16
AB  - The inhibition of methyltransferases is currently of high interest, particularly in the areas
AB  - of microbial infection and cell
AB  - proliferation, as there have been serious attempts to develop novel
AB  - anti-microbial agents. In the present investigation, a series of
AB  - 11S-adenosyl-L-homocysteine analogues have been synthesized and effect
AB  - of these analogues on DNA methylation catalyzed by DNA
AB  - methyltransferases was studied. It was found that, while
AB  - 5'-S-(propionic acid) 5-deoxy-9-(1'-beta-D-ribofuranosyl) 1,
AB  - 3-dideazaadenine was an activator of EcoP15I and HhaI DNA
AB  - methyltransferases, 5'-S-(propionic acid)
AB  - 5'-deoxy-9-(1'-beta-dribofuran osyl)adenine inhibited the
AB  - methyltransferases in a non-competitive manner. An understanding of the
AB  - binding of analogues to DNA methyltransferases will greatly assist the
AB  - design of novel anti-microbial compounds.
ER  -

TY  - JOUR
AU  - Kumar, R.A.
AU  - Vaze, M.B.
AU  - Chandra, N.R.
AU  - Vijayan, M.
AU  - Muniyappa, K.
TI  - Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis.
JO  - Biochemistry
PY  - 1996
SP  - 1793
EP  - 1802
VL  - 35
AB  - The recA locus of pathogenic mycobacteria differs from that of
AB  - nonpathogenic species because it contains large intervening sequences nested in the RecA
AB  - homology region that are excised by an unusual protein-splicing reaction.  In vivo assays
AB  - indicated that Mycobacterium tuberculosis recA partially complemented Escherichia coli
AB  - recA mutants for recombination and mutagenesis.  Further, splicing of the 85 kDa
AB  - precursor to 38 kDa MtRecA protein was necessary for the display of its activity, in vivo.
AB  - To gain insights into the molecular basis for partial and lack of complementation by
AB  - MtRecA and 85 kDa proteins, respectively, we purified both of them to homogeneity.
AB  - MtRecA protein, but not the 85 kDa form, bound stoichiometrically to single-stranded
AB  - DNA in the presence of ATP.  MtRecA protein was cross-linked to 8-azidoadenosine 5'-
AB  - triphosphate with reduced efficiency, and kinetic analysis of ATPase activity suggested that
AB  - it is due to decreased affinity for ATP.  In contrast, the 85 kDa form was unable to bind
AB  - ATP, in the presence or absence of ssDNA and, consequently, was entirely devoid of
AB  - ATPase activity.  Molecular modeling studies suggested that the decreased affinity of
AB  - MtRecA protein for ATP and the reduced efficiency of its hydrolysis might be due to the
AB  - widening of the cleft which alters the hydrogen bonds and the contact area between the
AB  - enzyme and the substrate and changes in the disposition of the amino acid residues around
AB  - the magnesium ion and the gamma-phosphate.  The formation of joint molecules promoted
AB  - by MtRecA protein was stimulated by SSB when the former was added first.  The
AB  - probability of an association between the lack and partial levels of biological activity of
AB  - RecA protein(s) to that of illegitimate recombination in pathogenic mycobacteria is
AB  - considered.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Bala, M.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14.
JO  - Genome Announcements
PY  - 2013
SP  - e0012913
EP  - e0012913
VL  - 1
AB  - We report the 5.8-Mb genome sequence of Rhodococcus triatomae BKS 15-14, isolated from an ant
AB  - hill soil sample, collected from Bhitarkanika Mangrove Reserve
AB  - Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349
AB  - bp, with a G+C content of 69%, 5,387 protein-coding genes, and 57 RNAs.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Cheng, X.
AU  - Klimasauskas, S.
AU  - Sha, M.
AU  - Posfai, J.
AU  - Roberts, R.J.
AU  - Wilson, G.G.
TI  - The DNA (cytosine-5) methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 1
EP  - 10
VL  - 22
AB  - A review of the m5C-methyltransferases relating sequence to structure and function.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Cheng, X.
AU  - Pflugrath, J.W.
AU  - Roberts, R.J.
TI  - Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex.
JO  - Biochemistry
PY  - 1992
SP  - 8648
EP  - 8653
VL  - 31
AB  - The type-II DNA-(cytosine-5)-methyltransferase M.HhaI was overexpressed in Escherichia coli
AB  - and purified to apparent homogeneity. The purification scheme exploits a unique high salt
AB  - back-extraction step to solubilize M.HhaI selectively, followed by FPLC chromatography. The
AB  - yield of purified protein was 0.75-1.0 mg per gram of bacterial paste. M.HhaI could be
AB  - isolated in two forms: bound with its cofactor S-adenosylmethionine (AdoMet) or devoid of the
AB  - cofactor. The AdoMet-bound form was capable of methylating DNA in vitro in the absence of
AB  - exogenous AdoMet. From kinetic studies of the purified enzyme, values for KmAdoMet(60 nM),
AB  - KiAdoHyc(0.4 nM), and Kcat (0.22s-1) were determined. The purified enzyme bound with its
AB  - cofactor was crystallized by the hanging drop vapor diffusion technique. Crystals were of
AB  - monoclinic space group P21 and had unit-cell dimensions of a = 55.3 A, b = 72.7 A, c = 91.0 A,
AB  - and B=102.5o, with two molecules of M.HhaI in each of the two asymmetric units. The crystals
AB  - diffract beyond 2.5 A and are suitable for structure determination.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Horton, J.R.
AU  - Jones, G.D.
AU  - Walker, R.T.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2773
EP  - 2783
VL  - 25
AB  - 4'-Thio-2'-deoxycytidine was synthesized as a 5'-protected phosphoramidite compatible with
AB  - solid phase DNA synthesis.  When incorporated as the target cytosine (C*) in the GC*GC
AB  - recognition sequence for the DNA methyltransferase M.HhaI, methyl transfer was strongly
AB  - inhibited.  In contrast, these same oligonucleotides were normal substrates for the cognate
AB  - restriction endonuclease R.HhaI and its isoschizomer R.HindP1I.  M.HhaI was able to bind both
AB  - 4'-thio-modified DNA and unmodified DNA to equivalent extents under equilibrium conditions.
AB  - However, the presence of 4'-thio-2'-deoxycytidine decreased the half-life of the complex by
AB  - >10-fold.  The crystal stucture of a ternary complex of M.HhaI, AdoMet and DNA containing
AB  - 4'-thio-2'-deoxycytidine was solved at 2.05 A resolution with a crystallographic R-factor of
AB  - 0.186 and R-free of 0.231.  The structure is not grossly different from previously solved
AB  - ternary complexes containing M.HhaI, DNA and AdoHcy.  The difference electron density suggests
AB  - partial methylation at C5 of the flipped target 4'-thio-2'-deoxycytidine.  The inhibitory
AB  - effect of the 4' sulfur atom on enzymatic activity may be traced to perturbation of a step in
AB  - the methylation reaction after DNA binding but prior to methyl transfer.  This inhibitory
AB  - effect can be partially overcome after a considerably long time in the crystal environment
AB  - where the packing prevents complex dissociation and the target is accurately positioned within
AB  - the active site.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Jangam, A.K.
AU  - Akhil, V.
AU  - Rajendran, V.
AU  - Katneni, V.K.
AU  - Sahaya, R.J.J.
AU  - Grover, M.
AU  - Nagaleekar, V.K.
AU  - Alavandi, S.V.
AU  - Vijayan, K.K.
TI  - Draft Genome Sequence of the Luminescent Strain Vibrio campbellii LB102, Isolated from a Black Tiger Shrimp (Penaeus monodon) Broodstock Rearing System.
JO  - Genome Announcements
PY  - 2017
SP  - e00342
EP  - e00317
VL  - 5
AB  - We report here the genome sequence of Vibrio campbellii LB102, isolated from the  broodstock
AB  - rearing system of a shrimp hatchery in India. Sequence analysis
AB  - revealed the presence of effector toxins of the type III (YopT, sharing 39%
AB  - identity with Yersinia pestis) and type VI (VgrG-3 and hemolysin coregulated
AB  - protein of V. cholerae) secretion systems.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Johnson, W.S.
AU  - Tomasz, M.
TI  - Orientation isomers of the mitomycin C interstrand cross-link in non-self-complementary DNA. Differential effect of the two isomers on restriction endonuclease cleavage at a nearby site.
JO  - Biochemistry
PY  - 1993
SP  - 1364
EP  - 1372
VL  - 32
AB  - Reductively activated mitomycin C (MC) forms DNA interstrand cross-links between two guanines
AB  - at CG.CG sequences. It is predictable that such cross-links should occur in two isomeric
AB  - strand orientations in duplex DNA (except when located in the center of a self-complementary
AB  - duplex). This was verified by the isolation and characterization of a pair of two isomeric
AB  - oligonucleotides in each case of five non-self-complementary duplexes of 8-bp length,
AB  - cross-linked by MC. Isomer separation was accomplished by reverse-phase HPLC. The isomers in a
AB  - pair were formed in approximately 1:1 proportion.Their structures were rigorously
AB  - characterized by a two-step cross-linking procedure: first 1-monoalkylation of each strand,
AB  - followed by conversion to a cross-linked duplex by annealing the monoalkylated strand to its
AB  - complement in the presence of a reducing agent. The resulting individual authentic orientation
AB  - isomers were used as standards for identification of the two isomers formed in the original
AB  - (one-step) cross-linking reactions. A 16-bp duplex oligonucleotide was synthesized featuring
AB  - the AluI cognate sequence, separated from a MC cross-link site by only 1 bp. Its two MC
AB  - cross-linked isomers were prepared separately, and their rate of cleavage by AluI was
AB  - determined using HPLC. Cleavage of both the unmodified and cross-linked duplexes was
AB  - nonsymmetrical. The isomer in which the 2-NH3+ of MC is oriented toward the AluI site was
AB  - cleaved essentially at the same rate as the control duplex, while cleavage of the isomer with
AB  - the MC indoloquinone group oriented toward the AluI site was inhibited 2-fold at the
AB  - faster-cleaved strand. This difference demonstrates that the two orientations of the MC
AB  - cross-link can exert differential effects on protein-DNA interactions. The modest inhibition
AB  - of AluI cleavage relative to that by CC-1065 [Hurley,L.H., Needham-VanDevanter,D.R., and
AB  - Lee,C.(1987)Proc. Natl. Acad. Sci. U.S.A. 84, 6412-6416] may indicate relatively low
AB  - distortion of DNA by the MC cross-link. This notion is supported by a comparison with psoralen
AB  - cross-links.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Karmakar, B.C.
AU  - Nagarajan, D.
AU  - Mukhopadhyay, A.K.
AU  - Morgan, R.D.
AU  - Rao, D.N.
TI  - N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 3429
EP  - 3445
VL  - 46
AB  - Many bacterial genomes exclusively display an N4-
AB  - methyl cytosine base (m4C), whose physiological
AB  - significance is not yet clear. Helicobacter pylori is
AB  - a carcinogenic bacterium and the leading cause of
AB  - gastric cancer in humans. Helicobacter pylori strain
AB  - 26695 harbors a single m4C cytosine methyltransferase,
AB  - M2.HpyAII which recognizes 5 TCTTC 3 sequence
AB  - and methylates the first cytosine residue. To
AB  - understand the role of m4C modification, M2.hpyAII
AB  - deletion strain was constructed. Deletion strain displayed
AB  - lower adherence to host AGS cells and reduced
AB  - potential to induce inflammation and apoptosis.
AB  - M2.hpyAII gene deletion strain exhibited reduced
AB  - capacity for natural transformation, which was
AB  - rescued in the complemented strain carrying an active
AB  - copy of M2.hpyAII gene in the genome. Genomewide
AB  - gene expression and proteomic analysis were
AB  - carried out to discern the possible reasons behind
AB  - the altered phenotype of the M2.hpyAII gene deletion
AB  - strain. Upon the loss of m4C modification a total
AB  - of 102 genes belonging to virulence, ribosome assembly
AB  - and cellular components were differentially
AB  - expressed. The present study adds a functional role
AB  - for the presence of m4C modification in H. pylori and
AB  - provides the first evidence that m4C signal acts as a
AB  - global epigenetic regulator in H. pylori.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Kaur, C.
AU  - Kimura, K.
AU  - Takeo, M.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658.
JO  - Genome Announcements
PY  - 2013
SP  - e00120
EP  - e00112
VL  - 1
AB  - We report the 5.0-Mb genome sequence of the type species of the genus Citrobacter, Citrobacter
AB  - freundii strain MTCC 1658, isolated from canal water. This draft genome sequence of C.
AB  - freundii strain MTCC 1658(T) consists of 5,001,265 bp with a G+C content of 51.61%, 4,691
AB  - protein-coding genes, 70 tRNAs, and 10 rRNAs.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Kaur, N.
AU  - Singh, N.K.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15.
JO  - Genome Announcements
PY  - 2013
SP  - e00150
EP  - e00113
VL  - 1
AB  - We report the 7.3-Mbp genome sequence of Streptomyces gancidicus strain BKS 13-15, isolated
AB  - from mangrove sediment samples collected from the Bhitar Kanika
AB  - Mangrove Reserve Forest, Odissha, India. The draft genome of strain Streptomyces
AB  - gancidicus strain BKS 13-15 consists of 7,300,479 bp with 72.6% G+C content,
AB  - 6,631 protein-coding genes, and 71 RNAs.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Lindquist, I.E.
AU  - Sundararajan, A.
AU  - Rajanna, C.
AU  - Floyd, J.T.
AU  - Smith, K.P.
AU  - Andersen, J.L.
AU  - He, G.
AU  - Ayers, R.M.
AU  - Johnson, J.A.
AU  - Werdann, J.J.
AU  - Sandoval, A.A.
AU  - Mojica, N.M.
AU  - Schilkey, F.D.
AU  - Mudge, J.
AU  - Varela, M.F.
TI  - Genome Sequence of Non-O1 Vibrio cholerae PS15.
JO  - Genome Announcements
PY  - 2013
SP  - e00227
EP  - e00212
VL  - 1
AB  - The draft genome sequence of a non-O1 Vibrio cholerae strain, PS15, organized into 3,512 open
AB  - reading frames within a 3.9-Mb genome, was determined. The PS15
AB  - genome sequence will allow for the study of the evolution of virulence and
AB  - environmental adaptation in V. cholerae.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Patil, P.P.
AU  - Midha, S.
AU  - Ray, P.
AU  - Patil, P.B.
AU  - Gautam, V.
TI  - Genome Sequence of Acinetobacter baumannii Strain 10441_14 Belonging to ST451, Isolated from India.
JO  - Genome Announcements
PY  - 2015
SP  - e01322
EP  - e01315
VL  - 3
AB  - Acinetobacter baumannii resistance to carbapenems is of global concern. Here, we  report the
AB  - 3.9 Mb draft genome of a cerebrospinal fluid isolate of A. baumannii
AB  - strain 10441_14 which is carbapenem resistant and belongs to ST451. This genome
AB  - will further help in the understanding of the drug resistance mechanism,
AB  - epidemiology, and pathology of this bacterium.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Patil, P.P.
AU  - Midha, S.
AU  - Ray, P.
AU  - Patil, P.B.
AU  - Gautam, V.
TI  - Genome Sequence of Acinetobacter baumannii Strain 5021_13, Isolated from Cerebrospinal Fluid.
JO  - Genome Announcements
PY  - 2015
SP  - e01213
EP  - e01215
VL  - 3
AB  - We report here the 4.1-Mb draft genome sequence of Acinetobacter baumannii strain 5021_13, a
AB  - cerebrospinal fluid isolate from northern India. This genome information will help studies
AB  - toward understanding the epidemiology and pathogenicity of this important nosocomial pathogen.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Subramanian, S.
AU  - Raghava, G.P.
AU  - Pinnaka, A.K.
TI  - Genome Sequence of the Marine Bacterium Marinilabilia salmonicolor JCM 21150T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3746
EP  - 3746
VL  - 194
AB  - We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150(T), which was
AB  - isolated from marine mud in the year 1961. The draft genome of strain
AB  - Marinilabilia salmonicolor JCM 21150(T) contains 4,982,627 bp with a G+C content
AB  - of 41.92% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Vikram, S.
AU  - Raghava, G.P.
TI  - Genome Sequence of the Nitroaromatic Compound-Degrading Bacterium Burkholderia sp. Strain SJ98.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3286
EP  - 3286
VL  - 194
AB  - We report the 7.85-Mb genome sequence of Burkholderia sp. strain SJ98, isolated from
AB  - agricultural fields of Assam, India. The draft genome of this strain will be
AB  - helpful in studying the genetic pathways involved in the degradation of aromatic
AB  - compounds.
ER  -

TY  - JOUR
AU  - Kumar, S.
AU  - Vikram, S.
AU  - Subramanian, S.
AU  - Raghava, G.P.
AU  - Pinnaka, A.K.
TI  - Genome Sequence of the Halotolerant Bacterium Imtechella halotolerans K1T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3731
EP  - 3731
VL  - 194
AB  - We report the 3.087-Mb genome sequence of Imtechella halotolerans K1(T), isolated from an
AB  - estuarine water sample collected from Kochi, Kerala, India. Strain K1 was
AB  - recently reported as a novel genus of the family Flavobacteriaceae.
ER  -

TY  - JOUR
AU  - Kumar-Pinnaka, P.A.
AU  - Ara, S.
AU  - Singh, A.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of Winogradskyella psychrotolerans RS-3T, Isolated from the Marine Transect of Kongsfjorden, Ny-Alesund, Svalbard, Arctic Ocean.
JO  - Genome Announcements
PY  - 2013
SP  - e00630
EP  - e00613
VL  - 1
AB  - The 4.3-Mb genome of Winogradskyella psychrotolerans strain RS-3(T), isolated from a sediment
AB  - sample of a marine transect of Kongsfjorden, Ny-Alesund, Svalbard, Arctic Ocean, is reported.
ER  -

TY  - JOUR
AU  - Kumar-Pinnaka, P.A.
AU  - Singh, A.
AU  - Ara, S.
AU  - Begum, Z.
AU  - Reddy, G.S.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of Leifsonia rubra Strain CMS 76RT, Isolated from a Cyanobacterial Mat Sample from a Pond in Wright Valley, McMurdo, Antarctica.
JO  - Genome Announcements
PY  - 2013
SP  - e00633
EP  - e00613
VL  - 1
AB  - The 2.7-Mb draft genome sequence of Leifsonia rubra strain CMS 76R(T), isolated from a
AB  - cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica, is reported.
ER  -

TY  - JOUR
AU  - Kumaravel, S.
AU  - Thankappan, S.
AU  - Raghupathi, S.
AU  - Uthandi, S.
TI  - Draft Genome Sequence of Plant Growth-Promoting and Drought-Tolerant Bacillus altitudinis FD48, Isolated from Rice Phylloplane.
JO  - Genome Announcements
PY  - 2018
SP  - e00019
EP  - e00018
VL  - 6
AB  - The genome sequence of a temperature-tolerant strain, Bacillus altitudinis FD48,  is described
AB  - here. The reads were assembled into contigs with a total size of 3.7
AB  - Mb. The genome information will aid in understanding its role in alleviating
AB  - stress in crop plants as a potential bioinoculant for agricultural applications.
ER  -

TY  - JOUR
AU  - Kumaresan, D.
AU  - Wischer, D.
AU  - Hillebrand-Voiculescu, A.M.
AU  - Murrell, J.C.
TI  - Draft Genome Sequences of Facultative Methylotrophs, Gemmobacter sp. Strain LW1 and Mesorhizobium sp. Strain 1M-11, Isolated from Movile Cave, Romania.
JO  - Genome Announcements
PY  - 2015
SP  - e01266
EP  - e01215
VL  - 3
AB  - Facultative methylotrophs belonging to the genera Gemmobacter and Mesorhizobium were isolated
AB  - from microbial mat and cave water samples obtained from the Movile
AB  - Cave ecosystem. Both bacteria can utilize methylated amines as their sole carbon
AB  - and nitrogen source. Here, we report the draft genome sequences of Gemmobacter
AB  - sp. strain LW1 and Mesorhizobium sp. strain IM1.
ER  -

TY  - JOUR
AU  - Kumari, M.
AU  - Swarnkar, M.K.
AU  - Kumar, S.
AU  - Singh, A.K.
AU  - Gupta, M.
TI  - Complete Genome Sequence of Potential Probiotic Lactobacillus sp. HFC8, Isolated  from Human Gut Using PacBio SMRT Sequencing.
JO  - Genome Announcements
PY  - 2015
SP  - e01337
EP  - e01315
VL  - 3
AB  - We report a 3.07-Mb complete genome sequence of a lactic acid bacterium, Lactobacillus sp.
AB  - HFC8. The gene-coding clusters are predicated for probiotic
AB  - characteristics, like bacteriocin production, cell adhesion, bile salt
AB  - hydrolysis, lactose metabolism, autoaggregation, and tolerance to oxidative
AB  - stress.
ER  -

TY  - JOUR
AU  - Kumari, M.
AU  - Swarnkar, M.K.
AU  - Kumar, S.
AU  - Singh, A.K.
AU  - Gupta, M.
TI  - Genome Sequence of a Potential Probiotic Strain, Lactobacillus fermentum HFB3, Isolated from a Human Gut.
JO  - Genome Announcements
PY  - 2015
SP  - e01296
EP  - e01215
VL  - 3
AB  - A draft genome sequence of 2.04 Mb is reported for Lactobacillus fermentum HFB3,  which is a
AB  - lactic acid bacterium with probiotic properties. The gene-coding
AB  - clusters also predicted the presence of genes responsible for probiotic
AB  - characteristics.
ER  -

TY  - JOUR
AU  - Kumari, P.
AU  - Badhai, J.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Marinomonas fungiae Strain AN44(T) (JCM 18476(T)), Isolated from the Coral Fungia echinata from the Andaman Sea.
JO  - Genome Announcements
PY  - 2018
SP  - e00112
EP  - e00118
VL  - 6
AB  - Marinomonas fungiae strain AN44(T) was isolated from mucus of the coral Fungia echinata
AB  - Optimum growth occurs at 3 to 5% NaCl. The draft genome is 4.2 Mb, with
AB  - 3,776 protein-coding genes. It harbors genes for the degradation of aromatic
AB  - compounds, such as quinate, ferulate, p-coumarate, protocatechuate, and
AB  - p-hydroxyphenylacetate.
ER  -

TY  - JOUR
AU  - Kumru, S.
AU  - Tekedar, H.C.
AU  - Griffin, M.J.
AU  - Waldbieser, G.C.
AU  - Liles, M.R.
AU  - Sonstegard, T.
AU  - Schroeder, S.G.
AU  - Lawrence, M.L.
AU  - Karsi, A.
TI  - Draft Genome Sequence of Fish Pathogen Aeromonas bestiarum GA97-22.
JO  - Genome Announcements
PY  - 2018
SP  - e00524
EP  - e00518
VL  - 6
AB  - Aeromonas bestiarum is a Gram-negative mesophilic motile bacterium causing acute  hemorrhagic
AB  - septicemia or chronic skin ulcers in fish. Here, we report the draft
AB  - genome sequence of A. bestiarum strain GA97-22, which was isolated from rainbow
AB  - trout in 1997. This genome sequence will improve our understanding of the complex
AB  - taxonomy of motile aeromonads.
ER  -

TY  - JOUR
AU  - Kumru, S.
AU  - Tekedar, H.C.
AU  - Waldbieser, G.C.
AU  - Karsi, A.
AU  - Lawrence, M.L.
TI  - Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar II Strain 94-081.
JO  - Genome Announcements
PY  - 2016
SP  - e00430
EP  - e00416
VL  - 4
AB  - Flavobacterium columnare causes columnaris disease in fresh and brackish water worldwide. F.
AB  - columnare strain 94-081 was isolated from a diseased channel
AB  - catfish in 1994; its genome sequence is the first completed genomovar II
AB  - sequence.
ER  -

TY  - JOUR
AU  - Kunadia, K.
AU  - Nathani, N.M.
AU  - Kothari, V.
AU  - Kotadia, R.J.
AU  - Kothari, C.R.
AU  - Joshi, A.
AU  - Rank, J.K.
AU  - Faldu, P.R.
AU  - Shekar, M.C.
AU  - Viroja, M.J.
AU  - Patel, P.A.
AU  - Jadeja, D.
AU  - Reddy, B.
AU  - Pal, S.R.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Kothari, R.K.
TI  - Draft Genome Sequence of Commercial Textile Dye-Decolorizing and -Degrading Bacillus subtilis Strain C3 Isolated in India.
JO  - Genome Announcements
PY  - 2016
SP  - e00104
EP  - e00116
VL  - 4
AB  - Bacillus subtilis C3, a commercial textile dye-decolorizing and -degrading bacterium, was
AB  - isolated from the common effluent treatment plant (CEPT) of the
AB  - Jetpur textile dyeing and printing industrial sector situated in the district of
AB  - Rajkot, Gujarat, India. Here, we present the annotated 4.18-Mb draft genome
AB  - sequence of B. subtilis C3, providing information about the metabolic pathways
AB  - involved in decolorization and degradation of several commercial textile azo
AB  - dyes. Thus, we confirm B. subtilis C3 as a potential candidate for bioremediation
AB  - of textile effluents.
ER  -

TY  - JOUR
AU  - Kunert, N.
TI  - Identification and characterization of IPOD, a novel interaction partner of the DNA methyltransferase Dnmt2 from Drosophila melanogaster.
JO  - Ph.D. Thesis, Germany
PY  - 2005
SP  - 1
EP  - 142
ER  -

TY  - JOUR
AU  - Kunkel, L.M.
AU  - Silberklang, M.
AU  - McCarthy, B.J.
TI  - A third restriction endonuclease from Xanthomonas malvacearum.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 133
EP  - 139
VL  - 132
AB  - An additional sequence-specific endonuclease, XmaIII, has been partially
AB  - purified from Xanthomonas malvacearum.  XmaIII recognizes ten cleavage sites in
AB  - adenovirus 2 DNA, two sites in bacteriophage lambda and no site in either
AB  - simian virus 40 DNA or PhiX174 DNA.  It recognizes the sequence 5' C-^G-G-C-C-G
AB  - 3' 3' G-C-C-G-G^-C 5' and cleaves at the sites indicated by the arrows.  No
AB  - other endonuclease with this particular nucleotide sequence specificity has
AB  - been reported.
ER  -

TY  - JOUR
AU  - Kunne, C.
AU  - Billion, A.
AU  - Mshana, S.E.
AU  - Schmiedel, J.
AU  - Domann, E.
AU  - Hossain, H.
AU  - Hain, T.
AU  - Imirzalioglu, C.
AU  - Chakraborty, T.
TI  - Complete Sequences of Plasmids from the Hemolytic-Uremic Syndrome-Associated Escherichia coli Strain HUSEC41.
JO  - J. Bacteriol.
PY  - 2012
SP  - 532
EP  - 533
VL  - 194
AB  - The complete and annotated sequences of four plasmids from a historical enteroaggregative
AB  - Shiga toxin-producing Escherichia coli (HUSEC) serotype
AB  - O104:H4 strain, HUSEC41/01-09591, isolated in 2001 in Germany are
AB  - reported.
ER  -

TY  - JOUR
AU  - Kunst, F. et al.
TI  - The complete genome sequence of the Gram-positive bacterium Bacillus subtilis.
JO  - Nature
PY  - 1997
SP  - 249
EP  - 256
VL  - 390
AB  - Bacillus subtilis is the best-characterized member of the Gram-positive bacteria.  Its genome
AB  - of 4,214,810 base pairs comprises 4,100 protein-coding genes.  Of these protein-coding genes,
AB  - 53% are represented once, while a quarter of the genome corresponds to several gene families
AB  - that have been greatly expanded by gene duplication, the largest family containing 77 putative
AB  - ATP-binding transport proeins.  In addition, a large proportion of the genetic capacity is
AB  - devoted to the utilization of a variety of carbon sources, including many plant-derived
AB  - molecules.  The identification of five signal peptidase genes, as well as several genes for
AB  - components of the secretion apparatus, is important given the capacity of Bacillus strains to
AB  - secrete large amounts of industrially important enzymes.  Many of the genes are involved in
AB  - the synthesis of secondary metabolites, including antibiotics, that are more typically
AB  - associated with Streptomyces species.  The genome contains at least ten prophages or remnants
AB  - of prophages, indicating that bacteriophage infection has played an important evolutionary
AB  - role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
ER  -

TY  - JOUR
AU  - Kunta, M.
AU  - Zheng, Z.
AU  - Wu, F.
AU  - da Graca, J.V.
AU  - Park, J.W.
AU  - Deng, X.
AU  - Chen, J.
TI  - Draft Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' Strain TX2351  Isolated from Asian Citrus Psyllids in Texas, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e00170
EP  - e00117
VL  - 5
AB  - We report here the draft genome sequence of 'Candidatus Liberibacter asiaticus' strain
AB  - TX2351, collected from Asian citrus psyllids in south Texas, USA. The
AB  - TX2351 genome has a size of 1,252,043 bp, a G+C content of 36.5%, 1,184 predicted
AB  - open reading frames, and 52 RNA genes.
ER  -

TY  - JOUR
AU  - Kunz, A.
AU  - Mackeldanz, P.
AU  - Mucke, M.
AU  - Meisel, A.
AU  - Reuter, M.
AU  - Schroeder, C.
AU  - Kruger, D.H.
TI  - Mutual activation of two restriction endonucleases: interaction of EcoPI and EcoP15.
JO  - Biol. Chem.
PY  - 1998
SP  - 617
EP  - 620
VL  - 379
AB  - Type III restriction endonucleases recognize nonsymmetric nucleotide sequences.  A necessary
AB  - condition for DNA cleavage is the presence of two unmethylated recognition sites which are
AB  - inversely ('head-to-head') oriented in the DNA double strand.  A DNA substrate possessing
AB  - one EcoP1 and one EcoP15 site in the head-to-head configuration could not be cleaved by the
AB  - individual enzymes, however, it was specifically digested in the simultaneous presence of both
AB  - enzymes.  In agreement with the tracking-collision model for the DNA interaction of type III
AB  - enzymes cleavage could be abolished by Lac repressor bound between the two sites.  We conclude
AB  - that two different type III enzymes can functionally cooperate in the cleavage of DNA.
ER  -

TY  - JOUR
AU  - Kunz, A.
AU  - Meisel, A.
AU  - Mackeldanz, P.
AU  - Reuter, M.
AU  - Kruger, D.H.
TI  - An experimental selection system to identify bacterial cells exhibiting a new DNA host specificity.
JO  - Biol. Chem.
PY  - 1998
SP  - 563
EP  - 566
VL  - 379
AB  - Restriction-modification enzymes interact with DNA sequences in a highly specific manner.
AB  - Mutations within the DNA binding region of the enzymes could be expected to produce enzyme
AB  - variants with changed DNA sequence specificities.  We developed an efficient in vivo selection
AB  - system that enabled us to detect one cell coding for a restriction-modification system with a
AB  - new DNA sequence specificity in a background of more than 10^6 cells with the original DNA
AB  - sequence specificity.
ER  -

TY  - JOUR
AU  - Kuo, V.
AU  - Shoemaker, W.R.
AU  - Muscarella, M.E.
AU  - Lennon, J.T.
TI  - Whole-Genome Sequence of the Soil Bacterium Micrococcus sp. KBS0714.<jour_book>Genome Announc.
JO  - 
PY  - 2017
SP  - e00697
EP  - e00617
VL  - 5
AB  - We present here a draft genome assembly of Micrococcus sp. KBS0714, which was isolated from
AB  - agricultural soil. The genome provides insight into the strategies
AB  - that Micrococcus spp. use to contend with environmental stressors such as
AB  - desiccation and starvation in environmental and host-associated ecosystems.
ER  -

TY  - JOUR
AU  - Kuosmanen, M.
AU  - Poso, H.
TI  - Inhibition of the activity of restriction endonucleases by spermidine and spermine.
JO  - FEBS Lett.
PY  - 1985
SP  - 17
EP  - 20
VL  - 179
AB  - Physiological concentrations (0.5-2.0 mM) of spermidine and spermine were
AB  - observed to inhibit the digestion in vitro of plasmid pJDB 207 by the
AB  - restriction endonucleases BamHI (EC 3.1.23.6), EcoRI (EC3.2.23.13), HindIII
AB  - (EC3.1.23.20), HpaI (EC3.1.23.23) and PstI (EC3.1.23.31).  The polyamines
AB  - protected all the tested restriction sequences of DNA, since the activity of
AB  - all endonucleases used was strongly inhibited.  These results show the need for
AB  - caution when using polyamines as experimental tools for recombinant DNA
AB  - chemistry.
ER  -

TY  - JOUR
AU  - Kupper, D.
AU  - Moncke-Buchner, E.
AU  - Reuter, M.
AU  - Kruger, D.H.
TI  - Oligonucleotide stimulators allow complete cleavage of agarose-embedded DNA by particular type II restriction endonucleases.
JO  - Anal. Biochem.
PY  - 1999
SP  - 275
EP  - 277
VL  - 272
AB  - In previous work we and others discovered several restriction endonucleases requiring the
AB  - simultaneous interaction with two copies of their respective recognition sequence for enzyme
AB  - activity.  EcoRII was the first restriction enzyme for which this special property has been
AB  - described, and the mechanism underlying the cooperative interaction with two sites in the
AB  - substrate DNA was studied in more detail.  Complete cleavage of a resistant DNA site (present
AB  - alone or at a great distance to a second site in a DNA molecule) can be achieved by providing
AB  - the required second copy of the recognition site on short synthetic oligonucleotide duplexes.
AB  - This principle has been verified for at least 12 restriction endonucleases so far (e.g.,
AB  - EcoRII, HpaII, NaeI, NarI, SfiI, and others).  In addition, the practical importance of
AB  - restriction enzyme stimulation by specific oligo duplexes for the reliable detection of
AB  - prokaryotic Dcm methylation by comparative DNA digestion with EcoRII/BstNI and of eukaryotic
AB  - CpG methylation with HpaII/MspI has been demonstrated.  Now we wanted to verify that the
AB  - technique of oligo duplex-based stimulation of those restriction endonucleases is also
AB  - applicable for digesting DNA being embedded in agarose as necessary for the handling of larger
AB  - genomic DNA.
ER  -

TY  - JOUR
AU  - Kupper, D.
AU  - Reuter, M.
AU  - Kruger, D.H.
TI  - Overproduction of His-tagged EcoRII restriction endonuclease and terminally deleted mutant proteins.
JO  - Gene
PY  - 1995
SP  - 97
EP  - 98
VL  - 157
AB  - EcoRII was the first restriction endonuclease (ENase) reported requiring the cooperative
AB  - interaction with at least two DNA sites for activity.  Using two different expression systems
AB  - the enzyme could be purified and its special substrate requirements were further analyzed.  At
AB  - the present state of knowledge we suggest a model of simultaneous binding of two DNA sites to
AB  - one dimeric enzyme molecule.
ER  -

TY  - JOUR
AU  - Kupper, D.
AU  - Reuter, M.
AU  - Mackeldanz, P.
AU  - Meisel, A.
AU  - Alves, J.
AU  - Schroeder, C.
AU  - Kruger, D.H.
TI  - Hyperexpressed EcoRII renatured from inclusion bodies and native enzyme both exhibit essential cooperativity with two DNA sites.
JO  - Protein Expr. Purif.
PY  - 1995
SP  - 1
EP  - 9
VL  - 6
AB  - EcoRII was the first restriction endonuclease (ENase) reported needing the cooperative
AB  - interaction with at least two DNA sites for activity. We constructed an EcoRII-overproducing
AB  - strain of Escherichia coli by placing the coding sequence under control of the T7 gene 10
AB  - regulatory elements. The yield of EcoRII expression could be increased to about 10% of total
AB  - soluble cellular protein. Inclusion bodies are formed that mainly consist of insoluble EcoRII
AB  - molecules. After solubilization by 6M guanidine hydrochloride refolding of the enzyme was
AB  - achieved by dilution into appropriate buffer. The endonuclease was purified to homogeneity
AB  - from both the soluble protein fraction and the protein renatured from inclusion bodies. Their
AB  - identity was proven by circular dichroism and analysis of enzyme activity with respect to the
AB  - special substrate requirements of EcoRII. It is shown that EcoRII cleavage of
AB  - oligodeoxyribonucleotide duplexes (oligo duplexes) with only one recognition site follows a
AB  - sigmoidal concentration dependence, i.e., they cannot be cleaved below a distinct low DNA
AB  - concentration where simultaneous interaction with two substrate molecules is no longer
AB  - possible. We demonstrate that the restriction of oligo duplexes containing two recognition
AB  - sites does not show this concentration dependence, confirming an intramolecular site
AB  - cooperativity.
ER  -

TY  - JOUR
AU  - Kupper, D.
AU  - Reuter, M.
AU  - Meisel, A.
AU  - Kruger, D.H.
TI  - Reliable detection of DNA CpG methylation profiles by the isoschizomers MspI/HpaII using oligonucleotide stimulators.
JO  - Biotechniques
PY  - 1997
SP  - 843
EP  - 846
VL  - 23
AB  - The increasing interest in methylation patterns of mammalian DNA demands a simple and reliable
AB  - method to clearly differentiate between cytosine and 5-methylcytosine within a specific DNA
AB  - region.  The simplest and most commonly used approach is the analysis with restriction
AB  - endonucleases exhibiting different methylation sensitivities, like the MspI/HpaII pair of
AB  - isoschizomeric enzymes.  Whereas MspI cleaves the recognition sequence 5'-CCGG independently
AB  - of the methylation state of the internal C, cleavage by HpaII is blocked by the presence of
AB  - 5-MeC at this site.  The method is compromised by the fact that methylation can be detected
AB  - only in those CpGs that are located within the tetranucleotide recognition sequence.
ER  -

TY  - JOUR
AU  - Kupper, D.
AU  - Zhou, J.-G.
AU  - Kiss, A.
AU  - Venetianer, P.
TI  - Cloning and structure of the M.BepI modification methyltransferase.
JO  - Gene
PY  - 1988
SP  - 33
EP  - 33
VL  - 74
AB  - Meeting abstract
ER  -

TY  - JOUR
AU  - Kupper, D.
AU  - Zhou, J.-G.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Cloning and structure of the BepI modification methylase.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 1077
EP  - 1088
VL  - 17
AB  - The gene coding for a CGCG specific DNA methylase has been cloned in E. coli from
AB  - Brevibacterium epidermidis.  The enzyme, named BepI methylase, is probably the cognate
AB  - methylase of the FnuDII isoschizomer BepI endonuclease isolated from this strain.  The
AB  - expression of BepI methylase in E. coli is dependent on the orientation of the cloned fragment
AB  - suggesting that the gene is transcribed from a promoter on the plasmid vector.  No BepI
AB  - endonuclease could be detected in the clones producing BepI methylase.  The nucleotide
AB  - sequence of the BepI methylase gene has been determined, it predicts a protein of 403 amino
AB  - acids (M:45,447).  Analysis of the amino acid sequence deduced from the nucleotide sequence
AB  - revealed similarities between the BepI methylase and other cytosine methylases.  M.BepI
AB  - methylates the external cytosine in its recognition sequence.
ER  -

TY  - JOUR
AU  - Kupriyanova, N.S.
AU  - Kirilenko, P.M.
AU  - Netchvolodov, K.K.
AU  - Ryskov, A.P.
TI  - Preferential cleavage sites for Sau3A restriction endonuclease in human ribosomal DNA.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2000
SP  - 11
EP  - 15
VL  - 274
AB  - Previous studies of cloned ribosomal DNA (rDNA) variants isolated from the cosmid library of
AB  - human chromosome 13 have revealed some disproportion in representativity of different rDNA
AB  - regions (N. S. Kupriyanova, K. K. Netchvolodov, P. M. Kirilenko, B. I. Kapanadze, N. K.
AB  - Yankovsky, and A. P. Ryskov, Mol. Biol. 30, 51-60, 1996). Here we show nonrandom cleavage of
AB  - human rDNA with Sau3A or its isoschizomer MboI under mild hydrolysis conditions. The
AB  - hypersensitive cleavage sites were found to be located in the ribosomal intergenic spacer
AB  - (rIGS), especially in the regions of about 5-5.5 and 11 kb upstream of the rRNA transcription
AB  - start point. This finding is based on sequence mapping of the rDNA insert ends in randomly
AB  - selected cosmid clones of human chromosome 13 and on the data of digestion kinetics of cloned
AB  - and noncloned human genomic rDNA with Sau3A and MboI. The results show that the methylation
AB  - status and superhelicity state of the rIGS have no effect on cleavage site sensitivity. It is
AB  - interesting that all primary cleavage sites are adjacent to or entering into Alu or Psi cdc 27
AB  - retroposons of the rIGS suggesting a possible role of neighboring sequences in nuclease
AB  - accessibility. The results explain nonequal representation of rDNA sequences in the human
AB  - genomic DNA library used for this study.
ER  -

TY  - JOUR
AU  - Kur, J.
TI  - Integration host factor (IHF) applied for partial digestion by restriction endonucleases in large DNA molecules (IARC procedure).
JO  - Acta Microbiol. Pol.
PY  - 1993
SP  - 145
EP  - 150
VL  - 42
AB  - The IHF protein of Escherichia coli was successfully used in IHF-mediated Achilles' Heel
AB  - Cleavage (IHF-AC) technique and leads to the generation of very rare restriction sites in
AB  - large DNA molecules. The first step of this procedure is methylation of DNA in the presence of
AB  - IHF, when the overlapping ihf/restriction sites are protected from methylation, and in the
AB  - second step the DNA is cut by the cognate restriction enzyme. The aim of the present study is
AB  - to develop a very exact and reproducible procedure to obtain only a few well-defined cuts with
AB  - the IHF-pre-treated DNA, depending on the variety of all parameters. This technique (IARC,
AB  - i.e., IHF-assisted rare cutters) employs the restriction enzyme and only one auxiliary protein
AB  - (IHF). The advantage of the IARC procedure is that no methylation is required (as opposed to
AB  - the IHF-AC method). Using the IARC approach, the effects of various IHF concentrations were
AB  - evaluated on the cleavage activity of the DraI, PacI, PmeI, and SwaI enzymes using DNA of
AB  - phage lambda or the entire genomic 4.7-Mb DNA of E. coli. At low IHF concentrations only a few
AB  - cut sites were eliminated by IHF binding, but a high IHF concentration, enzymes were able to
AB  - cut in only one or several specific sites.
ER  -

TY  - JOUR
AU  - Kur, J.
TI  - Use of IHF mediated achilles' heel cleavage (IHF-AC) method for mapping ihf sites.
JO  - Acta Microbiol. Pol.
PY  - 1993
SP  - 137
EP  - 144
VL  - 42
AB  - We have shown that Integration Host Factor of E. coli can successfully be used in the
AB  - IHF-mediated Achilles' Heel Cleavage (IHF-AC), for generating rare natural cleavage sites.
AB  - The first step of this procedure is methylation of DNA in the presence of IHF, when the
AB  - overlapping ihf/restriction sites are protected from methylation, and in the second step the
AB  - DNA is cut by the cognate restriction enzyme. The extent of cleavage could be controlled by
AB  - varying the IHF:DNA ratio and temperature. The aim of the present study is to demonstrate that
AB  - IHF-AC procedure might serve as a useful tool for finding new protein-binding sites which
AB  - overlap known restriction sites. I have used this approach in conjunction with several MTases
AB  - to find several other unknown IHF-binding sites.
ER  -

TY  - JOUR
AU  - Kur, J.
AU  - Koob, M.
AU  - Burkiewicz, A.
AU  - Szybalski, W.
TI  - A novel method for converting common restriction enzymes into rare cutters:  integration host factor-mediated Achilles' cleavage (IHF-AC).
JO  - Gene
PY  - 1992
SP  - 1
EP  - 7
VL  - 110
AB  - Integration host factor (IHF)-mediated protection against enzymatic methylation at
AB  - ihf-overlapping sites provides the basis for this novel application of the Achilles' cleavage
AB  - (AC) technique [Koob et al., Science 241 (1988) 1084-1086] for generating rare natural
AB  - cleavage sites. When applying IHF-AC to plasmid, phage lambda, Escherichia coli and yeast
AB  - genomes, only a few of the EcoRI, HinfI, and MboI sites (which overlapped the ihf sites)
AB  - remained cleavable after prior methylation with the cognate M.EcoRI, M.HinfI, or Dam
AB  - methyltransferases in the presence of IHF. Thus, IHF-AC essentially converted these enzymes
AB  - into very rare cutters. The extent of cleavage could be controlled by varying the IHF:DNA
AB  - ratio and temperature. Moreover, the method permits the genomic location and strength of the
AB  - ihf sites to be determined.
ER  -

TY  - JOUR
AU  - Kurakin, A.V.
AU  - Zaritskaya, L.S.
AU  - Metliskaya, A.Z.
AU  - Volodin, A.A.
AU  - Cherny, D.I.
TI  - BspRI methyltransferase as a marker for electron microscopic physical mapping.
JO  - Micron and Microscopica Acta
PY  - 1991
SP  - 213
EP  - 221
VL  - 22
AB  - An approach is described in this paper for direct physical mapping of DNA by
AB  - electron microscopy.  It implies visualization of specific
AB  - DNA-methyltransferase complexes followed by computer analysis of electron
AB  - micrographs.  The BspRI methylase (recognition site GGCC) was used as a marker
AB  - owing to the large difference (at least three orders of magnitude) between its
AB  - specific and non-specific interaction with DNA, as revealed by the gel
AB  - retardation technique.  For electron microscopic mapping the optimum conditions
AB  - were established in order to produce the maps practically without non-specific
AB  - noise.  The approach was tested with well-characterized plasmid DNAs-pA03,
AB  - pUC19 and pBR322 carrying 4,11 and 22 GGCC sites respectively. The results were
AB  - analyzed and the applications of the method are discussed.
ER  -

TY  - JOUR
AU  - Kurata, A.
AU  - Hirose, Y.
AU  - Misawa, N.
AU  - Hurunaka, K.
AU  - Kishimoto, N.
TI  - Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1.
JO  - Genome Announcements
PY  - 2014
SP  - e01051
EP  - e01014
VL  - 2
AB  - Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium,  Bacillus
AB  - amyloliquefaciens CMW1, which is newly isolated from a Japanese
AB  - fermented soybean paste. The genome sequence will allow for a characterization of
AB  - the molecular mechanism of its ionic liquid tolerance.
ER  -

TY  - JOUR
AU  - Kurata, A.
AU  - Nishimura, M.
AU  - Kishimoto, N.
AU  - Kobayashi, T.
TI  - Draft Genome Sequence of a Deep-Sea Bacterium, Bacillus niacini Strain JAM F8, Involved in the Degradation of Glycosaminoglycans.
JO  - Genome Announcements
PY  - 2014
SP  - e00983
EP  - e00914
VL  - 2
AB  - Here, we report the draft genome sequence of Bacillus niacini JAM F8, which was newly isolated
AB  - from deep-sea sediment at a depth of 2,759 m from the
AB  - Izu-Ogasawara Trench. An array of genes related to degradation of
AB  - glycosaminoglycans in this bacterium was identified by whole-genome analysis.
ER  -

TY  - JOUR
AU  - Kurilshikov, A.M.
AU  - Fomenko, N.V.
AU  - Stronin, O.V.
AU  - Tikunov, A.Y.
AU  - Kabilov, M.R.
AU  - Tupikin, A.E.
AU  - Tikunova, N.V.
TI  - Complete Genome Sequencing of Borrelia valaisiana and Borrelia afzelii Isolated from Ixodes persulcatus Ticks in Western Siberia.
JO  - Genome Announcements
PY  - 2014
SP  - e01315
EP  - e01314
VL  - 2
AB  - Lyme disease, caused by bacteria of the Borrelia burgdorferi sensu lato complex,  is the most
AB  - frequent tick-borne infection in Eurasia. Here, we report the
AB  - complete genome sequence of the Borrelia valaisiana Tom 4006 and Borrelia afzelii
AB  - Tom 3107 strains isolated from Ixodes persulcatus ticks in western Siberia.
ER  -

TY  - JOUR
AU  - Kurilung, A.
AU  - Keeratipusana, C.
AU  - Suriyaphol, P.
AU  - Prapasarakul, N.
TI  - Draft Genome Sequence of a Leptospira interrogans Strain Isolated from the Urine  of an Asymptomatic Dog in Thailand.
JO  - Genome Announcements
PY  - 2018
SP  - e01140
EP  - e01117
VL  - 6
AB  - In 2014, Leptospira interrogans strain CUDO8 was isolated from the urine of an asymptomatic
AB  - dog in Thailand. Here we report the draft genome sequence of this
AB  - pathogenic bacterium.
ER  -

TY  - JOUR
AU  - Kuroda, M. et al.
TI  - Whole genome sequencing of meticillin-resistant Staphylococcus aureus.
JO  - Lancet
PY  - 2001
SP  - 1225
EP  - 1240
VL  - 357
AB  - Staphylococcus aureus is one of the major causes of community-acquired and hospital-acquired
AB  - infections.  It produces numerous toxins including superantigens that cause unique disease
AB  - entities such as toxic-shock syndrome and staphylococcal scarlet fever, and has acquired
AB  - resistance to practically all antibiotics.  Whole genome analysis is a necessary step towards
AB  - future development of countermeasures against this organism.
ER  -

TY  - JOUR
AU  - Kuroda, M.
AU  - Ayano, H.
AU  - Sei, K.
AU  - Yamashita, M.
AU  - Ike, M.
TI  - Draft Genome Sequence of Bacillus selenatarsenatis SF-1T, a Promising Agent for Bioremediation of Environments Contaminated with Selenium and Arsenic.
JO  - Genome Announcements
PY  - 2015
SP  - e01466
EP  - e01414
VL  - 3
AB  - Bacillus selenatarsenatis sp. nov. strain SF-1(T) is a promising agent for bioremediation of
AB  - environments contaminated with selenium and arsenic. Here, we
AB  - report the draft genome sequence of this strain.
ER  -

TY  - JOUR
AU  - Kuroda, M.
AU  - Ogata, Y.
AU  - Yahara, T.
AU  - Yokoyama, T.
AU  - Ishizawa, H.
AU  - Takada, K.
AU  - Inoue, D.
AU  - Sei, K.
AU  - Ike, M.
TI  - Draft Genome Sequence of Sphingobium fuliginis OMI, a Bacterium That Degrades Alkylphenols and Bisphenols.
JO  - Genome Announcements
PY  - 2017
SP  - e01323
EP  - e01317
VL  - 5
AB  - Sphingobium fuliginis OMI is a bacterium that can degrade a variety of recalcitrant
AB  - alkylphenols and bisphenols. This study reports the draft genome
AB  - sequence of S. fuliginis OMI.
ER  -

TY  - JOUR
AU  - Kuroda, M.
AU  - Yamashita, A.
AU  - Hirakawa, H.
AU  - Kumano, M.
AU  - Morikawa, K.
AU  - Higashide, M.
AU  - Maruyama, A.
AU  - Inose, Y.
AU  - Matoba, K.
AU  - Toh, H.
AU  - Kuhara, S.
AU  - Hattori, M.
AU  - Ohta, T.
TI  - Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 13272
EP  - 13277
VL  - 102
AB  - Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from young
AB  - female outpatients presenting with uncomplicated
AB  - urinary tract infections. We sequenced the whole genome of S.
AB  - saprophyticus type strain ATCC 15305, which harbors a circular chromosome
AB  - of 2,516,575 bp with 2,446 ORFs and two plasmids. Comparative genomic
AB  - analyses with the strains of two other species, Staphylococcus aureus and
AB  - Staphylococcus epidermidis, as well as experimental data, revealed the
AB  - following characteristics of the S. saprophyticus genome. S. saprophyticus
AB  - does not possess any virulence factors found in S. aureus, such as
AB  - coagulase, enterotoxins, exoenzymes, and extracellular matrix-binding
AB  - proteins, although it does have a remarkable paralog expansion of
AB  - transport systems related to highly variable ion contents in the urinary
AB  - environment. A further unique feature is that only a single ORF is
AB  - predictable as a cell wall-anchored protein, and it shows positive
AB  - hemagglutination and adherence to human bladder cell associated with
AB  - initial colonization in the urinary tract. It also shows significantly
AB  - high urease activity in S. saprophyticus. The uropathogenicity of S.
AB  - saprophyticus can be attributed to its genome that is needed for its
AB  - survival in the human urinary tract by means of novel cell wall-anchored
AB  - adhesin and redundant uro-adaptive transport systems, together with
AB  - urease.
ER  -

TY  - JOUR
AU  - Kurokawa, S.
AU  - Bessho, Y.
AU  - Higashijima, K.
AU  - Shirouzu, M.
AU  - Yokoyama, S.
AU  - Watanabe, K.I.
AU  - Ohama, T.
TI  - Adaptation of intronic homing endonuclease for successful horizontal transmission.
JO  - FEBS J.
PY  - 2005
SP  - 2487
EP  - 2496
VL  - 272
AB  - Group I introns are thought to be self-propagating mobile elements, and are distributed over a
AB  - wide range of organisms through horizontal
AB  - transmission. Intron invasion is initiated through cleavage of a target
AB  - DNA by a homing endonuclease encoded in an open reading frame (ORF)
AB  - found within the intron. The intron is likely of no benefit to the host
AB  - cell and is not maintained over time, leading to the accumulation of
AB  - mutations after intron invasion. Therefore, regular invasional
AB  - transmission of the intron to a new species at least once before its
AB  - degeneration is likely essential for its evolutionary long-term
AB  - existence. In many cases, the target is in a protein-coding region
AB  - which is well conserved among organisms, but contains ambiguity at the
AB  - third nucleotide position of the codon. Consequently, the homing
AB  - endonuclease might be adapted to overcome sequence polymorphisms at the
AB  - target site. To address whether codon degeneracy affects horizontal
AB  - transmission, we investigated the recognition properties of a homing
AB  - enzyme, I-CsmI, that is encoded in the intronic ORF of a group I intron
AB  - located in the mitochondrial COB gene of the unicellular green alga
AB  - Chlamydomonas smithii. We successfully expressed and purified three
AB  - types of N-terminally truncated I-CsmI polypeptides, and assayed the
AB  - efficiency of cleavage for 81 substrates containing single nucleotide
AB  - substitutions. We found a slight but significant tendency that I-CsmI
AB  - cleaves substrates containing a silent or tolerated amino acid change
AB  - more efficiently than nonsilent or nontolerated ones. The published
AB  - recognition properties of I-SpomI, I-ScaI, and I-SceII were
AB  - reconsidered from this point of view, and we detected proficient
AB  - adaptation of I-SpomI, I-ScaI, and I-SceII for target site sequence
AB  - degeneracy. Based on the results described above, we propose that
AB  - intronic homing enzymes are adapted to cleave sequences that might
AB  - appear at the target region in various species, however, such
AB  - adaptation becomes less prominent in proportion to the time elapsed
AB  - after intron invasion into a new host.
ER  -

TY  - JOUR
AU  - Kurokawa, S.
AU  - Kabayama, J.
AU  - Nho, S.W.
AU  - Hwang, S.D.
AU  - Hikima, J.
AU  - Jung, T.S.
AU  - Kondo, H.
AU  - Hirono, I.
AU  - Takeyama, H.
AU  - Aoki, T.
TI  - Whole-Genome Sequence of Fish-Pathogenic Mycobacterium sp. Strain 012931, Isolated from Yellowtail (Seriola quinqueradiata).
JO  - Genome Announcements
PY  - 2013
SP  - e00534
EP  - e00513
VL  - 1
AB  - The genus Mycobacterium comprises a large number of well-characterized species, several of
AB  - which are human and animal pathogens. Here, we report the whole-genome
AB  - sequence of Mycobacterium sp. strain 012931, a fish pathogen responsible for huge
AB  - losses in aquaculture farms in Japan. The strain was isolated from a marine fish,
AB  - yellowtail (Seriola quinqueradiata).
ER  -

TY  - JOUR
AU  - Kuroyedov, A.A.
AU  - Grokhovsky, S.L.
AU  - Zhuze, A.L.
AU  - Nosikov, V.V.
AU  - Polyanovsky, O.L.
TI  - Distamycin A and its analogs as agents for blocking of endo R. EcoRI activity.
JO  - Gene
PY  - 1977
SP  - 389
EP  - 395
VL  - 1
AB  - Distamycin A (Dst) and its analogs protect the lambda phage DNA from cleavage
AB  - with endoR. EcoRI and show selective affinity for different recognition sites
AB  - of endoR. EcoRI on this DNA producing enlarged DNA fragments of various
AB  - composition and length.  The affinity of the antibiotic for DNA is influenced
AB  - by the number of pyrrol carboxamide units in Dst molecule and does not strongly
AB  - depend on the substitution of the N-methyl group by the N-propyl one.  Since in
AB  - the complex with DNA the antibiotics of the Dst type are localized in its minor
AB  - groove a conclusion can be made that the minor groove of DNA is needed for the
AB  - interaction of the restriction endonuclease with DNA.
ER  -

TY  - JOUR
AU  - Kurpiewski, M.R.
AU  - Engler, L.E.
AU  - Wozniak, L.A.
AU  - Kobylanska, A.
AU  - Koziolkiewicz, M.
AU  - Stec, W.J.
AU  - Jen-Jacobson, L.
TI  - Mechanisms of Coupling between DNA Recognition Specificity and Catalysis in EcoRI Endonuclease.
JO  - Structure
PY  - 2004
SP  - 1775
EP  - 1788
VL  - 12
AB  - Proteins that bind to specific sites on DNA often do so in order to carry out catalysis or
AB  - specific protein-protein interaction while bound to the
AB  - recognition site. Functional specificity is enhanced if this second
AB  - function is coupled to correct DNA site recognition. To analyze the
AB  - structural and energetic basis of coupling between recognition and
AB  - catalysis in EcoRI endonuclease, we have studied stereospecific
AB  - phosphorothioate (P(S)) or methylphosphonate (P(Me)) substitutions at the
AB  - scissile phosphate GpAATTC or at the adjacent phosphate GApATTC in
AB  - combination with molecular-dynamics simulations of the catalytic center
AB  - with bound Mg(2+). The results show the roles in catalysis of individual
AB  - phosphoryl oxygens and of DNA distortion and suggest that a "crosstalk
AB  - ring" in the complex couples recognition to catalysis and couples the two
AB  - catalytic sites to each other.
ER  -

TY  - JOUR
AU  - Kurpiewski, M.R.
AU  - Koziolkiewicz, M.
AU  - Wilk, A.
AU  - Stec, W.J.
AU  - Jen-Jacobson, L.
TI  - Chiral phosphorothioates as probes of protein interactions with individual DNA phosphoryl oxygens:  Essential interactions of EcoRI endonuclease with the phosphate at pGAATTC.
JO  - Biochemistry
PY  - 1996
SP  - 8846
EP  - 8854
VL  - 35
AB  - The contact between EcoRI endonuclease and the "primary clamp" phosphate of its recognition
AB  - site pGAATTC is absolutely required for recognition of the canonical and all variant DNA
AB  - sites.  We have probed this contact using oligonucleotides containing the single
AB  - stereospecific (Rp)- or (Sp)- phosphorothioates.  At the GAApTTC position, where the
AB  - endonuclease interacts with only one phosphoryl oxygen at the central DNA kink, Rp-Ps inhibits
AB  - and Sp-Ps stimulates binding and cleavage; in contrast, at the pGAATTC position both
AB  - diastereomers inhibit binding.  For single-strand substitution, the penalty in binding free
AB  - energy (delta delta Go bind) is slightly greater for Sp-Ps (+0.9 kcal/mol) than for Rp-Ps
AB  - (+0.7 kcal/mol).  Binding penalties are approximately additive for double-strand substitution
AB  - (Rp,Rp-Ps or Sp,Sp-Ps).  Neither Ps diastereomer in one DNA strand affects the first-order
AB  - rate constants for cleavage in the unmodified DNA strand, and only Sp-Ps inhibits the cleavage
AB  - rate constant (3-fold) in the modified DNA strand.  Thus, the second-order cleavage rate
AB  - (including binding and catalysis) is inhibited 14-fold by Sp-Ps and 45-fold by Sp,Sp-Ps.  In
AB  - the canonical complex, the phosphate at pGAATTC is completely surrounded by protein and each
AB  - nonbridging phosphoryl oxygen receives two hydrogen bonds from the endonuclease, such that in
AB  - either orientation the increased bond length of P-S- inhibits binding.  However, the pro-Sp
AB  - oxygen interacts with residues that are connected (by proximity or inter-side-chain hydrogen
AB  - bonding) to side chains with essential roles in catalysis, so cleavage is preferentially
AB  - inhibited when these side chains are slightly displaced by the Sp-Ps diastereomer.
ER  -

TY  - JOUR
AU  - Kurth, D.
AU  - Romero, C.M.
AU  - Fernandez, P.M.
AU  - Ferrero, M.A.
AU  - Martinez, M.A.
TI  - Draft Genome Sequence of Achromobacter sp. Strain AR476-2, Isolated from a Cellulolytic Consortium.
JO  - Genome Announcements
PY  - 2016
SP  - e00587
EP  - e00516
VL  - 4
AB  - Achromobacter sp. AR476-2 is a noncellulolytic strain previously isolated from a  cellulolytic
AB  - consortium selected from samples of insect gut. Its genome sequence
AB  - could contribute to the unraveling of the complex interaction of microorganisms
AB  - and enzymes involved in the biodegradation of lignocellulosic biomass in nature.
ER  -

TY  - JOUR
AU  - Kurylo, C.M.
AU  - Alexander, N.
AU  - Dass, R.A.
AU  - Parks, M.M.
AU  - Altman, R.A.
AU  - Vincent, C.T.
AU  - Mason, C.E.
AU  - Blanchard, S.C.
TI  - Genome sequence and analysis of Escherichia coli MRE600, a colicinogenic, nonmotile strain that lacks RNase I and the type I methyltransferase, EcoKI.
JO  - Genome Biol. Evol.
PY  - 2016
SP  - 742
EP  - 752
VL  - 8
AB  - Escherichia coli strain MRE600 was originally identified for its low RNase I
AB  - activity and has therefore been widely adopted by the biomedical research
AB  - community as a preferred source for the expression and purification of transfer
AB  - RNAs and ribosomes. Despite its widespread use, surprisingly little information
AB  - about its genome or genetic content exists. Here, we present the first de novo
AB  - assembly and description of the MRE600 genome and epigenome. To provide context
AB  - to these studies of MRE600, we include comparative analyses with E. coli K-12
AB  - MG1655 (K12). Pacific Biosciences Single Molecule, Real-Time (SMRT) sequence
AB  - reads were assembled into one large chromosome (4.83 Mb) and three smaller
AB  - plasmids (89.1 kb, 56.9 kb, and 7.1 kb). Interestingly, the 7.1 kb plasmid
AB  - possesses genes encoding a colicin E1 protein and its associated immunity
AB  - protein. The MRE600 genome has a G+C content of 50.8% and contains a total of
AB  - 5181 genes, including 4913 protein-encoding genes and 268 RNA genes. We
AB  - identified 41,469 modified DNA bases (0.83% of total) and found that MRE600 lacks
AB  - the gene for type I methyltransferase, EcoKI. Phylogenetic, taxonomic, and
AB  - genetic analyses demonstrate that MRE600 is a divergent E. coli strain that
AB  - shares features of the closely related genus, Shigella. Nevertheless, comparative
AB  - analyses between MRE600 and E. coli K12 show that these two strains exhibit
AB  - nearly identical ribosomal proteins, ribosomal RNAs, and highly homologous tRNA
AB  - species. Substantiating prior suggestions that MRE600 lacks RNase I activity, the
AB  - RNase I-encoding gene, rna, contains a single premature stop codon early in its
AB  - open reading frame.
ER  -

TY  - JOUR
AU  - Kusano, K.
AU  - Asami, Y.
AU  - Fujita, A.
AU  - Tanokura, M.
AU  - Kobayashi, I.
TI  - Type I restriction enzyme with RecA protein promotes illegitimate recombination.
JO  - Plasmid
PY  - 2003
SP  - 202
EP  - 212
VL  - 50
AB  - Illegitimate (non-homologous) recombination requires little or no sequence homology between
AB  - recombining DNAs and has been regarded as being a process
AB  - distinct from homologous recombination, which requires a long stretch of
AB  - homology between recombining DNAs. However, we have found a type of
AB  - illegitimate recombination that requires an interaction between long
AB  - homologous DNA sequences. It was detected when a plasmid that carried
AB  - 2-kb-long inverted repeats was subjected to type I (EcoKI) restriction in
AB  - vivo within a special mutant strain of Escherichia coli. In the present
AB  - work, we analyzed genetic requirements for this type of illegitimate
AB  - recombination in well-defined genetic backgrounds. Our analysis
AB  - demonstrated dependence on RecA function and on the presence of two EcoKI
AB  - sites on the substrate DNA. These results are in harmony with a model in
AB  - which EcoKI restriction enzyme attacks an intermediate of homologous
AB  - recombination to divert it to illegitimate recombination.
ER  -

TY  - JOUR
AU  - Kusano, K.
AU  - Naito, T.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Restriction-modification systems as genomic parasites in competition for specific sequences.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1995
SP  - 11095
EP  - 11099
VL  - 92
AB  - Restriction-modification (RM) systems are believed to have evolved to protect cells from
AB  - foreign DNA.  However, this hypothesis may not be sufficient to explain the diversity and
AB  - specificity in sequence recognition, as well as other properties, of these systems.  We report
AB  - that the EcoRI restriction endonuclease-modification methylase (rm) gene pair stabilizes
AB  - plasmids that carry it and that this stabilization is blocked by an RM of the same sequence
AB  - specificity (EcoRI or its isoschizomer, RsrI) but not by an RM of a different specificity
AB  - (PaeR7I) on another plasmid.  The PaeR7I rm likewise stabilizes plasmids, unless an rm gene
AB  - pair with identical sequence specificity is present.  Our analysis supports the following
AB  - model for stabilization and incompatibility: the descendants of cells that have lost an rm
AB  - gene pair expose the recognition sites in their chromosomes to lethal attack by any remaining
AB  - restriction enzymes unless modification by another RM system of the same specificity protects
AB  - these sites.  Competition for specific sequences among these selfish genes may have generated
AB  - the great diversity and specificity in sequence recognition among RM systems.  Such altruistic
AB  - suicide strategies, similar to those found in virus-infected cells, may have allowed selfish
AB  - RM systems to spread by effectively competing with other selfish genes.
ER  -

TY  - JOUR
AU  - Kusano, K.
AU  - Sakagami, K.
AU  - Yokochi, T.
AU  - Naito, T.
AU  - Tokinaga, Y.
AU  - Euda, E.
AU  - Kobayashi, I.
TI  - A new type of illegitimate recombination is dependent on restriction and homologous interaction.
JO  - J. Bacteriol.
PY  - 1997
SP  - 5380
EP  - 5390
VL  - 179
AB  - Illegitimate (nonhomologous) recombination requires little or no sequence homology between
AB  - recombining DNAs and has been regarded as being a process distinct from homologous
AB  - recombination, which requires a long stretch of homology between recombining DNAs.  Under
AB  - special conditions in Escherichia coli, we have found a new type of illegitimate recombination
AB  - that requires an interaction between homologous DNA sequences.  It was detected when a plasmid
AB  - that carried 2-kb-long inverted repeats was subjected to type II restriction in vitro and type
AB  - I (EcoKI) restriction in vivo within a delta-rac recBC recG ruvC strain.  Removal of one of
AB  - the repeats or its replacement with heterologous DNA resulted in a reduction in the level of
AB  - recombination.  The recombining sites themselves shared, at most a few base pairs of homology.
AB  - Many of the recombination events joined a site in one of the repeats with a site in another
AB  - repeat.  In two of the products, one of the recombining sites was at the end of one of the
AB  - repeats.  Removal of one of the EcoKI sites resulted in decreased recombination.  We discuss
AB  - the possibility that some structure made by homologous interaction between the long repeats is
AB  - used by the EcoKI restriction enzyme to promote illegitimate recombination.  The possible
AB  - roles and consequences of this type of homologous interaction are discussed.
ER  -

TY  - JOUR
AU  - Kusiak, M.
AU  - Price, C.
AU  - Rice, D.
AU  - Hornby, D.P.
TI  - The HsdS polypeptide of the Type IC restriction enzyme EcoR124 is a sequence-specific DNA-binding protein.
JO  - Mol. Microbiol.
PY  - 1992
SP  - 3251
EP  - 3256
VL  - 6
AB  - The HsdS and HsdM polypeptides of the type IC restriction enzyme EcoR124 have been purified
AB  - independently and used in a set of gel retardation experiments to determine the minimum
AB  - requirements for sequence-specific recognition of DNA by this enzyme. The HsdS polypeptide
AB  - alone is able to bind to DNA in a sequence-specific manner. In addition, whilst the presence
AB  - of the HsdM polypeptide gives rise to a stimulation of DNA binding by the HsdS subunit it is
AB  - not clear whether, under the conditions of the experiments reported here, the HsdS subunit
AB  - maintains the same interactions with the HsdM subunits observed in the absence of DNA.
ER  -

TY  - JOUR
AU  - Kuspa, A.
AU  - Loomis, W.F.
TI  - Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 8803
EP  - 8807
VL  - 89
AB  - Introduction of restriction enzyme along with linearized plasmid results in integration of
AB  - plasmid DNA at genomic restriction sites in a high proportion of the resulting transformants.
AB  - We have found that electroporating BamHI or EcoRI together with pyr5-6 plasmids cut with the
AB  - same enzyme stimulates the efficiency of transformation in Dictyostelium discoideum more than
AB  - 20-fold over the rate seen when plasmid DNA alone is introduced. Restriction enzyme-mediated
AB  - integration generates insertions into genomic restriction sites in an apparently random
AB  - manner, some of which cause mutations. About 1 in 400 of the Dictyostelium transformants
AB  - displayed arrested or aberrant development. The integrated plasmid, along with flanking
AB  - genomic DNA, was excised from some of these mutants, cloned in Escherichia coli, and used to
AB  - transform other Dictyostelium cells. Homologous recombination within the flanking sequences
AB  - resulted in the same phenotypes displayed by the original mutants, directly demonstrating that
AB  - the affected genes were responsible for the specific morphological phenotypes. This method of
AB  - insertional mutagenesis should be useful for tagging, and subsequent cloning, of many
AB  - developmentally important genes that can be identified by their mutant phenotypes.
ER  -

TY  - JOUR
AU  - Kusumoto, M.
AU  - Fukamizu, D.
AU  - Ogura, Y.
AU  - Yoshida, E.
AU  - Yamamoto, F.
AU  - Iwata, T.
AU  - Ooka, T.
AU  - Akiba, M.
AU  - Hayashi, T.
TI  - The lineage-specific distribution of IS-excision enhancer in enterotoxigenic Escherichia coli isolated from swine.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 1394
EP  - 1402
VL  - 80
AB  - Insertion sequences (ISs) are the simplest transposable elements and are widely distributed in
AB  - bacteria; however, they also play important roles in genome evolution. We recently identified
AB  - a protein called IS-excision enhancer (IEE) in enterohemorrhagic Escherichia coli (EHEC) O157.
AB  - IEE promotes the excision of IS elements belonging to the IS3 family, such as IS629, as well
AB  - as several other families. IEE-mediated IS excision
AB  - generates various genomic deletions that lead to the diversification of the bacterial genome.
AB  - IEE has been found in a broad range of bacterial species; however, among sequenced E. coli
AB  - strains, IEE is primarily found in EHEC isolates. In this study, we investigated non-EHEC
AB  - pathogenic E. coli strains isolated from domestic animals and found that IEE is distributed in
AB  - specific lineages of enterotoxigenic E. coli (ETEC) strains of serotypes O139
AB  - or O149 isolated from swine. The iee gene is located within integrative elements that are
AB  - similar to SpLE1 of EHEC O157. All iee-positive ETEC lineages also contained multiple copies
AB  - of IS629, a preferred substrate of IEE, and their genomic locations varied significantly
AB  - between strains, as observed in O157. These data suggest that IEE may have been transferred
AB  - among EHEC and ETEC in swine via SpLE1 or SpLE1-like integrative
AB  - elements. In addition, IS629 is actively moving in the ETEC O139 and O149 genomes, and as in
AB  - EHEC O157, is promoting the diversification of these genomes in combination with IEE.
ER  -

TY  - JOUR
AU  - Kutish, G.F.
AU  - Li, Y.
AU  - Lu, Z.
AU  - Furuta, M.
AU  - Rock, D.L.
AU  - Van Etten, J.L.
TI  - Analysis of 76 kb of the Chlorella virus PBCV-1 330-kb genome: Map positions 182 to 258.
JO  - Virology
PY  - 1996
SP  - 303
EP  - 317
VL  - 223
AB  - Analysis of 76 kb of newly sequencing DNA, located between map positions 182 and 258 kb in the
AB  - 330-kb chlorella virus PBCV-1 genome, revealed 175 open reading frames of 65 codons or longer.
AB  - One hundred and five of these 175 ORFs were considered major ORFs.  Twenty-one of the 105
AB  - major ORFs resembled proteins in databases including ribonucleotide reductase small subunit,
AB  - RNase III, thioredoxin, glutaredoxin, protein disulfide isomerase, deoxynucleoside kinase,
AB  - frog virus 3 ATPase, Acetobacter cellulose synthase, a bacteriophage encoded endonuclease, and
AB  - two C-5 cytosine DNA methyltransferases.  One of the ORFs was the PBCV-1 major capsid protein.
AB  - The 105 major ORFs were evenly distributed along the genome.  One set of ORFs was separated by
AB  - 543 nucleotides whereas 75 of the ORFs were separated by fewer than 100 nucleotides.  Nineteen
AB  - of the 175 ORFs resembled other PBCV-1 ORFs, suggesting that they represent either gene
AB  - duplications or gene families.
ER  -

TY  - JOUR
AU  - Kutter, E.
AU  - Rueger, W.
TI  - Structure, organization, and manipulation of the genome.
JO  - Bacteriophage T4
PY  - 1983
SP  - 277
EP  - 290
VL  - 0
AB  - Recent analysis of T4 transcription patterns, gene sequences, origins of replication, and
AB  - related data have taken advantage of the extensive restriction mapping of T4 and its
AB  - correlation with the genetic map.  Here we summarize the current data, including the locations
AB  - of those genes and specific transcripts that have now been mapped to within a few hundred base
AB  - pairs.  This is a continuing project; therefore, any additional sequence data, clone analyses,
AB  - and promoter mapping data will be greatly appreciated by the authors.  Sequence data should
AB  - also be submitted to the T4 sequence bank being maintained by Larry Gold, University of
AB  - Colorado, Boulder, Colo. 80309.
ER  -

TY  - JOUR
AU  - Kutter, E.
AU  - Stidham, T.
AU  - Guttman, B.
AU  - Kutter, E.
AU  - Batts, D.
AU  - Peterson, S.
AU  - Javakhishvili, T.D.
AU  - Arisaka, F.
AU  - Mesyanzhinov, V.
AU  - Rueger, W.
AU  - Mosig, G.
TI  - Genomic map of bacteriophage T4.
JO  - Molecular Biology of Bacteriophage T4
PY  - 1994
SP  - 491
EP  - 519
VL  - 0
AB  - The map presented here is based on the T4 DNA sequence, integrated with information from
AB  - genetic analysis.  In general, the results agree well with those initially determined by
AB  - restriction analysis and the genetic map of Wood and Revel.
ER  -

TY  - JOUR
AU  - Kutueva, L.I.
AU  - Ashapkin, V.V.
AU  - Vanyushin, B.F.
TI  - The methylation pattern of a cytosine DNA-methyltransferase gene in Arabidopsis thaliana plants.
JO  - Biochem. Mol. Biol. Int.
PY  - 1996
SP  - 347
EP  - 353
VL  - 40
AB  - Using a PCR-amplified 5'-end proximal 600-bp fragment and two cDNA clones of cytosine
AB  - DNA-methyltransferase gene of Arabidopsis thaliana as specific probes in hybridization with
AB  - plant DNA samples, hydrolyzed by methylation-sensitive restriction endonucleases HpaII and
AB  - MspI, it has been established that CCGG sites located in the 5'-end proximal part of cytosine
AB  - DNA-methyltransferase gene are highly methylated at internal C and less but detectably
AB  - methylated at external C residues.  On the contrary, all CCGG sites in 3'-terminal half of
AB  - the coding region were found to be unmethylated at both external and internal C residues.  No
AB  - significant differences between methylation patterns of cytosine DNA-methyltransferase gene in
AB  - various organs (leaf, stem, flower) of the Arabidopsis thaliana plant were detected.
ER  -

TY  - JOUR
AU  - Kutumbaka, K.K.
AU  - Han, S.
AU  - Mategko, J.
AU  - Nadala, C.
AU  - Buser, G.L.
AU  - Cassidy, M.P.
AU  - Beldavs, Z.G.
AU  - Weissman, S.J.
AU  - Morey, K.E.
AU  - Vega, R.
AU  - Samadpour, M.
TI  - Draft Genome Sequence of blaNDM-1-Positive Escherichia coli O25b-ST131 Clone Isolated from an Environmental Sample.
JO  - Genome Announcements
PY  - 2014
SP  - e00462
EP  - e00414
VL  - 2
AB  - A multidrug-resistant NDM-1 carbapenamase-producing Escherichia coli sequence type 131 (ST131)
AB  - organism was obtained from vacuum cleaner dust collected from
AB  - the home of a case patient. Here, we report the assembly and annotation of its
AB  - genome.
ER  -

TY  - JOUR
AU  - Kutumbaka, K.K.
AU  - Pasmowitz, J.
AU  - Mategko, J.
AU  - Reyes, D.
AU  - Friedrich, A.
AU  - Han, S.
AU  - Martens-Habbena, W.
AU  - Neal-McKinney, J.
AU  - Janagama, H.K.
AU  - Nadala, C.
AU  - Samadpour, M.
TI  - Draft Genome Sequence of the Beer Spoilage Bacterium Megasphaera cerevisiae Strain PAT 1T.
JO  - Genome Announcements
PY  - 2015
SP  - e01045
EP  - e01015
VL  - 3
AB  - The genus Megasphaera harbors important spoilage organisms that cause beer spoilage by
AB  - producing off flavors, undesirable aroma, and turbidity. Megasphaera  cerevisiae is mainly
AB  - found in nonpasteurized low-alcohol beer. In this study, we  report the draft genome of the
AB  - type strain of the genus, M. cerevisiae strain PAT 1(T).
ER  -

TY  - JOUR
AU  - Kuwahara, H.
AU  - Yuki, M.
AU  - Izawa, K.
AU  - Ohkuma, M.
AU  - Hongoh, Y.
TI  - Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut.
JO  - ISME J.
PY  - 2017
SP  - 766
EP  - 776
VL  - 11
AB  - The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts
AB  - two symbiotic bacteria, 'Candidatus Endomicrobium trichonymphae' and 'Candidatus
AB  - Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the
AB  - latter is almost intracellular but still connected to the outside via a small
AB  - pore. The complete genome of 'Ca. Endomicrobium trichonymphae' has previously
AB  - been reported, and we here present the complete genome of 'Ca. Desulfovibrio
AB  - trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and
AB  - retains biosynthetic pathways for various amino acids and cofactors, which are
AB  - partially complementary to those of 'Ca. Endomicrobium trichonymphae'. An amino
AB  - acid permease gene has apparently been transferred between the ancestors of these
AB  - two symbionts; a lateral gene transfer has affected their metabolic capacity.
AB  - Notably, 'Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize
AB  - hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates
AB  - common in desulfovibrios are pseudogenized or missing. Thus, 'Ca. Desulfovibrio
AB  - trichonymphae' is specialized to consume hydrogen that may otherwise inhibit
AB  - fermentation processes in both T. agilis and 'Ca. Endomicrobium trichonymphae'.
AB  - The small pore may be necessary to take up sulfate. This study depicts a
AB  - genome-based model of a multipartite symbiotic system within a cellulolytic
AB  - protist cell in the termite gut.The ISME Journal advance online publication, 1
AB  - November 2016; doi:10.1038/ismej.2016.143.
ER  -

TY  - JOUR
AU  - Kuwahara, T.
AU  - Ogura, Y.
AU  - Oshima, K.
AU  - Kurokawa, K.
AU  - Ooka, T.
AU  - Hirakawa, H.
AU  - Itoh, T.
AU  - Nakayama-Imaohji, H.
AU  - Ichimura, M.
AU  - Itoh, K.
AU  - Ishifune, C.
AU  - Maekawa, Y.
AU  - Yasutomo, K.
AU  - Hattori, M.
AU  - Hayashi, T.
TI  - The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing.
JO  - DNA Res.
PY  - 2011
SP  - 291
EP  - 303
VL  - 18
AB  - Numerous microbes inhabit the mammalian intestinal track and strongly impact host
AB  - physiology; however, our understanding of this ecosystem remains limited owing to
AB  - the high complexity of the microbial community and the presence of numerous
AB  - non-culturable microbes. Segmented filamentous bacteria (SFBs), which are
AB  - clostridia-related Gram-positive bacteria, are among such non-culturable
AB  - populations and are well known for their unique morphology and tight attachment
AB  - to intestinal epithelial cells. Recent studies have revealed that SFBs play
AB  - crucial roles in the post-natal maturation of gut immune function, especially the
AB  - induction of Th17 lymphocytes. Here, we report the complete genome sequence of
AB  - mouse SFBs. The genome, which comprises a single circular chromosome of 1 620 005
AB  - bp, lacks genes for the biosynthesis of almost all amino acids,
AB  - vitamins/cofactors and nucleotides, but contains a full set of genes for
AB  - sporulation/germination and, unexpectedly, for chemotaxis/flagella-based
AB  - motility. These findings suggest a triphasic lifestyle of the SFB, which
AB  - comprises two types of vegetative (swimming and epicellular parasitic) phases and
AB  - a dormant (spore) phase. Furthermore, SFBs encode four types of flagellin, three
AB  - of which are recognized by Toll-like receptor 5 and could elicit the innate
AB  - immune response. Our results reveal the non-culturability, lifestyle and
AB  - immunostimulation mechanisms of SFBs and provide a genetic basis for the future
AB  - development of the SFB cultivation and gene-manipulation techniques.
ER  -

TY  - JOUR
AU  - Kuwahara, T.
AU  - Yamashita, A.
AU  - Hirakawa, H.
AU  - Nakayama, H.
AU  - Toh, H.
AU  - Okada, N.
AU  - Kuhara, S.
AU  - Hattori, M.
AU  - Hayashi, T.
AU  - Ohnishi, Y.
TI  - Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 14919
EP  - 14924
VL  - 101
AB  - Bacteroides are predominant human colonic commensals, but the principal pathogenic species,
AB  - Bacteroides fragilis (BF), lives closely associated
AB  - with the mucosal surface, whereas a second major species, Bacteroides
AB  - thetaiotaomicron (BT), concentrates within the colon. We find
AB  - corresponding differences in their genomes, based on determination of the
AB  - genome sequence of BF and comparative analysis with BT. Both species have
AB  - acquired two mechanisms that contribute to their dominance among the
AB  - colonic microbiota: an exceptional capability to use a wide range of
AB  - dietary polysaccharides by gene amplification and the capacity to create
AB  - variable surface antigenicities by multiple DNA inversion systems.
AB  - However, the gene amplification for polysaccharide assimilation is more
AB  - developed in BT, in keeping with its internal localization. In contrast,
AB  - external antigenic structures can be changed more systematically in BF.
AB  - Thereby, at the mucosal surface, where microbes encounter continuous
AB  - attack by host defenses, BF evasion of the immune system is favored, and
AB  - its colonization and infectious potential are increased.
ER  -

TY  - JOUR
AU  - Kuzin, A.I.
AU  - Bolesnin, M.I.
AU  - Smolyaninov, V.V.
AU  - Azizbekyan, R.R.
TI  - Site specific restriction endonuclease BtcI from Bacillus thuringiensis var. canadensis.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1989
SP  - 36
EP  - 39
VL  - 0
AB  - Efficiency of bacteriophage Tp4 plating on Bacillus thuringiensis var.
AB  - canadensis H5 (Can) is decreased 10^7-fold as compared with the efficiency of
AB  - plating on Bacillus thuringiensis var. galleriae H5 (Gal).  Bacteriophage Tp4
AB  - having propagated for one cycle in Can cells can be further grown in this
AB  - strain without restriction.  The site specific restriction endonuclease BtcI
AB  - isolated from Bacillus thuringiensis var. canadensis recognises the same
AB  - nucleotide sequence GATC in DNA as recognised by restriction endonuclease
AB  - Sau3AI.
ER  -

TY  - JOUR
AU  - Kuzmanovic, N.
AU  - Pulawska, J.
AU  - Prokic, A.
AU  - Ivanovic, M.
AU  - Zlatkovic, N.
AU  - Gasic, K.
AU  - Obradovic, A.
TI  - Draft Genome Sequences of Agrobacterium nepotum Strain 39/7T and Agrobacterium sp. Strain KFB 330.
JO  - Genome Announcements
PY  - 2015
SP  - e00331
EP  - e00315
VL  - 3
AB  - Tumorigenic strains of Agrobacterium spp. are responsible for crown gall disease  of numerous
AB  - plant species. We present here draft genome sequences of
AB  - nonpathogenic Agrobacterium nepotum strain 39/7(T) (CFBP 7436(T), LMG 26435(T)),
AB  - isolated from crown gall tumor on Prunus cerasifera, and tumorigenic
AB  - Agrobacterium sp. strain KFB 330 (CFBP 8308, LMG 28674), isolated from galls on
AB  - raspberry.
ER  -

TY  - JOUR
AU  - Kuzmin, N.P.
AU  - Fodor, I.
AU  - Baev, A.A.
TI  - A specific endonuclease in Klebsiella pneumoniae OK8.
JO  - Dokl. Akad. Nauk.
PY  - 1977
SP  - 477
EP  - 480
VL  - 236
AB  - None
ER  -

TY  - JOUR
AU  - Kuzmin, N.P.
AU  - Loseva, S.P.
AU  - Belyaeva, R.K.
AU  - Kravets, A.N.
AU  - Solonin, A.S.
AU  - Tanyashin, V.I.
AU  - Baev, A.A.
TI  - Physical and catalytic properties of homogeneous restriction endonuclease EcoRV.
JO  - Mol. Biol. (Mosk)
PY  - 1984
SP  - 166
EP  - 173
VL  - 18
AB  - The characteristics of restriction endonuclease EcoRV, puried earlier to a homogeneous state
AB  - from a superproductive strain constructed in vitro, were determined by gel filtration and
AB  - electrophoresis in polyacrylamide gel under denaturing conditions.  The enzyme has a molecular
AB  - weight of 25,000. Restriction endonuclease EcoRV differs immunologically from the enzymes
AB  - EcoRI and EcoRII.  The catalytic properties of restriction endonuclease EcoRV were determined:
AB  - the dependence of the enzymatic activity on the pH of the medium, the ionic strength of the
AB  - solution, the temperature, and the presence of divalent metal cations (Mn2+, Mg2+, Co2+, Zn2+,
AB  - Ni2+, Cd2+), and organic solvents (glycerol, dimethylsulfoxide, ethanol).  It was found that
AB  - the specificity of EcoRV decreases when divalent magnesium ions are replaced by manganese or
AB  - when organic solvents are added.  The enzyme is capable of digesting "protected" DNAs of
AB  - T-even bacteriophages:  glycosylated and containing 5-hydroxmethylcytosine.  Methylated EcoRV
AB  - DNA of bacteriophage lambda, grown on a strain of E. coli containing an EcoRV
AB  - restriction-modification system, is cleaved by EcoRV on noncanonical cleavage sites under
AB  - conditions of a decrease in the specificity of the enzyme.  The DNA fragments formed upon
AB  - cleavage by EcoRV on noncanonical sites are inserted into canonical EcoRV site of cleavage of
AB  - the vector plasmid pBR322 DNA molecule.
ER  -

TY  - JOUR
AU  - Kuznetsov, B.B.
AU  - Ivanovsky, R.N.
AU  - Keppen, O.I.
AU  - Sukhacheva, M.V.
AU  - Bumazhkin, B.K.
AU  - Patutina, E.O.
AU  - Beletsky, A.V.
AU  - Mardanov, A.V.
AU  - Baslerov, R.V.
AU  - Panteleeva, A.N.
AU  - Kolganova, T.V.
AU  - Ravin, N.V.
AU  - Skryabin, K.G.
TI  - Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides ssp. DG-6.
JO  - J. Bacteriol.
PY  - 2010
SP  - 321
EP  - 322
VL  - 193
AB  - Oscillillochloris trichoides is a mesophilic filamentous photoautotrophic non-sulfur
AB  - diazotrophic bacterium which is capable for carbon dioxide fixation via the reductive pentose
AB  - phosphate cycle and possesses no assimilative sulfate reduction. Here we present the draft
AB  - genome sequence of Oscillillochloris trichoides ssp.DG6, the type strain of the specie, which
AB  - has permitted the prediction of genes for carbon and nitrogen metabolism and light harvesting
AB  - apparatus.
ER  -

TY  - JOUR
AU  - Kuznetsova, S.A.
AU  - Kubareva, E.A.
AU  - Oretskaya, T.S.
AU  - Dolinnaya, N.G.
AU  - Krynetskaya, N.F.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
AU  - Cech, D.
TI  - Interaction between EcoRII restriction/modification enzymes and synthetic DNA fragments. Synthesis of substrates containing a single recognition site.
JO  - Biopol. Kletka
PY  - 1987
SP  - 283
EP  - 289
VL  - 3
AB  - 9-16 membered oligodeoxyribonucleotides forming DNA-duplexes with one EcoRII
AB  - site (native or modified) were synthesized by the block triester method.  The
AB  - modifications involved the replacement of one (or two) cytidine or thymidine
AB  - moieties in duplexes for m5dC or f5dU, respectively.  30-membered DNA-duplex
AB  - was obtained by enzymatic ligation of five overlapping oligonucleotides.  The
AB  - substitutions introduced neither result in any significant destabilization nor
AB  - distort the double helix geometry as is evidenced by the UV- and
AB  - CD-spectroscopy methods.
ER  -

TY  - JOUR
AU  - Kvachadze, L.I.
AU  - Andriashvili, I.A.
AU  - Chanishvili, T.G.
AU  - Arutyunyan, E.E.
AU  - Nikolskaia, I.I.
AU  - Debov, S.S.
TI  - Identification of the system modification-restriction in Staphylococci.
JO  - Vopr. Med. Khim.
PY  - 1985
SP  - 121
EP  - 125
VL  - 31
AB  - A new system of host specificity of DNA, called Sau67 according to the available nomenclature,
AB  - was identified in Staphylococcus aureus 6782 strain by means of cross titration with
AB  - staphylophage 729 considering that the phage exhibited the highly effective absorption
AB  - properties.  A total preparation of Sau67 methylases was isolated using ammonium sulfate
AB  - fractionation.  The enzyme preparation contained methylases of cytosine and adenine, where the
AB  - activity of adenine methylases constituted only 5% of the total methylase activity.  As shown
AB  - by kinetics of methylation a low content of unspecific cellular nucleases was found in the St.
AB  - aureus 6782 strain; these reasons are important for isolation of restricting endonucleases
AB  - containing in the strain.  100 microg of protein of the total enzymatic fraction enabled the
AB  - methylation of the acceptor DNA at a maximal rate within 1.5 hr of incubation in phosphate
AB  - buffer, pH 7.9.  The fraction of cytosine methylases free of adenine methylating activity was
AB  - obtained after chromatography on Sepharose blue with NaCl concentration stepwise gradient.
ER  -

TY  - JOUR
AU  - Kwak, J.
AU  - Jiang, H.
AU  - Kendrick, K.E.
TI  - Transformation using in vivo and in vitro methylation in Streptomyces griseus.
JO  - FEMS Microbiol. Lett.
PY  - 2002
SP  - 243
EP  - 248
VL  - 209
AB  - Streptomyces griseus does not readily take up foreign DNA isolated from other Streptomyces
AB  - species or Escherichia coli, presumably due to its
AB  - unique restriction-modification systems that function as a barrier for
AB  - interspecific DNA transfer. To efficiently transform S. griseus by
AB  - avoiding the restriction barriers, we methylated incoming DNA in vivo
AB  - and in vitro and treated protoplasts with heat prior to transformation.
AB  - Whereas heat treatment of protoplasts or methylation of the E.
AB  - coli-Streptomyces shuttle vectors (pXE4 and pKK1443) did not
AB  - prominently improve the transformation efficiency, HpaII methylation of
AB  - the vectors from any E. coli strains tested in this study highly
AB  - increased the transformation efficiency. The highest transformation
AB  - efficiency was observed when the shuttle vectors were isolated from the
AB  - dam, hsd strain of E. coli (GM161) and methylated by AluI and HpaII
AB  - methyltransferases, and the efficiency was approximately the same as
AB  - that of the vectors from S. griseus. We identified several
AB  - restriction-modification systems that decrease the transformation
AB  - efficiency. This research also led us to understand methylation
AB  - profiles and restriction-modification systems in S. griseus.
ER  -

TY  - JOUR
AU  - Kwak, M.J.
AU  - Jeong, H.
AU  - Madhaiyan, M.
AU  - Lee, Y.
AU  - Sa, T.M.
AU  - Oh, T.K.
AU  - Kim, J.F.
TI  - Genome Information of Methylobacterium oryzae, a Plant-Probiotic Methylotroph in the Phyllosphere.
JO  - PLoS ONE
PY  - 2014
SP  - E106704
EP  - E106704
VL  - 9
AB  - Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the
AB  - environment, and many Methylobacterium species associated with plants produce
AB  - plant growth-promoting substances. To gain insights into the life style at the
AB  - phyllosphere and the genetic bases of plant growth promotion, we determined and
AB  - analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a
AB  - strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and
AB  - four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in
AB  - the chromosome, the bacterium has, besides most of the genes for the central
AB  - metabolism, all of the essential genes for the assimilation and dissimilation of
AB  - methanol that are either located in methylotrophy islands or dispersed. M. oryzae
AB  - is equipped with several kinds of genes for adaptation to plant surfaces such as
AB  - defense against UV radiation, oxidative stress, desiccation, or nutrient
AB  - deficiency, as well as high proportion of genes related to motility and
AB  - signaling. Moreover, it has an array of genes involved in metabolic pathways that
AB  - may contribute to promotion of plant growth; they include auxin biosynthesis,
AB  - cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of
AB  - heavy metals or decrease of metal toxicity, pyrroloquinoline quinone
AB  - biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate
AB  - solubilization, and thiosulfate oxidation. Through the genome analysis of M.
AB  - oryzae, we provide information on the full gene complement of M. oryzae that
AB  - resides in the aerial parts of plants and enhances plant growth. The
AB  - plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant
AB  - growth promotion, and its potential as a candidate for a bioinoculant targeted to
AB  - the phyllosphere and focused on phytostimulation are illuminated.
ER  -

TY  - JOUR
AU  - Kwak, M.J.
AU  - Kwon, S.K.
AU  - Kim, J.F.
TI  - Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 44
EP  - 44
VL  - 12
AB  - Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand
AB  - sediment of a beach in Dokdo, Korea, in 2005. In this study,
AB  - we determined the genome sequence of FR1436, the type strain of N. dokdonensis,
AB  - and analyzed its gene contents. The genome sequence is the second complete one in
AB  - the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a
AB  - 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence,
AB  - 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and
AB  - 71.38% of the genes were assigned putative functions. Through the sequence
AB  - analysis, dozens of genes involved in steroid metabolism, especially its
AB  - degradation, were detected. Most of the identified genes were located in large
AB  - gene clusters, which showed high similarities with the gene clusters in
AB  - Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated
AB  - with steroid catabolism indicate that it could be used for research and
AB  - application of steroids in science and industry.
ER  -

TY  - JOUR
AU  - Kwak, M.J.
AU  - Kwon, S.K.
AU  - Yoon, J.H.
AU  - Kim, J.F.
TI  - Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated  from soil in Dokdo, Korea.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 123
EP  - 123
VL  - 10
AB  - Lysobacter dokdonensis DS-58, belonging to the family Xanthomonadaceae, was isolated from a
AB  - soil sample in Dokdo, Korea in 2011. Strain DS-58 is the type
AB  - strain of L. dokdonensis. In this study, we determined the genome sequence to
AB  - describe the genomic features including annotation information and COG functional
AB  - categorization. The draft genome sequence consists of 25 contigs totaling
AB  - 3,274,406 bp (67.24 % G + C) and contains 3,155 protein coding genes, 2 copies of
AB  - ribosomal RNA operons, and 48 transfer RNA genes. Among the protein coding genes,
AB  - 75.91 % of the genes were annotated with a putative function and 87.39 % of the
AB  - genes were assigned to the COG category. In the genome of L. dokdonensis, a large
AB  - number of genes associated with protein degradation and antibiotic resistance
AB  - were detected.
ER  -

TY  - JOUR
AU  - Kwak, M.J.
AU  - Song, J.Y.
AU  - Kim, S.Y.
AU  - Jeong, H.
AU  - Kang, S.G.
AU  - Kim, B.K.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Yu, D.S.
AU  - Park, S.H.
AU  - Kim, J.F.
TI  - Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4432
EP  - 4433
VL  - 194
AB  - Endophytes live inside plant tissues without causing any harm and may even benefit plants.
AB  - Here, we provide the high-quality genome sequence of Burkholderia
AB  - sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The
AB  - 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains
AB  - genes related to plant growth promotion or degradation of aromatic compounds.
ER  -

TY  - JOUR
AU  - Kwak, Y.
AU  - Li, Q.X.
AU  - Shin, J.H.
TI  - Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated  soil in Hawaii.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 47
EP  - 47
VL  - 11
AB  - Mycobacterium rufum JS14(T) (=ATCC BAA-1377(T), CIP 109273(T), JCM 16372(T), DSM  45406(T)), a
AB  - type strain of the species Mycobacterium rufum sp. . belonging to
AB  - the family Mycobacteriaceae, was isolated from polycyclic aromatic hydrocarbon
AB  - (PAH)-contaminated soil in Hilo (HI, USA) because it harbors the capability of
AB  - degrading PAH. Here, we describe the first genome sequence of strain JS14(T),
AB  - with brief phenotypic characteristics. The genome is composed of 6,176,413 bp
AB  - with 69.25 % G + C content and contains 5810 protein-coding genes with 54 RNA
AB  - genes. The genome information on M. rufum JS14(T) will provide a better
AB  - understanding of the complexity of bacterial catabolic pathways for degradation
AB  - of specific chemicals.
ER  -

TY  - JOUR
AU  - Kwak, Y.
AU  - Park, G.S.
AU  - Shin, J.H.
TI  - High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 51
EP  - 51
VL  - 11
AB  - Pseudomonas lutea OK2(T) (=LMG 21974(T), CECT 5822(T)) is the type strain of the  species and
AB  - was isolated from the rhizosphere of grass growing in Spain in 2003
AB  - based on its phosphate-solubilizing capacity. In order to identify the functional
AB  - significance of phosphate solubilization in Pseudomonas Plant growth promoting
AB  - rhizobacteria, we describe here the phenotypic characteristics of strain OK2(T)
AB  - along with its high-quality draft genome sequence, its annotation, and analysis.
AB  - The genome is comprised of 5,647,497 bp with 60.15 % G + C content. The sequence
AB  - includes 4,846 protein-coding genes and 95 RNA genes.
ER  -

TY  - JOUR
AU  - Kwan, T.
AU  - Liu, J.
AU  - Dubow, M.
AU  - Gros, P.
AU  - Pelletier, J.
TI  - The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 5174
EP  - 5179
VL  - 102
AB  - Bacteriophages are the most abundant life forms in the biosphere. They
AB  - play important roles in bacterial ecology, evolution, adaptation to new
AB  - environments, and pathogenesis of human bacterial infections. Here, we
AB  - report the complete genomic sequences, and predicted proteins of 27
AB  - bacteriophages of the Gram-positive bacterium Staphylococcus aureus.
AB  - Comparative nucleotide and protein sequence analysis indicates that these
AB  - phages are a remarkable source of untapped genetic diversity, encoding
AB  - 2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated
AB  - for structure or function, and 522 are proteins with no similarity to
AB  - other phage or bacterial sequences. Based on their genome size,
AB  - organization of their gene map and comparative nucleotide and protein
AB  - sequence analysis, the S. aureus phages can be organized into three
AB  - groups. Comparison of their gene maps reveals extensive genome mosaicism,
AB  - hinting to a large reservoir of unidentified S. aureus phage genes. Among
AB  - the phages in the largest size class (178-214 kbp) that we characterized
AB  - is phage Twort, the first discovered bacteriophage (responsible for the
AB  - Twort-D'Herelle effect). These phage genomes offer an exciting opportunity
AB  - to discern molecular mechanisms of phage evolution and diversity.
ER  -

TY  - JOUR
AU  - Kwasiborski, A.
AU  - Mondy, S.
AU  - Beury-Cirou, A.
AU  - Faure, D.
TI  - Genome Sequence of the Quorum-Quenching Rhodococcus erythropolis Strain R138.
JO  - Genome Announcements
PY  - 2014
SP  - e00224
EP  - e00214
VL  - 2
AB  - Rhodococcus erythropolis strain R138 was isolated from the rhizosphere of Solanum tuberosum
AB  - and selected for its capacity to degrade N-acyl-homoserine lactones,
AB  - quorum-sensing signals used as communication molecules by the potato pathogens
AB  - Pectobacterium and Dickeya. Here, we report the genome sequence of Rhodococcus
AB  - erythropolis strain R138.
ER  -

TY  - JOUR
AU  - Kwasiborski, A.
AU  - Mondy, S.
AU  - Beury-Cirou, A.
AU  - Faure, D.
TI  - Genome Sequence of the Pectobacterium atrosepticum Strain CFBP6276, Causing Blackleg and Soft Rot Diseases on Potato Plants and Tubers.
JO  - Genome Announcements
PY  - 2013
SP  - e00374
EP  - e00313
VL  - 1
AB  - Pectobacterium atrosepticum strain CFBP6276 is a pectinolytic enterobacterium causing blackleg
AB  - and soft rot of the stem and tuber of Solanum tuberosum. Its
AB  - virulence is under the control of quorum sensing, with N-acylhomoserine lactones
AB  - as communication signals. Here, we report the genome sequence of P. atrosepticum
AB  - strain CFBP6276.
ER  -

TY  - JOUR
AU  - Kwiatek, A.
AU  - Bacal, P.
AU  - Wasiluk, A.
AU  - Trybunko, A.
AU  - Adamczyk-Poplawska, M.
TI  - The dam replacing gene product enhances Neisseria gonorrhoeae FA1090 viability and biofilm formation.
JO  - Front. Microbiol.
PY  - 2014
SP  - 712
EP  - 712
VL  - 5
AB  - Many Neisseriaceae do not exhibit Dam methyltransferase activity and, instead of the dam gene,
AB  - possess drg (dam replacing gene) inserted in the leuS/dam locus. The drg locus in Neisseria
AB  - gonorrhoeae FA1090 has a lower GC-pairs content (40.5%) compared to the whole genome of N.
AB  - gonorrhoeae FA1090 (52%). The gonococcal drg gene encodes a DNA endonuclease Drg, with GmeATC
AB  - specificity. Disruption of drg or insertion of the dam gene in gonococcal genome changes the
AB  - level of expression of genes as shown by transcriptome analysis. For the drg-deficient N.
AB  - gonorrhoeae mutant, a total of 195 (8.94% of the total gene pool) genes exhibited an altered
AB  - expression compared to the wt strain by at least 1.5 fold. In dam-expressing N. gonorrhoeae
AB  - mutant, the expression of 240 genes (11% of total genes) was deregulated. Most of these
AB  - deregulated genes were involved in translation, DNA repair, membrane biogenesis and energy
AB  - production as shown by cluster of orthologous group analysis. In vivo, the inactivation of drg
AB  - gene causes the decrease of the number of live neisserial cells and long lag phase of growth.
AB  - The insertion of dam gene instead of drg locus restores cell viability. We have also shown
AB  - that presence of the drg gene product is important for N. gonorrhoeae FA1090 in adhesion,
AB  - including human epithelial cells, and biofilm formation. Biofilm produced by drg-deficient
AB  - strain is formed by more dispersed cells, compared to this one formed by parental strain as
AB  - shown by scanning electron and confocal microscopy. Also adherence assays show a significantly
AB  - smaller biomass of formed biofilm (OD570 = 0.242 +/- 0.038) for drg-deficient strain, compared
AB  - to wild-type strain (OD570 = 0.378 +/- 0.057). Dam-expressing gonococcal cells produce
AB  - slightly weaker biofilm with cells embedded in an extracellular matrix. This strain has also a
AB  - five times reduced ability for adhesion to human epithelial cells. In this context, the
AB  - presence of Drg is more advantageous for N. gonorrhoeae biology than Dam presence.
ER  -

TY  - JOUR
AU  - Kwiatek, A.
AU  - Kobes, M.
AU  - Olejnik, K.
AU  - Piekarowicz, A.
TI  - DNA methyltransferases from Neisseria meningitidis and Neisseria gonorrhoeae FA1090 associated with mismatch nicking endonucleases.
JO  - Microbiology
PY  - 2004
SP  - 1713
EP  - 1722
VL  - 150
AB  - The genes encoding the DNA methyltransferases M.NmeDI and M.NmeAl from Neisseria meningitidis
AB  - associated with the genes encoding putative Vsr
AB  - endonucleases were overexpressed in Escherichia coli. The enzymes were
AB  - purified to apparent homogeneity on Ni-NTA agarose columns, yielding
AB  - proteins of 49  1 kDa and 39.6  1 kDa, respectively, under
AB  - denaturing conditions. M.NmeDI recognizes the degenerate sequence
AB  - 5'-RCCGGB-3'. It methylates the first 5' cytosine residue on both
AB  - strands within the core sequence CCGG. The enzyme shows higher affinity
AB  - with the hemimethylated degenerate sequence than with the unmethylated
AB  - degenerate sequence. Comparison of the amino acid sequence of the
AB  - target-recognizing domain of M.NmeDI with the closest neighbours
AB  - recognizing the sequence 5'-RCCGGY-3' showed the presence of the
AB  - homologous domain and an additional domain that may be responsible for
AB  - recognizing the degenerate sequence. M.NmeAl recognizes the sequence
AB  - 5'-CCGG-3' and methylates the second 5' cytosine residue on both DNA
AB  - strands. In Neisseria gonorrhoeae strain FA1090 the homologues of these
AB  - ORFs are truncated due to a variety of mutations.
ER  -

TY  - JOUR
AU  - Kwiatek, A.
AU  - Luczkiewicz, M.
AU  - Bandyra, K.
AU  - Stein, D.C.
AU  - Piekarowicz, A.
TI  - Neisseria gonorrhoeae FA1090 encodes two classes of Vsr endonucleases.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3951
EP  - 3960
VL  - 192
AB  - Very Short Patch repair systems prevent mutations resulting from deamination of
AB  - 5-methylcytosine to thymine. The Vsr endonuclease is the key enzyme of this system, providing
AB  - sequence specificity. We identified two genes encoding Vsr endonucleases from Neisseria
AB  - gonorrhoeae FA1090, V.NgoAXIII and V.NgoAXIV, based on DNA sequence similarity to genes
AB  - encoding Vsr endonucleases from other bacteria. After expression of the gonococcal genes in
AB  - Escherichia coli, the proteins were biochemically characterized and the endonucleolytic
AB  - activity and specificity of V.NgoAXIII and V.NgoAXIV were determined. V.NgoAXIII was found to
AB  - be multispecific and recognizes T:G mismatches in every tested nucleotide context whereas
AB  - V.NgoAXIV recognizes T:G mismatches in the following sequences: GTGG, CTGG, GTGC, ATGC or
AB  - CTGC. Alanine mutagenesis of conserved residues showed that Asp50 and His68 of V.NgoAXIII and
AB  - Asp51 and His69 of V.NgoAXIV are essential for hydrolytic activity. Glu25, His64 and Asp97 of
AB  - V.NgoAXIV and Glu24, Asp63 and Asp97 of V.NgoAXIII are important but not crucial for activity
AB  - V.NgoAXIII and V.NgoAXIV. However, Glu24 and Asp63 are also important for the specificity of
AB  - V.NgoAXIII. On the basis of our results, concerning features of Vsr endonucleases encoded by
AB  - N. gonorrhoeae FA1090, we postulate that at least two types of Vsr endonucleases can be
AB  - distinguished.
ER  -

TY  - JOUR
AU  - Kwiatek, A.
AU  - Piekarowicz, A.
TI  - The restriction endonuclease R.NmeDI from Neisseria meningitidis that recognizes a palindromic sequence and cuts the DNA on both sides of the  recognition sequence.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 6539
EP  - 6546
VL  - 35
AB  - The restriction endonuclease Type II R.NmeDI from Neisseria meningitidis 2120 (serogroup C,
AB  - ST-11 complex) was characterized. The cloned nmeDIR
AB  - gene was expressed in Escherichia coli cells, and the endonucleolytic and
AB  - restriction activities of R.NmeDI were then observed in vitro and in vivo.
AB  - The nmeDIR gene consists of 1056 bp coding 351 aa protein with a
AB  - calculated molecular weight of M((r)) = 39 000 +/- 1000 Da. The R.NmeDI
AB  - enzyme was purified to apparent homogeneity following overexpression,
AB  - using metal affinity chromatography. This enzyme recognizes a palindrome
AB  - sequence and cleaves double-stranded DNA upstream and downstream of its
AB  - recognition sequence (12/7) RCCGGY (7/12) (R = A/G, Y = C/T) cutting out a
AB  - 25-bp fragment. R.NmeDI cleaves in two steps. The enzyme cleaves the first
AB  - strand randomly on either side of the recognition sequence generating an
AB  - intermediate, and the second cleavage occurs more slowly and results in
AB  - the production of a final reaction product. The R.NmeDI endonuclease
AB  - requires two recognition sequences for effective cleavage. The tetramer is
AB  - an active form of the R.NmeDI enzyme.
ER  -

TY  - JOUR
AU  - Kwiatkowski, B.
AU  - Boschek, B.
AU  - Thiele, H.
AU  - Stirm, S.
TI  - Substrate specificity of two bacteriophage-associated endo-N-acetylneuraminidases.
JO  - J. Virol.
PY  - 1983
SP  - 367
EP  - 374
VL  - 45
AB  - For Escherichia coli Bos12 (O16:K92:H-), a bacteriophage (phi 92) has been
AB  - isolated which carries a depolymerase active on the K92 capsular polysaccharide.
AB  - As seen under the electron microscope, phi 92 belongs to Bradley's morphology
AB  - group A and is different from the phage phi 1.2 previously described (Kwiatkowski
AB  - et al., J. Virol. 43:697-704, 1982), which grows on E. coli K235 (O1:K1:H-),
AB  - depolymerizes colominic acid, and belongs to morphology group C. The specificity
AB  - of the phi 1.2- and phi 92-associated endo-N-acetylneuraminidases has been
AB  - studied with respect to the following substrates (all alkali treated, and where
AB  - NeuNAc represents N-acetylneuraminic acid): (i) [-alpha-NeuNAc-(2 leads to 8)-]n
AB  - (colominic acid), (ii) [-alpha-NeuNAc-(2 leads to 8)-alpha-NeuNAc-(2 leads to
AB  - 9)-]n (E. coli K92 polysaccharide), and (iii) [-alpha-NeuNAc-(2 leads to 9)-]n
AB  - (Neisseria meningitidis type C capsular polysaccharide). The increase in
AB  - periodate consumption of these glycans upon incubation with purified phi 1.2 or
AB  - phi 92 particles was measured, and the split products obtained from all
AB  - substrates after exhaustive degradation were analyzed by gel chromatography. It
AB  - was found that the Neisseria polysaccharide is not appreciably affected by either
AB  - virus enzyme and that phi 1.2 only depolymerizes a small fraction of the K92
AB  - glycan. Colominic acid, however, is completely degraded by both agents, phi 92
AB  - yielding smaller fragments (one to six NeuNAc residues) than phi 1.2 (two to
AB  - seven). Phage phi 92 additionally depolymerizes the K92 glycan, essentially to
AB  - oligosaccharides of two, four, and six residues. The size distribution of these
AB  - K92 oligosaccharides indicates that the phi 92 enzyme predominantly cleaves the
AB  - alpha(2 leads to 8) linkages in this polymer.
ER  -

TY  - JOUR
AU  - Kwoh, T.J.
AU  - Kwoh, D.Y.
AU  - McCue, A.W.
AU  - Davis, G.R.
AU  - Patrick, D.
AU  - Gingeras, T.R.
TI  - Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1986
SP  - 7713
EP  - 7717
VL  - 83
AB  - An approach is devised for studying the role of DNA methylation in eukaryotic
AB  - gene expression.  The approach is based on the expression of site-specific
AB  - bacterial methylase genes in animal cells.  A model system using the cloned
AB  - PaeR7 (an isoschizomer of XhoI) methylase gene was constructed to test the
AB  - feasibility of this approach.  Expression plasmids for the PaeR7 methylase gene
AB  - were introduced into mouse Ltk- cells by cotransfection with the cloned chicken
AB  - thymidine kinase (tk) gene.  Several of the cell strains derived from Tk+
AB  - colonies were found to express the PaeR7 gene as judged by four criteria:  the
AB  - cellular DNA of these strains showed increased resistance to cleavage by XhoI;
AB  - these strains contained cellular proteins that comigrated with pure PaeR7
AB  - methylase protein, as visualized by immunoblotting; PaeR7 methylase activity
AB  - was found in vitro in crude extracts of total cellular protein from these
AB  - strains; and murine adenovirus genomes grown on cells expressing PaeR7
AB  - methylase showed resistance to cleavage to PaeR7 endonuclease.  The potential
AB  - applications of this approach for the study of cellular and viral gene
AB  - regulation, DNA repair, and restriction modification are discussed.
ER  -

TY  - JOUR
AU  - Kwoh, T.J.
AU  - Obermiller, P.S.
AU  - McCue, A.W.
AU  - Kwoh, D.Y.
AU  - Sullivan, S.A.
AU  - Gingeras, T.R.
TI  - Introduction and expression of the bacterial PaeR7I restriction endonuclease gene in mouse cells containing the PaeR7I methylase.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 11489
EP  - 11506
VL  - 16
AB  - To study the factors essential for a functional restriction system, the PaeR7I
AB  - restriction-modification system has been introduced and expressed in murine
AB  - cells.  Transfer of this system was accomplished in two steps.  First, cells
AB  - containing sufficient PaeR7I methylase to completely methylate the mouse genome
AB  - were constructed.  In the second step, the mouse metallothionein
AB  - promoter-regulated, endonuclease expression vector linked to the hygromycin B
AB  - resistance selection marker was used to transfect the high methylase-expressing
AB  - cells.  Sixty percent of the clones isolated contained PaeR7I endonuclease
AB  - enzymatic activity.  Transfected cells expressing both methylase and
AB  - endonuclease were incapable of blocking infection by DNA viruses, and possible
AB  - explanations are discussed.
ER  -

TY  - JOUR
AU  - Kwok, J.S.
AU  - Ip, M.
AU  - Chan, T.F.
AU  - Lam, W.Y.
AU  - Tsui, S.K.
TI  - Draft Genome Sequence of Clostridium butyricum Strain NOR 33234, Isolated from an Elderly Patient with Diarrhea.
JO  - Genome Announcements
PY  - 2014
SP  - e01356
EP  - e01314
VL  - 2
AB  - Clostridium butyricum is one of the species frequently present in patients' stool samples.
AB  - However, the identification of this species is sometimes difficult.
AB  - Here, we present the draft genome of Clostridium butyricum NOR 33234, which was
AB  - isolated from a patient with suspected Clostridium difficile infection-associated
AB  - diarrhea and resembles Clostridium clostridioforme in biochemical tests.
ER  -

TY  - JOUR
AU  - Kwon, S.K.
AU  - Kim, B.K.
AU  - Song, J.Y.
AU  - Kwak, M.J.
AU  - Lee, C.H.
AU  - Yoon, J.H.
AU  - Oh, T.K.
AU  - Kim, J.F.
TI  - Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis DSW-6 and identification of a novel class of rhodopsins.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 187
EP  - 199
VL  - 5
AB  - Rhodopsin-containing marine microbes such as those in the class Flavobacteria
AB  - play a pivotal role in the biogeochemical cycle of the euphotic zone .
AB  - Deciphering the genome information of flavobacteria and accessing the diversity
AB  - and ecological impact of microbial rhodopsins is important in understanding and
AB  - preserving the global ecosystems. The genome sequence of the orange-pigmented
AB  - marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis)
AB  - DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its
AB  - genome physiological features that allow survival in marine oligotrophic
AB  - environments. The sequence analysis also uncovered a gene encoding an unexpected
AB  - type of microbial rhodopsin containing a unique motif in addition to a
AB  - proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs
AB  - of the novel rhodopsin gene were found in other flavobacteria,
AB  - alphaproteobacteria, a species of cytophaga, a deinococcus, and even a eukaryote
AB  - diatom. They all contain the characteristic NQ motif and form a phylogenetically
AB  - distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated
AB  - that it is induced at high NaCl concentrations, as well as in the presence of
AB  - light and the absence of nutrients. Genomic and metagenomic surveys demonstrate
AB  - the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the
AB  - encoding genes among microbial communities inhabiting hypersaline niches,
AB  - suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.
ER  -

TY  - JOUR
AU  - Kwon, T.
AU  - Cho, S.H.
TI  - Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157 NCCP15739, Isolated in the Republic of Korea.
JO  - Genome Announcements
PY  - 2015
SP  - e00522
EP  - e00515
VL  - 3
AB  - Enterohemorrhagic Escherichia coli (EHEC) is the main cause of the recent outbreaks of
AB  - diarrhea, hemolytic-uremic syndrome (HUS), and hemorrhagic colitis
AB  - worldwide. Herein, we present the draft genome sequence of the NCCP15739 isolate
AB  - from a patient in the Republic of Korea.
ER  -

TY  - JOUR
AU  - Kwon, T.
AU  - Han, S.J.
AU  - Yoo, W.G.
AU  - Yun, M.R.
AU  - Lee, S.
AU  - Lee, J.S.
AU  - Kim, D.W.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0184, Isolated in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e01755
EP  - e01715
VL  - 4
AB  - Here, we describe the draft genome sequence of Mycobacterium tuberculosis KT-0184, from the
AB  - Beijing family. This genome will provide insight into the
AB  - evolution and adaptation of M. tuberculosis KT-0184 in human hosts.
ER  -

TY  - JOUR
AU  - Kwon, T.
AU  - Han, S.J.
AU  - Yoo, W.G.
AU  - Yun, M.R.
AU  - Lee, S.
AU  - Lee, J.S.
AU  - Kim, D.W.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0133, Isolated in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e01731
EP  - e01715
VL  - 4
AB  - Here, we present the draft genome sequence of Mycobacterium tuberculosis KT-0133, which
AB  - belongs to the Korean-Beijing family. This sequence will provide a new
AB  - perspective on the evolution and accommodation of M. tuberculosis KT-0133 in
AB  - human hosts.
ER  -

TY  - JOUR
AU  - Kwon, T.
AU  - Yang, J.W.
AU  - Lee, S.
AU  - Yun, M.R.
AU  - Yoo, W.G.
AU  - Kim, H.S.
AU  - Cha, J.O.
AU  - Kim, D.W.
TI  - Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae KP617, Coproducing OXA-232 and NDM-1 Carbapenemases, Isolated in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e01550
EP  - e01515
VL  - 4
AB  - The prevalence of Klebsiella pneumoniae coproducing carbapenemase metallo-beta-lactamase 1
AB  - (NDM-1) and OXA-48 has been increasing globally since
AB  - 2013. The complete genome of KP617 was sequenced and assembled into a circular
AB  - chromosome and two plasmids. This sequence provides the genetic background for
AB  - understanding the evolution of carbapenemase genes in K. pneumoniae KP617.
ER  -

TY  - JOUR
AU  - Kwon, Y.K.
AU  - Kim, J.J.
AU  - Kim, J.H.
AU  - Jeon, S.M.
AU  - Ye, B.R.
AU  - Jang, J.
AU  - Heo, S.J.
AU  - Park, S.C.
AU  - Kang, D.H.
AU  - Oh, C.
TI  - Draft genome sequence of the xylan-degrading marine bacterium strain s124, representing a novel species of the genus oceanicola.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6325
EP  - 6325
VL  - 194
AB  - We isolated a xylan-degrading bacterium from seawater of Micronesia and identified it as
AB  - Oceanicola sp. strain S124. We sequenced the Oceanicola sp. S124
AB  - genome using GSFLX 454 pyrosequencing and predicted 4,433 open reading frames
AB  - (ORFs) including putative saccharification and phage-related genes.
ER  -

TY  - JOUR
AU  - Kwon, Y.M.
AU  - Kim, S.J.
TI  - Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13.
JO  - Genome Announcements
PY  - 2016
SP  - e01635
EP  - e01615
VL  - 4
AB  - Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we
AB  - present the first complete genome sequence of this genus,
AB  - which consists of 3,569,807 bp with 39.4% GC content. This strain contains
AB  - proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize
AB  - sunlight as an energy source.
ER  -

TY  - JOUR
AU  - Kwon, Y.T.
AU  - Jun, H.S.
AU  - Rho, H.M.
TI  - Characterization of BmaI methylase from Bacillus macerans.
JO  - Korean J. Microbiol.
PY  - 1988
SP  - 88
EP  - 92
VL  - 26
AB  - The isolation and characterization of a new type II methylase, BmaI methylase,
AB  - from Bacillus macerans ATCC 8244 were described.  BmaI methylase was isolated
AB  - by procedures of ammonium sulfate fractionation, DEAE-cellulose chromatography
AB  - and phosphocellulose chromatography.  Two types of methylases were present in
AB  - this strain and only one of the two was a site specific BmaI methylase.  The
AB  - pBR322 DNA methylated by BmaI methylase was not cleaved by BmaI endonuclease,
AB  - and pBR322 DNA cleaved by BmaI endonuclease was not methylated by BmaI
AB  - methylase.  The optimal pH for the BmaI methylase activity was 7.5, and optimal
AB  - NaCl concentration was about 50 mM.  BmaI methylase could methylate
AB  - single-stranded M13mp18 DNA.
ER  -

TY  - JOUR
AU  - Kwon, Y.T.
AU  - Jun, H.S.
AU  - Rho, H.M.
TI  - Characterization of BmaI endonuclease from Bacillus macerans ATCC 8244.
JO  - Korean J. Microbiol.
PY  - 1988
SP  - 1
EP  - 5
VL  - 26
AB  - The isolation and characterization of a new type II restriction endonuclease,
AB  - BmaI, from Bacillus macerans ATCC 8244 were described.  BmaI endonuclease was
AB  - partially purified by procedures of ammonium sulfate fractionation,
AB  - DEAE-cellulose and phosphocellulose chromatographies.  This enzyme recognized
AB  - one site on pBR322 DNA, two sites on Bluescribe DNA, three sites on lambda DNA
AB  - and no site on SV40 DNA.  The same cleavage patterns for various DNAs as PvuI
AB  - indicated that BmaI is an isoschizomer of PvuI whose recognition sequence is
AB  - 5'-CGATCG-3'.  The optimal pH for the BmaI endonuclease activity was about 7.0
AB  - and optimal NaCl concentration was about 100 mM.  Manganese ion could partially
AB  - replace magnesium as a cofactor, but calcium could not at all.
ER  -

TY  - JOUR
AU  - Kwong, S.M.
AU  - Yeo, C.C.
AU  - Suwanto, A.
AU  - Poh, C.L.
TI  - Characterization of the endogenous plasmid from Pseudomonas alcaligenes NCIB 9867: DNA sequence and mechanism of transfer.
JO  - J. Bacteriol.
PY  - 2000
SP  - 81
EP  - 90
VL  - 182
AB  - The endogenous plasmid pRA2 from Pseudomonas alcaligenes NCIB 9867 was determined to have
AB  - 32,743 bp with a G+C content of 59.8%, Sequence
AB  - analysis predicted a total of 29 open reading frames, with
AB  - approximately half of them contributing towards the functions of
AB  - plasmid replication, mobilization, and stability. The Pac25I
AB  - restriction-modification system and two mobile elements, Tn5563 and
AB  - IS1633, were physically localized. An additional eight open reading
AB  - frames with unknown functions were also detected. pRA2 was genetically
AB  - tagged with the Omega Str(r)/Spc(r) gene cassette by homologous
AB  - recombination, Intrastrain transfer of pRA2-encoded genetic markers
AB  - between isogenic mutants of P. alcaligenes NCIB 9867,were observed at
AB  - high frequencies (2.4 x 10(-4) per donor). This transfer aas determined
AB  - to be mediated by a natural transformation process that required
AB  - cell-cell contact and was completely sensitive to DNase I (1 mg/ml),
AB  - Efficient transformation was also observed when pRA2 DNA was applied
AB  - directly onto the cells, while transformation with foreign plasmid DNAs
AB  - was not observed. pRA2 could be conjugally transferred into Pseudomonas
AB  - putida RA713 and KT2440 recipients only when plasmid RK2/RP4 transfer
AB  - functions were provided in trams, Plasmid stability analysis
AB  - demonstrated that pRA2 could be stably maintained in its original host,
AB  - P. alcaligenes NCIB 9867, as well as in P. putida RA713 after 100
AB  - generations of nonselective growth. Disruption of the pRA2 pac25I
AB  - restriction endonuclease gene did not alter plasmid stability, while
AB  - the pRA2 minireplicon exhibited only partial stability, This indicates
AB  - that other pRA2-encoded determinants could have significant roles in
AB  - influencing plasmid stability.
ER  -

TY  - JOUR
AU  - Kwong, W.K.
AU  - Engel, P.
AU  - Koch, H.
AU  - Moran, N.A.
TI  - Genomics and host specialization of honey bee and bumble bee gut symbionts.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - 11509
EP  - 11514
VL  - 111
AB  - Gilliamella apicola and Snodgrassella alvi are dominant members of the honey bee  (Apis spp.)
AB  - and bumble bee (Bombus spp.) gut microbiota. We generated complete
AB  - genomes of the type strains G. apicola wkB1(T) and S. alvi wkB2(T) (isolated from
AB  - Apis), as well as draft genomes for four other strains from Bombus. G. apicola
AB  - and S. alvi were found to occupy very different metabolic niches: The former is a
AB  - saccharolytic fermenter, whereas the latter is an oxidizer of carboxylic acids.
AB  - Together, they may form a syntrophic network for partitioning of metabolic
AB  - resources. Both species possessed numerous genes [type 6 secretion systems,
AB  - repeats in toxin (RTX) toxins, RHS proteins, adhesins, and type IV pili] that
AB  - likely mediate cell-cell interactions and gut colonization. Variation in these
AB  - genes could account for the host fidelity of strains observed in previous
AB  - phylogenetic studies. Here, we also show the first experimental evidence, to our
AB  - knowledge, for this specificity in vivo: Strains of S. alvi were able to colonize
AB  - their native bee host but not bees of another genus. Consistent with specific,
AB  - long-term host association, comparative genomic analysis revealed a deep
AB  - divergence and little or no gene flow between Apis and Bombus gut symbionts.
AB  - However, within a host type (Apis or Bombus), we detected signs of horizontal
AB  - gene transfer between G. apicola and S. alvi, demonstrating the importance of the
AB  - broader gut community in shaping the evolution of any one member. Our results
AB  - show that host specificity is likely driven by multiple factors, including direct
AB  - host-microbe interactions, microbe-microbe interactions, and social transmission.
ER  -

TY  - JOUR
AU  - Kwong, W.K.
AU  - Mancenido, A.L.
AU  - Moran, N.A.
TI  - Genome Sequences of Lactobacillus sp. Strains wkB8 and wkB10, Members of the Firm-5 Clade, from Honey Bee Guts.
JO  - Genome Announcements
PY  - 2014
SP  - e01176
EP  - e01114
VL  - 2
AB  - We sequenced two strains from the Lactobacillus Firm-5 clade, a dominant group of symbionts in
AB  - the guts of honey bees and other social bees. The genome of strain
AB  - wkB8, comprising a 1.93-Mb chromosome and a 6.4-kb plasmid, was fully closed,
AB  - while strain wkB10 was assembled into 32 contigs. These genomes will provide
AB  - insights into how gut symbionts evolve and interact with their host species.
ER  -

TY  - JOUR
AU  - Kwun, M.J.
AU  - Cheng, J.
AU  - Yang, S.H.
AU  - Lee, D.R.
AU  - Suh, J.W.
AU  - Hong, H.J.
TI  - Draft Genome Sequence of Ristocetin-Producing Strain Amycolatopsis sp. Strain MJM2582 Isolated in South Korea.
JO  - Genome Announcements
PY  - 2014
SP  - e01091
EP  - e01014
VL  - 2
AB  - The draft genome sequence of a ristocetin-producing Amycolatopsis strain (sp. MJM2582)
AB  - isolated in South Korea is reported here. This strain has a genome of
AB  - approximately 8.9 Mb containing 7,933 predicted genes, including the ristocetin
AB  - cluster and 32 additional predicted secondary metabolite biosynthesis clusters.
ER  -

TY  - JOUR
AU  - Kwun, M.J.
AU  - Hong, H.J.
TI  - Draft Genome Sequence of Amycolatopsis lurida NRRL 2430, Producer of the Glycopeptide Family Antibiotic Ristocetin.
JO  - Genome Announcements
PY  - 2014
SP  - e01050
EP  - e01014
VL  - 2
AB  - We report here the first draft genome sequence for Amycolatopsis lurida NRRL 2430, the
AB  - producer of the glycopeptide antibiotic ristocetin. The 9-Mbp genome is
AB  - predicted to harbor 8,143 genes, including those belonging to the ristocetin
AB  - biosynthesis cluster and 31 additional predicted secondary metabolite gene
AB  - clusters.
ER  -

TY  - JOUR
AU  - Kwun, M.J.
AU  - Hong, H.J.
TI  - Genome Sequence of Streptomyces toyocaensis NRRL 15009, Producer of the Glycopeptide Antibiotic A47934.
JO  - Genome Announcements
PY  - 2014
SP  - e00749
EP  - e00714
VL  - 2
AB  - Here we report the draft genome sequence of Streptomyces toyocaensis strain NRRL  15009 which
AB  - is the producer of the glycopeptide antibiotic A47934. The genome
AB  - sequence is predicted to harbor a total of 26 secondary metabolite biosynthetic
AB  - gene clusters including the A47934 cluster.
ER  -

TY  - JOUR
AU  - Kyle, J.L.
AU  - Cummings, C.A.
AU  - Parker, C.T.
AU  - Quinones, B.
AU  - Vatta, P.
AU  - Newton, E.
AU  - Huynh, S.
AU  - Swimley, M.
AU  - Degoricija, L.
AU  - Barker, M.
AU  - Fontanoz, S.
AU  - Nguyen, K.
AU  - Patel, R.
AU  - Fang, R.
AU  - Tebbs, R.
AU  - Petrauskene, O.
AU  - Furtado, M.
AU  - Mandrell, R.E.
TI  - Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1885
EP  - 1896
VL  - 194
AB  - Enteropathogenic Escherichia coli (EPEC) continues to be a leading cause of
AB  - mortality and morbidity in children around the world. Two EPEC genomes have been
AB  - fully sequenced: those of EPEC O127:H6 strain E2348/69 (United Kingdom, 1969) and
AB  - EPEC O55:H7 strain CB9615 (Germany, 2003). The O55:H7 serotype is a recent
AB  - precursor to the virulent enterohemorrhagic E. coli O157:H7. To explore the
AB  - diversity of O55:H7 and better understand the clonal evolution of O157:H7, we
AB  - fully sequenced EPEC O55:H7 strain RM12579 (California, 1974), which was
AB  - collected 1 year before the first U.S. isolate of O157:H7 was identified in
AB  - California. Phage-related sequences accounted for nearly all differences between
AB  - the two O55:H7 strains. Additionally, O55:H7 and O157:H7 strains were tested for
AB  - the presence and insertion sites of Shiga toxin gene (stx)-containing
AB  - bacteriophages. Analysis of non-phage-associated genes supported core elements of
AB  - previous O157:H7 stepwise evolutionary models, whereas phage composition and
AB  - insertion analyses suggested a key refinement. Specifically, the placement and
AB  - presence of lambda-like bacteriophages (including those containing stx) should
AB  - not be considered stable evolutionary markers or be required in placing O55:H7
AB  - and O157:H7 strains within the stepwise evolutionary models. Additionally, we
AB  - suggest that a 10.9-kb region (block 172) previously believed unique to O55:H7
AB  - strains can be used to identify early O157:H7 strains. Finally, we defined two
AB  - subsets of O55:H7 strains that share an as-yet-unobserved or extinct common
AB  - ancestor with O157:H7 strains. Exploration of O55:H7 diversity improved our
AB  - understanding of the evolution of E. coli O157:H7 and suggested a key revision to
AB  - accommodate existing and future configurations of stx-containing bacteriophages
AB  - into current models.
ER  -

TY  - JOUR
AU  - L'abee-Lund, T.M.
AU  - Jorgensen, H.J.
AU  - O'Sullivan, K.
AU  - Bohlin, J.
AU  - Ligard, G.
AU  - Granum, P.E.
AU  - Lindback, T.
TI  - The Highly Virulent 2006 Norwegian EHEC O103:H25 Outbreak Strain Is Related to the 2011 German O104:H4 Outbreak Strain.
JO  - PLoS ONE
PY  - 2012
SP  - E31413
EP  - E31413
VL  - 7
AB  - In 2006, a severe foodborne EHEC outbreak occured in Norway. Seventeen cases were
AB  - recorded and the HUS frequency was 60%. The causative strain, Esherichia coli
AB  - O103:H25, is considered to be particularly virulent. Sequencing of the outbreak
AB  - strain revealed resemblance to the 2011 German outbreak strain E. coli O104:H4,
AB  - both in genome and Shiga toxin 2-encoding (Stx2) phage sequence. The nucleotide
AB  - identity between the Stx2 phages from the Norwegian and German outbreak strains
AB  - was 90%. During the 2006 outbreak, stx(2)-positive O103:H25 E. coli was isolated
AB  - from two patients. All the other outbreak associated isolates, including all food
AB  - isolates, were stx-negative, and carried a different phage replacing the Stx2
AB  - phage. This phage was of similar size to the Stx2 phage, but had a distinctive
AB  - early phage region and no stx gene. The sequence of the early region of this
AB  - phage was not retrieved from the bacterial host genome, and the origin of the
AB  - phage is unknown. The contaminated food most likely contained a mixture of E.
AB  - coli O103:H25 cells with either one of the phages.
ER  -

TY  - JOUR
AU  - L'Haridon, S.
AU  - Corre, E.
AU  - Guan, Y.
AU  - Vinu, M.
AU  - La Cono, V.
AU  - Yakimov, M.
AU  - Stingl, U.
AU  - Toffin, L.
AU  - Jebbar, M.
TI  - Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1(T).
JO  - Genome Announcements
PY  - 2018
SP  - e01482
EP  - e01417
VL  - 6
AB  - We report here the complete genome sequence (2.08 Mb) of Methanohalophilus portucalensis
AB  - strain FDF-1(T), a halophilic methylotrophic methanogen isolated
AB  - from the sediment of a saltern in Figeria da Foz, Portugal. The average
AB  - nucleotide identity and DNA-DNA hybridization analyses show that
AB  - Methanohalophilus mahii, M. halophilus, and M. portucalensis are three different
AB  - species within the Methanosarcinaceae family.
ER  -

TY  - JOUR
AU  - L'Haridon, S.
AU  - Corre, E.
AU  - Guan, Y.
AU  - Vinu, M.
AU  - La Cono, V.
AU  - Yakimov, M.
AU  - Stingl, U.
AU  - Toffin, L.
AU  - Jebbar, M.
TI  - Complete Genome Sequence of Methanohalophilus halophilus DSM 3094T, Isolated from a Cyanobacterial Mat and Bottom Deposits at Hamelin Pool, Shark Bay, Northwestern  Australia.
JO  - Genome Announcements
PY  - 2017
SP  - e01604
EP  - e01616
VL  - 5
AB  - The complete genome sequence of Methanohalophilus halophilus DSM 3094T, a member  of the
AB  - Methanosarcinaceae family and the Methanosarcianales order, consists of
AB  - 2,022,959 bp in one contig and contains 2,137 predicted genes. The genome is
AB  - consistent with a halophilic methylotrophic anaerobic lifestyle, including the
AB  - methylotrophic and CO2-H2 methanogensis pathways.
ER  -

TY  - JOUR
AU  - La Torre, A.
AU  - Bassi, D.
AU  - Zotta, T.
AU  - Orru, L.
AU  - Lamontanara, A.
AU  - Cocconcelli, P.S.
TI  - Draft Genome Sequence of Clostridium sporogenes Strain UC9000 Isolated from Raw Milk.
JO  - Genome Announcements
PY  - 2016
SP  - e00244
EP  - e00216
VL  - 4
AB  - Clostridium sporogenesis a causative agent of food spoilage and is often used as  the
AB  - nontoxigenic surrogate forClostridium botulinum Here, we described the draft
AB  - genome sequence and annotation ofC. sporogenesstrain UC9000 isolated from raw
AB  - milk.
ER  -

TY  - JOUR
AU  - Laayoun, A.
AU  - Baker, D.J.
AU  - Riley, J.
AU  - Smith, S.S.
TI  - The response of M.HpaII to heteroduplexes.
JO  - Gene
PY  - 1994
SP  - 195
EP  - 196
VL  - 150
AB  - Synthetic oligodeoxyribonucleotide duplexes have been used to study the methylation
AB  - specificity of M.HpaII, a bacterial DNA methyltransferase. Substrates of four types were
AB  - compared. A 30-mer containing a Watson-Crick paired CCGG recognition sequence was rapidly
AB  - methylated at the central cytosine on each strand in the recognition sequence. A 30-mer
AB  - containing an asymmetrically methylated recognition sequence, of the type transiently produced
AB  - by DNA replication, was rapidly methylated at the central cytosine on the unmethylated strand.
AB  - A heteroduplex containing an A.C mispair in the recognition sequence (CCGG/CCAG) was rapidly
AB  - methylated at the cytosine in the mispair. A heteroduplex containing an A.C and an adjacent
AB  - C.C mispair in the recognition sequence (CCGG/CCCA) was not methylated at a significant rate.
AB  - The results show that M.HpaII can tolerate a single mispair at its recognition site in a
AB  - heteroduplex without loss of activity or specificity.
ER  -

TY  - JOUR
AU  - Laayoun, A.
AU  - Smith, S.S.
TI  - Methylation of slipped duplexes, snapbacks and cruciforms by human DNA(cytosine-5)methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 1584
EP  - 1589
VL  - 23
AB  - When human DNA(cytosine-5)methyltransferase was used to methylate a series of snapback
AB  - oligodeoxynucleotides of differing stem lengths, each containing a centrally located CG
AB  - dinucleotide recognition site, the enzyme required a minimum of 22 base pairs in the stem for
AB  - maximum activity. Extrahelical cytosines in slipped duplexes that were 30 base pairs in length
AB  - acted as effective methyl acceptors and were more rapidly methylated than cytosines that were
AB  - Watson-Crick paired. Duplexes containing hairpins of CCG repeats in cruciform structures in
AB  - which the enzyme recognition sequence was disrupted by a C.C mispair were also more rapidly
AB  - methylated than control Watson-Crick-paired duplexes. Since enzymes have higher affinities for
AB  - their transition states than for their substrates, the results with extrahelical and mispaired
AB  - cytosines suggest that these structures can be viewed as analogs of the transition state
AB  - intermediates produced during catalysis by methyltransferases.
ER  -

TY  - JOUR
AU  - Labahn, J.
AU  - Granzin, J.
AU  - Schluckebier, G.
AU  - Robinson, D.P.
AU  - Jack, W.E.
AU  - Schildkraut, I.
AU  - Saenger, W.
TI  - Three-dimensional structure of the adenine-specific DNA methyltransferase M.TaqI in complex with the cofactor S-adenosylmethionine.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 10957
EP  - 10961
VL  - 91
AB  - The Thermus aquaticus DNA methyltransferase M.TaqI (EC 2.1.1.72) methylates N6 of adenine in
AB  - the specific double-helical DNA sequence TCGA by transfer of -CH3 from the cofactor
AB  - S-adenosyl-L-methionine. The x-ray crystal structure at 2.4 Angstrom resolution of this enzyme
AB  - in complex with S-adenosylmethionine shows alpha/beta folding of the polypeptide into two
AB  - domains of about equal size. They are arranged in the form of a C with a wide cleft suitable
AB  - to accommodate the DNA substrate. The N-terminal domain is dominated by a nine-stranded
AB  - beta-sheet; it contains the two conserved segments typical for N-methyltranferases which form
AB  - a pocket for cofactor binding. The C-terminal domain is formed by four small beta-sheets and
AB  - alpha-helices. The three-dimensional folding of M.TaqI is similar to that of the
AB  - cytosine-specific HhaI methyltransferase, where the large Beta-sheet in the N-terminal domain
AB  - contains all conserved segments and the enzymatically functional parts, and the smaller
AB  - C-terminal domain is less structured.
ER  -

TY  - JOUR
AU  - Labbe, D.
AU  - Holtke, H.J.
AU  - Lau, P.C.K.
TI  - Cloning and characterization of two tandemly arranged DNA methyltransferase genes of Neisseria lactamica: An adenine-specific M.NlaIII and a cytosine-type methylase.
JO  - Mol. Gen. Genet.
PY  - 1990
SP  - 101
EP  - 110
VL  - 224
AB  - The gene encoding the Neisseria lactamica III DNA methyltransferase (M.NlaIII) which
AB  - recognizes the sequence CATG has been cloned and expressed in Escherichia coli. DNA sequencing
AB  - of a 3.125 kb EcoRI-PstI fragment localizes the M.NlaIII gene to a 334 codon open reading
AB  - frame (ORF) and identifies, 468 bp downstream, a second ORF of 313 amino acids, which is
AB  - referred to as M.NlaX. Both proteins are detectable in the E. coli coupled in vitro
AB  - transcription-translation system; they are apparently expressed from separate N. lactamica
AB  - promoters. The N-terminal half of the previously characterized M.FokI, which methylates
AB  - adenine in one of the DNA strands with its asymmetric recognition sequence (GGATG), is found
AB  - to have 41% sequence identity and a further 11.7% sequence similarity with M.NlaIII. Among the
AB  - conserved amino acids is the well known DPPY sequence motif. With one exception, analysis of
AB  - the nucleotides coding for the DP dipeptide in all known DPPY sequences shows the presence of
AB  - an inherent DNA adenine methylation (dam) recognition site of GATC. A low level of expression
AB  - of M.NlaX in E. coli prevents the elucidation of its sequence recognition specificity.
AB  - Sequence analysis of M.NlaX shows that it is closely related to the group of monospecific
AB  - 5-methylcytosine DNA methyltransferases (M.EcoRII, Dcm, M.HpaII and M.HhaI) which all have a
AB  - modified cytosine at the second position of the recognition sequences. Both M.EcoRII and Dcm
AB  - amino acid sequences are about 50% identical with M.NlaX; a considerable degree of sequence
AB  - identity is found in the so-called variable region which is believed to be responsible for
AB  - sequence recognition specificity. M.NlaX is probably the counterpart to the E. coli Dcm in N.
AB  - lactamica.
ER  -

TY  - JOUR
AU  - Labbe, G.
AU  - Edirmanasinghe, R.
AU  - Ziebell, K.
AU  - Nash, J.H.
AU  - Bekal, S.
AU  - Parmley, E.J.
AU  - Mulvey, M.R.
AU  - Johnson, R.P.
TI  - Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources.
JO  - Genome Announcements
PY  - 2016
SP  - e01526
EP  - e01515
VL  - 4
AB  - Isolates of Salmonella enterica subsp. enterica serovar Heidelberg are often associated with
AB  - poultry products and may cause severe human illness. Here, we
AB  - report the fully assembled genome and plasmid sequences of three S. Heidelberg
AB  - strains with phage types 9, 29, and 41.
ER  -

TY  - JOUR
AU  - Labbe, G.
AU  - Ziebell, K.
AU  - Bekal, S.
AU  - Macdonald, K.A.
AU  - Parmley, E.J.
AU  - Agunos, A.
AU  - Desruisseau, A.
AU  - Daignault, D.
AU  - Slavic, D.
AU  - Hoang, L.
AU  - Ramsay, D.
AU  - Pollari, F.
AU  - Robertson, J.
AU  - Nash, J.H.
AU  - Johnson, R.P.
TI  - Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources.
JO  - Genome Announcements
PY  - 2016
SP  - e00990
EP  - e00916
VL  - 4
AB  - Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently
AB  - associated with foodborne illness. To facilitate subtyping efforts, we
AB  - report fully assembled genome sequences of 17 Canadian S Heidelberg isolates
AB  - including six pairs of epidemiologically related strains. The plasmid sequences
AB  - of eight isolates contain several drug resistance genes.
ER  -

TY  - JOUR
AU  - Labbe, S.
AU  - Xia, Y.
AU  - Roy, P.H.
TI  - BspMII and AccIII are an isoschizomer pair which differ in their sensitivity to cytosine methylation.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 7184
EP  - 7184
VL  - 16
AB  - The latest tabulation of restriction endonuclease sensitivities to
AB  - site-specific DNA methylation has shown that BspMII is able to cut the
AB  - methylated sequence TCCGGmA while AccIII is not.  We found that cellular DNA
AB  - from Acinetobacter calcoaceticus showed complete resistance to the action of
AB  - restriction endonuclease AccIII but sensitivity to the action of restriction
AB  - endonuclease BspMII, an isoschizomer of AccIII (results not shown).  This
AB  - experiment indicates that the methylation sensitivity of restriction enzymes
AB  - AccIII and BspMII are not the same.  We then tested both enzymes (AccIII and
AB  - BspMII) for sensitivity to cytosine methylation within their recognition sites
AB  - by using M.MspI (mCCGG) and M.HpaII (CmCGG) methylases on various DNA
AB  - substrates.  Adenovirus 2 DNA was used for this experiment (Fig. 1) and
AB  - additional tests were done with lambda DNA and pLQ61 DNA (which has 2 AccIII
AB  - sites and is derived from pBR328) (results not shown).  We conclude that BspMII
AB  - does not cleave the modified sequences TmCCGGA and TCmCGGA, and that
AB  - restriction by AccIII is not affected by methylation of either cytosine in the
AB  - same recognization sequence.  Thus, we suggest that the enzyme M.BspMII is a
AB  - DNA-cytosine-methyltransferase while M.AccIII is a
AB  - DNA-adenine-methyltransferase.
ER  -

TY  - JOUR
AU  - Labeots, L.A.
TI  - Structure and function of DNA phosphotriester substrates of the restriction endonuclease AluI.
JO  - Diss. Abstr.
PY  - 1993
SP  - 2842
EP  - 2842
VL  - 53
AB  - The duplex d(GGAAGCTAGG).d(CCTAGCTTCC) is a substrate for AluI, which cleaves at the center of
AB  - the AGCT recognition sequence when magnesium ion is present. Large scale synthesis of the
AB  - 2,2,2-trichloro-1,1-dimethylethyl phosphotriester derivative d(GGAAGp(TCDME)CTAGG) was done
AB  - using phosphite chemistry. The two diastereomers were separated on a large scale by HPLC. Both
AB  - diastereomers formed a stable heteroduplex with a complementary unmodified strand in the
AB  - hydrolysis buffer. Both modified duplexes bound to AluI with affinity similar to that of the
AB  - natural duplex, as determined by gel shift assays. When incubated with AluI under identical
AB  - conditions, one diastereomeric heteroduplex remained intact, while the other was hydrolyzed at
AB  - G-C in the unmodified strand. No cleavage of the modified strand was observed in either case,
AB  - nor was any hydrolysis detected when the single-stranded unmodified complement was treated.
AB  - The configuration at the phosphotriester sites was assigned from 2D NMR spectral data.
AB  - Resonance assignments for most nonexchangeable protons were made using DQF-COSY and NOESY.
AB  - Most resonances fell within expected ranges; however the central dG H3' and dC H5'{5'}
AB  - residues in the modified strands were shifted significantly downfield. The diastereomer
AB  - exhibiting NOE cross-relaxation between the methyl protons in the TCDME modification and the
AB  - C6 H6, C6 H4', C6 H5' H5{'}, G5 H3', and G5 H4' in the modified strand was assigned the
AB  - Rp configuration. The diastereomer showing cross-relaxation between the methyl protons of the
AB  - TCDME modification and the C6 H5'H5{'}, G5 H3', and G5 H4' in the modified strand was
AB  - assigned the Sp configuration. This assignment agrees with one based on chemical degradation
AB  - of the oligomers. The 3D structuers of the heteroduplexes were determined by integrating
AB  - resolved NOE cross-peaks and converting the volumes into distances for each mixing time. The
AB  - derived distances were applied to models and subjected to refinement. The refined structures
AB  - correspond to B-form DNA but with distortions in the region of the modified site. The triester
AB  - group of the Sp duplex projects out from the double helix into the aqueous environment,
AB  - whereas that of the Rp isomer points into the major groove.
ER  -

TY  - JOUR
AU  - Laborda, P.R.
AU  - Fonseca, F.S.
AU  - Angolini, C.F.
AU  - Oliveira, V.M.
AU  - Souza, A.P.
AU  - Marsaioli, A.J.
TI  - Genome Sequence of Bacillus safensis CFA06, Isolated from Biodegraded Petroleum in Brazil.
JO  - Genome Announcements
PY  - 2014
SP  - e00642
EP  - e00614
VL  - 2
AB  - Bacillus safensis is a microorganism recognized for its biotechnological and industrial
AB  - potential due to its interesting enzymatic portfolio. Here, as a means
AB  - of gathering information about the importance of this species in oil
AB  - biodegradation, we report a draft genome sequence of a strain isolated from
AB  - petroleum.
ER  -

TY  - JOUR
AU  - Labrador-Herrera, G.
AU  - Alvarez, R.
AU  - Lopez-Rojas, R.
AU  - Smani, Y.
AU  - Cebrero-Cangueiro, T.
AU  - Rueda, A.
AU  - Perez, F.J.
AU  - Pachon, J.
AU  - Pachon-Ibanez, M.E.
TI  - Draft Genome Sequences of Seven Multidrug-Resistant Acinetobacter baumannii Strains, Isolated from Respiratory Samples in Spain.
JO  - Genome Announcements
PY  - 2016
SP  - e00083
EP  - e00016
VL  - 4
AB  - The draft genome sequences of seven multidrug-resistantAcinetobacter baumanniiclinical strains
AB  - belonging to sequence types ST-208 and ST-218 are
AB  - reported in this study. They were isolated from tracheobronchial aspirate of
AB  - mechanically ventilated adult patients admitted to the intensive care unit of a
AB  - Spanish tertiary hospital during 2010 to 2011.
ER  -

TY  - JOUR
AU  - Labrie, S.J.
AU  - El Haddad, L.
AU  - Tremblay, D.M.
AU  - Plante, P.L.
AU  - Wasserscheid, J.
AU  - Dumaresq, J.
AU  - Dewar, K.
AU  - Corbeil, J.
AU  - Moineau, S.
TI  - First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture  and a Host to Propagate Staphylococcus aureus Phages.
JO  - Genome Announcements
PY  - 2014
SP  - e00671
EP  - e00614
VL  - 2
AB  - Staphylococcus xylosus is a bacterial species used in meat fermentation and a commensal
AB  - microorganism found on animals. We present the first complete circular
AB  - genome from this species. The genome is composed of 2,757,557 bp, with a G+C
AB  - content of 32.9%, and contains 2,514 genes and 79 structural RNAs.
ER  -

TY  - JOUR
AU  - Labrie, S.J.
AU  - Samson, J.E.
AU  - Moineau, S.
TI  - Bacteriophage resistance mechanisms.
JO  - Nat. Rev. Microbiol.
PY  - 2010
SP  - 317
EP  - 327
VL  - 8
AB  - Phages are now acknowledged as the most abundant microorganisms on the planet and are also
AB  - possibly the most diversified. This diversity is mostly driven by their dynamic adaptation
AB  - when facing selective pressure such as phage resistance mechanisms, which are widespread in
AB  - bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms,
AB  - and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in
AB  - order to thrive in most environments. In this Review, we highlight the most important
AB  - antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these
AB  - systems.
ER  -

TY  - JOUR
AU  - Labrie, S.J.
AU  - Tremblay, D.M.
AU  - Plante, P.L.
AU  - Wasserscheid, J.
AU  - Dewar, K.
AU  - Corbeil, J.
AU  - Moineau, S.
TI  - Complete Genome Sequence of Streptococcus thermophilus SMQ-301, a Model Strain for Phage-Host Interactions.
JO  - Genome Announcements
PY  - 2015
SP  - e00480
EP  - e00415
VL  - 3
AB  - Streptococcus thermophilus is used by the dairy industry to manufacture yogurt and several
AB  - cheeses. Using PacBio and Illumina platforms, we sequenced the genome
AB  - of S. thermophilus SMQ-301, the host of several virulent phages. The genome is
AB  - composed of 1,861,792 bp and contains 2,037 genes, 67 tRNAs, and 18 rRNAs.
ER  -

TY  - JOUR
AU  - Labudda, L.
AU  - Strapagiel, D.
AU  - Karczewska-Golec, J.
AU  - Golec, P.
TI  - Complete Annotated Genome Sequences of Four Klebsiella pneumoniae Phages Isolated from Sewage in Poland.
JO  - Genome Announcements
PY  - 2017
SP  - e00919
EP  - e00917
VL  - 5
AB  - Four lytic phages, vB_KpnP_BIS33, vB_KpnP_IL33, and vB_KpnP_PRA33 of the Podoviridae family
AB  - and vB_KpnM_BIS47 of the Myoviridae family, which act against
AB  - animal-pathogenic Klebsiella pneumoniae strains, were isolated from sewage plants
AB  - in Poland. They possess double-stranded DNA genomes of 41,697 bp, 41,335 bp,
AB  - 40,605 bp, and 147,443 bp, respectively.
ER  -

TY  - JOUR
AU  - Labutti, K. et al.
TI  - Complete genome sequence of Anaerococcus prevotii type strain (PC1).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 159
EP  - 165
VL  - 1
AB  - Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the
AB  - genus, and is of phylogenetic interest because of its arguable
AB  - assignment to the provisionally arranged family 'Peptostreptococcaceae'. A.
AB  - prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads.
AB  - The strain, whose genome is described here, was originally isolated from human
AB  - plasma; other strains of the species were also isolated from clinical specimen.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. This is the first completed genome sequence of a member
AB  - of the genus. Next to Finegoldia magna, A. prevotii is only the second species
AB  - from the family 'Peptostreptococcaceae' for which a complete genome sequence is
AB  - described. The 1,998,633 bp long genome (chromosome and one plasmid) with its
AB  - 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Labutti, K. et al.
TI  - Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 85
EP  - 92
VL  - 3
AB  - Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus
AB  - Dethiosulfovibrio of the family Synergistaceae in the recently created
AB  - phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing
AB  - bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids.
AB  - It was isolated from an offshore oil well where it was been reported to be
AB  - involved in pitting corrosion of mild steel. Initially, this bacterium was
AB  - described as a distant relative of the genus Thermoanaerobacter, but was not
AB  - assigned to a genus, it was subsequently placed into the novel phylum
AB  - Synergistetes. A large number of repeats in the genome sequence prevented an
AB  - economically justifiable closure of the last gaps. This is only the third
AB  - published genome from a member of the phylum Synergistetes. The 2,576,359 bp long
AB  - genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and
AB  - is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Labutti, K. et al.
TI  - Complete genome sequence of Planctomyces limnophilus type strain (Mu 290).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 47
EP  - 56
VL  - 3
AB  - Planctomyces limnophilus Hirsch and Muller 1986 belongs to the order Planctomycetales, which
AB  - differs from other bacterial taxa by several distinctive
AB  - features such as internal cell compartmentalization, multiplication by forming
AB  - buds directly from the spherical, ovoid or pear-shaped mother cell and a cell
AB  - wall which is stabilized by a proteinaceous layer rather than a peptidoglycan
AB  - layer. Besides Pirellula staleyi, this is the second completed genome sequence of
AB  - the family Planctomycetaceae. P. limnophilus is of interest because it differs
AB  - from Pirellula by the presence of a stalk and its structure of fibril bundles,
AB  - its cell shape and size, the formation of multicellular rosettes, low salt
AB  - tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304
AB  - protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Lacap-Bugler, D.C.
AU  - Jiang, J.
AU  - Huo, Y.B.
AU  - Chan, Y.
AU  - Leung, F.C.
AU  - Watt, R.M.
TI  - Complete Genome Sequence of the Oral Spirochete Bacterium Treponema putidum Strain OMZ 758T (ATCC 700334T).
JO  - Genome Announcements
PY  - 2014
SP  - e01076
EP  - e01014
VL  - 2
AB  - The oral spirochete bacterium Treponema putidum inhabits human periodontal niches. The
AB  - complete genome sequence of the OMZ 758(T) (ATCC 700334(T)) strain of
AB  - this species was determined, revealing a 2,796,913-bp chromosome, with a G+C
AB  - content of 37.30% and a single plasmid (pTPu1; 3,649 bp) identical to pTS1 from
AB  - Treponema denticola.
ER  -

TY  - JOUR
AU  - Lacey, J.A.
AU  - Allnutt, T.R.
AU  - Vezina, B.
AU  - Van, T.T.
AU  - Stent, T.
AU  - Han, X.
AU  - Rood, J.I.
AU  - Wade, B.
AU  - Keyburn, A.L.
AU  - Seemann, T.
AU  - Chen, H.
AU  - Haring, V.
AU  - Johanesen, P.A.
AU  - Lyras, D.
AU  - Moore, R.J.
TI  - Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.
JO  - BMC Genomics
PY  - 2018
SP  - 379
EP  - 379
VL  - 19
AB  - BACKGROUND: Clostridium perfringens causes a range of diseases in animals and
AB  - humans including necrotic enteritis in chickens and food poisoning and gas
AB  - gangrene in humans. Necrotic enteritis is of concern in commercial chicken
AB  - production due to the cost of the implementation of infection control measures
AB  - and to productivity losses. This study has focused on the genomic analysis of a
AB  - range of chicken-derived C. perfringens isolates, from around the world and from
AB  - different years. The genomes were sequenced and compared with 20 genomes
AB  - available from public databases, which were from a diverse collection of isolates
AB  - from chickens, other animals, and humans. We used a distance based phylogeny that
AB  - was constructed based on gene content rather than sequence identity. Similarity
AB  - between strains was defined as the number of genes that they have in common
AB  - divided by their total number of genes. In this type of phylogenetic analysis,
AB  - evolutionary distance can be interpreted in terms of evolutionary events such as
AB  - acquisition and loss of genes, whereas the underlying properties (the gene
AB  - content) can be interpreted in terms of function. We also compared these methods
AB  - to the sequence-based phylogeny of the core genome. RESULTS: Distinct pathogenic
AB  - clades of necrotic enteritis-causing C. perfringens were identified. They were
AB  - characterised by variable regions encoded on the chromosome, with predicted roles
AB  - in capsule production, adhesion, inhibition of related strains, phage
AB  - integration, and metabolism. Some strains have almost identical genomes, even
AB  - though they were isolated from different geographic regions at various times,
AB  - while other highly distant genomes appear to result in similar outcomes with
AB  - regard to virulence and pathogenesis. CONCLUSIONS: The high level of diversity in
AB  - chicken isolates suggests there is no reliable factor that defines a chicken
AB  - strain of C. perfringens, however, disease-causing strains can be defined by the
AB  - presence of netB-encoding plasmids. This study reveals that horizontal gene
AB  - transfer appears to play a significant role in genetic variation of the C.
AB  - perfringens chromosome as well as the plasmid content within strains.
ER  -

TY  - JOUR
AU  - Lackner, G.
AU  - Moebius, N.
AU  - Partida-Martinez, L.
AU  - Hertweck, C.
TI  - Complete Genome Sequence of Burkholderia rhizoxinica, the Endosymbiont of Rhizopus microsporus.
JO  - J. Bacteriol.
PY  - 2010
SP  - 783
EP  - 784
VL  - 193
AB  - Burkholderia rhizoxinica is an intracellular symbiont of the phytopathogenic fungus Rhizopus
AB  - microsporus. The vertically transmitted
AB  - endosymbiont not only delivers the antimitotic macrolide rhizoxin to its
AB  - host, but is also essential for vegetative spore formation of the fungus.
AB  - To shed light on the genetic equipment of this model organism, we
AB  - sequenced the whole genome of B. rhizoxinica HKI 0454, thus providing the
AB  - first genomic insight into of an intracellular mutualist of a fungal
AB  - species. The 3.75 Mb genome consists of a chromosome and two
AB  - strain-specific plasmids. Primary metabolism appears to be specialized for
AB  - the uptake of fungal metabolites. Besides the rhizoxin biosynthesis gene
AB  - cluster, there are 14 loci coding for nonribosomal peptide synthetase
AB  - (NRPS) assembly lines, which represent novel targets for genomic mining of
AB  - cryptic natural products. Furthermore, the endosymbionts are equipped with
AB  - a repertoire of virulence-related factors, which can now be studied to
AB  - elucidate molecular mechanisms underlying bacterial-fungal interaction.
ER  -

TY  - JOUR
AU  - Lacks, S.
AU  - Greenberg, B.
TI  - A deoxyribonuclease of Diplococcus pneumoniae specific for methylated DNA.
JO  - J. Biol. Chem.
PY  - 1975
SP  - 4060
EP  - 4066
VL  - 250
AB  - A deoxyribonuclease specific for methylated DNA was isolated from Diplococcus
AB  - pneumoniae.  The enzyme, an endonuclease, degrades DNA from Escherichia coli to
AB  - fragments of average molecular weight about half a million; it forms discrete
AB  - fragments from phage lambda DNA.  Methyl-deficient E. coli DNA is not attacked,
AB  - neither is DNA from Micrococcus radiodurans, which contains no methylated
AB  - adenine or cytosine.  Nor is DNA from D. pneumoniae or phage T7 attacked.
AB  - However, DNA from M. radiodurans, D. pneumoniae, and T7 is attacked after
AB  - methylation with an E. coli extract.  Methylated T7 DNA is degraded to discrete
AB  - fragments.  Although the genetic transforming activity of normal DNA from D.
AB  - pneumoniae is not affected by the enzyme, transforming activity of methylated
AB  - DNA is destroyed.  The enzyme is designated endonuclease R.DpnI.  Under certain
AB  - conditions another enzyme of complementary specificity can be isolated.  This
AB  - enzyme, designated endonuclease R.DpnII, produces a similar pattern of
AB  - fragments from the DNA of T7 without prior methylation of the DNA.  It also
AB  - degrades normal DNA from D. pneumoniae.  It is suggested that this pair of
AB  - enzymes plays a role in some unknown control process, which would involve a
AB  - large fraction of the specific base sequences that are methylated in E. coli
AB  - DNA and are present but not methylated in DNA from other sources.
ER  -

TY  - JOUR
AU  - Lacks, S.
AU  - Greenberg, B.
TI  - Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 153
EP  - 168
VL  - 114
AB  - Restriction endonucleases DpnI and DpnII are produced by two distinct strains of Diplococcus
AB  - pneumoniae. The two enzymes show complementary specificity with respect to methylation of
AB  - sites in DNA. From the identity of its cleavage site with that of MboI, it appears that DpnII
AB  - cleaves at the unmodified sequence 5'-G-A-T-C-3'. DpnI cleaves at the same sequence when the
AB  - adenine residue is methylated. Both enzymes produce only double-stranded breaks in susceptible
AB  - DNA. Their susceptibility to DpnI and not DpnII shows that essentially all the G-A-T-C
AB  - sequences are methylated in DNA from the pneumococcal strain that produces DpnII as well as in
AB  - DNA from Hemophilus influenzae and Escherichia coli. In the dam-3 mutant of E. coli none of
AB  - these sequences appear to be methylated. Residual adenine methylation in the dam-3 mutant DNA
AB  - most likely occurs at different sites. Different but characteristic degrees of methylation at
AB  - G-A-T-C sites are found in the DNA of bacterial viruses grown in E. coli. DNAs from mammalian
AB  - cells and viruses are not methylated at this sequence. Mitochondrial DNA from Paramecium
AB  - aurelia is not methylated, but a small proportion of G-A-T-C sequences in the macronuclear DNA
AB  - of this eukaryote appear to be methylated. Possible roles of sequence-specific methylation in
AB  - the accommodation of plasmids, in the replication of DNA, in the regulation of gene function
AB  - and in the restriction of viral infection are discussed.
ER  -

TY  - JOUR
AU  - Lacks, S.
AU  - Neuberger, M.
TI  - Membrane location of a deoxyribonuclease implicated in the genetic transformation of Diplococcus pneumoniae.
JO  - J. Bacteriol.
PY  - 1975
SP  - 1321
EP  - 1329
VL  - 124
AB  - The cellular localization of enzymes in Diplococcus pneumoniae was examined by
AB  - fractionation of spheroplasts.  A deoxyribonuclease implicated in the entry of
AB  - deoxyribonucleic acid (DNA) into the cell during genetic transformation was
AB  - located in the cell membrane.  This enzyme, the major endonuclease of the cell
AB  - (endonuclease I), which is necessary for the conversion of donor DNA to single
AB  - strands inside the cell and oligonucleotides outside, thus could act at the
AB  - cell surface.  Another enzyme, the cell wall lysin (autolysin), was also found
AB  - in the membrane fraction.  Other enzymes, including amylomaltase, two
AB  - exonucleases, an adenosine triphosphate-dependent deoxyribonuclease, and a
AB  - restriction type endonuclease, were predominantly periplasmic in location.
AB  - Spheroplasts were obtained spontaneously on incubation of pneumococcal cells in
AB  - concentrated sugar solutions.  The autolytic enzyme appears to be involved in
AB  - this process.  Cells that were physiologically competent to take up DNA formed
AB  - osmotically sensitive spheroplasts two to three times faster than cells that
AB  - were not in the competent state.  Although some genetically incompetent mutants
AB  - also formed spheroplasts more slowly, other such mutants formed them at the
AB  - faster rate.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
TI  - Purification and properties of the complementary endonucleases DpnI and DpnII.
JO  - Methods Enzymol.
PY  - 1980
SP  - 138
EP  - 146
VL  - 65
AB  - None
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Ayalew, S.
AU  - de la Campa, A.G.
AU  - Greenberg, B.
TI  - Regulation of competence for genetic transformation in Streptococcus pneumoniae: expression of dpnA, a late competence gene encoding a DNA methyltransferase of the DpnII restriction system.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 1089
EP  - 1098
VL  - 35
AB  - The chromosomal DpnII gene cassette of Streptococcus pneumoniae encodes two methyltransferases
AB  - and an endonuclease. One methyltransferase acts on double-stranded and the other on
AB  - single-stranded DNA. Two mRNAs are transcribed from the cassette. One, a SigA promoter
AB  - transcript, includes all three genes; the other includes a truncated form of the second
AB  - methyltransferase gene (dpnA) and the endonuclease gene. The truncated dpnA, which is
AB  - translated from the second start codon in the full gene, was shown to produce active enzyme. A
AB  - promoter reporter plasmid for S. pneumoniae was devised to characterize the promoter for the
AB  - second mRNA. This transcript was found to depend on a promoter that responded to the induction
AB  - of competence for genetic transformation. The promoter contains the combox sequence recognized
AB  - by a SigH-containing RNA polymerase. As part of the competence regulon, the dpnA gene makes a
AB  - product able to methylate incoming plasmid strands to protect them from the endonuclease and
AB  - allow plasmid establishment. Its function differs from most genes in the regulon, which are
AB  - involved in DNA uptake. Comparison of R6 and Rx strains of S. pneumoniae showed the
AB  - temperature dependence of transformation in R6 to result from temperature sensitivity of the
AB  - uptake apparatus and not the development of competence.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Dunn, J.J.
AU  - Greenberg, B.
TI  - Identification of base mismatches recognized by the heteroduplex-DNA-repair system of Streptococcus pneumoniae.
JO  - Cell
PY  - 1982
SP  - 327
EP  - 336
VL  - 31
AB  - The susceptibility to repair of particular base mismatches by the hex system of
AB  - Streptococcus pneumoniae was examined by comparison of the nucleotide sequence
AB  - of the wild-type and eight mutant alleles of the malM gene.  A detailed
AB  - restriction map was constructed for pLS70, and the nucleotide sequence was
AB  - determined for its 3475 bp chromosomal insert, which contains the entire malM
AB  - gene (encoding amylomaltase), portions of malX and malP (encoding a membrane
AB  - protein and a phosphorylase, respectively) and a control region.  Transition
AB  - mismatches were highly susceptible to repair; transversion mismatches, much
AB  - less so.  A mismatch caused by a single-nucleotide deletion was reparable, but
AB  - mismatches with longer deletions were not.  The hex system also reduced
AB  - spontaneous reversion of mutations corresponding to transitions.  It is
AB  - suggested that recognition of donor or nascent DNA strands by the hex system
AB  - depends on single-strand breaks in the target strand, and that the role of DNA
AB  - methylation in mismatch repair of Escherichia coli can be accommodated to this
AB  - model.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Greenberg, B.
TI  - Atypical ribosome binding sites and regulation of gene expression in the DpnII restriction enzyme system of S. pneumoniae.
JO  - FASEB J.
PY  - 1993
SP  - A1082
EP  - A1082
VL  - 7
AB  - Strains of Streptococcus pneumoniae express either the DpnI or DpnII restriction systems,
AB  - which are complementary in that DpnI cleaves methylated GATC sites, whereas DpnII cleaves
AB  - unmethylated GATC. The genes for each system are contained in a cassette located at one
AB  - particular position in the chromosome. The DpnII cassette contains three genes in an operon
AB  - that specifies two methylases, DpnM and DpnA, and the DpnII endonuclease. Translation of DpnM
AB  - and DpnA appears to depend on atypical ribosome binding sites, containing 5'-ATTTC-(5 or
AB  - 6n)-TATA-3' sequences located upstream of the start codon, rather than Shine-Dalgarno
AB  - sequences. Changes within this atypical sequence, but not outside it, block translation.
AB  - Proteins appear to be synthesized from atypical sites equally well in S. pneumoniae and E.
AB  - coli. The atypical sequence, also, is complementary to an unpaired region of 16S rRNA. These
AB  - unusual ribosome binding sites may play a role in the selective translation of methylases
AB  - prior to the endonuclease when the DpnII cassette is introduced into a cell.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Greenberg, B.
AU  - Sabelnikov, A.G.
TI  - Possible regulation of DNA methyltransferase expression by RNA processing in Streptococcus pneumoniae.
JO  - Gene
PY  - 1995
SP  - 209
EP  - 212
VL  - 157
AB  - Atypical ribosome-binding sites lacking Shine-Dalgarno sequences appear to be used for
AB  - translation of the DpnM and DpnA DNA methyltransferases of the DpnII restriction system.
AB  - Preliminary results indicate that the 5'-endpoints of DpnII system mRNAs result from
AB  - degradation of the original transcript.  These tentative findings serve as the basis for a
AB  - possible regulatory model that would accommodate the DpnII cassette either as a single copy in
AB  - the chromosome or on a multicopy plasmid.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Mannarelli, B.M.
AU  - Springhorn, S.S.
AU  - Greenberg, B.
TI  - Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae:  An intercellular cassette mechanism.
JO  - Cell
PY  - 1986
SP  - 993
EP  - 1000
VL  - 46
AB  - Cells of S. pneumoniae contain either DpnI, a restriction endonuclease that
AB  - cleaves only the methylated DNA sequence 5'-GmeATC-3', or DpnII, which cleaves
AB  - the same sequence when not methylated.  A chromosomal DNA segment containing
AB  - DpnII genes was cloned in S. pneumoniae.  Nucleotide sequencing of this segment
AB  - revealed genes encoding the methylase and endonuclease and a third protein of
AB  - unknown function.  When the plasmid was introduced into DpnI cells,
AB  - recombination during chromosomal facilitation of its establishment substituted
AB  - genes encoding the DpnI endonuclease and another protein in place of the DpnII
AB  - genes.  DNA hybridization and sequencing showed that the DpnI and DpnII
AB  - segments share homology on either side but not between themselves or with other
AB  - regions of the chromosome.  Thus, the complementary restriction systems are
AB  - found on nonhomologous and mutally exclusive cassettes that can be inserted
AB  - into a particular point in the chromosome of S. pneumoniae on the basis of
AB  - neighboring homology.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Mannarelli, B.M.
AU  - Springhorn, S.S.
AU  - Greenberg, B.
AU  - de la Campa, A.
TI  - Genetics of the complementary restriction systems DpnI and DpnII revealed by cloning and recombination in Streptococcus pneumoniae.
JO  - Streptococcal Genetics
PY  - 1987
SP  - 31
EP  - 41
VL  - 0
AB  - Restriction enzymes, because they are able to recognize and cleave specific
AB  - sequences in DNA, have had an enormous impact on genetic analysis and
AB  - engineering.  This review is concerned with some unusual restriction enzyme
AB  - systems found in Streptococcus pneumonia.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Sabelnikov, A.G.
AU  - Chen, J.-D.
AU  - Greenberg, B.
TI  - Gene expression in the DpnI and DpnII restriction enzyme systems of Streptococcus pneumoniae.
JO  - DNA Transfer and Gene Expression in Microorganisms
PY  - 1993
SP  - 169
EP  - 178
VL  - 0
AB  - Although a number of bacterial species are naturally transformable, that is, their cells are
AB  - able to take up external DNA in substantial amounts and integrate it into the chromosome
AB  - without artificial manipulation of the cell surface, Streptococcus pneumoniae, the first
AB  - species in which this phenomenon was detected, remains a prototype of such transformation.
AB  - This is partly because these bacteria do not appear to use other forms of genetic exchange for
AB  - transfer of chromosomal genes, such as conjugation and transduction, but rely solely on
AB  - DNA-mediated transformation.  Cells of S. pneumoniae also contain potent restriction
AB  - endonucleases able to severely restrict DNA introduced during viral infection.  Therefore, it
AB  - should be interesting to examine the effects of the restriction enzyme systems on transforming
AB  - DNA.  Our current understanding of the genetic basis of the complementary DpnI and DpnII
AB  - restriction systems and of the biochemistry of their component enzymes will be briefly
AB  - reviewed.  The manner in which these enzymes impinge on the transfer of chromosomal genes and
AB  - of plasmids will be examined in detail.  It will be seen that far from acting against
AB  - "foreign" DNA in general, the restriction systems seem to be designed to exclude only
AB  - infecting viral DNA.  The presence of complementary restriction systems in different cells of
AB  - S. pneumoniae enhances their effectiveness in blocking viral infection and promoting species
AB  - survival.  This enhanced effectiveness requires the expression of alternative restriction
AB  - systems.  Therefore, the ability of the cells to transfer the restriction enzyme genes and to
AB  - regulate their expression are important for survival of the species.  The final part of this
AB  - paper will present currently available information on this topic.  In particular, the
AB  - localization of the restriction genes in cassettes, their transcription products, and the role
AB  - of a possibly new class of ribosome binding sites will be examined in relation to the
AB  - regulation of restriction gene expression.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Springhorn, S.S.
TI  - Transfer of recombinant plasmids containing the gene for DpnII DNA methylase into strains of Streptococcus pneumoniae that produce DpnI or DpnII restriction endonucleases.
JO  - J. Bacteriol.
PY  - 1984
SP  - 905
EP  - 909
VL  - 158
AB  - Plasmid transfer via the transformation pathway of Streptococcus pneumoniae was
AB  - weakly restricted by the DpnI or DpnII restriction endonuclease, either of
AB  - which gave a reduction only to 0.4, compared with phage infection, which was
AB  - restricted to 10^-5.  The greater sensitivity of plasmid transfer compared with
AB  - chromosomal transformation, which was not at all restricted, can be attributed
AB  - to partially double-stranded intermediates formed from two complementary donor
AB  - fragments.  However, clustering of potential restriction sites in the plasmids
AB  - increased the probability of escape from restriction.  The recombinant plasmid
AB  - pMP10, in which the gene for the DpnII DNA methylase was cloned, can be
AB  - transferred to strains that contain neither restriction enzyme or that contain
AB  - DpnII as readily as can the vector pMP5.  Introduction of pMP10 raised the
AB  - level of methylase by five times the level normally present in DpnII strains.
AB  - Transfer of pMP10 to DpnI-containing strains was infrequent, presumably owing
AB  - to the suicidal methylation of DNA which rendered it susceptible to the host
AB  - endonuclease.  The few clones in which pMP10 was established had lost DpnI.
AB  - Loss of the plasmid after curing of the cell eliminated the methylase but did
AB  - not restore DpnI.  Although this loss of DpnI could result from spontaneous
AB  - mutation, its relatively high frequency, 0.1% suggested that the loss was due
AB  - to a regulatory shift.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Springhorn, S.S.
TI  - Cloning in Streptococcus pneumoniae of the gene for DpnII DNA methylase.
JO  - J. Bacteriol.
PY  - 1984
SP  - 934
EP  - 936
VL  - 157
AB  - The gene coding for the pneumococcal DNA adenine methylase that recognizes the
AB  - sequence 5'-GATC-3' was cloned in a strain of Streptococcus pneumoniae that
AB  - lacked both restriction endonucleases DpnI and DpnII.  The gene was cloned as a
AB  - 3.7-kilobase fragment of chromosomal DNA from a DpnII-containing strain
AB  - inserted in both possible orientations in the multicopy plasmid vector pMP5 to
AB  - give recombinant plasmids pMP8 and pMP10.  Recombinant plasmids were selected
AB  - by their resistance to DpnII cleavage.  Cells carrying the recombinant plasmids
AB  - modified phage in vivo so that it was restricted by DpnI-but not
AB  - DpnII-containing hosts.  They also showed levels of DNA methylase activity five
AB  - times higher than that in cells of the original DpnII strain.  No DpnII
AB  - activity was observed in the clones; therefore, it was concluded that the
AB  - insert did not contain an intact DpnII endonuclease gene and that methylation
AB  - of host DNA did not turn on a latent form of the gene.
ER  -

TY  - JOUR
AU  - Lacks, S.A.
AU  - Springhorn, S.S.
AU  - Cerritelli, S.
TI  - Restriction/Modification systems of Pneumococci:  Why two methylases in the DpnII system?
JO  - Genetics and Molecular Biology of Streptococci, Lactococci, and Enterococci
PY  - 1991
SP  - 71
EP  - 76
VL  - 8
AB  - None
ER  -

TY  - JOUR
AU  - Ladero, V.
AU  - Alvarez-Sieiro, P.
AU  - Redruello, B.
AU  - Del Rio, B.
AU  - Linares, D.M.
AU  - Martin, M.C.
AU  - Fernandez, M.
AU  - Alvarez, M.A.
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain IPLA 88.
JO  - Genome Announcements
PY  - 2013
SP  - e00524
EP  - e00513
VL  - 1
AB  - Here, we report a 3.2-Mbp draft assembly for the genome of Lactobacillus plantarum IPLA 88.
AB  - The sequence of this sourdough isolate provides insight into
AB  - the adaptation of this versatile species to different environments.
ER  -

TY  - JOUR
AU  - Ladero, V.
AU  - Del Rio, B.
AU  - Linares, D.M.
AU  - Fernandez, M.
AU  - Mayo, B.
AU  - Martin, M.C.
AU  - Alvarez, M.A.
TI  - Draft Genome Sequence of the Putrescine-Producing Strain Lactococcus lactis subsp. lactis 1AA59.
JO  - Genome Announcements
PY  - 2015
SP  - e00669
EP  - e00615
VL  - 3
AB  - We report here the 2,576,542-bp genome annotated draft assembly sequence of Lactococcus lactis
AB  - subsp. lactis 1AA59. This strain-isolated from a traditional
AB  - cheese-produces putrescine, one of the most frequently biogenic amines found in
AB  - dairy products.
ER  -

TY  - JOUR
AU  - Ladero, V.
AU  - Del Rio, B.
AU  - Linares, D.M.
AU  - Fernandez, M.
AU  - Mayo, B.
AU  - Martin, M.C.
AU  - Alvarez, M.A.
TI  - Genome Sequence Analysis of the Biogenic Amine-Producing Strain Lactococcus lactis subsp. cremoris CECT 8666 (Formerly GE2-14).
JO  - Genome Announcements
PY  - 2014
SP  - e01088
EP  - e01014
VL  - 2
AB  - We here report a 2,801,031-bp annotated draft assembly for the Lactococcus lactis subsp.
AB  - cremoris GE2-14 genome. This dairy strain produces the biogenic amine
AB  - putrescine. This sequence may help identify the mechanisms regulating putrescine
AB  - biosynthesis and throw light on ways to reduce its presence in fermented foods.
ER  -

TY  - JOUR
AU  - Ladero, V.
AU  - Herrero-Fresno, A.
AU  - Martinez, N.
AU  - Del Rio, B.
AU  - Linares, D.M.
AU  - Fernandez, M.
AU  - Martin, M.C.
AU  - Alvarez, M.A.
TI  - Genome Sequence Analysis of the Biogenic Amine-Degrading Strain Lactobacillus casei 5b.
JO  - Genome Announcements
PY  - 2014
SP  - e01199
EP  - e01113
VL  - 2
AB  - We here report a 3.02-Mbp annotated draft assembly of the Lactobacillus casei 5b  genome. The
AB  - sequence of this biogenic amine-degrading dairy isolate may help
AB  - identify the mechanisms involved in the catabolism of biogenic amines and perhaps
AB  - shed light on ways to reduce the presence of these toxic compounds in food.
ER  -

TY  - JOUR
AU  - Ladero, V.
AU  - Linares, D.M.
AU  - Del Rio, B.
AU  - Fernandez, M.
AU  - Martin, M.C.
AU  - Alvarez, M.A.
TI  - Draft Genome Sequence of the Tyramine Producer Enterococcus durans Strain IPLA 655.
JO  - Genome Announcements
PY  - 2013
SP  - e00265
EP  - e00213
VL  - 1
AB  - We here report a 3.059-Mbp draft assembly for the genome of Enterococcus durans strain IPLA
AB  - 655. This dairy isolate provides a model for studying the regulation
AB  - of the biosynthesis of tyramine (a toxic compound). These results should aid our
AB  - understanding of tyramine production and allow tyramine accumulation in food to
AB  - be reduced.
ER  -

TY  - JOUR
AU  - Ladner, J.T.
AU  - Welch, T.J.
AU  - Whitehouse, C.A.
AU  - Palacios, G.F.
TI  - Genome Sequence of Weissella ceti NC36, an Emerging Pathogen of Farmed Rainbow Trout in the United States.
JO  - Genome Announcements
PY  - 2013
SP  - e00187
EP  - e00112
VL  - 1
AB  - Novel Weissella sp. bacteria have recently been reported to be associated with disease
AB  - outbreaks in cultured rainbow trout (Oncorhynchus mykiss) at commercial
AB  - farms in China, Brazil, and the United States. Here we present the first genome
AB  - sequence of this novel Weissella species, isolated from the southeastern United
AB  - States.
ER  -

TY  - JOUR
AU  - Ladner, J.T.
AU  - Whitehouse, C.A.
AU  - Koroleva, G.I.
AU  - Palacios, G.F.
TI  - Genome Sequence of Moraxella macacae 0408225, a Novel Bacterial Species Isolated  from a Cynomolgus Macaque with Epistaxis.
JO  - Genome Announcements
PY  - 2013
SP  - e00188
EP  - e00112
VL  - 1
AB  - Moraxella macacae is a recently described bacterial species that has been associated with at
AB  - least two outbreaks of epistaxis in macaques. Here we present
AB  - the first genome sequence of this novel species, isolated from a symptomatic
AB  - cynomolgus macaque at the U.S. Army Medical Research Institute of Infectious
AB  - Diseases.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Alam, I.
AU  - Bisseling, T.
AU  - Geurts, R.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Acinetobacter  radioresistens Strain SA188 Isolated from the Desert Plant Indigofera argentea.
JO  - Genome Announcements
PY  - 2017
SP  - e01708
EP  - e01716
VL  - 5
AB  - Acinetobacter radioresistens strain SA188 is a plant endophytic bacterium, isolated from root
AB  - nodules of the desert plants Indigofera spp., collected in
AB  - Jizan, Saudi Arabia. Here, we report the 3.2-Mb draft genome sequence of strain
AB  - SA188, highlighting characteristic pathways for plant growth-promoting activity
AB  - and environmental adaptation.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Alam, I.
AU  - Geurts, R.
AU  - Bisseling, T.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of the Phosphate-Solubilizing Bacterium Pseudomonas argentinensis Strain SA190 Isolated from the Desert Plant Indigofera argentea.
JO  - Genome Announcements
PY  - 2016
SP  - e01431
EP  - e01416
VL  - 4
AB  - Pseudomonas argentinensis strain SA190 is a plant endophytic-inhabiting bacterium that was
AB  - isolated from root nodules of the desert plant Indigofera argentea collected from the Jizan
AB  - region of Saudi Arabia. Here, we report the genome sequence of SA190, highlighting several
AB  - functional genes related to plant growth-promoting activity, environment adaption, and
AB  - antifungal activity.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Alam, I.
AU  - Geurts, R.
AU  - Bisseling, T.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of Ochrobactrum intermedium Strain SA148, a Plant Growth-Promoting Desert Rhizobacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01707
EP  - e01716
VL  - 5
AB  - Ochrobactrum intermedium strain SA148 is a plant growth-promoting bacterium isolated from
AB  - sandy soil in the Jizan area of Saudi Arabia. Here, we report the
AB  - 4.9-Mb draft genome sequence of this strain, highlighting different pathways
AB  - characteristic of plant growth promotion activity and environmental adaptation of
AB  - SA148.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Alam, I.
AU  - Geurts, R.
AU  - Bisseling, T.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea.
JO  - Genome Announcements
PY  - 2017
SP  - e01638
EP  - e01616
VL  - 5
AB  - Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the
AB  - desert plant Indigofera argentea, collected from the Jizan region
AB  - of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting
AB  - several genes involved in plant growth-promoting activity and environmental
AB  - adaption.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - AlBladi, M.L.
AU  - Salem, N.M.
AU  - Al-Banna, L.
AU  - Alam, I.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan.
JO  - Genome Announcements
PY  - 2017
SP  - e01437
EP  - e01416
VL  - 5
AB  - Pseudomonas punonensis strain D1-6 was isolated from roots of the desert plant Erodium hirtum,
AB  - near the Dead Sea in Jordan. The genome of strain D1-6 reveals
AB  - several key plant growth-promoting and herbicide-resistance genes, indicating a
AB  - possible specialized role for this endophyte.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Bokhari, A.
AU  - Alam, I.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris.
JO  - Genome Announcements
PY  - 2016
SP  - e00678
EP  - e00616
VL  - 4
AB  - We isolated the plant endophytic bacterium Cupriavidus gilardii strain JZ4 from the roots of
AB  - the desert plant Tribulus terrestris, collected from the Jizan
AB  - region, Saudi Arabia. We report here the draft genome sequence of JZ4, together
AB  - with several enzymes related to plant growth-promoting activity, environmental
AB  - adaption, and antifungal activity.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Ramirez-Prado, J.S.
AU  - Alam, I.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta.
JO  - Genome Announcements
PY  - 2016
SP  - e01214
EP  - e01216
VL  - 4
AB  - Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated  from roots
AB  - of Cyperus conglomeratus collected at the Red Sea coast in Thuwal,
AB  - Saudi Arabia. Here, we present a draft genome sequence of this strain,
AB  - highlighting a number of pathways involved in plant growth promotion under salt
AB  - stress.
ER  -

TY  - JOUR
AU  - Lafi, F.F.
AU  - Ramirez-Prado, J.S.
AU  - Alam, I.
AU  - Bajic, V.B.
AU  - Hirt, H.
AU  - Saad, M.M.
TI  - Draft Genome Sequence of Plant Growth-Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia.
JO  - Genome Announcements
PY  - 2017
SP  - e01520
EP  - e01516
VL  - 5
AB  - Micrococcus luteus strain K39 is an endophyte bacterium isolated from roots of the desert
AB  - plant Cyperus conglomeratus collected from the Red Sea shore, Thuwal,
AB  - Saudi Arabia. The draft genome sequence of strain K39 revealed a number of
AB  - enzymes involved in salinity and oxidative stress tolerance or having
AB  - herbicide-resistance activity.
ER  -

TY  - JOUR
AU  - Lafleur, J.E.
AU  - Costa, S.K.
AU  - Bitzer, A.S.
AU  - Silby, M.W.
TI  - Draft Genome Sequence of Cellulophaga sp. E6, a Marine Algal Epibiont That Produces a Quorum-Sensing Inhibitory Compound Active against Pseudomonas  aeruginosa.
JO  - Genome Announcements
PY  - 2015
SP  - e01565
EP  - e01514
VL  - 3
AB  - The genus Cellulophaga is composed of obligate aerobic Gram-negative bacteria commonly found
AB  - in association with marine algae. We report the approximately
AB  - 4.42-Mbp draft genome sequence of Cellulophaga sp. E6, which inhibits
AB  - N-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C12-HSL)-mediated quorum sensing
AB  - (QS), lasB transcription, and biofilm formation by Pseudomonas aeruginosa.
ER  -

TY  - JOUR
AU  - Laganeckas, M.
AU  - Margelevicius, M.
AU  - Venclovas, C.
TI  - Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 1187
EP  - 1196
VL  - 39
AB  - PD-(D/E)XK nucleases, initially represented by only Type II restriction enzymes, now comprise
AB  - a large and extremely diverse superfamily of
AB  - proteins. They participate in many different nucleic acids transactions
AB  - including DNA degradation, recombination, repair and RNA processing.
AB  - Different PD-(D/E)XK families, although sharing a structurally conserved
AB  - core, typically display little or no detectable sequence similarity except
AB  - for the active site motifs. This makes the identification of new
AB  - superfamily members using standard homology search techniques challenging.
AB  - To tackle this problem, we developed a method for the detection of
AB  - PD-(D/E)XK families based on the binary classification of profile-profile
AB  - alignments using support vector machines (SVMs). Using a number of both
AB  - superfamily-specific and general features, SVMs were trained to identify
AB  - true positive alignments of PD-(D/E)XK representatives. With this method
AB  - we identified several PFAM families of uncharacterized proteins as
AB  - putative new members of the PD-(D/E)XK superfamily. In addition, we
AB  - assigned several unclassified restriction enzymes to the PD-(D/E)XK type.
AB  - Results show that the new method is able to make confident assignments
AB  - even for alignments that have statistically insignificant scores. We also
AB  - implemented the method as a freely accessible web server at
AB  - http://www.ibt.lt/bioinformatics/software/pdexk/.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - Armougom, F.
AU  - Mishra, A.K.
AU  - Nguyen, T.T.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 315
EP  - 324
VL  - 6
AB  - Alistipes timonensis strain JC136(T) sp. nov. is the type strain of A. timonensis sp. nov., a
AB  - new species within the genus Alistipes. This strain, whose genome is
AB  - described here, was isolated from the fecal flora of a healthy patient. A.
AB  - timonensis is an obligate anaerobic rod. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 3,497,779 bp long genome (one chromosome but no plasmid) contains 2,742
AB  - protein-coding and 50 RNA genes, including three rRNA genes.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - Bibi, F.
AU  - Ramasamy, D.
AU  - Azhar, E.I.
AU  - Robert, C.
AU  - Yasir, M.
AU  - Jiman-Fatani, A.A.
AU  - Alshali, K.Z.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1003
EP  - 1019
VL  - 9
AB  - Clostridium jeddahense strain JCD(T) (= CSUR P693 = DSM 27834) is the type strain of C.
AB  - jeddahense sp. nov. This strain, whose genome is described here, was
AB  - isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52
AB  - kg/m(2)). Clostridium jeddahense strain JCD(T) is an obligate Gram-positive
AB  - bacillus. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 3,613,503 bp long genome (1
AB  - chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462
AB  - protein-coding and 53 RNA genes, including 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - El Karkouri, K.
AU  - Mishra, A.K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 399
EP  - 412
VL  - 7
AB  - Enterobacter massiliensis strain JC163(T) sp. nov. is the type strain of E. massiliensis sp.
AB  - nov., a new species within the genus Enterobacter. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a healthy
AB  - Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a
AB  - G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes,
AB  - including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - El Karkouri, K.
AU  - Nguyen, T.T.
AU  - Armougom, F.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 116
EP  - 125
VL  - 6
AB  - Anaerococcus senegalensis strain JC48T sp. nov. is the type strain of A. senegalensis sp.
AB  - nov., a new species within the genus Anaerococcus. This strain, whose genome is described
AB  - here, was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate
AB  - anaerobic coccus. Here we describe the features of this organism, together with the complete
AB  - genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid)
AB  - contains 1,721 protein-coding and 53 RNA genes, including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - Elkarkouri, K.
AU  - Rivet, R.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 343
EP  - 356
VL  - 7
AB  - Senegalemassilia anaerobia strain JC110(T) sp.nov. is the type strain of Senegalemassilia
AB  - anaerobia gen. nov., sp. nov., the type species of a new genus
AB  - within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a healthy
AB  - Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 2,383,131 bp long genome contains 1,932
AB  - protein-coding and 58 RNA genes.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - Gimenez, G.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 200
EP  - 209
VL  - 7
AB  - Herbaspirillum massiliense strain JC206(T) sp. nov. is the type strain of H. massiliense sp.
AB  - nov., a new species within the genus Herbaspirillum. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a healthy
AB  - Senegalese patient. H. massiliense is an aerobic rod. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 4,186,486 bp long genome (one chromosome but no plasmid) contains
AB  - 3,847 protein-coding and 54 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - Khelaifia, S.
AU  - Azhar, E.I.
AU  - Croce, O.
AU  - Bibi, F.
AU  - Jiman-Fatani, A.A.
AU  - Yasir, M.
AU  - Helaby, H.B.
AU  - Robert, C.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 91
EP  - 91
VL  - 10
AB  - Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from
AB  - a mural painting. We demonstrate, for the first time, the culture
AB  - of human Oceanobacillus picturae, strain S1(T), whose genome is described here,
AB  - from a stool sample collected from a 25-year-old Saoudian healthy individual. We
AB  - used a slightly modified standard culture medium adding 100 g/L of NaCl. We
AB  - provide a short description of this strain including its MALDI-TOF spectrum, the
AB  - main identification tool currently used in clinical microbiology. The 3,675,175
AB  - bp long genome exhibits a G + C content of 39.15 % and contains 3666
AB  - protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus
AB  - picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb
AB  - versus 3.83 Mb). The G + C content was higher compared with Oceanobacillus
AB  - kimchii (respectively 39.15 % and 35.2 %). Oceanobacillus picturae shared almost
AB  - identical number of genes (3823 genes versus 3879 genes), with a similar ratio of
AB  - genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of
AB  - Oceanobacillus picturae strain S1 isolated for the first time in a human, will be
AB  - added to the 778 genome projects from the gastrointestinal tract listed by the
AB  - international consortium Human Microbiome Project.
ER  -

TY  - JOUR
AU  - Lagier, J.C.
AU  - Ramasamy, D.
AU  - Rivet, R.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 258
EP  - 270
VL  - 7
AB  - Cellulomonas massiliensis strain JC225(T) sp. nov. is the type strain of Cellulomonas
AB  - massiliensis sp., a new species within the genus Cellulomonas. This
AB  - strain, whose genome is described here, was isolated from the fecal flora of a
AB  - healthy Senegalese patient. C. massiliensis is an aerobic rod-shaped bacterium.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 3,407,283 bp long genome contains 3,083
AB  - protein-coding and 48 RNA genes.
ER  -

TY  - JOUR
AU  - Laging, M.
AU  - Lindner, E.
AU  - Fritz, H.-J.
AU  - Kramer, W.
TI  - Repair of hydrolytic DNA deamination damage in thermophilic bacteria: cloning and characterization of a Vsr endonuclease homolog from Bacillus stearothermophilus.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 1913
EP  - 1920
VL  - 31
AB  - Hydrolytic deamination of 5-methyl cytosine in double stranded DNA results in formation of a
AB  - T/G mismatch that-if left unrepaired-leads to a C-->T
AB  - transition mutation in half of the progeny. In addition to several
AB  - mismatch-specific glycosylases that have been found in both pro- and
AB  - eukaryotes to channel this lesion into base excision repair by removing
AB  - the T from the mismatch, Vsr endonuclease from Escherichia coli has been
AB  - described which initiates repair by an endonucleolytic strand incision 5'
AB  - to the mismatched T. We have isolated a gene coding for a homolog of
AB  - E.coli Vsr endonuclease from the thermophilic bacterium Bacillus
AB  - stearothermophilus H3 (Vsr.Bst) using a method that allows PCR
AB  - amplification with degenerated primers of gene segments which code for
AB  - only one highly conserved amino acid region. Vsr.Bst was produced
AB  - heterologously in E.coli and purified to apparent homogeneity. Vsr.Bst
AB  - specifically incises heteroduplex DNA with a preference for T/G
AB  - mismatches. The selectivity of Vsr.Bst for the sequence context of the T/G
AB  - mismatch appears less pronounced than for Vsr.Eco.
ER  -

TY  - JOUR
AU  - Lagonenko, A.L.
AU  - Komardina, V.S.
AU  - Nikolaichik, Y.A.
AU  - Evtushenkov, A.N.
TI  - First Report of Erwinia amylovora Fire Blight in Belarus.
JO  - J. Phytopathol.
PY  - 2008
SP  - 638
EP  - 640
VL  - 156
ER  -

TY  - JOUR
AU  - Laguerre, S.
AU  - Amari, M.
AU  - Vuillemin, M.
AU  - Robert, H.
AU  - Loux, V.
AU  - Klopp, C.
AU  - Morel, S.
AU  - Gabriel, B.
AU  - Remaud-Simeon, M.
AU  - Gabriel, V.
AU  - Moulis, C.
AU  - Fontagne-Faucher, C.
TI  - Genome Sequences of Three Leuconostoc citreum Strains, LBAE C10, LBAE C11, and LBAE E16, Isolated from Wheat Sourdoughs.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1610
EP  - 1611
VL  - 194
AB  - Leuconostoc citreum is a key microorganism in fermented foods of plant origin. Here we report
AB  - the draft genome sequence for three strains of Leuconostoc
AB  - citreum, LBAE C10, LBAE C11, and LBAE E16, which have been isolated from
AB  - traditional French wheat sourdoughs.
ER  -

TY  - JOUR
AU  - Lagunavicius, A.
TI  - DNA binding by MunI restriction endonuclease.
JO  - Biologija
PY  - 1997
SP  - 13
EP  - 20
VL  - 1
AB  - Investigation of DNA binding properties by gel shift assay indicated that in the absence of
AB  - cofactor at pH 8.0, WT MunI binds to DNA containing or lacking the recognition sequence with
AB  - similar affinity and only at a high excess of protein.  Contrary to the WT enzyme, E98A and
AB  - D83A mutants under the same conditions bound DNA containing the recognition sequence with high
AB  - affinity.  With noncognate DNA the latter mutants exhibited only a weak binding characteristic
AB  - of the WT MunI.  The increased affinity of the mutants to the cognate DNA suggest that E98A
AB  - and D83A replacements can mimic the effect of Mg2+ ion during the development of the
AB  - specificity of MunI restriction enzyme at the catalytic step.  An increased affinity of the WT
AB  - MunI to the cognate DNA was observed also at low pH or in the presence Ca2+ ions.  Indeed, in
AB  - contrast to the binding experiments at pH 8.0, gel-shift analysis at pH 6.5 indicated a tight
AB  - sequence-specific binding of WT MunI to the cognate DNA suggesting that the protonation of the
AB  - active site carboxylate residue(s) with anomalous high pKa value control the binding
AB  - specificity.  Interestingly, Ca2+ ions that did not support DNA cleavage by MunI were able to
AB  - induce DNA binding specificity of WT MunI at pH 8.0 and probably mimic the role of Mg2+ ions
AB  - in the development of sequence specific binding.  The relief of unfavorable repulsive
AB  - constraints either by replacement of carboxylate(s) lowering the pH or metal ion binding leads
AB  - to the manifestation of binding specificity by MunI.
ER  -

TY  - JOUR
AU  - Lagunavicius, A.
AU  - Grazulis, S.
AU  - Balciunaite, E.
AU  - Vainius, D.
AU  - Siksnys, V.
TI  - DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: Involvement of active site carboxylate residues.
JO  - Biochemistry
PY  - 1997
SP  - 11093
EP  - 11099
VL  - 36
AB  - Gel shift analysis reveals that at pH 8.3 in the absence of Mg2+, MunI restriction
AB  - endonuclease exhibits little DNA binding specificity, as compared with the D83A and E98A
AB  - mutants of MunI.  This suggests that charged carboxylate residue(s) influence the DNA binding
AB  - specificity of MunI.  In our efforts to establish the determinants of MunI binding
AB  - specificity, we investigated the possible role of the ionic milieu, and we found that lowering
AB  - pH or elevating Ca2+ levels per se induces specific DNA recognition by WT MunI.  In contrast
AB  - to the binding experiments at pH 8.3, gel shift analysis at pH 6.5 indicated tight
AB  - sequence-specific binding of WT MunI in the absence of Mg2+, suggesting that protonation of
AB  - active site carboxylate residue(s) which manifest anomalously high pKa value(s) control
AB  - binding specificity.  Interestingly, Ca2+ ion concentrations, which did not support DNA
AB  - cleavage by MunI also induced DNA binding specificity in WT MunI at pH 8.3.  To explore
AB  - possible structural changes upon DNA binding, we then used a limited proteolysis technique.
AB  - Trypsin cleavage of MunI--DNA complexes indicated that in the presence of cognate DNA the MunI
AB  - restriction endonuclease became resistant to proteolytic cleavage, suggesting that binding of
AB  - specific DNA induced a structural change.  CD measurements confirmed this observation,
AB  - suggesting minor secondary structural differences between complexes of MunI with cognate and
AB  - noncognate DNA. These results therefore suggest that binding of MunI to its recognition
AB  - sequence triggers a conformational transition that correctly juxtaposes active site
AB  - carboxylate residues, which then chelate Mg2+ ions.  In the absence of Mg2+ ions, at pH 8.3,
AB  - conditions in which carboxylate groups would be expected to be completely ionized,
AB  - electrostatic repulsion between charged carboxylates and phosphate oxygens is enhanced such as
AB  - to interfere with specific DNA binding.  Elimination of such repulsive constraints by
AB  - replacement of carboxylate residues, by lowering pH, or by metal ion binding, then promotes
AB  - MunI binding specificity.
ER  -

TY  - JOUR
AU  - Lagunavicius, A.
AU  - Sasnauskas, G.
AU  - Halford, S.E.
AU  - Siksnys, V.
TI  - The metal-independent type IIS restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 1051
EP  - 1064
VL  - 326
AB  - BfiI is a novel type IIs restriction endonuclease that, unlike all other restriction enzymes
AB  - characterised to date, cleaves DNA in the absence of
AB  - Mg(2+). The amino acid sequence of the N-terminal part of BfiI has some
AB  - similarities to Nuc of Salmonella typhimurium, an EDTA-resistant nuclease
AB  - akin to phospholipase D. The dimeric form of Nuc contains a single active
AB  - site composed of residues from both subunits. To examine the roles of the
AB  - amino acid residues of BfiI that align with the catalytic residues in Nuc,
AB  - a set of alanine replacement mutants was generated by site-directed
AB  - mutagenesis. The mutationally altered forms of BfiI were all catalytically
AB  - inactive but were still able to bind DNA specifically. The active site of
AB  - BfiI is thus likely to be similar to that of Nuc. BfiI was also found by
AB  - gel-filtration to be a dimer in solution. Both gel-shift and pull-down
AB  - assays indicated that the dimeric form of BfiI binds two copies of its
AB  - recognition sequence. In reactions on plasmids with either one or two
AB  - copies of its recognition sequence, BfiI cleaved the DNA with two sites
AB  - more rapidly than that with one site. Yet, when bound to two copies of its
AB  - recognition sequence, the BfiI dimer cleaved only one phosphodiester bond
AB  - at a time. The dimer thus seems to contain two DNA-binding domains but
AB  - only one active site.
ER  -

TY  - JOUR
AU  - Lagunavicius, A.
AU  - Siksnys, V.
TI  - Mutational analysis of MunI restriction endonuclease.
JO  - Biologija
PY  - 1996
SP  - 35
EP  - 38
VL  - 0
AB  - Mapping of the conserved sequence regions between MunI and EcoRI restriction endonucleases to
AB  - the known X-ray structure of the EcoRI restriction enzyme allowed us to identify a sequence
AB  - motif 82PDX14EXK as a putative catalytic site of MunI.  Site-directed mutagenesis was used to
AB  - test whether amino acids P82, D83, E98 and K100 were important for catalytic activity of MunI.
AB  - A set of MunI mutants (P82A, D83A, E98Q, E98Q, E98A, K100E, K100A) altered at the putative
AB  - catalytic site was obtained using site-directed mutagenesis, and the catalytic properties of
AB  - the mutants were studied in vivo and in vitro.  The phenotypes observed in vivo and in vitro
AB  - for the mutants of putative catalytic site residues of MunI were consistent with the proposed
AB  - active site function.  Investigation of the cleavage properties of these mutants revealed that
AB  - E98Q replacement in MunI resulted in alteration of metal ion binding.  Contrary to the wild
AB  - type enzyme, this mutant was activated by Mn2+ ions more effectively than by Mg2+ ions.
ER  -

TY  - JOUR
AU  - Lagunavicius, A.
AU  - Siksnys, V.
TI  - Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.
JO  - Biochemistry
PY  - 1997
SP  - 11086
EP  - 11092
VL  - 36
AB  - Mapping of the conserved sequence regions in the restriction endonucleases MunI (C/AATTG) and
AB  - EcoRI (G/AATTC) to the known X-ray structure of EcoRI allowed us to identify the sequence
AB  - motif 82PDX14EXK as the putative catalytic/Mg2+ ion binding site of MunI.  Site-directed
AB  - mutagenesis was then used to test whether amino acids P82, D83, E98, and K100 were important
AB  - for the catalytic activity of MunI.  Mutation P82A generated only a marginal effect on the
AB  - cleavage properties of the enzyme.  Investigation of the cleavage properties of the D83, E98,
AB  - and K100 substitution mutants, however, in vivo and in vitro, revealed either an absence of
AB  - catalytic activity or markedly reduced catalytic activity.  Interestingly, the deleterious
AB  - effect of the E98Q replacement in vitro was partially overcome by replacement of the metal
AB  - cofactor used.  Though the catalytic activity of the E98Q mutant was only 0.4% of WT under
AB  - standard conditions (in the presence of Mg2+ ions), the mutant exhibited 40% of WT catalytic
AB  - activity in buffer supplemented with Mn2+ ions.  Further, the DNA binding properties of these
AB  - substitution mutants were analyzed using the gel shift assay technique.  In the absence of
AB  - Mg2+ ions, WT MunI bound both cognate DNA and noncognate sequences with similar low
AB  - affinities.  The D83A and E98A mutants, in contrast, in the absence of Mg2+ ions, exhibited
AB  - significant specificity of binding to cognate DNA, suggesting that the substitutions made can
AB  - simulate the effect of the Mg2+ ion in conferring specificity to the MunI restriction enzyme.
ER  -

TY  - JOUR
AU  - Lahav, T.
AU  - Zchori-Fein, E.
AU  - Naor, V.
AU  - Freilich, S.
AU  - Iasur-Kruh, L.
TI  - Draft Genome Sequence of a Dyella-Like Bacterium from the Planthopper Hyalesthes  obsoletus.
JO  - Genome Announcements
PY  - 2016
SP  - e00686
EP  - e00616
VL  - 4
AB  - We report here the draft genome sequence of a Dyella-like bacterium (DLB) isolated from
AB  - Hyalesthes obsoletus, the insect vector of the uncultivable
AB  - mollicute bacterium 'Candidatus Phytoplasma.' This isolate inhibits Spiroplasma
AB  - melliferum, a cultivable mollicute. The draft genome of DLB consists of 4,196,214
AB  - bp, with a 68.6% G+C content, and 3,757 genes were predicted.
ER  -

TY  - JOUR
AU  - Lahlou, L.
AU  - El Mrimar, N.
AU  - Alouane, T.
AU  - Laamarti, M.
AU  - Karti, S.
AU  - Benhrif, O.
AU  - El Mesbahi, H.
AU  - Lemriss, H.
AU  - Bssaibis, F.
AU  - Maleb, A.
AU  - El Rarit, S.
AU  - Zegmout, A.
AU  - El Jaoudi, R.
AU  - Frikh, M.
AU  - Lemnouar, A.
AU  - Dakka, T.
AU  - Elouennass, M.
AU  - Ibrahimi, A.
TI  - Annotated Whole-Genome Shotgun Sequence of Multidrug-Resistant Mycobacterium tuberculosis MTB13_M Isolated from Morocco.
JO  - Genome Announcements
PY  - 2017
SP  - e01756
EP  - e01716
VL  - 5
AB  - Here, we describe the annotated genome sequence of Mycobacterium tuberculosis MTB13_M. The
AB  - organism was isolated from a sputum sample in Morocco.
ER  -

TY  - JOUR
AU  - Lahlou, L.
AU  - El Mrimar, N.
AU  - Laamarti, M.
AU  - Alouane, T.
AU  - Bendahou, M.A.
AU  - Bssaibis, F.
AU  - Ben Lahlou, Y.
AU  - Zegmout, A.
AU  - El Hafidi, N.
AU  - ElJaoudi, R.
AU  - Frikh, M.
AU  - Lemnouar, A.
AU  - Elouennass, M.
AU  - Ibrahimi, A.
TI  - Whole-Genome Shotgun Sequences of Three Multidrug-Resistant Mycobacterium tuberculosis Strains Isolated from Morocco.
JO  - Genome Announcements
PY  - 2017
SP  - e01275
EP  - e01217
VL  - 5
AB  - Tuberculosis is a contagious disease that usually attacks the lungs but sometimes attacks
AB  - other parts of the body, such as the kidneys, glands, and bones. It is an
AB  - endemic and major public health problem in Morocco. Tuberculosis is transmitted
AB  - through the airways via the inhalation of microdroplets containing Mycobacterium
AB  - tuberculosis We present here the whole-genome shotgun sequences of three
AB  - multidrug-resistant M. tuberculosis strains isolated from Morocco.
ER  -

TY  - JOUR
AU  - Lai, C.
AU  - Wu, X.
AU  - Chen, C.
AU  - Huang, T.
AU  - Xiong, X.
AU  - Wu, S.
AU  - Gu, M.
AU  - Deng, Z.
AU  - Chen, Xi.
AU  - Chen, S.
AU  - Wang, L.
TI  - In Vivo Mutational Characterization of DndE Involved in DNA Phosphorothioate Modification.
JO  - PLoS ONE
PY  - 2014
SP  - e107981
EP  - e107981
VL  - 9
AB  - DNA phosphorothioate (PT) modification is a recently identified epigenetic modification that
AB  - occurs in the sugar-phosphate backbone of prokaryotic DNA. Previous studies have demonstrated
AB  - that DNA PT modification is governed by the five DndABCDE proteins in a sequence-selective and
AB  - R-P stereo-specific manner. Bacteria may have acquired this physiological modification along
AB  - with dndFGH as a restriction-modification system. However, little is known about the
AB  - biological function of Dnd proteins, especially the smallest protein, DndE, in the PT
AB  - modification pathway. DndE was reported to be a DNA-binding protein with a preference for
AB  - nicked dsDNA in vitro; the binding of DndE to DNA occurs via six positively charged lysine
AB  - residues on its surface. The substitution of these key lysine residues significantly decreased
AB  - the DNA binding affinities of DndE proteins to undetectable levels. In this study, we
AB  - conducted site-directed mutagenesis of dndE on a plasmid and measured DNA PT modifications
AB  - under physiological conditions by mass spectrometry. We observed distinctive differences from
AB  - the in vitro binding assays. Several mutants with lysine residues mutated to alanine decreased
AB  - the total frequency of PT modifications, but none of the mutants completely eliminated PT
AB  - modification. Our results suggest that the nicked dsDNA-binding capacity of DndE may not be
AB  - crucial for PT modification and/or that DndE may have other biological functions in addition
AB  - to binding to dsDNA.
ER  -

TY  - JOUR
AU  - Lai, J.Y.
AU  - Zhang, H.
AU  - Chiang, M.H.
AU  - Yu, M.
AU  - Zhang, R.
AU  - Lau, S.C.
TI  - Draft Genome Sequence of Escherichia coli E1728 Isolated from Marine Sediment in  Hong Kong.
JO  - Genome Announcements
PY  - 2014
SP  - e00430
EP  - e00414
VL  - 2
AB  - Recent findings of Escherichia coli persisting autochthonously in environmental matrices
AB  - outside animal bodies have revealed largely unknown facets of the
AB  - lifestyle and ecophysiology of the species that have yet to be explored. Here, we
AB  - report the draft genome sequence of E. coli E1728 isolated from marine sediment.
ER  -

TY  - JOUR
AU  - Lai, J.Y.
AU  - Zhang, H.
AU  - Chiang, M.H.
AU  - Yu, M.
AU  - Zhang, R.
AU  - Lau, S.C.
TI  - Draft Genome Sequences of Three Escherichia coli Strains Investigated for the Effects of Lysogeny on Niche Diversification.
JO  - Genome Announcements
PY  - 2014
SP  - e00955
EP  - e00914
VL  - 2
AB  - During the course of investigating the effects of lysogeny on niche diversification of
AB  - Escherichia coli, we used the temperate phages induced from
AB  - one E. coli strain to infect another and created an isogenic lysogen of the
AB  - latter. The draft genome sequences of the three E. coli strains are reported
AB  - herein.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Cao, J.
AU  - Yuan, J.
AU  - Li, F.
AU  - Shao, Z.
TI  - Celeribacter indicus sp. nov. a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 4160
EP  - 4167
VL  - 64
AB  - A taxonomic study was carried out on strain P73(T), which was isolated from
AB  - deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic
AB  - hydrocarbons. The strain was able to degrade biphenyl, naphthalene,
AB  - 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene,
AB  - phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene
AB  - and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S
AB  - rRNA gene sequences showed that strain P73(T) formed a clade with the genera
AB  - Celeribacter and Huaishuia within the family Rhodobacteraceae, with highest
AB  - sequence similarity of 96.98 % to Celeribacter neptunius H 14(T), followed by
AB  - Huaishuia halophila ZXM137(T) (96.42 %). The bacterium was Gram-stain-negative,
AB  - oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at
AB  - salinities from 0.5 to 12 % and at temperatures from 10 to 41 degrees C. The
AB  - principal fatty acids (>10 %) of strain P73(T) were summed feature 8 (C18 :
AB  - 1omega7c/omega6c) and C19 : 0omega8c cyclo. The sole respiratory quinone was
AB  - Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one
AB  - unknown phospholipid and one unknown lipid; a second unknown phospholipid and one
AB  - unknown glycolipid were present as minor components. The G+C content of the
AB  - chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show
AB  - that strain P73(T) represents a novel species of the genus Celeribacter, for
AB  - which the name Celeribacter indicus sp. nov. is proposed. The type strain is
AB  - P73(T) ( = MCCC 1A01112(T) = LMG 27600(T) = DSM 27257(T)). Phylogenetic study and
AB  - existing phenotypic information also show that Huaishuia halophila should be
AB  - transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type
AB  - strain ZXM137(T) = MCCC 1A06432(T) = CGMCC 1.8891(T) = LMG 24854(T)).
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Li, C.
AU  - Shao, Z.
TI  - Genome Sequence of Galbibacter marinum Type Strain ck-I2-15.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6973
EP  - 6973
VL  - 194
AB  - Galbibacter marinum strain ck-I2-15(T) was isolated from an arsenite-resistant consortium
AB  - enriched from the deep sea sediment of a hydrothermal vent field on
AB  - the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain
AB  - ck-I2-15(T), which contains 3,572,447 bp with a G+C content of 37.04% and
AB  - contains 3,099 protein-coding genes and 38 tRNA genes.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Li, G.
AU  - Shao, Z.
TI  - Genome Sequence of Nitratireductor pacificus Type Strain pht-3B.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6958
EP  - 6958
VL  - 194
AB  - Nitratireductor pacificus strain pht-3B(T) was isolated from a pyrene-degrading consortium
AB  - enriched from the deep sea sediment of the Pacific Ocean. Here, we
AB  - present the draft genome of strain pht-3B(T), which contains 4,466,205 bp with a
AB  - G+C content of 65.51% and contains 4,197 protein-coding genes and 46 tRNA genes.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Li, G.
AU  - Yu, Z.
AU  - Shao, Z.
TI  - Genome Sequence of Nitratireductor indicus Type Strain C115.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6990
EP  - 6990
VL  - 194
AB  - Nitratireductor indicus strain C115(T) was isolated from a crude-oil-degrading consortium
AB  - enriched from deep seawater of the Indian Ocean. Here, we present the
AB  - draft genome of strain C115(T), which contains 4,992,479 bp with a G+C content of
AB  - 60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Li, W.
AU  - Shao, Z.
TI  - Complete Genome Sequence of Alcanivorax dieselolei Type Strain B5.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6674
EP  - 6674
VL  - 194
AB  - Alcanivorax dieselolei B5(T) was isolated from oil-contaminated surface water of  the Bohai
AB  - Sea of China and characterized by the efficient degradation of alkane
AB  - (C(5)-C(36)). Here we report the complete genome of B5(T) and genes associated
AB  - with alkane degradation.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Li, W.
AU  - Wang, B.
AU  - Yu, Z.
AU  - Shao, Z.
TI  - Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6677
EP  - 6677
VL  - 194
AB  - Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific  Ocean and
AB  - characterized as a unique bacterium in the degradation of pyrene, a
AB  - four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete
AB  - genome of P1 and genes associated with PAH degradation.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Liu, Y.
AU  - Shao, Z.
TI  - Genome Sequence of Bacillus sp. Strain HYC-10, Isolated from Intestinal Tract Contents from a Marine Fish (Mugil cephalus).
JO  - J. Bacteriol.
PY  - 2012
SP  - 6991
EP  - 6991
VL  - 194
AB  - Bacillus sp. strain HYC-10 was isolated with intestinal tract content of a fish,  Mugil
AB  - cephalus, captured from the sea close to Xiamen Island, China. Here, we
AB  - present the draft genome of strain HYC-10, which contains 3,611,918 bp with a G+C
AB  - content of 41.30% and contains 3,687 protein-coding genes and 33 tRNA genes.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6936
EP  - 6936
VL  - 194
AB  - Alcanivorax pacificus W11-5(T) was isolated from a pyrene-degrading consortium, enriched from
AB  - the deep sea sediment of the Pacific Ocean. Strain W11-5(T) can
AB  - degrade various n-alkanes. Here we report the draft genome of W11-5(T) and genes
AB  - associated with alkane degradation.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Genome Sequence of Oceanibaculum indicum Type Strain P24.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6942
EP  - 6942
VL  - 194
AB  - Oceanibaculum indicum type strain P24 was isolated from a
AB  - polycyclic-aromatic-hydrocarbon-degrading consortium enriched from a
AB  - deep-seawater sample collected from the Indian Ocean. Here we present the draft
AB  - genome of strain P24(T), which contains 3,952,792 bp with a G+C content of 65.5%
AB  - and contains 3,755 protein-coding genes and 45 tRNAs.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Genome Sequence of Thalassospira profundimaris Type Strain WP0211.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6956
EP  - 6956
VL  - 194
AB  - Thalassospira profundimaris WP0211(T) was isolated from a pyrene-degrading consortium,
AB  - enriched from deep-sea sediment collected from the West Pacific
AB  - Ocean. Here, we present the draft genome of strain WP0211(T), which contains
AB  - 4,380,232 bp with a G+C content of 55.19% and contains 4,040 protein-coding genes
AB  - and 45 tRNAs.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Genome Sequence of Thalassospira xiamenensis Type Strain M-5.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6957
EP  - 6957
VL  - 194
AB  - Thalassospira xiamenensis M-5(T) was isolated from the surface water of a waste oil pool at
AB  - the oil storage dock in the city of Xiamen, Fujian Province, China.
AB  - Here, we present the draft genome of strain M-5(T), which contains 4,705,237 bp
AB  - with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Genome Sequence of the Alkane-Degrading Bacterium Alcanivorax hongdengensis Type  Strain A-11-3.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6972
EP  - 6972
VL  - 194
AB  - Alcanivorax hongdengensis A-11-3(T) was isolated from an oil-enriched consortium  enriched
AB  - from the surface seawater of Hong-Deng dock in the Straits of Malacca
AB  - and Singapore. Strain A-11-3(T) can degrade n-alkane and produce a lipopeptide
AB  - biosurfactant. Here we report the genome of A-11-3(T) and the genes associated
AB  - with alkane degradation.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Wang, L.
AU  - Wang, W.
AU  - Shao, Z.
TI  - Genome Sequence of Gallaecimonas xiamenensis Type Strain 3-C-1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6937
EP  - 6937
VL  - 194
AB  - Gallaecimonas xiamenensis 3-C-1(T) was isolated from a crude-oil-degrading consortium enriched
AB  - from the surface seawater around Xiamen Island. Here, we
AB  - present the draft genome of strain 3-C-1(T), which contains 4,062,282 bp with a
AB  - G+C content of 60.58% and contains 3,798 protein-coding genes and 65 tRNAs.
ER  -

TY  - JOUR
AU  - Lai, Q.
AU  - Wang, L.
AU  - Wang, W.
AU  - Shao, Z.
TI  - Genome Sequence of Idiomarina xiamenensis Type Strain 10-D-4.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6938
EP  - 6938
VL  - 194
AB  - Idiomarina xiamenensis strain 10-D-4(T) was isolated from an oil-degrading consortium enriched
AB  - from surface seawater around the Xiamen island. Here, we
AB  - present the draft genome of strain 10-D-4(T), which contains 2,899,282 bp with a
AB  - G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes.
ER  -

TY  - JOUR
AU  - Lai, W.X.
AU  - Gan, H.M.
AU  - Hudson, A.O.
AU  - Savka, M.A.
TI  - Whole-Genome Sequencing Reveals a New Genospecies of Methylobacterium sp. GXS13,  Isolated from Vitis vinifera L. Xylem Sap.
JO  - Genome Announcements
PY  - 2016
SP  - e01695
EP  - e01615
VL  - 4
AB  - The whole-genome sequence of a new genospecies of Methylobacterium sp., named GXS13 and
AB  - isolated from grapevine xylem sap, is reported and demonstrates
AB  - potential for methylotrophy, cytokinin synthesis, and cell wall modification. In
AB  - addition, biosynthetic gene clusters were identified for cupriachelin,
AB  - carotenoid, and acyl-homoserine lactone using the antiSMASH server.
ER  -

TY  - JOUR
AU  - Lai, Y.C.
AU  - Yang, S.L.
AU  - Peng, H.L.
AU  - Chang, H.Y.
TI  - Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae.
JO  - Infect. Immun.
PY  - 2000
SP  - 7149
EP  - 7151
VL  - 68
AB  - Klebsiella pneumoniae is a common cause of septicemia and urinary tract infections. The
AB  - PCR-supported genomic subtractive hybridization was
AB  - employed to identify genes specifically present in a virulent strain of K.
AB  - pneumoniae. Analysis of 25 subtracted DNA clones has revealed 19 distinct
AB  - nucleotide sequences. Two of the sequences were found to be the genes
AB  - encoding the transposase of Tn3926 and a capsule polysaccharide exporting
AB  - enzyme. Three sequences displayed moderate homology with bvgAS, which
AB  - encodes a two-component signal transduction system in Bordetella
AB  - pertussis. The rest of the sequences did not exhibit homology with any
AB  - known genes. The distribution of these novel sequences varied greatly in
AB  - K. pneumoniae clinical isolates, reflecting the heterogeneous nature of
AB  - the K. pneumoniae population.
ER  -

TY  - JOUR
AU  - Laigret, F.
AU  - Gaurivaud, P.
AU  - Bove, J.-M.
TI  - The unique organization of the rpoB region of Spiroplasma citri: a restriction and modification system gene is adjacent to rpoB.
JO  - Gene
PY  - 1996
SP  - 95
EP  - 98
VL  - 171
AB  - A 6.5-kb DNA fragment containing the gene (rpoB) encoding the RNA polymerase (RNAP) beta
AB  - subunit, from the mollicute Spiroplasma citri (Sc), was cloned and sequenced.  The classical
AB  - eubacterial organization, with the genes (rplK, A, J and L) encoding ribosomal proteins L11,
AB  - L1, L10 and L12 located immediately upstream from rpoB, was not found in the Sc DNA.  Instead,
AB  - an open reading frame (hsdS) potentially encoding a component of a type I restriction and
AB  - modification system was identified upstream from rpoB, and sequences showing similarities with
AB  - insertion elements were found between hsdS and rpoB.
ER  -

TY  - JOUR
AU  - Lail, K. et al.
TI  - Complete genome sequence of Spirosoma linguale type strain (1).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 176
EP  - 185
VL  - 2
AB  - Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living
AB  - and non-pathogenic organism, known for its peculiar ringlike and
AB  - horseshoe-shaped cell morphology. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is only the third
AB  - completed genome sequence of a member of the family Cytophagaceae. The 8,491,258
AB  - bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Laino, J.E.
AU  - Hebert, E.M.
AU  - Savoy-de-Giori, G.
AU  - LeBlanc, J.G.
TI  - Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CRL871, a Folate-Producing Strain Isolated from a Northwestern Argentinian Yogurt.
JO  - Genome Announcements
PY  - 2015
SP  - e00693
EP  - e00615
VL  - 3
AB  - Lactobacillus delbrueckii subsp. bulgaricus CRL871 is the first strain of L. delbrueckii
AB  - subsp. bulgaricus reported as a folate-producing strain. We report
AB  - the draft genome sequence of L. delbrueckii subsp. bulgaricus CRL871 (2,063,981
AB  - bp, G+C content of 49.1%). This strain is of great biotechnological importance to
AB  - the dairy industry because it constitutes an alternative to folic acid
AB  - fortification.
ER  -

TY  - JOUR
AU  - Lainson, F.A.
AU  - Dagleish, M.P.
AU  - Fontaine, M.
AU  - Bayne, C.
AU  - Hodgson, J.C.
TI  - Draft Genome Sequences of Strains of Pasteurella multocida Isolated from the United Kingdom and the United States.
JO  - Genome Announcements
PY  - 2013
SP  - e00773
EP  - e00713
VL  - 1
AB  - Pasteurella multocida is a major pathogen of farm animals and has worldwide distribution. Here
AB  - we report the draft genome sequences of four strains that were
AB  - isolated from animals in the United Kingdom and the United States and represent
AB  - pathogenic and commensal presentation of the bacterium.
ER  -

TY  - JOUR
AU  - Lainson, F.A.
AU  - Dagleish, M.P.
AU  - Fontaine, M.C.
AU  - Bayne, C.
AU  - Hodgson, J.C.
TI  - Draft Genome Sequence of Pasteurella multocida A:3 Strain 671/90.
JO  - Genome Announcements
PY  - 2013
SP  - e00803
EP  - e00813
VL  - 1
AB  - Pasteurella multocida serogroup A is commonly isolated from nasal swabs of clinically healthy
AB  - calves and also from diseased lung tissue in bovine pneumonia.
AB  - Here, we report the draft genome sequence of the virulent strain P. multocida
AB  - 671/90, which has been characterized previously in experimental infections of
AB  - calves and mice.
ER  -

TY  - JOUR
AU  - Laird, P.W.
AU  - Jackson-Grusby, L.
AU  - Fazeli, A.
AU  - Dickinson, S.L.
AU  - Jung, W.E.
AU  - Li, E.
AU  - Weinberg, R.A.
AU  - Jaenisch, R.
TI  - Suppression of intestinal neoplasia by DNA hypomethylation.
JO  - Cell
PY  - 1995
SP  - 197
EP  - 205
VL  - 81
AB  - We have used a combination of genetics and pharmacology to assess the effects of reduced DNA
AB  - methyltransferase activity on ApcMin-induced intestinal neoplasia in mice. A reduction in the
AB  - DNA methyltransferase activity in Min mice due to heterozygosity of the DNA methyltransferase
AB  - gene, in conjunction with a weekly dose of the DNA methyltransferase inhibitor
AB  - 5-aza-deoxycytidine, reduced the average number of intestinal adenomas from 113 in the control
AB  - mice to only 2 polyps in the treated heterozygotes. Hence, DNA methyl-transferase activity
AB  - contributes substantially to tumor developments in this mouse model of intestinal neoplasia.
AB  - Our results argue against an oncogenic effect of DNA hypomethylation. Moreover, they are
AB  - consistent with a role for DNA methyltransferase in the generation of the C to T transitions
AB  - seen at high frequency in human colorectal tumors.
ER  -

TY  - JOUR
AU  - Laird, P.W.
AU  - Jaenisch, R.
TI  - The role of DNA methylation in cancer genetics and epigenetics.
JO  - Annu. Rev. Genet.
PY  - 1996
SP  - 441
EP  - 464
VL  - 30
AB  - The past few years have seen a wider acceptance of a role for DNA methylation in cancer.  This
AB  - can be attributed to three developments.  First, the documentation of the over-representation
AB  - of mutations at CpG dinucleotides has convincingly implicated DNA methylation in the
AB  - generation of oncogenic point mutations.  The second important advance has been the
AB  - demonstration of epigenetic silencing of tumor suppressor genes by DNA methylation.  The third
AB  - development has been the utilization of experimental methods to manipulate DNA methylation
AB  - levels.  These studies demonstrate that DNA methylation changes in cancer cells are not mere
AB  - by-products of malignant transformation, but can play an instrumental role in the cancer
AB  - process.  It seems clear that DNA methylation plays a variety of roles in different cancer
AB  - types and probably at different stages of oncogenesis.  DNA methylation is intricately
AB  - involved in a wide diversity of cellular processes.  Likewise, it appears to exert its
AB  - influence on the cancer process through a diverse array of mechanisms.  It is our task not
AB  - only to identify these mechanisms, but to determine their relative importance for each state
AB  - and type of cancer.  Our hope then will be to translate that knowledge into clinical
AB  - applications.
ER  -

TY  - JOUR
AU  - Laity, C.
AU  - Chater, K.F.
AU  - Lewis, C.G.
AU  - Buttner, M.J.
TI  - Genetic analysis of the phi C31-specific phage growth limitation (Pgl) system of  Streptomyces coelicolor A3(2).
JO  - Mol. Microbiol.
PY  - 1993
SP  - 329
EP  - 336
VL  - 7
AB  - The phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2) was shown to be
AB  - specific to phi C31 homo-immune phages, and to be absent from the
AB  - closely related strain Streptomyces lividans. A 16 kb fragment of S. coelicolor
AB  - A3(2) DNA was isolated which complemented the Pgl- phenotype of J1501, a pgl
AB  - mutant derivative of the Pglts S. coelicolor strain M130. The cloned DNA
AB  - complemented only half of the available pgl mutants, which therefore represented
AB  - at least two groups, designated Pgl class A and class B strains. It follows that
AB  - more than one kind of high-frequency genetic event can lead to the Pgl-
AB  - phenotype. Crosses between class A and class B strains yielded high frequencies
AB  - of Pgl+ recombinants. Crosses between strains of the same class gave no Pgl+
AB  - recombinants. The cloned DNA was altered by deletion or apparent point mutation
AB  - upon passage through the two class B strains tested, such that it was no longer
AB  - capable of complementing class A strains. This accumulation of mutations might
AB  - suggest that the expression of the cloned DNA is toxic to at least some class B
AB  - strains. The nature of the genetic instability associated with the Pgl system was
AB  - not detectable by Southern blot analysis.
ER  -

TY  - JOUR
AU  - Lajoie, M.J.
AU  - Rovner, A.J.
AU  - Goodman, D.B.
AU  - Aerni, H.-R.
AU  - Haimovich, A.D.
AU  - Kuznetsov, G.
AU  - Mercer, J.A.
AU  - Wang, H.H.
AU  - Carr, P.A.
AU  - Mosberg, J.A.
AU  - Rohland, N.
AU  - Schultz, P.G.
AU  - Jacobson, J.M.
AU  - Rinehart, J.
AU  - Church, G.M.
AU  - Isaacs, F.J.
TI  - Genomically Recoded Organisms Expand Biological Functions.
JO  - Science
PY  - 2013
SP  - 357
EP  - 360
VL  - 342
AB  - We describe the construction and characterization of a genomically recoded organism (GRO). We
AB  - replaced all known UAG stop codons in Escherichia coli MG1655 with synonymous UAA codons,
AB  - which permitted the deletion of release factor 1 and reassignment of UAG translation function.
AB  - This
AB  - GRO exhibited improved properties for incorporation of nonstandard amino acids that expand the
AB  - chemical diversity of proteins in vivo. The GRO also exhibited increased resistance to T7
AB  - bacteriophage, demonstrating that new genetic codes could enable increased viral resistance.
ER  -

TY  - JOUR
AU  - Laksanalamai, P.
AU  - Steyert, S.R.
AU  - Burall, L.S.
AU  - Datta, A.R.
TI  - Genome Sequences of Listeria monocytogenes Serotype 4b Variant Strains Isolated from Clinical and Environmental Sources.
JO  - Genome Announcements
PY  - 2013
SP  - e00771
EP  - e00713
VL  - 1
AB  - Listeria monocytogenes strains that show a novel PCR serotyping profile (IVb-v1)  have been
AB  - reported recently. Here, we announce the draft genome sequences of five
AB  - L. monocytogenes IVb-v1 strains isolated from the United States and Australia
AB  - that harbor a 6.3-kb DNA cassette characteristic of serotype 1/2a strains.
ER  -

TY  - JOUR
AU  - Lakshmipathy, D.
AU  - Vetrivel, U.
AU  - Irudayam, L.T.
AU  - Ramasubban, G.
AU  - Madhavan, H.N.
AU  - Sridhar, R.
AU  - Meenakshi, N.
TI  - Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Strain CWCFVRF MDRTB 670, Isolated from the Sputum of a Patient from Chennai, India,  with Clinically Suspected Tuberculosis.
JO  - Genome Announcements
PY  - 2014
SP  - e00475
EP  - e00414
VL  - 2
AB  - We announce the draft genome sequence of a multidrug-resistant Mycobacterium tuberculosis
AB  - strain (CWCFVRF MDRTB 670) isolated from sputum from a patient with
AB  - clinically suspected tuberculosis.
ER  -

TY  - JOUR
AU  - Lakshmipathy, D.
AU  - Vetrivel, U.
AU  - Ramasubban, G.
AU  - Kulandai, L.T.
AU  - Madhavan, H.N.
AU  - Sridhar, R.
AU  - Meenakshi, N.
TI  - Whole Genome Sequence of Polyresistant Mycobacterium tuberculosis CWCFVRF PRTB 19 Sputum Isolate from Chennai, India, Closely Clustering with East African Indian 5  Genogroup.
JO  - Genome Announcements
PY  - 2014
SP  - e00702
EP  - e00714
VL  - 2
AB  - We announce the draft genome sequence of a polyresistant Mycobacterium tuberculosis strain
AB  - (CWCFVRF PRTB 19) isolated from the sputum of a clinically
AB  - suspected tuberculosis patient, and it closely clusters to the East African
AB  - Indian 5 (EAI5) lineage.
ER  -

TY  - JOUR
AU  - Lal, S.
AU  - Ramachandran, U.
AU  - Zhang, X.
AU  - Munir, R.
AU  - Sparling, R.
AU  - Levin, D.B.
TI  - Draft Genome Sequence of the Cellulolytic, Mesophilic, Anaerobic Bacterium Clostridium termitidis Strain CT1112 (DSM 5398).
JO  - Genome Announcements
PY  - 2013
SP  - e00281
EP  - e00213
VL  - 1
AB  - Here, we report the draft genome sequence of Clostridium termitidis strain CT1112 (DSM 5398),
AB  - a mesophilic, cellulolytic bacterium that can utilize a variety of
AB  - sugars, as well as pure cellulose, as a sole carbon source; it also synthesizes
AB  - fermentation end products with potential industrial applications.
ER  -

TY  - JOUR
AU  - Lal, S.
AU  - Ramachandran, U.
AU  - Zhang, X.
AU  - Sparling, R.
AU  - Levin, D.B.
TI  - Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Bacterium Clostridium intestinale Strain URNW.
JO  - Genome Announcements
PY  - 2013
SP  - e00871
EP  - e00813
VL  - 1
AB  - Here, we report the draft genome sequence of Clostridium intestinale strain URNW, which can
AB  - convert biomass to useful products such as biofuels (hydrogen or
AB  - ethanol) and other soluble end products.
ER  -

TY  - JOUR
AU  - Lallement, A.
AU  - Besaury, L.
AU  - Eyheraguibel, B.
AU  - Amato, P.
AU  - Sancelme, M.
AU  - Mailhot, G.
AU  - Delort, A.M.
TI  - Draft Genome Sequence of Rhodococcus enclensis 23b-28, a Model Strain Isolated from Cloud Water.
JO  - Genome Announcements
PY  - 2017
SP  - e01199
EP  - e01117
VL  - 5
AB  - The whole genome of Rhodococcus enclensis 23b-28, a bacterial strain isolated from cloud
AB  - water, was sequenced. This microorganism is equipped with genes able
AB  - to degrade aromatic compounds and could thus play a role in complex organic
AB  - matter decomposition in cloud water.
ER  -

TY  - JOUR
AU  - Lam, M.C.
AU  - Seemann, T.
AU  - Bulach, D.M.
AU  - Gladman, S.L.
AU  - Chen, H.
AU  - Haring, V.
AU  - Moore, R.J.
AU  - Ballard, S.
AU  - Grayson, M.L.
AU  - Johnson, P.D.
AU  - Howden, B.P.
AU  - Stinear, T.P.
TI  - Comparative Analysis of the First Complete Enterococcus faecium Genome.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2334
EP  - 2334
VL  - 194
AB  - Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections
AB  - in healthcare facilities around the globe. In particular, infections caused by
AB  - vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and
AB  - functional genomic studies of E. faecium isolates have so far been limited owing to the lack
AB  - of a fully assembled E. faecium genome sequence. Here we address this issue and report the
AB  - complete 3.0 Mb genome sequence of the multi-locus sequence type 17 vancomycin-resistant
AB  - Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne,
AB  - Australia in 1998. The genome comprises a 2.9 Mb circular chromosome and three circular
AB  - plasmids. The chromosome harbours putative E. faecium virulence factors such as enterococcal
AB  - surface protein, hemolysin and collagen-binding adhesion. Aus0004 has a very large accessory
AB  - genome (38%) that includes, three prophage and two genomic islands absent among 22 other E.
AB  - faecium genomes. One of the prophage was present as inverted 50kb repeats that appear to have
AB  - facilitated a 683 kb chromosomal inversion across the replication terminus, resulting in a
AB  - striking replichore imbalance. Other distinctive features include 95 insertion sequence
AB  - elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin-resistance
AB  - element. A complete E. faecium genome will be a useful resource to assist our understanding of
AB  - this emerging nosocomial pathogen.
ER  -

TY  - JOUR
AU  - Lam, W.C.
AU  - Tsao, D.H.H.
AU  - Maki, A.H.
AU  - Maegley, K.A.
AU  - Reich, N.O.
TI  - Spectroscopic studies of arsenic(III) binding to Escherichia coli RI methyltransferase and to two mutants, C223S and W183F.
JO  - Biochemistry
PY  - 1992
SP  - 10438
EP  - 10442
VL  - 31
AB  - The interactions of an arsenic(III) reagent, (CH3)2AsSCH2CONH2, with two Escherichia coli RI
AB  - methyltransferase mutants, W183F and C223S, have been studied by phosphorescence, optically
AB  - detected magnetic resonance, and fluorescence spectroscopy. The phosphorescence specrum of the
AB  - W183F mutant containing only one tryptophan at position 225 reveals a single 0,0-band that is
AB  - red-shifted by 9.8 nm upon binding of As(III). Fluorescence titration of W183F with
AB  - (CH3)2AsSCH2CONH2 produces a large tryptophan fluorescence quenching. Analysis of the
AB  - quenching data points to a single high-affinity As(III) binding site that is associated with
AB  - the fluorescence quenching. Triplet-state kinetic measurements performed on the perturbed
AB  - tryptophan show large reductions in the lifetimes of the triplet sublevels, especially that of
AB  - the Tx sublevel. As(III) binding to the enzymes at a site very close to the Trp225 residue
AB  - induces an external heavy-atom effect, showing that the perturber atom is in van der Waals
AB  - contact with the indole chromophore. In the case of the C223S mutant, a single tryptophan
AB  - 0,0-band also is observed in the phosphorescence spectrum but no change occurs upon addition
AB  - of the As(III) reagent. Fluorescence titration of C223S with As(III) shows essentially no
AB  - quenching of tryptophan fluorescence, in contrast with W183F. These results along with
AB  - previous triplet-state and biochemical studies on the wild-type enzyme [Tsao,D.H>H., & Maki,
AB  - A.H. (1991) Biochemistry 30, 4565-4572], show that As(III) binds with high affinity to the
AB  - Cys223 residue and that the Trp225 side chain is located close enough to that of Cys223 to
AB  - produce a heavy-atom perturbation when As(III) is bound.
ER  -

TY  - JOUR
AU  - Lambert, A.R.
AU  - Hallinan, J.P.
AU  - Shen, B.W.
AU  - Chik, J.K.
AU  - Bolduc, J.M.
AU  - Kulshina, N.
AU  - Robins, L.I.
AU  - Kaiser, B.K.
AU  - Jarjour, J.
AU  - Havens, K.
AU  - Scharenberg, A.M.
AU  - Stoddard, B.L.
TI  - Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
JO  - Structure
PY  - 2016
SP  - 862
EP  - 873
VL  - 24
AB  - LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their
AB  - cleavage specificity can be altered using several protein engineering
AB  - and selection strategies, their overall targetability is limited by highly
AB  - specific indirect recognition of the central four base pairs within their
AB  - recognition sites. In order to examine the physical basis of indirect sequence
AB  - recognition and to expand the number of such nucleases available for genome
AB  - engineering, we have determined the target sites, DNA-bound structures, and
AB  - central four cleavage fidelities of nine related enzymes. Subsequent
AB  - crystallographic analyses of a meganuclease bound to two noncleavable target
AB  - sites, each containing a single inactivating base pair substitution at its
AB  - center, indicates that a localized slip of the mutated base pair causes a small
AB  - change in the DNA backbone conformation that results in a loss of metal occupancy
AB  - at one binding site, eliminating cleavage activity.
ER  -

TY  - JOUR
AU  - Lambert, A.R.
AU  - Sussman, D.
AU  - Shen, B.
AU  - Maunus, R.
AU  - Nix, J.
AU  - Samuelson, J.
AU  - Xu, S.Y.
AU  - Stoddard, B.L.
TI  - Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
JO  - Structure
PY  - 2008
SP  - 558
EP  - 569
VL  - 16
AB  - The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp
AB  - target 5'-GCGGCCGC-3', has been solved with and
AB  - without bound DNA. Because of its specificity (recognizing a site that
AB  - occurs once per 65 kb), NotI is used to generate large genomic fragments
AB  - and to map DNA methylation status. NotI contains a unique metal binding
AB  - fold, found in a variety of putative endonucleases, occupied by an iron
AB  - atom coordinated within a tetrahedral Cys4 motif. This domain positions
AB  - nearby protein elements for DNA recognition, and serves a structural role.
AB  - While recognition of the central six base pairs of the target is
AB  - accomplished via a saturated hydrogen bond network typical of restriction
AB  - enzymes, the most peripheral base pairs are engaged in a single direct
AB  - contact in the major groove, reflecting reduced pressure to recognize
AB  - those positions. NotI may represent an evolutionary intermediate between
AB  - mobile endonucleases (which recognize longer target sites) and canonical
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Lambert, G.R.
AU  - Carr, N.G.
TI  - Resistance of DNA from filamentous and unicellular cyanobacteria to restriction endonuclease cleavage.
JO  - Biochim. Biophys. Acta
PY  - 1984
SP  - 45
EP  - 55
VL  - 781
AB  - Chromosomal DNA from nine species of filamentous cyanobacteria as
AB  - diverse as Nostoc, Gloeotrichia and Plectonema is suggested to be extensively modified
AB  - (methylated) by its resistance to cleavage by a number of restriction endonucleases.  A
AB  - remarkably similar pattern of DNA modification in these species contrasts with the known
AB  - heterogeneity of their type II restriction endonuclease content.  In particular, Nostoc PCC
AB  - 73102, which lacks detectable sequence-specific endonucleases, is shown to possess
AB  - extensive DNA modification.  The use of isoschizomers demonstrates the presence of a
AB  - methylase in the filamentous strains analogous to the dam enzyme of Escherichia coli.  As a
AB  - preliminary to assessing the significance of the DNA modification, a study of susceptibility
AB  - to restriction endonuclease cleavage of the genomes of five unicellular cyanobacteria
AB  - revealed considerable variation between the different strains.  The significance of the DNA
AB  - modification patterns elucidated is discussed in terms of the restriction endonuclease
AB  - content and cellular differentiation of the relevant cyanobacterial strains.
ER  -

TY  - JOUR
AU  - Lambert, J.N.
TI  - The chemistry of biology: Molecular evolution, the total synthesis of proteins, and DNA restriction and modification.
JO  - Aust. J. Chem.
PY  - 1996
SP  - 1179
EP  - 1196
VL  - 49
AB  - Three topics of current interest in modern biological organic chemistry are presented:
AB  - molecular evolution, the total synthesis of proteins, and the study of DNA restriction and
AB  - modification systems.  These topics are used to illustrate the application of chemical
AB  - understanding to the study of chemistry in a biological context.
ER  -

TY  - JOUR
AU  - Lambie, S.C.
AU  - Altermann, E.
AU  - Leahy, S.C.
AU  - Kelly, W.J.
TI  - Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00107
EP  - e00114
VL  - 2
AB  - Lactococcus lactis subsp. cremoris HP(T) has been widely used in studies of the metabolism of
AB  - lactococcal dairy starter cultures. A comparison of the draft HP(T)
AB  - genome with those from other strains of L. lactis subsp. cremoris will aid our
AB  - understanding of the domestication and evolution of these important industrial
AB  - cultures.
ER  -

TY  - JOUR
AU  - Lambie, S.C.
AU  - Kelly, W.J.
AU  - Leahy, S.C.
AU  - Li, D.
AU  - Reilly, K.
AU  - McAllister, T.A.
AU  - Valle, E.R.
AU  - Attwood, G.T.
AU  - Altermann, E.
TI  - The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 57
EP  - 57
VL  - 10
AB  - Methanosarcina species are the most metabolically versatile of the methanogenic Archaea and
AB  - can obtain energy for growth by producing methane via the
AB  - hydrogenotrophic, acetoclastic or methylotrophic pathways. Methanosarcina barkeri
AB  - CM1 was isolated from the rumen of a New Zealand Friesian cow grazing a
AB  - ryegrass/clover pasture, and its genome has been sequenced to provide information
AB  - on the phylogenetic diversity of rumen methanogens with a view to developing
AB  - technologies for methane mitigation. The 4.5 Mb chromosome has an average G + C
AB  - content of 39 %, and encodes 3523 protein-coding genes, but has no plasmid or
AB  - prophage sequences. The gene content is very similar to that of M. barkeri Fusaro
AB  - which was isolated from freshwater sediment. CM1 has a full complement of genes
AB  - for all three methanogenesis pathways, but its genome shows many differences from
AB  - those of other sequenced rumen methanogens. Consequently strategies to mitigate
AB  - ruminant methane need to include information on the different methanogens that
AB  - occur in the rumen.
ER  -

TY  - JOUR
AU  - Lambowitz, A.M.
TI  - Infectious introns.
JO  - Cell
PY  - 1989
SP  - 323
EP  - 326
VL  - 56
AB  - Among the most vigorously debated questions in modern biology is whether introns were present
AB  - in primordial genes and subsequently lost from most present-day prokaryotes or whether they
AB  - are more recent additions to eukaryotic genes. While it is not necessarily true that all
AB  - introns originated in the same way from a common ancestor, recent studies, represented by four
AB  - papers in this issue of Cell, provide definitive evidence that a number of group I introns can
AB  - propagate themselves by insertion of group II introns and for relationships between these
AB  - introns and autonomous elements.
ER  -

TY  - JOUR
AU  - Lambowitz, A.M.
AU  - Belfort, M.
TI  - Introns as mobile genetic elements.
JO  - Annu. Rev. Biochem.
PY  - 1993
SP  - 587
EP  - 622
VL  - 62
AB  - *
AB  - Introduction
AB  - Intron Structure and Splicing Pathway
AB  - Group I introns
AB  - Group II introns
AB  - Archaeal introns
AB  - Intron Mobility
AB  - Intron distribution
AB  - Intron-encoded proteins
AB  - Intron acquisition or loss
AB  - Autonomous introns and intronlike elements
AB  - An autonomous Group II intron -- a-senDNA
AB  - Mitochondrial plasmids of neurospora
AB  - Intron evaluation
AB  - Introns early and late
AB  - ORF acquisition and evolution of group I intron mobility
AB  - Acquisition of group II intron ORFs
AB  - Regulation of intron mobility
AB  - Horizontal transmission?
AB  - Concluding remarks
AB  - 
ER  -

TY  - JOUR
AU  - Lambowitz, A.M.
AU  - Caprara, M.G.
AU  - Zimmerly, S.
AU  - Perlman, P.S.
TI  - Group I and Group II ribozymes as RNPs: Clues to the past and guides to the future.
JO  - The RNA World
PY  - 1999
SP  - 451
EP  - 485
AB  - Group I and group II introns are not only catalytic RNAs, but also mobile genetic elements.
AB  - The success of these introns as mobile elements almost certainly relates to their innate
AB  - self-splicing capability, which enables them to propagate by inserting into host genes while
AB  - only minimally impairing gene expression.  Nevertheless, both types of introns have become
AB  - dependent on proteins for efficient splicing in vivo to help fold the intron RNA into the
AB  - catalytically active structure.  A review.
ER  -

TY  - JOUR
AU  - Lambowitz, A.M.
AU  - Mohr, G.
AU  - Zimmerly, S.
TI  - Group II intron homing endonucleases: ribonucleoprotein complexes with programmable target specificity.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 121
EP  - 145
VL  - 16
AB  - Group II intron homing endonucleases are ribonucleoproteins consisting of a catalytically
AB  - active intron RNA and an intron-encoded protein, with reverse transcriptase and/or DNA
AB  - endonuclease activity.  The RNP is formed when the IEP binds to the intron in unspliced RNA
AB  - and promotes its splicing by stabilizing the catalytically active RNA structure.  Afterwards,
AB  - the IEP remains tightly bound to the excised intron RNA to constitute the homing endonuclease.
AB  - The homing endonuclease promotes intron mobility by a remarkable mechanism in which the intron
AB  - RNA reverse splices directly into a target DNA and is then reverse-transcribed by the IEP.
AB  - Importantly, the target site for intron insertion is determined mainly by base pairing between
AB  - short sequence elements in the intron RNA and target DNA, making it straightforward to change
AB  - the target specificity of the homing endonuclease simply by modifying the intron RNA.  This
AB  - feature combined with their very high specificity and insertion frequencies have made it
AB  - possible to develop mobile group II introns into gene targeting vectors, called "targetrons",
AB  - with programmable target specificity.
ER  -

TY  - JOUR
AU  - Lamontanara, A.
AU  - Caggianiello, G.
AU  - Orru, L.
AU  - Capozzi, V.
AU  - Michelotti, V.
AU  - Bayjanov, J.R.
AU  - Renckens, B.
AU  - van Hijum, S.A.
AU  - Cattivelli, L.
AU  - Spano, G.
TI  - Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine.
JO  - Genome Announcements
PY  - 2015
SP  - e00097
EP  - e00015
VL  - 3
AB  - Here, we describe the draft genome sequence and annotation of Lactobacillus plantarum strain
AB  - Lp90, the first sequenced genome of a L. plantarum strain
AB  - isolated from wine. This strain has a noticeable ropy phenotype and showed
AB  - potential probiotic properties. The genome consists of 3,324,076 bp (33 contigs)
AB  - and contains 3,155 protein coding genes, 34 pseudogenes, and 84 RNA genes.
ER  -

TY  - JOUR
AU  - Lamontanara, A.
AU  - Orru, L.
AU  - Cattivelli, L.
AU  - Russo, P.
AU  - Spano, G.
AU  - Capozzi, V.
TI  - Genome Sequence of Oenococcus oeni OM27, the First Fully Assembled Genome of a Strain Isolated from an Italian Wine.
JO  - Genome Announcements
PY  - 2014
SP  - e00658
EP  - e00614
VL  - 2
AB  - Oenococcus oeni OM27 is a strain selected from 'Nero di Troia' wine undergoing spontaneous
AB  - malolactic fermentation. 'Nero di Troia' is a wine made from 'Uva di
AB  - Troia' grapes, an autochthonous black grape variety from the Apulian region
AB  - (south of Italy). In this paper we present a 1.78-Mb assembly of the O. oeni OM27
AB  - genome, the first fully assembled genome of an O. oeni strain from an Italian
AB  - wine.
ER  -

TY  - JOUR
AU  - Lan, H.
AU  - Yang, H.
AU  - Li, P.
AU  - Wang, C.
AU  - Zhou, H.
AU  - Zhou, H.
AU  - Pan, H.
AU  - Yu, Y.
AU  - Lu, X.
AU  - Tian, Y.
TI  - Complete Genome Sequence of Enterobacter sp. Strain ODB01, a Bacterium That Degrades Crude Oil.
JO  - Genome Announcements
PY  - 2017
SP  - e01763
EP  - e01716
VL  - 5
AB  - Enterobacter sp. strain ODB01, which was isolated from the Changqing oil field, can degrade
AB  - crude oil efficiently and use crude oil as its sole source of carbon
AB  - and energy. We report the complete genome sequence of ODB01. The results promote
AB  - its application in the remediation of petroleum contaminants.
ER  -

TY  - JOUR
AU  - Lan, J.
AU  - Hua, S.
AU  - He, X.N.
AU  - Zhang, Y.
TI  - DNA methyltransferases and methyl-binding proteins of mammals.
JO  - Acta Biochim. Biophys. Sin.
PY  - 2010
SP  - 243
EP  - 252
VL  - 42
AB  - In mammals, DNA methylation, characterized by the transfer of the methyl group from
AB  - S-adenosylmethionines to a base (mainly referred to cytosine), acts as a major epigenetic
AB  - modification. In parallel to DNA sequences arrangement, modification of methylation to DNA
AB  - sequences has far-reaching influence on biological functions and activities, for it involves
AB  - controlling gene transcription, regulating chromatin structure, sustaining genome stability
AB  - and integrity, maintaining parental imprinting and X-chromosome inactivation, suppressing
AB  - homologous recombination as well as limiting transposable elements, during which DNA
AB  - methyltransferases (DNMTs) and methyl-binding proteins play important roles. Their aberrance
AB  - can give rise to dysregulation of gene expression, cell maltransformation and so on. Hence, it
AB  - is necessary to gain a good understanding of these two important kinds of proteins, which will
AB  - help to better investigate the epigenetic mechanisms and manipulate the modifications
AB  - according to our will based on its reversibility. Here we briefly review our current
AB  - understanding of DNMTs and methyl-binding proteins in mammals.
ER  -

TY  - JOUR
AU  - Lan, J.
AU  - Hua, S.
AU  - Liu, J.
AU  - Zhang, Y.
TI  - cDNA Cloning of Goat DNA Methyltransferase 1, Screening of shRNA Vectors and Influences to Development of Nuclear Transfer Embryos.
JO  - Agric. Sci. China
PY  - 2010
SP  - 1035
EP  - 1040
VL  - 9
AB  - This study was designed to clone cDNA of goat DNA methyltransferase 1 (DNMT1) gene, to screen
AB  - an effective shRNA-producing vector targeting
AB  - goat DNA methyltransferase 1 and to improve the developmental
AB  - competence of goat nuclear transfer embryos by decreasing the DNMT1
AB  - expression in donor cells. In this study, PCR primers were designed
AB  - against regions of high homology between bovine and sheep sequences and
AB  - then used to amplify the larger portions of the coding regions. Next, 3
AB  - RNAi oligonucleotides were designed based on the cloned sequences and
AB  - inserted into pRNAT-U6.1/Neo vector, acquiring 3 new vectors,
AB  - respectively termed pRNAD1, pRNAD2 and pRNAD3. Then the positive cells
AB  - were sorted by flow cytometry after transfection and detected by
AB  - real-time PCR analysis and sodium bisulfite genomic sequencing.
AB  - Finally, the developmental rates of nuclear transfer (NT) embryos
AB  - generated using donor cells with and without the effective shRNA vector
AB  - respectively, as well as in vitro fertilization (IVF) embryos were
AB  - observed and recorded. The results showed that the coding regions of
AB  - goat DNA methyltransferase 1 gene was successfully cloned (GenBank no.
AB  - FJ617538). Furthermore, an effective interfering shRNA (pRNAD2) was
AB  - obtained, with its interference effect being 47.88%. Finally, NT
AB  - embryos with shRNA vector harbored better developmental competence
AB  - during morula and blastocyst stage compared to controls (P<0.05),
AB  - reaching the similar rates to IVF embryos (P>0.05). In conclusion, goat
AB  - DNA methyltransferase 1 gene cDNA was cloned and sequenced, an
AB  - effective shRNA vector responsible for inhibiting DNA methyltransferase
AB  - 1 expression was developed and the developmental competence of goat
AB  - nuclear transfer morulae and blastcysts was significantly improved,
AB  - which provided a feasible pathway for improving goat nuclear transfer
AB  - embryo development competence by decreasing the methylation level in
AB  - donor cells through RNAi-mediated manner.
ER  -

TY  - JOUR
AU  - Lan, S.F.
AU  - Huang, C.H.
AU  - Chang, C.H.
AU  - Liao, W.C.
AU  - Lin, I.H.
AU  - Jian, W.N.
AU  - Wu, Y.G.
AU  - Chen, S.Y.
AU  - Wong, H.C.
TI  - Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 2659
EP  - 2667
VL  - 75
AB  - Vibrio parahaemolyticus is a common food-borne pathogen that is normally associated with
AB  - seafood. In 1996, a pandemic O3:K6 strain
AB  - abruptly appeared and caused the first pandemic of this pathogen to
AB  - spread throughout many Asian countries, America, Europe, and Africa.
AB  - The role of temperate bacteriophages in the evolution of this pathogen
AB  - is of great interest. In this work, a new temperate phage, VP882, from
AB  - a pandemic O3: K6 strain of V. parahaemolyticus was purified and
AB  - characterized after mitomycin C induction. VP882 was a Myoviridae
AB  - bacteriophage with a polyhedral head and a long rigid tail with a
AB  - sheath-like structure. It infected and lysed high proportions of V.
AB  - parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae strains. The
AB  - genome of phage VP882 was sequenced and was 38,197 bp long, and 71
AB  - putative open reading frames were identified, of which 27 were putative
AB  - functional phage or bacterial genes. VP882 had a linear plasmid-like
AB  - genome with a putative protelomerase gene and cohesive ends. The genome
AB  - does not integrate into the host chromosome but was maintained as a
AB  - plasmid in the lysogen. Analysis of the reaction sites of the
AB  - protelomerases in different plasmid-like phages revealed that VP882 and
AB  - Phi HAP-1 were highly similar, while N15, Phi KO2, and PY54 made up
AB  - another closely related group. The presence of DNA adenine methylase
AB  - and quorum-sensing transcriptional regulators in VP882 may play a
AB  - specific role in this phage or regulate physiological or
AB  - virulence-associated traits of the hosts. These genes may also be
AB  - remnants from the bacterial chromosome following transduction.
ER  -

TY  - JOUR
AU  - Lancaster, W.A.
AU  - Utturkar, S.M.
AU  - Poole, F.L.
AU  - Klingeman, D.M.
AU  - Elias, D.A.
AU  - Adams, M.W.
AU  - Brown, S.D.
TI  - Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.
JO  - Genome Announcements
PY  - 2016
SP  - e00229
EP  - e00216
VL  - 4
AB  - Clostridium paradoxum strain JW-YL-7 is a moderately thermophilic anaerobic alkaliphile
AB  - isolated from the municipal sewage treatment plant in Athens, GA. We
AB  - report the near-complete genome sequence of C. paradoxum strain JW-YL-7 obtained
AB  - by using PacBio DNA sequencing and Pilon for sequence assembly refinement with
AB  - Illumina data.
ER  -

TY  - JOUR
AU  - Lanclos, V.C.
AU  - Henson, M.W.
AU  - Pitre, D.M.
AU  - Thrash, J.C.
TI  - Draft Genome Sequence of Strain LSUCC0135, an Early Diverging Member of the Order Methylophilales in the Phylum Betaproteobacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e01231
EP  - e01216
VL  - 4
AB  - We present the draft genome of Methylophilales sp. strain LSUCC0135, isolated using
AB  - high-throughput dilution-to-extinction culturing methods from the coast of
AB  - Freshwater City, Louisiana, USA. The genome indicates metabolic flexibility for
AB  - differing oxygen concentrations and electron donors.
ER  -

TY  - JOUR
AU  - Land, M. et al.
TI  - Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 21
EP  - 28
VL  - 1
AB  - Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of
AB  - phylogenetic interest because of its isolated location in the actinobacterial
AB  - suborder Micrococcineae. B. cavernae HKI 0122(T) is a Gram-positive, non-motile,
AB  - non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae
AB  - grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell
AB  - wall peptidoglycan contains the diagnostic L-lysine <-- L-glutamate interpeptide
AB  - bridge. Here we describe the features of this organism, together with the
AB  - complete genome sequence, and annotation. This is the first completed genome
AB  - sequence from the poorly populated micrococcineal family Beutenbergiaceae, and
AB  - this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53
AB  - RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Land, M. et al.
TI  - Complete genome sequence of Actinosynnema mirum type strain (101).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 46
EP  - 53
VL  - 1
AB  - Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of
AB  - phylogenetic interest because of its central phylogenetic location in the
AB  - Actino-synnemataceae, a rapidly growing family within the actinobacterial
AB  - suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne
AB  - on synnemata and as a producer of nocardicin antibiotics. It is capable of
AB  - growing aerobically and under a moderate CO(2) atmosphere. The strain is a
AB  - Gram-positive, aerial and substrate mycelium producing bacterium, originally
AB  - isolated from a grass blade collected from the Raritan River, New Jersey. Here we
AB  - describe the features of this organism, together with the complete genome
AB  - sequence and annotation. This is the first complete genome sequence of a member
AB  - of the family Actinosynnemataceae, and only the second sequence from the
AB  - actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon
AB  - genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Land, M. et al.
TI  - Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 233
EP  - 243
VL  - 4
AB  - Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a
AB  - member of the family Bacteroidaceae. Members of the genus Bacteroides
AB  - in general are known as beneficial protectors of animal guts against pathogenic
AB  - microorganisms, and as contributors to the degradation of complex molecules such
AB  - as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of
AB  - a swine facility, but has not yet been found in an animal host. The species is of
AB  - interest solely because of its isolated phylogenetic location. The genome of B.
AB  - coprosuis is already the 5(th) sequenced type strain genome from the genus
AB  - Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78
AB  - RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Landry, D.
AU  - Barsomian, J.M.
AU  - Feehery, G.R.
AU  - Wilson, G.G.
TI  - Characterization of Type II DNA-Methyltransferases.
JO  - Methods Enzymol.
PY  - 1992
SP  - 244
EP  - 259
VL  - 216
ER  -

TY  - JOUR
AU  - Landry, D.
AU  - Looney, M.C.
AU  - Feehery, G.R.
AU  - Slatko, B.E.
AU  - Jack, W.E.
AU  - Schildkraut, I.
AU  - Wilson, G.G.
TI  - M.FokI methylates adenine in both strands of its asymmetric recognition sequence.
JO  - Gene
PY  - 1989
SP  - 1
EP  - 10
VL  - 77
AB  - M.FokI, a type-IIS modification enzyme from Flavobacterium okeanokoites, was purified, and its
AB  - activity was characterized in vitro.  The enzyme was found to be a DNA-adenine
AB  - methyltransferase and to methylate both strands of the asymmetric FokI recognition sequence:
AB  - M.FokI
AB  - 5'-GGATG / CCTAC-5' M.FokI-> 5'-GGm6ATG/CCTm6AC-5.  M.FokI does not methylate
AB  - single-stranded DNA, nor does it methylate double-stranded DNA at sequences other than FokI
AB  - sites.
ER  -

TY  - JOUR
AU  - Landthaler, M.
AU  - Begley, U.
AU  - Lau, N.C.
AU  - Shub, D.A.
TI  - Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 1935
EP  - 1943
VL  - 30
AB  - We have recently described three group I introns inserted into a single gene, orf142, of the
AB  - staphylococcal bacteriophage Twort and suggested the presence of at least two additional
AB  - self-splicing introns in this phage genome. Here we report that two previously uncharacterized
AB  - introns, 429 and 1087 nt in length, interrupt the Twort gene coding for the large subunit of
AB  - ribonucleotide reductase (nrdE). Reverse transcription-polymerase chain reaction (RT-PCR) of
AB  - RNA isolated from Staphylococcus aureus after phage infection indicates that the introns are
AB  - removed from the primary transcript in vivo. Both nrdE introns show sequence similarity to the
AB  - Twort orf142 introns I2 and I3, suggesting either a common origin of these introns or
AB  - shuffling of intron structural elements. Intron 2 encodes a DNA endonuclease, I-TwoI, with
AB  - similarity to homing endonucleases of the HNH family. Like I-HmuI and I-HmuII, intron-encoded
AB  - HNH endonucleases in Bacillus subtilis phages SPO1 and SP82, I-TwoI nicks only one strand of
AB  - its DNA recognition sequence. However, whereas I-HmuI and I-HmuII cleave the template strand
AB  - in exon 2, I-TwoI cleaves the coding strand in exon 1. In each case, the 3' OH created on the
AB  - cut strand is positioned to prime DNA synthesis towards the intron, suggesting that this
AB  - reaction contributes to the mechanism of intron homing. Both nrdE introns are inserted in
AB  - highly conserved regions of the ribonucleotide reductase gene, next to codons for functionally
AB  - important residues.
ER  -

TY  - JOUR
AU  - Landthaler, M.
AU  - Lau, N.C.
AU  - Shub, D.A.
TI  - Group I intron homing in Bacillus phages SPO1 and SP82: A gene conversion event initiated by a nicking homing endonuclease.
JO  - J. Bacteriol.
PY  - 2004
SP  - 4307
EP  - 4314
VL  - 186
AB  - Many group I introns encode endonucleases that promote intron homing by initiating a
AB  - double-stranded break-mediated homologous recombination event. In this work we describe intron
AB  - homing in Bacillus subtilis phages SPO1 and SP82. The introns encode the DNA endonucleases
AB  - I-HmuI and I-HmuII, respectively, which belong to the H-N-H endonuclease family and possess
AB  - nicking activity in vitro. Coinfections of B. subtilis with intron-minus and intron-plus
AB  - phages indicate that I-HmuI and I-HmuII are required for homing of the SPO1 and SP82 introns,
AB  - respectively. The homing process is a gene conversion event that does not require the major B.
AB  - subtilis recombination pathways, suggesting that the necessary functions are provided by
AB  - phage-encoded factors. Our results provide the first examples of H-N-H endonuclease-mediated
AB  - intron homing and the first demonstration of intron homing initiated by a nicking
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Landthaler, M.
AU  - Shen, B.W.
AU  - Stoddard, B.L.
AU  - Shub, D.A.
TI  - I-Basl and I-Hmul: Two phage intron-encoded endonucleases with homologous DNA recognition sequences but distinct DNA Specificities.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 1137
EP  - 1151
VL  - 358
AB  - I-HmuI and I-BasI are two highly similar nicking DNA endonucleases, which are each encoded by
AB  - a group I intron inserted into homologous sites within
AB  - the DNA polymerase genes of Bacillus phages SPO1 and Bastille,
AB  - respectively. Here, we present a comparison of the DNA specificities and
AB  - cleavage activities of these enconucleases with homologous target sites.
AB  - I-BasI has properties that are typical of homing endonucleases, nicking
AB  - the intron-minus polymerase genes in either host genome, three nucleotides
AB  - downstream of the intron insertion site. In contrast, I-HmuI nicks both
AB  - the intron-plus and intron-minus site in its own host genome, but does not
AB  - act on the target from Bastille phage. Although the enzymes have distinct
AB  - DNA substrate specificities, both bind to an identical 25bp region of
AB  - their respective intron-minus DNA polymerase genes surrounding the intron
AB  - insertion site. The endonucleases appear to interact with the DNA
AB  - substrates in the downstream exon 2 in a similar manner. However, whereas
AB  - I-HmuI is known to make its only base-specific contacts within this exon
AB  - region, structural modeling analyses predict that I-BasI might make
AB  - specific base contacts both upstream and downstream of the site of intron
AB  - insertion. The predicted requirement for base-specific contacts in exon 1
AB  - for cleavage by I-BasI was confirmed experimentally. This explains the
AB  - difference in substrate specificities between the two enzymes, including
AB  - the observation that the former enzyme is relatively insensitive to the
AB  - presence of an intron upstream of exon 2. These differences are likely a
AB  - consequence of divergent evolutionary constraints.
ER  -

TY  - JOUR
AU  - Landthaler, M.
AU  - Shub, D.A.
TI  - The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 3071
EP  - 3077
VL  - 31
AB  - Here we describe the discovery of a group I intron in the DNA polymerase gene of Bacillus
AB  - thuringiensis phage Bastille. Although the intron
AB  - insertion site is identical to that of the Bacillus subtilis phages SPO1
AB  - and SP82 introns, the Bastille intron differs from them substantially in
AB  - primary and secondary structure. Like the SPO1 and SP82 introns, the
AB  - Bastille intron encodes a nicking DNA endonuclease of the H-N-H family,
AB  - I-BasI, with a cleavage site identical to that of the SPO1-encoded enzyme
AB  - I-HmuI. Unlike I-HmuI, which nicks both intron-minus and intron-plus DNA,
AB  - I-BasI cleaves only intron-minus alleles, which is a characteristic of
AB  - typical homing endonucleases. Interestingly, the C-terminal portions of
AB  - these H-N-H phage endonucleases contain a conserved sequence motif, the
AB  - intron-encoded endonuclease repeat motif (IENR1) that also has been found
AB  - in endonucleases of the GIY-YIG family, and which likely comprises a small
AB  - DNA-binding module with a globular betabetaalphaalphabeta fold, suggestive
AB  - of module shuffling between different homing endonuclease families.
ER  -

TY  - JOUR
AU  - Landy, A.
AU  - Foeller, C.
AU  - Ross, W.
TI  - DNA fragments carrying genes for tRNATyrI.
JO  - Nature
PY  - 1974
SP  - 738
EP  - 742
VL  - 249
AB  - The duplicated genes coding for tRNA TyrI have been isolated using
AB  - site-specific nucleases and gel electrophoresis.  An unduplicated sequence of
AB  - 4-120 base pairs separates the two genes.  Specific DNA fragments can be
AB  - obtained in sizes appropriate for both functional and structural analysis of
AB  - the tRNA TyrI region.
ER  -

TY  - JOUR
AU  - Landy, A.
AU  - Olchowski, E.
AU  - Ross, W.
AU  - Reiness, G.
TI  - Isolation of a functional lac regulatory region.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 273
EP  - 281
VL  - 133
AB  - A DNA fragment containing the lac regulatory region has been isolated by
AB  - digestion of lambda plac 5 DNA with restriction endonuclease from Hemophilus
AB  - influenzae Rd followed by gel electrophoresis.  This DNA fragment, which is
AB  - approximately 660 base pairs, is identified by its ability to bind purified lac
AB  - repressor, and has been shown to be functional in a coupled
AB  - transcription-translation system.  A smaller repressor binding fragment of
AB  - approximately 174 base pairs has been derived from the larger fragment
AB  - utilizing a secondary digestion with restriction endonuclease from Hemophilus
AB  - aegyptius.
ER  -

TY  - JOUR
AU  - Landy, A.
AU  - Ruedisueli, E.
AU  - Robinson, L.
AU  - Foeller, C.
AU  - Ross, W.
TI  - Digestion of deoxyribonucleic acids from bacteriophage T7, lambda, and Phi80h with site-specific nucleases from Hemophilus influenzae strain Rc and strain Rd.
JO  - Biochemistry
PY  - 1974
SP  - 2134
EP  - 2142
VL  - 13
AB  - The digestion profiles of DNA from bacteriophage T7, lambda, and Phi80h by the
AB  - site-specific nucleases from Hemophilus influenzae strain Rc and strain Rd have
AB  - been analyzed.  The DNA fragments range in molecular weight from approximately
AB  - 0.02 to 3 Md and are resolved by polyacrylamide-agarose gel electrophoresis.
AB  - The digestion profiles thus produced are unique and characteristic for both the
AB  - DNA and the nuclease.  The T7 DNA digestion products produced by the Rc and Rd
AB  - nucleases are identical.  With Phi80h and lambda DNAs only 87 and 71%
AB  - respectively, of the total number of fragments produced by the Rd nuclease are
AB  - common to both nuclease digestions, the remaining DNA fragments being unique to
AB  - either the Rc or the Rd digestions.  Strain Rc possesses a site-specific
AB  - nuclease activity which is identical to an activity found in strain Rd.  In
AB  - addition strain Rd carries a second activity which is not found in strain Rc
AB  - and which elutes at slightly higher salt on phosphocellulose.  Protection
AB  - experiments with individual modification methylases of strain Rd (Roy, P.H. and
AB  - Smith, H.O. (1973), J. Mol. Biol. 81: 427) establish that the nuclease which is
AB  - common to both Rd and Rc is associated with methylase II.  This nuclease in
AB  - strain Rd is called HindII and in strain Rc is called HincII according to the
AB  - nomenclature proposed by Smith and Nathans (Smith, H.O., and Nathans, D.
AB  - (1973), J. Mol. Biol. 81: 419-423.  The additional activity which elutes second
AB  - from phosphocellulose is HindIII.  The HincII-HindII activity (i.e., HincII or
AB  - HindII) is best prepared from strain Rc.  It makes 34 cuts in lambda DNA, 43
AB  - cuts in Phi80h DNA, and 51 cuts in T7 DNA.  The HindIII nuclease makes no cuts
AB  - in T7 DNA and 6 and 4 cuts in lambda and Phi80h DNA, respectively.  A
AB  - nomenclature system for the DNA digestion products is proposed and all the DNA
AB  - fragments produced by Rc and Rd digestions of the three related phages, Phi80h
AB  - ambl, Phi80h psuIII+-, and Phi80h psuIII+ are identified and their molecular
AB  - weights are presented.
ER  -

TY  - JOUR
AU  - Lang, E. et al.
TI  - Complete genome sequence of Dyadobacter fermentans type strain (NS114).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 133
EP  - 140
VL  - 1
AB  - Dyadobacter fermentans (Chelius and Triplett, 2000) is the type species of the genus
AB  - Dyadobacter. It is of phylogenetic interest because of its location in the
AB  - Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D.
AB  - fermentans has a mainly respiratory metabolism, stains Gram-negative, is
AB  - non-motile and oxidase and catalase positive. It is characterized by the
AB  - production of cell filaments in aging cultures, a flexirubin-like pigment and its
AB  - ability to ferment glucose, which is almost unique in the aerobically living
AB  - members of this taxonomically difficult family. Here we describe the features of
AB  - this organism, together with the complete genome sequence, and its annotation.
AB  - This is the first complete genome sequence of the sphingobacterial genus
AB  - Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804
AB  - protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Lang, E. et al.
TI  - Complete genome sequence of Weeksella virosa type strain (9751).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 81
EP  - 90
VL  - 4
AB  - Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella
AB  - which belongs to the family Flavobacteriaceae of the phylum
AB  - Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided
AB  - the basis for the taxon description. While the species seems to be a saprophyte
AB  - of the mucous membranes of healthy man and warm-blooded animals a causal
AB  - relationship with disease has been reported in a few instances. Except for the
AB  - ability to produce indole and to hydrolyze Tween and proteins such as casein and
AB  - gelatin, this aerobic, non-motile, non-pigmented bacterial species is
AB  - metabolically inert in most traditional biochemical tests. The 2,272,954 bp long
AB  - genome with its 2,105 protein-coding and 76 RNA genes consists of one circular
AB  - chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Lange, C.
AU  - Jugel, A.
AU  - Walter, J.
AU  - Noyer-Weidner, M.
AU  - Trautner, T.A.
TI  - Pseudo domains in phage-encoded DNA methyltransferases.
JO  - Nature
PY  - 1991
SP  - 645
EP  - 648
VL  - 352
AB  - 5-Cytosine-DNA-methyltransferases, which are found in many organisms ranging
AB  - from bacteriophages to mammals, transfer a methyl group from
AB  - S-adenosylmethionine to the carbon-5 of a cytosine residue in specific DNA
AB  - target sequences.  Some phage-encoded methyltransferases methylate more than
AB  - one sequence:  these enzymes contain several independent target-recognizing
AB  - domains each responsible for recognizing a different site.  The amino-acid
AB  - sequences of these multispecific methyltransferases reveal that some enzymes in
AB  - addition carry domains that do not contribute to the enzymes' methylation
AB  - potential, but strongly resemble previously identified target-recognizing
AB  - domains.  Here we show that introducing defined amino-acid alterations into
AB  - these inactive domains endows these enzymes with additional methylation
AB  - specificities.  Gel retardation analysis demonstrates that these novel
AB  - methylation specificities correlate with the acquisition of additional
AB  - DNA-binding potential of the proteins.
ER  -

TY  - JOUR
AU  - Lange, C.
AU  - Noyer-Weidner, M.
AU  - Trautner, T.A.
AU  - Weiner, M.
AU  - Zahler, S.A.
TI  - M.H2I, a multispecific 5C-DNA methyltransferase encoded by Bacillus amyloliquefaciens phage H2.
JO  - Gene
PY  - 1991
SP  - 213
EP  - 218
VL  - 100
AB  - Bacillus amyloliquefaciens phage H2 codes for a multispecific
AB  - cytosine-5-DNA-methyltransferase (MTase), M.H2I, which methylates GGCC, GCNGC
AB  - and G(A/G/T)GC(T/C/A)C target sequences.  The gene coding for M.H2I was cloned
AB  - in Escherichia coli and its nucleotide (nt) sequence was determined.  It
AB  - consists of 1509 bp, corresponding to a protein of 503 amino acids (aa) with a
AB  - calculated Mr of 57,166.  A comparison of the aa sequence of M.H2I with those
AB  - of the multispecific MTases encoded by Bacillus subtilis phages SPR, Phi3T and
AB  - Rho11S, revealed that M.H2I is closely related to these enzymes.  A very high
AB  - degree of homology was observed between M.H2I and M.Rho11S, with 96.2% aa
AB  - identity and 97.8% nt identity of the corresponding genes.
ER  -

TY  - JOUR
AU  - Lange, C.
AU  - Wild, C.
AU  - Trautner, T.A.
TI  - Altered sequence recognition specificity of a C5-DNA methyltransferase carrying a chimeric 'target recognizing domain'.
JO  - Gene
PY  - 1995
SP  - 127
EP  - 128
VL  - 157
AB  - A MTase with a chimeric TRD with the N-terminal half derived from a TRD recognizing GCNGC, the
AB  - C-terminal half from one with CCWGG recognition, was constructed.  Its target specificity is
AB  - reported (hemimethylation of the first C in GCTGGC).
ER  -

TY  - JOUR
AU  - Lange, C.
AU  - Wild, C.
AU  - Trautner, T.A.
TI  - Identification of a subdomain within DNA-(cytosine-C5)-methyltransferases responsible for the recognition of the 5' part of their DNA target.
JO  - EMBO J.
PY  - 1996
SP  - 1443
EP  - 1450
VL  - 15
AB  - In previous work on DNA-(cytosine-C5)-methyltransferases (C5-MTases), domains had been
AB  - identified which are responsible for the sequence specificity of the different enzymes
AB  - (target-recognizing domains, TRDs).  Here we have analyzed the DNA methylation patterns of two
AB  - C5-MTases containing reciprocal chimeric TRDs, consisting of the N- and C-terminal parts
AB  - derived from two different parental TRDs specifying the recognition of 5'-CC(A/T)GG-3' and
AB  - 5'-GCNGC-3'.  Sequences recognized by these engineered MTases were non-symmetrical and
AB  - degenerate, but contained at their 5' part a consensus sequence which was very similar to the
AB  - 5' part of the target recognized by the parental TRD which contributed the N-terminal moiety
AB  - of the chimeric TRD.  The results are discussed in connection with the present understanding
AB  - of the mechanism of DNA target recognition of C5-MTases.  They demonstrate the possibility of
AB  - designing C5-MTases with novel DNA methylation specificities.
ER  -

TY  - JOUR
AU  - Lange, C.
AU  - Wild, C.
AU  - Trautner, T.A.
TI  - Colinearity between amino acids of the target recognizing domains of a C5-DNA-methyltransferase and the nucleotide sequence of its target.
JO  - FASEB J.
PY  - 1995
SP  - A1391
EP  - A1391
VL  - 9
AB  - Cytosine (C5)-DNA methyltransferases (C5-MTases) are composed of several highly conserved
AB  - domains involved in general steps of the methylation reaction and one variable target
AB  - recognizing domain (TRD), which is responsible for the recognition of the enzymes' specific
AB  - DNA targets.  TRDs have between about 30 and 50 amino acids of different composition.  We have
AB  - constructed two MTases with recombinant TRDs combining the amino- and carboxy terminal halves
AB  - of two (parental) TRDs, which recognize the pentameric sequences 5'-GCNGC (I) and
AB  - 5'-CC(A/T)GG (II).  DNA methylated by the recombinant enzymes was treated with bisulfite to
AB  - distinguish cytosines from methyl-cytosines and then sequenced.  We observe that the TRD whose
AB  - amino terminus was derived from enzyme (I) recognized hexameric, non-symmetrical sequences
AB  - with the consensus 5'-GCTGGC.  The reciprocal TRD was inactive, but could be activated by
AB  - site specific mutagenesis to recognize the target 5'-PyNCCPyPy.  Neither of the enzymes
AB  - methylated the parental sequence.  The results are compatible with the three dimensional
AB  - structure of M.HhaI complexed with its DNA target, where two sequential recognition loops of
AB  - the TRD interact with contiguous parts of the DNA target.
ER  -

TY  - JOUR
AU  - Langella, P.
AU  - Chopin, A.
TI  - Effect of restriction-modification systems on transfer of foreign DNA into Lactococcus lactis subsp. lactis.
JO  - FEMS Microbiol. Lett.
PY  - 1989
SP  - 301
EP  - 306
VL  - 59
AB  - The efficiency of transfer of plasmid pIP501 DNA into Restriction/Modification
AB  - (R/M) proficient strains of Lactococcus lactis subsp. lactis strongly depends
AB  - on the mode of transfer.  In two strains, each one containing a different R/M
AB  - system, the efficiency of protoplast transformation with unmodified pIP501 DNA
AB  - was restriction by more than 3 orders of magnitude when compared to pIP501
AB  - carrying the host modification.  By contrast, no difference was observed when
AB  - modified or unmodified DNA was introduced into the same hosts by
AB  - electroporation.  The pIP501 conjugation frequency between a R-/M- donor an an
AB  - isogenic recipient were also unaffected whether the recipient possesses a R/M
AB  - system or not.
ER  -

TY  - JOUR
AU  - Langhans, M.T.
AU  - Palladino, M.J.
TI  - Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.
JO  - Curr. Issues Mol. Biol.
PY  - 2008
SP  - 1
EP  - 12
VL  - 11
AB  - The utility of restriction endonucleases as a tool in molecular biology is in large part due
AB  - to the high degree of specificity with which they
AB  - cleave well-characterized DNA recognition sequences. The specificity of
AB  - restriction endonucleases is not absolute, yet many commonly used
AB  - assays of biological phenomena and contemporary molecular biology
AB  - techniques rely on the premise that restriction enzymes will cleave
AB  - only perfect cognate recognition sites. In vitro, mispaired
AB  - heteroduplex DNAs are commonly formed, especially subsequent to
AB  - polymerase chain reaction amplification. We investigated a panel of
AB  - restriction endonucleases to determine their ability to cleave
AB  - mispaired heteroduplex DNA substrates. Two straightforward,
AB  - non-radioactive assays are used to evaluate mispaired heteroduplex DNA
AB  - cleavage: a PCR amplification method and an oligonucleotide-based
AB  - assay. These assays demonstrated that most restriction endonucleases
AB  - are capable of site-specific double-strand cleavage with heteroduplex
AB  - mispaired DNA substrates, however, certain mispaired substrates do
AB  - effectively abrogate cleavage to undetectable levels. These data are
AB  - consistent with mispaired substrate cleavage previously reported for
AB  - Eco RI and, importantly, extend our knowledge of mispaired heteroduplex
AB  - substrate cleavage to 13 additional enzymes.
ER  -

TY  - JOUR
AU  - Langowski, J.
AU  - Alves, J.
AU  - Pingoud, A.
AU  - Maass, G.
TI  - Does the specific recognition of DNA by the restriction endonuclease EcoRI involve a linear diffusion step?  Investigation of the processivity of the EcoRI endonuclease.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 501
EP  - 513
VL  - 11
AB  - The time course of the EcoRI endonuclease catalysed cleavage of three
AB  - substrates, two plasmid DNAs and one oligonucleotide, each with two EcoRI
AB  - sites, was measured.  The two plasmid DNAs with the EcoRI sites 318 and 96 base
AB  - pairs apart are cut in a distributive fashion, while the oligonucleotide with
AB  - the EcoRI sites 8 base pairs apart is cut in a partially processive manner.  It
AB  - is concluded that a linear diffusion of the EcoRI endonuclease on its substrate
AB  - across long stretches of DNA is not likely to be operative during the
AB  - recognition process.  Microscopic dissociation-reassociation processes,
AB  - however, increase the probability of the enzyme to attack further sites located
AB  - in the immediate vicinity of a given site.
ER  -

TY  - JOUR
AU  - Langowski, J.
AU  - Pingoud, A.
AU  - Goppelt, M.
AU  - Maass, G.
TI  - Inhibition of EcoRI action by polynucleotides.  A characterization of the non-specific binding of the enzyme to DNA.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 4727
EP  - 4736
VL  - 8
AB  - The cleavage of the plasmid pBR322 by the restriction endonuclease EcoRI has
AB  - been studied in the presence of various polynucleotides and the double stranded
AB  - octanucleotide d-(GGAATTCC) in order to clarify whether there is a preferential
AB  - interation of EcoRI with DNA sequences other than -GAATTC-.  The steady state
AB  - kinetic analysis shows that all polynucleotides investigated with the possible
AB  - exception of poly-dG.poly-dC inhibit the cleavage competitively with Ki values
AB  - in the range of 10-4 to 10-5 [M nucleotides].  The Ki of d-(GGAATTCC) is
AB  - 1.5.10-6 [M nucleotides], indicating that the specific binding is approx. 2
AB  - orders of magnitude stronger than non-specific binding.
ER  -

TY  - JOUR
AU  - Langowski, J.
AU  - Urbanke, C.
AU  - Pingoud, A.
AU  - Maass, G.
TI  - Transient cleavage kinetics of the EcoRI restriction endonuclease measured in a pulsed quench-flow apparatus:  enzyme concentration-dependent activity change.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 3483
EP  - 3490
VL  - 9
AB  - We report measurements of the cleavage rate of pBR322 plasmid DNA by
AB  - restriction endonuclease EcoRI as a function of enzyme and DNA concentration.
AB  - The reaction, which at high excess of enzyme over DNA occurs between 0.2 and 5
AB  - seconds, was studied by the means of a microprocessor controlled pulsed
AB  - quench-flow apparatus.  Enzyme concentrations were between 1 and 100 nM with
AB  - DNA concentrations being 3 to 6 nM (specific EcoRI sites).  The catalytic
AB  - constants for cleavage of the first and second phosphodiester bonds as measured
AB  - at high enzyme concentration both have the same value of 0.35 sec-1 at 21C.  At
AB  - enzyme concentrations comparable to or less than DNA concentration, the rate of
AB  - the first cleavage is proportional to enzyme concentration, while the second
AB  - step is independent of concentration.  At approx. 10 nM EcoRI endonuclease
AB  - concentration, a rate increase shows up in both the first and the second
AB  - cleavage.  We suggest that this increase is due to the tetramerization reported
AB  - by Modrich & Zabel, which occurs in this concentration range.
ER  -

TY  - JOUR
AU  - Lanie, J.A.
AU  - Ng, W.L.
AU  - Kazmierczak, K.M.
AU  - Andrzejewski, T.M.
AU  - Davidsen, T.M.
AU  - Wayne, K.J.
AU  - Tettelin, H.
AU  - Glass, J.I.
AU  - Winkler, M.E.
TI  - Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain  R6.
JO  - J. Bacteriol.
PY  - 2007
SP  - 38
EP  - 51
VL  - 189
AB  - Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a
AB  - variety of serious mucosal and invasive diseases.
AB  - D39 is an historically important serotype 2 strain that was used in
AB  - experiments by Avery and coworkers to demonstrate that DNA is the genetic
AB  - material. Although isolated nearly a century ago, D39 remains extremely
AB  - virulent in murine infection models and is perhaps the strain used most
AB  - frequently in current studies of pneumococcal pathogenesis. To date, the
AB  - complete genome sequences have been reported for only two S. pneumoniae
AB  - strains: TIGR4, a recent serotype 4 clinical isolate, and laboratory
AB  - strain R6, an avirulent, unencapsulated derivative of strain D39. We
AB  - report here the genome sequences and new annotation of two different
AB  - isolates of strain D39 and the corrected sequence of strain R6.
AB  - Comparisons of these three related sequences allowed deduction of the
AB  - likely sequence of the D39 progenitor and mutations that arose in each
AB  - isolate. Despite its numerous repeated sequences and IS elements, the
AB  - serotype 2 genome has remained remarkably stable during cultivation, and
AB  - one of the D39 isolates contains only five relatively minor mutations
AB  - compared to the deduced D39 progenitor. In contrast, laboratory strain R6
AB  - contains 71 single-base-pair changes, six deletions, and four insertions
AB  - and has lost the cryptic pDP1 plasmid compared to the D39 progenitor
AB  - strain. Many of these mutations are in or affect the expression of genes
AB  - that play important roles in regulation, metabolism, and virulence. The
AB  - nature of the mutations that arose spontaneously in these three strains,
AB  - the relative global transcription patterns determined by microarray
AB  - analyses, and the implications of the D39 genome sequences to studies of
AB  - pneumococcal physiology and pathogenesis are presented and discussed.
ER  -

TY  - JOUR
AU  - Lanio, T.
AU  - Jeltsch, A.
TI  - PCR-based random mutagenesis method using spiked oligonucleotides to randomize selected parts of a gene without any wild-type background.
JO  - Biotechniques
PY  - 1998
SP  - 958
EP  - 965
VL  - 25
AB  - Site-directed mutagenesis is a common tool to analyze protein structure and function.  In
AB  - polymerase chain reaction (PCR)-based SDM methods, the mutation is introduced by a PCR primer.
AB  - Also, a restriction-enzyme-marker site is often introduced to allow fast and convenient
AB  - screening for the presence of the mutation.  Usually, each primer encodes only one particular
AB  - amino acid exchange.  In principle then, it is sufficient to identify one marker-positive
AB  - clone.  Under these circumstances, the level of background of nonmutated genes is not
AB  - important considering that more than approximately 20% of the clones carry the mutation.  If
AB  - only 20% of the transformants contained a mutated gene, then screening 10-20 of the clones
AB  - would be sufficient to identify at least one mutant, with a probability of 90%-99%.  However,
AB  - the approach of introducing nucleotide exchanges into a gene by a PCR primer can be easily
AB  - extended to randomize larger parts of the gene if spiked oligonucleotides, which contain some
AB  - degree of a mixture of all 4 nucleotides, are used.  Then, one usually intends to isolate as
AB  - many mutant clones as possible to obtain as large a library of mutated genes as possible.
AB  - Because it is impossible with respect to time and cost to screen more than a few hundred
AB  - clones, a method for mutagenesis that excludes the wild-type genes from the transformants with
AB  - high confidence is required.
ER  -

TY  - JOUR
AU  - Lanio, T.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Automated purification of His6-tagged proteins allows exhaustive screening of libraries generated by random mutagenesis.
JO  - Biotechniques
PY  - 2000
SP  - 338
EP  - 342
VL  - 29
AB  - In the course of site-directed mutagenesis or directed evolution
AB  - experiments, large numbers of
AB  - protein variants are often generated. To characterize functional properties of
AB  - individual
AB  - mutant proteins in vitro, a rapid and reliable protein purification system is
AB  - required. We
AB  - have developed an automated method for the parallel purification of 96 different
AB  - protein
AB  - variants that takes about two hours. Using a 96-well format, the whole process
AB  - can be
AB  - performed automatically by a pipetting robot. Coupled with a suitable assay,
AB  - again using a
AB  - 96-well format, all variants can be functionally characterized within a few
AB  - hours. The protein
AB  - purification procedure described here is based on the interaction between His6-
AB  - tagged proteins
AB  - and Ni-NTA-coated microplates. Typical yields are 3-8 pmol purified
AB  - protein/well, which is
AB  - sufficient to analyze most enzymatic activities. Using this procedure, we have
AB  - purified and
AB  - characterized variants of the restriction endonuclease EcoRV, which were
AB  - produced in an effort
AB  - to enhance the selectivity of this enzyme. For this purpose, three amino acid
AB  - residues were
AB  - randomized in a region known from the co-crystal structure to be located at the
AB  - protein-DNA
AB  - interface. From a library of about 1200 variants, predominantly single and
AB  - double mutants,
AB  - more than 1000 variants were purified and characterized in parallel, which
AB  - corresponds to an
AB  - almost complete screening of the library.
ER  -

TY  - JOUR
AU  - Lanio, T.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target.
JO  - Protein Eng.
PY  - 2000
SP  - 275
EP  - 281
VL  - 13
AB  - The restriction endonuclease EcoRV has been characterized in structural and functional terms
AB  - in great detail. Based on this detailed information we employed a structure-guided approach to
AB  - engineer variants of EcoRV that should be able to discriminate between differently flanked
AB  - EcoRV recognition sites. In crystal structures of EcoRV complexed with d(CGGGATATCCC)(2) and
AB  - d(AAAGATATCTT)(2), Lys104 and Ala181 closely approach the two base pairs flanking the GATATC
AB  - recognition site and thus were proposed to be a reasonable starting point for the rational
AB  - extension of site specificity in EcoRV [Horton,N.C. and Perona,J.J. (1998) J. Biol. Chem.,
AB  - 273, 21721-21729]. To test this proposal, several single (K104R, A181E, A181K) and double
AB  - mutants of EcoRV (K104R/A181E, K104R/A181K) were generated. A detailed characterization of all
AB  - variants examined shows that only the substitution of Ala181 by Glu leads to a considerably
AB  - altered selectivity with both oligodeoxynucleotide and macromolecular DNA substrates, but not
AB  - the predicted one, as these variants prefer cleavage of a TA flanked site over all other
AB  - sites, under all conditions tested. The substitution of Lys104 by Arg, in contrast, which
AB  - appeared to be very promising on the basis of the crystallographic analysis, does not lead to
AB  - variants which differ very much from the EcoRV wild-type enzyme with respect to the flanking
AB  - sequence preferences. The K104R/A181E and K104R/A181K double mutants show nearly the same
AB  - preferences as the A181E and A181K single mutants. We conclude that even for the very well
AB  - characterized restriction enzyme EcoRV, properties that determine specificity and selectivity
AB  - are difficult to model on the basis of the available structural information.
ER  -

TY  - JOUR
AU  - Lanio, T.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Towards the design of rare cutting restriction endonucleases: using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 59
EP  - 69
VL  - 283
AB  - The restriction endonuclease EcoRV cleaves DNA highly specifically within GATATC sequences. In
AB  - order to create EcoRV variants that have an extended recognition site we have employed a
AB  - semi-rational random mutagenesis/selection procedure. Twenty-two amino acid residues were
AB  - subjected to random mutagenesis and about 500 EcoRV variants representing three generations of
AB  - mutants were screened. Among these some highly active variants that strongly prefer AT-flanked
AB  - cleavage sites (e.g. S183A/Q224R, T93S/I103F/S183A/T222S or N97T/S183A/T222S) and others that
AB  - prefer GC flanks (e.g. K104N/A181T) were identified. As wild-type EcoRV does not discriminate
AB  - between these cleavage sites, the generation of these variants represents a significant first
AB  - step towards redesigning EcoRV to become an 8 or 10 bp cutter. Such enzymes, only very rarely
AB  - found in nature, could be extremely helpful for the manipulation of large DNA fragments.
ER  -

TY  - JOUR
AU  - Lanio, T.
AU  - Selent, U.
AU  - Wenz, C.
AU  - Wende, W.
AU  - Schulz, A.
AU  - Adiraj, M.
AU  - Katti, S.B.
AU  - Pingoud, A.
TI  - EcoRV-T94V: a mutant restriction endonucleaase with an altered substrate specificity towards modified oligodeoxynucleotides.
JO  - Protein Eng.
PY  - 1996
SP  - 1005
EP  - 1010
VL  - 9
AB  - Synthetic oligodeoxynucleotides with single methyl phosphonate substitutions were used for an
AB  - analysis of the contribution of phosphate contacts to the recognition of the cleavage site by
AB  - the restriction endonuclease EcoRV.  Only in the last position within the recognition
AB  - sequence, is the methyl phosphonate substitution tolerated by the enzyme.  The wild type
AB  - enzyme cleaves the SP diastereomer of the oligodeoxynucleotide GACGATATmpCGTC and the
AB  - unmodified sequence with equal rates, whereas the RP diastereomer is cleaved much more slowly.
AB  - Inspection of the crystal structure of an EcoRV-DNA complex revealed that the non-bridging
AB  - oxygen atoms of the phosphodiester bond between the T and C bases are in hydrogen bonding
AB  - distance of the hydroxyl group of the amino acid Thr94.  We therefore tried to engineer a
AB  - variant of EcoRV that would prefer a methyl phosphonate linkage over a normal phophodiester
AB  - bond and produced mutants with amino acid exchanges at position 94.  One of them, Thr94Val,
AB  - shows a dramatically reduced activity towards the unmodified DNA and does not accept the RP
AB  - diastereomer, but cleaves the SP diastereomer with the same rate as wild type EcoRV.  Its
AB  - selectivity, i.e. the ratio of cleavage rates determined for the unmodified and modified
AB  - substrates, differs by three orders of magnitude from that of the wild type enzyme.
ER  -

TY  - JOUR
AU  - Lannoy, N.N.
AU  - Hoet, P.P.
AU  - Cocito, C.G.
TI  - Cloning of DNA segments of phage 2C, which allows autonomous plasmid replication in Bacillus subtilis.
JO  - Eur. J. Biochem.
PY  - 1985
SP  - 137
EP  - 142
VL  - 152
AB  - The chromosome of Bacillus subtilis phage 2C is a 100-MDa double-stranded DNA molecule,
AB  - containing hydroxymethyluracil in place of thymine and carrying redundant ends each
AB  - encompassing 10% of the genome. 2C DNA was cleaved with EcoRI and HindIII, and cloned in the
AB  - shuttle plasmids pSC 540 and pCP 115, both containing segments originating from B. subtilis
AB  - and Escherichia coli plasmids. These chimaerical plasmids, carrying the chloramphenicol
AB  - resistance gene, were unable to replicate in B. subtilis; this ability was restored, however,
AB  - after the insertion of viral DNA segments. Physical maps of the recombinant plasmids were
AB  - made; a large deletion of the E. coli-derived segment of pSC 540 was observed (which
AB  - paralleled a loss of replication in this host), whereas addition of 2C DNA segments in pCP 115
AB  - was not accompanied by deletion (replication in E. coli was conserved in this case). Cloned
AB  - viral segments mapped mostly, but not exclusively, within the redundant ends of 2C DNA. It is
AB  - suggested that the thirteen recombinant clones carried the replication origin region of phage
AB  - 2C DNA, and that these sequences originated within or close to the redundant extremities of
AB  - the viral chromosome.
ER  -

TY  - JOUR
AU  - Lanois, A.
AU  - Ogier, J.C.
AU  - Gouzy, J.
AU  - Laroui, C.
AU  - Rouy, Z.
AU  - Givaudan, A.
AU  - Gaudriault, S.
TI  - Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1.
JO  - Genome Announcements
PY  - 2013
SP  - e00342
EP  - e00313
VL  - 1
AB  - We report the 4.3-Mb genome sequence of Xenorhabdus nematophila strain F1, a Gram-negative
AB  - bacterium that is a symbiont of the entomopathogenic nematode
AB  - Steinernema carpocapsae and pathogenic by direct injection for a wide variety of
AB  - insects.
ER  -

TY  - JOUR
AU  - Lanzarotti, E.
AU  - Pellizza, L.
AU  - Bercovich, A.
AU  - Foti, M.
AU  - Coria, S.H.
AU  - Vazquez, S.C.
AU  - Ruberto, L.
AU  - Hernandez, E.A.
AU  - Dias, R.L.
AU  - Mac, C.W.P.
AU  - Cicero, D.O.
AU  - Smal, C.
AU  - Nicolas, M.F.
AU  - Vasconcelos, A.T.
AU  - Marti, M.A.
AU  - Turjanski, A.G.
TI  - Draft Genome Sequence of Bizionia argentinensis, Isolated from Antarctic Surface Water.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6797
EP  - 6798
VL  - 193
AB  - A psychrotolerant marine bacterial strain, designated JUB59(T), was isolated from Antarctic
AB  - surface seawater and classified as a new species
AB  - of the genus Bizionia. Here, we present the first draft genome sequence
AB  - for this genus, which suggests interesting features such as UV resistance,
AB  - hydrolytic exoenzymes, and nitrogen metabolism.
ER  -

TY  - JOUR
AU  - Lao, W.
AU  - Chen, S.
TI  - HsaI:  A restriction enzyme from human being.
JO  - Sci. Sin.
PY  - 1986
SP  - 947
EP  - 953
VL  - 29
AB  - The HsaI restriction enzyme from the embryos of human, Homo sapiens, has been
AB  - isolated with both the tissue extract and nuclear extract.  It proves to be an
AB  - unusual enzyme, clearly related functionally to Type II endonuclease.  HsaI
AB  - seems to be an isoschizomer of EcoRI, but it has a distinctive property of
AB  - elution, differing from EcoRI.  Upon SDS-polyacrylamide gel electrophoresis,
AB  - the enzyme preparation showed Coomassie blue staining bands, having the
AB  - molecular weight of 65,000 and 22,000 daltons in size, respectively.
ER  -

TY  - JOUR
AU  - Lapidus, A. et al.
TI  - Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 86
EP  - 96
VL  - 5
AB  - Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the
AB  - family Deferribacteraceae. The species is of interest because
AB  - of its isolated phylogenetic location in a genomically under-characterized region
AB  - of the tree of life, and because of its origin from a multiply extreme
AB  - environment; the Atlantis Deep brines of the Red Sea, where it had to struggle
AB  - with high temperatures, high salinity, and a high concentrations of heavy metals.
AB  - This is the fourth completed genome sequence to be published of a type strain of
AB  - the family Deferribacteraceae. The 2,526,590 bp long genome with its 2,346
AB  - protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Lapidus, A. et al.
TI  - Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 3
EP  - 11
VL  - 1
AB  - Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of
AB  - phylogenetic interest because of its location in the Dermabacteraceae, a
AB  - rather isolated family within the actinobacterial suborder Micrococcineae. B.
AB  - faecium is known for its rod-coccus growth cycle and the ability to degrade uric
AB  - acid. It grows aerobically or weakly anaerobically. The strain described in this
AB  - report is a free-living, nonmotile, Gram-positive bacterium, originally isolated
AB  - from poultry deep litter. Here we describe the features of this organism,
AB  - together with the complete genome sequence, and annotation. This is the first
AB  - complete genome sequence of a member of the actinobacterial family
AB  - Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129
AB  - protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Lapidus, A. et al.
TI  - Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 398
EP  - 406
VL  - 5
AB  - Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and
AB  - Shinabarger 1983 is the type species of the genus Thiothrix in the
AB  - family Thiotrichaceae. The species is of interest not only because of its
AB  - isolated location in the yet to be genomically characterized region of the tree
AB  - of life, but also because of its life-style with gliding gonidia, the multilayer
AB  - sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype
AB  - strain of the species which was first observed by Rabenhorst in 1865 and later
AB  - reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is
AB  - the first completed (improved-high-quality-draft) genome sequence to be published
AB  - of a member of the family Thiotrichaceae. The genome in its current assembly
AB  - consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing
AB  - 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Lapidus, A.
AU  - Clum, A.
AU  - Labutti, K.
AU  - Kaluzhnaya, M.G.
AU  - Lim, S.
AU  - Beck, D.A.
AU  - Glavina del Rio, T.
AU  - Nolan, M.
AU  - Mavromatis, K.
AU  - Huntemann, M.
AU  - Lucas, S.
AU  - Lidstrom, M.E.
AU  - Ivanova, N.
AU  - Chistoserdova, L.
TI  - Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the Methylophilaceae.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3757
EP  - 3764
VL  - 193
AB  - The genomes of three representatives of the family Methylophilaceae, Methylotenera mobilis
AB  - JLW8, Methylotenera versatilis 301 and Methylovorus glucosetrophus SIP3-4, all isolated from a
AB  - single study site, Lake Washington in Seattle, were completely sequenced. These were compared
AB  - to each other and to the previously published genomes of Methylobacillus flagellatus KT and an
AB  - unclassified Methylophilales strain HTCC2181. Comparative analysis revealed that the core
AB  - genome of Methylophilaceae may be as small as approximately 600 genes while the pangenome may
AB  - be as large as approximately 6000 genes. Significant divergence between the genomes was
AB  - uncovered in terms of both gene content and gene and protein conservation, including varied
AB  - presence of certain genes involved in methylotrophy. Overall, our data demonstrate that
AB  - metabolic potentials can vary significantly between different species of Methylophilaceae,
AB  - including organisms inhabiting the very same environment. These data suggest that genetic
AB  - divergence among the members of this family may be responsible for their specialized and
AB  - non-redundant functions in C1 cycling and in turn suggest means for their successful
AB  - co-existence in their specific ecological niches.
ER  -

TY  - JOUR
AU  - Lapierre, P.
AU  - Halse, T.A.
AU  - Shea, J.
AU  - Escuyer, V.E.
AU  - Musser, K.A.
TI  - Draft Genome Sequence of Branchiibius sp. NY16-3462-2, Isolated from a Mixed Clinical Sample.
JO  - Genome Announcements
PY  - 2016
SP  - e00368
EP  - e00316
VL  - 4
AB  - Here, we report the release of a draft genome assembly of a Gram-positive cocci Branchiibius
AB  - sp. NY16-3462-2 with a high-GC content, sequenced from a mixed
AB  - clinical sample containing Mycobacterium tuberculosis This genome is the first
AB  - publicly available sequence from a representative of the genus Branchiibius.
ER  -

TY  - JOUR
AU  - Lapkouski, M.
AU  - Panjikar, S.
AU  - Janscak, P.
AU  - Smatanova, I.K.
AU  - Carey, J.
AU  - Ettrich, R.
AU  - Csefalvay, E.
TI  - Structure of the motor subunit of type I restriction-modification complex EcoR124I.
JO  - Nat. Struct. Mol. Biol.
PY  - 2009
SP  - 94
EP  - 95
VL  - 16
AB  - Type I restriction-modification enzymes act as conventional adenine methylases on
AB  - hemimethylated DNAs, but unmethylated recognition targets
AB  - induce them to translocate thousands of base pairs before cleaving
AB  - distant sites nonspecifically. The first crystal structure of a type I
AB  - motor subunit responsible for translocation and cleavage suggests how
AB  - the pentameric translocating complex is assembled and provides a
AB  - structural framework for translocation of duplex DNA by RecA-like
AB  - ATPase motors.
ER  -

TY  - JOUR
AU  - Lapkouski, M.
AU  - Panjikar, S.
AU  - Smatanova, I.K.
AU  - Csefalvay, E.
TI  - Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2007
SP  - 582
EP  - 585
VL  - 63
AB  - EcoR124I is a multicomplex enzyme belonging to the type I restriction-modification system from
AB  - Escherichia coli. Although
AB  - EcoR124I has been extensively characterized biochemically, there is no
AB  - direct structural information available about particular subunits. HsdR
AB  - is a motor subunit that is responsible for ATP hydrolysis, DNA
AB  - translocation and cleavage of the DNA substrate recognized by the
AB  - complex. Recombinant HsdR subunit was crystallized using the
AB  - sitting-drop vapour-diffusion method. Crystals belong to the primitive
AB  - monoclinic space group, with unit-cell parameters a = 85.75, b =
AB  - 124.71, c = 128.37 angstrom, beta = 108.14 degrees. Native data were
AB  - collected to 2.6 angstrom resolution at the X12 beamline of EMBL
AB  - Hamburg.
ER  -

TY  - JOUR
AU  - LaPorte, J.P.
AU  - Spinard, E.J.
AU  - Gomez-Chiarri, M.
AU  - Rowley, D.C.
AU  - Mekalanos, J.J.
AU  - Nelson, D.R.
TI  - Draft Genome Sequence of Bowmanella denitrificans JL63, a Bacterium Isolated from Whiteleg Shrimp (Litopenaeus vannamei) That Can Inhibit the Growth of Vibrio  parahaemolyticus.
JO  - Genome Announcements
PY  - 2018
SP  - e00215
EP  - e00218
VL  - 6
AB  - Bowmanella denitrificans strain JL63 was isolated from a whiteleg shrimp (Litopenaeus
AB  - vannamei) and was determined to have antibacterial activity against
AB  - an acute hepatopancreatic necrosis disease (AHPND) strain of Vibrio
AB  - parahaemolyticus Here, we report the draft genome sequence of this strain and
AB  - identify genes that are potentially involved in its antibacterial activity.
ER  -

TY  - JOUR
AU  - Lappalainen, I.
AU  - Vihinen, M.
TI  - Structural basis of ICF-causing mutations in the methyltransferase domain of DNMT3B.
JO  - Protein Eng.
PY  - 2002
SP  - 1005
EP  - 1014
VL  - 15
AB  - Mutations in the gene encoding for a de novo methyltransferase, DNMT3B, lead to an autosomal
AB  - recessive Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome. To
AB  - analyse the protein structure and consequences of ICF-causing mutations, we modelled the
AB  - structure of the DNMT3B methyltransferase domain based on Haemophilus haemolyticus protein in
AB  - complex with the cofactor AdoMet and the target DNA sequence. The structural model has a
AB  - two-subdomain fold where the DNA-binding region is situated between the subdomains on a
AB  - surface cleft having positive electrostatic potential. The smaller subdomains of the
AB  - methyltransferases differ in length and sequences and therefore only the target recognition
AB  - domain loop was modelled to show the location of an ICF-causing mutation. Based on the model,
AB  - the DNMT3B recognizes the GC sequence and flips the cytosine from the double-stranded DNA to
AB  - the catalytic pocket. The amino acids in the cofactor and target cytosine binding sites and
AB  - also the electrostatic properties of the binding pockets are conserved. In addition, a
AB  - registry of all known ICF-causing mutations, DNMT3Bbase, was constructed. The structural
AB  - principles of the pathogenic mutations based on the modelled structure and the analysis of chi
AB  - angle rotation changes of mutated side chains are discussed.
ER  -

TY  - JOUR
AU  - Lara, Y.
AU  - Durieu, B.
AU  - Cornet, L.
AU  - Verlaine, O.
AU  - Rippka, R.
AU  - Pessi, I.S.
AU  - Misztak, A.
AU  - Joris, B.
AU  - Javaux, E.J.
AU  - Baurain, D.
AU  - Wilmotte, A.
TI  - Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica).
JO  - Genome Announcements
PY  - 2017
SP  - e01546
EP  - e01516
VL  - 5
AB  - Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is
AB  - 5,684,389 bp long. It contains a total of 5,604 protein-encoding
AB  - genes, of which 22.2% have no clear homologues in known genomes. To date, this
AB  - draft genome is the first one ever determined for an axenic cyanobacterium from
AB  - Antarctica.
ER  -

TY  - JOUR
AU  - Larbi, D.
AU  - Decaris, B.
AU  - Simonet, J.M.
TI  - Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus.
JO  - J. Dairy Res.
PY  - 1992
SP  - 349
EP  - 357
VL  - 59
AB  - Streptococcus salivarius subsp. thermophilus strain NST5 exhibited a temperature-dependent
AB  - defence mechanism against the virulent bacteriophages phiB1.2 and phiA1.1. It was active at 42
AB  - degrees C but not at 30 degrees C as demonstrated by a significant increase of both plaque
AB  - size and efficiency of plaquing. This defence mechanism did not affect host-dependent phage
AB  - replication and did not interfere with phage adsorption to NST5. These results suggest that it
AB  - interfered with phage development. The phages phiT33, phiT58, phiD1, phiT21 and phiT9,
AB  - belonging to the same phage type as phiB1.2, were examined for their ability to infect NST3
AB  - and NST5. Restriction modification systems of different specificity were detected in NST3 and
AB  - NST5; host-dependent phage replication was detected at 30 and 42 degrees C; an abortive
AB  - defence mechanism was detected in NST5 which was active at 42 degrees C, but not 30 degreesC,
AB  - and was independent of restriction modification action or interference with phage adsorption.
AB  - Our investigations of phage-host interactions showed that the two Str. salivarius subsp.
AB  - thermophilus strains studied avoided attack by related bacteriophages by evolving at least
AB  - three different resistance systems.
ER  -

TY  - JOUR
AU  - Larimer, F.W.
TI  - Cleavage by ApaI is inhibited by overlapping dcm methylation.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 9087
EP  - 9087
VL  - 15
ER  -

TY  - JOUR
AU  - Lark, C.
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli.  XIII.  Breakdown of cellular DNA upon growth in ethionine of strains with r15+, r+P1 or r+N3 restriction phenotypes.
JO  - J. Mol. Biol.
PY  - 1970
SP  - 337
EP  - 348
VL  - 52
AB  - All methionine-requiring strains of Escherichia coli which have been tested show a two-fold
AB  - increase in DNA content when grown in the presence of ethionine or norleucine. In addition, E.
AB  - coli strains with the restriction phenotype r15+, rP1+ or rN3+ will degrade their
AB  - intracellular DNA when these methionine analogs are substituted for required methionine in the
AB  - growth medium. Degradation does not occur in restriction-deficient mutants and in strains
AB  - carrying the rK+, rA+ or rB+ phenotypes alone. Breakdown of DNA appears to be a characteristic
AB  - of the restriction gene products rather than of the location of these genes on plasmid or
AB  - chromosomal DNA molecules.
ER  -

TY  - JOUR
AU  - Larner-Svensson, H.
AU  - Worning, P.
AU  - Bartels, M.D.
AU  - Hestbjerg, H.L.
AU  - Boye, K.
AU  - Westh, H.
TI  - Complete Genome Sequence of Staphylococcus aureus Strain M1, a Unique t024-ST8-IVa Danish Methicillin-Resistant S. aureus Clone.
JO  - Genome Announcements
PY  - 2013
SP  - e00336
EP  - e00313
VL  - 1
AB  - We report the genome sequence, in five contigs, of a methicillin-resistant Staphylococcus
AB  - aureus isolate designated M1. This clinical isolate was from the
AB  - index patient of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in
AB  - Copenhagen, Denmark, that started in 2003. This strain is sequence type 8 (ST8),
AB  - spa type t024, and staphylococcal cassette chromosome mec element (SCCmec) type
AB  - IVa.
ER  -

TY  - JOUR
AU  - Larson, M.A.
AU  - Nalbantoglu, U.
AU  - Sayood, K.
AU  - Zentz, E.B.
AU  - Bartling, A.M.
AU  - Francesconi, S.C.
AU  - Fey, P.D.
AU  - Dempsey, M.P.
AU  - Hinrichs, S.H.
TI  - Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I.
JO  - PLoS ONE
PY  - 2015
SP  - E0124906
EP  - E0124906
VL  - 10
AB  - Although Francisella tularensis is considered a monomorphic intracellular
AB  - pathogen, molecular genotyping and virulence studies have demonstrated important
AB  - differences within the tularensis subspecies (type A). To evaluate genetic
AB  - variation within type A strains, sequencing and assembly of a new subtype A.II
AB  - genome was achieved for comparison to other completed F. tularensis type A
AB  - genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198,
AB  - NE061598, and TI0902), substantial genomic variation was observed between the
AB  - newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other
AB  - publically available A.II strain (WY96-3418). Genome differences between
AB  - WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580
AB  - indels, and 286 nucleotide substitutions of which 159 were observed in predicted
AB  - open reading frames and 127 were located in intergenic regions. The majority of
AB  - WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of
AB  - the insertions and substitutions occurred in predicted genes. Of the nucleotide
AB  - substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous.
AB  - WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T
AB  - allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the
AB  - A.II genomes contained a considerably higher number of intact genes and longer
AB  - repetitive sequences, including transposon remnants than the A.I genomes.
AB  - Together these findings support the premise that F. tularensis A.II may have a
AB  - fitness advantage compared to the A.I subtype due to the higher abundance of
AB  - functional genes and repeated chromosomal sequences. A better understanding of
AB  - the selective forces driving F. tularensis genetic diversity and plasticity is
AB  - needed.
ER  -

TY  - JOUR
AU  - Larsson, P.
AU  - Elfsmark, D.
AU  - Svensson, K.
AU  - Wikstrom, P.
AU  - Forsman, M.
AU  - Brettin, T.
AU  - Keim, P.
AU  - Johansson, A.
TI  - Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen.
JO  - PLoS Pathog.
PY  - 2009
SP  - e1000472
EP  - e1000472
VL  - 5
AB  - Francisella tularensis is a potent mammalian pathogen well adapted to intracellular habitats,
AB  - whereas F. novicida and F. philomiragia are less virulent
AB  - in mammals and appear to have less specialized lifecycles. We explored
AB  - adaptations within the genus that may be linked to increased host association, as
AB  - follows. First, we determined the genome sequence of F. tularensis subsp.
AB  - mediasiatica, the only subspecies that had not been previously sequenced. This
AB  - genome, and those of 12 other F. tularensis isolates, were then compared to the
AB  - genomes of F. novicida (three isolates) and F. philomiragia (one isolate). Signs
AB  - of homologous recombination were found in approximately 19.2% of F. novicida and
AB  - F. philomiragia genes, but none among F. tularensis genomes. In addition, random
AB  - insertions of insertion sequence elements appear to have provided raw materials
AB  - for secondary adaptive mutations in F. tularensis, e.g. for duplication of the
AB  - Francisella Pathogenicity Island and multiplication of a putative glycosyl
AB  - transferase gene. Further, the five major genetic branches of F. tularensis seem
AB  - to have converged along independent routes towards a common gene set via
AB  - independent losses of gene functions. Our observations suggest that despite an
AB  - average nucleotide identity of >97%, F. tularensis and F. novicida have evolved
AB  - as two distinct population lineages, the former characterized by clonal structure
AB  - with weak purifying selection, the latter by more frequent recombination and
AB  - strong purifying selection. F. tularensis and F. novicida could be considered the
AB  - same bacterial species, given their high similarity, but based on the
AB  - evolutionary analyses described in this work we propose retaining separate
AB  - species names.
ER  -

TY  - JOUR
AU  - Lartigue, C.
AU  - Vashee, S.
AU  - Algire, M.A.
AU  - Chuang, R.Y.
AU  - Benders, G.A.
AU  - Ma, L.
AU  - Noskov, V.N.
AU  - Denisova, E.A.
AU  - Gibson, D.G.
AU  - Assad-Garcia, N.
AU  - Alperovich, N.
AU  - Thomas, D.W.
AU  - Merryman, C.
AU  - Hutchison, C.A.I.I.I.
AU  - Smith, H.O.
AU  - Venter, J.C.
AU  - Glass, J.I.
TI  - Creating bacterial strains from genomes that have been cloned and engineered in yeast.
JO  - Science
PY  - 2009
SP  - 1693
EP  - 1696
VL  - 325
AB  - We recently reported the chemical synthesis, assembly, and cloning of a bacterial genome in
AB  - yeast. To produce a synthetic cell, the genome must be transferred from yeast to a receptive
AB  - cytoplasm. Here we describe methods to accomplish this. We cloned a Mycoplasma mycoides genome
AB  - as a yeast centromeric plasmid and then transplanted it into Mycoplasma capricolum to produce
AB  - a viable M. mycoides cell. While in yeast, the genome was altered by using yeast genetic
AB  - systems and then transplanted to produce a new strain of M. mycoides. These methods allow the
AB  - construction of strains that could not be produced with genetic tools available for this
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Lasa, A.
AU  - Gibas, C.J.
AU  - Romalde, J.L.
TI  - Draft Genome Sequence of Vibrio toranzoniae Strain CECT 7225T.
JO  - Genome Announcements
PY  - 2016
SP  - e00212
EP  - e00216
VL  - 4
AB  - Vibrio toranzoniae(CECT 7225(T)) was isolated from healthy reared carpet shell clams in
AB  - Galicia (Northwest Spain). In addition, this species has been recently
AB  - identified as a potential pathogen of red conger eel in Chile. The draft genome
AB  - sequence has 4.5 Mbp, a G+C content of 43.9%, and >3,800 protein-coding genes.
ER  -

TY  - JOUR
AU  - Lasek, R.
AU  - Dziewit, L.
AU  - Bartosik, D.
TI  - Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon.
JO  - Extremophiles
PY  - 2012
SP  - 363
EP  - 376
VL  - 16
AB  - The complete nucleotide sequence of plasmid pP62BP1 (34,467 bp), isolated from Arctic sp. DAB
AB  - AL62B, was determined and annotated. The
AB  - conserved plasmid backbone is composed of several genetic modules,
AB  - including a replication system (REP) with similarities to the REP
AB  - region of the iteron-containing plasmid pPS10 of . The additional
AB  - genetic load of pP62BP1 includes two highly related type II
AB  - restriction-modification systems and a set of genes () encoding enzymes
AB  - engaged in the metabolism of organic sulfates, plus a putative
AB  - transcriptional regulator (SlfR) of the AraC family. The pP62BP1 has a
AB  - compact and unique structure. It is predicted that the enzymes SlfC,
AB  - SlfH, SlfS and SlfL carry out a chain of reactions leading to the
AB  - transformation of alkyl sulfates into acyl-CoA, with dodecyl sulfate
AB  - (SDS) as a possible starting substrate. Comparative analysis of the
AB  - nucleotide sequences of pP62BP1 and other spp. plasmids revealed their
AB  - structural diversity. However, the presence of a few highly conserved
AB  - DNA segments in pP62BP1, plasmid 1 of K5 and pRWF-101 of sp. PRwf-1 is
AB  - indicative of recombinational shuffling of genetic information, and is
AB  - evidence of lateral gene transfer in the Arctic environment.
ER  -

TY  - JOUR
AU  - Lasko, D.D.
AU  - Basu, A.K.
AU  - Kadlubar, F.F.
AU  - Evans, F.E.
AU  - Lay, J.O.
AU  - Essigmann, J.M.
TI  - A probe for the mutagenic activity of the carcinogen 4-aminobiphenyl:  synthesis and characterization of an M13mp10 genome containing the major carcinogen-DNA adduct at a unique site.
JO  - Biochemistry
PY  - 1987
SP  - 3072
EP  - 3081
VL  - 26
AB  - The duplex genome of Escherichia coli virus M13mp10 was modified at a unique
AB  - site to contain N-(deoxyguanosin-8-yl)-4-aminobiphenyl (dG8-ABP), the major
AB  - carcinogen-DNA adduct of the human bladder carcinogen 4-aminobiphenyl.  A
AB  - tetradeoxynucleotide containing a single dG8-ABP residue was synthesized by
AB  - reacting 5'-d(TpGpCpA)-3' with N-acetoxy-N-(trifluoroacetyl)-4-aminobiphenyl,
AB  - followed by high-performance liquid chromatography purification of the
AB  - principal reaction product 5'-d(TpG8-ABPpCpA)-3' (yield 15-30%).
AB  - Characterization by fast atom bombardment mass spectrometry confirmed the
AB  - structure as an intact 4-aminobiphenyl-modified tetranucleotide, while 1H
AB  - nuclear magnetic resonance spectroscopy established the site of substitution
AB  - and the existence of ring stacking between the carcinogen residue and DNA
AB  - bases.  Both 5'-d(TpG8-ABPpCpA)-3' and 5'-d(TpGpCpA)-3' were 5'-phosphorylated
AB  - by use of bacteriophage T4 polynucleotide kinase and were incorporated into a
AB  - four-base gap uniquely positioned in the center of the recognition site for the
AB  - restriction endonuclease PstI, in an otherwise duplex genome of M13mp10.  In
AB  - the case of the adducted tetranucleotide, dG8-ABP was located in the minus
AB  - strand at genome position 6270.  Experiments in which the tetranucleotides were
AB  - 5' end labeled with [32P] phosphate revealed the following: (i) the adducted
AB  - oligomer, when incubated in a 1000-fold molar excess in the presence of T4 DNA
AB  - ligase and ATP, was found to be incorporated into the gapped DNA molecules with
AB  - an efficiency of approximately 30%, as compared to the unadducted d(pTpGpCpA),
AB  - which was incorporated with 60% ligation efficiency; (ii) radioactivity from
AB  - the 5' end of each tetranucleotide was physically mapped to a restriction
AB  - fragment that contained the PstI site and represented 0.2% of the genome; (iii)
AB  - the presence of the lesion within the PstI recognition site inhibited the
AB  - ability of PstI to cleave the genome at this site; (iv) in genomes in which
AB  - ligation occurred, T4 DNA ligase was capable of covalently joining both
AB  - modified and unmodified tetranucleotides to the gapped structures on both the
AB  - 5' and the 3' ends with at least 90% efficiency.  Evidence also is presented
AB  - showing that the dG8-ABP-modified tetranucleotide was stable to the conditions
AB  - of the recombinant DNA techniques used to insert it into the viral genome.  On
AB  - the basis of these and other data, the dG8-ABP-modified genome was judged to be
AB  - a useful probe for investigation of site-specific mutagenesis in E. coli.
ER  -

TY  - JOUR
AU  - Lassen, S.B.
AU  - Lomholt, H.B.
AU  - Bruggemann, H.
TI  - Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional  Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e00004
EP  - e00017
VL  - 5
AB  - Staphylococcus epidermidis is a Gram-positive bacterium that is prevalent on human skin. The
AB  - species is associated with skin health, as well as with
AB  - opportunistic infections. Here, we report the complete genome sequence of S.
AB  - epidermidis 14.1.R1, isolated from human skin. In bacterial interference assays,
AB  - the strain showed exceptional antimicrobial activity.
ER  -

TY  - JOUR
AU  - Lasserre, M.
AU  - Berna, L.
AU  - Greif, G.
AU  - Diaz-Viraque, F.
AU  - Iraola, G.
AU  - Naya, H.
AU  - Castro-Ramos, M.
AU  - Juambeltz, A.
AU  - Robello, C.
TI  - Whole-Genome Sequences of Mycobacterium bovis Strain MbURU-001, Isolated from Fresh Bovine Infected Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e01237
EP  - e01215
VL  - 3
AB  - Bovine tuberculosis in cattle has a high incidence in Uruguay, where it is considered a
AB  - disease of national importance. We present the genome sequence of
AB  - Mycobacterium bovis strain MbURU-001, isolated from pectoral lymph nodes of a
AB  - bovine host from a cattle farm.
ER  -

TY  - JOUR
AU  - Laszlo, V.G.
AU  - Rimanoczy, I.
TI  - Restriction and modification of Shigella flexneri phages by R factors.
JO  - Acta Microbiol. Acad. Sci. Hung.
PY  - 1976
SP  - 259
EP  - 270
VL  - 23
AB  - Out of 420 R factors derived from Shigella flexneri strains, 50.8% restricted Escherichia coli
AB  - and S. flexneri phages.  Phage restriction was produced both by fi- and fi+ R factors.  The R
AB  - factors were divided into nine groups on the basis of the efficiency of plating of S. flexneri
AB  - phages.  Changes of phage types were produced by transferring R factors of different
AB  - restrictive types.  The changes offered some information concerning the evolution of phage
AB  - types.  Studies on phage modification supported the grouping of R factors determined on the
AB  - basis of restriction.  R factors of different restrictive types were type-specific except for
AB  - types VIII and IX.  Modified phages proved to be highly practical for epidemiological
AB  - purposes.  The use of modified phages, as an additional phage-set besides the basic phage-set,
AB  - was suggested to trace the source of strains which changed their phage types as an effect of R
AB  - factors.
ER  -

TY  - JOUR
AU  - Lata, P.
AU  - Govindarajan, S.S.
AU  - Qi, F.
AU  - Li, J.L.
AU  - Maurya, S.K.
AU  - Sahoo, M.K.
TI  - Whole-Genome Sequence of Bacillus stratosphericus Strain 5Co, Isolated from Lichen Usnea florida in Central Florida, United States, with High Tolerance to  Salt and Heavy Metal.
JO  - Genome Announcements
PY  - 2017
SP  - e00500
EP  - e00517
VL  - 5
AB  - Bacillus stratosphericus strain 5Co was isolated from lichen Usnea florida in central Florida,
AB  - United States. Here, we report a draft genome sequence of this
AB  - strain, which consists of 159 contigs spanning 3,628,496 bp, with a G+C content
AB  - of 41.3% and comprises 3,729 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Lata, P.
AU  - Govindarajan, S.S.
AU  - Qi, F.
AU  - Li, J.L.
AU  - Maurya, S.K.
AU  - Sahoo, M.K.
TI  - Draft Genome Sequences of Extended-Spectrum-Beta-Lactamase-Producing Morganella morganii Strains AA1 and AV1, Isolated from a Freshwater Lake and  Eicchorniacrassipes Roots.
JO  - Genome Announcements
PY  - 2017
SP  - e00527
EP  - e00517
VL  - 5
AB  - Two strains of Morganella morganii, AA1 and AV1, were isolated from freshwater and Eicchornia
AB  - crassipes roots, respectively. Here, we report their draft genome
AB  - sequences, which are ~3.6 Mb and have 51% G+C content. The predicted coding
AB  - sequences (3,259 for strain AA1 and 3,345 for strain AV1) encode beta-lactamases,
AB  - transpeptidases, and penicillin-binding proteins.
ER  -

TY  - JOUR
AU  - Lata, P.
AU  - Govindarajan, S.S.
AU  - Qi, F.
AU  - Li, J.L.
AU  - Maurya, S.K.
AU  - Sahoo, M.K.
TI  - Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum beta-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora.
JO  - Genome Announcements
PY  - 2017
SP  - e01285
EP  - e01217
VL  - 5
AB  - Pantoea americana strain VS1, an extended-spectrum beta-lactamase-producing epibiont, was
AB  - isolated from Magnolia grandiflora in central Florida, USA. Here,
AB  - we report the de novo whole-genome sequence of this strain, which consists of a
AB  - total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and
AB  - comprising 4,836 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Lata, P.
AU  - Govindarajan, S.S.
AU  - Qi, F.
AU  - Li, J.L.
AU  - Maurya, S.K.
AU  - Sahoo, M.K.
TI  - De Novo Whole-Genome Sequence of Pantoea latae Strain AS1, Isolated from Zamia floridana Rhizosphere in Central Florida, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e00640
EP  - e00617
VL  - 5
AB  - Pantoea latae strain AS1 was isolated from the rhizophere of a cycad, Zamia floridana, in
AB  - central Florida, USA. Here, we report the de novo whole-genome
AB  - sequence of this strain, which consists of a total of 83 contigs spanning
AB  - 4,960,415 bp, with a G+C content of 59.6%, and comprising 4,527 predicted coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Lata, P.
AU  - Govindarajan, S.S.
AU  - Qi, F.
AU  - Li, J.L.
AU  - Sahoo, M.K.
TI  - Deep Sequencing-Identified Kanamycin-Resistant Paenibacillus sp. Strain KS1 Isolated from Epiphyte Tillandsia usneoides (Spanish Moss) in Central Florida,  USA.
JO  - Genome Announcements
PY  - 2017
SP  - e01523
EP  - e01516
VL  - 5
AB  - Paenibacillus sp. strain KS1 was isolated from an epiphyte, Tillandsia usneoides  (Spanish
AB  - moss), in central Florida, USA. Here, we report a draft genome sequence
AB  - of this strain, which consists of a total of 398 contigs spanning 6,508,195 bp,
AB  - with a G+C content of 46.5% and comprising 5,401 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Latif, H.
AU  - Lerman, J.A.
AU  - Portnoy, V.A.
AU  - Tarasova, Y.
AU  - Nagarajan, H.
AU  - Schrimpe-Rutledge, A.C.
AU  - Smith, R.D.
AU  - Adkins, J.N.
AU  - Lee, D.H.
AU  - Qiu, Y.
AU  - Zengler, K.
TI  - The Genome Organization of Thermotoga maritima Reflects Its Lifestyle.
JO  - PLoS Genet.
PY  - 2013
SP  - E1003485
EP  - E1003485
VL  - 9
AB  - The generation of genome-scale data is becoming more routine, yet the subsequent
AB  - analysis of omics data remains a significant challenge. Here, an approach that
AB  - integrates multiple omics datasets with bioinformatics tools was developed that
AB  - produces a detailed annotation of several microbial genomic features. This
AB  - methodology was used to characterize the genome of Thermotoga maritima-a
AB  - phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data
AB  - were generated for whole-genome resequencing, transcription start site (TSS)
AB  - determination, transcriptome profiling, and proteome profiling. These datasets,
AB  - analyzed in combination with bioinformatics tools, served as a basis for the
AB  - improvement of gene annotation, the elucidation of transcription units (TUs), the
AB  - identification of putative non-coding RNAs (ncRNAs), and the determination of
AB  - promoters and ribosome binding sites. This revealed many distinctive properties
AB  - of the T. maritima genome organization relative to other bacteria. This genome
AB  - has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and
AB  - few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and
AB  - ribosome binding sites showed increased sequence conservation relative to other
AB  - bacteria. The 5'UTRs follow an atypical bimodal length distribution comprised of
AB  - "Short" 5'UTRs (11-17 nt) and "Common" 5'UTRs (26-32 nt). Transcriptional
AB  - regulation is limited by a lack of intergenic space for the majority of TUs.
AB  - Lastly, a high fraction of annotated genes are expressed independent of growth
AB  - state and a linear correlation of mRNA/protein is observed (Pearson r = 0.63,
AB  - p<2.2x10(-16) t-test). These distinctive properties are hypothesized to be a
AB  - reflection of this organism's hyperthermophilic lifestyle and could yield novel
AB  - insights into the evolutionary trajectory of microbial life on earth.
ER  -

TY  - JOUR
AU  - Latif, H.
AU  - Li, H.J.
AU  - Charusanti, P.
AU  - Palsson, B.O.
AU  - Aziz, R.K.
TI  - A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli  O157:H7 Strain EDL933.
JO  - Genome Announcements
PY  - 2014
SP  - e00821
EP  - e00814
VL  - 2
AB  - Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype
AB  - O157:H7, associated with deadly food-borne outbreaks. Because the
AB  - publicly available sequence of the EDL933 genome has gaps and >6,000 ambiguous
AB  - base calls, we here present an updated high-quality, unambiguous genome sequence
AB  - with no assembly gaps.
ER  -

TY  - JOUR
AU  - Lau, E.Y.
AU  - Bruice, T.C.
TI  - Active site dynamics of the HhaI methyltransferase: Insights from computer simulation.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 9
EP  - 18
VL  - 293
AB  - A molecular dynamics study was performed on the DNA methyltransferase M.HhaI in a ternary
AB  - complex with DNA and AdoMet in solution. Methylation involves addition of the Cys81 sulfhydryl
AB  - anion to the 6-position of Cyt18, followed by a nucleophilic attack of the resultant carbanion
AB  - at C5 on the AdoMet methyl group. It was found in this simulation that the distances between
AB  - the sulfhydryl group (SG) of Cys81 to the C6 of Cyt18 (SG-C6) and methyl carbon (CH3) of
AB  - AdoMet to the C5 of cytosine (CH3-C5) are dependent on the dihedral angle chi
AB  - (O4'-C1'-N1-C2) of the nucleotide. When the chi angle of Cyt18 is low (<-80 degrees ), the
AB  - SG-C6 and CH3-C5 distances are large. A high chi angle (>-80 degrees ) for the target cytosine
AB  - residue reduces the distances for both SG-C6 and CH3-C5, and the angles formed between the
AB  - cytosine ring and AdoMet correspond well to values for the transition state structures formed
AB  - during methylation of cytosine from ab initio calculations. Two possible proton sources for
AB  - protonation of N3 of the cytosine residue upon formation of the covalent intermediate were
AB  - found in the simulation. The protonated amine group of AdoMet could provide a proton via a
AB  - water bridge, or Arg163 could also be the source of the proton for N3 via a water bridge. The
AB  - simulation provides insights into how the H5 of cytosine could go from the active site into
AB  - solvent. Conserved residues Asn304 and Gln82 stabilize a water network within the active site
AB  - of M.HhaI which provides a route for H5 to diffuse into bulk solvent. An initially distant
AB  - water molecule was able to diffuse into the active site of the enzyme and replace a position
AB  - of a crystallographic water molecule in close proximity to the C5 of cytosine. The movement of
AB  - this water molecule showed that a channel exists between Gln82 and the AdoMet in M.HhaI which
AB  - allows both water and protons to easily gain access to the active site of the enzyme.
ER  -

TY  - JOUR
AU  - Lau, N.S.
AU  - Sam, K.K.
AU  - Amirul, A.A.
TI  - Genome features of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 12
EP  - 12
VL  - 12
AB  - Yangia sp. CCB-MM3 was one of several halophilic bacteria isolated from soil sediment in the
AB  - estuarine Matang Mangrove, Malaysia. So far, no member from the
AB  - genus Yangia, a member of the Rhodobacteraceae family, has been reported
AB  - sequenced. In the current study, we present the first complete genome sequence of
AB  - Yangia sp. strain CCB-MM3. The genome includes two chromosomes and five plasmids
AB  - with a total length of 5,522,061 bp and an average GC content of 65%. Since a
AB  - different strain of Yangia sp. (ND199) was reported to produce a
AB  - polyhydroxyalkanoate copolymer, the ability for this production was tested in
AB  - vitro and confirmed for strain CCB-MM3. Analysis of its genome sequence confirmed
AB  - presence of a pathway for production of propionyl-CoA and gene cluster for PHA
AB  - production in the sequenced strain. The genome sequence described will be a
AB  - useful resource for understanding the physiology and metabolic potential of
AB  - Yangia as well as for comparative genomic analysis with other Rhodobacteraceae.
ER  -

TY  - JOUR
AU  - Lau, P.C.K.
AU  - Forghani, F.
AU  - Labbe, D.
AU  - Bergeron, H.
AU  - Brousseau, R.
AU  - Holtke, H.J.
TI  - The NlaIV restriction and modification genes of Neisseria lactamica are flanked by leucine biosynthesis genes.
JO  - Mol. Gen. Genet.
PY  - 1994
SP  - 24
EP  - 31
VL  - 243
AB  - The genes encoding the Neisseria lactamica restriction endonuclease IV (R.NlaIV) and its
AB  - cognate DNA methyltransferase (M.NlaIV), both of which recognize the sequence GGNNCC, have
AB  - been cloned in Escherichia coli and overexpressed using the T7 polymerase/promoter system.
AB  - Analysis of a sequenced 3.58kb fragment established the gene order, leuD-M.NlaIV-R.NlaIV-leuB.
AB  - The predicted primary sequence of M.NlaIV (423 amino acids) shows the highest degree of
AB  - identity to a pair of cytosine-specific methyltransferases, M.BanI (44.9%) and M.HgiCI
AB  - (44.3%), which recognize the sequence GGYRCC (Y, pyrimidines; R, purines). In contrast, the
AB  - R.NlaIV protein sequence (243 amino acids) is unique in the existing database, a situation
AB  - that holds for most endonucleases. Flanking the NlaIV modification and restriction genes are
AB  - homologues of the leuD and leuB genes of enteric bacteria, which code for enzymes in the
AB  - leucine biosynthesis pathway. This gene context implies a possible new mode of gene regulation
AB  - for the RM.NlaIV system, which would involve a mechanism similar to the recently discovered
AB  - leucine/Lrp regulon in E. coli.
ER  -

TY  - JOUR
AU  - Lau, R.H.
AU  - Doolittle, W.F.
TI  - AquI: a more easily purified isoschizomer of AvaI.
JO  - FEBS Lett.
PY  - 1980
SP  - 200
EP  - 202
VL  - 121
AB  - Since its first description by Murray and coworkers the restriction
AB  - endonuclease AvaI, which recognizes and cleaves at the sequence C^PyCGPuG, has
AB  - found wide use in DNA sequence studies.  There are, however, three difficulties
AB  - associated with preparation of this enzyme from its usual source, Anabaena
AB  - variabilis (Kutzing).  This sheathed filamentous cyanobacterium does not
AB  - readily yield single colonies on agar plates and is thus not easily rid of
AB  - contaminating bacteria.  It grows slowly (generation times of the order of
AB  - 24h).  Furthermore, it contains two additional restriction endonucleases, AvaII
AB  - and AvaIII.  We frequently find commercial preparations of AvaI to be
AB  - contaminated with one of these additional enzymes, and Roizes et al. were
AB  - unable to separate AvaI and AvaIII.  We report here that Agmenellum
AB  - quadruplicatum (strain PR-6) produces an isoschizomer of AvaI (AquI).  This
AB  - unicellular cyanobacterium is readily maintained in axenic condition, grows
AB  - rapidly (4-5h generation time at 37C) and contains only this single restriction
AB  - endonuclease activity.
ER  -

TY  - JOUR
AU  - Lau, R.H.
AU  - Visentin, L.P.
AU  - Martin, S.M.
AU  - Hofman, J.D.
AU  - Doolittle, W.F.
TI  - Site-specific restriction endonuclease from the filamentous cyanobacterium Nostoc sp. MAC PCC 8009.
JO  - FEBS Lett.
PY  - 1985
SP  - 129
EP  - 132
VL  - 179
AB  - We report here the presence of a type-II restriction endonuclease in the
AB  - filamentous cyanobacterium Nostoc sp. MAC PCC 8009.  This restriction enzyme,
AB  - Nsp MACI, is the first reported isoschizomer of BglII and is very readily
AB  - purified from non-specific deoxyribonuclease activity in the crude lysate by
AB  - one round of phosphocellulose column chromatography.
ER  -

TY  - JOUR
AU  - Lau, S.C.
AU  - Riedel, T.
AU  - Fiebig, A.
AU  - Han, J.
AU  - Huntemann, M.
AU  - Petersen, J.
AU  - Ivanova, N.N.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Goker, M.
AU  - Kyrpides, N.C.
AU  - Klenk, H.P.
AU  - Qian, P.Y.
TI  - Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 51
EP  - 51
VL  - 10
AB  - Loktanella hongkongensis UST950701-009P(T) is a Gram-negative, non-motile and rod-shaped
AB  - bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When
AB  - growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce
AB  - larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The
AB  - inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the
AB  - bacterial cells. In the  present study we describe the features of L. hongkongensis strain DSM
AB  - 17492(T) together with its genome sequence and annotation and novel aspects of its phenotype.
AB  - The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The
AB  - two unambiguously identified extrachromosomal replicons contain replication modules of the
AB  - RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.
ER  -

TY  - JOUR
AU  - Lau, S.K.
AU  - Teng, J.L.
AU  - Huang, Y.
AU  - Curreem, S.O.
AU  - Tsui, S.K.
AU  - Woo, P.C.
TI  - Draft Genome Sequence of Catabacter hongkongensis Type Strain HKU16T, Isolated from a Patient with Bacteremia and Intestinal Obstruction.
JO  - Genome Announcements
PY  - 2015
SP  - e00531
EP  - e00515
VL  - 3
AB  - We report the draft genome sequence of Catabacter hongkongensis, a catalase-positive bacterium
AB  - which causes bacteremia with high mortality. The
AB  - 3.2-Mb genome contains 3,161 protein coding sequences, including putative
AB  - catalase and motility-related proteins, and antibiotic resistance genes, which
AB  - could be important for its virulence and adaptation to diverse environments.
ER  -

TY  - JOUR
AU  - Laue, F.
AU  - Ankenbauer, W.
AU  - Schmitz, G.G.
AU  - Kessler, C.
TI  - The selective inhibitory effect of netropsin on relaxation of sequence specificity of restriction endonuclease SgrAI recognizing 5'-CR^CCGGYG-3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3421
EP  - 3421
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Laue, F.
AU  - Evans, L.R.
AU  - Jarsch, M.
AU  - Brown, N.L.
AU  - Kessler, C.
TI  - A complex family of class-II restriction endonucleases, DsaI-VI, in Dactylococcopsis salina.
JO  - Gene
PY  - 1991
SP  - 87
EP  - 95
VL  - 97
AB  - A series of class-II restriction endonucleases (ENases) was discovered in the halophilic,
AB  - phototrophic, gas-vacuolated cyanobacterium Dactylococcopsis salina sp. nov. The six novel
AB  - enzymes are characterized by the following recognition sequences and cut positions: 5'
AB  - -C^CRYGG-3' (DsaI); 5' -GG^CC-3' (DsaII); 5' -R^GATCY-3' (DsaIII); 5' -G^GWCC-3'
AB  - (DsaIV); 5' -^CCNGG-3' (DsaV); and 5' -GTMKAC-3' (DsaVI), where W = A or T, M = A or C, K
AB  - = G or T, and N = A, G, C or T. In addition, traces of further possible activity were
AB  - detected. DsaI has a novel sequence specificity and DsaV is an isoschizomer of ScrFI, but with
AB  - a novel cut specificity. A purification procedure was established to separate all six ENases,
AB  - resulting in their isolation free of contaminating nuclease activities. DsaI cleavage is
AB  - influenced by N6-methyladenine residues [derived from the Escherichia coli-encoded DNA
AB  - methyltransferase (MTase) M.Eco damI] within the overlapping sequence 5'-CCRYM/GGATC-3';
AB  - DsaV hydrolysis is inhibited by a C-5 methylcytosine residue in its recognition sequence
AB  - (5'-CM/CNGG-3'), generated in some DsaV sites by the E. coli-encoded MTase, M.Eco dcmI.
ER  -

TY  - JOUR
AU  - Lauer, A.C.
AU  - Humrighouse, B.W.
AU  - Loparev, V.
AU  - Shewmaker, P.L.
AU  - Whitney, A.M.
AU  - McQuiston, J.R.
AU  - McLaughlin, R.W.
TI  - Complete Genome Sequences of Enterococcus rotai LMG 26678T and Enterococcus silesiacus LMG 23085T.
JO  - Genome Announcements
PY  - 2016
SP  - e01387
EP  - e01316
VL  - 4
AB  - The inclusion of molecular methods in the characterization of the novel species Enterococcus
AB  - horridus necessitated the sequencing and assembly of the genomes of
AB  - the closely related Enterococcus rotai and Enterococcus silesiacus Sequencing
AB  - using Illumina technology in combination with optical mapping led to the
AB  - generation of closed genomes for both isolates.
ER  -

TY  - JOUR
AU  - Lauer, A.C.
AU  - Nicholson, A.C.
AU  - Humrighouse, B.W.
AU  - Emery, B.
AU  - Drobish, A.
AU  - Juieng, P.
AU  - Loparev, V.
AU  - McQuiston, J.R.
TI  - Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family.
JO  - Genome Announcements
PY  - 2015
SP  - e01474
EP  - e01415
VL  - 3
AB  - Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but
AB  - unidentified, isolates located in a historical collection at the
AB  - Centers for Disease Control and Prevention suggested that these isolates belong
AB  - to a novel genera of bacteria. The genomes of the bacteria, to be named
AB  - Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina
AB  - technology. Closed genomes were produced for all eight isolates.
ER  -

TY  - JOUR
AU  - Laugraud, A.
AU  - Young, S.
AU  - Gerard, E.
AU  - O'Callaghan, M.
AU  - Wakelin, S.
TI  - Draft Genome Sequence of the Clover (Trifolium repens L.) Root Endophyte Paraburkholderia sp. Strain A27.
JO  - Genome Announcements
PY  - 2017
SP  - e00466
EP  - e00417
VL  - 5
AB  - Paraburkholderia sp. strain A27, isolated from the root material of white clover, has plant
AB  - growth-promoting activity on a range of agriculturally important
AB  - plants. The draft genome of this bacterium is 7,393,089 bp and harbors a range of
AB  - genes putatively involved in host colonization.
ER  -

TY  - JOUR
AU  - Laugraud, A.
AU  - Young, S.
AU  - Gerard, E.
AU  - O'Callaghan, M.
AU  - Wakelin, S.
TI  - Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.
JO  - Genome Announcements
PY  - 2017
SP  - e00163
EP  - e00117
VL  - 5
AB  - Pseudomonas sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue
AB  - of Brassica oleracea L. grown in soil from Marlborough, New Zealand.
AB  - Its draft genome of 6,350,161 bp contains genes associated with plant growth
AB  - promotion and biological control.
ER  -

TY  - JOUR
AU  - Laurens, N.
AU  - Bellamy, S.R.
AU  - Harms, A.F.
AU  - Kovacheva, Y.S.
AU  - Halford, S.E.
AU  - Wuite, G.J.
TI  - Dissecting protein-induced DNA looping dynamics in real time.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5454
EP  - 5464
VL  - 37
AB  - Many proteins that interact with DNA perform or enhance their specific functions by binding
AB  - simultaneously to multiple target sites, thereby
AB  - inducing a loop in the DNA. The dynamics and energies involved in this
AB  - loop formation influence the reaction mechanism. Tethered particle motion
AB  - has proven a powerful technique to study in real time protein-induced DNA
AB  - looping dynamics while minimally perturbing the DNA-protein interactions.
AB  - In addition, it permits many single-molecule experiments to be performed
AB  - in parallel. Using as a model system the tetrameric Type II restriction
AB  - enzyme SfiI, that binds two copies of its recognition site, we show here
AB  - that we can determine the DNA-protein association and dissociation steps
AB  - as well as the actual process of protein-induced loop capture and release
AB  - on a single DNA molecule. The result of these experiments is a
AB  - quantitative reaction scheme for DNA looping by SfiI that is rigorously
AB  - compared to detailed biochemical studies of SfiI looping dynamics. We also
AB  - present novel methods for data analysis and compare and discuss these with
AB  - existing methods. The general applicability of the introduced techniques
AB  - will further enhance tethered particle motion as a tool to follow
AB  - DNA-protein dynamics in real time.
ER  -

TY  - JOUR
AU  - Laurens, N.
AU  - Rusling, D.A.
AU  - Pernstich, C.
AU  - Brouwer, I.
AU  - Halford, S.E.
AU  - Wuite, G.J.
TI  - DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 4988
EP  - 4997
VL  - 40
AB  - Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene
AB  - regulation and DNA replication. Here, we use
AB  - tethered-particle motion to examine the impact of DNA bending and twisting
AB  - rigidity on loop capture and release, using the restriction endonuclease FokI as
AB  - a test system. To cleave DNA efficiently, FokI bridges two copies of an
AB  - asymmetric sequence, invariably aligning the sites in parallel. On account of the
AB  - fixed alignment, the topology of the DNA loop is set by the orientation of the
AB  - sites along the DNA. We show that both the separation of the FokI sites and their
AB  - orientation, altering, respectively, the twisting and the bending of the DNA
AB  - needed to juxtapose the sites, have profound effects on the dynamics of the
AB  - looping interaction. Surprisingly, the presence of a nick within the loop does
AB  - not affect the observed rigidity of the DNA. In contrast, the introduction of a
AB  - 4-nt gap fully relaxes all of the torque present in the system but does not
AB  - necessarily enhance loop stability. FokI therefore employs torque to stabilise
AB  - its DNA-looping interaction by acting as a 'torsional' catch bond.
ER  -

TY  - JOUR
AU  - Laurent, J.P.
AU  - Faske, S.
AU  - Cangelosi, G.A.
TI  - Characterization of IS999, an unstable genetic element in Mycobacterium avium.
JO  - Gene
PY  - 2002
SP  - 249
EP  - 257
VL  - 294
AB  - An IS3-family insertion element, IS999, was identified in the opportunistic pathogen
AB  - Mycobacterium avium. The 1347 bp element has 29 bp
AB  - inverted repeats and two overlapping open reading frames coding for
AB  - putative transposases. It was detected in the genomes of ten of 12 M.
AB  - avium isolates examined. Copy numbers ranged from four to 16. IS999 is
AB  - less stable than IS1245, the most commonly-used marker for typing M. avium
AB  - isolates. Among 60 colonies picked from a single patient isolate, there
AB  - were two distinct IS1245 restriction fragment length polymorphism banding
AB  - patterns compared to eight distinct IS999 patterns (five in one IS1245
AB  - group and three in the other). In view of its instability, we asked
AB  - whether transposition of IS999 might have phenotypic consequences.
AB  - Nucleotide sequence analysis of insertion sites in four isolates revealed
AB  - 16 putative structural genes that were variably disrupted by IS999.
AB  - Insertions into hdhA, a gene that codes for a putative short chain alcohol
AB  - dehydrogenase, were distributed non-randomly between colony type variants,
AB  - consistent with phenotypic consequences that exert selective pressure.
AB  - These observations illustrate the genetic heterogeneity that can exist
AB  - within populations of M. avium that appear to be homogeneous by IS1245
AB  - analysis. IS999 may be a useful marker for tracking, at the sub-strain
AB  - level, the rapid genetic drift that M. avium isolates undergo in nature
AB  - and in the laboratory.
ER  -

TY  - JOUR
AU  - Laurino, P.
AU  - Tawfik, D.
TI  - Engineering DNA methyltransferases for a novel cofactor.
JO  - FEBS J.
PY  - 2013
SP  - 173
EP  - 174
VL  - 280
AB  - Cofactors are metals, or organic compounds, which play fundamental roles in enzymes.  Cofactor
AB  - engineering has only been partially pursued and rarely have natural cofactors been substituted
AB  - with synthetic organic molecules.  Herein, we have designed a synthetic compound presenting in
AB  - its structure few key modifications that, in turn, an engineered enzyme can exploit to achieve
AB  - cofactor specificity, tight binding and orthogonal recognition of it instead of the natural
AB  - cofactor.  The cofactor was designed considering aspects like cell permeability, which allows
AB  - extracellular administration of the cofactor, and the possibility to track the enzyme's
AB  - product.  The key candidate of our investigation is DNA methyltransferases, that use
AB  - S-adenosyl methionine as methyl donor to methylate specific DNA target sequences.  Although
AB  - these enzymes are key epigenetic mediators, their genomic targets are often unknown and their
AB  - cellular remain poorly understood.  To remodel the catalytic site for the new cofactor, a
AB  - protein engineering study ahs been carried out, using computational design as well as directed
AB  - evolution.  We believe that the evolved mammalian DNA methylases which will have acquired
AB  - orthogonality for the synthetic cofactor, as well as the ability to modify DNA with tractable
AB  - groups, will provide new insights regarding the role of this enzyme in epigentics, including
AB  - in dictating the genomic methylation patterns in cancer.
ER  -

TY  - JOUR
AU  - Lauro, F.M.
AU  - Chastain, R.A.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Yayanos, A.A.
AU  - Bartlett, D.H.
TI  - Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99.
JO  - Genome Announcements
PY  - 2013
SP  - e00210
EP  - e00213
VL  - 1
AB  - We report the draft genome sequence of the obligately piezophilic Shewanella benthica strain
AB  - KT99 isolated from the abyssal South Pacific Ocean. Strain KT99
AB  - is the first piezophilic isolate from the Tonga-Kermadec trench, and its genome
AB  - provides many clues on high-pressure adaptation and the evolution of deep-sea
AB  - piezophilic bacteria.
ER  -

TY  - JOUR
AU  - Lauro, F.M.
AU  - Stratton, T.K.
AU  - Chastain, R.A.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Goldberg, S.M.
AU  - Yayanos, A.A.
AU  - Bartlett, D.H.
TI  - Complete Genome Sequence of the Deep-Sea Bacterium Psychromonas Strain CNPT3.
JO  - Genome Announcements
PY  - 2013
SP  - e00304
EP  - e00313
VL  - 1
AB  - Members of the genus Psychromonas are commonly found in polar and deep-sea environments. Here
AB  - we present the genome of Psychromonas strain CNPT3.
AB  - Historically, it was the first bacterium shown to piezoregulate the composition
AB  - of its membrane lipids and to have a higher growth rate at 57 megapascals (MPa)
AB  - than at 0.1 MPa.
ER  -

TY  - JOUR
AU  - Lauster, R.
TI  - Duplication and variation as a phylogenetic principle of Type II DNA methyltransferases.
JO  - Gene
PY  - 1988
SP  - 243
EP  - 243
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Lauster, R.
TI  - Evolution of type II DNA methyltransferases:  A gene duplication model.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 313
EP  - 321
VL  - 206
AB  - On the basis of consensus sequences, which had previously been defined for two
AB  - groups of closely related cytosine-specific and adenine-specific DNA
AB  - methyltransferases, homologies can be detected that indicate a common origin
AB  - for these proteins.  Intramolecular comparisons of several of these enzymes
AB  - reveal homology relationships, which suggests that gene duplication is a
AB  - phylogenetic principle in the evolution of the Mtases.  One or two duplications
AB  - of an ancestral gene encoding a 12,000 to 16,000 Mr protein, followed by
AB  - divergent evolution, may have led to very different protein structures and
AB  - could explain the differences in amino acid sequences, molecular weights and
AB  - biochemical properties.  Intermolecular and intramolecular homologies were also
AB  - recognized in type II restriction endonucleases, suggesting a very similar
AB  - evolutionary pathway.
ER  -

TY  - JOUR
AU  - Lauster, R.
TI  - Close relationship between the HinfI and DpnA DNA-methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 4402
EP  - 4402
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Lauster, R.
AU  - Kriebardis, A.
AU  - Guschlbauer, W.
TI  - The GATATC-modification enzyme EcoRV is closely related to the GATC-recognizing methyltransferases DpnII and dam from E. coli and phage T4.
JO  - FEBS Lett.
PY  - 1987
SP  - 167
EP  - 176
VL  - 220
AB  - The amino acid sequence of EcoRV DNA methyltransferase which methylates the amino group of the
AB  - 5'-adenine residue of the target sequence GATATC has been found to be closely related to that
AB  - of three other adenine methyltransferases, DpnII, dam and damT4, the target sequence of which
AB  - is GATC. Despite large differences on the DNA level, the four sequences show four blocks of
AB  - homologies. One of these blocks has the sequence DVYXDPPY and is found with little
AB  - modification in numerous other DNA methyltransferases. It is speculated that it could be the
AB  - binding site of the methyl donor, S-adenosylmethionine. On the other hand, the identification
AB  - of a DNA-binding region is more tenuous. As expected, no analogies with (dimeric) repressors
AB  - and cro proteins which have the characteristic helix-turn-helix motif have been observed.
ER  -

TY  - JOUR
AU  - Lauster, R.
AU  - Trautner, T.A.
AU  - Noyer-Weidner, M.
TI  - Cytosine-specific type II DNA methyltransferases:  A conserved enzyme core with variable target-recognizing domains.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 305
EP  - 312
VL  - 206
AB  - Comparisons of the amino acid sequences of m5C DNA methyltransferases (Mtases)
AB  - from 11 prokaryotes and one eukaryote reveal a very similar organization.
AB  - Among all the enzymes one can distinguish highly conserved core sequences and
AB  - variable regions.  The core sequences apparently mediate steps of the
AB  - methylation reaction that are common to all the enzymes.  The major variable
AB  - region has been shown in our previous studies on multispecific phage Mtases to
AB  - contain the target-recognizing domains (TRDs) of these enzymes.  Here we have
AB  - compared the amino acid sequences of various TRDs from phage Mtases.  This has
AB  - revealed the presence of both highly conserved and variable amino acids.  We
AB  - postulate that the conserved residues represent a consensus sequence defining a
AB  - TRD, whereas the specificity of the TRD is determined by the variable residues.
AB  - We have observed similarity between this consensus sequence and sequences in
AB  - the variable region of the monospecific Mtases.  We predict that the regions
AB  - thus identified represent part of the TRDs of monospecific Mtases.
ER  -

TY  - JOUR
AU  - Lautenberger, J.
AU  - Eskin, B.
AU  - Linn, S.
TI  - The DNA modification methylase and restriction endonuclease of Escherichia coli B.
JO  - Fed. Proc.
PY  - 1972
SP  - 474
EP  - 474
VL  - 31
AB  - The modification and restriction enzymes from E. coli B have been extensively
AB  - purified.  As judged by SDS gel electrophoresis, the methylase contains two
AB  - subunits, beta and gamma, of molecular weights 60,000 and 55,000, respectively.
AB  - The endonuclease contains beta, gamma and a third subunit, alpha, of molecular
AB  - weight 135,000.  These results are consistent with the observations of Hubacek
AB  - and Glover [J. Mol. Biol. 50, 11, 1970] showing that the hss and hsm genes are
AB  - required for both activities, and in addition, the hsr gene is required for
AB  - restriction.  The methylase is isolated in an active 6S form, beta 1 gamma 1,
AB  - but it is able to disproportionate into an active 11S form, beta 3 gamma 1.
AB  - The endonuclease activity sediments in a broad peak around 15S and contains
AB  - alpha, beta, and gamma in the approximate ratio 2.5:2.5:1.  This material is a
AB  - mixture of active enzyme species, each containing the three subunits, but in
AB  - different proportions.  The methylase forms 6-methylaminopurine using
AB  - S-adenosylmethionine (SAM) as the methyl donor.  It acts optimally at pH 5.8,
AB  - and is stimulated 3- to 5-fold by Mg++, Mn++, or Ca++, and 30% by ATP.  The
AB  - endonuclease requires Mg++, SAM, and ATP, and unlike the methylase, it degrades
AB  - massive amounts of ATP to ADP and Pi during its action on DNA.  Both enzymes
AB  - are inhibited by S-adenosylethionine or 5'-methylthioadenosine, but not by
AB  - S-adenosylhomocysteine.
ER  -

TY  - JOUR
AU  - Lautenberger, J.A.
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
TI  - The nucleotide sequence recognized by the BstEII restriction endonuclease.
JO  - Gene
PY  - 1980
SP  - 171
EP  - 174
VL  - 12
AB  - The restriction site for the BstEII endonuclease is characterized by the
AB  - heptamer sequence: 5'-G-^G-T-N-A-C-C-3' 3'-C-C-A-N-T-G-^G-5' with five
AB  - nucleotide long cohesive termini.
ER  -

TY  - JOUR
AU  - Lautenberger, J.A.
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
TI  - The DNA sequence on bacteriophage G4 recognized by the Escherichia coli B restriction enzyme.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 871
EP  - 875
VL  - 131
AB  - Bacteriophage G4 possesses a single EcoB site located in the overlap between restriction
AB  - fragments HinfI-12 and HaeIII-6.  The sequence 5'-T-G-A...8N...T-G-C-T occurs once in this
AB  - segment and nowhere else in the DNA sequence of G4.  Four independent G4 mutants that were not
AB  - restricted by Escherichia coli B possessed the sequence 5'-T-G-A...8N...T-G-C-C.  The common
AB  - sequence shared by the previously mapped EcoB sites on PhiXsB1, simian virus 40, f1, and fd
AB  - DNAs is 5'-T-G-A...8N...T-G-C-T...9N...T.  However, the sequence in the region of the G4 EcoB
AB  - site contains an A instead of the final T conserved in these other examples.  When the G4 EcoB
AB  - site is aligned with the other EcoB sites, there are no conserved residues within 50 bases of
AB  - the common sequence, 5'-T-G-A...8N....T-G-C-T, except for those seven residues.  The analysis
AB  - of the EcoB site on G4 provides further evidence that only those seven bases are recognized by
AB  - the E. coli B restriction enzyme.
ER  -

TY  - JOUR
AU  - Lautenberger, J.A.
AU  - Kan, N.C.
AU  - Lackey, D.
AU  - Linn, S.
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
TI  - Recognition site of Escherichia coli B restriction enzyme on PhiXsB1 and simian virus 40 DNAs: An interrupted sequence.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1978
SP  - 2271
EP  - 2275
VL  - 75
AB  - Methyl groups placed on PhiXsB1 replicative form DNA by the Escherichia coli B
AB  - modification enzyme are located in the overlap between fragments MboII-3 and
AB  - AluI-2, a 61-base-pair DNA segment.  Mutations that led to loss of
AB  - susceptibility to restriction by E. coli B occurred within this segment at
AB  - three positions spanning 14 nucleotides.  A sequence difference between PhiXsB1
AB  - and PhiXam3cs70, a PhiX174 strain not restricted by E. coli B, occurs at one of
AB  - these positions.  The site on simian virus 40 DNA methylated by the
AB  - modification enzyme is located in the 115-base-pair overlap between fragments
AB  - HaeIII-I and AluI-G.  The sequences of these segments of PhiXsB1 and simian
AB  - virus 40 DNA and two regions of phage f1 DNA recognized by the E. coli B
AB  - restriction enzyme [Ravetch, J.V., Horiuchi, K. & Zinder, N.D. (1978) Proc.
AB  - Natl. Acad. Sci. USA 75, 2266-2270] contain a homology of nine bases in the
AB  - configuration:  5'-T-G-A...8N...T-G-C-G...9N...T-N-N-T-3'. The sequence
AB  - 5'-T-G-A...8N...T-G-C-T-3' may constitute the restriction enzyme recognition
AB  - site since it does not occur in PhiXam3cs70 DNA and occurs only once in simian
AB  - virus 40 DNA, and since all observed mutations leading to loss of the site
AB  - occur at one of the bases specified by this sequence.  Analysis of the sequence
AB  - of PhiXam3cs70 showed that if no other residues are recognizd, all seven of
AB  - these bases are essential for recognition and the interval between the two
AB  - groups of specified bases must be precisely eight.
ER  -

TY  - JOUR
AU  - Lautenberger, J.A.
AU  - Linn, S.
TI  - The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. I. Purification, subunit structure, and catalytic properties of the modification methylase.
JO  - J. Biol. Chem.
PY  - 1972
SP  - 6176
EP  - 6182
VL  - 247
AB  - The modification methylase of Escherichia coli B has been purified to apparent
AB  - homogeneity.  The enzyme can exist in several forms, each possessing two
AB  - nonidentical polypeptides, b and c, of molecular weights of 60,000 and 55,000,
AB  - respectively.  Freshly isolated enzyme has the structure b1c1, but upon storage
AB  - at neutral pH and low salt, it disproportionates, producing another form, b3c1.
AB  - Treatment at pH 5 converts the mixture of b3c1 and b1c1 to a mixture of b1c1
AB  - and another form b2c1, whereas exposure to high salt breaks down the b3c1
AB  - structure.  The enzyme is inhibited by S-adenosylethionine and
AB  - 5'-methylthioadenosine, but not by S-adenosylhomocysteine.  None of these
AB  - compounds can replace the required cofactor, S-adenosylmethionine.  The enzyme
AB  - can methylate a wide variety of DNAs, but not DNA produced by E. coli B.
ER  -

TY  - JOUR
AU  - Lautenberger, J.A.
AU  - White, C.T.
AU  - Haigwood, N.L.
AU  - Edgell, M.H.
AU  - Hutchison, C.A.
TI  - The recognition site of Type II restriction enzyme BglI is interrupted.
JO  - Gene
PY  - 1980
SP  - 213
EP  - 231
VL  - 9
AB  - The Type II restriction endonuclease BglI recognizes the interrupted DNA
AB  - sequence 5'-G-C-C-N-N-N-N-N-G-G-C-.  This sequence occurs at all locations in
AB  - over 33,000 base pairs of DNA sequence where the enzyme was found to cut DNA
AB  - and nowhere else.  All six of the specified bases are essential parts of the
AB  - site since all groups of five of the six bases occur in the DNA sequences
AB  - tested and none of them are cut by BglI.  The length of the block of
AB  - intervening unspecified positions must be exactly five since all other sizes
AB  - between zero and 15 occur in the DNA sequences searched and none are cut by
AB  - BglI.  The 5'-terminal nucleotides of BglI cleaved phage G4 replicative form
AB  - DNA and plasmid pER18 DNA were compared with the DNA sequences near the BglI
AB  - sites on these DNAs.  These results indicated that BglI cuts within the
AB  - intervening unspecified region and produces single-stranded 3' termini that are
AB  - three bases long.  The BglI recognition site and cleavage points can thus be
AB  - represented as follows: 5'-G-C-C-N-N-N-N-^-N-G-G-C-3'   This study of the BglI
AB  - recognition site was facilitated by the use of inexpensive microcomputers.  A
AB  - system of programs was developed that allowed analysis of over 33 kb of DNA
AB  - sequences stored on flexible magnetic disks or audio cassettes.  While these
AB  - programs were generally written in the higher level language BASIC, some
AB  - assembly language subroutines were utilized to reduce executive time.
ER  -

TY  - JOUR
AU  - Laverde-Gomez, J.A.
AU  - van Schaik, W.
AU  - Freitas, A.R.
AU  - Coque, T.M.
AU  - Weaver, K.E.
AU  - Francia, M.V.
AU  - Witte, W.
AU  - Werner, G.
TI  - A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates.
JO  - Int. J. Med. Microbiol.
PY  - 2011
SP  - 165
EP  - 175
VL  - 301
AB  - Enterococcus faecium is considered to be a nosocomial pathogen with
AB  - increasing medical importance. The putative virulence factor, hyl(Efm),
AB  - encoding a putative hyaluronidase, is enriched among the
AB  - hospital-associated polyclonal subpopulation of E. faecium.. The hyl(Efm)
AB  - gene is described to be part of a genomic island and was recently
AB  - identified to be plasmid-located. Here, we present a description of the
AB  - structure, localization, and distribution of the putative pathogenicity
AB  - factor hyl(Efm) and its putative island among 39 clinical isolates and
AB  - elucidate the composition and host range of pLG1, a hyl(Efm)
AB  - multiresistance plasmid of approximately 281.02kb. The hyl(Efm) gene was
AB  - located within a 17,824-bp element highly similar to the putative genomic
AB  - island (GI) structure that had been previously described. This genomic
AB  - region was conserved among 39 hyl(Efm)-positive strains with variation in
AB  - a specific region downstream of hyl(Efm) in 18 strains. The putative
AB  - hyl(Efm) was located on large plasmids (150-350kb) in 37 strains. pLG1
AB  - could be horizontally transferred into four different E. faecium recipient
AB  - strains (n=4) but not into E. faecalis (n=3). Sequencing of pLG1 resolved
AB  - putative plasmid replication, conjugation, and maintenance determinants as
AB  - well as a pilin gene cluster, carbon uptake and utilization genes, heavy
AB  - metal and antibiotic resistance clusters. The hyl(Efm) transferable
AB  - plasmid pLG1 bears additional putative pathogenicity factors and
AB  - antibiotic resistance genes. These findings suggest horizontal gene
AB  - transfer of virulence factors and antibiotic resistance gene clusters by a
AB  - single genetic event (conjugative transfer) which might be triggered by
AB  - heavy antibiotic use common in health care units where E. faecium is
AB  - increasingly prevalent.
ER  -

TY  - JOUR
AU  - Lavezzo, E.
AU  - Toppo, S.
AU  - Barzon, L.
AU  - Cobelli, C.
AU  - Di Camillo, B.
AU  - Finotello, F.
AU  - Franchin, E.
AU  - Peruzzo, D.
AU  - Toffolo, G.M.
AU  - Trevisan, M.
AU  - Palu, G.
TI  - Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5270
EP  - 5271
VL  - 192
AB  - Neisseria meningitidis is a human-specific pathogen known for its capability to cause sepsis
AB  - and meningitis. Here we report the availability
AB  - of 2 draft genome sequences obtained from patients infected during the
AB  - same epidemic outbreak. Both bacterial isolates belong to serogroup C, but
AB  - their genome sequences show local and remarkable differences compared with
AB  - each other or with the reference genome of strain FAM18.
ER  -

TY  - JOUR
AU  - Laviad, S.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Reddy, T.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Markowitz, V.M.
AU  - Pukall, R.
AU  - Klenk, H.P.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Halpern, M.
TI  - High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM  19883(T)) isolated from a Chironomus sp. egg mass.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 21
EP  - 21
VL  - 10
AB  - Leucobacter chironomi strain MM2LB(T) (Halpern et al., Int J Syst Evol Microbiol  59:665-70
AB  - 2009) is a Gram-positive, rod shaped, non-motile, aerobic,
AB  - chemoorganotroph bacterium. L. chironomi belongs to the family Microbacteriaceae,
AB  - a family within the class Actinobacteria. Strain MM2LB(T) was isolated from a
AB  - chironomid (Diptera; Chironomidae) egg mass that was sampled from a waste
AB  - stabilization pond in northern Israel. In a phylogenetic tree based on 16S rRNA
AB  - gene sequences, strain MM2LB(T) formed a distinct branch within the radiation
AB  - encompassing the genus Leucobacter. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The DNA GC
AB  - content is 69.90%. The chromosome length is 2,964,712 bp. It encodes 2,690
AB  - proteins and 61 RNA genes. L. chironomi genome is part of the Genomic
AB  - Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG)
AB  - project.
ER  -

TY  - JOUR
AU  - Laviad, S.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Haynes, M.
AU  - Reddy, T.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Mavromatis, K.
AU  - Lang, E.
AU  - Rohde, M.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Halpern, M.
TI  - High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 29
EP  - 29
VL  - 10
AB  - Brachymonas chironomi strain AIMA4(T) (Halpern et al., 2009) is a Gram-negative,  non-motile,
AB  - aerobic, chemoorganotroph bacterium. B. chironomi is a member of the
AB  - Comamonadaceae, a family within the class Betaproteobacteria. This species was
AB  - isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste
AB  - stabilization pond in northern Israel. Phylogenetic analysis based on the 16S
AB  - rRNA gene sequences placed strain AIMA4(T) in the genus Brachymonas. Here we
AB  - describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The DNA GC content is 63.5%. The chromosome length is
AB  - 2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi
AB  - genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one
AB  - thousand microbial genomes (KMG) project.
ER  -

TY  - JOUR
AU  - Laviad-Shitrit, S. et al.
TI  - High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 31
EP  - 31
VL  - 12
AB  - Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol
AB  - 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile,
AB  - facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the
AB  - Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when
AB  - psychrotolerant bacterial communities in raw milk and their proteolytic and
AB  - lipolytic traits were studied. Here we describe the features of this organism,
AB  - together with the draft genome sequence and annotation. The DNA G + C content is
AB  - 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105
AB  - RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type
AB  - Strains, Phase I: the one thousand microbial genomes study.
ER  -

TY  - JOUR
AU  - Law, J.A.
AU  - Jacobsen, S.E.
TI  - Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
JO  - Nat. Rev. Genet.
PY  - 2010
SP  - 204
EP  - 220
VL  - 11
AB  - Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse  biological
AB  - processes, including gene and transposon silencing, imprinting and X chromosome inactivation.
AB  - Recent findings in plants and animals have greatly increased our understanding of the pathways
AB  - used to accurately target, maintain and modify patterns of DNA methylation and have revealed
AB  - unanticipated mechanistic similarities between these organisms. Key roles have emerged for
AB  - small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these
AB  - processes. Drawing on insights from both plants and animals should deepen our understanding of
AB  - the regulation and biological significance of DNA methylation.
ER  -

TY  - JOUR
AU  - Lawrence, P.K.
AU  - Bey, R.F.
AU  - Wiener, B.
AU  - Kittichotirat, W.
AU  - Bumgarner, R.E.
TI  - Genome Sequence of a Presumptive Mannheimia haemolytica Strain with an A1/A6-Cross-Reactive Serotype from a White-Tailed Deer (Odocoileus virginianus).
JO  - Genome Announcements
PY  - 2014
SP  - e00114
EP  - e00114
VL  - 2
AB  - Mannheimia haemolytica is a Gram-negative bacterium and the principal etiological agent
AB  - associated mostly with bovine respiratory disease complex. However, we
AB  - report here the sequence of a strain with the novel A1/A6-cross-reactive
AB  - serotype, strain PKL10, isolated from white-tailed deer. PKL10 was isolated from
AB  - the spleen of farmed white-tailed deer showing clinical signs of pneumonia. The
AB  - genome structure of PKL10 is dramatically different from that of previously
AB  - sequenced isolates, which was demonstrated by genome alignments. In addition, the
AB  - coding sequences in PKL10 share approximately 86% sequence identity with the
AB  - coding sequences in other fully sequenced M. haemolytica strains. This suggests
AB  - that PKL10 is a novel Mannheimia species.
ER  -

TY  - JOUR
AU  - Lawrence, P.K.
AU  - Kittichotirat, W.
AU  - Bumgarner, R.E.
AU  - McDermott, J.E.
AU  - Herndon, D.R.
AU  - Knowles, D.P.
AU  - Srikumaran, S.
TI  - Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1167
EP  - 1168
VL  - 192
AB  - This report describes the genome sequences of Mannheimia haemolytica serotype A2
AB  - isolated from pneumonic lungs of two different ruminant species, one from Ovis
AB  - aries, designated ovine (O), and the other from Bos taurus, designated bovine
AB  - (B).
ER  -

TY  - JOUR
AU  - Lawrence, P.K.
AU  - Wiener, B.L.
AU  - Kolander-Bremer, T.
AU  - Bey, R.F.
AU  - Stine, D.L.
AU  - Kittichotirat, W.
AU  - Bumgarner, R.E.
TI  - Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00884
EP  - e00814
VL  - 2
AB  - Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs.
AB  - However, in conjunction with stress and/or viral infections, or in
AB  - immunocompromised animals, H. parasuis can transform into a pathogen causing
AB  - Glasser's disease, which is typically characterized by fibrinous polyserositis,
AB  - polyarthritis, meningitis, and sometimes acute pneumonia and septicemia. H.
AB  - parasuis serotype 5 is highly virulent and more frequently isolated from
AB  - respiratory and systemic infection in pigs. Recently Newport Laboratories
AB  - isolated highly virulent H. parasuis serotype 4 strains from the tissues of
AB  - diseased pigs. This study was undertaken to identify the genes responsible for H.
AB  - parasuis serotype 4 virulence. To achieve this objective we performed genome-wide
AB  - association studies (GWAS) across two virulent and three avirulent H. parasuis
AB  - serotype 4 strains.
ER  -

TY  - JOUR
AU  - Lawrenz, M.B.
AU  - Kawabata, H.
AU  - Norris, S.J.
TI  - Plasmid content determines the ability to transform Borrelia burgdorferi.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 179
EP  - 179
VL  - 102
AB  - The progress of research on Borrelia burgdorferi, the causative agent of Lyme disease, has
AB  - been hampered by the lack of genetic techniques that can
AB  - be used in the laboratory. Recent advancements in this field have included
AB  - the development of a reliable selection marker and the creation of both
AB  - stable shuttle vectors and a suicide vector to truncate linear plasmids.
AB  - To date, many researchers have published successful genetic manipulation
AB  - of high passage isolates of B. burgdorferi, but only very limited success
AB  - has been reported with low passage clones. Along with increased
AB  - transformation efficiency, high passage clones have also lost the ability
AB  - to infect the mammalian host, due to loss of plasmids during in vitro
AB  - passage. In this study, we have utilized the pBSV2 shuttle vector to
AB  - transform a library of low passage clones of B. burgdorferi B31 to
AB  - determine if the increased transformation efficiency seen in high passage
AB  - clones can be attributed to loss of one of the plasmids. Three
AB  - transformation phenotypes were identified that correlate with the presence
AB  - or absence of lp25 and/or lp56. Clones that lacked both plasmids yielded
AB  - greater than 1000 transformants per mug of DNA, whereas isolates that
AB  - possessed both plasmids yielded 0 to 5 transformants per mug of DNA. B.
AB  - burgdorferi that lacked either lp25 or lp56 had an intermediate
AB  - transformation efficiency. To date, all transformants isolated from
AB  - lp25-positive clones electroporated with pBSV2 lack lp25, consistent with
AB  - selective transformation of individual cells in which lp25 was missing.
AB  - This information indicates that lp25 and lp56 represent important barriers
AB  - against successful B. burgdorferi transformation, which may be related to
AB  - plasmid-encoded restriction modification systems.
ER  -

TY  - JOUR
AU  - Lawrenz, M.B.
AU  - Kawabata, H.
AU  - Purser, J.E.
AU  - Norris, S.J.
TI  - Decreased electroporation efficiency in Borrelia burgdorferi containing linear plasmids lp25 and lp56: impact on transformation of infectious  B. burgdorferi.
JO  - Infect. Immun.
PY  - 2002
SP  - 4798
EP  - 4804
VL  - 70
AB  - The presence of the linear plasmids lp25 and lp56 of Borrelia burgdorferi B31 was found to
AB  - dramatically decrease the rate of transformation by electroporation with the shuttle vector
AB  - pBSV2, an autonomously replicating plasmid that confers kanamycin resistance (P. E. Stewart,
AB  - R. Thalken, J. L. Bono, and P. Rosa, Mol. Microbiol. 39:714-721, 2001). B. burgdorferi B31
AB  - clones had transformation efficiencies that were either low, intermediate, or high, and this
AB  - phenotype correlated with the presence or absence of lp25 and lp56. Under the conditions
AB  - utilized in this study, no transformants were detected in clones that contained both lp25 and
AB  - lp56; the few kanamycin-resistant colonies isolated did not contain pBSV2, indicating that the
AB  - resistance was due to mutation. Intermediate electroporation rates (10 to 200 colonies per
AB  - micro g of DNA) were obtained with B31 clones that were either lp25(-) and lp56(+) or lp25(+)
AB  - and lp56(-). Clones in this group that initially contained lp25 lacked this plasmid in pBSV2
AB  - transformants, a finding consistent with selective transformation of lp25(-) variants. High
AB  - transformation rates (>1,000 colonies per micro g of DNA) occurred in clones that lacked both
AB  - lp25 and lp56. Sequence analysis indicated that lp25 and lp56 contain genes that may encode
AB  - restriction and/or modification systems that could result in the low transformation rates
AB  - obtained with strains containing these plasmids. The previously reported correlation between
AB  - lp25 and infectivity in mice, coupled with the barrier lp25 presents to transformation, may
AB  - explain the difficulty in obtaining virulent transformants of B. burgdorferi.
ER  -

TY  - JOUR
AU  - Lazarev, V.N. et al.
TI  - Complete Genome and Proteome of Acholeplasma laidlawii.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4943
EP  - 4953
VL  - 193
AB  - We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii
AB  - PG-8A: class Mollicutes, order Acholeplasmatales,
AB  - family Acholeplasmataceae. The genome of A. laidlawii is represented by a
AB  - single 1 496 992 b.p. circular chromosome with the average G+C content of
AB  - 31 mol%. This is the longest genome among the Mollicutes with a known
AB  - nucleotide sequence. It contains genes of polymerase type I, SOS-response,
AB  - and signal transduction systems, as well as RNA regulatory elements,
AB  - riboswitches and T-boxes. This demonstrates a significant capability for
AB  - the regulation of gene expression and mutagenic response to stress.
AB  - Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to
AB  - use the universal genetic code, in which UGA is a stop codon. Within the
AB  - Mollicutes group, only the sterol-nonrequiring Acholeplasma has the
AB  - capacity to synthesize saturated fatty acids de novo. Proteomic data was
AB  - used in the primary annotation of the genome, validating expression of
AB  - many predicted proteins. We also detected post-translational modifications
AB  - of A.laidlawii proteins: phosphorylation and acylation. Seventy four
AB  - candidate phosphorylated proteins were found: sixteen candidates are
AB  - proteins unique to A. laidlawii, and eleven of them are surface-anchored
AB  - or integral membrane proteins, which implies the presence of active
AB  - signaling pathways. Among twenty acylated proteins, fourteen contained
AB  - palmitic chains, and six, stearic chains. No residue of linoleic or oleic
AB  - acid was observed. Acylated proteins were mainly components of sugar and
AB  - inorganic ion transport systems, and were surface-anchored proteins with
AB  - unknown functions.
ER  -

TY  - JOUR
AU  - Lazarevic, V.
AU  - Dusterhoft, A.
AU  - Soldo, B.
AU  - Hilbert, H.
AU  - Mauel, C.
AU  - Karamata, D.
TI  - Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPbetaetac2.
JO  - Microbiology
PY  - 1999
SP  - 1055
EP  - 1067
VL  - 145
AB  - The Bacillus subtilis 168 chromosomal region extending from 184 degrees to 195 degrees,
AB  - corresponding to prophage SPbeta, has been completely sequenced using DNA of the
AB  - thermoinducible SPbetac2 mutant.  This 134416 bp segment comprises 187 putative ORFs which,
AB  - according to their orientation, were grouped into three clusters.  Compared to its host,
AB  - SPbetac2 is characterized by a lower G&C content, shorter mean ORF length, as well as a
AB  - different usage of start codons.  Nearly 75% of predicted ORFs do not share significant
AB  - homologies to sequences in available databases.  The only highly similar proteins to
AB  - SPbetac2-encoded ones are host paralogues.  SPbetac2 promoter regions contain SOS box
AB  - consensus sequences and a repeated motif, designated SPbeta repeated element, that is absent
AB  - from the host genome.  Gene sspC, encoding the small acid-soluble protein C, that has been
AB  - previously sequenced and mapped to the vicinity of the SPbeta region, was found to be part of
AB  - the prophage.
ER  -

TY  - JOUR
AU  - Lazarevic, V.
AU  - Soldo, B.
AU  - Dusterhoft, A.
AU  - Hilbert, H.
AU  - Mauel, C.
AU  - Karamata, D.
TI  - Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 1692
EP  - 1697
VL  - 95
AB  - The two putative ribonucleotide reductase subunits of the Bacillus subtilis bacteriophage
AB  - SPbeta are encoded by the bnrdE and bnrdF genes that are highly similar to corresponding host
AB  - paralogs, located on the opposite replication arm.  In contrast to their bacterial
AB  - counterparts, bnrdE and bnrdF each are interrupted by a group I intron, efficiently removed in
AB  - vivo by mRNA processing.  The bnrdF intron contains an ORF encoding a polypeptide similar to
AB  - homing endonucleases responsible for intron mobility, whereas the bnrdE intron has no obvious
AB  - trace of coding sequence.  The downstream bnrdE exon harbors an intervening sequence not
AB  - excised at the level of the primary transcript, which encodes an in-frame polypeptide
AB  - displaying all the features of an intein.  Presently, this is the only intein identified in
AB  - bacteriophages.  In addition, bnrdE provides an example of a group I intron and an intein
AB  - coding sequence within the same gene.
ER  -

TY  - JOUR
AU  - Lazareviciute, L.
AU  - Maneliene, Z.
AU  - Padegimiene, A.
AU  - Kiuduliene, L.
AU  - Laucys, V.
AU  - Bitinaite, J.
AU  - Gruber, I.M.
AU  - Polyachenko, V.M.
AU  - Butkus, V.
AU  - Janulaitus, A.
TI  - Isolation and characteristics of new restriction endonucleases from Haemophilus influenzae.
JO  - Bioorg. Khim.
PY  - 1990
SP  - 889
EP  - 897
VL  - 16
AB  - Various strains of Haemophilus influenzae have been examined for the presence
AB  - of site-specific endonuclease activities, and eleven restriction endonucleases
AB  - have been isolated from seven strains.  For all the endonucleases recognition
AB  - sequences were determined, for three of them cleavage sites being identified.
AB  - The enzymes proved to be isoschizomers of known endonucleases, viz. Hin1I,
AB  - Hin8I - AcyI; Hin1II, Hin8II-NlaIII; Hin2I, Hin5I-HpaII; Hin3I-CauII;
AB  - Hin5II-AsuI; Hin5III-HindIII; Hin6I, Hin7I-HhaI.  Restriction endonucleases
AB  - Hin1I, Hin1II and Hin6I recognize nucleotide sequences 5'GR^CGYC, 5'CATG^,
AB  - 5'G^CGC, respectively, and cleave them as indicated by the arrows.
ER  -

TY  - JOUR
AU  - Lazaro-Diez, M.
AU  - Acosta, F.
AU  - Remuzgo-Martinez, S.
AU  - Ocampo-Sosa, A.
AU  - Ocejo-Vinyals, J.G.
AU  - Bravo, J.
AU  - El Aamri, F.
AU  - Escuela, O.
AU  - Martinez-Martinez, L.
AU  - Ramos-Vivas, J.
TI  - Whole-Genome Sequence of Serratia liquefaciens HUMV-21, a Cytotoxic, Quorum-Sensing, and Biofilm-Producing Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00533
EP  - e00515
VL  - 3
AB  - A clinical isolate of Serratia liquefaciens (strain HUMV-21) was obtained from a  skin ulcer
AB  - of an adult patient. We report here its complete genome assembly using
AB  - PacBio single-molecule real-time (SMRT) sequencing, which resulted in a single
AB  - circular chromosome with 5.3 Mb. About 5,844 protein-coding genes are predicted
AB  - from this assembly.
ER  -

TY  - JOUR
AU  - Lazaro-Diez, M.
AU  - Redondo-Salvo, S.
AU  - Arboleya-Agudo, A.
AU  - Ocejo-Vinyals, J.G.
AU  - Chapartegui-Gonzalez, I.
AU  - Ocampo-Sosa, A.A.
AU  - Acosta, F.
AU  - Martinez-Martinez, L.
AU  - Ramos-Vivas, J.
TI  - Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00556
EP  - e00516
VL  - 4
AB  - A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an
AB  - adult patient. We report here its complete genome assembly using
AB  - PacBio single-molecule real-time (SMRT) sequencing, which resulted in a
AB  - chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding
AB  - genes are predicted from this assembly.
ER  -

TY  - JOUR
AU  - Lazaro-Perona, F.
AU  - Sotillo, A.
AU  - Troyano-Hernaez, P.
AU  - Gomez-Gil, R.
AU  - Vega-Bueno, A.
AU  - Mingorance, J.
TI  - Genomic path to panresistance in a clinical isolate of Klebsiella pneumoniae.
JO  - Int. J. Antimicrob. Agents
PY  - 2018
SP  - 713
EP  - 718
VL  - 52
AB  - Carbapenem-resistant Klebsiella pneumoniae (CRKP) have spread globally through
AB  - tertiary hospitals. Many CRKP clinical isolates are multi-drug resistant and may
AB  - become eventually pan-drug resistant (PDR). We present the closed genome of a
AB  - pan-drug resistant VIM-1-producer K. pneumoniae strain (KP1050) obtained in a
AB  - tertiary hospital . The isolate belonged to ST54 and had five extrachromosomal
AB  - elements, four plasmids and a circular phage genome. Most resistance genes were
AB  - located in two clusters borne by two of the plasmids, a class 1 integron that
AB  - contained up to fourteen genes, including a VIM-1 metallo-beta-lactamase gene,
AB  - and an IS26 transposon that contained a mobile element from A. baumannii encoding
AB  - the amikacin resistance gene aac(6')-Ian. A multi-drug resistant isolate obtained
AB  - six years before was identified retrospectively and sequenced. Comparison of the
AB  - two genomes showed that chromosomal mutations in outer membrane porins, ramR and
AB  - phoQ genes contributed to increase the resistance spectrum.
ER  -

TY  - JOUR
AU  - Lazarte, J.N.
AU  - Lopez, R.P.
AU  - Ghiringhelli, P.D.
AU  - Beron, C.M.
TI  - Bacillus wiedmannii biovar thuringiensis: A Specialized Mosquitocidal Pathogen with Plasmids from Diverse Origins.
JO  - Genome Biol. Evol.
PY  - 2018
SP  - 2823
EP  - 2833
VL  - 10
AB  - Bacillus cereus sensu lato also known as B. cereus group is composed of an
AB  - ecologically diverse bacterial group with an increasing number of related
AB  - species, some of which are medically or agriculturally important. Numerous e ff
AB  - orts have been undertaken to allow presumptive di ff erentiation of B. cereus
AB  - group species from one another. FCC41 is a Bacillus sp. strain toxic against
AB  - mosquito species like Aedes aegypti, Aedes (Ochlerotatus) albifasciatus, Culex
AB  - pipiens, Culex quinquefasciatus, and Culex apicinus, some of them responsible for
AB  - the transmission of vector-borne diseases. Here, we report the complete genome
AB  - sequence of FCC41 strain, which consists of one circular chromosome and eight
AB  - circular plasmids ranging in size from 8 to 490 kb. This strain harbors six
AB  - crystal protein genes, including cry24Ca, two cry4-like and two cry52-like, a
AB  - cry41-like parasporin gene and multiple virulence factors. The phylogenetic
AB  - analysis of the whole-genome sequence of this strain with molecular approaches
AB  - places this strain into the Bacillus wiedmannii cluster. However, according with
AB  - phenotypical characteristics such as the mosquitocidal activity due to the
AB  - presence of Cry proteins found in the parasporal body and cry genes encoded in
AB  - plasmids of different sizes, indicate that this strain could be renamed as B.
AB  - wiedmannii biovar thuringiensis strain FCC41.
ER  -

TY  - JOUR
AU  - Lazim, H.
AU  - Josephsen, J.
AU  - Ben Hassen, A.
AU  - Belhadj, O.
AU  - Limam, R.
TI  - Eco1524I, a type II restriction endonuclease - Isolation, partial purification, and characterization.
JO  - Appl. Biochem. Biotechnol.
PY  - 2005
SP  - 189
EP  - 199
VL  - 125
AB  - Various strains of Escherichia coli, isolated from different patients, were screened for type
AB  - II restriction endonuclease activity. In 1 out
AB  - of 23 patients, a type II restriction endonuclease activity was found.
AB  - The restriction endonuclease designated Eco1524I was purified to near
AB  - homogeneity, based on hydroxyapatite and heparin sepharose
AB  - chromatography. Eco1524I exhibited endonuclease restriction activity in
AB  - the pH range from 6.0 to 10.0 (maximum level at pH 8.0) and required
AB  - Mg2+ as divalent cation. The enzyme was stable till temperature 55
AB  - degrees C and pH range from 6.0 to 10.0. Eco1524I recognized the
AB  - sequence 6-bp palindromic 5'AGG|CCT 3', producing blunt end
AB  - and is found to be an isoschizomer of StuI.
ER  -

TY  - JOUR
AU  - Lazowska, J.
AU  - Meunier, B.
AU  - Macadre, C.
TI  - Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers.
JO  - EMBO J.
PY  - 1994
SP  - 4963
EP  - 4972
VL  - 13
AB  - Group II introns ai1 and ai2 of the Saccharomyces cerevisiae mitochondrial COX1 gene encode
AB  - proteins having a dual function (maturase and reverse transcriptase) and are mobile genetic
AB  - elements.  By construction of adequate donor genomes, we demonstrate that each of them is
AB  - self-sufficient and practices homing in the absence of homing-type endonucleases encoded by
AB  - either group I introns or the ENS2 gene.  Each of the S. cerevisiae group II self-mobile
AB  - introns was tested for its ability to invade mitochondrial DNA (mtDNA) from two related
AB  - Saccharomyces species.  Surprisingly, only ai2 was observed to integrate into both genomes.
AB  - The non-mobility of ai1 was clearly correlated with some polymorphic changes occurring in
AB  - sequences flanking its insertion sites in the recipient mtDNAs.  Importantly, studies of the
AB  - behavior of these introns in interspecific crosses demonstrate that flanking marker
AB  - co-conversion accompanying group II intron homing is unidirectional and efficient only in the
AB  - 3' to 5' direction towards the upstream exon.  Thus, the polar co-conversion and dependence
AB  - of the splicing proficiency of the intron reported previously by us are hallmarks of group II
AB  - intron homing, which significantly distinguish it from the strictly DNA-based group I intron
AB  - homing and strictly RNA-based group II intron transposition.
ER  -

TY  - JOUR
AU  - Lazowska, J.
AU  - Szczepanek, T.
AU  - Macadre, C.
AU  - Dakova, M.
TI  - Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in their open reading frames: one is mobile, the other is not.
JO  - C.R. Acad. Sci. III
PY  - 1992
SP  - 37
EP  - 41
VL  - 315
AB  - We have undertaken a comprehensive study of the gene conversion of all the mitochondrial
AB  - introns of Saccharomyces capensis.  The approach used involved the measurement of intron
AB  - transmission amongst the progeny of crosses between a recipient strain (Saccharomyces
AB  - cerevisiae intronless mitochondria) and various donor strains (Saccharomyces capensis, with
AB  - various combinations of mitochondrial introns).  We have shown that the S. capensis second
AB  - intron (bi2 of cytochrome b gene) is extremely active as a donor in gene conversion whereas
AB  - its homologous S. cerevisiae intron is not.  Determination of the sequence of the S. capensis
AB  - intron demonstrates that it differs from that of the homologous S. cerevisiae intron (bi2) by
AB  - a very small number of nucleotide substitutions.
ER  -

TY  - JOUR
AU  - Le Bars, H.
AU  - Bousarghin, L.
AU  - Bonnaure-Mallet, M.
AU  - Jolivet-Gougeon, A.
AU  - Barloy-Hubler, F.
TI  - Complete Genome Sequence of the Strong Mutator Salmonella enterica subsp. enterica Serotype Heidelberg Strain B182.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3537
EP  - 3538
VL  - 194
AB  - In bacteria, normal mutation frequencies are mostly around 10(-10) per base pair. However,
AB  - there exists natural isolates, called 'mutators,' that exhibit permanent
AB  - mutation occurrences up to 1,000-fold greater than usual. As mutations play
AB  - essential roles, particularly in the evolution of antibiotic resistance, bacteria
AB  - showing elevated mutation rates could have an important responsibility in the
AB  - emergence of antibiotic resistance, especially in the clinical background. In
AB  - this announcement, we report the first complete genome sequence of the Salmonella
AB  - enterica subsp. enterica serotype Heidelberg B182 mutator strain, isolated from
AB  - bovine feces (France), which consists of a 4,750,465-bp circular chromosome
AB  - (cB182_4750; GC, 52.2%) and one circular plasmid of 37,581 bp (pB182_37; GC,
AB  - 42.8%).
ER  -

TY  - JOUR
AU  - Le Gac, G.
AU  - Esteve, P.-O.
AU  - Ferec, C.
AU  - Pradhan, S.
TI  - DNA damage-induced down-regulation of human Cdc25C and Cdc2 is mediated by cooperation between p53 and maintenance DNA (Cytosine-5) methyltransferase 1.
JO  - J. Biol. Chem.
PY  - 2006
SP  - 24161
EP  - 24170
VL  - 281
AB  - The Cdc25C phosphatase mediates cellular entry into mitosis in mammalian cells. Cdc25C
AB  - activates Cdc2 for entry into mitosis by dephosphorylating Thr and Tyr at the site of
AB  - inhibitory phosphorylation. The Cdc25C gene contains tumor suppressor p53 binding sites and is
AB  - demonstrated to contribute to the p53-dependent cell cycle arrest upon DNA damage. Here we
AB  - show that both Cdc25C and Cdc2 were down-regulated in wild-type HCT116 cells but not in
AB  - p53-null, DNMT1-null or DNMT1and DNMT3b-null cells, upon p53 stabilization following
AB  - doxorubicin-mediated DNA damage. Furthermore, zebularine, a drug that selectively traps and
AB  - depletes nuclear DNMT1 and DNMT3b, relieved p53-mediated repression of endogenous Cdc25C and
AB  - Cdc2. Methylation analysis of the Cdc25C and Cdc2 promoter displayed internal CG methylation
AB  - proximal to the p53 binding site upon DNA damage in a p53-dependent manner. Chromatin
AB  - immunoprecipitation of doxorubicin treated wild-type HCT116 cells showed the presence of
AB  - DNMT1, p53, H3K9me2, and the transcriptional repressor HDAC1 on the Cdc25C and Cdc2 promoters,
AB  - suggesting their involvement as repressive complexes in Cdc25C and Cdc2 gene silencing. Thus,
AB  - the general mechanism of p53-mediated gene repression may involve recruitment of other
AB  - repressive factors.
ER  -

TY  - JOUR
AU  - Le Guen, L.
AU  - Santos, R.
AU  - Camadro, J.-M.
TI  - Functional analaysis of the hemK gene product involvement in protoporphyrinogen oxidase activity in yeast.
JO  - FEMS Microbiol. Lett.
PY  - 1999
SP  - 175
EP  - 182
VL  - 173
AB  - The Escherichia coli hemK gene has been described as being involved in protoporphyrinogen
AB  - oxidase activity; however, there is no biochemical evidence for this. In the context of
AB  - characterizing the mechanisms of protoporphyrinogen oxidation in the yeast Saccharomyces
AB  - cerevisiae, we investigated the yeast homolog of HemK, which is encoded by the ORF YNL063w, to
AB  - find out whether it has any protoporphyrinogen oxidase activity and/or whether it modulates
AB  - protoporphyrinogen oxidase activity. Phenotype analysis and enzyme activity measurements
AB  - indicated that the yeast HemK homolog is not involved in protoporphyrinogen oxidase activity.
AB  - Complementation assays in which the yeast HemK homolog is overproduced do not restore
AB  - wild-type phenotypes in a yeast strain with deficient protoporphyrinogen oxidase activity.
AB  - Protein sequence analysis of HemK-related proteins revealed consensus motif for
AB  - S-adenosyl-methionine-dependent methyltransferase.
ER  -

TY  - JOUR
AU  - Le Guern, R.
AU  - Grandjean, T.
AU  - Faure, K.
AU  - Bauduin, M.
AU  - Kipnis, E.
AU  - Dessein, R.
TI  - Draft Genome Sequences of Two Carbapenemase-Producing Klebsiella pneumoniae Strains Isolated from Blood Cultures.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01057
EP  - e01018
VL  - 7
AB  - Carbapenemase-producing Klebsiella pneumoniae represents an emerging public health issue.
AB  - Here, we present the draft whole-genome sequences of K. pneumoniae
AB  - clinical strains KPL0.1 (OXA-48 carbapenemase) and KPL0.2 (NDM-1 carbapenemase).
AB  - These genome sequences should help in investigating pathophysiological mechanisms
AB  - of digestive colonization or infection with these highly resistant bacteria.
ER  -

TY  - JOUR
AU  - Le Marechal, C.
AU  - Hernandez, D.
AU  - Schrenzel, J.
AU  - Even, S.
AU  - Berkova, N.
AU  - Thiery, R.
AU  - Vautor, E.
AU  - Fitzgerald, J.R.
AU  - Francois, P.
AU  - Le Loir, Y.
TI  - Genome Sequence of two Staphylococcus aureus ovine strains that induce severe (strain O11) and mild (strain O46) mastitis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2353
EP  - 2354
VL  - 193
AB  - Staphylococcus aureus is a major etiological agent of mastitis in ruminants. We report here
AB  - the genome sequences of two ovine strains that were isolated from gangrenous (strain O11) and
AB  - subclinical (strain O46) ewe mastitis. Both strains belong to the same clonal complex. Despite
AB  - this close genotypic relationship, the two isolates were shown to reproducibly induce highly
AB  - divergent type of infections, either severe (O11) or mild (O46) mastitis in experimental ewe
AB  - model.
ER  -

TY  - JOUR
AU  - le Roux, W.J.
AU  - Chan, W.Y.
AU  - De Maayer, P.
AU  - Venter, S.N.
TI  - Genome Sequence of Vibrio cholerae G4222, a South African Clinical Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e0004013
EP  - e0004013
VL  - 1
AB  - Vibrio cholerae, a Gram-negative pathogen autochthonous to the aquatic environment, is the
AB  - causative agent of cholera. Here, we report the complete
AB  - genome sequence of V. cholerae G4222, a clinical isolate from South Africa.
ER  -

TY  - JOUR
AU  - Le, Y.
AU  - Zhu, S.
TI  - Purification of restriction endonuclease MspI.
JO  - Huaxue Shiji
PY  - 1988
SP  - 35
EP  - 37
VL  - 10
AB  - A new procedure has been developed for the purification of restriction
AB  - endonuclease Msp I.  The procedure uses Sephadex G-200 gel filtration,
AB  - chromatography on phosphocellulose and heparin sepharose, and gives product
AB  - with sufficient purity to permit its use in genetic engineering.
ER  -

TY  - JOUR
AU  - Leahy, S.C.
AU  - Kelly, W.J.
AU  - Altermann, E.
AU  - Ronimus, R.S.
AU  - Yeoman, C.J.
AU  - Pacheco, D.M.
AU  - Li, D.
AU  - Kong, Z.
AU  - McTavish, S.
AU  - Sang, C.
AU  - Lambie, S.C.
AU  - Janssen, P.H.
AU  - Attwood, G.T.
TI  - The genome sequence of the rumen methanogen Methanobrevibacter ruminantium M1.
JO  - PLoS ONE
PY  - 2010
SP  - e8926
EP  - e8926
VL  - 5
AB  - Background: Methane (CH4) is a potent greenhouse gas (GHG), having a global warming potential
AB  - 21 times that of carbon dioxide (CO2). Methane emissions from agriculture represent around 40%
AB  - of the emissions produced by human-related activities, the single largest source being enteric
AB  - fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are
AB  - lacking. Ruminant methane is formed by the action of methanogenic archaea typified by
AB  - Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets
AB  - worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify
AB  - genes and proteins that can be targeted to reduce methane production, we have
AB  - sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be
AB  - completed.  Methodology/Principal Findings: The M1 genome was sequenced, annotated and
AB  - subjected to comparative genomic and
AB  - metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets
AB  - for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified.
AB  - The feasibility of using a synthetic peptidedirected vaccinology approach to target epitopes
AB  - of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic
AB  - enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted
AB  - stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated
AB  - up-regulation of methanogenesis genes during co-culture with a hydrogen (H2) producing rumen
AB  - bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium
AB  - M1, the first reported in archaeal species.  Conclusions/Significance: The M1 genome sequence
AB  - provides new insights into the lifestyle and cellular processes of this important rumen
AB  - methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen
AB  - methanogens and represents a significant contribution to worldwide efforts to mitigate
AB  - ruminant methane emissions and reduce production of anthropogenic greenhouse gases.
ER  -

TY  - JOUR
AU  - Leahy, S.C.
AU  - Kelly, W.J.
AU  - Li, D.
AU  - Li, Y.
AU  - Altermann, E.
AU  - Lambie, S.C.
AU  - Cox, F.
AU  - Attwood, G.T.
TI  - The Complete genome sequence of Methanobrevibacter sp. AbM4.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 215
EP  - 227
VL  - 8
AB  - Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and
AB  - was chosen as a representative of the
AB  - Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome
AB  - is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb
AB  - versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus
AB  - 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the
AB  - composition of the AbM4 genome is very similar to that of M1 suggesting
AB  - that the methanogenesis pathway and central metabolism of these strains
AB  - are highly similar, and both organisms are likely to be amenable to
AB  - inhibition by small molecule inhibitors and vaccine-based methane
AB  - mitigation technologies targeting these conserved features. The main
AB  - differences compared to M1 are that AbM4 has a complete coenzyme M
AB  - biosynthesis pathway and does not contain a prophage or non-ribosomal
AB  - peptide synthase genes. However, AbM4 has a large CRISPR region and
AB  - several type I and type II restriction-modification system components.
AB  - Unusually, DNA-directed RNA polymerase beta' and beta ' subunits of
AB  - AbM4 are joined, a feature only previously observed in some
AB  - thermophilic archaea. AbM4 has a much reduced complement of genes
AB  - encoding adhesin-like proteins which suggests it occupies a ruminal
AB  - niche different from that of M1.
ER  -

TY  - JOUR
AU  - Lean, S.S.
AU  - Yeo, C.C.
AU  - Suhaili, Z.
AU  - Thong, K.L.
TI  - Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance  Mechanism.
JO  - Front. Microbiol.
PY  - 2015
SP  - 1445
EP  - 1445
VL  - 6
AB  - Acinetobacter baumannii is a Gram-negative nosocomial pathogen of importance due  to its
AB  - uncanny ability to acquire resistance to most antimicrobials. These
AB  - include carbapenems, which are the drugs of choice for treating A. baumannii
AB  - infections, and polymyxins, the drugs of last resort. Whole genome sequencing was
AB  - performed on two clinical carbapenem-resistant A. baumannii AC29 and AC30 strains
AB  - which had an indistinguishable ApaI pulsotype but different susceptibilities to
AB  - polymyxin. Both genomes consisted of an approximately 3.8 Mbp circular chromosome
AB  - each and several plasmids. AC29 (susceptible to polymyxin) and AC30 (resistant to
AB  - polymyxin) belonged to the ST195 lineage and are phylogenetically clustered under
AB  - the International Clone II (IC-II) group. An AbaR4-type resistance island (RI)
AB  - interrupted the comM gene in the chromosomes of both strains and contained the
AB  - bla OXA-23 carbapenemase gene and determinants for tetracycline and streptomycin
AB  - resistance. AC29 harbored another copy of bla OXA-23 in a large (~74 kb)
AB  - conjugative plasmid, pAC29b, but this gene was absent in a similar plasmid
AB  - (pAC30c) found in AC30. A 7 kb Tn1548::armA RI which encodes determinants for
AB  - aminoglycoside and macrolide resistance, is chromosomally-located in AC29 but
AB  - found in a 16 kb plasmid in AC30, pAC30b. Analysis of known determinants for
AB  - polymyxin resistance in AC30 showed mutations in the pmrA gene encoding the
AB  - response regulator of the two-component pmrAB signal transduction system as well
AB  - as in the lpxD, lpxC, and lpsB genes that encode enzymes involved in the
AB  - biosynthesis of lipopolysaccharide (LPS). Experimental evidence indicated that
AB  - impairment of LPS along with overexpression of pmrAB may have contributed to the
AB  - development of polymyxin resistance in AC30. Cloning of a novel variant of the
AB  - bla AmpC gene from AC29 and AC30, and its subsequent expression in E. coli also
AB  - indicated its likely function as an extended-spectrum cephalosporinase.
ER  -

TY  - JOUR
AU  - Leandro, T.
AU  - da Costa, M.S.
AU  - Sanz, J.L.
AU  - Amils, R.
TI  - Complete Genome Sequence of Tessaracoccus sp. Strain T2.5-30 Isolated from 139.5  Meters Deep on the Subsurface of the Iberian Pyritic Belt.
JO  - Genome Announcements
PY  - 2017
SP  - e00238
EP  - e00217
VL  - 5
AB  - Here, we report the complete genome sequence of Tessaracoccus sp. strain T2.5-30, which
AB  - consists of a chromosome with 3.2 Mbp, 70.4% G+C content, and 3,005 coding
AB  - DNA sequences. The strain was isolated from a rock core retrieved at a depth of
AB  - 139.5 m in the subsurface of the Iberian Pyritic Belt (Spain).
ER  -

TY  - JOUR
AU  - Leao, S.C.
AU  - Matsumoto, C.K.
AU  - Viana-Niero, C.
AU  - Ramos, R.T.
AU  - Carneiro, A.R.
AU  - Barbosa, M.S.
AU  - Lima, K.V.
AU  - Lopes, M.L.
AU  - Azevedo, V.
AU  - Silva, A.
TI  - Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594.
JO  - Genome Announcements
PY  - 2013
SP  - e00896
EP  - e00813
VL  - 1
AB  - An epidemic of surgical-site infections by a single strain of Mycobacterium abscessus subsp.
AB  - bolletii affected >1,700 patients in Brazil from 2004 to 2008.
AB  - The genome of the epidemic prototype strain M. abscessus subsp. bolletii INCQS
AB  - 00594, deposited in the collection of the National Institute for Health Quality
AB  - Control (INCQS), was sequenced.
ER  -

TY  - JOUR
AU  - Leao, T.
AU  - Guimaraes, P.I.
AU  - de Melo, A.G.
AU  - Ramos, R.T.
AU  - Leao, P.N.
AU  - Silva, A.
AU  - Fiore, M.F.
AU  - Schneider, M.P.
TI  - Draft Genome Sequence of the N2-Fixing Cyanobacterium Nostoc piscinale CENA21, Isolated from the Brazilian Amazon Floodplain.
JO  - Genome Announcements
PY  - 2016
SP  - e00189
EP  - e00116
VL  - 4
AB  - We announce here the draft genome sequence ofNostoc piscinaleCENA21, a diazotrophic
AB  - heterocyst-forming cyanobacterium isolated from the Solimoes River,
AB  - Amazon Basin, Brazil. It consists of one circular chromosome scaffold with 11
AB  - contigs and total size of 7,094,556 bp. Secondary metabolite annotations indicate
AB  - a good source for the discovery of novel natural products.
ER  -

TY  - JOUR
AU  - Lebedev, L.R.
AU  - Afinogenova, G.N.
AU  - Andreeva, I.S.
AU  - Pustoshilova, N.M.
AU  - Pozdnyakov, S.G.
AU  - Chizhikov, V.E.
TI  - Determination of substrate specificity of a site-specific deoxyribonuclease RtrI.
JO  - Bioorg. Khim.
PY  - 1991
SP  - 277
EP  - 279
VL  - 17
AB  - A new site-specific deoxyribonuclease RtrI from Rhizobium trifolii has been
AB  - shown to recognize the sequence 5'-G^TCGAC-3' in double-stranded DNA and to
AB  - cleave it at the point indicated by an arrow.  Therefore the enzyme is a true
AB  - isoschizomer of the restriction endonuclease SalI.
ER  -

TY  - JOUR
AU  - Lebedev, L.R.
AU  - Pustoshilova, N.M.
AU  - Repin, V.E.
AU  - Degtyarev, S.K.
TI  - Isolation of restriction endonuclease RsaI from Rhodopseudomonas sphaeroides and study of its properties.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1991
SP  - 330
EP  - 337
VL  - 27
AB  - A technique is proposed for the isolation of the restrictase RsaI from
AB  - Rhodopseudomonas sphaeroides, which involves cultivation of the bacteria under
AB  - aerobic conditions, ultrasonic disruption of the cells, fractionation in the
AB  - PEG-dextran two-phase system, chromatography on phosphocellulose P-11 and
AB  - heparin-sepharose.  The enzyme yield from 1 g of wet cells is 35000 U.
AB  - Gel-filtration through Sephadex G-200 and electrophoresis in polyacrylamide gel
AB  - under denaturing conditions showed that RsaI in solution was a monomer with a
AB  - molecular weight of 24000 +/- 2000.  The optimal conditions for the highest
AB  - enzymatic activity are the following: NaCl concentration 0-20 mM; Mg2+
AB  - concentration 10-12 mM, pH 8.0-8.5; 37-50C.  Mg2+ ions cannot be replaced with
AB  - Mn2+, Zn2+, Ca2+ and Cu2+ ions.  Glycerol and ethanol at concentrations up to
AB  - 10%, and p-chloromercuric benzoate at concentrations up to 0.3 mM have no
AB  - inhibitory effect.
ER  -

TY  - JOUR
AU  - Lebenka, A.I.
AU  - Melvidas, V.I.
TI  - The sensitivity of E. coli and C. freundii strains to 5-azacytidine.
JO  - Vopr. Med. Khim.
PY  - 2001
SP  - 477
EP  - 482
VL  - 47
AB  - The sensitivity of E. coli and C. freundii strains to 5-azacytidine and restrictase activity
AB  - of partially purified cell-free extracts were investigated.  Restrictase activity was found
AB  - only in 5-azacytidine-sensitive strains.  In the 5-azacytidine-resistant strains restrictase
AB  - activity was not detected.
ER  -

TY  - JOUR
AU  - Lebenka, A.Y.
AU  - Chitavichyus, D.B.
TI  - Enzymes of DNA restriction-modification from Caulobacter fusiformis BC-25.
JO  - Biokhimiia
PY  - 1988
SP  - 1895
EP  - 1899
VL  - 53
AB  - The CfuII system of restriction-modification enzymes, as well as the methylase
AB  - CfuIII, was detected in cells of Caulobacter fusiformis BC-25.  R.CfuII
AB  - recognizes and cleaves the sequence 5'-CTGCA^G-3' (PstI).  This system has the
AB  - corresponding methylase CfuII, which protects the host DNA.  The manifestation
AB  - of R.CfuII activity requires Mg2+ or Mn2+.  M.CfuIII protects DNA from cleavage
AB  - by the restriction endonuclease EcoRI.  Modification of DNA by a Cfu of type
AB  - III is a generic characteristic of Caulobacter.
ER  -

TY  - JOUR
AU  - Lebenka, A.Y.
AU  - Kanopkaite, S.I.
AU  - Buryanov, Y.I.
TI  - DNA methylation in the cells of Escherichia coli MRE 600 in the presence of S-methylmethionine.
JO  - Biokhimiia
PY  - 1981
SP  - 2160
EP  - 2163
VL  - 46
AB  - The effect of S-methylmethionine, a methyl group donor, on enzymatic methylation of DNA in E.
AB  - coli MRE 600 cells was studied.  It was found that SMM can be used as a donor of methyl groups
AB  - during bacterial DNA methylation in vivo without changing the specificity of DNA methylation.
ER  -

TY  - JOUR
AU  - Lebenka, A.Y.
AU  - Rackus, Y.A.
TI  - DNA methylase Sau3AI:  isolation and properties.
JO  - Biokhimiia
PY  - 1989
SP  - 1009
EP  - 1014
VL  - 54
AB  - DNA-methylase Sau3AI has been isolated for the first time from Staphylococcus aureus 3A cells
AB  - and purified by column chromatography on phosphocellulose PII, heparin-Sepharose and blue
AB  - Sepharose. The purified enzyme methylates the GATC sequence with the formation of GATm5C as
AB  - can be evidenced from the protection of DNA from digestion with restrictases Sau3AI and BamHI,
AB  - the lack of the C3H3-group incorporation into Sau3AI DNA-restricts and the formation of a
AB  - single methylated base m5C. Sau3AI methylase modifies only double-stranded (but not
AB  - single-stranded) DNA. Thus, methylase Sau3AI modifies both DNA chains in the recognition site
AB  - during a single binding act. The 5-azacytidine-containing DNA inhibits by 95% the activity of
AB  - methylase Sau3AI. Ado-met is the single methyl group donor for methylase Sau3AI. The presence
AB  - of m6A in the recognition site does not affect the activity of methylase Sau3AI. The practical
AB  - recommendations for the use of M.Sau3AI, alongside with M.Eco dam, for the study of dam
AB  - methylation by additional methylation of the DNA in vitro in the presence of
AB  - [methyl-3H]-S-adenosyl-methionine are given.
ER  -

TY  - JOUR
AU  - Lebert, B.M.
AU  - Sanford, S.A.
AU  - Reisinger, L.M.
AU  - Forsman, A.M.
AU  - Savage, A.E.
TI  - Draft Genome Sequence of Xenophilus sp., a Novel Bacterium Isolated from the Skin of a Southern Leopard Frog (Rana sphenocephala) in Florida, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e01067
EP  - e01017
VL  - 5
AB  - We report here the draft genome sequence of a novel Xenophilus species cultured from the skin
AB  - of a southern leopard frog (Rana sphenocephala). Compared to
AB  - previously sequenced bacterial genomes, our novel isolate showed the most
AB  - significant homology with Xenophilus azovorans The assembled genome is 3,978,285
AB  - bp, with 3,704 predicted genes and one predicted plasmid.
ER  -

TY  - JOUR
AU  - Lebionka, A.Y.
AU  - Melvidas, V.I.
TI  - The ability of bacterial DNA methyltransferases to use methylcobalamine as a cofactor in DNA methylation reactions.
JO  - Bioorg. Khim.
PY  - 2007
SP  - 159
EP  - 163
VL  - 53
AB  - The ability of bacterial DNA methyltransferases Alu I, Cfr I, Cfr 6, Cfr 10, Eco RI, Eco RII,
AB  - Msp I, Mva I, Pvu I, Pvu II, and Sau 3A to use
AB  - methyl-cobalamine and methyl-methionine as cofactors of DNA methylation
AB  - in vitro. These bacterial DNA methyl transferase used
AB  - methyl-cobalamine, but not methylmethionine for DNA methylation.
ER  -

TY  - JOUR
AU  - LeBon, J.M.
AU  - Kado, C.I.
AU  - Rosenthal, L.J.
AU  - Chirikjian, J.G.
TI  - DNA modifying enzymes of Agrobacterium tumefaciens: Effect of DNA topoisomerase, restriction endonuclease, and unique DNA endonuclease on plasmid and plant DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1978
SP  - 4097
EP  - 4101
VL  - 75
AB  - Extracts from Agrobacterium tumefaciens strain 1D135 contain three enzymes that
AB  - have been characterized and partially purified.  The first enzyme, a DNA
AB  - topoisomerase, appeared to relax only negatively twisted DNA.  The second
AB  - enzyme, AtuI, a type II restriction endonuclease, generated the identical DNA
AB  - digestion pattern as EcoRII when several DNAs were used.  The third enzyme,
AB  - endonuclease A, showed a preference for superhelical DNAs as substrates.  When
AB  - plasmid pCK135DNA, obtained from the virulent strain 1D135 of A. tumefaciens,
AB  - or plant DNA was exposed to the three enzymes, changes in DNA patterns were
AB  - observed due to either conformational changes or digestion of the DNAs.  These
AB  - enzymes may function in vivo in the processing and incorporation of bacterial
AB  - DNA in plant cells.
ER  -

TY  - JOUR
AU  - Lebreton, F.
AU  - Valentino, M.D.
AU  - Duncan, L.B.
AU  - Zeng, Q.
AU  - Manson, Mc.G.A.
AU  - Earl, A.M.
AU  - Gilmore, M.S.
TI  - High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides.
JO  - Genome Announcements
PY  - 2013
SP  - e01087
EP  - e01013
VL  - 1
AB  - Vagococci are usually isolated from marine hosts and occasionally from endodontic infections.
AB  - Using 16S rRNA gene comparison, the closest relatives are members of
AB  - the genera Enterococcus and Carnobacterium. A draft sequence of Vagococcus lutrae
AB  - was generated to clarify the relationship of Vagococcus to these and other
AB  - related low-G+C Gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Lebreton, F.
AU  - van Schaik, W.
AU  - McGuire, A.M.
AU  - Godfrey, P.
AU  - Griggs, A.
AU  - Mazumdar, V.
AU  - Corander, J.
AU  - Cheng, L.
AU  - Saif, S.
AU  - Young, S.
AU  - Zeng, Q.
AU  - Wortman, J.
AU  - Birren, B.
AU  - Willems, R.J.
AU  - Earl, A.M.
AU  - Gilmore, M.S.
TI  - Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.
JO  - MBio
PY  - 2013
SP  - e00534
EP  - e00513
VL  - 4
AB  - UNLABELLED: Enterococcus faecium, natively a gut commensal organism, emerged as a leading
AB  - cause of multidrug-resistant hospital-acquired infection in the 1980s. As
AB  - the living record of its adaptation to changes in habitat, we sequenced the
AB  - genomes of 51 strains, isolated from various ecological environments, to
AB  - understand how E. faecium emerged as a leading hospital pathogen. Because of the
AB  - scale and diversity of the sampled strains, we were able to resolve the lineage
AB  - responsible for epidemic, multidrug-resistant human infection from other strains
AB  - and to measure the evolutionary distances between groups. We found that the
AB  - epidemic hospital-adapted lineage is rapidly evolving and emerged approximately
AB  - 75 years ago, concomitant with the introduction of antibiotics, from a population
AB  - that included the majority of animal strains, and not from human commensal lines.
AB  - We further found that the lineage that included most strains of animal origin
AB  - diverged from the main human commensal line approximately 3,000 years ago, a time
AB  - that corresponds to increasing urbanization of humans, development of hygienic
AB  - practices, and domestication of animals, which we speculate contributed to their
AB  - ecological separation. Each bifurcation was accompanied by the acquisition of new
AB  - metabolic capabilities and colonization traits on mobile elements and the loss of
AB  - function and genome remodeling associated with mobile element insertion and
AB  - movement. As a result, diversity within the species, in terms of sequence
AB  - divergence as well as gene content, spans a range usually associated with
AB  - speciation. IMPORTANCE: Enterococci, in particular vancomycin-resistant
AB  - Enterococcus faecium, recently emerged as a leading cause of hospital-acquired
AB  - infection worldwide. In this study, we examined genome sequence data to
AB  - understand the bacterial adaptations that accompanied this transformation from
AB  - microbes that existed for eons as members of host microbiota. We observed changes
AB  - in the genomes that paralleled changes in human behavior. An initial bifurcation
AB  - within the species appears to have occurred at a time that corresponds to the
AB  - urbanization of humans and domestication of animals, and a more recent
AB  - bifurcation parallels the introduction of antibiotics in medicine and
AB  - agriculture. In response to the opportunity to fill niches associated with
AB  - changes in human activity, a rapidly evolving lineage emerged, a lineage
AB  - responsible for the vast majority of multidrug-resistant E. faecium infections.
ER  -

TY  - JOUR
AU  - Lechner, M.
AU  - Frey, B.
AU  - Laue, F.
AU  - Ankenbauer, W.
AU  - Schmitz, G.
TI  - SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'.
JO  - Fresenius Z. Anal. Chem.
PY  - 1992
SP  - 121
EP  - 122
VL  - 343
AB  - Restriction endonucleases with low cutting frequencies are important tools in molecular
AB  - genetics. Analysis of complex DNA molecules e.g. chromosomes requires cutting of DNA into
AB  - fragments of megabase size range. Nucleases with low cutting frequencies either recognize
AB  - sequences which are under represented in chromosomal DNA or are characterized by recognition
AB  - sequences of more than six base pairs. We discovered and isolated SwaI a novel class-II
AB  - restriction endonuclease from Staphylococcus warneri whose recognition specificity requires
AB  - eight nucleotides.
ER  -

TY  - JOUR
AU  - Lechner, M.
AU  - Frey, B.
AU  - Laue, F.
AU  - Anton-Botella, J.
AU  - Smith, C.L.
AU  - Ankenbauer, W.
AU  - Schmitz, G.G.
TI  - SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2293
EP  - 2296
VL  - 20
AB  - A novel class-II restriction endonuclease designated SwaI was purified from Staphyloccus
AB  - warneri. This enzyme cleaves adenovirus 2 DNA, SV40 DNA and M13mp7 at one site each, but does
AB  - not cleave lambda, PhiX174, pBR322 or pBR328 DNA. SwaI recognizes the octanucleotide sequence
AB  - 5'-ATTTAAAT-3', cleaving in the center of the recognition sequence creating blunt ended DNA
AB  - fragments. SwaI was used to digest chromosomal DNA from various microorganisms and human
AB  - cells.
ER  -

TY  - JOUR
AU  - Leclercq, S.
AU  - Dittmer, J.
AU  - Bouchon, D.
AU  - Cordaux, R.
TI  - Phylogenomics of 'Candidatus Hepatoplasma crinochetorum,' a Lineage of Mollicutes Associated with Noninsect Arthropods.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 407
EP  - 415
VL  - 6
AB  - Bacterial gut communities of arthropods are highly diverse and tightly related to
AB  - host feeding habits. However, our understanding of the origin and role of the
AB  - symbionts is often hindered by the lack of genetic information. "Candidatus
AB  - Hepatoplasma crinochetorum" is a Mollicutes symbiont found in the midgut glands
AB  - of terrestrial isopods. The only available nucleotide sequence for this symbiont
AB  - is a partial 16S rRNA gene sequence. Here, we present the 657,101 bp assembled
AB  - genome of Candidatus Hepatoplasma crinochetorum isolated from the terrestrial
AB  - isopod Armadillidium vulgare. While previous 16S rRNA gene-based analyses have
AB  - provided inconclusive results regarding the phylogenetic position of Candidatus
AB  - Hepatoplasma crinochetorum within Mollicutes, we performed a phylogenomic
AB  - analysis of 127 Mollicutes orthologous genes which confidently branches the
AB  - species as a sister group to the Hominis group of Mycoplasma. Several genome
AB  - properties of Candidatus Hepatoplasma crinochetorum are also highlighted compared
AB  - with other Mollicutes genomes, including adjacent tryptophan tRNA genes, which
AB  - further our understanding of the evolutionary dynamics of these genes in
AB  - Mollicutes, and the presence of a probably inactivated CRISPR/Cas system, which
AB  - constitutes a testimony of past interactions between Candidatus Hepatoplasma
AB  - crinochetorum and mobile genetic elements, despite their current lack in this
AB  - streamlined genome. Overall, the availability of the complete genome sequence of
AB  - Candidatus Hepatoplasma crinochetorum paves the way for further investigation of
AB  - its ecology and evolution.
ER  -

TY  - JOUR
AU  - Lederberg, S.
TI  - Genetics of host-controlled restriction anad modification of deoxyribonucleic acid in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1966
SP  - 1029
EP  - 1036
VL  - 91
AB  - The locus for the host specific restriction and modification of
AB  - deoxyribonucleic acid in Escherichia coli has been mapped by matings between
AB  - mutants for these characters in strains K-12, C600, and B. Linkage analysis and
AB  - kinetics of marker transfer indicate that a single or closely linked multiple
AB  - chromosomal site located about 4 min counterclockwise to leucine is responsible
AB  - for these activities.  Secondary factors which affect the quantitative level of
AB  - restriction also were detected.  Wild-type recombinants were isolated in
AB  - crosses between rm- (restriction or modification, or both) mutants.  The
AB  - expression in zygotes of the restrictionless character of a rm- donor is masked
AB  - by a separate, physiological impairment of restriction, which results from
AB  - mating and is independent of the modification state of the donor.  The
AB  - relevance of the restriction character to mating incompatibilities in these and
AB  - other bacterial strains is considered.
ER  -

TY  - JOUR
AU  - Lederberg, S.
TI  - Host-controlled restriction and modification of deoxyribonucleic acid in Eschericia coli.
JO  - Virology
PY  - 1965
SP  - 378
EP  - 387
VL  - 27
AB  - In Escherichia coli strain C600 (which has the host specificity of K12),
AB  - restrictions against infection by phage lambda of host specificities B and C
AB  - have the same sensitivity to heat inactivation.  Likewise, in strain B,
AB  - restrictions against phage lambda of host specificities C600 and C have an
AB  - identical heat sensitivity.  Strain C600(P1) has a heat sensitivity for loss of
AB  - its P1-directed restriction different from that of its C600-controlled
AB  - restriction.  Mutants of K12-type strains and of B which are impaired in their
AB  - restriction and modification activities have been isolated.  In K12 strains,
AB  - restrictions toward phage lambda of host specificities C and B are impaired by
AB  - the same mutation.  In B, restrictions toward phage lambda of host
AB  - specificities C and C600 also are lost simultaneously by mutation.  The
AB  - coordinate changes in restriction by heat treatment and by mutation indicate
AB  - that a common mechanism for restriction of lambda of host specificities C and B
AB  - operates in K12 strains, and that a single mechanism for restriction of phage
AB  - lambda of host specificities C and K12 occurs in strain B.  Restrictionless
AB  - mutants of B, unlike their parent, act as fertile F- in crosses with K12 Hfr
AB  - strains.  Modificationless mutants of K12 Hfr, unlike their parent, are no
AB  - longer fertile with restricting C600 strains.  Thus, the same mutations affect
AB  - the modification and/or restriction of the DNA of bacteria as well as phage.
AB  - Models are proposed for host restriction and modfication.  The models visualize
AB  - restriction as either a screening of new DNA by a DNA-site specific degrading
AB  - activity-successful passage permitting the DNA to operate in that cell-or a
AB  - seavenging of new DNA by a nonspecific degrading activity when such DNA fails
AB  - to be complexed with a site-specific protecting agent.
ER  -

TY  - JOUR
AU  - Ledwaba, B.
AU  - Mafofo, J.
AU  - van Heerden, H.
TI  - Genome Sequences of Brucella abortus and Brucella suis Strains Isolated from Bovine in Zimbabwe.
JO  - Genome Announcements
PY  - 2014
SP  - e01063
EP  - e01014
VL  - 2
AB  - This is a report of whole-genome sequences of a Brucella abortus strain and two Brucella suis
AB  - strains isolated from bovine in Zimbabwe. These strains were
AB  - selected based on their origin and data obtained when using multiplex PCR assays,
AB  - then sequenced using next-generation sequencing technologies.
ER  -

TY  - JOUR
AU  - Lee, A.S.
AU  - Sinsheimer, R.L.
TI  - A cleavage map of bacteriophage PhiX174 genome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1974
SP  - 2882
EP  - 2886
VL  - 71
AB  - Restriction endonucleases isolated from Hemophilus influenzae, Hemophilus
AB  - parainfluenzae, and Hemophilus aegyptius were used to cleave PhiX174
AB  - replicative form DNA into three sets of specific DNA fragments.  The order of
AB  - these fragments in the PhiX replicative form molecule was determined by (1)
AB  - analysis of partial digest products, (2) analysis of overlapping sets of
AB  - fragments produced by two different restrictive enzymes.  On the basis of these
AB  - results, a detailed physical map of the PhiX174 genome has been constructed
AB  - with respect to the cleavage sites of all three enzymes.
ER  -

TY  - JOUR
AU  - Lee, B.
AU  - Muller, M.T.
TI  - SUMOylation enhances DNA methyltransferase 1 activity.
JO  - Biochem. J.
PY  - 2009
SP  - 449
EP  - 461
VL  - 421
AB  - DNA methylation regulates gene expression through Complex network of protein-protein and
AB  - protein-DNA interactions in chromatin. The
AB  - maintenance methylase, DNMT1 (DNA methyltransferase 1), is a prominent
AB  - enzyme in the process that is linked to DNA replication and drives the
AB  - heritable nature of epigenetic modifications. The mechanistic details
AB  - that explain how DNMT1 catalytic action is directed and regulated in
AB  - chromatin are important ill our overall understanding of gene control.
AB  - In this work, we show that DNMT1 is modified by SUMOylation and we have
AB  - mapped these SUMOylation sites by defined mutations. SUMOylated DNMT1
AB  - is catalytically active on genomic DNA in vivo and we find that
AB  - SUMOylation significantly enhances the methylase activity of DNMT1 both
AB  - in vitro and in chromatin. These data suggest that SUMOylation
AB  - modulates the endogenous activity of a prominent epigenetic maintenance
AB  - pathway in somatic cells.
ER  -

TY  - JOUR
AU  - Lee, B.H.
AU  - Yegnasubramanian, S.
AU  - Lin, X.H.
AU  - Nelson, W.G.
TI  - Procainamide is a specific inhibitor of DNA methyltransferase 1.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 40749
EP  - 40756
VL  - 280
AB  - CpG island hypermethylation occurs in most cases of cancer, typically resulting in the
AB  - transcriptional silencing of critical cancer genes.
AB  - Procainamide has been shown to inhibit DNA methyltransferase activity
AB  - and reactivate silenced gene expression in cancer cells by reversing
AB  - CpG island hypermethylation. We report here that procainamide
AB  - specifically inhibits the hemimethylase activity of DNA
AB  - methyltransferase 1 (DNMT1), the mammalian enzyme thought to be
AB  - responsible for maintaining DNA methylation patterns during
AB  - replication. At micromolar concentrations, procainamide was found to be
AB  - a partial competitive inhibitor of DNMT1, reducing the affinity of the
AB  - enzyme for its two substrates, hemimethylated DNA and
AB  - S-adenosyl-L-methionine. By doing so, procainamide significantly
AB  - decreased the processivity of DNMT1 on hemimethylated DNA. Procainamide
AB  - was not a potent inhibitor of the de novo methyltransferases DNMT3a and
AB  - DNMT3b2. As further evidence of the specificity of procainamide for
AB  - DNMT1, procainamide failed to lower genomic 5-methyl-2'-deoxycytidine
AB  - levels in HCT116 colorectal cancer cells when DNMT1 was genetically
AB  - deleted but significantly reduced genomic 5-methyl-2'-deoxycytidine
AB  - content in parental HCT116 cells and in HCT116 cells where DNMT3b was
AB  - genetically deleted. Because many reports have strongly linked DNMT1
AB  - with epigenetic alterations in carcinogenesis, procainamide may be a
AB  - useful drug in the prevention of cancer.
ER  -

TY  - JOUR
AU  - Lee, B.M.
AU  - Park, Y.J.
AU  - Park, D.S.
AU  - Kang, H.W.
AU  - Kim, J.G.
AU  - Song, E.S.
AU  - Park, I.C.
AU  - Yoon, U.H.
AU  - Hahn, J.H.
AU  - Koo, B.S.
AU  - Lee, G.B.
AU  - Kim, H.
AU  - Park, H.S.
AU  - Yoon, K.O.
AU  - Kim, J.H.
AU  - Jung, C.H.
AU  - Koh, N.H.
AU  - Seo, J.S.
AU  - Go, S.J.
TI  - The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 577
EP  - 586
VL  - 33
AB  - The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae
AB  - (Xoo) KACC10331, a bacterium that causes bacterial
AB  - blight in rice (Oryza sativa L.). The genome is comprised of a single, 4
AB  - 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome
AB  - includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be
AB  - assigned putative function. Orthologs for 80% of the predicted Xoo genes
AB  - were found in the previously reported X.axonopodis pv. citri (Xac) and
AB  - X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently
AB  - specific to Xoo were identified. Xoo genes likely to be associated with
AB  - pathogenesis include eight with similarity to Xanthomonas avirulence (avr)
AB  - genes, a set of hypersensitive reaction and pathogenicity (hrp) genes,
AB  - genes for exopolysaccharide production, and genes encoding extracellular
AB  - plant cell wall-degrading enzymes. The presence of these genes provides
AB  - insights into the interactions of this pathogen with its gramineous host.
ER  -

TY  - JOUR
AU  - Lee, C.
AU  - Peters, V.
AU  - Melefors, O.
AU  - Romling, U.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.
JO  - Genome Announcements
PY  - 2014
SP  - e00186
EP  - e00114
VL  - 2
AB  - Pseudomonas aeruginosa SG17M is an environmental isolate recovered from river water in the
AB  - city of Mulheim, Germany. SG17M belongs to clone C, which is
AB  - distributed worldwide. This is the first clone C strain whose genome sequence has
AB  - been determined.
ER  -

TY  - JOUR
AU  - Lee, C.G.
AU  - Yuki, M.
AU  - Iida, T.
AU  - Nakaho, K.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Tepidibacter mesophilus Strain JCM 16806T Isolated from  Soil Polluted by Crude Oil in China.
JO  - Genome Announcements
PY  - 2017
SP  - e01308
EP  - e01317
VL  - 5
AB  - Here, we report the draft genome sequence of Tepidibacter mesophilus strain JCM 16806T, which
AB  - was isolated from an oil field. It is composed of 3,310,272 bp and
AB  - contains 3,160 protein-coding genes, 8 5S rRNAs, 3 16S rRNAs, and 69 tRNAs.
ER  -

TY  - JOUR
AU  - Lee, D.
AU  - Kim, Y.K.
AU  - Kim, Y.S.
AU  - Kim, T.J.
TI  - Complete Genome Sequence of Elizabethkingia sp. BM10, a Symbiotic Bacterium of the Wood-Feeding Termite Reticulitermes speratus KMT1.
JO  - Genome Announcements
PY  - 2015
SP  - e01181
EP  - e01115
VL  - 3
AB  - Elizabethkingia sp. BM10 was isolated from the hindgut of the wood-feeding termite
AB  - Reticulitermes speratus KMT1. It had cellobiohydrolase and beta-glucosidase activities but not
AB  - endo-beta-glucanase activity. The complete sequence of its genome, which has a total size of
AB  - 4,242,519 bases, is reported here. The genomic analysis identified six beta-glucosidase
AB  - candidate genes and three beta-glucanase candidate genes.
ER  -

TY  - JOUR
AU  - Lee, D.
AU  - Seo, H.
AU  - Park, C.
AU  - Park, K.
TI  - WeGAS: a web-based microbial genome annotation system.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2009
SP  - 213
EP  - 216
VL  - 73
AB  - We have developed WeGAS, a Web based microbial Genome
AB  - Annotation System, which provides features that include gene prediction,
AB  - homology search, promoter/motif analysis, genome browsing, gene ontology
AB  - analysis based on the COGs and GO, and metabolic pathway analysis with
AB  - web-based interfaces. Most raw data and intermediate data from genome
AB  - projects can be managed with the WeGAS database system, and analysis
AB  - results, including information on each gene and final genome maps, are
AB  - provided by its visualization modules. Especially, a pie-view browser
AB  - displaying circular maps of contigs and a COG-GO combination browser are
AB  - very helpful for an overview of projects. Major public microbial genome
AB  - databases can be imported, searched, and browsed through the WeGAS
AB  - modules. WeGAS is freely accessible via web site
AB  - http://ns.smallsoft.co.kr:8051.
ER  -

TY  - JOUR
AU  - Lee, D.G.
AU  - Urbach, J.M.
AU  - Wu, G.
AU  - Liberati, N.T.
AU  - Feinbaum, R.L.
AU  - Miyata, S.
AU  - Diggins, L.T.
AU  - He, J.
AU  - Saucier, M.
AU  - Deziel, E.
AU  - Friedman, L.
AU  - Li, L.
AU  - Grills, G.
AU  - Montgomery, K.
AU  - Kucherlapati, R.
AU  - Rahme, L.G.
AU  - Ausubel, F.M.
TI  - Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.
JO  - Genome Biol.
PY  - 2006
SP  - R90
EP  - R90
VL  - 7
AB  - ABSTRACT: BACKGROUND: Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an
AB  - important opportunistic human pathogen. Generally, the
AB  - acquisition of genes in the form of pathogenicity islands distinguishes
AB  - pathogenic isolates from non-pathogens. We therefore sequenced a highly
AB  - virulent strain of P. aeruginosa, PA14, and compared it to a previously
AB  - sequenced (and less pathogenic) strain, PAO1, to identify novel virulence
AB  - genes. RESULTS: The PA14 and PAO1 genomes are remarkably similar, although
AB  - PA14 has a slightly larger genome (6.5 MB) than PAO1 (6.3 MB). We
AB  - identified 58 PA14 gene clusters that are absent in PAO1 to determine
AB  - which of these genes, if any, contribute to its enhanced virulence in a
AB  - Caenorhabditis elegans pathogenicity model. First, we tested 18 additional
AB  - diverse strains in the C. elegans model and observed a wide range of
AB  - pathogenic potential; however, genotyping these strains using a custom
AB  - microarray showed that the presence of PA14 genes absent in PAO1 did not
AB  - correlate with the virulence of these strains. Second we utilized a
AB  - full-genome non-redundant mutant library of PA14 to identify five genes
AB  - (absent in PAO1) required for C. elegans killing. Surprisingly, although
AB  - these five genes are present in many other P. aeruginosa strains, they do
AB  - not correlate with virulence in C. elegans. CONCLUSIONS: Genes required
AB  - for pathogenicity in one strain of P. aeruginosa are neither required for
AB  - nor predictive of virulence in other strains. We therefore propose that
AB  - virulence in this organism is multifactorial and combinatorial, the result
AB  - of a pool of pathogenicity-related genes that interact in various
AB  - combinations in different genetic backgrounds.
ER  -

TY  - JOUR
AU  - Lee, D.H.
AU  - Jin, S.G.
AU  - Cai, S.
AU  - Chen, Y.
AU  - Pfeifer, G.P.
AU  - O'Connor, T.R.
TI  - Repair of methylation damage in DNA and RNA by mammalian AlkB homologues.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 39448
EP  - 39459
VL  - 280
AB  - Human and Escherichia coli derivatives of AlkB enzymes remove methyl groups from
AB  - 1-methyladenine and 3-methylcytosine in nucleic acids via an
AB  - oxidative mechanism that releases the methyl group as formaldehyde. In
AB  - this report, we demonstrate that the mouse homologues of the
AB  - alpha-ketoglutarate Fe(II) oxygen-dependent enzymes mAbh2 and Abh3 have
AB  - activities comparable to those of their human counterparts. The mAbh2 and
AB  - mAbh3 release modified bases from both DNA and RNA. Comparison of the
AB  - activities of the homogenous ABH2 and ABH3 enzymes demonstrate that these
AB  - activities are shared by both sets of enzymes. An assay for the detection
AB  - of alpha-ketoglutarate Fe(II) dioxygenase activity using an
AB  - oligodeoxyribonucleotide with a unique modification shows activity for all
AB  - four enzymes studied and a loss of activity for eight mutant proteins.
AB  - Steady-state kinetics for removal of methyl groups from DNA substrates
AB  - indicates that the reactions of the proteins are close to the diffusion
AB  - limit. Moreover, mAbh2 or mAbh3 activity increases survival in a strain
AB  - defective in alkB. The mRNAs of AHB2 and ABH3 are expressed most in testis
AB  - for ABH2 and ABH3, whereas expression of the homologous mouse genes is
AB  - different. The mAbh3 is strongly expressed in testis, whereas highest
AB  - expression of mAbh2 is in heart. Other purified human AlkB homologue
AB  - proteins ABH4, ABH6, and ABH7 do not manifest activity. The demonstration
AB  - of mAbh2 and mAbh3 activities and their distributions provide data on
AB  - these mammalian homologues of AlkB that can be used in animal studies.
ER  -

TY  - JOUR
AU  - Lee, D.H.
AU  - Kim, H.R.
AU  - Chung, H.Y.
AU  - Lim, J.G.
AU  - Kim, S.
AU  - Kim, S.K.
AU  - Ku, H.J.
AU  - Kim, H.
AU  - Ryu, S.
AU  - Choi, S.H.
AU  - Lee, J.H.
TI  - Complete genome sequence of Bacillus cereus FORC_005, a food-borne pathogen from  the soy sauce braised fish-cake with quail-egg.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 97
EP  - 97
VL  - 10
AB  - Due to abundant contamination in various foods, the pathogenesis of Bacillus cereus has been
AB  - widely studied in physiological and molecular level. B. cereus
AB  - FORC_005 was isolated from a Korean side dish, soy sauce braised fish-cake with
AB  - quail-egg in South Korea. While 21 complete genome sequences of B. cereus has
AB  - been announced to date, this strain was completely sequenced, analyzed, and
AB  - compared with other complete genome sequences of B. cereus to elucidate the
AB  - distinct pathogenic features of a strain isolated in South Korea. The genomic DNA
AB  - containing a circular chromosome consists of 5,349,617-bp with a GC content of
AB  - 35.29 %. It was predicted to have 5170 open reading frames, 106 tRNA genes, and
AB  - 42 rRNA genes. Among the predicted ORFs, 3892 ORFs were annotated to encode
AB  - functional proteins (75.28 %) and 1278 ORFs were predicted to encode hypothetical
AB  - proteins (748 conserved and 530 non-conserved hypothetical proteins). This genome
AB  - information of B. cereus FORC_005 would extend our understanding of its
AB  - pathogenesis in genomic level for efficient control of its contamination in foods
AB  - and further food poisoning.
ER  -

TY  - JOUR
AU  - Lee, G.H.
AU  - Kumar, S.
AU  - Lee, J.H.
AU  - Chang, D.H.
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Rhee, M.S.
AU  - Lee, D.W.
AU  - Yoon, M.H.
AU  - Kim, B.C.
TI  - Genome Sequence of Oscillibacter ruminantium Strain GH1, Isolated from Rumen of Korean Native Cattle.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6362
EP  - 6362
VL  - 194
AB  - Oscillibacter ruminantium strain GH1 was isolated from the rumen of Korean native cattle
AB  - (HanWoo; Bos taurus coreanae). Here, we present the 3.07-Mb draft genome
AB  - of this strain, which could reveal the presence of certain fiber-specific
AB  - glycoside hydrolases and butyric acid-producing genes.
ER  -

TY  - JOUR
AU  - Lee, G.W.
AU  - Lee, K.J.
AU  - Chae, J.C.
TI  - Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4150
EP  - 4150
VL  - 194
AB  - Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites
AB  - australis on reclaimed land. Here we report the 5.05-Mb draft genome
AB  - sequence of the strain, providing bioinformation about the agronomic benefits of
AB  - this strain, such as multiple traits relevant to plant root colonization and
AB  - plant growth promotion.
ER  -

TY  - JOUR
AU  - Lee, H.
AU  - Kang, S.
AU  - Yim, J.-B.
AU  - Hwang, D.S.
TI  - Identification of hemimethylated DNA binding activity in the seqA mutant.
JO  - Korean J. Biol. Sci.
PY  - 1998
SP  - 351
EP  - 353
VL  - 2
AB  - A 245 bp segment of E. coli chromosomal replication origin, oriC, contains 11 repeats of the
AB  - GATC sequence in which adenine is methylated by Dam methylase.  Newly replicated oriC is
AB  - hemimethylated.  The parental strand of the newly replicated oriC is methylated, but the
AB  - nascent strand is not yet methylated until methylated by Dam methylase.  The hemimethylated
AB  - oriC plays an important role in the regulation of chromosomal replication.  Activity in the
AB  - seqA mutant was identified to bind preferentially to hemimethylated DNA, but not to
AB  - fully-methylated DNA.  This activity may participate in the sequestration of initiation of
AB  - chromosomal replication.
ER  -

TY  - JOUR
AU  - Lee, H.
AU  - Kim, B.J.
AU  - Kim, K.
AU  - Hong, S.H.
AU  - Kook, Y.H.
AU  - Kim, B.J.
TI  - Whole-Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-H4Y, Belonging to INT5 Genotype.
JO  - Genome Announcements
PY  - 2013
SP  - e00006
EP  - e00013
VL  - 1
AB  - Here, we report the draft genome sequence of the clinical strain MOTT-H4Y, grouped previously
AB  - into the INT5 genotype of the 5 genotypes of .
ER  -

TY  - JOUR
AU  - Lee, H.
AU  - Shin, S.C.
AU  - Lee, J.
AU  - Kim, S.J.
AU  - Kim, B.K.
AU  - Hong, S.G.
AU  - Kim, E.H.
AU  - Park, H.
TI  - Genome Sequence of Sphingomonas sp. Strain PAMC 26621, an Arctic-Lichen-Associated Bacterium Isolated from a Cetraria sp.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3030
EP  - 3030
VL  - 194
AB  - The lichen-associated bacterial strain Sphingomonas sp. PAMC 26621 was isolated from an Arctic
AB  - lichen Cetraria sp. on Svalbard Islands. Here we report the draft genome sequence of this
AB  - strain, which could provide novel insights into the molecular principles of lichen-microbe
AB  - interactions.
ER  -

TY  - JOUR
AU  - Lee, H.J.
AU  - Chun, B.H.
AU  - Jeon, H.H.
AU  - Kim, Y.B.
AU  - Lee, S.H.
TI  - Complete Genome Sequence of Bacillus velezensis YJ11-1-4, a Strain with Broad-Spectrum Antimicrobial Activity, Isolated from Traditional Korean Fermented  Soybean Paste.
JO  - Genome Announcements
PY  - 2017
SP  - e01352
EP  - e01317
VL  - 5
AB  - Bacillus velezensis YJ11-1-4 is a strain that exhibits broad-spectrum antimicrobial activity
AB  - against various pathogens. It was isolated from doenjang,
AB  - a traditional Korean fermented soybean paste. The genome comprises a single
AB  - circular chromosome of 4,006,637 bp with 46.42% G+C content without plasmids.
ER  -

TY  - JOUR
AU  - Lee, H.J.
AU  - Lee, S.H.
AU  - Lee, S.S.
AU  - Lee, J.S.
AU  - Kim, Y.
AU  - Kim, S.C.
AU  - Jeon, C.O.
TI  - Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 1317
EP  - 1322
VL  - 64
AB  - A Gram-staining-negative, strictly aerobic, white-colony-forming bacterium, designated strain
AB  - 5-10(T), was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile
AB  - rods or coccoids, showing oxidase- and catalase-positive reactions. Growth was observed at
AB  - 10-37 degrees C (optimum, 30 degrees C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence
AB  - of 0-1.0 % (w/v) NaCl (optimum, 0-0.5 %). The major cellular fatty acids were summed feature 3
AB  - (comprising C16 : 1omega6c and/or C16 : 1omega7c), C16 : 0, C10 : 0 3-OH and summed feature 8
AB  - (comprising C18 : 1omega6c and/or C18 : 1omega7c). The G+C content of the genomic DNA was 69.9
AB  - mol% and the only respiratory quinone detected was ubiquinone 8 (Q-8). Phylogenetic analysis
AB  - based on 16S rRNA gene sequences showed that strain 5-10(T) formed a tight phyletic lineage
AB  - with members of the genus Ramlibacter. Strain 5-10(T) was most closely related to Ramlibacter
AB  - tataouinensis TTB310(T) (97.3 %), but the DNA-DNA relatedness level between the two strains
AB  - was 38.2+/-1.8 %. Based on phenotypic, chemotaxonomic and molecular features, strain 5-10(T)
AB  - was shown to represent a novel species of the genus Ramlibacter, for which the name
AB  - Ramlibacter solisilvae sp. nov. is proposed. The type strain is 5-10(T) ( = KACC 17567(T) =
AB  - JCM 19319(T)). An emended description of the genus Ramlibacter is also proposed.
ER  -

TY  - JOUR
AU  - Lee, H.J.
AU  - Nishi, K.
AU  - Song, J.M.
AU  - Kim, J.S.
TI  - Expression, crystallization and preliminary X-ray diffraction analysis of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2009
SP  - 1271
EP  - 1273
VL  - 65
AB  - Modification (HsdM) and specificity (HsdS) subunits are constituents of an active
AB  - methyltransferase (MTase) of multifunctional type I
AB  - restriction enzymes. To provide a molecular background on HsdM, a
AB  - putative hsdM gene from Vibrio vulnificus YJ016 (HsdM Vv) was cloned
AB  - and the expressed protein was purified and crystallized from 22%(w/v)
AB  - polyethylene glycol 8000, 0.02 M imidazole pH 7.5 and 5 mM
AB  - beta-mercaptoethanol. Diffraction data were collected to 1.86 angstrom
AB  - resolution using synchrotron radiation. The crystal belonged to the
AB  - tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell
AB  - parameters a = b = 78.9, c = 165.8 angstrom. With one molecule in the
AB  - asymmetric unit, the crystal volume per unit protein weight was 2.12
AB  - angstrom(3) Da(-1), with a solvent content of 42%.
ER  -

TY  - JOUR
AU  - Lee, H.S.
AU  - Bae, S.S.
AU  - Kim, M.S.
AU  - Kwon, K.K.
AU  - Kang, S.G.
AU  - Lee, J.H.
TI  - Complete Genome Sequence of Hyperthermophilic Pyrococcus sp. Strain NA2, Isolated from Deep-Sea Hydrothermal Vent Area.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3666
EP  - 3667
VL  - 193
AB  - Pyrococcus sp. NA2, isolated from a deep-sea hydrothermal vent sample, is a novel marine
AB  - hyperthermophilic archaeon to grow optimally at 93 degrees C. The complete genome sequence of
AB  - the strain contains all genes for
AB  - tricarboxylic acid cycle except for succinate dehydrogease/fumarate reductase, but it doesn't
AB  - encode proteins involved in polysaccharide utilization.
ER  -

TY  - JOUR
AU  - Lee, H.S.
AU  - Kang, S.G.
AU  - Bae, S.S.
AU  - Lim, J.K.
AU  - Cho, Y.
AU  - Kim, Y.J.
AU  - Jeon, J.H.
AU  - Cha, S.S.
AU  - Kwon, K.K.
AU  - Kim, H.T.
AU  - Park, C.J.
AU  - Lee, H.W.
AU  - Kim, S.I.
AU  - Chun, J.
AU  - Colwell, R.R.
AU  - Kim, S.J.
AU  - Lee, J.H.
TI  - The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism.
JO  - J. Bacteriol.
PY  - 2008
SP  - 7491
EP  - 7499
VL  - 190
AB  - Members of the genus Thermococcus, sulfur-reducing
AB  - hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent
AB  - systems and are considered to play a significant role in the microbial consortia. We present
AB  - the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from
AB  - a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of
AB  - genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth
AB  - on peptides, amino acids, or sugars. More interesting was the discovery that the genome
AB  - encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation
AB  - of CO to CO(2), thereby providing a mechanistic basis for growth with CO as a substrate. This
AB  - lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose
AB  - 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy
AB  - supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the
AB  - surrounding of hydrothermal vents, providing the first genomic evidence for the
AB  - carboxydotrophy in Thermococcus.
ER  -

TY  - JOUR
AU  - Lee, H.S.
AU  - Kang, S.G.
AU  - Kwon, K.K.
AU  - Lee, J.H.
AU  - Kim, S.J.
TI  - Genome Sequence of the Algicidal Bacterium Kordia algicida OT-1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4031
EP  - 4032
VL  - 193
AB  - Kordia algicida OT-1 is an algicidal bacterium against the bloom-forming microalgae. The
AB  - genome sequence of K. algicida revealed a number of
AB  - interesting features, including degradation of macromolecules, the
AB  - biosynthesis of carotenoid pigment and secondary metabolites, and the
AB  - capacity for gliding motility, which might facilitate the understanding of
AB  - algicidal mechanisms.
ER  -

TY  - JOUR
AU  - Lee, H.W.
AU  - Kim, D.W.
AU  - Lee, M.H.
AU  - Kim, B.Y.
AU  - Cho, Y.J.
AU  - Yim, K.J.
AU  - Song, H.S.
AU  - Rhee, J.K.
AU  - Seo, M.J.
AU  - Choi, H.J.
AU  - Choi, J.S.
AU  - Lee, D.G.
AU  - Yoon, C.
AU  - Nam, Y.D.
AU  - Roh, S.W.
TI  - Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius  type strain D43(T) isolated from fermented seafood.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 53
EP  - 53
VL  - 10
AB  - An extremely halophilic archaeon, Haladaptatus cibarius D43(T), was isolated from traditional
AB  - Korean salt-rich fermented seafood. Strain D43(T) shows the highest 16S rRNA gene sequence
AB  - similarity (98.7 %) with Haladaptatus litoreus RO1-28(T),  is Gram-negative staining, motile,
AB  - and extremely halophilic. Despite potential industrial applications of extremely halophilic
AB  - archaea, their genome characteristics remain obscure. Here, we describe the whole genome
AB  - sequence and annotated features of strain D43(T). The 3,926,724 bp genome includes 4,092
AB  - protein-coding and 57 RNA genes (including 6 rRNA and 49 tRNA genes) with an average G + C
AB  - content of 57.76 %.
ER  -

TY  - JOUR
AU  - Lee, I.M.
AU  - Shao, J.
AU  - Bottner-Parker, K.D.
AU  - Gundersen-Rindal, D.E.
AU  - Zhao, Y.
AU  - Davis, R.E.
TI  - Draft Genome Sequence of 'Candidatus Phytoplasma pruni' Strain CX, a Plant-Pathogenic Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01117
EP  - e01115
VL  - 3
AB  - 'Candidatus Phytoplasma pruni' strain CX, belonging to subgroup 16SrIII-A, is a
AB  - plant-pathogenic bacterium causing economically important diseases in many fruit  crops. Here,
AB  - we report the draft genome sequence, which consists of 598,508 bases, with a G+C content of
AB  - 27.21 mol%.
ER  -

TY  - JOUR
AU  - Lee, J.
AU  - Cho, A.
AU  - Yang, J.Y.
AU  - Woo, J.
AU  - Lee, H.K.
AU  - Hong, S.G.
AU  - Kim, O.S.
TI  - Complete Genome Sequence of Cryobacterium arcticum Strain PAMC 27867, Isolated from a Sedimentary Rock Sample in Northern Victoria Land, Antarctica.
JO  - Genome Announcements
PY  - 2016
SP  - e00885
EP  - e00816
VL  - 4
AB  - Cryobacterium arcticum PAMC 27867, a psychrotolerant, Gram-positive bacterium, was isolated
AB  - from a sedimentary rock sample collected at Eureka Spurs in northern
AB  - Victoria Land, Antarctica. Here, we report the genome sequence of C. arcticum
AB  - PAMC 27867.
ER  -

TY  - JOUR
AU  - Lee, J.
AU  - Jang, Y.-S.
AU  - Han, M.-J.
AU  - Kim, J.Y.
AU  - Lee, S.Y.
TI  - Deciphering Clostridium tyrobutyricum metabolism based on the whole genome sequence and proteome analyses.
JO  - MBio
PY  - 2016
SP  - e00743
EP  - e00716
VL  - 7
AB  - Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces
AB  - butyric acid and is considered
AB  - a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the
AB  - genetic and metabolic
AB  - characteristics of this strain, however, little progress has been made in metabolic
AB  - engineering of this strain. Here we report
AB  - the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a
AB  - 3.07-Mbp chromosome
AB  - and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces
AB  - butyrate from butyrylcoenzyme
AB  - A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from
AB  - Clostridium acetobutylicum,
AB  - which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse
AB  - transcription-PCR
AB  - (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and
AB  - fed-batch fermentation. In addition,
AB  - the changes in protein expression levels during the course of batch fermentations on glucose
AB  - were examined by shotgun
AB  - proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic
AB  - and fermentative pathways
AB  - in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy
AB  - conservation
AB  - mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in
AB  - C. acetobutylicum, were
AB  - identified. Such features explain why this organism can produce butyric acid to a much higher
AB  - titer and better tolerate
AB  - toxic metabolites. This study presenting the complete genome sequence, global protein
AB  - expression profiles, and genomebased
AB  - metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable
AB  - in designing strategies
AB  - for metabolic engineering of this strain.
AB  - IMPORTANCE Bio-based production of chemicals from renewable biomass has become increasingly
AB  - important due to our concerns
AB  - on climate change and other environmental problems. C. tyrobutyricum has been used for
AB  - efficient butyric acid production.
AB  - In order to further increase the performance and expand the capabilities of this strain toward
AB  - production of other chemicals,
AB  - metabolic engineering needs to be performed. For this, better understanding on the metabolic
AB  - and physiological
AB  - characteristics of this bacterium at the genome level is needed. This work reporting the
AB  - results of complete genomic and proteomic
AB  - analyses together with new insights on butyric acid biosynthetic pathway and energy
AB  - conservation will allow development
AB  - of strategies for metabolic engineering of C. tyrobutyricum for the bio-based production of
AB  - various chemicals in addition
AB  - to butyric acid.
ER  -

TY  - JOUR
AU  - Lee, J.
AU  - Kwon, M.
AU  - Yang, J.Y.
AU  - Woo, J.
AU  - Lee, H.K.
AU  - Hong, S.G.
AU  - Kim, O.S.
TI  - Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample.
JO  - Genome Announcements
PY  - 2016
SP  - e00704
EP  - e00716
VL  - 4
AB  - Psychrobacter alimentarius PAMC 27889, a Gram-negative, psychrophilic bacterium,  was isolated
AB  - from an Antarctic rock sample. Here, we report the complete genome
AB  - of P. alimentarius PAMC 27889, which has the nonmevalonate methylerythritol
AB  - phosphate pathway of terpenoid biosynthesis and a complete gene cluster for
AB  - benzoate degradation.
ER  -

TY  - JOUR
AU  - Lee, J.
AU  - Roh, S.W.
AU  - Whon, T.W.
AU  - Shin, N.R.
AU  - Kim, Y.O.
AU  - Bae, J.W.
TI  - Genome Sequence of Strain TW15, a Novel Member of the Genus Ruegeria Belonging to the Marine Roseobacter Clade.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3401
EP  - 3402
VL  - 193
AB  - Ruegeria sp. TW15, which belongs to the family Rhodobacteraceae, was isolated from an ark clam
AB  - in the South Sea of Korea. Here is presented the
AB  - draft genome sequence of Ruegeria sp. TW15 (4,490,771 bp, with a G+C
AB  - content of 55.7%), a member of the marine Roseobacter clade, which
AB  - comprises up to 20% of bacterioplankton in the coastal and oceanic mixed
AB  - layer.
ER  -

TY  - JOUR
AU  - Lee, J.
AU  - Shin, S.C.
AU  - Kim, S.J.
AU  - Kim, B.K.
AU  - Hong, S.G.
AU  - Kim, E.H.
AU  - Park, H.
AU  - Lee, H.
TI  - Draft Genome Sequence of a Sphingomonas sp., an Endosymbiotic Bacterium Isolated  from an Arctic Lichen Umbilicaria sp.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3010
EP  - 3011
VL  - 194
AB  - Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on
AB  - the Svalbard Islands. Here we present the draft genome
AB  - sequence of this strain, which represents a valuable resource for understanding
AB  - the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in
AB  - extreme environments.
ER  -

TY  - JOUR
AU  - Lee, J.-H.
AU  - Shin, H.
AU  - Kim, H.
AU  - Ryu, S.
TI  - Complete Genome Sequence of Salmonella Bacteriophage SPN3US.
JO  - J. Virol.
PY  - 2011
SP  - 13470
EP  - 13471
VL  - 85
AB  - Salmonella bacteriophage SPN3US was isolated from a chicken fecal sample. It is a virulent
AB  - phage belonging
AB  - to the Myoviridae family and showing effective inhibition of Salmonella enterica and a few
AB  - Escherichia coli
AB  - O157:H7 strains. Here we announce the completely sequenced first genome of a Salmonella phage
AB  - using flagella
AB  - as receptors. It is the largest genome among Salmonella phages sequenced to date, and major
AB  - findings from its
AB  - annotation are described.
ER  -

TY  - JOUR
AU  - Lee, J.-I.
AU  - Yang, C.-H.
TI  - The purification and characterization of PvuII, restriction endonuclease.
JO  - Korean Biochem. J.
PY  - 1984
SP  - 357
EP  - 364
VL  - 17
AB  - Restriction endonuclease PvuII has been purified from Proteus vulgaris, aerobic
AB  - bacterium, by streptomycin sulfate fractionation, (NH4)SO4 precipitation, gel
AB  - filtration on Sephadex G-150, Phosphocellulose (P11) chromatography, and
AB  - DEAE-cellulose chromatography.
ER  -

TY  - JOUR
AU  - Lee, J.-T.
AU  - Cho, T.-J.
AU  - Lim, J.-Y.
TI  - Characterization of a restriction endonuclease AspJI from Alcaligenes sp. J-482.
JO  - Korean J. Microbiol.
PY  - 1994
SP  - 285
EP  - 290
VL  - 32
AB  - About 500 bacterial and fungal strains from a wide variety of natural habitats were screened
AB  - for a new type II restriction endonuclease.  Among the 500 species, we selected one species
AB  - that produced a new restriction endonuclease.  This strain has an optimum temperature of 30oC
AB  - for growth.  Morphological, cultural, and physiological characteristics were examined for
AB  - identification of the isolated strain J-482.  This strain was found to belong to the genus
AB  - Alcaligenes.  The restriction endonuclease was named as AspJI and partially purified from
AB  - Alcaligenes sp. J-482 by DEAE-Sephadex A-50 column chromatography and gel filtration.  Most of
AB  - other nucleases were removed by the purification steps.  The AspJI has a substrate
AB  - specificity to lambda DNA, pBR322 and Adenovirus-2 DNA.  For its maximal activity, the
AB  - isolated enzyme requires MgCl2, which should be at least 12.5  mM and it does not need any
AB  - other cofactors.  It is maximally active in the absence of NaCl and is completely inactivated
AB  - at 100 mM NaCl.  The pH and temperature optima for activity were pH 7.5 and 37oC,
AB  - respectively.  The DNA fragments generated by digesting lambda DNA, pBR322, and Adenovirus-2
AB  - DNA with AspJI were the same as that produced by AatII.  This suggests that AspJI is an
AB  - isoschizomer of AatII.
ER  -

TY  - JOUR
AU  - Lee, J.C.
AU  - Kim, D.S.
AU  - Moon, D.C.
AU  - Lee, J.H.
AU  - Kim, M.J.
AU  - Lee, S.M.
AU  - Lee, Y.S.
AU  - Kang, S.W.
AU  - Lee, E.J.
AU  - Kang, S.S.
AU  - Lee, E.
AU  - Hyun, S.H.
TI  - Prediction of bacterial proteins carrying a nuclear localization signal and nuclear targeting of HsdM from Klebsiella pneumoniae.
JO  - J. Microbiol.
PY  - 2009
SP  - 641
EP  - 645
VL  - 47
AB  - Nuclear targeting of bacterial proteins is an emerging pathogenic mechanism whereby bacterial
AB  - proteins can interact with nuclear
AB  - molecules and alter the physiology of host cells. The fully sequenced
AB  - bacterial genome can predict proteins that target the nuclei of host
AB  - cells based on the presence of nuclear localization signal (NLS). In
AB  - the present study, we predicted bacterial proteins with the NLS
AB  - sequences from Klebsiella pneumoniae by bioinformatic analysis, and 13
AB  - proteins were identified as carrying putative NLS sequences. Among
AB  - them, HsdM, a subunit of KpnAl that is a type I
AB  - restriction-modification system found in K. pneumoniae, was selected
AB  - for the experimental proof of nuclear targeting in host cells. HsdM
AB  - carried the NLS sequences, (7)KKAKAKK(13), in the N-terminus. A
AB  - transient expression of HsdM-EGFP in COS-1 cells exhibited exclusively
AB  - a nuclear localization of the fusion proteins, whereas the fusion
AB  - proteins of HsdM with substitutions in residues lysine to alanine in
AB  - the NLS sequences, (7)AAAKAAA(13), were localized in the cytoplasm.
AB  - HsdM was co-localized with importin o in the nuclei of host cells.
AB  - Recombinant HsdM alone methylated the eukaryotic DNA in vitro assay.
AB  - Although HsdM tested in this study has not been considered to be a
AB  - virulence factor, the prediction of NLS motifs from the full sequenced
AB  - genome of bacteria extends our knowledge of functional genomics to
AB  - understand subcellular targeting of bacterial proteins.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Bae, J.W.
AU  - Chun, J.
TI  - Draft Genome Sequence of Weissella koreensis KCTC 3621T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5711
EP  - 5712
VL  - 194
AB  - Weissella koreensis is a Gram-positive, rod-shaped, nonmotile, and facultative anaerobic
AB  - species belonging to the lactic acid bacteria (LAB). The members of
AB  - this species have been repeatedly isolated from kimchi (a traditional Korean
AB  - fermented food) and are known for their beneficial effects on human and animal
AB  - intestinal microflora through producing various clinically important amino acids
AB  - such as gamma-aminobutyric acid and ornithine. Here we report the genome sequence
AB  - of the type strain of W. koreensis (KCTC 3621(T)) to provide taxonomic and
AB  - functional insights into the species.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Chae, J.P.
AU  - Lee, J.Y.
AU  - Lim, J.S.
AU  - Kim, G.B.
AU  - Ham, J.S.
AU  - Chun, J.
AU  - Kang, D.K.
TI  - Genome Sequence of Lactobacillus johnsonii PF01, Isolated from Piglet Feces.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5030
EP  - 5031
VL  - 193
AB  - Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was
AB  - isolated from a fecal sample of piglet. The
AB  - strain adhered specifically to the duodenal and jejunal epithelial cells
AB  - of the piglet and had high bile resistance activity. Here, we report a
AB  - genomic sequence of L. johnsonii PF01.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Cheon, I.S.
AU  - Shim, B.S.
AU  - Kim, D.W.
AU  - Kim, S.W.
AU  - Chun, J.
AU  - Song, M.
TI  - Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5722
EP  - 5723
VL  - 194
AB  - Klebsiella pneumoniae is a Gram-negative, rod-shaped, nonmotile, and opportunistic pathogenic
AB  - species with clinical importance. It is a part of
AB  - natural flora of humans and animals. Here we report the draft genome sequence of
AB  - the type strain of Klebsiella pneumoniae subsp. pneumoniae (DSM 30104(T)) to
AB  - provide taxonomic and functional insights into the species.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Choi, Y.
AU  - Shin, H.
AU  - Lee, J.
AU  - Ryu, S.
TI  - Complete Genome Sequence of Cronobacter sakazakii Temperate Bacteriophage phiES15.
JO  - J. Virol.
PY  - 2012
SP  - 7713
EP  - 7714
VL  - 86
AB  - While most phage genome studies have been focused on the virulent phages, the
AB  - inducible temperate bacteriophage genome study provides more detailed information
AB  - about the interaction between the host strain and the phage. To study this
AB  - interaction in detail, UV-induced phiES15 bacteriophage was isolated from the
AB  - host strain Cronobacter sakazakii ES15 and its genome was completely sequenced.
AB  - Here we announce the genome sequence of phiES15 and report major findings from
AB  - the annotation.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Karamychev, V.N.
AU  - Kozyavkin, S.A.
AU  - Mills, D.
AU  - Pavlov, A.R.
AU  - Pavlova, N.V.
AU  - Polouchine, N.N.
AU  - Richardson, P.M.
AU  - Shakhova, V.V.
AU  - Slesarev, A.I.
AU  - Weimer, B.
AU  - O'Sullivan, D.J.
TI  - Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.
JO  - BMC Genomics
PY  - 2008
SP  - 247
EP  - 247
VL  - 9
AB  - BACKGROUND: Bifidobacteria are frequently proposed to be associated with good intestinal
AB  - health primarily because of their overriding dominance in
AB  - the feces of breast fed infants. However, clinical feeding studies with
AB  - exogenous bifidobacteria show they don't remain in the intestine,
AB  - suggesting they may lose competitive fitness when grown outside the gut.
AB  - RESULTS: To further the understanding of genetic attenuation that may be
AB  - occurring in bifidobacteria cultures, we obtained the complete genome
AB  - sequence of an intestinal isolate, Bifidobacterium longum DJO10A that was
AB  - minimally cultured in the laboratory, and compared it to that of a culture
AB  - collection strain, B. longum NCC2705. This comparison revealed colinear
AB  - genomes that exhibited high sequence identity, except for the presence of
AB  - 17 unique DNA regions in strain DJO10A and six in strain NCC2705. While
AB  - the majority of these unique regions encoded proteins of diverse function,
AB  - eight from the DJO10A genome and one from NCC2705, encoded gene clusters
AB  - predicted to be involved in diverse traits pertinent to the human
AB  - intestinal environment, specifically oligosaccharide and polyol
AB  - utilization, arsenic resistance and lantibiotic production. Seven of these
AB  - unique regions were suggested by a base deviation index analysis to have
AB  - been precisely deleted from strain NCC2705 and this is substantiated by a
AB  - DNA remnant from within one of the regions still remaining in the genome
AB  - of NCC2705 at the same locus. This targeted loss of genomic regions was
AB  - experimentally validated when growth of the intestinal B. longum in the
AB  - laboratory for 1,000 generations resulted in two large deletions, one in a
AB  - lantibiotic encoding region, analogous to a predicted deletion event for
AB  - NCC2705. A simulated fecal growth study showed a significant reduced
AB  - competitive ability of this deletion strain against Clostridium difficile
AB  - and E. coli. The deleted region was between two IS30 elements which were
AB  - experimentally demonstrated to be hyperactive within the genome. The other
AB  - deleted region bordered a novel class of mobile elements, termed mobile
AB  - integrase cassettes (MIC) substantiating the likely role of these elements
AB  - in genome deletion events. CONCLUSION: Deletion of genomic regions, often
AB  - facilitated by mobile elements, allows bifidobacteria to adapt to
AB  - fermentation environments in a very rapid manner (2 genome deletions per
AB  - 1,000 generations) and the concomitant loss of possible competitive
AB  - abilities in the gut.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Koh, H.Y.
AU  - Lee, S.G.
AU  - Doyle, S.
AU  - Christner, B.C.
AU  - Kim, H.J.
TI  - Draft Genome Sequence of Paenisporosarcina sp. Strain TG-20, a Psychrophilic Bacterium Isolated from the Basal Ice of Taylor Glacier.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6636
EP  - 6636
VL  - 194
AB  - We report the draft genome sequence of Paenisporosarcina sp. strain TG-20, which  is 4.12 Mb
AB  - in size and consists of 4,071 protein-coding genes and 76 RNA genes.
AB  - The genome sequence of Paenisporosarcina sp. TG-20 may provide useful information
AB  - about molecular adaptations that enhance survival in icy subsurface environments.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Rhee, M.S.
AU  - Kumar, S.
AU  - Lee, G.H.
AU  - Chang, D.H.
AU  - Kim, D.S.
AU  - Choi, S.H.
AU  - Lee, D.W.
AU  - Yoon, M.H.
AU  - Kim, B.C.
TI  - Genome Sequence of Methanobrevibacter sp. Strain JH1, Isolated from Rumen of Korean Native Cattle.
JO  - Genome Announcements
PY  - 2013
SP  - e00002
EP  - e00013
VL  - 1
AB  - The sp. strain JH1 was isolated from the rumen of Korean native cattle (HanWoo; ). Here, we
AB  - provide a 2.06-Mb draft genome sequence of strain JH1 that might
AB  - provide more information about the lifestyle of rumen methanogens and about the
AB  - genes and proteins that can be targeted to curb methane emissions.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Shin, H.
AU  - Choi, Y.
AU  - Ryu, S.
TI  - Complete genome sequence analysis of bacterial-flagellum-targeting bacteriophage chi.
JO  - Arch. Virol.
PY  - 2013
SP  - 2179
EP  - 2183
VL  - 158
AB  - Bacteriophage chi is a well-known phage that infects pathogens such as E. coli,
AB  - Salmonella, and Serratia via bacterial flagella. To further understand its
AB  - host-phage interaction and infection mechanism via host flagella, the genome was
AB  - completely sequenced and analyzed. The phage genome contains 59,407-bp-length DNA
AB  - with a GC content of 56.51 %, containing 75 open reading frames (ORFs) with no
AB  - tRNA genes. Its annotation and functional analysis revealed that chi is
AB  - evolutionarily very closely related to Enterobacter phage Enc34 and Providencia
AB  - phage Redjac. However, most of the annotated genes encode hypothetical proteins,
AB  - indicating that further genomic study of phage chi is required to elucidate the
AB  - bacterial-flagellum-targeting infection mechanism of phage chi.
ER  -

TY  - JOUR
AU  - Lee, J.H.
AU  - Valeriano, V.D.
AU  - Shin, Y.R.
AU  - Chae, J.P.
AU  - Kim, G.B.
AU  - Ham, J.S.
AU  - Chun, J.
AU  - Kang, D.K.
TI  - Genome Sequence of Lactobacillus mucosae LM1, Isolated from Piglet Feces.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4766
EP  - 4766
VL  - 194
AB  - Lactobacillus mucosae LM1, isolated from stool samples of a healthy piglet, displays good in
AB  - vitro mucin adhesion and antimicrobial activity against
AB  - pathogenic bacteria. To elucidate its antimicrobial effects and to find its
AB  - epithelial cell and mucin adhesion genes, the genomic sequence of L. mucosae LM1
AB  - was investigated.
ER  -

TY  - JOUR
AU  - Lee, J.J.
AU  - Srinivasan, S.
AU  - Lim, S.
AU  - Joe, M.
AU  - Im, S.
AU  - Bae, S.I.
AU  - Park, K.R.
AU  - Han, J.H.
AU  - Park, S.H.
AU  - Joo, B.M.
AU  - Park, S.J.
AU  - Kim, M.K.
TI  - Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.
JO  - Curr. Microbiol.
PY  - 2014
SP  - 286
EP  - 291
VL  - 69
AB  - A Gram-negative, short-rod-shaped bacterial strain with gliding motility,
AB  - designated as DG5A(T), was isolated from a rice field soil in South Korea.
AB  - Phylogenic analysis using 16S rRNA gene sequence of the new isolate showed that
AB  - strain DG5A(T) belong to the genus Spirosoma in the family Spirosomaceae, and the
AB  - highest sequence similarities were 95.5 % with Spirosoma linguale DSM 74(T), 93.4
AB  - % with Spirosoma rigui WPCB118(T), 92.8 % with Spirosoma luteum SPM-10(T), 92.7 %
AB  - with Spirosoma spitsbergense SPM-9(T), and 91.9 % with Spirosoma panaciterrae
AB  - Gsoil 1519(T). Strain DG5A(T) revealed resistance to gamma and UV radiation.
AB  - Chemotaxonomic data showed that the most abundant fatty acids were summed feature
AB  - C(16:1) omega7c/C(16:1) omega6c (36.90 %), C(16:1) omega5c (29.55 %), and
AB  - iso-C(15:0) (14.78 %), and the major polar lipid was phosphatidylethanolamine
AB  - (PE). The DNA G+C content of strain DG5A(T) was 49.1 mol%. Together, the
AB  - phenotypic, phylogenetic, and chemotaxonomic data supported that strain DG5A(T)
AB  - presents a novel species of the genus Spirosoma, for which the name Spirosoma
AB  - radiotolerans sp. nov., is proposed. The type strain is DG5A(T) (=KCTC 32455(T) =
AB  - JCM19447(T)).
ER  -

TY  - JOUR
AU  - Lee, J.Y.H.
AU  - Monk, I.R.
AU  - Pidot, S.J.
AU  - Singh, S.
AU  - Chua, K.Y.L.
AU  - Seemann, T.
AU  - Stinear, T.P.
AU  - Howden, B.P.
TI  - Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis.
JO  - Microbial Genomics
PY  - 2016
SP  - e000077
EP  - e000077
VL  - 2
AB  - Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage
AB  - is frequently multidrug-resistant and accounts for most of the
AB  - clinical disease worldwide. However, there are no publically available, closed
AB  - ST2 genomes and pathogenesis studies have not focused on these strains. We report
AB  - the complete genome and methylome of BPH0662, a multidrug-resistant,
AB  - hospital-adapted, ST2 S. epidermidis, and describe the correlation between
AB  - resistome and phenotype, as well as demonstrate its relationship to publically
AB  - available, international ST2 isolates. Furthermore, we delineate the methylome
AB  - determined by the two type I restriction modification systems present in BPH0662
AB  - through heterologous expression in Escherichia coli, allowing the assignment of
AB  - each system to its corresponding target recognition motif. As the first, to our
AB  - knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable
AB  - reference for future genomic studies of this clinically relevant lineage.
AB  - Defining the methylome and the construction of these E. coli hosts provides the
AB  - foundation for the development of molecular tools to bypass restriction
AB  - modification systems in this lineage that has hitherto proven intractable.
ER  -

TY  - JOUR
AU  - Lee, K.
AU  - Yi, H.
AU  - Cho, Y.J.
AU  - Jang, J.
AU  - Hur, H.G.
AU  - Chun, J.
TI  - Draft Genome Sequence of Escherichia coli AI27, a Porcine Isolate Belonging to Phylogenetic Group B1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6640
EP  - 6641
VL  - 194
AB  - Escherichia coli AI27 is a putatively commensal strain isolated from feces of a pig. Here we
AB  - report the draft genome sequence of E. coli AI27. This is the first
AB  - porcine strain in the phylogenetic group B1 whose genome sequence has been
AB  - determined.
ER  -

TY  - JOUR
AU  - Lee, K.-F.
AU  - Kam, K.-M.
AU  - Shaw, P.-C.
TI  - A bacterial methyltransferase M.EcoHK31I requires two proteins for in vitro methylation.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 103
EP  - 108
VL  - 23
AB  - The genes encoding the EcoHK31I restriction-modification (R-M) system were isolated from a
AB  - clinically-isolated Escherichia coli strain HK31. The entire R-M system of EcoHK31I is located
AB  - in a 2.1 kb fragment. R.EcoHK31I is an isoschizomer of EaeI which recognizes and cleaves
AB  - Y/GGCCR. M.EcoHK31I consists of two polypeptides alpha and beta with sizes 309 and 176 aa,
AB  - respectively. Polypeptide beta is encoded within an alternative reading frame of polypeptide
AB  - alpha. All the conserved motifs in mC5-MTases can be found in polypeptide alpha except motif
AB  - IX which is present in polypeptide beta. Polypeptides alpha and beta were separately
AB  - synthesized in a T7 promoter controlled over-expression system and in vitro methylation
AB  - occurred only when the two extracts were mixed and thus confirms that two polypeptides are
AB  - required for methylation.
ER  -

TY  - JOUR
AU  - Lee, K.-F.
AU  - Liaw, Y.-C.
AU  - Shaw, P.-C.
TI  - Overproduction, purification and characterization of M.EcoHK31I, a bacterial methyltransferase with two polypeptides.
JO  - Biochem. J.
PY  - 1996
SP  - 321
EP  - 326
VL  - 314
AB  - The two overlapping genes coding for EcoHK31I methyltransferase have previously been cloned,
AB  - sequenced and expressed.  Here we describe protocols developed to purify polypeptides alpha
AB  - and beta together or separately, to apparent homogeneity by various chromatographic media.
AB  - M.EcoHK31I is a heterodimer with a native molecular mass of 61 kDa.  Its specific activity
AB  - towards non-methylated lambda DNA was 3.0 x 105 units per mg of protein.  The respective
AB  - denatured molecular masses of polypeptides alpha and beta were 38 and 23 kDa, and their pI
AB  - values were 8.7 and 6.8.  Initial rate kinetic parameters of the native enzyme were 2.0 nM,
AB  - 0.58 uM and 3 min-1 for Km DNA, Km AdoMet and kcat, respectively, where AdoMet stands for
AB  - S-adenosyl-L-methionine.  Fully active enzyme was reconstituted by co-purifying the two
AB  - separately synthesized polypeptides, and activity assays confirmed our previous finding that
AB  - two polypeptides were needed to methylate substrate DNA.
ER  -

TY  - JOUR
AU  - Lee, K.-F.
AU  - Shaw, P.-C.
AU  - Picone, S.J.
AU  - Wilson, G.G.
AU  - Lunnen, K.D.
TI  - Sequence comparison of the EcoHK31I and EaeI restriction-modification systems suggests an intergenic transfer of genetic material.
JO  - Biol. Chem.
PY  - 1998
SP  - 437
EP  - 441
VL  - 379
AB  - The genes coding for the EcoHK31I and EaeI restriction-modification systems from Escherichia
AB  - coli strain HK31 and Enterobacter aerogenes, respectively, have been cloned and sequenced.
AB  - Both ENases recognize and cleave Y/GGCCR leaving 4 nucleotide 5'-protruding ends, while the
AB  - MTases modify the internal cytosine.  The systems were isolated on a 2.3 kb AseI fragment for
AB  - EcoHK31I, and a 4.6 kb HindIII fragment for EaeI.  The R and M genes of both systems converge
AB  - and overlap by 14 nucleotides.  Previously, we found that M.EcoHK31I consisted of two
AB  - subunits, (alpha and beta), with the beta subunit being translated from an alternative open
AB  - reading frame within the gene encoding the alpha subunit.  Sequence comparison between the
AB  - EcoHK31I and EaeI systems reveals striking similarity.  The aeaIM gene also encodes alpha and
AB  - beta polypeptides of 309 and 176 amino acids which share 95% and 97% identity, respectively,
AB  - with those of ecoHK31IM.  eCoHK31IR and aeaIR encode proteins of 318 and 315 aa, respectively,
AB  - which share 92% identity but are otherwise unique in the GenBank database.  The EaeI and the
AB  - EcoHK31I R-M systems were found to be flanked by genes coding for integrases.  It is possible
AB  - that these integrases have facilitated the transfer of this system among different bacterial
AB  - species.
ER  -

TY  - JOUR
AU  - Lee, K.-F.
AU  - Shi, S.-D.
AU  - Kam, K.-M.
AU  - Shaw, P.-C.
TI  - Restriction endonuclease from thermophilic bacterial species III.  Isolation and characterization of BsiHKAI.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 921
EP  - 921
VL  - 20
AB  - BsiHKAI is a type II restriction endonuclease from a Bacillus
AB  - stearothermophilus strain isolated from soil.  BsiHKAI in 1l culture (4.7 g wet
AB  - cells) was purified by a DEAE-sephacel column (30 ml bed volume).  Enzyme
AB  - eluted at about 0.3 M NaCl was dialysed against buffer A (1) and loaded onto a
AB  - heparin column (8 ml bed volume).  Enzyme eluted at 0.4 - 0.5 M NaCl was
AB  - dialysed against buffer B (1) and loaded onto an FPLC Mono Q anion exchange
AB  - column.  Enzyme was eluted at 0.3 - 0.4 M NaCl. The purified enzyme was used to
AB  - digest various DNA with known sequences (Fig. 1).  The sizes and numbers of
AB  - fragments produced are identical to those cleaved by mesophilic enzyme HgiAI
AB  - which recognizes 5'G(AT)GC(AT)C3' (2).  The cleavage site of BsiHKA I was
AB  - determined according to (3) using pUC18 DNA as the template and a 17 mer
AB  - oligonucleotide with sequence 5'CAGCACTGACCCTTTTG 3' as the primer.  The primer
AB  - was annealed to position 359-375 of the denatured pUC18 DNA and was extended
AB  - through the BsiHKAI site at position 444.  Figure 2 shows that the cleavage
AB  - product of reaction I comigrates with the band corresponding to nucleotide T in
AB  - the sequence GAGCTC and reaction II comigrates with the band corresponding to
AB  - the first G nucleotide.  Therefore, BsiHKAI recognizes and cleaves
AB  - 5'G(AT)GC(AT)!C3'.  The optimal buffer for this enzyme was medium salt (4) and
AB  - optimal reaction temperature 60C.
ER  -

TY  - JOUR
AU  - Lee, K.C.
AU  - Morgan, X.C.
AU  - Power, J.F.
AU  - Dunfield, P.F.
AU  - Huttenhower, C.
AU  - Stott, M.B.
TI  - Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 101
EP  - 101
VL  - 10
AB  - Strain K22(T) is the type species of the recently- described genus Pyrinomonas, in subdivision
AB  - 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014;
AB  - 64(1):220-7). It was isolated from geothermally-heated soil from Mt. Ngauruhoe,
AB  - New Zealand, using low-nutrient medium. P. methylaliphatogenes K22(T) has a
AB  - chemoheterotrophic metabolism; it can hydrolyze a limited range of simple
AB  - carbohydrates and polypeptides. Its cell membrane is dominated by iso-branching
AB  - fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether
AB  - lipids. It is obligately aerobic, thermophilic, moderately acidophilic, and
AB  - non-spore-forming. The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a
AB  - G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding
AB  - RNA genes. Genomic analysis was consistent with nutritional requirements; in
AB  - particular, the identified transporter classes reflect the oligotrophic nature of
AB  - this strain.
ER  -

TY  - JOUR
AU  - Lee, K.F.
AU  - Ling, J.M.-L.
AU  - Kam, K.-M.
AU  - Clark, D.R.
AU  - Shaw, P.-C.
TI  - Restriction endonucleases in clinical isolates of Shigella spp.
JO  - J. Med. Microbiol.
PY  - 1997
SP  - 949
EP  - 952
VL  - 46
AB  - Thirteen restriction endonuclease-containing strains were isolated from a collection of 186
AB  - clinical isolates of Shigella spp.  Among these, eight and five isolates carried isoschizomers
AB  - of EcoRII and NciI, respectively.  The former restriction-modification system was homologous
AB  - to that of EcoRII and was located on plasmids with sizes of 46.6 or 55.6 kb.  Isolates
AB  - producing NciI isoschizomers contained a 5.7-kb nontransferable plasmid.  Together with
AB  - antimicrobial susceptibility tests and plasmid profile studies, it is concluded that these two
AB  - R-M systems are not widely spread but confined to strains with similar antibiotic resistance
AB  - and plasmid profile.
ER  -

TY  - JOUR
AU  - Lee, K.S.
TI  - Cytotoxicity of patulin and its effect on lambda DNA cleavage by restriction endonuclease.
JO  - Korean J. Toxicol.
PY  - 1991
SP  - 157
EP  - 163
VL  - 7
AB  - The effect of patulin, a mycotoxin, on the growth of Escherichia coli cells was investigated.
AB  - E. coli cell elongation usually shown during SOS-response for DNA repair was induced by 20 ug
AB  - of patulin per ml. After staining the E. coli chromosome with a fluorescent dye (DAPI, 4',
AB  - 6-diamino-2-phenyl-indole), chromosomal DNA partitioning was not affected by patulin. This
AB  - observation indicates that patulin acts as a DNA damaging agent which is effective for E. coli
AB  - cell elongation introduced by the inhibition of septum formation. Moreover, patulin inhibits
AB  - the cleavage reaction of some restriction endonucleases (StyI, AsnI, BamHI, HindIII) on lambda
AB  - phage DNA. The restriction endonucleolytic fragments of lambda phage DNA preincubated with
AB  - patulin were larger than standard digestion products. The lambda DNA recognition site
AB  - (cleavage site) for StyI (C^CAAGG) was very sensitive to patulin, while the site for AsnI had
AB  - a very low reactivity with patulin. It seems likely that the cytosine of StyI recognition
AB  - sequences in lambda phage DNA would be a highly possible target nucleotide for patulin.
ER  -

TY  - JOUR
AU  - Lee, K.S.
AU  - Seo, S.Y.
AU  - Lee, S.W.
AU  - Rho, H.M.
TI  - Cloning and Expression of the Pst I Restriction Endonuclease Gene.
JO  - Korean Biochem. J.
PY  - 1982
SP  - 315
EP  - 329
VL  - 15
AB  - We report the cloning of the PstI restriction-modification system of
AB  - Providencia stuartii 164.  The DNA isolated from the native PstI producing
AB  - strain, P. stuartii 164, was completely digested with HindIII and inserted into
AB  - the HindIII target site of pBR322.  The cloned strain of E. coli was selected
AB  - on the basis of acquired resistance to bacteriophage Phi80 infection and PstI
AB  - endonuclease productivity.  Plasmid and host DNA from the cloned E. coli were
AB  - not digested by PstI, and the strain produced PstI restriction endonuclease.
AB  - These results indicated that both the restriction enzyme and modification
AB  - (methylase) genes had been cloned and were being expressed.  The plasmid (pRL
AB  - 829) isolated from the cloned strain contains an insert of approximately 3,700
AB  - base pairs.  The cloned E. coli produces approximately 15 times more PstI
AB  - endonuclease activity than does the native strain under similar conditions of
AB  - culture.
ER  -

TY  - JOUR
AU  - Lee, K.W.
AU  - Arumugam, K.
AU  - Purbojati, R.W.
AU  - Tay, Q.X.
AU  - Williams, R.B.
AU  - Kjelleberg, S.
AU  - Rice, S.A.
TI  - Draft Genome Sequence of Klebsiella pneumoniae Strain KP-1.
JO  - Genome Announcements
PY  - 2013
SP  - e01082
EP  - e01013
VL  - 1
AB  - Klebsiella pneumoniae is ubiquitous in the environment and is a member of a three-species
AB  - biofilm model. We compared the genome sequence of an environmental
AB  - isolate, K. pneumoniae strain KP-1, to those of two clinical strains (NTUH-K2044
AB  - and MGH 78578). KP-1 possesses strain-specific prophage sequences that
AB  - distinguish it from the clinical strains.
ER  -

TY  - JOUR
AU  - Lee, L.
AU  - Teh, L.
AU  - Zainuddin, Z.
AU  - Salleh, M.
TI  - The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 933
EP  - 939
VL  - 9
AB  - We report the genome sequence of a healthcare-associated MRSA type ST239 clone isolated from a
AB  - patient with septicemia in Malaysia. This clone typifies the
AB  - characteristics of ST239 lineage, including resistance to multiple antibiotics
AB  - and antiseptics.
ER  -

TY  - JOUR
AU  - Lee, L.L. et al.
TI  - Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and 'Thermoanaerobacter  cellulolyticus'.
JO  - Genome Announcements
PY  - 2015
SP  - e00440
EP  - e00415
VL  - 3
AB  - The genus Caldicellulosiruptor contains extremely thermophilic, cellulolytic bacteria capable
AB  - of lignocellulose deconstruction. Currently, complete genome
AB  - sequences for eleven Caldicellulosiruptor species are available. Here, we report
AB  - genome sequences for three additional Caldicellulosiruptor species: Rt8.B8 DSM
AB  - 8990 (New Zealand), Wai35.B1 DSM 8977 (New Zealand), and 'Thermoanaerobacter
AB  - cellulolyticus' strain NA10 DSM 8991 (Japan).
ER  -

TY  - JOUR
AU  - Lee, M.
AU  - Roh, S.W.
AU  - Lee, H.W.
AU  - Yim, K.J.
AU  - Kim, K.N.
AU  - Bae, J.W.
AU  - Choi, K.S.
AU  - Jeon, Y.J.
AU  - Jung, W.K.
AU  - Kang, H.
AU  - Hyun, C.G.
AU  - Kim, D.
TI  - Draft Genome Sequence of Pedobacter agri PB92T, Which Belongs to the Family Sphingobacteriaceae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3738
EP  - 3738
VL  - 194
AB  - Strain PB92(T) of Pedobacter agri, which belongs to the family Sphingobacteriaceae, was
AB  - isolated from soil in the Republic of Korea. The draft
AB  - genome of strain PB92(T) contains 5,141,552 bp, with a G+C content of 38.0%. This
AB  - is the third genome sequencing project of the type strains among the Pedobacter
AB  - species.
ER  -

TY  - JOUR
AU  - Lee, N.
AU  - Valinluck, B.
AU  - Randriamahefa, A.
AU  - Rutebuka, O.
AU  - Ryu, J.
TI  - Cloning and mapping of the hsdR genes of KpnAI and KpnBI restriction-modification systems of Klebsiella pneumoniae.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1993
SP  - 199
EP  - 199
VL  - 93
AB  - Two possible type I restriction-modification systems, KpnAI and KpnBI have been identified in
AB  - K. pneumoniae strains M5a1 and GM236 respectively (ASM Abstracts 1989, p180). The hsdR genes
AB  - from Sau3AI partially digested chromosomes of both strains were cloned into the BamHI site of
AB  - either pBR322 or pUC18. The clones expressing an r+ phenotype in r-m- recipients were
AB  - identified among the transformants resistant to non-modified phage SBS. A total of four clones
AB  - (8.8 to 14.8 kb) of KpnAI and two (5.8 and 6.2 kb) of KpnBI were obtained. The common portion
AB  - of these clones, which supposedly code for hsdR genes, were inferred as a 3.3 kb HindIII
AB  - fragment of KpnAI and a 3.9 kb EcoRI fragment for KpnBI respectively. Complementation results
AB  - with r-m- mutants suggest that the 6.2 kb fragment of the KpnBI clone contains a second gene
AB  - (either hsdM or hsdS) as well.
AB  - 
AB  - Clones of each type were hybridized to a membrane which contains pulsed-field gel
AB  - electrophoresed fragments of the chromosome of the corresponding strain. The KpnAI clone was
AB  - mapped on a 19 Kb XbaI fragment, located at about 40 min on the recently constructed physical
AB  - map of the M5a1 chromosome (ASM Abstracts 1992, p212). Similarly, the KpnBI clone was mapped
AB  - on a 40 kb XbaI fragment of the GM236 chromosome.
AB  - 
ER  -

TY  - JOUR
AU  - Lee, N.S.
AU  - Rutebuka, O.
AU  - Arakawa, T.
AU  - Bickle, T.A.
AU  - Ryu, J.
TI  - KpnAI, a new type I restriction-modification system in Klebsiella pneumoniae.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 342
EP  - 348
VL  - 271
AB  - The KpnAI restriction-modification system has been identified in Klebsiella pneumoniae strain
AB  - M5a1.  The restriction gene of KpnAI was first cloned into pBR322 using an r-m+ M5a1
AB  - derivative and phage SBS for screening.  Subsequently, an adjacent DNA fragment showing
AB  - modification activity was cloned into pUC19.  A total of 7.2 kb DNA sequencing data revealed
AB  - three open reading frames, corresponding to hsdR, hsdM and hsdS genes of type I R-M systems.
AB  - The predicted hsdR, hsdM and hsdS-coded peptides shared 95%, 98% and 44% identity,
AB  - respectively, with the corresponding peptides of the recently identified StySBLI system, a
AB  - prototype of the type ID family.  This high homology suggests that KpnAI is also a member of
AB  - the type ID family.  The KpnAI system seems to be the first type I system identified in
AB  - Klebsiella species.
ER  -

TY  - JOUR
AU  - Lee, N.S.
AU  - Ryu, J.
TI  - DNA sequence of the hsdR region of KpnBI R-M system of Klebsiella pneumoniae GM236.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 237
EP  - 237
VL  - 94
AB  - The hsdR gene of the KpnBI restriction-modification (R-M) system of Klebsiella pneumoniae
AB  - GM236 was cloned (ASM Abstracts 1993, p199). The DNA sequence of a 3.5 kb BamHI-EcoRI fragment
AB  - that includes the hsdR gene was determined by the Sanger's dideoxy method. An open reading
AB  - frame (ORF) of 3,039 bp (nucleotides 219 to 3,257) is the coding region for the HsdR
AB  - polypeptide. The 1,013 amino acid product deduced from the nucleotide sequence would have a
AB  - molecular weight of 116,312 daltons, in excellent agreement with the 116 kD size estimated
AB  - from the electrophoretic mobility of the putative HsdR protein in SDS polyacrylamide gels.
AB  - 
AB  - The nucleotide sequence of the hsdR gene showed no significant similarity to any other
AB  - sequence in the GenBank database. However, the amino acid sequence scored highly with
AB  - EcoR124/3I, a type I restriction enzyme. After alignment of the two proteins, two conserved
AB  - domains, an ATP binding and a DNA binding domain, were found.
AB  - 
AB  - Seven small ORFs were identified within a few kb on either side of the hsdR gene. When
AB  - subcloned, none of these ORFs showed any modification activity. This suggests that the KpnBI
AB  - system differs from other R-M systems where the hsdR and hsdM genes are adjacent. However,
AB  - complementation with an r-KpnBIm-KpnBI mutant suggests that one downstream ORF is a positive
AB  - effector for expression of the KpnBI modification activity. Therefore, a control gene for the
AB  - KpnBI modification genes may be located next to the hsdR gene.
AB  - 
ER  -

TY  - JOUR
AU  - Lee, R.D.
AU  - Jospin, G.
AU  - Coil, D.A.
AU  - Eisen, J.A.
TI  - Draft Genome Sequence of the Endosymbiont 'Candidatus Ruthia magnifica' UCD-CM (Phylum Proteobacteria).
JO  - Genome Announcements
PY  - 2014
SP  - e00717
EP  - e00714
VL  - 2
AB  - Here, we present the draft genome of the endosymbiont 'Candidatus Ruthia magnifica' UCD-CM,
AB  - a member of the phylum Proteobacteria, found from the gills of
AB  - a deep-sea giant clam, Calyptogena magnifica. The assembly consists of 1,160,249
AB  - bp contained in 18 contigs.
ER  -

TY  - JOUR
AU  - Lee, R.D.
AU  - Jospin, G.
AU  - Lang, J.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria).
JO  - Genome Announcements
PY  - 2015
SP  - e01276
EP  - e01215
VL  - 3
AB  - Here, we present the draft genome sequence of Pseudoalteromonas tetraodonis UCD-SED8, a marine
AB  - bacterium normally associated with the production of
AB  - tetrodotoxin in pufferfish. This strain was isolated from sediment samples
AB  - surrounding Zostera marina roots collected from Bodega Marine, California. The
AB  - assembly consists of 4,017,727 bp contained in 35 contigs.
ER  -

TY  - JOUR
AU  - Lee, R.D.
AU  - Jospin, G.
AU  - Lang, J.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment.
JO  - Genome Announcements
PY  - 2016
SP  - e00092
EP  - e00016
VL  - 4
AB  - Here, we present the draft genome sequences of Pseudoalteromonas porphyrae UCD-SED9 and
AB  - UCD-SED14 (phylum Proteobacteria). These strains were isolated from
AB  - sediment surrounding the roots of the seagrass, Zostera marina, collected near
AB  - the UC, Davis Bodega Marine Laboratory (Bodega Bay, California). The assemblies
AB  - contain 4,847,456 bp and 4,817,752 bp, respectively.
ER  -

TY  - JOUR
AU  - Lee, R.D.
AU  - Jospin, G.
AU  - Lang, J.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment.
JO  - Genome Announcements
PY  - 2016
SP  - e01769
EP  - e01715
VL  - 4
AB  - Here, we present the draft genome sequences of Vibrio splendidus UCD-SED7 and UCD-SED10
AB  - (phylum Proteobacteria). These strains were isolated from sediment
AB  - surrounding Zostera marina roots near the UC Davis Bodega Marine Laboratory
AB  - (Bodega, Bay, California). These assemblies contain 5,334,236 bp and 5,904,824
AB  - bp, respectively.
ER  -

TY  - JOUR
AU  - Lee, R.D.
AU  - Jospin, G.
AU  - Lang, J.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes).
JO  - Genome Announcements
PY  - 2015
SP  - e01376
EP  - e01315
VL  - 3
AB  - Here, we present the draft genome sequence of Bacillus vietnamensis UCD-SED5 (phylum
AB  - Firmicutes). This strain was isolated from sediment surrounding Zostera
AB  - marina roots near the UC Davis Bodega Marine Laboratory (Bodega Bay, California)
AB  - and represents the second genome of this species. The assembly consists of
AB  - 4,325,707 bp, in 108 contigs.
ER  -

TY  - JOUR
AU  - Lee, S.
AU  - Cho, Y.J.
AU  - Lee, A.H.
AU  - Chun, J.
AU  - Ha, N.J.
AU  - Ko, G.
TI  - Genomic sequence of Lactobacillus ruminis SPM0211, isolated from a fecal sample from a healthy Korean.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5034
EP  - 5034
VL  - 193
AB  - Lactobacillus ruminis SPM0211 is a potential probiotic strain that shows antimicrobial
AB  - activity against emerging pathogens. Here, we present the
AB  - draft genomic sequence of L. ruminis SPM0211, isolated from a fecal sample
AB  - from a healthy Korean, and we describe both the common and unique features
AB  - of this strain.
ER  -

TY  - JOUR
AU  - Lee, S.
AU  - Han, S.J.
AU  - Kwon, T.
AU  - Yoo, W.G.
AU  - Yun, M.R.
AU  - Lee, J.S.
AU  - Kim, D.W.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0192, Isolated in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e01601
EP  - e01615
VL  - 4
AB  - We report the draft genome sequence of totally drug-resistant (XDR) Mycobacterium tuberculosis
AB  - KT-0192. This sequence will provide new insights into the main cause
AB  - and evolution of drug resistance in M. tuberculosis KT-0192.
ER  -

TY  - JOUR
AU  - Lee, S.
AU  - Ward, T.J.
AU  - Siletzky, R.M.
AU  - Kathariou, S.
TI  - Two Novel Type II Restriction-Modification Systems Occupying Genomically Equivalent Locations on the Chromosomes of Listeria monocytogenes Strains.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 2623
EP  - 2630
VL  - 78
AB  - Listeria monocytogenes is responsible for the potentially life-threatening food-borne disease
AB  - listeriosis. One
AB  - epidemic-associated clonal group of L. monocytogenes, epidemic clone I
AB  - (ECI), harbors a Sau3AI-like restriction-modification (RM) system also
AB  - present in the same genomic region in certain strains of other
AB  - lineages. In this study, we identified and characterized two other,
AB  - novel type II RM systems, LmoJ2 and LmoJ3, at this same locus. LmoJ2
AB  - and LmoJ3 appeared to recognize GCWGC (W = A or T) and GCNGC,
AB  - respectively. Both RM systems consisted of genes with GC content below
AB  - the genome average and were in the same genomic region in strains of
AB  - different serotypes and lineages, suggesting site-specific horizontal
AB  - gene transfer. Genomic DNA from the LmoJ2 and LmoJ3 strains grown at
AB  - various temperatures (4 to 42 degrees C) was resistant to digestion
AB  - with restriction enzymes recognizing GCWGC or GCNGC, indicating that
AB  - the methyltransferases were expressed under these conditions. Phages
AB  - propagated in an LmoJ2-harboring strain exhibited moderately increased
AB  - infectivity for this strain at 4 and 8 degrees C but not at higher
AB  - temperatures, while phages propagated in an LmoJ3 strain had
AB  - dramatically increased infectivity for this strain at all temperatures.
AB  - Among the sequenced Listeria phages, lytic phages possessed
AB  - significantly fewer recognition sites for these RM systems than
AB  - lysogenic phages, suggesting that in lytic phages sequence content
AB  - evolved toward reduced susceptibility to such RM systems. The ability
AB  - of LmoJ2 and LmoJ3 to protect against phages may affect the efficiency
AB  - of phages as biocontrol agents for L. monocytogenes strains harboring
AB  - these RM systems.
ER  -

TY  - JOUR
AU  - Lee, S.
AU  - You, H.J.
AU  - Kwon, B.
AU  - Ko, G.
TI  - Complete Genome Sequence of the Plasmid-Bearing Lactobacillus fermentum Strain SNUV175, a Probiotic for Women's Health Isolated from the Vagina of a Healthy  South Korean Woman.
JO  - Genome Announcements
PY  - 2017
SP  - e00045
EP  - e00017
VL  - 5
AB  - Lactobacillus fermentum SNUV175 has been identified as a probiotic strain that inhibits
AB  - pathogenic microorganisms related to women's health. We present the
AB  - complete genomic sequence of the strain L. fermentum SNUV175 isolated from the
AB  - vagina of a South Korean woman. This genomic information may provide insight into
AB  - the functional activity of this strain.
ER  -

TY  - JOUR
AU  - Lee, S.
AU  - You, H.J.
AU  - Kwon, B.
AU  - Ko, G.
TI  - Complete Genome Sequence of Lactobacillus jensenii Strain SNUV360, a Probiotic for Treatment of Bacterial Vaginosis Isolated from the Vagina of a Healthy Korean  Woman.
JO  - Genome Announcements
PY  - 2017
SP  - e01757
EP  - e01716
VL  - 5
AB  - Lactobacillus jensenii SNUV360 is a potential probiotic strain that shows antimicrobial
AB  - activity for the treatment of bacterial vaginosis. Here, we present
AB  - the complete genomic sequence of L. jensenii SNUV360, isolated from a vaginal
AB  - sample from a healthy Korean woman. Analysis of the sequence may provide insight
AB  - into its functional activity.
ER  -

TY  - JOUR
AU  - Lee, S.F.
AU  - Forsberg, C.W.
AU  - Gibbins, A.M.
TI  - Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85.
JO  - J. Bacteriol.
PY  - 1992
SP  - 5275
EP  - 5283
VL  - 174
AB  - Fibrobacter succinogenes is an important cellulolytic bacterium found in the rumen and cecum
AB  - of herbivores.  Numerous attempts to introduce foreign DNA into F. succinogenes S85 have
AB  - failed, suggesting the presence of genetic barriers in this organism.  Results from this study
AB  - clearly demonstrate that F. succinogenes S85 possesses a type II restriction endonuclease,
AB  - FsuI, which recognizes the sequence 5'-GG(A/T)CC-3'.  Analysis of the restriction products
AB  - on sequencing gels showed that FsuI cleaves between the two deoxyguanosine residues, yielding
AB  - a 3-base 5' protruding end.  These data demonstrate that FsuI is an isoschizomer of AvaII.  A
AB  - methyltransferase activity has been identified in the cell extract of F. succinogenes S85.
AB  - This activity modified DNA in vitro and protected the DNA from restriction by FsuI and AvaII.
AB  - DNA modified in vivo by a cloned methylase gene, which codes for M.Eco47II, also protected the
AB  - DNA from restriction by FsuI, suggesting that FsuI is inhibited by methylation at one or both
AB  - deoxycytosine residues of the recognition sequence.  The methyltransferase activity in F.
AB  - succinogenes S85 is likely modifying the same deoxycytosine residues, but the exact site(s) is
AB  - unknown.  A highly active DNase (DNase A) was also isolated from the cell extract of this
AB  - organism.  DNase A is an endonuclease which showed high activity to all forms of DNA
AB  - (single-stranded, double-stranded, linear, and circular) but no activity on RNA.  In vitro,
AB  - the DNase A hydrolyzed F. succinogenes S85 DNA extensively, indicating the lack of protection
AB  - against hydrolysis by this enzyme.  In the presence of Mg2+, DNA was hydrolyzed to fragments
AB  - of 8 to 10 nucleotides in length.  The presence of DNase A and the type II
AB  - restriction-modification system of F. succinogenes S85 may be the barriers preventing the
AB  - introduction of foreign DNA into this bacterium.  Author agreed to change name to FssI to
AB  - avoid confusion with previous enzyme named FsuI.
ER  -

TY  - JOUR
AU  - Lee, S.G.
AU  - Koh, H.Y.
AU  - Lee, J.H.
AU  - Kang, S.H.
AU  - Kim, H.J.
TI  - Draft Genome Sequence of Moritella dasanensis Strain ArB 0140, a Psychrophilic Bacterium Isolated from the Arctic Ocean.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5452
EP  - 5453
VL  - 194
AB  - The psychrophilic bacterium Moritella dasanensis strain ArB 0140 was isolated near a glacier
AB  - in Kongsfjorden, Svalbard Archipelago, Norway. Here we report a
AB  - 4.89-Mb draft genome sequence of Moritella dasanensis ArB 0140, which could
AB  - provide comprehensive information on a psychrophilic mechanism in extreme
AB  - environments.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Choe, H.
AU  - Nasir, A.
AU  - Park, D.S.
AU  - Kim, K.M.
TI  - Complete Genome Sequence of Nitrilotriacetate-Degrading Aminobacter aminovorans KCTC 2477T.
JO  - Genome Announcements
PY  - 2016
SP  - e01363
EP  - e01316
VL  - 4
AB  - Aminobacter aminovorans is a Gram-negative, pleomorphic rod-shaped, flagellated,  and
AB  - obligately aerobic bacterium that was isolated from soil. Here, we report the
AB  - complete genome sequence of A. aminovorans KCTC 2477T, which degrades
AB  - nitrilotriacetate-metal complexes and iminodiacetate, a metabolic intermediate of
AB  - nitrilotriacetate.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Jin, H.M.
AU  - Lee, H.J.
AU  - Kim, J.M.
AU  - Jeon, C.O.
TI  - Complete Genome Sequence of the BTEX-Degrading Bacterium Pseudoxanthomonas spadix BD-a59.
JO  - J. Bacteriol.
PY  - 2012
SP  - 544
EP  - 544
VL  - 194
AB  - Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene,
AB  - ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated
AB  - from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb
AB  - genome sequence and annotation of strain BD-a59. These advance the
AB  - understanding of strain BD-a59's genomic properties and pollutant
AB  - metabolic versatility.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Jung, J.Y.
AU  - Jeon, C.O.
TI  - Draft Genome Sequence of Salimicrobium sp. Strain MJ3, Isolated from Myulchi-Jeot, Korean Fermented Seafood.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6695
EP  - 6695
VL  - 194
AB  - Salimicrobium sp. strain MJ3 was isolated from myulchi-jeot, traditional fermented seafood
AB  - made from anchovy in South Korea. Here we announce the draft
AB  - genome sequence of Salimicrobium sp. MJ3 with 2,717,782 bp, which consists of 45
AB  - contigs (>500 bp in size), and provide a description of their annotation.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Jung, J.Y.
AU  - Lee, S.H.
AU  - Jeon, C.O.
TI  - Complete Genome Sequence of Leuconostoc kimchii Strain C2, Isolated from Kimchi.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5548
EP  - 5548
VL  - 193
AB  - Leuconostoc kimchii strain C2 was isolated from fermented kimchi in Korea. Here we announce
AB  - the complete genome sequence of Leuconostoc kimchii
AB  - strain C2, consisting of a 1,877,174-bp chromosome with a G+C content of
AB  - 37.9% and no plasmid and describe major findings from its annotation.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Jung, M.Y.
AU  - Park, B.
AU  - Sung-Oh, S.
AU  - Park, H.W.
AU  - Choi, H.J.
AU  - Lee, J.H.
TI  - Complete Genome Sequence of Pediococcus pentosaceus Strain wikim 20, Isolated from Korean Kimchi.
JO  - Genome Announcements
PY  - 2016
SP  - e01233
EP  - e01216
VL  - 4
AB  - Pediococcus pentosaceus strain wikim 20 is a lactic acid bacterium that was isolated from
AB  - kimchi, a representative traditional Korean fermented food. Here,
AB  - we announce the complete genome sequence of P. pentosaceus strain wikim 20
AB  - consisting of a 1,830,629-bp chromosome and provide a description of its
AB  - annotation.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Jung, M.Y.
AU  - Song, J.H.
AU  - Lee, M.
AU  - Chang, J.Y.
TI  - Complete Genome Sequence of Lactobacillus curvatus Strain WiKim38 Isolated from Kimchi.
JO  - Genome Announcements
PY  - 2017
SP  - e00273
EP  - e00217
VL  - 5
AB  - Lactobacillus curvatus WiKim38 is a potential probiotic strain isolated from kimchi, a
AB  - traditional Korean fermented food. The complete genome of the WiKim38
AB  - strain consisted of a circular chromosome of 1,940,170 bp in length with a G+C
AB  - content of 41.93%.
ER  -

TY  - JOUR
AU  - Lee, S.H.
AU  - Rho, H.M.
TI  - Cloning of PstI methylase gene.
JO  - Korean J. Genet.
PY  - 1985
SP  - 42
EP  - 48
VL  - 7
AB  - The clonings of PstI restriction-modification system were reported in two cases.  One was by
AB  - Walder et al. (1981) and the other was by Lee et al. (1982). pRL829 constructed by Lee et al.
AB  - was a recombinant plasmid containing 3.7kb insert fragment at HindIII site of pBR322, which
AB  - encoded whole PstI restriction-modification system.  In this research, a new recombinant
AB  - plasmid, pRL830, containing only PstI methylase gene was constructed from pRL829 by partial
AB  - digestion with HincII.  pRL830 contained 2.2kb insert DNA out of 3.7kb insert of pRL829.  The
AB  - host DNA and plasmid from the cells transformed with pRL830 were not cleaved by PstI,
AB  - suggesting that PstI methylase gene was cloned and expressed in the cells.  However, E. coli
AB  - transformed with pRL830 was easily infected and lysed by bacteriophage Phi80, indicating that
AB  - PstI endonuclease gene was at least inactivated or removed from pRL830.  Soluble fractions
AB  - from the E. coli containing pRL830 were passed through the DEAE-cellulose and phosphocellulose
AB  - columns.  Eluted enzyme fraction with salt gradient were assayed for the PstI endonuclease and
AB  - methylase activities. Results showed that PstI methylase activity was detected, whereas PstI
AB  - endonuclease activity was not.  It was convinced pRL830 encoded PstI methylase gene, but not
AB  - endonuclease gene.
ER  -

TY  - JOUR
AU  - Lee, S.J.
AU  - Lee, Y.J.
AU  - Jeong, H.
AU  - Lee, S.J.
AU  - Lee, H.S.
AU  - Pan, J.G.
AU  - Kim, B.C.
AU  - Lee, D.W.
TI  - Draft Genome Sequence of Virgibacillus halodenitrificans 1806.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6332
EP  - 6333
VL  - 194
AB  - Virgibacillus halodenitrificans 1806 is an endospore-forming halophilic bacterium isolated
AB  - from salterns in Korea. Here, we report the draft genome sequence of V.
AB  - halodenitrificans 1806, which may reveal the molecular basis of osmoadaptation
AB  - and insights into carbon and anaerobic metabolism in moderate halophiles.
ER  -

TY  - JOUR
AU  - Lee, S.J.
AU  - Lee, Y.J.
AU  - Park, G.S.
AU  - Kim, B.C.
AU  - Lee, S.J.
AU  - Shin, J.H.
AU  - Lee, D.W.
TI  - Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream.
JO  - Genome Announcements
PY  - 2013
SP  - e00923
EP  - e00913
VL  - 1
AB  - Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium,
AB  - which was isolated from a geothermal hot stream in Indonesia. This
AB  - bacterium utilizes xylose and produces a variety of proteases. Here, we report
AB  - the draft genome sequence of C. yonseiensis, which reveals insights into the
AB  - pentose phosphate pathway and protein degradation metabolism in thermophilic
AB  - microorganisms.
ER  -

TY  - JOUR
AU  - Lee, S.J.
AU  - Lee, Y.J.
AU  - Ryu, N.
AU  - Park, S.
AU  - Jeong, H.
AU  - Lee, S.J.
AU  - Kim, B.C.
AU  - Lee, D.W.
AU  - Lee, H.S.
TI  - Draft Genome Sequence of the Thermophilic Bacterium Anoxybacillus kamchatkensis G10.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6684
EP  - 6685
VL  - 194
AB  - Anoxybacillus kamchatkensis G10 is a spore-forming thermophilic bacterium isolated from a hot
AB  - spring in Indonesia. Here, we report the draft genome
AB  - sequence of A. kamchatkensis G10 that may reveal insights into aerobic/anaerobic
AB  - metabolisms and carbon utilization in moderate thermophiles.
ER  -

TY  - JOUR
AU  - Lee, S.P.
AU  - Porter, D.
AU  - Chirikjian, J.G.
AU  - Knutson, J.R.
AU  - Han, M.K.
TI  - A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease.
JO  - Anal. Biochem.
PY  - 1994
SP  - 377
EP  - 383
VL  - 220
AB  - Fluorescently labeled oligonucleotides and DNA fragments have promise in nucleic acid research
AB  - with applications that include DNA hybridization, automated DNA sequencing, fluorescence
AB  - anisotropy, and resonance energy transfer studies. Past concerns with fluorescent-labeled DNA
AB  - arose from interactions between fluorophores and DNA that result in quenched fluorescence.
AB  - This quenching phenomenon is most problematic in fluorescence resonance energy transfer
AB  - studies because quenching of the donor fluorescence could result from either resonance energy
AB  - transfer or nontransfer effects. In the present study, relief of nontransfer quenching of a
AB  - 14-mer fluorescein 5-isothiocyanate (FITC)-labeled oliognucleotide containing the BamHI
AB  - restriction site was characterized with both steady-state and time-resolved fluorescence
AB  - techniques. The FITC-labeled single strand was best fit by a triexponential decay with
AB  - lifetimes of 0.5, 2.7, and 4.2 ns. The 4.2-ns component was found to contribute more than 80%
AB  - of the total steady-state intensity. Upon annealing with an unmodified complementary strand,
AB  - the contribution from the 4.2-ns component was significantly decreased, resulting in twofold
AB  - quenching of total fluorescence. We reasoned that this quenching phenomenon should be a
AB  - reversible process and could be employed to study strand separation processes in molecular
AB  - biology. Hence, cleavage of the fluorescently labeled substrate was examined using DNase I and
AB  - BamHI restriction endonuclease. Our results show that the quenched fluorescence is totally
AB  - recovered upon cleavage (compared to that of the single strand). The extent of cleavage
AB  - measured by fluorescence was confirmed by nondenaturing polyacrylamide gel electrophoresis
AB  - analysis. We believe this fluorescence dequenching technique may be used to quantify the
AB  - kinetics of other DNA strand separation and cleavage processes in molecular biology.
ER  -

TY  - JOUR
AU  - Lee, S.P.
AU  - Porter, D.K.
AU  - Chirikjian, J.G.
AU  - Knutson, J.R.
AU  - Han, M.K.
TI  - The development of a fluorescence assay for the BamHI restriction endonuclease utilizing modified oligonucleotides.
JO  - Biophys. J.
PY  - 1994
SP  - A163
EP  - A163
VL  - 66
AB  - Fluorescent labeled oigonucleotides and DNA fragments have promise in nucleic acid research
AB  - including DNA hybridization, automated DNA sequencing, and fluorescence anisotropy or
AB  - resonance energy transfer studies. One concern with fluorescent-labeled DNA is that the
AB  - interactions between fluorophores and DNA may result in quenching of the probe fluorescence.
AB  - This quenching phenomenon is most problematic in fluorescence enegy transfer studies because
AB  - donor quenching can occur as a result of both resonance transfer and these non-transfer
AB  - effects. In the present studies, the nontransfer quenching of a 14-mer FITC-labeled
AB  - oligonucleotide with the BamHI restriction site was characterized with both steady-state and
AB  - time-resolved fluoescence techniques. The FITC-labeled single strand was best fit by
AB  - triexponential decay with lifetimes of 0.5, 2.7, and 4.2 ns. The 4.2 ns component was found to
AB  - contribute more than 80% of total steady-state intensity. Upon annealing with an unmodified
AB  - complementary strand, the 4.2 ns component was significantly decreased, resulting in 2-fold
AB  - quenching of total fluorescence. We examined the reversible quenching process and applied our
AB  - findings to quantify DNA strand separation and cleavage processes. Utilizing this information,
AB  - we developed a continuous fluorescence assay for the restriction endonucleases reaction for
AB  - BamHI.
ER  -

TY  - JOUR
AU  - Lee, S.S.
AU  - Kongari, R.R.
AU  - Hernandez, A.C.
AU  - Kuty, E.G.F.
TI  - Complete Genome Sequence of Bacillus megaterium Siphophage Stills.
JO  - Genome Announcements
PY  - 2015
SP  - e00855
EP  - e00815
VL  - 3
AB  - Bacillus megaterium is a soil-dwelling bacterium frequently used in research as a model
AB  - organism and in industry in protein production applications. Bacteriophages
AB  - may be used to enhance the use of this bacterium. Here, we describe the complete
AB  - genome of B. megaterium siphophage Stills and its core features.
ER  -

TY  - JOUR
AU  - Lee, S.Y.
AU  - Kim, B.Y.
AU  - Ahn, J.H.
AU  - Song, J.
AU  - Seol, Y.J.
AU  - Kim, W.G.
AU  - Weon, H.Y.
TI  - Draft Genome Sequence of the Biocontrol Bacterium Bacillus amyloliquefaciens Strain M27.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6934
EP  - 6935
VL  - 194
AB  - Bacillus amyloliquefaciens strain M27 is a biocontrol agent with antagonistic activities
AB  - against a wide range of fungal pathogens. Here we present the 3.86-Mb
AB  - draft genome sequence of the bacterium with the aims of providing insights into
AB  - the genomic basis of its antifungal mechanism and facilitating its application in
AB  - the biocontrol of plant diseases.
ER  -

TY  - JOUR
AU  - Lee, S.Y.
AU  - Kim, S.H.
AU  - Lee, D.G.
AU  - Shin, S.
AU  - Yun, S.H.
AU  - Choi, C.W.
AU  - Chung, Y.H.
AU  - Choi, J.S.
AU  - Kahng, H.Y.
AU  - Kim, S.I.
TI  - Draft Genome Sequence of Petroleum Oil-Degrading Marine Bacterium Pseudomonas taeanensis Strain MS-3, Isolated from a Crude Oil-Contaminated Seashore.
JO  - Genome Announcements
PY  - 2014
SP  - e00818
EP  - e00813
VL  - 2
AB  - Pseudomonas taeanensis MS-3(T), isolated from a crude oil-contaminated seashore in South
AB  - Korea, is capable of degrading petroleum oils, such as gasoline, diesel,
AB  - and kerosene. Here, we report the draft genome sequence of this strain, which
AB  - consists of 5,477,045 bp, with a G+C content of 60.72%.
ER  -

TY  - JOUR
AU  - Lee, S.Y.
AU  - Mermelstein, L.D.
AU  - Bennett, G.N.
AU  - Papoutsakis, E.T.
TI  - Vector construction, transformation, and gene amplification in Clostridium acetobutylicum ATCC 824.
JO  - Ann. NY Acad. Sci.
PY  - 1992
SP  - 39
EP  - 51
VL  - 665
AB  - The acetone-butanol-ethanol fermentation by the gram-positive, endo-
AB  - spore-forming, obligate
AB  - anaerobe Clostridium acetobutylicum has received renewed interest because recombinant
AB  - DNA technology
AB  - offers the possibility of creating genetically engineered strains as potential producers of
AB  - these solvents from
AB  - renewable biomass.  The ability to express homologous and heterologous genes in C.
AB  - acetobutylicum and
AB  - alter the cellular metabolism in a beneficial way is critical to the creation of overproducing
AB  - strains for
AB  - industrial applications.  It is also necessary to understand the molecular mechanisms
AB  - involved in metabolic
AB  - regulation in order to rationally manipulate metabolic pathways using recDNA technology.
ER  -

TY  - JOUR
AU  - Lee, S.Y.
AU  - Yun, S.H.
AU  - Choi, C.W.
AU  - Lee, D.G.
AU  - Choi, J.S.
AU  - Kahng, H.Y.
AU  - Kim, S.I.
TI  - Draft Genome Sequence of an Aniline-Degrading Bacterium, Burkholderia sp. K24.
JO  - Genome Announcements
PY  - 2014
SP  - e01250
EP  - e01214
VL  - 2
AB  - Burkholderia sp. K24 is an aniline-degrading soil bacterium that utilizes aniline and its
AB  - analogues as sole carbon and nitrogen sources. Here, we report the draft
AB  - genome sequence of this strain that consists of 8,344,181 bp, with a G+C content
AB  - of 61.7%.
ER  -

TY  - JOUR
AU  - Lee, W.-K.
AU  - An, Y.-S.
AU  - Kim, K.-H.
AU  - Kim, S.-H.
AU  - Song, J.-Y.
AU  - Ryu, B.-D.
AU  - Choi, Y.-J.
AU  - Yoon, Y.-H.
AU  - Baik, S.-C.
AU  - Rhee, K.-H.
AU  - Cho, M.-J.
TI  - Construction of a Helicobacter pylori-Escherichia coli shuttle vector for gene transfer in Helicobacter pylori.
JO  - Appl. Environ. Microbiol.
PY  - 1997
SP  - 4866
EP  - 4871
VL  - 63
AB  - In this study, a Helicobacter pylori-Escherichia coli shuttle vector was constructed for
AB  - transferring DNA into H. pylori.  The smallest cryptic plasmid (1.2 kb), pHP489, among those
AB  - harbored by 77 H. pylori isolates was selected as a base replicon for constructing vectors.
AB  - HindIII-digested pHP-489 was ligated with a kanamycin resistance gene [aph(3')-III], which
AB  - originated from Campylobacter jejuni, to produce the recombinant plasmid pHP489K.  pHP489K was
AB  - efficiently transformed into and stably maintained in H. pylori strains.  The shuttle vector
AB  - pBHP489K (3.6kb) was constructed by the recombination of pHP489, ColE1, and aph(3')-III
AB  - sequences.  PBHP489K was reciprocally transformed into and maintained in both H. pylori and E.
AB  - coli.  Introduction of the shuttle vector clone DNA (pBHP489K/AB; 6.7 kb), containing the ureA
AB  - and ureB genes of H. pylori, into urease-negative mutants of H. pylori led to the restoration
AB  - of their urease activity.  The transformants were confirmed to contain the incoming plasmid
AB  - DNA.  PBHP489K satisfied the requirements for an H. pylori-E. coli shuttle vector, implying
AB  - that it might be a useful vector for investigating pathogenicity and restriction-modification
AB  - systems of H. pylori.
ER  -

TY  - JOUR
AU  - Lee, W.C.
AU  - Anton, B.P.
AU  - Wang, S.
AU  - Baybayan, P.
AU  - Singh, S.
AU  - Ashby, M.
AU  - Chua, E.G.
AU  - Tay, C.Y.
AU  - Thirriot, F.
AU  - Loke, M.F.
AU  - Goh, K.L.
AU  - Marshall, B.J.
AU  - Roberts, R.J.
AU  - Vadivelu, J.
TI  - The complete methylome of Helicobacter pylori UM032.
JO  - BMC Genomics
PY  - 2015
SP  - 424
EP  - 424
VL  - 16
AB  - BACKGROUND: The genome of the human gastric pathogen Helicobacter pylori encodes  a large
AB  - number of DNA methyltransferases (MTases), some of which are shared among
AB  - many strains, and others of which are unique to a given strain. The MTases have
AB  - potential roles in the survival of the bacterium. In this study, we sequenced a
AB  - Malaysian H. pylori clinical strain, designated UM032, by using a combination of
AB  - PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation
AB  - sequencing platforms, and used the SMRT data to characterize the set of
AB  - methylated bases (the methylome). RESULTS: The N4-methylcytosine and
AB  - N6-methyladenine modifications detected at single-base resolution using SMRT
AB  - technology revealed 17 methylated sequence motifs corresponding to one Type I and
AB  - 16 Type II restriction-modification (R-M) systems. Previously unassigned
AB  - methylation motifs were now assigned to their respective MTases-coding genes.
AB  - Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome
AB  - during normal growth was characterized by cloning. CONCLUSION: Consistent with
AB  - previously-studied H. pylori strains, we show that strain UM032 contains a
AB  - relatively large number of R-M systems, including some MTase activities with
AB  - novel specificities. Additional studies are underway to further elucidating the
AB  - biological significance of the R-M systems in the physiology and pathogenesis of
AB  - H. pylori.
ER  -

TY  - JOUR
AU  - Lee, Y.
TI  - Prediction of putative resistance islands in a carbapenem-resistant Acinetobacter baumannii global clone 2 clinical isolate.
JO  - Ann. Lab. Med.
PY  - 2016
SP  - 320
EP  - 324
VL  - 36
AB  - Background: We investigated the whole genome sequence (WGS) of a carbapenem-resistant
AB  - Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance
AB  - islands using a software tool.
AB  - Methods: A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with
AB  - sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System
AB  - (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were
AB  - analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively.
AB  - Results: The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids
AB  - (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent
AB  - with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following
AB  - resistance genes: four -lactamase genes blaADC-30, blaOXA-66, blaOXA-23, and blaTEM-1; armA,
AB  - aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6)Ib-cr for fluoroquinolone
AB  - resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for
AB  - phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative
AB  - resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed
AB  - two copies of Tn2009 carrying blaOXA-23, and PRI5 carried two copies of a class I integron
AB  - carrying sul1 and armA genes.
AB  - Conclusions: By prediction of resistance islands in the carbapenem-resistant A. baumannii
AB  - YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed
AB  - Tn2009 and class I integrons. The prediction of resistance islands using software tools was
AB  - useful for analysis of the WGS.
ER  -

TY  - JOUR
AU  - Lee, Y.
AU  - Jang, S.
TI  - Draft Genome Sequence of the Environmentally Isolated Acinetobacter pittii Strain IPK_TSA6.1.
JO  - Genome Announcements
PY  - 2016
SP  - e01028
EP  - e01016
VL  - 4
AB  - Acinetobacter pittii is an opportunistic pathogen frequently isolated from Acinetobacter
AB  - infections other than those from Acinetobacter baumannii Multidrug
AB  - resistance in A. pittii, including resistance to carbapenems, has been
AB  - increasingly reported worldwide. Here, we report the 4.14-Mbp draft genome
AB  - sequence of A. pittii IPK_TSA6.1 that was isolated from a nonhospital setting.
ER  -

TY  - JOUR
AU  - Lee, Y.
AU  - Nguyen, T.L.
AU  - Kim, A.
AU  - Kim, N.
AU  - Roh, H.J.
AU  - Han, H.J.
AU  - Jung, S.H.
AU  - Cho, M.Y.
AU  - Kang, H.Y.
AU  - Kim, D.H.
TI  - Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys  olivaceus).
JO  - Genome Announcements
PY  - 2018
SP  - e00248
EP  - e00218
VL  - 6
AB  - Here, we report the complete genome sequence of multiple-antibiotic-resistant Streptococcus
AB  - parauberis strain SPOF3K, isolated from the kidney of a diseased
AB  - olive flounder in South Korea in 2013. Sequencing using a PacBio platform yielded
AB  - a circular chromosome of 2,128,740 bp and a plasmid of 23,538 bp, harboring 2,123
AB  - and 24 protein-coding genes, respectively.
ER  -

TY  - JOUR
AU  - Lee, Y.-F.
AU  - Tawfik, D.S.
AU  - Griffiths, A.D.
TI  - Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalization.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 4937
EP  - 4944
VL  - 30
AB  - In vitro compartmentalisation (IVC), a technique for selecting genes encoding enzymes based on
AB  - compartmentalising gene translation and enzymatic reactions in emulsions, was used to
AB  - investigate the interaction of the DNA cytosine-5 methyltransferase M.HhaI with its target DNA
AB  - (5'-GCGC-3'). Crystallography shows that the active site loop from the large domain of
AB  - M.HhaI interacts with a flipped-out cytosine (the target for methylation) and two target
AB  - recognition loops (loops I and II) from the small domain make almost all the other
AB  - base-specific interactions. A library of M.HhaI genes was created by randomising all the loop
AB  - II residues thought to make base-specific interactions and directly determine target
AB  - specificity. The library was selected for 5'-GCGC-3' methylation. Interestingly, in 11
AB  - selected active clones, 10 different sequences were found and none were wild-type. At two of
AB  - the positions mutated (Ser252 and Tyr254) a number of different amino acids could be
AB  - tolerated. At the third position, however, all active mutants had a glycine, as in wild-type
AB  - M.HhaI, suggesting that Gly257 is crucial for DNA recognition and enzyme activity. Our results
AB  - suggest that recognition of base pairs 3 and 4 of the target site either relies entirely on
AB  - main chain interactions or that different residues from those identified in the crystal
AB  - structure contribute to DNA recognition.
ER  -

TY  - JOUR
AU  - Lee, Y.-H.
AU  - Blakesley, R.W.
AU  - Smith, L.A.
AU  - Chirikjian, J.G.
TI  - Preparation and properties of insolubilized restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 679
EP  - 689
VL  - 5
AB  - Type II restriction endonucleases BamHI and EcoRI were covalently coupled to
AB  - Sepharose.  These insolubilized enzymes generated fragment patterns for several
AB  - viral DNAs identical to those produced by the respective free enzymes.
AB  - Conditions for optimal activity were similar for both bound and unbound form of
AB  - the enzymes.  Insolubilization improved thermal stability of BamHI and EcoRI.
AB  - The bound enzyme can be recovered from reaction mixtures and reused several
AB  - times.  Upon storage at 4C, coupled endonucleases remained stable for several
AB  - months.
ER  -

TY  - JOUR
AU  - Lee, Y.-W.
AU  - Broday, L.
AU  - Costa, M.
TI  - Effects of nickel on DNA methyltransferase activity and genomic DNA methylation levels.
JO  - Mutat. Res.
PY  - 1998
SP  - 213
EP  - 218
VL  - 415
AB  - Methylation of DNA plays an important role in organizing the genome into transcriptionally
AB  - active and inactive zones.  Nickel compounds cause chromatin condensation and DNA methylation
AB  - in the transgenic gpt+ Chinese hamster cell line (G12).  Here we show that nickel is an
AB  - inhibitor of cytosine 5-methyltransferase activity in vivo and in vitro.  In living cells,
AB  - this inhibition is transient and following a recovery period after nickel treatment, Mtase
AB  - activity slightly rebounds.  Genomic DNA methylation levels are also somewhat decreased
AB  - following nickel treatment, but with time, there is an elevation of total DNA methylation
AB  - above basal levels and before any rebound of methyltransferase activity.  These results
AB  - suggest that nickel exposure can elevate total genomic DNA methylation levels even when DNA
AB  - methyltransferase activity is depressed.  These findings may explain the hypermethylation of
AB  - senescence and tumor suppressor genes found during nickel carcinogenesis and support the model
AB  - of a direct effect of Ni2+ on chromatin leading to de novo DNA methylation.
ER  -

TY  - JOUR
AU  - Lee, Y.D.
AU  - Chang, H.I.
AU  - Park, J.H.
TI  - Complete genomic sequence of virulent Cronobacter sakazakii phage ESSI-2 isolated from swine feces.
JO  - Arch. Virol.
PY  - 2011
SP  - 721
EP  - 724
VL  - 156
AB  - A newly identified virulent Cronobacter sakazakii phage, ESSI-2, was
AB  - isolated from fecal samples from swine. The morphological characteristics
AB  - evident under a transmission electron microscope indicated that phage
AB  - ESSI-2 belonged to the family Myoviridae. The genome of phage ESSI-2
AB  - comprised a double-stranded DNA of 28,765 bp with a G+C content of 55.17%.
AB  - Bioinformatic analysis of the phage genome identified 36 putative open
AB  - reading frames (ORFs). The genome of phage ESSI-2 was not significantly
AB  - similar to that of a previously reported bacteriophage of the members of
AB  - Enterobacteriaceae. A lysogeny module was found within the genome of this
AB  - virulent phage.
ER  -

TY  - JOUR
AU  - Lee, Y.H.
AU  - Blakesley, R.
AU  - Smith, L.A.
AU  - Chirikjian, G.
TI  - Preparation and properties of immobilized sequence specific endonucleases.
JO  - Methods Enzymol.
PY  - 1980
SP  - 173
EP  - 182
VL  - 65
AB  - The type II restriction endonucleases have become valuable reagents for research in molecular
AB  - biology.  This is primarily due to their unique property of cleaving DNAs at a limited number
AB  - of specific sites.  These enzymes have been employed for use in physical DNA mapping, plasmid
AB  - construction, and gene cloning.  Most of these enzymes recognize and cleave DNA at specific
AB  - sequences, which are usually in the form of a palindrome.  Since there is evidence implying
AB  - that these endonucleases are membrane bound, one approach to studying them is to determine
AB  - what effect insolubilization (i.e., mimicking membrane binding) has on their activity.
ER  -

TY  - JOUR
AU  - Lee, Y.H.
AU  - Chirikjian, J.G.
TI  - Sequence-specific endonuclease BglI.
JO  - J. Biol. Chem.
PY  - 1979
SP  - 6838
EP  - 6841
VL  - 254
AB  - The sequence-specific endonuclease BglI from Bacillus globigii (RUB561) has
AB  - been purified to homogeneity as determined by denaturing polyacrylamide gel
AB  - analysis.  The active form of the enzyme is a single polypeptide with a
AB  - molecular weight of 32,000.  The enzyme requires Mg2+ in the reaction mixture
AB  - and displays a broad pH and monovalent cation requirement.  BglI is not
AB  - sensitive to sulfhydryl reagents but was affected by reagents that modify
AB  - lysine and arginine residues.  When lysine residues were modified by pyridoxal
AB  - 5'-phosphate, both binding and catalysis were diminished while modification of
AB  - arginine residues by 2,3-butanedione inhibited the enzyme activity but had no
AB  - effect on its binding properties.
ER  -

TY  - JOUR
AU  - Lee, Y.H.
AU  - Smith, L.A.
AU  - Blakesley, R.W.
TI  - Preparation and properties of matrix-bound restriction endonucleases.
JO  - Fed. Proc.
PY  - 1978
SP  - 1414
EP  - 1414
VL  - 37
AB  - Properties of these specific endonucleases have made them valuable reagents for
AB  - several areas of research.  These enzymes are present in bacterial cells
AB  - although functions for most such enzymes are not known.  In as much as several
AB  - restriction endonucleases are potentially membrane bound, we have undertaken to
AB  - investigate the effect of insolubilization on their stability and reaction
AB  - characteristics.  Using cyanogen bromide activated sepharose we have covalently
AB  - coupled several enzymes including the widely used BamHI, EcoRI and HindIII.
AB  - Matrix bound ezymes digest DNAs, generating an identical pattern to those
AB  - produced by the respective free enzyme, indicating no change in specificity.
AB  - Specific activities for bound enzymes were 100-4000 units/ml of sepharose,
AB  - where a unit digests 1 microgram DNA at 37C in 1 hr.  Coupled enzymes display
AB  - high thermal stability making them useful in probing DNA structure at high
AB  - temperatures.  Coupled enzymes are reusable, can be removed rapidly from
AB  - reaction mixtures, and adapted to a flow-through system.
ER  -

TY  - JOUR
AU  - Lee, Y.J.
AU  - Jeong, H.
AU  - Park, G.S.
AU  - Kwak, Y.
AU  - Lee, S.J.
AU  - Lee, S.J.
AU  - Park, M.K.
AU  - Kim, J.Y.
AU  - Kang, H.K.
AU  - Shin, J.H.
AU  - Lee, D.W.
TI  - Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 71
EP  - 71
VL  - 10
AB  - Fervidobacterium islandicum AW-1 (KCTC 4680) is an extremely thermophilic anaerobe isolated
AB  - from a hot spring in Indonesia. This bacterium could degrade
AB  - native chicken feathers completely at 70 degrees C within 48 h, which is of
AB  - potential importance on the basis of relevant environmental and agricultural
AB  - issues in bioremediation and development of eco-friendly bioprocesses for the
AB  - treatment of native feathers. However, its genomic and phylogenetic analysis
AB  - remains unclear. Here, we report the high-quality draft genome sequence of an
AB  - extremely thermophilic anaerobe, F. islandicum AW-1. The genome consists of
AB  - 2,359,755 bp, which encodes 2,184 protein-coding genes and 64 RNA-encoding genes.
AB  - This may reveal insights into anaerobic metabolism for keratin degradation and
AB  - also provide a biological option for poultry waste treatments.
ER  -

TY  - JOUR
AU  - Lee, Y.J.
AU  - Lee, S.J.
AU  - Jeong, H.
AU  - Kim, H.J.
AU  - Ryu, N.
AU  - Kim, B.C.
AU  - Lee, H.S.
AU  - Lee, D.W.
AU  - Lee, S.J.
TI  - Draft Genome Sequence of Bacillus oceanisediminis 2691.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6351
EP  - 6352
VL  - 194
AB  - Bacillus oceanisediminis 2691 is an aerobic, Gram-positive, spore-forming, and moderately
AB  - halophilic bacterium that was isolated from marine sediment of the
AB  - Yellow Sea coast of South Korea. Here, we report the draft genome sequence of B.
AB  - oceanisediminis 2691 that may have an important role in the bioremediation of
AB  - marine sediment.
ER  -

TY  - JOUR
AU  - Lee, Y.J.
AU  - Lee, S.J.
AU  - Kim, S.H.
AU  - Lee, S.J.
AU  - Kim, B.C.
AU  - Lee, H.S.
AU  - Jeong, H.
AU  - Lee, D.W.
TI  - Draft Genome Sequence of Bacillus endophyticus 2102.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5705
EP  - 5706
VL  - 194
AB  - Bacillus endophyticus 2102 is an endospore-forming, plant growth-promoting rhizobacterium
AB  - isolated from a hypersaline pond in South Korea. Here we present
AB  - the draft sequence of B. endophyticus 2102, which is of interest because of its
AB  - potential use in the industrial production of algaecides and bioplastics and for
AB  - the treatment of industrial textile effluents.
ER  -

TY  - JOUR
AU  - Lee, Y.W.
AU  - Clanton, D.
AU  - Chirikjian, J.G.
TI  - Subpalindromic sequences as inhibitors for restriction endonucleases.
JO  - Fed. Proc.
PY  - 1979
SP  - 294
EP  - 294
VL  - 38
AB  - BglI from B. globigii was purified to homogeneity using several chromatographic
AB  - steps including phenyl-sepharose.  The enzyme is a single polypeptide chain of
AB  - 32,000 daltons as determined by calibrated techniques.  BglI activity required
AB  - Mg++ and was stimulated by NaCl.  When Mn++ replaced Mg++ in the reaction
AB  - mixture, no change in specificity was observed.  Arg, and lys, but not
AB  - sulfhydryl groups were necessary for activity.  The effect of subpalindromic
AB  - sequences to inhibit restriction endonuclease activity was examined using
AB  - purified BglI and BamHI.  The degree of inhibition on the BamHI (G7GATCC) was
AB  - found to be d(pG)2>d(pC)2>d(pApT) while d(pA)2, d(pGpA) and d(pCpT)2 had no
AB  - effect.  In addition, d(pTpC) > d(pG)2=d(pC)2 inhibited BglI GGCCG
AB  - AGGCGGCCCT^CGGCC CCGGC^TCCGCCCGGA GCCGG Application of this method in studies
AB  - on the mechanism of binding and catalysis for BamHI, BglI and other restriction
AB  - endonucleases as well as cognate methylases will be presented.
ER  -

TY  - JOUR
AU  - Lees, J.
AU  - Gladstone, R.A.
TI  - R-M systems go on the offensive.
JO  - Nat. Rev. Microbiol.
PY  - 2015
SP  - 131
EP  - 131
VL  - 13
AB  - Restriction-modification (R-M) systems protect bacteria against the integration of foreign DNA
AB  - from, for example, phages.  These systems rely on restriction enzymes that cleave foreign
AB  - unmethylated DNA at specific short sequence motifs; methylation of 'self' DNA protects the
AB  - bacterial genome from
AB  - its own restriction enzymes. Importantly, high frequency inversions in genes coding for R-M
AB  - systems in Bacteroides fragilis have been shown to affect the cleavage specificity of these
AB  - systems1. Now, Croucher et al.2
AB  - and Manso et al.3 describe a similar strategy in Streptococcus pneumoniae, and show that these
AB  - R-M systems are not limited to the defence against phages but can also regulate the expression
AB  - of genes involved in bacterial virulence.
ER  -

TY  - JOUR
AU  - Lees, N.D.
AU  - Welker, N.E.
TI  - Restriction and modification of bacteriophage in Bacillus stearothermophilus.
JO  - J. Virol.
PY  - 1973
SP  - 606
EP  - 609
VL  - 11
AB  - Host-controlled restriction and modification of TP-1C phage and infectious
AB  - phage DNA occurs in Bacillus stearothermophilus and is subject to control by
AB  - TP-8 or TP-12 prophage.
ER  -

TY  - JOUR
AU  - Lees-Murdock, D.J.
AU  - McLoughlin, G.A.
AU  - McDaid, J.R.
AU  - Quinn, L.M.
AU  - O'Doherty, A.
AU  - Hiripi, L.
AU  - Hack, C.J.
AU  - Walsh, C.P.
TI  - Identification of 11 pseudogenes in the DNA methyltransferase gene family in rodents and humans and implications for the functional loci.
JO  - Genomics
PY  - 2004
SP  - 193
EP  - 204
VL  - 84
AB  - DNA (cytosine-5-)-methyltransferase genes are important for normal development in mice and
AB  - humans. We describe here 11 pseudogenes spread
AB  - among human, mouse, and rat belonging to this gene family, ranging from
AB  - 1 pseudogene in humans to 7 in rat, all belonging to the Dnmt3
AB  - subfamily. All except 1 rat Dnmt3b pseudogene appear to be
AB  - transcriptionally silent. Dnmt3a2, a transcript variant of Dnmt3a
AB  - starting at an alternative promoter, had the highest number of
AB  - processed pseudogenes, while none were found for the canonical Dnmt3a,
AB  - suggesting the former transcript is more highly expressed in germ
AB  - cells. Comparison of human, mouse, and rat Dnmt3a2 sequences also
AB  - suggests that human exon 8 is a recent acquisition. Alignment of the
AB  - 3'UTR of Dnmt3a2 among the functional genes and the processed
AB  - pseudogenes suggested that a second polyadenylation site downstream of
AB  - the RefSeq poly(A) was being used in mice, resulting in a longer 3'UTR,
AB  - a finding confirmed by RT-PCR in mouse tissues. We also found conserved
AB  - cytoplasmic polyadenylation elements, usually implicated in regulating
AB  - translation in oocytes, in Dnmt3b and Dnmt1. Expression of DNMT3B in
AB  - the mouse oocyte was confirmed by immunocytochemistry. These results
AB  - clarify the structure of a number of loci in the three species examined
AB  - and provide some useful insights into the structure and evolution of
AB  - this gene family.
ER  -

TY  - JOUR
AU  - Lefebure, T.
AU  - Richards, V.P.
AU  - Lang, P.
AU  - Pavinski-Bitar, P.
AU  - Stanhope, M.J.
TI  - Gene Repertoire Evolution of Streptococcus pyogenes Inferred from Phylogenomic Analysis with Streptococcus canis and Streptococcus dysgalactiae.
JO  - PLoS ONE
PY  - 2012
SP  - E37607
EP  - E37607
VL  - 7
AB  - Streptococcus pyogenes, is an important human pathogen classified within the
AB  - pyogenic group of streptococci, exclusively adapted to the human host. Our goal
AB  - was to employ a comparative evolutionary approach to better understand the
AB  - genomic events concomitant with S. pyogenes human adaptation. As part of
AB  - ascertaining these events, we sequenced the genome of one of the potential sister
AB  - species, the agricultural pathogen S. canis, and combined it in a comparative
AB  - genomics reconciliation analysis with two other closely related species,
AB  - Streptococcus dysgalactiae and Streptococcus equi, to determine the genes that
AB  - were gained and lost during S. pyogenes evolution. Genome wide phylogenetic
AB  - analyses involving 15 Streptococcus species provided convincing support for a
AB  - clade of S. equi, S. pyogenes, S. dysgalactiae, and S. canis and suggested that
AB  - the most likely S. pyogenes sister species was S. dysgalactiae. The
AB  - reconciliation analysis identified 113 genes that were gained on the lineage
AB  - leading to S. pyogenes. Almost half (46%) of these gained genes were phage
AB  - associated and 14 showed significant matches to experimentally verified bacteria
AB  - virulence factors. Subsequent to the origin of S. pyogenes, over half of the
AB  - phage associated genes were involved in 90 different LGT events, mostly involving
AB  - different strains of S. pyogenes, but with a high proportion involving the horse
AB  - specific pathogen S. equi subsp. equi, with the directionality almost exclusively
AB  - (86%) in the S. pyogenes to S. equi direction. Streptococcus agalactiae appears
AB  - to have played an important role in the evolution of S. pyogenes with a high
AB  - proportion of LGTs originating from this species. Overall the analysis suggests
AB  - that S. pyogenes adaptation to the human host was achieved in part by (i) the
AB  - integration of new virulence factors (e.g. speB, and the sal locus) and (ii) the
AB  - construction of new regulation networks (e.g. rgg, and to some extent speB).
ER  -

TY  - JOUR
AU  - Lefort, F.
AU  - Calmin, G.
AU  - Crovadore, J.
AU  - Falquet, J.
AU  - Hurni, J.P.
AU  - Osteras, M.
AU  - Haldemann, F.
AU  - Farinelli, L.
TI  - Whole-Genome Shotgun Sequence of Arthrospira platensis Strain Paraca, a Cultivated and Edible Cyanobacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00751
EP  - e00714
VL  - 2
AB  - Here we report the whole-genome shotgun sequence of a Peruvian strain of Arthrospira platensis
AB  - (Paraca), a cultivated and edible haloalkaliphilic
AB  - cyanobacterium of great scientific, technical, and economic potential.
ER  -

TY  - JOUR
AU  - Lefort, F.
AU  - Calmin, G.
AU  - Crovadore, J.
AU  - Osteras, M.
AU  - Farinelli, L.
TI  - Whole-Genome Shotgun Sequence of Pseudomonas viridiflava, a Bacterium Species Pathogenic to Ararabidopsis thaliana.
JO  - Genome Announcements
PY  - 2013
SP  - e00116
EP  - e00112
VL  - 1
AB  - We report here the first whole-genome shotgun sequence of Pseudomonas viridiflava strain
AB  - UASWS38, a bacterium species pathogenic to the biological model plant Ararabidopsis thaliana
AB  - but also usable as a biological control agent and thus of great scientific interest for
AB  - understanding the genetics of plant-microbe interactions.
ER  -

TY  - JOUR
AU  - Lefort, F.
AU  - Calmin, G.
AU  - Pelleteret, P.
AU  - Farinelli, L.
AU  - Osteras, M.
AU  - Crovadore, J.
TI  - Whole-Genome Shotgun Sequence of Bacillus amyloliquefaciens Strain UASWS BA1, a Bacterium Antagonistic to Plant Pathogenic Fungi.
JO  - Genome Announcements
PY  - 2014
SP  - e00016
EP  - e00014
VL  - 2
AB  - We report here the whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS
AB  - BA1, isolated from inner wood tissues of a decaying Platanus x
AB  - acerifolia tree. This strain proved to be antagonistic to several plant
AB  - pathogenic fungi and oomycetes and can be developed as a biological control agent
AB  - in agriculture.
ER  -

TY  - JOUR
AU  - LeFrancois, J.
AU  - Gasc, A.-M.
AU  - Sicard, M.
TI  - Electrotransformation of Streptococcus pneumoniae: Evidence for restriction of the DNA on entry.
JO  - Microb. Drug Resist.
PY  - 1997
SP  - 101
EP  - 104
VL  - 3
AB  - Electrotransformation is a method generally used in biotechnology to introduce recombinant DNA
AB  - into a wide range of bacteria.  However the mechanism of DNA entry is poorly understood.  We
AB  - report that in Streptococcus pneumoniae, a naturally transformable species,
AB  - electrotransformation efficiently introduces a plasmid replicon.  DNA is strongly restricted
AB  - by the restriction-modification systems DpnI and DpnII which degrade methylated and
AB  - nonmethylated DNA respectively at GATC sequences.  This suggests that in electrotransformation
AB  - double-strand DNA penetrates into these bacteria without a single-strand step in contrast to
AB  - natural transformation.  Single-strand DNA by itself is able to electrotransform very weakly
AB  - and linearized double-stranded plasmid DNA yields barely detectable levels of transformants.
ER  -

TY  - JOUR
AU  - Lefrancois, J.
AU  - Sicard, A.M.
TI  - Electrotransformation of Streptococcus pneumoniae: evidence for restriction of DNA on entry.
JO  - Microbiology
PY  - 1997
SP  - 523
EP  - 526
VL  - 143
AB  - Electrotransformation is a method generally used in biotechnology to introduce recombinant DNA
AB  - into a wide range of bacteria.  However, the mechanism of DNA entry is poorly understood.  We
AB  - report that in Streptococcus pneumoniae, a naturally transformable species,
AB  - electrotransformation efficiently introduces a plasmid replicon.  DNA is strongly restricted
AB  - by the restriction-modification systems DpnI and DpnII which degrade methylated and
AB  - non-methylated DNA, respectively, at GATC sequences.  This suggests that in
AB  - electrotransformation double-stranded DNA penetrates into these bacteria without a
AB  - single-stranded DNA step in contrast to natural transformation.  Single-stranded DNA by itself
AB  - is able to electrotransform very weakly and linearized double-stranded plasmid DNA yields
AB  - barely detectable levels of transformants.
ER  -

TY  - JOUR
AU  - Leguizamon, M.
AU  - Draghi, W.O.
AU  - Montanaro, P.
AU  - Schneider, A.
AU  - Prieto, C.I.
AU  - Martina, P.
AU  - Lagares, A.
AU  - Lasch, P.
AU  - Bosch, A.
TI  - Draft Genome Sequence of Burkholderia puraquae Type Strain CAMPA 1040, Isolated from Hospital Settings in Cordoba, Argentina.
JO  - Genome Announcements
PY  - 2017
SP  - e01302
EP  - e01317
VL  - 5
AB  - We report here the draft genome sequence of Burkholderia puraquae type strain CAMPA 1040, a
AB  - member of the Burkholderia cepacia complex. This strain, isolated
AB  - from a hemodialysis water reservoir, harbors several stress tolerance genes, such
AB  - as the systems for low oxygen survival, for copper tolerance, and for osmotic
AB  - stress resistance.
ER  -

TY  - JOUR
AU  - Lehours, P.
AU  - Chaineux, J.
AU  - Dupouy, S.
AU  - Menard, A.
AU  - Morgner, A.
AU  - Megraud, F.
TI  - Identification of a new restriction modification system in Helicobacter pylori.
JO  - Int. J. Antimicrob. Agents
PY  - 2004
SP  - S211
EP  - S211
VL  - 24
AB  - Restriction modification systems are among the largest categories of specific genes in
AB  - Helicobacter pylori.  In an H. pylori strain isolated from a patient with gastric MALT
AB  - lymphoma, a new RMS was identified by subtractive hydridisation and chromosome walking.  This
AB  - RMS is present in a highly conserved area of the H. pylori genome of J99 and 26,695 reference
AB  - strains, but harbouring an ORF with unknown function and without homologies to a methylase or
AB  - an endonuclease.  This RMS was also described in parallel by Taiwanese researchers and named
AB  - HpyCII.  Its restriction site is identical to BccI (RMS type 1 of Bacteroides cacae).  Our
AB  - goal was to study the prevalence and the genetic evolution of this RMS in H. pylori.  The
AB  - prevalence of this new RMS was tested by PCR and dot blot hybridisation on a collection of
AB  - 62II.pylori strains isolated from patients with gastric MALT lymphoma.  The restriciton
AB  - profiles obtained with BccI on the chromosomal DNA of these strains were then compared to the
AB  - amplicon size obtained with primers designed on the ORF flanking HpyCII.  The prevalence of
AB  - HpyCII in our collection of H. pylori strains from gastric MALT lymphoma, was 66.1% (41/62).
AB  - For 35 strains (85.4%) the amplicons obtained had the expected size of 3831 bp indicating that
AB  - the RMS was complete.  In 30 out of 35 of these strains (85.7%), the DNA obtained was
AB  - protected from digestion by BccI as expected while in five cases a digestion was observed.
AB  - For six additional strains, a 1636 bp amplicon was obtained indicating that probably a
AB  - truncated RMS was prsent.  DNA from these six strains were digested by BccI.  For most H.
AB  - pylori strains harbouring HpyCII, this RMS is present in an active form.  The genetic
AB  - evolution from an active to an inactive form, then to its complete deletion as in reference
AB  - strains, remains to be determined.  To further investigate the question, amplicons from
AB  - strains with discrepant results will be sequenced.
ER  -

TY  - JOUR
AU  - Lehours, P.
AU  - Dupouy, S.
AU  - Chaineux, J.
AU  - Ruskone-Fourmestraux, A.
AU  - Delchier, J.C.
AU  - Morgner, A.
AU  - Megraud, F.
AU  - Menard, A.
TI  - Genetic diversity of the HpyC1I restriction modification system in Helicobacter pylori.
JO  - Res. Microbiol.
PY  - 2007
SP  - 265
EP  - 271
VL  - 158
AB  - Helicobacter pylori is unique because of the unusually high number and diversity of its
AB  - restriction modification (R-M) systems. HpyC1I R-M was
AB  - recently characterized and contains an endonuclease which is an
AB  - isoschizomer of the endonuclease BccI. This R-M is involved in
AB  - adherence to gastric epithelial cells, a crucial step in bacterial
AB  - pathogenesis. This observation illustrates the fact that R-M systems
AB  - have other putative biological functions in addition to protecting the
AB  - bacterial genome from external DNA. The genomic diversity of HpyC1I R-M
AB  - was evaluated more precisely on a large collection of H. pylori strains
AB  - by PCR, susceptibility to BccI digestion and sequencing. The results
AB  - obtained support the mechanism of gain and loss of this R-M system in
AB  - the H. pylori genome, and suggest that it is an ancestral system which
AB  - gradually disappears during H. pylori evolution, following successive
AB  - steps: (1) inactivation of the endonuclease gene, followed or
AB  - accompanied by: (2) inactivation of the methyltransferase genes, and
AB  - then: (3) definitive loss, leaving only short endonuclease remnant
AB  - sequences.
ER  -

TY  - JOUR
AU  - Lehours, P.
AU  - Vale, F.F.
AU  - Bjursell, M.K.
AU  - Melefors, O.
AU  - Advani, R.
AU  - Glavas, S.
AU  - Guegueniat, J.
AU  - Gontier, E.
AU  - Lacomme, S.
AU  - Alves, M.A.
AU  - Menard, A.
AU  - Megraud, F.
AU  - Engstrand, L.
AU  - Andersson, A.F.
TI  - Genome sequencing reveals a phage in Helicobacter pylori.
JO  - MBio
PY  - 2011
SP  - e00239
EP  - e00211
VL  - 2
AB  - Helicobacter pylori chronically infects the gastric mucosa in more than half of the human
AB  - population; in a subset of this population, its presence
AB  - is associated with development of severe disease, such as gastric cancer.
AB  - Genomic analysis of several strains has revealed an extensive H. pylori
AB  - pan-genome, likely to grow as more genomes are sampled. Here we describe
AB  - the draft genome sequence (63 contigs; 26x mean coverage) of H. pylori
AB  - strain B45, isolated from a patient with gastric mucosa-associated
AB  - lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage
AB  - integrated in the bacterial genome. The prophage shares most of its genes
AB  - (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba.
AB  - After UV treatment of liquid cultures, circular DNA carrying the prophage
AB  - integrase gene could be detected, and intracellular tailed phage-like
AB  - particles were observed in H. pylori cells by transmission electron
AB  - microscopy, indicating that phage production can be induced from the
AB  - prophage. PCR amplification and sequencing of the integrase gene from 341
AB  - H. pylori strains from different geographic regions revealed a high
AB  - prevalence of the prophage (21.4%). Phylogenetic reconstruction showed
AB  - four distinct clusters in the integrase gene, three of which tended to be
AB  - specific for geographic regions. Our study implies that phages may play
AB  - important roles in the ecology and evolution of H. pylori. IMPORTANCE:
AB  - Helicobacter pylori chronically infects the gastric mucosa in more than
AB  - half of the human population, and while most of the infected individuals
AB  - do not develop disease, H. pylori infection doubles the risk of developing
AB  - gastric cancer. An abundance and diversity of viruses (phages) infect
AB  - microbial populations in most environments and are important mediators of
AB  - microbial diversity. Our finding of a 24.6-kb prophage integrated inside
AB  - an H. pylori genome and the observation of circular integrase
AB  - gene-containing DNA and phage-like particles inside cells upon UV
AB  - treatment demonstrate that we have discovered a viable H. pylori phage.
AB  - The additional finding of integrase genes in a large proportion of
AB  - screened isolates of diverse geographic origins indicates that the
AB  - prevalence of prophages may have been underestimated in H. pylori. Since
AB  - phages are important drivers of microbial evolution, the discovery should
AB  - be important for understanding and predicting genetic diversity in H.
AB  - pylori.
ER  -

TY  - JOUR
AU  - Lehri, B.
AU  - Seddon, A.M.
AU  - Karlyshev, A.V.
TI  - Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 19
EP  - 19
VL  - 12
AB  - The article provides an overview of the genomic features of Lactobacillus fermentum strain
AB  - 3872. The genomic sequence reported here is one of three L.
AB  - fermentum genome sequences completed to date. Comparative genomic analysis
AB  - allowed the identification of genes that may be contributing to enhanced
AB  - probiotic properties of this strain. In particular, the genes encoding putative
AB  - mucus binding proteins, collagen-binding proteins, class III bacteriocin, as well
AB  - as exopolysaccharide and prophage-related genes were identified. Genes related to
AB  - bacterial aggregation and survival under harsh conditions in the gastrointestinal
AB  - tract, along with the genes required for vitamin production were also found.
ER  -

TY  - JOUR
AU  - Lei, H.
AU  - Oh, S.P.
AU  - Okano, M.
AU  - Juttermann, R.
AU  - Goss, K.A.
AU  - Jaenisch, R.
AU  - Li, E.
TI  - De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells.
JO  - Development
PY  - 1996
SP  - 3195
EP  - 3205
VL  - 122
AB  - It has been a controversial issue as to how many DNA cytosine methyltransferase mammalian
AB  - cells have and whether de novo methylation and maintenance methylation activities are encoded
AB  - by a single gene or two different genes.  To address these questions, we have generated a null
AB  - mutation of the only known mammalian DNA methyltransferase gene through homologous
AB  - recombination in mouse embryonic stem cells and found that the development of the homozygous
AB  - embryos is arrested prior to the 8-somite stage.  Surprisingly, the null mutant embryonic stem
AB  - cells are viable and contain low but stable levels of methyl cytosine and methyltransferase
AB  - activity, suggesting the existence of a second DNA methyltransferase in mammalian cells.
AB  - Further studies indicate that de novo methylation activity is not impaired by the mutation as
AB  - integrated provirus DNA in MoMuLV-infected homozygous embryonic stem cells become methylated
AB  - at a similar rate as in wild-type cells.  Differentiation of mutant cells results in further
AB  - reduction of methyl cytosine levels, consistent with the de novo methylation activity being
AB  - down regulated in differentiated cells.  These results provide the first evidence that an
AB  - independently encoded DNA methyltransferase is present in mammalian cells which is capable of
AB  - de novo methylating cellular and viral DNA in vivo.
ER  -

TY  - JOUR
AU  - Lei, M.
AU  - Lu, P.
AU  - Jin, L.
AU  - Wang, Y.
AU  - Qin, J.
AU  - Xu, X.
AU  - Zhang, L.
AU  - Wang, Y.
TI  - Complete Genome Sequence of Paenibacillus polymyxa CF05, a Strain of Plant Growth-Promoting Rhizobacterium with Elicitation of Induced Systemic Resistance.
JO  - Genome Announcements
PY  - 2015
SP  - e00198
EP  - e00115
VL  - 3
AB  - Paenibacillus polymyxa CF05 is a Gram-positive rod-shaped bacterium isolated from the interior
AB  - of an ancient tree, Cryptomeria fortunei, in China. This bacterium
AB  - displays potent biocontrol effects against certain soil-borne diseases and the
AB  - elicitation of induced systemic resistance in tomatoes. Here, we report the
AB  - complete genome sequence of P. polymyxa CF05.
ER  -

TY  - JOUR
AU  - Lei, X.
AU  - Yuan, F.
AU  - Shi, Y.
AU  - Li, X.
AU  - Wang, L.
AU  - Hong, B.
TI  - Draft Genome Sequence of Norvancomycin-Producing Strain Amycolatopsis orientalis  CPCC200066.
JO  - Genome Announcements
PY  - 2015
SP  - e00296
EP  - e00215
VL  - 3
AB  - Amycolatopsis orientalis CPCC200066 is an actinomycete that can produce the glycopeptide
AB  - antibiotic norvancomycin, which has significant inhibitory activity
AB  - against Gram-positive cocci and bacilli. Here, we report the draft genome
AB  - sequence of A. orientalis CPCC200066 and identified the genes involved in
AB  - norvancomycin biosynthesis.
ER  -

TY  - JOUR
AU  - Lei, X.Y.
AU  - Ou, T.
AU  - Zhu, R.L.
AU  - Zhang, Q.Y.
TI  - Sequencing and analysis of the complete genome of Rana grylio virus (RGV).
JO  - Arch. Virol.
PY  - 2012
SP  - 1559
EP  - 1564
VL  - 157
AB  - Infection with Rana grylio virus (RGV), an iridovirus isolated in China in 1995,
AB  - resulted in a high mortality rate in frogs. The complete genome sequence of RGV
AB  - was determined and analyzed. The genomic DNA was 105,791 bp long, with 106 open
AB  - reading frames (ORFs). Dot plot analysis showed that the gene order of RGV shared
AB  - colinearity with three completely sequenced ranaviruses. A phylogenetic tree was
AB  - constructed based on concatenated sequences of iridovirus 26 core-gene-encoded
AB  - proteins, and the result showed high bootstrap support for RGV being a member of
AB  - the genus Ranavirus and that iridoviruses of other genera also clustered closely.
AB  - A microRNA (miRNA) prediction revealed that RGV could encode 18 mature miRNAs,
AB  - many of which were located near genes associated with virus replication.
AB  - Thirty-three repeated sequences were found in the RGV genome. These results
AB  - provide insight into the genetic nature of RGV and are useful for laboratory
AB  - diagnosis for vertebrate iridoviruses.
ER  -

TY  - JOUR
AU  - Leimbach, A.
AU  - Poehlein, A.
AU  - Witten, A.
AU  - Scheutz, F.
AU  - Schukken, Y.
AU  - Daniel, R.
AU  - Dobrindt, U.
TI  - Complete Genome Sequences of Escherichia coli Strains 1303 and ECC-1470 Isolated  from Bovine Mastitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00182
EP  - e00115
VL  - 3
AB  - Escherichia coli is the leading causative agent of acute bovine mastitis. Here, we report the
AB  - complete genome sequence of E. coli O70:H32 strain 1303, isolated
AB  - from an acute case of bovine mastitis, and E. coli Ont:Hnt strain ECC-1470,
AB  - isolated from a persistent infection.
ER  -

TY  - JOUR
AU  - Leimbach, A.
AU  - Poehlein, A.
AU  - Witten, A.
AU  - Wellnitz, O.
AU  - Shpigel, N.
AU  - Petzl, W.
AU  - Zerbe, H.
AU  - Daniel, R.
AU  - Dobrindt, U.
TI  - Whole-Genome Draft Sequences of Six Commensal Fecal and Six Mastitis-Associated Escherichia coli Strains of Bovine Origin.
JO  - Genome Announcements
PY  - 2016
SP  - e00753
EP  - e00716
VL  - 4
AB  - The bovine gastrointestinal tract is a natural reservoir for commensal and pathogenic
AB  - Escherichia coli strains with the ability to cause mastitis. Here, we
AB  - report the whole-genome sequences of six E. coli isolates from acute mastitis
AB  - cases and six E. coli isolates from the feces of udder-healthy cows.
ER  -

TY  - JOUR
AU  - Leismann, O.
AU  - Roth, M.
AU  - Friedrich, T.
AU  - Wende, W.
AU  - Jeltsch, A.
TI  - The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase M.FokI is a tandem enzyme of two independent domains with very different kinetic properties.
JO  - Eur. J. Biochem.
PY  - 1998
SP  - 899
EP  - 906
VL  - 251
AB  - The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase, M.FokI, modifies
AB  - both adenine residues within its asymmetric recognition sequence 5'-GGATG/CATCC-3'.  It is a
AB  - fusion protein comprising two independent enzymes.  We have cloned, overexpressed and purified
AB  - full-length M.FokI as well as both individual domains and analyzed their kinetics of DNA
AB  - methylation using unmethylated and hemimethylated oligodeoxynucleotide substrates.  Our data
AB  - show that both domains of M.FokI methylate DNA independently of each other but cooperate in
AB  - DNA binding.  In agreement to former studies, the N-terminal domain of M.FokI modifies the
AB  - upper strand of the recognition sequence (GGATG).  It strongly prefers hemimethylated
AB  - (5'-GGATG/CmATCC-3'; mA=N6-methyladenosine) over unmethylated substrates.  In contrast, the
AB  - terminal domain prefers unmethylated DNA substrates.  Surprisingly, in addition to methylating
AB  - the lower strand of the recognition sequence (CATCC), M.FokI-(355-647) also modifies the upper
AB  - strand (GGATG), albeit with a lower activity.  In addition methylation was detected at CACCC
AB  - sites, but not at sites in which a central AT dinucleotide is flanked by at least one A.T or
AB  - T.A base pair.  These results suggests that M.FokI-(335-647) either has a very degenerate
AB  - specificity for (G/C)AT(G/C) and sites similar to CATCC or GGATG or, alternatively, that it
AB  - has a dual specificity for CATCC and GGATG.
ER  -

TY  - JOUR
AU  - Leite, L.R.
AU  - Medeiros, J.D.
AU  - Fernandes, G.R.
AU  - Araujo, F.
AU  - Pylro, V.S.
AU  - Salim, A.C.
AU  - Volpini, A.
AU  - Oliveira, G.
AU  - Cuadros-Orellana, S.
TI  - Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397T.
JO  - Genome Announcements
PY  - 2016
SP  - e00527
EP  - e00516
VL  - 4
AB  - We report the draft genome sequence of Hydrotalea flava CCUG 51397(T), the type strain of the
AB  - genus Hydrotalea (family Chitinophagaceae), isolated from water
AB  - samples in southern Sweden.
ER  -

TY  - JOUR
AU  - Lekota, K.E.
AU  - Mafofo, J.
AU  - Madoroba, E.
AU  - Rees, J.
AU  - van Heerden, H.
AU  - Muchadeyi, F.C.
TI  - Draft Genome Sequences of Two South African Bacillus anthracis Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01313
EP  - e01315
VL  - 3
AB  - Bacillus anthracis is a Gram-positive bacterium that causes anthrax, mainly in herbivores
AB  - through exotoxins and capsule produced on plasmids, pXO1 and pXO2.
AB  - This paper compares the whole-genome sequences of two B. anthracis strains from
AB  - an endemic region and a sporadic outbreak in South Africa. Sequencing was done
AB  - using next-generation sequencing technologies.
ER  -

TY  - JOUR
AU  - Lemieux, C.
AU  - Lee, R.W.
TI  - Nonreciprocal recombination between alleles of the chloroplast 23S rRNA gene in interspecific Chlamydomonas crosses.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1987
SP  - 4166
EP  - 4170
VL  - 84
AB  - The inheritance of six polymorphic loci mapping in the rRNA-encoding (rDNA) region of the
AB  - inverted repeat sequence of chloroplast DNA (cpDNA) was scored in hybrid subclones derived
AB  - from reciprocal interspecific crosses between the green algae Chlamydomonas eugametos and
AB  - Chlamydomonas moewusii. In order to enhance the detection of cells that had undergone
AB  - recombination between parental cpDNAs, hybrids were selected that inherited a chloroplast
AB  - antiboiotic-resistance marker contributed by the mating-type-minus (mt-) parent, the parent
AB  - that normally contributes fewer cpDNA molecules. The major findings of this study can be
AB  - summarized as follows. (i) The majority of the hybrids (14/17) were recombinant for cpDNA
AB  - markers in the 10-kilobase-pair rDNA region under study. (ii) Only one allele of each
AB  - polymorphic cpDNA locus was ever detected in the hybrids, thus suggesting that newly
AB  - recombined rDNA sequences in one copy of the inverted repeat are rapidly spread to the other
AB  - by a copy-correction mechanism. (iii) Chloroplast streptomycin-resistance (sr-2) and
AB  - erythromycin-resistance (er-nM1) loci, although showing litle or no genetic linkage, were
AB  - mapped to the 16S and 23S rRNA gene regions of the cpDNA, respectively, by virtue of their
AB  - perfect coinheritance with polymorphic markers within these genes. (iv) cpDNA markers
AB  - associated with a putative intron of the C. eugametos 23S rRNA gene were inherited by all 17
AB  - hybrids. Such a result is similar to that observed for certain alleles of the large rRNA gene
AB  - of yeast mitochrondria in crosses between Omega+ and Omega- strains.
ER  -

TY  - JOUR
AU  - Lemriss, H.
AU  - Dumont, Y.
AU  - Lemriss, S.
AU  - Martins-Simoes, P.
AU  - Butin, M.
AU  - Lahlou, L.
AU  - Rasigade, J.P.
AU  - El Kabbaj, S.
AU  - Laurent, F.
AU  - Ibrahimi, A.
TI  - Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C.
JO  - Genome Announcements
PY  - 2016
SP  - e00541
EP  - e00516
VL  - 4
AB  - Here, we report the draft genome sequences of methicillin-susceptible Staphylococcus captis
AB  - pulsotype NCRS-C (CR02 strain) and multiresistant
AB  - Staphylococcus captis pulsotype NCRS-A (CR07 strain).
ER  -

TY  - JOUR
AU  - Lemriss, H.
AU  - Lemriss, S.
AU  - Butin, M.
AU  - Ibrahimi, A.
AU  - El Kabbaj, S.
AU  - Rasigade, J.
AU  - Laurent, F.
TI  - Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1118
EP  - 1127
VL  - 9
AB  - Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the
AB  - human microflora. Recently, a clonal population of Staphylococcus
AB  - capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis
AB  - (LOS) in several neonatal intensive care units in France. Here, we report the
AB  - complete genome sequence and annotation of the prototype Staphylococcus capitis
AB  - NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids)
AB  - exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA
AB  - genes and 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Lemriss, H.
AU  - Lemriss, S.
AU  - Martins-Simoes, P.
AU  - Butin, M.
AU  - Lahlou, L.
AU  - Rasigade, J.P.
AU  - Kearns, A.
AU  - Denis, O.
AU  - Deighton, M.
AU  - Ibrahimi, A.
AU  - Laurent, F.
AU  - El Kabbaj, S.
TI  - Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units.
JO  - Genome Announcements
PY  - 2015
SP  - e00501
EP  - e00515
VL  - 3
AB  - Staphylococcus capitis pulsotype NRCS-A was previously reported as a frequent cause of
AB  - late-onset sepsis in neonatal intensive care units (NICUs) worldwide.
AB  - Here, we report the whole-genome shotgun sequences of four S. capitis pulsotype
AB  - NCRS-A strains, CR03, CR04, CR05, and CR09, isolated from Belgium, Australia, the
AB  - United Kingdom, and France, respectively.
ER  -

TY  - JOUR
AU  - Lenneman, E.M.
AU  - Barney, B.M.
TI  - Draft Genome Sequences of the Alga-Degrading Bacteria Aeromonas hydrophila Strain AD9 and Pseudomonas pseudoalcaligenes Strain AD6.
JO  - Genome Announcements
PY  - 2014
SP  - e00709
EP  - e00714
VL  - 2
AB  - Aeromonas hydrophila AD9 and Pseudomonas pseudoalcaligenes AD6 have been linked to algal cell
AB  - degradation. Here we report the draft genomes of A. hydrophila AD9
AB  - and P. pseudoalcaligenes AD6 for the investigation of causative agents for algal
AB  - cell degradation.
ER  -

TY  - JOUR
AU  - Lennen, R.M.
AU  - Nilsson, W.A.I.
AU  - Pedersen, M.
AU  - Bonde, M.
AU  - Luo, H.
AU  - Herrgard, M.J.
AU  - Sommer, M.O.
TI  - Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - e36
EP  - e36
VL  - 44
AB  - Homologous recombination of single-stranded oligonucleotides is a highly efficient process for
AB  - introducing precise mutations into the genome of E. coli
AB  - and other organisms when mismatch repair (MMR) is disabled. This can result in
AB  - the rapid accumulation of off-target mutations that can mask desired phenotypes,
AB  - especially when selections need to be employed following the generation of
AB  - combinatorial libraries. While the use of inducible mutator phenotypes or other
AB  - MMR evasion tactics have proven useful, reported methods either require
AB  - non-mobile genetic modifications or costly oligonucleotides that also result in
AB  - reduced efficiencies of replacement. Therefore a new system was developed,
AB  - Transient Mutator Multiplex Automated Genome Engineering (TM-MAGE), that solves
AB  - problems encountered in other methods for oligonucleotide-mediated recombination.
AB  - TM-MAGE enables nearly equivalent efficiencies of allelic replacement to the use
AB  - of strains with fully disabled MMR and with an approximately 12- to 33-fold lower
AB  - off-target mutation rate. Furthermore, growth temperatures are not restricted and
AB  - a version of the plasmid can be readily removed by sucrose counterselection.
AB  - TM-MAGE was used to combinatorially reconstruct mutations found in evolved
AB  - salt-tolerant strains, enabling the identification of causative mutations and
AB  - isolation of strains with up to 75% increases in growth rate and greatly reduced
AB  - lag times in 0.6 M NaCl.
ER  -

TY  - JOUR
AU  - Lentini, A.
AU  - Lagerwall, C.
AU  - Vikingsson, S.
AU  - Mjoseng, H.K.
AU  - Douvlataniotis, K.
AU  - Vogt, H.
AU  - Green, H.
AU  - Meehan, R.R.
AU  - Benson, M.
AU  - Nestor, C.E.
TI  - A reassessment of DNA-immunoprecipitation-based genomic profiling.
JO  - Nat. Methods
PY  - 2018
SP  - 499
EP  - 504
VL  - 15
AB  - DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for
AB  - profiling DNA modifications in mammalian genomes. However, the results
AB  - of independent DIP-seq studies often show considerable variation between profiles
AB  - of the same genome and between profiles obtained by alternative methods. Here we
AB  - show that these differences are primarily due to the intrinsic affinity of IgG
AB  - for short unmodified DNA repeats. This pervasive experimental error accounts for
AB  - 50-99% of regions identified as 'enriched' for DNA modifications in DIP-seq data.
AB  - Correction of this error profoundly altered DNA-modification profiles for
AB  - numerous cell types, including mouse embryonic stem cells, and subsequently
AB  - revealed novel associations among DNA modifications, chromatin modifications and
AB  - biological processes. We conclude that both matched input and IgG controls are
AB  - essential in order for the results of DIP-based assays to be interpreted
AB  - correctly, and that complementary, non-antibody-based techniques should be used
AB  - to validate DIP-based findings to avoid further misinterpretation of genome-wide
AB  - profiling data.
ER  -

TY  - JOUR
AU  - Lenz, A.
AU  - Tomkins, J.
AU  - Fabich, A.J.
TI  - Draft Genome Sequence of Citrobacter rodentium DBS100 (ATCC 51459), a Primary Model of Enterohemorrhagic Escherichia coli Virulence.
JO  - Genome Announcements
PY  - 2015
SP  - e00415
EP  - e00415
VL  - 3
AB  - Citrobacter rodentium is a Gram-negative bacterium which causes transmissible murine colonic
AB  - hyperplasia and models the virulence of enterohemorrhagic
AB  - Escherichia coli in vivo. Thus, C. rodentium is used to study human
AB  - gastrointestinal disease. We present the draft genome sequence of C. rodentium
AB  - strain ATCC 51459, also known as DBS100.
ER  -

TY  - JOUR
AU  - Lenz, T.
AU  - Bonnist, E.Y.M.
AU  - Pljevaljcic, G.
AU  - Neely, R.K.
AU  - Dryden, D.T.F.
AU  - Scheidig, A.J.
AU  - Jones, A.C.
AU  - Weinhold, E.
TI  - 2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence.
JO  - J. Am. Chem. Soc.
PY  - 2007
SP  - 6240
EP  - 6248
VL  - 129
AB  - We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed
AB  - with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix
AB  - and occupying virtually the same position in the active site as the natural target adenine.
AB  - Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this
AB  - state: base flipping is accompanied by the loss of the very short ( approximately 50 ps)
AB  - lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine
AB  - is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic
AB  - motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping
AB  - by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well
AB  - as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same
AB  - distinctive fluorescence response confirms complete destacking from DNA and is also observed
AB  - when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is
AB  - substituted by an abasic site analog. The corresponding cocrystal structure shows
AB  - 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not
AB  - essential for base flipping. However, in this structure, a shift of the 3' neighbor of the
AB  - target base into the vacancy left after base flipping is observed, apparently replicating a
AB  - stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide
AB  - quenching measurements of M.TaqI complexes in solution provide evidence for an alternative
AB  - binding site for the extra-helical target base within M.TaqI and suggest that the partner
AB  - thymine assists in delivering the target base into the active site.
ER  -

TY  - JOUR
AU  - Leon, M.J.
AU  - Ghai, R.
AU  - Fernandez, A.B.
AU  - Sanchez-Porro, C.
AU  - Rodriguez-Valera, F.
AU  - Ventosa, A.
TI  - Draft Genome of Spiribacter salinus M19-40, an Abundant Gammaproteobacterium in Aquatic Hypersaline Environments.
JO  - Genome Announcements
PY  - 2013
SP  - e00179
EP  - e00112
VL  - 1
AB  - We have previously used a de novo metagenomic assembly approach to describe the presence of an
AB  - abundant gammaproteobacterium comprising nearly 15% of the
AB  - microbial community in an intermediate salinity solar saltern pond. We have
AB  - obtained this microbe in pure culture and describe the genome sequencing of the
AB  - halophilic photoheterotrophic microbe, Spiribacter salinus M19-40.
ER  -

TY  - JOUR
AU  - Leonard, M.T.
AU  - Davis-Richardson, A.G.
AU  - Ardissone, A.N.
AU  - Kemppainen, K.M.
AU  - Drew, J.C.
AU  - Ilonen, J.
AU  - Knip, M.
AU  - Simell, O.
AU  - Toppari, J.
AU  - Veijola, R.
AU  - Hyoty, H.
AU  - Triplett, E.W.
TI  - The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei.
JO  - Front. Microbiol.
PY  - 2014
SP  - 361
EP  - 361
VL  - 5
AB  - Despite the large interest in the human microbiome in recent years, there are no reports of
AB  - bacterial DNA methylation in the microbiome.  Here metagenomic sequencing using the Pacific
AB  - Biosciences platform allowed for rapid identification of bacterial GATC methylation status of
AB  - a bacterial species in human stool samples.  For this work, two stool samples were chosen that
AB  - were dominated by a single species, Bacteroides dorei.  Based on 16S rRNA analysis, this
AB  - species represented over 45% of the bacteria present in these two samples.  The B. dorei
AB  - genome sequence from these samples was determined and the GATC methylation sites mapped.  The
AB  - Bacteroides dorei genome from one subject lacked any GATC methylation and lacked the DNA
AB  - adenine methyltransferase genes.  In contrast, B. dorei from another subject contained 20,551
AB  - methylated GATC sites.  Of the 4970 open reading frames identified in the GATC methylated B.
AB  - dorei genome, 3184 genes were methylated as well as 1735 GATC methylations in intergenic
AB  - regions.  These results suggest that DNA methylation patterns are important to consider in
AB  - multi-omic analyses of microbiome samples seeking to discover the diversity of bacterial
AB  - functions and may differ between disease states.
ER  -

TY  - JOUR
AU  - Leonard, M.T.
AU  - Fagen, J.R.
AU  - Davis-Richardson, A.G.
AU  - Davis, M.J.
AU  - Triplett, E.W.
TI  - Complete genome sequence of Liberibacter crescens BT-1.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 271
EP  - 283
VL  - 7
ER  -

TY  - JOUR
AU  - Leonard, M.T.
AU  - Panayotova, N.
AU  - Farmerie, W.G.
AU  - Triplett, E.W.
AU  - Nicholson, W.L.
TI  - Complete Genome Sequence of Carnobacterium gilichinskyi Strain WN1359T (DSM 27470T).
JO  - Genome Announcements
PY  - 2013
SP  - e00985
EP  - e00913
VL  - 1
AB  - We report the complete genome sequence of Carnobacterium gilichinskyi strain WN1359,
AB  - previously isolated from Siberian permafrost and capable of growth under
AB  - cold (0 degrees C), anoxic, CO2-dominated, low-pressure (0.7-kPa) conditions in a
AB  - simulation of the Mars atmosphere.
ER  -

TY  - JOUR
AU  - Leonard, M.T.
AU  - Valladares, R.B.
AU  - Ardissone, A.
AU  - Gonzalez, C.F.
AU  - Lorca, G.L.
AU  - Triplett, E.W.
TI  - Complete Genome Sequences of Lactobacillus johnsonii Strain N6.2 and Lactobacillus reuteri Strain TD1.
JO  - Genome Announcements
PY  - 2014
SP  - e00397
EP  - e00314
VL  - 2
AB  - We report here the complete genome sequences of Lactobacillus johnsonii strain N6.2, a
AB  - homofermentative lactic acid intestinal bacterium, and Lactobacillus
AB  - reuteri strain TD1, a heterofermentative lactic acid intestinal bacterium, both
AB  - isolated from a type 1 diabetes-resistant rat model.
ER  -

TY  - JOUR
AU  - Leonard, S.R.
AU  - Lacher, D.W.
AU  - Elkins, C.A.
AU  - Jung, C.M.
TI  - Draft Genome Sequence of the Multidrug-Resistant Escherichia coli Strain LR09, Isolated from a Wastewater Treatment Plant.
JO  - Genome Announcements
PY  - 2014
SP  - e00272
EP  - e00214
VL  - 2
AB  - We report the draft genome sequence of Escherichia coli O1:H6 strain LR09, which  was isolated
AB  - from a wastewater treatment plant and displays high resistance to five fluoroquinolone
AB  - antimicrobials. The assembled data determine that the strain clusters with E. coli phylogroup
AB  - F and harbors a plasmid conferring resistance to a broad spectrum of antibiotics.
ER  -

TY  - JOUR
AU  - Leonard, S.R.
AU  - Lacher, D.W.
AU  - Lampel, K.A.
TI  - Draft Genome Sequences of the Enteroinvasive Escherichia coli Strains M4163 and 4608-58.
JO  - Genome Announcements
PY  - 2015
SP  - e01395
EP  - e01314
VL  - 3
AB  - We report here the draft genome sequences of enteroinvasive Escherichia coli (EIEC) O124:H30
AB  - strain M4163 isolated from imported French cheese and EIEC
AB  - O143:H26 strain 4608-58. The assembled data determined that both strains contain
AB  - multiple copies of the ipaH gene, as well as the pINV A form of the invasion
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Leong, K.W.C.
AU  - Cooley, L.A.
AU  - O'Toole, R.F.
TI  - Draft Genome Sequence of New Vancomycin-Resistant Enterococcus faecium Sequence Type 1421.
JO  - Genome Announcements
PY  - 2018
SP  - e00438
EP  - e00418
VL  - 6
AB  - The spread of vancomycin-resistant Enterococcus faecium (VREfm) has become a challenge to
AB  - health care infection control worldwide. In 2015, a marked increase
AB  - in VREfm isolation was detected in acute public hospitals in Tasmania. We report
AB  - here the draft whole-genome sequence of a newly designated VREfm sequence type,
AB  - sequence type 1421 (ST1421).
ER  -

TY  - JOUR
AU  - Leong, L.E.X.
AU  - Shaw, D.
AU  - Papanicolas, L.
AU  - Lagana, D.
AU  - Bastian, I.
AU  - Rogers, G.B.
TI  - Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia.
JO  - Genome Announcements
PY  - 2017
SP  - e00756
EP  - e00717
VL  - 5
AB  - Enterobacter cloacae is a common member of the gut microbiota in healthy individuals. However,
AB  - it is also an opportunistic pathogen, capable of causing
AB  - bacteremia. We report the draft genomes of two Enterobacter cloacae subspecies
AB  - cloacae strains isolated from hematology patients with bacteremia. Both isolates
AB  - carry genes encoding extended-spectrum beta-lactamases.
ER  -

TY  - JOUR
AU  - Leonhardt, H.
AU  - Page, A.W.
AU  - Weier, H.U.
AU  - Bestor, T.H.
TI  - A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.
JO  - Cell
PY  - 1992
SP  - 865
EP  - 873
VL  - 71
AB  - Tissue-specific patterns of methylated deoxycytidine residues in the mammalian genome are
AB  - preserved by postreplicative methylation of newly synthesized DNA. DNA methyltransferase
AB  - (MTase) is here shown to associate with replication foci during S phase but to display a
AB  - difuse nucleoplasmic distribution in non-S phase cells. Analysis of DNA MTase-B-galactosidase
AB  - fusion proteins has shown that association with replication foci is mediated by a novel
AB  - targeting sequence located near the N-terminus of DNA MTase. This sequence has the properties
AB  - expected of a targeting sequence in that it is not required for enzymatic activity, prevents
AB  - proper targeting when deleted and, when fused to B-galactosidase, causes the fusion protein to
AB  - associate with replication foci in a cell cycle-dependent manner.
ER  -

TY  - JOUR
AU  - Leopold, S.R.
AU  - Magrini, V.
AU  - Holt, N.J.
AU  - Shaikh, N.
AU  - Mardis, E.R.
AU  - Cagno, J.
AU  - Ogura, Y.
AU  - Iguchi, A.
AU  - Hayashi, T.
AU  - Mellmann, A.
AU  - Karch, H.
AU  - Besser, T.E.
AU  - Sawyer, S.A.
AU  - Whittam, T.S.
AU  - Tarr, P.I.
TI  - A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 8713
EP  - 8718
VL  - 106
AB  - Single nucleotide polymorphisms (SNPs) in stable genome regions provide
AB  - durable measurements of species evolution. We systematically identified
AB  - each SNP in concatenations of all backbone ORFs in 7 newly or previously
AB  - sequenced evolutionarily instructive pathogenic Escherichia coli O157:H7,
AB  - O157:H(-), and O55:H7. The 1,113 synonymous SNPs demonstrate emergence of
AB  - the largest cluster of this pathogen only in the last millennium.
AB  - Unexpectedly, shared SNPs within circumscribed clusters of organisms
AB  - suggest severely restricted survival and limited effective population
AB  - sizes of pathogenic O157:H7, tenuous survival of these organisms in
AB  - nature, source-sink evolutionary dynamics, or, possibly, a limited number
AB  - of mutations that confer selective advantage. A single large segment
AB  - spanning the rfb-gnd gene cluster is the only backbone region convincingly
AB  - acquired by recombination as O157 emerged from O55. This concatenomic
AB  - analysis also supports using SNPs to differentiate closely related
AB  - pathogens for infection control and forensic purposes. However,
AB  - constrained radiations raise the possibility of making false associations
AB  - between isolates.
ER  -

TY  - JOUR
AU  - Lepcha, R.T.
AU  - Poddar, A.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Idiomarina woesei Strain W11T (DSM 27808T) Isolated from the Andaman Sea.
JO  - Genome Announcements
PY  - 2016
SP  - e00831
EP  - e00816
VL  - 4
AB  - Idiomarina woesei strain W11(T) was isolated from the Andaman Sea. Heterotrophic  growth was
AB  - observed at 30 to 37 degrees C and pH 7 to 9. It grows in the presence
AB  - of 0.5 to 12% (wt/vol) NaCl, and optimum growth occurred at 5 to 6% NaCl. The
AB  - estimated genome is 2.4 Mb and encodes 2,305 proteins.
ER  -

TY  - JOUR
AU  - Lephoto, T.E.
AU  - Featherston, J.
AU  - Gray, V.M.
TI  - Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius  sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa.
JO  - Genome Announcements
PY  - 2015
SP  - e00747
EP  - e00715
VL  - 3
AB  - Here, we report on the draft genome sequence of Serratia sp. strain TEL, associated with
AB  - Oscheius sp. TEL-2014 (Nematoda: Rhabditidae, KM492926) isolated
AB  - from a grassland in Suikerbosrand Nature Reserve near Johannesburg in South
AB  - Africa. Serratia sp. strain TEL has a genome size of 5,000,541 bp with 4,647
AB  - genes and a G+C content of 59.1%.
ER  -

TY  - JOUR
AU  - Lepikhov, K.
AU  - Tchernov, A.
AU  - Zheleznaja, L.
AU  - Matvienko, N.
AU  - Walter, J.
AU  - Trautner, T.A.
TI  - Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 4691
EP  - 4698
VL  - 29
AB  - We report the characterization and cloning of the genes for an unusual type IV
AB  - restriction-modification system, BspLU11III, from Bacillus sp. LU11. The system consists of
AB  - two methyltransferases and one endonuclease, which also possesses methyltransferase activity.
AB  - The three genes of the restriction-modification system, bsplu11IIIMa, bsplu11IIIMb and
AB  - bsplu11IIIR, are closely linked and tandemly arranged. The corresponding enzymes recognize the
AB  - dsDNA sequence 5'-GGGAC-3'/5'-GTCCC-3', with M.BspLU11IIIa modifying the A (underlined) of
AB  - one strand and M.BspLU11IIIb the inner C (underlined) of the other strand. R.BspLU11III has
AB  - both endonuclease and adenine-specific methyltransferase activities and is able to protect the
AB  - DNA against cleavage by itself. In contrast to all type IV restriction-modification systems
AB  - described so far, which have only one adenine-specific methyltransferase, BspLU11III is the
AB  - first type IV restriction-modification system that includes two methyltransferases, one of
AB  - them being cytosine specific.
ER  -

TY  - JOUR
AU  - Lepp, D.
AU  - Roxas, B.
AU  - Parreira, V.R.
AU  - Marri, P.R.
AU  - Rosey, E.L.
AU  - Gong, J.
AU  - Songer, J.G.
AU  - Vedantam, G.
AU  - Prescott, J.F.
TI  - Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis.
JO  - PLoS ONE
PY  - 2010
SP  - E10795
EP  - E10795
VL  - 5
AB  - Type A Clostridium perfringens causes poultry necrotic enteritis (NE), an
AB  - enteric disease of considerable economic importance, yet can also exist as
AB  - a member of the normal intestinal microbiota. A recently discovered
AB  - pore-forming toxin, NetB, is associated with pathogenesis in most, but not
AB  - all, NE isolates. This finding suggested that NE-causing strains may
AB  - possess other virulence gene(s) not present in commensal type A isolates.
AB  - We used high-throughput sequencing (HTS) technologies to generate draft
AB  - genome sequences of seven unrelated C. perfringens poultry NE isolates and
AB  - one isolate from a healthy bird, and identified additional novel
AB  - NE-associated genes by comparison with nine publicly available reference
AB  - genomes. Thirty-one open reading frames (ORFs) were unique to all NE
AB  - strains and formed the basis for three highly conserved NE-associated loci
AB  - that we designated NELoc-1 (42 kb), NELoc-2 (11.2 kb) and NELoc-3 (5.6
AB  - kb). The largest locus, NELoc-1, consisted of netB and 36 additional
AB  - genes, including those predicted to encode two leukocidins, an
AB  - internalin-like protein and a ricin-domain protein. Pulsed-field gel
AB  - electrophoresis (PFGE) and Southern blotting revealed that the NE strains
AB  - each carried 2 to 5 large plasmids, and that NELoc-1 and -3 were localized
AB  - on distinct plasmids of sizes approximately 85 and approximately 70 kb,
AB  - respectively. Sequencing of the regions flanking these loci revealed
AB  - similarity to previously characterized conjugative plasmids of C.
AB  - perfringens. These results provide significant insight into the
AB  - pathogenetic basis of poultry NE and are the first to demonstrate that
AB  - netB resides in a large, plasmid-encoded locus. Our findings strongly
AB  - suggest that poultry NE is caused by several novel virulence factors,
AB  - whose genes are clustered on discrete pathogenicity loci, some of which
AB  - are plasmid-borne.
ER  -

TY  - JOUR
AU  - Lepuschitz, S.
AU  - Mach, R.
AU  - Springer, B.
AU  - Allerberger, F.
AU  - Ruppitsch, W.
TI  - Draft Genome Sequence of a Community-Acquired Methicillin-Resistant Staphylococcus aureus USA300 Isolate from a River Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e01166
EP  - e01117
VL  - 5
AB  - The increasing emergence of multiresistant bacteria in health care settings in the community
AB  - and in the environment represents a major health threat worldwide.
AB  - Here, we report the draft genome sequence of a community-acquired
AB  - methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 isolate (W1) from a
AB  - small river in southern Austria.
ER  -

TY  - JOUR
AU  - Lepuschitz, S.
AU  - Pekard-Amenitsch, S.
AU  - Haunold, R.
AU  - Schill, S.
AU  - Schriebl, A.
AU  - Mach, R.
AU  - Allerberger, F.
AU  - Ruppitsch, W.
AU  - Forsythe, S.J.
TI  - Draft Genome Sequence of the First Documented Clinical Siccibacter turicensis Isolate in Austria.
JO  - Genome Announcements
PY  - 2018
SP  - e00380
EP  - e00318
VL  - 6
AB  - The nonpathogenic species Siccibacter turicensis is closely related to members of the
AB  - food-associated pathogenic genus Cronobacter and has been detected in fruit
AB  - powders, formula, spices, and herbs. Here, we report on the first clinical
AB  - isolate of S. turicensis, recovered from the labial angle of a patient with
AB  - angular cheilitis.
ER  -

TY  - JOUR
AU  - Lepuschitz, S.
AU  - Sorschag, S.
AU  - Springer, B.
AU  - Allerberger, F.
AU  - Ruppitsch, W.
TI  - Draft Genome Sequence of Carbapenemase-Producing Serratia marcescens Isolated from a Patient with Chronic Obstructive Pulmonary Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e01288
EP  - e01217
VL  - 5
AB  - The occurrence of multidrug-resistant Serratia marcescens strains producing
AB  - metallo-beta-lactamases or extended-spectrum beta-lactamases represents a serious
AB  - public health threat. Here, we report the draft genome sequence of a
AB  - multidrug-resistant carbapenemase-producing Serratia marcescens isolate recovered
AB  - from the bronchoalveolar lavage specimen of a patient suffering from chronic
AB  - obstructive pulmonary disease (COPD).
ER  -

TY  - JOUR
AU  - Lesaulnier, C.
AU  - Papamichail, D.
AU  - McCorkle, S.
AU  - Ollivier, B.
AU  - Skiena, S.
AU  - Taghavi, S.
AU  - Zak, D.
AU  - van der Lelie, D.
TI  - Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen.
JO  - Environ. Microbiol.
PY  - 2008
SP  - 926
EP  - 941
VL  - 10
AB  - The effects of elevated atmospheric CO(2) (560 p.p.m.) and subsequent
AB  - plant responses on the soil microbial community composition associated
AB  - with trembling aspen was assessed through the classification of 6996
AB  - complete ribosomal DNA sequences amplified from the Rhinelander WI
AB  - free-air CO(2) and O(3) enrichment (FACE) experiments microbial community
AB  - metagenome. This in-depth comparative analysis provides an unprecedented,
AB  - detailed and deep branching profile of population changes incurred as a
AB  - response to this environmental perturbation. Total bacterial and
AB  - eukaryotic abundance does not change; however, an increase in
AB  - heterotrophic decomposers and ectomycorrhizal fungi is observed. Nitrate
AB  - reducers of the domain bacteria and archaea, of the phylum Crenarchaea,
AB  - potentially implicated in ammonium oxidation, significantly decreased with
AB  - elevated CO(2). These changes in soil biota are evidence for altered
AB  - interactions between trembling aspen and the microorganisms in its
AB  - surrounding soil, and support the theory that greater plant detritus
AB  - production under elevated CO(2) significantly alters soil microbial
AB  - community composition.
ER  -

TY  - JOUR
AU  - Lescot, M.
AU  - Audic, S.
AU  - Robert, C.
AU  - Nguyen, T.T.
AU  - Blanc, G.
AU  - Cutler, S.J.
AU  - Wincker, P.
AU  - Couloux, A.
AU  - Claverie, J.M.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii.
JO  - PLoS Genet.
PY  - 2008
SP  - e1000185
EP  - e1000185
VL  - 4
AB  - In an effort to understand how a tick-borne pathogen adapts to the body louse, we sequenced
AB  - and compared the genomes of the recurrent fever agents
AB  - Borrelia recurrentis and B. duttonii. The 1,242,163-1,574,910-bp
AB  - fragmented genomes of B. recurrentis and B. duttonii contain a unique
AB  - 23-kb linear plasmid. This linear plasmid exhibits a large polyT track
AB  - within the promoter region of an intact variable large protein gene and a
AB  - telomere resolvase that is unique to Borrelia. The genome content is
AB  - characterized by several repeat families, including antigenic
AB  - lipoproteins. B. recurrentis exhibited a 20.4% genome size reduction and
AB  - appeared to be a strain of B. duttonii, with a decaying genome, possibly
AB  - due to the accumulation of genomic errors induced by the loss of recA and
AB  - mutS. Accompanying this were increases in the number of impaired genes and
AB  - a reduction in coding capacity, including surface-exposed lipoproteins and
AB  - putative virulence factors. Analysis of the reconstructed ancestral
AB  - sequence compared to B. duttonii and B. recurrentis was consistent with
AB  - the accelerated evolution observed in B. recurrentis. Vector
AB  - specialization of louse-borne pathogens responsible for major epidemics
AB  - was associated with rapid genome reduction. The correlation between gene
AB  - loss and increased virulence of B. recurrentis parallels that of
AB  - Rickettsia prowazekii, with both species being genomic subsets of
AB  - less-virulent strains.
ER  -

TY  - JOUR
AU  - Lesiak, J.M.
AU  - Liebl, W.
AU  - Ehrenreich, A.
TI  - Development of an in vivo methylation system for the solventogen Clostridium saccharobutylicum NCP 262 and analysis of two endonuclease mutants.
JO  - J. Biotechnol.
PY  - 2014
SP  - 97
EP  - 99
VL  - 188
AB  - The genome of the biotechnologically important solventogenic Clostridium saccharobutylicum NCP
AB  - 262 contains two operons coding for genes of presumed type I RM systems belonging to the
AB  - families A and C. They represent a limiting factor for the development of transformation and
AB  - conjugation protocols. We established an efficient triparental mating system to transfer DNA
AB  - to C. saccharobutylicum by conjugation, which includes an in vivo methylation of the donor
AB  - DNA. Furthermore we describe increased rates of conjugation in knock-out mutants of the
AB  - restrictase subunits of both RM systems.
ER  -

TY  - JOUR
AU  - Leski, T.A.
AU  - Taitt, C.R.
AU  - Bangura, U.
AU  - Ansumana, R.
AU  - Stenger, D.A.
AU  - Wang, Z.
AU  - Vora, G.J.
TI  - Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151.
JO  - Genome Announcements
PY  - 2016
SP  - e01225
EP  - e01216
VL  - 4
AB  - Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being
AB  - recognized as a causative agent of hospital-acquired urinary
AB  - tract infections and an important reservoir of antimicrobial resistance
AB  - determinants. In this report, we describe the finished genome sequence of C.
AB  - freundii strain SL151, a highly multidrug-resistant human urine isolate.
ER  -

TY  - JOUR
AU  - Lesnik, E.A.
AU  - Beschetnikova, Z.A.
AU  - Maslova, R.N.
AU  - Varshavsky, J.M.
TI  - The inhibition of restriction endonucleases due to Z-DNA in negatively supercoiled plasmids.
JO  - FEBS Lett.
PY  - 1991
SP  - 91
EP  - 93
VL  - 280
AB  - Plasmid pGC20 containing the (dGC) insert in the SmaI recognition site has been
AB  - used to study the inhibition of cleavage by different restriction endonucleases
AB  - due to Z-DNA formation in the (dCG) sequence of the negatively supercoiled
AB  - plasmid.  Data obtained indicate the different sensitivity of restriction
AB  - endonucleases to DNA conformational perturbations resulted from Z-DNA
AB  - formation.  Therefore, the inhibition of DNA cleavage by a particular
AB  - restriction endonuclease cannot serve as a criterion for the estimation of the
AB  - length of B-Z junctions in circular supercoiled DNAs.
ER  -

TY  - JOUR
AU  - Lesnik, E.A.
AU  - Beschetnikova, Z.A.
AU  - Maslova, R.N.
AU  - Varshavsky, J.M.
TI  - The influence of Z-DNA formation on the activity of restriction endonucleases.
JO  - J. Biomol. Struct. Dyn.
PY  - 1991
SP  - A118
EP  - A118
VL  - 8
AB  - Plasmid pGC20 containing the (dGC)9 insert in SmaI recognition site has been
AB  - used to study the inhibition of cleavage by six different restriction
AB  - endonucleases due to Z-DNA formation in negatively supercoiled plasmid.  The
AB  - recognition sites of the KpnI, SacI and EcoRI were located correspondingly at
AB  - 0, 6 and 12 b.p. away from Z-DNA.  The recognition sites of the BamHI, XbaI and
AB  - SalI were 1, 7 and 13 b.p. away from Z-DNA on the other side of it.  Formation
AB  - of Z-DNA in the (CG)10 sequence inhibited cleavage by restriction endonucleases
AB  - to different extents.  In the KpnI, SacI and EcoRI series the degree of enzyme
AB  - inhibition decreased as the distance between their recognition sites and the
AB  - insert increased.  Such a correlation was not observed in the BamHI, XbaI and
AB  - SalI series.  All three endonucleases were rather strongly inhibited.  These
AB  - data indicate on the different sensitivity of restriction endonucleases to DNA
AB  - conformational perturbations resulted from Z-DNA formation in the negatively
AB  - supercoiled plasmid.  Therefore, the inhibition of DNA cleavage by a particular
AB  - restriction endonuclease cannot serve as a criterion for the estimation of the
AB  - length of B-Z junctions in circular supercoiled DNAs.
ER  -

TY  - JOUR
AU  - Lesnik, E.A.
AU  - Khalimullina, Z.A.
TI  - The influence of Z-conformation of the enzyme activity of restriction endonucleases.
JO  - Mol. Biol. (Mosk)
PY  - 1989
SP  - 1638
EP  - 1644
VL  - 23
AB  - Recombinant plasmid pGC20 containing (GC)9-insert into the SmaI site of pUC19
AB  - has been used to study the inhibition of cleavage by six restriction
AB  - endonucleases; KpnI, SacI, EcoRI and also BamHI, XbaI and SalI, due to Z-DNA
AB  - formation in negatively supercoiled plasmids.  The recognition sites of these
AB  - enzymes were located at different distances on both side of the (CG)
AB  - 10-sequence.  It was shown that the inhibition of cleavage by KpnI, SacI and
AB  - EcoRI decreased in this series as fast as the distance between recognition site
AB  - and B-Z junction was increased, and no inhibition of cleavage by EcoRI was
AB  - found.  However, such a correlation was not found in the series of BamHI, XbaI
AB  - and SalI.  In contrast with EcoRI the cleavage by SalI was inhibited
AB  - completely.  These results indicate the difference in sensitivity of
AB  - restriction endonucleases to the structural perturbations of DNA associated
AB  - with B-Z junctions.  It seems to depend on features of the enzyme-substrate
AB  - interaction mechanisms and also on recognition and flanking sequences of DNA.
AB  - Consequently, experiments with the inhibition of the cleavage by any enzyme
AB  - cannot help to determine the dimension of the region of DNA with altered
AB  - structure.
ER  -

TY  - JOUR
AU  - Lesser, D.R.
AU  - Grajkowski, A.
AU  - Kurpiewski, M.R.
AU  - Koziolkiewicz, M.
AU  - Stec, W.J.
AU  - Jacobson, L.J.
TI  - Steroselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC Complex.
JO  - J. Biol. Chem.
PY  - 1992
SP  - 24810
EP  - 24818
VL  - 267
AB  - We have probed the contacts between EcoRI endonuclease and the central phosphate of its
AB  - recognition site GAApTTC, using synthetic oligonucleotides containing single sterospecific Rp-
AB  - or Sp-phosphorothioates (ps). These substitutions produce subtle sterospecific effects on
AB  - EcoRI endonuclease binding and cleavage. An Sp-Ps substitution in one strand of the DNA duplex
AB  - improves binding free energy by -1.5 kcal/mol, whereas the Rp-Ps substitution has an
AB  - unfavorable effect (+0.3 kcal/mol) on binding free energy. These effects derive principally
AB  - from changes in the first order rate constants for dissociation of the enzyme-DNA commplexes.
AB  - The first order rate constants for strand scission are also affected, in that a strand
AB  - containing Sp-Ps substitution is cleaved 2 to 3 times more rapidly than a strand containing a
AB  - normal prochiral phosphate, whereas a strand containing Rp-Ps substitution is cleaved about 3
AB  - times slower than normal. As a result, single-strand substitutions produce pronounced
AB  - asymmetry in the rates of cleavage of the two DNA strands, and this effect is exaggerated in
AB  - an Rp,Sp-heteroduplex. Ethylation-interference foot-printing indicates that none of the Ps
AB  - substitutions cause any major change in contacts between endonuclease and DNA phosphates. When
AB  - an Sp-Ps localizes P=O in the DNA major groove, a hydrogen -bonding interaction with the
AB  - backbone amide-NH of Gly116 of the endonuclease is improved relative to that with a prochiral
AB  - phosphate having intermediate P-O bond order and delocalized charge.
ER  -

TY  - JOUR
AU  - Lesser, D.R.
AU  - Kurpiewski, M.R.
AU  - Jen-Jacobson, L.
TI  - The energetic basis of specificity in the EcoRI endonuclease-DNA interaction.
JO  - Science
PY  - 1990
SP  - 776
EP  - 786
VL  - 250
AB  - High sequence selectivity in DNA-protein interactions was analyzed by measuring
AB  - discrimination by EcoRI endonuclease between the recognition site GAATTC and
AB  - systematically altered DNA sites.  Base analogue substitutions that preserve
AB  - the sequence-dependent conformational motif of the GAATTC site permit deletion
AB  - of single sites of protein-base contact at a cost of +1 to +2 kcal/mol.
AB  - However, the introduction of any one incorrect natural base pair costs +6 to
AB  - +13 kcal/mol in transition state interaction energy, the resultant of the
AB  - following interdependent factors:  deletion of one or two hydrogen bonds
AB  - between the protein and a purine base; unfavorable steric apposition between a
AB  - group on the protein and an incorrectly placed functional group on a base;
AB  - disruption of a pyrimidine contact with the protein; loss of some crucial
AB  - interactions between protein and DNA phosphates; and an increased energetic
AB  - cost of attaining the required DNA conformation in the transition state
AB  - complex.  EcoRI endonuclease thus achieves stringent discrimination by both
AB  - direct readout (protein-base contacts) and indirect readout (protein-phosphate
AB  - contacts and DNA conformation) of the DNA sequence.
ER  -

TY  - JOUR
AU  - Lesser, D.R.
AU  - Kurpiewski, M.R.
AU  - Waters, T.
AU  - Connolly, B.A.
AU  - Jen-Jacobson, L.
TI  - Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 7548
EP  - 7552
VL  - 90
AB  - We have measured the binding of EcoRI endonuclease to a complete set of purine-base analogue
AB  - sites, each of which deletes one functional group that forms a hydrogen bond with the
AB  - endonuclease in the canonical GAATTC complex. For five of six functional group deletions, the
AB  - observed penalty in binding free energy is +1.3 to +1.7 kcal/mol. For two of these cases
AB  - (replacement of adenine N7 with carbon) a single protein-base hydrogen bond is removed without
AB  - deleting an interstrand Watson-Crick hydrogen bond or causing structural adaptation in the
AB  - complex. This observation establishes that the incremental energetic contribution of one
AB  - protein-base hydrogen bond is about -1.5 kcal.mol. By contrast, deletion of the N6-amino group
AB  - of the inner adenine in the site improves binding by -1.0 kcal/mol because the penalty for
AB  - deleting a protein-base hydrogen bond is outweighed by facilitation of the required DNA
AB  - distortion (kinking) in the complex. This result provides direct evidence that the energetic
AB  - cost of distorting a DNA site can make an unfavorable contribution to protein-DNA binding.
ER  -

TY  - JOUR
AU  - Letek, M. et al.
TI  - The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.
JO  - PLoS Genet.
PY  - 2010
SP  - e1001145
EP  - e1001145
VL  - 6
AB  - We report the genome of the facultative intracellular parasite Rhodococcus equi, the only
AB  - animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The
AB  - 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci.
AB  - This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous
AB  - genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S
AB  - genome lacks the extensive catabolic and secondary metabolic complement of environmental
AB  - rhodococci, and it displays unique adaptations for host colonization and competition in the
AB  - short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs.
AB  - Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive
AB  - pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for
AB  - intramacrophage survival, most of the potential virulence-associated genes identified in R.
AB  - equi are conserved in environmental rhodococci or have homologs in nonpathogenic
AB  - Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of
AB  - existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We
AB  - tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by
AB  - global transcription profiling and expression network analysis. Two chromosomal genes
AB  - conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate
AB  - synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with
AB  - vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory
AB  - integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI
AB  - is thus an important element in the cooptive virulence of R. equi.
ER  -

TY  - JOUR
AU  - Leung, D.W.
AU  - Lui, A.C.P.
AU  - Merilees, H.
AU  - McBride, B.C.
AU  - Smith, M.
TI  - A restriction enzyme from Fusobacterium nucleatum 4H which recognizes GCNGC.
JO  - Nucleic Acids Res.
PY  - 1979
SP  - 17
EP  - 25
VL  - 6
AB  - A site-specific restriction endonuclease Fnu4HI isolated from Fusobacterium
AB  - nucleatum 4H recognizes the DNA nucleotide sequence 5'-G C^N G C-3' 3'-C G N^C
AB  - G-5' and cleaves as indicated by the arrows.
ER  -

TY  - JOUR
AU  - Leung, K.S.
AU  - Siu, G.K.
AU  - Tam, K.K.
AU  - To, S.W.
AU  - Rajwani, R.
AU  - Ho, P.L.
AU  - Wong, S.S.
AU  - Zhao, W.W.
AU  - Ma, O.C.
AU  - Yam, W.C.
TI  - Comparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing.
JO  - Front Cell Infect Microbiol
PY  - 2017
SP  - 478
EP  - 478
VL  - 7
AB  - Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to
AB  - global TB control. In this study, we focused on two consecutive MDR-TB isolated
AB  - from the same patient before and after the initiation of anti-TB treatment. To
AB  - better understand the genomic characteristics of MDR-TB, Single Molecule
AB  - Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to
AB  - identify mutations that contributed to the stepwise development of drug
AB  - resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs.
AB  - Result: Both pre-treatment and post-treatment strain demonstrated concordant
AB  - phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide,
AB  - streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and
AB  - para-aminosalicylic acid. However, although both strains carried identical
AB  - missense mutations at rpoB S531L, inhA C-15T, and embB M306V, MYCOTB Sensititre
AB  - assay showed that the post-treatment strain had 16-, 8-, and 4-fold elevation in
AB  - the minimum inhibitory concentrations (MICs) toward rifabutin, isoniazid, and
AB  - ethambutol respectively. The results have indicated the presence of additional
AB  - resistant-related mutations governing the stepwise development of MDR-TB. Further
AB  - comparative genomic analyses have identified three additional polymorphisms
AB  - between the clinical isolates. These include a single nucleotide deletion at
AB  - nucleotide position 360 of rv0888 in pre-treatment strain, and a missense
AB  - mutation at rv3303c (lpdA) V44I and a 6-bp inframe deletion at codon 67-68 in
AB  - rv2071c (cobM) in the post-treatment strain. Multiple sequence alignment showed
AB  - that these mutations were occurring at highly conserved regions among pathogenic
AB  - mycobacteria. Using structural-based and sequence-based algorithms, we further
AB  - predicted that the mutations potentially have deleterious effect on protein
AB  - function. Conclusion: This is the first study that compared the full genomes of
AB  - two clonally-related MDR-TB clinical isolates during the course of anti-TB
AB  - treatment. Our work has demonstrated the robustness of SMRT Sequencing in
AB  - identifying mutations among MDR-TB clinical isolates. Comparative genome analysis
AB  - also suggested novel mutations at rv0888, lpdA, and cobM that might explain the
AB  - difference in antibiotic resistance and growth pattern between the two MDR-TB
AB  - strains.
ER  -

TY  - JOUR
AU  - Leung, S.M.
AU  - Chan, K.Y.
AU  - Suen, Y.K.
AU  - Shaw, P.C.
TI  - Screening and characterization of restriction endonucleases from a bacterial culture collection in Hong Kong.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 10133
EP  - 10133
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Leung, S.M.
AU  - Kam, K.M.
AU  - Chan, K.Y.
AU  - Shaw, P.C.
TI  - Purification and characterization of restriction endonuclease BcoI from a soil isolate of Bacillus coagulans.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 153
EP  - 156
VL  - 66
AB  - A soil isolate identified as Bacillus coagulans is found to produce BcoI, an
AB  - isoschizomer of AvaI and with the same cleavage site.  This thermostable
AB  - enzyme, BcoI, is produced at high level and can be isolated by passing the
AB  - crude bacterial lysate through a DEAE-cellulose column.
ER  -

TY  - JOUR
AU  - Levasseur, A.
AU  - Asmar, S.
AU  - Robert, C.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T.
JO  - Genome Announcements
PY  - 2016
SP  - e00452
EP  - e00416
VL  - 4
AB  - Mycobacterium interjectum is a nontuberculosis species rarely responsible for human infection.
AB  - The draft genome of M. interjectum ATCC 51457(T) comprises
AB  - 5,927,979 bp, exhibiting 67.91% G+C content, 5,314 protein-coding genes, and 51
AB  - predicted RNA genes.
ER  -

TY  - JOUR
AU  - Levasseur, A.
AU  - Asmar, S.
AU  - Robert, C.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T.
JO  - Genome Announcements
PY  - 2016
SP  - e00443
EP  - e00416
VL  - 4
AB  - Mycobacterium houstonense is a nontuberculous species rarely responsible for human infection.
AB  - The draft genome of M. houstonense ATCC 49403(T) comprises
AB  - 6,451,020 bp, exhibiting a 66.96% G+C content, 5,881 protein-coding genes, and 65
AB  - predicted RNA genes.
ER  -

TY  - JOUR
AU  - Leveau, J.H.
AU  - Gerards, S.
AU  - de Boer, W.
AU  - van Veen, J.A.
TI  - Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH).
JO  - Environ. Microbiol.
PY  - 2004
SP  - 990
EP  - 998
VL  - 6
AB  - We assessed the utility of fluorescent in situ hybridization (FISH) in the
AB  - screening of clone libraries of (meta)genomic or environmental DNA for the
AB  - presence and expression of bacterial ribosomal RNA (rRNA) genes. To
AB  - establish proof-of-principle, we constructed a fosmid-based library in
AB  - Escherichia coli of large-sized genomic DNA fragments of the mycophagous
AB  - soil bacterium Collimonas fungivorans, and hybridized 768 library clones
AB  - with the Collimonas-specific fluorescent probe CTE998-1015. Critical to
AB  - the success of this approach (which we refer to as large-insert library
AB  - FISH or LIL-FISH) was the ability to induce fosmid copy number, the
AB  - exponential growth status of library clones in the FISH assay and the use
AB  - of a simple pooling strategy to reduce the number of hybridizations.
AB  - Twelve out of 768 E. coli clones were suspected to harbour and express
AB  - Collimonas 16S rRNA genes based on their hybridization to CTE998-1015.
AB  - This was confirmed by the finding that all 12 clones were also identified
AB  - in an independent polymerase chain reaction-based screening of the same
AB  - 768 clones using a primer set for the specific detection of Collimonas 16S
AB  - ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by
AB  - restriction analysis into two distinct contigs, confirming that C.
AB  - fungivorans harbours at least two 16S rRNA genes. For one contig,
AB  - representing 1-2% of the genome, the nucleotide sequence was determined,
AB  - providing us with a narrow but informative view of Collimonas genome
AB  - structure and content.
ER  -

TY  - JOUR
AU  - Levin, B.R.
TI  - Restriction-modification immunity and the maintenance of genetic diversity in bacterial populations.
JO  - Evolutionary Processes and Theory
PY  - 1986
SP  - 669
EP  - 688
VL  - 0
AB  - A simple model is presented of the population dynamics of phage and bacteria
AB  - with restriction-modification immunity.  The analysis of this model suggests
AB  - that: i) in phage-limited communities of bacteria, there are broad conditions
AB  - under which this type of immune system will maintain clonal diversity via
AB  - frequency-dependent selection that favors rare restriction-modification types;
AB  - and ii) when phage-resistant bacteria are present and the community is limited
AB  - by resources, the conditions for this mechanism to maintain clonal diversity
AB  - are much narrower.  Reviewing that which is known about the genetic structure
AB  - of natural populations of E. coli and the population biology of bacteriophage,
AB  - the proposition is evaluated that this type of phage-mediated,
AB  - frequency-dependent selection is responsible for maintaining the considerable
AB  - chromosomal gene and plasmid diversity found in this bacterial species.
AB  - Finally, the analogy is considered between this type of phage-mediated
AB  - selection on restriction-modification diversity and that postulated earlier for
AB  - parasite-mediated, frequency-dependent selection maintaining antigenic
AB  - diversity in vertebrates.
ER  -

TY  - JOUR
AU  - Levine, J.D.
AU  - Cech, C.L.
TI  - Low frequency restriction enzymes in pulsed field electrophoresis.
JO  - Biotechnology
PY  - 1989
SP  - 1033
EP  - 1036
VL  - 7
AB  - None
ER  -

TY  - JOUR
AU  - Levine, S.M.
AU  - Lin, E.A.
AU  - Emara, W.
AU  - Kang, J.
AU  - DiBenedetto, M.
AU  - Ando, T.
AU  - Falush, D.
AU  - Blaser, M.J.
TI  - Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation.
JO  - FASEB J.
PY  - 2007
SP  - 3458
EP  - 3467
VL  - 21
AB  - Helicobacter pylori, bacteria that colonize the human gastric mucosa, are naturally competent
AB  - for transformation by exogenous DNA, and show a
AB  - panmictic population structure. To understand the mechanisms involved
AB  - in its horizontal gene transfer, we sought to define the interval
AB  - required from exposure to substrate DNA until DNA uptake and expression
AB  - of a selectable phenotype, as well as the relationship of transforming
AB  - fragment length, concentration, homology, symmetry, and strandedness,
AB  - to the transformation frequency. We provide evidence that natural
AB  - transformation in H. pylori differs in efficiency among wild-type
AB  - strains but is saturable and varies with substrate DNA length,
AB  - symmetry, strandedness, and species origin. We show that H. pylori
AB  - cells can be transformed within one minute of contact with DNA, by DNA
AB  - fragments as small as 50 bp, and as few as 5 bp on one flank of a
AB  - selectable single nucleotide mutation is sufficient substrate for
AB  - recombination of a transforming fragment, and that double-stranded DNA
AB  - is the preferred (1000-fold > single-stranded) substrate. The high
AB  - efficiency of double-stranded DNA as transformation substrate, in
AB  - conjunction with strain-specific restriction endonucleases suggests a
AB  - model of short-fragment recombination favoring closest relatives,
AB  - consistent with the observed H. pylori population biology.
ER  -

TY  - JOUR
AU  - Levitz, R.
AU  - Chapman, D.
AU  - Amitsur, M.
AU  - Green, R.
AU  - Snyder, L.
AU  - Kaufmann, G.
TI  - The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease.
JO  - EMBO J.
PY  - 1990
SP  - 1383
EP  - 1389
VL  - 9
AB  - The optional Escherichia coli prr locus restricts phage T4 mutants lacking polynucleotide
AB  - kinase or RNA ligase.  Underlying this restriction is the specific manifestation of the
AB  - T4-induced anticodon nuclease, an enzyme which triggers the cleavage-ligation of the host
AB  - tRNALys.  We report here the molecular cloning, nucleotide sequence and mutational analysis of
AB  - prr-associated DNA.  The results indicate that prr encodes a latent form of anticodon nuclease
AB  - consisting of a core enzyme and cognate masking agents.  They suggest that the T4-encoded
AB  - factors of anticodon nuclease counteract the prr-encoded masking agents, thus activating the
AB  - latent enzyme.  The encoding of a tRNA cleavage-ligation pathway by two separate genetic
AB  - systems which cohabitate E. coli may provide a clue to the evolution of RNA splicing
AB  - mechanisms mediated by proteins.
ER  -

TY  - JOUR
AU  - Levy, W.P.
AU  - Welker, N.E.
TI  - Deoxyribonucleic acid modification methylase from Bacillus stearothermophilus.
JO  - Biochemistry
PY  - 1981
SP  - 1120
EP  - 1127
VL  - 20
AB  - A modification methylase was isolated from Bacillus stearothermophilus 1503-4R
AB  - (Bst153I) and purified to homogeneity.  The enzyme is an acidic protein and
AB  - composed of a subunit with a molecular weight of 105000, and only the
AB  - tetrameric form was detected in solution.  The methylase exhibited maximal
AB  - activity between 54 and 61C and between pH 8.1 and 9.3.  In contrast to
AB  - Bst1503I endonuclease [Catterall, J.F., & Welker, N.E. (1977) J. Bacteriol.
AB  - 129: 1110-1120], the methylase is completely inactivated when exposed to
AB  - temperatures near the optimal growth temperature (63-67C).  The methylase was
AB  - also inactivated when exposed to temperatures below the minimal growth
AB  - temperature (48-53C).  The thermostability of the methylase is significantly
AB  - enhanced by Na+, K+, or NH4+.  Membrane-bound methylase is resistant to heat
AB  - inactivation at temperatures near the maximum growth temperature (73-75C).  The
AB  - methylase functions as a tetramer.  The initial rates of methyl transfer are
AB  - first order in methylase concentration, and the enzyme obeys Michaelis-Menten
AB  - kinetics with respect to DNA but not to S-adenosyl-L-methionine.
ER  -

TY  - JOUR
AU  - Levy, W.P.
AU  - Welker, N.E.
TI  - Purification and properties of a modification methylase from Bacillus stearothermophilus (Meth M.Bst 1503).
JO  - Fed. Proc.
PY  - 1978
SP  - 1414
EP  - 1414
VL  - 37
AB  - A modification methylase has been isolated from B. stearothermophilus 1503-4R
AB  - Res+Mod+ (Math M.Bst 1503) and purified 500 fold from sonicated protoplasts
AB  - using ammonium sulfate fractionation, Bio Gel A5m gel filtration and
AB  - DEAE-cellulose ion exhange column chromatography.  Incurbation of Meth M.Pst
AB  - 1503 with various DNA substrates in the presence of S-adenosyl methionine
AB  - protects these substrates from the action of Endo R.Bst 1503.  Meth M.Bst 1503
AB  - has an apparent molecular weight between 400,000-450,000 daltons.  A single
AB  - protein staining band with a molecular weight of between 90,000-100,000 daltons
AB  - is obtained when the enzyme is analyzed by SDS polyacrylamide gel
AB  - electrohoresis.  Meth M.Bst 1503 does not exhibit restriction endonuclease
AB  - activity.  The enzyme in 50% glycerol can be stored at -25C for at least 3
AB  - weeks with no detectable loss of activity.  Data are presented which indicate
AB  - that Endo R.Bst 1503 and Meth M.Bst 1503 do not share a common polypeptide.
AB  - Temperature and pH profiles of enzymatic activity were determined.
ER  -

TY  - JOUR
AU  - Lewis, A.L.
AU  - Deitzler, G.E.
AU  - Ruiz, M.J.
AU  - Weimer, C.
AU  - Park, S.
AU  - Robinson, L.S.
AU  - Hallsworth-Pepin, K.
AU  - Wollam, A.
AU  - Mitreva, M.
AU  - Lewis, W.G.
TI  - Genome Sequences of 11 Human Vaginal Actinobacteria Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e00887
EP  - e00816
VL  - 4
AB  - The composition of the vaginal microbiota is an important health determinant. Several members
AB  - of the phylum Actinobacteria have been implicated in bacterial
AB  - vaginosis, a condition associated with many negative health outcomes. Here, we
AB  - present 11 strains of vaginal Actinobacteria (now available through BEI
AB  - Resources) along with draft genome sequences.
ER  -

TY  - JOUR
AU  - Lewis, L.K.
AU  - Lobachev, K.
AU  - Westmoreland, J.W.
AU  - Karthikeyan, G.
AU  - Williamson, K.M.J.J.J.
AU  - Resnick, M.A.
TI  - Use of a restriction endonuclease cytotoxicity assay to identify inducible GAL1 promoter variants with reduced basal activity - for use  in fucntional genomics.
JO  - Gene
PY  - 2005
SP  - 183
EP  - 192
VL  - 363
AB  - Inducible promoter fusions are commonly employed to study the biological functions of genes as
AB  - well as to investigate mechanisms of transcription regulation. A concern for many studies of
AB  - heterologous gene expression is that steady state transcription may be too high under
AB  - non-inducing conditions, producing undesired phenotypes prior to induction. Fusions containing
AB  - the galactose-inducible GAL1 promoter joined to PvuII, a bacterial DNA endonuclease gene, are
AB  - toxic to yeast cells even under non-inducing conditions, i.e., in glucose media. This toxicity
AB  - was utilized in conjunction with PCR-based mutagenesis of the GAL1 regulatory region to
AB  - isolate mutant promoters that retained high inducibility but exhibited reduced basal level
AB  - expression. The Mig1 repressor binding and putative TATA box regions were unchanged among four
AB  - mutant promoters examined in detail. However, each promoter contained one or more mutations
AB  - within previously identified binding sites for the Gal4 activator protein. Genetic assays
AB  - developed to monitor GAL1p::I-SceI endonuclease-induced recombination demonstrated that basal
AB  - expression from two of the new promoters (designated GAL1-V4 and GAL1-V10) was strongly
AB  - reduced. These experiments and additional quantitative luciferase reporter gene assays
AB  - demonstrate the utility of the approach for identifying promoters that permit more tightly
AB  - controlled gene expression.
ER  -

TY  - JOUR
AU  - Lewis, Z.A.
AU  - Adhvaryu, K.K.
AU  - Honda, S.
AU  - Shiver, A.L.
AU  - Knip, M.
AU  - Sack, R.
AU  - Selker, E.U.
TI  - DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC.
JO  - PLoS Genet.
PY  - 2010
SP  - e1001196
EP  - e1001196
VL  - 6
AB  - Methylation of DNA and of Lysine 9 on histone H3 (H3K9) is associated with gene silencing in
AB  - many animals, plants, and fungi. In Neurospora
AB  - crassa, methylation of H3K9 by DIM-5 directs cytosine methylation by
AB  - recruiting a complex containing Heterochromatin Protein-1 (HP1) and the
AB  - DIM-2 DNA methyltransferase. We report genetic, proteomic, and
AB  - biochemical investigations into how DIM-5 is controlled. These studies
AB  - revealed DCDC, a previously unknown protein complex including DIM-5,
AB  - DIM-7, DIM-9, CUL4, and DDB1. Components of DCDC are required for
AB  - H3K9me3, proper chromosome segregation, and DNA methylation.
AB  - DCDC-defective strains, but not HP1-defective strains, are
AB  - hypersensitive to MMS, revealing an HP1-independent function of H3K9
AB  - methylation. In addition to DDB1, DIM-7, and the WD40 domain protein
AB  - DIM-9, other presumptive DCAFs (DDB1/CUL4 associated factors)
AB  - co-purified with CUL4, suggesting that CUL4/DDB1 forms multiple
AB  - complexes with distinct functions. This conclusion was supported by
AB  - results of drug sensitivity tests. CUL4, DDB1, and DIM-9 are not
AB  - required for localization of DIM-5 to incipient heterochromatin
AB  - domains, indicating that recruitment of DIM-5 to chromatin is not
AB  - sufficient to direct H3K9me3. DIM-7 is required for DIM-5 localization
AB  - and mediates interaction of DIM-5 with DDB1/CUL4 through DIM-9. These
AB  - data support a two-step mechanism for H3K9 methylation in Neurospora.
ER  -

TY  - JOUR
AU  - Li, A.
AU  - Gai, Z.
AU  - Cui, D.
AU  - Ma, F.
AU  - Yang, J.
AU  - Zhang, X.
AU  - Sun, Y.
AU  - Ren, N.
TI  - Genome Sequence of a Highly Efficient Aerobic Denitrifying Bacterium, Pseudomonas stutzeri T13.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5720
EP  - 5720
VL  - 194
AB  - Pseudomonas stutzeri T13 is a highly efficient aerobic denitrifying bacterium. Information
AB  - about the genome of this aerobic denitrifying bacterium has been
AB  - limited until now. We present the draft genome of P. stutzeri T13. The results
AB  - could provide further insight into the aerobic denitrification mechanism in
AB  - strain T13.
ER  -

TY  - JOUR
AU  - Li, A.
AU  - Geng, J.
AU  - Cui, D.
AU  - Shu, C.
AU  - Zhang, S.
AU  - Yang, J.
AU  - Xing, J.
AU  - Wang, J.
AU  - Ma, F.
AU  - Hu, S.
TI  - Genome Sequence of Agrobacterium tumefaciens Strain F2, a Bioflocculant-Producing Bacterium.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5531
EP  - 5531
VL  - 193
AB  - Agrobacterium tumefaciens F2 is an efficient bioflocculant-producing bacterium. But the genes
AB  - related to the metabolic pathway of bioflocculant
AB  - biosynthesis in strain F2 are unknown. We present the draft genome of A.
AB  - tumefaciens F2. It could provide further insight into the biosynthetic
AB  - mechanism of polysaccharide-like bioflocculant in strain F2.
ER  -

TY  - JOUR
AU  - Li, B.
AU  - Brinks, E.
AU  - Franz, C.M.A.P.
AU  - Cho, G.S.
TI  - Draft Genome Sequence of Staphylococcus fleurettii Strain MBTS-1 Isolated from Cucumber.
JO  - Genome Announcements
PY  - 2017
SP  - e00335
EP  - e00317
VL  - 5
AB  - The draft genome of Staphylococcus fleurettii MBTS-1, isolated from cucumber in northern
AB  - Germany, was sequenced. Analysis showed that the assembled genome had a
AB  - size of 2,582,128 bp with a predicted total of 2,491 protein-encoding genes, 9
AB  - rRNAs, 5 ncRNAs, and 44 tRNAs. This strain did not contain plasmid DNA.
ER  -

TY  - JOUR
AU  - Li, B.
AU  - Chen, Y.
AU  - Liu, Q.
AU  - Hu, S.
AU  - Chen, X.
TI  - Complete Genome Analysis of Sulfobacillus acidophilus Strain TPY, Isolated from a Hydrothermal Vent in the Pacific Ocean.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5555
EP  - 5556
VL  - 193
AB  - Sulfobacillus acidophilus strain TPY is a moderately thermoacidophilic bacterium originally
AB  - isolated from a hydrothermal vent in the Pacific
AB  - Ocean. Ferrous iron and sulfur oxidation in acidic environments in strain
AB  - TPY have been confirmed. Here we report the genome sequence and annotation
AB  - of the strain TPY, which is the first complete genome of Sulfobacillus
AB  - acidophilus.
ER  -

TY  - JOUR
AU  - Li, B.
AU  - Shi, Y.
AU  - Ibrahim, M.
AU  - Liu, H.
AU  - Shan, C.
AU  - Wang, Y.
AU  - Kube, M.
AU  - Xie, G.L.
AU  - Sun, G.
TI  - Genome Sequence of the Rice Pathogen Dickeya zeae Strain ZJU1202.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4452
EP  - 4453
VL  - 194
AB  - Dickeya zeae is a phytopathogenic bacterium causing soft rot diseases in a wide range of
AB  - economically important crops. Here we present the draft genome sequence
AB  - of strain ZJU1202, which is the causal agent of rice foot rot in China. The draft
AB  - genome will contribute to epidemiological and comparative genomic studies and the
AB  - quarantine of this devastating phytopathogen.
ER  -

TY  - JOUR
AU  - Li, B.
AU  - Ye, M.
AU  - Guo, Q.
AU  - Zhang, Z.
AU  - Yang, S.
AU  - Ma, W.
AU  - Yu, F.
AU  - Chu, H.
TI  - Determination of MIC Distribution and Mechanisms of Decreased Susceptibility to Bedaquiline Among Clinical Isolates of Mycobacterium abscessus.
JO  - Antimicrob. Agents Chemother.
PY  - 2018
SP  - AAC.00175
EP  - AAC.00118
VL  - 0
AB  - Chemotherapeutic options are very limited against Mycobacterium abscessus infections.
AB  - Bedaquiline, a new anti-tuberculosis drug, is effective for the
AB  - treatment of multidrug-resistant TB. However, little data is available on
AB  - bedaquiline in treating M. abscessus infections. In this study, we reported the
AB  - in vitro susceptibility profile of M. abscessus clinical isolates to bedaquiline
AB  - and investigated the potential molecular mechanisms of decreased susceptibility.
AB  - A total of 197 M. abscessus clinical isolates were collected from sputum and
AB  - bronchoalveolar fluid of patients with lung infections. Standard broth
AB  - microdilution test revealed that bedaquiline exhibited high in vitro killing
AB  - activity against M. abscessus isolates, with MIC50 of 0.062 and MIC90 of 0.125
AB  - mg/L. Whole genome sequencing data showed that no nonsynonymous mutation occurred
AB  - in atpE, the gene encoding the bedaquiline targeted protein. However, of 6
AB  - strains with decreased susceptibility of bedaquiline (MIC=0.5-1 mg/L), 3 strains
AB  - had nonsynonymous mutations in mab_4384, the gene encoding the repressor of
AB  - efflux pump MmpS5/MmpL5. qRT-PCR analysis showed that the expression of
AB  - MmpS5/MmpL5 in the group with decreased susceptibility to bedaquiline were
AB  - significantly higher than those with medium MIC (MIC=0.125-0.5 mg/L) or low MIC
AB  - group (MIC</= 0.062 mg/L). Two isolates with increased MIC didn't show
AB  - overexpression of MmpS5/MmpL5, which couldn't be explained by known molecular
AB  - mechanisms. This is the first report showing the association of MmpS5/MmpL5 with
AB  - decreased bedaquiline susceptibility in M. abscessus clinical isolates, and
AB  - suggesting the presence of other yet-to-be identified mechanisms for decreased
AB  - bedaquiline susceptibility in M. abscessus.
ER  -

TY  - JOUR
AU  - Li, C.
AU  - Li, Y.H.
AU  - Zhang, X.M.
AU  - Stafford, P.
AU  - Dinu, V.
TI  - ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites.
JO  - BMC Bioinformatics
PY  - 2009
SP  - 286
EP  - 286
VL  - 10
AB  - Background: Restriction enzymes can produce easily definable segments from DNA sequences by
AB  - using a variety of cut patterns. There are,
AB  - however, no software tools that can aid in gene building - that is,
AB  - modifying wild-type DNA sequences to express the same wild-type amino
AB  - acid sequences but with enhanced codons, specific cut sites, unique
AB  - post-translational modifications, and other engineered-in components
AB  - for recombinant applications. A fast DNA pattern design algorithm,
AB  - ICRPfinder, is provided in this paper and applied to find or create
AB  - potential recognition sites in target coding sequences.
AB  - Results: ICRPfinder is applied to find or create restriction enzyme
AB  - recognition sites by introducing silent mutations. The algorithm is
AB  - shown capable of mapping existing cut-sites but importantly it also can
AB  - generate specified new unique cut-sites within a specified region that
AB  - are guaranteed not to be present elsewhere in the DNA sequence.
AB  - Conclusion: ICRPfinder is a powerful tool for finding or creating
AB  - specific DNA patterns in a given target coding sequence. ICRPfinder
AB  - finds or creates patterns, which can include restriction enzyme
AB  - recognition sites, without changing the translated protein sequence.
AB  - ICRPfinder is a browser-based JavaScript application and it can run on
AB  - any platform, in on-line or off-line mode.
ER  -

TY  - JOUR
AU  - Li, C.
AU  - Yan, X.
AU  - Lillehoj, H.S.
TI  - Complete Genome Sequence of Clostridium perfringens LLY_N11, a Necrotic Enteritis-Inducing Strain Isolated from a Healthy Chicken Intestine.
JO  - Genome Announcements
PY  - 2017
SP  - e01225
EP  - e01217
VL  - 5
AB  - Clostridium perfringens strain LLY_N11, a commensal bacterium, which previously induced
AB  - necrotic enteritis in an experimental study, was isolated from the
AB  - intestine of a young healthy chicken. Here, we present the complete genome
AB  - sequence of this strain, which may provide a better understanding of the
AB  - molecular mechanisms involved in necrotic enteritis pathogenesis.
ER  -

TY  - JOUR
AU  - Li, D.
AU  - Greenfield, P.
AU  - Rosewarne, C.P.
AU  - Midgley, D.J.
TI  - Draft Genome Sequence of Thermoanaerobacter sp. Strain A7A, Reconstructed from a  Metagenome Obtained from a High-Temperature Hydrocarbon Reservoir in the Bass  Strait, Australia.
JO  - Genome Announcements
PY  - 2013
SP  - e00701
EP  - e00713
VL  - 1
AB  - The draft genome sequence of Thermoanaerobacter sp. strain A7A was reconstructed  from a
AB  - metagenome of a microbial consortium obtained from the Tuna oil field in
AB  - the Gippsland Basin, Australia. The organism is a strict anaerobe that is
AB  - predicted to ferment a range of simple sugars and undertake sulfur reduction.
ER  -

TY  - JOUR
AU  - Li, E.
AU  - Beard, C.
AU  - Jaenisch, R.
TI  - Role for DNA methylation in genomic imprinting.
JO  - Nature
PY  - 1993
SP  - 362
EP  - 366
VL  - 366
AB  - The paternal and maternal genomes are not equivalent and both are required for mammalian
AB  - development. The difference between the parental genomes is believed to be due to
AB  - gametespecific differential modification, a process known as genomic imprinting. The study of
AB  - transgene methylation has shown that methylation patterns can be inherited in a
AB  - parent-of-origin-specific manner, suggesting that DNA mthylation may play a role in genomic
AB  - imprinting. The functional significance of DNA methylation in genomic imprinting was
AB  - strengthened by the recent finding that CpG islands (or sites) in three imprinted genes, H19,
AB  - insulin-like growth factor 2 (Igf-2), and Igf-2 receptor (Igf-2r), are differentially
AB  - methylated depending on their parental origin. We have examined the expression of these three
AB  - imprinted genes in mutant mice that are deficient in DNA methyltransferase activity. We report
AB  - here that expression of all three genes was affected in mutant embryos: the normally silent
AB  - paternal allele of the H19 gene was activated, whereas the normally active paternal allele of
AB  - the Igf-2 gene and the active maternal allele of the Igf-2r gene were repressed. Our results
AB  - demonstrate that a normal level of DNA methylation is required for controlling differential
AB  - expression of the paternal and maternal alleles of imprinted genes.
ER  -

TY  - JOUR
AU  - Li, E.
AU  - Bestor, T.H.
AU  - Jaenisch, R.
TI  - Targeted mutation of the DNA methyltransferase gene results in embryonic lethality.
JO  - Cell
PY  - 1992
SP  - 915
EP  - 926
VL  - 69
AB  - Gene targeting in embryonic stem (ES) cells has been used to mutate the murine DNA
AB  - methyltransferase gene. ES cell lines homozygous for the mutation were generated by
AB  - consecutive targeting of both wild-type alleles; the mutant cells were viable and showed no
AB  - obvious abnormalities with respect to growth rate or morphology, and had only trace levels of
AB  - DNA methyltransferase activity. A quantitative end-labeling assay showed that the level of m5C
AB  - in the DNA of homozygous mutant cells was about one-third that of wild-type cells, and
AB  - Southern blot analysis after cleavage of the DNA with a methylation-sensitive restriction
AB  - endonuclease revealed substantial demethylation of endogenous retroviral DNA. The mutation was
AB  - introduced into the germline of mice and found to cause a recessive lethal phenotype.
AB  - Homozygous embryos were stunted, delayed in development, and did not survive past
AB  - mid-gestation. The DNA of homozygous embryos showed a reduction of the level of m5C similar to
AB  - that of homozygous ES cells. These results indicate that while a 3-fold reduction in levels of
AB  - genomic m5C has no detectable effect on the viability or proliferation of ES cells in culture,
AB  - a similar reduction of DNA methylation in embryos causes abnormal development and embryonic
AB  - lethality.
ER  -

TY  - JOUR
AU  - Li, F.
AU  - Jiang, P.
AU  - Zheng, H.
AU  - Wang, S.
AU  - Zhao, G.
AU  - Qin, S.
AU  - Liu, Z.
TI  - Draft Genome Sequence of Marine bacterium Streptomyces griseoaurantiacus M045, which produces Novel Manumycin-type Antibiotics with a pABA Core Component.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3417
EP  - 3418
VL  - 193
AB  - Streptomyces griseoaurantiacus M045 isolated from marine sediment produces manumycin and
AB  - chinikomycin antibiotics. Here we present a high-quality
AB  - draft genome sequence of S. griseoaurantiacus M045, the first marine
AB  - Streptomyces species to be sequenced and annotated. The genome encodes
AB  - several gene clusters for biosynthesis of secondary metabolites and has
AB  - provided insight into genomic islands linking secondary metabolism to
AB  - functional adaptation in marine S. griseoaurantiacus M045.
ER  -

TY  - JOUR
AU  - Li, F.
AU  - Papworth, M.
AU  - Minczuk, M.
AU  - Rohde, C.
AU  - Zhang, Y.
AU  - Ragozin, S.
AU  - Jeltsch, A.
TI  - Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 100
EP  - 112
VL  - 35
AB  - Gene silencing by targeted DNA methylation has potential applications in basic research and
AB  - therapy. To establish targeted methylation in human
AB  - cell lines, the catalytic domains (CDs) of mouse Dnmt3a and Dnmt3b DNA
AB  - methyltransferases (MTases) were fused to different DNA binding domains
AB  - (DBD) of GAL4 and an engineered Cys2His2 zinc finger domain. We
AB  - demonstrated that (i) Dense DNA methylation can be targeted to specific
AB  - regions in gene promoters using chimeric DNA MTases. (ii) Site-specific
AB  - methylation leads to repression of genes controlled by various cellular or
AB  - viral promoters. (iii) Mutations affecting any of the DBD, MTase or target
AB  - DNA sequences reduce targeted methylation and gene silencing. (iv)
AB  - Targeted DNA methylation is effective in repressing Herpes Simplex Virus
AB  - type 1 (HSV-1) infection in cell culture with the viral titer reduced by
AB  - at least 18-fold in the presence of an MTase fused to an engineered zinc
AB  - finger DBD, which binds a single site in the promoter of HSV-1 gene
AB  - IE175k. In short, we show here that it is possible to direct DNA MTase
AB  - activity to predetermined sites in DNA, achieve targeted gene silencing in
AB  - mammalian cell lines and interfere with HSV-1 propagation.
ER  -

TY  - JOUR
AU  - Li, G.
AU  - Hu, F.Z.
AU  - Yang, X.
AU  - Cui, Y.
AU  - Yang, J.
AU  - Qu, F.
AU  - Gao, G.F.
AU  - Zhang, J.R.
TI  - Complete Genome Sequence of Streptococcus pneumoniae Strain ST556, a Multidrug-Resistant Isolate from an Otitis Media Patient.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3294
EP  - 3295
VL  - 194
AB  - Streptococcus pneumoniae is a major pathogen causing bacterial infection in the middle ear of
AB  - humans. We previously used S. pneumoniae strain ST556, a
AB  - low-passage 19F isolate from an otitis media patient, to perform a whole-genome
AB  - screen for ear infection-associated genes in a chinchilla model. This report
AB  - presents the complete genome sequence of ST556. The genome sequence will provide
AB  - information complementary to the experimental data from our genetic study of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Li, G.
AU  - Lu, S.
AU  - Shen, M.
AU  - Le, S.
AU  - Tan, Y.
AU  - Li, M.
AU  - Zhao, X.
AU  - Wang, J.
AU  - Shen, W.
AU  - Guo, K.
AU  - Yang, Y.
AU  - Zhu, H.
AU  - Li, S.
AU  - Zhu, J.
AU  - Rao, X.
AU  - Hu, F.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Phage-Resistant Variant PA1RG.
JO  - Genome Announcements
PY  - 2016
SP  - e01761
EP  - e01715
VL  - 4
AB  - Bacteria have evolved several defense systems against phage predation. Here, we report the
AB  - 6,500,439-bp complete genome sequence of the Pseudomonas aeruginosa
AB  - phage-resistant variant PA1RG. Single-molecule real-time (SMRT) sequencing and de
AB  - novo assembly revealed a single contig with 320-fold sequence coverage.
ER  -

TY  - JOUR
AU  - Li, G.
AU  - Mo, Z.
AU  - Li, J.
AU  - Xiao, P.
AU  - Hao, B.
TI  - Complete Genome Sequence of Vibrio anguillarum M3, a Serotype O1 Strain Isolated  from Japanese Flounder in China.
JO  - Genome Announcements
PY  - 2013
SP  - e00769
EP  - e00713
VL  - 1
AB  - Vibrio anguillarum is an important bacterial pathogen that causes vibriosis in marine fish. We
AB  - present the complete genome sequence of V. anguillarum M3, a
AB  - serotype O1 clinical strain isolated from Japanese flounder (Paralichthys
AB  - olivaceus) in Shandong, China.
ER  -

TY  - JOUR
AU  - Li, G.
AU  - Xie, F.
AU  - Zhang, Y.
AU  - Wang, C.
TI  - Draft Genome Sequence of Actinobacillus pleuropneumoniae Serotype 7 Strain S-8.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6606
EP  - 6607
VL  - 194
AB  - The Gram-negative bacterium Actinobacillus pleuropneumoniae is the etiological agent of
AB  - porcine pleuropneumonia, a respiratory disease that leads to severe
AB  - economic losses in the swine industry. For years, scientists working with it have
AB  - lacked a reliable genome sequence for comparison with other Actinobacillus
AB  - species. Here, we report the draft genome sequence of A. pleuropneumoniae
AB  - serotype 7 (strain S-8), isolated from swine lung in China in 1992.
ER  -

TY  - JOUR
AU  - Li, H.
AU  - Feng, Z.M.
AU  - Sun, Y.J.
AU  - Zhou, W.L.
AU  - Jiao, X.
AU  - Zhu, H.
TI  - Draft Genome Sequence of Sphingomonas sp. WG, a Welan Gum-Producing Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01709
EP  - e01715
VL  - 4
AB  - We report the draft genome sequence of Sphingomonas sp. WG, a high welan gum-producing strain
AB  - with a yield of 33 g/L. The core of wel cluster for welan
AB  - gum biosynthesis contained 24 coding sequences in the genome, which will provide
AB  - the genetic information on welan gum production.
ER  -

TY  - JOUR
AU  - Li, H.
AU  - Pellenz, S.
AU  - Ulge, U.
AU  - Stoddard, B.L.
AU  - Monnat, R.J. Jr.
TI  - Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 1650
EP  - 1662
VL  - 37
AB  - Homing endonucleases (HEs) cut long DNA target sites with high specificity to initiate and
AB  - target the lateral transfer of mobile introns or inteins.
AB  - This high site specificity of HEs makes them attractive reagents for gene
AB  - targeting to promote DNA modification or repair. We have generated several
AB  - hundred catalytically active, monomerized versions of the
AB  - well-characterized homodimeric I-CreI and I-MsoI LAGLIDADG family homing
AB  - endonuclease (LHE) proteins. Representative monomerized I-CreI and I-MsoI
AB  - proteins (collectively termed mCreIs or mMsoIs) were characterized in
AB  - detail by using a combination of biochemical, biophysical and structural
AB  - approaches. We also demonstrated that both mCreI and mMsoI proteins can
AB  - promote cleavage-dependent recombination in human cells. The use of single
AB  - chain LHEs should simplify gene modification and targeting by requiring
AB  - the expression of a single small protein in cells, rather than the
AB  - coordinate expression of two separate protein coding genes as is required
AB  - when using engineered heterodimeric zinc finger or homing endonuclease
AB  - proteins.
ER  -

TY  - JOUR
AU  - Li, H.
AU  - Tong, Y.
AU  - Huang, Y.
AU  - Bai, J.
AU  - Yang, H.
AU  - Liu, W.
AU  - Cao, W.
TI  - Complete Genome Sequence of Bartonella quintana, a Bacterium Isolated from Rhesus Macaques.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6347
EP  - 6347
VL  - 194
AB  - Bartonella quintana is a re-emerging pathogen and the causative agent of a broad  spectrum of
AB  - disease manifestations in humans. The present study reports the
AB  - complete genome of B. quintana strain RM_11, which was isolated from rhesus
AB  - macaques.
ER  -

TY  - JOUR
AU  - Li, H.
AU  - Ulge, U.Y.
AU  - Hovde, B.T.
AU  - Doyle, L.A.
AU  - Monnat, R.J. Jr.
TI  - Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 2587
EP  - 2598
VL  - 40
AB  - Homing endonucleases (HEs) promote the evolutionary persistence of selfish DNA elements by
AB  - catalyzing element lateral transfer into new host organisms. The high
AB  - site specificity of this lateral transfer reaction, termed homing, reflects both
AB  - the length (14-40 bp) and the limited tolerance of target or homing sites for
AB  - base pair changes. In order to better understand molecular determinants of
AB  - homing, we systematically determined the binding and cleavage properties of all
AB  - single base pair variant target sites of the canonical LAGLIDADG homing
AB  - endonucleases I-CreI and I-MsoI. These Chlorophyta algal HEs have very similar
AB  - three-dimensional folds and recognize nearly identical 22 bp target sites, but
AB  - use substantially different sets of DNA-protein contacts to mediate site-specific
AB  - recognition and cleavage. The site specificity differences between I-CreI and
AB  - I-MsoI suggest different evolutionary strategies for HE persistence. These
AB  - differences also provide practical guidance in target site finding, and in the
AB  - generation of HE variants with high site specificity and cleavage activity, to
AB  - enable genome engineering applications.
ER  -

TY  - JOUR
AU  - Li, H.
AU  - Zhou, S.
AU  - Johnson, T.
AU  - Vercruysse, K.
AU  - Ropelewski, A.J.
AU  - Thannhauser, T.W.
TI  - Draft Genome Sequence of New Bacillus cereus Strain tsu1.
JO  - Genome Announcements
PY  - 2014
SP  - e01294
EP  - e01214
VL  - 2
AB  - This paper reports the draft genome sequence of new Bacillus cereus strain tsu1,  isolated on
AB  - an agar-cellulose plate. The draft genome sequence is 5.81 Mb,
AB  - revealing 5,673 coding sequences. It contains genes for cellulose-degradation and
AB  - biosynthesis pathways of polyhydroxybutyrate (PHB) and 8 rRNA genes (5S, 16S, and
AB  - 23S).
ER  -

TY  - JOUR
AU  - Li, J.
AU  - Cheng, Y.
AU  - Wang, D.
AU  - Li, J.
AU  - Wang, Y.
AU  - Han, W.
AU  - Li, F.
TI  - Draft Genome Sequence of the Polysaccharide-Degrading Marine Bacterium Pseudoalteromonas sp. Strain A601.
JO  - Genome Announcements
PY  - 2017
SP  - e00590
EP  - e00517
VL  - 5
AB  - Pseudoalteromonas sp. strain A601 is a marine bacterium with excellent
AB  - polysaccharide-degrading capabilities. Here, we present a high-quality draft
AB  - genome sequence of strain A601 with a size of approximately 4.89 Mb and a mean
AB  - G+C content of 40.0%. Various putative polysaccharide-degrading genes were found
AB  - in the draft genome.
ER  -

TY  - JOUR
AU  - Li, J.
AU  - Guo, W.
AU  - Shi, M.
AU  - Cao, Y.
AU  - Wang, G.
TI  - High-quality-draft genomic sequence of Paenibacillus ferrarius CY1T with the potential to bioremediate Cd, Cr and Se contamination.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 60
EP  - 60
VL  - 12
AB  - Paenibacillus ferrarius CY1T (= KCTC 33419T = CCTCC AB2013369T) is a Gram-positive, aerobic,
AB  - endospore-forming, motile and rod-shaped bacterium
AB  - isolated from iron mineral soil. This bacterium reduces sulfate (SO42-) to S2-,
AB  - which reacts with Cd(II) to generate precipitated CdS. It also reduces the toxic
AB  - chromate [Cr(VI)] and selenite [Se(VI)] to the less bioavailable chromite
AB  - [Cr(III)] and selenium (Se0), respectively. Thus, strain CY1T has the potential
AB  - to bioremediate Cd, Cr and Se contamination, which is the main reason for the
AB  - interest in sequencing its genome. Here we describe the features of strain CY1T,
AB  - together with the draft genome sequence and its annotation. The 9,184,169 bp long
AB  - genome exhibits a G + C content of 45.6%, 7909 protein-coding genes and 81 RNA
AB  - genes. Nine putative Se(IV)-reducing genes, five putative Cr(VI) reductase and
AB  - nine putative sulfate-reducing genes were identified in the genome.
ER  -

TY  - JOUR
AU  - Li, J.
AU  - Lan, R.
AU  - Xiong, Y.
AU  - Ye, C.
AU  - Yuan, M.
AU  - Liu, X.
AU  - Chen, X.
AU  - Yu, D.
AU  - Liu, B.
AU  - Lin, W.
AU  - Bai, X.
AU  - Wang, Y.
AU  - Sun, Q.
AU  - Wang, Y.
AU  - Zhao, H.
AU  - Meng, Q.
AU  - Chen, Q.
AU  - Zhao, A.
AU  - Xu, J.
TI  - Sequential Isolation in a Patient of Raoultella planticola and Escherichia coli Bearing a Novel ISCR1 Element Carrying blaNDM-1.
JO  - PLoS ONE
PY  - 2014
SP  - E89893
EP  - E89893
VL  - 9
AB  - BACKGROUND: The gene for New Delhi metallo-beta-lactamase 1 (NDM-1) has been
AB  - reported to be transmitted via plasmids which are easily transferable and capable
AB  - of wide distribution. We report the isolation of two NDM-1 producing strains and
AB  - possible in vivo transfer of blaNDM-1 in a patient. METHODS: Clinical samples
AB  - were collected for bacterial culture and antibiotic susceptibility testing from a
AB  - patient during a 34-day hospitalization. The presence of blaNDM-1 was detected by
AB  - PCR and sequencing. Plasmids of interest were sequenced. Medical records were
AB  - reviewed for evidence of association between the administration of antibiotics
AB  - and the acquisition of the NDM-1 resistance. RESULTS: A NDM-1 positive Raoultella
AB  - planticola was isolated from blood on the ninth day of hospitalization without
AB  - administration of any carbapenem antibiotics and a NDM-1 positive Escherichia
AB  - coli was isolated from feces on the 29th day of hospitalization and eight days
AB  - after imipenem administration. The blaNDM-1 was carried by a 280 kb plasmid
AB  - pRpNDM1-1 in R. planticola and a 58 kb plasmid pEcNDM1-4 in E. coli. The two
AB  - plasmids shared a 4812 bp NDM-1-ISCR1 element which was found to be excisable
AB  - from the plasmid as a free form and transferrable in vitro to a NDM-1 negative
AB  - plasmid from E. coli. CONCLUSION: blaNDM-1 was embedded in an ISCR1 complex class
AB  - 1 integron as a novel 4812 bp NDM-1-ISCR1 element. The element was found to be
AB  - able to self excise to become a free form, which may provide a new vehicle for
AB  - NDM-1 dissemination. This mechanism could greatly accelerate the spread of NDM-1
AB  - mediated broad spectrum beta-lactam resistance.
ER  -

TY  - JOUR
AU  - Li, J.
AU  - Li, J.W.
AU  - Feng, Z.
AU  - Wang, J.
AU  - An, H.
AU  - Liu, Y.
AU  - Wang, Y.
AU  - Wang, K.
AU  - Zhang, X.
AU  - Miao, Z.
AU  - Liang, W.
AU  - Sebra, R.
AU  - Wang, G.
AU  - Wang, W.C.
AU  - Zhang, J.R.
TI  - Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.
JO  - PLoS Pathog.
PY  - 2016
SP  - e1005762
EP  - e1005762
VL  - 12
AB  - DNA methylation is an important epigenetic mechanism for phenotypic diversification in all
AB  - forms of life. We previously described remarkable
AB  - cell-to-cell heterogeneity in epigenetic pattern within a clonal population of
AB  - Streptococcus pneumoniae, a leading human pathogen. We here report that the
AB  - epigenetic diversity is caused by extensive DNA inversions among hsdSA, hsdSB,
AB  - and hsdSC, three methyltransferase hsdS genes in the Spn556II type-I restriction
AB  - modification (R-M) locus. Because hsdSA encodes the sequence recognition subunit
AB  - of this type-I R-M DNA methyltransferase, these site-specific recombinations
AB  - generate pneumococcal cells with variable HsdSA alleles and thereby diverse
AB  - genome methylation patterns. Most importantly, the DNA methylation pattern
AB  - specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas
AB  - the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this
AB  - HsdSA1-dependent phase variation requires intact DNA methylase activity encoded
AB  - by hsdM in the Spn556II (renamed colony opacity determinant or cod) locus. Thus,
AB  - the DNA inversion-driven ON/OFF switch of the hsdSA1 allele in the cod locus and
AB  - resulting epigenetic switch dictate the phase variation between the opaque and
AB  - transparent phenotypes. Phase variation has been well documented for its
AB  - importance in pneumococcal carriage and invasive infection, but its molecular
AB  - basis remains unclear. Our work has discovered a novel epigenetic cause for this
AB  - significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings
AB  - broadly represents a significant advancement in our understanding of bacterial
AB  - R-M systems and their potential in shaping epigenetic and phenotypic diversity of
AB  - the prokaryotic organisms because similar site-specific recombination systems
AB  - widely exist in many archaeal and bacterial species.
ER  -

TY  - JOUR
AU  - Li, J.
AU  - Peng, H.
AU  - Xu, L.G.
AU  - Xie, Y.Z.
AU  - Xuan, X.B.
AU  - Ma, C.X.
AU  - Hu, S.
AU  - Chen, Z.X.
AU  - Yang, W.
AU  - Xie, Y.P.
AU  - Pan, Y.
AU  - Tao, L.
TI  - Draft Genome Sequence of Haemophilus parasuis gx033, a Serotype 4 Strain Isolated from the Swine Lower Respiratory Tract.
JO  - Genome Announcements
PY  - 2013
SP  - e00224
EP  - e00213
VL  - 1
AB  - Haemophilus parasuis serotype 4 is a Gram-negative pathogen that is the most prevalent H.
AB  - parasuis serovar in the world, but its genome sequence information
AB  - has not yet been reported. Thus, we determined the genome of H. parasuis strain
AB  - gx033, a serovar 4 strain isolated from a lung specimen of a diseased piglet in
AB  - southwestern China. Here, we present the first draft genome sequence of this
AB  - species.
ER  -

TY  - JOUR
AU  - Li, J.
AU  - Yan, H.F.
AU  - Wang, K.M.
AU  - Tan, W.H.
AU  - Zhou, X.W.
TI  - Hairpin fluorescence DNA probe for real-time monitoring of DNA methylation.
JO  - Anal. Chem.
PY  - 2007
SP  - 1050
EP  - 1056
VL  - 79
AB  - DNA methylation catalyzed by methylase plays an important role in many biological events.
AB  - However, traditional methods of methylase activity
AB  - analysis by gel electrophoresis were laborious and discontinuous. In
AB  - this paper, we report a new strategy to study methylase activity using
AB  - fluorescent probes coupled with enzyme-linkage reactions. A hairpin DNA
AB  - probe is prepared with a fluorophore and a quencher linked at the 5'-
AB  - and 3'-terminus of the probe. A disturbance of the stem sequence by DNA
AB  - methylation would cause the separation of the fluorophore and the
AB  - quencher, resulting in the restoration of the fluorescence. We used DNA
AB  - adenine methylation (Dam) methyltransferase (MTase) and Dpn I
AB  - endonuclease, both having a 5'-G-A-T-C-3' recognition sequence. Dam
AB  - MTase catalyzed the methylation of the sequence of 5'-GATC-3', and Dpn
AB  - I cut the sequence of 5'-G-Am-T-C-3'. The fluorescence of the hairpin
AB  - probe was restored when it was cleaved by Dpn I endonuclease during the
AB  - course of methylation. Unlike traditional methods, this assay was done
AB  - in real time and could be used to monitor the dynamic process of
AB  - methylation. Our method is easy, simple, and nonradioactive, yet as
AB  - efficient as gel electrophoresis in detecting the activity of
AB  - methylase. It also had the potential to screen suitable inhibitor drugs
AB  - for Dam methylase.
ER  -

TY  - JOUR
AU  - Li, J.-K.
AU  - Tu, J.
TI  - Ssp RFI, a novel class-II restriction endonuclease from Synechococcus RF-1 recognizing 5'TT/CGAA-3' .
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4770
EP  - 4770
VL  - 19
AB  - A novel class II restriction endonuclease has been isolated from a
AB  - cyanobacterium Synechococcus RF-1, which shows a circadian rhythm in its
AB  - nitrogen fixation activity, and designated as SspRFI.  The enzyme recognizes
AB  - the palindrome 5'-TT/CGAA-3' and generates 5'-protruding CG-dinucleotides.  Its
AB  - isoschizomers have also been isolated from Streptomyces, Bacillus,
AB  - Lactobacillus and other cyanobacteria.  SspRFI favors low salt conditions and
AB  - can be inhibited by a methylation of the intter adenine residue.
ER  -

TY  - JOUR
AU  - Li, J.Y.
AU  - Pu, M.T.
AU  - Hirasawa, R.
AU  - Li, B.Z.
AU  - Huang, Y.N.
AU  - Zeng, R.
AU  - Jing, N.H.
AU  - Chen, T.
AU  - Li, E.
AU  - Sasaki, H.
AU  - Xu, G.L.
TI  - Synergistic function of DNA Methyltransferases dnmt3a and dnrnt3b in the methylation of Oct4 and Nanog.
JO  - Mol. Cell. Biol.
PY  - 2007
SP  - 8748
EP  - 8759
VL  - 27
AB  - DNA methylation plays an important role in gene silencing in mammals. Two de novo
AB  - methyltransferases, Dnmt3a and Dnmt3b, are required for the
AB  - establishment of genomic methylation patterns in development. However,
AB  - little is known about their coordinate function in the silencing of
AB  - genes critical for embryonic development and how their activity is
AB  - regulated. Here we show that Dnmt3a and Dnmt3b are the major components
AB  - of a native complex purified from embryonic stem cells. The two enzymes
AB  - directly interact and mutually stimulate each other both in vitro and
AB  - in vivo. The stimulatory effect is independent of the catalytic
AB  - activity of the enzyme. In differentiating embryonic carcinoma or
AB  - embryonic stem cells and mouse postimplantation embryos, they function
AB  - synergistically to methylate the promoters of the Oct4 and Nanog genes.
AB  - Inadequate methylation caused by ablating Dnmt3a and Dnmt3b is
AB  - associated with dysregulated expression of Oct4 and Nanog during the
AB  - differentiation of pluripotent cells and mouse embryonic development.
AB  - These results suggest that Dnmt3a and Dnmt3b form a complex through
AB  - direct contact in living cells and cooperate in the methylation of the
AB  - promoters of Oct4 and Nanog during cell differentiation. The physical
AB  - and functional interaction between Dnmt3a and Dnmt3b represents a novel
AB  - regulatory mechanism to ensure the proper establishment of genomic
AB  - methylation patterns for gene silencing in development.
ER  -

TY  - JOUR
AU  - Li, K.
AU  - Wang, S.
AU  - Shi, Y.
AU  - Qu, J.
AU  - Zhai, Y.
AU  - Xu, L.
AU  - Xu, Y.
AU  - Song, J.
AU  - Liu, L.
AU  - Rahman, M.A.
AU  - Yan, Y.
TI  - Genome Sequence of Paracoccus sp.TRP, a Chlorpyrifos Biodegrader.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1786
EP  - 1787
VL  - 193
AB  - A Paracoccus sp. strain TRP, isolated from activated sludge, could completely biodegrade
AB  - chlorpyrifos and 3,5,6-trichloro-2-pyridinol. Here, we report the draft genome sequence of
AB  - Paracoccus sp.strain TRP which could be used to predict genes for xenobiotics biodegradation
AB  - and metabolism.
ER  -

TY  - JOUR
AU  - Li, L.
TI  - Studies on FokI (a type IIS) restriction endonuclease.
JO  - Diss. Abstr.
PY  - 1994
SP  - 877B
EP  - 878B
VL  - 55
AB  - FokI restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide
AB  - 5'-GGATG-3'/5'-CATCC-3' in duplex DNA and cleaves 9 and 13 nucleotides away from the
AB  - recognition site. This implies that this enzyme has separate domains for DNA recognition and
AB  - cleavage. The fokIM and fokIR were subcloned into Escherichia coli. FokI endonuclease was
AB  - overexpressed and purified to homogeneity. The recognition and cleavage domains of FokI were
AB  - analyzed by trypsin digestion. FokI in the presence of a DNA substrate is cleaved into a 41
AB  - kDa amino-terminal fragment and a 25 kDA carboxyl-terminal fragment. Gel-mobility-shift assays
AB  - indicate that all the protein contacts necessary for the sequence-specific recognition of DNA
AB  - substrates are encoded within the 41 kDa fragment. On further digestion, the 41 kDa fragment
AB  - degrades into 30 kDa amino-terminal and 11 kDa carboxyl-terminal fragments which together bind
AB  - DNA substrates. Thus, the 41 kDa amino-terminal fragment constitutes the FokI recognition
AB  - domain. This was confirmed by the characterization of two carboxyl-terminal deletion mutant
AB  - proteins (41 kDa and 30 kDa, respectively) of FokI. The 41 kDa mutant protein binds the DNA
AB  - sequence 5'-GGATG-3':5' - CATCC-3' specifically like the wild-type FokI. The 30 kDa mutant
AB  - protein does not bind DNA. Addition of the HPLC-purified 11 kDa fragment to the 30 kDa mutant
AB  - protein restores its sequence specific DNA-binding property. The affinity of the 41 kDa mutant
AB  - protein for the DNA substrate is comparable to that of the wild-type FokI. The 41 kDa mutant
AB  - protein interacts with its substrate in a similar way compared to the wild-type enzyme as
AB  - revealed by hydroxyl radical footprinting experiments. The 25 kDa carboxyl-terminal fragment
AB  - of FokI cleaves DNA substrates non-specifically in the presence of MgCl2. Thus, the 25 kDa
AB  - fragment constitutes the FokI cleavage domain. Additional amino acids have been introduced
AB  - between the two domains of FokI by insertion mutagenesis. The mutant enzymes have the same DNA
AB  - sequence specificity as the wild-type FokI. However, compared with the wild-type enzyme, they
AB  - cleave one nucleotide further away from the recognition site on both strands of the DNA
AB  - substrates. Thus, it is possible to alter the cleavage distance of FokI by protein
AB  - engineering.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Bannantine, J.P.
AU  - Zhang, Q.
AU  - Amonsin, A.
AU  - May, B.J.
AU  - Alt, D.
AU  - Banerji, N.
AU  - Kanjilal, S.
AU  - Kapur, V.
TI  - The complete genome sequence of Mycobacterium avium subspecies paratuberculosis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 12344
EP  - 12349
VL  - 102
AB  - We describe here the complete genome sequence of a common clone of Mycobacterium avium
AB  - subspecies paratuberculosis (Map) strain K-10, the
AB  - causative agent of Johne's disease in cattle and other ruminants. The K-10
AB  - genome is a single circular chromosome of 4,829,781 base pairs and encodes
AB  - 4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis
AB  - identified >3,000 genes with homologs to the human pathogen, M.
AB  - tuberculosis (Mtb), and 161 unique genomic regions that encode 39
AB  - previously unknown Map genes. Analysis of nucleotide substitution rates
AB  - with Mtb homologs suggest overall strong selection for a vast majority of
AB  - these shared mycobacterial genes, with only 68 ORFs with a synonymous to
AB  - nonsynonymous substitution ratio of >2. Comparative sequence analysis
AB  - reveals several noteworthy features of the K-10 genome including: a
AB  - relative paucity of the PE/PPE family of sequences that are implicated as
AB  - virulence factors and known to be immunostimulatory during Mtb infection;
AB  - truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first
AB  - gene in the mycobactin biosynthesis gene cluster, providing a possible
AB  - explanation for mycobactin dependence of Map; and Map-specific sequences
AB  - that are likely to serve as potential targets for sensitive and specific
AB  - molecular and immunologic diagnostic tests. Taken together, the
AB  - availability of the complete genome sequence offers a foundation for the
AB  - study of the genetic basis for virulence and physiology in Map and enables
AB  - the development of new generations of diagnostic tests for bovine Johne's
AB  - disease.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Chandrasegaran, S.
TI  - Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 2764
EP  - 2768
VL  - 90
AB  - FokI restriction endonuclease recognizes the nonpalindromic pentadeoxyribonucleotide
AB  - 5'-GGATC-3'-5'CATCC-3' in duplex DNA and cleaves 9 and 13 nucleotides away from the
AB  - recognition site. Recently, we reported the presence of two distinct and separable protein
AB  - domains within this enzyme-one for the sequence-specific recognition and the other for
AB  - endonuclease activity. Here, we report the construction of two insertion mutants of FokI
AB  - endonuclease. The mutant enzymes were purified, and their cleavage properties were
AB  - characterized. The mutants have the same DNA sequence specificity as the wild-type enzyme.
AB  - However compared with the wild-type enzyme, they cleave one nucleotide further away from the
AB  - recognition site on both strands of the DNA substrates. Thus, it is possible to alter the
AB  - cleavage distance of FokI by protein engineering.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Cheng, C.K.
AU  - Cheung, M.K.
AU  - Law, P.T.
AU  - Ling, J.M.
AU  - Kam, K.M.
AU  - Cheung, W.M.
AU  - Kwan, H.S.
TI  - Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6319
EP  - 6320
VL  - 194
AB  - Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of  Salmonella
AB  - that causes human gastroenteritis. Here, we report the draft genome
AB  - sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative
AB  - genomic analysis unveiled three strain-specific genomic islands that potentially
AB  - confer the multidrug resistance and virulence of the strain.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Su, F.
AU  - Wang, Y.
AU  - Zhang, L.
AU  - Liu, C.
AU  - Li, J.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequences of Two Thermophilic Bacillus licheniformis Strains, Efficient Producers of Platform Chemical 2,3-Butanediol.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4133
EP  - 4134
VL  - 194
AB  - Both Bacillus licheniformis strains 10-1-A and 5-2-D are efficient producers of
AB  - 2,3-butanediol. Here we present 4.3-Mb and 4.2-Mb assemblies of their genomes.
AB  - The key genes for the regulation and metabolism of 2,3-butanediol production were
AB  - annotated, which may provide further insights into the molecular mechanism for
AB  - the production of 2,3-butanediol with high yield and productivity.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Wang, Y.
AU  - Li, K.
AU  - Su, F.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of meso-2,3-Butanediol-Producing Strain Serratia marcescens ATCC  14041.
JO  - Genome Announcements
PY  - 2014
SP  - e00590
EP  - e00514
VL  - 2
AB  - Serratia marcescens strain ATCC 14041 was found to be an efficient meso-2,3-butanediol
AB  - (meso-2,3-BD) producer from glucose and sucrose. Here we
AB  - present a 5.0-Mb assembly of its genome. We have annotated 4 coding sequences
AB  - (CDSs) for meso-2,3-BD fermentation and 2 complete operons including 6 CDSs for
AB  - sucrose utilization.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Wang, Y.
AU  - Wang, K.
AU  - Li, K.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Thermophilic Bacillus licheniformis Strain 3F-3, an Efficient  Pentose-Utilizing Producer of 2,3-Butanediol.
JO  - Genome Announcements
PY  - 2014
SP  - e00615
EP  - e00614
VL  - 2
AB  - Bacillus licheniformis strain 3F-3 is an efficient pentose-utilizing producer of  platform
AB  - chemical, 2,3-butanediol. Here we present a 4.1-Mb assembly of its
AB  - genome. The key genes for pentose utilization, regulation, and metabolism of
AB  - 2,3-butanediol were annotated, which may provide further insights into the
AB  - molecular mechanism of 2,3-butanediol production from biomass pentose.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Wu, L.P.
AU  - Chandrasegaran, S.
TI  - Functional domains in FokI restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 4275
EP  - 4279
VL  - 89
AB  - The PCR was used to alter transcriptional and translational signals surround the
AB  - Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high
AB  - expression in Escherichia coli. By changing the ribosome-binding site sequence preceding the
AB  - fokIR gene to match the consensus E. coli signal and by placing a positive retroregulator
AB  - stem-loop sequence downstream of the gene, FokI yield was increased to 5-8% of total cellular
AB  - protein. FokI was purified to homogeneity with phosphocellulose, DEAE-Sephadex, and gel
AB  - chromatography, yielding 50 mg of pure FokI endonuclease per liter of culture medium. The
AB  - recognition and cleavage domains of FokI were analyzed by trypsin digestion. FokI in the
AB  - absence of a DNA substrate cleaves into a 58-kDa carboxyl-terminal and 8-kDa amino-terminal
AB  - fragment. The 58-kDa fragment does not bind the DNA substrate. FokI in the presence of a DNA
AB  - substrate cleaves into a 41-kDa amino-terminal fragment and a 25-kDa carboxyl-terminal
AB  - fragment. On further digestion, the 41-kDa fragment degrades into 30-kDa amino terminal and
AB  - 11-kDa carboxyl-terminal fragments. The cleaved fragments both bind DNA substrates, as does
AB  - the 41-kDa fragment. Gel-mobility-shift assays indicate that all the protein contacts
AB  - necessary for the sequence-specific recognition of DNA substrates are encoded within the
AB  - 41-kDa fragment. Thus, the 41-kDa amino-terminal fragment constitutes the FokI recognition
AB  - domain. The 25-kDa fragment purified by using a DEAE-Sephadex column, cleaves nonspecifically
AB  - both methylated (pACYCfokIM) and nonmethylated (pTZ19R) DNA substrates in the presence of
AB  - MgCl2. Thus, the 25-kDa carboxyl-terminal fragment constitutes the FokI cleavage domain.
ER  -

TY  - JOUR
AU  - Li, L.
AU  - Wu, L.P.
AU  - Clarke, R.
AU  - Chandrasegaran, S.
TI  - C-terminal deletion mutants of the FokI restriction endonuclease.
JO  - Gene
PY  - 1993
SP  - 79
EP  - 84
VL  - 133
AB  - *
AB  - We have constructed two C-terminal deletion mutants of the FokI restriction endonuclease by
AB  - using the polymerase-chain-reaction technique and expressed them in Escherichia coli. The two
AB  - mutant proteins (MP) of 41 and 30 kDa, were purified to homogeneity and their DNA-binding
AB  - properties were characterized. The 41-kDa MP specifically binds the DNA sequence:
AB  - 
AB  -    5'GGATG
AB  -    3'CCTAC
AB  - 
AB  - like the wild-type (wt) FokI, but does not cleave DNA. The 30-kDa MP does not bind DNA. The
AB  - affinity of the 41-kDa MP for the DNA substrate is comparable to that of wt FokI. The 41-kDa
AB  - MP interacts with its substrate like the wt FokI, as revealed by hydroxyl radical footprinting
AB  - experiments. In the presence of a DNA substrate, the 41-kDa MP is cleaved by trypsin into a
AB  - 30-kDa N-terminal fragment and an 11-kDa C-terminal fragment. Addition of the HPLC-purified
AB  - 11-kDa C-terminal fragment to the 30-kDa MP restores its sequence-specific DNA binding
AB  - property.
AB  - These results confirm that the N-terminal 41-kDa fragment of the FokI ENase constitutes the
AB  - DNA recognition domain of the ENase.
AB  - 
ER  -

TY  - JOUR
AU  - Li, L.G.
AU  - Cai, L.
AU  - Zhang, T.
TI  - Genome of Cupriavidus sp. HMR-1, a Heavy Metal-Resistant Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00202
EP  - e00212
VL  - 1
AB  - Cupriavidus sp. HMR-1 was isolated from a heavy metal-enriched culture of activated sludge
AB  - from a wastewater treatment plant in Hong Kong. Here, we release
AB  - the HMR-1 genome to provide basic genetic characteristics for a better
AB  - understanding of its multiple heavy metal resistance properties.
ER  -

TY  - JOUR
AU  - Li, L.I.
AU  - Tanyashin, V.I.
AU  - Matvienko, N.I.
AU  - Bayev, A.A.
TI  - Production of Specific Fragments of T4 DNA by Endonuclease EcoRI.
JO  - Dokl. Akad. Nauk.
PY  - 1975
SP  - 1262
EP  - 1265
VL  - 223
AB  - Restriction enzyme EcoRI was used to cleave nonglucosylated bacteriophage T4
AB  - DNA in a minimum 41 fragments, which were separated on agarose gels.  The
AB  - fragments were estimated to fall within the size range of 8.2-0.38 Mdalton. It
AB  - was shown that either alpha- or beta-glucosylation protects fully T4 DNA
AB  - against EcoRI function. Recombinant cells E. coli K12 r 2,4-, r 6-(RI)/6
AB  - harbouring the RI plasmid were isolated.  The efficiency of plating of
AB  - different T4 mutants with nonglucosylated and partly glucosylated DNA on them
AB  - was not lower then on the strain E. coli K 12 r 2,4-,r6-.
ER  -

TY  - JOUR
AU  - Li, L.L.
AU  - Taghavi, S.
AU  - Izquierdo, J.A.
AU  - van der Lelie, D.
TI  - Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6982
EP  - 6983
VL  - 194
AB  - We present the full genome sequence of Clostridium sp. strain BNL1100, a Gram-positive,
AB  - endospore-forming, lignocellulolytic bacterium isolated from a
AB  - corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100
AB  - contains 4,025 putative protein-coding genes, of which 103 are glycoside
AB  - hydrolases, the highest detected number in cluster III clostridia.
ER  -

TY  - JOUR
AU  - Li, M.
AU  - Yang, S.
AU  - Lai, Q.
AU  - Shao, Z.
TI  - Draft Genome Sequence of Thalassospira xiamenensis Strain MCCC 1A03042T.
JO  - Genome Announcements
PY  - 2017
SP  - e01702
EP  - e01716
VL  - 5
AB  - Thalassospira xiamenensis strain MCCC 1A03042T was isolated from deep-sea sediment of the
AB  - Indian Ocean, and it was characterized with heavy-metal arsenic
AB  - tolerance. Here, we present the draft genome of strain MCCC 1A03042T, which
AB  - contains 4,786,207 bp with a G+C content of 52.6% and 4,359 protein-coding genes.
ER  -

TY  - JOUR
AU  - Li, M.Z.
AU  - Elledge, S.J.
TI  - MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules.
JO  - Nat. Genet.
PY  - 2005
SP  - 311
EP  - 319
VL  - 37
AB  - We describe a highly engineered in vivo cloning method, mating-assisted genetically integrated
AB  - cloning (MAGIC), that facilitates the rapid
AB  - construction of recombinant DNA molecules. MAGIC uses bacterial mating, in
AB  - vivo site-specific endonuclease cleavage and homologous recombination to
AB  - catalyze the transfer of a DNA fragment between a donor vector in one
AB  - bacterial strain and a recipient plasmid in a separate bacterial strain.
AB  - Recombination events are genetically selected and result in placement of
AB  - the gene of interest under the control of new regulatory elements with
AB  - high efficiency. MAGIC eliminates the need for restriction enzymes, DNA
AB  - ligases, preparation of DNA and all in vitro manipulations required for
AB  - subcloning and allows the rapid construction of multiple constructs with
AB  - minimal effort. We show that MAGIC can generate constructs for expression
AB  - in multiple organisms. As this new method requires only the simple mixing
AB  - of bacterial strains, it represents a substantial advance in
AB  - high-throughput recombinant DNA production that will save time, effort and
AB  - expense in functional genomics studies.
ER  -

TY  - JOUR
AU  - Li, N.
AU  - Zhang, J.
AU  - Zhang, L.Q.
AU  - Nie, P.
TI  - Difference in genes between a high virulence strain G4 and a low virulence strain G18 of Flavobacterium columnare by using suppression subtractive hybridization.
JO  - J. Fish Dis.
PY  - 2010
SP  - 403
EP  - 412
VL  - 33
AB  - Flavobacterium columnare is the causative agent of columnaris disease. Different genetic
AB  - groups of F. columnare show to some extent different degrees of virulence. To identify genetic
AB  - differences between
AB  - the high virulence strain G4 and the low virulence strain G18 of F. columnare, suppression
AB  - subtractive hybridization was used. A total of 46 genes were identified from the virulent
AB  - strain G4, 35 of which
AB  - showed some degree of homology with known proteins and can be classified into 11 categories:
AB  - DNA replication or recombination proteins, inorganic
AB  - ion transport proteins, outer membrane proteins, enterotoxin, binding proteins, YD repeat
AB  - proteins, transposase, chaperon, signal transduction-
AB  - related proteins, regulatory proteins, metabolism-
AB  - related proteins. Several putative virulence factors identified in other bacteria could also
AB  - be identified in the virulent strain G4, such as ferrous
AB  - iron transport protein, TonB-dependent receptor, transposases, as well as ABC transporter
AB  - permease protein. The flanking region of a putative transposase ISFclI was analysed, and a
AB  - putative Rhs element was located at the downstream of the putative transposase. The analysis
AB  - of isfcl I gene in
AB  - 24 strains of F. columnare isolated in China revealed that 11 strains have isfcl I, and all
AB  - the strains from Zhaoqing, Anhui and Qingjiang have
AB  - isfclI.
ER  -

TY  - JOUR
AU  - Li, N.
AU  - Zhang, L.Q.
AU  - Zhang, J.
AU  - Liu, Z.X.
AU  - Huang, B.
AU  - Zhang, S.H.
AU  - Nie, P.
TI  - Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare.
JO  - Vet. Microbiol.
PY  - 2012
SP  - 61
EP  - 68
VL  - 160
AB  - Flavobacterium columnare, the causative agent of columnaris disease, infects freshwater fish
AB  - worldwide. However, the pathogenicity of this
AB  - bacterium is poorly understood due possibly to the lack of an efficient
AB  - in-frame knockout technique. In order to improve electroporation
AB  - efficiency, the type I restriction-modification system (R-M system) was
AB  - cloned and its role in electroporation was examined in F. columnare
AB  - G(4) strain. The complete sequence of type I R-M system in the
AB  - bacterium, designated as Fcl, contains all three subunits of type I R-M
AB  - system, named as fclM, fclS, fclR, respectively, with the
AB  - identification of a hypothetical gene, fclX. Constitutive transcription
AB  - of the three genes was observed in F. columnare G(4) by RT-PCR. The ORF
AB  - of fclM and fclS was cloned into the plasmid pACYC184 and transformed
AB  - into Escherichia colt TOP10. The resultant E. coli strain, designated
AB  - as E. coli TOPmt, was transformed with the integrative plasmid pGL006
AB  - constructed for F. columnare G(4). The integrative plasmid was
AB  - re-isolated from TOPmt and incubated with the lysate of F. columnare
AB  - G(4). The re-isolated integrative plasmid, designated as pGL006',
AB  - showed higher resistance than pGL006. With pGL006', the electroporation
AB  - efficiency of the strain G(4) increased 2.6 times, while that of F.
AB  - columnare G(18) was not obviously improved. Furthermore, a method to
AB  - improve the electroporation efficiency of F. columnare G(4) was
AB  - developed using the integrative plasmid methylated by E. coil TOPmt
AB  - which contains the fclM and fclS gene of F. columnare G(4). Further
AB  - analyses showed that the fcl gene cluster may be a unique type I R-M
AB  - system in F. columnare G(4). It will be of significant interest to
AB  - examine the composition and diversity of R-M systems in strains of F.
AB  - columnare in order to set up a suitable genetic manipulation system for
AB  - the bacterium.
ER  -

TY  - JOUR
AU  - Li, N.Z.
AU  - Xia, T.
AU  - Xu, Y.L.
AU  - Qiu, R.R.
AU  - Xiang, H.
AU  - He, D.
AU  - Peng, Y.Y.
TI  - Genome Sequence of Paenibacillus sp. Strain Aloe-11, an Endophytic Bacterium with Broad Antimicrobial Activity and Intestinal Colonization Ability.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2117
EP  - 2118
VL  - 194
AB  - Paenibacillus sp. strain Aloe-11, a Gram-positive, spore-forming, facultatively anaerobic
AB  - bacterium isolated from the root of Aloe chinensis in the southwest
AB  - region of China, has excellent antibiotic activity and intestine colonization
AB  - ability. Here, we present the 5.8-Mb draft genome sequence of Paenibacillus sp.
AB  - strain Aloe-11.
ER  -

TY  - JOUR
AU  - Li, P.
AU  - Yang, C.
AU  - Wang, J.
AU  - Yi, S.
AU  - Li, H.
AU  - Wang, Y.
AU  - Qiu, S.
AU  - Song, H.
TI  - Draft Genome Sequence of a New Shigella flexneri Subserotype, 4S BJ10610.
JO  - Genome Announcements
PY  - 2014
SP  - e00715
EP  - e00714
VL  - 2
AB  - Shigella flexneri is of great concern in the prevalence of shigellosis and resistance to many
AB  - antibiotics in developing countries. Here, we report the draft
AB  - genome sequence of a new S. flexneri subserotype, 4S BJ10610, isolated from the
AB  - stool specimens of a patient in Beijing, China.
ER  -

TY  - JOUR
AU  - Li, P.Y.
AU  - Xie, B.B.
AU  - Zhang, X.Y.
AU  - Qin, Q.L.
AU  - Dang, H.Y.
AU  - Wang, X.M.
AU  - Chen, X.L.
AU  - Yu, J.
AU  - Zhang, Y.Z.
TI  - Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea.
JO  - Environ. Microbiol.
PY  - 2012
SP  - 467
EP  - 479
VL  - 14
AB  - Archaea of the Miscellaneous Crenarchaeotic Group (MCG) exist widely in soil,
AB  - freshwater and marine sediments of both surface and subsurface. However, current
AB  - knowledge about this group is limited to its phylogenetic diversity. An archaeal
AB  - 16S library was constructed from a sediment sample from the South China Sea,
AB  - which was dominated by MCG and Marine Group I (MG-I). A metagenomic library was
AB  - constructed from the same sediment sample, and three MCG fosmids (E6-3G, E37-7F
AB  - and E48-1C) containing 16S rRNA genes were screened. Annotation showed that the
AB  - three genomic fragments encode a variety of open reading frames (ORFs) that are
AB  - potentially homologous to important functional genes related to lipid
AB  - biosynthesis, energy metabolism, and resistance to oxidants. No colinear regions
AB  - were found between MCG fosmids and reported archaeal genomic fragments or
AB  - genomes, suggesting that the MCG archaea are quite different from the sequenced
AB  - archaea in gene arrangement. Analyses of both the phylogenies of 16S rRNA genes
AB  - and several informational processing genes and nucleotide frequencies showed that
AB  - MCG archaea are distinct from MG-I plus relatives. In addition, tetranucleotide
AB  - frequency analysis in combination with phylogenetic analysis suggested that some
AB  - fragments in the MCG fosmids are probably derived from non-MCG or non-archaeal
AB  - genomes.
ER  -

TY  - JOUR
AU  - Li, Q.
AU  - Hu, Y.
AU  - Xu, L.
AU  - Xie, X.
AU  - Tao, M.
AU  - Jiao, X.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Choleraesuis Vaccine Strain C500 Attenuated by Chemical Mutation.
JO  - Genome Announcements
PY  - 2014
SP  - e01022
EP  - e01014
VL  - 2
AB  - Salmonella enterica serovar Choleraesuis strain C500 is a live vaccine attenuated by chemical
AB  - methods. Here, we report the complete genome sequence of the strain,
AB  - which may be helpful for elucidating the attenuation mechanism of the vaccine
AB  - strain.
ER  -

TY  - JOUR
AU  - Li, Q.
AU  - Pan, Y.
AU  - Ding, L.
AU  - Hong, H.
AU  - Yan, S.
AU  - Wu, B.
AU  - Liang, Y.
TI  - Draft Genome Sequence of Lactobacillus brevis Strain 3M004, a Probiotic with Potential Quorum-Sensing Regulation.
JO  - Genome Announcements
PY  - 2017
SP  - e00675
EP  - e00617
VL  - 5
AB  - We present here the draft genome sequence of Lactobacillus brevis strain 3M004, a probiotic
AB  - that has potential for regulating quorum sensing. The strain was
AB  - obtained from a type of aquafeed. The assembly consists of 2,459,326 bp and
AB  - contains 33 contigs, with a G+C content of 45.10%.
ER  -

TY  - JOUR
AU  - Li, Q.
AU  - Xu, L.Z.
AU  - Zou, T.
AU  - Ai, P.
AU  - Huang, G.H.
AU  - Li, P.
AU  - Zheng, A.P.
TI  - Complete genome sequence of Bacillus thuringiensis strain HD521.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 62
EP  - 62
VL  - 10
AB  - Bacillus thuringiensis is the most widely used biological pesticide in the world. It belongs
AB  - to the Bacillus cereus sensu lato group, which contains six species. Among these six species,
AB  - B. thuringiensis, B. anthracis, and B. cereus have a low genetic diversity. B. thuringiensis
AB  - strain HD521 shows maroon colony which is different from most of the B. thuringiensis strains.
AB  - Strain HD521 also displays an ability to inhibit plant sheath blight disease pathogen
AB  - (Rhizoctonia solani AG1 IB) growth and can form bipyramidal parasporal crystals consisting of
AB  - three cry7 genes. These crystals have an insecticidal activity against Henosepilachna
AB  - vigintioctomaculata larva (Coleoptera). Here we report the complete genome sequence of strain
AB  - HD521, which has one chromosome and six circular plasmids.
ER  -

TY  - JOUR
AU  - Li, S.
AU  - Liu, F.
AU  - Sun, H.
AU  - Zhu, B.
AU  - Lv, N.
AU  - Xue, G.
TI  - Whole-Genome Sequencing of Macrolide-Resistant Mycoplasma pneumoniae Strain S355, Isolated in China.
JO  - Genome Announcements
PY  - 2016
SP  - e00087
EP  - e00016
VL  - 4
AB  - Macrolide-resistant Mycoplasma pneumoniae plays an important role in refractory M. pneumoniae
AB  - pneumonia. Here, we present the whole-genome sequencing of the
AB  - macrolide-resistant M. pneumoniae strain S355. The annotated full-genome sequence
AB  - might provide a new insight into drug resistance in M. pneumoniae and can help
AB  - pediatricians recognize the disease earlier.
ER  -

TY  - JOUR
AU  - Li, S.
AU  - Skov, R.L.
AU  - Han, X.
AU  - Larsen, A.R.
AU  - Larsen, J.
AU  - Sorum, M.
AU  - Wulf, M.
AU  - Voss, A.
AU  - Hiramatsu, K.
AU  - Ito, T.
TI  - Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 3046
EP  - 3050
VL  - 55
AB  - The structures of staphylococcal cassette chromosome mec (SCCmec) elements
AB  - carried by 31 clonal complex 398 (CC398) methicillin-resistant
AB  - Staphylococcus aureus (MRSA) strains isolated from the participants at a
AB  - conference were analyzed. The SCCmecs were classified into novel types,
AB  - namely, IX, X, V(5C2&5) subtype c, and IVa. Type V(5C2&5) subtype c, IX,
AB  - and X SCCmecs carried genes conferring resistance to metals. The
AB  - structures of SCCmecs from CC398 strains were distinct from those normally
AB  - found in humans, adding to the evidence that humans are not the original
AB  - host for CC398.
ER  -

TY  - JOUR
AU  - Li, S.
AU  - Sun, H.
AU  - Liu, F.
AU  - Zhao, H.
AU  - Zhu, B.
AU  - Lv, N.
TI  - Complete Genome Sequence of the Macrolide-Resistant Mycoplasma pneumoniae Strain  C267 in China.
JO  - Genome Announcements
PY  - 2016
SP  - e00236
EP  - e00216
VL  - 4
AB  - Macrolide-resistantMycoplasma pneumoniaestrains can cause severeM. pneumoniaepneumonia in
AB  - children. Here, we report the complete genome sequence of
AB  - the macrolide-resistantM. pneumoniaestrain C267, deposited in GenBank under
AB  - accession number CP014267, which provides new insights for other potential
AB  - macrolide-resistant mechanisms inM. pneumoniaeclinical isolates in China.
ER  -

TY  - JOUR
AU  - Li, S.
AU  - Yang, D.
AU  - Qiu, M.
AU  - Shao, J.
AU  - Guo, R.
AU  - Shen, B.
AU  - Yin, X.
AU  - Zhang, R.
AU  - Zhang, N.
AU  - Shen, Q.
TI  - Complete Genome Sequence of Paenibacillus polymyxa SQR-21, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity and Rhizosphere Colonization Ability.
JO  - Genome Announcements
PY  - 2014
SP  - e00281
EP  - e00214
VL  - 2
AB  - Here we report the complete genome sequence of a plant growth-promoting
AB  - rhizobacterium (PGPR), Paenibacillus polymyxa SQR-21, which consists of one
AB  - circular chromosome of 5,828,438 bp with 5,024 coding sequences (CDS). The data
AB  - presented highlight multiple sets of functional genes associated with its
AB  - plant-beneficial characteristics.
ER  -

TY  - JOUR
AU  - Li, S.
AU  - Zhao, H.
AU  - Li, Y.
AU  - Niu, S.
AU  - Cai, B.
TI  - Complete Genome Sequence of the Naphthalene-Degrading Pseudomonas putida Strain ND6.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5154
EP  - 5155
VL  - 194
AB  - Pseudomonas putida strain ND6 is an efficient naphthalene-degrading bacterium. The complete
AB  - genome of strain ND6 was sequenced and annotated. The genes encoding
AB  - the enzymes involved in catechol degradation by the ortho-cleavage pathway were
AB  - found in the chromosomal sequence, which indicated that strain ND6 is able to
AB  - metabolize naphthalene by the catechol meta- and ortho-cleavage pathways.
ER  -

TY  - JOUR
AU  - Li, T.
AU  - Chen, J.
AU  - Chang, D.
AU  - Fang, X.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Su, L.
AU  - Xu, G.
AU  - Wang, Y.
AU  - Chen, Z.
AU  - Liu, C.
TI  - Draft Genome Sequence of Escherichia coli Strain LCT-EC59.
JO  - Genome Announcements
PY  - 2013
SP  - e00242
EP  - e00212
VL  - 1
AB  - The space environment is a very special condition under which many organisms change many
AB  - features. is employed widely as a prokaryotic model organism in the
AB  - fields of biotechnology and microbiology. Here, we present the draft genome
AB  - sequence of strain LCT-EC59 exposed to space conditions.
ER  -

TY  - JOUR
AU  - Li, T.
AU  - Huang, S.
AU  - Jiang, W.Z.
AU  - Wright, D.
AU  - Spalding, M.H.
AU  - Weeks, D.P.
AU  - Yang, B.
TI  - TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 359
EP  - 372
VL  - 39
AB  - DNA double-strand breaks enhance homologous recombination in cells and have been exploited for
AB  - targeted genome editing through use of engineered
AB  - endonucleases. Here we report the creation and initial characterization of
AB  - a group of rare-cutting, site-specific DNA nucleases produced by fusion of
AB  - the restriction enzyme FokI endonuclease domain (FN) with the
AB  - high-specificity DNA-binding domains of AvrXa7 and PthXo1. AvrXa7 and
AB  - PthXo1 are members of the transcription activator-like (TAL) effector
AB  - family whose central repeat units dictate target DNA recognition and can
AB  - be modularly constructed to create novel DNA specificity. The hybrid
AB  - FN-AvrXa7, AvrXa7-FN and PthXo1-FN proteins retain both recognition
AB  - specificity for their target DNA (a 26 bp sequence for AvrXa7 and 24 bp
AB  - for PthXo1) and the double-stranded DNA cleaving activity of FokI and,
AB  - thus, are called TAL nucleases (TALNs). With all three TALNs, DNA is
AB  - cleaved adjacent to the TAL-binding site under optimal conditions in
AB  - vitro. When expressed in yeast, the TALNs promote DNA homologous
AB  - recombination of a LacZ gene containing paired AvrXa7 or asymmetric
AB  - AvrXa7/PthXo1 target sequences. Our results demonstrate the feasibility of
AB  - creating a tool box of novel TALNs with potential for targeted genome
AB  - modification in organisms lacking facile mechanisms for targeted gene
AB  - knockout and homologous recombination.
ER  -

TY  - JOUR
AU  - Li, T.
AU  - Pu, F.
AU  - Yang, R.
AU  - Fang, X.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Chang, D.
AU  - Su, L.
AU  - Guo, N.
AU  - Jiang, X.
AU  - Zhao, J.
AU  - Liu, C.
TI  - Draft Genome Sequence of Escherichia coli LCT-EC106.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4443
EP  - 4444
VL  - 194
AB  - Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found  in the
AB  - intestine of warm-blooded organisms. Most E. coli strains are harmless,
AB  - but some serotypes can cause serious food poisoning in humans. Here, we present
AB  - the complete genome sequence of Escherichia coli LCT-EC106, which was isolated
AB  - from CGMCC 1.2385.
ER  -

TY  - JOUR
AU  - Li, W.
AU  - Liu, L.
AU  - Qiu, D.
AU  - Chen, H.
AU  - Zhou, R.
TI  - Identification of Streptococcus suis serotype 2 genes preferentially expressed in the natural host.
JO  - Int. J. Med. Microbiol.
PY  - 2010
SP  - 482
EP  - 488
VL  - 300
AB  - Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen for swine
AB  - and humans. Previous research about the mechanism of SS2 infection was largely
AB  - established on in vitro or ex vivo models. In this study, we focused on the
AB  - identification of SS2 genes preferentially expressed in vivo during natural
AB  - infection in pigs. Eighty SS2 genes were identified to be up-regulated in the
AB  - porcine brains and lungs by selective capture of transcribed sequences (SCOTS)
AB  - and comparative dot blot analysis, followed by quantitative RT-PCR validation.
AB  - These genes could be classified into 5 functional categories: metabolism, cell
AB  - wall associated proteins, transporters, cell replication, and function unknown.
AB  - Some of these genes may contribute to the survival and pathogenesis of SS2 in the
AB  - host via the following strategies. First, SS2 evades the host innate immune
AB  - clearance through modifying its metabolism and cell wall composition as indicated
AB  - by the up-regulation of the corresponding gene ldh and pbp2A, respectively.
AB  - Secondly, SS2 adapts to the in vivo conditions by inducing the expression of the
AB  - two-component signal transduction system VicKR which may function on the target
AB  - genes such as pcsB involved in stress response and cell wall biosynthesis.
AB  - Thirdly, SS2 enhances its virulence in vivo by up-regulating the virulence genes,
AB  - such as sly, pdgA, ssp, gidA, gcp and hp1311. Further study of these in vivo
AB  - up-regulated genes will contribute to understanding the in vivo survival
AB  - mechanism and pathogenesis of SS2.
ER  -

TY  - JOUR
AU  - Li, W.
AU  - Shi, J.
AU  - Wang, X.
AU  - Han, Y.
AU  - Tong, W.
AU  - Ma, L.
AU  - Liu, B.
AU  - Cai, B.
TI  - Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6.
JO  - Gene
PY  - 2004
SP  - 231
EP  - 240
VL  - 336
AB  - Pseudomonas sp. strain ND6, which was isolated from industrial wastewater in
AB  - Tianjin, China, was capable of dissimilating naphthalene as sole carbon and
AB  - energy sources. We identified one plasmid, pND6-1, which was associated with the
AB  - metabolism of naphthalene and determined the complete nucleotide sequence of
AB  - pND6-1 (101,858 bp) using a whole-genome-shotgun approach. Computational analyses
AB  - indicated that the naphthalene metabolism of the strain ND6 is associated with
AB  - this plasmid. This is the first report of a complete sequence of naphthalene
AB  - catabolic plasmid. pND6-1 encodes 102 putative coding sequences (CDSs). Among
AB  - them, 23 CDSs were predicted to be involved in naphthalene catabolism, 14 were
AB  - predicted to be involved in transposition and integration, 2 encoded putative
AB  - transporters, 3 were putative transcriptional regulators, and 9 were proteins
AB  - necessary for plasmid replication and partitioning. Most of the naphthalene
AB  - catabolic genes of pND6-1 have 99-100% identity in amino acid sequences
AB  - homologous to their nearest counterparts found in plasmid pDTG1, NAH7 and in a
AB  - chromosome region in Pseudomonas stutzeri AN10 except for two duplicated genes
AB  - (ND013 and ND016). Results of this study indicated that globally distributed
AB  - naphthalene catabolic genes are highly conserved among different bacterial
AB  - species.
ER  -

TY  - JOUR
AU  - Li, W.
AU  - Wu, P.
AU  - Zhang, H.
AU  - Cai, C.X.
TI  - Signal Amplification of Graphene Oxide Combining with Restriction Endonuclease for Site-Specific Determination of DNA Methylation and Assay of Methyltransferase Activity.
JO  - Anal. Chem.
PY  - 2012
SP  - 7583
EP  - 7590
VL  - 84
AB  - Site-specific identification of DNA methylation and assay of MTase activity are important in
AB  - determining specific cancer types, providing
AB  - insights into the mechanism of gene repression, and developing novel
AB  - drugs to treat methylation-related diseases. This work reports an
AB  - electrochemical method for gene-specific methylation detection and
AB  - MTase activity assay using HpaII endonuclease to improve selectivity
AB  - and employing signal amplification of graphene oxide (GO) to enhance
AB  - the assay sensitivity. The method was developed by designing a probe
AB  - DNA, which was immobilized on electrode surface, to hybridize with
AB  - target DNA (one 137 mer DNA from exon 8 promoter region of the Homo
AB  - sapiens p53 gene, was extracted from HCT116 cells). The assay is based
AB  - on the electrochemical responses of the reporter (thionine), which was
AB  - conjugated to 3'-terminus of the probe DNA via GO, after the DNA hybrid
AB  - was methylated (under catalysis of M.SssI MTase) and cleaved by HpaII
AB  - endonuclease (a site-specific endonuclease recognizing the duplex
AB  - symmetrical sequence of 5'-CCGG-3' and catalyzing cleavage between the
AB  - cytosines). This model can determine DNA methylation at the site of CpG
AB  - and has an ability to discriminate the target DNA sequence from even
AB  - single-base mismatched sequence. The electrochemical signal has a
AB  - linear relationship with M.SssI activities ranging from 0.1 to 450 U/mL
AB  - with a detection limit of similar to(0.05 +/- 0.02) U/mL at a
AB  - signal/noise of 3. The advantages of this assay are ease of performance
AB  - having a good specificity and selectivity. In addition, we also
AB  - demonstrate the method can be used for rapid evaluation and screening
AB  - of the inhibitors of MTase and has a potential application in discovery
AB  - of new anticancer drugs.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Gong, J.
AU  - Hu, Y.
AU  - Cai, L.
AU  - Johnstone, L.
AU  - Grass, G.
AU  - Rensing, C.
AU  - Wang, G.
TI  - Genome Sequence of the Moderately Halotolerant, Arsenite-Oxidizing Bacterium Pseudomonas stutzeri TS44.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4473
EP  - 4474
VL  - 194
AB  - We present the draft genome sequence of Pseudomonas stutzeri TS44, a moderately halotolerant,
AB  - arsenite-oxidizing bacterium isolated from arsenic-contaminated
AB  - soil. The genome contains genes for arsenite oxidation, arsenic resistance, and
AB  - ectoine/hydroxyectoine biosynthesis. The genome information will be useful for
AB  - exploring adaptation of P. stutzeri TS44 to an arsenic-contaminated environment.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Gu, Q.
AU  - Lou, X.
AU  - Zhang, X.
AU  - Song, D.
AU  - Shen, L.
AU  - Zhao, Y.
TI  - Complete Genome Sequence of the Probiotic Lactobacillus plantarum Strain ZJ316.
JO  - Genome Announcements
PY  - 2013
SP  - e0009413
EP  - e0009413
VL  - 1
AB  - Lactobacillus plantarum strain ZJ316, a probiotic strain with several functions,  was isolated
AB  - from healthy newborn infant fecal samples. Here we report the
AB  - finished and annotated genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Hojberg, O.
AU  - Noel, S.J.
AU  - Canibe, N.
AU  - Jensen, B.B.
TI  - Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces.
JO  - Genome Announcements
PY  - 2016
SP  - e00042
EP  - e00016
VL  - 4
AB  - Olsenella scatoligenes SK9K4(T) is a strictly anaerobic bacterium isolated from pig feces that
AB  - produces the malodorous compounds 3-methylindole (skatole) and
AB  - 4-methylphenol (p-cresol). Here, we report the 2.47 Mbp draft genome sequence of
AB  - SK9K4(T), exploring pathways for the synthesis of skatole and p-cresol from the
AB  - amino acids tryptophan and tyrosine, respectively.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Hu, Y.
AU  - Gong, J.
AU  - Lin, Y.
AU  - Johnstone, L.
AU  - Rensiing, C.
AU  - Wang, G.
TI  - Genome sequence of the highly efficient arsenite-oxidizing bacterium Achromobacter arsenitoxydans SY8.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1243
EP  - 1244
VL  - 194
AB  - We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported
AB  - arsenite-oxidizing bacterium belonging to the genus Achromobacter and containing a genomic
AB  - arsenic island, an intact type III secretion system, and multiple metal(loid) transporters.
AB  - The genome may be helpful to explore the mechanisms intertwining metal(loid) resistance and
AB  - pathogenicity.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Hu, Y.
AU  - Gong, J.
AU  - Lin, Y.
AU  - Johnstone, L.
AU  - Rensing, C.
AU  - Wang, G.
TI  - Genome Sequence of the Highly Efficient Arsenite-Oxidizing Bacterium Achromobacter arsenitoxydans SY8.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1243
EP  - 1244
VL  - 194
AB  - We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported
AB  - arsenite-oxidizing bacterium belonging to the genus Achromobacter
AB  - and containing a genomic arsenic island, an intact type III secretion system, and
AB  - multiple metal(loid) transporters. The genome may be helpful to explore the
AB  - mechanisms intertwining metal(loid) resistance and pathogenicity.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Koblizek, M.
AU  - Feng, F.
AU  - Li, Y.
AU  - Jian, J.
AU  - Zeng, Y.
TI  - Whole-Genome Sequence of a Freshwater Aerobic Anoxygenic Phototroph, Porphyrobacter sp. Strain AAP82, Isolated from the Huguangyan Maar Lake in  Southern China.
JO  - Genome Announcements
PY  - 2013
SP  - e0007213
EP  - e0007213
VL  - 1
AB  - The Porphyrobacter genus (of the class Alphaproteobacteria) contains aerobic anoxygenic
AB  - phototrophic species. Here we report a draft genome sequence of a
AB  - freshwater bacterium, Porphyrobacter sp. strain AAP82. It contains a 38-kb-long
AB  - photosynthesis gene cluster, but carbon-fixation genes are absent. The presence
AB  - of respiratory enzymes, tricarboxylic acid (TCA) cycle, and the Entner-Doudoroff
AB  - pathway demonstrates its aerobic photoorganotrophic character.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Kot, W.
AU  - Wang, D.
AU  - Zheng, S.
AU  - Wang, G.
AU  - Hansen, L.H.
AU  - Rensing, C.
TI  - Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33.
JO  - Genome Announcements
PY  - 2015
SP  - e00406
EP  - e00415
VL  - 3
AB  - Pseudomonas migulae ES3-33 is a Gram-negative strain that strongly reduces Se(IV) and was
AB  - isolated from a selenium mining area in Enshi, southwest China. Here we
AB  - present the draft genome of this strain containing potential genes involved in
AB  - selenite reduction and a large number of genes encoding resistances to copper and
AB  - antibiotics.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Liu, F.
AU  - Hu, Y.
AU  - Mi, K.
TI  - Draft Genome Sequence of mc251, a Highly Hydrogen Peroxide-Resistant Mycobacterium smegmatis Mutant Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00092
EP  - e00014
VL  - 2
AB  - Here, we report the draft genome sequence of the Mycobacterium tuberculosis-like
AB  - Mycobacterium smegmatis mutant strain, mc(2)51, compared to that of wild-type
AB  - strain M. smegmatis mc(2)155. The draft genome sequence comprises 6,823,739 bp,
AB  - revealing 6,569 coding DNA sequences (CDSs) and 50 RNA genes (4 rRNA genes and 46
AB  - tRNA genes).
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Marshall, I.P.
AU  - Schreiber, L.
AU  - Hojberg, O.
AU  - Canibe, N.
AU  - Jensen, B.B.
TI  - Draft Genome Sequence of Megasphaera sp. Strain DJF_B143, an Isolate from Pig Hindgut Unable to Produce Skatole.
JO  - Genome Announcements
PY  - 2016
SP  - e00007
EP  - e00016
VL  - 4
AB  - The butyrate-producing Megasphaera spp. predominate in the pig hindgut and may play important
AB  - roles in gut health. Moreover, one Megasphaera isolate has been
AB  - reported to produce the boar taint compound, skatole. Here, we provide a 2.58-Mbp
AB  - draft genome of a pig hindgut isolate, Megasphaera sp. DJF_B143, unable to
AB  - produce skatole.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Song, C.
AU  - Zhao, M.
AU  - Li, Y.
TI  - Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction.
JO  - Anal. Biochem.
PY  - 2008
SP  - 1
EP  - 7
VL  - 381
AB  - We describe a method for sensitive monitoring of restriction endonuclease kinetics and
AB  - activity by use of a universal molecular beacon (U-MB) coupled with real-time polymerase chain
AB  - reaction (PCR). The method is used to monitor the progress of DNA cleavage in a sealed
AB  - reaction tube and offers more accurate and high-throughput detection. The template has a
AB  - universal tail hybridized with the U-MB and the remaining sequence is complementary to one of
AB  - the restriction endonuclease digestion products. The U-MB is replaced by the extension of
AB  - digested product and the fluorescence quenches. With this concept, one universal fluorescence
AB  - probe can be used in different enzyme analytical systems. In the work described here,
AB  - homogenous assays were performed with the restriction endonucleases AluI, EcoRI, XhoI, and
AB  - SacI at smoothly controlled temperature. Cleavage efficiencies were determined, and the
AB  - potential applications of this method were discussed. Furthermore, the AluI and EcoRI cleavage
AB  - reactions were monitored online at varying substrate concentrations at the molecular level,
AB  - and K(m), V(max), and K(cat) values were calculated. The results suggest that U-MB monitoring
AB  - of restriction endonuclease assays based on real-time PCR will be very useful for
AB  - high-throughput, sensitive, and precise assays for enzyme activity screening and evolutionary
AB  - biotechnology analysis.
ER  -

TY  - JOUR
AU  - Li, X.
AU  - Yuan, H.
AU  - Yang, J.
AU  - Li, B.
TI  - Genome Sequence of the Polyphosphate-Accumulating Organism Arthrobacter sp. Strain PAO19 Isolated from Maize Rhizosphere Soil.
JO  - Genome Announcements
PY  - 2013
SP  - e00566
EP  - e00513
VL  - 1
AB  - Arthrobacter sp. strain PAO19 is a polyphosphate-accumulating organism isolated from maize
AB  - rhizosphere soil. Here we report its genome sequence, which may shed
AB  - light on its role in phosphate removal from water bodies. To our knowledge, this
AB  - is the first genome announcement of a polyphosphate-accumulating strain of the
AB  - genus Arthrobacter.
ER  -

TY  - JOUR
AU  - Li, X.F.
AU  - Liao, X.Y.
AU  - Liu, Y.F.
AU  - Guo, L.Q.
AU  - Ye, Z.W.
AU  - Lin, J.F.
TI  - Complete Genome Sequence of Probiotic Lactobacillus plantarum Strain FMNP01, Isolated from Mango Fruit.
JO  - Genome Announcements
PY  - 2014
SP  - e01207
EP  - e01214
VL  - 2
AB  - Lactobacillus plantarum strain FMNP01 is a new strain with probiotic properties that was
AB  - isolated from fresh mango from Guangzhou, China. Here, we report the
AB  - complete genome of this organism.
ER  -

TY  - JOUR
AU  - Li, X.R.
AU  - Gong, F.M.
AU  - Zheng, H.J.
AU  - Zhang, Z.H.
AU  - Luo, Y.Y.
AU  - Liu, C.J.
TI  - Draft Genome Sequence of Lactobacillus plantarum Strain AY01, Isolated from the Raw Material of Fermented Goat Milk Cheese.
JO  - Genome Announcements
PY  - 2013
SP  - e00737
EP  - e00713
VL  - 1
AB  - Lactobacillus plantarum is an important probiotic that is isolated mostly from fermented
AB  - foods. Here, we report the first draft genome sequence of L. plantarum
AB  - strain AY01, isolated from the raw material of fermented goat milk cheese. This
AB  - bacterium, with optimum growth at 30 degrees C, has a G+C content of 43.68%.
ER  -

TY  - JOUR
AU  - Li, X.S.
AU  - Yuan, K.X.
AU  - Cullis, J.
AU  - Levesque, C.A.
AU  - Chen, W.
AU  - Lewis, C.T.
AU  - De Boer, S.H.
TI  - Draft Genome Sequences for Canadian Isolates of Pectobacterium carotovorum subsp. brasiliense with Weak Virulence on Potato.
JO  - Genome Announcements
PY  - 2015
SP  - e00240
EP  - e00215
VL  - 3
AB  - Pectobacterium carotovurum subsp. brasiliense causes soft rot and blackleg diseases on potato.
AB  - Here, we report the draft genome sequences of three weakly
AB  - virulent P. carotovurum subsp. brasiliense strains isolated in Canada. Analysis
AB  - of these genome sequences will help to pinpoint differences in virulence among P.
AB  - carotovurum subsp. brasiliense strains from tropical/subtropical and temperate
AB  - regions, such as Canada and United States. A small number of key factors for
AB  - adaptation to this bacterium's specific environmental niche were also evaluated.
ER  -

TY  - JOUR
AU  - Li, X.S.
AU  - Yuan, X.K.
TI  - Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.
JO  - Genome Announcements
PY  - 2017
SP  - e00721
EP  - e00717
VL  - 5
AB  - The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a
AB  - variety of agricultural crops, such as potato, tomato,
AB  - corn, barley, etc. Here, we report five new genome sequences, those of strains
AB  - CFIA-Cs3N, CFIA-CsR14, LMG 3663T, LMG 7333T, and ATCC 33566T, from different
AB  - subspecies of Clavibacter michiganensis All these genomic data will be used for
AB  - reclassification and niche-adapted feature comparisons.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Cao, B.
AU  - Zhang, Y.
AU  - Zhou, J.
AU  - Yang, B.
AU  - Wang, L.
TI  - Complete Genome Sequence of Staphylococcus aureus T0131, an ST239-MRSA-SCCmec type III Clone isolated in China.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3411
EP  - 3412
VL  - 193
AB  - We report here the complete genome sequence of Staphylococcus aureu T0131, which is a
AB  - multi-resistant clinical isolate recovered in China and the
AB  - first sequenced epidemic ST239-MRSA-SCCmec type III strain obtained in
AB  - Asia. Comparison with two published genomes of ST239 reveals the
AB  - polymorphism among strains of this type from different continents.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Fu, P.
AU  - Shi, L.-Y.
TI  - Study on a type II restriction endonuclease NcrI.
JO  - Chinese Biochem. J.
PY  - 1990
SP  - 309
EP  - 313
VL  - 6
AB  - NcrI isolated from Nocardia carnea C-212 strain is a type II restriction endonuclease.  By
AB  - comparing the NcrI digests of lambda DNA with that of the BglII and characterization of the
AB  - recognition specificity and its cleavage site, NcrI is identified as an isoschizomer of BglII,
AB  - with cleavage site the same as that of BglII at:
AB  - 5'...A^GATCT...3'
AB  - 3'...TCTAG^A...5'.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Guo, X.H.
AU  - Dang, Y.R.
AU  - Sun, L.L.
AU  - Zhang, X.Y.
AU  - Chen, X.L.
AU  - Qin, Q.L.
AU  - Wang, P.
TI  - Complete genome sequence of Arcticibacterium luteifluviistationis SM1504(T), a cytophagaceae bacterium isolated from Arctic surface seawater.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 33
EP  - 33
VL  - 13
AB  - Arcticibacterium luteifluviistationis SM1504(T) was isolated from Arctic surface  seawater and
AB  - classified as a novel genus of the phylum Bacteroides. To date, no
AB  - Arcticibacterium genomes have been reported, their genomic compositions and
AB  - metabolic features are still unknown. Here, we reported the complete genome
AB  - sequence of A. luteifluviistationis SM1504(T), which comprises 5,379,839 bp with
AB  - an average GC content of 37.20%. Genes related to various stress (such as
AB  - radiation, osmosis and antibiotics) resistance and gene clusters coding for
AB  - carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the
AB  - genome contained a 245-kb genomic island and a 15-kb incomplete prophage region.
AB  - A great percentage of proteins belonging to carbohydrate metabolism especially in
AB  - regard to polysaccharides utilization were found. These related genes and
AB  - metabolic characteristics revealed genetic basis for adapting to the diverse
AB  - extreme Arctic environments. The genome sequence of A. luteifluviistationis
AB  - SM1504(T) also implied that the genus Arcticibacterium may act as a vital organic
AB  - carbon matter decomposer in the Arctic seawater ecosystem.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Huang, C.C.
AU  - Zheng, J.B.
AU  - Qi, H.L.
TI  - Electrogenerated chemiluminescence biosensing method for the detection of DNA methylation and assay of the methyltransferase activity.
JO  - Biosensors and Bioelectronics
PY  - 2012
SP  - 407
EP  - 410
VL  - 38
AB  - A novel electrogenerated chemiluminescence (ECL) biosensing method for highly sensitive
AB  - detection of DNA methylation and assay of the CpG
AB  - methyltransferase (M. Sssl) activity was developed on basis of
AB  - enzyme-linkage reactions and ruthenium complex served as an ECL tag.
AB  - The ECL biosensing electrode was fabricated by self-assembling 5'-thiol
AB  - modified 32-mer single-strand DNA (ss-DNA)-tagged with ruthenium bis
AB  - (2,2'-bipyridine) (2,2'-bipyridine-4,4'-dicarboxylic
AB  - acid)-ethylenediamine on the surface of a gold electrode, and then
AB  - hybridized with complementary ss-DNA to form duplex DNA (ds-DNA). When
AB  - M. Sssl and S-adenosylmethionine were introduced, all cytosine residues
AB  - within 5'-CG-3' of ds-DNA on the biosensing electrode were methylated.
AB  - After the methylated biosensing electrode was treated by HpaII
AB  - endonuclease, the un-methylated cytosines were cleaved, thus led to
AB  - decrease ECL signal. The ECL intensity of ECL biosensing electrode is
AB  - related to the methylation level and M. Sssl activity in a fixed
AB  - concentration HpaII endonuclease. The increased ECL intensity was
AB  - direct proportion to M. Sssl activity in the range from 0.05 to 100
AB  - U/mL with a detection limit of 0.02 U/mL. This work demonstrates that
AB  - the combination of the enzyme-linkage reactions with a highly sensitive
AB  - ECL technique is a great promising approach for the detection of DNA
AB  - methylation level, assay of the activity of MTase, and evaluation of
AB  - the capability of inhibitors for the methyltransferase.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Leahy, S.C.
AU  - Jeyanathan, J.
AU  - Henderson, G.
AU  - Cox, F.
AU  - Altermann, E.
AU  - Kelly, W.J.
AU  - Lambie, S.C.
AU  - Janssen, P.H.
AU  - Rakonjac, J.
AU  - Attwood, G.T.
TI  - The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the  Methanomassiliicoccales.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 59
EP  - 59
VL  - 11
AB  - Methane emissions from agriculture represent around 9 % of global anthropogenic greenhouse
AB  - emissions. The single largest source of this methane is animal enteric
AB  - fermentation, predominantly from ruminant livestock where it is produced mainly
AB  - in their fermentative forestomach (or reticulo-rumen) by a group of archaea known
AB  - as methanogens. In order to reduce methane emissions from ruminants, it is
AB  - necessary to understand the role of methanogenic archaea in the rumen, and to
AB  - identify their distinguishing characteristics that can be used to develop methane
AB  - mitigation technologies. To gain insights into the role of methylotrophic
AB  - methanogens in the rumen environment, the genome of a methanogenic archaeon has
AB  - been sequenced. This isolate, strain ISO4-H5, was isolated from the ovine rumen
AB  - and belongs to the order Methanomassiliicoccales. Genomic analysis suggests
AB  - ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use
AB  - methanol and methylamines as substrates for methanogenesis. Like other organisms
AB  - within this order, ISO4-H5 does not possess genes required for the first six
AB  - steps of hydrogenotrophic methanogenesis. Comparison between the genomes of
AB  - different members of the order Methanomassiliicoccales revealed strong
AB  - conservation in energy metabolism, particularly in genes of the methylotrophic
AB  - methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine.
AB  - Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not
AB  - contain the genes required for production of coenzyme M, and so likely requires
AB  - external coenzyme M to survive.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Li, Q.
AU  - Li, Y.
AU  - Gao, J.
AU  - Fan, X.
TI  - Draft Genome Sequence of Paenibacillus polymyxa KF-1, an Excellent Producer of Microbicides.
JO  - Genome Announcements
PY  - 2016
SP  - e00727
EP  - e00716
VL  - 4
AB  - We report here the draft genome sequence of Paenibacillus polymyxa KF-1, which exhibits
AB  - excellent antimicrobial activity. It encodes the synthase of bacitracin,
AB  - kalimantacin, bacillomycin, iturin, fusaricidin, tridecaptin, and pelgipeptin and
AB  - biosynthetic pathways of antiviral curldan and levan polysaccharides. Also, a
AB  - novel prophage is involved in this genome that contains endolysin-encoding genes.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Li, S.
AU  - Chen, M.
AU  - Peng, G.
AU  - Tan, Z.
AU  - An, Q.
TI  - Complete genome sequence of Kosakonia oryzae type strain Ola 51T.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 28
EP  - 28
VL  - 12
AB  - Strain Ola 51T (=LMG 24251T = CGMCC 1.7012T) is the type strain of the species Kosakonia
AB  - oryzae and was isolated from surface-sterilized roots of the wild rice
AB  - species Oryza latifolia grown in Guangdong, China. Here we summarize the features
AB  - of the strain Ola 51T and describe its complete genome sequence. The genome
AB  - contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content,
AB  - 4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48
AB  - pseudo genes, and 1 CRISPR array.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Lin, Y.
AU  - Garvey, C.J.
AU  - Birch, D.
AU  - Corkery, R.W.
AU  - Loughlin, P.C.
AU  - Scheer, H.
AU  - Willows, R.D.
AU  - Chen, M.
TI  - Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris.
JO  - Biochim. Biophys. Acta
PY  - 2016
SP  - 107
EP  - 114
VL  - 1857
AB  - Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria
AB  - and some algae. It is commonly accepted that these complexes only absorb green
AB  - and orange light, complementing chlorophyll absorbance. Here, we present a new
AB  - phycobilisome derived complex that consists only of allophycocyanin core
AB  - subunits, having red-shifted absorption peaks of 653 and 712 nm. These
AB  - red-shifted phycobiliprotein complexes were isolated from the chlorophyll
AB  - f-containing cyanobacterium, Halomicronema hongdechloris, grown under
AB  - monochromatic 730 nm-wavelength (far-red) light. The 3D model obtained from
AB  - single particle analysis reveals a double disk assembly of 120-145 A with two
AB  - alpha/beta allophycocyanin trimers fitting into the two separated disks. They are
AB  - significantly smaller than typical phycobilisomes formed from allophycocyanin
AB  - subunits and core-membrane linker proteins, which fit well with a reduced
AB  - distance between thylakoid membranes observed from cells grown under far-red
AB  - light. Spectral analysis of the dissociated and denatured phycobiliprotein
AB  - complexes grown under both these light conditions shows that the same bilin
AB  - chromophore, phycocyanobilin, is exclusively used. Our findings show that
AB  - red-shifted phycobilisomes are required for assisting efficient far-red light
AB  - harvesting. Their discovery provides new insights into the molecular mechanisms
AB  - of light harvesting under extreme conditions for photosynthesis, as well as the
AB  - strategies involved in flexible chromatic acclimation to diverse light
AB  - conditions.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Liu, Y.
AU  - Zhou, Z.
AU  - Huang, H.
AU  - Ren, Y.
AU  - Zhang, Y.
AU  - Li, G.
AU  - Zhou, Z.
AU  - Wang, L.
TI  - Complete Genome Sequence of Aeromonas Veronii Strain B565.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3389
EP  - 3390
VL  - 193
AB  - Aeromonas veronii strain B565 was isolated from aquaculture pond sediment in China. We present
AB  - here the complete genome sequence of B565 and compare
AB  - it with 2 published genome sequences of pathogenic strains in Aeromonas
AB  - genus. The result represents an independent step-wise acquisition of
AB  - virulence factors of pathogenic strains in this genus.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Lu, Z.
AU  - Sun, L.
AU  - Ropp, S.
AU  - Kutish, G.F.
AU  - Rock, D.L.
AU  - Van Etten, J.L.
TI  - Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome.
JO  - Virology
PY  - 1997
SP  - 360
EP  - 377
VL  - 237
AB  - This report completes a preliminary analysis of the sequence of the 330,740-bp chlorella virus
AB  - PBCV-1 genome, the largest virus genome to be sequenced to date.  The PBCV-1 genome is 57% the
AB  - size of the genome from the smallest self-replicating organism, Mycoplasma genitalium,
AB  - Analysis of 74 kb of newly sequenced DNA, from the right terminus of the PBCV-1 genome,
AB  - revealed 153 open reading frames of 65 codons or longer.  Eighty-five of these ORFs, which are
AB  - evenly distributed on both strands of the DNA, were considered major ORFs.  Fifty-nine of the
AB  - major ORFs were separated by less than 100 bp.  The largest intergenic distance was 729 bp,
AB  - which occurred between two ORFs located in the 2.2-kb inverted terminal repeat region of the
AB  - PBCV-1 genome.  Twenty-seven of the 85 major ORFs resemble proteins in databases, including
AB  - the large subunit of ribonucleotide diphosphate reductase, ATP-dependent DNA ligase, type II
AB  - DNA topoisomerase, a helicase, histidine decarboxylase, dCMP deaminase, dUTP pyrophosphatase,
AB  - proliferating cell nuclear antigen, a transposase, fungal translation elongation factor 3, UDP
AB  - glucose dehydrogenase, a protein kinase, and an adeneine DNA methyltransferase and its
AB  - corresponding DNA site-specific endonuclease.  Seventeen of the 153 ORFs resembled other
AB  - PBCV-1 ORFs, suggesting that they represent either gene duplications or gene families.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Ng, I.S.
AU  - Zhang, X.
AU  - Wang, N.
TI  - Draft Genome Sequence of the Dye-Decolorizing and Nanowire-Producing Bacterium Shewanella xiamenensis BC01.
JO  - Genome Announcements
PY  - 2014
SP  - e00721
EP  - e00714
VL  - 2
AB  - Shewanella xiamenensis BC01 is an important biodecolorizing and nanowire-producing bacterium
AB  - which was found in Xiamen, China. Here, we present
AB  - the draft genome sequence consisting of 4,677,169 bp (GC content, 46.21%) and
AB  - 3,999 coded proteins. This information boosts insight into and understanding of
AB  - the genetic evolution of Shewanella species.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Wang, Y.
AU  - Wang, R.
AU  - Zhu, Y.
AU  - Liu, S.
AU  - Wang, Q.
AU  - Shao, J.
AU  - Chen, Y.
AU  - Gao, L.
AU  - Zhou, C.
AU  - Liu, H.
AU  - Wang, X.
AU  - Zheng, H.
AU  - Xin, J.
TI  - Changes in pathogenicity and immunogenicity of Mycoplasma mycoides subsp. mycoides strains revealed by comparative genomics analysis.
JO  - Sci. Rep.
PY  - 2016
SP  - 19081
EP  - 19081
VL  - 6
AB  - Mycoplasma mycoides subsp. mycoides is the causative agent of contagious bovine
AB  - pleuropneumonia. A pathogenic strain BEN-1 was isolated from bovine lung and
AB  - underwent continuous passages in rabbits for 468 generations. During this
AB  - process, the strain's strong virulence became weak and, gradually, it lost the
AB  - ability to confer protective immunity in cattle but developed virulence in
AB  - rabbits. In order to gain insight into the mechanisms behind the reduction in
AB  - virulence and the loss of immunogenicity, we sequenced five representative
AB  - strains of the BEN series, including the original strain (BEN-1), the strain
AB  - generation that first acquired virulence in rabbits (BEN-50), the two vaccine
AB  - strain generations (BEN-181 and BEN-326), and the strain generation showing the
AB  - greatest loss of immunogenicity (BEN-468). The gene mutation rate in the four
AB  - different propagation stages varied greatly, and over half of variations observed
AB  - in each generation were removed during the propagation process. However, the
AB  - variation maintained in the BEN-468 generation might contribute to its changes in
AB  - virulence and immunogenicity. We thus identified 18 genes associated with host
AB  - adaptation, six genes contributing to virulence in cattle, and 35 genes
AB  - participating in conferring immunity in cattle. These findings might help us
AB  - optimize the vaccine to obtain more effective immunization results.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Yan, Z.
AU  - Zheng, J.
AU  - Qi, H.
TI  - Label-free and amplified electrogenerated chemiluminescence biosensing method for the determination of DNA methyltransferase activity using signal reagent-assembled graphene oxide.
JO  - Electrochim. Acta.
PY  - 2014
SP  - 454
EP  - 461
VL  - 137
AB  - A novel label-free electrogenerated chemiluminescence (ECL) biosensing method for the
AB  - determination of DNA methyltransferase (MTase) activity was developed on base of
AB  - enzyme-linkage reactions and tris(1, 10-phenanthroline) ruthenium-assembled graphene oxide
AB  - (GO) served as an ECL signal compound. The ECL biosensing electrode was fabricated by
AB  - self-assembling 5'-thiol modified hairpin-capture DNA probe containing methylation
AB  - recognition site 5'-GATC-3' on the surface of a gold electrode. When DNA adenine methylation
AB  - (Dam) MTase and S-adenosyl-L-methionine were introduced, all adenine residues within
AB  - 5'-GATC-3' of hairpin-capture DNA probe on the biosensing electrode were methylated. After
AB  - the methylated biosensing electrode was treated by the methylation-sensitive restriction
AB  - endonuclease Dpn I, the methylated adenines were cleaved, methylation-induced scission of
AB  - hairpin-capture DNA probe would displace the hairpin section and remain the 'capture DNA
AB  - probe' section on the gold electrode, then a long ssDNA was immobilized via the partial
AB  - hybridization reaction between long ssDNA and hairpin-capture DNA probe remained section, the
AB  - more binding site allow tris(1, 10-phenanthroline) ruthenium-assembled GO to be more bound to
AB  - the long ssDNA on the electrode surface through both hydrophobic and pi-pi stacking
AB  - interaction, in conjunction with the generation of a increased ECL signal. The ECL intensity
AB  - versus the concentration of Dam MTase was linear in the range from 0.02 unit/mL to 10 unit/mL.
AB  - The detection limit was 0.01 unit/mL. This work demonstrates that using the different
AB  - affinities of GO for ssDNA and dsDNA for the fabrication of the label-free ECL biosensing
AB  - method for DNA MTase activity is promising approach.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Zhang, C.
AU  - Liu, C.
AU  - Ju, J.
AU  - Ma, J.
TI  - Genome Sequencing of Streptomyces atratus SCSIOZH16 and Activation Production of Nocardamine via Metabolic Engineering.
JO  - Front. Microbiol.
PY  - 2018
SP  - 1269
EP  - 1269
VL  - 9
AB  - The Actinomycetes are metabolically flexible microorganisms capable of producing
AB  - a wide range of interesting compounds, including but by no means limited to,
AB  - siderophores which have high affinity for ferric iron. In this study, we report
AB  - the complete genome sequence of marine-derived Streptomyces atratus ZH16 and the
AB  - activation of an embedded siderophore gene cluster via the application of
AB  - metabolic engineering methods. The S. atratus ZH16 genome reveals that this
AB  - strain has the potential to produce 26 categories of natural products (NPs)
AB  - barring the ilamycins. Our activation studies revealed S. atratus SCSIO ZH16 to
AB  - be a promising source of the production of nocardamine-type (desferrioxamine)
AB  - compounds which are important in treating acute iron intoxication and performing
AB  - ecological remediation. We conclude that metabolic engineering provides a highly
AB  - effective strategy by which to discover drug-like compounds and new NPs in the
AB  - genomic era.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Zheng, H.
AU  - Liu, Y.
AU  - Jiang, Y.
AU  - Xin, J.
AU  - Chen, W.
AU  - Song, Z.
TI  - The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1.
JO  - PLoS ONE
PY  - 2011
SP  - e20999
EP  - e20999
VL  - 6
AB  - Infection by Mycoplasma bovis (M. bovis) can induce diseases, such as pneumonia and otitis
AB  - media in young calves and
AB  - mastitis and arthritis in older animals. Here, we report the finished and annotated genome
AB  - sequence of M. bovis strain
AB  - Hubei-1, a strain isolated in 2008 that caused calf pneumonia on a Chinese farm. The genome of
AB  - M. bovis strain Hubei-1
AB  - contains a single circular chromosome of 953,114 bp with a 29.37% GC content. We identified
AB  - 803 open reading frames
AB  - (ORFs) that occupy 89.5% of the genome. While 34 ORFs were Hubei-1 specific, 662 ORFs had
AB  - orthologs in the M. bovis type
AB  - strain PG45 genome. Genome analysis validated lateral gene transfer between M. bovis and the
AB  - Mycoplasma mycoides
AB  - subspecies mycoides, while phylogenetic analysis found that the closest M. bovis neighbor is
AB  - Mycoplasma agalactiae.
AB  - Glycerol may be the main carbon and energy source of M. bovis, and most of the biosynthesis
AB  - pathways were incomplete.
AB  - We report that 47 lipoproteins, 12 extracellular proteins and 18 transmembrane proteins are
AB  - phase-variable and may help M.
AB  - bovis escape the immune response. Besides lipoproteins and phase-variable proteins, genomic
AB  - analysis found two possible
AB  - pathogenicity islands, which consist of four genes and 11 genes each, and several other
AB  - virulence factors including
AB  - hemolysin, lipoate protein ligase, dihydrolipoamide dehydrogenase, extracellular cysteine
AB  - protease and 59-nucleotidase.
ER  -

TY  - JOUR
AU  - Li, Y.
AU  - Zhu, H.
AU  - Li, C.
AU  - Zhang, H.
AU  - Chen, Z.
AU  - Zheng, W.
AU  - Xu, H.
AU  - Zheng, T.
TI  - Draft Genome Sequence of the Algicidal Bacterium Mangrovimonas yunxiaonensis Strain LY01.
JO  - Genome Announcements
PY  - 2014
SP  - e01234
EP  - e01214
VL  - 2
AB  - Mangrovimonas yunxiaonensis LY01, a novel bacterium isolated from mangrove sediment, showed
AB  - high algicidal effects on harmful algal blooms of Alexandrium
AB  - tamarense. Here, we present the first draft genome sequence of this strain to
AB  - further understanding of the functional genes related to algicidal activity.
ER  -

TY  - JOUR
AU  - Li, Y.Q.
AU  - Zhou, P.Z.
AU  - Zheng, X.D.
AU  - Walsh, C.P.
AU  - Xu, G.L.
TI  - Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 390
EP  - 400
VL  - 35
AB  - While methylcytosines serve as the fifth base encoding epigenetic information, they are also a
AB  - dangerous endogenous mutagen due to their
AB  - intrinsic instability. Methylcytosine undergoes spontaneous deamination,
AB  - at a rate much higher than cytosine, to generate thymine. In mammals, two
AB  - repair enzymes, thymine DNA glycosylase (TDG) and methyl-CpG binding
AB  - domain 4 (MBD4), have evolved to counteract the mutagenic effect of
AB  - methylcytosines. Both recognize G/T mismatches arising from methylcytosine
AB  - deamination and initiate base-excision repair that corrects them to G/C
AB  - pairs. However, the mechanism by which the methylation status of the
AB  - repaired cytosines is restored has remained unknown. We show here that the
AB  - DNA methyltransferase Dnmt3a interacts with TDG. Both the PWWP domain and
AB  - the catalytic domain of Dnmt3a are able to mediate the interaction with
AB  - TDG at its N-terminus. The interaction affects the enzymatic activity of
AB  - both proteins: Dnmt3a positively regulates the glycosylase activity of
AB  - TDG, while TDG inhibits the methylation activity of Dnmt3a in vitro. These
AB  - data suggest a mechanistic link between DNA repair and remethylation at
AB  - sites affected by methylcytosine deamination.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Cai, J.
AU  - Cao, X.
AU  - Lou, Z.
AU  - Chao, Y.
AU  - Kan, W.
AU  - Zhou, J.
TI  - Whole-Genome Sequence of Chlamydia abortus Strain GN6 Isolated from Aborted Yak Fetus.
JO  - Genome Announcements
PY  - 2017
SP  - e00893
EP  - e00817
VL  - 5
AB  - The obligate intracellular Gram-negative bacterium Chlamydia abortus is one of the causative
AB  - agents of abortion and fetal loss in sheep, goats, and cattle in
AB  - many countries. It also affects the reproductivity of yaks (Bos grunniens). This
AB  - study reports the whole-genome sequence of Chlamydia abortus strain GN6, which
AB  - was isolated from aborted yak fetus in Qinghai-Tibetan Plateau, China.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Chen, H.
AU  - Chen, X.
AU  - Zhou, T.
AU  - Zhao, L.
AU  - Zhang, C.
AU  - Jin, W.
TI  - Genome Sequence of the Human-Pathogenic Bacterium Vibrio vulnificus Type Strain ATCC 27562.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6954
EP  - 6955
VL  - 194
AB  - Vibrio vulnificus, which is the causative agent of cholera, is a Gram-negative, curved,
AB  - motile, and rod-shaped bacterium. Here, we present the draft genome
AB  - sequence of the type strain, ATCC 27562, which was the first isolated Vibrio
AB  - vulnificus strain.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Chen, M.
AU  - Ran, K.
AU  - Wang, J.
AU  - Zeng, Q.
AU  - Song, F.
TI  - Draft Genome Sequence of Bacillus velezensis Lzh-a42, a Plant Growth-Promoting Rhizobacterium Isolated from Tomato Rhizosphere.
JO  - Genome Announcements
PY  - 2018
SP  - e00161
EP  - e00118
VL  - 6
AB  - The plant growth-promoting rhizobacterium Bacillus velezensis strain Lzh-a42, which has
AB  - antimicrobial activity, was isolated from tomato rhizosphere. Here, we
AB  - report its genome sequence, which includes several predicted functional genes
AB  - related to secondary metabolite biosynthesis, antimicrobial activity, and biofilm
AB  - synthesis.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Li, X.
AU  - Zeng, Q.
AU  - Chen, M.
AU  - Liu, D.
AU  - Wang, J.
AU  - Shen, L.
AU  - Song, F.
TI  - Genome Sequence of Pseudomonas chlororaphis Lzh-T5, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2018
SP  - e00328
EP  - e00318
VL  - 6
AB  - Pseudomonas chlororaphis Lzh-T5 is a plant growth-promoting rhizobacterium (PGPR) with
AB  - antimicrobial activity isolated from tomato rhizosphere in the city of
AB  - Dezhou, Shandong Province, China. Here, the draft genome sequence of P.
AB  - chlororaphis Lzh-T5 is reported, and several functional genes related to
AB  - antifungal antibiotics and siderophore biosynthesis have been found in the
AB  - genome.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Ma, Z.
AU  - Hao, X.
AU  - Wei, G.
TI  - Draft Genome Sequence of Sinorhizobium meliloti CCNWSX0020, a Nitrogen-Fixing Symbiont with Copper Tolerance Capability Isolated from Lead-Zinc Mine Tailings.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1267
EP  - 1268
VL  - 194
AB  - Sinorhizobium meliloti CCNWSX0020 was isolated from Medicago lupulina plants growing in
AB  - lead-zinc mine tailings, which can establish a symbiotic relationship
AB  - with Medicago species. Also, the genome of this bacterium contains a number of
AB  - protein-coding sequences related to metal tolerance. We anticipate that the
AB  - genomic sequence provides valuable information to explore environmental
AB  - bioremediation.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Marsland, P.A.
AU  - Meek, R.T.
AU  - Eckmann, K.
AU  - Allard, M.W.
AU  - Perez-Osorio, A.C.
TI  - Draft Genome Sequences of Listeria monocytogenes Strains from Listeriosis Outbreaks Linked to Soft Cheese in Washington State.
JO  - Genome Announcements
PY  - 2017
SP  - e00936
EP  - e00917
VL  - 5
AB  - Listeria monocytogenes has caused listeriosis outbreaks linked to soft cheese. Here, we report
AB  - the draft genome sequences of seven L. monocytogenes isolates
AB  - from two possibly related outbreaks caused by soft cheese products in Washington
AB  - State.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Song, N.
AU  - Li, W.
AU  - Hardwidge, P.R.
AU  - Bu, Z.
AU  - Liu, S.
TI  - Complete Genome Sequences of Two Porcine Enterotoxigenic Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2018
SP  - e00059
EP  - e00018
VL  - 6
AB  - Enterotoxigenic Escherichia coli (ETEC) is one of the main causes of illness and  death in
AB  - neonatal and recently weaned pigs. Here, we sequenced the genomes of two
AB  - ETEC strains that were previously used as inactivated vaccines in China.
ER  -

TY  - JOUR
AU  - Li, Z.
AU  - Wu, S.
AU  - Bai, X.
AU  - Liu, Y.
AU  - Lu, J.
AU  - Liu, Y.
AU  - Xiao, B.
AU  - Lu, X.
AU  - Fan, L.
TI  - Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6088
EP  - 6089
VL  - 193
AB  - Ralstonia solanacearum is a causal agent of plant bacterial wilt with thousands of distinct
AB  - strains in a heterogeneous species complex. Here we
AB  - report the genome sequence of a phylotype IB strain, Y45, isolated from
AB  - tobacco (Nicotiana tabacum) in China. Compared with the published genomes
AB  - of eight strains which were isolated from other hosts and habitats, 794
AB  - specific genes and many rearrangements/inversion events were identified in
AB  - the tobacco strain, demonstrating that this strain represents an important
AB  - node within the R. solanacearum complex.
ER  -

TY  - JOUR
AU  - Li, Z.F.
AU  - Li, X.
AU  - Liu, H.
AU  - Liu, X.
AU  - Han, K.
AU  - Wu, Z.H.
AU  - Hu, W.
AU  - Li, F.F.
AU  - Li, Y.Z.
TI  - Genome Sequence of the Halotolerant Marine Bacterium Myxococcus fulvus HW-1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5015
EP  - 5016
VL  - 193
AB  - Myxococcus fulvus HW-1 (ATCC BAA-855) is a halotolerant marine myxobacterium. This strain
AB  - exhibits complex social behaviors in the
AB  - presence of low concentrations of seawater but adopts an asocial living
AB  - pattern under oceanic conditions. The whole genome of M. fulvus HW-1 will
AB  - enable us to further investigate the details of its evolution.
ER  -

TY  - JOUR
AU  - Liakopoulos, A.
AU  - Oikonomou, O.
AU  - Wareham, D.W.
TI  - Draft Genome Sequence of Providencia stuartii PS71, a Multidrug-Resistant Strain  Associated with Nosocomial Infections in Greece.
JO  - Genome Announcements
PY  - 2017
SP  - e00056
EP  - e00017
VL  - 5
AB  - Providencia stuartii is frequently associated with nosocomial outbreaks and displays intrinsic
AB  - resistance to many commonly used antimicrobials. We report
AB  - here the draft genome sequence of a P. stuartii strain carrying acquired
AB  - resistance genes conferring panresistance to cephalosporins (blaSHV-5 and
AB  - blaVEB-1), carbapenems (blaVIM-1), and aminoglycosides (rmtB) involved in an
AB  - outbreak in Greek hospitals.
ER  -

TY  - JOUR
AU  - Liang, G.
AU  - Chan, M.F.
AU  - Tomigahara, Y.
AU  - Tsai, Y.C.
AU  - Gonzales, F.A.
AU  - Li, E.
AU  - Laird, P.W.
AU  - Jones, P.A.
TI  - Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements.
JO  - Mol. Cell. Biol.
PY  - 2002
SP  - 480
EP  - 491
VL  - 22
AB  - We used mouse embryonic stem (ES) cells with systematic gene knockouts for DNA
AB  - methyltransferases to delineate the roles of DNA methyltransferase 1 (Dnmt1) and Dnmt3a and
AB  - Dnmt3b in maintaining methylation patterns in the mouse genome. Dnmt1 alone was able to
AB  - maintain
AB  - methylation of most CpG-poor regions analyzed. In contrast, both Dnmt1 and Dnmt3a and/or
AB  - Dnmt3b were required for methylation of a select class of sequences which included abundant
AB  - murine LINE-1 promoters. We used a novel hemimethylation assay to show that even in wild-type
AB  - cells these sequences contain high levels of hemimethylated DNA, suggestive of poor
AB  - maintenance methylation. We showed that Dnmt3a and/or -3b could restore methylation of these
AB  - sequences to pretreatment levels following transient exposure of cells to 5-aza-CdR, whereas
AB  - Dnmt1 by itself could not. We conclude that ongoing de novo methylation by Dnmt3a and/or
AB  - Dnmt3b compensates for inefficient maintenance methylation by Dnmt1 of these endogenous
AB  - repetitive sequences. Our results reveal a previously unrecognized degree of cooperativity
AB  - among mammalian DNA methyltransferases in ES cells.
ER  -

TY  - JOUR
AU  - Liang, J.
AU  - Blumenthal, R.M.
TI  - Naturally-occurring, dually-functional fusions between restriction endonucleases  and regulatory proteins.
JO  - BMC Evol. Biol.
PY  - 2013
SP  - 218
EP  - 218
VL  - 13
AB  - Background: Restriction-modification (RM) systems appear to play key roles in modulating gene
AB  - flow among bacteria and archaea. Because the restriction
AB  - endonuclease (REase) is potentially lethal to unmethylated new host cells,
AB  - regulation to ensure pre-expression of the protective DNA methyltransferase
AB  - (MTase) is essential to the spread of RM genes. This is particularly true for
AB  - Type IIP RM systems, in which the REase and MTase are separate,
AB  - independently-active proteins. A substantial subset of Type IIP RM systems are
AB  - controlled by an activator-repressor called C protein. In these systems, C
AB  - controls the promoter for its own gene, and for the downstream REase gene that
AB  - lacks its own promoter. Thus MTase is expressed immediately after the RM genes
AB  - enter a new cell, while expression of REase is delayed until sufficient C protein
AB  - accumulates. To study the variation in and evolution of this regulatory
AB  - mechanism, we searched for RM systems closely related to the well-studied C
AB  - protein-dependent PvuII RM system. Unexpectedly, among those found were several
AB  - in which the C protein and REase genes were fused. Results: The gene for
AB  - CR.NsoJS138I fusion protein (nsoJS138ICR, from the bacterium Niabella soli) was
AB  - cloned, and the fusion protein produced and partially purified. Western blots
AB  - provided no evidence that, under the conditions tested, anything other than
AB  - full-length fusion protein is produced. This protein had REase activity in vitro
AB  - and, as expected from the sequence similarity, its specificity was
AB  - indistinguishable from that for PvuII REase, though the optimal reaction
AB  - conditions were different. Furthermore, the fusion was active as a C protein, as
AB  - revealed by in vivo activation of a lacZ reporter fusion to the promoter region
AB  - for the nsoJS138ICR gene. Conclusions: Fusions between C proteins and REases have
AB  - not previously been characterized, though other fusions have (such as between
AB  - REases and MTases). These results reinforce the evidence for impressive
AB  - modularity among RM system proteins, and raise important questions about the
AB  - implications of the C-REase fusions on expression kinetics of these RM systems.
ER  -

TY  - JOUR
AU  - Liang, J.
AU  - Hoffrichter, A.
AU  - Brachmann, A.
AU  - Marin, M.
TI  - Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 36
EP  - 36
VL  - 13
AB  - Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic  interaction
AB  - with legume plants in which a bidirectional nutrient exchange takes
AB  - place. Occasionally, this interaction is suboptimal resulting in the formation of
AB  - ineffective nodules in which little or no atmospheric nitrogen fixation occurs.
AB  - Rhizobium leguminosarum Norway induces ineffective nodules in a wide range of
AB  - Lotus hosts. To investigate the basis of this phenotype, we sequenced the
AB  - complete genome of Rl Norway and compared it to the genome of the closely related
AB  - strain R. leguminosarum bv. viciae 3841. The genome comprises 7,788,085 bp,
AB  - distributed on a circular chromosome containing 63% of the genomic information
AB  - and five large circular plasmids. The functionally classified bacterial gene set
AB  - is distributed evenly among all replicons. All symbiotic genes (nod, fix, nif)
AB  - are located on the pRLN3 plasmid. Whole genome comparisons revealed differences
AB  - in the metabolic repertoire and in protein secretion systems, but not in
AB  - classical symbiotic genes.
ER  -

TY  - JOUR
AU  - Liang, J.
AU  - Wang, Z.
AU  - He, X.
AU  - Li, J.
AU  - Zhou, X.
AU  - Deng, Z.
TI  - DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2944
EP  - 2954
VL  - 35
AB  - The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in
AB  - Streptomyces lividans 1326, was strongly aggravated when one (dndB) of
AB  - the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding
AB  - patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear
AB  - change from a preferential modification site in strain 1326 to more random
AB  - modifications in the mutant. Fourteen randomly modifiable sites on pHZ209 were
AB  - localized, and each seemed to be able to be modified only once. Residues in a
AB  - region (5'-c-cGGCCgccg-3') including a highly conserved 4-bp central core
AB  - (5'-GGCC-3') in a well-documented preferential modification site were assessed
AB  - for their necessity by site-directed mutagenesis. While the central core (GGCC)
AB  - was found to be stringently required in 1326 and in the mutant, 'gccg' flanking
AB  - its right could either abolish or reduce the modification frequency only in the
AB  - mutant, and two separate nucleotides to the left had no dramatic effect. The lack
AB  - of essentiality of DndB for S-modification suggests that it might only be
AB  - required for enhancing or stabilizing the activity of a protein complex at the
AB  - required preferential modification site, or resolving secondary structures
AB  - flanking the modifiable site(s), known to constitute an obstacle for efficient
AB  - modification.
ER  -

TY  - JOUR
AU  - Liang, J.X.
AU  - Blumenthal, R.M.
TI  - Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins.
JO  - BMC Evol. Biol.
PY  - 2013
SP  - 0
EP  - 0
VL  - 13
AB  - Background: Restriction-modification (RM) systems appear to play key roles in modulating gene
AB  - flow among bacteria and archaea. Because the
AB  - restriction endonuclease (REase) is potentially lethal to unmethylated
AB  - new host cells, regulation to ensure pre-expression of the protective
AB  - DNA methyltransferase (MTase) is essential to the spread of RM genes.
AB  - This is particularly true for Type IIP RM systems, in which the REase
AB  - and MTase are separate, independently-active proteins. A substantial
AB  - subset of Type IIP RM systems are controlled by an activator-repressor
AB  - called C protein. In these systems, C controls the promoter for its own
AB  - gene, and for the downstream REase gene that lacks its own promoter.
AB  - Thus MTase is expressed immediately after the RM genes enter a new
AB  - cell, while expression of REase is delayed until sufficient C protein
AB  - accumulates. To study the variation in and evolution of this regulatory
AB  - mechanism, we searched for RM systems closely related to the
AB  - well-studied C protein-dependent PvuII RM system. Unexpectedly, among
AB  - those found were several in which the C protein and REase genes were
AB  - fused.
AB  - Results: The gene for CR. NsoJS138I fusion protein (nsoJS138ICR,
AB  - from the bacterium Niabella soli) was cloned, and the fusion protein
AB  - produced and partially purified. Western blots provided no evidence
AB  - that, under the conditions tested, anything other than full-length
AB  - fusion protein is produced. This protein had REase activity in vitro
AB  - and, as expected from the sequence similarity, its specificity was
AB  - indistinguishable from that for PvuII REase, though the optimal
AB  - reaction conditions were different. Furthermore, the fusion was active
AB  - as a C protein, as revealed by in vivo activation of a lacZ reporter
AB  - fusion to the promoter region for the nsoJS138ICR gene.
AB  - Conclusions: Fusions between C proteins and REases have not
AB  - previously been characterized, though other fusions have (such as
AB  - between REases and MTases). These results reinforce the evidence for
AB  - impressive modularity among RM system proteins, and raise important
AB  - questions about the implications of the C-REase fusions on expression
AB  - kinetics of these RM systems.
ER  -

TY  - JOUR
AU  - Liang, K.
AU  - Orata, F.D.
AU  - Winkjer, N.S.
AU  - Rowe, L.A.
AU  - Tarr, C.L.
AU  - Boucher, Y.
TI  - Complete Genome Sequence of Vibrio sp. Strain 2521-89, a Close Relative of Vibrio cholerae Isolated from Lake Water in New Mexico, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e00905
EP  - e00917
VL  - 5
AB  - Vibrio sp. strain 2521-89 is an environmental isolate from lake water in New Mexico, USA.
AB  - Average nucleotide identity, in silico DNA-DNA hybridization, and
AB  - core genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis
AB  - suggest that this may be a potentially novel species that is closely related to
AB  - Vibrio cholerae.
ER  -

TY  - JOUR
AU  - Liang, R.
AU  - Liu, H.
AU  - Tao, F.
AU  - Liu, Y.
AU  - Ma, C.
AU  - Liu, X.
AU  - Liu, J.
TI  - Genome Sequence of Pseudomonas putida Strain SJTE-1, a Bacterium Capable of Degrading Estrogens and Persistent Organic Pollutants.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4781
EP  - 4782
VL  - 194
AB  - Pseudomonas putida strain SJTE-1 can utilize 17beta-estradiol and other environmental
AB  - estrogens/toxicants, such as estrone, and naphthalene as sole
AB  - carbon sources. We report the draft genome sequence of strain SJTE-1 (5,551,505
AB  - bp, with a GC content of 62.25%) and major findings from its annotation, which
AB  - could provide insights into its biodegradation mechanisms.
ER  -

TY  - JOUR
AU  - Liang, S.
AU  - Jin, D.
AU  - Wang, X.
AU  - Fan, H.
AU  - Bai, Z.
TI  - Draft Genome Sequence of Paenibacillus polymyxa EBL06, a Plant Growth-Promoting Bacterium Isolated from Wheat Phyllosphere.
JO  - Genome Announcements
PY  - 2015
SP  - e00414
EP  - e00415
VL  - 3
AB  - Paenibacillus polymyxa strain EBL06 is a plant growth-promoting bacterium with high antifungal
AB  - activity. The estimated genome of this strain is 5.68 Mb in size
AB  - and harbors 4,792 coding sequences (CDSs).
ER  -

TY  - JOUR
AU  - Liang, X.
AU  - Jensen, K.
AU  - Frank-Kamenetskii, M.D.
TI  - Acceleration of de novo DNA synthesis by restriction enzymes.
JO  - J. Biomol. Struct. Dyn.
PY  - 2005
SP  - 766
EP  - 767
VL  - 22
AB  - We have found that in the presence of a restriction endonuclease, DNA polymerase efficiently
AB  - synthesizes and amplifies DNA in the absence of any added template and primer nucleic acid
AB  - under isothermal conditions.  In the presence of restriction endonuclease Tsp509I (recognition
AB  - sequence /AATT) or TspRI (recognition sequence: NNCAG(C)TGNN/), more than 90% of the available
AB  - dNTPs can be consumed by Vent (exo-) DNA polymerase in 1 h at 70oC.  The synthesized DNA has a
AB  - highly repetitive palindromic sequence containing recognition sites for the restriction
AB  - enzyme, e.g. (AAAAATTTTT)n and (ATACACTGTATATACAGTG-TAT)n.  Our data show that the high
AB  - efficiency of the restriction-endonuclease-DNA-polymerase (RE-pol) DNA synthesis results from
AB  - an efficient exponential amplification involving digestion-elongation cycles.
ER  -

TY  - JOUR
AU  - Liang, X.G.
AU  - Jensen, K.
AU  - Frank-Kamenetskii, M.D.
TI  - Very efficient template/primer-independent DNA synthesis by thermophilic DNA polymerase in the presence of a thermophilic  restriction endonuclease.
JO  - Biochemistry
PY  - 2004
SP  - 13459
EP  - 13466
VL  - 43
AB  - We have found that, in the presence of a thermophilic restriction endonuclease, thermophilic
AB  - DNA polymerase efficiently synthesizes and
AB  - amplifies DNA in the absence of any added template and primer nucleic
AB  - acid under isothermal conditions. More than 10 micrograms of DNA can be
AB  - synthesized by 1 unit of DNA polymerase in 1 h, and the reaction
AB  - proceeds until available dNTPs are consumed. We used mostly the Tsp509I
AB  - restriction endonuclease (recognition sequence: ^AATT), the
AB  - TspRI restriction endonuclease (recognition sequence: NNCA(G/C)TGNN^), and Vent (exo(-)) and
AB  - Vent DNA polymerase. The synthesized
AB  - double-stranded DNA has a highly repetitive palindromic sequence, e.g.
AB  - (AAAAATTTTT)(n) and (ATACACTGTATATACAGTGTAT)(n). In every repeating
AB  - unit, there are one or two recognition sites for the restriction
AB  - enzyme. Our data show that the high efficiency of the
AB  - restriction-endonuclease-DNA-polymerase (RE-pol) DNA synthesis results
AB  - from an efficient exponential amplification involving
AB  - digestion-elongation cycles: a longer DNA with numerous recognition
AB  - sites for the restriction enzyme is digested to short fragments, and
AB  - the short fragments are used as seeds for elongation to synthesize
AB  - longer DNA. A possible role of RE-pol DNA synthesis in the evolutionary
AB  - development of genetic materials is briefly discussed.
ER  -

TY  - JOUR
AU  - Liang, Z.
AU  - Li, G.
AU  - An, T.
AU  - Das, R.
TI  - Draft Genome Sequence of Bacillus sp. GZT, a 2,4,6-Tribromophenol-Degrading Strain Isolated from the River Sludge of an Electronic Waste-Dismantling Region.
JO  - Genome Announcements
PY  - 2016
SP  - e00474
EP  - e00416
VL  - 4
AB  - Here, we report the draft genome sequence of Bacillus sp. strain GZT, a 2,4,6-tribromophenol
AB  - (TBP)-degrading bacterium previously isolated from an
AB  - electronic waste-dismantling region. The draft genome sequence is 5.18 Mb and has
AB  - a G+C content of 35.1%. This is the first genome report of a brominated flame
AB  - retardant-degrading strain.
ER  -

TY  - JOUR
AU  - Liang, Z.
AU  - Li, G.
AU  - An, T.
AU  - Zhang, G.
AU  - Das, R.
TI  - Draft Genome Sequence of a Tetrabromobisphenol A-Degrading Strain, Ochrobactrum sp. T, Isolated from an Electronic Waste Recycling Site.
JO  - Genome Announcements
PY  - 2016
SP  - e00680
EP  - e00616
VL  - 4
AB  - Ochrobactrum sp. T was previously isolated from a sludge sample collected from an electronic
AB  - waste recycling site and characterized as a unique tetrabromobisphenol
AB  - A (TBBPA)-degrading bacterium. Here, the draft genome sequence (3.9 Mb) of
AB  - Ochrobactrum sp. T is reported to provide insights into its diversity and its
AB  - TBBPA biodegradation mechanism in polluted environments.
ER  -

TY  - JOUR
AU  - Liang, Z.
AU  - Stephens, M.
AU  - Ploplis, V.A.
AU  - Lee, S.W.
AU  - Castellino, F.J.
TI  - Draft Genome Sequences of Six Skin Isolates of Streptococcus pyogenes.
JO  - Genome Announcements
PY  - 2018
SP  - e00592
EP  - e00518
VL  - 6
AB  - Whole-genome shotgun sequences and bottom-up assembly of contigs of six skin isolates of
AB  - Streptococcus pyogenes, viz, NS88.3 (emm98.1), NS223 (emm91), NS455
AB  - (emm52), SS1448 (emm86.2), SS1572 (emm223), and SS1574 (emm224), are presented
AB  - here. All contigs were annotated, and the gene arrangements and the inferred
AB  - proteins were consistent with a pattern D classification.
ER  -

TY  - JOUR
AU  - Liao, H.M.
AU  - Chao, C.C.
AU  - Lei, H.
AU  - Li, B.
AU  - Tsai, S.
AU  - Hung, G.C.
AU  - Ching, W.M.
AU  - Lo, S.C.
TI  - Genomic Sequencing of Orientia tsutsugamushi Strain Karp, an Assembly Comparable  to the Genome Size of the Strain Ikeda.
JO  - Genome Announcements
PY  - 2016
SP  - e00702
EP  - e00716
VL  - 4
AB  - Orientia tsutsugamushi, an intracellular bacterium, belongs to the family Rickettsiaceae This
AB  - study presents the draft genome sequence of strain Karp, with
AB  - 2.0 Mb as the size of the completed genome. This nearly finished draft genome
AB  - sequence was annotated with the RAST server and the contents compared to those of
AB  - the other strains.
ER  -

TY  - JOUR
AU  - Liao, J.
AU  - Karnik, R.
AU  - Gu, H.
AU  - Ziller, M.J.
AU  - Clement, K.
AU  - Tsankov, A.M.
AU  - Akopian, V.
AU  - Gifford, C.A.
AU  - Donaghey, J.
AU  - Galonska, C.
AU  - Pop, R.
AU  - Reyon, D.
AU  - Tsai, S.Q.
AU  - Mallard, W.
AU  - Joung, J.K.
AU  - Rinn, J.L.
AU  - Gnirke, A.
AU  - Meissner, A.
TI  - Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.
JO  - Nat. Genet.
PY  - 2015
SP  - 469
EP  - 478
VL  - 47
AB  - DNA methylation is a key epigenetic modification involved in regulating gene expression and
AB  - maintaining genomic integrity. Here we inactivated all three
AB  - catalytically active DNA methyltransferases (DNMTs) in human embryonic stem cells
AB  - (ESCs) using CRISPR/Cas9 genome editing to further investigate the roles and
AB  - genomic targets of these enzymes. Disruption of DNMT3A or DNMT3B individually as
AB  - well as of both enzymes in tandem results in viable, pluripotent cell lines with
AB  - distinct effects on the DNA methylation landscape, as assessed by whole-genome
AB  - bisulfite sequencing. Surprisingly, in contrast to findings in mouse, deletion of
AB  - DNMT1 resulted in rapid cell death in human ESCs. To overcome this immediate
AB  - lethality, we generated a doxycycline-responsive tTA-DNMT1* rescue line and
AB  - readily obtained homozygous DNMT1-mutant lines. However, doxycycline-mediated
AB  - repression of exogenous DNMT1* initiates rapid, global loss of DNA methylation,
AB  - followed by extensive cell death. Our data provide a comprehensive
AB  - characterization of DNMT-mutant ESCs, including single-base genome-wide maps of
AB  - the targets of these enzymes.
ER  -

TY  - JOUR
AU  - Liao, T.L.
AU  - Lin, A.C.
AU  - Chen, E.
AU  - Huang, T.W.
AU  - Liu, Y.M.
AU  - Chang, Y.H.
AU  - Lai, J.F.
AU  - Lauderdale, T.L.
AU  - Wang, J.T.
AU  - Chang, S.C.
AU  - Tsai, S.F.
AU  - Chen, Y.T.
TI  - Complete Genome Sequence of Klebsiella oxytoca E718, a New Delhi Metallo-beta-Lactamase-1-Producing Nosocomial Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5454
EP  - 5454
VL  - 194
AB  - We report the complete genome sequence of Klebsiella oxytoca E718, a New Delhi
AB  - metallo-beta-lactamase-1 (NDM-1)-producing strain isolated from a renal
AB  - transplant patient. The genome contains a 6,097,032-bp chromosome and two
AB  - multidrug resistance plasmids with sizes of 324,906 bp and 110,781 bp.
ER  -

TY  - JOUR
AU  - Liao, Y.C.
AU  - Chen, Y.H.
AU  - Lin, H.H.
AU  - Mu, J.J.
AU  - Wu, H.S.
AU  - Chen, F.C.
AU  - Hsiung, C.A.
TI  - Draft Genome Sequence of NDM-1-Producing Klebsiella pneumoniae Clinical Isolate 303K.
JO  - Genome Announcements
PY  - 2013
SP  - e01069
EP  - e01013
VL  - 1
AB  - Multidrug-resistant New Delhi metallo-beta-lactamase 1 (NDM-1)-producing bacteria have spread
AB  - globally and become a major clinical and public health threat. We
AB  - report here the draft genome sequence of the Klebsiella pneumoniae clinical
AB  - isolate 303K, harboring an NDM-1 coding sequence.
ER  -

TY  - JOUR
AU  - Liao, Y.C.
AU  - Chen, Y.Y.
AU  - Lin, H.H.
AU  - Chang, J.R.
AU  - Su, I.J.
AU  - Huang, T.S.
AU  - Dou, H.Y.
TI  - Draft Genome Sequences of the Mycobacterium tuberculosis Clinical Strains A2 and  A4, Isolated from a Relapse Patient in Taiwan.
JO  - Genome Announcements
PY  - 2014
SP  - e00672
EP  - e00614
VL  - 2
AB  - The recurrence rate of Mycobacterium tuberculosis in Taiwan is 3%. Here, we present the draft
AB  - genome sequences of M. tuberculosis strains A2 and A4 from a
AB  - relapse patient. The draft genome sequences comprise 4,443,031 bp and 4,487,096
AB  - bp, revealing 4,220 and 4,143 coding sequences for A2 and A4, respectively, as
AB  - well as 49 tRNA genes for the both isolates.
ER  -

TY  - JOUR
AU  - Liao, Y.C.
AU  - Chen, Y.Y.
AU  - Lin, H.H.
AU  - Chang, J.R.
AU  - Su, I.J.
AU  - Huang, T.S.
AU  - Dou, H.Y.
TI  - Draft Genome Sequence of the Mycobacterium tuberculosis Clinical Isolate C2, Belonging to the Latin American-Mediterranean Family.
JO  - Genome Announcements
PY  - 2014
SP  - e00536
EP  - e00514
VL  - 2
AB  - Tuberculosis remains a major infectious disease in Taiwan. Here we present the draft genome
AB  - sequence of the Mycobacterium tuberculosis C2 strain, belonging to
AB  - the Latin American-Mediterranean lineage. The draft genome sequence comprises
AB  - 4,453,307 bp with a G+C content of 65.6%, revealing 4,390 coding genes and 45
AB  - tRNA genes.
ER  -

TY  - JOUR
AU  - Liao, Y.C.
AU  - Liu, T.T.
AU  - Chang, J.R.
AU  - Chen, Y.Y.
AU  - Lin, H.H.
AU  - Hsu, C.H.
AU  - Lin, C.Y.
AU  - Lo, Y.C.
AU  - Dou, H.Y.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain W06, a Prevalent Beijing Genotype Isolated in Taiwan.
JO  - Genome Announcements
PY  - 2015
SP  - e01460
EP  - e01415
VL  - 3
AB  - Mycobacterium tuberculosis strain W06, analyzed by molecular methods, was classified as a
AB  - modern Beijing M. tuberculosis strain, the most predominant
AB  - strain in Taiwan. To our knowledge, this is the first draft genome announcement
AB  - of a Beijing M. tuberculosis strain in Taiwan.
ER  -

TY  - JOUR
AU  - Liao, Z.
AU  - Ren, C.
AU  - Guo, X.
AU  - Yan, Y.
AU  - Li, J.
AU  - Zhao, B.
TI  - Draft Genome Sequence of Bacillus urumqiensis BZ-SZ-XJ18(T), a Moderately Haloalkaliphilic Bacterium Isolated from a Saline-Alkaline Lake.
JO  - Genome Announcements
PY  - 2018
SP  - e00460
EP  - e00418
VL  - 6
AB  - The moderately haloalkaliphilic bacterium Bacillus urumqiensis BZ-SZ-XJ18(T) was  isolated
AB  - from a saline-alkaline lake located in the Xinjiang Uyghur Autonomous
AB  - Region of China. Optimum growth occurred at the total Na(+) concentration of 1.08
AB  - M, with a broad optimum pH of 8.5 to 9.5. The draft genome consists of
AB  - approximately 3.28 Mb and contains 3,228 predicted genes. A number of genes
AB  - associated with adaptation strategies for osmotic balance and alkaline pH
AB  - homeostasis were identified, providing pertinent insight into specific
AB  - adaptations to the double-extreme environment.
ER  -

TY  - JOUR
AU  - Libuit, K.G.
AU  - Turner, L.
TI  - Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia.
JO  - Genome Announcements
PY  - 2018
SP  - e00329
EP  - e00318
VL  - 6
AB  - Antimicrobial-resistant (AMR) Salmonella infections pose a significant public health threat.
AB  - Here, we announce two draft genomes of Salmonella strains isolated
AB  - from wildlife harboring an alarming array of antibiotic resistance genes.
AB  - Continued investigations of these genomes will provide insight into the possible
AB  - attribution of AMR Salmonella infection of wild animals.
ER  -

TY  - JOUR
AU  - Licciardello, G.
AU  - Bella, P.
AU  - Devescovi, G.
AU  - Strano, C.P.
AU  - Sarris, P.F.
AU  - Catara, A.F.
AU  - Venturi, V.
AU  - Catara, V.
TI  - Draft Genome Sequence of Pseudomonas mediterranea Strain CFBP 5447T, a Producer of Filmable Medium-Chain-Length Polyhydroxyalkanoates.
JO  - Genome Announcements
PY  - 2014
SP  - e01260
EP  - e01214
VL  - 2
AB  - Pseudomonas mediterranea strain CFBP 5447(T) is a phytopathogenic bacterium isolated from
AB  - tomato plants affected by pith necrosis disease. Moreover, its
AB  - ability to produce medium-chain-length polyhydroxyalkanoates (mcl-PHAs) in
AB  - culture from different carbon sources and valuable microbial products, such as
AB  - cyclic lipopeptides, has been well documented. Here, we report the first draft
AB  - genome sequence of this species.
ER  -

TY  - JOUR
AU  - Lieb, M.
TI  - Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites.
JO  - J. Bacteriol.
PY  - 1987
SP  - 5241
EP  - 5246
VL  - 169
AB  - Certain amber mutationsn in the cI gene of bacteriophage lambda appear to recombine very
AB  - frequently with nearby mutations. The aberrant mutations included C-to-T transitiions at the
AB  - second cytosine in 5'CC(A/T)GG sequences (which are subject to methylation by bacterial
AB  - cytosine methylase) and in 5'CCAG and 5'CAGG sequences. Excess cI+ recombinants arising in
AB  - crosses that utilize these mutations are attributable to the correction of mismatches by a
AB  - bacterial very-short-patch (VSP) mismatch repair system. In the present study I found that two
AB  - genes required for methyladenine-directed (long-patch) mismatch repair, mutL and mutS, also
AB  - functioned in VSP mismatch repair; mutH and mutU (uvrD) were dispensable. VSP mismatch repair
AB  - was greatly reduced in a dcm Escherichia coli mutant, in which 5-methylcytosine was not
AB  - methylated. However, mismatches in heterduplexes prepared from lambda DNA lacking
AB  - 5-methylcytosine were repaired in dcm+ bacteria. These results indicate that the product of
AB  - gene dcm has a repair function in addition to its methylase activity.
ER  -

TY  - JOUR
AU  - Lieb, M.
TI  - Specific mismatch correction in bacteriophage lambda crosses by very short patch repair.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 118
EP  - 125
VL  - 191
AB  - In crosses under rec+, red+, gam+ conditions, mutation am6 in the cI
AB  - (repressor) gene of bacteriophage lambda recombines with other cI mutations
AB  - much more frequently than predicted by the physical distances involved.  In
AB  - four-factor crosses of am6 with mutations located 22-60 base pairs to the left,
AB  - cI+ recombinants that are expected to require three crossovers (triple
AB  - recombinants) are more frequent than recombinants that require only one
AB  - crossover.  However, when am6 is crossed with large insertions in cI, which may
AB  - be expected to interfere with the formation of heteroduplexes by branch
AB  - migration, the frequency of cI+ triple recombinants is very low.  In addition,
AB  - cI+ recombinants in crosses between am6 and adjacent mutations have a high
AB  - probability of retaining the flanking markers of the am6 parent.  These
AB  - findings suggest that am6 is particularly susceptible to mismatch repair in
AB  - heteroduplexes spanning cI.  A large fraction of such heteroduplexes are
AB  - presumed to be the result of branch migration from crossovers occuring at some
AB  - distance from am6.  The absence of co-repair when am6 is crossed with adjacent
AB  - cI mutations indicates that most repair tracts extend no farther than about 20
AB  - bp to either side of the mismatch.  The am6 mutation arose in the glutamine
AB  - codon in a CCAGG sequence, in which the central cytosines are methylated in K12
AB  - strains.  Their location in methylated sequences may make certain amber
AB  - mutations susceptible to a specific very short patch (VSP) repair.
ER  -

TY  - JOUR
AU  - Lieb, M.
TI  - Spontaneous Mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair.
JO  - Genetics
PY  - 1991
SP  - 23
EP  - 27
VL  - 128
AB  - In many strains of Escherichia coli, the product of gene dcm methylates the internal cytosines
AB  - in the sequence 5'CC(A or T)GG. Spontaneous deamination of 5-methylcytosine produces thymine
AB  - which, if not corrected, can result in a transition mutation. 5-Methylcytosines in the lacI
AB  - gene are hotspots for spontaneous C to T mutations. dcm is linked to vsr, a gene required for
AB  - very short patch (VSP) repair. VSP respir corrects T.G mispairs in the following contexts:
AB  - CTAGG/GGTCC, CTTGG/GGACC, TAGG/GTCC and CTAG/GGTC. I have investigated the relationships
AB  - between cytosine methylation, mutation, and VSP repair. Spontaneous mutations in the repressor
AB  - (cI) gene of lambda prophage were isolated in wild-type and mutant lysogens. A hotspot for
AB  - spontaneous mutation that corresponds with a 5-methylcytosine was observed in wild-type
AB  - lysogens but was not present in bacteria lacking both methylase and VSP repair activity.
AB  - Introduction of a plasmid containg dcm+ and vsr+ restored the mutation hotspot. If the added
AB  - plasmid carried only dcm+, the frequency of spontaneous mutations at the 5-methylcytosine was
AB  - over 10-fold higher than in Dcm+Vsr+ lysogens. The addition of vsr on a plasmid to a wild-type
AB  - lysogen resulted in a 4-fold reduciton in mutation at the hotspot. These findings support the
AB  - previously untested hypothesis that VSP repair prevents mutations resulting from deamination
AB  - of 5-methylcytosine.
ER  -

TY  - JOUR
AU  - Lieb, M.
AU  - Allen, E.
AU  - Read, D.
TI  - Very short patch mismatch repair in phage lambda: repair sites and length of repair tracts.
JO  - Genetics
PY  - 1986
SP  - 1041
EP  - 1060
VL  - 114
AB  - Five amber mutations in the repressor (cI) gene of bacteriophage lambda recombine anomalously
AB  - with nearby cI mutations.  When any of these markers is used in four-factor crosses, cI+
AB  - recombinants that are expected to require three crossovers occur at high frequencies.  These
AB  - recombinants are attributable to very-short-patch (VSP) repair of specific mismatches in DNA
AB  - heteroduplexes formed during recombination between the markers flanking cI.  The sites of the
AB  - repair-prone mutations and the lengths of repair tracts have now been determined.  Amber
AB  - mutations subject to VSP repair are C to T transitions in 5'CCA/TGG, the sequence methylated
AB  - by the product of gene dcm, and also in the related 5'CAGG or 5'CCAG sequences.  Ambers
AB  - arising in CAG sequences found in other contexts, or in codons other than CAG, were not
AB  - subject to VSP repair.  Rapair tracts rarely, if ever, exceed ten nucleotides in length, and
AB  - can be as short as two nucleotides.  A repair-prone mutation does not stimulate recombination
AB  - between flanking cI markers.
ER  -

TY  - JOUR
AU  - Lieb, M.
AU  - Bhagwat, A.S.
TI  - Very short patch repair: reducing the cost of cytosine methylation.
JO  - Mol. Microbiol.
PY  - 1996
SP  - 467
EP  - 473
VL  - 20
AB  - In Escherichia coli and related bacteria, the product of gene dcm methylates the second
AB  - cytosine of 5'-CCWGG sequences (where W is A or T).  Deamination of 5-methylcytosine results
AB  - in C to T mutations.  The mutagenic potential of 5meC is reduced by a system called very short
AB  - patch repair, which replaces T with C.  T:G and U:G mispairs in the methylatable sequence and
AB  - in related sequences are recognized by the product of vsr, a gene adjacent to dcm.  Vsr
AB  - creates a nick just 5' of the mispaired pyrimidine to initiate the repair.  Additional
AB  - products known to be required for VSP repair are DNA polymerase I and DNA ligase.  MutS and
AB  - MutL have a stimulatory role but are not required.  The ability of Vsr to recognize T:G
AB  - mispairs in sequences related to CCWGG is probably responsible for over- and
AB  - under-representation of certain tetranucleotides in the E. coli genome.  Although VSP repair
AB  - reduces spontaneous mutations at 5meCs in replicating bacteria, mutation hot-spots persist at
AB  - these sites. Under conditions that more accurately mimic the natural environment of E. coli,
AB  - VSP repair appears to be effective in preventing mutation at 5meC.
ER  -

TY  - JOUR
AU  - Lieb, M.
AU  - Bhagwat, A.S.
TI  - Very short patch mismatch repair activity associated with gene dcm is not conferred by a plasmid coding for EcoRII methylase.
JO  - J. Bacteriol.
PY  - 1988
SP  - 4967
EP  - 4968
VL  - 170
AB  - The only cytosine methylase in Escherichia coli K-12 methylates the second cytosine in the
AB  - sequence CC(A/T)GG and is encoded by gene dcm. Methylation and very short patch mismatch
AB  - repair activities lacking in a dcm mutant of E. coli were restored by a plasmid containing the
AB  - cloned dcm gene. In contrast, plasmids with the gene for EcoRII methylase, which is a homolog
AB  - of dcm, restored only cytosine methylase activity and not mismatch repair.
ER  -

TY  - JOUR
AU  - Lieb, M.
AU  - Rehmat, S.
TI  - 5-Methylcytosine is not a mutation hot spot in nondividing Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 940
EP  - 945
VL  - 94
AB  - Spontaneous deamination of 5-methylcytosine (5meC) causes hot spots of C.G-T.A mutations in
AB  - Escherichia coli and in human cells.  In E. coli, the resulting T.G mispairs can be corrected
AB  - to C.G by very short patch (VSP) repair, which requires the product of gene vsr.  Mutation hot
AB  - spots in genes of replicating vsr+ bacteria are attributable to low Vsr activity.  To
AB  - determine the rate of deamination of 5meC and the efficiency of VSP repair in nondividing
AB  - bacteria, we used kanamycin-sensitive (KanS) lysogens containing a lambda kan- prophage.
AB  - Deamination of a 5meC in the kan- gene resulted in mutation to kanamycin resistance (KanR).
AB  - Lysogens containing a single lambda kan- prophage per bacterial genome were grown in synthetic
AB  - medium with limiting amino acids and stored at 15oC or 37oC.  In the absence of VSP repair,
AB  - KanR mutants accumulated at the rate of approximately 1.3 x 10^-7 per bacterium per day at
AB  - 37oC.  This is similar to the 5meC--T mutation rate reported for DNA in solution.  In vsr+
AB  - bacteria, the KanR accumulation rate was 3 x 10^-9 per bacterium per day, which is not
AB  - significantly higher than the rate observed when the target cytosine was unmethylated.  The
AB  - increase in KanR mutants was barely detectable in vsr+ cultures stored at 15oC for 4 months.
AB  - It is likely that mutation hot spots at 5meC in rapidly dividing cells are attributable to
AB  - insufficient time for T.G correction in the interval between deamination of 5meC and
AB  - subsequent DNA replication.  DNA synthesis occurred in bacteria starved for amino acids and
AB  - this synthesis was not highly mutagenic.
ER  -

TY  - JOUR
AU  - Lieb, M.
AU  - Rehmat, S.
TI  - Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins.
JO  - J. Bacteriol.
PY  - 1995
SP  - 660
EP  - 666
VL  - 177
AB  - In Escherichia coli, T:G mismatches in specific contexts are corrected by a very short patch
AB  - (VSP) repair system. Previous studies have shown that the product of gene vsr mediates
AB  - correction of T:G to C:G in the 5'CTAGG/3'GGTCC context and in some related contexts. Amber
AB  - mutations that arose in CAG sequences in gene cI of bacteriophage lambda were used to
AB  - determine the effect of flanking bases on the repair of T:G mispairs arising during phage
AB  - recombination. The experimental findings were combined with published data on mismatch repair
AB  - of mutations in lambda gene P and E. coli gene lacI. While VSP repair was most efficient in
AB  - the context 5'CTAGG, there was very significant correction when either the 5' C or the 3' G
AB  - was replaced by another base. Some mismatch repair of TAG to CAG occurred in all contexts
AB  - tested. Reduction in VSP repair caused by the lack of MutL or MutS was fully complemented by
AB  - the addition of vsr+ plasmids when the T:G mispair was in the 5'CTAGG/3'GGTCC context. VSP
AB  - repair was decreased in bacteria containing mutS+ on a multicopy plasmid. It is suggested that
AB  - VSP repair maintains sequences such as the repetitive extragenic palindromic (REP) and Chi
AB  - sequences, which have important roles in E. coli and closely related bacteria.
ER  -

TY  - JOUR
AU  - Lieb, M.
AU  - Rehmat, S.
AU  - Bhagwat, A.S.
TI  - Interaction of MutS and Vsr: Some Dominant-Negative mutS Mutations That Disable Methyladenine-Directed Mismatch Repair Are Active in Very-Short-Patch Repair.
JO  - J. Bacteriol.
PY  - 2001
SP  - 6487
EP  - 6490
VL  - 183
AB  - In Escherichia coli and related bacteria, the very-short-patch (VSP) repair pathway uses an
AB  - endonuclease, Vsr, to correct T.G mismatches that result from the deamination of
AB  - 5-methylcytosines in DNA to C.G. The products of mutS and mutL, which are required for
AB  - adenine methylation-directed mismatch repair (MMR), enhance VSP repair. Multicopy plasmids
AB  - carrying mutS alleles that are dominant negative for MMR were tested for their effects on VSP
AB  - repair. Some mutS mutations (class I) did not lower VSP repair in a mutS(+) background, and
AB  - most class I mutations increased VSP repair in mutS cells more than plasmids containing
AB  - mutS(+). Other plasmid-borne mutS mutations (class II) and mutS(+) decreased VSP repair in the
AB  - mutS(+) background. Thus, MutS protein lacking functions required for MMR can still
AB  - participate in VSP repair, and our results are consistent with a model in which MutS binds
AB  - transiently to the mispair and then translocates away from the mispair to create a specialized
AB  - structure that enhances the binding of Vsr.
ER  -

TY  - JOUR
AU  - Liebert, K.
AU  - Hermann, A.
AU  - Schlickenrieder, M.
AU  - Jeltsch, A.
TI  - Stopped-flow and mutational analysis of base flipping by the Escherichia coli dam DNA-(adenine-N6)-methyltransferase.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 443
EP  - 454
VL  - 341
AB  - By stopped-flow kinetics using 2-aminopurine as a probe to detect base flipping, we show here
AB  - that base flipping by the Escherichia coli Dam
AB  - DNA-(adenine-N6)-methyltransferase (MTase) is a biphasic process:
AB  - target base flipping is very fast (k(flip) > 240 s(-1)), but binding of
AB  - the flipped base into the active site pocket of the enzyme is slow (k =
AB  - 0.1-2 s(-1)). Whereas base flipping occurs in the absence of
AB  - S-adenosyl-L-methionine (AdoMet), binding of the target base in the
AB  - active site pocket requires AdoMet. Our data suggest that the tyrosine
AB  - residue in the DPPY motif conserved in the active site of
AB  - DNA-(adenine-N6)-MTases stacks to the flipped target base. Substitution
AB  - of the aspartic acid residue of the DPPY motif by alanine abolished
AB  - base flipping, suggesting that this residue contacts and stabilizes the
AB  - flipped base. The exchange of Ser188 located in a loop next to the
AB  - active center by alanine led to a seven- to eightfold reduction of
AB  - k(flip), which was also reduced with substrates having altered GATC
AB  - recognition sites and in the absence of AdoMet. These findings provide
AB  - evidence that the enzyme actively initiates base flipping by
AB  - stabilizing the transition state of the process. Reduced rates of base
AB  - flipping in substrates containing the target base in a non-canonical
AB  - sequence demonstrate that DNA recognition by the MTase starts before
AB  - base flipping. DNA recognition, cofactor binding and base flipping are
AB  - correlated and efficient base flipping takes place only if the enzyme
AB  - has bound to a cognate target site and AdoMet is available.
ER  -

TY  - JOUR
AU  - Liebert, K.
AU  - Horton, J.R.
AU  - Chahar, S.
AU  - Orwick, M.
AU  - Cheng, X.D.
AU  - Jeltsch, A.
TI  - Two alternative conformations of S-Adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle.
JO  - J. Biol. Chem.
PY  - 2007
SP  - 22848
EP  - 22855
VL  - 282
AB  - The crystal structure of the Escherichia coli DNA adenine methyltransferase( EcoDam) in a
AB  - binary complex with the cofactor
AB  - product S-adenosyl-L-homocysteine ( AdoHcy) unexpectedly showed the
AB  - bound AdoHcy in two alternative conformations, extended or folded. The
AB  - extended conformation represents the catalytically competent
AB  - conformation, identical to that of EcoDam-DNA-AdoHcy ternary complex.
AB  - The folded conformation prevents catalysis, because the homocysteine
AB  - moiety occupies the target Ade binding pocket. The largest difference
AB  - between the binary and ternary structures is in the conformation of the
AB  - N-terminal hexapeptide ( (9)KWAGGK(14)). Cofactor binding leads to a
AB  - strong change in the fluorescence of Trp(10), whose indole ring
AB  - approaches the cofactor by 3.3 angstrom. Stopped-flow kinetics
AB  - andAdoMetcross-linking studies indicate that the cofactor prefers
AB  - binding to the enzyme after preincubation with DNA. In the presence of
AB  - DNA, AdoMet binding is similar to 2-fold stronger than AdoHcy binding.
AB  - In the binary complex the side chain of Lys(14) is disordered, whereas
AB  - Lys(14) stabilizes the active site in the ternary complex. Fluorescence
AB  - stopped-flow experiments indicate that Lys(14) is important for EcoDam
AB  - binding of the extrahelical target base into the active site pocket.
AB  - This suggests that the hexapeptide couples specific DNA binding
AB  - (Lys(9)), AdoMet binding (Trp(10)), and insertion of the flipped target
AB  - base into the active site pocket (Lys(14)).
ER  -

TY  - JOUR
AU  - Lienau, E.K.
AU  - Strain, E.
AU  - Wang, C.
AU  - Zheng, J.
AU  - Ottesen, A.R.
AU  - Keys, C.E.
AU  - Hammack, T.S.
AU  - Musser, S.M.
AU  - Brown, E.W.
AU  - Allard, M.W.
AU  - Cao, G.
AU  - Meng, J.
AU  - Stones, R.
TI  - Identification of a salmonellosis outbreak by means of molecular sequencing.
JO  - N. Engl. J. Med.
PY  - 2011
SP  - 981
EP  - 982
VL  - 364
ER  -

TY  - JOUR
AU  - Liesegang, H.
AU  - Kaster, A.K.
AU  - Wiezer, A.
AU  - Goenrich, M.
AU  - Wollherr, A.
AU  - Seedorf, H.
AU  - Gottschalk, G.
AU  - Thauer, R.K.
TI  - Complete Genome Sequence of Methanothermobacter marburgensis, a Methanoarchaeon Model Organism.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5850
EP  - 5851
VL  - 192
AB  - The circular genome sequence of the chemolithoautotrophic euryarchaeon Methanothermobacter
AB  - marburgensis, with 1,639,135 bp, was determined and
AB  - compared with that of Methanothermobacter thermautotrophicus. The genomes
AB  - of the two model methanogens differ substantially in protein coding
AB  - sequences, in insertion sequence (IS)-like elements, and in clustered
AB  - regularly interspaced short palindromic repeats (CRISPR) loci.
ER  -

TY  - JOUR
AU  - Liljeqvist, M.
AU  - Valdes, J.
AU  - Holmes, D.S.
AU  - Dopson, M.
TI  - Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4304
EP  - 4305
VL  - 193
AB  - Acidithiobacillus ferrivorans SS3 is a psychrotolerant acidophile capable of growth in the
AB  - range of 5 degrees  to 30 degrees C (optimum,
AB  - approximately 25 degrees C). It gains energy from the oxidation of ferrous
AB  - iron and inorganic sulfur compounds and obtains organic carbon from carbon
AB  - dioxide. Here, we present the draft genome sequence of A. ferrivorans SS3
AB  - that will permit investigation of genes involved in growth in acidic
AB  - environments at low temperatures.
ER  -

TY  - JOUR
AU  - Lilley, D.M.J.
TI  - Cisplatin adducts in DNA: distortion and recognition.
JO  - J. Biol. Inorg. Chem.
PY  - 1996
SP  - 189
EP  - 191
VL  - 1
AB  - cis-Diamminedichloroplatinum (II) (cisplatin) and derivatives are very successful anticancer
AB  - chemotherapeutic agents.  They crosslink cellular DNA, forming bifunctional adducts with the
AB  - N7 of guanine bases.  In this review, recent structures of cisplatin adducts are summarized,
AB  - and the significance for the recognition of DNA structure by proteins is discussed.  Two new
AB  - structures of intrastrand GpG adducts have been presented, showing a significant kinking of
AB  - the helix axis and a novel hybrid A-B helical geometry.  The relevance of this structure to
AB  - the recognition of HMG-box and related proteins is discussed.  A new structure of a
AB  - cross-strand cisplatin adduct reveals a major disruption of the local DNA structure.  The
AB  - basepairs containing the modified guanine bases are broken, with extrusion of the cytosine
AB  - bases into the solvent.  The backbone reverses direction locally, with the result that the
AB  - platinum adduct is located in what is the minor groove of the DNA overall.  The extrusion of
AB  - single bases out of the helix is strongly reminiscent of the effect of certain methylases on
AB  - their DNA targets.
ER  -

TY  - JOUR
AU  - Lim, H.I.
AU  - Lee, J.
AU  - Jang, J.Y.
AU  - Park, H.W.
AU  - Choi, H.J.
AU  - Kim, T.W.
AU  - Kang, M.R.
AU  - Lee, J.H.
TI  - Draft Genome Sequence of Lactobacillus sakei Strain wikim 22, Isolated from Kimchi in Chungcheong Province, South Korea.
JO  - Genome Announcements
PY  - 2014
SP  - e01296
EP  - e01214
VL  - 2
AB  - We report the draft genome sequence of Lactobacillus sakei strain wikim 22, a Lactobacillus
AB  - species isolated from kimchi in North Chungcheong Province, South
AB  - Korea, having 155 contigs with 2,447 genes and an average G+C content of 40.61%.
ER  -

TY  - JOUR
AU  - Lim, J.
AU  - Lee, T.H.
AU  - Nahm, B.H.
AU  - Choi, Y.D.
AU  - Kim, M.
AU  - Hwang, I.
TI  - Complete Genome Sequence of Burkholderia glumae BGR1.
JO  - J. Bacteriol.
PY  - 2009
SP  - 3758
EP  - 3759
VL  - 191
AB  - Burkholderia glumae is the causative agent of grain and seedling rot in rice and of bacterial
AB  - wilt in many field crops. Here, we report the complete genome sequence of B. glumae BGR1
AB  - isolated from a diseased rice panicle in Korea.
ER  -

TY  - JOUR
AU  - Lim, J.S.
AU  - Choi, B.S.
AU  - Choi, A.Y.
AU  - Kim, K.D.
AU  - Kim, D.I.
AU  - Choi, I.Y.
AU  - Ka, J.O.
TI  - Complete Genome Sequence of the Fenitrothion-Degrading Burkholderia sp. Strain YI23.
JO  - J. Bacteriol.
PY  - 2012
SP  - 896
EP  - 896
VL  - 194
AB  - Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated
AB  - from various environments have the potential
AB  - to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was
AB  - isolated from a golf course soil and identified as a
AB  - fenitrothion-degrading bacterium. In this study, we report the complete
AB  - genome sequence of Burkholderia sp. strain YI23.
ER  -

TY  - JOUR
AU  - Lim, J.Y.
AU  - Hwang, I.
AU  - Ganzorig, M.
AU  - Huang, S.L.
AU  - Cho, G.S.
AU  - Franz, C.M.A.P.
AU  - Lee, K.
TI  - Complete Genome Sequences of Three Moraxella osloensis Strains Isolated from Human Skin.
JO  - Genome Announcements
PY  - 2018
SP  - e01509
EP  - e01517
VL  - 6
AB  - Here, we present the complete whole-genome sequences of three Moraxella osloensis strains with
AB  - octylphenol polyethoxylate-degrading abilities. These strains were
AB  - isolated from human skin.
ER  -

TY  - JOUR
AU  - Lim, J.Y.
AU  - Hwang, I.
AU  - Ganzorig, M.
AU  - Pokhriyal, S.
AU  - Singh, R.
AU  - Lee, K.
TI  - Complete Genome Sequence of Paracoccus yeei TT13, Isolated from Human Skin.
JO  - Genome Announcements
PY  - 2018
SP  - e01514
EP  - e01517
VL  - 6
AB  - Paracoccus yeei TT13 was isolated from human skin because of its ability to degrade propylene
AB  - glycol. Here, we present the whole-genome sequence of this
AB  - strain; it possesses one 3.58-Mb chromosome and six plasmids. TT13 genome
AB  - analysis indicated that this bacterium has denitrification potential.
ER  -

TY  - JOUR
AU  - Lim, S.
AU  - Chang, D.H.
AU  - Ahn, S.
AU  - Kim, B.C.
TI  - Whole genome sequencing of 'Faecalibaculum rodentium' ALO17, isolated from C57BL/6J laboratory mouse feces.
JO  - Gut Pathog.
PY  - 2016
SP  - 3
EP  - 3
VL  - 8
AB  - BACKGROUND: Intestinal microorganisms affect host physiology, including ageing.
AB  - Given the difficulty in controlling for human studies of the gut microbiome, mouse models
AB  - provide an alternative avenue to study such relationships. In this study, we report on the
AB  - complete genome of "Faecalibaculum rodentium" ALO17, a bacterium that was isolated from the
AB  - faeces of a 9-month-old female C57BL/6J mouse. This strain will be utilized in future in vivo
AB  - studies detailing the relationships between the gut microbiome and ageing. RESULTS: The whole
AB  - genome sequence of "F. rodentium" ALO17 was obtained using single-molecule, real-time
AB  - (SMRT) technique on a PacBio instrument. The assembled genome consisted of
AB  - 2,542,486 base pairs of double-stranded DNA with a GC content of 54.0 % and no plasmids. The
AB  - genome was predicted to contain 2794 open reading frames, 55 tRNA genes, and 38 rRNA genes.
AB  - The 16S rRNA gene of ALO17 was 86.9 % similar to that of Allobaculum stercoricanis DSM
AB  - 13633(T), and the average overall nucleotide identity between strains ALO17 and DSM 13633(T)
AB  - was 66.8 %. After confirming the phylogenetic relationship between "F. rodentium" ALO17 and A.
AB  - stercoricanis DSM 13633(T), their whole genome sequences were compared, revealing that "F.
AB  - rodentium" ALO17 contains more fermentation-related genes than A. stercoricanis DSM 13633(T).
AB  - Furthermore, "F. rodentium" ALO17 produces higher levels of lactic acid than A. stercoricanis
AB  - DSM 13633(T) as determined by high-performance liquid chromatography. CONCLUSION: The
AB  - availability of the "F. rodentium" ALO17 whole genome sequence will enhance studies concerning
AB  - the gut microbiota and host physiology, especially when investigating the molecular
AB  - relationships between gut microbiota and ageing.
ER  -

TY  - JOUR
AU  - Lim, S.B.Y. et al.
TI  - Genome Sequence of Bacillus velezensis SGAir0473, Isolated from Tropical Air Collected in Singapore.
JO  - Genome Announcements
PY  - 2018
SP  - e00642
EP  - e00618
VL  - 6
AB  - Bacillus velezensis strain SGAir0473 (Firmicutes) was isolated from tropical air  collected in
AB  - Singapore. Its genome was assembled using short reads and
AB  - single-molecule real-time sequencing and comprises one chromosome with 4.18 Mb.
AB  - The genome consists of 3,937 protein-coding genes, 86 tRNAs, and 27 rRNAs.
ER  -

TY  - JOUR
AU  - Lim, S.K.
AU  - Kim, S.J.
AU  - Cha, S.H.
AU  - Oh, Y.K.
AU  - Rhee, H.J.
AU  - Kim, M.S.
AU  - Lee, J.K.
TI  - Complete genome sequence of Rhodobacter sphaeroides KD131.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1118
EP  - 1119
VL  - 191
AB  - Rhodobacter sphaeroides is a purple nonsulfur photosynthetic bacterium that is considered a
AB  - possible source of H(2) production. R. sphaeroides
AB  - KD131, which was isolated from sea mud in South Korea, was found to
AB  - produce high levels of H(2). Here we report the complete and annotated
AB  - genome sequence of R. sphaeroides KD131.
ER  -

TY  - JOUR
AU  - Lim, S.R.
AU  - Jeong, D.G.
AU  - Chi, W.J.
AU  - Kim, J.H.
TI  - Complete Genome Sequence of Lacinutrix venerupis DOK2-8 Isolated from Marine Sediment from the East Sea, Republic of Korea.
JO  - Genome Announcements
PY  - 2018
SP  - e01485
EP  - e01417
VL  - 6
AB  - Lacinutrix venerupis has recently been considered a potential fish pathogen. Here, we report
AB  - the complete genome sequence of L. venerupis DOK2-8, which
AB  - possesses several virulence-related genes. This strain may be potentially
AB  - virulent to other marine organisms, and its genomic information will provide
AB  - important insights into the biodiversity of the genus Lacinutrix.
ER  -

TY  - JOUR
AU  - Lim, Y.L.
AU  - Ee, R.
AU  - Yong, D.
AU  - Yu, C.Y.
AU  - Ang, G.Y.
AU  - Tee, K.K.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Complete Genome Sequence Analysis of Pandoraea pnomenusa Type Strain DSM 16536T Isolated from a Cystic Fibrosis Patient.
JO  - Front. Microbiol.
PY  - 2016
SP  - 109
EP  - 109
VL  - 7
AB  - The genus of Pandoraea was first proposed in 2000 following the isolation from the sputum of
AB  - cystic fibrosis patients (Coenye et al., 2000). Five species were initially assigned to the
AB  - novel genus namely Pandoraea apista, Pandoraea pulmonicola, Pandoraea pnomenusa, Pandoraea
AB  - sputorum, and Pandoraea norimbergensis but the description of four new species and another
AB  - four genomospecies in the subsequent years led to a total of nine species and four
AB  - genomospecies within the genus of Pandoraea (Daneshvar et al., 2001; Anandham et al., 2010;
AB  - Sahin et al., 2011). The isolation of Pandoraea spp. from various environmental samples such
AB  - as water, sludge, and soils have been reported, but to date, only P. pnomenusa, P. apista, P.
AB  - pulmonicola, and P. sputorum were isolated from clinical specimens such as blood, sputum and
AB  - bronchial fluid of patients with cystic fibrosis or chronic lung diseases (Coenye et al.,
AB  - 2000; Daneshvar et al., 2001; Stryjewski et al., 2003; Han-Jen et al., 2013). Members of
AB  - Pandoraea tend to exhibit broad resistance to ampicillin, extended-spectrum cephalosporins,
AB  - aztreonam, aminoglycosides, and meropenem but they are sensitive to imipenem (Daneshvar et
AB  - al., 2001; Stryjewski et al., 2003). However, the clinical significance and prevalence of
AB  - these multi-drug resistant bacteria among patients with cystic fibrosis or respiratory
AB  - diseases remained unknown since Pandoraea spp. are usually misidentified as Burkholderia
AB  - cepacia complex, Ralstonia pickettii, or Ralstonia paucula (Segonds et al., 2003). Ambiguity
AB  - in differentiating between B. cepacia complex, Ralstonia spp. and Pandoraea spp. can be
AB  - resolved by 16S ribosomal DNA-PCR (Coenye et al., 2001) and gyrB gene restriction fragment
AB  - length polymorphism (Coenye and LiPuma, 2002) but the limited use of molecular typing methods
AB  - in routine clinical microbiological laboratory has resulted in the underreporting of Pandoraea
AB  - spp. in clinical cases.
ER  -

TY  - JOUR
AU  - Lim, Y.L.
AU  - Roberts, R.J.
AU  - Ee, R.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile.
JO  - Genome Announcements
PY  - 2016
SP  - e00060
EP  - e00016
VL  - 4
AB  - In this report, we announce the complete genome sequence of Aeromonas hydrophila  strain YL17.
AB  - Single-molecule real-time (SMRT) DNA sequencing was used to generate
AB  - the complete genome sequence and the genome-wide DNA methylation profile of this
AB  - environmental isolate. A total of five unique DNA methyltransferase recognition
AB  - motifs were reported here.
ER  -

TY  - JOUR
AU  - Lima, A.C.
AU  - de Moura, V.A.
AU  - Pinheiro, K.D.
AU  - Paixao, C.T.
AU  - da Costa, W.L.
AU  - Folador, A.R.
AU  - Guaraldi, A.L.
AU  - Ramos, R.T.
AU  - Silva, A.
AU  - Marques, J.M.
TI  - Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA05 Isolated  from an Ovine Host in Para State, Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00082
EP  - e00017
VL  - 5
AB  - We report here the draft genome sequence of Corynebacterium pseudotuberculosis PA05, isolated
AB  - from an ovine host in Para State, Brazil. C. pseudotuberculosis is
AB  - an etiological agent of diseases with veterinary and medical importance. The
AB  - genome contains 2,435,137 bp, a G+C content of 52.2%, 2,295 coding sequences,
AB  - five pseudogenes, 53 tRNAs, and six rRNAs.
ER  -

TY  - JOUR
AU  - Lima, A.O.
AU  - Cabral, A.
AU  - Andreote, F.D.
AU  - Cavalett, A.
AU  - Pessatti, M.L.
AU  - Dini-Andreote, F.
AU  - da Silva, M.A.
TI  - Draft Genome Sequence of Bacillus stratosphericus LAMA 585, Isolated from the Atlantic Deep Sea.
JO  - Genome Announcements
PY  - 2013
SP  - e00204
EP  - e00213
VL  - 1
AB  - Bacillus stratosphericus LAMA 585 was isolated from the Mid-Atlantic-Ridge seafloor (5,500-m
AB  - depth). This bacterium presents the capacity for cellulase,
AB  - xylanase, and lipase production when growing aerobically in marine-broth media.
AB  - Genes involved in the tolerance of oligotrophic and extreme conditions and
AB  - prospection of biotechnological products were annotated in the draft genome (3.7
AB  - Mb).
ER  -

TY  - JOUR
AU  - Lima, A.R.
AU  - Siqueira, A.S.
AU  - Dos Santos, B.G.
AU  - da Silva, F.D.
AU  - Inada, D.T.
AU  - Lima, C.P.
AU  - Cardoso, J.F.
AU  - Vianez-Junior, J.L.
AU  - Nunes, M.R.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of Rhodobacter sp. Strain CACIA 14H1, a Heterotrophic Bacterium Obtained from a Nonaxenic Culture of a Cyanobium Species.
JO  - Genome Announcements
PY  - 2014
SP  - e01116
EP  - e01113
VL  - 2
AB  - Despite their prominent importance, few efforts have been paid to the genomic analysis of
AB  - heterotrophic bacteria associated with cyanobacteria. Thus, this work
AB  - presents the draft genome sequence (~3.9 Mbp) of a heterotrophic bacterium
AB  - (Rhodobacter sp. strain CACIA 14H1) recovered from a nonaxenic culture of a
AB  - Cyanobium species.
ER  -

TY  - JOUR
AU  - Lima, A.R.
AU  - Siqueira, A.S.
AU  - Dos Santos, B.G.
AU  - da Silva, F.D.
AU  - Lima, C.P.
AU  - Cardoso, J.F.
AU  - Vianez, J.J.L.
AU  - Dall'Agnol, L.T.
AU  - McCulloch, J.A.
AU  - Nunes, M.R.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of the Brazilian Cyanobium sp. Strain CACIAM 14.
JO  - Genome Announcements
PY  - 2014
SP  - e00669
EP  - e00614
VL  - 2
AB  - Given the scarcity of data pertaining to whole-genome sequences of cyanobacterial strains
AB  - isolated in Brazil, we hereby present the draft genome sequence of the
AB  - Cyanobium sp. strain CACIAM 14, isolated in southeastern Amazonia.
ER  -

TY  - JOUR
AU  - Lima, A.R.
AU  - Siqueira, A.S.
AU  - Dos Santos, B.G.
AU  - da Silva, F.D.
AU  - Lima, C.P.
AU  - Cardoso, J.F.
AU  - Vianez-Junior, J.L.
AU  - Nunes, M.R.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of Blastomonas sp. Strain CACIA 14H2, a Heterotrophic Bacterium Associated with Cyanobacteria.
JO  - Genome Announcements
PY  - 2014
SP  - e01200
EP  - e01213
VL  - 2
AB  - With the new methods for assembling sequence data from metagenomic samples, the genomic study
AB  - of heterotrophic bacterium-cyanobacterium associations can now be
AB  - improved. In this work, the draft genome sequence of Blastomonas sp. strain CACIA
AB  - 14H2, obtained from a nonaxenic culture of a Cyanobium sp., is presented.
ER  -

TY  - JOUR
AU  - Lima, A.R.J.
AU  - Castro, W.O.
AU  - Moraes, P.H.G.
AU  - Siqueira, A.S.
AU  - Aguiar, D.C.F.
AU  - de Lima, C.P.S.
AU  - Vianez-Junior, J.L.S.G.
AU  - Nunes, M.R.T.
AU  - Dall'Agnol, L.T.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of Alkalinema sp. Strain CACIAM 70d, a Cyanobacterium Isolated from an Amazonian Freshwater Environment.
JO  - Genome Announcements
PY  - 2017
SP  - e00635
EP  - e00617
VL  - 5
AB  - In order to increase the genomic data of cyanobacterial strains isolated in Brazil, we hereby
AB  - present the draft genome sequence of the Alkalinema sp. strain
AB  - CACIAM 70d, isolated from an Amazonian freshwater environment. This report
AB  - describes the first genome available for this genus.
ER  -

TY  - JOUR
AU  - Lima, N.B.
AU  - Gama, M.A.S.
AU  - Mariano, R.L.R.
AU  - Silva, W.J. Jr.
AU  - Farias, A.R.G.
AU  - Falcao, R.M.
AU  - Sousa-Paula, L.C.
AU  - Benko-Iseppon, A.M.
AU  - Paiva, S.S.L. Jr.
AU  - Balbino, V.Q.
AU  - Souza, E.B.
TI  - Complete Genome Sequence of Xanthomonas campestris pv. viticola Strain CCRMXCV 80 from Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e01263
EP  - e01217
VL  - 5
AB  - Here, we report the complete 5.3-Mb genome sequence of Xanthomonas campestris pv. viticola
AB  - (CCRMXCV 80), which causes grapevine (Vitis vinifera L.) bacterial
AB  - canker. Genome data will improve our understanding of the strain's comparative
AB  - genomics and epidemiology, and help to further define plant protection and
AB  - quarantine procedures.
ER  -

TY  - JOUR
AU  - Limsowtin, G.K.Y.
AU  - Heap, H.A.
AU  - Lawrence, R.C.
TI  - Heterogeneity among strains of lactic streptococci.
JO  - New Zealand J. Dairy Sci. Techn.
PY  - 1978
SP  - 1
EP  - 8
VL  - 13
AB  - Heterogeneity within lactic streptococcal cultures was studied with respect to
AB  - acid production and phage sensitivity.  All strains were found to accumulate
AB  - slow coagulating variants at different rates, depending upon the growth media
AB  - used.  Maintenance of cultures in M17 broth resulted in a significant
AB  - accumulation of slow coagulating variants for most strains studied.  In all but
AB  - one strain investigated, variants were detected which exhibited different phage
AB  - sensitivies.  When isolates from these cultures were examined four phenotypes
AB  - were observed:  1) Variants exhibiting host modification and restriction of
AB  - phages; 2) Variants which adsorbed but did not form plaques (with one or more
AB  - particular phages); 3) Variants resistant against one or more particular
AB  - phages; 4) Variants sensitive to different phages.  Generally only one or two
AB  - of these four phenotypes were recovered from any one strain but a detailed
AB  - investigation of strain 108 showed that all four phenotypes were present.  The
AB  - appearance of these variants was dependent upon the nature of subculturing
AB  - medium, being much more rapid in M17 broth than in autoclaved reconstituted
AB  - skim milk.  The commercial importance of these findings is discussed.
ER  -

TY  - JOUR
AU  - Lin, A.C.
AU  - Liao, T.L.
AU  - Lin, Y.C.
AU  - Lai, Y.C.
AU  - Lu, M.C.
AU  - Chen, Y.T.
TI  - Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6316
EP  - 6316
VL  - 194
AB  - We report the complete genome sequence of Klebsiella pneumoniae 1084, a
AB  - hypermucoviscosity-negative K1 clinical strain. Sequencing and annotation
AB  - revealed a 5,386,705-bp circular chromosome (57.4% G+C content), which contains
AB  - 4,962 protein-coding genes, 80 tRNA genes, and 25 rRNA genes.
ER  -

TY  - JOUR
AU  - Lin, B.
AU  - Lu, G.
AU  - Li, S.
AU  - Hu, Z.
AU  - Chen, H.
TI  - Draft Genome Sequence of the Novel Agarolytic Bacterium Aquimarina agarilytica ZC1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2769
EP  - 2769
VL  - 194
AB  - The marine bacterium ZC1 is the type strain of the recently identified novel species
AB  - Aquimarina agarilytica. It can produce multiple agarases. Here we report
AB  - the draft genome sequence of strain ZC1 (4,253,672 bp, with a GC content of
AB  - 32.8%) and major findings from its annotation. It is the first reported genome in
AB  - the genus Aquimarina.
ER  -

TY  - JOUR
AU  - Lin, B.-C.
AU  - Chien, M.-C.
AU  - Lou, S.-Y.
TI  - A sequence-specific endonuclease (XmnI) from Xanthomonas manihotis.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 6189
EP  - 6198
VL  - 8
AB  - A type II restriction endonuclease XmnI with a novel site specificity has been
AB  - isolated from Xanthomonas manihotis.  XmnI does not cleave SV40 DNA, but
AB  - cleaves PhiX174 DNA into three fragments, which constitute 76.61%, 18.08% and
AB  - 5.31% of the total length of 5386 base pairs, and cleaves pBR322 DNA into two
AB  - fragments of 55.71% and 44.29% of the entire 4362 base pairs.  The nucleotide
AB  - sequences around the cleavage sites made by XmnI are not exactly homologous,
AB  - but they have a common sequence of 5' GAANNNNTTC 3' according to a simple
AB  - computer program analysis on nucleotide sequences of PhiX174 DNA, pBR322 DNA
AB  - and SV40 DNA. The results suggest that the cleavage site of XmnI is located
AB  - within its recognition sequence of 5' GAANNNNTTC 3'.
ER  -

TY  - JOUR
AU  - Lin, C.
AU  - den Bakker, H.C.
AU  - Suzuki, H.
AU  - Lefebure, T.
AU  - Ponnala, L.
AU  - Sun, Q.
AU  - Stanhope, M.J.
AU  - Wiedmann, M.
AU  - Duhamel, G.E.
TI  - Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).
JO  - Genome Announcements
PY  - 2013
SP  - e00215
EP  - e00212
VL  - 1
AB  - Reported herein is the complete genome sequence of strain P43/6/78, isolated from a pig with
AB  - clinical disease. This sequence will aid in the study of genome-wide
AB  - comparison among species.
ER  -

TY  - JOUR
AU  - Lin, D.
AU  - Guo, Y.
AU  - Chen, C.
AU  - Fuzhu, Y.
AU  - Xiao, S.
AU  - Zhu, D.
AU  - Wang, M.
AU  - Xu, X.
TI  - Draft Genome Sequence of Linezolid-Resistant Enterococcus faecalis Clinical Isolate HS0914.
JO  - Genome Announcements
PY  - 2014
SP  - e00782
EP  - e00714
VL  - 2
AB  - We report the draft genome sequence of linezolid-resistant Enterococcus faecalis  strain
AB  - HS-0914 isolated from a teaching hospital in Shanghai, China. The draft
AB  - genome sequence is composed of 61 contigs for 2,816,079 bp. Ribosomal RNA
AB  - mutations and cfr, which mediates linezolid resistance, are not present.
ER  -

TY  - JOUR
AU  - Lin, H.
AU  - Coletta-Filho, H.D.
AU  - Han, C.S.
AU  - Lou, B.
AU  - Civerolo, E.L.
AU  - Machado, M.A.
AU  - Gupta, G.
TI  - Draft Genome Sequence of 'Candidatus Liberibacter americanus' Bacterium Associated with Citrus Huanglongbing in Brazil.
JO  - Genome Announcements
PY  - 2013
SP  - e00275
EP  - e00213
VL  - 1
AB  - We report here the draft genome sequence of 'Candidatus Liberibacter americanus'  strain
AB  - PW_SP. The 1,176,071-bp genome, with 31.6% G+C content, comprises 948 open
AB  - reading frames, 38 tRNAs, and three complete rRNAs.
ER  -

TY  - JOUR
AU  - Lin, H.
AU  - Han, C.S.
AU  - Liu, B.
AU  - Lou, B.
AU  - Bai, X.
AU  - Deng, C.
AU  - Civerolo, E.L.
AU  - Gupta, G.
TI  - Complete Genome Sequence of a Chinese Strain of 'Candidatus Liberibacter asiaticus'.
JO  - Genome Announcements
PY  - 2013
SP  - e00184
EP  - e00113
VL  - 1
AB  - We report here the complete genome sequence of 'Candidatus Liberibacter asiaticus' (strain
AB  - Guangxi-1). The 1,268,237-bp genome with a 36.5% G+C content
AB  - comprises 1,141 open reading frames, 44 tRNAs, and 3 complete rRNAs in a circular
AB  - chromosome.
ER  -

TY  - JOUR
AU  - Lin, H.
AU  - Pietersen, G.
AU  - Han, C.
AU  - Read, D.A.
AU  - Lou, B.
AU  - Gupta, G.
AU  - Civerolo, E.L.
TI  - Complete Genome Sequence of 'Candidatus Liberibacter africanus,' a Bacterium Associated with Citrus Huanglongbing.
JO  - Genome Announcements
PY  - 2015
SP  - e00733
EP  - e00715
VL  - 3
AB  - We report here the complete genome sequence of 'Candidatus Liberibacter africanus' strain
AB  - PTSAPSY. The 1,192,232-bp genome with 34.5% G+C content
AB  - comprises 1,017 open reading frames, 44 tRNAs, and three complete rRNAs in a
AB  - circular chromosome.
ER  -

TY  - JOUR
AU  - Lin, H.H.
AU  - Chen, Y.S.
AU  - Hsiao, H.W.
AU  - Hsueh, P.T.
AU  - Ni, W.F.
AU  - Chen, Y.L.
TI  - Two Genome Sequences of Klebsiella pneumoniae Strains with Sequence Type 23 and Capsular Serotype K1.
JO  - Genome Announcements
PY  - 2016
SP  - e01097
EP  - e01016
VL  - 4
AB  - Here, we report the whole-genome sequences of Klebsiella pneumoniae ED2 and ED23, isolated,
AB  - respectively, from bacteremic patients with liver abscesses (ED2) and
AB  - patients with primary liver abscess and metastatic meningitis (ED23). Both
AB  - strains were of multilocus sequence type 23 with capsule serotype K1.
ER  -

TY  - JOUR
AU  - Lin, I.-H.
AU  - Liu, T.-T.
AU  - Teng, Y.-T.
AU  - Wu, H.-L.
AU  - Liu, Y.-M.
AU  - Wu, K.-M.
AU  - Chang, C.-H.
AU  - Hsu, M.-T.
TI  - Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence.
JO  - PLoS ONE
PY  - 2011
SP  - e20519
EP  - e20519
VL  - 6
AB  - Streptococcus gallolyticus infections in humans are often associated with bacteremia,
AB  - infective endocarditis and colon cancers. The disease manifestations are different depending
AB  - on the subspecies of S. gallolyticus causing the infection. Here, we present the complete
AB  - genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype
AB  - II.2).  The genomic differences between the two biotypes were characterized with comparative
AB  - genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length
AB  - and encode 2246 and 1869 CDS respectively.  The organization and genomic contents of both
AB  - genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%)
AB  - and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively.
AB  - There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus
AB  - genus has a small core-genome (constitute around 30% of total CDS) and substantial
AB  - evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC
AB  - 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to
AB  - contribute to the fitness and virulence of each of the two subspecies. We have also predicted
AB  - putative cell-surface associated proteins that could play a role in adherence to host tissues,
AB  - leading to persistent infections causing sub-acute and chronic diseases in
AB  - humans. This study showed evidence that the S. gallolyticus still possesses genes making it
AB  - suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is
AB  - reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially
AB  - membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of
AB  - the two S. gallolyticus biotypes and the type of disease an infected patient eventually
AB  - develops.
ER  -

TY  - JOUR
AU  - Lin, I.G.
AU  - Han, L.
AU  - Taghva, A.
AU  - O'Brien, L.E.
AU  - Hsieh, C.L.
TI  - Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro.
JO  - Mol. Cell. Biol.
PY  - 2002
SP  - 704
EP  - 723
VL  - 22
AB  - CpG methylation is involved in a wide range of biological processes in vertebrates as well as
AB  - in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA
AB  - methyltransferase activity in mouse and human. It has been proposed that de novo methylation
AB  - observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b
AB  - methyltransferases, while Dntm1 is believed to be responsible for maintaining the established
AB  - methylation patterns upon replication. Analysis of the sites methylated in vivo using the
AB  - bisulfite genomic sequencing method confirms the previous finding that some regions of the
AB  - plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However,
AB  - the preferred targets of the enzyme cannot be determined due to the presence of other
AB  - methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of
AB  - Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed.
AB  - These analyses revealed that the two cDNA strands have distinctly different methylation
AB  - patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG
AB  - sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most
AB  - likely methylates one strand of DNA without concurrent methylation of the CpG site on the
AB  - complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites
AB  - more frequently than others, depending on the sequence context. Methylation of each DNA strand
AB  - independently and with possible sequence preference is a novel feature among the known DNA
AB  - methyltransferases.
ER  -

TY  - JOUR
AU  - Lin, J.
AU  - Vogt, V.M.
TI  - I-PpoI, the endonuclease encoded by the group I intron PpLSU3, is expressed from an RNA polymerase I transcript.
JO  - Mol. Cell. Biol.
PY  - 1998
SP  - 5809
EP  - 5817
VL  - 18
AB  - PpLSU3, a mobile group I intron in the rRNA genes of Physarum polycephalum, also can home into
AB  - yeast chromosomal ribosomal DNA (rDNA). By integrating PpLSU3 into the rDNA copies of a yeast
AB  - strain temperature sensitive for RNA polymerase I, we have shown that the I-PpoI homing
AB  - endonuclease encoded by PpLSU3 is expressed from an RNA polymerase I transcript. We have also
AB  - developed a method to integrate mutant forms of PpLSU3 as well as the Tetrahymena intron
AB  - TtLSU1 into rDNA, by expressing I-PpoI in trans. Analysis of I-PpoI expression levels in these
AB  - mutants, along with subcellular fractionation of intron RNA, strongly suggests that the
AB  - full-length excised intron RNA, but not RNAs that are further cleaved, serves as or gives rise
AB  - to the mRNA.
ER  -

TY  - JOUR
AU  - Lin, J.
AU  - Zhao, F.
AU  - Feng, Y.
AU  - Zong, Z.
TI  - Draft Genome Sequence of a High-Level Colistin-Resistant Clinical Strain of the Enterobacter cloacae Complex.
JO  - Genome Announcements
PY  - 2017
SP  - e00131
EP  - e00117
VL  - 5
AB  - Strain WCHECl-C4 of the Enterobacter cloacae complex, recovered from the blood of a patient
AB  - with peritonitis, was high-level resistant to colistin. Here, we report
AB  - its 5.1-Mb draft genome sequence, comprising 92 contigs with an average 55.74%
AB  - G+C content. The genome contained 4,783 coding sequences and 68 tRNA genes.
ER  -

TY  - JOUR
AU  - Lin, J.N.
AU  - Lai, C.H.
AU  - Yang, C.H.
AU  - Huang, Y.H.
AU  - Lin, H.H.
TI  - Complete Genome Sequence of Elizabethkingia miricola Strain EM798-26 Isolated from the Blood of a Cancer Patient.
JO  - Genome Announcements
PY  - 2018
SP  - e01408
EP  - e01417
VL  - 6
AB  - Elizabethkingia miricola EM798-26 was isolated from the blood of a patient with diffuse large
AB  - B-cell lymphoma in Taiwan. We report here the complete genome
AB  - sequence of EM798-26, which contains a G+C content of 35.7% and 3,877 candidate
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Lin, J.N.
AU  - Yang, C.H.
AU  - Lai, C.H.
AU  - Huang, Y.H.
AU  - Lin, H.H.
TI  - Draft Genome Sequence of Elizabethkingia anophelis Strain EM361-97 Isolated from  the Blood of a Cancer Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e01215
EP  - e01216
VL  - 4
AB  - Elizabethkingia anophelis EM361-97 was isolated from the blood of a patient with
AB  - nasopharyngeal carcinoma and lung cancer. We report the draft genome sequence of
AB  - EM361-97, which contains a G+C content of 35.7% and 3,611 candidate
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Lin, L.
AU  - Wei, C.
AU  - Chen, M.
AU  - Wang, H.
AU  - Li, Y.
AU  - Li, Y.
AU  - Yang, L.
AU  - An, Q.
TI  - Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 22
EP  - 22
VL  - 10
AB  - Klebsiella variicola strain DX120E (=CGMCC 1.14935) is an endophytic nitrogen-fixing bacterium
AB  - isolated from sugarcane crops grown in Guangxi, China
AB  - and promotes sugarcane growth. Here we summarize the features of the strain
AB  - DX120E and describe its complete genome sequence. The genome contains one
AB  - circular chromosome and two plasmids, and contains 5,718,434 nucleotides with
AB  - 57.1% GC content, 5,172 protein-coding genes, 25 rRNA genes, 87 tRNA genes, 7
AB  - ncRNA genes, 25 pseudo genes, and 2 CRISPR repeats.
ER  -

TY  - JOUR
AU  - Lin, L.
AU  - Xu, Q.
AU  - Zhang, Y.
AU  - Yin, B.
AU  - Fan, Y.
AU  - Luo, Y.
AU  - Han, S.
AU  - Zhang, Z.
AU  - Wu, G.
AU  - Shen, Y.
TI  - Alternative splicing of de novo methyltransferase gene 3b in adult and newborn mice.
JO  - Zhongguo Yixue Kexueyuan Xuebao
PY  - 2000
SP  - 312
EP  - 316
VL  - 22
AB  - Objective. To unravel the biological significance of the alternative splicing of de novo
AB  - methyltransferase 3b, expression of the Dnmt3b gene in various tissues and developmental
AB  - stages was investigated in postnatal mice.  Methods. RT-PCR and capillary electrophoresis were
AB  - employed to analyze the alternative splicing pattern of Dnmt3b in tissues of newborn and adult
AB  - mice.  The results had been further reaffirmed by repeating and statistics analysis.
AB  - Bioinformatics tools were used to predict the structure and hydrophobicity of the Dnmt3b
AB  - exon10 coding sequence.  Results. The isoform with Dnmt3b exon10 was the abundant form in the
AB  - lung of newborn mice and in the liver of both newborn and adult mice, while in other tissues
AB  - of newborn and adult mice, the spliced isoform was present as the predominant one.  The
AB  - peptide encoded by Dnmt3b exon10 was mainly random coil on the surface of Dnmt3b protein.
AB  - Conclusions. The data demonstrate that the specific expression of Dnmt3b exists in tissues and
AB  - developmental stages of postnatal mice.  The alternative splicing of the exon 10 of Dnmt3b is
AB  - possibly involved in the regulation of Dnmt3b's catalytic function.  These results provide an
AB  - insight into the developmental regulation and physiological function of the alternative
AB  - splicing of the Dnmt3b gene.
ER  -

TY  - JOUR
AU  - Lin, L.C.
AU  - Lin, G.H.
AU  - Tseng, Y.H.
AU  - Yu, M.S.
TI  - Draft Genome Sequence of Vibrio owensii GRA50-12, Isolated from Green Algae in the Intertidal Zone of Eastern Taiwan.
JO  - Genome Announcements
PY  - 2015
SP  - e01438
EP  - e01414
VL  - 3
AB  - Vibrio owensii GRA50-12 was isolated from symbiotic green algae of coral. The genome contains
AB  - genes encoding toxin production, virulence regulation, stress
AB  - response proteins, types II, IV, and VI secretion systems, and proteins for the
AB  - metabolism of aromatic compounds, which reflects its pathogenic potential and its
AB  - ecological roles in the ocean.
ER  -

TY  - JOUR
AU  - Lin, L.F.
AU  - Posfai, J.
AU  - Roberts, R.J.
AU  - Kong, H.M.
TI  - Comparative genomics of the restriction-modification systems in Helicobacter pylori.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 2740
EP  - 2745
VL  - 98
AB  - Helicpbacter pylori is a Gram-negative bacterial pathogen with a small genome of 1.64-1.67 Mb.
AB  - More than 20 putative DNA
AB  - restriction-modification (R-M) systems, comprising more than 4% of the
AB  - total genome, have been identified in the two completely sequenced H.
AB  - pylori strains, 26695 and J99, based on sequence similarities. In this
AB  - study, we have investigated the biochemical activities of 14 Type II
AB  - R-M systems in H. pylori 26695. Less than 30% of the Type II R-M
AB  - systems in 26695 are fully functional, similar to the results obtained
AB  - from strain J99. Although nearly 90% of the R-M genes are shared by the
AB  - two H. pylori strains, different sets of these R-M genes are
AB  - functionally active in each strain. Interestingly, all strain-specific
AB  - R-M genes are active, whereas most shared genes are inactive. This
AB  - agrees with the notion that strain-specific genes have been acquired
AB  - more recently through horizontal transfer from other bacteria and
AB  - selected far function. Thus, they are less likely to he impaired by
AB  - random mutations. Our results also show that H. pylori has extremely
AB  - diversified R-M systems in different strains, and that the diversity
AB  - may be maintained by constantly acquiring new R-M systems and by
AB  - inactivating and deleting the old ones.
ER  -

TY  - JOUR
AU  - Lin, M.J.
AU  - Lee, T.L.
AU  - Hsu, D.W.
AU  - Shen, C.K.
TI  - One-codon alternative splicing of the CpG MTase dnmt1 transcript in mouse somatic cells.
JO  - FEBS Lett.
PY  - 2000
SP  - 101
EP  - 104
VL  - 469
AB  - The genomic methylation patterns in the mammalian somatic cells are presumably maintained by a
AB  - single enzyme, dnmt1. In mouse, this DNA
AB  - (cytosine-5)-methyltransferase, or CpG MTase, is encoded by the Dnmt1 gene. We now present
AB  - evidence that in different tissues and cell types, the primary transcript of
AB  - mouse dnmt1 is alternatively spliced to generate two poly-(A) RNAs of approximately similar
AB  - abundance. This alternative splicing most likely originates from the existence
AB  - of two tandemly arranged acceptor sites separated by only 3 nt. The two Dnmt1 mRNAs thus
AB  - encode two CpG MTases differing by two amino acids. We discuss the
AB  - implications of the discovery of two dnmt1 isozymes, instead of one enzyme as previously
AB  - thought, in the somatic cells of both mouse and human.
ER  -

TY  - JOUR
AU  - Lin, M.J.
AU  - Tang, L.Y.
AU  - Reddy, M.N.
AU  - Shen, C.K.J.
TI  - DNA methyltransferase gene dDnmt2 and longevity of Drosophila.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 861
EP  - 864
VL  - 280
AB  - The DNA methylation program of the fruit fly Drosophila melanogaster is carried out by the
AB  - single DNA methyltransferase gene dDnmt2, the
AB  - function of which is unknown before. We present evidence that
AB  - intactness of the gene is required for maintenance of the normal life
AB  - span of the fruit flies. In contrast, overexpression of dDnmt2 could
AB  - extend Drosophila life span. The study links the Drosophila DNA
AB  - methylation program with the small heatshock proteins and longevity/
AB  - aging and has interesting implication on the eukaryotic DNA methylation
AB  - programs in general.
ER  -

TY  - JOUR
AU  - Lin, N.
AU  - Liu, Z.
AU  - Zhou, J.
AU  - Wang, S.
AU  - Fleming, J.
TI  - Draft Genome Sequences of Two Super-XDR Isolates of M. tuberculosis from China.
JO  - FEMS Microbiol. Lett.
PY  - 2013
SP  - 93
EP  - 96
VL  - 347
AB  - The prevalence of drug-resistance in Mycobacterium tuberculosis is already having a negative
AB  - impact on the control of TB. We report the draft genome sequences of
AB  - two super-extensively drug-resistant (S-XDR) Mycobacterium tuberculosis isolates
AB  - from China, FJ05194 (lineage 2) and GuangZ0019 (lineage 4), and compare them to
AB  - the H37Rv reference strain to identify possible sources of genetic variation
AB  - associated with their extensive drug resistance. Our results suggest that their
AB  - extensive drug resistance most likely results from the stepwise accumulation of
AB  - resistances to individual drugs. This article is protected by copyright. All
AB  - rights reserved.
ER  -

TY  - JOUR
AU  - Lin, P.M.
AU  - Lee, C.H.
AU  - Roberts, R.J.
TI  - Cloning and characterization of the genes encoding the MspI restriction modification system.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 3001
EP  - 3011
VL  - 17
AB  - The genes encoding the MspI restriction modification system, which recognizes
AB  - the sequence 5' CCGG, have been cloned into pUC9.  Selection was based on
AB  - expression of the cloned methylase gene which renders plasmid DNA insensitive
AB  - to MspI cleavage in vitro.  Initially, an insert of 15 kb was obtained which,
AB  - upon subcloning, yielded a 3 kb EcoRI to HindIII insert, carrying the genes for
AB  - both the methylase and the restriction enzyme.  This insert has been sequenced.
AB  - Based upon the sequence, together with appropriate subclones, it is shown that
AB  - the two genes are transcribed divergently with the methylase gene encoding a
AB  - polypeptide of 418 amino acids, while the restriction enzyme is composed of 262
AB  - amino acids.  Comparison of the sequence of the MspI methylase with other
AB  - cytosine methylases shows a striking degree of similarity.  Especially
AB  - noteworthy is the high degree of similarity with the HhaI and EcoRII
AB  - methylases.
ER  -

TY  - JOUR
AU  - Lin, S.Y.
AU  - Shieh, W.Y.
AU  - Chen, J.S.
AU  - Tang, S.L.
TI  - Complete Genome Sequence of Simiduia agarivorans SA1(T), a Marine Bacterium Able  To Degrade a Variety of Polysaccharides.
JO  - Genome Announcements
PY  - 2013
SP  - e00039
EP  - e00012
VL  - 1
AB  - Simiduia agarivorans strain SA1(T) is able to degrade a variety of polysaccharides found in
AB  - marine algae, plants, and animals. The genome of S. agarivorans SA1(T) consists of a single
AB  - chromosome (4,309,711 bp), and its information may provide insights into the
AB  - polysaccharide-degrading capability, cell division, flagellar motility, and chemotaxis of this
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Lin, T.L.
AU  - Shun, C.T.
AU  - Chang, K.C.
AU  - Wang, J.T.
TI  - Isolation and characterization of a HpyC1I restriction-modification system in Helicobacter pylori.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 11156
EP  - 11162
VL  - 279
AB  - Using transposon shuttle mutagenesis, we identified six Helicobacter pylori mutants from the
AB  - NTUH-C1 strain that exhibited decreased adherence and cell elongation. Inverse polymerase
AB  - chain reaction and DNA sequencing revealed that the same locus was interrupted in these six
AB  - mutants. Nucleotide and amino acid sequences showed no homologies with H. pylori 26695 and J99
AB  - strains. This novel open reading frame contained 1617 base pairs. The amino acid sequence
AB  - shared 24% identity with a putative nicking enzyme in Bacillus halodurans and 23 and 20%
AB  - identity with type IIS restriction endonucleases PleI and MlyI, respectively. The purified
AB  - protein, HpyC1I, showed endonuclease activity with the recognition and cleavage site
AB  - 5'-CCATC( 4/5)-3'. Two open reading frames were located upstream of the gene encoding
AB  - HpyC1I. Together, HpyC1I and these two putative methyltransferases (M1.HpyC1I and M2.HpyC1I)
AB  - function as a restriction-modification (R-M) system. The HpyC1I R-M genes were found in 9 of
AB  - the 15 H. pylori strains tested. When compared with the full genome, significantly lower G + C
AB  - content of HpyC1I R-M genes implied that these genes might have been acquired by horizontal
AB  - gene transfer. Plasmid DNA transformation efficiencies and chromosomal DNA digestion assays
AB  - demonstrated protection from HpyC1I digestion by the R-M system. In conclusion, we have
AB  - identified a novel R-M system present in similar to 60% of H. pylori strains. Disruption of
AB  - this R-M system results in cell elongation and susceptibility to HpyC1I digestion.
ER  -

TY  - JOUR
AU  - Lin, W.H.
AU  - Zheng, P.X.
AU  - Liu, T.
AU  - Tseng, C.C.
AU  - Chen, W.C.
AU  - Wang, M.C.
AU  - Wu, J.J.
TI  - Complete Genome Sequence of Community-Acquired Klebsiella pneumoniae KP36, a Strain Isolated from a Patient with an Upper Urinary Tract Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e01403
EP  - e01416
VL  - 4
AB  - Here, we announce the complete genome sequence of Klebsiella pneumoniae KP36, a strain
AB  - isolated from a patient with a severe community-acquired urinary tract
AB  - infection. This genome provides insights into the pathogenesis of a pandemic K.
AB  - pneumoniae strain from a community-acquired urinary tract infection.
ER  -

TY  - JOUR
AU  - Lin, X.
AU  - Wang, Z.
AU  - Li, Y.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain A2, an Isolate with High Antioxidative Activity from Arctic Seawater.
JO  - Genome Announcements
PY  - 2014
SP  - e00885
EP  - e00814
VL  - 2
AB  - Here we report the draft genome sequence of Pseudoalteromonas strain A2, isolated from Arctic
AB  - seawater in the pack-ice zone, which has high antioxidative activity
AB  - against H2O2. The genomics information of this strain will facilitate the study
AB  - of antioxidative mechanisms, cold adaptation properties, and evolution of this
AB  - genus.
ER  -

TY  - JOUR
AU  - Lin, Y.
AU  - Fan, H.
AU  - Hao, X.
AU  - Johnstone, L.
AU  - Hu, Y.
AU  - Wei, G.
AU  - Alwathnani, H.A.
AU  - Wang, G.
AU  - Rensing, C.
TI  - Draft genome sequence of Halomonas sp. Strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil.
JO  - J. Bacteriol.
PY  - 2011
SP  - 199
EP  - 200
VL  - 194
AB  - We report the draft genome sequence of arsenite-oxidizing Halomonas sp. strain HAL1, isolated
AB  - from the soil of a gold mine. Genes encoding proteins involved in arsenic resistance and
AB  - transformation, phosphate utilization and uptake, and betaine biosynthesis were identified.
AB  - Their identification might help in understanding how arsenic and phosphate metabolism are
AB  - intertwined.
ER  -

TY  - JOUR
AU  - Lin, Y.
AU  - Hao, X.
AU  - Johnstone, L.
AU  - Miller, S.J.
AU  - Baltrus, D.A.
AU  - Rensing, C.
AU  - Wei, G.
TI  - Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6408
EP  - 6409
VL  - 193
AB  - A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species
AB  - displaying a high level of resistance to zinc and
AB  - cadmium, is presented here. The genome contains a large number of genes
AB  - encoding proteins predicted to be involved in conferring metal resistance.
AB  - Many of these genes appear to have been acquired through horizontal gene
AB  - transfer.
ER  -

TY  - JOUR
AU  - Lin, Y.T.
AU  - Tsai, J.C.
AU  - Chen, H.J.
AU  - Hung, W.C.
AU  - Hsueh, P.R.
AU  - Teng, L.J.
TI  - A Novel Staphylococcal Cassette Chromosomal Element, SCCfusC, Carrying fusC and speG in Fusidic Acid-Resistant Methicillin-Resistant Staphylococcus aureus.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 1224
EP  - 1227
VL  - 58
AB  - A high prevalence of fusC (16/46, 59%) was found in fusidic acid-resistant
AB  - methicillin-resistant Staphylococcus aureus isolates collected from 2008 to 2010.
AB  - Nucleotide sequencing of fusC and flanking regions revealed a novel
AB  - staphylococcal cassette chromosome (SCC) structure, SCCfusC, which was integrated
AB  - into rlmH and located upstream from SCCmec. The SCCfusC element contained speG,
AB  - which may contribute to the polyamine resistance.
ER  -

TY  - JOUR
AU  - Lin, Z.
AU  - Liu, Z.
AU  - Yang, R.
AU  - Zou, Y.
AU  - Wan, D.
AU  - Chen, J.
AU  - Guo, M.
AU  - Zhao, J.
AU  - Fang, C.
AU  - Yang, R.
AU  - Liu, F.
TI  - Whole-Genome Sequencing of Lactobacillus shenzhenensis Strain LY-73T.
JO  - Genome Announcements
PY  - 2013
SP  - e00972
EP  - e00913
VL  - 1
AB  - Lactobacillus shenzhenensis strain LY-73T is a novel species which was first isolated from
AB  - fermented goods. Here, we report the draft genome sequence of
AB  - Lactobacillus shenzhenensis LY-73T.
ER  -

TY  - JOUR
AU  - Linares, D.M.
AU  - Arboleya, S.
AU  - Ross, R.P.
AU  - Stanton, C.
TI  - Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151.
JO  - Genome Announcements
PY  - 2017
SP  - e00205
EP  - e00217
VL  - 5
AB  - Here is presented the whole-genome sequence of Streptococcus thermophilus APC151, isolated
AB  - from a marine fish. This bacterium produces gamma-aminobutyric acid
AB  - (GABA) in high yields and is biotechnologically suitable to produce naturally
AB  - GABA-enriched biofunctional yogurt. Its complete genome comprises 2,097 genes and
AB  - 1,839,134 nucleotides, with an average G+C content of 39.1%.
ER  -

TY  - JOUR
AU  - Linares, D.M.
AU  - Kok, J.
AU  - Poolman, B.
TI  - Genome Sequences of Lactococcus lactis MG1363 (Revised) and NZ9000 and Comparative Physiological Studies.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5806
EP  - 5812
VL  - 192
AB  - Lactococcus lactis NZ9000 and its parent MG1363 are the most commonly used lactic acid
AB  - bacteria for expression and physiological studies. We noted
AB  - unexpected but significant differences in the growth behaviors of both
AB  - strains. We sequenced the entire genomes of the original NZ9000 and MG1363
AB  - strains using an ultradeep sequencing strategy. The analysis of the L.
AB  - lactis NZ9000 genome yielded 79 differences, mostly point mutations, with
AB  - the annotated genome sequence of L. lactis MG1363. Resequencing of the
AB  - MG1363 strain revealed that 73 out of the 79 differences were due to
AB  - errors in the published sequence. Comparative transcriptomic studies
AB  - revealed several differences in the regulation of genes involved in sugar
AB  - fermentation, which can be explained by two specific mutations in a region
AB  - of the ptcC promoter with a key role in the regulation of cellobiose and
AB  - glucose uptake.
ER  -

TY  - JOUR
AU  - Lincoln, S.A.
AU  - Hamilton, T.L.
AU  - Valladares, J.A.G.
AU  - Schedler, M.
AU  - Macalady, J.L.
AU  - Muller, R.
AU  - Freeman, K.H.
TI  - Draft Genome Sequence of the Piezotolerant and Crude Oil-Degrading Bacterium Rhodococcus qingshengii Strain TUHH-12.
JO  - Genome Announcements
PY  - 2015
SP  - e00268
EP  - e00215
VL  - 3
AB  - We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12. The
AB  - ability of this piezotolerant bacterium to grow on crude oil and
AB  - tetracosane as sole carbon sources at 150 x 10(5) Pa makes it useful in studies
AB  - of hydrocarbon degradation under simulated deep-sea conditions.
ER  -

TY  - JOUR
AU  - Lindahl, T.
TI  - Enzymatic methylation of DNA - Roles and prospects.
JO  - Biol. Chem.
PY  - 1998
SP  - 375
EP  - 376
VL  - 379
AB  - The occurrence of a fifth base in the DNA of mammalian cells and plant cells has been known
AB  - for close to fifty years.  However, the difficulties in relating 5-methylcytosine residues to
AB  - specific functional roles, and the apparent absence of such DNA residues in the intensely
AB  - studied eukaryotes Drosophila melanogaster and Saccharomyces cerevisiae, meant there were
AB  - relatively few investigations carried out on DNA methylation until recently.  New data on DNA
AB  - methylation as a mechanism for silencing of gene expression and its involvement in other
AB  - aspects of epigenetic control in mammalian cells, as well as the embryonic lethal phenotype of
AB  - gene knockout mouse constructs lacking the methyltransferase required for maintenance
AB  - methylation, have greatly increased the amount of activity in the field.  Nevertheless,
AB  - several potentially important aspects, such as the complicated perturbations of DNA
AB  - methylation patterns in cancer cells involving both hypermethylation and hypomethylation, and
AB  - the mechanisms of de novo methylation and demethylation, are still at very early stages of
AB  - investigation.  The merging data on eukaryotes may be contrasted with the, by now, well
AB  - established roles of DNA methylation in bacteria.  This occurs at DNA adenine as well as
AB  - cytosine residues, and serves to protect the genome from endogenous restriction endonucleases
AB  - as well as providing a strategy for strand discrimination in mismatch repair immediately after
AB  - DNA replication.
ER  -

TY  - JOUR
AU  - Linder, P.
AU  - Doelz, R.
AU  - Gubler, M.
AU  - Bickle, T.A.
TI  - An anticodon nuclease gene inserted into a hsd region encoding a type I DNA restriction system.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 7170
EP  - 7170
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Lindler, L.E.
AU  - Plano, G.V.
AU  - Burland, V.
AU  - Mayhew, G.F.
AU  - Blattner, F.R.
TI  - Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen.
JO  - Infect. Immun.
PY  - 1998
SP  - 5731
EP  - 5742
VL  - 66
AB  - Yersinia pestis, the causative agent of plague, harbors at least three plasmids necessary for
AB  - full virulence of the organism, two of which are
AB  - species specific. One of the Y. pestis-specific plasmids, pMT1, is thought
AB  - to promote deep tissue invasion, resulting in more acute onset of symptoms
AB  - and death. We determined the entire nucleotide sequence of Y. pestis KIM5
AB  - pMT1 and identified potential open reading frames (ORFs) encoded by the
AB  - 100,990-bp molecule. Based on codon usage for known yersinial genes,
AB  - homology with known proteins in the databases, and potential ribosome
AB  - binding sites, we determined that 115 of the potential ORFs which we
AB  - considered could encode polypeptides in Y. pestis. Five of these ORFs were
AB  - genes previously identified as being necessary for production of the
AB  - classic virulence factors, murine toxin (MT), and the fraction 1 (F1)
AB  - capsule antigen. The regions of pMT1 encoding MT and F1 were surrounded by
AB  - remnants of multiple transposition events and bacteriophage, respectively,
AB  - suggesting horizontal gene transfer of these virulence factors. We
AB  - identified seven new potential virulence factors that might interact with
AB  - the mammalian host or flea vector. Forty-three of the remaining 115
AB  - putative ORFs did not display any significant homology with proteins in
AB  - the current databases. Furthermore, DNA sequence analysis allowed the
AB  - determination of the putative replication and partitioning regions of
AB  - pMT1. We identified a single 2,450-bp region within pMT1 that could
AB  - function as the origin of replication, including a RepA-like protein
AB  - similar to RepFIB, RepHI1B, and P1 and P7 replicons. Plasmid partitioning
AB  - function was located ca. 36 kb from the putative origin of replication and
AB  - was most similar to the parABS bacteriophage P1 and P7 system. Y. pestis
AB  - pMT1 encoded potential genes with a high degree of similarity to a wide
AB  - variety of organisms, plasmids, and bacteriophage. Accordingly, our
AB  - analysis of the pMT1 DNA sequence emphasized the mosaic nature of this
AB  - large bacterial virulence plasmid and provided implications as to its
AB  - evolution.
ER  -

TY  - JOUR
AU  - Lindroth, A.M.
AU  - Cao, X.
AU  - Jackson, J.P.
AU  - Zilberman, D.
AU  - McCallum, C.M.
AU  - Henikoff, S.
AU  - Jacobsen, S.E.
TI  - Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
JO  - Science
PY  - 2001
SP  - 2077
EP  - 2080
VL  - 292
AB  - Epigenetic silenced alleles of the Arabidopsis SUPERMAN locus (the clark kent alleles) are
AB  - associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites,
AB  - where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent
AB  - mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3 (CMT3), a novel cytosine
AB  - methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit
AB  - decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They
AB  - also show reactivated expression of endogenous retrotransposon sequences. These results show
AB  - that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.
ER  -

TY  - JOUR
AU  - Lindsay, J.A.
TI  - Genomic variation and evolution of Staphylococcus aureus.
JO  - Int. J. Med. Microbiol.
PY  - 2010
SP  - 98
EP  - 103
VL  - 300
AB  - The evolution of new human and animal pathogenic strains of Staphylococcus aureus has been due
AB  - to the accumulation of mobile genetic elements (MGE) encoding methicillin resistance and
AB  - virulence factors into successful lineages. These include epidemic methicillin-resistant S.
AB  - aureus in hospitals (EMRSA), community-associated MRSA (CA-MRSA), fully vancomycin-resistant
AB  - MRSA (VRSA) and livestock-associated MRSA (LA-MRSA). The S. aureus population in humans is
AB  - dominated by about ten S. aureus lineages while animals generally have different lineages.
AB  - Individual isolates within each lineage have unique combination of MGE often encoding
AB  - virulence and resistance genes. S. aureus evolves due to point mutation and selection, but
AB  - also dramatically due to the horizontal transfer of these MGE between strains or from other
AB  - species or genera. Horizontal transfer, by conjugation or transduction, can be blocked by S.
AB  - aureus restriction modification systems which are lineage specific. Because of the mobility of
AB  - MGE, there are prospects for increasingly Virulent and resistant Strains to emerge that could
AB  - severely affect healthcare and agriculture more effectively than the current pathogens.
ER  -

TY  - JOUR
AU  - Lindsay, J.A.
TI  - Staphylococcus aureus genomics and the impact of horizontal gene transfer.
JO  - Int. J. Med. Microbiol.
PY  - 2014
SP  - 103
EP  - 109
VL  - 304
AB  - Whole genome sequencing and microarrays have revealed the population structure of
AB  - Staphylococcus aureus, and identified epidemiological shifts, transmission routes, and
AB  - adaptation of major clones. S. aureus genomes are highly diverse. This is partly due to a
AB  - population structure of conserved lineages, each with unique combinations of genes encoding
AB  - surface proteins, regulators, immune evasion and virulence pathways. Even more variable are
AB  - the mobile genetic elements (MGE), which encode key proteins for antibiotic resistance,
AB  - virulence and host-adaptation. MGEs can transfer at high frequency between isolates of the
AB  - same lineage by horizontal gene transfer (HGT). There is increasing evidence that HGT is key
AB  - to bacterial adaptation and success. Recent studies have shed light on new mechanisms of DNA
AB  - transfer such as transformation, the identification of receptors for transduction, on
AB  - integration of DNA pathways, mechanisms blocking transfer including CRISPR and new restriction
AB  - systems, strategies for evasion of restriction barriers, as well as factors influencing MGE
AB  - selection and stability. These studies have also lead to new tools enabling construction of
AB  - genetically modified clinical S. aureus isolates. This review will focus on HGT mechanisms and
AB  - their importance in shaping the evolution of new clones adapted to antibiotic resistance,
AB  - healthcare, communities and livestock.
ER  -

TY  - JOUR
AU  - Lindsey, R.L.
AU  - Batra, D.
AU  - Rowe, L.
AU  - Loparev, V.N.
AU  - Juieng, P.
AU  - Garcia-Toledo, L.
AU  - Bicknese, A.
AU  - Stripling, D.
AU  - Martin, H.
AU  - Chen, J.
AU  - Strockbine, N.
AU  - Trees, E.
TI  - High-Quality Draft Genome Sequences for Four Drug-Resistant or Outbreak-Associated Shigella sonnei Strains Generated with PacBio Sequencing and   Whole-Genome Maps.
JO  - Genome Announcements
PY  - 2017
SP  - e00906
EP  - e00917
VL  - 5
AB  - Drug-resistant Shigella sonnei poses a clinical and public health challenge. We report here
AB  - the high-quality draft whole-genome sequences of four
AB  - outbreak-associated S. sonnei isolates; three were resistant to two or more
AB  - antibiotics, and one was resistant to streptomycin only.
ER  -

TY  - JOUR
AU  - Lindsey, R.L.
AU  - Batra, D.
AU  - Rowe, L.
AU  - Loparev, V.N.
AU  - Stripling, D.
AU  - Garcia-Toledo, L.
AU  - Knipe, K.
AU  - Juieng, P.
AU  - Sheth, M.
AU  - Martin, H.
AU  - Laufer, H.A.
TI  - High-Quality Genome Sequence of an Escherichia coli O157 Strain Carrying an mcr-1 Resistance Gene Isolated from a Patient in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e01725
EP  - e01716
VL  - 5
AB  - Enterobacteriaceae carrying plasmid-mediated colistin resistance have been found  around the
AB  - world. We report here the high-quality whole-genome sequence of an
AB  - Escherichia coli O157:H48 isolate (2016C-3936C1) from Connecticut that carried
AB  - the mcr-1 resistance gene on an IncX4-type plasmid.
ER  -

TY  - JOUR
AU  - Lindsey, R.L.
AU  - Batra, D.
AU  - Smith, P.
AU  - Patel, P.N.
AU  - Tagg, K.A.
AU  - Garcia-Toledo, L.
AU  - Loparev, V.N.
AU  - Juieng, P.
AU  - Sheth, M.
AU  - Joung, Y.J.
AU  - Rowe, L.A.
TI  - PacBio Genome Sequences of Escherichia coli Serotype O157:H7, Diffusely Adherent  E. coli, and Salmonella enterica Strains, All Carrying Plasmids with an mcr-1 Resistance Gene.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01025
EP  - e01018
VL  - 7
AB  - We report here Illumina-corrected PacBio whole-genome sequences of an Escherichia coli
AB  - serotype O157:H7 strain (2017C-4109), an E. coli serotype O[undetermined]:H2
AB  - strain (2017C-4173W12), and a Salmonella enterica subsp. enterica serovar
AB  - Enteritidis strain (2017K-0021), all of which carried the mcr-1 resistance gene
AB  - on an IncI2 or IncX4 plasmid. We also determined that pMCR-1-CTSe is identical to
AB  - a previously published plasmid, pMCR-1-CT.
ER  -

TY  - JOUR
AU  - Lindsey, R.L.
AU  - Knipe, K.
AU  - Rowe, L.
AU  - Garcia-Toledo, L.
AU  - Loparev, V.
AU  - Juieng, P.
AU  - Trees, E.
AU  - Strockbine, N.
AU  - Stripling, D.
AU  - Gerner-Smidt, P.
TI  - Complete Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains from Serotypes O119:H4 and O165:H25.
JO  - Genome Announcements
PY  - 2015
SP  - e01496
EP  - e01415
VL  - 3
AB  - Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. Here, we
AB  - report complete whole-genome sequences for two STEC strains of serotypes
AB  - O119:H4 and O165:H25 isolated from clinical cases in the United States.
ER  -

TY  - JOUR
AU  - Lindsey, R.L.
AU  - Rowe, L.
AU  - Garcia-Toledo, L.
AU  - Loparev, V.
AU  - Knipe, K.
AU  - Stripling, D.
AU  - Martin, H.
AU  - Trees, E.
AU  - Juieng, P.
AU  - Batra, D.
AU  - Strockbine, N.
TI  - High-Quality Draft Genome Sequences for Five Non-O157 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing and Optical Maps.
JO  - Genome Announcements
PY  - 2016
SP  - e00626
EP  - e00616
VL  - 4
AB  - Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen. We report  here the
AB  - high-quality draft whole-genome sequences of five STEC strains isolated  from clinical cases
AB  - in the United States. This report is for STEC of serotypes O55:H7, O79:H7, O91:H14, O153:H2,
AB  - and O156:H25.
ER  -

TY  - JOUR
AU  - Lindsey, R.L.
AU  - Trees, E.
AU  - Sammons, S.
AU  - Loparev, V.
AU  - Frace, M.
AU  - Strockbine, N.
AU  - Sabol, A.L.
AU  - Sowers, E.
AU  - Stripling, D.
AU  - Martin, H.
AU  - Knipe, K.
AU  - Rowe, L.
AU  - Gerner-Smidt, P.
TI  - Draft Whole-Genome Sequences of Nine Non-O157 Shiga Toxin-Producing Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00501
EP  - e00514
VL  - 2
AB  - Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen. Here, we
AB  - report the draft whole-genome sequences of nine STEC strains
AB  - isolated from clinical cases in the United States. This is the first report of
AB  - such information for STEC of serotypes O69, H11, O145:H25, O118:H16, O91:H21,
AB  - O146:H21, O45:H2, O128:H2, and O121:H19.
ER  -

TY  - JOUR
AU  - Lindstrom, W.M. Jr.
TI  - The enzymology of bacterial dna methyltransferases.
JO  - Ph.D. Thesis, Univ. of California, Santa Barbara
PY  - 2000
SP  - 109
EP  - 109
AB  - DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzymne
AB  - specificity because catalysis requires the extrahelical stabilization of the target base
AB  - within the enzyme active site.  Equilibrium dissociation constants were determined for the
AB  - binding of the DNA (adenine-N6-)-methyltransferase M.EcoRI to DNA containing abasic sites and
AB  - base analogs incorporated at the target base.  Tighter binding to oligonucleotides containing
AB  - destabilized target base pairs was observed, corroborating spectroscopic evidence for
AB  - nucleoside flipping by that enzyme.
ER  -

TY  - JOUR
AU  - Lindstrom, W.M. Jr.
AU  - Flynn, J.
AU  - Reich, N.O.
TI  - HhaI DNA cytosine-C5 methyltransferase: Reconciling function and structure.
JO  - FASEB J.
PY  - 1999
SP  - A1443
EP  - A1443
VL  - 13
AB  - HhaI DNA methyltransferase utilizes S-adenosyl-L-methionine to modify the 5-carbon of the
AB  - inner cytosine in the cognate sequence 5'-GCGC-3'.  We directly demonstrate the catalytic
AB  - competence of the enzyme-DNA complex, and the catalytic incompetence of the enzyme-AdoMet
AB  - complex.  Formation of the dead-end enzyme-AdoMet complex is consistent with the AdoMet
AB  - binding observed by x-ray crystallographic analysis of the binary complex.  The enzyme has a
AB  - two-fold preference for unmethylated over hemimethylated DNA based on kcat/KmDNA.  The methyl
AB  - transfer step contributes little to this discrimination, in contrast to the mammalian DNA
AB  - cytosine methyltransferase.  Surprisingly, in the absence of any cofactor, the enzyme binds
AB  - hemimethylated DNA seven-fold more tightly than unmethylated DNA.  This overall DNA binding
AB  - affinity is increased 10,000-fold and the preference for hemimethylated DNA is enhanced to
AB  - greater than 140-fold in the ternary enzyme-DNA-cofactor complex.  The differential binding
AB  - affinities of hemi- and unmethylated substrates directly alter how the enzyme processes its
AB  - substrate during the catalytic cycle.  Our functional characterization is presented in the
AB  - context of the available co-crystal structures of the enzyme-hemimethylated DNA-cofactor,
AB  - enzyme-unmethylated DNA-cofactor, and enzyme-AdoMet complexes.  The combined functional and
AB  - structural analyses provide insight into the discrimination of hemi- and unmethylated DNA, and
AB  - the methyl transfer step, and comparisons with the mammalian DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Lindstrom, W.M. Jr.
AU  - Malygin, E.G.
AU  - Ovechkina, L.G.
AU  - Zinoviv, V.V.
AU  - Reich, N.O.
TI  - Functional analysis of BamHI DNA cytosine-N4 methyltransferase.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 711
EP  - 720
VL  - 325
AB  - We show that the kinetic mechanism of the DNA (cytosine-N(4)-)-methyltransferase M.BamHI,
AB  - which modifies the underlined
AB  - cytosine (GGATCC), differs from cytosine C(5) methyltransferases, and is
AB  - similar to that observed with adenine N(6) methyltransferases. This
AB  - suggests that the obligate order of ternary complex assembly and
AB  - disassembly depends on the type of methylation reaction. In contrast, the
AB  - single-turnover rate of catalysis for M.BamHI (0.10s(-1)) is closer to the
AB  - DNA (cytosine-C(5)-)-methyltransferases (0.14s(-1)) than the DNA
AB  - (adenine-N(6)-)-methyltransferases (>200s(-1)). The nucleotide flipping
AB  - transition dominates the single-turnover constant for adenine N(6)
AB  - methyltransferases, and, since the disruption of the guanine-cytosine
AB  - base-pair is essential for both types of cytosine DNA methyltransferases,
AB  - this transition may be a common, rate-limiting step for methylation for
AB  - these two enzyme subclasses. The similar overall rate of catalysis by
AB  - M.BamHI and other DNA methyltransferases is consistent with a common
AB  - rate-limiting catalytic step of product dissociation. Our analyses of
AB  - M.BamHI provide functional insights into the relationship between the
AB  - three different classes of DNA methyltransferases that complement both
AB  - prior structural and evolutionary insights.
ER  -

TY  - JOUR
AU  - Lindstrom, W.M.
AU  - Flynn, J.
AU  - Reich, N.O.
TI  - Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 4912
EP  - 4919
VL  - 275
AB  - Pre-steady state partitioning analysis of the HhaI DNA methyltransferase directly demonstrates
AB  - the catalytic competence of the
AB  - enzyme DNA complex and the lack of catalytic competence of the
AB  - enzyme-S-adenosyl-L-methionine (AdoMet) complex. The enzyme.AdoMet
AB  - complex does form, albeit with a 50-fold decrease in affinity compared
AB  - with the ternary enzyme.AdoMet.DNA complex. These findings reconcile
AB  - the distinct binding orientations previously observed within the binary
AB  - enzyme.AdoMet and ternary enzyme.S-adenosyl-L-homocysteine.DNA crystal
AB  - structures. The affinity of the enzyme for DNA is increased 900-fold in
AB  - the presence of its cofactor, and the preference for hemimethylated DNA
AB  - is increased to 12-fold over unmethylated DNA We suggest that this
AB  - preference is partially due to the energetic cost of retaining a cavity
AB  - in place of the B-methyl moiety in the ternary complex with the
AB  - unmethylated DNA, as revealed by the corresponding crystal structures.
AB  - The hemi- and unmethylated substrates alter the fates and lifetimes of
AB  - discrete enzyme substrate intermediates during the catalytic cycle.
AB  - Hemimethylated substrates partition toward product formation versus
AB  - dissociation significantly more than unmethylated substrates. The
AB  - mammalian DNA cytosine-C-5 methyltransferase Dnmt1 shows an even more
AB  - pronounced partitioning toward product formation.
ER  -

TY  - JOUR
AU  - Ling, J.
AU  - Lin, L.
AU  - Zhang, Y.
AU  - Lin, X.
AU  - Ahamad, M.
AU  - Zhou, W.
AU  - Dong, J.
TI  - Draft Genome Sequence of Marinobacter hydrocarbonoclasticus Strain STW2, a Polycyclic Aromatic Hydrocarbon-Degrading and Denitrifying Bacterium from the  Rhizosphere of Seagrass Enhalus acodoides.
JO  - Genome Announcements
PY  - 2017
SP  - e01412
EP  - e01416
VL  - 5
AB  - Here, we report the draft genome sequence of Marinobacter hydrocarbonoclasticus strain STW2,
AB  - which was isolated from the rhizosphere of seagrass Enhalus
AB  - acodoides This study will facilitate future studies on the genetic pathways of
AB  - marine microbes capable of both polycyclic aromatic hydrocarbon degradation and
AB  - nitrate reduction.
ER  -

TY  - JOUR
AU  - Ling, Y.
AU  - Sankpal, U.T.
AU  - Robertson, A.K.
AU  - McNally, J.G.
AU  - Karpova, T.
AU  - Robertson, K.D.
TI  - Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 598
EP  - 610
VL  - 32
AB  - The de novo DNA methyltransferase Dnmt3a is one of three mammalian DNA methyltransferases that
AB  - has been shown to play crucial roles in embryonic development, genomic imprinting and
AB  - transcriptional silencing. Despite its importance, very little is known about how the
AB  - enzymatic activity and transcriptional repression functions of Dnmt3a are regulated. Here we
AB  - show that Dnmt3a interacts with multiple components of the sumoylation machinery, namely the
AB  - E2 sumo conjugating enzyme Ubc9 and the E3 sumo ligases PIAS1 and PIASx , all of which are
AB  - involved in conjugating the small ubiquitin-like modifier polypeptide, SUMO-1, to its target
AB  - proteins. Dnmt3a is modified by SUMO-1 in vivo and in vitro and the region of Dnmt3a
AB  - responsible for interaction maps to the N-terminal regulatory domain. Functionally,
AB  - sumoylation of Dnmt3a disrupts its ability to interact with histone deacetylases (HDAC1/2),
AB  - but not with another interaction partner, Dnmt3b. Conditions that enhance the sumoylation of
AB  - Dnmt3a in vivo abolish its capacity to repress transcription. These studies reveal a new level
AB  - of regulation governing Dnmt3a whereby a post-translational modification can dramatically
AB  - regulate its interaction with specific protein partners and alter its ability to repress
AB  - transcription.
ER  -

TY  - JOUR
AU  - Ling, Y.H.
AU  - Nelson, J.A.
AU  - Chan, J.Y.
AU  - Beattie, K.L.
TI  - 6-Thioguanine substituted DNA as a substrate for restriction endonucleases and ligases.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1992
SP  - 543
EP  - 543
VL  - 33
ER  -

TY  - JOUR
AU  - Linn, S.
TI  - The 1978 Nobel prize in physiology or medicine.
JO  - Science
PY  - 1978
SP  - 1069
EP  - 1071
VL  - 202
AB  - The 1978 Nobel Prize in Physiology or Medicine was awarded to Werner Arber, 49, of the
AB  - Biozentrum in Basel, Switzerland; Hamilton O. Smith, 47 of Johns Hopkins University; and to
AB  - Daniel Nathans, 50, also of Johns Hopkins University.  The awards recognize the development of
AB  - restriction endonucleases, enzymes that can be used to study genetic organization and to
AB  - manipulate DNA for "genetic engineering".  Arber is credited with having first predicted the
AB  - existence of the enzymes, Smith with having isolated the first such enzyme and describing its
AB  - specific reaction, and Nathans with having first applied these enzymes to the study of gene
AB  - organization and regulation.
ER  -

TY  - JOUR
AU  - Linn, S.
AU  - Arber, W.
TI  - Host specificity of DNA produced by Escherichia coli, X.  In vitro restriction of phage fd replicative form.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1968
SP  - 1300
EP  - 1306
VL  - 59
AB  - An activity has been found in fractionated extracts from Escherichia coli which
AB  - reduces the infectivity of the replicative form of phage fd DNA.  It is
AB  - correlated with the in vivo restriction phenomenon by (1) its presence only in
AB  - fractions from restricting strains of bacteria and (2) its specificity for
AB  - nonmodified DNA.  The inactivation requires S-adenosylmethionine, ATP, Mg++,
AB  - and the products of at least two gene functions; it seems to be accompanied by
AB  - double-strand cleavage of the DNA.
ER  -

TY  - JOUR
AU  - Linn, S.
AU  - Lautenberger, J.A.
AU  - Eskin, B.
AU  - Lackey, D.
TI  - Host-controlled restriction and modification enzymes of Escherichia coli B1,2.
JO  - Fed. Proc.
PY  - 1974
SP  - 1128
EP  - 1134
VL  - 33
AB  - The Escherichia coli B modification methylase transfers a methyl group from
AB  - S-adenosylmethionine to DNA in a reaction wherein the enzyme may not turn over.
AB  - The corresponding restriction endonuclease puts one nick into the DNA, or
AB  - converts a previously placed restriction nick into a double-strand break in a
AB  - reaction which requires ATP and S-adenosylmethionine.  The DNA is not cleaved
AB  - at the specific recognition site, as demonstrated by centrifugational and
AB  - electrophoretic analyses and the fact that restricted DNA can be methylated by
AB  - the modification enzyme.  After the DNase event, the enzyme no longer cleaves
AB  - DNA, but forms a complex with S-adenosylmethionine and the DNA molecule which
AB  - it has restricted.  This complex actively hydrolyzes ATP to ADP and Pi.  The
AB  - modification enzyme exists in several forms, each having in some ratio the
AB  - polypeptides b and c, and a (molecular weight, 135,000).  In vitro
AB  - complementation analyses demonstrate that b and c from modification enzyme are
AB  - active in a restriction reaction when mixed with a factor that appears to be
AB  - the alpha-subunit.  These results are compatible with the genetic analysis of
AB  - the system.  The nature of the recognition site and the complexity of the
AB  - restriction reaction are discussed.
ER  -

TY  - JOUR
AU  - Linz, B.
AU  - Windsor, H.M.
AU  - Gajewski, J.P.
AU  - Hake, C.M.
AU  - Drautz, D.I.
AU  - Schuster, S.C.
AU  - Marshall, B.J.
TI  - Helicobacter pylori genomic microevolution during naturally occurring transmission between adults.
JO  - PLoS ONE
PY  - 2013
SP  - e82187
EP  - e82187
VL  - 8
AB  - The human gastric pathogen Helicobacter pylori is usually acquired during childhood and, in
AB  - the absence of treatment, chronic infection persists through most of the host's life.
AB  - However, the frequency and importance of H. pylori transmission between adults is
AB  - underestimated. Here we sequenced the complete genomes of H. pylori strains
AB  - that were transmitted between spouses and analysed the genomic changes. Similar to H. pylori
AB  - from chronic infection, a significantly high proportion of the determined 31 SNPs and 10
AB  - recombinant DNA fragments affected
AB  - genes of the hop family of outer membrane proteins, some of which are known to be adhesins. In
AB  - addition, changes in a fucosyltransferase gene modified the LPS component of the bacterial
AB  - cell surface, suggesting strong diversifying selection. In contrast, virulence factor genes
AB  - were not affected by the genomic changes. We propose a model of the genomic changes that are
AB  - associated with the transmission and adaptation of H. pylori to a new human host.
ER  -

TY  - JOUR
AU  - Linz, B.
AU  - Windsor, H.M.
AU  - McGraw, J.J.
AU  - Hansen, L.M.
AU  - Gajewski, J.P.
AU  - Tomsho, L.P.
AU  - Hake, C.M.
AU  - Solnick, J.V.
AU  - Schuster, S.C.
AU  - Marshall, B.J.
TI  - A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques.
JO  - Nat. Commun.
PY  - 2014
SP  - 4165
EP  - 4165
VL  - 5
AB  - The evolution rate and genetic changes that occur during chronic infection with Helicobacter
AB  - pylori have been analysed, but little is known about the genomic changes during the initial,
AB  - acute bacterial infection phase.  Here we analyse the rate and pattern of genome evolution in
AB  - H. pylori from the genomes of two input strains isolated from human volunteers with
AB  - asymptomatic infection, and the genomes of two output strains collected 20 and 44 days after
AB  - re-infection.  Similarly, we analyse genome evolution in bacteria from the genome sequences of
AB  - input and output strains sequentially taken after experimental infection of a rhesus macaque.
AB  - The estimated mutation rate reveals a mutation burst during the acute infection phase that is
AB  - over 10 times faster than the mutation rate during chronic infection, and orders of magnitude
AB  - faster than mutation rates in any other bacteria.  The elevated frequency of mutations in
AB  - outer membrane protein genes suggests that the mutation burst facilitates rapid host
AB  - adaptation of the bacteria.
ER  -

TY  - JOUR
AU  - Lio, P.
AU  - Vannucci, M.
TI  - Finding pathogenicity islands and gene transfer events in genome data.
JO  - Bioinformatics
PY  - 2000
SP  - 932
EP  - 940
VL  - 16
AB  - Motivation: There is a growing literature on wavelet theory and wavelet methods showing
AB  - improvements on more classical techniques, especially in the contexts of smoothing and
AB  - extraction of fundamental components of signals. G+C patterns occur at different lengths
AB  - (scales) and, for this reason, G+C plots are usually difficult to interpret. Current methods
AB  - for genome analysis choose a window size and compute a Chi-squared statistics of the average
AB  - value for each window with respect to the whole genome. Results: Firstly, wavelets are used to
AB  - smooth G+C profiles to locate characteristic patterns in genome sequences. The method we use
AB  - is based on performing a Chi-squared statistics on the wavelet coefficients of a profile; thus
AB  - we do not need to choose a fixed window size, in that the smoothing occurs at a set of
AB  - different scales. Secondly, a wavelet scalogram is used as a measure for sequence profile
AB  - comparison; this tool is very general and can be applied to other sequence profiles commonly
AB  - used in genome analysis. We show applications to the analysis of Deinococcus radiodurans
AB  - chromosome I, of two strains of Helicobacter pylori (26695, J99) and two of Neisseria
AB  - meningitidis (serogroup B strain MC58 and serogroup A strain Z2491).  We report a list of loci
AB  - that have different G+C content with respect to the nearby regions; the analysis of N.
AB  - meningitidis serogroup B shows two new large regions with low G+C content that are putative
AB  - pathogenicity islands. Availability: Software and numerical results (profiles, scalograms,
AB  - high and low frequency components) for all the genome sequences analyzed are available upon
AB  - request from the authors.
ER  -

TY  - JOUR
AU  - Liolios, K. et al.
TI  - Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 30
EP  - 40
VL  - 5
AB  - Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus  Pedobacter
AB  - within the family Sphingobacteriaceae. The species is of interest for
AB  - its isolated location in the tree of life. Like other members of the genus P.
AB  - saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing
AB  - motility and can be distinguished from other Pedobacter strains by their ability
AB  - to utilize glycerol and the inability to assimilate D-cellobiose. The genome
AB  - presented here is only the second completed genome sequence of a type strain from
AB  - a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long
AB  - genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome,
AB  - and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Liolios, K. et al.
TI  - Complete genome sequence of Thermobispora bispora type strain (R51).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 318
EP  - 326
VL  - 2
AB  - Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the  genus
AB  - Thermobispora. This genus is of great interest because it is strictly
AB  - thermophilic and because it has been shown for several of its members that the
AB  - genome contains substantially distinct (6.4% sequence difference) and
AB  - transcriptionally active 16S rRNA genes. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. This is the
AB  - second completed genome sequence of a member from the suborder
AB  - Streptosporangineae and the first genome sequence of a member of the genus
AB  - Thermobispora. The 4,189,976 bp long genome with its 3,596 protein-coding and 63
AB  - RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Liolos, K. et al.
TI  - Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 165
EP  - 176
VL  - 8
AB  - Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped
AB  - bacterium that is motile via periplasmic flagella. The type strain
AB  - of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom
AB  - in the brine under the trona layer in a shallow lagoon of the alkaline equatorial
AB  - Lake Magadi in Kenya. Here we describe the features of this organism, together
AB  - with the complete genome sequence, and annotation. Considering the pending
AB  - reclassification of S. caldaria to the genus Treponema, S. africana is only the
AB  - second 'true' member of the genus Spirochaeta with a genome-sequenced type strain
AB  - to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817
AB  - protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B
AB  - acteria and A rchaea project.
ER  -

TY  - JOUR
AU  - Liou, M.L.
AU  - Liu, C.C.
AU  - Lu, C.W.
AU  - Hsieh, M.F.
AU  - Chang, K.C.
AU  - Kuo, H.Y.
AU  - Lee, C.C.
AU  - Chang, C.T.
AU  - Yang, C.Y.
AU  - Tang, C.Y.
TI  - Genome Sequence of Acinetobacter baumannii TYTH-1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6974
EP  - 6974
VL  - 194
AB  - Acinetobacter baumannii has emerged recently as a major cause of health care-associated
AB  - infections due to the extent of its antimicrobial resistance and
AB  - its propensity to cause large nosocomial outbreaks. Here we report the genome
AB  - sequence of Acinetobacter baumannii TYTH-1 isolated in Taiwan during 2008.
ER  -

TY  - JOUR
AU  - Lippmann, J.E.
AU  - Wu, H.
AU  - Fives-Taylor, P.M.
TI  - Directed mutagenesis of the DNA-adenine-methyltransferase (DAM) gene in Actinobacillus actinomycetemcomitans (Aa) by conjugation.
JO  - J. Dent. Res.
PY  - 2002
SP  - A
EP  - 145
VL  - 81
AB  - Actinobacillus actinomycetemcomitans (Aa) is a slow growing, fastidious, Gram-negative,
AB  - capnophillic bacterium.  Of the over 500 different organisms in the oral cavity, Aa is one
AB  - which has been strongly implicated in juvenile and adult periodontis.  Aa manifests disease by
AB  - its ability to produce toxins, adhere to and invade epithelial cells.
AB  - DNA-adenine-methyltransferase (DAM) is generally associated with DNA modification, but it may
AB  - also act as a global regulator of gene expression in many organisms.  By adding methyl groups
AB  - to various sites along the genome, DAM alters the interactions of regulatory proteins with
AB  - their target genes.  Recently, virulence genes in Salmonella strains have been shown to be
AB  - modulated by DAM methylation.  Objectives:  To create a DAM minus strain of Aa SUNY465 for use
AB  - in evaluating the role of DAM in Aa virulence.  Methods: The dam gene was cloned and
AB  - sequenced.  The PCR-amplified gene was disrupted by insertion of an antibiotic cassette into a
AB  - unique blunt ended restriction site.  The disrupted gene was cloned into a conjugative plasmid
AB  - and transferred from E. coli SM10(lpir) to Aa.  Results: The insertional mutation resulted in
AB  - the loss of Dam methylation of the Aa genome as shown by restriction analysis using DpnI &
AB  - DpnII endonucleases, which cleave DNA at methylated and non-methylated sites, respectively.
AB  - Confirmation of the genetic mutation was confirmed by colony PCR and Southern blot analysis.
AB  - Conclusion: The chromosomal gene coding for DNA-adenine-methyltransferase of A.
AB  - actinomycetemcomitans has been cloned, sequenced, and disrupted.
ER  -

TY  - JOUR
AU  - Lippow, S.M.
AU  - Aha, P.M.
AU  - Parker, M.H.
AU  - Blake, W.J.
AU  - Baynes, B.M.
AU  - Lipovsek, D.
TI  - Creation of a type IIS restriction endonuclease with a long recognition sequence.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3061
EP  - 3073
VL  - 37
AB  - Type IIS restriction endonucleases cleave DNA outside their recognition sequences, and are
AB  - therefore particularly useful in the assembly of DNA
AB  - from smaller fragments. A limitation of type IIS restriction endonucleases
AB  - in assembly of long DNA sequences is the relative abundance of their
AB  - target sites. To facilitate ligation-based assembly of extremely long
AB  - pieces of DNA, we have engineered a new type IIS restriction endonuclease
AB  - that combines the specificity of the homing endonuclease I-SceI with the
AB  - type IIS cleavage pattern of FokI. We linked a non-cleaving mutant of
AB  - I-SceI, which conveys to the chimeric enzyme its specificity for an 18-bp
AB  - DNA sequence, to the catalytic domain of FokI, which cuts DNA at a defined
AB  - site outside the target site. Whereas previously described chimeric
AB  - endonucleases do not produce type IIS-like precise DNA overhangs suitable
AB  - for ligation, our chimeric endonuclease cleaves double-stranded DNA
AB  - exactly 2 and 6 nt from the target site to generate homogeneous, 5',
AB  - four-base overhangs, which can be ligated with 90% fidelity. We anticipate
AB  - that these enzymes will be particularly useful in manipulation of DNA
AB  - fragments larger than a thousand bases, which are very likely to contain
AB  - target sites for all natural type IIS restriction endonucleases.
ER  -

TY  - JOUR
AU  - Lippow, S.M.
AU  - Aha, P.M.
AU  - Parker, M.H.
AU  - Blake, W.J.
AU  - Baynes, B.M.
AU  - Lipovsek, D.
TI  - BIOT 7-Creation of a type IIS restriction endonuclease with a long recognition sequence.
JO  - ACS Abstracts
PY  - 2008
SP  - 0
EP  - 0
VL  - 236
AB  - We have engineered a novel family of type IIS restriction endonucleases that combines the high
AB  - specificity of the homing endonuclease I-SceI with the type-IIS cleavage of FokI. Our hybrid
AB  - endonucleases feature a non-cleaving mutant of I-SceI linked to the catalytic domain of FokI
AB  - through a series of peptide linkers. We find that length and composition of the linker affect
AB  - the cleavage specificity of the hybrid enzymes. The endonucleases containing the FokI native
AB  - linker or a 20-residue synthetic linker are the most specific, cutting double-stranded DNA
AB  - exactly two and seven nucleotides from the recognition sequence to generate homogeneous, 5',
AB  - five-base overhangs. These two hybrid endonucleases generate DNA cleavage products that can be
AB  - ligated with greater than 80% fidelity.
AB  - We anticipate that these novel enzymes will be particularly useful for manipulating or
AB  - assembling kilobase and longer DNA fragments, which are likely to contain recognition sites
AB  - for all natural type IIS restriction endonucleases.
ER  -

TY  - JOUR
AU  - Lipus, D.
AU  - Ross, D.
AU  - Bibby, K.
AU  - Gulliver, D.
TI  - Draft Genome Sequence of Pseudomonas sp. BDAL1 Reconstructed from a Bakken Shale  Hydraulic Fracturing-Produced Water Storage Tank Metagenome.
JO  - Genome Announcements
PY  - 2017
SP  - e00033
EP  - e00017
VL  - 5
AB  - We report the 5,425,832 bp draft genome of Pseudomonas sp. strain BDAL1, recovered from a
AB  - Bakken shale hydraulic fracturing-produced water tank
AB  - metagenome. Genome annotation revealed several key biofilm formation genes and
AB  - osmotic stress response mechanisms necessary for survival in hydraulic
AB  - fracturing-produced water.
ER  -

TY  - JOUR
AU  - Lipus, D.
AU  - Vikram, A.
AU  - Ross, D.E.
AU  - Bibby, K.
TI  - Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome.
JO  - Genome Announcements
PY  - 2016
SP  - e00899
EP  - e00816
VL  - 4
AB  - We report here the 1,882,100-bp draft genome sequence of Methanohalophilus mahii  strain DAL1,
AB  - recovered from Marcellus Shale hydraulic fracturing-produced water
AB  - using metagenomic contig binning. Genome annotation revealed several key
AB  - methanogenesis genes and provides valuable information on archaeal activity
AB  - associated with hydraulic fracturing-produced water environments.
ER  -

TY  - JOUR
AU  - Lira, F.
AU  - Garcia-Leon, G.
AU  - Oliver, A.
AU  - Martinez, J.L.
TI  - Draft Genome Sequences of Four Pseudomonas aeruginosa Isolates Obtained from Patients with Chronic Obstructive Pulmonary Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e00147
EP  - e00117
VL  - 5
AB  - Patients suffering chronic obstructive pulmonary disease are frequently infected  by
AB  - Pseudomonas aeruginosa Nevertheless, the number of sequenced isolates causing
AB  - this type of infection is low. Here, we present the draft genomes of four P.
AB  - aeruginosa isolates obtained from patients presenting chronic obstructive
AB  - pulmonary disease.
ER  -

TY  - JOUR
AU  - Lira, F.
AU  - Hernandez, A.
AU  - Belda, E.
AU  - Sanchez, M.B.
AU  - Moya, A.
AU  - Silva, F.J.
AU  - Martinez, J.L.
TI  - Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3563
EP  - 3564
VL  - 194
AB  - Stenotrophomonas maltophilia is an opportunistic pathogen with an environmental origin, and it
AB  - is an increasingly relevant cause of nosocomial infections. Here
AB  - we present the whole-genome sequence of S. maltophilia strain D457, a clinical
AB  - isolate that is being used as a model for studying antibiotic resistance in this
AB  - bacterial species.
ER  -

TY  - JOUR
AU  - Lisle, W.
AU  - Dutta, C.F.
AU  - Penner, M.
AU  - Amitsur, M.
AU  - Kaufmann, G.
AU  - Firman, K.
TI  - Phage T4-ancoded Stp alleviates the DNA restriction activity of EcoR124I endonuclease by affecting a critical step in the subunit assembly pathway.
JO  - Mol. Biol. Today
PY  - 2000
SP  - 57
EP  - 64
VL  - 1
AB  - The tRNA(Lys)-specific anticodon nuclease is kept latent by virtue of a physical
AB  - association with the type IC DNA
AB  - restriction-modification enzyme EcoprrI. Previous work in vivo has
AB  - indicated that the phage T4-encoded polypeptide Stp inhibits EcoprrI
AB  - DNA restriction and activates anticodon nuclease. These studies also
AB  - suggested that EcoprrI is the immediate target of Stp. The presumptive
AB  - interaction was investigated here in vitro using the synthetic Stp-like
AB  - polypeptide Stp sub(2-26). Stp sub(2-26) inhibited the DNA restriction
AB  - activity of both EcoprrI and the related type IC DNA restriction enzyme
AB  - EcoR124I in crude cell extracts more effectively than with purified
AB  - EcoR124I. However, complementation with an EcoR124I-free crude extract
AB  - fully restored Stp function, suggesting the existence of any
AB  - co-operating host factor(s). Stp sub(2-26) also enhanced limited
AB  - proteolysis of the purified EcoR124I holoenzyme (HsdR sub(2)M sub(2)S),
AB  - but not the HsdM sub(2)S subassembly indicating that the R subunit is
AB  - important for the interaction and, perhaps, serves as the immediate
AB  - target of Stp. Stp sub(2-26) also produced a subtle shift of the
AB  - equilibrium between the Hsd R2 M2 S1 and Hsd R1 M2
AB  - S1 subassembly towards the latter form. Since only the
AB  - holoenzyme is active as a restriction endonuclease, this effect can
AB  - account for the ability of Stp to inhibit the DNA restriction enzyme
AB  - and activate the appended anticodon nuclease.
ER  -

TY  - JOUR
AU  - Little, E.J.
AU  - Babic, A.C.
AU  - Horton, N.C.
TI  - Early interrogation and recognition of DNA sequence by indirect readout.
JO  - Structure
PY  - 2008
SP  - 1828
EP  - 1837
VL  - 16
AB  - Control of replication, transcription, recombination and repair requires proteins capable of
AB  - finding particular DNA sequences in a background of a large excess of nonspecific sequences.
AB  - Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in
AB  - some cases through the less well characterized indirect readout mechanisms. In order to
AB  - measure the relative contributions of direct and indirect readout by a sequence specific
AB  - endonuclease,  HincII, a mutant enzyme deficient in a direct contact, was characterized, and
AB  - surprisingly showed no loss of sequence specificity. The three dimensional crystal structure
AB  - shows the loss of most of the direct readout contacts to the DNA, possibly capturing an
AB  - early stage in target site recognition using predominately indirect readout to prescreen sites
AB  - before full sequence interrogation.
ER  -

TY  - JOUR
AU  - Little, E.J.
AU  - Horton, N.C.
TI  - DNA-induced conformational changes in type II restriction endonucleases: The structure of unliganded HincII.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 76
EP  - 88
VL  - 351
AB  - The 2.1 angstrom crystal structure of the unliganded type II restriction endonuclease, HincII,
AB  - is described. Although the asymmetric
AB  - unit contains only a single monomer, crystal lattice contacts bring two
AB  - monomers together to form a dimer very similar to that found in the DNA
AB  - bound form. Comparison with the published DNA bound structure reveals
AB  - that the DNA binding pocket is expanded in the unliganded structure.
AB  - Comparison of the unliganded and DNA liganded structures reveals a
AB  - simple rotation of subunits by 11 degrees each, or 22 degrees total, to
AB  - a more closed structure around the bound DNA. Comparison of this
AB  - conformational change to that observed in the other type II restriction
AB  - endonucleases where DNA bound and unliganded forms have both been
AB  - characterized, shows considerable variation in the types of
AB  - conformational changes that can occur. The conformational changes in
AB  - three can be described by a simple rotation of subunits, while in two
AB  - others both rotation and translation of subunits relative to one
AB  - another occurs. In addition, the endonucleases having subunits that
AB  - undergo the greatest amount of rotation upon DNA binding are found to
AB  - be those that distort the bound DNA the least, suggesting that DNA
AB  - bending may be less facile in dimers possessing greater flexibility (c)
AB  - 2005 Elsevier Ltd. All rights reserved.
ER  -

TY  - JOUR
AU  - Little, G.T.
AU  - Winzer, K.
AU  - Minton, N.P.
TI  - Genome Sequence of the Solvent-Producing Clostridium beijerinckii Strain 59B, Isolated from Staffordshire Garden Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00108
EP  - e00115
VL  - 3
AB  - The genome sequence of the solvent-producing, spore-forming, saccharolytic, mesophilic
AB  - bacterium Clostridium beijerinckii strain 59B, isolated from
AB  - Staffordshire garden soil, was obtained via a combination of sequencing with the
AB  - 454 and Illumina platforms. This information will allow for metabolic engineering
AB  - of a potentially industrially useful strain.
ER  -

TY  - JOUR
AU  - Little, J.W.
AU  - Mount, D.W.
TI  - Creating new restriction sites by silent changes in coding sequences.
JO  - Gene
PY  - 1984
SP  - 67
EP  - 73
VL  - 32
AB  - We present methods for identifying a useful type of DNA site - one that can be
AB  - mutated to create a new restriction site within a coding region without
AB  - changing the amino acid sequence.  These "latent sites" are abundant - silent
AB  - mutations creating one of 44 different 6-bp or 8-bp recognition sites were
AB  - found at relatively high density, roughly one latent site per 9 bp, in the
AB  - eleven genes tested.  Our analysis suggests that site-directed mutagenesis can
AB  - be used to refashion coding sequences at will for flexible analysis.
ER  -

TY  - JOUR
AU  - Liu, B.
AU  - Bian, C.
AU  - Huang, H.
AU  - Yin, Z.
AU  - Shi, Q.
AU  - Deng, X.
TI  - Complete Genome Sequence of a Marine Bacterium, Pseudomonas pseudoalcaligenes Strain S1, with High Mercury Resistance and Bioaccumulation Capacity.
JO  - Genome Announcements
PY  - 2016
SP  - e00381
EP  - e00316
VL  - 4
AB  - Pseudomonas pseudoalcaligenes S1, a marine bacterium, exhibited strong resistance to a high
AB  - concentration of Hg(2+) and remarkable Hg(2+) bioaccumulation capacity.
AB  - Here, we report the 6.9-Mb genome sequence of P. pseudoalcaligenes S1, which may
AB  - help clarify its phylogenetic status and provide further understanding of the
AB  - mechanisms of mercury bioremediation in a marine environment.
ER  -

TY  - JOUR
AU  - Liu, B.
AU  - Frostegard, A.
AU  - Shapleigh, J.P.
TI  - Draft genome sequences of five strains in the genus thauera.
JO  - Genome Announcements
PY  - 2013
SP  - e00052
EP  - e00012
VL  - 1
AB  - Thauera species are members of the betaproteobacteria and are most noted for their ability to
AB  - metabolize aromatic compounds under anoxic conditions. Here, we
AB  - announce the draft genome sequences of five Thauera strains in an effort to
AB  - provide further genetic information as a resource for understanding the
AB  - ecological function of this environmentally important genus.
ER  -

TY  - JOUR
AU  - Liu, B.
AU  - Ge, B.
AU  - Azhar, N.
AU  - Zhao, W.
AU  - Cui, H.
AU  - Zhang, K.
TI  - Complete Genome Sequence of Bacillus methylotrophicus Strain NKG-1, Isolated from the Changbai Mountains, China.
JO  - Genome Announcements
PY  - 2018
SP  - e01454
EP  - e01417
VL  - 6
AB  - We report here the complete genome sequence of Bacillus methylotrophicus NKG-1, isolated from
AB  - rare dormant volcanic soils on the Changbai Mountains in China. The
AB  - 4.20-Mb genome contains 4,432 genes and has a G+C content of 47.06%.
ER  -

TY  - JOUR
AU  - Liu, B.
AU  - Hu, B.
AU  - Zhou, Z.
AU  - Guo, D.
AU  - Guo, X.
AU  - Ding, P.
AU  - Feng, L.
AU  - Wang, L.
TI  - A novel non-homologous recombination-mediated mechanism for Escherichia coli unilateral flagellar phase variation.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 4530
EP  - 4538
VL  - 40
AB  - Flagella contribute to the virulence of bacteria through chemotaxis, adhesion to
AB  - and invasion of host surfaces. Flagellar phase variation is believed to
AB  - facilitate bacterial evasion of the host immune response. In this study, the flnA
AB  - gene that encodes Escherichia coli H17 flagellin was examined by whole genome
AB  - sequencing and genetic deletion analysis. Unilateral flagellar phase variation
AB  - has been reported in E. coli H3, H47 and H17 strains, although the mechanism for
AB  - phase variation in the H17 strain has not been previously understood. Analysis of
AB  - phase variants indicated that the flagellar phase variation in the H17 strain was
AB  - caused by the deletion of an approximately 35 kb DNA region containing the flnA
AB  - gene from diverse excision sites. The presence of covalently closed
AB  - extrachromosomal circular forms of this excised 35 kb region was confirmed by the
AB  - two-step polymerase chain reaction. The deletion and complementation test
AB  - revealed that the Int1157 integrase, a tyrosine recombinase, mediates the
AB  - excision of this region. Unlike most tyrosine recombinases, Int1157 is suggested
AB  - to recognize diverse sites and mediate recombination between non-homologous DNA
AB  - sequences. This is the first report of non-homologous recombination mediating
AB  - flagellar phase variation.
ER  -

TY  - JOUR
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Cetin, S.
AU  - Schumann, P.
AU  - Pan, Z.Z.
AU  - Chen, Q.Q.
TI  - Bacillus gobiensis sp. nov., isolated from a soil sample.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2016
SP  - 379
EP  - 384
VL  - 66
AB  - A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium
AB  - designated FJAT-4402T, was isolated from the weed rhizosphere soil of the Gobi
AB  - desert in the Xinjiang Autonomous Region in the north-west of China. Isolate
AB  - FJAT-4402T grew at 15-40 degrees C (optimum 30 degrees C), pH 5-10 (optimum pH 7)
AB  - and in 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses, based on 16S rRNA
AB  - gene sequences, showed that isolate FJAT-4402T was a member of the genus Bacillus
AB  - and was most closely related to Bacillus licheniformis DSM 13T (96.2 %). The
AB  - isolate showed 33.3 % DNA-DNA relatedness to the closest reference isolate, B.
AB  - licheniformis DSM 13T. The diagnostic diamino acid of the peptidoglycan of
AB  - isolate FJAT-4402T was meso-diaminopimelic acid and the predominant isoprenoid
AB  - quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (28.5 %),
AB  - iso-C15 : 0 (20.1 %), anteiso-C17 : 0 (14.3 %), iso-C16 : 0 (9.6 %), C16 : 0 (8.4
AB  - %), iso-C17 : 0 (6.2 %) and iso-C14 : 0 (4.7 %) and the DNA G+C content was 42.0
AB  - mol%. The phenotypic, chemotaxonomic and genotypic properties indicated that
AB  - strain FJAT-4402T represents a novel species within the genus Bacillus, for which
AB  - the name Bacillus gobiensis sp. nov. is proposed. The type strain is FJAT-4402T (
AB  - = DSM 29500T = CGMCC 1.12902T).
ER  -

TY  - JOUR
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Zhu, Y.J.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
AU  - Chen, Z.
TI  - Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T.
JO  - Genome Announcements
PY  - 2016
SP  - e01423
EP  - e01416
VL  - 4
AB  - Here, we report the draft genome sequences of Bacillus drentensis DSM 15600T and  Bacillus
AB  - novalis DSM 15603T with 5,305,306 bp and 5,667,584 bp, respectively,
AB  - which will provide useful information for the functional gene mining and
AB  - application of these two species. The average DNA G+C contents were 38.91% and
AB  - 40.01%, respectively.
ER  -

TY  - JOUR
AU  - Liu, C.
AU  - Hu, J.
AU  - Fang, X.
AU  - Zhang, D.
AU  - Chang, D.
AU  - Wang, J.
AU  - Li, T.
AU  - Guo, Y.
AU  - Dai, W.
AU  - Liu, C.
TI  - Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA41, with Changed Metabolism after Space Flight.
JO  - Genome Announcements
PY  - 2014
SP  - e01124
EP  - e01113
VL  - 2
AB  - To explore the effects of space flight on microorganisms, Pseudomonas aeruginosa  ATCC 27853
AB  - was sent into orbit for 398 h on the spacecraft ShenZhou VIII. Here,
AB  - we present the draft genome sequence of the P. aeruginosa strain LCT-PA41,
AB  - determined after space flight.
ER  -

TY  - JOUR
AU  - Liu, C.
AU  - Zheng, H.
AU  - Yang, M.
AU  - Xu, Z.
AU  - Wang, X.
AU  - Wei, L.
AU  - Tang, B.
AU  - Liu, F.
AU  - Zhang, Y.
AU  - Ding, Y.
AU  - Tang, X.
AU  - Wu, B.
AU  - Johnson, T.J.
AU  - Chen, H.
AU  - Tan, C.
TI  - Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033.
JO  - BMC Genomics
PY  - 2015
SP  - 717
EP  - 717
VL  - 16
AB  - BACKGROUND: Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can
AB  - invade and colonize extraintestinal sites and cause a wide range of infections.
AB  - Genomic analysis of ExPEC has mainly focused on isolates of human and avian
AB  - origins, with porcine ExPEC isolates yet to be sequenced. To better understand
AB  - the genomic attributes underlying the pathogenicity of porcine ExPEC, we isolated
AB  - two E. coli strains PCN033 and PCN061 from pigs, assessed their in vivo
AB  - virulence, and completed and compared their genomes. RESULTS: Animal experiments
AB  - demonstrated that strain PCN033, but not PCN061, was pathogenic in a pig model.
AB  - The chromosome of PCN033 was 384 kb larger than that of PCN061. Among the
AB  - PCN033-specific sequences, genes encoding adhesins, unique lipopolysaccharide,
AB  - unique capsular polysaccharide, iron acquisition and transport systems, and
AB  - metabolism were identified. Additionally, a large plasmid PCN033p3 harboring many
AB  - typical ExPEC virulence factors was identified in PCN033. Based on the genetic
AB  - variation between PCN033 and PCN061, corresponding phenotypic differences in
AB  - flagellum-dependent swarming motility and metabolism were verified. Furthermore,
AB  - the comparative genomic analyses showed that the PCN033 genome shared many
AB  - similarities with genomic sequences of human ExPEC strains. Additionally,
AB  - comparison of PCN033 genome with other nine characteristic E. coli genomes
AB  - revealed 425 PCN033-special coding sequences. Genes of this subset included those
AB  - encoding type I restriction-modification (R-M) system, type VI secretion system
AB  - (T6SS) and membrane-associated proteins. CONCLUSIONS: The genetic and phenotypic
AB  - differences between PCN033 and PCN061 could partially explain their differences
AB  - in virulence, and also provide insight towards the molecular mechanisms of
AB  - porcine ExPEC infections. Additionally, the similarities between the genomes of
AB  - PCN033 and human ExPEC strains suggest that some connections between porcine and
AB  - human ExPEC strains exist. The first completed genomic sequence for porcine ExPEC
AB  - and the genomic differences identified by comparative analyses provide a baseline
AB  - understanding of porcine ExPEC genetics and lay the foundation for their further
AB  - study.
ER  -

TY  - JOUR
AU  - Liu, D.
AU  - Zhou, Y.
AU  - Naito, M.
AU  - Yumoto, H.
AU  - Li, Q.
AU  - Miyake, Y.
AU  - Liang, J.
AU  - Shu, R.
TI  - Draft Genome Sequence of Porphyromonas gingivalis Strain SJD2, Isolated from the  Periodontal Pocket of a Patient with Periodontitis in China.
JO  - Genome Announcements
PY  - 2014
SP  - e01091
EP  - e01013
VL  - 2
AB  - Porphyromonas gingivalis strain SJD2 was isolated from subgingival plaque of a patient in
AB  - China with chronic periodontitis. Here, we report the draft genome of
AB  - this strain, with a size of 2,328,850 bp, average G+C content of 48.3%, and 2,020
AB  - predicted protein-coding sequences.
ER  -

TY  - JOUR
AU  - Liu, D.Y.
AU  - Li, Y.
AU  - Magarvey, N.A.
TI  - Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin.
JO  - Genome Announcements
PY  - 2016
SP  - e00173
EP  - e00116
VL  - 4
AB  - We present here the genome sequence ofStreptomyces canusATCC 12647, a producer of the
AB  - antibiotic telomycin, noted for its unique antibacterial activity against
AB  - cardiolipin. Genomic analysis using the bioinformatics tool PRISM revealed the
AB  - presence of multiple biosynthetic gene clusters, including those for telomycin
AB  - and other natural products of potential pharmacological interest.
ER  -

TY  - JOUR
AU  - Liu, F.
AU  - Li, J.
AU  - Li, Z.
TI  - Draft Genome Sequence of 'Candidatus Synechococcus spongiarum' m9, Binned from a  Metagenome of South China Sea Sponge Theonella swinhoei.
JO  - Genome Announcements
PY  - 2017
SP  - e01307
EP  - e01316
VL  - 5
AB  - 'Candidatus Synechococcus spongiarum' represents the widespread cyanobacterial symbionts
AB  - found in marine sponges with relatively high genomic variability and
AB  - likely important ecological roles. We present here the draft genome sequence of
AB  - 'Candidatus Synechococcus spongiarum' m9, which was assembled from a metagenome
AB  - of Theonella swinhoei sampled in the South China Sea.
ER  -

TY  - JOUR
AU  - Liu, F.
AU  - Ma, R.
AU  - Tay, C.Y.A.
AU  - Octavia, S.
AU  - Lan, R.
AU  - Chung, H.K.L.
AU  - Riordan, S.M.
AU  - Grimm, M.C.
AU  - Leong, R.W.
AU  - Tanaka, M.M.
AU  - Connor, S.
AU  - Zhang, L.
TI  - Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease.
JO  - Emerg. Microbes Infect.
PY  - 2018
SP  - 64
EP  - 64
VL  - 7
AB  - Campylobacter concisus is an oral bacterium that is associated with inflammatory
AB  - bowel disease (IBD) including Crohn's disease (CD) and ulcerative colitis (UC).
AB  - C. concisus consists of two genomospecies (GS) and diverse strains. This study
AB  - aimed to identify molecular markers to differentiate commensal and IBD-associated
AB  - C. concisus strains. The genomes of 63 oral C. concisus strains isolated from
AB  - patients with IBD and healthy controls were examined, of which 38 genomes were
AB  - sequenced in this study. We identified a novel secreted enterotoxin B homologue,
AB  - Csep1. The csep1 gene was found in 56% of GS2 C. concisus strains, presented in
AB  - the plasmid pICON or the chromosome. A six-nucleotide insertion at the position
AB  - 654-659 bp in csep1 (csep1-6bpi) was found. The presence of csep1-6bpi in oral C.
AB  - concisus strains isolated from patients with active CD (47%, 7/15) was
AB  - significantly higher than that in strains from healthy controls (0/29, P =
AB  - 0.0002), and the prevalence of csep1-6bpi positive C. concisus strains was
AB  - significantly higher in patients with active CD (67%, 4/6) as compared to healthy
AB  - controls (0/23, P = 0.0006). Proteomics analysis detected the Csep1 protein. A
AB  - csep1 gene hot spot in the chromosome of different C. concisus strains was found.
AB  - The pICON plasmid was only found in GS2 strains isolated from the two relapsed CD
AB  - patients with small bowel complications. This study reports a C. concisus
AB  - molecular marker (csep1-6bpi) that is associated with active CD.
ER  -

TY  - JOUR
AU  - Liu, F.
AU  - Yang, J.
AU  - Xiao, Y.
AU  - Li, L.
AU  - Yang, F.
AU  - Jin, Q.
TI  - Complete Genome Sequence of a Clinical Isolate of Enterobacter asburiae.
JO  - Genome Announcements
PY  - 2016
SP  - e00523
EP  - e00516
VL  - 4
AB  - We report here the complete genome sequence of Enterobacter asburiae strain ENIPBJ-CG1,
AB  - isolated from a bone marrow transplant patient. The size of the
AB  - genome sequence is approximately 4.65 Mb, with a G+C content of 55.76%, and it is
AB  - predicted to contain 4,790 protein-coding genes.
ER  -

TY  - JOUR
AU  - Liu, G.
AU  - Deng, C.
AU  - Song, L.
AU  - Peng, Q.
AU  - Zhang, J.
AU  - Lereclus, D.
AU  - Song, F.
TI  - Draft Genome Sequence of Bacillus thuringiensis Strain LM1212, Isolated from the  Cadaver of an Oryctes gigas Larva in Madagascar.
JO  - Genome Announcements
PY  - 2014
SP  - e00516
EP  - e00514
VL  - 2
AB  - We report the draft genome sequence of Bacillus thuringiensis strain LM1212, which
AB  - differentiates into crystal producers or spore formers during the
AB  - stationary phase. Availability of this genome sequence will facilitate the study
AB  - of spore formation, crystal formation, cell differentiation, and evolution of B.
AB  - thuringiensis.
ER  -

TY  - JOUR
AU  - Liu, G.
AU  - Liu, B.
AU  - Lin, N.
AU  - Tang, W.
AU  - Tang, J.
AU  - Lin, Y.
TI  - Genome Sequence of the Aerobic Bacterium Bacillus sp. Strain FJAT-13831.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6633
EP  - 6633
VL  - 194
AB  - Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's
AB  - Terracotta Warriors in Xi'an City, People's Republic of China. The isolate
AB  - showed a close relationship to the Bacillus cereus group. The draft genome
AB  - sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of
AB  - 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and
AB  - a G+C value of 36.36%.
ER  -

TY  - JOUR
AU  - Liu, G.
AU  - Liu, B.
AU  - Tang, W.
AU  - Che, J.
AU  - Lin, Y.
AU  - Zhu, Y.
AU  - Su, M.
AU  - Tang, J.
TI  - Genome Sequence of Bacillus sp. Strain FJAT-14515.
JO  - Genome Announcements
PY  - 2014
SP  - e01123
EP  - e01113
VL  - 2
AB  - We report the draft genome sequence of Bacillus sp. strain FJAT-14515. The genome is 5.44 Mb
AB  - in length. It covers 5,263 genes with an average length of 791 bp, has
AB  - a G+C value of 37.06%, and contains 67 tRNAs, 31 small RNAs, and 5 rRNA loci.
ER  -

TY  - JOUR
AU  - Liu, G.
AU  - Ou, H.Y.
AU  - Wang, T.
AU  - Li, L.
AU  - Tan, H.
AU  - Zhou, X.
AU  - Rajakumar, K.
AU  - Deng, Z.
AU  - He, X.
TI  - Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA.
JO  - PLoS Genet.
PY  - 2010
SP  - e1001253
EP  - e1001253
VL  - 6
AB  - Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a
AB  - non-bridging oxygen with a sulfur atom at specific sequences.
AB  - The biological implications of this DNA S-modification
AB  - (phosphorothioation) were unknown. We observed that simultaneous
AB  - expression of the dndA-E gene cluster from Streptomyces lividans 66, which
AB  - is responsible for the DNA S-modification, and the putative Streptomyces
AB  - coelicolor A(3)2 Type IV methyl-dependent restriction endonuclease
AB  - ScoA3McrA (Sco4631) leads to cell death in the same host. A His-tagged
AB  - derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA
AB  - in vitro near the respective modification sites. Double-strand cleavage
AB  - occurred 16-28 nucleotides away from the phosphorothioate links. DNase I
AB  - footprinting demonstrated binding of ScoA3McrA to the Dcm methylation
AB  - site, but no clear binding could be detected at the S-modified site under
AB  - cleavage conditions. This is the first report of in vitro endonuclease
AB  - activity of a McrA homologue and also the first demonstration of an enzyme
AB  - that specifically cleaves S-modified DNA.
ER  -

TY  - JOUR
AU  - Liu, G.
AU  - Song, L.
AU  - Shu, C.
AU  - Wang, P.
AU  - Deng, C.
AU  - Peng, Q.
AU  - Lereclus, D.
AU  - Wang, X.
AU  - Huang, D.
AU  - Zhang, J.
AU  - Song, F.
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD73.
JO  - Genome Announcements
PY  - 2013
SP  - e0008013
EP  - e0008013
VL  - 1
AB  - Bacillus thuringiensis is a Gram-positive bacterium that produces intracellular protein
AB  - crystals toxic to a wide variety of insect larvae. We report the complete
AB  - genome sequence of Bacillus thuringiensis subsp. kurstaki strain HD73 from the
AB  - Centre OILB (Institut Pasteur, France), which belongs to serotype 3ab and is
AB  - toxic to lepidopteran larvae.
ER  -

TY  - JOUR
AU  - Liu, G.
AU  - Zhang, W.
AU  - Lu, C.
TI  - Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6653
EP  - 6653
VL  - 194
AB  - This work describes a whole-genome sequence of Streptococcus agalactiae strain GD201008-001, a
AB  - pathogen causing meningoencephalitis in cultural tilapia in
AB  - China. The genome sequence provides opportunities to understand the piscine GBS
AB  - pathogenicity and its genetic basis associated with host tropism.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Tang, J.Y.
AU  - Che, J.M.
AU  - Zhu, Y.J.
AU  - Su, M.X.
AU  - Wang, J.P.
AU  - Chen, Q.Q.
TI  - Draft Genome Sequence of Bacillus fengqiuensis FJAT-14578, Isolated from a Soil Sample in China.
JO  - Genome Announcements
PY  - 2014
SP  - e01126
EP  - e01114
VL  - 2
AB  - Here, we report the first high-quality draft genome sequence of Bacillus fengqiuensis
AB  - FJAT-14578, isolated from a soil sample collected from China. The
AB  - genome size was 5,569,389 bp, with a 40.93 mol% G+C content. The number of tRNAs
AB  - was 69 and of rRNAs was 10 (5S, 16S, and 23S).
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
TI  - Complete Genome Sequence of a Potential Novel Bacillus sp. Strain, FJAT-18017, Isolated from a Potato Field.
JO  - Genome Announcements
PY  - 2017
SP  - e01424
EP  - e01416
VL  - 5
AB  - Bacillus sp. strain FJAT-18017 was isolated from a potato field in Xinjiang, China. This paper
AB  - is the first report, to our knowledge, to demonstrate the fully
AB  - sequenced and completely annotated genome of Bacillus sp. FJAT-18017. The genome
AB  - size is 5,265,521 bp. The average G+C content was 42.42%.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
AU  - Chen, Z.
TI  - High-Quality Genome Sequence of Bacillus vireti DSM 15602T for Setting Up Phylogenomics for the Genomic Taxonomy of Bacillus-Like Bacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e00864
EP  - e00815
VL  - 3
AB  - Bacillus vireti DSM 15602(T) is a Gram-negative, spore-forming, and facultatively anaerobic
AB  - bacterium. Here, we report the 5.309-Mb draft genome sequence of B.
AB  - vireti DSM 15602(T), which will provide useful information for setting up
AB  - phylogenomics for the genomic taxonomy of Bacillus-like bacteria, as well as for
AB  - the functional gene mining and application of B. vireti.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
AU  - Chen, Z.
TI  - Draft Genome Sequence of Bacillus simplex DSM 1321 for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00574
EP  - e00516
VL  - 4
AB  - Bacillus simplex DSM 1321 is a Gram-positive, spore-forming, and aerobic bacterium. Here, we
AB  - report the draft genome sequence of B. simplex DSM 1321, with
AB  - 6,494,937 bp, which will provide useful information for setting up phylogenomics
AB  - in genomic taxonomy of the Bacillus-like bacteria as well as for the functional
AB  - gene mining and application of B. simplex DSM 1321.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
AU  - Chen, Z.
AU  - Ge, C.B.
TI  - Genome Sequence of Type Strain Lysinibacillus macroides DSM 54T.
JO  - Genome Announcements
PY  - 2015
SP  - e01271
EP  - e01215
VL  - 3
AB  - Lysinibacillus macroides DSM 54(T) is a Gram-positive, spore-forming bacterium. Here, we
AB  - report the 4,866,035-bp genome sequence of Lysinibacillus macroides DSM
AB  - 54(T), which will accelerate the application of degrading xylan and provide
AB  - useful information for genomic taxonomy and phylogenomics of Bacillus-like
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
AU  - Zhu, Y.J.
TI  - Draft Genome Sequence of Bacillus sp. FJAT-27238 for Setting up Phylogenomic Analysis of Genomic Taxonomy of Bacillus-Like Bacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e00985
EP  - e00915
VL  - 3
AB  - Bacillus sp. FJAT-27238 is a Gram-positive, spore-forming, and aerobic bacterium. Here, we
AB  - report the draft genome sequence of Bacillus sp. FJAT-27238, with 6,134,829 bp, which will
AB  - provide useful information for setting up phylogenomic analysis of the genomic taxonomy of
AB  - Bacillus-like bacteria as well as for the functional gene mining and application of strain
AB  - FJAT-27238. The genomic DNA G+C  content was 47.37%.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Zheng, X.F.
AU  - Chen, Q.Q.
AU  - Ge, C.B.
TI  - Draft Genome Sequence of Type Strain Lysinibacillus xylanilyticus DSM 23493T.
JO  - Genome Announcements
PY  - 2015
SP  - e01037
EP  - e01015
VL  - 3
AB  - Lysinibacillus xylanilyticus DSM 23493(T) is a Gram-positive, spore-forming bacterium. Here,
AB  - we report the 5.22-Mb genome sequence of Lysinibacillus xylanilyticus DSM 23493(T), which will
AB  - accelerate the application of degrading xylan and provide useful information for genomic
AB  - taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Zhu, Y.J.
AU  - Chen, Q.Q.
AU  - Ruan, C.Q.
TI  - Genome Sequence of Paenibacillus sp. Strain FJAT-28004 for the Genome Sequencing  Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e00863
EP  - e00815
VL  - 3
AB  - Paenibacillus sp. strain FJAT-28004 is a spore forming and strictly aerobic bacterium. Here,
AB  - we report the draft 7,479,858-bp genome sequence of Paenibacillus sp. FJAT-28004, which will
AB  - provide useful information for genomic taxonomy and phylogenomics of the genus Paenibacillus,
AB  - as well as for the functional gene mining and application of Paenibacillus sp. FJAT-28004.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Wang, J.P.
AU  - Chen, Q.Q.
AU  - Che, J.M.
AU  - Zheng, X.F.
AU  - Ge, C.B.
TI  - Genome Sequence of Type Strain Bacillus decisifrondis E5HC-32T (DSM 11725T), Isolated from Soil Underlying the Decaying Leaf Litter of a Slash Pine Forest.
JO  - Genome Announcements
PY  - 2015
SP  - e01249
EP  - e01215
VL  - 3
AB  - Bacillus decisifrondis E5HC-32(T) (DSM 11725(T)) is a Gram-positive, subterminal  spherical
AB  - spore-forming, strictly aerobic bacterium. Here, we report the 5,613,728-bp genome sequence of
AB  - B. decisifrondis E5HC-32(T), which is the first genome information of this species and will
AB  - provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Liu, G.H.
AU  - Liu, B.
AU  - Zhu, Y.J.
AU  - Wang, J.P.
AU  - Che, J.M.
AU  - Chen, Q.Q.
AU  - Chen, Z.
TI  - Draft Genome Sequence of Bacillus mesonae FJAT-13985T (=DSM 25968T) for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00575
EP  - e00516
VL  - 4
AB  - Bacillus mesonae FJAT-13985(T) is a Gram-positive, spore-forming, and aerobic bacterium. Here,
AB  - we report the draft genome sequence of B. mesonae FJAT-13985(T)
AB  - with 5,807,726 bp, which will provide useful information for setting up
AB  - phylogenomics in the genomic taxonomy of the Bacillus-like bacteria, as well as
AB  - for the functional gene mining and application of B. mesonae FJAT-13985(T).
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Cheng, Y.
AU  - Gu, J.
AU  - Wang, Y.
AU  - Li, J.
AU  - Li, F.
AU  - Han, W.
TI  - Draft Genome Sequence of Paenibacillus sp. Strain MY03, a Terrestrial Bacterium Capable of Degrading Multiple Marine-Derived Polysaccharides.
JO  - Genome Announcements
PY  - 2017
SP  - e00678
EP  - e00617
VL  - 5
AB  - The bacterium Paenibacillus sp. strain MY03, isolated from the root soil of cypress, can
AB  - effectively degrade marine-derived polysaccharides such as agar,
AB  - alginate, and chitin. Here, we present the draft genome sequence of MY03.
AB  - Putative enzymes, including 3 agarases, 1 alginate lyase, and 1 chitinase, were
AB  - found.
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Liu, K.
AU  - Li, Y.
AU  - Wang, C.
AU  - Hou, Q.
AU  - Xu, W.
AU  - Fan, L.
AU  - Zhao, J.
AU  - Gou, J.
AU  - Du, B.
AU  - Ding, Y.
TI  - Complete Genome Sequence of Paenibacillus polymyxa YC0136, a Plant Growth-Promoting Rhizobacterium Isolated from Tobacco Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e01635
EP  - e01616
VL  - 5
AB  - Paenibacillus polymyxa strain YC0136 is a plant growth-promoting rhizobacterium with
AB  - antimicrobial activity, which was isolated from tobacco rhizosphere. Here,
AB  - we report the complete genome sequence of P. polymyxa YC0136. Several genes with
AB  - antifungal and antibacterial activity were discovered.
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Qiu, H.
AU  - Zhao, W.
AU  - Cui, Z.
AU  - Ibrahim, M.
AU  - Jin, G.
AU  - Li, B.
AU  - Zhu, B.
AU  - Xie, G.L.
TI  - Genome Sequence of the Plant Pathogen Pseudomonas syringae pv. panici LMG 2367.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5693
EP  - 5694
VL  - 194
AB  - Pseudomonas syringae pv. panici is a phytopathogenic bacterium causing brown stripe disease in
AB  - economically important crops worldwide. Here, we announce the
AB  - draft genome sequence of Pseudomonas syringae pv. panici LMG2367 to provide
AB  - further valuable insights for comparison of the pathovars among species
AB  - Pseudomonas syringae.
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Shan, W.
AU  - Zhou, Y.
AU  - Yu, X.
TI  - Draft Genome Sequence of Paenibacillus sp. XY044, a Potential Plant Growth Promoter Isolated from a Tea Plant.
JO  - Genome Announcements
PY  - 2017
SP  - e01016
EP  - e01017
VL  - 5
AB  - Paenibacillus sp. XY044 is an endophytic bacterium isolated from the stem of a tea plant
AB  - (Camellia sinensis cv. Maoxie). Here, we present the draft genome
AB  - sequence of XY044, which includes genes encoding features related to plant growth
AB  - promotion and biocontrol.
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Song, L.
AU  - Cai, Y.
AU  - Wang, Y.
AU  - Yu, L.
TI  - Draft Genome Sequence of Escherichia coli Strain SEC470, Isolated from a Piglet Experiencing Diarrhea.
JO  - Genome Announcements
PY  - 2016
SP  - e00088
EP  - e00016
VL  - 4
AB  - Escherichia coli strain SEC470 is a diarrhea-causing strain, isolated from a piglet
AB  - experiencing serious diarrhea in Jingxi Province, China. Here, we present
AB  - the draft genome of this strain, which provides the genetic basis for exploring
AB  - the mechanism of enterotoxigenic E. coli infections.
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Wang, C.
AU  - Li, Y.
AU  - Liu, K.
AU  - Hou, Q.
AU  - Xu, W.
AU  - Fan, L.
AU  - Zhao, J.
AU  - Gou, J.
AU  - Du, B.
AU  - Ding, Y.
TI  - Complete Genome Sequence of Paenibacillus polymyxa YC0573, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e01636
EP  - e01616
VL  - 5
AB  - Paenibacillus polymyxa strain YC0573 is a plant growth-promoting rhizobacterium with
AB  - antimicrobial activity, which was isolated from tobacco rhizosphere. Here,
AB  - we report the complete genome sequence of P. polymyxa YC0573. Antifungal and
AB  - antibacterial genes were discovered.
ER  -

TY  - JOUR
AU  - Liu, H.
AU  - Wu, Z.
AU  - Li, M.
AU  - Zhang, F.
AU  - Zheng, H.
AU  - Han, J.
AU  - Liu, J.
AU  - Zhou, J.
AU  - Wang, S.
AU  - Xiang, H.
TI  - Complete Genome Sequence of Haloarcula hispanica, a Model Haloarchaeon for Studying Genetics, Metabolism, and Virus-Host Interaction.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6086
EP  - 6087
VL  - 193
AB  - Haloarcula hispanica is an extremely halophilic archaeon that has an unusually low restriction
AB  - barrier and is therefore significant for
AB  - studying archaeal genetics, metabolism, and virus-host interactions. Here
AB  - we report the complete genome sequence (3,890,005 bp) of H. hispanica
AB  - strain CGMCC 1.2049, consisting of two chromosomes and one megaplasmid.
ER  -

TY  - JOUR
AU  - Liu, J.
AU  - Cheng, A.
AU  - Bangayan, N.J.
AU  - Barnard, E.
AU  - Curd, E.
AU  - Craft, N.
AU  - Li, H.
TI  - Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1.
JO  - Genome Announcements
PY  - 2014
SP  - e00740
EP  - e00714
VL  - 2
AB  - Propionibacterium acnes is a major skin commensal and is associated with acne vulgaris, the
AB  - most common skin disease. Here we report the draft genome sequences
AB  - of two P. acnes strains, the type strain ATCC6919 and an antibiotic-resistant
AB  - strain, HL411PA1.
ER  -

TY  - JOUR
AU  - Liu, J.
AU  - Li, L.
AU  - Peters, B.M.
AU  - Li, B.
AU  - Chen, D.
AU  - Xu, Z.
AU  - Shirtliff, M.E.
TI  - Complete genome sequence and bioinformatics analyses of Bacillus thuringiensis strain BM-BT15426.
JO  - Microb. Pathog.
PY  - 2017
SP  - 55
EP  - 60
VL  - 108
AB  - OBJECTIVES: This study aimed to investigate the genetic characteristics of
AB  - Bacillus thuringiensis strain BM-BT15426. METHODS: B. thuringiensis strain was
AB  - identified by sequencing the PCR product (amplifying 16S rRNA gene) using ABI
AB  - Prism 377 DNA Sequencer. The genome was sequenced using PacBio RS II sequencers
AB  - and assembled de novo using HGAP. Also, further genome annotation was performed.
AB  - RESULTS: The genome of B. thuringiensis strain BM-BT15426 has a length of
AB  - 5,246,329 bp and contains 5409 predicted genes with an average G + C content of
AB  - 35.40%. Three genes were involved in the "Infectious diseases: Amoebiasis"
AB  - pathway. A total of 21 virulence factors and 9 antibiotic resistant genes were
AB  - identified. CONCLUSIONS: The major pathogenic factors of B. thuringiensis strain
AB  - BM-BT15426 were identified through complete genome sequencing and bioinformatics
AB  - analyses which contributes to further study on pathogenic mechanism and phenotype
AB  - of B. thuringiensis.
ER  -

TY  - JOUR
AU  - Liu, J.
AU  - Xue, Y.
AU  - Meng, Y.
AU  - Zhao, X.
AU  - Cai, Y.
TI  - Expression detection and location analysis of BstNI isoschizomer restriction-modification system gene.
JO  - Wei Sheng Wu Xue Bao
PY  - 1999
SP  - 209
EP  - 214
VL  - 39
AB  - Some genetic markers of E. coli HB101 and JM110 were identified, two bacterial strains were
AB  - used as recipients respectively to detect the expression of a restriction endonuclease gene
AB  - and a methylase gene of BstNI isoschizomer restriction-modification system.  DNA fragment
AB  - containing the R-M genes was deleted unidirectionally with exoIII and 23 deletion subclones
AB  - were obtained.  According to the enzyme activity of each subclone, R and M gene were located
AB  - respectively at the regions of 0.2 to 1.4 kb and 1.5 to 3.3 kb from cloning site PstI.
AB  - Analysis showed that the R-M system belongs to type II, two genes are controlled by the
AB  - different promoters; the recognition sequence of this system is the same as that of
AB  - DNA-cytosine methyltransferase (Dcm), the latter's methylation function can resist the R
AB  - enzyme.  It was interesting that the recombinant plasmid with an R+M- genotype appeared to be
AB  - lethal to dcm+ hosts yet.  This indicated that the M gene closely linking to R gene is of
AB  - critical importance for the existence of the R-M system in process of evolution.
ER  -

TY  - JOUR
AU  - Liu, J.
AU  - Zhao, X.
AU  - Meng, Y.
AU  - Shen, J.
AU  - Xue, Y.
AU  - Shi, S.
AU  - Cai, Y.
TI  - Expression and deletion analysis of EcoRII endonuclease and methylase gene.
JO  - Zhongguo Yi Xue Ke Xue Yuan Xue Bao
PY  - 2000
SP  - 111
EP  - 114
VL  - 22
AB  - Objective. To clone the complete EcoRII restriction endonuclease gene (ecoRIIR) and
AB  - methyltransferase (ecoRIIM) gene into one vector and to analyze the expression of the whole
AB  - system.  Methods. Unidirectional deletion subclones, constructed with ExoIII, of the ecoRIIR/M
AB  - genes were preliminarily located in the cloned fragments according to the enzyme activities of
AB  - each subclone, exact deletion sites were determined by sequencing, and transcriptional start
AB  - sites were mapped by S1 mapping.  Results.  The DNA fragment which was cloned into pBluescript
AB  - SK+ contained the complete ecoRIIR gene and ecoRIIM gene, there are two transcriptional start
AB  - sites in the ecoRIIR gene, 132 bp to 458 bp from 3' end of the ecoRIIR gene are indispensable
AB  - to enzyme activities and deletion of 202 bp from the 3' end of the ecoRIIM gene made it lose
AB  - the capability to resist specific cleavage by EcoRIIR enzyme, deletion of coding region and
AB  - flanking sequence of one gene did not affect the expression of the other gene, the recombinant
AB  - only containing ecoRIIR gene appeared to be lethal to dcm+ host.  Conclusions. ecoRIIM gene
AB  - closely linked to the ecoRIIR gene was very important for the existence of the R-M system in
AB  - the process of evolution, but the key to make sure that the EcoRIIR enzyme is produced later
AB  - than the EcoRIIM enzyme does not exist at the transcriptional level.
ER  -

TY  - JOUR
AU  - Liu, J.
AU  - Zhao, X.
AU  - Meng, Y.
AU  - Shen, J.
AU  - Xue, Y.
AU  - Shi, S.
AU  - Cai, Y.
TI  - Expression and deletion analysis of EcoRII endonuclease and methylase gene.
JO  - Chin. Med. Sci. J.
PY  - 2001
SP  - 200
EP  - 203
VL  - 16
AB  - Objective. To clone complete EcoRII restriction endonuclease gene (ecoRIIR) and
AB  - methyltransferase gene (ecoRIIM) in one vector and to analyze the coordinated expression of
AB  - this whole R-M system.  Methods. Unidirectional deletion subclones were constructed with
AB  - ExoIII. ecoRIIR/M genes were preliminarily located in the cloned fragment according to the
AB  - enzyme activities of subclones.  Exact deletion sites were determined by sequencing, and
AB  - transcriptional start sites were determined by S1 mapping.  Results. The DNA fragment which
AB  - was cloned into pBluescript SK + contained intact ecoRIIR gene and ecoRIIM gene, and two
AB  - transcriptional start sites of ecoRIIIR gene were determined.  132bp to 458bp from 3' end of
AB  - ecoRIIR gene are indispensable to enzyme activities and deletion of 202bp from 3' end of
AB  - ecoRIIM gene made enzyme lose the capability in DNA protection to resist specific cut with
AB  - EcoRII endonuclease (EcoRII.R).  Deletion of the coding and flanking sequences of one gene did
AB  - not affect the expression of the other gene, and the recombinants only containing ecoRIIR gene
AB  - appeared to be lethal to dcm+ host.  Conclusion. ecoRIIIM gene linking closely to ecoRIIR gene
AB  - is very important for the existence of the R-M system in process of evolution, but the key to
AB  - control EcoRII R-M order may not exist in transcriptional level.
ER  -

TY  - JOUR
AU  - Liu, J.
AU  - Zhou, Q.
AU  - Ibrahim, M.
AU  - Liu, H.
AU  - Jin, G.
AU  - Zhu, B.
AU  - Xie, G.
TI  - Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6666
EP  - 6667
VL  - 194
AB  - Microbacterium barkeri strain 2011-R4 is a Gram-positive epiphyte which has been  confirmed as
AB  - a biocontrol agent against several plant pathogens in our previous
AB  - studies. Here, we present the draft genome sequence of this strain, which was
AB  - isolated from the rice rhizosphere in Tonglu city, Zhejiang province, China.
ER  -

TY  - JOUR
AU  - Liu, J.-Y.
AU  - Zhao, X.-J.
AU  - Cai, Y.Y.
AU  - Shen, J.
AU  - Meng, Y.
TI  - High expression and purification of EcoRII restriction endonuclease.
JO  - Chin. J. Biochem. Mol. Biol.
PY  - 2000
SP  - 417
EP  - 420
VL  - 16
AB  - EcoRII was the first restriction endonuclease ever found
AB  - requiring the cooperative interaction with the least two DNA sites for
AB  - digestion activity.  To study the specific activity, EcoRII was purified
AB  - from hyperexpression engineering bacteria in which the specific
AB  - expression products increased to about 20% of total cellular protein.
AB  - By using chromatography on DEAE-cellulose column, phosphocellulose
AB  - column and FPLC of Resource Q, the enzyme was purified from soluble
AB  - protein fraction.  The inclusion bodies were solved and renatured, and
AB  - the enzyme was purified from this part of protein with higher specific
AB  - activity by using FPLC of Resource Q.  Detection showed that the enzyme
AB  - was purified to homogeneity and was free of detectable contamination by
AB  - other DNase (exo and endo).
ER  -

TY  - JOUR
AU  - Liu, K.
AU  - Wang, Y.F.
AU  - Cantemir, C.
AU  - Muller, M.T.
TI  - Endogenous assays of DNA methyltransferases: Evidence for differential activities of DNMT1, DNMT2, and DNMT3 in mammalian cells in vivo.
JO  - Mol. Cell. Biol.
PY  - 2003
SP  - 2709
EP  - 2719
VL  - 23
AB  - While CpG methylation can be readily analyzed at the DNA sequence level in wild-type and
AB  - mutant cells, the actual DNA (cytosine-5) methyltransferases
AB  - (DNMTs) responsible for in vivo methylation on genomic DNA are less
AB  - tractable. We used an antibody-based method to identify specific
AB  - endogenous DNMTs (DNMT1, DNMT1b, DNMT2, DNMT3a, and DNMT3b) that stably
AB  - and selectively bind to genomic DNA containing 5-aza-2'-deoxycytidine
AB  - (aza-dC) in vivo. Selective binding to aza-dC-containing DNA suggests that
AB  - the engaged DNMT is catalytically active in the cell. DNMT1b is a splice
AB  - variant of the predominant maintenance activity DNMT1, while DNMT2 is a
AB  - well-conserved protein with homologs in plants, yeast, Drosophila, humans,
AB  - and mice. Despite the presence of motifs essential for transmethylation
AB  - activity, catalytic activity of DNMT2 has never been reported. The data
AB  - here suggest that DNMT2 is active in vivo when the endogenous genome is
AB  - the target, both in human and mouse cell lines. We quantified relative
AB  - global genomic activity of DNMT1, -2, -3a, and -3b in a mouse
AB  - teratocarcinoma cell line. DNMT1 and -3b displayed the greatest in vivo
AB  - binding avidity for aza-dC-containing genomic DNA in these cells. This
AB  - study demonstrates that individual DNMTs can be tracked and that their
AB  - binding to genomic DNA can be quantified in mammalian cells in vivo. The
AB  - different DNMTs display a wide spectrum of genomic DNA-directed activity.
AB  - The use of an antibody-based tracking method will allow specific DNMTs and
AB  - their DNA targets to be recovered and analyzed in a physiological setting
AB  - in chromatin.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Gao, P.
AU  - Chen, G.
AU  - Wang, L.
TI  - Draft Genome Sequence of Cellulose-Digesting Bacterium Sporocytophaga myxococcoides PG-01.
JO  - Genome Announcements
PY  - 2014
SP  - e01154
EP  - e01114
VL  - 2
AB  - Sporocytophaga myxococcoides, a Gram-negative bacterium isolated from soil, is an efficient
AB  - hydrolyzer of crystalline cellulose. Here, we report its draft genome
AB  - sequence, which may provide important genetic information regarding the
AB  - cellulolytic and hemicellulolytic enzymes that contribute to the
AB  - cellulose-degrading abilities of this bacterium.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Li, N.
AU  - Zhang, D.
AU  - Fu, X.
AU  - Shi, C.
AU  - Lin, Q.
TI  - Complete Genome Sequence of the Type Strain of Aeromonas schubertii, ATCC 43700.
JO  - Genome Announcements
PY  - 2016
SP  - e00012
EP  - e00016
VL  - 4
AB  - We sequenced the complete genome of the type strain of Aeromonas schubertii, ATCC 43700. The
AB  - full genome sequence of A. schubertii ATCC 43700 is 4,356,858 bp,
AB  - which encodes 3,842 proteins and contains 110 predicted RNA genes.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Li, N.
AU  - Zhang, D.
AU  - Fu, X.
AU  - Shi, C.
AU  - Lin, Q.
AU  - Hao, G.
TI  - Complete Genome Sequence of the Highly Virulent Aeromonas schubertii Strain WL1483, Isolated from Diseased Snakehead Fish (Channa argus) in China.
JO  - Genome Announcements
PY  - 2016
SP  - e01567
EP  - e01515
VL  - 4
AB  - We sequenced the complete genome of the highly virulent Aeromonas schubertii strain WL1483,
AB  - which was isolated from diseased snakehead fish (Channa argus) in
AB  - China. The full genome sequence of A. schubertii WL1483 is 4,400,034 bp, which
AB  - encodes 4,376 proteins and contains 195 predicted RNA genes.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Li, Y.
AU  - Zhang, J.
AU  - Zhou, Z.
AU  - Liu, J.
AU  - Li, X.
AU  - Zhou, J.
AU  - Du, G.
AU  - Wang, L.
AU  - Chen, J.
TI  - Complete Genome Sequence of the Industrial Strain Ketogulonicigenium vulgare WSH-001.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6108
EP  - 6109
VL  - 193
AB  - Ketogulonicigenium vulgare is an industrial organism commonly used in the vitamin C industry.
AB  - Here, we report the finished, annotated, and compared
AB  - 3.28-Mbp high-quality genome sequence of Ketogulonicigenium vulgare
AB  - WSH-001, a 2-keto-l-gulonic acid-producing industrial strain stocked in
AB  - our laboratory.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Li, Y.
AU  - Zhang, J.
AU  - Zou, W.
AU  - Zhou, Z.
AU  - Liu, J.
AU  - Li, X.
AU  - Wang, L.
AU  - Chen, J.
TI  - Complete Genome Sequence of the Industrial Strain Bacillus megaterium WSH-002.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6389
EP  - 6390
VL  - 193
AB  - Bacillus megaterium, an industrial strain, has been widely used in protein production and the
AB  - vitamin C industry. Here we reported a finished,
AB  - annotated, and compared 4.14-Mbp high-quality genome sequence of B.
AB  - megaterium WSH-002, which is the companion strain for Ketogulonicigenium
AB  - vulgare in the vitamin C industry and is stocked in our laboratory.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Santi, D.V.
TI  - Mutation of asparagine 229 to aspartate in thymidylate synthase converts the enzyme to a deoxycytidylate methylase.
JO  - Biochemistry
PY  - 1992
SP  - 5100
EP  - 5104
VL  - 31
AB  - The conserved Asn 229 of thymidylate synthase (TS) forms a cyclic hydrogen bond network with
AB  - the 3-NH and 4-O of the nucleotide substrate dUMP. The Asn 229 to Asp mutant of Lactobacillus
AB  - casei thymidylate synthase (TS N229D) has been prepared, purified, and investigated.
AB  - Steady-state kinetic parameters of TS N229D show 3.5- and 10-fold increases in the Km values
AB  - of CH2H4 folate and dUMP, respectively, and a 1000-fold decrease in kcat. Most important, the
AB  - Asp 229 mutation changes the substrate specificity of TS to an enzyme which recognizes and
AB  - methylates dCMP in preference to dUMP. With TS N229D the Km for dCMP is about 3-fold higher
AB  - than for dUMP, and the Km for CH2H4 folate is increased about 5-fold; however, the kcat for
AB  - dCMP methylation is 120-fold higher than that for dUMP methylation. Specificity for dCMP
AB  - versus dUMP, as measured by Kcat/Km, changes from negligible with wild-type TS to about a
AB  - 40-fold increase with TS N229D. TS N229D reacts with CH2H4 folate and FdUMP or FdCMP to form
AB  - ternary complexes which are analogous to the TS-FdUMP-CH2H4 folate complex. From what is known
AB  - of the mechanism and structure of TS, the dramatic change in substrate specificity of TS N229D
AB  - is proposed to involve a hydrogen bond network between Asp 229 and the 3-N and 4-NH2 of the
AB  - cytosine mechanism is proposed for related enzymes which catalyze one-carbone transfers to
AB  - cytosine heterocycles.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Xiao, J.
AU  - Xia, X.
AU  - Pan, Y.
AU  - Yan, S.
AU  - Wang, Y.
TI  - Draft Genome Sequence of Vibrio owensii Strain SH-14, Which Causes Shrimp Acute Hepatopancreatic Necrosis Disease.
JO  - Genome Announcements
PY  - 2015
SP  - e01395
EP  - e01315
VL  - 3
AB  - We sequenced Vibrio owensii strain SH-14, which causes serious acute hepatopancreatic necrosis
AB  - disease (AHPND) in shrimp. Sequence analysis showed a
AB  - large extrachromosomal plasmid, which encoded pir toxin genes and shared highly
AB  - sequence similarity with the one observed in AHPND-causing Vibrio
AB  - parahaemolyticus strains. The results suggest that this plasmid appears to play
AB  - an important role in shrimp AHPND.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Yang, F.
AU  - Li, X.
AU  - Luo, J.
AU  - Zhang, Z.
AU  - Li, H.
TI  - Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China.
JO  - Genome Announcements
PY  - 2017
SP  - e01389
EP  - e01316
VL  - 5
AB  - Streptococcus parauberis strain SP-llh was isolated from cows with mastitis in western China
AB  - in 2015. The 2,522,235-bp genome sequence consists of 46 large
AB  - contigs in 14 scaffolds and contains 2,620 predicted protein-coding genes, with a
AB  - G+C content of 35.3%.
ER  -

TY  - JOUR
AU  - Liu, L.
AU  - Zhang, S.
AU  - Luo, M.
AU  - Wang, G.
TI  - Genomic information of the arsenic-resistant bacterium Lysobacter arseniciresistens type strain ZS79(T) and comparison of Lysobacter draft genomes.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 88
EP  - 88
VL  - 10
AB  - Lysobacter arseniciresistens ZS79(T) is a highly arsenic-resistant,rod-shaped, motile,
AB  - non-spore-forming, aerobic, Gram-negative bacterium. In this study, four
AB  - Lysobacter type strains were sequenced and the genomic information of L.
AB  - arseniciresistens ZS79(T) and the comparative genomics results of the Lysobacter
AB  - strains were described. The draft genome sequence of the strain ZS79(T) consists
AB  - of 3,086,721 bp and is distributed in 109 contigs. It has a G+C content of 69.5 %
AB  - and contains 2,363 protein-coding genes including eight arsenic resistant genes.
ER  -

TY  - JOUR
AU  - Liu, L.J.
AU  - You, X.Y.
AU  - Zheng, H.J.
AU  - Wang, S.Y.
AU  - Jiang, C.Y.
AU  - Liu, S.J.
TI  - Complete genome sequence of Metallosphaera cuprina, a metal sulfide-oxidizing archaeon from hot spring.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3387
EP  - 3388
VL  - 193
AB  - The genome of metal sulfide oxidizing, thermoacidiphilic Metallosphaera cuprina Ar-4 has been
AB  - completely sequenced and annotated. Originally
AB  - isolated from a sulfuric hotspring, strain Ar-4 grows optimally at 65
AB  - degrees C and pH of 3.5. The M. cuprina genome has a 1,840,348 bp circular
AB  - chromosome (2029 ORFs) and is 16% smaller than the previously sequenced
AB  - Metallosphaera sedula genome. Compared to the M. sedula genome, there are
AB  - no counterpart genes in the M. cuprina genome for about 480 ORFs in the M.
AB  - sedula genome, of which 243 ORFs are annotated as hypothetical proteins.
AB  - Still, there are 235 ORFs uniquely occurring in M. cuprina. Genome
AB  - annotation supports that M. cuprina lives a facultative life on CO(2) and
AB  - organics, and obtains energy from oxidation of sulfidic ores and reduced
AB  - inorganic sulfuric compounds.
ER  -

TY  - JOUR
AU  - Liu, L.N.
AU  - Faulkner, M.
AU  - Liu, X.
AU  - Huang, F.
AU  - Darby, A.C.
AU  - Hall, N.
TI  - Revised Genome Sequence of the Purple Photosynthetic Bacterium Blastochloris viridis.
JO  - Genome Announcements
PY  - 2016
SP  - e01520
EP  - e01515
VL  - 4
AB  - Blastochloris viridis is a unique anaerobic, phototrophic purple bacterium that produces
AB  - bacteriochlorophyll b. Here we report an improved genome sequence of
AB  - Blastochloris viridis DSM133, which is instrumental to the studies of
AB  - photosynthesis, metabolic versatility, and genetic engineering of this
AB  - microorganism.
ER  -

TY  - JOUR
AU  - Liu, M.
AU  - Chen, S.
TI  - Draft Genome Sequence of Vibrio parahaemolyticus V110, Isolated from Shrimp in Hong Kong.
JO  - Genome Announcements
PY  - 2013
SP  - e00300
EP  - e00313
VL  - 1
AB  - We report the whole-genome sequence of a tdh- and trh-negative Vibrio parahaemolyticus strain,
AB  - V110, from shrimp. The major difference of V110 from
AB  - clinical strains was its lack of the type III secretion system T3SS2, a key
AB  - component of virulence. Further sequence comparison can shed light on the
AB  - pathogenesis of V. parahaemolyticus.
ER  -

TY  - JOUR
AU  - Liu, M.S.
AU  - Gingery, M.
AU  - Doulatov, S.R.
AU  - Liu, Y.C.
AU  - Hodes, A.
AU  - Baker, S.
AU  - Davis, P.
AU  - Simmonds, M.
AU  - Churcher, C.
AU  - Mungall, K.
AU  - Quail, M.A.
AU  - Preston, A.
AU  - Harvill, E.T.
AU  - Maskell, D.J.
AU  - Eiserling, F.A.
AU  - Parkhill, J.
AU  - Miller, J.F.
TI  - Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.
JO  - J. Bacteriol.
PY  - 2004
SP  - 1503
EP  - 1517
VL  - 186
AB  - Liu et al. recently described a group of related temperate bacteriophages that infect
AB  - Bordetella subspecies and undergo a unique
AB  - template-dependent, reverse transcriptase-mediated tropism switching
AB  - phenomenon (Liu et al., Science 295:2091-2094, 2002). Tropism switching
AB  - results from the introduction of single nucleotide substitutions at
AB  - defined locations in the VR1 (variable region 1) segment of the mtd
AB  - (major tropism determinant) gene, which determines specificity for
AB  - receptors on host bacteria. In this report, we describe the complete
AB  - nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA
AB  - genomes of three related phage isolates and characterize two additional
AB  - regions of variability. Forty-nine coding sequences were identified. Of
AB  - these coding sequences, bbp36 contained VR2 (variable region 2), which
AB  - is highly dynamic and consists of a variable number of identical 19-bp
AB  - repeats separated by one of three 5-bp spacers, and bpm encodes a DNA
AB  - adenine methylase with unusual site specificity and a homopolymer tract
AB  - that functions as a hotspot for frameshift mutations. Morphological and
AB  - sequence analysis suggests that these Bordetella phage are genetic
AB  - hybrids of P22 and T7 family genomes, lending further support to the
AB  - idea that regions encoding protein domains, single genes, or blocks of
AB  - genes are readily exchanged between bacterial and phage genomes.
AB  - Bordetella bacteriophages are capable of transducing genetic markers in
AB  - vitro, and by using animal models, we demonstrated that lysogenic
AB  - conversion can take place in the mouse respiratory tract during
AB  - infection.
ER  -

TY  - JOUR
AU  - Liu, P.
AU  - Li, P.
AU  - Jiang, X.
AU  - Bi, D.
AU  - Xie, Y.
AU  - Tai, C.
AU  - Deng, Z.
AU  - Rajakumar, K.
AU  - Ou, H.Y.
TI  - Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a Multidrug-Resistant Strain Isolated from Human Sputum.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1841
EP  - 1842
VL  - 194
AB  - Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic
AB  - infections. Here we report the genome sequence of a strain,
AB  - HS11286, isolated from human sputum in 2011 in Shanghai, China. It contains one
AB  - chromosome (5.3 Mb), three multidrug resistance plasmids ( approximately 110 kb),
AB  - including a carbapenemase producer, and three small plasmids ( approximately 3
AB  - kb).
ER  -

TY  - JOUR
AU  - Liu, P.
AU  - Yang, X.-Hai.
AU  - Wang, Q.
AU  - Huang, J.
AU  - Liu, J.-Bo.
AU  - Zhu, Y.
AU  - He, L.-L.
AU  - Wang, Ke.-Min.
TI  - Sensitive detection of DNA methyltransferase activity based on rolling circle amplification technology.
JO  - Chin. Chem. Lett.
PY  - 2014
SP  - 1047
EP  - 1051
VL  - 25
AB  - This work develops a fluorescence approach for sensitive detection of DNA methyltransferase
AB  - activity based on endonuclease and rolling circle amplification (RCA) technique. In the
AB  - presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of
AB  - hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease
AB  - Dpn I. The products cleaved by restriction endonuclease Dpn I then function as a signal primer
AB  - to initiate RCA reaction by hybridizing with the circular DNA template. Each RCA product
AB  - containing thousands of repeated sequences might hybridize with a large number of molecular
AB  - beacons (detection probes), resulting in an enhanced fluorescence signal. In the absence of
AB  - Dam MTase, neither methylation/cleavage nor RCA reaction can be initiated and no fluorescence
AB  - signal is observed. The proposed method exhibits a dynamic range from 0.5 U/mL to 30 U/mL and
AB  - a detection limit of 0.18 U/mL. This method can be used for the screening of antimicrobial
AB  - drugs and has a great potential to be further applied in early clinical diagnosis.
ER  -

TY  - JOUR
AU  - Liu, P.
AU  - Zheng, H.
AU  - Meng, Q.
AU  - Terahara, N.
AU  - Gu, W.
AU  - Wang, S.
AU  - Zhao, G.
AU  - Nakane, D.
AU  - Wang, W.
AU  - Miyata, M.
TI  - Chemotaxis without Conventional Two-Component System, Based on Cell Polarity and Aerobic Conditions in Helicity-Switching Swimming of Spiroplasma eriocheiris.
JO  - Front. Microbiol.
PY  - 2017
SP  - 58
EP  - 58
VL  - 8
AB  - Spiroplasma eriocheiris is a pathogen that causes mass mortality in Chinese
AB  - mitten crab, Eriocheir sinensis. S. eriocheiris causes tremor disease and infects
AB  - almost all of the artificial breeding crustaceans, resulting in disastrous
AB  - effects on the aquaculture economy in China. S. eriocheiris is a wall-less
AB  - helical bacterium, measuring 2.0 to 10.0 mum long, and can swim up to 5 mum per
AB  - second in a viscous medium without flagella by switching the cell helicity at a
AB  - kink traveling from the front to the tail. In this study, we showed that S.
AB  - eriocheiris performs chemotaxis without the conventional two-component system, a
AB  - system commonly found in bacterial chemotaxis. The chemotaxis of S. eriocheiris
AB  - was observed more clearly when the cells were cultivated under anaerobic
AB  - conditions. The cells were polarized as evidenced by a tip structure, swimming in
AB  - the direction of the tip, and were shown to reverse their swimming direction in
AB  - response to attractants. Triton X-100 treatment revealed the internal structure,
AB  - a dumbbell-shaped core in the tip that is connected by a flat ribbon, which
AB  - traces the shortest line in the helical cell shape from the tip to the other
AB  - pole. Sixteen proteins were identified as the components of the internal
AB  - structure by mass spectrometry, including Fibril protein and four types of MreB
AB  - proteins.
ER  -

TY  - JOUR
AU  - Liu, P.P.
AU  - Liu, Y.
AU  - Wang, L.H.
AU  - Wei, D.D.
AU  - Wan, L.G.
TI  - Draft Genome Sequence of an NDM-5-Producing Klebsiella pneumoniae Sequence Type 14 Strain of Serotype K2.
JO  - Genome Announcements
PY  - 2016
SP  - e01610
EP  - e01615
VL  - 4
AB  - We report here the draft genome sequence of uropathogenic Klebsiella pneumoniae sequence type
AB  - 14 strain of serotype K2 possessing blaNDM-5, isolated from a
AB  - 65-year-old male in China without a history of travel abroad.
ER  -

TY  - JOUR
AU  - Liu, P.Y.
AU  - Huang, Y.T.
AU  - Lin, S.Y.
AU  - Chang, G.C.
AU  - Chen, J.W.
TI  - Draft Genome Sequence of the Serratia marcescens Strain VGH107, a Taiwanese Clinical Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e00249
EP  - e00213
VL  - 1
AB  - Serratia marcescens, a member of the family Enterobacteriaceae, is the causative  agent of
AB  - various types of wound infections. We report a high-quality draft genome
AB  - sequence of S. marcescens strain VGH107, which was isolated from a patient with
AB  - an infection from a snakebite wound.
ER  -

TY  - JOUR
AU  - Liu, Q.
AU  - Chen, X.
AU  - Zhao, X.
AU  - Chen, Y.
AU  - Chen, D.
TI  - The effect of methylation outside the recognition sequence of restriction endonuclease PvuII on its cleavage efficiency.
JO  - Gene
PY  - 1992
SP  - 89
EP  - 93
VL  - 113
AB  - This study is to extend our earlier observation that Dam and Dcm methylation outside the PvuII
AB  - recognition sequence inhibited PvuII cleavage in one of the three PvuII sites of pGEM4Z-ras
AB  - DNA. In this paper, a new recombinant plasmid DNA, pGEM4-SV40ori-anti-ras, was constructed
AB  - which has only two PvuII sites, I and II. The Dam and Dcm-methylated and unmethylated DNAs
AB  - were produced in Escherichia coli and linearized by ScaI. The DNA molecules were digested with
AB  - different amounts of PvuII. The results show that by comparing the DNA fragment number and
AB  - intensity of the partial and final products in agarose gels, PvuII site I on the methylated
AB  - DNA molecule was digested four- to eight-fold more slowly than site II. In the unmethylated
AB  - plasmid DNA, the two PvuII sites were cleaved at about the same rate. The difference was
AB  - caused only by methylation of Dam and Dcm sites outside the PvuII recognition sequence. A
AB  - methylated Dam site immediately adjacent to the less efficiently cut PvuII site I may be
AB  - responsible for the inhibitory effect. We suggest that a new parameter, involving methylation
AB  - of sites outside the recognition sequence, be considered in kinetic experiments on cleavage.
ER  -

TY  - JOUR
AU  - Liu, Q.
AU  - Derbyshire, V.
AU  - Balfort, M.
AU  - Edgell, D.R.
TI  - Distance determination by GIY-YIG intron endonucleases: Discrimination between repression and cleavage functions.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 1755
EP  - 1755
VL  - 34
AB  - GIY-YIG homing endonucleases are modular proteins, with conserved N-terminal catalytic domains
AB  - connected by linkers to C-terminal DNA-binding domains. I-TevI, the T4 phage GIY-YIG intron
AB  - endonuclease, functions both in promoting td intron homing, and in acting as a transcriptional
AB  - autorepressor. Repression is achieved by binding to an operator, which is cleaved at 100-fold
AB  - reduced efficiency relative to the intronless homing site. The linker includes a zinc finger,
AB  - which functions in distance determination, to constrain the catalytic domain to cleave the
AB  - homing site at a fixed position. Here we show that I-BmoI, a related GIY-YIG endonuclease
AB  - lacking a zinc finger, also possesses some cleavage distance discrimination. Furthermore,
AB  - hybrid endonucleases constructed by swapping the domains of I-BmoI and I-TevI are active,
AB  - precise and demonstrate that features other than the zinc finger facilitate distance
AB  - determination. Most importantly, I-TevI zinc finger mutants cleave the operator more
AB  - efficiently than the homing site, the converse of wild-type protein. These results are
AB  - consistent with the zinc finger acting as a measuring device, directing efficient cleavage of
AB  - the homing site to promote intron mobility, while reducing cleavage at the operator to ensure
AB  - transcriptional autorepression and phage viability.
ER  -

TY  - JOUR
AU  - Liu, Q.
AU  - Wu, Y.H.
AU  - Cheng, H.
AU  - Xu, L.
AU  - Wang, C.S.
AU  - Xu, X.W.
TI  - Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 32
EP  - 32
VL  - 12
AB  - The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster.
AB  - Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic
AB  - freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as
AB  - well as grow under aerobic conditions. It is the type species of the genus
AB  - Porphyrobacter. Here we describe the characteristics of the strain DSM 9434,
AB  - including the genome sequence and annotation, synthesis of BChl a, and metabolic
AB  - pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp
AB  - and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain
AB  - DSM 9434 encodes 46 genes which participate in BChl a synthesis and this
AB  - investigation shed light on the evolution and functional implications regarding
AB  - bacteriochlorophyll synthesis.
ER  -

TY  - JOUR
AU  - Liu, Q.Q.
AU  - Dansereau, J.T.
AU  - Puttamadappa, S.S.
AU  - Shekhtman, A.
AU  - Derbyshire, V.
AU  - Belfort, M.
TI  - Role of the interdomain linker in distance determination for remote cleavage by homing endonuclease I-TevI.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 1094
EP  - 1106
VL  - 379
AB  - I-TevI is a modular intron-encoded endonuclease, consisting of an N-terminal catalytic domain
AB  - and a C-terminal DNA-binding domain, joined
AB  - by a 75 amino acid linker. This linker can be divided into three
AB  - regions, starting at the N terminus: the deletion-intolerant (DI)
AB  - region; the deletion-tolerant (DT) region; and a zinc finger, which
AB  - acts as a distance determinant for cleavage. To further explore linker
AB  - function, we generated deletion and substitution mutants that were
AB  - tested for their preference to cleave at a particular distance or at
AB  - the correct sequence. Our results demonstrate that the I-TevI linker is
AB  - multi-functional, a property that sets it apart from junction sequences
AB  - in most other proteins. First, the linker DI region has a role in
AB  - I-TevI cleavage activity. Second, the DT linker region participates in
AB  - distance determination, as evident from DT mutants that display a
AB  - phenotype similar to that of the zinc-finger mutants in their selection
AB  - of a cleavage site. Finally, NMR analysis of a freestanding 56 residue
AB  - linker segment showed an unstructured stretch corresponding to the DI
AB  - region and a portion of the DT region, followed by a beta-strand
AB  - corresponding to the remainder of the DT region and containing a key
AB  - distance-determining arginine, R129. Mutation of this arginine to
AB  - alanine abolished distance determination and disrupted the beta-strand,
AB  - indicating that the structure of the DT linker region has a role in
AB  - cleavage at a fixed distance.
ER  -

TY  - JOUR
AU  - Liu, S.
AU  - Wang, Y.
AU  - Xu, J.
AU  - Li, Y.
AU  - Guo, J.
AU  - Ke, Y.
AU  - Yuan, X.
AU  - Wang, L.
AU  - Du, X.
AU  - Wang, Z.
AU  - Huang, L.
AU  - Zhang, N.
AU  - Chen, Z.
TI  - Genome Sequence of an OXA23-Producing, Carbapenem-Resistant Acinetobacter baumannii Strain of Sequence Type ST75.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6000
EP  - 6001
VL  - 194
AB  - The increase of Acinetobacter baumannii resistance to carbapenems is of great concern. OXA23
AB  - is one of the most prevalent carbapenemases of A. baumannii that
AB  - causes outbreaks. Here, we announce the genome sequence of an OXA23-producing A.
AB  - baumannii strain assigned ST75, a newly emerged sequence type harboring
AB  - carbapenemase.
ER  -

TY  - JOUR
AU  - Liu, S.L.
AU  - Hessel, A.
AU  - Sanderson, K.E.
TI  - Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella ssp., Escherichia coli, and other bacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 6874
EP  - 6878
VL  - 90
AB  - Construction of physical maps of genomes by pulsed-field gel electrophoresis requires enxymes
AB  - which cut the genome into an analyzable number of fragments; most produce too many fragments.
AB  - The enzyme I-CeuI, encoded by a mobile intron in the chloroplast 23S ribosomal RNA (rrl) gene
AB  - of Chlamydomonas eugametos, cuts a 26-bp site in the rrl gene. This enzyme digests DNA of
AB  - Salmonella typhimurium at seven sites, each corresponding to one of the rrl genes of the rrn
AB  - operons, but at no other site. These seven fragments were located on the previously determined
AB  - XbaI physical map, and the I-CeuI sites, and thus the rrn genes of S. typhimurium, were mapped
AB  - on the 4800-kb chromosome. Escherichia coli K-12 also yields seven fragments of sizes similar
AB  - to those of S. typhimurium, indicating conservation of rrn genes and their location, and a
AB  - chromosome size of 4600 kb. The sizes of the E. coli fragments are close to the size predicted
AB  - from restriction maps and nucleotide sequence. The I-CeuI maps of Salmonella typhi were
AB  - deduced after digesting genomic DNA with I-CeuI and probing with DNA of S. typhimurium; the
AB  - data indicated strong conservation of rrn gene number and position and genome sizes up to 4950
AB  - kb. Digestion of DNA of other bacteria (species of Haemophilus, Neisseria, Proteus, and
AB  - Pasteurella) suggested that only rrn genes are cut in all these species. I-CeuI digestion
AB  - followed by pulsed-field gel electrophoresis is a powerful tool for determining genome
AB  - structure and evolution.
ER  -

TY  - JOUR
AU  - Liu, T.
AU  - Zhu, L.
AU  - Zhang, Z.
AU  - Jiang, L.
AU  - Huang, H.
TI  - Draft Genome Sequence of Myroides sp. N17-2, a Multidrug-Resistant Bacterium Isolated from Radiation-Polluted Soils.
JO  - Genome Announcements
PY  - 2017
SP  - e01301
EP  - e01317
VL  - 5
AB  - We report here the 4.29-Mb draft genome sequence of Myroides sp. N17-2, a new bacterium
AB  - isolated from radiation-polluted soils in Xinjiang, Uyghur Autonomous
AB  - Region, China. The acquisition of its genome will provide valuable information to
AB  - reveal the relationship between radiation and multidrug resistance.
ER  -

TY  - JOUR
AU  - Liu, T.-T.
AU  - Liu, J.-F.
AU  - Wang, W.-X.
AU  - Wang, H.
AU  - Wang, Z.-L.
AU  - Zeng, Z.-J.
AU  - Yan, W.-Y.
TI  - Cloning and expression profiling of the DNA methyltransferase Dnmt3 gene in the Chinese honeybee, Apis cerana cerana (Hymenoptera: Apidae).
JO  - Acta Entomologica Sinica
PY  - 2012
SP  - 284
EP  - 290
VL  - 55
AB  - To explore the pattern of methylation in the Chinese honeybee, Apis cerana cerana, the DNA
AB  - methyltransferase 3 (Dnmt3) gene in A. cerana
AB  - cerana was cloned by using RT-PCR, and the quantitative analysis of the
AB  - expression level of Dnmt3 mRNA in different developmental stages of
AB  - worker (4 d-old pupa, 1, 7 and 30 d-old workers, and laying worker) and
AB  - queen (4 d-old pupa, 1 d-old queen and laying queen) were conducted
AB  - using real-time qPCR. The full-length cDNA of Dnmt3 gene (GenBank
AB  - accession no. JQ740768) is 2 277 bp, encoding 758 amino acids, and the
AB  - predicted MW and pI are 88. 24 kD and 7. 85, respectively. Based on the
AB  - comparison of the domain and the phylogenetic tree of the amino acids
AB  - of Dnmt3 in A. cerana cerana and other species, the sequence obtained
AB  - has up to 99% identity with that of A. mellifera. The Dnmt3 transcript
AB  - was clearly detected in different developmental stages of worker and
AB  - queen, and it was expressed significantly higher in 30 d-old worker
AB  - than in 1 d- and 7 d-old worker (P < 0.05), while no difference existed
AB  - between 1 d- and 7 d-old worker (P > 0. 05). The Dnmt3 transcript was
AB  - expressed higher in queen pupae than in worker pupae (P < 0.05), and
AB  - was higher in 1 d-old queen than in 1 d-old worker (P <0. 05). The
AB  - expression level of Dnmt3 gene between laying worker and laying queen
AB  - had no significant difference. The results suggested that Dnmt3 may be
AB  - involved in the division of labor in workers and ovary development in
AB  - honeybees.
ER  -

TY  - JOUR
AU  - Liu, W.
TI  - Fluorescence studies of EcoRI restriction endonuclease structure and dynamics.
JO  - Diss. Abstr.
PY  - 1997
SP  - 681
EP  - 681
VL  - 58
AB  - Sequence specific protein-DNA interaction involves changes in protein conformation and
AB  - dynamics.  Research work involved in this thesis is the study of structure and dynamics of
AB  - EcoRI restriction endonuclease N-termini.  The N-termini of EcoRI endonuclease has been shown
AB  - to be essential for DNA cleavage and also stabilize EcoRI-DNA complex.  But they are not
AB  - resolved in the X-ray crystal structure.  An Asn3Cys mutation was made at the N-termini by
AB  - site-directed mutagenesis and the mutant was subjected to cysteine crosslinking, pyrene
AB  - labeling and fluorescence studies.  Chemical crosslinking of Asn3Cys mutant and steady-state
AB  - fluorescence studies of pyrene-labeled mutant indicated that the N-termini are in close
AB  - proximity and probably involved in the dimer interface.  Time resolved fluorescence
AB  - measurements revealed dynamics of the N-termini by examining the dissociation and reformation
AB  - of pyrene excimers as well as the monomer spectral shifts caused by N-terminal segment
AB  - movements.  Fluorescence anisotropy decay analysis indicated the N-termini are on the protein
AB  - surface and not totally disoriented in solution.  Substrate DNA binding, however, causes the
AB  - N-termini to be more mobile without affecting the proximity relationship.  Fluorescence energy
AB  - transfer experiments were carried out using a double-mutant Asn3Cys,Trp104Tyr.  The through
AB  - space distance between the fluorescent labels, MIANS or 1,5 -IAEDANS, and Trp246 is around 30
AB  - Angstroms.  Substrate DNA binding decreased the distance to 26 Angstroms but cofactor Mg2+ ion
AB  - did not cause any distance change.  Single Trp246 fluorescence in the double mutant also
AB  - revealed possible conformational changes upon substrate DNA or cofactor binding.  Experimental
AB  - evidence indicates that the N-termini are located at the dimer interface but distal to the DNA
AB  - binding site.  The findings provide further insight into the function of the N-termini of
AB  - EcoRI endonuclease.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Chen, Y.
AU  - Watrob, H.
AU  - Bartlett, S.G.
AU  - Jen-Jacobson, L.
AU  - Barkley, M.D.
TI  - N-termini of EcoRI restriction endonuclease dimer are in close proximity on the protein surface.
JO  - Biochemistry
PY  - 1998
SP  - 15457
EP  - 15465
VL  - 37
AB  - The N-terminal region of EcoRI endonuclease is essential for cleavage yet is invisible in the
AB  - 2.5 A crystal structure of endonuclease-DNA. We used site-directed fluorescence spectroscopy
AB  - and chemical cross-linking to locate the N-terminal region and assess its flexibility in the
AB  - absence and presence of DNA substrate. The second amino acid in each subunit of the homodimer
AB  - was replaced with cysteine and labeled with pyrene or reacted with bifunctional cross-linkers.
AB  - The broad absorption spectra and characteristic excimer emission bands of pyrene-labeled
AB  - muteins indicated stacking of the two pyrene rings in the homodimer. Proximity of N-terminal
AB  - cysteines was confirmed by disulfide bond formation and chemical cross-linking. The dynamics
AB  - of the N-terminal region were determined from time-resolved emission anisotropy measurements.
AB  - The anisotropy decay had two components: a fast component with rotational correlation time of
AB  - 0.3-3 ns representing probe internal motions and a slow component with 50-100 ns correlation
AB  - time representing overall tumbling of the protein conjugate. We conclude that the N-termini
AB  - are close together at the dimer interface with limited flexibility. Binding of Mg2+ cofactor
AB  - or DNA substrate did not affect the location or flexibility of the N-terminal region as sensed
AB  - by pyrene fluorescence and cross-linking, indicating that substrate binding is not accompanied
AB  - by folding or unfolding of the N-terminus.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Fang, L.
AU  - Li, S.
AU  - Li, Q.
AU  - Zhou, Z.
AU  - Feng, Z.
AU  - Luo, R.
AU  - Shao, G.
AU  - Wang, L.
AU  - Chen, H.
AU  - Xiao, S.
TI  - Complete Genome Sequence of Mycoplasma hyorhinis Strain HUB-1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5844
EP  - 5845
VL  - 192
AB  - Mycoplasma hyorhinis is generally considered a swine pathogen yet is most commonly found
AB  - infecting laboratory cell lines. An increasing body of
AB  - evidence suggests that chronic infections with M. hyorhinis may cause
AB  - oncogenic transformation. Here, we announce the complete genome sequence
AB  - of M. hyorhinis strain HUB-1.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Feng, Z.
AU  - Fang, L.
AU  - Zhou, Z.
AU  - Li, Q.
AU  - Li, S.
AU  - Luo, R.
AU  - Wang, L.
AU  - Chen, H.
AU  - Shao, G.
AU  - Xiao, S.
TI  - Complete Genome Sequence of Mycoplasma hyopneumoniae Strain 168.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1016
EP  - 1017
VL  - 193
AB  - Mycoplasma hyopneumoniae strain 168, a pathogenic strain prevalent in China, was isolated in
AB  - 1974. Although this strain has been widespread for
AB  - a long time, the genome sequence had not been determined. Here, we
AB  - announce the complete genome sequence of M. hyopneumoniae strain 168.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Jing, Z.
AU  - Ou, Q.
AU  - Cui, B.
AU  - He, Y.
AU  - Wu, Q.
TI  - Complete Genome Sequence of Brucella melitensis Biovar 3 Strain NI, Isolated from an Aborted Bovine Fetus.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6321
EP  - 6321
VL  - 194
AB  - From an aborted bovine fetus in China, a bacterial strain named NI was isolated and identified
AB  - as Brucella melitensis by a PCR assay. Strain NI was further
AB  - characterized as B. melitensis biovar 3 using biochemical assays. Here we report
AB  - the complete genome sequence of strain NI.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Liu, C.
AU  - Sun, D.
TI  - Complete Genome Sequence of a Novel Bioflocculant-Producing Strain, Microbacterium paludicola CC3.
JO  - Genome Announcements
PY  - 2017
SP  - e01008
EP  - e01017
VL  - 5
AB  - Microbacterium paludicola CC3 exhibits the capability to produce polysaccharide
AB  - bioflocculants. Here, we report the whole-genome sequence of M. paludicola CC3,
AB  - which may be helpful in understanding the genetic basis of the biosynthesis of
AB  - polysaccharide bioflocculants as well as in promoting its production and
AB  - application in industrial fields.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Xiao, S.
AU  - Li, M.
AU  - Guo, S.
AU  - Li, S.
AU  - Luo, R.
AU  - Feng, Z.
AU  - Li, B.
AU  - Zhou, Z.
AU  - Shao, G.
AU  - Chen, H.
AU  - Fang, L.
TI  - Comparative genomic analyses of Mycoplasma hyopneumoniae pathogenic 168 strain and its high-passaged attenuated strain.
JO  - BMC Genomics
PY  - 2013
SP  - 80
EP  - 80
VL  - 14
AB  - BACKGROUND: Mycoplasma hyopneumoniae is the causative agent of porcine enzootic
AB  - pneumonia (EP), a mild, chronic pneumonia of swine. Despite presenting with low
AB  - direct mortality, EP is responsible for major economic losses in the pig
AB  - industry. To identify the virulence-associated determinants of M. hyopneumoniae,
AB  - we determined the whole genome sequence of M. hyopneumoniae strain 168 and its
AB  - attenuated high-passage strain 168-L and carried out comparative genomic
AB  - analyses. RESULTS: We performed the first comprehensive analysis of M.
AB  - hyopneumoniae strain 168 and its attenuated strain and made a preliminary survey
AB  - of coding sequences (CDSs) that may be related to virulence. The 168-L genome has
AB  - a highly similar gene content and order to that of 168, but is 4,483 bp smaller
AB  - because there are 60 insertions and 43 deletions in 168-L. Besides these indels,
AB  - 227 single nucleotide variations (SNVs) were identified. We further investigated
AB  - the variants that affected CDSs, and compared them to reported virulence
AB  - determinants. Notably, almost all of the reported virulence determinants are
AB  - included in these variants affected CDSs. In addition to variations previously
AB  - described in mycoplasma adhesins (P97, P102, P146, P159, P216, and LppT), cell
AB  - envelope proteins (P95), cell surface antigens (P36), secreted proteins and
AB  - chaperone protein (DnaK), mutations in genes related to metabolism and growth may
AB  - also contribute to the attenuated virulence in 168-L. Furthermore, many mutations
AB  - were located in the previously described repeat motif, which may be of primary
AB  - importance for virulence. CONCLUSIONS: We studied the virulence attenuation
AB  - mechanism of M. hyopneumoniae by comparative genomic analysis of virulent strain
AB  - 168 and its attenuated high-passage strain 168-L. Our findings provide a
AB  - preliminary survey of CDSs that may be related to virulence. While these include
AB  - reported virulence-related genes, other novel virulence determinants were also
AB  - detected. This new information will form the foundation of future investigations
AB  - into the pathogenesis of M. hyopneumoniae and facilitate the design of new
AB  - vaccines.
ER  -

TY  - JOUR
AU  - Liu, W.
AU  - Yang, M.
AU  - Xu, Z.
AU  - Zheng, H.
AU  - Liang, W.
AU  - Zhou, R.
AU  - Wu, B.
AU  - Chen, H.
TI  - Complete Genome Sequence of Pasteurella multocida HN06, a Toxigenic Strain of Serogroup D.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3292
EP  - 3293
VL  - 194
AB  - Pasteurella multocida is an important etiological agent that can cause many economically
AB  - important diseases in a wide range of mammals and birds. Here, we
AB  - report the complete genome sequence of P. multocida HN06, a toxigenic serogroup D
AB  - strain isolated from a diseased pig in China.
ER  -

TY  - JOUR
AU  - Liu, W.B.
AU  - Yu, W.B.
AU  - Gao, S.H.
AU  - Ye, B.C.
TI  - Genome Sequence of Saccharopolyspora erythraea D, a Hyperproducer of Erythromycin.
JO  - Genome Announcements
PY  - 2013
SP  - e00718
EP  - e00713
VL  - 1
AB  - Saccharopolyspora erythraea is a Gram-positive bacterium that can produce antibiotics.
AB  - However, this microorganism must often be genetically improved for
AB  - higher production before it can be used in an industrial setting. Here, we report
AB  - the whole-genome sequence of the industrial hyperproducer strong mutator
AB  - Saccharopolyspora erythraea strain D.
ER  -

TY  - JOUR
AU  - Liu, W.Q.
AU  - Feng, Y.
AU  - Wang, Y.
AU  - Zou, Q.H.
AU  - Chen, F.
AU  - Guo, J.T.
AU  - Peng, Y.H.
AU  - Jin, Y.
AU  - Li, Y.G.
AU  - Hu, S.N.
AU  - Johnston, R.N.
AU  - Liu, G.R.
AU  - Liu, S.L.
TI  - Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi.
JO  - PLoS ONE
PY  - 2009
SP  - E4510
EP  - E4510
VL  - 4
AB  - BACKGROUND: Although over 1400 Salmonella serovars cause usually
AB  - self-limited gastroenteritis in humans, a few, e.g., Salmonella typhi and
AB  - S. paratyphi C, cause typhoid, a potentially fatal systemic infection. It
AB  - is not known whether the typhoid agents have evolved from a common
AB  - ancestor (by divergent processes) or acquired similar pathogenic traits
AB  - independently (by convergent processes). Comparison of different typhoid
AB  - agents with non-typhoidal Salmonella lineages will provide excellent
AB  - models for studies on how similar pathogens might have evolved.
AB  - METHODOLOGIES/PRINCIPAL FINDINGS: We sequenced a strain of S. paratyphi C,
AB  - RKS4594, and compared it with previously sequenced Salmonella strains.
AB  - RKS4594 contains a chromosome of 4,833,080 bp and a plasmid of 55,414 bp.
AB  - We predicted 4,640 intact coding sequences (4,578 in the chromosome and 62
AB  - in the plasmid) and 152 pseudogenes (149 in the chromosome and 3 in the
AB  - plasmid). RKS4594 shares as many as 4346 of the 4,640 genes with a strain
AB  - of S. choleraesuis, which is primarily a swine pathogen, but only 4008
AB  - genes with another human-adapted typhoid agent, S. typhi. Comparison of
AB  - 3691 genes shared by all six sequenced Salmonella strains placed S.
AB  - paratyphi C and S. choleraesuis together at one end, and S. typhi at the
AB  - opposite end, of the phylogenetic tree, demonstrating separate ancestries
AB  - of the human-adapted typhoid agents. S. paratyphi C seemed to have
AB  - suffered enormous selection pressures during its adaptation to man as
AB  - suggested by the differential nucleotide substitutions and different sets
AB  - of pseudogenes, between S. paratyphi C and S. choleraesuis. CONCLUSIONS:
AB  - S. paratyphi C does not share a common ancestor with other human-adapted
AB  - typhoid agents, supporting the convergent evolution model of the typhoid
AB  - agents. S. paratyphi C has diverged from a common ancestor with S.
AB  - choleraesuis by accumulating genomic novelty during adaptation to man.
ER  -

TY  - JOUR
AU  - Liu, W.Y.
AU  - Chung, K.M.
AU  - Wong, C.F.
AU  - Jiang, J.W.
AU  - Hui, R.K.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of the Endophytic Enterobacter cloacae subsp. cloacae Strain ENHKU01.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5965
EP  - 5965
VL  - 194
AB  - Enterobacter cloacae subsp. cloacae strain ENHKU01 is a Gram-negative endophyte isolated from
AB  - a diseased pepper (Capsicum annuum) plant in Hong Kong. This is the
AB  - first complete genome sequence report of a plant-endophytic strain of E. cloacae
AB  - subsp. cloacae.
ER  -

TY  - JOUR
AU  - Liu, X.
AU  - Arumugam, K.
AU  - Natarajan, G.
AU  - Seviour, T.W.
AU  - Drautz-Moses, D.I.
AU  - Wuertz, S.
AU  - Law, Y.
AU  - Williams, R.B.H.
TI  - Draft Genome Sequence of a 'Candidatus Brocadia' Bacterium Enriched from Activated Sludge Collected in a Tropical Climate.
JO  - Genome Announcements
PY  - 2018
SP  - e00406
EP  - e00418
VL  - 6
AB  - Here, we present the draft genome sequence of an anaerobic ammonium-oxidizing bacterium
AB  - (AnAOB), 'Candidatus Brocadia,' which was enriched in an anammox
AB  - reactor. A 3.2-Mb genome sequence comprising 168 contigs was assembled, in which
AB  - 2,765 protein-coding genes, 47 tRNAs, and one each of 5S, 16S, and 23S rRNAs were
AB  - annotated. No evidence for the presence of a nitric oxide-forming nitrite
AB  - reductase was found.
ER  -

TY  - JOUR
AU  - Liu, X.
AU  - Gai, Z.
AU  - Tao, F.
AU  - Yu, H.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R,  Two Efficient Carbazole-Degrading Strains.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5701
EP  - 5702
VL  - 194
AB  - Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R are two efficient
AB  - carbazole-degrading pseudomonad strains. Here we present 4.63- and 4.70-Mb
AB  - assemblies of their genomes. Their annotated key genes for carbazole catabolism
AB  - are similar, which may provide further insights into the molecular mechanism of
AB  - carbazole degradation in Pseudomonas.
ER  -

TY  - JOUR
AU  - Liu, X.
AU  - Huang, D.
AU  - Wu, J.
AU  - Yu, C.
AU  - Zhou, R.
AU  - Liu, C.
AU  - Zhang, W.
AU  - Yao, J.
AU  - Cheng, M.
AU  - Guo, S.
TI  - The Genome Sequence of Alcaligenes faecalis NBIB-017 Contains Genes with Potentially High Activities against Erwinia carotovora.
JO  - Genome Announcements
PY  - 2016
SP  - e00222
EP  - e00216
VL  - 4
AB  - Alcaligenes faecalisNBIB-017, a Gram-negative bacterium, was isolated from soil in China.
AB  - Here, we provide the complete genome sequence of this bacterium, which
AB  - possesses a high number of genes encoding antibacterial factors, including
AB  - proteins and small molecular peptides.
ER  -

TY  - JOUR
AU  - Liu, X.
AU  - Huang, Y.
AU  - Xu, X.
AU  - Zhao, Y.
AU  - Sun, Q.
AU  - Zhang, Z.
AU  - Zhang, X.
AU  - Wu, Y.
AU  - Wang, J.
AU  - Zhou, D.
AU  - An, X.
AU  - Pei, G.
AU  - Wang, Y.
AU  - Mi, Z.
AU  - Yin, Z.
AU  - Tong, Y.
TI  - Complete Genome Sequence of Multidrug-Resistant Citrobacter freundii Strain P10159, Isolated from Urine Samples from a Patient with Esophageal Carcinoma.
JO  - Genome Announcements
PY  - 2016
SP  - e01754
EP  - e01715
VL  - 4
AB  - Citrobacter freundii is an opportunistic pathogen that can cause diarrhea, septicemia,
AB  - meningitis, and urinary tract infections. We report here the complete
AB  - genome sequence of C. freundii strain P10159, isolated from urine samples from a
AB  - patient in China with esophageal carcinoma. The genome has 5,080,321 bp and 4,768
AB  - coding sequences, with a G+C content of 51.7%.
ER  -

TY  - JOUR
AU  - Liu, X.
AU  - Min, Y.
AU  - Huang, D.
AU  - Zhou, R.
AU  - Fang, W.
AU  - Liu, C.
AU  - Rao, B.
AU  - Zhang, G.
AU  - Wang, K.
AU  - Yang, Z.
TI  - Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum.
JO  - Genome Announcements
PY  - 2017
SP  - e01305
EP  - e01317
VL  - 5
AB  - Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in
AB  - Shangri-La, China. Here, we provide the complete genome sequence of this
AB  - bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding
AB  - genes and 195 RNA genes. This strain possesses a number of genes encoding
AB  - virulence factors of pathogens.
ER  -

TY  - JOUR
AU  - Liu, X.
AU  - Zhou, R.
AU  - Fu, G.
AU  - Zhang, W.
AU  - Min, Y.
AU  - Tian, Y.
AU  - Huang, D.
AU  - Wang, K.
AU  - Wan, Z.
AU  - Yao, J.
AU  - Yang, Z.
TI  - Draft Genome Sequence of Bacillus thuringiensis NBIN-866 with High Nematocidal Activity.
JO  - Genome Announcements
PY  - 2014
SP  - e00429
EP  - e00414
VL  - 2
AB  - Bacillus thuringiensis NBIN-866, a Gram-positive bacterium, was isolated from soil in China.
AB  - We announce here the draft genome sequence of strain B.
AB  - thuringiensis NBIN-866, which possesses highly nematocidal factors, such as
AB  - proteins and small molecular peptides.
ER  -

TY  - JOUR
AU  - Liu, X.-Q.
TI  - Protein-splicing intein: Genetic mobility, origin, and evolution.
JO  - Annu. Rev. Genet.
PY  - 2000
SP  - 61
EP  - 76
VL  - 34
AB  - Intein is the protein equivalent of intron and has been discovered in increasing numbers of
AB  - organisms and host proteins.  A self-splicing intein catalyzes its own removal from the host
AB  - protein through a posttranslational process of protein splicing.  A mobile intein displays a
AB  - site-specific endonuclease activity that confers genetic mobility to the intein through intein
AB  - homing.  Recent findings of intein structure and the mechanism of protein splicing illuminated
AB  - how inteins work and yielded clues regarding intein's origin, spread, and evolution.  Inteins
AB  - can evolve into new structures and new functions, such as split inteins that do
AB  - trans-splicing.  The structural basis of intein function needs to be identified for a full
AB  - understanding of the origin and evolution of this marvelous genetic element.
ER  -

TY  - JOUR
AU  - Liu, X.-Q.
AU  - Hu, Z.
TI  - A DnaB intein in Rhodothermus marinus: Indication of recent intein homing across remotely related organisms.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 7851
EP  - 7856
VL  - 94
AB  - A dnaB gene encoding a homologue of the Escherichia coli DNA helicase DnaB was cloned and
AB  - sequenced in the thermophilic eubacterium Rhodothermus marinus, predicting a DnaB protein that
AB  - harbors an intein.  This DnaB intein is 428 amino acid residues long, has several putative
AB  - intein sequence motifs (including two putative endonuclease motifs), and is capable of protein
AB  - splicing when produced in E. coli cells.  The R. marinus DnaB intein is a close homologue of a
AB  - DnaB intein in the cyanobacterium Synechocystis sp. strain PCC6803.  The two inteins are
AB  - positioned identically in their respective DnaB proteins.  They also share a 54% sequence
AB  - identity (74% sequence similarity) that is markedly higher than the 37% sequence identity
AB  - shared by the extein sequences of the two DnaB proteins.  Horizontal intein transfer (homing)
AB  - is therefore invoked to relate these two DnaB inteins.  The codon usage of R. marinus DnaB
AB  - intein coding sequence differs markedly from the codon usage of its flanking extein coding
AB  - sequences and other genes in the same genome, suggesting more recent acquisition of the DnaB
AB  - intein in this organism.
ER  -

TY  - JOUR
AU  - Liu, X.F.
AU  - Cao, Y.
AU  - Zhang, H.L.
AU  - Chen, Y.J.
AU  - Hu, C.J.
TI  - Complete Genome Sequence of Vibrio alginolyticus ATCC 17749T.
JO  - Genome Announcements
PY  - 2015
SP  - e01500
EP  - e01514
VL  - 3
AB  - Vibrio alginolyticus is a Gram-negative halophilic bacterium and has been recognized as an
AB  - opportunistic pathogen in both humans and marine animals. It is
AB  - the causative agent of food-borne diseases, such as gastroenteritis, and it
AB  - invades through wounds in predisposed individuals. In this study, we present the
AB  - completed genome of V. alginolyticus ATCC 17749(T) through high-throughput
AB  - sequencing.
ER  -

TY  - JOUR
AU  - Liu, X.Y.
AU  - Luo, X.J.
AU  - Li, C.X.
AU  - Lai, Q.L.
AU  - Xu, J.H.
TI  - Draft Genome Sequence of Burkholderia sp. Strain MP-1, a Methyl Parathion (MP)-Degrading Bacterium from MP-Contaminated Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e00344
EP  - e00314
VL  - 2
AB  - Burkholderia sp. strain MP-1 was isolated from pesticide-contaminated soil. Herein, we report
AB  - the draft genome sequence of strain MP-1, which contains 168
AB  - contigs of 8,611,053 bp, with a G+C content of 62.55% and 7,631 protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Liu, X.Y.
AU  - Min, Y.
AU  - Wang, K.M.
AU  - Wan, Z.Y.
AU  - Zhang, Z.G.
AU  - Cao, C.X.
AU  - Zhou, R.H.
AU  - Jiang, A.B.
AU  - Liu, C.J.
AU  - Zhang, G.Y.
AU  - Cheng, X.L.
AU  - Zhang, W.
AU  - Yang, Z.W.
TI  - Draft genome sequence of Bacillus amyloliquefaciens HB-26.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 775
EP  - 782
VL  - 9
AB  - Bacillus amyloliquefaciens HB-26, a Gram-positive bacterium was isolated from soil in China.
AB  - SDS-PAGE analysis showed this strain secreted six major protein
AB  - bands of 65, 60, 55, 34, 25 and 20 kDa. A bioassay of this strain reveals that it
AB  - shows specific activity against P. brassicae and nematode. Here we describe the
AB  - features of this organism, together with the draft genome sequence and
AB  - annotation. The 3,989,358 bp long genome (39 contigs) contains 4,001
AB  - protein-coding genes and 80 RNA genes.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Hu, A.
AU  - Shen, L.
AU  - Yao, T.
AU  - Jiao, N.
AU  - Wang, N.
AU  - Xu, B.
TI  - Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 883
EP  - 892
VL  - 9
AB  - Dyadobacter tibetensis Y620-1 is the type strain of the species Dyadobacter tibetensis,
AB  - isolated from ice at a depth of 59 m from a high altitude glacier in
AB  - China (5670 m above sea level). It is psychrotolerant with growth temperature
AB  - ranges of 4 to 35 degrees C. Here we describe the features of this organism,
AB  - together with the draft genome sequence and annotation. The 5,313,963 bp long
AB  - genome contains 4,828 protein-coding genes and 39 RNA genes. To the best of our
AB  - knowledge, this is the first Dyadobacter strain that was isolated from glacial
AB  - ice. This study provides genetic information of this organism to identify the
AB  - genes linked to its specific mechanisms for adaption to extreme glacial
AB  - environment.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Ichige, A.
AU  - Kobayashi, I.
TI  - Regulation of the EcoRI restriction-modification system: Identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene.
JO  - Gene
PY  - 2007
SP  - 140
EP  - 149
VL  - 400
AB  - Type II restriction-modification (R-M) systems are composed of linked restriction endonuclease
AB  - and modification methyltransferase genes and serve as barriers to horizontal gene transfer
AB  - even though they are mobile in themselves.  Their products kill host bacterial cells that have
AB  - lost the R-M genes, a process that helps to maintain the frequency of the R-M systems in the
AB  - viable cell population.  Their establishment and maintenance in a bacterial host are expected
AB  - to involve fine regulation of their gene expression.  In the present study, we analyzed
AB  - transcription of the modification gene and its regulation within the EcoRI R-M system.
AB  - Northern blotting revealed that the downstream ecoRIM gene is transcribed as a monocistronic
AB  - mRNA and as part of a larger bicistronic mRNA together with the upstream ecoRIR gene.  Primer
AB  - extension, RNase protection, and mutational analysis using lacZ gene fusions identified two
AB  - overlapping promoters for ecoRIM gene transcription within the ecoRIR gene.  Further
AB  - mutational analysis revealed that two upstream AT-rich elements within the ecoRIR gene,
AB  - "AATAAA" and "ATTATAAATATA", function as negative regulators of these promoters.  Simultaneous
AB  - substitution of these two elements resulted in a four-fold increase in beta-galactosidase
AB  - activity and a five-fold increase in transcript levels as measured by RNase protection assay.
AB  - RNA measurements of the ecoRIM transcript suggested that these elements decreased ecoRIM
AB  - expression by interfering with transcription initiation of the ecoRIM promoters.  Possible
AB  - roles for these ecoRIM promoters and their negative regulators in the EcoRI R-M system are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Lu, S.E.
AU  - Baird, S.M.
AU  - Qiao, J.
AU  - Du, Y.
TI  - Draft Genome Sequence of Pseudomonas chlororaphis YL-1, a Biocontrol Strain Suppressing Plant Microbial Pathogens.
JO  - Genome Announcements
PY  - 2014
SP  - e01225
EP  - e01213
VL  - 2
AB  - Pseudomonas chlororaphis YL-1 was isolated from soybean root tips and showed a broad range of
AB  - antagonistic activities to microbial plant pathogens. Here, we
AB  - report the high-quality draft genome sequence of YL-1, which consists of a
AB  - chromosome with an estimated size of 6.8 Mb with a G+C value of 63.09%.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Oakeley, E.J.
AU  - Sun, L.
AU  - Jost, J.-P.
TI  - Multiple domains are involved in the targeting of the mouse DNA methyltransferase to the DNA replication foci.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1038
EP  - 1045
VL  - 26
AB  - It has been shown that, during the S-phase of the cell cycle, the mouse DNA methyltransferase
AB  - is targeted to sites of DNA replication by an amino acid sequence (aa 207-455) lying in the
AB  - N-terminal domain of the enzyme.  In this paper it is shown, by using enhanced green
AB  - fluorescent protein fusions, that peptide sequences of DNA MTase are also involved in this
AB  - targeting.  The work focuses on a sequence, downstream of the reported targeting sequence,
AB  - which is homologous to the Polybromo-1 protein.  This motif (designated as PBHD) is separated
AB  - from the reported targeting sequence by a zinc-binding motif.  Primed in situ extension using
AB  - centromeric-specific primers was used to show that both the host DNA MTase and EGFP fusion
AB  - proteins containing the targeting sequences were localized to centromeric, but not telomeric,
AB  - regions during late S-phase and mitosis.  Also found was that, in ~10% of the S-phase cells,
AB  - the EGFP fusions did not co-localize with the centromeric regions.  Mutants containing either,
AB  - or both, of these targeting sequences could act as dominant negative mutants against the host
AB  - DNA MTase.  EGFP fusion proteins, containing the reported TS (aa 207-455), were targeted to
AB  - centromeric regions throughout the mitotic stage which lead to the discovery of similar
AB  - behavior of the endogenous DNA MTase although the host MTase showed much less intense staining
AB  - than in S-phase cells.  The biological role of the centromeric localization of DNA MTase
AB  - during mitosis is currently unknown.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Santi, D.V.
TI  - m5C RNA and m5C DNA methyl transferases use different cysteine residues as catalysts.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 8263
EP  - 8265
VL  - 97
AB  - A family of RNA m(5)C methyl transferases (MTases) containing over 55 members in eight
AB  - subfamilies has been identified recently by an iterative search of the genomic sequence
AB  - databases by using the known 16S rRNA m(5)C 967 MTase, Fmu, as an initial probe. The RNA m(5)C
AB  - MTase family contained sequence motifs that were highly homologous to motifs in the DNA m(5)C
AB  - MTases, including the ProCys sequence that contains the essential Cys catalyst of the
AB  - functionally similar DNA-modifying enzymes; it was reasonable to assign the Cys nucleophile to
AB  - be that in the conserved ProCys. The family also contained an additional conserved Cys residue
AB  - that aligns with the nucleophilic catalyst in m(5)U54 tRNA MTase. Surprisingly, the mutant of
AB  - the putative Cys catalyst in the ProCys sequence was active and formed a covalent complex with
AB  - 5-fluorocytosine-containing RNA, whereas the mutant at the other conserved Cys was inactive
AB  - and unable to form the complex. Thus, notwithstanding the highly homologous sequences and
AB  - similar functions, the RNA m(5)C MTase uses a different Cys as a catalytic nucleophile than
AB  - the DNA m(5)C MTases. The catalytic Cys seems to be determined, not by the target base that is
AB  - modified, but by whether the substrate is DNA or RNA. The function of the conserved ProCys
AB  - sequence in the RNA m(5)C MTases remains unknown.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Shen, W.
AU  - Shi, G.
AU  - Wang, Z.
TI  - Cloning, expression and nucleotide sequence analysis of gene encoding for BamHI methyltransferase from Bacillus amyloliquefaciens CICIM B2125.
JO  - Shengwu Jishu Tongbao
PY  - 2009
SP  - 65
EP  - 68
VL  - 11
AB  - A gene encoding for BamHI methyltransferase was cloned from Bacillus amyloliquefaciens CICIM
AB  - B2125.  The bamHIM was expressed under its own promoter in E. coli JM109.  The gene contained
AB  - an open reading frame of 1,271 bp, which encoded for 423 amino acid residues.  The molecular
AB  - weight of mature protein was 49 kD.  The BamHI site could be methylased by the enzyme M.BamHI.
AB  - The amino acid sequence analysis revealed that the enzyme contained a domain of Rossmann-fold
AB  - (NAD(P)(+)-binding proteins.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Sun, L.
AU  - Jost, J.-P.
TI  - In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2718
EP  - 2722
VL  - 24
AB  - Upon the onset of mouse myoblast differentiation there is a rapid drop in DNA
AB  - methyltransferase activity followed by a genome wide demethylation.  Here we show by using
AB  - specific antibodies directed against DNA methyltransferase that upon differentiation there was
AB  - a rapid drop in nuclear DNA methyltransferase whilst the internal control histone H1 remained
AB  - constant.  The loss of nuclear methyltransferase was not due to a translocation of the enzyme
AB  - from the nucleus to the cytoplasm where there was an increase in creatine phosphokinase
AB  - protein.  In vitro run on experiments carried out with growing and differentiating myoblast
AB  - nuclei showed no difference in the rate of DNA methyltransferase mRNA synthesis.  As measured
AB  - by Northern blot hybridization the relative half life of DNA methyltransferase mRNA in growing
AB  - and differentiating cells in the presence of Actinomycin D was 5h and 1h 30min, respectively,
AB  - whereas in the same cells the half life of histone H4 mRNA was in both cases 80 min.  As
AB  - measured by a combination of pulse chase experiments with labeled leucine and
AB  - immunoprecipitation, the relative half-life of DNA methyltransferase in growing and
AB  - differentiating cells was ~18h and 4h 30min, respectively.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Sun, L.
AU  - Jost, J.-P.
TI  - In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated.
JO  - Mol. Biol. Cell
PY  - 1996
SP  - 8a
EP  - 8a
VL  - 7
AB  - Upon the onset of mouse myoblast differentiation there is a rapid drop in DNA
AB  - methyltransferase activity followed by a genome wide demethylation.  Here we show by using
AB  - specific antibodies directed against DNA methyltransferase that upon differentiation there was
AB  - a rapid drop in nuclear DNA methyltransferase whilst the internal control Histone H1 remained
AB  - constant.  The loss of nuclear methyltransferase was not due to a translocation of the enzyme
AB  - from the nucleus to the cytoplasm where there was an increase in creatine phosphokinase
AB  - protein.  In vitro run on experiments carried out with growing and differentiating myoblast
AB  - nuclei showed no difference in the rate of DNA methyltransferase mRNA synthesis.  As measured
AB  - by Northern blot hybridization the relative half life of DNA methyltransferase mRNA in growing
AB  - and differentiating cells in the presence of Actinomycin D was 5 h and 1 h 30 min
AB  - respectively, whereas in the same cells the half life of Histone H4 mRNA was in both cases 80
AB  - minutes.  As measured by a combination of pulse chase experiments with labeled leucine and
AB  - immunoprecipitation, the relative half life of DNA methyltransferase in growing and
AB  - differentiating cells was approximately 18 h and 4 h 30 min respectively.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Wang, Y.
AU  - Schwarz, S.
AU  - Wang, S.
AU  - Chen, L.
AU  - Wu, C.
AU  - Shen, J.
TI  - Investigation of a multiresistance gene cfr that fails to mediate resistance to phenicols and oxazolidinones in Enterococcus faecalis.
JO  - J. Antimicrob. Chemother.
PY  - 2014
SP  - 892
EP  - 898
VL  - 69
AB  - OBJECTIVES: To investigate the basis of susceptibility to phenicols and
AB  - oxazolidinones of the porcine Enterococcus faecalis CPPF5 despite the presence of
AB  - the multiresistance gene cfr. METHODS: Southern blotting, conjugation and
AB  - transformation analyses were conducted to confirm the plasmid location and
AB  - transferability of cfr in CPPF5. The genetic environment of cfr was determined by
AB  - sequence analysis. Transcription and translation of cfr were examined by RT-PCR
AB  - and western blotting, respectively, and modifications at A2503 within the 23S
AB  - rRNA sequence were identified by primer extension. RESULTS: Electrotransformation
AB  - and Southern blotting indicated that CPPF5 and its transformant 5B2-3 contained
AB  - two cfr-carrying plasmids approximately 50 and approximately 12 kb in size. The
AB  - complete 12,270 bp sequence of the smaller plasmid, pCPPF5, was determined and
AB  - shared 99.9% (12,269/12,270 bp) identity with the corresponding region of the
AB  - cfr-carrying plasmid pEF-01 in E. faecalis of cattle origin. Moreover, the
AB  - genetic environment of cfr in the approximately 50 kb plasmid was the same as
AB  - that in pCPPF5 according to sequencing results. Although cfr mRNA, Cfr protein
AB  - and a modification at the A2503 site were detected, the cfr-carrying transformant
AB  - 5B2-3 did not have elevated MICs of chloramphenicol, florfenicol and linezolid,
AB  - indicating that cfr fails to mediate resistance to the respective antibiotics in
AB  - E. faecalis. CONCLUSIONS: This is the first report of the cfr gene failing to
AB  - elevate MICs of the corresponding antibiotics. Although the genetic basis for the
AB  - apparent 'no resistance' phenotype remains to be determined, this finding may
AB  - have implications for surveillance studies that target the cfr gene.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Yao, S.
AU  - Liu, Y.
AU  - Xu, Y.
AU  - Cheng, C.
TI  - Genome Sequence of Luteimonas huabeiensis HB-2, a Novel Species of Luteimonas with High Oil Displacement Efficiency.
JO  - Genome Announcements
PY  - 2014
SP  - e00152
EP  - e00114
VL  - 2
AB  - Luteimonas huabeiensis HB-2 is a novel and newly isolated strain, which shows a superior
AB  - property of oil displacement. Here, we present a 4.3-Mb assembly of its
AB  - genome. The key genes for phospholipid and fatty acid metabolism were annotated,
AB  - which are crucial for crude oil emulsification and recovery.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Ye, W.
AU  - Zheng, J.
AU  - Fang, L.
AU  - Peng, D.
AU  - Ruan, L.
AU  - Sun, M.
TI  - High-quality draft genome sequence of nematocidal Bacillus thuringiensis Sbt003.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 624
EP  - 631
VL  - 9
AB  - Bacillus thuringiensis represents one of the six species of 'Bacillus cereus group' in the
AB  - genus Bacillus within the family Bacillaceae. Strain Sbt003 was
AB  - isolated from soil and identified as B. thuringiensis. It harbors at least seven
AB  - plasmids and produces three shapes of parasporal crystals including oval,
AB  - bipyramidal and rice. SDS-PAGE analysis of spore-crystal suspension of this
AB  - strain reveals six major protein bands, which implies the presence of multiple
AB  - parasporal crystal genes. Bioassay of this strain reveals that it shows specific
AB  - activity against nematodes and human cancer cells. In this study, we report the
AB  - whole genomic shotgun sequences of Sbt003. The high-quality draft of the genome
AB  - is 6,175,670 bp long (including chromosome and plasmids) with 6,372
AB  - protein-coding and 80 RNA genes.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Yi, Z.
AU  - Zeng, R.
TI  - Draft Genome Sequence of a Symbiotic Bacterium, Rhizobium vignae CCBAU 05176T.
JO  - Genome Announcements
PY  - 2014
SP  - e00657
EP  - e00614
VL  - 2
AB  - The Rhizobium vignae strain CCBAU 05176(T) was isolated from a root nodule of Astragalus
AB  - dahuricus grown in Hebei Province, China. It grows on yeast mannitol
AB  - agar (YMA) supplemented with 0 to 2% (wt/vol) NaCl. We report the annotated
AB  - genome sequence of this strain in a 6.34-Mb scaffold.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Zeng, R.
AU  - Weng, B.
AU  - Luo, T.
AU  - Luo, Q.
AU  - Xu, L.
TI  - Draft Genome Sequence of Streptococcus sp. X13SY08, Isolated from Murray Cod (Maccullochella peelii peelii).
JO  - Genome Announcements
PY  - 2016
SP  - e01470
EP  - e01415
VL  - 4
AB  - Streptococcus sp. X13SY08, isolated from freshwater Murray cod fi sh, likely presents a novel
AB  - species of Streptococcus. Here, we present an annotated draft
AB  - genome sequence of this species, which will improve our understanding of its
AB  - physiology and pathogenesis.
ER  -

TY  - JOUR
AU  - Liu, Y.
AU  - Zheng, H.
AU  - Zhan, G.H.
AU  - Qin, W.
AU  - Tian, L.
AU  - Li, W.L.
TI  - Establishment of an efficient transformation protocol and its application in marine-derived Bacillus strain.
JO  - Sci. China C Life Sci.
PY  - 2014
SP  - 627
EP  - 635
VL  - 57
AB  - Marine-derived Bacillus strains have been proved to be a very promising source for natural
AB  - product leads. However, transformation of environmental strains is much more difficult than
AB  - that of domesticated strains. Here, we report the development of an efficient and robust
AB  - electroporation-based transformation system for marine-derived Bacillus marinus B-9987, which
AB  - is a macrolactin antibiotics producer and a very promising biological control agent against
AB  - fungal plant diseases. The transformation efficiency was greatly enhanced 10(3)-fold by using
AB  - unmethylated plasmid to bypass modification-restriction barrier, and using glycine betaine to
AB  - protect cells from electrical damages during electroporation. Addition of HEPES and 2 mmol L-1
AB  - MgCl2 further improved the efficiency by additional 2-fold, with a maximum value of 7.1x10(4)
AB  - cfu/mu g pHT3101. To demonstrate the feasibility and efficiency of the protocol, a green
AB  - fluorescent protein reporter system was constructed; furthermore, phosphopantetheinyl
AB  - transferase gene sfp, which is essential to the biosynthesis of polyketides and nonribosomal
AB  - peptides, was overexpressed in B-9987, leading to increased production of macrolactin A by
AB  - about 1.6-fold. In addition, this protocol is also applicable to marine-derived Bacillus
AB  - licheniforms EI-34-6, indicating it could be a reference for other undomesticated Bacillus
AB  - strains. To our knowledge, this is the first report regarding the transformation of
AB  - marine-derived Bacillus strain.
ER  -

TY  - JOUR
AU  - Liu, Y.C.
AU  - Wang, S.C.
AU  - Yu, Y.J.
AU  - Fung, K.M.
AU  - Yang, M.T.
AU  - Tseng, Y.H.
AU  - Tsai, S.F.
AU  - Sun, H.S.
AU  - Lyu, P.C.
AU  - Chou, S.H.
TI  - Complete Genome Sequence of Xanthomonas campestris pv. campestris Strain 17 from  Taiwan.
JO  - Genome Announcements
PY  - 2015
SP  - e01466
EP  - e01415
VL  - 3
AB  - Xanthomonas campestris pv. campestris 17 is a Gram-negative bacterium that is phytopathogenic
AB  - to cruciferous plants in Taiwan. The 4,994,426-bp-long genome
AB  - consists of 24 contigs with 4,050 protein-coding genes, 1 noncoding RNA (ncRNA)
AB  - gene, 6 rRNA genes, and 55 tRNA genes.
ER  -

TY  - JOUR
AU  - Liu, Y.P.
AU  - Kobayashi, I.
TI  - Negative regulation of the EcoRI restriction enzyme gene is associated with intragenic reverse promoters.
JO  - J. Bacteriol.
PY  - 2007
SP  - 6928
EP  - 6935
VL  - 189
AB  - Type 11 restriction-modification systems are expected to possess mechanisms for tight
AB  - regulation of their expression to suppress the
AB  - potential of lethal attack on their host bacteria when they establish
AB  - and maintain themselves within them. Although the EcoRI restriction
AB  - enzyme has been well characterized, regulation of its expression is
AB  - still poorly understood. In this study, mutational analysis with lacZ
AB  - gene fusion and primer extension assay identified a promoter for the
AB  - transcription of the ecoRIR gene. Further analyses revealed that an
AB  - intragenic region containing two overlapping reverse promoter-like
AB  - elements acted as a negative regulator for ecoRIR gene expression. The
AB  - activity of these putative reverse promoters was verified by
AB  - transcriptional gene fusion, primer extension and in vitro
AB  - transcription. Mutations in these reverse promoters resulted in
AB  - increased gene expression in both translational and transcriptional
AB  - gene fusions. An RNase protection assay revealed that the transcript
AB  - level of the wild type relative to that of the reverse promoter mutant
AB  - at the downstream regions was much lower than the level at the upstream
AB  - regions. This suggests that these reverse promoter-like elements affect
AB  - their downstream transcript level. The possible mechanisms of this kind
AB  - of negative regulation, in addition to their possible biological roles,
AB  - are discussed.
ER  -

TY  - JOUR
AU  - Liu, Y.P.
AU  - Tang, Q.
AU  - Zhang, J.Z.
AU  - Tian, L.F.
AU  - Gao, P.
AU  - Yan, X.X.
TI  - Structural basis underlying complex assembly and conformational transition of the type I R-M system.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2017
SP  - 11151
EP  - 11156
VL  - 114
AB  - Type I restriction-modification (R-M) systems are multisubunit enzymes with separate
AB  - DNA-recognition (S), methylation (M), and restriction (R) subunits. Despite extensive studies
AB  - spanning five decades, the detailed molecular mechanisms underlying subunit assembly and
AB  - conformational transition are still unclear due to the lack of high-resolution structural
AB  - information. Here, we report the atomic structure of a type I MTase complex (2M+1S) bound to
AB  - DNA and cofactor S-adenosyl methionine in the 'open' form. The intermolecular interactions
AB  - between M and S subunits are mediated by a four-helix bundle motif, which also determines the
AB  - specificity of the interaction. Structural comparison between open and previously reported
AB  - low-resolution 'closed' structures identifies the huge conformational changes within the
AB  - MTase complex. Furthermore, biochemical results show that R subunits prefer to load onto the
AB  - closed form MTase. Based on our results, we proposed an updated model for the complex
AB  - assembly. The work reported here provides guidelines for future applications in molecular
AB  - biology.
ER  -

TY  - JOUR
AU  - Liu, Z.
AU  - Muller, J.
AU  - Li, T.
AU  - Alvey, R.M.
AU  - Vogl, K.
AU  - Frigaard, N.U.
AU  - Rockwell, N.C.
AU  - Boyd, E.S.
AU  - Tomsho, L.P.
AU  - Schuster, S.C.
AU  - Henke, P.
AU  - Rohde, M.
AU  - Overmann, J.
AU  - Bryant, D.A.
TI  - Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium 'Chlorochromatium aggregatum'.
JO  - Genome Biol.
PY  - 2013
SP  - R127
EP  - R127
VL  - 14
AB  - BACKGROUND: 'Chlorochromatium aggregatum' is a phototrophic consortium, a
AB  - symbiosis that may represent the highest degree of mutual interdependence between
AB  - two unrelated bacteria not associated with a eukaryotic host. 'Chlorochromatium
AB  - aggregatum' is a motile, barrel-shaped aggregate formed from a single cell of
AB  - 'Candidatus Symbiobacter mobilis", a polarly flagellated, non-pigmented,
AB  - heterotrophic bacterium, which is surrounded by approximately 15 epibiont cells
AB  - of Chlorobium chlorochromatii, a non-motile photolithoautotrophic green sulfur
AB  - bacterium. RESULTS: We analyzed the complete genome sequences of both organisms
AB  - to understand the basis for this symbiosis. Chl. chlorochromatii has acquired
AB  - relatively few symbiosis-specific genes; most acquired genes are predicted to
AB  - modify the cell wall or function in cell-cell adhesion. In striking contrast,
AB  - 'Ca. S. mobilis' appears to have undergone massive gene loss, is probably no
AB  - longer capable of independent growth, and thus may only reproduce when consortia
AB  - divide. A detailed model for the energetic and metabolic bases of the dependency
AB  - of 'Ca. S. mobilis' on Chl. chlorochromatii is described. CONCLUSIONS: Genomic
AB  - analyses suggest that three types of interactions lead to a highly sophisticated
AB  - relationship between these two organisms. Firstly, extensive metabolic exchange,
AB  - involving carbon, nitrogen, and sulfur sources as well as vitamins, occurs from
AB  - the epibiont to the central bacterium. Secondly, 'Ca. S. mobilis' can sense and
AB  - move towards light and sulfide, resources that only directly benefit the
AB  - epibiont. Thirdly, electron cycling mechanisms, particularly those mediated by
AB  - quinones and potentially involving shared protonmotive force, could provide an
AB  - important basis for energy exchange in this and other symbiotic relationships.
ER  -

TY  - JOUR
AU  - Liutkeviciute, Z.
AU  - Kriukiene, E.
AU  - Grigaityte, I.
AU  - Masevicius, V.
AU  - Klimasauskas, S.
TI  - Methyltransferase-Directed Derivatization of 5-Hydroxymethylcytosine in DNA.
JO  - Angew. Chem. Int. Ed. Engl.
PY  - 2011
SP  - 2090
EP  - 2093
VL  - 50
AB  - The modification of cytosine by S-adenosylmethionine-dependent DNA methyltransferases is part
AB  - of an intricate epigenetic regulation mechanism in vertebrates.  DNA cytosine-5
AB  - methyltransferases (catalyze the transfer of a methyl group from S-adenosyl-L-methionine to
AB  - the cytosine residue in CpG dinucleotides.  Recent studies of genomic DNA from mouse embryonic
AB  - stem cells, neurons, and the brain found that a substantial fraction of 5-methylcytosine in CG
AB  - sequences is converted into 5-hydroxymethylcytosine by the action of 2-oxoglutarate- and
AB  - Fe2+-dependent oxygenases of the TET family.  As interactions of the 5-methyl- and
AB  - 5-hydroxymethyl groups with cellular proteins in DNA are distinct, hmC residues may play an
AB  - independent role in yet unknown epigenetic pathways during embryonic development, brain
AB  - functioning, and cancer progression.  However, further studies of these intriguing phenomena
AB  - are hampered by the lack of efficient analytical techniques for mapping hmC residues in the
AB  - genome.  Herein we show that C5-MTases can direct the condensation of exogenous thiols and
AB  - selenols with hmC in DNA to yield the corresponding 5-chalcogenomethyl derivatives.  These
AB  - transformations open new possibilities for the sequence-specific derivatization and analysis
AB  - of this newly discovered epigenetic mark in mammalian DNA.
ER  -

TY  - JOUR
AU  - Liutkeviciute, Z.
AU  - Kriukiene, E.
AU  - Grigaityte, I.
AU  - Vainorius, G.
AU  - Masevicius, V.
AU  - Klimasauskas, S.
TI  - Catalytic versatility of DNA cytosine-5 methyltransferases: reactions involving non-cofactor-like substrates.
JO  - FEBS J.
PY  - 2012
SP  - 540
EP  - 540
VL  - 279
AB  - DNA cytosine-5 methyltransferases catalyze site-specific transfers of a methyl group from the
AB  - cofactor S-adenosyl-L-methionine (SAM) onto the 5-position of their target cytosine residues
AB  - in DNA.  Recently we have shown that, in the absence of SAM, methyltranferases are able to add
AB  - formaldehyde to their target cytosines yielding 5-hydroxymethylcytosine.  This reaction can be
AB  - reversed yielding unmodified cytosine, or can be further extended by condensation with thiols
AB  - or selenols.  Lately hmC was discovered in mammals DNA but the biological role of this new
AB  - base is unclear because further studies are restricted by the lack of efficient analytical
AB  - techniques for mapping hmC residues in the genome.  These atypical reactions of DNA cytosine-5
AB  - methyltransferase open new ways for analysis of hnmC in genomic DNA and provide inroads into
AB  - active demethylation of 5-methylcytosine residues in the genome.
ER  -

TY  - JOUR
AU  - Liutkeviciute, Z.
AU  - Lukinavicius, G.
AU  - Masevicius, V.
AU  - Daujotyte, D.
AU  - Klimasauskas, S.
TI  - Cytosine-5-methyltransferases add aldehydes to DNA.
JO  - Nat. Chem. Biol.
PY  - 2009
SP  - 400
EP  - 402
VL  - 5
AB  - Targeted methylation of cytosine residues by S-adenosylmethionine-dependent DNA
AB  - methyltransferases modulates gene
AB  - expression in vertebrates. Here we show that
AB  - cytosine-5-methyltransferases catalyze reversible covalent addition of
AB  - exogenous aliphatic aldehydes to their target residues in DNA, thus
AB  - yielding corresponding 5-alpha-hydroxyalkylcytosines. Such atypical
AB  - enzymatic reactions with non-cofactor-like substrates open new ways for
AB  - sequence-specific derivatization of DNA and demonstrate enzymatic
AB  - exchange of 5-hydroxymethyl groups on cytosine in support of an
AB  - oxidative mechanism of DNA demethylation.
ER  -

TY  - JOUR
AU  - Llado, S.
AU  - Xu, Z.
AU  - Sorensen, S.J.
AU  - Baldrian, P.
TI  - Draft Genome Sequence of Burkholderia sordidicola S170, a Potential Plant Growth  Promoter Isolated from Coniferous Forest Soil in the Czech Republic.
JO  - Genome Announcements
PY  - 2014
SP  - e00810
EP  - e00814
VL  - 2
AB  - Burkholderia species are key players in the accumulation of carbon from cellulose
AB  - decomposition in coniferous forest ecosystems. We report here the draft genome of
AB  - Burkholderia sordidicola strain S170, containing features associated with known
AB  - genes involved in plant growth promotion, the biological control of plant
AB  - diseases, and green remediation technologies.
ER  -

TY  - JOUR
AU  - Lloyd, K.G.
AU  - Schreiber, L.
AU  - Petersen, D.G.
AU  - Kjeldsen, K.U.
AU  - Lever, M.A.
AU  - Steen, A.D.
AU  - Stepanauskas, R.
AU  - Richter, M.
AU  - Kleindienst, S.
AU  - Lenk, S.
AU  - Schramm, A.
AU  - Jorgensen, B.B.
TI  - Predominant archaea in marine sediments degrade detrital proteins.
JO  - Nature
PY  - 2013
SP  - 215
EP  - 218
VL  - 496
AB  - Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells
AB  - are members of the Archaea, single-celled prokaryotes in a domain of
AB  - life separate from Bacteria and Eukaryota. However, most of these archaea lack
AB  - cultured representatives, leaving their physiologies and placement on the tree of
AB  - life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal
AB  - group (MCG) and marine benthic group-D (MBG-D) are among the most numerous
AB  - archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell
AB  - of MCG and three cells of MBG-D indicated that they form new branches basal to
AB  - the archaeal phyla Thaumarchaeota and Aigarchaeota, for MCG, and the order
AB  - Thermoplasmatales, for MBG-D. All four cells encoded extracellular
AB  - protein-degrading enzymes such as gingipain and clostripain that are known to be
AB  - effective in environments chemically similar to marine sediments. Furthermore, we
AB  - found these two types of peptidase to be abundant and active in marine sediments,
AB  - indicating that uncultured archaea may have a previously undiscovered role in
AB  - protein remineralization in anoxic marine sediments.
ER  -

TY  - JOUR
AU  - Lloyd, R.S.
AU  - Cheng, X.
TI  - Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
JO  - Biopolymers
PY  - 1997
SP  - 139
EP  - 151
VL  - 44
AB  - Rotation of a DNA nucleotide out of the double helix and into a protein binding pocket ("base
AB  - flipping") was first observed in the structure of a DNA methyltransferase.  There is now
AB  - evidence that a variety of proteins, particularly DNA repair enzymes, use base flipping in
AB  - their interactions with DNA.  Though the mechanisms for base movement into extrahelical
AB  - positions are still unclear, the focus of this review is how base recognition is modulated by
AB  - the stringency of binding to the extrahelical base(s) or sugar moiety.
ER  -

TY  - JOUR
AU  - Lluch-Senar, M.
AU  - Luong, K.
AU  - Llorens-Rico, V.
AU  - Delgado, J.
AU  - Fang, G.
AU  - Spittle, K.
AU  - Clark, T.A.
AU  - Schadt, E.
AU  - Turner, S.W.
AU  - Korlach, J.
AU  - Serrano, L.
TI  - Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma  pneumoniae at Single-Base Resolution.
JO  - PLoS Genet.
PY  - 2013
SP  - e1003191
EP  - e1003191
VL  - 9
AB  - In the bacterial world, methylation is most commonly associated with restriction-modification
AB  - systems that provide a defense mechanism against
AB  - invading foreign genomes. In addition, it is known that methylation plays
AB  - functionally important roles, including timing of DNA replication, chromosome
AB  - partitioning, DNA repair, and regulation of gene expression. However, full DNA
AB  - methylome analyses are scarce due to a lack of a simple methodology for rapid and
AB  - sensitive detection of common epigenetic marks (ie N(6)-methyladenine (6 mA) and
AB  - N(4)-methylcytosine (4 mC)), in these organisms. Here, we use Single-Molecule
AB  - Real-Time (SMRT) sequencing to determine the methylomes of two related human
AB  - pathogen species, Mycoplasma genitalium G-37 and Mycoplasma pneumoniae M129, with
AB  - single-base resolution. Our analysis identified two new methylation motifs not
AB  - previously described in bacteria: a widespread 6 mA methylation motif common to
AB  - both bacteria (5'-CTAT-3'), as well as a more complex Type I m6A sequence motif
AB  - in M. pneumoniae (5'-GAN(7)TAY-3'/3'-CTN(7)ATR-5'). We identify the
AB  - methyltransferase responsible for the common motif and suggest the one involved
AB  - in M. pneumoniae only. Analysis of the distribution of methylation sites across
AB  - the genome of M. pneumoniae suggests a potential role for methylation in
AB  - regulating the cell cycle, as well as in regulation of gene expression. To our
AB  - knowledge, this is one of the first direct methylome profiling studies with
AB  - single-base resolution from a bacterial organism.
ER  -

TY  - JOUR
AU  - Lo, A.S.
AU  - Merrell, D.S.
AU  - Lei, H.
AU  - Sardi, A.
AU  - McAvoy, T.
AU  - Testerman, T.L.
TI  - A Novel Member of Chitinophagaceae Isolated from a Human Peritoneal Tumor.
JO  - Genome Announcements
PY  - 2015
SP  - e01297
EP  - e01215
VL  - 3
AB  - Peritoneal tumors from a rare malignancy, pseudomyxoma peritonei, frequently contain bacteria.
AB  - Evidence suggests that tumor-associated bacteria contribute to
AB  - pseudomyxoma peritonei development and/or progression. One unique isolate
AB  - (PMP191F) was characterized via whole-genome sequencing using the Illumina MiSeq
AB  - platform. PMP191F shows similarities to the Chitinophaga, Niastella, and
AB  - Flavitalea genera.
ER  -

TY  - JOUR
AU  - Lo, C.I.
AU  - Mishra, A.K.
AU  - Padhmanabhan, R.
AU  - Samb, B.
AU  - Sow, A.G.
AU  - Robert, C.
AU  - Couderc, C.
AU  - Faye, N.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Fenollar, F.
TI  - Non-contiguous finished genome sequence and description of Clostridium dakarense  sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 14
EP  - 27
VL  - 9
AB  - Clostridium dakarense strain FF1(T), is the type strain of Clostridium dakarense  sp. nov., a
AB  - new species within the genus Clostridium. This strain, whose genome
AB  - is described here, was isolated from the fecal flora of a 4-month-old Senegalese
AB  - child suffering from gastroenteritis. C. dakarense sp. nov. strain FF1(T) is an
AB  - obligate anaerobic Gram-positive bacillus. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 3,735,762 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of
AB  - 27.98% and contains 3,843 protein-coding and 73 RNA genes, including 8 rRNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Lo, C.I.
AU  - Padhmanabhan, R.
AU  - Mediannikov, O.
AU  - Nguyen, T.T.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Fenollar, F.
TI  - Genome sequence and description of Pantoea septica strain FF5.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 103
EP  - 103
VL  - 10
AB  - Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This
AB  - strain was identified as belonging to the species Pantoea septica
AB  - based on rpoB sequence identity of 99.7 % with Pantoea septica strain LMG 5345(T)
AB  - and a highest MALDI-TOF-MS score of 2.3 with Pantoea septica. Like P. septica,
AB  - this FF5 strain is a Gram-negative, aerobic, motile, and rod-shaped bacterium.
AB  - Currently, 17 genomes have been sequenced within the genus Pantoea but none for
AB  - Pantoea septica. Herein, we compared the genomic properties of strain FF5 to
AB  - those of other species within the genus Pantoea. The genome of this strain is
AB  - 4,548,444 bp in length (1 chromosome, no plasmid) with a G + C content of 59.1 %
AB  - containing 4125 protein-coding and 68 RNA genes (including 2 rRNA operons). We
AB  - also performed an extensive phenotypic analysis showing new phenotypic
AB  - characteristics such as the production of alkaline phosphatase, acid phosphatase
AB  - and naphthol-AS-BI-phosphohydrolase.
ER  -

TY  - JOUR
AU  - Lo, C.I.
AU  - Padhmanabhan, R.
AU  - Mediannikov, O.
AU  - Terras, J.
AU  - Robert, C.
AU  - Faye, N.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Fenollar, F.
TI  - High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 41
EP  - 41
VL  - 10
AB  - Strain FF4(T) was isolated from the skin flora of a 16-year-old healthy Senegalese female.
AB  - This strain exhibited a 16S rRNA sequence similarity of 97.5 %
AB  - with Bacillus fumarioli, the phylogenetically closest species with standing in
AB  - nomenclature and a poor MALDI-TOF-MS score (1.1 to 1.3) that does not allow any
AB  - identification. Using a polyphasic study consisting of phenotypic and genomic
AB  - analyses, strain FF4(T) was Gram-positive, aerobic, rod-shaped, and exhibited a
AB  - genome of 4,563,381 bp (1 chromosome but no plasmid) with a G + C content of 40.8
AB  - % that coded 4,308 protein-coding and 157 RNA genes (including 5 rRNA operons).
AB  - On the basis of these data, we propose the creation of Bacillus dielmoensis sp.
AB  - nov.
ER  -

TY  - JOUR
AU  - Lo, C.I.
AU  - Sankar, S.A.
AU  - Fall, B.
AU  - Sambe-Ba, B.
AU  - Diawara, S.
AU  - Gueye, M.W.
AU  - Mediannikov, O.
AU  - Blanc-Tailleur, C.
AU  - Wade, B.
AU  - Raoult, D.
AU  - Fournier, P.E.
AU  - Fenollar, F.
TI  - High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 31
EP  - 31
VL  - 11
AB  - Strain FF7(T) was isolated from the peritoneal fluid of a 44-year-old woman who suffered from
AB  - pelvic peritonitis. This strain exhibited a 16S rRNA sequence
AB  - similarity of 94.8 % 16S rRNA sequence identity with Haemophilus parasuis, the
AB  - phylogenetically closest species with a name with standing in nomenclature and a
AB  - poor MALDI-TOF MS score (1.32 to 1.56) that does not allow any reliable
AB  - identification. Using a polyphasic study made of phenotypic and genomic analyses,
AB  - strain FF7(T) was a Gram-negative, facultatively anaerobic rod and member of the
AB  - family Pasteurellaceae. It exhibited a genome of 2,442,548 bp long genome (one
AB  - chromosome but no plasmid) contains 2,319 protein-coding and 67 RNA genes,
AB  - including 6 rRNA operons. On the basis of these data, we propose the creation of
AB  - Haemophilus massiliensis sp. nov. with strain FF7(T) (= CSUR P859 = DSM 28247) as
AB  - the type strain.
ER  -

TY  - JOUR
AU  - Lo, I.
AU  - Denef, V.J.
AU  - Verberkmoes, N.C.
AU  - Shah, M.B.
AU  - Goltsman, D.
AU  - Dibartolo, G.
AU  - Tyson, G.W.
AU  - Allen, E.E.
AU  - Ram, R.J.
AU  - Detter, J.C.
AU  - Richardson, P.
AU  - Thelen, M.P.
AU  - Hettich, R.L.
AU  - Banfield, J.F.
TI  - Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.
JO  - Nature
PY  - 2007
SP  - 537
EP  - 541
VL  - 446
AB  - Microbes comprise the majority of extant organisms, yet much remains to be
AB  - learned about the nature and driving forces of microbial diversification.
AB  - Our understanding of how microorganisms adapt and evolve can be advanced
AB  - by genome-wide documentation of the patterns of genetic exchange,
AB  - particularly if analyses target coexisting members of natural communities.
AB  - Here we use community genomic data sets to identify, with strain
AB  - specificity, expressed proteins from the dominant member of a genomically
AB  - uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a
AB  - genome shaped by recombination involving chromosomal regions of tens to
AB  - hundreds of kilobases long that are derived from two closely related
AB  - bacterial populations. Inter-population genetic exchange was confirmed by
AB  - multilocus sequence typing of isolates and of uncultivated natural
AB  - consortia. The findings suggest that exchange of large blocks of gene
AB  - variants is crucial for the adaptation to specific ecological niches
AB  - within the very acidic, metal-rich environment. Mass-spectrometry-based
AB  - discrimination of expressed protein products that differ by as little as a
AB  - single amino acid enables us to distinguish the behaviour of closely
AB  - related coexisting organisms. This is important, given that microorganisms
AB  - grouped together as a single species may have quite distinct roles in
AB  - natural systems and their interactions might be key to ecosystem
AB  - optimization. Because proteomic data simultaneously convey information
AB  - about genome type and activity, strain-resolved community proteomics is an
AB  - important complement to cultivation-independent genomic (metagenomic)
AB  - analysis of microorganisms in the natural environment.
ER  -

TY  - JOUR
AU  - Lo, J.R.
AU  - Lang, J.M.
AU  - Darling, A.E.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of an Actinobacterium, Brachybacterium muris Strain UCD-AY4.
JO  - Genome Announcements
PY  - 2013
SP  - e0008613
EP  - e0008613
VL  - 1
AB  - Here we present the draft genome of an actinobacterium, Brachybacterium muris UCD-AY4. The
AB  - assembly contains 3,257,338 bp and has a GC content of 70%. This
AB  - strain was isolated from a residential bath towel and has a 16S rRNA gene 99.7%
AB  - identical to that of the original B. muris strain, C3H-21.
ER  -

TY  - JOUR
AU  - Lo, R.
AU  - Stanton-Cook, M.J.
AU  - Beatson, S.A.
AU  - Turner, M.S.
AU  - Bansal, N.
TI  - Draft Genome Sequence of Pseudomonas fluorescens SRM1, an Isolate from Spoiled Raw Milk.
JO  - Genome Announcements
PY  - 2015
SP  - e00138
EP  - e00115
VL  - 3
AB  - Pseudomonas fluorescens is considered a major milk spoilage organism due to its psychrotrophic
AB  - nature and ability to produce heat-stable proteases and lipases.
AB  - Here, we report the draft genome and annotation of P. fluorescens SRM1 isolated
AB  - from spoiled raw milk and the presence of an operon encoding spoilage enzymes.
ER  -

TY  - JOUR
AU  - Lo, W.-S.
AU  - Ku, C.
AU  - Chen, L.-L.
AU  - Chang, T.-H.
AU  - Kuo, C.-H.
TI  - Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 1512
EP  - 1523
VL  - 5
AB  - Mosquitoes are hosts of several Spiroplasma species that belong to different serogroups. To
AB  - investigate the genetic mechanisms that may be involved in the utilization of similar hosts in
AB  - these phylogenetically distinct bacteria, we determined the complete genome sequences of S.
AB  - diminutum and S. taiwanense for comparative analysis. The genome alignment indicates that
AB  - their chromosomal organization is highly conserved,
AB  - which is in sharp contrast to the elevated genome instabilities observed in other Spiroplasma
AB  - lineages. Examination of the substrate utilization strategies revealed that S. diminutum can
AB  - use a wide range of carbohydrates, suggesting that it is well suited to living in the gut (and
AB  - possibly the circulatory system) of its mosquito hosts. In comparison, S. taiwanense has lost
AB  - several carbohydrate utilization genes and acquired additional sets of oligopeptide
AB  - transporter genes through tandem duplications, suggesting
AB  - that proteins from digested blood meal or lysed host cells may be an important nutrient
AB  - source. Moreover, one glycerol-3-phosphate oxidase gene (glpO) was found in S. taiwanense but
AB  - not S. diminutum. This gene is linked to the production of reactive oxygen species and has
AB  - been shown to be a major virulence factor in Mycoplasma mycoides. This finding may explain the
AB  - pathogenicity of S. taiwanense observed in previous artificial infection experiments, while no
AB  - apparent effect was found for S. diminutum. To infer the gene content evolution at deeper
AB  - divergence levels, we incorporated other Mollicutes genomes for comparative analyses. The
AB  - results suggest that the losses of biosynthetic pathways are a recurrent theme in these
AB  - host-associated bacteria.
ER  -

TY  - JOUR
AU  - Lo, W.S.
AU  - Chen, H.
AU  - Chen, C.Y.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan.
JO  - Genome Announcements
PY  - 2014
SP  - e01005
EP  - e01014
VL  - 2
AB  - Vibrio vulnificus 93U204 is a bacterium isolated from a moribund tilapia collected in
AB  - Kaohsiung, Taiwan. Here, we report the complete genome sequence of
AB  - this bacterium to facilitate the investigation of its pathogenicity and for
AB  - comparative analyses with human-pathogenic strains within the same species.
ER  -

TY  - JOUR
AU  - Lo, W.S.
AU  - Gasparich, G.E.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.).
JO  - Genome Announcements
PY  - 2016
SP  - e01010
EP  - e01016
VL  - 4
AB  - Spiroplasma turonicum Tab4c(T) was isolated from a horse fly (Haematopota sp.; probably
AB  - Haematopota pluvialis) collected at Champchevrier, Indre-et-Loire,
AB  - Touraine, France, in 1991. Here, we report the complete genome sequence of this
AB  - bacterium to facilitate the investigation of its biology and the comparative
AB  - genomics among Spiroplasma spp.
ER  -

TY  - JOUR
AU  - Lo, W.S.
AU  - Haryono, M.
AU  - Gasparich, G.E.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma sp. TU-14.
JO  - Genome Announcements
PY  - 2017
SP  - e01465
EP  - e01416
VL  - 5
AB  - Spiroplasma sp. TU-14 was isolated from a contaminated sample of Entomoplasma lucivorax
AB  - PIPN-2T obtained from the International Organization for Mycoplasmology
AB  - collection. Here, we report the complete genome sequence of this bacterium to
AB  - facilitate the investigation of its biology and the comparative genomics among
AB  - Spiroplasma spp.
ER  -

TY  - JOUR
AU  - Lo, W.S.
AU  - Lai, Y.C.
AU  - Lien, Y.W.
AU  - Wang, T.H.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma litorale TN-1T (DSM 21781), a Bacterium Isolated from a Green-Eyed Horsefly (Tabanus nigrovittatus).
JO  - Genome Announcements
PY  - 2015
SP  - e01116
EP  - e01115
VL  - 3
AB  - Spiroplasma litorale TN-1(T) (DSM 21781) was isolated from the gut of a green-eyed horsefly
AB  - (Tabanus nigrovittatus), collected at Ocracoke Island in North Carolina in 1983. Here, we
AB  - report the complete genome sequence of this bacterium to facilitate the investigation of its
AB  - biology.
ER  -

TY  - JOUR
AU  - Lo, W.S.
AU  - Liu, P.Y.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a Bacterium Isolated from Soldier Beetle (Cantharis carolinus).
JO  - Genome Announcements
PY  - 2015
SP  - e01253
EP  - e01215
VL  - 3
AB  - Spiroplasma cantharicola CC-1(T) (DSM 21588) was isolated from the gut of a soldier beetle
AB  - (Cantharis carolinus) collected in Maryland, USA. Here, we report  the complete genome
AB  - sequence of this bacterium to facilitate the investigation of its biology.
ER  -

TY  - JOUR
AU  - Lobner-Olesen, A.
AU  - Boye, E.
AU  - Marinus, M.G.
TI  - Expression of the Escherichia coli dam gene.
JO  - Mol. Microbiol.
PY  - 1992
SP  - 1841
EP  - 1851
VL  - 6
AB  - The Escherichia coli dam gene and upstream sequences were cloned from the Kohara phage 4D4.
AB  - Five promoters were found to contribute to dam gene transcription.  P1 and P2 (the major
AB  - promoter) were situated approximately 3.5 kb upstream of the structural gene, P3 was within
AB  - the aroB gene, P4 was within the urf74.3 gene, and P5 was in the urf74.3-dam intergenic
AB  - region.  The nucleotide sequence of 2280 bp of DNA containing P1 and P2 was determined and
AB  - shown to have the potential to encode a protein of approximately 16 kDa between P1, P2 and the
AB  - aroB gene.  This 16 kDa open reading frame has been identified as aroK, the gene for shikimic
AB  - acid kinase I.  Thus the dam gene is part of an operon containing aroK, aroB, urf74.3, and
AB  - dam.  The transcriptional start points of the promoters were determined.  A comparison of
AB  - their nucleotide sequences suggested that P1-P4 were all recognized by the sigma 70 subunit of
AB  - the RNA polymerase.
ER  -

TY  - JOUR
AU  - Lobner-Olesen, A.
AU  - Skovgaard, O.
AU  - Marinus, M.G.
TI  - Dam methylation: coordinating cellular processes.
JO  - Curr. Opin. Microbiol.
PY  - 2005
SP  - 154
EP  - 160
VL  - 8
AB  - GATC sequences in Escherichia coli DNA are methylated at the adenine residue by DNA adenine
AB  - methyltransferase (DamMT). These methylated
AB  - residues and/or the level of DamMT can influence cellular functions
AB  - such as gene transcription, DNA mismatch repair, initiation of
AB  - chromosome replication and nucleoid structure. In certain bacteria,
AB  - unlike E coli, DamMT is essential for viability perhaps owing to its
AB  - role in chromosome replication. DamMT has also been implicated as a
AB  - virulence factor in bacterial pathogenesis. The origin and phylogeny of
AB  - DamMT, based on sequenced genomes, has been deduced.
ER  -

TY  - JOUR
AU  - Lobner-Olesen, A.
AU  - von Freiesleben, U.
TI  - Chromosomal replication incompatibility in Dam methyltransferase deficient Escherichia coli cells.
JO  - EMBO J.
PY  - 1996
SP  - 5999
EP  - 6008
VL  - 15
AB  - Dam methyltransferase deficient Escherichia coli cells containing minichromosomes were
AB  - constructed.  Free plasmid DNA could not be detected in these cells and the minichromosomes
AB  - were found to be integrated in multiple copies in the origin of replication (oriC) region of
AB  - the host chromosome.  The absence of the initiation cascade in Dam- cells is proposed to
AB  - account for this observation of apparent incompatibility between plasmid and chromosomal
AB  - copies of oriC.  Studies using oriC-pBR322 chimeric plasmids and their deletion derivatives
AB  - indicated that the incompatibility determinant is an intact and functional oriC sequence.  The
AB  - seqA2 mutation was found to overcome the incompatibility phenotype by increasing the cellular
AB  - oriC copy number 3-fold thereby allowing minichromosomes to coexist with the chromosome.  The
AB  - replication pattern of a wild-type strain with multiple integrated minichromosomes in the oriC
AB  - region of the chromosome, led to the conclusion that initiation of DNA replication commences
AB  - at a fixed cell mass, irrespective of the number of origins contained on the chromosome.
ER  -

TY  - JOUR
AU  - Lobocka, M.B.
AU  - Rose, D.J.
AU  - Rusin, M.
AU  - Plunkett, G. III
AU  - Samojedny, A.
AU  - Lehnherr, H.
AU  - Yarmolinsky, M.B.
AU  - Blattner, F.R.
TI  - Genome of bacteriophage P1.
JO  - J. Bacteriol.
PY  - 2004
SP  - 7032
EP  - 7068
VL  - 186
AB  - P1 is a bacteriophage of Escherichia coli and other enteric bacteria.
AB  - It lysogenizes its hosts as a circular, low-copy-number plasmid. We have
AB  - determined the complete nucleotide sequences of two strains of a P1
AB  - thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at
AB  - least 117 genes, of which almost two-thirds had not been sequenced
AB  - previously and 49 have no homologs in other organisms. Protein-coding
AB  - genes occupy 92% of the genome and are organized in 45 operons, of which
AB  - four are decisive for the choice between lysis and lysogeny. Four others
AB  - ensure plasmid maintenance. The majority of the remaining 37 operons are
AB  - involved in lytic development. Seventeen operons are transcribed from
AB  - sigma(70) promoters directly controlled by the master phage repressor C1.
AB  - Late operons are transcribed from promoters recognized by the E. coli RNA
AB  - polymerase holoenzyme in the presence of the Lpa protein, the product of a
AB  - C1-controlled P1 gene. Three species of P1-encoded tRNAs provide
AB  - differential controls of translation, and a P1-encoded DNA
AB  - methyltransferase with putative bifunctionality influences transcription,
AB  - replication, and DNA packaging. The genome is particularly rich in Chi
AB  - recombinogenic sites. The base content and distribution in P1 DNA indicate
AB  - that replication of P1 from its plasmid origin had more impact on the base
AB  - compositional asymmetries of the P1 genome than replication from the lytic
AB  - origin of replication.
ER  -

TY  - JOUR
AU  - Lobos, C.
AU  - Vasquez, C.
TI  - Purification and characterisation of BstLVI restriction endonuclease, a thermostable isoschizomer of ClaI from Bacillus stearothermophilus LV.
JO  - Biochim. Biophys. Acta
PY  - 1993
SP  - 295
EP  - 298
VL  - 1171
AB  - This work describes the purification and biochemical characterization of BstLVI restriction
AB  - endonuclease, a thermostable isoschizomer of ClaI, from Bacillus stearothermophilus LV. The
AB  - enzyme was purified by successive DEAE-cellulose, Affi-Gel Blue and Heparin-Sepharose CL-6B
AB  - column chromatography. A molecular weight of 37000 was determined for BstLVI by gel
AB  - filtration. As expected for thermophilic proteins, the enzyme showed a high stability towards
AB  - heat and also to other known protein-denaturing agents.
ER  -

TY  - JOUR
AU  - Lodwick, D.
AU  - Ross, H.N.M.
AU  - Harris, J.E.
AU  - Almond, J.W.
AU  - Grant, W.D.
TI  - dam Methylation in the archaebacteria.
JO  - J. Gen. Microbiol.
PY  - 1986
SP  - 3055
EP  - 3059
VL  - 132
AB  - The DNA of certain species of halophilic and methanogenic archaebacteria is dam methylated, as
AB  - shown by restriction endonuclease sensitivities. The Dam+ phenotype appears to be confined to
AB  - particular taxonomic groupings defined by DNA:rRNA hybridization or 16S RNA oligonucleotide
AB  - cataloging.
ER  -

TY  - JOUR
AU  - Loeffler, J.M.
AU  - Fischetti, V.A.
TI  - Lysogeny of Streptococcus pneumoniae with MM1 Phage: Improved Adherence and Other Phenotypic Changes.
JO  - Infect. Immun.
PY  - 2006
SP  - 4486
EP  - 4495
VL  - 74
AB  - Pneumococcal prophages are extremely frequent, but no role in pathogenesis has so far been
AB  - attributed to them. We isolated a variant of phage MM1, named MM1-1998, from a serotype 24
AB  - strain of Streptococcus pneumoniae. We created three isogenic strain pairs (serotypes 3, 4,
AB  - and 24) that differed only by the lysogenic presence of the MM1-1998 phage and did a
AB  - phenotypic comparison. Lysogeny led to improved adherence to inert surfaces and pharyngeal
AB  - cells compared to that with the cured variants of the strains. We found that lysogeny with
AB  - MM1-1998 coincided with a more transparent phenotype and phage curing with more opaque
AB  - colonies in all strain pairs, and we discovered that transparency was associated with more
AB  - successful and stable lysogeny. Since transparency alone was possibly responsible for the
AB  - adherence difference, we further compared the TIGR4 lysogen with an equally transparent
AB  - variant of TIGR4 in order to reassess the role of phage or transparency separately. The
AB  - results revealed that improved adherence was independently associated with lysogeny with the
AB  - MM1-1998 phage. Other phenotypic differences such as faster growth, increased autolysis, and
AB  - decreased intracellular hemolytic activity were more likely due to transparency. By improving
AB  - the adherence of pneumococci, this prophage may contribute to their fitness and possibly to
AB  - their persistence in humans.
ER  -

TY  - JOUR
AU  - Loenen, W.
AU  - Murray, N.
TI  - Modification Enhancement by Restriction Alleviation Protein (Ral) of Bacteriophage lambda.
JO  - J. Mol. Biol.
PY  - 1986
SP  - 11
EP  - 22
VL  - 190
AB  - The product of the lambda ral gene alleviates restriction and enhances
AB  - modification by the Escherichia coli K-12 restriction and modification system.
AB  - An open reading frame (orf) located between genes N and Ealpha10 has been
AB  - assigned to the ral gene.  We have cloned this orf in a plasmid where its
AB  - transcription is controlled by a thermolabile lambda repressor.  Inactivation
AB  - of the lambda repressor caused a 1000-fold reduction in K-specific restriction
AB  - of unmodified lambda phage and a 100-fold increase in modification.  In
AB  - minicells transformed with ral+ plasmids, derepression resulted in the
AB  - appearance of a polypeptide with a lower mobility than that predicted for a
AB  - protein encoded by the orf attributed to ral; in a transcription and
AB  - translation system in vitro DNA from a ral+ plasmid encoded a polypeptide with
AB  - the same mobility.  This polypeptide was absent when the plasmid DNA carried a
AB  - mutant ral gene.  The nucleotide sequence of this mutant gene defined two base
AB  - changes, one of which inactivates the initiation codon of the orf.  The K
AB  - restriction endonuclease, which is also a K-specific methylase, is encoded by
AB  - three genes designated hsdR, hsdM and hsdS, although the hsdR polypeptide is
AB  - not essential for the methylase activity.  We show that Ral enchances
AB  - modification in a host strain lacking the entire hsdR gene, and lambda phages
AB  - carrying the hsdM and S genes modify their their own DNA inefficiently in the
AB  - absence of Ral, despite the fact that derivatives of these phages provide
AB  - efficient amplification of the K-specific methylase.  Our data support a model
AB  - in which, as a consequence of the interaction of Ral with either the hsdM or
AB  - the hsdS polypeptide, the conformation of the enzyme is changed and the
AB  - efficiency of methylation of unmodified target sites is enhanced.  It has been
AB  - postulated that Ral counteracts Rho, but in our experiments Ral did not relieve
AB  - transcriptional polarity.
ER  -

TY  - JOUR
AU  - Loenen, W.A.
AU  - Dryden, D.T.
AU  - Raleigh, E.A.
AU  - Wilson, G.G.
TI  - Type I restriction enzymes and their relatives.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 20
EP  - 44
VL  - 42
AB  - Type I restriction enzymes (REases) are large pentameric proteins with separate restriction
AB  - (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to
AB  - be discovered and purified, but unlike the enormously useful Type II REases, they have yet to
AB  - find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been
AB  - difficult to characterize, but this is changing as genome analysis reveals their genes, and
AB  - methylome analysis reveals their recognition sequences. Several Type I REases have been
AB  - studied in detail and what has been learned about them invites greater attention. In this
AB  - article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and
AB  - of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases
AB  - have a remarkable ability to change sequence specificity by domain shuffling and
AB  - rearrangements. We summarize the classic experiments and observations that led to this
AB  - discovery, and we discuss how this ability depends on the modular organizations of the enzymes
AB  - and of their S subunits. Finally, we describe examples of Type II restriction-modification
AB  - systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Loenen, W.A.
AU  - Dryden, D.T.
AU  - Raleigh, E.A.
AU  - Wilson, G.G.
AU  - Murray, N.E.
TI  - Highlights of the DNA cutters: a short history of the restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 3
EP  - 19
VL  - 42
AB  - In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a
AB  - non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the
AB  - ability of progeny virus to grow on other hosts by either restricting or enlarging their host
AB  - range. Unlike mutation, this change was reversible, and one cycle of growth in the previous
AB  - host returned the virus to its original form. These simple observations heralded the discovery
AB  - of the endonuclease and methyltransferase activities of what are now termed Type I, II, III
AB  - and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave
AB  - rise to recombinant DNA technology that has transformed molecular biology and medicine. This
AB  - review traces the discovery of restriction enzymes and their continuing impact on molecular
AB  - biology and medicine.
ER  -

TY  - JOUR
AU  - Loenen, W.A.
AU  - Raleigh, E.A.
TI  - The other face of restriction: modification-dependent enzymes.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 56
EP  - 69
VL  - 42
AB  - The 1952 observation of host-induced non-hereditary variation in bacteriophages by Salvador
AB  - Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that glucosylate
AB  - hydroxymethylcytosine in T-even phages and of genes encoding corresponding host activities
AB  - that restrict non-glucosylated phage DNA: rglA and rglB (restricts glucoseless phage). In the
AB  - 1980's, appreciation of the biological scope of these activities was dramatically expanded
AB  - with the demonstration that plant and animal DNA was also sensitive to restriction in cloning
AB  - experiments. The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction). The
AB  - new class of modification-dependent restriction enzymes was named Type IV, as distinct from
AB  - the familiar modification-blocked Types I-III. A third Escherichia coli enzyme, mrr (modified
AB  - DNA rejection and restriction) recognizes both methylcytosine and methyladenine. In recent
AB  - years, the universe of modification-dependent enzymes has expanded greatly. Technical advances
AB  - allow use of Type IV enzymes to study epigenetic mechanisms in mammals and plants. Type IV
AB  - enzymes recognize modified DNA with low sequence selectivity and have emerged many times
AB  - independently during evolution. Here, we review biochemical and structural data on these
AB  - proteins, the resurgent interest in Type IV enzymes as tools for epigenetic research and the
AB  - evolutionary pressures on these systems.
ER  -

TY  - JOUR
AU  - Loenen, W.A.M.
TI  - Tracking EcoKI and DNA fifty years on: a golden story full of surprises.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 7059
EP  - 7069
VL  - 31
AB  - 1953 was a historical year for biology, as it marked the birth of the DNA helix, but also a
AB  - report by Bertani and Weigle on 'a barrier to infection'
AB  - of bacteriophage lambda in its natural host, Escherichia coli K-12, that
AB  - could be lifted by 'host-controlled variation' of the virus. This paper
AB  - lay dormant till Nobel laureate Arber and PhD student Dussoix showed that
AB  - the lambda DNA was rejected and degraded upon infection of different
AB  - bacterial hosts, unless it carried host-specific modification of that DNA,
AB  - thus laying the foundations for the phenomenon of restriction and
AB  - modification (R-M). The restriction enzyme of E.coli K-12, EcoKI, was
AB  - purified in 1968 and required S-adenosylmethionine (AdoMet) and ATP as
AB  - cofactors. By the end of the decade there was substantial evidence for a
AB  - chromosomal locus hsdK with three genes encoding restriction (R),
AB  - modification (M) and specificity (S) subunits that assembled into a large
AB  - complex of >400 kDa. The 1970s brought the message that EcoKI cut away
AB  - from its DNA recognition target, to which site the enzyme remained bound
AB  - while translocating the DNA past itself, with concomitant ATP hydrolysis
AB  - and subsequent double-strand nicks. This translocation event created
AB  - clearly visible DNA loops in the electron microscope. EcoKI became the
AB  - archetypal Type I R-M enzyme with curious DNA translocating properties
AB  - reminiscent of helicases, recognizing the bipartite asymmetric site
AB  - AAC(N6)GTGC. Cloning of the hsdK locus in 1976 facilitated molecular
AB  - understanding of this sophisticated R-M complex and in an elegant 'pas de
AB  - deux' Murray and Dryden constructed the present model based on a large
AB  - body of experimental data plus bioinformatics. This review celebrates the
AB  - golden anniversary of EcoKI and ends with the exciting progress on the
AB  - vital issue of restriction alleviation after DNA damage, also first
AB  - reported in 1953, which involves intricate control of R subunit activity
AB  - by the bacterial proteasome ClpXP, important results that will keep
AB  - scientists on the EcoKI track for another 50 years to come.
ER  -

TY  - JOUR
AU  - Loenen, W.A.M.
AU  - Daniel, A.S.
AU  - Braymer, H.D.
AU  - Murray, N.E.
TI  - Organization and sequence of the hsd genes of Escherichia coli K12.
JO  - J. Mol. Biol.
PY  - 1987
SP  - 159
EP  - 170
VL  - 198
AB  - The nucleotide sequence of the hsdR and M genes, together with that for hsdS
AB  - comprises an 8400 base segment spanning the entire hsd region of Escherichia
AB  - coli K-12.  The three hsd genes are transcribed in the same direction, but from
AB  - two promoters.  hsdR and hsdM are separated by 492 base-pairs, whereas the
AB  - termination codon of hsdM overlaps the initiation codon of hsdS.  pres precedes
AB  - hsdR, and our data indicate a transcription termination signal in the interval
AB  - between hsdR and -mod, as expected if transcription of hsdM and S is dependent
AB  - on pmod.  Transcription from pres is not influenced by the products of the hsdM
AB  - and S genes, and the mechanism whereby restriction is prevented when the hsd
AB  - region is transferred to a modification-deficient cell remains to be
AB  - elucidated.  A segment of the predicted amino acid sequence of the M
AB  - polypeptide shares homology with a variety of adenine methylases and may
AB  - identify part of the active site for methylation of specific adenine residues.
AB  - The R polypeptide shows homology with a variety of ATPases, and pronounced
AB  - regions of alpha-helical structure are predicted, one of which is amphipathic.
ER  -

TY  - JOUR
AU  - Loessner, M.J.
AU  - Wendlinger, G.
AU  - Scherer, S.
TI  - Heterogeneous endolysins in Listeria monocytogenes bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes.
JO  - Mol. Microbiol.
PY  - 1995
SP  - 1231
EP  - 1241
VL  - 16
AB  - Listeria monocytogenes bacteriophages A118, A500 and A511 are members of three distinct phage
AB  - groups with characteristic host ranges. Their endolysin (ply) genes were cloned and expressed
AB  - in Escherichia coli as demonstrated by the conferred lytic phenotype when colonies of
AB  - recombinant cells were overlaid with a lawn of Listeria cells. The nucleotide sequences of the
AB  - cloned DNA fragments were determined and the individual enzymes (PLY118, 30.8 kDa; PLY500,
AB  - 33.4 kDa; PLY511, 36.5 kDa) were shown to have varying degrees of homology within their
AB  - N-terminal or C-terminal domains. Transcriptional analysis revealed them to be 'late' genes
AB  - with transcription beginning 15-20 min post-infection. The enzymes were overexpressed and
AB  - partially purified and their individual specificities examined. When applied exogenously, the
AB  - lysins induced rapid lysis of Listeria strains from all species but generally did not affect
AB  - other bacteria. Using hydrolysis of purified listerial cell walls, PLY511 was characterized as
AB  - an N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) and shows homology in its N-terminal
AB  - domain to other enzymes of this type. In contrast, PLY118 and PLY500 were shown to represent a
AB  - new class of cell wall lytic enzymes which cleave between the L-alanine and D-glutamate
AB  - residues of listerial peptidoglycan; these were designated as L-alanoyl-D-glutamate
AB  - peptidases. These two enzymes share homology in the N-terminal domain which we propose
AB  - determines hydrolytic specificity. Highly conserved holin (hol) gene sequences are present
AB  - upstream of ply118 and ply500. They encode proteins of structural similarity to the product of
AB  - phage lambda gene S, and are predicted to be membrane proteins which form pores to allow
AB  - access of the lysins to their peptidoglycan substrates. This arrangement of conserved holin
AB  - genes with downstream lysin genes among the siphoviral lysis cassettes explains why the
AB  - cytoplasmic endolysins alone are not lethal, since they require a specific transport function
AB  - across the cell membrane.
ER  -

TY  - JOUR
AU  - Loewen, P.C.
AU  - Alsaadi, Y.
AU  - Fernando, D.
AU  - Kumar, A.
TI  - Genome Sequence of a Tigecycline-Resistant Clinical Isolate of Acinetobacter baumannii Strain AB031 Obtained from a Bloodstream Infection.
JO  - Genome Announcements
PY  - 2014
SP  - e01036
EP  - e01014
VL  - 2
AB  - We report here the 3.8-Mbp genome sequence of a blood isolate of Acinetobacter baumannii
AB  - strain AB031.
ER  -

TY  - JOUR
AU  - Loewen, P.C.
AU  - Alsaadi, Y.
AU  - Fernando, D.
AU  - Kumar, A.
TI  - Genome Sequence of an Extremely Drug-Resistant Clinical Isolate of Acinetobacter  baumannii Strain AB030.
JO  - Genome Announcements
PY  - 2014
SP  - e01035
EP  - e01014
VL  - 2
AB  - We report the 4.3-Mbp genome sequence of a blood isolate of Acinetobacter baumannii strain
AB  - AB030.
ER  -

TY  - JOUR
AU  - Loewen, P.C.
AU  - Switala, J.
AU  - Fernando, W.G.
AU  - de Kievit, T.
TI  - Genome Sequence of Pseudomonas brassicacearum DF41.
JO  - Genome Announcements
PY  - 2014
SP  - e00390
EP  - e00314
VL  - 2
AB  - Pseudomonas brassicacearum DF41, a Gram-negative soil bacterium, is able to suppress the
AB  - fungal pathogen Sclerotinia sclerotiorum through a process known as
AB  - biological control. Here, we present a 6.8-Mb assembly of its genome, which is
AB  - the second fully assembled genome of a P. brassicacearum strain.
ER  -

TY  - JOUR
AU  - Loewen, P.C.
AU  - Villenueva, J.
AU  - Fernando, W.G.
AU  - de Kievit, T.
TI  - Genome Sequence of Pseudomonas chlororaphis Strain PA23.
JO  - Genome Announcements
PY  - 2014
SP  - e00689
EP  - e00614
VL  - 2
AB  - Pseudomonas chlororaphis strain PA23 is a plant-beneficial bacterium that is able to suppress
AB  - disease caused by the fungal pathogen Sclerotinia sclerotiorum
AB  - through a process known as biological control. Here we present a 7.1-Mb assembly
AB  - of the PA23 genome.
ER  -

TY  - JOUR
AU  - Loftie-Eaton, W.
AU  - Suzuki, H.
AU  - Bashford, K.
AU  - Heuer, H.
AU  - Stragier, P.
AU  - De Vos, P.
AU  - Settles, M.L.
AU  - Top, E.M.
TI  - Draft Genome Sequence of Pseudomonas sp. nov. H2.
JO  - Genome Announcements
PY  - 2015
SP  - e00241
EP  - e00215
VL  - 3
AB  - We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment
AB  - in Moscow, ID, USA. The strain is most closely related to
AB  - Pseudomonas putida. However, it has a slightly smaller genome that appears to
AB  - have been impacted by horizontal gene transfer and poorly maintains IncP-1
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Loftus, B. et al.
TI  - The genome of the protist parasite Entamoeba histolytica.
JO  - Nature
PY  - 2005
SP  - 865
EP  - 868
VL  - 433
AB  - Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which
AB  - is a significant source of morbidity and mortality in developing countries. Here we present
AB  - the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two
AB  - other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These
AB  - adaptations include reduction or elimination of most mitochondrial metabolic pathways and the
AB  - use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic
AB  - analysis identifies evidence for lateral gene transfer of bacterial genes into the E.
AB  - histolytica genome, the effects of which centre on expanding aspects of E. histolytica's
AB  - metabolic repertoire. The presence of these genes and the potential for novel metabolic
AB  - pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The
AB  - genome encodes a large number of novel receptor kinases and contains expansions of a variety
AB  - of gene families, including those associated with virulence. Additional genome features
AB  - include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a
AB  - structural function in the genome. Analysis of the genome provides new insights into the
AB  - workings and genome evolution of a major human pathogen.
ER  -

TY  - JOUR
AU  - Loizos, N.
AU  - Silva, G.H.
AU  - Belfort, M.
TI  - Intron-encoded endonuclease I-TevII binds across the minor groove and induces two distinct conformational changes in its DNA substrate.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 412
EP  - 424
VL  - 255
AB  - I-TevII is the homing endonuclease encoded by the sunY intron of bacteriophage T4.  The enzyme
AB  - cleaves an intronless sunY gene near the exon I-exon II junction, thereby initiating intron
AB  - homing into its cognate intronless allele.  Specifically, I-TevII cleaves its DNA target 13 to
AB  - 15 nucleotides downstream of the sunY intron insertion site, generating 2-nt 3'-OH
AB  - extensions.  Here, we present evidence that I-TevII makes predominantly minor groove contacts
AB  - in two regions of its recognition sequence, as does I-TevI, the other homing endonuclease
AB  - encoded by phage T4.  Following cleavage, I-TevII was shown to remain bound to one of its DNA
AB  - products, suggesting possible additional roles for the endonuclease in the mobility process.
AB  - Interestingly, two distinct conformational changes were detected by gel analysis in the DNA
AB  - substrate following binding by I-TevII, one occurring in the absence of Mg2+, the second being
AB  - dependent on the presence of Mg2+.  The Mg2+-induced distortion accompanies a nick in one
AB  - strand, and may serve to bring the cleavage site on the other strand into proximity with the
AB  - catalytic domain of the protein.
ER  -

TY  - JOUR
AU  - Loizos, N.
AU  - Tillier, E.R.M.
AU  - Belfort, M.
TI  - Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 11983
EP  - 11987
VL  - 91
AB  - Mobile group I introns are hypothesized to have arisen after invasion by endonuclease-encoding
AB  - open reading frames (ORFs) which mediate their mobility. Consistent with an endonuclease-ORF
AB  - invasion event, we report similarity between exon junction sequences (the recognition site for
AB  - the mobility endonuclease) and intron sequences flanking the endonuclease ORF in the sunY gene
AB  - of phage T4. Furthermore, we have demonstrated the ability of the intron-encoded endonuclease
AB  - to recognize and cleave these intron sequences when present in fused form in synthetic
AB  - constructs. These observations and accompanying splicing data are consistent with models in
AB  - which the invading endonuclease ORF is provided safe haven within a splicing element. In turn
AB  - the intron is afforded immunity to the endonuclease product, which imparts mobility to the
AB  - intron.
ER  -

TY  - JOUR
AU  - Loman, N.J.
AU  - Snyder, L.A.
AU  - Linton, J.D.
AU  - Langdon, R.
AU  - Lawson, A.J.
AU  - Weinstock, G.M.
AU  - Wren, B.W.
AU  - Pallen, M.J.
TI  - Genome sequence of the emerging pathogen Helicobacter canadensis.
JO  - J. Bacteriol.
PY  - 2009
SP  - 5566
EP  - 5567
VL  - 191
AB  - We determined the genome sequence of the type strain of Helicobacter
AB  - canadensis, an emerging human pathogen with diverse animal reservoirs.
AB  - Potential virulence determinants carried by the genome include systems for
AB  - N-linked glycosylation and capsular export. A protein-based phylogenetic
AB  - analysis places H. canadensis close to Wolinella succinogenes.
ER  -

TY  - JOUR
AU  - Lomonaco, S.
AU  - Gallina, S.
AU  - Filipello, V.
AU  - Sanchez, L.M.
AU  - Kastanis, G.J.
AU  - Allard, M.
AU  - Brown, E.
AU  - Amato, E.
AU  - Pontello, M.
AU  - Decastelli, L.
TI  - Draft Genome Sequences of 510 Listeria monocytogenes Strains from Food Isolates and Human Listeriosis Cases from Northern Italy.
JO  - Genome Announcements
PY  - 2018
SP  - e01276
EP  - e01217
VL  - 6
AB  - Listeriosis outbreaks are frequently multistate/multicountry outbreaks, underlining the
AB  - importance of molecular typing data for several diverse and
AB  - well-characterized isolates. Large-scale whole-genome sequencing studies on
AB  - Listeria monocytogenes isolates from non-U.S. locations have been limited.
AB  - Herein, we describe the draft genome sequences of 510 L. monocytogenes isolates
AB  - from northern Italy from different sources.
ER  -

TY  - JOUR
AU  - Lomovskaya, N.D.
AU  - Chater, K.F.
AU  - Mkrtumian, N.M.
TI  - Genetics and Molecular Biology of Streptomyces Bacteriophages.
JO  - Microbiol. Rev.
PY  - 1980
SP  - 206
EP  - 229
VL  - 44
AB  - The streptomycetes are genetically among the most tractable of bacteria.  In
AB  - the best-studied strain, Streptomyces coelicolor A3, chromosome mapping is
AB  - straightforward, and a single circular linkage map of more than 100 markers has
AB  - been established.  Extremely efficient protoplast fusion can be induced by
AB  - polyethylene glycol.  Plasmids have been demonstrated both physically and
AB  - genetically, and some of them are self-transmissible sex factors having a
AB  - variety of interactions with the host chromosome.  Reintroduction
AB  - (transformation) of isolated plasmid deoxyribonucleic acid (DNA) into
AB  - protoplasts occurs at high frequency in the presence of polyethylene glycol.
AB  - These features are important in the study of several special characteristics of
AB  - streptomycetes, in particular, their remarkable status as antibiotic producers
AB  - and their morphological complexity.  Much greater progress will be possible in
AB  - these investigations when the techniques already available are supplemented by
AB  - gene cloning and transposon genetics and by systems for fine-structure mapping.
AB  - Among the important requirements for the development and optimum exploitation
AB  - of such techniques is an understanding of Streptomyces phages, particularly of
AB  - their genetics and DNA. About a decade ago it was possible for major reviews of
AB  - S. coelicolor genetics and Streptomyces phages to be completely independent of
AB  - each other; the potential benefits of using a genetically studied host in phage
AB  - studies, and vice versa, were unfulfilled.  More recently, considerable
AB  - advances have been made in the genetic and physical analysis of these phages
AB  - and their interactions with their hosts.  Thus, when temperate phages acting on
AB  - S. coelicolor A3 were isolated, it became possible to initiate studies of such
AB  - problems as the relationship between phages and differentiated bacteria,
AB  - comparison with model eubacterial phage-host systems, the genetic basis of
AB  - lysogenization in streptomycetes, the structure and function of the genomes of
AB  - Streptomyces phages, and the development of Streptomyces phages as DNA-cloning
AB  - vectors.  Both temperate and virulent phages have been instrumental in
AB  - understanding Streptomyces host-controlled restriction and modification (RM)
AB  - systems, and they have also helped in various aspects of the genetic analysis
AB  - of streptomycetes. The most extensive studies have been of the temperate phage
AB  - UC31, and we will focus on this phage as a main theme, with occasional
AB  - variations provided by observations on some other phages.  We shall then
AB  - consider these and other results in the context of the use of phages as vectors
AB  - for the introduction of particular DNA segments into streptomycetes, and
AB  - finally review interactions between the phages and host-controlled RM systems.
ER  -

TY  - JOUR
AU  - Long, M.
AU  - Ruan, L.
AU  - Yu, Z.
AU  - Xu, X.
TI  - Genome sequence of Pseudomonas sp. S9, an extracellular arylsulfatase producing bacterium isolated from the mangrove soil.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4041
EP  - 4041
VL  - 193
AB  - Pseudomonas sp. S9 was originally isolated from the mangrove soil in Xiamen, China. It is an
AB  - aerobic bacterium which shows extracellular
AB  - arylsulfatase activity. Here, we describe the 4.8 Mb draft genome sequence
AB  - of Pseudomonas sp. S9 which exhibits novel cysteine-type sulfatases.
ER  -

TY  - JOUR
AU  - Long, S.W.
AU  - Kachroo, P.
AU  - Musser, J.M.
AU  - Olsen, R.J.
TI  - Whole-Genome Sequencing of a Human Clinical Isolate of emm28 Streptococcus pyogenes Causing Necrotizing Fasciitis Acquired Contemporaneously with Hurricane   Harvey.
JO  - Genome Announcements
PY  - 2017
SP  - e01269
EP  - e01217
VL  - 5
AB  - We discovered an emm28 Streptococcus pyogenes isolate causing necrotizing fasciitis in a
AB  - patient exposed to the floodwaters of Hurricane Harvey in the
AB  - Houston, TX, metropolitan area in August 2017. The Oxford Nanopore MinION
AB  - instrument provided sufficient genome sequence data within 1 h of beginning
AB  - sequencing to close the genome.
ER  -

TY  - JOUR
AU  - Long, S.W.
AU  - Linson, S.E.
AU  - Ojeda, S.M.
AU  - Cantu, C.
AU  - Davis, J.J.
AU  - Brettin, T.
AU  - Olsen, R.J.
TI  - Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov.
JO  - Genome Announcements
PY  - 2017
SP  - e01057
EP  - e01017
VL  - 5
AB  - In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all
AB  - recognized Klebsiella spp. We closed the genome of strain KPN1705 using
AB  - a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For
AB  - this novel species, we propose the name Klebsiella quasivariicola sp. nov.
ER  -

TY  - JOUR
AU  - Long, S.W.
AU  - Olsen, R.J.
AU  - Eagar, T.N.
AU  - Beres, S.B.
AU  - Zhao, P.
AU  - Davis, J.J.
AU  - Brettin, T.
AU  - Xia, F.
AU  - Musser, J.M.
TI  - Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307.
JO  - MBio
PY  - 2017
SP  - e00489
EP  - e00417
VL  - 8
AB  - Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality
AB  - rates. The emergence and spread of strains resistant to multiple
AB  - antimicrobial agents and documented large nosocomial outbreaks are especially
AB  - concerning. To develop new therapeutic strategies for K. pneumoniae, it is
AB  - imperative to understand the population genomic structure of strains causing
AB  - human infections. To address this knowledge gap, we sequenced the genomes of
AB  - 1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured
AB  - from patients in the 2,000-bed Houston Methodist Hospital system between
AB  - September 2011 and May 2015, representing a comprehensive, population-based
AB  - strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused
AB  - more infections than those of well-studied epidemic CG258. Strains varied
AB  - markedly in gene content and had an extensive array of small and very large
AB  - plasmids, often containing antimicrobial resistance genes. Some patients with
AB  - multiple strains cultured over time were infected with genetically distinct
AB  - clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase
AB  - 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam
AB  - antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse
AB  - strains showed that the global transcriptome of each strain was unique and highly
AB  - variable. Experimental mouse infection provided new information about
AB  - immunological parameters of host-pathogen interaction. We exploited the large
AB  - data set to develop whole-genome sequence-based classifiers that accurately
AB  - predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We
AB  - conclude that analysis of large, comprehensive, population-based strain samples
AB  - can assist understanding of the molecular diversity of these organisms and
AB  - contribute to enhanced translational research.IMPORTANCEKlebsiella pneumoniae
AB  - causes human infections that are increasingly difficult to treat because many
AB  - strains are resistant to multiple antibiotics. Clonal group 258 (CG258) organisms
AB  - have caused outbreaks in health care settings worldwide. Using a comprehensive
AB  - population-based sample of extended-spectrum beta-lactamase (ESBL)-producing K.
AB  - pneumoniae strains, we show that a relatively uncommon clonal type, CG307, caused
AB  - the plurality of ESBL-producing K. pneumoniae infections in our patients. We
AB  - discovered that CG307 strains have been abundant in Houston for many years. As
AB  - assessed by experimental mouse infection, CG307 strains were as virulent as
AB  - pandemic CG258 strains. Our results may portend the emergence of an especially
AB  - successful clonal group of antibiotic-resistant K. pneumoniae.
ER  -

TY  - JOUR
AU  - Longley, M.J.
AU  - Mosbaugh, D.W.
TI  - Characterization of DNA metabolizing enzymes in situ following polyacrylamide gel electrophoresis.
JO  - Biochemistry
PY  - 1991
SP  - 2655
EP  - 2664
VL  - 30
AB  - We have detected the in situ activities of DNA glycosylase, endonuclease, DNA
AB  - polymerase, and DNA ligase using a novel polyacrylamide activity gel
AB  - electrophoresis procedure.  DNA metabolizing enzymes were resolved through
AB  - either native or SDS-polyacrylamide gels containing defined 32P-labeled
AB  - oligonucleotides annealed to M13 DNA.  After electrophoresis, these enzymes
AB  - catalyzed in situ reactions and their [32P]DNA products were resolved from the
AB  - gel by a second dimension of electrophoresis through a denaturing DNA
AB  - sequencing gel.  Detection of modified (degraded or elongated) oligonucleotide
AB  - chains was used to locate various enzyme activities.  The catalytic and
AB  - physical properties of Novikoff hepatoma DNA polymerase beta were found to be
AB  - similar under both in vitro and in situ conditions.  With 3'-terminally matched
AB  - and mismatched [32P]DNA substrates in the same activity gel, DNA polymerase
AB  - and/or 3' to 5' exonuclease activities of Escherichia coli DNA polymerase I
AB  - (large fragment), DNA polymerase III (holoenzyme), and exonuclease III were
AB  - detected and characterized.  In addition, use of matched and mismatched DNA
AB  - primers permitted the uncoupling of mismatch excision and chain extension
AB  - steps.  Activities first detected in nondenaturing activity gels as either
AB  - multifunctional or multimeric enzymes were also identified in denaturing
AB  - activity gels, and assignment of activities to specific polypeptides suggested
AB  - subunit composition.  Furthermore, DNA substrates cast within polyacrylamide
AB  - gels were successfully modified by the exogenous enzymes polynucleotide kinase
AB  - and alkaline phosphatase before and after in situ detection of E. coli DNA
AB  - ligase activity, respectively.  Several restriction endonucleases and the
AB  - tripeptide (Lys-Trp-Lys), which acts as an apurinic/apyrimidinic endonuclease,
AB  - were able to diffuse into gels and modify DNA.  This ability to create
AB  - intermediate substrates within activity gels could prove extremely useful in
AB  - delineating the steps of DNA replication and repair pathways.
ER  -

TY  - JOUR
AU  - Longo, M.
AU  - De Jode, M.
AU  - Plainvert, C.
AU  - Weckel, A.
AU  - Hua, A.
AU  - Chateau, A.
AU  - Glaser, P.
AU  - Poyart, C.
AU  - Fouet, A.
TI  - Complete Genome Sequence of Streptococcus pyogenes emm28 Clinical Isolate M28PF1, Responsible for a Puerperal Fever.
JO  - Genome Announcements
PY  - 2015
SP  - e00750
EP  - e00715
VL  - 3
AB  - We report the sequence of the Streptococcus pyogenes emm28 strain M28PF1, isolated from a
AB  - patient with postpartum endometritis. The M28 protein is smaller
AB  - than that of MGAS6180 (NC_007296.1). Furthermore, the 1,896,976-bp-long
AB  - chromosome presents, compared to that of MGAS6180, an inversion between the two
AB  - comX genes.
ER  -

TY  - JOUR
AU  - Looft, T.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Stanton, T.B.
TI  - Complete Genome Sequence of Coriobacteriaceae Strain 68-1-3, a Novel Mucus-Degrading Isolate from the Swine Intestinal Tract.
JO  - Genome Announcements
PY  - 2015
SP  - e01143
EP  - e01115
VL  - 3
AB  - A novel Coriobacteriaceae bacterium (strain 68-1-3) was isolated from the ileum of the swine
AB  - intestinal tract using a selective mucus-based medium. Here we present the finished genome
AB  - sequence for the swine commensal, totaling 1.97 Mb in size.
ER  -

TY  - JOUR
AU  - Looney, M.C.
AU  - Moran, L.S.
AU  - Jack, W.E.
AU  - Feehery, G.R.
AU  - Benner, J.S.
AU  - Slatko, B.E.
AU  - Wilson, G.G.
TI  - Nucleotide sequence of the FokI restriction-modification system:  separate strand-specificity domains in the methyltransferase.
JO  - Gene
PY  - 1989
SP  - 193
EP  - 208
VL  - 80
AB  - The genes for FokI, a type-IIS restriction-modification system from
AB  - Flavobacterium okeanokoites (asymmetric recognition sequence:
AB  - 5'-GGATG/3'-CCTAC), were cloned into Escherichia coli.  Recombinants carrying
AB  - the fokIR and fokIM genes were found to modify their DNA completely, and to
AB  - restrict lambdoid phages weakly.  The nucleotide sequences of the genes were
AB  - determined, and the probable start codons were confirmed by amino acid
AB  - sequencing.  The FokI endonuclease (R.FokI) and methyltransferase (M.FokI) are
AB  - encoded by single, adjacent genes, aligned in the same orientation, in the
AB  - order M then R.  The genes are large by the standards of type-II systems, 1.9
AB  - kb for the M gene, and 1.7 kb for the R gene.  Preceding each gene is a pair of
AB  - FokI recognition sites; it is conceivable that interactions between the sites
AB  - and the FokI proteins could regulate expression of the genes.
ER  -

TY  - JOUR
AU  - Lopatina, N.
AU  - Haskell, J.F.
AU  - Andrews, L.G.
AU  - Poole, J.C.
AU  - Saldanha, S.
AU  - Tollefsbol, T.
TI  - Differential maintenance and de novo methylating activity by three DNA methyltransferases in aging and immortalized fibroblasts.
JO  - J. Cell. Biochem.
PY  - 2002
SP  - 324
EP  - 334
VL  - 84
AB  - Genomic methylation, which influences many cellular processes such as gene expression and
AB  - chromatin organization, generally declines with
AB  - cellular senescence although some genes undergo paradoxical
AB  - hypermethylation during cellular aging and immortalization. To explore
AB  - potential mechanisms for this process, we analyzed the methylating
AB  - activity of three DNA methyltransferases (Dnmts) in aging and
AB  - immortalized WI-38 fibroblasts. Overall maintenance methylating
AB  - activity by the Dnmts greatly decreased during cellular senescence. In
AB  - immortalized WI-38 cells, maintenance methylating activity was similar
AB  - to that of normal young cells. Combined de novo methylation activity of
AB  - the Dnmts initially decreased but later increased as WI-38 cells aged
AB  - and was strikingly elevated in immortalized cells. To further elucidate
AB  - the mechanisms for changes in DNA methylation in aging and immortalized
AB  - cells, the individual Dnmts were separated and individually assessed
AB  - for maintenance and de novo methylating activity. We resolved three
AB  - Dnmt fractions, one of which was the major maintenance
AB  - methyltransferase, Dnmt1, which declined steadily in activity with
AB  - cellular senescence and immortalization. However, a more basic Dnmt,
AB  - which has significant de novo methylating activity, increased markedly
AB  - in activity in aging and immortalized cells. We have identified this
AB  - methyltransferase as Dnmt3b which has an important role in neoplastic
AB  - transformation but its role in cellular senescence and immortalization
AB  - has not previously been reported. An acidic Dnmt we isolated also had
AB  - increased de novo methylating activity in senescent and immortalized
AB  - WI-38 cells. These studies indicate that reduced genome-wide
AB  - methylation in aging cells may be attributed to attenuated Dnmt1
AB  - activity but that regional or gene-localized hypermethylation in aging
AB  - and immortalized cells may be linked to increased de novo methylation
AB  - by Dnmts other than the maintenance methyltransferase.
ER  -

TY  - JOUR
AU  - Lopatina, N.G.
AU  - Kirnos, M.D.
AU  - Suchkov, S.V.
AU  - Vanyushin, B.F.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Determination of the recognition site for adenine-specific methylase of Shigella sonnei 47 by hydrazinolysis of DNA, followed by separation of the purine oligonucleotides by thin-layer chromatography on DEAE-cellulose.
JO  - Biokhimiia
PY  - 1985
SP  - 495
EP  - 502
VL  - 50
AB  - A method has been developed for the separation of oligopurine units according
AB  - to length and composition by two-dimensional thin-layer chromatography on
AB  - plates with DEAE-cellulose, permitting a comparative analysis of the content of
AB  - various purine isopliths in DNA of different origin.  In the case of the
AB  - analysis of methylated DNA, the method permits a comparison of the substrate
AB  - specificity of various enzymes of methylation of the adenine residues in DNA.
AB  - In conjunction with enzymatic treatment of labeled methylated isopliths, the
AB  - method permits determination of the methylatable sequence and in a number of
AB  - cases an ascertainment of the recognition site for adenine-specific methylase
AB  - as a whole.  The proposed method was used to establish the fact that the
AB  - methylase SsoI recognizes the sequence 5' ...G-*A-A-T-T-C...3' and methylates
AB  - the adenine residue closest to its 5'-end.
ER  -

TY  - JOUR
AU  - Lopatina, N.G.
AU  - Lopareva, E.N.
AU  - Posypanova, A.M.
AU  - Nikolskaya, A.
AU  - Debov, S.S.
TI  - Cytosine DNA-methylase SsoII from Shigella sonnei 47 cells.
JO  - Biokhimiia
PY  - 1988
SP  - 1265
EP  - 1269
VL  - 53
AB  - Shigella sonnei 47 cells were found to contain DNA-methylase SsoII which is a
AB  - modifying component of the system of host specificity of SsoII.  The
AB  - recognition sequence (RS) of methylase SsoII is represented by a five-member
AB  - palindromic structure -5'...CCNGG...3'- with a degenerate central nucleotide.
AB  - Modification of SsoII affords protection of acceptor DNA not only from SsoII
AB  - type restriction, but also from other restrictases, e.g., EcoRII having an
AB  - analogous RS but with a less degenerate central nucleotide pair.  A simple and
AB  - rapid procedure for isolation and purification of DNA-methylase SsoII, which
AB  - employs hydrophobic chromatography on phenyl-Sepharose, has been developed.
AB  - The enzyme preparation does not contain trace amounts of specific and
AB  - nonspecific endonucleases and keeps stable on storage in 30% glycerol over a
AB  - period of one year.
ER  -

TY  - JOUR
AU  - Lopatina, N.G.
AU  - Nikolskaya, I.I.
AU  - Buryanov, Y.I.
AU  - Debov, S.S.
TI  - Presence of 2 DNA-methylases of cytosine in Escherichia coli CK cells.
JO  - Dokl. Akad. Nauk.
PY  - 1978
SP  - 1475
EP  - 1477
VL  - 240
ER  -

TY  - JOUR
AU  - Lopatina, N.G.
AU  - Nikolskaya, I.I.
AU  - Sverdiov, E.D.
AU  - Debov, S.S.
TI  - Determination of the recognition sites of adenine DNA-methylases from Escherichia coli CK.
JO  - Vopr. Med. Khim.
PY  - 1981
SP  - 220
EP  - 223
VL  - 27
AB  - DNA-methylases from a strain of E. coli CK were studied.  Three adenine methylases were found
AB  - in the strain studied, which were eluted by 0.16M, 0.23M and 0.7M NaCl in phosphocellulose
AB  - P-11 chromatography.  According to this, the enzymes were designated as DM-A16, DM-A23 and
AB  - DM-A-70.  Indirect data on the presence of adenine specific methylases dissimilar in their
AB  - recognition sites in cells of E. coli CK were obtained using the test of additional
AB  - methylation modified by I.I. Nikolskaya.  These conclusions were confirmed, when the
AB  - dinucleotide sequence was determined in the recognition site using DM-A23 and DM-A70.  The
AB  - methylase DM-A23 was shown to recognize the dinucleotide sequence 5'...A-G...3'.
ER  -

TY  - JOUR
AU  - Lopatina, N.G.
AU  - Suchkov, S.V.
AU  - Kulikov, S.M.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Site-specificity of DNA methylases from Shigella sonnei 47 cells.
JO  - Biokhimiia
PY  - 1985
SP  - 1694
EP  - 1701
VL  - 50
AB  - A complex approach involving isoplith analysis, enzymatic treatment of methylated isopliths
AB  - and computer analysis of experimental data has been used to determine site specificity of six
AB  - methylases from Shigella sonnei 47 cells termed according to their base specificity and pI as
AB  - MC4.2, MC5.3, MC6.2, MC7.4, MC8.4 and MA9.5.  It has been found that the recognition site of
AB  - MA9.5 is a palindrome of the 5' ...GAATTC...3' type and that this enzyme is an isomethylomer
AB  - of M.EcoRI.  It has been demonstrated for the first time for methylases that the recognition
AB  - site of MC4.2 is represented by a non-symmetrical four-member sequence, 5'...NCCCCN...3'
AB  - characterized by unique blocking of cytosines.  MC8.4 possesses a broad specificity of
AB  - substrate recognition and methylates the cytosine residue within the non-symmetrical unique
AB  - sequence 5'...N(C/Pu) CCN...3', whose 5'-terminal base is depleted in three nucleotides.
AB  - MC5.3 methylates the 3'-terminal cytosine residue within the composition of the
AB  - pentanucleotide palindrome recognition site, 5'...CCNGG...3' MC6.2 and MC7.4 possess
AB  - identical pentanucleotide recognition sites, 5'...(Py)CNG(Pu)...3', but are distinguished by
AB  - pI.  The latter finding has been shown for the first time for different methylases within one
AB  - strain.
ER  -

TY  - JOUR
AU  - Loper, J.E. et al.
TI  - Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions.
JO  - PLoS Genet.
PY  - 2012
SP  - E1002784
EP  - E1002784
VL  - 8
AB  - We provide here a comparative genome analysis of ten strains within the
AB  - Pseudomonas fluorescens group including seven new genomic sequences. These
AB  - strains exhibit a diverse spectrum of traits involved in biological control and
AB  - other multitrophic interactions with plants, microbes, and insects. Multilocus
AB  - sequence analysis placed the strains in three sub-clades, which was reinforced by
AB  - high levels of synteny, size of core genomes, and relatedness of orthologous
AB  - genes between strains within a sub-clade. The heterogeneity of the P. fluorescens
AB  - group was reflected in the large size of its pan-genome, which makes up
AB  - approximately 54% of the pan-genome of the genus as a whole, and a core genome
AB  - representing only 45-52% of the genome of any individual strain. We discovered
AB  - genes for traits that were not known previously in the strains, including genes
AB  - for the biosynthesis of the siderophores achromobactin and pseudomonine and the
AB  - antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III,
AB  - and VI secretion systems; and insect toxins. Certain gene clusters, such as those
AB  - for two type III secretion systems, are present only in specific sub-clades,
AB  - suggesting vertical inheritance. Almost all of the genes associated with
AB  - multitrophic interactions map to genomic regions present in only a subset of the
AB  - strains or unique to a specific strain. To explore the evolutionary origin of
AB  - these genes, we mapped their distributions relative to the locations of mobile
AB  - genetic elements and repetitive extragenic palindromic (REP) elements in each
AB  - genome. The mobile genetic elements and many strain-specific genes fall into
AB  - regions devoid of REP elements (i.e., REP deserts) and regions displaying
AB  - atypical tri-nucleotide composition, possibly indicating relatively recent
AB  - acquisition of these loci. Collectively, the results of this study highlight the
AB  - enormous heterogeneity of the P. fluorescens group and the importance of the
AB  - variable genome in tailoring individual strains to their specific lifestyles and
AB  - functional repertoire.
ER  -

TY  - JOUR
AU  - Lopes, E.F.
AU  - Da Costa, J.G.
AU  - Wolf, I.R.
AU  - Lima, J.P.A.
AU  - Astolfi-Filho, S.
TI  - Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum  Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00301
EP  - e00318
VL  - 6
AB  - Burkholderia gladioli Coa14 is a bacterium isolated from water collected from Coari Lake
AB  - (Amazonas, Brazil) that shows a capacity for survival in a medium
AB  - containing only oil as a carbon source. Here, we report its draft genome
AB  - sequence, highlighting some genes involved with petroleum derivative degradation.
ER  -

TY  - JOUR
AU  - Lopes, E.M.
AU  - Kishi, L.T.
AU  - Fernandes, C.C.
AU  - Paganelli, F.L.
AU  - Alves, L.M.
AU  - Lemos, E.G.
AU  - de Souza, J.A.
TI  - Draft Genome Sequence of Bradyrhizobium elkanii TnphoA 33, a Producer of Polyhydroxyalkanoates.
JO  - Genome Announcements
PY  - 2017
SP  - e01502
EP  - e01516
VL  - 5
AB  - The genus Bradyrhizobium comprises bacteria with the ability to form nitrogen-fixing symbioses
AB  - with legumes. They are of great interest in
AB  - agriculture, as well as for the production of biopolymers such as
AB  - polyhydroxyalkanoates. Here, we report the draft genome assembly of
AB  - Bradyrhizobium elkanii TnphoA 33 comprising 9 Mb, 1,124 contigs, and 9,418 open
AB  - reading frames.
ER  -

TY  - JOUR
AU  - Lopes, T. et al.
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3567
EP  - 3568
VL  - 194
AB  - In this work we report the genome of Corynebacterium pseudotuberculosis strain 267, isolated
AB  - from a llama. This pathogen is of great veterinary and economic
AB  - importance, as it is the cause of caseous lymphadenitis in several livestock
AB  - species around the world and causes significant losses due to the high cost of
AB  - treatment.
ER  -

TY  - JOUR
AU  - Lopes-Santos, L.
AU  - Castro, D.B.
AU  - Ottoboni, L.M.
AU  - Park, D.
AU  - Weir, B.S.
AU  - Destefano, S.A.
TI  - Draft Genome Sequence of Burkholderia andropogonis Type Strain ICMP2807, Isolated from Sorghum bicolor.
JO  - Genome Announcements
PY  - 2015
SP  - e00455
EP  - e00415
VL  - 3
AB  - Here, we report the draft genome sequence of Burkholderia andropogonis ICMP2807,  a
AB  - phytopathogenic bacterium isolated from Sorghum bicolor plants in the United
AB  - States.
ER  -

TY  - JOUR
AU  - Lopez, G.
AU  - Diaz-Cardenas, C.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - David, A.J.
AU  - Gonzalez, L.N.
AU  - Restrepo, S.
AU  - Baena, S.
TI  - Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 78
EP  - 78
VL  - 12
AB  - Here we present the physiological features of Pseudomonas extremaustralis strain  USBA-GBX-515
AB  - (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000
AB  - m.a.s.l, in the northern Andes of South America, as well as the thorough analysis
AB  - of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium
AB  - of 1.0-3.0 mum x 0.5-1 mum, motile and unable to form spores, it grows
AB  - aerobically and cells show one single flagellum. Several genetic indices, the
AB  - phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic
AB  - characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus
AB  - and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis
AB  - strain CT14-3(T). The draft genome of P. extremaustralis strain USBA-GBX-515
AB  - consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665
AB  - genes were predicted and of those, 5544 were protein coding genes and 121 were
AB  - RNA genes. The distribution of genes into COG functional categories showed that
AB  - most genes were classified in the category of amino acid transport and metabolism
AB  - (10.5%) followed by transcription (8.4%) and signal transduction mechanisms
AB  - (7.3%). We performed experimental analyses of the lipolytic activity and results
AB  - showed activity mainly on short chain fatty acids. The genome analysis
AB  - demonstrated the existence of two genes, lip515A and est515A, related to a
AB  - triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes
AB  - were also observed, mainly nitrate reductase genes. Genes related with synthesis
AB  - of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were
AB  - detected. The phaABC and phbABC operons also appeared complete in the genome. P.
AB  - extremaustralis strain USBA-GBX-515 conserves the same gene organization of the
AB  - type strain CT14-3(T). We also thoroughly analyzed the potential for production
AB  - of secondary metabolites finding close to 400 genes in 32 biosynthetic gene
AB  - clusters involved in their production.
ER  -

TY  - JOUR
AU  - Lopez, L.L.
AU  - Rusconi, B.
AU  - Gildersleeve, H.
AU  - Qi, C.
AU  - McLaughlin, M.
AU  - Scheetz, M.H.
AU  - Seshu, J.
AU  - Eppinger, M.
TI  - Genome Sequences of Five Clinical Isolates of Klebsiella pneumoniae.
JO  - Genome Announcements
PY  - 2016
SP  - e00040
EP  - e00016
VL  - 4
AB  - Klebsiella pneumoniae is a nosocomial pathogen of emerging importance and displays resistance
AB  - to broad-spectrum antibiotics, such as carbapenems. Here, we
AB  - report the genome sequences of five clinical K. pneumoniae isolates, four of
AB  - which are carbapenem resistant. Carbapenem resistance is conferred by hydrolyzing
AB  - class A beta-lactamases found adjacent to transposases.
ER  -

TY  - JOUR
AU  - Lopez, M.
AU  - Alvarez-Fraga, L.
AU  - Gato, E.
AU  - Blasco, L.
AU  - Poza, M.
AU  - Fernandez-Garcia, L.
AU  - Bou, G.
AU  - Tomas, M.
TI  - Genome Sequence of a Clinical Strain of Acinetobacter baumannii Belonging to the  ST79/PFGE-HUI-1 Clone Lacking the AdeABC (Resistance-Nodulation-Cell  Division-Type) Efflux Pump.
JO  - Genome Announcements
PY  - 2016
SP  - e00962
EP  - e00916
VL  - 4
AB  - Increased expression of chromosomal genes for resistance-nodulation-cell division-type efflux
AB  - systems plays a major role in the multidrug resistance of
AB  - Acinetobacter baumannii Little is known about the genetic characteristics of
AB  - clinical strains of Acinetobacter baumannii lacking the AdeABC pump. In this
AB  - study, we sequenced the genome of clinical strain Ab421 GEIH-2010 (belonging to
AB  - clone ST79/PFGE-HUI-1 from the GEIH-REIPI Ab. 2010 project) which lacks this
AB  - efflux pump.
ER  -

TY  - JOUR
AU  - Lopez, M.
AU  - Rueda, A.
AU  - Florido, J.P.
AU  - Blasco, L.
AU  - Gato, E.
AU  - Fernandez-Garcia, L.
AU  - Martinez-Martinez, L.
AU  - Fernandez-Cuenca, F.
AU  - Pachon, J.
AU  - Cisneros, J.M.
AU  - Garnacho-Montero, J.
AU  - Vila, J.
AU  - Rodriguez-Bano, J.
AU  - Pascual, A.
AU  - Bou, G.
AU  - Tomas, M.
TI  - Genomic Evolution of Two Acinetobacter baumannii Clinical Strains from ST-2 Clones Isolated in 2000 and 2010 (ST-2_clon_2000 and ST-2_clon_2010).
JO  - Genome Announcements
PY  - 2016
SP  - e01182
EP  - e01116
VL  - 4
AB  - Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in
AB  - hospital environments by acquiring mobile elements such as
AB  - transposons, plasmids, and phages. In this study, we compared two genomes of A.
AB  - baumannii clinical strains isolated in 2000 (ST-2_clon_2000) and 2010
AB  - (ST-2_clon_2010) from GenBank project PRJNA308422.
ER  -

TY  - JOUR
AU  - Lopez, O.J.
AU  - Quintanar, A.
AU  - Padhye, N.V.
AU  - Nelson, M.
TI  - Genotyping of DNA using sequence-specific methyltransferases followed by immunochemical detection.
JO  - J. Immunoassay Immunochem.
PY  - 2003
SP  - 11
EP  - 28
VL  - 24
AB  - Modern molecular genetics relies on the ability to map the positions of genes on chromosomes,
AB  - relative to known DNA markers. The first such DNA
AB  - markers described were Restriction Fragment Length Polymorphisms, but any
AB  - restriction endonuclease used for RFLP mapping is just one member of a
AB  - restriction-modification pair. For each restriction endonuclease, there is
AB  - a companion methyltransferase (MTase) that has the same DNA sequence
AB  - specificity. Therefore, in principle, it should be possible to use MTases
AB  - rather than restriction enzymes to detect polymorphic sites in DNA. We
AB  - have used sequence-specific DNA MTases to detect polym orphisms in closely
AB  - related viral pathogens. If at least one MTase recognition site is present
AB  - in PCR-amplified DNA, then methyl groups are incorporated; if no MTase
AB  - site is present, then methyl groups are not incorporated. When several
AB  - different sequence-specific DNA MTase reactions are carried out, the
AB  - pattern of methyl incorporation defines a DNA MTase genotype. DNA MTase
AB  - Genotyping (DMG) can be used to rapidly diagnose heritable or infectious
AB  - diseases, to immunochemically detect DNA at defined 2 to 8 base pair
AB  - sites, or to characterize the amplicons by constructing ordered maps.
ER  -

TY  - JOUR
AU  - Lopez-Alonso, V.
AU  - Ortiz, S.
AU  - Martinez-Suarez, J.V.
TI  - Genome Sequences of Five Disinfectant-Resistant Listeria monocytogenes Strains from Two Iberian Pork-Processing Plants.
JO  - Genome Announcements
PY  - 2015
SP  - e00077
EP  - e00015
VL  - 3
AB  - We announce the draft genome sequences of five Listeria monocytogenes strains from two Iberian
AB  - pork-processing plants located in Spain that were distinguished
AB  - by their resistance to benzalkonium chloride. These strains seem highly adapted
AB  - to the meat-processing environment according to their persistence and
AB  - transmission capabilities.
ER  -

TY  - JOUR
AU  - Lopez-Garrido, J.
AU  - Casadesus, J.
TI  - Regulation of Salmonella enterica Pathogenicity Island 1 by DNA Adenine Methylation.
JO  - Genetics
PY  - 2010
SP  - 637
EP  - 649
VL  - 184
AB  - DNA adenine methylase (Dam ) mutants of Salmonella enterica are attenuated in the mouse model
AB  - and present multiple virulence-related
AB  - defects. Impaired interaction of Salmonella Dam mutants with the
AB  - intestinal epithelium has been tentatively correlated with reduced
AB  - secretion of pathogenicity island 1 (SPI-1) effectors. In this study,
AB  - we show that S. enterica Dam mutants contain lowered levels of the
AB  - SPI-1 transcriptional regulators HilA, HilC, HilD, and InvF. Epistasis
AB  - analysis indicates that Dam-dependent regulation of SPI-1 requires
AB  - HilD, while HilA, HilC, and InvF are dispensable. A transcriptional
AB  - hilD::lac fusion is expressed at similar levels in Dam(+) and Dam
AB  - hosts. However, lower levels of hilD mRNA are found in a Dam
AB  - background, thus providing unsuspected evidence that Dam methylation
AB  - might exert post-transcriptional regulation of hilD expression. This
AB  - hypothesis is supported by the following lines of evidence: (i) lowered
AB  - levels of hilD mRNA are found in Salmonella Dam mutants when hilD is
AB  - transcribed from a heterologous promoter; (ii) increased hilD mRNA
AB  - turnover is observed in Dam mutants; (iii) lack of the Hfq RNA
AB  - chaperone enhances hilD mRNA instability in Dam mutants; and (iv) lack
AB  - of the RNA degradosome components polynucleotide phosphorylase and
AB  - ribonuclease E suppresses hilD mRNA instability in a Dam background.
AB  - Our report of Dam-dependent control of hilD mRNA stability suggests
AB  - that DNA adenine methylation plays hitherto unknown roles in
AB  - post-transcriptional control of gene expression.
ER  -

TY  - JOUR
AU  - Lopez-Hermoso, C.
AU  - de la Haba, R.R.
AU  - Sanchez-Porro, C.
AU  - Bayliss, S.C.
AU  - Feil, E.J.
AU  - Ventosa, A.
TI  - Draft Genome Sequences of Salinivibrio proteolyticus, Salinivibrio sharmensis, Salinivibrio siamensis, Salinivibrio costicola subsp. alcaliphilus, Salinivibrio costicola subsp. vallismortis, and 29 New Isolates Belonging to the Genus Salinivibrio.
JO  - Genome Announcements
PY  - 2017
SP  - e00244
EP  - e00217
VL  - 5
AB  - The draft genome sequences of 5 type strains of species of the halophilic genus Salinivibrio
AB  - and 29 new isolates from different hypersaline habitats belonging to
AB  - the genus Salinivibrio have been determined. The genomes have 3,123,148 to
AB  - 3,641,359 bp, a G+C content of 49.2 to 50.9%, and 2,898 to 3,404 open reading
AB  - frames (ORFs).
ER  -

TY  - JOUR
AU  - Lopez-Lopez, A.
AU  - Richter, M.
AU  - Pena, A.
AU  - Tamames, J.
AU  - Rossello-Mora, R.
TI  - New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach.
JO  - Syst. Appl. Microbiol.
PY  - 2013
SP  - 205
EP  - 214
VL  - 36
AB  - A metagenomic approach was carried out in order to study the genetic pool of a
AB  - hypersaline microbial mat, paying more attention to the archaeal community and,
AB  - specifically, to the putatively methanogenic members. The main aim of the work
AB  - was to expand the knowledge of a likely ecologically important archaeal lineage,
AB  - candidate division MSBL1, which is probably involved in methanogenesis at very
AB  - high salinities. The results obtained in this study were in accordance with our
AB  - previous report on the bacterial diversity encountered by using a number of
AB  - molecular techniques, but remarkable differences were found in the archaeal
AB  - diversity retrieval by each of the procedures used (metagenomics and 16S
AB  - rRNA-based methods). The lack of synteny for most of the metagenomic fragments
AB  - with known genomes, together with the low degree of similarity of the annotated
AB  - open reading frames (ORFs) with the sequences in the databases, reflected the
AB  - high degree of novelty in the mat community studied. Linking the sequenced clones
AB  - with representatives of division MSBL1 was not possible because of the lack of
AB  - additional information concerning this archaeal group in the public gene
AB  - repositories. However, given the high abundance of representatives of this
AB  - division in the 16S rRNA clone libraries and the low identity of the archaeal
AB  - clones with known genomes, it was hypothesized that some of them could arise from
AB  - MSBL1 genomes. In addition, other prokaryotic groups known to be relevant in
AB  - organic matter mineralization at high salinities were detected.
ER  -

TY  - JOUR
AU  - Lopez-Perez, M.
AU  - Gonzaga, A.
AU  - Rodriguez-Valera, F.
TI  - Genomic Diversity of 'Deep Ecotype' Alteromonas macleodii Isolates: Evidence for Pan-Mediterranean Clonal Frames.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 1220
EP  - 1232
VL  - 5
AB  - We have compared genomes of Alteromonas macleodii "deep ecotype" isolates from
AB  - two deep Mediterranean sites and two surface samples from the Aegean and the
AB  - English Channel. A total of nine different genomes were analyzed. They belong to
AB  - five clonal frames (CFs) that differ among them by approximately 30,000
AB  - single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs
AB  - contain three strains each with nearly identical genomes ( approximately 100 SNPs
AB  - over the core genome). One of the CFs had representatives that were isolated from
AB  - samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These
AB  - data mark the longest proven persistence of a CF in nature (outside of clinical
AB  - settings). We have found evidence for frequent recombination events between or
AB  - within CFs and even with the distantly related A. macleodii surface ecotype. The
AB  - different CFs had different flexible genomic islands. They can be classified into
AB  - two groups; one type is additive, that is, containing different numbers of gene
AB  - cassettes, and is very variable in short time periods (they often varied even
AB  - within a single CF). The other type was more stable and produced the complete
AB  - replacement of a genomic fragment by another with different genes. Although this
AB  - type was more conserved within each CF, we found examples of recombination among
AB  - distantly related CFs including English Channel and Mediterranean isolates.
ER  -

TY  - JOUR
AU  - Lopez-Perez, M.
AU  - Rodriguez-Valera, F.
AU  - Webb, H.K.
AU  - Crawford, R.J.
AU  - Ivanova, E.P.
TI  - Genome Sequence of 'Thalassospira australica' NP3b2T Isolated from St. Kilda Beach, Tasman Sea.
JO  - Genome Announcements
PY  - 2014
SP  - e01139
EP  - e01114
VL  - 2
AB  - Here, we present the draft genome of 'Thalassospira australica' NP3b2(T), a potential
AB  - poly(ethylene terephthalate) (PET) plastic biodegrader. This genomic
AB  - information will enhance information on the genetic basis of metabolic pathways
AB  - for the degradation of PET plastic.
ER  -

TY  - JOUR
AU  - Lorenz, S.C.
AU  - Kotewicz, M.L.
AU  - Hoffmann, M.
AU  - Gonzalez-Escalona, N.
AU  - Fischer, M.
AU  - Kase, J.A.
TI  - Complete Genome Sequences of Four Enterohemolysin-Positive (ehxA) Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e00846
EP  - e00816
VL  - 4
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are important foodborne pathogens
AB  - associated with human disease. Most disease-associated STEC strains
AB  - carry the locus of enterocyte effacement (LEE); however, regularly LEE-negative
AB  - STEC strains are recovered from ill patients. Few reference sequences are
AB  - available for these isolate types. Here, we report here the complete genome
AB  - sequences for four LEE-negative STEC strains.
ER  -

TY  - JOUR
AU  - Lorenzi, A.S.
AU  - Silva, G.G.
AU  - Lopes, F.A.
AU  - Chia, M.A.
AU  - Edwards, R.A.
AU  - Bittencourt-Oliveira, M.C.
TI  - Draft Genome Sequence of Cylindrospermopsis raciborskii (Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin  and Cylindrospermopsin Synthetase Genes.
JO  - Genome Announcements
PY  - 2016
SP  - e00228
EP  - e00216
VL  - 4
AB  - Cylindrospermopsis raciborskii ITEP-A1 is a saxitoxin-producing cyanobacterium. We report the
AB  - draft genome sequence of ITEP-A1, which comprised 195 contigs that
AB  - were assembled with SPAdes and annotated with Rapid Annotation using Subsystem
AB  - Technology. The identified genome sequence had 3,605,836 bp, 40.1% G+C, and
AB  - predicted 3,553 coding sequences (including the synthetase genes).
ER  -

TY  - JOUR
AU  - Lorincz, M.C.
AU  - Groudine, M.
TI  - CmC(a/t)GG methylation: a new epigenetic mark in mammalian DNA?
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 10034
EP  - 10036
VL  - 98
AB  - Twenty-five years ago, based on the knowledge of cytosine methylation in higher organisms and
AB  - the newly discovered bacterial adenine methyltransferase, Riggs and Holliday and Pugh
AB  - independently proposed that the covalent modification of DNA by methylation might serve as a
AB  - means to propagate heritable expression states in eukaryotes.  In the years since, the
AB  - association between cytosine methylation and transcriptional silencing in mammalian cells has
AB  - become well established, and a number of proteins that catalyze the transfer of a methyl group
AB  - to the 5-carbon of the cytosine pyrimidine ring have been cloned and characterized.  These DNA
AB  - methyltransferases (m5C-MTases) are encoded by a diverse family of genes found in prokaryotes
AB  - as well as all four groups of eukaryotes.
ER  -

TY  - JOUR
AU  - Lorincz, M.C.
AU  - Schubeler, D.
AU  - Hutchinson, S.R.
AU  - Dickerson, D.R.
AU  - Groudine, M.
TI  - DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation.
JO  - Mol. Cell. Biol.
PY  - 2002
SP  - 7572
EP  - 7580
VL  - 22
AB  - DNA methylation plays an important role in transcriptional repression. To gain insight into
AB  - the dynamics of demethylation and de novo methylation, we introduced a proviral reporter,
AB  - premethylated at different densities, into a defined chromosomal site in murine
AB  - erythroleukemia cells and monitored the stability of the introduced methylation and reporter
AB  - gene expression. A high density of methylation was faithfully propagated in vivo. In contrast,
AB  - a low level of methylation was not stable, with complete demethylation and associated
AB  - transcriptional activation or maintenance-coupled de novo methylation and associated silencing
AB  - occurring with equal probability. Deletion of the proviral enhancer increased the probability
AB  - of maintenance-coupled de novo methylation, suggesting that this enhancer functions in part to
AB  - antagonize such methylation. The DNA methyltransferases (MTases) Dnmt3a and Dnmt3b are thought
AB  - to be the sole de novo MTases in the mammalian genome. To determine whether these enzymes are
AB  - responsible for maintenance-coupled de novo methylation, the unmethylated or premethylated
AB  - proviral reporter was introduced into DNA MTase-deficient embryonic stem cells. These studies
AB  - revealed the presence of a Dnmt3a/Dnmt3b-independent de novo methyltransferase activity that
AB  - is stimulated by the presence of preexisting methylation.
ER  -

TY  - JOUR
AU  - Loscar, M.E.
AU  - Huptas, C.
AU  - Wenning, M.
AU  - Sieber, V.
AU  - Schmid, J.
TI  - Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86.
JO  - Genome Announcements
PY  - 2016
SP  - e01317
EP  - e01316
VL  - 4
AB  - Lysinibacillus xylanilyticus belongs to the family Bacillaceae and was first described in 2010
AB  - with the type strain L. xylanilyticus XDB9. It is able to both
AB  - degrade xylan and use it as the sole carbon source. Here, we describe the 4.8-Mb
AB  - genome of the strain L. xylanilyticus SR-86, which was isolated from organic
AB  - waste.
ER  -

TY  - JOUR
AU  - Lou, S.
AU  - Wu, L.
TI  - Isolation of thermostable restriction endonuclease from thermophilic Synechococcus elongatus T3.
JO  - J. Xiamen Univ.
PY  - 1997
SP  - 272
EP  - 275
VL  - 36
AB  - A restriction endonuclease was isolated from thermophilic cyanobacterium Synechococcus
AB  - elongatus T3, which was named SelI.  This restriction endonuclease was characterized as an
AB  - isoschizomer of Sau96I, its recognition sequences is GGNCC.  Bu the reaction conditions of
AB  - SelI are different from that of Sau96I.  SalI is a thermostable restriction endonuclease with
AB  - optimal reaction temperature 50-70oC.
ER  -

TY  - JOUR
AU  - Loucif, L.
AU  - Michelle, C.
AU  - Terras, J.
AU  - Rolain, J.M.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Streptomyces specialis Type Strain GW41-1564 (DSM 41924).
JO  - Genome Announcements
PY  - 2017
SP  - e00101
EP  - e00117
VL  - 5
AB  - Here, we report the draft genome sequence of Streptomyces specialis type strain GW41-1564,
AB  - which was isolated from soil. This 5.87-Mb genome exhibits a high G+C
AB  - content of 72.72% and contains 5,486 protein-coding genes.
ER  -

TY  - JOUR
AU  - Louie, T.S.
AU  - Giovannelli, D.
AU  - Yee, N.
AU  - Narasingarao, P.
AU  - Starovoytov, V.
AU  - Goker, M.
AU  - Klenk, H.P.
AU  - Lang, E.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Bini, E.
AU  - Haggblom, M.M.
TI  - High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 66
EP  - 66
VL  - 11
AB  - Sedimenticola selenatireducens strain AK4OH1T (= DSM 17993T = ATCC BAA-1233T) is  a
AB  - microaerophilic bacterium isolated from sediment from the Arthur Kill
AB  - intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens
AB  - is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1T was the
AB  - first representative of its genus to be isolated for its unique coupling of the
AB  - oxidation of aromatic acids to the respiration of selenate. It is a versatile
AB  - heterotroph and can use a variety of carbon compounds, but can also grow
AB  - lithoautotrophically under hypoxic and anaerobic conditions. The draft genome
AB  - comprises 4,588,530 bp and 4276 predicted protein-coding genes including genes
AB  - for the anaerobic degradation of 4-hydroxybenzoate and benzoate. Here we report
AB  - the main features of the genome of S. selenatireducens strain AK4OH1T.
ER  -

TY  - JOUR
AU  - Loureiro, D.
AU  - Portela, R.W.
AU  - Sousa, T.J.
AU  - Rocha, F.
AU  - Pereira, F.L.
AU  - Dorella, F.A.
AU  - Carvalho, A.F.
AU  - Menezes, N.
AU  - Macedo, E.S.
AU  - Moura-Costa, L.F.
AU  - Meyer, R.
AU  - Leal, C.A.
AU  - Figueiredo, H.C.
AU  - Azevedo, V.
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Viscerotropic Strain N1.
JO  - Genome Announcements
PY  - 2016
SP  - e01673
EP  - e01615
VL  - 4
AB  - We present the complete genome sequence of Corynebacterium pseudotuberculosis strain N1. The
AB  - sequencing was performed with the Ion Torrent Personal Genome
AB  - Machine system. The genome is a circular chromosome with 2,337,845 bp, a G+C
AB  - content of 52.85%, and a total of 2,045 coding sequences, 12 rRNAs, 49 tRNAs, and
AB  - 58 pseudogenes.
ER  -

TY  - JOUR
AU  - Loux, V.
AU  - Coeuret, G.
AU  - Zagorec, M.
AU  - Champomier, V.M.C.
AU  - Chaillou, S.
TI  - Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected  from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes.
JO  - Genome Announcements
PY  - 2018
SP  - e00082
EP  - e00018
VL  - 6
AB  - We present here the complete and draft genome sequences of nine Lactobacillus sakei strains,
AB  - selected from the entire range of clonal complexes from the three
AB  - known lineages of the species. The strains were chosen to provide a wide view of
AB  - pangenomic and plasmidic diversity for this important foodborne species.
ER  -

TY  - JOUR
AU  - Loux, V.
AU  - Mariadassou, M.
AU  - Almeida, S.
AU  - Chiapello, H.
AU  - Hammani, A.
AU  - Buratti, J.
AU  - Gendrault, A.
AU  - Barbe, V.
AU  - Aury, J.M.
AU  - Deutsch, S.M.
AU  - Parayre, S.
AU  - Madec, M.N.
AU  - Chuat, V.
AU  - Jan, G.
AU  - Peterlongo, P.
AU  - Azevedo, V.
AU  - Le Loir, Y.
AU  - Falentin, H.
TI  - Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii.
JO  - BMC Genomics
PY  - 2015
SP  - 296
EP  - 296
VL  - 16
AB  - BACKGROUND: Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese
AB  - technology and for its probiotic properties. PF is also extremely
AB  - adaptable to several ecological niches and can grow on a variety of carbon and
AB  - nitrogen sources. The aim of this work was to discover the genetic basis for
AB  - strain-dependent traits related to its ability to use specific carbon sources.
AB  - High-throughput sequencing technologies were ideal for this purpose as they have
AB  - the potential to decipher genomic diversity at a moderate cost. RESULTS: 21
AB  - strains of PF were sequenced and the genomes were assembled de novo. Scaffolds
AB  - were ordered by comparison with the complete reference genome CIRM-BIA1, obtained
AB  - previously using traditional Sanger sequencing. Automatic functional annotation
AB  - and manual curation were performed. Each gene was attributed to either the core
AB  - genome or an accessory genome. The ability of the 21 strains to degrade 50
AB  - different sugars was evaluated. Thirty-three sugars were degraded by none of the
AB  - sequenced strains whereas eight sugars were degraded by all of them. The
AB  - corresponding genes were present in the core genome. Lactose, melibiose and
AB  - xylitol were only used by some strains. In this case, the presence/absence of
AB  - genes responsible for carbon uptake and degradation correlated well with the
AB  - phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence
AB  - of these genes was in line the metabolic pathways described previously in other
AB  - species. We also considered the genetic origin (transduction, rearrangement) of
AB  - the corresponding genomic islands. Ribose and gluconate were degraded to a
AB  - greater or lesser extent (quantitative phenotype) by some strains. For these
AB  - sugars, the phenotypes could not be explained by the presence/absence of a gene
AB  - but correlated with the premature appearance of a stop codon interrupting protein
AB  - synthesis and preventing the catabolism of corresponding carbon sources.
AB  - CONCLUSION: These results illustrate (i) the power of correlation studies to
AB  - discover the genetic basis of binary strain-dependent traits, and (ii) the
AB  - plasticity of PF chromosomes, probably resulting from horizontal transfers,
AB  - duplications, transpositions and an accumulation of mutations. Knowledge of the
AB  - genetic basis of nitrogen and sugar degradation opens up new strategies for the
AB  - screening of PF strain collections to enable optimum cheese starter, probiotic
AB  - and white biotechnology applications.
ER  -

TY  - JOUR
AU  - Lovett, S.
AU  - Chase, K.
AU  - Koroleva, G.
AU  - Palacios, G.
AU  - Rozak, D.
AU  - Ladner, J.T.
TI  - Complete Genome Sequence of Pigmentation-Negative Yersinia pestis Strain Cadman.
JO  - Genome Announcements
PY  - 2016
SP  - e01207
EP  - e01216
VL  - 4
AB  - Here, we report the genome sequence of Yersinia pestis strain Cadman, an attenuated strain
AB  - lacking the pgm locus. Y. pestis is the causative agent of
AB  - plague and generally must be worked with under biosafety level 3 (BSL-3)
AB  - conditions. However, strains lacking the pgm locus are considered safe to work
AB  - with under BSL-2 conditions.
ER  -

TY  - JOUR
AU  - Low, D.A.
AU  - Casadesus, J.
TI  - Clocks and switches: bacterial gene regulation by DNA adenine methylation.
JO  - Curr. Opin. Microbiol.
PY  - 2008
SP  - 106
EP  - 112
VL  - 11
AB  - N(6) methylation in adenosine moieties causes changes in DNA structure and can modulate
AB  - DNA-protein interactions. In both alpha-Proteobacteria and gamma-Proteobacteria,
AB  - postreplicative formation of N(6)-methyl-adenine regulates transcription of specific genes and
AB  - provides two general types of controls: (i) clock-like controls that permit transient gene
AB  - transcription during a specific stage of DNA replication; (ii) switch-like controls in which
AB  - transcription is regulated by a DNA methylation pattern. DNA adenine methylation may also
AB  - regulate gene expression by affecting nucleoid topology. Recent transcriptomic studies have
AB  - unveiled novel cases of genes regulated by DNA adenine methylation, including virulence genes
AB  - of bacterial pathogens.
ER  -

TY  - JOUR
AU  - Low, D.A.
AU  - Weyand, N.J.
AU  - Mahan, M.J.
TI  - Roles of DNA adenine methylation in regulating bacterial gene expression and virulence.
JO  - Infect. Immun.
PY  - 2001
SP  - 7197
EP  - 7204
VL  - 69
AB  - DNA methylation provides a mechanism by which additional information is imparted to DNA, and
AB  - such epigenetic information can alter the timing and targeting of cellular events.  DNA
AB  - methylation occurs throughout the living world, including bacteria, plants, and mammals. Until
AB  - recently, methylated DNA sequences were not detected in the fruit fly, in brewer's yeast, or
AB  - in the nematode.  However, analysis by Lyko and colleagues showed that Drosophila melanogaster
AB  - does contain methylated DNA, and thus it is possible that yeast and worms may also have it.
AB  - In this review, we focus our attention on the roles of DNA methylation in regulating bacterial
AB  - gene expression and virulence.  Although some background information about DNA methylation is
AB  - presented, we refer the reader to excellent reviews on the subject.  DNA methylation occurs at
AB  - the C-5 or N-4 positions of cytosine and at the N-6 position of adenine and is catalyzed by
AB  - enzymes known as DNA methyltransferases (Mtases).  All MTases use S-adenosyl methionine as a
AB  - methyl donor.  DNA methylation has historically been associated with DNA
AB  - restriction-modification systems thought to be important in protecting cells from foreign DNAs
AB  - such as transposons and viral DNAs.  Restriction-modification systems contain a DNA methylase
AB  - that protects host DNA sequences from restriction with their cognate restriction enzymes,
AB  - which digest unmodified foreign DNAs.  Certain MTases, including DNA cytosine MTase (Dcm),
AB  - which methylates the C-5 position of cytosine in CC(A/T)GG sequences, DNA adenine methylase
AB  - (Dam), which methylates N-6 of adenine in GATC sequences, and cell cycle-regulated methylase
AB  - (CcrM), which methylates the N-6 adenine of GAnTC, do not have cognate restriction enzymes
AB  - associated with them.  These methylases participate in cellular regulatory events, including
AB  - those that control bacterial virulence, which are the primary focus of this review.
ER  -

TY  - JOUR
AU  - Loy, J.D.
AU  - Dickey, A.M.
AU  - Clawson, M.L.
TI  - Complete Genome Sequence of Moraxella bovis Strain Epp-63 (300), an Etiologic Agent of Infectious Bovine Keratoconjunctivitis.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01004
EP  - e01018
VL  - 7
AB  - We report here the complete closed genome sequence of Moraxella bovis strain Epp-63 (300)
AB  - (Epp63). This strain was isolated from an infectious bovine
AB  - keratoconjunctivitis (IBK) case in 1963. Since then, Epp63 has been used
AB  - extensively for IBK research. Consequently, the genome sequence of Epp63 should
AB  - help elucidate IBK host-pathogen interactions.
ER  -

TY  - JOUR
AU  - Loyola, C.
AU  - Saavedra, C.
AU  - Gomez, I.
AU  - Vasquez, C.
TI  - The amino acidic substitution of cysteine 167 by serine (C167S) in BstVI restriction endonuclease of Bacillus stearothermophilus V affects its conformation and thermostability.
JO  - Biochimie
PY  - 1999
SP  - 261
EP  - 266
VL  - 81
AB  - The restriction endonuclease BstVI from Bacillus stearothermophilus V contains three cysteine
AB  - residues at positions 134, 167 and 180. Titration of Cys residues with DTNB showed that none
AB  - of them are involved in disulphide bond formation. Cysteine triplets 134 and 167 were modified
AB  - by recombinant PCR to introduce a serine residue in each case. The mutated genes were cloned
AB  - into pGEM-T vector and transformed into E. coli JM109. Even though pGEM-T is not designed for
AB  - expression, the mutant proteins were efficiently expressed in E. coli. The endonuclease
AB  - carrying the mutation C134S was purified to homogeneity but appeared to be very unstable. In
AB  - contrast, the C167S mutant enzyme was stable when pure and was studied biochemically. This
AB  - mutant enzyme was as stable and resistant to protein-denaturing agents as the wild type
AB  - enzyme. The activity of both enzymes was not affected by preincubations of 2 h at 80 degrees
AB  - C. A short preincubation at 95 degrees C caused a complete inactivation of the mutant enzyme
AB  - while the wild type endonuclease retained 30% of its activity. Moreover, the C167S BstVI was
AB  - more susceptible to be hydrolyzed by proteinase K and trypsin compared to the wild type
AB  - endonuclease. These results show that the substitution Cys --> Ser at position 167 affects the
AB  - configuration and thermostability of BstVI restriction endonuclease.
ER  -

TY  - JOUR
AU  - Lozano, G.L.
AU  - Bravo, J.I.
AU  - Handelsman, J.
TI  - Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus 'Hitchhiker' from the Soybean Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e00570
EP  - e00517
VL  - 5
AB  - Pseudomonas koreensis CI12 was coisolated with Bacillus cereus from a root of a soybean plant
AB  - grown in a field in Arlington, WI. Here, we report the draft genome
AB  - sequence of P. koreensis CI12 obtained by Illumina sequencing.
ER  -

TY  - JOUR
AU  - Lozano, G.L.
AU  - Holt, J.
AU  - Ravel, J.
AU  - Rasko, D.A.
AU  - Thomas, M.G.
AU  - Handelsman, J.
TI  - Draft Genome Sequence of Biocontrol Agent Bacillus cereus UW85.
JO  - Genome Announcements
PY  - 2016
SP  - e00910
EP  - e00916
VL  - 4
AB  - Bacillus cereus UW85 was isolated from a root of a field-grown alfalfa plant from Arlington,
AB  - WI, and identified for its ability to suppress damping off, a disease
AB  - caused by Phytophthora megasperma f. sp. medicaginis on alfalfa. Here, we report
AB  - the draft genome sequence of B. cereus UW85, obtained by a combination of Sanger
AB  - and Illumina sequencing.
ER  -

TY  - JOUR
AU  - Lu, A.-L.
AU  - Jack, W.E.
AU  - Modrich, P.
TI  - DNA determinants important in sequence recognition by EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 13200
EP  - 13206
VL  - 256
AB  - Alkylation interference and protection methods (Siebenlist, U., and Gilbert,
AB  - W., (1980) Proc. Natl. Acad. Sci. USA 77, 122-126) have been utilized to deduce
AB  - potential DNA contracts involved in specific complex formation between EcoRI
AB  - endonuclease and its recognition sequence.  The endonuclease protected the N7
AB  - position (major groove) of the dG and the N3 position (minor groove) of both dA
AB  - residues within the EcoRI sequence against alkylation by dimethylsulfate,
AB  - d(7Gp7Ap7ApTpTpC), suggesting the presence of polypeptide in both grooves in
AB  - the vicinity of affected nitrogens.  Results of methylation interference
AB  - analysis suggest that the N7 of the EcoRI site dG and the N3 of the central dA,
AB  - d(7GpAp7ApTpTpC), are utilized as contacts by the enzyme.  The failure to
AB  - observe interference upon methylation of the 5'-penultimate dA within the
AB  - sequence implies that the endonuclease does not bond to the N3 of this residue,
AB  - despite the fact that it is protected against alkylation by the protein.
AB  - Ethylation interference patterns suggest four major phosphate contacts between
AB  - endonuclease and each DNA strand.  Two of these phosphates are 5'-external to
AB  - the EcoRI sequence, d(7pN7pG7pApA7pTpTpC), suggesting involvement of outside
AB  - phosphates in electrostatic interactions.  Moreover, alkylation protection and
AB  - interference effects on the two DNA strands display perfect 2-fold symmetry.
AB  - Thus, the endonuclease interacts with a minimum of 10 nucleotide pairs to yield
AB  - a DNA-protein complex characterized by elements of symmetry.  In contrast,
AB  - specific alkylation effects were not observed in comparable experiments with
AB  - the endonuclease and a DNA which had been previously methylated by the EcoRI
AB  - modification enzyme.
ER  -

TY  - JOUR
AU  - Lu, A.L.
AU  - Cheng, S.C.
AU  - Jack, W.E.
AU  - Modrich, P.
TI  - DNA contacts and mechanism of specific site location of EcoRI endonuclease, and effects of modification methylation on DNA helix conformation.
JO  - Fed. Proc.
PY  - 1982
SP  - 1199
EP  - 1199
VL  - 41
AB  - Alkylation interference and protection methods have been utilized to deduce
AB  - potential DNA contacts involved in specific complex formation between EcoRI
AB  - endonuclease and its recognition sequence.  The endonuclease interacts
AB  - symmetrically with a minimum of 10 nucleotide pairs, including nitrogens in
AB  - both major and minor grooves and phosphate groups along the DNA backbone.
AB  - Dissociation and association rates for site-specific EcoRI endonuclease-DNA
AB  - complexes increase with increasing DNA chain length up to a plateau.  Since
AB  - intrinsic EcoRI site Keq are identical for the different length DNA fragments,
AB  - outside DNA sequences must form the basis for observed kinetic differences.
AB  - Thus, outside DNA sequences lie on the major kinetic pathway by which EcoRI
AB  - endonuclease locates and leaves its recognition site.  Conformational changes
AB  - associated with DNA biological methylation was investigated (using the
AB  - electrophoresis band shift method).  The DNA helix was found to be unwound
AB  - about 0.5 degree for each methyl group introduced to the N6 position of
AB  - adenine.  No detectable effect (< 0.2 degree) was observed when methyl group
AB  - was introduced to DNA on C5 of cytosine.
ER  -

TY  - JOUR
AU  - Lu, C.
AU  - Marjanovic, O.
AU  - Morales, C.
AU  - Kiang, D.
TI  - Genome Sequences of Two Listeria monocytogenes Strains from Nectarines Associated with Listeriosis in 2014.
JO  - Genome Announcements
PY  - 2017
SP  - e00389
EP  - e00317
VL  - 5
AB  - Listeria monocytogenes is an important foodborne pathogen. Here, we present the annotated
AB  - whole genome of Listeria monocytogenes strains F14M01297-C2 and
AB  - F14M01297-C4, isolated from nectarines distributed by a packing facility in
AB  - California during an investigation of listeriosis associated with stone fruit in
AB  - 2014.
ER  -

TY  - JOUR
AU  - Lu, H.
AU  - Graham, D.
AU  - Xiao, S.D.
AU  - Gutierrez, O.
AU  - Yamaoka, Y.
TI  - Relationship between Helicobacter pylori restriction endonuclease-replacing gene, Hrga and clinical outcome.
JO  - Gastroenterology
PY  - 2003
SP  - A270
EP  - A270
VL  - 124
AB  - Background: Recently, polymorphisms in the hpyIII locus in Helicobacter pylori have been
AB  - identified and the presence of a new gene, hrgA, that had replaced hpyIIIR, was reported to be
AB  - related to gastric cancer in Asian strains.  However, this relation was data-derived and the
AB  - hypothesis has not yet been confirmed.  Aims: To confirm the relationship between hrgA allelic
AB  - type and clinical outcome in strains from both Asian and Western countries.  Methods: We
AB  - examined H. pylori strains from Asia (Korea, Hong Kong, Thailand, Taiwan, and Vietnam) and
AB  - Western countries (Columbia, Canada, France, and Italy).  hrgA and hpyIIIR status were
AB  - determined by polymerase chain reaction.  Results: There were 332 strains including as 172
AB  - Asian (49 cancer, 123 non-cancer) and 160 Western strains (50 gastric cancer, 90 non-cancer).
AB  - The prevalence of hrgA gene was significantly higher in Western strains 46.8% than Asian
AB  - strains (33.7%) irrespective of the clinical outcome (P = 0.01).  In Asian, the prevalence of
AB  - hrgA gene was 34.78% in strains from cancer and 33.3% from non-cancer.  In western countries,
AB  - the prevalence of hrgA gene was 50% in strains from cancer and 45% from non-cancer.
AB  - Discussion: We were unable to confirm the hypothesis that the hrgA gene was related to gastric
AB  - cancer.  We found no relationship between the prevalence of the hrgA gene and clinical outcome
AB  - in either Asian or Western countries.  The prevalence of hrgA gene was higher in Western
AB  - strains compared with Asian strains which are the opposite of other important putative
AB  - virulence factors such as cag pathogenicity island, vacA s1 genotype, babA2 genotypes and oipA
AB  - "on" types.
ER  -

TY  - JOUR
AU  - Lu, J.J.
AU  - Wang, J.F.
AU  - Hu, X.F.
TI  - Genome Sequence of Growth-Improving Paenibacillus mucilaginosus Strain KNP414.
JO  - Genome Announcements
PY  - 2013
SP  - e00881
EP  - e00813
VL  - 1
AB  - Paenibacillus mucilaginosus is a critical growth-improving silicate bacterium. Here, we report
AB  - the complete genome sequence of P. mucilaginosus strain KNP414.
AB  - This information will provide us with the opportunity to understand its molecular
AB  - mechanisms and develop more effective utilization of the strain.
ER  -

TY  - JOUR
AU  - Lu, L.
AU  - Patel, H.
AU  - Bissler, J.J.
TI  - Optimizing DpnI digestion conditions to detect replicated DNA.
JO  - Biotechniques
PY  - 2002
SP  - 316
EP  - 318
VL  - 33
AB  - In vitro replication systems are powerful tools for studying DNA replication and repair.
AB  - Replication competent cellular extracts can be used with reporter plasmids that contain the
AB  - simian virus 40 (SV40) DNA replication origin.  Replication is initiated by the addition of
AB  - the large T antigen.  By using plasmid DNA prepared in bacteria expressing adenosine methylase
AB  - as substrate, processive eukaryotic replication involving polymerase alpha, beta and epsilon
AB  - can be distinguished from gap-filling reactions mediated by other DNA polymerases such as
AB  - polymerase beta by the methylation status of the resulting DNA (Figure 1).  The bacterially
AB  - derived plasmid will contain methyladenosine at the DpnI restriction site, GATC, making the
AB  - plasmid susceptible to DpnI cleavage.  The complete absence of methylation profoundly
AB  - suppresses DNA cleavage by DpnI.  However, after a single round of semi-conservative
AB  - replication, the DNA is only hemimethylated.  The susceptibility of hemimethylated DNA has not
AB  - been well studied, though previous work suggests that replicated DNA also may be susceptible
AB  - to cleavage.  We demonstrate that under conditions of enzyme excess, long duration digestion,
AB  - or small DNA amounts, the hemimethylated DNA is susceptible to DpnI cleavage.  Other
AB  - investigators have identified that DpnI digestions can be difficult to interpret. For the
AB  - analysis of DNA replication, we optimized the digestion conditions so that only fully
AB  - methylated DNA would be digested, preserving hemimethylated DNA for analyses.
ER  -

TY  - JOUR
AU  - Lu, L.
AU  - Zhou, S.Y.
AU  - Chen, C.
AU  - Weng, S.P.
AU  - Chan, S.M.
AU  - He, J.G.
TI  - Complete genome sequence analysis of an iridovirus isolated from the orange-spotted grouper, Epinephelus coioides.
JO  - Virology
PY  - 2005
SP  - 81
EP  - 100
VL  - 339
AB  - Orange-spotted grouper iridovirus (OSGIV) was the causative agent of
AB  - serious systemic diseases with high mortality in the cultured
AB  - orange-spotted grouper, Epinephelus coioides. Here we report the complete
AB  - genome sequence of OSGIV. The OSGIV genome consists of 112,636 bp with a
AB  - G+C content of 54%. 121 putative open reading frames (ORF) were identified
AB  - with coding capacities for polypeptides varying from 40 to 1168 amino
AB  - acids. The majority of OSGIV shared homologies to other iridovirus genes.
AB  - Phylogenetic analysis of the major capsid protein, ATPase, cytosine DNA
AB  - methyl transferase and DNA polymerase indicated that OSGIV was closely
AB  - related to infectious spleen and kidney necrosis virus (ISKNV) and rock
AB  - bream iridovirus (RBIV), but differed from lymphocytisvirus and ranavirus.
AB  - The determination of the genome of OSGIV will facilitate a better
AB  - understanding of the molecular mechanism underlying the pathogenesis of
AB  - the OSGIV and may provide useful information to develop diagnosis method
AB  - and strategies to control outbreak of OSGIV.
ER  -

TY  - JOUR
AU  - Lu, M.G.
AU  - Jiang, J.
AU  - Liu, L.
AU  - Ma, A.P.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of Klebsiella variicola Strain HKUOPLA, a Cellulose-Degrading Bacterium Isolated from Giant Panda Feces.
JO  - Genome Announcements
PY  - 2015
SP  - e01200
EP  - e01215
VL  - 3
AB  - We report here the complete genome sequence of Klebsiella variicola strain HKUOPLA, isolated
AB  - from a giant panda feces sample collected from Ocean Park, Hong Kong. The complete genome of
AB  - this bacterium may contribute toward the discovery of efficient cellulose-degrading pathways.
ER  -

TY  - JOUR
AU  - Lu, M.G.
AU  - Jiang, J.
AU  - Liu, L.
AU  - Ma, A.P.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of Klebsiella pneumoniae Strain HKUOPLC, a Cellulose-Degrading Bacterium Isolated from Giant Panda Feces.
JO  - Genome Announcements
PY  - 2015
SP  - e01318
EP  - e01315
VL  - 3
AB  - We report here the complete genome sequence of Klebsiella pneumoniae strain HKUOPLC, isolated
AB  - from a giant panda fecal sample collected from Ocean Park, Hong
AB  - Kong. The complete genome of this bacterium may contribute to the discovery of
AB  - efficient cellulose-degrading pathways.
ER  -

TY  - JOUR
AU  - Lu, P.
AU  - Lei, M.
AU  - Xiao, F.
AU  - Zhang, L.
AU  - Wang, Y.
TI  - Complete Genome Sequence of Terribacillus aidingensis Strain MP602, a Moderately  Halophilic Bacterium Isolated from Cryptomeria fortunei in Tianmu Mountain in  China.
JO  - Genome Announcements
PY  - 2015
SP  - e00126
EP  - e00115
VL  - 3
AB  - Terribacillus aidingensis strain MP602, which was isolated from an ancient tree (Cryptomeria
AB  - forunei) in Tianmu Mountain in China, has antagonistic activity
AB  - against several certain phytopathogenic fungi. Here, we report the genome
AB  - sequence of this strain. This is the first complete genome report of the
AB  - Terribacillus genus.
ER  -

TY  - JOUR
AU  - Lu, S.
AU  - Le, S.
AU  - Li, G.
AU  - Shen, M.
AU  - Tan, Y.
AU  - Zhao, X.
AU  - Wang, J.
AU  - Shen, W.
AU  - Guo, K.
AU  - Yang, Y.
AU  - Zhu, H.
AU  - Li, S.
AU  - Li, M.
AU  - Zhu, J.
AU  - Rao, X.
AU  - Hu, F.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection.
JO  - Genome Announcements
PY  - 2015
SP  - e01453
EP  - e01415
VL  - 3
AB  - We report the 6,498,072-bp complete genome sequence of Pseudomonas aeruginosa PA1, which was
AB  - isolated from a patient with a respiratory tract infection in
AB  - Chongqing, People's Republic of China. Whole-genome sequencing was performed
AB  - using single-molecule real-time (SMRT) technology, and de novo assembly revealed
AB  - a single contig with 396-fold sequence coverage.
ER  -

TY  - JOUR
AU  - Lu, S.
AU  - Zhang, X.
AU  - Zhu, Y.
AU  - Kim, K.S.
AU  - Yang, J.
AU  - Jin, Q.
TI  - Complete Genome Sequence of the Neonatal-Meningitis-Associated Escherichia coli Strain CE10.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7005
EP  - 7005
VL  - 193
AB  - Neonatal bacterial meningitis continues to be an important cause of mortality and morbidity
AB  - worldwide. Escherichia coli possessing the K1
AB  - capsular polysaccharide is the most common Gram-negative pathogen causing
AB  - neonatal meningitis. Here we present the complete genome sequence of
AB  - neonatal meningitis-associated E. coli strain CE10, a unique K1 strain
AB  - with a functional type III secretion system. Functional analysis of the
AB  - genome should enhance our knowledge of the pathogenesis of neonatal E.
AB  - coli K1 meningitis.
ER  -

TY  - JOUR
AU  - Lu, W.
AU  - Wise, M.J.
AU  - Tay, C.Y.
AU  - Windsor, H.M.
AU  - Marshall, B.J.
AU  - Peacock, C.
AU  - Perkins, T.
TI  - Comparative analysis of the full genome of the Helicobacter pylori isolate, Sahul64, identifies genes of high divergence.
JO  - J. Bacteriol.
PY  - 2013
SP  - 1073
EP  - 1083
VL  - 196
AB  - Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity
AB  - and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to
AB  - play a functional role in persistence and colonisation of diverse human populations. To
AB  - provide further genomic evidence in the lineage of H. pylori and to further characterise
AB  - diverse strains of this pathogen in different human populations, we report the finished genome
AB  - sequence of Sahul64, an H. pylori strain isolated from an Indigenous Australian. Our analysis
AB  - identified highly divergent genes, when compared to the 38 publically available genomes, which
AB  - include genes involved in the biosynthesis and modification of lipopolysaccharide, putative
AB  - prophage genes, restriction modification components and hypothetical genes. Furthermore, the
AB  - virulence associated vacA locus is a pseudogene and the cagPAI is not present. However, the
AB  - genome does contain a gene cluster associated with pathogenicity including dupA. Our analysis
AB  - found that with the addition of Sahul64 to the 38 genomes, the core genome content of H.
AB  - pylori is reduced by approximately 14% ( approximately 170 genes) and the pan-genome has
AB  - expanded from 2070 to 2238 genes. We have identified three putative horizontally acquired
AB  - regions, including one that is likely to have been acquired prior to speciation from the
AB  - closely related Helicobacter cetorum. Our results suggest that Sahul64, with the absence of
AB  - cagPAI, highly divergent cell envelope proteins and a predicted non-transportable VacA, could
AB  - be more highly adapted to ancient indigenous Australian people but with lower virulence
AB  - potential compared to other sequenced and cagPAI positive H. pylori strains.
ER  -

TY  - JOUR
AU  - Lu, W.D.
AU  - Pang, H.Q.
AU  - Guo, L.Z.
TI  - Genome Sequence of the Fructan-Degrading Organism Marinimicrobium sp. Strain LS-A18, Isolated from a Marine Solar Saltern.
JO  - Genome Announcements
PY  - 2013
SP  - e00776
EP  - e00713
VL  - 1
AB  - Marinimicrobium sp. strain LS-A18 is a fructan-degrading organism isolated from a brine sample
AB  - from a marine solar saltern in Jiaozhou Bay, China. The draft genome
AB  - sequence of this bacterium is 3,815,107 bp in length, with a G+C content of
AB  - 59.03%. To our knowledge, this is the first genome announcement of a
AB  - fructan-degrading strain of the genus Marinimicrobium.
ER  -

TY  - JOUR
AU  - Lu, Y.
AU  - Samac, D.A.
AU  - Glazebrook, J.
AU  - Ishimaru, C.A.
TI  - Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e00396
EP  - e00315
VL  - 3
AB  - We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus
AB  - R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de
AB  - novo assembly of PacBio sequencing data, is the first complete genome sequence
AB  - available for this subspecies.
ER  -

TY  - JOUR
AU  - Lu, Z.
AU  - Li, Y.
AU  - Que, Q.
AU  - Kutish, G.F.
AU  - Rock, D.L.
AU  - Van Etten, J.L.
TI  - Analysis of 94 kb of the chlorella virus PBCV-1 330-kb genome: Map positions 88 to 182.
JO  - Virology
PY  - 1996
SP  - 102
EP  - 123
VL  - 216
AB  - Analysis of 94 kb of DNA, located between map positions 88 and 182 kb in the 330-kb chlorella
AB  - virus PBCV-1 genome, revealed 195 open reading frames 65 codons or longer.  One hundred and
AB  - five of the 195 ORFs were considered major ORFs.  Twenty-six of the 105 major ORFs resembled
AB  - genes in the databases including three chitinases, a chitosanase, three serine/threonine
AB  - protein kinases, two additional protein kinases, a tyrosine protein phosphatase, two ankyrins,
AB  - an ornithine decarboxylase, a copper/zinc-superoxide dismutase, a proliferating cell nuclear
AB  - antigen, a DNA polymerase, a fibronectin-binding protein, the yeast Ski2 protein, an adenine
AB  - DNA methyltransferase and its corresponding DNA site-specific endonuclease, and an amidase.
AB  - The genes for the 105 major ORFs were evenly distributed along the genome and, except for one
AB  - noncoding 1788-nucleotide stretch, the genes were close together.  Unexpectedly, a 900-bp
AB  - region in the 1788-bp noncoding sequence resembled a CpG island.
ER  -

TY  - JOUR
AU  - Lu, Z.
AU  - Lu, Y.
TI  - Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2398
EP  - 2399
VL  - 194
AB  - Members of the order Methanocellales play a key role in methane emissions in paddy fields.
AB  - Because of their slow growth and fastidious culture conditions,
AB  - pure cultures are difficult to isolate and have been unavailable until recently.
AB  - Here we report the complete genome sequence of a novel isolate in this group,
AB  - Methanocella conradii strain HZ254.
ER  -

TY  - JOUR
AU  - Luan, X.
AU  - Cui, Z.
AU  - Gao, W.
AU  - Li, Q.
AU  - Yin, X.
AU  - Zheng, L.
TI  - Genome Sequence of the Petroleum Hydrocarbon-Degrading Bacterium Alcanivorax sp.  Strain 97CO-5.
JO  - Genome Announcements
PY  - 2014
SP  - e01277
EP  - e01214
VL  - 2
AB  - Alcanivorax sp. strain 97CO-5 was isolated from a crude-oil-degrading consortium, enriched
AB  - from Yellow Sea sediment of China. Here, we present the draft genome of
AB  - strain 97CO-5, which comprises 3,251,558 bp with a G+C content of 54.54% and
AB  - contains 2,962 protein-coding genes and 42 tRNAs.
ER  -

TY  - JOUR
AU  - Lubys, A.
AU  - Janulaitis, A.
TI  - Cloning and analysis of the plasmid-borne genes encoding the Bsp6I restriction and modification enzymes.
JO  - Gene
PY  - 1995
SP  - 25
EP  - 29
VL  - 157
AB  - The Bsp6I restriction and modification (R-M) system has been localized on the plasmid pXH13,
AB  - naturally occurring in the Bacillus sp. strain RFL6.  The genes coding for the Bsp6I-R-M
AB  - system, an Fnu4HI isoschizomer recognizing the sequence GCNGC, have been cloned in Escherichia
AB  - coli by two steps.  The nucleotide sequence of a 2126-bp region containing the genes for
AB  - restriction endonuclease (ENase; bsp6IR) and DNA methyltransferase (MTase; bsp6IM) has been
AB  - determined.  The genes are separated by 99 bp and are arranged tandemly with bsp6IR preceding
AB  - bsp6IM.  The DNA sequence predicts an ENase of 174 amino acids (19.9 kDa) and a MTase of 315
AB  - aa (36.3 kDa).  M.Bsp6I contains all the conserved aa sequence motifs characteristic for
AB  - m5C-MTases.  In addition, its variable region exhibits a slight similarity to the
AB  - 5'-GCNGC-3'-specific target-recognition domain from M.Phi3T.  No aa sequence similarity was
AB  - found between R.Bsp6I and M.Bsp6I, nor among R.Bsp6I and other known ENases.  We have tested
AB  - recombinant plasmids carrying the complete R-M system for their ability to transform native
AB  - and pre-methylated Escherichia coli hosts.  The results indicate that pre-methylation
AB  - increases the efficiency of establishment of the complete R-M system.  In addition, we have
AB  - obtained orientation-dependent differences in transformation efficiency.
ER  -

TY  - JOUR
AU  - Lubys, A.
AU  - Jurenaite, S.
AU  - Janulaitis, A.
TI  - Structural organization and regulation of the plasmid-borne type II restriction-modification system Kpn21 from Klebsiella pneumoniae RFL2.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 4228
EP  - 4234
VL  - 27
AB  - Kpn2I enzymes of a type II restriction-modification (R-M) system from the bacterium Klebsiella
AB  - pneumoniae strain RFL2 recognize the sequence 5'-TCCGGA-3'. The Kpn2I R-M genes have been
AB  - cloned and expressed in Escherichia coli. DNA sequence analysis revealed the presence of two
AB  - convergently transcribed open reading frames (ORFs) coding for a restriction endonuclease
AB  - (Enase) of 301 amino acids (34.8 kDa) and methyltransferase (Mtase) of 375 amino acids (42.1
AB  - kDa). The 3'-terminal ends of these genes ( kpn2IR and kpn2IM, respectively) overlap by 11
AB  - bp. In addition, a small ORF (gene kpn2IC ) capable of coding for a protein of 96 amino acids
AB  - in length (10.6 kDa) was found upstream of kpn2IM. The direction of kpn2IC transcription is
AB  - opposite to that of kpn2IM. The predicted amino acid sequence of this ORF includes a probable
AB  - helix-turn-helix motif. We show that the product of kpn2IC represses expression of the Kpn2I
AB  - Mtase but has no influence on expression of the Enase gene. Such a mode of regulation is
AB  - unique among R-M systems analyzed so far. The Kpn2I R-M is located on the K.pneumoniae RFL2
AB  - plasmid pKp4.3, which is able to replicate in E.coli cells.
ER  -

TY  - JOUR
AU  - Lubys, A.
AU  - Lubiene, J.
TI  - Cloning of the genes encoding type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.
JO  - Biologija
PY  - 1996
SP  - 39
EP  - 41
VL  - 0
AB  - The restriction-modification system HphI from Haemophilus parahaemolyticus was cloned into E.
AB  - coli and sequenced.  Five open reading frames aligned in the same orientation were found.  The
AB  - first ORF, orfX, is incomplete and encodes an unknown protein.  The next is the gene for
AB  - C5-methylcytosine forming HphI methylase (hphIMC).  The third gene codes for the
AB  - N6-methyladenine forming HphI methylase (hphIMA).  The fourth gene encodes HphI restriction
AB  - endonuclease.  The expression of hphIR was obtained only after the subcloning of this gene
AB  - under the control of T7 RNA polymerase promoter.  The last gene, menB, codes for the
AB  - dihydroxynaphthoate synthase.
ER  -

TY  - JOUR
AU  - Lubys, A.
AU  - Lubiene, J.
AU  - Kulakauskas, S.
AU  - Stankevicius, K.
AU  - Timinskas, A.
AU  - Janulaitis, A.
TI  - Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2760
EP  - 2766
VL  - 24
AB  - The genomic region encoding the type IIS restriction-modification (R-M) system HphI (enzymes
AB  - recognizing the asymmetric sequence 5'-GGTGA-3'/5'-TCACC-3') from Haemophilus
AB  - parahaemolyticus were cloned into Escherichia coli and sequenced.  Sequence analysis of the
AB  - R-M HphI system revealed three adjacent genes aligned in the same orientation: a cytosine 5
AB  - methyltransferase (gene hphIMC), an adenine N6 methyltransferase (hphIMA) and the HphI
AB  - restriction endonuclease (gene hphIR).  Either methyltransferase is capable of protecting
AB  - plasmid DNA in vivo against the action of the cognate restriction endonuclease.  hphIMA
AB  - methylation renders plasmid DNA resistant to R.HindIII at overlapping sites, suggesting that
AB  - the adenine methyltransferase modifies the 3'-terminal A residue on the GGTGA strand.  Strong
AB  - homology was found between the N-terminal part of the m6A methyltransferase and an
AB  - unidentified reading frame interrupted by an incomplete galE gene of Neisseria meningitidis.
AB  - The HphI R-M genes are flanked by a copy of a 56 bp direct nucleotide repeat on each side.
AB  - Similar sequences have also been identified in the non-coding regions of H.influenzae Rd DNA.
AB  - Possible involvement of the repeat sequences in the mobility of the HphI R-M system is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Lubys, A.
AU  - Menkevicius, S.
AU  - Timinskas, A.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system.
JO  - Gene
PY  - 1994
SP  - 85
EP  - 89
VL  - 141
AB  - The complete type-II Cfr9I restriction-modification (R-M) system of Citrobacter freundii
AB  - strain RFL9, recognizing the DNA sequence CCCGGG, has been cloned and expressed, and
AB  - functionally active enzymes have been produced in Escherichia coli. Both the methyltransferase
AB  - (MTase; M.Cfr9I) and restriction endonuclease (ENase; R.Cfr9I) were found to be encoded on a
AB  - 2.3-kb cloned fragment in the same transcriptional orientation, but differing in translational
AB  - phases. The last codon (underlined) (ATGA) of the MTase-encoding gene (Cf9IM) overlaps with
AB  - the start codon for the ENase-encoding gene (overlined) Cfr9IR). A nucleotide sequence
AB  - complementary to a predicted Shine-Dalgarno sequence preceeding cfr9IR is within this gene.
AB  - Predicted free energy (deltaG) for formation of the mRNA secondary structure involving these
AB  - complementary sequences was found to be - 16.1 kcal mol. Amino-acid sequence homology of 80%
AB  - was found between R.Cfr9I and R.XcyI.
ER  -

TY  - JOUR
AU  - Lucas, P.
AU  - Jouy, E.
AU  - Le Devendec, L.
AU  - de Boisseson, C.
AU  - Perrin-Guyomard, A.
AU  - Jove, T.
AU  - Blanchard, Y.
AU  - Touzain, F.
AU  - Kempf, I.
TI  - Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs.
JO  - Vet. Microbiol.
PY  - 2018
SP  - 100
EP  - 106
VL  - 224
AB  - Resistance to extended-spectrum cephalosporins is prevalent in French pig E. coli
AB  - isolates. The aim of this study was to characterize the plasmids and genes
AB  - present in pathogenic and commensal extended-spectrum cephalosporins -resistant
AB  - isolates. The resistance plasmids of 26 strains were sequenced and then analyzed
AB  - to identify resistance and virulence genes. Results showed that resistance to
AB  - extended-spectrum cephalosporins in French pig E. coli isolates is-as in other
AB  - food animals in France-mainly carried by highly similar blaCTX-M-1 IncI1/ST3
AB  - plasmids. These plasmids very often bear other resistance genes such as
AB  - resistance to sulphonamides (sul2), trimethoprim (dfrA17) and aminoglycosides
AB  - (aadA5), and occasionally to tetracycline (tet(A)), macrolides (mph(A) and erm
AB  - genes), phenicols (floR) or streptomycin (strA, strB). Few virulence genes were
AB  - detected, including colicins, heat-stable enterotoxins, adhesins or
AB  - temperature-sensitive hemagglutinins. The other cefotaximases detected were
AB  - blaCTX-M-27 and blaCTX-M-14, the latter being on an IncF plasmid which showed
AB  - very close identity to a human epidemic plasmid. Importantly, resistance genes
AB  - for quinolones or polymyxins were never detected on the extended-spectrum
AB  - cephalosporins resistance plasmids. These results are helpful to evidence the
AB  - risk of co-selecting cephalosporins -resistance using antibiotics outside this
AB  - group. They also highlight the occasional presence in pigs of human epidemic
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Lucas, P.
AU  - Otis, C.
AU  - Mercier, J.-P.
AU  - Turmel, M.
AU  - Lemieux, C.
TI  - Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 960
EP  - 969
VL  - 29
AB  - Sequence analysis of chloroplast and mitochondrial large subunit rRNA genes from over 75 green
AB  - algae disclosed 28 new group I intron-encoded proteins carrying a single LAGLIDADG motif.
AB  - These putative homing endonucleases form four subfamilies of homologous enzymes, with the
AB  - members of each subfamily being encoded by introns sharing the same insertion site. We showed
AB  - that four divergent endonucleases from the I-CreI subfamily cleave the same DNA substrates.
AB  - Mapping of the 66 amino acids that are conserved among the members of this subfamily on the
AB  - 3-dimensional structure of I-CreI bound to its recognition sequence revealed that these
AB  - residues participate in protein folding, homodimerization, DNA recognition and catalysis.
AB  - Surprisingly, only seven of the 21 I-CreI amino acids interacting with DNA are conserved,
AB  - suggesting that I-CreI and its homologs use different subsets of residues to recognize the
AB  - same DNA sequence. Our sequence comparison of all 45 single-LAGLIDADG proteins identified so
AB  - far suggests that these proteins share related structures and that there is a weak pressure in
AB  - each subfamily to maintain identical protein-DNA contacts. The high sequence variability we
AB  - observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into
AB  - how these proteins evolve new DNA specificity.
ER  -

TY  - JOUR
AU  - Lucas, S. et al.
TI  - Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5974
EP  - 5975
VL  - 194
AB  - Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing
AB  - bacterium isolated from the Grandbonum deep-sea hydrothermal vent
AB  - site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M.
AB  - piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp
AB  - circular plasmid. This genome was sequenced within Department of Energy Joint
AB  - Genome Institute CSP 2010.
ER  -

TY  - JOUR
AU  - Lucas-Elio, P.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Pitluck, S.
AU  - Nolan, M.
AU  - Kyrpides, N.C.
AU  - Detter, J.C.
AU  - Copeland, A.
AU  - Lu, M.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, S.
AU  - Land, M.L.
AU  - Ivanova, N.
AU  - Mikhailova, N.
AU  - Johnston, A.W.
AU  - Sanchez-Amat, A.
TI  - Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 31
EP  - 43
VL  - 7
AB  - IVIA-Po-181 Lucas-Elio 2011 belongs to the family within the phylum . Different species of the
AB  - genus can be readily isolated from the seagrass . is among the
AB  - most abundant species of the genus detected in the cultured microbiota of
AB  - suggesting a close relationship with this plant, which has a great ecological
AB  - value in the Mediterranean Sea, covering an estimated surface of 38,000 Km. Here
AB  - we describe the genomic features of . The 3,899,940 bp long genome harbors 3,544
AB  - protein-coding genes and 107 RNA genes and is a part of the project.
ER  -

TY  - JOUR
AU  - Lucas-Elio, P.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Pitluck, S.
AU  - Nolan, M.
AU  - Kyrpides, N.C.
AU  - Detter, J.C.
AU  - Copeland, A.
AU  - Teshima, H.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, S.
AU  - Land, M.L.
AU  - Ivanova, N.
AU  - Mikhailova, N.
AU  - Johnston, A.W.
AU  - Sanchez-Amat, A.
TI  - Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 63
EP  - 73
VL  - 6
AB  - Marinomonas mediterranea MMB-1(T) Solano & Sanchez-Amat 1999 belongs to the family
AB  - Oceanospirillaceae within the phylum Proteobacteria. This species is of
AB  - interest because it is the only species described in the genus Marinomonas to
AB  - date that can synthesize melanin pigments, which is mediated by the activity of a
AB  - tyrosinase. M. mediterranea expresses other oxidases of biotechnological
AB  - interest, such as a multicopper oxidase with laccase activity and a novel
AB  - L-lysine-epsilon-oxidase. The 4,684,316 bp long genome harbors 4,228
AB  - protein-coding genes and 98 RNA genes and is a part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Lucas-Elio, P.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Pitluck, S.
AU  - Nolan, M.
AU  - Kyrpides, N.C.
AU  - Detter, J.C.
AU  - Copeland, A.
AU  - Teshima, H.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, S.
AU  - Land, M.L.
AU  - Ivanova, N.
AU  - Mikhailova, N.
AU  - Johnston, A.W.B.
AU  - Sanchez-Amat, A.
TI  - Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1T).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 63
EP  - 73
VL  - 5
ER  -

TY  - JOUR
AU  - Lucchini, S.
AU  - Sidoti, J.
AU  - Brussow, H.
TI  - Broad-range bacteriophage resistance in Streptococcus thermophilus by insertional mutagenesis.
JO  - Virology
PY  - 2000
SP  - 267
EP  - 277
VL  - 275
AB  - Streptococcus thermophilus is a lactic acid bacterium used in industrial milk fermentation. To
AB  - obtain phage-resistant starters, S. thermophilus strain Sfi1 was submitted to mutagenesis with
AB  - the thermolabile insertional vector pG(+)host9:ISS1 followed by a challenge with the lytic S.
AB  - thermophilus phage Sfi19.  Vector insertions into four distinct sites led to a
AB  - phage-resistance phenotype. Three mutants were characterized further. They were protected
AB  - against the homologous challenging phage and 14 heterologous phages. All three mutants
AB  - adsorbed phages. No intracellular phage DNA synthesis was observed in mutants R7 and R71,
AB  - while mutant R24 showed a delayed and diminished phage DNA synthesis compared to the parental
AB  - Sfi1 strain. In mutant R7 a short deletion occurred next to the insertion site which removed
AB  - the upstream sequences and the 15 initial codons from orf 394, encoding a likely transmembrane
AB  - protein.  Analogy with other phage systems suggests an involvement of this protein in the
AB  - phage DNA injection process. In mutant R24 the vector was inserted into orf 269 predicting an
AB  - oxido-reductase. When the vector sequence was removed via homologous recombination across the
AB  - duplicated insertion elements, mutant R24 returned to the phage susceptibility of the parental
AB  - strain. This observation suggested that inactivation of orf  269 was not crucial for the
AB  - resistance phenotype. A gene encoding a likely restriction subunit of a type I
AB  - restriction-modification system was located directly downstream of the insertion site in
AB  - mutant R24. HsdM and hsdS genes encoding the modification and specificity subunits of a type I
AB  - R-M system and biological evidence for an active R-M system were detected in strain Sfi1,
AB  - suggesting involvement of a type I R-M system in the resistance phenotype of R24.
ER  -

TY  - JOUR
AU  - Lucid, A.
AU  - Bullman, S.
AU  - Koziel, M.
AU  - Corcoran, G.D.
AU  - Cotter, P.D.
AU  - Sleator, R.D.
AU  - Lucey, B.
TI  - Draft Genome Sequence of Campylobacter ureolyticus Strain CIT007, the First Whole-Genome Sequence of a Clinical Isolate.
JO  - Genome Announcements
PY  - 2014
SP  - e00262
EP  - e00214
VL  - 2
AB  - Herein, we present the draft genome sequence of Campylobacter ureolyticus. Strain CIT007 was
AB  - isolated from a stool sample from an elderly female presenting with diarrheal illness and
AB  - end-stage chronic renal disease.
ER  -

TY  - JOUR
AU  - Lucker, S.
AU  - Wagner, M.
AU  - Maixner, F.
AU  - Pelletier, E.
AU  - Koch, H.
AU  - Vacherie, B.
AU  - Rattei, T.
AU  - Damste, J.S.
AU  - Spieck, E.
AU  - Le Paslier, D.
AU  - Daims, H.
TI  - A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 13479
EP  - 13484
VL  - 107
AB  - Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are,
AB  - according to molecular data, among the most diverse
AB  - and widespread nitrifiers in natural ecosystems and biological wastewater
AB  - treatment. Here, environmental genomics was used to reconstruct the
AB  - complete genome of 'Candidatus Nitrospira defluvii' from an activated
AB  - sludge enrichment culture. On the basis of this first-deciphered
AB  - Nitrospira genome and of experimental data, we show that Ca. N. defluvii
AB  - differs dramatically from other known nitrite oxidizers in the key enzyme
AB  - nitrite oxidoreductase (NXR), in the composition of the respiratory chain,
AB  - and in the pathway used for autotrophic carbon fixation, suggesting
AB  - multiple independent evolution of chemolithoautotrophic nitrite oxidation.
AB  - Adaptations of Ca. N. defluvii to substrate-limited conditions include an
AB  - unusual periplasmic NXR, which is constitutively expressed, and pathways
AB  - for the transport, oxidation, and assimilation of simple organic compounds
AB  - that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle
AB  - as the pathway for CO(2) fixation and the lack of most classical defense
AB  - mechanisms against oxidative stress suggest that Nitrospira evolved from
AB  - microaerophilic or even anaerobic ancestors. Unexpectedly, comparative
AB  - genomic analyses indicate functionally significant lateral gene-transfer
AB  - events between the genus Nitrospira and anaerobic ammonium-oxidizing
AB  - planctomycetes, which share highly similar forms of NXR and other proteins
AB  - reflecting that two key processes of the nitrogen cycle are evolutionarily
AB  - connected.
ER  -

TY  - JOUR
AU  - Luckwu-de-Lucena, B.T.
AU  - Silva, G.G.
AU  - Manoel-Dos-Santos, B.
AU  - Dias, G.M.
AU  - Amaral, G.R.
AU  - Moreira, A.P.
AU  - de Morais, J.M.A.
AU  - Dutilh, B.E.
AU  - Edwards, R.A.
AU  - Balbino, V.
AU  - Thompson, C.C.
AU  - Thompson, F.L.
TI  - Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3018
EP  - 3018
VL  - 194
AB  - We report on the genome sequences of Lactobacillus vini type strain LMG 23202(T)(DSM
AB  - 20605)isolated from fermenting grape musts in Spain) and the industrial strain L. vini JP7.8.9
AB  - (isolated from a bioethanol plant in northeast Brazil.  All contigs were assembled using
AB  - gsAssembler, and genes were predicted and annotated using Rapid Annotation using Subsystem
AB  - Technology (RAST). The identified genome sequence of LMG 23202(T) had 2.201.333 bp, 37.6% G+C,
AB  - and 1,833 genes, whereas the identified genome sequence of JP7.8.9 had 2.301.037 bp, 37.8%
AB  - G+C, and 1,739 genes. The gene repertoire of the species L. vini offers promising
AB  - opportunities for biotechnological applications.
ER  -

TY  - JOUR
AU  - Ludannyy, R.
AU  - Alvarez, F.M.
AU  - Levi, D.
AU  - Markelov, M.
AU  - Dedkov, V.
AU  - Aleksandrova, N.
AU  - Shipulin, G.
TI  - Whole-Genome Sequence of Mycobacterium bovis BCG-1 (Russia).
JO  - Genome Announcements
PY  - 2015
SP  - e01320
EP  - e01315
VL  - 3
AB  - BCG vaccine (Mycobacterium bovis BCG-1 [Russia]) is the most important component  of
AB  - tuberculosis prophylaxis in Russia. This study represents the complete genome
AB  - sequence and genetic characteristics of M. bovis BCG-1 (Russia), which has been
AB  - used to manufacture BCG vaccine in Russia and in some other countries.
ER  -

TY  - JOUR
AU  - Ludeke, C.H.
AU  - Kong, N.
AU  - Weimer, B.C.
AU  - Fischer, M.
AU  - Jones, J.L.
TI  - Complete Genome Sequences of a Clinical Isolate and an Environmental Isolate of Vibrio parahaemolyticus.
JO  - Genome Announcements
PY  - 2015
SP  - e00216
EP  - e00215
VL  - 3
AB  - Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States.
AB  - We report complete genome sequences for two V. parahaemolyticus
AB  - strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin,
AB  - respectively. These two sequences might assist in the investigation of
AB  - differential virulence of this organism.
ER  -

TY  - JOUR
AU  - Luedin, S.M.
AU  - Pothier, J.F.
AU  - Danza, F.
AU  - Storelli, N.
AU  - Frigaard, N.U.
AU  - Wittwer, M.
AU  - Tonolla, M.
TI  - Complete genome sequence of 'Thiodictyon syntrophicum' sp. nov. strain Cad16(T),  a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 14
EP  - 14
VL  - 13
AB  - 'Thiodictyon syntrophicum' sp. nov. strain Cad16(T) is a photoautotrophic purple  sulfur
AB  - bacterium belonging to the family of Chromatiaceae in the class of
AB  - Gammaproteobacteria. The type strain Cad16(T) was isolated from the chemocline of
AB  - the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16(T) represents a
AB  - key species within this sulfur-driven bacterial ecosystem with respect to carbon
AB  - fixation. The 7.74-Mbp genome of strain Cad16(T) has been sequenced and
AB  - annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences.
AB  - Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans
AB  - strain DSM 232(T) the most closely related species. Genes involved in sulfur
AB  - oxidation, central carbon metabolism and transmembrane transport were found.
AB  - Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment
AB  - biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed
AB  - insight into the Cad16(T) genome and analyze it in the context of the microbial
AB  - ecosystem of Lake Cadagno.
ER  -

TY  - JOUR
AU  - Lugli, G.A.
AU  - Duranti, S.
AU  - Milani, C.
AU  - Turroni, F.
AU  - Viappiani, A.
AU  - Mangifesta, M.
AU  - van Sinderen, D.
AU  - Ventura, M.
TI  - The Genome Sequence of Bifidobacterium moukalabense DSM 27321 Highlights the Close Phylogenetic Relatedness with the Bifidobacterium dentium Taxon.
JO  - Genome Announcements
PY  - 2014
SP  - e00048
EP  - e00014
VL  - 2
AB  - Bifidobacterium moukalabense DSM 27321 is the reference strain for a recently described new
AB  - bifidobacterial species that has been isolated from a wild west
AB  - lowland gorilla. Here, we report the whole-genome sequence of DSM 27321, which
AB  - supports very close phylogenetic relatedness with members of the Bifidobacterium
AB  - adolescentis phylogenetic group and, in particular, the Bifidobacterium dentium
AB  - taxon.
ER  -

TY  - JOUR
AU  - Luhtanen, A.M.
AU  - Eronen-Rasimus, E.
AU  - Kaartokallio, H.
AU  - Rintala, J.M.
AU  - Autio, R.
AU  - Roine, E.
TI  - Isolation and characterization of phage-host systems from the Baltic Sea ice.
JO  - Extremophiles
PY  - 2014
SP  - 121
EP  - 130
VL  - 18
AB  - In search for sea ice bacteria and their phages from the Baltic Sea ice, two ice
AB  - samples were collected from land-fast ice in a south-west Finland coastal site in
AB  - February and March 2011. Bacteria were isolated from the melted sea ice samples
AB  - and phages were screened from the same samples for 43 purified isolates.
AB  - Plaque-producing phages were found for 15 bacterial isolates at 3 degrees C. Ten
AB  - phage isolates were successfully plaque purified and eight of them were chosen
AB  - for particle purification to analyze their morphology and structural proteins.
AB  - Phage 1/32 infecting an isolate affiliated to phylum Bacteroidetes
AB  - (Flavobacterium sp.) is a siphovirus and six phages infecting isolates affiliated
AB  - to gamma-Proteobacteria (Shewanella sp.) hosts were myoviruses. Cross titrations
AB  - between the hosts showed that all studied phages are host specific. Phage
AB  - solutions, host growth and phage infection were tested in different temperatures
AB  - revealing phage temperature tolerance up to 45 degrees C, whereas phage infection
AB  - was in most of the cases retarded above 15 degrees C. This study is the first to
AB  - report isolation and cultivation of ice bacteria and cold-active phages from the
AB  - Baltic Sea ice.
ER  -

TY  - JOUR
AU  - Luhung, I. et al.
TI  - Genome Sequence of Pantoea ananatis SGAir0210, Isolated from Outdoor Air in Singapore.
JO  - Genome Announcements
PY  - 2018
SP  - e00643
EP  - e00618
VL  - 6
AB  - Pantoea ananatis SGAir0210 was isolated from outdoor air collected in Singapore.  The genome
AB  - was assembled from long reads generated by single-molecule real-time
AB  - sequencing complemented with short reads. The genome size was approximately 4.81
AB  - Mb, with 4,303 protein-coding genes, 80 tRNAs, and 22 rRNAs identified.
ER  -

TY  - JOUR
AU  - Lui, A.C.P.
AU  - McBride, B.C.
AU  - Vovis, G.F.
AU  - Smith, M.
TI  - Site specific endonuclease from Fusobacterium nucleatum.
JO  - Nucleic Acids Res.
PY  - 1979
SP  - 1
EP  - 15
VL  - 6
AB  - Four different isolates of Fusobacterium nucleatum (A,C,D and E) contain
AB  - restriction endonucleases of differing specificity.  Whilst many of the
AB  - endonucleases are isochizomers of known enzymes, two novel activities are Fnu
AB  - DII which recognizes and cleaves the sequence 5'-CG^CG-3' 3'-GC^GC-5' and Fnu
AB  - EI which recognizes and cleaves the sequence 5'-^GATC-3' 3'-CTAG^-5'
AB  - irrespective of the extent of methylation of the adenine residues.
ER  -

TY  - JOUR
AU  - Lujan, A.M.
AU  - Feliziani, S.
AU  - Smania, A.M.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain Hex1T Isolated from Soils  Contaminated with Used Lubricating Oil in Argentina.
JO  - Genome Announcements
PY  - 2017
SP  - e01473
EP  - e01416
VL  - 5
AB  - Pseudomonas aeruginosa Hex1T was isolated from soils contaminated with used lubricating oil
AB  - from a garage in Cordoba, Argentina. This strain is capable of
AB  - utilizing this pollutant as the sole carbon and energy source. Here, we present
AB  - the 6.9-Mb draft genome sequence of Hex1T, which contains many heavy
AB  - metal-resistance genes.
ER  -

TY  - JOUR
AU  - Lujan, K.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Tenacibaculum soleae UCD-KL19.
JO  - Genome Announcements
PY  - 2016
SP  - e01120
EP  - e01116
VL  - 4
AB  - Here, we present the draft genome sequence of Tenacibaculum soleae strain UCD-KL19. The
AB  - assembly contains 3,012,701 bp in 46 contigs. This strain was
AB  - isolated from a seagrass leaf (Zostera marina) collected from Bodega Bay, CA, as
AB  - a part of an undergraduate student research project on isolating bacteria from
AB  - seagrass.
ER  -

TY  - JOUR
AU  - Lujan, K.M.
AU  - Eisen, J.A.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and  Shewanella sp. Strain UCD-KL21, Isolated from Seagrass.
JO  - Genome Announcements
PY  - 2017
SP  - e00023
EP  - e00017
VL  - 5
AB  - Here, we present the draft genome sequences for five bacterial strains. These strains were all
AB  - isolated from seagrass (Zostera marina) collected from Bodega
AB  - Bay, CA, as a part of an undergraduate research project focused on
AB  - seagrass-associated microbes.
ER  -

TY  - JOUR
AU  - Lukacs, C.M.
AU  - Aggarwal, A.K.
TI  - BglII and MunI: what a difference a base makes.
JO  - Curr. Opin. Struct. Biol.
PY  - 2001
SP  - 14
EP  - 18
VL  - 11
AB  - Restriction endonucleases are resilient to alterations in their DNA-binding specificities.
AB  - Structures of the BglII and MunI endonucleases bound to their palindromic DNA sites, which
AB  - differ by only their outer base pairs from the recognition sequences of BamHI and EcoRI,
AB  - respectively, have recently been determined. A comparison of these complexes reveals
AB  - surprising differences and similarities in structure, and provides a basis for understanding
AB  - the immutability of restriction endonucleases.
ER  -

TY  - JOUR
AU  - Lukacs, C.M.
AU  - Kucera, R.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5A resolution.
JO  - Nat. Struct. Biol.
PY  - 2000
SP  - 134
EP  - 140
VL  - 7
AB  - Restriction endonucleases are remarkably resilient to alterations in their DNA binding
AB  - specificity. To understand the basis of this immutability, we have determined the crystal
AB  - structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A
AB  - resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a
AB  - closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core,
AB  - but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to
AB  - provide extra specificity.  Remarkably, the DNA is contorted differently in the two
AB  - structures, leading to different protein-DNA contacts for even the common base pairs.
AB  - Furthermore, the BglII active site contains  a glutamine in place of the glutamate at the
AB  - general base position in BamHI, and only a single metal is found coordinated to the putative
AB  - nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows
AB  - that different strategies can be successful in achieving site-specific recognition and
AB  - catalysis in restriction endonucleases.
ER  -

TY  - JOUR
AU  - Luke, P.A.
AU  - Halford, S.E.
TI  - Fluorescent labelling of EcoRI and EcoRV.
JO  - Biochem. Soc. Trans.
PY  - 1986
SP  - 259
EP  - 260
VL  - 14
AB  - Fluorescent chromophores, covalently attached to proteins, have been widely used as reporter
AB  - groups to monitor associations of proteins with ligands, either by observing perturbations to
AB  - fluorescence spectra or by fluorescence polarization methods.  In the latter, given excitation
AB  - with light polarized in the vertical plane and measurements of emission in both horizontal and
AB  - vertical planes, the binding of a ligand that increases the rotational correlation time of the
AB  - protein (relative to the excited state lifetime of the fluorophore) may reduce the H/V ratio.
ER  -

TY  - JOUR
AU  - Luke, P.A.
AU  - Halford, S.E.
TI  - Solubility of the EcoRI restriction endonuclease and its purification from an over-producing strain.
JO  - Gene
PY  - 1985
SP  - 241
EP  - 246
VL  - 37
AB  - The solubility of the EcoRI restriction endonuclease was measured in solutions
AB  - of varying NaCl concentrations, at different temperatures and in the presence
AB  - of DNA.  The precipitation of the protein was enhanced by low NaCl
AB  - concentrations, by elevated temperatures, and by the addition of DNA.  These
AB  - observations are discussed in relationship to the interaction of this protein
AB  - with DNA.  The purification of the EcoRI restriction enzyme from a strain of
AB  - Escherichia coli that over-produces this enzyme was hampered by the
AB  - insolubility of the protein, and hence the purification procedure was modified
AB  - to optimize the recovery of active enzyme.
ER  -

TY  - JOUR
AU  - Luke, P.A.
AU  - McCallum, S.A.
AU  - Halford, S.E.
TI  - The EcoRV restriction endonuclease.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 185
EP  - 207
VL  - 5
AB  - Type II restriction endonucleases have attracted attention for two main
AB  - reasons:  firstly, their many applications in the dissection of DNA and in the
AB  - construction of novel DNA molecules; secondly, as systems for studying the
AB  - interactions of proteins with specific DNA sequences.  With respect to the
AB  - latter, the EcoRI restriction endonuclease has been examined in greater depth
AB  - than any other type II enzyme.  However, the EcoRI enzyme has a major
AB  - disadvantage as a system for studying DNA-protein interactions:  the protein
AB  - has a remarkably low solubility.  The solutions in which EcoRI shows maximal
AB  - activity, and also affinity for its recognition site, are saturated at less
AB  - than 0.5 microM of this protein.  Consequently, many techniques that have been
AB  - developed to study protein-ligand interactions but which require high
AB  - concentrations of the protein in solution, such as NMR spectroscopy, cannot be
AB  - used on EcoRI.  But this drawback does not apply to all type II restriction
AB  - enzymes.  A different enzyme, the EcoRV restriction endonuclease, has special
AB  - advantages as a system for studying DNA-protein interactions.  In particular,
AB  - this is the only type II restriction enzyme (apart from EcoRI) for which
AB  - crystals of the protein have been reported.
ER  -

TY  - JOUR
AU  - Lukinavicius, G.
AU  - Klimasauskas, S.
AU  - Dalhoff, C.
AU  - Weinhold, E.
TI  - Conversion of DNA methyltransferases to alkyltransferases via cofactor engineering.
JO  - FEBS Lett.
PY  - 2006
SP  - 336
EP  - 337
VL  - 273
AB  - S-Adenosyl-L-methionine (AdoMet) is a biological sulfonium compound known as the major methyl
AB  - donor in the cell.  AdoMet-dependent methyltransferases (MTases) catalyze the transfer of the
AB  - methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to defined positions within
AB  - various substrates like DNA, RNA, proteins and other biomolecules.  A series of new AdoMet
AB  - analogs with extended linear carbon chains replacing the methyl group was obtained by chemical
AB  - synthesis.  Remarkably, we find that extended groups containing a double or triple
AB  - carbon-carbon bond one unit away from the sulfonium center, was opposed to saturated carbon
AB  - chains, are readily transferred onto DNA owing to conjugative stabilization of the SN2-like
AB  - transition state.  The MTase-assisted transalkylations of DNA are truly catalytic, efficient
AB  - and proceed in a sequence-specific manner yielding corresponding adenine-N-6, cytosine-N4 or
AB  - cytosine-5 derivatives.
ER  -

TY  - JOUR
AU  - Lukinavicius, G.
AU  - Lapiene, V.
AU  - Stasevskij, Z.
AU  - Dalhoff, C.
AU  - Weinhold, E.
AU  - Klimasauskas, S.
TI  - Targeted labeling of DNA by methyltransferase-directed transfer of activated groups (mTAG).
JO  - J. Am. Chem. Soc.
PY  - 2007
SP  - 2758
EP  - 2759
VL  - 129
AB  - Methyltransferases catalyze highly specific transfers of methyl groups from the ubiquitous
AB  - cofactor S-adenosyl-L-methionine (AdoMet) to
AB  - various biopolymers like DNA, RNA, and proteins. Here we describe the
AB  - first synthetic analogue of AdoMet with an activated side chain
AB  - carrying a primary amino group that permits efficient
AB  - methyltransferase-directed functionalization of DNA and subsequent
AB  - amine-specific chemoligations with various reporter groups. The
AB  - demonstrated two-step sequence-specific labeling of natural DNA offers
AB  - a facile way to query the methylation status of the target sites and
AB  - envisions numerous applications in functional studies and medical
AB  - diagnostics.
ER  -

TY  - JOUR
AU  - Lukinavicius, G.
AU  - Lapinaite, A.
AU  - Urbanaviciute, G.
AU  - Gerasimaite, R.
AU  - Klimasauskas, S.
TI  - Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 11594
EP  - 11602
VL  - 40
AB  - DNA methyltransferases catalyse the transfer of a methyl group from the ubiquitous cofactor
AB  - S-adenosyl-L-methionine (AdoMet) onto specific target sites
AB  - on DNA and play important roles in organisms from bacteria to humans. AdoMet
AB  - analogs with extended propargylic side chains have been chemically produced for
AB  - methyltransferase-directed transfer of activated groups (mTAG) onto DNA, although
AB  - the efficiency of reactions with synthetic analogs remained low. We performed
AB  - steric engineering of the cofactor pocket in a model DNA cytosine-5
AB  - methyltransferase (C5-MTase), M.HhaI, by systematic replacement of three
AB  - non-essential positions, located in two conserved sequence motifs and in a
AB  - variable region, with smaller residues. We found that double and triple
AB  - replacements lead to a substantial improvement of the transalkylation activity,
AB  - which manifests itself in a mild increase of cofactor binding affinity and a
AB  - larger increase of the rate of alkyl transfer. These effects are accompanied with
AB  - reduction of both the stability of the product DNA-M.HhaI-AdoHcy complex and the
AB  - rate of methylation, permitting competitive mTAG labeling in the presence of
AB  - AdoMet. Analogous replacements of two conserved residues in M.HpaII and M2.Eco31I
AB  - also resulted in improved transalkylation activity attesting a general
AB  - applicability of the homology-guided engineering to the C5-MTase family and
AB  - expanding the repertoire of sequence-specific tools for covalent in vitro and ex
AB  - vivo labeling of DNA.
ER  -

TY  - JOUR
AU  - Lukinavicius, G.
AU  - Tomkuviene, M.
AU  - Masevicius, V.
AU  - Klimasauskas, S.
TI  - Enhanced Chemical Stability of AdoMet Analogues for Improved Methyltransferase-Directed Labeling of DNA.
JO  - ACS Chem. Biol.
PY  - 2013
SP  - 1134
EP  - 1139
VL  - 8
AB  - Methyltransferases catalyze specific transfers of methyl groups from the ubiquitous cofactor
AB  - S-adenosyl-L-methionine (AdoMet) to various
AB  - nucleophilic positions in biopolymers like DNA, RNA, and proteins. We
AB  - had previously described synthesis and application of AdoMet analogues
AB  - carrying sulfonium-bound 4-substituted but-2-ynyl side chains for
AB  - transfer by methyltransferases. Although useful in certain
AB  - applications, these cofactor analogues exhibited short lifetimes in
AB  - physiological buffers. Examination of the reaction kinetics and
AB  - products showed that their fast inactivation followed a different
AB  - pathway than observed for AdoMet and rather involved a pH-dependent
AB  - addition of a water molecule to the side chain. This side reaction was
AB  - eradicated by synthesis of a series of cofactor analogues in which the
AB  - separation between an electronegative group and the triple bond was
AB  - increased from one to three carbon units. The designed hex-2-ynyl
AB  - moiety-based cofactor analogues with terminal amino, azide, or alkyne
AB  - groups showed a markedly improved enzymatic transalkylation activity
AB  - and proved well suitable for methyltransferase-directed
AB  - sequence-specific labeling of DNA in vitro and in bacterial cell
AB  - lysates.
ER  -

TY  - JOUR
AU  - Lukyanchuk, V.
AU  - Reva, O.
AU  - Polishchuk, L.
TI  - Restriction endonucleases of type II from two endophytic strains of Bacillus.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A181
EP  - A181
VL  - 28
AB  - Restriction modification systems were found in more than 3000 bacterial species.  It is
AB  - generally accepted that their primary role is to protect host bacteria against phage
AB  - infection.  We used a simple technique proposed by Belavin with our modification, for
AB  - detection of bacterial restriction endonucleases.  Endonucleases activity of 24 Bacillus
AB  - strains isolated from inner tissues of cotton plants was tested by this method.  Enzyme of
AB  - Bacillus licheniformis IMB B-55O8B (Bli55O8B) cuts DNA of lambda phage at 2 sites and DNA of
AB  - T7 phage at 29 sites.  We found that computer calculated numbers of DNAs fragments and their
AB  - molecular sizes that would be generated at the sequence GGTCTC, correlated with the observed
AB  - cleavage frequency of the both mentioned substrates.  We suppose a new isoschisomer of type II
AB  - endonuclease of restriction Eco31I was isolated from Bacillus licheniformis IMB B-55O8B.  A
AB  - restriction endonuclease of Bacillus subtilis IMB 5044B (Bsu5044B) cut DNA at M13mp18 at four
AB  - sites, DNA of pUC19 at six sites and DNA of pBR322 at fifteen sites.  We found that computer
AB  - calculated number of fragments that would be generated the sequence 5'-GGNCC-3' correlated
AB  - with the observed cleavage frequency of the above mentioned substrates.  Recently this
AB  - sequence was determined for restrictase Asu1.  Similarity of digestion profiles of gel
AB  - electrophoresis of T7 and lambda DNA fragments obtained after treating by Cfr13I (isoschizomer
AB  - of AsuI) and Bsu5O44B was evidence of Bsu5044B could be new isoschizomer of AsuI.  Thus two
AB  - endophytic strains of Bacillus were found to produce endonucleases of restriction.  Found
AB  - enzymes were isoschizomers of well known enzymes AsuI and EcoR31I.
ER  -

TY  - JOUR
AU  - Lukyanchuk, V.V.
AU  - Polishchuk, L.V.
AU  - Strizhkova, G.M.
AU  - Kopieiko, O.P.
AU  - Matselyukh, B.P.
TI  - Determination of site-specificity of the II type restriction endonuclease in Streptomyces sp. 48.
JO  - Mikrobiol. Zh.
PY  - 1999
SP  - 80
EP  - 83
VL  - 61
AB  - The activity of a restriction endonuclease which splits DNA of lambda and T7 phages into 8
AB  - fragments has been detected in the mycelium lysates of the 2-days culture of Streptomyces sp.
AB  - 48.  The fragments dimensions according to the data of agarose gel electrophoresis, coincide
AB  - with those of AsuII fragments of DNA of lambda and T7 phages.  This allows the studied Ssp48
AB  - restrictase to be considered the isoschizomer of AsuII restriction endonuclease.
ER  -

TY  - JOUR
AU  - Lukyanchuk, V.V.
AU  - Reva, O.M.
AU  - Polishchuk, L.V.
TI  - Type-II site-specific restriction endonucleases in endophytic strains of the genus Bacillus.
JO  - Mikrobiol. Zh.
PY  - 1999
SP  - 28
EP  - 30
VL  - 61
AB  - Using a modified Belavin's method the site-specific II type restriction endonucleases were
AB  - determined for two endophytic strains of the Bacillus genus from the inner tissues of cotton
AB  - plants.
ER  -

TY  - JOUR
AU  - Lukyanchuk, V.V.
AU  - Reva, O.N.
AU  - Polishchuk, L.V.
TI  - Endophytic bacilli producing type II restriction endonucleases.
JO  - Mikrobiologiia
PY  - 2002
SP  - 491
EP  - 493
VL  - 71
AB  - Two of thirteen bacillar strains isolated from the inner tissues of cotton plants were found
AB  - to produce type II restriction endonucleases. The investigation of the site specificity of
AB  - these enzymes showed that they are AsuI and Eco31I isoschizomers.
ER  -

TY  - JOUR
AU  - Lukyanchuk, V.V.
AU  - Strizhkova, G.M.
AU  - Polishchuk, L.V.
AU  - Kopeyko, O.P.
AU  - Matselyukh, B.P.
TI  - Search for site-specific endonucleases of the II type restriction among Streptomycetes.
JO  - Mikrobiol. Zh.
PY  - 1998
SP  - 33
EP  - 35
VL  - 60
AB  - Three Streptomycetes strains producing endonucleases of restriction of II type have been found
AB  - using the modified method of Belavin.
ER  -

TY  - JOUR
AU  - Lukyanchuk, V.V.
AU  - Suchanoff, S.M.
AU  - Polishchuk, L.V.
AU  - Matselyukh, B.P.
TI  - Isolation of site-specific endonuclease of Streptomyces sp. 48.
JO  - Biopol. Kletka
PY  - 2000
SP  - 559
EP  - 561
VL  - 16
AB  - A method of isolation and purification of site-specific endonuclease of the II type S. sp. 48
AB  - has been worked out.  It has been determined that the S. sp. 48 lysate contains only one
AB  - enzyme with site-specific activity.  Maximum elution of the endonuclease was made by buffer
AB  - with ionic strength of 350 mM NaCl.  This method provides sufficient purification and
AB  - concentration of this enzyme with preservation of its specific activity.
ER  -

TY  - JOUR
AU  - Lulitanond, A.
AU  - Ito, T.
AU  - Li, S.
AU  - Han, X.
AU  - Ma, X.X.
AU  - Engchanil, C.
AU  - Chanawong, A.
AU  - Wilailuckana, C.
AU  - Jiwakanon, N.
AU  - Hiramatsu, K.
TI  - ST9 MRSA strains carrying a variant of type IX SCCmec identified in the Thai community.
JO  - BMC Infect. Dis.
PY  - 2013
SP  - 214
EP  - 214
VL  - 13
AB  - BACKGROUND: Infections caused by methicillin-resistant Staphylococcus aureus
AB  - (MRSA) in Thailand occur most frequently in healthcare facilities. However,
AB  - reports of community-associated MRSA are limited. METHODS: We characterized 14
AB  - MRSA isolates from outpatients (O-1 to O-14) by phenotypic and genotypic methods
AB  - and compared them with 5 isolates from inpatients (I-1 to I-5). Thai MRSA
AB  - isolates from a healthcare worker (N-1) and a pig (P-1) were also included as ST9
AB  - MRSA strains from other sources. RESULTS: All MRSA isolates from the outpatients
AB  - and inpatients were multidrug-resistant (resistant to >/=3 classes of
AB  - antimicrobials). All of them except strains O-2 and I-3 carried type III SCCmec
AB  - and belonged to agrI, coagulase IV, spa type t037 or t233, which related to
AB  - ST239. The strain O-2 (JCSC6690) carried type IX SCCmec and belonged to agrII,
AB  - coagulaseXIc, spa type t337 and ST9, whereas the strain I-3 carried a type III
AB  - SCCmec and belonged to ST1429. Nucleotide sequence determination revealed that
AB  - the type IX SCCmec element in strain O-2 was distinct from that in a Thai ST398
AB  - strain (JCSC6943) previously identified in 2011; nucleotide identities of ccrA
AB  - and ccrB were 93 and 91%, respectively and several open reading frames (ORFs) at
AB  - the joining regions were different. PCR experiments suggested that strain O-2 and
AB  - N-1 carried similar SCCmec element, whereas that of strain P-1 was different,
AB  - suggesting that distinct ST9-MRSA-IX clones might be spreading in this province.
AB  - CONCLUSIONS: The SCCmecIX-ST9 MRSA clones of distinct SCCmec subtypes might have
AB  - emerged in the Thai community and might also have disseminated into the hospital.
ER  -

TY  - JOUR
AU  - Lumactud, R.
AU  - Fulthorpe, R.
AU  - Sentchilo, V.
AU  - van der Meer, J.R.
TI  - Draft Genome Sequence of Microbacterium foliorum Strain 122 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.
JO  - Genome Announcements
PY  - 2017
SP  - e00434
EP  - e00417
VL  - 5
AB  - Microbacterium foliorum strain 122 is a bacterial endophyte isolated from a Dactylis glomerata
AB  - plant growing in a natural oil seep soil located in Oil
AB  - Springs, Ontario, Canada. We present here a draft genome sequence of an
AB  - endophytic strain that has promising potential in hydrocarbon degradation and
AB  - plant growth promotion.
ER  -

TY  - JOUR
AU  - Lumactud, R.
AU  - Fulthorpe, R.
AU  - Sentchilo, V.
AU  - van der Meer, J.R.
TI  - Draft Genome Sequence of Plantibacterflavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site.
JO  - Genome Announcements
PY  - 2017
SP  - e00276
EP  - e00217
VL  - 5
AB  - Plantibacter flavus isolate 251 is a bacterial endophyte isolated from an Achillea millefolium
AB  - plant growing in a natural oil seep soil located in Oil
AB  - Springs, Ontario, Canada. We present here a draft genome sequence of an
AB  - infrequently reported genus Plantibacter, highlighting an endophytic lifestyle
AB  - and biotechnological potential.
ER  -

TY  - JOUR
AU  - Luna-Flores, C.H.
AU  - Nielsen, L.K.
AU  - Marcellin, E.
TI  - Genome Sequence of Propionibacterium acidipropionici ATCC 55737.
JO  - Genome Announcements
PY  - 2016
SP  - e00248
EP  - e00216
VL  - 4
AB  - Propionibacterium acidipropionici produces propionic acid as its main fermentation product.
AB  - Traditionally derived from fossil fuels, environmental and
AB  - sustainable issues have revived the interest in producing propionic acid using
AB  - biological resources. Here, we present the closed sequence of Propionibacterium
AB  - acidipropionici ATCC 55737, an efficient propionic acid producer.
ER  -

TY  - JOUR
AU  - Luna-Flores, C.H.
AU  - Palfreyman, R.W.
AU  - Kromer, J.O.
AU  - Nielsen, L.K.
AU  - Marcellin, E.
TI  - Improved production of propionic acid using genome shuffling.
JO  - Biotechnol. J.
PY  - 2017
SP  - 0
EP  - 0
VL  - 12
AB  - Traditionally derived from fossil fuels, biological production of propionic acid
AB  - has recently gained interest. Propionibacterium species produce propionic acid as
AB  - their main fermentation product. Production of other organic acids reduces
AB  - propionic acid yield and productivity, pointing to by-products gene-knockout
AB  - strategies as a logical solution to increase yield. However, removing by-product
AB  - formation has seen limited success due to our inability to genetically engineer
AB  - the best producing strains (i.e. Propionibacterium acidipropionici). To overcome
AB  - this limitation, random mutagenesis continues to be the best path towards
AB  - improving strains for biological propionic acid production. Recent advances in
AB  - next generation sequencing opened new avenues to understand improved strains. In
AB  - this work, we use genome shuffling on two wild type strains to generate a better
AB  - propionic acid producing strain. Using next generation sequencing, we mapped the
AB  - genomic changes leading to the improved phenotype. The best strain produced 25%
AB  - more propionic acid than the wild type strain. Sequencing of the strains showed
AB  - that genomic changes were restricted to single point mutations and gene
AB  - duplications in well-conserved regions in the genomes. Such results confirm the
AB  - involvement of gene conversion in genome shuffling as opposed to long genomic
AB  - insertions.
ER  -

TY  - JOUR
AU  - Lund, L.C.
AU  - Sydenham, T.V.
AU  - Hogh, S.V.
AU  - Skov, M.
AU  - Kemp, M.
AU  - Justesen, U.S.
TI  - Draft Genome Sequence of 'Terrisporobacter othiniensis' Isolated from a Blood Culture from a Human Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e00042
EP  - e00015
VL  - 3
AB  - 'Terrisporobacter othiniensis' (proposed species) was isolated from a blood culture. Genomic
AB  - DNA was sequenced using a MiSeq benchtop sequencer (Illumina)
AB  - and assembled using the SPAdes genome assembler. This resulted in a draft genome
AB  - sequence comprising 3,980,019 bp in 167 contigs containing 3,449 coding
AB  - sequences, 7 rRNAs, and 58 tRNAs.
ER  -

TY  - JOUR
AU  - Lundin, A.
AU  - Bjorkholm, B.
AU  - Kupershmidt, I.
AU  - Unemo, M.
AU  - Nilsson, P.
AU  - Andersson, D.I.
AU  - Engstrand, L.
TI  - Slow genetic divergence of Helicobacter pylori strains during long-term colonization.
JO  - Infect. Immun.
PY  - 2005
SP  - 4818
EP  - 4822
VL  - 73
AB  - The genetic variability of Helicobacter pylori is known to be high compared to that of many
AB  - other bacterial species. H. pylori is adapted to
AB  - the human stomach, where it persists for decades, and adaptation to each
AB  - host results in every individual harboring a distinctive bacterial
AB  - population. Although clonal variants may exist within such a population,
AB  - all isolates are generally genetically related and thus derived from a
AB  - common ancestor. We sought to determine the rate of genetic change of H.
AB  - pylori over 9 years in two asymptomatic adult patients. Arbitrary primed
AB  - PCR confirmed the relatedness of individual subclones within a patient.
AB  - Furthermore, sequencing of 10 loci ( approximately 6,000 bp) in three
AB  - subclones per time and patient revealed only two base pair changes among
AB  - the subclones from patient I. All sequences were identical among the
AB  - patient II subclones. However, PCR amplification of the highly divergent
AB  - gene amiA revealed great variation in the size of the gene between the
AB  - subclones within each patient. Thus, both patients harbored a single
AB  - strain with clonal variants at both times. We also studied genetic changes
AB  - in culture- and mouse-passaged strains, and under both conditions no
AB  - genetic divergence was found. These results suggest that previous
AB  - estimates of the rate of genetic change in H. pylori within an individual
AB  - might be overestimates.
ER  -

TY  - JOUR
AU  - Lunnen, K.D.
AU  - Barsomian, J.M.
AU  - Camp, R.R.
AU  - Card, C.O.
AU  - Chen, S.-Z.
AU  - Croft, R.
AU  - Looney, M.C.
AU  - Meda, M.M.
AU  - Moran, L.S.
AU  - Nwankwo, D.O.
AU  - Slatko, B.E.
AU  - Van Cott, E.M.
AU  - Wilson, G.G.
TI  - Cloning Type II restriction and modification genes.
JO  - Gene
PY  - 1988
SP  - 25
EP  - 32
VL  - 74
AB  - We have cloned into Escherichia coli the genes for 38 type-II bacterial
AB  - modification methyltransferases.  The clones were isolated by selecting in
AB  - vitro for protectively modified recombinants.  Most of the clones modify their
AB  - DNA fully but a substantial number modify only partially.  In approximately
AB  - one-half of the clones, the genes for the corresponding endonucleases are also
AB  - present.  Some of these clones restrict infecting phages and others do not.
AB  - Clones carrying endonuclease genes but lacking methyltransferase genes have
AB  - been found, in several instances, to be viable.
ER  -

TY  - JOUR
AU  - Lunnen, K.D.
AU  - Morgan, R.D.
AU  - Timan, C.J.
AU  - Krzycki, J.A.
AU  - Reeve, J.N.
AU  - Wilson, G.G.
TI  - Characterization and cloning of MwoI (GCN7GC), a new type-II restriction-modification system from Methanobacterium wolfei.
JO  - Gene
PY  - 1989
SP  - 11
EP  - 19
VL  - 77
AB  - R.MwoI, a type-II restriction enzyme with the new specificity 5'-GCN7GC-3', was
AB  - found in extracts of the thermophilic archaebacterium, Methanobacterium wolfei.
AB  - R.MwoI cleaves duplex DNA producing fragments with 3-nt, 3'-terminal
AB  - extensions, thus: GCN5/N2GC.  The genes coding for the MwoI restriction and
AB  - modification enzymes were cloned into Escherichia coli on the plasmid vector
AB  - pBR322.  The clones synthesize a low level of R.MwoI endonuclease.  The
AB  - plasmids display incomplete MwoI-specific modification, suggesting that the
AB  - clones synthesize a low level of the M.MwoI methyltransferases, too.
ER  -

TY  - JOUR
AU  - Luo, C.
AU  - Walk, S.T.
AU  - Gordon, D.M.
AU  - Feldgarden, M.
AU  - Tiedje, J.M.
AU  - Konstantinidis, K.T.
TI  - Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 7200
EP  - 7205
VL  - 108
AB  - Defining bacterial species remains a challenging problem even for the model
AB  - bacterium Escherichia coli and has major practical consequences for reliable
AB  - diagnosis of infectious disease agents and regulations for transport and
AB  - possession of organisms of economic importance. E. coli traditionally is thought
AB  - to live within the gastrointestinal tract of humans and other warm-blooded
AB  - animals and not to survive for extended periods outside its host; this
AB  - understanding is the basis for its widespread use as a fecal contamination
AB  - indicator. Here, we report the genome sequences of nine environmentally adapted
AB  - strains that are phenotypically and taxonomically indistinguishable from typical
AB  - E. coli (commensal or pathogenic). We find, however, that the commensal genomes
AB  - encode for more functions that are important for fitness in the human gut, do not
AB  - exchange genetic material with their environmental counterparts, and hence do not
AB  - evolve according to the recently proposed fragmented speciation model. These
AB  - findings are consistent with a more stringent and ecologic definition for
AB  - bacterial species than the current definition and provide means to start
AB  - replacing traditional approaches of defining distinctive phenotypes for new
AB  - species with omics-based procedures. They also have important implications for
AB  - reliable diagnosis and regulation of pathogenic E. coli and for the coliform
AB  - cell-counting test.
ER  -

TY  - JOUR
AU  - Luo, F.
AU  - Zou, Y.
AU  - Huang, T.
AU  - Lin, S.
TI  - Draft Genome Sequence of Streptomyces sp. B9173, a Producer of Indole Diketopiperazine Maremycins.
JO  - Genome Announcements
PY  - 2017
SP  - e00447
EP  - e00417
VL  - 5
AB  - Streptomyces sp. B9173 is a producer of maremycins, a group of naturally occurring
AB  - 2,5-diketopiperazines. Here, we report the draft genome sequence of
AB  - Streptomyces sp. B9173, which comprises ~8.77 Mb, with a G+C content of 71.8%.
ER  -

TY  - JOUR
AU  - Luo, G.Z.
AU  - Wang, F.
AU  - Weng, X.
AU  - Chen, K.
AU  - Hao, Z.
AU  - Yu, M.
AU  - Deng, X.
AU  - Liu, J.
AU  - He, C.
TI  - Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing.
JO  - Nat. Commun.
PY  - 2016
SP  - 11301
EP  - 11301
VL  - 7
AB  - Although extensively studied in prokaryotes, the prevalence and significance of DNA
AB  - N6-methyladenine (6mA or m6dA) in eukaryotes had been underappreciated until
AB  - recent studies, which have demonstrated that 6mA regulates gene expression as a
AB  - potential heritable mark. To interrogate 6mA sites at single-base resolution, we
AB  - report DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an approach that
AB  - uses DpnI to cleave methylated adenine sites in duplex DNA. We find that DpnI
AB  - cuts other sequence motifs besides the canonical GATC restriction sites, thereby
AB  - expanding the utility of this method. DA-6mA-seq achieves higher sensitivity with
AB  - nanograms of input DNA and lower sequencing depth than conventional approaches.
AB  - We study 6mA at base resolution in the Chlamydomonas genome and apply the new
AB  - method to two other eukaryotic organisms, Plasmodium and Penicillium. Combined
AB  - with conventional approaches, our method further shows that most 6mA sites are
AB  - fully methylated on both strands of DNA at various sequence contexts.
ER  -

TY  - JOUR
AU  - Luo, J.
AU  - Bruice, T.C.
TI  - Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 16194
EP  - 16198
VL  - 102
AB  - The results of normal-mode analyses are in accord with the proposal that a low-frequency
AB  - motion of the HhaI methyltransferase enzyme is responsible for base flipping in bound DNA. The
AB  - vectors of the low-frequency normal mode of residues Ser-85 and Ile-86 point directly to the
AB  - phosphate and ribose moieties of the DNA backbone near the target base in position to rotate
AB  - the dihedral angles and flip the base out of the DNA duplex. The vector of residue Gln-237 on
AB  - the major groove is in the proper orientation to assist base separation. Our results favor the
AB  - major groove pathway and the protein active process in base flipping.
ER  -

TY  - JOUR
AU  - Luo, W.Y.
AU  - Tu, A.H.T.
AU  - Cao, Z.H.
AU  - Yu, H.L.
AU  - Dybvig, K.
TI  - Identification of an isoschizomer of the HhaI DNA methyltransferase in Mycoplasma arthritidis.
JO  - FEMS Microbiol. Lett.
PY  - 2009
SP  - 195
EP  - 198
VL  - 290
AB  - The genome of Mycoplasma arthritidis strain 158 has modified cytosine residues at AGCT
AB  - sequences that render the DNA resistant to digestion
AB  - with the AluI restriction endonuclease. The DNA methyltransferase
AB  - responsible for the base modification has previously been designated
AB  - MarI. From the complete genome sequence of M. arthritidis, we identify
AB  - Marth orf138 as a candidate marI gene. Marth orf138 was cloned in
AB  - Escherichia coli and its TGA codons converted to TGG. DNA isolated from
AB  - E. coli cells expressing the modified Marth orf138 gene was degraded by
AB  - the AluI nuclease, indicating that Marth orf138 does not code for MarI.
AB  - However, the DNA from E. coli was found to have acquired resistance to
AB  - the restriction endonuclease HhaI. Genomic DNA from M. arthritidis was
AB  - also found to be resistant to HhaI (recognizes GCGC). The M.
AB  - arthritidis isoschizomer of the HhaI DNA methyltransferase, coded by
AB  - Marth orf138, is designated MarII. Transformation of M. arthritidis was
AB  - not significantly affected by modification of plasmid at HhaI sites,
AB  - indicating that the mycoplasma lacks a restriction endonuclease that
AB  - recognizes GCGC sites.
ER  -

TY  - JOUR
AU  - Luo, X.
AU  - Wan, C.
AU  - Zhang, L.
TI  - Draft Genome Sequence of Streptomyces mutabilis TRM45540, Isolated from a Hypersaline Soil Sample.
JO  - Genome Announcements
PY  - 2015
SP  - e01465
EP  - e01415
VL  - 3
AB  - We report here the draft genome sequence of Streptomyces mutabilis TRM45540, a strain isolated
AB  - from a soil sample from Xinjiang, China. Analysis of the genome
AB  - using the bioinformatics tool antiSMASH showed the presence of many unique
AB  - natural-product biosynthetic pathways.
ER  -

TY  - JOUR
AU  - Luo, Y.
AU  - Kong, Q.
AU  - Yang, J.
AU  - Golden, G.
AU  - Wanda, S.Y.
AU  - Jensen, R.V.
AU  - Ernst, P.B.
AU  - Curtiss, R.I.I.I.
TI  - Complete Genome Sequence of the Universal Killer, Salmonella enterica serovar Typhimurium UK-1 (ATCC 68169).
JO  - J. Bacteriol.
PY  - 2011
SP  - 4035
EP  - 4036
VL  - 193
AB  - The Salmonella enterica serovar Typhimurium strain UK-1 presents the highest invasion and
AB  - virulence attributes among the most frequently
AB  - studied strains. S. Typhimurium UK-1 has been used as the foundation for
AB  - developing recombinant vaccines and been extensively used on virulence and
AB  - colonization studies in chickens and mice. We describe here the complete
AB  - genome sequence of S. Typhimurium UK-1. Comparative genomics of Salmonella
AB  - Typhimurium will provide insight into factors that determine virulence and
AB  - invasion.
ER  -

TY  - JOUR
AU  - Luo, Y.
AU  - Wang, C.
AU  - Allard, S.
AU  - Strain, E.
AU  - Allard, M.W.
AU  - Brown, E.W.
AU  - Zheng, J.
TI  - Draft Genome Sequences of Paenibacillus alvei A6-6i and TS-15.
JO  - Genome Announcements
PY  - 2013
SP  - e00673
EP  - e00613
VL  - 1
AB  - Here, we report draft genomes of Paenibacillus alvei strains A6-6i and TS-15, which were
AB  - isolated, respectively, from plant material and soil in the Virginia
AB  - Eastern Shore (VES) tomato growing area. An array of genes related to
AB  - antimicrobial biosynthetic pathways have been identified with whole-genome
AB  - analyses of these strains.
ER  -

TY  - JOUR
AU  - Luo, Y.
AU  - Xu, X.
AU  - Ding, Z.
AU  - Liu, Z.
AU  - Zhang, B.
AU  - Yan, Z.
AU  - Sun, J.
AU  - Hu, S.
AU  - Hu, X.
TI  - Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line  K562.
JO  - BMC Genomics
PY  - 2008
SP  - 386
EP  - 386
VL  - 9
AB  - BACKGROUND: Phenylobacterium zucineum is a recently identified facultative intracellular
AB  - species isolated from the human leukemia cell line K562.
AB  - Unlike the known intracellular pathogens, P. zucineum maintains a stable
AB  - association with its host cell without affecting the growth and morphology
AB  - of the latter. RESULTS: Here, we report the whole genome sequence of the
AB  - type strain HLK1T. The genome consists of a circular chromosome (3,996,255
AB  - bp) and a circular plasmid (382,976 bp). It encodes 3,861 putative
AB  - proteins, 42 tRNAs, and a 16S-23S-5S rRNA operon. Comparative genomic
AB  - analysis revealed that it is phylogenetically closest to Caulobacter
AB  - crescentus, a model species for cell cycle research. Notably, P. zucineum
AB  - has a gene that is strikingly similar, both structurally and functionally,
AB  - to the cell cycle master regulator CtrA of C. crescentus, and most of the
AB  - genes directly regulated by CtrA in the latter have orthologs in the
AB  - former. CONCLUSION: This work presents the first complete bacterial genome
AB  - in the genus Phenylobacterium. Comparative genomic analysis indicated that
AB  - the CtrA regulon is well conserved between C. crescentus and P. zucineum.
ER  -

TY  - JOUR
AU  - Luo, Y.R.
AU  - Kang, S.G.
AU  - Kim, S.J.
AU  - Kim, M.R.
AU  - Li, N.
AU  - Lee, J.H.
AU  - Kwon, K.K.
TI  - Genome Sequence of Benzo(a)pyrene-Degrading Bacterium Novosphingobium pentaromativorans US6-1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 907
EP  - 907
VL  - 194
AB  - Novosphingobium pentaromativorans US6-1 showed a good ability to degrade high-molecular-weight
AB  - polycyclic aromatic hydrocarbons. We report the
AB  - draft genome sequence of strain US6-1, which contains a main chromosome
AB  - (5,096,413 bp, G+C content of 63.1%) and two plasmids (188,476 and 60,085
AB  - bp). The majority of the aromatic-hydrocarbon-degrading genes are encoded
AB  - in the larger plasmid.
ER  -

TY  - JOUR
AU  - Lupker, H.S.C.
AU  - Dekker, B.M.M.
TI  - Purification of the sequence-specific endonuclease SinI from Salmonella infantis.
JO  - Biochim. Biophys. Acta
PY  - 1981
SP  - 297
EP  - 299
VL  - 654
AB  - A sequence-specific endonuclease was isolated from a strain of Salmonella
AB  - infantis.  Its recognition sequence proved to be identical to that of
AB  - restriction endonuclease AvaII (an endonuclease from the blue-green alga
AB  - Anabaena variabilis), G^G(A/T)CC.
ER  -

TY  - JOUR
AU  - Luria, S.E.
TI  - Host-induced modifications of viruses.
JO  - Cold Spring Harb. Symp. Quant. Biol.
PY  - 1953
SP  - 237
EP  - 244
VL  - 18
AB  - Viruses exhibit extensive adaptability to growth in various hosts or tissues.
AB  - It was widely held in the past that virus adaptability reflected a peculiar
AB  - plasticity of virus heredity, which allowed it to be directly influenced by its
AB  - host cells.  The alternative interpretation of virus adaptation to new host
AB  - cells as due to spontaneous mutations, which provide a range of genotypes for
AB  - the new hosts to select from, always had authoritative proponents (see Findlay,
AB  - 1939).  This viewpoint finally gained wide recognition (see Burnet, 1946),
AB  - partly as a consequence of the development of phage genetics and of the
AB  - interpenetration of various branches of virology.  It is now recognized that
AB  - most variation in virus properties is caused by viral mutations, and that virus
AB  - plasticity results from the variety of genotypes present in the large viral
AB  - populations.  It was, therefore, an unexpected development when a new type of
AB  - virus variation was discovered in bacteriophages.  This has been called
AB  - host-induced or host-controlled variation (Luria and Human, 1952; Ralston and
AB  - Krueger, 1952; Anderson and Felix, 1952; Bertani and Weigle, 1953).  Its
AB  - outstanding characteristics are that is is strictly phenotypic, non-hereditary,
AB  - and that it is determined by the host cell in which a virus has been produced.
AB  - In this paper, I shall summarize the features of this phenomenon; I shall
AB  - compare it with other instances of nonhereditary phage variation; and I shall
AB  - attempt to assess its possible bearing on certain problems in other areas of
AB  - virology.
ER  -

TY  - JOUR
AU  - Luria, S.E.
TI  - The recognition of DNA in Bacteria.
JO  - Sci. Am.
PY  - 1970
SP  - 88
EP  - 102
VL  - 222
AB  - Some bacteria have enzyme systems that scan invading DNA molecules injected by
AB  - viruses and break them unless they are chemically marked at specific
AB  - recognition sites.
ER  -

TY  - JOUR
AU  - Luria, S.E.
AU  - Human, M.L.
TI  - A nonhereditary, host-induced variation of bacterial viruses.
JO  - J. Bacteriol.
PY  - 1952
SP  - 557
EP  - 569
VL  - 64
AB  - One of virology's most generally valid rules is that the properties of virus particles are
AB  - unaffected by the host in which they grow.  Host adaptation and tissue adaptation, the
AB  - apparent exceptions, are explained today by selective reproduction of virus mutants in new
AB  - hosts or in new tissues.  In analyzing the relation between certain phages and certain mutants
AB  - of their bacterial hosts, we have encountered a novel situation: the genotype of the host in
AB  - which a virus reproduces affects the phenotype of the new virus.  The phenotypic change
AB  - suppresses the ability of the virus to reproduce in certain hosts but not in others.  It is a
AB  - transient change, in the sense that one cycle of growth in a suitable host returns the virus
AB  - to its original form.  Both the growth ability of the modified virus and, in some cases, its
AB  - production from normal virus are controlled in part by the physiological state of the host
AB  - cell.  The present paper describes these findings and discusses their general implications.
AB  - Other instances of host-controlled phenotypic changes in bacteriophages have recently been
AB  - discovered (Bertani and Weigle, 1952).
ER  -

TY  - JOUR
AU  - Lushnikov, A.Y.
AU  - Potaman, V.N.
AU  - Oussatcheva, E.A.
AU  - Sinden, R.R.
AU  - Lyubchenko, Y.L.
TI  - DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis.
JO  - Biochemistry
PY  - 2006
SP  - 152
EP  - 158
VL  - 45
AB  - The SfiI restriction enzyme binds to DNA as a tetramer holding two usually distant DNA
AB  - recognition sites together before cleavage of the four DNA strands. To elucidate structural
AB  - properties of the SfiI-DNA complex, atomic force microscopy (AFM) imaging of the complexes
AB  - under noncleaving conditions (Ca2+ instead of Mg2+ in the reaction buffer) was performed.
AB  - Intramolecular complexes formed by protein interaction between two binding sites in one DNA
AB  - molecule (cis interaction) as well as complexes formed by the interaction of two sites in
AB  - different molecules (trans interaction) were analyzed. Complexes were identified unambiguously
AB  - by the presence of a tall spherical blob at the DNA intersections. To characterize the path of
AB  - DNA within the complex, the angles between the DNA helices in the proximity of the complex
AB  - were systematically analyzed. All the data show clear-cut bimodal distributions centered
AB  - around peak values corresponding to 60 degrees and 120 degrees. To unambiguously distinguish
AB  - between the crossed and bent models for the DNA orientation within the complex, DNA molecules
AB  - with different arm lengths flanking the SfiI binding site were designed. The analysis of the
AB  - AFM images for complexes of this type led to the conclusion that the DNA recognition sites
AB  - within the complex are crossed. The angles of 60 degrees or 120 degrees between the DNA
AB  - helices correspond to a complex in which one of the helices is flipped with respect to the
AB  - orientation of the other. Complexes formed by five different recognition sequences
AB  - (5'-GGCCNNNNNGGCC-3'), with different central base pairs, were also analyzed. Our results
AB  - showed that complexes containing the two possible orientations of the helices were formed
AB  - almost equally. This suggests no preferential orientation of the DNA cognate site within the
AB  - complex, suggesting that the central part of the DNA binding site does not form strong
AB  - sequence specific contacts with the protein.
ER  -

TY  - JOUR
AU  - Lusk, B.G.
AU  - Badalamenti, J.P.
AU  - Parameswaran, P.
AU  - Bond, D.R.
AU  - Torres, C.I.
TI  - Draft Genome Sequence of the Gram-Positive Thermophilic Iron Reducer Thermincola  ferriacetica Strain Z-0001T.
JO  - Genome Announcements
PY  - 2015
SP  - e01072
EP  - e01015
VL  - 3
AB  - A 3.19-Mbp draft genome of the Gram-positive thermophilic iron-reducing Firmicutes isolate
AB  - from the Peptococcaceae family, Thermincola ferriacetica Z-0001, was assembled at ~100x
AB  - coverage from 100-bp paired-end Illumina reads. The draft genome contains 3,274 predicted
AB  - genes (3,187 protein coding genes) and  putative multiheme c-type cytochromes.
ER  -

TY  - JOUR
AU  - Luthje, F.L.
AU  - Hasman, H.
AU  - Aarestrup, F.M.
AU  - Alwathnani, H.A.
AU  - Rensing, C.
TI  - Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs.
JO  - Genome Announcements
PY  - 2014
SP  - e01341
EP  - e01314
VL  - 2
AB  - The draft genome sequences of two copper-resistant Escherichia coli strains were  determined.
AB  - These had been isolated from copper-fed pigs and contained additional
AB  - putative operons conferring copper and other metal and metalloid resistances.
ER  -

TY  - JOUR
AU  - Lutsenko, E.
AU  - Bhagwat, A.S.
TI  - Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells.  A model, its experimental support and implications.
JO  - Mutat. Res.
PY  - 1999
SP  - 11
EP  - 20
VL  - 437
AB  - In Escherichia coli and human cells, many sites of cytosine methylation in DNA are hot spots
AB  - for C to T mutations. It is generally believed that T.G mismatches created by the hydrolytic
AB  - deamination of 5-methylcytosines (5meC) are intermediates in the mutagenic pathway. A number
AB  - of hypotheses have been proposed regarding the source of the mispaired thymine and how the
AB  - cells deal with the mispairs. We have constructed a genetic reversion assay that utilizes a
AB  - gene on a mini-F to compare the frequency of occurrence of C to T mutations in different
AB  - genetic backgrounds in exponentially growing E. coli. The results identify at least two causes
AB  - for the hot spot at a 5meC: (1) the higher rate of deamination of 5meC compared to C generates
AB  - more T.G than uracil.G (U.G) mismatches, and (2) inefficient repair of T.G mismatches by the
AB  - very short-patch (VSP) repair system compared to the repair of U. G mismatches by the
AB  - uracil-DNA glycosylase (Ung). This combination of increased DNA damage when the cytosines are
AB  - methylated coupled with the relative inefficiency in the post-replicative repair of T.G
AB  - mismatches can be quantitatively modeled to explain the occurrence of the hot spot at 5meC.
AB  - This model has implications for mutational hot and cold spots in all organisms.
ER  -

TY  - JOUR
AU  - Lutz, C.
AU  - Martin, T.Q.X.
AU  - Sun, S.
AU  - McDougald, D.
TI  - Draft Genome Sequence of Shewanella sp. Strain CP20.
JO  - Genome Announcements
PY  - 2015
SP  - e00256
EP  - e00215
VL  - 3
AB  - Shewanella sp. CP20 is a marine bacterium that survives ingestion by Tetrahymena  pyriformis
AB  - and is expelled from the protozoan within membrane-bound vacuoles,
AB  - where the bacterial cells show long-term survival. Here, we report the draft
AB  - genome sequence of Shewanella sp. CP20 and discuss the potential mechanisms
AB  - facilitating intraprotozoan survival.
ER  -

TY  - JOUR
AU  - Lux, T.M.
AU  - Lee, R.
AU  - Love, J.
TI  - Complete Genome Sequence of a Free-Living Vibrio furnissii sp. nov. Strain (NCTC 11218).
JO  - J. Bacteriol.
PY  - 2011
SP  - 1487
EP  - 1488
VL  - 193
AB  - The Vibrionales are widespread, free-living, Gram-negative proteobacteria that have been
AB  - linked to pathogenicity in animals and gastroenteric infection in humans.  We report the
AB  - annotated genome sequence of a free-living strain of Vibrio furnissii (NCTC 11218) harvested
AB  - from an estuarine environment.  It consists of two circular chromosomes (3.2 Mb and 1.6 Mb)
AB  - and reveals novel genes likely to be involved in pathogenicity.
ER  -

TY  - JOUR
AU  - Lv, R.
AU  - Yang, X.
AU  - Fang, N.
AU  - Song, Y.
AU  - Luo, X.
AU  - Guo, J.
AU  - Peng, F.
AU  - Yang, R.
AU  - Cui, Y.
AU  - Fang, C.
AU  - Song, Y.
TI  - Draft Genome Sequence of 'Paramesorhizobium deserti' A-3-ET, a Strain Highly Resistant to Diverse beta-Lactam Antibiotics.
JO  - Genome Announcements
PY  - 2016
SP  - e00311
EP  - e00316
VL  - 4
AB  - Here, we report the draft genome sequence of 'Paramesorhizobium deserti' A-3-E(T), a strain
AB  - isolated from the Taklimakan Desert of Xinjiang, China, which
AB  - is resistant to multiple beta-lactam antibiotics and other antibiotics
AB  - (kanamycin, erythromycin, streptomycin, etc.) as well.
ER  -

TY  - JOUR
AU  - Lv, Y.
AU  - Liao, J.
AU  - Wu, Z.
AU  - Han, S.
AU  - Lin, Y.
AU  - Zheng, S.
TI  - Genome Sequence of Corynebacterium glutamicum ATCC 14067, Which Provides Insight into Amino Acid Biosynthesis in Coryneform Bacteria.
JO  - J. Bacteriol.
PY  - 2012
SP  - 742
EP  - 743
VL  - 194
AB  - We report the genome sequence of Corynebacterium glutamicum ATCC 14067 (once named
AB  - Brevibacterium flavum), which is useful for taxonomy research
AB  - and further molecular breeding in amino acid production. Preliminary
AB  - comparison with those of the reported coryneform strains revealed some
AB  - notable differences that might be related to the difficulties in molecular
AB  - manipulation.
ER  -

TY  - JOUR
AU  - Lv, Y.
AU  - Wu, Z.
AU  - Han, S.
AU  - Lin, Y.
AU  - Zheng, S.
TI  - Genome Sequence of Corynebacterium glutamicum S9114, a Strain for Industrial Production of Glutamate.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6096
EP  - 6097
VL  - 193
AB  - Here we report the genome sequence of Corynebacterium glutamicum S9114, an industrial producer
AB  - widely used in production of glutamate in China.
AB  - Preliminary comparison with the sequences of the Corynebacterium
AB  - glutamicum strains ATCC 13032 and R revealed some notable mutagenesis that
AB  - might be related to the high yield of glutamate.
ER  -

TY  - JOUR
AU  - Ly, L.K.
AU  - Underwood, G.E.
AU  - McCully, L.M.
AU  - Bitzer, A.S.
AU  - Godino, A.
AU  - Bucci, V.
AU  - Brigham, C.J.
AU  - Principe, A.
AU  - Fischer, S.E.
AU  - Silby, M.W.
TI  - Draft Genome Sequences of Pseudomonas fluorescens Strains SF39a and SF4c, Potential Plant Growth Promotion and Biocontrol Agents.
JO  - Genome Announcements
PY  - 2015
SP  - e00219
EP  - e00215
VL  - 3
AB  - Pseudomonas fluorescens SF4c and SF39a, strains isolated from wheat rhizosphere,  have
AB  - potential applications in plant growth promotion and biocontrol of fungal
AB  - diseases of crop plants. We report the draft genome sequences of SF4c and SF39a
AB  - with estimated sizes of 6.5 Mb and 5.9 Mb, respectively.
ER  -

TY  - JOUR
AU  - Lycksell, P.O.
AU  - Graslund, A.
AU  - Claesens, F.
AU  - McLaughlin, L.W.
AU  - Larsson, U.
AU  - Rigler, R.
TI  - Base pair opening dynamics of a 2-aminopurine substituted EcoRI restriction sequence and its unsubstituted counterpart in oligonucleotides.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 9011
EP  - 9025
VL  - 15
AB  - Studies of 1H NMR selective recovery were performed to determine the imino
AB  - proton exchange with solvent water of the base pairs in the EcoRI endonuclease
AB  - recognition sequence GAATTC, placed at the center of self-complementary decamer
AB  - and dodecamer oligonucleotides.  In one oligonucleotide the innermost adenine
AB  - was replaced by the fluorescent base analogue 2-aminopurine (2AP).  From the
AB  - measurements at different concentrations of TRIS buffer acting as proton
AB  - exchange catalyst, base pair lifetimes were evaluated.  The results at 25C show
AB  - that the AT base pairs have lifetimes of the order of a few ms, whereas the
AB  - surrounding GC base pairs in a dodecamer have lifetimes of about 100 ms.  The
AB  - (2AP)T base pair has a shorter lifetime than the corresponding AT base pair.
AB  - The temperature dependent optical absorption, and for the 2AP containing
AB  - oligonucleotide fluorescence, were used to study the single strand-duplex
AB  - equilibrium of the decamers.  The results indicate that NMR and the optical
AB  - techniques, although applied at very different concentrations, monitor the same
AB  - conformational transition of the oligonucleotide.
ER  -

TY  - JOUR
AU  - Lykidis, A.
AU  - Mavromatis, K.
AU  - Ivanova, N.
AU  - Anderson, I.
AU  - Land, M.
AU  - DiBartolo, G.
AU  - Martinez, M.
AU  - Lapidus, A.
AU  - Lucas, S.
AU  - Copeland, A.
AU  - Richardson, P.
AU  - Wilson, D.B.
AU  - Kyrpides, N.
TI  - Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX.
JO  - J. Bacteriol.
PY  - 2007
SP  - 2477
EP  - 2486
VL  - 189
AB  - Thermobifida fusca is a moderately thermophilic soil bacterium that belongs to Actinobacteria.
AB  - It is a major degrader of plant cell walls and
AB  - has been used as a model organism for the study of secreted, thermostable
AB  - cellulases. The complete genome sequence showed that T. fusca has a single
AB  - circular chromosome of 3,642,249 bp predicted to encode 3,117 proteins and
AB  - 65 RNA species with a coding density of 85%. Genome analysis revealed the
AB  - existence of 29 putative glycoside hydrolases in addition to the
AB  - previously identified cellulases and xylanases. The glycosyl hydrolases
AB  - include enzymes predicted to exhibit mainly dextran/starch- and
AB  - xylan-degrading functions. T. fusca possesses two protein secretion
AB  - systems: the sec general secretion system and the twin-arginine
AB  - translocation system. Several of the secreted cellulases have sequence
AB  - signatures indicating their secretion may be mediated by the twin-arginine
AB  - translocation system. T. fusca has extensive transport systems for import
AB  - of carbohydrates coupled to transcriptional regulators controlling the
AB  - expression of the transporters and glycosylhydrolases. In addition to
AB  - providing an overview of the physiology of a soil actinomycete, this study
AB  - presents insights on the transcriptional regulation and secretion of
AB  - cellulases which may facilitate the industrial exploitation of these
AB  - systems.
ER  -

TY  - JOUR
AU  - Lykke-Andersen, J.
AU  - Garrett, R.A.
AU  - Kjems, J.
TI  - Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 3982
EP  - 3989
VL  - 24
AB  - The archaeal intron-encoded homing enzymes I-PorI and I-DmoI belong to a family of
AB  - endonucleases that contain two copies of a characteristic LAGLIDADG motif.  These
AB  - endonucleases cleave their intron- or intein- alleles site-specifically, and thereby
AB  - facilitate homing of the introns or inteins which encode them.  The protein structure and the
AB  - mechanism of DNA recognition of these homing enzymes is largely unknown.  Therefore, we
AB  - examined these properties of I-PorI and I-DmoI by protein footprinting.  Both proteins were
AB  - susceptible to proteolytic cleavage within regions that are equidistant from each of the two
AB  - LAGLIDADG motifs.  When complexed with their DNA substrates, a characteristic subset of the
AB  - exposed sites, located in regions immediately after and 40-60 amino acids after each of the
AB  - LAGLIDADG motifs, were protected.  Our data suggest that the enzymes are structured into two,
AB  - tandemly repeated, domains, each containing both the LAGLIDADG motif and two putative DNA
AB  - binding regions.  The latter contains a potentially novel DNA binding motif conserved in
AB  - archaeal homing enzymes.  The results are consistent with a model where the LAGLIDADG
AB  - endonucleases bind to their non-palindromic substrates as monomeric enzymes, with each of the
AB  - two domains recognizing one half of the DNA substrate.
ER  -

TY  - JOUR
AU  - Lykke-Andersen, J.
AU  - Garrett, R.A.
AU  - Kjems, J.
TI  - Mapping metal ions at the catalytic centres of two intron-encoded endonucleases.
JO  - EMBO J.
PY  - 1997
SP  - 3272
EP  - 3281
VL  - 16
AB  - Divalent metal ions play a crucial role in forming the catalytic centres of DNA endonucleases.
AB  - Substitution of Mg2+ ions by Fe2+ ions in two archaeal intron-encoded homing endonucleases,
AB  - I-DmoI and I-PorI, yielded functional enzymes and enabled the generation of reactive hydroxyl
AB  - radicals within the metal ion binding sites.  Specific hydroxyl radical-induced cleavage was
AB  - observed within, and immediately after, two conserved LAGLIDADG motifs in both proteins and at
AB  - sites at, and near, the scissile phosphates of the corresponding DNA substrates.  Titration of
AB  - Fe2+-containing protein-DNA complexes with Ca2+ ions, which are unable to support
AB  - endonucleolytic activity, was performed to distinguish between the individual metal ions in
AB  - the complex.  Mutations of single amino acids in this region impaired catalytic activity and
AB  - caused the preferential loss of a subset of hydroxyl radical cleavages in both the protein and
AB  - the DNA substrate, suggesting an active role in metal ion coordination for these amino acids.
AB  - The data indicate that the endonucleases cleave their DNA substrates as monomeric enzymes, and
AB  - contain a minimum of four divalent metal ions located at or near the catalytic centres of each
AB  - endonuclease.  The metal ions involved in cleaving the coding and the non-coding strand are
AB  - positioned immediately after the N- and C-terminally located LAGLIDADG motifs, respectively.
AB  - The dual protein/nucleic acid footprinting approach described here is generally applicable to
AB  - other protein-nucleic acid complexes when the natural metal ion can be replaced by Fe2+.
ER  -

TY  - JOUR
AU  - Lykke-Andersen, J.
AU  - Thi-Ngoc, H.P.
AU  - Garrett, R.A.
TI  - DNA substrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 4583
EP  - 4590
VL  - 22
AB  - The protein encoded by intron 1 of the single 23S rRNA gene of the archaeal hyperthermophile
AB  - Pyrobaculum organotrophum was isolated and shown to constitute a homing-type DNA endonuclease,
AB  - I-PorI. It cleaves the intron- 23S rDNA of the closely related organism Pyrobaculum islandicum
AB  - near the site of intron insertion in Pb. organotrophum. In contrast, no endonuclease activity
AB  - was detected for the protein product of intron 2 of the same gene of Pb. organotrophum which,
AB  - like I-PorI, carries the LAGLI-DADG motif, common to group I intron-encoded homing enzymes.
AB  - I-PorI cleaves optimally at 80oC, with kcat and km values of about 2 min-1 and 4 nM,
AB  - respectively, and generates four nucleotide 3'-overhangs and 5'-phosphates. It can cleave a
AB  - 25 base pair DNA fragment encompassing the intron insertion site. A mutation-selection study
AB  - established the base pair specificity of the endonuclease within a 17 bp region, from
AB  - positions -6 to +11 with respect to the intron-insertion site. Four of the essential base
AB  - pairs encode the sequence involved in the intron-exon interaction in the pre-rRNA that is
AB  - required for recognition by the RNA splicing enzymes. Properties of the enzyme are compared
AB  - and contrasted with those of eucaryotic homing endonucleases.
ER  -

TY  - JOUR
AU  - Lyko, F.
AU  - Brown, R.
TI  - DNA methyltransferase inhibitors and the development of epigenetic cancer therapies.
JO  - J. Natl. Cancer Inst.
PY  - 2005
SP  - 1498
EP  - 1506
VL  - 97
AB  - Epimutations, such as the hypermethylation and epigenetic silencing of tumor suppressor genes,
AB  - play a role in the etiology of human cancers.
AB  - In contrast to DNA mutations, which are passively inherited through DNA
AB  - replication, epimutations must be actively maintained because they are
AB  - reversible. In fact, the reversibility of epimutations by
AB  - small-molecule inhibitors provides the foundation for the use of such
AB  - inhibitors in novel cancer therapy strategies. Among the compounds that
AB  - inhibit epigenetic processes, the most extensively studied are DNA
AB  - methyltransferase inhibitors. In this review, we examine the literature
AB  - on DNA methyltransferase inhibitors and discuss the efficacy of such
AB  - compounds as antitumor agents, as evaluated in phase I-III clinical
AB  - trials. We also discuss future areas of research, including the
AB  - development of nonnucleoside inhibitors, the application of novel
AB  - bioanalytical tools for DNA methylation analysis (which will be
AB  - important for the clinical application of these compounds by allowing
AB  - rational approaches to trial design), the need to optimize treatment
AB  - schedules for maximal biologic effectiveness, and the need to define
AB  - molecular endpoints so that changes induced by demethylating drugs in
AB  - patients can be monitored during treatment. Assays for genome-wide and
AB  - tumor-specific DNA methylation also need to be further developed to
AB  - establish the pharmacodynamic parameters of DNA methyltransferase
AB  - inhibitors in patients and to provide rational approaches to maximizing
AB  - the therapeutic efficacy of these compounds.
ER  -

TY  - JOUR
AU  - Lyko, F.
AU  - Ramsahoye, B.H.
AU  - Jaenisch, R.
TI  - DNA methylation in Drosophila melanogaster.
JO  - Nature
PY  - 2000
SP  - 538
EP  - 540
VL  - 408
AB  - Certain cytosine residues of eukaryotic DNA are methylated in inactive regions of the genome.
AB  - For a long time the fruitfly Drosophila was thought to be an exception, but now the evidence
AB  - points to the existence of a functional DNA-methylation system in Drosophila as well.  Here we
AB  - show that DNA is methylated, but that Drosophila genomic methylation is restriction to the
AB  - early stages of development.
ER  -

TY  - JOUR
AU  - Lyko, F.
AU  - Ramsahoye, B.H.
AU  - Kashevsky, H.
AU  - Tudor, M.
AU  - Mastrangelo, M.A.
AU  - Orr-Weaver, T.L.
AU  - Jaenisch, R.
TI  - Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in drosophila.
JO  - Nat. Genet.
PY  - 1999
SP  - 363
EP  - 366
VL  - 23
AB  - CpG methylation is essential for mouse development as well as gene regulation and genome
AB  - stability. Many features of mammalian DNA methylation are consistent with the action of a de
AB  - novo methyltransferase that establishes methylation patterns during early development and the
AB  - post-replicative maintenance of these patterns by a maintenance methyltransferase. The mouse
AB  - methyltransferase Dnmt1 (encoded by Dnmt) shows a preference for hemimethylated substrates in
AB  - vitro, making the enzyme a candidate for a maintenance methyltransferase. Dnmt1 also has de
AB  - novo methylation activity in vitro, but the significance of this finding is unclear, because
AB  - mouse embryonic stem (ES) cells contain a de novo methylating activity unrelated to Dnmt1
AB  - (ref. 10). Recently, the Dnmt3 family of methyltransferases has been identified and shown in
AB  - vitro to catalyse de novo methylation. To analyse the function of these enzymes, we expressed
AB  - Dnmt and Dnmt3a in transgenic Drosophila melanogaster. The absence of endogenous methylation
AB  - in Drosophila facilitates detection of experimentally induced methylation changes. In this
AB  - system, Dnmt3a functioned as a de novo methyltransferase, whereas Dnmt1 had no detectable de
AB  - novo methylation activity. When co-expressed, Dnmt1 and Dnmt3a cooperated to establish and
AB  - maintain methylation patterns. Genomic DNA methylation impaired the viability of transgenic
AB  - flies, suggesting that cytosine methylation has functional consequences for Drosophila
AB  - development.
ER  -

TY  - JOUR
AU  - Lyko, F.
AU  - Whittaker, A.J.
AU  - Orr-Weaver, T.L.
AU  - Jaenisch, R.
TI  - The putative Drosophila methyltransferase gene dDnmt2 is contained in a transposon-like element and is expressed specifically in ovaries.
JO  - Mech. Dev.
PY  - 2000
SP  - 215
EP  - 217
VL  - 95
AB  - Several organisms, including Drosophila melanogaster, are apparently devoid of DNA
AB  - methylation. This might reflect a highly restricted activity of DNA methyltransferases, a loss
AB  - of methyltransferase activity during evolution or the dispensability of DNA methylation due to
AB  - an efficient substitute mechanism. Vestiges of a Drosophila DNA methylation system have been
AB  - identified recently. We show here that the putative DNA methyltransferase gene, dDnmt2, is the
AB  - component of a transposon-like element. This element also contains a second, novel open
AB  - reading frame with homologies to a yeast protein involved in RNA processing. Both open reading
AB  - frames are coordinately expressed and transcripts are present specifically in ovarian nurse
AB  - cells as well as during early stages of embryonic development.
ER  -

TY  - JOUR
AU  - Lylloff, J.E.
AU  - Hansen, L.B.
AU  - Jepsen, M.
AU  - Hallin, P.F.
AU  - Sorensen, S.J.
AU  - Stougaard, P.
AU  - Glaring, M.A.
TI  - Draft genome sequences of two protease-producing strains of arsukibacterium, isolated from two cold and alkaline environments.
JO  - Genome Announcements
PY  - 2015
SP  - e00585
EP  - e00515
VL  - 3
AB  - Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated
AB  - from two cold and alkaline environments as producers of
AB  - extracellular proteolytic enzymes active at high pH and low temperature. This
AB  - report describes the two draft genome sequences, which may serve as sources of
AB  - future industrial enzymes.
ER  -

TY  - JOUR
AU  - Lymperopoulou, D.S.
AU  - Coil, D.A.
AU  - Schichnes, D.
AU  - Lindow, S.E.
AU  - Jospin, G.
AU  - Eisen, J.A.
AU  - Adams, R.I.
TI  - Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62,  S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum  strain H39, Plan.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 17
EP  - 17
VL  - 12
AB  - We report here the draft genome sequences of eight bacterial strains of the genera
AB  - Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and
AB  - Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of
AB  - five residences in the San Francisco Bay area. Taxonomic classifications as well
AB  - as the genome sequence and gene annotation of the isolates are described. As part
AB  - of the 'Built Environment Reference Genome' project, these isolates and
AB  - associated genome data provide valuable resources for studying the microbiology
AB  - of the built environment.
ER  -

TY  - JOUR
AU  - Lynch, K.H.
AU  - Stothard, P.
AU  - Dennis, J.J.
TI  - Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex.
JO  - BMC Genomics
PY  - 2010
SP  - 599
EP  - 599
VL  - 11
AB  - Background: The Burkholderia cepacia complex (BCC) is comprised of at least seventeen
AB  - Gram-negative species that cause infections in cystic
AB  - fibrosis patients. Because BCC bacteria are broadly antibiotic
AB  - resistant, phage therapy is currently being investigated as a possible
AB  - alternative treatment for these infections. The purpose of our study
AB  - was to sequence and characterize three novel BCC-specific phages: KS5
AB  - (vB BceM-KS5 or vB BmuZ-ATCC 17616), KS14 (vB BceM-KS14) and KL3 (vB
AB  - BamM-KL3 or vB BceZ-CEP511).
AB  - Results: KS5, KS14 and KL3 are myoviruses with the A1 morphotype.
AB  - The genomes of these phages are between 32317 and 40555 base pairs in
AB  - length and are predicted to encode between 44 and 52 proteins. These
AB  - phages have over 50% of their proteins in common with enterobacteria
AB  - phage P2 and so can be classified as members of the Peduovirinae
AB  - subfamily and the 'P2-like viruses' genus. The BCC phage proteins
AB  - similar to those encoded by P2 are predominantly structural components
AB  - involved in virion morphogenesis. As prophages, KS5 and KL3 integrate
AB  - into an AMP nucleosidase gene and a threonine tRNA gene, respectively.
AB  - Unlike other P2-like viruses, the KS14 prophage is maintained as a
AB  - plasmid. The P2 E+E' translational frameshift site is conserved among
AB  - these three phages and so they are predicted to use frameshifting for
AB  - expression of two of their tail proteins. The lysBC genes of KS14 and
AB  - KL3 are similar to those of P2, but in KS5 the organization of these
AB  - genes suggests that they may have been acquired via horizontal transfer
AB  - from a phage similar to l. KS5 contains two sequence elements that are
AB  - unique among these three phages: an ISBmu2-like insertion sequence and
AB  - a reverse transcriptase gene. KL3 encodes an EcoRII-C
AB  - endonuclease/methylase pair and Vsr endonuclease that are predicted to
AB  - function during the lytic cycle to cleave non-self DNA, protect the
AB  - phage genome and repair methylation-induced mutations.
AB  - Conclusions: KS5, KS14 and KL3 are the first BCC-specific phages to
AB  - be identified as P2-like. As KS14 has previously been shown to be
AB  - active against Burkholderia cenocepacia in vivo, genomic
AB  - characterization of these phages is a crucial first step in the
AB  - development of these and similar phages for clinical use against the
AB  - BCC.
ER  -

TY  - JOUR
AU  - Lynch, K.H.
AU  - Stothard, P.
AU  - Dennis, J.J.
TI  - Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages.
JO  - BMC Genomics
PY  - 2012
SP  - 223
EP  - 223
VL  - 13
AB  - ABSTRACT: BACKGROUND: Genomic analysis of bacteriophages infecting the
AB  - Burkholderia cepacia complex (BCC) is an important preliminary step in the
AB  - development of a phage therapy protocol for these opportunistic pathogens. The
AB  - objective of this study was to characterize KL1 (vB_BceS_KL1) and AH2
AB  - (vB_BceS_AH2), two novel Burkholderia cenocepacia-specific siphoviruses isolated
AB  - from environmental samples. RESULTS: KL1 and AH2 exhibit several unique
AB  - phenotypic similarities: they infect the same B. cenocepacia strains, they
AB  - require prolonged incubation at 30degreesC for the formation of plaques at low
AB  - titres, and they do not form plaques at similar titres following incubation at
AB  - 37degreesC. However, despite these similarities, we have determined using
AB  - whole-genome pyrosequencing that these phages show minimal relatedness to one
AB  - another. The KL1 genome is 42,832 base pairs (bp) in length and is most closely
AB  - related to Pseudomonas phage 73 (PA73). In contrast, the AH2 genome is 58,065 bp
AB  - in length and is most closely related to Burkholderia phage BcepNazgul. Using
AB  - both BLASTP and HHpred analysis, we have identified and analyzed the putative
AB  - virion morphogenesis, lysis, DNA binding, and MazG proteins of these two phages.
AB  - Notably, MazG homologs identified in cyanophages have been predicted to
AB  - facilitate infection of stationary phase cells and may contribute to the unique
AB  - lysis phenotype of KL1 and AH2. CONCLUSIONS: The nearly indistinguishable
AB  - phenotypes but distinct genomes of KL1 and AH2 provide further evidence of both
AB  - vast diversity and convergent evolution in the BCC-specific phage population.
ER  -

TY  - JOUR
AU  - Lynch, K.H.
AU  - Stothard, P.
AU  - Dennis, J.J.
TI  - Characterization of DC1, a broad-host-range Bcep22-like podovirus.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 889
EP  - 891
VL  - 78
AB  - Bcep22-like phages are a recently described group of podoviruses that infect
AB  - strains of Burkholderia cenocepacia. We have isolated and characterized a novel
AB  - member of this group named DC1. This podovirus shows many genomic similarities to
AB  - BcepIL02 and Bcep22, but it infects strains belonging to multiple Burkholderia
AB  - cepacia complex (BCC) species.
ER  -

TY  - JOUR
AU  - Lynch, T.W.
AU  - Sligar, S.G.
TI  - Macromolecular Hydration Changes Associated with BamHI Binding and Catalysis.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 30561
EP  - 30565
VL  - 275
AB  - In this report, the effects of osmotic pressure on BamHI cognate binding and catalysis were
AB  - investigated and compared with a previous study on EcoRI (Robinson, C. R. and Sligar, S. G.
AB  - (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 2186-2191). Our observation of the dependence of
AB  - binding and catalytic parameters on osmotic pressure has allowed for the comparison of
AB  - hydration changes associated with site-specific DNA recognition for both endonucleases. Over a
AB  - large range of osmotic pressures (pi), the dependence of BamHI on osmotic stress during
AB  - cognate binding and catalysis was very different from that of the related endonuclease EcoRI.
AB  - The binding of EcoRI to cognate DNA was dominated by a dehydration of the endonuclease-DNA
AB  - complex, whereas binding by BamHI to its cognate sequence was accompanied by a solvent release
AB  - corresponding to some 125 fewer waters. Catalytic analysis at elevated osmotic pressures
AB  - indicated that both endonucleases had undergone a net hydration of the complex with BamHI
AB  - displaying a much greater dependence on osmotic stress than EcoRI. Although the enzymes shared
AB  - core structural motifs, comparisons of high resolution x-ray structures revealed many
AB  - different secondary structural features of the complexed endonucleases. The large difference
AB  - in hydration changes by both BamHI and EcoRI could be attributed to these dissimilar secondary
AB  - structural features, as well as the functional differences of the two endonucleases during
AB  - site-specific DNA recognition.
ER  -

TY  - JOUR
AU  - Lyngstadaas, A.
AU  - Lobner-Olesen, A.
AU  - Boye, E.
TI  - Characterization of three genes in the dam-containing operon of Escherichia coli.
JO  - Mol. Gen. Genet.
PY  - 1995
SP  - 546
EP  - 554
VL  - 247
AB  - The dam-containing operon in Escherichia coli is located at 74 min on the chromosomal map and
AB  - contains the genes aroK, aroB, a gene called urf74.3,
AB  - dam and trpS. We have determined the nucleotide sequence between the dam
AB  - and trpS genes and show that it encodes two proteins with molecular
AB  - weights of 24 and 27 kDa. Furthermore, we characterize the three genes
AB  - urf74.3, 24kDa, 27kDa and the proteins they encode. The predicted amino
AB  - acid sequences of the 24 and 27 kDa proteins are similar to those of the
AB  - CbbE and CbbZ proteins, respectively, of the Alcaligenes eutrophus cbb
AB  - operon, which encodes enzymes involved in the Calvin cycle. In separate
AB  - experiments, we have shown that the 24 kDa protein has
AB  - d-ribulose-5-phosphate epimerase activity (similar to CbbE), and we call
AB  - the gene rpe. Similarly, the 27 kDa protein has 2-phosphoglycolate
AB  - phosphatase activity (similar to CbbZ), and we name the gene gph. The
AB  - Urf74.3 protein, with a predicted molecular weight of 46 kDa, migrated as
AB  - a 70 kDa product under denaturing conditions. Overexpression of Urf74.3
AB  - induced cell filamentation, indicating that Urf74.3 directly or indirectly
AB  - interferes with cell division. We present evidence for translational
AB  - coupling between aroB and urf74.3 and also between rpe and gph. Proteins
AB  - encoded in the dam superoperon appear to be largely unrelated: Dam, and
AB  - perhaps Urf74.3, are involved in cell cycle regulation, AroK, AroB, and
AB  - TrpS function in aromatic amino acid biosynthesis, whereas Rpe and Gph are
AB  - involved in carbohydrate metabolism.
ER  -

TY  - JOUR
AU  - Lynn, S.P.
AU  - Cohen, L.K.
AU  - Gardner, J.F.
AU  - Kaplan, S.
TI  - Characterization of a site-specific restriction endonuclease from Rhodopseudomonas sphaeroides.
JO  - J. Bacteriol.
PY  - 1979
SP  - 505
EP  - 509
VL  - 138
AB  - A type II restriction endonuclease, RshI, has been partially purified from
AB  - photoheterotrophically grown Rhodopseudomonas sphaeroides strain 2.4.1.  The
AB  - enzyme preparation, after a single DE-52 column fractionation, is free of 5'
AB  - exonuclease and phospatase activities but contains a trace of 3' exonuclease
AB  - activity.  Based upon deoxyribonucleic acid (DNA) sequencing data in the
AB  - vicinity of the enzyme-promoted cleavage of pBR322 DNA, we have concluded that
AB  - RshI probably recognizes the palinodromic hexanucleotide sequence 5'-CGATCG-3'
AB  - and cleaves between the T and C.  Lambda cI857 DNA contains three RshI sites,
AB  - two of which lie in the replaceable region.  The plasmid pBR322, which carries
AB  - resistances to ampicillin and tetracycline, contains a single RshI site in the
AB  - ampicillin resistance determinant.  Insertion of DNA into the RshI site of
AB  - pBR322 results in loss of ampicillin resistance but retention of tetracycline
AB  - resistance, thereby providing a convenient screening procedure for recombinant
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Lynn, S.P.
AU  - Cohen, L.K.
AU  - Kaplan, S.
AU  - Gardner, J.F.
TI  - RsaI: a new sequence-specific endonuclease activity from Rhodopseudomonas sphaeroides.
JO  - J. Bacteriol.
PY  - 1980
SP  - 380
EP  - 383
VL  - 142
AB  - A new type II sequence-specific endonuclease, RsaI, has been identified from
AB  - Rhodopseudomonas sphaeroides strain 28/5.  An RsaI purification scheme that
AB  - yields enzyme which is free of contaminating exonuclease and phosphatase
AB  - activities after a single column fractionation has been developed.  The enzyme
AB  - recognized the tetranucleotide sequence 5'-GTAC-3' and cleaved between the T
AB  - and A, thereby generating flush ends.  RsaI should be extremely useful in
AB  - deoxyribonucleic acid sequencing experiments.
ER  -

TY  - JOUR
AU  - Lyra, C.
AU  - Halme, T.
AU  - Torsti, A.-M.
AU  - Tenkanen, T.
AU  - Sivonen, K.
TI  - Site-specific restriction endonucleases in cyanobacteria.
JO  - J. Appl. Microbiol.
PY  - 2000
SP  - 979
EP  - 991
VL  - 89
AB  - Aim: Planktic cyanobacteria were screened for endodeoxyribonucleases. Principal component
AB  - analysis (PCA) was employed to demonstrate a
AB  - potential relationship between certain enzymes and a group of
AB  - cyanobacteria. The data were obtained from a data bank and this study.
AB  - Methods and Results: Enzymes were partially purified using column
AB  - chromatography. Anabaena strains contained Asp83/1I(5'-TTCGAA-3'),
AB  - Asp83/1II (5'-GGCC-3'), Asp90I (5'-ACRYGT-3') and five isoschizomeric
AB  - enzymes (5'-ATCGAT-3'). Aphanizomenon and Microcystis strains contained
AB  - ApcTR183I (5'-TGCGCA-3') and Msp199I (5'-CCGG-3'), respectively.
AB  - Planktothrix strains possessed Psc2I (5'-GAANNNNTTC-3'), Psc27I and
AB  - Psc28I (5'-TTCGAA-3'). PCA showed that the most common cyanobacterial
AB  - endonuclease types were AvaII, AvaI and AsuII.
AB  - Conclusions: All planktic cyanobacteria studied contained
AB  - restriction endonucleases. The defined restriction endonucleases were
AB  - isoschizomers of known enzymes. The Nostoc and the Spirulina genera had
AB  - an association, while the majority of the genera had no association
AB  - with certain endonuclease type(s).
AB  - Significance and Impact of the Study: The defined enzymes in this
AB  - study and the estimated trend in the endonuclease type distribution
AB  - allow more efficient avoidance of cynobacterial restriction barriers.
ER  -

TY  - JOUR
AU  - Lyu, W.
AU  - Wu, Y.
AU  - Liu, Y.
AU  - Lyu, Z.
TI  - Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (Sophora japonica) Forest Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01059
EP  - e01016
VL  - 4
AB  - Bacillus litoralis C44 can hydrolyze rutin to produce isoquercetin by the enzyme
AB  - alpha-l-rhamnosidase. We report here the genome sequence and annotation result of
AB  - strain C44. The genomic information will serve as references to the physiology,
AB  - genetics, and evolution of this species and further genetic engineering research
AB  - in this species.
ER  -

TY  - JOUR
AU  - Lyumkis, D.
AU  - Talley, H.
AU  - Stewart, A.
AU  - Shah, S.
AU  - Park, C.K.
AU  - Tama, F.
AU  - Potter, C.S.
AU  - Carragher, B.
AU  - Horton, N.C.
TI  - Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization.
JO  - Structure
PY  - 2013
SP  - 1848
EP  - 1858
VL  - 21
AB  - SgrAI is a sequence specific DNA endonuclease that functions through an unusual enzymatic
AB  - mechanism that is allosterically activated 200- to 500-fold by effector
AB  - DNA, with a concomitant expansion of its DNA sequence specificity. Using
AB  - single-particle transmission electron microscopy to reconstruct distinct
AB  - populations of SgrAI oligomers, we show that in the presence of allosteric,
AB  - activating DNA, the enzyme forms regular, repeating helical structures
AB  - characterized by the addition of DNA-binding dimeric SgrAI subunits in a run-on
AB  - manner. We also present the structure of oligomeric SgrAI at 8.6 A resolution,
AB  - demonstrating the conformational state of SgrAI in its activated form. Activated
AB  - and oligomeric SgrAI displays key protein-protein interactions near the helix
AB  - axis between its N termini, as well as allosteric protein-DNA interactions that
AB  - are required for enzymatic activation. The hybrid approach reveals an unusual
AB  - mechanism of enzyme activation that explains SgrAI's oligomerization and
AB  - allosteric behavior.
ER  -

TY  - JOUR
AU  - Lyutzkanova, D.
AU  - Stoilova-Disheva, M.
AU  - Peltekova, V.
TI  - The restriction-modification system in Streptomyces flavopersicus.
JO  - Folia Microbiol. (Praha)
PY  - 2001
SP  - 119
EP  - 122
VL  - 46
AB  - To clone bifunctional vectors in streptomycetes, it was necessary to define the
AB  - restriction-modification system of Streptomyces
AB  - flavopersicus. Plasmid DNA from bifunctional vectors pIJ699 and
AB  - pXED3-13, isolated from E. coli strains with different methylation
AB  - systems: E. coli DH5 alpha (dam(+) dcm(+)), E. coli MB5386 (dam dcm), E.
AB  - coli CB51 (dam dcm(+)), E. coli NM544 (dam(+) dcm), was used for
AB  - transformation of protoplasts from strain S. flavopersicus. Restriction
AB  - of dcm-methylated DNA from S. flavopersicus was established. As a host
AB  - in the intermediate cloning strain E.coli NM544 (dam(+) dcm) should be
AB  - used, as the dcm-transmethylase-dependent strain S. flavopersicus does
AB  - not process DNA from this strain.
ER  -

TY  - JOUR
AU  - Ma, A.P.
AU  - Jiang, J.
AU  - Tun, H.M.
AU  - Mauroo, N.F.
AU  - Yuen, C.S.
AU  - Leung, F.C.
TI  - Complete Genome Sequence of Staphylococcus xylosus HKUOPL8, a Potential Opportunistic Pathogen of Mammals.
JO  - Genome Announcements
PY  - 2014
SP  - e00653
EP  - e00614
VL  - 2
AB  - We report here the first complete genome sequence of Staphylococcus xylosus strain HKUOPL8,
AB  - isolated from giant panda feces. The whole genome sequence of
AB  - this strain will provide an important framework for investigating the genes
AB  - responsible for potential opportunistic infections with this species, as well as
AB  - its survival in various environments.
ER  -

TY  - JOUR
AU  - Ma, B.
AU  - Ma, J.
AU  - Liu, D.
AU  - Guo, L.
AU  - Chen, H.
AU  - Ding, J.
AU  - Liu, W.
AU  - Zhang, H.
TI  - Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori.
JO  - Oncotarget
PY  - 2016
SP  - 40965
EP  - 40977
VL  - 7
AB  - DNA N6-methyladenine modification plays an important role in regulating a variety of
AB  - biological functions in bacteria. However, the mechanism of sequence-specific
AB  - recognition in N6-methyladenine modification remains elusive. M1.HpyAVI, a DNA
AB  - N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous
AB  - substrate specificity than other enzymes. Here, we present the crystal structures
AB  - of cofactor-free and AdoMet-bound structures of this enzyme, which were
AB  - determined at resolutions of 3.0 A and 3.1 A, respectively. The core structure of
AB  - M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative
AB  - DNA binding regions considerably differ from those of the other MTases, which may
AB  - account for the substrate promiscuity of this enzyme. Site-directed mutagenesis
AB  - experiments identified residues D29 and E216 as crucial amino acids for cofactor
AB  - binding and the methyl transfer activity of the enzyme, while P41, located in a
AB  - highly flexible loop, playing a determinant role for substrate specificity. Taken
AB  - together, our data revealed the structural basis underlying DNA N6-adenine
AB  - methyltransferase substrate promiscuity.
ER  -

TY  - JOUR
AU  - Ma, B.C.
AU  - Wang, J.
AU  - Fang, X.H.
TI  - Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase.
JO  - J. Phys. Chem. B
PY  - 2006
SP  - 19647
EP  - 19651
VL  - 110
AB  - We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET)
AB  - techniques to study the interaction between
AB  - EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution.
AB  - Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip
AB  - out the second adenine for methylation. The binding affinity of M.
AB  - EcoRI to two dsDNA fragments (20 and 38 bp) was studied with
AB  - fluorescence anisotropy. Their binding constants at different
AB  - temperatures from 20 to 40 degrees C were obtained, and the
AB  - thermodynamic parameters of binding were derived. The results showed
AB  - that M.EcoRI had a higher binding affinity to the short dsDNA strand
AB  - than to the long one, and its binding to DNA was primarily
AB  - entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two
AB  - fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we
AB  - were able to monitor the enhanced TMR fluorescence in the presence of
AB  - M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET
AB  - efficiency was changed from 72.4 to 63.4 angstrom, and the DNA bending
AB  - angle was estimated as 57.8 degrees.
ER  -

TY  - JOUR
AU  - Ma, C.B.
AU  - Tang, Z.W.
AU  - Wang, K.M.
AU  - Tan, W.H.
AU  - Yang, X.H.
AU  - Li, W.
AU  - Li, Z.H.
AU  - Lv, X.Y.
TI  - Real-time monitoring of restriction endonuclease activity using molecular beacon.
JO  - Anal. Biochem.
PY  - 2007
SP  - 294
EP  - 296
VL  - 363
AB  - Restriction endonucleases are one of the most important enzymes in molecular biology.  These
AB  - enzymes are essential in recombinant technology, genotyping, mapping, and sequencing of large
AB  - strands of DNA.  Because of the biological importance of restriction endonucleases and their
AB  - wide use, restriction endonuclease activity assays are essential.  Traditional methods for
AB  - assaying activity of restriciton endonucleases, such as gel electrophoresis, filter binding,
AB  - high-performance liquid chromatography, and enzyme-linked immunosorbent assay, have been used.
AB  - All of these methods, however, are discontinuous, time-consuming, and laborious, and they
AB  - usually require isotope labeling.  Several spectroscopic methods using fluorescence
AB  - measurements have been developed.  These assays are continuous.  However, up to now all of
AB  - them have been designed only for doubly labeled DNA substrates with very large fluorophores
AB  - that may interfere with recognition and reactivity with certain restriction endonucleases.
AB  - Furthermore, the potential for achieving high sensitivity through fluorescent resonance energy
AB  - transfer has not been fully realized.  Therefore, it is necessary to develop a sensitive,
AB  - convenient, and non-isotope-labeled method for assaying restriction endonuclease activity.
ER  -

TY  - JOUR
AU  - Ma, D.
AU  - Bai, J.
AU  - Deng, G.
AU  - Li, S.
TI  - Sequence analysis of DNA methyltransferase gene from Largemouth bass ulcerative syndrome virus and its expression in prokaryote.
JO  - Nong Ye Sheng Wu Ji Shu Xue Bao
PY  - 2011
SP  - 342
EP  - 349
VL  - 19
AB  - In order to further reveal the characteristics of Largemouth bass ulcerative syndrome virus
AB  - (LBUSV) isolated recently, a further study the group of LBUSV, DFV (Doctor fish virus) and
AB  - LMBV (Largemouth bass virus), the full-length DNA methyltransferase (DNA MTase) gene was
AB  - analyzed and expressed using prokaryotic system.  A about 200 bp core fragment was amplified
AB  - and sequenced, and the full-length of DNA MTase was identified by genome walking.  The open
AB  - reading frame (ORF) of DNA MTase gene was 663 bp encoding 220 amino acids (GenBank accession
AB  - No. GU256634).  Motif analysis indicated that LBUSV DNA MTase protein contained blocks I, IV,
AB  - VI and VIII, and cofactor binding sites, substrate interacting sites and DNA binding sites
AB  - were also found in LBUSV DNA MTase, and the proline-proline-cysteine tripeptide was proposed
AB  - catalytic site.  Additionally, the primers were designed according to DNA MTase ORF, and the
AB  - PCR products were inserted in vector pBV220 and transformed to host Escherichia coli DH5a.
AB  - After temperature inducement and SDS-PAGE analysis, the recombinant expression bacteria
AB  - produced a special proein about 25 kD in molecular weight.  The analysis, the recombinant
AB  - expression bacteria produced a special protein about 25 kD in molecular weight.  The
AB  - proportion of recombinant protein in total bacterial protein was about 30%.  Characteristic
AB  - analysis of DNA MTase gene showed that the predicted protein may play a role of DNA
AB  - methyltransferase, and confirmed that the taxonomic status of LBUSV is genus Ranavirus of the
AB  - family Iridoviridae.
ER  -

TY  - JOUR
AU  - Ma, D.
AU  - Hao, Z.
AU  - Sun, R.
AU  - Bartlam, M.
AU  - Wang, Y.
TI  - Genome Sequence of a Typical Ultramicrobacterium, Curvibacter sp. Strain PAE-UM,  Capable of Phthalate Ester Degradation.
JO  - Genome Announcements
PY  - 2016
SP  - e01510
EP  - e01515
VL  - 4
AB  - Curvibacter sp. strain PAE-UM, isolated from river sediment, is a typical ultramicrobacterium
AB  - capable of phthalate ester degradation. The genome of
AB  - Curvibacter sp. PAE-UM consists of 3,284,473 bp, and its information will provide
AB  - insights into the molecular mechanisms underlying its degradation ability.
ER  -

TY  - JOUR
AU  - Ma, D.P.
AU  - King, Y.T.
AU  - Kim, Y.
AU  - Luckett, S.
TI  - The group I intron of apocytochrome b gene from Chlamydomonas smithii encodes a site-specific endonuclease.
JO  - Plant Mol. Biol.
PY  - 1992
SP  - 1001
EP  - 1004
VL  - 18
AB  - The mitochondrial DNA molecules of two interfertile algal species, Chlamydomonas smithii and
AB  - C. reinhardtii, are co-linear except for a 1075 bp intron (the alpha-insert) that is present
AB  - in the cob gene of C. smithii. The alpha-insert, a group I intron (Cs cob.1) containing an
AB  - open reading frame (ORF) which encodes a basic, hydrophilic protein of 237 amino acids, is
AB  - unidirectionally transmitted to all diploid progeny during interspecific crosses. In this
AB  - report, we show that the Cs cob.1-encoded protein is a site-specific endonuclease (I-Csm I)
AB  - which could mediate intron transfer via the gene conversion mechanism. The Cs cob.1 ORF was
AB  - cloned into the vector pMALcr1 and over-expressed as a hybrid protein fused to maltose-binding
AB  - protein (MBP). This fusion protein exhibited an in vivo endonuclease activity which
AB  - specifically cleaved the intron homing site within the intronless cob gene.
ER  -

TY  - JOUR
AU  - Ma, J.
AU  - He, Y.
AU  - Hu, B.
AU  - Luo, Z.Q.
TI  - Genome Sequence of an Environmental Isolate of the Bacterial Pathogen Legionella  pneumophila.
JO  - Genome Announcements
PY  - 2013
SP  - e00320
EP  - e00313
VL  - 1
AB  - We report here the genomic sequence of Legionella pneumophila strain LPE509 from  the water
AB  - distribution system of a hospital in Shanghai, China. This is the first
AB  - complete genome sequence of an environmental L. pneumophila isolate. Genomic
AB  - analyses identified approximately 600 genes unique to LPE509 compared to those of
AB  - the 7 available L. pneumophila genomes.
ER  -

TY  - JOUR
AU  - Ma, J.
AU  - Liu, H.
AU  - Liu, K.
AU  - Wang, C.
AU  - Li, Y.
AU  - Hou, Q.
AU  - Yao, L.
AU  - Cui, Y.
AU  - Zhang, T.
AU  - Wang, H.
AU  - Wang, B.
AU  - Wang, Y.
AU  - Ge, R.
AU  - Xu, B.
AU  - Yao, G.
AU  - Xu, W.
AU  - Fan, L.
AU  - Ding, Y.
AU  - Du, B.
TI  - Complete Genome Sequence of Bacillus velezensis GQJK49, a Plant Growth-Promoting  Rhizobacterium with Antifungal Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e00922
EP  - e00917
VL  - 5
AB  - Bacillus velezensis GQJK49 is a plant growth-promoting rhizobacterium with antifungal
AB  - activity, which was isolated from Lycium barbarum L. rhizosphere.
AB  - Here, we report the complete genome sequence of B. velezensis GQJK49. Twelve gene
AB  - clusters related to its biosynthesis of secondary metabolites, including
AB  - antifungal and antibacterial antibiotics, were predicted.
ER  -

TY  - JOUR
AU  - Ma, J.
AU  - Liu, H.
AU  - Wang, C.
AU  - Xia, Z.
AU  - Liu, K.
AU  - Hou, Q.
AU  - Li, Y.
AU  - Zhang, T.
AU  - Wang, H.
AU  - Wang, B.
AU  - Wang, Y.
AU  - Ge, R.
AU  - Xu, B.
AU  - Yao, G.
AU  - Jiang, Z.
AU  - Hou, W.
AU  - Ding, Y.
AU  - Du, B.
TI  - Complete Genome Sequence of Bacillus subtilis GQJK2, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e00467
EP  - e00417
VL  - 5
AB  - Bacillus subtilis GQJK2 is a plant growth-promoting rhizobacterium with antifungal activity
AB  - which was isolated from Lycium barbarum L. rhizosphere. Here,
AB  - we report the complete genome sequence of B. subtilis GQJK2. Ten gene clusters
AB  - involved in the biosynthesis of antagonistic compounds were predicted.
ER  -

TY  - JOUR
AU  - Ma, L.
AU  - Chen, K.
AU  - Clarke, D.J.
AU  - Nortcliffe, C.P.
AU  - Wilson, G.G.
AU  - Edwardson, J.M.
AU  - Morton, A.J.
AU  - Jones, A.C.
AU  - Dryden, D.T.F.
TI  - Resriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 4999
EP  - 5009
VL  - 41
AB  - The type II restriction endonuclease TseI recognizes the DNA target sequence 5'-G^CWGC-3'
AB  - (where W=A or T) and cleaves after the first G to produce fragments with three-base
AB  - 5'-overhangs.  We have determined that it is a dimeric protein capable of cleaving not only
AB  - its target sequence but also one containing A:A or T:T mismatches at the central base pair in
AB  - the target sequence.  The cleavage of targets containing these mismatches is as efficient as
AB  - cleavage of the correct target sequence containing a central A:T base pair.  The cleavage
AB  - mechanism does not apparently use a base flipping mechanism as found for some other type II
AB  - restriction endonuclease recognizing similarly degenerate target sequences.  The ability of
AB  - TseI to cleave targets with mismatches means that it can cleave the unusual DNA hairpin
AB  - structures containing A:A or T:T mismatches formed by the repetitive DNA sequences associated
AB  - with Huntington's disease (CAG repeats) and myotonic dystrophy type 1 (CTG repeats).
ER  -

TY  - JOUR
AU  - Ma, L.
AU  - Wu, X.
AU  - Wilson, G.G.
AU  - Jones, A.C.
AU  - Dryden, D.T.F.
TI  - Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction-modification enzyme.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2014
SP  - 120
EP  - 125
VL  - 449
AB  - EcoP15I is a Type III DNA restriction and modification enzyme of Escherichia coli. We show
AB  - that it contains two modification (Mod) subunits for sequence-specific methylation of DNA and
AB  - one copy of a restriction endonuclease (Res) subunit for cleavage of DNA containing
AB  - unmethylated target sequences. Previously the Mod(2) dimer in the presence of cofactors was
AB  - shown to use nucleotide flipping to gain access to the adenine base targeted for methylation
AB  - (Reddy and Rao, J. Mol. Biol. 298 (2000) 597-610.). Surprisingly the Mod(2) enzyme also
AB  - appeared to flip a second adenine in the target sequence, one which was not subject to
AB  - methylation. We show using fluorescence lifetime measurements of the adenine analogue,
AB  - 2-aminopurine, that only the methylatable adenine undergoes flipping by the complete
AB  - Res(1)Mod(2) enzyme and that this occurs even in the absence of cofactors. We suggest that
AB  - this is due to activation of the Mod(2) core by the Res subunit.
ER  -

TY  - JOUR
AU  - Ma, L.
AU  - Zhu, Z.
AU  - Li, T.
AU  - Wang, Z.
TI  - Assaying multiple restriction endonucleases functionalities and inhibitions on DNA microarray with multifunctional gold nanoparticle probes.
JO  - Biosensors and Bioelectronics
PY  - 2014
SP  - 118
EP  - 118
VL  - 52
AB  - Herein, a double-stranded (ds) DNA microarray-based resonance light scattering (RLS) assay
AB  - with multifunctional gold nanoparticle (GNP) probes has been developed for studying
AB  - restriction endonuclease functionality and inhibition. Because of decreasing significantly
AB  - melting temperature, the enzyme-cleaved dsDNAs easily unwind to form single-stranded (ss)
AB  - DNAs. The ssDNAs are hybridized with multiplex complementary ssDNAs functionalized GNP probes
AB  - followed by silver enhancement and RLS detection. Thre restriction endonucleases (EcoRI, BamHI
AB  - and EcoRV) and three potential inhibitors (doxorubicin hydrochloride (DOX), ethidium bromide
AB  - (EB) and an EcoRI-derived helical peptide (alpha 4)) were selected to demonstrate capability
AB  - of the assay. Enzyme activities of restriction endonucleases are detected simultaneously with
AB  - high specificity down to the limits of 2.0 x 10(-2) U/mL for EcoRI, 1.1 x 10(-2) U/mL for
AB  - BamHI and 1.6 x 10(-2) U/mL for EcoRV, respectively. More importantly, the inhibitory
AB  - potencies of t hree inhibitors are showed quantitatively, indicating that our approach has
AB  - great promise for high-throughput screening of restriction endonuclease inhibitors.
ER  -

TY  - JOUR
AU  - Ma, M.
AU  - Wang, C.
AU  - Ding, Y.
AU  - Li, L.
AU  - Shen, D.
AU  - Jiang, X.
AU  - Guan, D.
AU  - Cao, F.
AU  - Chen, H.
AU  - Feng, R.
AU  - Wang, X.
AU  - Ge, Y.
AU  - Yao, L.
AU  - Bing, X.
AU  - Yang, X.
AU  - Li, J.
AU  - Du, B.
TI  - Complete Genome Sequence of Paenibacillus polymyxa SC2, a Strain of Plant Growth Promoting Rhizobacteria with Broad-Spectrum Antimicrobial Activity.
JO  - J. Bacteriol.
PY  - 2010
SP  - 311
EP  - 312
VL  - 193
AB  - Paenibacillus polymyxa SC2 is an important plant growth promoting rhizobacterium (PGPR). Here
AB  - we report the complete genome sequence of P. polymyxa SC2. Multiple sets of functional genes
AB  - have been found in the genome. As far as we know, this is the first complete genome sequence
AB  - of Paenibacillus polymyxa.
ER  -

TY  - JOUR
AU  - Ma, Q.
AU  - Qu, Y.
AU  - Tang, H.
AU  - Yu, H.
AU  - Ma, F.
AU  - Shi, S.
AU  - Zhang, X.
AU  - Zhou, H.
AU  - Zhou, J.
AU  - Xu, P.
TI  - Genome Sequence of a Novel Indigo-Producing Strain, Pseudomonas monteilii QM.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4459
EP  - 4460
VL  - 194
AB  - Pseudomonas monteilii is a versatile bacterium found in various niches. A newly isolated
AB  - strain, P. monteilii QM, can effectively produce indigoids from indoles.
AB  - Here we present a 5.76-Mb assembly of the P. monteilii genome for the first time.
AB  - It may provide abundant molecular information for the transformation of
AB  - aromatics.
ER  -

TY  - JOUR
AU  - Ma, Q.
AU  - Qu, Y.
AU  - Zhang, Z.
AU  - Li, P.
AU  - Tang, H.
TI  - Genome Sequence of an Efficient Indole-Degrading Bacterium, Cupriavidus sp. Strain IDO, with Potential Polyhydroxyalkanoate Production Applications.
JO  - Genome Announcements
PY  - 2015
SP  - e00102
EP  - e00115
VL  - 3
AB  - Cupriavidus sp. strain IDO has been shown to efficiently transform indole, and the genus of
AB  - Cupriavidus has been described as a promising cell factory for
AB  - polyhydroxyalkanoate synthesis from low-cost wastes. Here, we report the draft
AB  - genome sequence of strain IDO, which may provide useful genetic information on
AB  - indole metabolism and polyhydroxyalkanoate production.
ER  -

TY  - JOUR
AU  - Ma, R.
AU  - Wang, J.
AU  - Wang, Q.
AU  - Ma, Z.
AU  - Li, J.
AU  - Chen, L.
TI  - Draft Genome Sequence of Loktanella cinnabarina Strain XM1 Isolated from Coastal  Surface Water.
JO  - Genome Announcements
PY  - 2017
SP  - e01310
EP  - e01317
VL  - 5
AB  - We report here the draft genome sequence of Loktanella cinnabarina strain XM1, which was
AB  - isolated from coastal surface water and shared 99.43% 16S rRNA gene
AB  - sequence identity with the deep-sea bacterium L. cinnabarina LL-001(T) The
AB  - estimated genome size of strain XM1 is 3,782,785 bp, with a G+C content of 67.9%.
ER  -

TY  - JOUR
AU  - Ma, X.X.
AU  - Ito, T.
AU  - Tiensasitorn, C.
AU  - Jamklang, M.
AU  - Chongtrakool, P.
AU  - Boyle-Vavra, S.
AU  - Daum, R.S.
AU  - Hiramatsu, K.
TI  - Novel Type of Staphylococcal Cassette Chromosome mec Identified in Community-Acquired Methicillin-Resistant Staphylococcus aureus Strains.
JO  - Antimicrob. Agents Chemother.
PY  - 2002
SP  - 1147
EP  - 1152
VL  - 46
AB  - We identified a new type of staphylococcal cassette chromosome mec
AB  - (SCCmec) from two community-acquired methicillin-resistant Staphylococcus
AB  - aureus (MRSA) strains. The novel element, designated type IV SCCmec, had a
AB  - unique combination of the class B mec gene complex and the type 2 ccr gene
AB  - complex and was much smaller in size (21 to 24 kb) than previously
AB  - identified SCCmec elements of hospital-acquired MRSA. Consistent with the
AB  - strains' susceptibilities to various non-beta-lactam antibiotics, the type
AB  - IV SCCmec was devoid of any antibiotic resistance genes other than the
AB  - mecA gene.
ER  -

TY  - JOUR
AU  - Ma, Y.F.
AU  - Zhang, Y.
AU  - Zhang, J.Y.
AU  - Chen, D.W.
AU  - Zhu, Y.
AU  - Zheng, H.
AU  - Wang, S.Y.
AU  - Jiang, C.Y.
AU  - Zhao, G.P.
AU  - Liu, S.J.
TI  - The Complete Genome of Comamonas testosteroni Reveals Its Genetic Adaptations to Changing Environments.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 6812
EP  - 6819
VL  - 75
AB  - Members of the gram-negative, strictly aerobic genus Comamonas occur in
AB  - various environments. Here we report the complete genome of Comamonas
AB  - testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is
AB  - 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open
AB  - reading frames (ORFs) were identified; 3,514 of these ORFs are
AB  - functionally assigned to energy production, cell growth, signal
AB  - transduction, or transportation, while 866 ORFs encode hypothetical
AB  - proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2
AB  - genome has many genes for transportation (22%) and signal transduction
AB  - (6%), which allows the cells to respond and adapt to changing
AB  - environments. Strain CNB-2 does not assimilate carbohydrates due to the
AB  - lack of genes encoding proteins involved in glycolysis and pentose
AB  - phosphate pathways, and it contains many genes encoding proteins involved
AB  - in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T
AB  - systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to
AB  - take up and metabolize a range of carboxylic acids. This nutritional bias
AB  - for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy
AB  - unique niches in environments. Four different sets of terminal oxidases
AB  - for the respiratory system were identified, and they putatively functioned
AB  - at different oxygen concentrations. This study conclusively revealed at
AB  - the genomic level that the genetic versatility of C. testosteroni is vital
AB  - for competition with other bacteria in its special niches.
ER  -

TY  - JOUR
AU  - Ma, Y.L.
AU  - Xia, J.L.
AU  - Yang, Y.
AU  - Nie, Z.Y.
AU  - Liu, H.C.
AU  - Liu, L.Z.
TI  - Complete Genome Sequence of the Extremely Thermoacidophilic Archaeon Acidianus manzaensis YN-25.
JO  - Genome Announcements
PY  - 2017
SP  - e00438
EP  - e00417
VL  - 5
AB  - The complete genome of Acidianus manzaensis YN-25 consists of a chromosome of 2,687,463 bp,
AB  - with a G+C content of 30.62% and 2,746 coding DNA sequences. This
AB  - archaeon contains a series of specific genes involved in the oxidation of
AB  - elemental sulfur and reduced inorganic sulfur compounds.
ER  -

TY  - JOUR
AU  - Ma, Z.
AU  - Geng, J.
AU  - Zhang, H.
AU  - Yu, H.
AU  - Yi, L.
AU  - Lei, M.
AU  - Lu, C.P.
AU  - Fan, H.J.
AU  - Hu, S.
TI  - Complete Genome Sequence of Streptococcus equi subsp. zooepidemicus Strain ATCC 35246.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5583
EP  - 5584
VL  - 193
AB  - Streptococcus equi subsp. zooepidemicus is an opportunistic pathogen. It has caused a very
AB  - large economic loss in the swine industry of China and
AB  - has become a threat to human health. We announce the complete genome
AB  - sequence of S. equi subsp. zooepidemicus strain ATCC 35246, which provides
AB  - opportunities to understand its pathogenesis mechanism and genetic basis.
ER  -

TY  - JOUR
AU  - Ma, Z.
AU  - Geng, J.N.
AU  - Yi, L.
AU  - Xu, B.
AU  - Jia, R.Y.
AU  - Li, Y.
AU  - Meng, Q.S.
AU  - Fan, H.J.
AU  - Hu, S.N.
TI  - Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp zooepidemicus strain ATCC35246.
JO  - BMC Genomics
PY  - 2013
SP  - 377
EP  - 377
VL  - 14
AB  - Background: Streptococcus equi ssp. zooepidemicus (S. zooepidemicus) is an important pathogen
AB  - causing swine streptococcosis in China. Pathogenicity islands (PAIs) of S. zooepidemicus have
AB  - been transferred among bacteria through horizontal gene transfer (HGT) and play important
AB  - roles in the adaptation and increased virulence of S. zooepidemicus. The present study used
AB  - comparative genomics to examine the different pathogenicities of S. zooepidemicus. Results:
AB  - Genome of S. zooepidemicus ATCC35246 (Sz35246) comprises 2,167,264-bp of a single circular
AB  - chromosome, with a GC content of 41.65%. Comparative genome analysis of Sz35246, S.
AB  - zooepidemicus MGCS10565 (Sz10565), Streptococcus equi. ssp. equi. 4047 (Se4047) and S.
AB  - zooepidemicus H70 (Sz70) identified 320 Sz35246-specific genes, clustered into three
AB  - toxin-antitoxin (TA) systems PAIs and one restriction modification system (RM system) PAI.
AB  - These four acquired PAIs encode proteins that may contribute to the overall pathogenic
AB  - capacity and fitness of this bacterium to adapt to different hosts. Analysis of the in vivo
AB  - and in vitro transcriptomes of this bacterium revealed differentially expressed PAI genes and
AB  - non-PAI genes, suggesting that Sz35246 possess mechanisms for infecting animals and adapting
AB  - to a wide range of host environments. Analysis of the genome identified potential Sz35246
AB  - virulence genes. Genes of the Fim III operon were presumed to be involved in breaking the
AB  - host-restriction of Sz35246. Conclusion: Genome wide comparisons of Sz35246 with three other
AB  - strains and transcriptome analysis revealed novel genes related to bacterial virulence and
AB  - breaking the host-restriction. Four specific PAIs, which were judged to have been transferred
AB  - into Sz35246 genome through HGT, were identified for the first time. Further analysis of the
AB  - TA and RM systems in the PAIs will improve our understanding of the pathogenicity of this
AB  - bacterium and could lead to the development of diagnostics and vaccines.
ER  -

TY  - JOUR
AU  - Ma, Z.
AU  - Shen, X.
AU  - Hu, H.
AU  - Wang, W.
AU  - Peng, H.
AU  - Xu, P.
AU  - Zhang, X.
TI  - Genome Sequence of Sphingomonas wittichii DP58, the First Reported Phenazine-1-Carboxylic Acid-Degrading Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3535
EP  - 3536
VL  - 194
AB  - Sphingomonas wittichii DP58 (CCTCC M 2012027), the first reported phenazine-1-carboxylic acid
AB  - (PCA)-degrading strain, was isolated from pimiento
AB  - rhizosphere soils. Here we present a 5.6-Mb assembly of its genome. This sequence
AB  - would contribute to the elucidation of the molecular mechanism of PCA degradation
AB  - to improve the antifungal's effectiveness or remove superfluous PCA.
ER  -

TY  - JOUR
AU  - Maaloum, M.
AU  - Diop, A.
AU  - Ndongo, S.
AU  - Nguyen, T.T.
AU  - Cadoret, F.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota.
JO  - Genome Announcements
PY  - 2018
SP  - e01459
EP  - e01417
VL  - 6
AB  - In this article, we present the draft genome sequence of Megamonas funiformis strain
AB  - Marseille-P3344, isolated from a human fecal sample. The genome described
AB  - here is composed of 2,464,704 nucleotides, with 2,230 protein-coding genes and 76
AB  - RNA genes.
ER  -

TY  - JOUR
AU  - Maas, R.
TI  - Change in plasmid DNA structure, hypermethylation, and lon-proteolysis as steps in a replicative cascade.
JO  - Cell
PY  - 2001
SP  - 945
EP  - 955
VL  - 105
AB  - I have defined conditions under which RepFIC plasmid DNA can be maintained in a state of
AB  - lowered helical density.  In exponentially growing cultures, the DNA of lowered helical
AB  - density is present in small amounts but never totally absent, suggesting that it is a normal
AB  - variant of plasmid maintenance.  It is fully methylated at frequent sites by
AB  - dam-methyltransferase, some not previously recognized, further suggesting that the variant is
AB  - a precursor of replication.  The low-helical density plasmid is present in dam hosts,
AB  - indicating that methylation is not essential for the change in helical density.  The lowered
AB  - helical density is stabilized in lon hosts, suggesting that Lon-protease may remove both the
AB  - protein(s) that lower the helical density and the dam-methyltransferase after each round of
AB  - replication.
ER  -

TY  - JOUR
AU  - Maass, G.
TI  - Recognition of DNA sequences by restriction endonucleases.
JO  - NATO ASI Ser.
PY  - 1987
SP  - 225
EP  - 237
VL  - 137
AB  - Type II restriction endonucleases recognize DNA sequences 4 or 6 base pairs
AB  - long with very high specificity in a vast excess of non-specific DNA binding
AB  - sites.  They cleave the DNA within or in the immediate vicinity of the
AB  - recognition sequence.  Because of the immense importance of these enzymes in
AB  - analysis, preparation and in vitro recombination of DNA many investigations
AB  - have been carried out to understand the structural and mechanistic features
AB  - underlying their mode of recognition.  Among approximately 500 type II
AB  - restriction endonucleases described, EcoRI is the so far best studied enzyme.
AB  - EcoRI is a dimeric protein with two identical subunits, the aminoacid sequence
AB  - of which is known.  It recognizes the palindromic sequence -G^AATTC- -CTTAA^G-
AB  - and cleaves the DNA double strand at the marked positions.  For its enzymatic
AB  - activity it needs Mg2+ as a co-factor.  It was the first DNA-binding protein
AB  - that was co-crystallized with its substrate TCGCGAATTCGCG by Frederick et al.
AB  - in the absence of Mg2+.  The 3A X-ray analysis revealed a complementary
AB  - interface between the enzyme and the major groove of the DNA.  The binding of
AB  - the enzyme introduces distortions of the DNA, so called neo-kinks, and thereby
AB  - widens the major groove.  In a more recent though preliminary presentation, a
AB  - more detailed interpretation of the 3A-structure was given by J. Rosenberg, who
AB  - suggested that EcoRI interacts with its canonical sequence via 12 hydrogen
AB  - bonds between glutamic acid and arginine residues and the guanine and adenine
AB  - residues of GAATTC.  However, the data available at present are not yet
AB  - sufficient to understand the molecular basis of the EcoRI action.  A more
AB  - detailed knowledge of the thermodynamic, kinetic and structural aspects of the
AB  - EcoRI-DNA interaction is needed.  This contribution intends to present
AB  - physicochemical studies on the binding and catalytic properties of EcoRI and to
AB  - discuss structural aspects of the interaction.
ER  -

TY  - JOUR
AU  - Maass, G.
AU  - Alves, J.
AU  - Fliess, A.
AU  - Pingoud, A.
AU  - Wolfes, H.
TI  - Recognition of DNA-sequences by restriction endonucleases.
JO  - Hoppe Seylers Z. Physiol. Chem.
PY  - 1986
SP  - 47
EP  - 47
VL  - 367
AB  - Class II restriction endonucleases cleave DNA specifically at defined sites.
AB  - EcoRI, e.g., which recognizes the sequence GAATTC, cleaves at sites differing
AB  - in one base pair from this sequence by a factor of 103 to 105 more slowly than
AB  - at its canonical site.  This specificity is a complex function of thermodynamic
AB  - and kinetic parameters which govern the non-specific and specific binding of
AB  - EcoRI to DNA, the linear diffusion of the protein along DNA and conformational
AB  - changes of the enzyme and substrate.  We have been interested in the
AB  - thermodynamics, kinetics as well as structural aspects of these processes in
AB  - order to understand how DNA recognizing proteins interacting with DNA select
AB  - their specific site in a huge excess of nonspecific sites.  The initial contact
AB  - between EcoRI and its substrate is to nonspecific sites, binding to these sites
AB  - in the presence of Mg2+ is by a least a factor of 100 weaker than to the
AB  - specific site.  After nonspecific association EcoRI "slides" along the DNA in a
AB  - random fashion:  at physiological Mg2+ concentrations EcoRI cleave several
AB  - EcoRI sites in close proximity processively.  At high Mg2+ or at high ionic
AB  - strength dissociation is favoured over linear diffusion, and consequently,
AB  - processivity is suppressed.  Discrimination between specific and non-specific
AB  - sites resides in several unique contacts that can only be formed in the
AB  - specific complex.  Many studies have been carried out to define structural
AB  - elements on the DNA important for recognition, few studies, however, were
AB  - concerned with the identification of the regions of the protein important for
AB  - specific binding.  Using bromodeoxyuridine containing oligodeoxynucleotides
AB  - EcoRI was photo-crosslinked to its substrate via Met 157 demonstrating the
AB  - involvement of this region in the recognition complex.  This identification was
AB  - confirmed by the interference of antibodies against this region of EcoRI with
AB  - the catalytic action of EcoRI.  Met 157 is at the end of a sequence which shows
AB  - a striking homology to the sequence of the recognition helix of gene regulatory
AB  - proteins.  We are currently probing the importance of individual amino acid
AB  - residues for the catalytic action of EcoRI by site directed mutagenesis.
ER  -

TY  - JOUR
AU  - Maass, G.
AU  - Ruter, T.
AU  - Oelgeschlager, T.
AU  - Alves, J.
AU  - Wolfes, H.
AU  - Pingoud, A.
TI  - Site-directed mutagenesis studies suggest that Asp91 is part of the catalytic center of the restriction endonuclease EcoRI.
JO  - J. Biomol. Struct. Dyn.
PY  - 1991
SP  - A126
EP  - A126
VL  - 8
AB  - The comparison of the structures of EcoRI and EcoRV has revealed an interesting
AB  - homology which presumably concerns the active center of the two enzymes:
AB  - EcoRI:  90 - P D....... 111 E A K
AB  - EcoRV:  73 - P D.......  90 D I K
AB  - In the crystal structure of EcoRI Glu111 is near the bond cleaved.
ER  -

TY  - JOUR
AU  - Mac Aogain, M.
AU  - Bower, J.E.
AU  - Basu, I.
AU  - Freeman, J.T.
AU  - O'Toole, R.F.
TI  - Draft Genome Sequence of a Drug-Susceptible New Zealand Isolate of Mycobacterium  tuberculosis Lineage 3.
JO  - Genome Announcements
PY  - 2015
SP  - e00499
EP  - e00415
VL  - 3
AB  - We report here the draft whole-genome sequence of a drug-susceptible lineage 3 (East-African
AB  - Indian) isolate of Mycobacterium tuberculosis from New Zealand (NZ3DS1) and compare it to a
AB  - multidrug-resistant lineage 3 isolate (NZ3MDR1) with an identical 24-locus mycobacterial
AB  - interspersed repetitive-unit-variable-number tandem-repeat profile.
ER  -

TY  - JOUR
AU  - Mac Aogain, M.
AU  - Fennelly, N.
AU  - Walsh, A.
AU  - Lynagh, Y.
AU  - Bekaert, M.
AU  - Lawlor, B.
AU  - Walsh, P.
AU  - Kelly, B.
AU  - Rogers, T.R.
AU  - Crowley, B.
TI  - Fourteen Draft Genome Sequences for the First Reported Cases of Azithromycin-Resistant Neisseria gonorrhoeae in Ireland.
JO  - Genome Announcements
PY  - 2017
SP  - e00403
EP  - e00417
VL  - 5
AB  - Here, we report the draft genome assemblies of 14 azithromycin-resistant Neisseria gonorrhoeae
AB  - clinical isolates, representing the first such strains
AB  - identified in Ireland. Among these isolates are the first reported highly
AB  - resistant strains (MIC >256 mg/liter), which both belonged to the ST1580 sequence
AB  - type.
ER  -

TY  - JOUR
AU  - Mac Aogain, M.
AU  - Gautam, S.S.
AU  - Bower, J.E.
AU  - Basu, I.
AU  - O'Toole, R.F.
TI  - Draft Genome Sequence of a New Zealand Rangipo Strain of Mycobacterium tuberculosis.
JO  - Genome Announcements
PY  - 2016
SP  - e00657
EP  - e00616
VL  - 4
AB  - The Rangipo genotype of the Mycobacterium tuberculosis complex has been associated with a
AB  - number of tuberculosis (TB) outbreaks in New Zealand. We report
AB  - here the draft whole-genome sequence of a representative isolate of this strain.
ER  -

TY  - JOUR
AU  - Mac, A.M.
AU  - Roycroft, E.
AU  - Raftery, P.
AU  - Mok, S.
AU  - Fitzgibbon, M.
AU  - Rogers, T.R.
TI  - Draft Genome Sequences of Three Mycobacterium chimaera Respiratory Isolates.
JO  - Genome Announcements
PY  - 2015
SP  - e01409
EP  - e01415
VL  - 3
AB  - Mycobacterium chimaera is an opportunistic human pathogen implicated in both pulmonary and
AB  - cardiovascular infections. Here, we report the draft genome
AB  - sequences of three strains isolated from human respiratory specimens.
ER  -

TY  - JOUR
AU  - Macaluso, A.
AU  - Mettus, A.-M.
TI  - Efficient transformation of Bacillus thuringiensis requires nonmethylated plasmid DNA.
JO  - J. Bacteriol.
PY  - 1991
SP  - 1353
EP  - 1356
VL  - 173
AB  - The transformation efficiency of Bacillus thuringiensis depends upon the source of plasmid
AB  - DNA. DNA isolated from B. thuringiensis, Bacillus megaterium, or a Dam-Dcm- Escherichia coli
AB  - strain efficiently transformed several B. thuringiensis strains. B. thuringiensis strains were
AB  - grouped according to which B. thuringiensis backgrounds were suitable sources of DNA for
AB  - transformation of other B. thuringiensis strains, suggesting that B. thuringiensis strains
AB  - differ in DNA modification and restriction. Efficient transformation allowed the demonstration
AB  - of developmental regulation of cloned crystal protein genes in B. thuringiensis.
ER  -

TY  - JOUR
AU  - MacAogain, M.
AU  - Johari, B.M.
AU  - Bower, J.E.
AU  - O'Toole, R.F.
TI  - Draft Genome Sequence of a Multidrug-Resistant New Zealand Isolate of Mycobacterium tuberculosis Lineage 3.
JO  - Genome Announcements
PY  - 2014
SP  - e01017
EP  - e01014
VL  - 2
AB  - Multidrug resistance constitutes a threat worldwide to the management of tuberculosis (TB). We
AB  - report the draft whole-genome sequence of a lineage 3 (East-African Indian) isolate of
AB  - Mycobacterium tuberculosis which presented as multidrug resistant in New Zealand, and describe
AB  - a number of single-nucleotide polymorphisms in genes relating to drug resistance.
ER  -

TY  - JOUR
AU  - Macdonald, P.M.
AU  - Mosig, G.
TI  - Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication.
JO  - EMBO J.
PY  - 1984
SP  - 2863
EP  - 2871
VL  - 3
AB  - We have determined the DNA sequence and transcription patterns in a 3-kb segment (between 15
AB  - and 18 kb on the standard phage T4 map) spanning an origin of DNA replication. A new gene, 69,
AB  - spans this origin. Gene 69 codes for two overlapping proteins that share a common C-terminal
AB  - segment. Defective DNA replication in an appropriate amber mutant shows that at least the
AB  - larger of the two proteins is required for efficient T4 DNA replication. The two proteins
AB  - coded by gene 69 are expressed from different transcripts that are under different regulation.
AB  - The smaller protein, gp69*, can be expressed immediately from an Escherichia coli-like
AB  - promoter, whereas expression of the larger protein, gp69, must be delayed since its middle
AB  - promoter requires T4 coded proteins, most likely gp mot, for activation. We discuss the
AB  - possible significance of two overlapping proteins in the assembly of replisomes. Gene 69 is
AB  - bracketed by the nonessential early gene dam (DNA adenine methylase) and the late gene soc
AB  - (small outer capsid protein). Transcripts through this region are interdigitated in a complex
AB  - pattern, which reveals all elements that are thought to be important in regulation of
AB  - pre-replicative and post-replicative T4 genes.
ER  -

TY  - JOUR
AU  - Macdonald, S.E.
AU  - Gundogdu, O.
AU  - Dorrell, N.
AU  - Wren, B.W.
AU  - Blake, D.
AU  - Stabler, R.
TI  - Draft Genome Sequence of Campylobacter jejuni 11168H.
JO  - Genome Announcements
PY  - 2017
SP  - e01556
EP  - e01516
VL  - 5
AB  - Campylobacter jejuni is the most prevalent cause of food-borne gastroenteritis in the
AB  - developed world. The reference and original sequenced strain C. jejuni
AB  - NCTC11168 has low levels of motility compared to clinical isolates. Here, we
AB  - describe the draft genome of the laboratory derived hypermotile variant named
AB  - 11168H.
ER  -

TY  - JOUR
AU  - Macey, M.C.
AU  - Pratscher, J.
AU  - Crombie, A.
AU  - Murrell, J.C.
TI  - Draft Genome Sequences of Obligate Methylotrophs Methylovorus sp. Strain MM2 and  Methylobacillus sp. Strain MM3, Isolated from Grassland Soil.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00824
EP  - e00818
VL  - 7
AB  - Methylotrophs of the family Methylophilaceae were isolated from grassland soil. Here, we
AB  - report the draft genome sequences of two obligate methylotrophs,
AB  - Methylovorus sp. strain MM2 and Methylobacillus sp. strain MM3. These genome
AB  - sequences provide further insights into the genetic and metabolic diversity of
AB  - the Methylophilaceae.
ER  -

TY  - JOUR
AU  - MacGregor, B.J.
AU  - Biddle, J.F.
AU  - Siebert, J.R.
AU  - Staunton, E.
AU  - Hegg, E.L.
AU  - Matthysse, A.G.
AU  - Teske, A.
TI  - Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome    with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 1183
EP  - 1190
VL  - 79
AB  - Orange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of
AB  - microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments
AB  - typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in
AB  - pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing
AB  - bacteria. The nearly complete genome sequence of a single orange Beggiatoa ("Candidatus
AB  - Maribeggiatoa") filament from a microbial mat sample collected in 2008 at a hydrothermal site
AB  - in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the
AB  - gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples
AB  - (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid
AB  - chromatography (HPLC) nano-electrospray tandem mass spectrometry (muLC-MS-MS) of a pigmented
AB  - band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related
AB  - to a large group of octaheme cytochromes whose few characterized representatives are
AB  - hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro
AB  - assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities.
AB  - From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo
AB  - role of the octaheme protein, but future experiments are required to confirm this tentative
AB  - conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise
AB  - identification of an abundant mat protein, and its potential activities could be assayed,
AB  - proof of its physiological role remains elusive in the absence of a pure culture that can be
AB  - genetically manipulated.
ER  -

TY  - JOUR
AU  - MacGregor, B.J.
AU  - Biddle, J.F.
AU  - Teske, A.
TI  - Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa ('Candidatus Maribeggiatoa') sp Draft Genome: Evidence for Genetic Exchange with Cyanobacteria.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 3974
EP  - 3985
VL  - 79
AB  - The draft genome sequence of a single orange Beggiatoa ('Candidatus Maribeggiatoa') filament
AB  - collected from a microbial mat at a
AB  - hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows
AB  - evidence of extensive genetic exchange with cyanobacteria, in
AB  - particular for sensory and signal transduction genes. A putative homing
AB  - endonuclease gene and group I intron within the 23S rRNA gene; several
AB  - group II catalytic introns; GyrB and DnaE inteins, also encoding homing
AB  - endonucleases; multiple copies of sequences similar to the fdxN
AB  - excision elements XisH and XisI (required for heterocyst
AB  - differentiation in some cyanobacteria); and multiple sequences related
AB  - to an open reading frame (ORF) (00024 0693) of unknown function all
AB  - have close non-Beggiatoaceae matches with cyanobacterial sequences.
AB  - Sequences similar to the uncharacterized ORF and Xis elements are found
AB  - in other Beggiatoaceae genomes, a variety of cyanobacteria, and a few
AB  - phylogenetically dispersed pleiomorphic or filamentous bacteria. We
AB  - speculate that elements shared among filamentous bacterial species may
AB  - have been exchanged in microbial mats and that some of them may be
AB  - involved in cell differentiation.
ER  -

TY  - JOUR
AU  - Macgregor, R.B.
TI  - Reversible inhibition of EcoRI with elevated pressure.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1990
SP  - 775
EP  - 778
VL  - 170
AB  - The endonuclease activity of EcoRI is completely inhibited at 200 MPa, 37C
AB  - using the plasmid pBR322 as a substrate.  When assayed at 133 MPa approximately
AB  - half the activity at atmospheric pressure was observed; from these data the
AB  - standard molar volume change is estimated to be -80 cm3  mol-1.  Upon return to
AB  - atmospheric pressure the enzyme reacted in a standard manner with its
AB  - restriction site in pBR322.  Pressurization did not decrease the specificity of
AB  - the endonuclease activity of the enzyme for its canonical site.  These results
AB  - are discussed in terms of the role of ionic interactions in protein-DNA
AB  - interactions.
ER  -

TY  - JOUR
AU  - Machado, H.
AU  - Mansson, M.
AU  - Gram, L.
TI  - Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites.
JO  - Genome Announcements
PY  - 2014
SP  - e00535
EP  - e00514
VL  - 2
AB  - We report here the whole draft genome sequence of marine isolate Photobacterium halotolerans
AB  - S2753, which produces the known antibiotic holomycin and also
AB  - ngercheumicins and solonamides A and B, which interfere with virulence of
AB  - methicillin-resistant Staphylococcus aureus strains by interacting with the
AB  - quorum-sensing system.
ER  -

TY  - JOUR
AU  - Machado, V.S.
AU  - Bicalho, R.C.
TI  - Complete Genome Sequence of Trueperella pyogenes, an Important Opportunistic Pathogen of Livestock.
JO  - Genome Announcements
PY  - 2014
SP  - e00400
EP  - e00414
VL  - 2
AB  - Here, we report the complete genome sequence of Trueperella pyogenes TP6375, a strain isolated
AB  - from the uterus of a dairy cow affected with metritis. The
AB  - complete circular genome is 2,338,390 bp and contains several genes needed for
AB  - pathogenicity.
ER  -

TY  - JOUR
AU  - Machnicka, M.A.
AU  - Kaminska, K.H.
AU  - Dunin-Horkawicz, S.
AU  - Bujnicki, J.M.
TI  - Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
JO  - BMC Bioinformatics
PY  - 2015
SP  - 336
EP  - 336
VL  - 16
AB  - BACKGROUND: GmrSD is a modification-dependent restriction endonuclease that specifically
AB  - targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC)
AB  - modified DNA. It is encoded either as two separate single-domain GmrS and GmrD
AB  - proteins or as a single protein carrying both domains. Previous studies suggested
AB  - that GmrS acts as endonuclease and NTPase whereas GmrD binds DNA. METHODS: In
AB  - this work we applied homology detection, sequence conservation analysis, fold
AB  - recognition and homology modeling methods to study sequence-structure-function
AB  - relationships in the GmrSD restriction endonucleases family. We also analyzed the
AB  - phylogeny and genomic context of the family members. RESULTS: Results of our
AB  - comparative genomics study show that GmrS exhibits similarity to proteins from
AB  - the ParB/Srx fold which can have both NTPase and nuclease activity. In contrast
AB  - to the previous studies though, we attribute the nuclease activity also to GmrD
AB  - as we found it to contain the HNH endonuclease motif. We revealed residues
AB  - potentially important for structure and function in both domains. Moreover, we
AB  - found that GmrSD systems exist predominantly as a fused, double-domain form
AB  - rather than as a heterodimer and that their homologs are often encoded in regions
AB  - enriched in defense and gene mobility-related elements. Finally, phylogenetic
AB  - reconstructions of GmrS and GmrD domains revealed that they coevolved and only
AB  - few GmrSD systems appear to be assembled from distantly related GmrS and GmrD
AB  - components. CONCLUSIONS: Our study provides insight into
AB  - sequence-structure-function relationships in the yet poorly characterized family
AB  - of Type IV restriction enzymes. Comparative genomics allowed to propose possible
AB  - role of GmrD domain in the function of the GmrSD enzyme and possible active sites
AB  - of both GmrS and GmrD domains. Presented results can guide further experimental
AB  - characterization of these enzymes.
ER  -

TY  - JOUR
AU  - Macickova-Cahova, H.
AU  - Hocek, M.
TI  - Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 7612
EP  - 7622
VL  - 37
AB  - A set of 6 base-modified 2'-deoxyadenosine derivatives was incorporated to diverse DNA
AB  - sequences by primer extension using Vent (exo-) polymerase and
AB  - the influence of the modification on cleavage by diverse restriction
AB  - endonucleases was studied. While 8-substituted (Br or methyl) adenine
AB  - derivatives were well tolerated by the restriction enzymes and the
AB  - corresponding sequences were cleaved, the presence of 7-substituted
AB  - 7-deazaadenine in the recognition sequence resulted in blocking of
AB  - cleavage by some enzymes depending on the nature and size of the
AB  - 7-substituent. All sequences with modifications outside of the recognition
AB  - sequence were perfectly cleaved by all the restriction enzymes. The
AB  - results are useful both for protection of some sequences from cleavage and
AB  - for manipulation of functionalized DNA by restriction cleavage.
ER  -

TY  - JOUR
AU  - Macickova-Cahova, H.
AU  - Pohl, R.
AU  - Hocek, M.
TI  - Cleavage of Functionalized DNA Containing 5-Modified Pyrimidines by Type II Restriction Endonucleases.
JO  - Chembiochem
PY  - 2011
SP  - 431
EP  - 438
VL  - 12
AB  - A series of six pyrimidine-modified dNTPs-5-ethynyl-, 5-phenyl-, and
AB  - 5-(3-nitrophenyl)deoxycitidine and -deoxyuridine triphosphates-were
AB  - prepared and incorporated by primer extension with Vent
AB  - (exo-)polymerase to specific DNA sequences within or next to the
AB  - recognition sequences of selected restriction endonucleases. The
AB  - cleavage of these pyrimidine-modified DNA sequences by 13 restriction
AB  - enzymes was then studied. Whereas the presence of any modified C within
AB  - the target sequence completely prevented any restriction cleavage, most
AB  - enzymes tolerated the presence of 5-ethynylU and two of them even the
AB  - presence of 5-phenyl- and 5-(3-nitrophenyl)U. Modifications outside the
AB  - recognition sequence were tolerated except in the case of phenyl
AB  - derivatives with the PvuII enzyme. 5-EthynylC was used for protection
AB  - of the recognition sequence from cleavage in the presence of the second
AB  - unmodified copy of the same sequence that was cleaved.
ER  -

TY  - JOUR
AU  - Macinnes, J.I.
AU  - Mackinnon, J.
AU  - Bujold, A.R.
AU  - Ziebell, K.
AU  - Kropinski, A.M.
AU  - Nash, J.H.
TI  - Complete Genome Sequence of Actinobacillus suis H91-0380, a Virulent Serotype O2  Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6686
EP  - 6687
VL  - 194
AB  - Here, we report the first complete genome sequence of Actinobacillus suis, an important
AB  - opportunistic pathogen of swine. By comparing the genome sequence of A.
AB  - suis with those of other members of the family Pasteurellaceae, we hope to better
AB  - understand the role of these organisms in health and disease in swine.
ER  -

TY  - JOUR
AU  - Macintyre, G.
AU  - Atwood, C.V.
AU  - Cupples, C.G.
TI  - Lowering S-adenosylmethionine levels in Escherichia coli modulates C-to-T transition mutations.
JO  - J. Bacteriol.
PY  - 2001
SP  - 921
EP  - 927
VL  - 183
AB  - Deoxycytosine methylase (Dcm) enzyme activity causes mutagenesis in vitro either directly by
AB  - enzyme-induced deamination of cytosine to uracil in the absence of the methyl donor,
AB  - S-adenosylmethionine (SAM), or indirectly through spontaneous deamination of
AB  - [5-methyl]cytosine to thymine. Using a Lac reversion assay, we investigated the contribution
AB  - of the first mechanism to Dcm mutagenesis in vivo by lowering the levels of SAM. Escherichia
AB  - coli SAM levels were lowered by reducing SAM synthetase activity via the introduction of a
AB  - metK84 allele or by hydrolyzing SAM using the bacteriophage T3 SAM hydrolase.  The metK84
AB  - strains exhibited increased C-to-T mutagenesis. Expression of the T3 SAM hydrolase gene, under
AB  - the control of the arabinose-inducible P(BAD) promoter, effectively reduced Dcm-mediated
AB  - genomic DNA methylation. However, increased mutagenesis was not observed until extremely high
AB  - arabinose concentrations were used, and genome methylation at Dcm sites was negligible.
ER  -

TY  - JOUR
AU  - Macintyre, G.
AU  - Doiron, K.
AU  - Cupples, G.
TI  - Analysis of the levels of Dcm and Vsr in E. coli.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1997
SP  - 294
EP  - 294
VL  - 97
AB  - In Escherichia coli, T/G mismatches at C(T/G)WGG are cleaved by Vsr endonuclease, this is the
AB  - initial step in the very short patch repair process which repairs the T/G mismatch to C/G.
AB  - Since Dcm cytosine methylase methylates the second C in CCWGG, the function of VSP repair is
AB  - probably the prevention of CG to TA mutations caused by deamination of 5-methylcytosine to
AB  - thymine.  The dcm and vsr genes overlap, and are expressed from a single promoter situated
AB  - upstream of dcm.  The cellular levels of Dcm and Vsr are unknown.  We are investigating the
AB  - consequences of altering the levels of these two proteins.  Overexpression of Vsr in E. coli
AB  - stimulates transition and frameshift mutations.  Overexpression of dcm does not stimulate
AB  - mutations in cells with a functional vsr; in vsr-deleted cells, high levels of Dcm stimulate C
AB  - to T transitions at 5-methylcytosines.  Thus the expression of a single copy of vsr on the
AB  - chromosome is sufficient to counteract the mutagenic effect of even high levels of Dcm.  Since
AB  - Vsr is mutagenic, the organization of these two genes may reflect the need to produce low
AB  - levels of Vsr.  This would allow Vsr to counteract the mutagenic effects of Dcm, while
AB  - minimizing the mutagenic effect of Vsr.  We have constructed plasmids which allow the
AB  - purification of 6his-Dcm and 6his-Vsr.  The purified Dcm and Vsr will be used to produce
AB  - antibodies, to analyse the relative levels of Dcm and Vsr in E. coli by Western blot analysis.
ER  -

TY  - JOUR
AU  - Macintyre, G.
AU  - Doiron, K.M.J.
AU  - Cupples, C.G.
TI  - The Vsr endonuclease of Escherichia coli: an efficient DNA repair enzyme and a potent mutagen.
JO  - J. Bacteriol.
PY  - 1997
SP  - 6048
EP  - 6052
VL  - 179
AB  - The Vsr endonuclease of Escherichia coli initiates the repair of T/G mismatches caused by
AB  - deamination of 5-methylcytosine to thymine.  In this paper, we examine the capacity of Vsr to
AB  - prevent CG-to-TA mutations in cells with increased transcription of the cytosine methylase
AB  - gene (dcm).  We find that sufficient Vsr is produced by a single chromosomal copy of vsr to
AB  - prevent mutagenesis.  We also investigate the cause of the transition and frameshift mutations
AB  - in cells overproducing Vsr.  Neither the absence of the dcm methylase nor its overproduction
AB  - affects Vsr-stimulated mutagenesis.  However, addition of mutS, mutL, or mutH on multicopy
AB  - plasmids has a significant effect: mutL or mutH decreases the number of mutations, while mutS
AB  - stimulates mutagenesis.  The mut-containing plasmids have the same effect in cells treated
AB  - with 2-aminopurine and in cells made defective in DNA proofreading, two experimental
AB  - situations known to cause transition and frameshift mutations by saturating mismatch repair.
ER  -

TY  - JOUR
AU  - Macintyre, G.
AU  - Pitsikas, P.
AU  - Cupples, C.G.
TI  - Growth phase-dependent regulation of Vsr endonuclease may contribute to 5-methylcytosine mutational hot spots in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1999
SP  - 4435
EP  - 4436
VL  - 181
AB  - Using rabbit polyclonal antibodies, we have shown that the Dcm cytosine methylase of
AB  - Escherichia coli is maintained at a constant level during cell growth, while Vsr endonuclease
AB  - levels are growth phase dependent. Decreased production of Vsr relative to Dcm during the log
AB  - phase may contribute substantially to the mutability of 5-methylcytosine.
ER  -

TY  - JOUR
AU  - Mackeldanz, P.
AU  - Alves, J.
AU  - Moncke-Buchner, E.
AU  - Wyszomirski, K.H.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Functional consequences of mutating conserved SF2 helicase motifs in the Type III restriction endonuclease EcoP15I translocase domain.
JO  - Biochimie
PY  - 2013
SP  - 817
EP  - 823
VL  - 95
AB  - For efficient DNA hydrolysis, Type III restriction endonuclease EcoP15I interacts with two
AB  - inversely oriented recognition sites in an
AB  - ATP-dependent process. EcoP15I consists of two methylation (Mod)
AB  - subunits and a single restriction (Res) subunit yielding a
AB  - multifunctional enzyme complex able to methylate or to hydrolyse DNA.
AB  - Comprehensive sequence alignments, limited proteolysis and mass
AB  - spectroscopy suggested that the Res subunit is a fusion of a motor or
AB  - translocase (Tr) domain of superfamily II helicases and an endonuclease
AB  - domain with a catalytic PD...EXK motif. In the Tr domain, seven
AB  - predicted helicase motifs (I, la, II VI), a recently discovered Q-tip
AB  - motif and three additional regions (Ilia, IVa, Va) conserved among Type
AB  - III restriction enzymes have been identified that are predicted to be
AB  - involved in DNA binding and ATP hydrolysis. Because DNA unwinding
AB  - activity for EcoP15I (as for bona fide helicases) has never been found
AB  - and EcoP15I ATPase rates are only low, the functional importance of the
AB  - helicase motifs and regions was questionable and has never been probed
AB  - systematically. Therefore, we mutated all helicase motifs and conserved
AB  - regions predicted in Type III restriction enzyme EcoP15I and examined
AB  - the functional consequences on EcoP15I enzyme activity and the
AB  - structural integrity of the variants by CD spectroscopy. The resulting
AB  - eleven enzyme variants all, except variant IVa, are properly folded
AB  - showing the same secondary structure distribution as the wild-type
AB  - enzyme. Classical helicase motifs I VI are important for ATP and DNA
AB  - cleavage by EcoP15I and mutations therein led to complete loss of
AB  - ATPase and cleavage activity. Among the catalytically inactive enzyme
AB  - variants three preserved the ability to bind ATP. In contrast, newly
AB  - assigned motifs Q-tip, Ia and Va are not essential for EcoP15I activity
AB  - and the corresponding enzyme variants were still catalytically active.
AB  - DNA binding was only marginally reduced (2-7 fold) in all enzyme
AB  - variants tested.
ER  -

TY  - JOUR
AU  - Mackenzie, D.A.
AU  - McLay, K.
AU  - Roos, S.
AU  - Walter, J.
AU  - Swarbreck, D.
AU  - Drou, N.
AU  - Crossman, L.C.
AU  - Juge, N.
TI  - Draft Genome Sequence of a Novel Lactobacillus salivarius Strain Isolated from Piglet.
JO  - Genome Announcements
PY  - 2014
SP  - e01231
EP  - e01213
VL  - 2
AB  - Lactobacillus salivarius is part of the vertebrate indigenous microbiota of the
AB  - gastrointestinal tract, oral cavity, and milk. The properties associated with
AB  - some L. salivarius strains have led to their use as probiotics. Here we describe
AB  - the draft genome of the pig isolate L. salivarius cp400, providing insights into
AB  - host-niche specialization.
ER  -

TY  - JOUR
AU  - Macklaim, J.M.
AU  - Gloor, G.B.
AU  - Anukam, K.C.
AU  - Cribby, S.
AU  - Reid, G.
TI  - At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 4688
EP  - 4695
VL  - 108
AB  - Lactobacilli have long been regarded as important constituents of the healthy
AB  - human vagina. Lactobacillus iners is the most frequently detected bacterial
AB  - species in the vagina, but little is known about its characteristics. We report a
AB  - description of the whole-genome sequence of L. iners AB-1 along with comparative
AB  - analysis of published genomes of closely related strains of lactobacilli. The
AB  - genome is the smallest Lactobacillus reported to date, with a 1.3-Mbp single
AB  - chromosome. The genome seems to have undergone one or more rapid evolution events
AB  - that resulted in large-scale gene loss and horizontal acquisition of a number of
AB  - genes for survival in the vagina. L. iners may exhibit specialized adaptation
AB  - mechanisms to the vaginal environment, such as an iron-sulfur cluster assembly
AB  - system, and several unique sigma factors to regulate gene transcription in this
AB  - fluctuating environment. A potentially highly expressed homolog of a
AB  - cholesterol-binding lysin may also contribute to host cell adhesion or act as a
AB  - defense mechanism against other microbes. Notably, there is a lack of apparent
AB  - adhesion proteins, but several cell-anchor proteins were identified and may be
AB  - important for interaction with the host mucosal tissues. L. iners is widely
AB  - present in healthy females as well as those suffering from bacterial vaginosis or
AB  - who have undergone antimicrobial therapy, suggesting that it is an important
AB  - indigenous species of the vagina.
ER  -

TY  - JOUR
AU  - Mackova, M.
AU  - Pohl, R.
AU  - Hocek, M.
TI  - Polymerase Synthesis of DNAs Bearing Vinyl Groups in the Major Groove and their Cleavage by Restriction Endonucleases.
JO  - Chembiochem
PY  - 2014
SP  - 2306
EP  - 2312
VL  - 15
AB  - DNA molecules containing 5-vinyluracil, 5-vinylcytosine, or 7-deaza-7-vinyladenine were
AB  - prepared by polymerase incorporation of the corresponding vinyl-modified 2-deoxyribonucleoside
AB  - triphosphates, and the influence of the vinyl group in the major groove of DNA on the cleavage
AB  - by diverse type II restriction endonucleases (REs) was studied. The presence of 5-vinyluracil
AB  - was tolerated by most of the REs, whereas only some REs were able to cleave sequences
AB  - containing 7-deaza-7-vinyladenine. The enzyme ScaI was found to cleave DNA containing
AB  - 5-vinylcytosine efficiently but not DNA containing the related 5-ethynylcytosine. All other
AB  - REs failed to cleave sequences containing any cytosine modifications.
ER  -

TY  - JOUR
AU  - MacLea, K.S.
AU  - Trachtenberg, A.M.
TI  - Complete Genome Sequence of Staphylococcus epidermidis ATCC 12228 Chromosome and  Plasmids, Generated by Long-Read Sequencing.
JO  - Genome Announcements
PY  - 2017
SP  - e00954
EP  - e00917
VL  - 5
AB  - Staphylococcus epidermidis ATCC 12228 was sequenced using a long-read method to generate a
AB  - complete genome sequence, including some plasmid sequences. Some
AB  - differences from the previously generated short-read sequence of this
AB  - nonpathogenic and non-biofilm-forming strain were noted. The assembly size was
AB  - 2,570,371 bp with a total G+C% content of 32.08%.
ER  -

TY  - JOUR
AU  - MacLeod, A.R.
AU  - Szyf, M.
TI  - Expression of antisense to DNA methyltransferase mRNA induces DNA demethylation and inhibits tumorigenesis.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 8037
EP  - 8043
VL  - 270
AB  - Many tumor cell lines overexpress DNA methyltransferase (MeTase) activity; however it is still
AB  - unclear whether this increase in DNA MeTase activity plays a casual role in naturally
AB  - occurring tumors and cell lines, whether it is critical for the maintenance of transformed
AB  - phenotypes, and whether inhibition of the DNA MeTase in tumor cells can reverse
AB  - transformation. To address these basic questions, we transfected a murine adrenocortical tumor
AB  - cell line Y1 with a chimeric construct expressing 600 base pairs from the 5' of the DNA
AB  - MeTase cDNA in the antisense orientation. The antisense transfectants show DNA demethylation,
AB  - distinct morphological alterations, are inhibited in their ability to grow in an
AB  - anchorage-independent manner, and exhibit decreased tumorigenicity in syngeneic mice. Ex vivo,
AB  - cells expressing the antisense construct show increased serum requirements, decreased rate of
AB  - growth, and induction of an apoptotic death program upon serum deprivation.
AB  - 5-Azadeoxycytidine-treated cells exhibit a similar dose-dependent reversal of the transformed
AB  - phenotype. These results support the hypothesis that the DNA MeTase is actively involved in
AB  - oncogenic transformation.
ER  -

TY  - JOUR
AU  - MacMillan, A.M.
AU  - Chen, L.
AU  - Verdine, G.L.
TI  - Synthesis of an oligonucleotide suicide substrate for DNA methyltransferases.
JO  - J. Org. Chem.
PY  - 1992
SP  - 2989
EP  - 2991
VL  - 57
AB  - The large-scale chemical synthesis of an oligodeoxynucleotide containing
AB  - 5-fluoro-2'-deoxycytidine (FdC)and its characterization are described. The FdC residue is
AB  - introduced via the corresponding 4-O-(2,4,6-trimethylphenyl)-2'-deoxyuridine derivative,
AB  - which undergoes clean conversion to FdC during removal of the oligonucleotide protecting
AB  - groups with ammonia. A double-stranded oligodeoxynucleotide containing FdC inactivated the DNA
AB  - methyltransferase enzyme M.HaeIII by irreversible formation of a covalent protein-DNA complex.
ER  -

TY  - JOUR
AU  - MacNeil, D.
TI  - Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1988
SP  - 156
EP  - 156
VL  - 88
AB  - Streptomyces avermitilis contains a restriction system that restricts plasmid DNA containing
AB  - N6-methyladenine or 5-methylcytosine. This system restricts DNA isolated from strains with DNA
AB  - methylases. Shuttle vectors iolated from Escherichia coli, or plasmids isolated from
AB  - modification proficient Streptomyces cannot be directly introduced into S. avermitilis. S.
AB  - lividans appears to lack the ability to modify DNA. Plasmids isolated from S. lividans which
AB  - have been modified in vitro with DNA methylases are restricted by S. avermitilis. The
AB  - transformation frequency is reduced 1000-fold when plasmid DNA is modified by dam or TaqI
AB  - methylases to contain N6-methyladenine, or by AluI, HhaI, or HphI methylases to contain
AB  - 5-methylcytosine. Methyl-specific restriction appears to be common in Streptomyces, since
AB  - either N6-methyladenine-specific restriction, or 5-methylcytosine-specific restriction was
AB  - observed in 7 of 9 strains tested. S. avermitilis is unique in that it restricts both
AB  - N6-methyladenine and 5-methylcytosine containing DNA.
ER  -

TY  - JOUR
AU  - MacNeil, D.J.
TI  - Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis.
JO  - J. Bacteriol.
PY  - 1988
SP  - 5607
EP  - 5612
VL  - 170
AB  - Streptomyces avermitilis contains a unique restriction system that restricts plasmid DNA
AB  - containing N6-methyladenine or 5-methylcytosine. Shuttle vectors isolated from Escherichia
AB  - coli RR1 or plasmids isolated from modification-proficient Streptomyces spp. cannot be
AB  - directly introduced into S. avermitilis. This restriction barrier can be overcome by first
AB  - transferring plasmids into Streptomyces lividans or a modification-deficient E. coli strain
AB  - and then into S. avermitilis. The transformation frequency was reduced ->1,000-fold when
AB  - plasmid DNA was modified by dam or TaqI methylases to contain N6-methyladenine or by AluI,
AB  - HhaI, or HphI methylases to contain 5-methylcytosine. Methyl-specific restriction appears to
AB  - be common in Streptomyces spp., since either N6-methyladenine-specific or
AB  - 5-methylcytosine-specific restriction was observed in seven of nine strains tested.
ER  -

TY  - JOUR
AU  - Macori, G.
AU  - Romano, A.
AU  - Adriano, D.
AU  - Razzuoli, E.
AU  - Bianchi, D.M.
AU  - Gallina, S.
AU  - Bellio, A.
AU  - Decastelli, L.
TI  - Draft Genome Sequences of Four Yersinia enterocolitica Strains, Isolated from Wild Ungulate Carcasses.
JO  - Genome Announcements
PY  - 2017
SP  - e00192
EP  - e00117
VL  - 5
AB  - This study describes the draft genome sequences of four Yersinia enterocolitica strains,
AB  - originally isolated from ungulate carcasses. These isolates were typed
AB  - biochemically and two were determined to be highly virulent (biotype 1B). The
AB  - draft genome sequences had a mean size of 4.77 Mb and a mean G+C content of
AB  - 47.1%.
ER  -

TY  - JOUR
AU  - Macreadie, I.G.
AU  - Scott, R.M.
AU  - Zinn, A.R.
AU  - Butow, R.A.
TI  - Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.
JO  - Cell
PY  - 1985
SP  - 395
EP  - 402
VL  - 41
AB  - The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (Omega+) is nearly
AB  - quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (Omega-). The
AB  - intron contains an open reading frame that can encode a protein of 235 amino acids, but no
AB  - function has been ascribed to this sequence. We previously found an in vivo double-strand
AB  - break in Omega- DNA at or close to the intron insertion site only in zygotes of Omega+ x
AB  - Omega- crosses that appears with the same kinetics as intron insertion. We now show that
AB  - mutations in the intron open reading frame that would alter the translation product
AB  - simulataneously inhibit nonreciprocal Omega recombination and the in vivo double-strand break
AB  - in Omega- DNA. These results provide evidence that the open reading frame encodes a protein
AB  - required for intron transposition and support the role of the double strand break in the
AB  - process.
ER  -

TY  - JOUR
AU  - MacWilliams, M.
AU  - Meister, J.
AU  - Jutte, H.
AU  - Bickle, T.
TI  - Generation of a new type-I restriction-modification specificity by transposition.
JO  - J. Cell Biochem. Suppl.
PY  - 1994
SP  - 136
EP  - 136
VL  - 18C
AB  - *
AB  - We have characterised a novel mutant of EcoDXXI, a type IC DNA restriction and modification
AB  - system, in which the specificity has been altered due to a Tn5 insertion into the middle of
AB  - hsdS, the gene which codes the polypepide that confers DNA sequence specificity to both the
AB  - restriction and modification reactions. With the type IR-M systems, both the DNA restriction
AB  - and modification functions are carried out by a single enzyme composed of 3 subunits: hsdS
AB  - (DNA binding specificity), hsdM (modification/methylation), and hsdR (restriction). A complex
AB  - of only hsdS and hsdM can catalyse methylation but not restriction. Type I restriction of
AB  - unmodified DNA occurs a great distance from the enzyme's recognition site and is accompanied
AB  - by large amounts of ATP hydrolysis. It is proposed that the ATP hydrolysis fuels the "pumping"
AB  - of the DNA past the bound enzyme to reach the cleavage site.
AB  - 
AB  - Like other type I enzymes, the wild type EcoDXXI recognises a sequence composed of two
AB  - asymmetrical half sites separated by a spacer region: TCA(N7)RTTC. Purification of the EcoDXXI
AB  - mutant methylase and subsequent in vitro DNA methylation assays, identified the mutant
AB  - recognition sequence as an interrupted palindrome. TCA(N8)TGA, in which the 5' half site of
AB  - the wild type site is repeated in inverse orientation. The additional base pair in the
AB  - non-specific spacer of the mutant recognition sequence maintains the proper spacing between
AB  - the two methylatable adenine groups.
AB  - 
AB  - Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion
AB  - occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl
AB  - DNA binding domain which recognises the 3' half of the EcoDXXI binding site. Subsequent
AB  - deletion analysis demonstrated that the Tn5 element as well as the distal hsdS3' sequence are
AB  - dispensible; an additional 65 bp of the hsdS sequence could also be removed without loss of
AB  - methylation or restriction activity. The minimum characterised hsdS fragment encodes both the
AB  - amino terminal DNA binding domain as well as the conserved repeated sequence that defines the
AB  - length of the recognition site spacer region. The predicted 205 amino acid peptide must
AB  - contain all the information necessary for DNA binding and subunit interactions. We propose
AB  - that the EcoDXXI mutant methylase utilises two truncated hsdS subunits to recognise its
AB  - binding site. The implications of this finding in terms of subunit interactions and the
AB  - malleability of the type I R-M system will be discussed.
AB  - 
ER  -

TY  - JOUR
AU  - MacWilliams, M.P.
AU  - Bickle, T.A.
TI  - Generation of new DNA binding specificity by truncation of the type IC EcoDXXI hsdS gene.
JO  - EMBO J.
PY  - 1996
SP  - 4775
EP  - 4783
VL  - 15
AB  - The hsdS subunit of a type IC restriction-modification enzyme is responsible for the enzyme's
AB  - DNA binding specificity.  Type I recognition sites are characterized by two defined half-sites
AB  - separated by a non-specific spacer of defined length.  The hsdS subunit contains two
AB  - independent DNA binding domains, each targeted towards one DNA half-site.  We have shown
AB  - previously that the 5' half of hsdS can code for a functional substitute of the full-length
AB  - hsdS.  Here we demonstrate that the 3' half of the gene, when fused to the appropriate
AB  - transcriptional and translational start signals, also codes for a peptide which imparts DNA
AB  - binding specificity to the enzyme.  About half the natural hsdS size, the mutant peptide
AB  - contains a single DNA recognition domain flanked by one copy of each internal repeat found in
AB  - the full-length hsdS.  Deletion of either repeat sequence results in loss of activity.  Like
AB  - the 5' hsdS mutant, the 3' mutant recognizes an interrupted palindrome, GAAYN5RTTC,
AB  - suggesting that two truncated subunits participate in DNA recognition.  Coexpression of the
AB  - 5' hsdS mutant and the 3' hsdS mutant along with hsdM regenerates the wild-type methylation
AB  - specificity.  Thus, there is a free assortment of subunits in the cell.
ER  -

TY  - JOUR
AU  - Madani, N.
AU  - Giraud, P.
AU  - Mendy, C.
AU  - Colaneri, C.
AU  - Cherchame, E.
AU  - Cherfa, M.A.
AU  - Richomme, C.
AU  - Decors, A.
AU  - Girault, G.
TI  - First Draft Genome Sequences of Three Strains of Francisella tularensis subsp. holarctica, Isolated from Hares and a Tick in France.
JO  - Genome Announcements
PY  - 2017
SP  - e00993
EP  - e00917
VL  - 5
AB  - Here, we report the complete genome sequences of three strains of Francisella tularensis
AB  - subsp. holarctica (11-789-5S, 11-935-13S, and 11-930-9S), isolated
AB  - from brown hares and a tick during a tularemia outbreak in France, where
AB  - tularemia is endemic.
ER  -

TY  - JOUR
AU  - Madhaiyan, M.
AU  - Chan, K.L.
AU  - Ji, L.
TI  - Draft Genome Sequence of Methylobacterium sp. Strain L2-4, a Leaf-Associated Endophytic N-Fixing Bacterium Isolated from Jatropha curcas L.
JO  - Genome Announcements
PY  - 2014
SP  - e01306
EP  - e01314
VL  - 2
AB  - Methylobacterium sp. strain L2-4 is an efficient nitrogen-fixing leaf colonizer of biofuel
AB  - crop Jatropha curcas. This strain is able to greatly improve the
AB  - growth and seed yield of Jatropha curcas and is the second reported genome
AB  - sequence of plant growth-promoting bacteria isolated from Jatropha curcas.
ER  -

TY  - JOUR
AU  - Madhaiyan, M.
AU  - Peng, N.
AU  - Ji, L.
TI  - Complete Genome Sequence of Enterobacter sp. Strain R4-368, an Endophytic N-Fixing Gammaproteobacterium Isolated from Surface-Sterilized Roots of Jatropha   curcas L.
JO  - Genome Announcements
PY  - 2013
SP  - e00544
EP  - e00513
VL  - 1
AB  - Enterobacter sp. strain R4-368 is one of the few characterized Jatropha endophytic
AB  - diazotrophic bacteria and was isolated from surface-sterilized roots.
AB  - This bacterium shows strong growth-promoting effects, being able to increase
AB  - plant biomass and seed yields. Enterobacter sp. R4-368 is the second fully
AB  - sequenced diazotrophic Enterobacter species. The sequence information shall
AB  - facilitate the elucidation of the molecular mechanisms of plant growth promotion,
AB  - nitrogen fixation in nonlegume plant species, and evolution of biological
AB  - nitrogen fixation systems.
ER  -

TY  - JOUR
AU  - Madhavan, T.P.
AU  - Steen, J.A.
AU  - Hugenholtz, P.
AU  - Sakellaris, H.
TI  - Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C.
JO  - Genome Announcements
PY  - 2014
SP  - e00247
EP  - e00214
VL  - 2
AB  - Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease around the
AB  - globe, causing an estimated 380,000 deaths annually. The disease is caused by a wide variety
AB  - of strains. Here, we report the genome sequence of ETEC strain B2C, which was isolated from an
AB  - American soldier in Vietnam.
ER  -

TY  - JOUR
AU  - Madhavilatha, G.K.
AU  - Joseph, B.V.
AU  - Paul, L.K.
AU  - Kumar, R.A.
AU  - Hariharan, R.
AU  - Mundayoor, S.
TI  - Whole-Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Kerala, South India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4430
EP  - 4430
VL  - 194
AB  - We report the annotated genome sequence of two clinical isolates of Mycobacterium tuberculosis
AB  - isolated from Kerala, India.
ER  -

TY  - JOUR
AU  - Madhusoodanan, J.
AU  - Seo, K.S.
AU  - Remortel, B.
AU  - Park, J.Y.
AU  - Hwang, S.Y.
AU  - Fox, L.K.
AU  - Park, Y.H.
AU  - Deobald, C.F.
AU  - Wang, D.
AU  - Liu, S.
AU  - Daugherty, S.C.
AU  - Gill, A.L.
AU  - Bohach, G.A.
AU  - Gill, S.R.
TI  - An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1854
EP  - 1862
VL  - 193
AB  - Cocolonization of human mucosal surfaces causes frequent encounters
AB  - between various staphylococcal species, creating opportunities for the
AB  - horizontal acquisition of mobile genetic elements. The majority of
AB  - Staphylococcus aureus toxins and virulence factors are encoded on S.
AB  - aureus pathogenicity islands (SaPIs). Horizontal movement of SaPIs between
AB  - S. aureus strains plays a role in the evolution of virulent clinical
AB  - isolates. Although there have been reports of the production of toxic
AB  - shock syndrome toxin 1 (TSST-1), enterotoxin, and other superantigens by
AB  - coagulase-negative staphylococci, no associated pathogenicity islands have
AB  - been found in the genome of Staphylococcus epidermidis, a generally less
AB  - virulent relative of S. aureus. We show here the first evidence of a
AB  - composite S. epidermidis pathogenicity island (SePI), the product of
AB  - multiple insertions in the genome of a clinical isolate. The taxonomic
AB  - placement of S. epidermidis strain FRI909 was confirmed by a number of
AB  - biochemical tests and multilocus sequence typing. The genome sequence of
AB  - this strain was analyzed for other unique gene clusters and their
AB  - locations. This pathogenicity island encodes and expresses staphylococcal
AB  - enterotoxin C3 (SEC3) and staphylococcal enterotoxin-like toxin L (SElL),
AB  - as confirmed by quantitative reverse transcription-PCR (qRT-PCR) and
AB  - immunoblotting. We present here an initial characterization of this novel
AB  - pathogenicity island, and we establish that it is stable, expresses
AB  - enterotoxins, and is not obviously transmissible by phage transduction. We
AB  - also describe the genome sequence, excision, replication, and packaging of
AB  - a novel bacteriophage in S. epidermidis FRI909, as well as attempts to
AB  - mobilize the SePI element by this phage.
ER  -

TY  - JOUR
AU  - Madhusoodanan, U.K.
AU  - Rao, D.N.
TI  - Diversity of DNA methyltransferases that recognize asymmetric target sequences.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 2010
SP  - 125
EP  - 145
VL  - 45
AB  - DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer
AB  - from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases
AB  - usually recognize palindromic DNA sequences and add a methyl group to the target base (either
AB  - adenine or cytosine) on both strands. However, there are a number of MTases that recognize
AB  - asymmetric target sequences and differ in their subunit organization. In a bacterial cell,
AB  - after each round of replication, the substrate for any MTase is hemimethylated DNA, and it
AB  - therefore needs only a single methylation event to restore the fully methylated state. This is
AB  - in consistent with the fact that most of the DNA MTases studied exist as monomers in solution.
AB  - Multiple lines of evidence suggest that some DNA MTases function as dimers. Further,
AB  - functional analysis of many restriction-modification systems showed the presence of more than
AB  - one or fused MTase genes. It was proposed that presence of two MTases responsible for the
AB  - recognition and methylation of asymmetric sequences would protect the nascent strands
AB  - generated during DNA replication from cognate restriction endonuclease. In this review, MTases
AB  - recognizing asymmetric sequences have been grouped into different subgroups based on their
AB  - unique properties. Detailed characterization of these unusual MTases would help in better
AB  - understanding of their specific biological roles and mechanisms of action. The rapid progress
AB  - made by the genome sequencing of bacteria and archaea may accelerate the identification and
AB  - study of species- and strain-specific MTases of host-adapted bacteria and their roles in
AB  - pathogenic mechanisms.</.
ER  -

TY  - JOUR
AU  - Madsen, A.
AU  - Josephsen, J.
TI  - The LlaGI restriction and modification system of Lactococcus lactis W10 consists of only one single polypeptide.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 91
EP  - 96
VL  - 200
AB  - The naturally occurring 12.1-kb plasmid, pEW104, in Lactococcus lactis ssp. cremoris W10 was
AB  - found to confer decreased bacteriophage sensitivity to its host. Plasmid pEW104 encodes a
AB  - non-classic restriction and modification (R/M) system, named LlaGI, consisting of only one
AB  - single polypeptide. Analysis of the amino acid sequence revealed the presence of a catalytic
AB  - motif and seven helicase-like motifs (DEAD-box motifs) characteristic of type I and III
AB  - endonucleases, followed by four conserved methylase motifs characteristic of
AB  - adenine-methylases. A comparison between LlaGI and the very similar R/M system, LlaBIII,
AB  - suggests that the C-terminal region of LlaGI, apparently containing no known motifs, could
AB  - possibly specify target DNA recognition. Conceivably, the LlaGI gene is included in the operon
AB  - of the plasmid replication machinery. Finally, it is proposed that LlaGI represents a variant
AB  - of the type I R/M systems.
ER  -

TY  - JOUR
AU  - Madsen, A.
AU  - Josephsen, J.
TI  - Characterization of LlaCI, a new restriction-modification system from Lactococcus lactis subsp. cremoris W15.
JO  - Biol. Chem.
PY  - 1998
SP  - 443
EP  - 449
VL  - 379
AB  - The genes encoding the restriction-modification system LlaCI have been found on the naturally
AB  - occurring 7.0 kb plasmid pAW153 in L. lactis subsp. cremoris W15.  The R/M system was isolated
AB  - on a chloramphenicol resistant derivative of the wild type plasmid (pAW153cat).  Plasmid
AB  - pAW153cat and a 2.4 kb HincII-SphI fragment cloned into a high- and a low-copy vector
AB  - conferred decreased sensitivity in L. lactis LM2301 and L. lactis SMQ86 against small
AB  - isometric-headed phages of the 936 or P335 species, respectively.  Increased plasmid copy
AB  - number enhanced the level of phage restriction.  Sequencing the 2.4 kb HincII-SphI fragment
AB  - revealed two open reading frames arranged convergently with a 94 bp separation.  IIaCIM showed
AB  - 66% identity to hindIIIM, and IlaCIR showed 45% identity to hindIIIR.  The organization of the
AB  - LlaCI operon differs from the HindIII operon, where the endonuclease and methylase genes
AB  - overlap and are transcribed in the same direction.  The LlaCI methylase is predicted to be 296
AB  - amino acids long, with 63% identity to the HindIII methylase, while the LlaCI endonuclease is
AB  - predicted to consist of  324 or 332 amino acids, depending on the position of the start codon.
AB  - It shows 24% identity to the HindIII endonuclease.
ER  -

TY  - JOUR
AU  - Madsen, A.
AU  - Josephsen, J.
TI  - Cloning and characterization of the lactococcal plasmid-encoded type II restriction/modification system, LlaDII.
JO  - Appl. Environ. Microbiol.
PY  - 1998
SP  - 2424
EP  - 2431
VL  - 64
AB  - The LlaDII restriction/modification system was found on the naturally occurring 8.9-kb plasmid
AB  - pHW393 in Lactococcus lactis subsp. cremoris W39.  A 2.4-kb PstI-EcoRI fragment inserted into
AB  - the Escherichia coli-L.lactis shuttle vector pCI3340 conferred to L. lactis LM2301 and L.
AB  - lactis SMQ86 resistance against representatives of the three most common lactococcal phage
AB  - species: 936, P335, and c2.  The LlaDII endonuclease was partially purified and found to
AB  - recognize and cleave the sequence 5'-GC/NGC-3', where the arrow indicates the cleavage site.
AB  - It is thus an isoschizomer of the commercially available restriction endonuclease Fnu4HI.
AB  - Sequencing of the 2.4-kb PstI-EcoRI fragment revealed two open reading frames-arranged
AB  - tandemly and separated by a 105-bp intergenic region.  The endonuclease gene of 543 bp
AB  - preceded the methylase gene of 954 bop.  The deduced amino acid sequence of the LlaDII R/M
AB  - system showed high homology to that of its only sequence isoschizomer, Bsp6I from Bacillus sp.
AB  - strain RFL6, with 41% identity between the endonucleases and 60% identity between the
AB  - methylases.  The genetic organizations of the LlaDII and Bsp6I R/M systems are identical.
AB  - Both methylases have two recognition sites (5'-GCGGC-3' and 5'-GCCGC-3') forming a
AB  - putative stem-loop structure spanning part of the presumed -35 sequence and part of the
AB  - intervening region between the -35 and -10 sequences.  Alignment of the LlaDII and Bsp6I
AB  - methylases with other m5C methylases showed that the protein primary structures possessed the
AB  - same organization.
ER  -

TY  - JOUR
AU  - Madsen, A.
AU  - Nellemann, L.J.
AU  - Josephsen, J.
TI  - The restriction and modification system LlaCI and its use in the development of phage resistant lactococcal starter cultures.
JO  - FASEB J.
PY  - 1997
SP  - A1035
EP  - A1035
VL  - 11
AB  - The mixed Cheddar starter culture, TK5, consisting of Lactococcus lactis strains, is highly
AB  - bacteriophage resistant, and has been used for cheese production for 12 years.  One of the
AB  - major problems encountered in the dairy industry is infection of the starter cultures by lytic
AB  - phages.  It is possible to obtain plasmids encoding phage defense mechanisms from bacterial
AB  - isolates of TK5.  The 7 kb plasmid, pAW153, from isolate W15, encodes the type II R/M system,
AB  - LlaCI with recognition sequence AAGCTT, an isoschizomer of HindIII.  LlaCI restricts the small
AB  - isometric headed lactococcal phage p2 with an EOP of 10^-2, this effect, together with other
AB  - bacteriophage resistance mechanisms, will be utilized in experiments for the development of
AB  - phage resistant starter cultures.  A 2.4 kb HincII-SphI fragment containing LlaCI was
AB  - subcloned from pAW153 into pC13340 to generate pCAC1.  The nucleotide sequence of this
AB  - fragment encoding the LlaCI activity has been determined.  Analysis of the DNA sequence
AB  - predicts; A, a methylase of 296 amino acids showing 62% identity to M.HindIII, and B, an
AB  - endonuclease of 332 amino acids showing 24% identity to R.HindIII.  The methylase is an
AB  - adenine methylase containing the I-D-PY, LK, T-KP-L, and LD-F-GSGTT-A motifs characteristic of
AB  - this class of adenine methylases.  Upstream of the two genes, putative ribosome binding sites
AB  - and promoter regions are situated.
ER  -

TY  - JOUR
AU  - Madsen, A.
AU  - Westphal, C.
AU  - Josephsen, J.
TI  - Characterization of a novel plasmid-encoded HsdS subunit, S.LlaW12I, from Lactococcus lactis W12.
JO  - Plasmid
PY  - 2000
SP  - 196
EP  - 200
VL  - 44
AB  - A novel type I restriction-modification specificity subunit, S.LlaW12I, has been identified on
AB  - the naturally occurring 8.0-kb plasmid pAW122 in the lactic acid bacterium Lactococcus lactis
AB  - subsp. cremoris W12. Presence of the HsdS protein together with a complete type I
AB  - restriction-modification system conferred increased phage restriction to the host, indicating
AB  - exchange of specificity subunits. Sequence analysis showed that the S.LlaW12I subunit is most
AB  - probably of type IC. Presumably, the hsdS gene is organized together with the repB gene on one
AB  - transcriptional unit.
ER  -

TY  - JOUR
AU  - Madueno, L.
AU  - Macchi, M.
AU  - Morelli, I.S.
AU  - Coppotelli, B.M.
TI  - Draft Whole-Genome Sequence of Sphingobium sp. 22B, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium from Semiarid Patagonia, Argentina.
JO  - Genome Announcements
PY  - 2016
SP  - e00488
EP  - e00416
VL  - 4
AB  - Sphingobium sp. 22B is a polycyclic aromatic hydrocarbon-degrading strain isolated from
AB  - Patagonia, Argentina, with capabilities to withstand the
AB  - environmental factors of that semiarid region. The draft genome shows the
AB  - presence of genes related with responses to carbon starvation and drying
AB  - environmental conditions.
ER  -

TY  - JOUR
AU  - Maeda, A.H.
AU  - Nishi, S.
AU  - Ishii, S.
AU  - Shimane, Y.
AU  - Kobayashi, H.
AU  - Ichikawa, J.
AU  - Kurosawa, K.
AU  - Arai, W.
AU  - Takami, H.
AU  - Ohta, Y.
TI  - Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off  Kashima, Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00200
EP  - e00218
VL  - 6
AB  - Altererythrobacter sp. strain B11 is an aromatic monomer-degrading bacterium newly isolated
AB  - from sediment under the seabed off Kashima, Japan, at a depth of
AB  - 2,100 m. Here, we report the complete nucleotide sequence of the genome of strain
AB  - B11.
ER  -

TY  - JOUR
AU  - Maeda, A.H.
AU  - Nishi, S.
AU  - Ozeki, Y.
AU  - Ohta, Y.
AU  - Hatada, Y.
AU  - Kanaly, R.A.
TI  - Draft Genome Sequence of Sphingobium sp. Strain KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Isolated from Cattle Pasture   Soil.
JO  - Genome Announcements
PY  - 2013
SP  - e00911
EP  - e00913
VL  - 1
AB  - Sphingobium sp. strain KK22 was isolated from a bacterial consortium that originated from
AB  - cattle pasture soil from Texas. Strain KK22 grows on phenanthrene
AB  - and has been shown to biotransform the high-molecular-weight (HMW) polycyclic
AB  - aromatic hydrocarbon (PAH) benz[a]anthracene. The genome of strain KK22 was
AB  - sequenced to investigate the genes involved in aromatic pollutant
AB  - biotransformation.
ER  -

TY  - JOUR
AU  - Maeder, D.L.
AU  - Anderson, I.
AU  - Brettin, T.S.
AU  - Bruce, D.C.
AU  - Gilna, P.
AU  - Han, C.S.
AU  - Lapidus, A.
AU  - Metcalf, W.W.
AU  - Saunders, E.
AU  - Tapia, R.
AU  - Sowers, K.R.
TI  - The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive  rearrangement within methanosarcinal genomes.
JO  - J. Bacteriol.
PY  - 2006
SP  - 7922
EP  - 7931
VL  - 188
AB  - We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with
AB  - those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is
AB  - distinguished by having an organization that is well conserved with respect to the other
AB  - Methanosarcina spp. in the region proximal to the origin of replication, with interspecies
AB  - gene similarities as high as 95%. However, it is disordered and marked by increased
AB  - transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of
AB  - the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80%
AB  - identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique
AB  - (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes
AB  - required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a
AB  - bacterial-like P450-specific ferredoxin reductase cluster not previously observed or
AB  - characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene
AB  - flanked by a presumptive origin of replication consisting of 38 tandem repeats of a
AB  - 143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals
AB  - differing mechanisms for the accrual of changes. Elongation of the relatively large M.
AB  - acetivorans genome is the result of uniformly distributed multiple gene scale insertions and
AB  - duplications, while the M. barkeri genome is characterized by localized inversions associated
AB  - with the loss of gene content. In contrast, the short M. mazei genome most closely
AB  - approximates the putative ancestral organizational state of these species.
ER  -

TY  - JOUR
AU  - Maeder, D.L.
AU  - Weiss, R.B.
AU  - Dunn, D.M.
AU  - Cherry, J.L.
AU  - Gonzalez, J.M.
AU  - DiRuggiero, J.
AU  - Robb, F.T.
TI  - Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.
JO  - Genetics
PY  - 1999
SP  - 1299
EP  - 1305
VL  - 152
AB  - Divergence of the hyperthermophilic Archaea, Pyrococcus furiosus and Pyrococcus horikoshii,
AB  - was assessed by analysis of complete genomic sequences of both
AB  - species. The average nucleotide identity between the genomic sequences is 70-75%
AB  - within ORFs. The P. furiosus genome (1.908 mbp) is 170 kbp larger than the P.
AB  - horikoshii genome (1.738 mbp) and the latter displays significant deletions in
AB  - coding regions, including the trp, his, aro, leu-ile-val, arg, pro, cys, thr, and
AB  - mal operons. P. horikoshii is auxotrophic for tryptophan and histidine and is
AB  - unable to utilize maltose, unlike P. furiosus. In addition, the genomes differ
AB  - considerably in gene order, displaying displacements and inversions. Six allelic
AB  - intein sites are common to both Pyrococcus genomes, and two intein insertions
AB  - occur in each species and not the other. The bacteria-like methylated chemotaxis
AB  - proteins form a functional group in P. horikoshii, but are absent in P. furiosus.
AB  - Two paralogous families of ferredoxin oxidoreductases provide evidence of gene
AB  - duplication preceding the divergence of the Pyrococcus species.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Reich, N.O.
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
JO  - FASEB J.
PY  - 1992
SP  - A61
EP  - A61
VL  - 6
AB  - The EcoRI DNA methyltransferase is part of a type II restriction modification
AB  - system and methylates the second adenine in the recognition sequence GAATTC.
AB  - Cys223 was implicated as a critical residue by our previous protein chemical
AB  - data ((1990) J. Biol. Chem. 265,17713-17719) and by homology to other DNA
AB  - methyltransferases.  Substitution of Cys223 with Ser, Ala, and Gly by site
AB  - directed methods produced three mutant enzymes all with altered substrate
AB  - specificity.  Kinetic analysis of the mutant enzymes yields kcat and kmDNA
AB  - values for the canonical site, that do not significantly differ from those of
AB  - the wild type enzyme.  However, a significant decrease in the methylation of
AB  - non-canonical sequences is observed with the mutant enzymes both in vitro and
AB  - in vivo.  Our results suggest that either Cys223 is near the DNA binding region
AB  - or that flexibility in the region of Cys223 may be important for specificity.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Reich, N.O.
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
JO  - Biophys. J.
PY  - 1992
SP  - A61
EP  - A61
VL  - 61
AB  - The EcoRI DNA methyltransferase is part of a type II restriction modification
AB  - system and methylates the second adenine in the recognition sequence GAATTC.
AB  - Cys223 was implicated as a critical residue by our previous protein chemical
AB  - data [1990] J. Biol. Chem. 265, 17713-17719) and by homology to other DNA
AB  - methyltransferases.  Substitution of Cys223 with Ser, Ala, and Gly by site
AB  - directed methods produced three mutant enzymes all with altered substrate
AB  - specificity.  Kinetic analysis of the mutant enzymes yields kcat and kmDNA
AB  - values for the canonical site, that do not significantly differ from those of
AB  - the wild type enzyme.  However, a significant decrease in the methylation of
AB  - non-canonical sequences is observed with the mutant enzymes both in vitro and
AB  - in vivo.  Our results suggest that either Cys223 is near the DNA binding region
AB  - or that flexibility in the region of Cys223 may be important for specificity.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Reich, N.O.
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
JO  - Biochemistry
PY  - 1992
SP  - 2197
EP  - 2197
VL  - 31
AB  - The EcoRI DNA methyltransferase is part of a type-II restriction modification
AB  - system and methylates the second adenine in the recognition sequence GAATTC.
AB  - Cys223 was implicated as a critical residue by our previous protein chemical
AB  - data [1990] J. Biol. Chem. 265, 17713-17719] and by homology to other DNA
AB  - methyltransferases.  Substitution of Cys223 with Ser, Ala, and Gly by
AB  - site-directed methods produced three mutant enzymes, all with altered substrate
AB  - specificity.  Kinetic analysis of the mutant enzymes yields Kcat and KmDNA
AB  - values for the canonical site that do not significantly differ from those of
AB  - the wild type enzyme.  However, a significant decrease in the methylation of
AB  - noncanonical sequences is observed with the mutant enzymes both in vitro and in
AB  - vivo.  Our results suggest that either Cys223 is near the DNA binding region or
AB  - that flexibility in the region of Cys223 may be important for specificity.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Reich, N.O.
TI  - Enhanced substrate specificity observed in EcoRI DNA methyltransferase upon mutagenesis of cysteine 223.
JO  - ACS Abstracts
PY  - 1992
SP  - 57
EP  - BIOL
VL  - 203
AB  - The EcoRI DNA methyltransferase is part of a type II restriction-modification system and
AB  - methylates the second adenine in the recognition sequence GAATTC. Cys223 was implicated as a
AB  - critical residue by our previous protein chemical data (JBC, 1990, 265: 17713-17719) and by
AB  - homology to other DNA methyltransferases. Substitution of Cys223 with Ser, Ala and Gly by
AB  - site-directed methods produced three mutant enzymes all with altered substrate specificity.
AB  - Kinetic analysis of the mutant enzymes yields Kcat and KmDNA values for the cannonical site
AB  - that do not significantly differ from those of the wild type enzyme. However, a significant
AB  - decrease in the methylation of non-canonical sequences is observed with the mutant enzymes
AB  - both in vitro and in vivo. Our results suggest that either Cys223 is near the DNA binding
AB  - region or that flexibility in the region of Cys223 may be important for specificity.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Reich, N.O.
TI  - Enhanced substrate discriminiation and identification of an essential catalytic residue of the EcoRI DNA methyltransferase by site directed mutagenesis.
JO  - FASEB J.
PY  - 1993
SP  - A1197
EP  - A1197
VL  - 7
AB  - The EcoRI DNA methyltransferase (Mtase) is part of a type II restriction modification system
AB  - and catalyzes the AdoMet dependent methylation of the ds-DNA sequence GAATTC. Cys223 was
AB  - implicated as a critical functional residue by prevous protein chemical data [(1990) J. Biol.
AB  - Chem. 265, 17713-17719] and by sequence homology. Substitution of Cys223 with Ser, Ala, and
AB  - Gly by site directed mutagenesis produced three mutant Mtases with enhanced sequence
AB  - specificity. Further characterization of the mutants has indicated possible mechanistic
AB  - reasons for the enhanced specificity. Chemical modification with DEPC has identified one
AB  - histidine residue with a pKa of approx 6, which is critical for catalysis. Site directed
AB  - mutagenesis was used to identify which histidine is critical and to better understand the role
AB  - of histidine in the chemical mechanism of the Mtase. Limited proteolysis of the Mtase in the
AB  - presence of DNA and the AdoMet analog sinefungin produced a 26 kDa (p26) and a 12 kDa (p12)
AB  - fragment [(1991) Biochemistry 30, 2940-2946]. Preliminary results suggested that the p26
AB  - fragment retained significant activity. Therefore, p26 (aa's 105-end) was genetically
AB  - produced, expressed and characterized.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Shoemaker, D.
AU  - Everett, B.
AU  - Reich, N.O.
TI  - Limited proteolysis of EcoRI DNA methylase.
JO  - FASEB J.
PY  - 1990
SP  - A1793
EP  - A1793
VL  - 4
AB  - Limited proteolysis by soybean trpsin in the presence of various combinations
AB  - of ligands was used to probe the domain structure of the EcoRI DNA methylase
AB  - and its interactions with DNA, S-adenosyl methionine (AdoMet), S-Adenosyl
AB  - homocysteine (AdoHcy) and sinefungin (an AdoMet analog).  Proteolysis at 37C
AB  - initially results in cleavage at Lys-14 and Lys-16 followed by cleaving at
AB  - Arg-217.  The resultant fragments (14,22,22.5 Kilodaltons) are relatively
AB  - resistant to further cleavage.  This cleavage pattern was also found with
AB  - proteases of different specificities.  This data suggests a tertiary structure
AB  - consisting of two domains connected by a tether region.  In the presence of
AB  - AdoMet, AdoHcy, or DNA the 22K and 14K fragments are formed, but the rate of
AB  - proteolysis is slowed by as much as 100-fold.  Although AdoMet and sinefungin
AB  - have comparable affinities for the methylase, sinefungin shows no ability to
AB  - slow the rate of proteolysis.  Thus the methylase-sinefungin complex is
AB  - conformationally distinct from the methylase-AdoMet complex.  In the presence
AB  - of both DNA and sinefungin, proteolysis results in the cleavage of the first
AB  - 105 amino acids generating fragments of 12 and 26K.  These fragments show the
AB  - greatest resistance to further proteolysis and initial results suggest that the
AB  - 26K fragment is active.
ER  -

TY  - JOUR
AU  - Maegley, K.
AU  - Shoemaker, D.
AU  - Reich, N.O.
TI  - Covalent intermediate in EcoRI DNA methyltransferase investigated by site directed mutagenesis.
JO  - J. Cell. Biochem.
PY  - 1991
SP  - 175
EP  - 175
VL  - 15G
AB  - EcoRI DNA methyltransferase catalyses the methylation of the second adenine in
AB  - the recognition sequence GAATTC, at the N6 position.  Our protein modification
AB  - studies have implicated cysteine 223 as an important residue in the chemical
AB  - mechanism of the methyltransferase (JBC 265, 17713-17719).  Cytosine N4 and
AB  - adenine N6 methyltransferases are two unrelated classes of enzymes that
AB  - catalyze similar reactions and our analyses show homology between both types of
AB  - methyltransferases in the region of cysteine 223.  Based on these results and
AB  - the fact that the N6 of adenine is a poor nucleophile, we have proposed a
AB  - chemical mechanism involving a covalent enzyme-DNA intermediate.  Three mutants
AB  - have been constructed to test the proposed mechanism; ser223, ala223 and
AB  - gly223.  Characterization of these mutants will be described.
ER  -

TY  - JOUR
AU  - Maegley, K.A.
TI  - Structural and functional characterization of the EcoRI DNA methyltransferase.
JO  - Diss. Abstr.
PY  - 1995
SP  - 3293B
EP  - 3293B
VL  - 55
AB  - *
AB  - This dissertation describes continued structural and functional characterization of the EcoRI
AB  - DNA Methyltransferase (MTase). The MTase catalyzes the transfer of a methyl group from
AB  - S-adenosyl-L-methionine (AdoMet) to the N6 position of the second adenine in the DNA sequence
AB  - 5' GAATTC 3'. Previously, little structural information was available on this MTase. Only
AB  - recently has a crystal structure been solved for an AdoMet-dependent enzyme. Structural
AB  - characterization of the MTase was performed using the techniques of limited proteolysis and
AB  - fluorescence spectroscopy. Site-directed mutagenesis was used to investigate the role of
AB  - Cys223 in the chemical mechanism of the MTase.
AB  - 
AB  -         Limited proteolysis of the MTase with trypsin suggests that the MTase is a two domain
AB  - protein consisting of a large N-terminal domain connected to a smaller C-terminal domain by a
AB  - flexible, solvent-exposed region. This "hinge" region contains part of the AdoMet binding site
AB  - and is close to two residues discussed below, Trp225 and Cys223. Structural dynamics of the
AB  - MTase were probed by performing proteolysis in the presence of the following ligands: AdoMet,
AB  - S-adenosyl-L-homocysteine (AdoHcy), sinefungin (an AdoMet analog) and DNA. All of the ligands
AB  - except sinefungin protected the Mtase from digestion, with AdoMet affording the greatest
AB  - protection (approx. 1000-fold). These results imply that there are structural differences
AB  - between the MTase-AdoMet, MTase-AdoHcy and MTase-sinefungin binary complexes.
AB  - 
AB  -         Fluorescence spectroscopy of the wild-type and tryptophan 183 to phenylalanine (WF183)
AB  - mutant MTases suggests that the two tryptophans within the MTase (W183 and W225) are partially
AB  - buried within the protein. Changes in the MTase emission spectrum upon AdoMet, AdoHcy,
AB  - adenosine, or adenine binding are not consistent with a ligand induced conformational change.
AB  - Therefore, the protection from proteolysis seen upon AdoMet binding is likely due to steric
AB  - obstruction of the cleavage site by the bound cofactor or by increaased rigidity of the hinge
AB  - region when AdoMet is bound.
AB  - 
AB  -         The fluorescence intensity of the wild-type MTase is substantially increased by the
AB  - formation of the MTase-DNA complex, whereas the fluorescence intensity of the WF183 MTase-DNA
AB  - complex decreases slightly upon DNA binding. This indicates that the fluorescence of
AB  - tryptophan 225 is greatly enhanced upon DNA binding. DNA binding may cause a conformational
AB  - change which results in the movement of tryptophan 225 away from a positively charged residue
AB  - such as arginine or lysine. Alternatively, the negatively charged phosphate backbone of the
AB  - DNA may form salt bridges with positively charged residues near tryptophan 225, thereby
AB  - causing the fluorescence intensity to increase.
AB  - 
AB  -         Protein modification studies with the MTase implicated Cys223 as being critical for
AB  - catalysis. Therefore, three mutant MTases were constructed, cysteine 223 to serine (CS223),
AB  - alanine (CA223), and glycine (CG223). Kinetic analysis of the mutants indicates that their
AB  - ability to methylate the canonical site remains unchanged, while their ability to methylate
AB  - closely related non-canonical sites is significantly decreased. The mutant MTases are enhanced
AB  - in their specificity. Detailed analysis of the CG223 mutant suggests that Cys223 does not
AB  - directly contact the DNA. Initial velocity and single turnover kinetics showed that a
AB  - significant portion of the enhanced specificity is due to a 5-fold decrease in the rate of
AB  - methyl transfer (kmeth). For both the wild-type and CG223 MTases kmeth is substantially faster
AB  - than kcat for canonical site methylation, whereas kmeth determines kcat for non-canonical
AB  - methylation.
AB  - 
ER  -

TY  - JOUR
AU  - Maegley, K.A.
AU  - Gonzalez, L.
AU  - Smith, D.W.
AU  - Reich, N.O.
TI  - Cofactor and DNA interactions in EcoRI DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 1992
SP  - 18527
EP  - 18532
VL  - 267
AB  - EcoRI DNA methyltransferase contains tryptophans at positions 183 and 225. Tryptophan 225 is
AB  - adjacent to residues previously implicated in S-adenosylmethionine (AdoMet) binding and to
AB  - cysteine 223, previously shown to be the site of N-ethyl maleimide-mediated inactivation of
AB  - the enyzme (Reich,N.O, and Everett,E. (1990) J. Biol Chem. 265, 8929-8934; Everett,E.A.,
AB  - Falick, A.M., and Reich, N.O. (1990) J. Biol Chem 265, 17713-17719). The fluorescence spectra
AB  - of the wild-type enzyme is centered at 338 nm indicating partial tryptophan solvent
AB  - accessibility. Substitution of tryptophan 183 with phenylalanine results n a 45% drop in
AB  - fluorescence intensity, but no shift in lambdamax. DNA binding to the wild-type
AB  - methyltransferase caused an increase in the fluorescence intensity, while binding to the
AB  - tryptophan 183 mutant had a quenching effect, suggesting that DNA binding induces a
AB  - conformational change near both tryptophans. Binding of AdoMet and various AdoMet analogs to
AB  - the wild-type methyltransferase results in no change in the fluorescence spectrum when
AB  - excitation occurs at 295 nm, suggesting that no conformational change occurs, and AdoMet does
AB  - not interact with either tryptophan. In contrast, quenching was observed when excitation
AB  - occurred at 280 nm, suggesting that AdoMet and its analogs may be quenching tyrosine to
AB  - tryptophan energy transfer. Protein-ligand complexes were titrated with acrylamide, and the
AB  - data also implicate conformational changes upon DNA binding but not upon AdoMet binding,
AB  - consistent with previous limited proteolysis results (Reich, N.O., Maegley, K.A., Shoemaker,
AB  - D.D. and Everett, E. (1991) Biochemistry 30 2940-2946).
ER  -

TY  - JOUR
AU  - Maehara, T.
AU  - Itaya, M.
AU  - Ogura, M.
AU  - Tanaka, T.
TI  - Effect of Bacillus subtilis BsuM restriction-modification on plasmid transfer by polyethylene glycol-induced protoplast fusion.
JO  - FEMS Microbiol. Lett.
PY  - 2011
SP  - 49
EP  - 55
VL  - 325
AB  - Polyethylene glycol (PEG)-induced cell fusion is a promising method to transfer larger DNA
AB  - from one cell to another than conventional genetic
AB  - DNA transfer systems. The laboratory strain Bacillus subtilis 168
AB  - contains a restriction (R) and modification (M) system, BsuM, which
AB  - recognizes the sequence 5'-CTCGAG-3'. To study whether the BsuM system
AB  - affects DNA transfer by the PEG-induced cell fusion between R+M+ and
AB  - R-M- strains, we examined transfer of plasmids pHV33 and pLS32neo
AB  - carrying no and eight BsuM sites, respectively. It was shown that
AB  - although the transfer of pLS32neo but not pHV33 from the R-M- to R+M+
AB  - cells was severely restricted, significant levels of transfer of both
AB  - plasmids from the R+M+ to R-M- cells were observed. The latter result
AB  - shows that the chromosomal DNA in the R-M- cell used as the recipient
AB  - partially survived restriction from the donor R+M+ cell, indicating
AB  - that the BsuM R-M- strain is useful as a host for accepting DNA from
AB  - cells carrying a restriction system(s). Two such examples were
AB  - manifested for plasmid transfer from Bacillus circulans and Bacillus
AB  - stearothermophilus strains to a BsuM-deficient mutant, B. subtilis
AB  - RM125.
ER  -

TY  - JOUR
AU  - Maekawa, Y.
AU  - Kawakami, B.
TI  - The relaxation of specificity of BanI restriction endonuclease from Bacillus aneurinolyticus IAM 1077.
JO  - J. Ferment. Bioeng.
PY  - 1990
SP  - 57
EP  - 59
VL  - 69
AB  - The restriction endonuclease BanI from Bacillus aneurinolyticus IAM 1077, which
AB  - recognizes 5'-GGPyPuCC-3' and cleaves between G and G within this sequence, has
AB  - decreased substrate specificity at high nuclease concentrations.  The
AB  - relaxation of its specificity was enhanced during modified reactions:
AB  - digestion of pBR322 DNA or lambda DNA in the presence of high glycerol and
AB  - dimethyl-sulfoxide (DMSO) produced additional fragments in addition to the
AB  - inherent fragments.  Therefore, it is required to check the reaction conditions
AB  - carefully for generation of inherent fragments.
ER  -

TY  - JOUR
AU  - Maekawa, Y.
AU  - Kawakami, B.
TI  - Cloning and expression in Escherichia coli of the BanI and BanIII restriction-modification systems from Bacillus aneurinolyticus.
JO  - J. Ferment. Bioeng.
PY  - 1990
SP  - 195
EP  - 198
VL  - 69
AB  - The genes coding for the GGPyPuCC-specific (BanI) and ATCGAT-specific (BanIII)
AB  - restriction-modification systems of Bacillus aneurinolyticus IAM1077 were
AB  - cloned and expressed in Escherichia coli using pBR322 as a vector.  The
AB  - plasmids carrying the BanI and BanIII restriction-modification genes were
AB  - designated pBanIRM8 and pBanIIIRM12, respectively.  The restriction maps of
AB  - these recombinant plasmids were constructed.  These two plasmids were stably
AB  - maintained in E. coli HB101.  However, when E. coli JM109 was used as a host,
AB  - pBanIIIRM12 was efficiently propagated but pBanIRM8 was not. The HB101 cells
AB  - carrying only the restriction gene of BanIII were viable, but the BanI
AB  - restriction gene carrier could not form colonies on agar plates.  The growth of
AB  - bacteriophage lambda was strongly restricted only in the E. coli HB101 cells
AB  - harboring pBanIRM8.  These facts indicate that the BanI restriction enzyme is
AB  - expressed and functions more efficiently than BanI modification enzyme in E.
AB  - coli.
ER  -

TY  - JOUR
AU  - Maekawa, Y.
AU  - Yasukawa, H.
AU  - Kawakami, B.
TI  - Cloning and nucleotide sequences of the BanI restriction-modification genes in Bacillus aneurinolyticus.
JO  - J. Biochem. (Tokyo)
PY  - 1990
SP  - 645
EP  - 649
VL  - 107
AB  - The genes of the BanI restriction-modification system specific for GGPyPuCC were cloned from
AB  - the chromosomal DNA of Bacillus aneurinolyticus IAM107, and the coding regions were assigned
AB  - on the nucleotide sequence on the basis of the N-terminal amino acid sequences and molecular
AB  - weights of the enzymes. The restriction and modification genes coded for polypeptides with
AB  - calculated molecular weights of 39,841 and 42,637, respectively. Both the enzymes were coded
AB  - by the same DNA strand. The restriction gene was located upstream of the methylase gene,
AB  - separated by 21 bp. The cloned genes were significantly expressed in E. coli cells, so that
AB  - the respective enzymes could be purified to homogeneity. Analysis by sodium dodecyl sulfate
AB  - polyacrylamide gel electrophoresis and gel filtration indicated that the catalytically active
AB  - form of the endonuclease was dimeric and that of the methylase was monomeric. Comparison of
AB  - the amino acid sequences revealed no significant homology between the endonuclease and
AB  - methylase, though both enzymes recognize the same target sequence. Sequence comparison with
AB  - other related enzymes indicated that BanI methylase contains sequences common to
AB  - cytosine-specific methylases.
ER  -

TY  - JOUR
AU  - Magana-Lizarraga, J.A.
AU  - Ahumada-Santos, Y.P.
AU  - Parra-Unda, J.R.
AU  - Uribe-Beltran, M.J.
AU  - Gomez-Gil, B.
AU  - Baez-Flores, M.E.
TI  - Draft Genome Sequence of Escherichia coli Strain M15-4, a Typical Enteropathogenic E. coli Strain Isolated in Mexico.
JO  - Genome Announcements
PY  - 2018
SP  - e01522
EP  - e01517
VL  - 6
AB  - We present here the first draft genome sequence of a typical enteropathogenic Escherichia coli
AB  - serotype O55:H51 strain, M15-4, isolated from a 2-month-old
AB  - infant girl with acute diarrhea. The study of this Mexican isolate will provide
AB  - insights to the virulence and drug resistance traits involved in its pathogenic
AB  - potential.
ER  -

TY  - JOUR
AU  - Magana-Lizarraga, J.A.
AU  - Hernandez-Peinado, J.V.
AU  - Ahumada-Santos, Y.P.
AU  - Parra-Unda, J.R.
AU  - Uribe-Beltran, M.J.
AU  - Gomez-Gil, B.
AU  - Baez-Flores, M.E.
TI  - Draft Genome Sequence of a Mexican Community-Associated Methicillin-Resistant Staphylococcus epidermidis Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e01236
EP  - e01217
VL  - 5
AB  - We report here the first draft genome sequence of a Mexican communitarian
AB  - methicillin-resistant Staphylococcus epidermidis (MRSE) strain whose genome
AB  - harbors a wide variety of resistance determinants. The availability of this
AB  - genome will allow the study of antibiotic resistance in Mexican staphylococci
AB  - from a genomic perspective.
ER  -

TY  - JOUR
AU  - Maggini, V.
AU  - Presta, L.
AU  - Miceli, E.
AU  - Fondi, M.
AU  - Bosi, E.
AU  - Chiellini, C.
AU  - Fagorzi, C.
AU  - Bogani, P.
AU  - Di Pilato, V.
AU  - Rossolini, G.M.
AU  - Mengoni, A.
AU  - Firenzuoli, F.
AU  - Perrin, E.
AU  - Fani, R.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic  Pathogens Belonging to the Burkholderia cepacia Complex.
JO  - Genome Announcements
PY  - 2017
SP  - e00351
EP  - e00317
VL  - 5
AB  - In this announcement, we detail the draft genome sequence of the Pseudomonas sp.  strain Ep
AB  - R1, isolated from the roots of the medicinal plant Echinacea purpurea
AB  - The elucidation of this genome sequence may allow the identification of genes
AB  - associated with the production of antimicrobial compounds.
ER  -

TY  - JOUR
AU  - Magni, C.
AU  - Espeche, C.
AU  - Repizo, G.D.
AU  - Saavedra, L.
AU  - Suarez, C.A.
AU  - Blancato, V.S.
AU  - Espariz, M.
AU  - Esteban, L.
AU  - Raya, R.R.
AU  - Font-de-Valdez, G.
AU  - Vignolo, G.
AU  - Mozzi, F.
AU  - Taranto, M.P.
AU  - Hebert, E.M.
AU  - Nader-Macias, M.E.
AU  - Sesma, F.
TI  - Draft Genome Sequence of Enterococcus mundtii CRL1656.
JO  - J. Bacteriol.
PY  - 2012
SP  - 550
EP  - 550
VL  - 194
AB  - We report the draft genome sequence of Enterococcus mundtii CRL1656, which was isolated from
AB  - the stripping milk of a clinically healthy adult
AB  - Holstein dairy cow from a dairy farm of the northwestern region of Tucuman
AB  - (Argentina). The 3.10-Mb genome sequence consists of 450 large contigs and
AB  - contains 2,741 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Magno-Perez-Bryan, M.C.
AU  - Martinez-Garcia, P.M.
AU  - Hierrezuelo, J.
AU  - Rodriguez-Palenzuela, P.
AU  - Arrebola, E.
AU  - Ramos, C.
AU  - de Vicente, A.
AU  - Perez-Garcia, A.
AU  - Romero, D.
TI  - Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains.
JO  - Mol. Plant Microbe Interact.
PY  - 2015
SP  - 1102
EP  - 1116
VL  - 28
AB  - Bacillus amyloliquefaciens CECT 8237 and CECT 8238, formerly known as Bacillus
AB  - subtilis UMAF6639 and UMAF6614, respectively, contribute to plant health by
AB  - facing microbial pathogens or inducing the plant's defense mechanisms. We
AB  - sequenced their genomes and developed a set of ad hoc scripts that allowed us to
AB  - search for the features implicated in their beneficial interaction with plants.
AB  - We define a core set of genes that should ideally be found in any beneficial
AB  - Bacillus strain, including the production of secondary metabolites, volatile
AB  - compounds, metabolic plasticity, cell-to-cell communication systems, and biofilm
AB  - formation. We experimentally prove that some of these genetic elements are
AB  - active, such as i) the production of known secondary metabolites or ii) acetoin
AB  - and 2-3-butanediol, compounds that stimulate plant growth and host defense
AB  - responses. A comparison with other Bacillus genomes permits us to find
AB  - differences in the cell-to-cell communication system and biofilm formation and to
AB  - hypothesize variations in their persistence and resistance ability in diverse
AB  - environmental conditions. In addition, the major protection provided by CECT 8237
AB  - and CECT 8238, which is different from other Bacillus strains against bacterial
AB  - and fungal melon diseases, permits us to propose a correlation with their
AB  - singular genetic background and determine the need to search for additional blind
AB  - biocontrol-related features.
ER  -

TY  - JOUR
AU  - Magrini, V.
AU  - Salmi, D.
AU  - Thomas, D.
AU  - Herbert, S.K.
AU  - Hartzell, P.L.
AU  - Youderian, P.
TI  - Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox.
JO  - J. Bacteriol.
PY  - 1997
SP  - 4254
EP  - 4263
VL  - 179
AB  - Temperate bacteriophage Mx8 of Myxococcus xanthus encapsidates terminally repetitious DNA,
AB  - packaged as circular permutations of its 49-kbp genome.  During both lytic and lysogenic
AB  - development, Mx8 expresses a nonessential DNA methylase, Mox, which modifies adenine residues
AB  - in occurrences of XhoI and PstI recognition sites, CTCGAG and CTGCAG, respectively, on both
AB  - phage DNA and the host chromosome.  The mox gene is necessary for methylase activity in vivo,
AB  - because an amber mutation in the mox gene abolishes activity.  The mox gene is the only phage
AB  - gene required for methylase activity in vivo, because ectopic expression of mox as part of the
AB  - M. xanthus mglBA operon results in partial methylation of the host chromosome.  The predicted
AB  - amino acid sequence of Mox is related most closely to that of the methylase involved in the
AB  - cell cycle control of Caulobacter crescentus.  We speculate that Mox acts to protect Mx8 phage
AB  - DNA against restriction upon infection of a subset of natural M. xanthus hosts.  One natural
AB  - isolate of M. xanthus, the lysogenic source of related phage Mx81, produces a restriction
AB  - endonuclease with the cleavage specificity of endonuclease BstBI.
ER  -

TY  - JOUR
AU  - Mahalingam, N.
AU  - Manivannan, B.
AU  - Jadhao, S.
AU  - Mishra, G.
AU  - Nilawe, P.
AU  - Pradeep, B.E.
TI  - Draft Genome Sequences of Two Extensively Drug-Resistant Acinetobacter baumannii  Strains Isolated from Pus Samples.
JO  - Genome Announcements
PY  - 2016
SP  - e00161
EP  - e00116
VL  - 4
AB  - We report the draft genomes of two extensively drug-resistant (XDR)Acinetobacter
AB  - baumanniistrains isolated from pus samples of two patients with surgical site
AB  - infections at Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram,
AB  - India. The average genomic size and G+C content are 4 Mbp and 38.96% (AB28) and 4
AB  - Mbp and 38.94% (AB30), respectively.
ER  -

TY  - JOUR
AU  - Mahan, K.M.
AU  - Klingeman, D.M.
AU  - Hettich, R.L.
AU  - Parry, R.J.
AU  - Graham, D.E.
TI  - Draft Genome Sequence of Streptomyces vitaminophilus ATCC 31673, a Producer of Pyrrolomycin Antibiotics, Some of Which Contain a Nitro Group.
JO  - Genome Announcements
PY  - 2016
SP  - e01582
EP  - e01515
VL  - 4
AB  - Streptomyces vitaminophilus produces pyrrolomycins, which are halogenated polyketide
AB  - antibiotics. Some of the pyrrolomycins contain a rare nitro group
AB  - located on the pyrrole ring. The 6.5-Mbp genome encodes 5,941 predicted
AB  - protein-coding sequences in 39 contigs with a 71.9% G+C content.
ER  -

TY  - JOUR
AU  - Mahan, M.J.
AU  - Low, D.A.
TI  - DNA methylation regulates bacterial gene expression and virulence.
JO  - ASM News
PY  - 2001
SP  - 356
EP  - 361
VL  - 67
AB  - DNA adenine methylase (Dam) plays a pivotal role in bacteria such as Escherichia coli and
AB  - Salmonella - acting as a global regulator of gene expression and affecting a wide range of
AB  - critical cellular functions, including DNA replication, DNA repair, transposition, and
AB  - segregation of chromosomal DNA.  This extraordinary versatility stems from the inherent
AB  - biochemical activity of Dam.  Thus, by adding methyl groups to various sites along the
AB  - cellular DNA, Dam alters interactions of a variety of regulatory proteins with their
AB  - designated gene targets and, in the process, effectively controls expression of those genes.
AB  - In some cases, such changes modulate bacterial virulence and also serve to elicit protective
AB  - immune responses in host organisms that Salmonella or other bacterial pathogens may infect.
ER  -

TY  - JOUR
AU  - Mahato, N.K.
AU  - Tripathi, C.
AU  - Verma, H.
AU  - Singh, N.
AU  - Lal, R.
TI  - Draft Genome Sequence of Deinococcus sp. Strain RL Isolated from Sediments of a Hot Water Spring.
JO  - Genome Announcements
PY  - 2014
SP  - e00703
EP  - e00714
VL  - 2
AB  - Deinococcus sp. strain RL, a moderately thermophilic bacterium, was isolated from sediments of
AB  - a hot water spring in Manikaran, India. Here, we report the draft
AB  - genome (2.79 Mbp) of this strain, which contains 62 contigs and 2,614 coding DNA
AB  - sequences, with an average G+C content of 69.4%.
ER  -

TY  - JOUR
AU  - Maher, L.J. III
TI  - DNA triple-helix formation: an approach to artificial gene repressors?
JO  - Bioessays
PY  - 1992
SP  - 807
EP  - 815
VL  - 14
AB  - Certain sequences of double-helical DNA can be recognized and tightly bound by
AB  - oligonucleotides. The effects of such triple-helical structures
AB  - on DNA binding proteins have been studied. Stabilities of DNA
AB  - triple-helices at or near physiological conditions are sufficient to
AB  - inhibit DNA binding proteins directed to overlapping sites. Such proteins
AB  - include restriction endonucleases, methylases, transcription factors, and
AB  - RNA polymerases. These and other results suggest that
AB  - oligonucleotide-directed triple-helix formation could provide the basis
AB  - for designing artificial gene repressors. The general question of whether
AB  - biological systems employ RNA molecules for recognition and regulation of
AB  - double-helical DNA is discussed.
ER  -

TY  - JOUR
AU  - Maher, L.J.
AU  - Wold, B.
AU  - Dervan, P.B.
TI  - Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation.
JO  - Science
PY  - 1989
SP  - 725
EP  - 733
VL  - 245
AB  - Oligonucleotides that bind to duplex DNA in a sequence-specific manner by
AB  - triple helix formation offer an approach to the experimental manipulation of
AB  - sequence-specific protein binding.  Micromolar concentrations of pyrimidine
AB  - oligodeoxyribonucleotides are shown to block recognition of double helical DNA
AB  - by prokaryotic modifying enzymes and a eukaryotic transcription factor at a
AB  - homopurine target site.  Inhibition is sequence-specific.  Oligonucleotides
AB  - containing 5-methylcytosine provide substantially more efficient inhibition
AB  - than oligonucleotides containing cytosine.  The results have implications for
AB  - gene-specific repression by oligonucleotides or their analogs.
ER  -

TY  - JOUR
AU  - Maheux, A.F.
AU  - Berube, E.
AU  - Boudreau, D.K.
AU  - Raymond, F.
AU  - Corbeil, J.
AU  - Roy, P.H.
AU  - Boissinot, M.
AU  - Omar, R.F.
TI  - Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial  Vaginosis.
JO  - Genome Announcements
PY  - 2016
SP  - e00959
EP  - e00916
VL  - 4
AB  - Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567 is the type strain of the new genus
AB  - Criibacterium The strain was isolated from a woman with bacterial
AB  - vaginosis. The genome assembly comprised 2,384,460 bp, with 34.4% G+C content.
AB  - This is the first genome announcement of a strain belonging to the genus
AB  - Criibacterium.
ER  -

TY  - JOUR
AU  - Maheux, A.F.
AU  - Boudreau, D.K.
AU  - Berube, E.
AU  - Boissinot, M.
AU  - Cantin, P.
AU  - Raymond, F.
AU  - Corbeil, J.
AU  - Omar, R.F.
AU  - Bergeron, M.G.
TI  - Draft Genome Sequence of Romboutsia weinsteinii sp. nov. Strain CCRI-19649T Isolated from Surface Water.
JO  - Genome Announcements
PY  - 2017
SP  - e00901
EP  - e00917
VL  - 5
AB  - Romboutsia weinsteinii sp. nov. CCRI-19649T belongs to the genus Romboutsia The strain was
AB  - isolated from a water sample harvested in Quebec City, Quebec, Canada.
AB  - The genome assembly comprised 4,134,593 bp with a 29.3% GC content. This is the
AB  - first documentation that reports the genome sequence of R. weinsteinii.
ER  -

TY  - JOUR
AU  - Maheux, A.F.
AU  - Boudreau, D.K.
AU  - Berube, E.
AU  - Boissinot, M.
AU  - Raymond, F.
AU  - Brodeur, S.
AU  - Corbeil, J.
AU  - Brightwell, G.
AU  - Broda, D.
AU  - Omar, R.F.
AU  - Bergeron, M.G.
TI  - Draft Genome Sequence of Romboutsia maritimum sp. nov. Strain CCRI-22766T, Isolated from Coastal Estuarine Mud.
JO  - Genome Announcements
PY  - 2017
SP  - e01044
EP  - e01017
VL  - 5
AB  - The Romboutsia maritimum sp. nov. CCRI-22766T strain was isolated from coastal estuarine mud
AB  - in New Zealand. The genome assembly comprised 2,854,352 bp, with
AB  - 27.1% G+C content. This is the first documentation that reports the genome
AB  - sequence of R. maritimum.
ER  -

TY  - JOUR
AU  - Maheux, A.F.
AU  - Boudreau, D.K.
AU  - Berube, E.
AU  - Boissinot, M.
AU  - Raymond, F.
AU  - Brodeur, S.
AU  - Corbeil, J.
AU  - Isabel, S.
AU  - Omar, R.F.
AU  - Bergeron, M.G.
TI  - Draft Genome Sequence of a Sporulating and Motile Strain of Lachnotalea glycerini Isolated from Water in Quebec City, Canada.
JO  - Genome Announcements
PY  - 2017
SP  - e01059
EP  - e01017
VL  - 5
AB  - Lachnotalea glycerini CCRI-19302 belongs to the genus Lachnotalea The strain was  isolated
AB  - from a water sample harvested in Quebec City, Canada. The genome
AB  - assembly comprised 4,694,231 bp, with 34.6% GC content. This is the first
AB  - documentation to report the genome sequence of a sporulating and motile strain of
AB  - L. glycerini.
ER  -

TY  - JOUR
AU  - Mahony, J.
AU  - Bottacini, F.
AU  - van Sinderen, D.
AU  - Fitzgerald, G.F.
TI  - Progress in lactic acid bacterial phage research.
JO  - Microb. Cell Fact.
PY  - 2014
SP  - S1
EP  - S1
VL  - 13
AB  - Research on lactic acid bacteria (LAB) has advanced significantly over the past number of
AB  - decades and these developments have been driven by the parallel advances in technologies such
AB  - as genomics, bioinformatics, protein expression systems and structural biology, combined with
AB  - the ever increasing commercial relevance of this group of microorganisms. Some of the more
AB  - significant and impressive outputs have been in the domain of bacteriophage-host interactions
AB  - which provides a prime example of the cutting-edge model systems represented by LAB research.
AB  - Here, we present a retrospective overview of the key advances in LAB phage research including
AB  - phage-host interactions and co-evolution. We describe how in many instances this knowledge can
AB  - be pivotal in creating real improvements in the application of LAB cultures in commercial
AB  - practice.
ER  -

TY  - JOUR
AU  - Mahowald, M.A. et al.
TI  - Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 5859
EP  - 5864
VL  - 106
AB  - The adult human distal gut microbial community is typically dominated by 2
AB  - bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little
AB  - is known about the factors that govern the interactions between their
AB  - members. Here, we examine the niches of representatives of both phyla in
AB  - vivo. Finished genome sequences were generated from Eubacterium rectale
AB  - and E. eligens, which belong to Clostridium Cluster XIVa, one of the most
AB  - common gut Firmicute clades. Comparison of these and 25 other gut
AB  - Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller
AB  - genomes and a disproportionately smaller number of glycan-degrading
AB  - enzymes. Germ-free mice were then colonized with E. rectale and/or a
AB  - prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed
AB  - by whole-genome transcriptional profiling, high-resolution proteomic
AB  - analysis, and biochemical assays of microbial-microbial and microbial-host
AB  - interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating
AB  - expression of a variety of polysaccharide utilization loci encoding
AB  - numerous glycoside hydrolases, and by signaling the host to produce
AB  - mucosal glycans that it, but not E. rectale, can access. E. rectale adapts
AB  - to B. thetaiotaomicron by decreasing production of its glycan-degrading
AB  - enzymes, increasing expression of selected amino acid and sugar
AB  - transporters, and facilitating glycolysis by reducing levels of NADH, in
AB  - part via generation of butyrate from acetate, which in turn is used by the
AB  - gut epithelium. This simplified model of the human gut microbiota
AB  - illustrates niche specialization and functional redundancy within members
AB  - of its major bacterial phyla, and the importance of host glycans as a
AB  - nutrient foundation that ensures ecosystem stability.
ER  -

TY  - JOUR
AU  - Mai-Prochnow, A.
AU  - Bradbury, M.
AU  - Murphy, A.B.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027 (DSM 1128), an Important Rhamnolipid Surfactant Producer and Sterility Testing Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01259
EP  - e01215
VL  - 3
AB  - Pseudomonas aeruginosa ATCC 9027 (DSM1128) is often used as a quality-control strain for
AB  - sterility and microbial contamination testing and is an important
AB  - biosurfactant producer. Here, we present the 6.4-Mb draft genome sequence and
AB  - highlight some genomic differences to its closest relative, P. aeruginosa strain
AB  - PA7.
ER  -

TY  - JOUR
AU  - Maida, I.
AU  - Bosi, E.
AU  - Perrin, E.
AU  - Papaleo, M.C.
AU  - Orlandini, V.
AU  - Fondi, M.
AU  - Fani, R.
AU  - Wiegel, J.
AU  - Bianconi, G.
AU  - Canganella, F.
TI  - Draft Genome Sequence of the Fast-Growing Bacterium Vibrio natriegens Strain DSMZ 759.
JO  - Genome Announcements
PY  - 2013
SP  - e00648
EP  - e00613
VL  - 1
AB  - Vibrio natriegens is a Gram-negative bacterium known for its extremely short doubling time.
AB  - Here we present the annotated draft genome sequence of Vibrio
AB  - natriegens strain DSMZ 759, with the aim of providing insights about its high
AB  - growth rate.
ER  -

TY  - JOUR
AU  - Mainardi, R.M.
AU  - Lima, J.E.A.
AU  - Ribeiro, J.J.C.
AU  - Beloti, V.
AU  - Carmo, A.O.
AU  - Kalapothakis, E.
AU  - Goncalves, D.D.
AU  - Padua, S.B.
AU  - Pereira, U.P.
TI  - Complete Genome Sequence of Streptococcus agalactiae Strain S25 Isolated from Peritoneal Liquid of Nile Tilapia.
JO  - Genome Announcements
PY  - 2016
SP  - e00784
EP  - e00716
VL  - 4
AB  - Streptococcus agalactiae (Lancefield group B; GBS) is one of the major pathogens  in fish
AB  - production, especially in Nile tilapia (Oreochromis niloticus). The
AB  - genomic characteristics of GBS isolated from fish must be more explored. Thus, we
AB  - present here the genome of GBS S25, isolated from Nile tilapia from Brazil.
ER  -

TY  - JOUR
AU  - Mairhofer, J.
AU  - Krempl, P.M.
AU  - Thallinger, G.G.
AU  - Striedner, G.
TI  - Finished Genome Sequence of Escherichia coli K-12 Strain HMS174 (ATCC 47011).
JO  - Genome Announcements
PY  - 2014
SP  - e00975
EP  - e00914
VL  - 2
AB  - Escherichia coli strain K-12 substrain HMS174 is an engineered descendant of the  E. coli K-12
AB  - wild-type strain. Like its ancestor, it is an important organism in
AB  - biotechnological research and is used in fermentation processes for heterologous
AB  - protein production. Here, we report the complete genome sequence of E. coli
AB  - HMS174 (ATCC 47011).
ER  -

TY  - JOUR
AU  - Maita, C.
AU  - Matushita, M.
AU  - Okubo, T.
AU  - Matsuo, J.
AU  - Miyake, M.
AU  - Nagai, H.
AU  - Yamaguchi, H.
TI  - Draft Genome Sequences of Legionella pneumophila JR32 and Lp01 Laboratory Strains Domesticated in Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e00791
EP  - e00716
VL  - 4
AB  - We report here the draft genome sequences of two Legionella pneumophila variant strains (JR32
AB  - and Lp01_666) originally derived from a Philadelphia-1 clinical
AB  - isolate, domesticated in Japan, with distinct susceptibility to amoebae. Detailed
AB  - genomic analysis will allow us to better understand Legionella adaptation and
AB  - survival mechanisms in host cells.
ER  -

TY  - JOUR
AU  - Maitra, N.
AU  - Whitman, W.B.
AU  - Ayyampalayam, S.
AU  - Samanta, S.
AU  - Sarkar, K.
AU  - Bandopadhyay, C.
AU  - Aftabuddin, M.
AU  - Sharma, A.P.
AU  - Manna, S.K.
TI  - Draft Genome Sequence of the Aquatic Phosphorus-Solubilizing and -Mineralizing Bacterium Bacillus sp. Strain CPSM8.
JO  - Genome Announcements
PY  - 2014
SP  - e01265
EP  - e01213
VL  - 2
AB  - Bacillus sp. strain CPSM8 is an efficient solubilizer and mineralizer of phosphorus. Here, we
AB  - present the 4.39-Mb draft genome sequence of the strain,
AB  - providing insight into the phosphorus-releasing genes related to productivity in
AB  - aquatic habitats.
ER  -

TY  - JOUR
AU  - Maizel, D.
AU  - Utturkar, S.M.
AU  - Brown, S.D.
AU  - Ferrero, M.A.
AU  - Rosen, B.P.
TI  - Draft Genome Sequence of Brevibacterium linens AE038-8, an Extremely Arsenic-Resistant Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00316
EP  - e00315
VL  - 3
AB  - To understand the arsenic biogeocycles in the groundwaters at Tucuman, Argentina, we isolated
AB  - Brevibacterium linens sp. strain AE38-8, obtained from
AB  - arsenic-contaminated well water. This strain is extremely resistant to arsenicals
AB  - and has arsenic resistance (ars) genes in its genome. Here, we report the draft
AB  - genome sequence of B. linens AE38-8.
ER  -

TY  - JOUR
AU  - Majid, M.
AU  - Kumar, N.
AU  - Qureshi, A.
AU  - Yerra, P.
AU  - Kumar, A.
AU  - Kumar, M.K.
AU  - Tiruvayipati, S.
AU  - Baddam, R.
AU  - Shaik, S.
AU  - Srikantam, A.
AU  - Ahmed, N.
TI  - Genomes of Two Clinical Isolates of Mycobacterium tuberculosis from Odisha, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00199
EP  - e00114
VL  - 2
AB  - We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis
AB  - isolated from patients in Odisha, India. The sequence analysis
AB  - revealed that these isolates are of an ancestral type and might represent some of
AB  - the 'pristine' isolates in India that have not admixed with other lineages.
ER  -

TY  - JOUR
AU  - Majumder, K.
TI  - The importance of flanking sequences in the sequence specific cleavage by the restriction endonucleases RsaI, AluI and HaeIII.
JO  - Biophys. J.
PY  - 1989
SP  - 48a
EP  - 48a
VL  - 55
AB  - Recent discoveries on the dependence in the sensitivity of some of restriction
AB  - enzymes (REs) on conformational changes in DNA indicate a complex diversity in
AB  - the nature of RE-DNA interaction.  Although the bases around these recognition
AB  - sequences are believed to be of considerable importance, not much data is
AB  - available in this regard.  We have studied the importance of flanking sequences
AB  - in the sequence specific cleavage by the REs - RsaI, AluI and HaeIII.  The
AB  - oligomers d(ACGTACGT), d(CGTACGTACG), poly d(ACGT), d(AGCTAGCT), poly d(AGCT),
AB  - d(GGCC) and d(CCGGCCGG) were used as the substrates for the relevant enzymes.
AB  - We have found that in the absence of the flanking bases the REs - RsaI, AluI
AB  - and HaeIII fail to cleave the corresponding recognition sites.  The minimum
AB  - number of such flanking bases (termed as flanking number or FN) has been found
AB  - to be two (i.e., FN=2) for RsaI.  Preliminary indications showed that the
AB  - flanking bases play an important role in the case of several other REs also.
AB  - It appears to us that in the sequence specific cleavage of DNA by RE the
AB  - flanking bases play two roles viz. (i) provide better binding and improved
AB  - kinetic stability to the enzyme-DNA complex formed prior to cleavage and (ii)
AB  - stabilization of the local active conformation by buffering out the
AB  - neighbouring influences like fraying or altered structure.
ER  -

TY  - JOUR
AU  - Mak, A.N.
AU  - Lambert, A.R.
AU  - Stoddard, B.L.
TI  - Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
JO  - Structure
PY  - 2010
SP  - 1321
EP  - 1331
VL  - 18
AB  - The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of
AB  - functions; none have been visualized bound to DNA. The
AB  - structure of the GIY-YIG restriction endonuclease R.Eco29kI has been
AB  - solved both alone and bound to its target site. The protein displays a
AB  - domain-swapped homodimeric structure with several extended surface loops
AB  - encircling the DNA. Only three side chains from each protein subunit
AB  - contact DNA bases, two directly and one via a bridging solvent molecule.
AB  - Both tyrosine residues within the GIY-YIG motif are positioned in the
AB  - catalytic center near a putative nucleophilic water; the remainder of the
AB  - active site resembles the HNH endonuclease family. The structure
AB  - illustrates how the GIY-YIG scaffold has been adapted for the highly
AB  - specific recognition of a DNA restriction site, in contrast to nonspecific
AB  - DNA cleavage by GIY-YIG domains in homing endonucleases or
AB  - structure-specific cleavage by DNA repair enzymes such as UvrC.
ER  -

TY  - JOUR
AU  - Mak, A.N.S.
AU  - Fung, W.T.
AU  - Kong, K.P.S.
AU  - Poon, A.W.S.
AU  - Ngai, S.M.
AU  - Shaw, P.C.
TI  - Characterization of the large subunit of EcoHK31I methyltransferase by structural modeling and mutagenesis.
JO  - Biol. Chem.
PY  - 2007
SP  - 265
EP  - 271
VL  - 388
AB  - M.EcoHK31I is a naturally occurring mC5-methyltransferase with a large alpha polypeptide and a
AB  - small beta polypeptide. Polypeptide alpha
AB  - contains conserved motifs I-VIII and X, and polypeptide beta contains
AB  - motif IX. To understand how polypeptide alpha carries out its function,
AB  - a molecular model of the large domain of polypeptide a was generated
AB  - using M.Hhal and M.Haelll as templates. The large domain is a mixed
AB  - alpha/beta structure. Residues 15-19 in motif I (Phe-Naa-Gly-Naa) are
AB  - conserved for cofactor binding. The key catalytic residue Cys-79 in
AB  - motif IV is also conserved in comparison with other C-5 MTases.
AB  - Comparing polypeptide a with M.Hhal and M.Haelll revealed a unique
AB  - region upstream of motif X. To understand the role of this region, 14
AB  - charged residues between R224 and E271 in the putative small domain
AB  - were mutated. Activity assays indicated that most of these charges can
AB  - be eliminated or changed conservatively. Among these charged residues,
AB  - R224, E240, D245 and D251 may take part in proper interaction with DNA
AB  - in the presence of polypeptide beta.
ER  -

TY  - JOUR
AU  - Mak, T.N.
AU  - Sfanos, K.S.
AU  - Bruggemann, H.
TI  - Draft Genome Sequences of Two Strains of Propionibacterium acnes Isolated from Radical Prostatectomy Specimens.
JO  - Genome Announcements
PY  - 2013
SP  - e01071
EP  - e01013
VL  - 1
AB  - Propionibacterium acnes is a Gram-positive bacterium that is closely associated with various
AB  - parts of the human body, in particular with sebaceous follicles of
AB  - the skin. It has also been frequently isolated from diseased human prostates.
AB  - Here, we report draft genome sequences of two P. acnes strains, P6 and PA2,
AB  - isolated from radical prostatectomy specimens.
ER  -

TY  - JOUR
AU  - Makarova, K. et al.
TI  - Comparative genomics of the lactic acid bacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 15611
EP  - 15616
VL  - 103
AB  - Lactic acid-producing bacteria are associated with various plant and animal niches and play a
AB  - key role in the production of fermented foods and
AB  - beverages. We report nine genome sequences representing the phylogenetic
AB  - and functional diversity of these bacteria. The small genomes of lactic
AB  - acid bacteria encode a broad repertoire of transporters for efficient
AB  - carbon and nitrogen acquisition from the nutritionally rich environments
AB  - they inhabit and reflect a limited range of biosynthetic capabilities that
AB  - indicate both prototrophic and auxotrophic strains. Phylogenetic analyses,
AB  - comparison of gene content across the group, and reconstruction of
AB  - ancestral gene sets indicate a combination of extensive gene loss and key
AB  - gene acquisitions via horizontal gene transfer during the coevolution of
AB  - lactic acid bacteria with their habitats.
ER  -

TY  - JOUR
AU  - Makarova, K.S.
AU  - Wolf, Y.I.
AU  - Koonin, E.V.
TI  - Comparative genomics of defense systems in archaea and bacteria.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 4360
EP  - 4377
VL  - 41
AB  - Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative
AB  - genomic analysis, followed by experimental validation. This expansion is both quantitative,
AB  - including the discovery of diverse new examples of known types of defense systems, such as
AB  - restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery
AB  - of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale
AB  - statistical analysis reveals that the distribution of different defense systems in bacterial
AB  - and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect
AB  - to the overall abundance and the balance between specific types of defense systems. The genes
AB  - encoding defense system components in bacterial and archaea typically cluster in defense
AB  - islands. In addition to genes encoding known defense systems, these islands contain numerous
AB  - uncharacterized genes, which are candidates for new types of defense systems. The tight
AB  - association of the genes encoding immunity systems and dormancy- or cell death-inducing
AB  - defense systems in prokaryotic genomes suggests that these two major types of defense are
AB  - functionally coupled, providing for effective protection at the population level.
ER  -

TY  - JOUR
AU  - Makarova, K.S.
AU  - Wolf, Y.I.
AU  - Snir, S.
AU  - Koonin, E.V.
TI  - Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6039
EP  - 6056
VL  - 193
AB  - The arms race between cellular life forms and viruses is a major driving force of evolution. A
AB  - substantial fraction of bacterial and archaeal
AB  - genomes is dedicated to antivirus defense. We analyzed the distribution of
AB  - defense genes and typical mobilome components (such as viral and
AB  - transposon genes) in bacterial and archaeal genomes, and demonstrated
AB  - statistically significant clustering of antivirus defense systems and
AB  - mobile genes and elements in genomic islands. The defense islands are
AB  - enriched in putative operons and contain numerous over-represented gene
AB  - families. A detailed sequence analysis of the proteins encoded by genes in
AB  - these families shows that many of them are diverged variants of known
AB  - defense system components, whereas others show features, such as
AB  - characteristic operonic organization, that are suggestive of novel defense
AB  - systems. Thus, genomic islands provide abundant material for experimental
AB  - study of bacterial and archaeal antivirus defense. Except for the
AB  - CRISPR-Cas systems, different classes of defense systems, in particular
AB  - toxin-antitoxin and restriction-modification systems, show non-random
AB  - clustering in defense islands. It remains unclear to what extant these
AB  - associations reflect functional cooperation between different defense
AB  - systems and to what extent the islands are genomic 'sinks' that accumulate
AB  - diverse non-essential genes, particularly those acquired via HGT. The
AB  - characteristics of defense islands resemble those of mobilome islands.
AB  - Defense and mobilome genes are non-randomly associated in islands,
AB  - suggesting non-adaptive evolution of the islands via a preferential
AB  - attachment-like mechanism underpinned by the addictive properties of
AB  - defense systems such as toxins-antitoxins and an important role of
AB  - horizontal mobility in the evolution of these islands.
ER  -

TY  - JOUR
AU  - Makarova, O.
AU  - Johnston, P.
AU  - Walther, B.
AU  - Rolff, J.
AU  - Roesler, U.
TI  - Complete Genome Sequence of the Livestock-Associated Methicillin-Resistant Strain Staphylococcus aureus subsp. aureus 08S00974 (Sequence Type 398).
JO  - Genome Announcements
PY  - 2017
SP  - e00294
EP  - e00217
VL  - 5
AB  - We report here the complete genome sequence of the livestock-associated methicillin-resistant
AB  - Staphylococcus aureus strain 08S00974 from sequence type
AB  - 398 (ST398 LA-MRSA) isolated from a fatting pig at a farm in Germany.
ER  -

TY  - JOUR
AU  - Makarova, O.
AU  - Johnston, P.
AU  - Walther, B.
AU  - Rolff, J.
AU  - Roesler, U.
TI  - Complete Genome Sequence of the Disinfectant Susceptibility Testing Reference Strain Staphylococcus aureus subsp. aureus ATCC 6538.
JO  - Genome Announcements
PY  - 2017
SP  - e00293
EP  - e00217
VL  - 5
AB  - We report here the complete genome sequence of the methicillin-sensitive Staphylococcus aureus
AB  - subsp. aureus strain ATCC 6538 (FDA 209, DSM 799, WDCM
AB  - 00032, and NCTC 10788).
ER  -

TY  - JOUR
AU  - Maker, A.
AU  - Hemp, J.
AU  - Pace, L.A.
AU  - Ward, L.M.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the Bacilli Class of Firmicutes.
JO  - Genome Announcements
PY  - 2017
SP  - e00380
EP  - e00316
VL  - 5
AB  - We report here the draft genome sequence of Hydrogenibacillus schlegelii MA48, a  thermophilic
AB  - facultative anaerobe that can oxidize hydrogen aerobically. H.
AB  - schlegelii MA48 belongs to a deep-branching clade of the Bacilli class and
AB  - provides important insight into the acquisition of aerobic respiration within the
AB  - Firmicutes phylum.
ER  -

TY  - JOUR
AU  - Maki, A.H.
AU  - Tsao, D.H.H.
TI  - Microwave-optical study of an As(III) derivative of EcoRI methylase.
JO  - Biomol. Spectroscopy II
PY  - 1991
SP  - 119
EP  - 128
VL  - 1432
AB  - We report on the formation of an unusually stable As(III)-thiolate with a
AB  - single high-affinity cysteine (Cys) of E. coli RI methylase, monitored via its
AB  - influence on a neighboring tryptophan (Trp) residue in the enzyme structure.
AB  - The binding was studied by Trp fluorescence quenching, low temperature
AB  - phosphorescence and triplet state optically detected magnetic resonance (ODMR)
AB  - of the intrinsic Trp residue(s).  The affected Trp is subject to an external
AB  - heavy atom effect (HAE) from arsenic, quenching its fluorescence and reducing
AB  - its phosphorescence lifetime from 6 sec to ca. 70 msec.  The enzyme high
AB  - affinity binding site has at least 27 times the affinity for As(III) as does a
AB  - typical sulfhydryl reagent, HSCH2CONH2.  The accessibility of the arsenical to
AB  - this Cys site was reduced upon formation of the ternary complex
AB  - methylase-DNA-sinefungin, suggesting a local conformational change in the
AB  - enzyme when DNA is bound.  The enzymatic activity assay of methylase is not
AB  - affected by the addition of a 1:1 molar ratio of the arsenical to the
AB  - methylase, but incubation with an excess of As(III) causes complete loss of
AB  - enzymatic activity.  This suggests that the high-affinity Cys residue is not a
AB  - part of the active site of the enzyme, but the addition of a molar excess of
AB  - arsenical to the enzyme derivatizes the Cys residue known to be located in the
AB  - active site.
ER  -

TY  - JOUR
AU  - Makino, K.
AU  - Ishii, K.
AU  - Yasunaga, T.
AU  - Hattori, M.
AU  - Yokoyama, K.
AU  - Yutsudo, H.C.
AU  - Kubota, Y.
AU  - Yamaichi, Y.
AU  - Iida, T.
AU  - Yamamoto, K.
AU  - Honda, T.
AU  - Han, C.G.
AU  - Ohtsubo, E.
AU  - Kasamatsu, M.
AU  - Hayashi, T.
AU  - Kuhara, S.
AU  - Shinagawa, H.
TI  - Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak.
JO  - DNA Res.
PY  - 1998
SP  - 1
EP  - 9
VL  - 5
AB  - Enterohemorrhagic Escherichia coli (EHEC) O157:H7, derived from an
AB  - outbreak in Sakai city, Japan in 1996, possesses two kinds of plasmids: a
AB  - 93-kb plasmid termed pO157, found in clinical EHEC isolates world-wide and
AB  - a 3.3-kb plasmid termed pOSAK1, prevalent in EHEC strains isolated in
AB  - Japan. Complete nucleotide sequences of both plasmids have been
AB  - determined, and the putative functions of the encoded proteins and the
AB  - cis-acting DNA sequences have been analyzed. pO157 shares strikingly
AB  - similar genes and DNA sequences with F-factor and the transmissible
AB  - drug-resistant plasmid R100 for DNA replication, copy number control,
AB  - plasmid segregation, conjugative functions and stable maintenance in the
AB  - host, although it is defective in DNA transfer by conjugation due to the
AB  - truncation and deletion of the required genes and DNA sequences. In
AB  - addition, it encodes several proteins implicated in EHEC pathogenicity
AB  - such as an EHEC hemolysin (HlyA), a catalase-peroxidase (KatP), a serine
AB  - protease (EspP) and type II secretion system. pOSAK1 possesses a
AB  - ColE1-like replication system, and the DNA sequence is extremely similar
AB  - to that of a drug-resistant plasmid, NTP16, derived from Salmonella
AB  - typhimurium except that it lacks drug resistance transposons.
ER  -

TY  - JOUR
AU  - Makino, K.
AU  - Oshima, K.
AU  - Kurokawa, K.
AU  - Yokoyama, K.
AU  - Uda, T.
AU  - Tagomori, K.
AU  - Iijima, Y.
AU  - Najima, M.
AU  - Nakano, M.
AU  - Yamashita, A.
AU  - Kubota, Y.
AU  - Kimura, S.
AU  - Yasunaga, T.
AU  - Honda, T.
AU  - Shinagawa, H.
AU  - Hattori, M.
AU  - Iida, T.
TI  - Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae.
JO  - Lancet
PY  - 2003
SP  - 743
EP  - 749
VL  - 361
AB  - BACKGROUND: Vibrio parahaemolyticus, a gram-negative marine bacterium, is a worldwide cause of
AB  - food-borne gastroenteritis. V parahaemolyticus
AB  - strains of a few specific serotypes, probably derived from a common clonal
AB  - ancestor, have lately caused a pandemic of gastroenteritis. The organism
AB  - is phylogenetically close to V cholerae, the causative agent of cholera.
AB  - METHODS: The whole genome sequence of a clinical V parahaemolyticus strain
AB  - RIMD2210633 was established by shotgun sequencing. The coding sequences
AB  - were identified by use of Gambler and Glimmer programs. Comparative
AB  - analysis with the V cholerae genome was undertaken with MUMmer. FINDINGS:
AB  - The genome consisted of two circular chromosomes of 3288558 bp and 1877212
AB  - bp; it contained 4832 genes. Comparison of the V parahaemolyticus genome
AB  - with that of V cholerae showed many rearrangements within and between the
AB  - two chromosomes. Genes for the type III secretion system (TTSS) were
AB  - identified in the genome of V parahaemolyticus; V cholerae does not have
AB  - these genes. INTERPRETATION: The TTSS is a central virulence factor of
AB  - diarrhoea-causing bacteria such as shigella, salmonella, and
AB  - enteropathogenic Escherichia coli, which cause gastroenteritis by invading
AB  - or intimately interacting with intestinal epithelial cells. Our results
AB  - suggest that V parahaemolyticus and V cholerae use distinct mechanisms to
AB  - establish infection. This finding explains clinical features of V
AB  - parahaemolyticus infections, which commonly include inflammatory diarrhoea
AB  - and in some cases systemic manifestations such as septicaemia, distinct
AB  - from those of V cholerae infections, which are generally associated with
AB  - non-inflammatory diarrhoea.
ER  -

TY  - JOUR
AU  - Makino, K.
AU  - Yokoyama, K.
AU  - Kubota, Y.
AU  - Watanabe, M.
AU  - Kimura, S.
AU  - Yutsudo, C.H.
AU  - Kurokawa, K.
AU  - Ishii, K.
AU  - Hattori, M.
AU  - Abe, H.
AU  - Yamamoto, K.
AU  - Hayashi, T.
AU  - Yasunaga, T.
AU  - Honda, T.
AU  - Sasakawa, C.
AU  - Shinagawa, H.
TI  - Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak.
JO  - Genes Genet. Syst.
PY  - 1999
SP  - 227
EP  - 239
VL  - 74
AB  - The enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain RIMD 0509952, derived from an
AB  - outbreak in Sakai city, Japan, in 1996, produces two kinds of verotoxins, VT1 and VT2, encoded
AB  - by the stx1 and stx2 genes. In the EHEC strains, as well as in other VT-producing E. coli
AB  - strains, the toxins are encoded by lysogenic bacteriophages. The EHEC O157:H7 strain RIMD
AB  - 0509952 did not produce plaque-forming phage particles upon inducing treatments. We have
AB  - determined the complete nucleotide sequence of a prophage, VT2-Sakai, carrying the stx2A and
AB  - stx2B genes on the chromosome, and presumed the putative functions of the encoded proteins and
AB  - the cis-acting DNA elements based on sequence homology data. To our surprise, the sequences in
AB  - the regions of VT2-Sakai corresponding to the early gene regulators and replication proteins,
AB  - and the DNA sequences recognized by the regulators share very limited homology to those of the
AB  - VT2-encoding 933W phage carried by the EHEC O157:H7 strain EDL933 reported by Plunkett et al.
AB  - (J. Bacteriol., p1767-1778, 181, 1999), although the sequences corresponding to the structural
AB  - components are almost identical. These data suggest that these two phages were derived from a
AB  - common ancestral phage and that either or both of them underwent multiple genetic
AB  - rearrangements. An IS629 insertion was found downstream of the stx2B gene and upstream of the
AB  - lysis gene S, and this might be responsible for the absence of plaque-forming activity in the
AB  - lysate obtained after inducing treatments.
ER  -

TY  - JOUR
AU  - Makino, O.
AU  - Kawamura, F.
AU  - Saito, H.
AU  - Ikeda, Y.
TI  - Inactivation of restriction endonuclease BamNx after infection with phage UNR2.
JO  - Nature
PY  - 1979
SP  - 64
EP  - 65
VL  - 277
AB  - A host-controlled restriction-modification system is a means of protection by a
AB  - host against attacks of bacteriophages.  Recently, coliphage T3 and T7 have
AB  - been found to overcome the host-controlled restriction-modification systems of
AB  - their host strains Escherichia coli B and K, but details of the mechanism are
AB  - not well understood at present.  We have found that a Bacillus subtilis phage
AB  - UNR2rH, a mutant of UNR2, also has the ability to overcome the
AB  - restriction-modification system of B. amyloliquefaciens strain N, and detected
AB  - a BamNx inhibitor in cells infected with UNR2rH.
ER  -

TY  - JOUR
AU  - Makino, O.
AU  - Saito, H.
AU  - Ando, T.
TI  - Bacillus subtilis-Phage Phi1 overcomes host-controlled restriction by producing BamNx inhibitor protein.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 463
EP  - 468
VL  - 179
AB  - Bacillus amyloliquefaciens N produces two restriction enzymes, BamNI and BamNX.
AB  - Subtilis-phage Phi1 is strongly restricted by BamNx.  We isolated Phi1rH, a
AB  - mutant of phage Phi1, which overcame the BamNx-restriction by producing
AB  - inhibitor.  This inhibitor inactivated BamNx specifically and reversibly.  The
AB  - inhibitor directly interacted with BamNx and the inactivation might be the
AB  - result of formation of a binary complex.  The inhibitory activity was sensitive
AB  - to treatment with trypsin.  The molecular weight of the inhibitor protein was
AB  - estimated to be approximately 20,000 daltons by gel filtration.
ER  -

TY  - JOUR
AU  - Makita, H.
AU  - Nishi, S.
AU  - Takaki, Y.
AU  - Tanaka, E.
AU  - Nunoura, T.
AU  - Mitsunobu, S.
AU  - Takai, K.
TI  - Draft Genome Sequence of Mariprofundus micogutta Strain ET2.
JO  - Genome Announcements
PY  - 2018
SP  - e00342
EP  - e00318
VL  - 6
AB  - Mariprofundus micogutta strain ET2 was isolated in 2014 from a deep-sea hydrothermal field on
AB  - the Bayonnaise Knoll of the Izu-Ogasawara arc. Here, we
AB  - report its draft genome, which comprises 2,497,805 bp and contains 2,417
AB  - predicted coding sequences.
ER  -

TY  - JOUR
AU  - Makovets, S.
AU  - Doronina, V.A.
AU  - Murray, N.E.
TI  - Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 9757
EP  - 9762
VL  - 96
AB  - ClpXP-dependent proteolysis has been implicated in the delayed detection of restriction
AB  - activity after the acquisition of the genes (hsdR, hsdM, and hsdS) that specify EcoKI and
AB  - EcoAI, representatives of two families of type I restriction and modification (R-M) systems.
AB  - Modification, once established, has been assumed to provide adequate protection against a
AB  - resident restriction system. However, unmodified targets may be generated in the DNA of an
AB  - hsd(+) bacterium as the result of replication errors or recombination-dependent repair. We
AB  - show that ClpXP-dependent regulation of the endonuclease activity enables bacteria that
AB  - acquire unmodified chromosomal target sequences to survive. In such bacteria, HsdR, the
AB  - polypeptide of the R-M complex essential for restriction but not modification, is degraded in
AB  - the presence of ClpXP. A mutation that blocks only the modification activity of EcoKI, leaving
AB  - the cell with approximately 600 unmodified targets, is not lethal provided that ClpXP is
AB  - present. Our data support a model in which the HsdR component of a type I restriction
AB  - endonuclease becomes a substrate for proteolysis after the endonuclease has bound to
AB  - unmodified target sequences, but before completion of the pathway that would result in DNA
AB  - breakage.
ER  -

TY  - JOUR
AU  - Makovets, S.
AU  - Powell, L.M.
AU  - Titheradge, A.J.B.
AU  - Blakely, G.W.
AU  - Murray, N.E.
TI  - Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?
JO  - Mol. Microbiol.
PY  - 2004
SP  - 135
EP  - 147
VL  - 51
AB  - It has been generally accepted that DNA modification protects the chromosome of a bacterium
AB  - encoding a restriction and modification
AB  - system. But, when target sequences within the chromosome of one such
AB  - bacterium (Escherichia coli K-12) are unmodified, the cell does not
AB  - destroy its own DNA; instead, ClpXP inactivates the nuclease, and
AB  - restriction is said to be alleviated. Thus, the resident chromosome is
AB  - recognized as 'self' rather than 'foreign' even in the absence of
AB  - modification. We now provide evidence that restriction alleviation may
AB  - be a characteristic of Type I restriction-modification systems, and
AB  - that it can be achieved by different mechanisms. Our experiments
AB  - support disassembly of active endonuclease complexes as a potential
AB  - mechanism. We identify amino acid substitutions in a restriction
AB  - endonuclease, which impair restriction alleviation in response to
AB  - treatment with a mutagen, and demonstrate that restriction alleviation
AB  - serves to protect the chromosome even in the absence of mutagenic
AB  - treatment. In the absence of efficient restriction alleviation, a Type
AB  - I restriction enzyme cleaves host DNA and, under these conditions,
AB  - homologous recombination maintains the integrity of the bacterial
AB  - chromosome.
ER  -

TY  - JOUR
AU  - Makovets, S.
AU  - Titheradge, A.J.B.
AU  - Murray, N.E.
TI  - ClpX and ClpP are essential for the efficient acquisition of genes specifying type IA and IB restriction systems.
JO  - Mol. Microbiol.
PY  - 1998
SP  - 25
EP  - 35
VL  - 28
AB  - Efficient acquisition of genes that encode a restriction and modification system with
AB  - specificities different from any already present in the recipient bacterium requires the
AB  - sequential production of the new modification enzyme followed by the restriction activity in
AB  - order that the chromosome of the recipient bacterium is protected against attack by the
AB  - restriction endonuclease.  We show that ClpX and ClpP, the components of ClpXP protease, are
AB  - necessary for the efficient transmission of the genes encoding EcoKI and EcoAI,
AB  - representatives of two families of type I R-M systems, thus implicating ClpXP in the
AB  - modulation of restriction activity.  Loss of ClpX imposed a bigger barrier than loss of ClpP,
AB  - consistent with a dual role for ClpX, possibly as a chaperone and as a component of the ClpXP
AB  - protease.  Transmission of genes specifying EcoKI was more dependent on ClpX and ClpP than
AB  - transmission of the genes for EcoAI.  Sensitivity to absence of the protease was also
AB  - influenced by the mode of gene transfer; conjugative transfer and transformation were more
AB  - dependent on ClpXP than transduction.  In the absence of either ClpX or ClpP transfer of the
AB  - EcoKI genes by P1-mediated transduction was impaired, transfer of the EcoAI genes was not.
ER  -

TY  - JOUR
AU  - Maksimenko, A.
AU  - Gottikh, M.B.
AU  - Kubareva, E.A.
AU  - Fedorova, O.A.
AU  - Shabarova, Z.A.
TI  - Restriction endonucleases can be used to confirm a structure of unusual DNA duplexes.
JO  - Biol. Chem.
PY  - 1998
SP  - 625
EP  - 630
VL  - 379
AB  - Cyclic and polycyclic oligonucleotides were synthesized using chemical ligation.  Two types of
AB  - catenanes with one and several intertwinings were produced.  The yield of these molecules
AB  - depended on the ligation conditions and nucleotide sequence of the ligated oligonucleotide and
AB  - its template.  Structure of ligation products was investigated and confirmed using restriction
AB  - endonuclease MvaI.  Interaction of the synthesized molecules with restriction endonucleases
AB  - SsoII, EcoRII and HindIII was also studied.
ER  -

TY  - JOUR
AU  - Makula, R.A.
AU  - Meagher, R.B.
TI  - A new restriction endonuclease from the anaerobic bacterium, Desulfovibrio desulfuricans, Norway.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 3125
EP  - 3131
VL  - 8
AB  - The purification and characterization of a new restriction endonuclease, DdeI,
AB  - from a sulfate-reducing, anaerobic bacterium, Desulfovibrio desulfuricans,
AB  - Norway, is reported.  The enzyme recognizes the sequence 5'-C-^T-N-A-G-3'
AB  - 3'-G-A-N-T-^C-5' and cleaves at the position indicated by the arrows.  The
AB  - enzyme preparation obtained is suitable for restriction mapping and ligation.
ER  -

TY  - JOUR
AU  - Malagnac, F.
AU  - Gregoire, A.
AU  - Goyon, C.
AU  - Rossignol, J.-L.
AU  - Faugeron, G.
TI  - Masc2, a gene from Ascobolus encoding a protein with a DNA-methyltransferase activity in vitro, is dispensable for in vivo methylation.
JO  - Mol. Microbiol.
PY  - 1999
SP  - 331
EP  - 338
VL  - 31
AB  - We have shown previously that masc1, a gene encoding a putative C5-DNA-methyltransferase, was
AB  - necessary for the de novo 'Methylation Induced Premeiotically' (MIP) process and sexual
AB  - reproduction in Ascobolus, whereas it was dispensable for maintenance methylation.  A second
AB  - MTase gene from Asobolus, masc2, encodes a protein, Masc2, which possesses the large
AB  - amino-terminal part characteristic of eukaryotic maintenance MTases.  In vitro assays have
AB  - shown that Masc2 displays a methylation activity, suggesting that it might be the MTase
AB  - responsible for maintenance methylation.  To check its function in vivo, we engineered a
AB  - disruption of the masc2 gene.  The resulting mutant strains did not exhibit any particular
AB  - phenotype during either vegetative growth or sexual reproduction.  Neither the masc2 mutation
AB  - nor the double masc1 masc2 mutation had any detectable effect upon the maintenance of the
AB  - pre-existing methylation of single gene copies previously subjected to MIP, natural
AB  - retroelement-like repeats and tandemly repeated rDNA.  The masc2 mutation did not alter either
AB  - MIP or the other de novo methylation process that operates in vegetative cells.  Nor did it
AB  - impair the meiotic process of methylation transfer.  These results suggest that at least a
AB  - third MTase gene responsible for maintenance and vegetative de novo methylation is present in
AB  - Asobolus.
ER  -

TY  - JOUR
AU  - Malagnac, F.
AU  - Wendel, B.
AU  - Goyon, C.
AU  - Faugeron, G.
AU  - Zickler, D.
AU  - Rossignol, J.-L.
AU  - Noyer-Weidner, M.
AU  - Vollmayr, P.
AU  - Trautner, T.A.
AU  - Walter, J.
TI  - A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure.
JO  - Cell
PY  - 1997
SP  - 281
EP  - 290
VL  - 91
AB  - Molecular mechanisms determining methylation patterns in eukaryotic genomes still remain
AB  - unresolved.  We have characterized, in Ascobolus, a gene for de novo methylation.  This novel
AB  - eukaryotic gene, masc1, encodes a protein that has all motifs of the catalytic domain of
AB  - eukaryotic C5-DNA-methyltransferases but is unique in that it lacks a regulatory N-terminal
AB  - domain.  The disruption of masc1 has no effect on viability or methylation maintenance but
AB  - prevents the de novo methylation of DNA repeats, which takes place after fertilization,
AB  - through the methylation induced premeiotically (MIP) process.  Crosses between parents
AB  - harboring the masc1 disruption are arrested at an early stage of sexual reproduction,
AB  - indicating that the activity of Masc1, the product of the gene, is crucial in this
AB  - developmental process.
ER  -

TY  - JOUR
AU  - Malathi, J.
AU  - Murugan, N.
AU  - Umashankar, V.
AU  - Bagyalakshmi, R.
AU  - Madhavan, H.N.
TI  - Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India.
JO  - Genome Announcements
PY  - 2013
SP  - e00425
EP  - e00413
VL  - 1
AB  - Multidrug-resistant Pseudomonas aeruginosa strains, which are notable nosocomial  pathogens,
AB  - have greatly increased the mortality rate of septicemic patients due
AB  - to treatment failure. Here, we report the draft genome sequence of P. aeruginosa
AB  - strain VRFPA02, a human bloodstream isolate that has phenotypically proven to be
AB  - resistant to a broad spectrum of antibiotics.
ER  -

TY  - JOUR
AU  - Malcolm, A.D.B.
TI  - The use of restriction enzymes in genetic engineering.
JO  - Genet. Eng. (N Y)
PY  - 1981
SP  - 129
EP  - 173
VL  - 2
AB  - When the coliphage lambda is grown on E. coli strain C and then attempts are
AB  - made to grow it in E. coli K12, it grows very poorly (Bertani and Weigle, 1953.
AB  - It was shown that this was caused by a response of the host to the phage.
AB  - Since the growth of the phage was restricted, the mechanism used by the E. coli
AB  - was called a "restriction system".  Phage grown originally on K12 could be
AB  - regrown efficiently on K12, and this implies that the host also possessed a
AB  - means of protecting the phage from this restriction and the mechanism became a
AB  - "restriction-modification system".  Meselson and Yuan (1968) incubated lambda
AB  - DNA, which had been grown in E. coli K12, and lambda DNA from E. coli C with an
AB  - extract from K12.  Analysis by sedimentation through a sucrose gradient showed
AB  - that the k.K DNA was unaffected but that k.C DNA was degraded.  This
AB  - degradation was limited in extent and suggested that the restriction system
AB  - (enzyme) only hydrolysed the DNA at a small number of sites.  As it happens the
AB  - restriction enzyme from E. coli K does not cut the DNA at specific sequences
AB  - and hence has not been greatly exploited for genetic engineering. 	The first
AB  - site specific restriction enzyme was discovered by Smith and Wilcox (1970)
AB  - during their studies on recombination in Haemophilus influenzae.  They showed
AB  - by viscometry that a Haemophilus cell extract degraded DNA from the
AB  - bacteriophage P22 but had no effect on DNA from Haemophilus itself.  Using the
AB  - purified enzyme Kelly and Smith (1970) showed that the breaks produced in T7
AB  - DNA all occurred at the symmetrical sequence       5' ....G p T p Py^p Pu p A p
AB  - C....3'	       3' ....C p A p Pu p^ Py p T p G...5' where the hydrolysis occurs
AB  - at the phosphodiester bonds indicated by the arrows.  A catalogue of
AB  - restriction endonucleases isolated since then now numbers over 250 examples,
AB  - although it is not certain that all these are in fact different enzymes (Table
AB  - 1).  Excellent earlier reviews are by Roberts (1976) and Modrich (1979).
ER  -

TY  - JOUR
AU  - Malcolm, A.D.B.
TI  - Binding sites of restriction endonucleases.
JO  - Biochem. Soc. Trans.
PY  - 1986
SP  - 202
EP  - 204
VL  - 14
AB  - There are now more than 600 known restriction endonucleases and these enzymes recognize more
AB  - than 100 different base sequences in their DNA substrates.  When considering binding sites we
AB  - must, of course, consider both the protein and the nucleic acid.  Many, but by no means all,
AB  - of the nucleic acid sequences recognized show a two-fold rotational axis of symmetry, for
AB  - example, BamHI recognizes GGATCCCCTAGG and HindIII cleaves at AAGCTTTTCGAA.   One might
AB  - therefore expect this symmetry to be reflected in the protein's subunit structure and
AB  - disposition of active sites.  While this probably holds in most cases, it is certainly not
AB  - universally true because some of the nucleases are active as monomers (Koncz et al., 1978). 	
AB  - Another feature worthy of comment is the predominance of G-C base-pairs in the recognition
AB  - sites.  This can be illustrated by the fact that, although many enzymes (e.g. ApaI, SacII,
AB  - BsePI, NarI, NaeI, SmaI) which recognize sequences composed entirely of GC's have been known
AB  - for some time, the first all AT-recognizing enzyme (AhaIII) was only discovered very recently
AB  - (Whitehead & Brown, 1982).  It is, of course, possible that the reasons for this bias are
AB  - evolutionary rather then mechanistic, but to date there are no useful suggestions under either
AB  - heading to account for this.
ER  -

TY  - JOUR
AU  - Malcolm, A.D.B.
AU  - Mofatt, J.R.
TI  - Measurement of differential reactivities at restriction endonuclease sites.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 734
EP  - 735
VL  - 8
AB  - Type II restriction endonucleases recognize and hydrolyse DNA at specific sites, often a
AB  - symmetrical four- or six-base-pair sequence.  Although the presence of the unmethylated
AB  - recognition sequence is both a necessary and sufficient condition for cleavage, it has been
AB  - recognized for some time that the rate of cleavage is not constant and presumably depends on
AB  - neighboring sequences.  Only a few attempts have so far been made to quantify these
AB  - observations, but the methods used, involving either the use of deletion mutants or analysis
AB  - of the data by a comparatively sophisticated computer analysis, may not be suitable for
AB  - routine use.
ER  -

TY  - JOUR
AU  - Malcolm, A.D.B.
AU  - Moffat, J.R.
TI  - Differential reactivities at restriction enzyme sites.
JO  - Biochim. Biophys. Acta
PY  - 1981
SP  - 128
EP  - 135
VL  - 655
AB  - A method has been developed to measure the rates of digestion by restriction
AB  - enzymes at individual sites.  This involves a simple arithmetical treatment of
AB  - the integrated areas from a densitometer scan of an ethidium bromide stained
AB  - gel.  We have used this method to study the digestion by HpaI, HincII and SalI
AB  - of pBR322 and PhiX174 DNA, and the effect of various DNA binding ligands.  One
AB  - of the two HpaI sites in PhiX174 DNA is much more sensitive to inhibition by
AB  - ligands such as netropsin, which display a preference for AT base pairs, than
AB  - is the other site.  Inspection of the sequences flanking the restriction sites
AB  - shows that the former contains a much higher proportion of AT base-pairs than
AB  - does the latter.  The opposite phenomenon is observed with the two HincII sites
AB  - in pBR322.  This illustrates the importance of neighbouring sequences in the
AB  - interaction between restriction enzymes and their cleavage sites in DNA.
ER  -

TY  - JOUR
AU  - Malcolm, A.D.B.
AU  - Moffatt, J.R.
AU  - Fox, K.R.
AU  - Waring, M.J.
TI  - Differential inhibition of a restriction enzyme by quinoxaline antibiotics.
JO  - Biochim. Biophys. Acta
PY  - 1982
SP  - 211
EP  - 216
VL  - 699
AB  - The inhibition of cleavage by HpaI at two well-defined restriction sites in
AB  - linearised PhiX174-RF DNA by quinoxaline antibiotics has been investigated.
AB  - Echinomycin, which displays a certain preference for binding to GC basepairs,
AB  - inhibits cleavage at one site much more than the other, whereas triostin A,
AB  - which displays less pronounced sequence-selectivity, inhibits both sites about
AB  - equally.  Other congeners inhibit reaction at the two sites with varying
AB  - effectiveness.  The results demonstrate the usefulness of studying inhibition
AB  - of cleavage at specific sites by restriction enzymes as a means of exploring
AB  - the specificity of DNA-ligand interactions.
ER  -

TY  - JOUR
AU  - Malcolm, A.D.B.
AU  - Snounou, G.
TI  - Restriction enzymes and DNA.
JO  - Top. Mol. Struct. Biol.
PY  - 1987
SP  - 193
EP  - 222
VL  - 9
AB  - The discovery of restriction and modification enzymes, which proved to be a
AB  - major turning point in the progress of molecular biology, was a consequence of
AB  - a bacteriological observation in the early 1950s (Luria and Human, 1952;
AB  - Bertani and Weigle, 1953).  The two groups reported the curious behaviour of
AB  - phage grown on two different strains of bacteria.  Phages propagated on one
AB  - strain were found to grow poorly on the second and vice versa.  However, the
AB  - few phages that escaped restriction could then grow well on the new host, thus
AB  - being modifified in a way that afforded them protection from the restriction
AB  - imposed by the host.
ER  -

TY  - JOUR
AU  - Maldonado-Barragan, A.
AU  - Caballero-Guerrero, B.
AU  - Lucena-Padros, H.
AU  - Ruiz-Barba, J.L.
TI  - Genome Sequence of Lactobacillus pentosus IG1, a Strain Isolated from Spanish-Style Green Olive Fermentations.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5605
EP  - 5605
VL  - 193
AB  - Lactobacillus pentosus is the most prevalent lactic acid bacterium in Spanish-style green
AB  - olive fermentations. Here we present the draft genome
AB  - sequence of L. pentosus IG1, a bacteriocin-producing strain with
AB  - biotechnological and probiotic properties isolated from this food
AB  - fermentations.
ER  -

TY  - JOUR
AU  - Maldonado-Contreras, A.
AU  - Mane, S.P.
AU  - Zhang, X.-S.
AU  - Pericchi, L.
AU  - Alarcon, T.
AU  - Contreras, M.
AU  - Linz, B.
AU  - Blaser, M.J.
AU  - Dominguez-Bello, M.G.
TI  - Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance.
JO  - BMC Microbiol.
PY  - 2013
SP  - 14
EP  - 14
VL  - 13
AB  - Background: Helicobacter pylori has diverged in parallel to its human host, leading to
AB  - distinct phylogeographic populations. Recent evidence suggests that in the current human
AB  - mixing in Latin America, European H. pylori (hpEurope) are increasingly dominant at the
AB  - expense of Amerindian haplotypes (hspAmerind). This phenomenon might occur via DNA
AB  - recombination, modulated by restriction-modification systems (RMS), in which differences in
AB  - cognate recognition sites (CRS) and in active methylases will det rmine direction and
AB  - frequency of gene flow. We hypothesized that genomes from hspAmerind strains that evolved from
AB  - a small founder population have lost CRS for RMS and active methylases, promoting hpEurope's
AB  - DNA invasion. We determined the observed and expected frequencies of CRS for RMS in DNA from 7
AB  - H. pylori whole genomes and 110 multilocus sequences. We also measured the number of active
AB  - methylases by resistance to in vitro digestion by 16 restriction enzymes of genomic DNA from 9
AB  - hpEurope and 9 hspAme rind strains, and determined the direction of DNA uptake in co-culture
AB  - experiments of hspAmerind and hpEurope strains.Results: Most of the CRS were underrepresented
AB  - with consistency between whole genomes and multilocus sequences. Although neither the
AB  - frequency of CRS nor the number of active methylases differ among the bacterial populations
AB  - (average 8.6 +/- 2.6), hspAmerind strains had a restriction profile distinct from that in
AB  - hpEurope strains, with 15 recognition sites accounting for the differences. Am erindians
AB  - strains also exhibited higher transformation rates than European strains, and were more
AB  - susceptible to be subverted by larger DNA hpEurope-fragments than vice versa.Conclusions: The
AB  - geographical variation in the pattern of CRS provides evidence for ancestral differences in
AB  - RMS representation and function, and the transformation findings support the hypothesis of
AB  - Europeanization of the Amerindian strains in Latin America via DNA recombination.
ER  -

TY  - JOUR
AU  - Maldonado-Contreras, A.L.
AU  - Olagibel, L.
AU  - Dominguez-Bello, M.G.
TI  - Geographical differences in restriction-modification system cognate recognition sites in Helicobacter pylori.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2007
SP  - 656
EP  - 656
VL  - 107
AB  - Restriction-modification systems provide a barrier to horizontal gene transfer. Restriction
AB  - Endonucleases (RE) identify cognate DNA sequences and cleave the DNA, unless it is methylated.
AB  - H. pylori, an obligate bacterium of the human stomach, is highly recombinant. But in which
AB  - direction does recombination occurs? As human hosts mix, H. pylori strains (showing geographic
AB  - clusters) also mix, but there seems to be a shift towards predominance of European alleles in
AB  - cultured strains from Latin America. Why are Amerindian strains being lost? Are they being
AB  - subverted by recombination? We hypothesize that European strains would have lower number of
AB  - restriction sites than Amerindian strains, and an increased capability to subvert them. To
AB  - test this hypothesis, we compared the number of cognate restriction sites in the DNA from H.
AB  - pylori strains from Asian, European, African and Amerindian hosts. We analyzed in silico the
AB  - restriction profiles of DNA sequences corresponding to 7 concatenated housekeeping gene
AB  - sequences. DNA was digested in silico with 16 restriction enzymes (RE) previously reported to
AB  - be present in H. pylori strains. Phylogenetic analysis showed 4 clusters by host origin, with
AB  - Amerindian strains close to Asian strains. There was high variability in the number of cognate
AB  - RE sites within and between the phylogroups. All strains had cognate sequences for at least 13
AB  - of the 16 tested RE, and there were no significant differences in the number of cognate sites
AB  - by phylogroup (p>0.05). The average number of restriction sites was 5.3 for European strains,
AB  - 5.2 for Amerindian, 5.5 for Asian and 4.9 for African strains. The results show little
AB  - differences based in the number of cognate restriction sites between the phylogroups. However
AB  - the possibility of RM differences among strain phylogroups given by the number of active
AB  - methylases cannot be assessed in silico. In vitro assays need to be performed to test for the
AB  - real susceptibility to RE digestion, which assesses the methylase functions.
ER  -

TY  - JOUR
AU  - Malfatti, S. et al.
TI  - Complete genome sequence of Halogeometricum borinquense type strain (PR3).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 150
EP  - 159
VL  - 1
AB  - Halogeometricum borinquense Montalvo-Rodriguez et al. 1998 is the type species of the genus,
AB  - and is of phylogenetic interest because of its distinct location
AB  - between the halobacterial genera Haloquadratum and Halosarcina. H. borinquense
AB  - requires extremely high salt (NaCl) concentrations for growth. It can not only
AB  - grow aerobically but also anaerobically using nitrate as electron acceptor. The
AB  - strain described in this report is a free-living, motile, pleomorphic,
AB  - euryarchaeon, which was originally isolated from the solar salterns of Cabo Rojo,
AB  - Puerto Rico. Here we describe the features of this organism, together with the
AB  - complete genome sequence, and annotation. This is the first complete genome
AB  - sequence of the halobacterial genus Halogeometricum, and this 3,944,467 bp long
AB  - six replicon genome with its 3937 protein-coding and 57 RNA genes is part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Malhotra, J.
AU  - Dua, A.
AU  - Saxena, A.
AU  - Sangwan, N.
AU  - Mukherjee, U.
AU  - Pandey, N.
AU  - Rajagopal, R.
AU  - Khurana, P.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5156
EP  - 5156
VL  - 194
AB  - In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar
AB  - larva of Helicoverpa armigera. Here, we report the draft genome
AB  - sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911
AB  - predicted coding sequences, and a G+C content of 41%.
ER  -

TY  - JOUR
AU  - Malik, G.
AU  - Dangwal, M.
AU  - Kapoor, S.
AU  - Kapoor, M.
TI  - Role of DNA methylation in growth and differentiation in Physcomitrella patens and characterization of cytosine DNA methyltransferases.
JO  - FEBS J.
PY  - 2012
SP  - 4081
EP  - 4094
VL  - 279
AB  - Epigenetic mechanisms such as DNA methylation are known to regulate important developmental
AB  - processes in higher eukaryotes. However, little
AB  - is known about the necessity and role of this process in early land
AB  - plants. Using the methyltransferase (MTase) inhibitor zebularine
AB  - (1-(beta-d-ribofuranosyl)-1,2-dihydropyrimidine-2-one), the impact of
AB  - loss of genome-wide methylation on the overall development in
AB  - Physcomitrellapatens was analyzed. It is observed that various aspects
AB  - of growth and differentiation during gametophyte development become
AB  - aberrant. A search for the core molecular components of methylation
AB  - machinery, cytosine DNA MTases, revealed the presence of seven loci in
AB  - the P.patens genome. Five of the loci code for MTases that are similar
AB  - to corresponding proteins in higher plants, while two MTases appear
AB  - specific to P.patens and are closely related to human DNMT3a and
AB  - DNMT3b, respectively. These proteins possess all the conserved
AB  - catalytic motifs characteristic of MTases and a domain of unknown
AB  - function, DUF3444. Association of these highly conserved motifs with a
AB  - DUF has not been reported in any of the MTases known so far. All the
AB  - seven genes are differentially but ubiquitously expressed in
AB  - gametophytes at low levels. Subcellular localization of GFP-fused
AB  - proteins shows patterns of distribution that can be correlated with
AB  - their putative cellular functions. This work bridges the knowledge of
AB  - MTases in P.patens and makes this simple model plant accessible for
AB  - studies on epigenetic aspects that remain intractable in higher plants.
ER  -

TY  - JOUR
AU  - Malik, S.
AU  - Siezen, R.J.
AU  - Renckens, B.
AU  - Vaneechoutte, M.
AU  - Vanderleyden, J.
AU  - Lebeer, S.
TI  - Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a Human Vaginal Isolate.
JO  - Genome Announcements
PY  - 2014
SP  - e01149
EP  - e01114
VL  - 2
AB  - The draft genome of a highly auto-aggregating Lactobacillus plantarum strain isolated from a
AB  - human vagina is reported. The peculiar phenotype also provides an
AB  - adhesive and co-aggregative potential with various pathogens, which could be of
AB  - significance in the vaginal niche. Detailed genome analysis could aid in
AB  - identifying the adhesins of the strain.
ER  -

TY  - JOUR
AU  - Malin, G.
AU  - Iakobashvili, R.
AU  - Lapidot, A.
TI  - Effect of tetrahydropyrimidine derivatives on protein-nucleic acids interaction.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 6920
EP  - 6929
VL  - 274
AB  - 2-Methyl-4-carboxy,5-hydroxy-3,4,5,5-tetrahydropyrimidine (THP(A) or hydroxyectoine) and
AB  - 2-methyl,4-carboxy-3,4,5,6-tetrahydropyrimidine (THP(B) or ectoine) are now recognized as
AB  - ubiquitous bacterial osmoprotectants.  To evaluate the impact of tetrahydropyrimidine
AB  - derivatives on protein-DNA interaction and on restriction-modification systems, we have
AB  - examined their effect on the cleavage of plasmid DNA by 10 type II restriction endonucleases.
AB  - THP(A) completely arrested the cleavage of plasmid and bacteriophage lambda DNA by EcoRI
AB  - endonuclease at 0.4 mM and the oligonucleotide (d(CGCGAATTCGCG))2 at about 4.0 mM.  THP(B) was
AB  - 10-fold less effective than THP(A), whereas for betaine and proline, a notable inhibition was
AB  - observed only at 100 mM.  Similar effects of THP(A) were observed for all tested restriction
AB  - endonucleases, except for SmaI and PvuII, which were inhibited only partially at 50mM THP(A).
AB  - No effect of THP(A) on the activity of DNase I, RNase A, and Taq DNA polymerase was noticed.
AB  - Gel shift assays showed that THP(A) inhibited the EcoRI-(d-(CGCGAATTCGCG))2 complex formation,
AB  - whereas facilitated diffusion of EcoRI along the DNA was not affected.  Methylation of the
AB  - carboxy group significantly decreased the activity of THPs, suggesting that their zwitterionic
AB  - character is essential for the inhibition effect.  Possible mechanisms of inhibition, role of
AB  - THPs in the modulation of the protein-DNA interaction, and the in vivo relevance of the
AB  - observed phenomena are discussed.
ER  -

TY  - JOUR
AU  - Malinga, L.A.
AU  - Abeel, T.
AU  - Desjardins, C.A.
AU  - Dlamini, T.C.
AU  - Cassell, G.
AU  - Chapman, S.B.
AU  - Birren, B.W.
AU  - Earl, A.M.
AU  - van der Walt, M.
TI  - Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.
JO  - Genome Announcements
PY  - 2016
SP  - e01771
EP  - e01715
VL  - 4
AB  - We report the whole-genome sequencing of two extensively drug-resistant tuberculosis strains
AB  - belonging to the Euro-American S lineage. The RSA 114 strain
AB  - showed single-nucleotide polymorphisms predicted to have drug efflux activity.
ER  -

TY  - JOUR
AU  - Mallamaci, M.A.
AU  - Bascoy, M.L.
AU  - Brown, J.
AU  - Combates, N.J.
AU  - Winkle, S.A.
TI  - Locating binding sites for the carcinogen N-acetoxy-N-acetyl-2-aminofluorene using restriction enzyme inhibition assays.
JO  - J. Biomol. Struct. Dyn.
PY  - 1992
SP  - 83
EP  - 96
VL  - 10
AB  - Restriction enzyme inhibition studies have been employed to map the locations of high affinity
AB  - binding sites of the carcinogen N-acetoxy-N-acetyl-2-aminofluorene (acetoxyAAF) on pBR322,
AB  - phiX174 and SV40 DNAs. Bound carcinogen levels were kept low (less than 20 bound AAF moieties
AB  - per DNA molecule) in order to observe only the binding to the high affinity sites. Inhibition
AB  - of certain restriction enzymes was observed in a limited number of locations on these DNAs.
AB  - Inhibition increased as bound AAF increased and the particular restriction enzymes inhibited
AB  - varied with location. On all three DNAs, activities of these enzymes was not affected in other
AB  - locations. Comparison of the sequences at the sites of inhibition on the three DNAs indicates
AB  - that all sites have common sequence elements: the presence of either the sequence
AB  - T(C/G)TT(G/C) or the sequence T(G/C)CTT(G/C).
ER  -

TY  - JOUR
AU  - Malone, C.S.
AU  - Miner, M.D.
AU  - Doerr, J.R.
AU  - Jackson, J.P.
AU  - Jacobsen, S.E.
AU  - Wall, R.
AU  - Teitell, M.
TI  - CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 10404
EP  - 10409
VL  - 98
AB  - DNA methylation has been linked to gene silencing in cancer. Primary effusion lymphoma (PEL)
AB  - and myeloma are lymphoid malignancies that arise
AB  - from terminally differentiated B cells. Interestingly, PEL do not express
AB  - immunoglobulins or most B lineage-specific genes. The B cell-specific B29
AB  - (Igbeta/CD79b) gene is silenced in PEL and some myelomas but is expressed
AB  - in other normal and malignant B cells. B29 expression was reactivated in
AB  - PEL by demethylating and histone deacetylase inhibiting treatments.
AB  - Bisulfite sequencing revealed two types of DNA methylation in silenced B29
AB  - promoters: at conventional CpG and at CC(A/T)GG B29 promoter sites. The
AB  - pattern of methylated CpG ((m)CpG) and C(m)C(A/T)GG B29 promoter
AB  - methylation observed was similar to that recently reported for epigenetic
AB  - silencing of an integrated retrovirus. Methylation of C(m)C(A/T)GG sites
AB  - in the B29 promoter significantly repressed in vivo transcriptional
AB  - activity. Also, methylation of a central conserved C(m)CTGG B29 promoter
AB  - site blocked the binding of early B cell factor. This methylated motif
AB  - formed DNA-protein complexes with nuclear extracts from all cell types
AB  - examined. Therefore, C(m)C(A/T)GG methylation may represent an important
AB  - type of epigenetic marker on mammalian DNA that impacts transcription by
AB  - altering DNA-protein complex formation.
ER  -

TY  - JOUR
AU  - Malone, K.M.
AU  - Farrell, D.
AU  - Stuber, T.P.
AU  - Schubert, O.T.
AU  - Aebersold, R.
AU  - Robbe-Austerman, S.
AU  - Gordon, S.V.
TI  - Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97.
JO  - Genome Announcements
PY  - 2017
SP  - e00157
EP  - e00117
VL  - 5
AB  - We report here an update to the reference genome sequence of the bovine tuberculosis bacillus
AB  - Mycobacterium bovis AF2122/97, generated using an
AB  - integrative multiomics approach. The update includes 42 new coding sequences
AB  - (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP)
AB  - corrections, and disclosure that the RD900 locus, previously described as absent
AB  - from the genome, is in fact present.
ER  -

TY  - JOUR
AU  - Malone, T.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyl-transferases, and suggests a catalytic mechanism for these enzymes.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 618
EP  - 632
VL  - 253
AB  - Previous X-ray crystallographic studies have revealed that the catalytic domain of a DNA
AB  - methyltransferase (Mtase) generating C5-methylcytosine bears a striking structural similarity
AB  - to that of a Mtase generating N6-methyladenine.  Guided by this common structure, we performed
AB  - a multiple sequence alignment of 42 amino-Mtases (N6-adenine and N4-cytosine).  This
AB  - comparison revealed nine conserved motifs, corresponding to the motifs I to VIII and X
AB  - previously defined in C5-cytosine Mtases.  The amino and C5-cytosine Mtases thus appear to be
AB  - more closely related than has been appreciated.  The amino Mtases could be divided into three
AB  - groups, based on the sequential order of motifs, and this variation in order may explain why
AB  - only two motifs were previously recognized in the amino Mtases.  The amino and C5-cytosine
AB  - Mtases thus appear to be more closely related than has been appreciated.  The amino Mtases
AB  - could be divided into three groups, based on the sequential order of motifs, and this
AB  - variation in order may explain why only two motifs were previously recognized in the amino
AB  - Mtases.  The Mtases grouped in this way show several other group-specific properties,
AB  - including differences in amino acid sequence, molecular mass and DNA sequence specificity.
AB  - Surprisingly, the N4-cytosine and N6-adenine Mtases do not form separate groups.  These
AB  - results have implications for the catalytic mechanisms, evolution and diversification of ths
AB  - family of enzymes.  Furthermore, a comparative analysis of the S-adenosyl-L-methionine and
AB  - adenine/cytosine binding pockets suggests that, stucturally and functionally, they are
AB  - remarkably similar to one another.
ER  -

TY  - JOUR
AU  - Maltchenko, S.
TI  - The target recognition domains from the methyltransferases of II class have common subdomains.
JO  - Protein Engineering Suppl.
PY  - 1993
SP  - 46
EP  - 46
VL  - 6
AB  - The proteins of the class II restriction-modification systems are very interesting objects for
AB  - biotechnology. Both endonuclease and methyltransferase enzymes recognize identical DNA target
AB  - sites, but they are not significantly similar in their amino acid sequences. Recently,
AB  - alignment for m5C-methyltransferases (m5C-Mets) was done and common domains (from 1 to 10) for
AB  - these proteins were identified. The target recognition domain (TRDs) for BsuPhi3T and SprI
AB  - m5C-Mets which recognize a specific DNA site were determined by site-directed mutagenesis. The
AB  - location of TRDs is between domains 8 and 9, which were determined from the alignment of
AB  - m5C-Met sequences. The size of TRDs varies from 86 to 274 amino acids. It was shown that some
AB  - of the homologous sequences are within the TRD. We analyzed TRDs from 18 m5C-Met sequences for
AB  - the presence of common subsequences and compared the subsequences with the restriction and
AB  - methyltransferase enzyme sequences.
ER  -

TY  - JOUR
AU  - Maltseva, D.V.
AU  - Baykov, A.A.
AU  - Jeltsch, A.
AU  - Gromova, E.S.
TI  - Impact of 7,8-Dihydro-8-oxoguanine on Methylation of the CpG Site by Dnmt3a (dagger).
JO  - Biochemistry
PY  - 2009
SP  - 1361
EP  - 1368
VL  - 48
AB  - 7,8-Dihydro-8-oxoguanine (8-oxoG) is a ubiquitous oxidative DNA lesion resulting from injury
AB  - to DNA via reactive oxygen species. 8-oxoG lesions
AB  - may play a role in the formation of aberrant DNA methylation patterns
AB  - during carcinogenesis. In this study, we assessed the effects of 8-oxoG on
AB  - methylation and complex formation of nine 30-mer oligodeoxynucleotide
AB  - duplexes by the catalytic domain of murine Dnmt3a DNA methyltransferase
AB  - (Dnmt3a-CD). The effects of 8-oxoG on the methylation rate of
AB  - hemimethylated duplexes varied from a 25-fold decrease to a 1.8-fold
AB  - increase, depending on the position of the lesion relative to the
AB  - Dnmt3a-CD recognition site (CpG) and target cytosine (C). The most
AB  - significant effect was observed when 8-oxoG replaced guanine within the
AB  - recognition site immediately downstream of the target cytosine.
AB  - Fluorescence polarization experiments with fluorescein-labeled duplexes
AB  - revealed that two molecules of Dnmt3a-CD bind per duplex, generating
AB  - sigmoid binding curves. Duplexes exhibiting the highest apparent binding
AB  - cooperativity formed the least stable 1:2 complexes with Dnmt3a-CD and
AB  - were methylated at the lowest rate. Kinetic analyses disclosed the
AB  - formation of very stable nonproductive enzyme-substrate complexes with
AB  - hemimethylated duplexes that act as suicide substrates of Dnmt3a-CD. The
AB  - presence of 8-oxoG within the CpG site downstream of the target cytosine
AB  - markedly diminished productive versus nonproductive binding. We propose
AB  - that 8-oxoG located adjacent to the target cytosine interferes with
AB  - methylation by weakening the affinity of DNA for Dnmt3a-CD, thereby
AB  - favoring a nonproductive binding mode.
ER  -

TY  - JOUR
AU  - Maluta, R.P.
AU  - Nicholson, B.
AU  - Logue, C.M.
AU  - Nolan, L.K.
AU  - Rojas, T.C.
AU  - Dias-da-Silveira, W.
TI  - Complete Genomic Sequence of an Avian Pathogenic Escherichia coli Strain of Serotype O7:HNT.
JO  - Genome Announcements
PY  - 2016
SP  - e01611
EP  - e01615
VL  - 4
AB  - Avian pathogenic Escherichia coli (APEC) is associated with colibacillosis in poultry. Here,
AB  - we present the first complete sequence of an APEC strain of the
AB  - O7:HNT serotype and ST73 sequence type, isolated from a broiler with cellulitis.
AB  - Complete genomes of APEC with distinct genetic backgrounds may be useful for
AB  - comparative analysis.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Evdokimov, A.A.
AU  - Hattman, S.
TI  - Dimeric/oligomeric DNA methyltransferases: an unfinished story.
JO  - Biol. Chem.
PY  - 2009
SP  - 835
EP  - 844
VL  - 390
AB  - DNA methyltransferases (MTases) are enzymes that carry out post-replicative sequence-specific
AB  - modifications. The initial
AB  - experimental data on the structure and kinetic characteristics of the
AB  - EcoRI MTase led to the paradigm that type II systems comprise dimeric
AB  - endonucleases and monomeric MTases. In retrospect, this was logical
AB  - because, while the biological substrate of the restriction endonuclease
AB  - is two-fold symmetrical, the in vivo substrate for the MTase is
AB  - generally hemi-methylated and, hence, inherently asymmetric. Thus, the
AB  - paradigm was extended to include all DNA MTases except the more complex
AB  - bifunctional type I and type III enzymes. Nevertheless, a gradual
AB  - enlightenment grew over the last decade that has changed the accepted
AB  - view on the structure of DNA MTases. These results necessitate a more
AB  - complex view of the structure and function of these important enzymes.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Evdokimov, A.A.
AU  - Zinoviev, V.V.
AU  - Ovechkina, L.G.
AU  - Lindstrom, W.M.
AU  - Reich, N.O.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 2361
EP  - 2369
VL  - 29
AB  - The fluorescence of 2-aminopurine (2A)-substituted duplexes (contained in the GATC target
AB  - site) was investigated by titration with T4 Dam DNA-(N6-adenine)-methyltransferase. With an
AB  - unmethylated target (2A/A duplex) or its methylated derivative (2A/mA duplex), T4 Dam produced
AB  - up to a 50-fold increase in fluorescence, consistent with 2A being flipped out of the DNA
AB  - helix. Though neither S-adenosyl-L-homocysteine nor sinefungin had any significant effect,
AB  - addition of substrate S-adenosyl-L-methionine (AdoMet) sharply reduced the Dam-induced
AB  - fluorescence with these complexes. In contrast, AdoMet had no effect on the fluorescence
AB  - increase produced with an 2A/2A double-substituted duplex. Since the 2A/mA duplex cannot be
AB  - methylated, the AdoMet-induced decrease in fluorescence cannot be due to methylation per se.
AB  - We propose that T4 Dam alone randomly binds to the asymmetric 2A/A and 2A/mA duplexes, and
AB  - that AdoMet induces an allosteric T4 Dam conformational change that promotes reorientation of
AB  - the enzyme to the strand containing the native base. Thus, AdoMet increases enzyme
AB  - binding-specificity, in addition to serving as the methyl donor. The results of
AB  - pre-steady-state methylation kinetics are consistent with this model.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Hattman, S.
TI  - DNA methyltransferases: Mechanistic models derived from kinetic analysis.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 2012
SP  - 97
EP  - 193
VL  - 47
AB  - The sequence-specific transfer of methyl groups from donor S-adenosyl-L-methionine (AdoMet) to
AB  - certain positions of DNA-adenine or
AB  - -cytosine residues by DNA methyltransferases (MTases) is a major form
AB  - of epigenetic modification. It is virtually ubiquitous, except for some
AB  - notable exceptions. Site-specific methylation can be regarded as a
AB  - means to increase DNA information capacity and is involved in a large
AB  - spectrum of biological processes. The importance of these functions
AB  - necessitates a deeper understanding of the enzymatic mechanism(s) of
AB  - DNA methylation. DNA MTases fall into one of two general classes; viz.
AB  - amino-MTases and [C5-cytosine]-MTases. Amino-MTases, common in
AB  - prokaryotes and lower eukaryotes, catalyze methylation of the exocyclic
AB  - amino group of adenine ([N6-adenine]-MTase) or cytosine
AB  - ([N4-cytosine]-MTase). In contrast, [C5-cytosine]-MTases methylate the
AB  - cyclic carbon-5 atom of cytosine. Characteristics of DNA MTases are
AB  - highly variable, differing in their affinity to their substrates or
AB  - reaction products, their kinetic parameters, or other characteristics
AB  - (order of substrate binding, rate limiting step in the overall
AB  - reaction). It is not possible to present a unifying account of the
AB  - published kinetic analyses of DNA methylation because different authors
AB  - have used different substrate DNAs and/or reaction conditions.
AB  - Nevertheless, it would be useful to describe those kinetic data and the
AB  - mechanistic models that have been derived from them. Thus, this review
AB  - considers in turn studies carried out with the most consistently and
AB  - extensively investigated [N6-adenine]-, [N4-cytosine]- and
AB  - [C5-cytosine]-DNA MTases.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Lindstrom, W.M. Jr.
AU  - Schlagman, S.L.
AU  - Hattman, S.
AU  - Reich, N.O.
TI  - Pre-steady state kinetics of bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase: interaction with native (GATC) or modified sites.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 4207
EP  - 4211
VL  - 28
AB  - The DNA methyltransferase of bacteriophage T4 (T4 Dam MTase) recognizes the palindromic
AB  - sequence GATC, and catalyzes transfer of the methyl group from S-adenosyl-L-methionine
AB  - (AdoMet) to the N(6)-position of adenine [generating N(6)-methyladenine and
AB  - S-adenosyl-L-homocysteine (AdoHcy)].  Pre-steady state kinetic analysis revealed that the
AB  - methylation rate constant k(meth) for unmethylated and hemimethylated substrates (0.56 and
AB  - 0.47 s(-1), respectively) was at least 20-fold larger than the overall reaction rate constant
AB  - k(cat) (0.023 s(-1)). This indicates that the release of products is the rate-limiting step in
AB  - the reaction. Destabilization of the target-base pair did not alter the methylation rate,
AB  - indicating that the rate of target nucleoside flipping does not limit k(meth). Preformed T4
AB  - Dam MTase-DNA complexes are less efficient than preformed T4 Dam MTase-AdoMet complexes in the
AB  - first round of catalysis. Thus, this data is consistent with a preferred route of reaction for
AB  - T4 Dam MTase in which AdoMet is bound first; this preferred reaction route is not observed
AB  - with the DNA-[C5-cytosine]-MTases.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Lindstrom, W.M.
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Schlagman, S.L.
AU  - Reich, N.O.
AU  - Hattman, S.
TI  - Bacteriophage T4Dam (DNA-(adenine-N6)-methyltransferase). Evidence for two distinct stages of methylation under single turnover conditions.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 41749
EP  - 41755
VL  - 278
AB  - We compared the (pre)steady-state and single turnover methylation kinetics of bacteriophage
AB  - T4Dam (DNA-(adenine-N6)-methyltransferase)-mediated
AB  - methyl group transfer from S-adenosyl-l-methionine (AdoMet) to
AB  - oligodeoxynucleotide duplexes containing a single recognition site
AB  - (palindrome 5'-GATC/5'-GATC) or some modified variant. T4Dam-AdoMet
AB  - functions as a monomer under steady-state conditions (enzyme/DNA << 1),
AB  - whereas under single turnover conditions (enzyme/DNA > 1), a catalytically
AB  - active complex containing two Dam-AdoMet molecules is formed initially,
AB  - and two methyl groups are transferred per duplex (to produce a methylated
AB  - duplex and S-adenosyl-l-homocysteine (AdoHcy)). We propose that the single
AB  - turnover reaction proceeds in two stages. First, two preformed
AB  - T4Dam-AdoMet complexes bind opposite strands of the unmodified target
AB  - site, and one enzyme molecule catalyzes the rapid transfer of the
AB  - AdoMet-methyl group (kmeth1 = 0.21 s-1); this is 2.5-fold slower than the
AB  - rate observed with monomeric T4Dam-AdoMet bound under pre-steady-state
AB  - conditions for burst determination. In the second stage, methyl transfer
AB  - to adenine in GATC on the complementary strand occurs at a rate that is 1
AB  - order of magnitude slower (kmeth2 = 0.023 s-1). We suggest that under
AB  - single turnover conditions, methylation of the second strand is
AB  - rate-limited by Dam-AdoHcy dissociation or its clearance from the
AB  - methylated complementary strand. The hemimethylated duplex 5'-GATC/5'-GMTC
AB  - also interacts with T4Dam-AdoMet complexes in two stages under single
AB  - turnover reaction conditions. The first stage (kmeth1) reflects
AB  - methylation by dimeric T4Dam-AdoMet productively oriented to the strand
AB  - with the adenine residue capable of methylation. The slower second stage
AB  - (kmeth2) reflects methylation by enzyme molecules non-productively
AB  - oriented to the GMTC chain, which then have to re-orient to the opposite
AB  - productive chain. Substitutions of bases and deletions in the recognition
AB  - site affect the kinetic parameters in different fashions. When the GAT
AB  - portion of GATC was disrupted, the proportion of the initial productive
AB  - enzyme-substrate complexes was sharply reduced.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Ovechkina, L.G.
AU  - Evdokimov, A.A.
AU  - Zinoviev, V.V.
TI  - Single turnover kinetics of methylation by T4 DNA-(N6-adenine)-methyltransferase.
JO  - Mol. Biol. (Mosk)
PY  - 2001
SP  - 65
EP  - 78
VL  - 35
AB  - Interaction of T4 DNA-(N6-adenine)-methyltransferase was studied with a variety of synthetic
AB  - oligonucleotide substrates containing the native
AB  - recognition site GATC or its modified variants. The data obtained in
AB  - the decisecond and second intervals of the reaction course allowed for
AB  - the first time the substrate methylation rates to be compared with the
AB  - parameters of the steady-state reaction. It was established that the
AB  - substrate reaction proceeds in two stages. Because it is shown that in
AB  - steady-state conditions T4 MTase forms a dimeric structure, the
AB  - following sequence of events is assumed. Upon collision of a T4 MTase
AB  - monomer with an oligonucleotide duplex, an asymmetrical complex forms
AB  - in which the enzyme randomly oriented relative to one of the strands of
AB  - the specific recognition site catalyzes a fast transfer of the methyl
AB  - group from S-adenosylmethionine to the adenosine residue (k(1) = 0.21
AB  - s(-1)). Simultaneously, a second T4 MTase subunit is added to the
AB  - complex, providing for the continuation of the reaction. In the course
AB  - of a second stage, which is by an order of magnitude slower (k(2) =
AB  - 0.023 s(-1) for duplex with the native site), the dimeric T4 MTase
AB  - switches over to the second strand and the methylation of the second
AB  - residue, target. The rate of the methyl group transfer from donor,
AB  - S-adenosylmethionine, to DNA is much higher than the overall rate of
AB  - the T4 MTase-catalyzed steady-state reaction, although this difference
AB  - is considerably less than that shown for EcoRI MTase. Base
AB  - substitutions and deletions in the recognition site affect the
AB  - substrate parameters in different fashions. When the GAT sequence is
AB  - disrupted, the proportion of the initial productive enzyme-substrate
AB  - complexes is usually sharply reduced. The flipping of the adenosine
AB  - residue to be modified in the recognition site upon interaction with
AB  - the enzyme, revealed by fluorescence titration, supports the existing
AB  - notions about the involvement of such a DNA deformation in reactions
AB  - catalyzed by various DNA-MTases.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Ovechkina, L.G.
AU  - Zinoviev, V.V.
AU  - Linstrem, U.M.
AU  - Reich, N.O.
TI  - DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens: kinetic and substrate-binding properties.
JO  - Mol. Biol. (Mosk)
PY  - 2001
SP  - 42
EP  - 51
VL  - 35
AB  - Interaction of DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens (BamHI
AB  - MTase, 49 kDa) with a 20-mer duplex containing
AB  - a palindromic recognition site GGATCC was studied by methods of
AB  - steady-state and pre-steady-state kinetics of the methyl group
AB  - transfer, gel retardation, and crosslinking of the enzyme subunits with
AB  - glutaraldehyde. In steady-state conditions, BamHI MTase displays a
AB  - simple kinetic behavior toward the 20-mer substrate. A linear
AB  - dependence was observed for the reaction rate on the enzyme
AB  - concentration and a Michaelis dependence of the reaction rate on the
AB  - concentration of both substrates: S-adenosyl-L-methionine (SAM), the
AB  - methyl group donor, and DNA, the methyl group acceptor. In independent
AB  - experiments, the concentration of the 20-mer duplex or SAM was changed,
AB  - the enzyme concentration being substantially lower than the
AB  - concentrations of substrates. The k(cat) values determined in these
AB  - conditions are in good agreement with one another and approximately
AB  - equal to 0.05 s(-1). The K-M values for the duplex and SAM are 0.35 and
AB  - 1.6 nM, respectively. An analysis of single turnover kinetics (at
AB  - limiting concentration of the 20-mer duplex) revealed the following
AB  - characteristics of the BamHI MTase-dependent methylation of DNA. The
AB  - value of the rate constant of the DNA methylation step at the enzyme
AB  - saturating concentration is on average 0.085 s(-1), which is only 1.6
AB  - times higher than the value determined in steady-state conditions. Only
AB  - one of two target cytidine residues was methylated in a single turnover
AB  - of the enzyme, which coincides with the earlier data on EcoRI MTase.
AB  - Regardless of the order of enzyme preincubation with SAM and DNA, both
AB  - curves for the single turnover methylation are comparable. These
AB  - results are consistent with the model of the random order of the
AB  - productive ternary enzyme-substrate complex formation. In contrast to
AB  - the relatively simple kinetic behavior of BamHI MTase in the
AB  - steady-state reaction are the data on the enzyme binding with DNA. In
AB  - gel retardation experiments, there was no stoichiometrically simple
AB  - complex with the oligonucleotide duplex even at low enzyme
AB  - concentrations. The molecular mass of the complexes was so high that
AB  - they did not enter 12% PAG. In experiments on crosslinking of the BamHI
AB  - MTase subunits, it was shown that the enzyme in a free state exists as
AB  - a dimer. Introduction of substoichiometric amounts of DNA into the
AB  - reaction mixture results in pronounced multimerization of the enzyme.
AB  - However, addition of SAM in saturating concentration at an excess of
AB  - the oligonucleotide duplex over BamHI MTase converts most of the enzyme
AB  - into a monomeric state.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Petrov, N.A.
AU  - Gorbunov, Y.A.
AU  - Kossykh, V.G.
AU  - Hattman, S.
TI  - Interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with oligonucleotides containing native or modified (defective) recognition sites.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4393
EP  - 4399
VL  - 25
AB  - The DNA-[N6-adenine]-methyltransferase of phage T4 catalyzes methyl group transfer from
AB  - S-adenosyl-L-methionine to the N6-position of adenine in the palindromic sequence, GATC.  We
AB  - have used a gel shift assay to monitor complex formation between T4 Dam and various synthetic
AB  - duplex oligonucleotides, either native or modified/defective.  The results are summarized as
AB  - follows.  (i) T4 Dam bound with ~100-fold higher affinity to a 20mer specific
AB  - (GATC-containing) duplex containing the canonical palindromic methylation sequence, GATC, than
AB  - to a non-specific duplex containing another palindrome, GTAC.  (ii) Compared with the
AB  - unmethylated duplex, the hemimethylated 20mer specific duplex had a slightly increased
AB  - (~2-fold) ability to form complexes with T4 Dam.  (iii) No stable complex was formed with a
AB  - synthetic 12mer specific (GATC-containing) duplex, although T4 Dam can methylate it.  This
AB  - indicates that there is no relation between formation of a catalytically competent 12mer-Dam
AB  - complex and one stable to gel electrophoresis.  (iv) Formation of a stable complex did not
AB  - require that both strands be contiguous or completely complementary.  Absence of a single
AB  - internucleotide phosphate strongly reduced complex formation only when missing between the T
AB  - and C residues.  This suggests that if T4 Dam makes critical contact(s) with a backbone
AB  - phosphate(s), then the one between T and C is the only likely candidate.  Having only one half
AB  - of the recognition site intact on one strand was sufficient for stable complex formation
AB  - provided that the 5' G.C base-pairs be present at both ends of the palindromic, GATC.  Since
AB  - absence of either a G or C abolished T4 Dam binding, we conclude that both strands are
AB  - recognized by T4 Dam.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Sclavi, B.
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Hattman, S.
AU  - Buckle, M.
TI  - Bacteriophage T4Dam DNA-(adenine-N-6)-methyltransferase - Comparison of pre-steady state and single turnover methylation of 40-mer duplexes  containing two (un)modified target sites.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 50012
EP  - 50018
VL  - 279
AB  - We analyzed pre-steady state and single turnover kinetics of bacteriophage T4Dam
AB  - DNA-(adenine-N-6)methyltransferase- mediated methyl
AB  - group transfer from S-adenosyl-L-methionine ( AdoMet) to 40-mer
AB  - duplexes containing native recognition sites (5'-GATC/5'- GATC) or some
AB  - modified variant(s). The results extend a model from studies with
AB  - single-site 20-mer duplexes. Under pre-steady state conditions,
AB  - monomeric T4Dam methyltransferase- AdoMet complexes were capable of
AB  - rapid methylation of adenine residues in 40-mer duplexes containing two
AB  - sites. During processive movement of T4Dam to the next site, the
AB  - rate-limiting step was the exchange of the product
AB  - S-adenosyl-L-homocysteine ( AdoHcy) for AdoMet without T4Dam
AB  - dissociating from the duplex. Consequently, instead of a single
AB  - exponential rate dependence, complex methylation curves were obtained
AB  - with at least two pre-steady state steps. With 40-mer duplexes
AB  - containing a single target site, the kinetics were simpler, fitting a
AB  - single exponential followed by a linear steady state phase. Single
AB  - turnover methylation of 40-mer duplexes also proceeded in two stages.
AB  - First, two dimeric T4Dam-AdoMet molecules bound, and each catalyzed a
AB  - two-step methylation. Instead of processive movement of T4Dam, a
AB  - conformational adaptation occurred. We propose that following methyl
AB  - transfer to one strand, dimeric ( T4Dam-AdoMet)-(T4Dam-AdoHcy) was
AB  - capable of rapidly reorienting itself and catalyzing methyl transfer to
AB  - the target adenine on the complementary, unmethylated strand. This
AB  - second stage methyl transfer occurred at a rate about 25-fold slower
AB  - than in the first step; it was rate-limited by Dam-AdoHcy dissociation
AB  - or its clearance from the methylated complementary strand. Under single
AB  - turnover conditions, there was complete methylation of all target
AB  - adenine residues with each of the two-site 40-mer duplexes.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Zinovev, V.V.
TI  - Studies of the role of symmetry in the specific recognition of natural and synthetic DNA by type II restriction and modification enzymes.
JO  - Sov. Sci. Rev. D. Physiochem. Biol.
PY  - 1989
SP  - 87
EP  - 142
VL  - 9
AB  - Type II restriction endonucleases and methylases are site-specific enzymes acting on synthetic
AB  - and natural DNAs. In prokaryotic cells they make up a unique system of
AB  - restriction-modification which destroys any foreign DNA penetrating the cell. The overwhelming
AB  - majority of restrictases and methylases recognize palindromic sites with a second-order
AB  - symmetry axis. Two alternative mechanisms for this recognition exist: (i) symmetric
AB  - recognition by way of double-sided symmetrical contacts of the enzyme with non-overlapping
AB  - nucleotide groups of the duplex site; (ii) asymmetric recognition is brought about through
AB  - asymmetrical contact between the DNA chain and the enzyme molecule. The majority of
AB  - restrictases have a subunit structure, the number of subunits being even. All type II
AB  - methylases which have been isolated up to now consist of a single polypeptide chain, a monomer
AB  - being their stable form in solution. A central theme that has emerged from the data is that
AB  - multiple mechanisms exist for discrimination of base pairs. Hence, the elucidation of such
AB  - enzyme-DNA binding schemes as may be employed in sequence discrimination requires the analysis
AB  - of multiple systems. This review deals with our data on the interaction of restriction
AB  - endonucleases and Ecodam methylase with various natural and synthetic substrates containing
AB  - either completely symmetrical recognition sites or their asymmetrical variations. Our results
AB  - concerning the properties of different substrates confirm a symetrical model of interaction
AB  - between DNA and type II enzymes and demonstrate the probable interdependence of the active
AB  - centers in the cases of the BamHI and Sau3AI endonuclease just as there is with Ecodam
AB  - methylase. Dimerization of monomeric Ecodam methylase and endonuclease MvaI induced by the
AB  - oligonucleotide substrate has been demonstrated by gel filtration, ultracentrifugation and
AB  - small angle X-ray scattering methods. Thus, the catalytically active form of Ecodam methylase
AB  - and other monomeric type II enzymes seems to be a dimer. In discussing the results, attention
AB  - has mainly been paid to the significance of symmetry in the structures of both substrate DNs
AB  - and type II enzymes with respect to providing a productive interaction.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Zinovev, V.V.
AU  - Gorbunov, Y.A.
AU  - Popov, S.G.
AU  - Rechkunova, N.I.
AU  - Buryanov, Y.I.
AU  - Nesternko, V.F.
AU  - Baev, A.A.
TI  - Influence of the structure of oligonucleotide substrates on the interaction with Eco dam methylase.
JO  - Biokhimiia
PY  - 1988
SP  - 1639
EP  - 1647
VL  - 53
AB  - The interaction of Eco dam methylase with synthetic substrates containing various damages in
AB  - the recognition site of the enzyme was investigated. The imperfect oligonucleotide complexes
AB  - contained a complete GATC recognition seuqence in one strand, but various defects in the
AB  - complementary strand in the recognition site: omission of one or several nucleotides, the
AB  - presence of an S-methylthiophosphate residue at the site of a break in the oligonucleotide
AB  - strand. The presence of the S-methyl-thiophosphate residue has no significant effect on
AB  - methylation in comparison with analogous substrates that did not contain an internucleotide
AB  - phosphate. A productive enzyme-substrate interaction occurred only with oligonucleotide
AB  - complexes containing both GA pairs in the recognition site of Eco dam methylase. The data
AB  - obtained suggest that Eco dam methylase, like type II restriction endonucleases, can form a
AB  - symmetrical structure in the enzyme-substrate complex.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Lindstrom, W.M. Jr.
AU  - Reich, N.O.
AU  - Hattman, S.
TI  - DNA (cytosine-N4-)- and -(adenine-N6-)-methyltransferases have different kinetic mechanisms but the same reaction route. A comparison of M.BamHI and T4 Dam.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 15713
EP  - 15719
VL  - 278
AB  - We studied the kinetics of methyl group transfer by the BamHI
AB  - DNA-(cytosine-N(4)-)-methyltransferase (MTase) from Bacillus
AB  - amyloliquefaciens to a 20-mer oligodeoxynucleotide duplex containing the
AB  - palindromic recognition site GGATCC. Under steady state conditions the
AB  - BamHI MTase displayed a simple kinetic behavior toward the 20-mer duplex.
AB  - There was no apparent substrate inhibition at concentrations much higher
AB  - than the K(m) for either DNA (100-fold higher) or S-adenosyl-l-methionine
AB  - (AdoMet) (20-fold higher); this indicates that dead-end complexes did not
AB  - form in the course of the methylation reaction. The DNA methylation rate
AB  - was analyzed as a function of both substrate and product concentrations.
AB  - It was found to exhibit product inhibition patterns consistent with a
AB  - steady state random bi-bi mechanism in which the dominant order of
AB  - substrate binding and product release (methylated DNA, DNA(Me), and
AB  - S-adenosyl-l-homocysteine, AdoHcy) was Ado-Met DNA DNA(Me) AdoHcy. The
AB  - M.BamHI kinetic scheme was compared with that for the T4 Dam
AB  - (adenine-N(6)-)-MTase. The two differed with respect to an effector action
AB  - of substrates and in the rate-limiting step of the reaction (product
AB  - inhibition patterns are the same for the both MTases). From this we
AB  - conclude that the common chemical step in the methylation reaction, methyl
AB  - transfer from AdoMet to a free exocyclic amino group, is not sufficient to
AB  - dictate a common kinetic scheme even though both MTases follow the same
AB  - reaction route.
ER  -

TY  - JOUR
AU  - Malygin, E.G.
AU  - Zinoviev, V.V.
AU  - Petrov, N.A.
AU  - Evdokimov, A.A.
AU  - Jen-Jacobson, L.
AU  - Kossykh, V.G.
AU  - Hattman, S.
TI  - Effect of base analog substitutions in the specific GATC site on binding and methylation of oligonucleotide duplexes by the bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 1135
EP  - 1144
VL  - 27
AB  - The interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with 24mer synthetic
AB  - oligonucleotide duplexes having different purine base substitutions in the palindromic
AB  - recognition sequence, GATC, was investigated by means of gel shift and methyl transfer assays.
AB  - The substitutions were introduced in either the upper or lower strand: guanine by
AB  - 7-deazaguanine (G-D) or 2-aminopurine (G-N) and target adenine by purine (A-P) or
AB  - 2-aminopurine (A-N).  The effects of each base modification on binding/methylation were
AB  - approximately equivalent for both strands.  G-D and G-N substitutions resulted in a sharp
AB  - decrease in binary complex formation.  This suggests that T4 Dam makes hydrogen bonds with
AB  - either the N7- or O6-keto groups (or both) in forming the complex.  In contrast, A-P and A-N
AB  - substitutions were much more tolerant for complex formation.  This confirms our earlier
AB  - observations that the presence of intact 5'-G:C base pairs at both ends of the methylation
AB  - site is critical, but that base substitutions within the central A:T base pairs show less
AB  - inhibition of complex formation.  Addition of T4 Dam to a complete substrate mixture resulted
AB  - in a burst of [3H]methylated product.  In all cases the substrate dependencies of bursts and
AB  - methylation rates were proportional to each other.  For the perfect 24mer kcat=0.014/s and
AB  - Km=7.7 nM was obtained.  In contrast to binary complex formation the two guanine substitutions
AB  - exerted relatively minor effects on catalytic turnover (the kcat was reduced at most
AB  - 2.5-fold), while the two adenine substitutions showed stronger effects (5- to 15-fold
AB  - reduction in kcat).  The effects of base analog substitutions on Km(DNA) were more variable:
AB  - A-P (decreased); A-N and G-D (unchanged); G-N (increased).
ER  -

TY  - JOUR
AU  - Malyguine, E.
AU  - Vannier, P.
AU  - Yot, P.
TI  - Alteration of the specificity of restriction endonucleases in the presence of organic solvents.
JO  - Gene
PY  - 1980
SP  - 163
EP  - 177
VL  - 8
AB  - The specificity of XbaI, SalI, HhaI, PstI, BamHI and SstI is relaxed in the
AB  - presence of an organic solvent, such as 20% glycerol or 8% dimethylsulfoxide
AB  - (DMSO).  This alteration, very pronounced in some cases, requires an excess of
AB  - enzyme, varies from one kind of enzyme to another and is highly dependent on
AB  - the pH, the ionic strength, the nature of the metallic cofactor and/or the
AB  - presence of a second organic solvent.  Preliminary data concerning XbaI and
AB  - BamHI used under conditions where the relaxation of specificity is moderate,
AB  - suggest that some of the new ("pseudo") sites correspond to shortened sequences
AB  - derived from the normal recognition sequence cleaved under the standard
AB  - conditions of the reaction.
ER  -

TY  - JOUR
AU  - Mamelak, L.
AU  - Boyer, H.W.
TI  - Genetic control of the secondary modification of deoxyribonucleic acid in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1970
SP  - 57
EP  - 62
VL  - 104
AB  - The wild-type restriction and modification alleles of Escherichia coli K-12 and
AB  - B were found to have no measurable effect on the patterns of methylated bases
AB  - in the deoxyribonucleic acid (DNA) of these strains.  The genetic region
AB  - controlling the methylation of cytosine in E. coli K-12 was mapped close to
AB  - his, and the presence or absence of this gene in E. coli B or E. coli K had no
AB  - effect on the restriction and modification properties of these strains.  Thus,
AB  - only a few of the methylated bases in the DNA of these strains are involved in
AB  - host modification, and the biological role of the remainder remains obscure.
ER  -

TY  - JOUR
AU  - Manachini, P.L.
AU  - Parini, C.
AU  - Fortina, M.G.
AU  - Benazzi, L.
TI  - BliI, a restriction endonuclease from Bacillus licheniformis.
JO  - FEBS Lett.
PY  - 1987
SP  - 305
EP  - 307
VL  - 214
AB  - From Bacillus licheniformis a site-specific restriction endonuclease, named
AB  - BliI, has been purified and characterized.  BliI was able to digest lambda DNA
AB  - at pH 9.1 over a wide temperature range (25-65C).  Digestion of lambda and
AB  - PhiX174 DNAs with BliI produced banding patterns identical to those seen with
AB  - HaeIII.  Therefore, BliI and HaeIII endonucleases are isoschizomers.
ER  -

TY  - JOUR
AU  - Manageiro, V.
AU  - Clemente, L.
AU  - Duarte, S.
AU  - Vieira, L.
AU  - Canica, M.
TI  - Draft Genome Sequence of an Escherichia coli Strain Isolated from a Gallus gallus Broiler Producing the Novel CTX-M-166 Variant.
JO  - Genome Announcements
PY  - 2016
SP  - e01029
EP  - e01016
VL  - 4
AB  - We report here the draft genome sequence of the CTX-M-166-harboring O6:H16 sequence type 48
AB  - (ST48)-fimH34 Escherichia coli strain recovered from a Gallus
AB  - gallus broiler. Sequence analyses revealed the presence of an
AB  - IncI1/ST103-ISEcp1-blaCTX-M-166-orf477 plasmid region and of diverse antibiotic
AB  - resistance and virulence-acquired genes.
ER  -

TY  - JOUR
AU  - Manageiro, V.
AU  - Sampaio, D.A.
AU  - Pereira, P.
AU  - Rodrigues, P.
AU  - Vieira, L.
AU  - Palos, C.
AU  - Canica, M.
TI  - Draft Genome Sequence of the First NDM-1-Producing Providencia stuartii Strain Isolated in Portugal.
JO  - Genome Announcements
PY  - 2015
SP  - e01077
EP  - e01015
VL  - 3
AB  - We report here the draft genome sequence of the first NDM-1-producing Providencia stuartii
AB  - strain isolated in Portugal. Sequence analyses revealed the presence of  an incompatibility
AB  - group A/C2 (IncA/C2) plasmid and of diverse acquired genes conferring resistance to
AB  - beta-lactams, aminoglycosides, tetracycline, macrolides, chloramphenicol, and sulfonamides.
AB  - This sequence contributes to the evaluation of the spread of NDM-1 producers.
ER  -

TY  - JOUR
AU  - Manakova, E.
AU  - Golovenko, D.
AU  - Grazulis, S.
AU  - Zaremba, M.
AU  - Siksnys, V.
TI  - Structural mechanism of cognate DNA recognition by the BfiI restriction enzyme.
JO  - FEBS J.
PY  - 2012
SP  - 446
EP  - 447
VL  - 279
AB  - Restriction endonuclease BfiI recognizes and cleaves the asymmetric DNA sequence
AB  - 5'-ACTGGG-3' downstream of the site independently of Mg-ions.  BfiI is evolved as a fusion
AB  - of two domains: the C-terminal DNA binding domain similar to DNHA binding domans of EcoRII and
AB  - B3 family of plant transcription factors, and the N-terminal catalytic domain, which is
AB  - similar to the Nuc nuclease of S. thyphimurium.  We have solved the crystal structure of the
AB  - BfiI DNA binding domjain in complex with the specific DNA to reveal the mechanism of the
AB  - specific DNA recognition. Superposition of the apoBfiI structure with the DNA bound C-domain
AB  - suggests that BfiI must change its conformation to accommopdate the scissile phosphate in the
AB  - active site.  To get a glimpse on the structural changes occurring upon BfiI binding to
AB  - cognate DNA we have performed the X-ray small angle scatterinhg measurements of apo and DNA
AB  - bound BfiI.  Ab initio shape determination as well as rigid body modeling using the
AB  - crystallographic data suggest that apo BfiI retains the similar conformation in the solution
AB  - as in a crystal, whereas DNA bound BfiI shows a conformational flexibility.  The truncated
AB  - heterodimar of BfiI which lacks one of the two DNHA-bidning domains was constructed in order
AB  - to simplify the system for SAXS experiments.
ER  -

TY  - JOUR
AU  - Manakova, E.
AU  - Grazulis, S.
AU  - Zaremba, M.
AU  - Tamulaitiene, G.
AU  - Golovenko, D.
AU  - Siksnys, V.
TI  - Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 6741
EP  - 6751
VL  - 40
AB  - Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence
AB  - 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a
AB  - cleavage position). Here, we report the crystal structures of the Bse634I R226A
AB  - mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites,
AB  - respectively. In the crystal, all potential H-bond donor and acceptor atoms on
AB  - the base edges of the conserved CCGG core are engaged in the interactions with
AB  - Bse634I amino acid residues located on the alpha6 helix. In contrast, direct
AB  - contacts between the protein and outer base pairs are limited to van der Waals
AB  - contact between the purine nucleobase and Pro203 residue in the major groove and
AB  - a single H-bond between the O2 atom of the outer pyrimidine and the side chain of
AB  - the Asn73 residue in the minor groove. Structural data coupled with biochemical
AB  - experiments suggest that both van der Waals interactions and indirect readout
AB  - contribute to the discrimination of the degenerate base pair by Bse634I.
AB  - Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC)
AB  - and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a
AB  - conserved structural core.
ER  -

TY  - JOUR
AU  - Manavalan, P.
AU  - Johnson, W.C. Jr.
AU  - Modrich, P.
TI  - Prediction of secondary structure for EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 11666
EP  - 11667
VL  - 259
AB  - The circular dichroism of EcoRI restriction endonuclease was measured to 178 nm
AB  - and analyzed for secondary structure.  The results (33% alpha-helix, 25%
AB  - beta-sheet, 17% turns, and 25% other structures) compare well with our joint
AB  - prediction from sequence data.
ER  -

TY  - JOUR
AU  - Mancini, S.
AU  - Abicht, H.K.
AU  - Karnachuk, O.V.
AU  - Solioz, M.
TI  - Genome Sequence of Desulfovibrio sp. A2, a Highly Copper Resistant, Sulfate-Reducing Bacterium Isolated from Effluents of a Zinc Smelter at  the Urals.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6793
EP  - 6794
VL  - 193
AB  - Desulfovibrio sp. A2 is an anaerobic Gram-negative sulfate-reducing bacterium with remarkable
AB  - tolerance to copper. It was isolated from
AB  - wastewater effluents of a zinc smelter at the Urals. Here, we report the
AB  - 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify
AB  - potential copper resistance mechanisms.
ER  -

TY  - JOUR
AU  - Mandape, S.N.
AU  - Marshall, D.R.
AU  - Dent, L.L.
AU  - Pratap, S.
TI  - Draft Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain MMC4, Isolated from a Patient in Tennessee.
JO  - Genome Announcements
PY  - 2014
SP  - e00051
EP  - e00014
VL  - 2
AB  - Acinetobacter baumannii multidrug-resistant strain MMC4 was isolated from a bronchoalveolar
AB  - lavage fluid sample from a patient in Nashville, TN, USA. Here,
AB  - we report a draft genome sequence with a size of 3,985,367 bp, an average G+C
AB  - content of 39.8%, and 3,863 predicted protein-coding sequences.
ER  -

TY  - JOUR
AU  - Mandelli, F.
AU  - Oliveira, R.B.
AU  - Couger, M.B.
AU  - Paixao, D.A.
AU  - Camilo, C.M.
AU  - Polikarpov, I.
AU  - Prade, R.
AU  - Riano-Pachon, D.M.
AU  - Squina, F.M.
TI  - Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer  of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest.
JO  - Genome Announcements
PY  - 2015
SP  - e00475
EP  - e00415
VL  - 3
AB  - Here, we present the draft genome sequence of Thermus fi liformis strain ATCC 43280, a
AB  - thermophile bacterium capable of producing glycosylated carotenoids
AB  - acylated with branched fatty acids and enzymes of biotechnological potential.
ER  -

TY  - JOUR
AU  - Mane, S.P. et al.
TI  - Host-interactive genes in amerindian Helicobacter pylori diverge from their old world homologs and mediate inflammatory responses.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3078
EP  - 3092
VL  - 192
AB  - Helicobacter pylori is the dominant member of the gastric microbiota and
AB  - has been associated with an increased risk of gastric cancer and peptic
AB  - ulcers in adults. H. pylori populations have migrated and diverged with
AB  - human populations, and health effects vary. Here, we describe the whole
AB  - genome of the cag-positive strain V225d, cultured from a Venezuelan Piaroa
AB  - Amerindian subject. To gain insight into the evolution and host adaptation
AB  - of this bacterium, we undertook comparative H. pylori genomic analyses. A
AB  - robust multiprotein phylogenetic tree reflects the major human migration
AB  - out of Africa, across Europe, through Asia, and into the New World,
AB  - placing Amerindian H. pylori as a particularly close sister group to East
AB  - Asian H. pylori. In contrast, phylogenetic analysis of the
AB  - host-interactive genes vacA and cagA shows substantial divergence of
AB  - Amerindian from Old World forms and indicates new genotypes (e.g., VacA
AB  - m3) involving these loci. Despite deletions in CagA EPIYA and CRPIA
AB  - domains, V225d stimulates interleukin-8 secretion and the hummingbird
AB  - phenotype in AGS cells. However, following a 33-week passage in the mouse
AB  - stomach, these phenotypes were lost in isolate V225-RE, which had a 15-kb
AB  - deletion in the cag pathogenicity island that truncated CagA and
AB  - eliminated some of the type IV secretion system genes. Thus, the unusual
AB  - V225d cag architecture was fully functional via conserved elements, but
AB  - the natural deletion of 13 cag pathogenicity island genes and the
AB  - truncation of CagA impaired the ability to induce inflammation.
ER  -

TY  - JOUR
AU  - Manfredi, P.
AU  - Pagni, M.
AU  - Cornelis, G.R.
TI  - Complete Genome Sequence of the Dog Commensal and Human Pathogen Capnocytophaga canimorsus Strain 5.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5558
EP  - 5559
VL  - 193
AB  - Capnocytophaga canimorsus is a commensal Gram-negative bacterium, originally isolated from a
AB  - dog's mouth, that causes septicemia in humans.
AB  - C. canimorsus has the unusual ability to feed on host cells, including
AB  - phagocytes. This capacity depends on surface-exposed glycan-foraging
AB  - systems. Here we present the first complete genome sequence of a C.
AB  - canimorsus strain (Cc5).
ER  -

TY  - JOUR
AU  - Manfredi, P.
AU  - Renzi, F.
AU  - Cornelis, G.R.
TI  - Draft Genome Sequences of Three Capnocytophaga cynodegmi Strains Isolated from the Oral Cavity of Healthy Dogs.
JO  - Genome Announcements
PY  - 2015
SP  - e00200
EP  - e00215
VL  - 3
AB  - Here, we present the draft genome sequences of three strains of Capnocytophaga cynodegmi. In
AB  - contrast to the very close relationship among them, C. cynodegmi
AB  - and Capnocytophaga canimorsus differ dramatically in terms of virulence in
AB  - humans. Comparative genomics provided some understanding on how Capnocytophaga
AB  - species may switch from being dog commensals to human pathogens.
ER  -

TY  - JOUR
AU  - Manfredi, P.
AU  - Renzi, F.
AU  - Cornelis, G.R.
TI  - Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Healthy Canine Oral Cavities.
JO  - Genome Announcements
PY  - 2015
SP  - e00199
EP  - e00115
VL  - 3
AB  - Here, we present the draft genome sequences of three strains of Capnocytophaga canimorsus,
AB  - each isolated from a different dog's mouth. Genome analysis provided
AB  - evidence that these organisms may belong to a different nonpathogenic subtype of
AB  - C. canimorsus.
ER  -

TY  - JOUR
AU  - Manfredi, P.
AU  - Renzi, F.
AU  - Cornelis, G.R.
TI  - Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Septic Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e00193
EP  - e00115
VL  - 3
AB  - Capnocytophaga canimorsus is a bacterium from the normal oral flora of dogs and cats that
AB  - causes rare generalized infections in humans. In an attempt to
AB  - determine whether infections could be caused by a subset of strains and to
AB  - identify pathogenicity factors, we sequenced the genomes of three strains
AB  - isolated from human infections.
ER  -

TY  - JOUR
AU  - Mangiamele, P.
AU  - Nicholson, B.
AU  - Wannemuehler, Y.
AU  - Seemann, T.
AU  - Logue, C.M.
AU  - Li, G.
AU  - Tivendale, K.A.
AU  - Nolan, L.K.
TI  - Complete Genome Sequence of the Avian Pathogenic Escherichia coli Strain APEC O78.
JO  - Genome Announcements
PY  - 2013
SP  - e0002613
EP  - e0002613
VL  - 1
AB  - Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is a significant disease,
AB  - causing extensive animal and financial losses globally.
AB  - Because of the significance of this disease, more knowledge is needed regarding
AB  - APEC's mechanisms of virulence. Here, we present the fully closed genome sequence
AB  - of a typical avian pathogenic E. coli strain belonging to the serogroup O78.
ER  -

TY  - JOUR
AU  - Manichanh, C.
AU  - Chapple, C.E.
AU  - Frangeul, L.
AU  - Gloux, K.
AU  - Guigo, R.
AU  - Dore, J.
TI  - A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 5180
EP  - 5188
VL  - 36
AB  - The construction of metagenomic libraries has permitted the study of
AB  - microorganisms resistant to isolation and the analysis of 16S rDNA
AB  - sequences has been used for over two decades to examine bacterial
AB  - biodiversity. Here, we show that the analysis of random sequence reads
AB  - (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity
AB  - of a bacterial community from metagenomic libraries. We generated 10,010
AB  - RSRs from a metagenomic library of microorganisms found in human faecal
AB  - samples. Then searched them using the program BLASTN against a prokaryotic
AB  - sequence database to assign a taxon to each RSR. The results were compared
AB  - with those obtained by screening and analysing the clones containing 16S
AB  - rDNA sequences in the whole library. We found that the biodiversity
AB  - observed by RSR analysis is consistent with that obtained by 16S rDNA. We
AB  - also show that RSRs are suitable to compare the biodiversity between
AB  - different metagenomic libraries. RSRs can thus provide a good estimate of
AB  - the biodiversity of a metagenomic library and, as an alternative to 16S,
AB  - this approach is both faster and cheaper.
ER  -

TY  - JOUR
AU  - Maniloff, J.
AU  - Dybvig, K.
AU  - Sladek, T.L.
TI  - Mycoplasma DNA Restriction and Modification.
JO  - Mycoplasmas: Molecular Biology and Pathogenesis
PY  - 1992
SP  - 325
EP  - 330
VL  - 0
AB  - *
AB  - Mycoplasma DNA Restriction and Modification
AB  - Introduction
AB  - Restriction and Modification in Eubacteria
AB  - Restriction-Modification Systems
AB  - Restriction and Modification in Mycoplasmas
AB  - Mycoplasma Restriction-modification systems
AB  - A. laidlawii K2
AB  - A. laidlawii JA1
AB  - A. laidlawii JA1 Restriction and recA Mutants
AB  - S. citri ASP2
AB  - M. fermentans
AB  - U. urealyticum 960
AB  - Mycoplasma methylases
AB  - Restriction-modification systems and Mycoplasma Evolution
AB  - Acknowledgments
AB  - References
AB  - 
ER  -

TY  - JOUR
AU  - Manivannan, B.
AU  - Mahalingam, N.
AU  - Jadhao, S.
AU  - Mishra, A.
AU  - Nilawe, P.
AU  - Pradeep, B.E.
TI  - Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00162
EP  - e00116
VL  - 4
AB  - We present the draft genome assembly of an extensively drug-resistant (XDR)Pseudomonas
AB  - aeruginosastrain isolated from a patient with a history of
AB  - genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content
AB  - of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm
AB  - formation, virulence, and antibiotic resistance.
ER  -

TY  - JOUR
AU  - Manivasakam, P.
AU  - Aubrecht, J.
AU  - Sidhom, S.
AU  - Schiestl, R.H.
TI  - Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 4826
EP  - 4833
VL  - 29
AB  - Mammalian cells repair DNA double-strand breaks by illegitimate end-joining or by homologous
AB  - recombination. We investigated the effects
AB  - of restriction enzymes on illegitimate and homologous DNA integration
AB  - in mammalian cells. A plasmid containing the neoR expression cassette,
AB  - which confers G418 resistance, was used to select for illegitimate
AB  - integration events in CHO wild-type and xrcc5 mutant cells.
AB  - Co-transfection with the restriction enzymes BamHI, Bglll, EcoRI and
AB  - Kpnl increased the efficiency of linearized plasmid integration up to
AB  - 5-fold in CHO cells. In contrast, the restriction enzymes did not
AB  - increase the integration efficiency in xrcc5 mutant cells. Effects of
AB  - restriction enzymes on illegitimate and homologous integration were
AB  - also studied in mouse embryonic stem (ES) cells using a plasmid
AB  - containing the neoR gene flanked by exon 3 of Hprt. The enzymes BamHI,
AB  - Bglll and EcoRI increased the illegitimate integration efficiency of
AB  - transforming DNA several-fold, similar to the results for CHO cells.
AB  - However, all three enzymes decreased the absolute frequency of
AB  - homologous integration apprx2-fold, and the percentage of homologous
AB  - integration decreased >10-fold. This suggests that random DNA breaks
AB  - attract illegitimate recombination (IR) events that compete with
AB  - homology search.
ER  -

TY  - JOUR
AU  - Manivasakam, P.
AU  - Schiestl, R.H.
TI  - Nonhomologous end joining during restriction enzyme-mediated DNA integration in Saccharomyces cerevisiae.
JO  - Mol. Cell. Biol.
PY  - 1998
SP  - 1736
EP  - 1745
VL  - 18
AB  - The BamHI restriction enzyme mediates integration of nonhomologous DNA into the Saccharomyces
AB  - cerevisiae genome (R. H. Schiestl and T. D. Petes,
AB  - Proc. Natl. Acad. Sci. USA 88:7585-7589, 1991). The present study
AB  - investigates the mechanism of such events: in particular, the mediating
AB  - activity of various restriction enzymes and the processing of resultant
AB  - fragment ends. Our results show that in addition to BamHI, BglII and KpnI
AB  - increase DNA integration efficiencies severalfold, while Asp718, HindIII,
AB  - EcoRI, SalI, SmaI, HpaI, MscI, and SnaBI do not. Secondly, the three
AB  - active enzymes stimulated integrations only of fragments containing 5' or
AB  - 3' overhangs but not of blunt-ended fragments. Thirdly, integrations
AB  - mediated by one enzyme and utilizing a substrate created by another
AB  - required at least 2 bp of homology. Furthermore, an Asp718 fragment
AB  - possessing a 5' overhang integrated into a KpnI (isoschizomer) site
AB  - possessing a 3' overhang, most likely by filling of the 5' overhang
AB  - followed by 5' exonuclease digestion to produce a 3' end. We classified
AB  - and analyzed the restriction enzyme-mediated integration events in the
AB  - context of their genomic positions. The majority of events integrated into
AB  - single sites. In the remaining 6 of 19 cases each end of the plasmid
AB  - inserted into a different sequence, producing rearrangements such as
AB  - duplications, deletions, and translocations.
ER  -

TY  - JOUR
AU  - Mann, A.J.
AU  - Hahnke, R.L.
AU  - Huang, S.
AU  - Werner, J.
AU  - Xing, P.
AU  - Barbeyron, T.
AU  - Huettel, B.
AU  - Stueber, K.
AU  - Reinhardt, R.
AU  - Harder, J.
AU  - Gloeckner, F.O.
AU  - Amann, R.I.
AU  - Teeling, H.
TI  - The genome of the algae-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for the degradation of algal polysaccharides.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 6813
EP  - 6813
VL  - 79
AB  - In recent years, representatives of the Bacteroidetes have been increasingly recognized as
AB  - specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus
AB  - within the class Flavobacteria, whose members have been found in marine habitats with high
AB  - levels of organic matter, such as an association with algae, invertebrates and fecal pellets.
AB  - Here we report on the generation and analysis of the genome of the type strain of Formosa
AB  - agariphila(KMM 3901T) - an isolate from the green algae Acrosiphonia sonderi.  F. agariphila
AB  - is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification.
AB  - Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced
AB  - specialization on the degradation of protein, polysaccharides and glycoproteins.  65 of the
AB  - glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci,
AB  - where they are clustered with TonB-dependent receptors, SusD-like proteins,
AB  - sensors/transcription factors, transporters and oftentimes sulfatases.  These loci play a
AB  - pivotal role in bacteroidetal polysaccharide biodegradation, and in the case of F. agariphila
AB  - revealed the capacity to degrade a wide range of algal polysaccharides from green, red and
AB  - brown algae and thus a strong specialization of towards an algae-associated lifestyle.  This
AB  - was corroborated by growth experiments, which confirmed usage of particularly those
AB  - monosaccharides that constitute the building blocks of abundant agal polysaccharides as well
AB  - as of distinct algal polysaccharides such as laminarins, xylans and k-carrageenans.
ER  -

TY  - JOUR
AU  - Mann, M.B.
TI  - The cloned HhaII restriction-modification system.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 229
EP  - 237
VL  - 1
AB  - I. Procedure for cloning restriction-modification (R-M) systems.  II. A clone that
AB  - overproduces the HhaII R-M gene products.
AB  - III. Biologic properties of the cloned HhaII R-M system.
AB  - IV. The problem of site-specific DNA-protein interaction.
AB  - V. HhaII*, a form of HhaII with grossly altered site specificity.
ER  -

TY  - JOUR
AU  - Mann, M.B.
AU  - Rao, R.N.
AU  - Smith, H.O.
TI  - Cloning of restriction and modification genes in E. coli: the HhaII system from Haemophilus haemolyticus.
JO  - Gene
PY  - 1978
SP  - 97
EP  - 112
VL  - 3
AB  - The genes for a Class II restriction-modification system (HhaII) from
AB  - Haemophilus haemolyticus have been cloned in Escherichia coli.  The vector used
AB  - for cloning was plasmid pBR322 which confers resistance to tetracycline and
AB  - ampicillin and contains a single endonuclease R-PstI site,
AB  - (5')C-T-G-C-A7-G(3'), in the ampicillin gene.  The procedure developed by
AB  - Bolivar et al. (1977) was used to form DNA recombinants.  H. haemolyticus DNA
AB  - was cleaved with PstI endonuclease and poly(dC) extensions were added to the
AB  - 3'-OH termini using terminal deoxynucleotidyl transferase.  Circular pBR322 DNA
AB  - was cleaved to linear molecules with PstI endonuclease and poly(dG) extensions
AB  - were added to the 3'-OH termini, thus regenerating the PstI cleavage site
AB  - sequence.  Recombinant molecules, formed by annealing the two DNAs, were used
AB  - to transfect a restriction and modification-deficient strain of E. coli (HB101
AB  - r-m-recA).  Tetracycline-resistant clones were tested for acquisition of
AB  - restriction phenotype (as measured by growth on plates seeded with phage
AB  - lambdacI-0).  A single phage-resistant clone was found.  The recombinant
AB  - plasmid, pDI10, isolated from this clone, had acquired 3 kilobases of
AB  - additional DNA which could be excised with PstI endonuclease.  In addition to
AB  - the restriction function, cells carrying the plasmid expressed the HhaII
AB  - modification function.  Both activities have been partially purified by
AB  - single-stranded DNA-agarose chromatography.  The cloned HhaII restriction
AB  - activity yields cleavage patterns identical to HinfI. A restriction map of the
AB  - cloned DNA segment is presented.
ER  -

TY  - JOUR
AU  - Mann, M.B.
AU  - Smith, H.O.
TI  - Specificity of DNA Methylases from Haemophilus Sp.
JO  - Proceedings of the Conference on Transmethylation
PY  - 1979
SP  - 483
EP  - 492
VL  - 0
AB  - We have studied the specificity of three DNA cytosine methylases found in
AB  - Haemophilus sp., which have the common property of acting at tetranucleotide
AB  - sites containing cytosine and guanine residues.  The methylases belong to the
AB  - three restriction and modification systems:  HhaI, HpaII, and HaeIII, for which
AB  - the restriction endonuclease recognition sites are (5') pG-C-G-C, (5')
AB  - pC-C-G-G, and (5') pG-G-C-C.  The sequence specificity and position of cytosine
AB  - methylation within the recognition sequence for M.HpaII and M.HaeIII have been
AB  - previously reported as (5') pC-CmC.1  Here we present comparable data for
AB  - M.HhaI.  In addition, we determine the ability of each of the three methylases
AB  - to utilize as substrates a variety of polymers containing base analogues.
AB  - Judging from their behaviour on these substrates, we conclude that the
AB  - mechanism for discriminating a given base pair varies from one enzyme to
AB  - another.
ER  -

TY  - JOUR
AU  - Mann, M.B.
AU  - Smith, H.O.
TI  - Size of 5'-terminal fragments cleaved from poly(dG-dC) by EndoR.HhaI.
JO  - Nucleic Acid - Protein Recognition
PY  - 1977
SP  - 269
EP  - 271
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Mann, M.B.
AU  - Smith, H.O.
TI  - Specificity of HpaII and HaeIII DNA methylases.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 4211
EP  - 4221
VL  - 4
AB  - The methylases M HaeIII and M HpaII recognize the tetranucleotide sequences
AB  - (5') G/C-G/C*-C*/G-C/G (5') and (5') C/G-C*/G-G/C*-G/C (5') respectively, in
AB  - DNA, and transfer a methyl group from S-adenosylmethionine to the 5-position of
AB  - cytosine on each strand as indicated by the asterisks.  Restriction
AB  - endonuclease R HaeIII does not cleave the methylated sequence G/C-G/Cm-Cm/G-C/G
AB  - but can cleave G/Cm-G/C-C/G-Cm/G in which methylation is introduced on the
AB  - unnatural external cytosine positions.  Similarly, R HpaII does not cleave
AB  - C/G-Cm/G-G/Cm-G/C but can cleave Cm/G-C/G-G/C-G/C.
ER  -

TY  - JOUR
AU  - Mannala, G.K.
AU  - Hain, T.
AU  - Sproer, C.
AU  - Bunk, B.
AU  - Overmann, J.
AU  - Alt, V.
AU  - Domann, E.
TI  - Complete Genome and Plasmid Sequences of Staphylococcus aureus EDCC 5055 (DSM 28763), Used To Study Implant-Associated Infections.
JO  - Genome Announcements
PY  - 2017
SP  - e01698
EP  - e01616
VL  - 5
AB  - Staphylococcus aureus EDCC 5055 (DSM 28763) is a human clinical wound isolate intensively used
AB  - to study implant-associated infections in rabbit and rat
AB  - infection models. Here, we report its complete genome sequence (2,794,437 bp)
AB  - along with that of one plasmid (27,437 bp). This strain belongs to sequence type
AB  - 8 and contains a mecA gene.
ER  -

TY  - JOUR
AU  - Mannarelli, B.M.
AU  - Balganesh, T.S.
AU  - Greenberg, B.
AU  - Springhorn, S.S.
AU  - Lacks, S.A.
TI  - Nucleotide sequence of the DpnII DNA methylase gene of Streptococcus pneumoniae and its relationship to the dam gene of Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1985
SP  - 4468
EP  - 4472
VL  - 82
AB  - The structural gene (dpnM) for the DpnII DNA methylase of Streptococcus pneumoniae, which is
AB  - part of the DpnII restriction system and methylates adenine in the sequence 5'-G-A-T-C-3',
AB  - was identified by subcloning fragments of a chromosomal segment from a DpnII-producing strain
AB  - in an S. pneumoniae host/vector cloning system and demonstrating function of the gene also in
AB  - Bacillus subtilis. Determination of the nucleotide sequence of the gene and adjacent DNA
AB  - indicates that it encodes a polypeptide of 32,903 daltons. A putative promoter for
AB  - transcription of the gene lies within a hundred nucleotides of the polypeptide start codon.
AB  - Comparison of the coding sequence to that of the dam gene of Escherichia coli, which encodes a
AB  - similar methylase, revealed 30% of the amino acid residues in the two enzymes to be identical.
AB  - This homology presumably reflects a common origin of the two genes prior to the divergence of
AB  - Gram-positive and Gram-negative bacteria. it is suggested that the restriction function of the
AB  - gene is primitive, and that the homologous restriction system in E. coli has evolved to play
AB  - an accessory role in heteroduplex DNA base mismatch repair.
ER  -

TY  - JOUR
AU  - Manninger, P.
AU  - Koziol, A.
AU  - Carrillo, C.D.
TI  - Draft Whole-Genome Sequences of Escherichia fergusonii Strains Isolated from Beef Trim (GTA-EF02), Ground Beef (GTA-EF03), and Chopped Kale (GTA-EF04).
JO  - Genome Announcements
PY  - 2016
SP  - e00185
EP  - e00116
VL  - 4
AB  - Escherichia fergusoniiis a Gram-negative, rod-shaped, non-spore-forming member of
AB  - theEnterobacteriaceaefamily and is a bacterium with both biotechnological
AB  - applications and implication in human clinical disease. Here, we report the draft
AB  - genome sequences of three isolates ofE. fergusoniifrom beef trim (GTA-EF02),
AB  - ground beef (GTA-EF03), and chopped kale (GTA-EF04).
ER  -

TY  - JOUR
AU  - Mannino, S.J.
AU  - Jenkins, C.L.
AU  - Raines, R.T.
TI  - Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI.
JO  - Biochemistry
PY  - 1999
SP  - 16178
EP  - 16186
VL  - 38
AB  - Homing endonucleases are distinguished by their ability to catalyze the cleavage of
AB  - double-stranded DNA with extremely high specificity. I-PpoI endonuclease, a homing
AB  - endonuclease from the slime mold Physarum polycephalum, is a small enzyme (2 x 20 kDa) of
AB  - known three-dimensional structure that catalyzes the cleavage of a long target DNA sequence
AB  - (15 base pairs). Here, a detailed chemical mechanism for catalysis of DNA cleavage by I-PpoI
AB  - endonuclease is proposed and tested by creating six variants in which active-site residues are
AB  - replaced with alanine. The side chains of three residues (Arg61, His98, and Asn119) are found
AB  - to be important for efficient catalysis of DNA cleavage. This finding is consistent with the
AB  - proposed mechanism in which His98 abstracts a proton from an attacking water molecule bound by
AB  - an adjacent phosphoryl oxygen, Arg61 and Asn119 stabilize the pentavalent transition state,
AB  - and Asn119 also binds to the essential divalent metal cation (e.g., Mg(2+) ion), which
AB  - interacts with the 3'-oxygen leaving group. Because Mg(2+) is required for cleavage of a
AB  - substrate with a good leaving group (p-nitrophenolate), Mg(2+) likely stabilizes the
AB  - pentavalent transition state. The pH-dependence of k(cat) for catalysis by I-PpoI reveals a
AB  - macroscopic pK(a) of 8.4 for titratable groups that modulate product release. I-PpoI appears
AB  - to be unique among known restriction endonucleases and homing endonucleases in its use of a
AB  - histidine residue to activate the attacking water molecule for in-line displacement of the
AB  - 3'-leaving group.
ER  -

TY  - JOUR
AU  - Mannion, A.
AU  - Shen, Z.
AU  - Feng, Y.
AU  - Garcia, A.
AU  - Fox, J.G.
TI  - Draft Genome Sequences of Five Novel Polyketide Synthetase-Containing Mouse Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e01082
EP  - e01016
VL  - 4
AB  - We report herein the draft genomes of five novel Escherichia coli strains isolated from
AB  - surveillance and experimental mice housed at MIT and the Whitehead
AB  - Institute and describe their genomic characteristics in context with the
AB  - polyketide synthetase (PKS)-containing pathogenic E. coli strains NC101, IHE3034,
AB  - and A192PP.
ER  -

TY  - JOUR
AU  - Mansilla, S.
AU  - Garcia-Ferrer, I.
AU  - Mendez, C.
AU  - Salas, J.A.
AU  - Portugal, J.
TI  - Differential inhibition of restriction enzyme cleavage by chromophore-modified analogues of the antitumour antibiotics mithramycin and chromomycin reveals structure-activity relationships.
JO  - Biochem. Pharmacol.
PY  - 2010
SP  - 1418
EP  - 1427
VL  - 79
AB  - Differential cleavage at three restriction enzyme sites was used to determine the specific
AB  - binding to DNA of the antitumour antibiotics
AB  - mithramycin A (MTA), chromomycin A(3) (CRO) and six
AB  - chromophore-modified analogues bearing shorter side chains attached at
AB  - C-3, instead of the pentyl chain All these antibiotics were obtained
AB  - through combinatorial biosynthesis in the producer organisms. MTA, CRO
AB  - and their six analogues showed differences in their capacity for
AB  - inhibiting the rate of cleavage by restriction enzymes that recognize
AB  - C/G-rich tracts. Changes in DNA melting temperature produced by these
AB  - molecules were also analyzed, as well as their antiproliferative
AB  - activities against a panel of colon, ovarian and prostate human
AB  - carcinoma cell lines. Moreover, the cellular uptake of several
AB  - analogues was examined to identify whether intracellular retention was
AB  - related to cytotoxicity These experimental approaches provided mutually
AB  - consistent evidence of a seeming correlation between the strength of
AB  - binding to DNA and the antiproliferative activity of the
AB  - chromophore-modified molecules Four of the analogues (mithramycin SK,
AB  - mithramycin SDK, chromomycin SK and chromomycin SDK) showed promising
AB  - biological profiles.
ER  -

TY  - JOUR
AU  - Manso, A.S.
AU  - Chai, M.H.
AU  - Atack, J.M.
AU  - Furi, L.
AU  - De Ste, C.M.
AU  - Haigh, R.
AU  - Trappetti, C.
AU  - Ogunniyi, A.D.
AU  - Shewell, L.K.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Blades, M.
AU  - Mirkes, E.
AU  - Gorban, A.N.
AU  - Paton, J.C.
AU  - Jennings, M.P.
AU  - Oggioni, M.R.
TI  - A random six-phase switch regulates pneumococcal virulence via global epigenetic  changes.
JO  - Nat. Commun.
PY  - 2014
SP  - 5055
EP  - 5055
VL  - 5
AB  - Streptococcus pneumoniae (the pneumococcus) is the world's foremost bacterial pathogen in
AB  - both morbidity and mortality. Switching between phenotypic forms (or
AB  - 'phases') that favour asymptomatic carriage or invasive disease was first
AB  - reported in 1933. Here, we show that the underlying mechanism for such phase
AB  - variation consists of genetic rearrangements in a Type I restriction-modification
AB  - system (SpnD39III). The rearrangements generate six alternative specificities
AB  - with distinct methylation patterns, as defined by single-molecule, real-time
AB  - (SMRT) methylomics. The SpnD39III variants have distinct gene expression
AB  - profiles. We demonstrate distinct virulence in experimental infection and in vivo
AB  - selection for switching between SpnD39III variants. SpnD39III is ubiquitous in
AB  - pneumococci, indicating an essential role in its biology. Future studies must
AB  - recognize the potential for switching between these heretofore undetectable,
AB  - differentiated pneumococcal subpopulations in vitro and in vivo. Similar systems
AB  - exist in other bacterial genera, indicating the potential for broad exploitation
AB  - of epigenetic gene regulation.
ER  -

TY  - JOUR
AU  - Manso-Silvan, L. et al.
TI  - Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for  Cattle.
JO  - Genome Announcements
PY  - 2013
SP  - e00348
EP  - e00313
VL  - 1
AB  - We report here the draft genome sequences of Mycoplasma alkalescens, Mycoplasma arginini, and
AB  - Mycoplasma bovigenitalium. These three species are regularly
AB  - isolated from bovine clinical specimens, although their role in disease is
AB  - unclear.
ER  -

TY  - JOUR
AU  - Mansor, M.
AU  - Macalady, J.L.
TI  - Draft Genome Sequence of Lampenflora Chlorobium limicola Strain Frasassi in a Sulfidic Cave System.
JO  - Genome Announcements
PY  - 2016
SP  - e00357
EP  - e00316
VL  - 4
AB  - The draft genome sequence of Chlorobium limicola strain Frasassi was assembled from
AB  - metagenomic sequencing of a green mat in an artificially lighted aquarium
AB  - inside the Frasassi caves in Italy. The genome is 2.08 Mbp in size and contains
AB  - the necessary genes for anoxygenic photosynthesis and CO2 fixation.
ER  -

TY  - JOUR
AU  - Mansour, C.A.
AU  - Doiron, K.M.
AU  - Cupples, C.G.
TI  - Characterization of functional interactions among the Escherichia coli mismatch repair proteins using a bacterial two-hybrid assay.
JO  - Mutat. Res.
PY  - 2001
SP  - 331
EP  - 338
VL  - 485
AB  - Vsr mediates very short patch repair in Escherichia coli, correcting T/G mismatches caused by
AB  - deamination of 5-methylcytosine to thymine. MutS and
AB  - MutL, part of the post-replication mismatch repair system, stimulate VSP
AB  - repair. In this study, we use a bacterial two-hybrid assay to show that
AB  - MutL interacts with Vsr. We also show that interaction between Vsr and
AB  - MutL inhibits the ability of MutL to dimerize, to interact with MutS and
AB  - MutH and to mediate a previously unknown interaction between MutS and
AB  - MutH. This inhibition may explain why high levels of Vsr are mutagenic in
AB  - vivo. In addition, we show that the Mut fusion proteins are repair
AB  - proficient in the bacterial two-hybrid assay, making it possible to study
AB  - their interactions in various genetic backgrounds, or in the presence of
AB  - DNA damaging agents.
ER  -

TY  - JOUR
AU  - Mansour, S.R.
AU  - Oshone, R.
AU  - Hurst, S.G.I.V.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Draft Genome Sequence of Frankia sp. Strain CcI6, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Casuarina cunninghamiana.
JO  - Genome Announcements
PY  - 2014
SP  - e01205
EP  - e01213
VL  - 2
AB  - Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different
AB  - families of actinorhizal plants. We report a 5.57-Mbp draft genome
AB  - sequence for Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixing
AB  - actinobacterium isolated from root nodules of Casurina cunninghamiana grown in
AB  - Egyptian soils.
ER  -

TY  - JOUR
AU  - Manwaring, N.P.
AU  - Skurray, R.A.
AU  - Firth, N.
TI  - Nucleotide sequence of the F plasmid leading region.
JO  - Plasmid
PY  - 1999
SP  - 219
EP  - 225
VL  - 41
AB  - The entire nucleotide sequence of the first DNA segment of the conjugative
AB  - F plasmid to enter the recipient cell, the leading region, is described.
AB  - Analysis of the sequence provides further evidence that products encoded
AB  - within the 13.2-kb leading region are likely to be expressed and perform
AB  - functions associated with the transferred strand in the recipient cell.
ER  -

TY  - JOUR
AU  - Manzanera, M.
AU  - Garcia-Fontana, C.
AU  - Vilchez, J.I.
AU  - Gonzalez-Lopez, J.
TI  - Genome Sequence of Rhodococcus sp. 4J2A2, a Desiccation-Tolerant Bacterium Involved in Biodegradation of Aromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2015
SP  - e00592
EP  - e00515
VL  - 3
AB  - The genome sequence for Rhodococcus sp. 4J2A2, a newly described desiccation-tolerant strain
AB  - that removes aromatic hydrocarbons, is reported here.
AB  - The genome is estimated to be around 7.5 Mb in size, with an average G+C content
AB  - of 60.77% and a predicted number of protein-coding sequences of 6,354.
ER  -

TY  - JOUR
AU  - Manzanera, M.
AU  - Garcia-Fontana, C.
AU  - Vilchez, J.I.
AU  - Narvaez-Reinaldo, J.J.
AU  - Gonzalez-Lopez, J.
TI  - Genome Sequence of Microbacterium sp. Strain 3J1, a Highly Desiccation-Tolerant Bacterium That Promotes Plant Growth.
JO  - Genome Announcements
PY  - 2015
SP  - e00713
EP  - e00715
VL  - 3
AB  - The genome sequence for Microbacterium sp. strain 3J1, a desiccation-tolerant organism
AB  - isolated from the Nerium oleander rhizosphere, is reported here. The genome is estimated to be
AB  - approximately 3.5 Mb in size, with an average G+C content of 67.7% and a predicted number of
AB  - protein-coding sequences of 3,310.
ER  -

TY  - JOUR
AU  - Manzanera, M.
AU  - Narvaez-Reinaldo, J.J.
AU  - Garcia-Fontana, C.
AU  - Vilchez, J.I.
AU  - Gonzalez-Lopez, J.
TI  - Genome Sequence of Arthrobacter koreensis 5J12A, a Plant Growth-Promoting and Desiccation-Tolerant Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00648
EP  - e00615
VL  - 3
AB  - Arthrobacter koreensis 5J12A is a desiccation-tolerant organism isolated from the Nerium
AB  - oleander rhizosphere. Here, we report its genome sequence, which may shed
AB  - light on its role in plant growth promotion. This is believed to be the first
AB  - published genome of a desiccation-tolerant plant growth promoter from the genus
AB  - Arthrobacter.
ER  -

TY  - JOUR
AU  - Manzanera, M.
AU  - Santa-Cruz-Calvo, L.
AU  - Vilchez, J.I.
AU  - Garcia-Fontana, C.
AU  - Silva-Castro, G.A.
AU  - Calvo, C.
AU  - Gonzalez-Lopez, J.
TI  - Genome Sequence of Arthrobacter siccitolerans 4J27, a Xeroprotectant-Producing Desiccation-Tolerant Microorganism.
JO  - Genome Announcements
PY  - 2014
SP  - e00526
EP  - e00514
VL  - 2
AB  - We report the first genome sequence for Arthrobacter siccitolerans 4J27, a newly  described
AB  - desiccation-tolerant species. The complete genome of A. siccitolerans
AB  - 4J27 has been sequenced and is estimated to be around 5.3 Mb in size, with an
AB  - average GC content of 65.13%. We predict 4,480 protein-coding sequences (CDSs).
ER  -

TY  - JOUR
AU  - Manzanera, M.
AU  - Vilchez, J.I.
AU  - Garcia-Fontana, C.
AU  - Calvo, C.
AU  - Gonzalez-Lopez, J.
TI  - Genome Sequence of Leucobacter sp. 4J7B1, a Plant-Osmoprotectant Soil Microorganism.
JO  - Genome Announcements
PY  - 2015
SP  - e00398
EP  - e00315
VL  - 3
AB  - We report the first genome sequence for Leucobacter sp. 4J7B1, a newly described
AB  - desiccation-tolerant strain. The complete genome sequence of Leucobacter sp.
AB  - 4J7B1 has been sequenced and is estimated to be around 3.5 Mb in size, with an
AB  - average GC content of 62.18%. We predict 2,953 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Manzano-Marin, A.
AU  - Latorre, A.
TI  - Settling down: the genome of Serratia symbiotica from the aphid Cinara tujafilina zooms in on the process of accommodation to a cooperative intracellular life.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 1683
EP  - 1698
VL  - 6
AB  - Particularly interesting cases of mutualistic endosymbioses come from the
AB  - establishment of co-obligate associations of more than one species of
AB  - endosymbiotic bacteria. Throughout symbiotic accommodation from a free-living
AB  - bacterium, passing through a facultative stage and ending as an obligate
AB  - intracellular one, the symbiont experiences massive genomic losses and phenotypic
AB  - adjustments. Here, we scrutinized the changes in the coevolution of Serratia
AB  - symbiotica and Buchnera aphidicola endosymbionts in aphids, paying particular
AB  - attention to the transformations undergone by S. symbiotica to become an obligate
AB  - endosymbiont. Although it is already known that S. symbiotica is facultative in
AB  - Acyrthosiphon pisum, in Cinara cedri it has established a co-obligate
AB  - endosymbiotic consortium along with B. aphidicola to fulfill the aphid's
AB  - nutritional requirements. The state of this association in C. tujafilina, an
AB  - aphid belonging to the same subfamily (Lachninae) that C. cedri, remained
AB  - unknown. Here, we report the genome of S. symbiotica strain SCt-VLC from the
AB  - aphid C. tujafilina. While being phylogenetically and genomically very closely
AB  - related to the facultative endosymbiont S. symbiotica from the aphid A. pisum, it
AB  - shows a variety of metabolic, genetic, and architectural features, which point
AB  - toward this endosymbiont being one step closer to an obligate intracellular one.
AB  - We also describe in depth the process of genome rearrangements suffered by S.
AB  - symbiotica and the role mobile elements play in gene inactivations. Finally, we
AB  - postulate the supply to the host of the essential riboflavin (vitamin B2) as key
AB  - to the establishment of S. symbiotica as a co-obligate endosymbiont in the aphids
AB  - belonging to the subfamily Lachninane.
ER  -

TY  - JOUR
AU  - Manzella, M.P.
AU  - Holmes, D.E.
AU  - Rocheleau, J.M.
AU  - Chung, A.
AU  - Reguera, G.
AU  - Kashefi, K.
TI  - The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon 'Geoglobus ahangari' strain 234(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 77
EP  - 77
VL  - 10
AB  - 'Geoglobus ahangari' strain 234(T) is an obligate Fe(III)-reducing member of the
AB  - Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the
AB  - Guaymas Basin hydrothermal system. It grows optimally at 88 degrees C by coupling
AB  - the reduction of Fe(III) oxides to the oxidation of a wide range of compounds,
AB  - including long-chain fatty acids, and also grows autotrophically with hydrogen
AB  - and Fe(III). It is the first archaeon reported to use a direct contact mechanism
AB  - for Fe(III) oxide reduction, relying on a single archaellum for locomotion,
AB  - numerous curled extracellular appendages for attachment, and outer-surface
AB  - heme-containing proteins for electron transfer to the insoluble Fe(III) oxides.
AB  - Here we describe the annotation of the genome of 'G. ahangari' strain 234(T) and
AB  - identify components critical to its versatility in electron donor utilization and
AB  - obligate Fe(III) respiratory metabolism at high temperatures. The genome
AB  - comprises a single, circular chromosome of 1,770,093 base pairs containing 2034
AB  - protein-coding genes and 52 RNA genes. In addition, emended descriptions of the
AB  - genus 'Geoglobus' and species 'G. ahangari' are described.
ER  -

TY  - JOUR
AU  - Manzoor, S.
AU  - Bongcam-Rudloff, E.
AU  - Schnurer, A.
AU  - Muller, B.
TI  - First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.
JO  - Genome Announcements
PY  - 2013
SP  - e00213
EP  - e00212
VL  - 1
AB  - Syntrophic acetate-oxidizing bacteria (SAOB) have been identified as key organisms for
AB  - efficient biogas production from protein-rich materials. is the
AB  - first reported SAOB for which the genome has been sequenced. Genome analysis will
AB  - aid us in understanding the mechanisms regulating syntrophy, particularly
AB  - energy-conserving and electron transfer mechanisms.
ER  -

TY  - JOUR
AU  - Manzoor, S.
AU  - Muller, B.
AU  - Niazi, A.
AU  - Bongcam-Rudloff, E.
AU  - Schnurer, A.
TI  - Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e0010713
EP  - e0010713
VL  - 1
AB  - Clostridium ultunense strain Esp belongs to the functional group of syntrophic
AB  - acetate-oxidizing bacteria (SAOB), which have been identified as key organisms
AB  - for efficient biogas production from protein-rich materials. Genome analysis and
AB  - comparative genomics might aid us to define physiological features that are
AB  - essential for maintaining this particular syntrophic lifestyle.
ER  -

TY  - JOUR
AU  - Manzoor, S.
AU  - Muller, B.
AU  - Niazi, A.
AU  - Schnurer, A.
AU  - Bongcam-Rudloff, E.
TI  - Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 99
EP  - 99
VL  - 10
AB  - Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium,
AB  - belonging to the Clostridia class within the phylum Firmicutes,
AB  - originally isolated from a mesophilic methanogenic digester. It has been shown to
AB  - oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming
AB  - methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open
AB  - reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA
AB  - genes. Here, we are presenting assembly and annotation features as well as basic
AB  - genomic properties of the type strain Sp3.
ER  -

TY  - JOUR
AU  - Manzoor, S.
AU  - Niazi, A.
AU  - Bejai, S.
AU  - Meijer, J.
AU  - Bongcam-Rudloff, E.
TI  - Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.
JO  - Genome Announcements
PY  - 2013
SP  - e0011113
EP  - e0011113
VL  - 1
AB  - We announce here the genome sequence of Bacillus amyloliquefaciens strain UCMB5036, a plant
AB  - growth-promoting bacterium isolated from a cotton plant. Its
AB  - genome contains gene clusters involved in nonribosomal synthesis of secondary
AB  - metabolites known for their antimicrobial activities. The availability of this
AB  - genome will provide novel insights into plant-bacterium-associated activities.
ER  -

TY  - JOUR
AU  - Manzoor, S.
AU  - Schnurer, A.
AU  - Bongcam-Rudloff, E.
AU  - Muller, B.
TI  - Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 80
EP  - 80
VL  - 11
AB  - Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of
AB  - mesophilic acetate-oxidising bacteria, a syntrophic relationship
AB  - operating close to the thermodynamic equilibrium and of considerable importance
AB  - in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain
AB  - MAB1 belongs to the order Methanomicrobiales, family Methanomicrobiaceae, within
AB  - the phylum Euryarchaeota. The genome shows a total size of 2,859,299 bp encoding
AB  - 3450 predicted protein-encoding genes, of which only 1472 (43 %) have been
AB  - assigned tentative functions. The genome encodes further 44 tRNA genes and three
AB  - rRNA genes (5S, 16S and 23S rRNA). This study presents assembling and annotation
AB  - features as well as genomic traits related to ammonia tolerance and
AB  - methanogenesis.
ER  -

TY  - JOUR
AU  - Mao, D.
AU  - Grogan, D.
TI  - Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species.
JO  - ISME J.
PY  - 2012
SP  - 1613
EP  - 1616
VL  - 6
AB  - Local populations of Sulfolobus islandicus diverge genetically with geographical
AB  - separation, and this has been attributed to restricted transfer of propagules
AB  - imposed by the unfavorable spatial distribution of acidic geothermal habitat. We
AB  - tested the generality of genetic divergence with distance in Sulfolobus species
AB  - by analyzing genomes of Sulfolobus acidocaldarius drawn from three populations
AB  - separated by more than 8000 km. In sharp contrast to S. islandicus, the
AB  - geographically diverse S. acidocaldarius genomes proved to be nearly identical.
AB  - We could not link the difference in genome conservation between the two species
AB  - to a corresponding difference in genome stability or ecological factors affecting
AB  - propagule dispersal. The results provide the first evidence that genetic
AB  - isolation of local populations does not result primarily from properties
AB  - intrinsic to Sulfolobus and the severe discontinuity of its geothermal habitat,
AB  - but varies with species, and thus may reflect biotic interactions that act after
AB  - propagule dispersal.
ER  -

TY  - JOUR
AU  - Mao, M.
AU  - Yang, X.
AU  - Poff, K.
AU  - Bennett, G.
TI  - Comparative genomics of the dual-obligate symbionts from the treehopper, Entylia carinata (Hemiptera: Membracidae), provide insight into the origins and evolution of an ancient symbioses.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 1803
EP  - 1815
VL  - 9
ER  -

TY  - JOUR
AU  - Mao, X.H.
AU  - Wei, M.
AU  - Zhu, C.F.
AU  - Lu, J.X.
AU  - Gao, J.M.
AU  - Simon, A.J.
AU  - Shi, J.Y.
AU  - Huang, Q.
AU  - Fan, C.H.
TI  - Real Time in Vitro Regulation of DNA Methylation Using a 5-Fluorouracil Conjugated DNA-Based Stimuli-Responsive Platform.
JO  - ACS Appl. Mater. Inter.
PY  - 2013
SP  - 2604
EP  - 2609
VL  - 5
AB  - DNA methylation, catalyzed by methylases, plays a critical role in many biological processes,
AB  - and many methylases have been regarded as
AB  - promising targets for antimicrobial drugs. In this work, we report a
AB  - stimulus responsive, self-regulating anticancer drug release platform,
AB  - comprising a multifunctional DNA that upon methylation by
AB  - methyltransferase (MTase) releases 5-fluorouracil (5-Fu) and in turn
AB  - inhibits subsequent expression of MTase. The multifunctional DNA with
AB  - anticancer drug are first methylated by DNA adenine methylation (DAM)
AB  - methyltransferase (MTase) and then cut by the methylation-sensitive
AB  - restriction endonuclease Dpn I. Removal of duplex from the functional
AB  - DNA by the methylation/cleavage process will release the anticancer
AB  - drug, resulting in inhibition of the activity of DAM in turn.
AB  - Consequently, the enzyme activity of DAM MTase can be self-regulated.
AB  - Furthermore, we found that the inhibition efficiency of 5-Fu
AB  - significantly increase as it is functionalized with DNA.
ER  -

TY  - JOUR
AU  - Mao, Y.
AU  - Chen, M.
AU  - Horvath, P.
TI  - Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.
JO  - Genome Announcements
PY  - 2015
SP  - e00821
EP  - e00815
VL  - 3
AB  - Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC
AB  - AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The
AB  - total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol%
AB  - and 2,797 predicted coding sequences (CDSs).
ER  -

TY  - JOUR
AU  - Mao, Z.
AU  - Li, M.
AU  - Chen, J.
TI  - Draft Genome Sequence of Pseudomonas plecoglossicida Strain NB2011, the Causative Agent of White Nodules in Large Yellow Croaker (Larimichthys crocea).
JO  - Genome Announcements
PY  - 2013
SP  - e00586
EP  - e00513
VL  - 1
AB  - We describe the draft genome sequence of Pseudomonas plecoglossicida strain NB2011, the
AB  - causative agent of white nodules in cultured large yellow croaker
AB  - (Larimichthys crocea) in China. The draft genome sequence of the bacterium
AB  - consists of 5.41 million bp, with a G+C content of 62.8%. A total of 4,952 genes
AB  - were identified.
ER  -

TY  - JOUR
AU  - Mappley, L.J.
AU  - Black, M.L.
AU  - Abuoun, M.
AU  - Darby, A.C.
AU  - Woodward, M.J.
AU  - Parkhill, J.
AU  - Turner, A.K.
AU  - Bellgard, M.I.
AU  - La, T.
AU  - Phillips, N.D.
AU  - La Ragione, R.M.
AU  - Hampson, D.J.
TI  - Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.
JO  - BMC Genomics
PY  - 2012
SP  - 454
EP  - 454
VL  - 13
AB  - ABSTRACT: BACKGROUND: The anaerobic spirochaete Brachyspira pilosicoli causes
AB  - enteric disease in avian, porcine and human hosts, amongst others. To date, the
AB  - only available genome sequence of B. pilosicoli is that of strain 95/1000, a
AB  - porcine isolate. In the first intra-species genome comparison within the
AB  - Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an
AB  - avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human
AB  - isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on
AB  - incomplete genome sequences from three other Brachyspira species. Finally we
AB  - report the first application of the high-throughput Biolog phenotype screening
AB  - tool on the B. pilosicoli strains for detailed comparisons between genotype and
AB  - phenotype. RESULTS: Feature and sequence genome comparisons revealed a high
AB  - degree of similarity between the three B. pilosicoli strains, although the
AB  - genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and
AB  - 2.596 Mb, respectively). Genome rearrangements were observed which correlated
AB  - largely with the positions of mobile genetic elements. Through comparison of the
AB  - B2904 and WesB genomes with the 95/1000 genome, features that we propose are
AB  - non-essential due to their absence from 95/1000 include a peptidase, glycine
AB  - reductase complex components and transposases. Novel bacteriophages were detected
AB  - in the newly-sequenced genomes, which appeared to have involvement in intra- and
AB  - inter-species horizontal gene transfer. Phenotypic differences predicted from
AB  - genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000,
AB  - were confirmed by phenotyping. CONCLUSIONS: The availability of multiple B.
AB  - pilosicoli genome sequences has allowed us to demonstrate the substantial genomic
AB  - variation that exists between these strains, and provides an insight into genetic
AB  - events that are shaping the species. In addition, phenotype screening allowed
AB  - determination of how genotypic differences translated to phenotype. Further
AB  - application of such comparisons will improve understanding of the metabolic
AB  - capabilities of Brachyspira species.
ER  -

TY  - JOUR
AU  - Marasa, B.S.
AU  - Khan, S.
AU  - Iram, S.
AU  - Sung, K.
AU  - Xu, J.
TI  - Draft Genome Sequence of Methicillin-Resistant Clinical Staphylococcus aureus Isolate 51S (Sequence Type 291).
JO  - Genome Announcements
PY  - 2015
SP  - e01050
EP  - e01015
VL  - 3
AB  - We report the draft genome sequence of a methicillin-resistant clinical Staphylococcus aureus
AB  - isolate with a novel spa type and sequence type (ST291), isolated from a renal failure patient
AB  - in Rawalpindi, Pakistan.
ER  -

TY  - JOUR
AU  - Marasa, B.S.
AU  - Revollo, J.
AU  - Iram, S.
AU  - Sung, K.
AU  - Xu, J.
AU  - Khan, S.
TI  - Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus ST1413 Strain for Studying Genetic Mechanisms of Antibiotic Resistance.
JO  - Genome Announcements
PY  - 2014
SP  - e00162
EP  - e00114
VL  - 2
AB  - Here we report the whole draft genome sequence of a methicillin-resistant Staphylococcus
AB  - aureus ST1413 strain. Determining the distribution and arrangement
AB  - of various genes associated with drug resistance, toxicity, and diseases will
AB  - enhance our understanding about its adaptability to thrive in different
AB  - ecological niches and help in the development of effective treatments for
AB  - enterotoxigenic staphylococcal infections.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Abo-Shama, U.H.
AU  - Fakhr, M.K.
TI  - Complete Genome Sequences of Salmonella enterica Serovars Anatum and Anatum var.  15+, Isolated from Retail Ground Turkey.
JO  - Genome Announcements
PY  - 2016
SP  - e01619
EP  - e01615
VL  - 4
AB  - The complete genome sequences of two isolates of Salmonella enterica serovars Anatum and
AB  - Anatum var. 15+ revealed the presence of two plasmids of 112 kb and 3
AB  - kb in size in each. The chromosome of Salmonella Anatum (4.83 Mb) was slightly
AB  - smaller than that of Salmonella Anatum var. 15+ (4.88 Mb).
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Abo-Shama, U.H.
AU  - Fakhr, M.K.
TI  - Whole-Genome Sequencing of Salmonella enterica subsp. enterica Serovar Ouakam Isolated from Ground Turkey.
JO  - Genome Announcements
PY  - 2016
SP  - e01618
EP  - e01615
VL  - 4
AB  - In this report, we announce the first whole-genome sequencing of Salmonella enterica subsp.
AB  - enterica serovar Ouakam strain GNT-01, isolated from ground
AB  - turkey retail meat. The strain has a chromosome of 5,088,451 bp long, with a G+C
AB  - content of 52.3%, and a plasmid of 109,715 bp.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Cornell, C.R.
AU  - Oyewole, O.
AU  - Sheaff, R.J.
AU  - Fakhr, M.K.
TI  - The Whole-Genome Sequence of Bacillus velezensis Strain SB1216 Isolated from the  Great Salt Plains of Oklahoma Reveals the Presence of a Novel Extracellular RNase  with Antitumor Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e01343
EP  - e01317
VL  - 5
AB  - The whole-genome sequence of Bacillus velezensis strain SB1216, isolated from the Great Salt
AB  - Plains of Oklahoma, showed the presence of a 3,814,720-bp circular
AB  - chromosome and no plasmids. The presence of a novel 870-bp extracellular RNase
AB  - gene is predicted to be responsible for this strain's antitumor activity.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Complete Genome Sequences of the Plasmid-Bearing Campylobacter coli Strains HC2-48, CF2-75, and CO2-160 Isolated from Retail Beef Liver.
JO  - Genome Announcements
PY  - 2016
SP  - e01004
EP  - e01016
VL  - 4
AB  - The complete genome sequences of Campylobacter coli strains HC2-48, CF2-75, and CO2-160,
AB  - isolated from retail beef liver, showed the presence of 1,663,782-,
AB  - 1,711,393-, and 1,683,224-bp circular chromosomes and 44,064-, 44,233-, and
AB  - 44,228-bp circular plasmids, respectively. This is the first reported
AB  - Campylobacter coli genome sequence isolated from retail beef liver.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Complete Genome Sequences of Plasmid-Bearing Campylobacter coli and Campylobacter jejuni Strains Isolated from Retail Chicken Liver.
JO  - Genome Announcements
PY  - 2017
SP  - e01350
EP  - e01317
VL  - 5
AB  - Complete genome sequences of Campylobacter coli strains WA333, YF2105, BG2108, MG1116, and
AB  - BP3183 and Campylobacter jejuni strain IF1100 isolated from retail
AB  - chicken liver showed the presence of 1,841,551-, 1,687,232-, 1,695,638-,
AB  - 1,665,146-, 1,695,360-, and 1,744,171-bp circular chromosomes, respectively.
AB  - These isolates also contained plasmids ranging in size from 5,209 to 55,122 bp.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Complete Genome Sequences of Campylobacter jejuni Strains OD267 and WP2202 Isolated from Retail Chicken Livers and Gizzards Reveal the Presence of Novel  116-Kilobase and 119-Kilobase Megaplasmids with Type VI Secretion Systems.
JO  - Genome Announcements
PY  - 2016
SP  - e01060
EP  - e01016
VL  - 4
AB  - Genome sequences of Campylobacter jejuni strains OD267 and WP2202, isolated from  chicken
AB  - livers and gizzards, showed the presence of novel 116-kb and 119-kb
AB  - megaplasmids, respectively. The two megaplasmids carry a type VI secretion system
AB  - and tetracycline resistance genes. These are the largest sequenced Campylobacter
AB  - plasmids to date.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Whole-Genome Sequencing of a Campylobacter jejuni Strain Isolated from Retail Chicken Meat Reveals the Presence of a Megaplasmid with Mu-Like Prophage and  Multidrug Resistance Genes.
JO  - Genome Announcements
PY  - 2016
SP  - e00460
EP  - e00416
VL  - 4
AB  - Genome sequencing of Campylobacter jejuni strain T1-21 isolated from retail chicken meat
AB  - revealed the presence of a chromosome of 1,565,978 bp and a
AB  - megaplasmid of 82,732 bp that contains Mu-like prophage and multidrug resistance
AB  - genes. This is the first reported sequence of a Campylobacter megaplasmid >55 kb.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Complete Genome Sequences of Plasmid-Bearing Multidrug-Resistant Campylobacter jejuni and Campylobacter coli Strains with Type VI Secretion Systems, Isolated  from Retail Turkey and Pork.
JO  - Genome Announcements
PY  - 2017
SP  - e01360
EP  - e01317
VL  - 5
AB  - We report the complete genome sequences of multidrug-resistant Campylobacter jejuni and
AB  - Campylobacter coli isolated from retail turkey and pork, respectively.
AB  - The chromosomes of these two isolates contained type VI secretion system genes.
AB  - The two isolates also harbored large plasmids with antimicrobial resistance genes
AB  - possibly contributing to their multidrug resistance.
ER  -

TY  - JOUR
AU  - Marasini, D.
AU  - Fakhr, M.K.
TI  - Complete Genome Sequences of Campylobacter jejuni Strains Isolated from Retail Chicken and Chicken Gizzards.
JO  - Genome Announcements
PY  - 2017
SP  - e01351
EP  - e01317
VL  - 5
AB  - Genome sequences of Campylobacter jejuni FJ3124 and ZP3204 isolated from retail chicken
AB  - gizzards and Campylobacter jejuni TS1218 isolated from retail chicken
AB  - showed the presence of 1,694,324-, 1,763,161-, and 1,762,596-bp circular
AB  - chromosomes, respectively. Campylobacter jejuni ZP3204 and TS1218 harbored large
AB  - tetracycline resistance plasmids with type IV secretion systems.
ER  -

TY  - JOUR
AU  - Marcaida, M.J. et al.
TI  - Homing endonucleases: from basics to therapeutic applications.
JO  - Cell. Mol. Life Sci.
PY  - 2010
SP  - 727
EP  - 748
VL  - 67
AB  - Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites
AB  - (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their
AB  - recognition sites are extremely rare, with none or only a few of these sites present in a
AB  - mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases,
AB  - tolerate some sequence degeneracy within their recognition sequence. Several members of this
AB  - enzyme family have been used as templates to engineer tools to cleave DNA sequences that
AB  - differ from their original wild-type targets. These custom HEs can be used to stimulate
AB  - double-strand break homologous recombination in cells, to induce the repair of defective genes
AB  - with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene
AB  - therapy in patients with monogenic diseases that can be treated ex vivo. This review provides
AB  - an overview of recent advances in this field.
ER  -

TY  - JOUR
AU  - Marcaida, M.J.
AU  - Prieto, J.
AU  - Redondo, P.
AU  - Nadra, A.D.
AU  - Alibes, A.
AU  - Serrano, L.
AU  - Grizot, S.
AU  - Duchateau, P.
AU  - Paques, F.
AU  - Blanco, F.J.
AU  - Montoya, G.
TI  - Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 16888
EP  - 16893
VL  - 105
AB  - Homing endonucleases, also known as meganucleases, are sequence-specific enzymes with large
AB  - DNA recognition sites. These enzymes can be used to
AB  - induce efficient homologous gene targeting in cells and plants, opening
AB  - perspectives for genome engineering with applications in a wide series of
AB  - fields, ranging from biotechnology to gene therapy. Here, we report the
AB  - crystal structures at 2.0 and 2.1 A resolution of the I-DmoI meganuclease
AB  - in complex with its substrate DNA before and after cleavage, providing
AB  - snapshots of the catalytic process. Our study suggests that I-DmoI
AB  - requires only 2 cations instead of 3 for DNA cleavage. The structure sheds
AB  - light onto the basis of DNA binding, indicating key residues responsible
AB  - for nonpalindromic target DNA recognition. In silico and in vivo analysis
AB  - of the I-DmoI DNA cleavage specificity suggests that despite the
AB  - relatively few protein-base contacts, I-DmoI is highly specific when
AB  - compared with other meganucleases. Our data open the door toward the
AB  - generation of custom endonucleases for targeted genome engineering using
AB  - the monomeric I-DmoI scaffold.
ER  -

TY  - JOUR
AU  - March, J.B.
AU  - Clark, J.
TI  - Enzymes by post-restriction enzyme stability.
JO  - Nat. Biotechnol.
PY  - 2000
SP  - 243
EP  - 243
VL  - 18
AB  - The authors suggest that many restriction enzymes are sufficiently stable at room temperature
AB  - that they could be transported abroad without expensive ice-packs or dry ice.
ER  -

TY  - JOUR
AU  - Marche, L.
AU  - Saraoui, T.
AU  - Remenant, B.
AU  - Zagorec, M.
AU  - Prevost, H.
AU  - Delbarre-Ladrat, C.
AU  - Leroi, F.
AU  - Pilet, M.F.
TI  - Complete Genome Sequence of Lactococcus piscium CNCM I-4031, a Bioprotective Strain for Seafood Products.
JO  - Genome Announcements
PY  - 2017
SP  - e01510
EP  - e01516
VL  - 5
AB  - Lactococcus piscium CNCM I-4031 is a psychotrophic foodborne lactic acid bacterium showing
AB  - potential interest for the biopreservation of seafood products
AB  - due to its inhibition properties toward pathogenic and spoilage bacteria. The
AB  - analysis of its genome will provide a better understanding of the mechanisms of
AB  - interaction between these bacteria.
ER  -

TY  - JOUR
AU  - Marchionni, M.A.
AU  - Roufa, D.J.
TI  - Digestion of 5-bromodeoxyuridine-substituted lambda-DNA by restriction endonucleases.
JO  - J. Biol. Chem.
PY  - 1978
SP  - 9075
EP  - 9081
VL  - 253
AB  - 5-bromodeoxyuridine (BrdUrd) DNA from bacteriophage lambda affects both the
AB  - rates and sites of cleavage by Endo R.EcoRI, HindIII, and SmaI.  Endonucleases
AB  - EcoRI and HindIII, both of which recognize nucleotide sequences that contain 4
AB  - thymidine residues, cleaved fully substituted BrdUrd-DNA at the same sites as
AB  - unsubstituted DNA.  However, when treated with limiting amounts of either of
AB  - the two endonucleases, BrdUrd-DNA was digested more slowly than was the
AB  - unsubstituted DNA.  Endo R.SmaI, which recognizes a nucleotide sequence that
AB  - does not contain thymidine digested BrdUrd-DNA at approximately the same rate
AB  - as unsubstituted DNA.  Surprisingly, one of the three SmaI sites in lambda-DNA
AB  - (located at 0.656 on the genome's physical map) appeared to be highly resistant
AB  - to cleavage by SmaI in substituted DNA.  Hence, cleavage of BrdUrd-DNA by SmaI
AB  - generated three restriction products instead of the expected four products
AB  - derived from unsubstituted DNA.  These BrdUrd-DNA products were identified as
AB  - the characteristic SmaI.A and C fragments as well as an unusual, large product
AB  - that contained the fused B and D fragments.  Therefore, the SmaI cleavage site
AB  - at the junction of the B-D fragments appears to differ from the other two sites
AB  - by aspects of DNA structure determined outside of the canonical SmaI
AB  - recognition sequence.  This finding indicates that site-specific DNA enzymes
AB  - can be influenced by DNA determinants that reside outside of the accepted
AB  - recognition sequences of the enyzmes.
ER  -

TY  - JOUR
AU  - Marcial-Coba, M.S.
AU  - Marshall, I.P.G.
AU  - Schreiber, L.
AU  - Nielsen, D.S.
TI  - High-Quality Draft Genome Sequence of Lactobacillus casei Strain Z11, Isolated from a Human Adult Intestinal Biopsy Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e00634
EP  - e00617
VL  - 5
AB  - Several Lactobacillus casei strains are used as probiotics. L. casei strain Z11,  isolated
AB  - from a human colon biopsy sample, has been suggested as a probiotic
AB  - candidate based on promising properties in vitro Here, we present a 2.74-Mbp
AB  - high-quality draft genome sequence for this strain.
ER  -

TY  - JOUR
AU  - Marcoleta, A.
AU  - Gutierrez-Cortez, S.
AU  - Maturana, D.
AU  - Monasterio, O.
AU  - Lagos, R.
TI  - Whole-Genome Sequence of the Microcin E492-Producing Strain Klebsiella pneumoniae RYC492.
JO  - Genome Announcements
PY  - 2013
SP  - e00178
EP  - e00113
VL  - 1
AB  - Here, we report the draft genome sequence of the Gram-negative strain Klebsiella  pneumoniae
AB  - RYC492, which produces the amyloid-forming and antibacterial peptide
AB  - microcin E492. The sequenced genome consists of a 5,095,761-bp assembled open
AB  - chromosome where the gene cluster for microcin production is located in a
AB  - putative 31-kb genomic island flanked by sequence repeats and containing a
AB  - putative integrase-coding gene.
ER  -

TY  - JOUR
AU  - Marcon, J.
AU  - Taketani, R.G.
AU  - Dini-Andreote, F.
AU  - Mazzero, G.I.
AU  - Soares, F.L.J.
AU  - Melo, I.S.
AU  - Azevedo, J.L.
AU  - Andreote, F.D.
TI  - Draft Genome Sequence of Bacillus thuringiensis Strain BrMgv02-JM63, a Chitinolytic Bacterium Isolated from Oil-Contaminated Mangrove Soil in Brazil.
JO  - Genome Announcements
PY  - 2014
SP  - e01264
EP  - e01213
VL  - 2
AB  - Here, we report the draft genome sequence and the automatic annotation of Bacillus
AB  - thuringiensis strain BrMgv02-JM63. This genome comprises a set of genes
AB  - involved in the metabolism of chitin and N-acetylglucosamine utilization, thus
AB  - suggesting the possible role of this strain in the cycling of organic matter in
AB  - mangrove soils.
ER  -

TY  - JOUR
AU  - Marczynski, G.T.
TI  - Chromosome methylation and measurement of faithful, once and only once per cell cycle chromosome replication in Caulobacter crescentus.
JO  - J. Bacteriol.
PY  - 1999
SP  - 1984
EP  - 1993
VL  - 181
AB  - Caulobacter crescentus exhibits cell-type-specific control of chromosome replication and DNA
AB  - methylation.  Asymmetric cell division yields a replicating stalked cell and a nonreplicating
AB  - swarmer cell.  The motile swarmer cell must differentiate into a sessile stalked cell in order
AB  - to replicate and execute asymmetric cell division.  This program of cell division implies that
AB  - chromosome replication initiates in the stalked cell only once per cell cycle.  DNA
AB  - methylation is restricted to the predivisional cell stage, and since DNA synthesis produces an
AB  - unmethylated nascent strand, late DNA methylation also implies that DNA near the replication
AB  - origin remains hemimethylated longer than DNA located further away.  In this report, both
AB  - assumptions are tested with an engineered Tn5-based transposon, Tn5omega-MP.  This allows a
AB  - sensitive Southern blot assay that measures fully methylated, hemimethylated, and unmethylated
AB  - DNA duplexes.  Tn5omega-MP DNA near the replication origin remained hemimethylated longer than
AB  - DNA located further away.  One Tn5omega-MP placed near the replication origin revealed small
AB  - but detectable amounts of unmethylated duplex DNA in replicating stalked cells.  Extra DNA
AB  - synthesis produces a second unmethylated nascent strand.  Therefore, measurement of
AB  - unmethylated DNA is a critical test of the "once and only once per cell cycle" rule of
AB  - chromosome replication in C. crescentus.  Fewer than 1 in 1,000 stalked cells prematurely
AB  - initiate a second round of chromosome replication.  The implications for very precise negative
AB  - control of chromosome replication are discussed with respect to the bacterial cell cycle.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Beletskii, A.V.
AU  - Gumerov, V.M.
AU  - Karbysheva, E.A.
AU  - Mikheeva, L.E.
TI  - New low-copy plasmid in cyanobacterium Anabaena variabilis.
JO  - Genetika
PY  - 2013
SP  - 798
EP  - 805
VL  - 49
AB  - Complete genome sequencing was performed for Anabaena variabilis ATCC 29413 from the
AB  - collection of the Chair of Genetics, Department of
AB  - Biology, Moscow State University, Russia. In addition to known plasmids
AB  - A, B, and C, a new circular low-copy plasmid was detected and named D.
AB  - It was also sequenced completely and found to have 27051 bp. The
AB  - plasmid contained the parA and parB genes of the partition system, two
AB  - genes that encode replication proteins, a gene for site-specific
AB  - recombinase, a type-I restriction-modification system, and several
AB  - genes with unknown functions. Analysis by PCR revealed the presence of
AB  - plasmid D in two epiphytic strains from Vietnam, i.e., Anabaena sp. 182
AB  - and Anabaena sp. 281, as well as in Anabaena sp. V5 and A. azollae
AB  - (Newton's isolate).
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Eldarov, M.A.
AU  - Sklyarenko, A.V.
AU  - Dumina, M.V.
AU  - Beletsky, A.V.
AU  - Yarotsky, S.V.
AU  - Ravin, N.V.
TI  - Draft Genome Sequence of Escherichia coli Strain VKPM B-10182, Producing the Enzyme for Synthesis of Cephalosporin Acids.
JO  - Genome Announcements
PY  - 2014
SP  - e01222
EP  - e01214
VL  - 2
AB  - Escherichia coli strain VKPM B-10182, obtained by chemical mutagenesis from E. coli strain
AB  - ATCC 9637, produces cephalosporin acid synthetase employed in the
AB  - synthesis of beta-lactam antibiotics, such as cefazolin. The draft genome
AB  - sequence of strain VKPM B-10182 revealed 32 indels and 1,780 point mutations that
AB  - might account for the improvement in antibiotic synthesis that we observed.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Gumerov, V.M.
AU  - Beletsky, A.V.
AU  - Prokofeva, M.I.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Ravin, N.V.
AU  - Skryabin, K.G.
TI  - Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3156
EP  - 3157
VL  - 193
AB  - Thermoproteus uzoniensis 768-20 is a thermoacidophilic anaerobic crenarchaeon isolated from a
AB  - solfataric field in Kamchatka, Russia. The
AB  - complete genome sequence reveals genes for protein and carbohydrate-active
AB  - enzymes, beta-oxidation of fatty acids, the Embden-Meyerhof and
AB  - Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid
AB  - cycle, the dicarboxylate/4-hydroxybutyrate cycle, hydrogenase and sulfur
AB  - reductase.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Gumerov, V.M.
AU  - Slobodkina, G.B.
AU  - Beletsky, A.V.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Ravin, N.V.
AU  - Skryabin, K.G.
TI  - Complete genome sequence of strain 1860, a crenarchaeon of the genus pyrobaculum able to grow with various electron acceptors.
JO  - J. Bacteriol.
PY  - 2012
SP  - 727
EP  - 728
VL  - 194
AB  - Strain 1860, a novel member of the genus Pyrobaculum, is a hyperthermophilic organotrophic
AB  - crenarchaeon growing anaerobically with
AB  - various electron acceptors. The complete genome sequence reveals genes for
AB  - several membrane-bound oxidoreductases, the Embden-Meyerhof and
AB  - Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid
AB  - cycle, the glyoxylate cycle, and the dicarboxylate/4-hydroxybutyrate
AB  - cycle.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Kochetkova, T.V.
AU  - Beletsky, A.V.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Ravin, N.V.
AU  - Skryabin, K.G.
TI  - Complete Genome Sequence of the Hyperthermophilic Cellulolytic Crenarchaeon 'Thermogladius cellulolyticus' 1633.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4446
EP  - 4447
VL  - 194
AB  - Strain 1633, a novel member of the genus Thermogladius, isolated from a freshwater hot spring,
AB  - is an anaerobic hyperthermophilic crenarchaeon capable of
AB  - fermenting proteinaceous and cellulose substrates. The complete genome sequence
AB  - reveals genes for protein and carbohydrate-active enzymes, the Embden-Meyerhof
AB  - pathway for glucose metabolism, cytoplasmic NADP-dependent hydrogenase, and
AB  - several energy-coupling membrane-bound oxidoreductases.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Ravin, N.V.
AU  - Svetlitchnyi, V.A.
AU  - Beletsky, A.V.
AU  - Miroshnichenko, M.L.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Skryabin, K.G.
TI  - Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 4580
EP  - 4588
VL  - 75
AB  - Thermococcus species are widely distributed in terrestrial and marine
AB  - hydrothermal areas, as well as in deep subsurface oil reservoirs.
AB  - Thermococcus sibiricus is a hyperthermophilic anaerobic archaeon isolated
AB  - from a well of the never flooded oil-bearing Jurassic horizon of a
AB  - high-temperature oil reservoir. To obtain insight into the genome of an
AB  - archaeon inhabiting the oil reservoir, we have determined and annotated
AB  - the complete 1,845,800-base genome of T. sibiricus. A total of 2,061
AB  - protein-coding genes have been identified, 387 of which are absent in
AB  - other members of the order Thermococcales. Physiological features and
AB  - genomic data reveal numerous hydrolytic enzymes (e.g., cellulolytic
AB  - enzymes, agarase, laminarinase, and lipases) and metabolic pathways,
AB  - support the proposal of the indigenous origin of T. sibiricus in the oil
AB  - reservoir, and explain its survival over geologic time and its
AB  - proliferation in this habitat. Indeed, in addition to proteinaceous
AB  - compounds known previously to be present in oil reservoirs at limiting
AB  - concentrations, its growth was stimulated by cellulose, agarose, and
AB  - triacylglycerides, as well as by alkanes. Two polysaccharide degradation
AB  - loci were probably acquired by T. sibiricus from thermophilic bacteria
AB  - following lateral gene transfer events. The first, a "saccharolytic gene
AB  - island" absent in the genomes of other members of the order
AB  - Thermococcales, contains the complete set of genes responsible for the
AB  - hydrolysis of cellulose and beta-linked polysaccharides. The second
AB  - harbors genes for maltose and trehalose degradation. Considering that
AB  - agarose and laminarin are components of algae, the encoded enzymes and the
AB  - substrate spectrum of T. sibiricus indicate the ability to metabolize the
AB  - buried organic matter from the original oceanic sediment.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Slododkina, G.B.
AU  - Slobodkin, A.I.
AU  - Beletsky, A.V.
AU  - Gavrilov, S.N.
AU  - Kublanov, I.V.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Skryabin, K.G.
AU  - Ravin, N.V.
TI  - The genome of Geoglobus acetivorans: Fe(III) reduction, acetate utilization, autotrophic growth and degradation of aromatic compounds in a hyperthermophilic archaeon.
JO  - Appl. Environ. Microbiol.
PY  - 2015
SP  - 1003
EP  - 1012
VL  - 81
AB  - Geoglobus acetivorans is a hyperthermophilic anaerobic euryarchaeon of the order
AB  - Archaeoglobales isolated from deep-sea hydrothermal vents. A unique physiological
AB  - feature of the members of the genus Geoglobus is their obligate dependence on
AB  - Fe(III) reduction, which plays an important role in the geochemistry of
AB  - hydrothermal systems. The features of this organism and its complete 1,860,815-bp
AB  - genome sequence are described in this report. Genome analysis revealed pathways
AB  - enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids,
AB  - aromatic compounds, n-alkanes and organic acids including acetate, through
AB  - anaerobic respiration linked to Fe(III) reduction. Consistent with the inability
AB  - of G. acetivorans to grow on carbohydrates, the modified Embden-Meyerhof pathway
AB  - encoded by the genome is incomplete. Autotrophic CO2 fixation is enabled by the
AB  - Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide
AB  - depends on the transfer of electrons from the quinone pool to multiheme c-type
AB  - cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III)
AB  - oxide particles could be facilitated by pili-like appendages. Genome analysis
AB  - indicated the presence of metabolic pathways for anaerobic degradation of
AB  - aromatic compounds and n-alkanes, although the ability of G. acetivorans to grow
AB  - on these substrates was not observed in laboratory experiments. Overall, our
AB  - results suggest that Geoglobus species could play an important role in microbial
AB  - communities of deep-sea hydrothermal vents as lithoautotrophic producers. An
AB  - additional role as decomposers would close the biogeochemical cycle of carbon
AB  - through complete mineralization of various organic compounds via Fe(III)
AB  - respiration.
ER  -

TY  - JOUR
AU  - Mardanov, A.V.
AU  - Svetlitchnyi, V.A.
AU  - Beletsky, A.V.
AU  - Prokofeva, M.I.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Ravin, N.V.
AU  - Skryabin, K.G.
TI  - The Genome Sequence of the Crenarchaeon Acidilobus saccharovorans Supports a New Order, Acidilobales, and Suggests an Important Ecological Role in Terrestrial Acidic Hot Springs.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 5652
EP  - 5657
VL  - 76
AB  - Acidilobus saccharovorans is an anaerobic, organotrophic,
AB  - thermoacidophilic crenarchaeon isolated from a terrestrial hot spring. We
AB  - report the complete genome sequence of A. saccharovorans, which has
AB  - permitted the prediction of genes for Embden-Meyerhof and Entner-Doudoroff
AB  - pathways and genes associated with the oxidative tricarboxylic acid cycle.
AB  - The electron transfer chain is branched with two sites of proton
AB  - translocation and is linked to the reduction of elemental sulfur and
AB  - thiosulfate. The genomic data suggest an important role of the order
AB  - Acidilobales in thermoacidophilic ecosystems whereby its members can
AB  - perform a complete oxidation of organic substrates, closing the anaerobic
AB  - carbon cycle.
ER  -

TY  - JOUR
AU  - Mardanova, A.M.
AU  - Toymentseva, A.A.
AU  - Gilyazeva, A.G.
AU  - Kazakov, S.V.
AU  - Shagimardanova, E.I.
AU  - Khaitlina, S.Y.
AU  - Sharipova, M.R.
TI  - Draft Genome Sequence of Serratia grimesii Strain A2.
JO  - Genome Announcements
PY  - 2014
SP  - e00937
EP  - e00914
VL  - 2
AB  - We report the first draft genome assembly of Serratia grimesii strain A2, previously
AB  - identified as Escherichia coli strain A2, which produces protease
AB  - ECP32 with a high specificity toward actin. S. grimesii strain A2 has multidrug
AB  - resistance associated with a number of efflux pump genes.
ER  -

TY  - JOUR
AU  - Marenda, M.S.
AU  - Sagne, E.
AU  - Poumarat, F.
AU  - Citti, C.
TI  - Suppression subtractive hybridization as a basis to assess Mycoplasma agalactiae and Mycoplasma bovis genomic diversity and species-specific sequences.
JO  - Microbiology
PY  - 2005
SP  - 475
EP  - 489
VL  - 151
AB  - The phylogenically related Mycoplasma agalactiae and Mycoplasma bovis
AB  - species are two ruminant pathogens difficult to differentiate and for
AB  - which a limited amount of sequence data are available. To assess the
AB  - degree of genomic diversity existing between and within these mycoplasma
AB  - species, sets of DNA fragments specific for M. bovis type-strain PG45 or
AB  - for M. agalactiae type-strain PG2 were isolated by suppression subtractive
AB  - hybridization and used as probes on a panel of M. agalactiae and M. bovis
AB  - field isolates. Results indicated that approximately 70 % of the DNA
AB  - fragments specific to one or the other type strain are represented in all
AB  - field isolates of the corresponding species. Only one M. bovis isolate,
AB  - which was first classified as M. agalactiae, reacted with 15 % of the
AB  - PG2-specific probes, while several M. agalactiae isolates reacted with 15
AB  - % of the PG45-specific probes. Sequence analyses indicated that most of
AB  - the genomic diversity observed within one species is related to ORFs with
AB  - (i) no homologies to proteins recorded in the databases or (ii) homologies
AB  - to proteins encoded by restriction modification systems. Reminiscent of
AB  - gene transfer as a means for genomic diversity, a PG45-specific DNA
AB  - fragment with significant homologies to a central protein of an
AB  - integrative conjugative element of Mycoplasma fermentans (ICEF) was found
AB  - in most M. bovis field isolates and in a few M. agalactiae isolates.
AB  - Finally, sequences encoding part of DNA polymerase III were found in both
AB  - sets of M. agalactiae- and M. bovis-specific DNA fragments and were used
AB  - to design a species-specific PCR assay for the identification and
AB  - differentiation of M. agalactiae and M. bovis.
ER  -

TY  - JOUR
AU  - Maresca, D.
AU  - De Filippis, F.
AU  - Tytgat, H.L.P.
AU  - de Vos, W.M.
AU  - Mauriello, G.
TI  - Draft Genome Sequences of the Aerobic Strains Lactobacillus gasseri AL3 and AL5.
JO  - Genome Announcements
PY  - 2017
SP  - e00213
EP  - e00217
VL  - 5
AB  - Adaptation to the aerobic environment has been investigated in heterofermentative
AB  - lactobacilli, while data on how homofermentative lactobacilli adapt to oxygen are
AB  - limited. We report here the draft genome sequences of the aerobic strains
AB  - Lactobacillus gasseri AL3 and AL5 that allow an in-depth investigation of the
AB  - genes involved in oxidative metabolism and the stress response.
ER  -

TY  - JOUR
AU  - Margolles, A.
AU  - Gueimonde, M.
AU  - Sanchez, B.
TI  - Genome Sequence of the Antarctic Psychrophile Bacterium Planococcus antarcticus DSM 14505.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4465
EP  - 4465
VL  - 194
AB  - Planococcus antarcticus DSM 14505 is a psychrophile bacterium that was isolated from
AB  - cyanobacterial mat samples, originally collected from ponds in McMurdo,
AB  - Antarctica. This orange-pigmented bacterium grows at 4 degrees C and may possess
AB  - interesting enzymatic activities at low temperatures. Here we report the first
AB  - genomic sequence of P. antarcticus DSM 14505.
ER  -

TY  - JOUR
AU  - Margos, G.
AU  - Hepner, S.
AU  - Mang, C.
AU  - Sing, A.
AU  - Liebl, B.
AU  - Fingerle, V.
TI  - Completed Genome Sequences of Borrelia burgdorferi Sensu Stricto B31(NRZ) and Closely Related Patient Isolates from Europe.
JO  - Genome Announcements
PY  - 2017
SP  - e00637
EP  - e00617
VL  - 5
AB  - Borrelia burgdorferi sensu stricto is a causative agent of human Lyme borreliosis in the
AB  - United States and Europe. We report here the completed genome sequences of
AB  - strain B31 isolated from a tick in the United States and two closely related
AB  - strains from Europe, PAli and PAbe, which were isolated from patients with
AB  - erythema migrans and neuroborreliosis, respectively.
ER  -

TY  - JOUR
AU  - Margot, J.B.
AU  - Aguirre-Arteta, A.M.
AU  - Di Giacco, B.V.
AU  - Pradhan, S.
AU  - Roberts, R.J.
AU  - Cardoso, M.C.
AU  - Leonhardt, H.
TI  - Structure and Function of the Mouse DNA Methyltransferase Gene: Dnmt1 shows a Tripartite Structure.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 293
EP  - 300
VL  - 297
AB  - Dnmt1 is the predominant DNA methyltransferase (MTase) in mammals. The C-terminal domain of
AB  - Dnmt1 clearly shares sequence similarity with many
AB  - prokaryotic 5mC methyltransferases, and had been proposed to be sufficient for catalytic
AB  - activity. We show here by deletion analysis that the C-terminal domain alone is not
AB  - sufficient for methylating activity, but that a large part of the N-terminal domain is
AB  - required in addition. Since this complex structure of Dnmt1 raises issues about its
AB  - evolutionary origin, we have compared several eukaryotic MTases and have determined the
AB  - genomic organization of the mouse Dnmt1 gene. The 5' most part of the
AB  - N-terminal domain is dispensible for enzyme activity, includes the major nuclear import signal
AB  - and comprises tissue-specific exons. Interestingly, the functional subdivision
AB  - of Dnmt1 correlates well with the structure of the Dnmt1 gene in terms of intron/exon size
AB  - distribution as well as sequence conservation. Our results, based on functional,
AB  - structural and sequence comparison data, suggest that the gene has evolved from the fusion of
AB  - at least three genes.
ER  -

TY  - JOUR
AU  - Margot, J.B.
AU  - Cardoso, M.C.
AU  - Leonhardt, H.
TI  - Mammalian DNA methyltransferases show different subnuclear distributions.
JO  - J. Cell. Biochem.
PY  - 2001
SP  - 373
EP  - 379
VL  - 83
AB  - In mammalian cells, DNA methylation patterns are precisely maintained after DNA replication
AB  - with defined changes occurring during development. The major DNA methyltransferase (Dnmt1) is
AB  - associated with nuclear replication sites during S-phase, which is consistent with a role in
AB  - maintenance methylation. The subcellular distribution of the recently discovered de novo DNA
AB  - methyltransferases, Dnmt3a and Dnmt3b, was investigated by immunofluorescence and by epitope
AB  - tagging. We now show that both Dnmt3a and Dnmt3b are distributed throughout the nucleoplasm
AB  - but are not associated with nuclear DNA replication sites during S-phase. These results
AB  - suggest that de novo methylation by Dnmt3a and Dnmt3b occurs independently of the replication
AB  - process and might involve an alternative mechanism for accessing the target DNA. The different
AB  - subcellular distribution of mammalian DNA methyltransferases might thus contribute to the
AB  - regulation of DNA methylation.
ER  -

TY  - JOUR
AU  - Margot, J.B.
AU  - Ehrenhofer-Murray, A.E.
AU  - Leonhardt, H.
TI  - Interactions within the mammalian DNA methyltransferase family.
JO  - BMC Mol. Biol.
PY  - 2003
SP  - 7
EP  - 7
VL  - 4
AB  - BACKGROUND: In mammals, epigenetic information is established and maintained via the
AB  - postreplicative methylation of cytosine residues by the
AB  - DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Dnmt1 is required for
AB  - maintenance methylation whereas Dnmt3a and Dnmt3b are responsible for de
AB  - novo methylation. Contrary to Dnmt3a or Dnmt3b, the isolated C-terminal
AB  - region of Dnmt1 is catalytically inactive, despite the presence of the
AB  - sequence motifs typical of active DNA methyltransferases. Deletion
AB  - analysis has revealed that a large part of the N-terminal domain is
AB  - required for enzymatic activity. RESULTS: The role played by the
AB  - N-terminal domain in this regulation has been investigated using the yeast
AB  - two-hybrid system. We show here the presence of an intra-molecular
AB  - interaction in Dnmt1 but not in Dnmt3a or Dnmt3b. This interaction was
AB  - confirmed by immunoprecipitation and was localized by deletion mapping.
AB  - Furthermore, a systematic analysis of interactions among the Dnmt family
AB  - members has revealed that DNMT3L interacts with the C-terminal domain of
AB  - Dnmt3a and Dnmt3b. CONCLUSIONS: The lack of methylating ability of the
AB  - isolated C-terminal domain of Dnmt1 could be explained in part by a
AB  - physical interaction between N- and C-terminal domains that apparently is
AB  - required for activation of the catalytic domain. Our deletion analysis
AB  - suggests that the tertiary structure of Dnmt1 is important in this process
AB  - rather than a particular sequence motif. Furthermore, the interaction
AB  - between DNMT3L and the C-terminal domains of Dnmt3a and Dnmt3b suggests a
AB  - mechanism whereby the enzymatically inactive DNMT3L brings about the
AB  - methylation of its substrate by recruiting an active methylase.
ER  -

TY  - JOUR
AU  - Margulies, M. et al.
TI  - Genome sequencing in microfabricated high-density picolitre reactors.
JO  - Nature
PY  - 2005
SP  - 376
EP  - 380
VL  - 437
AB  - The proliferation of large-scale DNA-sequencing projects in recent years has
AB  - driven a search for alternative methods to reduce time and cost. Here we describe
AB  - a scalable, highly parallel sequencing system with raw throughput significantly
AB  - greater than that of state-of-the-art capillary electrophoresis instruments. The
AB  - apparatus uses a novel fibre-optic slide of individual wells and is able to
AB  - sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To
AB  - achieve an approximately 100-fold increase in throughput over current Sanger
AB  - sequencing technology, we have developed an emulsion method for DNA amplification
AB  - and an instrument for sequencing by synthesis using a pyrosequencing protocol
AB  - optimized for solid support and picolitre-scale volumes. Here we show the
AB  - utility, throughput, accuracy and robustness of this system by shotgun sequencing
AB  - and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at
AB  - 99.96% accuracy in one run of the machine.
ER  -

TY  - JOUR
AU  - Mariita, R.M.
AU  - Bhatnagar, S.
AU  - Hanselmann, K.
AU  - Hossain, M.J.
AU  - Korlach, J.
AU  - Boitano, M.
AU  - Roberts, R.J.
AU  - Liles, M.R.
AU  - Moss, A.G.
AU  - Leadbetter, J.R.
AU  - Newman, D.K.
AU  - Dawson, S.C.
TI  - Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.
JO  - Genome Announcements
PY  - 2015
SP  - e01506
EP  - e01515
VL  - 3
AB  - Here, we present the complete genome sequence of Streptomyces sp. strain CCM_MD2014 (phylum
AB  - Actinobacteria), isolated from surface soil in Woods Hole, MA.
AB  - Its single linear chromosome of 8,274,043 bp in length has a 72.13% G+C content
AB  - and contains 6,948 coding sequences.
ER  -

TY  - JOUR
AU  - Mariita, R.M.
AU  - Bhatnagar, S.
AU  - Hanselmann, K.
AU  - Hossain, M.J.
AU  - Korlach, J.
AU  - Boitano, M.
AU  - Roberts, R.J.
AU  - Liles, M.R.
AU  - Moss, A.G.
AU  - Leadbetter, J.R.
AU  - Newman, D.K.
AU  - Dawson, S.C.
TI  - Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts.
JO  - Genome Announcements
PY  - 2015
SP  - e01504
EP  - e01515
VL  - 3
AB  - Here, we present the 3,443,800-bp complete genome sequence of Curtobacterium sp.  strain
AB  - MR_MD2014 (phylum Actinobacteria). This strain was isolated from soil in
AB  - Woods Hole, MA, as part of the 2014 Microbial Diversity Summer Program at the
AB  - Marine Biological Laboratory in Woods Hole, MA.
ER  -

TY  - JOUR
AU  - Marin, M.A.
AU  - Fonseca, E.L.
AU  - Andrade, B.N.
AU  - Cabral, A.C.
AU  - Vicente, A.C.
TI  - Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1.
JO  - PLoS ONE
PY  - 2014
SP  - E108728
EP  - E108728
VL  - 9
AB  - In the last decades, there has been an increase of cholera epidemics caused by
AB  - multidrug resistant strains. Particularly, the integrative and conjugative
AB  - element (ICE) seems to play a major role in the emergence of multidrug resistant
AB  - Vibrio cholerae. This study fully characterized, by whole genome sequencing, new
AB  - ICEs carried by multidrug resistant V. cholerae O1 strains from Nigeria (2010)
AB  - (ICEVchNig1) and Nepal (1994) (ICEVchNep1). The gene content and gene order of
AB  - these two ICEs are the same, and identical to ICEVchInd5, ICEVchBan5 and
AB  - ICEVchHai1 previously identified in multidrug resistant V. cholerae O1. This ICE
AB  - is characterized by dfrA1, sul2, strAB and floR antimicrobial resistance genes,
AB  - and by unique gene content in HS4 and HS5 ICE regions. Screening for ICEs, in
AB  - publicly available V. cholerae genomes, revealed the occurrence and widespread
AB  - distribution of this ICE among V. cholerae O1. Metagenomic analysis found
AB  - segments of this ICE in marine environments far from the direct influence of the
AB  - cholera epidemic. Therefore, this study revealed the epidemiology of a
AB  - spatio-temporal prevalent ICE in V. cholerae O1. Its occurrence and dispersion in
AB  - V. cholerae O1 strains from different continents throughout more than two decades
AB  - can be indicative of its role in the fitness of the current pandemic lineage.
ER  -

TY  - JOUR
AU  - Marinho-Almeida, D.
AU  - Dini-Andreote, F.
AU  - Camargo-Neves, A.A.
AU  - Juca-Ramos, R.T.
AU  - Andreote, F.D.
AU  - Carneiro, A.R.
AU  - Oliveira-de-Souza, L.A.
AU  - Caracciolo-Gomes-de-Sa, P.H.
AU  - Ribeiro-Barbosa, M.S.
AU  - Araujo, W.L.
AU  - Silva, A.
TI  - Draft Genome Sequence of Methylobacterium mesophilicum Strain SR1.6/6, Isolated from Citrus sinensis.
JO  - Genome Announcements
PY  - 2013
SP  - e00356
EP  - e00313
VL  - 1
AB  - Methylobacterium mesophilicum strain SR1.6/6 is an endophytic bacterium isolated  from a
AB  - surface-sterilized Citrus sinensis branch. Ecological and biotechnological
AB  - aspects of this bacterium, such as the genes involved in its association with the
AB  - host plant and the primary oxidation of methanol, were annotated in the draft
AB  - genome.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - DNA Methylation.
JO  - Methylation of DNA in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology
PY  - 1996
SP  - 782
EP  - 791
VL  - 0
AB  - DNA methylation in bacteria is most often thought of in its
AB  - role to protect DNA from restriction endonucleases.  In addition to this
AB  - role, however, studies in Escherichia coli have shown that methylated
AB  - bases have other biological functions.  As described below, DNA adenine
AB  - methylation is frequently used to control the rate at which these
AB  - functions exert their effects.  Thus it is primarily used for regulatory
AB  - purposes.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - Methylation of DNA.
JO  - Escherichia coli and Salmonella typhimurium: Cellular and molecular biology.
PY  - 1987
SP  - 697
EP  - 702
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - Methylation of prokaryotic DNA.
JO  - DNA Methylation. Biochemistry and Biological Significance.
PY  - 1984
SP  - 81
EP  - 109
VL  - 0
AB  - The biological function of methylated bases in DNA of prokaryotes appears to be
AB  - quite different than that of eukaryotes.  In this chapter, most of the
AB  - information presented is derived fom studies with Escherichia coli K-12 simply
AB  - because more is known about DNA methylation in this organism than in any other
AB  - one.  Some data from certain E. coli bacteriophages also will be reviewed, in
AB  - addition to selected aspects about DNA methylation in certain other
AB  - prokaryotes.  Other recent reviews that complement this one are by Razin and
AB  - Friedman (1981) and Hattman (1981).
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - Recombination is essential for viability of an Escherichia coli dam (DNA adenine methyltransferase) mutant.
JO  - J. Bacteriol.
PY  - 2000
SP  - 463
EP  - 468
VL  - 182
AB  - Double mutants of Escherichia coli dam (DNA adenine methyltransferase) strains with ruvA,
AB  - ruvB, or ruvC could not be constructed, whereas dam derivatives with recD, recF, recJ, and
AB  - recR were viable.  The ruv gene products are required for Holliday junction translocation and
AB  - resolution of recombination intermediates.  A dam recG (Holliday junction translocation)
AB  - mutant strain was isolated but at a very much lower frequency than expected.  The inviability
AB  - of a dam lexA (Ind-) host was abrogated by the simultaneous presence of plasmids encoding both
AB  - recA and ruvAB.  This result indicates that of more than 20 SOS genes, only recA and ruvAB
AB  - need to be derepressed to allow for dam mutant survival.  The presence of mutS or mutL
AB  - mutations allowed the construction of dam lexA (Ind-) derivatives.  The requirement for recA,
AB  - recB, recC, ruvA, ruvB, ruvC, and possibly recG gene expression indicates that recombination
AB  - is essential for viability of dam bacteria probably to repair DNA double-strand breaks.  The
AB  - effect of mutS and mutL mutations indicates that DNA mismatch repair is the ultimate source of
AB  - most of these DNA breaks.  The requirement for recombination also suggests an explanation for
AB  - the sensitivity of dam cells to certain DNA-damaging agents.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - DNA methylation in Escherichia coli.
JO  - Annu. Rev. Genet.
PY  - 1987
SP  - 113
EP  - 131
VL  - 21
AB  - None
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - DNA methylation influences trpR promoter activity in Escherichia coli K-12.
JO  - Mol. Gen. Genet.
PY  - 1985
SP  - 185
EP  - 186
VL  - 200
AB  - Methylation of adenine in the GATC-sequence of the -35 region of the trpR
AB  - promoter decreases activity by 2-3 fold.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - Location of DNA methylase genes on the Escherichia coli K-12 genetic map.
JO  - Mol. Gen. Genet.
PY  - 1973
SP  - 47
EP  - 55
VL  - 127
AB  - The genes responsible for DNA adenine methylation (dam) and DNA cytosine methylation (dcm)
AB  - have been mapped on the E. coli K-12 genetic map. The dam gene is situated at min 65 and the
AB  - gene order cysG-(trpS, dam)-aroB inferred. The dcm gene is located at min 37.5 and the gene
AB  - order is supD-dcm-flaA1. In F' merodiploids, the dam and dcm alleles are recessive.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - Adenine methylation of Okazaki fragments in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1976
SP  - 853
EP  - 854
VL  - 128
AB  - In Escherichia coli polA lig-4 bacteria, the moles percent 6-methyladenine
AB  - content of 10S deoxyribonucleic acid (Okazaki fragments) is 0.96 compared with
AB  - 1.4 for bulk desoxyribonucleic acid.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
TI  - Influence of uvrD3, uvrE502, and recL152 mutations on the phenotypes of Escherichia coli K-12 dam mutants.
JO  - J. Bacteriol.
PY  - 1980
SP  - 223
EP  - 226
VL  - 141
AB  - The recF143 allele did not alter the phenotypes of dam mutants of Escherichia coli. The uvrD3,
AB  - uvrE502, and recL152 mutations did alter some of the phenotypes of dam bacteria. It was
AB  - concluded that the uvrD, uvrE, and recL gene products are involved in the same
AB  - deoxyribonucleic acid repair pathway as the dam gene product.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Carraway, M.
AU  - Frey, A.Z.
AU  - Brown, L.
AU  - Arraj, J.A.
TI  - Insertion mutations in the dam gene of Escherichia coli K-12.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 288
EP  - 289
VL  - 192
AB  - The dam gene of E. coli can be inactivated by insertion of Tn9 or Mud phage. Strains bearing
AB  - these mutations are viable indicating that the dam gene product is dispensable.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Casadesus, J.
TI  - Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.
JO  - FEMS Microbiol. Rev.
PY  - 2009
SP  - 488
EP  - 503
VL  - 33
AB  - The DNA adenine methyltransferase (Dam methylase) of Gammaproteobacteria and the cell
AB  - cycle-regulated methyltransferase (CcrM) methylase of Alphaproteobacteria catalyze an
AB  - identical reaction (methylation of adenosine moieties using S-adenosyl-methionine as a methyl
AB  - donor) at similar DNA targets (GATC and GANTC, respectively). Dam and CcrM are of independent
AB  - evolutionary origin. Each may have evolved from an ancestral restriction-modification system
AB  - that lost its restriction component, leaving an 'orphan' methylase devoted solely to
AB  - epigenetic genome modification. The formation of 6-methyladenine reduces the thermodynamic
AB  - stability of DNA and changes DNA curvature. As a consequence, the methylation state of
AB  - specific adenosine moieties can affect DNA-protein interactions. Well-known examples include
AB  - binding of the replication initiation complex to the methylated oriC, recognition of
AB  - hemimethylated GATCs in newly replicated DNA by the MutHLS mismatch repair complex, and
AB  - discrimination of methylation states in promoters and regulatory DNA motifs by RNA polymerase
AB  - and transcription factors. In recent years, Dam and CcrM have been shown to play roles in
AB  - host-pathogen interactions. These roles are diverse and have only partially been understood.
AB  - Especially intriguing is the evidence that Dam methylation regulates virulence genes in
AB  - Escherichia coli, Salmonella, and Yersinia at the posttranscriptional level.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Konrad, E.B.
TI  - Hyper-recombination in dam mutants of Escherichia coli K-12.
JO  - Mol. Gen. Genet.
PY  - 1976
SP  - 273
EP  - 277
VL  - 149
AB  - F-prime heterogenotes of dam-3 bacteria segregate F-prime homogenotes at a frequency 30-200
AB  - times higher than the isogenic dam+ strain. A hyperrecombination mutant which shows increased
AB  - recombination between chromosomal duplications was characterized as a dam mutant. The dam-3
AB  - allele causes a reduction in linkage of proximal unselected markers in transconjugants and
AB  - increases the recombination frequency between a pair of closely linked markers. It is
AB  - concluded that dam mutations confer a hyperrecombination phenotype to the cell.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Lobner-Olesen, A.
TI  - DNA Methylation.
JO  - EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology
PY  - 2009
SP  - 1
EP  - 51
AB  - DNA methylation in bacteria is most often thought of in its role to protect DNA from
AB  - restriction endonucleases.  In addition to this role, however, studies in Escherichia coli,
AB  - Salmonella enteric serovar Typhimurium (referred to as serovar Typhimurium hereafter), and
AB  - Caulobacter crescentus have shown that methylated bases have other biological functions.  In
AB  - these cases, the methylated bases are not part of a restriction/modification system and the
AB  - enzymes that produce them are often referred to as orphan or solitary DNA methyltransferases.
AB  - The postreplicative DNA methylation produced by this enzyme superimposes on the primary DNA
AB  - sequence secondary information that has significance for DNA transactions such as
AB  - transcription, transposition, initiation of chromosome replication, mRNA utilization, and
AB  - prevention of mutations by DNA repair.  These alterations are brought about in two ways, the
AB  - first being simply a change in the steady-state level of the methyltransferase either up or
AB  - down from normal.  The second mechanism is through the configuration of the nucleotide
AB  - sequence subject to methylation; it can exist as symmetrically methylated, unmethylated, or
AB  - two possible hemi-methylated arrangements.  The details about the changes in DNA transactions
AB  - through alteration of methyltransferase levels or state of methylation sequences form the bulk
AB  - of this review.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Morris, N.R.
TI  - Biological function for 6-methyladenine residues in the DNA of Escherichia coli K12.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 309
EP  - 322
VL  - 85
AB  - A strain of Escherichia coli K12 mutant at the dam-3 site contains 0.08 mole % 6-methyl
AB  - adenine as compared to 0.5 mole % in the wild type, and the residual DNA methylation is not
AB  - due to the K12 modification methylase specified by the hsp genes. The dam-3 mutant is more
AB  - sensitive to ultraviolet irradiation and to mitomycin C than the wild type and also shows a
AB  - higher mutability. DNA isolated from the dam-3 mutant contains single stranded breaks that are
AB  - amplified in dam-3 polA12 and dam-3 lig-7 double mutants. A function of dam-specified 6-methyl
AB  - adenine residues in DNA would, therefore, appear to be the protection of DNA from nuclease(s)
AB  - that causes the development of breaks. Combination of dam-3 with polA,recA,recB and recC is
AB  - lethal.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Morris, N.R.
TI  - Pleiotropic effects of a DNA adenine methylation mutation (dam-3) in Escherichia coli K12.
JO  - Mutat. Res.
PY  - 1975
SP  - 15
EP  - 26
VL  - 28
AB  - The dam-3 mutation results in a five-fold reduction in the number of 6-methyladenine (6-meA)
AB  - residues in the DNA of E. coli K12 or phage lambda. The DNA of phage fd appears to be devoid
AB  - of 6-meA when propagated on dam-3 bacteria. The phenotypic differences between dam-3 and dam+
AB  - bacteria include: (1) increased free phage in lysogenic dam-3 cultures, (2) increased
AB  - sensitivity to methyl methanesulfonate (MMS), (3) inviability of dam-3 lex-I strains, (4)
AB  - lower molecular weight of DNA in dam-3 bacteria in the absence of DNA ligase and (5) increased
AB  - rate of DNA degradation in dam-3 recA strains.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Morris, N.R.
TI  - Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1973
SP  - 1143
EP  - 1150
VL  - 114
AB  - Fourteen deoxyribonucleic acid (DNA) and 10 ribonucleic acid (RNA) methylation mutants were
AB  - isolated from Escherichia coli K-12 by examining the ability of nucleic acids prepared from
AB  - clones of unselected mutagenized cells to accept methyl groups from wild-type crude extract.
AB  - Eleven of the DNA methylation mutants were deficient in 5-methylcytosine (5-MeC) and were
AB  - designated Dcm. Three DNA methylation mutants were deficient in N6-methyladenine (N6-MeA) and
AB  - were designated Dam. Extracts of the mutants were tested for DNA-cytosine:S-adenosylmethione
AB  - and DNA-adenine:S-adenosylmethionine methyltransferase activities. With one exception, all of
AB  - the mutants had reduced or absent activity. A representative Dcm mutation was located at 36 to
AB  - 37 min and a representative Dam mutation was located in the 60- to 66-min region on the
AB  - genetic map. The Dcm mutants had no obvious associated phenotypic abnormality. The Dam mutants
AB  - were defective in their ability to restrict lambda. None of the mutations had the effect of
AB  - being lethal.
ER  -

TY  - JOUR
AU  - Marinus, M.G.
AU  - Poteete, A.
AU  - Arraj, J.A.
TI  - Correlation of DNA adenine methylase activity with spontaneous mutability in Escherichia coli K-12.
JO  - Gene
PY  - 1984
SP  - 123
EP  - 125
VL  - 28
AB  - Using a multicopy plasmid in which the tac promoter has been placed in front of the dam gene
AB  - of Escherichia coli K-12, we show that levels of DNA adenine methylase activity are correlated
AB  - with the spontaneous mutation frequency.
ER  -

TY  - JOUR
AU  - Mark, K.-K.
AU  - Studier, F.W.
TI  - Purification of the gene 0.3 protein of bacteriophage T7, an inhibitor of the DNA restriction system of Escherichia coli.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 2573
EP  - 2578
VL  - 256
AB  - The gene 0.3 protein of bacteriophage T7 prevents the DNA restriction system of
AB  - Escherichia coli from interfering with T7 infection.  A mutant strain of T7
AB  - that greatly overproduces the 0.3 protein has been constructed and used for
AB  - purification of this protein.  The 0.3 protein was found to be extremely acidic
AB  - and can be separated from virtually all other proteins of the infected cell by
AB  - chromatography on DEAE-cellulose.  Residual contaminating proteins and nucleic
AB  - acids can be removed by gel filtration, but an even simpler final purification
AB  - is possible, because under appropriate conditions the 0.3 protein is soluble in
AB  - high concentrations of ethanol.  Thus, a simple, essentially two-step
AB  - purification can produce about 50 mg of pure 0.3 protein from 30 liters of
AB  - culture.  The purified protein appears to be a dimer of identical subunits.  As
AB  - expected from its known function during infection, the purified 0.3 protein
AB  - inhibits the nuclease and ATPase activities of partially purified EcoB, the DNA
AB  - restriction enzyme of E. coli B, but it does not interfere with several
AB  - different type II restriction endonucleases tested.  The inhibition of EcoB
AB  - appears to require stoichiometric rather than catalytic amounts of 0.3 protein.
ER  -

TY  - JOUR
AU  - Markell, J.A.
AU  - Koziol, A.G.
AU  - Lambert, D.
TI  - Draft Genome Sequence of Escherichia coli O157:H7 ATCC 35150 and a Nalidixic Acid-Resistant Mutant Derivative.
JO  - Genome Announcements
PY  - 2015
SP  - e00734
EP  - e00715
VL  - 3
AB  - Shiga toxin-producing Escherichia coli strains, occasionally isolated from food,  are of
AB  - public health importance. Here, we report on the 5.30-Mbp draft genome
AB  - sequence of E. coli O157:H7 EDL931 (strain ATCC 35150) and the 5.32-Mbp draft
AB  - genome sequence of a nalidixic acid-resistant mutant derivative used as a
AB  - distinguishable control strain in food-testing laboratories.
ER  -

TY  - JOUR
AU  - Markie, D.
AU  - Tvrdeich, G.
AU  - Hill, D.F.
AU  - Poulter, R.
TI  - The response of Type II restriction endonucleases to single base pair mismatches in heteroduplex DNA.
JO  - Proc. Univ. Otago Med. Sch.
PY  - 1986
SP  - 13
EP  - 14
VL  - 64
AB  - The Type II restriction endonucleases cleave double-stranded DNA at specific sites within
AB  - short recognition sequences and have proven invaluable in the analysis and manipulation of
AB  - genetic material.  In contrast, the Type I endonucleases, which cleave DNA non-specifically at
AB  - varying distances from their recognition sequences, have played only a minor role in modern
AB  - molecular genetics.  Factors affecting DNA recognition and cleavage have been carefully
AB  - defined.  The resistance of mismatched heteroduplex DNA to digestion was initially reported
AB  - for a Type I enzyme (EcoBI) and this has since been confirmed for a single Type II enzyme
AB  - (EcoRI).  In this paper we extend this finding to four more Type II restriction enzymes,
AB  - BamHI, AccI, KpnI and SmaI, using a novel assay for digestion of heteroduplex DNA.
ER  -

TY  - JOUR
AU  - Marks, P.
AU  - McGeehan, J.
AU  - Kneale, G.
TI  - A novel strategy for the expression and purification of the DNA methyltransferase, M.AhdI.
JO  - Protein Expr. Purif.
PY  - 2004
SP  - 236
EP  - 242
VL  - 37
AB  - Biochemical and structural studies of the methylase from the type 1 1/2 R-M system AhdI
AB  - require the ability to purify this multisubunit enzyme
AB  - in significant quantities in a soluble and active form. Several
AB  - Escherichia coli expression systems were tested for their ability to
AB  - produce the intact methylase but this could not be achieved in a simple
AB  - co-expression system. Expression experiments were optimised to produce
AB  - high yields of soluble M and S subunits as individual proteins.
AB  - Temperature and conditions of induction proved to be the most useful
AB  - factors and although purification of the S subunit was successful, an
AB  - efficient strategy for the M subunit remained elusive. A novel strategy
AB  - was developed in which individual subunits are expressed separately and
AB  - the bacterial cells mixed before lysis. This method produced a high
AB  - yield of the multi-subunit methylase when purified to homogeneity by
AB  - means of heparin and size-exclusion chromatography. It was found to be
AB  - essential, however, to remove tightly bound DNA by ammonium sulphate
AB  - precipitation in 1 M NaCl. The intact methylase can now be consistently
AB  - produced, avoiding the use of fusion proteins. The purified enzyme is
AB  - stable over long time periods, unlike the individual subunits. This
AB  - method may be of general application where the expression of
AB  - multi-subunit proteins, or indeed their individual components, is
AB  - problematic.
ER  -

TY  - JOUR
AU  - Marks, P.
AU  - McGeehan, J.
AU  - Wilson, G.
AU  - Errington, N.
AU  - Kneale, G.
TI  - Purification and characterization of a novel DNA methyltransferase, M.AhdI.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 2803
EP  - 2810
VL  - 31
AB  - We have cloned the M and S genes of the restriction-modification (R-M) system AhdI and have
AB  - purified the resulting methyltransferase to
AB  - homogeneity. M.AhdI is found to form a 170 kDa tetrameric enzyme having a
AB  - subunit stoichiometry M2S2 (where the M and S subunits are responsible for
AB  - methylation and DNA sequence specificity, respectively). Sedimentation
AB  - equilibrium experiments show that the tetrameric enzyme dissociates to
AB  - form a heterodimer at low concentration, with K(d) approximately 2 microM.
AB  - The intact (tetrameric) enzyme binds specifically to a 30 bp DNA duplex
AB  - containing the AhdI recognition sequence GACN5GTC with high affinity (K(d)
AB  - approximately 50 nM), but at low enzyme concentration the DNA binding
AB  - activity is governed by the dissociation of the tetramer into dimers,
AB  - leading to a sigmoidal DNA binding curve. In contrast, only non-specific
AB  - binding is observed if the duplex lacks the recognition sequence.
AB  - Methylation activity of the purified enzyme was assessed by its ability to
AB  - prevent restriction by the cognate endonuclease. The subunit structure of
AB  - the M.AhdI methyltransferase resembles that of type I MTases, in contrast
AB  - to the R.AhdI endonuclease which is typical of type II systems. AhdI
AB  - appears to be a novel R-M system with properties intermediate between
AB  - simple type II systems and more complex type I systems, and may represent
AB  - an intermediate in the evolution of R-M systems.
ER  -

TY  - JOUR
AU  - Marques, C.
AU  - Franceschi, C.
AU  - Collin, V.
AU  - Laurent, F.
AU  - Chatellier, S.
AU  - Forestier, C.
TI  - Genome Sequence of a Clinical Staphylococcus aureus Strain from a Prosthetic Joint Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e00198
EP  - e00116
VL  - 4
AB  - Here, we report the genome sequence ofStaphylococcus aureusLYO-S2, an isolate with sequence
AB  - type (ST) 45 that was isolated in 2001 from a prosthetic joint
AB  - infection.
ER  -

TY  - JOUR
AU  - Marques, J.M.
AU  - de Moura, V.A.
AU  - Lima, A.C.
AU  - Paixao, C.T.
AU  - Lobato, A.R.
AU  - Alves, J.T.
AU  - Guaraldi, A.L.
AU  - Folador, A.R.
AU  - Ramos, R.T.
AU  - Silva, A.
TI  - Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA06 Isolated  from a Subauricular Abscess in an Ovine Host.
JO  - Genome Announcements
PY  - 2017
SP  - e00083
EP  - e00017
VL  - 5
AB  - We report here the draft genome sequence of Corynebacterium pseudotuberculosis PA06, isolated
AB  - from a subauricular abscess in an ovine host. C.
AB  - pseudotuberculosis is a worldwide pathogen of small and large ruminants. The
AB  - genome comprises 2,320,074 bp, with a G+C content of 52.2%, 2,195 coding
AB  - sequences, 48 tRNAs, and three rRNAs.
ER  -

TY  - JOUR
AU  - Marques, L.M.
AU  - Guimaraes, A.M.
AU  - Martins, H.B.
AU  - Rezende, I.S.
AU  - Barbosa, M.S.
AU  - Campos, G.B.
AU  - do Nascimento, N.C.
AU  - Dos Santos, A.P.
AU  - Amorim, A.T.
AU  - Santos, V.M.
AU  - Messick, J.B.
AU  - Timenetsky, J.
TI  - Genome Sequence of Ureaplasma diversum Strain ATCC 49782.
JO  - Genome Announcements
PY  - 2015
SP  - e00314
EP  - e00315
VL  - 3
AB  - Here, we report the complete genome sequence of Ureaplasma diversum strain ATCC 49782. This
AB  - species is of bovine origin, having an association with reproductive
AB  - disorders in cattle, including placentitis, fetal alveolitis, abortion, and birth
AB  - of weak calves. It has a small circular chromosome of 975,425 bp.
ER  -

TY  - JOUR
AU  - Marquez, V.E.
AU  - Eritja, R.
AU  - Kelley, J.A.
AU  - Vanbemmel, D.
AU  - Christman, J.
TI  - Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (Zebularine) at the G(C)under-barGC recognition domain.
JO  - Therapeutic Oligonucleotides
PY  - 2003
SP  - 154
EP  - 164
VL  - 1002
AB  - A short oligodeoxynucleotide (ODN) with 2-(1H)-pyrimidinone at the HhaI DNA methyltransferase
AB  - target site (GCGC) is shown to induce a level of inhibition of methyl transfer and thermal
AB  - stability of the complex with the enzyme identical to that achieved with a similar ODN
AB  - substituted with 5-azacytosine. The drugs responsible for these effects-zebularine and
AB  - 5-azacytidine/2'-deoxy-5-azacytidine-are contrasted in terms of chemical stability and
AB  - possible metabolic activation by a brief structure-activit analysis.
ER  -

TY  - JOUR
AU  - Marquez, V.E.
AU  - Eritja, R.
AU  - Kelley, J.A.
AU  - Vanbemmel, D.
AU  - Christman, J.K.
TI  - Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (Zebularine) at the GCGC recognition domain.
JO  - Ann. NY Acad. Sci.
PY  - 2003
SP  - 154
EP  - 164
VL  - 1002
AB  - A short oligodeoxynucleotide (ODN) with 2-(1H)-pyrimidinone at the HhaI DNA methyltransferase
AB  - target site (GCGC) is shown to induce a level of
AB  - inhibition of methyl transfer and thermal stability of the complex with
AB  - the enzyme identical to that achieved with a similar ODN substituted with
AB  - 5-azacytosine. The drugs responsible for these effects-zebularine and
AB  - 5-azacytidine/2'-deoxy-5-azacytidine-are contrasted in terms of chemical
AB  - stability and possible metabolic activation by a brief structure-activity
AB  - analysis.
ER  -

TY  - JOUR
AU  - Marquez, V.E.
AU  - Goddard, A.
AU  - Alvarez, E.
AU  - Ford, H. Jr.
AU  - Christman, J.K.
AU  - Sheikhnejad, G.
AU  - Brank, A.
AU  - Marasco, C.J.
AU  - Suffrin, J.R.
AU  - O'Gara, M.
AU  - Cheng, X.
TI  - Oligonucleotides containing 5,6-dihydro-5-azacytosine at CpG sites can produce potent inhibition of DNA cytosine-C5-methyltransferase without covalently binding to the enzyme.
JO  - Antisense Nucleic Acid Drug Dev.
PY  - 1999
SP  - 415
EP  - 421
VL  - 9
AB  - C5-cytosine methylation of DNA at CpG sites is catalyzed by DNA cytosine-C5-methyltransferase
AB  - in both prokaryotes and eukaryotes.  The mechanism of transfer of the methyl group from the
AB  - cofactor S-adenosyl-L-methionine to the target cytosine occurs in a similar fashion in most
AB  - (if not all) C5-MTases, which share highly conserved sequence motifs in the catalytic and
AB  - AdoMet binding regions.  In mammals, the enzyme is responsible for the maintenance of
AB  - methylation patterns in the genome.  However, aberrant DNA methylation patterns are associated
AB  - with tumorigenesis and are common in cancer.
ER  -

TY  - JOUR
AU  - Marquez, V.E.
AU  - Wang, P.Y.
AU  - Nicklaus, M.C.
AU  - Maier, M.
AU  - Manoharan, M.
AU  - Christman, J.K.
AU  - Banavali, N.K.
AU  - Mackerell, A.D.
TI  - Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained  (bicyclo[3.1.0]hexane) abasic sites.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2001
SP  - 451
EP  - 459
VL  - 20
AB  - Pseudorotationally locked sugar analogues based on bicyclo[3.1.0]-hexane templates were placed
AB  - in DNA duplexes as abasic target sites in the M.HhaI recognition sequence. The binding
AB  - affinity
AB  - of the enzyme increases when the abasic site is constrained to the
AB  - South conformation and decreases when it is constrained to the North
AB  - conformation. A structural understanding of these differences is
AB  - provided.
ER  -

TY  - JOUR
AU  - Marquez-Ortiz, R.A.
AU  - Haggerty, L.
AU  - Sim, E.M.
AU  - Duarte, C.
AU  - Castro-Cardozo, B.E.
AU  - Beltran, M.
AU  - Saavedra, S.
AU  - Vanegas, N.
AU  - Escobar-Perez, J.
AU  - Petty, N.K.
TI  - First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151.
JO  - Genome Announcements
PY  - 2017
SP  - e01472
EP  - e01416
VL  - 5
AB  - Providencia rettgeri is an opportunistic bacterial pathogen of clinical significance due to
AB  - its association with urinary tract infections and multidrug
AB  - resistance. Here, we report the first complete genome sequence of P. rettgeri The
AB  - genome of strain RB151 consists of a 4.8-Mbp chromosome and a 108-kbp
AB  - blaNDM-1-positive plasmid.
ER  -

TY  - JOUR
AU  - Marra, A.
AU  - Shuman, H.A.
TI  - Isolation of a Legionella pneumophila restriction mutant with increased ability to act as a recipient in heterospecific matings.
JO  - J. Bacteriol.
PY  - 1989
SP  - 2238
EP  - 2240
VL  - 171
AB  - The ability of Legionella pneumophila to act as a recipient of IncP and IncQ
AB  - plasmids in matings with Escherichia coli varies widely from strain to strain.
AB  - We found that the low efficiency of mating of the Philadelphia-1 strain is due
AB  - to a type II restriction-modification system, and we isolated and characterized
AB  - a Philadelphia-1 mutant that lacks the restriction enzyme activity.
ER  -

TY  - JOUR
AU  - Marrero, R.
AU  - Welkos, S.L.
TI  - The transformation frequency of plasmids into Bacillus anthracis is affected by adenine methylation.
JO  - Gene
PY  - 1995
SP  - 75
EP  - 78
VL  - 152
AB  - Plasmids pLTV1 and pHV33, capable of replicating in both Gram+ and Gram- bacterial hosts
AB  - (shuttle vectors), when derived from the Escherichia coli strain HB101, were inactive in an
AB  - electro-transformation assay employing the Bacillus anthracis strains delta Ames-1 and delta
AB  - V1B-1 as recipients.  The same plasmids isolated from the DNA methyltransferase
AB  - (MTase)-deficient E. coli strain GM2929 (dam,dcm), were able to transform the B. anthracis
AB  - strains at a frequency of 10/2-10/3 transformants/ug of plasmid DNA.  Efficient transformation
AB  - was also obtained when the plasmids were propagated in strains of B. subtilis 168 (10/2-10/4
AB  - transformants/ug of plasmid DNA).  The B. subtilis strains used are known to harbor
AB  - restriction/modification systems that recognize cytosine as a target for methylation.  In
AB  - contrast, no adenine methylation activities have been reported for these strains.  The data
AB  - presented indicate that DNA containing methylated adenine residues is restricted in the B.
AB  - anthracis strains studied here, resulting in decreased plasmid DNA-mediated transformation
AB  - frequencies.  This inhibition could be alleviated by propagating plasmid species in
AB  - MTase-deficient (dam) strains of E. coli or B. subtilis 168, before their introduction into
AB  - strains of B. anthracis.
ER  -

TY  - JOUR
AU  - Marsan, D.
AU  - Wommack, K.E.
AU  - Ravel, J.
AU  - Chen, F.
TI  - Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary.
JO  - Genome Announcements
PY  - 2014
SP  - e01111
EP  - e01113
VL  - 2
AB  - Here, we report the draft genome sequence of the estuarine Synechococcus sp. strain CB0101.
AB  - The genomics information of this strain will facilitate the study
AB  - of the poorly understood Synechococcus subcluster 5.2 and how this strain is
AB  - capable of thriving in a dynamic estuarine system, such as the Chesapeake Bay.
ER  -

TY  - JOUR
AU  - Marsh, J.W.
AU  - Krauland, M.G.
AU  - Nelson, J.S.
AU  - Schlackman, J.L.
AU  - Brooks, A.M.
AU  - Pasculle, A.W.
AU  - Shutt, K.A.
AU  - Doi, Y.
AU  - Querry, A.M.
AU  - Muto, C.A.
AU  - Harrison, L.H.
TI  - Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae.
JO  - PLoS ONE
PY  - 2015
SP  - E0144310
EP  - E0144310
VL  - 10
AB  - Increased incidence of infections due to Klebsiella pneumoniae carbapenemase
AB  - (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients
AB  - undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single
AB  - hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing,
AB  - extended-spectrum beta-lactamase (ESBL)-producing Kp in cultures from 2
AB  - endoscopes. Genotyping was performed on patient and endoscope isolates to
AB  - characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp
AB  - isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel
AB  - electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2
AB  - endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding
AB  - plasmids were characterized by single molecule, real-time sequencing. Plasmid
AB  - diversity was assessed by endonuclease digestion. Genomic and epidemiologic data
AB  - were used in conjunction to investigate the outbreak source. Two clusters of Kp
AB  - patient isolates were genetically related to endoscope isolates by PFGE. A subset
AB  - of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a
AB  - possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates
AB  - supported ERCP as a potential source of transmission. Differences in gene content
AB  - defined 5 ST258 subclades and identified 2 of the subclades as
AB  - outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track
AB  - one endoscope-associated ST258 subclade. WGS demonstrated high genetic
AB  - relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated
AB  - transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak
AB  - from endemic ST258 populations and assisted with the molecular epidemiologic
AB  - investigation of an extended KPC-Kp outbreak.
ER  -

TY  - JOUR
AU  - Marshall, J.J.
AU  - Gowers, D.M.
AU  - Halford, S.E.
TI  - Restriction Endonucleases that Bridge and Excise Two Recognition Sites from DNA.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 419
EP  - 431
VL  - 367
AB  - Most restriction endonucleases bridge two target sites before cleaving DNA: examples include
AB  - all of the translocating Type I and Type III
AB  - systems, and many Type II nucleases acting at their sites. A subset of
AB  - Type II enzymes, the IIB systems, recognise bipartite sequences, like Type
AB  - I sites, but cut specified phosphodiester bonds near their sites, like
AB  - Type IIS enzymes. However, they make two double-strand breaks, one either
AB  - side of the site, to release the recognition sequence on a short DNA
AB  - fragment; 34 bp long in the case of the archetype, BcgI. It has been
AB  - suggested that BcgI needs to interact with two recognition sites to cleave
AB  - DNA but whether this is a general requirement for Type IIB enzymes had yet
AB  - to be established. Ten Type IIB nucleases were tested against DNA
AB  - substrates with one or two copies of the requisite sequences. With one
AB  - exception, they all bridged two sites before cutting the DNA, usually in
AB  - concerted reactions at both sites. The sites were ideally positioned in
AB  - cis rather than in trans and were bridged through 3-D space, like Type II
AB  - enzymes, rather than along the 1-D contour of the DNA, as seen with Type I
AB  - enzymes. The standard mode of action for the restriction enzymes that
AB  - excise their recognition sites from DNA thus involves concurrent action at
AB  - two DNA sites.
ER  -

TY  - JOUR
AU  - Marshall, J.J.
AU  - Smith, R.M.
AU  - Ganguly, S.
AU  - Halford, S.E.
TI  - Concerted action at eight phosphodiester bonds by the BcgI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 7630
EP  - 7640
VL  - 39
AB  - The BcgI endonuclease exemplifies a subset of restriction enzymes, the Type IIB class, which
AB  - make two double-strand breaks (DSBs) at each copy of
AB  - their recognition sequence, one either side of the site, to excise the
AB  - sequence from the remainder of the DNA. In this study, we show that BcgI
AB  - is essentially inactive when bound to a single site and that to cleave a
AB  - DNA with one copy of its recognition sequence, it has to act in trans,
AB  - bridging two separate DNA molecules. We also show that BcgI makes the two
AB  - DSBs at an individual site in a highly concerted manner. Intermediates cut
AB  - on one side of the site do not accumulate during the course of the
AB  - reaction: instead, the DNA is converted straight to the final products cut
AB  - on both sides. On DNA with two sites, BcgI bridges the sites in cis and
AB  - then generally proceeds to cut both strands on both sides of both sites
AB  - without leaving the DNA. The BcgI restriction enzyme can thus excise two
AB  - DNA segments together, by cleaving eight phosphodiester bonds within a
AB  - single-DNA binding event.
ER  -

TY  - JOUR
AU  - Marshall, J.J.T.
AU  - Halford, S.E.
TI  - The Type IIB restriction endonucleases.
JO  - Biochem. Soc. Trans.
PY  - 2010
SP  - 410
EP  - 416
VL  - 38
AB  - The endonucleases from the Type IIB restriction-modification systems differ from all other
AB  - restriction enzymes. The Type IIB enzymes cleave
AB  - both DNA strands at specified locations distant from their recognition
AB  - sequences, like Type IIS nucleases, but they are unique in that they do
AB  - so on both sides of the site, to liberate the site from the remainder
AB  - of the DNA on a short duplex. The fact that these enzymes cut DNA at
AB  - specific locations mark them as Type II systems, as opposed to the Type
AB  - I enzymes that cut DNA randomly, but in terms of gene organization and
AB  - protein assembly, most Type IIB restriction-modification systems have
AB  - more in common with Type I than with other Type II systems. Our current
AB  - knowledge of the Type IIB systems is reviewed in the present paper.
ER  -

TY  - JOUR
AU  - Marshall, K.T.
AU  - Morris, R.M.
TI  - Genome Sequence of 'Candidatus Thioglobus singularis' Strain PS1, a Mixotroph from the SUP05 Clade of Marine Gammaproteobacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e01155
EP  - e01115
VL  - 3
AB  - Mixotrophic marine bacteria from the SUP05 clade are ubiquitous in the ocean. Here, we
AB  - announce the complete genome sequence of 'Candidatus Thioglobus singularis' strain PS1, the
AB  - first cultured mixotrophic representative from the SUP05 clade.
ER  -

TY  - JOUR
AU  - Marshall, P.
AU  - Davis, T.B.
AU  - Lemieux, C.
TI  - The I-CeuI endonuclease: purification and potential role in the evolution of Chlamydomonas group I introns.
JO  - Eur. J. Biochem.
PY  - 1994
SP  - 855
EP  - 859
VL  - 220
AB  - During genetic crosses between the interfertile green algae Chlamydomonas eugametos and
AB  - Chlamydomonas moewusii, the I-CeuI endonuclease encoded by the fifth group I intron (CeLSU.5)
AB  - in the C. eugametos chloroplast large subunit rRNA gene mediates the mobility of this intron
AB  - by introducing a double-strand break near the insertion site of the intron in the
AB  - corresponding C. moewusii intronless allele.  To characterize the biochemical properties of
AB  - this endonuclease, we have purified I-CeuI and determined the optimal reaction conditions for
AB  - cleavage.  I-CeuI activity is maximal at 50oC, pH 10.0, 2.5 mM MgCl2 and in the absence of
AB  - NaCl.  Unlike the well-characterized I-SceI endonuclease, I-CeuI remains stable following
AB  - preincubation in the absence of substrate.  We discuss the role that homing endonucleases may
AB  - have played in the evolution of Chlamydomonas chloroplast group I introns.
ER  -

TY  - JOUR
AU  - Marshall, P.
AU  - Lemieux, C.
TI  - The I-CeuI endonuclease recognizes a sequence of 19 base pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit rRNA gene.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6401
EP  - 6407
VL  - 20
AB  - The I-CeuI endonuclease is a member of the growing family of homing endonucleases that
AB  - catalyse mobility of group I introns by making a double-strand break at the homing site of
AB  - these introns in cognate intronless alleles during genetics crosses. In a previous study, we
AB  - have shown that a short DNA fragment of 26 bp, encompassing the homing site of the fifth
AB  - intron in the Chlamydomonas eugametos chloroplast large subunit rRNA gene (Ce LSU.5), was
AB  - sufficient for I-CeuI recognition and cleavage. Here, we report the recognition sequence of
AB  - the I-CeuI endonuclease, as determined by random mutagenesis of nucleotide positions adjacent
AB  - to the I-CeuI cleavage site. Single-base substitutions that completely abolish endonuclease
AB  - activity delimit a 15-bp sequence whereas those that reduce the cleavage rate define a 19-bp
AB  - sequence that extends from position -7 to position +12 with respect to the Ce LSU.5 intron
AB  - insertion site. As the other homing endonucleases that have been studied so far, the I-CeuI
AB  - endonuclease recognizes a non-symmetric degenerate sequence. The top strand of the recognition
AB  - sequence is preferred for I-CeuI cleavage and the bottom strand most likely determines the
AB  - rate of double-strand breaks.
ER  -

TY  - JOUR
AU  - Marshall, P.
AU  - Lemieux, C.
TI  - Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos.
JO  - Gene
PY  - 1991
SP  - 241
EP  - 245
VL  - 104
AB  - The fifth group-I intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas
AB  - eugametos (CeLSU.5) is mobile during interspecific crosses between C. eugametos and
AB  - Chlamydomonas moewusii. Like the six other mobile introns that have been well characterized so
AB  - far, CeLSU.5 contains a long open reading frame (ceuIR) coding for a site-specific
AB  - endonuclease (I-CeuI) that cleaves the C. moewsuii intronless gene in the vicinity of the
AB  - intron-insertion site. This stimulates gap repair and mediates efficient transfer of the
AB  - intron at its cognate site. By expressing the ceuIR gene in the Escherichia coli vectors
AB  - pKK233-2 and pTRC-99A, we recently demonstrated that the endonuclease is highly toxic to E.
AB  - coli. To eliminate this problem and characterize the cleavage pattern and recognition sequence
AB  - of the I-CeuI endonuclease, we have expressed the ceuIR gene in E. coli under the control of a
AB  - bacteriophage T7 promoter in a tightly regulated M13 system, and developed an in vitro system
AB  - to assay partially purified I-CeuI activity. This allowed us to determine that I-CeuI
AB  - recognizes a sequence of less than 26 bp centered around the insertion site and produces a
AB  - staggered cut 5 bp downstream from this site, yielding 4-nucleotide (CTAA), 3'-OH overhangs.
ER  -

TY  - JOUR
AU  - Marston, M.F.
AU  - Pierciey, F.J. Jr.
AU  - Shepard, A.
AU  - Gearin, G.
AU  - Qi, J.
AU  - Yandava, C.
AU  - Schuster, S.C.
AU  - Henn, M.R.
AU  - Martiny, J.B.
TI  - Rapid diversification of coevolving marine Synechococcus and a virus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 4544
EP  - 4549
VL  - 109
AB  - Marine viruses impose a heavy mortality on their host bacteria, whereas at the
AB  - same time the degree of viral resistance in marine bacteria appears to be high.
AB  - Antagonistic coevolution-the reciprocal evolutionary change of interacting
AB  - species-might reconcile these observations, if it leads to rapid and dynamic
AB  - levels of viral resistance. Here we demonstrate the potential for extensive
AB  - antagonistic coevolution between the ecologically important marine cyanobacterium
AB  - Synechococcus and a lytic virus. In a 6-mo-long replicated chemostat experiment,
AB  - Synechococcus sp. WH7803 and the virus (RIM8) underwent multiple coevolutionary
AB  - cycles, leading to the rapid diversification of both host and virus. Over the
AB  - course of the experiment, we detected between 4 and 13 newly evolved viral
AB  - phenotypes (differing in host range) and between 4 and 11 newly evolved
AB  - Synechococcus phenotypes (differing in viral resistance) in each chemostat.
AB  - Genomic analysis of isolates identified several candidate genes in both the host
AB  - and virus that might influence their interactions. Notably, none of the viral
AB  - candidates were tail fiber genes, thought to be the primary determinants of host
AB  - range in tailed bacteriophages, highlighting the difficulty in generalizing
AB  - results from bacteriophage infecting gamma-Proteobacteria. Finally, we show that
AB  - pairwise virus-host coevolution may have broader community consequences;
AB  - coevolution in the chemostat altered the sensitivity of Synechoccocus to a
AB  - diverse suite of viruses, as well as the virus' ability to infect additional
AB  - Synechococcus strains. Our results indicate that rapid coevolution may contribute
AB  - to the generation and maintenance of Synechococcus and virus diversity and
AB  - thereby influence viral-mediated mortality of these key marine bacteria.
ER  -

TY  - JOUR
AU  - Marti, R.
AU  - Hagens, S.
AU  - Loessner, M.J.
AU  - Klumpp, J.
TI  - Genome Sequence of Salmonella bongori Strain N268-08.
JO  - Genome Announcements
PY  - 2013
SP  - e01018
EP  - e01013
VL  - 1
AB  - Volume 1, no. 4, e00580-13, 2013. Page 1: The article title should read as given above. After
AB  - the publication of this article, we were
AB  - made aware of the fact that strain N268-08 was not isolated from a clinical sample.
ER  -

TY  - JOUR
AU  - Marti, R.
AU  - Hagens, S.
AU  - Loessner, M.J.
AU  - Klumpp, J.
TI  - Genome Sequence of Salmonella bongori Strain N268-08, a Rare Clinical Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e00580
EP  - e00513
VL  - 1
AB  - Salmonella bongori is a close relative of the highly virulent members of S. enterica
AB  - subspecies enterica, encompassing more than 2,500 serovars, most of
AB  - which cause human salmonellosis, one of the leading food-borne illnesses. S.
AB  - bongori is only very rarely implicated in infections. We here present the
AB  - sequence of a clinical isolate from Switzerland, S. bongori strain N268-08.
ER  -

TY  - JOUR
AU  - Marti, R.
AU  - Schmid, M.
AU  - Kulli, S.
AU  - Schneeberger, K.
AU  - Naskova, J.
AU  - Knochel, S.
AU  - Ahrens, C.H.
AU  - Hummerjohann, J.
TI  - Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845.
JO  - Appl. Environ. Microbiol.
PY  - 2017
SP  - e00628
EP  - e00617
VL  - 83
AB  - We tested the biofilm formation potential of 30 heat-resistant and 6 heat-sensitive
AB  - Escherichia coli dairy isolates. Production of curli and
AB  - cellulose, static biofilm formation on polystyrene (PS) and stainless steel
AB  - surfaces, biofilm formation under dynamic conditions (Bioflux), and initial
AB  - adhesion rates (IAR) were evaluated. Biofilm formation varied greatly between
AB  - strains, media, and assays. Our results highlight the importance of the
AB  - experimental setup in determining biofilm formation under conditions of interest,
AB  - as correlation between different assays was often not a given. The
AB  - heat-resistant, multidrug-resistant (MDR) strain FAM21845 showed the strongest
AB  - biofilm formation on PS and the highest IAR and was the only strain that formed
AB  - significant biofilms on stainless steel under conditions relevant to the dairy
AB  - industry, and it was therefore fully sequenced. Its chromosome is 4.9 Mb long,
AB  - and it harbors a total of five plasmids (147.2, 54.2, 5.8, 2.5, and 1.9 kb). The
AB  - strain carries a broad range of genes relevant to antimicrobial resistance and
AB  - biofilm formation, including some on its two large conjugative plasmids, as
AB  - demonstrated in plate mating assays.IMPORTANCE In biofilms, cells are embedded in
AB  - an extracellular matrix that protects them from stresses, such as UV radiation,
AB  - osmotic shock, desiccation, antibiotics, and predation. Biofilm formation is a
AB  - major bacterial persistence factor of great concern in the clinic and the food
AB  - industry. Many tested strains formed strong biofilms, and especially strains such
AB  - as the heat-resistant, MDR strain FAM21845 may pose a serious issue for food
AB  - production. Strong biofilm formation combined with diverse resistances (some
AB  - encoded on conjugative plasmids) may allow for increased persistence,
AB  - coselection, and possible transfer of these resistance factors. Horizontal gene
AB  - transfer may conceivably occur in the food production setting or the
AB  - gastrointestinal tract after consumption.
ER  -

TY  - JOUR
AU  - Marti, R.
AU  - Stephan, R.
AU  - Klumpp, J.
AU  - Nuesch-Inderbinen, M.
AU  - Hummerjohann, J.
AU  - Bagutti, C.
AU  - Zurfluh, K.
TI  - Draft Genome Sequence of Klebsiella pneumoniae 704SK6, an OXA-48- and CTX-M-15-Encoding Wastewater Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00831
EP  - e00817
VL  - 5
AB  - The Swiss wastewater isolate Klebsiella pneumoniae 704SK6, encoding OXA-48 and CTX-M-15
AB  - beta-lactamases, was fully sequenced. The assembly resulted in an open
AB  - chromosome of 5,208,104 bp in size (G+C content, 57.6%) and four closed plasmid
AB  - sequences of 209,651, 197,670, 65,998, and 63,605 bp in size.
ER  -

TY  - JOUR
AU  - Marti, R.
AU  - Stephan, R.
AU  - Klumpp, J.
AU  - Nuesch-Inderbinen, M.
AU  - Hummerjohann, J.
AU  - Bagutti, C.
AU  - Zurfluh, K.
TI  - Complete Genome Sequence of Enterobacter cloacae 704SK10, an OXA-48-Encoding Wastewater Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00830
EP  - e00817
VL  - 5
AB  - Here we present the complete genome sequence of Enterobacter cloacae 704SK10, a Swiss
AB  - wastewater isolate encoding an OXA-48 carbapenemase. Assembly resulted in
AB  - closed sequences of the 4,876,946-bp chromosome, a 111,184-bp IncF plasmid, and
AB  - an OXA-48-encoding IncL plasmid (63,458 bp) nearly identical to the previously
AB  - described plasmid pOXA-48.
ER  -

TY  - JOUR
AU  - Martienssen, R.
TI  - Chipping away at chromatin.
JO  - Nat. Genet.
PY  - 2001
SP  - 240
EP  - 241
VL  - 27
AB  - When DNA-binding proteins are tethered to dam methylase from Escherichia coli. adenine
AB  - methylation is directed to eukaryotic target
AB  - sites in vivo. Hybridization of methylated DNA to microarrays allows
AB  - binding sites to be displayed genome-wide, providing a versatile
AB  - alternative to chromatin immunoprecipitation.
ER  -

TY  - JOUR
AU  - Martienssen, R.A.
AU  - Colot, V.
TI  - DNA methylation and epigenetic inheritance in plants and filamentous fungi.
JO  - Science
PY  - 2001
SP  - 1070
EP  - 1074
VL  - 293
AB  - Plants and filamentous fungi share with mammals enzymes responsible for DNA methylation. In
AB  - these organisms, DNA methylation is associated with gene silencing and transposon control.
AB  - However, plants and fungi differ from mammals in the genomic distribution, sequence
AB  - specificity, and heritability of methylation. We consider the role that transposons play in
AB  - establishing methylation patterns and the epigenetic consequences of their perturbation.
ER  -

TY  - JOUR
AU  - Martienssen, R.A.
AU  - Richards, E.J.
TI  - DNA methylation in eukaryotes.
JO  - Curr. Opin. Genet. Dev.
PY  - 1995
SP  - 234
EP  - 242
VL  - 5
AB  - Recent advances have expanded our understanding of the processes underlying the establishment,
AB  - maintenance, and elaboration of DNA methylation patterns in eukaryotes.  The functional
AB  - significance of DNA methylation is sought in a comparison of results on a variety of
AB  - epigenetic phenomena in different eukaryotes.  The recent development of DNA methylation
AB  - mutants in mice, Neurospora, and Arabadopsis will allow traditional genetic dissection to be
AB  - applied to long-standing problems regarding the function and regulation of eukaryotic DNA
AB  - methylation.  Although methylation appears to be important for maintenance of different
AB  - epigenetic states, the mechanism that establishes these states is likely to involve additional
AB  - processes.
ER  -

TY  - JOUR
AU  - Martin, A.M.
AU  - Horton, N.C.
AU  - Luseti, S.
AU  - Reich, N.O.
AU  - Perona, J.J.
TI  - Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.
JO  - Biochemistry
PY  - 1999
SP  - 8430
EP  - 8439
VL  - 38
AB  - Measurements of binding equilibria of EcoRV endonuclease to DNA, for a series of base-analogue
AB  - substrates, demonstrate that expression of sequence selectivity is strongly enhanced by the
AB  - presence of Ca2+ ions. Binding constants were determined for short duplex
AB  - oligodeoxynucleotides containing the cognate DNA site, three cleavable noncognate sites, and a
AB  - fully nonspecific site. At pH 7.5 and 100 mM NaCl, the full range of specificity from the
AB  - specific (tightest binding) to nonspecific (weakest binding) sites is 0.9 kcal/mol in the
AB  - absence of metal ions and 5.8 kcal/mol in the presence of Ca2+. Precise determination of
AB  - binding affinities in the presence of the active Mg2+ cofactor was found to be possible for
AB  - substrates retaining up to 1.6% of wild-type activity, as determined by the rate of phosphoryl
AB  - transfer. These measurements show that Ca2+ is a near-perfect analogue for Mg2+ in binding
AB  - reactions of the wild-type enzyme with DNA base-analogue substrates, as it provides identical
AB  - DeltaDeltaG degrees bind values among the cleavable noncognate sites. Equilibrium dissociation
AB  - constants of wild-type and base-analogue sites were also measured for the weakly active EcoRV
AB  - mutant K38A, in the presence of either Mg2+ or Ca2+. In this case, Ca2+ allows expression of a
AB  - greater degree of specificity than does Mg2+. DeltaDeltaG degrees/bind values of K38A toward
AB  - specific versus nonspecific sites are 6.1 kcal/mol with Ca2+ and 3.9 kcal/mol with Mg2+,
AB  - perhaps reflecting metal-specific conformational changes in the ground-state ternary
AB  - complexes. The enhancement of binding specificity provided by divalent metal ions is likely to
AB  - be general to many restriction endonucleases and other metal-dependent nucleic acid-modifying
AB  - enzymes. These results strongly suggest that measurements of DNA binding affinities for EcoRV,
AB  - and likely for many other restriction endonucleases, should be performed in the presence of
AB  - divalent metal ions.
ER  -

TY  - JOUR
AU  - Martin, A.M.
AU  - Sam, M.D.
AU  - Reich, N.O.
AU  - Perona, J.J.
TI  - Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.
JO  - Nat. Struct. Biol.
PY  - 1999
SP  - 269
EP  - 277
VL  - 6
AB  - Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the
AB  - center TA step occurs solely via hydrophobic interaction with thymine methyl groups.
AB  - Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that
AB  - direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal
AB  - mol(-1) arising from indirect readout. Crystal structures of several base analog complexes
AB  - show that the major-groove hydrophobic contacts are crucial to forming required divalent
AB  - metal-binding sites, and that indirect readout operates in part through the sequence-dependent
AB  - free-energy cost of unstacking the center base-pair step of the DNA.
ER  -

TY  - JOUR
AU  - Martin, J.L.
AU  - McMillan, F.M.
TI  - SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold.
JO  - Curr. Opin. Struct. Biol.
PY  - 2002
SP  - 783
EP  - 793
VL  - 12
AB  - The S-adenosylmethionine-dependent methyltransferase enzymes share little sequence identity,
AB  - but incorporate a highly conserved structural
AB  - fold. Surprisingly, residues that bind the common cofactor are poorly
AB  - conserved, although the binding site is localised to the same region of
AB  - the fold. The substrate-binding region of the fold varies enormously.
AB  - Over the past two years, there has been a significant increase in the
AB  - number of structures that are known to incorporate this fold, including
AB  - several uncharacterised proteins and two proteins that lack
AB  - methyltransferase activity.
ER  -

TY  - JOUR
AU  - Martin, P.
AU  - Boulukos, K.E.
AU  - Pognonec, P.
TI  - REtools: a laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance.
JO  - BMC Bioinformatics
PY  - 2006
SP  - 98
EP  - 98
VL  - 7
AB  - ABSTRACT : BACKGROUND : Restriction enzymes are one of the everyday tools used in molecular
AB  - biology. The continuously expanding panel of known
AB  - restriction enzymes (several thousands) renders their optimal use
AB  - virtually impossible without computerized assistance. Several
AB  - manufacturers propose on-line sites that assist scientists in their
AB  - restriction enzyme work, however, none of these sites meet all the actual
AB  - needs of laboratory workers, and they do not take into account the enzymes
AB  - actually present in one's own laboratory. RESULTS : Using FileMaker Pro,
AB  - we developed a stand-alone application which can run on both PCs and
AB  - Macintoshes. We called it REtools, for Restriction Enzyme tools. This
AB  - program, which references all currently known enzymes (>3500), permits the
AB  - creation and update of a personalized list of restriction enzymes actually
AB  - available in one's own laboratory. Upon opening the program, scientists
AB  - will be presented with a user friendly interface that will direct them to
AB  - different menus, each one corresponding to different situations that
AB  - restriction enzyme users commonly encounter. We particularly emphasized
AB  - the ease of use to make REtools a solution that laboratory members would
AB  - actually want to use. CONCLUSION : REtools, a user friendly and easily
AB  - customized program to organize any laboratory enzyme stock, brings a
AB  - software solution that will make restriction enzyme use and reaction
AB  - condition determination straightforward and efficient. The usually
AB  - unexplored potential of isoschizomers also becomes accessible to all,
AB  - since REtools proposes all possible enzymes similar to the one(s) chosen
AB  - by the user. Finally, many of the commonly overlooked subtleties of
AB  - restriction enzyme work, such as methylation requirement, unusual reaction
AB  - conditions, or the number of flanking bases required for cleavage, are
AB  - automatically provided by REtools.
ER  -

TY  - JOUR
AU  - Martin, R.N.A.
AU  - McGeehan, J.E.
AU  - Ball, N.J.
AU  - Streeter, S.D.
AU  - Thresh, S.J.
AU  - Kneale, G.G.
TI  - Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2013
SP  - 962
EP  - 966
VL  - 69
AB  - The controller protein of the type II restriction-modification (RM) system Esp1396I binds to
AB  - three distinct DNA operator sequences upstream
AB  - of the methyltransferase and endonuclease genes in order to regulate
AB  - their expression. Previous biophysical and crystallographic studies
AB  - have shown molecular details of how the controller protein binds to the
AB  - operator sites with very different affinities. Here, two protein-DNA
AB  - co-crystal structures containing portions of unbound DNA from native
AB  - operator sites are reported. The DNA in both complexes shows
AB  - significant distortion in the region between the conserved symmetric
AB  - sequences, similar to that of a DNA duplex when bound by the controller
AB  - protein (C-protein), indicating that the naked DNA has an intrinsic
AB  - tendency to bend when not bound to the C-protein. Moreover, the width
AB  - of the major groove of the DNA adjacent to a bound C-protein dimer is
AB  - observed to be significantly increased, supporting the idea that this
AB  - DNA distortion contributes to the substantial cooperativity found when
AB  - a second C-protein dimer binds to the operator to form the tetrameric
AB  - repression complex.
ER  -

TY  - JOUR
AU  - Martin, R.N.A.
AU  - McGeehan, J.E.
AU  - Kneale, G.
TI  - Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I.
JO  - PLoS ONE
PY  - 2014
SP  - e98365
EP  - e98365
VL  - 9
AB  - Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic
AB  - activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation
AB  - and DNA restriction. These two activities are tightly regulated to prevent over-methylation or
AB  - auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional
AB  - regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All
AB  - high-resolution structures of C-protein/DNA-protein complexes solved to date relate to
AB  - C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or
AB  - the phosphate backbone could be observed. Here we present both structural and DNA binding data
AB  - for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate
AB  - that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding
AB  - affinity than mutations to those residues that bind directly to the bases (T36, R46), and the
AB  - contributions of each side chain to the binding energies are compared. High-resolution X-ray
AB  - crystal structures of the mutant and native proteins showed that the fold of the proteins was
AB  - unaffected by the mutations, but also revealed variation in the flexible loop conformations
AB  - associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA
AB  - bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA
AB  - complex by X-ray crystallography to allow us to directly compare the structure of the DNA in
AB  - the mutant and native complexes.
ER  -

TY  - JOUR
AU  - Martin, V.
AU  - Cardenas, N.
AU  - Jimenez, E.
AU  - Maldonado, A.
AU  - Rodriguez, J.M.
AU  - Fernandez, L.
TI  - Genome Sequence of Lactobacillus gastricus PS3, a Strain Isolated from Human Milk.
JO  - Genome Announcements
PY  - 2013
SP  - e00489
EP  - e00413
VL  - 1
AB  - Lactobacillus gastricus is a mostly unknown lactobacilli species associated with  mucosal
AB  - surfaces. We present the draft annotated genome sequence of L. gastricus
AB  - strain PS3, isolated from a human milk sample, to provide new insights into its
AB  - biology and to characterize those genes related to advantageous technological and
AB  - beneficial properties.
ER  -

TY  - JOUR
AU  - Martin, V.
AU  - Maldonado-Barragan, A.
AU  - Jimenez, E.
AU  - Ruas-Madiedo, P.
AU  - Fernandez, L.
AU  - Rodriguez, J.M.
TI  - Complete Genome Sequence of Streptococcus salivarius PS4, a Strain Isolated from  Human Milk.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4466
EP  - 4467
VL  - 194
AB  - Streptococcus salivarius is a commensal species commonly found in the human oropharyngeal
AB  - tract. Some strains of this species have been developed for use as
AB  - oral probiotics, while others have been associated with a variety of
AB  - opportunistic human infections. Here, we report the complete sequence of strain
AB  - PS4, which was isolated from breast milk of a healthy woman.
ER  -

TY  - JOUR
AU  - Martin-Cuadrado, A.B.
AU  - Lopez-Garcia, P.
AU  - Alba, J.C.
AU  - Moreira, D.
AU  - Monticelli, L.
AU  - Strittmatter, A.
AU  - Gottschalk, G.
AU  - Rodriguez-Valera, F.
TI  - Metagenomics of the deep mediterranean, a warm bathypelagic habitat.
JO  - PLoS ONE
PY  - 2007
SP  - e914
EP  - e914
VL  - 2
AB  - BACKGROUND: Metagenomics is emerging as a powerful method to study the
AB  - function and physiology of the unexplored microbial biosphere, and is
AB  - causing us to re-evaluate basic precepts of microbial ecology and
AB  - evolution. Most marine metagenomic analyses have been nearly exclusively
AB  - devoted to photic waters. METHODOLOGY/PRINCIPAL FINDINGS: We constructed a
AB  - metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which
AB  - is much warmer (approximately 14 degrees C) than waters of similar depth
AB  - in open oceans (approximately 2 degrees C). We analyzed the library both
AB  - by phylogenetic screening based on 16S rRNA gene amplification from clone
AB  - pools and by sequencing both insert extremities of ca. 5,000 fosmids.
AB  - Genome recruitment strategies showed that the majority of high scoring
AB  - pairs corresponded to genomes from Rhizobiales within the
AB  - Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria,
AB  - Chloroflexi and Gammaproteobacteria. We have found a community structure
AB  - similar to that found in the aphotic zone of the Pacific. However, the
AB  - similarities were significantly higher to the mesopelagic (500-700 m deep)
AB  - in the Pacific than to the single 4000 m deep sample studied at this
AB  - location. Metabolic genes were mostly related to catabolism, transport and
AB  - degradation of complex organic molecules, in agreement with a prevalent
AB  - heterotrophic lifestyle for deep-sea microbes. However, we observed a high
AB  - percentage of genes encoding dehydrogenases and, among them, cox genes,
AB  - suggesting that aerobic carbon monoxide oxidation may be important in the
AB  - deep ocean as an additional energy source. CONCLUSIONS/SIGNIFICANCE: The
AB  - comparison of metagenomic libraries from the deep Mediterranean and the
AB  - Pacific ALOHA water column showed that bathypelagic Mediterranean
AB  - communities resemble more mesopelagic communities in the Pacific, and
AB  - suggests that, in the absence of light, temperature is a major stratifying
AB  - factor in the oceanic water column, overriding pressure at least over 4000
AB  - m deep. Several chemolithotrophic metabolic pathways could supplement
AB  - organic matter degradation in this most depleted habitat.
ER  -

TY  - JOUR
AU  - Martin-Cuadrado, A.B.
AU  - Rodriguez-Valera, F.
AU  - Moreira, D.
AU  - Alba, J.C.
AU  - Ivars-Martinez, E.
AU  - Henn, M.R.
AU  - Talla, E.
AU  - Lopez-Garcia, P.
TI  - Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions.
JO  - ISME J.
PY  - 2008
SP  - 865
EP  - 886
VL  - 2
AB  - Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite
AB  - their obvious ecological importance, little is known about them. Metagenomic analyses of large
AB  - genome fragments allow access to both gene content and genome structure from single
AB  - individuals of these cultivation-reluctant organisms. We present the comparative analysis of
AB  - 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic
AB  - libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South
AB  - Atlantic, Antarctic Polar Front,
AB  - Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent
AB  - archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones
AB  - from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we
AB  - analysed
AB  - clones that had identical or nearly identical 16S rRNA genes and that were retrieved from
AB  - distant geographical locations, that is, that defined pan-oceanic operational taxonomic units
AB  - (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes
AB  - involved in
AB  - carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could
AB  - confirm the idea that these are mixotrophic. A two-component system resembling that found in
AB  - ammoniaoxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic
AB  - respiratory
AB  - chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high,
AB  - and recombination and gene shuffling extensive within and between OTUs in Group I
AB  - Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II
AB  - Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota
AB  - and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant
AB  - genome-shaping forces. These observations, along with variations in GC content, led us to
AB  - hypothesize that the two groups of organisms have fundamentally different lifestyles.
ER  -

TY  - JOUR
AU  - Martin-Laurent, F.
AU  - Marti, R.
AU  - Waglechner, N.
AU  - Wright, G.D.
AU  - Topp, E.
TI  - Draft Genome Sequence of the Sulfonamide Antibiotic-Degrading Microbacterium sp.  Strain C448.
JO  - Genome Announcements
PY  - 2014
SP  - e01113
EP  - e01113
VL  - 2
AB  - We report the draft genome sequence of Microbacterium sp. strain C448, isolated from
AB  - agricultural soil with a decade of exposure to veterinary antibiotics on the
AB  - basis of using sulfamethazine and other antibiotics as the sole sources of
AB  - carbon. The genome sequence revealed that strain C448 harbors several antibiotic
AB  - resistance genes, including sulI.
ER  -

TY  - JOUR
AU  - Martineau, C.
AU  - Villeneuve, C.
AU  - Mauffrey, F.
AU  - Villemur, R.
TI  - Complete Genome Sequence of Hyphomicrobium nitrativorans Strain NL23, a Denitrifying Bacterium Isolated from Biofilm of a Methanol-Fed Denitrification  System Treating Seawater at the Montreal Biodome.
JO  - Genome Announcements
PY  - 2014
SP  - e01165
EP  - e01113
VL  - 2
AB  - Hyphomicrobium nitrativorans strain NL23 has been isolated from the biofilm of a
AB  - denitrification system treating seawater. This strain has the capacity to
AB  - denitrify using methanol as a carbon source. Here, we report the complete genome
AB  - sequence of this strain in an effort to increase understanding of the function of
AB  - this bacterium within the biofilm.
ER  -

TY  - JOUR
AU  - Martinet, N.
AU  - Michel, B.Y.
AU  - Bertrand, P.
AU  - Benhida, R.
TI  - Small molecules DNA methyltransferases inhibitors.
JO  - MedChemComm
PY  - 2012
SP  - 263
EP  - 273
VL  - 3
AB  - Methylation catalyzed by the DNA methyltransferases affects the C5 position of cytosine
AB  - residues in DNA. This physiological process is
AB  - active from the embryo conception, throughout all its developmental
AB  - steps, and also later for the maintenance of the adult organism. Excess
AB  - methylated cytosine in tumor suppressor genes is a consistent hallmark
AB  - of human cancers. However, DNA methylation variation is now
AB  - acknowledged to significantly contribute to genetic and common
AB  - diseases. DNA methyltransferases became attractive therapeutic targets
AB  - as DNA demethylation, in vitro, brought cancer cell differentiation and
AB  - apoptosis. Inhibitors are already in use, alone or in combination, to
AB  - treat myeloid malignancies, while clinical assays are ongoing for other
AB  - diseases. DNA methylation and histone modifications are intimately
AB  - correlated with epigenetic heritable modifications of gene expression
AB  - that are independent of changes in the genetic sequence. Common
AB  - initiatives for epigenetic research have built public databases with
AB  - useful resources. The recent discovery of 5-hydroxymethyl cytosine has
AB  - added new questions and challenges for the epigenome community. We
AB  - review here knowledge about DNA methylation to provide researchers with
AB  - the information needed to make more active inhibitors for the benefit
AB  - of patients. Because of space limitations, many important works cannot
AB  - be cited. We refer the reader to reviews containing these references.
ER  -

TY  - JOUR
AU  - Martinez, N.
AU  - Luque, R.
AU  - Olivares, M.M.
AU  - Margolles, A.
AU  - Banuelos, O.
TI  - Resequencing the Genome of Bifidobacterium breve Strain CECT7263.
JO  - Genome Announcements
PY  - 2017
SP  - e00299
EP  - e00217
VL  - 5
AB  - The probiotic properties of Bifidobacterium breve CECT7263, as well as its safety, have been
AB  - the focus of in several studies since 2008, including the
AB  - sequencing of its genome in 2012. This study aims to complete the available
AB  - genomic data to deepen the knowledge of some phenotypic characteristics of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Martinez, R.J.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Goodwin, L.A.
AU  - Han, J.
AU  - Han, C.S.
AU  - Held, B.
AU  - Land, M.L.
AU  - Mikhailova, N.
AU  - Nolan, M.
AU  - Pennacchio, L.
AU  - Pitluck, S.
AU  - Tapia, R.
AU  - Woyke, T.
AU  - Sobecky, P.A.
TI  - Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2113
EP  - 2114
VL  - 194
AB  - Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface
AB  - soils that is capable of promoting uranium phosphate mineralization as
AB  - a result of constitutive phosphatase activity. Here we report the first complete
AB  - genome sequence of an isolate belonging to the genus Rahnella.
ER  -

TY  - JOUR
AU  - Martinez, R.J.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Goodwin, L.A.
AU  - Han, J.
AU  - Han, C.S.
AU  - Held, B.
AU  - Land, M.L.
AU  - Mikhailova, N.
AU  - Nolan, M.
AU  - Pennacchio, L.
AU  - Pitluck, S.
AU  - Tapia, R.
AU  - Woyke, T.
AU  - Sobecky, P.A.
TI  - Complete Genome Sequence of Rahnella aquatilis CIP 78.65.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3020
EP  - 3021
VL  - 194
AB  - Rahnella aquatilis CIP 78.65 is a gammaproteobacterium isolated from a drinking water source
AB  - in Lille, France. Here we report the complete genome sequence of Rahnella aquatilis CIP 78.65,
AB  - the type strain of R. aquatilis.
ER  -

TY  - JOUR
AU  - Martinez, T.
AU  - Ropelewski, A.J.
AU  - Gonzalez-Mendez, R.
AU  - Vazquez, G.J.
AU  - Robledo, I.E.
TI  - Draft Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Strain M3AC9-7, Isolated from Puerto Rico.
JO  - Genome Announcements
PY  - 2015
SP  - e00274
EP  - e00215
VL  - 3
AB  - We report the draft genome of a multidrug resistant, Klebsiella pneumoniae carbapenemase
AB  - (KPC)-producing Acinetobacter baumannii strain M3AC9-7 that belongs
AB  - to the novel sequence type, ST250. The draft genome consists of a total length of
AB  - 4.09 Mbp and a G+C content of 38.95%.
ER  -

TY  - JOUR
AU  - Martinez, T.
AU  - Ropelewski, A.J.
AU  - Gonzalez-Mendez, R.
AU  - Vazquez, G.J.
AU  - Robledo, I.E.
TI  - Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from  Puerto Rico.
JO  - Genome Announcements
PY  - 2016
SP  - e00758
EP  - e00716
VL  - 4
AB  - We report here the draft genome sequence of Acinetobacter baumannii strain M3AC14-8, sequence
AB  - type 2 (ST2), carrying a chromosomally carried blaKPC-2 gene.
AB  - The draft genome consists of a total length of 4.11 Mbp and a G+C content of
AB  - 39.25%.
ER  -

TY  - JOUR
AU  - Martinez, V.
AU  - Hormigo, D.
AU  - Del Cerro, C.
AU  - Gomez-de-Santos, P.
AU  - Garcia-Hidalgo, J.
AU  - Arroyo, M.
AU  - Prieto, A.
AU  - Garcia, J.L.
AU  - de la Mata, I.
TI  - Genome Sequence of Streptomyces exfoliatus DSMZ 41693, a Source of Poly(3-Hydroxyalkanoate)-Degrading Enzymes.
JO  - Genome Announcements
PY  - 2014
SP  - e01272
EP  - e01213
VL  - 2
AB  - Here we report the draft genome sequence of Streptomyces exfoliatus DSMZ 41693, which includes
AB  - a gene encoding a poly(3-hydroxyoctanoate) depolymerase, an enzyme
AB  - which can be used for the industrial synthesis of chiral (R)-3-hydroxyalkanoic
AB  - acids. In addition, the genome carries numerous genes involved in the
AB  - biosynthesis of secondary metabolites, including polyketides and terpenes.
ER  -

TY  - JOUR
AU  - Martinez-Abarca, F.
AU  - Garcia-Rodriguez, F.M.
AU  - Toro, N.
TI  - Homing of a bacterial group II intron with an intron-encoded protein lacking a recognizable endonuclease domain.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 1405
EP  - 1412
VL  - 35
AB  - RmInt1 is a functional group II intron found in Sinorhizobium meliloti where it interrupts a
AB  - group of IS elements of the IS630-Tc1 family. In contrast to many other group II introns, the
AB  - intron-encoded protein (IEP) of RmInt1 lacks the characteristic conserved part of the Zn
AB  - domain associated with the IEP endonuclease activity. Nevertheless, in this study, we show
AB  - that RmInt1 is capable of inserting into a vector containing the DNA spanning the RmInt1
AB  - target site from the genome of S. meliloti. Efficient homing was also observed in the absence
AB  - of homologous recombination (RecA- strains). In addition, it is shown that RmInt1 is able to
AB  - move to its target in a heterologous host (S. medicae). Homing of RmInt1 occurs very
AB  - efficiently upon DNA target uptake (conjugation/electroporation) by the host cell resulting in
AB  - a proportion of invaded target of 11-30%. Afterwards, the remaining intronless target DNA is
AB  - protected from intron invasion.
ER  -

TY  - JOUR
AU  - Martinez-Abarca, F.
AU  - Martinez-Rodriguez, L.
AU  - Lopez-Contreras, J.A.
AU  - Jimenez-Zurdo, J.I.
AU  - Toro, N.
TI  - Complete Genome Sequence of the Alfalfa Symbiont Sinorhizobium/Ensifer meliloti Strain GR4.
JO  - Genome Announcements
PY  - 2013
SP  - e00174
EP  - e00112
VL  - 1
AB  - We present the complete nucleotide sequence of the multipartite genome of
AB  - Sinorhizobium/Ensifer meliloti GR4, a predominant rhizobial strain in an
AB  - agricultural field site. The genome (total size, 7.14 Mb) consists of five
AB  - replicons: one chromosome, two expected symbiotic megaplasmids (pRmeGR4c and
AB  - pRmeGR4d), and two accessory plasmids (pRmeGR4a and pRmeGR4b).
ER  -

TY  - JOUR
AU  - Martinez-Ballesteros, I.
AU  - Arizaga, Y.
AU  - Bikandi, J.
AU  - Garaizar, J.
AU  - Ganau, G.
AU  - Paglietti, B.
AU  - Murgia, M.
AU  - Deligios, M.
AU  - Rubino, S.
TI  - Draft Genome Sequence of an Oceanobacillus sp. Strain Isolated from Soil in a Burial Crypt.
JO  - Genome Announcements
PY  - 2016
SP  - e00701
EP  - e00716
VL  - 4
AB  - We present the draft genome of an Oceanobacillus sp. strain isolated from spores  found in
AB  - soil samples from a burial crypt of the Cathedral of Sant'Antonio Abate
AB  - in Castelsardo, Italy. The data obtained indicated the closest relation of the
AB  - strain with Oceanobacillus caeni.
ER  -

TY  - JOUR
AU  - Martinez-Blanch, J.F.
AU  - Ramon, D.
AU  - Beltran, D.
AU  - Romo-Vaquero, M.
AU  - Garcia-Villalba, R.
AU  - Espin, J.C.
AU  - Tomas-Barberan, F.A.
AU  - Codoner, F.M.
AU  - Selma, M.V.
TI  - Complete Genome Sequence of the New Urolithin-Producing Bacterium Gordonibacter urolithinfaciens DSM 27213(T).
JO  - Genome Announcements
PY  - 2017
SP  - e01120
EP  - e01117
VL  - 5
AB  - Gordonibacter urolithinfaciens DSM 27213(T) was isolated from human feces and is  able to
AB  - metabolize ellagic acid (a dietary phenolic compound present in various
AB  - fruits) to urolithins. Here, we report the finished and annotated genome sequence
AB  - of this organism.
ER  -

TY  - JOUR
AU  - Martinez-Garcia, P.M.
AU  - Rodriguez-Palenzuela, P.
AU  - Arrebola, E.
AU  - Carrion, V.J.
AU  - Gutierrez-Barranquero, J.A.
AU  - Perez-Garcia, A.
AU  - Ramos, C.
AU  - Cazorla, F.M.
AU  - Vicente, Ad.
TI  - Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle.
JO  - PLoS ONE
PY  - 2015
SP  - E0136101
EP  - E0136101
VL  - 10
AB  - The genome sequence of more than 100 Pseudomonas syringae strains has been
AB  - sequenced to date; however only few of them have been fully assembled, including
AB  - P. syringae pv. syringae B728a. Different strains of pv. syringae cause different
AB  - diseases and have different host specificities; so, UMAF0158 is a P. syringae pv.
AB  - syringae strain related to B728a but instead of being a bean pathogen it causes
AB  - apical necrosis of mango trees, and the two strains belong to different
AB  - phylotypes of pv.syringae and clades of P. syringae. In this study we report the
AB  - complete sequence and annotation of P. syringae pv. syringae UMAF0158 chromosome
AB  - and plasmid pPSS158. A comparative analysis with the available sequenced genomes
AB  - of other 25 P. syringae strains, both closed (the reference genomes DC3000, 1448A
AB  - and B728a) and draft genomes was performed. The 5.8 Mb UMAF0158 chromosome has
AB  - 59.3% GC content and comprises 5017 predicted protein-coding genes.
AB  - Bioinformatics analysis revealed the presence of genes potentially implicated in
AB  - the virulence and epiphytic fitness of this strain. We identified several genetic
AB  - features, which are absent in B728a, that may explain the ability of UMAF0158 to
AB  - colonize and infect mango trees: the mangotoxin biosynthetic operon mbo, a gene
AB  - cluster for cellulose production, two different type III and two type VI
AB  - secretion systems, and a particular T3SS effector repertoire. A mutant strain
AB  - defective in the rhizobial-like T3SS Rhc showed no differences compared to
AB  - wild-type during its interaction with host and non-host plants and worms. Here we
AB  - report the first complete sequence of the chromosome of a pv. syringae strain
AB  - pathogenic to a woody plant host. Our data also shed light on the genetic factors
AB  - that possibly determine the pathogenic and epiphytic lifestyle of UMAF0158. This
AB  - work provides the basis for further analysis on specific mechanisms that enable
AB  - this strain to infect woody plants and for the functional analysis of host
AB  - specificity in the P. syringae complex.
ER  -

TY  - JOUR
AU  - Martinez-Garcia, P.M.
AU  - Ruano-Rosa, D.
AU  - Schiliro, E.
AU  - Prieto, P.
AU  - Ramos, C.
AU  - Rodriguez-Palenzuela, P.
AU  - Mercado-Blanco, J.
TI  - Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent  against Verticillium dahliae.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 10
EP  - 10
VL  - 10
AB  - Pseudomonas fluorescens strain PICF7 is a native endophyte of olive roots. Previous studies
AB  - have shown this motile, Gram-negative, non-sporulating bacterium
AB  - is an effective biocontrol agent against the soil-borne fungus Verticillium
AB  - dahliae, the causal agent of one of the most devastating diseases for olive (Olea
AB  - europaea L.) cultivation. Here, we announce and describe the complete genome
AB  - sequence of Pseudomonas fluorescens strain PICF7 consisting of a circular
AB  - chromosome of 6,136,735 bp that encodes 5,567 protein-coding genes and 88
AB  - RNA-only encoding genes. Genome analysis revealed genes predicting factors such
AB  - as secretion systems, siderophores, detoxifying compounds or volatile components.
AB  - Further analysis of the genome sequence of PICF7 will help in gaining insights
AB  - into biocontrol and endophytism.
ER  -

TY  - JOUR
AU  - Martinez-Ocampo, F.
AU  - Fernandez, L.M.G.
AU  - Lozano-Aguirre, B.L.F.
AU  - Popoca-Ursino, E.C.
AU  - Ortiz-Hernandez, M.L.
AU  - Sanchez-Salinas, E.
AU  - Ramos, Q.F.
AU  - Villalobos-Lopez, M.A.
AU  - Dantan-Gonzalez, E.
TI  - Draft Genome Sequence of Burkholderia cenocepacia Strain CEIB S5-2, a Methyl Parathion- and p-Nitrophenol-Degrading Bacterium, Isolated from Agricultural  Soils in Morelos, Mexico.
JO  - Genome Announcements
PY  - 2016
SP  - e00220
EP  - e00216
VL  - 4
AB  - Burkholderia cenocepacia is an opportunistic pathogen that belongs to Burkholderia cepacia
AB  - complex (BCC). Burkholderia cenocepacia strain CEIB S5-2 was
AB  - isolated from agricultural soils in Morelos, Mexico, and previously has shown its
AB  - abilities for bioremediation. In this study, we report the draft genome sequence
AB  - of Burkholderia cenocepacia strain CEIB S5-2.
ER  -

TY  - JOUR
AU  - Martinez-Ocampo, F.
AU  - Lozano-Aguirre, B.L.F.
AU  - Hernandez-Mendoza, A.
AU  - Rojas-Espinoza, L.E.
AU  - Popoca-Ursino, E.C.
AU  - Ortiz-Hernandez, M.L.
AU  - Sanchez-Salinas, E.
AU  - Ramos, Q.F.
AU  - Dantan-Gonzalez, E.
TI  - Burkholderia cenocepacia Strain CEIB S5-1, a Rhizosphere-Inhabiting Bacterium with Potential in Bioremediation.
JO  - Genome Announcements
PY  - 2015
SP  - e00056
EP  - e00015
VL  - 3
AB  - Burkholderia cenocepacia is considered an opportunistic pathogen from humans and  may cause
AB  - disease in plants. A bioprospection from a plaguicide-contaminated
AB  - agricultural field in Mexico identified several methyl parathion-degrading
AB  - bacteria. Here, we report the draft genome sequence of B. cenocepacia strain CEIB
AB  - S5-1, which gave us clues into ecological biodiversity.
ER  -

TY  - JOUR
AU  - Martinez-Ocampo, F.
AU  - Rodriguez-Camarillo, S.D.
AU  - Amaro-Estrada, I.
AU  - Quiroz-Castaneda, R.E.
TI  - Draft Genome Sequence of 'Candidatus Mycoplasma haemobos,' a Hemotropic Mycoplasma Identified in Cattle in Mexico.
JO  - Genome Announcements
PY  - 2016
SP  - e00656
EP  - e00616
VL  - 4
AB  - We present here the draft genome sequence of the first 'Candidatus Mycoplasma haemobos'
AB  - strain found in cattle in Mexico. This hemotropic mycoplasma causes
AB  - acute and chronic disease in animals. This genome is a starting point for
AB  - studying the role of this mycoplasma in coinfections and synergistic mechanisms
AB  - associated with the disease.
ER  -

TY  - JOUR
AU  - Martinez-Penafiel, E.
AU  - Fernandez-Ramirez, F.
AU  - Ishida, C.
AU  - Reyes-Cortes, R.
AU  - Sepulveda-Robles, O.
AU  - Guarneros-Pena, G.
AU  - Bermudez-Cruz, R.M.
AU  - Kameyama, L.
TI  - Overexpression of Ipe protein from the coliphage mEp021 induces pleiotropic effects involving hemolysis by HlyE-containing vesicles and cell death.
JO  - Biochimie
PY  - 2012
SP  - 1262
EP  - 1273
VL  - 94
AB  - Lysogenic Escherichia coli K-12 harbouring the prophage mEp021 displays haemolytic activity.
AB  - From a genomic library of mEp021, we identified an open reading frame (ORF 4) that was
AB  - responsible for the haemolytic activity. However, the ORF 4 sequence contains four initiation
AB  - codons in the same frame: ORF 4.1-ORF 4.4, coding for 83-a.a., 82-a.a., 77-a.a. and 72-a.a.
AB  - products, respectively. The expression of the cloned ORF 4.3, or inducer of pleiotropic
AB  - effects (ipe), reproduced the haemolytic phenotype in a native strain carrying the gene hlyE+,
AB  - but not in the mutant hlyE- strain. The overexpression of Ipe induced several pleiotropic
AB  - effects, such as the inhibition of cell growth and the deregulation of cell division, which
AB  - resulted in a mixture of normal and desiccated-like cells: normal-filamentous,
AB  - desiccated-likefilamentous bacilli, minicells etc. Other effects included abnormalities of the
AB  - cell membrane, the production of vesicles containing HlyE, and finally, cell death. These
AB  - events were analysed at the molecular level by microarray assays. The global transcription
AB  - profile of E. coli K-12 strain MC4100, which expressed Ipe after 4 h, revealed differential
AB  - expression of various genes, most of which were related either to cell membrane and murein
AB  - biosynthesis or to cell division. The up-regulation of some of these transcripts was confirmed
AB  - by qRT-PCR. Additional research is needed to determine whether these effects are directly
AB  - related to Ipe activity or are consequences of the cellular responses to putative structural
AB  - damage induced by Ipe.
ER  -

TY  - JOUR
AU  - Martinez-Raudales, I.
AU  - De La Cruz-Rodriguez, Y.
AU  - Alvarado-Gutierrez, A.
AU  - Vega-Arreguin, J.
AU  - Fraire-Mayorga, A.
AU  - Alvarado-Rodriguez, M.
AU  - Balderas-Hernandez, V.
AU  - Fraire-Velazquez, S.
TI  - Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against  root rot causing phytopathogens.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 73
EP  - 73
VL  - 12
AB  - A Bacillus velezensis strain from the rhizosphere of Sporobolus airoides (Torr.)  Torr., a
AB  - grass in central-north Mexico, was isolated during a biocontrol of
AB  - phytopathogens scrutiny study. The 2A-2B strain exhibited at least 60% of growth
AB  - inhibition of virulent isolates of phytopathogens causing root rot. These
AB  - phytopathogens include Phytophthora capsici, Fusarium solani, Fusarium oxysporum
AB  - and Rhizoctonia solani. Furthermore, the 2A-2B strain is an indolacetic acid
AB  - producer, and a plant inducer of PR1, which is an induced systemic resistance
AB  - related gene in chili pepper plantlets. Whole genome sequencing was performed to
AB  - generate a draft genome assembly of 3.953 MB with 46.36% of GC content, and a N50
AB  - of 294,737. The genome contains 3713 protein coding genes and 89 RNA genes.
AB  - Moreover, comparative genome analysis revealed that the 2A-2B strain had the
AB  - greatest identity (98.4%) with Bacillus velezensis.
ER  -

TY  - JOUR
AU  - Martinez-Raudales, I.
AU  - De La Cruz-Rodriguez, Y.
AU  - Vega-Arreguin, J.
AU  - Alvarado-Gutierrez, A.
AU  - Fraire-Mayorga, A.
AU  - Alvarado-Rodriguez, M.
AU  - Balderas-Hernandez, V.
AU  - Gomez-Soto, J.M.
AU  - Fraire-Velazquez, S.
TI  - Draft Genome Sequence of Bacillus velezensis 3A-25B, a Strain with Biocontrol Activity against Fungal and Oomycete Root Plant Phytopathogens, Isolated from  Grassland Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e01021
EP  - e01017
VL  - 5
AB  - Here, we present the draft genome of Bacillus velezensis 3A-25B, which totaled 4.01 Mb with 36
AB  - contigs, 3,948 genes, and a GC content of 46.34%. This strain,
AB  - which demonstrates biocontrol activity against root rot causal phytopathogens in
AB  - horticultural crops and friendly interactions in roots of pepper plantlets, was
AB  - obtained from grassland soil in Zacatecas Province, Mexico.
ER  -

TY  - JOUR
AU  - Martinez-Romero, E.
AU  - Silva-Sanchez, J.
AU  - Barrios, H.
AU  - Rodriguez-Medina, N.
AU  - Martinez-Barnetche, J.
AU  - Tellez-Sosa, J.
AU  - Gomez-Barreto, R.E.
AU  - Garza-Ramos, U.
TI  - Draft Genome Sequences of Klebsiella variicola Plant Isolates.
JO  - Genome Announcements
PY  - 2015
SP  - e01015
EP  - e01015
VL  - 3
AB  - Three endophytic Klebsiella variicola isolates-T29A, 3, and 6A2, obtained from sugar cane
AB  - stem, maize shoots, and banana leaves, respectively-were used for whole-genome sequencing.
AB  - Here, we report the draft genome sequences of circular chromosomes and plasmids. The genomes
AB  - contain plant colonization and cellulases genes. This study will help toward understanding the
AB  - genomic basis of K. variicola interaction with plant hosts.
ER  -

TY  - JOUR
AU  - Martinez-Steele, L.
AU  - Lowe, C.G.
AU  - Okihiro, M.S.
AU  - Berlemont, R.
TI  - Draft Genome Sequences of Nine New Carnobacterium maltaromaticum Strains Isolated from Diseased Sharks.
JO  - Genome Announcements
PY  - 2018
SP  - e00354
EP  - e00318
VL  - 6
AB  - Here, we report the draft genome sequences of 9 strains of Carnobacterium maltaromaticum
AB  - (SK_LD1 to SK_LD3 and SK_AV1 to SK_AV6), a member of the
AB  - Carnobacteriaceae family (phylum Firmicutes). These strains were isolated from
AB  - the brain and the inner ear of three diseased thresher sharks and two diseased
AB  - salmon sharks. The genome assembly resulted in an average of 3,306,205.9 +/-
AB  - 29,143.9 bp and 3,085 +/- 32.67 coding DNA sequences (CDS).
ER  -

TY  - JOUR
AU  - Martino, G.P.
AU  - Quintana, I.M.
AU  - Espariz, M.
AU  - Blancato, V.S.
AU  - Gallina, N.G.
AU  - Esteban, L.
AU  - Magni, C.
TI  - Draft Genome Sequences of Four Enterococcus faecium Strains Isolated from Argentine Cheese.
JO  - Genome Announcements
PY  - 2016
SP  - e01576
EP  - e01515
VL  - 4
AB  - We report the draft genome sequences of four Enterococcus faecium strains isolated from
AB  - Argentine regional cheeses. These strains were selected based on
AB  - their technological properties, i.e., their ability to produce aroma compounds
AB  - (diacetyl, acetoin, and 2,3-butanediol) from citrate. The goal of our study is to
AB  - provide further genetic evidence for the rational selection of enterococci
AB  - strains based on their pheno- and genotype in order to be used in cheese
AB  - production.
ER  -

TY  - JOUR
AU  - Martino, M.E.
AU  - Bayjanov, J.R.
AU  - Joncour, P.
AU  - Hughes, S.
AU  - Gillet, B.
AU  - Kleerebezem, M.
AU  - Siezen, R.
AU  - van Hijum, S.A.
AU  - Leulier, F.
TI  - Resequencing of the Lactobacillus plantarum Strain WJL Genome.
JO  - Genome Announcements
PY  - 2015
SP  - e01382
EP  - e01315
VL  - 3
AB  - Lactobacillus plantarum strain WJL is a symbiont isolated from the Drosophila melanogaster
AB  - gut. The genome of L. plantarum WJL, first sequenced in 2013, was
AB  - resequenced and rescaffolded in this study. A combination of Sanger and Illumina
AB  - sequencing allowed us to reduce the number of contigs from 102 to 13. This work
AB  - contributes to a better understanding of the genome and function of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Martino, M.E.
AU  - Bayjanov, J.R.
AU  - Joncour, P.
AU  - Hughes, S.
AU  - Gillet, B.
AU  - Kleerebezem, M.
AU  - Siezen, R.
AU  - van Hijum, S.A.
AU  - Leulier, F.
TI  - Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877.
JO  - Genome Announcements
PY  - 2015
SP  - e01370
EP  - e01315
VL  - 3
AB  - Lactobacillus plantarum is a versatile bacterial species that is isolated mostly  from foods.
AB  - Here, we present the first genome sequence of L. plantarum strain
AB  - NIZO2877 isolated from a hot dog in Vietnam. Its two contigs represent a nearly
AB  - complete genome sequence.
ER  -

TY  - JOUR
AU  - Maruyama, F.
AU  - Kobata, M.
AU  - Kurokawa, K.
AU  - Nishida, K.
AU  - Sakurai, A.
AU  - Nakano, K.
AU  - Nomura, R.
AU  - Kawabata, S.
AU  - Ooshima, T.
AU  - Nakai, K.
AU  - Hattori, M.
AU  - Hamada, S.
AU  - Nakagawa, I.
TI  - Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.
JO  - BMC Genomics
PY  - 2009
SP  - 358
EP  - 358
VL  - 10
AB  - Background: Streptococcus mutans is the major pathogen of dental caries, and it occasionally
AB  - causes infective endocarditis. While the
AB  - pathogenicity of this species is distinct from other human pathogenic
AB  - streptococci, the species-specific evolution of the genus Streptococcus
AB  - and its genomic diversity are poorly understood.Results: We have
AB  - sequenced the complete genome of S. mutans serotype c strain NN2025,
AB  - and compared it with the genome of UA159. The NN2025 genome is composed
AB  - of 2,013,587 bp, and the two strains show highly conserved core-genome.
AB  - However, comparison of the two S. mutans strains showed a large genomic
AB  - inversion across the replication axis producing an X-shaped symmetrical
AB  - DNA dot plot. This phenomenon was also observed between other
AB  - streptococcal species, indicating that streptococcal genetic
AB  - rearrangements across the replication axis play an important role in
AB  - Streptococcus genetic shuffling. We further confirmed the genomic
AB  - diversity among 95 clinical isolates using long-PCR analysis. Genomic
AB  - diversity in S. mutans appears to occur frequently between insertion
AB  - sequence (IS) elements and transposons, and these diversity regions
AB  - consist of restriction/modification systems, antimicrobial peptide
AB  - synthesis systems, and transporters. S. mutans may preferentially
AB  - reject the phage infection by clustered regularly interspaced short
AB  - palindromic repeats (CRISPRs). In particular, the CRISPR-2 region,
AB  - which is highly divergent between strains, in NN2025 has long repeated
AB  - spacer sequences corresponding to the streptococcal phage
AB  - genome.Conclusion: These observations suggest that S. mutans strains
AB  - evolve through chromosomal shuffling and that phage infection is not
AB  - needed for gene acquisition. In contrast, S. pyogenes tolerates phage
AB  - infection for acquisition of virulence determinants for niche
AB  - adaptation.
ER  -

TY  - JOUR
AU  - Marvig, R.L.
AU  - Jochumsen, N.
AU  - Johansen, H.K.
AU  - Hoiby, N.
AU  - Molin, S.
AU  - Sommer, M.O.
AU  - Jelsbak, L.
AU  - Folkesson, A.
TI  - Draft Genome Sequences of Pseudomonas aeruginosa B3 Strains Isolated from a Cystic Fibrosis Patient Undergoing Antibiotic Chemotherapy.
JO  - Genome Announcements
PY  - 2013
SP  - e00804
EP  - e00813
VL  - 1
AB  - Pseudomonas aeruginosa frequently establishes chronic infections in the airways of patients
AB  - suffering from cystic fibrosis (CF). Here, we report the draft genome
AB  - sequences of four P. aeruginosa B3 strains isolated from a chronically infected
AB  - CF patient undergoing antibiotic chemotherapy.
ER  -

TY  - JOUR
AU  - Marx, C.J. et al.
TI  - Complete genome sequences of six strains of the genus methylobacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4746
EP  - 4748
VL  - 194
AB  - The complete and assembled genome sequences were determined for six strains of the
AB  - alphaproteobacterial genus Methylobacterium, chosen for their key adaptations
AB  - to different plant-associated niches and environmental constraints.
ER  -

TY  - JOUR
AU  - Marx, H.
AU  - Graf, A.B.
AU  - Tatto, N.E.
AU  - Thallinger, G.G.
AU  - Mattanovich, D.
AU  - Sauer, M.
TI  - Genome Sequence of the Ruminal Bacterium Megasphaera elsdenii.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5578
EP  - 5579
VL  - 193
AB  - Megasphaera elsdenii is a Gram-negative ruminal bacterium. It is being investigated as a
AB  - probiotic supplement for ruminants as it may provide
AB  - benefits for energy balance and animal productivity. Furthermore, it is of
AB  - biotechnological interest due to its capability of producing various
AB  - volatile fatty acids. Here we report the complete genome sequence of M.
AB  - elsdenii DSM 20460, the type strain for the species.
ER  -

TY  - JOUR
AU  - Marx, J.L.
TI  - Restriction enzymes:  new tools for studying DNA.
JO  - Science
PY  - 1973
SP  - 482
EP  - 485
VL  - 180
AB  - None
ER  -

TY  - JOUR
AU  - Marzabal, S.
AU  - DuBois, S.
AU  - Thielking, V.
AU  - Cano, A.
AU  - Eritja, R.
AU  - Guschlbauer, W.
TI  - Dam methylase from Escherichia coli: kinetic studies using modified DNA oligomers: hemimethylated substrates.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 3648
EP  - 3655
VL  - 23
AB  - We have measured steady-state kinetics of the N6-adenine methyltransferase Dam Mtase using as
AB  - substrates non-selfcomplementary tetradecamer duplexes (d[GCCGGATCTAGACG].d[CGTCTAGATCCGGC])
AB  - containing the hemimethylated GATC target sequence in one or the other strand and
AB  - modifications in the GATC target sequence of the complementary strands.  Modifications
AB  - included substitution of guanine by hypoxanthine (I), thymine by uracil (U) or 5-ethyl-uracil
AB  - (E) and adenine by 2,6-diamino-purine (D).  Thermodynamic parameters were obtained from the
AB  - concentration dependence of the melting temperature (Tm) of the duplexes.  Large differences
AB  - in DNA methylation of duplexes containing single dl for dG substitution of the Dam recognition
AB  - site were observed compared with the canonical substrate, if the substitution involved the
AB  - top strand (on the G.C rich side).  Substitution in either strand by uracil (dU) or
AB  - 5-ethyl-uracil (dE) resulted in small perturbation of the methylation patterns.  When
AB  - 2,5-diamino-purine (dD) replaced the adenine to be methylated, small, but significant
AB  - methylation was observed.  The kinetic parameters of the methylation reaction were compared
AB  - with the thermodynamic free energies and significant correlation was observed.
ER  -

TY  - JOUR
AU  - Mas-Llado, M.
AU  - Pina-Villalonga, J.M.
AU  - Brunet-Galmes, I.
AU  - Nogales, B.
AU  - Bosch, R.
TI  - Draft Genome Sequences of Thalassobacter Strains 1CONIMAR09 and 16PALIMAR09, Two  Members of the Roseobacter Lineage Isolated from Coastal Areas of the  Mediterranean Sea around Mallorca Island.
JO  - Genome Announcements
PY  - 2015
SP  - e00041
EP  - e00015
VL  - 3
AB  - We report the draft genome sequence of two new members of the Roseobacter lineage,
AB  - Thalassobacter strains 1CONIMAR09 and 16PALIMAR09, which were isolated
AB  - from the seawater coast of Mallorca Island. Each genome harbored putative genes
AB  - for obtaining energy by chemolithotrophy and making aerobic anoxygenic
AB  - photosynthesis.
ER  -

TY  - JOUR
AU  - Mas-Llado, M.
AU  - Pina-Villalonga, J.M.
AU  - Brunet-Galmes, I.
AU  - Nogales, B.
AU  - Bosch, R.
TI  - Draft Genome Sequences of Two Isolates of the Roseobacter Group, Sulfitobacter sp. Strains 3SOLIMAR09 and 1FIGIMAR09, from Harbors of Mallorca Island  (Mediterranean Sea).
JO  - Genome Announcements
PY  - 2014
SP  - e00350
EP  - e00314
VL  - 2
AB  - We present the draft genome sequences of two isolates of the Roseobacter lineage, 3SOLIMAR09
AB  - and 1FIGIMAR09, which were obtained from harbors of Mallorca Island,
AB  - Spain, and are affiliated with the Sulfitobacter genus. Both isolates harbor the
AB  - complete gene set for protocatechuate catabolism and incomplete pathways for
AB  - several additional monoaromatic compounds.
ER  -

TY  - JOUR
AU  - Masai, E.
AU  - Kamimura, N.
AU  - Kasai, D.
AU  - Oguchi, A.
AU  - Ankai, A.
AU  - Fukui, S.
AU  - Takahashi, M.
AU  - Yashiro, I.
AU  - Sasaki, H.
AU  - Harada, T.
AU  - Nakamura, S.
AU  - Katano, Y.
AU  - Narita-Yamada, S.
AU  - Nakazawa, H.
AU  - Hara, H.
AU  - Katayama, Y.
AU  - Fukuda, M.
AU  - Yamazaki, S.
AU  - Fujita, N.
TI  - Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls.
JO  - J. Bacteriol.
PY  - 2012
SP  - 534
EP  - 535
VL  - 194
AB  - Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls
AB  - and monoaryls, and the catabolic genes for these
AB  - compounds are useful for the production of industrially valuable
AB  - metabolites from lignin. Here we report the complete nucleotide sequence
AB  - of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and
AB  - the 148,801-bp-long plasmid.
ER  -

TY  - JOUR
AU  - Mascarenhas, D.S.A.C.
AU  - Jie, R.
AU  - Antunes, G.H.
AU  - Alves, M.
AU  - Pombert, J.F.
TI  - Complete Genome Sequences of the Potential Zoonotic Pathogens Staphylococcus felis and Staphylococcus kloosii.
JO  - Genome Announcements
PY  - 2018
SP  - e00404
EP  - e00418
VL  - 6
AB  - Coagulase-negative staphylococci (CoNS) are opportunistic pathogens frequently encountered in
AB  - nosocomial infections. Animal-associated CoNS pose a zoonotic risk
AB  - and constitute a potential reservoir for virulence and antimicrobial resistance
AB  - genes. To improve our knowledge of animal-associated CoNS, we sequenced the
AB  - complete genomes of Staphylococcus felis (ATCC 49168) and Staphylococcus kloosii
AB  - (ATCC 43959).
ER  -

TY  - JOUR
AU  - Mashhoon, N.
TI  - Kinetic and chemical mechanisms of the EcoRI DNA (N6-adenine) methyltransferase.
JO  - Diss. Abstr.
PY  - 1994
SP  - 5132B
EP  - 5133B
VL  - 54
AB  - A kinetic analysis of the EcoRI DNA N6-adenine methyltransferase (Mtase) is presented. The
AB  - enzyme catalyzes the S-adenosylmethionine (AdoMet)-dependent methylation of a short, synthetic
AB  - 14 base pair DNA substrate and plasmid pBR322 DNA substrate with kcat/Km values of 0.51 x 10/8
AB  - and 4.1 x 10/8 s-1 M-1, respectively. The Mtase is thus one of the most efficient biocatalysts
AB  - known. The steady state kinetic data are consistent with an ordered bi-bi steady-state
AB  - mechanism in which AdoMet binds first, followed by (AdoHcy), is an uncompetitive inhibitor
AB  - with respect to DNA and a competitive inhibitor with respect to AdoMet. Thus, initial DNA
AB  - binding followed by AdoHcy binding leads to formation of a ternary deadend complex
AB  - (Mtase-AdoHcy binding leads to formation of a ternary dead-end complex (Mtase-DNA-AdoHcy). The
AB  - product inhibition patterns and apparent order of substrate binding can be reconciled by a
AB  - mechanism in which the Mtase binds AdoMet and noncanonical DNA randomly but that recognition
AB  - of the canonical site requires AdoMet to be bound. Presteady-state and isotope partition
AB  - analyses starting with the binary Mtase-AdoMet complex confirm its catalytic competence. In
AB  - summary, it was determined that the EcoRI DNA Mtase binds AdoMet and noncanonical DNA randomly
AB  - but recognition of the canonical site requires AdoMet to be bound. It was shown that step(s)
AB  - after methyl transfer limit the overall reaction rate and that methyl transfer at the N6 amino
AB  - moiety of adenine on each strand requires a single binding orientation. Furthermore, it was
AB  - demonstrated that no critical protein residues undergo ionization state changes in the pH
AB  - range 5.5-8.0. However, above pH 8.5 at least four residues in the free enzyme and AdoMet
AB  - bound enzyme and two residues in the central complex (Mtase-DNA-AdoMet) are implicated to be
AB  - critical in binding and/or catalysis; candidate amino acid residues are cysteine (other than
AB  - cysteine 223), lysine, tyrosine, and/or arginine.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Carroll, M.
AU  - Pruss, C.
AU  - Eberhard, J.
AU  - Ishikawa, S.
AU  - Estabrook, R.A.
AU  - Reich, N.
TI  - Functional Characterization of Escherichia coli DNA Adenine Methyltransferase, a Novel Target for Antibiotics.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 52075
EP  - 52081
VL  - 279
AB  - We have characterized Escherichia coli DNA adenine methyltransferase, a critical regulator of
AB  - bacterial virulence. Steady-state kinetics, product
AB  - inhibition, and isotope exchange studies are consistent with a kinetic
AB  - mechanism in which the cofactor S-adenosylmethionine binds first, followed
AB  - by sequence-specific DNA binding and catalysis. The enzyme has a fast
AB  - methyl transfer step followed by slower product release steps, and we
AB  - directly demonstrate the competence of the enzyme cofactor complex.
AB  - Methylation of adjacent GATC sites is distributive with DNA derived from a
AB  - genetic element that controls the transcription of the adjacent genes.
AB  - This indicates that the first methylation event is followed by enzyme
AB  - release. The affinity of the enzyme for both DNA and S-adenosylmethionine
AB  - was determined. Our studies provide a basis for further structural and
AB  - functional analysis of this important enzyme and for the identification of
AB  - inhibitors for potential therapeutic applications.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Pruss, C.
AU  - Carroll, M.
AU  - Johnson, P.H.
AU  - Reich, N.O.
TI  - Selective inhibitors of bacterial DNA adenine methyltransferases.
JO  - J. Biomol. Screen.
PY  - 2006
SP  - 497
EP  - 510
VL  - 11
AB  - The authors describe the discovery and characterization of several structural classes of
AB  - small-molecule inhibitors of bacterial DNA
AB  - adenine methyltransferases. These enzymes are essential for bacterial
AB  - virulence (DNA adenine methyltransferase [DAM]) and cell viability
AB  - (cell cycle-regulated methyltransferase [CcrM]). Using a novel
AB  - high-throughput fluorescence-based assay and recombinant DAM and CcrM,
AB  - the authors screened a diverse chemical library. They identified 5
AB  - major structural classes of inhibitors composed of more than 350
AB  - compounds: cyclopentaquinolines, phenyl vinyl furans,
AB  - pyrimidine-diones, thiazolidine-4-ones, and phenyl-pyrroles. DNA
AB  - binding assays were used to identify compounds that interact directly
AB  - with DNA. Potent compounds selective for the bacterial target were
AB  - identified, whereas other compounds showed greater selectivity for the
AB  - mammalian DNA cytosine methyltransferase, Dnmt1. Enzyme inhibition
AB  - analysis identified mechanistically distinct compounds that interfered
AB  - with DNA or cofactor binding. Selected compounds demonstrated
AB  - cell-based efficacy. These small-molecule DNA methyltransferase
AB  - inhibitors provide useful reagents to probe the role of DNA methylation
AB  - and may form the basis of developing novel antibiotics.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Reich, N.O.
TI  - Investigation of ionizable residues critical for sequence-specific enzymatic DNA modification: Protein modification and steady-state and pre-steady-state kinetic pH analyses of EcoRI DNA methyltransferase.
JO  - Biochemistry
PY  - 1994
SP  - 7113
EP  - 7119
VL  - 33
AB  - Steady- and pre-steady-state pH kinetic analyses are widely used methods to investigate
AB  - important ionizable groups in enzyme-catalyzed reactions. The first such analysis to identify
AB  - ionizable residues critical for sequence-specific modification of DNA is presented. EcoRI DNA
AB  - methyltransferase uses S-adenosyl-L-methionine (AdoMet) to catalyze the N6 methylation of the
AB  - second adenine in the double-stranded DNA sequence GAATTC. The kinetic mechanism was
AB  - previously shown to be steady-state-ordered bi bi in which AdoMet binds first followed by DNA
AB  - addition (Reich, N.O. & Mashhoon, N. (1991) Biochemistry 30, 2933-2939). Steady-state
AB  - parameters are strongly dependent on pH and implicate at least four residues with pKa values
AB  - between 8.2 and 8.9 in the free enzyme and AdoMet-bound enzyme and one residue with an
AB  - apparent pKa of 6.0. The data obtained aer consistent with the enzyme binding the form of
AB  - AdoMet in which the alpha amino group is protonated. Two protein residues with an apparent pKa
AB  - between 8.9 and 9.2 were implicated within the central complex (enzyme-DNA-AdoMet). The
AB  - general insensitivity of all steady-state parameters to pH changes between pH 6.0 and 8.0
AB  - suggests that no critical protein residues undergo ionization-state changes in this range. The
AB  - lack of significant pH-dependent changes in protein fluorescence and DNA thermal stability
AB  - suggests minimal structural changes in either macromolecule. In support of the steady-state
AB  - results single-turnover experiments reveal minimal pH dependence of the methylation rate
AB  - constant between pH 5.53 and 8.6. Thus, no amino acids critical for catalysis undergo
AB  - ionization-state changes in this range. The previously identified site of NEM-mediated
AB  - inactivation of the methyltransferase, cysteine 223 (Everett et al. (1990) J. Biol. Chem. 265,
AB  - 17713-17719), has a pKa of 7.9; on the basis of the steady- and pre-steady-state pH
AB  - dependences this cysteine does not directly contribute to catalysis and substrate binding. The
AB  - results are discussed in the context of the requirement for significant enzymatic activation
AB  - of the poorly nucleophilic N6 position.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Reich, N.O.
TI  - A kinetic study of DNA methylation by EcoRI methylase.
JO  - J. Cell Biol.
PY  - 1988
SP  - 838a
EP  - 838a
VL  - 107
AB  - The ability of a protein to recognize and subsequently modify a specific
AB  - sequence of bases in DNA is a fundamental biochemical question that is being
AB  - addressed in our laboratory by studying the EcoRI DNA methylase.  EcoRI
AB  - methylase, a 38 kilodalton bacterial protein, requires S-adenosyl methionine
AB  - (AdoMet) to methylate the double stranded DNA sequence GAATTC at the second
AB  - adenine.  Methylation of DNA serves to protect the organism's DNA against
AB  - cleavage by the corresponding endonuclease.  Little is known about the enzyme's
AB  - kinetic mechanism, the order of substrate binding and product release, and the
AB  - rate limiting step in the reaction.  Steady state and pre-steady state analysis
AB  - were used to determine the kinetic mechanism.  Product inhibition with
AB  - S-adenosyl homocysteine is competitive with respect to AdoMet, whereas it is
AB  - non-competititve with respect to DNA.  Data will be presented on the steady
AB  - state kinetic parameters for AdoMet and DNA, the rate limiting step in the
AB  - reaction, and the order of substrate binding and product release.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Reich, N.O.
TI  - An investigation of the chemical mechanism of the EcoRI DNA methyltransferase.
JO  - FASEB J.
PY  - 1992
SP  - A333
EP  - A333
VL  - 6
AB  - The pH dependence of the EcoRI DNA methyltransferase activity was studied under
AB  - steady state and pre-steady state conditions, and with chemical modification
AB  - analysis.  Steady state pH analysis suggests that a residue with a pKa of
AB  - 8.5-9.0 is necessary in its protonated form for enzyme activity.  KmDNA
AB  - increases over 250 fold as pH increases from 5.5 to 9.5 and kcat decreases over
AB  - 20 fold.  Pre-steady state experiments were performed to measure the
AB  - methylation rate constant under single turnover conditions (>1 s-1 compared to
AB  - the kcat of .124 s-1) and to determine how pH affects this methylation rate
AB  - constant.  Chemical modification of the methylase with N-ethylmaleimide was
AB  - carried out to substantiate the steady state experimental findings.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Reich, N.O.
TI  - Analysis of the kinetic and chemical mechanisms of EcoRI methylase.
JO  - FASEB J.
PY  - 1990
SP  - A1979
EP  - A1979
VL  - 4
AB  - Our goal is to elucidate the kinetic and chemical mechanisms of the EcoRI DNA
AB  - (adenine-N6)-methyltransferase.  Steady state and pre-steady state kinetic
AB  - experiments suggest an ordered bi bi mechanism in which S-Adenosylmethionine
AB  - (AdoMet) binds first, followed by DNA substrate.  After methyl transfer,
AB  - S-Adenosylhomocysteine (AdoHcy) dissociates followed by methylated DNA.  The
AB  - methyl transfer step is at least nine fold faster than the catalytic turnover
AB  - (kcat).  The kcat and Michaelis constants (Km) for AdoMet with a short 14 base
AB  - pair (14mer) and a long 4363 base pair plasmid DNA substrates are similar (150
AB  - nM).  In contrast, the Km for the plasmid DNA is fifty fold lower than 14mer.
AB  - The specificity constant (kcat/Km) for plasmid DNA is about 50 fold greater
AB  - than for the 14mer, suggesting that EcoRI methylase is a processive enzyme.
AB  - With a kcat/Km ratio of 2.9x10/8 M-1 sec-1 for plasmid DNA, EcoRI methylase is
AB  - among the most efficient enzymes reported.  pH studies implicating specific
AB  - amino acid residues in catalysis and (or) substrate binding will be presented.
ER  -

TY  - JOUR
AU  - Mashhoon, N.
AU  - Reich, N.O.
TI  - A kinetic study of DNA methylation by EcoRI methylase.
JO  - ACS Abstracts
PY  - 1988
SP  - 96
EP  - 96
VL  - 196
AB  - The ability of a protein to recognize and subsequently modify a specific
AB  - sequence of bases in DNA is a fundamental biochemical question that is being
AB  - addressed in our laboratory by studying the EcoRI DNA methylase.  EcoRI
AB  - methylase, a 38 kilodalton bacterial protein, requires S-adenosyl methionine
AB  - (AdoMet) to methylate the double stranded DNA sequence GAATTC at the second
AB  - adenine.  Methylation of DNA serves to protect the organism's DNA against
AB  - cleavage by the corresponding endonuclease.  Little is known about the enzyme's
AB  - kinetic mechanism, the order of substrate binding and product release and the
AB  - rate limiting step in the reaction.  Steady state and pre-steady state analysis
AB  - were used to determine the kinetic mechanism.  Product inhibition with
AB  - S-adenosyl homocysteine is competitive with respect to AdoMet, whereas it is
AB  - non-competitive with respect to DNA.  Data will be presented on the steady
AB  - state kinetic parameters for AdoMet and DNA, the rate limiting step in the
AB  - reaction, and the order of substrate binding and product release.
ER  -

TY  - JOUR
AU  - Mashima, I.
AU  - Liao, Y.C.
AU  - Sabharwal, A.
AU  - Haase, E.M.
AU  - Nakazawa, F.
AU  - Scannapieco, F.A.
TI  - Draft Genome Sequences of Four Strains of Recently Established Novel Veillonella  Species Isolated from Human Oral Cavities.
JO  - Genome Announcements
PY  - 2018
SP  - e00259
EP  - e00218
VL  - 6
AB  - Veillonella species are known to contribute to the formation of early oral biofilms and tend
AB  - to be prevalent in people with poor oral hygiene status. Here,
AB  - we report the draft genome sequences of 4 oral Veillonella strains that were
AB  - established recently as novel species.
ER  -

TY  - JOUR
AU  - Mashima, I.
AU  - Nakazawa, F.
TI  - Draft Genome Sequence of Veillonella tobetsuensis ATCC BAA-2400T Isolated from Human Tongue Biofilm.
JO  - Genome Announcements
PY  - 2015
SP  - e00808
EP  - e00815
VL  - 3
AB  - Here, we report the draft genome sequence of Veillonella tobetsuensis ATCC-BAA 2400(T). This
AB  - bacterium has the remarkable ability to form oral biofilms. The
AB  - genome is predicted to encode the necessary enzymes involved in the pathway that
AB  - facilitates the conversion of lactate to propionate.
ER  -

TY  - JOUR
AU  - Mashimo, C.
AU  - Yamane, K.
AU  - Yamanaka, T.
AU  - Maruyama, H.
AU  - Wang, P.L.
AU  - Komasa, S.
AU  - Okazaki, J.
AU  - Nambu, T.
TI  - Genome Sequence of Actinomyces naeslundii Strain ATCC 27039, Isolated from an Abdominal Wound Abscess.
JO  - Genome Announcements
PY  - 2016
SP  - e01443
EP  - e01416
VL  - 4
AB  - Here, we present the complete genome sequence of Actinomyces naeslundii strain ATCC 27039,
AB  - isolated from an abdominal wound abscess. This strain is genetically
AB  - transformable and will thus provide valuable information related to its crucial
AB  - role in oral multispecies biofilm development.
ER  -

TY  - JOUR
AU  - Maslov, A.
AU  - Metrikin, M.
AU  - Vijg, J.
TI  - A dual-activation, adenoviral-based system for the controlled induction of DNa double-strand breaks by the restriction endonuclease SacI.
JO  - Biotechniques
PY  - 2009
SP  - 847
EP  - 854
VL  - 47
AB  - Spontaneous damage to DNA is frequent and may lead to cell death, cell senescence, or
AB  - mutations.  DNA double-strand breaks are of special interest because they are highly toxic and
AB  - have been implicated in neurodegeneration, cancer, and aging.  Until now, there has not been a
AB  - reliable system allowing tunable induction of random DSBs without affecting other
AB  - macromolecules or cell functions.  Here, we describe an adenoviral-based,
AB  - doxycycline-mediated, and tamoxifen-dependent system for quantitative introduction of DSBs in
AB  - mammalian cells.  We generated a single adenoviral vector containing a tet-inducible,
AB  - composite SalI restriction endonuclease/estrogen receptor gene, and a constitutively expressed
AB  - reverse transactivator gene.  Transduced mouse embryonic fibroblasts - as well as mouse liver
AB  - cells in vivo - demonstrated a high level of DSBs in response to treatment with doxycycline
AB  - and tamoxifen.  We show that the amount of induced DSBs can be titrated by doxycycline dose
AB  - and duration of treatment.  This system should be useful for studying the processing of
AB  - randomly induced DSBs and their effects on cell fate, without the side effects normally
AB  - associated with radiation or chemical treatment.
ER  -

TY  - JOUR
AU  - Maslov, D.A.
AU  - Shur, K.V.
AU  - Bekker, O.B.
AU  - Zakharevich, N.V.
AU  - Zaichikova, M.V.
AU  - Klimina, K.M.
AU  - Smirnova, T.G.
AU  - Zhang, Y.
AU  - Chernousova, L.N.
AU  - Danilenko, V.N.
TI  - Draft Genome Sequences of Two Pyrazinamide-Resistant Clinical Isolates, Mycobacterium tuberculosis 13-4152 and 13-2459.
JO  - Genome Announcements
PY  - 2015
SP  - e00758
EP  - e00715
VL  - 3
AB  - We report draft genome sequences of two pyrazinamide (PZA)-resistant isolates, Mycobacterium
AB  - tuberculosis 13-4152 and 13-2459. Isolate 13-4152 is PZA resistant,
AB  - though it lacks mutations in known genes of PZA resistance. The comparative
AB  - analysis of these genomes with those stored in GenBank revealed unique mutations,
AB  - which may elucidate new mechanisms of PZA resistance.
ER  -

TY  - JOUR
AU  - Masood, N.
AU  - Jackson, E.
AU  - Moore, K.
AU  - Farbos, A.
AU  - Paszkiewicz, K.
AU  - Dickins, B.
AU  - McNally, A.
AU  - Forsythe, S.
TI  - Draft Genome Sequence of 'Candidatus Cronobacter colletis' NCTC 14934T, a New Species in the Genus Cronobacter.
JO  - Genome Announcements
PY  - 2014
SP  - e00585
EP  - e00514
VL  - 2
AB  - Members of the Cronobacter genus are associated with serious infections in neonates. This is
AB  - the first report of the draft genome sequence for the newly
AB  - proposed species Cronobacter colletis.
ER  -

TY  - JOUR
AU  - Masood, N.
AU  - Moore, K.
AU  - Farbos, A.
AU  - Hariri, S.
AU  - Block, C.
AU  - Paszkiewicz, K.
AU  - Dickins, B.
AU  - McNally, A.
AU  - Forsythe, S.
TI  - Draft Genome Sequence of a Meningitic Isolate of Cronobacter sakazakii Clonal Complex 4, Strain 8399.
JO  - Genome Announcements
PY  - 2013
SP  - e00833
EP  - e00813
VL  - 1
AB  - The Cronobacter sakazakii clonal lineage defined as clonal complex 4 (CC4), composed of nine
AB  - sequence types, is associated with severe cases of neonatal
AB  - meningitis. To date, only closely related C. sakazakii sequence type 4 (ST4)
AB  - strains have been sequenced. C. sakazakii strain 8399, isolated from a case of
AB  - neonatal meningitis, was sequenced as the first non-ST4 C. sakazakii strain.
ER  -

TY  - JOUR
AU  - Masood, N.
AU  - Moore, K.
AU  - Farbos, A.
AU  - Hariri, S.
AU  - Paszkiewicz, K.
AU  - Dickins, B.
AU  - McNally, A.
AU  - Forsythe, S.
TI  - Draft Genome Sequences of Three Newly Identified Species in the Genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis  LMG23730T.
JO  - Genome Announcements
PY  - 2013
SP  - e00783
EP  - e00713
VL  - 1
AB  - Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described
AB  - species in the Cronobacter genus, which is associated with
AB  - serious infections of neonates. This is the first report of draft genome
AB  - sequences for these species.
ER  -

TY  - JOUR
AU  - Masood, N.
AU  - Moore, K.
AU  - Farbos, A.
AU  - Hariri, S.
AU  - Paszkiewicz, K.
AU  - Dickins, B.
AU  - McNally, A.
AU  - Forsythe, S.
TI  - Draft Genome Sequence of the Earliest Cronobacter sakazakii Sequence Type 4 Strain, NCIMB 8272.
JO  - Genome Announcements
PY  - 2013
SP  - e00782
EP  - e00713
VL  - 1
AB  - The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with
AB  - severe cases of neonatal meningitis and persistence in powdered
AB  - infant formula. For genome sequencing of the earliest deposited culture
AB  - collection strain of Cronobacter sakazakii ST4, we used the strain NCIMB 8272,
AB  - originally isolated from milk powder in 1950.
ER  -

TY  - JOUR
AU  - Master, S.S.
TI  - What is the origin and role of the large variable region in the M-AluI DNA-(cytosine c5) methyltransferase?
JO  - Diss. Abstr.
PY  - 1996
SP  - 1626
EP  - 1626
VL  - 57
AB  - AluI DNA-(cytosine C5)-methyltransferase is part of a restriction-modification system, and
AB  - methylates the 5-carbon of cytosine in the sequence 5'-AGCT-3'.  The amino acid sequences of
AB  - all known 5mC MTases contain ten conserved motifs, and between Motifs VIII and IX have a
AB  - variable region containing one or more Target Recognizing Domains.  TRDs are responsible for
AB  - DNA sequence specificity: monospecific MTases appear to have only one, while multispecific
AB  - MTases have as many as five.  M.AluI has the second largest variable region of all known 5mC
AB  - MTases, and sequence comparisons reveal four candidate TRDs in its variable region.  What is
AB  - the origin and role of this large variable region?  One possibility is that M.AluI evolved
AB  - from a multispecific MTase, or imported its variable region from a multispecific MTase.
AB  - Alternatively, it may have evolved from a monospecific MTase, expanding its variable region by
AB  - partial duplications.  Phylogenetic parsimony analysis and FASTA followed by Spearman's rank
AB  - order correlation coefficient suggested that neither M.AluI nor its variable region is closely
AB  - related to the known multispecific MTases.  The M.AluI pattern, however, is consistent with
AB  - importation of the variable region.  Methylation of AGCT sites accounted for 85-90% of the
AB  - methylating activity, but M.HhaI gave no unexplained methylating activity.  Various insertions
AB  - or deletion mutants failed to identify dispensable portions of the variable region, but a
AB  - sensitive in vivo assay based on McrBC restriction did reveal that the central portion is
AB  - particularly important for activity.  If M.AluI is like the multispecific MTases, which it
AB  - resembles in size, then it might be expected to accommodate a TRD from a multispecific MTase.
AB  - When such a TRD was moved into two locations in the M.AluI variable region, neither construct
AB  - gained a new specificity and both had greatly reduced activity.  Hence, M.AluI behaves in most
AB  - respects like a monospecific MTase, and the remarkable size of its variable region remains to
AB  - be explained.
ER  -

TY  - JOUR
AU  - Master, S.S.
AU  - Blumenthal, R.M.
TI  - A genetic and functional analysis of the unusually large variable region in the M.AluI DNA-(cytosine C5)-methyltransferase.
JO  - Mol. Gen. Genet.
PY  - 1997
SP  - 14
EP  - 22
VL  - 257
AB  - The M.AluI DNA-(cytosine C5)-methyltransferase (5mC methylase) acts on the sequence
AB  - 5'-AGCT-3'.  The amino acid sequences of known 5mC methylases contain ten conserved motifs,
AB  - with a variable region between Motifs VIII and IX that contains one or more
AB  - "target-recognizing domains" responsible for DNA sequence specificity.  Monospecific 5mC
AB  - methylases are believed to have only one TRD, while multi-specific 5mC methylases have as many
AB  - as five.  M.AluI has the second-largest variable region of all known 5mC methylase, and
AB  - sequence analysis reveals five candidate TRDs.  In testing whether M.AluI is in fact
AB  - monospecific it was found that AGCT methylation represents only 80-90% of the methylating
AB  - activity of this enzyme, while control experiments with the enzyme M.HhaI gave no unexplained
AB  - activity.  Because individual TRDs can be deleted from multispecific methylases without
AB  - general loss of activity, a series of insertion and deletion mutants of the M.AluI variable
AB  - region were prepared.  All deletions that removed more than single amino acids from the
AB  - variable region caused significant loss of activity; a sensitive in vivo assay for methylase
AB  - activity based on McrBC restriction suggested that the central portion of the variable region
AB  - is particularly important.  In some cases, multispecific methylases can accommodate a TRD from
AB  - another multispecific methylase, thereby acquiring an additional specificity.  When TRDs were
AB  - removed from a multispecific methylase into two different locations in the variable region of
AB  - M.AluI, all hybrid enzymes had greatly reduced activity and no new specificities.  M.AluI thus
AB  - behaves in most respects as a monospecific methylase despite the remarkable sizeof its
AB  - variable region.
ER  -

TY  - JOUR
AU  - Master, S.S.
AU  - Blumenthal, R.M.
TI  - Is the M.AluI DNA-(cytosine C5)-methyltransferase monospecific or multispecific?
JO  - FASEB J.
PY  - 1995
SP  - A1399
EP  - A1399
VL  - 9
AB  - The AluI DNA-(cytosine C5)-methyltransferase (M.AluI) is part of a type II
AB  - restriction-modification system and methylates cytosine at the 5-carbon position in the
AB  - sequence 5'-AGCT-3'. The predicted amino acid sequences of all known 5-methylcytosine (5mC)
AB  - MTases contain ten conserved motifs, and a variable region which lies between motifs VIII and
AB  - IX. This variable region contains one or more Target Recognition Domains (TRDs) responsible
AB  - for the DNA sequence specificity of the MTase. Monospecific 5mC MTases are believed to have
AB  - only one TRD, while multispecific 5mC methylases have as many as four. M.AluI has the
AB  - second-largest variable region of all known 5mC MTases, and sequence comparisons with the TRDs
AB  - of multispecific MTases reveal four candidate TRDs in the M.AluI variable region. We have
AB  - confirmed that M.AluI is monospecific. Furthermore, we have constructed a series of insertion
AB  - and deletion mutants in order to identify a single contiguous region as the candidate TRD
AB  - responsible for M.AluI 5'-AGCT-3' specificity. In multispecific MTases a TRD is necessary
AB  - and sufficient to confer the cognate specificity, as shown by moving the TRD into another
AB  - multispecific MTase. In monospecific MTases, however, the TRD alone is not sufficient to
AB  - confer the required specificity but requires the presence of at least motif IX from the parent
AB  - MTase. Is M.AluI functionally more closely related to the multispecifics than to other
AB  - monospecifics. We are testing this in collaboration with another laboratory. If M.AluI is like
AB  - the multispecific MTases, than it should accommodate a TRD from a multispecific MTase. When a
AB  - TRD was moved from a multispecific MTase into two different locations in the variable region
AB  - of M.AluI, neither construct gained a new specificity and both had greatly reduced activity.
AB  - To test if the candidate M.AluI TRD is sufficient to confer specificity we are moving it into
AB  - the variable region of a multispecific MTase. From the existing data, it seems as if M.AluI
AB  - behaves in all respects as a monospecific MTase, and the remarkable size of its variable
AB  - region remains to be explained.
ER  -

TY  - JOUR
AU  - Masuda, H.
AU  - Shiwa, Y.
AU  - Yoshikawa, H.
AU  - Zylstra, G.J.
TI  - Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1.
JO  - Genome Announcements
PY  - 2014
SP  - e01271
EP  - e01214
VL  - 2
AB  - The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of
AB  - utilizing both liquid and solid alkanes, was deciphered. This is the
AB  - first report of an Aquabacterium genome sequence.
ER  -

TY  - JOUR
AU  - Masuda, S.
AU  - Hori, K.
AU  - Maruyama, F.
AU  - Ren, S.
AU  - Sugimoto, S.
AU  - Yamamoto, N.
AU  - Mori, H.
AU  - Yamada, T.
AU  - Sato, S.
AU  - Tabata, S.
AU  - Ohta, H.
AU  - Kurokawa, K.
TI  - Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4.
JO  - Genome Announcements
PY  - 2013
SP  - e00577
EP  - e00513
VL  - 1
AB  - We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum
AB  - sulfidophilum. The photosynthesis gene cluster comprises two
AB  - segments-a unique feature among photosynthesis gene clusters of purple bacteria.
AB  - The genome information will be useful for further analysis of bacterial
AB  - photosynthesis.
ER  -

TY  - JOUR
AU  - Matejkova, P.
AU  - Strouhal, M.
AU  - Smajs, D.
AU  - Norris, S.J.
AU  - Palzkill, T.
AU  - Petrosino, J.F.
AU  - Sodergren, E.
AU  - Norton, J.E.
AU  - Singh, J.
AU  - Richmond, T.A.
AU  - Molla, M.N.
AU  - Albert, T.J.
AU  - Weinstock, G.M.
TI  - Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays.
JO  - BMC Microbiol.
PY  - 2008
SP  - 76
EP  - 76
VL  - 8
AB  - BACKGROUND: Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic
AB  - pathogen, since no virulence factors have been identified
AB  - and the pathogenesis of the disease is poorly understood. Increasing rates
AB  - of new syphilis cases per year have been observed recently. RESULTS: The
AB  - genome of the SS14 strain was sequenced to high accuracy by an
AB  - oligonucleotide array strategy requiring hybridization to only three
AB  - arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting
AB  - sequence were filled with targeted dideoxy-terminators (DDT) sequencing
AB  - and the sequence was confirmed by whole genome fingerprinting (WGF). When
AB  - compared to the Nichols strain, 327 single nucleotide substitutions (224
AB  - transitions, 103 transversions), 14 deletions, and 18 insertions were
AB  - found. On the proteome level, the highest frequency of amino acid-altering
AB  - substitution polymorphisms was in novel genes, while the lowest was in
AB  - housekeeping genes, as expected by their evolutionary conservation.
AB  - Evidence was also found for hypervariable regions and multiple regions
AB  - showing intrastrain heterogeneity in the T. pallidum chromosome.
AB  - CONCLUSION: The observed genetic changes do not have influence on the
AB  - ability of Treponema pallidum to cause syphilitic infection, since both
AB  - SS14 and Nichols are virulent in rabbit. However, this is the first
AB  - assessment of the degree of variation between the two syphilis pathogens
AB  - and paves the way for phylogenetic studies of this fascinating organism.
ER  -

TY  - JOUR
AU  - Mateos-Rivera, A.
AU  - Islam, T.
AU  - Marshall, I.P.G.
AU  - Schreiber, L.
AU  - Ovreas, L.
TI  - High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 10
EP  - 10
VL  - 13
AB  - Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph
AB  - isolated from Hardangervidda national park (Norway). This strain
AB  - represents the second of the two validly published species genus with a sequenced
AB  - genome. The other is M. miyakonense HT12, which is the type strain of the species
AB  - and the type species of the genus Methylovulum. We present the genome of M.
AB  - psychrotolerants str. HV10-M2 and discuss the differences between M.
AB  - psychrotolerans and M. miyakonense. The genome size of M. psychrotolerans str.
AB  - HV10-M2 is 4,923,400 bp and contains 4415 protein-coding genes, 50 RNA genes and
AB  - an average GC content of 50.88%.
ER  -

TY  - JOUR
AU  - Mather, A.E. et al.
TI  - Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.
JO  - Science
PY  - 2013
SP  - 1514
EP  - 1517
VL  - 341
AB  - The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides
AB  - an important example, both in terms of the agent and its resistance, of a widely
AB  - disseminated zoonotic pathogen. Here, with an unprecedented national collection
AB  - of isolates collected contemporaneously from humans and animals and including a
AB  - sample of internationally derived isolates, we have used whole-genome sequencing
AB  - to dissect the phylogenetic associations of the bacterium and its antimicrobial
AB  - resistance genes through the course of an epidemic. Contrary to current tenets
AB  - supporting a single homogeneous epidemic, we demonstrate that the bacterium and
AB  - its resistance genes were largely maintained within animal and human populations
AB  - separately and that there was limited transmission, in either direction. We also
AB  - show considerable variation in the resistance profiles, in contrast to the
AB  - largely stable bacterial core genome, which emphasizes the critical importance of
AB  - integrated genotypic data sets in understanding the ecology of bacterial zoonoses
AB  - and antimicrobial resistance.
ER  -

TY  - JOUR
AU  - Mathers, A.J.
AU  - Stoesser, N.
AU  - Sheppard, A.E.
AU  - Pankhurst, L.
AU  - Giess, A.
AU  - Yeh, A.J.
AU  - Didelot, X.
AU  - Turner, S.D.
AU  - Sebra, R.
AU  - Kasarskis, A.
AU  - Peto, T.
AU  - Crook, D.
AU  - Sifri, C.D.
TI  - Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.
JO  - Antimicrob. Agents Chemother.
PY  - 2015
SP  - 1656
EP  - 1663
VL  - 59
AB  - The global emergence of Klebsiella pneumoniae carbapenemase-producing K.
AB  - pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is
AB  - known about the molecular and epidemiological details of non-ST258 K. pneumoniae
AB  - in the setting of an outbreak mediated by an endemic plasmid. We describe the
AB  - interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to
AB  - the location of acquisition in a U.S. health care institution. Whole-genome
AB  - sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from
AB  - a single institution over 5 years following the introduction of blaKPC in August
AB  - 2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16
AB  - distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01
AB  - and pKPC_UVA02), carried by the hospital index case, accounted for the presence
AB  - of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an
AB  - emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02
AB  - in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258,
AB  - mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using
AB  - WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate
AB  - the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital
AB  - through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp
AB  - was imported into the institution on numerous occasions, with other blaKPC
AB  - plasmid vectors and without sustained transmission. Instead, a newly recognized
AB  - KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and
AB  - spread locally, making it a future candidate for clinical persistence and
AB  - dissemination.
ER  -

TY  - JOUR
AU  - Mathew, D.C.
AU  - Lo, S.C.
AU  - Mathew, G.M.
AU  - Chang, K.H.
AU  - Huang, C.C.
TI  - Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 56
EP  - 56
VL  - 11
AB  - Mercury impacts the function and development of the central nervous system in both humans and
AB  - wildlife by being a potent neurotoxin. Microbial bioremediation
AB  - is an important means of remediation of mercury-contaminated soil. The
AB  - rhizospheric Photobacterium halotolerans strain MELD1 was isolated from mercury
AB  - and dioxin contaminated site from Tainan, Taiwan. It has been shown to reduce
AB  - Hg(2+) to Hg(0). The 4,758,027 bp genome of P. halotolerans MELD1 has a G + C
AB  - content of 50.88 % and contains 4198 protein-coding and 106 RNA genes. Genomic
AB  - analysis revealed the presence of a number of interesting gene cluster that maybe
AB  - involved in heavy metal resistance, rhizosphere competence and colonization of
AB  - the host plant.
ER  -

TY  - JOUR
AU  - Mathew, D.C.
AU  - Mathew, G.M.
AU  - Gicana, R.G.
AU  - Huang, C.C.
TI  - Genome Sequence of Photobacterium halotolerans MELD1, with Mercury Reductase (merA), Isolated from Phragmites australis.
JO  - Genome Announcements
PY  - 2015
SP  - e00530
EP  - e00515
VL  - 3
AB  - Here, we present the whole-genome sequence of Photobacterium halotolerans strain, MELD1,
AB  - isolated from the roots of a terrestrial plant Phragmites australis grown
AB  - in soil heavily contaminated with mercury and dioxin. The genome provides further
AB  - insight into the adaptation of bacteria to the toxic environment from where it
AB  - was isolated.
ER  -

TY  - JOUR
AU  - Mathew, M.J.
AU  - Subramanian, G.
AU  - Nguyen, T.T.
AU  - Robert, C.
AU  - Mediannikov, O.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Genome Sequence of Diplorickettsia massiliensis, an Emerging Ixodes ricinus-Associated Human Pathogen.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3287
EP  - 3287
VL  - 194
AB  - Diplorickettsia massiliensis is a gammaproteobacterium in the order Legionellales and an agent
AB  - of tick-borne infection. We sequenced the genome from strain 20B,
AB  - isolated from an Ixodes ricinus tick. The genome consists of a 1,727,973-bp
AB  - chromosome but no plasmid and includes 2,269 protein-coding genes and 42 RNA
AB  - genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Mathews, S.L.
AU  - Pawlak, J.
AU  - Grunden, A.M.
TI  - Draft Genome Sequences of Two Strains of Paenibacillus glucanolyticus with the Ability To Degrade Lignocellulose.
JO  - Genome Announcements
PY  - 2016
SP  - e00423
EP  - e00416
VL  - 4
AB  - Paenibacillus glucanolyticus 5162, a bacterium isolated from soil, and Paenibacillus
AB  - glucanolyticus SLM1, a bacterium isolated from pulp mill waste, can
AB  - utilize cellulose, hemicellulose and lignin as sole carbon sources for growth.
AB  - These two strains of Paenibacillus glucanolyticus were sequenced using PacBio and
AB  - Illumina MiSeq technologies.
ER  -

TY  - JOUR
AU  - Mathimaran, N.
AU  - Srivastava, R.
AU  - Wiemken, A.
AU  - Sharma, A.K.
AU  - Boller, T.
TI  - Genome sequences of two plant growth-promoting fluorescent pseudomonas strains, r62 and r81.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3272
EP  - 3273
VL  - 194
AB  - Plant growth-promoting rhizobacterial (PGPR) strains R62 and R81 have previously  been
AB  - isolated and characterized as part of the Indo-Swiss Collaboration in
AB  - Biotechnology. Here we present the draft genome sequences of these two PGPR
AB  - strains, with the aim of unraveling the mechanisms behind their ability to
AB  - promote wheat growth.
ER  -

TY  - JOUR
AU  - Mathur, P.
AU  - Veeraraghavan, B.
AU  - Devanga, R.N.K.
AU  - Inbanathan, F.Y.
AU  - Khurana, S.
AU  - Bhardwaj, N.
AU  - Kumar, S.
AU  - Sagar, S.
AU  - Gupta, A.
TI  - First Report on a Cluster of Colistin-Resistant Klebsiella pneumoniae Strains Isolated from a Tertiary Care Center in India: Whole-Genome Shotgun Sequencing.
JO  - Genome Announcements
PY  - 2017
SP  - e01466
EP  - e01416
VL  - 5
AB  - Klebsiella pneumoniae is a nosocomial pathogen with clinical importance due to its increasing
AB  - resistance to carbapenems and colistin. Here, we report the genome
AB  - sequences of eight colistin-resistant K. pneumoniae strains which might help in
AB  - understanding the molecular mechanism of the species. The sequence data indicate
AB  - genomes of ~5.2 to 5.4 Mb, along with several plasmids.
ER  -

TY  - JOUR
AU  - Matic, I.
AU  - Taddei, F.
AU  - Radman, M.
TI  - Genetic barriers among bacteria.
JO  - Trends Microbiol.
PY  - 1996
SP  - 69
EP  - 73
VL  - 4
AB  - Barriers to chromosomal gene transfer between bacterial species control their genetic
AB  - isolation.  These barriers, such as different microhabitats, the host ranges of genetic
AB  - exchange vectors and restriction-modification systems, limit gene exchange, but the major
AB  - limitation is genomic sequence divergence.  The mismatch-repair system inhibits interspecies
AB  - recombination, the inducible SOS system stimulates interspecies recombination, while natural
AB  - selection determines the effective recombination frequencies.
ER  -

TY  - JOUR
AU  - Matilla, M.A.
AU  - Drew, A.
AU  - Udaondo, Z.
AU  - Krell, T.
AU  - Salmond, G.P.
TI  - Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and  Andrimid.
JO  - Genome Announcements
PY  - 2016
SP  - e00373
EP  - e00316
VL  - 4
AB  - The rhizobacterium Serratia plymuthica A153 is a Gram-negative bacterium belonging to the
AB  - family Enterobacteriaceae Here, we present the genome sequence
AB  - of this strain, which produces multiple bioactive secondary metabolites,
AB  - including the halogenated macrolide oocydin A, the polyamino antibiotic zeamine,
AB  - and the bacterial acetyl-CoA carboxylase inhibitor andrimid.
ER  -

TY  - JOUR
AU  - Matilla, M.A.
AU  - Pizarro-Tobias, P.
AU  - Roca, A.
AU  - Fernandez, M.
AU  - Duque, E.
AU  - Molina, L.
AU  - Wu, X.
AU  - van der Lelie, D.
AU  - Gomez, M.J.
AU  - Segura, A.
AU  - Ramos, J.L.
TI  - Complete genome of the plant-growth promoting rhizobacterium Pseudomonas putida BIRD-1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1290
EP  - 1290
VL  - 193
AB  - We report the complete sequence of the 5.7-Mbp of Pseudomonas putida BIRD-1, a
AB  - metabolically-versatile plant growth-promoting rhizobacterium that is highly tolerant to
AB  - desiccation, capable of solubilizing inorganic phosphate and iron, and of synthesizing
AB  - phytohormones that stimulate seed germination and plant growth.
ER  -

TY  - JOUR
AU  - Matilla, M.A.
AU  - Udaondo, Z.
AU  - Krell, T.
AU  - Salmond, G.P.
TI  - Genome Sequence of Serratia marcescens MSU97, a Plant-Associated Bacterium That Makes Multiple Antibiotics.
JO  - Genome Announcements
PY  - 2017
SP  - e01752
EP  - e01716
VL  - 5
AB  - Serratia marcescens MSU97 was isolated from the Guayana region of Venezuela due to its ability
AB  - to suppress plant-pathogenic oomycetes. Here, we report the genome
AB  - sequence of MSU97, which produces various antibiotics, including the bacterial
AB  - acetyl-coenzyme A (acetyl-CoA) carboxylase inhibitor andrimid, the chlorinated
AB  - macrolide oocydin A, and the red linear tripyrrole antibiotic prodigiosin.
ER  -

TY  - JOUR
AU  - Matin, M.M.
AU  - Hornby, D.P.
TI  - A positive selection vector combining tetracycline resistance that eliminates the need for bacterial plating comprising a modified version of the gene encoding the cytosine-specific DNA-methyltransferase and a modified form of the plasmid pBR322 tetA(C).
JO  - Anal. Biochem.
PY  - 2000
SP  - 46
EP  - 51
VL  - 278
AB  - The construction of plasmid pMTet1 that combined positive selection with
AB  - tetracycline-resistance was described. The vector comprised a
AB  - modified version of the gene encoding the cytosine(C-5)-specific
AB  - DNA-methyltransferase (C5-Mtase) MspI and a modified form of the
AB  - plasmid pBR322 tetA(C) gene. This combination of a C5-Mtase gene and
AB  - the tetA(C) derived from plasmid pBR322 permitted the isolation of
AB  - recombinant plasmids in liquid culture which for the first time
AB  - eliminated the need to isolate single, antibiotic-resistant colonies
AB  - and therefore significantly accelerated recombinant plasmid isolation.
AB  - Furthermore, the application of this novel cloning vector, in
AB  - conjunction with chromatographic DNA fractionation, for the
AB  - construction of size-selected recombinant molecules was reported. The
AB  - construction of the plasmid pMTet1 was followed by the DNA
AB  - amplification reaction and nucleic acid chromatography. The plasmid
AB  - pMTet1 facilitated the rapid cloning of DNA molecules generated by
AB  - proof-reading DNA-polymerases and restriction digests using enzymes
AB  - that produced noncohesive termini.
ER  -

TY  - JOUR
AU  - Matin, M.M.
AU  - Hornby, D.P.
TI  - Exploring the structural flexibility of 5m-cytosine-DNA methyltransferases.
JO  - Biochem. Soc. Trans.
PY  - 1998
SP  - S394
EP  - S394
VL  - 26
AB  - DNA methyltransferases are found in organisms ranging from bacteria to mammals.  They
AB  - recognize specific DNA sequences and transfer a methyl group to adenine or cytosine residues.
AB  - 5m-cytosine methyltransferases form the basis of the work considered here, they belong to type
AB  - II restriction-modification systems, which use S-adenosyl-L-methionine as a cofactor to add
AB  - methyl groups to the 5 position of cytosine.  Two families of 5mC Mtases are known;
AB  - mono-specific methyltransferases which recognize and methylate a single DNA sequence, and
AB  - multi-specific Mtases that recognize and modify more than one DNA sequence.
ER  -

TY  - JOUR
AU  - Matje, D.M.
AU  - Coughlin, D.F.
AU  - Connolly, B.A.
AU  - Dahlquist, F.W.
AU  - Reich, N.O.
TI  - Determinants of Precatalytic Conformational Transitions in the DNA Cytosine Methyltransferase M.HhaI.
JO  - Biochemistry
PY  - 2011
SP  - 1465
EP  - 1473
VL  - 50
AB  - The DNA methyltransferase M.HhaI is an excellent model for understanding how recognition of a
AB  - nucleic acid substrate is translated
AB  - into site-specific modification. In this study, we utilize direct,
AB  - real-time monitoring of the catalytic loop position via engineered
AB  - tryptophan fluorescence reporters to dissect the conformational
AB  - transitions that occur in both enzyme and DNA substrate prior to
AB  - methylation of the target cytosine. Using nucleobase analogues in place
AB  - of the target and orphan bases, the kinetics of the base flipping and
AB  - catalytic loop closure rates were determined, revealing that base
AB  - flipping precedes loop closure as the rate-determining step prior to
AB  - methyl transfer. To determine the mechanism by which individual
AB  - specific hydrogen bond contacts at the enzyme DNA interface mediate
AB  - these conformational transitions, nucleobase analogues lacking hydrogen
AB  - bonding groups were incorporated into the recognition sequence to
AB  - disrupt the major groove recognition elements. The consequences of
AB  - binding, loop closure, and catalysis were determined for four contacts,
AB  - revealing large differences in the contribution of individual hydrogen
AB  - bonds to DNA recognition and conformational transitions on the path to
AB  - catalysis. Our results describe how M.HhaI utilizes direct readout
AB  - contacts to accelerate extrication of the target base that offer new
AB  - insights into the evolutionary history of this important class of
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Matje, D.M.
AU  - Zhou, H.
AU  - Smith, D.A.
AU  - Neely, R.K.
AU  - Dryden, D.T.
AU  - Jones, A.C.
AU  - Dahlquist, F.W.
AU  - Reich, N.O.
TI  - Enzyme-Promoted Base Flipping Controls DNA Methylation Fidelity.
JO  - Biochemistry
PY  - 2013
SP  - 1677
EP  - 1685
VL  - 52
AB  - A quantitative understanding of how conformational transitions contribute to enzyme catalysis
AB  - and specificity remains a fundamental challenge. A suite of
AB  - biophysical approaches was used to reveal several transient states of the
AB  - enzyme-substrate complexes of the model DNA cytosine methyltransferase M.HhaI.
AB  - Multidimensional, transverse relaxation-optimized nuclear magnetic resonance
AB  - (NMR) experiments show that M.HhaI has the same conformation with noncognate and
AB  - cognate DNA sequences. The high-affinity cognatelike mode requires the formation
AB  - of a subset of protein-DNA interactions that drive the flipping of the target
AB  - base from the helix to the active site. Noncognate substrates lacking these
AB  - interactions undergo slow base flipping, and fluorescence tracking of the
AB  - catalytic loop corroborates the NMR evidence of a loose, nonspecific binding mode
AB  - prior to base flipping and subsequent closure of the catalytic loop. This slow
AB  - flipping transition defines the rate-limiting step for the methylation of
AB  - noncognate sequences. Additionally, we present spectroscopic evidence of an
AB  - intermediate along the base flipping pathway that has been predicted but never
AB  - previously observed. These findings provide important details of how
AB  - conformational rearrangements are used to balance specificity with catalytic
AB  - efficiency.
ER  -

TY  - JOUR
AU  - Matney, T.S.
AU  - MacDougall, N.L.T.
AU  - Butler, M.A.
AU  - Suit, J.C.
TI  - Host-induced modification/restriction and the utilization of 5-bromouracil by thymineless mutants of Escherichia coli.
JO  - J. Bacteriol.
PY  - 1970
SP  - 606
EP  - 607
VL  - 104
AB  - An mk-rk- mutation exerted no measurable effect on 5-bromouracil incorporation
AB  - by a thymineless derivative of Escherichia coli K.
ER  -

TY  - JOUR
AU  - Matrosova, V.Y. et al.
TI  - High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 46
EP  - 46
VL  - 12
AB  - The genetic platforms of Deinococcus species remain the only systems in which massive ionizing
AB  - radiation (IR)-induced genome damage can be investigated in vivo
AB  - at exposures commensurate with cellular survival. We report the whole genome
AB  - sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS
AB  - 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been
AB  - studied since 1987, first under the name Deinobacter grandis, then Deinococcus
AB  - grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC
AB  - content and 3894 predicted genes) divided into six genome partitions, five of
AB  - which are confirmed to be circular. Circularity was determined manually by mate
AB  - pair linkage. Approximately 76% of the predicted proteins contained identifiable
AB  - Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79%
AB  - and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus
AB  - geothermalis DSM 11300, respectively. The most striking differences between D.
AB  - ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG
AB  - pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation
AB  - present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in
AB  - nitrogen metabolism, including nitrate and nitrite reductases, that D.
AB  - radiodurans lacks. Moreover, genes previously considered to be important to IR
AB  - resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp,
AB  - and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus
AB  - deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
ER  -

TY  - JOUR
AU  - Matselyukh, A.B.
TI  - Genetic transformation of Streptomyces globisporus 1912 strains: restriction barrier and plasmid compatibility.
JO  - Mikrobiol. Zh.
PY  - 2001
SP  - 15
EP  - 21
VL  - 63
AB  - Low efficiency of genetic transformation of protoplasts of different strains of Streptomyces
AB  - globisporus 1912 by means of DNA preparations
AB  - of three vectors pIJ487, pGM160 and pWHM4 is explained by the presence of
AB  - a restriction barrier in the recipients. This obstacle can be
AB  - overcome by the use of modified DNA of the same vectors, isolated from
AB  - not numerous transformants. The frequency of transformation by such
AB  - modified vector DNA was increased by two-three orders in comparison
AB  - with initial DNA, isolated from Streptomyces lividans TK24, losing
AB  - restriction-modification system. The vector pCNB4001, containing the
AB  - replicon of endogeneous plasmid pSG1912-1, effectively transformed the
AB  - protoplasts of all S. globisporus 1912 strains. Compatibility of pIJ487
AB  - and pSG1912-1 plasmids and incompatibility of the latter and pWHM4 was
AB  - shown.
ER  -

TY  - JOUR
AU  - Matson, E.G.
AU  - Zhang, X.
AU  - Leadbetter, J.R.
TI  - Selenium controls transcription of paralogous formate dehydrogenase genes in the termite gut acetogen, Treponema primitia.
JO  - Environ. Microbiol.
PY  - 2010
SP  - 2245
EP  - 2258
VL  - 12
AB  - Summary The termite gut spirochete, Treponema primitia, is a CO(2)-reductive acetogen that is
AB  - phylogenetically distinct from other distantly related and more extensively studied acetogens
AB  - such as Moorella thermoacetica. Research on T. primitia has revealed details about the role of
AB  - spirochetes in CO(2)-reductive acetogenesis, a process important to the mutualism occurring
AB  - between termites and their gut microbial communities. Here, a locus of the T. primitia genome
AB  - containing Wood-Ljungdahl pathway genes for CO(2)-reductive acetogenesis was sequenced. This
AB  - locus contained methyl-branch genes of the pathway (i.e. for the reduction of CO(2) to the
AB  - level of methyl-tetrahydrofolate) including paralogous genes for cysteine and selenocysteine
AB  - (Sec) variants of formate dehydrogenase (FDH) and genes for Sec incorporation. The FDH
AB  - variants affiliated phylogenetically with hydrogenase-linked FDH enzymes, suggesting that T.
AB  - primitia FDH enzymes utilize electrons derived directly from molecular H(2). Sub-nanomolar
AB  - concentrations of selenium decreased transcript levels of the cysteine variant FDH gene.
AB  - Selenium concentration did not markedly influence the level of mRNA upstream of the Sec-codon
AB  - in the Sec variant FDH; however, the level of transcript extending downstream of the Sec-codon
AB  - increased incrementally with increasing selenium concentrations. The features and regulation
AB  - of these FDH genes are an indication that T. primitia may experience dynamic selenium
AB  - availability in its H(2)-rich gut environment.
ER  -

TY  - JOUR
AU  - Matsui, H.
AU  - Takahashi, T.
AU  - Murayama, S.Y.
AU  - Uchiyama, I.
AU  - Yamaguchi, K.
AU  - Shigenobu, S.
AU  - Suzuki, M.
AU  - Rimbara, E.
AU  - Shibayama, K.
AU  - Overby, A.
AU  - Nakamura, M.
TI  - Draft Genome Sequence of Helicobacter suis Strain SNTW101, Isolated from a Japanese Patient with Nodular Gastritis.
JO  - Genome Announcements
PY  - 2016
SP  - e00934
EP  - e00916
VL  - 4
AB  - We present here the draft whole-genome shotgun sequence of an uncultivated strain SNTW101 of
AB  - Helicobacter suis, which has been maintained in the stomachs of mice.
AB  - This strain was originally isolated from gastric biopsy specimens of a urea
AB  - breath test-negative Japanese patient suffering from nodular gastritis.
ER  -

TY  - JOUR
AU  - Matsui, M.
AU  - Mise, K.
AU  - Yoshida, Y.
AU  - Ishidate, M.
TI  - Production of restriction endonucleases from various Salmonella strains of human origin.
JO  - Eisei Shikenjo Hokoku
PY  - 1986
SP  - 92
EP  - 96
VL  - 104
AB  - Using a safe procedure for the detection of restriction endonuclease-producing
AB  - strains, 21 restriction-positive strains were found among 120 Salmonella
AB  - strains of human origin.  The designation of the restriction endonucleases and
AB  - their producers was SinI and SinII in Salmonella infantis (11 strains), SblI in
AB  - Salmonella blockley (3 strains), StmI in Salmonella typhimurium, SbaI in
AB  - Salmonella bareilly, SscI in Salmonella schwarzengrund, SthI in Salmonella
AB  - thompson, SanI in Salmonella anatum, SisI in Salmonella Isangi and SbrI in
AB  - Salmonella bredeney.  Activity of all the endonucleases was very high.  No Hsd
AB  - plasmids has been isolated from these restriction endonuclease-producing
AB  - strains in spite of several trials, indicating that the hsd+ gene might be
AB  - carried on chromosomal DNA.
ER  -

TY  - JOUR
AU  - Matsumoto, A.
AU  - Igo, M.M.
TI  - Species-Specific Type II Restriction-Modification System of Xylella fastidiosa Temecula1.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 4092
EP  - 4095
VL  - 76
AB  - The transformation efficiency of Xylella fastidiosa can be increased by interfering with
AB  - restriction by the strain-specific type II system
AB  - encoded by the PD1607 and PD1608 genes. Here, we report results for two
AB  - strategies: in vitro methylation using M. SssI and isolation of DNA
AB  - from an Escherichia coli strain expressing the methylase PD1607.
ER  -

TY  - JOUR
AU  - Matsumura, H.
AU  - Takahashi, H.
AU  - Inoue, T.
AU  - Yamamoto, T.
AU  - Hashimoto, H.
AU  - Nishioka, M.
AU  - Fujiwara, S.
AU  - Takagi, M.
AU  - Imanaka, T.
AU  - Kai, Y.
TI  - Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1.
JO  - Proteins
PY  - 2006
SP  - 711
EP  - 715
VL  - 63
ER  -

TY  - JOUR
AU  - Matsumura, Y.
AU  - Peirano, G.
AU  - Pitout, J.D.D.
TI  - Complete Genome Sequence of Escherichia coli J53, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments.
JO  - Genome Announcements
PY  - 2018
SP  - e00433
EP  - e00418
VL  - 6
AB  - We report here the complete genome sequence of Escherichia coli J53, which is used as a
AB  - recipient in conjugation experiments and is a laboratory strain derived
AB  - from E. coli K-12. This genome sequence will help in the development of a
AB  - comprehensive genetic analysis of conjugative elements.
ER  -

TY  - JOUR
AU  - Matsumura, Y.
AU  - Yamamoto, M.
AU  - Nakano, S.
AU  - Nagao, M.
TI  - Complete Genome Sequence of Escherichia coli ME8067, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments.
JO  - Genome Announcements
PY  - 2018
SP  - e00515
EP  - e00518
VL  - 6
AB  - We report here the complete genome sequence of Escherichia coli ME8067, an azide-resistant
AB  - laboratory strain used for conjugation experiments. The ME8067
AB  - genome was closely related to E. coli strain K-12 substrain W3110. This genome
AB  - sequence will support further genetic analysis of conjugative elements.
ER  -

TY  - JOUR
AU  - Matsunaga, E.
AU  - Higuchi, Y.
AU  - Mori, K.
AU  - Tashiro, K.
AU  - Kuhara, S.
AU  - Takegawa, K.
TI  - Draft Genome Sequence of Streptomyces sp. JHA19, a Strain That Possesses beta-d-Galactofuranosidase Activity.
JO  - Genome Announcements
PY  - 2015
SP  - e01171
EP  - e01115
VL  - 3
AB  - By screening for microbes that exhibit beta-d-galactofuranosidase (Galf-ase) activity, a
AB  - Streptomyces sp. strain, named JHA19, was isolated from a soil sample from Kagawa University,
AB  - Japan, in 2010. Here, we report the results of whole-genome shotgun sequencing and found that
AB  - the strain has four predicted Galf-ase genes.
ER  -

TY  - JOUR
AU  - Matsunaga, E.
AU  - Higuchi, Y.
AU  - Mori, K.
AU  - Tashiro, K.
AU  - Takegawa, K.
TI  - Draft Genome Sequence of Streptomyces sp. JHA26, a Strain That Harbors a PA14 Domain Containing beta-d-Galactofuranosidase.
JO  - Genome Announcements
PY  - 2017
SP  - e00190
EP  - e00117
VL  - 5
AB  - The genome sequence of Streptomyces sp. strain JHA26, the culture supernatant of  which
AB  - exhibited beta-d-galactofuranosidase (Galf-ase) activity, was analyzed to
AB  - search for a Galf-ase-encoding gene. We report here the results of whole-genome
AB  - shotgun sequencing and reveal the identity of a new Galf-ase gene.
ER  -

TY  - JOUR
AU  - Matsunaga, T.
AU  - Okamura, Y.
AU  - Fukuda, Y.
AU  - Wahyudi, A.T.
AU  - Murase, Y.
AU  - Takeyama, H.
TI  - Complete Genome Sequence of the Facultative Anaerobic Magnetotactic Bacterium Magnetospirillum sp. strain AMB-1.
JO  - DNA Res.
PY  - 2005
SP  - 157
EP  - 166
VL  - 12
AB  - Magnetospirillum sp. strain AMB-1 is a Gram-negative alpha-proteobacterium that synthesizes
AB  - nano-sized magnetites, referred to as magnetosomes,
AB  - aligned intracellularly in a chain. The potential of this nano-sized
AB  - material is growing and will be applicable to broad research areas. It has
AB  - been expected that genome analysis would elucidate the mechanism of
AB  - magnetosome formation by magnetic bacteria. Here we describe the genome of
AB  - Magnetospirillum sp. AMB-1 wild type, which consists of a single circular
AB  - chromosome of 4967148 bp. For identification of genes required for
AB  - magnetosome formation, transposon mutagenesis and determination of
AB  - magnetosome membrane proteins were performed. Analysis of a non-magnetic
AB  - transposon mutant library focused on three unknown genes from 2752 unknown
AB  - genes and three genes from 205 signal transduction genes. Partial proteome
AB  - analysis of the magnetosome membrane revealed that the membrane contains
AB  - numerous oxidation/reduction proteins and a signal response regulator that
AB  - may function in magnetotaxis. Thus, oxidation/reduction proteins and
AB  - elaborate multidomain signaling proteins were analyzed. This comprehensive
AB  - genome analysis will enable resolution of the mechanisms of magnetosome
AB  - formation and provide a template to determine how magnetic bacteria
AB  - maintain a species-specific, nano-sized, magnetic single domain and
AB  - paramagnetic morphology.
ER  -

TY  - JOUR
AU  - Matsuo, K.
AU  - Silke, J.
AU  - Gramatikoff, K.
AU  - Schaffner, W.
TI  - The CpG-specific methylase SssI has topoisomerase activity in the presence of Mg2+.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 5354
EP  - 5359
VL  - 22
AB  - A prokaryotic CpG-specific methylase from Spiroplasma, SssI methylase, is now widely used to
AB  - study the effect of CpG methylation in mammalian cells, and can processively modify cytosines
AB  - in CpG dinucleotides in the absence of Mg2+. In the presence of Mg2+, we found (i) that the
AB  - methylation reaction is distributive rather than processive as a result of the decreased
AB  - affinity of SssI methylase for DNA, and (ii) that a type I-like topoisomerase activity is
AB  - present in SssI methylase preparations. This topoisomerase activity was still present in SssI
AB  - methylase further purified by either SDS-polyacrylamide or isoelectric focusing gel
AB  - electrophoresis. We show that methylase and topoisomerase activities are not functionally
AB  - interdependent, since conditions exist where only one or the other enzymatic activity is
AB  - detectable. The catalytic domains of SssI methylase and prokaryotic topoisomerases show
AB  - similarity at the amino acid level, further supporting the idea that the topoisomerase
AB  - activity is a genuine activity of SssI methylase. Mycoplasmas, including Spiroplasma, have the
AB  - smallest genomes of all living organisms; thus, this condensation of two enzymatic activities
AB  - into the same protein may be a result of genome economy, and may also have functional
AB  - implications for the mechanism of methylation.
ER  -

TY  - JOUR
AU  - Matsuoka, S.
AU  - Asai, K.
AU  - Sadaie, Y.
TI  - Restriction and modification of SP10 phage by BsuM of Bacillus subtilis Marburg.
JO  - FEMS Microbiol. Lett.
PY  - 2005
SP  - 335
EP  - 339
VL  - 244
AB  - Bacillus subtilis Marburg has only one intrinsic restriction and modification system BsuM that
AB  - recognizes the CTCGAG (XhoI site)
AB  - sequence. It consists of two operons, BsuMM operon for two cytosine DNA
AB  - methyltransferases, and BsuMR operon for a restriction nuclease and two
AB  - associated proteins of unknown function. In this communication, we
AB  - analyzed the BsuM system by utilizing phage SPIO that possesses more
AB  - than twenty BsuM target sequences on the phage genome. SPIO phages
AB  - grown in the restriction and modification-deficient strain could not
AB  - make plaques on the restriction-proficient BsuMR(+) indicator strain.
AB  - An enforced expression of the wild type BsuMM operon in the BsuMR(+)
AB  - indicator strain, however, allowed more than thousand times more
AB  - plaques. DNA extracted from SPIO phages, thus, propagated became more
AB  - but not completely refractory to XhoI digestion in vitro. Thus, the
AB  - SPIO phage genome DNA is able to be nearly full-methylated but some
AB  - BsuM sites are considered to be unmethylated.
ER  -

TY  - JOUR
AU  - Matsushima, P.
AU  - Baltz, R.H.
TI  - Streptomyces lipmanii expresses two restriction systems that inhibit plasmid transformation and bacteriophage plaque formation.
JO  - J. Bacteriol.
PY  - 1989
SP  - 3128
EP  - 3132
VL  - 171
AB  - Bacteriophage host range studies suggested that several beta-lactam-producing streptomycetes
AB  - express similar restriction-modification systems.  Streptomyces lipmanii LE32 expressed two
AB  - restriction-modification systems, designated SliI and SliII.  A mutant strain, PM87, was
AB  - defective only in SliI restriction but expressed both SliI and SliII modification.
AB  - Streptomyces sp. strain A57986, a natural isolate partially deficient in the expression of
AB  - SliI and SliII restriction, nevertheless modified bacteriophage DNA for both SliI and SliII
AB  - specificities.  Protoplasts of PM87 and A57986 were transformed by several plasmids, and the
AB  - modified plasmids isolated from these strains transformed wild-type S. lipmanii efficiently.
ER  -

TY  - JOUR
AU  - Matsushima, P.
AU  - Baltz, R.H.
TI  - Restriction and modification in Streptomyces lipmanii.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 361
EP  - 361
VL  - 89
AB  - Steptomyces lipmanii and several other beta-lactam antibiotic-producing
AB  - streptomycetes express restriction systems that inhibit plasmid transformation
AB  - and bacteriophage plaque formation.  Bacteriophage host range studies suggested
AB  - that many beta-lactam producers express some common restriction system(s).  We
AB  - isolated a mutant, S. lipmanii PM87, defective in one restriction system (SliI)
AB  - and analyzed restriction and modification of several different bacteriophages
AB  - in PM87 and its parent strain, LE32.  PM87 appears to be proficient in SliI
AB  - modification and expresses a second restriction/modification system, designated
AB  - SliII.  Another beta-lactam producing streptomycete, strain A57986, which was
AB  - naturally less restricting than S. lipmanii, expressed only SliI restriction
AB  - and modification.  PM87 and A57986 were readily transformed by many unmodified
AB  - plasmids; once modified in these hosts the same plasmids were efficiently
AB  - introduced into more restricting strains by transformation.
ER  -

TY  - JOUR
AU  - Matsushima, P.
AU  - Cox, K.L.
AU  - Baltz, R.H.
TI  - Highly transformable mutants of Streptomyces fradiae defective in several restriction systems.
JO  - Mol. Gen. Genet.
PY  - 1987
SP  - 393
EP  - 400
VL  - 206
AB  - Streptomyces fradiae JS85 is a mutant defective in tylosin production and an
AB  - efficient recipient for conjugal transfer of tylosin genes.  JS85 was
AB  - mutagenized with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and derivatives
AB  - defective in restriction were isolated by sequential selection for increased
AB  - transformability by several plasmid DNAs.  From the number of mutation and
AB  - selection cycles required to eliminate most restriction, it was estimated that
AB  - wild type S. fradiae expressed at least five restriction systems.  From the
AB  - patterns of restriction enzyme digestion of chromosomal DNA observed in the
AB  - series of mutants that became progressively less restricting, it was suggested
AB  - that wild type S. fradiae normally expresses modification (and presumably
AB  - restriction) systems similar or analogous to PstI, XhoI, ScaI and EcoRI.  The
AB  - least restricting mutant of S. fradiae was readily transformable by many
AB  - plasmids, including a bifunctional cosmid vector containing a large insert of
AB  - Streptomyces DNA.
ER  -

TY  - JOUR
AU  - Matsushima, P.
AU  - McHenney, M.A.
AU  - Baltz, R.H.
TI  - Efficient transformation of Amycolatopsis orientalis (Nocardia orientalis) protoplasts by Streptomyces plasmids.
JO  - J. Bacteriol.
PY  - 1987
SP  - 2298
EP  - 2300
VL  - 169
AB  - Conditions for efficient transformation of Amycolatopsis orientalis (Nocardia
AB  - orientalis) protoplasts by Streptomyces plasmid cloning vectors were
AB  - identified.  Three streptomycete plasmid origins of replication function in A.
AB  - orientalis, as do the apramycin resistance gene from Escherichia coli, the
AB  - thiostrepton resistance gene from Streptomyces azureus, and the tyrosinase gene
AB  - from Streptomyces antibioticus.  A. orientalis appears to express some
AB  - restriction and modification, because highest transformation frequencies
AB  - (1000000/microgram DNA) were obtained when plasmid pIJ702 was modified in A.
ER  -

TY  - JOUR
AU  - Matsushima, P.
AU  - McHenney, M.A.
AU  - Baltz, R.H.
TI  - Transduction and transformation of plasmid DNA in Streptomyces fradiae strains that express different levels of restriction.
JO  - J. Bacteriol.
PY  - 1989
SP  - 3080
EP  - 3084
VL  - 171
AB  - We constructed nonrestricting strains of Streptomyces fradiae blocked in
AB  - different steps in tylosin biosynthesis.  Plasmid transformation frequencies
AB  - were 10/3 to 10/4-fold higher and bacteriophage plating efficiences were 10/4
AB  - to 10/8-fold higher in the nonrestricting strains than in the restricting
AB  - strains.  The efficiences of transduction of plasmid pRHB101 in S. fradiae
AB  - strains varied by over 1,000-fold, depending on growth conditions, and optimum
AB  - transduction frequencies were obtained when cells were grown to mid-exponential
AB  - phase at 39C.  Under these conditions, restricting and nonrestricting strains
AB  - were transduced at frequencies that differed by only two- to fivefold.
ER  -

TY  - JOUR
AU  - Matsushita, S.
AU  - Nakano, M.
AU  - Aoi, Y.
AU  - Kindaichi, T.
AU  - Ozaki, N.
AU  - Ohashi, A.
TI  - Draft Genome Sequence of Mn(II)-Oxidizing Pseudomonas resinovorans Strain MO-1.
JO  - Genome Announcements
PY  - 2018
SP  - e00088
EP  - e00018
VL  - 6
AB  - Pseudomonas resinovorans strain MO-1, which possesses a high ability to oxidize Mn(II), has
AB  - been isolated from oligotrophic pond sediment. The draft genome
AB  - sequence consists of 6,252,942 bp and has a G+C content of 63.4%. Strain MO-1 has
AB  - 5,694 coding sequences, including 13 putative Mn(II) oxidation genes.
ER  -

TY  - JOUR
AU  - Matsutani, M.
AU  - Hirakawa, H.
AU  - Nishikura, M.
AU  - Soemphol, W.
AU  - Ali, I.A.
AU  - Yakushi, T.
AU  - Matsushita, K.
TI  - Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2011
SP  - 120
EP  - 124
VL  - 409
AB  - Thermotolerant acetic acid bacteria (AAB), Acetobacter tropicalis SKU1100,
AB  - can grow above 40 degrees C. To investigate the basis of its
AB  - thermotolerance, we compared the genome of A. tropicalis SKU1100 with that
AB  - of mesophilic AAB strain Acetobacter pasteurianus IFO3283-01. The
AB  - comparative genomic study showed that amino acid substitutions from large
AB  - to small residue and Lys to Arg occur in many orthologous genes.
AB  - Furthermore, comparative modeling study was carried out with the
AB  - orthologous proteins between SKU1100 and IFO3283-01 strains, indicating
AB  - that the number of Arg-based salt bridges increased in protein models.
AB  - Since it has been reported that Arg-based salt bridges are important
AB  - factor for thermo-stability of protein structure, our results strongly
AB  - suggest that the increased number of Arg-based salt bridges may
AB  - contributes to the thermotolerance of A. tropicalis SKU1100 (the
AB  - thermo-stability of proteins in A. tropicalis SKU1100).
ER  -

TY  - JOUR
AU  - Matsutani, M.
AU  - Kawajiri, E.
AU  - Yakushi, T.
AU  - Adachi, O.
AU  - Matsushita, K.
TI  - Draft Genome Sequence of Dihydroxyacetone-Producing Gluconobacter thailandicus Strain NBRC 3255.
JO  - Genome Announcements
PY  - 2013
SP  - e00118
EP  - e00113
VL  - 1
AB  - Here, we report the draft genome sequence of the acetic acid bacterium Glucnobacter
AB  - thailandicus strain NBRC 3255. The draft genome sequence is composed
AB  - of 109 contigs in 3,305,227 bp and contains 3,225 protein-coding genes. Two
AB  - paralogous sets of sldAB operons, which are responsible for dihydroxyacetone
AB  - production from glycerol, were identified.
ER  -

TY  - JOUR
AU  - Matsutani, M.
AU  - Shirakihara, Y.
AU  - Imada, K.
AU  - Yakushi, T.
AU  - Matsushita, K.
TI  - Draft Genome Sequence of a Thermophilic Member of the Bacillaceae, Anoxybacillus  flavithermus Strain Kn10, Isolated from the Kan-nawa Hot Spring in Japan.
JO  - Genome Announcements
PY  - 2013
SP  - e00311
EP  - e00313
VL  - 1
AB  - Here, we report the draft genome sequence of the Anoxybacillus flavithermus Kn10  strain (NBRC
AB  - 109594), isolated from a water drain of the Kan-nawa Hot Spring in
AB  - Japan. The draft genome sequence is composed of 90 contigs for 2,772,624 bp with
AB  - 41.6% G+C content and contains 2,883 protein-coding genes and 80 tRNA genes.
ER  -

TY  - JOUR
AU  - Matsutani, M.
AU  - Suzuki, H.
AU  - Yakushi, T.
AU  - Matsushita, K.
TI  - Draft genome sequence of Gluconobacter thailandicus NBRC 3257.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 614
EP  - 623
VL  - 9
AB  - Gluconobacter thailandicus strain NBRC 3257, isolated from downy cherry (Prunus tomentosa), is
AB  - a strict aerobic rod-shaped Gram-negative bacterium. Here, we
AB  - report the features of this organism, together with the draft genome sequence and
AB  - annotation. The draft genome sequence is composed of 107 contigs for 3,446,046 bp
AB  - with 56.17% G+C content and contains 3,360 protein-coding genes and 54 RNA genes.
ER  -

TY  - JOUR
AU  - Matsuura, M.
AU  - Saldanha, R.
AU  - Ma, H.
AU  - Wank, H.
AU  - Yang, J.
AU  - Mohr, G.
AU  - Cavangh, S.
AU  - Dunny, G.M.
AU  - Belfort, M.
AU  - Lambowitz, A.M.
TI  - A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron.
JO  - Genes Dev.
PY  - 1997
SP  - 2910
EP  - 2924
VL  - 11
AB  - The Lactococcus lactis group II intron Ll.ltrB is similar to mobile yeast mtDNA group II
AB  - introns, which encode reverse transcriptase, RNA maturase, and DNA endonuclease activities for
AB  - site-specific DNA insertion. Here, we show that the Lactococcal intron can be expressed and
AB  - spliced efficiently in Escherichia coli. The intron-encoded protein LtrA has reverse
AB  - transcriptase and RNA maturase activities, with the latter activity shown both in vivo and in
AB  - vitro, a first for any group II intron-encoded protein. As for the yeast mtDNA introns, the
AB  - DNA endonuclease activity of the Lactococcal intron is associated with RNP particles
AB  - containing both the intron-encoded protein and the excised intron RNA. Also, the intron RNA
AB  - cleaves the sense-strand of the recipient DNA by a reverse splicing reaction, whereas the
AB  - intron-encoded protein cleaves the antisense strand. The Lactococcal intron endonuclease can
AB  - be obtained in large quantities by coexpression of the LtrA protein with the intron RNA in E.
AB  - coli or reconstituted in vitro by incubating the expressed LtrA protein with in
AB  - vitro-synthesized intron RNA. Furthermore, the specificity of the endonuclease and reverse
AB  - splicing reactions can be changed predictably by modifying the RNA component. Expression in E.
AB  - coli facilitates the use of group II introns for the targeting of specific foreign sequences
AB  - to a desired site in DNA.
ER  -

TY  - JOUR
AU  - Matsuura, N.
AU  - Ohashi, A.
AU  - Tourlousse, D.M.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of Thermodesulfovibrio aggregans TGE-P1T, an Obligately Anaerobic, Thermophilic, Sulfate-Reducing Bacterium in the Phylum Nitrospirae.
JO  - Genome Announcements
PY  - 2016
SP  - e00089
EP  - e00016
VL  - 4
AB  - We report a high-quality draft genome sequence of the type strain (TGE-P1(T)) of
AB  - Thermodesulfovibrio aggregans, an obligately anaerobic, thermophilic,
AB  - sulfate-reducing bacterium in the phylum Nitrospirae. The genome comprises 2.00
AB  - Mb in 16 contigs (3 scaffolds), has a G+C content of 34.5%, and contains 1,998
AB  - predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Matsuura, N.
AU  - Ohashi, A.
AU  - Tourlousse, D.M.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of the Syntrophic Lactate-Degrading Bacterium Tepidanaerobacter syntrophicus JLT.
JO  - Genome Announcements
PY  - 2016
SP  - e01712
EP  - e01715
VL  - 4
AB  - We report here a high-quality draft genome sequence of the type strain (JL) of
AB  - Tepidanaerobacter syntrophicus, an obligately anaerobic and moderately
AB  - thermophilic bacterium, which is able to perform syntrophic lactate degradation
AB  - with hydrogenotrophic methanogens. The genome comprises 2.43 Mb in 9 scaffolds,
AB  - with a G+C content of 38.6%.
ER  -

TY  - JOUR
AU  - Matsuura, N.
AU  - Tourlousse, D.M.
AU  - Ohashi, A.
AU  - Hugenholtz, P.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae (Chloroflex.
JO  - Genome Announcements
PY  - 2015
SP  - e00975
EP  - e00915
VL  - 3
AB  - Members of the class Anaerolineae in the bacterial phylum Chloroflexi are widespread in a
AB  - range of ecosystems but remain poorly understood. We present here the draft genome sequences
AB  - of the type strains of five Anaerolineae species, Anaerolinea thermolimosa IMO-1, Bellilinea
AB  - caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, and
AB  - Longilinea arvoryzae KOME-1.
ER  -

TY  - JOUR
AU  - Matsuura, N.
AU  - Tourlousse, D.M.
AU  - Sun, L.
AU  - Toyonaga, M.
AU  - Kuroda, K.
AU  - Ohashi, A.
AU  - Cruz, R.
AU  - Yamaguchi, T.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.
JO  - Genome Announcements
PY  - 2015
SP  - e01104
EP  - e01115
VL  - 3
AB  - We report the draft genome sequence of Anaerolineae bacterium strain TC1, newly isolated from
AB  - a methanogenic wastewater treatment system. The assembly contains 16 contigs in 3 scaffolds
AB  - representing 3,510,630 bp in total with a G+C content of 41.35%. The genome is predicted to
AB  - contain 2,793 protein-coding genes and 56 RNAs.
ER  -

TY  - JOUR
AU  - Matsuura, S.-I.
AU  - Hirano, K.
AU  - Zako, T.
AU  - Katsura, S.
AU  - Nagamune, T.
AU  - Mizuno, A.
TI  - Direct observation of sliding of restriction endonuclease EcoRI on a single DNA molecule.
JO  - Eur. Biophys. J.
PY  - 2000
SP  - 255
EP  - 255
VL  - 29
AB  - In recent years, a fluorescence microscopy technique has been used to image the dynamics of
AB  - individual DNA and protein molecules.  For the advanced investigation of the molecular
AB  - mechanism in DNA-protein interactions such as sliding of restriction endonucleases on DNA
AB  - molecules, direct observation of a single protein molecule will be significant.  To observe
AB  - dynamics of individual proteins under a fluorescence microscopy on real-time, it requires
AB  - labeling proteins with a fluorescent dye.  In this study, therefore, we developed fluorescent
AB  - labeling system for a restriction endonuclease EcoRI as a model to label DNA binding proteins.
AB  - EcoRI bound on DNA molecules was treated with amine-reactive dye Oregon-Green500.
AB  - Consequently, we found that restriction endonuclease activity of labeled EcoRI was retained,
AB  - even though EcoRI was fluorescently labeled.  Moreover, when DNA-staining dye YOYO-1
AB  - concentration was YOYO-1 : nucleotide pair = 1:100 in molar ratio, EcoRI digested the DNA
AB  - molecules as unstained DNA.  Finally, we observed that fluorescent labeled EcoRI slid on
AB  - stained DNA straightening on 3-APTES-treated cover glass in the absence of Mg2+ using a
AB  - fluorescence microscopy.
ER  -

TY  - JOUR
AU  - Matsuzaki, S.
AU  - Inoue, T.
AU  - Tanaka, S.
TI  - Evidence for the existence of a restriction-modification system common to several species of the family Vibronaceae.
JO  - FEMS Microbiol. Lett.
PY  - 1992
SP  - 191
EP  - 194
VL  - 94
AB  - A broad-host-range vibriophage KVP40 originally isolated on Vibrio parahaemolyticus 1010 was
AB  - restricted and modified by strains of at least five Vibrio and one Photobacterium species.
AB  - 1010 was a non-restricting host. An anti-restriction mutant KVP40 aar1 was isolated after
AB  - propagating the phage on a restricting host, V. anguillarum VIB36, as well as the parental
AB  - phage grown on VIB36, showed much higher efficiencies of plating on all the restricting hosts
AB  - as compared with the parental phage grown on 1010, indicating that these restricting hosts
AB  - probably share a common restriction-modification system active in vivo on KVP40.
ER  -

TY  - JOUR
AU  - Matsuzawa, T.
AU  - Mori, K.
AU  - Kadowaki, T.
AU  - Shimada, M.
AU  - Tashiro, K.
AU  - Kuhara, S.
AU  - Inagawa, H.
AU  - Soma, G.
AU  - Takegawa, K.
TI  - Genome Sequence of Pantoea agglomerans Strain IG1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1258
EP  - 1259
VL  - 194
AB  - Pantoea agglomerans is a Gram-negative bacterium that grows symbiotically with various plants.
AB  - Here we report the 4.8-Mb genome sequence of P. agglomerans
AB  - strain IG1. The lipopolysaccharides derived from P. agglomerans IG1 have been
AB  - shown to be effective in the prevention of various diseases, such as bacterial or
AB  - viral infection, lifestyle-related diseases. This genome sequence represents a
AB  - substantial step toward the elucidation of pathways for production of
AB  - lipopolysaccharides.
ER  -

TY  - JOUR
AU  - Mattos-Guaraldi, A.L.
AU  - Guimaraes, L.C.
AU  - Santos, C.S.
AU  - Veras, A.A.
AU  - Carneiro, A.R.
AU  - Soares, S.C.
AU  - Ramos, J.N.
AU  - Souza, C.
AU  - Vieira, V.V.
AU  - Hirata, R. Jr.
AU  - Azevedo, V.
AU  - Pacheco, L.G.
AU  - Silva, A.
AU  - Ramos, R.T.
TI  - Draft Genome Sequence of Corynebacterium striatum 1961 BR-RJ/09, a Multidrug-Susceptible Strain Isolated from the Urine of a Hospitalized  37-Year-Old Female Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e00869
EP  - e00815
VL  - 3
AB  - Corynebacterium striatum commonly colonizes the normal skin and nasopharyngeal tract of
AB  - humans; however, this potentially pathogenic bacterium has been
AB  - identified as the causative agent of several nosocomial infections. The current
AB  - study describes the draft genome of strain 1961 BR-RJ/09, isolated from the urine
AB  - of a hospitalized patient from Brazil.
ER  -

TY  - JOUR
AU  - Maturrano, L.
AU  - Aleman, M.
AU  - Carhuaricra, D.
AU  - Maximiliano, J.
AU  - Siuce, J.
AU  - Luna, L.
AU  - Rosadio, R.
TI  - Draft Genome Sequences of Enterohemorrhagic and Enteropathogenic Escherichia coli Strains Isolated from Alpacas in Peru.
JO  - Genome Announcements
PY  - 2018
SP  - e01391
EP  - e01317
VL  - 6
AB  - The draft genome sequences of two strains of Escherichia coli, isolated from alpacas in Peru,
AB  - are reported here. ECA1 has been determined to be a strain of
AB  - enterohemorrhagic E. coli and ECB1 a strain of enteropathogenic E. coli These
AB  - pathogens are responsible for hemolytic-uremic syndrome in humans and diarrhea in
AB  - different mammals, respectively.
ER  -

TY  - JOUR
AU  - Matveyev, A.V.
AU  - Young, K.T.
AU  - Meng, A.
AU  - Elhai, J.
TI  - DNA methyltransferases of the cyanobacterium Anabaena PCC 7120.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 1491
EP  - 1506
VL  - 29
AB  - From the characterization of enzyme activities and the analysis of genomic sequences, the
AB  - complement of DNA methyltransferases (MTases) possessed by the cyanobacterium Anabaena PCC
AB  - 7120 has been deduced. Anabaena has nine DNA MTases. Four are associated with Type II
AB  - restriction enzymes (AvaI, AvaII, AvaIII and the newly recognized inactive AvaIV), and five
AB  - are not. Of the latter, four may be classified as solitary MTases, those whose function lies
AB  - outside of a restriction/modification system. The group is defined here based on biochemical
AB  - and genetic characteristics. The four solitary MTases, DmtA/M.AvaVI, DmtB/M.AvaVII,
AB  - DmtC/M.AvaVIII and DmtD/M.AvaIX, methylate at GATC, GGCC, CGATCG and RCCGGY, respectively.
AB  - DmtB methylates cytosines at the N4 position, but its sequence is more similar to N6-adenine
AB  - MTases than to cytosine-specific enzymes, indicating that it may have evolved from the former.
AB  - The solitary MTases, appear to be of ancient origin within cyanobacteria, while the
AB  - restriction MTases appear to have arrived by recent horizontal transfer as did five now
AB  - inactive Type I restriction systems. One Mtase, M.AvaV, cannot reliably be classified as
AB  - either a solitary or restriction MTase. It is structurally unusual and along with a few
AB  - proteins of prokaryotic and eukaryotic origin defines a structural class of MTases distinct
AB  - from all previously described.
ER  -

TY  - JOUR
AU  - Matvienko, N.I.
AU  - Kramarov, V.M.
AU  - Irismetov, A.A.
TI  - Isolation and characterization of a DNA-methylase from Flavobacterium okeanokoites.
JO  - Bioorg. Khim.
PY  - 1985
SP  - 953
EP  - 956
VL  - 11
AB  - FokI DNA methylase has been isolated from a cell extract of Flavobacterium
AB  - okeanokoites by gel filtration followed by gel chromatography on
AB  - hydroxylapatite.  The purified enzyme methylated the DNA of plasmid pBR322,
AB  - making it resistant to the subsequent action of the site-specific FokI
AB  - endonuclease.  It has been shown that it is the cytosine residues that are
AB  - methylated.  This modification does not protect the DNA from hydrolysis by
AB  - BbvI, BmeI, and EcoRII endonucleases, the recognition sites of which contain
AB  - cytosine, which shows the specific nature of the methylation of DNA by the FokI
AB  - methylase.
ER  -

TY  - JOUR
AU  - Matvienko, N.I.
AU  - Kramarov, V.M.
AU  - Pachkunov, D.M.
TI  - Isolation and some properties of the site-specific endonuclease and methylase Bme216I from Bacillus megaterium 216.
JO  - Eur. J. Biochem.
PY  - 1987
SP  - 565
EP  - 570
VL  - 165
AB  - The site-specific endonuclease Bme216I was isolated as a homogeneous
AB  - preparation by chromatography on phosphocellulose, hydroxyapatite and
AB  - heparin-agarose.  The molecular mass of the enzyme, determined by gel
AB  - filtration and by electrophoresis under denaturing conditions, was found to be
AB  - 60 kDa and 30 kDa respectively.  These data indicate that the native enzyme
AB  - consists of two identical subunits.  The enzyme recognized the pentanucleotide
AB  - sequence 5'-G^GACC-3' . 3'-CCTG^G-5' and cleaves the sequence as indicated by
AB  - arrows.  The optimal concentration for endonuclease reaction is 6-7 mM Mg2+.
AB  - The endonuclease relaxes its specificity in the presence of glycerol or
AB  - dimethyl sulfoxide at low Mg2+ concentration (1-3 mM).  Methylase Bme216I,
AB  - which protects DNA against endonuclease Bme216I action by DNA methylation, was
AB  - isolated from the same bacterial strain.
ER  -

TY  - JOUR
AU  - Matvienko, N.I.
AU  - Pachkunov, D.M.
AU  - Kramarov, V.M.
TI  - The recognition sequence of site-specific endonuclease BbvII from Bacillus brevis 80.
JO  - FEBS Lett.
PY  - 1984
SP  - 23
EP  - 26
VL  - 177
AB  - Site-specific endonuclease BbvII from Bacillus brevis 80 recognizes the
AB  - non-symmetrical hexanucleotide and cleaves DNA at distances of 2 and 6
AB  - nucleotides from the recognition site:5'-GAAGACNN^ 3'-CTTCTGNNNNNN^This enzyme
AB  - may be used in molecular cloning for vectors with multiple restriction sites.
ER  -

TY  - JOUR
AU  - Matvienko, N.N.
AU  - Kramarov, V.M.
AU  - Ivanov, L.Y.
AU  - Matvienko, N.I.
TI  - Bce83I, a restriction endonuclease from Bacillus cereus 83 which recognizes novel nonpalindromic sequence 5'-CTTGAG-3' and is stimulated by S-adenosylmethionine.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1803
EP  - 1803
VL  - 20
AB  - Restriction endonuclease Bce83I has been purified by chromatography on blue-sepharose and
AB  - hydroxyapatite. It recognizes 4,6,5,13 and more than 20 sites on pUC18, pBR322, M13mp18,
AB  - lambda and T7 DNA, respectively.
ER  -

TY  - JOUR
AU  - Matvienko, N.N.
AU  - Kramarov, V.M.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - New site-specific endonuclease and methylase from Bacillus licheniformis 736.
JO  - Biokhimiia
PY  - 1993
SP  - 1139
EP  - 1153
VL  - 58
AB  - *
AB  - The site-specific endonuclease R.Bli736I and methylase M.Bli736I have been isolated from the
AB  - Bacilus licheniformis strain 736 by blue-agarose, hydroxyapatite-Ultragel and
AB  - heparin-Sepharose
AB  - chromatography. The enzymes are free from interfering impurities. R.Bli736I recognizes the
AB  - sequence:
AB  - 
AB  -    5'-GGTCTCN^-3'
AB  -    3'-CCAGAGNNNNN^-5'
AB  - 
AB  - on the DNA and cleaves the DNA as indicated by arrows to form single-stranded 4-nucleotide
AB  - 5'-protruding termini. This enzyme is an isoschizomer of Eco31I isolated from E.coli.
AB  - 
ER  -

TY  - JOUR
AU  - Matvienko, N.N.
AU  - Kramarov, V.M.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Isolation of site-specific endonuclease and methylase from Bacillus cereus 83.
JO  - Biokhimiia
PY  - 1993
SP  - 1845
EP  - 1860
VL  - 58
AB  - 
AB  -  The site-specific endonuclease R.Bce83I and methylase M.Bce83I were isolated from Bacillus
AB  -  cereus 83 by three consecutive chromatographies on blue agarose, hydroxyapatite and
AB  -  heparin-Sepharose. R.Bce83I recognizes the
AB  -  
AB  - 
AB  -      5'-CTTGAG16N^-3'
AB  -      3'-GAACTC14N^-5'
AB  -  
AB  - 
AB  -  sequences on the DNA and cleaves the DNA as indicated by the arrows. The endonuclease is
AB  -  stimulated by S-adenosyl-L-methionine and may consequently be referred to as a type IV
AB  -  restriction enzyme.
AB  - 
ER  -

TY  - JOUR
AU  - Matvienko, N.N.
AU  - Zeleznaja, L.A.
AU  - Matvienko, N.I.
TI  - BspLU11I, a novel site specific endonuclease which cleaves 5'-ACATGT-3'.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 1495
EP  - 1495
VL  - 21
ER  -

TY  - JOUR
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Chernyshova, E.E.
AU  - Buryanov, Y.I.
AU  - Matvienko, N.I.
TI  - Peculiarities of gene expression of the EcoRII modification-restriction system.
JO  - Biokhimiia
PY  - 1997
SP  - 1314
EP  - 1318
VL  - 62
AB  - The restriction-modification genes of the EcoRII system have been cloned into plasmids under
AB  - control of phage-specific promoters T7 and SP6.  The transcription was induced by cell
AB  - infection with the recombinant M13 phages with the corresponding genes of phage
AB  - RNA-polymerases under control of the Plac-promoter in the presence of IPTG.  The induction
AB  - yields significant amounts of EcoRII DNA-methylase for both phage-specific promoters.  In both
AB  - cases no increase in EcoRII endonuclease expression could be achieved.  We hypothesize that
AB  - the expression of the endonuclease gene is regulated on the translational level.
ER  -

TY  - JOUR
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Zelinskaya, N.V.
AU  - Matvienko, N.I.
TI  - Site-specific DNA-methylase M.BspST5I methylates only one strand of the recognized site.
JO  - Biokhimiia
PY  - 1997
SP  - 304
EP  - 306
VL  - 62
AB  - We recently isolated a site-specific adenine DNA-methylase, M.BspST5I, which methylates only
AB  - one strand of the recognized site GCA*TC.  The methylated base is indicated by an asterisk.
ER  -

TY  - JOUR
AU  - Matyi, S.A.
AU  - Hoyt, P.R.
AU  - Ayoubi-Canaan, P.
AU  - Hasan, N.A.
AU  - Gustafson, J.E.
TI  - Draft Genome Sequence of Strain ATCC 33958, Reported To Be Elizabethkingia miricola.
JO  - Genome Announcements
PY  - 2015
SP  - e00828
EP  - e00815
VL  - 3
AB  - We report the draft genome of Elizabethkingia strain ATCC 33958, which has been classified as
AB  - Elizabethkingia miricola. Similar to other Elizabethkingia species,
AB  - the ATCC 33958 draft genome contains numerous beta-lactamase genes. ATCC 33958
AB  - also harbors a urease gene cluster which supports classification as E. miricola.
ER  -

TY  - JOUR
AU  - Matyi, S.A.
AU  - Hoyt, P.R.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Gustafson, J.E.
TI  - Draft Genome Sequences of Elizabethkingia meningoseptica.
JO  - Genome Announcements
PY  - 2013
SP  - e00444
EP  - e00413
VL  - 1
AB  - Elizabethkingia meningoseptica is ubiquitous in nature, exhibits a multiple-antibiotic
AB  - resistance phenotype, and causes rare opportunistic
AB  - infections. We now report two draft genome sequences of E. meningoseptica type
AB  - strains that were sequenced independently in two laboratories.
ER  -

TY  - JOUR
AU  - Matyi, S.A.
AU  - Ramaraj, T.
AU  - Sundararajan, A.
AU  - Lindquist, I.E.
AU  - Devitt, N.P.
AU  - Schilkey, F.D.
AU  - Lamichhane-Khadka, R.
AU  - Hoyt, P.R.
AU  - Mudge, J.
AU  - Gustafson, J.E.
TI  - Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.
JO  - Genome Announcements
PY  - 2014
SP  - e00688
EP  - e00614
VL  - 2
AB  - The draft genomes of heterogeneous vancomycin-intermediate Staphylococcus aureus  (hVISA)
AB  - strain MM66 and MM66 isolates demonstrating altered vancomycin resistance
AB  - levels were produced in an effort to provide information on mutations
AB  - contributing to the vancomycin resistance levels observed in these strains.
ER  -

TY  - JOUR
AU  - Matz, L.M.
AU  - Kamdar, K.Y.
AU  - Holder, M.E.
AU  - Metcalf, G.A.
AU  - Weissenberger, G.M.
AU  - Meng, Q.
AU  - Vee, V.
AU  - Han, Y.
AU  - Muzny, D.M.
AU  - Gibbs, R.A.
AU  - Johnson, C.L.
AU  - Revell, P.A.
AU  - Petrosino, J.F.
TI  - Challenges of Francisella classification exemplified by an atypical clinical isolate.
JO  - Diagn. Microbiol. Infect. Dis.
PY  - 2018
SP  - 241
EP  - 247
VL  - 90
AB  - The accumulation of sequenced Francisella strains has made it increasingly apparent that the
AB  - 16S rRNA gene alone is not enough to stratify the Francisella
AB  - genus into precise and clinically useful classifications. Continued whole-genome
AB  - sequencing of isolates will provide a larger base of knowledge for targeted
AB  - approaches with broad applicability. Additionally, examination of genomic
AB  - information on a case-by-case basis will help resolve outstanding questions
AB  - regarding strain stratification. We report the complete genome sequence of a
AB  - clinical isolate, designated here as F. novicida-like strain TCH2015, acquired
AB  - from the lymph node of a 6-year-old male. Two features were atypical for F.
AB  - novicida: exhibition of functional oxidase activity and additional gene content,
AB  - including proposed virulence determinants. These differences, which could
AB  - potentially impact virulence and clinical diagnosis, emphasize the need for more
AB  - comprehensive methods to profile Francisella isolates. This study highlights the
AB  - value of whole-genome sequencing, which will lead to a more robust database of
AB  - environmental and clinical genomes and inform strategies to improve detection and
AB  - classification of Francisella strains.
ER  -

TY  - JOUR
AU  - Maus, I.
AU  - Wibberg, D.
AU  - Stantscheff, R.
AU  - Eikmeyer, F.G.
AU  - Seffner, A.
AU  - Boelter, J.
AU  - Szczepanowski, R.
AU  - Blom, J.
AU  - Jaenicke, S.
AU  - Konig, H.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5487
EP  - 5488
VL  - 194
AB  - Methanoculleus bourgensis, of the order Methanomicrobiales, is a dominant methanogenic
AB  - archaeon in many biogas-producing reactor systems fed with renewable
AB  - primary products. It is capable of synthesizing methane via the hydrogenotrophic
AB  - pathway utilizing hydrogen and carbon dioxide or formate as the substrates. Here
AB  - we report the complete and finished genome sequence of M. bourgensis strain
AB  - MS2(T), isolated from a sewage sludge digester.
ER  -

TY  - JOUR
AU  - Maus, I.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Puhler, A.
AU  - Schnurer, A.
AU  - Schluter, A.
TI  - Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.
JO  - Genome Announcements
PY  - 2016
SP  - e00568
EP  - e00516
VL  - 4
AB  - Methanoculleus bourgensis BA1, a hydrogenotrophic methanogen, was isolated from a
AB  - laboratory-scale biogas reactor operating under an elevated ammonium
AB  - concentration. Here, the complete genome sequence of M. bourgensis BA1 is
AB  - reported. The availability of the BA1 genome sequence enables detailed
AB  - comparative analyses involving other Methanoculleus spp. representing important
AB  - members of microbial biogas communities.
ER  -

TY  - JOUR
AU  - Mavian, C.
AU  - Lopez-Bueno, A.
AU  - Balseiro, A.
AU  - Casais, R.
AU  - Alcami, A.
AU  - Alejo, A.
TI  - The Genome Sequence of the Emerging Common Midwife Toad Virus Identifies an Evolutionary Intermediate within Ranaviruses.
JO  - J. Virol.
PY  - 2012
SP  - 3617
EP  - 3625
VL  - 86
AB  - Worldwide amphibian population declines have been ascribed to global warming,
AB  - increasing pollution levels, and other factors directly related to human
AB  - activities. These factors may additionally be favoring the emergence of novel
AB  - pathogens. In this report, we have determined the complete genome sequence of the
AB  - emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in
AB  - several amphibian species across Europe. Phylogenetic and gene content analyses
AB  - of the first complete genomic sequence from a ranavirus isolated in Europe show
AB  - that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome
AB  - structure is novel and represents an intermediate evolutionary stage between the
AB  - two previously described ALRV groups. We find that CMTV clusters with several
AB  - other ranaviruses isolated from different hosts and locations which might also be
AB  - included in this novel ranavirus group. This work sheds light on the phylogenetic
AB  - relationships within this complex group of emerging, disease-causing viruses.
ER  -

TY  - JOUR
AU  - Mavian, C.
AU  - Lopez-Bueno, A.
AU  - Fernandez-Somalo, M.P.
AU  - Alcami, A.
AU  - Alejo, A.
TI  - Complete genome sequence of European sheatfish virus.
JO  - J. Virol.
PY  - 2012
SP  - 6365
EP  - 6366
VL  - 86
AB  - Viral diseases are an increasing threat to the thriving aquaculture industry worldwide. An
AB  - emerging group of fish pathogens is formed by several ranaviruses, which have been isolated at
AB  - different locations from freshwater and seawater fish species since 1985.  We report the
AB  - complete genome sequence of European sheatfish ranavirus (ESV), the first ranavirus isolated
AB  - in Europe, which causes high mortality rates in infected sheatfish (Silurus glanis) and in
AB  - other species. Analysis of the genome sequence shows that ESV belongs to the amphibian-like
AB  - ranaviruses and is closely related to the epizootic hematopoietic necrosis virus (EHNV), a
AB  - disease agent geographically confined to the Australian continent and notifiable to the World
AB  - Organization for Animal Health.
ER  -

TY  - JOUR
AU  - Mavrodi, D.V.
AU  - Mavrodi, O.V.
AU  - McSpadden-Gardener, B.B.
AU  - Landa, B.B.
AU  - Weller, D.M.
AU  - Thomashow, L.S.
TI  - Identification of Differences in Genome Content among phlD-Positive Pseudomonas fluorescens Strains by Using PCR-Based Subtractive Hybridization.
JO  - Appl. Environ. Microbiol.
PY  - 2002
SP  - 5170
EP  - 5176
VL  - 68
AB  - Certain 2,4-diacetylphloroglucinol-producing strains of Pseudomonas
AB  - fluorescens colonize roots and suppress soilborne diseases more
AB  - effectively than others from which they are otherwise phenotypically
AB  - almost indistinguishable. We recovered DNA fragments present in the
AB  - superior colonizer P. fluorescens Q8r1-96 but not in the less
AB  - rhizosphere-competent strain Q2-87. Of the open reading frames in 32
AB  - independent Q8r1-96-specific clones, 1 was similar to colicin M from
AB  - Escherichia coli, 3 resembled known regulatory proteins, and 28 had no
AB  - significant match with sequences of known function. Seven clones
AB  - hybridized preferentially to DNA from strains with superior rhizosphere
AB  - competence, and sequences in two others were highly expressed in vitro and
AB  - in the rhizosphere.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of Cryptobacterium curtum type strain (12-3).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 93
EP  - 100
VL  - 1
AB  - Cryptobacterium curtum Nakazawa etal. 1999 is the type species of the genus, and  is of
AB  - phylogenetic interest because of its very distant and isolated position within the family
AB  - Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical
AB  - occurrence in the oral cavity, involved in dental and oral infections like periodontitis,
AB  - inflammations and abscesses. Here we describe the features of this organism, together with the
AB  - complete genome sequence, and annotation. This is the first complete genome sequence of the
AB  - actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome
AB  - with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 9
EP  - 18
VL  - 2
AB  - Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of
AB  - the two genera in the bacillal family 'Alicyclobacillaceae'. A.
AB  - acidocaldarius is a free-living and non-pathogenic organism, but may also be
AB  - associated with food and fruit spoilage. Due to its acidophilic nature, several
AB  - enzymes from this species have since long been subjected to detailed molecular
AB  - and biochemical studies. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. This is the first completed
AB  - genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome
AB  - (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 210
EP  - 219
VL  - 6
AB  - Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the  class
AB  - 'Sphingobacteria' that remains poorly characterized at the genomic level.
AB  - The species is known for preying on other marine bacteria via 'ixotrophy'. S.
AB  - grandis strain Sa g1 was isolated from decaying crab carapace in France and was
AB  - selected for genome sequencing because of its isolated location in the tree of
AB  - life. Only one type strain genome has been published so far from the
AB  - Saprospiraceae, while the sequence of strain Sa g1 represents the second genome
AB  - to be published from a non-type strain of S. grandis. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with
AB  - its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 290
EP  - 299
VL  - 2
AB  - Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus
AB  - Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative,
AB  - non-spore-forming, non-motile, spherical bacterium that was isolated from
AB  - seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of
AB  - special interest because of its phylogenetic position in a genomically
AB  - under-studied area of the bacterial diversity. Here we describe the features of
AB  - this organism, together with the complete genome sequence, and annotation. This
AB  - is the first complete genome sequence of a member of the family Puniceicoccaceae.
AB  - The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of Vulcanisaeta distributa type strain (IC-017).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 117
EP  - 125
VL  - 3
AB  - Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum
AB  - Crenarchaeota. The genus Vulcanisaeta is characterized by a global
AB  - distribution in hot and acidic springs. This is the first genome sequence from a
AB  - member of the genus Vulcanisaeta and seventh genome sequence in the family
AB  - Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and
AB  - 49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 136
EP  - 144
VL  - 3
AB  - Spirochaeta smaragdinae Magot et al. 1998 belongs to the family Spirochaetaceae.  The species
AB  - is Gram-negative, motile, obligately halophilic and strictly
AB  - anaerobic and is of interest because it is able to ferment numerous
AB  - polysaccharides. S. smaragdinae is the only species of the family Spirochaetaceae
AB  - known to reduce thiosulfate or element sulfur to sulfide. This is the first
AB  - complete genome sequence in the family Spirochaetaceae. The 4,653,970 bp long
AB  - genome with its 4,363 protein-coding and 57 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 144
EP  - 153
VL  - 4
AB  - Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species
AB  - of the genus Riemerella, which belongs to the family
AB  - Flavobacteriaceae. The species is of interest because of the position of the
AB  - genus in the phylogenetic tree and because of its role as a pathogen of
AB  - commercially important avian species worldwide. This is the first completed
AB  - genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome
AB  - with its 2,001 protein-coding and 51 RNA genes consists of one circular
AB  - chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 47
EP  - 57
VL  - 8
AB  - Anaerobaculum mobile Menes and Muxi 2002 is one of three described species of the genus
AB  - Anaerobaculum, family Synergistaceae, phylum Synergistetes. This anaerobic
AB  - and motile bacterium ferments a range of carbohydrates and mono- and dicarboxylic
AB  - acids with acetate, hydrogen and CO2 as end products. A. mobile NGA(T) is the
AB  - first member of the genus Anaerobaculum and the sixth member of the phylum
AB  - Synergistetes with a completely sequenced genome. Here we describe the features
AB  - of this bacterium, together with the complete genome sequence, and annotation.
AB  - The 2,160,700 bp long single replicon genome with its 2,053 protein-coding and 56
AB  - RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K. et al.
TI  - Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 26
EP  - 36
VL  - 8
AB  - Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with  a validly
AB  - published name: family Rikenellaceae, order Bacteroidetes, class
AB  - Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic
AB  - organism has been isolated mostly from human tissues. Here we describe the
AB  - features of the type strain of this species, together with the complete genome
AB  - sequence, and annotation. A. finegoldii is the first member of the genus
AB  - Alistipes for which the complete genome sequence of its type strain is now
AB  - available. The 3,734,239 bp long single replicon genome with its 3,302
AB  - protein-coding and 68 RNA genes is part of the G enomic E ncyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Mavromatis, K.
AU  - Doyle, C.K.
AU  - Lykidis, A.
AU  - Ivanova, N.
AU  - Francino, M.P.
AU  - Chain, P.
AU  - Shin, M.
AU  - Malfatti, S.
AU  - Larimer, F.
AU  - Copeland, A.
AU  - Detter, J.C.
AU  - Land, M.
AU  - Richardson, P.M.
AU  - Yu, X.J.
AU  - Walker, D.H.
AU  - McBride, J.W.
AU  - Kyrpides, N.C.
TI  - The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion  strategies.
JO  - J. Bacteriol.
PY  - 2006
SP  - 4015
EP  - 4023
VL  - 188
AB  - Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative,
AB  - alpha-proteobacterium, is the primary etiologic agent of
AB  - globally distributed canine monocytic ehrlichiosis. Complete genome
AB  - sequencing revealed that the E. canis genome consists of a single circular
AB  - chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA
AB  - species, 17 putative pseudogenes, and a substantial proportion of
AB  - noncoding sequence (27%). Interesting genome features include a large set
AB  - of proteins with transmembrane helices and/or signal sequences and a
AB  - unique serine-threonine bias associated with the potential for O
AB  - glycosylation that was prominent in proteins associated with pathogen-host
AB  - interactions. Furthermore, two paralogous protein families associated with
AB  - immune evasion were identified, one of which contains poly(G-C) tracts,
AB  - suggesting that they may play a role in phase variation and facilitation
AB  - of persistent infections. Genes associated with pathogen-host interactions
AB  - were identified, including a small group encoding proteins (n = 12) with
AB  - tandem repeats and another group encoding proteins with eukaryote-like
AB  - ankyrin domains (n = 7).
ER  -

TY  - JOUR
AU  - Mavrommatis, K. et al.
TI  - Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 101
EP  - 109
VL  - 1
AB  - Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 is the type species of the
AB  - genus Capnocytophaga. It is of interest because of its location in
AB  - the Flavobacteriaceae, a genomically not yet charted family within the order
AB  - Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to
AB  - form clumps and are able to move by gliding. C. ochracea is known as a
AB  - capnophilic (CO(2)-requiring) organism with the ability to grow under anaerobic
AB  - as well as aerobic conditions (oxygen concentration larger than 15%), here only
AB  - in the presence of 5% CO(2). Strain VPI 2845(T), the type strain of the species,
AB  - is portrayed in this report as a gliding, Gram-negative bacterium, originally
AB  - isolated from a human oral cavity. Here we describe the features of this
AB  - organism, together with the complete genome sequence, and annotation. This is the
AB  - first completed genome sequence from the flavobacterial genus Capnocytophaga, and
AB  - the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59
AB  - RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Maxwell, A.
AU  - Halford, S.E.
TI  - The SalGI restriction endonuclease.  (Enzyme specificity).
JO  - Biochem. J.
PY  - 1982
SP  - 93
EP  - 98
VL  - 203
AB  - We have analysed the kinetics of DNA cleavage in the reaction between the SalGI
AB  - restriction endonuclease and plasmid pMB9.  This reaction is subject to
AB  - competitive inhibiton by DNA sequences outside the SalGI recognition site; we
AB  - have determined the Km and Vmax. for the reaction of this enzyme at its
AB  - recognition site and the KI for its interaction at other DNA sequences.  We
AB  - conclude that the specificity of DNA cleavage by the enzyme is only partly
AB  - determined by the discrimination it shows for binding at its recognition
AB  - sequence compared with binding to other DNA sequences.
ER  -

TY  - JOUR
AU  - Maxwell, A.
AU  - Halford, S.E.
TI  - The SalGI restriction endonuclease.  (Purification and properties).
JO  - Biochem. J.
PY  - 1982
SP  - 77
EP  - 84
VL  - 203
AB  - The type II restriction endonuclease SalGI has been purified to near
AB  - homogeneity.  At least 80% of the protein remaining after the final stage of
AB  - the preparation is SalGI restriction endonuclease; no contaminating nucleases
AB  - remain detectable.  The principal form of the protein under both native and
AB  - denaturing conditions is a monomer of Mr about 29000. The optimal conditions
AB  - for both enzyme stability and enzyme activity have been determined.
ER  -

TY  - JOUR
AU  - Maxwell, A.
AU  - Halford, S.E.
TI  - The mechanism of DNA cleavage by restriction endonuclease SalGI.
JO  - Biochem. Soc. Trans.
PY  - 1981
SP  - 227P
EP  - 227P
VL  - 9
AB  - The SalGI restriction endonuclease cleaves duplex DNA only at its recognition
AB  - site.  Under optimal conditions (pH 8, 10 mM MgCl2), both strands of the DNA
AB  - are cleaved in one concerted reaction:  a covalently closed DNA molecule with
AB  - one SalGI recognition site is converted directly to linear DNA.  But under
AB  - other conditions (viz 1 mM MgCl2), each reaction of this enzyme cleaves either
AB  - one or both strands of the DNA; the covalently closed DNA is now converted into
AB  - either the open-circle or the linear forms, the two being produced
AB  - simultaneously rather than consecutively.  The enzyme will also cleave the DNA
AB  - nicked at the SalGI recognition site but this second reaction is much slower
AB  - than the first.  The SalGI restriction enzyme therefore interacts with DNA by a
AB  - fundamentally different mechanism from some other restriction enzymes such as
AB  - EcoRI.
ER  -

TY  - JOUR
AU  - Maxwell, A.
AU  - Halford, S.E.
TI  - The SalGI restriction endonuclease.  Mechanism of DNA cleavage.
JO  - Biochem. J.
PY  - 1982
SP  - 85
EP  - 92
VL  - 203
AB  - The cleavage of supercoiled DNA of plasmid pMB9 by restriction endonuclease
AB  - SalGI has been studied.  Under the optimal conditions for this reaction, the
AB  - only product is the linear form of the DNA, in which both strands of the duplex
AB  - have been cleaved at the SalGI recognition site.  DNA molecules cleaved in one
AB  - strand at this site were found to be poor substrates for the SalGI enzyme.
AB  - Thus, both strands of the DNA appear to be cleaved in a concerted reaction.
AB  - However, under other conditions, the enzyme cleaves either one or both strands
AB  - of the DNA; the supercoiled substrate is then converted to either open-circle
AB  - or linear forms, the two being produced simultaneously rather than
AB  - consecutively.  We propose a mechanism for the SalGI restriction endonuclease
AB  - which accounts fo the reactions of this enzyme under both optimal and other
AB  - conditions.  These reactions were unaffected by the tertiary structure of the
AB  - DNA.
ER  -

TY  - JOUR
AU  - May, A.C.
AU  - Ehrlich, R.L.
AU  - Balashov, S.
AU  - Ehrlich, G.D.
AU  - Shanmugam, M.
AU  - Fine, D.H.
AU  - Ramasubbu, N.
AU  - Mell, J.C.
AU  - Cugini, C.
TI  - Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781.
JO  - Genome Announcements
PY  - 2016
SP  - e01285
EP  - e01216
VL  - 4
AB  - We report here the complete genomic sequence and methylome of Aggregatibacter
AB  - actinomycetemcomitans strain IDH781. This rough strain is used extensively as a
AB  - model organism to characterize localized aggressive periodontitis pathogenesis,
AB  - the basic biology and oral cavity colonization of A. actinomycetemcomitans, and
AB  - its interactions with other members of the oral microbiome.
ER  -

TY  - JOUR
AU  - May, A.C.
AU  - Ohta, H.
AU  - Maeda, H.
AU  - Kokeguchi, S.
AU  - Cugini, C.
TI  - Draft Genome Sequences of Aggregatibacter actinomycetemcomitans Strains 310a and  310b.
JO  - Genome Announcements
PY  - 2017
SP  - e01282
EP  - e01217
VL  - 5
AB  - We report the draft genome sequences of Aggregatibacter actinomycetemcomitans strains 310a
AB  - (310-TR) and 310b (310-OS). Strain 310a is a clinical isolate with a
AB  - rough phenotype. Strain 310b is a laboratory-adapted isolate derived from the
AB  - passage of 310a and displays a smooth phenotype.
ER  -

TY  - JOUR
AU  - May, B.J.
AU  - Zhang, Q.
AU  - Li, L.L.
AU  - Paustian, M.L.
AU  - Whittam, T.S.
AU  - Kapur, V.
TI  - Complete genomic sequence of Pasteurella multocida, Pm70.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 3460
EP  - 3465
VL  - 98
AB  - We present here the complete genome sequence of a common avian clone of Pasteurella multocida,
AB  - Pm70. The genome of Pm70 is a single circular chromosome 2,257,487 base pairs in length and
AB  - contains 2,014 predicted coding regions, 6 ribosomal RNA operons, and 57 tRNAs. Genome-scale
AB  - evolutionary analyses based on pairwise comparisons of 1,197 orthologous sequences between P.
AB  - multocida, Haemophilus influenzae, and Escherichia coli suggest that P. multocida and H.
AB  - influenzae diverged approximately 270 million years ago and the gamma subdivision of the
AB  - proteobacteria radiated about 680 million years ago. Two previously undescribed open reading
AB  - frames, accounting for approximately 1% of the genome, encode large proteins with homology to
AB  - the virulence-associated filamentous hemagglutinin of Bordetella pertussis. Consistent with
AB  - the critical role of iron in the survival of many microbial pathogens, in silico and
AB  - whole-genome microarray analyses identified more than 50 Pm70 genes with a potential role in
AB  - iron acquisition and metabolism. Overall, the complete genomic sequence and preliminary
AB  - functional analyses provide a foundation for future research into the mechanisms of
AB  - pathogenesis and host specificity of this important multispecies pathogen.
ER  -

TY  - JOUR
AU  - May, C.E.
AU  - Schulman, M.L.
AU  - Howell, P.G.
AU  - Lourens, C.W.
AU  - Gouws, J.
AU  - Joone, C.
AU  - Monyai, M.S.
AU  - le Grange, M.
AU  - Bezuidt, O.K.
AU  - Harper, C.K.
AU  - Guthrie, A.J.
TI  - Draft Genome Sequence of Taylorella equigenitalis Strain ERC_G2224 Isolated from  the Semen of a Lipizzaner Stallion in South Africa.
JO  - Genome Announcements
PY  - 2015
SP  - e01205
EP  - e01215
VL  - 3
AB  - Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a
AB  - sexually transmitted infection of horses. We report here the genome sequence of T.
AB  - equigenitalis strain ERC_G2224, isolated in 2015 from a semen sample collected in 1996 from a
AB  - Lipizzaner stallion in South Africa.
ER  -

TY  - JOUR
AU  - May, M.A.
AU  - Kutish, G.F.
AU  - Barbet, A.F.
AU  - Michaels, D.L.
AU  - Brown, D.R.
TI  - Complete Genome Sequence of Mycoplasma synoviae Strain WVU 1853T.
JO  - Genome Announcements
PY  - 2015
SP  - e00563
EP  - e00515
VL  - 3
AB  - A hybrid sequence assembly of the complete Mycoplasma synoviae type strain WVU 1853(T) genome
AB  - was compared to that of strain MS53. The findings support prior
AB  - conclusions about M. synoviae, based on the genome of that otherwise
AB  - uncharacterized field strain, and provide the first evidence of epigenetic
AB  - modifications in M. synoviae.
ER  -

TY  - JOUR
AU  - May, M.S.
AU  - Hattman, S.
TI  - Deoxyribonucleic acid-cytosine methylation by host- and plasmid-controlled enzymes.
JO  - J. Bacteriol.
PY  - 1975
SP  - 129
EP  - 138
VL  - 122
AB  - Deoxyribonucleic acid (DNA)-cytosine methylation specified by the wild-type Escherichia coli
AB  - K12 mec+ gene and by the N-3 drug resistance (R) factor was studied in vivo and in vitro.
AB  - Phage lambda and fd were propagated in the presence of L-[methyl-3H]methionine in various host
AB  - bacteria. The in vivo labeled DNA was isolated from purified phage and depurinated by formic
AB  - acid-diphenylamine treatment. The resulting pyrimidine oligonucleotide tracts were separated
AB  - according to size and base composition by chromatography on diethylaminoethyl-cellulose in 7 M
AB  - urea at pH 5.5 and 3.5, respectively. The distribution of labeled 5-methylcytosine in DNA
AB  - pyrimidine tracts was identical for phage grown in mec+ and mec- (N-3) cells. For phage lambda
AB  - the major 5-methylcytosine-containing tract was the tripyrimidine, C2T; for both fd.mec- (N-3)
AB  - DNA and fd.mec+ DNA, C2T was the sole 5-methylcytosine-containing tract. When various lambda
AB  - DNAs were methylated to saturation in vitro by crude extracts from mec+ and mec- (N-3) cells,
AB  - the extent of cytosine methylation was the same. This is in contrast to in vivo methylation
AB  - where k.mec- (N-3) DNA contains twice as many 5-methylcytosines per genome as k.mec+ DNA.
AB  - Therefore, we suggest that the K12 met+ cytosine methylase and the N-3 plasmid modification
AB  - methylases are capable of recognizing the same nucleotide sequences, but that the in vivo
AB  - methylation rate is lower in mec+ cells.
ER  -

TY  - JOUR
AU  - May, M.S.
AU  - Hattman, S.
TI  - Analysis of bacteriophage deoxyribonucleic acid sequences methylated by host- and R-factor-controlled enzymes.
JO  - J. Bacteriol.
PY  - 1975
SP  - 768
EP  - 770
VL  - 123
AB  - Phages lambda and fd were propagated in Escherichia coli strains that have
AB  - either host K-12 or the N-3 R-factor deoxyribonucleic acid-cytosine methylase
AB  - activity.  Pyrimidine tracts containing 3H-labeled 5-methylcytosine (MeC) were
AB  - analyzed; in all cases, the major methylated sequence was 5'...C-MeC-T ...3'.
ER  -

TY  - JOUR
AU  - Mayer, A.
AU  - Barany, F.
TI  - DNA photoaffinity crosslinking to TaqI endonuclease by a phosphorothioate-linked aryl azide.
JO  - FASEB J.
PY  - 1992
SP  - A487
EP  - A487
VL  - 6
AB  - To identify amino acid residues required for the function of TaqI endonuclease
AB  - (cleaves T^CGA), a new type of DNA photoaffinity crosslinking reagent was
AB  - designed.  DNA (16-mer) was chemically synthesized in which a sulphur atom
AB  - replaced a non-bridging phosphate oxygen at the position 5' to the C (scissile
AB  - phosphate).  The two resulting phosphorothioate diasteriomers were separated
AB  - using HPLC (C-18 column) and then alkylated with p-azidophenacyl bromide.  The
AB  - endonuclease bound the modified substrates in a sequence-nonspecific manner and
AB  - was crosslinked in the presence of UV light (366nm) with an efficiency of 25%.
AB  - The TaqI-DNA crosslink was purified from unreacted material by FPLC (MonoQ).
AB  - This species has proven highly resistant to a variety of proteases, and efforts
AB  - are underway to effectively fragment the protein and identify the crosslinked
AB  - residue.  The approach described here should be generally applicable to the
AB  - study of other DNA binding proteins, given the facility of reagent synthesis
AB  - and the flexibility of photoactive crosslinker placement.
ER  -

TY  - JOUR
AU  - Mayer, A.N.
TI  - Defining the contacts between Taq endonuclease and the DNA phosphate backbone.
JO  - Diss. Abstr.
PY  - 1996
SP  - 2359B
EP  - 2359B
VL  - 57
AB  - The restriction endonuclease TaqI exhibits extreme specificity for its cognate sequence, TCGA,
AB  - but a direct readout model fails to account for this property.  This study examines the role
AB  - of phosphate contacts in the enzyme-substrate and transition-state complexes.  An S-methyl
AB  - group was introduced into each of the pTpCpGpApNpN internucleotide linkages using a hybrid
AB  - chemical-enzymatic synthesis, in which sulfur substitutions of non-bridging phosphate oxygens
AB  - directed the placement of methyl groups.  The resulting twelve diastereomerically pure
AB  - phosphate-modified substrates were tested for binding and cleavage by TaqI endonuclease.  The
AB  - largest binding effects were produced by pro-Sp methylations at the pTpCpGA phosphates, which
AB  - destablized the enzyme-substrate complex by 1.0-1.6 kcal/mol.  Cleavage of the modified strand
AB  - was inhibited completely by modifications at the TpCpGpA phosphates, and inhibited
AB  - significantly at the TCGApNp phosphates.  Cleavage of both strands was completely inhibited by
AB  - modification of the TCGpA linkage.  Effects on the cleavage of the unmodified strand
AB  - implicated phosphate modifications which caused global perturbations in the structure of the
AB  - transition-state complex.  These results support a model to account for the specificity of
AB  - TaqI, in which sequence-specific phosphate contacts are formed in the transition state, thus
AB  - amplifying the apparent contribution of base contacts to the transition-state complex.  To
AB  - identify amino acid residues which are in contact with the DNA, a sequence-specific
AB  - photoaffinity reagent was designed which exploits the finding that modification of the Rp
AB  - oxygen of the scissile phosphate does not interfere with substrate binding.  Accordingly, the
AB  - scissile phosphate was substituted with an Rp phosphorothioate group to direct the placement
AB  - of the bifunctional reagent, p-azidophenacyl bromide.  TaqI bound the photoaffinity reagent
AB  - specifically and formed a covalent adduct with the enzyme in the presence of UV light.  Upon
AB  - digestion of the covalent complex and isolation of a labeled peptide, the modified amino acid
AB  - was identified as Tyr161.  This residue was changed to phenylalanine by site-directed
AB  - mutagenesis, and the resulting Y161F mutant was characterized.  Removal of the Tyr161 hydroxyl
AB  - group lowered both the kcat and the KM 5-fold, indicating that while this residue may be near
AB  - the scissile phosphate, it is not critically required for catalysis.
ER  -

TY  - JOUR
AU  - Mayer, A.N.
AU  - Barany, F.
TI  - Interaction of TaqI endonuclease with the phosphate backbone.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 29067
EP  - 29076
VL  - 269
AB  - The restriction endonuclease TaqI exhibits extreme specificity for its cognate sequence, TCGA,
AB  - but a direct hydrogen bond readout model fails to account for this property. The present study
AB  - examines the role of phosphate contacts in the enzyme-substrate and transition state
AB  - complexes. An S-methyl group was introduced into each of the pTpCpGpApNpN internucleotide
AB  - linkages using a hybrid chemical-enzymatic synthesis, in which sulfur substitutions of
AB  - nonbridging phosphate oxygens directed the placement of methyl groups. The resulting 12
AB  - diastereomerically pure phosphate-modified substrates were tested for binding and cleavage by
AB  - TaqI. The largest binding effects were induced by pro-Sp methylations at the pTpCpGA
AB  - phosphates, which destabilized the enzyme-substrate complex by 1.0-1.6 kcal/mol. Cleavage of
AB  - the modified strand was inhibited completely by modifications at the TpCpGpA phosphates and
AB  - inhibited significantly at the TCGApNp phosphates. Cleavage of both strands was completely
AB  - inhibited by modification of the TCGpA linkage. Effects on the cleavage of the unmodified
AB  - strand were used to implicate phosphate modifications that caused global perturbations in the
AB  - structure of the transition state complex. These results lend support for a model for the
AB  - specificity of TaqI, in which sequence-specific phosphate contacts are formed in the
AB  - transition state, thus amplifying the apparent contribution of base contacts to transition
AB  - state stabilization.
ER  -

TY  - JOUR
AU  - Mayer, A.N.
AU  - Barany, F.
TI  - Photoaffinity cross-linking of TaqI restriction endonuclease using an aryl azide linked to the phosphate backbone.
JO  - Gene
PY  - 1995
SP  - 1
EP  - 8
VL  - 153
AB  - In an effort to identify amino acid (aa) residues near the active site of TaqI restriction
AB  - endonuclease (ENase), a sequence-specific photoaffinity reagent was designed. This reagent
AB  - exploits the finding that modification of the Rp oxygen of the scissile phosphate does not
AB  - interfere with substrate binding. The TpCGA phosphate was substituted with an Rp
AB  - phosphorothioate group to direct the placement of the heterobifunctional reagent
AB  - p-azidophenacyl bromide. TaqI bound the photoaffinity reagent specifically and formed a
AB  - covalent adduct with the ENase in the presence of UV light. The modified aa was identified as
AB  - Tyr161. This aa was changed to Phe by site-directed mutagenesis, and the resulting Y161F
AB  - mutant was characterized. Removal of the Tyr161 hydroxyl group lowered both the kcat and the
AB  - Km five-fold, indicating that, while this aa may be near the scissile phosphate, it is not
AB  - critically rquired for catalysis.
ER  -

TY  - JOUR
AU  - Mayer, H.
TI  - Optimization of the EcoRI* activity of EcoRI endonuclease.
JO  - FEBS Lett.
PY  - 1978
SP  - 341
EP  - 344
VL  - 90
AB  - None
ER  -

TY  - JOUR
AU  - Mayer, H.
AU  - Goebel, W.
TI  - Isolierung der Restriktionsendonuclease EcoRI aus einem Antibiotka-Resistenz-freien Stamm von Escherichia coli.
JO  - Hoppe Seylers Z. Physiol. Chem.
PY  - 1975
SP  - 253
EP  - 254
VL  - 356
AB  - Der Antibiotikaresistenz-(R-Faktor R1drd16 ist ein durch Deletionsmutation
AB  - entstandenes Derivat des ursprunglichen R1-Faktors, der das Restriktionsenzym
AB  - EcoRI kodiert.  Der R1drd16-Faktor determiniert nur noch Resistenz gegen
AB  - Kanamycin.  Durch weitere Mutation konnte ein Plasmid erhalten werden, das
AB  - keine Antibiotikaresistenz, wohl aber noch die Synthese von EcoRI determiniert.
AB  - Im Grobfermentationsannsatz konnte der E.-coli-Stamm, der diesen mutierten
AB  - R-Faktor tragt, mit einer Ausbeute von 35 g Bakterienfeuchtmasse/Igezuchtet
AB  - werden, ohne dab ein erkennbarer Verlust des Plasmids zu beobachten wr.  Nach
AB  - Zellaufschlub wurden in einem einzigen Fallungsschritt mit
AB  - Cetyltrimetylam-moniumbromid Zellmembran und DNA entfernt.  Bei der
AB  - Chromatographie an  Phosphocellulose und Hydroxyl-apatit verhalt sich das
AB  - Exonuclease-freie Enzym wie EcoRI des ursprunglichen Plasmids.  Auch die
AB  - Spaltungs-produkte von verschiedenen bakteriellen DNAs mit beiden
AB  - Enzympraparationen sind identisch.
ER  -

TY  - JOUR
AU  - Mayer, H.
AU  - Grosschedl, R.
AU  - Schutte, H.
AU  - Hobom, G.
TI  - ClaI, a new restriction endonuclease from Caryophanon latum L.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 4833
EP  - 4845
VL  - 9
AB  - From Caryophanon latum L a site specific restriction endonuclease (ClaI) has been purified,
AB  - which recognises the DNA hexanucleotide palindrome 5'-A-T-^C-G-A-T-3'. Staggered cleavage
AB  - generates DNA restriction fragments with 5'-terminal pCG extensions. A ClaI map of
AB  - bacteriophage lambda has been determined, which indicates cleavage inhibition due to adenine
AB  - methylation at overlapping ClaI-GATC recognition sequences. Plasmid pBR322 is cut only once,
AB  - in the tetracycline promoter region, and can, therefore, be used as a vector system for
AB  - cloning fragments derived from ClaI digestions, and in addition for fragments generated by
AB  - TaqI, HpaII, and several other enzymes.
ER  -

TY  - JOUR
AU  - Mayer, H.
AU  - Reichenbach, H.
TI  - Restriction Endonucleases: General Survey Procedure and Survey of Gliding Bacteria.
JO  - J. Bacteriol.
PY  - 1978
SP  - 708
EP  - 713
VL  - 136
AB  - Among 120 strains of gliding bacteria which were screened for restriction
AB  - endonucleases, 27 were found positive.  Additionally, three strains carried
AB  - enzymes able to release the supercoiled state of closed circular DNA.  By using
AB  - a new rapid method, restriction endonuclease activity was released by stirring
AB  - about 0.5 g of cells (fresh weight) in a motor-driven glass homogenizer in
AB  - buffer containing Triton X-101, ethylenediaminetetraacetic acid, and
AB  - mercaptoethanol.  A yield from 60 to 80% of the total activity present in the
AB  - cells was obtained with minimal destruction of the cells.  The enzyme activity
AB  - in the crude extract was measured semi-quantitatively be digestion of DNA and
AB  - subsequent separation of the fragments on an agarose slab gel.  The method
AB  - appears to be generally applicable for the extraction of restriction
AB  - endonucleases from gram-negative bacteria on an analytical scale and in a
AB  - modified form for large-scale preparation of restriction enzymes.
ER  -

TY  - JOUR
AU  - Mayer, M.J.
AU  - Narbad, A.
AU  - Gasson, M.J.
TI  - Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin.
JO  - J. Bacteriol.
PY  - 2008
SP  - 6734
EP  - 6740
VL  - 190
AB  - Clostridium difficile infection is increasing in both frequency and
AB  - severity, with the emergence of new highly virulent strains highlighting
AB  - the need for more rapid and effective methods of control. Here, we show
AB  - that bacteriophage endolysin can be used to inhibit and kill C. difficile.
AB  - The genome sequence of a novel bacteriophage that is active against C.
AB  - difficile was determined, and the bacteriophage endolysin gene was
AB  - subcloned and expressed in Escherichia coli. The partially purified
AB  - endolysin was active against 30 diverse strains of C. difficile, and
AB  - importantly, this group included strains of the major epidemic ribotype
AB  - 027 (B1/NAP1). In contrast, a range of commensal species that inhabit the
AB  - gastrointestinal tract, including several representatives of the
AB  - clostridium-like Firmicutes, were insensitive to the endolysin. This
AB  - endolysin provides a platform for the generation of both therapeutic and
AB  - detection systems to combat the C. difficile problem. To investigate a
AB  - method for the protected delivery and production of the lysin in the
AB  - gastrointestinal tract, we demonstrated the expression of active CD27L
AB  - endolysin in the lactic acid bacterium Lactococcus lactis MG1363.
ER  -

TY  - JOUR
AU  - Mayer, M.J.
AU  - Payne, J.
AU  - Gasson, M.J.
AU  - Narbad, A.
TI  - Genomic Sequence and Characterization of the Virulent Bacteriophage {phi}CTP1 from Clostridium tyrobutyricum and Heterologous Expression of Its Endolysin.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 5415
EP  - 5422
VL  - 76
AB  - The growth of Clostridium tyrobutyricum in developing cheese leads to
AB  - spoilage and cheese blowing. Bacteriophages or their specific lytic
AB  - enzymes may provide a biological control method for eliminating such
AB  - undesirable organisms without affecting other microflora. We isolated the
AB  - virulent bacteriophage phiCTP1 belonging to the Siphoviridae and have
AB  - shown that it is effective in causing lysis of sensitive strains. The
AB  - double-stranded DNA genome of phiCTP1 is 59,199 bp, and sequence analysis
AB  - indicated that it has 86 open reading frames. orf29 was identified as the
AB  - gene coding for the phage endolysin responsible for cell wall degradation
AB  - prior to virion release. We cloned and expressed the ctp1l gene in E. coli
AB  - and demonstrated that the partially purified protein induced lysis of C.
AB  - tyrobutyricum cells and reduced viable counts both in buffer and in milk.
AB  - The endolysin was inactive against a range of clostridial species but did
AB  - show lysis of Clostridium sporogenes, another potential spoilage organism.
AB  - Removal of the C-terminal portion of the endolysin completely abolished
AB  - lytic activity.
ER  -

TY  - JOUR
AU  - Mayer, W.
AU  - Niveleau, A.
AU  - Walter, J.
AU  - Fundele, R.
AU  - Haaf, T.
TI  - Demethylation of the zygotic paternal genome.
JO  - Nature
PY  - 2000
SP  - 501
EP  - 502
VL  - 403
AB  - In mammals, both parental genomes undergo dramatic epigenetic changes after fertilization to
AB  - form the diploid somatic genome.  Here we show that the paternal genome in the mouse is
AB  - significantly and actively demethylated within 6-8 hours of fertilization, before the onset of
AB  - DNA replication, whereas the maternal genome is demethylated after several cleavage divisions.
AB  - This active demethylation of the paternal genome may be associated with epigenetic remodelling
AB  - of sperm chromatin, in order to establish parent-specific developmental programmes during
AB  - early embryogenesis.
ER  -

TY  - JOUR
AU  - Maynard-Smith, M.D.
AU  - McKelvie, J.C.
AU  - Wood, R.J.
AU  - Harmer, J.E.
AU  - Ranasinghe, R.T.
AU  - Williams, C.L.
AU  - Coomber, D.M.
AU  - Stares, A.F.
AU  - Roach, P.L.
TI  - Direct and continuous fluorescence-based measurements of Pyrococcus horikoshii DNA N-6 adenine methyltransferase activity.
JO  - Anal. Biochem.
PY  - 2011
SP  - 204
EP  - 212
VL  - 418
AB  - N-6 methylation of adenine destabilises duplex DNA and this can increase the proportion of DNA
AB  - that dissociates into single strands. We
AB  - have investigated utilising this property to measure the DNA adenine
AB  - methyltransferase-catalyzed conversion of hemimethylated to fully
AB  - methylated DNA through a simple, direct, fluorescence-based assay. The
AB  - effects of methylation on the kinetics and thermodynamics of
AB  - hybridisation were measured by comparing a fully methylated
AB  - oligonucleotide product and a hemimethylated oligonucleotide substrate
AB  - using a 13-bp duplex labeled on adjacent strands with a fluorophore
AB  - (fluorescein) and quencher (dabcyl). Enzymatic methylation of the
AB  - hemimethylated GATC site resulted in destabilisation of the duplex,
AB  - increasing the proportion of dissociated DNA, and producing an
AB  - observable increase in fluorescence. The assay provides a direct
AB  - measurement of methylation rate in real time and is highly
AB  - reproducible, with a coefficient of variance over 48 independent
AB  - measurements of 3.6%. DNA methylation rates can be measured as low as
AB  - 3.55 +/- 1.84 fmol s(-1) in a 96-well plate format, and the assay has
AB  - been used to kinetically characterise the Pyrococcus horikoshii DNA
AB  - adenine methyltransferase.
ER  -

TY  - JOUR
AU  - Mayo, B.
AU  - Hardisson, C.
AU  - Brana, A.F.
TI  - Nucleolytic activities in Lactococcus lactis subsp. lactis NCDO 497.
JO  - FEMS Microbiol. Lett.
PY  - 1991
SP  - 195
EP  - 198
VL  - 79
AB  - Two nucleolytic activities were detected in Lactococcus lactis subsp. lactis NCDO 497. One of
AB  - them was a specific endonuclease, located in the cytoplasm, with the typical characteristics
AB  - of type II restriction endonucleases. The second activity was a non-specific deoxyribonuclease
AB  - with exocytoplasmic location.
ER  -

TY  - JOUR
AU  - Maze, A. et al.
TI  - Complete genome sequence of the probiotic Lactobacillus casei strain BL23.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2647
EP  - 2648
VL  - 192
AB  - The entire genome of Lactobacillus casei BL23, a strain with probiotic properties, has been
AB  - sequenced. The genomes of BL23 and the industrially
AB  - used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar.
ER  -

TY  - JOUR
AU  - Mazin, A.L.
AU  - Vanyushin, B.F.
TI  - Possible origin and evolution of enzymatic methylation of eukaryotic DNA.  Methylation of cytosine residues in three families of palindromes: RYRY, YYRR, and YYRYRR.
JO  - Mol. Biol. (Mosk)
PY  - 1990
SP  - 16
EP  - 35
VL  - 24
AB  - On the basis of an analysis of the experimental data on the closest neighbors of the
AB  - 5-methylcytosine residues in eukaryotic DNA it was established that the regions of methylation
AB  - CG and CNG may be included in three families of palindromes: RYRY, YYRR and YYRYRR.  It was
AB  - shown that the entire variety of methylated sequences detectable in their DNA can arise as a
AB  - result of mutational substitutions 5-MeC -> T, which occur in the deamination of 5-MeC
AB  - residues in prototype portions of each of these families: GCGC, CCGG and CCGCGG.  The question
AB  - of the multiplicity of DNA-methyltransferases in eukaryotes and their evolutionary origin from
AB  - prokaryotic methylases of the second type, which recognize analogous sequences in DNA, is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Mazuet, C.
AU  - Bouchier, C.
AU  - Popoff, M.R.
TI  - Draft Genome Sequence of Clostridium botulinum Strain 277-00 Type B2.
JO  - Genome Announcements
PY  - 2015
SP  - e00211
EP  - e00215
VL  - 3
AB  - We report the draft genome sequence of Clostridium botulinum strain 277-00, which encodes a
AB  - botulinum neurotoxin B2 associated with a ha gene locus. Strain 277-00
AB  - was isolated from a cheese responsible for an outbreak of botulism in Iran in
AB  - 1997. This strain is closed to the bivalent B2/FA strain IBCA10-7060.
ER  -

TY  - JOUR
AU  - Mazur, A.
AU  - De Meyer, S.E.
AU  - Tian, R.
AU  - Wielbo, J.
AU  - Zebracki, K.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 36
EP  - 36
VL  - 10
AB  - Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that can exist as a soil saprophyte or as a legume
AB  - microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule
AB  - recovered from the roots of Pisum sativum growing at Janow. GB30 is also an
AB  - effective microsymbiont of the annual forage legumes vetch and pea. Here we
AB  - describe the features of R. leguminosarum bv. viciae strain GB30, together with
AB  - sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is
AB  - arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and
AB  - 75 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
ER  -

TY  - JOUR
AU  - Mazurek, M.
AU  - Sowers, L.C.
TI  - The paradoxical influence of thymine analogues on restriction endonuclease cleavage of oligodeoxynucleotides.
JO  - Biochemistry
PY  - 1996
SP  - 11522
EP  - 11528
VL  - 35
AB  - Thymine residues in the DNA of eukaryotes may be replaced occasionally by uracil (U) or
AB  - 5-(hydroxymethyl)uracil (H) as consequences of dUMP misincorporation or thymine oxidation,
AB  - respectively.  In this study, we constructed a series of 44-base oligonucleotides containing
AB  - site-specific U or H residues and 5'-fluorescein labels in order to probe the influence of
AB  - such modifications on sequence-specific DNA-protein interactions using several type II
AB  - restriction endonucleases.  We find that substitution within the recognition sites of several
AB  - restriction endonucleases increases initial cleavage velocity by up to an order of magnitude.
AB  - These results contrast dramatically with several previous studies which demonstrated that U
AB  - substitution in short oligonucleotides inhibits or prevents nuclease cleavage.  We propose
AB  - that this apparent paradox results because the rate-limiting step in the cleavage of longer
AB  - oligonucleotides is product release whereas for shorter oligonucelotides substrate binding is
AB  - most probably rate-limiting.  For longer oligonucleotides and DNA, more rapid release of the
AB  - cleaved, substituted oligonucleotides results in more rapid turnover and a faster apparent
AB  - cleavage rate.  The sequence length at which the transition is rate-limiting step occurs
AB  - likely corresponds to the size of th enzyme footprint on its DNA recognition site.  We
AB  - conclude that both U and H do perturb sequence-specific DNA - protein interactions, and the
AB  - magnitude of this effect is site-dependent.
ER  -

TY  - JOUR
AU  - Mazzarelli, J.
AU  - Scholtissek, S.
AU  - McLaughlin, L.W.
TI  - Effects of functional group changes in the EcoRV recognition site on the cleavage reaction catalyzed by the endonuclease.
JO  - Biochemistry
PY  - 1989
SP  - 4616
EP  - 4622
VL  - 28
AB  - Oligodeoxynucleotides have been prepared which contain changes in the
AB  - functional group pattern present in the EcoRV recognition site d(GATATC).
AB  - These modifications involve the deletion of specific functional groups or the
AB  - reversal of the relative positions of functional groups within the canonical
AB  - six base pair recognition site.  The duplex stability of these modified
AB  - oligodeoxynucleotides has been assessed by determining the thermodynamic
AB  - parameters characterizing helix formation.  Steady-state kinetic parameters
AB  - have been used to characterize the interaction of the modified
AB  - oligodeoxynucleotides with the EcoRV endonuclease.  The enzyme is very
AB  - sensitive to the deletion of either of the adenine amino or thymine methyl
AB  - groups, or the reversal of the relative positions of the adenine amino group
AB  - and thymine carboxy group which form an interstrand hydrogen bond in the major
AB  - groove of the B-DNA helix.  Conversely, deletion of the guanine amino group had
AB  - only minimal effects upon the measured kinetic parameters.  Deletion of the
AB  - exocyclic amino group from the inner dA-dT base pair resulted in the fragment
AB  - which interacted with the enzyme on the basis of observed inhibition
AB  - experiments but was not cleaved.  The results suggest that the endonuclease
AB  - interacts with its recognition sequence via contacts in the major groove of the
AB  - B-DNA helix and that both hydrogen bonding to the adenine amino groups and also
AB  - hydrophobic interactions with the thymine methyl groups are involved.
ER  -

TY  - JOUR
AU  - Mbelle, N.M.
AU  - Maningi, N.E.
AU  - Tshisevhe, V.
AU  - Modipane, L.
AU  - Amoako, D.G.
AU  - Osei, S.J.
TI  - Draft Genome Sequence of a Clinical Enterococcus faecium Sequence Type 18 Strain  from South Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e01381
EP  - e01317
VL  - 5
AB  - We report the first draft genome sequence of an Enterococcus faecium sequence type 18 (ST18)
AB  - strain isolated from a tuberculosis patient in Africa. The genome
AB  - is comprised of 3,202,539 bp, 501 contigs, 37.70% GC content, 3,202
AB  - protein-encoding genes, and 61 RNA genes. The resistome and virulome of this
AB  - important pathogen are presented herein.
ER  -

TY  - JOUR
AU  - Mbelle, N.M.
AU  - Maningi, N.E.
AU  - Tshisevhe, V.
AU  - Modipane, L.
AU  - Amoako, D.G.
AU  - Osei, S.J.
TI  - First Report of a Whole-Genome Shotgun Sequence of a Clinical Enterococcus faecalis Sequence Type 6 Strain from South Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e01382
EP  - e01317
VL  - 5
AB  - Enterococcus faecalis is a lactic acid-producing Gram-positive bacterium commonly found in the
AB  - intestinal tract of humans and animals; it is implicated in
AB  - multidrug-resistant nosocomial infections. The draft genome of this E. faecalis
AB  - sequence type 6 (ST6) strain consists of 3,215,228 bp, with 37.20% GC content,
AB  - 3,048 predicted coding sequences, and 61 RNA genes.
ER  -

TY  - JOUR
AU  - McCallum, C.M.
TI  - TILLING for Arabidopsis chromomethylase function.
JO  - Ph.D. Thesis, University of Washington, Seattle, USA
PY  - 2005
SP  - 1
EP  - 66
AB  - In contrast to prokaryotic methyltransferases, comparatively little is known about the
AB  - detailed structure and function of eukaryotic cytosine-5-methyltransferase enzymes.  During
AB  - the course of my thesis work, I identified two DNA methyltransferase homologs that also
AB  - contained a chromodomain (termed "chromomethylases") in Arabidopsis thaliana.  It is thought
AB  - that chromodomains target proteins to interact with specific chromatin determinants; thus
AB  - chromomethylases might be involved in epigenetic silencing by linking chromatin structure to
AB  - DNA methylation.  In addition, the unique structure of the chromomethylases suggest they may
AB  - not play a general role in maintaining CpG DNA methylation patterns, as may be true for the
AB  - Arabidopsis methylase MET1 but, instead, may play a more specialized role in either
AB  - establishing methylation or maintaining methylation on CpNpG or other nonsymmetrical sites.
AB  - The two new genes, CMT2 and CMT3, were studied to determine their biological functions.  The
AB  - goal of my thesis work was to characterize the chromomethylase genes specifically in hopes of
AB  - determining the function of DNA methylation in plants.  Along the way I developed the reverse
AB  - genetics method TILLING (Targeting Induced Local Lesions IN Genomes) and explored genome wide
AB  - methylation targets of CMT3 using methylation profiling.  This work revealed that cmt3 mutants
AB  - appear to have decreased CpNpG methylation while CpG methylation is unaffected.
ER  -

TY  - JOUR
AU  - McCallum, C.M.
AU  - Comai, L.
AU  - Greene, E.A.
AU  - Henikoff, S.
TI  - Targeted screening for induced mutations.
JO  - Nat. Biotechnol.
PY  - 2000
SP  - 455
EP  - 459
VL  - 18
AB  - With the accumulation of large-scale sequence data, emphasis in genomics has shifted from
AB  - determining gene structure to testing gene function, and this relies on reverse genetic
AB  - methodology. Here we explore the feasibility of screening for chemically induced mutations in
AB  - target sequences in Arabidopsis thaliana. Our TILLING (Targeting Induced Local Lesions IN
AB  - Genomes) method combines the efficiency of ethyl methanesulfonate (EMS)-induced mutagenesis
AB  - with the ability of denaturing high-performance liquid chromatography (DHPLC) to detect base
AB  - pair changes by heteroduplex analysis. Importantly, this method generates a wide range of
AB  - mutant alleles, is fast and automatable, and is applicable to any organism that can be
AB  - chemically mutagenized.
ER  -

TY  - JOUR
AU  - McCann, H.C.
AU  - Rikkerink, E.H.
AU  - Bertels, F.
AU  - Fiers, M.
AU  - Lu, A.
AU  - Rees-George, J.
AU  - Andersen, M.T.
AU  - Gleave, A.P.
AU  - Haubold, B.
AU  - Wohlers, M.W.
AU  - Guttman, D.S.
AU  - Wang, P.W.
AU  - Straub, C.
AU  - Vanneste, J.L.
AU  - Rainey, P.B.
AU  - Templeton, M.D.
TI  - Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.
JO  - PLoS Pathog.
PY  - 2013
SP  - E1003503
EP  - E1003503
VL  - 9
AB  - The origins of crop diseases are linked to domestication of plants. Most crops
AB  - were domesticated centuries--even millennia--ago, thus limiting opportunity to
AB  - understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an
AB  - exception: domestication began in the 1930s with outbreaks of canker disease
AB  - caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on
AB  - SNP analyses of two circularized and 34 draft genomes, we show that Psa is
AB  - comprised of distinct clades exhibiting negligible within-clade diversity,
AB  - consistent with disease arising by independent samplings from a source
AB  - population. Three clades correspond to their geographical source of isolation; a
AB  - fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now
AB  - globally distributed. Psa has an overall clonal population structure, however,
AB  - genomes carry a marked signature of within-pathovar recombination. SNP analysis
AB  - of Psa-V reveals hundreds of polymorphisms; however, most reside within
AB  - PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome.
AB  - Removal of SNPs due to recombination yields an uninformative (star-like)
AB  - phylogeny consistent with diversification of Psa-V from a single clone within the
AB  - last ten years. Growth assays provide evidence of cultivar specificity, with
AB  - rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show
AB  - a dynamic genome with evidence of positive selection on type III effectors and
AB  - other candidate virulence genes. Each clade has highly varied complements of
AB  - accessory genes encoding effectors and toxins with evidence of gain and loss via
AB  - multiple genetic routes. Genes with orthologs in vascular pathogens were found
AB  - exclusively within Psa-V. Our analyses capture a pathogen in the early stages of
AB  - emergence from a predicted source population associated with wild Actinidia
AB  - species. In addition to candidate genes as targets for resistance breeding
AB  - programs, our findings highlight the importance of the source population as a
AB  - reservoir of new disease.
ER  -

TY  - JOUR
AU  - McCarren, J.
AU  - DeLong, E.F.
TI  - Proteorhodopsin photosystem gene clusters exhibit co-evolutionary trends and shared ancestry among diverse marine microbial phyla.
JO  - Environ. Microbiol.
PY  - 2007
SP  - 846
EP  - 858
VL  - 9
AB  - Since the recent discovery of retinylidene proteins in marine bacteria (proteorhodopsins), the
AB  - estimated abundance and diversity of this gene
AB  - family has expanded rapidly. To explore proteorhodopsin photosystem
AB  - evolutionary and distributional trends, we identified and compared 16
AB  - different proteorhodopsin-containing genome fragments recovered from
AB  - naturally occurring bacterioplankton populations. In addition to finding
AB  - several deep-branching proteorhodopsin sequences, proteorhodopsins were
AB  - found in novel taxonomic contexts, including a betaproteobacterium and a
AB  - planctomycete. Approximately one-third of the proteorhodopsin-containing
AB  - genome fragments analysed, as well as a number of recently reported marine
AB  - bacterial whole genome sequences, contained a linked set of genes required
AB  - for biosynthesis of the rhodopsin chromophore, retinal. Phylogenetic
AB  - analyses of the retinal biosynthetic genes suggested their co-evolution
AB  - and probable coordinated lateral gene transfer into disparate lineages,
AB  - including Euryarchaeota, Planctomycetales, and three different
AB  - proteobacterial lineages. The lateral transfer and retention of genes
AB  - required to assemble a functional proteorhodopsin photosystem appears to
AB  - be a coordinated and relatively frequent evolutionary event. Strong
AB  - selection pressure apparently acts to preserve these light-dependent
AB  - photosystems in diverse marine microbial lineages.
ER  -

TY  - JOUR
AU  - McCarthy, A.J.
AU  - Lindsay, J.A.
TI  - The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated.
JO  - BMC Microbiol.
PY  - 2012
SP  - 104
EP  - 104
VL  - 12
AB  - Background: Staphylococcus aureus is major human and animal pathogen. Plasmids often carry
AB  - resistance genes and virulence genes that can
AB  - disseminate through S. aureus populations by horizontal gene transfer
AB  - (HGT) mechanisms. Sequences of S. aureus plasmids in the public domain
AB  - and data from multi-strain microarrays were analysed to investigate (i)
AB  - the distribution of resistance genes and virulence genes on S. aureus
AB  - plasmids, and (ii) the distribution of plasmids between S. aureus
AB  - lineages.
AB  - Results: A total of 21 plasmid rep gene families, of which 13 were
AB  - novel to this study, were characterised using a previously proposed
AB  - classification system. 243 sequenced plasmids were assigned to 39
AB  - plasmid groups that each possessed a unique combination of rep genes.
AB  - We show some resistance genes (including ermC and cat) and virulence
AB  - genes (including entA, entG, entJ, entP) were associated with specific
AB  - plasmid groups suggesting there are genetic pressures preventing
AB  - recombination of these genes into novel plasmid groups. Whole genome
AB  - microarray analysis revealed that plasmid rep, resistance and virulence
AB  - genes were associated with S. aureus lineages, suggesting
AB  - restriction-modification (RM) barriers to HGT of plasmids between
AB  - strains exist. Conjugation transfer (tra) complex genes were rare.
AB  - Conclusion: This study argues that genetic pressures are
AB  - restraining the spread of resistance and virulence genes amongst S.
AB  - aureus plasmids, and amongst S. aureus populations, delaying the
AB  - emergence of fully virulent and resistant strains.
ER  -

TY  - JOUR
AU  - McCarthy, C.B.
AU  - Romanowski, V.
TI  - Digestion of I-PpoI recognition sites in unfavorable sequence contexts achieved by changing the reaction conditions.
JO  - Biochem. Genet.
PY  - 2006
SP  - 61
EP  - 67
VL  - 44
ER  -

TY  - JOUR
AU  - McCarthy, K.L.
AU  - Jennison, A.
AU  - Wailan, A.M.
AU  - Paterson, D.L.
TI  - Draft Genome Sequence of an IMP-7-Producing Pseudomonas aeruginosa Bloodstream Infection Isolate from Australia.
JO  - Genome Announcements
PY  - 2017
SP  - e00596
EP  - e00517
VL  - 5
AB  - IMP-7 is one of the two IMP-type carbapenemases that in Pseudomonas aeruginosa are not limited
AB  - to a geographic area, but it has not been previously reported in
AB  - the Australian setting. We report here the draft genome sequence of an Australian
AB  - P. aeruginosa bloodstream infection isolate that contains IMP-7.
ER  -

TY  - JOUR
AU  - McCarthy, K.L.
AU  - Jennison, A.V.
AU  - Wailan, A.M.
AU  - Paterson, D.L.
TI  - Draft Genome Sequences of Two Pseudomonas aeruginosa Bloodstream Infection Isolates Associated with Rapid Patient Death.
JO  - Genome Announcements
PY  - 2017
SP  - e00597
EP  - e00517
VL  - 5
AB  - The morbidity and mortality associated with Pseudomonas aeruginosa bloodstream infections are
AB  - significant. New strategies are required to treat such infections.
AB  - We report here the draft genome sequences of two antibiotic-sensitive P.
AB  - aeruginosa bloodstream infection isolates that were associated with rapid death
AB  - in nonneutropenic patients.
ER  -

TY  - JOUR
AU  - McCarthy, S.
AU  - Gradnigo, J.
AU  - Johnson, T.
AU  - Payne, S.
AU  - Lipzen, A.
AU  - Martin, J.
AU  - Schackwitz, W.
AU  - Moriyama, E.
AU  - Blum, P.
TI  - Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives.
JO  - Genome Announcements
PY  - 2015
SP  - e00549
EP  - e00515
VL  - 3
AB  - Sulfolobus solfataricus is a thermoacidophilic crenarcheote with a 3.0-Mb genome. Here, we
AB  - report the genome sequence of S. solfataricus strain 98/2, along with
AB  - several evolved derivatives generated through experimental microbial evolution
AB  - for enhanced thermoacidophily.
ER  -

TY  - JOUR
AU  - McClain, M.S.
AU  - Shaffer, C.L.
AU  - Israel, D.A.
AU  - Peek, R.M. Jr.
AU  - Cover, T.L.
TI  - Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer.
JO  - BMC Genomics
PY  - 2009
SP  - 3
EP  - 3
VL  - 10
AB  - BACKGROUND: Persistent colonization of the human stomach by Helicobacter
AB  - pylori is associated with asymptomatic gastric inflammation (gastritis)
AB  - and an increased risk of duodenal ulceration, gastric ulceration, and
AB  - non-cardia gastric cancer. In previous studies, the genome sequences of H.
AB  - pylori strains from patients with gastritis or duodenal ulcer disease have
AB  - been analyzed. In this study, we analyzed the genome sequences of an H.
AB  - pylori strain (98-10) isolated from a patient with gastric cancer and an
AB  - H. pylori strain (B128) isolated from a patient with gastric ulcer
AB  - disease. RESULTS: Based on multilocus sequence typing, strain 98-10 was
AB  - most closely related to H. pylori strains of East Asian origin and strain
AB  - B128 was most closely related to strains of European origin. Strain 98-10
AB  - contained multiple features characteristic of East Asian strains,
AB  - including a type s1c vacA allele and a cagA allele encoding an EPIYA-D
AB  - tyrosine phosphorylation motif. A core genome of 1237 genes was present in
AB  - all five strains for which genome sequences were available. Among the 1237
AB  - core genes, a subset of alleles was highly divergent in the East Asian
AB  - strain 98-10, encoding proteins that exhibited <90% amino acid sequence
AB  - identity compared to corresponding proteins in the other four strains.
AB  - Unique strain-specific genes were identified in each of the newly
AB  - sequenced strains, and a set of strain-specific genes was shared among H.
AB  - pylori strains associated with gastric cancer or premalignant gastric
AB  - lesions. CONCLUSION: These data provide insight into the diversity that
AB  - exists among H. pylori strains from diverse clinical and geographic
AB  - origins. Highly divergent alleles and strain-specific genes identified in
AB  - this study may represent useful biomarkers for analyzing geographic
AB  - partitioning of H. pylori and for identifying strains capable of inducing
AB  - malignant or premalignant gastric lesions.
ER  -

TY  - JOUR
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Grable, J.
AU  - Samudzi, C.T.
AU  - Wang, B.-C.
AU  - Greene, P.
AU  - Boyer, H.W.
AU  - Rosenberg, J.M.
TI  - Structural studies on a DNA-EcoRI endonuclease recognition complex.
JO  - Biomolecular Sterodynamics
PY  - 1986
SP  - 45
EP  - 68
VL  - 3
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
AB  - endonuclease and the cognate oligonucleotide TCGCGAATTCGCG was solved by the
AB  - ISIRT method using a platinum isomorphous derivative.  The complex possesses a
AB  - common two-fold symmetry axis which relates both strands of the
AB  - self-complementary oligonucleotide and the two identical subunits of the
AB  - protein dimer.  Each subunit is organized into an alpha/beta domain based on a
AB  - five stranded beta-sheet and an extension, called the arm, which wraps around
AB  - the DNA.  The primary beta-sheet consists of anti-parallel and parallel
AB  - segments which, respectively, contain the sites of DNA strand scission and
AB  - sequence recognition.  (DNA hydrolysis was inhibited via omission of
AB  - magnesium).  The DNA departs significantly from the conformations seen in the
AB  - absence of protein, suggesting that binding of the enzyme is required for their
AB  - stability.  These are termed neo-conformations to distinguish them from those
AB  - which are intrinsically stable in the absence of protein and include the
AB  - torsional type-1 neo-kink which unwinds the DNA by approximately 25 degrees.
AB  - This separates the DNA backbones by approximately 3.5 angstrom without
AB  - unstacking the bases, and is a structural requirement for the recognition
AB  - modules of the protein to gain access to the edges of the bases exposed at the
AB  - bottom of the major groove.  We suspect that there are a finite number of
AB  - structurally feasible neo-conformations which are important for DNA-protein
AB  - interactions in general.
ER  -

TY  - JOUR
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Wang, B.C.
AU  - Greene, P.
AU  - Boyer, H.W.
AU  - Grable, J.
AU  - Rosenberg, J.M.
TI  - Structure of the DNA-EcoRI endonuclease recognition complex at 3 angstrom resolution.
JO  - Science
PY  - 1986
SP  - 1526
EP  - 1541
VL  - 234
AB  - The crystal structure of the complex between EcoRI endonuclease and the cognate
AB  - oligonucleotide TCGC-GAATTCGCG provides a detailed example of the structural basis of
AB  - sequence-specific DNA-protein interactions.  The structure was determined, to 3 angstrom
AB  - resolution, by the ISIR (iterative single isomorphous replacement) method with a platinum
AB  - isomorphous derivative.  The complex has twofold symmetry.  Each subunit of the endonuclease
AB  - is organized into an a/b domain consisting of a five-stranded beta sheet, alpha helices, and
AB  - an extension, called the "arm," which wraps around the DNA.  The large beta sheet consists of
AB  - antiparallel and parallel motifs that form the foundations for loops and alpha helices
AB  - responsible for DNA strand scission and sequence-specific recognition, respectively.  The DNA
AB  - cleavage site is located in a cleft that binds the DNA backbone in the vicinity of the
AB  - scissile bond. Sequence specificity is mediated by 12 hydrogen bonds originating from alpha
AB  - helical recognition modules.  Arg200 forms two hydrogen bonds with guanine while Glu144 and
AB  - Arg145 form four hydrogen bonds to adjacent adenine residues. These interactions discriminate
AB  - the EcoRI hexanucleotide GAATTC from all other hexanucleotides because any base substitution
AB  - would require rupture of at least one of these hydrogen bonds.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - Site-specific cleavage of DNA at 8-, 9-, and 10-bp sequences.
JO  - Methods Enzymol.
PY  - 1987
SP  - 22
EP  - 33
VL  - 155
AB  - Site-specific cleavage of DNA at 8-, 9-, and 10-bp sequences had been reported.
AB  - This technique relies on a restriction enzyme, DpnI, which only cuts the sequence
AB  - GATC when both strands are methylated at adenine 3,4;
AB  -     5'...GmA T C...3'
AB  -     3'...C TmA G...5'
AB  - DpnI does not cut the DNA of most species because they lack this methylated sequence.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - Selection against dam methylation sites in the genomes of DNA of enterobacteriophages.
JO  - J. Mol. Evol.
PY  - 1984
SP  - 317
EP  - 322
VL  - 21
AB  - Post replicative methylation of adenine in Escherichia coli DNA to produce G6mATC (where 6mA
AB  - is 6-methyladenine) has been associated with preferential daughter-strand repair and possibly
AB  - regulation of replication. An analysis was undertaken to determine if these, or other, as yet
AB  - unknown roles of GATC, have had an effect on the frequency of GATC in E. coli or bacteriophage
AB  - DNA. It was first ascertained that the most accurate predictions of GATC frequency were based
AB  - on the observed frequencies of GAT and ATC, which would be expected since these predictors
AB  - take into account preferences in codon usage. The predicted frequencies were compared with
AB  - observed GATC frequencies in all available bacterial and phage nucleotide sequences. The
AB  - frequency of GATC was close to the predicted frequency in most genes of E. coli and its RNA
AB  - bacteriophages and in the genes of nonenteric bacteria and their bacteriophages. However, for
AB  - DNA enterobacteriophages the observed frequency of GATC was generally significantly lower than
AB  - predicted when assessed by the chi square test. No elevation in the rate of mutation of 6mA in
AB  - GATC relative to other bases was found when pairs of DNA sequences from closely related phages
AB  - or pairs of homologous genes from enterobacteria were compared, nor was any preferred pathway
AB  - for mutation of 6mA evident in the E. coli DNA bacteriophages. This situation contrasts with
AB  - that of 5-methylcytosine, which is hypermutable, with a preferred pathway to thymine. Thus,
AB  - the low level of GATC in enterobacteriophages is probably due not to 6mA hypermutability, but
AB  - to selection against GATC in order to bypass a GATC mediated host function.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - The effect of sequence specific DNA methylation on restriction endonuclease cleavage.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 5859
EP  - 5866
VL  - 9
AB  - Sequence specific DNA methylation sometimes results in the protection of some
AB  - or all of a restriction endonucleases' cleavage sites.  This is usually, but
AB  - not always, the result of methylation of one or both strands of DNA at the site
AB  - characteristic of the corresponding "cognate" modification methylase.  The
AB  - known effects of sequence methylation on restriction endonucleases are
AB  - compiled.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - Purification and characterization of two new modification methylases: M.ClaI from Caryophanon latum and M.TaqI from Thermus aquaticus YTI.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 6795
EP  - 6804
VL  - 9
AB  - A method for detecting Type II modification methylases and determining their methylation site
AB  - by assaying the ability of methylated DNA to be cleaved by heterologous restriction enzymes is
AB  - described and applied to the isolation of the restriction modification methylases from Thermus
AB  - thermophilus HB8, Thermus aquaticus YTI and Caryophanon latum L.  M.TaqI is shown to have a
AB  - methylation specificity identical to M.TthI (TCGmeA). M.ClaI methylates at adenine and
AB  - protects a subset of TthI sites indicating that it methylates the sequence ATCGmeAT.
AB  - Methylation by M.TthI also protects against cleavage by SalI, XhoI and at some HindII, AccI
AB  - and MboI sites.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - The effect of site specific methylation on restriction endonuclease cleavage (update).
JO  - Nucleic Acids Res.
PY  - 1983
SP  - r169
EP  - r173
VL  - 11
AB  - I present here an update of the compilation published in 1981 in this journal
AB  - on the effects of site specific methylation on restriction endonuclease
AB  - cleavage.  The amount of information available has increased by nearly 50%
AB  - since that time.  Table 1 is organized by length of restriction endonuclease
AB  - recognition sequence and then alphabetically by sequence.  Isoschizomers are
AB  - listed alphabetically by name.  Only the effects of methylation at the N6
AB  - position of adenine and C5 of cytosine are considered.  References to the
AB  - purification of restriction enzymes and the determination of their recognition
AB  - sequences can be found in R.J. Roberts review.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes.
JO  - J. Mol. Evol.
PY  - 1983
SP  - 346
EP  - 354
VL  - 19
AB  - Methylation of higher plant DNA occurs at up to 25% of all cytosines, primarily
AB  - in the sequences CpG and CpNpG, both of which are over 80% methylated in wheat
AB  - and tobacco (Gruenbaum et al. 1981).  CpG and CpNpG frequencies and
AB  - distributions in the known sequences of cloned genes of leguminous plants were
AB  - analyzed.  In this sample CpG occurred at only 49% of the frequency expected if
AB  - the bases were distributed at random.  This lower frequency may be attributed
AB  - to the fixation of mutations generated by a high rate of deamination of
AB  - 5-methylcytosine to thymine (Salser 1977).  Consistent with this hypothesis,
AB  - the product of CpG transitions, TpG and CpA, were significantly above their
AB  - expected frequency.  However CpNpG occurred at approximately expected levels
AB  - and there was no significant increase in its transition products CpNpA and
AB  - TpNpG.  Possible explanations for this phenomenon are discussed.  An analysis
AB  - of the distribution of di- and trinucleotides across functionally classified
AB  - regions of genes showed CpG to be asymmetrically distributed.  CpG was on
AB  - average significantly enriched in the 3' flanking regions compared to other
AB  - regions.  This may reflect a methylation-mediated regulatory role for this
AB  - region in some legume genes.
ER  -

TY  - JOUR
AU  - McClelland, M.
TI  - Recognition sequences of Type II restriction systems are constrained by the G+C content of host genomes.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 2283
EP  - 2294
VL  - 16
AB  - I show that the recognition sequences of Type II restriction systems are
AB  - correlated with the G+C content of the host bacterial DNA.  Almost all
AB  - restriction systems with G+C rich tetranucleotide recognition sequences are
AB  - found in species with A+T rich genomes, whereas G+C rich hexanucleotide and
AB  - octanucleotide recognition sequences are found almost exclusively in speciies
AB  - with G+C rich genomes.  Most hexanucleotide recognition sequences found in
AB  - species with A+T rich genomes are A+T rich.  This distribution eliminates a
AB  - substantial proportion of the potential variance in the frequency of
AB  - restriction recognition sequences in the host genomes.  As a consequence,
AB  - almost all restriction recognition sequences, including those eight base pairs
AB  - in length (NotI and SfiI), are predicted to occur with a frequency ranging from
AB  - once every 300 to once every 5,000 base pairs in the host genome.  Since the
AB  - G+C content of bacteriophage DNA and of the host genome are also correlated,
AB  - the data presented is evidence that most TypeII "restriction systems" are
AB  - indeed involved in phage restriction.
ER  -

TY  - JOUR
AU  - McClelland, M. et al.
TI  - Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.
JO  - Nat. Genet.
PY  - 2004
SP  - 1268
EP  - 1274
VL  - 36
AB  - Salmonella enterica serovars often have a broad host range, and some cause both
AB  - gastrointestinal and systemic disease. But the serovars Paratyphi A
AB  - and Typhi are restricted to humans and cause only systemic disease. It has
AB  - been estimated that Typhi arose in the last few thousand years. The
AB  - sequence and microarray analysis of the Paratyphi A genome indicates that
AB  - it is similar to the Typhi genome but suggests that it has a more recent
AB  - evolutionary origin. Both genomes have independently accumulated many
AB  - pseudogenes among their approximately 4,400 protein coding sequences: 173
AB  - in Paratyphi A and approximately 210 in Typhi. The recent convergence of
AB  - these two similar genomes on a similar phenotype is subtly reflected in
AB  - their genotypes: only 30 genes are degraded in both serovars.
AB  - Nevertheless, these 30 genes include three known to be important in
AB  - gastroenteritis, which does not occur in these serovars, and four for
AB  - Salmonella-translocated effectors, which are normally secreted into host
AB  - cells to subvert host functions. Loss of function also occurs by mutation
AB  - in different genes in the same pathway (e.g., in chemotaxis and in the
AB  - production of fimbriae).
ER  -

TY  - JOUR
AU  - McClelland, M. et al.
TI  - Complete genome sequence of Salmonella enterica serovar typhimurium LT2.
JO  - Nature
PY  - 2001
SP  - 852
EP  - 856
VL  - 413
AB  - Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of
AB  - human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of
AB  - non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many
AB  - deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome
AB  - and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues
AB  - of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously
AB  - completed genomes of three related bacteria, sample sequencing of both S. enterica serovar
AB  - Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced
AB  - genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent,
AB  - with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi),
AB  - and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2
AB  - confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are
AB  - useful for studies of epidemiology, host specificity and pathogenesis. Most of these
AB  - homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane,
AB  - rendering them accessible as therapeutic or vaccine targets.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Bhagwat, A.S.
TI  - Biased DNA repair.
JO  - Nature
PY  - 1992
SP  - 595
EP  - 596
VL  - 355
AB  - Hennecke et al. report the first in vitro characterization of a DNA mismatch
AB  - endonuclease.  This enzyme, the vsr gene product, initiates very short patch
AB  - repair of E. coli by nicking one strand of the duplex next to the T at a
AB  - mismatched T:G in the sequence CTWG or TWGG.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Hanish, J.
AU  - Nelson, M.
AU  - Patel, Y.
TI  - KGB: a single buffer for all restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 364
EP  - 364
VL  - 16
AB  - Most recommended restriction buffers contain Na+ and Cl-.  However, in bacteria
AB  - the most abundant intracellular cation and anion are usually potassium and
AB  - glutamate, respectively.  Furthermore, restriction endonucleases cleave DNA in
AB  - potassium glutamate (KGlu) over a much broader concentration range than they do
AB  - in NaCl.  These facts encouraged us to investigate the possibility that we
AB  - could use KGlu in a chloride-free buffer and achieve normal levels of activity
AB  - for all restriction endonucleases.  We have tested fifty-five restriction
AB  - endonucleases for their ability to cleave DNA in a series of KGlu buffers (KGB,
AB  - see Table 1) and compared the level of activity with that found under
AB  - conditions recommended by the vendors (New England Biolabs, Boehringer Mannheim
AB  - Biochem. and International Biotech. Inc.).  Assays were performed as partial
AB  - digests (0.2 units per ug of DNA in 30 ul for 30 min.) and as overnight
AB  - digestions with excess enzyme to ensure that no loss of specificity (start
AB  - activity) occurred.  Most restriction endonucleases, polymerases and ligase
AB  - showed broad KGlu concentration optima and all enzymes functioned in 100 mM
AB  - KGlu (1X KGB).  Reducing agent was not normally required.  Some enzymes worked
AB  - well in concentrations of KGlu over 400 mM (data not presented).  KGB can be
AB  - used to simplify laboratory procedures including double digests, DNA cleavage
AB  - followed by end-labeling, or the digestion of DNA embedded in agarose prior to
AB  - pulsed field gel electrophoresis.  DNA in KGB can be phenol extracted and
AB  - ethanol precipitated using standard protocols.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Jones, R.
AU  - Patel, Y.
AU  - Nelson, M.
TI  - Restriction endonucleases for pulsed field mapping of bacterial genomes.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 5985
EP  - 6005
VL  - 15
AB  - Fundamental to many bacterial genome mapping strategies currently under
AB  - development is the need to cleave the genome into a few large DNA fragments
AB  - that can be resolved by pulsed field gel electrophoresis.  Identification of
AB  - endonucleases that infrequently cut a genome is of key importance in this
AB  - process.  We show that the tetranucleotide CTAG is extremely rare in most
AB  - bacterial genomes with G+C contents above 45%.  As a consequence, most of the
AB  - sixteen bacterial genomes we have tested are cleaved less than once every
AB  - 100,000 base pairs by one or more endonucleases that have CTAG in their
AB  - recognition sequences:  XbaI (TCTAGA), SpeI (ACTAGT), AvrII (CCTAGG) and NheI
AB  - (GCTAGC).  Similarily, CCG and CGG are the rarest trinucleotides in many
AB  - genomes with G+C content of less than 45%.  Thus, SmaI (CCCGGG), RsrII
AB  - (CGGWCCG), NaeI (GCCGGC) and SacII (CCGCGG) are often suitable endonucleases
AB  - for producing fragments that average over 100,000 base pairs from such genomes.
AB  - Pulsed field gel electrophoresis of the fragments that result from cleavage
AB  - witih endonucleases that cleave only a few times per genome should assist in
AB  - the physical mapping of many prokaryotic genomes.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Kessler, L.G.
AU  - Bittner, M.
TI  - Site-specific cleavage of DNA at 8- and 10-base pair sequences.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 983
EP  - 987
VL  - 81
AB  - A method is described for cutting DNA at specific sites that are 8 and 10 base
AB  - pairs long.  The DNA is first treated with a specific methylase, either the
AB  - restriction-modification enzyme M. TaqI, which converts the 4-base sequence
AB  - T-C-G-A to T-C-G-mA, or the similar enzyme M. ClaI, which converts the 6-base
AB  - sequence A-T-C-G-A-T to A-T-C-G-mA-T.  The DNA is then cleaved with DpnI, a
AB  - restriction endonuclease that recognizes the sequence G-mA-T-C.  DpnI is unique
AB  - in that it cuts only DNA that is methylated at adenine in both strands of its
AB  - recognition sequence.  In DNAs that are not otherwise methylated at adenine in
AB  - both strands of the sequence G-A-T-C, cleavage by DpnI occurs only at the
AB  - following sequences: 	in the case of M. TaqI methylation, 5' T-C-G-mA- T-C-G-mA
AB  - 3'3'mA-G-C- T-mA-G-C- T 5'; in the case of M. ClaI methylation, 5' A- T-C-G-mA-
AB  - T-C-G-mA-T 3'3' T-mA-G-C -T-mA-G-C -T-A 5'.  Specific cutting and cloning at
AB  - these methylase/DpnI-generated sites is shown experimentally.  Further, we
AB  - describe how the above technique can be extended to generate DpnI cleavage
AB  - sites of up to 12 base pairs.  In DNA that contains equal amounts of each base
AB  - distributed at random, 8- and 10-base pair recognition sequences occur, on the
AB  - average, approximately once every 65,000 and 1,000,000 base pairs,
AB  - respectively.  Potential applications, including the development of cloning
AB  - vectors and a rapid method for chromosome walking, are discussed.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
TI  - Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2145
EP  - 2157
VL  - 20
AB  - We present in Table I an updated list of the sensitivities of over 280 restriction
AB  - endonucleases to the site-specific DNA modifications m4C, m5C, hm5C, and m6A, four
AB  - modifications that are common in DNA prokaryotes, eukaryotes, and their viruses. Table II is a
AB  - list of over 190 characterized DNA methyltransferases. A detailed list of cloned
AB  - restriction-modification genes has been made by Wilson. Table III lists the sensitivities of
AB  - over 20 Type II DNA methyltransferases to m4C, m5C, hm5C, and m6A modification. Most DNA
AB  - methyltransferases are sensitive to non-canonical modifications within their recognition
AB  - sequences, and this sensitivity may differ from that of their restriction endonuclease
AB  - partners. Finally, several restriction endonuclease isoschizomers are known to differ in their
AB  - ability to cleave DNA which has been methylated. Table IV lists over 20 known isoschizomer
AB  - pairs and one isomethylator pair, along with the modified recognition sites at which they
AB  - differ.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
TI  - Enhancement of the apparent cleavage specificities of restriction endonucleases:  applications to megabase mapping of chromosomes.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 257
EP  - 282
VL  - 5
AB  - Restriction endonucleases generally recognize DNA sequences of four to six base
AB  - pairs.  Therefore, these enzymes cut DNA that contains equal amounts of A,C,G
AB  - and T, distributed at random, into fragments with an average size of 4/4 to 4/6
AB  - base pairs, (256 to 4096 base pairs).  Accordingly, restriction endonuclease
AB  - mapping techniques are appropriate for the analysis of gene-sized DNA
AB  - molecules.  For example, a restriction endonuclease with a six base specificity
AB  - will cut the human genome into approximately 750,000 fragments averaging 4
AB  - kilobase pairs.  However, more specific DNA cutting methods would yield fewer
AB  - and larger fragments, suitable for the analysis of large, complex genomes.
AB  - Techniques have been described for the preparation and separation of DNA
AB  - molecules of one megabase pair or more.  To produce fragments of this size from
AB  - random DNA one must have a recognition sequence which is the log (base 4) of
AB  - 1,000,000; approximately ten base pairs.  The genome sizes of various organisms
AB  - and the number of fragments generated by cleavage systems of varying
AB  - specificities are presented in Table 1.  We describe here a number of
AB  - strategies which can be used to increase the apparent specificity of
AB  - restriction endonucleases to produce Average Fragment Sizes (AFS) in the range
AB  - fo 6,000 to 270,000,000 base pairs.  These are:  (1) protection of restriction
AB  - endonuclease recognition sites from cleavage by sequence-specific DNA
AB  - methylation. (2) generation of cleavage sites using sequence-specific DNA
AB  - methylation and a methylation-dependent restriction endonuclease, DpnI.  (3)
AB  - blocking DNA methylases by other methylases.  (4) prediction of rare
AB  - restriction recognition sites for particular genomes based on the non-random
AB  - sequence arrangement of natural DNAs.  We believe that combinations of the
AB  - above-mentioned three methods will provide a framework for the eventual
AB  - molecular dissection of large, complex, DNA molecules.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
TI  - The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases - a review.
JO  - Gene
PY  - 1988
SP  - 291
EP  - 304
VL  - 74
AB  - Review of methylation sensitivity.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
TI  - The 5'-GGATCC-3' cleavage specificity of BamHI is increased to 5'-CCGGATCCGG-3' by sequential double methylation with M.HpaII and M.BamHI.
JO  - Gene
PY  - 1988
SP  - 169
EP  - 176
VL  - 74
AB  - Site-specific DNA methylation is known to block cleavage by a number of
AB  - restriction endonucleases.  We show that methylation at non-canonical DNA
AB  - modification sites can also block methylation by five of 13 DNA
AB  - methyltransferases (MTases) tested.  Furthermore, MTases and endonucleases that
AB  - recognize the same nucleotide sequence can differ in their sensitivity to
AB  - non-canonical methylation.  In particular, BamHI endonuclease can cut
AB  - 5'-GGATCm5C efficiently, whereas M.BamHI cannot methylate this modified
AB  - sequence.  Methyltransferase/endonuclease pairs which differ in their
AB  - sensitivity to non-canonical methylation can be exploited to generate rare DNA
AB  - cleavage sites.  For example, we show that M.HpaII, M.BamHI, and BamHI can be
AB  - used sequentially in a three-step procedure to specifically cleave DNA at the
AB  - 10-bp sequence 5'-CCGGATCCGG.  Several highly selective DNA cutting strategies
AB  - are made possible by these sequential double methylation-blocking reactions.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
TI  - The effect of site specific methylation on restriction endonuclease digestion.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - r201
EP  - r207
VL  - 13
AB  - None
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
AU  - Cantor, C.R.
TI  - Purification of MboII methylase (GAAGmA) from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 7171
EP  - 7182
VL  - 13
AB  - The restriction modification methylase M.MboII has been purified using a sensitive
AB  - oligonucleotide linker assay.  The enzyme methylates the MboII recognition sequence GAAGA at
AB  - adenine to produce GAAGmA.  M.MboII can be used in conjunction with the methylation dependent
AB  - restriction endonuclease DpnI (GmATC) to produce cleavage at the 10 base sequence GAAGATCTTC.
AB  - When M.MboII is used in combination with M.ClaI (ATCGATCGAT), GAAGATCTTC, GAAGATCGAT,
AB  - ATCGATCTTC and ATCGATCGAT, which is equivalent to a nine base recognition site. The use of
AB  - combinations of adenine methylases and DpnI to generate highly selective DNA cleavages at a
AB  - variety of sequences up to fourteen base pairs is discussed.
ER  -

TY  - JOUR
AU  - McClelland, M.
AU  - Nelson, M.
AU  - Raschke, E.
TI  - Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 3640
EP  - 3659
VL  - 22
AB  - Restriction endonucleases have site-specific interactions with DNA that can often be inhibited
AB  - by site-specific DNA methylation and other site-specific DNA modifications. However, such
AB  - inhibition cannot generally be predicted. The empirically acquired data on these effects are
AB  - tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific
AB  - DNA modification methyltransferases and their specificities is presented along with EMBL
AB  - database accession numbers for cloned genes.
ER  -

TY  - JOUR
AU  - McClelland, S.E.
AU  - Dryden, D.T.F.
AU  - Szczelkun, M.D.
TI  - Continuous assays for DNA translocation using fluorescent triplex dissociation: Application to type I restriction endonucleases.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 895
EP  - 915
VL  - 348
AB  - Fluorescent assays and accompanying kinetic models are described for the analysis of DNA
AB  - translocation independent of duplex unwinding. A
AB  - triplex binding site (TBS) was introduced into DNA substrates at
AB  - precise loci downstream of recognition sequences for type IA, IB and IC
AB  - restriction endonucleases (EcoKI, EcoAI and EcoR1241, respectively).
AB  - Each endonuclease was incubated (without ATP) with substrates on which
AB  - a hexachlorofluoroscein-labelled triplex-forming oligonucleotide
AB  - (HEX-TFO) was pre-bound. Following addition of ATP, 1-D enzyme motion
AB  - resulted in collision with, and displacement of, the HEX-TFO, producing
AB  - a > twofold increase in fluorescent intensity. Alternatively, a
AB  - decrease in anisotropy following displacement of a rhodamine-labelled
AB  - TFO was monitored. Using rapid mixing in a stopped-flow fluorimeter,
AB  - continuous kinetic profiles were produced in which displacement is
AB  - preceded by a lag-phase, directly proportional to the distance moved.
AB  - For each enzyme, we obtained not only the translocation. rate but also
AB  - information on slow isomerisation step(s) at initiation. Furthermore,
AB  - we demonstrated that enzymes deficient in DNA cleavage but with maximal
AB  - ATPase activity showed initiation and translocation rates identical to
AB  - wild-type, confirming that DNA strand breaks are not a pre-requisite of
AB  - motion.
ER  -

TY  - JOUR
AU  - McClelland, S.E.
AU  - Szczelkun, M.D.
TI  - The type I and III restriction endonucleases: Structural elements in the molecular motors that process DNA.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 111
EP  - 135
VL  - 14
AB  - The Type I and III restriction endonucleases are larger, multimeric protein complexes with
AB  - four enzyme activities; DNA methyltransferase, DNA endonuclease, ATPase and DNA translocase.
AB  - It has been demonstrated that ATP-dependent protein motion along DNA is necessary for
AB  - endonuclease activity.  Studies have shown that Type I enzymes remain bound to their
AB  - recognition sites whilst simultaneously translocating adjacent non-specific dsDNA past a
AB  - stationary complex.  This occurs bi-directionally so that two DNA loops are extruded.  An
AB  - equivalent unidirectional mechanism has been suggested for the Type III enzymes.  DNA cleavage
AB  - generally results when the enzymes stall against another restriction enzyme complex.  Both the
AB  - HsdR subunits of the Type I enzymes and the Res subunits of the Type III enzymes carry amino
AB  - acid motifs characteristic of superfamily 2 helicases.  In this review, the structural and
AB  - mechanistic implications of this relationship are discussed and models s!
AB  - uggested for how the ATP-dependent restriction enzymes might couple chemical energy to
AB  - mechanical motion on DNA.
ER  -

TY  - JOUR
AU  - McClelland, W.D.
AU  - Trachtenberg, A.M.
AU  - Brennan, M.A.
AU  - MacLea, K.S.
TI  - Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832T.
JO  - Genome Announcements
PY  - 2017
SP  - e01007
EP  - e01017
VL  - 5
AB  - The aerobic phenol-degrading Gram-negative rod Oceanimonas baumannii ATCC 700832T was first
AB  - isolated from estuary mud from the River Wear, United Kingdom, in 1983.
AB  - Information on the draft genome sequence for O. baumannii ATCC 700832T is
AB  - included in this announcement. The predicted genome size is 3,809,332 bp, with
AB  - 55.88% G+C content.
ER  -

TY  - JOUR
AU  - McClure, J.A.
AU  - Shideler, S.M.
AU  - Zhang, K.
TI  - Complete Genome Sequences of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Strains CMRSA3 and CMRSA6.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00892
EP  - e00818
VL  - 7
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 8 (CC8) sequence type 239
AB  - (ST239) represents a predominant hospital-associated MRSA
AB  - sublineage present worldwide. The Canadian epidemic MRSA strains CMRSA3 and
AB  - CMRSA6 are moderately virulent members of this group but are closely related to
AB  - the highly virulent strain TW20. Whole-genome sequencing of CMRSA3 and CMRSA6 was
AB  - conducted to identify genetic determinants associated with their virulence.
ER  -

TY  - JOUR
AU  - McClure, J.A.
AU  - Zhang, K.
TI  - Complete Genome Sequence of a Community-Associated Methicillin-Resistant Staphylococcus aureus Hypervirulent Strain, USA300-C2406, Isolated from a Patient  with a Lethal Case of Necrotizing Pneumonia.
JO  - Genome Announcements
PY  - 2017
SP  - e00461
EP  - e00417
VL  - 5
AB  - USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus
AB  - strain causing significant morbidity and mortality. We present here the
AB  - full annotated genome of a USA300 hypervirulent clinical strain, USA300-C2406,
AB  - isolated from a patient with a lethal case of necrotizing pneumonia, to gain a
AB  - better understanding of USA300 hypervirulence.
ER  -

TY  - JOUR
AU  - McClure, J.A.
AU  - Zhang, K.
TI  - Complete Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Colonizing Strain M92.
JO  - Genome Announcements
PY  - 2017
SP  - e00478
EP  - e00417
VL  - 5
AB  - M92 is a methicillin-resistant Staphylococcus aureus (MRSA) colonizing strain belonging to
AB  - ST239-MRSA-III. It frequently shows local nasal colonization in our
AB  - hospital staff, but has never been associated with infection. We sequenced the
AB  - complete genome of M92, in order to compare it to highly virulent MRSA strains to
AB  - gain insight into MRSA virulence factors.
ER  -

TY  - JOUR
AU  - McClure, J.A.
AU  - Zhang, K.
TI  - Complete Genome Sequences of Five Representative Staphylococcus aureus ST398 Strains from Five Major Sequence Heterogeneity Groups of a Diverse Isolate  Collection.
JO  - Genome Announcements
PY  - 2017
SP  - e00473
EP  - e00417
VL  - 5
AB  - Staphylococcus aureus sequence type 398 (ST398) is a rapidly emerging livestock-associated
AB  - strain causing zoonotic disease in humans. The course of
AB  - pathogen evolution remains unclear, prompting whole-genome comparative studies in
AB  - attempts to elucidate this issue. We present the full, annotated genomes of five
AB  - newly isolated representative ST398 strains from five major sequence
AB  - heterogeneity groups of our diverse isolate collection.
ER  -

TY  - JOUR
AU  - McConnell, D.J.
AU  - Searcy, D.G.
AU  - Sutcliffe, J.G.
TI  - A restriction enzyme ThaI from the thermophilic mycoplasma Thermoplasma acidophilum.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 1729
EP  - 1739
VL  - 5
AB  - A type II restriction enzyme (ThaI) has been isolated from the thermophilic
AB  - mycoplasma Thermoplasma acidophilum.  A new method of general application was
AB  - used to determine the DNA sequence cleaved by the enzyme.  ThaI cuts DNA in the
AB  - centre of the sequence CGCG.  Single-stranded DNA is not a substrate.  ThaI
AB  - does not cut T. acidophilum DNA which is presumably modified.  This is the
AB  - first description of a restriction enzyme from a mycoplasma.  Because ThaI is
AB  - easily prepared in large amounts of approximately 105 units per gram of cells,
AB  - it will be a valuable addition to the battery of restriction enzymes used in
AB  - studies of DNA sequences.  It is active at high temperatures and may therefore
AB  - be useful for special purposes requiring more extreme conditions.
ER  -

TY  - JOUR
AU  - McConnell, S.A.
AU  - Takeuchi, R.
AU  - Pellenz, S.
AU  - Davis, L.
AU  - Maizels, N.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
TI  - Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 5099
EP  - 5104
VL  - 106
AB  - Homing endonucleases stimulate gene conversion by generating site-specific DNA double-strand
AB  - breaks that are repaired by homologous recombination.
AB  - These enzymes are potentially valuable tools for targeted gene correction
AB  - and genome engineering. We have engineered a variant of the I-AniI homing
AB  - endonuclease that nicks its cognate target site. This variant contains a
AB  - mutation of a basic residue essential for proton transfer and solvent
AB  - activation in one active site. The cleavage mechanism, DNA-binding
AB  - affinity, and substrate specificity profile of the nickase are similar to
AB  - the wild-type enzyme. I-AniI nickase stimulates targeted gene correction
AB  - in human cells, in cis and in trans, at approximately 1/4 the efficiency
AB  - of the wild-type enzyme. The development of sequence-specific nicking
AB  - enzymes like the I-AniI nickase will facilitate comparative analyses of
AB  - DNA repair and mutagenesis induced by single- or double-strand breaks.
ER  -

TY  - JOUR
AU  - McCulloch, J.A.
AU  - de Oliveira, V.M.
AU  - de Almeida, P.A.V.
AU  - Perez-Chaparro, P.J.
AU  - de Almeida, L.M.
AU  - de Vasconcelos, J.M.
AU  - de Oliveira, L.F.
AU  - da Silva, D.E.
AU  - Rogez, H.L.
AU  - Cretenet, M.
AU  - Mamizuka, E.M.
AU  - Nunes, M.R.
TI  - Complete Genome Sequence of Lactococcus lactis Strain AI06, an Endophyte of the Amazonian Acai Palm.
JO  - Genome Announcements
PY  - 2014
SP  - e01225
EP  - e01214
VL  - 2
AB  - We report the genome, in a single chromosome, of Lactococcus lactis strain AI06,  isolated
AB  - from the mesocarp of the acai fruit (Euterpe oleracea) in eastern
AB  - Amazonia, Brazil. This strain is an endophyte of the acai palm and also a
AB  - component of the microbiota of the edible food product.
ER  -

TY  - JOUR
AU  - McCulloch, J.A.
AU  - Silveira, A.C.
AU  - da Costa-Lima-Moraes, A.
AU  - Perez-Chaparro, P.J.
AU  - Ferreira, S.M.
AU  - Almeida, L.M.
AU  - d'Azevedo, P.A.
AU  - Mamizuka, E.M.
TI  - Complete Genome Sequence of Staphylococcus aureus FCFHV36, a Methicillin-Resistant Strain Heterogeneously Resistant to Vancomycin.
JO  - Genome Announcements
PY  - 2015
SP  - e00893
EP  - e00815
VL  - 3
AB  - We report here the sequence of the entire chromosome of Staphylococcus aureus strain FCFHV36,
AB  - a methicillin-resistant strain heterogeneously intermediate to
AB  - vancomycin, bearing a type II staphylococcal chromosome cassette mec element
AB  - (SCCmec), belonging to multilocus sequence type (MLST) 105, and isolated from a
AB  - vertebra of a patient with osteomyelitis.
ER  -

TY  - JOUR
AU  - McCully, L.M.
AU  - Bitzer, A.S.
AU  - Spence, C.A.
AU  - Bais, H.P.
AU  - Silby, M.W.
TI  - Draft Genome Sequence of Rice Isolate Pseudomonas chlororaphis EA105.
JO  - Genome Announcements
PY  - 2014
SP  - e01342
EP  - e01314
VL  - 2
AB  - Pseudomonas chlororaphis EA105, a strain isolated from rice rhizosphere, has shown
AB  - antagonistic activities against a rice fungal pathogen, and could be
AB  - important in defense against rice blast. We report the draft genome sequence of
AB  - EA105, which is an estimated size of 6.6 Mb.
ER  -

TY  - JOUR
AU  - McCusker, M.P.
AU  - Hokamp, K.
AU  - Buckley, J.F.
AU  - Wall, P.G.
AU  - Martins, M.
AU  - Fanning, S.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak.
JO  - Genome Announcements
PY  - 2014
SP  - e01219
EP  - e01213
VL  - 2
AB  - Salmonella enterica serovar Agona is in the top 10 most common nontyphoidal serovars reported
AB  - in humans in the European Union. Here we report the complete
AB  - genome sequence of an S. enterica serovar Agona isolate, designated 24249, that
AB  - was the cause of a pan-European outbreak in 2008 with 163 confirmed cases
AB  - reported.
ER  -

TY  - JOUR
AU  - McDermott, P.F.
AU  - Crawford, J.T.
TI  - A plasmid-encoded restriction-modification system in Mycobacterium avium.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 167
EP  - 167
VL  - 89
AB  - We previously described an R-M system in M. avium strain LR25.  This system was
AB  - demonstrated by restriction and host-induced modification of phage JF2.  Curing
AB  - of the plasmids of LR25 produced a strain, LR163, that lacks the R-M system.
AB  - We have now demonstrated the presence of a restriction endonuclease, designated
AB  - MavI, in extracts of LR25 and other M. avium strains.  Cells were grown in
AB  - 7H9-Av broth and treated with cycloserine for 16 hr.  Cells were harvested and
AB  - then lysed by sonication.  Debris was removed by centrifugation, and the DNA
AB  - was precipitated with streptomycin sulfate.  The crude lysates were assayed for
AB  - endonuclease activity using various test DNAs.  The digest patterns obtained
AB  - with the extract of LR25 were the same as those produced by XhoI.  Further
AB  - studies showed that MavI cleaves at the same site as XhoI, C^TCGAG.  The enzyme
AB  - was demonstrated in several plasmid-containing strains but was absent from
AB  - LR163.  DNA isolated from the strains having MavI activity ws found to be
AB  - resistant to cleavage by XhoI but sensitive to other endonucleases indicating
AB  - the expected modification.  Modification of some SalI sites was also observed,
AB  - but no corresponding endonuclease activity was detected.
ER  -

TY  - JOUR
AU  - McDonald, R.R.
AU  - Golding, G.R.
AU  - Irvine, J.
AU  - Graham, M.R.
AU  - Tyler, S.
AU  - Mulvey, M.R.
AU  - Levett, P.N.
TI  - Draft Genome Sequence of Methicillin-Susceptible Staphylococcus aureus Strain 06BA18369, a Pathogen Associated with Skin and Soft Tissue Infections in Northern  Saskatchewan, Canada.
JO  - Genome Announcements
PY  - 2013
SP  - e00389
EP  - e00313
VL  - 1
AB  - Here, we announce the draft sequence of a representative methicillin-susceptible
AB  - Staphylococcus aureus (MSSA) isolate (06BA18369) whose strain type (spa type
AB  - t311) was commonly isolated from skin and soft tissue coinfections with
AB  - Streptococcus pyogenes. This strain sequence provides insight into a highly
AB  - successful community-associated MSSA strain type.
ER  -

TY  - JOUR
AU  - McDonald, R.R.
AU  - Golding, G.R.
AU  - Irvine, J.
AU  - Graham, M.R.
AU  - Tyler, S.
AU  - Mulvey, M.R.
AU  - Levett, P.N.
TI  - Draft Genome Sequence of Streptococcus pyogenes Strain 06BA18369, a Human Pathogen Associated with Skin and Soft Tissue Infections in Northern Canada.
JO  - Genome Announcements
PY  - 2013
SP  - e00387
EP  - e00313
VL  - 1
AB  - We report the draft sequence of Streptococcus pyogenes 06BA18369 (emm type 41.2,  sequence
AB  - type 579 [ST579]), isolated from a skin and soft tissue infection (SSTI)
AB  - mixed with Staphylococcus aureus. This genome provides insight into the genetic
AB  - composition of S. pyogenes strains associated with mixed SSTIs.
ER  -

TY  - JOUR
AU  - McDowell, A.
AU  - Hunyadkurti, J.
AU  - Horvath, B.
AU  - Voros, A.
AU  - Barnard, E.
AU  - Patrick, S.
AU  - Nagy, I.
TI  - Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain,  PRP-38, from the Novel Type IC Cluster.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3260
EP  - 3261
VL  - 194
AB  - Propionibacterium acnes, a non-spore-forming, anaerobic Gram-positive bacterium,  is most
AB  - notably recognized for its association with acne vulgaris (I. Kurokawa et
AB  - al., Exp. Dermatol. 18:821-832, 2009). We now present the draft genome sequence
AB  - of an antibiotic-resistant P. acnes strain, PRP-38, isolated from an acne patient
AB  - in the United Kingdom and belonging to the novel type IC cluster.
ER  -

TY  - JOUR
AU  - McGann, P.
AU  - Hang, J.
AU  - Clifford, R.J.
AU  - Yang, Y.
AU  - Kwak, Y.I.
AU  - Kuschner, R.A.
AU  - Lesho, E.P.
AU  - Waterman, P.E.
TI  - Complete Sequence of a Novel 178-Kilobase Plasmid Carrying blaNDM-1 in a Providencia stuartii Strain Isolated in Afghanistan.
JO  - Antimicrob. Agents Chemother.
PY  - 2012
SP  - 1673
EP  - 1679
VL  - 56
AB  - In response to global concerns over the spread of the New Delhi metallo-beta-lactamase gene 1,
AB  - bla(NDM-1), a monthly surveillance program was initiated in September 2010. All
AB  - carbapenem-resistant Gram-negative strains forwarded to our facility are screened for this
AB  - gene. To date, 321 carbapenem-resistant isolates, encompassing 11 bacterial species, have been
AB  - tested. In February 2011, two strains of Providencia stuartii, submitted from a military
AB  - hospital in Afghanistan, tested positive for bla(NDM-1). Both strains were identical by
AB  - pulsed-field gel electrophoresis (PFGE). bla(NDM-1) was carried on a large plasmid, pMR0211,
AB  - which was sequenced by emulsion PCR and pyrosequencing. pMR0211 is 178,277 bp in size and
AB  - belongs to incompatibility group A/C. The plasmid consists of a backbone with considerable
AB  - homology to pAR060302 from Escherichia coli, and it retains many of the antibiotic resistance
AB  - genes associated with it. The plasmid also shares common elements with the pNDM-HK plasmid,
AB  - including bla(NDM-1), armA, and sul1. However, gene orientation is reversed, and a 3-kb
AB  - fragment from this region is absent from pMR0211. pMR0211 also contains additional genes,
AB  - including the aminoglycoside-modifying enzyme loci aadA and aac(6'), the quinolone resistance
AB  - gene qnrA, a gene with highest homology to a U32 family peptidase from Shewanella amazonensis,
AB  - and the bla(OXA-10) gene. The finding of this gene in an intrinsically colistin-resistant
AB  - species such as Providencia stuartii is especially worrisome, as it renders the organism
AB  - resistant to nearly every available antibiotic. The presence of multiple insertion sequences
AB  - and transposons flanking the region containing the bla(NDM-1) gene further highlights the
AB  - potential mobility associated with this gene.
ER  -

TY  - JOUR
AU  - McGeehan, J.E.
AU  - Ball, N.J.
AU  - Streeter, S.D.
AU  - Thresh, S.J.
AU  - Kneale, G.G.
TI  - Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 4158
EP  - 4167
VL  - 40
AB  - The controller protein C.Esp1396I regulates the timing of gene expression of the
AB  - restriction-modification (RM) genes of the RM system Esp1396I. The molecular
AB  - recognition of promoter sequences by such transcriptional regulators is poorly
AB  - understood, in part because the DNA sequence motifs do not conform to a
AB  - well-defined symmetry. We report here the crystal structure of the controller
AB  - protein bound to a DNA operator site. The structure reveals how two different
AB  - symmetries within the operator are simultaneously recognized by the homo-dimeric
AB  - protein, underpinned by a conformational change in one of the protein subunits.
AB  - The recognition of two different DNA symmetries through movement of a flexible
AB  - loop in one of the protein subunits may represent a general mechanism for the
AB  - recognition of pseudo-symmetric DNA sequences.
ER  -

TY  - JOUR
AU  - McGeehan, J.E.
AU  - Papapanagiotou, I.
AU  - Streeter, S.D.
AU  - Kneale, G.G.
TI  - Cooperative Binding of the C.AhdI Controller Protein to the C/R Promoter and its Role in Endonuclease Gene Expression.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 523
EP  - 531
VL  - 358
AB  - The controller (C) proteins of a wide variety of restriction-modification (R-M) systems are
AB  - thought to regulate expression of the endonuclease (R) gene by a genetic switch that ensures
AB  - that methylation precedes endonuclease expression. Previous DNA footprinting experiments with
AB  - C.AhdI have located the binding site upstream of the C and R genes in the AhdI R-M system, and
AB  - the structure of C.AhdI has recently been determined. Here, we provide evidence that the
AB  - binding site can accommodate either one or two dimers of C.AhdI in a concentration-dependent
AB  - manner The dimer binding site is adjacent to the -35 hexamer site required for the interaction
AB  - with RNA polymerase (RNAP); however, co-operative binding of a second dimer blocks this site.
AB  - Optimum DNA binding site sizes for dimer and tetramer formation were determined to be ca 21 bp
AB  - and 34 bp, respectively. The stoichiometry and affinities of relevant DNA-protein complexes
AB  - have been characterised by sedimentation velocity and EMSA using native and mutant promoter
AB  - sequences. Molecular models of the dimer and tetramer complexes have been constructed that are
AB  - consistent with the hydrodynamic data. Our results suggest a mechanism for both positive and
AB  - negative regulation of endonuclease expression, whereby at moderate levels of C.AhdI, the
AB  - protein binds to the promoter as a dimer and stimulates transcription by the interaction with
AB  - RNAP. As the levels of C.AhdI increase further, binding of the second dimer competes with
AB  - RNAP, thus down-regulating transcription of its own gene, and hence that of the endonuclease.
ER  -

TY  - JOUR
AU  - McGeehan, J.E.
AU  - Streeter, S.
AU  - Cooper, J.B.
AU  - Mohammed, F.
AU  - Fox, G.C.
AU  - Kneale, G.G.
TI  - Crystallization and preliminary X-ray analysis of the controller protein C.Ahdl from Aeromonas hydrophilia.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2004
SP  - 323
EP  - 325
VL  - 60
AB  - Single crystals of purified homodimeric controller protein from Aeromonas hydrophilia (C.AhdI)
AB  - have been grown under several different
AB  - conditions using vapour diffusion. X-ray diffraction data have been
AB  - collected using synchrotron radiation from crystals of both the native
AB  - and a selenomethionine (SeMet) derivative of the protein. The native
AB  - crystal form belongs to space group P2(1) and data were collected to a
AB  - resolution of 2.2 Angstrom. Two crystal forms of the SeMet protein have
AB  - been obtained and were found to belong to space groups P1 and P2(1);
AB  - data have been recorded to 2.0 and 1.7 Angstrom resolution,
AB  - respectively, for the two crystal forms. Three-wavelength MAD data were
AB  - collected to 1.7 Angstrom for the SeMet derivative crystal, which is
AB  - isomorphous with the native P2(1) crystal.
ER  -

TY  - JOUR
AU  - McGeehan, J.E.
AU  - Streeter, S.
AU  - Papapanagiotou, I.
AU  - Fox, G.C.
AU  - Kneale, G.G.
TI  - High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 689
EP  - 701
VL  - 346
AB  - Restriction/modification (R/M) systems serve to protect the host bacterium from invading
AB  - bacteriophage. The multi-component system includes a methyltransferase, which recognizes and
AB  - methylates a specific DNA sequence, and an endonuclease which recognises the same sequence and
AB  - cleaves within or close to this site. The endonuclease will only cleave DNA that is
AB  - unmethylated at the specific site, thus host DNA is protected while non-host DNA is cleaved.
AB  - However, following DNA replication, expression of the endonuclease must be delayed until the
AB  - host DNA is appropriately methylated. In many R/M systems, this regulation is achieved at the
AB  - transcriptional level via the controller protein, or C-protein.  We have solved the first
AB  - X-ray structure of an R/M controller protein, C.AhdI, to 1.69  resolution using
AB  - selenomethionine MAD. C.AhdI is part of a Type IIH R/M system from the pathogen Aeromonas
AB  - hydrophila. The structure reveals an all-B protein that contains a classical helix-turn-helix
AB  - (HTH) domain and can be assigned to the Xre family of transcriptional regulators. Unlike its
AB  - monomeric structural homologues, an extended helix generates an interface that results in
AB  - dimerisation of the free protein. The dimer is electrostatically polarised and a positively
AB  - charged surface corresponds to the position of the DNA recognition helices of the HTH domain.
AB  - Comparison with the structure of the cI ternary complex suggests that C.AhdI activates
AB  - transcription through direct contact with the 70 subunit of RNA polymerase.
ER  -

TY  - JOUR
AU  - McGeehan, J.E.
AU  - Streeter, S.D.
AU  - Thresh, S.J.
AU  - Ball, N.
AU  - Ravelli, R.B.
AU  - Kneale, G.G.
TI  - Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 4778
EP  - 4787
VL  - 36
AB  - Controller (C) proteins regulate the timing of the expression of restriction and modification
AB  - (R-M) genes through a combination of positive and negative feedback circuits. A single dimer
AB  - bound to the operator switches on transcription of the C-gene and the endonuclease gene; at
AB  - higher concentrations, a second dimer bound adjacently switches off these genes. Here we
AB  - report the first structure of a C protein-DNA operator complex, consisting of two C protein
AB  - dimers bound to the native 35 bp operator sequence of the R-M system Esp1396I. The structure
AB  - reveals a role for both direct and indirect DNA sequence recognition. The structure of the DNA
AB  - in the complex is highly distorted, with severe compression of the minor groove resulting in a
AB  - 50 degrees bend within each operator site, together with a large expansion of the major groove
AB  - in the centre of the DNA sequence. Cooperative binding between dimers governs the
AB  - concentration-dependent activation-repression switch and arises, in part, from the interaction
AB  - of Glu25 and Arg35 side chains at the dimer-dimer interface. Competition between Arg35 and an
AB  - equivalent residue of the sigma(70) subunit of RNA polymerase for the Glu25 site underpins the
AB  - switch from activation to repression of the endonuclease gene.
ER  -

TY  - JOUR
AU  - McGeehan, J.E.
AU  - Streeter, S.D.
AU  - Thresh, S.J.
AU  - Taylor, J.E.
AU  - Shevtsov, M.B.
AU  - Kneale, G.G.
TI  - Structural Analysis of a Novel Class of R-M Controller Proteins: C.Csp231I from Citrobacter sp. RFL231.
JO  - J. Mol. Biol.
PY  - 2011
SP  - 177
EP  - 188
VL  - 409
AB  - Controller proteins play a key role in the temporal regulation of gene expression in bacterial
AB  - restriction-modification (R-M) systems and are
AB  - important mediators of horizontal gene transfer. They form the basis of a
AB  - highly cooperative, concentration-dependent genetic switch involved in
AB  - both activation and repression of R-M genes. Here we present biophysical,
AB  - biochemical, and high-resolution structural analysis of a novel class of
AB  - controller proteins, exemplified by C.Csp231I. In contrast to all
AB  - previously solved C-protein structures, each protein subunit has two extra
AB  - helices at the C-terminus, which play a large part in maintaining the
AB  - dimer interface. The DNA binding site of the protein is also novel, having
AB  - largely AAAA tracts between the palindromic recognition half-sites,
AB  - suggesting tight bending of the DNA. The protein structure shows an
AB  - unusual positively charged surface that could form the basis for wrapping
AB  - the DNA completely around the C-protein dimer.
ER  -

TY  - JOUR
AU  - McGillivary, G.
AU  - Tomaras, A.P.
AU  - Rhodes, E.R.
AU  - Actis, L.A.
TI  - Cloning and sequencing of a genomic island found in the Brazilian purpuric fever clone of Haemophilus influenzae biogroup aegyptius.
JO  - Infect. Immun.
PY  - 2005
SP  - 1927
EP  - 1938
VL  - 73
AB  - A genomic island was identified in the Haemophilus influenzae biogroup
AB  - aegyptius Brazilian purpuric fever (BPF) strain F3031. This island, which
AB  - was also found in other BPF isolates, could not be detected in non-BPF
AB  - biogroup aegyptius strains or in nontypeable or typeable H. influenzae
AB  - strains, with the exception of a region present in the type b Eagan
AB  - strain. This 34,378-bp island is inserted, in reference to H. influenzae
AB  - Rd KW20, within a choline transport gene and contains a mosaic structure
AB  - of Mu-like prophage genes, several hypothetical genes, and genes
AB  - potentially encoding an Erwinia carotovora carotovoricin Er-like
AB  - bacteriocin. The product of the tail fiber ORF in the bacteriocin-like
AB  - region shows a hybrid structure where the C terminus is similar to an H.
AB  - influenzae phage HP1 tail protein implicating this open reading frame in
AB  - altering host specificity for a putative bacteriocin. Significant synteny
AB  - is seen in the entire genomic island with genomic regions from Salmonella
AB  - enterica subsp. enterica serovar Typhi CT18, Photorhabdus luminescens
AB  - subsp. laumondii TT01, Chromobacterium violaceum, and to a lesser extent
AB  - Haemophilus ducreyi 35000HP. In a previous work, we isolated several
AB  - BPF-specific DNA fragments through a genome subtraction procedure, and we
AB  - have found that a majority of these fragments map to this locus. In
AB  - addition, several subtracted fragments generated from an independent
AB  - laboratory by using different but related strains also map to this island.
AB  - These findings underscore the importance of this BPF-specific chromosomal
AB  - region in explaining some of the genomic differences between highly
AB  - invasive BPF strains and non-BPF isolates of biogroup aegyptius.
ER  -

TY  - JOUR
AU  - McGrath, K.C.
AU  - Thomas-Hall, S.R.
AU  - Cheng, C.T.
AU  - Leo, L.
AU  - Alexa, A.
AU  - Schmidt, S.
AU  - Schenk, P.M.
TI  - Isolation and analysis of mRNA from environmental microbial communities.
JO  - J. Microbiol. Methods
PY  - 2008
SP  - 172
EP  - 176
VL  - 75
AB  - The advent of metagenomics has revealed that our planet harbors millions
AB  - of previously undiscovered microbial species. However, functional insights
AB  - into the activities of microbial communities cannot easily be obtained
AB  - using metagenomics. Using transcriptional analyses to study microbial gene
AB  - functions is currently problematic due to difficulties working with
AB  - unstable microbial mRNA as a small fraction of total cellular RNA. Current
AB  - techniques can be expensive and time consuming, and still result in
AB  - significant levels of rRNA contamination. We have adapted techniques to
AB  - rapidly isolate high high-quality RNA from environmental samples and
AB  - developed a simple method for specific isolation of mRNA by size
AB  - separation. This new technique was evaluated by constructing cDNA
AB  - libraries directly from uncultured environmental microbial communities,
AB  - including agricultural soil samples, aquatic flocculants, organic
AB  - composts, mammalian oral and faecal samples, and wastewater sludge. The
AB  - sequencing of a fraction of these cDNA clones revealed a high degree of
AB  - novelty, demonstrating the potential of this approach to capture a large
AB  - number of unique transcripts directly from the environment. To our
AB  - knowledge, this is the first study that uses gel electrophoresis to
AB  - isolate mRNA from microbial communities. We conclude that this method
AB  - could be used to provide insights into the microbial 'metatranscriptome'
AB  - of entire microbial communities. Coupled with high-throughput sequencing
AB  - or the construction of cDNA microarrays, this approach will provide a
AB  - useful tool to study the transcriptional activities of microorganisms,
AB  - including those of entire microbial communities and of non-culturable
AB  - microorganisms.
ER  -

TY  - JOUR
AU  - McGrath, S.
AU  - Seegers, J.F.M.L.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
TI  - Molecular characterization of a phage-encoded resistance system in Lactococcus lactis.
JO  - Appl. Environ. Microbiol.
PY  - 1999
SP  - 1891
EP  - 1899
VL  - 65
AB  - A specific fragment of the genome of Tuc2009, a temperate lactococcal bacteriophage, was shown
AB  - to contain several open reading frames, whose deduced protein products exhibited similarities
AB  - to proteins known to be involved in DNA replication and modification.  In this way, a putative
AB  - single-stranded binding protein, replisome organizer protein, topoisomerase I, and a methylase
AB  - were identified.  When the genetic information coding for the putative replisome organizer
AB  - protein of Tuc2009, Rep2009, was supplied on a high-copy-number plasmid vector, it was shown
AB  - to confer a phage-encoded resistance (Per) phenotype on its lactococcal host UC509.9.  The
AB  - presence of this recombinant plasmid was shown to cause a marked reduction in Tuc2009 DNA
AB  - replication, suggesting that the observed phage resistance was due to titration of a factor,
AB  - or factors, required for Tuc2009 DNA replication.  Further experiments delineated the phage
AB  - resistance-conferring region to a 160-bp fragment rich in direct repeats.  Gel retardation
AB  - experiments, which indicated a protein-DNA interaction between this 160-bp fragment and the
AB  - Rep2009 protein, were performed.  UC509.9 strains harboring plasmids with randomly mutated
AB  - versions of this fragment were shown to display a variable phage resistance phenotype,
AB  - depending on the position of the mutations.
ER  -

TY  - JOUR
AU  - McGraw, B.R.
AU  - Marinus, M.G.
TI  - Isolation and characterization of Dam+ revertants and suppressor mutations that modify secondary phenotypes of dam-3 strains of Escherichia coli K-12.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 309
EP  - 315
VL  - 178
AB  - Bacteria mutant in the dam (DNA adenine methylation) gene and in either recA or recB or recC
AB  - genes are inviable (Virm- phenotype). From crosses between dam-3 bacteria and recA1 or recB21
AB  - recC22 strains, Vrm+ recombinants were recovered. Among these recombinants, Dam+ revertants
AB  - were present which did not show the phenotypes normally associated with dam-3 bacteria. Three
AB  - classes of indirectly suppressed strains (dam 3 genotype) were also recovered which showed
AB  - alterations in the secondary phenotypes normally associated with dam-3 bacteria. These strains
AB  - contained a second unlinked mutation in either mutL or mutS or sin. In addition, mutation in
AB  - either sbcA or sbcB supresses the Vrm-phenotype of dam-3 recB21 recC22 strains.
ER  -

TY  - JOUR
AU  - McIlroy, S.J.
AU  - Lapidus, A.
AU  - Thomsen, T.R.
AU  - Han, J.
AU  - Haynes, M.
AU  - Lobos, E.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Markowitz, V.
AU  - Verbarg, S.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.
AU  - Nielsen, P.H.
TI  - High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 23
EP  - 23
VL  - 10
AB  - Meganema perideroedes Gr1(T) is a filamentous bacterium isolated from an activated sludge
AB  - wastewater treatment plant where it is implicated in poor sludge
AB  - settleability (bulking). M. perideroedes is the sole described species of the
AB  - genus Meganema and of the proposed novel family 'Meganemaceae'. Here we describe
AB  - the features of the type strain Gr1(T) along with its annotated genome sequence.
AB  - The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033
AB  - protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type
AB  - Strains, Phase I: the one thousand microbial genomes KMG project. Notably, genome
AB  - annotation indicated the potential for facultative methylotrophy. However, the
AB  - ability to utilize methanol as a carbon source could not be empirically
AB  - demonstrated for the type strain or for in situ Meganema spp. strains.
ER  -

TY  - JOUR
AU  - McInerney, M.J.
AU  - Rohlin, L.
AU  - Mouttaki, H.
AU  - Kim, U.
AU  - Krupp, R.S.
AU  - Rios-Hernandez, L.
AU  - Sieber, J.
AU  - Struchtemeyer, C.G.
AU  - Bhattacharyya, A.
AU  - Campbell, J.W.
AU  - Gunsalus, R.P.
TI  - The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 7600
EP  - 7605
VL  - 104
AB  - Biochemically, the syntrophic bacteria constitute the missing link in our understanding of
AB  - anaerobic flow of carbon in the biosphere. The completed genome sequence of Syntrophus
AB  - aciditrophicus SB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium,
AB  - provides a glimpse of the composition and architecture of the electron transfer and
AB  - energy-transducing systems needed to exist on marginal energy economies of a syntrophic
AB  - lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were
AB  - assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most
AB  - biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature
AB  - of syntrophic metabolism is the need for reverse electron transport; the presence of a unique
AB  - Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S
AB  - proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish
AB  - this task. Previously undescribed approaches to degrade fatty and aromatic acids, including
AB  - multiple AMP-forming CoA ligases and acyl-CoA synthetases seem to be present as ways to form
AB  - and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus,
AB  - although nutritionally self-sufficient, seems to be a syntrophic specialist with limited
AB  - fermentative and respiratory metabolism. Genomic analysis confirms the S. aciditrophicus
AB  - metabolic and regulatory commitment to a nonconventional mode of life compared with our
AB  - prevailing understanding of microbiology.
ER  -

TY  - JOUR
AU  - McKane, M.
AU  - Milkman, R.
TI  - Transduction, restriction and recombination patterns in Escherichia coli.
JO  - Genetics
PY  - 1995
SP  - 35
EP  - 43
VL  - 139
AB  - Chromosomal DNA from several Escherichia coli reference (ECOR) strains was transducted by
AB  - bacteriophage P1 into E. coli strain K12 W3110 trpA33. Recombination patterns of the
AB  - transductants were determined by restriction fragment length polymorphism over a 40-kb region
AB  - centering on a single marker (trpA+) in the tryptophan operon. These experiments demonstrate
AB  - that transduction between different strains of E. coli can result in recombinational
AB  - replacements that are small in comparison to the entrant molecule (replacements average 8-14
AB  - kb, whereas P1 packages approximately 100 kb) often in a series of discrete segments. The
AB  - transduction patterns generated resemble the natural mosaic sequence patterns of the ECOR
AB  - strains described in previous work. Extensive polymorphisms in the restriction-modification
AB  - systems of the ECOR strains are a possible explanation for the sequence patterns in nature. To
AB  - test this possibility, two transductants were back-transduced into strain K12 W3110 trpA33.
AB  - The resulting patterns were strikingly different from the original transductions. The size of
AB  - the replacements was greater, and no multiple replacements were observed, suggesting a role
AB  - for restriction-modification systems in the transduction patterns and perhaps for the mosaic
AB  - sequence patterns in nature.
ER  -

TY  - JOUR
AU  - McKay, L.L.
AU  - Bohanon, M.J.
AU  - Polzin, K.M.
AU  - Rule, P.L.
AU  - Baldwin, K.A.
TI  - Localization of separate genetic loci for reduced sensitivity towards small isometric-headed bacteriophage sk1 and prolate-headed bacteriophage c2 on pGBK17 from Lactococcus lactis subsp. lactis KR2.
JO  - Appl. Environ. Microbiol.
PY  - 1989
SP  - 2702
EP  - 2709
VL  - 55
AB  - The mechanism of reduced sensitivity to the small isometric-headed bacteriophage sk1 encoded
AB  - on a 19-kilobase (kb) HpaII fragment subcloned from pKR223 of Lactococcus lactis subsp. lactis
AB  - KR2 was examined. The reduced sensitivity to phage sk1 was due to a modest
AB  - restriction/modification (R/M) system that was not active against prolate-headed phage c2. The
AB  - genetic loci for the R/M system against sk1 and the abortive phage infection (Abi) mechanism
AB  - effective against phage c2 were then localized by restriction mapping, subcloning, and
AB  - deletion analysis. The restriction gene was localized to a region of a 2.7-kb EcoRV fragment
AB  - and included an EcoRI site within that fragment. The modification gene was found to be
AB  - physically separate from the restriction gene and was present on a 1.75-kb BstEII-XbaI
AB  - fragment. The genetic locus for the Abi phenotype against phage c2 was localized to a region
AB  - containing a 1.3-kb EcoRI fragment. Attempts to clone the c2 Abi mechanism independent of the
AB  - sk1 R/M system were unsuccessful, suggesting that expression of the abi genes required
AB  - sequences upstream of the modification gene. Some pGBK17 (vector pGB301 plus a 19-kb HpaII
AB  - insert fragment) transformants exhibited the R/M system against phage sk1 but lost the Abi
AB  - mechanism against phage c2. These transformants contained a 1.2-1.3-kb insertion in the Abi
AB  - region. The data identified genetic loci on a cloned 19-kb HpaII fragment responsible for
AB  - restriction activity and for modification activity against a small isometric-headed phage and
AB  - for Abi activity against prolate-headed phage c2. A putative insertion element was also found
AB  - to inactivate the abi gene(s).
ER  -

TY  - JOUR
AU  - McKelvie, J.C.
AU  - Richards, M.I.
AU  - Harmer, J.E.
AU  - Milne, T.S.
AU  - Roach, P.L.
AU  - Oyston, P.C.F.
TI  - Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents.
JO  - Br. J. Pharmacol.
PY  - 2013
SP  - 172
EP  - 188
VL  - 168
AB  - Background and Purpose Multiple antibiotic resistant strains of plague are emerging, driving a
AB  - need for the development of novel antibiotics
AB  - effective against Yersinia pestis. DNA adenine methylation regulates
AB  - numerous fundamental processes in bacteria and alteration of DNA
AB  - adenine methlytransferase (Dam) expression is attenuating for several
AB  - pathogens, including Y. pestis. The lack of a functionally similar
AB  - enzyme in humans makes Dam a suitable target for development of novel
AB  - therapeutics for plague. Experimental Approach Compounds were evaluated
AB  - for their ability to inhibit Dam activity in a high-throughput
AB  - screening assay. DNA was isolated from Yersinia grown in the presence
AB  - of lead compounds and restricted to determine the effect of inhibitors
AB  - on DNA methylation. Transcriptional analysis was undertaken to
AB  - determine the effect of an active inhibitor on virulence-associated
AB  - phenotypes. Key Results We have identified a series of aryl stibonic
AB  - acids which inhibit Dam in vitro. The most active,
AB  - 4-stibonobenzenesulfonic acid, exhibited a competitive mode of
AB  - inhibition with respect to DNA and a Ki of 6.46 nM. One compound was
AB  - found to inhibit DNA methylation in cultured Y. pestis. The effects of
AB  - this inhibition on the physiology of the cell were widespread, and
AB  - included altered expression of known virulence traits, including iron
AB  - acquisition and Type III secretion. Conclusions and Implications We
AB  - have identified a novel class of potent Dam inhibitors. Treatment of
AB  - bacterial cell cultures with these inhibitors resulted in a decrease in
AB  - DNA methylation. Expression of virulence factors was affected,
AB  - suggesting these inhibitors may attenuate bacterial infectivity and
AB  - function as antibiotics.
ER  -

TY  - JOUR
AU  - McKenna, W.G.
AU  - Brown, F.L.
AU  - Musich, P.R.
AU  - Maio, J.J.
TI  - Cleavage of mammalian repetitive deoxyribonucleic acids by a mammalian site-specific endodeoxyribonuclease.
JO  - J. Mol. Biol.
PY  - 1982
SP  - 379
EP  - 384
VL  - 154
AB  - We probed the structure of mammalian repetitive DNAs with a site-specific
AB  - mammalian endodeoxyribonuclease, which we recently identified, and which
AB  - apparently represents a common enzyme activity among the mammals (McKenna et
AB  - al., 1981).  With several of the DNAs (e.g. mouse satellite, guinea pig
AB  - beta-satellite, variable repeated spacer DNA from mouse ribosomal genes and
AB  - primate alphoid sequences), the endonuclease activity gave highly specific
AB  - cleavage patterns when the digestion products were analyzed by gel
AB  - electrophoresis.  These patterns were not always identical to those produced by
AB  - microbial restriction enzymes.  However, in other cases (e.g. bovid and caprid
AB  - satellites and guinea pig alpha-satellite) the repetitive DNAs appeared to be
AB  - degraded randomly.  Thus, the mammalian enzyme reveals structural features of
AB  - the repetitive sequences that are not rendered immediately obvious by microbial
AB  - restriction enzyme analysis.  Evidence from mapping data presented here
AB  - suggests that the mammalian site-specific endonucleases are not sequence
AB  - specific but have special affinity for imperfect or hyphenated palindromic
AB  - sequences in repetitive DNAs and in other eukaryrotic DNA sequences.
ER  -

TY  - JOUR
AU  - McKenna, W.G.
AU  - Maio, J.J.
AU  - Brown, F.L.
TI  - Purification and properties of a mammalian endonuclease showing site-specific cleavage of DNA.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 6435
EP  - 6443
VL  - 256
AB  - An endonuclease activity has been identified from a variety of mammalian
AB  - sources which cleaves native viral DNAs (adenovirus-2, SV40) and mammalian
AB  - repetitive DNA to yield specific, double-stranded DNA segments when the
AB  - cleavage products are analyzed by gel electrophoresis.  The activity has been
AB  - purified 750-fold from bull testes by ammonium sulfate precipitations and ion
AB  - exchange chromatography.  The enzyme has a pH optimum of 7.5 and shows an
AB  - absolute requirement for Mg2+ or Mn2+ and reducing agents in the reaction
AB  - buffer.  It is strongly inhibited by salt and stimulated by glycerol or
AB  - dimethyl sulfoxide.  By glycerol gradient analysis it has a sedimentation
AB  - coefficient of 4.5 S (65,000 daltons if globular) and it may exist as a dimer
AB  - of 6.4 S (130,000 daltons).  The enzyme liberates 3'-OH and 5'-P termini in its
AB  - cleavage of mammalian viral and repetitive DNAs and there is a clear
AB  - nonrandomness in the 5'-terminal nucleotides: purines and 5'-pG in particular
AB  - predominate.  The similarities between the mammalian endonuclease activity and
AB  - the bacterial restriction enzymes may be superficial.  By gel electrophoresis
AB  - the mammalian endonuclease produces its most characteristic series of segments
AB  - with viral DNAs in the molecular weight range of 150,000 to 1,500.000  These
AB  - are true double-stranded intermediate products in the cleavage of high
AB  - molecular weight DNA but they are not end products in the reaction as they
AB  - would be in the case of the bacterial restriction enzymes.  With time, the
AB  - endonuclease degrades viral DNA to shorter and shorter segments without
AB  - releasing acid-soluble nucleotides at any stage in the digestion and the final
AB  - end products are about 120 base pairs long.  The enzyme degrades both double-
AB  - and single-stranded DNA endonucleolytically though it shows site specificity
AB  - (production of discrete segments upon gel electrophoresis) only with the
AB  - double-stranded DNA substrates.
ER  -

TY  - JOUR
AU  - McKenney, P.T.
AU  - Ling, L.
AU  - Wang, G.
AU  - Mane, S.
AU  - Pamer, E.G.
TI  - Complete Genome Sequence of Enterococcus faecium ATCC 700221.
JO  - Genome Announcements
PY  - 2016
SP  - e00386
EP  - e00316
VL  - 4
AB  - We report the complete genome sequence of a vancomycin-resistant isolate of Enterococcus
AB  - faecium derived from human feces. The genome comprises one
AB  - chromosome of 2.9 Mb and three plasmids. The strain harbors a plasmid-borne
AB  - vanA-type vancomycin resistance locus and is a member of multilocus sequencing
AB  - type (MLST) cluster ST-17.
ER  -

TY  - JOUR
AU  - McKernan, K.J.
AU  - Spangler, J.
AU  - Helbert, Y.
AU  - Zhang, L.
AU  - Tadigotla, V.
TI  - DREAMing of a patent-free human genome for clinical sequencing.
JO  - Nat. Biotechnol.
PY  - 2013
SP  - 884
EP  - 887
VL  - 31
AB  - Can methylation be the key to challenging the interpretation of existing gene patent claims?
AB  - And can a novel PCR method be used to enable the sequencing of hundreds of genes?  The case
AB  - for the perils of gene patents and the negative impact of a profit motive in scientific
AB  - endeavors has been made.  Often, gene patent discussions will conflate economic and ethical
AB  - concerns while failing to properly define the scope of property or the influence of profit
AB  - motivations.  In an attempt to untangle these two topics, we review the impact of methylation
AB  - on the scope of gene patent property rights and suggest a simple PCR strategy that may
AB  - challenge the interpretation of many patent claims still in force after the US Supreme
AB  - Court's decision in Associaton for Moleuclar Pathology v. Mayriad Genetics.  We also offer an
AB  - alternatie economic perspective on profit motivation and its impact on the ethics of gene
AB  - patents.
ER  -

TY  - JOUR
AU  - McLaughlin, L.W.
AU  - Benseler, F.
AU  - Graeser, E.
AU  - Piel, N.
AU  - Scholtissek, S.
TI  - Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease.
JO  - Biochemistry
PY  - 1987
SP  - 7238
EP  - 7245
VL  - 26
AB  - Oligodeoxynucleotides have been prepared that contain changes in the functional
AB  - group pattern present in the EcoRI recognition site.  These changes involve
AB  - functional group deletions, functional group reversals, and displaced
AB  - functional groups.  Steady-state kinetic parameters have been used to
AB  - characterize the interaction of these modified recognition sites with the EcoRI
AB  - endonuclease.  Changes in the functional group pattern have varying effects
AB  - upon the cleavage reaction.  Both the exocyclic amino groups of the two adenine
AB  - residues and the methyl groups of the thymine residues appear to interact with
AB  - the endonuclease quite differently.  In both cases efficient catalysis was
AB  - observed when these functional groups were present at the outer dA-dT base
AB  - pair.  Selectivity was decreased by over an order of magnitude largely via
AB  - increases in Km when these functional groups were deleted.  Similar
AB  - modifications at the inner dA-dT base pair did not alter the kinetic parameters
AB  - significantly from those observed with the native sequence.  Addition of an
AB  - amino group to the minor groove at the outer dA-dT base pair resulted in a
AB  - modified recognition site that interacted with the enzyme, on the basis of
AB  - observed competitive inhibition kinetics, but was not cleaved.
ER  -

TY  - JOUR
AU  - McLaughlin, R.W. et al.
TI  - Draft Genome Sequence of Clostridium mangenotii TR, Isolated from the Fecal Material of a Timber Rattlesnake.
JO  - Genome Announcements
PY  - 2014
SP  - e01107
EP  - e01113
VL  - 2
AB  - Here, we report the draft genome sequence of Clostridium mangenotii strain TR, which was
AB  - isolated from the fecal material of a timber rattlesnake. This
AB  - bacterium is nonpathogenic but contains 68 genes involved in virulence, disease,
AB  - and defense.
ER  -

TY  - JOUR
AU  - McLean, J.S.
AU  - Liu, Q.
AU  - Bor, B.
AU  - Bedree, J.K.
AU  - Cen, L.
AU  - Watling, M.
AU  - To, T.T.
AU  - Bumgarner, R.E.
AU  - He, X.
AU  - Shi, W.
TI  - Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain  XH001, the Basibiont of an Oral TM7 Epibiont.
JO  - Genome Announcements
PY  - 2016
SP  - e01685
EP  - e01615
VL  - 4
AB  - Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter
AB  - strain XH001, isolated from the human oral cavity. Uniquely, it
AB  - was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the
AB  - first cultivated member of 'Candidatus Saccharibacteria' (formerly candidate
AB  - phylum TM7).
ER  -

TY  - JOUR
AU  - McLean, J.S.
AU  - Liu, Q.
AU  - Thompson, J.
AU  - Edlund, A.
AU  - Kelley, S.
TI  - Draft Genome Sequence of 'Candidatus Bacteroides periocalifornicus,' a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis  Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e01485
EP  - e01415
VL  - 3
AB  - Here we present the draft genome of a distantly related member within the phylum
AB  - Bacteriodetes, 'Candidatus Bacteroides periocalifornicus.' The draft genome
AB  - sequence was assembled with metagenomic data from a patient with periodontitis.
AB  - The closest relative has less than 68% average nucleic identity, supporting a
AB  - novel family within Bacteriodetes.
ER  -

TY  - JOUR
AU  - McLeod, A.
AU  - Brede, D.A.
AU  - Rud, I.
AU  - Axelsson, L.
TI  - Genome Sequence of Lactobacillus sakei subsp. sakei LS25, a Commercial Starter Culture Strain for Fermented Sausage.
JO  - Genome Announcements
PY  - 2013
SP  - e00475
EP  - e00413
VL  - 1
AB  - Lactobacillus sakei is a lactic acid bacterium associated primarily with fermented meat and
AB  - fish. Here, we present the draft genome sequence of L. sakei
AB  - subsp. sakei strain LS25, a commercial starter culture strain for fermented
AB  - sausage.
ER  -

TY  - JOUR
AU  - McLeod, M.P. et al.
TI  - The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 15582
EP  - 15587
VL  - 103
AB  - Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete
AB  - that catabolizes a wide range of compounds and
AB  - represents a genus of considerable industrial interest. RHA1 has one of
AB  - the largest bacterial genomes sequenced to date, comprising 9,702,737 bp
AB  - (67% G+C) arranged in a linear chromosome and three linear plasmids. A
AB  - targeted insertion methodology was developed to determine the telomeric
AB  - sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally
AB  - rich in oxygenases (203) and ligases (192). Many of the oxygenases occur
AB  - in the numerous pathways predicted to degrade aromatic compounds (30) or
AB  - steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes,
AB  - six of which exceed 25 kbp, and seven polyketide synthase genes, providing
AB  - evidence that rhodococci harbor an extensive secondary metabolism. Among
AB  - sequenced genomes, RHA1 is most similar to those of nocardial and
AB  - mycobacterial strains. The genome contains few recent gene duplications.
AB  - Moreover, three different analyses indicate that RHA1 has acquired fewer
AB  - genes by recent horizontal transfer than most bacteria characterized to
AB  - date and far fewer than Burkholderia xenovorans LB400, whose genome size
AB  - and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear
AB  - to demonstrate that ecologically similar bacteria can evolve large genomes
AB  - by different means. Overall, RHA1 appears to have evolved to
AB  - simultaneously catabolize a diverse range of plant-derived compounds in an
AB  - O(2)-rich environment. In addition to establishing RHA1 as an important
AB  - model for studying actinomycete physiology, this study provides critical
AB  - insights that facilitate the exploitation of these industrially important
AB  - microorganisms.
ER  -

TY  - JOUR
AU  - McMahon, S.A.
AU  - Roberts, G.A.
AU  - Johnson, K.A.
AU  - Cooper, L.P.
AU  - Liu, H.
AU  - White, J.H.
AU  - Carter, L.G.
AU  - Sanghvi, B.
AU  - Oke, M.
AU  - Walkinshaw, M.D.
AU  - Blakely, G.W.
AU  - Naismith, J.H.
AU  - Dryden, D.T.
TI  - Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 4887
EP  - 4897
VL  - 37
AB  - The ardA gene, found in many prokaryotes including important pathogenic species, allows
AB  - associated mobile genetic elements to evade the ubiquitous
AB  - Type I DNA restriction systems and thereby assist the spread of resistance
AB  - genes in bacterial populations. As such, ardA contributes to a major
AB  - healthcare problem. We have solved the structure of the ArdA protein from
AB  - the conjugative transposon Tn916 and find that it has a novel extremely
AB  - elongated curved cylindrical structure with defined helical grooves. The
AB  - high density of aspartate and glutamate residues on the surface follow a
AB  - helical pattern and the whole protein mimics a 42-base pair stretch of
AB  - B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of
AB  - this dimeric structure comprises three alpha-beta domains, each with a
AB  - different fold. These domains have the same fold as previously determined
AB  - proteins possessing entirely different functions. This DNA mimicry
AB  - explains how ArdA can bind and inhibit the Type I restriction enzymes and
AB  - we demonstrate that 6 different ardA from pathogenic bacteria can function
AB  - in Escherichia coli hosting a range of different Type I restriction
AB  - systems.
ER  -

TY  - JOUR
AU  - McMillan, K.
AU  - Allnutt, T.R.
AU  - Fox, E.M.
TI  - Draft Genome Sequences of 15 Staphylococcus aureus Isolates Recovered from Raw Milk and Associated Milk Filters from Victoria, Australia.
JO  - Genome Announcements
PY  - 2017
SP  - e01463
EP  - e01416
VL  - 5
AB  - This study describes draft whole genomes of 15 Staphylococcus aureus isolates from dairy farms
AB  - located in Victoria, Australia. Two novel sequence types (ST3183
AB  - and ST3184) were identified among these isolates.
ER  -

TY  - JOUR
AU  - McMullen, P.D.
AU  - Gillaspy, A.F.
AU  - Gipson, J.
AU  - Bobo, L.D.
AU  - Skiest, D.J.
AU  - Freitag, N.E.
TI  - Genome Sequence of Listeria monocytogenes 07PF0776, a Cardiotropic Serovar 4b Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3552
EP  - 3552
VL  - 194
AB  - Listeria monocytogenes is a food-borne bacterial pathogen commonly associated with serious
AB  - invasive infections of the central nervous system or of the
AB  - developing fetus. We present the genome sequence of Listeria monocytogenes
AB  - 07PF0776, a serovar 4b isolate from a human myocardial abscess that exhibits
AB  - enhanced invasion of cardiac tissue.
ER  -

TY  - JOUR
AU  - McMurdie, P.J.
AU  - Behrens, S.F.
AU  - Muller, J.A.
AU  - Goke, J.
AU  - Ritalahti, K.M.
AU  - Wagner, R.
AU  - Goltsman, E.
AU  - Lapidus, A.
AU  - Holmes, S.
AU  - Loffler, F.E.
AU  - Spormann, A.M.
TI  - Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides.
JO  - PLoS Genet.
PY  - 2009
SP  - E1000714
EP  - E1000714
VL  - 5
AB  - Vinyl chloride (VC) is a human carcinogen and widespread priority
AB  - pollutant. Here we report the first, to our knowledge, complete genome
AB  - sequences of microorganisms able to respire VC, Dehalococcoides sp.
AB  - strains VS and BAV1. Notably, the respective VC reductase encoding genes,
AB  - vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs)
AB  - with different predicted integration sites, suggesting that these genes
AB  - were acquired horizontally and independently by distinct mechanisms. A
AB  - comparative analysis that included two previously sequenced
AB  - Dehalococcoides genomes revealed a contextually conserved core that is
AB  - interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs
AB  - contain the majority of GEIs and strain-specific genes identified in the
AB  - four Dehalococcoides genomes, an elevated number of repeated elements
AB  - including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that
AB  - putatively encode terminal reductases in organohalide respiration. Only
AB  - three core rdhA orthologous groups were identified, and only one of these
AB  - groups is supported by synteny. The low number of core rdhAB, contrasted
AB  - with the high rdhAB numbers per genome (up to 36 in strain VS), as well as
AB  - their colocalization with GEIs and other signatures for horizontal
AB  - transfer, suggests that niche adaptation via organohalide respiration is a
AB  - fundamental ecological strategy in Dehalococccoides. This adaptation has
AB  - been exacted through multiple mechanisms of recombination that are mainly
AB  - confined within HPRs of an otherwise remarkably stable, syntenic,
AB  - streamlined genome among the smallest of any free-living microorganism.
ER  -

TY  - JOUR
AU  - McMurrough, T.A.
AU  - Dickson, R.J.
AU  - Thibert, S.M.F.
AU  - Gloor, G.B.
AU  - Edgell, D.R.
TI  - Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - E2376
EP  - E2383
VL  - 111
AB  - The active sites of enzymes consist of residues necessary for catalysis and structurally
AB  - important noncatalytic residues that together maintain the architecture and function of the
AB  - active site. Examples of evolutionary interactions between catalytic and non-catalytic
AB  - residues have been difficult to define and experimentally validate due to a general
AB  - intolerance of these residues to substitution. Here, using computational methods to predict
AB  - coevolving residues, we identify a network of positions consisting of two catalytic
AB  - metal-binding residues and two adjacent noncatalytic residues in LAGLIDADG homing
AB  - endonucleases (LHEs). Distinct combinations of the four residues in the network map to
AB  - distinct LHE subfamilies, with a striking distribution of the metal-binding Asp (D) and Glu
AB  - (E) residues. Mutation of these four positions in three LHEs-I-LtrI, I-OnuI, and
AB  - I-HjeMI-indicate that the combinations of residues tolerated are specific to each enzyme.
AB  - Kinetic analyses under single-turnover conditions revealed that I-LtrI activity could be
AB  - modulated over an similar to 100-fold range by mutation of residues in the coevolving network.
AB  - I-LtrI catalytic site variants with low activity could be rescued by compensatory mutations at
AB  - adjacent noncatalytic sites that restore an optimal coevolving network and vice versa. Our
AB  - results demonstrate that LHE activity is constrained by an evolutionary barrier of residues
AB  - with strong context-dependent effects. Creation of optimal coevolving active-site networks is
AB  - therefore an important consideration in engineering of LHEs and other enzymes.
ER  -

TY  - JOUR
AU  - McNamara, A.R.
AU  - Hurd, P.J.
AU  - Smith, A.E.F.
AU  - Ford, K.G.
TI  - Characterisation of site-biased DNA methyltransferases: specificity, affinity and subsite relationships.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3818
EP  - 3830
VL  - 30
AB  - DNA methylation is now seen as a primary signal in the cell for mediating transcriptional
AB  - repression through chromatin formation. The construction and evaluation of enzymes capable of
AB  - influencing this process in vivo is therefore of significant interest. We have fused the
AB  - C5-cytosine DNA methyltransferases, M.HhaI and M.HpaII, which both methylate 4 bp sequences
AB  - containing a CpG dinucleotide, to a three zinc finger protein recognising a 9 bp DNA sequence.
AB  - DNA methylation analyses demonstrate specific DNA methylation by both enzymes at target sites
AB  - comprising adjacent methyltransferase and zinc finger subsites, targeted M.HpaII being the
AB  - most specific. Binding analysis of the targeted M.HpaII enzyme reveals an 8-fold preference
AB  - for binding to its target site, compared to binding to a zinc finger site alone, and an
AB  - 18-fold preference over binding to a methyltransferase site alone, thereby demonstrating
AB  - enhanced binding by the fusion protein, compared to its component proteins. Both DNA binding
AB  - and methylation are specific for the target site up to separations of approximately 40 bp
AB  - between the zinc finger and methyltransferase subsites. Ex vivo plasmid methylation
AB  - experiments are also described that demonstrate targeted methylation. These targeted enzymes,
AB  - however, are shown to be not fully mono-functional, retaining a significant non-targeted
AB  - activity most evident at elevated protein concentrations.
ER  -

TY  - JOUR
AU  - McNulty, N.P. et al.
TI  - The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins.
JO  - Sci. Transl. Med.
PY  - 2011
SP  - 106RA106
EP  - 106RA106
VL  - 3
AB  - Understanding how the human gut microbiota and host are affected by probiotic bacterial
AB  - strains requires carefully controlled studies in humans and in mouse models of the gut
AB  - ecosystem where potentially confounding variables that are difficult to control in humans can
AB  - be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of
AB  - adult female monozygotic twin pairs through repeated sampling 4 weeks before, 7 weeks during,
AB  - and 4 weeks after consumption of a commercially available fermented milk product (FMP)
AB  - containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of
AB  - Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and
AB  - Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human
AB  - gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were
AB  - studied before and after gavage with all five sequenced FMP strains. No significant changes in
AB  - bacterial species composition or in the proportional representation of genes encoding known
AB  - enzymes were observed in the feces of humans consuming the FMP. Only minimal changes in
AB  - microbiota configuration were noted in mice after single or repeated gavage with the FMP
AB  - consortium. However, RNA-Seq analysis of fecal samples and follow-up mass spectrometry of
AB  - urinary metabolites disclosed that introducing the FMP strains into mice results in
AB  - significant changes in expression of microbiome-encoded enzymes involved in numerous metabolic
AB  - pathways, most prominently those related to carbohydrate metabolism. B. animalis subsp.
AB  - lactis, the dominant persistent member of the FMP consortium in gnotobiotic mice, up-regulates
AB  - a locus in vivo that is involved in the catabolism of xylooligosaccharides, a class of glycans
AB  - widely distributed in fruits, vegetables, and other foods, underscoring the importance of
AB  - these sugars to this bacterial species. The human fecal metatranscriptome exhibited
AB  - significant changes, confined to the period of FMP consumption, that mirror changes in
AB  - gnotobiotic mice, including those related to plant polysaccharide metabolism. These
AB  - experiments illustrate a translational research pipeline for characterizing the effects of
AB  - FMPs on the human gut microbiome.
ER  -

TY  - JOUR
AU  - McShan, W.M.
AU  - Ferretti, J.J.
AU  - Karasawa, T.
AU  - Suvorov, A.N.
AU  - Lin, S.
AU  - Qin, B.
AU  - Jia, H.
AU  - Kenton, S.
AU  - Najar, F.
AU  - Wu, H.
AU  - Scott, J.
AU  - Roe, B.A.
AU  - Savic, D.J.
TI  - Genome Sequence of a Nephritogenic and Highly Transformable M49 Strain of Streptococcus pyogenes.
JO  - J. Bacteriol.
PY  - 2008
SP  - 7773
EP  - 7785
VL  - 190
AB  - The 1,815,783-bp genome of a serotype M49 strain of Streptococcus pyogenes
AB  - (group A streptococcus [GAS]), strain NZ131, has been determined. This GAS
AB  - strain (FCT type 3; emm pattern E), originally isolated from a case of
AB  - acute post-streptococcal glomerulonephritis, is unusually competent for
AB  - electrotransformation and has been used extensively as a model organism
AB  - for both basic genetic and pathogenesis investigations. As with the
AB  - previously sequenced S. pyogenes genomes, three unique prophages are a
AB  - major source of genetic diversity. Two clustered regularly interspaced
AB  - short palindromic repeat (CRISPR) regions were present in the genome,
AB  - providing genetic information on previous prophage encounters. A unique
AB  - cluster of genes was found in the pathogenicity island-like emm region
AB  - that included a novel Nudix hydrolase, and, further, this cluster appears
AB  - to be specific for serotype M49 and M82 strains. Nudix hydrolases
AB  - eliminate potentially hazardous materials or prevent the unbalanced
AB  - accumulation of normal metabolites; in bacteria, these enzymes may play a
AB  - role in host cell invasion. Since M49 S. pyogenes strains have been known
AB  - to be associated with skin infections, the Nudix hydrolase and its
AB  - associated genes may have a role in facilitating survival in an
AB  - environment that is more variable and unpredictable than the uniform
AB  - warmth and moisture of the throat. The genome of NZ131 continues to shed
AB  - light upon the evolutionary history of this human pathogen. Apparent
AB  - horizontal transfer of genetic material has led to the existence of highly
AB  - variable virulence-associated regions that are marked by multiple
AB  - rearrangements and genetic diversification while other regions, even those
AB  - associated with virulence, vary little between genomes. The genome regions
AB  - that encode surface gene products that will interact with host targets or
AB  - aid in immune avoidance are the ones that display the most sequence
AB  - diversity. Thus, while natural selection favors stability in much of the
AB  - genome, it favors diversity in these regions.
ER  -

TY  - JOUR
AU  - McTaggart, T.L.
AU  - Benuska, G.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Chistoserdova, L.
TI  - Draft genome sequences of five new strains of methylophilaceae isolated from lake washington sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e01511
EP  - e01514
VL  - 3
AB  - We sequenced the genomes of five new Methylophilaceae strains isolated from Lake  Washington
AB  - sediment. We used the new sequences to sort these new strains into
AB  - specific Methylophilaceae ecotypes, including one novel ecotype. The new genomes
AB  - expand the known diversity of Methylophilaceae and provide new models for
AB  - studying the ecology of methylotrophy.
ER  -

TY  - JOUR
AU  - McTaggart, T.L.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Chistoserdova, L.
TI  - Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e01588
EP  - e01514
VL  - 3
AB  - Sequencing the genome of Janthinobacterium sp. RA13 from Lake Washington sediment is
AB  - announced. From the genome content, a versatile life-style is predicted, but
AB  - not bona fide methylotrophy. With the availability of its genomic sequence,
AB  - Janthinobacterium sp. RA13 presents a prospective model for studying microbial
AB  - communities in lake sediments.
ER  -

TY  - JOUR
AU  - McTaggart, T.L.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Chistoserdova, L.
TI  - Draft genomes of two strains of flavobacterium isolated from lake washington sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e01597
EP  - e01514
VL  - 3
AB  - We report sequencing the genomes of two new Flavobacterium strains isolated from Lake
AB  - Washington sediment. From genomic contents, versatile lifestyles were predicted but not bona
AB  - fide methylotrophy. With the availability of their genomic sequences, the new Flavobacterium
AB  - strains present prospective models for studying microbial communities in lake sediments.
ER  -

TY  - JOUR
AU  - McTaggart, T.L.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Chistoserdova, L.
TI  - Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e01587
EP  - e01514
VL  - 3
AB  - We announce here the genome sequencing of Pseudomonas sp. strain 11/12A from Lake Washington
AB  - sediment. From the genome content, a versatile lifestyle is predicted  but not one of bona
AB  - fide methylotrophy. With the availability of its genomic sequence, Pseudomonas sp. 11/12A
AB  - presents a prospective model for studying microbial communities in lake sediments.
ER  -

TY  - JOUR
AU  - Mead, D.A. et al.
TI  - Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 381
EP  - 400
VL  - 6
AB  - Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring,
AB  - Yellowstone National Park, Montana, USA under permit from the
AB  - National Park Service. The isolate was initially classified as a Geobacillus sp.
AB  - Y412MC10 based on its isolation conditions and similarity to other organisms
AB  - isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA
AB  - sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered
AB  - with Paenibacillus species, and the organism was most closely related to
AB  - Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was
AB  - sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome
AB  - sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of
AB  - Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp
AB  - with an average G+C content of 51.2%. Comparison to other Paenibacillus species
AB  - shows the organism lacks nitrogen fixation, antibiotic production and social
AB  - interaction genes reported in other paenibacilli. The Y412MC10 genome shows a
AB  - high level of synteny and homology to the draft sequence of Paenibacillus sp.
AB  - HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes.
AB  - This, combined with genomic CAZyme analysis, suggests an intestinal, rather than
AB  - environmental origin for Y412MC10.
ER  -

TY  - JOUR
AU  - Medema, M.H.
AU  - Trefzer, A.
AU  - Kovalchuk, A.
AU  - van den Berg, M.
AU  - Muller, U.
AU  - Heijne, W.
AU  - Wu, L.
AU  - Alam, M.T.
AU  - Ronning, C.M.
AU  - Nierman, W.C.
AU  - Bovenberg, R.A.
AU  - Breitling, R.
AU  - Takano, E.
TI  - The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways.
JO  - Genome Biol. Evol.
PY  - 2010
SP  - 212
EP  - 224
VL  - 2
AB  - Plasmids are mobile genetic elements that play a key role in the evolution
AB  - of bacteria by mediating genome plasticity and lateral transfer of useful
AB  - genetic information. Although originally considered to be exclusively
AB  - circular, linear plasmids have also been identified in certain bacterial
AB  - phyla, notably the actinomycetes. In some cases, linear plasmids engage
AB  - with chromosomes in an intricate evolutionary interplay, facilitating the
AB  - emergence of new genome configurations by transfer and recombination or
AB  - plasmid integration. Genome sequencing of Streptomyces clavuligerus ATCC
AB  - 27064, a Gram-positive soil bacterium known for its production of a
AB  - diverse array of biotechnologically important secondary metabolites,
AB  - revealed a giant linear plasmid of 1.8 Mb in length. This megaplasmid
AB  - (pSCL4) is one of the largest plasmids ever identified and the largest
AB  - linear plasmid to be sequenced. It contains more than 20% of the putative
AB  - protein-coding genes of the species, but none of these is predicted to be
AB  - essential for primary metabolism. Instead, the plasmid is densely packed
AB  - with an exceptionally large number of gene clusters for the potential
AB  - production of secondary metabolites, including a large number of putative
AB  - antibiotics, such as staurosporine, moenomycin, beta-lactams, and
AB  - enediynes. Interestingly, cross-regulation occurs between chromosomal and
AB  - plasmid-encoded genes. Several factors suggest that the megaplasmid came
AB  - into existence through recombination of a smaller plasmid with the arms of
AB  - the main chromosome. Phylogenetic analysis indicates that heavy traffic of
AB  - genetic information between Streptomyces plasmids and chromosomes may
AB  - facilitate the rapid evolution of secondary metabolite repertoires in
AB  - these bacteria.
ER  -

TY  - JOUR
AU  - Medhi, K.
AU  - Mishra, A.
AU  - Thakur, I.S.
TI  - Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus  denitrificans Strain ISTOD1, Isolated from Wastewater.
JO  - Genome Announcements
PY  - 2018
SP  - e00210
EP  - e00218
VL  - 6
AB  - We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb,
AB  - isolated from wastewater. It has been identified as a
AB  - heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis
AB  - revealed genes related to nitrogen and phosphorus removal, showing that the
AB  - strain holds potential for bioremediation and biorefinery uses.
ER  -

TY  - JOUR
AU  - Mediannikov, O.
AU  - El Karkouri, K.
AU  - Diatta, G.
AU  - Robert, C.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Bartonella senegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 279
EP  - 289
VL  - 8
AB  - Bartonella senegalensis sp. nov. strain OS02(T) is the type strain of B. senegalensis sp.
AB  - nov., a new species within the genus Bartonella. This strain,
AB  - whose genome is described here, was isolated in Senegal from the soft tick
AB  - Ornithodoros sonrai, the vector of relapsing fever. B. senegalensis is an
AB  - aerobic, rod-shaped, Gram-negative bacterium. Here we describe the features of
AB  - this organism, together with the complete genome sequence and its annotation. The
AB  - 1,966,996 bp-long genome contains 1,710 protein-coding and 46 RNA genes,
AB  - including 6 rRNA genes.
ER  -

TY  - JOUR
AU  - Mediannikov, O.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Bartonella florenciae  sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 185
EP  - 196
VL  - 9
AB  - Bartonella florenciae sp. nov. strain R4(T) is the type strain of B. florenciae sp. nov., a
AB  - new species within the genus Bartonella. This strain, whose genome is
AB  - described here, was isolated in France from the spleen of the shrew Crocidura
AB  - russula. B. florenciae is an aerobic, rod-shaped, Gram-negative bacterium. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence and its annotation. The 2,010,844 bp-long genome contains 1,909
AB  - protein-coding and 46 RNA genes, including two rRNA operons.
ER  -

TY  - JOUR
AU  - Mediannikov, O.
AU  - Nguyen, T.T.
AU  - Bell-Sakyi, L.
AU  - Padmanabhan, R.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 9
EP  - 9
VL  - 9
AB  - The family Rickettsiaceae currently includes two genera: Orientia that contains one species,
AB  - Orientia tsutsugamushi, and Rickettsia that contains 28 species.
AB  - Occidentia massiliensis gen. nov., sp. nov. strain OS118(T) is the type strain of
AB  - O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia
AB  - gen. nov. within the family Rickettsiaceae. This strain, whose genome is
AB  - described here, was isolated in France from the soft tick Ornithodoros sonrai
AB  - collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative,
AB  - obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here
AB  - we describe the features of O. massiliensis, together with the complete genomic
AB  - sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no
AB  - plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA
AB  - operon.
ER  -

TY  - JOUR
AU  - Medigue, C. et al.
TI  - Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.
JO  - Genome Res.
PY  - 2005
SP  - 1325
EP  - 1335
VL  - 15
AB  - A considerable fraction of life develops in the sea at temperatures lower than 15 degrees C.
AB  - Little is known about the adaptive features selected
AB  - under those conditions. We present the analysis of the genome sequence of
AB  - the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis
AB  - TAC125. We find that it copes with the increased solubility of oxygen at
AB  - low temperature by multiplying dioxygen scavenging while deleting whole
AB  - pathways producing reactive oxygen species. Dioxygen-consuming lipid
AB  - desaturases achieve both protection against oxygen and synthesis of lipids
AB  - making the membrane fluid. A remarkable strategy for avoidance of reactive
AB  - oxygen species generation is developed by P. haloplanktis, with
AB  - elimination of the ubiquitous molybdopterin-dependent metabolism. The P.
AB  - haloplanktis proteome reveals a concerted amino acid usage bias specific
AB  - to psychrophiles, consistently appearing apt to accommodate asparagine, a
AB  - residue prone to make proteins age. Adding to its originality, P.
AB  - haloplanktis further differs from its marine counterparts with recruitment
AB  - of a plasmid origin of replication for its second chromosome.
ER  -

TY  - JOUR
AU  - Medina-Cordoba, L.K.
AU  - Chande, A.T.
AU  - Rishishwar, L.
AU  - Mayer, L.W.
AU  - Marino-Ramirez, L.
AU  - Valderrama-Aguirre, L.C.
AU  - Valderrama-Aguirre, A.
AU  - Kostka, J.E.
AU  - Jordan, I.K.
TI  - Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia's Cauca Valley.
JO  - Genome Announcements
PY  - 2018
SP  - e00104
EP  - e00118
VL  - 6
AB  - Members of the Klebsiella genus promote plant growth. We report here draft whole-genome
AB  - sequences for 15 Klebsiella sp. isolates from sugarcane fields in
AB  - the Cauca Valley of Colombia. The genomes of these isolates were characterized as
AB  - part of a broader effort to evaluate their utility as endemic plant
AB  - growth-promoting biofertilizers.
ER  -

TY  - JOUR
AU  - Medina-Franco, J.L.
AU  - Caulfield, T.
TI  - Advances in the computational development of DNA methyltransferase inhibitors.
JO  - Drug Discovery Today
PY  - 2011
SP  - 418
EP  - 425
VL  - 16
AB  - DNA methylation is an epigenetic change that results in the addition of a methyl group at the
AB  - carbon-5 position of cytosine residues. The process is mediated by DNA methyltransferases
AB  - (DNMTs), a family of enzymes for which inhibition is a promising strategy for the treatment of
AB  - cancer and other diseases. Here, we review the current status of the computational studies
AB  - directed to rationalize, at the molecular level, the enzymatic activity of DNMT inhibitors. We
AB  - also review successful virtual screenings to identify inhibitors with novel scaffolds as well
AB  - as the emerging efforts to characterize the dynamic behavior of DNMTs. Thus, computational
AB  - approaches form part of multidisciplinary efforts to further advance epigenetic therapies.
ER  -

TY  - JOUR
AU  - Medina-Franco, J.L.
AU  - Yoo, J.
TI  - Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases.
JO  - Mol. Diversity
PY  - 2013
SP  - 337
EP  - 344
VL  - 17
AB  - Inhibitors of DNA methyltransferase (DNMT) are attractive compounds not only as potential
AB  - therapeutic agents for the treatment of cancer and
AB  - other diseases, but also as research tools to investigate the role of
AB  - DNMTs in epigenetic events. Recent advances in high-throughput
AB  - screening (HTS) for epigenetic targets and the availability of the
AB  - first crystallographic structure of human DNMT1 encourage the
AB  - integration of research strategies to uncover and optimize the activity
AB  - of DNMT inhibitors. Herein, we present a binding model of a novel
AB  - small-molecule DNMT1 inhibitor obtained by HTS, recently released in a
AB  - public database. The docking model is in agreement with key
AB  - interactions previously identified for established inhibitors using
AB  - extensive computational studies including molecular dynamics and
AB  - structure-based pharmacophore modeling. Based on the chemical structure
AB  - of the novel inhibitor, a sequential computational screening of five
AB  - chemical databases was performed to identify candidate compounds for
AB  - testing. Similarity searching followed by molecular docking of chemical
AB  - databases such as approved drugs, natural products, a DNMT-focused
AB  - library, and a general screening collection, identified at least 108
AB  - molecules with promising DNMT inhibitory activity. The chemical
AB  - structures of all hit compounds are disclosed to encourage the research
AB  - community working on epigenetics to test experimentally the enzymatic
AB  - and demethylating activity in vivo. Five candidate hits are drugs
AB  - approved for other indications and represent potential starting points
AB  - of a drug repurposing strategy.
ER  -

TY  - JOUR
AU  - Medrano, E.G.
AU  - Bell, A.A.
TI  - Genome Sequence of Pantoea sp. Strain Sc 1, an Opportunistic Cotton Pathogen.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3019
EP  - 3019
VL  - 194
AB  - Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we
AB  - provide an annotated genome sequence of Pantoea sp. strain Sc 1, which
AB  - was isolated from a diseased cotton boll. This research provides the first genome
AB  - sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen.
ER  -

TY  - JOUR
AU  - Medrano, E.G.
AU  - Bell, A.A.
TI  - Genome Sequence of Pantoea ananatis Strain CFH 7-1, Which Is Associated with a Vector-Borne Cotton Fruit Disease.
JO  - Genome Announcements
PY  - 2015
SP  - e01029
EP  - e01015
VL  - 3
AB  - Pantoea ananatis is a bacterium with versatile niches that vary from pathogenic to beneficial.
AB  - We present the genome of strain CFH 7-1, which was recovered from  a diseased greenhouse
AB  - cotton boll previously caged with a field-collected cotton  fleahopper (Pseudatomoscelis
AB  - seriatus). These data will assist in deciphering the infection process.
ER  -

TY  - JOUR
AU  - Medrano, E.G.
AU  - Forray, M.M.
AU  - Bell, A.A.
TI  - Complete Genome Sequence of a Klebsiella pneumoniae Strain Isolated from a Known  Cotton Insect Boll Vector.
JO  - Genome Announcements
PY  - 2014
SP  - e00850
EP  - e00814
VL  - 2
AB  - Klebsiella pneumoniae (associated with bacterial pneumonia) was previously isolated from
AB  - Nezara viridula, a significant vector of cotton boll-rot pathogens.
AB  - We provide the first annotated genome sequence of the cotton opportunistic strain
AB  - K. pneumoniae 5-1. This data provides guidance to study the bases of cotton
AB  - pathogenesis by bacteria associated with vectors.
ER  -

TY  - JOUR
AU  - Medrano-Felix, A.
AU  - Estrada-Acosta, M.
AU  - Jimenez, M.
AU  - Gomez-Gil, B.
AU  - Leon-Felix, J.
AU  - Amarillas, L.
AU  - Chaidez, C.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Oranienburg Strain S-76, Isolated from an Aquatic Environment.
JO  - Genome Announcements
PY  - 2013
SP  - e01017
EP  - e01013
VL  - 1
AB  - Salmonella is a widespread microorganism and a common causative agent of food-borne illnesses.
AB  - Salmonella enterica subsp. enterica serotype Oranienburg is
AB  - highly prevalent in surface water from tropical ecosystems and is not commonly
AB  - related to illnesses. Here, we report the first genome sequence of Salmonella
AB  - Oranienburg strain S-76, isolated from an aquatic environment.
ER  -

TY  - JOUR
AU  - Medvedeva, E.S.
AU  - Siniagina, M.N.
AU  - Malanin, S.Y.
AU  - Boulygina, E.A.
AU  - Malygina, T.Y.
AU  - Baranova, N.B.
AU  - Mouzykantov, A.A.
AU  - Davydova, M.N.
AU  - Chernova, O.A.
AU  - Chernov, V.M.
TI  - Genome Sequences of Acholeplasma laidlawii Strains Differing in Sensitivity to Ciprofloxacin.
JO  - Genome Announcements
PY  - 2017
SP  - e01189
EP  - e01117
VL  - 5
AB  - Acholeplasma laidlawii is a well-suited model for study of the molecular basis of the
AB  - adaptation of mollicutes to environmental conditions. Here we present the
AB  - whole-genome sequences of four strains of A. laidlawii with differential
AB  - sensitivity to ciprofloxacin.
ER  -

TY  - JOUR
AU  - Meehan, R.R.
AU  - Ulrich, E.
AU  - Bird, A.P.
TI  - Restriction endonuclease NciI is not blocked by CpG methylation.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 5517
EP  - 5518
VL  - 21
AB  - Vertebrate DNA is highly methylated at cytosines in the dinucleotide sequence CpG. Many
AB  - restriction enzymes are unable to cleave DNA if their recognition sequences contain methylated
AB  - CpG, and this property has been used to study the pattern of DNA methylation in higher
AB  - eukaryotes. An enzyme that has recently been used in this way is NciI (recognition sequence
AB  - CCSGG, where S is C or G). It was reported that this enzyme cannot cleave a region of the
AB  - mouse actin promoter when the CpG in its recognition site is methylated on both strands, but
AB  - can cleave when either one or both strands are unmethylated. As a result, NciI has been used
AB  - to monitor the conversion of symmetrically methylated DNA to hemi-methylated DNA in a number
AB  - of systems. Its general use for this purpose depends upon the idea that NciI cannot cleave any
AB  - symmetrically methylated site. We have digested symmetrically methylated and non-methylated
AB  - DNA with NciI, and find that it can cleave both forms to completion, though at markedly
AB  - different rates.
ER  -

TY  - JOUR
AU  - Meessen-Pinard, M.
AU  - Sekulovic, O.
AU  - Fortier, L.C.
TI  - Evidence of in vivo prophage induction during Clostridium difficile infection.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 7662
EP  - 7670
VL  - 78
AB  - Prophages contribute to the evolution and virulence of most bacterial pathogens,
AB  - but their role in Clostridium difficile is unclear. Here we describe the
AB  - isolation of four Myoviridae phages, MMP01, MMP02, MMP03, and MMP04, that were
AB  - recovered as free viral particles in the filter-sterilized stool supernatants of
AB  - patients suffering from C. difficile infection (CDI). Furthermore, identical
AB  - prophages were found in the chromosomes of C. difficile isolated from the
AB  - corresponding fecal samples. We therefore provide, for the first time, evidence
AB  - of in vivo prophage induction during CDI. We completely sequenced the genomes of
AB  - MMP02 and MMP04, and bioinformatics analyses did not reveal the presence of
AB  - virulence factors but underlined the unique character of MMP04. We also studied
AB  - the mobility of MMP02 and MMP04 prophages in vitro. Both prophages were
AB  - spontaneously induced, with 4 to 5 log PFU/ml detected in the culture
AB  - supernatants of the corresponding lysogens. When lysogens were grown in the
AB  - presence of subinhibitory concentrations of ciprofloxacin, moxifloxacin,
AB  - levofloxacin, or mitomycin C, the phage titers further increased, reaching 8 to 9
AB  - log PFU/ml in the case of MMP04. In summary, our study highlights the extensive
AB  - genetic diversity and mobility of C. difficile prophages. Moreover, antibiotics
AB  - known to represent risk factors for CDI, such as quinolones, can stimulate
AB  - prophage mobility in vitro and probably in vivo as well, which underscores their
AB  - potential impact on phage-mediated horizontal gene transfer events and the
AB  - evolution of C. difficile.
ER  -

TY  - JOUR
AU  - Mefferd, C.C. et al.
TI  - High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China.
JO  - Genome Announcements
PY  - 2016
SP  - e00312
EP  - e00316
VL  - 4
AB  - The draft genomes of Thermus tengchongensis YIM 77401 and T. caliditerrae YIM 77777 are
AB  - 2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes,
AB  - respectively. Gene content and growth experiments demonstrate broad metabolic
AB  - capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation,
AB  - incomplete denitrification, and polysulfide reduction.
ER  -

TY  - JOUR
AU  - Megaw, J.
AU  - Gilmore, B.F.
TI  - Draft Genome Sequence of Staphylococcus succinus Strain CSM-77, a Moderately Halophilic Bacterium Isolated from a Triassic Salt Mine.
JO  - Genome Announcements
PY  - 2016
SP  - e00532
EP  - e00516
VL  - 4
AB  - Here, we report the draft genome sequence of Staphylococcus succinus strain CSM-77. This
AB  - moderately halophilic bacterium was isolated from the surface of a
AB  - halite sample obtained from a Triassic salt mine.
ER  -

TY  - JOUR
AU  - Megias, E.
AU  - Dos Reis, J.F.B.
AU  - Ribeiro, R.A.
AU  - Ollero, F.J.
AU  - Megias, M.
AU  - Hungria, M.
TI  - Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from  the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential  as an Inoculant.
JO  - Genome Announcements
PY  - 2018
SP  - e01547
EP  - e01517
VL  - 6
AB  - Pantoea ananatis 1.38 is a strain isolated from the rhizosphere of irrigated rice in southern
AB  - Spain. Its genome was estimated at 4,869,281 bp, with 4,644 coding
AB  - sequences (CDSs). The genome encompasses several CDSs related to plant growth
AB  - promotion, such as that for siderophore metabolism, and virulence genes
AB  - characteristic of pathogenic Pantoea spp. are absent.
ER  -

TY  - JOUR
AU  - Megias, E.
AU  - Megias, M.
AU  - Ollero, F.J.
AU  - Hungria, M.
TI  - Draft Genome Sequence of Pantoea ananatis Strain AMG521, a Rice Plant Growth-Promoting Bacterial Endophyte Isolated from the Guadalquivir Marshes in  Southern Spain.
JO  - Genome Announcements
PY  - 2016
SP  - e01681
EP  - e01615
VL  - 4
AB  - The rice endophyte Pantoea ananatis AMG521 shows several plant growth-promoting properties and
AB  - promotes rice yield increases. Its draft genome was estimated at
AB  - 4,891,568 bp with 4,704 coding sequences (CDS). The genome encodes genes for
AB  - N-acylhomoserine lactone (AHL) synthases, AHL hydrolases, hyperadherence (yidQ,
AB  - yidP, and yidR), fusaric acid resistance, and oxidation of lignin, highlighting
AB  - its biotechnological potential.
ER  -

TY  - JOUR
AU  - Megias, E.
AU  - Reis, J.F.B.
AU  - Ribeiro, R.A.
AU  - Megias, M.
AU  - Ollero, F.J.
AU  - Hungria, M.
TI  - Genome Sequence of Pantoea sp. Strain 1.19, Isolated from Rice Rhizosphere, with  the Capacity To Promote Growth of Legumes and Nonlegumes.
JO  - Genome Announcements
PY  - 2017
SP  - e00707
EP  - e00717
VL  - 5
AB  - Pantoea sp. 1.19, a plant growth-promoting bacterium (PGPB), was isolated from the rhizosphere
AB  - of rice plants in Spain. Its genome, estimated at 3,771,065 bp,
AB  - encodes 3,535 coding sequences (CDSs), carrying genes for synthesis of auxins,
AB  - homoserine lactones, enzymes, siderophores, and quorum sensing. Several CDSs
AB  - emphasize its biotechnological potential as an agriculture inoculant.
ER  -

TY  - JOUR
AU  - Megias, E.
AU  - Reis, J.F.B.
AU  - Ribeiro, R.A.
AU  - Ollero, F.J.
AU  - Megias, M.
AU  - Hungria, M.
TI  - Genome Sequence of Pantoea ananatis Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain.
JO  - Genome Announcements
PY  - 2017
SP  - e00848
EP  - e00817
VL  - 5
AB  - Pantoea ananatis AMG 501 is a plant growth-promoting bacterium isolated from rice leaves. Its
AB  - genome was estimated at 5,102,640 bp with 4,994 coding sequences,
AB  - encompassing genes related to the metabolism of carbohydrates, to the synthesis
AB  - of auxins, siderophores, and homoserine lactones, and to the type I, II, III, IV,
AB  - and VI secretion systems.
ER  -

TY  - JOUR
AU  - Mehari, Y.T.
AU  - Arivett, B.A.
AU  - Farone, A.L.
AU  - Gunderson, J.H.
AU  - Farone, M.B.
TI  - Draft Genome Sequences of Two Novel Amoeba-Resistant Intranuclear Bacteria, 'Candidatus Berkiella cookevillensis' and 'Candidatus Berkiella aquae'.
JO  - Genome Announcements
PY  - 2016
SP  - e01732
EP  - e01715
VL  - 4
AB  - 'Candidatus Berkiella cookevillensis' and 'Candidatus Berkiella aquae' are obligate
AB  - intranuclear endosymbionts of freshwater amoebae. Here, we present the
AB  - draft genome sequences of these two bacteria, with total sizes of 2,990,361 bp
AB  - and 3,626,027 bp, respectively.
ER  -

TY  - JOUR
AU  - Mehdizadeh-Gohari, I.
AU  - Kropinski, A.M.
AU  - Weese, S.J.
AU  - Parreira, V.R.
AU  - Whitehead, A.E.
AU  - Boerlin, P.
AU  - Prescott, J.F.
TI  - Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.
JO  - PLoS ONE
PY  - 2016
SP  - E0148344
EP  - E0148344
VL  - 11
AB  - The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly
AB  - associated with canine and foal necrotizing enteritis should improve our
AB  - understanding of the role of type A Clostridium perfringens associated disease in
AB  - these animals. The current study presents the complete genome sequence of two
AB  - netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal
AB  - necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively.
AB  - Genome sequencing was done using Single Molecule, Real-Time (SMRT)
AB  - technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a
AB  - single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include
AB  - five circular plasmids. Plasmid annotation revealed that three plasmids were
AB  - shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding
AB  - tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a
AB  - putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin
AB  - genes, netF, netE and netG, were located in unique pathogenicity loci on
AB  - tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825
AB  - protein-coding genes whereas the chromosome of JFP838 contains 3,014
AB  - protein-encoding genes. Comparison of these two chromosomes with three available
AB  - reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81
AB  - (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these
AB  - divergent genomic regions in both chromosomes are phage- and plasmid-related
AB  - segments. Sixteen of these unique chromosomal regions (~69 kb) were shared
AB  - between the two isolates. Five of these shared regions formed a mosaic of
AB  - plasmid-integrated segments, suggesting that these elements were acquired early
AB  - in a clonal lineage of netF-positive C. perfringens strains. These results
AB  - provide significant insight into the basis of canine and foal necrotizing
AB  - enteritis and are the first to demonstrate that netF resides on a large and
AB  - unique plasmid-encoded locus.
ER  -

TY  - JOUR
AU  - Mehershahi, K.S.
AU  - Abraham, S.N.
AU  - Chen, S.L.
TI  - Complete Genome Sequence of Uropathogenic Escherichia coli Strain CI5.
JO  - Genome Announcements
PY  - 2015
SP  - e00558
EP  - e00515
VL  - 3
AB  - Escherichia coli represents the primary etiological agent responsible for urinary tract
AB  - infections, one of the most common infections in humans. We report here the
AB  - complete genome sequence of uropathogenic Escherichia coli strain CI5, a clinical
AB  - pyelonephritis isolate used for studying pathogenesis.
ER  -

TY  - JOUR
AU  - Mehershahi, K.S.
AU  - Chen, S.L.
TI  - Complete Genome Sequence of the Uropathogenic Escherichia coli Strain NU14.
JO  - Genome Announcements
PY  - 2017
SP  - e00306
EP  - e00317
VL  - 5
AB  - Escherichia coli is the most common bacterium causing urinary tract infections in humans. We
AB  - report here the complete genome sequence of the uropathogenic
AB  - Escherichia coli strain NU14, a clinical pyelonephritis isolate used for studying
AB  - pathogenesis.
ER  -

TY  - JOUR
AU  - Mehershahi, K.S.
AU  - Hsu, L.Y.
AU  - Koh, T.H.
AU  - Chen, S.L.
TI  - Complete Genome Sequence of Streptococcus agalactiae Serotype III, Multilocus Sequence Type 283 Strain SG-M1.
JO  - Genome Announcements
PY  - 2015
SP  - e01188
EP  - e01115
VL  - 3
AB  - Streptococcus agalactiae (group B Streptococcus) is a common commensal strain in  the human
AB  - gastrointestinal tract that can also cause invasive disease in humans and other animals. We
AB  - report here the complete genome sequence of S. agalactiae SG-M1, a serotype III, multilocus
AB  - sequence type 283 strain, isolated from a Singaporean patient suffering from meningitis.
ER  -

TY  - JOUR
AU  - Mehling, J.S.
AU  - Lavender, H.
AU  - Clegg, S.
TI  - A Dam methylation mutant of Klebsiella pneumoniae is partially attenuated.
JO  - FEMS Microbiol. Lett.
PY  - 2007
SP  - 187
EP  - 193
VL  - 268
AB  - In Klebsiella pneumoniae, a chromosomal insertion mutation was constructed in the dam gene,
AB  - which encodes DNA adenine methylase (Dam),
AB  - resulting in a mutant unable to methylate specific nucleotides. In some
AB  - bacteria, the Dam methylase has been shown to play an important role in
AB  - virulence gene regulation as well as in methyl-directed mismatch repair
AB  - and the regulation of replication initiation. Disruption of the normal
AB  - Dam function by either eliminating or greatly increasing expression in
AB  - several organisms has been shown to cause attenuation of virulence in
AB  - murine models of infection. In K. pneumoniae, a mutation-eliminating
AB  - Dam function is shown here to result in only partial attenuation
AB  - following intranasal and intraperitoneal infection of Balb/C mice.
ER  -

TY  - JOUR
AU  - Mehnaz, S.
AU  - Bauer, J.S.
AU  - Gross, H.
TI  - Complete Genome Sequence of the Sugar Cane Endophyte Pseudomonas aurantiaca PB-St2, a Disease-Suppressive Bacterium with Antifungal Activity toward the Plant  Pathogen Colletotrichum falcatum.
JO  - Genome Announcements
PY  - 2014
SP  - e01108
EP  - e01113
VL  - 2
AB  - The endophytic bacterium Pseudomonas aurantiaca PB-St2 exhibits antifungal activity and
AB  - represents a biocontrol agent to suppress red rot disease of sugar
AB  - cane. Here, we report the completely sequenced 6.6-Mb genome of P. aurantiaca
AB  - PB-St2. The sequence contains a repertoire of biosynthetic genes for secondary
AB  - metabolites that putatively contribute to its antagonistic activity and its
AB  - plant-microbe interactions.
ER  -

TY  - JOUR
AU  - Mehra, R.S.
AU  - Malhotra, V.P.
AU  - Rembhotkar, G.W.
TI  - Rapid purification of a restriction endonuclease from Escherichia coli RY13.
JO  - Biotechnol. Tech.
PY  - 1993
SP  - 411
EP  - 414
VL  - 7
AB  - A two step method for the purification of the restriction endonuclease EcoRI was developed.
AB  - The first step involved the purification of the enzyme on a Cibacron Blue-F3GA-agarose column,
AB  - followed by a hydroxyapatite column. The enzyme was homogeneous on SDS-PAGE and completely
AB  - free from contaminating nucleases and phosphatases, and can be used for direct DNA hydrolysis.
ER  -

TY  - JOUR
AU  - Mehrabadi, J.F.
AU  - Mirzaie, A.
AU  - Ahangar, N.
AU  - Rahimi, A.
AU  - Rokni-Zadeh, H.
TI  - Draft Genome Sequence of Kocuria rhizophila RF, a Radiation-Resistant Soil Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00095
EP  - e00016
VL  - 4
AB  - Kocuria rhizophila RF, a soil isolate from Iran, is a radiation-resistant bacterium. Only a
AB  - limited amount of genomic information for radiation-resistant
AB  - bacteria is currently available. Here, we report the draft genome sequence of
AB  - this bacterium, providing knowledge to aid in the discovery of the genomic basis
AB  - of its resistance to radiation.
ER  -

TY  - JOUR
AU  - Mei, Y.
AU  - Sun, Y.
AU  - He, J.
AU  - Wang, Q.
AU  - Sun, Y.
AU  - Shao, W.
TI  - Genome Sequences of Pseudomonas fragi Strains A22 and B25.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3276
EP  - 3277
VL  - 194
AB  - Pseudomonas fragi A22 is a novel isolate that produces bead-like particles (A22B) in its cell
AB  - wall. To explore the genetic basis for the formation of A22B, P.
AB  - fragi A22 and the type strain of the species, P. fragi B25, were subjected to
AB  - genome sequence analysis. Here, we report the draft genome sequences and
AB  - automatic annotation of both strains. These data offer a solid base for related
AB  - studies of P. fragi, including comparative genomics, proteomics, and gene mining.
ER  -

TY  - JOUR
AU  - Meidler, R.
AU  - Morad, I.
AU  - Amitsur, M.
AU  - Inokuchi, H.
AU  - Kaufmann, G.
TI  - Detection of anticodon nuclease residues involved in tRNALys cleavage specificity.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 499
EP  - 510
VL  - 287
AB  - The tRNALys-specific anticodon
AB  - nuclease exists in latent form in Escherichia coli strains containing
AB  - the optional prr locus. The latency is a result of a masking
AB  - interaction between the anticodon nuclease core-polypeptide PrrC and
AB  - the Type IC DNA restriction-modification enzyme EcoprrI. Activation of
AB  - the latent enzyme by phage T4-infection elicits cleavage of tRNALys 5'
AB  - to the wobble base, yielding 5'-OH and 2', 3'-cyclic phosphate termini.
AB  - The N-proximal half of PrrC has been implicated with (A/G) TPase and
AB  - EcoprrI interfacing activities. Therefore, residues involved in
AB  - recognition and cleavage of tRNALys were searched for at the C-half.
AB  - Random mutagenesis of the low-G+C portion encoding PrrC residues
AB  - 200-313 was performed, followed by selection for loss of anticodon
AB  - nuclease-dependent lethality and production of full-sized PrrC-like
AB  - protein. This process yielded a cluster of missense mutations mapping
AB  - to a region highly conserved between PrrC and two putative Neisseria
AB  - meningitidis MC58 homologues. This cluster included two adjacent
AB  - members that relaxed the inherent enzyme's cleavage specificity. We
AB  - also describe another mode of relaxed specificity, due to mere
AB  - overexpression of PrrC. This mode was shared by wild-type PrrC and the
AB  - other mutant alleles. The additional substrates recognised under the
AB  - promiscuous conditions had, in general, anticodons resembling that of
AB  - tRNALys. Taken together, the data suggest that the anticodon of tRNALys
AB  - harbours anticodon nuclease identity elements and implicates a
AB  - conserved region in PrrC in their recognition.
ER  -

TY  - JOUR
AU  - Meier-Kolthoff, J.P. et al.
TI  - Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial  taxonomy.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 2
EP  - 2
VL  - 9
AB  - Although Escherichia coli is the most widely studied bacterial model organism and often
AB  - considered to be the model bacterium per se, its type strain was until now
AB  - forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B
AB  - acteria and A rchaea project, we here describe the features of E. coli DSM
AB  - 30083(T) together with its genome sequence and annotation as well as novel
AB  - aspects of its phenotype. The 5,038,133 bp containing genome sequence includes
AB  - 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid.
AB  - Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and
AB  - outgroup strains to the type strain of E. coli was investigated using digital
AB  - DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content.
AB  - As in the majority of previous studies, results show Shigella spp. embedded
AB  - within E. coli and in most cases forming a single subgroup of it. Phylogenomic
AB  - trees also recover the proposed E. coli phylotypes as monophyla with minor
AB  - exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest
AB  - neighbor. The widely used lab strain K-12 is not only genomically but also
AB  - physiologically strongly different from the type strain. The phylotypes do not
AB  - express a uniform level of character divergence as measured using dDDH, however,
AB  - thus an alternative arrangement is proposed and discussed in the context of
AB  - bacterial subspecies. Analyses of the genome sequences of a large number of E.
AB  - coli strains and of strains from > 100 other bacterial genera indicate a value of
AB  - 79-80% dDDH as the most promising threshold for delineating subspecies, which in
AB  - turn suggests the presence of five subspecies within E. coli.
ER  -

TY  - JOUR
AU  - Meier-Kolthoff, J.P.
AU  - Lu, M.
AU  - Huntemann, M.
AU  - Lucas, S.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Pitluck, S.
AU  - Goodwin, L.A.
AU  - Han, C.
AU  - Tapia, R.
AU  - Potter, G.
AU  - Land, M.
AU  - Ivanova, N.
AU  - Rohde, M.
AU  - Goker, M.
AU  - Detter, J.C.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Klenk, H.P.
TI  - Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 28
EP  - 41
VL  - 9
AB  - Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the
AB  - family Pseudonocardiaceae that is moderately well
AB  - characterized at the genome level thus far. Members of the genus
AB  - Saccharomonospora are of interest because they originate from diverse habitats,
AB  - such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated
AB  - grain, and ocean sediment, where they probably play a role in the primary
AB  - degradation of plant material by attacking hemicellulose. Species of the genus
AB  - Saccharomonospora are usually Gram-positive, non-acid fast, and are classified
AB  - among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue)
AB  - aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only
AB  - the fourth member in the genus for which a completely sequenced (non-contiguous
AB  - finished draft status) type strain genome will be published. Here we describe the
AB  - features of this organism, together with the draft genome sequence, and
AB  - annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57
AB  - RNA genes was sequenced as part of the DOE funded Community Sequencing Program
AB  - (CSP) 2010 at the Joint Genome Institute (JGI).
ER  -

TY  - JOUR
AU  - Meincke, L. et al.
TI  - Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 74
EP  - 83
VL  - 6
AB  - Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic
AB  - freshwater bacterium affiliated with the family Burkholderiaceae
AB  - (class Betaproteobacteria). This strain is of interest because it represents a
AB  - subspecies with cosmopolitan and ubiquitous distribution in standing freshwater
AB  - systems. The 16S-23S ITS genotype represented by the sequenced strain comprised
AB  - on average more than 10% of bacterioplankton in its home habitat. While all
AB  - strains of the subspecies P. necessarius asymbioticus are free-living freshwater
AB  - bacteria, strains belonging to the only other subspecies, P. necessarius subsp.
AB  - necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The
AB  - two subspecies of P. necessarius are the instances of two closely related
AB  - subspecies that differ in their lifestyle (free-living vs. obligate
AB  - endosymbiont), and they are the only members of the genus Polynucleobacter with
AB  - completely sequenced genomes. Here we describe the features of P. necessarius
AB  - subsp. asymbioticus, together with the complete genome sequence and annotation.
AB  - The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA
AB  - genes is the first completed genome sequence of the genus Polynucleobacter to be
AB  - published and was sequenced as part of the DOE Joint Genome Institute Community
AB  - Sequencing Program 2006.
ER  -

TY  - JOUR
AU  - Meinersmann, R.J.
AU  - Bono, J.L.
AU  - Lindsey, R.L.
AU  - Genzlinger, L.L.
AU  - Loparev, V.N.
AU  - Oakley, B.B.
TI  - Genome Sequence of a Urease-Positive Campylobacter lari Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01191
EP  - e01115
VL  - 3
AB  - Campylobacter lari is frequently isolated from shore birds and can cause illness  in humans.
AB  - Here, we report the draft whole-genome sequence of a urease-positive strain of C. lari that
AB  - was isolated in estuarial water on the coast of Delaware,  USA.
ER  -

TY  - JOUR
AU  - Meinersmann, R.J.
AU  - Ladely, S.R.
AU  - Bono, J.L.
AU  - Plumblee, J.R.
AU  - Hall, M.C.
AU  - Genzlinger, L.L.
AU  - Cook, K.L.
TI  - Complete Genome Sequence of a Colistin Resistance Gene (mcr-1)-Bearing Isolate of Escherichia coli from the United States.
JO  - Genome Announcements
PY  - 2016
SP  - e01283
EP  - e01216
VL  - 4
AB  - Transmissible colistin resistance conferred by the mcr-1 gene-bearing IncI2 plasmid has been
AB  - recently reported in Escherichia coli in the United States. We
AB  - report here the completed genome sequence of a second E. coli strain isolated
AB  - from swine in the United States that carried the mcr-1 gene on an IncI2-type
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Meinersmann, R.J.
AU  - Ladely, S.R.
AU  - Plumblee, J.R.
AU  - Hall, M.C.
AU  - Simpson, S.A.
AU  - Ballard, L.L.
AU  - Scheffler, B.E.
AU  - Genzlinger, L.L.
AU  - Cook, K.L.
TI  - Colistin Resistance mcr-1-Gene-Bearing Escherichia coli Strain from the United States.
JO  - Genome Announcements
PY  - 2016
SP  - e00898
EP  - e00816
VL  - 4
AB  - Transmissible colistin resistance in the form of an mcr-1-gene-bearing plasmid has been
AB  - recently reported in Enterobacteriaceae in several parts of the world.
AB  - We report here the completed genome sequence of an Escherichia coli strain
AB  - isolated from swine in the United States that carried the mcr-1 gene on an
AB  - IncI2-type plasmid.
ER  -

TY  - JOUR
AU  - Meints, G.A.
AU  - Drobny, G.P.
TI  - Dynamic impact of methylation at the m. hhai target site: a solid-state deuterium nmr study.
JO  - Biochemistry
PY  - 2001
SP  - 12436
EP  - 12443
VL  - 40
AB  - Base methylation plays an important role in numerous biological functions of DNA, from
AB  - inhibition of cleavage by endonucleases to inhibition of transcription factor binding. Studies
AB  - of nucleic acid structure have shown little differences in unmethylated DNAs and the identical
AB  - sequence containing methylated analogues. We have investigated changes in the local dynamics
AB  - of DNA upon substitution of a methylated cytosine analogue for cytosine using solid-state
AB  - deuterium NMR. In particular, we have observed changes in the local dynamics at the target
AB  - site of the M.HhaI restriction system. These studies observe changes in the amplitudes of the
AB  - local backbone dynamics at the actual target site of the HhaI methyltransferase. This
AB  - conclusion is another indication that the significant result of base methylation is to perturb
AB  - the local dynamics, and therefore the local conformational flexibility, of the DNA helix,
AB  - inhibiting or restricting the protein's ability to manipulate the DNA helix in order to
AB  - perform its chemical alterations.
ER  -

TY  - JOUR
AU  - Meints, R.H.
AU  - Schuster, A.M.
AU  - Van Etten, J.L.
TI  - Chlorella Viruses.
JO  - Plant Mol. Biol. Rep.
PY  - 1985
SP  - 180
EP  - 187
VL  - 3
AB  - Although viruses that infect blue-green algae (cyanobacteria) have been
AB  - extensively studied (Sherman and Brown, 1978), little is known about viruses of
AB  - eukaryotic algae (see reviews, Lemke, 1976, Sherman and Brown, 1978, Dodds,
AB  - 1979, and Dodds, 1983).  Most viruses or virus-like particles (VLP) in
AB  - eukaryotic algae have been detected by ultrastructural studies, and only a few
AB  - attempts have been made to characterize these particles, primarily because they
AB  - are difficult to obtain in reasonable quantities.  Several factors contribute
AB  - to this lack of material: (i) usually only a few algal cells contained
AB  - particles, (ii) usually the cells only contained particles at one stage of the
AB  - algal life cycle, (iii) usually the cells that had particles did not lyse, and
AB  - (iv) in most cases the particles were not infectious.  These factors, plus the
AB  - fact that some of these particles were present in multicellular filamentous
AB  - algae, have hindered the development of a biological assay for them.  Thus it
AB  - is interesting that we have recently discovered a group of large (negatively
AB  - stained particles are 150 to 190 nm in diameter) polyhedral, dsDNA-containing
AB  - viruses which infect and replicate in certain strains of unicellular,
AB  - eukaryotic, exsymbiont Chlorella-like green algae.  These viruses can be
AB  - produced in large quantities and, most importantly, the viruses can be assayed
AB  - by plaque formation on lawns of the host Chlorella.  These viruses, therefore,
AB  - have the potential to serve as excellent model systems for studying gene
AB  - regulation in a photosynthetic eukaryote in the manner that bacterio phages
AB  - served as model systems for studying gene regulation in bacteria.  This review
AB  - will briefly describe some of the pertinent properties of these viruses,
AB  - focusing primarily on the most studied virus PBCV-1.  A more comprehensive
AB  - review of these viruses is in press (Van Etten et al., 1986).
ER  -

TY  - JOUR
AU  - Meiron, H.
AU  - Nahon, E.
AU  - Raveh, D.
TI  - Identification of the heterothallic mutation in HO-endonuclease of S. cerevisiae using HO/ho chimeric genes.
JO  - Curr. Genet.
PY  - 1995
SP  - 367
EP  - 373
VL  - 28
AB  - HO-endonuclease initiates a mating-type switch in the yeast S. cerevisiae by making a
AB  - double-strand cleavage in the DNA of the mating-type gene, MAT.  Heterothallic strains of
AB  - yeast have a stable mating type and contain a recessive ho allele.  Here we report the
AB  - sequence of the ho allele; ho has four point mutations all of which encode for substitute
AB  - amino acids.  The fourth mutation is a leucine to histidine substitution within a presumptive
AB  - zinc finger.  Chimeric HO/ho genes were constructed in vivo by converting different parts of
AB  - the sequence of the genomic ho allele to the HO sequence by gene conversion.  HO activity was
AB  - assessed by three bioassays: a mating-type switch, extinction of expression of an a-specific
AB  - reporter gene, and the appearance of Canr Ade- papillae resulting from excision of an
AB  - engineered Ty element containing the HO-endonuclease target site and a SUP4o gene.  We found
AB  - that the replacement of the fourth point mutation in ho to the HO sequence restored HO
AB  - activity to the chimeric endonuclease.
ER  -

TY  - JOUR
AU  - Meisel, A.
AU  - Bickle, T.A.
AU  - Kruger, D.H.
AU  - Schroeder, C.
TI  - Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage.
JO  - Nature
PY  - 1992
SP  - 467
EP  - 469
VL  - 355
AB  - Type III restriction/modification enzymes recognize short, nonpalindromic
AB  - sequences that can be methylated on only one strand, with the paradoxical
AB  - consequence that during replication of what is in effect hemimethylated DNA
AB  - totally unmodified sites arise.  Why the unmodified sites are not subject to
AB  - suicidal restriction was not clear.  Here we show that restriction requires two
AB  - unmodified recognition sites that can be separated by different distances but
AB  - which must be in inverse orientation.  All of the unmodified sites in newly
AB  - replicated DNA are of course in the same orientation, which explains why they
AB  - are not restricted.  This result may be of relevance to other manifestations of
AB  - anisotropy in double-stranded DNA, such as genetic imprinting.
ER  -

TY  - JOUR
AU  - Meisel, A.
AU  - Kruger, D.H.
AU  - Bickle, T.A.
TI  - M.EcoP15I methylates the second adenine in its recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 3997
EP  - 3997
VL  - 19
AB  - The type III restriction/modification system EcoP15I recognizes the
AB  - non-palindromic sequence 5'-CAGCAG-3'.  The restriction enzyme cleaves the DNA
AB  - 25-27 bp to the right of the sequence as written.  The modification methylase
AB  - methylates one of the two adenine residues in the recognition sequence.
AB  - Attempts to determine which of the adenines is methylated by the enzyme were
AB  - foiled by the internal repeated symmetry of the recognition sequence.
ER  -

TY  - JOUR
AU  - Meisel, A.
AU  - Mackeldanz, P.
AU  - Bickle, T.A.
AU  - Kruger, D.H.
AU  - Schroeder, C.
TI  - Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis.
JO  - EMBO J.
PY  - 1995
SP  - 2958
EP  - 2966
VL  - 14
AB  - Type III restriction/modification systems recognize short non-palindromic sequences, only one
AB  - strand of which can be methylated. Replication of type III-modified DNA produces completely
AB  - unmethylated recognition sites which, according to classical mechanisms of restriction, should
AB  - be signals for restriction. We have shown previously that suicidal restriction by the type III
AB  - enzyme EcoP15I is prevented if all the unmodified sites are in the same orientation:
AB  - restriction by EcoP15I requires a pair of unmethylated, inversely oriented recognition sites.
AB  - We have now addressed the molecular mechanism of site orientation-specific DNA restriction.
AB  - EcoP15I is demonstrated to possess an intrinsic ATPase activity, the potential driving force
AB  - of DNA translocation. The ATPase activity is uniquely recognition site-specific, but
AB  - EcoP15I-modified sites also support the reaction. EcoP15I DNA restriction patterns are shown
AB  - to be predetermined by the enzyme-to-site ratio, in that site-saturating enzyme levels elicit
AB  - cleavage exclusively between the closest pair of head-to-head oriented sites. DNA restriction
AB  - is blocked by Lac repressor bound in the intervening sequence between the two EcoP15I sites.
AB  - These results rule out DNA looping and strongly suggest that cleavage is triggered by the
AB  - close proximity of two convergently tracking EcoP15I-DNA complexes.
ER  -

TY  - JOUR
AU  - Meister, G.E.
TI  - Non-associating heterodimeric DNA methyltransferases as a platform for developing designer methyltransferases.
JO  - Ph.D. Thesis, Johns Hopkins University, USA
PY  - 2009
AB  - The ability to site-specifically methylate a unique DNA sequence within a genome has numerous
AB  - potential uses including 1) a tool for the study of DNA methylation patterns, 2) a tool to
AB  - silence genes of interest, and 3) a potential gene therapy device to correct conditions caused
AB  - by hypomethylation. Current approaches include linking methyltransferases to DNA binding
AB  - domains to localize enzymes next to a target site. This approach has achieved site-biased
AB  - methylation, however the engineered methyltransferases are still active in the absence of
AB  - binding their intended target and methylate non-target sites. We demonstrate an alternative
AB  - strategy in which fragments of a DNA methyltransferase, compromised in their ability to
AB  - methylate DNA, are fused to two zinc fingers designed to bind 9 bp sites flanking a
AB  - methylation site. Using the naturally heterodimeric methyltransferase M.EcoHK31I, we have
AB  - demonstrated that this strategy can yield a methyltransferase capable of a high level of
AB  - methylation at the target site with undetectable levels of methylation at the non-target sites
AB  - in E. coli. The two zinc fingers acted synergistically to target methylation to the desired
AB  - site. However, some nontarget methylation could be detected at higher expression levels of the
AB  - zinc fingermethyltransferase indicating that further improvements will be necessary to attain
AB  - the desired exclusive target specificity.
ER  -

TY  - JOUR
AU  - Meister, G.E.
AU  - Chandrasegaran, S.
AU  - Ostermeier, M.
TI  - An engineered split M.Hhal-zinc finger fusion lacks the intended methyltransferase specificity.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2008
SP  - 226
EP  - 230
VL  - 377
AB  - The ability to site-specifically methylate DNA in vivo would have wide applicability to the
AB  - study of basic biomedical problems as well as
AB  - enable studies on the potential of site-specific DNA methylation as a
AB  - therapeutic strategy for the treatment of diseases. Natural DNA
AB  - methyltransferases lack the specificity required for these
AB  - applications. Nomura and Barbas [W. Nomura, C.F. Barbas 3rd, In vivo
AB  - site-specific DNA methylation with a designed sequence-enabled DNA
AB  - methylase, J. Am. Chem. Soc. 129 (2007) 8676-8677] have reported that
AB  - an engineered DNA methyltransferase comprised of fragments of M.Hhal
AB  - methyltransferase and zinc finger proteins has very high specificity
AB  - for the chosen target site. Our analysis of this engineered enzyme
AB  - shows that the fusion protein methylates target and non-target sites
AB  - with similar efficiency.
ER  -

TY  - JOUR
AU  - Meister, G.E.
AU  - Chandrasegaran, S.
AU  - Ostermeier, M.
TI  - Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 1749
EP  - 1759
VL  - 38
AB  - The ability to target methylation to specific genomic sites would further the study of DNA
AB  - methylation's biological role and potentially offer a
AB  - tool for silencing gene expression and for treating diseases involving
AB  - abnormal hypomethylation. The end-to-end fusion of DNA methyltransferases
AB  - to zinc fingers has been shown to bias methylation to desired regions.
AB  - However, the strategy is inherently limited because the methyltransferase
AB  - domain remains active regardless of whether the zinc finger domain is
AB  - bound at its cognate site and can methylate non-target sites. We
AB  - demonstrate an alternative strategy in which fragments of a DNA
AB  - methyltransferase, compromised in their ability to methylate DNA, are
AB  - fused to two zinc fingers designed to bind 9 bp sites flanking a
AB  - methylation target site. Using the naturally heterodimeric DNA
AB  - methyltransferase M.EcoHK31I, which methylates the inner cytosine of
AB  - 5'-YGGCCR-3', we demonstrate that this strategy can yield a
AB  - methyltransferase capable of significant levels of methylation at the
AB  - target site with undetectable levels of methylation at non-target sites in
AB  - Escherichia coli. However, some non-target methylation could be detected
AB  - at higher expression levels of the zinc finger methyltransferase
AB  - indicating that further improvements will be necessary to attain the
AB  - desired exclusive target specificity.
ER  -

TY  - JOUR
AU  - Meister, G.E.
AU  - Chandrasegaran, S.
AU  - Ostermeier, M.
TI  - BIOT 149-Heterodimeric DNA methyltransferases.
JO  - ACS Abstracts
PY  - 2008
SP  - 0
EP  - 0
VL  - 236
AB  - DNA methylation patterns play an important role in determining gene expression patterns. These
AB  - patterns are of particular interest in embryonic development and in cancer cells, which often
AB  - exhibit abnormal methylation patterns. The ability to control the activity and specificity of
AB  - DNA methyltransferases would have applications in the study of DNA methylation in cells, would
AB  - offer an avenue to control gene expression epigenetically and potentially would allow the
AB  - correction of abnormal methylation patterns for therapeutic purposes. Most known DNA
AB  - methyltransferases are encoded in a single polypeptide chain.  DNA methyltransferases in which
AB  - the activity is encoded by heterodimerizing peptides, offer unique platform for engineering
AB  - DNA methyltransferases with novel properties. The C5-methylcytosine methyltransferases M. AquI
AB  - and M. EcoHK31I each have alpha and beta peptide chains that associate to create a functional
AB  - enzyme. Methylation is not possible without the association of the two fragments.   Truncated
AB  - version of these fragments exhibit decreased association in vitro. We have used an in vivo
AB  - method to determine if the fragment's association is more or less sensitive to these
AB  - truncations in the cellular environment.  Select fragments formed the basis for designed
AB  - methyltransferase libraries that will methylate unique sites.
ER  -

TY  - JOUR
AU  - Meister, J.
AU  - MacWilliams, M.
AU  - Hubner, P.
AU  - Jutte, H.
AU  - Skrzypek, E.
AU  - Piekarowicz, A.
AU  - Bickle, T.A.
TI  - Macroevolution by transposition: drastic modification of DNA recognition by the type I restriction enzyme following Tn5 transposition.
JO  - EMBO J.
PY  - 1993
SP  - 4585
EP  - 4591
VL  - 12
AB  - We have characterized a novel mutant of EcoDXXI, a type IC DNA restriction and modification
AB  - (R-M) system, in which the specificity has been altered due to a Tn5 insertion into the middle
AB  - of hsdS, the gene which encodes the polypeptide that confers DNA sequence specificity to both
AB  - the restriction and the modification reactions. Like other type I enzymes, the wild type
AB  - EcoDXXI recognizes a sequence composed of two asymmetrical half sites separated by a spacer
AB  - region: TCA(N7)RTTC. Purification of the EcoDXXI mutant methylase and subsequent in vitro DNA
AB  - methylation assays identified the mutant recognition sequence as an interrupted palindrome,
AB  - TCA(N8)TGA, in which the 5' half site of the wild type site is repeated in inverse
AB  - orientation. The additional base pair in the non-specific spacer of the mutant recognition
AB  - sequence maintains the proper spacing between the two methylatable adenine groups. Sequencing
AB  - of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion occurred at
AB  - nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl-terminal DNA
AB  - binding domain which recognizes the 3' half of the EcoDXXI binding site. The truncated hsdS
AB  - gene still encodes both the amino-terminal DNA binding domain and the conserved repeated
AB  - sequence that defines the length of the recognition site spacer region. We propose that the
AB  - EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize its binding site.
AB  - The implications of this finding in terms of subunit interactions and the malleability of the
AB  - type I R-M systems will be discussed.
ER  -

TY  - JOUR
AU  - Mejean, A.
AU  - Mazmouz, R.
AU  - Mann, S.
AU  - Calteau, A.
AU  - Medigue, C.
AU  - Ploux, O.
TI  - The genome sequence of the cyanobacterium Oscillatoria sp. PCC 6506 reveals several gene clusters responsible for the biosynthesis of toxins  and secondary metabolites.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5264
EP  - 5265
VL  - 192
AB  - We report a draft sequence of the genome of Oscillatoria sp. PCC 6506, a cyanobacterium that
AB  - produces anatoxin-a and homoanatoxin-a, two
AB  - neurotoxins, and cylindrospermopsin, a cytotoxin. Beside the clusters of
AB  - genes responsible for the biosynthesis of these toxins, we have found
AB  - other clusters of genes likely involved in the biosynthesis of
AB  - not-yet-identified secondary metabolites.
ER  -

TY  - JOUR
AU  - Melcher, U.
AU  - Fletcher, J.
TI  - Inactivation of a Spiroplasma citri DNA modification methylase by a virus-like insertion element suggested by DNA sequence.
JO  - J. Plant Pathol.
PY  - 2000
SP  - 71
EP  - 71
VL  - 82
AB  - A partial SpV1-like viral DNA sequence in the Spiroplasma citri chromosome, the D3 progenitor,
AB  - was previously implicated as the donor of viral DNA sequences causing recombinational
AB  - instability of insert-containing virus vectors.  Re-examination of the D3 progenitor sequence
AB  - suggested that the virus-like sequence had inserted into a DNA adenine modification methylase
AB  - gene, inactivating it.  Comparison of the D3 progenitor sequence with SpV1-C74 revealed that
AB  - it was more closely related to this virus than to SpV1-R8A2 B and that the point of insertion
AB  - corresponded to an inverted terminal repeat similar to those terminating elements of the IS3
AB  - family of insertion sequences.  The transposases most similar to the SpV1-C74 is probably an
AB  - encapsilated insertion element.
ER  -

TY  - JOUR
AU  - Melcher, U.
AU  - Sha, Y.
AU  - Ye, F.
AU  - Fletcher, J.
TI  - Mechanisms of Spiroplasma genome variation associated with SpV1-like viral DNA inferred from sequence comparisons.
JO  - Microb. Comp. Genomics
PY  - 1999
SP  - 29
EP  - 46
VL  - 4
AB  - Genomes of Spiroplasma citri strains have rearranged frequently during their evolution, partly
AB  - due to multiple integrated sequences of spiroplasma viruses. To understand better the role of
AB  - viral sequences in genome evolution, we examined available nucleotide sequences of viruslike
AB  - elements in the S. citri chromosome. Comparison of integrated and nonintegrated sequences of
AB  - spiroplasma virus SpV1-C74 DNA suggested that it is an encapsidated form of the circular
AB  - transposition intermediate belonging to an insertion sequence (IS3) family member. One
AB  - SpV1-C74 viral DNA fragment was identified as interrupting the remains of a DNA adenine
AB  - modification methylase gene. A viral DNA insertion of SpV1-R8A2 B DNA had hallmarks of having
AB  - suffered an internal deletion by a site-specific recombination system. Homologous
AB  - recombination likely was responsible for several deletions within viral DNA. A homologous
AB  - recombination event was inferred between part of a viral DNA insertion and a similar
AB  - chromosomal sequence. Dispersed sequences from SpV1-like C4 open reading frames (ORFs) were
AB  - identified as involved in a complex deletion-inversion event. Thus, SpV1-like sequences likely
AB  - have altered spiroplasma genomes by inserting within active genes, destroying their function,
AB  - by providing targets for site-specific recombination, by mediating deletions of sequences
AB  - adjacent to their integration sites, and by providing targets for homologous recombination,
AB  - leading to inversions.
ER  -

TY  - JOUR
AU  - Mell, J.C.
AU  - Sinha, S.
AU  - Balashov, S.
AU  - Viadas, C.
AU  - Grassa, C.J.
AU  - Ehrlich, G.D.
AU  - Nislow, C.
AU  - Redfield, R.J.
AU  - Garmendia, J.
TI  - Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media.
JO  - Genome Announcements
PY  - 2014
SP  - e01245
EP  - e01214
VL  - 2
AB  - Originally isolated from a pediatric patient with otitis media, Haemophilus influenzae strain
AB  - 375 (Hi375) has been extensively studied as a model system for
AB  - intracellular invasion of airway epithelial cells and other pathogenesis traits.
AB  - Here, we report its complete genome sequence and methylome.
ER  -

TY  - JOUR
AU  - Mellbye, B.L.
AU  - Davis, E.W.I.I.
AU  - Spieck, E.
AU  - Chang, J.H.
AU  - Bottomley, P.J.
AU  - Sayavedra-Soto, L.A.
TI  - Draft Genome Sequence of Nitrobacter vulgaris Strain Ab1, a Nitrite-Oxidizing Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00290
EP  - e00217
VL  - 5
AB  - Here, we present the 3.9-Mb draft genome sequence of Nitrobacter vulgaris strain  Ab1, which
AB  - was isolated from a sewage system in Hamburg, Germany. The analysis of
AB  - its genome sequence will contribute to our knowledge of nitrite-oxidizing
AB  - bacteria and acyl-homoserine lactone quorum sensing in nitrifying bacteria.
ER  -

TY  - JOUR
AU  - Mellmann, A.
AU  - Spindler-Raffel, E.
AU  - Bletz, S.
AU  - Prax, M.
AU  - Bekeredjian-Ding, I.
TI  - Genome Sequences of the First WHO Repository of Platelet Transfusion-Relevant Bacterial Reference Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00001
EP  - e00017
VL  - 5
AB  - To develop novel techniques for improving blood safety, dedicated bacterial strains, which are
AB  - able to persist and to proliferate in blood platelet
AB  - concentrates, are needed. Here, we present draft genome sequences of the four
AB  - bacterial strains approved for the first WHO repository of platelet
AB  - transfusion-relevant bacterial reference strains.
ER  -

TY  - JOUR
AU  - Melnik, A.I.
AU  - Rebentish, B.A.
AU  - Bolotin, A.V.
AU  - Mendzhul, M.I.
TI  - Two site-specific endonucleases of the Cyanobacterium Nostoc linckia.
JO  - Mikrobiol. Zh.
PY  - 1991
SP  - 24
EP  - 28
VL  - 53
AB  - Two restrictases Nli387/7I and Nli387/7II have been isolated from
AB  - cyanobacterium Nostoc linckia using chromatography on phosphocellulose, <Mono
AB  - Q> column, and heparin sepharose 4B.  The preparations are described by the
AB  - method of electrophoresis in polyacrylamide gels under denaturating conditions.
AB  - The catalytic properties of the restrictases have been determined:  optimal
AB  - pH 9.0 - 9.5, optimal concentration of Na+ - 5 mM, that of Mg2+ - 6 mM, optimal
AB  - temperature - 37C.  The isolated enzymes are isoschizomers of the restrictases
AB  - AvaI and AvaII.  The point of cutting is determined for enzyme Nli387/7 I.  It
AB  - is shown that restrictase Nli387/7 I is a false isoschizomer of AvaI.
ER  -

TY  - JOUR
AU  - Melton, E.D.
AU  - Sorokin, D.Y.
AU  - Overmars, L.
AU  - Chertkov, O.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Ivanova, N.
AU  - Shapiro, N.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Lapidus, A.L.
AU  - Muyzer, G.
TI  - Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 67
EP  - 67
VL  - 11
AB  - Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic
AB  - haloalkaliphile isolated from a composite sediment sample of eight hypersaline
AB  - alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D.
AB  - alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae
AB  - within the Deltaproteobacteria. Here we report its genome sequence, which
AB  - contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2(T) is adapted to survive
AB  - under highly alkaline and moderately saline conditions and therefore, is relevant
AB  - to the biotechnology industry and life under extreme conditions. For these
AB  - reasons, D. alkaliphilus AHT2(T) was sequenced by the DOE Joint Genome Institute
AB  - as part of the Community Science Program.
ER  -

TY  - JOUR
AU  - Melton, E.D.
AU  - Sorokin, D.Y.
AU  - Overmars, L.
AU  - Lapidus, A.L.
AU  - Pillay, M.
AU  - Ivanova, N.
AU  - Del Rio, T.G.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
AU  - Muyzer, G.
TI  - Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive  sulfidogenic polyextremophile.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 57
EP  - 57
VL  - 12
AB  - Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately
AB  - salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake
AB  - sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC
AB  - content, within the phylum Firmicutes. Here we report its draft genome sequence,
AB  - which consists of 34 contigs with a total sequence length of 3.12 Mbp. D.
AB  - alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as
AB  - part of the Community Science Program due to its relevance to bioremediation and
AB  - biotechnological applications.
ER  -

TY  - JOUR
AU  - Mendez-Tenorio, A.
AU  - Larios-Serrato, V.
AU  - Olguin-Ruiz, G.E.
AU  - Sanchez-Vallejo, C.J.
AU  - Torres-Lopez, R.C.
AU  - Aviles-Jimenez, F.
AU  - Camorlinga-Ponce, M.
AU  - Torres, J.
TI  - Genome Sequence of a Helicobacter pylori Strain Isolated from a Mexican Patient with Intestinal Gastric Cancer.
JO  - Genome Announcements
PY  - 2014
SP  - e01214
EP  - e01213
VL  - 2
AB  - Helicobacter pylori strains are the major risk factor for gastric cancer. Strains vary in
AB  - their content of disease-associated genes, so genome-wide analysis of
AB  - cancer-isolated strains will help elucidate their pathogenesis and genetic
AB  - diversity. We present the draft genome sequence of H. pylori isolated from a
AB  - Mexican patient with intestinal gastric cancer.
ER  -

TY  - JOUR
AU  - Mendoza, L.M.
AU  - Saavedra, L.
AU  - Raya, R.R.
TI  - Draft Genome Sequence of Oenococcus oeni Strain X2L (CRL1947), Isolated from Red  Wine of Northwest Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e01376
EP  - e01314
VL  - 3
AB  - We report the draft genome sequence of Oenococcus oeni strain X2L, a potential starter culture
AB  - of malolactic fermentation, isolated from Malbec wine of
AB  - Argentina. Genes encoding for enzymes involved in the metabolism of malate,
AB  - citrate, and nitrogen compounds, as well as aroma compounds, were found in this
AB  - genome, showing its ability to improve the sensorial characteristics of wines.
ER  -

TY  - JOUR
AU  - Mendoza-Olazaran, S.
AU  - Garcia-Mazcorro, J.F.
AU  - Morfin-Otero, R.
AU  - Villarreal-Trevino, L.
AU  - Camacho-Ortiz, A.
AU  - Rodriguez-Noriega, E.
AU  - Bocanegra-Ibarias, P.
AU  - Maldonado-Garza, H.J.
AU  - Dowd, S.E.
AU  - Garza-Gonzalez, E.
TI  - Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus  cohnii isolated from human patients.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 49
EP  - 49
VL  - 12
AB  - Herein, we report the draft-genome sequences and annotation of two opportunistic  pathogenic
AB  - strains of Staphylococcus cohnii isolated from humans. One strain
AB  - (SC-57) was isolated from blood from a male patient in May 2006 and the other
AB  - (SC-532) from a catheter from a male patient in June 2006. Similar to other
AB  - genomes of Staphylococcus species, most genes (42%) of both strains are involved
AB  - in metabolism of amino acids and derivatives, carbohydrates and proteins. Eighty
AB  - (4%) genes are involved in virulence, disease, and defense and both species show
AB  - phenotypic low biofilm production and evidence of increased antibiotic resistance
AB  - associated to biofilm production. From both isolates, a new Staphylococcal
AB  - Cassette Chromosome mec was detected: mec class A, ccr type 1. This is the first
AB  - report of whole genome sequences of opportunistic S. cohnii isolated from human
AB  - patients.
ER  -

TY  - JOUR
AU  - Mendzhul, M.I.
AU  - Moshinsky, I.D.
AU  - Syrchin, S.A.
TI  - Endonuclease activity in cyanobacteria Anabaena variabilis and Plectonema boryanum involving restriction endonuclease and nuclease.
JO  - Mikrobiol. Zh.
PY  - 1999
SP  - 10
EP  - 14
VL  - 61
AB  - Site-specific endodeoxyribonuclease activity was found in crude cell-free extracts of
AB  - cyanobacteria Plectonema boryanum CALU 465 and
AB  - Plectonema edaphycum CALU 262. Cyanobacterium Anabaena variabilis CALU
AB  - 458 was shown to possess restriction site-specific endonuclease Ava458I
AB  - which was probably an isoschizomer of CfrI with the recognition site
AB  - PyGGCCPu.
ER  -

TY  - JOUR
AU  - Mendzhul, M.I.
AU  - Syrchin, S.A.
AU  - Averkiev, A.A.
AU  - Rebentish, B.A.
TI  - The way of defense of cyanophage LPP-3 DNA against restriction-modification systems in the cells of the cyanobacterium Plectonema boryanum.
JO  - Biopol. Kletka
PY  - 1993
SP  - 54
EP  - 61
VL  - 9
AB  - The HPLC method was used to study some peculiarities of the DNA composition of the
AB  - cyanobacterium Plectonema boryanum and cyanophage LPP-3. Analysis of the elution profile of
AB  - the products of DNA acid hydrolysis allow the identification in P. boryanum DNA, in addition
AB  - to the canonical bases, of the presence of 4.5% N-6-methyladenine and 1.2% 5-methyl-cytosine;
AB  - DNA from LPP-3 has 0.8% 5-methycytosine and no N-6-methyladenine. The presence of
AB  - 5-methylcytosine was detected only by the application of a modified hydrolysis method using
AB  - HF. Restriction endonuclease isoschizomers, whose hydrolysis of DNA depends on the presence of
AB  - methylated bases in the recognition sites, were used to detect site-specific methylation. The
AB  - comparison of the products of the DNA LPP-3 and P. boryanum fermentative hydrolysis by MspI
AB  - and HpaII; Sau3AI, MboI and DpnI; Apyl and MvaI restrictases enabled the determination that
AB  - DNA from LPP-3 and P. boryanum has a high degree of methylation of the inner cytosine in
AB  - CC(A/T)GG sequences and in P. boryanum the adenine in the GATC site; CCGG sites were not
AB  - methylated in either DNA. It is concluded that dam- and dcm-like modification systems are in
AB  - P. boryanum. The defense of viral DNA against host R-M systems occurs by cytosine methylation
AB  - in the sequence CmC(A/T)GG and counter-selection at BamHI sites.
ER  -

TY  - JOUR
AU  - Mendzhul, M.I.
AU  - Syrchin, S.A.
AU  - Rebentish, B.A.
AU  - Averkiev, A.A.
AU  - Busakhina, I.V.
TI  - The resistance of the DNA of cyanophage LPP-3 to the action of different restriction endonucleases.
JO  - Mikrobiol. Zh.
PY  - 1993
SP  - 47
EP  - 53
VL  - 55
AB  - Data on the study of structural peculiarities of cyanophage LPP-3 DNA are presented in the
AB  - work. The length of cyanophage DNA calculated by means of the enzymatic hydrolysis by
AB  - restrictases is 40+/-3.5 thousand base pairs. Cyanophage LPP-3 DNA was hydrolysed by more than
AB  - 50 different restrictases. As a result of screening it was found out that the great number of
AB  - restrictases, which recognized hexanucleotide sequences did not hydrolyse DNA of cyanophage
AB  - LPP-3. A considerable deviation of the number of the observed sites of restriction from their
AB  - theoretically expected number for restrictases, which recognized hexanucleotide sequences did
AB  - not hydrolyse DNA of cyanophage LPP-3. A considerable deviation of the number of the observed
AB  - sites of restriction from their theoretically expected number for restrictases HaeIII and
AB  - Cfr131 was established. Restrictases-isoschizomers with different sensitivity to the
AB  - methylation of the recognition sites -- MspI, HpaII and Sau3A, MboI and DpnI were used to
AB  - check the availability of methylated bases in LPP-3 DNA. Absence of methylated adenine in the
AB  - site GATC and methylated cytosine in the second position of the site CCGG were established.
AB  - The results obtained permit supposing that the expressed counterselection by the sites of
AB  - recognition of many restriction endonucleases takes place in cyanophage LPP-3 DNA. It is
AB  - supposed that apparently, this method of protection of its genome in LPP-3 is one of most
AB  - important but the inconsiderable percentage of site-specific methylation of the virus DNA
AB  - cannot be completely excluded.
ER  -

TY  - JOUR
AU  - Meneghel, J.
AU  - Dugat-Bony, E.
AU  - Irlinger, F.
AU  - Loux, V.
AU  - Vidal, M.
AU  - Passot, S.
AU  - Beal, C.
AU  - Layec, S.
AU  - Fonseca, F.
TI  - Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk.
JO  - Genome Announcements
PY  - 2016
SP  - e00052
EP  - e00016
VL  - 4
AB  - Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a lactic acid bacterium widely
AB  - used for the production of yogurt and cheeses. Here, we report
AB  - the genome sequence of L. bulgaricus CFL1 to improve our knowledge on its
AB  - stress-induced damages following production and end-use processes.
ER  -

TY  - JOUR
AU  - Menendez, C.
AU  - Bournat, J.C.
AU  - Ramirez, J.L.
TI  - Cloning and overexpression of EcoRI methylase.
JO  - Interciencia
PY  - 1989
SP  - 37
EP  - 40
VL  - 14
AB  - The author cloned a HindIII fragment of pMB3 plasmid containing part of the coding region for
AB  - EcoRI endonuclease, and the entire sequence for EcoRI methylase downstream of the PL promoter
AB  - of the expression vector pcp 40.  The recombinant was introduced into a lysogenic E. coli
AB  - strain, harboring a lambda phage with a temperature sensitive mutation for the repressor gene
AB  - (c1857). After heat induction, a protein band of apparent molecular mass of 39 Kd, increased
AB  - continuously during 8 hours.  After four hours of thermal induction, the band represented
AB  - nearly 50% of the soluble proteins observed by gel electrophoresis.  At the maximum induction
AB  - time, the methylase activity registered a 15 fold increment over the non-induced state.
ER  -

TY  - JOUR
AU  - Meng, J.
AU  - Sun, X.
AU  - Li, S.
AU  - Liang, H.
TI  - Draft Genome Sequence of Paenarthrobacter nicotinovorans Hce-1.
JO  - Genome Announcements
PY  - 2017
SP  - e00727
EP  - e00717
VL  - 5
AB  - Paenarthrobacter nicotinovorans Hce-1 is a Gram-positive obligate aerobe actinomycete. We
AB  - report here the complete genome sequence of this organism. The
AB  - genome has a length of 4,174,362 bp and contains 4,568 protein-coding genes, 64
AB  - tRNA operons, and 22 rRNA operons. Its GC content in the gene region is 63.4%.
ER  -

TY  - JOUR
AU  - Meng, X.
AU  - Bertani, I.
AU  - Abbruscato, P.
AU  - Piffanelli, P.
AU  - Licastro, D.
AU  - Wang, C.
AU  - Venturi, V.
TI  - Draft Genome Sequence of Rice Endophyte-Associated Isolate Kosakonia oryzae KO348.
JO  - Genome Announcements
PY  - 2015
SP  - e00594
EP  - e00515
VL  - 3
AB  - Kosakonia oryzae KO348 is an endophytic and plant growth-promoting strain isolated from the
AB  - roots of rice in Italy. Here, we report the draft genome
AB  - sequence of Kosakonia oryzae KO348.
ER  -

TY  - JOUR
AU  - Meng, X.
AU  - Cai, W.
AU  - Schwartz, D.C.
TI  - Inhibition of restriction endonuclease activity by DNA binding fluorochromes.
JO  - J. Biomol. Struct. Dyn.
PY  - 1996
SP  - 945
EP  - 951
VL  - 13
AB  - Activity of type II restriction endonucleases is affected by many common factors including
AB  - buffer composition and sequences flanking the recognition site.  The successful development of
AB  - Optical Mapping relied on optimization of light microscope-based imaging of fluorescently
AB  - labeled DNA molecules during restriction endonuclease digestion.  Little was known about the
AB  - effects of commonly used DNA-fluorochromes on restriction endonuclease activity.  Thus, we
AB  - developed an enzyme activity assay using lambda bacteriophage DNA or adenovirus-2 DNA to
AB  - evaluate the effects of five DNA binding fluorochromes (4'-6-daimidine-2-phenylindole (DAPI),
AB  - ethidium bromide (EtdBr), ethidium bromide homodimer (EthD-1), bis-benzimide (H33258) and
AB  - benzothiazolium-4-quinolinium dimer (TOTO-1)) on the enzymatic activities of eleven type II
AB  - restriction endonucleases (AscI, CspI, DraI, EcoRI, HhaI, HindIII, NotI, RsrII, SfiI, SgrAI
AB  - and SmaI).  We found that the minor groove binding fluorochrome, DAPI, did not measurably
AB  - inhibit activity of this group, with the exception of DraI.  Similarly, another minor groove
AB  - binding fluorochrome H33258 inhibited DraI and NotI (slightly).  The three intercalating
AB  - fluorochromes EtdBr, EthD-1 and TOTO-1, however, variably inhibited the other enzymes.  Since
AB  - beta-mercaptoethanol (BME) is used to discourage photodamage of stained DNA molecules, we also
AB  - assessed its effect on restriction endonuclease activity.  Interestingly, DraI, EcoRI, HhaI,
AB  - HindIII, SfiI and SmaI retained full activities at high concentration of BME (5%), but AscI,
AB  - CspI, NotI, RsrII and SgrAI showed varying sensitivities to the BME.  Isoschizomers CspI and
AB  - RsrII behaved differently to both fluorochromes and BME.  The results presented here should
AB  - provide a basis for further development of new Optical Mapping-based techniques requiring
AB  - fluorescence labeling of other actively imaged enzymatic reactions.
ER  -

TY  - JOUR
AU  - Meramveliotaki, C.
AU  - Kotsifaki, D.
AU  - Androulaki, M.
AU  - Hountas, A.
AU  - Eliopoulos, E.
AU  - Kokkinidis, M.
TI  - Purification, crystallization, x-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2007
SP  - 836
EP  - 838
VL  - 63
AB  - The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type
AB  - homodimeric form into the enzymatically
AB  - active single-chain variant scPvuII by tandemly joining the two
AB  - subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is
AB  - suitable for the development of programmed restriction endonucleases
AB  - for highly specific DNA cleavage, was purified and crystallized. The
AB  - crystals diffract to a resolution of 2.35 angstrom and belong to space
AB  - group P4(2), with unit-cell parameters a = b = 101.92, c = 100.28
AB  - angstrom and two molecules per asymmetric unit. Phasing was
AB  - successfully performed by molecular replacement.
ER  -

TY  - JOUR
AU  - Mercante, J.W.
AU  - Morrison, S.S.
AU  - Desai, H.P.
AU  - Raphael, B.H.
AU  - Winchell, J.M.
TI  - Genomic Analysis Reveals Novel Diversity among the 1976 Philadelphia Legionnaires' Disease Outbreak Isolates and Additional ST36 Strains.
JO  - PLoS ONE
PY  - 2016
SP  - E0164074
EP  - E0164074
VL  - 11
AB  - Legionella pneumophila was first recognized as a cause of severe and potentially
AB  - fatal pneumonia during a large-scale outbreak of Legionnaires' disease (LD) at a
AB  - Pennsylvania veterans' convention in Philadelphia, 1976. The ensuing
AB  - investigation and recovery of four clinical isolates launched the fields of
AB  - Legionella epidemiology and scientific research. Only one of the original
AB  - isolates, "Philadelphia-1", has been widely distributed or extensively studied.
AB  - Here we describe the whole-genome sequencing (WGS), complete assembly, and
AB  - comparative analysis of all Philadelphia LD strains recovered from that
AB  - investigation, along with L. pneumophila isolates sharing the Philadelphia
AB  - sequence type (ST36). Analyses revealed that the 1976 outbreak was due to
AB  - multiple serogroup 1 strains within the same genetic lineage, differentiated by
AB  - an actively mobilized, self-replicating episome that is shared with L.
AB  - pneumophila str. Paris, and two large, horizontally-transferred genomic loci,
AB  - among other polymorphisms. We also found a completely unassociated ST36 strain
AB  - that displayed remarkable genetic similarity to the historical Philadelphia
AB  - isolates. This similar strain implies the presence of a potential clonal
AB  - population, and suggests important implications may exist for considering
AB  - epidemiological context when interpreting phylogenetic relationships among
AB  - outbreak-associated isolates. Additional extensive archival research identified
AB  - the Philadelphia isolate associated with a non-Legionnaire case of "Broad Street
AB  - pneumonia", and provided new historical and genetic insights into the 1976
AB  - epidemic. This retrospective analysis has underscored the utility of
AB  - fully-assembled WGS data for Legionella outbreak investigations, highlighting the
AB  - increased resolution that comes from long-read sequencing and a sequence
AB  - type-matched genomic data set.
ER  -

TY  - JOUR
AU  - Mercante, J.W.
AU  - Morrison, S.S.
AU  - Raphael, B.H.
AU  - Winchell, J.M.
TI  - Complete Genome Sequences of the Historical Legionella pneumophila Strains OLDA and Pontiac.
JO  - Genome Announcements
PY  - 2016
SP  - e00866
EP  - e00816
VL  - 4
AB  - Here, we report the complete genome sequences of Legionella pneumophila serogroup 1 strains
AB  - OLDA and Pontiac, which predate the 1976 Philadelphia Legionnaires'
AB  - disease outbreak. Strain OLDA was isolated in 1947 from an apparent sporadic
AB  - case, and strain Pontiac caused an explosive outbreak at a Michigan health
AB  - department in 1968.
ER  -

TY  - JOUR
AU  - Mercier, C.
AU  - Lossouarn, J.
AU  - Haverkamp, T.
AU  - Bienvenu, N.
AU  - Godfroy, A.
AU  - Cueff-Gauchard, V.
AU  - Geslin, C.
AU  - Nesbo, C.
TI  - Draft Genome Sequences of Two Marinitoga camini Isolates Producing Bacterioviruses.
JO  - Genome Announcements
PY  - 2016
SP  - e01261
EP  - e01216
VL  - 4
AB  - Here, we present the draft genome sequences of two thermophilic Marinitoga strain members of
AB  - the Thermotogales order, Marinitoga camini DV1155 and Marinitoga
AB  - camini DV1197. These strains were isolated from deep-sea hydrothermal vents of
AB  - the Mid-Atlantic Ridge.
ER  -

TY  - JOUR
AU  - Merga, J.Y.
AU  - Winstanley, C.
AU  - Williams, N.J.
AU  - Yee, E.
AU  - Miller, W.G.
TI  - Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h.
JO  - Genome Announcements
PY  - 2013
SP  - e00655
EP  - e00613
VL  - 1
AB  - Arcobacter butzleri strain 7h1h was isolated in the United Kingdom from the feces of a
AB  - clinically healthy dairy cow. The genome of this isolate was sequenced to
AB  - completion. Here, we present the annotation and analysis of the completed 7h1h
AB  - genome, along with a comparison of this genome to the existing A. butzleri
AB  - genomes.
ER  -

TY  - JOUR
AU  - Merhej, V.
AU  - Armougom, F.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Genome Sequence of Lactobacillus ingluviei, a Bacterium Associated with Weight Gain in Animals.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5697
EP  - 5697
VL  - 194
AB  - We report the draft genome sequence of Lactobacillus ingluviei strain Autruche 4  (CSURP209)
AB  - isolated from an ostrich. L. ingluviei is associated with weight gain
AB  - in mice. This genome sequence may help us understand the obesity-induced
AB  - mechanisms of intestinal bacteria.
ER  -

TY  - JOUR
AU  - Merhej, V.
AU  - Croce, O.
AU  - Robert, C.
AU  - Rolain, J.M.
AU  - Raoult, D.
TI  - Genome Sequence of Bartonella rattaustraliani, a Bacterium Isolated from an Australian Rat.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7012
EP  - 7012
VL  - 194
AB  - Bartonella rattaustraliani is a facultative intracellular bacterium isolated from the blood of
AB  - a Rattus sp. in Australia. The present study reports the draft
AB  - genome of B. rattaustraliani strain AUST/NH4 (CSUR B609(T)).
ER  -

TY  - JOUR
AU  - Merhej, V.
AU  - Croce, O.
AU  - Robert, C.
AU  - Rolain, J.M.
AU  - Raoult, D.
TI  - Genome Sequence of Bartonella rattimassiliensis, a Bacterium Isolated from European Rattus norvegicus.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7013
EP  - 7013
VL  - 194
AB  - Bartonella rattimassiliensis is a facultative intracellular bacterium isolated from the blood
AB  - of Rattus norvegicus in Marseille. The present study reports the
AB  - draft genome of B. rattimassiliensis strain 15908 (CIP 107705(T)).
ER  -

TY  - JOUR
AU  - Merhej, V.
AU  - Pfleiderer, A.
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Michelle, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 63
EP  - 63
VL  - 10
AB  - Clostridium ihumii strain AP5(T) sp. nov. is a new species within the genus Clostridium. This
AB  - strain, whose genome is described here, was isolated from the stool sample of a 21-year-old
AB  - French Caucasian female with anorexia nervosa. C. ihumii is a Gram-positive, anaerobic
AB  - bacillus. Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 4,433,668 bp long genome contains 4,076 protein-coding and 85 RNA
AB  - genes, including 9 rRNA genes.
ER  -

TY  - JOUR
AU  - Merino, A.
AU  - Gamba, G.
TI  - Biologia molecular en medicina.  II. Enzimas de restriccion.
JO  - Rev. Invest. Clin.
PY  - 1996
SP  - 159
EP  - 163
VL  - 48
ER  -

TY  - JOUR
AU  - Merino, M.
AU  - Alvarez-Fraga, L.
AU  - Gomez, M.J.
AU  - Aransay, A.M.
AU  - Lavin, J.L.
AU  - Chaves, F.
AU  - Bou, G.
AU  - Poza, M.
TI  - Complete Genome Sequence of the Multiresistant Acinetobacter baumannii Strain AbH12O-A2, Isolated during a Large Outbreak in Spain.
JO  - Genome Announcements
PY  - 2014
SP  - e01182
EP  - e01114
VL  - 2
AB  - We report the complete genome sequence of Acinetobacter baumannii strain AbH12O-A2, isolated
AB  - during a large outbreak in Spain. The genome has 3,875,775 bp
AB  - and 3,526 coding sequences, with 39.4% G+C content. The availability of this
AB  - genome will facilitate the study of the pathogenicity of the Acinetobacter
AB  - species.
ER  -

TY  - JOUR
AU  - Merkiene, E.
AU  - Klimasauskas, S.
TI  - Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 307
EP  - 315
VL  - 33
AB  - DNA methylation plays important roles via regulation of numerous cellular mechanisms in
AB  - diverse organisms, including humans. The paradigm bacterial methyltransferase (MTase) HhaI
AB  - (M.HhaI) catalyzes the transfer of a methyl group from the cofactor S-adenosyl-L-methionine
AB  - (AdoMet) onto the target cytosine in DNA, yielding 5-methylcytosine and
AB  - S-adenosyl-L-homocysteine (AdoHcy). The turnover rate (kcat) of M.HhaI, and the other two
AB  - cytosine-5 MTases examined, is limited by a step subsequent to methyl transfer; however, no
AB  - such step has so far been identified. To elucidate the role of cofactor interactions during
AB  - catalysis, eight mutants of Trp41, which is located in the cofactor binding pocket, were
AB  - constructed and characterized. The mutants show full proficiency in DNA binding and
AB  - base-flipping, and little variation is observed in the apparent methyl transfer rate kchem as
AB  - determined by rapid-quench experiments using immobilized fluorescent-labeled DNA. However, the
AB  - Trp41 replacements with short side chains substantially perturb cofactor binding (100-fold
AB  - higher KD(AdoMet)and KM(AdoMet))leading to a faster turnover of the enzyme (10-fold higher
AB  - kcat). Our analysis indicates that the rate-limiting breakdown of a long-lived ternary product
AB  - complex is initiated by the dissociation of AdoHcy or the opening of the catalytic loop in the
AB  - enzyme.
ER  -

TY  - JOUR
AU  - Merkiene, E.
AU  - Lukinavicius, G.
AU  - Klimasauskas, S.
TI  - Synergy of substrate binding, base flipping and catalytic loop motions in a DNA methyltransferase.
JO  - Eur. Biophys. J.
PY  - 2005
SP  - 617
EP  - 617
VL  - 34
AB  - The HhaI methyltransferase transfers a methyl group from cofactor AdoMet onto its target
AB  - cytosine residue in DNA.  Crystal structures revealed that M.HhaI flips its target base out of
AB  - the DNA helix.  This transition is accompanied by a massive motion of a loop in the protein
AB  - which locks the flipped out base in the catalytic site.  We used fluorescence of a unique
AB  - tryptophan residue to specifically monitor cofactor binding.  Equilibrium binding studies
AB  - revealed a highly improved binding of the cofactor AdoMet and the reaction product AdoHcy in
AB  - the presence of specific DNA.  No such effect was observed with non-specific DNA in the case
AB  - of AdoMet, but surprisingly, led to a substantial drop in binding affinity in the case of
AB  - AdoHcy!  To elucidate the role of the catalytic loop in substrate binding we constructed two
AB  - variants of M.HhaI in which large segments of the catalytic loop were entirely removed.
AB  - Although the binary interactions with the substrates and base flipping was almost unaffected
AB  - by the deletions, the synergy of substrate binding in the ternary complexes were completely
AB  - lost.  To 'visualize' the loop motions directly during the reaction cycle we prepared a
AB  - series of double mutants in which a unique tryptophan residue was placed in selected positions
AB  - on the mobile catalytic loop.  Single turnover stopped flow kinetic studies of the mutants
AB  - revealed two conformational transitions of the loop which coincide with the formation of the
AB  - tight ternary complex and the release of products.
ER  -

TY  - JOUR
AU  - Merkiene, E.
AU  - Vilkaitis, G.
AU  - Klimasauskas, S.
TI  - Coexistence of single-strand and double-strand DNA cytosine-N4-methyltransferases in the BcnI restriction-modification system.
JO  - Biologija
PY  - 1997
SP  - 5
EP  - 8
VL  - 1
AB  - Sequence analysis of the BcnI RM system, besides the previously characterized restriction
AB  - endonuclease (bcnIR) and cytosine-N4-methyltransferase (bcnIB), revealed the presence of a
AB  - large open reading frame potentially encoding a second cytosine-N4-methyltransferase (bcnIA).
AB  - The bcnIA gene, when subcloned in E. coli on the pUC19 vector, rendered protection of the
AB  - 5'CC(C/G)GG-3' sites against cleavage by the cognate BcnI endonuclease.  The two
AB  - methyltransferases were partially purified, and their activities in vitro were compared using
AB  - various DNA substrates.  Both enzymes act on 5'-CC(C/G)GG-3' sites in double-stranded DNA,
AB  - however, BcnIA can also, at a comparable rate, modify the specific targets in single-stranded
AB  - DNA.  Biological significance of the presence of two distinct methyltransferases in the BcnI
AB  - RM system is discussed.
ER  -

TY  - JOUR
AU  - Merkiene, E.
AU  - Vilkaitis, G.
AU  - Klimasauskas, S.
TI  - A pair of single-strand and double-strand DNA cytosine-N4 methyltransferases from Bacillus centrosporus.
JO  - Biol. Chem.
PY  - 1998
SP  - 569
EP  - 571
VL  - 379
AB  - Sequence analysis of the BcnI restriction-modification system revealed the presence of an open
AB  - reading frame encoding a second cytosine-N4 methyltransferase, M.BcnIA, in the vicinity of the
AB  - genes specifying the previously characterized cytosine-N4 methyltransferase M.BcnIB and
AB  - restriction endonuclease R.BcnI.  Both methyltransferases were purified from the E. coli cells
AB  - expressing the individual genes, and their enzymatic efficiencies in vitro were compared with
AB  - a variety of DNA substrates.  Both enzymes act on 5'-CC(C/G)GG-3' sites in double-stranded
AB  - DNA, however, M.BcnIA can also, with a comparable efficiency, modify the specific targets in
AB  - single-stranded DNA.  The biological significance of the presence of the tandem
AB  - methyltransferases in the BcnI system is discussed.
ER  -

TY  - JOUR
AU  - Merkiene, E.
AU  - Weinhold, E.
AU  - Klimasauskas, S.
TI  - Kinetics of cofactor binding and catalytic loop movements of HhaI methyltransferase.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A464
EP  - A464
VL  - 28
AB  - HhaI methyltransferase (M.HhaI) flips its target cytosine out of the DNA helix and into a
AB  - catalytic site in the enzyme.  This conformational transition of bound DNA is accompanied by a
AB  - large movement of the catalytic loop (over 20 Angstrom) in the enzyme itself.  Our studies
AB  - concentrated on the motions of the catalytic loop and interaction between M.HhaI and its
AB  - cofactor S-adenosyl-L-methionine (AdoMet) which serves as the methyl group donor in the MTase
AB  - reaction.  We found that the intrinsic fluorescence of a unique tryptophan residue (W41) is
AB  - significantly quenched upon binding of cofactor, but is unaffected upon binding of DNA.  A
AB  - series of kinetic association and equilibrium binding studies in the presence of various DNA
AB  - substrates permitted direct determination of kinetic parameters for cofactor binding.  We find
AB  - that non-specific DNA causes a substantial decrease in the affinity of the enzyme toward the
AB  - product AdoHcy but not toward cofactor AdoMet, which suggests a mechanism for cofactor
AB  - reloading during diffusion of MTase over regions of non-specific DNA.  Single-turnover
AB  - experiments revealed a concentration independent transient (2 s^-1) which we tentatively
AB  - attribute to the aforementioned conformational rearrangement of the catalytic loop.  To
AB  - 'visualize' the loop motions directly we prepared a series of double mutants in which the
AB  - unique Trp was placed in selected positions on the mobile catalytic loop.  Preliminary
AB  - characterization of the mutant proteins indicates that they are suitable for direct kinetic
AB  - measurement of conformational transitions in the catalytic loop.  Kinetic analysis of these
AB  - transitions using global fitting and simulation is now underway.
ER  -

TY  - JOUR
AU  - Merkl, R.
AU  - Fritz, H.J.
TI  - Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in Haemophilus influenzae Rd.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 4146
EP  - 4151
VL  - 24
AB  - Markov chain analysis of the Haemophilus influenzae Rd genome reveals striking
AB  - under-representation of three palindromic tetranucleotide strings (CCGG, GGCC and CATG),
AB  - accompanied by over-representation of six tetranucleotide strings that are derived from the
AB  - former by exchanging strand location of the two residues making up a G/C nucleotide pair at
AB  - the terminal palindrome position.  Constraints are outlined for a molecular model able to
AB  - explain the phenomenon as the result of sequence-targeted, enzyme-driven G/C to C/G
AB  - transversion mutagenesis.  Possible participation in the process by components of known DNA
AB  - mismatch repair or restriction/modification systems (in particular, cytosine methylation) is
AB  - discussed.  The effect widens the spectrum of enzyme-driven, specific mutagenesis beyond the
AB  - formerly described C/G to T/A transition (VSP repair of Escherichia coli).  Potential
AB  - evolutionary benefits of enzymatic pathways of specific mutagenesis can be envisioned.
ER  -

TY  - JOUR
AU  - Merkl, R.
AU  - Kroeger, M.
AU  - Rice, P.
AU  - Fritz, H.-J.
TI  - Statistical evaluation and biological interpretation of non-random abundance in the E. coli K-12 genome of tetra- and pentanucleotide sequences related to VSP DNA mismatch repair.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1657
EP  - 1662
VL  - 20
AB  - The abundance of all tetra- and pentanucleotide sequences is calculated for a set of DNA
AB  - sequence data comprising 767,393 nucleotides of the E. coli K-12 genome.  Observed frequencies
AB  - are compared to those expected from a Markov chain prediction algorithm.  Systematic and
AB  - extreme non-random representations are found for special sets of sequences.  These are
AB  - interpreted as arising from incorporation of a 2'-deoxyguanosine residue opposite thymidine
AB  - during replication which, in special sequence contexts, leads to a T/G mismatch that is
AB  - simultaneously substrate for two competing DNA mismatch repair systems: the mutHLS and the VSP
AB  - pathway.  Processing by the former leads to error correction, by the latter to mutation
AB  - fixation.  The significance of the latter process, as demonstrated here, makes it unlikely
AB  - that VSP repair has evolved mainly as a mutation avoidance mechanism.  It is proposed that in
AB  - E. coli K-12, VSP repair, together with DNA cytosine methylation, constitutes a
AB  - mutagenesis/recombination system capable of promoting gene-conversion-like unidirectional
AB  - transfer of short stretches of DNA sequence.
ER  -

TY  - JOUR
AU  - Merlo, D.J.
AU  - Thompson, D.V.
TI  - In vitro sodium bisulfite mutagenesis of restriction endonuclease recognition sites.
JO  - Anal. Biochem.
PY  - 1987
SP  - 79
EP  - 87
VL  - 163
AB  - Sodium bisulfite treatment of single-stranded DNA deaminates exposed cytosine
AB  - residues to form uracil, resulting in cytosine-to-thymidine transition
AB  - mutations following DNA replication.  We have used this reaction in vitro to
AB  - destroy the recognition sequences for the restriction endonucleases HindIII and
AB  - XmaI in the aminoglycoside 3'-phosphotransferase I coding region of plasmid
AB  - pUC4K.  This procedure should be applicable to the mutation of any recognition
AB  - sequence of restriction endonucleases which generate cytosine-containing
AB  - single-stranded ends.  The possibility of mutagenesis of restriction sites to
AB  - generate stop codons in coding regions is discussed.
ER  -

TY  - JOUR
AU  - Mermelstein, L.D.
AU  - Popoutsakis, E.T.
TI  - In vivo methylation in Escherichia coli by the Bacillus subtilis phage Phi3T methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824.
JO  - Appl. Environ. Microbiol.
PY  - 1993
SP  - 1077
EP  - 1081
VL  - 59
AB  - The restriction endonuclease Cac824I has been shown to be a major barrier to
AB  - electrotransformation of Clostridium acetobutylicum ATCC 824 (L.D. Mermelstein, N.E. Welker,
AB  - G.N. Bennett, and E.T. Popoutsakis, BioTechnology 10:190-195, 1992). Methylation by the Phi3T
AB  - I methyltransferase encoded by Bacillus subtilis phage Phi3T was shown to protect plasmid DNA
AB  - from restriction by Cac824I. Expression in Escherichia coli of the phi3tI gene (which encodes
AB  - the Phi3TI methyltransferase) from pAN1, which replicates via the p15A origin of replication,
AB  - was sufficient to completely methylate coresident E. coli-C. acetobutylicum shuttle vectors
AB  - with ColE1 origins of replication. Three shuttle vectors (pIMP1, pSYL2, and pSYL7) methylated
AB  - in this manner were used to efficiently electrotransform strain ATCC 824. These vectors could
AB  - not be introduced into strain ATCC 824 when unmethylated because the E. coli portions of the
AB  - plasmids contain a large number of Cac824I sites. This method obviates the need to use B.
AB  - subtilis-C. acetobutylicum shuttle vectors with few Cac824I sites to introduce DNA into C.
AB  - acetobutylicum ATCC 824.
ER  -

TY  - JOUR
AU  - Mermelstein, L.D.
AU  - Welker, N.E.
AU  - Bennett, G.N.
AU  - Papoutsakis, E.T.
TI  - Expression of cloned homologous genes in Clostridium acetobutylicum ATCC 824.
JO  - Biotechnology
PY  - 1992
SP  - 190
EP  - 195
VL  - 10
AB  - We have previously cloned the acetone-formation pathway gene, encoding acetoacetate
AB  - deacarboxylase (adc), and butyrate-formation pathway gene, encoding phosphtransbutyrylase
AB  - (ptb), of Clostridium acetobutylicum ATCC 824 in Escherichia coli. Here we report their
AB  - subcloning in Bacillus subtilis and transfer to strain ATCC 824 via electrotransformation,
AB  - where the corresponding enzyme activities were expressed at elevated levels, using pFNK1, a
AB  - new B. subtilis/C. acetobutylicum shuttle vector. Plasmid pFNK1 was used because shuttle
AB  - vectors that function in E. coli were unable to electrotransform ATCC 824 unless they became
AB  - deleted in the E. coli-plasmid regions. The difficulties with shuttle vectors that function in
AB  - E. coli are probably due to the presence of a restriction endonuclease in ATCC 824. This
AB  - endonuclease recognizes the sequence 5'-GCNGC-3', which is prevalent in E. coli plasmids,
AB  - but occurs infrequently in pFNK1 and C. acetobutylicum genes. Cloning of genes in C.
AB  - acetobutylicum is critical for redirecting the cellular metabolism (metabolic engineering) as
AB  - well as for genetic studies of this industrial organism.
ER  -

TY  - JOUR
AU  - Mernagh, D.
AU  - Marks, P.
AU  - Kneale, G.
TI  - AhdI, a new class of restriction-modification system?
JO  - Biochem. Soc. Trans.
PY  - 1999
SP  - A126
EP  - A126
VL  - 27
AB  - Bacterial restriction-modification systems have traditionally been divided into three distinct
AB  - classes, types I, II and III.  Here we report a study of what appears to be a new class of R-M
AB  - systems, exemplified by AhdI.  Analysis of the DNA sequence and gene organization of AhdI has
AB  - revealed that the methyltransferase more closely resembles a type I MTase than a type II.  In
AB  - contrast, the AhdI endonuclease is more characteristic of a type II R-M system.  It is
AB  - possible that the AhdI R-M system is an evolutionary intermediate made up of a type II-like
AB  - endonuclease and a methyltransferase that resembles those found in the multisubunit type I
AB  - systems.  This new class of R-M system has been named type 1-1/2.  The AhdI methyltransferase
AB  - is a multisubunit enzyme containing two subunits, one that shares some degree of sequence
AB  - homology with the type I HsdM subunit and the other with the HsdS subunit found in type I
AB  - MTases.  Whereas the M subunit of AhdI closely resembles a type I HsdM subunit in the sequence
AB  - and size of the protein, the S subunit is only half the size of the type I counterpart.  We
AB  - report here the cloning and characterization of the AhdI methyltransferase.  With experimental
AB  - evidence obtained from gel electrophoresis and analytical gel filtration we have determined
AB  - the stoichiometry of the enzyme and with the use of gel retardation and surface plasmon
AB  - resonance we will address the relationship of the subunit composition to DNA binding by the
AB  - AhdI MTase.
ER  -

TY  - JOUR
AU  - Mernagh, D.R.
AU  - Janscak, P.
AU  - Firman, K.
AU  - Kneale, G.G.
TI  - Protein-protein and protein-DNA interactions in the type I restriction endonuclease R.EcoR124I.
JO  - Biol. Chem.
PY  - 1998
SP  - 497
EP  - 503
VL  - 379
AB  - The type I restriction-modification system EcoR124I recognizes and binds to the split DNA
AB  - recognition sequence 5'-GAAN6RTCG-3'.  The methyltransferase, consisting of HsdM and HsdS
AB  - subunits with the composition M2S, can interact with one or more subunits of the HsdR subunit
AB  - to form the endonuclease.  The interaction of the methyltransferase with HsdR has been
AB  - investigated by surface plasmon resonance, showing that there are two non-equivalent binding
AB  - sites for hsdR which differ in binding affinity by at least two orders of magnitude.  DNA
AB  - footprinting experiments using exonuclease III suggest that the addition of HsdR to the
AB  - methyltransferase (at a stoichiometry of either 1:1 or 2:1) increases the stability of the
AB  - resulting DNA-protein complex but does not increase the size of the footprint.  More extensive
AB  - in situ footprinting experiments using copper-phenanthroline on the DNA-protein complexes
AB  - formed by M2S, R1M2S and R2M2S also show no difference in the detailed cleavage pattern, with
AB  - ~18 nucleotides protected on both strands in each complex.  Thus the HsdR subunit(s) of the
AB  - endonuclease stabilize the interaction of the M2S complex with DNA, but do not directly
AB  - contribute to DNA binding.  In addition, the thymidine nucleotide in the tetranucleotide
AB  - recognition sequence GTCG is hyper-reactive to cleavage in each case, suggesting that the DNA
AB  - structure in this region is altered in these complexes.
ER  -

TY  - JOUR
AU  - Mernagh, D.R.
AU  - Kneale, G.G.
TI  - High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 4853
EP  - 4858
VL  - 24
AB  - The type I DNA methyltransferase M.EcoR124I is a multi-subunit enzyme that binds to the
AB  - sequence GAAN6RTCG, transferring a methyl group from S-adenosylmethionine to a specific
AB  - adenine on each DNA strand.  We have investigated the protein-DNA interactions in the complex
AB  - by DNase I and hydroxyl radical footprinting.  The DNase I footprint is unusually large: the
AB  - protein protects the DNA on both strands for at least two complete turns of the helix,
AB  - indicating that the enzyme completely encloses the DNA in the complex.  The higher resolution
AB  - hydroxyl radical probe shows a smaller, but still extensive, 18 bp footprint encompassing the
AB  - recognition site.  Within this region, however, there is a remarkably hyper-reactive site on
AB  - each strand.  The two sites of enhanced cleavage are co-incident with the two adenines that
AB  - are the target bases for methylation, showing that the DNA is both accessible and highly
AB  - distorted at these sites.  The hydroxyl radical footprint is unaffected by the presence of the
AB  - cofactor S-adenosylmethionine, showing that the distorted DNA structure induced by M.EcoR124I
AB  - is formed during the initial DNA binding reaction and not as a transient intermediate in the
AB  - reaction pathway.
ER  -

TY  - JOUR
AU  - Mernagh, D.R.
AU  - Reynolds, L.A.
AU  - Kneale, G.G.
TI  - DNA binding and subunit interactions in the type I methyltransferase M.EcoR124I.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 987
EP  - 991
VL  - 25
AB  - The type I DNA methyltransferase M.EcoR124I consists of two methylation subunits (hsdM) and
AB  - one DNA recognition subunit (HsdS).  When expressed independently, HsdS is insoluble, but this
AB  - subunit can be obtained in soluble form as a GST fusion protein.  We show that the HsdS
AB  - subunit, even as a fusion protein, is unable to form a discrete complex with its DNA
AB  - recognition sequence.  When HsdM is added to the HsdS fusion protein, discrete complexes are
AB  - formed but these are unable to methylate DNA.  The two complexes formed correspond to species
AB  - with one or two copies of the HsdM subunit, indicating that blocking the N-terminus of hsdS
AB  - affects one of the HsdM binding sites.  However, removal of the GST moiety from such complexes
AB  - results in tight and specific DNA binding and restores full methylation activity.  The results
AB  - clearly demonstrate the importance of the HsdM subunit for DNA binding, in addition to its
AB  - catalytic role in the methyltransferase reaction.
ER  -

TY  - JOUR
AU  - Mernagh, D.R.
AU  - Taylor, I.A.
AU  - Kneale, G.G.
TI  - Interaction of the type I methyltransferase M.EcoR124I with modified DNA substrates: sequence discrimination and base flipping.
JO  - Biochem. J.
PY  - 1998
SP  - 719
EP  - 725
VL  - 336
AB  - We have analyzed the DNA-protein contacts made between the type I DNA methyltransferase
AB  - M.EcoR124I and its recognition sequence.  The effects of base modifications have been probed
AB  - by measuring the affinity of M.EcoR124I for the modified sequences relative to that for the
AB  - wild-type sequence by using gel-retardation competition assays.  These results, along with
AB  - those from methylation interference footprinting and photo-affinity cross-linking have
AB  - identified the location of potential DNA contacts within the DNA recognition site.
AB  - Substitution of 6-thioguanosine for each of the three specific guanines in the recognition
AB  - sequence leads to a large (10-20-fold) decrease in the strength of DNA binding, indicating the
AB  - importance of hydrogen-bonding interactions in the major groove of DNA.  In contrast,
AB  - replacement of either (or both) of the adenine at the target site for methylation by the
AB  - enzyme, to produce either a base pair mismatch or loss of the base, leads to a marked increase
AB  - in DNA-binding affinity.  The results strongly support the proposal that type I
AB  - methyltransferases employ a base-flipping mechanism to methylate their target base.
ER  -

TY  - JOUR
AU  - Merritt, J.
AU  - Qi, F.X.
AU  - Shi, W.Y.
TI  - A unique nine-gene comY operon in Streptococcus mutans.
JO  - Microbiology
PY  - 2005
SP  - 157
EP  - 166
VL  - 151
AB  - Many Gram-positive and Gram-negative bacteria possess natural competence mechanisms for DNA
AB  - capture and internalization. In Bacillus
AB  - subtilis, natural competence is absolutely dependent upon the presence
AB  - of a seven-gene operon known as the comG operon (comGA-G). In species
AB  - of Streptococcus, this function has been described for a four-gene
AB  - operon (comYA-D in Streptococcus gordonii and cglA-D in Streptococcus
AB  - pneumoniae). In this study, a nine-orf operon (named comYA-I) required
AB  - for natural competence in Streptococcus mutans was identified and
AB  - characterized. Orf analysis of this operon indicates that the first
AB  - four Orfs (ComYA-D) share strong homology with ComYA-D of S. gordonii
AB  - and CgIA-D of S. pneumoniae, the fifth to seventh Orfs (ComYE-G) match
AB  - conserved hypothetical proteins from various species of Streptococcus
AB  - with ComYF possessing a predicted ComGF domain, the eighth Orf (ComYH)
AB  - shows a strong homology to numerous DNA methyltransferases from
AB  - restriction/modification systems, and the ninth Orf (ComYI) is
AB  - homologous to acetate kinase (AckA). RT-PCR analysis of the orf
AB  - junctions confirmed that all nine orfs were present in a single
AB  - transcript, while real-time RT-PCR analysis demonstrated that these
AB  - orfs were expressed at a level very similar to that of the first orf in
AB  - the operon. Mutations were constructed in all nine putative orfs. The
AB  - first seven genes (comYA-G) were found to be essential for natural
AB  - competence, while comYH and comYI had reduced and normal natural
AB  - competence ability, respectively. Analyses of S. mutans comY-luciferase
AB  - reporter fusions indicated that comY expression is growth-phase
AB  - dependent, with maximal expression at an OD600 of about 0(.)2, while
AB  - mutations in ciaH, comC and luxS reduced the level of comY expression.
AB  - In addition, comY operon expression appears to be correlated with
AB  - natural competence ability.
ER  -

TY  - JOUR
AU  - Merten, M.
AU  - Brinkrolf, K.
AU  - Albersmeier, A.
AU  - Kutter, Y.
AU  - Ruckert, C.
AU  - Tauch, A.
TI  - Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen.
JO  - Genome Announcements
PY  - 2015
SP  - e00183
EP  - e00115
VL  - 3
AB  - Corynebacterium singulare DSM 44357 is a urease-positive microorganism isolated from human
AB  - semen. The complete genome sequence of C. singulare DSM 44357
AB  - comprises 2,830,519 bp with a mean G+C content of 60.12% and 2,581 protein-coding
AB  - genes. The deduced antibiotic resistance pattern of this strain includes
AB  - macrolides, lincosamides, aminoglycosides, chloramphenicol, and tetracyline.
ER  -

TY  - JOUR
AU  - Mertineit, C.
AU  - Yoder, J.A.
AU  - Taketo, T.
AU  - Laird, D.W.
AU  - Trasler, J.M.
AU  - Bestor, T.H.
TI  - Sex-specific exons control DNA methyltransferase in mammalian germ cells.
JO  - Development
PY  - 1998
SP  - 889
EP  - 897
VL  - 125
AB  - The spermatozoon and oocyte genomes bear sex-specific methylation patterns that are
AB  - established during gametogenesis and are required for the allele-specific expression of
AB  - imprinted genes in somatic tissues.  The mRNA for Dnmt1, the predominant maintenance and de
AB  - novo DNA (cytosine-5)-methyl transferase in mammals, is present at high levels in postmitotic
AB  - murine germ cells but undergoes alternative splicing of sex-specific 5' exons, which controls
AB  - the production and localization of enzyme during specific stages of gametogenesis.  An
AB  - oocyte-specific 5' exon is associated with the production of very large amounts of active
AB  - Dnmt1 protein, which is truncated at the N terminus and sequestered in the cytoplasm during
AB  - the later stages of oocyte growth, while a spermatocyte-specific 5' exon interferes with
AB  - translation and prevents production of Dnmt1 during the prolonged crossing-over stages of male
AB  - meiosis.  During the course of postnatal oogenesis, Dnmt1 is present at high levels in nuclei
AB  - only in growing dictyate oocytes, a stage during which gynogenetic developmental potential is
AB  - lost and biparental developmental potential is gained.
ER  -

TY  - JOUR
AU  - Mertz, J.E.
AU  - Davis, R.W.
TI  - Cleavage of DNA by EcoRI restriction endonuclease generates cohesive ends.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3370
EP  - 3374
VL  - 69
AB  - EcoRI restriction endonuclease cleaves duplex DNA at a specific sequence,
AB  - probably 6 nucleotide pairs in length, by making two single-strand staggered
AB  - cleavages, generating 5'-phosphoryl and 3'-hydroxyl termini.  The single-strand
AB  - ends produced at each break have identical and complementary sequences of 4 or
AB  - 6 nucleotides in length.  Therefore, the cleavage site possesses a 2-fold
AB  - rotational axis of symmetry perpendicular to the helix axis.  The ends of
AB  - full-length linear SV40 DNA, generated by EcoRI endonuclease cleavage, can be
AB  - joined by Escherichia coli ligase to regenerate duplex, fully infectious,
AB  - covalently-closed circular molecules.  It was further found that all EcoRI
AB  - endonuclease-generated ends are identical and complementary.  Therefore, any
AB  - two DNA molecules with EcoRI sites can be "recombined" at their restriction
AB  - sites by the sequential action of EcoRI endonuclease and DNA ligase to generate
AB  - hybrid DNA molecules.
ER  -

TY  - JOUR
AU  - Meselson, M.
AU  - Yuan, R.
TI  - DNA-restriction enzyme from E. coli K.
JO  - Procedures in Nucleic Acids Research
PY  - 1972
SP  - 889
EP  - 895
VL  - 2
AB  - Most strains of E. coli are able to recognize and degrade DNA from foreign E.
AB  - coli strains.  Whether a foreign DNA molecule is degraded depends on certain
AB  - nonheritable properties imparted by the cell from which it is obtained.  These
AB  - properties are called host-controlled modifications.  For example, the result
AB  - of infecting E. coli strain K with phage lambda depends on the host in which
AB  - the phages were last grown.  Phages grown in bacteria possessing the
AB  - modification character mk multiply successfully, but phages from bacteria
AB  - lacking mk do not.  Instead, their DNA is quickly degraded on entering cells of
AB  - strain K.  The ability of strain K to degrade or "restrict" DNA from cells
AB  - lacking mk is itself under genetic control, the responsible character being
AB  - designated rk.  An endonuclease has been shown to be responsible for
AB  - restriction in E. coli K.  It is specifically active against lambda DNA from
AB  - strains lacking mk and is called endonuclease R.K.
ER  -

TY  - JOUR
AU  - Meselson, M.
AU  - Yuan, R.
TI  - DNA restriction enzyme from E. coli.
JO  - Nature
PY  - 1968
SP  - 1110
EP  - 1114
VL  - 217
AB  - An endonuclease which degrades foreign DNA has been isolated.  The enzyme
AB  - requires S-adenosylmethionine, ATP and Mg++.
ER  -

TY  - JOUR
AU  - Meselson, M.
AU  - Yuan, R.
AU  - Heywood, J.
TI  - Restriction and modification of DNA.
JO  - Annu. Rev. Biochem.
PY  - 1972
SP  - 447
EP  - 466
VL  - 41
AB  - None
ER  -

TY  - JOUR
AU  - Meslier, V.
AU  - Loux, V.
AU  - Renault, P.
TI  - Genome Sequence of Lactococcus raffinolactis Strain 4877, Isolated from Natural Dairy Starter Culture.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6364
EP  - 6364
VL  - 194
AB  - The nonstarter lactic acid bacterium Lactococcus raffinolactis is prevalent in a  wide range
AB  - of environments, such as the dairy environment, but little is known
AB  - about this species. Here, we present the draft genome of Lactococcus
AB  - raffinolactis strain 4877, isolated from a natural mesophilic dairy starter
AB  - culture.
ER  -

TY  - JOUR
AU  - Meslier, V.
AU  - Loux, V.
AU  - Renault, P.
TI  - Genome Sequence of Leuconostoc pseudomesenteroides Strain 4882, Isolated from a Dairy Starter Culture.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6637
EP  - 6637
VL  - 194
AB  - The nonstarter lactic acid bacterium Leuconostoc pseudomesenteroides is a species widely found
AB  - in the dairy industry and plays a key role in the formation of
AB  - aromatic compounds. Here, we report the first genome sequence of a dairy strain
AB  - of Leuconostoc pseudomesenteroides, which is 2 Mb.
ER  -

TY  - JOUR
AU  - Messer, W.
AU  - Noyer-Weidner, M.
TI  - Timing and targeting: the biological functions of Dam methylation in E. coli.
JO  - Cell
PY  - 1988
SP  - 735
EP  - 737
VL  - 54
AB  - Postreplicative DNA methylation superimposes on the fixed primary information of the DNA
AB  - sequence secondary information that has significance in the regulation of a variety of
AB  - cellular processes in prokaryotes and eukaryotes.  In many eukaryotes, methylation of cytosine
AB  - residues in defined regions of the genome is involved in a global control of gene activity.
AB  - The methylation pattern may change during development, but once established, it can be stably
AB  - transmitted to daughter cells by the activity of maintenance methyltransferases.  Highly
AB  - methylated regions are often transcriptionally inactive.  In contrast to the situation in
AB  - eukaryotes, the regulatory effects of Dam methylation in Escherichia coli do not arise from
AB  - selective methylation of defined regions of the genome. The Dam DNA methyltransferase
AB  - methylates the N6 position of adenine at all GATC sites.  However, because there is a lag
AB  - between replication and methylation, newly replicated DNA is hemimethylated and therefore
AB  - distinct from the rest of the genome.  The hemimethylated status of new DNA provides a time
AB  - window during which certain cellular processes are activated or suppressed, thus linking these
AB  - processes to the cell cycle.  Moreover, the methylation asymmetry in this window allows
AB  - distinction between parental (methylated) and daughter (unmethylated) DNA strands.  Here we
AB  - discuss the regulatory potential of these two forms of superimposed information.
ER  -

TY  - JOUR
AU  - Messick, J.B.
AU  - Santos, A.P.
AU  - Guimaraes, A.M.
TI  - Complete Genome Sequences of Two Hemotropic Mycoplasmas, Mycoplasma haemofelis Strain Ohio2 and Mycoplasma suis Strain Illinois.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2068
EP  - 2069
VL  - 193
AB  - We report the complete and fully assembled genomes of Mycoplasma haemofelis strain Ohio2 and
AB  - Mycoplasma suis strain Illinois, which are the
AB  - first available genomes of these uncultivatable hemoplasma species. The
AB  - single circular chromosomes of 1,152,484 bp and 742,431 bp for M.
AB  - haemofelis and M. suis, respectively, are typical of mycoplasma species,
AB  - having reduced size and low G+C content (38.8% for M. haemofelis and 31.1%
AB  - for M. suis). Their metabolic pathways are reduced, with evidence of
AB  - adaption to the blood environment.
ER  -

TY  - JOUR
AU  - Messina, E.
AU  - Sorokin, D.Y.
AU  - Kublanov, I.V.
AU  - Toshchakov, S.
AU  - Lopatina, A.
AU  - Arcadi, E.
AU  - Smedile, F.
AU  - La Spada, G.
AU  - La Cono, V.
AU  - Yakimov, M.M.
TI  - Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 35
EP  - 35
VL  - 11
AB  - Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which
AB  - represents one of the most hostile extreme environments on our planet. On
AB  - the basis of physiological studies and phylogenetic positioning this extremely
AB  - halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the
AB  - family Halobacteriaceae. All members of this genus cultivated so far are strict
AB  - anaerobes using acetate as the sole carbon and energy source and elemental sulfur
AB  - as electron acceptor. Here we report the complete genome sequence of the strain
AB  - M27-SA2 which is composed of a 2,129,244-bp chromosome and a 124,256-bp plasmid.
AB  - This is the second complete genome sequence within the genus Halanaeroarchaeum.
AB  - We demonstrate that genome of 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors
AB  - complete metabolic pathways for acetate and sulfur catabolism and for de novo
AB  - biosynthesis of 19 amino acids. The genomic analysis also reveals that
AB  - 'Halanaeroarchaeum sulfurireducens' M27-SA2 harbors two prophage loci and one
AB  - CRISPR locus, highly similar to that of Kulunda Steppe (Altai, Russia) isolate
AB  - 'H. sulfurireducens' HSR2(T). The discovery of sulfur-respiring acetate-utilizing
AB  - haloarchaeon in deep-sea hypersaline anoxic lakes has certain significance for
AB  - understanding the biogeochemical functioning of these harsh ecosystems, which are
AB  - incompatible with life for common organisms. Moreover, isolations of
AB  - Halanaeroarchaeum members from geographically distant salt-saturated sites of
AB  - different origin suggest a high degree of evolutionary success in their
AB  - adaptation to this type of extreme biotopes around the world.
ER  -

TY  - JOUR
AU  - Metcalf, W.W.
TI  - Genetic analysis in the domain Archaea.
JO  - Methods Microbiol.
PY  - 1999
SP  - 277
EP  - 326
VL  - 29
AB  - The recognition of the Archaea as a phylogenetic domain at the same hierarchical level as the
AB  - Bacteria or Eukarya is a relatively recent development in the biological sciences.  This
AB  - revision of the classical prokaryotic vs. eukaryotic phylogeny stems largely from the work of
AB  - Carl Woese and his collaborators, and originated in the late 1970's from the study of what
AB  - were then known as methane-producing bacteria.  Utilizing 16S RNA as a molecular marker for
AB  - determining phylogenetic relationships between organisms, Woese and his collaborators showed
AB  - that these organisms were vastly different from the known bacterial species and proposed they
AB  - should be considered as a separate group, designated the Archaebacteria.  Although this
AB  - assertion was hotly contested for many years, its validity has been gradually substantiated by
AB  - a variety of methods and is now widely accepted.  The term Archaebacteria has been replaced by
AB  - Archaea to emphasize the important point that these are not Bacteria.
ER  -

TY  - JOUR
AU  - Methe, B.A. et al.
TI  - The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 10913
EP  - 10918
VL  - 102
AB  - The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium
AB  - Colwellia psychrerythraea 34H, a model for the study of life in permanently cold environments,
AB  - reveals capabilities important to carbon and nutrient cycling, bioremediation, production of
AB  - secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation
AB  - is suggested in several broad categories involving changes to the cell membrane fluidity,
AB  - uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome
AB  - temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein
AB  - homology from bacteria representing a range of optimal growth temperatures suggests changes to
AB  - proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative
AB  - genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a
AB  - unique set of genes but by a collection of synergistic changes in overall genome content and
AB  - amino acid composition.
ER  -

TY  - JOUR
AU  - Methe, B.A. et al.
TI  - Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.
JO  - Science
PY  - 2003
SP  - 1967
EP  - 1969
VL  - 302
AB  - The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals
AB  - unsuspected capabilities, including
AB  - evidence of aerobic metabolism, one-carbon and complex carbon metabolism,
AB  - motility, and chemotactic behavior. These characteristics, coupled with
AB  - the possession of many two-component sensors and many c-type cytochromes,
AB  - reveal an ability to create alternative, redundant, electron transport
AB  - networks and offer insights into the process of metal ion reduction in
AB  - subsurface environments. As well as playing roles in the global cycling of
AB  - metals and carbon, this organism clearly has the potential for use in
AB  - bioremediation of radioactive metals and in the generation of electricity.
ER  -

TY  - JOUR
AU  - Meunier, B.
AU  - Tian, G.-L.
AU  - Macadre, C.
AU  - Slonimski, P.P.
AU  - Lazowska, J.
TI  - Group II introns transpose in yeast mitochondria.
JO  - Structure, function and biogenesis of energy transfer systems.
PY  - 1990
SP  - 169
EP  - 174
VL  - 0
AB  - There is a set of genetic phenomena which, first discovered in yeast mitochondrial genetics
AB  - twenty years ago, is still of considerable interest for molecular biologists.  Variously
AB  - described as polarity of transmission and recombination of genetic markers, unidirectional
AB  - gene conversion with coconversion of flanking markers, intron gene conversion, duplicative
AB  - transposition, homing or intron infectivity these phenomena have one feature in common: a
AB  - specific portion of the donor mitochondrial genome, is preferentially transmitted to the
AB  - progeny when compared to other parts of the same genome.  The leading element of this gene
AB  - conversion is an intron and the process is initiated by an intron-encoded-protein which has a
AB  - specific double strand DNA endonuclease activity that cleaves an intronless recipient
AB  - mitochondrial genome at (or in the vicinity of) the site of intron insertion.  For many years
AB  - the phenomenon was restricted to the omega+ intron located in the large rRNA gene but more
AB  - recently it was observed for the ai4 intron of the COX1 gene.  Both omega+ and ai4 belong to
AB  - the group I of intronic RNA structure and code for proteins which share several polypeptide
AB  - motifs in common with RNA maturases.
ER  -

TY  - JOUR
AU  - Mevada, V.A.
AU  - Patel, S.
AU  - Pandya, J.V.
AU  - Joshi, H.
AU  - Patel, R.K.
TI  - Whole Genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from coastal region of Gujarat.
JO  - Genomics Data
PY  - 2017
SP  - 30
EP  - 34
VL  - 13
AB  - Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample
AB  - collected from the coastal region of Gujarat, India, from a surface water stream. Based on
AB  - 16sRNA sequencing, the organism was identi and #64257;ed as Salinicoccus sp. BAB3246 (Genebank
AB  - ID:KF889285). The present work was performed to determine the whole genome sequence of the
AB  - organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench
AB  - and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp
AB  - identi and #64257;ed by with second largest size for Salinicoccus sp. reported in the NCBI
AB  - genome database. A total of 652 degradative pathways were identi and #64257;ed by KEGG map
AB  - analysis. Comparative genomic analysis revealed Salinicoccus sp.BAB3246 as mosthighly related
AB  - to Salinicoccushalodurans H3B36. Data mining identi and #64257;ed stress response genes and
AB  - operator pathway for degradation of various environmental pollutants. Annotation data and
AB  - analysis indicate potential use in pollution control in industrial in and #64258;uent and
AB  - saline environment.
ER  -

TY  - JOUR
AU  - Meyer, J.L.
AU  - Dillard, B.A.
AU  - Rodgers, J.M.
AU  - Ritchie, K.B.
AU  - Paul, V.J.
AU  - Teplitski, M.
TI  - Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 75
EP  - 75
VL  - 10
AB  - Members of the gammaproteobacterial genus Halomonas are common in marine environments.
AB  - Halomonas and other members of the Oceanospirillales have recently
AB  - been identified as prominent members of the surface microbiota of reef-building
AB  - corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer
AB  - of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This
AB  - strain was chosen for genome sequencing to provide insight into the role of
AB  - commensal heterotrophic bacteria in the coral holobiont. The draft genome
AB  - consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Meyer, P.
TI  - DNA methylation of flower color transgenes in Petunia hybrida.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 305
EP  - 317
VL  - 0
AB  - Inactivation of transgene constructs that have been introduced into plants is a frequently
AB  - reported phenomenon.  Many such silencing events are associated with DNA methylation, although
AB  - it is still a matter of debate whether de novo methylation is the cause or the consequence of
AB  - gene inactivation.  A correlation between DNA methylation and gene inactivation is not limited
AB  - to transgenes but is also observed for transposable elements and for some, but not all,
AB  - endogenous genes.  Interestingly, changes in methylation patterns that correlate with changes
AB  - in tissue-specific expression have been found in distant upstream regions of some genes,
AB  - indicating that methylation-mediated control of gene expression does not exclusively affect
AB  - promoter regions.
ER  -

TY  - JOUR
AU  - Meyer-Cifuentes, I.
AU  - Fiedler, S.
AU  - Muller, J.A.
AU  - Kappelmeyer, U.
AU  - Mausezahl, I.
AU  - Heipieper, H.J.
TI  - Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor.
JO  - Genome Announcements
PY  - 2017
SP  - e00764
EP  - e00717
VL  - 5
AB  - Here, we report the draft genome sequence of Magnetospirillum sp. 15-1. This strain was
AB  - isolated from a planted fixed-bed reactor based on its ability to
AB  - degrade toluene under anaerobic conditions. The genome assembly consists of 5.4
AB  - Mb in 28 contigs and 5,095 coding sequences containing the genes involved in
AB  - anaerobic toluene degradation.
ER  -

TY  - JOUR
AU  - Meyerdierks, A.
AU  - Kube, M.
AU  - Kostadinov, I.
AU  - Teeling, H.
AU  - Glockner, F.O.
AU  - Reinhardt, R.
AU  - Amann, R.
TI  - Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group.
JO  - Environ. Microbiol.
PY  - 2010
SP  - 422
EP  - 439
VL  - 12
AB  - Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of
AB  - methanotrophic Archaea (ANME) and Bacteria related
AB  - to sulfate-reducing Deltaproteobacteria. Cultured representatives are not
AB  - available for any of the three ANME clades. Therefore, a metagenomic
AB  - approach was applied to assess the genetic potential of ANME-1 archaea. In
AB  - total, 3.4 Mbp sequence information was generated based on metagenomic
AB  - fosmid libraries constructed directly from a methanotrophic microbial mat
AB  - in the Black Sea. These sequence data represent, in 30 contigs, about
AB  - 82-90% of a composite ANME-1 genome. The dataset supports the hypothesis
AB  - of a reversal of the methanogenesis pathway. Indications for an
AB  - assimilatory, but not for a dissimilatory sulfate reduction pathway in
AB  - ANME-1, were found. Draft genome and expression analyses are consistent
AB  - with acetate and formate as putative electron shuttles. Moreover, the
AB  - dataset points towards downstream electron-accepting redox components
AB  - different from the ones known from methanogenic archaea. Whereas catalytic
AB  - subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an
AB  - [FeFe]-hydrogenase homologue were identified, not yet described to be
AB  - present in methanogenic archaea. Clustered genes annotated as secreted
AB  - multiheme c-type cytochromes were identified, which have not yet been
AB  - correlated with methanogenesis-related steps. The genes were shown to be
AB  - expressed, suggesting direct electron transfer as an additional possible
AB  - mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing
AB  - partner.
ER  -

TY  - JOUR
AU  - Meyerink, J.H.
AU  - Retel, J.
TI  - Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases.  II. The physical map of EcoRI fragments.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 2697
EP  - 2707
VL  - 3
AB  - Yeast ribosomal DNA (rDNA) was digested with the restriction endonuclease
AB  - EcoRI.  Eight distinct fragments were obtained with a molecular weight of 4.35
AB  - (1), 1.75 (2), 1.45 (3), 1.07 (4), 0.42 (5), 0.37 (6), 0.26 (7) and 0.22 (8)
AB  - Mdaltons, respectively.  Except for fragment 1 with a molecular wieght of 4.35
AB  - Mdaltons, all fragments are derived from the multiple ribosomal transcription
AB  - units.  The 'spacer' sequences, on the other hand, gave rise to digestion
AB  - products which are very heterogeneous in size.  By analysis of the partial
AB  - digestion products, together with the data obtained by digestion with a
AB  - combination of two restriction enzymes (EcoRI and HindII or HindIII) and
AB  - redigation of the HindII- and HindIII-fragments with EcoRI, the physical map of
AB  - the EcoRI cleavage sites in the ribosomal transcription unit could be
AB  - established.
ER  -

TY  - JOUR
AU  - Meyerink, J.H.
AU  - Retel, J.
AU  - Planta, R.J.
AU  - Heidekamp, F.
TI  - Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases.
JO  - Mol. Biol. Rep.
PY  - 1976
SP  - 393
EP  - 400
VL  - 2
AB  - Yeast ribosomal DNA (rDNA) was digested with the restriction enzymes HindIII,
AB  - HindII and a mixture of HindII and HindIII.  The cleavage products were
AB  - analyzed by electrophoresis on 1.5% agarose gels.  Several distinct bands could
AB  - be observed, which are derived from the redundant ribosomal transcription unit.
AB  - They are superimposed on a rather broad smear of background DNA, representing
AB  - the heterogenous 'spacer' sequences.  From the restriction maps, together with
AB  - data obtained by partial digestion, a physical map for the ribosomal
AB  - transcription unit in yeast could be constructed.
ER  -

TY  - JOUR
AU  - Meyertons, J.L.
TI  - Actinophages and restriction endonucleases from Micromonospora species (Actinomycetales).
JO  - Diss. Abstr.
PY  - 1988
SP  - 1888
EP  - 1888
VL  - 48
AB  - In the course of developing a screening procedure for the detection of
AB  - restriction endonucleases in micromonosporae, an economically important group
AB  - of actinomycetes, previously undiscovered actinophages were isolated from soils
AB  - enriched with Micromonospora species. The majority of the actinophages belonged
AB  - to Ackermann's type B1 since they had isometric heads, hexagonal in shape, and
AB  - long, noncontractile tails. The tails were often flexible and striated, and
AB  - some had terminal bulbs. One actinophage was classified as type C1 because of
AB  - the very short, noncontractile tail and the isometric head. The actinophages
AB  - all contained double-stranded DNA and had genome sizes ranging from
AB  - approximately 40 to 60 kilobases. All actinophages were polyvalent except for
AB  - one monovalent isolate specific for M. coerulea (NRRL B16092). The host-ranges
AB  - of the actinophages were determined on thirty species of Micromonospora.
AB  - Certain actinophages were also capable of infecting strains of
AB  - Amorphosporangium, Ampullariella and Catellatospora which are Actinomycetes of
AB  - the same cell wall chemotype as Micromonosporae (type II). Whole-cell sugar
AB  - analyses were performed on the Micromonospora species using a newly developed
AB  - thin-layer chromatography (TLC) method. The TLC method used an
AB  - acetonitrile:water development system, and N-naphthylethylenediamine
AB  - hydrochloride or acid aniline phthalate to visualize hexoses or pentoses,
AB  - respectively. A comparison of host-range studies and whole-cell sugar analyses
AB  - suggested that xylose may be involved in actinophage receptors for
AB  - Micromonospora species. The actinophages were used in efficiency of plating
AB  - studies as biological indicators of host-controlled restriction-modification
AB  - activity. Restriction enzymes were detected and isolated from three strains of
AB  - Micromonospora. Type II restriction endonucleases were isolated from
AB  - Micromonospora echinospora ssp. echinospora (ATCC 15837), M. purpurea (ATCC
AB  - 15835) and M. zionensis (LL-100-125), and were designed MecI, MpuI and MziI,
AB  - respectively. Restriction enzymes MecI and MpuI are isoschizomers of XhoI (from
AB  - Xanthomonas holcicola), while MziI is an isoschizomer of PvuII (from Proteus
AB  - vulgaris). One can speculate that a number of R-M systems remain to be
AB  - identified in Micromonospora species and that the discovery of an enzyme with a
AB  - novel recognition sequence is possible.
ER  -

TY  - JOUR
AU  - Meyertons, J.L.
TI  - Actinophages and restriction endonucleases from Micromonospora species (Actinomycetales).
JO  - Ph.D. Thesis, Rutgers University, USA
PY  - 1987
SP  - 1
EP  - 117
AB  - In the course of developing a screening procedure for the detection of
AB  - restriction endonucleases in Micromonosporae, an economically important group
AB  - of actinomycetes, previously undiscovered actinophages were isolated from soils
AB  - enriched with Micromonospora species.  The majority of the actinophages
AB  - belonged to Ackermann's type B1 since they had isometric heads, hexagonal in
AB  - shape, and long, noncontractile tails.  The tails were often flexible and
AB  - striated, and some had terminal bulbs.  One actinophage was classified as type
AB  - C1 because of the very short, noncontractile tail and the isometric head.  The
AB  - actinophages all contained double-stranded DNA and had genome sizes ranging
AB  - from approximately 40 to 60 kilobases.  All actinophages were polyvalent except
AB  - for one monovalent isolate specific for M. coerulea (NRRL B16093).  The
AB  - host-ranges of the actinophages were determined on thirty species of
AB  - Micromonospora.  Certain actinophages were also capable of infecting strains of
AB  - Amorphosporangium, Ampullariella and Catellatospora which are actinomycetes of
AB  - the same cell wall chemotype as Micromonosporae (type II).  Whole-cell sugar
AB  - analyses were performed on the Micromonospora species using a newly developed
AB  - thin-layer chromatography (TLC) method.  The TLC method used an
AB  - acetonitrile:water development system, and N-naphthylethylenediamine
AB  - hydrochloride or acid aniline phthalate to visualize hexoses or pentoses,
AB  - respectively.  A comparison of host-range studies and whole-cell sugar analyses
AB  - suggested that xylose may be involved in actinophage receptors for
AB  - Micromonospora species.  The actinophages were used in efficiency of plating
AB  - studies as biological indicators of host-controlled restriction-modification
AB  - activity.  Restriction enzymes were detected and isolated from three strains of
AB  - Micromonospora.  Type II restriction endonucleases werre isolated from
AB  - Micromonospora echinospora ssp. echinospora (ATCC 15837), M. purpurea (ATCC
AB  - 15835) and M. zionensis (LL-100-125), and were designated MecI, MpuI and MziI,
AB  - respectively.  Restriction enzymes MecI and MpuI are isoschizomers of XhoI
AB  - (from Xanthomonas holcicola), while MziI is an isoschizomer of PvuII (from
AB  - Proteus vulgaris).  One can speculate that a number of R-M systems remain to be
AB  - identified in Micromonospora species and that the discovery of an enzyme with a
AB  - novel recognition sequence is possible.
ER  -

TY  - JOUR
AU  - Meyertons, J.L.
AU  - Tilley, B.C.
AU  - Lechevalier, M.P.
AU  - Lechevalier, H.A.
TI  - Actinophages and restriction enzymes from Micromonospora species (Actinomycetales).
JO  - J. Ind. Microbiol.
PY  - 1987
SP  - 293
EP  - 303
VL  - 2
AB  - To develop a screening procedure for the detection of restriction endonucleases
AB  - in Micromonosporae and Catellatosporae based on efficiency of plating, eight
AB  - different actinophages were isolated from soils enriched with Micromonospora
AB  - species and one from Catellatospora-enriched soil.  The lytic actinophages all
AB  - contained double-stranded DNA and the majority appeared, when examined by
AB  - electron microscopy, to belong to Ackermann's type B1 since they had isometric
AB  - heads and noncontractile tails.  One actinophage was classified as type C1
AB  - because of its isometric head and very short noncontractile tail.  The host
AB  - ranges of the actinophages were determined on strains of Micromonospora and
AB  - selected species from other actinomycete genera of cell wall chemotype II.
AB  - Type II restriction enzymes were isolated from M. echinospora ssp. echinospora
AB  - (ATCC 15837), M. purpurea (ATCC 15835) and M. zionensis (LL-100-125) and were
AB  - designated MecI, MpuI, and MziI, respectively.  Restriction enzymes MecI and
AB  - MpuI are isoschizomers of XhoI, while MziI is an isoschizomer of PvuII.
ER  -

TY  - JOUR
AU  - Meygret, A.
AU  - Vincent, P.
AU  - Moullec, S.
AU  - Nacazume, J.
AU  - Adnani, Y.
AU  - Lavenier, D.
AU  - Kayal, S.
AU  - Faili, A.
TI  - Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021,  Isolated from Clonal Clustered Cases in French Brittany.
JO  - Genome Announcements
PY  - 2016
SP  - e00689
EP  - e00616
VL  - 4
AB  - Here, we announce the complete annotated genome sequence of the invasive Streptococcus
AB  - pyogenes strain M/emm66, isolated in 2013 from a subcutaneous
AB  - abscess in new clustered cases in French Brittany.
ER  -

TY  - JOUR
AU  - Mhamdi, R.
AU  - Ardley, J.
AU  - Tian, R.
AU  - Seshadri, R.
AU  - Reddy, T.B.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an  effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 34
EP  - 34
VL  - 10
AB  - Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can
AB  - exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris).
AB  - Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from
AB  - the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at
AB  - fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together
AB  - with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent
AB  - draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes
AB  - and 72 RNA-only encoding genes, and is one of the rhizobial  genomes sequenced as part of the
AB  - DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule
AB  - Bacteria (GEBA-RNB) project proposal.
ER  -

TY  - JOUR
AU  - Mhanni, A.A.
AU  - Yoder, J.A.
AU  - Dubesky, C.
AU  - McGowan, R.A.
TI  - Cloning and sequence analysis of a zebrafish cDNA encoding DNA (cytosine-5)-methyltransferase-1.
JO  - Genesis
PY  - 2001
SP  - 213
EP  - 219
VL  - 30
AB  - Summary: The zebrafish has become a well-established animal model for the analysis of
AB  - development and of several disease phenotypes. Several of the favorable traits that make it a
AB  - popular model organism would also be beneficial for the study of normal and abnormal
AB  - vertebrate development in which DNA methylation may play a role. We report the determination
AB  - of the full-length cDNA sequence corresponding to the zebrafish DNA (cytosine-5-)
AB  - methyltransferase gene, Dnmt1. It is 4,907 bases long and has an open reading frame predicted
AB  - to encode a 1,499 amino acid protein that is similar in size and sequence to a number of other
AB  - methyltransferases identified in other organisms.
ER  -

TY  - JOUR
AU  - Mi, S.
AU  - Alonso, D.
AU  - Roberts, R.J.
TI  - Functional analysis of Gln-237 mutants of HhaI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 620
EP  - 627
VL  - 23
AB  - When the HhaI (cytosine-5) methyltransferase (M.HhaI) binds DNA it causes the target cytosine
AB  - to be flipped 180 degrees out of the helix. The space becomes occupied by two amino acids,
AB  - Ser-87 and Gln-237, which enter the helix from opposite sides and form a hydrogen bond to each
AB  - other. Gln-237 may be involved in specific sequence recognition since it forms three hydrogen
AB  - bonds to the orphan guanosine, which is the partner of the target cytosine. We have prepared
AB  - all 19 mutants of Gln-237 and tested their biochemical properties. We find that mutations of
AB  - this residue greatly affect the stability of the M.HhaI-DNA complex without affecting the
AB  - enzyme's specificity for the target sequence. Surprisingly, all mutants retain detectable
AB  - levels of enzymatic activity.
ER  -

TY  - JOUR
AU  - Mi, S.
AU  - Roberts, R.J.
TI  - The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2459
EP  - 2464
VL  - 21
AB  - The HhaI methyltransferase recognizes the sequence GCGC and transfers a methyl group to C5 of
AB  - the first cytosine residue. All m5C-methyltransferases contain a highly conserved sequence
AB  - motif called the P-C motif. The cysteine residue of this motif is involved in catalysis by
AB  - forming a covalent bond with the 6-position of cytosine prior to methyl group transfer. For
AB  - the EcoRII methyltransferase, it has been shown that substitution of this catalytic cysteine
AB  - by glycine is cytotoxic to E.coli cells expressing the mutant methyltransferase (Wyszynski et
AB  - al. Nucl. Acids. Res. 20:319,1992). We now show that this observation can be extended to the
AB  - HhaI system and suggest that the cytotoxicity is due to abnormally tight DNA binding by the
AB  - mutant methyltransferase, which probably interferes with replication or transcription.
ER  -

TY  - JOUR
AU  - Mi, S.
AU  - Roberts, R.J.
TI  - How M.MspI and M.HpaII decide which base to methylate.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4811
EP  - 4816
VL  - 20
AB  - The HpaII methylase (M.HpaII) recognizes the sequence CCGG and methylates the inner cytosine
AB  - residue. The MspI methylase (MspI) recognizes the same sequence but methylates the outer
AB  - cytosine residue. Both methylases have the usual architecture of 10 well-conserved motifs
AB  - surrounding a variable region, responsible for sequence specific recognition, that is quite
AB  - different in the two methylases. We hav constructed hybrids between these two methylases and
AB  - studied their methylation properties. A hybrid containing the variable region and C-terminal
AB  - sequences from M.MspI methylates the outer cytosine residue. A second hybrid identical to the
AB  - first except that the variable region derives from the M.HpaII methylates the inner cytosine
AB  - residue. Thus the choice of base to be methylated within the recognition sequence is
AB  - determined by the variable region.
ER  -

TY  - JOUR
AU  - Mi, S.
AU  - Song, J.
AU  - Lin, J.
AU  - Che, Y.
AU  - Zheng, H.
AU  - Lin, J.
TI  - Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation.
JO  - J. Microbiol.
PY  - 2011
SP  - 890
EP  - 901
VL  - 49
AB  - Leptospirillum ferriphilum has been identified as the dominant, moderately
AB  - thermophilic, bioleaching microorganism in bioleaching processes. It is an acidic
AB  - and chemolithoautrophic bacterium that gains electrons from ferrous iron
AB  - oxidation for energy production and cell growth. Genetic information about this
AB  - microorganism has been limited until now, which has hindered its further
AB  - exploration. In this study, the complete genome of L. ferripilum ML-04 is
AB  - sequenced and annotated. The bacterium has a single circular chromosome of
AB  - 2,406,157 bp containing 2,471 coding sequences (CDS), 2 rRNA operons, 48 tRNA
AB  - genes, a large number of mobile genetic elements and 2 genomic islands. In silico
AB  - analysis shows L. ferriphilum ML-04 fixes carbon through a reductive citric acid
AB  - (rTCA) cycle, and obtains nitrogen through ammonium assimilation. The genes
AB  - related to "cell envelope biogenesis, outer membrane" (6.9%) and "DNA
AB  - replication, recombination and repair" (5.6%) are abundant, and a large number of
AB  - genes related to heavy metal detoxification, oxidative and acidic stress defense,
AB  - and signal transduction pathways were detected. The genomic plasticity, plentiful
AB  - cell envelope components, inorganic element metabolic abilities and stress
AB  - response mechanisms found the base for this organism's survival in the
AB  - bioleaching niche.
ER  -

TY  - JOUR
AU  - Miao, S.
AU  - Li, F.
AU  - Zhang, M.
AU  - Wang, X.
AU  - He, J.
AU  - Jiang, J.
TI  - Molecular cloning and sequence analysis of Rana tigrina ranavirus (RTV) DNA methyltransferase gene.
JO  - Shuichan Xuebao
PY  - 2002
SP  - 157
EP  - 160
VL  - 26
AB  - The complete gene of RTV DNA methyltransferase (MTase) was amplified, cloned and sequenced.
AB  - The ORF consists of 642 bp, which codes for a protein of 214 aa with a predicted molecular
AB  - mass
AB  - of 24.8kD.  Sequence analysis of MTase gene shows much higher identity to the species of genus
AB  - Ranavirus (96%-97%) than to lymphocystis disease virus (56%), the type species of the genus
AB  - Lymphocystivirus, indicating again that RTV was the member of the genus Ranavirus; just as the
AB  - other vertebrate iridoviruses, the MTase gene of RTV contains the first four highly conserved
AB  - motifs of cytosine MTases but the fifth motif, responsible for DNA binding specificity, is
AB  - missing; among the virus of RTV, doctor fish iridovirus and largemouth bass ranavirus, the
AB  - very
AB  - different identity between MTase and MCP gene suggests that the gene used as target to
AB  - estimate the evolution of the iridoviruses should be suitable.
ER  -

TY  - JOUR
AU  - Miao, Y.
AU  - Zhou, X.
AU  - Xu, Y.
AU  - Yu, S.
TI  - Draft Genome Sequence of Gluconobacter oxydans NL71, a Strain That Efficiently Biocatalyzes Xylose to Xylonic Acid at a High Concentration.
JO  - Genome Announcements
PY  - 2015
SP  - e00615
EP  - e00615
VL  - 3
AB  - Gluconobacter oxydans NL71, a selected strain in the crude lignocellulosic hydrolysate,
AB  - catalyzed 600 g/liter xylose to 586.3 g/liter xylonic acid at 95.1%
AB  - yield. The biocatalysis of xylose yielded three times higher than the best
AB  - previous output, providing a possibility of the industrial scale utilization of
AB  - lignocellulosic xylose. Due to its promising industrial applications, we
AB  - sequenced the complete genome of strain G. oxydans NL71 to further our
AB  - understanding of its overall metabolism.
ER  -

TY  - JOUR
AU  - Miceli, E.
AU  - Presta, L.
AU  - Maggini, V.
AU  - Fondi, M.
AU  - Bosi, E.
AU  - Chiellini, C.
AU  - Fagorzi, C.
AU  - Bogani, P.
AU  - Di Pilato, V.
AU  - Rossolini, G.M.
AU  - Mengoni, A.
AU  - Firenzuoli, F.
AU  - Perrin, E.
AU  - Fani, R.
TI  - New Genome Sequence of an Echinaceapurpurea Endophyte, Arthrobacter sp. Strain EpSL27, Able To Inhibit Human-Opportunistic Pathogens.
JO  - Genome Announcements
PY  - 2017
SP  - e00565
EP  - e00517
VL  - 5
AB  - We announce here the draft genome sequence of Arthrobacter sp. strain EpSL27, isolated from
AB  - the stem and leaves of the medicinal plant Echinacea purpurea and
AB  - able to inhibit human-pathogenic bacterial strains. The genome sequencing of this
AB  - strain may lead to the identification of genes involved in the production of
AB  - antimicrobial molecules.
ER  -

TY  - JOUR
AU  - Michael, G.B.
AU  - Kadlec, K.
AU  - Sweeney, M.T.
AU  - Brzuszkiewicz, E.
AU  - Liesegang, H.
AU  - Daniel, R.
AU  - Murray, R.W.
AU  - Watts, J.L.
AU  - Schwarz, S.
TI  - ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer.
JO  - J. Antimicrob. Chemother.
PY  - 2012
SP  - 91
EP  - 100
VL  - 67
AB  - BackgroundIntegrative and conjugative elements (ICEs) have not been
AB  - detected in Pasteurella multocida. In this study the multiresistance
AB  - ICEPmu1 from bovine P. multocida was analysed for its core genes and its
AB  - ability to conjugatively transfer into strains of the same and different
AB  - genera.MethodsICEPmu1 was identified during whole genome sequencing.
AB  - Coding sequences were predicted by bioinformatic tools and manually
AB  - curated using the annotation software ERGO. Conjugation into P. multocida,
AB  - Mannheimia haemolytica and Escherichia coli recipients was performed by
AB  - mating assays. The presence of ICEPmu1 and its circular intermediate in
AB  - the recipient strains was confirmed by PCR and sequence analysis.
AB  - Integration sites were sequenced. Susceptibility testing of the
AB  - ICEPmu1-carrying recipients was conducted by broth
AB  - microdilution.ResultsThe 82 214 bp ICEPmu1 harbours 88 genes. The core
AB  - genes of ICEPmu1, which are involved in excision/integration and
AB  - conjugative transfer, resemble those found in a 66 641 bp ICE from
AB  - Histophilus somni. ICEPmu1 integrates into a tRNA(Leu) and is flanked by
AB  - 13 bp direct repeats. It is able to conjugatively transfer to P.
AB  - multocida, M. haemolytica and E. coli, where it also uses a tRNA(Leu) for
AB  - integration and produces closely related 13 bp direct repeats. PCR assays
AB  - and susceptibility testing confirmed the presence and the functional
AB  - activity of the ICEPmu1-associated resistance genes in the recipient
AB  - strains.ConclusionsThe observation that the multiresistance ICEPmu1 is
AB  - present in a bovine P. multocida and can easily spread across strain and
AB  - genus boundaries underlines the risk of a rapid dissemination of multiple
AB  - resistance genes, which will distinctly decrease the therapeutic options.
ER  -

TY  - JOUR
AU  - Michel, F.
AU  - Dujon, B.
TI  - Genetic exchanges between bacteriophage T4 and filamentous fungi?
JO  - Cell
PY  - 1986
SP  - 323
EP  - 323
VL  - 46
AB  - Note the sequence similarity between I-TevI and a protein encoded by a class 1 intron in the
AB  - NADH-dehydrogenase gene of Neurospora crassa.
ER  -

TY  - JOUR
AU  - Michiels, J.E.
AU  - Van den Bergh, B.
AU  - Fauvart, M.
AU  - Michiels, J.
TI  - Draft genome sequence of Enterococcus faecium strain LMG 8148.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 63
EP  - 63
VL  - 11
AB  - Enterococcus faecium, traditionally considered a harmless gut commensal, is emerging as an
AB  - important nosocomial pathogen showing increasing rates of
AB  - multidrug resistance. We report the draft genome sequence of E. faecium strain
AB  - LMG 8148, isolated in 1968 from a human in Gothenburg, Sweden. The draft genome
AB  - has a total length of 2,697,490 bp, a GC-content of 38.3 %, and 2,402 predicted
AB  - protein-coding sequences. The isolation of this strain predates the emergence of
AB  - E. faecium as a nosocomial pathogen. Consequently, its genome can be useful in
AB  - comparative genomic studies investigating the evolution of E. faecium as a
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Michiels, J.E.
AU  - Van den Bergh, B.
AU  - Fauvart, M.
AU  - Michiels, J.
TI  - Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 57
EP  - 57
VL  - 11
AB  - Acinetobacter baumannii is a pathogen that is becoming increasingly important and causes
AB  - serious hospital-acquired infections. We sequenced the genome of A.
AB  - baumannii NCTC 13423, a multidrug-resistant strain belonging to the international
AB  - clone II group, isolated from a human infection in the United Kingdom in 2003.
AB  - The 3,937,944 bp draft genome has a GC-content of 39.0 % and a total of 3672
AB  - predicted protein-coding sequences. The availability of genome sequences of
AB  - multidrug-resistant A. baumannii isolates will fuel comparative genomic studies
AB  - to help understand the worrying spread of multidrug resistance in this pathogen.
ER  -

TY  - JOUR
AU  - Mick, J.M.
AU  - Beck, D.J.
TI  - Diamminedichloroplatinum(II) modification of DNA inhibits cutting by restriction endonucleases in a sequence specific manner.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1988
SP  - 164
EP  - 164
VL  - 88
AB  - cis-Diamminedichloroplatinum(II), cis-DDP, is a potent antitumor agent while
AB  - the trans-isomer is ineffective.  Both have been shown to bind to DNA
AB  - preferentially at guanine.  In this study, [32P]-end-labeled DNA modified with
AB  - cis-DDP or trans-DDP was digested with restriction endonucleases having
AB  - recognition sequences at which DDP is capable of reacting to form bifunctional
AB  - adducts:  BstUI, GG^CG; HinPI, G^CGC; HhaI, GCG^C; and BamHI, G^GATCC.
AB  - Inhibition of cutting by these enzymes was compared to that for ClaI, AT^CGAT,
AB  - as DDP reacts with bases of its recognition site in a monofunctional manner.
AB  - Restriction fragments were subjected to electrophoresis and the amounts of
AB  - radioactivity in each were quantitated by densitometry and liquid scintillation
AB  - spectrophotometry.  Inhibition by trans-DDP was greatest when the base sequence
AB  - GXG was adjacent to, or occluding the cut site.  Thus, two guanines separated
AB  - by a third base appears to be a biologically inhibitory adduct of trans-DDP
AB  - while cis-DDP forms such adducts at lower frequency.  Inhibition by cis-DDP was
AB  - greatest at the BamHI site where it can form crosslinks between adjacent
AB  - guanines.
ER  -

TY  - JOUR
AU  - Middleton, D.R.
AU  - Lorenz, W.
AU  - Avci, F.Y.
TI  - Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352.
JO  - Genome Announcements
PY  - 2017
SP  - e00289
EP  - e00217
VL  - 5
AB  - Here, we report the complete genome sequence for the Bacillus circulans Jordan strain 32352.
AB  - This species is a soil dwelling bacterium that expresses glycosyl
AB  - hydrolase enzymes degrading pneumococcal capsular polysaccharides.
ER  -

TY  - JOUR
AU  - Middleton, J.H.
TI  - Restriction endonucleases from Haemophilus species: Enzymes for specific fragmentation of DNA.
JO  - Ph.D. Thesis
PY  - 1973
AB  - Restriction endodeoxyribonucleases cleave DNA at specific recognition sites.  We proposed to
AB  - employ such enzymes as reagents for analysis of DNA.  Screening procedures were begun to
AB  - identify restriction enzymes that would cleave OmegaX174 DNA into unique fragments.
ER  -

TY  - JOUR
AU  - Middleton, J.H.
AU  - Edgell, M.H.
AU  - Hutchison, C.A. III
TI  - Specific fragments of PhiX174 deoxyribonucleic acid produced by a restriction enzyme from Haemophilus aegyptius, endonuclease Z.
JO  - J. Virol.
PY  - 1972
SP  - 42
EP  - 50
VL  - 10
AB  - A restriction-like enzyme has been purified from Haemophilus aegyptius.  This
AB  - nuclease, endonuclease Z, produces a rapid decrease in the viscosity of native
AB  - calf thymus and H. influenzae deoxyribonucleic acids (DNA), but does not
AB  - degrade homologous DNA.  The specificity of endonuclease Z is different from
AB  - that of the similar endonuclease isolated from H. influenzae (endonuclease R).
AB  - The purified enzyme cleaves the double-stranded replicative form DNA of
AB  - bacteriophage PhiX174 (PhiX174 RF DNA) into at least 11 specific limit
AB  - fragments whose molecular sizes have been estimated by gel electrophoresis.
AB  - The position of these fragments with respect to the genetic map of PhiX174 can
AB  - be determined by using the genetic assay for small fragments of PhiX174 DNA.
ER  -

TY  - JOUR
AU  - Midha, S.
AU  - Ranjan, M.
AU  - Sharma, V.
AU  - Kumari, A.
AU  - Singh, P.K.
AU  - Korpole, S.
AU  - Patil, P.B.
TI  - Genome Sequence of Pediococcus pentosaceus Strain IE-3.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4468
EP  - 4468
VL  - 194
AB  - We report the 1.8-Mb genome sequence of Pediococcus pentosaceus strain IE-3, isolated from a
AB  - dairy effluent sample. The whole-genome sequence of this strain
AB  - will aid in comparative genomics of Pediococcus pentosaceus strains of diverse
AB  - ecological origins and their biotechnological applications.
ER  -

TY  - JOUR
AU  - Midha, S.
AU  - Ranjan, M.
AU  - Sharma, V.
AU  - Pinnaka, A.K.
AU  - Patil, P.B.
TI  - Genome Sequence of Xanthomonas citri pv. mangiferaeindicae Strain LMG 941.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3031
EP  - 3031
VL  - 194
AB  - We report the 5.1-Mb genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG
AB  - 941, the causal agent of bacterial black spot in mango. Apart from evolutionary studies, the
AB  - draft genome will be a valuable resource for the epidemiological studies and quarantine of
AB  - this phytopathogen.
ER  -

TY  - JOUR
AU  - Mierzejewska, K.
AU  - Bochtler, M.
AU  - Czapinska, H.
TI  - On the role of steric clashes in methylation control of restriction endonuclease  activity.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 485
EP  - 495
VL  - 44
AB  - Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA
AB  - against the endonuclease activity by methylation. It is widely believed that the methylated
AB  - DNA would not 'fit' into the binding site of the endonuclease in the productive orientation,
AB  - and thus steric clashes should account for most of the protection. We test this concept
AB  - statistically by grafting methyl groups in silico onto non-methylated DNA in co-crystal
AB  - structures with restriction endonucleases. Clash scores are significantly higher for
AB  - protective than non-protective methylation (P < 0.05% according to the Wilcoxon rank sum
AB  - test). Structural data alone are sufficient to distinguish between protective and
AB  - non-protective DNA methylation with 90% confidence and decision thresholds of 1.1 A and 48 A3
AB  - for the most severe distance-based and cumulative volume-based clash with the protein,
AB  - respectively (0.1 A was deducted from each interatomic distance to allow for coordinate
AB  - errors). The most severe clashes are more pronounced for protective methyl groups attached to
AB  - the nitrogen atoms (N6-methyladenines and N4-methylcytosines) than for C5-methyl groups on
AB  - cytosines. Cumulative clashes are comparable for all three types of protective methylation.
ER  -

TY  - JOUR
AU  - Mierzejewska, K.
AU  - Siwek, W.
AU  - Czapinska, H.
AU  - Kaus-Drobek, M.
AU  - Radlinska, M.
AU  - Skowronek, K.
AU  - Bujnicki, J.M.
AU  - Dadlez, M.
AU  - Bochtler, M.
TI  - Structural basis of the methylation specificity of R.DpnI.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 8745
EP  - 8754
VL  - 42
AB  - R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that  are
AB  - separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we
AB  - present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic
AB  - and winged helix domains and identify the catalytic domain residues that are
AB  - involved in interactions with the substrate methyl groups. We show that these
AB  - methyl groups in the Gm6ATC target sequence are positioned very close to each
AB  - other. We further show that the presence of the two methyl groups requires a
AB  - deviation from B-DNA conformation to avoid steric conflict. The methylation
AB  - compatible DNA conformation is complementary with binding sites of both R.DpnI
AB  - domains. This indirect readout of methylation adds to the specificity mediated by
AB  - direct favorable interactions with the methyl groups and solvation/desolvation
AB  - effects. We also present hydrogen/deuterium exchange data that support
AB  - 'crosstalk' between the two domains in the identification of methylated DNA,
AB  - which should further enhance R.DpnI methylation specificity.
ER  -

TY  - JOUR
AU  - Mierzejewska, K.
AU  - Siwek, W.
AU  - Czapinska, H.
AU  - Skowronek, K.
AU  - Bujnicki, J.
AU  - Bochtler, M.
TI  - Molecular basis of 6-methyladenine recognition by R.DpnI restriction endonuclease.
JO  - FEBS J.
PY  - 2013
SP  - 122
EP  - 123
VL  - 280
AB  - The 6-methyladenine is one of the key epigenetic modifications in prokaryotes.  R.DpnI is the
AB  - best known 6 mA-dependent restriction endonuclease, specific for Dam methylated G6 mATC sites
AB  - and widely used for site-directed mutagenesis.  Our previous studies have shown that R.DpnI
AB  - consists of two domains, an N-terminal catalytic PD-D/E_XK domain and a C-terminal winged
AB  - helix domain and that both independently read out DNA sequence and methylation status.  In our
AB  - first structure of R.DpnI-DNA complex, there is only one substrate oligoduplex per enzyme
AB  - molecule, which is specifically bound to the wH domain and distant from the calalytic domain.
AB  - Hence, the question remained open how the catalytic domain of R.DpnI interacts with its
AB  - target, and how it specifically recognizes the methyl groups which license DNA cleavage.  Such
AB  - a process is difficult to realize with stringency, because attractive van der Waals
AB  - interactions with the small hydrophobic group are relatively weak when compared to repulsive
AB  - ones.  The structures depicting the phenomenon are rare and there is still relatively little
AB  - known about the mechanism of recognition by modification dependent enzymes.  Here, we present
AB  - a high resolution structure of R.DpnI which features both protein domains bound to the target
AB  - DNA.  Recognition of the 6mAs by the catalytic domain is carried out without flipping bases
AB  - out of the helix.  A previously disordered loop wraps around the major groove of the target
AB  - DNA, where both methyl groups are located in close proximity to each other.  The PD-D/E)XK
AB  - domain places the 6mAs in a hydrophobic pocket formed by residues Leu129 and Trp 138.  To the
AB  - best of our knowledge this is the first structure showing how a protein can efficiently detect
AB  - two 6mA modified sites together.
ER  -

TY  - JOUR
AU  - Mignolet, J.
AU  - Fontaine, L.
AU  - Kleerebezem, M.
AU  - Hols, P.
TI  - Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract.
JO  - Genome Announcements
PY  - 2016
SP  - e01637
EP  - e01615
VL  - 4
AB  - The human commensal bacterium Streptococcus salivarius plays a major role in the  equilibrium
AB  - of microbial communities of the digestive tract. Here, we report the
AB  - first complete genome sequence of a Streptococcus salivarius strain isolated from
AB  - the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903
AB  - coding sequences and 2,100,988 nucleotides.
ER  -

TY  - JOUR
AU  - Miki, T.
AU  - Okada, N.
TI  - Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e01047
EP  - e01014
VL  - 2
AB  - Chromobacterium haemolyticum is a Gram-negative bacterium displaying remarkable hemolysis
AB  - against human and sheep erythrocytes. In addition, C. haemolyticum
AB  - infects humans, in which the infection mechanism remains unknown. We report here
AB  - the draft genome sequence of C. haemolyticum strain T124, isolated from a young
AB  - patient with sepsis in Japan.
ER  -

TY  - JOUR
AU  - Milani, C.
AU  - Duranti, S.
AU  - Lugli, G.A.
AU  - Bottacini, F.
AU  - Strati, F.
AU  - Arioli, S.
AU  - Foroni, E.
AU  - Turroni, F.
AU  - van Sinderen, D.
AU  - Ventura, M.
TI  - Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 4304
EP  - 4315
VL  - 79
AB  - Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by
AB  - the food industry as health-promoting bacteria, although the genetic variability
AB  - of members belonging to this taxon has so far not received much scientific
AB  - attention. In this article, we describe the complete genetic makeup of the B.
AB  - animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this
AB  - strain with other sequenced strains belonging to this taxon. Moreover, a detailed
AB  - comparative genomic analysis of B. animalis subsp. lactis genomes was performed,
AB  - which revealed a closely related and isogenic nature of all currently available
AB  - B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome
AB  - structure of this bacterial group.
ER  -

TY  - JOUR
AU  - Milani, C.
AU  - Lugli, G.A.
AU  - Duranti, S.
AU  - Turroni, F.
AU  - Bottacini, F.
AU  - Mangifesta, M.
AU  - Sanchez, B.
AU  - Viappiani, A.
AU  - Mancabelli, L.
AU  - Taminiau, B.
AU  - Delcenserie, V.
AU  - Barrangou, R.
AU  - Margolles, A.
AU  - van Sinderen, D.
AU  - Ventura, M.
TI  - Genome encyclopaedia of type strains of the genus Bifidobacterium.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 6290
EP  - 6302
VL  - 80
AB  - Bifidobacteria represent one of the dominant microbial groups that are present in the gut of
AB  - various animals, being particularly prevalent during the suckling stage of life of humans and
AB  - other mammals.  However, the overall genome structure of this group of microorganisms remains
AB  - largely unexplored.  Here, we sequenced the genomes of 42 representative (sub)species across
AB  - the Bifidobacterium genus, and used this information to explore the overall genetic picture of
AB  - this bacterial group.  Furthermore, the here described genomic data were used to reconstruct
AB  - the evolutionary development of the Bifidobacterium genus.  This reconstruction suggests that
AB  - its evolution was substantially influenced by genetic adaptations to obtain access to glycans,
AB  - thereby representing a common and potent evolutionary force in shaping bifidobacterial
AB  - genomes.
ER  -

TY  - JOUR
AU  - Militello, K.T.
AU  - Mandarano, A.H.
AU  - Varechtchouk, O.
AU  - Simon, R.D.
TI  - Cytosine DNA methylation influences drug resistance in Escherichia coli through increased sugE expression.
JO  - FEMS Microbiol. Lett.
PY  - 2014
SP  - 100
EP  - 106
VL  - 350
AB  - Escherichia coli K-12 strains contain the orphan cytosine-5 DNA methyltransferase enzyme Dcm
AB  - (DNA cytosine methyltransferase). Two recent reports indicate that Dcm
AB  - has an influence on stationary phase gene expression in E. coli. Herein, we
AB  - demonstrate that dcm knockout cells overexpress the drug resistance transporter
AB  - SugE, which has been linked to ethidium bromide (ETBR) resistance. SugE
AB  - expression also increased in the presence of the DNA methylation inhibitor
AB  - 5-azacytidine, suggesting that Dcm-mediated DNA methylation normally represses
AB  - sugE expression. The effect of Dcm on sugE expression is primarily restricted to
AB  - early stationary phase, and RpoS is required for robust sugE expression. Dcm
AB  - knockout cells are more resistant to ETBR than wild-type cells, and
AB  - complementation with a plasmid-borne dcm gene restores ETBR sensitivity. SugE
AB  - knockout cells are more sensitive to ETBR than wild-type cells. These data
AB  - indicate that Dcm influences the sensitivity to an antimicrobial compound through
AB  - changes in gene expression.
ER  -

TY  - JOUR
AU  - Militello, K.T.
AU  - Simon, R.D.
AU  - Qureshi, M.
AU  - Maines, R.
AU  - VanHorne, M.L.
AU  - Hennick, S.M.
AU  - Jayakar, S.K.
AU  - Pounder, S.
TI  - Dcm-mediated cytosine DNA methylation is conserved in Escherichia coli and influences the expression of ribosomal protein genes.
JO  - FASEB J.
PY  - 2010
SP  - 78
EP  - 85
VL  - 24
AB  - In Escherichia coli, cytosine DNA methylation is catalyzed by the Dcm (DNA cytosine methylase)
AB  - protein and occurs at the second cytosine in the sequence 5'CCWGG3'. Although the presence
AB  - of cytosine DNA methylation was reported over 35 years ago, the biological role of
AB  - 5-methylcytosine in E. coli remains unclear. There is data indicating that Dcm can protect the
AB  - genome against attack by a restriction enzyme that cleaves the same sequence, yet DNA
AB  - methyltransferases in eukaryotes often influence gene expression. In order to gain insight
AB  - into the potential roles of cytosine DNA methylation in E. coli, we: (a) screened 162 strains
AB  - including laboratory strains, pathogens, and recently isolated environmental samples for the
AB  - presence of the full-length dcm gene using the polymerase chain reaction; (b) examined the
AB  - same strains for the presence of 5-methylcytosine at 5'CCWGG3' sites using a restriction
AB  - enzyme isoschizomer digestion assay; and (c) quantified the levels of
AB  - 5-methyl-2'-deoxycytidine in selected strains using liquid chromatography tandem mass
AB  - spectrometry. Dcm-mediated cytosine DNA methylation is conserved in all 162 strains examined,
AB  - and the level of 5-methylcytosine ranges from 0.8-1.2% of the cytosines. We also tested the
AB  - hypothesis that Dcm influences gene expression. Gene expression in wild-type and dcm knockout
AB  - cells was compared via qPCR. We focused on ribosomal protein genes, as they have been
AB  - previously demonstrated to contain numerous 5'CCWGG3' sites. We demonstrate that Dcm
AB  - represses expression of ribosomal protein genes during stationary phase, and this may explain
AB  - the ubiquitous presence of this DNA modification pathway. Support for this work was provided
AB  - by the Geneseo Foundation and NIH grant R15AI074035-01.
ER  -

TY  - JOUR
AU  - Militello, K.T.
AU  - Simon, R.D.
AU  - Qureshi, M.
AU  - Maines, R.
AU  - VanHorne, M.L.
AU  - Hennick, S.M.
AU  - Jayakar, S.K.
AU  - Pounder, S.
TI  - Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli.
JO  - FEMS Microbiol. Lett.
PY  - 2012
SP  - 78
EP  - 85
VL  - 328
AB  - In Escherichia coli, cytosine DNA methylation is catalyzed by the DNA cytosine
AB  - methyltransferase (Dcm) protein and occurs at the second
AB  - cytosine in the sequence 5'CCWGG3'. Although the presence of cytosine
AB  - DNA methylation was reported over 35years ago, the biological role of
AB  - 5-methylcytosine in E.coli remains unclear. To gain insight into the
AB  - role of cytosine DNA methylation in E.coli, we (1) screened the 72
AB  - strains of the ECOR collection and 90 recently isolated environmental
AB  - samples for the presence of the full-length dcm gene using the
AB  - polymerase chain reaction; (2) examined the same strains for the
AB  - presence of 5-methylcytosine at 5'CCWGG3' sites using a restriction
AB  - enzyme isoschizomer digestion assay; and (3) quantified the levels of
AB  - 5-methyl-2'-deoxycytidine in selected strains using liquid
AB  - chromatography tandem mass spectrometry. Dcm-mediated cytosine DNA
AB  - methylation is conserved in all 162 strains examined, and the level of
AB  - 5-methylcytosine ranges from 0.86% to 1.30% of the cytosines. We also
AB  - demonstrate that Dcm reduces the expression of ribosomal protein genes
AB  - during stationary phase, and this may explain the highly conserved
AB  - nature of this DNA modification pathway.
ER  -

TY  - JOUR
AU  - Milkman, R.
TI  - Recombination and population structure in Escherichia coli.
JO  - Genetics
PY  - 1997
SP  - 745
EP  - 750
VL  - 146
AB  - A major focus of population genetics, and now of molecular evolution, is the study of gene
AB  - lineages.  Population genetic parameters usually apply to small chromosomal regions rather
AB  - than to the genome as a whole, although genes do not always descend independently of their
AB  - surroundings.  The genome of Escherichia coli strikes me as an unusually favorable theater in
AB  - which to observe the lineages of genes and their relationships with the evolutionary processes
AB  - that operate at the population level.  I should like to trace the developing understanding of
AB  - E. coli's population genetics in  the coexistence of clonality and recombination, the
AB  - recognition of restriction as important to recombination, and the emerging features of its
AB  - genomic structure.
ER  -

TY  - JOUR
AU  - Milkman, R.
AU  - Jaeger, E.
AU  - McBride, R.D.
TI  - Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination.
JO  - Genetics
PY  - 2003
SP  - 475
EP  - 483
VL  - 163
AB  - Two 6- to 8-min regions, centered respectively near 45 min (O-antigen region) and 99 min
AB  - (restriction-modification region) on the Escherichia
AB  - coli chromosome, display unusually high variability among 11 otherwise
AB  - very similar strains. This variation, revealed by restriction fragment
AB  - length polymorphism (RFLP) and nucleotide sequence comparisons, appears to
AB  - be due to a great local increase in the retention frequency of recombinant
AB  - replacements. We infer a two-step mechanism. The first step is the
AB  - acquisition of a small stretch of DNA from a phylogenetically distant
AB  - source. The second is the successful retransmission of the imported DNA,
AB  - together with flanking native DNA, to other strains of E. coli. Each cell
AB  - containing the newly transferred DNA has a very high selective advantage
AB  - until it reaches a high frequency and (in the O-antigen case) is
AB  - recognized by the new host's immune system. A high selective advantage
AB  - increases the probability of retention greatly; the effective
AB  - recombination rate is the product of the basic recombination rate and the
AB  - probability of retention. Nearby nucleotide sequences clockwise from the
AB  - O-antigen (rfb) region are correlated with specific O antigens, confirming
AB  - local hitchhiking. Comparable selection involving imported restriction
AB  - endonuclease genes is proposed for the region near 99 min.
ER  -

TY  - JOUR
AU  - Milkman, R.
AU  - Raleigh, E.A.
AU  - McKane, M.
AU  - Cryderman, D.
AU  - Bilodeau, P.
AU  - McWeeny, K.
TI  - Molecular evolution of the escherichia coli chromosome. V. Recombination patterns among strains of diverse origin.
JO  - Genetics
PY  - 1999
SP  - 539
EP  - 554
VL  - 153
AB  - Incorporation patterns of donor DNA into recipient chromosomes following transduction or
AB  - conjugation have been studied in the progeny of a variety of Escherichia coli crosses in which
AB  - donor and recipient nucleotide sequences differ by 1-3%. Series of contiguous or variously
AB  - spaced PCR fragments have been amplified from each recombinant chromosome and digested with a
AB  - commercial restriction endonuclease previously shown to distinguish the respective parents in
AB  - a given fragment. We conclude that entering donor DNA fragments are frequently abridged (cut
AB  - and shortened) before incorporation, the cutting being due to restriction systems, and the
AB  - shortening presumably due to exonuclease activity. Analysis of several backcrosses confirms,
AB  - and extends to conjugation, the importance of restriction in E. coli recombination in nature.
AB  - The transmission patterns in conjugation are similar to those of transduction, but (as
AB  - expected) on a much larger scale. Asymmetric results of reciprocal crosses imply that mismatch
AB  - frequency is not a major factor. Marked differences among the results of simple crosses
AB  - according to parental strain combinations are consistent with observations that E. coli
AB  - strains in nature vary dramatically in their restriction-modification systems.
ER  -

TY  - JOUR
AU  - Milla, M.A.
AU  - Spears, P.A.
AU  - Pearson, R.E.
AU  - Walker, G.T.
TI  - Use of the restriction enzyme AvaI and Exo- Bst polymerase in strand displacement amplification.
JO  - Biotechniques
PY  - 1998
SP  - 392
EP  - 396
VL  - 24
AB  - Strand displacement amplification is an isothermal in vitro method of amplifying DNA.  This
AB  - technique is based on the ability of a restriction enzyme to nick one strand of a
AB  - hemiphosphorothioated form of its double-stranded recognition site and the ability of a
AB  - polymerase to initiate synthesis at the nick and displace the downstream DNA strand during
AB  - replication.  The method consists of two parts: (i) a target generation process that makes
AB  - copies of the target sequence flanked by nickable restriction sites and (ii) the exponential
AB  - amplification of these modified target sequences by repeated nicking, strand displacement and
AB  - priming of displaced strands, as depicted in Figure 1.  The first SDA system we developed used
AB  - the restriction enzyme HincII and the 3'-5' exonuclease-deficient Klenow fragment of E. coli
AB  - polymerase I.  This system achieves 10^8-fold amplification in 2h at 37-40 C.  More recently,
AB  - we have developed a thermophilic SDA system that operates at 60 C and uses a restriction
AB  - enzyme from Bacillus stearothermophilus and a 3'-5' exonuclease-deficient Klenow fragment of
AB  - a DNA polymerase from B. caldotenax.  This system is faster and more powerful, achieving a
AB  - 10^10-fold amplification in 15 min.  It is also more specific, with a significant reduction in
AB  - background amplification.
ER  -

TY  - JOUR
AU  - Millar, J.A.
AU  - Beare, P.A.
AU  - Moses, A.S.
AU  - Martens, C.A.
AU  - Heinzen, R.A.
AU  - Raghavan, R.
TI  - Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4),  a Laboratory Workhorse Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e00471
EP  - e00417
VL  - 5
AB  - Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II,
AB  - clone 4), a laboratory strain used extensively to investigate the
AB  - biology of this intracellular bacterial pathogen. The genome consists of a
AB  - 1.97-Mb chromosome and a 37.32-kb plasmid.
ER  -

TY  - JOUR
AU  - Millard, A.
AU  - Clokie, M.R.
AU  - Shub, D.A.
AU  - Mann, N.H.
TI  - Genetic organization of the psbAD region in phages infecting marine Synechococcus strains.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 11007
EP  - 11012
VL  - 101
AB  - The discovery of the genes psbA and psbD, encoding the D1 and D2 core components  of the
AB  - photosynthetic reaction center PSII (photosystem II), in the genome of the
AB  - bacteriophage S-PM2 (a cyanomyovirus) that infects marine cyanobacteria begs the
AB  - question as to how these genes were acquired. In an attempt to answer this
AB  - question, it was established that the occurrence of the genes is widespread among
AB  - marine cyanomyovirus isolates and may even extend to podoviruses. The phage psbA
AB  - genes fall into a clade that includes the psbA genes from their potential
AB  - Synechococcus and Prochlorococcus hosts, and thus, this phylogenetic analysis
AB  - provides evidence to support the idea of the acquisition of these genes by
AB  - horizontal gene transfer from their cyanobacterial hosts. However, the phage psbA
AB  - genes form distinct subclades within this lineage, which suggests that their
AB  - acquisition was not very recent. The psbA genes of two phages contain identical
AB  - 212-bp insertions that exhibit all of the canonical structural features of a
AB  - group I self-splicing intron. The different patterns of genetic organization of
AB  - the psbAD region are consistent with the idea that the psbA and psbD genes were
AB  - acquired more than once by cyanomyoviruses and that their horizontal transfer
AB  - between phages via a common phage gene pool, as part of mobile genetic modules,
AB  - may be a continuing process. In addition, genes were discovered encoding a
AB  - high-light inducible protein and a putative key enzyme of dark metabolism,
AB  - transaldolase, extending the areas of host-cell metabolism that may be affected
AB  - by phage infection.
ER  -

TY  - JOUR
AU  - Millard, A.D.
AU  - Westblade, L.F.
AU  - LiPuma, J.J.
AU  - Vavikolanu, K.
AU  - Read, T.D.
AU  - Pallen, M.J.
AU  - Burd, E.M.
AU  - Constantinidou, C.I.
TI  - Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01300
EP  - e01315
VL  - 3
AB  - Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant
AB  - pathogens in persons with cystic fibrosis (CF). To aid in
AB  - understanding the role of P. apista in CF lung disease, we used Illumina MiSeq
AB  - and nanopore MinION technology to sequence the whole genome of the P. apista LMG
AB  - 16407(T).
ER  -

TY  - JOUR
AU  - Millard, J.T.
AU  - Beachy, T.M.
TI  - Cytosine methylation enhances mitomycin C cross-linking.
JO  - Biochemistry
PY  - 1993
SP  - 12850
EP  - 12856
VL  - 32
AB  - MitomycinC (M) is a powerful antitumor agent that targets the DNA sequence CpG. Because it is
AB  - likely that this dinucleotide will contain 5-methylcytosine in vivo, we have compared the
AB  - cross-linking efficiency of MC for DNA containing either 5-methylcytosine or normal cytosine
AB  - embedded in random sequence DNA oligomers. We have found that mitomycin C displays a small but
AB  - significant preference for methylated DNA. Recognition of an abnormal methylation pattern in
AB  - the DNA of transformed cells may therefore be one mechanism by which MC exerts its
AB  - chemotherapeutic effects.
ER  -

TY  - JOUR
AU  - Miller, C.A.
AU  - Cohen, S.N.
TI  - Phenotypically cryptic EcoRI endonuclease specified by the ColE1 plasmid.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1978
SP  - 1265
EP  - 1269
VL  - 75
AB  - An endonuclease having EcoRI specificity is produced by bacteria containing the
AB  - ColE1 plasmid.  Such bacterial cells fail to express restriction or
AB  - modification functions in vivo, and phage or plasmid DNA obtained from
AB  - ColE1-containing cells has unmodified EcoRI sites that are extracted from
AB  - bacteria that carry ColE1.  No EcoRI DNA methylase activity associated with
AB  - ColE1 has been detected.  The finding of phenotypically cryptic ColE1-dependent
AB  - EcoRI endonuclease activity and the absence of any detectable EcoRI
AB  - modification system in ColE1-containing cells suggest a control mechanism that
AB  - appears to prevent functional expression of the ColE1-determined enzyme in
AB  - vivo.
ER  -

TY  - JOUR
AU  - Miller, C.L.
AU  - Chen, T.
AU  - Chen, P.
AU  - Leung, K.P.
TI  - Genome Sequence of Highly Virulent Pseudomonas aeruginosa Strain VA-134, Isolated from a Burn Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e01662
EP  - e01615
VL  - 4
AB  - Infection with Pseudomonas aeruginosa leads to impairment of healing and many deaths in severe
AB  - burn patients. The phenotypic diversity of P. aeruginosa strains
AB  - makes it difficult to define a therapeutic strategy. Here we report the genome
AB  - sequence of a highly virulent strain of P. aeruginosa, VA-134, isolated from a
AB  - burn patient.
ER  -

TY  - JOUR
AU  - Miller, D.A. et al.
TI  - Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2357
EP  - 2358
VL  - 193
AB  - Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the
AB  - Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium;
AB  - originally isolated from estuarine sediment of a river that received both domestic and paper
AB  - mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors
AB  - that influence degradation rates.
ER  -

TY  - JOUR
AU  - Miller, J.C.
AU  - Holmes, M.C.
AU  - Wang, J.
AU  - Guschin, D.Y.
AU  - Lee, Y.L.
AU  - Rupniewski, I.
AU  - Beausejour, C.M.
AU  - Waite, A.J.
AU  - Wang, N.S.
AU  - Kim, K.A.
AU  - Gregory, P.D.
AU  - Pabo, C.O.
AU  - Rebar, E.J.
TI  - An improved zinc-finger nuclease architecture for highly specific genome editing.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 778
EP  - 785
VL  - 25
AB  - Genome editing driven by zinc-finger nucleases (ZFNs) yields high gene-modification
AB  - efficiencies (>10%) by introducing a recombinogenic
AB  - double-strand break into the targeted gene. The cleavage event is induced
AB  - using two custom-designed ZFNs that heterodimerize upon binding DNA to
AB  - form a catalytically active nuclease complex. Using the current ZFN
AB  - architecture, however, cleavage-competent homodimers may also form that
AB  - can limit safety or efficacy via off-target cleavage. Here we develop an
AB  - improved ZFN architecture that eliminates this problem. Using
AB  - structure-based design, we engineer two variant ZFNs that efficiently
AB  - cleave DNA only when paired as a heterodimer. These ZFNs modify a native
AB  - endogenous locus as efficiently as the parental architecture, but with a
AB  - >40-fold reduction in homodimer function and much lower levels of
AB  - genome-wide cleavage. This architecture provides a general means for
AB  - improving the specificity of ZFNs as gene modification reagents.
ER  -

TY  - JOUR
AU  - Miller, J.F.
AU  - Dower, W.J.
AU  - Tompkins, L.S.
TI  - High-voltage electroporation of bacteria:  Genetic transformation of Campylobacter jejuni with plasmid DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1988
SP  - 856
EP  - 860
VL  - 85
AB  - Electroporation permits the uptake of DNA by mammalian cells and plant
AB  - protoplasts because it induces transient permeability of the cell membrane.  We
AB  - investigated the utility of high-voltage electroporation as a method for
AB  - genetic transformation of intact bacterial cells by using the enteric pathogen
AB  - Campylobacter jejuni as a model system.  This report demonstrates that the
AB  - application of high-voltage discharges to bacterial cells permits genetic
AB  - transformation.  Our method involves exposure of a Campylobacter cell
AB  - suspension to a high-voltage exponential decay discharge (5-13 kV/cm) for a
AB  - brief period of time (resistance-capacitance time constant = 2.4-26 msec) in
AB  - the presence of plasmid DNA.  Electrical transformation of C. jejuni results in
AB  - frequencies as high as 1.2 x 10/6 transformants per microgram of DNA.  We have
AB  - investigated the effects of pulse amplitude and duration, cell growth
AB  - conditions, divalent cations, and DNA concentration on the efficiency of
AB  - transformation.  Transformants of C. jejuni obtained by electroporation
AB  - contained structurally intact plasmid molecules.  In addition, evidence is
AB  - presented that indicates that C. jejuni possesses DNA restriction and
AB  - modification systems.  The use of electroporation as a method for transforming
AB  - other bacterial species and guidelines for its implementation are also
AB  - discussed.
ER  -

TY  - JOUR
AU  - Miller, P.A.
AU  - Shajani, Z.
AU  - Meints, G.A.
AU  - Caplow, D.
AU  - Goobes, G.
AU  - Varani, G.
AU  - Drobny, G.P.
TI  - Contrasting Views of the Internal Dynamics of the HhaI Methyltransferase Target DNA Reported by Solution and Solid-State NMR Spectroscopy.
JO  - J. Am. Chem. Soc.
PY  - 2006
SP  - 15970
EP  - 15971
VL  - 128
AB  - The enzymatic methylation of deoxyribonucleic acid is essential for many biological processes
AB  - and has therefore been studied in considerable detail.  The structure of the ternary complex
AB  - of the HhaI methyltransferase with its DNA target [5'-(dGATAGCGCTATC)-3']2 and the
AB  - methyl-donating cofactor S-adenosyl L-methionine demonstrated that the substrate cytosine is
AB  - extruded from its normally base-paired position.  Through this confirmational change, the
AB  - carbon at the C5 position on the base of the underlined cytosine becomes accessible in the
AB  - enzyme's catalytic pocket.  The interactions observed between the protein and the extruded
AB  - base explain the stabilization of this highly distorted structure but do not provide a
AB  - mechanism or pathway to flip the base outside of the double helix.  What are the energetically
AB  - favorable pathways that allow base extrusion?  Are they sequence dependent?
ER  -

TY  - JOUR
AU  - Miller, P.B.
AU  - Wakarchuk, W.W.
AU  - Warren, R.A.J.
TI  - Alpha-putrescinylthymine and the sensitivity of bacteriophage Phi W-14 DNA to restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 2559
EP  - 2568
VL  - 13
AB  - The modified base alpha-putrescinylthymine (putT) in Phi W-14 DNA blocks
AB  - cleavage of the DNA by 17 of 32 Type II restriction endonucleases.  The enzymes
AB  - cleaving the DNA do so to widely varying extents.  The frequencies of cleavage
AB  - of three altered forms of the DNA show that putT blocks recognition sites
AB  - either when it occurs within the site or when it is in a sequence flanking the
AB  - site.  The blocking is dependent on both charge and steric factors.  The charge
AB  - effects can be greater than the steric effects for some of the enzymes tested.
AB  - All the enzymes cleaving Phi W-14 DNA release discrete fragments, showing that
AB  - the distribution of putT is ordered.  The cleavage frequencies for different
AB  - enzymes suggest that the sequence CAputTG occurs frequently in DNA.  Only TaqI
AB  - of the enzymes tested appeared not to be blocked by putT, but it was slowed
AB  - down.  TaqI generated fragments are joinable by T4 DNA ligase.
ER  -

TY  - JOUR
AU  - Miller, T.R.
AU  - Delcher, A.L.
AU  - Salzberg, S.L.
AU  - Saunders, E.
AU  - Detter, J.C.
AU  - Halden, R.U.
TI  - Genome Sequence of the Dioxin-Mineralizing Bacterium Sphingomonas wittichii RW1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6101
EP  - 6102
VL  - 192
AB  - Pollutants such as polychlorinated biphenyls and dioxins pose a serious threat to human and
AB  - environmental health. Natural attenuation of these
AB  - compounds by microorganisms provides one promising avenue for their
AB  - removal from contaminated areas. Over the past 2 decades, studies of the
AB  - bacterium Sphingomonas wittichii RW1 have provided a wealth of knowledge
AB  - about how bacteria metabolize chlorinated aromatic hydrocarbons. Here we
AB  - describe the finished genome sequence of S. wittichii RW1 and major
AB  - findings from its annotation.
ER  -

TY  - JOUR
AU  - Miller, W.G.
TI  - Characterization of multiple Campylobacter jejuni type I restriction-modification loci.
JO  - Int. J. Med. Microbiol.
PY  - 2001
SP  - 79
EP  - 79
VL  - 291
AB  - Type I restriction-modification systems have been found in many bacterial taxa.  Type I
AB  - enzymes are composed of three subunits, encoded by the hsdR, hsdS, and hsdM genes.  All three
AB  - gene products are necessary for restriction, whereas the hsdM and hsdS gene products are
AB  - sufficient for methylation.  To characterize the Campylobacter jejuni type I
AB  - restriction-modification systems, the hsd loci from eight C. jejuni strains were cloned and
AB  - sequence.  The enteric hsd genes and the H. pylori hsd genes are contiguous; however, in C.
AB  - jejuni, intervening ORFs are present between hsdR and hsdS and between hsdS and hsdM.  The
AB  - function of the "RS"  ORF is unknown and the "SM" ORF probably serves no function since it is
AB  - absent in at least two loci.  Based on DNA homology and complementation, the enteric hsd loci
AB  - have been subdivided into five families (IA, IB, IC, ID, and IE).  The hsd loci of C. jejuni
AB  - can also be divided into families: BLAST analysis suggests that the hsd locus of NCTC 81116 is
AB  - homologous to the IB family and the hsd loci of NCTC 11168 and 81-176 are homologous to the ID
AB  - family.  The hsdM gene of C. jejuni RM1221 ("IB") is more homologous to its enteric
AB  - counterparts (E-e-74) than to the hsdM genes of NCTC 11168 (E=e-24) and H. pylori 26695
AB  - (E=e-22).  To determine if additional families exist or if some strains have multiple loci, 39
AB  - C. jejuni strains were amplified with "IB" - and "ID"-specific probes.  Twelve strains could
AB  - not be assigned to either the "IB" or "ID" family, suggesting that at least one additional
AB  - family may exist.  Also, no strain amplified with both the "IB" and "ID" probes; however, the
AB  - presence of one or more strains that contain multiple loci of the same family cannot be
AB  - eliminated.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Chapman, M.H.
AU  - Yee, E.
AU  - Revez, J.
AU  - Bono, J.L.
AU  - Rossi, M.
TI  - Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591.
JO  - Genome Announcements
PY  - 2017
SP  - e01221
EP  - e01217
VL  - 5
AB  - Campylobacter avium is a thermotolerant Campylobacter species that has been isolated from
AB  - poultry. C. avium was also the second hippuricase-positive species
AB  - to be identified within Campylobacter Here, we present the genome sequence of the
AB  - C. avium type strain LMG 24591 (=CCUG 56292T), isolated in 2006 from a broiler
AB  - chicken in Italy.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Huynh, S.
AU  - Parker, C.T.
AU  - Niedermeyer, J.A.
AU  - Kathariou, S.
TI  - Complete Genome Sequences of Multidrug-Resistant Campylobacter jejuni Strain 14980A (Turkey Feces) and Campylobacter coli Strain 14983A (Housefly from a  Turkey Farm), Harboring a Novel Gentamicin Resistance Mobile Element.
JO  - Genome Announcements
PY  - 2016
SP  - e01175
EP  - e01116
VL  - 4
AB  - Multidrug resistance (MDR) in foodborne pathogens is a major food safety and public health
AB  - issue. Here we describe whole-genome sequences of two MDR strains
AB  - of Campylobacter jejuni and Campylobacter coli from turkey feces and a housefly
AB  - from a turkey farm. Both strains harbor a novel chromosomal gentamicin resistance
AB  - mobile element.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Keech, A.M.
AU  - Pearson, B.M.
AU  - Wells, J.M.
AU  - Kapitonov, V.V.
AU  - Konkel, M.E.
AU  - Mandrell, R.E.
TI  - Diversity of Campylobacter type I restriction-modification loci: Induction of hsdS by exogenous DNA.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2004
SP  - 210
EP  - 210
VL  - 104
AB  - Restriction-modification systems are found in many bacterial taxa and are believed to provide
AB  - a barrier against foreign DNA and bacteriophages.  R-M systems have been classified into three
AB  - types, type I, II, and III.  The type I enzyme is a bifunctional, multi-subunit complex
AB  - containing HsrR, HsdS, and HsdM.  Restriction and modification are represented by the HsdR and
AB  - HsdM proteins, respectively.  HsdS interacts with the target sequence as part of both the
AB  - restriction and modification complexes.  The type I restriction-modification (hsd) genes of 62
AB  - Campylobacter jejuni strains were characterized by DNA sequencing and amplification.  No
AB  - evidence was found that C. jejuni strains contain multiple hsd loci.  Unlike many
AB  - characterized hsd loci from other taxa, intervening open reading frames are present between
AB  - hsdS and the hsdR and hsdM genes.  These ORFs, designated as rlo (R-linked ORF) and mlo
AB  - (M-linked ORF), have no defined function but association of rlo genes with particular hsdS
AB  - alleles may suggest a role in R-M function.  Based on parsimony analysis of amino-acid
AB  - sequences, the C. jejuni hsd loci were assigned to one of three families: 'IAB', 'IC', or
AB  - 'IF'.  HsdM proteins within a family are strongly conserved but share little homology with
AB  - HsdM proteins from the other two families.  Also, there is significant diversity within the
AB  - 'IAB' hsd family: 8 different 'IAB' hsdS alleles and 7 different 'IAB' rlo alleles have
AB  - been characterized.  Finally, RT-PCR analysis using hsdS-specific primer sets was used to
AB  - assess whether the unique hsdS alleles were expressed.  Expression of only two hsdS alleles
AB  - was detected by RT-PCR from cultures grown on rich media; however, expression of 7 additional
AB  - hsdS alleles was detected after the addition of exogenous DNA to the C. jejuni cells.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Pearson, B.M.
AU  - Wells, J.M.
AU  - Parker, C.T.
AU  - Kapitonov, V.V.
AU  - Mandrell, R.E.
TI  - Diversity within the Campylobacter jejuni type I restriction - modification loci.
JO  - Microbiology
PY  - 2005
SP  - 337
EP  - 351
VL  - 151
AB  - The type I restriction-modification (hsd) systems of 73 Campylobacter jejuni strains were
AB  - characterized according to their DNA and amino acid
AB  - sequences, and/or gene organization. A number of new genes were
AB  - identified which are not present in the sequenced strain NCTC 11168.
AB  - The closely related organism Helicobacter pylori has three type I
AB  - systems; however, no evidence was found that C. jejuni strains contain
AB  - multiple type I systems, although hsd loci are present in at least two
AB  - different chromosomal locations. Also, unlike H. pylori, intervening
AB  - ORFs are present, in some strains, between hsdR and hsdS and between
AB  - hsdS and hsdM. No definitive function can be ascribed to these ORFs,
AB  - designated here as rloA-H ((R) under bar-(l) under bar inked (O) under
AB  - bar RF) and mloA-B ((M) under bar-(l) under bar inked (O) under bar
AB  - RF). Based on parsimony analysis of amino acid sequences to assess
AB  - character relatedness, the C. jejuni type I R-M systems are assigned to
AB  - one of three families: 'IAB', 'IC' or 'IF'. This study confirms that
AB  - HsdM proteins within a family are highly conserved but share little
AB  - homology with HsdM proteins from other families. The 'IC' hsd loci are
AB  - > 99% identical at the nucleoticle level, as are the 'IF' hsd loci.
AB  - Additionally, whereas the nucleoticle sequences of the 'IAB' hsdR and
AB  - hsdM genes show a high degree of similarity, the nucleoticle sequences
AB  - of the 'IAB' hsdS and no genes vary considerably. This diversity
AB  - suggests that recombination between 'IAB' hsd loci would lead not only
AB  - to new hsdS alleles but also to the exchange of no genes; five C.
AB  - jejuni hsd loci are presumably the result of such recombination. The
AB  - importance of these findings with regard to the evolution of C. jejuni
AB  - type I R-M systems is discussed.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Wang, G.
AU  - Binnewies, T.T.
AU  - Parker, C.T.
TI  - The complete genome sequence and analysis of the human pathogen Campylobacter lari.
JO  - Foodborne Pathog. Dis.
PY  - 2008
SP  - 371
EP  - 386
VL  - 5
AB  - Campylobacter lari is a member of the epsilon subdivision of the Proteobacteria and is part of
AB  - the thermotolerant Campylobacter group, a
AB  - clade that includes the human pathogen C. jejuni. Here we present the
AB  - complete genome sequence of the human clinical isolate, C. lari RM2100.
AB  - The genome of strain RM2100 is approximately 1.53 Mb and includes the 46
AB  - kb megaplasmid pCL2100. Also present within the strain RM2100 genome is a
AB  - 36 kb putative prophage, termed CLIE1, which is similar to CJIE4, a
AB  - putative prophage present within the C. jejuni RM1221 genome. Nearly all
AB  - (90%) of the gene content in strain RM2100 is similar to genes present in
AB  - the genomes of other characterized thermotolerant campylobacters. However,
AB  - several genes involved in amino acid biosynthesis and energy metabolism,
AB  - identified previously in other Campylobacter genomes, are absent from the
AB  - C. lari RM2100 genome. Therefore, C. lari RM2100 is predicted to be
AB  - multiply auxotrophic, unable to synthesize eight different amino acids,
AB  - acetyl-coA, and pantothenate. Additionally, strain RM2100 does not contain
AB  - a complete TCA cycle and is missing the CydAB terminal oxidase of the
AB  - respiratory chain. Defects in the amino acid biosynthetic pathways in this
AB  - organism could be potentially compensated by the large number of encoded
AB  - peptidases. Nevertheless, the apparent absence of certain key enzymatic
AB  - functions in strain RM2100 would be expected to have an impact on C. lari
AB  - biology. It is also possible that the reduction in the C. lari metabolic
AB  - machinery is related to its environmental range and host preference.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
TI  - Complete Genome Sequence of Campylobacter gracilis ATCC 33236T.
JO  - Genome Announcements
PY  - 2015
SP  - e01087
EP  - e01015
VL  - 3
AB  - The human oral pathogen Campylobacter gracilis has been isolated from periodontal and
AB  - endodontal infections, and also from nonoral head, neck, or lung infections.  This study
AB  - describes the whole-genome sequence of the human periodontal isolate ATCC 33236(T) (=FDC
AB  - 1084), which is the first closed genome for C. gracilis.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Bono, J.L.
TI  - Complete Genome Sequence of the Campylobacter helveticus Type Strain ATCC 51209.
JO  - Genome Announcements
PY  - 2017
SP  - e00398
EP  - e00317
VL  - 5
AB  - Campylobacter helveticus has been isolated from domestic dogs and cats. Although  C.
AB  - helveticus is closely related to the emerging human pathogen C. upsaliensis,
AB  - no C. helveticus-associated cases of human illness have been reported. This study
AB  - describes the whole-genome sequence of the C. helveticus type strain ATCC 51209
AB  - (=CCUG 30682T).
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Chapman, M.H.
TI  - Complete Genome Sequences of Campylobacter hyointestinalis subsp. hyointestinalis Strain LMG 9260 and C. hyointestinalis subsp. lawsonii Strain LMG 15993.
JO  - Genome Announcements
PY  - 2016
SP  - e00665
EP  - e00616
VL  - 4
AB  - Campylobacter hyointestinalis is isolated primarily from ruminants and swine, but is also
AB  - occasionally isolated from humans. C. hyointestinalis is currently
AB  - divided into two subspecies, C. hyointestinalis subsp. hyointestinalis and C.
AB  - hyointestinalis subsp. lawsonii This study describes the first closed
AB  - whole-genome sequences of C. hyointestinalis subsp. hyointestinalis isolate LMG
AB  - 9260 and C. hyointestinalis subsp. lawsonii isolate LMG 15993.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Chapman, M.H.
AU  - Bono, J.L.
TI  - Comparative genomics of all three Campylobacter sputorum biovars and a novel cattle-associated C. sputorum clade.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 1513
EP  - 1518
VL  - 9
AB  - Campylobacter sputorum is a non-thermotolerant campylobacter that is primarily
AB  - isolated from food animals such as cattle and sheep. C. sputorum is also
AB  - infrequently associated with human illness. Based on catalase and urease
AB  - activity, three biovars are currently recognized within C. sputorum: bv. sputorum
AB  - (catalase negative, urease negative), bv. fecalis (catalase positive, urease
AB  - negative), and bv. paraureolyticus (catalase negative, urease positive). A
AB  - multi-locus sequence typing (MLST) method was recently constructed for C.
AB  - sputorum. MLST typing of several cattle-associated C. sputorum isolates suggested
AB  - that they are members of a divergent C. sputorum clade. Although catalase
AB  - positive, and thus technically bv. fecalis, the taxonomic position of these
AB  - strains could not be determined solely by MLST. To further characterize C.
AB  - sputorum, the genomes of four strains, representing all three biovars and the
AB  - divergent clade, were sequenced to completion. Here we present a comparative
AB  - genomic analysis of the four C. sputorum genomes. This analysis indicates that
AB  - the three biovars and the cattle-associated strains are highly-related at the
AB  - genome level with similarities in gene content. Furthermore, the four genomes are
AB  - strongly syntenic with one or two minor inversions. However, substantial
AB  - differences in gene content were observed among the three biovars. Finally,
AB  - although the strain representing the cattle-associated isolates was shown to be
AB  - C. sputorum, it is possible that this strain is a member of a novel C. sputorum
AB  - subspecies; thus, these cattle-associated strains may form a second taxon within
AB  - C. sputorum.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Chapman, M.H.
AU  - Smith, T.P.
AU  - Bono, J.L.
AU  - Huynh, S.
AU  - Parker, C.T.
AU  - Vandamme, P.
AU  - Luong, K.
AU  - Korlach, J.
TI  - Comparative genomics of the Campylobacter lari group.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 3252
EP  - 3266
VL  - 6
AB  - The Campylobacter lari group is a phylogenetic clade within the epsilon
AB  - subdivision of the Proteobacteria and is part of the thermotolerant Campylobacter
AB  - spp., a division within the genus that includes the human pathogen Campylobacter
AB  - jejuni. The C. lari group is currently composed of five species (C. lari,
AB  - Campylobacter insulaenigrae, Campylobacter volucris, Campylobacter
AB  - subantarcticus, and Campylobacter peloridis), as well as a group of strains
AB  - termed the urease-positive thermophilic Campylobacter (UPTC) and other C.
AB  - lari-like strains. Here we present the complete genome sequences of 11 C. lari
AB  - group strains, including the five C. lari group species, four UPTC strains, and a
AB  - lari-like strain isolated in this study. The genome of C. lari subsp. lari strain
AB  - RM2100 was described previously. Analysis of the C. lari group genomes indicates
AB  - that this group is highly related at the genome level. Furthermore, these genomes
AB  - are strongly syntenic with minor rearrangements occurring only in 4 of the 12
AB  - genomes studied. The C. lari group can be bifurcated, based on the flagella and
AB  - flagellar modification genes. Genomic analysis of the UPTC strains indicated that
AB  - these organisms are variable but highly similar, closely related to but distinct
AB  - from C. lari. Additionally, the C. lari group contains multiple genes encoding
AB  - hemagglutination domain proteins, which are either contingency genes or linked to
AB  - conserved contingency genes. Many of the features identified in strain RM2100,
AB  - such as major deficiencies in amino acid biosynthesis and energy metabolism, are
AB  - conserved across all 12 genomes, suggesting that these common features may play a
AB  - role in the association of the C. lari group with coastal environments and
AB  - watersheds.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Huynh, S.
AU  - Chapman, M.H.
AU  - Parker, C.T.
TI  - Complete Genome Sequence of Campylobacter iguaniorum Strain RM11343, Isolated from an Alpaca.
JO  - Genome Announcements
PY  - 2016
SP  - e00646
EP  - e00616
VL  - 4
AB  - Campylobacter iguaniorum is a member of the C. fetus group of campylobacters and  is one of
AB  - two Campylobacter taxa isolated from reptiles. This study describes the whole-genome sequence
AB  - of the C. iguaniorum strain RM11343, which was isolated from a California alpaca fecal sample.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Lopes, B.S.
AU  - Chapman, M.H.
AU  - Huynh, S.
AU  - Bono, J.L.
AU  - Parker, C.T.
AU  - Forbes, K.J.
TI  - Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 1843
EP  - 1858
VL  - 9
AB  - The nonthermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum, and
AB  - C. lanienae form a distinct phylogenetic clusterwithin the genus.  These species are primarily
AB  - isolated from foraging(swine)or grazing (e.g.,cattle, sheep) animals and cause sporadic and
AB  - infrequent human illness. Previous typing studies identi and #64257;ed three putative novel
AB  - C.lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize
AB  - these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either
AB  - to completion or to draft level.  The segenomes represent 26 C.lanienae strains and 50 strains
AB  - of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were
AB  - previously sequenced to completion; therefore, a comparative genomic analysis across the
AB  - entire C. fetus group was conducted (including average nucleotide identity analysis) that
AB  - supports the initial identi and #64257;cation of these three novel Campylobacterspecies.
AB  - Furthermore, C. lanienae and the three putative novel species form a discrete clade within the
AB  - C. fetus group, which we have termed the C. lanienaeclade.  This clade is distinguished from
AB  - other members of the C. fetus group by a reduced genome size and distinct CRISPR/Cas systems.
AB  - Moreover, there are two signature characteristics of the C. lanienae clade. C. lanienae clade
AB  - genomes carry four toten unlinked and similar, but non-identical,  and #64258;agellin genes.
AB  - Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of
AB  - genes related to selenium metabolism, including genes encoding the selenocysteine insertion
AB  - machinery, selenoproteins, and the selenocysteinyl tRNA.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - On, S.L.
AU  - Andersen, L.P.
AU  - Bono, J.L.
TI  - Complete Genome Sequence of the Campylobacter ureolyticus Clinical Isolate RIGS 9880.
JO  - Genome Announcements
PY  - 2015
SP  - e01291
EP  - e01215
VL  - 3
AB  - The emerging pathogen Campylobacter ureolyticus has been isolated from human and  animal
AB  - genital infections, human periodontal disease, domestic and food animals,
AB  - and from cases of human gastroenteritis. We report the whole-genome sequence of
AB  - the human clinical isolate RIGS 9880, which is the first closed genome for C.
AB  - ureolyticus.
ER  -

TY  - JOUR
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Revez, J.
AU  - Bono, J.L.
AU  - Rossi, M.
TI  - Complete Genome Sequence of the Campylobacter cuniculorum Type Strain LMG 24588.
JO  - Genome Announcements
PY  - 2017
SP  - e00543
EP  - e00517
VL  - 5
AB  - Campylobacter cuniculorum is a thermotolerant species isolated from farmed rabbits
AB  - (Oryctolagus cuniculus). Although C. cuniculorum is highly prevalent in
AB  - rabbits farmed for human consumption, the pathogenicity of this organism in
AB  - humans is still unknown. This study describes the whole-genome sequence of the C.
AB  - cuniculorum type strain LMG 24588 (=CCUG 56289T).
ER  -

TY  - JOUR
AU  - Mills, D.A.
AU  - Manias, D.A.
AU  - McKay, L.L.
AU  - Dunny, G.M.
TI  - Homing of a group II intron from Lactococcus lactis subsp. lactis ML3.
JO  - J. Bacteriol.
PY  - 1997
SP  - 6107
EP  - 6111
VL  - 179
AB  - Ll.ltrB is a functional group II intron located within a gene (ltrB) encoding a conjugative
AB  - relaxase essential for transfer of the lactococcal element pRS01.  In this work, the Ll.ltrB
AB  - intron was shown to be an independent mobile element capable of inserting into an intronless
AB  - allele of the ltrB gene.  Ll.ltrB was not observed to insert into a deletion derivative of the
AB  - ltrB gene in which the intron splice site was removed. In contrast, a second vector containing
AB  - a 271-nucleotide segment of ltrB spanning the Ll.ltrB splice site was shown to be a proficient
AB  - recipient of intron insertion.  Efficient homing was observed in the absence of a functional
AB  - host homologous recombination system.  This work demonstrates that the Ll.ltrB intron is a
AB  - novel site-specific mobile element in lactococci and that group II intron self-transfer is a
AB  - mechanism for intron dissemination among bacteria.
ER  -

TY  - JOUR
AU  - Mills, D.A.
AU  - McKay, L.L.
AU  - Dunny, G.M.
TI  - Splicing of a group II intron involved in the conjugative transfer of pRS01 in Lactococci.
JO  - J. Bacteriol.
PY  - 1996
SP  - 3531
EP  - 3538
VL  - 178
AB  - Analysis of a region involved in the conjugative transfer of the lactococcal conjugative
AB  - element pRS01 has revealed a bacterial group II intron.  Splicing of this lactococcal intron
AB  - (designated Ll.ltrB) in vivo resulted in the ligation of two exon messages (ltrBE1 and ltrBE2)
AB  - which encoded a putative conjugative relaxase essential for the transfer of pRS01.  Like many
AB  - group II introns, the Ll.ltrB intron possessed an open reading frame (ltrA) with homology to
AB  - reverse transcriptases.  Remarkably, sequence analysis of ltrA suggested a greater similarity
AB  - to open reading frames encoded by eukaryotic mitochondrial group II introns than to those
AB  - identified to date from other bacteria.  Several insertional mutations within ltrA resulted in
AB  - plasmids exhibiting a conjugative transfer-deficient phenotype.  These results provide the
AB  - first direct evidence for splicing of a prokaryotic group II intron in vivo and suggest that
AB  - conjugative transfer is a mechanism for group II intron dissemination in bacteria.
ER  -

TY  - JOUR
AU  - Mills, H.J.
AU  - Eisen, J.
AU  - Sobecky, P.A.
TI  - Insights into the role of cryptic marine plasmids based on sequence analysis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2003
SP  - N
EP  - 147
VL  - 103
AB  - Knowledge has been gained from the intensive study of a limited group of bacterial plasmids
AB  - particularly those from clinical settings and
AB  - terrestrial environments. The molecular characterization of plasmid
AB  - populations occurring in a wider range of habitats, especially marine,
AB  - is necessary to provide knowledge on plasmid ecology and their
AB  - contributions to the genetic plasticity of microbial communities. DNA
AB  - sequencing and analysis have greatly facilitated the determination of
AB  - putative functions to otherwise 'cryptic' marine plasmids. In
AB  - collaboration with TIGR, we have undertaken whole plasmid sequencing to
AB  - elucidate putative gene functions to gain a better understanding of
AB  - plasmid diversity and ecological roles. A random shotgun method was
AB  - used to obtain DNA sequences from five 'cryptic' marine plasmids
AB  - ranging in size from 9-kb to 80-kb from Vibrio and Shewanella. A
AB  - comparative and systematic analysis of the marine plasmid sequences
AB  - have indicated that p172, a 28.8-kb plasmid from marine Vibrio sp. 172
AB  - encodes partitioning elements, colicin-mediated cell killing,
AB  - restriction modification systems, and natural competence. A co-resident
AB  - replicon in Vibrio sp. 172, p172-A, is a 9.0-kb element that appears to
AB  - be the replicative form of a previously identified Vibrio
AB  - parahaemolyticus phage. A second marine Vibrio strain designated 09022,
AB  - contains a 31.0-kb plasmid, p09022, that remains mostly cryptic,
AB  - however p09022 does encode partitioning elements and a restriction
AB  - modification system related to similar genes on p172. A majority of the
AB  - putative genes from p23023 (52.1-kb) resident in a third Vibrio sp.,
AB  - and p0908 (81.4-kb) isolated from a Shewenella sp., possesses no
AB  - homology to any known ORFs. However, p23023 encodes a putative cell
AB  - adhesion operon, previously reported in non-marine bacterial hosts.
AB  - Sequence analysis demonstrates the capacity to assign putative function
AB  - to cryptic plasmids, but also exemplifies the need for additional
AB  - sequencing and analyzing of marine genes. Such plasmid-encoded
AB  - adhesion, competency and colicin production traits likely provide hosts
AB  - with competitive advantages in marine ecosystems.
ER  -

TY  - JOUR
AU  - Mills, K.I.
AU  - Ramsahoye, B.H.
TI  - Methods in Molecular Biology. DNA methylation protocols.
JO  - Methods Mol. Biol.
PY  - 2002
SP  - 1
EP  - 7
VL  - 200
AB  - This book provides a set of reproducible protocols for the analysis of DNA methylation and
AB  - methylases. Each technique includes a summary of the basic
AB  - theory, a materials list, step-by-step instructions, and notes for
AB  - avoiding pitfalls. It was written for all researchers investigating
AB  - replication, transcription, growth, differentiation, and carcinogenesis.
AB  - Bibliographical references, illustrations, and an index are included.
ER  -

TY  - JOUR
AU  - Mills, K.V.
AU  - Paulus, H.
TI  - Biochemical mechanisms of intein-mediated protein splicing.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 233
EP  - 255
VL  - 16
AB  - This chapter discusses the mechanism of the self-catalyzed process by which inteins promote
AB  - both their own excision from a host protein and the direct linkage of the flanking host
AB  - protein segments, the N- and C-exteins, by a peptide bond.  The majority of inteins have a
AB  - nucleophilic amino acid at their N-terminus and asparagine at their C-terminus and are linked
AB  - to a C-extein with an N-terminal nucleophilic amino acid.  These canonical inteins promote
AB  - protein splicing by a four-step mechanism of sequential acyl rearrangements.  Non-canonical
AB  - inteins, which lack either the N-terminal nucleophile or the C-terminal asparagine, promote
AB  - protein splicing by a variant of this mechanism or promote protein cleavage rather than
AB  - splicing.  A remarkable feature of the protein splicing process is that it involves multiple
AB  - steps that are chemically autonomous yet proceed in a highly coordinated manner without side
AB  - reactions unless perturbed by mutation, unnatural exteins, or non-physiological conditions.
AB  - The factors that may serve to integrate protein splicing into a system that ordinarily
AB  - operates efficiently without side reactions are discussed.
ER  -

TY  - JOUR
AU  - Mills, S.
AU  - Griffin, C.
AU  - O'Sullivan, O.
AU  - Coffey, A.
AU  - McAuliffe, O.E.
AU  - Meijer, W.C.
AU  - Serrano, L.M.
AU  - Ross, R.P.
TI  - A new phage on the 'Mozzarella' block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages.
JO  - Int. Dairy Journal
PY  - 2011
SP  - 963
EP  - 969
VL  - 21
AB  - Streptococcus thermophilus bacteriophage 5093 is a virulent phage that infects the industrial
AB  - Mozzarella starter CSK939. The genome of phage
AB  - 5093 is 37,184 base pairs (bps) containing 50 open reading frames
AB  - (orfs). Genetic analysis revealed that the genome of phage 5093 is
AB  - highly mosaic when compared with other sequenced S. thermophilus
AB  - phages. This is particularly apparent in the late gene cluster with
AB  - regions displaying high homology to prophage sequences of non-dairy
AB  - streptococci and limited homology to either pac or cos-type S.
AB  - thermophilus phages. In addition, a definitive antireceptor gene was
AB  - not observed - suggesting that phage 5093 may have developed a
AB  - different system for host recognition. Interestingly, the phage does
AB  - contain a methylase domain that probably evolved as a phage
AB  - counter-defence mechanism. These findings suggest that phage 5093 may
AB  - represent a third group of S. thermophilus phage and provide the link
AB  - between phages that infect S. thermophilus and its non-dairy ancestors.
ER  -

TY  - JOUR
AU  - Mills, S.
AU  - McAuliffe, O.E.
AU  - Coffey, A.
AU  - Fitzgerald, G.F.
AU  - Ross, R.P.
TI  - Plasmids of lactococci - genetic accessories or genetic necessities?
JO  - FEMS Microbiol. Rev.
PY  - 2006
SP  - 243
EP  - 273
VL  - 30
AB  - Lactococci are one of the most exploited microorganisms used in the manufacture of food.
AB  - These intensively used cultures are generally characterized by having a rich plasmid
AB  - complement.  It could be argued that it is the plasmid complement of commercially utilized
AB  - cultures that gives them their technical superiority and individuality.  Consequently, it is
AB  - timely to reflect on the desirable characteristics encoded on lactococcal plasmids.  It is
AB  - argued that plasmids play a key role in the evolution of modern starter strains and are a lot
AB  - more than just selfish replicosomes but more essential necessities of intensively used
AB  - commercial starters.  Moreover, the study of plasmid biology provides a genetic blueprint that
AB  - has proved essential for the generation of molecular tools for the genetic improvement of
AB  - Lactococcus lactis.
ER  -

TY  - JOUR
AU  - Milsom, S.E.
AU  - Halford, S.E.
AU  - Embleton, M.L.
AU  - Szczelkun, M.D.
TI  - Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 515
EP  - 527
VL  - 311
AB  - Before cleaving DNA substrates with two recognition sites, the Cfr10I, NgoMIV, NaeI and SfiI
AB  - restriction endonucleases bridge the two sites
AB  - through 3D space, looping out the intervening DNA. To characterise
AB  - their looping interactions, the enzymes were added to plasmids with two
AB  - recognition sites interspersed with two res sites for site-specific
AB  - recombination by Tn21 resolvase, in buffers that contained either EDTA
AB  - or CaCl2 so as to preclude DNA cleavage by the endonuclease; the extent
AB  - to which the res sites were sequestered into separate loops was
AB  - evaluated from the degree of inhibition of resolvase. With Cfr10I, a
AB  - looped complex was detected in the presence but not in the absence of
AB  - Ca2+; it had a lifetime of about 90 seconds. Neither NgoMIV nor NaeI
AB  - gave looped complexes of sufficient stability to be detected by this
AB  - method. In contrast, SfiI with Ca++ produced a looped complex that survived for more than
AB  - seven hours, whereas its looping interaction in
AB  - EDTA lasts for about four minutes. When resolvase was added to a SfiI
AB  - binding reaction in EDTA followed immediately by CaCl2, the looped DNA
AB  - was blocked from recombination while the unlooped DNA underwent
AB  - recombination. By measuring the distribution between looped and
AB  - unlooped DNA at various SfiI concentrations, and by fitting the data to
AB  - a model for DNA binding by a tetrameric protein to two sites in cis, an
AB  - equilibrium constant for the looping interaction was determined. The
AB  - equilibrium constant was essentially independent of the length of DNA
AB  - between the SfiI sites.
ER  -

TY  - JOUR
AU  - Minami, T.
AU  - Ohtsubo, Y.
AU  - Anda, M.
AU  - Nagata, Y.
AU  - Tsuda, M.
AU  - Mitsui, H.
AU  - Sugawara, M.
AU  - Minamisawa, K.
TI  - Complete Genome Sequence of Methylobacterium sp. Strain AMS5, an Isolate from a Soybean Stem.
JO  - Genome Announcements
PY  - 2016
SP  - e00144
EP  - e00116
VL  - 4
AB  - Nonrhizobial Methylobacterium spp. inhabit the phyllosphere of a wide variety of  plants. We
AB  - report here the complete genome sequence of Methylobacterium sp. AMS5,
AB  - which was isolated from a soybean stem. The information is useful for
AB  - understanding the molecular mechanisms of the interaction between nonrhizobial
AB  - Methylobacterium spp. and plants.
ER  -

TY  - JOUR
AU  - Minarovits, J.
TI  - MICROBE-INDUCED EPIGENETIC ALTERATIONS IN HOST CELLS: THE COMING ERA OF PATHO-EPIGENETICS OF MICROBIAL INFECTIONS A REVIEW.
JO  - Acta Microbiol. Immunol. Hung.
PY  - 2009
SP  - 1
EP  - 19
VL  - 56
AB  - It is well documented that the double-stranded DNA (dsDNA) genomes of certain viruses and the
AB  - proviral genomes of retroviruses are regularly
AB  - targeted by epigenetic regulatory mechanisms (DNA methylation, histone
AB  - modifications, binding of regulatory proteins) in infected cells. In
AB  - parallel, proteins encoded by viral genomes may affect the activity of
AB  - a set of cellular promoters by interacting with the very same
AB  - epigenetic regulatory machinery. This may result in epigenetic
AB  - dysregulation and subsequent cellular dysfunctions that may manifest in
AB  - or contribute to the development of pathological changes (e. g.
AB  - initiation and progression of malignant neoplasms; immunodeficiency).
AB  - Bacteria infecting mammals may cause diseases in a similar manner, by
AB  - causing hypermethylation of key cellular promoters at CpG dinucleotides
AB  - (promoter silencing, e. g. by Campylobacter rectus in the placenta or
AB  - by Helicobacter pylori in gastric mucosa). I suggest that in addition
AB  - to viruses and bacteria, other microparasites (protozoa) as well as
AB  - macroparasites (helminths, arthropods, fungi) may induce pathological
AB  - changes by epigenetic reprogramming of host cells they are interacting
AB  - with. Elucidation of the epigenetic consequences of microbe-host
AB  - interactions (the emerging new field of patho-epigenetics) may have
AB  - important therapeutic implications because epigenetic processes can be
AB  - reverted and elimination of microbes inducing patho-epigenetic changes
AB  - may prevent disease development.
ER  -

TY  - JOUR
AU  - Minczuk, M.
AU  - Papworth, M.A.
AU  - Kolasinska, P.
AU  - Murphy, M.P.
AU  - Klug, A.
TI  - Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 19689
EP  - 19694
VL  - 103
AB  - We used engineered zinc finger peptides (ZFPs) to bind selectively to predetermined sequences
AB  - in human mtDNA. Surprisingly, we found that
AB  - engineered ZFPs cannot be reliably routed to mitochondria by using only
AB  - conventional mitochondrial targeting sequences. We here show that addition
AB  - of a nuclear export signal allows zinc finger chimeric enzymes to be
AB  - imported into human mitochondria. The selective binding of
AB  - mitochondria-specific ZFPs to mtDNA was exemplified by targeting the
AB  - T8993G mutation, which causes two mitochondrial diseases, neurogenic
AB  - muscle weakness, ataxia, and retinitis pigmentosa (NARP) and also
AB  - maternally inherited Leigh's syndrome. To develop a system that allows the
AB  - monitoring of site-specific alteration of mtDNA we combined a ZFP with the
AB  - easily assayed DNA-modifying activity of hDNMT3a methylase. Expression of
AB  - the mutation-specific chimeric methylase resulted in the selective
AB  - methylation of cytosines adjacent to the mutation site. This is a proof of
AB  - principle that it is possible to target and alter mtDNA in a
AB  - sequence-specific manner by using zinc finger technology.
ER  -

TY  - JOUR
AU  - Mindlin, S.
AU  - Petrenko, A.
AU  - Kurakov, A.
AU  - Beletsky, A.
AU  - Mardanov, A.
AU  - Petrova, M.
TI  - Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis.
JO  - Biomed. Res. Int.
PY  - 2016
SP  - 3970831
EP  - 3970831
VL  - 2016
AB  - We performed whole-genome sequencing of five permafrost strains of Acinetobacter
AB  - lwoffii (frozen for 15-3000 thousand years) and analyzed their resistance genes
AB  - found in plasmids and chromosomes. Four strains contained multiple plasmids
AB  - (8-12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic
AB  - structure; the fifth strain contained only two plasmids. All large plasmids and
AB  - some medium-size and small plasmids contained genes encoding resistance to
AB  - various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium,
AB  - and arsenic compounds. Most resistance genes found in the ancient strains of A.
AB  - lwoffii had their closely related counterparts in modern clinical A. lwoffii
AB  - strains that were also located on plasmids. The vast majority of the chromosomal
AB  - resistance determinants did not possess complete sets of the resistance genes or
AB  - contained truncated genes. Comparative analysis of various A. lwoffii and of A.
AB  - baumannii strains discovered a number of differences between them: (i) chromosome
AB  - sizes in A. baumannii exceeded those in A. lwoffii by about 20%; (ii) on the
AB  - contrary, the number of plasmids in A. lwoffii and their total size were much
AB  - higher than those in A. baumannii; (iii) heavy metal resistance genes in the
AB  - environmental A. lwoffii strains surpassed those in A. baumannii strains in the
AB  - number and diversity and were predominantly located on plasmids. Possible reasons
AB  - for these differences are discussed.
ER  -

TY  - JOUR
AU  - Minegishi, K.
AU  - Aikawa, C.
AU  - Furukawa, A.
AU  - Watanabe, T.
AU  - Nakano, T.
AU  - Ogura, Y.
AU  - Ohtsubo, Y.
AU  - Kurokawa, K.
AU  - Hayashi, T.
AU  - Maruyama, F.
AU  - Nakagawa, I.
AU  - Eishi, Y.
TI  - Complete Genome Sequence of a Propionibacterium acnes Isolate from a Sarcoidosis  Patient.
JO  - Genome Announcements
PY  - 2013
SP  - e00016
EP  - e00012
VL  - 1
AB  - Propionibacterium acnes is a human skin commensal that resides preferentially within sebaceous
AB  - follicles and is the only microorganism that has been isolated from sarcoid lesions. We report
AB  - the complete genome sequence of P. acnes, which was isolated from a Japanese patient with
AB  - sarcoidosis.
ER  -

TY  - JOUR
AU  - Miner, Z.
TI  - Comparative analysis of the T2 and T4 DNA [N6-adenine] methyltransferase (dam) genes and characterization of single amino acid substitutions that alter the sequence specificity of their encoded proteins.
JO  - Diss. Abstr.
PY  - 1990
SP  - 588B
EP  - 588B
VL  - 51
AB  - Bacteriophage T4 encodes a DNA-[N6-adenine]methyltransferase (Dam) which recognizes primarily
AB  - the sequence GATC in both cytosine- and hydroxymethylcytosine-containing DNA. The
AB  - corresponding enzyme encoded by the related bacteriophage T2 is able to methylate both
AB  - substrates to a greater extent than T4 Dam. The T2 dam gene has been cloned and sequenced, and
AB  - the sequence compared with that of the T4 dam gene. From the coding region, I infer there are
AB  - three amino acid differences, two of which are located in a region of homology (I) that is
AB  - shared by T2 and T4 Dam, Escherichia coli Dam, and the modification enzyme of Streptococcus
AB  - pneumoniae, all of which methylate the sequence 5' GATC 3'. Although the T2 and T4 dam
AB  - promoters are not identical, gene fusion experiments indicate that the T4 promoter produces
AB  - about two-fold more Beta-galactosidase activity than does the T2 promoter. T2 and T4 dam give
AB  - rise to hypermethylating mutants (damh) which exhibit an alteration in sequence specificity;
AB  - that is, they are readily able to methylate non-canonical sites. I have determined that the
AB  - damh mutation in T4 produces a single amino acid change (Pro126 to Ser126) in another region
AB  - of homology (III) shared by the four DNA-adenine methyltransferases. Another mutant, damc, is
AB  - described which methylates GATC in cytosine-containing DNA, but not in
AB  - hydroxymethylcytosine-containing DNA. This mutation alters a single amino acid (Phe127 to
AB  - Val127). The effect of several different amino acids at residue 126 was examined by creating
AB  - an amber codon at that position and comparing the methylation capability of partially purified
AB  - enzymes produced in the presence of various suppressors. No enzyme activity is observed for
AB  - proteins containing phenylalanine, glutamic acid, or histidine at position 126. However,
AB  - insertion of alanine, cysteine, or glycine at residue 126 produces enzymatic activity similar
AB  - to that of Damh. These results suggest that at least two regions of the Dam protein are
AB  - involved in sequence recognition. These regions may be in close proximity to one another in
AB  - the native protein to form a domain that is involved in nucleotide recognition and protein-DNA
AB  - interation.
ER  -

TY  - JOUR
AU  - Miner, Z.
AU  - Hattman, S.
TI  - Molecular cloning, sequencing, and mapping of the bacteriophage T2 dam gene.
JO  - J. Bacteriol.
PY  - 1988
SP  - 5177
EP  - 5184
VL  - 170
AB  - Bacteriophage T2 codes for a DNA-(adenine-N6) methyltransferase (Dam), which is able to
AB  - methylate both cytosine- and hydroxymethylcytosine-containing DNAs to a greater extent than
AB  - the corresponding methyltransferase encoded by bacteriophage T4. We have cloned and sequenced
AB  - the T2 dam gene and compared it with the T4 dam gene. In the Dam coding region, there are 22
AB  - nucleotide differences, 4 of which result in three coding differences (2 are in the same
AB  - codon). Two of the amino acid alterations are located in a region of homology that is shared
AB  - by T2 and T4 Dam, Escherichia coli Dam, and the modification enzyme of Streptococcus
AB  - pneumoniae, all of which methylate the sequence 5'GATC3'. The T2 dam and T4 dam promoters
AB  - are not identical and appear to have slightly different efficiencies; when fused to the E.
AB  - coli lacZ gene, the T4 promoter produces about twofold more beta-galactosidase activity than
AB  - does the T2 promoter. In our first attempt to isolate T2 dam, a truncated gene was cloned on a
AB  - 1.67-kilobase XbaI fragment. This construct produces a chimeric protein composed of the first
AB  - 163 amino acids of T2 Dam followed by 83 amino acids coded by the pUC18 vector. Surprisingly,
AB  - the chimera has Dam activity, but only on cytosine-containing DNA. Genetic and physical
AB  - analyses place the T2 dam gene at the same respective map location as the T4 dam gene.
AB  - However, relative to T4, T2 contains an insertion of 536 base pairs 5' to the dam gene.
AB  - Southern blot hybridization and computer analysis failed to reveal any homology between this
AB  - insert and either T4 or E. coli DNA.
ER  -

TY  - JOUR
AU  - Miner, Z.
AU  - Schlagman, S.
AU  - Hattman, S.
TI  - Single amino acid changes which alter the sequence specificity of the T4 and T2 (Dam) DNA-adenine methyltransferases.
JO  - Gene
PY  - 1988
SP  - 275
EP  - 276
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Miner, Z.
AU  - Schlagman, S.
AU  - Hattman, S.
TI  - Single amino acid changes which alter the sequence specificity of the T4 (dam) DNA-adenine methyltransferase.
JO  - Biochem. Pharmacol.
PY  - 1988
SP  - 1811
EP  - 1812
VL  - 37
AB  - Many enteric bacteria contain a DNA adenine methyltransferase (Dam) that methylates the A
AB  - residue in the sequence, GATC. The related T-even phages, T2 and T4 (but not T6), also encode
AB  - Dam methylases; the normal substrate for these enzymes is 5-hydroxymethylcytosine
AB  - (hmC)-containing DNA, since these viruses contain this base in place of C, and the hmC is
AB  - modified further by glucosylation. Nonglucosylating mutants (gt-) have been isolated that are
AB  - different from their gt+ parents in that they are unable to grow on certain strains, such as
AB  - P1 lysogenic hosts. Derivatives of T2 gt- and T4 gt- phage capable of growth on P1 lysogens
AB  - have been isolated; these are designated damh because they exhibit hypermethylation of their
AB  - DNA. Thus, Damh, but not Dam+, methylation protects against P1 restriction of the asymmetric
AB  - sequence, AGACC.
ER  -

TY  - JOUR
AU  - Miner, Z.
AU  - Schlagman, S.
AU  - Hattman, S.
TI  - The dam DNA-methyltransferases of E. coli and its phages T2 and T4.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 199
EP  - 199
VL  - 13D
AB  - DNA (adenine-N6) methyltransferases (MTases) recognizing the palindromic tetranucleotide
AB  - sequence, 5'-GATC-3', are encoded by (dam) genes of various bacteriophages (e.g.
AB  - T2,T4,T1,P1) and bacteria (e.g. Escherichia, Salmonella, Neisseria, Streptococcus).  Cloning
AB  - and nucleotide sequence analysis has revealed that these Dam polypeptides contain several
AB  - regions of considerable amino acid sequence homology; and one of these regions (IV) contains a
AB  - sequence motif, (Asp/Asn)-Pro-Pro-(Phe/Tyr), also found in MTases that methylate adenine in
AB  - sequences other than GATC.  The conservation of amino acid sequences among these enzymes
AB  - suggests that they are in domains important for MTase function and specificity; i.e. substrate
AB  - (S-adenosylmethionine, AdoMet) and DNA-nucleotide sequence recognition/interaction.  We have
AB  - been focusing on the Dam MTases of phages T2 and T4, particularly because mutants (dam^h) are
AB  - known that methylate DNA to higher extents than the enzyme from the wild-type (dam+) parent.
AB  - In addition, second site mutants (dam^h dam-x) have been isolated that abolish all DNA
AB  - methylation ability.  The normal substrate for the phage DNA MTases is DNA containing
AB  - 5-hydroxymethylcytosine (hmC), because the viruses contain this base in place of C; however,
AB  - C-DNA is still a good substrate for these enzymes.  The two wild-type phage MTases differ in
AB  - that the T2 enzyme adds about twice as many methyl groups per unit DNA than does the T4
AB  - enzyme.  A comparison of the wild-type T2 and T4 Dam+ encoded polypeptides revealed three
AB  - amino acid differences; viz., at positions 20,26,188.  The latter is a conserved changed
AB  - (Asp->Glu) and does not appear to be involved in sequence specificity.  The other two changes
AB  - are located in homology region I, implicating this domain in nucleotide sequence recognition.
AB  - Current efforts to prove this include production of chimeric enzymes and site-directed
AB  - mutagenesis.  We have shown that the dam+ -> dam^h mutation produces a Pro ->Ser change at
AB  - amino acid residue 126.  A Phe -> Val change at residue 127 prevents the MTase from
AB  - methylating hmC-DNA, but not C-DNA.  These two residues are contained in homology region III,
AB  - also implicating this domain in nucleotide sequence recognition.
ER  -

TY  - JOUR
AU  - Miner, Z.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Single amino acid changes that alter the DNA sequence specificity of the DNA-[N/6-adenine] methyltransferase (Dam) of bacteriophage T4.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8149
EP  - 8157
VL  - 17
AB  - Bacteriophage T4 codes for a DNA-[N/6-adenine] methyltransferase (Dam) which
AB  - recognizes primarily the sequence GATC in both cytosine-and
AB  - hydroxymethylcytosine-containing DNA.  Hypermethylating mutants, dam/h, exhibit
AB  - a relaxation in sequence specificity, that is, they are readily able to
AB  - methylate non-canonical sites.  We have determined that the dam/h mutation
AB  - produces a single amino acid change (Pro/126 to Ser/126) in a region of
AB  - homology (III) shared by three DNA-adenine methyltransferases; viz, T4 Dam,
AB  - Escherichia coli Dam, and the DpnII modification enzyme of Streptococcus
AB  - pneumoniae.  We also describe another mutant, dam/c, which methylates GATC in
AB  - cytosine-containing DNA, but not in hydroxymethylcytosine-containing DNA.  This
AB  - mutation also alters a single amino acid (Phe/127 to Val/127).  These results
AB  - implicate homology region III as a domain involved in DNA sequence recognition.
AB  - The effect of several different amino acids at residue 126 was examined by
AB  - creating a polypeptide chain terminating codon at that position and comparing
AB  - the methylation capability of partially purified enzymes produced in the
AB  - presence of various suppressors.  No enzyme activity is detected when
AB  - phenylalanine, glutamic acid, or histidine is inserted at position 126.
AB  - However, insertion of alanine, cysteine, or glycine at residue 126 produces
AB  - enzymatic activity similar to Dam/h.
ER  -

TY  - JOUR
AU  - Minion, F.C.
AU  - Lefkowitz, E.J.
AU  - Madsen, M.L.
AU  - Cleary, B.J.
AU  - Swartzell, S.M.
AU  - Mahairas, G.G.
TI  - The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis.
JO  - J. Bacteriol.
PY  - 2004
SP  - 7123
EP  - 7133
VL  - 186
AB  - We present the complete genome sequence of Mycoplasma hyopneumoniae, an important member of
AB  - the porcine respiratory disease complex. The genome is
AB  - composed of 892,758 bp and has an average G+C content of 28.6 mol%. There
AB  - are 692 predicted protein coding sequences, the average protein size is
AB  - 388 amino acids, and the mean coding density is 91%. Functions have been
AB  - assigned to 304 (44%) of the predicted protein coding sequences, while 261
AB  - (38%) of the proteins are conserved hypothetical proteins and 127 (18%)
AB  - are unique hypothetical proteins. There is a single 16S-23S rRNA operon,
AB  - and there are 30 tRNA coding sequences. The cilium adhesin gene has six
AB  - paralogs in the genome, only one of which contains the cilium binding
AB  - site. The companion gene, P102, also has six paralogs. Gene families
AB  - constitute 26.3% of the total coding sequences, and the largest family is
AB  - the 34-member ABC transporter family. Protein secretion occurs through a
AB  - truncated pathway consisting of SecA, SecY, SecD, PrsA, DnaK, Tig, and
AB  - LepA. Some highly conserved eubacterial proteins, such as GroEL and GroES,
AB  - are notably absent. The DnaK-DnaJ-GrpR complex is intact, providing the
AB  - only control over protein folding. There are several proteases that might
AB  - serve as virulence factors, and there are 53 coding sequences with
AB  - prokaryotic lipoprotein lipid attachment sites. Unlike other mycoplasmas,
AB  - M. hyopneumoniae contains few genes with tandem repeat sequences that
AB  - could be involved in phase switching or antigenic variation. Thus, it is
AB  - not clear how M. hyopneumoniae evades the immune response and establishes
AB  - a chronic infection.
ER  -

TY  - JOUR
AU  - Minko, I.
AU  - Hattman, S.
AU  - Lloyd, R.S.
AU  - Kossykh, V.
TI  - Methylation by a mutant T2 DNA [N6-adenine] methyltransferase expands the usage of RecA-assisted endonuclease (RARE) cleavage.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 1484
EP  - 1490
VL  - 29
AB  - Properties of a mutant bacteriophage T2 DNA [N6-adenine] methyltransferase (T2 Dam MTase) have
AB  - been investigated for its potential utilization in RecA-assisted restriction endonuclease
AB  - (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that,
AB  - compared to wild-type T4 Dam, both wild-type T2 Dam and mutant T2 Dam P126S had a 1.5-fold
AB  - higher kcat in methylating canonical GATC sites. Additionally, T2 Dam P126S showed increased
AB  - efficiencies in methylation of non-canonical GAY sites relative to the wild-type enzymes. In
AB  - agreement with these steady-state kinetic data, when bacteriophage  DNA was used as a
AB  - substrate, maximal protection from restriction nuclease cleavage in vitro was achieved on the
AB  - sequences GATC, GATN and GACY, while protection of GACR sequences was less efficient.
AB  - Collectively, our data suggest that T2 Dam P126S can modify 28 recognition sequences. The
AB  - feasibility of using the mutant enzyme in RARE cleavage with BclI and EcoRV endonucleases has
AB  - been shown on phage  DNA and with BclI and DpnII endonucleases on yeast chromosomal DNA
AB  - embedded in agarose.
ER  -

TY  - JOUR
AU  - Minogue, T.D. et al.
TI  - Whole-genome sequences of 24 Brucella strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00915
EP  - e00914
VL  - 2
AB  - Brucella species are intracellular zoonotic pathogens which cause, among other pathologies,
AB  - increased rates of abortion in ruminants. Human infections are
AB  - generally associated with exposure to contaminated and unpasteurized dairy
AB  - products; however Brucellae have been developed as bioweapons. Here we present 17
AB  - complete and 7 scaffolded genome assemblies of Brucella strains.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.A.
AU  - Davenport, K.W.
AU  - Bishop-Lilly, K.A.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Chertkov, O.
AU  - Coyne, S.R.
AU  - Freitas, T.
AU  - Frey, K.G.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Redden, C.L.
AU  - Rosenzweig, C.N.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference  Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00969
EP  - e00914
VL  - 2
AB  - We present the complete genome assembly of Escherichia coli ATCC 25922 as submitted to NCBI
AB  - under accession no. CP009072. This strain was originally
AB  - isolated from a clinical sample in Seattle, Washington (1946), and is often used
AB  - in quality control testing. The assembled genome is 5.20 Mb (50.4% G+C content)
AB  - and includes two plasmids.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.A.
AU  - Davenport, K.W.
AU  - Bishop-Lilly, K.A.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Chertkov, O.
AU  - Coyne, S.R.
AU  - Freitas, T.
AU  - Frey, K.G.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Redden, C.L.
AU  - Rosenzweig, C.N.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of Streptococcus pyogenes ATCC 19615, a Group A beta-Hemolytic Reference Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00976
EP  - e00914
VL  - 2
AB  - We present the complete genome assembly of Streptococcus pyogenes ATCC 19615 (Rosenbach) as
AB  - submitted to GenBank under accession number CP008926. This group A
AB  - nonmotile beta-hemolytic clinical isolate is used for quality control in a
AB  - variety of commercially available tests. The assembled genome is 1.84 Mb (38.5%
AB  - G+C content) and contains 1,788 coding regions.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.A.
AU  - Davenport, K.W.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Chertkov, O.
AU  - Coyne, S.R.
AU  - Freitas, T.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687.
JO  - Genome Announcements
PY  - 2014
SP  - e00962
EP  - e00914
VL  - 2
AB  - Ochrobactrum anthropi is an occasional cause of nosocomial infections; however, interest in
AB  - the organism lies in its phylogenetic proximity to the genus
AB  - Brucella. Here, we present the 4.9-Mb finished genome of Ochrobactrum anthropi
AB  - ATCC 49687, most commonly used as an exclusionary reference organism.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.A.
AU  - Davenport, K.W.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Chertkov, O.
AU  - Coyne, S.R.
AU  - Freitas, T.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Neisseria lactamica Type Strain A7515.
JO  - Genome Announcements
PY  - 2014
SP  - e00951
EP  - e00914
VL  - 2
AB  - We present the scaffolded genome assembly of Neisseria lactamica type strain A7515 (ATCC
AB  - 23970) as submitted to NCBI under accession no. JOVI00000000. This
AB  - type strain of the lactose-fermenting Neisseria species is often used in quality
AB  - control testing and intra-genus phylogenetic analyses. The assembly includes four
AB  - contigs placed into a single scaffold.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Chertkov, O.
AU  - Freitas, T.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01.
JO  - Genome Announcements
PY  - 2014
SP  - e01073
EP  - e01014
VL  - 2
AB  - The Enterobacteriaceae are environmental and enteric microbes. We sequenced the genomes of two
AB  - Enterobacter reference strains, E. aerogenes CDC 6003-71 and E.
AB  - cloacae CDC 442-68, as well as one near neighbor used as an exclusionary
AB  - reference for diagnostics, Pantoea agglomerans CDC UA0804-01. The genome sizes
AB  - range from 4.72 to 5.55 Mbp and have G+C contents from 54.6 to 55.1%.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Bishop-Lilly, K.A.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Chertkov, O.
AU  - Freitas, T.
AU  - Frey, K.G.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Palacios, G.F.
AU  - Redden, C.L.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC  49132.
JO  - Genome Announcements
PY  - 2014
SP  - e01064
EP  - e01014
VL  - 2
AB  - The pleomorphic swarming bacilli of the genus Proteus are common human gut commensal organisms
AB  - but also the causative agents of recurrent urinary tract
AB  - infections and bacteremia. We sequenced and assembled the 3.99-Mbp genome of
AB  - Proteus mirabilis ATCC 7002 (accession no. JOVJ00000000) and the 3.97-Mbp genome
AB  - of Proteus vulgaris ATCC 49132 (accession no. JPIX00000000), both of which are
AB  - commonly used reference strains.
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Chertkov, O.
AU  - Freitas, T.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Koroleva, G.I.
AU  - Ladner, J.T.
AU  - Palacios, G.F.
AU  - Rosenzweig, C.N.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00968
EP  - e00914
VL  - 2
AB  - Enterococcus faecalis is a nonmotile Gram-positive coccus, found both as a commensal organism
AB  - in healthy humans and animals and as a causative agent of
AB  - multiple diseases, in particular endocarditis. We sequenced the genome of E.
AB  - faecalis ATCC 29212, a commonly used reference strain in laboratory studies, to
AB  - complete 'finished' annotated assembly (3 Mb).
ER  -

TY  - JOUR
AU  - Minogue, T.D.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Broomall, S.M.
AU  - Bruce, D.C.
AU  - Chain, P.S.
AU  - Coyne, S.R.
AU  - Gibbons, H.S.
AU  - Jaissle, J.
AU  - Chertkov, O.
AU  - Freitas, T.
AU  - Rosenzweig, C.N.
AU  - Xu, Y.
AU  - Johnson, S.L.
TI  - Draft Genome Assembly of Pseudomonas aeruginosa Quality Control Reference Strain  Boston 41501.
JO  - Genome Announcements
PY  - 2014
SP  - e00960
EP  - e00914
VL  - 2
AB  - We present the scaffolded genome assembly of Pseudomonas aeruginosa Boston 41501, now publicly
AB  - available in GenBank (JOVK00000000) in 10 contigs placed into a
AB  - single scaffold. The 6.82-Mbp genome contains 66.1% G+C content and 6,295 coding
AB  - sequences, including type 4 pilus and type 3 secretion system production genes.
ER  -

TY  - JOUR
AU  - Minot, S.
AU  - Grunberg, S.
AU  - Wu, G.
AU  - Lewis, J.
AU  - Bushman, F.
TI  - Hypervariable loci in the human gut virome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 3962
EP  - 3966
VL  - 109
AB  - Genetic variation is critical in microbial immune evasion and drug resistance, but variation
AB  - has rarely been studied in complex heterogeneous communities such as the human microbiome. To
AB  - begin to study natural variation, we analyzed DNA viruses present in the lower
AB  - gastrointestinal tract of 12 human volunteers by determining 48 billion bases of viral DNA
AB  - sequence. Viral genomes mostly showed low variation, but 51 loci of approximately 100 bp
AB  - showed extremely high variation, so that up to 96% of the viral genomes encoded unique amino
AB  - acid sequences. Some hotspots of hypervariation were in genes homologous to the bacteriophage
AB  - BPP-1 viral tail-fiber gene, which is known to be hypermutagenized by a unique
AB  - reverse-transcriptase (RT)-based mechanism. Unexpectedly, other hypervariable loci in our data
AB  - were in previously undescribed gene types, including genes encoding predicted Ig-superfamily
AB  - proteins. Most of the hypervariable loci were linked to genes encoding RTs of a single clade,
AB  - which we find is the most abundant clade among gut viruses but only a minor component of
AB  - bacterial RT populations. Hypervariation was targeted to 5'-AAY-3' asparagine codons, which
AB  - allows maximal chemical diversification of the encoded amino acids while avoiding formation of
AB  - stop codons. These findings document widespread targeted hypervariation in the human gut
AB  - virome, identify previously undescribed types of genes targeted for hypervariation, clarify
AB  - association with RT gene clades, and motivate studies of hypervariation in the full human
AB  - microbiome.
ER  -

TY  - JOUR
AU  - Minton, N.
AU  - Carter, G.
AU  - Herbert, M.
AU  - O'Keeffe, T.
AU  - Purdy, D.
AU  - Elmore, M.
AU  - Ostrowski, A.
AU  - Pennington, O.
AU  - Davis, I.
TI  - The development of Clostridium difficile genetic systems.
JO  - Anaerobe
PY  - 2004
SP  - 75
EP  - 84
VL  - 10
AB  - Clostridum difficile is a major cause of healthcare-associated disease in the western world,
AB  - and is particularly prominent in the elderly. Its
AB  - incidence is rising concomitant with increasing longevity. More
AB  - effective countermeasures are required. However, the pathogenesis of C.
AB  - difficile infection is poorly understood. The lack of effective genetic
AB  - tools is a principal reason for this ignorance. For many years. the
AB  - only tools available for the transfer of genes into C. difficile have
AB  - been conjugative transposons, such as Tn916, delivered via filter
AB  - mating from Bacillus subtilis donors. They insert into a preferred site
AB  - within the genome. Therefore, they may not be employed for classical
AB  - mutagenesis studies, but can be employed to modulate gene function
AB  - through the delivery of antisense RNA. Attempts to develop
AB  - transformation procedures have so far met with little success. However,
AB  - in recent years the situation has been dramatically improved through
AB  - the demonstration of efficient conjugative transfer of both
AB  - replication-proficient and replication-deficient plasmids from
AB  - Escherichia coli donors. This efficient transfer can only be achieved
AB  - in certain strains through negation of the indigenous restriction
AB  - barrier, and is generally most effective when the plasmid employed is
AB  - based on the replicon of the C. difficile plasmid. pCD6.
ER  -

TY  - JOUR
AU  - Mirajkar, N.S.
AU  - Johnson, T.J.
AU  - Gebhart, C.J.
TI  - Complete Genome Sequence of Brachyspira hyodysenteriae Type Strain B-78 (ATCC 27164).
JO  - Genome Announcements
PY  - 2016
SP  - e00840
EP  - e00816
VL  - 4
AB  - Reported herein is the complete genome sequence of the type strain B-78 (ATCC 27164) of
AB  - Brachyspira hyodysenteriae, the etiological agent of swine dysentery.
AB  - The 3.1-Mb genome consists of a 3.056-Mb chromosome and a 45-kb plasmid, with
AB  - 2,617 protein-coding genes, 39 RNA genes, and 40 pseudogenes.
ER  -

TY  - JOUR
AU  - Mirajkar, N.S.
AU  - Kelley, M.R.
AU  - Gebhart, C.J.
TI  - Draft Genome Sequence of Lawsonia intracellularis Strain E40504, Isolated from a  Horse Diagnosed with Equine Proliferative Enteropathy.
JO  - Genome Announcements
PY  - 2017
SP  - e00330
EP  - e00317
VL  - 5
AB  - Reported herein is the draft genome sequence of equine-origin Lawsonia intracellularis strain
AB  - E40504, an obligate intracellular bacterium and the
AB  - etiological agent of equine proliferative enteropathy. The 1.69-Mb draft genome
AB  - sequence includes 1,380 protein-coding genes and 49 RNA genes, and it lacks a
AB  - genomic island reported in swine-origin L. intracellularis strain PHE/MN1-00.
ER  -

TY  - JOUR
AU  - Miranda-Rios, J.A.
AU  - Ramirez-Trujillo, J.A.
AU  - Nova-Franco, B.
AU  - Lozano-Aguirre, B.L.F.
AU  - Iturriaga, G.
AU  - Suarez-Rodriguez, R.
TI  - Draft Genome Sequence of Arthrobacter chlorophenolicus Strain Mor30.16, Isolated  from the Bean Rhizosphere.
JO  - Genome Announcements
PY  - 2015
SP  - e00360
EP  - e00315
VL  - 3
AB  - Bacteria of the genus Arthrobacter are commonly found in the soil and plant rhizosphere. In
AB  - this study we report the draft genome of Arthrobacter
AB  - chlorophenolicus strain Mor30.16 that was isolated from rhizosphere of beans
AB  - grown in Cuernavaca Morelos, Mexico. This strain promotes growth and ameliorates
AB  - drought stress in bean plants.
ER  -

TY  - JOUR
AU  - Miriagou, V.
AU  - Papagiannitsis, C.C.
AU  - Kotsakis, S.D.
AU  - Loli, A.
AU  - Tzelepi, E.
AU  - Legakis, N.J.
AU  - Tzouvelekis, L.S.
TI  - Sequence of pNL194, a 79.3-Kilobase IncN Plasmid Carrying the blaVIM-1 Metallo-{beta}-Lactamase Gene in Klebsiella pneumoniae.
JO  - Antimicrob. Agents Chemother.
PY  - 2010
SP  - 4497
EP  - 4502
VL  - 54
AB  - The nucleotide sequence of pNL194, a VIM-1-encoding plasmid, is described.
AB  - pNL194 (79,307-bp) comprised an IncN characteristic segment (38,940-bp)
AB  - and a mosaic structure (40,367-bp) including blaVIM-1, aacA7, aadA1,
AB  - dfrA1, dfrA12, aphA1, strA, strB, and sul1. Tn1000 or Tn5501 insertion
AB  - within fipA probably facilitated recruitment of additional mobile elements
AB  - carrying resistance genes.
ER  -

TY  - JOUR
AU  - Mironov, K.S.
AU  - Sinetova, M.A.
AU  - Bolatkhan, K.
AU  - Zayadan, B.K.
AU  - Ustinova, V.V.
AU  - Kupriyanova, E.V.
AU  - Skrypnik, A.N.
AU  - Gogoleva, N.E.
AU  - Gogolev, Y.V.
AU  - Los, D.A.
TI  - Draft Genome Sequence of the Thermotolerant Cyanobacterium Desertifilum sp. IPPAS B-1220.
JO  - Genome Announcements
PY  - 2016
SP  - e01304
EP  - e01316
VL  - 4
AB  - Here, we report the draft genome of the filamentous cyanobacterium Desertifilum sp. strain
AB  - IPPAS B-1220, isolated from Lake Shar-Nuur, Mongolia. The genome of
AB  - 6.1 Mb codes for 5,113 genes. Genome mining revealed 10 clusters for the
AB  - synthesis of bioactive compounds (nonribosomal peptides, polyketides,
AB  - bacteriocins, and lantipeptides) with potential biotechnological or medical
AB  - importance.
ER  -

TY  - JOUR
AU  - Mironov, K.S.
AU  - Sinetova, M.A.
AU  - Kupriyanova, E.V.
AU  - Ustinova, V.V.
AU  - Kozlova, A.Y.
AU  - Messineva, E.M.
AU  - Gabrielyan, D.A.
AU  - Bedbenov, V.S.
AU  - Zayadan, B.K.
AU  - Los, D.A.
TI  - Draft Genome Sequences of Two Thermotolerant Cyanobacterial Strains Isolated from Hot Springs.
JO  - Genome Announcements
PY  - 2018
SP  - e01548
EP  - e01517
VL  - 6
AB  - We report here two draft cyanobacterial genome sequences, those of Cyanobacterium aponinum
AB  - IPPAS B-1201, isolated from a hot spring in the Turgen Gorge
AB  - (Kazakhstan), and the uncharacterized cyanobacterium IPPAS B-1203, isolated from
AB  - a hot spring in Karlovy Vary (Czech Republic). These two strains were deposited
AB  - at the Collection of Microalgae (IPPAS) of the Timiryazev Institute of Plant
AB  - Physiology.
ER  -

TY  - JOUR
AU  - Miroshnichenko, B.A.
AU  - Naroditskii, B.S.
AU  - Khilko, S.N.
AU  - Platonova, N.
AU  - Gruber, I.M.
AU  - Tikhonenko, T.I.
TI  - Purification of specific endonucleases EcoRI and BglII by affinity chromatography.
JO  - Biokhimiia
PY  - 1982
SP  - 686
EP  - 694
VL  - 47
AB  - Highly active preparations of specific endonucleases EcoRI from E. coli cells and BglII from
AB  - Bacillus globigii cells were obtained by affinity chromatography.  The isolation and
AB  - purification procedures included ultrasonic disintegration of the cells, high-speed
AB  - centrifugation, and chromatography. Dextran blue-Sepharose, folate-Sepharose, and
AB  - phenyl-Sepharose were used as affinity sorbents.  The optimum conditions for sorption and
AB  - elution of the endonucleases without intermediate steps of dialysis and concentration were
AB  - selected.  The consecutive combining of the above-mentioned sorbents with various ligands made
AB  - it possible to achieve highly efficient purification.  The purified enzyme preparations do not
AB  - contain nonspecific nucleases or phosphatases, they are fairly concentrated, and can be used
AB  - for the specific hydrolysis of DNA.
ER  -

TY  - JOUR
AU  - Miroshnikov, K.K. et al.
TI  - Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00504
EP  - e00517
VL  - 5
AB  - Methylocapsa palsarum NE2T is an aerobic, mildly acidophilic, obligate methanotroph. Similar
AB  - to other Methylocapsa species, it possesses only a
AB  - particulate methane monooxygenase and is capable of atmospheric nitrogen
AB  - fixation. The genome sequence of this typical inhabitant of subarctic wetlands
AB  - and soils also contains genes indicative of aerobic anoxygenic photosynthesis.
ER  -

TY  - JOUR
AU  - Misaki, W.
TI  - A recombinant lactobacillus strain expressing genes coding for restriction enzymes cleaving the HIV genomes for use as a live  microbicide strategy against heterosexual transmission of HIV.
JO  - Afr. J. Biotechnol.
PY  - 2007
SP  - 1750
EP  - 1756
VL  - 6
AB  - Using genetically engineered endogenous lactobacillus strains colonizing the vagina mucosa to
AB  - express heterogenous proteins has of
AB  - late joined the novel strategies aimed at developing a microbicides
AB  - against HIV. Using the lactobacillus metabolic genome pathway, we found
AB  - that these bacteria do not naturally produce restriction enzymes, but
AB  - rather, have a number of putative alien genes of the type. In view of
AB  - the antiviral defence role of restriction modification systems (RMS),
AB  - we searched for enzymes that cleave HIV-1, 2 and other SIV genomes
AB  - using theoretical computational methods. With over 200 such enzymes
AB  - identified, we present herein a plasmid vector mediated strategy for
AB  - modifying lactobacillus strains to express RMS islands as an approach
AB  - to developing a live HIV microbicide. This model is transferable to
AB  - other viral infections that find their way into humans through mucosal
AB  - orifices.
ER  -

TY  - JOUR
AU  - Misaki, W.
TI  - Why bacteria derived R-M nucleic enzymatic peptides are likely efficient therapeutic molecules for use in the design and development of novel HIV inhibitory strategies.
JO  - Afr. J. Biotechnol.
PY  - 2008
SP  - 1791
EP  - 1796
VL  - 7
AB  - In the past, we have identified, described and isolated over 200 bacteria derived Restriction
AB  - Modification (R-M) nucleic enzymatic peptides as efficient therapeutic molecules for use in
AB  - the development of novel HIV inhibitory strategies. In the issuing months of our publications,
AB  - 3 questions have been directed to our work; (1) HIV is an RNA virus, thus restriction peptides
AB  - are impotent as defense peptides. (2) HIV genome is encapsulated in nuclear capsid and viral
AB  - envelope, making access impossible. (3) Human genome contains several palindromes recognizable
AB  - by R-M peptides, making safety delineation critical. This paper serves to provide succinct
AB  - responses to these issues, and highlight critical strategies being employed in ensuring the
AB  - development of safe Microbides and therapeutic vaccines based on this approach.
ER  -

TY  - JOUR
AU  - Misaki, W.
AU  - Wilson, B.
AU  - Henry, K.
TI  - Frequency and site mapping of HIV-1/SIVcpz, HIV2/SIVsmm and other SIV gene sequence cleavage by various bacteria restriction enzymes:  Precursors for a novel HIV inhibitory product.
JO  - Afr. J. Biotechnol.
PY  - 2007
SP  - 1225
EP  - 1232
VL  - 6
AB  - Resistance, toxicity and virologic failure have underlined the need to develop new HIV
AB  - inhibitory products. Base on the natural bacteria
AB  - "restriction modification system" antiviral immune model, we set out to
AB  - analyze the effects of various restriction enzymes on the HIV genome. A
AB  - computer simulated model using Web cutter Version 2.0, and cytogenetic
AB  - analysis. 339 restriction enzymes from Promega database, 10
AB  - HIV-1/SIVcpz genes, 10 HIV-2/SIVsmm genes and 10 other SIV genes. Gene
AB  - sequences were fed into Web cutter 2.0 set to search enzymes with at
AB  - least 6 recognition base pairs ( palindromes). A background in vitro
AB  - cytogenetic control analysis using HIV-1/ SIVcpz GAG, POL and ENV genes
AB  - was done. Of the 339 enzymes used, 238 ( 70.2%) cleaved the HIV-1/
AB  - SIVcpz A1. BY. 97.97BL006  AF193275 genome with 9037 bp compared to 225
AB  - ( 66.4%) and 219 ( 64.6%) for the HIV-2/SIVsmm genome ( 9713 bp) and
AB  - other SIV B. FR. 83. HXB2  LAI  IIIB  BRU  K03455 genome ( 9719 bp),
AB  - respectively. Individual genes had differing but potent susceptibility
AB  - to the enzymes, with a 98.9% Web cutter PPV ( 95% CI, 97.2%99.6%) for
AB  - in vitro cytogenetics. The natural bacteria RMS antiviral immune model
AB  - offers precursors for developing novel HIV and other viral therapeutic
AB  - molecules.
ER  -

TY  - JOUR
AU  - Mise, K.
AU  - Miyahara, M.
TI  - Restriction endonucleases: Their characteristics and distribution in pathogenic bacteria.
JO  - Eisei Shikenjo Hokoku
PY  - 1993
SP  - 1
EP  - 12
VL  - 111
AB  - Restriction endonucleases have been widely employed in almost all fields of genetic
AB  - engineering including DNA mapping, cloning, sequencing, hybridization, amplification and
AB  - diagnosis. The general characteristics of restriction endonucleases and their reactions are
AB  - reviewed in this paper, together with their distribution in pathogenic bacteria. Many
AB  - restriction endonucleases with novel specificity have been found in these bacteria in our
AB  - laboratory. Some of them are commercially available and have been employed for the molecular
AB  - biologist. Rapid method for detection of restriction endonucleases in pathogenic bacteria is
AB  - also described.
ER  -

TY  - JOUR
AU  - Mise, K.
AU  - Miyahara, M.
AU  - Maruyama, T.
AU  - Kudoh, Y.
AU  - Ohashi, M.
TI  - Usefulness in the epidemiology of food poisoning cases of detection of specific restriction endonucleases in some serotypes of Salmonella and Yersinia.
JO  - Microbial Toxins in Foods and Feeds: Cell. Mol. Modes Action
PY  - 1990
SP  - 127
EP  - 129
VL  - 0
AB  - Restriction endonucleases have been employed as an extremely important tool in
AB  - recombinant DNA technology.  To date, the occurrence of more than 100
AB  - restriction endonucleases with different specificities has been reported.
AB  - Restriction endonucleases have been screened in this laboratory for pathogenic
AB  - bacteria belonging to the Enterobacteriaceae in the hope that: (i) the
AB  - detection of a specific restriction endonuclease is found at a high frequency
AB  - in the species; and (ii) new restriction endonucleases with novel specificities
AB  - might be found in pathogenic bacteria, since screening for restriction
AB  - endonucleases has rarely been carried out.  Here, we report that four
AB  - clinically important food-poisoning bacteria produce specific restriction
AB  - endonucleases at high frequencies.  Some of these are expected to be useful for
AB  - recombinant DNA technology after cloning of their gene into Escherichia coli
AB  - K-12.
ER  -

TY  - JOUR
AU  - Mise, K.
AU  - Nakajima, K.
TI  - Purification of a new restriction endonuclease, StyI, from Escherichia coli carrying the hsd+ miniplasmid.
JO  - Gene
PY  - 1985
SP  - 357
EP  - 361
VL  - 33
AB  - A new restriction endonuclease, StyI, free of contaminating nuclease
AB  - activities, has been isolated from Escherichia coli carrying the hsd+
AB  - miniplasmid of Salmonella typhi origin.  In the presence of 10 mM Mg2+, it
AB  - recognizes and cleaves a hexanucleotide sequence of 5'-C^C(A/T)(A/T)GG.  The
AB  - advantages of the StyI endonuclease include its stability, high yield (more
AB  - than 2 x 103 units/g of wet cells), easy handling of producer cells, and the
AB  - ability to recognize new sequences, CCAAGG and CCTTGG.
ER  -

TY  - JOUR
AU  - Mise, K.
AU  - Nakajima, K.
TI  - Isolation of restriction enzyme EcoVIII, an isoschizomer of HindIII, produced by Escherichia coli E1585-68.
JO  - Gene
PY  - 1984
SP  - 79
EP  - 85
VL  - 30
AB  - A restriction endonuclease designated EcoVIII, an isoschizomer of HindIII, was
AB  - isolated from Escherichia coli E1585-68 and purified by dextran-polyethylene
AB  - glycol (DPG) phase partitiion, ammonium sulfate precipitation, phospho- and
AB  - DEAE-cellulose chromatography, and hydroxylapatite chromatography.  The
AB  - purified EcoVIII was stable during the purification procedure and its high
AB  - specific activity required 10 mM Mg2+.  Unlike HindIII, EcoVIII exhibited a
AB  - high specific activity even at low pH (pH 6.3) and showed the highest activity
AB  - at 48C.  Transformation of purified plasmid DNA from E. coli E1585-68 into K-12
AB  - indicated that the EcoVIII gene was carried on a multicopy 4.4-kb miniplasmid.
AB  - EcoVIII seems to be preferable to HindIII for its production and use because of
AB  - easier handling of producer cells and a wider range of activity.
ER  -

TY  - JOUR
AU  - Mise, K.
AU  - Nakajima, K.
TI  - Restriction endonuclease EcoO109 from Escherichia coli H709c with heptanucleotide recognition site 5'-PuG^GNCCPy.
JO  - Gene
PY  - 1985
SP  - 363
EP  - 367
VL  - 36
AB  - A new restriction endonuclease, EcoO109, has been isolated from Escherichia
AB  - coli H709c by polyethylenemine (PEI) precipitation, DEAE-cellulose
AB  - chromatography and heparin agarose chromatography.  The yield was high, more
AB  - than 3000 units/g of wet cells.  The EcoO109 endonuclease recognizes and
AB  - cleaves a nucleotide sequence of 5'-PuG^GN C CPy-3' 3'-PyC CN'G^GPu-5'in the
AB  - presence of 10 mM Mg2+.  The enzyme will be useful for structural analysis and
AB  - molecular cloning of DNA because of the stability, high yield and easy handling
AB  - of the producer strain.
ER  -

TY  - JOUR
AU  - Mise, K.
AU  - Nakajima, K.
AU  - Terakado, N.
AU  - Ishidate, M.
TI  - Production of restriction endonucleases using multicopy Hsd plasmids occurring naturally in pathogenic Escherichia coli and Shigella boydii.
JO  - Gene
PY  - 1986
SP  - 165
EP  - 169
VL  - 44
AB  - A convenient procedure has been devised for detection of restriction
AB  - endonucleases in the Escherichia coli-Shigella group.  With this procedure, two
AB  - restriction endonucleases, designated Sbo13 and EcoT22, were found and later
AB  - were identified as isoschizomers of NruI and AvaIII, respectively.  These
AB  - endonucleases were shown to be produced from small multicopy plasmids.  They
AB  - were isolated from nonpathogenic E. coli into which the plasmids had been
AB  - introduced by transformation, and purified from contaminating nuclease
AB  - activity.  The yield was high, 1000 units/g of wet cells for Sbo13 and 500
AB  - units/g for EcoT22.  Sbo13 and EcoT22 should be preferable to NruI and AvaIII
AB  - because of the high yield and ease in handling the producer cells.
ER  -

TY  - JOUR
AU  - Mishra, A.
AU  - Jha, G.
AU  - Thakur, I.S.
TI  - Draft Genome Sequence of Zhihengliuella sp. Strain ISTPL4, a Psychrotolerant and  Halotolerant Bacterium Isolated from Pangong Lake, India.
JO  - Genome Announcements
PY  - 2018
SP  - e01533
EP  - e01517
VL  - 6
AB  - Zhihengliuella sp. strain ISTPL4, a psychrotolerant bacterium, was isolated from  brackish
AB  - water of the high-altitude Pangong Lake in India. In this study, we
AB  - report its draft genome sequence, which contains 3,529,629 bp with a G+C content
AB  - of 69.84%. The genome is enriched in genes associated with cold adaptation and
AB  - plant growth promotion.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Edouard, S.
AU  - Dangui, N.P.
AU  - Lagier, J.C.
AU  - Caputo, A.
AU  - Blanc-Tailleur, C.
AU  - Ravaux, I.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 205
EP  - 219
VL  - 9
AB  - Nosocomiicoccus massiliensis strain NP2(T) sp. nov. is the type strain of a new species within
AB  - the genus Nosocomiicoccus. This strain, whose genome is described
AB  - here, was isolated from the fecal flora of an AIDS-infected patient living in
AB  - Marseille, France. N. massiliensis is a Gram-positive aerobic coccus. Here we
AB  - describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 1,645,244 bp long genome (one chromosome but no
AB  - plasmid) contains 1,738 protein-coding and 45 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Gimenez, G.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome sequence and description of Alistipes senegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 1
EP  - 16
VL  - 6
AB  - Alistipes senegalensis strain JC50(T) is the type strain of A. senegalensis sp. nov., a new
AB  - species within the Alistipes genus. This strain, whose genome is
AB  - described here, was isolated from the fecal flora of an asymptomatic patient. A.
AB  - senegalensis is an anaerobic Gram-negative rod-shaped bacterium. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 4,017,609 bp long genome (1 chromosome, but no plasmid) contains
AB  - 3,113 protein-coding and 50 RNA genes, including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Hugon, P.
AU  - Lagier, J.C.
AU  - Nguyen, T.T.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 290
EP  - 305
VL  - 8
AB  - Enorma massiliensis strain phI(T) is the type strain of E. massiliensis gen. nov., sp. nov.,
AB  - the type species of a new genus within the family
AB  - Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here,
AB  - was isolated from the fecal flora of a 26-year-old woman suffering from morbid
AB  - obesity. E. massiliensis strain phI(T) is a Gram-positive, obligately anaerobic
AB  - bacillus. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 2,280,571 bp long genome (1
AB  - chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901
AB  - protein-coding and 51 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Hugon, P.
AU  - Lagier, J.C.
AU  - Nguyen, T.T.
AU  - Robert, C.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 357
EP  - 369
VL  - 7
AB  - Peptoniphilus obesi strain ph1(T) sp. nov., is the type strain of P. obesi sp. nov., a new
AB  - species within the genus Peptoniphilus. This strain, whose genome is
AB  - described here, was isolated from the fecal flora of a 26-year-old woman
AB  - suffering from morbid obesity. P. obesi strain ph1(T) is a Gram-positive,
AB  - obligate anaerobic coccus. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. The 1,774,150 bp long
AB  - genome (1 chromosome but no plasmid) contains 1,689 protein-coding and 29 RNA
AB  - genes, including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Hugon, P.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 320
EP  - 330
VL  - 7
AB  - Peptoniphilus grossensis strain ph5(T) sp. nov., is the type strain of Peptoniphilus
AB  - grossensis sp. nov., a new species within the Peptoniphilus genus.
AB  - This strain, whose genome is described here, was isolated from the fecal flora of
AB  - a 26-year-old woman suffering from morbid obesity. P. grossensis strain ph5 is a
AB  - Gram-positive obligate anaerobic coccus. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 2,101,866-bp long genome (1 chromosome but no plasmid) exhibits a G+C content of
AB  - 33.9% and contains 2,041 protein-coding and 29 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Nguyen, T.T.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 370
EP  - 381
VL  - 7
AB  - Peptoniphilus senegalensis strain JC140(T) sp. nov., is the type strain of P. senegalensis sp.
AB  - nov., a new species within the genus Peptoniphilus. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a healthy
AB  - patient. P. senegalensis strain JC140(T) is an obligate Gram-positive anaerobic
AB  - coccus. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 1,840,641 bp long genome (1
AB  - chromosome but no plasmid) exhibits a G+C content of 32.2% and contains 1,744
AB  - protein-coding and 23 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Pfleiderer, A.
AU  - Nguyen, T.T.
AU  - Caputo, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 395
EP  - 409
VL  - 9
AB  - Holdemania massiliensis strain AP2(T) sp. nov. is the type strain of H. massiliensis sp. nov.,
AB  - a new species within the genus Holdemania. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a
AB  - 21-year-old French Caucasian female suffering from severe restrictive anorexia
AB  - nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains
AB  - 3,461 protein-coding and 49 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Rivet, R.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 70
EP  - 81
VL  - 7
AB  - strain JC66, is the type strain of sp. nov., a new species within the genus . This strain,
AB  - whose genome is described here, was isolated from the fecal flora of
AB  - a healthy patient. strain JC66 is a facultative Gram-negative anaerobic
AB  - rod-shaped bacterium. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 5,581,254 bp long genome (1
AB  - chromosome but no plasmid) exhibits a G+C content of 48.2% and contains 5,008
AB  - protein-coding and 51 RNA genes, including 9 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 1
EP  - 11
VL  - 7
AB  - strain JC401 sp. nov. is the type strain of sp. nov., a new species within the genus. This
AB  - strain, whose genome is described here, was isolated from the fecal
AB  - flora of a healthy patient. is an obligate Gram-positive anaerobic coccus. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 1,758,598 bp long genome (1 chromosome, no plasmid)
AB  - contains 1,922 protein-coding and 22 RNA genes, including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 386
EP  - 395
VL  - 6
AB  - Clostridium senegalense strain JC122(T), is the type strain of Clostridium senegalense sp.
AB  - nov., a new species within the genus Clostridium. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a healthy
AB  - patient. C. senegalense strain JC122(T) is an obligate anaerobic Gram-positive
AB  - rod-shaped bacterium. Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 3,893,008 bp long genome (1
AB  - chromosome but no plasmid) exhibits a G+C content of 26.8% and contains 3,704
AB  - protein-coding and 57 RNA genes, including 6 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a  new member of the suborder Micrococcinae.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 318
EP  - 335
VL  - 8
AB  - Timonella senegalensis strain JC301(T) gen. nov., sp. nov. is the type strain of  T.
AB  - senegalensis gen. nov., sp. nov., a new species within the newly proposed
AB  - genus Timonella. This bacterial strain was isolated from the fecal flora of a
AB  - healthy Senegalese patient. In this report, we detail the features of this
AB  - organism, together with the complete genome sequence and annotation. Timonella
AB  - senegalensis strain JC301(T) exhibits the highest 16S rRNA similarity (95%) with
AB  - Sanguibacter marinus, the closest validly published bacterial species. The genome
AB  - of T. senegalensis strain JC301(T) is 3,010,102-bp long, with one chromosome and
AB  - no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes,
AB  - including 5 rRNA genes. The genomic annotation revealed that T. senegalensis
AB  - strain JC301(T) possesses the complete complement of enzymes necessary for the de
AB  - novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin),
AB  - as well as the enzymes involved in the metabolism of various carbon sources,
AB  - chaperone genes, and genes involved in the regulation of polyphosphate and
AB  - glycogen levels.
ER  -

TY  - JOUR
AU  - Mishra, A.K.
AU  - Pfleiderer, A.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 465
EP  - 479
VL  - 8
AB  - Bacillus massilioanorexius strain AP8(T) sp. nov. is the type strain of B. massilioanorexius
AB  - sp. nov., a new species within the genus Bacillus. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a
AB  - 21-year-old Caucasian French female suffering from a severe form of anorexia
AB  - nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive
AB  - aerobic bacillus. Here we describe the features of this organism, together with
AB  - the complete genome sequence and annotation. The 4,616,135 bp long genome (one
AB  - chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes,
AB  - including 8 rRNA genes.
ER  -

TY  - JOUR
AU  - Mishra, M.
AU  - Patole, S.
AU  - Mohapatra, H.
TI  - Draft Genome Sequences of Nonclinical and Clinical Enterobacter cloacae Isolates  Exhibiting Multiple Antibiotic Resistance and Virulence Factors.
JO  - Genome Announcements
PY  - 2017
SP  - e01218
EP  - e01217
VL  - 5
AB  - Enterobacter spp. have been implicated as opportunistic pathogens which over the  years have
AB  - gained resistance toward most of the available therapeutic drugs. We
AB  - sequenced two multidrug-resistant Enterobacter cloacae isolates harboring
AB  - multiple efflux pump genes. These isolates exhibited strain-specific modulation
AB  - of efflux pump protein expression.
ER  -

TY  - JOUR
AU  - Mishra, N.C.
TI  - Restriction Endonucleases.
JO  - Nucleases. Molecular Biology and Applications.
PY  - 2002
SP  - 62
EP  - 80
AB  - Luria and Human first described the phenomenon of host-controlled specificity in T-even
AB  - phages.  This was immediately confirmed by Bertani and Weigle in lambda and P2 phages.  In
AB  - these studies it was shown that a particular bacteriophage possessed different efficiencies of
AB  - infection on several closely related strains of bacteria.  However, the progeny of
AB  - bacteriophage which initially plated with a low efficiency was later found to plate
AB  - efficiently after one generation of plating on the same bacterium.  This phenomenon of
AB  - host-controlled specificity was first discovered in T-even phages by Luria and Human  and in
AB  - lambda and P2 phages by Bertani and Weigle.  The epigenetic nature of such host range
AB  - specificity was indicated by the fact that the newly acquired high efficiency of plating on a
AB  - particular bacterial host was lost by the progeny of the same bacteriophage when plated on
AB  - different hosts.  The first host modification unique to T-even phages involved the
AB  - glycosylation of hydroxymethyl cytosine residue.  However, the modification introduced in
AB  - lambda phages was found to be of universal occurrence.  The molecular basis of such host range
AB  - specificity depended on the restriction or modification of certain DNA sequences by
AB  - restriction and modification enzymes (Arber and Dussoix, 1962; Arbor and Linn, 1969).  Foreign
AB  - DNA molecules (lacking appropriate modification) were cleaved by the host restriction
AB  - endonuclease upon entry into the bacterial cell.  During this process some of the phage DNA
AB  - may escape restriction by host endonucleases and instead get modified by methylation of
AB  - adenine or cytosine moieties in DNA and thus acquire the ability to infect the same host
AB  - efficiently in subsequent rounds of infection.  In these series of events, bacterial DNAs
AB  - remain protected because of previous modification of the DNA sequences by methylase.  This
AB  - molecular scenario for the host range specificity by Arber and Dussoix was confirmed by the
AB  - discovery of bacterial restriction-modification enzymes.  The restriction endonucleases widely
AB  - differ in terms of subunit composition, cofactor requirements, and interaction with DNA
AB  - substrate in addition to their specificity for nucleotide sequence as sites of recognition and
AB  - of cleavage or modification.  They are classified under three categories.  These are: type I
AB  - restriction endonuclease, type II restriction endonuclease, and type III restriction
AB  - endonuclease.  Among these three types of restriction endonuclease, type I and type III
AB  - enzymes can be referred to as ATP-dependent restriction endonucleases and the type II enzymes
AB  - can be referred to as ATP-independent restriction endonucleases.  The physiological roles of
AB  - the ATP-dependent restriction endonucleases in biological restriction and modification have
AB  - been genetically identified.  The physiological role of the ATP-independent endonucleases
AB  - remains to be elucidated.  However, the discovery of this group of restriction endonucleases
AB  - has revolutionized molecular biology by facilitating the physical mapping and nucleotide
AB  - sequencing of DNA segments and their amplification by molecular cloning.  The properties of
AB  - the three types of restriction enzymes are compared in Table 4.1.
ER  -

TY  - JOUR
AU  - Mishra, S.R.
AU  - Panda, A.N.
AU  - Ray, L.
AU  - Sahu, N.
AU  - Mishra, G.
AU  - Jadhao, S.
AU  - Suar, M.
AU  - Adhya, T.K.
AU  - Rastogi, G.
AU  - Pattnaik, A.K.
AU  - Raina, V.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain BMS12, a Plant Growth-Promoting and Protease-Producing Bacterium, Isolated from the Rhizosphere Sediment of Phragmites karka of Chilika Lake, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00342
EP  - e00316
VL  - 4
AB  - We report the 4.51 Mb draft genome of Pseudomonas sp. strain BMS12, a Gram-negative bacterium
AB  - in the class of Gammaproteobacteria, isolated from the rhizospheric sediment of Phragmites
AB  - karka, an invasive weed in Chilika Lake, Odisha, India. The Pseudomonas sp. strain BMS12 is
AB  - capable of producing proteases and is also an efficient plant growth promoter that can be
AB  - useful for various phytoremedial and industrial applications.
ER  -

TY  - JOUR
AU  - Mishra, S.R.
AU  - Ray, L.
AU  - Panda, A.N.
AU  - Sahu, N.
AU  - Xess, S.S.
AU  - Jadhao, S.
AU  - Suar, M.
AU  - Adhya, T.K.
AU  - Rastogi, G.
AU  - Pattnaik, A.K.
AU  - Raina, V.
TI  - Draft Genome Sequence of Acinetobacter sp. Strain BMW17, a Cellulolytic and Plant Growth-Promoting Bacterium Isolated from the Rhizospheric Region of Phragmites karka of Chilika Lake, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00395
EP  - e00316
VL  - 4
AB  - We report the 3.16 Mb draft genome of Acinetobacter sp. strain BMW17, a Gram-negative
AB  - bacterium in the class of Gammaproteobacteria, isolated from the rhizospheric region of
AB  - Phragmites karka, an invasive weed in Chilika Lake, Odisha, India. The strain BMW17(T) is
AB  - capable of degrading cellulose and is also  an efficient plant growth promoter that can be
AB  - useful for various phytoremedial and commercial applications.
ER  -

TY  - JOUR
AU  - Misic, A.M.
AU  - Cain, C.L.
AU  - Morris, D.O.
AU  - Rankin, S.C.
AU  - Beiting, D.P.
TI  - Complete Genome Sequence and Methylome of Staphylococcus schleiferi, an Important Cause of Skin and Ear Infections in Veterinary Medicine.
JO  - Genome Announcements
PY  - 2015
SP  - e01011
EP  - e01015
VL  - 3
AB  - Staphylococcus schleiferi, a Gram-positive and coagulase-variable organism, is an
AB  - opportunistic human pathogen and a major cause of skin and soft tissue infections in dogs.
AB  - Here, we report the first S. schleiferi genome sequence and methylome from four canine
AB  - clinical isolates.
ER  -

TY  - JOUR
AU  - Misra, V.K.
AU  - Hecht, J.L.
AU  - Sharp, K.A.
AU  - Friedman, R.A.
AU  - Honig, B.
TI  - Salt effects on protein-DNA interactions.  The lambdacI repressor and EcoRI endonuclease.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 264
EP  - 280
VL  - 238
AB  - In this paper, finite-difference solutions to the nonlinear Poisson-Boltzmann (NLPB) equation
AB  - are used to calculate the salt dependent contribution to the electrostatic DNA binding free
AB  - energy for both the lambdacI repressor and the EcoRI endonuclease. For the protein-DNA systems
AB  - studied, the NLPB method describes nonspecific univalent salt dependent effects on the binding
AB  - free energy which are in excellent agreement with experimental results. In these systems, the
AB  - contribution of the ion atmosphere to the binding free energy substantially destabilizes the
AB  - protein-DNA complexes. The magnitude of this effect involves a macromolecular structure
AB  - dependent redistribution of both cations and anions around the protein and the DNA which is
AB  - dominated by long range electrostatic interactions. We find that the free energy associated
AB  - with global ion redistribution upon binding is more important than changes associated with
AB  - local protein-DNA interactions (ion-pairs) in determining salt effects. The NLPB model reveals
AB  - how long range salt effects can play a significant role on the relative stability of
AB  - protein-DNA complexes with different structures.
ER  -

TY  - JOUR
AU  - Mithoefer, S.
AU  - Rheaume, B.A.
AU  - MacLea, K.S.
TI  - Draft Whole-Genome Sequence of the Marine Bacterium Idiomarina zobellii KMM 231T.
JO  - Genome Announcements
PY  - 2015
SP  - e01257
EP  - e01215
VL  - 3
AB  - Idiomarina zobellii was isolated from the northwest Pacific Ocean at a depth of 4,000 to 5,000
AB  - m in 1985. The draft whole-genome shotgun sequence of I. zobellii
AB  - KMM 231(T) described in this paper has a predicted length of 2,602,160 bp,
AB  - containing 2,570 total genes, 52 tRNAs, and a G+C content of 47.10%.
ER  -

TY  - JOUR
AU  - Mitra, A.
AU  - Higgins, D.W.
TI  - The Chlorella virus adenine methyltransferase gene is a strong promoter in plants.
JO  - Plant Mol. Biol.
PY  - 1994
SP  - 85
EP  - 93
VL  - 26
AB  - An upstream region isolated from a eukaryotic algal virus adenine methyltransferase gene was
AB  - tested for promoter function in plants. Fusion of this region to the chloramphenicol
AB  - acetyltransferase reporter gene resulted in significantly higher expression than fusion with
AB  - the cauliflower mosaic virus 35S promoter. Strong levels of expression were also found in
AB  - electroporated monocot plant cells. The promoter activity in transgenic tobacco plants showed
AB  - tissue-specific expression. Leaves had the highest expression followed by stems and flowers.
AB  - The promoter activity was not detected in root tissue. Environmental cues, such as light, and
AB  - the phytohormones auxin and cytokinines had no effect on the promoter's expression. This
AB  - promoter might be utilized to achieve high levels of expression of introduced genes in higher
AB  - plants.
ER  -

TY  - JOUR
AU  - Mitra, A.
AU  - Que, Q.
TI  - Ectopic expression of a viral adenine methyltransferase gene in tobacco.
JO  - Biochim. Biophys. Acta
PY  - 1994
SP  - 244
EP  - 249
VL  - 1219
AB  - Plant genomes contain both methylated adenine and cytosine residues although the roles of
AB  - these methylations are not well understood. A Chlorella virus adenine methyltransferase gene
AB  - under the control of cauliflower mosaic virus 35S promoter in a binary plant transformation
AB  - vector was expressed both in transgenic tobacco plants and transformed tobacco calli. The
AB  - transgenic plants as well as transformed calli produced functional adenine methyltransferase
AB  - enzyme, but the level of expression was higher in tobacco calli. A transgenic tobacco cell
AB  - line that expressed the methyltransferase enzyme and carried an Arabidopsis cab3 gene
AB  - containing a single target site for the adenine methyltransferase enzyme showed that the
AB  - adenine residue was not methylated. HPLC analysis of genomic DNA from transgenic calli also
AB  - showed no detectable levels of methylated adenine residues.
ER  -

TY  - JOUR
AU  - Mitrovic, J.
AU  - Siewert, C.
AU  - Duduk, B.
AU  - Hecht, J.
AU  - Moelling, K.
AU  - Broecker, F.
AU  - Beyerlein, P.
AU  - Buettner, C.
AU  - Bertaccini, A.
AU  - Kube, M.
TI  - Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates.
JO  - J. Mol. Microbiol. Biotechnol.
PY  - 2014
SP  - 1
EP  - 11
VL  - 24
AB  - Phytoplasma-associated diseases are reported for more than 1,000 plant species worldwide.
AB  - Only a few genome sequences are available in contrast to the economical importance of these
AB  - bacterial pathogens.  A new strategy was used to retrieve phytoplasma strain-specifric genome
AB  - data.  Multiple displacement amplification was performed on DNA obtained from <3 g of plant
AB  - tissue from tobacco and parsley samples infected with 'stolbur' strains.  Random hexamers
AB  - and Phi29 polymerase were evaluated with and without supplementation by group-assigned
AB  - oligonucleotides providing templates for Illumina's sequencing approach.  Metagenomic drafts
AB  - derived from individual and pooled strain-specific de novo assembles were analyzed.
AB  - Supplementation of the Phi29 reaction with the group-assigned oligonucleotides resulted in an
AB  - about 2-fold enrichment of the percentage of phytoplasma-assigned reads and thereby improved
AB  - assembly results.  The obtained genomic drafts represent the largest datasets available from
AB  - 'stolbur' phytoplasmas.  Sequences of the two strains (558 kb, 448 proeins and 516 kb, 346
AB  - proteins, respectively) were annotated allowing the identification of prominent membrane
AB  - proteins and reconstruction of core pathways.  Analysis of a putative truncated sucrose
AB  - phosphorylase provides hints on sugar degradation.  Furthermore, it is shown that drafts
AB  - obtained from repetitive-rich genomes allow only limited analysis on multicopy regions and
AB  - genome completeness.
ER  -

TY  - JOUR
AU  - Mittal, P.
AU  - Saxena, R.
AU  - Sharma, V.K.
TI  - Draft Genome Sequence of Anoxybacillus mongoliensis Strain MB4, a Sulfur-Utilizing Aerobic Thermophile Isolated from a Hot Spring in Tattapani,  Central India.
JO  - Genome Announcements
PY  - 2017
SP  - e01709
EP  - e01716
VL  - 5
AB  - Anoxybacillus mongoliensis strain MB4, an aerobic thermophile, was isolated from  a hot spring
AB  - located in central India. Its first draft genome sequence reported
AB  - in this study comprises 2,807,516 bp and 2,853 protein-coding genes. Detailed
AB  - genomic analysis indicates that it is capable of performing sulfur metabolism.
ER  -

TY  - JOUR
AU  - Miura, T.
AU  - Kusada, H.
AU  - Kamagata, Y.
AU  - Hanada, S.
AU  - Kimura, N.
TI  - Genome Sequence of the Multiple-beta-Lactam-Antibiotic-Resistant Bacterium Acidovorax sp. Strain MR-S7.
JO  - Genome Announcements
PY  - 2013
SP  - e00412
EP  - e00413
VL  - 1
AB  - Acidovorax sp. strain MR-S7 was isolated from activated sludge in a treatment system for
AB  - wastewater containing beta-lactam antibiotic pollutants. Strain MR-S7
AB  - demonstrates multidrug resistance for various types of beta-lactam antibiotics at
AB  - high levels of MIC. The draft genome sequence clarified that strain MR-S7 harbors
AB  - unique beta-lactamase genes.
ER  -

TY  - JOUR
AU  - Miura, T.
AU  - Tsuchikane, K.
AU  - Numata, M.
AU  - Hashimoto, M.
AU  - Hosoyama, A.
AU  - Ohji, S.
AU  - Yamazoe, A.
AU  - Fujita, N.
TI  - Complete Genome Sequence of an Alkane Degrader, Alcanivorax sp. Strain NBRC 101098.
JO  - Genome Announcements
PY  - 2014
SP  - e00766
EP  - e00714
VL  - 2
AB  - Alcanivorax sp. strain NBRC 101098 was isolated from seawater in Japan. Strain NBRC 101098 is
AB  - able to degrade various types of n-alkanes. Here, we report the
AB  - complete genome of strain NBRC 101098.
ER  -

TY  - JOUR
AU  - Miura, T.
AU  - Uchino, Y.
AU  - Tsuchikane, K.
AU  - Ohtsubo, Y.
AU  - Ohji, S.
AU  - Hosoyama, A.
AU  - Ito, M.
AU  - Takahata, Y.
AU  - Yamazoe, A.
AU  - Suzuki, K.
AU  - Fujita, N.
TI  - Complete Genome Sequences of Sulfurospirillum Strains UCH001 and UCH003 Isolated  from Groundwater in Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e00236
EP  - e00215
VL  - 3
AB  - Sulfurospirillum strains UCH001 and UCH003 were isolated from anaerobic
AB  - cis-1,2-dichloroethene-dechlorinating microbial consortia derived from
AB  - groundwater in Japan. Here, we report the complete genome sequences of strains
AB  - UCH001 and UCH003.
ER  -

TY  - JOUR
AU  - Miyada, C.G.
AU  - Born, T.L.
TI  - A DNA sequence for the discrimination of Neisseria gonorrhoeae from other Neisseria species.
JO  - Mol. Cell. Probes
PY  - 1991
SP  - 327
EP  - 335
VL  - 5
AB  - A 350 base pair Neisseria gonorrhoeae DNA restriction fragment was cloned after subtractive
AB  - hybridization to Neisseria meningitidis DNA.  This restriction fragment hybridized to 105 out
AB  - of 106 N. gonorrhoeae strains tested.  While three N. meningitidis strains did not hybridize
AB  - to this probe, Neisseria mucosa DNA exhibited cross-hybridization.  This particular clone was
AB  - used to screen a N. gonorrhoeae genomic DNA library.  A positive 2-4 kilobase pair clone was
AB  - shown by DNA sequencing to contain two long open reading frames.  One open reading frame did
AB  - not hybridize to N. mucosa and other Neisseria species, while it retained specificity for the
AB  - original 105 N. gonorrhoeae strains.  This open reading frame also showed significant homology
AB  - to cytosine DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Miyagi, T.
AU  - Javorsky, P.
AU  - Pristas, P.
AU  - Karita, S.
AU  - Sakka, K.
AU  - Ohmiya, K.
TI  - Partial purification and characterization of RalF40I, a class II restriction endonuclease from Ruminococcus albus F-40, which recognizes and cleaves 5'-/GATC-3'.
JO  - FEMS Microbiol. Lett.
PY  - 1998
SP  - 215
EP  - 218
VL  - 164
AB  - Restriction endonuclease RalF40I was purified from cell-free extracts of the rumen
AB  - cellulolytic bacterium Ruminococcus albus F-40 by heparin-Sepharose chromatography.  The
AB  - preparation was active only on DNA substrates that were not Dam-methylated.  RalF40I
AB  - recognizes the 4-bp palindrome, 5'-/GATC-3', and cleaves DNA at the 5' side of G in the
AB  - sequence, producing 5' tetranucleotide protruding ends.  RalF40I is a class II restriction
AB  - endonuclease and an isoschizomer of MboI and DpnII.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Fujiwara, R.
AU  - Mise, K.
AU  - Shimada, T.
AU  - Matsushita, S.
AU  - Kudoh, Y.
AU  - Ishiwata, N.
AU  - Tanimura, A.
TI  - Characterization of restriction endonucleases from Vibrio parahaemolyticus.
JO  - J. Food. Hyg. Sci. Japan
PY  - 1994
SP  - 605
EP  - 609
VL  - 35
AB  - Forty-six restriction endonuclease (ENase)-positive strains were found among 270 strains of
AB  - Vibrio parahaemolyticus tested. Thirty-six ENases were purified and 7 different specificities
AB  - were identified. All are isoschizomers of already-known ENases, i.e., isoschizomers of AvaII,
AB  - AsuI, PmaCI, PstI, Eco31I, EarI, and SapI. It is noteworthy that the majority of V.
AB  - parahaemolyticus ENases recognize non-palindromic or interrupted palindromic sequences.
AB  - Specific ENases with the same specificity were found at a high frequency in some serotypes of
AB  - V. parahaemolyticus.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Ishiwata, N.
AU  - Yoshida, Y.
TI  - StyD4I restriction-modification system of Salmonella typhi D4: Cloning and sequence analysis.
JO  - Biol. Pharm. Bull.
PY  - 1997
SP  - 201
EP  - 203
VL  - 20
AB  - A plasmid (5.4 kbp) from Salmonella Typhi D4 has been identified as encoding a restriction and
AB  - modification (R-M) system.  DNA fragments (2537 bp) that carried the genes for the restriction
AB  - endonuclease and methyltransferase encoded on the plasmid were sequenced.  Two divergently
AB  - arranged open reading frames of 957 bp for the restriction endonuclease consisting of 318 aa
AB  - (amino acids) and 1140 bp for the DNA methyltransferase consisting of 379 aa were identified.
AB  - These sequences were similar to the sequences of the SsoII R-M system, including the
AB  - interspace between the two genes.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Kimizuka, F.
AU  - Kita, A.
AU  - Matsushita, S.
AU  - Kudo, Y.
AU  - Shimada, T.
AU  - Mise, K.
TI  - Isolation and characterization of restriction endonuclease in Plesiomonas shigelloides and Aeromonas species.
JO  - Biol. Pharm. Bull.
PY  - 1996
SP  - 1506
EP  - 1507
VL  - 19
AB  - Five restriction endonucleases (ENases) and one ENase were found in a screen of 196 strains of
AB  - Plesiomonas shigelloides and 147 strains of Aeromonas species.  Plesiomonas and Aeromonas
AB  - species are classified as Vibrionaceae, identified as food-poisoning bacteria, are closely
AB  - genetically related to each other, and their ENases producing abilities have not been
AB  - reported.  ENases were detected at relatively low frequencies in these species as compared to
AB  - those in other species, such as Salmonella species and Vibrio parahaemolyticus.  All ENases
AB  - were shown to be isoschizomers of already known ENases.  One of the Plesiomonas ENases,
AB  - designated PshBI, recognizing the sequence 5'-AT/TAAT-3' should be useful, since PshBI ENase
AB  - is produced at a high yield of 7000 units/g of wet cells.  The specificities of other ENases
AB  - are also described in this paper.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Kudoh, Y.
AU  - Mise, K.
TI  - Widespread occurrence of specific restriction endonucleases in Salmonella infantis, Salmonella thompson, and Salmonella blockley isolated from humans in Japan.
JO  - Appl. Environ. Microbiol.
PY  - 1990
SP  - 2248
EP  - 2250
VL  - 56
AB  - Specific restriction endonucleases were detected in three serotypes of
AB  - Salmonella spp. isolated from humans in Japan from 1970 to 1987: an
AB  - isoschizomer of AvaII endonuclease at a frequency of 0.91 in Salmonella
AB  - infantis, an isoschizomer of KpnI at a frequency of 0.34 in Salmonella
AB  - thompson, and an isoschziomer of StyI at a frequency of 0.30 in Salmonella
AB  - blockley.  Of interest is that restriction endonuclease-producing S. thompson
AB  - was detected at high frequencies in the 1970s but at low frequencies in the
AB  - 1980s.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Maruyama, T.
AU  - Wake, A.
AU  - Mise, K.
TI  - Widespread occurrence of the restriction endonuclease YenI, an isoschizomer of PstI, in Yersinia enterocolitica serotype 08.
JO  - Appl. Environ. Microbiol.
PY  - 1988
SP  - 577
EP  - 580
VL  - 54
AB  - The cold-active restriction endonuclease YenI, an isoschizomer of PstI, was
AB  - found in 12 of 14 Yersinia enterocolitica serotype 08 strains of different
AB  - origins, but not in other serotypes of Y. enterocolitica, Yersinia
AB  - pseudotuberculosis, or Yersinia pestis.  In spite of the limited number of
AB  - strains tested, the result suggests that the detection of YenI endonuclease or
AB  - the gene might result in more rapid determination of the prominently pathogenic
AB  - serotype of Y. enterocolitica.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Mise, K.
TI  - Rapid method for detection of restriction endonuclease-producing strains in enteropathogenic bacteria.
JO  - Anal. Chim. Acta
PY  - 1988
SP  - 273
EP  - 277
VL  - 213
AB  - An improved rapid method is described for the detection of restriction
AB  - endonucleases in enteropathogenic bacteria including Salmonella and Escherichia
AB  - coli.  With the improved method, at least six restriction endonucleases with
AB  - different specificity were found in 415 strains tested.  Five of them were
AB  - shown to be isoschizomers of known restriction endonucleases, while one seemed
AB  - to be novel.  Among the isoschizomers, SthI endonuclease (isoschizomer of KpnI)
AB  - in Salmonella thompson appears to be useful; unlike KpnI, SthI generates DNA
AB  - fragments with a 5'-protruding end.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Mise, K.
TI  - Isolation and characterization of the StyD4I restriction endonuclease a neoschizomer of ScrFI, from Escherichia coli K-12 carrying a small multicopy Hsd Plasmid of Salmonella typhi origin.
JO  - Gene
PY  - 1993
SP  - 83
EP  - 86
VL  - 129
AB  - A restriction endonuclease designated StyD4I, a neoschizomer of ScrFI, has been isolated from
AB  - Escherichia coli K-12 carrying a small multicopy host specificity for DNA (Hsd) plasmid of
AB  - Salmonella typhi D4 origin. In the presence of 10 mM Mg2+, StyD4I cleaves the sequence
AB  - 5'-/CCNGG-3' and generates a 5-nucleotide cohesive end. StyD4I should be useful for
AB  - recombinant DNA technology, because of the stability and ease in handling the producer cells.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Mise, K.
AU  - Kimizuka, F.
AU  - Matsumoto, H.
AU  - Terawaki, Y.
TI  - Purification of restriction endonuclease EcoO128I produced by an enteropathogenic Escherichia coli O128Ly3.
JO  - Gene
PY  - 1992
SP  - 135
EP  - 136
VL  - 113
AB  - Restriction endonuclease EcoO128I, an isoschizomer of BstEII, was purified from a rough mutant
AB  - of Escherichia coli O128Ly3. EcoO128I should be more convenient for recombinant DNA
AB  - applications than BstEII, because of its improved cleavage activity at 37C.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Nakajima, K.
AU  - Kawanishi, T.
AU  - Mise, K.
TI  - SshAI restriction endonuclease from Salmonella shikmonah.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 245
EP  - 248
VL  - 66
AB  - A new type II restriction endonuclease, SshAI, was purified from Salmonella shikmonah TK139 of
AB  - kangaroo origin.  The recognition and cleavage specificity of SshAI was determined to be
AB  - 5'-CC/TNAGG-3', identical to that of SauI from Streptomyces aureofaciens and Bsu36I from
AB  - Bacillus subtilis.  Based on closely related and in part overlapping recognition specificities
AB  - of SshAI and other restriction endonucleases, a close evolutionary relationship is proposed
AB  - for all known Salmonella restriction endonucleases.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Nakajima, K.
AU  - Shimada, T.
AU  - Mise, K.
TI  - Restriction endonuclease PshAI from Plesiomonas shigelloides with the novel recognition site 5'-GACNN/NNGTC.
JO  - Gene
PY  - 1990
SP  - 119
EP  - 122
VL  - 87
AB  - A new restriction endonuclease (ENase), PshAI, has been isolated from
AB  - Plesiomonas shigelloides 319-73, an organism that causes food poisoning in
AB  - humans.  The enzyme was stable and produced a yield of 410 units/g of cells.
AB  - In the presence of 10 mM MgCl2, PshAI recognizes and cleaves the nucleotide
AB  - sequence 5'-GACNN/NNGTC, producing blunt ends.  PshAI will be useful for
AB  - structural analysis and molecular cloning of DNA, because no ENases recognizing
AB  - the sequence GACNNNNGTC have been previously described.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Nakamura, A.
AU  - Mise, K.
TI  - Characterization of two restriction endonucleases, SenPT14bI and SenPT16I, in standard phage-type strains of Salmonella enteritidis.
JO  - Biol. Pharm. Bull.
PY  - 1997
SP  - 1212
EP  - 1214
VL  - 20
AB  - Two restriction endonucleases were found by screening 38 standard phage strains of Salmonella
AB  - enteritidis.  An isoschizomer of SacII Enase that recognizes the sequence 5'-CCGC/GG-3' was
AB  - identified in S. enteritidis PT14b, and an isoschizomer of XmaIII ENase (5'-C/GGCCG-3') was
AB  - found in S. enteritidis PT16.  It is of special interest that the recognition specifities of
AB  - all known ENases in Salmonella, including those of the S. enteritidis ENases, are very similar
AB  - to each other.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Shimada, T.
AU  - Kotani, H.
AU  - Mise, K.
TI  - Isolation and characterization of new restriction endonucleases from Vibrio parahaemolyticus: VpaK32I enzyme with the class-IIS heptanucleotide specificity, GCTCTTCN1/N4.
JO  - Gene
PY  - 1992
SP  - 103
EP  - 106
VL  - 117
AB  - Six restriction endonucleases (ENases), classified into four different specificities, were
AB  - found in a screen among 68 reference strains of Vibrio parahaemolyticus of human origin. Five
AB  - of these ENases are isoschizomers of well-know ENases, while the remaining one, designated
AB  - VpaK321, is a novel and highly efficient class-IIS ENase with the heptanucleotide recognition
AB  - site, 5'-GCTCTTC(1/4)-3'.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Shimada, T.
AU  - Mise, K.
TI  - Characterization of restriction endonucleases from Vibrio cholerae non 01.
JO  - J. Food. Hyg. Sci. Japan
PY  - 1994
SP  - 599
EP  - 604
VL  - 35
AB  - Fourteen restriction endonucleases (ENases) were found by screening of 118 O antigen reference
AB  - strains of Vibrio cholerae. Ten of these ENases were partially purified and classified into
AB  - eight specificity categories. All of them were isoschizomers of already-known ENases. It is of
AB  - interest that the isoschizomer of EcoRI ENase designated VchO2I was found in V. cholerae O2,
AB  - since VchO2I, as well as EcoRI, shows high activity at pH 8-9, and most V. cholerae strains
AB  - can grow well in this pH range.
ER  -

TY  - JOUR
AU  - Miyahara, M.
AU  - Shinohara, N.
AU  - Mise, K.
TI  - Purification of EcoO44I restriction endonuclease in Escherichia coli O44 isolated from an affected human.
JO  - Eisei Shikenjo Hokoku
PY  - 1996
SP  - 13
EP  - 15
VL  - 114
AB  - A restriction endonuclease (Enase) designated EcoO44I  was purified without non-specific
AB  - nucleases from enteropathogenic Escherichia coli O44 Hiromi strain of affected human origin.
AB  - The yield was 1,100 units/g of wet cells.  The EcoO44I Enase recognized and cleaved the
AB  - specific sequence 5'-GGTCTC-3' (1/5) as was the case with Eco31I or BsaI Enase.  Because of
AB  - the stability and high yield, EcoO44I would be useful for recombinant DNA technology after
AB  - isolation of EcoO44-positive, avirulent mutant strains of E. coli O44 Hiromi.
ER  -

TY  - JOUR
AU  - Miyake, M.
AU  - Kotani, H.
AU  - Asada, Y.
TI  - Isolation and identification of restriction endonuclease, SelI from a cyanobacterium, Synechococcus elongatus.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2605
EP  - 2605
VL  - 20
AB  - A restriction endonuclease, SelI has been isolated from a thermophilic and unicellular
AB  - cyanobacterium, Synechococcus elongatus. SelI, an isoschizomer of FnuDII, recognizes and
AB  - cleaves at the sequence, 5'-|CGCG-3'.
ER  -

TY  - JOUR
AU  - Miyake, T.
AU  - Hiraishi, H.
AU  - Sammoto, H.
AU  - Ono, B.-I.
TI  - Involvement of the VDE homing endonuclease and rapamycin in regulation of the Saccharomyces cerevisiae GSH11 gene encoding the high affinity  glutathione transporter.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 39632
EP  - 39636
VL  - 278
AB  - The Saccharomyces cerevisiae gene HGT1/GSH11 encodes the high affinity glutathione transporter
AB  - and is repressed by cysteine added to the culture
AB  - medium. It has been found previously that a 5'-upstream cis-element,
AB  - CCGCCACAC, is responsible for regulating GSH11 expression and that several
AB  - proteins bind to this element (Miyake, T., Kanayama, M., Sammoto, H., and
AB  - Ono, B. (2002) Mol. Genet. Genomics 266, 1004-1011). In this report we
AB  - present evidence that the most prominent of these proteins is VDE, known
AB  - previously as the homing endonuclease encoded by VMA1. We show also that
AB  - GSH11 is not expressed in a VDE-deleted strain and that inability to
AB  - express the GSH11 of this strain is overcome by introduction of the coding
AB  - region of VDE or the entire VMA1 gene. It is also found that VDE does not
AB  - cut DNA in the vicinity of the GSH11 cis-element. Rapamycin, an inhibitor
AB  - of the target of rapamycin (TOR) signal-transduction system, is found to
AB  - enhance expression of GSH11 in a VDE-dependent manner under conditions of
AB  - sulfur starvation. These results indicate that GSH11 is regulated by a
AB  - system sensitive to sulfur starvation (presumably via cysteine depletion)
AB  - and a more general system involving the nutritional starvation signal
AB  - mediated by the TOR system. Both systems need to be operational
AB  - (inhibition of TOR and sulfur starvation) for full expression of GSH11.
ER  -

TY  - JOUR
AU  - Miyamoto, H.
AU  - Nakai, W.
AU  - Yajima, N.
AU  - Fujibayashi, A.
AU  - Higuchi, T.
AU  - Sato, K.
AU  - Matsushiro, A.
TI  - Sequence analysis of Stx2-converting phage VT2-Sa shows a great divergence in early regulation and replication regions.
JO  - DNA Res.
PY  - 1999
SP  - 235
EP  - 240
VL  - 6
AB  - In enterohemorrhagic Escherichia coli, Shiga toxin is produced by lysogenic prophages. We have
AB  - isolated the prophage VT2-Sa that is responsible for production of Shiga toxin type 2 protein,
AB  - and determined the complete nucleotide sequence of this phage DNA. The entire DNA sequence
AB  - consisted of 60,942 bp, exhibiting marked similarity to the 933W phage genome. However,
AB  - several differences were observed in the immunity and replication regions, where cI, cII,
AB  - cIII, N, cro, O, and P genes were present: Predicted amino acid sequences of N, cI, cro, O and
AB  - P in the VT2-Sa genome did not show significant similarity to the counterparts of the 933W
AB  - genome; however its cI showed higher similarity to lambda. Furthermore, O and P closely
AB  - resembled those of phage HK022. These observations suggest that the various degrees of
AB  - homology observed in the immunity and replication regions of VT2-Sa could have resulted from
AB  - frequent recombination events among the lambdoid phages, and that these regions play a key
AB  - role as a functional unit for phage propagation in competition with other lambdoid phages.
ER  -

TY  - JOUR
AU  - Miyamoto, K.
AU  - Chakrabarti, G.
AU  - Morino, Y.
AU  - McClane, B.A.
TI  - Organization of the plasmid cpe locus in Clostridium perfringens type A isolates.
JO  - Infect. Immun.
PY  - 2002
SP  - 4261
EP  - 4272
VL  - 70
AB  - Clostridium perfringens type A isolates causing food poisoning have a chromosomal enterotoxin
AB  - gene (cpe), while C. perfringens type A isolates
AB  - responsible for non-food-borne human gastrointestinal diseases carry a
AB  - plasmid cpe gene. In the present study, the plasmid cpe locus of the
AB  - type A non-food-borne-disease isolate F4969 was sequenced to design
AB  - primers and probes for comparative PCR and Southern blot studies of the
AB  - cpe locus in other type A isolates. Those analyses determined that the
AB  - region upstream of the plasmid cpe gene is highly conserved among type
AB  - A isolates carrying a cpe plasmid. The organization of the type A
AB  - plasmid cpe locus was also found to be unique, as it contains IS1469
AB  - sequences located similarly to those in the chromosomal cpe locus but
AB  - lacks the IS1470 sequences found upstream of IS1469 in the chromosomal
AB  - cpe locus. Instead of those upstream IS1470 sequences, a partial open
AB  - reading frame potentially encoding cytosine methylase (dcm) was
AB  - identified upstream of IS1469 in the plasmid cpe locus of all type A
AB  - isolates tested. Similar dcm sequences were also detected in several
AB  - cpe-negative C. perfringens isolates carrying plasmids but not in type
AB  - A isolates carrying a chromosomal cpe gene. Contrary to previous
AB  - reports, sequences homologous to IS1470, rather than IS1151, were found downstream of the
AB  - plasmid cpe gene in most type A isolates
AB  - tested. Those IS1470-like sequences reside in about the same position
AB  - but are oppositely oriented and defective relative to the IS1470
AB  - sequences found downstream of the chromosomal cpe gene. Collectively,
AB  - these and previous results suggest that the cpe plasmid of many type A
AB  - isolates originated from integration of a cpe-containing genetic
AB  - element near the dcm sequences of a C. perfringens plasmid. The
AB  - similarity of the plasmid cpe locus in many type A isolates is
AB  - consistent with horizontal transfer of a common cpe plasmid among C.
AB  - perfringens type A strains.
ER  -

TY  - JOUR
AU  - Miyamoto, K.
AU  - Fisher, D.J.
AU  - Li, J.
AU  - Sayeed, S.
AU  - Akimoto, S.
AU  - McClane, B.A.
TI  - Complete Sequencing and Diversity Analysis of the Enterotoxin-Encoding Plasmids in Clostridium perfringens Type A Non-Food-Borne Human Gastrointestinal Disease Isolates.
JO  - J. Bacteriol.
PY  - 2006
SP  - 1585
EP  - 1598
VL  - 188
AB  - Enterotoxin-producing Clostridium perfringens type A isolates are an
AB  - important cause of food poisoning and non-food-borne human
AB  - gastrointestinal diseases, e.g., sporadic diarrhea (SPOR) and
AB  - antibiotic-associated diarrhea (AAD). The enterotoxin gene (cpe) is
AB  - usually chromosomal in food poisoning isolates but plasmid-borne in
AB  - AAD/SPOR isolates. Previous studies determined that type A SPOR isolate
AB  - F5603 has a plasmid (pCPF5603) carrying cpe, IS1151, and the beta2 toxin
AB  - gene (cpb2), while type A SPOR isolate F4969 has a plasmid (pCPF4969)
AB  - lacking cpb2 and IS1151 but carrying cpe and IS1470-like sequences. By
AB  - completely sequencing these two cpe plasmids, the current study identified
AB  - pCPF5603 as a 75.3-kb plasmid carrying 73 open reading frames (ORFs) and
AB  - pCPF4969 as a 70.5-kb plasmid carrying 62 ORFs. These plasmids share an
AB  - approximately 35-kb conserved region that potentially encodes virulence
AB  - factors and carries ORFs found on the conjugative transposon Tn916. The
AB  - 34.5-kb pCPF4969 variable region contains ORFs that putatively encode two
AB  - bacteriocins and a two-component regulator similar to VirR/VirS, while the
AB  - approximately 43.6-kb pCPF5603 variable region contains a functional cpb2
AB  - gene and several metabolic genes. Diversity studies indicated that other
AB  - type A plasmid cpe(+)/IS1151 SPOR/AAD isolates carry a pCPF5603-like
AB  - plasmid, while other type A plasmid cpe(+)/IS1470-like SPOR/AAD isolates
AB  - carry a pCPF4969-like plasmid. Tn916-related ORFs similar to those in
AB  - pCPF4969 (known to transfer conjugatively) were detected in the cpe
AB  - plasmids of other type A SPOR/AAD isolates, as well as in representative
AB  - C. perfringens type B to D isolates carrying other virulence plasmids,
AB  - possibly suggesting that most or all C. perfringens virulence plasmids
AB  - transfer conjugatively.
ER  -

TY  - JOUR
AU  - Miyamoto, K.
AU  - Yumine, N.
AU  - Mimura, K.
AU  - Nagahama, M.
AU  - Li, J.
AU  - McClane, B.A.
AU  - Akimoto, S.
TI  - Identification of Novel Clostridium perfringens Type E Strains That Carry an Iota Toxin Plasmid with a Functional Enterotoxin Gene.
JO  - PLoS ONE
PY  - 2011
SP  - E20376
EP  - E20376
VL  - 6
AB  - Clostridium perfringens enterotoxin (CPE) is a major virulence factor for
AB  - human gastrointestinal diseases, such as food poisoning and antibiotic
AB  - associated diarrhea. The CPE-encoding gene (cpe) can be chromosomal or
AB  - plasmid-borne. Recent development of conventional PCR cpe-genotyping
AB  - assays makes it possible to identify cpe location (chromosomal or plasmid)
AB  - in type A isolates. Initial studies for developing cpe genotyping assays
AB  - indicated that all cpe-positive strains isolated from sickened patients
AB  - were typable by cpe-genotypes, but surveys of C. perfringens environmental
AB  - strains or strains from feces of healthy people suggested that this assay
AB  - might not be useful for some cpe-carrying type A isolates. In the current
AB  - study, a pulsed-field gel electrophoresis Southern blot assay showed that
AB  - four cpe-genotype untypable isolates carried their cpe gene on a plasmid
AB  - of  approximately 65 kb. Complete sequence analysis of the  approximately
AB  - 65 kb variant cpe-carrying plasmid revealed no intact IS elements and a
AB  - disrupted cytosine methyltransferase (dcm) gene. More importantly, this
AB  - plasmid contains a conjugative transfer region, a variant cpe gene and
AB  - variant iota toxin genes. The toxin genes encoded by this plasmid are
AB  - expressed based upon the results of RT-PCR assays. The  approximately 65
AB  - kb plasmid is closely related to the pCPF4969 cpe plasmid of type A
AB  - isolates. MLST analyses indicated these isolates belong to a unique
AB  - cluster of C. perfringens. Overall, these isolates carrying a variant
AB  - functional cpe gene and iota toxin genes represent unique type E strains.
ER  -

TY  - JOUR
AU  - Miyamoto, S.
AU  - Mizutani, R.
AU  - Satow, Y.
AU  - Kawasaki, M.
AU  - Ohya, Y.
AU  - Anraku, Y.
TI  - Recognition and cleavage of double-stranded DNA by yeast VMA1-derived endonuclease.
JO  - Nucleic Acids Symp. Ser.
PY  - 1999
SP  - 197
EP  - 198
VL  - 42
AB  - DNA endonuclease derived from the yeast VMA1-gene product recognizes and cleaves 31 base-pairs
AB  - of double-stranded DNA (dsDNA). Mixtures of the endonuclease (VDE) with a full DNA substrate
AB  - consisting of 34 base-pairs, with nicked substrates each having a nick in either DNA chain,
AB  - and with cleaved substrates each having a cleaved-off chain are prepared. Molecular weights
AB  - (MWs) of eluted peaks from gel filtration columns were estimated from elution profiles in the
AB  - presence of Mg2+ ions. Each mixture exhibited an eluted peak at about 63k MW, larger than the
AB  - MW of VDE unbound to dsDNA. This indicates that VDE and dsDNA substrates form stable
AB  - complexes. The mixture of VDE either with the full substrate or with the nicked substrate
AB  - having a nick in the anti-sense chain eluted an additional 25k-MW peak, which presumably
AB  - corresponds to a cleaved product. The complex of VDE with the full substrate was eluted at
AB  - 62k-MW location in the absence of Mg2+ ions and yielded a single crystal. Stable complexes of
AB  - VDE either with the dsDNA substrates or with the cleaved products are obtainable.
ER  -

TY  - JOUR
AU  - Miyauchi, T.
AU  - Kouzuma, A.
AU  - Abe, T.
AU  - Watanabe, K.
TI  - Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01028
EP  - e01018
VL  - 7
AB  - Acidithiobacillus ferridurans is an acidophilic chemolithotrophic bacterium that  can grow in
AB  - the presence of high concentrations of ferrous iron. Here, we present
AB  - the complete 2,921,399-bp genome sequence of the strain A. ferridurans JCM
AB  - 18981(T), isolated from uranium mine drainage water.
ER  -

TY  - JOUR
AU  - Miyazaki, R.
AU  - Sato, Y.
AU  - Ito, M.
AU  - Ohtsubo, Y.
AU  - Nagata, Y.
AU  - Tsuda, M.
TI  - Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in .gamma.-hexachlorocyclohexane degradation.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 6923
EP  - 6933
VL  - 72
AB  - The alpha-proteobacterial strain Sphingobium japonicum UT26 utilizes a highly chlorinated
AB  - pesticide, gamma-hexachlorocyclohexane (gamma-HCH), as a sole source of carbon and energy, and
AB  - haloalkane dehalogenase LinB catalyzes the second step of gamma-HCH degradation in UT26.
AB  - Functional complementation of a linB mutant of UT26, UT26DB, was performed by the exogenous
AB  - plasmid isolation technique using HCH-contaminated soil, leading to our successful
AB  - identification of a plasmid, pLB1, carrying the linB gene. Complete sequencing analysis of
AB  - pLB1, with a size of 65,998 bp, revealed that it carries (i) 50 totally annotated coding
AB  - sequences, (ii) an IS6100 composite transposon containing two copies of linB, and (iii)
AB  - potential genes for replication, maintenance, and conjugative transfer with low levels of
AB  - similarity to other homologues. A minireplicon assay demonstrated that a 2-kb region
AB  - containing the predicted repA gene and its upstream region of pLB1 functions as an
AB  - autonomously replicating unit in UT26. Furthermore, pLB1 was conjugally transferred from
AB  - UT26DB to other alpha-proteobacterial strains but not to any of the beta- or
AB  - gamma-proteobacterial strains examined to date. These results suggest that this exogenously
AB  - isolated novel plasmid contributes to the dissemination of at least some genes for gamma-HCH
AB  - degradation in the natural environment. To the best of our knowledge, this is the first
AB  - detailed report of a plasmid involved in gamma-HCH degradation.
ER  -

TY  - JOUR
AU  - Miyazono, K.
AU  - Furuta, Y.
AU  - Watanabe-Matsui, M.
AU  - Miyakawa, T.
AU  - Ito, T.
AU  - Kobayashi, I.
AU  - Tanokura, M.
TI  - A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.
JO  - Nat. Commun.
PY  - 2014
SP  - 3178
EP  - 3178
VL  - 5
AB  - Restriction-modification systems consist of genes that encode a restriction enzyme and a
AB  - cognate methyltransferase. Thus far, it was believed that restriction enzymes are
AB  - sequence-specific endonucleases that introduce double-strand breaks at specific sites by
AB  - catalysing the cleavages of phosphodiester bonds. Here we report that based on the crystal
AB  - structure and enzymatic activity, one of the restriction enzymes, R.PabI, is not an
AB  - endonuclease but a sequence-specific adenine DNA glycosylase. The structure of the R.PabI-DNA
AB  - complex shows that R.PabI unwinds DNA at a 5'-GTAC-3' site and flips the guanine and adenine
AB  - bases out of the DNA helix to recognize the sequence. R.PabI catalyses the hydrolysis of the
AB  - N-glycosidic bond between the adenine base and the sugar in the DNA and produces two opposing
AB  - apurinic/apyrimidinic (AP) sites. The opposing AP sites are cleaved by heat-promoted beta
AB  - elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand
AB  - break.
ER  -

TY  - JOUR
AU  - Miyazono, K.
AU  - Watanabe, M.
AU  - Kosinski, J.
AU  - Ishikawa, K.
AU  - Kamo, M.
AU  - Sawasaki, T.
AU  - Nagata, K.
AU  - Bujnicki, J.M.
AU  - Endo, Y.
AU  - Tanokura, M.
AU  - Kobayashi, I.
TI  - Novel protein fold discovered in the PabI family of restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 1908
EP  - 1918
VL  - 35
AB  - Although structures of many DNA-binding proteins have been solved, they fall into a limited
AB  - number of folds. Here, we describe an approach that
AB  - led to the finding of a novel DNA-binding fold. Based on the behavior of
AB  - Type II restriction-modification gene complexes as mobile elements, our
AB  - earlier work identified a restriction enzyme, R.PabI, and its cognate
AB  - modification enzyme in Pyrococcus abyssi through comparison of closely
AB  - related genomes. While the modification methyltransferase was easily
AB  - recognized, R.PabI was predicted to have a novel 3D structure. We
AB  - expressed cytotoxic R.PabI in a wheat-germ-based cell-free translation
AB  - system and determined its crystal structure. R.PabI turned out to adopt a
AB  - novel protein fold. Homodimeric R.PabI has a curved anti-parallel
AB  - beta-sheet that forms a 'half pipe'. Mutational and in silico DNA-binding
AB  - analyses have assigned it as the double-strand DNA-binding site. Unlike
AB  - most restriction enzymes analyzed, R.PabI is able to cleave DNA in the
AB  - absence of Mg(2+). These results demonstrate the value of genome
AB  - comparison and the wheat-germ-based system in finding a novel DNA-binding
AB  - motif in mobile DNases and, in general, a novel protein fold in
AB  - horizontally transferred genes.
ER  -

TY  - JOUR
AU  - Miyoshi-Akiyama, T.
AU  - Kuwahara, T.
AU  - Tada, T.
AU  - Kitao, T.
AU  - Kirikae, T.
TI  - Complete Genome Sequence of Highly Multidrug-Resistant Pseudomonas aeruginosa NCGM2.S1, a Representative Strain of a Cluster Endemic to  Japan.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7010
EP  - 7010
VL  - 193
AB  - We report the completely annotated genome sequence of Pseudomonas aeruginosa NCGM2.S1, a
AB  - representative strain of a cluster endemic to Japan
AB  - with a high level of resistance to carbapenem (MIC >/= 128 mug/ml),
AB  - amikacin (MIC >/= 128 mug/ml), and fluoroquinolone (MIC >/= 128 mug/ml).
ER  -

TY  - JOUR
AU  - Miyoshi-Akiyama, T.
AU  - Matsumura, K.
AU  - Iwai, H.
AU  - Funatogawa, K.
AU  - Kirikae, T.
TI  - Complete Annotated Genome Sequence of Mycobacterium tuberculosis Erdman.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2770
EP  - 2770
VL  - 194
AB  - We report the completely annotated genome sequence of Mycobacterium tuberculosis  Erdman (TMC
AB  - 107; ATCC 35801), which is a well-known laboratory strain of M.
AB  - tuberculosis.
ER  -

TY  - JOUR
AU  - Miyoshi-Akiyama, T.
AU  - Matsumura, K.
AU  - Kobayashi, N.
AU  - Maeda, S.
AU  - Kirikae, T.
TI  - Genome Sequence of Clinical Isolate Mycobacterium tuberculosis NCGM2209.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6792
EP  - 6792
VL  - 193
AB  - We report the annotated genome sequence of a clinical isolate, Mycobacterium tuberculosis
AB  - strain NCGM2209, which belongs to the 'Beijing
AB  - family' and was isolated in Japan.
ER  -

TY  - JOUR
AU  - Miyoshi-Akiyama, T.
AU  - Satou, K.
AU  - Kato, M.
AU  - Shiroma, A.
AU  - Matsumura, K.
AU  - Tamotsu, H.
AU  - Iwai, H.
AU  - Teruya, K.
AU  - Funatogawa, K.
AU  - Hirano, T.
AU  - Kirikae, T.
TI  - Complete annotated genome sequence of Mycobacterium tuberculosis (Zopf) Lehmann and Neumann (ATCC35812) (Kurono).
JO  - Tuberculosis
PY  - 2014
SP  - 37
EP  - 39
VL  - 95
AB  - We report the completely annotated genome sequence of Mycobacterium tuberculosis
AB  - (Zopf) Lehmann and Neumann (ATCC35812) (Kurono), which is a used for virulence
AB  - and/or immunization studies. The complete genome sequence of M. tuberculosis
AB  - Kurono was determined with a length of 4,415,078 bp and a G+C content of 65.60%.
AB  - The chromosome was shown to contain a total of 4,340 protein-coding genes, 53
AB  - tRNA genes, one transfer messenger RNA for all amino acids, and 1 rrn operon.
AB  - Lineage analysis based on large sequence polymorphisms indicated that M.
AB  - tuberculosis Kurono belongs to the Euro-American lineage (lineage 4).
AB  - Phylogenetic analysis using whole genome sequences of M. tuberculosis Kurono in
AB  - addition to 22 M. tuberculosis complex strains indicated that H37Rv is the
AB  - closest relative of Kurono based on the results of phylogenetic analysis. These
AB  - findings provide a basis for research using M. tuberculosis Kurono, especially in
AB  - animal models.
ER  -

TY  - JOUR
AU  - Miyoshi-Akiyama, T.
AU  - Takeshita, N.
AU  - Ohmagari, N.
AU  - Kirikae, T.
TI  - Complete Genome Sequence of Helicobacter cinaedi Type Strain ATCC BAA-847.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5692
EP  - 5692
VL  - 194
AB  - Here we report the completely annotated genome sequence of the Helicobacter cinaedi type
AB  - strain (ATCC BAA-847), which is an emerging pathogen that causes
AB  - cellulitis and bacteremia. The genome sequence will provide new insights into the
AB  - diagnosis, pathogenic mechanisms, and drug resistance of H. cinaedi.
ER  -

TY  - JOUR
AU  - Miyoshi-Akiyama, T.
AU  - Watanabe, S.
AU  - Kirikae, T.
TI  - Complete Genome Sequence of Streptococcus pyogenes M1 476, Isolated from a Patient with Streptococcal Toxic Shock Syndrome.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5466
EP  - 5466
VL  - 194
AB  - Here, we report the completely annotated genome sequence of Streptococcus pyogenes M1 476
AB  - isolated from a patient with streptococcal toxic shock syndrome
AB  - (STSS) during pregnancy. The genome sequence will provide new insights into the
AB  - mechanisms underlying STSS.
ER  -

TY  - JOUR
AU  - Mizumura, H.
AU  - Shibata, T.
AU  - Morishima, N.
TI  - Association of HSP70 with endonucleases allows the expression of otherwise silent mutations.
JO  - FEBS Lett.
PY  - 2002
SP  - 177
EP  - 182
VL  - 522
AB  - A subpopulation of the 70 kDa heat shock protein (HSP70) found within the mitochondria of
AB  - Saccharomyces cerevisiae functions as a stable
AB  - binding partner of the endonuclease SceI. We have previously found that
AB  - the SceI endonuclease monomer recognizes and cleaves a unique, 26 bp
AB  - sequence in vitro. Dimerization with HSP70 changes the specificity of
AB  - SceI, allowing it to cleave at multiple sequences. This study shows
AB  - that SuvI, an ortholog of SceI isolated from a different yeast strain,
AB  - contains two amino acid substitutions, yet it shows the same uni-site
AB  - specificity in its monomeric form. Binding of HSP70 to the SuvI monomer
AB  - confers multi-site specificity that is different from that exhibited by
AB  - the HSP70/SceI heterodimer. Mutation of single residues of SceI to the
AB  - corresponding residue in SuvI provides enzymes with specificities
AB  - intermediate between SceI and SuvI when complexed with HSP70. These
AB  - results suggest that HSP70 interaction with certain endonucleases
AB  - allows the expression of otherwise silent mutations in them, causing a
AB  - change in enzyme cleavage specificity.
ER  -

TY  - JOUR
AU  - Mizumura, H.
AU  - Shibata, T.
AU  - Morishima, N.
TI  - Stable association of 70-kDa heat shock protein induces latent multisite specificity of a unisite-specific endonuclease in yeast mitochondria.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 25682
EP  - 25690
VL  - 274
AB  - The multisite-specific endonuclease Endo.SceI of yeast mitochondria is unique among
AB  - endonucleases because its 50-kDa subunit forms a stable dimer with the mitochondrial 70-kDa
AB  - heat shock protein (mtHSP70), which otherwise fulfills a chaperone function by binding
AB  - transiently to unfolded proteins. Here we show that the mtHSP70 subunit confers broader
AB  - sequence specificity, greater stability, and higher activity on the 50-kDa subunit. The 50-kDa
AB  - subunit alone displayed weaker activity and highly sequence-specific endonuclease activity.
AB  - The 50-kDa protein exists as a heterodimer with mtHSP70 in vivo, allowing Endo.SceI to cleave
AB  - specifically at multiple sites on mitochondrial DNA. Endo.SceI may have evolved from a highly
AB  - specific endonuclease that gained broader sequence specificity after becoming a stable partner
AB  - of mtHSP70.
ER  -

TY  - JOUR
AU  - Mizuno, C.M.
AU  - Rodriguez-Valera, F.
AU  - Garcia-Heredia, I.
AU  - Martin-Cuadrado, A.B.
AU  - Ghai, R.
TI  - Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 688
EP  - 695
VL  - 79
AB  - Cellular metagenomes are primarily used for investigating microbial community
AB  - structure and function. However, cloned fosmids from such metagenomes capture
AB  - phage genome fragments that can be used as a source of phage genomes. We show
AB  - that fosmid cloning from cellular metagenomes and sequencing at a high coverage
AB  - is a credible alternative to constructing metaviriomes and allows capturing and
AB  - assembling novel, complete phage genomes. It is likely that phages recovered from
AB  - cellular metagenomes are those replicating within cells during sample collection
AB  - and represent "active" phages, naturally amplifying their genomic DNA and
AB  - increasing chances for cloning. We describe five sets of siphoviral contigs
AB  - (MEDS1, MEDS2, MEDS3, MEDS4 and MEDS5), obtained by sequencing fosmids from the
AB  - cellular metagenome of the deep chlorophyll maximum in the Mediterranean. Three
AB  - of these represent complete siphoviral genomes and two partial ones. These are
AB  - the first set of phage genomes assembled directly from cellular metagenomic
AB  - fosmid libraries. They exhibit low sequence similarities to one another and to
AB  - known siphoviruses, but are remarkably similar in overall genome architecture. We
AB  - present evidence suggesting they infect picocyanobacteria, likely Synechococcus.
AB  - Four of these sets also define a novel branch in the phylogenetic tree of phage
AB  - large subunit terminases. Moreover, some of these siphoviral groups are globally
AB  - distributed and abundant in the oceans, comparable to some known myoviruses and
AB  - podoviruses. This suggests that as more siphoviral genomes become available, we
AB  - will be better able to assess the abundance and influence of this diverse and
AB  - polyphyletic group in the marine habitat.
ER  -

TY  - JOUR
AU  - Mizuno, C.M.
AU  - Rodriguez-Valera, F.
AU  - Kimes, N.E.
AU  - Ghai, R.
TI  - Expanding the marine virosphere using metagenomics.
JO  - PLoS Genet.
PY  - 2013
SP  - e1003987
EP  - e1003987
VL  - 9
AB  - Viruses infecting prokaryotic cells (phages) are the most abundant entities of the biosphere
AB  - and contain a largely uncharted
AB  - wealth of genomic diversity. They play a critical role in the biology of their hosts and in
AB  - ecosystem functioning at large. The
AB  - classical approaches studying phages require isolation from a pure culture of the host. Direct
AB  - sequencing approaches have
AB  - been hampered by the small amounts of phage DNA present in most natural habitats and the
AB  - difficulty in applying metaomic
AB  - approaches, such as annotation of small reads and assembly. Serendipitously, it has been
AB  - discovered that cellular
AB  - metagenomes of highly productive ocean waters (the deep chlorophyll maximum) contain
AB  - significant amounts of viral DNA
AB  - derived from cells undergoing the lytic cycle. We have taken advantage of this phenomenon to
AB  - retrieve metagenomic
AB  - fosmids containing viral DNA from a Mediterranean deep chlorophyll maximum sample. This method
AB  - allowed description of
AB  - complete genomes of 208 new marine phages. The diversity of these genomes was remarkable,
AB  - contributing 21 genomic
AB  - groups of tailed bacteriophages of which 10 are completely new. Sequence based methods have
AB  - allowed host assignment
AB  - to many of them. These predicted hosts represent a wide variety of important marine
AB  - prokaryotic microbes like members of
AB  - SAR11 and SAR116 clades, Cyanobacteria and also the newly described low GC Actinobacteria. A
AB  - metavirome constructed
AB  - from the same habitat showed that many of the new phage genomes were abundantly represented.
AB  - Furthermore, other
AB  - available metaviromes also indicated that some of the new phages are globally distributed in
AB  - low to medium latitude ocean
AB  - waters. The availability of many genomes from the same sample allows a direct approach to
AB  - viral population genomics
AB  - confirming the remarkable mosaicism of phage genomes.
ER  -

TY  - JOUR
AU  - Mizuno, H.
AU  - Suzuki, T.
AU  - Akagawa, M.
AU  - Yamasato, K.
AU  - Yamada, Y.
TI  - Purification, properties and determination of recognition sequence and cleavage site of restriction endonuclease from Agrobacterium gelatinovorum IAM 12617, a marine bacterium (AgeI).
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 1797
EP  - 1802
VL  - 54
AB  - A new restriction endonuclease, designated as AgeI, was purified from cell-free
AB  - extracts of a marine bacterium, Agrobacterium gelatinovorum IAM 12617 by
AB  - streptomycin treatment, ammonium sulfate fractionation, combined column
AB  - chromatographies on heparin-Sepharose CL-6B and DEAE-Sepharose CL-6B and FPLC
AB  - on Mono Q (HR 5/5) and Superose 12 (HR 10/30).  The purified enzyme was
AB  - homogenous on SDS-polyacrylamide gel disc electrophoresis and free from other
AB  - phosphatase and exonuclease activities on ligation-recutting test.  The
AB  - relative molecular mass of the enzyme was 24,000 daltons by SDS-polyacrylamide
AB  - gel disc electrophoresis.  The gel filtration using Superose 12 (HR 10/30) gave
AB  - the same calculation (23,000 daltons).  These data indicated that the enzyme is
AB  - a monomer.  The isoelectric point of the enzyme was 6.5.  The purified enzyme
AB  - cleaved lambda and Ad2 DNAs at 10 or more and 5 sites, respectively.  However,
AB  - the purified enzyme did not cleave SV40, PhiX174 RF I, M13mp18 RF I or pBR322
AB  - DNAs.  pBR328 DNA was cleaved at 1 site by the purified enzyme.  The purified
AB  - enzyme worked best at 37C and pH 7.5 in a reaction mixture (50 microliters)
AB  - containing 1.0 micrograms lambda DNA, 10 mM Tris-HCl, 7 mM 2-mercaptoethanol, 7
AB  - mM MgCl2 and 50 mM NaCl.  The purified enzyme did not require monovalent
AB  - cations necessarily for the enzyme reaction.  The enzyme recognized the
AB  - palindromic hexanucleotide DNA sequence 5'-ACCGGT-3' and cut between A and C,
AB  - producing a 5'-cohesive tetranucleotide extension.
ER  -

TY  - JOUR
AU  - Mizuno, H.
AU  - Suzuki, T.
AU  - Yamada, Y.
AU  - Akagawa, M.
AU  - Yamasato, K.
TI  - Purification and properties of restriction endonuclease from Deleya marina IAM 14114, a marine bacterium (DmaI).
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 2863
EP  - 2867
VL  - 54
AB  - A restriction endonuclease, designated as DmaI, was purified from cell-free
AB  - extracts of Deleya marina IAM 14114 by streptomycin treatment, ammonium sulfate
AB  - fractionation and two steps of chromatographicy on Heparin-Sepharose CL-6B and
AB  - Mono Q (HR 5/5, FPLC).  The purified enzyme was homogeneous on
AB  - SDS-polyacrylamide gel disk electrophoresis and a ligation-recutting test.  The
AB  - relative molecular mass measurements of the purified enzyme gave 28,000 daltons
AB  - by SDS-polyacrylamide gel disk electrophoresis and 56,000 daltons by gel
AB  - filtration.  These data indicated that the purified enzyme (56,000 daltons) has
AB  - a dimeric structure composed of two 28,000-dalton subunits.  The isoelectric
AB  - point was 5.5.  The purified enzyme worked best at 37C in a reaction mixture
AB  - (50 microliters) containing 1.0 microgram lambda DNA, 10 mM Tris-HCI, 7 mM
AB  - 2-mercaptoethanol, 7 mM MgCl2 and 100 mM NaCl (pH 7.5).  The enzyme was stable
AB  - up to 55C and between pH 7.0 and 9.0.  The purified enzyme recognizes the
AB  - palindromic hexanucleotide DNA sequence 5'-CAGCTG-3', cuts between G and C and
AB  - produces a flush end (isoschizomer of PvuII).
ER  -

TY  - JOUR
AU  - Mizutani, R.
AU  - Anraku, Y.
AU  - Satow, Y.
TI  - Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.
JO  - J. Synchrotron Radiat.
PY  - 2004
SP  - 109
EP  - 112
VL  - 11
AB  - Protein splicing precisely excises out an internal intein segment from a protein precursor,
AB  - and concomitantly ligates the N- and C-terminal extein polypeptides flanking the intein.  A
AB  - recombinant X10SNS bearing N- and C-extein polypeptides has been prepared for the intein
AB  - endonuclease derived from the Saccharomyces cerevisiae VMA1 gene.  X10SNS has replacements of
AB  - C284S, H362N, and C738S, and forms the intein and extein segments in the crystal lattice.  The
AB  - crystal structure of X10SNS revealed a linkage between the N- and C-extein segments, and
AB  - showed that the C284 amino group of the resultant intein segment is in interaction with the
AB  - G283 O atom of the N-extein segment.  A mechanism for the final S-N acyl shift step proposes
AB  - that a tetrahedral intermediate involves a five-membered thiazolidine ring at G283-C738
AB  - junction.  An oxyanion of the thiazolidine intermediate is to be stabilized by the C284 N
AB  - atom.
ER  -

TY  - JOUR
AU  - Mizutani, R.
AU  - Nogami, S.
AU  - Kawasaki, M.
AU  - Ohya, Y.
AU  - Anraku, Y.
AU  - Satow, Y.
TI  - Protein-splicing reaction via a thiazolidine intermediate: Crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal  propeptides.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 919
EP  - 929
VL  - 316
AB  - Protein splicing excises an internal intein segment from a protein precursor precisely, and
AB  - concomitantly ligates flanking N and C-extein
AB  - polypeptides at the respective sides of the precursor. Here, a series
AB  - of precursor recombinants bearing 11 N-extein and ten C-extein residues
AB  - is prepared for the intein of the Saccharomyces cerevisiae VMAI-derived
AB  - homing endonuclease referred to as VIDE and as PI-SceI. The recombinant
AB  - with replacements of C284S, H362N, N737S, and C738S is chosen as a
AB  - splice-able precursor model and is then subjected to a 2.1 Angstrom
AB  - resolution crystallographic analysis. The crystal structure shows that
AB  - the introduced extein polypeptides are located in the vicinity of the
AB  - splicing site, and that each of their peptide bonds is in the trans
AB  - conformation. The S284 O-gamma atom located at a distance of 3.1
AB  - Angstrom from the G283 C atom in the N-terminal junction suggests that
AB  - a nucleophilic attack of the C284 S-gamma atom on the G283 C atom forms
AB  - a tetrahedral intermediate containing a five-membered thiazolidine
AB  - ring. The tetrahedral intermediate is supposedly resolved into a
AB  - thioester acyl group upon the cleavage of the linkage between the G283
AB  - C and C284 N atoms, and this thioester acyl formation completes the
AB  - initial steps of N --> S acyl shift at the junction between the
AB  - N-extein and intein. The S738 O-gamma atom in the C-terminal junction
AB  - is placed in close proximity to the S284 O-gamma atom at a distance of
AB  - 3.6 Angstrom, and is well suited for another nucleophilic attack on the
AB  - resultant thioester acyl group that is then subjected to the
AB  - transesterification in the next step. The reaction steps proposed for
AB  - the acyl shift are driven entirely by protonation and deprotonation, in
AB  - which proton ingress and egress is balanced within the splicing site.
ER  -

TY  - JOUR
AU  - Mizutani, Y.
AU  - Tanaka, R.
TI  - Genome Sequence of Arcobacter sp. Strain LA11, Isolated from the Abalone Haliotis discus.
JO  - Genome Announcements
PY  - 2017
SP  - e00032
EP  - e00017
VL  - 5
AB  - Arcobacter sp. strain LA11 was isolated from the gut of the abalone Haliotis discus Here, we
AB  - present the annotation and analysis of the draft genome of this
AB  - strain, which is involved in nitrogen metabolism.
ER  -

TY  - JOUR
AU  - Mizuuchi, K.
AU  - Nobbs, T.J.
AU  - Halford, S.E.
AU  - Adzuma, K.
AU  - Qin, J.
TI  - A new method for determining the Stereochemistry of DNA cleavage reactions: Application to the SfiI and HpaII restriction endonucleases and to the MuA transposase.
JO  - Biochemistry
PY  - 1999
SP  - 4640
EP  - 4648
VL  - 38
AB  - A new method was developed for tracking the stereochemical path of enzymatic cleavage of DNA.
AB  - DNA with a phosphorothioate of known chirality at the scissile bond is cleaved by the enzyme
AB  - in H218O. The cleavage produces a DNA molecule with the 5'-[16O,18O, S]-thiophosphoryl group,
AB  - whose chirality depends on whether the cleavage reaction proceeds by a single-step hydrolysis
AB  - mechanism or by a two-step mechanism involving a protein-DNA covalent intermediate. To
AB  - determine this chirality, the cleaved DNA is joined to an oligonucleotide by DNA ligase. Given
AB  - the strict stereochemistry of the DNA ligase reaction, determined here, the original chirality
AB  - of the phosphorothioate dictates whether the 18O is retained or lost in the ligation product,
AB  - which can be determined by mass spectrometry. This method has advantages over previous methods
AB  - in that it is not restricted to particular DNA sequences, requires substantially less
AB  - material, and avoids purification of the products at intermediate stages in the procedure. The
AB  - method was validated by confirming that DNA cleavage by the EcoRI restriction endonuclease
AB  - causes inversion of configuration at the scissile phosphate. It was then applied to the
AB  - reactions of the SfiI and HpaII endonucleases and the MuA transposase. In all three cases, DNA
AB  - cleavage proceeded with inversion of configuration, indicating direct hydrolysis of the
AB  - phosphodiester bond by water as opposed to a reaction involving a covalent enzyme-DNA
AB  - intermediate.
ER  -

TY  - JOUR
AU  - Mo, D.
AU  - Wu, L.
AU  - Xu, Y.
AU  - Ren, J.
AU  - Wang, L.
AU  - Huang, L.
AU  - Wu, Q.-J.
AU  - Bao, P.
AU  - Xie, M.-H.
AU  - Yin, P.
AU  - Liu, B.-F.
AU  - Liang, Y.
AU  - Zhang, Y.
TI  - A maturase that specifically stabilizes and activates its cognate group  I intron at high temperatures.
JO  - Biochimie
PY  - 2011
SP  - 533
EP  - 541
VL  - 93
AB  - Folding of large structured RNAs into their functional tertiary structures at high
AB  - temperatures is challenging. Here we show that
AB  - I-Tnal protein, a small LAGLIDADG homing endonuclease encoded by a
AB  - group I intron from a hyperthermophilic bacterium, acts as a maturase
AB  - that is essential for the catalytic activity of this intron at high
AB  - temperatures and physiological cationic conditions. I-Tnal specifically
AB  - binds to and induces tertiary packing of the P4-P6 domain of the
AB  - intron: this RNA protein complex might serve as a thermostable platform
AB  - for active folding of the entire intron. Interestingly, the binding
AB  - affinity of I-Tnal to its cognate intron RNA largely increases with
AB  - temperature; over 30-fold stronger binding at higher temperatures
AB  - relative to 37 degrees C correlates with a switch from an
AB  - entropy-driven (37 degrees C) to an enthalpydriven (55-60 degrees C)
AB  - interaction mode. This binding mode may represent a novel strategy how
AB  - an RNA binding protein can promote the function of its target RNA
AB  - specifically at high temperatures.
ER  -

TY  - JOUR
AU  - Mo, S.
AU  - Kim, B.S.
AU  - Yun, S.J.
AU  - Lee, J.J.
AU  - Yoon, S.H.
AU  - Oh, C.H.
TI  - Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces.
JO  - Gut Pathog.
PY  - 2015
SP  - 8
EP  - 8
VL  - 7
AB  - BACKGROUND: Clostridium butyricum is a butyric acid-producing anaerobic
AB  - bacteriuma, and commonly present as gut microbiota in humans. This species has
AB  - been used as a probiotic for the prevention of diarrhea in humans. In this study,
AB  - we report the draft genome of C. butyricum DKU-01, which was isolated from infant
AB  - feces, to better understand the characteristics of this strain so that it can
AB  - later be used in the development of probiotic products. RESULTS: A total of 79
AB  - contigs generated by hybrid assembly of sequences obtained from Roche 454 and
AB  - Illumina Miseq sequencing systems were investigated. The assembled genome of
AB  - strain DKU-01 consisted of 4,519,722 bp (28.62% G + C content) with a N50 contig
AB  - length of 108,221 bp and 4,037 predicted CDSs. The extracted 16S rRNA gene from
AB  - genome sequences of DKU-01 was similar to Clostridium butyricum with 99.63%
AB  - pairwise similarity. The sequence of strain DKU-01 was compared with previously
AB  - reported genome sequences of C. butyricum. The value of average nucleotide
AB  - identity between strains DKU-01 and C. butyricum 60E3 was 98.74%, making it the
AB  - most similar strain to DKU-01. CONCLUSIONS: We sequenced the DKU-01 strain
AB  - isolated from infant feces, and compared it with the available genomes of C.
AB  - butyricum on a public database. Genes related to Fructooligosaccharide
AB  - utilization were detected in the genome of strain DKU-01 and compared with other
AB  - genera, such as Bifidobacterium and Streptococcus. We found that strain DKU-01
AB  - can metabolize a wide range of carbohydrates in comparative genome result.
AB  - Further analyses of the comparative genome and fermentation study can provide the
AB  - information necessary for the development of strain DKU-01 for probiotics.
ER  -

TY  - JOUR
AU  - Mo, X.
AU  - Pei, J.
AU  - Guo, Y.
AU  - Lin, L.
AU  - Peng, L.
AU  - Kou, C.
AU  - Fan, D.
AU  - Pang, H.
TI  - Genome Sequence of Clostridium acetobutylicum GXAS18-1, a Novel Biobutanol Production Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00033
EP  - e00015
VL  - 3
AB  - Clostridium acetobutylicum is an organism involved in the production of acetone and butanol by
AB  - traditional acetone-butanol-ethanol fermentation (ABE). We report
AB  - the draft genome sequence of C. acetobutylicum strain GXAS18-1, which can produce
AB  - ABE directly from cassava flour.
ER  -

TY  - JOUR
AU  - Mobberley, J.M.
AU  - Authement, R.N.
AU  - Segall, A.M.
AU  - Paul, J.H.
TI  - The temperate marine phage PhiHAP-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome.
JO  - J. Virol.
PY  - 2008
SP  - 6618
EP  - 6630
VL  - 82
AB  - A myovirus-like temperate phage, PhiHAP-1, was induced with mitomycin C
AB  - from a Halomonas aquamarina strain isolated from surface waters in the
AB  - Gulf of Mexico. The induced cultures produced significantly more
AB  - virus-like particles (VLPs) (3.73 x 10(10) VLP ml(-1)) than control
AB  - cultures (3.83 x 10(7) VLP ml(-1)) when observed with epifluorescence
AB  - microscopy. The induced phage was sequenced by using linker-amplified
AB  - shotgun libraries and contained a genome 39,245 nucleotides in length with
AB  - a G+C content of 59%. The PhiHAP-1 genome contained 46 putative open
AB  - reading frames (ORFs), with 76% sharing significant similarity (E value of
AB  - <10(-3)) at the protein level with other sequences in GenBank. Putative
AB  - functional gene assignments included small and large terminase subunits,
AB  - capsid and tail genes, an N6-DNA adenine methyltransferase, and
AB  - lysogeny-related genes. Although no integrase was found, the PhiHAP-1
AB  - genome contained ORFs similar to protelomerase and parA genes found in
AB  - linear plasmid-like phages with telomeric ends. Southern probing and PCR
AB  - analysis of host genomic, plasmid, and PhiHAP-1 DNA indicated a lack of
AB  - integration of the prophage with the host chromosome and a difference in
AB  - genome arrangement between the prophage and virion forms. The linear
AB  - plasmid prophage form of PhiHAP-1 begins with the protelomerase gene,
AB  - presumably due to the activity of the protelomerase, while the induced
AB  - phage particle has a circularly permuted genome that begins with the
AB  - terminase genes. The PhiHAP-1 genome shares synteny and gene similarity
AB  - with coliphage N15 and vibriophages VP882 and VHML, suggesting an
AB  - evolutionary heritage from an N15-like linear plasmid prophage ancestor.
ER  -

TY  - JOUR
AU  - Mobberley, J.M.
AU  - Romine, M.F.
AU  - Cole, J.K.
AU  - Maezato, Y.
AU  - Lindemann, S.R.
AU  - Nelson, W.C.
TI  - Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake.
JO  - Genome Announcements
PY  - 2018
SP  - e01583
EP  - e01517
VL  - 6
AB  - The complete genome sequence of Cyanobacterium sp. strain HL-69 consists of 3,155,247 bp and
AB  - contains 2,897 predicted genes comprising a chromosome and two
AB  - plasmids. The genome is consistent with a halophilic nondiazotrophic phototrophic
AB  - lifestyle, and this organism is able to synthesize most B vitamins and produces
AB  - several secondary metabolites.
ER  -

TY  - JOUR
AU  - Mobius, P.
AU  - Holzer, M.
AU  - Felder, M.
AU  - Nordsiek, G.
AU  - Groth, M.
AU  - Kohler, H.
AU  - Reichwald, K.
AU  - Platzer, M.
AU  - Marz, M.
TI  - Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany.
JO  - Genome Biol. Evol.
PY  - 2015
SP  - 2585
EP  - 2601
VL  - 7
AB  - Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) - the etiologic agent of Johne's
AB  - disease - affects cattle, sheep and other ruminants worldwide. To decipher phenotypic
AB  - differences among sheep and cattle strains (belonging to MAP-S [Type-I/III] respectively MAP-C
AB  - [Type-II]) comparative genome analysis needs data from diverse isolates originating from
AB  - different geographic regions of the world. The current study presents the so far best
AB  - assembled genome of a MAP-S-strain: sheep isolate JIII-386 from Germany. One newly sequenced
AB  - cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from U.S.
AB  - and Australia and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement
AB  - and comparisons. All genomes were annotated by BacProt and results compared with NCBI
AB  - annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that
AB  - were exclusively determined either by NCBI or BacProt. A new Shine-Dalgarno sequence motif
AB  - (5'AGCTGG3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80
AB  - non-coding RNAs exhibiting high sequence conservation are presented. Previously found genetic
AB  - differences between MAP-types are partially revised. Four out of ten assumed MAP-S-specific
AB  - large sequence polymorphism regions (LSPSs) are still present in MAP-C strains; new LSPSs were
AB  - identified. Independently of the regional origin of the strains, the number of individual CDSs
AB  - and single nucleotide variants confirm the strong similarity of MAP-C strains and show higher
AB  - diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis
AB  - that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a
AB  - higher similarity of MAP to MAH than to M. intracellulare.
ER  -

TY  - JOUR
AU  - Mobius, P.
AU  - Nordsiek, G.
AU  - Holzer, M.
AU  - Jarek, M.
AU  - Marz, M.
AU  - Kohler, H.
TI  - Complete Genome Sequence of JII-1961, a Bovine Mycobacterium avium subsp. paratuberculosis Field Isolate from Germany.
JO  - Genome Announcements
PY  - 2017
SP  - e00870
EP  - e00817
VL  - 5
AB  - Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants and was also
AB  - detected in nonruminant species, including human beings, and in milk
AB  - products. We announce here the 4.829-Mb complete genome sequence of the
AB  - cattle-type strain JII-1961 from Germany, which is very similar to cattle-type
AB  - strains recovered from different continents.
ER  -

TY  - JOUR
AU  - Mochizuki, A.
AU  - Yahara, K.
AU  - Kobayashi, I.
AU  - Iwasa, Y.
TI  - Genetic addiction: selfish gene's strategy for symbiosis in the genome.
JO  - Genetics
PY  - 2006
SP  - 1309
EP  - 1323
VL  - 172
AB  - The evolution and maintenance of the phenomenon of postsegregational host killing or genetic
AB  - addiction are paradoxical. In this phenomenon, a gene complex, once
AB  - established in a genome, programs death of a host cell that has eliminated it.
AB  - The intact form of the gene complex would survive in other members of the host
AB  - population. It is controversial as to why these genetic elements are maintained,
AB  - due to the lethal effects of host killing, or perhaps some other properties are
AB  - beneficial to the host. We analyzed their population dynamics by analytical
AB  - methods and computer simulations. Genetic addiction turned out to be advantageous
AB  - to the gene complex in the presence of a competitor genetic element. The
AB  - advantage is, however, limited in a population without spatial structure, such as
AB  - that in a well-mixed liquid culture. In contrast, in a structured habitat, such
AB  - as the surface of a solid medium, the addiction gene complex can increase in
AB  - frequency, irrespective of its initial density. Our demonstration that genomes
AB  - can evolve through acquisition of addiction genes has implications for the
AB  - general question of how a genome can evolve as a community of potentially selfish
AB  - genes.
ER  -

TY  - JOUR
AU  - Modise, T.
AU  - Ryder, C.
AU  - Mane, S.P.
AU  - Bandara, A.B.
AU  - Jensen, R.V.
AU  - Inzana, T.J.
TI  - Genomic Comparison between a Virulent Type A1 Strain of Francisella tularensis and Its Attenuated O-Antigen Mutant.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2775
EP  - 2776
VL  - 194
AB  - We report the complete genome sequences of TI0902, a highly virulent type A1 strain, and
AB  - TIGB03, a related, attenuated chemical mutant strain. Compared to the
AB  - wild type, the mutant strain had 45 point mutations and a 75.9-kb duplicated
AB  - region that had not been previously observed in Francisella species.
ER  -

TY  - JOUR
AU  - Modrich, P.
TI  - Studies on sequence recognition by type II restriction and modification enzymes.
JO  - CRC Crit. Rev. Biochem.
PY  - 1982
SP  - 287
EP  - 323
VL  - 13
AB  - DNA restriction endonucleases and modification methylases are strain-specific
AB  - enzymes responsible for the host-specific barriers to interstrain transfer of
AB  - DNA that have been identified in numerous prokaryotic cell types.  Foreign DNA
AB  - entering a bacterial cell is subject to rapid endonucleolytic hydrolysis if it
AB  - is devoid of the modification characteristic of the particular bacterial
AB  - strain.  The strain specific modification enzyme catalyzes methyl transfer from
AB  - S-adenosyl-L-methionine (AdoMet) to a specific DNA sequence which is
AB  - characteristic of the particular host specificity system.  Thus, cellular DNA
AB  - is rendered resistant to attack by the endogenous restriction enzyme by virtue
AB  - of being methylated at DNA sites that are also recognized by the endonuclease.
ER  -

TY  - JOUR
AU  - Modrich, P.
TI  - Structures and mechanisms of DNA restriction and modification enzymes.
JO  - Q. Rev. Biophys.
PY  - 1979
SP  - 315
EP  - 369
VL  - 12
AB  - Although the phenomenon of host specificity was initially observed in the early
AB  - 1950s (Luria & Human, 1952; Bertani & Weigle, 1953), it was nearly a decade
AB  - later that Arber and his colleagues accurately predicted the molecular basis of
AB  - the phenomenon.  Their experiments with bacteriophage lambda demonstrated that
AB  - a given host-specificity system imparts a specific modification of the viral
AB  - DNA, and further, that restriction of DNA lacking the appropriate modificaton
AB  - is a consequence of nucleolytic hydrolysis upon entry into the host cell (Arber
AB  - & Dussoix, 1962; Dussoix & Arber, 1962; Arber, Hattman & Dussoix, 1963).  These
AB  - observations led to their proposal that host specificity is based on a
AB  - two-enzyme system.  They suggested that cells of a given host specificity
AB  - possess a restriction endodeoxyribonuclease that recognizes a unique sequence
AB  - of nucleotide pairs and introduces double strand breaks into unmodified DNA.
AB  - The second component of the system, a modification enzyme, was proposed to
AB  - recognize the same nucleotide sequence and to modify the DNA, yielding a
AB  - species which is no longer subject to hydrolysis by the restriction
AB  - endonuclease.  Moreover, a variety of biological experiments suggested a
AB  - correlation between the phenomenon of modifications and polynucleotide
AB  - methylation (Arber, 1965; Klein & Sauerbier, 1965; Arber & Smith, 1966).  Thus,
AB  - cellular DNA would be resistant to restriction cleavage by virtue of being
AB  - appropriately methylated.  DNA foreign to the cell and lacking the appropriate
AB  - modification would, however, be specifically recognized and hydrolysed by the
AB  - restriction endonuclease.  Such systems then could account for the observed
AB  - barriers to transfer of unmodified DNA elements between prokaryotic cell types.
ER  -

TY  - JOUR
AU  - Modrich, P.
AU  - Roberts, R.J.
TI  - Type-II restriction and modification enzymes.
JO  - Nucleases
PY  - 1982
SP  - 109
EP  - 154
VL  - 0
AB  - I. IntroductionII. Structure of type-II restriction and modification enzymes.III. Methyl
AB  - transfer by type-II modification enzymes.IV. Fidelity of type-II restriction and modification
AB  - enzymes.V. Type-II enzyme-DNA interaction: thermodynamic and Kinetic parameters.VI. Type-II
AB  - enzyme-DNA interaction: DNA determinants important in specific recognition.VII. Concluding
AB  - remarks.
ER  -

TY  - JOUR
AU  - Modrich, P.
AU  - Rubin, R.A.
TI  - Role of the 2-amino group of deoxyguanosine in sequence recognition by EcoRI restriction and modifcation enzymes.
JO  - J. Biol. Chem.
PY  - 1977
SP  - 7273
EP  - 7278
VL  - 252
AB  - The dG residues within the EcoRI recognition sequence of ColE1 DNA have been
AB  - selectively replaced with dI.  Methylation of the altered sequence by the EcoRI
AB  - modification enzyme is extremely slow as compared with methyl transfer to the
AB  - natural recognition site.  Since the affinity of the modification enzyme for
AB  - the dI-containing sequence is considerably less than that for the nature
AB  - sequence, we have concluded that the 2-amino group of dG has an important role
AB  - in DNA site recognition by this enzyme.  In contrast, the altered site is
AB  - subject to cleavage by EcoRI endonuclease at rates essentially identical with
AB  - those observed with the natural sequence.  These results strongly suggest that
AB  - the two enzymes utilize different contacts within the EcoRI site and are
AB  - consistent with our conclusion (Rubin, R.A., and Modrich, P. (1977) J. Biol.
AB  - Chem. 252, 7265-7272) that the two proteins interact with their common
AB  - recognition sequence in different ways.
ER  -

TY  - JOUR
AU  - Modrich, P.
AU  - Zabel, D.
TI  - EcoRI endonuclease.  Physical and catalytic properties of the homogeneous enzyme.
JO  - J. Biol. Chem.
PY  - 1976
SP  - 5866
EP  - 5874
VL  - 251
AB  - A procedure for large scale isolation of Escherichia coli RI endonuclease in
AB  - high yield has been developed.  The purified enzyme is homogenous as judged by
AB  - polyacrylamide gel electrophoresis and analytical sedimentation.  The denatured
AB  - and reduced form of the enzyme has a molecular weight of 28,500 -/+ 500.  In
AB  - solution the enzyme exists as a mixture of dimers and tetramers of molecular
AB  - weights 57,000 and 114,000, respectively.  We estimate the dissociation
AB  - constant for tetramer to dimer transition to be less than or approximately
AB  - equal to 1 x 10-7 M.  Steady state kinetic analysis of the endonuclease with
AB  - ColE1 DNA as substrate showed that the enzyme obeys Michaelis-Menten kinetics.
AB  - At 37C the turnover number is four double strand scissions per min, and the Km
AB  - for ColE1 molecules is 8 x 10-9 M.  At 0C the major product of endonuclease
AB  - action contains only one single strand break in the RI site, and such molecules
AB  - can dissociate from the enzyme.  In contrast, at 30C or 37C, two single strand
AB  - breaks are introduced into the RI sequence prior to dissociation of the enzyme.
AB  - A transient enzyme-bound intermediate containing only one break in the RI site
AB  - was observed in studies of a single turnover at 30C.  Kinetic analysis of this
AB  - reaction indicates that the first break is introduced into the RI site with a
AB  - first order rate constant of at elast 40 min-1, while the second cleavage
AB  - occurs with a rate constant of 14 min-1.  Since the turnover number of the
AB  - enzyme at 30C is only 0.72 min-1, these results indicate that the rate-limiting
AB  - step is release of endonuclease from its DNA product.
ER  -

TY  - JOUR
AU  - Moencke-Buchner, E.
AU  - Mackeldanz, P.
AU  - Krueger, D.H.
AU  - Reuter, M.
TI  - Overexpression and affinity chromatography purification of the Type III restriction endonuclease EcoP15I for use in transcriptome analysis.
JO  - J. Biotechnol.
PY  - 2004
SP  - 99
EP  - 106
VL  - 114
AB  - The Type III restriction endonuclease EcoP15I is a multifunctional hetero-oligomeric enzyme
AB  - that recognizes the non-symmetric DNA sequence 5'-CAGCAG. For efficient cleavage, EcoP15I
AB  - needs the interaction with two copies of the recognition sequence that have to be inversely
AB  - oriented in the DNA double strand. The enzyme cuts the upper DNA strand 25-26bp and the lower
AB  - DNA strand 27-28bp, respectively, downstream of the recognition sequence-a distinct feature
AB  - that makes the enzyme particularly valuable for gene expression profiling methods relying on
AB  - the SAGE procedure (Matsumura et al., PNAS 100, 15718, 2003). Because the broader use of this
AB  - transcriptome analysis method requires the availability of larger amounts of restriction
AB  - endonuclease EcoP15I and the enzyme is not commercially available, we have cloned the genes
AB  - coding for the EcoP15I restriction endonuclease into pQE-16 plasmid vector that provides the
AB  - enzyme with a C-terminal 6xHis-tag. After Ni-NTA affinity chromatography and ion exchange
AB  - chromatography on heparin sepharose, we obtained 5mg homogeneous EcoP15I per gram cell pellet
AB  - within 1-2 day(s). Moreover, the C-terminally 6xHis-tagged EcoP15I restriction endonuclease
AB  - shows comparable enzymatic activity as the untagged enzyme.
ER  -

TY  - JOUR
AU  - Moffatt, B.A.
AU  - Studier, F.W.
TI  - Entry of bacteriophage T7 DNA into the cell and escape from host restriction.
JO  - J. Bacteriol.
PY  - 1988
SP  - 2095
EP  - 2105
VL  - 170
AB  - T7 DNA did not become susceptible to degradation by the host restriction
AB  - enzymes EcoB, EcoK, or EcoP1 until 6 to 7 min. after infection (at 30C).
AB  - During this period, T7 gene 0.3 protein is made and inactivates EcoB and EcoK,
AB  - allowing wild-type T7, or even a mutant that has recognition sites flanking
AB  - gene 0.3, to escape restriction by these enzymes.  However, T7 failed to escape
AB  - restriction by EcoP1 even though 0.3 protein was made, evidently because 0.3
AB  - protein is unable to inactivate EcoP1.  How T7 DNA can be accessible to
AB  - transcription but not restriction in the first few minutes of infection is not
AB  - yet understood, but we favor the idea that the entering DNA is initially
AB  - segregated in a special place.  Entry of T7 DNA into the cell is normally
AB  - coupled to transcription.  Tests of degradation of DNAs having their first
AB  - restriction sites different distances from the end of the DNA indicated that
AB  - only the first 1,000 or so base pairs (2.5%) of the molecule enter the cell
AB  - without transcription.  An exception was the only mutant tested that lacks base
AB  - pairs 343 to 393 of T7 DNA; most or all of this DNA entered the cell without
AB  - being transcribed, apparently because it lacks a sequence that normally arrests
AB  - entry.  This block to DNA entry would normally be relieved by the host RNA
AB  - polymerase transcribing from an appropriately situated promoter, but the block
AB  - can also be relieved by T7 RNA polymerase, if supplied by the host cell.  T7
AB  - mutants that lack all three strong early promoters A1, A2, and A3 could grow by
AB  - using a secondary promoter.
ER  -

TY  - JOUR
AU  - Moghadam, M.S.
AU  - Albersmeier, A.
AU  - Winkler, A.
AU  - Cimmino, L.
AU  - Rise, K.
AU  - Hohmann-Marriott, M.F.
AU  - Kalinowski, J.
AU  - Ruckert, C.
AU  - Wentzel, A.
AU  - Lale, R.
TI  - Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity.
JO  - BMC Genomics
PY  - 2016
SP  - 117
EP  - 117
VL  - 17
AB  - BACKGROUND: Marine cold-temperature environments are an invaluable source of
AB  - psychrophilic microbial life for new biodiscoveries. An Arctic marine bacterial
AB  - strain collection was established consisting of 1448 individual isolates
AB  - originating from biota, water and sediment samples taken at a various depth in
AB  - the Barents Sea, North of mainland Norway, with an all year round seawater
AB  - temperature of 4 degrees C. The entire collection was subjected to
AB  - high-throughput screening for detection of extracellular laccase activity with
AB  - guaiacol as a substrate. RESULTS: In total, 13 laccase-positive isolates were
AB  - identified, all belonging to the Psychrobacter genus. From the most diverse four
AB  - strains, based on 16S rRNA gene sequence analysis, all originating from the same
AB  - Botryllus sp. colonial ascidian tunicate sample, genomic DNA was isolated and
AB  - genome sequenced using a combined approach of whole genome shotgun and 8 kb
AB  - mate-pair library sequencing on an Illumina MiSeq platform. The genomes were
AB  - assembled and revealed genome sizes between 3.29 and 3.52 Mbp with an average G +
AB  - C content of around 42 %, with one to seven plasmids present in the four strains.
AB  - Bioinformatics based genome mining was performed to describe the metabolic
AB  - potential of these four strains and to identify gene candidates potentially
AB  - responsible for the observed laccase-positive phenotype. Up to two different
AB  - laccase-like multicopper oxidase (LMCO) encoding gene candidates were identified
AB  - in each of the four strains. Heterologous expression of P11F6-LMCO and
AB  - P11G5-LMCO2 in Escherichia coli BL21 (DE3) resulted in recombinant proteins
AB  - exhibiting 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and
AB  - guaiacol oxidizing activity. CONCLUSIONS: Thirteen Psychrobacter species with
AB  - laccase-positive phenotype were isolated from a collection of Arctic marine
AB  - bacteria. Four of the isolates were genome sequenced. The overall genome features
AB  - were similar to other publicly available Psychrobacter genome sequences except
AB  - for P11G5 harboring seven plasmids. However, there were differences at the
AB  - pathway level as genes associated with degradation of phenolic compounds,
AB  - nicotine, phenylalanine, styrene, ethylbenzene, and ethanolamine were detected
AB  - only in the Psychrobacter strains reported in this study while they were absent
AB  - among the other publicly available Psychrobacter genomes. In addition, six gene
AB  - candidates were identified by genome mining and shown to possess T1, T2 and T3
AB  - copper binding sites as the main signature of the three-domain laccases.
AB  - P11F6-LMCO and P11G5-LMCO2 were recombinantly expressed and shown to be active
AB  - when ABTS and guaiacol were used as substrates.
ER  -

TY  - JOUR
AU  - Moghaddam, J.A.
AU  - Poehlein, A.
AU  - Fisch, K.
AU  - Alanjary, M.
AU  - Daniel, R.
AU  - Konig, G.M.
AU  - Schaberle, T.F.
TI  - Draft Genome Sequences of the Obligatory Marine Myxobacterial Strains Enhygromyxa salina SWB005 and SWB007.
JO  - Genome Announcements
PY  - 2018
SP  - e00324
EP  - e00318
VL  - 6
AB  - The two marine myxobacterial strains Enhygromyxa salina SWB005 and SWB007 were isolated from
AB  - coastal soil samples using Escherichia coli as bait for these predatory strains. These strains
AB  - produce unique specialized metabolites. Genomes were assembled into 312 contigs for E. salina
AB  - SWB005 (9.0 Mbp) and 192 contigs for E. salina SWB007 (10.6 Mbp).
ER  -

TY  - JOUR
AU  - Mogila, V.A.
AU  - Bellaiche, Y.
AU  - Perrimon, N.
TI  - Expression of I-SceI in Drosophila to induce DNA double-strand breaks.
JO  - Methods Mol. Biol.
PY  - 1999
SP  - 439
EP  - 445
VL  - 113
AB  - Generation of double-strand breaks in chromosomal DNA induces repair machinery of a cell, and
AB  - is also a necessary step for recombination events.  A system for the directed introduction of
AB  - DSBs into a genome could substantially facilitate progress in understanding DSB repair
AB  - mechanisms and could be used for efficient gene targeting.  The most successful attempts
AB  - toward this goal in Drosophila have utilized the P element transposition system.  However,
AB  - directed introduction of DSBs is still neither highly precise nor efficient, probably in part
AB  - owing to the innate properties of the P element transposase, which although being a
AB  - site-specific DNA binding protein, also has an affinity for nonspecific DNA sequences in
AB  - vitro.  As a result, DSBs generated by P element transposase are distributed randomly in the
AB  - Drosophila genome with the highest frequency close to or at the P element ends.  Site-specific
AB  - endonucleases with sufficiently long recognition sequences potentially could provide a
AB  - solution to this problem.  Among the most specific is the I-SceI endonuclease.  It recognizes
AB  - an 18-bp nonpalindromic sequence and has very low tolerance to nucleotide substitution.
AB  - Theoretically, this recognition site should appear only once in every 6.87 x 10^10 bp, which
AB  - exceeds the size of the Drosophila genome by about 400 times.
ER  -

TY  - JOUR
AU  - Moh, T.H.
AU  - Lau, N.S.
AU  - Furusawa, G.
AU  - Amirul, A.A.
TI  - Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from  Matang Mangrove Forest, Malaysia.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 36
EP  - 36
VL  - 12
AB  - Microbulbifer sp. CCB-MM1 is a halophile isolated from estuarine sediment of Matang Mangrove
AB  - Forest, Malaysia. Based on 16S rRNA gene sequence analysis,
AB  - strain CCB-MM1 is a potentially new species of genus Microbulbifer. Here we
AB  - describe its features and present its complete genome sequence with annotation.
AB  - The genome sequence is 3.86 Mb in size with GC content of 58.85%, harbouring 3313
AB  - protein coding genes and 92 RNA genes. A total of 71 genes associated with
AB  - carbohydrate active enzymes were found using dbCAN. Ectoine biosynthetic genes,
AB  - ectABC operon and ask_ect were detected using antiSMASH 3.0. Cell shape
AB  - determination genes, mreBCD operon, rodA and rodZ were annotated, congruent with
AB  - the rod-coccus cell cycle of the strain CCB-MM1. In addition, putative mreBCD
AB  - operon regulatory gene, bolA was detected, which might be associated with the
AB  - regulation of rod-coccus cell cycle observed from the strain.
ER  -

TY  - JOUR
AU  - Mohamad, N.I.
AU  - Tan, W.S.
AU  - Chang, C.Y.
AU  - Keng, T.K.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Analysis of Quorum-Sensing Pantoea stewartii Strain M073A through Whole-Genome Sequencing.
JO  - Genome Announcements
PY  - 2015
SP  - e00022
EP  - e00015
VL  - 3
AB  - Pantoea stewartii strain M073a is a Gram-negative bacterium isolated from a tropical
AB  - waterfall. This strain exhibits quorum-sensing activity. Here, the assembly and annotation of
AB  - its genome are presented.
ER  -

TY  - JOUR
AU  - Mohamad, N.I.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Whole-Genome Sequence of Quorum-Sensing Vibrio tubiashii Strain T33.
JO  - Genome Announcements
PY  - 2015
SP  - e01362
EP  - e01314
VL  - 3
AB  - Vibrio tubiashii strain T33 was isolated from the coastal waters of Morib, Malaysia, and was
AB  - shown to possess quorum-sensing activity similar to that of its famous relative Vibrio
AB  - fischeri. Here, the assembly and annotation of its genome are presented.
ER  -

TY  - JOUR
AU  - Mohamed, S.B.
AU  - Ali, M.S.
AU  - Alamir, F.M.
AU  - Alyas, T.B.
AU  - Ahmed, A.E.
AU  - Seed, A.O.
AU  - Omer, R.A.
TI  - First Complete Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Khartoum, Sudan.
JO  - Genome Announcements
PY  - 2017
SP  - e00945
EP  - e00917
VL  - 5
AB  - Methicillin-resistant Staphylococcus aureus is increasingly becoming resistant to most
AB  - antibiotics and consequently has become a challenging public health problem
AB  - in Sudan. The present study documented the first complete genome sequence of
AB  - strain SO-1977, isolated from a contaminated wound in Sudan.
ER  -

TY  - JOUR
AU  - Mohamed-Nor, N.H.
AU  - Tan, B.F.
AU  - Te, S.H.
AU  - Thompson, J.R.
AU  - Gin, K.Y.
TI  - Draft Genome Sequence of Cylindrospermopsis sp. Strain CR12 Extracted from the Minimetagenome of a Nonaxenic Unialgal Culture from a Tropical Freshwater Lake.
JO  - Genome Announcements
PY  - 2016
SP  - e01726
EP  - e01715
VL  - 4
AB  - Cylindrospermopsis is known to be one of the major bloom-forming cyanobacterial genera in many
AB  - freshwater environments. We report here the draft genome sequence of a tropical
AB  - Cylindrospermopsis sp. strain, CR12, which is capable of producing the hepatotoxic
AB  - cylindrospermopsin.
ER  -

TY  - JOUR
AU  - Mohan, A.
AU  - Bhosle, A.
AU  - Chandra, N.
TI  - Complete Genome Sequences of an Escherichia coli Laboratory Strain and Trimethoprim-Resistant (TMP32XR) Mutant Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01434
EP  - e01415
VL  - 3
AB  - We report the whole-genome sequences of an Escherichia coli laboratory wild-type  strain and
AB  - trimethoprim-resistant strains (two biological replicates, TMP32XR1
AB  - and TMP32XR2). Compared to the U00096.3 strain, a widely used strain in
AB  - laboratory experiments, the laboratory wild-type strain and the drug-resistant
AB  - strains evolved from this (TMP32XR1 and TMP32XR2) are 13, 24, and 37 bp longer,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Mohan, A.
AU  - Padiadpu, J.
AU  - Baloni, P.
AU  - Chandra, N.
TI  - Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01520
EP  - e01514
VL  - 3
AB  - We report the whole genome sequences of a Mycobacterium smegmatis laboratory wild-type strain
AB  - (MC(2) 155) and mutants (4XR1, 4XR2) resistant to isoniazid.
AB  - Compared to Mycobacterium smegmatis MC(2) 155 (NC_008596), a widely used strain
AB  - in laboratory experiments, the MC(2) 155, 4XR1, and 4XR2 strains are 60, 128 and
AB  - 93 bp longer, respectively.
ER  -

TY  - JOUR
AU  - Mohan, K.N.
AU  - Chaillet, J.R.
TI  - Cell and Molecular Biology of DNA Methyltransferase 1.
JO  - Int. Rev. Cell Mol. Biol.
PY  - 2013
SP  - 1
EP  - 42
VL  - 306
AB  - The DNA cytosine methyltransferase 1 (DNMT1) is a ubiquitous nuclear enzyme that catalyzes the
AB  - well-established reaction of placing methyl
AB  - groups on the unmethylated cytosines in methyl-CpG:CpG base pairs in
AB  - the hemimethylated DNA formed by methylated parent and unmethylated
AB  - daughter strands. This activity regenerates fully methylated
AB  - methyl-CpG:methyl-CpG pairs. Despite the straightforward nature of its
AB  - catalytic activity, detailed biochemical, genetic, and developmental
AB  - studies revealed intricate details of the central regulatory role of
AB  - DNMT1 in governing the epigenetic makeup of the nuclear genome. DNMT1
AB  - mediates demethylation and also participates in seemingly wide cellular
AB  - functions unrelated to maintenance DNA methylation. This review brings
AB  - together mechanistic details of maintenance methylation by DNMT1, its
AB  - regulation at transcriptional and posttranscriptional levels, and the
AB  - seemingly unexpected functions of DNMT1 in the context of DNA
AB  - methylation which is central to epigenetic changes that occur during
AB  - development and the process of cell differentiation.
ER  -

TY  - JOUR
AU  - Mohn, W.W.
AU  - Teather, R.M.
TI  - Partial purification and characterisation of Bfi57I and Bfi89I, restriction endonucleases from different strains of Butyrivibrio fibrisolvens.
JO  - Gene
PY  - 1995
SP  - 131
EP  - 132
VL  - 155
AB  - Two class-II restriction endonucleases (ENases), Bfi57I and Bfi89I, were partially purified
AB  - from Butyrivibrio fibrisolvens OB157 and OB189, respectively. Bfi57I (isoschizomer Sau3AI) had
AB  - the DNA recognition/cleavage sequence 5'-/GATC-3'; it is not inhibited by Dam methylation,
AB  - but is partially inhibited by M.BamHI methylation. Bfi89I (isoschizomer EaeI) had the
AB  - recognition/cleavage sequence 5'Y/GGCCR-3'; unlike the EaeI isoschizomer it is not fully
AB  - inhibited by M.HaeIII methylation.
ER  -

TY  - JOUR
AU  - Mohr, G.
AU  - Smith, D.
AU  - Belfort, M.
AU  - Lambowitz, A.M.
TI  - Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences.
JO  - Genes Dev.
PY  - 2000
SP  - 559
EP  - 573
VL  - 14
AB  - Group II intron homing occurs primarily by a mechanism in which the intron RNA reverse splices
AB  - into a DNA target site and is then reverse transcribed by the intron-encoded protein. The DNA
AB  - target site is recognized by an RNP complex containing the intron-encoded protein and the
AB  - excised intron RNA. Here, we analyzed DNA target-site requirements for the Lactococcus lactis
AB  - Ll.LtrB group II intron in vitro and in vivo. Our results suggest a model similar to yeast
AB  - mtDNA introns, in which the intron-encoded protein first recognizes a small number of
AB  - nucleotide residues in double-stranded DNA and causes DNA unwinding, enabling the intron RNA
AB  - to base-pair with the DNA for reverse splicing. Antisense-strand cleavage requires additional
AB  - interactions between the protein and 3' exon. Key nucleotide residues are recognized directly
AB  - by the intron-encoded protein independent of sequence context, and there is a stringent
AB  - requirement for fixed spacing between target site elements recognized by the protein and RNA
AB  - components of the endonuclease. Experiments with DNA substrates containing GC-clamps or
AB  - "bubbles" indicate a requirement for DNA unwinding in the 3' exon but not the distal 5' exon
AB  - region. Finally, by applying the target-site recognition rules, we show that the L1.LtrB
AB  - intron can be modified to insert at new sites in a plasmid-borne thyA gene in Escherichia
AB  - coli. This strategy should be generally applicable to retargeting group II introns and to
AB  - delivering foreign sequences to specific sites in heterologous genomes.
ER  -

TY  - JOUR
AU  - Moine, D.
AU  - Kassam, M.
AU  - Baert, L.
AU  - Tang, Y.
AU  - Barretto, C.
AU  - Ngom, B.C.
AU  - Klijn, A.
AU  - Descombes, P.
TI  - Fully Closed Genome Sequences of Five Type Strains of the Genus Cronobacter and One Cronobacter sakazakii Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00142
EP  - e00116
VL  - 4
AB  - Cronobacteris associated with infant infections and the consumption of reconstituted infant
AB  - formula. Here we sequenced and closed six genomes ofC.
AB  - condimenti(T),C. muytjensii(T),C. universalis(T),C. malonaticus(T),C.
AB  - dublinensis(T), andC. sakazakiithat can be used as reference genomes in single
AB  - nucleotide polymorphism (SNP)-based next-generation sequencing (NGS) analysis for
AB  - source tracking investigations.
ER  -

TY  - JOUR
AU  - Moineau, S.
AU  - D'Amelio, G.E.
AU  - Pandian, S.
AU  - Klaenhammer, T.R.
TI  - The susceptibility of evolving dairy bacteriophages to restriction enzymes and lactococcal R/M system.
JO  - J. Dairy Sci.
PY  - 1992
SP  - 114
EP  - 114
VL  - 75
AB  - One approach to limit phage development during milk fermentation is to use strains insensitive
AB  - to predominant phage species present in cheese plants, particularly prolate (c2) and small
AB  - isometric-headed (P008) species. However this may lead to the emergence of other phage
AB  - species. Recently, we have isolated 7 industrial phages (phi48, phi50,al,bl, cs, d1 from USA
AB  - and UL36 from Canada) able to propagate on Lactococcus lactis LMA12, and except for UL36, also
AB  - on its pTR2030 transconjugants. Electron microscopy and DNA homology studies have placed these
AB  - phages within the P335 species (composed of lytic and temperate types). Molecular analyses
AB  - have shown a relatively high number of restriction sites in their genomes for many
AB  - endonucleases, including ScrFI. The industrial phages, compared to phages sk1, p2, jj50 (P008
AB  - species) and c2, were highly sensitive to 4 plasmid-encoded R/M systems (pTN20, pTRK12,
AB  - pTRK30, pTRK68). The paucity of restriction sites in many phage genomes has been proposed as
AB  - an antirestriction response which has evolved in some lactococcal phages. Since the 7 phages
AB  - studied herein are more sensitive to R/M and their DNA cuts more frequently, this group may
AB  - represent a younger generation of phages that have just recently evolved to lactococci.
ER  -

TY  - JOUR
AU  - Moineau, S.
AU  - Pandian, S.
AU  - Klaenhammer, T.R.
TI  - Restriction/modification systems and restriction endonucleases are more effective on lactococcal bacteriophages that have emerged recently in the dairy industry.
JO  - Appl. Environ. Microbiol.
PY  - 1993
SP  - 197
EP  - 202
VL  - 59
AB  - Recently, eight lytic small isometric-headed bacteriophages were isolated from
AB  - cheese-manufacturing plants throughout North America. The eight phages were different, but all
AB  - propagated on one strain, Lactococcus lactis NCK203. On the basis of DNA homology, they were
AB  - classified in the P335 species. Digestion of their genomes in vitro with restriction enzymes
AB  - resulted in an unusually high number of type II endonuclease sites compared with the more
AB  - common lytic phages of the 936 (small isometric-headed) and c2 (prolate-headed) species. In
AB  - vivo, the P335 phages were more sensitive to four distinct lactococcal restriction and
AB  - modification (R/M) systems than phages belonging to the 936 and c2 species. A significant
AB  - correlation was found between the number of restriction sites for endonucleases (purified from
AB  - other bacterial genera) and the relative susceptibility of phages to lactococcal R/M systems.
AB  - Comparisons among these three phage species indicate that the P335 species may have emerged
AB  - most recently in the dairy industry.
ER  -

TY  - JOUR
AU  - Moineau, S.
AU  - Walker, S.A.
AU  - Holler, B.J.
AU  - Vedamuthu, E.R.
AU  - Vandenbergh, P.A.
TI  - Expression of a Lactococcus lactis phage resistance mechanism by Streptococcus thermophilus.
JO  - Appl. Environ. Microbiol.
PY  - 1995
SP  - 2461
EP  - 2466
VL  - 61
AB  - The 7.8-kb lactococcal plasmid pSRQ700 encodes the LlaII restriction/modification system which
AB  - recognizes and cleaves the sequence 3'-GATC-5'. When the plasmid pSRQ700 is introduced into
AB  - a phage-sensitive Lactococcus lactis strain, strong phage resistance is conferred by the LlaII
AB  - system. In this report, we show that pSRQ700 cannot replicate in Streptococcus thermophilus.
AB  - However, if cloned into the vector pNZ123, the native LlaII system is expressed and strong
AB  - phage resistance is conferred to various industrial S. thermophilus strains. Resistance
AB  - against phages isolated from yogurt and mozzarella wheys was observed. To our knowledge, this
AB  - is the first report of increased phage resistance in S. thermophilus.
ER  -

TY  - JOUR
AU  - Moineau, S.
AU  - Walker, S.A.
AU  - Vedamuthu, E.R.
AU  - Vandenbergh, P.A.
TI  - Cloning and sequencing of LlaII restriction/modification genes from Lactococcus lactis and relatedness of this system to the Streptococcus pneumoniae DpnII system.
JO  - Appl. Environ. Microbiol.
PY  - 1995
SP  - 2193
EP  - 2202
VL  - 61
AB  - The natural 7.8-kb plasmid pSRQ700 was isolated from Lactococcus lactis subsp. cremoris DCH-4.
AB  - It encodes a restriction/modification system named LlaII. When introduced into a
AB  - phage-sensitive L. lactis strain, pSRQ700 confers strong phage resistance against the three
AB  - most common lactococcal phage species, namely, 936, c2, and P335. The LlaII endonuclease was
AB  - purified and found to cleave the palindromic sequence 5'-GATC-3'. It is an isoschizomer of
AB  - Streptococcus pneumoniae DpnII. The plasmid pSRQ700 was mapped, and the genetic organization
AB  - of LlaII was localized. Cloning and sequencing of the entire LlaII system allowed the
AB  - identification of three open reading frames. The three genes (llaIIA, llaIIB, and llaIIC)
AB  - overlapped and are under one putative promoter. A putative terminator was found at the end of
AB  - llaIIC. The genes llaIIA and llaIIB coded for m6A methyltransferases, and llaIIC coded for an
AB  - endonuclease. The LlaII system shares strong genetic similarities with the DpnII system. The
AB  - deduced amino acid sequence of M.LlaIIA was 75% identical with that of M.DpnII, whereas
AB  - M.LlaIIB was 88% identical with M.DpnA. However, R.LlaII shared only 31% identity with
AB  - R.DpnII.
ER  -

TY  - JOUR
AU  - Moissidou, A.
AU  - Rina, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction BshKI.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8884
EP  - 8884
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Mok, Y.K.
AU  - Clark, D.R.
AU  - Kam, K.M.
AU  - Shaw, P.C.
TI  - Restriction endonuclease from thermophilic bacterial species I.  Isolation and characterization of BsiEI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4954
EP  - 4954
VL  - 18
ER  -

TY  - JOUR
AU  - Mok, Y.K.
AU  - Clark, D.R.
AU  - Kam, K.M.
AU  - Shaw, P.C.
TI  - Restriction endonuclease from thermophilic bacterial species II. Isolation and characterization of BsiBl.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6740
EP  - 6740
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Mok, Y.K.
AU  - Clark, D.R.
AU  - Kam, K.M.
AU  - Shaw, P.C.
TI  - BsiYI, a novel thermophilic restriction endonuclease that recognizes 5' CCNNNNNNNGG3' and the discovery of a wrongly sequenced site in pACYC177 .
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2321
EP  - 2323
VL  - 19
AB  - A new type II restriction endonuclease designated BsiYI has been purified from
AB  - a thermophilic soil Bacillus stearothermophilus strain.  This enzyme recognizes
AB  - and cleaves the highly degenerate sequence 5'CCNNNNN^NNGG3'.  During the
AB  - identification of the recognition sequence of BsiYI, we discovered that there
AB  - should be five G nucleotides instead of four at position 1227 - 1230 of the
AB  - plasmid pACYC177.
ER  -

TY  - JOUR
AU  - Mokrishcheva, M.L.
AU  - Kertesz-Farkas, A.
AU  - Nikitin, D.V.
TI  - New bifunctional restriction-modification enzyme AloI isoschizomer (PcoI): Bioinformatics analysis, purification and activity confirmation.
JO  - Gene
PY  - 2018
SP  - 8
EP  - 12
VL  - 660
AB  - Type II restriction endonucleases and modification DNA-methyltransferases are key instruments
AB  - of genetic engineering. Recently the number of proteins assigned to
AB  - this group exceeds 8500. Subtype IIC organizes bifunctional
AB  - endonuclease-methyltransferase enzymes and currently consists of 16 described
AB  - members. Here we present phylogenetic tree of 22 new potential bifunctional
AB  - endonucleases. The majority of them are thought to be fusions of a restriction
AB  - nuclease with a DNA-methyltransferase and a target recognition subunit of type I
AB  - restriction-modification systems (R-M-S structure). A RM.AloI isoschizomer from
AB  - Prevotella copri DSM-18205, PcoI, has been cloned, purified and its REase
AB  - activity demonstrated. It cuts DNA in magnesium-dependent manner and demonstrates
AB  - high affinity to DNA, which probably reflects its mechanism of action. This work
AB  - provides additional proves that gene fusion might play an important role in
AB  - evolution of restriction-modification systems and other DNA-modifying proteins.
ER  -

TY  - JOUR
AU  - Mokrishcheva, M.L.
AU  - Solonin, A.S.
AU  - Nikitin, D.V.
TI  - Role of gene fusion in evolution of restriction endonucleases.
JO  - Protein Purification and Analysis
PY  - 2012
SP  - 163
EP  - 181
AB  - DNA restriction-modification systems (RMS) are prokaryotic tools against invasion of foreign
AB  - DNAs into
AB  - cells (Williams, 2003). They play an important evolutionary role as subcellular barriers
AB  - restricting horizontal
AB  - gene transfer and thereby providing microbial biodiversity. Usually, RMS comprise of a
AB  - restriction
AB  - endonuclease (REase) and modification DNA methyltransferase (MTase) enzyme recognizing
AB  - the same short 4-8 nucleotide sequence. RMS functioning includes methylation of recognition
AB  - DNA sequences
AB  - by MTase. All non-modified sites can be cut by a cognate REase (Williams, 2003). Type II
AB  - REases are indispensable tools in creating recombinant DNA molecules (Skowronek and Bujnicki,
AB  - 2007).
AB  - Their widespread practical application has stimulated research to discover and characterize
AB  - more of these
AB  - systems. Currently, more than 10000 different sequences corresponding to REases of type II
AB  - alone are
AB  - listed in REBASE, the database holding all known and many putative RMS (Roberts et al., 2010).
AB  - The high number of known RMS is reflected also in high diversity of their organisation or
AB  - functioning
AB  - and, hypothetically, in multiplicity of their evolutionary pathways. One of these pathways
AB  - could be fusion
AB  - of preexisting ORFs with formation of a gene capable of producing a protein with an array of
AB  - new
AB  - activities and functions. It could be suggested that type IIC RMS carrying both REase and
AB  - MTase in a
AB  - single polypeptide might appear by this mechanism (Roberts et al., 2003). Here we present
AB  - direct evidence
AB  - how a fully functional type IIC REase could appear by fusion of the appropriate genes as a
AB  - result
AB  - of a few point mutations.
ER  -

TY  - JOUR
AU  - Mokrishcheva, M.L.
AU  - Solonin, A.S.
AU  - Nikitin, D.V.
TI  - Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems.
JO  - BMC Evol. Biol.
PY  - 2011
SP  - 35
EP  - 35
VL  - 11
AB  - Background: The discovery of restriction endonucleases and modification DNA
AB  - methyltransferases, key instruments of genetic engineering, opened
AB  - a new era of molecular biology through development of the recombinant
AB  - DNA technology. Today, the number of potential proteins assigned to
AB  - type II restriction enzymes alone is beyond 6000, which probably
AB  - reflects the high diversity of evolutionary pathways. Here we present
AB  - experimental evidence that a new type IIC restriction and modification
AB  - enzymes carrying both activities in a single polypeptide could result
AB  - from fusion of the appropriate genes from preexisting bipartite
AB  - restriction-modification systems.
AB  - Results: Fusion of eco29kIR and M ORFs gave a novel gene encoding
AB  - for a fully functional hybrid polypeptide that carried both restriction
AB  - endonuclease and DNA methyltransferase activities. It has been placed
AB  - into a subclass of type II restriction and modification enzymes - type
AB  - IIC. Its MTase activity, 80% that of the M.Eco29kI enzyme, remained
AB  - almost unchanged, while its REase activity decreased by three times,
AB  - concurrently with changed reaction optima, which presumably can be
AB  - caused by increased steric hindrance in interaction with the substrate.
AB  - In vitro the enzyme preferentially cuts DNA, with only a low level of
AB  - DNA modification detected. In vivo new RMS can provide a 10(2)-fold
AB  - less protection of host cells against phage invasion.
AB  - Conclusions: We propose a molecular mechanism of appearing of type
AB  - IIC restriction-modification and M.SsoII-related enzymes, as well as
AB  - other multifunctional proteins. As shown, gene fusion could play an
AB  - important role in evolution of restriction-modification systems and be
AB  - responsible for the enzyme subclass interconversion. Based on the
AB  - proposed approach, hundreds of new type IIC enzymes can be generated
AB  - using head-to-tail oriented type I, II, and III restriction and
AB  - modification genes. These bifunctional polypeptides can serve a basis
AB  - for enzymes with altered recognition specificities. Lastly, this study
AB  - demonstrates that protein fusion may change biochemical properties of
AB  - the involved enzymes, thus giving a starting point for their further
AB  - evolutionary divergence.
ER  -

TY  - JOUR
AU  - Mol, C.D.
AU  - Arvai, A.S.
AU  - Begley, T.J.
AU  - Cunningham, R.P.
AU  - Tainer, J.A.
TI  - Structure and activity of a thermostable thymine-DNA glycosylase: Evidence for base twisting to remove mismatched normal DNA bases.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 373
EP  - 384
VL  - 315
AB  - The repair of T:G mismatches in DNA is key for maintaining bacterial restriction/modification
AB  - systems and gene silencing in higher eukaryotes. T:G mismatch repair can be initiated by a
AB  - specific mismatch glycosylase (MIG) that is homologous to the helix-hairpin-helix (HhH) DNA
AB  - repair enzymes. Here, we present a 2.0 A resolution crystal structure and complementary
AB  - mutagenesis results for this thermophilic HhH MIG enzyme. The results suggest that MIG
AB  - distorts the target thymine nucleotide by twisting the thymine base approximately 90 degrees
AB  - away from its normal anti position within DNA. We propose that functionally significant
AB  - differences exist in DNA repair enzyme extrahelical nucleotide binding and catalysis that are
AB  - characteristic of whether the target base is damaged or is a normal base within a mispair.
AB  - These results explain why pure HhH DNA glycosylases and combined glycosylase/AP lyases cannot
AB  - be interconverted by simply altering their functional group chemistry, and how
AB  - broad-specificity DNA glycosylase enzymes may weaken the glycosylic linkage to allow a variety
AB  - of damaged DNA bases to be excised.
ER  -

TY  - JOUR
AU  - Molemans, F.
AU  - van Emmelo, J.
AU  - Fiers, W.
TI  - The sequence specificity of endonucleases CauI and CauII isolated from Chloroflexus aurantiacus.
JO  - Gene
PY  - 1982
SP  - 93
EP  - 96
VL  - 18
AB  - The type II restriction enzymes CauI and CauII, isolated from Chloroflexus
AB  - aurantiacus, recognize and cleave (at the position indicated by an arrow) the
AB  - sequences G^GA/TCC and CC^G/CGG, respectively.  These conclusions are supported
AB  - by the results from restriction site mapping, sequence analysis by partial
AB  - chemical degradation, end-group analysis after lambda exonuclease treatment and
AB  - computer-assisted comparison of DNA sequence data.
ER  -

TY  - JOUR
AU  - Molenda, O.
AU  - Tang, S.
AU  - Edwards, E.A.
TI  - Complete Genome Sequence of Dehalococcoides mccartyi Strain WBC-2, Capable of Anaerobic Reductive Dechlorination of Vinyl Chloride.
JO  - Genome Announcements
PY  - 2016
SP  - e01375
EP  - e01316
VL  - 4
AB  - Dehalococcoides mccartyi strain WBC-2 dechlorinates carcinogen vinyl chloride to  ethene in
AB  - the West Branch Canal Creek (WBC-2) microbial consortium used for bioaugmentation. We
AB  - assembled and closed the complete genome sequence of this prokaryote using metagenomic
AB  - sequencing from an enrichment culture.
ER  -

TY  - JOUR
AU  - Molholt, B.
AU  - Fraser, D.
TI  - Host-controlled restriction of T-even bacteriophages:  relation of endonuclease I and T-even-induced nucleases to restriction.
JO  - J. Virol.
PY  - 1968
SP  - 313
EP  - 319
VL  - 2
AB  - Restriction of nonglucosylated T2 phage (T*2) as a function of bacterial growth
AB  - state was the same for endonuclease I-containing and endonuclease I-deficient
AB  - strains of Escherichia coli B.  Furthermore, E. coli strains with various
AB  - levels of restriction for T2 had comparable endonuclease I activities.  It was
AB  - also found that a T4 mutant temperature-sensitive for gene 46 and 47 functions
AB  - was fully restricted at 42 C.  It therefore appears that neither endonuclease I
AB  - nor the phage-induced nucleases whose activities are blocked by mutations in
AB  - genes 46 and 47 catalyze the initial event in restriction of nonglucosylated
AB  - T-even phages.
ER  -

TY  - JOUR
AU  - Molina, L.
AU  - Bernal, P.
AU  - Udaondo, Z.
AU  - Segura, A.
AU  - Ramos, J.L.
TI  - Complete Genome Sequence of a Pseudomonas putida Clinical Isolate, Strain H8234.
JO  - Genome Announcements
PY  - 2013
SP  - e00496
EP  - e00413
VL  - 1
AB  - We report the complete genome sequence of Pseudomonas putida strain H8234, which  was isolated
AB  - from a hospital patient presenting with bacteremia. This strain has
AB  - a single chromosome (6,870,827 bp) that contains 6,305 open reading frames. The
AB  - strain is not a pathogen but exhibits multidrug resistance associated with 40
AB  - genomic islands.
ER  -

TY  - JOUR
AU  - Molina, R.
AU  - Marcaida, M.J.
AU  - Redondo, P.
AU  - Marenchino, M.
AU  - Duchateau, P.
AU  - D'Abramo, M.
AU  - Montoya, G.
AU  - Prieto, J.
TI  - Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold.
JO  - J. Biol. Chem.
PY  - 2015
SP  - 18534
EP  - 18544
VL  - 290
AB  - Homing endonucleases are useful tools for genome modification because of their capability to
AB  - recognize and cleave specifically large DNA targets. These
AB  - endonucleases generate a DNA double strand break that can be repaired by the DNA
AB  - damage response machinery. The break can be repaired by homologous recombination,
AB  - an error-free mechanism, or by non-homologous end joining, a process susceptible
AB  - to introducing errors in the repaired sequence. The type of DNA cleavage might
AB  - alter the balance between these two alternatives. The use of 'nickases' producing
AB  - a specific single strand break instead of a double strand break could be an
AB  - approach to reduce the toxicity associated with non-homologous end joining by
AB  - promoting the use of homologous recombination to repair the cleavage of a single
AB  - DNA break. Taking advantage of the sequential DNA cleavage mechanism of I-DmoI
AB  - LAGLIDADG homing endonuclease, we have developed a new variant that is able to
AB  - cut preferentially the coding DNA strand, generating a nicked DNA target. Our
AB  - structural and biochemical analysis shows that by decoupling the action of the
AB  - catalytic residues acting on each strand we can inhibit one of them while keeping
AB  - the other functional.
ER  -

TY  - JOUR
AU  - Molina, R.
AU  - Redondo, P.
AU  - Stella, S.
AU  - Marenchino, M.
AU  - D'Abramo, M.
AU  - Gervasio, F.L.
AU  - Charles, E.J.
AU  - Valton, J.
AU  - Grizot, S.
AU  - Duchateau, P.
AU  - Prieto, J.
AU  - Montoya, G.
TI  - Non-specific protein-DNA interactions control I-CreI target binding and cleavage.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 6936
EP  - 6945
VL  - 40
AB  - Homing endonucleases represent protein scaffolds that provide powerful tools for  genome
AB  - manipulation, as these enzymes possess a very low frequency of DNA
AB  - cleavage in eukaryotic genomes due to their high specificity. The basis of
AB  - protein-DNA recognition must be understood to generate tailored enzymes that
AB  - target the DNA at sites of interest. Protein-DNA interaction engineering of
AB  - homing endonucleases has demonstrated the potential of these approaches to create
AB  - new specific instruments to target genes for inactivation or repair. Protein-DNA
AB  - interface studies have been focused mostly on specific contacts between amino
AB  - acid side chains and bases to redesign the binding interface. However, it has
AB  - been shown that 4 bp in the central DNA sequence of the 22-bp substrate of a
AB  - homing endonuclease (I-CreI), which do not show specific protein-DNA
AB  - interactions, is not devoid of content information. Here, we analyze the
AB  - mechanism of target discrimination in this substrate region by the I-CreI
AB  - protein, determining how it can occur independently of the specific protein-DNA
AB  - interactions. Our data suggest the important role of indirect readout in this
AB  - substrate region, opening the possibility for a fully rational search of new
AB  - target sequences, thus improving the development of redesigned enzymes for
AB  - therapeutic and biotechnological applications.
ER  -

TY  - JOUR
AU  - Molina, R.
AU  - Stella, S.
AU  - Redondo, P.
AU  - Gomez, H.
AU  - Marcaida, M.J.
AU  - Orozco, M.
AU  - Prieto, J.
AU  - Montoya, G.
TI  - Visualizing phosphodiester-bond hydrolysis by an endonuclease.
JO  - Nat. Struct. Mol. Biol.
PY  - 2015
SP  - 65
EP  - 72
VL  - 22
AB  - The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical
AB  - reaction has not yet been observed. Here we follow the generation of
AB  - a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing
AB  - endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage
AB  - mechanism. We captured intermediates of the different catalytic steps, and this
AB  - allowed us to watch the reaction by 'freezing' multiple states. We observed the
AB  - successive entry of two metals involved in the reaction and the arrival of a
AB  - third cation in a central position of the active site. This third metal ion has a
AB  - crucial role, triggering the consecutive hydrolysis of the targeted
AB  - phosphodiester bonds in the DNA strands and leaving its position once the DSB is
AB  - generated. The multiple structures show the orchestrated conformational changes
AB  - in the protein residues, nucleotides and metals during catalysis.
ER  -

TY  - JOUR
AU  - Mollmann, S.
AU  - Albersmeier, A.
AU  - Ruckert, C.
AU  - Tauch, A.
TI  - Complete Genome Sequence of Corynebacterium imitans DSM 44264, Isolated from a Five-Month-Old Boy with Suspected Pharyngeal Diphtheria.
JO  - Genome Announcements
PY  - 2014
SP  - e01210
EP  - e01214
VL  - 2
AB  - The complete genome sequence of the type strain Corynebacterium imitans DSM 44264 comprises
AB  - 2,565,321 bp with a mean G+C content of 64.26%. The detection of the
AB  - antibiotic resistance genes erm(X), aphA1-IAB, strA-strB, and cmx is fully
AB  - consistent with the previously observed multidrug-resistant pattern of C. imitans
AB  - isolates.
ER  -

TY  - JOUR
AU  - Molloy, P.L.
AU  - Symons, R.H.
TI  - Cleavage of DNA.RNA hybrids by Type II restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 2939
EP  - 2946
VL  - 8
AB  - The action of a number of restriction enzymes on DNA.RNA hybrids has been examined using
AB  - hybrids synthesised with RNAs of cucumber mosaic virus as templates. The enzymes EcoRI,
AB  - HindII, SalI, MspI, HhaI, AluI, TaqI and HaeIII cleaved the DNA strand of the hybrids (and
AB  - possibly also the RNA strand) into specific fragments. For four of these enzymes, HhaI, AluI,
AB  - TaqI and HaeIII, comparison of the restriction fragments produced with the known sequences of
AB  - the viral RNAs confirmed that they were recognising and cleaving the DNA strand of the hybrids
AB  - at their correct recognition sequences. It is likely that the ability to utilise DNA.RNA
AB  - hybrids as substrates is a general property of Type II restriction enzymes.
ER  -

TY  - JOUR
AU  - Molloy, P.L.
AU  - Watt, F.
TI  - Effect of cytosine methylation on cutting by the restriction enzyme MaeII.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 2335
EP  - 2335
VL  - 16
AB  - The restriction enzyme MaeII, isolated from Methanococcus aeolicus, recognizes
AB  - and cuts within the sequence ACGT.  The susceptibility of MaeII to inhibition
AB  - by cytosine methylation of interest for studies of gene expression as its
AB  - recognition sequence contains a CG dinucleotide which has the potential to be
AB  - methylated in vertebrate DNA.  In particular its recognition sequence is found
AB  - within the binding sites for at least three mammalian transcription factors -
AB  - the adenovirus major late gene upstream element, CCACGTGA, the cAMP responsive
AB  - element, TGACGTCA, and an adenovirus E2 factor binding site, (T/A)CGTCA.
ER  -

TY  - JOUR
AU  - Molnar, A.
AU  - Geck, P.
AU  - Orosz, A.
AU  - Kulcsar, P.
AU  - Nasz, I.
TI  - Purification of a new restriction endonuclese from Streptococcus mutans and identification of its recognition sequence.
JO  - Acta Microbiol. Hung.
PY  - 1991
SP  - 55
EP  - 60
VL  - 38
AB  - SmuEI, a type II restriction endonuclease, has been isolated from Streptococcus mutans
AB  - serotype E, which is an isoschizomer of AvaII recognizes the palindromic pentanucleotide
AB  - sequence 5' GGWCC 3'. Similarly to AvaII, SmuEI cleaves the sequence, G^GWCC generating 5'
AB  - protruding fragment termini.
ER  -

TY  - JOUR
AU  - Molnarova, V.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - Occurrence of restriction and modification systems in ruminal Selenomonades.
JO  - Chemical Papers-Chemicke Zvesti
PY  - 1998
SP  - 284
EP  - 284
VL  - 52
AB  - Bacterial restriction and modification systems consist of a restriction endonuclease plus a
AB  - "cognate" modification methyltransferase having the same specificity. The biological function
AB  - of restriction and modification systems is to protect bacteria from invading phage and plasmid
AB  - DNA. The rumen is one of the most complex and best studied of all microbial ecosystems. In
AB  - addition to protozoa, bacteria and fungi the rumen is known to contain a large and diverse
AB  - population of bacteriophages. These phages probably play a significant role in the population
AB  - dynamics of ruminal bacteria. Thus under ruminal condition possession of restriction and
AB  - modification system can provide bacteria with a selective advantage.
ER  -

TY  - JOUR
AU  - Molnarova, V.
AU  - Pristas, P.
AU  - Javorsky, P.
TI  - Prevalence of CTGCAG recognizing restriction and modification systems in ruminal selenomonades.
JO  - Anaerobe
PY  - 1999
SP  - 37
EP  - 41
VL  - 5
AB  - Analysis of restriction and modification activities in natural population of Selenomonas
AB  - ruminantium have revealed the prevalence of CTGCAG (PstI isoschizomers) recognizing
AB  - restriction and/or modification systems in these bacteria.  PstI isoschizomeric restriction
AB  - endonucleases were detected in 4 out of 15 strains tested.  In one strain, the PstI
AB  - isoschizomeric restriction system was accompanied by another restriction and modification
AB  - system recognizing the sequence GAATTC (EcoRI isoschizomer).  Four other strains contained
AB  - CTGCAG specific methylases which lacked cognate endonuclease activities.  The presence of
AB  - identical restriction and modification systems in both subspecies of S. ruminantium, as well
AB  - as the occurrence of PstI isoschizomers in various combinations, indicate the possibility of
AB  - horizontal transfer of genes coding for these systems.
ER  -

TY  - JOUR
AU  - Molohon, K.J.
AU  - Blair, P.M.
AU  - Park, S.
AU  - Doroghazi, J.R.
AU  - Maxson, T.
AU  - Hershfield, J.R.
AU  - Flatt, K.M.
AU  - Schroeder, N.E.
AU  - Ha, T.
AU  - Mitchell, D.A.
TI  - Plantazolicin is an ultra-narrow spectrum antibiotic that targets the membrane.
JO  - ACS Infect Dis
PY  - 2016
SP  - 207
EP  - 220
VL  - 2
AB  - Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified natural
AB  - product from Bacillus methylotrophicus FZB42 and Bacillus pumilus. Extensive tailoring to
AB  - twelve of the fourteen amino acid residues in the mature natural product endows PZN with not
AB  - only a rigid, polyheterocyclic structure, but also antibacterial activity. Here we report a
AB  - remarkably discriminatory activity of PZN toward Bacillus anthracis, which rivals a
AB  - previously-described gamma (gamma) phage lysis assay in distinguishing B.
AB  - anthracis from other members of the Bacillus cereus group. We evaluate the underlying cause of
AB  - this selective activity by measuring the RNA expression profile of PZN-treated B. anthracis,
AB  - which revealed significant upregulation of genes within the cell envelope stress response. PZN
AB  - depolarizes the B. anthracis membrane like other cell envelope-acting compounds but uniquely
AB  - localizes to distinct foci within the envelope. Selection and whole-genome sequencing of
AB  - PZN-resistant mutants of B. anthracis implicate a relationship between the action of PZN and
AB  - cardiolipin (CL) within the membrane. Exogenous CL increases the potency of PZN in wild type
AB  - B. anthracis and promotes the incorporation of fluorescently tagged PZN in the cell envelope.
AB  - We propose that PZN localizes to and exacerbates structurally compromised regions of the
AB  - bacterial membrane, which ultimately results in cell lysis.
ER  -

TY  - JOUR
AU  - Momparler, R.L.
AU  - Bovenzi, V.
TI  - DNA methylation and cancer.
JO  - J. Cell. Physiol.
PY  - 2000
SP  - 145
EP  - 154
VL  - 183
AB  - The methylation of DNA is an epigenetic modification that can play an important role in the
AB  - control of gene expression in mammalian cells. The enzyme involved in this process is DNA
AB  - methyltransferase, which catalyzes the transfer of a methyl group from S-adenosyl-methionine
AB  - to cytosine residues to form 5-methylcytosine, a modified base that is found mostly at CpG
AB  - sites in the genome. The presence of methylated CpG islands in the promoter region of genes
AB  - can suppress their expression. This process may be due to the presence of 5-methylcytosine
AB  - that apparently interferes with the binding of transcription factors or other DNA-binding
AB  - proteins to block transcription. In different types of tumors, aberrant or accidental
AB  - methylation of CpG islands in the promoter region has been observed for many cancer-related
AB  - genes resulting in the silencing of their expression. How this aberrant hypermethylation takes
AB  - place is not known. The genes involved include tumor suppressor genes, genes that suppress
AB  - metastasis and angiogenesis, and genes that repair DNA suggesting that epigenetics plays an
AB  - important role in tumorigenesis. The potent and specific inhibitor of DNA methylation,
AB  - 5-aza-2'-deoxycytidine (5-AZA-CdR) has been demonstrated to reactivate the expression most of
AB  - these "malignancy" suppressor genes in human tumor cell lines. These genes may be interesting
AB  - targets for chemotherapy with inhibitors of DNA methylation in patients with cancer and this
AB  - may help clarify the importance of this epigenetic mechanism in tumorigenesis.
ER  -

TY  - JOUR
AU  - Momynaliev, K.
AU  - Chelysheva, V.
AU  - Selezneva, O.
AU  - Akopian, T.
AU  - Alexeev, D.
AU  - Govorun, V.
TI  - Complete Genome Sequences of Helicobacter pylori Rifampin-Resistant Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00446
EP  - e00413
VL  - 1
AB  - Here we present the complete genome sequences of two Helicobacter pylori rifampin-resistant
AB  - (Rif(r)) strains (Rif1 and Rif2). Rif(r) strains were obtained
AB  - by in vitro selection of H. pylori 26695 on agar plates with 20 microg/ml
AB  - rifampin. The genome data provide insights on the genomic diversity of H. pylori
AB  - under selection by rifampin.
ER  -

TY  - JOUR
AU  - Momynaliev, K.T.
AU  - Rogov, S.I.
AU  - Govorun, V.M.
TI  - Nucleotide correspondence between protein-coding sequences of Helicobacter pylori 26695 and J99 strains.
JO  - Mol. Biol. (Mosk)
PY  - 2005
SP  - 945
EP  - 951
VL  - 39
AB  - Comparison of open-reading frames (ORFs) H. pylori 26695 and J99 strains has been revealed
AB  - prevalence of nucleotide replacements as transitions (more than 3%) above transversions (less
AB  - than 1%). Prevalence of nucleotide transitions is caused by high speed of C : G to T : A
AB  - transitions in a coding strand of DNA (3.5-5.3%) and not coding strand (2.9-3.9%). The
AB  - correspondence rate of transversion (A --> C, A --> T, C --> A, C --> G, G --> C, G --> T, T
AB  - --> A and T --> G) did not exceed 0.84%. The highest correspondence frequency between C and T
AB  - was detected in ACGT-ATGT (28.3%) - the site of methylation by active methyltransferase
AB  - M.Hpy99XI in H. pylori 26695 and J99. Thus one can speculate that predominant transition
AB  - taking place in H. pylori is mutation of C into T, which is realized through cytosine
AB  - methylation-deamination mechanism.
ER  -

TY  - JOUR
AU  - Momynaliev, K.T.
AU  - Smirnova, O.V.
AU  - Kudryavtseva, L.V.
AU  - Govorun, V.M.
TI  - Comparative genome analysis of Helicobacter pylori strains.
JO  - Mol. Biol. (Mosk)
PY  - 2003
SP  - 529
EP  - 536
VL  - 37
AB  - DNA macroarrays were used to characterize 17 Helicobacter pylori strains isolated in four
AB  - geographic regions of Russia (Moscow, St.
AB  - Petersburg, Kazan, and Novosibirsk). Of all genes, 1272 (81%) proved to
AB  - occur in all strains and to constitute a functional core of the genome,
AB  - and 293 (18.7%) were strain-specific and greatly varied among the H.
AB  - pylori strains. Most (71%) of the latter had unknown functions; the
AB  - remainder included restriction-modification genes (3-9%), transposition
AB  - genes (2-4%), and genes coding for outer membrane proteins (2-4%). The
AB  - Russian H. pylori strains did not differ in genome organization or in
AB  - the number and distribution of strain-specific genes from strains
AB  - isolated in other countries.
ER  -

TY  - JOUR
AU  - Monastiriakos, S.K.
AU  - Doiron, K.M.
AU  - Siponen, M.I.
AU  - Cupples, C.G.
TI  - Functional interactions between the MutL and Vsr proteins of Escherichia coli are dependent on the N-terminus of Vsr.
JO  - DNA Repair
PY  - 2004
SP  - 639
EP  - 647
VL  - 3
AB  - The crystal structure of the Escherichia coli Vsr endonuclease bound to a C(T/G)AGG substrate
AB  - revealed that the DNA is held by a pincer composed of
AB  - a trio of aromatic residues which intercalate into the major groove, and
AB  - an N-terminus alpha helix which lies across the minor groove. We have
AB  - constructed an N-terminus truncation (Delta14) which removes most of the
AB  - alpha helix. The mutant is still fairly proficient in mediating very short
AB  - patch repair. However, its endonuclease activity is considerably reduced
AB  - and, in contrast to that of the wild type protein, cannot be stimulated by
AB  - MutL. We had shown previously that excess Vsr in vivo causes mutagenesis,
AB  - probably by inhibiting the participation of MutL in mismatch repair. The
AB  - Delta14 mutant has diminished mutagenicity. In contrast, four
AB  - enzymatically inactive mutants, with intact N-termini, are as mutagenic as
AB  - the wild type protein. On the basis of these results we suggest that MutL
AB  - causes a conformational change in the N-terminus of Vsr which enhances Vsr
AB  - activity, and that this functional interaction between Vsr and MutL
AB  - decreases the ability of MutL to carry out mismatch repair.
ER  -

TY  - JOUR
AU  - Monastyrskaya, G.S.
AU  - Fushan, A.A.
AU  - Abaev, I.V.
AU  - Filyukova, O.B.
AU  - Kostina, M.B.
AU  - Pecherskih, E.
AU  - Sverdlov, E.D.
TI  - Genome-wide comparison reveals great inter- and intraspecies variability in B. pseudomallei and B. mallei pathogens.
JO  - Res. Microbiol.
PY  - 2004
SP  - 781
EP  - 793
VL  - 155
AB  - Burkholderia mallei and B. pseudomallei, closely related Gram-negative
AB  - bacteria, are causative agents of serious infectious diseases of humans
AB  - and animals: glanders and melioidosis, respectively. Despite numerous
AB  - studies of these pathogens, the detailed mechanism of their pathogenesis
AB  - is still unknown. The problem is even more complicated due to natural
AB  - variability of B. pseudomallei and B. mallei strains, the understanding of
AB  - which is a prerequisite for rational design of tools for diagnostics,
AB  - prophylaxis and therapy of the diseases. Using a subtractive hybridization
AB  - technique, we compared the genomes of B. pseudomallei C-141 and B. mallei
AB  - C-5 strains. A subtracted library of DNA fragments specific for B.
AB  - pseudomallei C-141 and absent from B. mallei C-5 was obtained and
AB  - analyzed. A variety of differences have been detected and mapped on the
AB  - recently sequenced genome of B. pseudomallei K96243. A comparative
AB  - sequence analysis also revealed considerable genomic differences between
AB  - B. pseudomallei C-141 and B. mallei ATCC 23344 strains sequenced at The
AB  - Institute for Genomic Research (TIGR). We also observed significant
AB  - genomic differences between B. pseudomallei C-141 and B. pseudomallei
AB  - K96243. Some of the differential DNA fragments displayed similarity to
AB  - different mobile elements which have not yet been described for B.
AB  - pseudomallei, whereas the others matched various prophage components,
AB  - components of active transport systems, different enzymes and
AB  - transcription regulators. A substantial proportion of the differential
AB  - clones had no database matches either at the nucleotide or protein level.
AB  - The results provide evidence for great genome-wide variability of B.
AB  - pseudomallei, further confirmed by Southern blot analysis of various B.
AB  - pseudomallei strains. The data obtained can be useful for future
AB  - development of efficient diagnostic tools allowing rapid identification of
AB  - species, strains and isolates of B. mallei and B. pseudomallei.
ER  -

TY  - JOUR
AU  - Moncke-Buchner, E.
AU  - Rothenberg, M.
AU  - Reich, S.
AU  - Wagenfuhr, K.
AU  - Matsumura, H.
AU  - Terauchi, R.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Functional Characterization and Modulation of the DNA Cleavage Efficiency of Type III Restriction Endonuclease EcoP15I in Its Interaction with Two  Sites in the DNA Target.
JO  - J. Mol. Biol.
PY  - 2009
SP  - 1309
EP  - 1319
VL  - 387
AB  - EcoP15I is a Type III restriction endonuclease requiring the interaction with two inversely
AB  - oriented 5'-CAGCAG recognition sites for efficient DNA
AB  - cleavage. Diverse models have been developed to explain how enzyme
AB  - complexes bound to both sites move toward each other, DNA translocation,
AB  - DNA looping and simple diffusion along the DNA. Conflicting data also
AB  - exist about the impact of cofactor S-adenosyl-l-methionine (AdoMet), the
AB  - AdoMet analogue sinefungin and the bases flanking the DNA recognition
AB  - sequence on EcoP15I enzyme activity. To clarify the functional role of
AB  - these questionable parameters on EcoP15I activity and to optimize the
AB  - enzymatic reaction, we investigated the influence of cofactors, ionic
AB  - conditions, bases flanking the recognition sequence and enzyme
AB  - concentration. We found that AdoMet is not necessary for DNA cleavage.
AB  - Moreover, the presence of AdoMet dramatically impaired DNA cleavage due to
AB  - competing DNA methylation. Sinefungin neither had an appreciable effect on
AB  - DNA cleavage by EcoP15I nor compensated for the second recognition site.
AB  - Moreover, we discovered that adenine stretches on the 5' or 3' side of
AB  - CAGCAG led to preferred cleavage of this site. The length of the adenine
AB  - stretch was pivotal and had to be different on the two sides for most
AB  - efficient cleavage. In the absence of AdoMet and with enzyme in molar
AB  - excess over recognition sites, we observed minor cleavage at two
AB  - communicating DNA sites simultaneously. These results could also be
AB  - exploited in the high-throughput, quantitative transcriptome analysis
AB  - method SuperSAGE to optimize the crucial EcoP15I digestion step.
ER  -

TY  - JOUR
AU  - Mondo, S.J. et al.
TI  - Widespread adenine N6-methylation of active genes in fungi.
JO  - Nat. Genet.
PY  - 2017
SP  - 964
EP  - 968
VL  - 49
AB  - N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in
AB  - plant and animal genomes, but its prevalence and association with
AB  - genome function in other eukaryotic lineages remains poorly understood. Here we
AB  - report that abundant 6mA is associated with transcriptionally active genes in
AB  - early-diverging fungal lineages. Using single-molecule long-read sequencing of 16
AB  - diverse fungal genomes, we observed that up to 2.8% of all adenines were
AB  - methylated in early-diverging fungi, far exceeding levels observed in other
AB  - eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT
AB  - dinucleotides and was concentrated in dense methylated adenine clusters
AB  - surrounding the transcriptional start sites of expressed genes; its distribution
AB  - was inversely correlated with that of 5-methylcytosine. Our results show a
AB  - striking contrast in the genomic distributions of 6mA and 5-methylcytosine and
AB  - reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark
AB  - in eukaryotes.
ER  -

TY  - JOUR
AU  - Mondragon, E.
AU  - Maher, L.J. III
TI  - RNA aptamer inhibitors of a restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 7544
EP  - 7555
VL  - 43
AB  - Restriction endonucleases (REases) recognize and cleave short palindromic DNA sequences,
AB  - protecting bacterial cells against bacteriophage infection by
AB  - attacking foreign DNA. We are interested in the potential of folded RNA to mimic
AB  - DNA, a concept that might be applied to inhibition of DNA-binding proteins. As a
AB  - model system, we sought RNA aptamers against the REases BamHI, PacI and KpnI
AB  - using systematic evolution of ligands by exponential enrichment (SELEX). After 20
AB  - rounds of selection under different stringent conditions, we identified the 10
AB  - most enriched RNA aptamers for each REase. Aptamers were screened for binding and
AB  - specificity, and assayed for REase inhibition. We obtained eight high-affinity
AB  - (Kd approximately 12-30 nM) selective competitive inhibitors (IC50 approximately
AB  - 20-150 nM) for KpnI. Predicted RNA secondary structures were confirmed by in-line
AB  - attack assay and a 38-nt derivative of the best anti-KpnI aptamer was sufficient
AB  - for inhibition. These competitive inhibitors presumably act as KpnI binding site
AB  - analogs, but lack the primary consensus KpnI cleavage sequence and are not
AB  - cleaved by KpnI, making their potential mode of DNA mimicry fascinating.
AB  - Anti-REase RNA aptamers could have value in studies of REase mechanism and may
AB  - give clues to a code for designing RNAs that competitively inhibit DNA binding
AB  - proteins including transcription factors.
ER  -

TY  - JOUR
AU  - Mondy, S.
AU  - Lalouche, O.
AU  - Dessaux, Y.
AU  - Faure, D.
TI  - Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31.
JO  - Genome Announcements
PY  - 2013
SP  - e00653
EP  - e00613
VL  - 1
AB  - Agrobacterium tumefaciens strain WRT31 is a quorum-sensing signal-degrading bacterium that has
AB  - been isolated from the rhizosphere of tobacco plants. This
AB  - strain belongs to A. tumefaciens genomovar G1, is avirulent on various putative
AB  - host plants, devoid of Ti plasmid, and contains the blcC gene encoding a
AB  - gamma-butyrolactonase.
ER  -

TY  - JOUR
AU  - Mondy, S.
AU  - Lalouche, O.
AU  - Dessaux, Y.
AU  - Faure, D.
TI  - Genome Sequence of the Quorum-Sensing-Signal-Producing Nonpathogen Agrobacterium  tumefaciens Strain P4.
JO  - Genome Announcements
PY  - 2013
SP  - e00798
EP  - e00713
VL  - 1
AB  - Agrobacterium tumefaciens P4 is a quorum-sensing-signal-producing bacterium that  has been
AB  - isolated from the tobacco rhizosphere. This strain belongs to
AB  - genomospecies 1 of the A. tumefaciens complex; it is avirulent on various
AB  - putative host plants, devoid of the Ti plasmid, and contains a luxI homolog on
AB  - the At plasmid.
ER  -

TY  - JOUR
AU  - Mones, L.
AU  - Kulhanek, P.
AU  - Florian, J.
AU  - Simon, I.
AU  - Fuxreiter, M.
TI  - Probing the two-metal ion mechanism in the restriction endonuclease BamHI.
JO  - Biochemistry
PY  - 2007
SP  - 14514
EP  - 14523
VL  - 46
AB  - The choreography of restriction endonuclease catalysis is a long-standing paradigm in
AB  - molecular biology. Bivalent metal ions are
AB  - required almost for all PD..D/ExK type enzymes, but the number of
AB  - cofactors essential for the DNA backbone scission remained ambiguous.
AB  - On the basis of crystal structures and biochemical data for various
AB  - restriction enzymes, three models have been developed that assign
AB  - critical roles for one, two, or three metal ions during the
AB  - phosphodiester hydrolysis. To resolve this apparent controversy, we
AB  - investigated the mechanism of BamHI catalysis using quantum
AB  - mechanical/molecular mechanical simulation techniques and determined
AB  - the activation barriers of three possible pathways that involve a
AB  - Glu-113 or a neighboring water molecule as a general base or an
AB  - external nucleophile that penetrated from bulk solution. The extrinsic
AB  - mechanism was found to be the most favorable with an activation free
AB  - energy of 23.4 kcal/mol, in reasonable agreement with the experimental
AB  - data. On the basis of the effect of the individual metal ions on the
AB  - activation barrier, metal ion A was concluded to be pivotal for the
AB  - reaction, while the enzyme lacking metal ion B still has moderate
AB  - efficiency. Thus, we propose that the catalytic scheme of BamHI does
AB  - not involve a general base for nucleophile generation and requires one
AB  - obligatory metal ion for catalysis that stabilizes the attacking
AB  - nucleophile and coordinates it throughout the nucleophilic attack. Such
AB  - a model may also explain the variation in the number of metal ions in
AB  - the crystal structures and thus could serve as a framework for a
AB  - unified catalytic scheme of type II restriction endonucleases.
ER  -

TY  - JOUR
AU  - Mones, L.
AU  - Simon, I.
AU  - Fuxreiter, M.
TI  - Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
JO  - Biol. Chem.
PY  - 2007
SP  - 73
EP  - 78
VL  - 388
AB  - The number of metal ions required for phosphoryl transfer in restriction endonucleases is
AB  - still an unresolved question in molecular
AB  - biology. The two Ca2+ and Mn2+ ions observed in the pre- and
AB  - post-reactive complexes of BamHI conform to the classical two-metal ion
AB  - choreography. We probed the Mg2+ cofactor positions at the active site
AB  - of BamHI by molecular dynamics simulations with one and two metal ions
AB  - present and identified several catalytically relevant sites. These can
AB  - mark the pathway of a single ion during catalysis, suggesting its
AB  - critical role, while a regulatory function is proposed for a possible
AB  - second ion.
ER  -

TY  - JOUR
AU  - Mongodin, E.F. et al.
TI  - The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 18147
EP  - 18152
VL  - 102
AB  - Saturated thalassic brines are among the most physically demanding habitats on Earth: few
AB  - microbes survive in them. Salinibacter ruber is among these organisms and has been found
AB  - repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of
AB  - this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The
AB  - genome sequence suggests that this resemblance has arisen through convergence at the
AB  - physiological level (different genes producing similar overall phenotype) and the molecular
AB  - level (independent mutations yielding similar sequences or structures). Several genes and gene
AB  - clusters also derive by lateral transfer from (or may have been laterally transferred to)
AB  - haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and
AB  - three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The
AB  - impact of these modular adaptive elements on the cell biology and ecology of S. ruber is
AB  - substantial, affecting salt adaptation, bioenergetics, and photobiology.
ER  -

TY  - JOUR
AU  - Mongodin, E.F.
AU  - Hittle, L.L.
AU  - Nadendla, S.
AU  - Brinkman, C.C.
AU  - Xiong, Y.
AU  - Bromberg, J.S.
TI  - Complete Genome Sequence of a Strain of Bifidobacterium pseudolongum Isolated from Mouse Feces and Associated with Improved Organ Transplant Outcome.
JO  - Genome Announcements
PY  - 2017
SP  - e01089
EP  - e01017
VL  - 5
AB  - Here, we report the complete genome sequence of Bifidobacterium pseudolongum strain
AB  - UMB-MBP-01, isolated from the feces of C57BL/6J mice. This strain was
AB  - identified in microbiome profiling studies and associated with improved
AB  - transplant outcome in a murine model of cardiac heterotypic transplantation.
ER  -

TY  - JOUR
AU  - Mongodin, E.F.
AU  - Shapir, N.
AU  - Daugherty, S.C.
AU  - DeBoy, R.T.
AU  - Emerson, J.B.
AU  - Shvartsbeyn, A.
AU  - Radune, D.
AU  - Vamathevan, J.
AU  - Riggs, F.
AU  - Grinberg, V.
AU  - Khouri, H.M.
AU  - Wackett, L.P.
AU  - Nelson, K.E.
AU  - Sadowsky, M.J.
TI  - Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1.
JO  - PLoS Genet.
PY  - 2006
SP  - e214
EP  - e214
VL  - 2
AB  - Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial
AB  - genera found in soils. Member of the genus are metabolically and ecologically diverse and have
AB  - the ability to survive in environmentally harsh conditions for extended periods of time. The
AB  - genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an
AB  - atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and
AB  - two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over
AB  - 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a
AB  - putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting
AB  - niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia,
AB  - Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has
AB  - expanded its metabolic abilities by relying on the duplication of catabolic genes and by
AB  - funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded
AB  - pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be
AB  - due to its ability to survive under stressful conditions induced by starvation, ionizing
AB  - radiation, oxygen radicals, and toxic chemicals.
ER  -

TY  - JOUR
AU  - Moniruzzaman, M.
AU  - LeCleir, G.R.
AU  - Brown, C.M.
AU  - Gobler, C.J.
AU  - Bidle, K.D.
AU  - Wilson, W.H.
AU  - Wilhelm, S.W.
TI  - Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution.
JO  - Virology
PY  - 2014
SP  - 60
EP  - 70
VL  - 466-467
AB  - Aureococcus anophagefferens causes economically and ecologically destructive
AB  - "brown tides" in the United States, China and South Africa. Here we report the
AB  - 370,920bp genomic sequence of AaV, a virus capable of infecting and lysing A.
AB  - anophagefferens. AaV is a member of the nucleocytoplasmic large DNA virus (NCLDV)
AB  - group, harboring 377 putative coding sequences and 8 tRNAs. Despite being an
AB  - algal virus, AaV shows no phylogenetic affinity to the Phycodnaviridae family, to
AB  - which most algae-infecting viruses belong. Core gene phylogenies, shared gene
AB  - content and genome-wide similarities suggest AaV is the smallest member of the
AB  - emerging clade "Megaviridae". The genomic architecture of AaV demonstrates that
AB  - the ancestral virus had an even smaller genome, which expanded through gene
AB  - duplication and assimilation of genes from diverse sources including the host
AB  - itself - some of which probably modulate important host processes. AaV also
AB  - harbors a number of genes exclusive to phycodnaviruses - reinforcing the
AB  - hypothesis that Phycodna- and Mimiviridae share a common ancestor.
ER  -

TY  - JOUR
AU  - Monk, I.R.
AU  - Foster, T.J.
TI  - Genetic manipulation of Staphylococci-breaking through the barrier.
JO  - Front Cell Infect Microbiol
PY  - 2012
SP  - 49
EP  - 49
VL  - 2
AB  - Most strains of Staphylococcus aureus and Staphylococcus epidermidis possess a strong
AB  - restriction barrier that hinders exchange of DNA. Recently, major advances have been made in
AB  - identifying and characterizing the restriction-modification (RM) systems involved. In
AB  - particular a novel type IV restriction enzyme that recognizes cytosine methylated DNA has been
AB  - shown to be the major barrier to transfer of plasmid DNA from Escherichia coli into S. aureus
AB  - and S. epidermidis. While the conserved type I RM system provides a further barrier. Here we
AB  - review the recent advances in understanding of restriction systems in staphylococci and
AB  - highlight how this has been exploited to improve our ability to manipulate genetically
AB  - previously untransformable strains.
ER  -

TY  - JOUR
AU  - Monk, I.R.
AU  - Shah, I.M.
AU  - Xu, M.
AU  - Tan, M.W.
AU  - Foster, T.J.
TI  - Transforming the Untransformable: Application of Direct Transformation To Manipulate Genetically Staphylococcus aureus and Staphylococcus epidermidis.
JO  - MBio
PY  - 2012
SP  - e00277
EP  - e00277
VL  - 3
AB  - The strong restriction barrier present in Staphylococcus aureus and Staphylococcus epidermidis
AB  - has limited functional genomic analysis to a
AB  - small subset of strains that are amenable to genetic manipulation.
AB  - Recently, a conserved type IV restriction system termed SauUSI (which
AB  - specifically recognizes cytosine methylated DNA) was identified as the
AB  - major barrier to transformation with foreign DNA. Here we have
AB  - independently corroborated these findings in a widely used laboratory
AB  - strain of S. aureus. Additionally, we have constructed a DNA cytosine
AB  - methyltransferase mutant in the high-efficiency Escherichia coli
AB  - cloning strain DH10B (called DC10B). Plasmids isolated from DC10B can
AB  - be directly transformed into clinical isolates of S. aureus and S.
AB  - epidermidis. We also show that the loss of restriction (both type I and
AB  - IV) in an S. aureus USA300 strain does not have an impact on virulence.
AB  - Circumventing the SauUSI restriction barrier, combined with an improved
AB  - deletion and transformation protocol, has allowed the genetic
AB  - manipulation of previously untransformable strains of these important
AB  - opportunistic pathogens.
AB  - IMPORTANCE Staphylococcal infections place a huge burden on the
AB  - health care sector due both to their severity and also to the economic
AB  - impact of treating the infections because of prolonged hospitalization.
AB  - To improve the understanding of Staphylococcus aureus and
AB  - Staphylococcus epidermidis infections, we have developed a series of
AB  - improved techniques that allow the genetic manipulation of strains that
AB  - were previously refractory to transformation. These developments will
AB  - speed up the process of mutant construction and increase our
AB  - understanding of these species as a whole, rather than just a small
AB  - subset of strains that could previously be manipulated.
ER  -

TY  - JOUR
AU  - Monk, I.R.
AU  - Tree, J.J.
AU  - Howden, B.P.
AU  - Stinear, T.P.
AU  - Foster, T.J.
TI  - Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages.
JO  - MBio
PY  - 2015
SP  - e00308
EP  - e00315
VL  - 6
AB  - Staphylococcus aureus is a prominent global nosocomial and community-acquired bacterial
AB  - pathogen. A strong restriction barrier presents a major hurdle for the
AB  - introduction of recombinant DNA into clinical isolates of S. aureus. Here, we
AB  - describe the construction and characterization of the IMXXB series of Escherichia
AB  - coli strains that mimic the type I adenine methylation profiles of S. aureus
AB  - clonal complexes 1, 8, 30, and ST93. The IMXXB strains enable direct,
AB  - high-efficiency transformation and streamlined genetic manipulation of major S.
AB  - aureus lineages. IMPORTANCE: The genetic manipulation of clinical S. aureus
AB  - isolates has been hampered due to the presence of restriction modification
AB  - barriers that detect and subsequently degrade inappropriately methylated DNA.
AB  - Current methods allow the introduction of plasmid DNA into a limited subset of S.
AB  - aureus strains at high efficiency after passage of plasmid DNA through the
AB  - restriction-negative, modification-proficient strain RN4220. Here, we have
AB  - constructed and validated a suite of E. coli strains that mimic the adenine
AB  - methylation profiles of different clonal complexes and show high-efficiency
AB  - plasmid DNA transfer. The ability to bypass RN4220 will reduce the cost and time
AB  - involved for plasmid transfer into S. aureus. The IMXXB series of E. coli strains
AB  - should expedite the process of mutant construction in diverse genetic backgrounds
AB  - and allow the application of new techniques to the genetic manipulation of S.
AB  - aureus.
ER  -

TY  - JOUR
AU  - Monnat, R.J. Jr.
AU  - Hackmann, A.F.M.
AU  - Cantrell, M.A.
TI  - Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1999
SP  - 88
EP  - 93
VL  - 255
AB  - We have determined the ability of two well-characterized eukaryotic homing endonucleases,
AB  - I-PpoI from the myxomycete Physarum polycephalum and I-CreI from the green alga Chlamydomonas
AB  - reinhardtii, to generate site-specific DNA double-strand breaks in human cells. These 18-kDa
AB  - proteins cleave highly conserved 15- or 24-bp rDNA homing sites in their respective hosts to
AB  - generate homogeneous 4-base, 3' ends that initiate target intron transposition or "homing."
AB  - We show that both endonucleases can be expressed in human cells and can generate site-specific
AB  - DNA double-strand breaks in 28S rDNA and homing site plasmids. These endonuclease-induced
AB  - breaks can be repaired in vivo, although break repair is mutagenic with the frequent
AB  - generation of short deletions or insertions. I-PpoI and I-CreI should be useful for analyzing
AB  - DNA double-strand break repair in human cells and rDNA.
ER  -

TY  - JOUR
AU  - Monnerat, M.-P.
AU  - Thiaucourt, F.
AU  - Nicolet, J.
AU  - Frey, J.
TI  - Comparative analysis of the lppA locus in Mycoplasma capricolum subsp. capricolum and Mycoplasma capricolum subsp. capripneumoniae.
JO  - Vet. Microbiol.
PY  - 1999
SP  - 157
EP  - 172
VL  - 69
AB  - The lppA gene, encoding the lipoprotein named LppA[Mcaca] was characterised in Mycoplasma
AB  - capricolum subsp. capricolum.  It encodes a lipoprotein with an apparent molecular mass of 57
AB  - kDa as determined by SDS-PAGE. Using antibodies directed against recombinant LppA[Mcaca], we
AB  - showed the expression of this lipoprotein in all M. capricolum subsp. capricolum by immunoblot
AB  - analysis. The serum did not cross-react with other members of the Mycoplasma mycoides cluster,
AB  - hence showing that LppA[Mcaca] was antigenically specific to M. capricolum subsp. capricolum.
AB  - The lppA gene was conserved within the subspecies and was used for the development of a
AB  - specific PCR assay for the identification of M. capricolum subsp. capricolum.
AB  - The taxonomically related Mycoplasma capricolum subsp. capripneumoniae (F38) was found to
AB  - contain an lppA-pseudo-gene.  It showed high similarity to functional lppA genes of other
AB  - mycoplasmas in the M. mycoides cluster. However, it contained interrupted open reading frames.
AB  - Moreover, the nucleotide sequence of the lppA pseudo-genes in different strains of M.
AB  - capricolum subsp. capripneumoniae were quite variable. Interestingly, the lppA pseudo-gene had
AB  - a size similar to that of the functional lppA genes of other mycoplasmas of the M. mycoides
AB  - cluster and occupied the same genomic location as the latter ones in the vicinity of the mtlD
AB  - genes. This study showed that all members of the M. mycoides cluster contain each a species-,
AB  - subspecies- respectively type- specific lppA gene analogue which encodes a lipoprotein that
AB  - has structural and functional relationship to the surface lipoprotein LppA [MmymySC],
AB  - previously named P72, of M. mycoides subsp mycoides SC, with the exceptionof M. capricolum
AB  - subsp. capripneumoniae which seems not to express an LppA analogue.
ER  -

TY  - JOUR
AU  - Monnerat, M.P.
AU  - Thiaucourt, F.
AU  - Poveda, J.B.
AU  - Nicolet, J.
AU  - Frey, J.
TI  - Genetic and serological analysis of lipoprotein LppA in Mycoplasma mycoides subsp. mycoides LC and Mycoplasma mycoides subsp. capri.
JO  - Clin. Diagn. Lab. Immunol.
PY  - 1999
SP  - 224
EP  - 230
VL  - 6
AB  - The genes encoding the 62-kDa lipoproteins from the Mycoplasma mycoides subsp. mycoides
AB  - large-colony type (LC) strain Y-goat and the M. mycoides subsp. capri strain PG3 were cloned
AB  - and analyzed by sequencing. These two lipoproteins have been named LppA[MmymyLC] and
AB  - LppA[Mmyca], and their corresponding genes have been named lppA[MmymyLC] and lppA[Mmyca],
AB  - respectively. The nucleotide and deduced amino acid sequences of these two lipoproteins showed
AB  - a very high degree of similarity between these two mycoplasmas. Given the sequence data,
AB  - LppA seems to fulfill the same structural functions as the previously described major
AB  - lipoproteins P72 of M. mycoides subsp. mycoides small-colony type and P67 of the Mycoplasma
AB  - species bovine group 7. Based on lppA gene sequences of M. mycoides subsp. mycoides LC and M.
AB  - mycoides subsp. capri type strains, a specific PCR assay was developed so that it amplified
AB  - this gene in all field strains of the two species analyzed in this study but not in the other
AB  - members of the M. mycoides cluster. Analysis of the PCR-amplified lppA genes with frequently
AB  - cutting restriction
AB  - enzymes showed a certain degree of genetic variability which, however, did not cluster the two
AB  - subspecies. This PCR therefore allows a rapid identification of M. mycoides subsp. mycoides LC
AB  - and M. mycoides subsp. capri but does not distinguish between these two closely related
AB  - subspecies. LppA was expressed in Escherichia coli K-12 and used for the production of
AB  - polyclonal mouse antiserum. Antibodies against recombinant LppA[MmymyLC] reacted with a 62 kDa
AB  - protein in all M. mycoides subsp. mycoides LC and M. mycoides subsp. capri type strains and
AB  - field strains tested but not with the other members of the M. mycoides cluster, thus showing
AB  - the antigenic specificity of LppA and further supporting the concept that a close relationship
AB  - exists between these two mycoplasmas.
ER  -

TY  - JOUR
AU  - Monnet, C.
AU  - Loux, V.
AU  - Bento, P.
AU  - Gibrat, J.F.
AU  - Straub, C.
AU  - Bonnarme, P.
AU  - Landaud, S.
AU  - Irlinger, F.
TI  - Genome Sequence of Corynebacterium casei UCMA 3821, Isolated from a Smear-Ripened Cheese.
JO  - J. Bacteriol.
PY  - 2012
SP  - 738
EP  - 739
VL  - 194
AB  - Corynebacterium casei is one of the most prevalent species present on the surfaces of
AB  - smear-ripened cheeses, where it contributes to the production
AB  - of the desired organoleptic properties. Here, we report the draft genome
AB  - sequence of Corynebacterium casei UCMA 3821 to provide insights into its
AB  - physiology.
ER  -

TY  - JOUR
AU  - Monno, S.
AU  - Sugiura, H.
AU  - Yamashita, H.
AU  - Kato, Y.
AU  - Morimitu, K.
AU  - Imajoh, M.
TI  - Draft Genome Sequence of Vibrio harveyi Strain GAN1709, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00611
EP  - e00618
VL  - 6
AB  - Vibrio harveyi strain GAN1709 was isolated from a diseased greater amberjack farmed in Nomi
AB  - Bay, Japan. Here, we report the draft genome sequence of this
AB  - strain, which comprises 6,265,473 bp, with a G+C content of 44.8%.
ER  -

TY  - JOUR
AU  - Monsieurs, P.
AU  - Mijnendonckx, K.
AU  - Provoost, A.
AU  - Venkateswaran, K.
AU  - Ott, C.M.
AU  - Leys, N.
AU  - Van Houdt, R.
TI  - Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment.
JO  - Genome Announcements
PY  - 2014
SP  - e00719
EP  - e00714
VL  - 2
AB  - Cupriavidus metallidurans NA1, NA4, and NE12 were isolated from space and
AB  - spacecraft-associated environments. Here, we report their draft genome sequences
AB  - with the aim of gaining insight into their potential to adapt to these
AB  - environments.
ER  -

TY  - JOUR
AU  - Monsieurs, P.
AU  - Mijnendonckx, K.
AU  - Provoost, A.
AU  - Venkateswaran, K.
AU  - Ott, C.M.
AU  - Leys, N.
AU  - Van Houdt, R.
TI  - Draft Genome Sequences of Ralstonia pickettii Strains SSH4 and CW2, Isolated from Space Equipment.
JO  - Genome Announcements
PY  - 2014
SP  - e00887
EP  - e00814
VL  - 2
AB  - Ralstonia pickettii SSH4 and CW2 were isolated from space equipment. Here, we report their
AB  - draft genome sequences with the aim of gaining insight into their
AB  - potential to adapt to these environments.
ER  -

TY  - JOUR
AU  - Monsieurs, P.
AU  - Provoost, A.
AU  - Mijnendonckx, K.
AU  - Leys, N.
AU  - Gaudreau, C.
AU  - Van Houdt, R.
TI  - Genome Sequence of Cupriavidus metallidurans Strain H1130, Isolated from an Invasive Human Infection.
JO  - Genome Announcements
PY  - 2013
SP  - e01051
EP  - e01013
VL  - 1
AB  - Cupriavidus metallidurans H1130 was repeatedly isolated from different blood culture sets
AB  - taken from a patient suffering from significant nosocomial
AB  - septicemia. Here, we announce the H1130 genome sequence for use in comparative
AB  - analyses and for exploring the adaptation and pathogenic potential of this
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Monson, R.E.
AU  - Honger, J.
AU  - Rawlinson, A.
AU  - Salmond, G.P.C.
TI  - Draft Genome Sequences of Enterobacter cloacae Strains CAPREx E7 and CAPREx E2-2.
JO  - Genome Announcements
PY  - 2017
SP  - e00488
EP  - e00417
VL  - 5
AB  - Enterobacter cloacae strains CAPREx E7 and CAPREx E2-2 were isolated from Ghanaian yams at a
AB  - London market. The draft genome sequences indicate that the
AB  - two strains are similar, with genomes of 5,042,838 and 5,039,930 bp and 56.19%
AB  - and 55.05% G+C content, respectively. Both strains encoded three different
AB  - beta-lactamases, including one of the AmpC family.
ER  -

TY  - JOUR
AU  - Monte, D.F.
AU  - Fernandes, M.R.
AU  - Cerdeira, L.
AU  - de Souza, T.A.
AU  - Mem, A.
AU  - Franco, B.D.G.M.
AU  - Landgraf, M.
AU  - Lincopan, N.
TI  - Draft Genome Sequences of Colistin-Resistant MCR-1-Producing Escherichia coli ST1850 and ST74 Strains Isolated from Commercial Chicken Meat.
JO  - Genome Announcements
PY  - 2017
SP  - e00329
EP  - e00317
VL  - 5
AB  - We present here the draft genome sequences of two colistin-resistant mcr-1-carrying
AB  - Escherichia coli strains belonging to sequence type 74 (ST74) and
AB  - ST1850, isolated from commercial chicken meat in Brazil. Assembly of this draft
AB  - genome resulted in 5,022,083 and 4,950,681 bp, respectively, revealing the
AB  - presence of the IncX4 plasmid-mediated mcr-1 gene responsible for resistance to
AB  - colistin.
ER  -

TY  - JOUR
AU  - Montecillo, A.D.
AU  - Raymundo, A.K.
AU  - Papa, I.A.
AU  - Aquino, G.M.B.
AU  - Rosana, A.R.R.
TI  - Complete Genome Sequence of Rhizobium sp. Strain 11515TR, Isolated from Tomato Rhizosphere in the Philippines.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00903
EP  - e00918
VL  - 7
AB  - Rhizobium sp. strain 11515TR was isolated from the rhizosphere of tomato in Laguna,
AB  - Philippines. The 7.07-Mb complete genome comprises three replicons, one
AB  - chromosome, and two plasmids, with a G+C content of 59.4% and 6,720
AB  - protein-coding genes. The genome encodes gene clusters supporting rhizosphere
AB  - processes, plant symbiosis, and secondary bioactive metabolites.
ER  -

TY  - JOUR
AU  - Monteilhet, C.
AU  - Dziadkowiec, D.
AU  - Szczepanek, T.
AU  - Lazowska, J.
TI  - Purification and characterization of the DNA cleavage and recognition site of I-ScaI mitochondrial group I intron encoded endonuclease produced in Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 1245
EP  - 1251
VL  - 28
AB  - The second intron in the mitochondrial cytb gene of Saccharomyces capensis, belonging to group
AB  - I, encodes a 280 amino acid protein containing two LAGLIDADG motifs. Genetic and molecular
AB  - studies have previously shown that this protein has a dual function in the wild-type strain.
AB  - It acts as a specific homing endonuclease I-ScaI promoting intron mobility and as a maturase
AB  - promoting intron splicing. Here we describe the synthesis of a universal code equivalent to
AB  - the mitochondrial sequence coding for this protein and the in vitro characterization of I-ScaI
AB  - endonuclease activity, using a truncated mutant form of the protein p28bi2 produced in
AB  - Escherichia coli. We have also determined the cleavage pattern as well as the recognition site
AB  - of p28bi2. It was found that p28bi2 generates a double-strand cleavage downstream from the
AB  - intron insertion site with 4 nt long 3'-overhangs. Mutational analysis of the DNA target site
AB  - shows that p28bi2 recognizes a 16-19 bp sequence from positions -11 to +8 with respect to the
AB  - intron insertion site.
ER  -

TY  - JOUR
AU  - Monteilhet, C.
AU  - Perrin, A.
AU  - Thierry, A.
AU  - Colleaux, L.
AU  - Dujon, B.
TI  - Purification and characterization of the in vitro activity of I-Sce I, a novel and highly specific endonuclease encoded by a group I intron.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1407
EP  - 1413
VL  - 18
AB  - Group I intron encoded proteins represent a novel class of site specific double
AB  - strand endonucleases.  The endonuclease activity of this class of proteins has
AB  - been first demonstrated in vivo for I-Sce I which is encoded  by a
AB  - mitochondrial intron of Saccharomyces cerevisiae.  Assays using crude cell
AB  - extracts have shown that I-Sce I can be used in vitro as a restriction
AB  - endonuclease potentially useful for recombinant DNA technology owing to its
AB  - large recognition sequence (18 nucleotides).  We report here the purification
AB  - and the first detailed analysis of the in vitro activity and properties of
AB  - I-Sce I.
ER  -

TY  - JOUR
AU  - Monteiro-Vitorello, C.B. et al.
TI  - The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.
JO  - Mol. Plant Microbe Interact.
PY  - 2004
SP  - 827
EP  - 836
VL  - 17
AB  - The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and
AB  - affects sugarcane worldwide, was determined. The
AB  - single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb
AB  - in length with a GC content of 68% and 2,044 predicted open reading
AB  - frames. The analysis also revealed 307 predicted pseudogenes, which is
AB  - more than any bacterial plant pathogen sequenced to date. Many of these
AB  - pseudogenes, if functional, would likely be involved in the degradation of
AB  - plant heteropolysaccharides, uptake of free sugars, and synthesis of amino
AB  - acids. Although L. xyli subsp. xyli has only been identified colonizing
AB  - the xylem vessels of sugarcane, the numbers of predicted regulatory genes
AB  - and sugar transporters are similar to those in free-living organisms. Some
AB  - of the predicted pathogenicity genes appear to have been acquired by
AB  - lateral transfer and include genes for cellulase, pectinase, wilt-inducing
AB  - protein, lysozyme, and desaturase. The presence of the latter may
AB  - contribute to stunting, since it is likely involved in the synthesis of
AB  - abscisic acid, a hormone that arrests growth. Our findings are consistent
AB  - with the nutritionally fastidious behavior exhibited by L. xyli subsp.
AB  - xyli and suggest an ongoing adaptation to the restricted ecological niche
AB  - it inhabits.
ER  -

TY  - JOUR
AU  - Monteiro-Vitorello, C.B.
AU  - Zerillo, M.M.
AU  - Van Sluys, M.A.
AU  - Camargo, L.E.
AU  - Kitajima, J.P.
TI  - Complete Genome Sequence of Leifsonia xyli subsp. cynodontis Strain DSM46306, a Gram-Positive Bacterial Pathogen of Grasses.
JO  - Genome Announcements
PY  - 2013
SP  - e00915
EP  - e00913
VL  - 1
AB  - We announce the complete genome sequence of Leifsonia xyli subsp. cynodontis, a vascular
AB  - pathogen of Bermuda grass. The species also comprises Leifsonia xyli
AB  - subsp. xyli, a sugarcane pathogen. Since these two subspecies have genome
AB  - sequences available, a comparative analysis will contribute to our understanding
AB  - of the differences in their biology and host specificity.
ER  -

TY  - JOUR
AU  - Montenegro, M.A.
AU  - Pawlek, B.
AU  - Behrens, B.
AU  - Trautner, T.A.
TI  - Restriction and modification in Bacillus subtilis:  expression of the cloned methyltransferase gene from B. subtilis phage SPR in E. coli and B. subtilis.
JO  - Mol. Gen. Genet.
PY  - 1983
SP  - 17
EP  - 20
VL  - 189
AB  - Expression of the SPR methyltransferase gene from B. subtilis phage SPR cloned
AB  - into lambda and SPP1 was studied by analyzing the sensitivity of the hybrid
AB  - phage DNAs to restriction by the enzymes HaeIII, MspI, and HpaII.  The
AB  - following results were obtained:  (1) The genes were expressed both in the
AB  - homologous (B. subtilis) and heterologous (E. coli) host. (2) The specificity
AB  - of the expression of the cloned gene was identical to that of the gene in SPR.
AB  - (3) Expression depended on the orientation of the cloned segment within the
AB  - vector DNAs suggesting that vector promoters were involved in transcription.
AB  - The coding strand of the cloned DNA was identified through hybridization with
AB  - SPR mRNA.
ER  -

TY  - JOUR
AU  - Montes, C.
AU  - Altimira, F.
AU  - Canchignia, H.
AU  - Castro, A.
AU  - Sanchez, E.
AU  - Miccono, M.
AU  - Tapia, E.
AU  - Sequeida, A.
AU  - Valdes, J.
AU  - Tapia, P.
AU  - Gonzalez, C.
AU  - Prieto, H.
TI  - A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 76
EP  - 76
VL  - 11
AB  - A new plant commensal Pseudomonas veronii isolate (strain R4) was identified from a Xiphinema
AB  - index biocontrol screen. Isolated from grapevine roots from vineyards
AB  - in central Chile, the strain R4 exhibited a slower yet equivalently effective
AB  - nematicide activity as the well-characterized P. protegens CHA0. Whole genome
AB  - sequencing of strain R4 and comparative analysis among the available Pseudomonas
AB  - spp. genomes allowed for the identification of gene clusters that encode putative
AB  - extracellular proteases and lipase synthesis and secretion systems, which are
AB  - proposed to mediate-at least in part-the observed nematicidal activity. In
AB  - addition, R4 strain presented relevant gene clusters related to metal tolerance,
AB  - which is typical in P. veronii. Bioinformatics analyses also showed gene clusters
AB  - associated with plant growth promoting activity, such as indole-3-acetic acid
AB  - synthesis. In addition, the strain R4 genome presented a metabolic gene clusters
AB  - associated with phosphate and ammonia biotransformation from soil, which could
AB  - improve their availability for plants.
ER  -

TY  - JOUR
AU  - Montor-Antonio, J.J.
AU  - Sachman-Ruiz, B.
AU  - Lozano, L.
AU  - Del Moral, S.
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens JJC33M, Isolated from Sugarcane Soils in the Papaloapan Region, Mexico.
JO  - Genome Announcements
PY  - 2015
SP  - e01519
EP  - e01514
VL  - 3
AB  - Bacillus amyloliquefaciens strain JJC33M is a bacterium that produces alpha-amylase (EC
AB  - 3.2.1.1) and was isolated from sugarcane soil. Its estimated
AB  - genome size is 3.96 Mb, and it harbors 4,048 coding genes (CDSs).
ER  -

TY  - JOUR
AU  - Moodley, A.
AU  - Riley, M.C.
AU  - Kania, S.A.
AU  - Guardabassi, L.
TI  - Genome Sequence of Staphylococcus pseudintermedius Strain E140, an ST71 European-Associated Methicillin-Resistant Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e0020712
EP  - e0020712
VL  - 1
AB  - We report the first genome sequence of the methicillin-resistant Staphylococcus
AB  - pseudintermedius (MRSP) strain E140, isolated from a canine bite wound infection
AB  - in Denmark. This strain represents the dominant clonal lineage associated with
AB  - canine MRSP infections in Europe.
ER  -

TY  - JOUR
AU  - Moon, B.J.
AU  - Kim, S.K.
AU  - Kim, N.H.
AU  - Kwon, O.S.
TI  - Synthesis and characterization of dodecanucleotides containing the XhoI recognition sequence with a phosphorothioate group at the cleavage site.
JO  - Bull. Korean Chem. Soc.
PY  - 1996
SP  - 1031
EP  - 1036
VL  - 17
AB  - The synthesis and characterization of diastereomeric dodecanucleotides, d[GATCp(s)TCGAGATC],
AB  - containing the recognition sequence of the XhoI restriction endonuclease with a
AB  - phosphorothioate internucleotidic linkage at the cleavage sites are described.  Rp and Sp
AB  - forms of each diastereomerically pure dinucleoside phosphorothioates d[Cp(S)T] were
AB  - presynthesized and used for the addition to the growing oligonucleotide chain as a block.  The
AB  - stereochemistry of dinucleoside phosphorothioate was assigned by 31P NMR spectroscopy, enzyme
AB  - digestion, and reverse-phase HPLC.  XhoI restriction endonuclease cuts only theRp diastereomer
AB  - d[GATCp(s)TCGAGATC].  The rate of hydrolysis is slower than that of the unmodified dodecamer
AB  - d[GATCTCGAGATC].  The phosphorothioate nucleotide is used for determination of the
AB  - stereochemical course of the XhoI catalyzed reaction.
ER  -

TY  - JOUR
AU  - Moon, B.J.
AU  - Vipond, I.B.
AU  - Halford, S.E.
TI  - Site-directed mutagenesis studies with restriction endonuclease EcoRV to identify the role of Ile91 in recognition and catalysis.
JO  - J. Biochem. Mol. Biol.
PY  - 1996
SP  - 99
EP  - 104
VL  - 29
AB  - Site-directed substitutions were made to change the Ile91 of restriction endonuclease EcoRV to
AB  - either Val, Ala or Gly to identify the role of Ile91 in recognition and catalysis, since
AB  - substitution of Ile91 with Leu afforded dramatic effects on the activity and properties of
AB  - restriction endonuclease EcoRV.  These changes alter the size of the hydrophobic side chain at
AB  - position 91 and thus might have revealed the reason for the altered phenotype of Ile91 Leu.
AB  - However, the properties of Ile91Val and Ile91Ala mutants were much like wild type EcoRV, in
AB  - both activity and metal ion preference.  Ile91Gly had very little activity with either Mg2+ or
AB  - Mn2- as cofactors.  To try to understand the unusual Mn2+ profile of the Ile91Leu mutant, two
AB  - double mutants, Ile91Leu;Asp90Asn and Ile91Leu;Glu45Met were created.  Both double mutants
AB  - were seriously disabled by the second amino acid change. Ile91Leu;Glu45Met had some residual
AB  - activity in the Mn2+ reaction buffer, whereas the Ile91Leu;Asp90Asn displayed no detectable
AB  - activity.
ER  -

TY  - JOUR
AU  - Moon, B.J.
AU  - Vipond, I.B.
AU  - Halford, S.E.
TI  - Site-directed mutagenesis of Ile91 of restriction endonuclease EcoRV: Dramatic consequences on the activity and the properties of the enzyme.
JO  - J. Biochem. Mol. Biol.
PY  - 1996
SP  - 17
EP  - 21
VL  - 29
AB  - Ile91 of restriction endonuclease EcoRV, which has not been known to take part directly in
AB  - catalytic activity, was substituted with Leu by site-directed mutagenesis.  The Ile91Leu
AB  - mutant shows over 1000-fold less activity than the wild type EcoRV under standard reaction
AB  - condition.  The metal ion dependency of the reaction was altered.  In contrast to the wild
AB  - type EcoRV, the mutant prefers Mn2+ to Mg2+ as the cofactor.  In Mn2+ buffer the mutant is as
AB  - active as the wild type enzyme in Mg2+ buffer.  Like the wild type enzyme, the mutant shows an
AB  - unspecific binding of DNA in gel shift experiments.  In contrast to the wild type enzyme, the
AB  - mutant did not cleave at noncognate sites of DNA under star condition.  Note: this paper was
AB  - published without Dr. S. Halford's knowledge.
ER  -

TY  - JOUR
AU  - Moon, D.C.
AU  - Kim, B.Y.
AU  - Tamang, M.D.
AU  - Nam, H.M.
AU  - Jang, G.C.
AU  - Jung, S.C.
AU  - Lee, H.S.
AU  - Park, Y.H.
AU  - Lim, S.K.
TI  - Genome Sequence of a Unique t2247-ST692-III Livestock-Associated Methicillin-Resistant Staphylococcus aureus Strain from Chicken Carcass.
JO  - Genome Announcements
PY  - 2016
SP  - e00026
EP  - e00016
VL  - 4
AB  - We report the draft genome sequence of a novel livestock-associated t2247-ST692-III
AB  - methicillin-resistant Staphylococcus aureus strain designated
AB  - K12S0375, which was isolated from a chicken carcass in South Korea. The K12S0375
AB  - strain contains uncommon genes, including antimicrobial resistance genes (tetL
AB  - and tetS) and leukotoxin (lukED), and the genomic distance indicates a single
AB  - lineage in a genome-based phylogenetic tree compared with 459 S. aureus genome
AB  - sequences. This genome sequence will contribute to understanding epidemiological
AB  - and genomic features of the ST692 lineage, including antimicrobial resistance and
AB  - virulence genes.
ER  -

TY  - JOUR
AU  - Moon, W.J.
AU  - Cho, J.-Y.
AU  - Chae, Y.K.
TI  - Recombinant expression, purification, and characterization of XorKII: A restriction endonuclease from Xanthomonas oryzae pv. oryzae.
JO  - Protein Expr. Purif.
PY  - 2008
SP  - 230
EP  - 234
VL  - 62
AB  - An endonuclease from Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, XorKII, was
AB  - recombinantlyproduced in Escherichia coli by applying the stationary state induction method,
AB  - which was necessary toprevent the unwanted lysis of E. coli cells. XorKII was purified by
AB  - immobilized metal affinity chromatographyon an FPLC system. The yield was 3.5 mg of XorKII per
AB  - liter of LB medium. The purified recombinantXorKII showed that it recognized and cleaved to
AB  - the same site as PstI. It behaved as a dimer as evidenced
AB  - by the size exclusion chromatography. The specific activity of the purified XorKII was
AB  - determined to be31,300 U/mg. The enzyme activity was monitored by cleaving lambda DNA or YEp24
AB  - plasmid as substrates. The enzyme was the most active at 10 mM Tris-HCl pH 7.0, 10 mM MgCl2, 1
AB  - mM dithiothreitol
AB  - at 37 oC. XorKII was easily inactivated by heating at 65 oC for 5 min, but retained most of
AB  - the original activity after incubation at 37oC for 24 h.
ER  -

TY  - JOUR
AU  - Moore, A.M.
AU  - Patel, S.
AU  - Forsberg, K.J.
AU  - Wang, B.
AU  - Bentley, G.
AU  - Razia, Y.
AU  - Qin, X.
AU  - Tarr, P.I.
AU  - Dantas, G.
TI  - Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes.
JO  - PLoS ONE
PY  - 2013
SP  - E78822
EP  - E78822
VL  - 8
AB  - Emerging antibiotic resistance threatens human health. Gut microbes are an
AB  - epidemiologically important reservoir of resistance genes (resistome), yet prior
AB  - studies indicate that the true diversity of gut-associated resistomes has been
AB  - underestimated. To deeply characterize the pediatric gut-associated resistome, we
AB  - created metagenomic recombinant libraries in an Escherichia coli host using fecal
AB  - DNA from 22 healthy infants and children (most without recent antibiotic
AB  - exposure), and performed functional selections for resistance to 18 antibiotics
AB  - from eight drug classes. Resistance-conferring DNA fragments were sequenced
AB  - (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS
AB  - computational pipeline. Resistance to 14 of the 18 antibiotics was found in
AB  - stools of infants and children. Recovered genes included chloramphenicol
AB  - acetyltransferases, drug-resistant dihydrofolate reductases, rRNA
AB  - methyltransferases, transcriptional regulators, multidrug efflux pumps, and every
AB  - major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline
AB  - resistance protein. Many resistance-conferring sequences were mobilizable; some
AB  - had low identity to any known organism, emphasizing cryptic organisms as
AB  - potentially important resistance reservoirs. We functionally confirmed three
AB  - novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside
AB  - resistance, and two tetracycline-resistance proteins nearly identical to a
AB  - bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the
AB  - first report to our knowledge of resistance to folate-synthesis inhibitors
AB  - conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway).
AB  - This functional metagenomic survey of gut-associated resistomes, the largest of
AB  - its kind to date, demonstrates that fecal resistomes of healthy children are far
AB  - more diverse than previously suspected, that clinically relevant resistance genes
AB  - are present even without recent selective antibiotic pressure in the human host,
AB  - and that cryptic gut microbes are an important resistance reservoir. The observed
AB  - transferability of gut-associated resistance genes to a gram-negative (E. coli)
AB  - host also suggests that the potential for gut-associated resistomes to threaten
AB  - human health by mediating antibiotic resistance in pathogens warrants further
AB  - investigation.
ER  -

TY  - JOUR
AU  - Moore, G.P.
AU  - Moore, A.R.
TI  - The average spacing of restriction enzyme recognition sites in DNA.
JO  - J. Theor. Biol.
PY  - 1982
SP  - 165
EP  - 169
VL  - 98
AB  - The discovery of naturally occurring enzymes which cleave DNA at sites specific to particular
AB  - nucleotide sequences has had a great impact on molecular biology.  The function of these
AB  - enzymes in vivo is to protect bacterial cells from viral invasion by degradation of foreign
AB  - DNA.  Several hundred of these "restriction" enzymes are known and they are a very common tool
AB  - both for analysis and manipulation of DNA.  The overwhelming majority of restriction enzyme
AB  - recognition sites are four to six nucleotides in length and have the remarkable property of
AB  - internal symmetry with respect to nucleotide sequence (i.e. diad symmetry).  A major practical
AB  - offshoot of the characterization of restriction enzymes has been their use in DNA cloning.  In
AB  - addition, comparison of restriction enzyme cleavage patterns has been used analytically to
AB  - assess the similarity of DNA from related organisms-particularly mitochondrial DNA.  As an aid
AB  - in these studies, a number of statistical methods have been devised to analyze data generated
AB  - by comparison of restriction enzyme digestion patterns.  The first of these studies was
AB  - carried out by Upholt and Upholt & Dawid.  This work was revised by Nei & Li and by Gotoh et
AB  - al.  The intent of this note is to add practical detail to these analyses.
ER  -

TY  - JOUR
AU  - Moore, K.H.
AU  - Johnson, P.H.
AU  - Chandler, E.W.
AU  - Grossman, L.I.
TI  - A restriction endonuclease cleavage map of mouse mitochondrial DNA.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 1273
EP  - 1289
VL  - 4
AB  - A restriction endonuclease cleavage map is presented for mouse mitochrondrial DNA.  This map
AB  - was constructed by electron microscopic measurements on partial digests containing fixed
AB  - D-loops, and by electrophoretic analysis of partial and complete single enzyme digests, and of
AB  - double digests.  No map differences were detected between mitochrondrial DNA from cultured LA9
AB  - cells and an inbred mouse line for the six endonucleases used.  Three cleavage sites
AB  - recognized by HpaI, five sites recognized by HincII, two sites recognized by PstI and four
AB  - sites recognized by BamI were located with respect to the origin of replication and the EcoRI
AB  - and HinIII sites previously determined by others.  No cleavages were produced by KpnI or SalI.
AB  - The migration of linear DNA with a molecular weight greater than 1 x 10^6 was not a linear
AB  - function of log molecular weight in 1% agarose gels run at 6.6 volts/cm.
ER  -

TY  - JOUR
AU  - Moore, S.P.
AU  - McAleer, M.A.
AU  - Moss, S.H.
TI  - Restriction enzyme cleavage of UV-irradiated DNA:  A comparison of far-UV and mid-UV wavelengths.
JO  - Photochem. Photobiol.
PY  - 1987
SP  - 253
EP  - 263
VL  - 45
AB  - UV-irradiated DNA is less susceptible to restriction by Type II endonucleases
AB  - than unirradiated DNA presumably due to photolesions formed in the recognition
AB  - sites.  Previous reported studies have used 254 nm radiation or 313 nm plus
AB  - acetophenone, both treatments which introduce pyrimidine dimers in preference
AB  - to other photolesions.  To assess the effect of a longer wavelength, at which
AB  - the ratio of pyrimidine dimer formation to the formation of other photolesions
AB  - is reduced, two different DNAs were irradiated with UV of either 254 or 313 nm
AB  - and restricted with suitable restriction endonucleases.  Restriction patterns
AB  - were analysed for novel fragments resulting from UV-induced alteration of
AB  - enzyme recognition sites.  EcoRI restriction of 254 nm irradiated lambda DNA
AB  - produced six novel bands, only three of which were observed following
AB  - restriction of 313 nm irradiated lambda.  These three represented the largest
AB  - fragments resulting from single site blocks.  Novel fragments involving
AB  - adjacent site blocks observed at 254 nm were not found with 313 nm radiation.
AB  - Comparison of 254 nm irradiated pSVgpt to that irradiated at 313 nm, both
AB  - restricted with DraI, revealed a more complex pattern.  Although all sites were
AB  - singly blocked by radiation of both wavelengths, multiple site blocks produced
AB  - by 313 nm radiation did not occur in the order predicted by the 254 nm
AB  - radiation dose response.  These data suggest that certain sites in pSVgpt may
AB  - be more refractory to multiple site blocks than others when irradiated at 313
AB  - nm.
ER  -

TY  - JOUR
AU  - Morad, I.
AU  - Chapman-Shimshoni, D.
AU  - Amitsur, M.
AU  - Kaufmann, G.
TI  - Functional expression and properties of tRNALys-specific core anticodon nuclease encoded by Escherichia coli prrC.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 26842
EP  - 26849
VL  - 268
AB  - Escherichia coli carrying the optional locus prr harbor a latent, tRNALys-specific anticodon
AB  - nuclease, activated by the product of phage T4 stp.  Anticodon nuclease latency is ascribed to
AB  - the masking of prrC, implicated with the enzymatic activity, by flanking, type Ic DNA
AB  - restriction modification genes (prrA, B&D-hsdM, S&R).  Overexpression of plasmid-borne prrC
AB  - elicited anticodon nuclease activity in uninfected E. coli.  In vitro, the prrC-coded core
AB  - activity was indifferent to a synthetic Stp polypeptide, GTP, ATP, and endogenous DNA,
AB  - effectors that synergistically activate the latent enzyme.  Several facts suggested that PrrC
AB  - is highly labile in the absence of the masking proteins.  The core activity decayed with t1/2
AB  - below 1 min at 30oC, and the PrrC portion of a fusion protein was unstable.  Moreover,
AB  - expression of prrC from its own promoter at low plasmid copy number did not allow detection of
AB  - core activity.  Yet, it sufficed for establishment of a latent, T4-inducible enzyme when
AB  - complemented by the masking Hsd proteins, which were provided by another replicon.
AB  - Interaction between the antagonistic components of latent anticodon nuclease was also
AB  - demonstrated immunochemically.  The coupling of anticodon nuclease with a DNA restriction
AB  - modification system may serve to ward off its inadvertent toxicity and maintain it as an
AB  - antiviral contingency.
ER  -

TY  - JOUR
AU  - Moraes, P.H.
AU  - Lima, A.R.
AU  - Siqueira, A.S.
AU  - Dall'Agnol, L.T.
AU  - Barauna, A.R.
AU  - Aguiar, D.C.
AU  - Fuzii, H.T.
AU  - Albuquerque, K.C.
AU  - de Lima, C.P.
AU  - Nunes, M.R.
AU  - Vianez-Junior, J.L.
AU  - Goncalves, E.C.
TI  - Draft Genome Sequence of Flavihumibacter sp. Strain CACIAM 22H1, a Heterotrophic  Bacterium Associated with Cyanobacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e00400
EP  - e00416
VL  - 4
AB  - Here, we present a draft genome and annotation of Flavihumibacter sp. CACIAM 22H1, isolated
AB  - from Bolonha Lake, Brazil, which will provide further insight into
AB  - the production of substances of biotechnological interest.
ER  -

TY  - JOUR
AU  - Morais, L.L.
AU  - Garza, D.R.
AU  - Loureiro, E.C.
AU  - Nunes, K.N.
AU  - Vellasco, R.S.
AU  - da Silva, C.P.
AU  - Nunes, M.R.
AU  - Thompson, C.C.
AU  - Vicente, A.C.
AU  - Santos, E.C.
TI  - Complete Genome Sequence of a Sucrose-Nonfermenting Epidemic Strain of Vibrio cholerae O1 from Brazil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2772
EP  - 2772
VL  - 194
AB  - We report the genome sequence of Vibrio cholerae strain IEC224, which fails to ferment
AB  - sucrose. It was isolated from a cholera outbreak in the Amazon. The
AB  - defective sucrose phenotype was determined to be due to a frameshift mutation,
AB  - and a molecular marker of the Latin American main epidemic lineage was
AB  - identified.
ER  -

TY  - JOUR
AU  - Morais-Silva, F.O.
AU  - Santos, C.I.
AU  - Rodrigues, R.
AU  - Pereira, I.A.
AU  - Rodrigues-Pousada, C.
TI  - Role of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas.
JO  - J. Bacteriol.
PY  - 2013
SP  - 4753
EP  - 4753
VL  - 195
AB  - Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been
AB  - proposed to contribute to the overall energy metabolism of the cell, but exactly in what role
AB  - is not clear. Desulfovibrio spp. can produce or consume H2 when growing on organic or
AB  - inorganic substrates in the presence or absence of sulfate. Because of the presence of only
AB  - two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech
AB  - hydrogenases, Desulfovibrio gigas is an excellent model organism for investigation of the
AB  - specific function of each of these enzymes during growth. In this study, we analyzed the
AB  - physiological response to the deletion of the genes that encode the two hydrogenases in D.
AB  - gigas, through the generation of DeltaechBC and DeltahynAB single mutant strains. These
AB  - strains were analyzed for the ability to grow on different substrates, such as lactate,
AB  - pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the
AB  - expression of both hydrogenase genes in the three strains studied was assessed through
AB  - quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is
AB  - essential for growth on lactate-sulfate, indicating that hydrogen cycling is not
AB  - indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is
AB  - required for growth on H2 or by fermentation of pyruvate. Therefore, this enzyme seems to play
AB  - a dominant role in D. gigas hydrogen metabolism.
ER  -

TY  - JOUR
AU  - Moran, J.C.
AU  - Horsburgh, M.J.
TI  - Whole-Genome Sequence of Staphylococcus epidermidis Tu3298.
JO  - Genome Announcements
PY  - 2016
SP  - e00112
EP  - e00116
VL  - 4
AB  - Staphylococcus epidermidis Tu3298 is a frequently used laboratory strain, known for its
AB  - production of epidermin and absence of the icaABCD operon. We report the
AB  - whole-genome sequence of this strain, a 2.5-kb genome containing 2,332 genes.
ER  -

TY  - JOUR
AU  - Moran, J.V.
AU  - Mecklenburg, K.L.
AU  - Sass, P.
AU  - Belcher, S.M.
AU  - Mahnke, D.
AU  - Lewin, A.
AU  - Perlman, P.
TI  - Splicing defective mutants of the COXI gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron AI2.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 2057
EP  - 2064
VL  - 22
AB  - Six mutations blocking the function of a seven intron form of the mitochondrial gene encoding
AB  - subunit I of cytochrome c oxidase (COXI) and mapping upstream of exon 3 were isolated and
AB  - characterized.  A cis-dominant mutant of the group IIA intron 1 defines a helical portion of
AB  - the C1 substructure of domain 1 as essential for splicing.  A trans-recessive mutant confirms
AB  - that the intron 1 reading frame encodes a maturase function.  A cis-dominant mutant in exon 2
AB  - was found to have no effect on the splicing of intron 1 or 2.  A trans-recessive mutant,
AB  - located in the group IIA intron 2, demonstrates for the first time that intron 2 encodes a
AB  - maturase.  A genetic dissection of the five missense mutations present in the intron 2 reading
AB  - frame of that strain demonstrates that the maturase defect results from one or both of the
AB  - missense mutations in a newly-recognized conserved sequence called domain X.
ER  -

TY  - JOUR
AU  - Moran, J.V.
AU  - Wernette, C.M.
AU  - Mecklenburg, K.L.
AU  - Butow, R.A.
AU  - Perlman, P.S.
TI  - Intron 5a of the COXI gene of yeast mitochondrial DNA is a mobile group I intron.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4069
EP  - 4076
VL  - 20
AB  - We have found that intron 5a of the COXI gene (aI5a) of yeast mtDNA is a mobile group I intron
AB  - in crosses between strains having or lacking the intron. We have demonstrated the following
AB  - hallmarks of that process: 1) co-conversion of flanking optional intron markers; 2) mutations
AB  - that truncate the intron open reading frame block intron mobility; and 3) the intron open
AB  - reading frame encodes an endonuclease activity that is required for intron movement. The
AB  - endonuclease activity, termed I-SceIV, cleaves the COXI allele lacking aI5a near the site of
AB  - intron insertion, making a four-base staggered cut with 3' OH overhangs. Three cloned DNAs
AB  - derived from different forms of the COXI gene, which differ in primary sequence at up to seven
AB  - nucleotides around the cleavage site, are all good substrates for in vitro I-SceIV cleavage
AB  - activity. Two of the strains from which these substrates derived were tested in crosses and
AB  - are comparably efficient as aI5a recipients. When compared with omega mobility occurring
AB  - simultaneously in one cross, aI5a is less efficient as a mobile element.
ER  -

TY  - JOUR
AU  - Moran, J.V.
AU  - Zimmerly, S.
AU  - Eskes, R.
AU  - Kennell, J.C.
AU  - Lambowitz, A.M.
AU  - Butow, R.A.
AU  - Perlman, P.S.
TI  - Mobile group II introns of yeast mitochrondrial DNA are novel site-specific retroelements.
JO  - Mol. Cell. Biol.
PY  - 1995
SP  - 2828
EP  - 2838
VL  - 15
AB  - Group II introns aI1 and aI2 of the yeast mitochondrial COX1 gene are mobile elements that
AB  - encode an intron-specific reverse transcriptase (RT) activity.  We show here that the introns
AB  - of Saccharomyces cerevisiae ID41-6/161 insert site specifically into intronless alleles.  The
AB  - mobility is accompanied by efficient, but highly asymmetric, coconversion of nearby flanking
AB  - exon sequences.  Analysis of mutants shows that the aI2 protein is required for the mobility
AB  - of both aI1 and aI2.  Efficient mobility is dependent on both the RT activity of the
AB  - aI2-encoded protein and a separate function, a putative DNA endonuclease, that is associated
AB  - with the Zn2+ finger-like region of the intron reading frame.  Surprisingly, there appear to
AB  - be two  mobility modes: the major one involves cDNAs reverse transcribed from unspliced
AB  - precursor RNA; the minor one, observed in two mutants lacking detectable RT activity, appears
AB  - to involve DNA level recombination.  A cis-dominant splicing-defective mutant of aI2 continues
AB  - to synthesize cDNAs containing the introns but is completely defective in both mobility modes,
AB  - indicating that the splicing or the structure of the intron is required.  Our results
AB  - demonstrate that the yeast group II intron aI2 is a retroelement that uses novel mobility
AB  - mechanisms.
ER  -

TY  - JOUR
AU  - Moran, M.A. et al.
TI  - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.
JO  - Nature
PY  - 2004
SP  - 910
EP  - 913
VL  - 432
AB  - Since the recognition of prokaryotes as essential components of the oceanic food web,
AB  - bacterioplankton have been acknowledged as catalysts of
AB  - most major biogeochemical processes in the sea. Studying heterotrophic
AB  - bacterioplankton has been challenging, however, as most major clades have
AB  - never been cultured or have only been grown to low densities in sea water.
AB  - Here we describe the genome sequence of Silicibacter pomeroyi, a member of
AB  - the marine Roseobacter clade (Fig. 1), the relatives of which comprise
AB  - approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton.
AB  - This first genome sequence from any major heterotrophic clade consists of
AB  - a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs).
AB  - Genome analysis indicates that this organism relies upon a
AB  - lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide
AB  - and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has
AB  - genes advantageous for associations with plankton and suspended particles,
AB  - including genes for uptake of algal-derived compounds, use of metabolites
AB  - from reducing microzones, rapid growth and cell-density-dependent
AB  - regulation. This bacterium has a physiology distinct from that of marine
AB  - oligotrophs, adding a new strategy to the recognized repertoire for coping
AB  - with a nutrient-poor ocean.
ER  -

TY  - JOUR
AU  - Moran, N.A.
AU  - Degnan, P.H.
AU  - Santos, S.R.
AU  - Dunbar, H.E.
AU  - Ochman, H.
TI  - The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 16919
EP  - 16926
VL  - 102
AB  - Aphids maintain mutualistic symbioses involving consortia of coinherited
AB  - organisms. All possess a primary endosymbiont, Buchnera, which compensates
AB  - for dietary deficiencies; many also contain secondary symbionts, such as
AB  - Hamiltonella defensa, which confers defense against natural enemies.
AB  - Genome sequences of uncultivable secondary symbionts have been refractory
AB  - to analysis due to the difficulties of isolating adequate DNA samples. By
AB  - amplifying DNA from hemolymph of infected pea aphids, we obtained a set of
AB  - genomic sequences of H. defensa and an associated bacteriophage. H.
AB  - defensa harbors two type III secretion systems, related to those that
AB  - mediate host cell entry by enteric pathogens. The phage, called APSE-2, is
AB  - a close relative of the previously sequenced APSE-1 but contains intact
AB  - homologs of the gene encoding cytolethal distending toxin (cdtB), which
AB  - interrupts the eukaryotic cell cycle and which is known from a variety of
AB  - mammalian pathogens. The cdtB homolog is highly expressed, and its genomic
AB  - position corresponds to that of a homolog of stx (encoding Shiga-toxin)
AB  - within APSE-1. APSE-2 genomes were consistently abundant in infected pea
AB  - aphids, and related phages were found in all tested isolates of H.
AB  - defensa, from numerous insect species. Based on their ubiquity and
AB  - abundance, these phages appear to be an obligate component of the H.
AB  - defensa life cycle. We propose that, in these mutualistic symbionts,
AB  - phage-borne toxin genes provide defense to the aphid host and are a basis
AB  - for the observed protection against eukaryotic parasites.
ER  -

TY  - JOUR
AU  - Morcrette, H.
AU  - Morgan, M.S.
AU  - Farbos, A.
AU  - O'Neill, P.
AU  - Moore, K.
AU  - Titball, R.W.
AU  - Studholme, D.J.
TI  - Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis.
JO  - Genome Announcements
PY  - 2018
SP  - e00623
EP  - e00618
VL  - 6
AB  - Here, we present the genome sequence of Staphylococcus aureus Ex1, isolated in 2015 from a
AB  - patient with spinal osteomyelitis at the Royal Devon and Exeter
AB  - Hospital in the United Kingdom. The availability of the Ex1 genome sequence
AB  - provides a resource for studying the basis for spinal infection and horizontal
AB  - gene transfer in S. aureus.
ER  -

TY  - JOUR
AU  - Mordasini, T.
AU  - Curioni, A.
AU  - Andreoni, W.
TI  - Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 4381
EP  - 4384
VL  - 278
AB  - Divalent metal ions are essential to many enzymatic reactions involving nucleic acids, but
AB  - their critical and specific role still needs to be uncovered. Restriction endonucleases are a
AB  - prominent group of such metal-requiring enzymes. Large-scale accurate simulations of Mg- and
AB  - Ca-BamHI elucidate the mechanism of the catalytic reaction leading to DNA cleavage and show
AB  - that it involves the concerted action of two metal ions and water molecules. It is also
AB  - established that what is decisive for the dramatically different behavior of magnesium (a
AB  - cocatalyst) and calcium (an inhibitor) are kinetic factors and not the properties of the
AB  - pre-reactive states of the enzymes. A new perspective is opened for the understanding of the
AB  - functional role of metal ions in biological processes.
ER  -

TY  - JOUR
AU  - Moreau, H.
AU  - Piganeau, G.
AU  - Desdevises, Y.
AU  - Cooke, R.
AU  - Derelle, E.
AU  - Grimsley, N.
TI  - Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer.
JO  - J. Virol.
PY  - 2010
SP  - 12555
EP  - 12563
VL  - 84
AB  - Although marine picophytoplankton are at the base of the global food
AB  - chain, accounting for half of the planetary primary production, they are
AB  - outnumbered 10 to 1 and are largely controlled by hugely diverse
AB  - populations of viruses. Eukaryotic microalgae form a ubiquitous and
AB  - particularly dynamic fraction of such plankton, with environmental clone
AB  - libraries from coastal regions sometimes being dominated by one or more of
AB  - the three genera Bathycoccus, Micromonas, and Ostreococcus (class
AB  - Prasinophyceae). The complete sequences of two double-stranded (dsDNA)
AB  - Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus
AB  - genomes are described. Genome comparison of these giant viruses revealed a
AB  - high degree of conservation, both for orthologous genes and for synteny,
AB  - except for one 36-kb inversion in the Ostreococcus lucimarinus virus and
AB  - two very large predicted proteins in Bathycoccus prasinos viruses. These
AB  - viruses encode a gene repertoire of certain amino acid biosynthesis
AB  - pathways never previously observed in viruses that are likely to have been
AB  - acquired from lateral gene transfer from their host or from bacteria.
AB  - Pairwise comparisons of whole genomes using all coding sequences with
AB  - homologous counterparts, either between viruses or between their
AB  - corresponding hosts, revealed that the evolutionary divergences between
AB  - viruses are lower than those between their hosts, suggesting either
AB  - multiple recent host transfers or lower viral evolution rates.
ER  -

TY  - JOUR
AU  - Moreau, M.R.
AU  - Wijetunge, D.S.
AU  - Kurundu, H.E.M.
AU  - Jayarao, B.M.
AU  - Kariyawasam, S.
TI  - Genome Sequences of Two Strains of Salmonella enterica Serovar Enteritidis Isolated from Shell Eggs.
JO  - Genome Announcements
PY  - 2015
SP  - e00954
EP  - e00915
VL  - 3
AB  - This report presents the complete genome sequences of two Salmonella enterica serovar
AB  - Enteritidis strains bearing the pulsed-field gel electrophoresis profile  JEGX01.0004, which
AB  - were isolated from the internal contents of eggs.
ER  -

TY  - JOUR
AU  - Moreira, A.S.
AU  - Germaine, K.J.
AU  - Lloyd, A.
AU  - Lally, R.D.
AU  - Galbally, P.T.
AU  - Ryan, D.
AU  - Dowling, D.N.
TI  - Draft Genome Sequence of Three Endophyte Strains of Pseudomonas fluorescens Isolated from Miscanthus giganteus.
JO  - Genome Announcements
PY  - 2016
SP  - e00965
EP  - e00916
VL  - 4
AB  - We report here the draft genome sequence of three Pseudomonas fluorescens strains (L111, L228,
AB  - and L321) isolated from Miscanthus giganteus The draft genome
AB  - analyses uncovered a group of genes involved in the biosynthesis of secondary
AB  - metabolites and for plant growth promotion.
ER  -

TY  - JOUR
AU  - Moreira, R.F.
AU  - Noren, C.J.
TI  - Minimum duplex requirements for restriction enzyme cleavage near the termini of linear DNA fragments.
JO  - Biotechniques
PY  - 1995
SP  - 56
EP  - 59
VL  - 19
AB  - Restriction endonucleases differ in their ability to cleave close to the ends of linear DNA
AB  - fragments, each requiring a characteristic minimum number of base pairs adjacent to their
AB  - recognition sites for efficient cleavage. Quantitative cleavage close to either end of a
AB  - linear DNA fragment is crucial when carrying out digests at adjacent restriction sites within
AB  - cloning vector polylinkers or when trimming the ends of polymerase chain reaction (PCR)
AB  - products prior to cloning. In the former case, incomplete digestion by the second restriction
AB  - enzyme (following linearization by the first) would be undetectable by gel electrophoresis,
AB  - yet could result in an unacceptably high background level of transformants following ligation
AB  - of the insert. In the latter case, recovery of a cloned PCR product is dependent upon
AB  - generation of the desired overhangs at either end of the amplified product prior to cloning.
AB  - Incorporation of restriction sites within PCR primers for future cloning steps has become an
AB  - important factor in primer design: If not enough bases are added upstream from each site, then
AB  - the corresponding enzyme will not cut the PCR product.
ER  -

TY  - JOUR
AU  - Moreno, E.
AU  - Parks, M.
AU  - Pinnell, L.J.
AU  - Tallman, J.J.
AU  - Turner, J.W.
TI  - Draft Genome Sequence of a Vibrio harveyi Strain Associated with Vibriosis in Pacific White Shrimp (Litopenaeus vannamei).
JO  - Genome Announcements
PY  - 2017
SP  - e01662
EP  - e01616
VL  - 5
AB  - Vibrio harveyi is a Gram-negative bacterium associated with vibriosis in penaeid  shrimp.
AB  - Here, we report the draft genome sequence of a V. harveyi strain isolated
AB  - from Pacific white shrimp (Litopenaeus vannamei) during a vibriosis outbreak. The
AB  - availability of this genome will aid future studies of vibriosis in shrimp
AB  - aquaculture.
ER  -

TY  - JOUR
AU  - Moreno, L.Z.
AU  - Knobl, T.
AU  - Grespan, A.A.
AU  - Felizardo, M.R.
AU  - Gomes, C.R.
AU  - Ferreira, T.S.
AU  - Xavier-de-Oliveira, M.G.
AU  - Myriantheus, L.
AU  - Moreno, A.M.
TI  - Draft Genome Sequence of Bordetella avium Nh1210, an Outbreak Strain of Lockjaw Syndrome.
JO  - Genome Announcements
PY  - 2015
SP  - e00120
EP  - e00115
VL  - 3
AB  - Bordetella avium is a highly contagious bacterium that infects the upper respiratory tract of
AB  - birds. B. avium Nh1210 is an outbreak strain of lockjaw
AB  - syndrome in juvenile cockatiel chicks (Nymphicus hollandicus). Here, we report
AB  - the draft genome sequence of strain Nh1210.
ER  -

TY  - JOUR
AU  - Moreno, L.Z.
AU  - Loureiro, A.P.
AU  - Miraglia, F.
AU  - Matajira, C.E.
AU  - Kremer, F.S.
AU  - Eslabao, M.R.
AU  - Dellagostin, O.A.
AU  - Lilenbaum, W.
AU  - Moreno, A.M.
TI  - Draft Genome Sequence of Brazilian Leptospira noguchii Serogroup Panama Strain U73, Isolated from Cattle.
JO  - Genome Announcements
PY  - 2015
SP  - e01179
EP  - e01115
VL  - 3
AB  - Leptospira noguchii is a current zoonotic pathogen in Brazil. Here, we report the draft genome
AB  - sequence of the Brazilian L. noguchii serogroup Panama strain U73, isolated from asymptomatic
AB  - cattle urine.
ER  -

TY  - JOUR
AU  - Moreno, L.Z.
AU  - Miraglia, F.
AU  - de Oliveira, C.H.
AU  - Vasconcellos, S.A.
AU  - Heinemann, M.B.
AU  - Moreno, A.M.
TI  - Draft Genome Sequence of Brazilian Leptospira interrogans Serovar Pomona Strain GR5, Isolated from Apparently Healthy Gilt.
JO  - Genome Announcements
PY  - 2018
SP  - e00491
EP  - e00418
VL  - 6
AB  - Leptospira interrogans serovar Pomona is one of the most important serovars associated with
AB  - worldwide porcine leptospirosis, and its infection is
AB  - characterized by high antibody titers and the establishment of a renal carrier
AB  - state. Here, we present the draft genome sequence of Leptospira interrogans
AB  - serovar Pomona strain GR5 isolated from apparently healthy gilt in Brazil.
ER  -

TY  - JOUR
AU  - Moreno-Avitia, F.
AU  - Lozano, L.
AU  - Utrilla, J.
AU  - Bolivar, F.
AU  - Escalante, A.
TI  - Draft Genome Sequence of Pseudomonas chlororaphis ATCC 9446, a Nonpathogenic Bacterium with Bioremediation and Industrial Potential.
JO  - Genome Announcements
PY  - 2017
SP  - e00474
EP  - e00417
VL  - 5
AB  - Pseudomonas chlororaphis strain ATCC 9446 is a biocontrol-related organism. We report here its
AB  - draft genome sequence assembled into 35 contigs consisting of
AB  - 6,783,030 bp. Genome annotation predicted a total of 6,200 genes, 6,128 coding
AB  - sequences, 81 pseudogenes, 58 tRNAs, 4 noncoding RNAs (ncRNAs), and 41
AB  - frameshifted genes.
ER  -

TY  - JOUR
AU  - Moreno-Switt, A.I.
AU  - Andrus, A.D.
AU  - Ranieri, M.L.
AU  - Orsi, R.H.
AU  - Ivy, R.
AU  - den Bakker, H.C.
AU  - Martin, N.H.
AU  - Wiedmann, M.
AU  - Boor, K.J.
TI  - Genomic comparison of sporeforming bacilli isolated from milk.
JO  - BMC Genomics
PY  - 2014
SP  - 26
EP  - 26
VL  - 15
AB  - BACKGROUND: Sporeformers in the order Bacillales are important contributors to spoilage of
AB  - pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6
AB  - degrees C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under
AB  - these conditions. To gain a better understanding of genomic features of these important
AB  - spoilage organisms and to identify candidate genomic features that may facilitate cold growth
AB  - in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers
AB  - representing isolates that can and cannot grow in milk at 6 degrees C. RESULTS: The genomes
AB  - for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were
AB  - sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial
AB  - resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide
AB  - antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and
AB  - Viridibacillus into three distinct well supported clades and further classified the
AB  - Paenibacillus strains characterized here into three distinct clades, including (i) clade I,
AB  - which contains one strain able to grow at 6 degrees C in skim milk broth and one strain not
AB  - able to grow under these conditions, (ii) clade II, which contains three strains able to grow
AB  - at 6 degrees C in skim milk broth, and (iii) clade III, which contains two strains unable to
AB  - grow under these conditions. While all Paenibacillus genomes were found to include multiple
AB  - copies of genes encoding beta-galactosidases, clade II strains showed significantly higher
AB  - numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of
AB  - strains able to grow at 6 degrees C and strains unable to grow at this temperature identified
AB  - numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at
AB  - 6 degrees C, including peptidases with cold-adapted features (flexibility and disorder regions
AB  - in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone
AB  - DnaJ). CONCLUSIONS: Through a comparative genomics approach we identified a number of genomic
AB  - features that may relate to the ability of selected Paenibacillus strains to cause spoilage of
AB  - refrigerated fluid milk. With additional experimental evidence, these data will facilitate
AB  - identification of targets to detect and control Gram positive spore formers in fluid milk.
ER  -

TY  - JOUR
AU  - Moreno-Switt, A.I.
AU  - Orsi, R.H.
AU  - den Bakker, H.C.
AU  - Vongkamjan, K.
AU  - Altier, C.
AU  - Wiedmann, M.
TI  - Genomic characterization provides new insight into Salmonella phage diversity.
JO  - BMC Genomics
PY  - 2013
SP  - 481
EP  - 481
VL  - 14
AB  - Background Salmonella is a widely distributed foodborne pathogen that causes tens of millions
AB  - of salmonellosis cases globally every year. While the genomic diversity of Salmonella is
AB  - increasingly well studied, our knowledge of Salmonella phage genomic diversity is still rather
AB  - limited, despite the contributions of both lysogenic and lytic phages to Salmonella virulence,
AB  - diversity and ecology (e.g., through horizontal gene transfer and Salmonella lysis). To gain a
AB  - better understanding of phage diversity in a specific ecological niche, we sequenced 22
AB  - Salmonella phages isolated from a number of dairy farms from New York State (United States)
AB  - and analyzed them using a comparative genomics approach. Results Classification of the 22
AB  - phages according to the presence/absence of orthologous genes allowed for classification into
AB  - 8 well supported clusters. In addition to two phage clusters that represent novel virulent
AB  - Salmonella phages, we also identified four phage clusters that each contained previously
AB  - characterized phages from multiple continents. Our analyses also identified two clusters of
AB  - phages that carry putative virulence (e.g., adhesins) and antimicrobial resistance (tellurite
AB  - and bicyclomycin) genes as well as virulent and temperate transducing phages. Insights into
AB  - phage evolution from our analyses include (i) identification of DNA metabolism genes that may
AB  - facilitate nucleotide synthesis in phages with a G+C % distinct from Salmonella, and (ii)
AB  - evidence of Salmonella phage tailspike and fiber diversity due to both single nucleotide
AB  - polymorphisms and major re-arrangements, which may affect the host specificity of Salmonella
AB  - phages. Conclusions Genomics-based characterization of 22 Salmonella phages isolated from
AB  - dairy farms allowed for identification of a number of novel Salmonella phages. While the
AB  - comparative genomics analyses of these phages provide a number of new insights in the
AB  - evolution and diversity of Salmonella phages, they only represent a first glimpse into the
AB  - diversity of Salmonella phages that is likely to be discovered when phages from different
AB  - environments are characterized.
ER  -

TY  - JOUR
AU  - Moretti, C.
AU  - Cortese, C.
AU  - Passos-da-Silva, D.
AU  - Venturi, V.
AU  - Firrao, G.
AU  - Buonaurio, R.
TI  - Draft Genome Sequence of Erwinia oleae, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi.
JO  - Genome Announcements
PY  - 2014
SP  - e01308
EP  - e01314
VL  - 2
AB  - Erwinia oleae is a nonpathogenic bacterial species isolated from olive knots caused by
AB  - Pseudomonas savastanoi pv. savastanoi. Since the presence of E. oleae
AB  - in the knots increases disease severity, interspecies interactions with the
AB  - pathogen are hypothesized. Here, we report the first draft genome sequence of the
AB  - E. oleae type strain.
ER  -

TY  - JOUR
AU  - Moretti, C.
AU  - Cortese, C.
AU  - Passos-da-Silva, D.
AU  - Venturi, V.
AU  - Ramos, C.
AU  - Firrao, G.
AU  - Buonaurio, R.
TI  - Draft Genome Sequence of Pseudomonas savastanoi pv. savastanoi Strain DAPP-PG 722, Isolated in Italy from an Olive Plant Affected by Knot Disease.
JO  - Genome Announcements
PY  - 2014
SP  - e00864
EP  - e00814
VL  - 2
AB  - Olive knot disease, caused by the bacterium Pseudomonas savastanoi pv. savastanoi, seriously
AB  - affects olive trees in the Mediterranean basin. Here, we
AB  - report the draft genome sequence of P. savastanoi pv. savastanoi DAPP-PG 722, a
AB  - strain isolated in Italy from an olive plant affected by knot disease.
ER  -

TY  - JOUR
AU  - Moretti, C.
AU  - Cortese, C.
AU  - Passos-da-Silva, D.
AU  - Venturi, V.
AU  - Torelli, E.
AU  - Firrao, G.
AU  - Buonaurio, R.
TI  - Draft Genome Sequence of a Hypersensitive Reaction-Inducing Pantoea agglomerans Strain Isolated from Olive Knots Caused by Pseudomonas savastanoi pv. savastanoi.
JO  - Genome Announcements
PY  - 2014
SP  - e00774
EP  - e00714
VL  - 2
AB  - Pantoea agglomerans strains inducing a hypersensitive reaction in tobacco leaves  are
AB  - frequently isolated inside olive knots caused by Pseudomonas savastanoi pv.
AB  - savastanoi. Here, we report the draft genome sequence of the Italian P.
AB  - agglomerans strain, which is able to increase olive knot disease severity when
AB  - coinoculated with P. savastanoi pv. savastanoi.
ER  -

TY  - JOUR
AU  - Morgado, S.M.
AU  - Vicente, A.C.
TI  - Beyond the Limits: tRNA Array Units in Mycobacterium Genomes.
JO  - Front. Microbiol.
PY  - 2018
SP  - 1042
EP  - 1042
VL  - 9
AB  - tRNA array unit, a genomic region presenting an intriguing high tRNA gene number
AB  - and density, was supposed to occur only in few bacteria phyla, particularly
AB  - Firmicutes. Here, we identified and characterized an abundance and diversity of
AB  - tRNA array units in Mycobacterium associated genomes. These genomes comprised
AB  - chromosome, bacteriophages and plasmids from mycobacteria. Firstly, we had
AB  - identified 32 tRNA genes organized in an array unit within a mycobacteria plasmid
AB  - genome and therefore, we hypothesized the presence of such structures in
AB  - Mycobacterium genus. However, at the time, bioinformatics tools only predict tRNA
AB  - genes, not characterizing their arrangement as arrays. In order to test our
AB  - hypothesis, we developed and applied an in-house Perl script that identified tRNA
AB  - genes organization as an array unit. This survey included a total of 7,670
AB  - complete and drafts genomes of Mycobacterium genus, 4312 mycobacteriophage
AB  - genomes and 40 mycobacteria plasmids. We showed that tRNA array units are
AB  - abundant in genomes associated to the Mycobacterium genus, mainly in
AB  - Mycobacterium abscessus complex species, being spread in chromosome, prophage,
AB  - and plasmid genomes. Moreover, other non-coding RNA species (tmRNA and structured
AB  - RNA) were also identified in these regions. Our results revealed that tRNA array
AB  - units are not restrict, as previously assumed, to few bacteria phyla and genomes
AB  - being present in one of the most diverse bacteria genus. We also provide a
AB  - bioinformatics tool that allows further exploration of this issue in huge genomic
AB  - databases. The presence of tRNA array units in plasmids and bacteriophages,
AB  - associated with horizontal gene transfer, and in a bacteria genus that explores
AB  - diverse niches, are indicatives that tRNA array units have impact in the bacteria
AB  - biology.
ER  -

TY  - JOUR
AU  - Morgan, R.
AU  - Xiao, J.-P.
AU  - Xu, S.-Y.
TI  - Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli.
JO  - Appl. Environ. Microbiol.
PY  - 1998
SP  - 3669
EP  - 3673
VL  - 64
AB  - An extremely thermostable restriction endonuclease, PspGI, was purified from Pyrococcus sp.
AB  - strain GI-H.  PspGI is an isoschizomer of EcoRII and cleaves DNA before the first C in the
AB  - sequence 5' ^CCWGG 3' (W is A or T).  PspGI digestion can be carried out at 65 to 85 C.  To
AB  - express PspGI at high levels, the PspGI restriction-modification genes (pspGIR and pspGIM)
AB  - were cloned in Escherichia coli.  M.PspGI contains the conserved sequence motifs of
AB  - alpha-aminomethyltransferases; therefore, it must be an N4-cytosine methylase.  M.PspGI shows
AB  - 53% similarity to (44% identity with) its isoschizomer, M.MvaI from Micrococcus variabilis.
AB  - In a segment of 87 amino acid residues, PspGI shows significant sequence similarity to EcoRII
AB  - and to regions of SsoII and StyD4I which have a closely related recognition sequence (5'
AB  - ^CCNGG 3').  PspGI was expressed in E. coli via a T7 expression system.  Recombinant PspGI
AB  - was purified to near homogeneity and had a half-life of 2 h at 95 C.  PspGI remained active
AB  - following 30 cycles of thermocycling; thus, it can be used in DNA-based diagnostic
AB  - applications.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
TI  - MseI, a unique restriction endonuclease from Micrococcus species which recognizes 5'T^TAA 3'.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 3104
EP  - 3104
VL  - 16
AB  - A new typeII restriction endonuclease, MseI, has been isolated from Micrococcus
AB  - species (NEB446).  MseI recognizes the palindromic sequence 5'TTAA3' and
AB  - cleaves between the two T residues to produce a 2 base 5' extension: T/TAA.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
TI  - Complete Genome Sequence and Methylome Analysis of Bacillus globigii ATCC 49760.
JO  - Genome Announcements
PY  - 2016
SP  - e00427
EP  - e00416
VL  - 4
AB  - Bacillus subtilis (Ehrenburg) Cohn ATCC 49760, deposited as Bacillus globigii, is the source
AB  - strain for the restriction enzymes BglI and BglII. Its complete
AB  - sequence and full methylome were determined using single-molecule real-time
AB  - (SMRT) sequencing.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
TI  - Rational engineering of DNA binding and cleavage specificity in a family of Type II restriction endonucleases.
JO  - Ph.D. Thesis, Boston University
PY  - 2009
SP  - 1
EP  - 190
AB  - Type II restriction endonucleases serve as important tools for molecular biology. Although
AB  - enzymes recognizing 274 unique sequences are known, it would be desirable to be able to create
AB  - 'designer endonucleases' to cut at sequences of choice rather than rely on the limited
AB  - number of natural isolates. However, these endonucleases have proved remarkably resistant to
AB  - all attempts to engineer changes in their recognition specificity. The Type II endonucleases
AB  - typically exhibit little sequence similarity. This study has identified a new family of
AB  - unusual Type II endonucleases through genome mining that do share a great deal of sequence
AB  - conservation. Twenty individual members of this family were biochemically characterized and
AB  - all recognize unique DNA sequences. These enzymes also employ a unique mode of modification,
AB  - in that they modify only one DNA strand for host protection against the action of the
AB  - endonuclease. This family of single-strand-modifying enzymes serves as the archetype for a new
AB  - restriction endonuclease subclass, the Type IIL group. Because these enzymes encode
AB  - endonuclease, methyltransferase and specificity functions in the same polypeptide, alterations
AB  - to the recognition domain result in a coordinated change in specificity for both host
AB  - protection and endonuclease activity. To alter recognition specificity, multiple sequence
AB  - alignments of the recognition sequences and protein sequences were created and interrogated to
AB  - identify correlations between position-specific amino acid residues and position-specific DNA
AB  - base recognition. Correlations were identified between pairs of amino acid positions and the
AB  - DNA bases recognized at three separate recognition positions. Enzymes having new recognition
AB  - specificity were then created by altering the amino acid residues at the correlating positions
AB  - to residues correlated with recognition of a desired new DNA base. Using this approach three
AB  - positions in the recognition sequences have been altered singly and in combination to create a
AB  - dozen novel Type II endonucleases having predictable new recognition sequences. From this work
AB  - it is now possible to rationally engineer hundreds of new Type II restriction endonucleases
AB  - specificities. These results move us closer to the goal of creating 'designer restriction
AB  - endonucleases' that recognize and cleave at any desired DNA sequence.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Bhatia, T.K.
AU  - Lovasco, L.
AU  - Davis, T.B.
TI  - MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 6558
EP  - 6570
VL  - 36
AB  - MmeI is an unusual Type II restriction enzyme that is useful for generating long sequence
AB  - tags. We have cloned the MmeI
AB  - restriction-modification (R-M) system and found it to consist of a single
AB  - protein having both endonuclease and DNA methyltransferase activities. The
AB  - protein comprises an amino-terminal endonuclease domain, a central DNA
AB  - methyltransferase domain and C-terminal DNA recognition domain. The
AB  - endonuclease cuts the two DNA strands at one site simultaneously, with
AB  - enzyme bound at two sites interacting to accomplish scission. Cleavage
AB  - occurs more rapidly than methyl transfer on unmodified DNA. MmeI modifies
AB  - only the adenine in the top strand, 5'-TCCRAC-3'. MmeI endonuclease
AB  - activity is blocked by this top strand adenine methylation and is
AB  - unaffected by methylation of the adenine in the complementary strand,
AB  - 5'-GTYGGA-3'. There is no additional DNA modification associated with the
AB  - MmeI R-M system, as is required for previously characterized Type IIG R-M
AB  - systems. The MmeI R-M system thus uses modification on only one of the two
AB  - DNA strands for host protection. The MmeI architecture represents a
AB  - minimal approach to assembling a restriction-modification system wherein a
AB  - single DNA recognition domain targets both the endonuclease and DNA
AB  - methyltransferase activities.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Calvet, C.
AU  - Demeter, M.
AU  - Agra, R.
AU  - Kong, H.M.
TI  - Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI.
JO  - Biol. Chem.
PY  - 2000
SP  - 1123
EP  - 1125
VL  - 381
AB  - N.BstNBI is a unique restriction endonuclease isolated from Bacillus stearothermophilus, We
AB  - have characterized the recognition sequence and
AB  - the cleavage site of N.BstNBI. Mapping of cleavage sites of N.BstNBI
AB  - showed that it recognizes an asymmetric sequence, 5' GAGTC 3', and
AB  - cleaves only on the top strand 4 base pairs away from its recognition
AB  - sequence. To verify the nicking activity of N.BstNBI, we have
AB  - constructed two plasmids containing a single recognition sequence
AB  - (pNB1) or no recognition site (pNB0). When pNB1 and pNB0 were incubated
AB  - with the enzyme, N.BstNBI nicked only the plasmid pNB1, suggesting that
AB  - N.BstNBI is a specific nicking endonuclease.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Camp, R.R.
AU  - Wilson, G.G.
AU  - Xu, S.-Y.
TI  - Molecular cloning and expression of NlaIII restriction-modification system in E. coli.
JO  - Gene
PY  - 1996
SP  - 215
EP  - 218
VL  - 183
AB  - The NlaIII restriction enzyme isolated from Neisseria lactamica recognizes the sequence
AB  - 5'-CATG-3', cleaving after the G to generate a four base 3' overhang.  The NlaIII methylase
AB  - and a portion of the NlaIII endonuclease gene were cloned into E. coli by the methylase
AB  - selection method, and the remaining portion of the NlaIII endonuclease gene was cloned by
AB  - inverse PCR.  The nucleotide sequence of the endonuclease gene and the methylase gene were
AB  - determined.  The NlaIII endonuclease gene is 693 bp, encoding a protein with a predicted
AB  - molecular weight of 26,487.  The NlaIII methylase gene was identical with that previously
AB  - reported [Labbe, D., Joltke, H.J. and Lau, P.C. (1990)  Cloning and characterization of two
AB  - tandemly arranged DNA methyltransferase genes of Neisseria lactamica: an adenine-specific
AB  - M.NlaIII and a cytosine-type methylase.  Mol. Gen. genet. 224, 101-110].  The endonuclease and
AB  - methylase genes overlap by four bases and are transcribed in the same orientation.  The
AB  - endonuclease gene was cloned into an improved T7 vector, and a high level of NlaIII
AB  - endonuclease expression was achieved in E. coli.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Dalton, M.
AU  - Stote, R.
TI  - A unique type II restriction endonuclease from Acinetobacter lwoffi N.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 7201
EP  - 7201
VL  - 15
AB  - A new type II restriction endonuclease, AlwN I, has been isolated from
AB  - Acinetobacter lwoffi N (NEB 419).  AlwN I recognizes the interrupted
AB  - palindromic sequence 5' CAGNNNCTG 3' and cleaves between the 3' N and C to
AB  - produce a 3 base 3' extension.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Dwinell, E.A.
AU  - Bhatia, T.K.
AU  - Lang, E.M.
AU  - Luyten, Y.A.
TI  - The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5208
EP  - 5221
VL  - 37
AB  - The type II restriction endonucleases form one of the largest families of
AB  - biochemically-characterized proteins. These endonucleases typically share
AB  - little sequence similarity, except among isoschizomers that recognize the
AB  - same sequence. MmeI is an unusual type II restriction endonuclease that
AB  - combines endonuclease and methyltransferase activities in a single
AB  - polypeptide. MmeI cuts DNA 20 bases from its recognition sequence and
AB  - modifies just one DNA strand for host protection. Using MmeI as query we
AB  - have identified numerous putative genes highly similar to MmeI in database
AB  - sequences. We have cloned and characterized 20 of these MmeI homologs.
AB  - Each cuts DNA at the same distance as MmeI and each modifies a conserved
AB  - adenine on only one DNA strand for host protection. However each enzyme
AB  - recognizes a unique DNA sequence, suggesting these enzymes are undergoing
AB  - rapid evolution of DNA specificity. The MmeI family thus provides a rich
AB  - source of novel endonucleases while affording an opportunity to observe
AB  - the evolution of DNA specificity. Because the MmeI family enzymes employ
AB  - modification of only one DNA strand for host protection, unlike previously
AB  - described type II systems, we propose that such single-strand modification
AB  - systems be classified as a new subgroup, the type IIL enzymes, for Lone
AB  - strand DNA modification.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Luyten, Y.A.
TI  - Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5222
EP  - 5233
VL  - 37
AB  - The type II restriction endonucleases are indispensible tools for molecular biology. Although
AB  - enzymes recognizing nearly 300 unique
AB  - sequences are known, the ability to engineer enzymes to recognize any
AB  - sequence of choice would be valuable. However, previous attempts to
AB  - engineer new recognition specificity have met limited success. Here we
AB  - report the rational engineering of multiple new type II specificities. We
AB  - recently identified a family of MmeI-like type II endonucleases that have
AB  - highly similar protein sequences but different recognition specificity. We
AB  - identified the amino-acid positions within these enzymes that determine
AB  - position specific DNA base recognition at three positions within their
AB  - recognition sequences through correlations between their aligned
AB  - amino-acid residues and aligned recognition sequences. We then altered the
AB  - amino acids at the identified positions to those correlated with
AB  - recognition of a desired new base to create enzymes that recognize and cut
AB  - at predictable new DNA sequences. The enzymes so altered have similar
AB  - levels of endonuclease activity compared to the wild-type enzymes. Using
AB  - simple and predictable mutagenesis in this family it is now possible to
AB  - create hundreds of unique new type II restriction endonuclease
AB  - specificities. The findings suggest a simple mechanism for the evolution
AB  - of new DNA specificity in Nature.
ER  -

TY  - JOUR
AU  - Morgan, R.D.
AU  - Luyten, Y.A.
AU  - Johnson, S.A.
AU  - Clough, E.M.
AU  - Clark, T.A.
AU  - Roberts, R.J.
TI  - Novel m4C modification in type I restriction-modification systems.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 9413
EP  - 9425
VL  - 44
AB  - We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in
AB  - one DNA strand and adenine in the opposite strand for host
AB  - protection. Recognition specificity has been determined for ten systems using
AB  - SMRT sequencing and each recognizes a novel DNA sequence motif. Previously
AB  - characterized Type I systems use two identical copies of a single
AB  - methyltransferase (MTase) subunit, with one bound at each half site of the
AB  - specificity (S) subunit to form the MTase. The new m4C-producing Type I systems
AB  - we describe have two separate yet highly similar MTase subunits that form a
AB  - heterodimeric M1M2S MTase. The MTase subunits from these systems group into two
AB  - families, one of which has NPPF in the highly conserved catalytic motif IV and
AB  - modifies adenine to m6A, and one having an NPPY catalytic motif IV and modifying
AB  - cytosine to m4C. The high degree of similarity among their cytosine-recognizing
AB  - components (MTase and S) suggest they have recently evolved, most likely from the
AB  - far more common m6A Type I systems. Type I enzymes that modify cytosine
AB  - exclusively were formed by replacing the adenine target recognition domain (TRD)
AB  - with a cytosine-recognizing TRD. These are the first examples of m4C modification
AB  - in Type I RM systems.
ER  -

TY  - JOUR
AU  - Morgan, W.F.
AU  - Fero, M.L.
AU  - Land, M.C.
AU  - Winegar, R.A.
TI  - Inducible expression and cytogenic effects of the EcoRI restriction endonuclease in chinese hamster ovary cells.
JO  - Mol. Cell. Biol.
PY  - 1988
SP  - 4204
EP  - 4211
VL  - 8
AB  - The cytogenic endpoints of sister chromatid exchange (SCE) and chromosome
AB  - aberrations are widely used as indicators of DNA damage induced by mutagenic
AB  - carcinogens.  Chromosome aberrations appear to result directly from DNA
AB  - double-strand breaks, but the lesion(s) giving rise to SCE formation remains
AB  - unknown.  Most compounds that induce SCEs induce a spectrum of lesions in DNA.
AB  - To investigate the role of double-strand breakage in SCE formation, we
AB  - constructed a plasmid that gives rise to one specific lesion, a staggered-end
AB  - ("cohesive") DNA double-strand break.  This plasmid, designated pMENs, contains
AB  - a selectable marker, neo, which is a bacterial gene for neomycin resistance,
AB  - and the coding sequence for the bacterial restriction endonuclease EcoRI
AB  - attached to the mouse metallothionein gene promoter.  EcoRI recognizes G^AATTC
AB  - sequences in DNA and makes DNA double-strand breaks with four nucleotides
AB  - overhanging as staggered ends.  Cells transfected with pMENS were resistant to
AB  - the antibiotic G418 and contained an integrated copy of the EcoRI gene,
AB  - detectable by DNA filter hybridization.  The addition of the heavy metal CdSO4
AB  - resulted in the intracellular production of EcoRI, as measured by an anti-EcoRI
AB  - antibody.  Cytogenetic analysis after the addition of CdSO4 indicated a
AB  - dramatic increase in the frequency of chromosome aberrations but very little
AB  - effect on SCE frequency.  Although there was some intercellular heterogeneity,
AB  - these results confirm that DNA double-strand breaks do result in chromosome
AB  - aberrations but that these breaks are not sufficient to give rise to SCE
AB  - formation.
ER  -

TY  - JOUR
AU  - Mori, K.
AU  - Kadooka, C.
AU  - Masuda, C.
AU  - Muto, A.
AU  - Okutsu, K.
AU  - Yoshizaki, Y.
AU  - Takamine, K.
AU  - Futagami, T.
AU  - Tamaki, H.
TI  - Genome Sequence of Saccharomyces cerevisiae Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shochu.
JO  - Genome Announcements
PY  - 2017
SP  - e01126
EP  - e01117
VL  - 5
ER  -

TY  - JOUR
AU  - Mori, K.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Ohji, S.
AU  - Fujita, N.
AU  - Ishibashi, J.
AU  - Kimura, H.
AU  - Suzuki, K.
TI  - Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 2128
EP  - 2136
VL  - 64
AB  - Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains
AB  - AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan.
AB  - The optimum growth conditions for strain AZM34c06(T) were 60 degrees C, pH 7.4 and 0 %
AB  - additional NaCl, and those for strain AZM44c09(T) were 70 degrees C, pH
AB  - 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains,
AB  - revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic
AB  - analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences
AB  - of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The
AB  - closest relatives of strains
AB  - AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0 % similarity
AB  - based on the 16S rRNA gene and 84.1 % similarity based on ribosomal
AB  - proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively.
AB  - Using blast, the average nucleotide identity was 70.4-70.5 % when comparing strain AZM34c06(T)
AB  - and T. lettingae TMO(T) and 76.6 % when comparing strain
AB  - AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95 % threshold value
AB  - for species delineation. In view of these data, we propose the inclusion of the two isolates
AB  - in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain
AB  - AZM34c06(T) = NBRC 106115(T) = DSM
AB  - 23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC
AB  - 106116(T) = DSM 23272(T)).
ER  -

TY  - JOUR
AU  - Mori, T.
AU  - Takahashi, M.
AU  - Tanaka, R.
AU  - Shibata, T.
AU  - Kuroda, K.
AU  - Ueda, M.
AU  - Takeyama, H.
TI  - Draft Genome Sequence of Falsirhodobacter sp. Strain alg1, an Alginate-Degrading  Bacterium Isolated from Fermented Brown Algae.
JO  - Genome Announcements
PY  - 2014
SP  - e00826
EP  - e00814
VL  - 2
AB  - Falsirhodobacter sp. alg1 is an alginate-degrading bacterium, the second species  from the
AB  - nonphototrophic bacterial genus Falsirhodobacter. We report the first
AB  - draft genome of a bacterium from this genus and point out possible important
AB  - features related to alginate assimilation and its evolutionary aspects.
ER  -

TY  - JOUR
AU  - Moriel, B.
AU  - Cruz, L.M.
AU  - Dallagassa, C.B.
AU  - Faoro, H.
AU  - de Souza, E.M.
AU  - Pedrosa, F.O.
AU  - Rego, F.G.
AU  - Picheth, G.
AU  - Fadel-Picheth, C.M.
TI  - Draft Genome Sequence of Aeromonas caviae 8LM, Isolated from Stool Culture of a Child with Diarrhea.
JO  - Genome Announcements
PY  - 2015
SP  - e00524
EP  - e00515
VL  - 3
AB  - Aeromonas spp. are Gram-negative rods ubiquitous in aquatic environments; however, some
AB  - species are able to cause a variety of infections in humans. Here,
AB  - we report the draft genome sequence of Aeromonas caviae 8LM isolated from stool
AB  - culture from a child with diarrhea in southern Brazil.
ER  -

TY  - JOUR
AU  - Moriel, D.G. et al.
TI  - Identification of protective and broadly conserved vaccine antigens from the genome of Extraintestinal Pathogenic Escherichia coli (ExPEC).
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 9072
EP  - 9077
VL  - 107
AB  - Extraintestinal pathogenic Escherichia coli (ExPEC) are a common cause of disease in both
AB  - mammals and birds. A vaccine to prevent such infections would be desirable given the
AB  - increasing antibiotic resistance of these bacteria. We have determined the genome
AB  - sequence of ExPEC IHE3034 (ST95) isolated from a case of neonatal
AB  - meningitis and compared this to available genome sequences of
AB  - other ExPEC strains and a few nonpathogenic E. coli. We found
AB  - 19 genomic islands present in the genome of IHE3034, which are
AB  - absent in the nonpathogenic E. coli isolates. By using subtractive
AB  - reverse vaccinology we identified 230 antigens present in ExPEC
AB  - but absent (or present with low similarity) in nonpathogenic
AB  - strains. Nine antigens were protective in a mouse challenge model.
AB  - Some of them were also present in other pathogenic non-ExPEC
AB  - strains, suggesting that a broadly protective E. coli vaccine may
AB  - be possible. The gene encoding the most protective antigen was
AB  - detected in most of the E. coli isolates, highly conserved in
AB  - sequence and found to be exported by a type II secretion system
AB  - which seems to be nonfunctional in nonpathogenic strains.
ER  -

TY  - JOUR
AU  - Morikawa, K.
AU  - Shirakawa, M.
TI  - Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.
JO  - Mutat. Res.
PY  - 2000
SP  - 257
EP  - 275
VL  - 460
AB  - Genetic information is frequently disturbed by introduction of modified or mismatch bases into
AB  - duplex DNA, and hence all organisms contain DNA repair systems to restore normal genetic
AB  - information by removing such damaged bases or nucleotides and replacing them by correct ones.
AB  - The understanding of this repair mechanism is a central subject in cell biology. This review
AB  - focuses on the three-dimensional structural views of damaged DNA recognition by three
AB  - proteins. The first protein is T4 endonuclease V (T4 endo V), which catalyzes the first
AB  - reaction step of the excision repair pathway to remove pyrimidine-dimers (PD) produced within
AB  - duplex DNA by UV irradiation. The crystal structure of this enzyme complexed with DNA
AB  - containing a thymidine-dimer provided the first direct view of DNA lesion recognition by a
AB  - repair enzyme, indicating that the DNA kink coupled with base flipping-out is important for
AB  - damaged DNA recognition. The second is very short patch repair (Vsr) endonuclease, which
AB  - recognizes a TG mismatch within the five base pair consensus sequence. The crystal structure
AB  - of this enzyme in complex with duplex DNA containing a TG mismatch revealed a novel mismatch
AB  - base pair recognition scheme, where three aromatic residues intercalate from the major groove
AB  - into the DNA to strikingly deform the base pair stacking but the base flipping-out does not
AB  - occur. The third is human nucleotide excision repair (NER) factor XPA, which is a major
AB  - component of a large protein complex. This protein has been shown to bind preferentially to
AB  - UV- or chemical carcinogen-damaged DNA. The solution structure of the XPA central domain,
AB  - essential for the interaction of damaged DNA, was determined by NMR. This domain was found to
AB  - be divided mainly into a (Cys)4-type zinc-finger motif subdomain for replication protein A
AB  - (RPA) recognition and the carboxyl terminal subdomain responsible for DNA binding.
ER  -

TY  - JOUR
AU  - Morishima, N.
AU  - Nakagawa, K.-I.
AU  - Shibata, T.
TI  - A sequence-specific endonuclease, Endo.SceI, can efficiently induce gene conversion in yeast mitochondria lacking a major exonuclease.
JO  - Curr. Genet.
PY  - 1993
SP  - 537
EP  - 541
VL  - 23
AB  - Endo.SceI most likely initiates homologous recombination of the yeast mitochondrial genome
AB  - through sequence-specific double-strand scission of DNA.  According to the double-strand
AB  - break-repair model for the mechanism of homologous recombination, DNA ends created by
AB  - sequence-specific endonucleases have to be processed by exonucleases.  The major mitochondrial
AB  - exonuclease (encoded by NUC1) has been shown to greatly affect the length of conversion tracts
AB  - at the 21S rRNA locus when site-specific gene conversion is induced by omega endonuclease.  In
AB  - order to examine the role of the NUC1 nuclease in the Endo.SceI-induced recombination,
AB  - recombination frequencies were measured after crossing of parental strains either in the
AB  - presence or absence of NUC1 nuclease activity.  The frequency of gene conversion in the oli2
AB  - locus induced by Endo.SceI was not reduced by disruption of the NUC1 gene.  This result
AB  - strongly implicates the presence of multiple exonucleases for the processing of the DNA ends
AB  - created by sequence-specific endonucleases.
ER  -

TY  - JOUR
AU  - Morishima, N.
AU  - Nakagawa, K.-I.
AU  - Yamamoto, E.
AU  - Shibata, T.
TI  - A subunit of yeast site-specific endonuclease SceI is a mitochondrial version of the 70-kDa heat shock protein.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 15189
EP  - 15197
VL  - 265
AB  - Endo.SceI of Saccharomyces cerevisiae is a heterodimeric site-specific
AB  - endonuclease, which is distinguishable from prokaryotic restriction
AB  - endonucleases in the mode of recognition of its cleavage site.  We have used
AB  - monoclonal antibodies specific to the larger subunit (75 kDa) of Endo.SceI to
AB  - isolate the gene for the subunit (ENS1) from S. cerevisiae.  Unexpectedly ENS1
AB  - was found to encode a 70-kDa heat shock protein-related polypeptide and to be
AB  - identical to recently cloned SSC1.  Subcellular fractionation experiments on
AB  - yeast cells revealed that the primary target site of the larger subunit is
AB  - mitochondria, where almost all the Endo.SceI activity is localized.  Molecular
AB  - genetic analysis of ENS1 demonstrated its indispensability for growth and the
AB  - requirement of a high level of its expression at the sporulation and
AB  - germination stages.  The data suggest that ENS1 plays an important role,
AB  - especially at these differentiation stages.
ER  -

TY  - JOUR
AU  - Morishima, N.
AU  - Shibata, T.
TI  - SceI: an endonuclease with multiple cutting sites induces homologous genetic recombination.
JO  - Seikagaku
PY  - 1992
SP  - 1420
EP  - 1431
VL  - 64
AB  - A review.
ER  -

TY  - JOUR
AU  - Morishima, N.
AU  - Shibata, T.
TI  - Sequence-specific endonucleases involved in genetic recombination.
JO  - Tanpakushitsu Kakusan Koso
PY  - 1991
SP  - 1716
EP  - 1720
VL  - 36
ER  -

TY  - JOUR
AU  - Morita, H.
AU  - Toh, H.
AU  - Fukuda, S.
AU  - Horikawa, H.
AU  - Oshima, K.
AU  - Suzuki, T.
AU  - Murakami, M.
AU  - Hisamatsu, S.
AU  - Kato, Y.
AU  - Takizawa, T.
AU  - Fukuoka, H.
AU  - Yoshimura, T.
AU  - Itoh, K.
AU  - O'Sullivan, D.J.
AU  - McKay, L.L.
AU  - Ohno, H.
AU  - Kikuchi, J.
AU  - Masaoka, T.
AU  - Hattori, M.
TI  - Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production.
JO  - DNA Res.
PY  - 2008
SP  - 151
EP  - 161
VL  - 15
AB  - Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits
AB  - the gut of humans and other animals. The probiotic
AB  - effects of L. reuteri have been proposed to be largely associated with the
AB  - production of the broad-spectrum antimicrobial compound reuterin during
AB  - anaerobic metabolism of glycerol. We determined the complete genome
AB  - sequences of the reuterin-producing L. reuteri JCM 1112(T) and its closely
AB  - related species Lactobacillus fermentum IFO 3956. Both are in the same
AB  - phylogenetic group within the genus Lactobacillus. Comparative genome
AB  - analysis revealed that L. reuteri JCM 1112(T) has a unique cluster of 58
AB  - genes for the biosynthesis of reuterin and cobalamin (vitamin B(12)). The
AB  - 58-gene cluster has a lower GC content and is apparently inserted into the
AB  - conserved region, suggesting that the cluster represents a genomic island
AB  - acquired from an anomalous source. Two-dimensional nuclear magnetic
AB  - resonance (2D-NMR) with (13)C(3)-glycerol demonstrated that L. reuteri JCM
AB  - 1112(T) could convert glycerol to reuterin in vivo, substantiating the
AB  - potential of L. reuteri JCM 1112(T) to produce reuterin in the intestine.
AB  - Given that glycerol is shown to be naturally present in feces, the
AB  - acquired ability to produce reuterin and cobalamin is an adaptive
AB  - evolutionary response that likely contributes to the probiotic properties
AB  - of L. reuteri.
ER  -

TY  - JOUR
AU  - Morita, H.
AU  - Toh, H.
AU  - Nakano, A.
AU  - Oshima, K.
AU  - Takagi, M.
AU  - Suda, W.
AU  - Tanabe, S.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Bifidobacterium kashiwanohense JCM 15439T, Isolated from Feces from a Healthy Japanese Infant.
JO  - Genome Announcements
PY  - 2015
SP  - e00255
EP  - e00215
VL  - 3
AB  - We isolated Bifidobacterium kashiwanohense JCM 15439 from the feces of a healthy  Japanese
AB  - infant and proposed it as the type strain of a novel species within the
AB  - genus Bifidobacterium. Here, we report the complete genome sequence of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Morita, H.
AU  - Toh, H.
AU  - Oshima, K.
AU  - Murakami, M.
AU  - Taylor, T.D.
AU  - Igimi, S.
AU  - Hattori, M.
TI  - Complete genome sequence of probiotic Lactobacillus rhamnosus ATCC 53103.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7630
EP  - 7631
VL  - 191
AB  - Lactobacillus rhamnosus is a facultatively heterofermentative lactic acid bacterium and is
AB  - frequently isolated from human gastrointestinal mucosa of healthy individuals. L. rhamnosus
AB  - ATCC 53103 isolated from a healthy human intestinal flora is one of the most widely used and
AB  - well-documented probiotics. Here we report the finished and annotated genome sequence of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Morita, H.
AU  - Toh, H.
AU  - Oshima, K.
AU  - Nakano, A.
AU  - Hano, C.
AU  - Yoshida, S.
AU  - Bolormaa, T.
AU  - Burenjargal, S.
AU  - Nguyen, C.T.
AU  - Tashiro, K.
AU  - Arakawa, K.
AU  - Miyamoto, T.
TI  - Draft Genome Sequence of Leuconostoc mesenteroides 213M0, Isolated from Traditional Fermented Mare Milk Airag in Bulgan Aimag, Mongolia.
JO  - Genome Announcements
PY  - 2016
SP  - e00178
EP  - e00116
VL  - 4
AB  - Leuconostoc mesenteroides213M0 was isolated from traditional fermented mare milk  airag in
AB  - Bulgan Aimag, Mongolia. This strain produces a listericidal
AB  - bacteriocin-like inhibitory substance. Here, we report the draft genome sequence
AB  - of this organism.
ER  -

TY  - JOUR
AU  - Morita, H.
AU  - Toh, H.
AU  - Oshima, K.
AU  - Nakano, A.
AU  - Hano, C.
AU  - Yoshida, S.
AU  - Nguyen, T.T.
AU  - Wulijideligen, T.K.
AU  - Arakawa, K.
AU  - Miyamoto, T.
TI  - Draft Genome Sequence of Leuconostoc mesenteroides 406 Isolated from the Traditional Fermented Mare Milk Airag in Tuv Aimag, Mongolia.
JO  - Genome Announcements
PY  - 2016
SP  - e00166
EP  - e00116
VL  - 4
AB  - Leuconostoc mesenteroides406 was isolated from the traditional fermented mare milk airag in
AB  - Tuv Aimag, Mongolia. This strain produces an antilisterial
AB  - bacteriocin. Here, we report the draft genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Morita, H.
AU  - Toh, H.
AU  - Oshima, K.
AU  - Yoshizaki, M.
AU  - Kawanishi, M.
AU  - Nakaya, K.
AU  - Suzuki, T.
AU  - Miyauchi, E.
AU  - Ishii, Y.
AU  - Tanabe, S.
AU  - Murakami, M.
AU  - Hattori, M.
TI  - Complete Genome Sequence and Comparative Analysis of the Fish Pathogen Lactococcus garvieae.
JO  - PLoS ONE
PY  - 2011
SP  - E23184
EP  - E23184
VL  - 6
AB  - Lactococcus garvieae causes fatal haemorrhagic septicaemia in fish such as
AB  - yellowtail. The comparative analysis of genomes of a virulent strain Lg2
AB  - and a non-virulent strain ATCC 49156 of L. garvieae revealed that the two
AB  - strains shared a high degree of sequence identity, but Lg2 had a 16.5-kb
AB  - capsule gene cluster that is absent in ATCC 49156. The capsule gene
AB  - cluster was composed of 15 genes, of which eight genes are highly
AB  - conserved with those in exopolysaccharide biosynthesis gene cluster often
AB  - found in Lactococcus lactis strains. Sequence analysis of the capsule gene
AB  - cluster in the less virulent strain L. garvieae Lg2-S, Lg2-derived strain,
AB  - showed that two conserved genes were disrupted by a single base pair
AB  - deletion, respectively. These results strongly suggest that the capsule is
AB  - crucial for virulence of Lg2. The capsule gene cluster of Lg2 may be a
AB  - genomic island from several features such as the presence of insertion
AB  - sequences flanked on both ends, different GC content from the chromosomal
AB  - average, integration into the locus syntenic to other lactococcal genome
AB  - sequences, and distribution in human gut microbiomes. The analysis also
AB  - predicted other potential virulence factors such as haemolysin. The
AB  - present study provides new insights into understanding of the virulence
AB  - mechanisms of L. garvieae in fish.
ER  -

TY  - JOUR
AU  - Morita, R.
AU  - Ishikawa, H.
AU  - Nakagawa, N.
AU  - Kuramitsu, S.
AU  - Masui, R.
TI  - Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8.
JO  - Proteins
PY  - 2008
SP  - 259
EP  - 264
VL  - 73
AB  - To protect the cell from exogenous DNA, most species have DNA modification methylase.  It is
AB  - also reported that DNA methylation is essentially involved in bacterial virulence.  Many
AB  - restriction-modification systems have been researched, and several three-dimensional
AB  - structures of R-M enzymes have been determined.  DNA modification methylases catalyze the
AB  - transfer of a methyl group to DNA from S-adenosyl-L-methionine, which is consequently
AB  - converted to S-adenosyl-L-homocysteine.  These enzymes are categorized into the following two
AB  - classes based on the position of the transferred methyl group on the DNA bases: endocyclic
AB  - MTases and exocyclic amino MTases.  Endocyclic MTases methylate the C5 position of a cytosine
AB  - base, whereas exocyclic amino MTases methylate the N6 position of an adenine base or N4
AB  - position of a cytosine base.  Furtermore, the exocyclic amino MTases are subdivided into six
AB  - classes, namely, alpha, beta, gamma, delta and epsilon, based on their amino acid sequences.
ER  -

TY  - JOUR
AU  - Moriya, N. et al.
TI  - Complete Genome Sequence of Lactobacillus plantarum Strain LQ80, Selected for Preparation of Fermented Liquid Feed for Pigs.
JO  - Genome Announcements
PY  - 2018
SP  - e00530
EP  - e00518
VL  - 6
AB  - Lactobacillus plantarum LQ80 is a strain isolated from liquid feed for pigs. We determined the
AB  - complete genome sequence of this strain using the PacBio RS II
AB  - platform. LQ80 contained a single circular chromosome of 3,230,192 bp, with
AB  - 44.66% G+C content and seven plasmids.
ER  -

TY  - JOUR
AU  - Moriya, S.
AU  - Yanagawa, S.
AU  - Aoki, N.
AU  - Iwabuchi, M.
AU  - Inoue, T.
AU  - Ando, T.
TI  - Isolation and characterization of a restriction enzyme BspO4I from an alkalophilic bacterium.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3781
EP  - 3781
VL  - 20
AB  - A type II restriction enzyme, BspO4I, has been isolated from Bacillus sp 0-4 (ATCC 21536), an
AB  - alkalophilic bacterium. The enzyme was an isoschizomer of PvuII, recognizing the six base
AB  - palindromic sequence of 5'CAGCTG3' and cleaves between G and C residues to produce
AB  - blunt-ended cleavage products. Bsp04I was partially purified from a cell-free extract using
AB  - column chromatography on DEAE-cellulose, heparin-cellulofine and phosphocellulose. Optimal
AB  - conditions for the enzyme activity were pH 8.5, 20 mM MgCl2, 250 mM monovalent cation (NaCl or
AB  - KCl), 10 mM 2-mercaptoethanol at 40oC. The cleavage site of BspO4I was determined by primer
AB  - extension experiments and indicated that BspO4I recognizes and cleaves the following sequence:
AB  - 5'CAG^CTG3'
AB  - 3'GTC^GAC5'.
ER  -

TY  - JOUR
AU  - Morohoshi, T.
AU  - Ikeda, T.
TI  - Complete Genome Sequence of Methylobacterium populi P-1M, Isolated from Pink-Pigmented Household Biofilm.
JO  - Genome Announcements
PY  - 2016
SP  - e00458
EP  - e00416
VL  - 4
AB  - Methylobacterium populi P-1M is isolated from the pink-pigmented household biofilm. Here, we
AB  - present the complete genome sequence of P-1M, consisting of one
AB  - chromosome of 5,705,640 bp and five plasmids of 64,864 bp, 59,879 bp, 42,569 bp,
AB  - 41,417 bp, and 29,506 bp.
ER  -

TY  - JOUR
AU  - Morohoshi, T.
AU  - Kato, T.
AU  - Someya, N.
AU  - Ikeda, T.
TI  - Complete Genome Sequence of N-Acylhomoserine Lactone-Producing Pseudomonas sp. Strain StFLB209, Isolated from Potato Phyllosphere.
JO  - Genome Announcements
PY  - 2014
SP  - e01037
EP  - e01014
VL  - 2
AB  - Pseudomonas sp. strain StFLB209 is isolated from the potato leaf and produces N-acylhomoserine
AB  - lactone quorum-sensing signal compounds. Here, we present the
AB  - 6,332,373-bp complete genome sequence of StFLB209, with a G+C content of 60.7%,
AB  - which carries 5,598 protein-coding genes, 6 rRNA operons, and 69 tRNA genes.
ER  -

TY  - JOUR
AU  - Morohoshi, T.
AU  - Wang, W.Z.
AU  - Someya, N.
AU  - Ikeda, T.
TI  - Complete Genome Sequence of Chryseobacterium sp. Strain StRB126, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Root.
JO  - Genome Announcements
PY  - 2014
SP  - e00952
EP  - e00914
VL  - 2
AB  - Chryseobacterium sp. strain StRB126 was isolated from a potato root and showed
AB  - N-acylhomoserine lactone-degrading activity. Here, we present the complete
AB  - 5,503,743-bp genome sequence of StRB126, which has a G+C content of 35.6% and
AB  - carries 4,828 protein-coding genes, six rRNA operons, and 80 tRNA genes.
ER  -

TY  - JOUR
AU  - Morohoshi, T.
AU  - Wang, W.Z.
AU  - Someya, N.
AU  - Ikeda, T.
TI  - Genome Sequence of Microbacterium testaceum StLB037, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Leaves.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2072
EP  - 2073
VL  - 193
AB  - Microbacterium testaceum is an endophytic Gram-positive bacterium that resides within plant
AB  - hosts. M. testaceum StLB037 was isolated from potato
AB  - leaves and shows N-acylhomoserine lactone-degrading activity. Here, we
AB  - present the 3.98-Mb complete genome sequence of StLB037, with an average
AB  - GC content of 70.28%.
ER  -

TY  - JOUR
AU  - Morozova, N.
AU  - Sabantsev, A.
AU  - Bogdanova, E.
AU  - Fedorova, Y.
AU  - Maikova, A.
AU  - Vedyaykin, A.
AU  - Rodic, A.
AU  - Djordjevic, M.
AU  - Khodorkovskii, M.
AU  - Severinov, K.
TI  - Temporal dynamics of methyltransferase and restriction endonuclease accumulation  in individual cells after introducing a restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 790
EP  - 800
VL  - 44
AB  - Type II restriction-modification (R-M) systems encode a restriction endonuclease  that cleaves
AB  - DNA at specific sites, and a methyltransferase that modifies same
AB  - sites protecting them from restriction endonuclease cleavage. Type II R-M systems
AB  - benefit bacteria by protecting them from bacteriophages. Many type II R-M systems
AB  - are plasmid-based and thus capable of horizontal transfer. Upon the entry of such
AB  - plasmids into a naive host with unmodified genomic recognition sites,
AB  - methyltransferase should be synthesized first and given sufficient time to
AB  - methylate recognition sites in the bacterial genome before the toxic restriction
AB  - endonuclease activity appears. Here, we directly demonstrate a delay in
AB  - restriction endonuclease synthesis after transformation of Escherichia coli cells
AB  - with a plasmid carrying the Esp1396I type II R-M system, using single-cell
AB  - microscopy. We further demonstrate that before the appearance of the Esp1396I
AB  - restriction endonuclease the intracellular concentration of Esp1396I
AB  - methyltransferase undergoes a sharp peak, which should allow rapid methylation of
AB  - host genome recognition sites. A mathematical model that satisfactorily describes
AB  - the observed dynamics of both Esp1396I enzymes is presented. The results reported
AB  - here were obtained using a functional Esp1396I type II R-M system encoding both
AB  - enzymes fused to fluorescent proteins. Similar approaches should be applicable to
AB  - the studies of other R-M systems at single-cell level.
ER  -

TY  - JOUR
AU  - Morris, D.W.
AU  - Parish, J.H.
TI  - Restriction in Myxococcus virescens.
JO  - Arch. Microbiol.
PY  - 1976
SP  - 227
EP  - 230
VL  - 108
AB  - 1.  The plating efficiency of bacteriophage MX-1 on Myococcus xanthus strains A
AB  - and B and M. virescens V2 were compared.  Comparison of strains V2 and A
AB  - suggest that V2 is restrictive and A is not (restriction coefficient was
AB  - approximately 8).  A derivative of M. virescens V2 (strain V2-9) was obtained
AB  - by repeated exposure of strain V2 to ultraviolet radiation.  Strain V2-9 was
AB  - also unrestrictive.  Strain B is apparently unrestrictive too but analysis of
AB  - phenotypic changes in phage derived from hosts V2, B and A suggested that some
AB  - of the host-cell processes differ from orthodox restriction and modification.
AB  - 2.  Cell-free extracts from M. virescens V2 were fractionated by ion-exchange
AB  - chromatography and two restriction endonucleases, R. MviV2I and R. MviV2II were
AB  - identified.  Nuclease I was found to hydrolyse coliphage lambda DNA at
AB  - apparently one site only and MX-1 DNA at approximately 10 sites; nuclease II
AB  - was found to hydrolyse MX-1 DNA at a very large number of sites and its
AB  - restriction sequence was of comparable frequency with that of R.EcoRII.
AB  - "Modified MX-1 DNA", obtained from phage whose last host was M. virescens V2
AB  - was hydroxlysed by nuclease II but not by nuclease I.  The significance of
AB  - these findings for restriction in myxococci is discussed.
ER  -

TY  - JOUR
AU  - Morris, P.
AU  - Marinelli, L.J.
AU  - Jacobs-Sera, D.
AU  - Hendrix, R.W.
AU  - Hatfull, G.F.
TI  - Genomic characterization of mycobacteriophage giles: evidence for phage acquisition of host DNA by illegitimate recombination.
JO  - J. Bacteriol.
PY  - 2008
SP  - 2172
EP  - 2182
VL  - 190
AB  - A characteristic feature of bacteriophage genomes is that they are
AB  - architecturally mosaic, with each individual genome representing a unique
AB  - assemblage of individual exchangeable modules. Plausible mechanisms for
AB  - generating mosaicism include homologous recombination at shared boundary
AB  - sequences of module junctions, illegitimate recombination in a
AB  - non-sequence-directed process, and site-specific recombination. Analysis
AB  - of the novel mycobacteriophage Giles genome not only extends our current
AB  - perspective on bacteriophage genetic diversity, with more than 60% of the
AB  - genes unrelated to other mycobacteriophages, but offers novel insights
AB  - into how mosaic genomes are created. In one example, the
AB  - integration/excision cassette is atypically situated within the structural
AB  - gene operon and could have moved there either by illegitimate
AB  - recombination or more plausibly via integrase-mediated site-specific
AB  - recombination. In a second example, a DNA segment has been recently
AB  - acquired from the host bacterial chromosome by illegitimate recombination,
AB  - providing further evidence that phage genomic mosaicism is generated by
AB  - nontargeted recombination processes.
ER  -

TY  - JOUR
AU  - Morrison, C.K.
AU  - Novinscak, A.
AU  - Gadkar, V.J.
AU  - Joly, D.L.
AU  - Filion, M.
TI  - Complete Genome Sequence of Pseudomonas fluorescens LBUM636, a Strain with Biocontrol Capabilities against Late Blight of Potato.
JO  - Genome Announcements
PY  - 2016
SP  - e00446
EP  - e00416
VL  - 4
AB  - Herein provided is the full-genome sequence of Pseudomonas fluorescens LBUM636. This strain is
AB  - a plant growth-promoting rhizobacterium (PGPR) which produces
AB  - phenazine-1-carboxylic acid, an antibiotic involved in the biocontrol of numerous
AB  - plant pathogens, including late blight of potato caused by the plant pathogen
AB  - Phytophthora infestans.
ER  -

TY  - JOUR
AU  - Morrison, E.A.
AU  - Garner, S.
AU  - Echaubard, P.
AU  - Lesbarreres, D.
AU  - Kyle, C.J.
AU  - Brunetti, C.R.
TI  - Complete genome analysis of a frog virus 3 (FV3) isolate and sequence comparison with isolates of differing levels of virulence.
JO  - Virol. J.
PY  - 2014
SP  - 46
EP  - 46
VL  - 11
AB  - BACKGROUND: Frog virus 3 (FV3) is the type species of the genus Ranavirus, and in
AB  - the past few decades, FV3 infections have resulted in considerable morbidity and
AB  - mortality in a range of wild and cultivated amphibian species in the Americas,
AB  - Europe, and Asia. The reasons for the pathogenicity of FV3 are not well
AB  - understood. FINDINGS: We investigated three FV3 isolates designated SSME, wt-FV3,
AB  - and aza-Cr, and reported that our wt-FV3 and aza-Cr strains showed similar levels
AB  - of virulence, while SSME was the least virulent in an in vivo study with
AB  - Lithiobates pipiens tadpoles. Using 454 GS-FLX sequencing technology, we
AB  - sequenced SSME and compared it to the published wt-FV3 genome. SSME had multiple
AB  - amino acid deletions in ORFs 49/50L, 65L, 66L, and 87L, which may explain its
AB  - reduced virulence. We also investigated repeat regions and found that repeat copy
AB  - number differed between isolates, with only one group of 3 isolates and 1 pair of
AB  - isolates being identical at all 3 locations. CONCLUSIONS: In this study we have
AB  - shown that genetic variability is present between closely related FV3 isolates,
AB  - both in terms of deletions/insertions, and even more so at select repeat
AB  - locations. These genomic areas with deletions/insertions may represent regions
AB  - that affect virulence, and therefore require investigation. Furthermore, we have
AB  - identified repeat regions that may prove useful in future phylogeographical
AB  - tracking and identification of ranaviral strains across different environmental
AB  - regions.
ER  -

TY  - JOUR
AU  - Morrison, H.A.
AU  - Seligman, L.M.
TI  - Homing endonuclease I-CreI mutants with substitutions at residues 30, 32 and 38 include altered specificity derivatives.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2004
SP  - 313
EP  - 313
VL  - 104
AB  - The homing endonuclease I-CreI recognizes and cleaves a specific 22 base pair DNA sequence.
AB  - The amino acid contacts responsible for DNA recognition have been identified; three such
AB  - residues that cooperate to interact with a particular target site base pair are N30, S32, and
AB  - Q38.  In order to study how these residues function in DNA recognition and cleavage, as well
AB  - as the interactions bertween the residues themselves, we employed site-directed mutagenesis to
AB  - alter the amino acids at these positions.  Resulting I-CreI derivatives were then assayed in
AB  - vivo in an Escherichia coli based system for cleavage activity against appropriate DNA
AB  - targets.  A number of active I-CreI derivatives altered at these positions have been isolated
AB  - and characterized both in vivo and in vitro.  Our results demonstrate that it is possible to
AB  - isolate derivatives of I-CreI altered at residues 30, 32 and 38 that exhibit novel DNA
AB  - recognition properties.
ER  -

TY  - JOUR
AU  - Morrison, M.
TI  - Deoxyribonucleic acid restriction/modification systems and gene transfer strategies in Ruminococcus albus 8 and Ruminococcus flavofaciens FD-1.
JO  - Ph.D. Thesis, University of Illinois, USA
PY  - 1991
SP  - 1
EP  - 134
AB  - One goal critical to the use of recombinant DNA technologies with rumen bacteria is the
AB  - establishment of a stable DNA transfer system. Research to date has shown that Ruminococcus
AB  - can be classified as a genus resistant to transformation, and that electroporation may offer
AB  - the only means to introduce foreign DNA. This thesis aims to elucidate and solve limitations
AB  - to the utilization of electroporation with Ruminococcus albus 8 and Ruminococcus flavefaciens
AB  - FD-1. The limited degradation of DNA by restriction enzymes and confirmation of plasmid uptake
AB  - were given priority, although the consequences of incompatible plasmid replicons and failure
AB  - in the expression of selectable markers cannot be overlooked. Fluorescent labelled dextrans
AB  - were used in place of plasmid DNA and indicated that electroporation resulted in the uptake of
AB  - macromolecules. Type-II endonuclease activities were present in most strains of Ruminococcus
AB  - tested. However, the cell-free extract of R. flavefaciens FD-1 did not provide a simple DNA
AB  - protection strategy, so the restriction/modification systems of R. albus 8 and R. flavefaciens
AB  - FD-1 were studied in more detail. Plasmids derived from a dam proficient Escherichia coli
AB  - background are protected against the Type-IIS restriction enzyme of R. albus 8. Adenine
AB  - methylation by M.TaqI and a methylase from Chlorella will inhibit DNA cleavage by RflFI and
AB  - RFlFII, respectively. The initial electroporation experiments utilizing methylated DNA were
AB  - unsuccessful in yielding phenotypic transformants of R. albus 8. Plasmid DNA isolated directly
AB  - from Ruminococcus would be a valuable tool in addressing some of the problems still affecting
AB  - gene transfer. The plasmid pBAW301, present in R. flavefaciens strain R13c2, was isolated and
AB  - is sufficiently small to facilitate construction of potential shuttle vectors as well as broad
AB  - host range, chimeric plasmids. Knowledge of DNA modification in Ruminococcus has been
AB  - obtained. Other species possessing stable plasmids and gene/s encoding antibiotic resistance
AB  - have also been identified. Greater emphasis can now be placed on the electroporation technique
AB  - itself, as well as a wider range of selective markers. Ruminococcus ssp. required further
AB  - investigation if model genetic systems are to be developed and some of the proposed goals of
AB  - molecular biology research for this genus are to be fully realized.
ER  -

TY  - JOUR
AU  - Morrison, M.
AU  - Mackie, R.I.
AU  - White, B.A.
TI  - The restriction endonuclease RflFII, isolated from Ruminococcus flavefaciens FD-1, recognizes the sequence 5'-AGTACT-3', and is inhibited by site-specific adenine methylation.
JO  - FEMS Microbiol. Lett.
PY  - 1994
SP  - 181
EP  - 185
VL  - 122
AB  - Molecular studies of the rumen bacterium Ruminococcus flavefaciens are constrained by the lack
AB  - of stable gene transfer system. We report here on the characterization of RflFII, a
AB  - restriction endonuclease isolated from R. flavefaciens FD-1. The enzyme is an isoschizomer of
AB  - ScaI, and cleavage of the DNA is blunt-ended, between the internal TA dinucleotide sequence of
AB  - 5'-AGTACT-3'. Chromosomal DNA preparations were used to demonstrate that adenine methylation
AB  - of DNA within the sequence 5'-GTAC-3' inhibits both RflFII and the restriction endonucleases
AB  - RsaI and ScaI. Chromosomal DNA from R. flavefaciens FD-1 is also host modified to protect
AB  - against cleavage by ScaI.
ER  -

TY  - JOUR
AU  - Morrison, M.
AU  - Mackie, R.I.
AU  - White, B.A.
TI  - Partial characterization of a DNA restriction endonuclease from Ruminococcus flavefaciens FD-1 and its inhibition by site-specific adenine methylation.
JO  - Appl. Environ. Microbiol.
PY  - 1992
SP  - 66
EP  - 69
VL  - 58
AB  - The principal DNA restriction-modification system of the cellulolytic ruminal
AB  - bacterium Ruminococcus flavefaciens FD-1 is described.  The restriction
AB  - endonuclease RflFI could be separated from cell extracts by phosphocellulose
AB  - and heparin-sepharose chromatography.  Restriction enzyme digests utilizing
AB  - RflFI alone or in combination with SalI, a restriction enzyme isolated from
AB  - Streptomyces albus G, showed that the DNA sequence recognized by RflFI either
AB  - overlapped or was the same as that recognized by SalI.  DNA sequence analysis
AB  - confirmed that RflFI was identical in activity to SalI, with the recognition
AB  - sequence being 5'-GTCGAC-3' and cleavage occurring between G and T.  Adenine
AB  - methylation within this sequence can be catalyzed in vitro by TaqI methylase,
AB  - and this inhibited the cleavage of plasmid DNA molecules by RflFI and SalI.
AB  - Chromosomal DNA from R. flavefaciens FD-1 is also methylated within this DNA
AB  - sequence because neither restriction endonuclease could degrade this DNA
AB  - substrate.  These findings provide a means to protect plasmid molecules from
AB  - degradation prior to gene transfer experiments with R. flavefaciens FD-1.
ER  -

TY  - JOUR
AU  - Morrison, M.
AU  - Mackie, R.I.
AU  - White, B.A.
TI  - Partial purification and characterization of Ral8I, a class-IIS restriction endonuclease from Ruminococcus albus 8 which recognizes 5'-GGATC .
JO  - Gene
PY  - 1992
SP  - 105
EP  - 108
VL  - 111
AB  - Heparin-agarose chromatography was used to isolate a restriction endonuclease (ENase) from the
AB  - cellulolytic Gram + anaerobe, Ruminococcus albus 8. The enzyme, Ral8I, was eluted from the
AB  - column using 230-310 mM Na+. However, the preparation was active only with DNA substrates that
AB  - were not Dam-methylated. Moreover the restriction fragment pattern generated from simian virus
AB  - 40 (SV40) DNA was not consistent with the expected number of Dam-methylation sites. Alignment
AB  - of the Dam-methylation sites in SV40 DNA indicated that Ral8I may actually recognize the
AB  - asymmetric sequence, GGATC. This was confirmed by nucleotide (nt) sequence analysis and,
AB  - further, Ral8I was found to cause cleavage of the DNA approx. 5 nt downstream from the
AB  - recognition sequence. Ral8I can therefore be classified as a type-IIS restriction endonuclease
AB  - and is an isoschizomer of AlwI, BinI and BthII.
ER  -

TY  - JOUR
AU  - Morrison, M.
AU  - Mackie, R.I.
AU  - White, B.A.
TI  - Restriction-modification systems in Ruminococcus and development of a gene transfer system.
JO  - Aust. Microbiol.
PY  - 1992
SP  - 301
EP  - 303
VL  - 0
ER  -

TY  - JOUR
AU  - Morrison, S.S.
AU  - Desai, H.P.
AU  - Mercante, J.W.
AU  - Lapierre, P.
AU  - Raphael, B.H.
AU  - Musser, K.
AU  - Winchell, J.M.
TI  - Complete Genome Sequences of Three Outbreak-Associated Legionella pneumophila Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e00696
EP  - e00616
VL  - 4
AB  - We report here the complete genome sequences of three Legionella pneumophila isolates that are
AB  - associated with a Legionnaires' disease outbreak in New York in
AB  - 2012. Two clinical isolates (D7630 and D7632) and one environmental isolate
AB  - (D7631) were recovered from this outbreak. A single isolate-specific virulence
AB  - gene was found in D7632. These isolates were included in a large study evaluating
AB  - the genomic resolution of various bioinformatics approaches for L. pneumophila
AB  - serogroup 1 isolates.
ER  -

TY  - JOUR
AU  - Morrison, S.S.
AU  - Kozak-Muiznieks, N.A.
AU  - Sammons, S.
AU  - Rowe, L.A.
AU  - Frace, M.
AU  - Winchell, J.M.
TI  - Draft Genome Sequence of Legionella pneumophila D-5864, a Serogroup 6 Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01379
EP  - e01314
VL  - 3
AB  - Legionella pneumophila is the leading etiology of legionellosis infections in North America
AB  - and Europe. Here we report the draft genome sequence of L.
AB  - pneumophila D-5864, a serogroup 6 strain, which was isolated from a bronchial
AB  - alveolar lavage specimen of a male patient from Arizona in 2009. Genes within the
AB  - lipopolysaccharide (LPS)-biosynthesis region could potentially be determinants of
AB  - serogroup specificity.
ER  -

TY  - JOUR
AU  - Morrow, J.F.
AU  - Berg, P.
TI  - Cleavage of Simian Virus 40 DNA at a unique site by a bacterial restriction enzyme.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3365
EP  - 3369
VL  - 69
AB  - The RI restriction endonuclease of Escherichia coli converts covalently-closed
AB  - circular Simian Virus 40 (SV40) DNA to unit-length linear duplex molecules.
AB  - Cleavage occurs at a unique site, since denaturation and renaturation of these
AB  - linear molecules yield linear but no circular molecules.  The distance from the
AB  - cleavage site to the SV40 DNA sequence contained in the adenovirus-SV40 hybrid,
AB  - Ad2+ND1, is 0.11 of the length of SV40 DNA.  T4 gene 32 protein binds to SV40
AB  - DNA in a region 0.45 of the length of SV40 DNA from the RI cleavage site.  E.
AB  - coli B restriction endonuclease can cleave SV40 DNA at several sites.
ER  -

TY  - JOUR
AU  - Mortusewicz, O.
AU  - Schermelleh, L.
AU  - Walter, J.
AU  - Cardoso, M.C.
AU  - Leonhardt, H.
TI  - Recruitment of DNA methyltransferase I to DNA repair sites.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 8905
EP  - 8909
VL  - 102
AB  - In mammalian cells, the replication of genetic and epigenetic information is directly coupled;
AB  - however, little is known about the maintenance of epigenetic information in DNA repair. Using
AB  - a laser microirradiation system to introduce DNA lesions at defined subnuclear sites, we
AB  - tested whether the major DNA methyltransferase (Dnmt1) or one of the two de novo
AB  - methyltransferases (Dnmt3a, Dnmt3b) are recruited to sites of DNA repair in vivo. Time lapse
AB  - microscopy of microirradiated mammalian cells expressing GFP-tagged Dnmt1, Dnmt3a, or Dnmt3b1
AB  - together with red fluorescent protein-tagged proliferating cell nuclear antigen (PCNA)
AB  - revealed that Dnmt1 and PCNA accumulate at DNA damage sites as early as 1 min after
AB  - irradiation in S and non-S phase cells, whereas recruitment of Dnmt3a and Dnmt3b was not
AB  - observed. Deletion analysis showed that Dnmt1 recruitment was mediated by the PCNA-binding
AB  - domain. These data point to a direct role of Dnmt1 in the restoration of epigenetic
AB  - information during DNA repair.
ER  -

TY  - JOUR
AU  - Moser, D.
AU  - Kallas, T.
TI  - Characteristics of a restriction endonuclease from the Cyanobacterium Nostoc PCC 7121 and protection of DNA with Eco 47 II methylase.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - 155
EP  - 155
VL  - 91
AB  - In order to investigate the structure and function of the cytochrome b6-f
AB  - complex, we are trying to develop procedures for gene transfer into and gene
AB  - replacement in Nostoc PCC 7121, a heterotrophic cyanobacterium from which the
AB  - cytochrome b6-f genes have been cloned and sequenced.  Restriction
AB  - endonucleases in Nostoc are being investigated as possible barriers to
AB  - transformation.  A restriction endonuclease which we designated Nsp7121I has
AB  - been isolated and partially purified.  The DNA recognition sequence (GGNCC) for
AB  - this endonuclease was established by comparison of Nsp7171I restriction digests
AB  - of plasmid and bacteriophage DNAs with computer generated restriction fragment
AB  - profiles.  Plasmid encoded Eco47II methylase protected DNA against restriction
AB  - by the Nostoc endonuclease.  Unmodified plasmids previously used in
AB  - transformation attempts were cleaved at multiple sites.  Thus one barrier to
AB  - transformation has been identified and a modification methylase is available
AB  - for its circumvention.  Work is in progress to test transformation of Nostoc
AB  - PCC 7121 with Eco47II protected DNA.
ER  -

TY  - JOUR
AU  - Moser, D.P.
AU  - Zarka, D.
AU  - Kallas, T.
TI  - Characterization of a restriction barrier and electrotransformation of the cyanobacterium Nostoc PCC-7121.
JO  - Arch. Microbiol.
PY  - 1993
SP  - 229
EP  - 237
VL  - 160
AB  - We have investigated host restriction as a barrier to transformation and developed a method
AB  - for gene transfer into the previously untransformable, heterotrophic cyanobacterium Nostoc PCC
AB  - 7121. A restriction endonuclease, designed Nsp7121I, has been partialy purified by
AB  - phosphocellulose chromatography of Nostoc cell extracts. Comparisons of Nsp7121I digests of
AB  - bacteriophage lambda and plasmid DNAs with computer-generated restriction fragment profiles
AB  - showed that Nsp7121I is an isoschizomer of restriction endonucleases, such as AsuI, Nsp75241V,
AB  - Sau96I, and Eco4711, that recognize the sequence GGNCC. Cleavage by Nsp71211 within this
AB  - sequence was confirmed by sequence analysis of DNA fragments cleaved at a unique Nsp7121I
AB  - site. These date further suggested that cleavage occurs after the first G (5'-G/GNCC-3') in
AB  - this site to generate a three base 5' overhang. Nsp7121I degraded all plasmids used in
AB  - previous transformation attempts but modification of these DNA molecules by Eco47II methylase
AB  - effectively prevented digestion by Nsp7121I. Plasmids premethylated by passage through
AB  - Escherichia coli carrying a plasmid-encoded Eco47II methylase have now been used in an
AB  - electroporation procedure to transform Nostoc PCC 7121 to neomycin resistance at frequencies
AB  - as high as one transformant per 1000 viable cells. Transformation and stable replication
AB  - within Nostoc of one of the transforming plasmids (pRL25), was confirmed by recovery of pRL25,
AB  - in its original form, from transformants. Conjugal transfer of pRL25 from E. coli into Nostoc
AB  - was also possible but at much lower efficiency than by electroporation. These findings
AB  - establish the basis for genetic analysis of Nostoc PCC 7121, from which genes for
AB  - photosynthetic electron transport have been cloned.
ER  -

TY  - JOUR
AU  - Moses, P.
AU  - Horiuchi, K.
TI  - Specific Recombination in Vitro Promoted by the Restriction Endonuclease HgaI.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 517
EP  - 524
VL  - 135
AB  - We describe the use of the restriction endonuclease HgaI from Haemophilus
AB  - gallinarum for the efficient construction in vitro of recombinant molecules.
AB  - Using bacteriophage f1 DNA, we show that only HgaI fragments that were
AB  - orginally adjacent on the genome are ligated, that upon ligation infectious
AB  - molecules are reassembled with high efficiency, and that recombinant genomes
AB  - can thus be easily constructed.  The method relies upon the unique properties
AB  - of HgaI and is applicable to any viral or plasmid DNA that contains several
AB  - HgaI recognition sites.
ER  -

TY  - JOUR
AU  - Mosier, A.C.
AU  - Allen, E.E.
AU  - Kim, M.
AU  - Ferriera, S.
AU  - Francis, C.A.
TI  - Genome Sequence of 'Candidatus Nitrosopumilus salaria' BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2121
EP  - 2122
VL  - 194
AB  - Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine
AB  - and terrestrial ecosystems. Here, we present the draft genome
AB  - sequence for the ammonia-oxidizing archaeon 'Candidatus Nitrosopumilus salaria'
AB  - BD31, which was enriched in culture from sediments of the San Francisco Bay
AB  - estuary. The genome sequences revealed many similarities to the genome of
AB  - Nitrosopumilus maritimus.
ER  -

TY  - JOUR
AU  - Mosier, A.C.
AU  - Allen, E.E.
AU  - Kim, M.
AU  - Ferriera, S.
AU  - Francis, C.A.
TI  - Genome Sequence of 'Candidatus Nitrosoarchaeum limnia' BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2119
EP  - 2120
VL  - 194
AB  - Here, we present the draft genome sequence of 'Candidatus Nitrosoarchaeum limnia' BG20, an
AB  - ammonia-oxidizing archaeon enriched in culture from low-salinity
AB  - sediments of the San Francisco Bay estuary. The genome sequence revealed many
AB  - similarities to the previously sequenced genome of 'Ca. Nitrosoarchaeum limnia'
AB  - SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of
AB  - a clade of ammonia-oxidizing archaea (AOA) found in low-salinity habitats
AB  - worldwide.
ER  -

TY  - JOUR
AU  - Motamedchaboki, K.
TI  - Characterization of a restriction endonuclease isolated from Bacillus subtilis F2.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 457
EP  - 457
VL  - 101
AB  - Usefulness of restriction system with their high substrate specificities for ds-DNA, and the
AB  - processing of the free or packaged
AB  - DNA during uptake into Bacillus subtilis cells made us study about the
AB  - restriction enzyme activity of one of our laboratory isolate, Bacillus
AB  - subtilis F2 which have been used for the propagation of the newly
AB  - isolated PAK phage. During the life cycle of PAK phage in Bacillus
AB  - subtilis F2 host, it has been noticed that DNA of phage get fragmented
AB  - in vivo, therefore, it becomes important to explore the endonuclease
AB  - activity in this strain. A cell bound enzyme was isolated from Bacillus
AB  - subtilis F2, and was characterized in crude extract of bacterial cell
AB  - pellet. The enzyme showed to have endonuclease activity on
AB  - bacteriophage lambda DNA and other DNA as well. Interestingly, lambda
AB  - DNA seems to have very few cut sites. Another important characteristic
AB  - of this enzyme is to have optimum pH shifted toward alkaline range,
AB  - which is 8.5 among of 182 known restriction enzymes. The optimum
AB  - temperature found to be 40 C. It seems to work at high salt
AB  - concentration. Lysates extracted at pH 6 and 6.5 have shown
AB  - endonuclease activity with a new profile of lambda DNA fragmentation of
AB  - lysate extracted at pH 7.5. Hence BsuF2 is a type II restriction enzyme
AB  - it seems to have high potential to be used as a genetic tool in
AB  - molecular biology.
ER  -

TY  - JOUR
AU  - Mothupi, B.
AU  - Featherston, J.
AU  - Gray, V.
TI  - Draft Whole-Genome Sequence and Annotation of Xenorhabdus griffiniae Strain BMMCB Associated with the South African Entomopathogenic Nematode Steinernema khoisanae  Strain BMMCB.
JO  - Genome Announcements
PY  - 2015
SP  - e00785
EP  - e00715
VL  - 3
AB  - Xenorhabdus griffiniae strain BMMCB (LDNM00000000) belongs to the family Enterobacteriaceae
AB  - and was isolated from the South African entomopathogenic
AB  - nematode Steinernema khoisanae strain BMMCB (GenBank accession no. KT027382).
AB  - Here, we report the draft whole-genome sequence of X. griffinae strain BMMCB with
AB  - a genome size of 4,183,779 bp and 44.7% G+C content. The NCBI Prokaryotic
AB  - Automatic Annotation Pipeline (PGAAP) revealed 3,970 genes.
ER  -

TY  - JOUR
AU  - Motoshima, K.
AU  - Ishikawa, M.
AU  - Hashimoto, Y.
AU  - Sugita, K.
TI  - Inhibition of Restriction Enzymes EcoRI, BamHI and HindIII by Phenethylphenylphthalimides Derived from Thalidomide.
JO  - Chem. Pharm. Bull. (Tokyo)
PY  - 2011
SP  - 880
EP  - 884
VL  - 59
AB  - We discovered inhibitors of the restriction enzymes EcoRI, BamHI and HindIII by screening our
AB  - library of compounds with a
AB  - phenethylphenylphthalimide skeleton, based on alpha-glucosidase
AB  - inhibitors and liver X receptor antagonists derived from thalidomide.
AB  - Structural development afforded the potent restriction enzyme
AB  - inhibitors 25 and 26.
ER  -

TY  - JOUR
AU  - Motta, E.V.S.
AU  - Kwong, W.K.
AU  - Moran, N.A.
TI  - Glyphosate perturbs the gut microbiota of honey bees.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2018
SP  - 10305
EP  - 10310
VL  - 115
AB  - Glyphosate, the primary herbicide used globally for weed control, targets the
AB  - 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS)
AB  - enzyme in the shikimate pathway found in plants and some
AB  - microorganisms. Thus, glyphosate may affect bacterial symbionts
AB  - of animals living near agricultural sites, including pollinators such
AB  - as bees. The honey bee gut microbiota is dominated by eight
AB  - bacterial species that promote weight gain and reduce pathogen
AB  - susceptibility. The gene encoding EPSPS is present in almost all
AB  - sequenced genomes of bee gut bacteria, indicating that they are
AB  - potentially susceptible to glyphosate. We demonstrated that the
AB  - relative and absolute abundances of dominant gut microbiota
AB  - species are decreased in bees exposed to glyphosate at concentrations
AB  - documented in the environment. Glyphosate exposure of
AB  - young workers increased mortality of bees subsequently exposed
AB  - to the opportunistic pathogen Serratia marcescens. Members of
AB  - the bee gut microbiota varied in susceptibility to glyphosate,
AB  - largely corresponding to whether they possessed an EPSPS of class
AB  - I (sensitive to glyphosate) or class II (insensitive to glyphosate).
AB  - This basis for differences in sensitivity was confirmed using
AB  - in vitro experiments in which the EPSPS gene from bee gut bacteria
AB  - was cloned into Escherichia coli. All strains of the core bee gut
AB  - species, Snodgrassella alvi, encode a sensitive class I EPSPS, and
AB  - reduction in S. alvi levels was a consistent experimental result.
AB  - However, some S. alvi strains appear to possess an alternative
AB  - mechanism of glyphosate resistance. Thus, exposure of bees to
AB  - glyphosate can perturb their beneficial gut microbiota, potentially
AB  - affecting bee health and their effectiveness as pollinators.
ER  -

TY  - JOUR
AU  - Mottawea, W.
AU  - Chen, S.
AU  - Saleh-Lakha, S.
AU  - Belanger, S.
AU  - Ogunremi, D.
TI  - Complete Genome Sequences of 12 Isolates of Listeria monocytogenes Belonging to Serotypes 1/2a, 1/2b, and 4b Obtained from Food Products and Food-Processing  Environments in Canada.
JO  - Genome Announcements
PY  - 2017
SP  - e00258
EP  - e00217
VL  - 5
AB  - Listeria monocytogenes is the etiological agent for an often fatal foodborne illness known as
AB  - listeriosis. Here, we present the complete genome sequences of
AB  - 12 L. monocytogenes isolates representing the three most common serotypes of this
AB  - pathogen (1/2a, 1/2b, and 4b), collected in Canada from different food products
AB  - and environmental sources.
ER  -

TY  - JOUR
AU  - Mou, K.T.
AU  - Muppirala, U.K.
AU  - Severin, A.J.
AU  - Clark, T.A.
AU  - Boitano, M.
AU  - Plummer, P.J.
TI  - A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data.
JO  - Front. Microbiol.
PY  - 2014
SP  - 782
EP  - 782
VL  - 5
AB  - Campylobacter jejuni is a leading cause of human gastrointestinal disease and small ruminant
AB  - abortions in the United States. The recent emergence of a highly
AB  - virulent, tetracycline-resistant C. jejuni subsp. jejuni sheep abortion clone
AB  - (clone SA) in the United States, and that strain's association with human
AB  - disease, has resulted in a heightened awareness of the zoonotic potential of this
AB  - organism. Pacific Biosciences' Single Molecule, Real-Time sequencing technology
AB  - was used to explore the variation in the genome-wide methylation patterns of the
AB  - abortifacient clone SA (IA3902) and phenotypically distinct
AB  - gastrointestinal-specific C. jejuni strains (NCTC 11168 and 81-176). Several
AB  - notable differences were discovered that distinguished the methylome of IA3902
AB  - from that of 11168 and 81-176: identification of motifs novel to IA3902,
AB  - genome-specific hypo- and hypermethylated regions, strain level variability in
AB  - genes methylated, and differences in the types of methylation motifs present in
AB  - each strain. These observations suggest a possible role of methylation in the
AB  - contrasting disease presentations of these three C. jejuni strains. In addition,
AB  - the methylation profiles between IA3902 and a luxS mutant were explored to
AB  - determine if variations in methylation patterns could be identified that might
AB  - explain the role of LuxS-dependent methyl recycling in IA3902 abortifacient
AB  - potential.
ER  -

TY  - JOUR
AU  - Moulin, L. et al.
TI  - Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 763
EP  - 774
VL  - 9
AB  - Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with
AB  - species of the legume genus Mimosa, and is frequently found
AB  - associated specifically with Mimosa pudica. The type strain of the species, STM
AB  - 815(T), was isolated from a root nodule in French Guiana in 2000. The strain is
AB  - an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly
AB  - competitive strain for nodulation compared to other Mimosa symbionts, as it also
AB  - nodulates a broad range of other legume genera and species. The 8,676,562 bp
AB  - genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid
AB  - (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).
ER  -

TY  - JOUR
AU  - Moulin, L.
AU  - Mornico, D.
AU  - Melkonian, R.
AU  - Klonowska, A.
TI  - Draft Genome Sequence of Rhizobium mesoamericanum STM3625, a Nitrogen-Fixing Symbiont of Mimosa pudica Isolated in French Guiana (South America).
JO  - Genome Announcements
PY  - 2013
SP  - e00066
EP  - e00012
VL  - 1
AB  - Rhizobium mesoamericanum STM3625 is a Mimosa pudica symbiont isolated in French Guiana. This
AB  - strain serves as a model bacterium for comparison of adaptation to mutualism (symbiotic
AB  - traits, bacterial genetic programs for plant infection) between alpha and beta rhizobial
AB  - symbionts of Mimosa pudica.
ER  -

TY  - JOUR
AU  - Moure, C.M.
AU  - Gimble, F.S.
AU  - Quiocho, F.A.
TI  - Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 3287
EP  - 3296
VL  - 36
AB  - I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI
AB  - exhibits a strong preference for cleaving the bottom strand DNA. The published structure of
AB  - I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but
AB  - not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we
AB  - determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in
AB  - either the top or bottom strands. The structures resemble intermediates along the DNA cleavage
AB  - reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal
AB  - ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that
AB  - cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand
AB  - is cleaved first or second. In the structure containing a nick in the bottom strand, a new
AB  - metal binding site is present in the active site that cleaves the top strand. This new metal
AB  - and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand
AB  - following bottom strand cleavage, providing a plausible mechanism for top strand cleavage.
ER  -

TY  - JOUR
AU  - Moure, C.M.
AU  - Gimble, F.S.
AU  - Quiocho, F.A.
TI  - The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 685
EP  - 695
VL  - 334
AB  - The I-SceI homing endonuclease enhances gene targeting by introducing double-strand breaks at
AB  - specific chromosomal loci, thereby increasing the
AB  - recombination frequency. Here, we report the crystal structure of the
AB  - enzyme complexed to its DNA substrate and Ca(2+) determined at 2.25A
AB  - resolution. The structure shows the prototypical beta-saddle of LAGLIDADG
AB  - homing endonucleases that is contributed by two pseudo-symmetric domains.
AB  - The high specificity of I-SceI is explained by the large number of
AB  - protein-DNA contacts, many that are made by a long beta-hairpin loop that
AB  - reaches into the major groove of the DNA. The DNA minor groove is
AB  - compressed at the catalytic center, bringing the two scissile
AB  - phosphodiester bonds into close proximity. The protein-Ca(2+)-DNA
AB  - structure shows the protein bound to its DNA substrate in a pre-reactive
AB  - state that is defined by the presence of two asymmetric active sites, one
AB  - of which appears poised to first cleave the DNA bottom strand.
ER  -

TY  - JOUR
AU  - Moure, C.M.
AU  - Gimble, F.S.
AU  - Quiocho, F.A.
TI  - Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.
JO  - Nat. Struct. Biol.
PY  - 2002
SP  - 764
EP  - 770
VL  - 9
AB  - The first X-ray structures of an intein-DNA complex, that of the two-domain homing
AB  - endonuclease PI-SceI bound to its 36-base pair DNA substrate, have been determined in the
AB  - presence and absence of Ca(2+). The DNA shows an asymmetric bending pattern, with a major 50
AB  - degrees bend in the endonuclease domain and a minor 22 degrees bend in the splicing domain
AB  - region. Distortions of the DNA bound to the endonuclease domain cause the insertion of the two
AB  - cleavage sites in the catalytic center. DNA binding induces changes in the protein
AB  - conformation. The two overlapping non-identical active sites in the endonucleolytic center
AB  - contain two Ca(+2) ions that coordinate to the catalytic Asp residues. Structure analysis
AB  - indicates that the top strand may be cleaved first.
ER  -

TY  - JOUR
AU  - Moure, C.M.
AU  - Quiocho, F.A.
TI  - The structure and function of intein-associated homing endonucleases.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 257
EP  - 271
VL  - 16
AB  - Homing endonucleases are a large group of proteins that are characterized by their ability to
AB  - recognize long (14-40 base pairs, bp) asymmetric or pseudo-palindromic double-stranded DNA
AB  - sequences as cleavage sites.  By cleaving DNA, they assist in the homing process of their
AB  - encoding genes into other genes.  Homing endonucleases include both intron-encoded and intein-
AB  - (for intervening protein) associated members that self-splice at the mRNA and protein level,
AB  - respectively.  Those inteins that contain associated endonuclease domains are especially
AB  - interesting due to their bifunctionality and their exceptionally long DNA recognition
AB  - abilities.  With two exceptions, all of the approximately 160 inteins that have been
AB  - characterized to date are associated with the LAGLIDADG homing endonuclease subfamily, which
AB  - also includes numerous intron-encoded endonucleases.  This chapter is devoted mainly to the
AB  - structural studies of intein-associated LAGLIDADG homing endonucleases that have revealed the
AB  - domain organization and architecture of this type of protein, providing insights into the
AB  - combination of protein splicing and site-specific DNA recognition and cleavage across a single
AB  - peptide chain.  The knowledge gained in these structure-function studies has been successfully
AB  - exploited in biotechnology to devise systems for protein purification and to study
AB  - protein-protein interactions using the splicing capability of inteins, and in gene targeting
AB  - studies, which use their rare-cutting endonuclease properties.  These applications are
AB  - discussed in other chapters in this volume.
ER  -

TY  - JOUR
AU  - Moxon, E.R.
AU  - Rainey, P.B.
AU  - Nowak, M.A.
AU  - Lenski, R.E.
TI  - Adaptive evolution of highly mutable loci in pathogenic bacteria.
JO  - Curr. Biol.
PY  - 1994
SP  - 24
EP  - 33
VL  - 4
AB  - Bacteria have specific loci that are highly mutable.  We argue that the coexistence within
AB  - bacterial genomes of such 'contingency' genes with high mutation rates, and 'housekeeping'
AB  - genes with low mutation rates, is the result of adaptive evolution, and facilitates the
AB  - efficient exploration of phenotypic solutions to unpredictable aspects of the host environment
AB  - while minimizing deleterious effects on fitness.
ER  -

TY  - JOUR
AU  - Moya-Beltran, A.
AU  - Cardenas, J.P.
AU  - Covarrubias, P.C.
AU  - Issotta, F.
AU  - Ossandon, F.J.
AU  - Grail, B.M.
AU  - Holmes, D.S.
AU  - Quatrini, R.
AU  - Johnson, D.B.
TI  - Draft Genome Sequence of the Nominated Type Strain of 'Ferrovum myxofaciens,' an  Acidophilic, Iron-Oxidizing Betaproteobacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00834
EP  - e00814
VL  - 2
AB  - 'Ferrovum myxofaciens' is an iron-oxidizing betaproteobacterium with widespread distribution
AB  - in acidic low-temperature environments, such as acid mine drainage
AB  - streams. Here, we describe the genomic features of this novel acidophile and
AB  - investigate the relevant metabolic pathways that enable its survival in these
AB  - environments.
ER  -

TY  - JOUR
AU  - Mrazek, J.
AU  - Karlin, S.
TI  - Detecting alien genes in bacterial genomes.
JO  - Ann. NY Acad. Sci.
PY  - 1999
SP  - 314
EP  - 329
VL  - 870
AB  - We present new methods for calculating codon bias of a group of genes or an individual gene
AB  - relative to a standard gene class.  This method is suitable for identifying alien (e.g.,
AB  - horizonatally transferred) and highly expressed genes.  In yeast and several bacterial
AB  - genomes, highly expressed genes typically include ribosomal protein genes, elongation factors,
AB  - chaperonins (heat shock proteins), and a subset of genes involved in glycolysis generally
AB  - essential in exponential growth.  Highly expressed genes of the Synechocystis genome feature
AB  - several photosystem II genes, and highly expressed genes in several methanogens (Methanococcus
AB  - jannaschii, M. thermoautotrophicum) are essential for methanogenesis.  Alien genes mostly
AB  - consist of ORFs of unknown function, transposases, prophage genes, and
AB  - restriction/modification enzymes.  Notably, nuclear ribosomal proteins of yeast are highly
AB  - expressed, whereas mitochondrial ribosomal protein genes appear to be alien genes.  Alien
AB  - genes often occur in clusters, suggesting in these cases that transfer events entail several
AB  - genes.
ER  -

TY  - JOUR
AU  - Mrazek, J.
AU  - Piknova, M.
AU  - Pristas, P.
AU  - Kopecny, J.
TI  - Occurrence of restriction-modification systems in ruminal butyrate-producing bacteria.
JO  - Anaerobe
PY  - 2005
SP  - 280
EP  - 284
VL  - 11
AB  - Thirty-five strains of ruminal bacteria belonging to the former Butyrivibrio fibrisolvens
AB  - species were screened for the presence of
AB  - site-specific restriction endonuclease and modification
AB  - methyltransferase activities. Seven strains possessed endonuclease
AB  - activities detectable in crude cell extracts. The recognition sequences
AB  - and optimal reaction conditions for seven of them were determined. Five
AB  - enzymes were found to be isoschizomers of type II endonucleases (EcoRV,
AB  - Nsil, Asel (2x) and Saul), one was type IIS (FokI) and two remained
AB  - unknown. The optimal reaction buffer was found to be a low ionic
AB  - strength buffer and all enzymes possessed sufficient activity at 39
AB  - degrees C. The presence of DNA modification among all strains was also
AB  - determined. Most of the methylation activities correlated with
AB  - restriction activities, yet some strains possessed unaccompanied
AB  - modification methyltransferases.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Blumenthal, R.M.
TI  - Real-time kinetics of restriction-modification gene expression after entry into a new host cell.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 2581
EP  - 2593
VL  - 36
AB  - Most type II restriction-modification (R-M) systems produce separate restriction endonuclease
AB  - (REase) and methyltransferase (MTase) proteins.
AB  - After R-M system genes enter a new cell, protective MTase must appear
AB  - before REase to avoid host chromosome cleavage. The basis for this
AB  - apparent temporal regulation is not well understood. PvuII and some other
AB  - R-M systems appear to achieve this delay by cotranscribing the REase gene
AB  - with the gene for an autogenous transcription activator/repressor (the 'C'
AB  - protein C.PvuII). To test this model, bacteriophage M13 was used to
AB  - introduce the PvuII genes into a bacterial population in a relatively
AB  - synchronous manner. REase mRNA and activity appeared approximately 10 min
AB  - after those of the MTase, but never rose if there was an inactivating
AB  - pvuIIC mutation. Infection with recombinant M13pvuII phage had little
AB  - effect on cell growth, relative to infection with parental M13. However,
AB  - infection of cells pre-expressing C.PvuII led to cessation of growth. This
AB  - study presents the first direct demonstration of delayed REase expression,
AB  - relative to MTase, when type II R-M genes enter a new host cell.
AB  - Surprisingly, though the C and REase genes are cotranscribed, the pvuIIC
AB  - portion of the mRNA was more abundant than the pvuIIR portion after stable
AB  - establishment of the R-M system.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Blumenthal, R.M.
TI  - Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 983
EP  - 998
VL  - 37
AB  - Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and
AB  - methyltransferase (MTase) proteins. After R-M
AB  - genes enter a new cell, MTase activity must appear before REase or the
AB  - host chromosome will be cleaved. Temporal control of these genes thus has
AB  - life-or-death consequences. PvuII and some other R-M systems delay
AB  - endonuclease expression by cotranscribing the REase gene with the upstream
AB  - gene for an autogenous activator/repressor (C protein). C.PvuII was
AB  - previously shown to have low levels early, but positive feedback later
AB  - boosts transcription of the C and REase genes. The MTase is expressed
AB  - without delay, and protects the host DNA. C.PvuII binds to two sites
AB  - upstream of its gene: O(L), associated with activation, and O(R),
AB  - associated with repression. Even when symmetry elements of each operator
AB  - are made identical, C.PvuII binds preferentially to O(L). In this study,
AB  - the intra-operator spacers are shown to modulate relative C.PvuII
AB  - affinity. In light of a recently reported C.Esp1396I-DNA co-crystal
AB  - structure, in vitro and in vivo effects of altering O(L) and O(R) spacers
AB  - were determined. The results suggest that the GACTnnnAGTC consensus is the
AB  - primary determinant of C.PvuII binding affinity, with intra-operator
AB  - spacers playing a fine-tuning role that affects mobility of this R-M
AB  - system.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Cichowicz, M.
AU  - Kaczorowski, T.
TI  - Characterization of the LlaCl methyltransferase from Lactococcus lactis subsp cremoris W15 provides new insights into the biology of type II  restriction-modification systems.
JO  - Microbiology
PY  - 2003
SP  - 3331
EP  - 3341
VL  - 149
AB  - The gene encoding the LlaCI methyltransferase (M.LlaCI) from Lactococcus lactis subsp.
AB  - cremoris W15 was overexpressed in Escherichia coli. The
AB  - enzyme was purified to apparent homogeneity using three consecutive steps
AB  - of chromatography on phosphocellulose, blue-agarose and Superose 12HR,
AB  - yielding a protein of M(r) 31 300+/-1000 under denaturing conditions. The
AB  - exact position of the start codon AUG was determined by protein
AB  - microsequencing. This enzyme recognizes the specific palindromic sequence
AB  - 5'-AAGCTT-3'. Purified M.LlaCI was characterized. Unlike many other
AB  - methyltransferases, M.LlaCI exists in solution predominantly as a dimer.
AB  - It modifies the first adenine residue at the 5' end of the specific
AB  - sequence to N(6)-methyladenine and thus is functionally identical to the
AB  - corresponding methyltransferases of the HindIII (Haemophilus influenzae
AB  - Rd) and EcoVIII (Escherichia coli E1585-68) restriction-modification
AB  - systems. This is reflected in the identity of M.LlaCI with M.HindIII and
AB  - M.EcoVIII noted at the amino acid sequence level (50 % and 62 %,
AB  - respectively) and in the presence of nine sequence motifs conserved among
AB  - N(6)-adenine beta-class methyltransferases. However, polyclonal antibodies
AB  - raised against M.EcoVIII cross-reacted with M.LlaCI but not with
AB  - M.HindIII. Restriction endonucleases require Mg(2+) for phosphodiester
AB  - bond cleavage. Mg(2+) was shown to be a strong inhibitor of the M.LlaCI
AB  - enzyme and its isospecific homologues. This observation suggests that
AB  - sensitivity of the M.LlaCI to Mg(2+) may strengthen the restriction
AB  - activity of the cognate endonuclease in the bacterial cell. Other
AB  - biological implications of this finding are also discussed.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Kaczorowski, T.
TI  - A rapid and efficient method for cloning genes of type II restriction-modification systems by use of a killer plasmid.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 4286
EP  - 4293
VL  - 73
AB  - We present a method for cloning restriction-modification (R-M) systems that is based on the
AB  - use of a lethal plasmid (pKILLER). The plasmid
AB  - carries a functional gene for a restriction endonuclease having the
AB  - same DNA specificity as the R-M system of interest. The first step is
AB  - the standard preparation of a representative, plasmid-borne genomic
AB  - library. Then this library is transformed with the killer plasmid. The
AB  - only surviving bacteria are those which carry the gene specifying a
AB  - protective DNA methyltransferase. Conceptually, this in vivo selection
AB  - approach resembles earlier methods in which a plasmid library was
AB  - selected in vitro by digestion with a suitable restriction
AB  - endonuclease, but it is much more efficient than those methods. The new
AB  - method was successfully used to clone two R-M systems, BstZ1II from
AB  - Bacillus stearothermophilus 14P and Csp231I from Citrobacter sp. strain
AB  - RFL231, both isospecific to the prototype HindIII R-M system.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Kaczorowski, T.
TI  - Genetic organization and molecular analysis of the EcoVIII restriction-modification system of Escherichia coli E1585-68 and its comparison with isospecific homologs.
JO  - Appl. Environ. Microbiol.
PY  - 2003
SP  - 2638
EP  - 2650
VL  - 69
AB  - The EcoVIII restriction-modification (R-M) system is carried by the Escherichia coli E1585-68
AB  - natural plasmid pEC156 (4,312 bp). The two genes
AB  - were cloned and characterized. The G+C content of the EcoVIII R-M system
AB  - is 36.1%, which is significantly lower than the average G+C content of
AB  - either plasmid pEC156 (43.6%) or E. coli genomic DNA (50.8%). The
AB  - difference suggests that there is a possibility that the EcoVIII R-M
AB  - system was recently acquired by the genome. The 921-bp EcoVIII
AB  - endonuclease (R. EcoVIII) gene (ecoVIIIR) encodes a 307-amino-acid protein
AB  - with an M(r) of 35,554. The convergently oriented EcoVIII
AB  - methyltransferase (M. EcoVIII) gene (ecoVIIIM) consists of 912 bp that
AB  - code for a 304-amino-acid protein with an M(r) of 33,930. The exact
AB  - positions of the start codon AUG were determined by protein
AB  - microsequencing. Both enzymes recognize the specific palindromic sequence
AB  - 5'-AAGCTT-3'. Preparations of EcoVIII R-M enzymes purified to homogeneity
AB  - were characterized. R. EcoVIII acts as a dimer and cleaves a specific
AB  - sequence between two adenine residues, leaving 4-nucleotide 5' protruding
AB  - ends. M. EcoVIII functions as a monomer and modifies the first adenine
AB  - residue at the 5' end of the specific sequence to N(6)-methyladenine.
AB  - These enzymes are thus functionally identical to the corresponding enzymes
AB  - of the HindIII (Haemophilus influenzae Rd) and LlaCI (Lactococcus lactis
AB  - subsp. cremoris W15) R-M systems. This finding is reflected by the levels
AB  - of homology of M. EcoVIII with M. HindIII and M. LlaCI at the amino acid
AB  - sequence level (50 and 62%, respectively) and by the presence of nine
AB  - sequence motifs conserved among m(6) N-adenine beta-class
AB  - methyltransferases. The deduced amino acid sequence of R. EcoVIII shows
AB  - weak homology with its two isoschizomers, R. HindIII (26%) and R. LlaCI
AB  - (17%). A catalytic sequence motif characteristic of restriction
AB  - endonucleases was found in the primary structure of R. EcoVIII
AB  - (D(108)X(12)DXK(123)), as well as in the primary structures of R. LlaCI
AB  - and R. HindIII. Polyclonal antibodies raised against R. EcoVIII did not
AB  - react with R. HindIII, while anti-M. EcoVIII antibodies cross-reacted with
AB  - M. LlaCI but not with M. HindIII. R. EcoVIII requires Mg(II) ions for
AB  - phosphodiester bond cleavage. We found that the same ions are strong
AB  - inhibitors of the M. EcoVIII enzyme. The biological implications of this
AB  - finding are discussed.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Kobayashi, I.
TI  - To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 70
EP  - 86
VL  - 42
AB  - One of the simplest classes of genes involved in programmed death is that containing the
AB  - toxin-antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular
AB  - toxin and an antitoxin that neutralizes its effect. These systems, now classified into five
AB  - types, were initially discovered because some of them allow the stable maintenance of mobile
AB  - genetic elements in a microbial population through postsegregational killing or the death of
AB  - cells that have lost these systems. Here, we demonstrate parallels between some TA systems and
AB  - restriction-modification systems (RM systems). RM systems are composed of a restriction enzyme
AB  - (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with
AB  - different epigenetic identities, as defined by sequence-specific DNA methylation. The
AB  - similarities between these systems include their postsegregational killing and their effects
AB  - on global gene expression. Both require the finely regulated expression of a toxin and
AB  - antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional
AB  - regulator. A regulatory antisense RNA recently identified in an RM system can be compared with
AB  - those RNAs in TA systems. This review is intended to generalize the concept of TA systems in
AB  - studies of stress responses, programmed death, genetic conflict and epigenetics.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Liu, Y.
AU  - Ge, L.
AU  - Kobayashi, I.
TI  - Antisense RNA associated with biological regulation of a restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 5622
EP  - 5632
VL  - 39
AB  - Restriction-modification systems consist of a modification enzyme that methylates a specific
AB  - DNA sequence and a restriction endonuclease that cleaves DNA lacking this epigenetic
AB  - signature. Their gene expression should be finely regulated because their potential to attack
AB  - the host bacterial genome needs to be controlled. In the EcoRI system, where the restriction
AB  - gene is located upstream of the modification gene in the same orientation, we previously
AB  - identified intragenic reverse promoters affecting gene expression. In the present work, we
AB  - identified a small (88 nt) antisense RNA (Rna0) transcribed from a reverse promoter (P(REV0))
AB  - at the 3' end of the restriction gene. Its antisense transcription, as measured by
AB  - transcriptional gene fusion, appeared to be terminated by the P(M1,M2) promoter. P(M1,M2)
AB  - promoter-initiated transcription, in turn, appeared to be inhibited by P(REV0). Mutational
AB  - inactivation of P(REV0) increased expression of the restriction gene. The biological
AB  - significance of this antisense transcription is 2-fold. First, a mutation in P(REV0) increased
AB  - restriction of incoming DNA. Second, the presence of the antisense RNA gene (ecoRIA) in trans
AB  - alleviated cell killing after loss of the EcoRI plasmid (post-segregational killing). Taken
AB  - together, these results strongly suggested the involvement of an antisense RNA in the
AB  - biological regulation of this restriction-modification system.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Rajesh, P.
AU  - Blumenthal, R.M.
TI  - Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII  restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 6935
EP  - 6952
VL  - 35
AB  - Type II restriction-modification (R-M) systems comprise a restriction endonuclease (REase) and
AB  - a protective methyltransferase (MTase). After R-M
AB  - genes enter a new cell, MTase must appear before REase or the chromosome
AB  - will be cleaved. PvuII and some other R-M systems achieve this delay by
AB  - cotranscribing the REase gene with the gene for an autogenous
AB  - transcription activator (the controlling or 'C' protein C.PvuII). This
AB  - study reveals, through in vivo titration, that C.PvuII is not only an
AB  - activator but also a repressor for its own gene. In other systems, this
AB  - type of circuit can result in oscillatory behavior. Despite the use of
AB  - identical, symmetrical C protein-binding sequences (C-boxes) in the left
AB  - and right operators, C.PvuII showed higher in vitro affinity for O(L) than
AB  - for O(R), implicating the spacer sequences in this difference. Mutational
AB  - analysis associated the repression with O(R), which overlaps the promoter
AB  - -35 hexamer but is otherwise dispensable for activation. A nonrepressing
AB  - mutant exhibited poor establishment in new cells. Comparing
AB  - promoter-operator regions from PvuII and 29 R-M systems controlled by C
AB  - proteins revealed that the most-highly conserved sequence is the
AB  - tetranucleotide spacer separating O(L) from O(R). Any changes in that
AB  - spacer reduced the stability of C.PvuII-operator complexes and abolished
AB  - activation.
ER  -

TY  - JOUR
AU  - Mruk, I.
AU  - Sektas, M.
AU  - Kaczorowski, T.
TI  - Characterization of pEC156, a ColE1-Type Plasmid from Escherichia coli E1585-68 That Carries Genes of the EcoVIII Restriction-Modification System.
JO  - Plasmid
PY  - 2001
SP  - 128
EP  - 139
VL  - 46
AB  - The complete 4312-bp sequence of the pEC156 plasmid from Escherichia coli E1585-68, which
AB  - carries genes encoding the EcoVIII restriction-modification (R-M) system, an isoschizomer of
AB  - HindIII from Haemophilus influenzae, has been determined. Two clustered and convergently
AB  - oriented open reading frames, large enough to encode genes of the EcoVIII R-M system, were
AB  - found. The transcriptional start points were mapped by the primer extension method. The
AB  - relative molecular masses of the EcoVIII endonuclease and EcoVIII methyltransferase deduced
AB  - from the nucleotide sequence are 35,554 and 33,910, respectively. Nucleotide sequence analysis
AB  - of pEC156 suggests that this plasmid is a ColE1-type replicon. It consists of an origin of
AB  - replication and two untranslated genes encoding RNA I and RNA II, both involved in the
AB  - regulation of plasmid DNA replication. The replication region also contains the gene encoding
AB  - a 64-aa Rom-like protein. Inactivation of the putative rom gene by insertion of a
AB  - kanamycin-resistance cassette resulted in 4.5-fold increase in pEC156-derived plasmid copy
AB  - number in E. coli cells. All of these elements (RNA I, RNA II, and rom) reveal a high level of
AB  - similarity to ColE1 homologs. The replication of all ColE1-type plasmids is dependent on the
AB  - activity of E. coli DNA polymerase I. It was shown that a pEC156 derivative (pIB8) carrying an
AB  - antibiotic resistance gene indeed failed to replicate in an E. coli polA12(ts) mutant at 43
AB  - degrees C, and its copy number was reduced in the E. coli pcnB80 mutant. These results prove
AB  - that pEC156 is a ColE1-type replicon. Copyright 2001 Academic Press.
ER  -

TY  - JOUR
AU  - Mu, D.
AU  - Zhao, J.
AU  - Wang, Z.
AU  - Chen, G.
AU  - Du, Z.
TI  - Draft Genome Sequence of Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China.
JO  - Genome Announcements
PY  - 2016
SP  - e01555
EP  - e01515
VL  - 4
AB  - Algoriphagus sp. NH1 is a multidrug-resistant bacterium isolated from coastal sediments of the
AB  - northern Yellow Sea in China. Here, we report the draft genome
AB  - sequence of NH1, with a size of 6,131,579 bp, average G+C content of 42.68%, and
AB  - 5,746 predicted protein-coding sequences.
ER  -

TY  - JOUR
AU  - Muchaamba, F.
AU  - Guldimann, C.
AU  - Tasara, T.
AU  - Mota, M.I.
AU  - Braga, V.
AU  - Varela, G.
AU  - Algorta, G.
AU  - Klumpp, J.
AU  - Jermini, M.
AU  - Stephan, R.
TI  - Full-Genome Sequence of Listeria monocytogenes Strain H34, Isolated from a Newborn with Sepsis in Uruguay.
JO  - Genome Announcements
PY  - 2017
SP  - e00544
EP  - e00517
VL  - 5
AB  - The foodborne pathogen Listeria monocytogenes causes severe disease mainly in the vulnerable
AB  - populations of the young, old, pregnant, and immunocompromised. Here,
AB  - we present the genome sequence of L. monocytogenes H34, a serotype 1/2b, lineage
AB  - I, sequence type 489 (ST489) strain, isolated from a neonatal sepsis case in
AB  - Uruguay.
ER  -

TY  - JOUR
AU  - Muchova, J.
AU  - Lacova, B.
AU  - Godany, A.
AU  - Sevcikova, B.
TI  - High transformable mutants of Streptomyces aureofaciens containing restriction-modification systems.
JO  - J. Basic Microbiol.
PY  - 1991
SP  - 141
EP  - 147
VL  - 31
AB  - Streptomyces aureofaciens 13 is a mutant defective in chlortetracycline
AB  - production. It was chosen as a potentially useful host for gene cloning in
AB  - investigations of the organization of the biosynthetic genes for the
AB  - tetracycline antibiotic pathway.  From the Streptomyces aureofaciens 13 strain,
AB  - three suitable clones were used for our work.  The conditions for optimal
AB  - formation and efficient transformation of protoplasts with plasmid DNAs have
AB  - been determined.  Transformation frequencies of about 10/4 to 10/5 per
AB  - microgram of plasmid DNA were obtained when plasmids were isolated from
AB  - Streptomyces strains.  From the patterns of restriction enzyme digestion of
AB  - plasmid DNA isolated from Streptomyces aureofaciens transformants, it was
AB  - observed that the clones express modification systems which render plasmid DNAs
AB  - resistant to cleavage by HindIII and EcoRI.  Additionally, one of the clones
AB  - produces the restriction endonuclease Sau13I (isoschizomer of SauI).  The
AB  - presence of the restriction-modification system of Sau13I does not reduce the
AB  - efficiency of plasmid transformation.  Note: Sau13I is already used for an
AB  - isoschizomer of AsuI from Staphylococcus aureus.
ER  -

TY  - JOUR
AU  - Mucito-Varela, E.
AU  - Castillo-Rojas, G.
AU  - Cevallos, M.A.
AU  - Lozano, L.
AU  - Merino, E.
AU  - Lopez-Leal, G.
AU  - Lopez-Vidal, Y.
TI  - Complete Genome Sequence of Helicobacter pylori Strain 29CaP Isolated from a Mexican Patient with Gastric Cancer.
JO  - Genome Announcements
PY  - 2016
SP  - e01512
EP  - e01515
VL  - 4
AB  - Helicobacter pylori infection is a risk factor for the development of gastric cancer and other
AB  - gastroduodenal diseases. We report here the complete genome
AB  - sequence of H. pylori strain 29CaP, isolated from a Mexican patient with gastric
AB  - cancer. The genomic data analysis revealed a cag-negative H. pylori strain that
AB  - contains a prophage sequence.
ER  -

TY  - JOUR
AU  - Mucito-Varela, E.
AU  - Castillo-Rojas, G.
AU  - Cevallos, M.A.
AU  - Lozano, L.
AU  - Merino, E.
AU  - Lopez-Leal, G.
AU  - Lopez-Vidal, Y.
TI  - Complete Genome Sequence of Helicobacter pylori Strain 7C Isolated from a Mexican Patient with Chronic Gastritis.
JO  - Genome Announcements
PY  - 2016
SP  - e01503
EP  - e01515
VL  - 4
AB  - Helicobacter pylori-induced gastritis is a risk factor for developing gastric pathologies.
AB  - Here, we report the complete genome sequence of a
AB  - multidrug-resistant H. pylori strain isolated from a chronic gastritis patient in
AB  - Mexico City, Mexico. Nonvirulent VacA and cag-pathogenicity island (PAI)
AB  - genotypes were found, but the presence of a potential mobilizable plasmid
AB  - carrying an IS605 element is of outstanding interest.
ER  -

TY  - JOUR
AU  - Mucke, M.
AU  - Grelle, G.
AU  - Behlke, J.
AU  - Kraft, R.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - EcoRII: a restriction enzyme evolving recombination functions?
JO  - EMBO J.
PY  - 2002
SP  - 5262
EP  - 5268
VL  - 21
AB  - The restriction endonuclease EcoRII requires the cooperative interaction with two copies of
AB  - the sequence 5'CCWGG for DNA cleavage. We found by limited proteolysis that EcoRII has a
AB  - two-domain structure that enables this particular mode of protein-DNA interaction. The
AB  - C-terminal domain is a new restriction endonuclease, EcoRII-C. In contrast to the wild-type
AB  - enzyme, EcoRII-C cleaves DNA specifically at single 5'CCWGG sites. Moreover, substrates
AB  - containing two or more cooperative 5'CCWGG sites are cleaved much more efficiently by
AB  - EcoRII-C than by EcoRII. The N-terminal domain binds DNA specifically and attenuates the
AB  - activity of EcoRII by making the enzyme dependent on a second 5'CCWGG site. Therefore, we
AB  - suggest that a precursor EcoRII endonuclease acquired an additional DNA-binding domain to
AB  - enable the interaction with two 5'CCWGG sites. The current EcoRII molecule could be an
AB  - evolutionary intermediate between a site-specific endonuclease and a protein that functions
AB  - specifically with two DNA sites such as recombinases and transposases. The combination of
AB  - these functions may enable EcoRII to accomplish its own propagation similarly to transposons.
ER  -

TY  - JOUR
AU  - Mucke, M.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Diversity of Type II restriction endonucleases that require two DNA recognition sites.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 6079
EP  - 6084
VL  - 31
AB  - Orthodox Type IIP restriction endonucleases, which are commonly used in molecular biological
AB  - work, recognize a single palindromic DNA recognition
AB  - sequence and cleave within or near this sequence. Several new studies have
AB  - reported on structural and biochemical peculiarities of restriction
AB  - endonucleases that differ from the orthodox in that they require two
AB  - copies of a particular DNA recognition sequence to cleave the DNA. These
AB  - two sites requiring restriction endonucleases belong to different subtypes
AB  - of Type II restriction endonucleases, namely Types IIE, IIF and IIS. We
AB  - compare enzymes of these three types with regard to their DNA recognition
AB  - and cleavage properties. The simultaneous recognition of two identical DNA
AB  - sites by these restriction endonucleases ensures that single unmethylated
AB  - recognition sites do not lead to chromosomal DNA cleavage, and might
AB  - reflect evolutionary connections to other DNA processing proteins that
AB  - specifically function with two sites.
ER  -

TY  - JOUR
AU  - Mucke, M.
AU  - Lurz, R.
AU  - Mackeldanz, P.
AU  - Behlke, J.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 30631
EP  - 30637
VL  - 275
AB  - EcoRII is a type IIE restriction endonuclease characterized by a highly cooperative reaction
AB  - mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of
AB  - its DNA recognition site. Transmission electron microscopy provided direct evidence that
AB  - EcoRII mediates loop formation of linear DNA containing two EcoRII recognition sites. Specific
AB  - DNA binding of EcoRII revealed a symmetrical DNase I footprint occupying 16-18 bases. Single
AB  - amino acid replacement of Val(258) by Asn yielded a mutant enzyme that was unaffected in
AB  - substrate affinity and DNase I footprinting properties, but exhibited a profound decrease in
AB  - cooperative DNA binding and cleavage activity. Because the electrophoretic mobility of the
AB  - mutant enzyme-DNA complexes was significantly higher than that of the wild-type, we
AB  - investigated if mutant V258N binds as a monomer to the substrate DNA. Analysis of the
AB  - molecular mass of mutant V258N showed a high percentage of protein monomers in solution. The
AB  - dissociation constant of mutant V258N confirmed a 350-fold decrease of the enzyme dimerization
AB  - capability. We conclude that Val(258) is located in a region of EcoRII involved in
AB  - homodimerization. This is the first report of a specific amino acid replacement in a
AB  - restriction endonuclease leading to the loss of dimerization and DNA cleavage while retaining
AB  - specific DNA binding.
ER  -

TY  - JOUR
AU  - Mucke, M.
AU  - Pingoud, V.
AU  - Grelle, G.
AU  - Kraft, R.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 14288
EP  - 14293
VL  - 277
AB  - The EcoRII homodimer engages two of its recognition sequences (5'-CCWGG) simultaneously and
AB  - is therefore a type IIE restriction endonuclease. To identify the amino acids of EcoRII that
AB  - interact specifically with the recognition sequence, we photocross-linked EcoRII with
AB  - oligonucleotide substrates that contained only one recognition sequence for EcoRII. In this
AB  - recognition sequence, we substituted either 5-iododeoxycytidine for each C or
AB  - 5-iododeoxyuridine for A, G, or T. These iodopyrimidine bases were excited using a UV laser to
AB  - result in covalent cross-linking products. The yield of EcoRII photocross-linked to the 5'-C
AB  - of the 5'-CCAGG strand of the recognition sequence was 45%. However, we could not
AB  - photocross-link EcoRII to the 5'-C of the 5'-CCTGG strand. Thus, the contact of EcoRII to
AB  - the bases of the recognition sequence appears to be asymmetric, unlike that expected for most
AB  - type II restriction endonucleases. Tryptic digestion of free and of cross-linked EcoRII,
AB  - followed by high performance liquid chromatography (HPLC) separation of the individual
AB  - peptides and Edman degradation, identified amino acids 25-49 of EcoRII as the cross-linking
AB  - peptide. Mutational analysis of the electron-rich amino acids His(36) and Tyr(41) of this
AB  - peptide indicates that Tyr(41) is the amino acid involved in the cross-link and that it
AB  - therefore contributes to specific DNA recognition by EcoRII.
ER  -

TY  - JOUR
AU  - Mucke, M.
AU  - Reich, S.
AU  - Moncke-Buchner, E.
AU  - Reuter, M.
AU  - Kruger, D.H.
TI  - DNA cleavage by type II restriction-modification enzyme EcoP15I is independent of spacer distance between two head to head oriented recognition sites.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 687
EP  - 698
VL  - 312
AB  - The type III restriction-modification enzyme EcoP15I requires the interaction of two
AB  - unmethylated, inversely oriented recognition sites 5'-CAGCAG in head to head configuration to
AB  - allow an efficient DNA cleavage. It has been hypothesized that two convergent
AB  - DNA-translocating enzyme-substrate complexes interact to form the active cleavage complex and
AB  - that translocation is driven by ATP hydrolysis. Using a half-automated, fluorescence-based
AB  - detection method, we investigated how the distance between two inversely oriented recognition
AB  - sites affects DNA cleavage efficiency. We determined that EcoP15I cleaves DNA efficiently even
AB  - for two adjacent head to head or tail to tail oriented target sites. Hence, DNA translocation
AB  - appears not to be required for initiating DNA cleavage in these cases. Furthermore, we report
AB  - here that EcoP15I is able to cleave single-site substrates. When we analyzed the interaction
AB  - of EcoP15I with DNA substrates containing adjacent target sites in the presence of
AB  - non-hydrolyzable ATP analogues, we found that cleavage depended on the hydrolysis of ATP.
AB  - Moreover, we show that cleavage occurs at only one of the two possible cleavage positions of
AB  - an interacting pair of target sequences. When EcoP15I bound to a DNA substrate containing one
AB  - recognition site in the absence of ATP, we observed a 36 nucleotide DNaseI-footprint that is
AB  - asymmetric on both strands. All of our footprinting experiments showed that the enzyme did not
AB  - cover the region around the cleavage site. Analyzing a DNA fragment with two head to head
AB  - oriented recognition sites, EcoP15I protected 27-33 nucleotides around the recognition
AB  - sequence, including an additional region of 26 bp between both cleavage sites. For all DNA
AB  - substrates examined, the presence of ATP caused altered footprinting patterns. We assume that
AB  - the altered patterns are most likely due to a conformational change of the enzyme. Overall,
AB  - our data further refine the tracking-collision model for type III restriction enzymes.
ER  -

TY  - JOUR
AU  - Muckerman, C.C.
AU  - Springhorn, S.S.
AU  - Greenberg, B.
AU  - Lacks, S.A.
TI  - Transformation of restriction endonuclease phenotype in Streptococcus pneumoniae.
JO  - J. Bacteriol.
PY  - 1982
SP  - 183
EP  - 190
VL  - 152
AB  - The genetic basis of the unique restriction endonuclease DpnI, that cleaves
AB  - only at a methylated sequence, 5'-GmeATC-3', and of the complementary
AB  - endonuclease DpnII, which cleaves at the same sequence when it is not
AB  - methylated, was investigated.  Different strains of Streptococcus pneumoniae
AB  - isolated from patients contained either DpnI (two isolates) or DpnII (six
AB  - isolates).  The latter strains also contained DNA methylated at the 5'-GATC-3'
AB  - sequence.  A restrictable bacteriophage, HB-3, was used to characterize the
AB  - various strains and to select for transformants.  One laboratory strain
AB  - contained neither DpnI nor DpnII.  It was probably derived from a
AB  - DpnI-containing strain, and its DNA was not methylated at 5'-GATC-3'.  Cells of
AB  - this strain were transformed to the DpnI restriction phenotype by DNA from a
AB  - DpnI-containing strain and to the DpnII restriction phenotype by DNA from
AB  - DpnII-containing strain.  Neither cross-transformation, that is, transformation
AB  - to one phenotype by DNA from a strain of the other phenotype, nor spontaneous
AB  - conversion was observed.  Extracts of transformants to the new restriction
AB  - phenotype were shown to contain the corresponding endonuclease.
ER  -

TY  - JOUR
AU  - Mueller, J.E.
AU  - Bryk, M.
AU  - Loizos, N.
AU  - Belfort, M.
TI  - Homing endonucleases.
JO  - Nucleases
PY  - 1993
SP  - 111
EP  - 143
VL  - 0
AB  - *
AB  - I. Introduction
AB  - II. Historic review
AB  - III. General characteristics of homing endonucleases
AB  -         A. Endonuclease-mediated homing
AB  -         B. Endonuclease ORF location
AB  -         C. Endonuclease expression
AB  -         D. Sequence motifs
AB  -                 1. The LAGLI-DADG motif
AB  -                 2. The GIY-YIG motif
AB  -                 3. The zinc finger motif
AB  -                 4. Unclassified
AB  -         E. Target recognition and cleavage specificity
AB  -                 1. General properties
AB  -                 2. Genetic studies
AB  -                 3. Physical studies
AB  - IV. Evolutionary considerations
AB  -         A. Evidence for mobility of endonuclease genes
AB  -         B. Invasion and its aftermath
AB  -         C. Endonuclease properties that potentiate invasiveness
AB  -         D. Down-regulation of endonuclease expression
AB  -         E. Cross-species transfer
AB  - 
ER  -

TY  - JOUR
AU  - Mueller, J.E.
AU  - Clyman, J.
AU  - Huang, Y.-J.
AU  - Parker, M.M.
AU  - Belfort, M.
TI  - Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways.
JO  - Genes Dev.
PY  - 1996
SP  - 351
EP  - 364
VL  - 10
AB  - Numerous group I introns in both prokaryotes and euykaryotes behave as mobile genetic
AB  - elements.  The functional requirements for intron mobility were determined in the T4 phage
AB  - system using an in vivo assay to measure intron homing with wild-type and mutant derivatives.
AB  - Thus, it was demonstrated that intron mobility occurs in the context of phage
AB  - recombination-dependent replication, a pathway that uses overlapping subsets of replication
AB  - and recombination functions.  The functional requirements for intron homing and the nature of
AB  - recombinant products are only partially consistent with the accepted double-strand-break
AB  - repair model for intron inheritance, and implicate additional homing pathways.  Whereas
AB  - ambiguities in resolvase requirements and underrepresentation of crossover recombination
AB  - products are difficult to rationalize strictly by DSBR, these properties are most readily
AB  - consistent with a synthesis-dependent strand annealing pathway.  The pathways share common
AB  - features in the strand invasion steps, but differ in subsequent repair synthesis and
AB  - resolution steps, influencing the genetic consequences of the intron transfer event.
ER  -

TY  - JOUR
AU  - Mueller, J.E.
AU  - Smith, D.
AU  - Belfort, M.
TI  - Exon coconversion biases accompanying intron homing: battle of the nucleases.
JO  - Genes Dev.
PY  - 1996
SP  - 2158
EP  - 2166
VL  - 10
AB  - Intron homing in phage T4 occurs in the context of recombination-dependent replication, by
AB  - virtue of intron-encoded endonucleolytic activity.  After the td intron endonuclease I-TevI
AB  - cleaves the intronless recipient 23 and 25 nucleotides upstream of the intron insertion site,
AB  - exonucleolytic degradation is required for recombination to proceed.  This resection process
AB  - results in coconversion of exon sequences flanking the intron.  In a genetic system designed
AB  - to study coconversion of flanking markers, we demonstrate that although there is a
AB  - bidirectional polarity gradient, coconversion can be highly asymmetric.  Furthermore, we show
AB  - that the coconversion of flanking markers favors exon I sequences, upstream of the I-TevI
AB  - cleavage site.  These data are consistent with the asymmetric features of the homing pathways
AB  - that have been invoked for intron mobility in phage T4.  Moreover, these results are in accord
AB  - with the finding that once the td homing-site substrate is cleaved, I-TevI remains bound to
AB  - the downstream cleavage product, protecting against exonucleolytic degradation, and thereby
AB  - limiting the extent of coconversion into exon II.  The results suggest that recombination
AB  - events are influenced by a competition between the homing endonuclease and exonucleases for
AB  - sequences downstream of the I-TevI cleavage site, thereby implying a role for the homing
AB  - endonuclease in the repair process.
ER  -

TY  - JOUR
AU  - Mueller, J.E.
AU  - Smith, D.
AU  - Bryk, M.
AU  - Belfort, M.
TI  - Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site.
JO  - EMBO J.
PY  - 1995
SP  - 5724
EP  - 5735
VL  - 14
AB  - I-TevI, the intron-encoded endonuclease from the thymidylate synthase (td) gene of
AB  - bacteriophage T4, binds its DNA substrate across the minor groove in a sequence-tolerant
AB  - fashion.  We demonstrate here that the 28 kDa I-TevI binds the extensive 37 bp td homing site
AB  - as a monomer and significantly distorts its substrate.  In situ cleavage assays and phasing
AB  - analyses indicate that upon nicking the bottom strand of the td homing site, I-TevI induces a
AB  - directed bend of 38o towards the major groove near the cleavage site.  Formation of the bent
AB  - I-TevI-DNA complex is proposed to promote top-strand cleavage of the homing site.
AB  - Furthermore, reductions in the degree of distortion and in the efficiency of binding
AB  - base-substitution variants of the td homing site indicate that sequences flanking the cleavage
AB  - site contribute to the I-TevI-induced conformational change.  These results, combined with
AB  - genetic, physical and computer-modeling studies, form the basis of a model, wherein I-TevI
AB  - acts as a hinged monomer to induce a distortion that widens the minor groove, facilitating
AB  - access to the top-strand cleavage site.  The model is compatible with both unmodified DNA and
AB  - glucosylated hydroxymethylcytosine-containing DNA, as exists in the T-even phages.
ER  -

TY  - JOUR
AU  - Muge, G.R.
AU  - Veras, A.A.
AU  - de Sa, P.H.
AU  - Cavalcante, A.L.
AU  - Alves, J.T.
AU  - Morais, E.
AU  - Silva, A.G.
AU  - Guimaraes, L.C.
AU  - Azevedo, V.
AU  - Folador, A.R.
AU  - Silva, A.
AU  - Ramos, R.T.
TI  - Genome Sequence of Corynebacterium pseudotuberculosis Strain PA02 Isolated from an Ovine Host in the Amazon.
JO  - Genome Announcements
PY  - 2016
SP  - e00838
EP  - e00816
VL  - 4
AB  - In this work, we report the complete genome sequence of Corynebacterium pseudotuberculosis
AB  - strain PA02 isolated from an ovine host. The genome contains
AB  - 2,328,435 bp, a 52.2% G+C content, 2,035 coding sequences, 12 rRNA operons, 45
AB  - tRNAs, and 14 predicted pseudogenes.
ER  -

TY  - JOUR
AU  - Muhd, S.M.K.
AU  - Abdul, R.A.Y.
AU  - Saito, J.A.
AU  - Hou, S.
AU  - Alam, M.
TI  - Complete Genome Sequence of the Thermophilic Bacterium Geobacillus thermoleovorans CCB_US3_UF5.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1239
EP  - 1239
VL  - 194
AB  - Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring
AB  - in Malaysia. Here, we report the complete genome of G.
AB  - thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of
AB  - Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.
ER  -

TY  - JOUR
AU  - Muir, R.S.
AU  - Flores, H.
AU  - Zinder, N.D.
AU  - Model, P.
AU  - Soberon, X.
AU  - Heitman, J.
TI  - Temperature-sensitive mutants of the EcoRI endonuclease.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 722
EP  - 737
VL  - 274
AB  - The EcoRI endonuclease is an important recombinant DNA tool and a paradigm of
AB  - sequence-specific DNA-protein interactions.  We have isolated temperature sensitive EcoRI
AB  - endonuclease mutants (R56Q, G78D, P90S, V97I, R105K, M157I, C218Y, A235E, M255I, T261I and
AB  - L263F) and characterized activity in vivo and in vitro.  Although the majority were TS for
AB  - function in vivo, all of the mutant enzymes were stably expressed and largely soluble at both
AB  - 30oC and 42oC in vivo and none of the mutants was found to be TS in vitro.  These findings
AB  - suggest that these mutations may affect folding of the enzyme at elevated temperature in vivo.
AB  - Both non-conservative and conservative substitutions occurred but were not correlated with
AB  - severity of the mutation.  Of the 12 residues identified, 11 are conserved between EcoRI and
AB  - the isoschizomer RsrI (which shares 50% identity), a further indication that these residues
AB  - are critical for EcoRI structure and function.  Inspection of the 2.8 A resolution X-ray
AB  - crystal structure of the wild-type EcoRI endonuclease-DNA complex revealed that: (1) the TS
AB  - mutations cluster in one half of the globular enzyme; (2) several of the substituted residues
AB  - interact with each other; (3) most mutations would be predicted to disrupt local structures;
AB  - (4) two mutations may affect the dimer interface (G78D and A235E); (5) one mutation (P90S)
AB  - occurred in a residue that is part of, or immediately adjacent to, the EcoRI active site and
AB  - which is conserved in the distantly related EcoRV endonuclease.  Finally, one class of mutants
AB  - restricted phage in vivo and was active in vitro, whereas a second class did not restrict and
AB  - was inactive in vitro.  The two classes of mutants may differ in kinetic properties or
AB  - cleavage mechanism.  In summary, these mutations provide insights into EcoRI structure and
AB  - function, and complement previous genetic, biochemical, and structural analyses.
ER  -

TY  - JOUR
AU  - Mukherjee, A.
AU  - Chettri, B.
AU  - Langpoklakpam, J.S.
AU  - Singh, A.K.
AU  - Chattopadhyay, D.
TI  - Draft Genome Sequence of Hydrocarbon-Degrading Staphylococcus saprophyticus Strain CNV2, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil  Refinery, Guwahati, Assam, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00370
EP  - e00316
VL  - 4
AB  - Here, we report the 2.6 Mb draft genome sequence of hydrocarbon-degrading Staphylococcus
AB  - saprophyticus strain CNV2, isolated from oil-contaminated soil in
AB  - Guwahati, India. CNV2 contains 2,545 coding sequences and has a G+C content of
AB  - 33.2%. This is the first report of the genome sequence of an S. saprophyticus
AB  - adapted to an oil-contaminated environment.
ER  -

TY  - JOUR
AU  - Mukherjee, A.
AU  - Chettri, B.
AU  - Langpoklakpam, J.S.
AU  - Singh, A.K.
AU  - Chattopadhyay, D.
TI  - Draft Genome Sequence of Hydrocarbon-Degrading Enterobacter cloacae Strain S1:CND1, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil  Refinery, Guwahati, Assam, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00367
EP  - e00316
VL  - 4
AB  - We report here the 4.57-Mb draft genome sequence of hydrocarbon-degrading Enterobacter cloacae
AB  - strain S1:CND1 isolated from oil-contaminated soil in
AB  - Guwahati, India. S1:CND1 contains 4,205 coding sequences and has a G+C content of
AB  - 57.45%. This is the first report of the genome sequence of an E. cloacae adapted
AB  - to an oil-contaminated environment.
ER  -

TY  - JOUR
AU  - Mukherjee, S. et al.
TI  - High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 8
EP  - 8
VL  - 10
AB  - Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia.
AB  - While the type species of the genus Pontibacter actiniarum was
AB  - isolated in 2005 from a marine environment, subsequent species of the same genus
AB  - have been found in different types of habitats ranging from seawater, sediment,
AB  - desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here
AB  - we describe the features of Pontibacter roseus strain SRC-1(T) along with its
AB  - complete genome sequence and annotation from a culture of DSM 17521(T). The
AB  - 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding
AB  - and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I
AB  - project.
ER  -

TY  - JOUR
AU  - Mukherjee, S. et al.
TI  - 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
JO  - Nat. Biotechnol.
PY  - 2017
SP  - 676
EP  - 683
VL  - 35
AB  - We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea (GEBA) initiative, selected to maximize
AB  - sequence coverage of phylogenetic space. These genomes double the number of
AB  - existing type strains and expand their overall phylogenetic diversity by 25%.
AB  - Comparative analyses with previously available finished and draft genomes reveal
AB  - a 10.5% increase in novel protein families as a function of phylogenetic
AB  - diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic
AB  - proteins from 4,650 samples, improving their phylogenetic and functional
AB  - interpretation. We identify numerous biosynthetic clusters and experimentally
AB  - validate a divergent phenazine cluster with potential new chemical structure and
AB  - antimicrobial activity. This Resource is the largest single release of reference
AB  - genomes to date. Bacterial and archaeal isolate sequence space is still far from
AB  - saturated, and future endeavors in this direction will continue to be a valuable
AB  - resource for scientific discovery.
ER  -

TY  - JOUR
AU  - Mukherjee, T.
AU  - Bose, S.
AU  - Sen, U.
AU  - Roy, C.
AU  - Rameez, M.J.
AU  - Ghosh, W.
AU  - Mukhopadhyay, S.K.
TI  - Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00629
EP  - e00616
VL  - 4
AB  - Here we report the draft genome sequence of Meiothermus taiwanensis strain RP (MCC 2966),
AB  - isolated from the Paniphala hot spring of India, which contains genes encoding for enzymes of
AB  - the methyl erythritol 4-phosphate (MEP) pathway of isoprenoid biosynthesis and carotenoid
AB  - backbone synthesis.
ER  -

TY  - JOUR
AU  - Mukherjee, U.
AU  - Kumar, R.
AU  - Mahato, N.K.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane.
JO  - Genome Announcements
PY  - 2013
SP  - e00749
EP  - e00713
VL  - 1
AB  - Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and
AB  - degraded HCH isomers rapidly. The draft genome sequence of HDIPO4
AB  - (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of
AB  - 65%.
ER  -

TY  - JOUR
AU  - Mukherjee, U.
AU  - Saxena, A.
AU  - Kumari, R.
AU  - Singh, P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Amycolatopsis mediterranei DSM 40773, a Tangible Antibiotic Producer.
JO  - Genome Announcements
PY  - 2014
SP  - e00752
EP  - e00714
VL  - 2
AB  - Amycolatopsis mediterranei DSM 40773 has been of special interest as successors of this strain
AB  - are in use for the commercial production of rifamycin B. Here we
AB  - present the draft genome sequence (~10 Mb) of this strain, which contains 108
AB  - contigs, 9,198 genes, and has a G+C content of 71.3%.
ER  -

TY  - JOUR
AU  - Mukhopadhyay, A.K.
AU  - Kersulyte, D.
AU  - Jeong, J.Y.
AU  - Datta, S.
AU  - Ito, Y.
AU  - Chowdhury, A.
AU  - Chowdhury, S.
AU  - Santra, A.
AU  - Bhattacharya, S.K.
AU  - Azuma, T.
AU  - Nair, G.B.
AU  - Berg, D.E.
TI  - Distinctiveness of genotypes of Helicobacter pylori in Calcutta India.
JO  - J. Bacteriol.
PY  - 2000
SP  - 3219
EP  - 3227
VL  - 182
AB  - The genotypes of 78 strains of Helicobacter pylori from Calcutta, India (55 from ulcer
AB  - patients and 23 from more-benign infections), were studied, with a focus on putative virulence
AB  - genes and neutral DNA markers that were likely to be phylogenetically informative. PCR tests
AB  - indicated that 80 to 90% of Calcutta strains carried the cag pathogenicity island (PAI) and
AB  - potentially toxigenic vacAs1 alleles of the vacuolating cytotoxin gene (vacA), independent of
AB  - disease status. This was higher than in the West (where cag PAI(+) vacAs1 genotypes are
AB  - disease associated) but lower than in east Asia. The iceA2 gene was weakly disease associated
AB  - in Calcutta, whereas in the West the alternative but unrelated iceA1 gene at the same locus is
AB  - weakly disease associated. DNA sequence motifs of vacAm1 (middle region) alleles formed a
AB  - cluster that was distinct from those of east Asia and the West, whereas the cagA sequences of
AB  - Calcutta and Western strains were closely related. An internal deletion found in 20% of
AB  - Calcutta iceA1 genes was not seen in any of approximately 200 strains studied from other
AB  - geographic regions and thus seemed to be unique to this H. pylori population. Two mobile DNAs
AB  - that were rare in east Asian strains were also common in Calcutta. About 90% of Calcutta
AB  - strains were metronidazole resistant. These findings support the idea that H. pylori gene
AB  - pools differ regionally and emphasize the potential importance of studies of Indian and other
AB  - non-Western H. pylori populations in developing a global understanding of this gastric
AB  - pathogen and associated disease.
ER  -

TY  - JOUR
AU  - Mukhopadhyay, C.
AU  - Vandana, K.E.
AU  - Chaitanya, T.A.
AU  - Shaw, T.
AU  - Bhat, H.V.
AU  - Chakrabarty, S.
AU  - Paul, B.
AU  - Mallya, S.
AU  - Murali, T.S.
AU  - Satyamoorthy, K.
TI  - Genome Sequence of a Burkholderia pseudomallei Clinical Isolate from a Patient with Community-Acquired Pneumonia and Septicemia.
JO  - Genome Announcements
PY  - 2015
SP  - e00915
EP  - e00915
VL  - 3
AB  - Here, we report the draft genome sequence of Burkholderia pseudomallei CM_Manipal, the
AB  - causative agent of melioidosis isolated from a diabetic patient
AB  - in Manipal, southern India. The draft genome consists of 107 contigs and is
AB  - 7,209,157 bp long. A total of 5,600 coding sequences (CDSs), 60 tRNAs, 12 rRNAs,
AB  - and one noncoding RNA (ncRNA) were predicted from this assembly.
ER  -

TY  - JOUR
AU  - Mukhopadhyay, P.
AU  - Roy, K.B.
TI  - Protein engineering of BamHI restriction endonuclease: replacement of Cys54 by Ala enhances catalytic activity.
JO  - Protein Eng.
PY  - 1998
SP  - 931
EP  - 935
VL  - 11
AB  - Chemical modification studies of BamHI endonuclease indicated the importance of the cysteine
AB  - residue in catalysis.  Of the three cysteine residues at position 34, 54 and 64 in the BamHI
AB  - endonuclease Cys54 and Cys64 are at the DNA-protein interface.  The co-crystal structure of
AB  - the BamHI-DNA complex, however, does not indicate any role of cysteines either in binding or
AB  - catalysis.  In the context of strong biochemical evidence, Cys54 in BamHI was changed to Ala54
AB  - to investigate its role in catalysis.  The mutation was carried out by PCR overlap extension,
AB  - the mutant gene was cloned and characterized by sequencing.  The mutant BamHI was expressed
AB  - and purified to homogeneity and the kinetic parameters (KM and kcat) of the wild type and the
AB  - C54A mutant were determined.  The mutation results in up to ~40% enhancement of kcat and some
AB  - increase in KM.  These in vitro results were also supported by in vivo SOS induction assays:
AB  - the C54A mutant gene under the T7 promoter caused complete lysis in JH139 in absence of T7 RNA
AB  - polymerase whereas the wild-type gene gave deep blue colonies under the same conditions.  The
AB  - results suggest no direct role in Cys54 in catalysis, but it can influence the catalytic
AB  - activity through Val57 backbone contact seen in the co-crystal structure.
ER  -

TY  - JOUR
AU  - Mukhopadhyay, R.
AU  - Joaquin, J.
AU  - Hogue, R.
AU  - Fitzgerald, S.
AU  - Jospin, G.
AU  - Mars, K.
AU  - Eisen, J.A.
AU  - Chaturvedi, V.
TI  - Complete Genome Sequence of Dolosigranulum pigrum from a Patient with Interstitial Lung Disease Using Single-Molecule Real-Time Sequencing Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e00317
EP  - e00317
VL  - 5
AB  - The whole genome sequence of Dolosigranulum pigrum isolated from the blood of a patient with
AB  - interstitial lung disease was sequenced with the Pacific Biosciences
AB  - RS II platform. The genome size is 2.1 Mb with 2,127 annotated coding sequences;
AB  - it contained two clustered regularly interspaced short palindromic repeats
AB  - (CRISPR)/CRISPR-associated proteins (Cas) systems.
ER  -

TY  - JOUR
AU  - Mukhopadhyay, R.
AU  - Joaquin, J.
AU  - Hogue, R.
AU  - Kilaru, A.
AU  - Jospin, G.
AU  - Mars, K.
AU  - Eisen, J.A.
AU  - Chaturvedi, V.
TI  - Complete Genome Sequence of a Paenalcaligenes hominis Strain Isolated from a Paraplegic Patient with Neurogenic Bladder Using Single-Molecule Real-Time  Sequencing Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e00252
EP  - e00217
VL  - 5
AB  - The genome of Paenalcaligenes hominis, isolated from a paraplegic patient with neurogenic
AB  - bladder, was sequenced with the Pacific Biosciences RSII platform. The
AB  - genome size is 2.68 Mb and includes 3,096 annotated coding sequences, including
AB  - genes associated with quinone cofactors, which play crucial roles in the
AB  - virulence of Gram-negative bacteria.
ER  -

TY  - JOUR
AU  - Mukhopadhyay, S.
AU  - Thomason, M.K.
AU  - Lentz, S.
AU  - Nolan, N.
AU  - Willner, K.
AU  - Gee, J.E.
AU  - Glass, M.B.
AU  - Inglis, T.J.
AU  - Merritt, A.
AU  - Levy, A.
AU  - Sozhamannan, S.
AU  - Mateczun, A.
AU  - Read, T.D.
TI  - High-redundancy draft sequencing of 15 clinical and environmental burkholderia strains.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6313
EP  - 6314
VL  - 192
AB  - The Gram-negative Burkholderia genus includes several species of intracellular bacterial
AB  - pathogens that pose substantial risk to humans. In
AB  - this study, we have generated draft genome sequences of 15 strains of B.
AB  - oklahomensis, B. pseudomallei, B. thailandensis, and B. ubonensis to an
AB  - average sequence read coverage of 25- to 40-fold.
ER  -

TY  - JOUR
AU  - Mukhtar, T.
AU  - Afridi, M.S.
AU  - McArthur, R.
AU  - Van Hamme, J.D.
AU  - Rineau, F.
AU  - Mahmood, T.
AU  - Amna, S.
AU  - Zahid, M.
AU  - Salam, A.
AU  - Khan, M.N.
AU  - Ali, F.
AU  - Mehmood, S.
AU  - Bangash, N.
AU  - Chaudhary, H.J.
TI  - Draft Genome Sequence of Bacillus pumilus SCAL1, an Endophytic Heat-Tolerant Plant Growth-Promoting Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00306
EP  - e00318
VL  - 6
AB  - Bacillus pumilus strain SCAL1 is an endophytic, thermophilic plant that was isolated from the
AB  - leaf of a plant, Solanum lycopersicum L., in Sindh, Pakistan.
AB  - B. pumilus strain SCAL1 has usually exhibited high resistance to environmental
AB  - stresses, with a growth temperature ranging from 30 to 60 degrees C. An
AB  - approximately 3.75-Mb draft genome was assembled into 68 contigs.
ER  -

TY  - JOUR
AU  - Mukund, M.A.
TI  - Restriction and modification systems: unrestricted frontiers.
JO  - Curr. Sci.
PY  - 1993
SP  - 509
EP  - 511
VL  - 65
AB  - Report on Saxton's River Meeting, July 1993
ER  -

TY  - JOUR
AU  - Mulder, C.
AU  - Delius, H.
TI  - Specificity of the break produced by restricting endonuclease R in Simian virus 40 DNA, as revealed by partial denaturation mapping.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 3215
EP  - 3219
VL  - 69
AB  - Superhelical circular (form 1) SV40 DNA was converted to linear molecules by
AB  - the action of a partially purified restriction enzyme of resistance transfer
AB  - factor-R of Escherichia coli.  The resulting linear DNA molecules are full
AB  - length, as judged by their sedimentation through alkaline sucrose gradient and
AB  - by direct observation in an electron microscope.  Nicked circular (form II) DNA
AB  - was found as an intermediate in the conversion of form I DNA to linear DNA.
AB  - Analysis of partial denaturation maps obtained by alkaline denaturation of the
AB  - unit-length linear molecules showed that the break in SV40 DNA occurred at a
AB  - specific site on the DNA.
ER  -

TY  - JOUR
AU  - Mulla, S.I.
AU  - Hu, A.
AU  - Xu, H.
AU  - Yu, C.P.
TI  - Draft Genome Sequence of Triclosan-Degrading Bacterium Sphingomonas sp. Strain YL-JM2C, Isolated from a Wastewater Treatment Plant in China.
JO  - Genome Announcements
PY  - 2015
SP  - e00603
EP  - e00615
VL  - 3
AB  - Sphingomonas sp. strain YL-JM2C was isolated from a wastewater treatment plant in Xiamen,
AB  - China, by enrichment on triclosan. The bacterium is of special interest
AB  - because of its ability to degrade triclosan. Here, we present a draft genome
AB  - sequence of the microorganism and its functional annotation. To our best
AB  - knowledge, this is the first report of a draft genome sequence of a
AB  - triclosan-degrading bacterium.
ER  -

TY  - JOUR
AU  - Muller, A.
AU  - Huptas, C.
AU  - Wenning, M.
AU  - Schmidt, H.
AU  - Weiss, A.
TI  - Draft Genome Sequence of Staphylococcus carnosus subsp. utilis LTH 7013, Isolated from South Tyrolean Ham.
JO  - Genome Announcements
PY  - 2015
SP  - e00456
EP  - e00415
VL  - 3
AB  - Staphylococcus carnosus is used as a starter culture in meat fermentation, where  it
AB  - contributes to color formation and produces aromatic compounds. Here, we
AB  - report the first draft genome sequence of an S. carnosus subsp. utilis strain,
AB  - LTH 7013, isolated from South Tyrolean ham, with potential application as a
AB  - starter culture.
ER  -

TY  - JOUR
AU  - Muller, A.
AU  - Klumpp, J.
AU  - Schmidt, H.
AU  - Weiss, A.
TI  - Complete Genome Sequence of Staphylococcus carnosus LTH 3730.
JO  - Genome Announcements
PY  - 2016
SP  - e01038
EP  - e01016
VL  - 4
AB  - Specific strains of the apathogenic coagulase-negative species Staphylococcus carnosus are
AB  - frequently used as meat starter cultures, as they contribute to
AB  - color formation and the production of aroma compounds. Here, we report the
AB  - complete genome sequence of S. carnosus LTH 3730, a strain isolated from a
AB  - fermented fish product.
ER  -

TY  - JOUR
AU  - Muller, D. et al.
TI  - A tale of two oxidation states: bacterial colonization of arsenic-rich environments.
JO  - PLoS Genet.
PY  - 2007
SP  - e53
EP  - e53
VL  - 3
AB  - Microbial biotransformations have a major impact on contamination by toxic elements, which
AB  - threatens public health in developing and industrial
AB  - countries. Finding a means of preserving natural environments-including
AB  - ground and surface waters-from arsenic constitutes a major challenge
AB  - facing modern society. Although this metalloid is ubiquitous on Earth,
AB  - thus far no bacterium thriving in arsenic-contaminated environments has
AB  - been fully characterized. In-depth exploration of the genome of the
AB  - beta-proteobacterium Herminiimonas arsenicoxydans with regard to
AB  - physiology, genetics, and proteomics, revealed that it possesses
AB  - heretofore unsuspected mechanisms for coping with arsenic. Aside from
AB  - multiple biochemical processes such as arsenic oxidation, reduction, and
AB  - efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility
AB  - towards arsenic and metalloid scavenging by exopolysaccharides. These
AB  - observations demonstrate the existence of a novel strategy to efficiently
AB  - colonize arsenic-rich environments, which extends beyond oxidoreduction
AB  - reactions. Such a microbial mechanism of detoxification, which is possibly
AB  - exploitable for bioremediation applications of contaminated sites, may
AB  - have played a crucial role in the occupation of ancient ecological niches
AB  - on earth.
ER  -

TY  - JOUR
AU  - Muller, E.E.
AU  - Pinel, N.
AU  - Gillece, J.D.
AU  - Schupp, J.M.
AU  - Price, L.B.
AU  - Engelthaler, D.M.
AU  - Levantesi, C.
AU  - Tandoi, V.
AU  - Luong, K.
AU  - Baliga, N.S.
AU  - Korlach, J.
AU  - Keim, P.S.
AU  - Wilmes, P.
TI  - Genome Sequence of 'Candidatus Microthrix parvicella' Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological    Wastewater Treatment Plant.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6670
EP  - 6671
VL  - 194
AB  - 'Candidatus Microthrix' bacteria are deeply branching filamentous actinobacteria  which
AB  - occur at the water-air interface of biological wastewater treatment plants,
AB  - where they are often responsible for foaming and bulking. Here, we report the
AB  - first draft genome sequence of a strain from this genus: 'Candidatus Microthrix
AB  - parvicella' strain Bio17-1.
ER  -

TY  - JOUR
AU  - Muller, E.E.L.
AU  - Narayanasamy, S.
AU  - Zeimes, M.
AU  - Laczny, C.C.
AU  - Lebrun, L.A.
AU  - Herold, M.
AU  - Hicks, N.D.
AU  - Gillece, J.D.
AU  - Schupp, J.M.
AU  - Keim, P.
AU  - Wilmes, P.
TI  - First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 64
EP  - 64
VL  - 12
AB  - The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated
AB  - from foaming activated sludge of a municipal wastewater treatment plant.
AB  - Here, we describe its draft genome sequence and annotation together with a
AB  - general physiological and genomic analysis, as the first sequenced representative
AB  - of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment
AB  - is described using metatranscriptomic data obtained from the same treatment
AB  - plant. The presented genomic and transcriptomic information demonstrate a
AB  - pronounced capacity of this genus to synthesize poly-beta-hydroxyalkanoate within
AB  - wastewater.
ER  -

TY  - JOUR
AU  - Muller, H.
AU  - Furnkranz, M.
AU  - Grube, M.
AU  - Berg, G.
TI  - Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination- and Plant-Growth-Promoting Activity from the Flower of Styrian Oil Pumpkin.
JO  - Genome Announcements
PY  - 2013
SP  - e00594
EP  - e00513
VL  - 1
AB  - The bacterium Serratia plymuthica strain S13 was demonstrated to colonize various
AB  - plant-associated microhabitats and to suppress damping-off diseases. The
AB  - completed genome sequence has a size of 5.5 Mb, containing 4,957 putative
AB  - protein-encoding regions, and will be used to identify genetic determinants
AB  - enabling the bacterium to escort a plant's entire life cycle.
ER  -

TY  - JOUR
AU  - Muller, H.
AU  - Zachow, C.
AU  - Alavi, M.
AU  - Tilcher, R.
AU  - Krempl, P.M.
AU  - Thallinger, G.G.
AU  - Berg, G.
TI  - Complete Genome Sequence of the Sugar Beet Endophyte Pseudomonas poae RE*1-1-14,  a Disease-Suppressive Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e0002013
EP  - e0002013
VL  - 1
AB  - The endophytic bacterium Pseudomonas poae RE*1-1-14 shows broad antagonistic activity and is
AB  - applied to seeds as a biocontrol agent to suppress late root rot
AB  - in the sugar beet. The completely sequenced 5.5-Mb genome reveals genes that
AB  - putatively contribute to this antagonistic activity and the intimate
AB  - plant-microbe interaction.
ER  -

TY  - JOUR
AU  - Muller, I.
AU  - Kube, M.
AU  - Reinhardt, R.
AU  - Jelkmann, W.
AU  - Geider, K.
TI  - The Complete Genome Sequences of three Erwinia amylovora Phages Isolated in North America and a Bacteriophage Induced from an Erwinia tasmaniensis  Strain.
JO  - J. Bacteriol.
PY  - 2010
SP  - 795
EP  - 796
VL  - 193
AB  - Fire blight, a plant disease of economical importance caused by Erwinia amylovora, may be
AB  - controlled by application of bacteriophages. Here we
AB  - provide the complete genome sequences and the annotation of three E.
AB  - amylovora-specific phages isolated in North America and genomic
AB  - information about a bacteriophage induced by mitomycin C-treatment of an
AB  - E. tasmaniensis strain, antagonistic for E. amylovora. The American phages
AB  - resemble two already described viral genomes, whereas the E. tasmaniensis
AB  - phage displays a singular genomic sequence in BLAST searches.
ER  -

TY  - JOUR
AU  - Muller, S.
AU  - Willett, J.W.
AU  - Bahr, S.M.
AU  - Darnell, C.L.
AU  - Hummels, K.R.
AU  - Dong, C.K.
AU  - Vlamakis, H.C.
AU  - Kirby, J.R.
TI  - Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development.
JO  - Genome Announcements
PY  - 2013
SP  - e00217
EP  - e00213
VL  - 1
AB  - Myxococcus xanthus is a member of the Myxococcales order within the Deltaproteobacteria
AB  - subdivision. The myxobacteria reside in soil, have relatively
AB  - large genomes, and display complex life cycles. Here, we report the whole-genome
AB  - shotgun sequence of strain DZ2, which includes unique genes not found previously
AB  - in strain DK1622.
ER  -

TY  - JOUR
AU  - Muller, S.
AU  - Willett, J.W.
AU  - Bahr, S.M.
AU  - Scott, J.C.
AU  - Wilson, J.M.
AU  - Darnell, C.L.
AU  - Vlamakis, H.C.
AU  - Kirby, J.R.
TI  - Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1.
JO  - Genome Announcements
PY  - 2013
SP  - e00392
EP  - e00313
VL  - 1
AB  - Myxococcus xanthus is a member of the Myxococcales order within the deltaproteobacterial
AB  - subdivision. Here, we report the whole-genome shotgun
AB  - sequence of the type IV pilus (T4P) defective strain DZF1, which includes many
AB  - genes found in strain DZ2 but absent from strain DK1622.
ER  -

TY  - JOUR
AU  - Mulligan, E.A.
AU  - Dunn, J.J.
TI  - Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease.
JO  - Protein Expr. Purif.
PY  - 2008
SP  - 98
EP  - 103
VL  - 62
AB  - Expression strains of Escherichia coli BL21(DE3) overproducing the E. coli m(5)C McrA
AB  - restriction protein were produced by cloning the mcrA coding
AB  - sequence behind a T7 promoter. The recombinant mcrA minus BL21(DE3) host
AB  - produces active McrA as evidenced by its acquired ability to selectively
AB  - restrict the growth of T7 phage containing DNA methylated in vitro by
AB  - HpaII methylase. The mcrA coding region contains several non-optimal E.
AB  - coli triplets. Addition of the pACYC-RIL tRNA encoding plasmid to the
AB  - BL21(DE3) host increased the yield of recombinant McrA (rMcrA) upon
AB  - induction about 5- to 10-fold. McrA protein expressed at 37 degrees C is
AB  - insoluble but a significant fraction is recovered as soluble protein after
AB  - autoinduction at 20 degrees C. rMcrA protein, which is predicted to
AB  - contain a Cys(4)-Zn(2+) finger and a catalytically important histidine
AB  - triad in its putative nuclease domain, binds to several metal chelate
AB  - resins without addition of a poly-histidine affinity tag. This feature was
AB  - used to develop an efficient protocol for the rapid purification of nearly
AB  - homogeneous rMcrA. The native protein is a dimer with a high alpha-helical
AB  - content as measured by circular dichroism analysis. Under all conditions
AB  - tested purified rMcrA does not have measurable nuclease activity on HpaII
AB  - methylated (Cm(5)CGG) DNA, although the purified protein does specifically
AB  - bind HpaII methylated DNA. These results have implications for
AB  - understanding the in vivo activity of McrA in "restricting"
AB  - m(5)C-containing DNA and suggest that rMcrA may have utility as a reagent
AB  - for affinity purification of DNA fragments containing m(5)C residues.
ER  -

TY  - JOUR
AU  - Mulligan, E.A.
AU  - Hatchwell, E.
AU  - McCorkle, S.R.
AU  - Dunn, J.J.
TI  - Differential binding of Escherichia coli McrA protein to DNA sequences that contain the dinucleotide m5CpG.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 1997
EP  - 2005
VL  - 38
AB  - The Escherichia coli McrA protein, a putative C(5)-methylcytosine/C(5)-hydroxyl
AB  - methylcytosine-specific nuclease, binds
AB  - DNA with symmetrically methylated HpaII sequences (Cm5CGG), but its
AB  - precise recognition sequence remains undefined. To determine McrA's
AB  - binding specificity, we cloned and expressed recombinant McrA with a
AB  - C-terminal StrepII tag (rMcrA-S) to facilitate protein purification and
AB  - affinity capture of human DNA fragments with m5C residues. Sequence
AB  - analysis of a subset of these fragments and electrophoretic mobility shift
AB  - assays with model methylated and unmethylated oligonucleotides suggest
AB  - that N(Y > R) m5CGR is the canonical binding site for rMcrA-S. In addition
AB  - to binding HpaII-methylated double-stranded DNA, rMcrA-S binds DNA
AB  - containing a single, hemimethylated HpaII site; however, it does not bind
AB  - if A, C, T or U is placed across from the m5C residue, but does if I is
AB  - opposite the m5C. These results provide the first systematic analysis of
AB  - McrA's in vitro binding specificity.
ER  -

TY  - JOUR
AU  - Mullineux, S.T.
AU  - Costa, M.
AU  - Bassi, G.S.
AU  - Michel, F.
AU  - Hausner, G.
TI  - A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions.
JO  - RNA
PY  - 2010
SP  - 1818
EP  - 1831
VL  - 16
AB  - A group II intron encoding a protein belonging to the LAGLIDADG family of homing endonucleases
AB  - was identified in the mitochondrial rns gene of
AB  - the filamentous fungus Leptographium truncatum, and the catalytic
AB  - activities of both the intron and its encoded protein were
AB  - characterized. A model of the RNA secondary structure indicates that
AB  - the intron is a member of the IIB1 subclass and the open reading frame
AB  - is inserted in ribozyme domain III. In vitro assays carried out with
AB  - two versions of the intron, one in which the open reading frame was
AB  - removed and the other in which it was present, demonstrate that both
AB  - versions of the intron readily self-splice at 37 degrees C and at a
AB  - concentration of MgCl2 as low as 6 mM. The open reading frame encodes a
AB  - functional LAGLIDADG homing endonuclease that cleaves 2 (top strand)
AB  - and 6 (bottom strand) nucleotides (nt) upstream of the intron insertion
AB  - site, generating 4 nt 3' OH overhangs. In vitro splicing assays carried
AB  - out in the absence and presence of the intron-encoded protein indicate
AB  - that the protein does not enhance intron splicing, and RNA-binding
AB  - assays show that the protein does not appear to bind to the intron RNA
AB  - precursor transcript. These findings raise intriguing questions
AB  - concerning the functional and evolutionary relationships of the two
AB  - components of this unique composite element.
ER  -

TY  - JOUR
AU  - Mullings, R.
AU  - Bennett, S.P.
AU  - Brown, N.L.
TI  - Investigation of sequence homology in a group of type-II restriction/modification isoschizomers.
JO  - Gene
PY  - 1988
SP  - 245
EP  - 251
VL  - 74
AB  - We have dissected the cloned PstI M and R genes to make DNA hybridization
AB  - probes spanning most of the sequence.  These subclones, and also the intact
AB  - sequence, were used to search for nucleic acid homology by Southern blot in the
AB  - DNA from twelve organisms which produce PstI isoschizomers.  One of these
AB  - probes, a 206-bp fragment from the N-terminal domain of the endonuclease,
AB  - showed significant hybridisation in four strains (Escherichia coli strains
AB  - RFL48, RFL49 and RFL83, and Streptomyces albus P).  No significant
AB  - hybridisation was detected with other parts  of the PstI proteins and the known
AB  - sequences of other type-II systems that recognise different sites.  We
AB  - postulate a possible recognition domain within the M.PstI methyltransferase
AB  - based on similarity to the M.PaeR7 and M.TaqI methyltransferases.
ER  -

TY  - JOUR
AU  - Mullings, R.
AU  - Evans, L.R.
AU  - Brown, N.L.
TI  - Type II restriction endonucleases from Bacillus sphaericus.
JO  - FEMS Microbiol. Lett.
PY  - 1986
SP  - 237
EP  - 240
VL  - 37
AB  - We report the isolation and characterisation of 3 Type II restriction
AB  - endonucleases from Bacillus sphaericus.  These are BspAI (an isoschizomer of
AB  - Sau3AI) in strain JL4B; BspBI and BspBII (isoschizomers of PstI and AsuI) in
AB  - strain JL14.  These are the first reports of these activities in B. sphaericus
AB  - and the first citation of an AsuI isoschizomer in a member of the genus
AB  - Bacillus.  We briefly discuss the possible uses in vitro and significance in
AB  - vivo of these enzymes.
ER  -

TY  - JOUR
AU  - Mullins, M.A.
AU  - Register, K.B.
AU  - Bayles, D.O.
AU  - Dyer, D.W.
AU  - Kuehn, J.S.
AU  - Phillips, G.J.
TI  - Genome sequence of Haemophilus parasuis strain 29755.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 61
EP  - 68
VL  - 5
AB  - Haemophilus parasuis is a member of the family Pasteurellaceae and is the etiologic agent of
AB  - Glasser's disease in pigs, a systemic syndrome associated with
AB  - only a subset of isolates. The genetic basis for virulence and systemic spread of
AB  - particular H. parasuis isolates is currently unknown. Strain 29755 is an invasive
AB  - isolate that has long been used in the study of Glasser's disease. Accordingly,
AB  - the genome sequence of strain 29755 is of considerable importance to
AB  - investigators endeavoring to understand the molecular pathogenesis of H.
AB  - parasuis. Here we describe the features of the 2,224,137 bp draft genome sequence
AB  - of strain 29755 generated from 454-FLX pyrosequencing. These data comprise the
AB  - first publicly available genome sequence for this bacterium.
ER  -

TY  - JOUR
AU  - Mund, C.
AU  - Musch, T.
AU  - Strodicke, M.
AU  - Assmann, B.
AU  - Li, E.
AU  - Lyko, F.
TI  - Comparative analysis of DNA methylation patterns in transgenic Drosophila overexpressing mouse DNA methyltransferases.
JO  - Biochem. J.
PY  - 2003
SP  - 763
EP  - 768
VL  - 378
AB  - DNA methyltransferases (Dnmts) mediate the epigenetic modification of eukaryotic genomes.
AB  - Mammalian DNA methylation patterns are established and
AB  - maintained by co-operative interactions among the Dnmt proteins Dnmt1,
AB  - Dnmt3a and Dnmt3b. Owing to their simultaneous presence in mammalian
AB  - cells, the activities of individual Dnmt have not yet been determined.
AB  - This includes a fourth putative Dnmt, namely Dnmt2, which has failed to
AB  - reveal any activity in previous assays. We have now established transgenic
AB  - Drosophila strains that allow for individual overexpression of all known
AB  - mouse Dnmts. Quantitative analysis of genomic cytosine methylation levels
AB  - demonstrated a robust Dnmt activity for the de novo methyltransferases
AB  - Dnmt3a and Dnmt3b. In addition, we also detected a weak but significant
AB  - activity for Dnmt2. Subsequent methylation tract analysis by genomic
AB  - bisulphite sequencing revealed that Dnmt3 enzymes preferentially
AB  - methylated CpG dinucleotides in a processive manner, whereas Dnmt2
AB  - methylated isolated cytosine residues in a non-CpG dinucleotide context.
AB  - Our results allow a direct comparison of the activities of mammalian Dnmts
AB  - and suggest a significant functional specialization of these enzymes.
ER  -

TY  - JOUR
AU  - Mundo, S.L.
AU  - Gilardoni, L.R.
AU  - Hoffman, F.J.
AU  - Lopez, O.J.
TI  - Rapid and Sensitive Method To Identify Mycobacterium avium subsp paratuberculosis in Cow's Milk by DNA Methylase Genotyping.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 1612
EP  - 1618
VL  - 79
AB  - Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants,
AB  - caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily
AB  - through feces of infected cows but can be also excreted in colostrum and milk and might
AB  - survive pasteurization. Since an association of genomic sequences of M. avium subsp.
AB  - paratuberculosis in patients with Crohn's disease has been described; it is of interest to
AB  - rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion
AB  - is used as a target for PCR amplification to identify the presence of M. avium subsp.
AB  - paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and
AB  - IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis
AB  - strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk
AB  - samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized
AB  - using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and
AB  - digested with restriction enzymes to confirm their identity. The methylated amplicons from 100
AB  - CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an
AB  - anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled
AB  - to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp.
AB  - paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation
AB  - and thus multiple samples can be tested at the same time.
ER  -

TY  - JOUR
AU  - Muniesa, M.
AU  - Recktenwald, J.
AU  - Bielaszewska, M.
AU  - Karch, H.
AU  - Schmidt, H.
TI  - Characterization of a shiga toxin 2e-converting bacteriophage from an Escherichia coli strain of human origin.
JO  - Infect. Immun.
PY  - 2000
SP  - 4850
EP  - 4855
VL  - 68
AB  - An infectious Shiga toxin (Stx) 2e-converting bacteriophage (phiP27) was
AB  - isolated from Stx2e-producing Escherichia coli ONT:H(-) isolate 2771/97
AB  - originating from a patient with diarrhea. The phage could be transduced to
AB  - E. coli laboratory strain DH5alpha, and we could show that lysogens were
AB  - able to produce biologically active toxin in a recA-dependent manner. By
AB  - DNA sequence analysis of a 6,388-bp HindIII restriction fragment of
AB  - phiP27, we demonstrated that the stx(2e) gene was located directly
AB  - downstream of ileZ and argO tRNA genes. Although no analogue of an
AB  - antiterminator Q encoding gene was present on this fragment, a lysis
AB  - cassette comprising two holin genes which are related to the holin genes
AB  - of Pseudomonas aeruginosa phage phiCTX and a gene homologous to the
AB  - endolysin gene gp19 of phage PS3 were detected. The results of our study
AB  - demonstrated for the first time that Stx2e can be encoded in the genome of
AB  - an infectious bacteriophage.
ER  -

TY  - JOUR
AU  - Munk, A.C. et al.
TI  - Complete genome sequence of Rhodospirillum rubrum type strain (S1).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 293
EP  - 302
VL  - 4
AB  - Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus
AB  - Rhodospirillum, which is the type genus of the family Rhodospirillaceae in
AB  - the class Alphaproteobacteria. The species is of special interest because it is
AB  - an anoxygenic phototroph that produces extracellular elemental sulfur (instead of
AB  - oxygen) while harvesting light. It contains one of the most simple photosynthetic
AB  - systems currently known, lacking light harvesting complex 2. Strain S1(T) can
AB  - grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed
AB  - entries, R. rubrum is one of the most intensively studied microbial species, in
AB  - particular for physiological and genetic studies. Next to R. centenum strain SW,
AB  - the genome sequence of strain S1(T) is only the second genome of a member of the
AB  - genus Rhodospirillum to be published, but the first type strain genome from the
AB  - genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of
AB  - 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint
AB  - Genome Institute Program DOEM 2002.
ER  -

TY  - JOUR
AU  - Munk, A.C. et al.
TI  - Complete genome sequence of Tsukamurella paurometabola type strain (no. 33).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 342
EP  - 351
VL  - 4
AB  - Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of
AB  - the genus Tsukamurella, which is the type genus to the family
AB  - Tsukamurellaceae. The species is not only of interest because of its isolated
AB  - phylogenetic location, but also because it is a human opportunistic pathogen with
AB  - some strains of the species reported to cause lung infection, lethal meningitis,
AB  - and necrotizing tenosynovitis. This is the first completed genome sequence of a
AB  - member of the genus Tsukamurella and the first genome sequence of a member of the
AB  - family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long
AB  - plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of
AB  - the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Munk, C. et al.
TI  - Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 234
EP  - 241
VL  - 1
AB  - Stackebrandtia nassauensis Labeda and Kroppenstedt (2005) is the type species of  the genus
AB  - Stackebrandtia, and a member of the actinobacterial family
AB  - Glycomycetaceae. Stackebrandtia currently contains two species, which are
AB  - differentiated from Glycomyces spp. by cellular fatty acid and menaquinone
AB  - composition. Strain LLR-40K-21(T) is Gram-positive, aerobic, and nonmotile, with
AB  - a branched substrate mycelium and on some media an aerial mycelium. The strain
AB  - was originally isolated from a soil sample collected from a road side in Nassau,
AB  - Bahamas. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. This is the first complete genome
AB  - sequence of the actinobacterial suborder Glycomycineae. The 6,841,557 bp long
AB  - single replicon genome with its 6487 protein-coding and 53 RNA genes is part of
AB  - the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Munoz, B.A.
AU  - Santillana, G.
AU  - Mavrodieva, V.
AU  - Liu, Z.
AU  - Nakhla, M.
AU  - Gabriel, D.W.
TI  - Complete Genome Sequences of Three Xanthomonas citri Strains from Texas.
JO  - Genome Announcements
PY  - 2017
SP  - e00609
EP  - e00617
VL  - 5
AB  - The complete genome sequences of three Xanthomonas citri strains isolated from lime trees in
AB  - Texas were found to belong to the Aw group. All carried nearly
AB  - identical large plasmids with similarity to those of a citrus canker strain from
AB  - India and to xanthomonads from Africa and Colombia. All three strains harbored
AB  - unusual pthA homologs.
ER  -

TY  - JOUR
AU  - Munoz, I.G. et al.
TI  - Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 729
EP  - 743
VL  - 39
AB  - Homing endonucleases recognize long target DNA sequences generating an accurate double-strand
AB  - break that promotes gene targeting through
AB  - homologous recombination. We have modified the homodimeric I-CreI
AB  - endonuclease through protein engineering to target a specific DNA sequence
AB  - within the human RAG1 gene. Mutations in RAG1 produce severe combined
AB  - immunodeficiency (SCID), a monogenic disease leading to defective immune
AB  - response in the individuals, leaving them vulnerable to infectious
AB  - diseases. The structures of two engineered heterodimeric variants and one
AB  - single-chain variant of I-CreI, in complex with a 24-bp oligonucleotide of
AB  - the human RAG1 gene sequence, show how the DNA binding is achieved through
AB  - interactions in the major groove. In addition, the introduction of the
AB  - G19S mutation in the neighborhood of the catalytic site lowers the
AB  - reaction energy barrier for DNA cleavage without compromising DNA
AB  - recognition. Gene-targeting experiments in human cell lines show that the
AB  - designed single-chain molecule preserves its in vivo activity with higher
AB  - specificity, further enhanced by the G19S mutation. This is the first time
AB  - that an engineered meganuclease variant targets the human RAG1 locus by
AB  - stimulating homologous recombination in human cell lines up to 265 bp away
AB  - from the cleavage site. Our analysis illustrates the key features for a la
AB  - carte procedure in protein-DNA recognition design, opening new
AB  - possibilities for SCID patients whose illness can be treated ex vivo.
ER  -

TY  - JOUR
AU  - Munoz-Moreno, C.Y.
AU  - De La Cruz-Rodriguez, Y.
AU  - Vega-Arreguin, J.
AU  - Alvarado-Rodriguez, M.
AU  - Gomez-Soto, J.M.
AU  - Alvarado-Gutierrez, A.
AU  - Fraire-Velazquez, S.
TI  - Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn.
JO  - Genome Announcements
PY  - 2018
SP  - e01502
EP  - e01517
VL  - 6
AB  - Bacillus subtilis 2C-9B, obtained from the rhizosphere of wild grass, exhibits inhibition
AB  - against root rot causal pathogens in Capsicum annuum, Pb and Zn
AB  - tolerance, and plant growth promotion in medium supplemented with Pb. The genome
AB  - of B. subtilis 2C-9B was sequenced and the draft genome assembled, with a length
AB  - of 4,215,855 bp and 4,723 coding genes.
ER  -

TY  - JOUR
AU  - Munson, R.S.
AU  - Harrison, A.
AU  - Gillaspy, A.
AU  - Ray, W.C.
AU  - Carson, M.
AU  - Armbruster, D.
AU  - Gipson, J.
AU  - Gipson, M.
AU  - Johnson, L.
AU  - Lewis, L.
AU  - Dyer, D.W.
AU  - Bakaletz, L.O.
TI  - Partial analysis of the genomes of two nontypeable Haemophilus influenzae otitis media isolates.
JO  - Infect. Immun.
PY  - 2004
SP  - 3002
EP  - 3010
VL  - 72
AB  - In 1995, The Institute for Genomic Research completed the genomic sequence of a rough
AB  - derivative of Haemophilus influenzae serotype d,
AB  - strain KW20. This sequence, though extremely useful in understanding
AB  - the basic biology of H. influenzae, has yet to provide significant
AB  - insight into our understanding of disease caused by nontypeable H.
AB  - influenzae (NTHI), because serotype d strains are not generally
AB  - pathogens. In contrast, NTHI strains are frequently mucosal pathogens
AB  - and are the primary pathogens of chronic otitis media as well as a
AB  - significant cause of acute otitis media in children. Thus, it is of
AB  - great importance to further understand their biology. We used a
AB  - DNA-based microarray approach to identify genes present in a clinical
AB  - isolate of NTHI that were absent from strain Rd. We also sequenced the
AB  - genome of a second NTHI isolate from a child with chronic otitis media
AB  - to threefold coverage and then used an array of bioinformatics tools to
AB  - identify genes present in this NTHI strain but absent from strain Rd.
AB  - These methods were complementary in approach and results. We
AB  - identified, in both strains, homologues of H. influenzae lav, an
AB  - autotransported protein of unknown function; tna4, which encodes
AB  - tryptophanase; as well as a homologue of Pasteurella multocida tsaA,
AB  - which encodes an alkyl peroxidase that may play a role in protection
AB  - against reactive oxygen species. We also identified a number of
AB  - putative restriction-modification systems, bacteriophage genes and
AB  - transposon-related genes. These data provide new insight that
AB  - complements and extends our ongoing analysis of NTHI virulence
AB  - determinants.
ER  -

TY  - JOUR
AU  - Muraguchi, Y.
AU  - Kushimoto, K.
AU  - Ohtsubo, Y.
AU  - Suzuki, T.
AU  - Dohra, H.
AU  - Kimbara, K.
AU  - Shintani, M.
TI  - Complete Genome Sequence of Algoriphagus sp. Strain M8-2, Isolated from a Brackish Lake.
JO  - Genome Announcements
PY  - 2016
SP  - e00347
EP  - e00316
VL  - 4
AB  - Algoriphagus sp. strain M8-2 was isolated from a brackish lake, Lake Sanaru, in Hamamatsu,
AB  - Japan, as a filterable bacterium through a 0.22-microm-pore-size
AB  - membrane filter. We report here the complete nucleotide sequence of the M8-2
AB  - genome (a 3,882,610-bp chromosome).
ER  -

TY  - JOUR
AU  - Murakami, A.
AU  - Yamamoto, Y.
AU  - Namba, M.
AU  - Iwase, R.
AU  - Yamaoka, T.
TI  - Photo-cross-linked oligonucleotide duplex as a decoy-DNA for inhibition of restriction endonuclease activity.
JO  - Bioorg. Chem.
PY  - 2001
SP  - 223
EP  - 233
VL  - 29
AB  - As a novel type of regulator molecule for DNA-recognizing proteins, a photo-cross-linked
AB  - oligonucleotide duplex was designed and synthesized,
AB  - The molecule regulated the activity of a restriction endonuclease by
AB  - being recognized as a substrate. This type of regulating molecule is
AB  - regarded as a decoy-DNA. 4,5',8-[4-Aminoethylaminomethyl]-trioxaten
AB  - (aeAMT) was conjugated with art oligodeoxyribonucleotide (ODN) at the 5'-end and the aeAMT
AB  - was cross-linked with the thymine residue of the
AB  - complementary oligonucleotide upon UVA irradiation. The terminally
AB  - cross-linked oligonucleotides, singly clipped (SC) decoy-DNA, acquired
AB  - thermal stability, An oligonucleoside phosphorothioate (OPT) was also
AB  - introduced as one or both components, yielding three types of
AB  - decoy-DNAs, SC-ODN-ODN (SC.DD), SC-OPT-ODN (SC.SD). and SC-OPT-OPT
AB  - (SC.SS). The SC decoy-DNAs inhibited the function of the restriction
AB  - endonuclease, AatII, in a sequence-specific and concentration-dependent
AB  - manner with an appreciable IC50 value (1.3 microM for SC.DD, 0.016 microM for
AB  - SC.SD. 0.002 microM for SC.SS). The SC decoy-DNAs were found to be
AB  - effective for regulating the DNA recognizing proteins.
ER  -

TY  - JOUR
AU  - Murakami, M.
AU  - Mizuno, H.
AU  - Yamada, Y.
TI  - The restriction endonuclease GinI of Gluconobacter cerinus IFO 3260, an isoschizomer of BamHI, has a monomeric structure.
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 2747
EP  - 2749
VL  - 54
AB  - Type II restriction endonucleases, which are indispensable for gene
AB  - manipulation and gene analysis, are widely found in the Procaryotae such as
AB  - bacteria and cyanobacteria.  During the course of our studies, we reported a
AB  - new restriction endonuclease ApaLI from cells of Acetobacter pasteurianus IFO
AB  - 13753.  We have found that the restriction endonuclease GceinI, an isoschizomer
AB  - of BamHI, has a monomeric structure different from the BamHI endonuclease.
AB  - This paper is concerned with the purification and properties of the restriction
AB  - endonuclease GceinI of Gluconobacter cerinus.  Note this enzyme is incorrectly
AB  - called GceinI in this paper.  It should be GinI.
ER  -

TY  - JOUR
AU  - Murakami, M.
AU  - Ozawa, O.
AU  - Kanematsu, T.
AU  - Yamada, Y.
TI  - A new restriction endonuclease from Bacteroides distasonis (BdiI).
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 275
EP  - 277
VL  - 54
AB  - Authors have changed the name to BdiSI to avoid confusion.
ER  -

TY  - JOUR
AU  - Murakami, M.
AU  - Ozawa, O.
AU  - Kanematsu, T.
AU  - Yamada, Y.
TI  - Characterization of restriction endonuclease CbiI, an isoschizomer of AsuII, from Clostridium bifermentans strain B-4.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 3458
EP  - 3458
VL  - 19
AB  - We have found that an extremely large amount of a restriction endonuclease, designated CbiI,
AB  - is produced within the cells of Clostridium bifermentans strain B-4.  CbiI was purified from
AB  - cell extracts by combined high performance liquid chromatographies on DEAE-Toyopearlpak 650M.
AB  - TSKgel DEAE-5PW, TSKgel HA-1000 and TSKgel G3000SW.  The purified enzyme (0.4 mg protein from
AB  - 1.7 g cell extract) was homogeneous on polyacrylamide gel disc electrophoresis (PAGDE).  The
AB  - relative molecular mass of the enzyme was calculated as 49,000 daltons by gel filtration and
AB  - by SDS-PAGE.  These data indicated that CbiI has a monomeric structure.
ER  -

TY  - JOUR
AU  - Murakami, M.
AU  - Ozawa, O.
AU  - Kanematsu, T.
AU  - Yamada, Y.
TI  - Characterization of restriction endonuclease BdiSI, an isoschizomer of SfeI, from Bacteroides distasonis strain S-7.
JO  - Agric. Biol. Chem.
PY  - 1991
SP  - 261
EP  - 263
VL  - 55
AB  - This paper describes the purification and properties of the restriction
AB  - endonuclease BdiSI, an isoschizomer of SfeI (CTRYAG).
ER  -

TY  - JOUR
AU  - Murakami, M.
AU  - Yamada, Y.
TI  - Purification, properties and recognition sequence and cleavage site determinations of restriction endonuclease from Acetobacter pasteurianus IFO 13753 (ApaLI).
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 1791
EP  - 1796
VL  - 54
AB  - A new restriction endonuclease, designated as ApaLI, was purified from
AB  - cell-free extracts of Acetobacter pasteurianus IFO 13753 by streptomycin
AB  - treatment, ammonium sulfate fractionation, combined column chromatographies on
AB  - heparin-Sepharose CL-6B and DEAE-Sepharose CL-6B and Fast Protein Liquid
AB  - Chromatography on Mono Q HR 5/5.  The purified enzyme was homogenous on
AB  - polyacrylamide gel disc electrophoresis.  The molecular weight of the purified
AB  - enzyme was calculated as 26,000 daltons by gel filtration using Sephadex G-200,
AB  - and the isoelectric point of the purified enzyme was 4.8 by ampholine
AB  - sucrose-density gradient isoelectric focusing.  The purified enzyme cleaves
AB  - lambda, Ad2, SV40, M13mp18 RF I, PhiX174 RF I and pBR322 DNAs at 4, 7, 0, 0, 1
AB  - and 3 sites, respectively.  The purified enzyme worked best at 37C and pH 8.0
AB  - in a reaction mixture (50 microliters) containing 1.0 micrograms lambda DNA, 10
AB  - mM Tris-HCI, 7 mM 2-mercaptoethanol, 7 mM MgCl2 and 25 mM NaCl.  However, the
AB  - purified enzyme did not require NaCl necessarily for the enzyme reaction.  The
AB  - purified enzyme recognized the palindromic hexanucleotide DNA sequence,
AB  - 5'-GTGCAC-3' and cut between G and T, producing a 5'-cohesive tetranucleotide
AB  - extension.
ER  -

TY  - JOUR
AU  - Mural, R.J.
TI  - Cleavage by the restriction endonuclease Asp718, an isoschizomer of KpnI, is sensitive to Escherichia coli Dcm methylation.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 9085
EP  - 9085
VL  - 15
AB  - While attempting to use Asp718, a KpnI isoschizomer, to subclone KpnI fragments from pAn602, a
AB  - plasmid known to have two KpnI sites, I found that one of these sites was cut very poorly by
AB  - this enzyme. DNA sequence analysis showed that the poorly cut site overlapped the sequence
AB  - CCAGG, an Escherichia coli Dcm methylation site. When this plasmid DNA was propagated in E.
AB  - coli GM31 (dcm-6), a host which does not methylate this site, and digested with either Asp718
AB  - or KpnI both sites were cut to completion.
ER  -

TY  - JOUR
AU  - Murali, T.S.
AU  - Paul, B.
AU  - Parikh, H.
AU  - Singh, R.P.
AU  - Kavitha, S.
AU  - Bhat, M.K.
AU  - Satyamoorthy, K.
TI  - Genome Sequences of Four Clinical Staphylococcus aureus Strains with Diverse Drug Resistance Profiles Isolated from Diabetic Foot Ulcers.
JO  - Genome Announcements
PY  - 2014
SP  - e00204
EP  - e00214
VL  - 2
AB  - Staphylococcus aureus is a major pathogen associated with diabetic foot ulcer infections. To
AB  - gain insight into their pathogenicity and virulence potential, we
AB  - report draft genome sequences of four strains of Staphylococcus aureus, isolated
AB  - from diabetic foot ulcers, showing profiles with various degrees of resistance to
AB  - common antibiotics.
ER  -

TY  - JOUR
AU  - Murata, T.
AU  - Ohnishi, M.
AU  - Ara, T.
AU  - Kaneko, J.
AU  - Han, C.G.
AU  - Li, Y.F.
AU  - Takashima, K.
AU  - Nojima, H.
AU  - Nakayama, K.
AU  - Kaji, A.
AU  - Kamio, Y.
AU  - Miki, T.
AU  - Mori, H.
AU  - Ohtsubo, E.
AU  - Terawaki, Y.
AU  - Hayashi, T.
TI  - Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes.
JO  - J. Bacteriol.
PY  - 2002
SP  - 3194
EP  - 3202
VL  - 184
AB  - Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype
AB  - for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the
AB  - complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300
AB  - potential open reading frames                        (ORFs). Among these, the products of 141
AB  - ORFs, including 9 previously identified genes, displayed significant sequence similarity to
AB  - known proteins. The set of genes responsible for the conjugation function of Rts1 has been
AB  - identified. A broad array of genes related to diverse processes of DNA metabolism were also
AB  - identified. Of particular interest was the presence of tus-like genes that could be involved
AB  - in replication termination. Inspection of the overall genome organization revealed that the
AB  - Rts1 genome is composed of four large modules, providing an example of modular evolution of
AB  - plasmid genomes.
ER  -

TY  - JOUR
AU  - Murawska, E.
AU  - Fiedoruk, K.
AU  - Bideshi, D.K.
AU  - Swiecicka, I.
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. thuringiensis Strain IS5056, an Isolate Highly Toxic to Trichoplusia ni.
JO  - Genome Announcements
PY  - 2013
SP  - e0010813
EP  - e0010813
VL  - 1
AB  - The genome sequence of the entomopathogen Bacillus thuringiensis subsp. thuringiensis strain
AB  - IS5056 was determined. The chromosome is composed of
AB  - 5,491,935 bp. In addition, IS5056 harbors 14 plasmids ranging from 6,880 to
AB  - 328,151 bp, four of which contain nine insecticidal protein genes, cry1Aa3,
AB  - cry1Ab21, cry1Ba1, cry1Ia14, cry2Aa9, cry2Ab1, vip1, vip2, and vip3Aa10.
ER  -

TY  - JOUR
AU  - Murchie, A.I.H.
AU  - Portugal, J.
AU  - Lilley, D.M.J.
TI  - Cleavage of a four-way DNA function by a restriction enzyme spanning the point of strand exchange.
JO  - EMBO J.
PY  - 1991
SP  - 713
EP  - 718
VL  - 10
AB  - The four-way DNA junction is believed to fold in the presence of metal ions
AB  - into an X-shaped structure, in which there is pairwise coaxial stacking of
AB  - helical arms.  A restriction enzyme MboII has been used to probe this
AB  - structure.  A junction was constructed containing a recognition site for MboII
AB  - in one helical arm, positioned such that stacking of arms would result in
AB  - cleavage in a neighbouring arm.  Strong cleavage was observed, at the sites
AB  - expected on the basis of coaxial stacking.  An additional cleavage was seen
AB  - corresponding to the formation of an alternative stacking isomer, suggesting
AB  - that the two isomeric forms are in dynamic equilibrium in solution.
ER  -

TY  - JOUR
AU  - Muro-Pastor, A.M.
AU  - Herrero, A.
AU  - Flores, E.
TI  - Sequence-specific endonucleases from the cyanobacterium Nostoc sp. ATCC 29132.
JO  - FEMS Microbiol. Lett.
PY  - 1991
SP  - 1
EP  - 4
VL  - 77
AB  - The nitrogen-fixing cyanobacterium Nostoc sp. ATCC 29132 was shown to contain
AB  - two sequence-specific endonucleases.  Nsp(29132) I was an isoschizomer of
AB  - AsuII, and Nsp(29132) II was an isoschizomer of BamHI.  Nsp(29132) II was shown
AB  - to generate ends that could be ligated to those generated by BamHI.
ER  -

TY  - JOUR
AU  - Murphy, J.
AU  - Klumpp, J.
AU  - Mahony, J.
AU  - O'Connell-Motherway, M.
AU  - Nauta, A.
AU  - van Sinderen, D.
TI  - Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity.
JO  - BMC Genomics
PY  - 2014
SP  - 831
EP  - 831
VL  - 15
AB  - Background: So-called 936-type phages are among the most frequently isolated phages in dairy
AB  - facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control
AB  - phage proliferation and decades of research, these phages continue to negatively impact cheese
AB  - production in terms of the final product quality and consequently, monetary return.Results:
AB  - Whole genome sequencing and in silico analysis of three 936-type phage genomes identified
AB  - several putative (orphan) methyltransferase (MTase)-encoding genes located within the
AB  - packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis
AB  - was performed on all three phages, allowing the identification of adenine modifications
AB  - consistent with N-6 methyladenine sequence methylation, which in some cases could be
AB  - attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.
AB  - Phi145I/M. Phi93I and M. Phi93DAM, encoded by genes located within the packaging module,
AB  - provide protection against the restriction enzymes HphI and DpnII, respectively, representing
AB  - the first functional MTases identified in members of 936-type phages.Conclusions: SMRT
AB  - sequencing technology enabled the identification of the target motifs of MTases encoded by the
AB  - genomes of three lytic 936-type phages and these MTases represent the first functional MTases
AB  - identified in this species of phage. The presence of these MTase-encoding genes on 936-type
AB  - phage genomes is assumed to represent an adaptive response to circumvent host encoded
AB  - restriction-modification systems thereby increasing the fitness of the phages in a dynamic
AB  - dairy environment.
ER  -

TY  - JOUR
AU  - Murphy, J.
AU  - Mahony, J.
AU  - Ainsworth, S.
AU  - Nauta, A.
AU  - van Sinderen, D.
TI  - Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 7547
EP  - 7547
VL  - 79
AB  - Type II DNA methyltransferases (MTases) are enzymes found ubiquitously in the prokaryotic
AB  - world, where they play important roles in several cellular processes, such as host protection
AB  - and epigenetic regulation. Three classes of type II MTases have been identified thus far in
AB  - bacteria which function in transferring a methyl group from S-adenosyl-L-methionine (SAM) to a
AB  - target nucleotide base, forming N-6-methyladenine (class I), N-4-methylcytosine (class II), or
AB  - C-5-methylcytosine (class III). Often, these MTases are associated with a cognate restriction
AB  - endonuclease (REase) to form a restriction-modification (R-M) system protecting bacterial
AB  - cells from invasion by foreign DNA. When MTases exist alone, which are then termed orphan
AB  - MTases, they are believed to be mainly involved in regulatory activities in the bacterial
AB  - cell. Genomes of various lytic and lysogenic phages have been shown to encode multi-and
AB  - mono-specific orphan MTases that have the ability to confer protection from restriction
AB  - endonuclea ses of their bacterial host(s). The ability of a phage to overcome R-M and other
AB  - phage-targeting resistance systems can be detrimental to particular biotechnological processes
AB  - such as dairy fermentations. Conversely, as phages may also be beneficial in certain areas
AB  - such as phage therapy, phages with additional resistance to host defenses may prolong the
AB  - effectiveness of the therapy. This minireview will focus on bacteriophage-encoded MTases,
AB  - their prevalence and diversity, as well as their potential origi n and function.
ER  -

TY  - JOUR
AU  - Murphy, K.C.
AU  - Ritchie, J.M.
AU  - Waldor, M.K.
AU  - Lobner-Olesen, A.
AU  - Marinus, M.G.
TI  - Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157 : H7.
JO  - J. Bacteriol.
PY  - 2008
SP  - 438
EP  - 441
VL  - 190
AB  - Shiga toxin 2 (Stx2), one of the principal virulence factors of enterohemorrhagic Escherichia
AB  - coli, is encoded by 933W, a lambda-like
AB  - prophage. 933W prophage induction contributes to Stx2 production, and
AB  - here, we provide evidence that Dam methyltransferase is essential for
AB  - maintenance of 933W lysogeny. Our findings are consistent with the idea
AB  - that the 933W prophage has a relatively low threshold for induction,
AB  - which may promote Stx2 production during infection.
ER  -

TY  - JOUR
AU  - Murphy, M.
AU  - Schmid, N.S.
AU  - Bickle, T.A.
TI  - Lack of regulation of the modification-dependent restriction enzyme McrBC in Escherichia coli.
JO  - J. Bacteriol.
PY  - 2002
SP  - 1794
EP  - 1795
VL  - 184
AB  - Restriction alleviation (RA) by the type I restriction enzyme EcoKI is caused by treatments
AB  - that damage DNA. RA is due to proteolysis of the EcoKI HsdR subunit by the ClpXP ATP-dependent
AB  - protease. Here we show that the modification-dependent enzyme McrBC is not subject to RA,
AB  - although it is moderately sensitive to ClpAP.
ER  -

TY  - JOUR
AU  - Murphy, R.A.
AU  - Boyd, E.F.
TI  - Three pathogenicity islands of Vibrio cholerae can excise from the chromosome and form circular intermediates.
JO  - J. Bacteriol.
PY  - 2008
SP  - 636
EP  - 647
VL  - 190
AB  - Vbrio pathogenicity island-2 (VPI-2) is a 57-kb region integrated at a transfer RNA
AB  - (tRNA)-serine locus that encompasses VC1758 to VC1809 on
AB  - the V. cholerae N16961 genome and is present in pandemic isolates.
AB  - VPI-2 encodes a P4-like integrase, a restriction modification system, a
AB  - Mu phage-like region, and a sialic acid metabolism region, as well as
AB  - neuraminidase (VC1784), which is a glycosylhydrolase known to release
AB  - sialic acid from sialoglycoconjugates to unmask GM1 gangliosides, the
AB  - receptor for cholera toxin. We examined the tRNA-serine locus among the
AB  - sequenced V. cholerae genomes and identified five variant VPI-2
AB  - regions, four of which retained the sialometabolism region. Three
AB  - variant VPI-2 regions contained a type three secretion system. By using
AB  - an inverse nested PCR approach, we found that the VPI-2 region can form
AB  - an extrachromosomal circular intermediate (CI) molecule after precise
AB  - excision from its tRNA-serine attachment site. We constructed a
AB  - knockout mutant of VC1758 (int) with V. cholerae strain N16961 and
AB  - found that no excision PCR product was produced, indicating that a
AB  - functional cognate, VPI-2 integrase, is required for excision. The
AB  - Vibrio seventh pandemic island-I (VSP-I) and VSP-II regions are present
AB  - in V. cholerae 01 El Tor and 0139 serogroup isolates. Novel regions are
AB  - present at the VSP-I insertion site in strain MZO-3 and at the VSP-II
AB  - insertion site in strain 623-39. VSP-II is a 27-kb region that
AB  - integrates at a tRNA-methionine locus, is flanked by direct repeats,
AB  - and encodes a P4-like integrase. We show that VSP-II can excise and
AB  - form a CI and that the cognate VSP-II integrase is required for
AB  - excision. Interestingly, VSP-I is not inserted at a tRNA locus and does
AB  - encode a XerDC-like recombinase, but similar to VPI-2 and VSP-II, VSP-I
AB  - does excise from the genome to form a CI. These results show that all
AB  - three pathogenicity islands can excise from the chromosome, which is
AB  - likely a first step in their horizontal transfer.
ER  -

TY  - JOUR
AU  - Murray, I.A.
AU  - Clark, T.A.
AU  - Morgan, R.D.
AU  - Boitano, M.
AU  - Anton, B.P.
AU  - Luong, K.
AU  - Fomenkov, A.
AU  - Turner, S.W.
AU  - Korlach, J.
AU  - Roberts, R.J.
TI  - The methylomes of six bacteria.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 11450
EP  - 11462
VL  - 40
AB  - Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio
AB  - breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and C.
AB  - jejuni NCTC 11168, all of which had previously been sequenced using other platforms were
AB  - re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their
AB  - methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C)
AB  - methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for
AB  - those methylation patterns were assigned. In 15 cases, it was possible to match MTase genes
AB  - with MTase recognition sequences without further sub-cloning. Two Type I restriction systems
AB  - required sub-cloning to differentiate their recognition sequences, while four MTase genes that
AB  - were not expressed in the native organism were sub-cloned to test for viability and
AB  - recognition sequences. Two of these proved active. No attempt was made to detect 5-
AB  - methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this
AB  - modification produces weaker signals using current methods.  However, all predicted m6A and
AB  - m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing
AB  - to traditional sequencing approaches gives a wealth of useful functional information about a
AB  - genome showing not only which MTase genes are active but also revealing their recognition
AB  - sequences.
ER  -

TY  - JOUR
AU  - Murray, I.A.
AU  - Morgan, R.D.
AU  - Luyten, Y.
AU  - Fomenkov, A.
AU  - Correa, I.R. Jr.
AU  - Dai, N.
AU  - Allaw, M.B.
AU  - Zhang, X.
AU  - Cheng, X.
AU  - Roberts, R.J.
TI  - The non-specific adenine DNA methyltransferase M.EcoGII.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 840
EP  - 848
VL  - 46
AB  - We describe the cloning, expression and characterization of the first truly non-specific
AB  - adenine DNA methyltransferase, M.EcoGII. It is encoded in the genome
AB  - of the pathogenic strain Escherichia coli O104:H4 C227-11, where it appears to
AB  - reside on a cryptic prophage, but is not expressed. However, when the gene
AB  - encoding M.EcoGII is expressed in vivo - using a high copy pRRS plasmid vector
AB  - and a methylation-deficient E. coli host-extensive in vivo adenine methylation
AB  - activity is revealed. M.EcoGII methylates adenine residues in any DNA sequence
AB  - context and this activity extends to dA and rA bases in either strand of a
AB  - DNA:RNA-hybrid oligonucleotide duplex and to rA bases in RNAs prepared by in
AB  - vitro transcription. Using oligonucleotide and bacteriophage M13mp18 virion DNA
AB  - substrates, we find that M.EcoGII also methylates single-stranded DNA in vitro
AB  - and that this activity is only slightly less robust than that observed using
AB  - equivalent double-stranded DNAs. In vitro assays, using purified recombinant
AB  - M.EcoGII enzyme, demonstrate that up to 99% of dA bases in duplex DNA substrates
AB  - can be methylated thereby rendering them insensitive to cleavage by multiple
AB  - restriction endonucleases. These properties suggest that the enzyme could also be
AB  - used for high resolution mapping of protein binding sites in DNA and RNA
AB  - substrates.
ER  -

TY  - JOUR
AU  - Murray, I.A.
AU  - Stickel, S.K.
AU  - Roberts, R.J.
TI  - Sequence-specific cleavage of RNA by Type II restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 8257
EP  - 8268
VL  - 38
AB  - The ability of 223 Type II restriction endonucleases to hydrolyze RNA-DNA heteroduplex
AB  - oligonucleotide substrates was assessed. Despite the
AB  - significant topological and sequence asymmetry introduced when one strand
AB  - of a DNA duplex is substituted by RNA we find that six restriction enzymes
AB  - (AvaII, AvrII, BanI, HaeIII, HinfI and TaqI), exclusively of the Type IIP
AB  - class that recognize palindromic or interrupted-palindromic DNA sequences,
AB  - catalyze robust and specific cleavage of both RNA and DNA strands of such
AB  - a substrate. Time-course analyses indicate that some endonucleases
AB  - hydrolyze phosphodiester bonds in both strands simultaneously whereas
AB  - others appear to catalyze sequential reactions in which either the DNA or
AB  - RNA product accumulates more rapidly. Such strand-specific variation in
AB  - cleavage susceptibility is both significant (up to orders of magnitude
AB  - difference) and somewhat sequence dependent, notably in relation to the
AB  - presence or absence of uracil residues in the RNA strand. Hybridization to
AB  - DNA oligonucleotides that contain endonuclease recognition sites can be
AB  - used to achieve targeted hydrolysis of extended RNA substrates produced by
AB  - in vitro transcription. The ability to 'restrict' an RNA-DNA hybrid,
AB  - albeit with a limited number of restriction endonucleases, provides a
AB  - method whereby individual RNA molecules can be targeted for site-specific
AB  - cleavage in vitro.
ER  -

TY  - JOUR
AU  - Murray, K.
AU  - Hughes, S.G.
AU  - Brown, J.S.
AU  - Bruce, S.A.
TI  - Isolation and characterization of two sequence-specific endonucleases from Anabaena variabilis.
JO  - Biochem. J.
PY  - 1976
SP  - 317
EP  - 322
VL  - 159
AB  - Two endonucleases, AvaI and AvaII, were isolated from Anabaena variabilis on
AB  - the basis of their ability to make a limited number of breaks at specific
AB  - points in bacteriophage lambda DNA.  Neither enzyme has cofactor requirements
AB  - beyond Mg2+.  Endonuclease AvaI makes eight breaks in the phage lambda
AB  - chromosome at which the 5'-terminal sequence is pPy-C-G-N.  AvaII endonuclease
AB  - cuts phage lambda DNA more extensively, yielding fragments with the 5'-terminal
AB  - sequence G-T-C-N or G-A-C-N.  Neither enzyme generates cohesive ends.
ER  -

TY  - JOUR
AU  - Murray, K.
AU  - Murray, N.E.
AU  - Brammar, W.J.
TI  - Restriction enzymes and the cloning of eukaryotic DNA.
JO  - FEBS J.
PY  - 1975
SP  - 193
EP  - 207
VL  - 10
AB  - If bacteriophage lambda that has been grown on Escherichia coli strain C is transferred to E.
AB  - coli strain K, its efficiency of growth is impaired by several orders of magnitude, but those
AB  - phage that survive on strain K subsequently grow normally upon it.  If the surviving phage are
AB  - then transferred back to strain C they grow with normal efficiency, but if after this growth
AB  - on strain C they are again transferred to strain K, the reduced efficiency of growth is once
AB  - more observed.  This is an example of the general phenomenon of host-controlled restriction.
AB  - Experiments with 32P-labelled phage showed that the impairment of phage growth was correlated
AB  - with the ability of the restricting host strain to degrade the phage DNA to acid-soluble
AB  - products, a property that the original host strain lacked and which was attributed to a
AB  - host-specific endonuclease.  It is clearly necessary for the bacterial cell to protect its own
AB  - DNA from the action of this enzyme and this it does by methylation of certain bases (adenine
AB  - to 6-methylamino purine or, less commonly, cytosine to 5-methyl cytosine) as was demonstrated
AB  - by the analysis of DNA from phage f1 that had been propagated on restricting and
AB  - non-restricting strains of E. coli.  This process of host-controlled modification explains why
AB  - those phage that survive restriction subsequently grow normally upon the restricting strain:
AB  - their DNA is methylated by the host modification methylase and therefore survives attack by
AB  - the restriction endonuclease.
ER  -

TY  - JOUR
AU  - Murray, K.
AU  - Old, R.W.
TI  - The primary structure of DNA.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 1974
SP  - 117
EP  - 185
VL  - 14
AB  - Brown and Todd, in 1952, summarized the evidence then available and proposed
AB  - the now generally accepted structure for deoxyribonucleic acid, in which the
AB  - deoxynucleoside units are linked by 3',5'-phosphodiester bonds.
ER  -

TY  - JOUR
AU  - Murray, N.E.
TI  - Immigration control of DNA in bacteria: self versus non-self.
JO  - Microbiology
PY  - 2002
SP  - 3
EP  - 20
VL  - 148
AB  - Bacteria commonly endow their DNA with an identity mark.  When DNA is transferred from one
AB  - bacterium to another strain of the same species, DNA that lacks the identification mark of the
AB  - recipient strain is recognized as 'foreign' rather than 'self'.  Foreign DNA is commonly
AB  - degraded.  The first evidence for this discriminatory process was the demonstration of a
AB  - barrier, albeit incomplete, to the productive infection of Escherichia coli strain K-12 by
AB  - bacteriophage lambda previously propagated in either E. coli strain C or E. coli strain B.
AB  - Much later it was proven that the growth of phages in E. coli K-12 can be 'restricted' by an
AB  - endonuclease, a restriction enzyme (EcoKI), which attacks foreign DNA.  Occasionally phages
AB  - escape restriction and they, like the resident bacterial chromosome, acquire a protective
AB  - identification mark from a strain-specific modification enzyme that methylates defined bases
AB  - within a specific target sequence.  This sequence-specific modification identifies the
AB  - immediate provenance of bacterial, or phage, DNA.
ER  -

TY  - JOUR
AU  - Murray, N.E.
TI  - Type I restriction systems: sophisticated molecular machines.
JO  - Microbiol. Mol. Biol. Rev.
PY  - 2000
SP  - 412
EP  - 434
VL  - 64
AB  - Restriction enzymes are well known as reagents widely used by molecular biologists for genetic
AB  - manipulation and analysis, but these reagents represent only one class (type II) of a wider
AB  - range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the
AB  - provenance of the DNA on the basis of specific modifications to their target sequence. Type I
AB  - restriction and modification (R-M) systems are complex; a single multifunctional enzyme can
AB  - respond to the modification state of its target sequence with the alternative activities of
AB  - modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves
AB  - like a molecular motor, translocating vast stretches of DNA towards itself before eventually
AB  - breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which
AB  - will emphasize those aspects that give insights into more general problems of molecular and
AB  - microbial biology. Current molecular experiments explore target recognition, intramolecular
AB  - communication, and enzyme activities, including DNA translocation. Type I R-M systems are
AB  - notable for their ability to evolve new specificities, even in laboratory cultures. This
AB  - observation raises the important question of how bacteria protect their chromosomes from
AB  - destruction by newly acquired restriction specifities. Recent experiments demonstrate
AB  - proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their
AB  - chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the
AB  - present impact of genomic sequences on a field that has previously derived information almost
AB  - exclusively from the analysis of bacteria commonly studied in the laboratory.
ER  -

TY  - JOUR
AU  - Murray, N.E.
TI  - The impact of phage lambda: from restriction to recombineering.
JO  - Biochem. Soc. Trans.
PY  - 2006
SP  - 203
EP  - 207
VL  - 34
AB  - Experiments using phage lambda provided early insights into important molecular mechanisms,
AB  - including genetic recombination and the control of
AB  - gene expression. Before recombinant DNA technology, the use of lambda,
AB  - most particularly lambda transducing phages, illustrated the importance of
AB  - cloning bacterial genes, already providing some insight into how to use
AB  - cloned genes to advantage. Subsequently, lambda made significant
AB  - contributions to recombinant DNA technology, including the early
AB  - generation of genomic and cDNA libraries. More recently, lambda genes
AB  - associated with recombination have enabled techniques referred to as
AB  - 'recombineering' to be developed. These techniques permit the refined
AB  - manipulation, including mutation, of foreign genes in Escherichia coli and
AB  - their subsequent return to the donor organism.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - Barcus, V.A.
AU  - Campbell, A.J.B.
AU  - Dryden, D.T.F.
AU  - Kelleher, J.E.
AU  - Powell, L.M.
AU  - Willcock, D.
AU  - Sharp, P.M.
TI  - Type I restriction enzymes of enteric bacteria.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 152
EP  - 152
VL  - 17C
AB  - The multifunctional type I restriction and modification (R/M) enzymes are encoded by three
AB  - genes (hsdR, hsdM and hsdS). These enzymes recognize asymmetric, bipartite target sequences
AB  - and their alternative responses of either restriction or modification are determined by the
AB  - methylation state of the target sequence. Three discrete families of type I R/M systems have
AB  - been described (A,B and C), and we now present evidence for a fourth. This new system and the
AB  - enzymes of families IA and IB are all encoded by allelic genes. Members of a family are highly
AB  - conserved, but differ in their specificity (A) subunits; each of two recognition domains of
AB  - the S subunit confers specificity for one of the two components of the target sequence.
AB  - Members of different families are dissimilar in all of their three subunits. Even when encoded
AB  - by allelic genes, amino acid identity may be only about 20%. The diversity of type I R/M
AB  - systems will be reviewed in relation to their natural distribution and their evolutionary
AB  - relationships. Horizontal transfer of hsd genes between species and frequency-dependent
AB  - selection for alternative specificities are invoked to explain the high levels of variability.
AB  - Comparative analyses of polypeptides identify conserved sequences within the M polypeptides
AB  - common to methyltransferases (mtases) in general and adenine mtases in particular, and within
AB  - the R polypeptides features in common with ATP-dependent helicases. We have made mutations in
AB  - some of these conserved regions and have isolated other mutants on the basis of a change in
AB  - response to the methylation state of the target sequence. The latter mutations mimic the
AB  - effect of a phage encoded polypeptide (Ral) that can enhance modification and ameliorate
AB  - restriction. The mtase component of EcoK, the type I R/M system found in E.coli K-12, has been
AB  - purified and characterized, particularly in terms of binding to target sequences and to the
AB  - cofactor S-adenosylmethionine. The properties of the wild-type mtase and some mutant
AB  - derivatives will be reported.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - Batten, P.L.
AU  - Murray, K.
TI  - Restriction of bacteriophage lambda by Escherichia coli K.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 395
EP  - 407
VL  - 81
AB  - Derivatives of phage lambda, for which the numbers and positions of the
AB  - recognition sites for endonuclease R, EcoK are known, were used as substrates
AB  - for the Escherichia coli K restriction system in vivo and in vitro.  A single
AB  - unmodified recognition site was sufficient for a DNA molecule to be bound and
AB  - broken by the K restriction enzyme.  Although discrete fragments of DNA were
AB  - not produced, the breaks were made preferentially in the proximity of the
AB  - recognition site.  Breakage of a DNA molecule with only one recognition site
AB  - required a 10 to 40-fold higher concentration of restriction enzyme than
AB  - breakage of a DNA molecule with two or more recognition sites, but these
AB  - substrates were all equally effective in a binding assay for the enzyme.  The
AB  - polynucleotide kinase reaction provided no evidence for new 5'-terminal
AB  - sequences generated by restriction in vitro; the 5' termini were either
AB  - refractory to the polynucleotide kinase reaction or had no sequence
AB  - specificity.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - Brammar, W.J.
TI  - The trpE gene of Escherichia coli K contains a recognition sequence for the K-restriction system.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 615
EP  - 624
VL  - 77
AB  - A recognition sequence for the K-restriction system has been localized within
AB  - the trpE gene of Escherichia coli.  Mutations conferring resistance to
AB  - restriction do not always inactivate the E gene.  By selecting for phage
AB  - mutants which have simultaneously lost two restriction-recognition sites, one
AB  - in trpE and the other near gene N of phage lambda, we have isolated deletions
AB  - which localize a site of action of the N protein betwen cIII and N itself.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - Daniel, A.S.
AU  - Cowan, G.M.
AU  - Sharp, P.M.
TI  - Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes.
JO  - Mol. Microbiol.
PY  - 1993
SP  - 133
EP  - 143
VL  - 9
AB  - Type I restriction enzymes comprise three subunits encoded by genes designated hsdR, hsdM, and
AB  - hsdS; S confers sequence specificity. Three families of enzymes are known and within families,
AB  - but not between, hsdM and hsdR are conserved. Consequently, interfamily comparisons of M and R
AB  - sequences focus on regions of putative functional significance, , while both inter- and
AB  - intrafamily comparisons address the origin, nature and role of diversity of type I restriction
AB  - systems. We have determined the sequence of the hsdR gene for EcoAI, thus making available
AB  - sequences of all three hsd genes of one representative from each family. The predicted R
AB  - polypeptide sequences share conserved regions with one superfamily of putative helicases,
AB  - so-called DEAD box proteins; these conserved sequences may be associated with the
AB  - ATP-dependent translocation of DNA that precedes restriction. We also present hsdM and hsdR
AB  - sequences for EcoEI, a member of the same family as EcoAI. The sequences of the M and R genes
AB  - of EcoAI and EcoEI are at least as divergent as typical genes from Escherichia coli and
AB  - Salmonella, perhaps as the result of selection favouring diversity of restriction
AB  - specificities combined with lateral transfer among different species.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - de Ritis, P.M.
AU  - Foster, L.A.
TI  - DNA targets for the Escherichia coli K restriction system analysed genetically in recombinants between phages Phi80 and lambda.
JO  - Mol. Gen. Genet.
PY  - 1973
SP  - 261
EP  - 281
VL  - 120
AB  - Genetic analyses demonstrate the segregation of three targets for the K
AB  - restriction system in h80-lambda hybrid phages.  Mutations in each of these
AB  - three targets have been isolated and shown to confer resistance in cis but not
AB  - in trans.  Two of the three targets (sk-1 and sk-2) have been located on the
AB  - lambda genome:  sk-1 is right of gene R and sk-2 is between genes cIII and N.
AB  - The third target is in the phi80 genome right of, but close to, att.  Phage
AB  - lambda lacking both sk-1 and sk-2 retains at least 3 targets for the K
AB  - restriction system.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - Gough, J.A.
AU  - Suri, B.
AU  - Bickle, T.A.
TI  - Structural homologies among type I restriction-modification systems.
JO  - EMBO J.
PY  - 1982
SP  - 535
EP  - 539
VL  - 1
AB  - Structural homologies among different restriction systems of Escherichia coli
AB  - and several Salmonella species have been investigated by immunological methods
AB  - using antibodies prepared against two subunits of the E. coli K12 restriction
AB  - enzyme, and by DNA hybridization experiments using different fragments of the
AB  - E. coli K12 hsd genes as probes.  The results with both techniques show a
AB  - strong homology between the E. coli K12 and B restriction-modification systems,
AB  - weaker but nevertheless marked homology between E. coli K12 and the Salmonella
AB  - systems SB, SP, and SQ and, surprisingly, no homology between the E. coli K12
AB  - and A systems.
ER  -

TY  - JOUR
AU  - Murray, N.E.
AU  - Murray, K.
TI  - Manipulation of restriction targets in phage lambda to form receptor chromosomes for DNA fragments.
JO  - Nature
PY  - 1974
SP  - 476
EP  - 481
VL  - 251
AB  - Fragments of DNA from derivatives of phage lambda having either one or two
AB  - targets for R.EcoRI have been joined in new combinations to give biologically
AB  - active phage genomes.  These include two classes of deletion mutants; in one,
AB  - only the DNA between targets is deleted, but in the second the deletions are
AB  - more extensive.  Other fragments of DNA have been inserted into these phage
AB  - chromosomes.
ER  -

TY  - JOUR
AU  - Murthy, T.
AU  - Rolfs, A.
AU  - Hu, Y.
AU  - Shi, Z.
AU  - Raphael, J.
AU  - Moreira, D.
AU  - Kelley, F.
AU  - McCarron, S.
AU  - Jepson, D.
AU  - Taycher, E.
AU  - Zuo, D.
AU  - Mohr, S.E.
AU  - Fernandez, M.
AU  - Brizuela, L.
AU  - Labaer, J.
TI  - A Full-Genomic Sequence-Verified Protein-Coding Gene Collection for Francisella tularensis.
JO  - PLoS ONE
PY  - 2007
SP  - E577
EP  - E577
VL  - 2
AB  - The rapid development of new technologies for the high throughput (HT)
AB  - study of proteins has increased the demand for comprehensive plasmid clone
AB  - resources that support protein expression. These clones must be
AB  - full-length, sequence-verified and in a flexible format. The generation of
AB  - these resources requires automated pipelines supported by software
AB  - management systems. Although the availability of clone resources is
AB  - growing, current collections are either not complete or not fully
AB  - sequence-verified. We report an automated pipeline, supported by several
AB  - software applications that enabled the construction of the first
AB  - comprehensive sequence-verified plasmid clone resource for more than 96%
AB  - of protein coding sequences of the genome of F. tularensis, a highly
AB  - virulent human pathogen and the causative agent of tularemia. This clone
AB  - resource was applied to a HT protein purification pipeline successfully
AB  - producing recombinant proteins for 72% of the genes. These methods and
AB  - resources represent significant technological steps towards exploiting the
AB  - genomic information of F. tularensis in discovery applications.
ER  -

TY  - JOUR
AU  - Murugan, N.
AU  - Malathi, J.
AU  - Umashankar, V.
AU  - Madhavan, H.N.
TI  - Comparative Genomic Analysis of Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates VRFPA06 and VRFPA08 with VRFPA07.
JO  - Genome Announcements
PY  - 2014
SP  - e00140
EP  - e00114
VL  - 2
AB  - Pseudomonas aeruginosa isolates harboring acquired drug-resistant genes lead to increased
AB  - mortality. Here, we have sequenced and annotated the genomes of two
AB  - multidrug-resistant (MDR) P. aeruginosa isolates and a susceptible P. aeruginosa
AB  - clinical isolate evidencing divergent antibiotic susceptibilities. Genomic
AB  - analysis showed insight on the different genomic strategies adapted by P.
AB  - aeruginosa to combat antimicrobial effects.
ER  -

TY  - JOUR
AU  - Murugapiran, S.K. et al.
TI  - Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 449
EP  - 468
VL  - 7
AB  - The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a
AB  - circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two
AB  - plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18
AB  - chromosome with those from other strains of T. thermophilus revealed a high
AB  - degree of synteny, whereas the megaplasmids from the same strains were highly
AB  - plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no
AB  - synteny with other sequenced Thermus strains. Phylogenomic analyses using a
AB  - concatenated set of conserved proteins confirmed the phylogenetic and taxonomic
AB  - assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete
AB  - glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus
AB  - glucosidases, glycosidases, proteases, and peptidases, highlighting highly
AB  - versatile heterotrophic capabilities. Megaplasmids of both strains contained a
AB  - gene cluster encoding enzymes predicted to catalyze the sequential reduction of
AB  - nitrate to nitrous oxide; however, the nitrous oxide reductase required for the
AB  - terminal step in denitrification was absent, consistent with their incomplete
AB  - denitrification phenotypes. A sox gene cluster was identified in both
AB  - chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene
AB  - clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and
AB  - polysulfide reduction as possible modes of anaerobic respiration.
ER  -

TY  - JOUR
AU  - Murugapiran, S.K. et al.
TI  - Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin.
JO  - Genome Announcements
PY  - 2013
SP  - e00106
EP  - e00112
VL  - 1
AB  - The strains Thermus oshimai JL-2 and Thermus thermophilus JL-18 each have a circular
AB  - chromosome, 2.07 Mb and 1.9 Mb in size, respectively, and each has two plasmids ranging from
AB  - 0.27 Mb to 57.2 kb. The megaplasmid of each strain contains a gene cluster for the reduction
AB  - of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.
ER  -

TY  - JOUR
AU  - Muscarella, D.E.
AU  - Ellison, E.L.
AU  - Ruoff, B.M.
AU  - Vogt, V.M.
TI  - Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum.
JO  - Mol. Cell. Biol.
PY  - 1990
SP  - 3386
EP  - 3396
VL  - 10
AB  - A novel and only recently recognized class of enzymes is composed of the site-specific
AB  - endonucleases encoded by some group I introns. We have characterized several aspects of I-Ppo,
AB  - the endonuclease that mediates the mobility of intron 3 in the ribosomal DNA of Physarum
AB  - polycephalum. This intron is unique among mobile group I introns in that it is located in
AB  - nuclear DNA. We found that I-Ppo is encoded by an open reading frame in the 5' half of intron
AB  - 3, upstream of the sequences required for self-splicing of group I introns. Either of two AUG
AB  - initiation codons could start this reading frame, one near the beginning of the intron and the
AB  - other in the upstream exon, leading to predicted polypeptides of 138 and 160 amino acid
AB  - residues. The longer polypeptide was the major form translated in vitro in a reticulocyte
AB  - extract. From nuclease assays of proteins synthesized in vitro with partially deleted DNAs, we
AB  - conclude that both polypeptides possess endonuclease activity. We also have expressed I-Ppo in
AB  - Escherichia coli, using a bacteriophage T7 RNA polymerase expression system. The longer
AB  - polypeptide also was the predominant form made in this system. It showed enzymatic activity in
AB  - bacteria in vivo, as demonstrated by the cleavage of a plasmid carrying the target site. Like
AB  - several other intron-encoded endonucleases, I-Ppo makes a four-base staggered cut in its
AB  - ribosomal DNA target sequence, very near the site where intron 3 becomes integrated in crosses
AB  - of intron 3-containing and intron 3-lacking Physarum strains.
ER  -

TY  - JOUR
AU  - Muscarella, D.E.
AU  - Vogt, V.M.
TI  - A mobile group I intron in the nuclear DNA of Physarum polycephalum.
JO  - Cell
PY  - 1989
SP  - 443
EP  - 454
VL  - 56
AB  - We have shown that a strain-specific group I intron (intron 3) in the nuclear extrachromosomal
AB  - rDNA of Physarum polycephalum is a mobile element. Shortly after mating of amoebae from
AB  - intron-lacking and intron-containing strains, intron 3 transposes in a site-specific manner
AB  - into all available recipient molecules. The transposition appears to occur by gene conversion,
AB  - as evidenced by the co-conversion of adjacent sequences and by double strand breakage observed
AB  - in some of the recipient rDNA molecules. We infer that the double strand break is induced by
AB  - an endonuclease encoded by intron 3, since in vitro transcription and translation of the
AB  - cloned intron leads to the synthesis of an enzymatically active, site-specific nuclease. This
AB  - is the first demonstration of the transposition of a nuclear intron in an experimental
AB  - setting, and provides a rare example of a protein encoded by an RNA polymerase I transcript.
ER  -

TY  - JOUR
AU  - Mushtaq, M.
AU  - Manzoor, S.
AU  - Pringle, M.
AU  - Rosander, A.
AU  - Bongcam-Rudloff, E.
TI  - Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 67
EP  - 67
VL  - 10
AB  - 'Treponema phagedenis' is considered to be a key agent in the pathogenesis of bovine digital
AB  - dermatitis, an infectious foot condition of economic and animal welfare importance. We hereby
AB  - report the draft sequence of 'T. phagedenis' strain V1. The draft genome assembly consists
AB  - of 51 scaffolds comprising 3,129,551 bp and a GC-content of 39.9 %. Putative pathogenicity
AB  - related factors have been identified in the genome that can be used in future studies to gain
AB  - insight into  the pathogenic mechanisms of 'T. phagedenis'.
ER  -

TY  - JOUR
AU  - Mushtaq, R.
AU  - Naeem, S.
AU  - Sohail, A.
AU  - Riazuddin, S.
TI  - BseRI a novel restriction endonuclease from a Bacillus species which recognizes the sequence 5'...GAGGAG...3'.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3585
EP  - 3585
VL  - 21
AB  - BseRI, a unique Type IIS restriction endonuclease, has been isolated from Bacillus species R
AB  - (CAMB 2669). BseRI recognizes a six base pair non-palindromic sequence 5'-GAGGAG-3' and
AB  - cleaves double stranded DNA ten nucleotides beyond this sequence on the top strand and eight
AB  - nucleotides beyond the sequence on the complementary strand to produce a two nucleotide 3'
AB  - extension.
ER  -

TY  - JOUR
AU  - Musich, P.R.
TI  - Effects of cytosine methylation on the activity of restriction enzymes.
JO  - J. Cell Biol.
PY  - 1987
SP  - 155a
EP  - 155a
VL  - 105
AB  - Restriction cleavage of DNA is a major tool in the characterization eukaryotic
AB  - genes.  Cleavage by a restriction enzyme requires only that the DNA contain the
AB  - recognition site for the enzyme and that it not be modified so as to prohibit
AB  - the hydrolytic reaction.  In mammals, the DNA is modified in some of the
AB  - 5'-CG-3' doublets by C5 methylation of cytosine (5mC).  The 5mC inhibits the
AB  - cleavage activity of some nucleases, but does not affect others.  However, the
AB  - effect of 5mC on most restriction enzyme activities has not been thoroughly
AB  - documented.  The studies presented address this need.  Single stranded pTZ19U
AB  - and pTZ19R plasmid DNAs were hybridized with the universal and reverse M13
AB  - sequencing primers, respectively.  These primed templates were extended by DNA
AB  - polI with dATP, dGTP, dTTP and either dCTP or d5mCTP, generating double strand
AB  - substrates in which one strand was completely methylated at all cytosine
AB  - positions.  These substrates were treated with 12 restriction enzymes, each
AB  - with a single cleavage site in the polyclonal region of these vectors.  AccI,
AB  - Asp718, SacI, SalI and SmaI were inactive on the hemimethylated substrates.
AB  - HindIII, KpnI, PstI and XbaI were active but exhibited modified specificities.
AB  - BamHI, EcoRI and HincII activitiies were not affected by 5mC.  These results
AB  - indicate that cytosine methylation can affect restriction cleavage either by
AB  - inhibition or by alteration of the selected cleavage site.  In addition, the
AB  - data confirm that isoschizomers are affected differently by methylation of the
AB  - same site.
ER  -

TY  - JOUR
AU  - Mussa, H.J.
AU  - VanWagoner, T.M.
AU  - Morton, D.J.
AU  - Seale, T.W.
AU  - Whitby, P.W.
AU  - Stull, T.L.
TI  - Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme.
JO  - Genome Announcements
PY  - 2015
SP  - e01374
EP  - e01315
VL  - 3
AB  - Nontypeable Haemophilus influenzae is an important cause of human disease. Strains were
AB  - selected for genome sequencing to represent the breadth of
AB  - nontypeable strains within the species, as previously defined by the
AB  - electrophoretic mobility of 16 metabolic enzymes.
ER  -

TY  - JOUR
AU  - Mustapha, M.M.
AU  - Li, B.
AU  - Pacey, M.P.
AU  - Mettus, R.T.
AU  - McElheny, C.L.
AU  - Marshall, C.W.
AU  - Ernst, R.K.
AU  - Cooper, V.S.
AU  - Doi, Y.
TI  - Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii.
JO  - J. Antimicrob. Chemother.
PY  - 2018
SP  - 2952
EP  - 2959
VL  - 73
AB  - Background: Acinetobacter baumannii is a healthcare-associated pathogen with high rates of
AB  - carbapenem resistance. Colistin is now routinely used for treatment of
AB  - infections by this pathogen. However, colistin use has been associated with
AB  - development of resistance to this agent. Objectives: To elucidate the
AB  - phylogenomics of colistin-susceptible and -resistant A. baumannii strain pairs
AB  - from a cohort of hospitalized patients at a tertiary medical centre in the USA.
AB  - Methods: WGS data from 21 pairs of colistin-susceptible and -resistant, XDR
AB  - clinical strains were obtained and compared using phylogeny of aligned genome
AB  - sequences, assessment of pairwise SNP differences and gene content. Results:
AB  - Fourteen patients had colistin-resistant strains that were highly genetically
AB  - related to their own original susceptible strain with a median pairwise SNP
AB  - distance of 5.5 (range 1-40 SNPs), while seven other strain pairs were divergent
AB  - with >/=84 SNP differences. In addition, several strains from different patients
AB  - formed distinct clusters on the phylogeny in keeping with closely linked
AB  - transmission chains. The majority of colistin-resistant strains contained
AB  - non-synonymous mutations within the pmrAB locus suggesting a central role for
AB  - pmrAB mutations in colistin resistance. Excellent genotype-phenotype correlation
AB  - was also observed for carbapenems, aminoglycosides and tetracyclines.
AB  - Conclusions: The findings suggest that colistin resistance in the clinical
AB  - setting arises through both in vivo evolution from colistin-susceptible strains
AB  - and reinfection by unrelated colistin-resistant strains, the latter of which may
AB  - involve patient-to-patient transmission.
ER  -

TY  - JOUR
AU  - Mustapha, M.M.
AU  - Marsh, J.W.
AU  - Ezeonwuka, C.D.
AU  - Pasculle, A.W.
AU  - Pacey, M.P.
AU  - Querry, A.M.
AU  - Muto, C.A.
AU  - Harrison, L.H.
TI  - Draft Genome Sequences of Four Hospital-Associated Pseudomonas putida Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e01039
EP  - e01016
VL  - 4
AB  - We present here the draft genome sequences of four Pseudomonas putida isolates belonging to a
AB  - single clone suspected for nosocomial transmission between
AB  - patients and a bronchoscope in a tertiary hospital. The four genome sequences
AB  - belong to a single lineage but contain differences in their mobile genetic
AB  - elements.
ER  -

TY  - JOUR
AU  - Mutti, M.
AU  - Sonnevend, A.
AU  - Pal, T.
AU  - Junttila, S.
AU  - Ekker, H.
AU  - Galik, B.
AU  - Gyenesei, A.
AU  - Nagy, G.
AU  - Nagy, E.
AU  - Szijarto, V.
TI  - Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug-Resistant Phenotype.
JO  - Genome Announcements
PY  - 2018
SP  - e00056
EP  - e00018
VL  - 6
AB  - The sequence type 131 (ST131)-H30 clone is responsible for a significant proportion of
AB  - multidrug-resistant extraintestinal Escherichia coli infections.
AB  - Recently, the C1-M27 clade of ST131-H30, associated with blaCTX-M-27, has
AB  - emerged. The complete genome sequence of E. coli isolate 81009 belonging to this
AB  - clone, previously used during the development of ST131-specific monoclonal
AB  - antibodies, is reported here.
ER  -

TY  - JOUR
AU  - Muyyarikkandy, M.S.
AU  - Alqahtani, F.H.
AU  - Mandoiu, I.
AU  - Amalaradjou, M.A.
TI  - Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits Potent Antipathogenic Effects against Salmonella enterica Serovars Enteritidis,  Typhimurium, and Heidelberg.
JO  - Genome Announcements
PY  - 2018
SP  - e00065
EP  - e00018
VL  - 6
AB  - Lactobacillus paracasei DUP 13076 demonstrates antagonistic effects against the foodborne
AB  - pathogens Salmonella enterica serovars Enteritidis, Typhimurium, and
AB  - Heidelberg in coculture and in vitro experiments. Here, we report the draft
AB  - genome sequence of Lactobacillus paracasei DUP 13076, which has a circular
AB  - chromosome of 3,048,314 bp and a G+C content of 46.3%.
ER  -

TY  - JOUR
AU  - Muyyarikkandy, M.S.
AU  - Alqahtani, F.H.
AU  - Mandoiu, I.
AU  - Amalaradjou, M.A.
TI  - Draft Genome Sequence of Lactobacillus rhamnosus NRRL B-442, a Potential Probiotic Strain.
JO  - Genome Announcements
PY  - 2018
SP  - e00046
EP  - e00018
VL  - 6
AB  - Lactic acid bacteria are known to exhibit probiotic properties through various mechanisms,
AB  - including competitive exclusion, pathogen inhibition, production of
AB  - antimicrobial substances, and maintenance of eubiosis. Here, we present the draft
AB  - genome sequence of a novel probiotic strain, Lactobacillus rhamnosus strain NRRL
AB  - B-442, which exhibits potent antivirulence activity against Salmonella enterica.
ER  -

TY  - JOUR
AU  - Muyzer, G.
AU  - Sorokin, D.Y.
AU  - Mavromatis, K.
AU  - Lapidus, A.
AU  - Clum, A.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - d'Haeseleer, P.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
TI  - Complete genome sequence of 'Thioalkalivibrio sulfidophilus' HL-EbGr7.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 23
EP  - 35
VL  - 4
AB  - 'Thioalkalivibrio sulfidophilus' HL-EbGr7 is an obligately chemolithoautotrophic,
AB  - haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the
AB  - Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor,
AB  - removing sulfide from biogas. Here we report the complete genome sequence of
AB  - strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint
AB  - Genome Institute Community Sequencing Program, because of its relevance to the
AB  - sustainable removal of sulfide from bio- and industrial waste gases.
ER  -

TY  - JOUR
AU  - Muyzer, G.
AU  - Sorokin, D.Y.
AU  - Mavromatis, K.
AU  - Lapidus, A.
AU  - Foster, B.
AU  - Sun, H.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - D'haeseleer, P.
AU  - Woyke, T.
AU  - Kyripides, N.C.
TI  - Complete genome sequence of Thioalkalivibrio sp. K90mix.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 341
EP  - 355
VL  - 5
AB  - Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic
AB  - sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the
AB  - Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from
AB  - different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme
AB  - potassium carbonate tolerance as an enrichment method. Here we report the complete ge-nome
AB  - sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome
AB  - Institute Community Sequencing Program, because of its relevance to the sus-tainable removal
AB  - of sulfide from wastewater and gas streams.
ER  -

TY  - JOUR
AU  - Myers, G.S. et al.
TI  - Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.
JO  - Genome Res.
PY  - 2006
SP  - 1031
EP  - 1040
VL  - 16
AB  - Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found
AB  - in soil, sediments, and the human
AB  - gastrointestinal tract. C. perfringens is responsible for a wide spectrum
AB  - of disease, including food poisoning, gas gangrene (clostridial
AB  - myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal
AB  - infections. The complete genome sequences of Clostridium perfringens
AB  - strain ATCC 13124, a gas gangrene isolate and the species type strain, and
AB  - the enterotoxin-producing food poisoning strain SM101, were determined and
AB  - compared with the published C. perfringens strain 13 genome. Comparison of
AB  - the three genomes revealed considerable genomic diversity with >300 unique
AB  - "genomic islands" identified, with the majority of these islands unusually
AB  - clustered on one replichore. PCR-based analysis indicated that the large
AB  - genomic islands are widely variable across a large collection of C.
AB  - perfringens strains. These islands encode genes that correlate to
AB  - differences in virulence and phenotypic characteristics of these strains.
AB  - Significant differences between the strains include numerous novel mobile
AB  - elements and genes encoding metabolic capabilities, strain-specific
AB  - extracellular polysaccharide capsule, sporulation factors, toxins, and
AB  - other secreted enzymes, providing substantial insight into this medically
AB  - important bacterial pathogen.
ER  -

TY  - JOUR
AU  - Nabhan, S.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Liu, Z.
AU  - Bryant, D.A.
AU  - Overmann, J.
TI  - Genome Sequence of Prosthecochloris sp. Strain CIB 2401 of the Phylum Chlorobi.
JO  - Genome Announcements
PY  - 2016
SP  - e01222
EP  - e01216
VL  - 4
AB  - To date, only 13 genomes of green sulfur bacteria (family Chlorobiaceae) have been sequenced.
AB  - The sequenced strains do not cover the full phylogenetic
AB  - diversity of the family. We determined the complete genome sequence of
AB  - Prosthecochloris sp. strain CIB 2401, thereby increasing the genome information
AB  - for the poorly represented marine Chlorobiaceae.
ER  -

TY  - JOUR
AU  - Nacke, H.
AU  - Daniel, R.
AU  - Poehlein, A.
TI  - Genome Sequence of Creatinine-Fermenting Tissierella creatinophila Strain KRE 4T  (DSM 6911).
JO  - Genome Announcements
PY  - 2017
SP  - e00051
EP  - e00017
VL  - 5
AB  - Tissierella creatinophila strain KRE 4T (DSM 6911) is a strictly anaerobic,
AB  - creatinine-fermenting, and creatine-fermenting organism, which has been isolated
AB  - from sewage sludge. The draft genome consists of one circular chromosome (2.5 Mb)
AB  - and harbors 2,533 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Nadeev, A.N.
AU  - Chernukhin, V.A.
AU  - Sevastyanova, O.O.
AU  - Tomilova, Y.E.
AU  - Shinkarenko, N.M.
AU  - Evdokimov, A.A.
AU  - Degtyarev, S.K.
TI  - BstKTI, a new dam-sensitive neoschizomer of restriction endonuclease MboI, which is able to cleave 5 hemimethylated substrate.
JO  - Biotekhnologiya
PY  - 2006
SP  - 5
EP  - 10
VL  - 0
AB  - The strain Bacillus stearothermophilus KT, a producer of a new restriction endonuclease
AB  - BstKTI, which is the neoschizomer of restrictase MboI that recognizes the sequence
AB  - 5'-GATC-3', has been found. The preparation of the enzyme was obtained, and its properties
AB  - were studied including substrate specificity and cleavage position in DNA. It was shown that
AB  - DNA hydrolysis occurred in position 5'-GAT^C-3'. Unlike the other isoschizomers of the
AB  - restriction endonuclease MboI, BstKTI is sensitive to dam-methylation, but it is able to
AB  - cleave the adenine-hemimethylated substrate. Moreover, BstKTI is capable of cleaving the
AB  - sequence 5'-GATC-3' that contains the modified cytosine in position C5.
ER  -

TY  - JOUR
AU  - Naderer, M.
AU  - Brust, J.R.
AU  - Knowle, D.
AU  - Blumenthal, R.M.
TI  - Mobility of a restriction-modification system revealed by its genetic context in three hosts.
JO  - J. Bacteriol.
PY  - 2002
SP  - 2411
EP  - 2419
VL  - 184
AB  - The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution,
AB  - and restriction-modification systems can modulate this flow. However, relatively little is
AB  - known about the distribution and movement of restriction-modification systems themselves. We
AB  - have isolated and characterized the genes for restriction-modification systems from two
AB  - species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both
AB  - systems are closely related to the PvuII restriction-modification system and share its target
AB  - specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is
AB  - inactive, apparently due to a mutation in the subunit interface region. Unlike the
AB  - chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed
AB  - the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris,
AB  - making this the first completely sequenced plasmid from the genus Proteus. Despite the
AB  - pronounced similarity of the three restriction-modification systems, the flanking sequences in
AB  - Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an
AB  - equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative
AB  - integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination
AB  - (cer) site.
ER  -

TY  - JOUR
AU  - Nadig, S.
AU  - Velusamy, N.
AU  - Lalitha, P.
AU  - Kar, S.
AU  - Sharma, S.
AU  - Arakere, G.
TI  - Staphylococcus aureus eye infections in two Indian hospitals: emergence of ST772 as a major clone.
JO  - Clinical Ophthalmology
PY  - 2012
SP  - 165
EP  - 173
VL  - 6
AB  - PURPOSE: The purpose of this study was to perform molecular characterization of Staphylococcus
AB  - aureus isolates causing a variety of eye infections from two major eye care hospitals in
AB  - India. METHODS: Twenty-four isolates from Aravind Eye Hospital, Madurai, India, and nine
AB  - isolates from LV Prasad Eye Institute, Bhubaneswar, India, representing severe to nonsevere
AB  - eye infections like microbial keratitis to lacrimal sac abscess, were characterized.
AB  - Staphylococcal cassette chromosome mec typing, multilocus sequence typing, accessory gene
AB  - regulator typing, staphylococcal protein A typing, and pulsed field gel electrophoresis were
AB  - used, along with determination of the presence of Panton-Valentine leucocidin toxin and
AB  - endotoxin gene cluster among each sequence type. RESULTS: The majority of eye infections, both
AB  - severe and nonsevere, were caused by sequence type (ST)772, positive for the Panton-Valentine
AB  - leucocidin gene, and carrying methicillin-resistant staphylococcal cassette chromosome mec
AB  - type V cassette (22/33, 67%). Some of the other sequence types that caused severe eye
AB  - infections were ST1 (9%), 5 (3%), 72 (6%), 88 (3%), 121 (3%), and 672 (3%).
AB  - This is the first report of the presence of ST1 and 88 in India. CONCLUSION:
AB  - Although the number of isolates included in this study was small, most of the eye infections
AB  - were caused by community-associated S. aureus where patients had no history of hospitalization
AB  - or treatment in the past year. In the case of six severe infections, patients were admitted
AB  - for surgeries and there is probability of hospital infection. In addition, only
AB  - methicillin-resistant S. aureus isolates carrying staphylococcal cassette chromosome mec type
AB  - V were detected. Epidemic methicillin-resistant Staphylococcus aureus 15 (ST22) is a major ST
AB  - found in health care as well as community settings in non-eye infections in India, but only
AB  - one methicillin-sensitive S. aureus isolate belonging to ST22 was detected.
AB  - Predominantly ST772, along with a few other STs, caused the 33 eye infections studied.
ER  -

TY  - JOUR
AU  - Nadiga, M.
AU  - Vaidyanathan, V.V.
AU  - Thayumanavan, T.
TI  - Draft Genome Sequence of Aeromonas dhakensis Strain F2S2-1, Isolated from the Skin Surface of an Indian Oil Sardine (Sardinella longiceps).
JO  - Genome Announcements
PY  - 2016
SP  - e00494
EP  - e00416
VL  - 4
AB  - Draft genome sequencing of Aeromonas dhakensis strain F2S2-1, isolated from the skin surface
AB  - of an Indian oil sardine (Sardinella longiceps), has been carried
AB  - out. The draft genome was roughly 4.7 Mb in size with 61.7% G+C content.
AB  - Annotation of the genome yielded 4,337 genes coding for proteins, tRNAs, and
AB  - rRNAs. Annotation also revealed the presence of 52 genes linked to resistance to
AB  - antibiotics/toxic compounds. Pathway analysis revealed the presence of novobiocin
AB  - biosynthetic genes and genes for biosynthesis of a siderophore group on
AB  - nonsynthetic peptides.
ER  -

TY  - JOUR
AU  - Nagai, Y.
AU  - Nogami, S.
AU  - Kumagai-Sano, F.
AU  - Ohya, Y.
TI  - Karyopherin-mediated nuclear import of the homing endonuclease VMA1-derived endonuclease is required for self-propagation of the  coding region.
JO  - Mol. Cell. Biol.
PY  - 2003
SP  - 1726
EP  - 1736
VL  - 23
AB  - VMA1-derived endonuclease (VDE), a site-specific endonuclease in Saccharomyces cerevisiae,
AB  - enters the nucleus to generate a double-strand
AB  - break in the VDE-negative allelic locus, mediating the self-propagating
AB  - gene conversion called homing. Although VDE is excluded from the nucleus
AB  - in mitotic cells, it relocalizes at premeiosis, becoming localized in both
AB  - the nucleus and the cytoplasm in meiosis. The nuclear localization of VDE
AB  - is induced by inactivation of TOR kinases, which constitute central
AB  - regulators of cell differentiation in S. cerevisiae, and by nutrient
AB  - depletion. A functional genomic approach revealed that at least two
AB  - karyopherins, Srp1p and Kap142p, are required for the nuclear localization
AB  - pattern. Genetic and physical interactions between Srp1p and VDE imply
AB  - direct involvement of karyopherin-mediated nuclear transport in this
AB  - process. Inactivation of TOR signaling or acquisition of an extra nuclear
AB  - localization signal in the VDE coding region leads to artificial nuclear
AB  - localization of VDE and thereby induces homing even during mitosis. These
AB  - results serve as evidence that VDE utilizes the host systems of nutrient
AB  - signal transduction and nucleocytoplasmic transport to ensure the
AB  - propagation of its coding region.
ER  -

TY  - JOUR
AU  - Nagamalleswari, E.
AU  - Nagaraja, V.
TI  - Draft Genome Sequence of Klebsiella pneumoniae OK8, a Multidrug-Resistant Mouse and Human Pathogen.
JO  - Genome Announcements
PY  - 2017
SP  - e01018
EP  - e01017
VL  - 5
AB  - We report here the draft genome sequence of Klebsiella pneumoniae OK8, a multidrug-resistant
AB  - strain which was isolated in 1976 from a human and is known
AB  - to be a mouse pathogen.
ER  -

TY  - JOUR
AU  - Nagamalleswari, E.
AU  - Rao, S.
AU  - Vasu, K.
AU  - Nagaraja, V.
TI  - Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 8423
EP  - 8434
VL  - 45
AB  - Programmed cell death (PCD) under certain conditions is one of the features of bacterial
AB  - altruism. Given the bacterial diversity and varied life style,
AB  - different PCD mechanisms must be operational that remain largely unexplored. We
AB  - describe restriction endonuclease (REase) mediated cell death by an apoptotic
AB  - pathway, beneficial for isogenic bacterial communities. Cell death is pronounced
AB  - in stationary phase and when the enzyme exhibits promiscuous DNA cleavage
AB  - activity. We have elucidated the molecular mechanism of REase mediated cell
AB  - killing and demonstrate that released nutrients from dying cells support the
AB  - growth of the remaining cells in the population. These findings illustrate a new
AB  - intracellular moonlighting role for REases which are otherwise established host
AB  - defence arsenals. REase induced PCD appears to be a cellular design to replenish
AB  - nutrients for cells undergoing starvation stress and the phenomenon could be wide
AB  - spread in bacteria, given the abundance of restriction-modification (R-M) systems
AB  - in the microbial population.
ER  -

TY  - JOUR
AU  - Nagamalleswari, E.
AU  - Vasu, K.
AU  - Nagaraja, V.
TI  - Ca(2+) binding to the ExDxD motif regulates the DNA cleavage specificity of a promiscuous endonuclease.
JO  - Biochemistry
PY  - 2012
SP  - 8939
EP  - 8949
VL  - 51
AB  - Most of the restriction endonucleases (REases) are dependent on Mg(2+) for DNA cleavage, and
AB  - in general, Ca(2+) inhibits their activity. R.KpnI, an HNH active
AB  - site containing betabetaalpha-Me finger nuclease, is an exception. In presence of
AB  - Ca(2+), the enzyme exhibits high-fidelity DNA cleavage and complete suppression
AB  - of Mg(2+)-induced promiscuous activity. To elucidate the mechanism of unusual
AB  - Ca(2+)-mediated activity, we generated alanine variants in the putative Ca(2+)
AB  - binding motif, E(132)xD(134)xD(136), of the enzyme. Mutants showed decreased
AB  - levels of DNA cleavage in the presence of Ca(2+). We demonstrate that ExDxD
AB  - residues are involved in Ca(2+) coordination; however, the invariant His of the
AB  - catalytic HNH motif acts as a general base for nucleophile activation, and the
AB  - other two active site residues, D148 and Q175, also participate in
AB  - Ca(2+)-mediated cleavage. Insertion of a 10-amino acid linker to disrupt the
AB  - spatial organization of the ExDxD and HNH motifs impairs Ca(2+) binding and
AB  - affects DNA cleavage by the enzyme. Although ExDxD mutant enzymes retained
AB  - efficient cleavage at the canonical sites in the presence of Mg(2+), the
AB  - promiscuous activity was greatly reduced, indicating that the carboxyl residues
AB  - of the acidic triad play an important role in sequence recognition by the enzyme.
AB  - Thus, the distinct Ca(2+) binding motif that confers site specific cleavage upon
AB  - Ca(2+) binding is also critical for the promiscuous activity of the Mg(2+)-bound
AB  - enzyme, revealing its role in metal ion-mediated modulation of DNA cleavage.
ER  -

TY  - JOUR
AU  - Nagao, K.
AU  - Suzuki, K.
AU  - Hamada, S.
AU  - Yahara, S.
AU  - Yamamura, R.
AU  - Uyeda, M.
TI  - 1513-DMIa and 1513-DMIb, DNA methyltransferase inhibitors produced by Streptomyces sp. strain no. 1513.
JO  - J. Enzym. Inhib.
PY  - 1998
SP  - 135
EP  - 146
VL  - 13
AB  - Two new methyltransferase inhibitors were isolated from the culture filtrate of Streptomyces
AB  - sp. strain No. 1513 and named 1513-DMIa and 1513-DMIb.  1513-DMIa and 1513-DMIb were
AB  - distinguished in certain properties from DMI-1, DMI-2, DMI-3 and DMI-4 previously reported.
AB  - The molecular weight of 1513-DMIa and 1513-DMIb were estimated to be 576 and 8400 from the
AB  - results of FAB-MS and gel filtration, respectively.  The inhibitory activities of 1513-DMIa
AB  - and 1513-DMIb were shown to be pH- and temperature-dependent and both inhibited M.EcoRI in an
AB  - uncompetitive manner with respect to DNA or S-adenosylmethionine (SAM).
ER  -

TY  - JOUR
AU  - Nagao, K.
AU  - Suzuki, K.
AU  - Tokunaga, J.
AU  - Miyazaki, H.
AU  - Katayama, N.
AU  - Mitsuyama, R.
AU  - Uyeda, M.
TI  - DMI-2 and DMI-3, DNA methyltransferase inhibitors produced by Streptomyces sp. strain no. 560.
JO  - J. Enzym. Inhib.
PY  - 1996
SP  - 115
EP  - 124
VL  - 10
AB  - Streptomyces sp. strain no. 560 produces several types of DNA methyltransferase inhibitors in
AB  - the culture filtrate.  Two of them, DMI-2 and DMI-3, were distinguished from the previously
AB  - reported DMI-1 by their inhibitory spectrum and inhibition characteristics against DNA
AB  - methyltransferase.  The molecular weights of DMI-2 and DMI-3 were 854 and 435, respectively.
AB  - The structure of DMI-2 was determined to be
AB  - 4R,6aR,10S,10aS-8-acetyl-6a.10a-d:hydroxy-2-methoxy-12-methyl-10-[4-[3-hydroxy-3,5-dimethy
AB  - tetrahydropyran-1-yloxy)-5-methylcyclohexan-1-yloxyl-1,4,6,7,9-pentaoxo-1,4,6,6a,7,8,9,10,10a
AB  - The chemical structure of DMI-2 was established as a tautomer of duiomycin which is an
AB  - antitumor antibiotic produced by Streptomyces sp. 1725.  DMI-2 and DMI-3 showed strong
AB  - inhibition against N6-methyladenine-DNA methyltransferase (M.EcoRI).  DMI-2 inhibited M.EcoRI
AB  - in a competitive manner with respect to plasmid pUC19 used as DNA substrate and in an
AB  - uncompetitive manner with respect to S-adenosylmethionine (SAM) used as methyl donor.  DMI-3
AB  - inhibited M.EcoRI in a competitive manner with respect to plasmid pUC19 and SAM.  The
AB  - inhibitory activities of both inhibitors depended upon the pH and temperature in the assay
AB  - media.
ER  -

TY  - JOUR
AU  - Nagao, N.
AU  - Hirose, Y.
AU  - Misawa, N.
AU  - Ohtsubo, Y.
AU  - Umekage, S.
AU  - Kikuchi, Y.
TI  - Complete Genome Sequence of Rhodovulum sulfidophilum DSM 2351, an Extracellular Nucleic Acid-Producing Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00388
EP  - e00315
VL  - 3
AB  - Rhodovulum sulfidophilum DSM 2351 is the nonsulfur photosynthetic bacterium that  efficiently
AB  - releases nucleic acids into the extracellular milieu, which leads to
AB  - flocculation. In this study, we determined the complete genome sequence of R.
AB  - sulfidophilum DSM 2351, which will provide new insights into the mechanism of its
AB  - unique nucleic acid release.
ER  -

TY  - JOUR
AU  - Nagaraja, V.
AU  - Shepherd, J.C.W.
AU  - Bickle, T.A.
TI  - A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity.
JO  - Nature
PY  - 1985
SP  - 371
EP  - 372
VL  - 316
AB  - Early attempts to generate new restriction specificities by recombination
AB  - between allelic restriction-modification systems have been unsuccessful.
AB  - Bullas et al. succeeded in isolating a new specificity, SQ, in Salmonella that
AB  - they interpreted as being the result of a recombination event betwen the
AB  - parental strains, Salmonella typhimurium and S. potsdam, which encode the SB
AB  - and SP restriction systems, respectively.  This interpretation has recently
AB  - been confirmed by DNA heteroduplex studies with the SB, SP and SQ structural
AB  - genes.  We have determined the DNA sequences recognized by the SB and SP
AB  - enzymes and found that, like all type I restriction sequences, they are split
AB  - into two specific domains by a spacer of nonspecific sequence that, for both SB
AB  - and SP, is 6 base pairs (bp) long.  We have now determined the sequence
AB  - recognized by the recombinant SQ enzyme and find that it is a hybrid between
AB  - the SB and SP sequences, containing one specific domain from each parental
AB  - strain.  This result implies that each of the two specific domains is
AB  - recognized by a physically distinct part of the enzyme.
ER  -

TY  - JOUR
AU  - Nagaraja, V.
AU  - Shepherd, J.C.W.
AU  - Pripfl, T.
AU  - Bickle, T.A.
TI  - Two Type I restriction enzymes from Salmonella species.  Purification and DNA recognition sequences.
JO  - J. Mol. Biol.
PY  - 1985
SP  - 579
EP  - 587
VL  - 182
AB  - We have purified the type I restriction enzymes SB and SP from Salmonella typhimurium and S.
AB  - potsdam, respectively, and determined the DNA sequences that they recognize.  These sequences
AB  - resemble those previously determined for the type I enzymes, EcoB, EcoK and EcoA, in that the
AB  - specific part of the sequence is divided into two domains by a spacer of non-specific sequence
AB  - that has a fixed length for each enzyme.  Two main differences from the previously determined
AB  - sequences are seen.  Both of the new sequences are degenerate and one of them, SB, has one
AB  - trinucleotide and one pentanucleotide-specific domain rather than the trinucleotide and
AB  - tetranucleotide domains seen for all of the other enzymes.  The only conserved features of the
AB  - recognition sequences are the adenosyl residues that are methylated in the modification
AB  - reaction.  For all of the enzymes these are situated ten or 11 base-pairs apart, one on each
AB  - strand of the DNA.  This suggests that the enzymes bind to DNA along one face of the double
AB  - helix making protein-DNA interaction in two successive major grooves with most of the
AB  - non-specific spacer sequence in the intervening minor groove.
ER  -

TY  - JOUR
AU  - Nagaraja, V.
AU  - Stieger, M.
AU  - Nager, C.
AU  - Hadi, S.M.
AU  - Bickle, T.A.
TI  - The nucleotide sequence recognized by the Escherichia coli D type I restriction and modification enzyme.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 389
EP  - 399
VL  - 13
AB  - A type I restriction endonuclease from a new isolate of Escherichia coli (E.
AB  - coli E166) has been purified and characterized.  The enzyme, EcoD, has a
AB  - recognition sequence similar in overall structure to the previously determined
AB  - type I enzyme sequences, an exception being that it is degenerate.  The
AB  - sequence is 5'-T-T-A-N-N-N-N-N-N-N-N-G-T-C-Y-3'
AB  - 3'-A-A-T-N-N-N-N-N-N-N-N-C-A-G-R-5'where Y is a pyrimidine, R is a purine and N
AB  - can be any nucleotide.  The enzyme methylates adenosyl residues in both strands
AB  - of the DNA that are separated by ten base pairs, suggesting that the enzyme
AB  - interacts with DNA along one face of the helix making contacts in two
AB  - successive major grooves.
ER  -

TY  - JOUR
AU  - Nagaraja, V.
AU  - Suri, B.
AU  - Shepherd, J.C.W.
AU  - Bickle, T.A.
TI  - New variations of an old theme:  Type I restriction enzymes and their recognition sequences.
JO  - Gene Manipulation and Expression
PY  - 1985
SP  - 62
EP  - 78
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Nagarajan, H.
AU  - Butler, J.E.
AU  - Klimes, A.
AU  - Qiu, Y.
AU  - Zengler, K.
AU  - Ward, J.
AU  - Young, N.D.
AU  - Methe, B.A.
AU  - Palsson, B.O.
AU  - Lovley, D.R.
AU  - Barrett, C.L.
TI  - De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
JO  - PLoS ONE
PY  - 2010
SP  - E10922
EP  - E10922
VL  - 5
AB  - State-of-the-art DNA sequencing technologies are transforming the life
AB  - sciences due to their ability to generate nucleotide sequence information
AB  - with a speed and quantity that is unapproachable with traditional Sanger
AB  - sequencing. Genome sequencing is a principal application of this
AB  - technology, where the ultimate goal is the full and complete sequence of
AB  - the organism of interest. Due to the nature of the raw data produced by
AB  - these technologies, a full genomic sequence attained without the aid of
AB  - Sanger sequencing has yet to be demonstrated.We have successfully
AB  - developed a four-phase strategy for using only next-generation sequencing
AB  - technologies (Illumina and 454) to assemble a complete microbial genome de
AB  - novo. We applied this approach to completely assemble the 3.7 Mb genome of
AB  - a rare Geobacter variant (KN400) that is capable of unprecedented current
AB  - production at an electrode. Two key components of our strategy enabled us
AB  - to achieve this result. First, we integrated the two data types early in
AB  - the process to maximally leverage their complementary characteristics. And
AB  - second, we used the output of different short read assembly programs in
AB  - such a way so as to leverage the complementary nature of their different
AB  - underlying algorithms or of their different implementations of the same
AB  - underlying algorithm.The significance of our result is that it
AB  - demonstrates a general approach for maximizing the efficiency and success
AB  - of genome assembly projects as new sequencing technologies and new
AB  - assembly algorithms are introduced. The general approach is a meta
AB  - strategy, wherein sequencing data are integrated as early as possible and
AB  - in particular ways and wherein multiple assembly algorithms are
AB  - judiciously applied such that the deficiencies in one are complemented by
AB  - another.
ER  -

TY  - JOUR
AU  - Nagarjuna, D.
AU  - Gaind, R.
AU  - Dhanda, R.S.
AU  - Yadav, M.
TI  - Whole-Genome Shotgun Sequence of Escherichia coli Strain MN067 from India, a Commensal Bacterium with Potent Pathogenic Ability.
JO  - Genome Announcements
PY  - 2017
SP  - e00054
EP  - e00017
VL  - 5
AB  - Escherichia coli is one of the most frequently prevalent pathogens, causing infections in
AB  - health care settings throughout the world. Here, we report the
AB  - whole-genome sequence of MN067, a commensal bacterium with a pathogenic
AB  - potential.
ER  -

TY  - JOUR
AU  - Nagashima, S.
AU  - Kamimura, A.
AU  - Shimizu, T.
AU  - Nakamura-Isaki, S.
AU  - Aono, E.
AU  - Sakamoto, K.
AU  - Ichikawa, N.
AU  - Nakazawa, H.
AU  - Sekine, M.
AU  - Yamazaki, S.
AU  - Fujita, N.
AU  - Shimada, K.
AU  - Hanada, S.
AU  - Nagashima, K.V.
TI  - Complete Genome Sequence of Phototrophic Betaproteobacterium Rubrivivax gelatinosus IL144.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3541
EP  - 3542
VL  - 194
AB  - Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in
AB  - freshwater ponds, sewage ditches, activated sludge, and food processing
AB  - wastewater. There have not been many studies on photosynthetic
AB  - betaproteobacteria. Here we announce the complete genome sequence of the
AB  - best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC
AB  - 100245).
ER  -

TY  - JOUR
AU  - Nagata, Y.
AU  - Ohtsubo, Y.
AU  - Endo, R.
AU  - Ichikawa, N.
AU  - Ankai, A.
AU  - Oguchi, A.
AU  - Fukui, S.
AU  - Fujita, N.
AU  - Tsuda, M.
TI  - Complete Genome Sequence of the Representative {gamma}-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum  UT26.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5852
EP  - 5853
VL  - 192
AB  - Sphingobium japonicum strain UT26 utilizes gamma-hexachlorocyclohexane (gamma-HCH), a man-made
AB  - chlorinated pesticide that causes serious
AB  - environmental problems due to its toxicity and long persistence, as a sole
AB  - source of carbon and energy. Here, we report the complete genome sequence
AB  - of UT26, which consists of two chromosomes and three plasmids. The 15 lin
AB  - genes involved in gamma-HCH degradation are dispersed on the two
AB  - chromosomes and one of the three plasmids.
ER  -

TY  - JOUR
AU  - Nagornykh, M.
AU  - Zakharova, M.
AU  - Protsenko, A.
AU  - Bogdanova, E.
AU  - Solonin, A.S.
AU  - Severinov, K.
TI  - Regulation of gene expression in restriction-modification system Eco29kI.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 4653
EP  - 4663
VL  - 39
AB  - The Eco29kI restriction-modification (R-M) system consists of two partially overlapping genes,
AB  - eco29kIR, encoding a restriction endonuclease
AB  - and eco29kIM, encoding methyltransferase. The two genes are thought to
AB  - form an operon with the eco29kIR gene preceding the eco29kIM gene. Such an
AB  - organization is expected to complicate establishment of plasmids
AB  - containing this R-M system in naive hosts, since common logic dictates
AB  - that methyltransferase should be synthesized first to protect the DNA from
AB  - cleavage by the endonuclease. Here, we characterize the Eco29kI gene
AB  - transcription. We show that a separate promoter located within the
AB  - eco29kIR gene is sufficient to synthesize enough methyltransferase to
AB  - completely modify host DNA. We further show that transcription from two
AB  - intragenic antisense promoters strongly decreases the levels of eco29kIR
AB  - gene transcripts. The antisense transcripts act by preventing translation
AB  - initiation from the bicistronic eco29kIR-eco29kIM mRNA and causing its
AB  - degradation. Both eco29kIM and antisense promoters are necessary for
AB  - Eco29kI genes establishment and/or stable maintenance, indicating that
AB  - they jointly contribute to coordinated expression of Eco29kI genes.
ER  -

TY  - JOUR
AU  - Nagornykh, M.O.
AU  - Bogdanova, E.S.
AU  - Protsenko, A.S.
AU  - Solonin, A.S.
AU  - Zakharova, M.V.
AU  - Severinov, K.V.
TI  - Regulation of gene expression in a type II restriction-modification system.
JO  - Genetika
PY  - 2008
SP  - 606
EP  - 615
VL  - 44
AB  - Type II restriction-modification systems are comprised of a restriction endonuclease and
AB  - methyltransferase. The enzymes are coded by individual genes and recognize the same DNA
AB  - sequence. Endonuclease makes a double-stranded break in the recognition site, and
AB  - methyltransferase covalently modifies DNA bases within the recognition site, thereby
AB  - preventing cleavage by the endonuclease. The concerted action of these enzymes plays the role
AB  - of a primitive immune system and protects the bacterial host cell from invasion by foreign
AB  - (for example, viral) DNA. However, uncontrolled expression of restriction-modification system
AB  - genes can result in the death of a bacterial host cell because of endonuclease cleavage of the
AB  - host DNA. In the present review, data on the regulation of expression of the type II
AB  - restriction-modification enzymes genes are discussed.
ER  -

TY  - JOUR
AU  - Nagymihaly, M.
AU  - Vasarhelyi, B.M.
AU  - Barriere, Q.
AU  - Chong, T.M.
AU  - Balint, B.
AU  - Bihari, P.
AU  - Hong, K.W.
AU  - Horvath, B.
AU  - Ibijbijen, J.
AU  - Amar, M.
AU  - Farkas, A.
AU  - Kondorosi, E.
AU  - Chan, K.G.
AU  - Gruber, V.
AU  - Ratet, P.
AU  - Mergaert, P.
AU  - Kereszt, A.
TI  - The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 75
EP  - 75
VL  - 12
AB  - Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing
AB  - bacterium isolated from the nodules of the legume Medicago
AB  - arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen
AB  - fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is
AB  - exceptional because it is a highly effective symbiotic partner of the two most
AB  - widely used accessions, A17 and R108, of the model legume Medicago truncatula
AB  - Gaertn. Based on 16S rRNA gene sequence, multilocus sequence and average
AB  - nucleotide identity analyses, FSM-MA is identified as a new Ensifer meliloti
AB  - strain. The genome is 6,70 Mbp and is comprised of the chromosome (3,64 Mbp)
AB  - harboring 3574 predicted genes and two megaplasmids, pSymA (1,42 Mbp) and pSymB
AB  - (1,64 Mbp) with respectively 1481 and 1595 predicted genes. The average GC
AB  - content of the genome is 61.93%. The FSM-MA genome structure is highly similar
AB  - and co-linear to other E. meliloti strains in the chromosome and the pSymB
AB  - megaplasmid while, in contrast, it shows high variability in the pSymA plasmid.
AB  - The large number of strain-specific sequences in pSymA as well as strain-specific
AB  - genes on pSymB involved in the biosynthesis of the lipopolysaccharide and
AB  - capsular polysaccharide surface polysaccharides may encode novel symbiotic
AB  - functions explaining the high symbiotic performance of FSM-MA.
ER  -

TY  - JOUR
AU  - Nahar, A.
AU  - Baker, A.L.
AU  - Bowman, J.P.
AU  - Britz, M.L.
TI  - Draft Genome Sequences of Two Lactobacillus casei Strains Isolated from Cheddar Cheese and a Fermented Milk Drink.
JO  - Genome Announcements
PY  - 2017
SP  - e01235
EP  - e01217
VL  - 5
AB  - MiSeq Illumina shotgun sequencing technology was used to sequence two Lactobacillus casei
AB  - strains, designated strains GCRL 163 and MJA 12. The
AB  - estimated genome sizes for GCRL 163 and MJA 12 were 2.9 Mb and 3.1 Mb, with
AB  - 46.35% and 46.31% GC contents, respectively.
ER  -

TY  - JOUR
AU  - Nahar, A.
AU  - Baker, A.L.
AU  - Charleston, M.A.
AU  - Bowman, J.P.
AU  - Britz, M.L.
TI  - Draft Genome Sequences of Three Sub-Antarctic Rhodococcus spp., Including Two Novel Psychrophilic Genomospecies.
JO  - Genome Announcements
PY  - 2017
SP  - e00898
EP  - e00817
VL  - 5
AB  - The draft genome sequences of three sub-Antarctic Rhodococcus sp. strains-1159, 1163, and
AB  - 1168-are reported here. The estimated genome sizes were 7.09 Mb with a
AB  - 62.3% GC content for strain 1159, 4.45 Mb with a 62.3% GC content for strain
AB  - 1163, and 5.06 Mb with a 62.10% GC content for strain 1168.
ER  -

TY  - JOUR
AU  - Nahar, A.
AU  - Baker, A.L.
AU  - Charleston, M.A.
AU  - Bowman, J.P.
AU  - Britz, M.L.
TI  - Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species.
JO  - Genome Announcements
PY  - 2017
SP  - e01047
EP  - e01017
VL  - 5
AB  - Illumina MiSeq shotgun sequencing technology was used to sequence the genomes of  two novel
AB  - sub-Antarctic Williamsia species, designated strains 1135 and 1138. The
AB  - estimated genome sizes for strains 1135 and 1138 are 5.99 Mb and 6.08 Mb,
AB  - respectively. This genome sequence information will aid in understanding the
AB  - lipid metabolic pathways of cold-tolerant Williamsia species.
ER  -

TY  - JOUR
AU  - Nahar, A.
AU  - Baker, A.L.
AU  - Charleston, M.A.
AU  - Britz, M.L.
TI  - Draft Genome Sequence of Subantarctic Rhodococcus sp. Strain 1139.
JO  - Genome Announcements
PY  - 2017
SP  - e00090
EP  - e00017
VL  - 5
AB  - The draft genome sequence of subantarctic Rhodococcus sp. strain 1139 is reported here. The
AB  - genome size is 7.04 Mb with high G+C content (62.3%) and it contains a
AB  - large number of genes involved in lipid synthesis. This lipid synthesis system is
AB  - characteristic of oleaginous Actinobacteria, which are of interest for biofuel
AB  - production.
ER  -

TY  - JOUR
AU  - Nahid, F.
AU  - Zahra, R.
AU  - Sandegren, L.
TI  - A blaOXA-181-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance.
JO  - PLoS ONE
PY  - 2017
SP  - e0189438
EP  - e0189438
VL  - 12
AB  - Carbapenem resistant Klebsiella pneumoniae (CR-KP) infections are an
AB  - ever-increasing global issue, especially in the Indian subcontinent. Here we
AB  - report genetic insight into a blaOXA-181 harbouring Klebsiella pneumoniae,
AB  - belonging to the pandemic lineage ST147, that represents an intermediate stage
AB  - towards pan-drug resistance. The CR-KP isolate DA48896 was isolated from a
AB  - patient from Pakistan and was susceptible only to tigecycline and colistin. It
AB  - harboured blaOXA-181 and was assigned to sequence type ST147. Analysis from whole
AB  - genome sequencing revealed a very high sequence similarity to the previously
AB  - sequenced pan-resistant K. pneumoniae isolate MS6671 from the United Arab
AB  - Emirates. The two isolates are very closely related with only 46 chromosomal
AB  - nucleotide differences, 14 indels and differences in plasmid content. Both carry
AB  - a substantial number of plasmid-borne and chromosomally encoded resistance
AB  - determinants. Interestingly, the two differences in susceptibility between the
AB  - isolates could be attributed to DA48896 lacking an insertion of blaOXA-181 into
AB  - the mgrB gene that results in colistin resistance in MS6671 and SNPs affecting
AB  - AcrAB efflux pump expression likely to result in tigecycline resistance. These
AB  - differences between the otherwise very similar isolates indicate that strong
AB  - selection has occurred for resistance towards these last-resort drugs and
AB  - illustrates the trajectory of resistance evolution of OXA-181-producing versions
AB  - of the ST147 international risk clone.
ER  -

TY  - JOUR
AU  - Nahon, E.
AU  - Raveh, D.
TI  - Targeting a truncated Ho-endonuclease of yeast to novel DNA sites with foreign zinc fingers.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1233
EP  - 1239
VL  - 26
AB  - Ho-endonuclease of the yeast, Saccharomyces cerevisiae, initiates a mating type switch by
AB  - making a site-specific double strand break in the mating type gene, MAT.  Ho is a dodecamer
AB  - endonuclease and shares six of the seven intein motifs with PI-SceI endonuclease, an intein
AB  - encoded by the VMAI gene.  We show that a 113 residue truncated Ho-endonuclease starting at
AB  - intein motif C initiates a mating type switch in yeast.  Ho is the only dodecamer endonuclease
AB  - with zinc finers.  To see whether they have a role in determining site specificity we
AB  - exchanged them for zinc fingers of the yeast transcription factor, Swi5.  A chimeric
AB  - endonuclease comprising the dodecamer motifs of Ho (C-E) and the zinc finger domain of Swi5
AB  - cleaves a Swi5 substrate plasmid in vivo.  A similar chimera with the zinc fingers of Sp1
AB  - cleaves a GC box rich substrate plasmid.  These experiments delineate a catalytic fragment of
AB  - Ho-endonuclease that can be fused to various DNA binding moieties in the design of chimeric
AB  - endonucleases with new site specificities.
ER  -

TY  - JOUR
AU  - Naidoo, S.
AU  - Featherston, J.
AU  - Gray, V.M.
TI  - Draft Whole-Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus khoisanae Strain MCB.
JO  - Genome Announcements
PY  - 2015
SP  - e00872
EP  - e00815
VL  - 3
AB  - We report here the draft genome sequence of Xenorhabdus khoisanae strain MCB, a Gram-negative
AB  - bacterium and symbiont of a Steinernema entomopathogenic nematode.
AB  - The genome assembly consists of 266 contigs covering 4.68 Mb. Genome annotation
AB  - revealed 3,869 protein-coding sequences, with a G+C content of 43.5%.
ER  -

TY  - JOUR
AU  - Naidoo, S.
AU  - Mothupi, B.
AU  - Featherston, J.
AU  - Mpangase, P.T.
AU  - Gray, V.M.
TI  - Draft Genome Sequence and Assembly of Photorhabdus heterorhabditis Strain VMG, a  Bacterial Symbiont Associated with the Entomopathogenic Nematode Heterorhabditis   zealandica.
JO  - Genome Announcements
PY  - 2015
SP  - e01279
EP  - e01215
VL  - 3
AB  - Here, we report the draft genome sequence of Photorhabdus heterorhabditis strain  VMG, a
AB  - symbiont of the entomopathogenic nematode Heterorhabditis zealandica in
AB  - South Africa. The draft genome sequence is 4,878,919 bp long and contains 4,023
AB  - protein-coding genes. The genome assembly contains 262 contigs with a G+C content
AB  - of 42.22%.
ER  -

TY  - JOUR
AU  - Nair, D.
AU  - Memmi, G.
AU  - Hernandez, D.
AU  - Bard, J.
AU  - Beaume, M.
AU  - Gill, S.
AU  - Francois, P.
AU  - Cheung, A.L.
TI  - Whole genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that  affect not only virulence factors but also the fitness of the strain.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2332
EP  - 2335
VL  - 193
AB  - S. aureus RN4220, a cloning intermediate, is sometimes used in virulence, resistance and
AB  - metabolic studies. Using whole genome sequencing, we showed that RN4220 differs from NCTC8325
AB  - and contains a number of genetic polymorphisms that affect both virulence and general fitness,
AB  - thus implying caution in using this strain for these studies.
ER  -

TY  - JOUR
AU  - Naito, M.
AU  - Hirakawa, H.
AU  - Yamashita, A.
AU  - Ohara, N.
AU  - Shoji, M.
AU  - Yukitake, H.
AU  - Nakayama, K.
AU  - Toh, H.
AU  - Yoshimura, F.
AU  - Kuhara, S.
AU  - Hattori, M.
AU  - Hayashi, T.
AU  - Nakayama, K.
TI  - Genome sequence determination of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis.
JO  - DNA Res.
PY  - 2008
SP  - 215
EP  - 225
VL  - 15
AB  - The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of
AB  - chronic periodontitis. Porphyromonas gingivalis strains
AB  - have been classified into virulent and less-virulent strains by mouse
AB  - subcutaneous soft tissue abscess model analysis. Here, we present the
AB  - whole genome sequence of P. gingivalis ATCC 33277, which is classified as
AB  - a less-virulent strain. We identified 2090 protein-coding sequences
AB  - (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By
AB  - genomic comparison with the virulent strain W83, we identified 461 ATCC
AB  - 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements
AB  - were observed between the two strains: 175 regions in which genomic
AB  - rearrangements have occurred were identified. Thirty-five of those genomic
AB  - rearrangements were inversion or translocation and 140 were simple
AB  - insertion, deletion, or replacement. Both strains contained large numbers
AB  - of mobile elements, such as insertion sequences, miniature inverted-repeat
AB  - transposable elements (MITEs), and conjugative transposons, which are
AB  - frequently associated with genomic rearrangements. These findings indicate
AB  - that the mobile genetic elements have been deeply involved in the
AB  - extensive genome rearrangement of P. gingivalis and the occurrence of many
AB  - of the strain-specific CDSs. We also describe here a very unique feature
AB  - of MITE400, which we renamed MITEPgRS (MITE of P. gingivalis with
AB  - Repeating Sequences).
ER  -

TY  - JOUR
AU  - Naito, M.
AU  - Ogura, Y.
AU  - Itoh, T.
AU  - Shoji, M.
AU  - Okamoto, M.
AU  - Hayashi, T.
AU  - Nakayama, K.
TI  - The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and a novel Prevotella-lineage-specific repeat.
JO  - DNA Res.
PY  - 2015
SP  - dsv032
EP  - dsv032
VL  - 0
AB  - Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we
AB  - present the complete genome sequence of a clinical strain, OMA14, of
AB  - this bacterium along with the results of comparative genome analysis with strain
AB  - 17 of the same species whose genome has also been sequenced, but not fully
AB  - analysed yet. The genomes of both strains consist of two circular chromosomes:
AB  - the larger chromosomes are similar in size and exhibit a high overall linearity
AB  - of gene organizations, whereas the smaller chromosomes show a significant size
AB  - variation and have undergone remarkable genome rearrangements. Unique features of
AB  - the Pre. intermedia genomes are the presence of a remarkable number of essential
AB  - genes on the second chromosomes and the abundance of conjugative and mobilizable
AB  - transposons (CTns and MTns). The CTns/MTns are particularly abundant in the
AB  - second chromosomes, involved in its extensive genome rearrangement, and have
AB  - introduced a number of strain-specific genes into each strain. We also found a
AB  - novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia
AB  - and are specifically distributed among the Pre. intermedia-related species. These
AB  - findings expand our understanding of the genetic features of Pre. intermedia and
AB  - the roles of CTns and MTns in the evolution of bacteria.
ER  -

TY  - JOUR
AU  - Naito, T.
AU  - Kobayashi, I.
TI  - Cell death programmed by selfish genes -- or, why are there restriction enzymes?
JO  - Jikken Igaku
PY  - 1995
SP  - 1444
EP  - 1447
VL  - 13
ER  -

TY  - JOUR
AU  - Naito, T.
AU  - Kusano, K.
AU  - Kobayashi, I.
TI  - Selfish behavior of restriction-modification systems.
JO  - Science
PY  - 1995
SP  - 897
EP  - 899
VL  - 267
AB  - Plasmids carrying gene pairs encoding type II DNA restriction endonucleases and their cognate
AB  - modification enzymes were shown to have increased stability in Escherichia coli. The
AB  - descendants of cells that had lost these genes appeared unable to modify a sufficient number
AB  - of recognition sites in their chromosomes to protect them from lethal attack by the remaining
AB  - restriction enzyme molecules. The capacity of these genes to act as a selfish symbiont is
AB  - likely to have contributed to the evolution of restriction-modification gene pairs.
ER  -

TY  - JOUR
AU  - Naito, Y.
AU  - Naito, T.
AU  - Kobayashi, I.
TI  - Selfish restriction modification genes: Resistance of a resident R/M plasmid to displacement by an incompatible plasmid mediated by host killing.
JO  - Biol. Chem.
PY  - 1998
SP  - 429
EP  - 436
VL  - 379
AB  - Previous work from this laboratory demonstrated that plasmids carrying a type II
AB  - restriction-modification gene complex are not easily lost from their bacterial host because
AB  - plasmid-free segregant cells are killed through chromosome cleavage.  Here, we have followed
AB  - the course of events that takes place when an Escherichia coli recBC sbcA strain carrying a
AB  - plasmid coding for the PaeR7I restriction-modification gene complex is transformed by a
AB  - plasmid with an identical origin of replication.  The number of transformants that appeared
AB  - was far fewer than with the restriction-minus (r-) control.  Most of the transformants were
AB  - very small.  After prolonged incubation, the number and the size of the colonies increased,
AB  - but this increase never attained the level of the r- control.  Most of the transformed
AB  - colonies retained the drug-resistance of the resident, r+m+ plasmid.  These results indicate
AB  - that post-segregational host killing occurs when a plasmid bearing an R/M gene complex is
AB  - displaced by an incompatible plasmid.  Such cell killing eliminates the competitor plasmid
AB  - along with the host and, thus, would allow persistence of the R/M plasmid in the neighboring,
AB  - clonal host cells in nature.  This phenomenon is reminiscent of mammalian apoptosis and other
AB  - forms of altruistic cell death strategy against infection.  This type of resistance to
AB  - displacement was also studied in a wild type Escherichia coli strain that was normal for
AB  - homologous recombination.  A number of differences between the recBC sbcA strain and the rec+
AB  - strain were observed and these will be discussed.
ER  -

TY  - JOUR
AU  - Najah, S.
AU  - Chong, T.M.
AU  - Gerbaud, C.
AU  - Chan, K.G.
AU  - Mellouli, L.
AU  - Pernodet, J.L.
TI  - Complete Genome Sequence of Streptomyces sp. TN58, a Producer of Acyl Alpha-l-Rhamnopyranosides.
JO  - Genome Announcements
PY  - 2017
SP  - e00828
EP  - e00817
VL  - 5
AB  - Streptomyces sp. TN58, isolated from a Tunisian soil sample, produces several natural
AB  - products, including acyl alpha-l-rhamnopyranosides. It possesses a 7.6-Mb
AB  - linear chromosome. This is, to our knowledge, the first genome sequence of a
AB  - microorganism known to produce acyl alpha-l-rhamnopyranosides, and it will be
AB  - helpful to study the biosynthesis of these specialized metabolites.
ER  -

TY  - JOUR
AU  - Najera-Hernandez, S.
AU  - Sanchez-Alonso, M.P.
AU  - Anastacio-Marcelino, E.
AU  - Negrete-Abascal, E.
AU  - Vazquez-Cruz, C.
TI  - Draft Genome Sequence of Escherichia coli Strain SN137, a Bacterium with Extracellular Proteolytic Activity on Immunoglobulins and Persistence in Human  Tissue Blood.
JO  - Genome Announcements
PY  - 2018
SP  - e01455
EP  - e01417
VL  - 6
AB  - The draft genome sequence of Escherichia coli strain SN137 is reported here. The  genome
AB  - comprises 172 contigs, corresponding to 4.9 Mb with 50% G+C content, and
AB  - contains several genes related to pathogenicity that explain its survival in
AB  - human hematic tissue.
ER  -

TY  - JOUR
AU  - Naka, H.
AU  - Dias, G.M.
AU  - Thompson, C.C.
AU  - Dubay, C.
AU  - Thompson, F.L.
AU  - Crossa, J.H.
TI  - Complete genome sequence of the marine fish pathogen Vibrio anguillarum harboring the pJM1 virulence plasmid and genomic comparison with other virulent strans of V. anguillarum and V. ordalii.
JO  - Infect. Immun.
PY  - 2011
SP  - 2889
EP  - 2900
VL  - 79
AB  - We dissected the complete genome sequence of the O1 serotype strain Vibrio anguillarum
AB  - 775(pJM1) and determined the draft genomic sequences of plasmidless strains of serotype O1
AB  - (strain 96F) and O2B (strain RV22) and V. ordalii. All strains harbor two chromosomes, but 775
AB  - also harbors the virulence plasmid pJM1, which carries the anguibactin-producing and cognate
AB  - transport genes, one of the main virulence factors of V. anguillarum. Genomic analysis
AB  - identified eight genomic islands in chromosome 1 of V. anguillarum 775(pJM1) and two in
AB  - chromosome 2. Some of them carried potential virulence genes for the biosynthesis of O
AB  - antigens, hemolysins, and exonucleases as well as others for sugar transport and metabolism.
AB  - The majority of genes for essential cell functions and pathogenicity are located on chromosome
AB  - 1. In contrast, chromosome 2 contains a larger fraction (59%) of hypothetical genes than does
AB  - chromosome 1 (42%). Chromosome 2 also harbors a superintegron, as well as host "addiction"
AB  - genes that are typically found on plasmids. Unique distinctive properties include homologues
AB  - of type III secretion system genes in 96F, homologues of V. cholerae zot and ace toxin genes
AB  - in RV22, and the biofilm formation syp genes in V. ordalii. Mobile genetic elements, some of
AB  - them possibly originated in the pJM1 plasmid, were very abundant in 775, resulting in the
AB  - silencing of specific genes, with only few insertions in the 96F and RV22 chromosomes.
ER  -

TY  - JOUR
AU  - Nakagawa, K.-I.
AU  - Hashikawa, J.-I.
AU  - Makino, O.
AU  - Ando, T.
AU  - Shibata, T.
TI  - Subunit structure of a yeast site-specific endodeoxyribonuclease, endoSceI.  A study using monoclonal antibodies.
JO  - Eur. J. Biochem.
PY  - 1988
SP  - 23
EP  - 23
VL  - 171
AB  - EndoSceI is a eucaryotic site-specific endoDNase of 120 kDa that causes
AB  - double-stranded scission at well-defined sites, but is distinguishable from
AB  - procaryotic restriction endonucleases by its mode of sequence recognition and
AB  - lack of related specific DNA modification.  In purified preparations of
AB  - endoSceI, only two polypeptide species of 75 kDa (75-kDa peptide) and 50 kDa
AB  - (50-kDa peptide) are detected in apparently equal amounts.  We prepared mouse
AB  - monoclonal IgGs that bound specifically to the 75-kDa peptide (but not the
AB  - 50-kDa peptide) without inhibiting the endoSceI activity.  Immunoprecipitation
AB  - experiments with these IgGs revealed that the 75-kDa peptide and the 50-kDa
AB  - peptide are physically associated with each other and with the endonucleolytic
AB  - activity.  Full endoSceI activity was recovered by mixing the purified 75-kDa
AB  - peptide and the partially purified 50-kDa peptide, each of which exhibited
AB  - little or no endonuclease activity alone.  These observations indicate that
AB  - endoSceI consists of two non-identical subunits of 75 kDa and 50 kDa, and that
AB  - both subunits are required for full enzyme activity.
ER  -

TY  - JOUR
AU  - Nakagawa, K.-I.
AU  - Morishima, N.
AU  - Shibata, T.
TI  - An endonuclease with multiple cutting sites, Endo.SceI, initiates genetic recombination at its cutting site in yeast mitochondria.
JO  - EMBO J.
PY  - 1992
SP  - 2707
EP  - 2715
VL  - 11
AB  - Endo.SceI is a mitochondrial sequence-specific endonuclease which has multiple cutting sites.
AB  - In order to examine the possible role of Endo.SceI in homologus recombination, we analyzed the
AB  - mode of recombination upon mating using antibiotic resistance markers on the mitochondrial
AB  - genome. The segregation of a marker located very close to one of the Endo.SceI cutting sites
AB  - showed a disparity (polarized segregation, i.e. gene conversion). This gene conversion
AB  - depended on the presence of the functional Endo.SceI gene. In vivo cutting of mitochondrial
AB  - DNA upon mating was detected at the cutting site in the antibiotic marker region, which also
AB  - depended on the Endo.SceI activity. These results suggest that mitochrondrial recombination is
AB  - induced by cleavage of mitochondrial DNA by this sequence-specific endonuclease. This is the
AB  - first demonstration that a sequence-specific endonuclease with multiple cutting sites induces
AB  - genetic recombination.
ER  -

TY  - JOUR
AU  - Nakagawa, K.-I.
AU  - Morishima, N.
AU  - Shibata, T.
TI  - A maturase-like subunit of the sequence-specific endonuclease Endo.SceI from yeast mitochondria.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 1977
EP  - 1984
VL  - 266
AB  - Some yeast strains possess a sequence-specific endonuclease, Endo.SceI, which is a
AB  - heterodimeric enzyme localized in mitochondria.  The larger subunit (75 kDa) of Endo.SceI,
AB  - encoded by a nuclear gene (ENS1), is transported from the cytosol into the mitochondria.  In
AB  - this study, we determined the partial amino acid sequence of the smaller subunit (50 kDa) of
AB  - Endo.SceI.  The determined sequence matched well the partial sequence deduced from a
AB  - mitochondrial open reading frame (RF3).  The RF3 locus is known to exhibit polymorphism since
AB  - this reading frame in some yeast strains is supposed to encode a maturase-like protein,
AB  - whereas in other strains, the frame is interrupted by GC clusters, which thus break the frame.
AB  - Southern blot analysis of various yeast strains showed that the continuity of RF3 is
AB  - correlated with the presence of Endo.SceI activity.  These data indicate that the continuous
AB  - RF3 sequence is a functional gene (ENS2) coding for the smaller subunit of Endo.SceI.  The
AB  - results of cytoduction, by which the continuous RF3 sequence was transferred into a yeast
AB  - strain lacking mitochondrial DNA, confirmed this conclusion.  This study suggests the
AB  - involvement of Endo.SceI in genetic recombination of mitochondrial DNA.
ER  -

TY  - JOUR
AU  - Nakagawa, S.
AU  - Shimamura, S.
AU  - Takaki, Y.
AU  - Suzuki, Y.
AU  - Murakami, S.
AU  - Watanabe, T.
AU  - Fujiyoshi, S.
AU  - Mino, S.
AU  - Sawabe, T.
AU  - Maeda, T.
AU  - Makita, H.
AU  - Nemoto, S.
AU  - Nishimura, S.
AU  - Watanabe, H.
AU  - Watsuji, T.
AU  - Takai, K.
TI  - Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont.
JO  - ISME J.
PY  - 2014
SP  - 40
EP  - 51
VL  - 8
AB  - Deep-sea vents harbor dense populations of various animals that have their specific symbiotic
AB  - bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides
AB  - of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and
AB  - diverse epibionts on the surface of their scales.  In this study, we report the complete
AB  - genome sequencing of gammaproteobacterial endosymbiont.  The endosymbiont genome displays
AB  - features consistent with ongoing genome reduction such as large proportions of pseudogenes and
AB  - insertion elements.  The genome encodes functions commonly found in deep-sea vent
AB  - chemoautotrophs such as sulfur oxidation and carbon fixation.  Stable carbon isotope
AB  - (13C)-labeling experiments confirmed the endosymbiont chemoautotrophy.  The genome also
AB  - includes an intact hydrogenase gene cluster that potentially has been horizontally transferred
AB  - from phylogenetically distant bacteria.  Notable findings include the presence and
AB  - transcription of genes for flagellar assembly, through which proteins are potentially exported
AB  - from bacterium to the host.  Symbionts of snail individuals exhibited extreme genetic
AB  - homogeneity, showing only two synonymous changes in 19 different genes (13810 positions in
AB  - total) determined for 32 individual gastropods collected from a single colony at one time.
AB  - The extremely low genetic individuality in endosymbionts probably reflects that the stringent
AB  - symbiont selection by host prevents the random genetic drift in the small population of
AB  - horizontally transmitted symbiont.  This study is the first complete genome analysis of
AB  - gastropod endosymbiont and offers an opportunity to study genome evolution in a recently
AB  - evolved endosymbiont.
ER  -

TY  - JOUR
AU  - Nakagawa, S.
AU  - Takaki, Y.
AU  - Shimamura, S.
AU  - Reysenbach, A.L.
AU  - Takai, K.
AU  - Horikoshi, K.
TI  - Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 12146
EP  - 12150
VL  - 104
AB  - Deep-sea vents are the light-independent, highly productive ecosystems driven primarily by
AB  - chemolithoautotrophic microorganisms, in particular by
AB  - epsilon-Proteobacteria phylogenetically related to important pathogens. We
AB  - analyzed genomes of two deep-sea vent epsilon-Proteobacteria strains,
AB  - Sulfurovum sp. NBC37-1 and Nitratiruptor sp. SB155-2, which provide
AB  - insights not only into their unusual niche on the seafloor, but also into
AB  - the origins of virulence in their pathogenic relatives, Helicobacter and
AB  - Campylobacter species. The deep-sea vent epsilon-proteobacterial genomes
AB  - encode for multiple systems for respiration, sensing and responding to
AB  - environment, and detoxifying heavy metals, reflecting their adaptation to
AB  - the deep-sea vent environment. Although they are nonpathogenic, both
AB  - deep-sea vent epsilon-Proteobacteria share many virulence genes with
AB  - pathogenic epsilon-Proteobacteria, including genes for virulence factor
AB  - MviN, hemolysin, invasion antigen CiaB, and the N-linked glycosylation
AB  - gene cluster. In addition, some virulence determinants (such as the
AB  - H(2)-uptake hydrogenase) and genomic plasticity of the pathogenic
AB  - descendants appear to have roots in deep-sea vent epsilon-Proteobacteria.
AB  - These provide ecological advantages for hydrothermal vent
AB  - epsilon-Proteobacteria who thrive in their deep-sea habitat and are
AB  - essential for both the efficient colonization and persistent infections of
AB  - their pathogenic relatives. Our comparative genomic analysis suggests that
AB  - there are previously unrecognized evolutionary links between important
AB  - human/animal pathogens and their nonpathogenic, symbiotic,
AB  - chemolithoautotrophic deep-sea relatives.
ER  -

TY  - JOUR
AU  - Nakagawahara, K.
AU  - Mori, M.
AU  - Mioka, C.
TI  - Types and uses of restriction enzymes.
JO  - Rinsho Kensa
PY  - 1996
SP  - 826
EP  - 835
VL  - 40
AB  - A review (in japanese).
ER  -

TY  - JOUR
AU  - Nakahigashi, K.
AU  - Kubo, N.
AU  - Narita, S.
AU  - Shimaoka, T.
AU  - Goto, S.
AU  - Oshima, T.
AU  - Mori, H.
AU  - Maeda, M.
AU  - Wada, C.
AU  - Inokuchi, H.
TI  - HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 1473
EP  - 1478
VL  - 99
AB  - HemK, a universally conserved protein of unknown function, has high amino acid similarity with
AB  - DNA-(adenine-N6) methyl transferases (MTases). A certain mutation in hemK gene rescues the
AB  - photosensitive phenotype of a ferrochelatase-deficient (hemH) mutant in Escherichia coli. A
AB  - hemK knockout strain of E. coli not only suffered severe growth defects, but also showed a
AB  - global shift in gene expression to anaerobic respiration, as determined by microarray
AB  - analysis, and this shift may lead to the abrogation of photosensitivity by reducing the
AB  - oxidative stress. Suppressor mutations that abrogated the growth defects of the hemK knockout
AB  - strain were isolated and shown to be caused by a threonine to alanine change at codon 246 of
AB  - polypeptide chain release factor (RF) 2, indicating that hemK plays a role in translational
AB  - termination. Consistent with such a role, the hemK knockout strain showed an enhanced rate of
AB  - read-through of nonsense codons and induction of transfer-mRNA-mediated tagging of proteins
AB  - within the cell. By analysis of the methylation of RF1 and RF2 in vivo and in vitro, we showed
AB  - that HemK methylates RF1 and RF2 in vitro within the tryptic fragment containing the conserved
AB  - GGQ motif, and that hemK is required for the methylation within the same fragment of, at
AB  - least, RF1 in vivo. This is an example of a protein MTase containing the DNA MTase motif and
AB  - also a protein-(glutamine-N5) MTase.
ER  -

TY  - JOUR
AU  - Nakai, R.
AU  - Fujisawa, T.
AU  - Nakamura, Y.
AU  - Baba, T.
AU  - Nishijima, M.
AU  - Karray, F.
AU  - Sayadi, S.
AU  - Isoda, H.
AU  - Naganuma, T.
AU  - Niki, H.
TI  - Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 90
EP  - 90
VL  - 11
AB  - Oligoflexus tunisiensis Shr3T is the first strain described in the newest (eighth) class
AB  - Oligoflexia of the phylum Proteobacteria. This strain was isolated
AB  - from the 0.2-mum filtrate of a suspension of sand gravels collected in the Sahara
AB  - Desert in the Republic of Tunisia. The genome of O. tunisiensis Shr3T is
AB  - 7,569,109 bp long and consists of one scaffold with a 54.3% G + C content. A
AB  - total of 6,463 genes were predicted, comprising 6,406 protein-coding and 57 RNA
AB  - genes. Genome sequence analysis suggested that strain Shr3T had multiple terminal
AB  - oxidases for aerobic respiration and various transporters, including the
AB  - resistance-nodulation-cell division-type efflux pumps. Additionally, gene
AB  - sequences related to the incomplete denitrification pathway lacking the final
AB  - step to reduce nitrous oxide (N2O) to nitrogen gas (N2) were found in the O.
AB  - tunisiensis Shr3T genome. The results presented herein provide insight into the
AB  - metabolic versatility and N2O-producing activity of Oligoflexus species.
ER  -

TY  - JOUR
AU  - Nakai, R.
AU  - Fujisawa, T.
AU  - Nakamura, Y.
AU  - Nishide, H.
AU  - Uchiyama, I.
AU  - Baba, T.
AU  - Toyoda, A.
AU  - Fujiyama, A.
AU  - Naganuma, T.
AU  - Niki, H.
TI  - Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water.
JO  - Genome Announcements
PY  - 2016
SP  - e00616
EP  - e00616
VL  - 4
AB  - Aurantimicrobium minutum type strain KNC(T) is a planktonic ultramicrobacterium isolated from
AB  - river water in western Japan. Strain KNC(T) has an extremely small, streamlined genome of
AB  - 1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that
AB  - strain KNC(T) has an actinorhodopsin-based photometabolism.
ER  -

TY  - JOUR
AU  - Nakajima, T.
AU  - Matsubara, K.
AU  - Ueno, H.
AU  - Kagawa, S.
AU  - Moore, J.E.
AU  - Millar, B.C.
AU  - Matsuda, M.
TI  - Molecular identification and characterization of type III restriction-modification (R-M) gene cluster in Campylobacter lari.
JO  - Ann. Microbiol. (Paris)
PY  - 2013
SP  - 1629
EP  - 1637
VL  - 63
AB  - Although the human clinical strain of Campylobacter lari (RM2100) has been shown not to carry
AB  - any type III restriction-modification (R-M) systems, an R-M genes cluster was identified
AB  - downstream of the full-length cytolethal distending toxin gene operon in the urease-positive
AB  - thermophilic Campylobacter (UPTC) CF89-12 strain. Two possible open reading frames (ORFs) for
AB  - restriction endonuclease and methyltransferase were predicted to encode peptides of 947 and
AB  - 613 amino acid residues with calculated mo ecular weights of 111 and 70.8 kDa, respectively.
AB  - Two putative promoters consisting of the consensus sequences and two probable ribosome binding
AB  - sites for the two ORFs were also identified. Reverse transcription PCR identified
AB  - co-transcription of the R-M genes in the cells. The existence of an S-adenosyl
AB  - methionine-binding motif in the N-terminal conserved region of the possible ORF for the M
AB  - gene, and seven conserved helicase motifs in the R gene were also identified. PCR and Southern
AB  - blot hybridization a nalyses for type III R-M enzyme genes with some of the C. lari isolates
AB  - including UPTC gave positive signals. UPTC isolates were shown to carry type III R-M enzyme
AB  - genes, with a relatively high frequency.
ER  -

TY  - JOUR
AU  - Nakajima, Y.
AU  - Yoshizawa, S.
AU  - Nakamura, K.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Kogure, K.
TI  - Draft Genome Sequences of Tersicoccus phoenicis DSM 30849T, Isolated from a Cleanroom for Spacecraft Assembly, and Tersicoccus sp. Strain Bi-70, Isolated  from a Freshwater Lake.
JO  - Genome Announcements
PY  - 2017
SP  - e00079
EP  - e00017
VL  - 5
AB  - Here, we report the draft genome sequences of Tersicoccus phoenicis DSM 30849T, isolated from
AB  - a spacecraft assembly cleanroom at the National Aeronautics and
AB  - Space Administration (NASA), and Tersicoccus sp. strain Bi-70, isolated from Lake
AB  - Biwa, the largest lake in Japan. These genome sequences facilitate our
AB  - understanding of the adaptation of these closely related strains to different
AB  - habitats.
ER  -

TY  - JOUR
AU  - Nakajima, Y.
AU  - Yoshizawa, S.
AU  - Park, S.
AU  - Kumagai, Y.
AU  - Wong, S.K.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Kogure, K.
TI  - Draft Genome Sequence of Rubricoccus marinus SG-29T, a Marine Bacterium within the Family Rhodothermaceae, Which Contains Two Different Rhodopsin Genes.
JO  - Genome Announcements
PY  - 2017
SP  - e00990
EP  - e00917
VL  - 5
AB  - Here, we report the draft genome sequence of Rubricoccus marinus SG-29T, a bacterium isolated
AB  - from the western North Pacific Ocean. R. marinus SG-29T
AB  - possesses two different types of rhodopsin genes and belongs to the family
AB  - Rhodothermaceae, with which halophilic, thermophilic, and marine bacteria are
AB  - associated.
ER  -

TY  - JOUR
AU  - Nakamaye, K.L.
AU  - Eckstein, F.
TI  - Inhibition of restriction endonuclease NciI cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 9679
EP  - 9698
VL  - 14
AB  - M13 RF IV DNA where phosphorothioate groups are incorporated at restriction
AB  - endonuclease NciI recognition sites in the (-)strand is efficiently nicked by
AB  - the action of this enzyme.  Incubation of such nicked DNA with exonuclease III
AB  - produces gapped DNA.  The gap can be filled by reaction with deoxynucleoside
AB  - triphosphates and DNA polymerase I.  When this sequence of reactions is
AB  - performed with DNA containing a mismatch oligonucleotide primer in the
AB  - (-)-strand mutational frequencies of 70 - 90% can be obtained upon
AB  - transformation.  The general nature of this methodology has been further shown
AB  - to be applicable to other restriction enzymes such as HindII, PstI and FspI.
AB  - The mutational frequency obtained using these enzymes is between 40 - 80%
AB  - mainly because of less efficient nicking and gapping.  Studies on inhibition of
AB  - NciI cleavage show that in addition to a phosphorothioate group at the position
AB  - of cleavage an additional group in the 5'-neighbouring position is necessary
AB  - for complete inhibition.
ER  -

TY  - JOUR
AU  - Nakamura, S.
AU  - Ikehata, H.
AU  - Ono, T.
TI  - Characteristics of mutations generated through digestion with restriction enzyme and ligation in plasmid DNA.
JO  - Environ. Mol. Mutagen.
PY  - 2001
SP  - 46
EP  - 54
VL  - 38
AB  - Recently, the use of restriction enzymes has been extended to studies in which rare events
AB  - such as mutation and mistakes in DNA repair are
AB  - examined. In these studies, the specificity of restriction enzymes
AB  - becomes critical. To clarify the nature of the rare unexpected events
AB  - occurring in the process of cutting of DNA with restriction enzymes
AB  - then ligating it, we studied the molecular characteristics of
AB  - unexpected plasmid DNAs that were retrieved as mutants of the plasmid
AB  - after transfection to E. coli. The plasmid used was pUR288, containing
AB  - lacZ as a marker of mutation. It was digested with restriction enzymes
AB  - under the conditions recommended by the supplier of the enzymes and
AB  - under the presence of DMSO, which is known to induce star activity of
AB  - the enzymes. Comparisons of mutant frequencies and of nucleotide
AB  - sequences of the mutants found in the different conditions indicated
AB  - that nonspecific endonucleolytic activity similar to that found under
AB  - star activity was present under the recommended conditions and,
AB  - further, was responsible for the creation of deletion-type mutations.
AB  - The frequency of these events ranged from 10^-5 to 10^-3, depending
AB  - on the kind of restriction enzymes analyzed. Although the levels of the
AB  - nonspecificity were not high, they should be considered in assays such
AB  - as mutation and mistakes in DNA repair, where rare events are examined.
ER  -

TY  - JOUR
AU  - Nakamura, T.
AU  - Maeda, Y.
AU  - Oka, T.
AU  - Tabata, H.
AU  - Futai, M.
AU  - Kawai, T.
TI  - Atomic force microscope observation of plasmid deoxyribose nucleic acid with restriction enzyme.
JO  - J. Vac. Sci. Technol. B
PY  - 1999
SP  - 288
EP  - 293
VL  - 17
AB  - We have observed plasmid deoxyribose nucleic acid, in real space images, before and after
AB  - treating with restriction enzyme (PvuII or HincII) using an atomic force microscope.  The
AB  - enzyme is recognized on DNA even in the absence of Mg2+ ions.  In the presence of Mg2+, on the
AB  - other hand, direct evidence was obtained that the enzyme could bind to circular plasmid DNA
AB  - without cutting and cleaved it at the site corresponding to the specificity.  Lengths of the
AB  - DNA fragments observed by AFM were consistent with the values estimated by agarose gel
AB  - electrophoresis.  In addition, as substrates for the AFM observation, rutile TiO2(110) single
AB  - crystal surface was found to be effective in expanding and fixing the DNA molecules as
AB  - straight chains along the stepped surface.
ER  -

TY  - JOUR
AU  - Nakamura, Y. et al.
TI  - Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids.
JO  - DNA Res.
PY  - 2003
SP  - 137
EP  - 145
VL  - 10
AB  - The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC
AB  - 7421 was determined. The genome of G. violaceus
AB  - was a single circular chromosome 4,659,019 bp long with an average GC
AB  - content of 62%. No plasmid was detected. The chromosome comprises 4430
AB  - potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes
AB  - representing 44 tRNA species and genes for tmRNA, B subunit of RNase P,
AB  - SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding
AB  - genes showed sequence similarity to genes of known function, 37% to
AB  - hypothetical genes, and the remaining 22% had no apparent similarity to
AB  - reported genes. Comparison of the assigned gene components with those of
AB  - other cyanobacteria has unveiled distinctive features of the G. violaceus
AB  - genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY,
AB  - PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO,
AB  - PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide
AB  - for phycobilisomes and nblA related to the degradation of phycobilisomes
AB  - were also missing. Potential signal peptides of the presumptive products
AB  - of petJ and petE for soluble electron transfer catalysts were less
AB  - conserved than the remaining portions. These observations may be related
AB  - to the fact that photosynthesis in G. violaceus takes place not in
AB  - thylakoid membranes but in the cytoplasmic membrane. A large number of
AB  - genes for sigma factors and transcription factors in the LuxR, LysR, PadR,
AB  - TetR, and MarR families could be identified, while those for major
AB  - elements for circadian clock, kaiABC were not found. These differences may
AB  - reflect the phylogenetic distance between G. violaceus and other
AB  - cyanobacteria.
ER  -

TY  - JOUR
AU  - Nakamura, Y. et al.
TI  - Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (supplement).
JO  - DNA Res.
PY  - 2002
SP  - 135
EP  - 148
VL  - 9
AB  - none
ER  -

TY  - JOUR
AU  - Nakamura, Y. et al.
TI  - Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1.
JO  - DNA Res.
PY  - 2002
SP  - 123
EP  - 130
VL  - 9
AB  - The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus
AB  - BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no
AB  - plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes,
AB  - 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned
AB  - to the chromosome by similarity search and computer prediction. The translated products of 56%
AB  - of the potential protein-encoding genes showed sequence similarity to experimentally
AB  - identified and predicted proteins of known function, and the products of 34% of these genes
AB  - showed sequence similarity to the translated products of hypothetical genes. The remaining 10%
AB  - lacked significant similarity to genes for predicted proteins in the public DNA databases.
AB  - Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those
AB  - of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were
AB  - unique to this species, indicating a high degree of divergence of the gene information among
AB  - cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence
AB  - of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be
AB  - genomic features of thermophilic strains. A remarkable feature of the genome is the presence
AB  - of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse
AB  - transcriptase. A trace of genome rearrangement mediated by the group II introns was also
AB  - observed.
ER  -

TY  - JOUR
AU  - Nakanishi, M.
AU  - Meirelles, P.
AU  - Suzuki, R.
AU  - Takatani, N.
AU  - Mino, S.
AU  - Suda, W.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Ohkuma, M.
AU  - Hosokawa, M.
AU  - Miyashita, K.
AU  - Thompson, F.L.
AU  - Niwa, A.
AU  - Sawabe, T.
AU  - Sawabe, T.
TI  - Draft Genome Sequences of Marine Flavobacterium Nonlabens Strains NR17, NR24, NR27, NR32, NR33, and Ara13.
JO  - Genome Announcements
PY  - 2014
SP  - e01165
EP  - e01114
VL  - 2
AB  - Here, we present the draft genome sequences of six carotenoid producers affiliated with
AB  - Nonlabens spp. isolated from marine environments in both the
AB  - northern and southern parts of Japan. The genomic information will help to
AB  - elucidate the function and evolution of carotenoid synthetic gene clusters not
AB  - only in the genus Nonlabens but also in the family Flavobacteriaceae.
ER  -

TY  - JOUR
AU  - Nakanishi, S.
AU  - Tazumi, A.
AU  - Moore, J.E.
AU  - Millar, B.C.
AU  - Matsuda, M.
TI  - Molecular and comparative analyses of the full-length cytolethal distending toxin (cdt) gene operon and its adjacent genetic loci from urease-positive thermophilic  Campylobacter (UPTC) organisms.
JO  - Br. J. Biomed. Sci.
PY  - 2010
SP  - 208
EP  - 215
VL  - 67
AB  - Molecular and comparative analyses of the full-length cytolethal distending toxin (cdt) gene
AB  - operon and its adjacent genetic loci (2.7-9.4 kilo base pairs in
AB  - length) are carried out with 12 urease-positive thermophilic Campylobacter (UPTC)
AB  - isolates using several polymerase chain reaction (PCR) primer pairs. Three
AB  - putative open reading frames (ORFs) for cdtA, cdtB and cdtC, two putative
AB  - promoters and a hypothetically intrinsic rho-independent transcription terminator
AB  - were identified in all the operons of the 12 UPTC isolates examined. Although the
AB  - number of amino acid residues slightly varied for the putative cdtA and cdtC
AB  - ORFs, those for the cdtB were similar among all the UPTC isolates, as well as the
AB  - six urease-negative (UN) C. lari examined previously. Regarding the cdt genes in
AB  - UPTC CF89-12, each ORF commenced with an ATG start codon and terminated with a
AB  - TAG stop codon for cdtA and cdtB and a TAA for cdtC. Start and stop codons of the
AB  - three ORFs for the other 11 UPTC isolates were identical to those from the UPTC
AB  - CF89-12 isolate except for the TTG start codon for cdtC in the two isolates
AB  - (NCTC12892 and 12893) and the TGA stop codon for cdtA in five isolates (A1, A2,
AB  - A3, 89049 and 92251). Two putative promoter structures, consisting of sequences
AB  - at the -35-like (TTAATA) and -10-like (TATTAA) regions, as well as the start
AB  - codon (ATG), were identified for the transcriptional promoter, immediately
AB  - upstream of the cdtA gene in all the 12 isolates, Although the genetic
AB  - heterogeneity of the cdtB gene locus occurred in all 28 C. lari isolates (n = 16
AB  - UN C. lari; n = 12 UPTC) examined, all nine amino acid-specific DNase residues
AB  - were completely conserved in all their cdtB genes. Variable gene insertions with
AB  - heterogeneous order and combinations occurred between cdtC and lpxB genes in the
AB  - all UPTC organisms examined.
ER  -

TY  - JOUR
AU  - Nakano, K. et al.
TI  - First Complete Genome Sequence of the Skin-Improving Lactobacillus curvatus Strain FBA2, Isolated from Fermented Vegetables, Determined by PacBio  Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2016
SP  - e00884
EP  - e00816
VL  - 4
AB  - The first complete genome sequence of Lactobacillus curvatus was determined by PacBio RS II.
AB  - The single circular chromosome (1,848,756 bp, G+C content of 42.1%)
AB  - of L. curvatus FBA2, isolated from fermented vegetables, contained low G+C
AB  - regions (26.9% minimum) and 43 sets of >1,000-bp identical sequence pairs. No
AB  - plasmids were detected.
ER  -

TY  - JOUR
AU  - Nakano, K.
AU  - Minami, M.
AU  - Shinzato, M.
AU  - Shimoji, M.
AU  - Ashimine, N.
AU  - Shiroma, A.
AU  - Ohki, S.
AU  - Nakanishi, T.
AU  - Tamotsu, H.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Moriya, N.
AU  - Kimoto-Nira, H.
AU  - Kobayashi, M.
AU  - Hagi, T.
AU  - Nomura, M.
AU  - Suzuki, C.
AU  - Hirano, T.
TI  - Complete Genome Sequence of Lactococcus lactis subsp. lactis G50 with Immunostimulating Activity, Isolated from Napier Grass.
JO  - Genome Announcements
PY  - 2018
SP  - e00069
EP  - e00018
VL  - 6
AB  - Lactococcus lactis subsp. lactis G50 is a strain with immunostimulating activity, isolated
AB  - from Napier grass (Pennisetum purpureum). We determined the complete
AB  - genome sequence of this strain using the PacBio RS II platform. The single
AB  - circular chromosome consists of 2,346,663 bp, with 35.03% G+C content and no
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Nakano, K.
AU  - Terabayashi, Y.
AU  - Shiroma, A.
AU  - Shimoji, M.
AU  - Tamotsu, H.
AU  - Ashimine, N.
AU  - Ohki, S.
AU  - Shinzato, M.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Hirano, T.
TI  - First Complete Genome Sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula  1900 (DSM 50071T), Determined Using PacBio Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e00932
EP  - e00915
VL  - 3
AB  - The first complete genome sequence of the type strain Pseudomonas aeruginosa (Schroeter 1872)
AB  - Migula 1900 (DSM 50071(T)) was determined in a single contig by
AB  - PacBio RS II. The genome (6,317,050 bp, G+C content of 66.52%) contained 10 sets
AB  - of >1,000-bp identical sequence pairs and 183 tandem repeats.
ER  -

TY  - JOUR
AU  - Nakano, K.
AU  - Terabayashi, Y.
AU  - Shiroma, A.
AU  - Shimoji, M.
AU  - Tamotsu, H.
AU  - Ashimine, N.
AU  - Ohki, S.
AU  - Shinzato, M.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Hirano, T.
TI  - First Complete Genome Sequence of Clostridium sporogenes DSM 795T, a Nontoxigenic Surrogate for Clostridium botulinum, Determined Using PacBio Single-Molecule  Real-Time Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e00832
EP  - e00815
VL  - 3
AB  - The first complete genome sequence of Clostridium sporogenes DSM 795(T), a nontoxigenic
AB  - surrogate for Clostridium botulinum, was determined in a single
AB  - contig using the PacBio single-molecule real-time technology. The genome
AB  - (4,142,990 bp; G+C content, 27.98%) included 86 sets of >1,000-bp identical
AB  - sequence pairs and 380 tandem repeats.
ER  -

TY  - JOUR
AU  - Nakano, Y.
AU  - Steward, N.
AU  - Sekine, M.
AU  - Kusano, T.
AU  - Sano, H.
TI  - A tobacco NtMET1 cDNA encoding a DNA methyltransferase: Molecular characterization and abnormal phenotypes of transgenic tobacco plants.
JO  - Plant Cell Physiol.
PY  - 2000
SP  - 448
EP  - 457
VL  - 41
AB  - A cDNA encoding a DNA methyltransferase, with a predicted polypeptide of 1556 amino acid
AB  - residues containing all motifs conserved in this
AB  - enzyme family, was isolated from tobacco plants, and the corresponding
AB  - gene was designated as NtMET1, RNA blot analysis indicated NtMET1
AB  - transcripts to accumulate in dividing tissues of tobacco plants, and
AB  - they could be detected during the S phase in synchronized dividing BY2
AB  - cells. In situ hybridization revealed the transcripts to be localized
AB  - exclusively in actively proliferating tissues around axillary apical
AB  - meristem. In order to ascertain physiological roles, transgenic tobacco
AB  - plants that had the antisense construct were made and examined for
AB  - phenotypes. Methylation levels of genomic DNA from transgenic plants
AB  - significantly decreased in comparison with wild-type levels, and
AB  - distinct phenotypic changes including small leaves, short internodes
AB  - and abnormal flower morphology were noted. Microscopic observation
AB  - revealed that leaf structure differed between transgenic and wild-type
AB  - plants. These results suggest that NtMET1 functions during DNA
AB  - replication, and that DNA methylation plays an important role in plant
AB  - morphogenesis.
ER  -

TY  - JOUR
AU  - Nakao, K.
AU  - Chinen, A.
AU  - Nobusato, A.
AU  - Fujitani, Y.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Relation between restriction modification genes and genome rearrangements suggested from genome sequence comparison within genus  Neisseria.
JO  - Genome Inf. Ser.
PY  - 2001
SP  - 398
EP  - 399
VL  - 12
AB  - Restriction-modification gene complexes, such as EcoRI, encode two enzymatic functions,
AB  - restriction and modification.  A restriction enzyme will recognize a specific sequence in DNA
AB  - and cut the DNA unless it is methylated by a cognate modification enzyme.  RM systems will
AB  - defend bacterial cells by attacking incoming foreign DNA.  It is widely held that bacteria
AB  - have evolved RM systems and maintain them in order to protect their genome from invasion by
AB  - foreign DNA such as bacteriophages and plasmids.
ER  -

TY  - JOUR
AU  - Nakao, R.
AU  - Jongejan, F.
AU  - Sugimoto, C.
TI  - Draft Genome Sequences of Three Strains of Ehrlichia ruminantium, a Tick-Borne Pathogen of Ruminants, Isolated from Zimbabwe, The Gambia, and Ghana.
JO  - Genome Announcements
PY  - 2016
SP  - e00453
EP  - e00416
VL  - 4
AB  - The rickettsial bacterium Ehrlichia ruminantium is the causative pathogen of heartwater in
AB  - ruminants. Here, we report the draft genome sequences of three
AB  - strains of E. ruminantium, namely, the Crystal Springs strain from Zimbabwe, the
AB  - Kerr Seringe strain from The Gambia, and the Sankat 430 strain from Ghana.
ER  -

TY  - JOUR
AU  - Nakashima, N.
AU  - Tamura, T.
TI  - Whole-Genome Sequence of Acetobacter orientalis Strain FAN1, Isolated from Caucasian Yogurt.
JO  - Genome Announcements
PY  - 2018
SP  - e00201
EP  - e00218
VL  - 6
AB  - In traditional Caucasian yogurt, Acetobacter orientalis bacteria play important roles in the
AB  - fermentation of milk in concert with Lactococcus bacteria. In this
AB  - study, an A. orientalis strain, FAN1, was newly isolated from commercially
AB  - available Caucasian yogurt, and its whole-genome sequence was determined,
AB  - identifying two circular DNAs.
ER  -

TY  - JOUR
AU  - Nakatsu, C.H.
AU  - Barabote, R.
AU  - Thompson, S.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Brettin, T.
AU  - Han, C.
AU  - Beasley, F.
AU  - Chen, W.
AU  - Konopka, A.
AU  - Xie, G.
TI  - Complete genome sequence of Arthrobacter sp. strain FB24.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 106
EP  - 116
VL  - 9
AB  - Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in
AB  - the family Micrococcaceae and class Actinobacteria. A number of
AB  - Arthrobacter genome sequences have been completed because of their important role
AB  - in soil, especially bioremediation. This isolate is of special interest because
AB  - it is tolerant to multiple metals and it is extremely resistant to elevated
AB  - concentrations of chromate. The genome consists of a 4,698,945 bp circular
AB  - chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of
AB  - 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function.
AB  - This genome was sequenced as part of the DOE Joint Genome Institute Program.
ER  -

TY  - JOUR
AU  - Nakayama, H.
AU  - Morinaga, Y.
AU  - Nomura, N.
AU  - Nunoura, T.
AU  - Sako, Y.
AU  - Uchida, A.
TI  - An archaeal homing endonuclease I-PogI cleaves at the insertion site of the neighboring intron, which has no nested open reading frame.
JO  - FEBS Lett.
PY  - 2003
SP  - 165
EP  - 170
VL  - 544
AB  - Homing endonucleases (HEs) of the LAGLIDADG family cleave intron/inteinless cognate DNA at, or
AB  - near, the insertion site (IS) of
AB  - their own intron/intein. Here, we describe a notable exception to this
AB  - rule. Two introns, Pog.S1205 (length 32 bp) and Pog.S1213 (664 bp), whose
AB  - ISs are 8 bp apart, exist within the 16S rRNA gene of the archaeon
AB  - Pyrobaculum oguniense. Pog.S1213 harbors a nested open reading frame (ORF)
AB  - encoding a 22 kDa monomeric protein, I-PogI, which contains two LAGLIDADG
AB  - motifs and has optimal DNA cleavage activity at 90 degrees C.
AB  - Intriguingly, I-PogI cleaves the Pog.S1205-less substrate DNA in the
AB  - presence or absence of Pog.S1213. The cleavage site (CS) of I-PogI does
AB  - not coincide with the IS of Pog.S1213 but with that of Pog.S1205. Thus,
AB  - I-PogI activity both promotes the homing of its own intron, Pog.S1213, and
AB  - guarantees co-conversion of the ORF-less intron Pog.S1205.
ER  -

TY  - JOUR
AU  - Nakayama, H.
AU  - Shimamura, T.
AU  - Imagawa, T.
AU  - Shirai, N.
AU  - Itoh, T.
AU  - Sako, Y.
AU  - Miyano, M.
AU  - Sakuraba, H.
AU  - Ohshima, T.
AU  - Nomura, N.
AU  - Tsuge, H.
TI  - Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: Contribution of cross-domain polar networks to thermostability.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 362
EP  - 378
VL  - 365
AB  - A novel LAGLIDADG-type homing endonuclease (HEase), I-TspO61I, from the hyperthermophilic
AB  - archaeon Thermoproteus sp. IC-061 16 S rRNA gene
AB  - (rDNA) intron was characterized with respect to its structure,
AB  - catalytic properties and thermostability. It was found that I-Tsp061I
AB  - is a HEase isoschizomer of the previously described I-PogI and exhibits
AB  - the highest thermostability among the known LAGLIDADG-type HEases.
AB  - Determination of the crystal structure of I-Tsp061I at 2.1 A resolution
AB  - using the multiple isomorphous replacement and anomalous scattering
AB  - method revealed that the overall fold is similar to that of other known
AB  - LAGLIDADG-type HEases, despite little sequence similarity between
AB  - I-TspO61I and those HEases. However, I-Tsp061I contains important
AB  - cross-domain polar networks, unlike its mesophilic counterparts.
AB  - Notably, the polar network Tyr6-Asp104-His180-107O-HOH12-104O-Asn177
AB  - exists across the two packed a-helices containing both the LAGLIDADG
AB  - catalytic motif and the GxxxG hydrophobic helix bundle motif. Another
AB  - important structural feature is the salt-bridge network
AB  - Asp29-Arg31-GIu182 across N and C-terminal domain interface, which
AB  - appears to contribute to the stability of the domain/domain packing. On
AB  - the basis of these structural analyses and extensive mutational
AB  - studies, we conclude that such cross-domain polar networks play key
AB  - roles in stabilizing the catalytic center and domain packing, and
AB  - underlie the hyperthermostability of T-Tsp061I.
ER  -

TY  - JOUR
AU  - Nakayama, K.
AU  - Endo, M.
AU  - Fujitsuka, M.
AU  - Majima, T.
TI  - Monitoring of three distinct structures of restriction enzyme complexes using characteristic fluorescence from site-selectively incorporated solvatochromic probe.
JO  - Photochem. Photobiolog.
PY  - 2007
SP  - 836
EP  - 841
VL  - 6
AB  - The local change in the three different structures of restriction enzyme BamHI, which include
AB  - DNA-free dimer and non-specific and
AB  - specific complexes with DNA, were detected by the fluorescence from a
AB  - site-selectively introduced solvatochromic fluorophore
AB  - N-beta-L-alanyl-5-(N,N-dimethylamino)naphthalene-1-sulfonamide
AB  - (DanAla). According to the crystal structure, alpha-helices of the
AB  - non-specific complex containing Ile82, Glu86 and Trp206 residues are
AB  - converted into random coil by the formation of specific complex with a
AB  - substrate. To understand the microenvironmental change caused by the
AB  - structural transition around these positions, the DanAla probe was
AB  - site-specifically introduced into the positions, and steady-state and
AB  - time-resolved fluorescence was observed. The steady-state fluorescence
AB  - gave us information that the rigidity of the polypeptide chains would
AB  - be enhanced by the formation of the specific complex. The time-resolved
AB  - fluorescence supported that the change in a water molecule-accessible
AB  - space was induced by DNA-binding. We revealed that the change in
AB  - rigidity and solvation around the specific positions was detected by
AB  - the characteristic fluorescence using the combination of steady-state
AB  - and time-resolved fluorescence techniques.
ER  -

TY  - JOUR
AU  - Nakayama, K.
AU  - Endo, M.
AU  - Majima, T.
TI  - Photochemical regulation of the activity of a restriction enzyme BamHI using an azobenzene moiety incorporated into the dimer interface.
JO  - ACS Abstracts
PY  - 2005
SP  - U399
EP  - U400
VL  - 229
AB  - We describe the control of enzymatic activity by photochemical regulation of protein-protein
AB  - interaction.  Restriction enzyme BamHI has a typical dimer interface with salt-bridge network
AB  - and need the dimer formation to show the activity.  Using this enzyme, we designed the
AB  - photochemically controllable BamHI, which has a photofunctional molecule in the dimer
AB  - interface for inactivation, and initiates the activity with photoirradiation (366 nm).
AB  - Photoisomerizable trans-phenylazophenylalanine (trans-azoAla) was site-selectively introduced
AB  - at 132 position in the dimer interface.  The photofunctional BamHI showed no activity, and the
AB  - following photoisomerization induced the activity.  These results suggest that, the bulky
AB  - trans-azoAla may induce the misalignment of the two BamHI monomers as an inactive dimer form,
AB  - while the compact cis-azoAla may allow the specific hydrogen bondings in the dimer interface
AB  - as similar to the wild-type BamHI.  By employing the phosoisomerization of azoAla residue, we
AB  - have successfully constructed photofunctional BamHI which is activated by photoirradiation.
ER  -

TY  - JOUR
AU  - Nakayama, K.
AU  - Endo, M.
AU  - Majima, T.
TI  - A hydrophilic azobenzene-bearing amino acid for photochemical control of a restriction enzyme BamHI.
JO  - Bioconjugate Chem.
PY  - 2005
SP  - 1360
EP  - 1366
VL  - 16
AB  - A novel hydrophilic and negatively charged azobenzene-bearing amino acid,
AB  - 4'-carboxyphenylazophenylalanine (azoAla 1), has been designed
AB  - and synthesized for investigation of the photochemical regulation of
AB  - the enzyme activity. The properties of photoisomerization and thermal
AB  - stability of the cis-isomer were similar to those of a commonly used
AB  - phenylazophenylalanine (azoAla 2). For photochemical control of the
AB  - enzyme, these two azobenzene-bearing amino acids were incorporated into
AB  - the specific position at the dimer interface of a restriction enzyme
AB  - BamHI. These trans-azobenzene derivatives in the BamHI suppressed the
AB  - enzymatic activity, and the following photoirradiation at 366 nm
AB  - induced the recovery of its activity. Although the activities of both
AB  - azoAla-BamHI mutants were same level after a long time irradiation, the
AB  - recovery of the activity of azoAla 1-BamHI was faster than that of
AB  - azoAla 2-BamHI with a short time irradiation. This result suggests that
AB  - the negatively charged carboxylate group introduced into an azobenzene
AB  - moiety affects the behavior of azoAla in the protein scaffold during
AB  - the trans-cis photoisomerization.
ER  -

TY  - JOUR
AU  - Nakayama, K.
AU  - Yamashita, A.
AU  - Kurokawa, K.
AU  - Morimoto, T.
AU  - Ogawa, M.
AU  - Fukuhara, M.
AU  - Urakami, H.
AU  - Ohnishi, M.
AU  - Uchiyama, I.
AU  - Ogura, Y.
AU  - Ooka, T.
AU  - Oshima, K.
AU  - Tamura, A.
AU  - Hattori, M.
AU  - Hayashi, T.
TI  - The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During  Reductive Genome Evolution.
JO  - DNA Res.
PY  - 2008
SP  - 185
EP  - 199
VL  - 15
AB  - Scrub typhus ('Tsutsugamushi' disease in Japanese) is a mite-borne infectious disease. The
AB  - causative agent is Orientia tsutsugamushi, an
AB  - obligate intracellular bacterium belonging to the family Rickettsiaceae of
AB  - the subdivision alpha-Proteobacteria. In this study, we determined the
AB  - complete genome sequence of O. tsutsugamushi strain Ikeda, which comprises
AB  - a single chromosome of 2 008 987 bp and contains 1967 protein coding
AB  - sequences (CDSs). The chromosome is much larger than those of other
AB  - members of Rickettsiaceae, and 46.7% of the sequence was occupied by
AB  - repetitive sequences derived from an integrative and conjugative element,
AB  - 10 types of transposable elements, and seven types of short repeats of
AB  - unknown origins. The massive amplification and degradation of these
AB  - elements have generated a huge number of repeated genes (1196 CDSs,
AB  - categorized into 85 families), many of which are pseudogenes (766 CDSs),
AB  - and also induced intensive genome shuffling. By comparing the gene content
AB  - with those of other family members of Rickettsiacea, we identified the
AB  - core gene set of the family Rickettsiaceae and found that, while much more
AB  - extensive gene loss has taken place among the housekeeping genes of
AB  - Orientia than those of Rickettsia, O. tsutsugamushi has acquired a large
AB  - number of foreign genes. The O. tsutsugamushi genome sequence is thus a
AB  - prominent example of the high plasticity of bacterial genomes, and
AB  - provides the genetic basis for a better understanding of the biology of O.
AB  - tsutsugamushi and the pathogenesis of 'Tsutsugamushi' disease.
ER  -

TY  - JOUR
AU  - Nakayama, T.
AU  - Inagaki, Y.
TI  - Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.
JO  - Sci. Rep.
PY  - 2017
SP  - 13075
EP  - 13075
VL  - 7
AB  - Organelle acquisitions via endosymbioses with prokaryotes were milestones in the
AB  - evolution of eukaryotes. Still, quite a few uncertainties have remained for the
AB  - evolution in the early stage of organellogenesis. In this respect, rhopalodiacean
AB  - diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies,
AB  - are emerging as new models for the study of organellogenesis. The genome for the
AB  - spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its
AB  - unique metabolic nature lacking the photosynthetic ability. Nevertheless, the
AB  - genome sequence of a spheroid body from a single lineage may not be sufficient to
AB  - depict the evolution of these cyanobacterium-derived intracellular structures as
AB  - a whole. Here, we report on the complete genome for the spheroid body of
AB  - Rhopalodia gibberula, a lineage distinct from E. turgida, of which genome has
AB  - been fully determined. Overall, features in genome structure and metabolic
AB  - capacity, including a lack of photosynthetic ability, were highly conserved
AB  - between the two spheroid bodies. However, our comparative genomic analyses
AB  - revealed that the genome of the R. gibberula spheroid body exhibits a lower
AB  - non-synonymous substitution rate and a slower progression of pseudogenisation
AB  - than those of E. turgida, suggesting that a certain degree of diversity exists
AB  - amongst the genomes of obligate endosymbionts in unicellular eukaryotes.
ER  -

TY  - JOUR
AU  - Nakayama, T.
AU  - Kamikawa, R.
AU  - Tanifuji, G.
AU  - Kashiyama, Y.
AU  - Ohkouchi, N.
AU  - Archibald, J.M.
AU  - Inagaki, Y.
TI  - Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - 11407
EP  - 11412
VL  - 111
AB  - The evolution of mitochondria and plastids from bacterial endosymbionts were key
AB  - events in the origin and diversification of eukaryotic cells. Although the
AB  - ancient nature of these organelles makes it difficult to understand the earliest
AB  - events that led to their establishment, the study of eukaryotic cells with
AB  - recently evolved obligate endosymbiotic bacteria has the potential to provide
AB  - important insight into the transformation of endosymbionts into organelles.
AB  - Diatoms belonging to the family Rhopalodiaceae and their endosymbionts of
AB  - cyanobacterial origin (i.e., "spheroid bodies") are emerging as a useful model
AB  - system in this regard. The spheroid bodies, which appear to enable rhopalodiacean
AB  - diatoms to use gaseous nitrogen, became established after the divergence of
AB  - extant diatom families. Here we report what is, to our knowledge, the first
AB  - complete genome sequence of a spheroid body, that of the rhopalodiacean diatom
AB  - Epithemia turgida. The E. turgida spheroid body (EtSB) genome was found to
AB  - possess a gene set for nitrogen fixation, as anticipated, but is reduced in size
AB  - and gene repertoire compared with the genomes of their closest known free-living
AB  - relatives. The presence of numerous pseudogenes in the EtSB genome suggests that
AB  - genome reduction is ongoing. Most strikingly, our genomic data convincingly show
AB  - that the EtSB has lost photosynthetic ability and is metabolically dependent on
AB  - its host cell, unprecedented characteristics among cyanobacteria, and
AB  - cyanobacterial symbionts. The diatom-spheroid body endosymbiosis is thus a unique
AB  - system for investigating the processes underlying the integration of a bacterial
AB  - endosymbiont into eukaryotic cells.
ER  -

TY  - JOUR
AU  - Nakayama, Y.
AU  - Kobayashi, I.
TI  - Restriction-modification gene complexes as selfish gene entities: roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 6442
EP  - 6447
VL  - 95
AB  - We have reported some type II restriction-modification gene complexes on plasmids resist
AB  - displacement by an incompatible plasmid through postsegregational host killing.  Such selfish
AB  - behavior may have contributed to the spread and maintenance of RM systems.  Here we analyze
AB  - the role of regulatory genes, often found linked to RM gene complexes, in their interaction
AB  - with the host and the other RM gene complexes.  We identified the C gene of EcoRV as a
AB  - positive regulator of restriction.  A C mutation eliminated postsegregational killing by
AB  - EcoRV.  The C system has been proposed to allow establishment of RM systems in new hosts by
AB  - delaying the appearance of restriction activity.  Consistent with this proposal, bacteria
AB  - pre-expressing ecoRVC were transformed at a reduced efficiency by plasmids carrying the EcoRV
AB  - RM gene complex.  Cells carrying the BamHI RM gene complex were transformed at a reduced
AB  - efficiency by a plasmid carrying a PvuII RM gene complex, which shares the same C specificity.
AB  - The reduction most likely was caused by chromosome cleavage at unmodified PvuII sites by
AB  - prematurely expressed PvuII restriction enzyme.  Therefore, association of the C genes of the
AB  - same specificity with RM gene complexes of different sequence specificities can confer on a
AB  - resident RM gene complex the capacity to abort establishment of a second, incoming RM gene
AB  - complex.  This phenomenon, termed "apoptotic mutual exclusion," is reminiscent of suicidal
AB  - defense against virus infection programmed by other selfish elements.  PvuIIC and bamHIC genes
AB  - define one incompatibility group of exclusion whereas ecoRVC gene defines another.
ER  -

TY  - JOUR
AU  - Nakayashiki, T.
AU  - Nishimura, K.
AU  - Inokuchi, H.
TI  - Cloning and sequencing of a previously unidentified gene that is involved in the biosynthesis of heme in Escherichia coli.
JO  - Gene
PY  - 1995
SP  - 67
EP  - 70
VL  - 153
AB  - We have isolated a number of porphyrin (Por)-synthesis mutants as light-resistant revertants
AB  - of a light-sensitive strain delta visA (hemH) of Escherichia coli that accumulates protoPor IX
AB  - in the cell.  Among such mutants, we found a double mutant (H103) with mutations in hemA and
AB  - in a new gene downstream of hemA. This new gene, designated hemK, was located at 27 min on the
AB  - linkage map of the E. coli chromosome. By nucleotide (nt) sequencing, it was demonstrated that
AB  - hemK forms part of the hemA-prfA-hemK operon and encodes 225 amino acids that show no
AB  - significant homology to any protein in the standard databases. The mutant strain H103 formed
AB  - small colonies and showed no catalase activity even in the presence of 5-aminolevulinic acid
AB  - (ALA), indicating its inability to catalyze a step in the biosynthesis of heme from ALA. An
AB  - extract of H103 cells has readily detectable ALA dehydratase and porphobilinogen deaminase
AB  - activities. H103 cells carrying a plasmid that included only hemA as an insert accumulated
AB  - protoPor and coproPor, but showed no sensitivity to light, a result that suggests that it may
AB  - be deficient in protoporphyrinogen oxidase activity.
ER  -

TY  - JOUR
AU  - Nakonieczna, J.
AU  - Kaczorowski, T.
AU  - Obarska-Kosinska, A.
AU  - Bujnicki, J.M.
TI  - Functional Analysis of MmeI from Methanol Utilizer Methylophilus methylotrophus, a Subtype IIC Restriction-Modification Enzyme Related to Type I Enzymes.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 212
EP  - 223
VL  - 75
AB  - MmeI from Methylophilus methylotrophus belongs to the type II restriction-modification
AB  - enzymes. It recognizes an asymmetric DNA
AB  - sequence, 5'-TCCRAC-3' (R indicates G or A), and cuts both strands at
AB  - fixed positions downstream of the specific site. This particular
AB  - feature has been exploited in transcript profiling of complex genomes
AB  - (using serial analysis of gene expression technology). We have shown
AB  - previously that the endonucleolytic activity of MmeI is strongly
AB  - dependent on the presence of S-adenosyl-L-methionine (J. Nakonieczna,
AB  - J. W. Zmijewski, B. Banecki, and A. J. Podhajska, Mol. Biotechnol. 37:
AB  - 127-135, 2007), which puts MmeI in subtype IIG. The same cofactor is
AB  - used by MmeI as a methyl group donor for modification of an adenine in
AB  - the upper strand of the recognition site to N-6-methyladenine. Both
AB  - enzymatic activities reside in a single polypeptide (919 amino acids
AB  - [aa]), which puts MmeI also in subtype IIC of the
AB  - restriction-modification systems. Based on a molecular model, generated
AB  - with the use of bioinformatic tools and validated by site-directed
AB  - mutagenesis, we were able to localize three functional domains in the
AB  - structure of the MmeI enzyme: (i) the N-terminal portion containing the
AB  - endonucleolytic domain with the catalytic Mg2+-binding motif
AB  - D-70-X-9-EXK82, characteristic for the PD-(D/E)XK superfamily of
AB  - nucleases; (ii) a central portion (aa 310 to 610) containing nine
AB  - sequence motifs conserved among N-6-adenine gamma-class DNA
AB  - methyltransferases; (iii) the C-terminal portion (aa 610 to 919)
AB  - containing a putative target recognition domain. Interestingly, all
AB  - three domains showed highest similarity to the corresponding elements
AB  - of type I enzymes rather than to classical type II enzymes. We have
AB  - found that MmeI variants deficient in restriction activity (D70A, E80A,
AB  - and K82A) can bind and methylate specific nucleotide sequence. This
AB  - suggests that domains of MmeI responsible for DNA restriction and
AB  - modification can act independently. Moreover, we have shown that a
AB  - single amino acid residue substitution within the putative target
AB  - recognition domain (S807A) resulted in a MmeI variant with a higher
AB  - endonucleolytic activity than the wild-type enzyme.
ER  -

TY  - JOUR
AU  - Nakonieczna, J.
AU  - Zmijewski, J.W.
AU  - Banecki, B.
AU  - Podhajska, A.J.
TI  - Binding of MmeI restriction-modification enzyme to its specific recognition sequence is stimulated by S-adenosyl-L-methionine.
JO  - Mol. Biotechnol.
PY  - 2007
SP  - 127
EP  - 135
VL  - 37
AB  - Restriction endonucleases serve as a very good model for studying specific protein-DNA
AB  - interaction. MmeI is a very interesting
AB  - restriction endonuclease, but although it is useful in Serial Analysis
AB  - of Gene Expression, still very little is known about the mechanism of
AB  - its interaction with DNA. MmeI is a unique enzyme as besides cleaving
AB  - DNA it also methylates specific sequence. For endonucleolytic activity
AB  - MmeI requires Mg(II) and S-adenosyl-L-methionine (AdoMet). AdoMet is a
AB  - methyl donor in the methylation reaction, but its requirement for DNA
AB  - cleavage remains unclear. In the present article we investigated MmeI
AB  - interaction with DNA with the use of numerous methods. Our
AB  - electrophoretic mobility shift assay revealed formation of two types of
AB  - specific protein-DNA complexes. We speculate that faster migrating
AB  - complex consists of one protein molecule and one DNA fragment whereas,
AB  - slower migrating complex, which appears in the presence of AdoMet, may
AB  - be a dimer or multimer form of MmeI interacting with specific DNA.
AB  - Additionally, using spectrophotometric measurements we showed that in
AB  - the presence of AdoMet, MmeI protein undergoes conformational changes.
AB  - We think that such change in the enzyme structure, upon addition of
AB  - AdoMet, may enhance its specific binding to DNA. In the absence of
AB  - AdoMet MmeI binds DNA to the much lower extent.
ER  -

TY  - JOUR
AU  - Nally, J.E.
AU  - Bayles, D.O.
AU  - Hurley, D.
AU  - Fanning, S.
AU  - McMahon, B.J.
AU  - Arent, Z.
TI  - Complete Genome Sequence of Leptospira alstonii Serovar Room22 Strain GWTS #1.
JO  - Genome Announcements
PY  - 2016
SP  - e01230
EP  - e01216
VL  - 4
AB  - We report here the complete genome sequence of Leptospira alstonii serovar Room22 strain GWTS
AB  - #1. This is the first isolate of L. alstonii to be cultured from a
AB  - mammal and in western Europe, and it represents a new serovar of pathogenic
AB  - leptospires.
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, D.S.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Leuconostoc fallax KCTC 3537.
JO  - J. Bacteriol.
PY  - 2010
SP  - 588
EP  - 589
VL  - 193
AB  - Leuconostoc fallax is known to be present during the manufacturing process of kimchi, the
AB  - best-known traditional Korean dish. Here, we present the
AB  - draft genome sequence of the type strain Leuconostoc fallax KCTC 3537
AB  - (1,638,971 bp, with a G+C content of 37.5%), which consists of 30 large
AB  - contigs (>100 bp in size).
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, D.S.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1014
EP  - 1015
VL  - 193
AB  - Lactobacillus coryniformis subsp. coryniformis is known to be present during the manufacturing
AB  - process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome
AB  - sequence of Lactobacillus coryniformis subsp. coryniformis type strain KCTC 3167 (2,964,752
AB  - bp, with a G+C content of 42.8%), which consists of 55 scaffolds.
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Kim, D.S.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus farciminis KCTC 3681.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1790
EP  - 1791
VL  - 193
AB  - Lactobacillus farciminis is one of the most prevalent lactic acid bacteria present during the
AB  - manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the
AB  - draft genome sequence of the type strain Lactobacillus farciminis KCTC 3681 (2,498,309 bp,
AB  - with a G+C content of 36.4%), which consists of 5 scaffolds.
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Kim, D.S.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus animalis KCTC 3501.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1280
EP  - 1281
VL  - 193
AB  - Lactobacillus animalis is one of the most prevalent lactic acid bacteria present during the
AB  - manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the
AB  - draft genome sequence of the type strain Lactobacillus animalis KCTC 3501 (1,882,795 bp, with
AB  - a G+C content of 41.1%), which consists of 7 scaffolds.
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Leuconostoc argentinum KCTC 3773.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6490
EP  - 6491
VL  - 192
AB  - Leuconostoc argentinum is one of the most prevalent lactic acid bacteria present during the
AB  - manufacturing process of kimchi, the best-known
AB  - traditional Korean dish. Here, we present the draft genome sequence of
AB  - type strain KCTC 3773 of Leuconostoc argentinum (1,720,683 bp, with a G+C
AB  - content of 42.9%), which consists of 98 large contigs (>100 bp in size).
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Kim, D.S.
AU  - Kim, A.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus suebicus KCTC 3549.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5532
EP  - 5533
VL  - 193
AB  - Lactobacillus suebicus is important in the generation of particular flavors and in other
AB  - ripening processes associated with apple mash. Here,
AB  - we present the draft genome sequence of the type strain Lactobacillus
AB  - suebicus KCTC 3549 (2,656,936 bp, with a G+C content of 39.0%), which
AB  - consists of 143 large contigs (>100 bp).
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Lee, K.S.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Kim, D.S.
AU  - Park, H.S.
TI  - Genome Sequence of Lactobacillus fructivorans KCTC 3543.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2111
EP  - 2112
VL  - 194
AB  - Lactobacillus fructivorans is important in the generation of particular flavors and in other
AB  - ripening processes associated with fermented food. Here, we present
AB  - the draft genome sequence of the type strain Lactobacillus fructivorans KCTC 3543
AB  - (1,373,326 bp, with a G+C content of 38.9%), which consists of 5 scaffolds. The
AB  - genome sequence was obtained by using a whole-genome shotgun strategy with Roche
AB  - 454 GS (FLX Titanium) pyrosequencing, and all of the reads were assembled using
AB  - Newbler Assembler 2.3.
ER  -

TY  - JOUR
AU  - Nam, S.H.
AU  - Kim, A.
AU  - Choi, S.H.
AU  - Kang, A.
AU  - Kim, D.W.
AU  - Kim, R.N.
AU  - Kim, D.S.
AU  - Park, H.S.
TI  - Genome Sequence of Leuconostoc carnosum KCTC 3525.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6100
EP  - 6101
VL  - 193
AB  - We announce the draft genome sequence of the type strain Leuconostoc carnosum KCTC 3525
AB  - (3,234,408 bp with a G+C content of 40.9%), one of the
AB  - most prevalent lactic acid bacteria present during the manufacturing
AB  - process of vacuum-packaged meats, which consists of 2,407 large contigs
AB  - (>500 bp in size). The genome sequence was obtained by a whole-genome
AB  - shotgun strategy using Roche 454 GS (FLX Titanium) pyrosequencing, and all
AB  - of the reads were assembled using Newbler Assembler 2.3.
ER  -

TY  - JOUR
AU  - Nam, Y.D.
AU  - Chung, W.H.
AU  - Seo, M.J.
AU  - Lim, S.I.
TI  - Draft Genome Sequence of Staphylococcus vitulinus F1028, a Strain Isolated from a Block of Fermented Soybean.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5961
EP  - 5962
VL  - 194
AB  - Staphylococcus vitulinus is a coagulase-negative staphylococcus in the family
AB  - Staphylococcaceae. This report describes the draft genome sequence of S.
AB  - vitulinus F1028, which was isolated from a traditional Korean soybean food
AB  - (meju). This 2.56-Mbp genome sequence is the first S. vitulinus genome of a
AB  - strain isolated from a fermented soybean product.
ER  -

TY  - JOUR
AU  - Nam, Y.D.
AU  - Chung, W.H.
AU  - Seo, M.J.
AU  - Lim, S.I.
AU  - Yi, S.H.
TI  - Genome Sequence of Staphylococcus lentus F1142, a Strain Isolated from Korean Soybean Paste.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5987
EP  - 5987
VL  - 194
AB  - This report describes the draft genome sequence of Staphylococcus lentus F1142, which was
AB  - isolated from a Korean fermented soybean paste (doenjang). The draft
AB  - genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first
AB  - S. lentus genome to be reported.
ER  -

TY  - JOUR
AU  - Nam, Y.D.
AU  - Lee, H.W.
AU  - Lee, M.
AU  - Yim, K.J.
AU  - Kim, K.N.
AU  - Roh, S.W.
AU  - Kim, D.
TI  - Draft Genome Sequence of Gillisia sp. Strain CBA3202, a Novel Member of the Genus Gillisia, Which Belongs to the Family Flavobacteriaceae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3739
EP  - 3739
VL  - 194
AB  - Gillisia sp. strain CBA3202, which belongs to the family Flavobacteriaceae, was isolated from
AB  - sand of the seashore on Jeju Island, Republic of Korea. The draft
AB  - genome of Gillisia sp. CBA3202 contains 2,981,404 bp with a G+C content of 34.9%.
AB  - This is the second genome sequence of the Gillisia strains.
ER  -

TY  - JOUR
AU  - Nam, Y.D.
AU  - Seo, M.J.
AU  - Lim, S.I.
AU  - Lee, S.Y.
TI  - Genome Sequence of Lysinibacillus boronitolerans F1182, Isolated from a Traditional Korean Fermented Soybean Product.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5988
EP  - 5988
VL  - 194
AB  - Lysinibacillus is a Gram-positive, rod-shaped, and round-spore-forming bacterial  genus of the
AB  - family Bacillaceae. We analyzed the genome sequence of
AB  - Lysinibacillus boronitolerans F1182, isolated from a traditional Korean fermented
AB  - soybean product. The genome sequence contained 4.46 Mbp with a G+C content of
AB  - 37.5%. This is the first report of an L. boronitolerans genome.
ER  -

TY  - JOUR
AU  - Nam, Y.D.
AU  - Seo, M.J.
AU  - Lim, S.I.
AU  - Park, S.L.
TI  - Genome Sequence of Kocuria atrinae C3-8, Isolated from Jeotgal, a Traditional Korean Fermented Seafood.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5996
EP  - 5996
VL  - 194
AB  - Kocuria is a Gram-positive coccus, catalase-positive, coagulase-negative, strictly aerobic
AB  - bacterial genus in the family Micrococcaceae. Kocuria atrinae
AB  - C3-8 was isolated from a traditional Korean fermented seafood. This study
AB  - describes the first genome sequence of K. atrinae strain C3-8, which has a
AB  - 3.19-Mbp genome and a G+C content of 63.8%.
ER  -

TY  - JOUR
AU  - Nambu, T.
AU  - Tsuzukibashi, O.
AU  - Uchibori, S.
AU  - Mashimo, C.
TI  - Complete Genome Sequence of Rothia mucilaginosa Strain NUM-Rm6536, Isolated from  a Human Oral Cavity.
JO  - Genome Announcements
PY  - 2015
SP  - e01122
EP  - e01115
VL  - 3
AB  - Here, we present the complete genome sequence of Rothia mucilaginosa NUM-Rm6536,  a strain
AB  - isolated from the tongue plaque of a healthy human adult. This strain is amenable to genetic
AB  - manipulation by transformation and so provides a useful foundation for more detailed
AB  - investigation of this species.
ER  -

TY  - JOUR
AU  - Nambu, T.
AU  - Tsuzukibashi, O.
AU  - Uchibori, S.
AU  - Yamane, K.
AU  - Yamanaka, T.
AU  - Maruyama, H.
AU  - Wang, P.L.
AU  - Mugita, N.
AU  - Morioka, H.
AU  - Takahashi, K.
AU  - Komasa, Y.
AU  - Mashimo, C.
TI  - Complete Genome Sequence of Rothia aeria Type Strain JCM 11412, Isolated from Air in the Russian Space Laboratory Mir.
JO  - Genome Announcements
PY  - 2016
SP  - e01444
EP  - e01416
VL  - 4
AB  - Here, we present the complete genome sequence of Rothia aeria type strain JCM 11412, isolated
AB  - from air in the Russian space laboratory Mir. Recently, there has
AB  - been an increasing number of reports on infections caused by R. aeria The genomic
AB  - information will enable researchers to identify the pathogenicity of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Nambu, T.
AU  - Yamane, K.
AU  - Maruyama, H.
AU  - Mashimo, C.
AU  - Yamanaka, T.
TI  - Complete Genome Sequence of Prevotella intermedia Strain 17-2.
JO  - Genome Announcements
PY  - 2015
SP  - e00951
EP  - e00915
VL  - 3
AB  - Prevotella intermedia, a Gram-negative black-pigmented anaerobic rod, is frequently isolated
AB  - from not only periodontal pockets but also purulent
AB  - infections. We report here the complete genome sequence of P. intermedia strain
AB  - 17-2, which is a non-exopolysaccharide-producing variant obtained from
AB  - exopolysaccharide (EPS)-producing P. intermedia strain 17 stock culture.
ER  -

TY  - JOUR
AU  - Nan, X.
AU  - Ng, H.-H.
AU  - Johnson, C.A.
AU  - Laherty, C.D.
AU  - Turner, B.M.
AU  - Eisenman, R.N.
AU  - Bird, A.
TI  - Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex.
JO  - Nature
PY  - 1998
SP  - 386
EP  - 389
VL  - 393
AB  - Cytosine residues in the sequence 5'CpG (cytosine-guanine) are often postsynthetically
AB  - methylated in animal genomes.  CpG methylation is involved in long-term silencing of certain
AB  - genes during mammalian development and in repression of viral genomes.  The methyl-CpG-binding
AB  - proteins MeCP1 and MeCP2 interact specifically with methylated DNA and mediate transcriptional
AB  - repression.  Here we study the mechanism of repression by MeCP2, an abundant nuclear protein
AB  - that is essential for mouse embryogenesis.  MeCP2 binds tightly to chromosomes in a
AB  - methylation-dependent manner.  It contains a transcriptional-repression domain that can
AB  - function at a distance in vitro and in vivo.  We show that a region of MeCP2 that localizes
AB  - with the TRD associates with a corepressor complex containing the transcriptional repressor
AB  - mSin3A and histone deacetylases.  Transcriptional repression in vivo is relieved by the
AB  - deacetylase inhibitor trichostatin A, indicating the deacetylation of histones (and/or of
AB  - other proteins) is an essential component of this repression mechanism.  The data suggest that
AB  - two global mechanisms of gene regulation, DNA methylation and histone deacetylation, can be
AB  - linked by MeCP2.
ER  -

TY  - JOUR
AU  - Nancucheo, I.
AU  - Oliveira, R.
AU  - Dall'Agnol, H.
AU  - Johnson, D.B.
AU  - Grail, B.
AU  - Holanda, R.
AU  - Nunes, G.L.
AU  - Cuadros-Orellana, S.
AU  - Oliveira, G.
TI  - Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, 'Acidibacillus ferrooxidans' (SLC66T).
JO  - Genome Announcements
PY  - 2016
SP  - e00383
EP  - e00316
VL  - 4
AB  - Here, we present the draft genome sequence of the type strain of 'Acidibacillus
AB  - ferrooxidans,' a mesophilic, heterotrophic, and acidophilic bacterium that was
AB  - isolated from mine spoilage subjected to accelerated weathering in humidity cell
AB  - tests carried out by the former U.S. Bureau of Mines in Salt Lake City, UT.
ER  -

TY  - JOUR
AU  - Nandasena, K. et al.
TI  - Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 462
EP  - 472
VL  - 9
AB  - Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) was isolated from root nodules of the
AB  - pasture legume Biserrula pelecinus growing in the Mediterranean
AB  - basin. Previous studies have shown this aerobic, motile, Gram negative,
AB  - non-spore-forming rod preferably nodulates B. pelecinus - a legume with many
AB  - beneficial agronomic attributes for sustainable agriculture in Australia. We
AB  - describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271(T)
AB  - consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together
AB  - encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
ER  -

TY  - JOUR
AU  - Nandi, T. et al.
TI  - Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.
JO  - Genome Res.
PY  - 2015
SP  - 129
EP  - 141
VL  - 25
AB  - Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis.
AB  - To investigate population diversity, recombination, and horizontal
AB  - gene transfer in closely related Bp isolates, we performed whole-genome
AB  - sequencing (WGS) on 106 clinical, animal, and environmental strains from a
AB  - restricted Asian locale. Whole-genome phylogenies resolved multiple genomic
AB  - clades of Bp, largely congruent with multilocus sequence typing (MLST). We
AB  - discovered widespread recombination in the Bp core genome, involving hundreds of
AB  - regions associated with multiple haplotypes. Highly recombinant regions exhibited
AB  - functional enrichments that may contribute to virulence. We observed
AB  - clade-specific patterns of recombination and accessory gene exchange, and provide
AB  - evidence that this is likely due to ongoing recombination between clade members.
AB  - Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms
AB  - restricting gene flow between clades. Interrogation of accessory elements
AB  - revealed that each clade harbored a distinct complement of
AB  - restriction-modification (RM) systems, predicted to cause clade-specific patterns
AB  - of DNA methylation. Using methylome sequencing, we confirmed that representative
AB  - strains from separate clades indeed exhibit distinct methylation profiles.
AB  - Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit
AB  - uptake of non-self DNA. Our data suggest that RM systems borne on mobile
AB  - elements, besides preventing foreign DNA invasion, may also contribute to
AB  - limiting exchanges of genetic material between individuals of the same species.
AB  - Genomic clades may thus represent functional units of genetic isolation in Bp,
AB  - modulating intraspecies genetic diversity.
ER  -

TY  - JOUR
AU  - Nannan, C.
AU  - Gillis, A.
AU  - Caulier, S.
AU  - Mahillon, J.
TI  - Complete Genome Sequence of Bacillus velezensis CN026 Exhibiting Antagonistic Activity against Gram-Negative Foodborne Pathogens.
JO  - Genome Announcements
PY  - 2018
SP  - e01543
EP  - e01517
VL  - 6
AB  - We report here the complete genome sequence of Bacillus velezensis strain CN026,  a member of
AB  - the B. subtilis group, which is known for its many industrial
AB  - applications. The genome contains 3,995,812 bp and displays six gene clusters
AB  - potentially involved in strain CN026's activity against Gram-negative foodborne
AB  - pathogens.
ER  -

TY  - JOUR
AU  - Naome, A.
AU  - Maciejewska, M.
AU  - Calusinska, M.
AU  - Martinet, L.
AU  - Anderssen, S.
AU  - Adam, D.
AU  - Tenconi, E.
AU  - Deflandre, B.
AU  - Coppieters, W.
AU  - Karim, L.
AU  - Hanikenne, M.
AU  - Baurain, D.
AU  - Delfosse, P.
AU  - van Wezel, G.P.
AU  - Rigali, S.
TI  - Complete Genome Sequence of Streptomyces lunaelactis MM109(T), Isolated from Cave Moonmilk Deposits.
JO  - Genome Announcements
PY  - 2018
SP  - e00435
EP  - e00418
VL  - 6
AB  - Streptomyces lunaelactis MM109(T) is a ferroverdin A (anticholesterol) producer isolated from
AB  - cave moonmilk deposits. The complete genome sequence of MM109(T)
AB  - was obtained by combining Oxford Nanopore MinION and Illumina HiSeq and MiSeq
AB  - technologies, revealing an 8.4-Mb linear chromosome and two plasmids, pSLUN1
AB  - (127,264 bp, linear) and pSLUN2 (46,827 bp, circular).
ER  -

TY  - JOUR
AU  - Naor, A.
AU  - Lazary, R.
AU  - Barzel, A.
AU  - Papke, R.T.
AU  - Gophna, U.
TI  - In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.
JO  - PLoS ONE
PY  - 2011
SP  - e15833
EP  - e15833
VL  - 6
AB  - Inteins are parasitic genetic elements, analogous to introns that excise themselves at the
AB  - protein level by self-splicing, allowing the formation
AB  - of functional non-disrupted proteins. Many inteins contain a homing
AB  - endonuclease (HEN) gene, and rely on its activity for horizontal
AB  - propagation. In the halophilic archaeon, Haloferax volcanii, the gene
AB  - encoding DNA polymerase B (polB) contains an intein with an annotated but
AB  - uncharacterized HEN. Here we examine the activity of the polB HEN in vivo,
AB  - within its natural archaeal host. We show that this HEN is highly active,
AB  - and able to insert the intein into both a chromosomal target and an
AB  - extra-chromosomal plasmid target, by gene conversion. We also demonstrate
AB  - that the frequency of its incorporation depends on the length of the
AB  - flanking homologous sequences around the target site, reflecting its
AB  - dependence on the homologous recombination machinery. Although several
AB  - evolutionary models predict that the presence of an intein involves a
AB  - change in the fitness of the host organism, our results show that a strain
AB  - deleted for the intein sequence shows no significant changes in growth
AB  - rate compared to the wild type.
ER  -

TY  - JOUR
AU  - Napier, B.A.
AU  - Band, V.
AU  - Burd, E.M.
AU  - Weiss, D.S.
TI  - Colistin heteroresistance in Enterobacter cloacae is associated with cross-resistance to the host antimicrobial lysozyme.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 5594
EP  - 5597
VL  - 58
AB  - Here, we describe the first identification of colistin-heteroresistant
AB  - Enterobacter cloacae in the United States. Treatment of this isolate with
AB  - colistin increased the frequency of the resistant subpopulation and induced
AB  - cross-resistance to the host antimicrobial lysozyme. This is the first
AB  - description of heteroresistance conferring cross-resistance to a host
AB  - antimicrobial and suggests that clinical treatment with colistin may
AB  - inadvertently select for bacteria that are resistant to components of the host
AB  - innate immune system.
ER  -

TY  - JOUR
AU  - Narayan, K.D.
AU  - Badhai, J.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Comamonas thiooxydans Strain S23T (DSM 17888T), a Thiosulfate-Oxidizing Bacterium Isolated from a Sulfur Spring in India.
JO  - Genome Announcements
PY  - 2016
SP  - e00834
EP  - e00816
VL  - 4
AB  - The genus Comamonas contains species isolated from various environments, such as  termite
AB  - guts, wetlands, activated sludge, soil, humans, and fresh water. Here, we
AB  - report the draft genome sequence of Comamonas thiooxydans strain S23(T) capable
AB  - of oxidizing thiosulfate under mixotrophic growth conditions. Based upon draft
AB  - genome sequencing, the genome is 5.3 Mb and encodes 4,767 proteins. The Comamonas
AB  - thiooxydans whole-genome sequence will help understand the metabolic diversity in
AB  - sulfur oxidation pathways.
ER  -

TY  - JOUR
AU  - Narayanan, S.
AU  - Deshpande, U.
TI  - Whole-Genome Sequences of Four Clinical Isolates of Mycobacterium tuberculosis from Tamil Nadu, South India.
JO  - Genome Announcements
PY  - 2013
SP  - e00186
EP  - e00113
VL  - 1
AB  - We report the annotated genome sequences of four clinical isolates of Mycobacterium
AB  - tuberculosis from Tamil Nadu, India.
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - Blakesley, R.
TI  - A new type II restriction enzyme from Haemophilus influenzae.
JO  - Fed. Proc.
PY  - 1981
SP  - 1848
EP  - 1848
VL  - 40
AB  - We have previously reported a new Type II restriction activity (Hin GUII) from
AB  - Haemophilus influenzae (Fed. Proc. 27: 1415, 1978).  These cells also possess
AB  - an isoschizomer of HhaI.  These two enzyme activities can be separated by
AB  - chromatography of the cell extract on phosphocellulose and single-stranded DNA
AB  - agarose.  Two possible recognition sequences were predicted for Hin GUII by the
AB  - computer program RESITE (Tolstoshev, C. and Blakesley, R., manuscript in prep.)
AB  - from the lengths of the eight fragments generated by digestion of PhiX174 RF
AB  - DNA.  By comparison of digestion products of SV40 (11 fragments) and pBR322 (12
AB  - fragments) DNAs, the sequence GGATG/CATCC was predicted.  This was confirmed by
AB  - mapping each on the Hin GUII sites PhiX174 RF DNA and direct DNA sequencing of
AB  - 3 cleavage sites on PhiX174 RF and one site on pBR322 DNAs.  Hin GUII is a
AB  - member of a unique group of Type II restriction enzymes which bind to a
AB  - specific sequence and cleave at another site.  The Hin GUII cleavage site is
AB  - situated 9-11 bases 3' to the recognition sequence GGATG/CATCC.
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - Chirikjian, J.G.
TI  - The enzymes of the BamHI restriction-modification system.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 147
EP  - 184
VL  - 5
AB  - The remarkable sequence specificity of Type II restriction endonucleases and
AB  - their cognate methyl transferases has recently placed them under the scrutiny
AB  - of nucleic acid enzymology.  From a biochemical perspective, their
AB  - comparatively uncomplicated reaction requirements, intermediate size and
AB  - concise, well-defined recognition sites has made them attractive models for the
AB  - investigation of specific protein-nucleic acid interactions.  The solution of
AB  - the same DNA sequence recognition problem by the enzymes of a
AB  - restriction-modification system has led to interesting questions concerning
AB  - structure-function relationships between these genetically distinct proteins.
AB  - Further study of restriction-modification enzymes should promote a better
AB  - understanding of the patterns and principles of protein-nucleic acid
AB  - interactions.  The type II restriction-modification enzymes of Bacillus
AB  - amyloliquefaciens H recognizes the duplex, symmetrical sequence 5'-GGATCC-3'.
AB  - In the presence of Mg+2 the endonuclease catalyzes double stranded cleavage
AB  - between the guanines, generating 5'-phophoryl and 3'-hydroxyl staggered
AB  - termini.  The methylase catalyzes methyl group transfer from
AB  - S-adenosyl-L-methionine to the C5 position of the internal cytosines.
AB  - Methylation prevents cleavage by the endonuclease and is the presumed host
AB  - controlled mechanism for the protection of endogenous DNA.  The specificity of
AB  - the methyl acceptor must be as stringent as the position of strand scission
AB  - since methylation of the external cytosines or the 6-amino groups of the
AB  - adenines does not prevent cleavage.  We have been involved with the
AB  - purification and characterization of these enzymes.  Emphasis has been placed
AB  - on their catalytic properties and mechanisms of sequence discrimination.
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - Connaughton, J.F.
AU  - Kaloss, W.
AU  - Chirikjian, J.G.
TI  - Changes in the kinetics of the BamHI restriction/modification enzymes with systematic alterations of the bases flanking the recognition site.
JO  - FASEB J.
PY  - 1990
SP  - A1794
EP  - A1794
VL  - 4
AB  - Several type II restriction enzymes exhibit different reaction kinetics with
AB  - identical recognition sites in a given DNA molecule.  Kinetic preferences have
AB  - been ascribed to different sequences flanking each recognition site.  Using
AB  - site-specific mutagenesis, we have made 30 M13mp8 linear DNA substrates having
AB  - mutations within the first 3 nucleotides on both flanks of the single BamHI
AB  - site.  The advantages of these substrates are the constant position of the
AB  - BamHI site relative to the DNA termini, the elimination of changes in secondary
AB  - structure induced by supercoiling and the retention of all the flanking
AB  - sequences except for the specified base changes.  Initial reaction velocities
AB  - were determined in the presence of saturating DNA.  The greater difference in
AB  - cleavage rates was 5 fold.  No correlation was found between flanking G/C
AB  - content and reaction kinetics.  The endonuclease was sensitive to the position
AB  - of base substitution.  C and T in flanking positions 1 and 2 produced the
AB  - greatest reduction in velocites.  A in the second position of either flank
AB  - produced the greatest increase in velocity.  Double or triple substitutions of
AB  - A or T did not generate additive kinetic effects.  The methylase prefers
AB  - substrates containing A in flanking positions 1 and 2 but is inhibited by this
AB  - base in position 3.  T substitutions reduced methylation rates.
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - George, J.
AU  - Chirikjian, J.G.
TI  - Differences in the Kinetic Properties of BamHI Endonuclease and Methylase with Linear DNA Substrates.
JO  - J. Biol. Chem.
PY  - 1986
SP  - 12128
EP  - 12133
VL  - 261
AB  - BamHI endonuclease and methylase were found to exhibit a kinetic preference for linear pBR322
AB  - DNA substrates containing the recognition site in a central location.  The Km values for
AB  - substrates having the recognition site in a terminal location were approximately 3-fold
AB  - greater than those with a centrally located site.  This phenomenon may be partially due to
AB  - facilitated transfer of the enzymes to the recognition site over nonspecific flanking
AB  - sequences.  The exploitation of facilitated transfer by these enzymes has been inferred from
AB  - studies demonstrating kinetic preferences for longer DNA substrates.  The reaction rates of
AB  - the endonuclease were 9-fold greater with full-length pBR322 DNA than with a 74-base pair
AB  - derivative.  The methylase exhibits a kinetic preference for longer substrates but only under
AB  - conditions of comparatively higher DNA concentrations.  In addition, the methylase has the
AB  - property of increasing long chain preference with increasing salt concentrations up to 120 mM.
AB  - Increasing salt concentrations decreased the endonuclease's preference for longer substrates.
AB  - Nonspecific inhibition studies revealed qualitative and quantitative differences between the
AB  - two enzymes under catalytic conditions. These studies suggest that BamHI endonuclease and
AB  - methylase interact with nonspecific DNA in different ways.
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - George, J.
AU  - Chirikjian, J.G.
TI  - Sequence-specific BamHI methylase.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 10357
EP  - 10362
VL  - 259
AB  - BamHI methylase has been purified to apparent homogeneity.  The isolated form
AB  - of the enzyme is a single polypeptide with a molecular weight of 56,000 as
AB  - determined by sodium dodecyl sulfate-polyacrylamide electrophoresis.  Unlike
AB  - BamHI endonuclease, which is isolated as a dimer and higher aggregates, the
AB  - methylase has no apparent higher form.  The methylase requires
AB  - S-adenosyl-L-methionine as the methyl-group donor and is inhibited by Mg2+.
AB  - The enzyme is also inhibited by 2,3-butanedione and reagents specific for
AB  - sulfhydryl groups, such as N-ethylmaleimide, which suggests a role for arginine
AB  - and cysteine residues, respectively.  DNA efficiently protects the enzyme
AB  - against the butanedione modification while S-adeno-sylmethionine has no effect.
AB  - In contrast, S-adenosyl-methionine protects against cysteine modification
AB  - while DNA produces only small amounts of protection.  Studies on the mechanism
AB  - of methylation indicate that both strands of the recognition sequence are
AB  - modified in a single binding event.  The sequence specificity of the methylase
AB  - is relaxed upon the addition of glycerol in the reaction mixture.  In the
AB  - presence of 30% glycerol the enzyme methylates sequences that are also
AB  - recognized by BamHI endonuclease when acting under conditions of relaxed
AB  - specificity.
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - Wastney, M.
AU  - Hensley, P.
AU  - Chirikjian, J.G.
TI  - Kinetics of BamHI endonuclease cleavage of form I SV40 DNA.
JO  - Fed. Proc.
PY  - 1986
SP  - 1504
EP  - 1504
VL  - 45
AB  - BamHI endonuclease recognizes the symmetrical, duplex sequence 5'-GGATCC-3' and cleaves
AB  - between the guanines on both strands.  The kinetic mechanism of the enzyme was investigated
AB  - with form [3H]-SV40 DNA which contains a single BamHI site.  The time course data was analyzed
AB  - by numerical integration of the rate equation and a coordinated non-linear least squares
AB  - analysis in terms of the rate constants.  The kinetic model used was that postulated for the
AB  - EcoRI endonuclease.  	k1	k2	k3	k4E + 1 - EI 5 EII 5 EIII5 E + III	k1k-567 k5E + II	To simplify
AB  - the analysis it was assumed that k1 and k-1 were large with respect to k2 and that k4 were not
AB  - distinguished.  In reactions containing 12 nM DNA 2 nM endonuclease an excellent fit to the
AB  - model was obtained with k2 = 0.192 min-1 +/- 0.0019, k3 (k4) = 1.190 +/- 0.042 and k5/k-5 =
AB  - 1.07 +- 0.067.  Unlike EcoRI endonuclease, the cleavage of the first strand is slower with
AB  - this substrate. This analysis is useful in substantiating the model as well as providing
AB  - self-consistent values for the rate constants.  These studies wre being extended to other DNA
AB  - substrates (supported by USPS Grant GM 27701).
ER  -

TY  - JOUR
AU  - Nardone, G.
AU  - Wastney, M.E.
AU  - Hensley, P.
TI  - DNA structural polymorphism modulates the kinetics of superhelical DNA cleavage by BamHI restriction endonucleases.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 15308
EP  - 15315
VL  - 265
AB  - A compartmental model developed by Hensley (Hensley, P., Nardone, G.,
AB  - Chirikjian, J.G., and Wastney, M.E., (1990) J. Biol. Chem. 265, 15300-15307)
AB  - for analysis of the time courses of the cleavage of superhelical DNA substrates
AB  - by the restriction endonuclease, BamHI, has been used to quantify the effects
AB  - of changes in temperature, ionic strength, superhelical density, and the DNA
AB  - substrate on the binding and strand cleavage processes.  Studies reported here
AB  - indicate that changes in topology may be introduced into the DNA substrate
AB  - solely as a result of the plasmid preparation process and in the absence of
AB  - covalent bond cleavage and ligation.  These changes in topology have
AB  - qualitatively different effects on the kinetics than those promoted by changes
AB  - in the superhelical density.  The former are removed by briefly warming the DNA
AB  - prior to assay, suggesting that they are only kinetically stable, while the
AB  - latter changes are not affected by heating.  Increasing the [NaCl] from 0.0 M
AB  - to 0.1 M increases the overall rate of plasmid cleavage by increasing both the
AB  - rates of cleavage and enzyme DNA association.  To describe the decrease in the
AB  - overall cleavage rate observed in 0.15 M NaCl, an ionic strength-dependent
AB  - rate-determining structural transition in the DNA substrate was incorporated
AB  - into the model.  The largest changes in the rate of the cleavage process
AB  - resulted from changes in the DNA substrate.  For the SV40 substrate compared to
AB  - pBR322, the rate constants describing the two association processes and the
AB  - first bond cleavage event were increased 6- to 7-fold.  The rate of the second
AB  - bond cleavage process was not affected.  These changes may be due to
AB  - differences in the flanking sequences.
ER  -

TY  - JOUR
AU  - Narendra-Kumar, P.
AU  - Swapna, T.H.
AU  - Sathi, R.K.
AU  - Archana, K.
AU  - Nageshwar, L.
AU  - Nalini, S.
AU  - Khan, M.Y.
AU  - Hameeda, B.
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens Strain RHNK22, Isolated from  Rhizosphere with Biosurfactant (Surfactin, Iturin, and Fengycin) and Antifungal  Activity.
JO  - Genome Announcements
PY  - 2016
SP  - e01682
EP  - e01615
VL  - 4
AB  - Bacillus amyloliquefaciens strain RHNK22 isolated from groundnut rhizosphere showed direct and
AB  - indirect plant growth-promoting traits along with biosurfactant activity and reduction in
AB  - surface tension of water. Biosurfactants were identified as lipopeptides (surfactin, iturin,
AB  - and fengycin) by molecular and biochemical analysis in our studies.
ER  -

TY  - JOUR
AU  - Narendrakumar, L.
AU  - Suryaletha, K.
AU  - Reghunathan, D.
AU  - Prasannakumar, M.
AU  - Thomas, S.
TI  - Insights into the Draft Genome Sequence of a Haitian Variant Vibrio cholerae Strain Isolated from a Clinical Setting in Kerala, South India.
JO  - Genome Announcements
PY  - 2017
SP  - e00843
EP  - e00817
VL  - 5
AB  - We report here the draft genome sequence of a Haitian variant Vibrio cholerae strain, W4-13,
AB  - isolated from Kerala, South India, possessing cholera toxin gene
AB  - in chromosomes I and II. The sequence will be useful to achieve a profound
AB  - understanding on its evolution, with emphasis on its pathogenesis and antibiotic
AB  - resistance.
ER  -

TY  - JOUR
AU  - Narihiro, T.
AU  - Kusada, H.
AU  - Yoneda, Y.
AU  - Tamaki, H.
TI  - Draft Genome Sequences of Methanoculleus horonobensis Strain JCM 15517, Methanoculleus thermophilus Strain DSM 2373, and Methanofollis ethanolicus Strain  JCM 15103, Hydrogenotrophic Methanogens Belonging to the Family  Methanomicrobiaceae.
JO  - Genome Announcements
PY  - 2016
SP  - e00199
EP  - e00116
VL  - 4
AB  - The familyMethanomicrobiaceaecomprises hydrogen- and formate-utilizing methanogens. Genome
AB  - sequencing of nine species ofMethanomicrobiaceaehas been
AB  - conducted so far. Here, we report three additional draft genome sequences
AB  - ofMethanomicrobiaceae, those ofMethanoculleus horonobensisJCM 15517
AB  - (=T10(T)),Methanoculleus thermophilusDSM 2373 (=CR-1(T)), andMethanofollis
AB  - ethanolicusJCM 15103 (=HASU(T)).
ER  -

TY  - JOUR
AU  - Narihiro, T.
AU  - Nobu, M.K.
AU  - Tamaki, H.
AU  - Kamagata, Y.
AU  - Liu, W.T.
TI  - Draft Genome Sequence of Syntrophomonas wolfei subsp. methylbutyratica Strain 4J5T (JCM 14075), a Mesophilic Butyrate- and 2-Methylbutyrate-Degrading Syntroph.
JO  - Genome Announcements
PY  - 2016
SP  - e00047
EP  - e00016
VL  - 4
AB  - Syntrophomonas wolfei subsp. methylbutyratica strain 4J5(T) (=JCM 14075(T)) is a  mesophilic
AB  - bacterium capable of degrading butyrate and 2-methylbutyrate through
AB  - syntrophic cooperation with a partner methanogen. The draft genome sequence is
AB  - 3.2 Mb, with a G+C content of 45.5%.
ER  -

TY  - JOUR
AU  - Naroditsky, B.S.
AU  - Khilko, S.N.
AU  - Loparev, V.N.
TI  - Current methods for the isolation of specific endonucleases.
JO  - Vestn. Akad. Med. Nauk SSSR
PY  - 1981
SP  - 26
EP  - 28
VL  - 2
AB  - Various schemes and methods used to isolate specific endonucleases from bacteria are
AB  - discussed.  The advantages of employing affinity chromatography to purify restrictases are
AB  - shown with special reference to the isolation of a set of enzymes from B. globigii.  In
AB  - particular, the utilization, in the first stage of purification, of Sepharose 4 B with the
AB  - group-specific ligand Cibacron blue "sewed on" to it, made it possible to eliminate nucleic
AB  - acids and the bulk of protein and to obtain, already after this stage, an enzyme suitable for
AB  - physical mapping.  Additional purification of the enzyme activity maintaining fractions made
AB  - it possible to achieve mutual separation of the enzymes BglI and BglII and BglI and BglIII and
AB  - at the same time to ride of admixtures of nonspecific activities (the purification was done on
AB  - heparin Sepharose).  It is concluded that using affinity chromatography enzymes suitable for
AB  - genetic engineering work can be obtained rapidly and with a high recovery rate.
ER  -

TY  - JOUR
AU  - Narsing-Rao, M.P.
AU  - Jiao, J.Y.
AU  - Liu, L.
AU  - Fang, B.Z.
AU  - Zhang, X.T.
AU  - Chen, W.
AU  - Zhao, J.
AU  - Xiao, M.
AU  - Li, W.J.
TI  - Draft Genome Sequence of MPKL 26, the Type Strain of the Novel Species Sinomonas  mesophila.
JO  - Genome Announcements
PY  - 2017
SP  - e00247
EP  - e00217
VL  - 5
AB  - Sinomonas mesophila MPKL 26T can produce silver nanoparticles. Here, we present the 4.0-Mb
AB  - genome of this type strain, which contains 47 scaffolds with an N50 scaffold length of 261,266
AB  - bp. The availability of the genome sequence will provide a better understanding of strain MPKL
AB  - 26T and the genus Sinomonas.
ER  -

TY  - JOUR
AU  - Narva, K.E.
AU  - Skrdla, M.P.
AU  - Wendell, D.L.
AU  - Van Etten, J.L.
TI  - Isolation of a DNA methyltransferase gene, M.CviBIII, from Chlorella virus NC-1A.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1987
SP  - 314
EP  - 314
VL  - 87
AB  - As an initial step in the study of DNA restriction-modification systems of
AB  - viruses which infect a eucaryotic green alga, Chlorella, we have isolated the
AB  - gene for one methyltransferase, M.CviBIII, from virus NC-1A in Escherichia coli
AB  - plasmid pUC8.  M.CviBIII methylates A in TCGA sequences.  DNA from E. coli
AB  - strains harboring the recombinant plasmid, pNC-1A.14, is resistant to digestion
AB  - by SalI (GTCGAC) and TaqI (TCGA) as well as methylation by the bacterial
AB  - methylase, M.TaqI.  M.CviBIII activity in crude extracts from these E. coli
AB  - strains methylates SalI sites in lambda DNA in an in vitro protection assay.
AB  - Transposon Tn5 mutagenesis localized the M.CviBIII gene to a 1.5 kbp region on
AB  - pNC-1A.14.  Nucleic acid hybridization studies have produced several findings:
AB  - (i) Five of the 29 other Chlorella viruses described in the literature contain
AB  - a gene homologous to M.CviBIII. (ii) Spontaneous mutants of NC-1A, the DNA from
AB  - which is sensitive to TaqI and SalI, have the M.CviBIII gene deleted.  (iii)
AB  - Transcription of the M.CviBIII gene is under temporal control; a 1.4 kb mRNA
AB  - species can be detected with pNC-1A.14 probes only during the early stages of
AB  - NC-1A infection of Chlorella cells.
ER  -

TY  - JOUR
AU  - Narva, K.E.
AU  - Van Etten, J.L.
AU  - Slatko, B.E.
AU  - Benner, J.S.
TI  - The amino acid sequence of the eukaryotic DNA [N6-adenine]methyltransferase, M.CviBIII, has regions of similarity with the prokaryotic isoschizomer M.TaqI and other DNA [N6-adenine] methyltransferases.
JO  - Gene
PY  - 1988
SP  - 253
EP  - 259
VL  - 74
AB  - the sequences of the genes encoding M.CviBIII (from virus NC-1A which infects a
AB  - eukaryotic alga) [Narva et al., Nucleic Acids Res. 15 (1987) 9807-9823] and
AB  - M.TaqI (from the bacterium Thermus aquaticus) [Slatko et al., Nucleic Acids
AB  - Res. 15 (1987) 9781-9796] have been determined recently.  Both enzymes
AB  - methylate adenine in the sequence TCGA.  We have compared the predicted amino
AB  - acid sequences of these two methyltransferases (MTases), with each other and
AB  - with ten other N6A-MTases and find regions of similarity.  M.CviBIII and M.TaqI
AB  - were most closely related followed by M.PaeR7, whose recognition sequence
AB  - (CTCGAG) contains the M.TaqI/M.CviBIII recognition sequence TCGA, and M.PstI,
AB  - whose recognition sequence is CTGCAG.  All of the N6-MTases contain the
AB  - sequence Asp/Asn-Pro-Pro-Tyr (B-P-P-Y) referred to by Hattman et al. [J.
AB  - Bacteriol. 164 (1985) 932-937] as region IV.  The predicted secondary structure
AB  - of this region forms a finger-like structure (Beta finger) containing a
AB  - Beta-pleated sheet (...XXXB), two Beta-turns (P-P) followed by another
AB  - Beta-pleated sheet [Y/FXXX...].
ER  -

TY  - JOUR
AU  - Narva, K.E.
AU  - Wendell, D.L.
AU  - Skrdla, M.P.
AU  - Van Etten, J.L.
TI  - Molecular cloning and characterization of the gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 9807
EP  - 9823
VL  - 15
AB  - The gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A was cloned
AB  - and expressed in E. coli plasmid pUC8. Plasmid (pNC-1A.14.8) encoded M.CviBIII methylates
AB  - adenine in TCGA sequences both in vivo in E. coli and in vitro. Transposon Tn5 mutagenesis
AB  - localized the M.CviBIII functional domain to a 1.5 kbp region of pNC-1A.14.8 and also
AB  - indicated that a virus promoter directs transcription of the gene in E. coli. The 2.1 kbp
AB  - insert containing the M.CviBIII gene was sequenced and a single open reading frame of 1131 bp
AB  - was identified within the domain determined by Tn5 mutagenesis. When the M.CviBIII gene was
AB  - fused in-frame with the 19 amino-terminal codons of lacZ a 45 kD polypeptide was identified in
AB  - maxicells as predicted by the DNA sequence. The M.CviBIII gene was not essential for virus
AB  - replication since a virus M.CviBIII deletion mutant also replicated in Chlorella.
ER  -

TY  - JOUR
AU  - Nascimento, A.L. et al.
TI  - Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis.
JO  - J. Bacteriol.
PY  - 2004
SP  - 2164
EP  - 2172
VL  - 186
AB  - Leptospira species colonize a significant proportion of rodent populations
AB  - worldwide and produce life-threatening infections in accidental hosts,
AB  - including humans. Complete genome sequencing of Leptospira interrogans
AB  - serovar Copenhageni and comparative analysis with the available Leptospira
AB  - interrogans serovar Lai genome reveal that despite overall genetic
AB  - similarity there are significant structural differences, including a large
AB  - chromosomal inversion and extensive variation in the number and
AB  - distribution of insertion sequence elements. Genome sequence analysis
AB  - elucidates many of the novel aspects of leptospiral physiology relating to
AB  - energy metabolism, oxygen tolerance, two-component signal transduction
AB  - systems, and mechanisms of pathogenesis. A broad array of transcriptional
AB  - regulation proteins and two new families of afimbrial adhesins which
AB  - contribute to host tissue colonization in the early steps of infection
AB  - were identified. Differences in genes involved in the biosynthesis of
AB  - lipopolysaccharide O side chains between the Copenhageni and Lai serovars
AB  - were identified, offering an important starting point for the elucidation
AB  - of the organism's complex polysaccharide surface antigens. Differences in
AB  - adhesins and in lipopolysaccharide might be associated with the adaptation
AB  - of serovars Copenhageni and Lai to different animal hosts. Hundreds of
AB  - genes encoding surface-exposed lipoproteins and transmembrane outer
AB  - membrane proteins were identified as candidates for development of
AB  - vaccines for the prevention of leptospirosis.
ER  -

TY  - JOUR
AU  - Nasfi, Z.
AU  - Poehlein, A.
AU  - Harms, H.
AU  - Goralski, E.
AU  - Fisch, K.M.
AU  - Daniel, R.
AU  - Konig, G.M.
AU  - Schaberle, T.F.
AU  - Bachoual, R.
TI  - Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of  Matmata, Tunisia.
JO  - Genome Announcements
PY  - 2018
SP  - e00323
EP  - e00318
VL  - 6
AB  - Bacillus sp. strain M21 was isolated from an environmental sample. In antibacterial
AB  - screenings, the strain inhibited growth of Gram-positive and
AB  - Gram-negative test strains. The genome was assembled into 69 contigs with a total
AB  - size of 5.178 Mb. The strain contains at least nine biosynthetic gene clusters
AB  - for the production of specialized metabolites.
ER  -

TY  - JOUR
AU  - Nash, J.H.
AU  - Villegas, A.
AU  - Kropinski, A.M.
AU  - Aguilar-Valenzuela, R.
AU  - Konczy, P.
AU  - Mascarenhas, M.
AU  - Ziebell, K.
AU  - Torres, A.G.
AU  - Karmali, M.A.
AU  - Coombes, B.K.
TI  - Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes.
JO  - BMC Genomics
PY  - 2010
SP  - 667
EP  - 667
VL  - 11
AB  - ABSTRACT: BACKGROUND: Adherent and invasive Escherichia coli (AIEC) are
AB  - commonly found in ileal lesions of Crohn's Disease (CD) patients, where
AB  - they adhere to intestinal epithelial cells and invade into and survive in
AB  - epithelial cells and macrophages, thereby gaining access to a typically
AB  - restricted host niche. Colonization leads to strong inflammatory responses
AB  - in the gut suggesting that AIEC could play a role in CD immunopathology.
AB  - Despite extensive investigation, the genetic determinants accounting for
AB  - the AIEC phenotype remain poorly defined. To address this, we present the
AB  - complete genome sequence of an AIEC, revealing the genetic blueprint for
AB  - this disease-associated E. coli pathotype. Results - We sequenced the
AB  - complete genome of E. coli NRG857c (O83:H1), a clinical isolate of AIEC
AB  - from the ileum of a Crohn's Disease patient. Our sequence data confirmed a
AB  - phylogenetic linkage between AIEC and extraintestinal pathogenic E. coli
AB  - causing urinary tract infections and neonatal meningitis. The comparison
AB  - of the NRG857c AIEC genome with other pathogenic and commensal E. coli
AB  - allowed for the identification of unique genetic features of the AIEC
AB  - pathotype, including 41 genomic islands, and unique genes that are found
AB  - only in strains exhibiting the adherent and invasive phenotype.
AB  - CONCLUSIONS: Up to now, the virulence-like features associated with AIEC
AB  - are detectable only phenotypically. AIEC genome sequence data will
AB  - facilitate the identification of genetic determinants implicated in
AB  - invasion and intracellular growth, as well as enable functional genomic
AB  - studies of AIEC gene expression during health and disease.
ER  -

TY  - JOUR
AU  - Nash, J.H.
AU  - Young, N.M.
TI  - Draft Whole-Genome Sequence of Morganella morganii Serotype O:1ab.
JO  - Genome Announcements
PY  - 2015
SP  - e00453
EP  - e00415
VL  - 3
AB  - Morganella morganii is a facultative pathogen of humans, causing urinary tract and
AB  - postsurgical infections. Here, we report a high-quality draft assembly of the
AB  - O:1ab serotype.
ER  -

TY  - JOUR
AU  - Nasri, M.
AU  - Sayadi, S.
AU  - Thomas, D.
TI  - Relaxation of PvuII recognition sequence.
JO  - FEBS Lett.
PY  - 1985
SP  - 101
EP  - 104
VL  - 185
AB  - The substrate specificity of PvuII endonuclease is relaxed in the presence of
AB  - dimethyl sulfoxide.  The new recognition sequences cleaved in pBR322 DNA have
AB  - been found to be CCGCTG, CATCTG, CAGATG, CAGGTG and CAGCGG.
ER  -

TY  - JOUR
AU  - Nasri, M.
AU  - Thomas, D.
TI  - Alteration of the specificity of PvuII restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 7677
EP  - 7687
VL  - 15
AB  - The restriction endonuclease PvuII which cleaves the sequence CAG^CTG, at the
AB  - position indicated by the arrow, was found to decrease its substrate
AB  - specificity in the presence of organic solvents.  Thirty-three sites, that we
AB  - have named PvuII* sites, were identified on the nucleotide sequence of pBR322
AB  - DNA.  The new recognition sequences cleaved in pBR322 DNA, at the positions
AB  - indicated by the arrows, were shown to be AAGCTG, GAGCTG, CNGCTG, CANCTG,
AB  - CAGNTG, CAGCNG, CAGCTC and CAGCTT.  (TAGCTG and the complementary sequence
AB  - CAGCTA are not present in pBR322 DNA).  From these recognition sequences, we
AB  - deduced that PvuII* activity recognizes and cleaves degenerate sequences which
AB  - differ from the standard PvuII sequence CAGCTG at only one of the recognition
AB  - site.  Any substitution can occur at any one of the six positions in the
AB  - hexanucleotide sequence.  The optimum incubation medium for PvuII* activity was
AB  - found to be:  10-50 mM Tris-HCl, pH 8.5, 12-15 mM MgCl2, 50 mM NaCl, 10%
AB  - ethanol + 10% dimethylsulfoxide (DMSO).
ER  -

TY  - JOUR
AU  - Nasri, M.
AU  - Thomas, D.
TI  - Increase of the potentialities of restriction endonucleases by specificity relaxation in the presence of organic solvents.
JO  - Ann. NY Acad. Sci.
PY  - 1988
SP  - 255
EP  - 265
VL  - 542
AB  - None
ER  -

TY  - JOUR
AU  - Nasri, M.
AU  - Thomas, D.
TI  - Relaxation of recognition sequence of specific endonuclease HindIII.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 811
EP  - 821
VL  - 14
AB  - Under the standard reaction conditions, the restriction endonuclease HindIII
AB  - cleaves double-stranded DNA, within the recognition sequence -A^AGCTT- at the
AB  - position indicated by the arrow.  In the presence of Dimethyl sulfoxide the
AB  - substrate specificity of this enzyme is reduced and cleavages occur at
AB  - additional sites.  We have determined the secondary sites in pBR322 DNA
AB  - recognized by HindIII endonuclease under relaxed conditions and found that it
AB  - cleaves the hexanucleotides:  G^AGCTT, A^GGCTT, A^TGCTT, A^ATCTT, A^AGCAT,
AB  - A^AGCGT, A^AGCTC,  at the positions indicated by the arrows, producing
AB  - fragments with cohesive ends.
ER  -

TY  - JOUR
AU  - Nasri, M.
AU  - Thomas, D.
TI  - The reactions of SacI, PvuII and EcoRI endonucleases.
JO  - Biomed. Biochim. Acta
PY  - 1986
SP  - 997
EP  - 1005
VL  - 45
AB  - A new approach to the mechanism study of DNA restriction is suggested.  It is
AB  - based on enzymatic hydrolysis of DNA in the presence of organic solvent.  We
AB  - found that in the presence of DMSO (10% v/v), the superhelical cleavage of
AB  - pBR322 DNA by restriction endonucleases SacI and EcoRI proceeds with extensive
AB  - accumulation of an intermediate, the single-nicked circular DNA, while with
AB  - PvuII endonuclease the superhelical form is converted directly to the linear
AB  - form.
ER  -

TY  - JOUR
AU  - Nasri, M.
AU  - Thomas, D.
TI  - Immobilization of the restriction endonucleases PvuII and HindIII.
JO  - Appl. Biochem. Biotechnol.
PY  - 1987
SP  - 119
EP  - 130
VL  - 15
AB  - The effects of several chemical reagents on the activity of the restriction
AB  - endonucleases PvuII and HindIII were investigated.  Carbodiimide, which reacts
AB  - preferentially with carboxyl groups, was found to inactivate these enzymes.
AB  - This specific effect could be prevented by Mg2+ cation.  pBR322 DNA, which
AB  - contains PvuII and PvuII sites and HindIII and HindIII sites, did not protect
AB  - the enzymes from the carbodiimide.  On the other hand, glutaraldehyde, which
AB  - reacts primarily with lysine residues, inactivates PvuII and HindIII enzymes.
AB  - This specific effect could not be prevented by pBR322 DNA.  Preincubation with
AB  - high concentrations of N-ethylmaleimide, which reacts with sulfhydryl groups,
AB  - caused slight inhibition of PvuII activity, but had no effect on the activity
AB  - of HindIII enzyme.  The effects of glutaraldehyde , carbodiimide, and
AB  - N-ethylmaleimide on other restriction endonucleases were also investigated.
AB  - Restriction endonucleases PvuII and HindIII were immobilized by covalent
AB  - coupling to various insoluble carriers.  Both immobilized enzymes retained
AB  - partial enzyme activities, when immobilized through phenolic groups and were
AB  - stable for at least two months.
ER  -

TY  - JOUR
AU  - Nasrin, S.
AU  - Hossain, M.J.
AU  - Liles, M.R.
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens AP183 with Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus.
JO  - Genome Announcements
PY  - 2015
SP  - e00162
EP  - e00115
VL  - 3
AB  - Bacillus amyloliquefaciens AP183 expresses secondary metabolites that inhibit the growth of
AB  - methicillin-resistant Staphylococcus aureus (MRSA). Here, we present a
AB  - ~3.99-Mbp draft genome sequence of AP183 with the aims of providing insights into
AB  - the genomic basis of its antibacterial mechanisms and exploring its potential use
AB  - in preventing MRSA skin colonization.
ER  -

TY  - JOUR
AU  - Nasser, K.
AU  - Mustafa, A.S.
AU  - Khan, M.W.
AU  - Purohit, P.
AU  - Al-Obaid, I.
AU  - Dhar, R.
AU  - Al-Fouzan, W.
TI  - Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait.
JO  - Genome Announcements
PY  - 2018
SP  - e00264
EP  - e00218
VL  - 6
AB  - Acinetobacter baumannii is an important opportunistic pathogen in global health care settings.
AB  - Its dissemination and multidrug resistance pose an issue with
AB  - treatment and outbreak control. Here, we present draft genome assemblies of six
AB  - multidrug-resistant clinical strains of A. baumannii isolated from patients
AB  - admitted to one of two major hospitals in Kuwait.
ER  -

TY  - JOUR
AU  - Nastri, H.G.
AU  - Evans, P.D.
AU  - Walker, I.H.
AU  - Riggs, P.D.
TI  - Catalytic and DNA binding properties of PvuII restriction endonuclease mutants.
JO  - J. Biol. Chem.
PY  - 1997
SP  - 25761
EP  - 25767
VL  - 272
AB  - The role of particular residues of the PvuII endonuclease in DNA binding and cleavage was
AB  - studied by mutational analysis using a number of in vivo and in vitro approaches.  While
AB  - confirming the importance of residues predicted to be involved directly in function by the
AB  - crystal structure, the analysis led to several striking results. Aspartate 34, which contacts
AB  - the central base pair of the PvuII site (5'-CAGCTG-3') through the minor groove, plays a
AB  - critical role in binding specificity.  A D34G mutant binds with high affinity to any of the
AB  - sequences in the set CANNTG, although its low level of cleavage activity acts only on the
AB  - wild-type site.  In addition, a His to Ala mutation at the residue that contacts the central
AB  - G, and is predicted to be blocked by PvuII methylation, still requires the PvuII methylase to
AB  - be maintained in vivo, arguing against this hypothesis as the only mechanism for methylation
AB  - protection.  Finally, four of the five mutations that reduce cleavage activity while still
AB  - exhibiting binding in the gel shift assay are at residues that form DNA- or subunit-subunit
AB  - contacts rather than in the catalytic center.  This provides further evidence for a strong
AB  - linkage between specific binding and catalysis.
ER  -

TY  - JOUR
AU  - Nath, K.
TI  - Effect of sulfhydryl group inhibitors on restriction endonuclease activities.
JO  - Arch. Biochem. Biophys.
PY  - 1981
SP  - 611
EP  - 617
VL  - 212
AB  - The activity of restriction endonuclease BamHI was abolished by
AB  - p-mercuribenzoate and 5,5'-dithiobis(2-nitrobenzoic acid).  The activity of
AB  - restriction endonuclease PvuI was abolished by p-mercuribenzoate.  The activity
AB  - of none of the eight other restriction endonucleases tested could be abolished
AB  - by the sulfydryl group inhibitors.  Despite the general practice of inclusion
AB  - of sulfhydryl reducing agents in reaction mixtures containing restriction
AB  - endonucleases it appears that most of these enzymes function without the active
AB  - participation of a -SH moiety.
ER  -

TY  - JOUR
AU  - Nath, K.
AU  - Azzolina, B.A.
TI  - Cleavage properties of site-specific restriction endonucleases.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 113
EP  - 130
VL  - 1
AB  - *
AB  -   I. Introduction
AB  -  II. Site preference by restriction endonucleases
AB  - III. Perturbations in restriction-endonuclease cleavage properties
AB  -  IV. Application of manipulated restriction endonuclease cleavage
AB  -   V. Summary
AB  - 
ER  -

TY  - JOUR
AU  - Nath, K.
AU  - Bollon, A.P.
TI  - Generation of discrete yeast DNA fragments by endonuclease RI.
JO  - Nature
PY  - 1975
SP  - 155
EP  - 157
VL  - 257
AB  - Fine structure genetic analysis has shown that the ilv1 gene of yeast,
AB  - Saccharomyces cerevisiae, is multifunctional.  The ilv1 gene product, threonine
AB  - deaminase, shows catalytic activity, as well as participating in multivalent
AB  - repression of other enzymes involved in isoleucine-valine biosynthetic
AB  - pathways.  A better understanding of the regulatory role of the ilv1 gene
AB  - product and other proteins, such as isoleucyl-tRNA synthetase, which in
AB  - addition to the ilv1 gene product seems to regulate ilv2 and ilv3 gene
AB  - expression, could be obtained if a pure preparation of the various ilv genes
AB  - were isolated in large quantities.  One way of isolating the genes would be to
AB  - use restriction enzymes to cleave yeast DNA which contains normal ilv genes and
AB  - join the fragments to a bacterial plasmid.  Because of the similarity of the
AB  - isoleucine-valine pathways in yeast and Escherichia coli, the fused DNA could
AB  - then be transformed into a strain of E. coli with a deletion in the particular
AB  - ilv gene.  Restriction enzyme-cleaved DNA from various sources has been
AB  - amplified by growth in E. coli.  We have found that restriction enzyme EcoRI
AB  - treatment of yeast DNA results in not only a reduction in the size of total DNA
AB  - but also the generation of several distinct species of homogeneous size DNAs
AB  - some of which are derived from ribosomal genes and others from mitochondrial
AB  - genes.
ER  -

TY  - JOUR
AU  - Nathan, D.
AU  - Crothers, D.M.
TI  - Bending and flexibility of methylated and unmethylated EcoRI DNA.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 7
EP  - 17
VL  - 316
AB  - We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural
AB  - model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with
AB  - recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven
AB  - degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that
AB  - the sequence has a higher flexibility, assumed to be isotropic, compared to that of a
AB  - "generic" DNA sequence. This model was used as a starting point for the investigation of the
AB  - effect of cytosine methylation on DNA bending and flexibility. While methylation did not
AB  - affect bend magnitude or direction, it resulted in a reduction in bending flexibility and
AB  - under-winding of the methylated nucleotides. We demonstrate that our approach can augment the
AB  - understanding of DNA structure and dynamics by adding information about the global structure
AB  - and flexibility of the sequence. We also show that cyclization kinetics can be used to study
AB  - the properties of modified nucleotides.
ER  -

TY  - JOUR
AU  - Nathan, P.D.
AU  - Brooks, J.E.
TI  - Characterization of clones of the BamHI methyltransferase gene.
JO  - Gene
PY  - 1988
SP  - 35
EP  - 36
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Nathan, P.D.
AU  - Brooks, J.E.
TI  - Characterization of clones of the BamHI methyltransferase gene.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 212
EP  - 212
VL  - 13D
AB  - The BamHI type II restriction-modification system from Bacillus
AB  - amyloliquefaciensH, recognizes the sequence 5'-GGATCC.  We are characterizing
AB  - different subclones of the BamHI methyltransferase (MTase) gene.  One clone
AB  - carries a 2.2-kb HindIII fragment (pBamM2.2) that contains the MTase gene and
AB  - the N-terminal end of the endonuclease gene.  A second clone carries a 1.8-kb
AB  - XmnI-HindIII fragment (pBamM1.8) that contains the MTase gene and a portion of
AB  - the ORF located in the intergenic region.  These two clones differ in their
AB  - compatibility with McrB (modified cytosine restriction).  Only the plasmid
AB  - pBamM1.8 is restricted by McrB+ hosts.  Two approaches are being used to
AB  - investigate the different McrB compatibilites.  First, we have found that cells
AB  - containing pBamM1.8 produce significantly greater amounts of BamHI MTase than
AB  - cells containing pBamM2.2.  Second, we have found that a disruption of plasmid
AB  - pBamM2.2 in the intergenic ORF results in the loss of McrB compatibility.
AB  - Together, these results suggest that the higher level of MTase from pBamM1.8 is
AB  - responsible for the McrB restriction, and that the region located between the
AB  - two genes affects the level of MTase produced.
ER  -

TY  - JOUR
AU  - Nathan, P.D.
AU  - Brooks, J.E.
TI  - Regulation of the BamHI restriction-modification system.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 180
EP  - 180
VL  - 89
AB  - The BamHI restriction-modification (RM) system recognizes the sequence
AB  - 5'-GGATCC.  The endonuclease cleaves to leave a 5' GATC extension.  The
AB  - methyltransferase (MTase) modifies the internal cytosine residue to give
AB  - GGATmCC.  We have investigated clones of the BamHI MTase gene, pBamM1.8 and
AB  - pBamM2.2, that differ in their restriction by the McrB (modified cytosine
AB  - restriction) system of Escherichia coli, only pBamM1.8 is restricted by McrB+
AB  - cells.  We have found that cells containing pBamM1.8 produce more MTase than
AB  - cells containing pBamM2.2.  We suggest that the higher expression of MTase by
AB  - cells containing pBamM1.8 is responsible for the McrB restriction.  By using
AB  - linkers to disrupt the plasmid pBamM2.2, we have identified and subcloned a
AB  - genetic region involved in the McrB effect.  This region contains a small open
AB  - reading frame (ORF) that lies between the BamHI RM genes.  Recently we have
AB  - investigated the effect of the ORF region on the endonuclease gene.  Cells that
AB  - contain a plasmid with the BamHI RM system disrupted in the ORF region produce
AB  - a lower level of endonuclease.  Moreover, endonuclease levels are restored when
AB  - the cells are cotransformed with the ORF containing plasmid.  These results
AB  - syggest that the region located between the two genes is important in
AB  - controlling the expression of both BamHI MTase and endonuclease.
ER  -

TY  - JOUR
AU  - Nathans, D.
AU  - Adler, S.P.
AU  - Brockman, W.W.
AU  - Danna, K.J.
AU  - Lee, T.N.H.
AU  - Sack, G.H. Jr.
TI  - Use of restriction endonucleases in analyzing the genome of simian virus 40.
JO  - Fed. Proc.
PY  - 1974
SP  - 1135
EP  - 1138
VL  - 33
AB  - Bacterial restriction endonucleases have been used to cleave SV40 DNA at
AB  - specific sites.  The resulting fragments have been ordered in the molecule,
AB  - resulting in a physical cleavage map of the SV40 chromosome.  With this map as
AB  - a reference, sites of initiation and termination of DNA replication have been
AB  - located, as have regions of the genome expressed early and late in productively
AB  - infected cells.  The 5' - 3' orientation of each strand of SV40 DNA has also
AB  - been determined; from this information and prior identification of the early
AB  - and late template strands, the direction of early and late transcription could
AB  - be deduced.
ER  -

TY  - JOUR
AU  - Nathans, D.
AU  - Smith, H.O.
TI  - Restriction endonucleases in the analysis and restructuring of DNA molecules.
JO  - Annu. Rev. Biochem.
PY  - 1975
SP  - 273
EP  - 293
VL  - 44
AB  - Restriction enzymes are endodeoxyribonucleases that recognize specific
AB  - nucleotide sequences in double stranded DNA and cleave both strands of the
AB  - duplex.  In the cell of origin each restriction enzyme is part of a
AB  - restriction-modification (R-M) system, consisting of the restriction
AB  - endonuclease and a matched modification enzyme which recognizes and modifies
AB  - (generally by methylation) the same nucleotide sequence in DNA recognized by
AB  - the restriction enzyme.  Modification thus protects cellular DNA from
AB  - restriction; however, foreign (unmodified) DNA is cleaved by the restriction
AB  - endonuclease and further degraded by other enzymes.  Such R-M systems, first
AB  - detected by phage restriction and modification, are widespread in bacteria and
AB  - are thought to play a role in eliminating foreign DNA that gains entrance to
AB  - the cell via viruses or as naked DNA.  The biochemistry and genetics of R-M
AB  - systems have recently been reviewed.  The usefulness of restriction
AB  - endonucleases in the analysis and restructuring of DNA, which is the topic of
AB  - this review, rests on the fact that some of the restriction enzymes cleave DNA
AB  - at specific nucleotide sequences.  These cleavage site-specific endonucleases
AB  - are thus analogous to specific proteolytic enzymes and are proving as useful in
AB  - the study of DNA structure and function as trypsin and chymotrypsin have been
AB  - in protein analysis.  After the first characterization of a restriction
AB  - endonuclease from Escherichia coli strain K in 1968, there was a curious lag in
AB  - the application of restriction enzymes as analytical tools.  In a sense this
AB  - delay was fortunate, since the enzymes isolated initially are in the class now
AB  - known to be nonspecific in their cleavage sites.  However, after the discovery
AB  - of cleavage site-specific endonucleases, there was immediate applicaton of
AB  - these enzymes to the analysis of viral genomes.  In the past three years there
AB  - has been an almost explosive rate of discovery of new site-specific restriction
AB  - enzymes and rapid application to physical mapping of chromosomes, nucleotide
AB  - sequence analysis of DNA, isolation of genes, and restructuring of DNA
AB  - molecules.  Our purpose is to review these recent developments.
ER  -

TY  - JOUR
AU  - Naughton, S.
AU  - Parker, D.
AU  - Seemann, T.
AU  - Thomas, T.
AU  - Turnbull, L.
AU  - Rose, B.
AU  - Bye, P.
AU  - Cordwell, S.
AU  - Whitchurch, C.
AU  - Manos, J.
TI  - Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung.
JO  - PLoS ONE
PY  - 2011
SP  - E24526
EP  - E24526
VL  - 6
AB  - Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people
AB  - with cystic fibrosis (CF), adapts for survival in the CF lung through both
AB  - mutation and gene expression changes. Frequent clonal strains such as the
AB  - Australian Epidemic Strain-1 (AES-1), have increased ability to establish
AB  - infection in the CF lung and to superimpose and replace infrequent clonal
AB  - strains. Little is known about the factors underpinning these properties.
AB  - Analysis has been hampered by lack of expression array templates containing
AB  - CF-strain specific genes. We sequenced the genome of an acute infection AES-1
AB  - isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array
AB  - (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The
AB  - unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes,
AB  - including 338 not found in the other seven genomes. The PANarray contained 12,543
AB  - gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326
AB  - quality-control probes and 70 probes for non-P. aeruginosa genes, including phage
AB  - and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same
AB  - patient 10.5 years later and not eradicated in the intervening period, in our
AB  - validated artificial sputum medium (ASMDM) and used the PANarray to compare gene
AB  - expression of both in duplicate. 675 genes were differentially expressed between
AB  - the isogenic pairs, including upregulation of alginate, biofilm, persistence
AB  - genes and virulence-related genes such as dihydroorotase, uridylate kinase and
AB  - cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included
AB  - pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and
AB  - numerous phage genes. Elucidation of these genes' roles could lead to targeted
AB  - treatment strategies for chronically infected CF patients.
ER  -

TY  - JOUR
AU  - Naumann, T.A.
AU  - Tavassoli, A.
AU  - Benkovic, S.J.
TI  - Genetic selection of cyclic peptide dam methyltransferase inhibitors.
JO  - Chembiochem
PY  - 2008
SP  - 194
EP  - 197
VL  - 9
AB  - Enzymatic methylation of specific DNA bases is fundamental to the survival and propagation of
AB  - a variety of organisms, including humans.  DNA methyltransferases control and regulate a
AB  - variety of cellular processes, and due to the central role these processes play in the
AB  - organism's lifecycle, bacterial methyltransferases are attractive targets for the development
AB  - of new antibiotics.  The Escherichia coli dam methyltransferase protein is an N-6 adenine
AB  - methyltransferase that methylates the GATC palindrome by transfer of a methyl group from
AB  - S-adenosyl-L-methionine.  EcoDam functions in a number of diverse and important cellular
AB  - processes, the most well studied being postreplicative DNA mismatch repair and control of DNA
AB  - replication.  In uropathogenic E. coli, EcoDam activity is required for conversion to and
AB  - maintenance of the virulent phenotype.
ER  -

TY  - JOUR
AU  - Naumann, U.
AU  - Daxinger, L.
AU  - Kanno, T.
AU  - Eun, C.
AU  - Long, Q.A.
AU  - Lorkovic, Z.J.
AU  - Matzke, M.
AU  - Matzke, A.J.M.
TI  - Genetic Evidence That DNA Methyltransferase DRM2 Has a Direct Catalytic Role in RNA-Directed DNA Methylation in Arabidopsis thaliana.
JO  - Genetics
PY  - 2011
SP  - 977
EP  - 979
VL  - 187
AB  - RNA-directed DNA methylation (RdDM) is a small RNA-mediated epigenetic modification in plants.
AB  - We report here the identification of DOMAINS
AB  - REARRANGED METHYLTRANSFERASE 2 (DRM2) in a forward screen for mutants
AB  - defective in RdDM in Arabidopsis thaliana. The finding of a mutation in
AB  - the presumptive active site argues in favor of direct catalytic
AB  - activity for DRM2.
ER  -

TY  - JOUR
AU  - Navas, E.
AU  - Bohle, H.
AU  - Henriquez, P.
AU  - Grothusen, H.
AU  - Bustamante, F.
AU  - Bustos, P.
AU  - Mancilla, M.
TI  - Draft Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 37551, Serotype O1b, Isolated from Diseased, Vaccinated Atlantic Salmon (Salmo salar) in  Chile.
JO  - Genome Announcements
PY  - 2014
SP  - e00858
EP  - e00814
VL  - 2
AB  - We sequenced the genome of a motile O1b Yersinia ruckeri field isolate from Chile, which is
AB  - causing enteric redmouth disease (ERM) in vaccinated Atlantic
AB  - salmon (Salmo salar). The draft genome has 3,775,486 bp, a G+C content of 47.1%,
AB  - and is predicted to contain 3,406 coding sequences.
ER  -

TY  - JOUR
AU  - Navas, L.E.
AU  - Berretta, M.F.
AU  - Ortiz, E.M.
AU  - Benintende, G.B.
AU  - Amadio, A.F.
AU  - Zandomeni, R.O.
TI  - Draft Genome Sequence of Thermus sp. Isolate 2.9, Obtained from a Hot Water Spring Located in Salta, Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e01414
EP  - e01414
VL  - 3
AB  - Thermus sp. isolate 2.9 was obtained from a hot water spring in Salta, Argentina. Here, we
AB  - report the draft genome sequence (2,485,434 bp) of this isolate, which
AB  - consists of 11 scaffolds of >10 kbp and 2,719 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Navas, L.E.
AU  - Berretta, M.F.
AU  - Ortiz, E.M.
AU  - Sauka, D.H.
AU  - Benintende, G.B.
AU  - Zandomeni, R.O.
AU  - Amadio, A.F.
TI  - Draft Genome Sequence of Bacillus thuringiensis INTA Fr7-4.
JO  - Genome Announcements
PY  - 2017
SP  - e00076
EP  - e00017
VL  - 5
AB  - We report here the complete annotated 6,035,547-bp draft genome sequence of Bacillus
AB  - thuringiensis INTA Fr7-4. This strain contains three cry8 and two vip1
AB  - and vip2 insecticidal toxin genes.
ER  -

TY  - JOUR
AU  - Naz, S.
AU  - Tareb, R.
AU  - Bernardeau, M.
AU  - Vaisse, M.
AU  - Lucchetti-Miganeh, C.
AU  - Rechenmann, M.
AU  - Vernoux, J.P.
TI  - Genome Sequence of Lactobacillus plantarum Strain UCMA 3037.
JO  - Genome Announcements
PY  - 2013
SP  - e00251
EP  - e00213
VL  - 1
AB  - Nucleic acid of the strain Lactobacillus plantarum UCMA 3037, isolated from raw milk camembert
AB  - cheese in our laboratory, was sequenced. We present its draft
AB  - genome sequence with the aim of studying its functional properties and
AB  - relationship to the cheese ecosystem.
ER  -

TY  - JOUR
AU  - Nazarenko, I.A.
AU  - Gorbunov, Y.A.
AU  - Malysgin, E.G.
TI  - Cleavage of synthetic RNA-DNA hybrids with restriction endonucleases BamHI and Sau3AI.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 928
EP  - 933
VL  - 13
AB  - Synthetic oligodeoxyribonucleotides, containing one or two ribonucleotides in
AB  - the recognition sequence, and RNA-DNA hybrids were tested for their activity in
AB  - cleavage with BamHI and Sau3AI endonucleases.  The replacement of dG with G in
AB  - the first position of BamHI-site (GGATCC) of one of the chains does not affect
AB  - the rate of the BamHI hydrolysis.  The similar heteroduplex, containing G
AB  - residue in the second position, displays a decreased rate of the BamHI
AB  - hydrolysis of the modified strand and to a lesser extent, of the unmodified
AB  - complementary strand.  Oligodeoxyribonucleotides in complex with
AB  - oligoribonucleotides can be cleaved with the excess of BamHI and Sau3AI
AB  - oligoribonucleotides remaining intact.
ER  -

TY  - JOUR
AU  - Nazari, B.
AU  - Forneris, C.C.
AU  - Gibson, M.I.
AU  - Moon, K.
AU  - Schramma, K.R.
AU  - Setedsayamdost, M.R.
TI  - Nonomuraea sp. ATCC 55076 harbors the largest actinomycete chromosome to date and the kistamicin biosynthetic gene cluster.
JO  - MedChemComm
PY  - 2017
SP  - 780
EP  - 788
VL  - 8
AB  - Glycopeptide antibiotics (GPAs) have served as potent clinical drugs and as an inspiration to
AB  - chemists in various disciplines. Among known GPAs, complestatin, chloropeptin, and kistamicin
AB  - are unique in that they contain an unusual indole-phenol crosslink. The mechanism of formation
AB  - of this linkage is unknown, and to date, the biosynthetic gene cluster of only one GPA with an
AB  - indole-phenol crosslink, that of complestatin, has been identified. Here, we report the genome
AB  - sequence of the kistamicin producer Nonomuraea sp. ATCC 55076. We find that this strain
AB  - harbours the largest actinobacterial chromosome to date, consisting of a single linear
AB  - chromosome of 13.1 Mbp. AntiSMASH analysis shows that 32 biosynthetic gene clusters and 10% of
AB  - the genome are devoted to production of secondary metabolites, which include
AB  - 1,6-dihydroxyphenazine and nomuricin, a new anthraquinone-type pentacyclic compound that we
AB  - report herein. The kistamicin gene cluster (kis) was identified bioinformatically. A unique
AB  - feature of kis is that it contains two cytochrome P450 enzymes, which likely catalyze three
AB  - crosslinking reactions. These findings set the stage for examining the biosynthesis of
AB  - kistamicin and its unusual indole-phenol crosslink in the future.
ER  -

TY  - JOUR
AU  - Nazir, R.
AU  - Hansen, M.A.
AU  - Sorensen, S.
AU  - van Elsas, J.D.
TI  - Draft Genome Sequence of the Soil Bacterium Burkholderia terrae Strain BS001, Which Interacts with Fungal Surface Structures.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4480
EP  - 4481
VL  - 194
AB  - Burkholderia terrae BS001 is a soil bacterium which was originally isolated from  the
AB  - mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a
AB  - range of fungus-interacting traits which reveal its propensity to actively
AB  - interact at fungal interfaces. Here, we present the approximately 11.5-Mb (G+C
AB  - content, 61.52%) draft genome sequence of B. terrae BS001 with the aim of
AB  - providing insight into the genomic basis of its ecological success in
AB  - fungus-affected soil settings.
ER  -

TY  - JOUR
AU  - Neave, M.J.
AU  - Michell, C.T.
AU  - Apprill, A.
AU  - Voolstra, C.R.
TI  - Whole-genome sequences of three symbiotic endozoicomonas strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00802
EP  - e00814
VL  - 2
AB  - Members of the genus Endozoicomonas associate with a wide range of marine organisms. Here, we
AB  - report on the whole-genome sequencing, assembly, and
AB  - annotation of three Endozoicomonas type strains. These data will assist in
AB  - exploring interactions between Endozoicomonas organisms and their hosts, and it
AB  - will aid in the assembly of genomes from uncultivated Endozoicomonas spp.
ER  -

TY  - JOUR
AU  - Neaves, K.J.
AU  - Cooper, L.P.
AU  - White, J.H.
AU  - Carnally, S.M.
AU  - Dryden, D.T.
AU  - Edwardson, J.M.
AU  - Henderson, R.M.
TI  - Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 2053
EP  - 2063
VL  - 37
AB  - Atomic force microscopy (AFM) allows the study of single protein-DNA interactions such as
AB  - those observed with the Type I
AB  - Restriction-Modification systems. The mechanisms employed by these systems
AB  - are complicated and understanding them has proved problematic. It has been
AB  - known for years that these enzymes translocate DNA during the restriction
AB  - reaction, but more recent AFM work suggested that the archetypal EcoKI
AB  - protein went through an additional dimerization stage before the onset of
AB  - translocation. The results presented here extend earlier findings
AB  - confirming the dimerization. Dimerization is particularly common if the
AB  - DNA molecule contains two EcoKI recognition sites. DNA loops with dimers
AB  - at their apex form if the DNA is sufficiently long, and also form in the
AB  - presence of ATPgammaS, a non-hydrolysable analogue of the ATP required for
AB  - translocation, indicating that the looping is on the reaction pathway of
AB  - the enzyme. Visualization of specific DNA loops in the protein-DNA
AB  - constructs was achieved by improved sample preparation and analysis
AB  - techniques. The reported dimerization and looping mechanism is unlikely to
AB  - be exclusive to EcoKI, and offers greater insight into the detailed
AB  - functioning of this and other higher order assemblies of proteins
AB  - operating by bringing distant sites on DNA into close proximity via DNA
AB  - looping.
ER  -

TY  - JOUR
AU  - Nebendahl, A.
AU  - Baumlein, H.
TI  - Analysis of overlapping cDNA clones specific for a putative second DNA methyltransferase-encoding gene in Arabidopsis thaliana.
JO  - Gene
PY  - 1995
SP  - 269
EP  - 272
VL  - 157
AB  - We have isolated and sequenced overlapping cDNA clones specific for a putative second DNA
AB  - methyltransferase (MTase)-encoding gene (MTase11) from Arabidopsis thaliana (At) recently
AB  - described as a genomic DNA fragment.  The gene seems to be present as a single copy in the At
AB  - genome and is transcribed into a 2.2-kb messenger detectable only in young seedlings.  Using
AB  - sequence comparison we found structural differences between the cDNA clones and the previously
AB  - reported genomic fragment.  The amino-acid sequence deduced from the 1.8-kb cDNA sequence
AB  - shows the occurrence of the conserved motif number VI characteristic for m5C-MTases.  Northern
AB  - and Southern analysis detects no cross-hybridization with the originally described
AB  - MTase-encoding At gene (MTase1).
ER  -

TY  - JOUR
AU  - Nechaeva, A.A.
AU  - Kalinina, N.A.
AU  - Sukhodolets, V.V.
TI  - Plasmid profiles and stability of industrial strains of lactococci.
JO  - Genetika
PY  - 1995
SP  - 1210
EP  - 1217
VL  - 31
AB  - Industrial lactococci strains, usually cultivated on agar with hydrolized milk, are
AB  - characterized by an increased instability with respect to their ability to utilize lactose on
AB  - an enriched M21 medium.  Plasmid profiles of 14 industrial strains of Lactococcus lactis subs.
AB  - lactis and of a large number of segregants phenotypically differing in sugar-fermenting
AB  - ability and phage sensitivity were examined.  Four out of 14 strains segregated Lac-Gal-
AB  - clones, i.e., simultaneously lost the ability to utilize lactose and galactose.  All
AB  - phage-sensitive segregants retained systems of DNA restriction and modification.  Segregants
AB  - sensitive to the phage lethal effect were found.  These segregants possibly retained the
AB  - defense mechanism against phages manifested as an abortive infection.  In the majority of lac-
AB  - segregants, large plasmids of 40 to 55 kb were lost, although changes in plasmid profiles of
AB  - many Lac- segregants were not detected.
ER  -

TY  - JOUR
AU  - Needels, M.C.
AU  - Fried, S.R.
AU  - Love, R.
AU  - Rosenberg, J.M.
AU  - Boyer, H.W.
AU  - Greene, P.J.
TI  - Determinants of EcoRI endonuclease sequence discrimination.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1989
SP  - 3579
EP  - 3583
VL  - 86
AB  - The arginine at position 200 of EcoRI endonuclease is thought to make two
AB  - hydrogen bonds to the guanine of the sequence GAATTC and thus be an important
AB  - determinant of sequence discrimination.  Arg-200 was replaced by each of the
AB  - other 29 naturally occurring amino acids, and the mutant endonucleases were
AB  - assessed for activities in vivo and in vitro.  The mutant endonuclease with
AB  - lysine at position 200 exhibits the most in vivo activity of all the position
AB  - 200 mutants, although the in vitro activity is less than 1/100th of wild-type
AB  - activity.  Five other mutants show more drastically reduced levels of in vivo
AB  - activity (Cys, Pro, Val, Ser, and Trp).  The Cys, Val, and Ser mutant enzymes
AB  - appear to have in vivo activity which is specific for the wild-type canonical
AB  - site despite the loss of hydrogen bonding potential at position 200.  The Pro
AB  - and Trp mutants retain in vivo activity which is independent of the presence of
AB  - the EcoRI methylase.  In crude cell lysates, only the Cys mutant shows a very
AB  - low level of in vitro activity.  None of the mutant enzymes show a preference
AB  - for alternative sites in assays in vitro.  The implications of these results
AB  - are discussed.
ER  -

TY  - JOUR
AU  - Needels, M.C.
AU  - Reich, N.O.
AU  - Boyer, H.W.
AU  - Greene, P.
TI  - Cassette mutagenesis of EcoRI endonuclease.
JO  - J. Cell Biochem. Suppl.
PY  - 1987
SP  - 209
EP  - 209
VL  - 11C
AB  - From inspection of the x-ray crystal structure of the DNA-EcoRI endonuclease
AB  - recognition complex, regions of the protein which are responsible for binding
AB  - specificity and catalysis were inferred.  Based on this structural information,
AB  - we have subjected the EcoRI endonuclease gene to site directed mutagenesis.  In
AB  - the first round of mutagenesis we used mismatched oligonucleotides to introduce
AB  - a small number of conservative substitutions into the putative recognition
AB  - regions.  In order to extend this analysis, we have now engineered several
AB  - unique restriction sites into the EcoRI endonuclease gene bracketing
AB  - potentially important regions.  For example, we have introduced sites which
AB  - bracket the N-terminal residues of each of the recognition helices.  Also, the
AB  - introduction of flanking BstEII and SpeI sites around residue 130 has allowed
AB  - us to test a model for the mechanism of phosphodiester hydrolysis.  Based on
AB  - the crystal structure of the protein-DNA complex, it is possible that Lys 130
AB  - participates in general acid catalysis of this reaction.  Employing cassette
AB  - mutagenesis, we have generated mutants of the EcoRI endonuclease gene which
AB  - encode a variety of different amino acids at position 130.  The mutant gene
AB  - products are being characterized and the effect on catalysis of different
AB  - substitutions at position 130 is being assessed.
ER  -

TY  - JOUR
AU  - Neely, C.
AU  - Bou, K.C.
AU  - Cervantes, A.
AU  - Diaz, R.
AU  - Escobar, A.
AU  - Ho, K.
AU  - Hoefler, S.
AU  - Smith, H.H.
AU  - Abuyen, K.
AU  - Savalia, P.
AU  - Nealson, K.H.
AU  - Emerson, D.
AU  - Tully, B.
AU  - Barco, R.A.
AU  - Amend, J.
TI  - Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer.
JO  - Genome Announcements
PY  - 2018
SP  - e01581
EP  - e01517
VL  - 6
AB  - Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine
AB  - surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated
AB  - autotrophic growth through the oxidation of thiosulfate and iron. Here, we
AB  - present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Neely, R.K.
AU  - Daujotyte, D.
AU  - Grazulis, S.
AU  - Magennis, S.W.
AU  - Dryden, D.T.F.
AU  - Klimasauskas, S.
AU  - Jones, A.C.
TI  - Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 6953
EP  - 6960
VL  - 33
AB  - DNA base flipping is an important mechanism in molecular enzymology, but its study is limited
AB  - by the lack of an accessible and reliable diagnostic technique. A series of crystalline
AB  - complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent
AB  - nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target
AB  - flipped base, have been prepared and their structures determined at higher than 2 A
AB  - resolution. From time-resolved fluorescence measurements of these single crystals, we have
AB  - established that the fluorescence decay function of AP shows a pronounced, characteristic
AB  - response to base flipping: the loss of the very short (approximately 100 ps) decay component
AB  - and the large increase in the amplitude of the long (approximately 10 ns) component. When AP
AB  - is positioned at sites other than the target site, this response is not seen. Most
AB  - significantly, we have shown that the same clear response is apparent when M.HhaI complexes
AB  - with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP
AB  - fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes
AB  - that cannot be discerned from the present X-ray structures.
ER  -

TY  - JOUR
AU  - Neely, R.K.
AU  - Roberts, R.J.
TI  - The BsaHI Restriction-Modification System: Cloning, Sequencing and Analysis of Conserved Motifs.
JO  - BMC Mol. Biol.
PY  - 2008
SP  - 48
EP  - 48
VL  - 9
AB  - ABSTRACT: BACKGROUND: Restriction and modification enzymes typically recognise short DNA
AB  - sequences of between two and eight bases in length.
AB  - Understanding the mechanism of this recognition represents a significant
AB  - challenge that we begin to address for the BsaHI restriction-modification
AB  - system, which recognises the six base sequence GRCGYC. RESULTS: The DNA
AB  - sequences of the genes for the BsaHI methyltransferase, bsaHIM, and
AB  - restriction endonuclease, bsaHIR, have been determined (GenBank accession
AB  - #EU386360), cloned and expressed in E.coli. Both the restriction
AB  - endonuclease and methyltransferase enzymes share significant homology with
AB  - a group of 6 other enzymes comprising the RM systems HgiDI and HgiGI and
AB  - the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP RM systems. A
AB  - sequence alignment of these homologues shows that their amino acid
AB  - sequences are largely conserved and highlights several motifs of interest.
AB  - One such conserved motif was identified at the C-terminal end of the
AB  - bsaHIR gene as a potential DNA-recognising region of the enzyme. A
AB  - mutational analysis of these amino acids is consistent with this
AB  - assignment. Sequence alignment of the methyltransferase gene reveals a
AB  - motif that may be used as a diagnostic tool to define the recognition
AB  - sequences of the cytosine C5 methyltransferases. CONCLUSIONS: We have
AB  - identified a region of the R.BsaHI enzyme that is likely involved in DNA
AB  - recognition. Analysis of the amino acid sequence of the BsaHI
AB  - methyltransferase enzyme led us to propose two new motifs that can be used
AB  - in the diagnosis of the recognition sequence of the cytosine
AB  - C5-methyltransferases.
ER  -

TY  - JOUR
AU  - Neely, R.K.
AU  - Tamulaitis, G.
AU  - Chen, K.
AU  - Kubala, M.
AU  - Siksnys, V.
AU  - Jones, A.C.
TI  - Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 6859
EP  - 6870
VL  - 37
AB  - Restriction enzymes Ecl18kI, PspGI and EcoRII-C, specific for interrupted 5-bp target
AB  - sequences, flip the central base pair of these sequences into
AB  - their protein pockets to facilitate sequence recognition and adjust the
AB  - DNA cleavage pattern. We have used time-resolved fluorescence spectroscopy
AB  - of 2-aminopurine-labelled DNA in complex with each of these enzymes in
AB  - solution to explore the nucleotide flipping mechanism and to obtain a
AB  - detailed picture of the molecular environment of the extrahelical bases.
AB  - We also report the first study of the 7-bp cutter, PfoI, whose recognition
AB  - sequence (T/CCNGGA) overlaps with that of the Ecl18kI-type enzymes, and
AB  - for which the crystal structure is unknown. The time-resolved fluorescence
AB  - experiments reveal that PfoI also uses base flipping as part of its DNA
AB  - recognition mechanism and that the extrahelical bases are captured by PfoI
AB  - in binding pockets whose structures are quite different to those of the
AB  - structurally characterized enzymes Ecl18kI, PspGI and EcoRII-C. The
AB  - fluorescence decay parameters of all the enzyme-DNA complexes are
AB  - interpreted to provide insight into the mechanisms used by these four
AB  - restriction enzymes to flip and recognize bases and the relationship
AB  - between nucleotide flipping and DNA cleavage.
ER  -

TY  - JOUR
AU  - Neesen, K.
AU  - Volckaert, G.
TI  - Construction and shuttling of novel bifunctional vectors for Streptomyces spp. and Escherichia coli.
JO  - J. Bacteriol.
PY  - 1989
SP  - 1569
EP  - 1573
VL  - 171
AB  - Shuttle vectors for gene transfer between Streptomyces spp. and Escherichia
AB  - coli have been constructed by fusion of an artificial multicopy E. coli
AB  - replicon and DNA fragments of pIJ702.  Stable transfer to Streptomyces lividans
AB  - was obtained.  Marked differences in transformation efficiency were observed
AB  - when plasmid DNA isolated from E. coli GM119 was used instead of that from
AB  - strain HB101.
ER  -

TY  - JOUR
AU  - Neff, N.F.
TI  - Protein splicing: selfish genes invade cellular proteins.
JO  - Curr. Opin. Cell Biol.
PY  - 1993
SP  - 971
EP  - 976
VL  - 5
AB  - Protein splicing is a series of enzymatic events involving intramolecular
AB  - protein breakage, rejoining and intron homing, in which introns are able to promote the
AB  - recombinative transposition of their own coding sequences.  Eukaryotic and prokaryotic
AB  - spliced proteins have conserved similar gene structure, but little amino acid identity.  The
AB  - genes coding for these spliced proteins contain internal in-frame introns that encode
AB  - polypeptides that apparently self-excise from the resulting host protein sequences.
AB  - Excision of the 'protein intron' is coupled with joining of the two flanking protein regions
AB  - encoded by exons of the host gene.  Some introns of this type encode DNA endonucleases,
AB  - related to Group I RNA intron gene products, that stimulate gene conversion and self-
AB  - transmission.
ER  -

TY  - JOUR
AU  - Negi, V.
AU  - Lata, P.
AU  - Sangwan, N.
AU  - Kumar-Gupta, S.
AU  - Das, S.
AU  - Rao, D.L.
AU  - Lal, R.
TI  - Draft Genome Sequence of Hexachlorohexane (HCH)-Degrading Sphingobium lucknowense Strain F2T, Isolated from an HCH Dumpsite.
JO  - Genome Announcements
PY  - 2014
SP  - e00788
EP  - e00714
VL  - 2
AB  - Sphingobium lucknowense F2(T), isolated from the hexachlorocylcohexane (HCH) dumpsite located
AB  - in Ummari village, Lucknow, India, rapidly degrades HCH isomers.
AB  - Here we report the draft genome of strain F2 (4.4 Mbp), consisting of 4,910
AB  - protein coding genes with an average G+C content of 64.3%.
ER  -

TY  - JOUR
AU  - Negrete-Abascal, E.
AU  - Montes-Garcia, F.
AU  - Vaca-Pacheco, S.
AU  - Leyto-Gil, A.M.
AU  - Fragoso-Garcia, E.
AU  - Carvente-Garcia, R.
AU  - Perez-Agueros, S.
AU  - Castelan-Sanchez, H.G.
AU  - Garcia-Molina, A.
AU  - Villamar, T.E.
AU  - Sanchez-Alonso, P.
AU  - Vazquez-Cruz, C.
TI  - Genome Sequence of Actinobacillus seminis Strain ATCC 15768, a Reference Strain of Ovine Pathogens That Causes Infections in Reproductive Organs.
JO  - Genome Announcements
PY  - 2018
SP  - e01453
EP  - e01417
VL  - 6
AB  - The draft genome sequence of Actinobacillus seminis strain ATCC 15768 is reported here. The
AB  - genome comprises 22 contigs corresponding to 2.36 Mb with 40.7% G+C
AB  - content and contains several genes related to virulence, including a putative RTX
AB  - protein.
ER  -

TY  - JOUR
AU  - Neiger, R.
AU  - Thomas, M.
AU  - Das, S.
AU  - Barnes, M.
AU  - Fletcher, B.
AU  - Snekvik, K.
AU  - Thompson, J.
AU  - Scaria, J.
TI  - Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Coldwater Disease Outbreaks at Three Production Hatcheries.
JO  - Genome Announcements
PY  - 2016
SP  - e00035
EP  - e00016
VL  - 4
AB  - We report here the genome sequences of three Flavobacterium psychrophilum strains causing a
AB  - bacterial coldwater disease (BCWD) outbreak, isolated from infected
AB  - rainbow trout from hatcheries in Montana and South Dakota. The availability of
AB  - these virulent outbreak-causing strain genome sequences will help further
AB  - understand the pathogenesis of BCWD.
ER  -

TY  - JOUR
AU  - Nejedly, K.
AU  - Matyasek, R.
AU  - Palecek, E.
TI  - Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing.
JO  - J. Biomol. Struct. Dyn.
PY  - 1988
SP  - 261
EP  - 273
VL  - 6
AB  - Structural distortions on the boundary between right-handed and left-
AB  - handed segments in the superhelical plasmid pPK2 (a derivative of pUC19 containing (dC-
AB  - dG)n segments cloned into polylinker) were studied by means of chemical probes.  Strong
AB  - osmium tetroxide, pyridine (Os,py) modification of DNA at native superhelical density (sigma)
AB  - was found in four thymines surrounding the (dC-dG)13 segment.  These results correlated  with
AB  - restriction cleavage inhibition (due to modification): BamHI cleavage was strongly  inhibited,
AB  - unlike the neighboring XbaI and SalI (weak or no inhibition).  In the (dC-dG)8  segment
AB  - considerably weaker modification of the B-Z junctions was observed,
AB  - accompanied by weak inhibition of BamHI cleavage, while the neighboring SmaI and KpnI
AB  - were not affected.  Os,py modification of DNA at native sigma was not detected by nuclease S1
AB  - cleavage at and (dC-dG)n segment.  However, this enzyme recognized and cleaved at the  B-Z
AB  - junction, osmium modified at more negative sigma.  The results obtained with the glyoxal  and
AB  - diethyl pyrocarbonate modification support the idea of very narrow B-Z junctions at  native
AB  - sigma.
ER  -

TY  - JOUR
AU  - Nekrasov, S.V.
AU  - Agafonova, O.V.
AU  - Belogurova, N.G.
AU  - Delver, E.P.
AU  - Belogurov, A.A.
TI  - Plasmid-encoded Antirestriction Protein ArdA Can Discriminate between Type I Methyltransferase and Complete Restriction-Modification System.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 284
EP  - 297
VL  - 365
AB  - Many promiscuous plasmids encode the antirestriction proteins ArdA (alleviation of restriction
AB  - of DNA) that specifically affect the
AB  - restriction activity of heterooligomeric type I restriction-modification
AB  - (R-M) systems in Escherichia coli cells. In addition, a lot of the
AB  - putative ardA genes encoded by plasmids and bacterial chromosomes are
AB  - found as a result of sequencing of complete genomic sequences, suggesting
AB  - that ArdA proteins and type I R-M systems that seem to be widespread among
AB  - bacteria may be involved in the regulation of gene transfer among
AB  - bacterial genomes. Here, the mechanism of antirestriction action of ArdA
AB  - encoded by IncI plasmid ColIb-P9 has been investigated in comparison with
AB  - that of well-studied T7 phage-encoded antirestriction protein Ocr using
AB  - the mutational analysis, retardation assay and His-tag affinity
AB  - chromatography. Like Ocr, ArdA protein was shown to be able to efficiently
AB  - interact with EcoKI R-M complex and affect its in vivo and in vitro
AB  - restriction activity by preventing its interaction with specific DNA.
AB  - However, unlike Ocr, ArdA protein has a low binding affinity to EcoKI
AB  - Mtase and the additional C-terminal tail region (VF-motif) is needed for
AB  - ArdA to efficiently interact with the type I R-M enzymes. It seems likely
AB  - that this ArdA feature is a basis for its ability to discriminate between
AB  - activities of EcoKI Mtase (modification) and complete R-M system
AB  - (restriction) which may interact with unmodified DNA in the cells
AB  - independently. These findings suggest that ArdA may provide a very
AB  - effective and delicate control for the restriction and modification
AB  - activities of type I systems and its ability to discriminate against DNA
AB  - restriction in favour of the specific modification of DNA may give some
AB  - advantage for efficient transmission of the ardA-encoding promiscuous
AB  - plasmids among different bacterial populations.
ER  -

TY  - JOUR
AU  - Nell, S.
AU  - Estibariz, I.
AU  - Krebes, J.
AU  - Bunk, B.
AU  - Graham, D.Y.
AU  - Overmann, J.
AU  - Song, Y.
AU  - Sproer, C.
AU  - Yang, I.
AU  - Wex, T.
AU  - Korlach, J.
AU  - Malfertheiner, P.
AU  - Suerbaum, S.
TI  - Genome and Methylome Variation in Helicobacter pylori With a cag Pathogenicity Island During Early Stages of Human Infection.
JO  - Gastroenterology
PY  - 2018
SP  - 612
EP  - 623.e7
VL  - 154
AB  - BACKGROUND and AIMS: Helicobacter pylori is remarkable for its genetic variation; yet, little
AB  - is known about its genetic changes during early stages of human
AB  - infection, as the bacteria adapt to their new environment. We analyzed genome and
AB  - methylome variations in a fully virulent strain of H pylori during experimental
AB  - infection. METHODS: We performed a randomized Phase I/II, observer-blind,
AB  - placebo-controlled study of 12 healthy, H pylori-negative adults in Germany from
AB  - October 2008 through March 2010. The volunteers were given a prophylactic vaccine
AB  - candidate (n = 7) or placebo (n = 5) and then challenged with H pylori strain
AB  - BCM-300. Biopsy samples were collected and H pylori were isolated. Genomes of the
AB  - challenge strain and 12 reisolates, obtained 12 weeks after (or in 1 case, 62
AB  - weeks after) infection were sequenced by single-molecule, real-time technology,
AB  - which, in parallel, permitted determination of genome-wide methylation patterns
AB  - for all strains. Functional effects of genetic changes observed in H pylori
AB  - strains during human infection were assessed by measuring release of interleukin
AB  - 8 from AGS cells (to detect cag pathogenicity island function), neutral red
AB  - uptake (to detect vacuolating cytotoxin activity), and adhesion assays. RESULTS:
AB  - The observed mutation rate was in agreement with rates previously determined from
AB  - patients with chronic H pylori infections, without evidence of a mutation burst.
AB  - A loss of cag pathogenicity island function was observed in 3 reisolates. In
AB  - addition, 3 reisolates from the vaccine group acquired mutations in the
AB  - vacuolating cytotoxin gene vacA, resulting in loss of vacuolization activity. We
AB  - observed interstrain variation in methylomes due to phase variation in genes
AB  - encoding methyltransferases. CONCLUSIONS: We analyzed adaptation of a fully
AB  - virulent strain of H pylori to 12 different volunteers to obtain a robust
AB  - estimate of the frequency of genetic and epigenetic changes in the absence of
AB  - interstrain recombination. Our findings indicate that the large amount of genetic
AB  - variation in H pylori poses a challenge to vaccine development.
AB  - ClinicalTrials.gov no: NCT00736476.
ER  -

TY  - JOUR
AU  - Nellemann, L.J.
AU  - Aamand, J.L.
AU  - Madsen, A.
AU  - Josephsen, J.
TI  - Characterization of a non-type II restriction/modification system on plasmid PJW565 from Lactococcus lactis subsp. cremoris W56.
JO  - FASEB J.
PY  - 1997
SP  - A1035
EP  - A1035
VL  - 11
AB  - Lactococcus lactis subsp. cremoris W56 contains several plasmid encoded
AB  - restriction-modification systems.  The 12.826 kb plasmid pJW565 exhibits a non-type II
AB  - activity, designated LlaBII, and displays resistance against small-isometric-headed phages p2
AB  - and SK1.  The entire plasmid has been sequenced.  Sequence analysis revealed that the R/M
AB  - system was encoded by at least two genes, carrying code for the 231 amino acid protein
AB  - designated llabiiM, and the 1376 amino acid protein designated llabiiR.  Both genes were
AB  - preceded by putative promoter and RBS sequences.  The two genes were separated by 1
AB  - nucleotide, indicating polycistronic transcription.  The predicted proteins (M.LlaBII and
AB  - R.LlaBII) showed homology to several adenine-specific methyltransferases and an E. coli type I
AB  - restriction enzyme, respectively.  Apart from the putative genes involved in the R/M system
AB  - activity and the genes involved in replication, pJW565 contained several open reading frames
AB  - with no known function or homology to existing sequencing data in the EMBL or Genbank
AB  - databases.  In vitro studies of LlaBII activity revealed that the cofactor ATP was essential,
AB  - and the methyl-group donor Adomet stimulated LlaBII endonuclease activity.
ER  -

TY  - JOUR
AU  - Nelson, B.A.
AU  - Ramaiya, P.
AU  - Lopez-de-Leon, A.
AU  - Kumar, R.
AU  - Crinklaw, A.
AU  - Jolkovsky, E.
AU  - Crane, J.M.
AU  - Bergstrom, G.C.
AU  - Rey, M.W.
TI  - Complete Genome Sequence for the Fusarium Head Blight Antagonist Bacillus amyloliquefaciens Strain TrigoCor 1448.
JO  - Genome Announcements
PY  - 2014
SP  - e00219
EP  - e00214
VL  - 2
AB  - We present the complete genome sequence for Bacillus amyloliquefaciens TrigoCor 1448 (ATCC
AB  - 202152), a bacterial biological control agent for Fusarium head blight
AB  - in wheat. We compare it to its closest relative, B. amyloliquefaciens strain
AB  - AS43.3.
ER  -

TY  - JOUR
AU  - Nelson, H.C.M.
AU  - Bestor, T.H.
TI  - Base eversion and shuffling by DNA methyltransferases.
JO  - Chem. Biol.
PY  - 1996
SP  - 419
EP  - 423
VL  - 3
AB  - The structures of two DNA cytosine methyltransferases reveal two novel methods of gaining
AB  - access to the substrate cytosine residue, both of which involve eversion of the cytosine in a
AB  - process that may require DNA bending.  In one instance there is also widespread base shuffling
AB  - and distortion of the DNA.
ER  -

TY  - JOUR
AU  - Nelson, J.M.
AU  - Miceli, S.M.
AU  - Lechevalier, M.P.
AU  - Roberts, R.J.
TI  - FseI, a new type II restriction endonuclease that recognizes the octanucleotide sequence 5' GGCCGGCC 3' .
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 2061
EP  - 2064
VL  - 18
AB  - A Type II restriction endonuclease, designated FseI, has been partially purified from a
AB  - Frankia species (NRRL 18528). This enzyme cleaves Adenovirus 2 DNA at three sites, but does
AB  - not cleave the DNAs from bacteriophages lambda, T7 and PhiX174, the animal virus SV40, pUC18
AB  - and pBR322. FseI recognizes the octanucleotide sequence 5' GGCCGG^CC 3' and cleaves as
AB  - indicated by the arrow. The frequency of occurrence of FseI sites within sequenced regions of
AB  - the human genome is similar to that for NotI sites.
ER  -

TY  - JOUR
AU  - Nelson, K.E. et al.
TI  - Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83.
JO  - J. Bacteriol.
PY  - 2003
SP  - 5591
EP  - 5601
VL  - 185
AB  - The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium
AB  - Porphyromonas gingivalis strain W83, a major contributor to
AB  - periodontal disease, was determined. Whole-genome comparative analysis
AB  - with other available complete genome sequences confirms the close
AB  - relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum
AB  - and the green-sulfur bacteria. Within the CFB phyla, the genomes most
AB  - similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron
AB  - and B. fragilis. Outside of the CFB phyla the most similar genome to P.
AB  - gingivalis is that of Chlorobium tepidum, supporting the previous
AB  - phylogenetic studies that indicated that the Chlorobia and CFB phyla are
AB  - related, albeit distantly. Genome analysis of strain W83 reveals a range
AB  - of pathways and virulence determinants that relate to the novel biology of
AB  - this oral pathogen. Among these determinants are at least six putative
AB  - hemagglutinin-like genes and 36 previously unidentified peptidases. Genome
AB  - analysis also reveals that P. gingivalis can metabolize a range of amino
AB  - acids and generate a number of metabolic end products that are toxic to
AB  - the human host or human gingival tissue and contribute to the development
AB  - of periodontal disease.
ER  -

TY  - JOUR
AU  - Nelson, K.E. et al.
TI  - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome   components of this species.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 2386
EP  - 2395
VL  - 32
AB  - The genomes of three strains of Listeria monocytogenes that have been associated with
AB  - food-borne illness in the USA were subjected to whole
AB  - genome comparative analysis. A total of 51, 97 and 69 strain-specific
AB  - genes were identified in L.monocytogenes strains F2365 (serotype 4b,
AB  - cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858
AB  - (serotype 4b, meat isolate), respectively. Eighty-three genes were
AB  - restricted to serotype 1/2a and 51 to serotype 4b strains. These strain-
AB  - and serotype-specific genes probably contribute to observed differences in
AB  - pathogenicity, and the ability of the organisms to survive and grow in
AB  - their respective environmental niches. The serotype 1/2a-specific genes
AB  - include an operon that encodes the rhamnose biosynthetic pathway that is
AB  - associated with teichoic acid biosynthesis, as well as operons for five
AB  - glycosyl transferases and an adenine-specific DNA methyltransferase. A
AB  - total of 8603 and 105 050 high quality single nucleotide polymorphisms
AB  - (SNPs) were found on the draft genome sequences of strain H7858 and strain
AB  - F6854, respectively, when compared with strain F2365. Whole genome
AB  - comparative analyses revealed that the L.monocytogenes genomes are
AB  - essentially syntenic, with the majority of genomic differences consisting
AB  - of phage insertions, transposable elements and SNPs.
ER  -

TY  - JOUR
AU  - Nelson, K.E. et al.
TI  - Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
JO  - Nature
PY  - 1999
SP  - 323
EP  - 329
VL  - 399
AB  - The 1,860,725-base pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding
AB  - regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of
AB  - unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars
AB  - and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other
AB  - thermophilic Eubacteria and Archaea.  Of the Eubacteria sequenced to date, T. maritima has the
AB  - highest percentage (24%) of genes that are most similar to archaeal genes.  Eighty-one
AB  - archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size
AB  - from 4 to 20 kilobases.  Conservation of gene order between T. maritima and Archaea in many of
AB  - the clustered regions suggests that lateral gene transfer may have occurred between
AB  - thermophilic Eubacteria and Archaea.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - Burbank, D.E.
AU  - Van Etten, J.L.
TI  - Chlorella viruses encode multiple DNA methyltransferases.
JO  - Biol. Chem.
PY  - 1998
SP  - 423
EP  - 428
VL  - 379
AB  - The >320 kb dsDNA genomes of 16 viruses which infect Chlorella strain NC64A and 5 viruses
AB  - infecting Chlorella strain Pbi were tested for their sensitivity/resistance to more than 80
AB  - DNA restriction endonucleases.  From the known methylation sensitivities of these enzymes to
AB  - site-specific 5-methylcytosine and N6-methyladenine DNA modifications, we deduce that the 16
AB  - NC64A viruses encode at least 13 different sequence-specific DNA methyltransferases and the 5
AB  - Pbi viruses encode at least 7 sequence-specific DNA methyltransferases.  Each DNA
AB  - methyltransferase has a 2 to 4 base pair DNA recognition sequence.  Some individual viruses
AB  - encode as many as ten different DNA methyltransferases, making these chlorella virus genomes
AB  - among the most concentrated sources of DNA methyltransferase genes known.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - Christ, C.
AU  - Schildkraut, I.
TI  - Alteration of apparent restriction endonuclease recognition specificities by DNA methylases.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 5165
EP  - 5173
VL  - 12
AB  - An in vitro method of altering the apparent cleavage specificities of
AB  - restriction endonucleases was developed using DNA modification methylases.
AB  - This method was used to reduce the number of cleavage sites for 34 restriction
AB  - endonucleases.  In particular, single-site cleavages were achieved for NheI in
AB  - Adeno-2 DNA and for AccI and HincII in pBR322 DNA by specifically methylating
AB  - all but one recognition sequence.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - McClelland, M.
TI  - The effect of site-specific methylation on restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - r219
EP  - r230
VL  - 15
AB  - Previous tabulations of restriction endonuclease sensitivities to site-specific
AB  - DNA methylation have shown that these endonucleases cannot cut particular DNA
AB  - recognition sequences which have been methylated at 4mC, 5mC or 6mA.  Since our
AB  - previous tabulation in this journal the major new additions are extensive data
AB  - on 4mC.  We have altered our notation to incorporate the 4mC data and added a
AB  - number of footnotes.  Fine structural details of cleavage reactions, rate
AB  - differences on hemi- and bi-methylated substrates, and experimental
AB  - discrepancies are noted where such data is available.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - McClelland, M.
TI  - Purification and assay of Type II DNA methylases.
JO  - Methods Enzymol.
PY  - 1987
SP  - 32
EP  - 41
VL  - 155
AB  - Site-specific DNA methylases (S-adenosylmethionine:  DNA methyltransferases)
AB  - have a variety of uses in DNA analytical procedures.  Methylases may be used as
AB  - probes for DNA conformation, in recombinant DNA cloning strategies, or in
AB  - combination with restriction endonucleases to generate rare or novel DNA
AB  - cleavage specificities.  DNA methylases have been purified from a number of
AB  - different sources.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - McClelland, M.
TI  - Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - r389
EP  - r415
VL  - 17
AB  - Review of the effects of methylation.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - McClelland, M.
TI  - Site-specific methylation: effect on DNA modification methyltransferases and restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2045
EP  - 2071
VL  - 19
AB  - We present in Table I an updated list of the sensitivities of over 240
AB  - restriction endonucleases to the site-specific DNA modifications m4C, m5C,
AB  - hm5C, and m6A, four modifications that are common in DNA prokaryotes,
AB  - eukaryotes, and their viruses (Mc2, Mc5, Mc8, Mc11, Ne3, Ne4).  Table II is a
AB  - list of over 130 characterized DNA methyltransferases.  A detailed list of
AB  - cloned restriction-modification genes has been made Wilson (Wi4).  Table III
AB  - lists the sensitivities of over 20 Type II DNA methyltransferases to m4C, m5C,
AB  - hm5C, and m6A modification.  Most DNA methyltransferases are sensitive to
AB  - non-canonical modifications within their recognition sequences (Bu5, Mc10, Ne3,
AB  - Po4), and this sensitivity may differ from that of their restriction
AB  - endonuclease partners.  Finally, several restriction endonuclease isoschizomers
AB  - are known to differ in their ability to cleave DNA which has been methylated.
AB  - Table IV lists over 20 known isoschizomer pairs and one isomethylator pair,
AB  - along with the modified recognition sites at which they differ.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - McClelland, M.
TI  - Chromosome mapping at the megabase level: Guidelines for choosing restriction endonucleases for pulsed field gel mapping.
JO  - Promega Notes
PY  - 1989
SP  - 1
EP  - 3
VL  - 18
AB  - A review.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - McClelland, M.
TI  - Use of DNA methyltransferase/endonuclease enzyme combinations for megabase mapping of chromosomes.
JO  - Methods Enzymol.
PY  - 1992
SP  - 279
EP  - 303
VL  - 216
AB  - Based on a knowledge of the methylation sensitivities of restriction-modification enzymes, and
AB  - the specificities of bacterial DNA methyltransferases, it is possible to mix and match
AB  - site-specific DNA methylation and restriction endonuclease cleavage reactions to produce rare
AB  - or novel DNA cleavages (Dobritsa and Dobritsa, 1980); Nelson et al., 1984; McClelland et al.,
AB  - 1985) Detailed procedures for the purification, assay and use of methylase/endonuclease
AB  - combinations in sequential two-step reactions were described in a previous volume of this
AB  - series (McClelland, 1987, Nelson and McClelland, 1987; Nelson and Shildkraut, 1987).
AB  - Three-step procedures have also been described, based upon methylase/endonuclease combinations
AB  - and sequence-specific masking by bacterial repressor proteins (Koob and Szybalski, 1980,
AB  - polypyrimidine triplexes (Maher et al, 1989; Hanvey et al 1989), or other DNA
AB  - methyltransferases (McClelland and Nelson, 1987; McClelland and Nelson, 1988a; Posfai and
AB  - Szybalski, 1988). This article describes four selected DNA methylase/ endonuclease
AB  - combinations which may be used for megabase mapping of chromosome fragments in the size range
AB  - from 100 kb-2000 kb, paying special attention to features of these reactions which have
AB  - sometimes proven problematic.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - Raschke, E.
AU  - McClelland, M.
TI  - Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3139
EP  - 3154
VL  - 21
AB  - We present in Table I an updated list of the sensitivities of 298 restriction endonucleases
AB  - and 20 DNA methyltransferases to site-specific modification at 4-methylcytosine (m4C),
AB  - 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), and 6-methyladenine (m6A), four
AB  - modifications that are common in the DNA of prokaryotes, eukaryotes, and their viruses. In
AB  - addition, new information is included on restriction endonuclease cleavage at sites modified
AB  - with 5-hydroxymethyluracil (hm5U). Knowledge of the sensitivity of restriction endonucleases
AB  - to site-specific modification can be used to study cellular DNA methylation. Several
AB  - restriction-modification enzymes share the same recognition sequence specificity, but have
AB  - different sensitivities to site-specific methylation. Table II lists 32 known isoschizomer
AB  - pairs and one isomethylator pair, along with the modified recognition sites at which they
AB  - differ.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - Schildkraut, I.
TI  - The use of DNA methylases to alter the apparent recognition specificities of restriction endonucleases.
JO  - Methods Enzymol.
PY  - 1987
SP  - 41
EP  - 48
VL  - 155
AB  - DNA methylases can be used to alter the apparent recognition specificity of
AB  - restriction endonucleases.  These altered specificities are unique and increase
AB  - the list of cleavage sequences which can be utilized by molecular biologists.
ER  -

TY  - JOUR
AU  - Nelson, M.
AU  - Zhang, Y.
AU  - Van Etten, J.L.
TI  - DNA methyltransferases and DNA-site-specific endonucleases encoded by chlorella viruses.
JO  - DNA Methylation: Molecular Biology and Biological Significance
PY  - 1993
SP  - 186
EP  - 211
VL  - 0
AB  - Large polyhedral (diameter of 150 to 190 nm) dsDNA-containing (>30 kbp) viruses which infect
AB  - certain unicellular, eukaryotic, chlorella-like green algae are common in fresh water
AB  - collected throught the world (Van Etten et al, 1985; Schuster et al. 1986; Zhang et al., 1988;
AB  - Reisser et al., 1988; Yamada et al., 1991). The hosts for these lytic chlorella viruses are
AB  - exsymbiotic Chlorella strains NC64A and Pbi, originally isolated from the protozoan Paramecium
AB  - bursaria. Chlorella viruses, which can be produced in large quantities, are the first viruses
AB  - infecting a photosynthetic eukaryotic organism which can be plaque assayed (Van Etten et al.,
AB  - 1983) and have been given family status with the name Phycodnaviridae (Francki et al., 1991).
AB  - A comprehensive review on the chlorella viruses has recently been published (Van Etten et al.,
AB  - 1991).
ER  -

TY  - JOUR
AU  - Nelson, M.C.
AU  - Bomar, L.
AU  - Graf, J.
TI  - Complete Genome Sequence of the Novel Leech Symbiont Mucinivorans hirudinis M3T.
JO  - Genome Announcements
PY  - 2015
SP  - e01530
EP  - e01514
VL  - 3
AB  - Mucinivorans hirudinis M3(T) was isolated from the digestive tract of the medicinal leech,
AB  - Hirudo verbana, and is the type species of a new genus within
AB  - the Rikenellaceae. Here, we report the complete annotated genome sequence of this
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Nelson, M.C.
AU  - LaPatra, S.E.
AU  - Welch, T.J.
AU  - Graf, J.
TI  - Complete Genome Sequence of Yersinia ruckeri Strain CSF007-82, Etiologic Agent of Red Mouth Disease in Salmonid Fish.
JO  - Genome Announcements
PY  - 2015
SP  - e01491
EP  - e01414
VL  - 3
AB  - We present the complete, closed, and finished chromosomal and extrachromosomal genome
AB  - sequences of Yersinia ruckeri strain CSF007-82, the etiologic agent of
AB  - enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a
AB  - G+C content of 47.5% and encodes 3,530 predicted coding sequences (CDS), 7
AB  - ribosomal operons, and 80 tRNAs.
ER  -

TY  - JOUR
AU  - Nelson, M.C.
AU  - Varney, J.S.
AU  - Welch, T.J.
AU  - Graf, J.
TI  - Draft Genome Sequence of Lactococcus garvieae Strain PAQ102015-99, an Outbreak Strain Isolated from a Commercial Trout Farm in the Northwestern United States.
JO  - Genome Announcements
PY  - 2016
SP  - e00781
EP  - e00716
VL  - 4
AB  - We announce the draft genome assembly of Lactococcus garvieae strain PAQ102015-99, a recently
AB  - isolated strain from an outbreak of lactococcosis at a
AB  - commercial trout farm in the northwestern United States. The draft genome
AB  - comprises 14 contigs totaling 2,068,357 bp with an N50 of 496,618 bp and average
AB  - G+C content of 38%.
ER  -

TY  - JOUR
AU  - Nelson, P.S.
AU  - Papas, T.S.
AU  - Schweinfest, C.W.
TI  - Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 681
EP  - 686
VL  - 21
AB  - We have investigated the ability of a large number of restriction enzymes to digest
AB  - non-canonically hemimethylated DNA at high enzyme-to-substrate ratios. A single-stranded
AB  - unmethylated phagemid was used as a template to complete synthesis of the second strand using
AB  - 5-methyl-dCTP to substitute for all the deoxycytosine residues. A fragment of this
AB  - double-stranded hemimethylated DNA which contains the multiple cloning site region was used as
AB  - a substrate. For all the enzymes tested, at least some degree of protection from digestion is
AB  - observed. Sites completely protected from digestion by their cognate enzymes are SalI, BstXI,
AB  - SacI, SacII, SmaI, SstI, XhoI, PstI, HinfI, BamHI and AccI. Sites partially protected from
AB  - digestion by their cognate enzymes are XbaI, HindIII, KpnI, SpeI, ClaI, EcoRI and PvuII.
AB  - Knowledge of the sensitivity of commonly used restriction enzymes to hemimethylated substrates
AB  - is useful for several applications, which will be discussed.
ER  -

TY  - JOUR
AU  - Nelson, R.L.
AU  - Castro, M.A.
AU  - Katti, M.
AU  - Eisen, J.A.
AU  - Van Laar, T.A.
TI  - Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus, CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos.
JO  - Genome Announcements
PY  - 2016
SP  - e00807
EP  - e00816
VL  - 4
AB  - Avian species have the potential to serve as important reservoirs for the spread  of
AB  - pathogenic microorganisms. Here, we report the genome sequence of a
AB  - drug-resistant strain of Bacillus pumilus, CB01, isolated from the feces of an
AB  - American crow, Corvus brachyrhynchos.
ER  -

TY  - JOUR
AU  - Nemet, Z.
AU  - Albert, E.
AU  - Nagy, T.
AU  - Olasz, F.
AU  - Barta, E.
AU  - Kiss, J.
AU  - Dan, A.
AU  - Banyai, K.
AU  - Hermans, K.
AU  - Biksi, I.
TI  - Draft Genome Sequence of a Highly Virulent Rabbit Staphylococcus aureus Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e00461
EP  - e00415
VL  - 3
AB  - We report the draft genome sequence of Staphylococcus aureus Sp17, a typical highly virulent
AB  - (HV) rabbit strain. As current medicine apparently fails to
AB  - effectively reduce disease and economical losses caused by this organism, it is
AB  - essential to gain better insight on its genomic arrangement.
ER  -

TY  - JOUR
AU  - Neoh, H.M.
AU  - Mohamed-Hussein, Z.A.
AU  - Tan, X.E.
AU  - Abd-Rahman, B.R.R.M.
AU  - Hussin, S.
AU  - Mohamad, Z.N.
AU  - Jamal, R.
TI  - Draft Genome Sequences of Four Nosocomial Methicillin-Resistant Staphylococcus aureus (MRSA) Strains (PPUKM-261-2009, PPUKM-332-2009, PPUKM-377-2009, and  PPUKM-775-2009) Representative of Dominant MRSA Pulsotypes Circulating in a  Malaysian University T.
JO  - Genome Announcements
PY  - 2013
SP  - e00103
EP  - e00112
VL  - 1
AB  - Here, we report the draft genome sequences of four nosocomial methicillin-resistant
AB  - Staphylococcus aureus strains (PPUKM-261-2009, PPUKM-332-2009, PPUKM-377-2009, and
AB  - PPUKM-775-2009) isolated from a university teaching hospital in Malaysia. Three of the strains
AB  - belong to sequence type 239 (ST239), which has been associated with sustained hospital
AB  - epidemics worldwide.
ER  -

TY  - JOUR
AU  - Nerdal, W.
AU  - Hare, D.R.
AU  - Reid, B.R.
TI  - Solution structure of the EcoRI DNA sequence: Refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations.
JO  - Biochemistry
PY  - 1989
SP  - 10008
EP  - 10021
VL  - 28
AB  - The solution structure of the self-complementary DNA duplex [d(CGCGAATTCGCG)]2,
AB  - which contains the EcoRI restriction site sequence GAATTC at the center, has
AB  - been studied by two-dimensional nuclear magnetic resonance spectroscopy.
AB  - Time-dependent nuclear Overhauser effect spectra were used to obtain the
AB  - initial cross-relaxation rates between 155 pairs of protons.  These initial
AB  - cross-relaxation rates were converted into interproton distances and entered
AB  - into a distance (bounds) matrix.  A distance geometry algorithm (DSPACE) was
AB  - used to create embedded starting structures and to refine these structures
AB  - until they showed good agreement with the distance matrix; symmetry constraints
AB  - were included in the refinement procedure, making the two strands in the
AB  - refined distanced geometry structures virtually identical and significantly
AB  - improving the agreement with the distance matrix.  The NOESY spectrum for one
AB  - of these distance geometry was then calculated from the explicit coordinates by
AB  - numerically integrating all the z-magnetization transfer pathways among
AB  - neighboring protons within a specified radius. Distances in this distance
AB  - geometry structure that did not agree with the experimental NOESY time course
AB  - were then adjusted accordingly.  This process was iterated until a good
AB  - agreement between calculated and experimental NOESY spectra was reached.  The
AB  - final structure, which generates good agreement with the experimental NOESY
AB  - spectrum, display kinks at the C3-G4 base step and at the A6-T7 base step that
AB  - appear to be similar to those reported for the EcoRI restriction site DNA bound
AB  - to its endonuclease.  The solution structure is not the same as the crystal
AB  - structure of this DNA duplex.
ER  -

TY  - JOUR
AU  - Neri, A.
AU  - Fazio, C.
AU  - Ciammaruconi, A.
AU  - Anselmo, A.
AU  - Fortunato, A.
AU  - Palozzi, A.
AU  - Vacca, P.
AU  - Fillo, S.
AU  - Lista, F.
AU  - Stefanelli, P.
TI  - Draft Genome Sequence of C:P1.5-1,10-8:F3-6:ST-11 Meningococcal Clinical Isolate  Associated with a Cluster on a Cruise Ship.
JO  - Genome Announcements
PY  - 2014
SP  - e01263
EP  - e01214
VL  - 2
AB  - Meningococcal serogroup C strains, in particular those belonging to the ST-11 clonal complex,
AB  - are known to cause invasive diseases worldwide. We report the
AB  - genome sequence of a Neisseria meningitidis strain linked to a cluster of cases
AB  - of invasive meningococcal disease on a cruise ship that was described in 2012.
ER  -

TY  - JOUR
AU  - Neri, F.
AU  - Krepelova, A.
AU  - Incarnato, D.
AU  - Maldotti, M.
AU  - Parlato, C.
AU  - Galvagni, F.
AU  - Matarese, F.
AU  - Stunnenberg, H.G.
AU  - Oliviero, S.
TI  - Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs.
JO  - Cell
PY  - 2013
SP  - 121
EP  - 134
VL  - 155
AB  - The de novo DNA methyltransferase 3-like (Dnmt3L) is a catalytically inactive DNA
AB  - methyltransferase that cooperates with Dnmt3a and Dnmt3b to methylate DNA. Dnmt3L
AB  - is highly expressed in mouse embryonic stem cells (ESCs), but its function in
AB  - these cells is unknown. Through genome-wide analysis of Dnmt3L knockdown in ESCs,
AB  - we found that Dnmt3L is a positive regulator of methylation at the gene bodies of
AB  - housekeeping genes and, more surprisingly, is also a negative regulator of
AB  - methylation at promoters of bivalent genes. Dnmt3L is required for the
AB  - differentiation of ESCs into primordial germ cells (PGCs) through the activation
AB  - of the homeotic gene Rhox5. We demonstrate that Dnmt3L interacts with the
AB  - Polycomb PRC2 complex in competition with the DNA methyltransferases Dnmt3a and
AB  - Dnmt3b to maintain low methylation levels at the H3K27me3 regions. Thus, in ESCs,
AB  - Dnmt3L counteracts the activity of de novo DNA methylases to maintain
AB  - hypomethylation at promoters of bivalent developmental genes.
ER  -

TY  - JOUR
AU  - Nesbo, C.L.
AU  - Boucher, Y.
AU  - Dlutek, M.
AU  - Doolittle, W.F.
TI  - Lateral gene transfer and phylogenetic assignment of environmental fosmid clones.
JO  - Environ. Microbiol.
PY  - 2005
SP  - 2011
EP  - 2026
VL  - 7
AB  - Metagenomic data, especially sequence data from large insert clones, are
AB  - most useful when reasonable inferences about phylogenetic origins of
AB  - inserts can be made. Often, clones that bear phylotypic markers (usually
AB  - ribosomal RNA genes) are sought, but sometimes phylogenetic assignments
AB  - have been based on the preponderance of blast hits obtained with predicted
AB  - protein coding sequences (CDSs). Here we use a cloning method which
AB  - greatly enriches for ribosomal RNA-bearing fosmid clones to ask two
AB  - questions: (i) how reliably can we judge the phylogenetic origin of a
AB  - clone (that is, its RNA phylotype) from the sequences of its CDSs? and
AB  - (ii) how much lateral gene transfer (LGT) do we see, as assessed by CDSs
AB  - of different phylogenetic origins on the same fosmid? We sequenced 12 rRNA
AB  - containing fosmid clones, obtained from libraries constructed using DNA
AB  - isolated from Baltimore harbour sediments. Three of the clones are from
AB  - bacterial candidate divisions for which no cultured representatives are
AB  - available, and thus represent the first protein coding sequences from
AB  - these major bacterial lineages. The amount of LGT was assessed by making
AB  - phylogenetic trees of all the CDSs in the fosmid clones and comparing the
AB  - phylogenetic position of the CDS to the rRNA phylotype. We find that the
AB  - majority of CDSs in each fosmid, 57-96%, agree with their respective rRNA
AB  - genes. However, we also find that a significant fraction of the CDSs in
AB  - each fosmid, 7-44%, has been acquired by LGT. In several cases, we can
AB  - infer co-transfer of functionally related genes, and generate hypotheses
AB  - about mechanism and ecological significance of transfer.
ER  -

TY  - JOUR
AU  - Nesemann, K.
AU  - Braus-Stromeyer, S.A.
AU  - Thuermer, A.
AU  - Daniel, R.
AU  - Braus, G.H.
TI  - Draft Genome Sequence of the Beneficial Rhizobacterium Pseudomonas fluorescens DSM 8569, a Natural Isolate of Oilseed Rape (Brassica napus).
JO  - Genome Announcements
PY  - 2015
SP  - e00137
EP  - e00115
VL  - 3
AB  - Pseudomonas fluorescens DSM 8569 represents a natural isolate of the rhizosphere  of oilseed
AB  - rape (Brassica napus) in Germany and possesses antagonistic potential
AB  - toward the fungal pathogen Verticillium. We report here the draft genome sequence
AB  - of strain DSM 8569, which comprises 5,914 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Nesemann, K.
AU  - Braus-Stromeyer, S.A.
AU  - Thuermer, A.
AU  - Daniel, R.
AU  - Mavrodi, D.V.
AU  - Thomashow, L.S.
AU  - Weller, D.M.
AU  - Braus, G.H.
TI  - Draft Genome Sequence of the Phenazine-Producing Pseudomonas fluorescens Strain 2-79.
JO  - Genome Announcements
PY  - 2015
SP  - e00130
EP  - e00115
VL  - 3
AB  - Pseudomonas fluorescens strain 2-79, a natural isolate of the rhizosphere of wheat (Triticum
AB  - aestivum L.), possesses antagonistic potential toward several
AB  - fungal pathogens. We report the draft genome sequence of strain 2-79, which
AB  - comprises 5,674 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Nesme, J.
AU  - Cania, B.
AU  - Zadel, U.
AU  - Scholer, A.
AU  - Plaza, G.A.
AU  - Schloter, M.
TI  - Complete Genome Sequences of Two Plant-Associated Pseudomonas putida Isolates with Increased Heavy-Metal Tolerance.
JO  - Genome Announcements
PY  - 2017
SP  - e01330
EP  - e01317
VL  - 5
AB  - We report here the complete genome sequences of two Pseudomonas putida isolates recovered from
AB  - surface-sterilized roots of Sida hermaphrodita The two isolates
AB  - were characterized by an increased tolerance to zinc, cadmium, and lead.
AB  - Furthermore, the strains showed typical plant growth-promoting properties, such
AB  - as the production of indole acetic acid, cellulolytic enzymes, and siderophores.
ER  -

TY  - JOUR
AU  - Nesterenko, V.F.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Isolation and properties of DNA-cytosine-methylase I from Escherichia coli MRE 600.
JO  - Biokhimiia
PY  - 1979
SP  - 130
EP  - 140
VL  - 44
AB  - DNA-cytosine-methylase I was isolated and purified to homogeneity.  The yield
AB  - made up to about 30% of total activity.  The enzyme molecular weight as
AB  - determined by centrifugation in a sucrose gradient, by gel filtration and by
AB  - electrophoresis in polyacrylamide gel in the presence of sodium dodecyl sulfate
AB  - was found to be 45000.  The Michaelis constant was 1,8.10-6 M for SAM and
AB  - 2.10-4 M for DNA.  DNA-cytosine-methylase I modifies phage lambda DNA in 60
AB  - sites.  This modification does not protect DNA from the effects of restriction
AB  - endonucleases HpaII and BsuRI.  The enzyme methylates DNA in the nucleotide
AB  - sequence: 5'...Pu-MC-C-G-G-Py...3'.
ER  -

TY  - JOUR
AU  - Nesterenko, V.F.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Determination of DNA-cytosine methylase I (M. Eco MRE600I) in plasmid CoLA.
JO  - Dokl. Akad. Nauk.
PY  - 1980
SP  - 1265
EP  - 1267
VL  - 250
AB  - None
ER  -

TY  - JOUR
AU  - Nestor, C.
AU  - Ruzov, A.
AU  - Meehan, R.R.
AU  - Dunican, D.S.
TI  - Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.
JO  - Biotechniques
PY  - 2010
SP  - 317
EP  - 319
VL  - 48
AB  - DNA cytosine methylation (5mC) is highly abundant in mammalian cells and is associated with
AB  - transcriptional repression. Recently, hydroxymethylcytosine
AB  - (hmC) has been detected at high levels in certain human cell types; however,
AB  - its roles are unknown. Due to the structural similarity between 5mC and hmC,
AB  - it is unclear whether 5mC analyses can discriminate between these nucleotides.
AB  - Here we show that 5mC and hmC are experimentally indistinguishable using
AB  - established 5mC mapping methods, thereby implying that existing 5mC data
AB  - sets will require careful re-evaluation in the context of the possible presence of
AB  - hmC. Potential differential enrichment of 5mC and hmC DNA sequences
AB  - may be facilitated using a 5mC monoclonal antibody.
ER  -

TY  - JOUR
AU  - Netesov, S.V.
AU  - Grachev, S.A.
TI  - An effective method for isolation of restriction endonucleases.
JO  - Bioorg. Khim.
PY  - 1981
SP  - 790
EP  - 791
VL  - 7
AB  - A modification of the published method for isolating the restriction
AB  - endonucleases is proposed.  The modification involves the use of Triton X-100
AB  - containing buffers at all steps of the isolation procedure which results in a
AB  - 2-12-fold increase in the yield of enzymes depending on the strain of bacteria.
ER  -

TY  - JOUR
AU  - Netesova, N.A.
AU  - Golikova, L.N.
AU  - Ovetchkina, L.G.
AU  - Evdokimov, A.A.
AU  - Malygin, E.G.
AU  - Gololobova, N.S.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Comparative study of the M.BstF5I-1 and M.BstF5I-3 DNA methyltransferases from the Bacillus stearothermophilus F5 restriction-modification system.
JO  - Mol. Biol. (Mosk)
PY  - 2002
SP  - 136
EP  - 143
VL  - 36
AB  - The BstF5I restriction-modification system from Bacillus stearothermophilus F5, unlike all
AB  - known restriction-modification
AB  - systems, contains three genes encoding DNA methyltransferases. In
AB  - addition to revealing two DNA methylases responsible for modification
AB  - of adenine in different DNA strands, it has been first shown that one
AB  - bacterial cell has two DNA methylases, M.BstF5I-1 and M.BstF5I-3, with
AB  - similar substrate specificity. The boundaries of the gene for DNA
AB  - methyltransferase M.BstF5I-1 have been verified. The bstF5IM-1 gene was
AB  - cloned in pJW and expressed in Escherichia coli. Homogeneous samples of
AB  - M.BstF5I-1 and M.BstF5I-3 were obtained by chromatography with
AB  - different sorbents. The main kinetic parameters have been determined
AB  - for M.BstF5I-1 and M.BstF5I-3, both modifying adenine in the
AB  - recognition site 5'-GGATG-3'.
ER  -

TY  - JOUR
AU  - Neupane, S. et al.
TI  - Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 441
EP  - 449
VL  - 8
AB  - Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild
AB  - Equisetum sp., has the ability to stimulate plant growth and
AB  - to suppress the growth of several soil-borne fungal pathogens of economically
AB  - important crops. Here we present the non-contiguous, finished genome sequence of
AB  - S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a
AB  - 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while
AB  - the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as
AB  - protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58
AB  - pseudogenes. This genome is a part of the project 'Genomics of four rapeseed
AB  - plant growth-promoting bacteria with antagonistic effect on plant pathogens'
AB  - awarded through the 2010 DOE-JGI's Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Neupane, S. et al.
TI  - Complete genome sequence of the plant-associated Serratia plymuthica strain AS13.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 22
EP  - 30
VL  - 7
AB  - AS13 is a plant-associated , isolated from rapeseed roots. It is of special interest because
AB  - of its ability to inhibit fungal pathogens of rapeseed and to
AB  - promote plant growth. The complete genome of AS13 consists of a 5,442,549 bp
AB  - circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA
AB  - genes and 7 rRNA operons. This genome was sequenced as part of the project
AB  - entitled 'Genomics of four rapeseed plant growth promoting bacteria with
AB  - antagonistic effect on plant pathogens' within the 2010 DOE-JGI Community
AB  - Sequencing Program (CSP2010).
ER  -

TY  - JOUR
AU  - Neupane, S. et al.
TI  - Complete genome sequence of Serratia plymuthica strain AS12.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 165
EP  - 173
VL  - 6
AB  - A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12
AB  - was isolated from rapeseed roots. It is of scientific interest
AB  - because it promotes plant growth and inhibits plant pathogens. The genome of S.
AB  - plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists
AB  - of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was
AB  - sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part
AB  - of the project entitled 'Genomics of four rapeseed plant growth promoting
AB  - bacteria with antagonistic effect on plant pathogens'.
ER  -

TY  - JOUR
AU  - Neupane, S. et al.
TI  - Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 54
EP  - 62
VL  - 6
AB  - Serratia plymuthica are plant-associated, plant beneficial species belonging to the family
AB  - Enterobacteriaceae. The members of the genus Serratia are ubiquitous
AB  - in nature and their life style varies from endophytic to free-living. S.
AB  - plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens
AB  - of rapeseed and to promote plant growth. The genome of S. plymuthica AS9
AB  - comprises a 5,442,880 bp long circular chromosome that consists of 4,952
AB  - protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of
AB  - the project entitled 'Genomics of four rapeseed plant growth promoting bacteria
AB  - with antagonistic effect on plant pathogens' awarded through the 2010 DOE-JGI
AB  - Community Sequencing Program (CSP2010).
ER  -

TY  - JOUR
AU  - Neurgaonkar, P.S.
AU  - Dharne, M.S.
AU  - Dastager, S.G.
TI  - Draft Genome Sequence of Arthrobacter enclensis NCIM 5488T for Secondary Metabolism.
JO  - Genome Announcements
PY  - 2016
SP  - e00497
EP  - e00416
VL  - 4
AB  - Here, we report the draft genome sequence of Arthrobacter enclensis NCIM 5488(T), an
AB  - actinobacterium isolated from a marine sediment sample from Chorao Island,
AB  - Goa, India. This draft genome sequence consists of 4,226,231 bp with a G+C
AB  - content of 67.08%, 3,888 protein-coding genes, 50 tRNAs, and 10 rRNAs. Analysis
AB  - of the genome using bioinformatics tools such as antiSMASH and NaPDoS showed the
AB  - presence of many unique natural product biosynthetic gene clusters.
ER  -

TY  - JOUR
AU  - Newby, A.E.R.
AU  - Lau, E.Y.
AU  - Bruice, T.C.
TI  - A theoretical examination of the factors controlling the catalytic efficiency of the DNA-(adenine-N6)-methyltransferase from Thermus aquaticus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 7922
EP  - 7927
VL  - 99
AB  - Ab initio and density functional calculations have been carried out to more fully understand
AB  - the factors controlling the catalytic activity of the Thermus aquaticus DNA methyltransferase
AB  - (M.TaqI) in the N-methylation at the N6 of an adenine nucleobase. The noncatalyzed reaction
AB  - was modeled as a methyl transfer from trimethylsulfonium to the N6 of adenine. Activation
AB  - barriers of 32.0 kcal/mol and 24.0 kcal/mol were predicted for the noncatalyzed reaction in
AB  - the gas phase by MP2/6-31+G(d,p)//HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) calculations,
AB  - respectively. Calculations performed to evaluate the effect of substrate positioning in the
AB  - active site of MTaqI on the reaction determine the barrier to be 23.4 kcal/mol and 17.3
AB  - kcal/mol for the MP2/6-31+G(d,p)//HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) gas phase calculations,
AB  - respectively. The effect of hydrogen bonding between the N6 of adenine and the terminal oxygen
AB  - of Asn-105 on the activation barrier was also studied. A formamide molecule was modeled into
AB  - the system to mimic the function of active site residue Asn-105. The activation barrier for
AB  - this reaction was found to be 21.8 kcal/mol and 15.8 kcal/mol as determined from the
AB  - MP2/6-31+G(d,p)//HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) calculations, respectively. This result
AB  - predicts a contribution of less than 2 kcal/mol to the lowering of the activation barrier from
AB  - amide hydrogen bonding between formamide and N6 of adenine. Comparison of the reaction
AB  - coordinates suggest that it is not the hydrogen bonding of the Asn-105 that lends to the
AB  - catalytic prowess of the enzyme since the organization of the substrates in the active site of
AB  - the enzyme has a far greater effect on reducing the activation barrier. The results also
AB  - suggest a stepwise mechanism for the removal of the hydrogen from the N6 of adenine as opposed
AB  - to a concerted reaction in which a proton is abstracted simultaneously with the transfer of
AB  - the methyl group. The hydrogen on the N6 of the intermediate methyl adenine product is far
AB  - more acidic than in the reactant complex and may be subsequently abstracted by basic groups in
AB  - the active site that are too weak to abstract the proton before the full sp3 hybridization of
AB  - the attacking nitrogen.
ER  -

TY  - JOUR
AU  - Newman, A.K.
AU  - Rubin, R.A.
AU  - Kim, S.H.
AU  - Modrich, P.
TI  - DNA Sequences of Structural Genes for EcoRI DNA Restriction and Modified Enzymes.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 2131
EP  - 2139
VL  - 256
AB  - We have determined the sequence of a 2210-base pair DNA segment containing genes required for
AB  - expression of EcoRI DNA restriction and modification phenotypes.  Polypeptide sequences
AB  - encoded within the two longest open reading frames in this region are in agreement with NH2-
AB  - and C00H-terminal sequences of the two EcoRI enzymes (Rubin, R.A., Modrich, P., and Vanaman,
AB  - T.C. (1981) J. Biol. Chem. 256, 2140-2142), indicating that these are structural genes for the
AB  - two proteins.  The DNA sequence encoding EcoRI endonuclease specifies a 277-residue
AB  - polypeoptide (Mr = 31,063) while the methylase gene encodes a 326-residue protein (Mr =
AB  - 38,048).  Genes for the two proteins are nonoverlapping, being separated by a 29-nucleotide
AB  - intercistronic region. Analysis of each polypeptide and its gene sequence for internal regions
AB  - of homology led to identification of a striking 4-fold repeat of Leu-Ile-Lys within the
AB  - methylase and a tandem repeat within the endonuclease, both of which are unlikely on the basis
AB  - of chance.  Comparison of DNA and polypeptide sequences also demonstrated a limited, but
AB  - statistically significant, region of homology between EcoRI endonuclease and methylase primary
AB  - structures. However, the general lack of homology between the two polypeptides suggests
AB  - different evolutionary origins for the two proteins.  The two enzymes also differ markedly at
AB  - higher levels of structure as judged by circular dichroism and prediction of secondary
AB  - structure by the probabilistic method of Chou and Fasman (Chou, P.Y., and Fasman, G.D. (1978)
AB  - Adv. Enzymol. 47, 45-148).  Thus, despite their ability to interact with the same DNA
AB  - sequence, the EcoRI enzymes have quite distinct structural properties.
ER  -

TY  - JOUR
AU  - Newman, M.
AU  - Lunnen, K.
AU  - Wilson, G.
AU  - Greci, J.
AU  - Schildkraut, I.
AU  - Phillips, S.E.V.
TI  - Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
JO  - EMBO J.
PY  - 1998
SP  - 5466
EP  - 5476
VL  - 17
AB  - The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its
AB  - specific recognition sequence has been determined at 2.2 A resolution.  This is the first
AB  - structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA
AB  - sequence, producing 3' overhanging ends.  BglI is a homodimer that binds its specific DNA
AB  - sequence with the minor groove facing the protein.  Parts of the enzyme reach into both the
AB  - major and minor grooves to contact the edges of the bases within the recognition half-sites.
AB  - The arrangement of active site residues is strikingly similar to other restriction
AB  - endonucleases, but the coordination of two calcium ions at the active site gives new insight
AB  - into the catalytic mechanism.  Surprisingly, the core of a BglI subunit displays a striking
AB  - similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different.
AB  - The BglI DNA complex demonstrates, for the first time, that a conserved subunit fold can
AB  - dimerize in more than one way, resulting in different DNA cleavage patterns.
ER  -

TY  - JOUR
AU  - Newman, M.
AU  - Strzelecka, T.
AU  - Dorner, L.F.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Structure of restriction endonuclease BamHI phased at 1.95 A resolution by MAD analysis.
JO  - Structure
PY  - 1994
SP  - 439
EP  - 452
VL  - 2
AB  - Type II restriction endonucleases recognize DNA sequences that vary between four to eight base
AB  - pairs, and require only Mg2+ as a cofactor to catalyze the hydrolysis of DNA. Their protein
AB  - sequences display a surprising lack of similarity, and no recurring structural motif analogous
AB  - to the helix-turn-helix or the zinc finger of transcription factors, has yet been discovered.
AB  - We have determined the crystal structure of restriction endonuclease BamHI at 1.95 A
AB  - resolution. The structure was solved by combining phase information derived from
AB  - multi-wavelength X-ray data by algebraic and maximum likelihood methods. The BamHI subunit
AB  - consists of a central beta-sheet with alpha-helices on both sides. The dimer configuration
AB  - reveals a large cleft which could accommodate B-form DNA. Mutants of the enzyme that are
AB  - deficient in cleavage are located at or near the putative DNA-binding cleft. BamHI and
AB  - endonuclease EcoRI share a common core motif (CCM) consisting of five beta-strands and two
AB  - helices. It remains to be determined if other restriction enzymes also contain the CCM. The
AB  - structure of BamHI provides the first clear evidence that there may be substantial structural
AB  - homology amongst restriction enzymes, even though it is undetectable at the sequence level.
ER  -

TY  - JOUR
AU  - Newman, M.
AU  - Strzelecka, T.
AU  - Dorner, L.F.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding.
JO  - Science
PY  - 1995
SP  - 656
EP  - 663
VL  - 269
AB  - The crystal structure of restriction endonuclease BamHI complexed to DNA has been determined
AB  - at 2.2 angstrom resolution.  The DNA binds in the cleft and retains a B-DNA type of
AB  - conformation.  The enzyme, however, undergoes a series of conformational changes, including
AB  - rotation of subunits and folding of disordered regions.  The most striking conformational
AB  - change is the unraveling of carboxyl-terminal alpha helices to form partially disordered
AB  - "arms".  The arm from one subunit fits into the minor groove while the arm from the symmetry
AB  - related subunit follows the DNA sugar-phosphate backbone.  Recognition of DNA base pairs
AB  - occurs primarily in the major groove, with a few interactions occurring in the minor groove.
AB  - Tightly bound water molecules play an equally important role as side chain and main chain
AB  - atoms in the recognition of base pairs.  The complex also provides new insights into the
AB  - mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.
ER  -

TY  - JOUR
AU  - Newman, M.
AU  - Strzelecka, T.
AU  - Dorner, L.F.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Structure of restriction endonuclease BamHI and its relationship to EcoRI.
JO  - Nature
PY  - 1994
SP  - 660
EP  - 664
VL  - 368
AB  - Type II restriction endonucleases are characterized by the remarkable specificity with which
AB  - they cleave specific DNA sequences. Surprisingly, their protein sequences are in most cases
AB  - unrelated, and no recurring structural motif has yet been identified. We have determined the
AB  - structure of restriction endonuclease BamHI at 1.95 angstrom resolution. BamHI shows striking
AB  - resemblance to the structure of endonuclease EcoRI, despite the lack of sequence similarity
AB  - between them. We also observe some curious differences between the two structures, and propose
AB  - an evolutionary scheme that may explain them. The active site of BamHI is structurally similar
AB  - to the active sites of EcoRI and EcoRV, but the mechanism by which BamHI activates a water
AB  - molecule for nucleophilic attack may be different.
ER  -

TY  - JOUR
AU  - Newman, P.C.
TI  - Investigation of the sequence-specific DNA/protein interactions of the EcoRV restriction enzyme.
JO  - Diss. Abstr.
PY  - 1991
SP  - 3366B
EP  - 3366B
VL  - 51
AB  - The EcoRV restriction enzyme from Escherichia coli recognises the sequence GATATC on double
AB  - stranded DNA and cuts between the central residues with very high specificity.  The self
AB  - complementary dodecadeoxynucleotide dGACGATATCGTC which contains the EcoRV recognition site
AB  - (underlined) is also a substrate for the endonuclease.  The thesis describes the synthesis of
AB  - fourteen dodecamers of the above parent sequence in which the functional groups of the central
AB  - ATAT residues accessible to the protein via the DNA major and minor grooves have been
AB  - systematically and sequentially deleted.  Conservative contact deletions were achieved by the
AB  - substitution of the two deoxyadenosine residues in turn with the base analogues purine
AB  - deoxyriboside (dP), 7-deazadeoxyadenosine (d7CA) and 3-deazadeoxyadenosine (d3CA).  Similarly
AB  - the two thymidine residues were substituted with deoxyuridine (dU), 5-methyl-2-pyrimidinone
AB  - deoxyriboside (d4HT), 4-thiothymidine (d4ST) and 2-thiothymidine (d2ST).  To obtain the
AB  - complete set of analogues, efficient synthetic routes for the formation of derivatives of
AB  - d4HT, d4ST and d2ST suitable for oligodeoxynucleotide synthesis using the cyanoethyl
AB  - phosphoramidite approach are described (also see Connolly
ER  -

TY  - JOUR
AU  - Newman, P.C.
AU  - Nwosu, V.U.
AU  - Williams, D.M.
AU  - Cosstick, R.
AU  - Seela, F.
AU  - Connolly, B.A.
TI  - Incorporation of a complete set of deoxyadenosine and thymidine analogues suitable for the study of protein nucleic acid interactions into oligodeoxynucleotides.  Application to the EcoRV restriction endonuclease and modification methylase.
JO  - Biochemistry
PY  - 1990
SP  - 9891
EP  - 9901
VL  - 29
AB  - A complete set of dA and T analogues designed for the study of protein DNA
AB  - interactions has been prepared.  These modified bases have been designed by
AB  - considering the groups on the dA and T bases that are accessible to proteins
AB  - when these bases are incorporated into double-helical B-DNA [Seeman, N.C.,
AB  - Rosenberg, J.M. and Rich, A. (1976) Proc. Natl. Acad. Sci. USA 73, 804-808].
AB  - Each of the positions on the two bases, having the potential to interact with
AB  - proteins, have been subject to nondisruptive, conservative change.  Typically a
AB  - particular group (e.g., the 6-amino group of dA or the 5-methyl of T) has been
AB  - replaced with a hydrogen atom.  Occasionally keto groups (the 2- and 4-keto
AB  - oxygen atoms of T) have been replaced with sulfur.  The base set has been
AB  - incorporated into the self-complementary dodecamer d(GACGATATCGTC) at the
AB  - central d(ATAT) sequence.  Melting temperature determination shows that the
AB  - modified bases do not destabilize the double helix.  Additionally, circular
AB  - dichroism spectroscoy shows that almost all the altered bases have very little
AB  - effect on overall oligodeoxynucleotide conformation and that most of the
AB  - modified oligomers have a B-DNA type structure.  d(GATATC) is the recognition
AB  - sequence for the EcoRV restriction modification system.  Initial rate
AB  - measurements (at a single oligodeoxynucleotide concentration of 20 microM) have
AB  - been carried out with both the EcoRV restriction endonuclease and modification
AB  - methylase.  This has enabled a preliminary identification of the groups of the
AB  - dA and T bases within the d(GATATC) sequence that make important contacts to
AB  - both proteins.
ER  -

TY  - JOUR
AU  - Newman, P.C.
AU  - Williams, D.M.
AU  - Cosstick, R.
AU  - Seela, F.
AU  - Connolly, B.A.
TI  - Interaction of the EcoRV restriction endonuclease with the deoxyadenosine and thymidine bases in its recognition hexamer d(GATATC).
JO  - Biochemistry
PY  - 1990
SP  - 9902
EP  - 9910
VL  - 29
AB  - A set of dA and T analogues suitable for the study of protein DNA interactions
AB  - have been incorporated into the central d(ATAT) sequence within
AB  - d(GACGATATCGTC).  The individual analogues have one potential protein contact
AB  - (either a hydrogen-bonding group or a CH3 group capable of a van der Waals
AB  - interaction) deleted.  In general, the modified bases do not perturb the
AB  - overall structure of the dodecamer, enabling results obtained to be simply
AB  - interpreted in terms of loss of protein DNA contacts.  We have used the
AB  - modified oligodeoxynucleotide set to study the recognition of DNA by the EcoRV
AB  - restriction endonuclease [recognition sequence d(GATATC)].  The kcat and Km
AB  - values for the set have been determined, and a comparison with results seen
AB  - with the parent oligodeoxynucleotide (containing no modified bases) has been
AB  - carried out.  Three classes of results are seen.  First, some analogues lead to
AB  - no change in kinetic parameters, meaning no enzyme contact at the altered site.
AB  - Second (this is seen for most of the modified oligodeoxynucleotides), a drop
AB  - in the kcat/Km ratio relative to the parent is observed.  This comes mainly
AB  - from a decrease in kcat, implying that the endonuclease uses the interaction
AB  - under study to lower the transition-state barrier rather than to bind the
AB  - substrate.  Analyses of these results show that the drop in kcat/Km is what
AB  - would be expected for the simple loss of a hydrogen bond or a CH3 contact
AB  - between the enzyme and the oligodeoxynucleotide.  This implies a contact of
AB  - these types at these sites.  Third, some analogue-containing
AB  - oligodeoxynucleotides are not substrates; i.e., the kcat/Km drop is much
AB  - greater than would be expected for loss of a single hydrogen bond or CH3
AB  - contact.  These results are interpreted in terms of a cooperative mechanism
AB  - whereby the loss of one interaction causes a rearrangement at the enzyme active
AB  - site leading to a consequent loss of further protein substrate contacts.
AB  - However, in these cases gross structural changes in the oligodeoxynucleotide
AB  - conformation cannot be excluded.  It is found that the endonuclease makes very
AB  - many interactions to the d(ATAT) sequence within its d(GATATC) recognition
AB  - site, and these occur in both the major and minor grooves.  The results
AB  - obtained have been used to explain how the enzyme achieves the high degree of
AB  - cleavage specificity for d(GATATC) as compared to all other sequences.
ER  -

TY  - JOUR
AU  - Ng, E.K.O.
AU  - Tsang, W.P.
AU  - Ng, S.S.M.
AU  - Jin, H.C.
AU  - Yu, J.
AU  - Li, J.J.
AU  - Roecken, C.
AU  - Ebert, M.P.A.
AU  - Kwok, T.T.
AU  - Sung, J.J.Y.
TI  - MicroRNA-143 targets DNA methyltransferases 3A in colorectal cancer.
JO  - Br. J. Cancer
PY  - 2009
SP  - 699
EP  - 706
VL  - 101
AB  - BACKGROUND: MicroRNAs (miRNAs) are 19-25-nucleotides regulatory non-protein-coding RNA
AB  - molecules that regulate the expressions of a
AB  - wide variety of genes, including some involved in cancer development.
AB  - In this study, we investigated the possible role of miR-143 in
AB  - colorectal cancer (CRC).METHODS: Expression levels of human mature
AB  - miRNAs were examined using real-time PCR-based expression arrays on
AB  - paired colorectal carcinomas and adjacent non-cancerous colonic
AB  - tissues. The downregulation of miR-143 was further evaluated in colon
AB  - cancer cell lines and in paired CRC and adjacent non-cancerous colonic
AB  - tissues by qRT-PCR. Potential targets of miR-143 were defined. The
AB  - functional effect of miR-143 and its targets was investigated in human
AB  - colon cancer cell lines to confirm miRNA-target association.RESULTS:
AB  - Both real-time PCR-based expression arrays and qRT-PCR showed that
AB  - miR-143 was frequently downregulated in 87.5% (35 of 40) of colorectal
AB  - carcinoma tissues compared with their adjacent non-cancerous colonic
AB  - tissues. Using in silico predictions, DNA methyltranferase 3A (DNMT3A)
AB  - was defined as a potential target of miR-143. Restoration of the
AB  - miR-143 expression in colon cell lines decreased tumour cell growth and
AB  - soft-agar colony formation, and downregulated the DNMT3A expression in
AB  - both mRNA and protein levels. DNMT3A was shown to be a direct target of
AB  - miR-143 by luciferase reporter assay. Furthermore, the miR-143
AB  - expression was observed to be inversely correlated with DNMT3A mRNA and
AB  - protein expression in CRC tissues.CONCLUSION: Our findings suggest that
AB  - miR-143 regulates DNMT3A in CRC. These findings elucidated a
AB  - tumour-suppressive role of miR-143 in the epigenetic aberration of CRC,
AB  - providing a potential development of miRNA-based targeted approaches
AB  - for CRC therapy. British Journal of Cancer (2009) 101, 699-706. doi:
AB  - 10.1038/sj.bjc.6605195 www.bjcancer.com Published online 28 July 2009
ER  -

TY  - JOUR
AU  - Ng, H.F.
AU  - Tan, J.L.
AU  - Zin, T.
AU  - Yap, S.F.
AU  - Ngeow, Y.F.
TI  - A mutation in anti-sigma factor MAB_3542c may be responsible for tigecycline resistance in Mycobacterium abscessus.
JO  - J. Med. Microbiol.
PY  - 2018
SP  - 1676
EP  - 1681
VL  - 67
AB  - In this study, we characterized 7C, a spontaneous mutant selected from tigecycline-susceptible
AB  - Mycobacterium abscessus
AB  - ATCC 19977. Whole-genome sequencing (WGS) was used to identify possible resistance
AB  - determinants in this mutant.
AB  - Compared to the wild-type, 7C demonstrated resistance to tigecycline as well as
AB  - cross-resistance to imipenem, and had a
AB  - slightly retarded growth rate. WGS and subsequent biological verifications showed that these
AB  - phenotypes were caused by a
AB  - point mutation in MAB_3542c, which encodes an RshA-like protein. In Mycobacterium
AB  - tuberculosis, RshA is an anti-sigma
AB  - factor that negatively regulates the heat/oxidative stress response mechanisms. The MAB_3542c
AB  - mutation may represent a
AB  - novel determinant of tigecycline resistance. We hypothesize that this mutation may dysregulate
AB  - the stress-response
AB  - pathways which have been shown to be linked to antibiotic resistance in previous studies.
ER  -

TY  - JOUR
AU  - Ng, K.P.
AU  - Yew, S.M.
AU  - Chan, C.L.
AU  - Chong, J.
AU  - Tang, S.N.
AU  - Soo-Hoo, T.S.
AU  - Na, S.L.
AU  - Hassan, H.
AU  - Ngeow, Y.F.
AU  - Hoh, C.C.
AU  - Lee, K.W.
AU  - Yee, W.Y.
TI  - Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia.
JO  - Genome Announcements
PY  - 2013
SP  - e00056
EP  - e00012
VL  - 1
AB  - The emergence of the global threat of extensively drug-resistant (XDR) Mycobacterium
AB  - tuberculosis reveals weaknesses in tuberculosis management and diagnostic services. We report
AB  - the draft genome sequence of the first extensively drug-resistant Mycobacterium tuberculosis
AB  - strain isolated in Malaysia. The sequence was also compared against a reference strain to
AB  - elucidate the polymorphism that is related to their extensive resistance.
ER  -

TY  - JOUR
AU  - Ng, W.V. et al.
TI  - Genome sequence of Halobacterium species NRC-1.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 12176
EP  - 12181
VL  - 97
AB  - We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a
AB  - dynamic 2,571,010-bp genome containing 91 insertion sequences
AB  - representing 12 families and organized into a large chromosome and 2 related
AB  - minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted
AB  - proteins, 36% of which are unrelated to any previously reported. Analysis of the
AB  - genome sequence shows the presence of pathways for uptake and utilization of
AB  - amino acids, active sodium-proton antiporter and potassium uptake systems,
AB  - sophisticated photosensory and signal transduction pathways, and DNA replication,
AB  - transcription, and translation systems resembling more complex eukaryotic
AB  - organisms. Whole proteome comparisons show the definite archaeal nature of this
AB  - halophile with additional similarities to the Gram-positive Bacillus subtilis and
AB  - other bacteria. The ease of culturing Halobacterium and the availability of
AB  - methods for its genetic manipulation in the laboratory, including construction of
AB  - gene knockouts and replacements, indicate this halophile can serve as an
AB  - excellent model system among the archaea.
ER  -

TY  - JOUR
AU  - Ng, W.V.
AU  - Ciufo, S.A.
AU  - Smith, T.M.
AU  - Bumgarner, R.E.
AU  - Baskin, D.
AU  - Faust, J.
AU  - Hall, B.
AU  - Loretz, C.
AU  - Seto, J.
AU  - Slagel, J.
AU  - Hood, L.
AU  - DasSarma, S.
TI  - Snapshot of a large dynamic replicon in a halophilic archaeon: Megaplasmid or minichromosome?
JO  - Genome Res.
PY  - 1998
SP  - 1131
EP  - 1141
VL  - 8
AB  - Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain
AB  - a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100,
AB  - in Halobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence
AB  - element-mediated insertions and deletions, as well as inversions via recombination between
AB  - 39-kb-long inverted repeats. Now, the complete sequencing of pNRC100, a 191,346-bp circle, has
AB  - shown the presence of 27 IS elements representing eight families.  A total of 176 ORFs or
AB  - likely genes of 850-bp average size were found, 39 of which were repeated within the large
AB  - IRs. More than one-half of the ORFs are likely to represent novel genes that have no known
AB  - homologs in the databases. Among ORFs with previously characterized homologs, three different
AB  - copies of putative plasmid replication and four copies of partitioning genes were found,
AB  - suggesting that pNRC100 evolved from IS element-mediated fusions of several smaller plasmids.
AB  - Consistent with this idea, putative genes typically found on plasmids, including those
AB  - encoding a restriction-modification system and arsenic resistance, as well as buoyant
AB  - gas-filled vesicles and a two-component regulatory system, were found on pNRC100.  However,
AB  - additional putative genes not expected on an extrachromosomal element, such as those encoding
AB  - an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin
AB  - and thioredoxin reductase, and eukaryotic-like TATA-binding protein transcription factors and
AB  - a chromosomal replication initiator protein were also found.  A multi-step IS element-mediated
AB  - process is proposed to account for the acquisition of these chromosomal genes.  The finding of
AB  - essential genes on pNRC100 and its property of resistance to curing suggest that this replicon
AB  - may be evolving into a new chromosome.
ER  -

TY  - JOUR
AU  - Ngeow, Y.F.
AU  - Leong, M.L.
AU  - Wong, Y.L.
AU  - Wong, G.J.
AU  - Tan, J.L.
AU  - Wee, W.Y.
AU  - Ong, C.S.
AU  - Pang, Y.K.
AU  - Choo, S.W.
TI  - Draft Genome Sequence of Mycobacterium massiliense Strain M159, Showing Phenotypic Resistance to beta-Lactam and Tetracycline Antibiotics.
JO  - Genome Announcements
PY  - 2013
SP  - e00669
EP  - e00613
VL  - 1
AB  - Mycobacterium massiliense is a nontuberculous mycobacterium associated with human infections.
AB  - We report here the draft genome sequence of M. massiliense strain
AB  - M159, isolated from the bronchial aspirate of a patient who had a pulmonary
AB  - infection. This strain showed genotypic and in vitro resistance to a number of
AB  - tetracyclines and beta-lactam antibiotics.
ER  -

TY  - JOUR
AU  - Ngeow, Y.F.
AU  - Wee, W.Y.
AU  - Wong, Y.L.
AU  - Tan, J.L.
AU  - Ongi, C.S.
AU  - Ng, K.P.
AU  - Choo, S.W.
TI  - Genomic Analysis of Mycobacterium abscessus Strain M139, Which Has an Ambiguous Subspecies Taxonomic Position.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6002
EP  - 6003
VL  - 194
AB  - Mycobacterium abscessus is a ubiquitous, rapidly growing species of nontuberculous
AB  - mycobacteria that colonizes organic surfaces and is frequently
AB  - associated with opportunistic infections in humans. We report here the draft
AB  - genome sequence of Mycobacterium abscessus strain M139, which shows genomic
AB  - features reported to be characteristic of both Mycobacterium abscessus subsp.
AB  - abscessus and Mycobacterium abscessus subsp. massiliense.
ER  -

TY  - JOUR
AU  - Ngeow, Y.F.
AU  - Wong, Y.L.
AU  - Lokanathan, N.
AU  - Wong, G.J.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Choo, S.W.
TI  - Genomic Analysis of Mycobacterium massiliense Strain M115, an Isolate from Human  Sputum.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4786
EP  - 4786
VL  - 194
AB  - We report the draft genome sequence of a clinical isolate, strain M115, identified as
AB  - Mycobacterium massiliense, a member of the newly created taxon of
AB  - Mycobacterium abscessus subspecies bolletii comb. nov.
ER  -

TY  - JOUR
AU  - Ngeow, Y.F.
AU  - Wong, Y.L.
AU  - Tan, J.L.
AU  - Arumugam, R.
AU  - Wong, G.J.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Choo, S.W.
TI  - Genome Sequence of Mycobacterium massiliense M18, Isolated from a Lymph Node Biopsy Specimen.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4125
EP  - 4125
VL  - 194
AB  - Mycobacterium massiliense is a rapidly growing mycobacterial species. The pathogenicity of
AB  - this subspecies is not well known. We report here the annotated
AB  - genome sequence of M. massiliense strain M18, which was isolated from a lymph
AB  - node biopsy specimen from a Malaysian patient suspected of having tuberculous
AB  - cervical lymphadenitis.
ER  -

TY  - JOUR
AU  - Ngeow, Y.F.
AU  - Wong, Y.L.
AU  - Tan, J.L.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Choo, S.W.
TI  - Genome Sequence of Mycobacterium abscessus Strain M152.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6662
EP  - 6662
VL  - 194
AB  - Mycobacterium abscessus is an environmental bacterium with increasing clinical relevance.
AB  - Here, we report the annotated whole-genome sequence of M. abscessus
AB  - strain M152.
ER  -

TY  - JOUR
AU  - Ngom, M.
AU  - Oshone, R.
AU  - Hurst, S.G. IV
AU  - Abebe-Akele, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Sy, M.O.
AU  - Champion, A.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in  Senegal.
JO  - Genome Announcements
PY  - 2016
SP  - e00265
EP  - e00216
VL  - 4
AB  - Frankiastrain CeD is a member ofFrankialineage Ib that is able to reinfect plants of
AB  - theCasuarinafamilies. Here, we report a 5.0-Mbp draft genome sequence with a
AB  - G+C content of 70.1% and 3,847 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Ngugi, D.K.
AU  - Stingl, U.
TI  - High-Quality Draft Single-Cell Genome Sequence of the NS5 Marine Group from the Coastal Red Sea.
JO  - Genome Announcements
PY  - 2018
SP  - e00565
EP  - e00518
VL  - 6
AB  - The uncultured NS5 marine group represents one of the most ubiquitous flavobacterial
AB  - bacterioplankton associated with marine blooms in the pelagic
AB  - ocean. Here, we present a single-cell genome sampled from coastal waters in the
AB  - Red Sea that represents the first high-quality draft genome sequence within the
AB  - NS5 lineage.
ER  -

TY  - JOUR
AU  - Ngugi, D.K.
AU  - Stingl, U.
TI  - High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea.
JO  - Genome Announcements
PY  - 2018
SP  - e00383
EP  - e00318
VL  - 6
AB  - Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in
AB  - deep hypersaline anoxic brines around the globe. Recently, the
AB  - genome sequences of two cultivated representatives from hypersaline soda lake
AB  - sediments were published. Here, we present a single-cell genome sequence from
AB  - Nereus Deep in the Red Sea that represents a putatively novel family within SA1.
ER  -

TY  - JOUR
AU  - Nguyen, D.T.
AU  - Lessor, L.E.
AU  - Cahill, J.L.
AU  - Rasche, E.S.
AU  - Kuty, E.G.F.
TI  - Complete Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Siphophage Sushi.
JO  - Genome Announcements
PY  - 2015
SP  - e00994
EP  - e00915
VL  - 3
AB  - Klebsiella pneumoniae is a Gram-negative bacterium in the family Enterobacteriaceae. It is
AB  - associated with numerous nosocomial infections, including respiratory and urinary tract
AB  - infections in humans. The following reports the complete genome sequence of K. pneumoniae
AB  - carbapenemase-producing K. pneumoniae T1-like siphophage Sushi and describes its major
AB  - features.
ER  -

TY  - JOUR
AU  - Nguyen, L.D.
AU  - Cajthamlova, K.
AU  - Nguyen, H.T.
AU  - Weiser, J.
AU  - Holubova, I.
AU  - Weiserova, M.
TI  - Identification of the EcoKI and EcoR124I type I restriction-modification enzyme subunits by non-equilibrium pH gradient two-dimensional gel electrophoresis.
JO  - Folia Microbiol. (Praha)
PY  - 2002
SP  - 641
EP  - 648
VL  - 47
AB  - Effectively optimized and reproducible procedure for monitoring the composition of type I
AB  - restriction-modification endonucleases EcoKI and
AB  - EcoR124I by non-equilibrium pH gradient two-dimensional (2-D) gel
AB  - electrophoresis is described. Three subunits of the enzyme complex,
AB  - which widely differ from one another in their isoelectric points and
AB  - molar mass, were identified in crude cell extracts of E. coli. For the
AB  - first time all three subunits of both EcoKI and EcoR124I were detected
AB  - as distinct spots on a single 2-D gel. A sensitive immunoblotting
AB  - procedure was suggested suitable for routine use in determining the
AB  - identity of individual subunits. Potential application of this method
AB  - for detailed studies of regulation of the function and stoichiometry of
AB  - the enzyme complexes is discussed.
ER  -

TY  - JOUR
AU  - Nguyen, S.V.
AU  - Harhay, D.M.
AU  - Bono, J.L.
AU  - Smith, T.P.
AU  - Fields, P.I.
AU  - Dinsmore, B.A.
AU  - Santovenia, M.
AU  - Kelley, C.M.
AU  - Wang, R.
AU  - Bosilevac, J.M.
AU  - Harhay, G.P.
TI  - Complete and Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Anatum Isolates from Human and Bovine Sources.
JO  - Genome Announcements
PY  - 2016
SP  - e00447
EP  - e00416
VL  - 4
AB  - Salmonella enterica is an important pathogen transmitted by numerous vectors. Genomic
AB  - comparisons of Salmonella strains from disparate hosts have the potential
AB  - to further our understanding of mechanisms underlying host specificities and
AB  - virulence. Here, we present the closed genome and plasmid sequences of 10
AB  - Salmonella enterica subsp. enterica serovar Anatum isolates from bovine and human
AB  - sources.
ER  -

TY  - JOUR
AU  - Nguyen, S.V.
AU  - Harhay, D.M.
AU  - Bono, J.L.
AU  - Smith, T.P.
AU  - Fields, P.I.
AU  - Dinsmore, B.A.
AU  - Santovenia, M.
AU  - Kelley, C.M.
AU  - Wang, R.
AU  - Bosilevac, J.M.
AU  - Harhay, G.P.
TI  - Complete, Closed Genome Sequences of 10 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Human and Bovine Sources.
JO  - Genome Announcements
PY  - 2016
SP  - e01212
EP  - e01216
VL  - 4
AB  - Salmonella enterica is a leading cause of enterocolitis for humans and animals. S. enterica
AB  - subsp. enterica serovar Typhimurium infects a broad range of hosts.
AB  - To facilitate genomic comparisons among isolates from different sources, we
AB  - present the complete genome sequences of 10 S Typhimurium strains, 5 each
AB  - isolated from human and bovine sources.
ER  -

TY  - JOUR
AU  - Nguyen, T.P.
AU  - De Mot, R.
AU  - Springael, D.
TI  - Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2.
JO  - Genome Announcements
PY  - 2015
SP  - e00764
EP  - e00715
VL  - 3
AB  - Complete mineralization of the N-methylcarbamate insecticide carbofuran, including
AB  - mineralization of the aromatic moiety, appears to be confined to
AB  - sphingomonad isolates. Here, we report the first draft genome sequence of such a
AB  - sphingomonad strain, i.e., Novosphingobium sp. KN65.2, isolated from
AB  - carbofuran-exposed agricultural soil in Vietnam.
ER  -

TY  - JOUR
AU  - Nho, S.W.
AU  - Hikima, J.I.
AU  - Cha, I.S.
AU  - Park, S.B.
AU  - Jang, H.B.
AU  - Del Castillo, C.S.
AU  - Kondo, H.
AU  - Hirono, I.
AU  - Aoki, T.
AU  - Jung, T.S.
TI  - Complete genome sequence and immunoproteomic analyses of the fish bacterial pathogen Streptococcus parauberis.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3356
EP  - 3366
VL  - 193
AB  - Although Streptococcus parauberis is known as a bacterial pathogen associated with bovine
AB  - udder mastitis, it has recently become one of the
AB  - major causative agents of olive flounder (Paralichthys olivaceus)
AB  - streptococcosis in northeast Asia, causing massive mortality resulting in
AB  - severe economic losses. S. parauberis contains two serotypes, and it is
AB  - likely that capsular polysaccharide antigens serve to differentiate the
AB  - serotypes. In the present study, the complete genome sequence of S.
AB  - parauberis (serotype I) was determined using the GS-FLX system to
AB  - investigate its phylogeny, virulence factors, and antigenic proteins. S.
AB  - parauberis possesses a single chromosome of 2,143,887 bp containing 1,868
AB  - predicted coding sequences (CDSs) with an average GC content of 35.6%.
AB  - Whole-genome dot plot analysis and phylogenetic analysis of a 60 kDa
AB  - chaperonin-encoding gene and the GAPDH-encoding gene showed that the
AB  - strain was evolutionarily closely related to S. uberis. S. parauberis
AB  - antigenic proteins were analyzed using an immunoproteomic technique.
AB  - Twenty-one antigenic protein spots were identified in S. parauberis, by
AB  - reaction with an antiserum obtained from S. parauberis-challenged olive
AB  - flounder. This work provides the foundation needed to understand more
AB  - clearly the relationship between pathogen and host, and develops new
AB  - approaches toward prophylactic and therapeutic strategies to deal with
AB  - streptococcosis in fish. The work also provides a better understanding of
AB  - the physiology and evolution of a significant representative of the
AB  - Streptococcaceae.
ER  -

TY  - JOUR
AU  - Niazi, A.
AU  - Manzoor, S.
AU  - Bejai, S.
AU  - Meijer, J.
AU  - Bongcam-Rudloff, E.
TI  - Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 718
EP  - 725
VL  - 9
AB  - Bacillus amyloliquefaciens subsp. plantarum UCMB5033 is of special interest for its ability to
AB  - promote host plant growth through production of stimulating
AB  - compounds and suppression of soil borne pathogens by synthesizing antibacterial
AB  - and antifungal metabolites or priming plant defense as induced systemic
AB  - resistance. The genome of B. amyloliquefaciens UCMB5033 comprises a 4,071,167 bp
AB  - long circular chromosome that consists of 3,912 protein-coding genes, 86 tRNA
AB  - genes and 10 rRNA operons.
ER  -

TY  - JOUR
AU  - Nicholls, C.
AU  - Kump, A.
AU  - Ford, S.
AU  - Gonser, R.
AU  - Cho, K.H.
TI  - Draft Genome Sequence of Streptococcus pyogenes Strain M3KCL.
JO  - Genome Announcements
PY  - 2017
SP  - e00610
EP  - e00617
VL  - 5
AB  - We present here the draft genome sequence of Streptococcus pyogenes strain M3KCL. The assembly
AB  - contains 1,864,059 bp in 60 contigs. This strain is an M3 strain
AB  - close to MGAS315 but produces SpeB. It was isolated from the blood of a human
AB  - patient with an invasive infection in 2009.
ER  -

TY  - JOUR
AU  - Nichols, M.
AU  - Topaz, N.
AU  - Wang, X.
AU  - Wang, X.
AU  - Boxrud, D.
TI  - Draft Genome Sequences for a Diverse Set of Isolates from 10 Neisseria Species.
JO  - Genome Announcements
PY  - 2018
SP  - e00409
EP  - e00418
VL  - 6
AB  - Neisseria is a diverse genus that includes commensal and pathogenic species that  pose a
AB  - public health threat. While the pathogenic species have been studied
AB  - extensively, many of the commensals have limited genomic information available.
AB  - Here, we present draft genome sequences for a diverse set of 37 isolates from 10
AB  - Neisseria species.
ER  -

TY  - JOUR
AU  - Nicholson, A.C.
AU  - Bell, M.
AU  - Humrighouse, B.W.
AU  - McQuiston, J.R.
TI  - Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical  Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e01462
EP  - e01415
VL  - 3
AB  - Here we report the complete genome sequences of two strains of the novel fastidious, partially
AB  - acid-fast, Gram-positive bacillus 'Lawsonella
AB  - clevelandensis' (proposed). Their clinical relevance and unusual growth
AB  - characteristics make them intriguing candidates for whole-genome sequencing.
ER  -

TY  - JOUR
AU  - Nicholson, A.C.
AU  - Humrighouse, B.W.
AU  - Graziano, J.C.
AU  - Emery, B.
AU  - McQuiston, J.R.
TI  - Draft Genome Sequences of Strains Representing Each of the Elizabethkingia Genomospecies Previously Determined by DNA-DNA Hybridization.
JO  - Genome Announcements
PY  - 2016
SP  - e00045
EP  - e00016
VL  - 4
AB  - Draft genome sequences of Elizabethkingia meningoseptica and representatives of each of its
AB  - four historically described genomospecies were sequenced here.
AB  - Preliminary analysis suggests that Elizabethkingia miricola belongs to
AB  - genomospecies 2, and both Elizabethkingia anophelis and Elizabethkingia
AB  - endophytica are most similar to genomospecies 1.
ER  -

TY  - JOUR
AU  - Nicholson, A.C.
AU  - Whitney, A.M.
AU  - Emery, B.D.
AU  - Bell, M.E.
AU  - Gartin, J.T.
AU  - Humrighouse, B.W.
AU  - Loparev, V.N.
AU  - Batra, D.
AU  - Sheth, M.
AU  - Rowe, L.A.
AU  - Juieng, P.
AU  - Knipe, K.
AU  - Gulvik, C.
AU  - McQuiston, J.R.
TI  - Complete Genome Sequences of Four Strains from the 2015-2016 Elizabethkingia anophelis Outbreak.
JO  - Genome Announcements
PY  - 2016
SP  - e00563
EP  - e00516
VL  - 4
AB  - The complete circularized genome sequences of selected specimens from the largest known
AB  - Elizabethkingia anophelis outbreak to date are described here. Genomic
AB  - rearrangements observed among the outbreak strains are discussed.
ER  -

TY  - JOUR
AU  - Nicholson, A.C.
AU  - Whitney, A.M.
AU  - Humrighouse, B.
AU  - Emery, B.
AU  - Loparev, V.
AU  - McQuiston, J.R.
TI  - Complete Genome Sequence of Strain H5989 of a Novel Devosia Species.
JO  - Genome Announcements
PY  - 2015
SP  - e00934
EP  - e00915
VL  - 3
AB  - The CDC Special Bacteriology Reference Laboratory (SBRL) collection of human clinical
AB  - pathogens contains several strains from the genus Devosia, usually found environmentally. We
AB  - provide here the complete genome of strain H5989, which was isolated from a human
AB  - cerebrospinal fluid (CSF) specimen and represents a putative novel species in the genus
AB  - Devosia.
ER  -

TY  - JOUR
AU  - Nicholson, B.A.
AU  - Wannemuehler, Y.M.
AU  - Logue, C.M.
AU  - Li, G.
AU  - Nolan, L.K.
TI  - Complete Genome Sequence of the Neonatal Meningitis-Causing Escherichia coli Strain NMEC O18.
JO  - Genome Announcements
PY  - 2016
SP  - e01239
EP  - e01216
VL  - 4
AB  - Neonatal meningitis Escherichia coli (NMEC) is a common agent of neonatal bacterial
AB  - meningitis, causing high neonatal mortality and neurologic sequelae in
AB  - its victims. Here, we present the complete genome sequence of NMEC O18 (also
AB  - known as NMEC 58), a highly virulent (O18ac:K1, ST416) strain.
ER  -

TY  - JOUR
AU  - Nicholson, B.A.
AU  - Wannemuehler, Y.M.
AU  - Logue, C.M.
AU  - Li, G.
AU  - Nolan, L.K.
TI  - Complete Genome Sequence of the Avian-Pathogenic Escherichia coli Strain APEC O18.
JO  - Genome Announcements
PY  - 2016
SP  - e01213
EP  - e01216
VL  - 4
AB  - Avian-pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, a disease
AB  - that affects all facets of poultry production
AB  - worldwide, resulting in multimillion dollar losses annually. Here, we report the
AB  - genome sequence of an APEC O18 sequence type 95 (ST95) strain associated with
AB  - disease in a chicken.
ER  -

TY  - JOUR
AU  - Nicholson, T.L.
AU  - Shore, S.M.
AU  - Bayles, D.O.
AU  - Register, K.B.
AU  - Kingsley, R.A.
TI  - Draft Genome Sequence of the Bordetella bronchiseptica Swine Isolate KM22.
JO  - Genome Announcements
PY  - 2014
SP  - e00670
EP  - e00614
VL  - 2
AB  - Bordetella bronchiseptica swine isolate KM22 has been used in experimental infections of swine
AB  - as a model of clinical B. bronchiseptica infections within
AB  - swine herds and to study host-to-host transmission. Here we report the draft
AB  - genome sequence of KM22.
ER  -

TY  - JOUR
AU  - Nicholson, W.L.
AU  - Davis, C.L.
AU  - Shapiro, N.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Reddy, T.B.
AU  - Pillay, M.
AU  - Markowitz, V.
AU  - Varghese, N.
AU  - Pati, A.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Woyke, T.
TI  - An improved high-quality draft genome sequence of Carnobacterium inhibens subsp.  inhibens strain K1(T).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 65
EP  - 65
VL  - 11
AB  - Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium
AB  - remains rather sparsely characterized at the genome level.
AB  - Carnobacterium inhibens K1(T) is a member of the Carnobacteriaceae family within
AB  - the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated
AB  - from the intestine of an Atlantic salmon. The present study determined the genome
AB  - sequence and annotation of Carnobacterium inhibens K1(T). The genome comprised
AB  - 2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding
AB  - genes and 116 RNA genes. The strain contained five contigs corresponding to
AB  - presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.
ER  -

TY  - JOUR
AU  - Nicholson, W.L.
AU  - Leonard, M.T.
AU  - Fajardo-Cavazos, P.
AU  - Panayotova, N.
AU  - Farmerie, W.G.
AU  - Triplett, E.W.
AU  - Schuerger, A.C.
TI  - Complete Genome Sequence of Serratia liquefaciens Strain ATCC 27592.
JO  - Genome Announcements
PY  - 2013
SP  - e00548
EP  - e00513
VL  - 1
AB  - We report the complete genome sequence of Serratia liquefaciens strain ATCC 27592, which was
AB  - previously identified as capable of growth under low-pressure
AB  - conditions. To the best of our knowledge, this is the first announcement of the
AB  - complete genome sequence of an S. liquefaciens strain.
ER  -

TY  - JOUR
AU  - Nickoloff, J.A.
TI  - Converting restriction sites by filling in 5' extensions.
JO  - Biotechniques
PY  - 1992
SP  - 512
EP  - 514
VL  - 12
AB  - None
ER  -

TY  - JOUR
AU  - Nickoloff, J.A.
AU  - Chen, E.Y.
AU  - Heffron, F.
TI  - A 23-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1986
SP  - 7831
EP  - 7835
VL  - 83
AB  - HO nuclease is a site-specific double-strand endonuclease present in haploid Saccharomyces
AB  - cerevisiae undergoing mating type interconversion. HO nuclease initiates mating type
AB  - interconversion by making a double-strand break within the MAT locus. To define the
AB  - recognition site for the enzyme in vitro, we have constructed a number of point mutations and
AB  - deletions within or adjacent to the HO recognition site. Digestion of these substrates with HO
AB  - in vitro reveals that the minimal recognition site is 18 base pairs long, although several
AB  - shorter substrates and substrates containing point mutations are cleaved at low levels in
AB  - vitro. A 24-base-pair HO recognition site stimulates homologous recombination when present in
AB  - a region unrelated to MAT. Recombinants arise from both gene conversion and crossover events.
AB  - The identification of the HO recognition site provides a way of introducing a defined
AB  - initiation site for recombination.
ER  -

TY  - JOUR
AU  - Nie, H.
AU  - Yang, F.
AU  - Zhang, X.
AU  - Yang, J.
AU  - Chen, L.
AU  - Wang, J.
AU  - Xiong, Z.
AU  - Peng, J.
AU  - Sun, L.
AU  - Dong, J.
AU  - Xue, Y.
AU  - Xu, X.
AU  - Chen, S.
AU  - Yao, Z.
AU  - Shen, Y.
AU  - Jin, Q.
TI  - Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a.
JO  - BMC Genomics
PY  - 2006
SP  - 173
EP  - 173
VL  - 7
AB  - ABSTRACT: BACKGROUND: Shigella bacteria cause dysentery, which remains a significant threat to
AB  - public health. Shigella flexneri is the most common
AB  - species in both developing and developed countries. Five Shigella genomes
AB  - have been sequenced, revealing dynamic and diverse features. To
AB  - investigate the intra-species diversity of S. flexneri genomes further, we
AB  - have sequenced the complete genome of S. flexneri 5b strain 8401
AB  - (abbreviated Sf8401) and compared it with S. flexneri 2a (Sf301). RESULTS:
AB  - The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of
AB  - Sf301, mainly because the former lacks the SHI-1 pathogenicity island
AB  - (PAI). Compared with Sf301, there are 6 inversions and one translocation
AB  - in Sf8401, which are probably mediated by insertion sequences (IS). There
AB  - are clear differences in the known PAIs between these two genomes. The
AB  - bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger
AB  - than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from
AB  - Sf8401 but a specific related protein is found next to the pheV locus.
AB  - SHI-2 is involved in one intra-replichore inversion near the origin of
AB  - replication, which may change the expression of iut/iuc genes. Moreover,
AB  - genes related to the glycine-betaine biosynthesis pathway are present only
AB  - in Sf8401 among the known Shigella genomes. CONCLUSIONS: Our data show
AB  - that the two S. flexneri genomes are very similar, which suggests a high
AB  - level of structural and functional conservation between the two serotypes.
AB  - The differences reflect different selection pressures during evolution.
AB  - The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O
AB  - was integrated and the serotypes diverged. SHI-1 was subsequently deleted
AB  - from the S. flexneri 5b genome by recombination, but stabilized in the S.
AB  - flexneri 2a genome. These events may have contributed to the differences
AB  - in pathogenicity and epidemicity between the two serotypes of S. flexneri.
ER  -

TY  - JOUR
AU  - Nielsen, H.
AU  - Einvik, C.
AU  - Lentz, T.E.
AU  - Hedegaard, M.M.
AU  - Johansen, S.D.
TI  - A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA.
JO  - RNA
PY  - 2009
SP  - 958
EP  - 967
VL  - 15
AB  - DiGIR1 is a group I-like cleavage ribozyme found as a structural domain within a nuclear
AB  - twin-ribozyme group I intron. DiGIR1 catalyzes
AB  - cleavage by branching at an Internal Processing Site (IPS) leading to
AB  - formation of a lariat cap at the 5'-end of the 3'-cleavage product. The
AB  - 3'-cleavage product is subsequently processed into an mRNA encoding a
AB  - homing endonuclease. By analysis of combinations of 5'- and
AB  - 3'-deletions, we identify a hairpin in the 5'-UTR of the mRNA (HEG P1)
AB  - that is formed by conformational switching following cleavage. The
AB  - formation of HEG P1 inhibits the reversal of the branching reaction,
AB  - thus giving it directionality. Furthermore, the release of the mRNA is
AB  - a consequence of branching rather than hydrolytic cleavage. A model is
AB  - put forward that explains the release of the I-DirI mRNA with a lariat
AB  - cap and a structured 5'-UTR as a direct consequence of the DiGIR1
AB  - branching reaction. The role of HEG P1 in GIR1 branching is reminiscent
AB  - of that of hairpin P-1 in splicing of the Tetrahymena rRNA group I
AB  - intron and illustrates a general principle in RNA-directed RNA
AB  - processing.
ER  -

TY  - JOUR
AU  - Nielsen, H.
AU  - Westhof, E.
AU  - Johansen, S.
TI  - An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme.
JO  - Science
PY  - 2005
SP  - 1584
EP  - 1587
VL  - 309
AB  - Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in
AB  - some ribosomal RNA transcripts. The group I-like
AB  - ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger
AB  - RNA in the slime mold Didymium iridis. We demonstrate that this cleavage
AB  - occurs by a transesterification reaction with the joining of the first and
AB  - the third nucleotide of the messenger by a 2',5'-phosphodiester linkage.
AB  - Thus, a group I-like ribozyme catalyzes an RNA branching reaction similar
AB  - to the first step of splicing in group II introns and spliceosomal
AB  - introns. The resulting short lariat, by forming a protective 5' cap, might
AB  - have been useful in a primitive RNA world.
ER  -

TY  - JOUR
AU  - Nielsen, M.
AU  - Schreiber, L.
AU  - Finster, K.
AU  - Schramm, A.
TI  - Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 23
EP  - 23
VL  - 9
AB  - Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate
AB  - denitrifier, which can also produce N2 by co-denitrification. Oxygen is
AB  - consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and
AB  - contains key genes for both denitrification and dissimilatory nitrate reduction
AB  - to ammonium.
ER  -

TY  - JOUR
AU  - Nielsen, M.
AU  - Schreiber, L.
AU  - Finster, K.
AU  - Schramm, A.
TI  - Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 4
EP  - 4
VL  - 10
AB  - Bacillus azotoformans MEV2011, isolated from soil, is a microaerotolerant obligate
AB  - denitrifier, which can also produce N2 by co-denitrification. Oxygen is
AB  - consumed but not growth-supportive. The draft genome has a size of 4.7 Mb and
AB  - contains key genes for both denitrification and dissimilatory nitrate reduction
AB  - to ammonium.
ER  -

TY  - JOUR
AU  - Nielsen, P.E.
AU  - Egholm, M.
AU  - Berg, R.H.
AU  - Buchardt, O.
TI  - Sequence-selective recognition of DNA by strand displacement with a Thymine-substituted polyamide.
JO  - Science
PY  - 1991
SP  - 1497
EP  - 1500
VL  - 254
AB  - A polyamide nucleic acid (PNA) was designed by detaching the deoxyribose
AB  - phosphate backbone of DNA in a computer model and replacing it with an achiral
AB  - polyamide backbone.  On the basis of this model, oligomers consisting of
AB  - thymine-linked aminoethylglycyl units were prepared.  These oligomers recognize
AB  - their complementary target in double-stranded DNA by strand displacement.  The
AB  - displacement is made possible by the extraordinarily high stability of the
AB  - PNA-DNA hybrids.  The results show that the backbone of DNA can be replaced by
AB  - a polyamide, with the resulting oligomer retaining base-specificity
AB  - hybridization.
ER  -

TY  - JOUR
AU  - Nielsen, P.E.
AU  - Egholm, M.
AU  - Berg, R.H.
AU  - Buchardt, O.
TI  - Sequence specific inhibition of DNA restriction enzyme cleavage by PNA.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 197
EP  - 200
VL  - 21
AB  - Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets
AB  - proximally flanked by two restriction enzyme sites were challenged with the complementary PNA
AB  - or PNAs having one or two mismatches, and the effect on the restriction enzyme cleavage of the
AB  - flanking sites was assayed. The following PNAs were used: T10-LysNH2, T5CT4-LysNH2 and
AB  - T2CT2CT4-LysNH2 and the corresponding targets cloned into pUC19 were flanked by BamHI, SalI or
AB  - PstI sites, respectively. In all cases it was found that complete inhibition of restriction
AB  - enzyme cleavage was obtained with the complementary PNA, a significantly reduced effect was
AB  - seen with a PNA having one mismatch, and no effect was seen with a PNA having two mismatches.
AB  - These results show that PNA can be used as sequence specific blockers of DNA recognizing
AB  - proteins.
ER  -

TY  - JOUR
AU  - Nielsen, T.K.
AU  - Kot, W.
AU  - Sorensen, S.R.
AU  - Hansen, L.H.
TI  - Draft Genome Sequence of MCPA-Degrading Sphingomonas sp. Strain ERG5, Isolated from a Groundwater Aquifer in Denmark.
JO  - Genome Announcements
PY  - 2015
SP  - e01529
EP  - e01514
VL  - 3
AB  - Sphingomonas sp. strain ERG5 was isolated from a bacterial community, originating from a
AB  - groundwater aquifer polluted with low pesticide concentrations. This
AB  - bacterium degrades 2-methyl-4-chlorophenoxyacetic acid (MCPA) in a wide spectrum
AB  - of concentrations and has been shown to function in bioaugmented sand filters.
AB  - Genes associated with MCPA degradation are situated on a putative conjugative
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Nielsen, T.K.
AU  - Sorensen, S.R.
AU  - Hansen, L.H.
TI  - Draft Genome Sequence of Isoproturon-Mineralizing Sphingomonas sp. SRS2, Isolated from an Agricultural Field in the United Kingdom.
JO  - Genome Announcements
PY  - 2015
SP  - e00569
EP  - e00515
VL  - 3
AB  - Sphingomonas sp. SRS2 was the first described pure strain that is capable of mineralizing the
AB  - phenylurea herbicide isoproturon and some of its related
AB  - compounds. This strain has been studied thoroughly and shows potential for
AB  - bioremediation purposes. We present the draft genome sequence of this bacterium,
AB  - which will aid future studies.
ER  -

TY  - JOUR
AU  - Niemi, O.
AU  - Laine, P.
AU  - Koskinen, P.
AU  - Pasanen, M.
AU  - Pennanen, V.
AU  - Harjunpaa, H.
AU  - Nykyri, J.
AU  - Holm, L.
AU  - Paulin, L.
AU  - Auvinen, P.
AU  - Palva, E.T.
AU  - Pirhonen, M.
TI  - Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 87
EP  - 87
VL  - 12
AB  - Bacteria of the genus Pectobacterium are economically important plant pathogens that cause
AB  - soft rot disease on a wide variety of plant species. Here, we report
AB  - the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot
AB  - model strain isolated from a diseased potato tuber in the early 1980's. The
AB  - genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one
AB  - circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349
AB  - are protein coding and 102 are RNA genes.
ER  -

TY  - JOUR
AU  - Nierman, W.C. et al.
TI  - Structural flexibility in the Burkholderia mallei genome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 14246
EP  - 14251
VL  - 101
AB  - The complete genome sequence of Burkholderia mallei ATCC 23344 provides
AB  - insight into this highly infectious bacterium's pathogenicity and
AB  - evolutionary history. B. mallei, the etiologic agent of glanders, has come
AB  - under renewed scientific investigation as a result of recent concerns
AB  - about its past and potential future use as a biological weapon. Genome
AB  - analysis identified a number of putative virulence factors whose function
AB  - was supported by comparative genome hybridization and expression profiling
AB  - of the bacterium in hamster liver in vivo. The genome contains numerous
AB  - insertion sequence elements that have mediated extensive deletions and
AB  - rearrangements of the genome relative to Burkholderia pseudomallei. The
AB  - genome also contains a vast number (>12,000) of simple sequence repeats.
AB  - Variation in simple sequence repeats in key genes can provide a mechanism
AB  - for generating antigenic variation that may account for the mammalian
AB  - host's inability to mount a durable adaptive immune response to a B.
AB  - mallei infection.
ER  -

TY  - JOUR
AU  - Nierman, W.C. et al.
TI  - Complete genome sequence of Caulobacter crescentus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 4136
EP  - 4141
VL  - 98
AB  - The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base
AB  - pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a
AB  - dilute aquatic environment, coordinates the cell division cycle and multiple cell
AB  - differentiation events. With the annotated genome sequence, a full description of the genetic
AB  - network that controls bacterial differentiation, cell growth, and cell cycle progression is
AB  - within reach. Two-component signal transduction proteins are known to play a significant role
AB  - in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a
AB  - significantly higher number of these signaling proteins (105) than any bacterial genome
AB  - sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA
AB  - methylation. The occurrence of the recognition sequence for an essential DNA methylating
AB  - enzyme that is required for cell cycle regulation is severely limited and shows a bias to
AB  - intergenic regions. The genome contains multiple clusters of genes encoding proteins essential
AB  - for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer
AB  - membrane channel function, degradation of aromatic ring compounds, and the breakdown of
AB  - plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors,
AB  - providing the organism with the ability to respond to a wide range of environmental
AB  - fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class
AB  - proteobacterium to be sequenced and will serve as a foundation for exploring the biology of
AB  - this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia
AB  - prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen
AB  - Brucella abortus.
ER  -

TY  - JOUR
AU  - Niharika, N.
AU  - Sangwan, N.
AU  - Ahmad, S.
AU  - Singh, P.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite.
JO  - Genome Announcements
PY  - 2013
SP  - e00680
EP  - e00613
VL  - 1
AB  - Sphingobium chinhatense strain IP26(T) is a conducive hexachlorocyclohexane (HCH) degrader
AB  - isolated from a heavily contaminated (450 mg HCH/g soil) HCH dumpsite.
AB  - IP26(T) degrades alpha-, beta-, gamma-, and delta-HCH, which are highly
AB  - persistent in the environment. Here we report the draft genome sequence (~5.8
AB  - Mbp) of this strain.
ER  -

TY  - JOUR
AU  - Nikiforov, T.T.
AU  - Connolly, B.A.
TI  - Oligodeoxynucleotides containing 4-thiothymidine and 6-thiodeoxyguanosine as affinity labels for the Eco RV restriction endonuclease and modification methylase.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1209
EP  - 1214
VL  - 20
AB  - 4-Thiothymidine and 6-thiodeoxyguanosine were incorporated into synthetic
AB  - dodecamers containing the recognition site d(GATATC) of the enzymes EcoRV
AB  - endonuclease and EcoRV methyltransferase.  Upon irradiation with long
AB  - wavelength UV light (340- 360 nm), these oligodeoxynucleotides were
AB  - photochemically crosslinked to both enzymes.  The yields were up to 35% with
AB  - the methyltransferase, but lower (up to 6%) with the endonuclease.
AB  - Oligodeoxynucleotides containing 4-thiothymidine generally gave higher yields
AB  - of crosslinking than those containing 6-thiodeoxyguanosine.  Although both
AB  - specific (i.e. those containing the d(GATATC) sequence) and non-specific
AB  - (lacking this sequence) photoreactive oligodeoxynucleotides gave rise to
AB  - crosslinked products, the use of a non-reactive, competitive substrate
AB  - oligodeoxynucleotide suppressed the crosslinking, indicating that the reaction
AB  - takes place at the enzymes' active sites.  Oligodeoxynucleotides containing
AB  - 4-thiocyanatothymidine or 6-thiocyanatodeoxyguanosine were also prepared by
AB  - treatment of the title oligomers with CNBr and KCN.  The dodecamers containing
AB  - 4-thiocyanatothymidine were found to covalently modify both enzymes under
AB  - study, with levels of crosslinking reaching up to 42% with the endonuclease and
AB  - up to 12% with the methyltransferase.  No crosslinking was observed with
AB  - oligodeoxynucleotides containing 6-thiocyanatodeoxyguanosine.
ER  -

TY  - JOUR
AU  - Nikitin, D.
AU  - Mokrishcheva, M.
AU  - Denjmukhametov, M.
AU  - Pertzev, A.
AU  - Zakharova, M.
AU  - Solonin, A.
TI  - Construction of an overproducing strain, purification, and biochemical characterization of the 6His-Eco29kI restriction endonuclease.
JO  - Protein Expr. Purif.
PY  - 2003
SP  - 26
EP  - 31
VL  - 30
AB  - We constructed a strain of Escherichia coli overproducing 6His-tagged Eco29kI by placing the
AB  - coding sequence under control of a strong
AB  - bacteriophage T5 promoter. The yield of 6His-Eco29kI restriction
AB  - endonuclease expression could be increased to about 20% of the total
AB  - cellular protein, but inclusion bodies formed consisting of insoluble
AB  - 6His-Eco29kI protein. We developed a fast and effective protocol for
AB  - purification of the homogeneous enzyme from both soluble and insoluble
AB  - fractions and established their identity by catalytic activity assay. The
AB  - isolated enzymes were tested for recognition specificity and optimal
AB  - reaction conditions as a function of NaCl and KCl concentrations,
AB  - temperature, and pH compared with the native Eco29kI restriction
AB  - endonuclease. The 6His-tagged enzyme retained the specificity of the
AB  - native protein but had an altered optimum of its catalytic reaction.
ER  -

TY  - JOUR
AU  - Nikitin, D.
AU  - Mokrishcheva, M.
AU  - Solonin, A.
TI  - 6His-Eco29kI methyltransferase methylation site and kinetic mechanism characterization.
JO  - Biochim. Biophys. Acta
PY  - 2007
SP  - 1014
EP  - 1019
VL  - 1774
AB  - A new type 11 6His-Eco29kI DNA methyltransferase was tested for methylation site (CC(Me)GCGG)
AB  - and catalytic reaction optimal
AB  - conditions. With high substrate concentrations, an inhibitory effect of
AB  - DNA, but not AdoMet, on its activity was observed. Isotope partitioning
AB  - and substrate preincubation assays showed that the enzyme-AdoMet
AB  - complex is catalytically active. Considering effect of different
AB  - concentrations of DNA and AdoMet on initial velocity, ping-pong
AB  - mechanisms were ruled out. According to data obtained, the enzyme
AB  - appears to work by preferred ordered bi-bi mechanism with AdoMet as
AB  - leading substrate.
ER  -

TY  - JOUR
AU  - Nikitin, D.V.
AU  - Kertesz-Farkas, A.
AU  - Solonin, A.S.
AU  - Mokrishcheva, M.L.
TI  - Bifunctional prokaryotic DNA-methyltransferases.
JO  - Methylation - from DNA, RNa and histones to diseases and treatment
PY  - 2012
SP  - 71
EP  - 87
VL  - 0
AB  - Restriction-modification systems are prokaryotic tools against invasion of foreign DNAs into
AB  - cells.  They reduce horizontal gene transfer, thus stimulating microbial biodiversity.
AB  - Usually, they consist of a restriction endonuclease and a modification DNA methyltransferase
AB  - enzyme recognizing the same short 4-8 nucleotide sequence.  MTase is responsible for methyl
AB  - group transfer to adenine or cytosine nucleotides within the target sequence, thus preventing
AB  - its hydrolysis by cognate REase.  Up to now, more than 20 000 different RMS have been
AB  - collected in the REBASE, the database holding all known, and many putative RMS.  Many of these
AB  - RMS have head-to-tail gene orientation, thus providing, by our hypothesis, the possibility of
AB  - gene fusion through point mutations or genome rearrangements such as deletions, insertions,
AB  - inversions or translocation.  These events could be responsible for the origin of bifunctional
AB  - restriction enzymes of type IIC such as AloI, BcgI, BseMII, BseRI, BsgI, BspLU11III, CjeI,
AB  - Eco57I, HaeIV, MmeI, PpiI, TstI and TspWGI; bifunctional MTases such as FokI and LlaI, and
AB  - regulatory SsoII-related MTases.
ER  -

TY  - JOUR
AU  - Nikitin, D.V.
AU  - Mokrishcheva, M.L.
AU  - Solonin, A.S.
TI  - Binding of DNA methyltransferase M.Ecl18 to operator-promoter region decreases its methylating activity.
JO  - Biokhimiia
PY  - 2012
SP  - 392
EP  - 397
VL  - 77
AB  - The type II bifunctional DNA methyltransferase (MTase) Ecl18 that is able to control
AB  - transcription of its own gene was studied kinetically. Based on initial velocity dependences
AB  - from S-adenosyl-L-methionine (AdoMet) and target DNA and substrate preincubation assays, it is
AB  - proposed that the enzyme apparently works by a rapid equilibrium ordered bi-bi mechanism with
AB  - DNA binding first. By measuring the enzyme activity depending on DNA and AdoMet at different
AB  - fixed concentrations of the operator sequence oligonucleotide, it was found that its binding
AB  - has noncompetitive inhibitory effect on Ecl18 MTase activity.
ER  -

TY  - JOUR
AU  - Nikitin, D.V.
AU  - Mokrishcheva, M.L.
AU  - Solonin, A.S.
TI  - Binding of DNA methyltransferase M.Ecl18 to operator-promoter region decreases its methylating activity.
JO  - Biochemistry
PY  - 2012
SP  - 307
EP  - 311
VL  - 77
AB  - The type II bifunctional DNA methyltransferase (MTase) Ecl18 that is able to control
AB  - transcription of its own gene was studied kinetically.
AB  - Based on initial velocity dependences from S-adenosyl-L-methionine
AB  - (AdoMet) and target DNA and substrate preincubation assays, it is
AB  - proposed that the enzyme apparently works by a rapid equilibrium
AB  - ordered bi-bi mechanism with DNA binding first. By measuring the enzyme
AB  - activity depending on DNA and AdoMet at different fixed concentrations
AB  - of the operator sequence oligonucleotide, it was found that its binding
AB  - has noncompetitive inhibitory effect on Ecl18 MTase activity.
ER  -

TY  - JOUR
AU  - Nikitina, A.S.
AU  - Kharlampieva, D.D.
AU  - Babenko, V.V.
AU  - Shirokov, D.A.
AU  - Vakhitova, M.T.
AU  - Manolov, A.I.
AU  - Shkoporov, A.N.
AU  - Taraskina, A.E.
AU  - Manuvera, V.A.
AU  - Lazarev, V.N.
AU  - Kostryukova, E.S.
TI  - Complete Genome Sequence of an Enterotoxigenic Bacteroides fragilis Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00450
EP  - e00415
VL  - 3
AB  - Here we present the complete genome sequence of Bacteroides fragilis isolate BOB25. It is an
AB  - enterotoxigenic isolate that was obtained from a stool sample of
AB  - a patient with dysbiosis.
ER  -

TY  - JOUR
AU  - Nikolaichik, Y.
AU  - Gorshkov, V.
AU  - Gogolev, Y.
AU  - Valentovich, L.
AU  - Evtushenkov, A.
TI  - Genome Sequence of Pectobacterium atrosepticum Strain 21A.
JO  - Genome Announcements
PY  - 2014
SP  - e00935
EP  - e00914
VL  - 2
AB  - We report the annotated genome sequence of the enterobacterial plant pathogen Pectobacterium
AB  - atrosepticum strain 21A, isolated in Belarus from potato stem with
AB  - blackleg symptoms.
ER  -

TY  - JOUR
AU  - Nikolajewa, S.
AU  - Byer, A.
AU  - Friedel, M.
AU  - Hollunder, J.
AU  - Wilhelm, T.
TI  - Common patterns in type II restriction enzyme binding sites.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 2726
EP  - 2733
VL  - 33
AB  - Restriction enzymes are among the best studied examples of DNA binding proteins. In order to
AB  - find general patterns in DNA recognition sites, which may reflect important properties of
AB  - protein-DNA interaction, we analyse the binding sites of all known type II restriction
AB  - endonucleases. We find a significantly enhanced GC content and discuss three explanations for
AB  - this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our
AB  - analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We
AB  - discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond
AB  - donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking
AB  - energy. These features make RR/YY steps particularly accessible for specific protein-DNA
AB  - interactions. Finally, we show that the recognition sites of type II restriction enzymes are
AB  - underrepresented in host genomes and in phage genomes.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.
AU  - Lopatina, N.
AU  - Suchkov, S.
AU  - Kartashova, I.
AU  - Debov, S.
TI  - Sequence Specificity of Isolated DNA-Cytosine Methylases from Shigella Sonnei 47 Cells.
JO  - Biochem. Int.
PY  - 1984
SP  - 771
EP  - 781
VL  - 9
AB  - Five individual DNA-cytosine methylases differing in pI (isoelectric point) values are present
AB  - in Shigella sonnei 47 cells.  The sequence specificity of each of those was determined 'in
AB  - vitro' by a highly efficient combined approach that included pyrimidine tract (isostic)
AB  - analysis, identification of the immediate neighborhood of the methylated base within the
AB  - recognition sequence and the calculation method.  The enzyme with pI 5.3 (Msso 5,3) is the
AB  - counterpart of the RSso 47II in the Sso 47II restriction-modification system and methylates
AB  - the internal cytosine residue of the 'palindromic' 5'-C-C-N-G-G-3' sequence.  The enzymes
AB  - with pI 6.2 (Msso 6,2) and 7.4 (MSso 7,4) exhibit identical specificity upon methylation of
AB  - the 'palindromic' 5'-Py-C-N-G-Pu-3' sequence, but differ in the pI values of the proteins.
AB  - The enzyme with pI 4.2 (MSso 4,2) recognizes the unique tetranucleotide 5'-C-C-C-C-3'
AB  - sequence and methylates the second cytosine residue at the 5'-end of the sequence.  The
AB  - enzyme with pI 8.4 (MSso 8,4) methylates the centrol cytosine residue within the degenerative
AB  - trinucleotide 5'-(Pu)-C-C-3' sequence. MSso5,3', MSso6,2', and MSso7,4 are presumed to
AB  - belong to the 'family' of sequence-specific (EcoRII-like) enzymes. These DNA-cytosine
AB  - methylases are likely to be evolutionarily related to EcoRII and to have undergone a
AB  - sufficient genetic drift so as to recognize similar (but more degenerative) nucleotide
AB  - sequences.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.
AU  - Tediashvili, M.
AU  - Lopatina, N.
AU  - Chanishvili, T.G.
AU  - Debov, S.
TI  - Specificity and functions of guanine methylase of Shigella sonnei DDVI phage.
JO  - Biochim. Biophys. Acta
PY  - 1979
SP  - 232
EP  - 239
VL  - 561
AB  - DNA methylase methylating adenine with formation of 6-methylamino-purine has
AB  - been identified in Shigella sonnei 1188 cells which are the natural host of
AB  - DDVI phage.  At the same time, in DNA of DDVI phage replicating both in Sh.
AB  - sonnei 1188 cells and Escherichia coli B cells 7-methylguanine was found as the
AB  - only minor base in amounts of 0.25 and 0.27 mol per 100 mos of nucleotides,
AB  - respectively.  The extract of the infected cells was found to contain both
AB  - kinds of DNA methylases; virus-specific guanine methylase and cellular adenine
AB  - methylase.  The place of 6-methylaminopurine in DNA of this phage is explained
AB  - by reversible inhibition of the cell enzyme in the infected cells.  The amount
AB  - of methyl groups transferred by DDVI-specific methylase on DNA does not depend
AB  - on the specifics of the infected cells and is similar in the case of unmodified
AB  - SD phage DNA and DNA of T2 phase methylated by E. coli B enzyme.  Guanine
AB  - methylase has been shown to be a DDVI-induced modification enzyme and to
AB  - protect against restriction of B-type. It methylates double-stranded DNAs only
AB  - and is inhibited by S-adenosylhomocysteine.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Aleksandrova, S.S.
AU  - Lopatina, N.G.
AU  - Debov, S.S.
TI  - Fractionation and purification of DNA methylases and specific endonucleases from cells of Escherichia coli SK.
JO  - Biokhimiia
PY  - 1977
SP  - 598
EP  - 608
VL  - 42
AB  - Fractionation and purification of DNA methylases and specific endonucleases from cells of
AB  - Escherichia coli SK responsible for DNA specificity to host prokaryotic cells were studied.
AB  - The most efficient purification was achieved by precipitation of proteins by 60% saturated
AB  - ammonium sulfate with subsequent chromatography on CM-cellulose and concentration of fractions
AB  - by dialysis against glycerol.  Under these conditions the methylase activity produced 4
AB  - discrete fractions.  Due to purification the specific activity of methylases increased
AB  - 11-20-fold in various fractions.  Methylase from the first (A) and fourth (BII) peaks
AB  - catalyzed the methylation of cytosine to produce 5-methylcytosine; methylase from the third
AB  - peak (BI) methylated adenine to produce 6-methylaminopurine.  The chemical specificity of the
AB  - second peak (B) methylase could not be established due to very high lability of the enzyme in
AB  - this fraction.  Specific endonuclease was found in the gradient zones eluted by 0.1-0.2M and
AB  - 0.65-0.75M NaCl.   It is assumed that those enzymes providing for DNA hydrolysis up to the
AB  - formation of high-molecular discrete fragments, are restriction endonucleases of the SK
AB  - system.  The results obtained strongly suggest the existence of several types of methylases
AB  - and restricting endonucleases in E. coli SK cells.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Aleksandrova, S.S.
AU  - Lopatina, N.G.
AU  - Debov, S.S.
TI  - Fractionation and specificity of DNA methylases from the Escherichia coli SK cells.
JO  - Mol. Cell. Biochem.
PY  - 1978
SP  - 17
EP  - 24
VL  - 20
AB  - Specificity of DNA methylation enzymes from the E. coli SK cells and conditions for their
AB  - separation have been investigated.  Column chromatography on carboxymethylcellulose permits
AB  - fractionation of methylase activity into six discrete peaks whose specificity to the
AB  - methylated base has been determined in vitro with H3-SAM as precursor.  All methylases
AB  - specific for adenine produced 6'-methylaminopurine, all methylases specific for cytosine
AB  - yielded 5'-methylcytosine.  The first enzymatic activity peak containing cytosine methylase
AB  - free of traces of adenine-methylating activity (E1), and the second peak containing both the
AB  - enzymes (E2) were not adsorbed on the ion exchanger and went off the column with the effluent
AB  - (column buffer).  Adenine specific methylase E2 is retarded to a small extent during the
AB  - passage through the column.  The second adenine methylase (W) was characterized by weak bonds
AB  - with the ion exchanger and was removed when washing the column with column buffer.  The
AB  - elution with NaCl gradient produced successively three enzymatic activity peaks: adenine
AB  - methylase (GI), cytosine methylase (GII), and one more adenine methylase (GIII) removed from
AB  - the column by 0.16M, 0.24M and 0.43M NaCl respectively.  Using a new modification of the
AB  - complementary methylation test, the specificity with regard to recognition site was examined
AB  - for all enzymes, except for W and GIII, which were extremely unstable.  The adenine methylases
AB  - E2 and GI and the cytosine methylases E1 and GII were shown to recognize different sites and
AB  - to be different enzymes.  In view of the drastic differences in their chromatographic behavior
AB  - and physical stability, the adenine methylases W and GIII are probably also different enzymes.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Molecular and medical aspects of DNA modification.
JO  - Vestn. Akad. Med. Nauk SSSR
PY  - 1987
SP  - 23
EP  - 29
VL  - 0
AB  - The role of methylation in the cell's life cycle is considered with special
AB  - reference to regulation of transcription in pro- and eukaryotes.  In
AB  - eukaryotes, an inverse correlation exists between levels of gene expression and
AB  - methylation, as is illustrated by experiments with eukaryotic viruses.  In the
AB  - case of bacteriophages, the expression of viral genes may be regulated through
AB  - methylation both negatively and positively.  The modifying role of methylation
AB  - enzymes in prokaryotes, based on the identity or overlap of recognition sites
AB  - in methylases and restriction endonucleses, is analyzed at length.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Karpetz, L.Z.
AU  - Kartashova, M.
AU  - Lopatina, N.G.
AU  - Skripkin, E.A.
AU  - Suchkov, S.V.
AU  - Uporova, T.M.
AU  - Gruber, I.M.
AU  - Debov, S.S.
TI  - Enzymes of the new system of the host specificity Sso47II.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1983
SP  - 5
EP  - 10
VL  - 0
AB  - The DNA host specificity systems SsoI and SsoII are present in Sh. sonnei 47 cells.  The
AB  - R.SsoII and M.SsoII were isolated from these cells and purified by means of affinity,
AB  - ion-exchange, hydrophobic chromatography and isoelectric focusing.  The fine structure of
AB  - R.SsoII and M.SsoII recognition sites was the following: ^CC*NGG.  The pI of M.SsoII was found
AB  - to be 5.3 as determined by isoelectric focusing.  M.SsoII transfers methyl groups to the inner
AB  - cytosine in the recognition sequence CC*NGG.  R.SsoII and M.SsoII are isoshiso- and
AB  - isomethymeric of EcoRII type correspondingly with the SsoII recognition sequence being more
AB  - degenerative.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Anikeicheva, N.V.
AU  - Debov, S.S.
TI  - Determination of the recognition sites of cytosine DNA-methylases from Escherichia coli SK.
JO  - Nucleic Acids Res.
PY  - 1979
SP  - 517
EP  - 528
VL  - 7
AB  - Two different cytosine DNA-methylases, NI and GII, are present in Escherichia
AB  - coli SK.  The GII methylase recognizes the five-member symmetric sequence:
AB  - 5'...NpCpCpApGpGpN...3'.  This sequence is identical with the recognition site
AB  - of the hsp II type determined by RII plasmid but, in contrast to RII methylase,
AB  - the GII enzyme methylates cytosine located on the 5' side of the site.  By
AB  - analogy with the isoshizomery of the restricting endonucleases, RII and GII DNA
AB  - methylaeses may be called isomethymers which recognize the same site but
AB  - methylate different bases.  Since the phage of the SK and hsp II phenotypes is
AB  - effectively restricted in respective cells it may be assumed that the
AB  - isomethymeric modification does not provide any protection against the
AB  - corresponding restrictases.  NI methylase recognizes the five-member symmetric
AB  - site which represents an inverted sequence of the GII site:
AB  - 5'...NpGpGpApCpCpN...3'.  In this case cytosine at the 3'-end of the
AB  - recognition site is methylated.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Chaplygina, N.M.
AU  - Debov, S.S.
TI  - The host specificity system in Escherichia coli SK.
JO  - Mol. Cell. Biochem.
PY  - 1976
SP  - 79
EP  - 87
VL  - 13
AB  - E. coli SK has its own enzyme system providing DNA host specificity which differs from the
AB  - known types of specificity in E. coli K12 and E. coli B.  Modification and restriction are
AB  - observed when the PBVI or PBV3 phages are transferred from E. coli SK to E. coli B or K12 (and
AB  - back).  A methylase has been isolated from E. coli SK cells and partly purified.  This
AB  - methylase catalyzes in vitro transfer of the labeled methyl groups from S-adenosylmethionine
AB  - to DNA of both phage and tissue origin which gives rise to 5'-methylcytosine and
AB  - 6'-methylaminopurine.  The methylase preparations isolated from the cells at stationary phase
AB  - have proved to be 1.5-1.7 times as active as the enzyme from cells at the logarithmic growth
AB  - stage.  The extract of E. coli SK cells infected with the phage SD cannot methylate DNA in
AB  - vitro.  This fact is due to de novo synthesis of the enzyme which degrades SAM to
AB  - 5'-methylthioadenosine and homoserine.  This enzyme is not found in cells infected with the
AB  - SD phage in the presence of chloroamphenicol.  The activity of the enzyme which degrades SAM
AB  - is highest between the 4th and the 5th minutes of infection.  Thus it may be assumed that this
AB  - enzyme, most probably, is an early virus specific protein and prevents in vivo methylation of
AB  - the phage DNA.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Debov, S.S.
TI  - On heterogeneity of DNA methylases from Escherichia coli SK cells.
JO  - Mol. Cell. Biochem.
PY  - 1981
SP  - 3
EP  - 10
VL  - 35
AB  - The presence in E. coli SK cells of five different DNA-methylases differing in specificity to
AB  - the methylated sequence is documented has been proven.  Two enzymes methylate cytosine with
AB  - the formation of 5'-methylcytosine and three enzymes methylate adenine with formation of
AB  - 6'-methylaminopurine.  A method for simultaneous isolation of the five individual enzymes
AB  - including gel filtration on Biogel A-0.5 M is proposed.  The direct evidence has been
AB  - presented showing that the additional methylation test in our method modification actually can
AB  - discriminate between enzymes differing in sensitive sites.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Dedov, S.S.
TI  - Some peculiarities of phage DDVI-specific methylases.
JO  - Biokhimiia
PY  - 1977
SP  - 828
EP  - 832
VL  - 42
AB  - Two types of methylases are found in the cellular extract of Escherichia coli B, infected with
AB  - phage DDVI.  One of them is a cellular enzyme, which methylates adenine to form
AB  - 6-methylaminopurine and is repressed in the infected cell in vivo.  The second type, which is
AB  - not found in the non-infected cell, is specific for phage DDVI and induces the formation of
AB  - 7-methylguanine.  Both enzymes recognize various sites, which accounts for variation in the
AB  - ratio 6-MAP/7-MG in heterologous DNAs between 2.07 in phage Sd DNA and 0.40 in phage DDII DNA.
AB  - During in vitro incubation with homologous methylases phage DDVI DNA and especially phage T2
AB  - DNA are subjected to further methylation, which is probably indicative of their
AB  - undermethylation in vivo.  The DDVI-specific enzyme, similar to B-specific type, methylates
AB  - DNA with a normal set of nitrogenous bases (phages Sd and DDII0, as well as DNAs containing
AB  - 5-oxymethylcytosine and glucose (phages T2 and DDVI).  Both methylases under study use only
AB  - native double-helical DNA as substrate and are strongly inhibited by S-adenosylhomocysteine.
AB  - Phage DDVI methylase is characterized by low stability.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Lopareva, E.N.
AU  - Posypanova, A.M.
AU  - Debov, S.S.
TI  - Modifying methylase SsoI from Shigella sonnei 47 cells.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1988
SP  - 26
EP  - 30
VL  - 10
AB  - A simple and fast method for isolation and purification of SsoI methylase from
AB  - the bacterial strain Shigella sonnei 47 has been proposed.  The enzyme is a
AB  - modifying component of the host cell specificity system and protects the
AB  - acceptor DNA from hydrolysis by restriction endonuclease SsoI and EcoRI.  The
AB  - method is based on hydrophobic chromatography of ammonium sulphate fraction on
AB  - phenylsepharose.  The enzyme preparation obtained is devoid of specific and
AB  - nonspecific endonucleases and is stable at storage in 30% glycerol during a
AB  - year.  The conditions of manifestation of "star" activity by the enzyme were
AB  - studied.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Rekunova, V.N.
AU  - Yurkevich, A.M.
AU  - Debov, S.S.
TI  - On the effect of S-nucleosyl homocysteines on activity of several DNA methylases.
JO  - Vopr. Med. Khim.
PY  - 1978
SP  - 252
EP  - 255
VL  - 24
AB  - The effect was studied of S-adenosyl, -uridyl, -cytidyl and -inosyl homocysteines on the
AB  - activity of bacterial adenine and cytosine methylases from E. coli CK as well as on guanine
AB  - methylase specific for DDVI phage.  S-adenosyl homocysteine was shown to be a strong inhibitor
AB  - of methylation; 10 microM of the substance inhibited all the enzymes studied by 98-99%.  Use
AB  - of total enzymatic preparations did not show any difference in the affinity of S-uridyl,
AB  - -cytidyl and -inosyl homocysteines to various DNA methylases studied.  All these preparations
AB  - inhibited DNA methylases by 55-65%.  Increase in the concentration of inhibitor up to 20
AB  - microM did not elevate the inhibitory effect.  Action of S-nucleosyl homocysteines did not
AB  - depend on the type of acceptor DNA.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Lopatina, N.G.
AU  - Sharkova, E.V.
AU  - Suchkov, S.V.
AU  - Somodi, P.
AU  - Foldes, I.
AU  - Debov, S.S.
TI  - Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells.
JO  - Biochem. Int.
PY  - 1985
SP  - 405
EP  - 413
VL  - 10
AB  - A set of four individual DNA-adenine methylases differing in pI (isoelectric point) values
AB  - (MMbu4.2', MMbu6.4', MMbu7.3' and MMbu8.7), and a sole methylating enzyme with the same
AB  - base specificity (MSso9.5) are present in M. smegmatis (butyricum) and S. sonnei 47 cells,
AB  - respectively.  The sequence specificity of each of those was studied in vitro by a combined
AB  - approach that comprised isostich (purine tract) analysis and identification of the immediate
AB  - neighbourhood of the methylated base within the sequence methylated.  The MSso9.5 recognition
AB  - site has been established as the hexanucleotide 'palindromic' 5'-G-A*-A-T-T-C-3' sequence
AB  - which is structurally similar to the analogous M.EcoRI recognition site.  However, in contrast
AB  - to M.EcoRI, MSso 9.5 methylates the 5'-end adenine residue in the sequence and thus it
AB  - appears to be an isometimer of M.EcoRI.  By means of the same approach, the partial nucleotide
AB  - sequences methylated by each of the four individual M. butyricum enzymes were determined.
AB  - MMbu7.3 and MMbu8.7 exhibit the identical sequence specificity upon methylation of the
AB  - degenerative trinucleotide 5'-Py-A*-Py-3' sequence and thus these enzymes are assumed to
AB  - represent the different molecular forms of the methylase.  MMbu4.2 methylates the
AB  - 5'-G-G-A*-3' sequence and thus it is of a great value as the tool for negating effects of
AB  - the R.BamHI and R.AvaII-type restriction.  MMbu6.4 is of a particular interest on account of
AB  - its unique DNA methylation pattern which is distinguished in the pronounced clustering of
AB  - purine bases in the 5'-Pu-Pu-Pu-Pu-Pu-3' sequence methylated.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Sharkova, E.V.
AU  - Suchkov, S.V.
AU  - Karpets, L.Z.
AU  - Debov, S.S.
AU  - Somodi, P.
AU  - Foldes, I.
TI  - Isoelectric focusing of bacterial DNA methylases.
JO  - Biochem. Int.
PY  - 1983
SP  - 605
EP  - 615
VL  - 7
AB  - The multiplicity of bacterial DNA methylases has been shown for new microorganisms,
AB  - Mycobacteria and Shigella, by a double-step procedure including column chromatography followed
AB  - by isoelectric focusing of the total methylase fraction.  The profiles of the DNA methylating
AB  - activity of Sh.sonnei 47 and M. butyricum strains were studied.  Sh. Sonnei 47 cells were
AB  - found to contain five different proteins responsible for DNA methylation and having pI 4.2,
AB  - 5.3, 6.2, 8.4 and 9.2.  Four M. butyricum methylases were represented by proteins with pI 4.2,
AB  - 6.0, 8.0 and 9.0.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Sharkova, E.V.
AU  - Suchkov, S.V.
AU  - Lopatina, N.G.
AU  - Habar, K.
AU  - Somodi, P.
AU  - Foldes, I.
AU  - Debov, S.S.
TI  - Factors of activation and stabilization of DNA-methylases from Shigella Sonnei 47 and Mycobacterium smegmatis butyricum cells.
JO  - Biochem. Int.
PY  - 1987
SP  - 127
EP  - 138
VL  - 15
AB  - A comparative study of factors of activation and stabilization of individual
AB  - DNA-methylases from two bacterial strains - Shigella sonnei 47 and
AB  - Mycobacterium smegmatis butyricum - isolated by isoelectrofocusing in a pH
AB  - gradient has been carried out.  Storage of enzymes at +4C (pH 7.5) is
AB  - accompanied by periodic changes in the methylating activity.  No such changes
AB  - are observed when the enzymes are stored at pI of the protein.  In this case
AB  - the methylases with alkaline or close to neutral values of pI remain stable
AB  - over a period of at least two weeks, whereas acidic proteins are irreversibly
AB  - inactivated by the end of a two-week period.  A stabilizing effect of BSA on
AB  - DNA-methylases of Sso47 and Mbu strains has been demonstrated.  A direct
AB  - correlation between the stabilizing effect of BSA and the degree of enzyme
AB  - purity has been established.  Ca2+ appear to be a universal activator of
AB  - methylases of the above strains; these cations produce a potent, although a
AB  - short-term effect and can be used in the production of enzyme preparations with
AB  - a high specific activity in DNA recombinant technology.  Protease inhibitors do
AB  - not exert any appreciable effect on the methylase activity upon storage.
AB  - Storage at -20C and at neutral pH leads to complete inactivation of all
AB  - DNA-methylases within 24 hours.  In this case glycerol is fairly ineffective as
AB  - a stabiliziing agent.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Tediashvili, M.G.
AU  - Vasileva, M.B.
AU  - Chanishvili, T.G.
AU  - Debov, S.S.
TI  - System of host specificity and the DNA methylases of Shigellae and their phages.
JO  - Vopr. Virusol.
PY  - 1978
SP  - 724
EP  - 731
VL  - 6
AB  - In Shigella sonnei cells there is a host DNA specificity system responsible for modification
AB  - and restriction of DDII phage.  DNA methylase from Shigella stutzeri cells is specific for
AB  - adenine and catalyses the appearance of 6'-methylaminopurine in the acceptory DNA.
AB  - Methylases from Shigella sonnei cells are specific for adenine and cytosine and provide for
AB  - the presence of 6'-methylaminopurine and 5'-methylcytosine in DNA.  The modifying activity
AB  - of these cells may be equally likely associated with both the enzymes.  A simplified version
AB  - of the additional methylation test has been developed for the study of enzyme specificity.
AB  - The results of additional and cross methylation suggest that several adenine methylases are
AB  - present in the cells of these Shigella, one of these enzymes being shared by Shigella stutzeri
AB  - and Shigella sonnei.  The DNA's isolated from Shigella sonnei and Shigella stutzeri cells are
AB  - undermethylated and in vitro undergo additional methylation upon incubation with the
AB  - appropriate enzyme.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Tediashvili, M.I.
AU  - Chanishvili, T.G.
AU  - Debov, S.S.
TI  - Investigation of methylation character and DNA methylases specificity in Shigella.
JO  - Biokhimiia
PY  - 1978
SP  - 1228
EP  - 1232
VL  - 43
AB  - The nature and content of minor bases in DNA of 3 Shigella strains are investigated.  DNA's
AB  - from Shigella stutzeri 2, S. sonnei 1188 and S. sonnei 311 are found to contain 0.43, 0.56 and
AB  - 0.45 mol. % of N6-methyladenine respectively.  5-methylcytosine (0.16%) is discovered in S.
AB  - sonnei 311.  Substrate specificity of adenine methylase from S. sonnei 1188 with respect to
AB  - phage DNA's of different host modification is investigated.  Recognition sites for guanine
AB  - methylase of DDVI phage and for adenine methylase of S. sonnei 1188 turned out to be
AB  - different.  DNA of DDII phage grown in S. stutzeri 2 cells does not accept methyl groups under
AB  - the treatment with S. sonnei 1188 extracts, but it is methylated by Escherichia coli extract.
AB  - Adenine methylases of S. sonnei 1188 and S. stutzeri 2 are suggested to be either the same
AB  - enzyme, or enzymes, which recognition sites are partially overlapped.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Uporova, T.M.
AU  - Tereshina, E.V.
AU  - Gruber, I.M.
AU  - Zhdanova, L.G.
AU  - Debov, S.S.
TI  - Specificity and properties of DNA methylases in Shigella.
JO  - Vestn. Akad. Med. Nauk SSSR
PY  - 1981
SP  - 16
EP  - 21
VL  - 2
AB  - The specificity of and several properties of whole DNA methylase preparations from two
AB  - Shigella strains, S. sonnei 47843 and S. flexneri, were studied.  Both kinds of preparation
AB  - contained adenine and cytosine methylases which led to the presence of 6-methylaminopurine and
AB  - 5-methylcytosine in the bacterial DNAs.  The concentrations of these in the S. sonnei DNA were
AB  - 0.47 and 0.43 mole per 100 moles of nucleotides, respectively; the corresponding figures for
AB  - the S. flexneri DNAs were 0.42 and 0.38.  In vitro study of substrate specificity showed both
AB  - DNAs to be undermethylated in vivo and to be sensitive substrates for their "own" enzyme.  The
AB  - best acceptors for methyl groups were the thymus and phage Cd DNAs.  The denatured DNA
AB  - specimens did not undergo methylation.  The methylase activities of both strains were
AB  - inhibited by 95-97% by S-adenosylhomocysteine present in an amount of 10 micromoles.
ER  -

TY  - JOUR
AU  - Nikolskaya, I.I.
AU  - Vanyushin, B.F.
AU  - Mardashev, S.R.
TI  - Identification of DNA methylases in cells of Escherichia coli CK.
JO  - Biokhimiia
PY  - 1975
SP  - 1081
EP  - 1086
VL  - 40
AB  - It was established that E. coli CK cells contain a methylase which catalyzes
AB  - the incorporation of CH3 groups into tissue and phage DNAs in vitro in the
AB  - presence of the methyl group donor S-adenosyl-L-methionine.  During isolation
AB  - and purification the enzyme was found in the fraction of 30-60% saturation by
AB  - ammonium sulfate and its specific activity increased 1.9-fold.  The methylase
AB  - was active in both phosphate and tris-HCl buffers at pH 6.5-7.5 and did not
AB  - require Mg ions, EDTA, or dithiothreitol.  The enzyme recognized specific
AB  - nucleotide sequences in all the DNAs investigated and had broader substrate
AB  - specificity than the analogous enzyme from E. coli B.  The methylase of E. coli
AB  - CK was most active with thymus DNA.  The methylase from rat liver nuclei was
AB  - inactive in relation to the DNA of bacteriophages.
ER  -

TY  - JOUR
AU  - Nilsson, M.-G.
AU  - Skarped, C.
AU  - Magnusson, G.
TI  - Structure at restriction endonuclease MboI cleavage sites protected by actinomycin D or distamycin A.
JO  - FEBS Lett.
PY  - 1982
SP  - 360
EP  - 364
VL  - 145
AB  - Restriction endonuclease MboI cleavage of DNA was inhibited by actinomycin D
AB  - and distamycin A.  The two inhibitors protected different subsets of the 8
AB  - cleavage sites in polyoma DNA.  The cleavage reactions were analyzed both in
AB  - the presence of minimal inhibitory concentrations of the compounds and at
AB  - higher concentrations, allowing cleavage at only 1 site/DNA molecule.  The
AB  - experiments showed that cleavage sites most efficiently protected by
AB  - actinomycin D had putative inhibitor binding sites as a distance of 1-2 base
AB  - pairs from the MboI recognition sequence.  Distamycin A, in contrast,
AB  - apparently has to bind immediately adjacent to the MboI recognition sequence to
AB  - protect from cleavage.
ER  -

TY  - JOUR
AU  - Nirwan, N.
AU  - Singh, P.
AU  - Mishra, G.G.
AU  - Johnson, C.M.
AU  - Szczelkun, M.D.
AU  - Inoue, K.
AU  - Vinothkumar, K.R.
AU  - Saikrishnan, K.
TI  - Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity.
JO  - Nucleic Acids Res.
PY  - 2018
AB  - McrBC is one of the three modification-dependent restriction enzymes encoded by the
AB  - Escherichia coli K12 chromosome. Amongst restriction enzymes, McrBC and its
AB  - close homologues are unique in employing the AAA+ domain for GTP
AB  - hydrolysis-dependent activation of DNA cleavage. The GTPase activity of McrB is
AB  - stimulated by the endonuclease subunit McrC. It had been reported previously that
AB  - McrB and McrC subunits oligomerise together into a high molecular weight species.
AB  - Here we conclusively demonstrate using size exclusion chromatography coupled
AB  - multi-angle light scattering (SEC-MALS) and images obtained by electron
AB  - cryomicroscopy that McrB exists as a hexamer in solution. Furthermore, based on
AB  - SEC-MALS and SAXS analyses of McrBC and the structure of McrB, we propose that
AB  - McrBC is a complex of two McrB hexamers bridged by two subunits of McrC, and that
AB  - the complete assembly of this complex is integral to its enzymatic activity. We
AB  - show that the nucleotide-dependent oligomerisation of McrB precedes GTP
AB  - hydrolysis. Mutational studies show that, unlike other AAA+ proteins, the
AB  - catalytic Walker B aspartate is required for oligomerisation.
ER  -

TY  - JOUR
AU  - Nishi, S.
AU  - Tsubouchi, T.
AU  - Takaki, Y.
AU  - Koyanagi, R.
AU  - Satoh, N.
AU  - Maruyama, T.
AU  - Hatada, Y.
TI  - Draft Genome Sequence of Loktanella cinnabarina LL-001T, Isolated from Deep-Sea Floor Sediment.
JO  - Genome Announcements
PY  - 2013
SP  - e00927
EP  - e00913
VL  - 1
AB  - This report describes the draft genome sequence of Loktanella cinnabarina LL-001(T), which was
AB  - the first isolated strain from deep-sea floor sediment of
AB  - the genus Loktanella. The draft genome sequence contains 3,896,245 bp, with a G+C
AB  - content of 66.7%.
ER  -

TY  - JOUR
AU  - Nishibe, C.
AU  - Canevari, C.A.B.
AU  - Dalla, C.R.
AU  - Pinto, B.J.
AU  - Varuzza, L.
AU  - Cataldi, A.A.
AU  - Bernardelli, A.
AU  - Bigi, F.
AU  - Blanco, F.C.
AU  - Zumarraga, M.J.
AU  - Almeida, N.F.
AU  - Araujo, F.R.
TI  - Draft Genome Sequence of Mycobacterium bovis 04-303, a Highly Virulent Strain from Argentina.
JO  - Genome Announcements
PY  - 2013
SP  - e00931
EP  - e00913
VL  - 1
AB  - Mycobacterium bovis strain 04-303 was isolated from a wild boar living in a free-ranging field
AB  - in Argentina. This work reports the draft genome sequence of
AB  - this highly virulent strain and the genomic comparison of its major
AB  - virulence-related genes with those of M. bovis strain AF2122/97 and Mycobacterium
AB  - tuberculosis strain H37Rv.
ER  -

TY  - JOUR
AU  - Nishida, H.
TI  - Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea.
JO  - Curr. Issues Mol. Biol.
PY  - 2013
SP  - 19
EP  - 24
VL  - 15
AB  - Comparative genomics has revealed that variations in bacterial and archaeal genome DNA
AB  - sequences cannot be explained by only neutral mutations. Virus resistance and plasmid
AB  - distribution systems have resulted in changes in bacterial and archaeal genome sequences
AB  - during evolution. The restriction-modification system, a virus resistance system, leads to
AB  - avoidance of palindromic DNA sequences in genomes. Clustered, regularly interspaced, short
AB  - palindromic repeats (CRISPRs) found in genomes represent yet another virus resistance system.
AB  - Comparative genomics has shown that bacteria and archaea have failed to gain any DNA with GC
AB  - content higher than the GC content of their chromosomes. Thus, horizontally transferred DNA
AB  - regions have lower GC content than the host chromosomal DNA does. Some nucleoid-associated
AB  - proteins bind DNA regions with low GC content and inhibit the expression of genes contained in
AB  - those regions. This form of gene repression is another type of virus resistance system. On the
AB  - other hand, bacteria and archaea have used plasmids to gain additional genes. Virus resistance
AB  - systems influence plasmid distribution. Interestingly, the restriction-modification system and
AB  - nucleoid-associated protein genes have been distributed via plasmids. Thus, GC content and
AB  - genomic signatures do not reflect bacterial and archaeal evolutionary relationships.
ER  -

TY  - JOUR
AU  - Nishigaki, K.
AU  - Kaneko, Y.
AU  - Wakuda, H.
AU  - Husimi, Y.
AU  - Tanaka, T.
TI  - Type II restriction endonucleases cleave single-stranded DNAs in general.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 5747
EP  - 5759
VL  - 13
AB  - Restriction endonucleases (13 out of 18 species used for the test) were
AB  - certified to cleave single-stranded(ss)DNA.  Such enzymes as AvaII, HaeII,
AB  - DdeI, AluI, Sau3AI, AccII, TthHB81 and HapII were newly reported to cleave
AB  - ssDNA.  A model to account for the cleavage of ssDNA by restriction enzyes was
AB  - proposed with supportive data.  The essential part of the model was that
AB  - restriction enzymes preferentially cleave transiently formed secondary
AB  - structures (called canonical structures) in ssDNA composed of two recognition
AB  - sequences with two fold rotational symmetry.  This means that a restriction
AB  - enzyme can cleave ssDNAs in general so far as the DNAs have the sequences of
AB  - restriction sites for the enzyme, and that the rate of cleavage depends on the
AB  - stabilities of canonical structures.
ER  -

TY  - JOUR
AU  - Nishikawa, S.
AU  - Ogawa, Y.
AU  - Eguchi, M.
AU  - Rambukkana, A.
AU  - Shimoji, Y.
TI  - Draft Genome Sequences of Lawsonia intracellularis Swine Strains Causing Proliferative Enteropathy in Japan.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01021
EP  - e01018
VL  - 7
AB  - The draft genome sequences of three strains of Lawsonia intracellularis, an obligate
AB  - intracellular animal pathogen responsible for causing proliferative
AB  - enteropathy, obtained from swine in different prefectures in Japan revealed the
AB  - absence of a genomic island previously reported to be linked to host adaptation
AB  - and to high genomic diversity, despite geographical proximity.
ER  -

TY  - JOUR
AU  - Nishiki, I.
AU  - Oinaka, D.
AU  - Iwasaki, Y.
AU  - Yasuike, M.
AU  - Nakamura, Y.
AU  - Yoshida, T.
AU  - Fujiwara, A.
AU  - Nagai, S.
AU  - Katoh, M.
AU  - Kobayashi, T.
TI  - Complete Genome Sequence of Nonagglutinating Lactococcus garvieae Strain 122061 Isolated from Yellowtail in Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e00592
EP  - e00516
VL  - 4
AB  - Nonagglutinating Lactococcus garvieae has been isolated from diseased farmed yellowtail in
AB  - Japan since 2012. In this study, the complete genome and plasmid
AB  - sequence of nonagglutinating L. garvieae strain 122061 was determined, to our
AB  - knowledge, for the first time.
ER  -

TY  - JOUR
AU  - Nishimura, Y.
AU  - Tsuboi, M.
TI  - A possible correlation between DNA conformation and the mode of action of restriction enzymes.
JO  - J. Biochem. (Tokyo)
PY  - 1984
SP  - 1807
EP  - 1811
VL  - 96
AB  - The cutting modes of restriction endonucleases which recognize
AB  - tetradeoxyribonucleotide sequences are classified into two groups.  d(GGCC) and
AB  - d(CGCG), for example, are cut to produce blunt ends, while d(CCGG) and d(GCGC)
AB  - are cut to produce two-base-long cohesive ends.  A conformational analysis by
AB  - the Calladine-Dickerson method indicates that d(GGCC) and d(CGCG) should have a
AB  - roll angle of successive base-pairs open towards the major groove at the
AB  - central (second) base-pair step.  On the other hand, d(CCGG) and d(GCGC) have
AB  - such open roll angles at the first and third base-pair steps.  It is suggested
AB  - that, in general, the cutting mode of a tetramer-specific enzyme depends
AB  - primarily upon the substrate conformation, rather than upon the enzyme.
AB  - Similar correlations between the mode of action and substrate conformation are
AB  - also suggested for hexamer-specific enzymes.
ER  -

TY  - JOUR
AU  - Nishio, Y.
AU  - Nakamura, Y.
AU  - Kawarabayasi, Y.
AU  - Usuda, Y.
AU  - Kimura, E.
AU  - Sugimoto, S.
AU  - Matsui, K.
AU  - Yamagishi, A.
AU  - Kikuchi, H.
AU  - Ikeo, K.
AU  - Gojobori, T.
TI  - Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens.
JO  - Genome Res.
PY  - 2003
SP  - 1572
EP  - 1579
VL  - 13
AB  - Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum,  a species
AB  - widely used for the industrial production of amino acids. C. efficiens
AB  - but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C.
AB  - efficiens genome to investigate the basis of its thermostability by comparing its
AB  - genome with that of C. glutamicum. The difference in GC content between the
AB  - species was reflected in codon usage and nucleotide substitutions. Our
AB  - comparative genomic study clearly showed that there was tremendous bias in amino
AB  - acid substitutions in all orthologous ORFs. Analysis of the direction of the
AB  - amino acid substitutions suggested that three substitutions are important for the
AB  - stability of the C. efficiens proteins: from lysine to arginine, serine to
AB  - alanine, and serine to threonine. Our results strongly suggest that the
AB  - accumulation of these three types of amino acid substitutions correlates with the
AB  - acquisition of thermostability and is responsible for the greater GC content of
AB  - C. efficiens.
ER  -

TY  - JOUR
AU  - Nishioka, M.
AU  - Fujiwara, S.
AU  - Takagi, M.
AU  - Imanaka, T.
TI  - Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 4409
EP  - 4412
VL  - 26
AB  - Two intein endonucleases, denoted PI-PkoI and PI-PkoII, in the DNA polymerase gene of the
AB  - hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 were expressed in Escherichia coli
AB  - and the recombinant endonucleases were characterized.  Both endonucleases were thermostable
AB  - and cleaved their inteinless DNA sequences leaving four base 3'-hydroxyl overhangs.  PI-PkoII
AB  - and the activity of PI-PkoII was enhanced at higher potassium ion concentrations (1M).
AB  - Recognition sequences were also determined using synthetic oligonucleotides inserted into
AB  - plasmid pUC19.  It was shown that DNA sequences of 19 and 16 bp are needed for cleavage by
AB  - PI-PkoI and PI-PkoII, respectively.  PI-PkoII could cleave the downstream junction region
AB  - between intein-encoding and mature DNA polymerase regions and cleavage by PI-PkoII could be
AB  - detected even when chromosomal DNA of P. kodakaraensis KOD1 was used as substrate.  Therefore,
AB  - it is suggested that these endonucleases are switching endonucleases whose function lies in
AB  - the rearrangement of chromosomal DNA.
ER  -

TY  - JOUR
AU  - Nishiyama, R.
AU  - Ito, M.
AU  - Yamaguchi, Y.
AU  - Koizumi, N.
AU  - Sano, H.
TI  - Correlation between maternal inheritance of chloroplast genes and a chloroplast-resident DNA methyltransferase in the green alga, Chlamydomonas reinhardtii.
JO  - Plant Cell Physiol.
PY  - 2002
SP  - s32
EP  - s32
VL  - 43
AB  - Chloroplast DNA of Chlamydomonas reinhardtii is maternally inherited.  Methylation mapping and
AB  - indirect immunofluorescence analyses revealed that chloroplast DNA of mating type plus (mt+)
AB  - gametes is heavily methylated while that of mating type minus (mt-) gametes is not.  To
AB  - clarify the relationship between methylation and maternal inheritance of chloroplast DNA, we
AB  - isolated a cDNA encoding a DNA methyltransferase.  The deduced protein, CrMET1 was transferred
AB  - to chloroplasts, shown by GFP analyses.  Upon gametogenesis, CrMET1 transcripts clearly
AB  - increased in mt+ but not in mt- cells.  These experiments suggest that the CrMET1 protein is
AB  - located in chloroplasts and that it specifically methylates chloroplast DNA in mt+ gametes.
AB  - This conclusion was further strengthened by the observation that, during gametogenesis, CrMET1
AB  - is expressed in a mt- mutant, mat-1, whose chloroplast DNA is heavily methylated in gametes
AB  - and paternally inherited.  The results provide evidence that cytosine methylation plays a
AB  - critical role in maternal inheritance of chloroplast genes.
ER  -

TY  - JOUR
AU  - Nishiyama, R.
AU  - Ito, M.
AU  - Yamaguchi, Y.
AU  - Koizumi, N.
AU  - Sano, H.
TI  - A chloroplast-resident DNA methyltransferase is responsible for hypermethylation of chloroplast genes in Chlamydomonas maternal gametes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 5925
EP  - 5930
VL  - 99
AB  - Chloroplast DNA of the green alga Chlamydomonas reinhardtii is maternally inherited.
AB  - Methylation mapping directly revealed that,
AB  - before mating, chloroplast DNA of maternal (mating type plus; mt(+))
AB  - gametes is heavily methylated whereas that of paternal (mating type
AB  - minus; mt(-)) gametes is not. Indirect immunofluorescence analyses with
AB  - anti-5-methylcytosine mAbs visually showed methylation to occur
AB  - exclusively in chloroplast DNA of mt+ gametes, and not in mt- gametes
AB  - or nuclear DNA of either mt. To clarify the relationship between
AB  - methylation and maternal inheritance of chloroplast DNA, we have
AB  - isolated and characterized a cDNA encoding a DNA methyltransferase. The
AB  - deduced protein, CrMET1, consists of 1,344 aa and contains a conserved
AB  - catalytic domain at the C terminal and a nonconserved N-terminal
AB  - region. The predicted N-terminal region has an arginine-rich domain,
AB  - suggesting CrMET1 is transferred to chloroplasts. This finding could be
AB  - directly shown by green fluorescent protein epifluorescence microscopy
AB  - analyses. CrMET1 transcripts were found to be absent in both mt(+) and
AB  - mt(-) vegetative cells. Upon gametogenesis, however, transcript levels
AB  - clearly increased in mt(+) but not mt(-) cells. These experiments
AB  - suggest that the CrMET1 protein is located in chloroplasts and that it
AB  - specifically methylates cytosine residues of chloroplast DNA in mt+
AB  - gametes. This conclusion was further strengthened by the observation
AB  - that, during gametogenesis, CrMET1 is expressed in a mt(-) mutant,
AB  - mat-1, whose chloroplast DNA is heavily methylated in gametes and
AB  - paternally inherited. The results provide evidence that cytosine
AB  - methylation plays a critical role in maternal inheritance of
AB  - chloroplast genes in C. reinhardtii.
ER  -

TY  - JOUR
AU  - Nishiyama, R.
AU  - Wada, Y.
AU  - Mibu, M.
AU  - Yamaguchi, Y.
AU  - Shimogawara, K.
AU  - Sano, H.
TI  - Role of a nonselective de novo DNA methyltransferase in maternal inheritance of chloroplast genes in the green alga, Chlamydomonas  reinhardtii.
JO  - Genetics
PY  - 2004
SP  - 809
EP  - 816
VL  - 168
AB  - In the green alga, Chlamydomonas, chloroplast DNA is maternally transmitted to the offspring.
AB  - We previously hypothesized that the
AB  - underlying molecular mechanism involves specific methylation of
AB  - maternal gamete DNA before mating, protecting against degradation. To
AB  - obtain direct evidence for this, we focused on a DNA methyltransferase,
AB  - DMT1, which was previously shown to be localized in chloroplasts. The
AB  - full-length DMT1 protein with a molecular mass of 150 kD was expressed
AB  - in insect cells, and its catalytic activity was determined. In vitro
AB  - assays using synthetic DNA indicated methylation of all cytosine
AB  - residues, with no clear selectivity in terms of the neighboring
AB  - nucleotides. Subsequently, transgenic paternal cells constitutively
AB  - expressing DMTI were constructed and direct methylation mapping assays
AB  - of their DNA showed a clear nonselective methylation of chloroplast
AB  - DNA. When transgenic paternal cells were crossed with wild-type
AB  - maternal cells, the frequency of biparental and paternal offspring of
AB  - chloroplasts increased up to 23% while between wild-type strains it was
AB  - similar to3%. The results indicate that DMT1 is a novel type of DNA
AB  - methyltransferase with a nonselective cytosine methylation activity,
AB  - and that chloroplast DNA methylation by DMT1 is one of factors
AB  - influencing maternal inheritance of chloroplast genes.
ER  -

TY  - JOUR
AU  - Nishizawa, A.
AU  - Arshad, A.B.
AU  - Nishizawa, T.
AU  - Asayama, M.
AU  - Fujii, K.
AU  - Nakano, T.
AU  - Harada, K.
AU  - Shirai, M.
TI  - Cloning and characterization of a new hetero-gene cluster of nonribosomal peptide synthetase and polyketide synthase from the cyanobacterium Microcystis aeruginosa K-139.
JO  - J. Gen. Appl. Microbiol.
PY  - 2007
SP  - 17
EP  - 27
VL  - 53
AB  - Two nonribosomal peptide synthetase genes responsible for the biosynthesis
AB  - of microcystin and micropeptin in Microcystis aeruginosa K-139 have been
AB  - identified. A new nonribosomal peptide synthetase gene, psm3, was
AB  - identified in M. aeruginosa K-139. The gene is a cluster extending 30 kb
AB  - and comprising 13 bidirectionally transcribed open reading frames arranged
AB  - in two putative operons. psm3 encodes four adenylation proteins, one
AB  - polyketide synthase, and several unique proteins, especially Psm3L
AB  - consisting of halogenase, acyl-CoA binding protein-like protein, and acyl
AB  - carrier protein. Alignment of the binding pocket of the adenylation domain
AB  - and an ATP-PPi exchange analysis using a recombinant protein with the
AB  - adenylation domain of Psm3B showed that Psm3G and Psm3B activate aspartic
AB  - acid and tyrosine, respectively. Although disruption of psm3 did not
AB  - reveal the product produced by Psm3, we identified microviridin B and
AB  - aeruginosin K139 in the cells of M. aeruginosa K-139. The above-mentioned
AB  - results indicated that M. aeruginosa possesses at least five nonribosomal
AB  - peptide synthetase gene clusters.
ER  -

TY  - JOUR
AU  - Nishizawa, T.
AU  - Hanami, T.
AU  - Hirano, E.
AU  - Miura, T.
AU  - Watanabe, Y.
AU  - Takanezawa, A.
AU  - Komatsuzaki, M.
AU  - Ohta, H.
AU  - Shirai, M.
AU  - Asayama, M.
TI  - Isolation and Molecular Characterization of a Multicellular Cyanobacterium, Limnothrix/Pseudanabaena sp Strain ABRG5-3.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2010
SP  - 1827
EP  - 1835
VL  - 74
AB  - A cyanobacterium, semi-filamentous multicellular strain ABRG5-3, was isolated and its unique
AB  - nature was characterized. This axenic strain
AB  - formal colonies and was motile on an agarose plate. The 16S rRNA gene
AB  - of ABRG5-3 exhibited similarities to those of the Limnothrix and
AB  - Pseudanabaena strains, which are known as filamentous and
AB  - nonheterocystous cyanobacteria. Peaks in absorbance for the
AB  - accumulation of chlorophyll a, phycocyanin, and phycoerythrin were
AB  - observed in the cell extract. Natural separation of the pigments
AB  - occurred in the supernatant of the autolysed cells. The cell lysis was
AB  - promoted by osmotic shocks and lysozyme treatments. Chlorophyll a and
AB  - total DNA were abundantly recovered from the cells. Analysis of the
AB  - restriction-modification system for genomic DNA revealed novel
AB  - diversity. Moreover, we made a successful attempt to create
AB  - antibiotic-resistant strains by conjugation with a foreign plasmid,
AB  - which indicates that strain ABRG5-3 is transformable.
ER  -

TY  - JOUR
AU  - Nishizawa, T.
AU  - Miura, T.
AU  - Harada, C.
AU  - Guo, Y.
AU  - Narisawa, K.
AU  - Ohta, H.
AU  - Takahashi, H.
AU  - Shirai, M.
TI  - Complete Genome Sequence of Streptomyces parvulus 2297, Integrating Site-Specifically with Actinophage R4.
JO  - Genome Announcements
PY  - 2016
SP  - e00875
EP  - e00816
VL  - 4
AB  - Streptomyces parvulus 2297, which is a host for site-specific recombination according to
AB  - actinophage R4, is derived from the type strain ATCC 12434. Species
AB  - of S. parvulus are known as producers of polypeptide antibiotic actinomycins and
AB  - have been considered for industrial applications. We herein report for the first
AB  - time the complete genome sequence of S. parvulus 2297.
ER  -

TY  - JOUR
AU  - Nishizawa, T.
AU  - Tago, K.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Ishii, S.
AU  - Otsuka, S.
AU  - Senoo, K.
TI  - Complete Genome Sequence of the Denitrifying and N2O-Reducing Bacterium Azoarcus  sp. Strain KH32C.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1255
EP  - 1255
VL  - 194
AB  - We report the finished and annotated genome sequence of a denitrifying and N(2)O-reducing
AB  - betaproteobacterium, Azoarcus sp. strain KH32C. The genome is
AB  - composed of one chromosome and one megaplasmid and contains genes for
AB  - plant-microbe interactions and the gene clusters for aromatic-compound
AB  - degradations.
ER  -

TY  - JOUR
AU  - Niu, B.
AU  - Kolter, R.
TI  - Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community  of Maize Roots.
JO  - Genome Announcements
PY  - 2017
SP  - e00997
EP  - e00917
VL  - 5
AB  - Previously, we assembled a model bacterial community of maize roots. Here, we report the
AB  - complete genome sequences of the seven strains composing the
AB  - community.
ER  -

TY  - JOUR
AU  - Niu, B.
AU  - Rueckert, C.
AU  - Blom, J.
AU  - Wang, Q.
AU  - Borriss, R.
TI  - The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of  Lipopeptides and Polyketides.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5862
EP  - 5863
VL  - 193
AB  - The genome of Paenibacillus polymyxa M-1 consisted of a 5.8-Mb chromosome and a 360-kb
AB  - plasmid. Nine sites were dedicated to nonribosomal synthesis
AB  - of lipopeptides and polyketides. Eight of them were located at the
AB  - chromosome, while one gene cluster predicted to encode an unknown
AB  - secondary metabolite was present on the plasmid.
ER  -

TY  - JOUR
AU  - Niu, Y.
AU  - Tenney, K.
AU  - Li, H.
AU  - Gimble, F.S.
TI  - Engineering Variants of the I-SceI Homing Endonuclease with Strand-specific and Site-specific DNA-nicking Activity.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 188
EP  - 202
VL  - 382
AB  - The number of strand-specific nicking endonucleases that are currently available for
AB  - laboratory procedures and applications in vivo is limited,
AB  - and none is sufficiently specific to nick single target sites within
AB  - complex genomes. The extreme target specificity of homing endonucleases
AB  - makes them attractive candidates for engineering high-specificity nicking
AB  - endonucleases. I-SceI is a monomeric homing enzyme that recognizes an 18
AB  - bp asymmetric target sequence, and cleaves both DNA strands to leave
AB  - 3'-overhangs of 4 bp. In single turnover experiments using plasmid
AB  - substrates, I-SceI generates transient open circle intermediates during
AB  - the conversion of supercoiled to linear DNA, indicating that the enzyme
AB  - cleaves the two DNA strands sequentially. A novel hairpin substrate was
AB  - used to demonstrate that although wild-type I-SceI cleaves either the top
AB  - or bottom DNA strand first to generate two nicked DNA intermediates, the
AB  - enzyme has a preference for cleaving the bottom strand. The kinetics data
AB  - are consistent with a parallel sequential reaction mechanism. Substitution
AB  - of two pseudo-symmetric residues, Lys122 and Lys223, markedly reduces top
AB  - and bottom-strand cleavage, respectively, to generate enzymes with
AB  - significant strand- and sequence-specific nicking activity. The two active
AB  - sites are partially interdependent, since alterations to one site affect
AB  - the second. The kinetics analysis is consistent with X-ray crystal
AB  - structures of I-SceI/DNA complexes that reveal a role for the lysines in
AB  - establishing important solvent networks that include nucleophilic water
AB  - molecules thought to attack the scissile phosphodiester bonds.
ER  -

TY  - JOUR
AU  - Niv, M.Y.
AU  - Ripoll, D.R.
AU  - Vila, J.A.
AU  - Liwo, A.
AU  - Vanamee, E.S.
AU  - Aggarwal, A.K.
AU  - Weinstein, H.
AU  - Scheraga, H.A.
TI  - Topology of Type II REases revisited; structural classes and the common conserved core.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2227
EP  - 2237
VL  - 35
AB  - Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences
AB  - with remarkable specificity. Type II REases are highly divergent in sequence as well as in
AB  - topology, i.e. the connectivity of secondary structure elements. A widely held assumption is
AB  - that a structural core of five beta-strands flanked by two alpha-helices is common to these
AB  - enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an
AB  - unambiguous and reproducible way, and use it to analyze the currently available X-ray
AB  - structures of Type II REases. Based on this analysis, we propose an alternative definition of
AB  - the core, which we term the alphabetaalpha-core. The alphabetaalpha-core includes the most
AB  - frequently observed secondary structure elements and is not a sandwich, as it consists of a
AB  - five-strand beta-sheet and two alpha-helices on the same face of the beta-sheet. We use the
AB  - alphabetaalpha-core connectivity as a basis for grouping the Type II REases into distinct
AB  - structural classes. In these new structural classes, the connectivity correlates with the
AB  - angles between the secondary structure elements and with the cleavage patterns of the REases.
AB  - We show that there exists a substructure of the alphabetaalpha-core, namely a common conserved
AB  - core, ccc, defined here as one alpha-helix and four beta-strands common to all Type II REase
AB  - of known structure.
ER  -

TY  - JOUR
AU  - Niv, M.Y.
AU  - Skrabanek, L.
AU  - Roberts, R.J.
AU  - Scheraga, H.A.
AU  - Weinstein, H.
TI  - Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with  optional secondary structure constraints.
JO  - Proteins
PY  - 2008
SP  - 631
EP  - 640
VL  - 71
AB  - Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable
AB  - tools in molecular biology. Type II REases are highly divergent in
AB  - sequence despite their common structural core, function and, in some cases,
AB  - common specificities towards DNA sequences. This makes it difficult to identify
AB  - and classify them functionally based on sequence, and has hampered the efforts of
AB  - specificity-engineering. Here, we define novel REase sequence motifs, which
AB  - extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure
AB  - information. The automated search using these motifs is carried out with a newly
AB  - developed fast regular expression matching algorithm that accommodates long
AB  - patterns with optional secondary structure constraints. Using this new tool,
AB  - named Scan2S, motifs derived from REases with specificity towards GATC- and
AB  - CGGG-containing DNA sequences successfully identify REases of the same
AB  - specificity. Notably, some of these sequences are not identified by standard
AB  - sequence detection tools. The new motifs highlight potential
AB  - specificity-determining positions that do not fully overlap for the GATC- and the
AB  - CCGG-recognizing REases and are candidates for specificity re-engineering.
ER  -

TY  - JOUR
AU  - Niza, B.
AU  - Merfa, M.V.
AU  - Alencar, V.C.
AU  - Menegidio, F.B.
AU  - Nunes, L.R.
AU  - Machado, M.A.
AU  - Takita, M.A.
AU  - de Souza, A.A.
TI  - Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa.
JO  - Genome Announcements
PY  - 2016
SP  - e01124
EP  - e01116
VL  - 4
AB  - The draft genome of Xylella fastidiosa subsp. pauca strain 11399, a transformable
AB  - citrus-pathogenic strain, is reported here. The 11399 genome size is 2,690,704 bp
AB  - and has a G+C content of 52.7%. The draft genome of 11399 reveals the absence of
AB  - four type I restriction-modification system genes.
ER  -

TY  - JOUR
AU  - Nkenfou, C.
TI  - Cloning and studying of the cleavage flexibility of some type IIs  restriction endonucleases.
JO  - Ph.D. Thesis, University of Yaounde I, Cameroon
PY  - 2002
SP  - 1
EP  - 226
AB  - More than 3000 bacterial samples were screened for restriction
AB  - enzymes.  Three new specificities were found and a few isoschizomers with
AB  - interesting properties.  Two of these isoschizomers: BceAI, an isoschizomer
AB  - of BcefI (ACGGC) and BspCNI, an isoschizomer of BseMII (CTCAG), belonging
AB  - to the subgroup of Type IIs restriction enzymes were cloned as well as the
AB  - prototype of BceAI, BcefI.  These two cloned isoschizomers and one other,
AB  - BpuCI, a neoschizomer of Ecil (GGCGGA), were studied for their cleavage
AB  - flexibility alongside that of their prototypes.  These studies were carried
AB  - out on different DNA substrates.  The conformation as well as the bending
AB  - mode of these DNA substrates were predicted using computer programs.  The
AB  - flexibility of the 3 pairs of enzymes studied was as follows:  For BceAI
AB  - and BcefI, their preferred site was 12/14 and their alternative site was
AB  - 11/13.  For BspCNI and BseMII, for some sequences their preferred site was
AB  - 10/8, for other sequences the preferred site was 9/7 and some sequences
AB  - were cleaved at both positions with the same rate.  For BpuCI and Ecil, the
AB  - preferred site for BpuCI was 12/10 and its alternative site was 13/11.  The
AB  - preferred site for EciI was 11/9 and its alternative site was 12/10.  These
AB  - cleavage positions and rates were determined to be sequence-dependent as
AB  - well as influenced by the conformation of the protein (enzyme).  Based on
AB  - the prediction of the conformation and bending mode of the different
AB  - substrates together with the results of the cleavage positions and rates,
AB  - allowed the following conclusions.  For sequences presenting an anisotropic
AB  - bending mode, the cleavage position tended to be further away from the
AB  - recognition sequence.  For sequences presenting an isotropic bending mode,
AB  - the cleavage tended to occur closer to the recognition sequence.
ER  -

TY  - JOUR
AU  - Noar, J.
AU  - Makwana, S.T.
AU  - Bruno-Barcena, J.M.
TI  - Complete Genome Sequence of Solvent-Tolerant Clostridium beijerinckii Strain SA-1.
JO  - Genome Announcements
PY  - 2014
SP  - e01310
EP  - e01314
VL  - 2
AB  - We report the complete genome sequence of Clostridium beijerinckii SA-1, derived  by directed
AB  - evolution from C. beijerinckii NCIMB 8052, selecting for enhanced
AB  - solvent tolerance. This sequence allows for accurate placement of SA-1 as C.
AB  - beijerinckii, permits functional analyses of mutant phenotypes, and suggests
AB  - methods for distinguishing SA-1 from its parent.
ER  -

TY  - JOUR
AU  - Noar, J.D.
AU  - Bruno-Barcena, J.M.
TI  - Complete Genome Sequences of Azotobacter vinelandii Wild-Type Strain CA and Tungsten-Tolerant Mutant Strain CA6.
JO  - Genome Announcements
PY  - 2013
SP  - e00313
EP  - e00313
VL  - 1
AB  - We report the complete genome sequences of Azotobacter vinelandii mutant strain CA6 and its
AB  - parent wild-type strain, CA. When fixing nitrogen, strain CA6
AB  - displays slow growth and impaired molybdate uptake, tolerance to tungstates, and
AB  - production of hydrogen gas, compared to results for strain CA. Comparing these
AB  - genome sequences may provide a genetic basis for these mutant phenotypes.
ER  -

TY  - JOUR
AU  - Nobbs, T.F.
AU  - Wentzell, L.M.
AU  - Szczelkum, M.D.
AU  - Halford, S.E.
TI  - SfiI: An unconventional restriction enzyme.
JO  - The NEB Transcript
PY  - 1997
SP  - 10
EP  - 11
VL  - 8
AB  - Abrief review of SfiI
ER  -

TY  - JOUR
AU  - Nobbs, T.J.
AU  - Halford, S.E.
TI  - DNA cleavage at two recognition sites by the SfiI restriction endonuclease: Salt dependence of Cis and Trans interactions between distant DNA sites.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 399
EP  - 411
VL  - 252
AB  - At low ionic strength, the SfiI restriction enzyme cleaved at similar rates both supercoiled
AB  - and linear DNA with two SfiI sites and linear DNA with one SfiI site.  For the substrates with
AB  - two sites, the majority of the DNA was converted directly to products cut at both sites; the
AB  - enzyme appears to bind to two sites before catalyzing its reactions, looping out the
AB  - intervening DNA.  At high ionic strength, linear DNA with one SfiI site was not cut at all,
AB  - linear DNA with two sites was cleaved slowly while supercoiled DNA with two sites was cleaved
AB  - rapidly, though only half of the DNA with two sites was cut at both sites; the DNA that had
AB  - been cut at one site was not cleaved again at the remaining site.  The singly cut product must
AB  - therefore have been generated by a reaction incorporating both sites.  All DNA cleavage
AB  - reactions by SfiI thus involve the tetrameric enzyme bound to two copies of its recognition
AB  - sequence, but weakened DNA-protein interactions at high ionic strength can cause this complex
AB  - to dissociate before cleaving both sites.  Intramolecular interactions between distant DNA
AB  - sites are generally thought to be enhanced by supercoiling and to be more stable than
AB  - intermolecular interactions.  The preference of SfiI at high ionic strength for substrates
AB  - with two sites over substrates with one site and, in the former case, for supercoiled over
AB  - linear DNA, validates this view.  At low ionic strength, the similar rates with the different
AB  - substrates may be due to rate-limiting product dissociation.
ER  -

TY  - JOUR
AU  - Nobbs, T.J.
AU  - Szczelkun, M.D.
AU  - Wentzell, L.M.
AU  - Halford, S.E.
TI  - DNA excision by the SfiI restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 419
EP  - 432
VL  - 281
AB  - A mechanism for the precise excision of DNA between two target sites was elucidated by
AB  - analyzing the individual steps during the reactions of the SfiI endonuclease on a plasmid with
AB  - two SfiI sites.  Previous studies had indicated that SfiI is a tetrameric protein that binds
AB  - to two copies of its recognition site before cleaving both sites in both strands.  In this
AB  - study, the concerted cleavage of four phosphodiester bonds was shown to arise from four
AB  - consecutive reactions that had similar values for their intrinsic rate constants.  Each
AB  - reaction is presumably mediated by one of the four active sites in the tetramer and all four
AB  - were generally completed within the life-time of the complex between the protein and two
AB  - recognition sites, though products cleaved in one or two phosphodiester bonds were also
AB  - detected following premature dissociation of the enzyme-substrate complex at elevated
AB  - temperatures.  At the physiological temperature for this enzyme, all four bonds were cleaved
AB  - within one minute but the subsequent dissociation of the enzyme-product complex, liberating
AB  - the excised segment of DNA, took about one hour.  The tetrameric structure of SfiI was
AB  - confirmed by equilibrium centrifugation.
ER  -

TY  - JOUR
AU  - Nobbs, T.J.
AU  - Williams, S.A.
AU  - Connolly, B.A.
AU  - Halford, S.E.
TI  - Phosphorothioate substrates for the SfiI restriction endonuclease.
JO  - Biol. Chem.
PY  - 1998
SP  - 599
EP  - 604
VL  - 379
AB  - Oligodeoxynucleotides carrying the recognition sequence for the SfiI endonuclease were
AB  - synthesized with phosphorothioates at the cleavage site.  The Rp and Sp diasteroisomers of the
AB  - oligonucleotides were separated by HPLC using a mobile phase containing L-cysteine.  The
AB  - duplex with Rp phosphorothioates was cleaved very slowly in the presence of Mg2+, though
AB  - virtually complete cleavage was obtained with Mn2+.  No significant cleavage of the duplex
AB  - with Sp phosphorothioates occurred with either Mg2+ or Mn2+.  When added to a plasmid with one
AB  - SfiI site, the duplexes with either Rp or Sp phosphorothioates inhibited the rate at which
AB  - SfiI cleaved the plasmid: a control duplex with oxyester linkages enhanced the rate of plasmid
AB  - cleavage.  In contrast to type IIe nucleases such as EcoRII and NaeI, which can be activated
AB  - by non-hydrolysable analogues of their substrates, SfiI reactions require four susceptible
AB  - phosphodiester bonds.
ER  -

TY  - JOUR
AU  - Nobile, C.
TI  - An improved method for partial restriction digestion of ultraviolet irradiated DNA.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4288
EP  - 4288
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Nobu, M.K.
AU  - Narihiro, T.
AU  - Tamaki, H.
AU  - Qiu, Y.L.
AU  - Sekiguchi, Y.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Davenport, K.W.
AU  - Kamagata, Y.
AU  - Liu, W.T.
TI  - Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph.
JO  - Genome Announcements
PY  - 2014
SP  - e01064
EP  - e01013
VL  - 2
AB  - Syntrophorhabdus aromaticivorans strain UI is a mesophilic bacterium capable of degrading
AB  - aromatic substrates in syntrophic cooperation with a partner
AB  - methanogen. The draft genome sequence is 3.7 Mb, with a G+C content of 52.0%.
ER  -

TY  - JOUR
AU  - Nobusato, A.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Diversity of restriction-modification gene homologues in Helicobacter pylori.
JO  - Gene
PY  - 2000
SP  - 89
EP  - 98
VL  - 259
AB  - The complete genome sequences of two Helicobacter pylori strains have recently become
AB  - available. We have searched them for homologues of restriction-modification genes. One strain
AB  - (26695) carried 52 such homologues, and the other (J99) carried 53. Their sequence alignments
AB  - were arranged in the form of a phylogenetic tree and compared with the tree based on rRNA. The
AB  - trees showed that the homologues are scattered among diverse groups of bacteria. They also
AB  - revealed high polymorphism within the species - there are 42 pairs with high homology, 10
AB  - specific to 26695, and 11 specific to J99. Many of the restriction-modification homologues
AB  - were characterized by a GC content lower than that of the average gene in the genome. Some of
AB  - the restriction-modification homologues showed a different codon use bias from the average
AB  - genes. These observations are interpreted in terms of horizontal transfer of the
AB  - restriction-modification genes.
ER  -

TY  - JOUR
AU  - Nobusato, A.
AU  - Uchiyama, I.
AU  - Ohashi, S.
AU  - Kobayashi, I.
TI  - Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes.
JO  - Gene
PY  - 2000
SP  - 99
EP  - 108
VL  - 259
AB  - The complete genome sequences of two closely related organisms - two Helicobacter pylori
AB  - strains - have recently become available. Comparison of these genomes at single base pair
AB  - level has suggested the presence of a mechanism for bacterial gene mobility - insertion with
AB  - long target duplications. This mechanism is formally similar to classical transposon
AB  - insertion, but the duplication is much longer, often in the range of 100bp.  Restriction
AB  - and/or modification enzyme genes are often within or adjacent to the insertion. A similar
AB  - process may have mediated insertion of the cag+ pathogenicity island in H. pylori. A similar
AB  - structure was identified in comparisons between Neisseria meningitidis and Neisseria
AB  - gonorrhoeae genomes. We hypothesize that this mechanism, as well as two other types of
AB  - polymorphism linked with restriction-modification genes (insertion accompanied by target
AB  - deletion and a tripartite structure composed of  substitution/inversion/deletion), have
AB  - resulted from attack by restriction enzymes on the chromosome.
ER  -

TY  - JOUR
AU  - Noda, M.
AU  - Shiraga, M.
AU  - Kumagai, T.
AU  - Danshiitsoodol, N.
AU  - Sugiyama, M.
TI  - Characterization of the SN35N Strain-Specific Exopolysaccharide Encoded in the Whole Circular Genome of a Plant-Derived Lactobacillus plantarum.
JO  - Biol. Pharm. Bull.
PY  - 2018
SP  - 536
EP  - 545
VL  - 41
AB  - Lactobacillus plantarum SN35N, which has been previously isolated from pear,
AB  - secretes exopolysaccharide (EPS). The aim of the present study is to characterize
AB  - the EPS chemically and to find the EPS-biosynthesizing gene cluster. The present
AB  - study demonstrates that the strain produces an acidic EPS carrying phosphate
AB  - residue, which is composed of glucose, galactose, and mannose at a molecular
AB  - ratio of 15.0 : 5.7 : 1.0. We also show that acidic EPS strongly inhibits the
AB  - catalytic activity of hyaluronidase (EC 3.2.1.35), promoting an inflammatory
AB  - reaction. In the present study, we also determined the complete genome sequence
AB  - of the SN35N strain, demonstrating that the genome is a circular DNA with 3267626
AB  - bp, and the number of predicted coding genes is 3146, with a GC content of
AB  - 44.51%. In addition, the strain harbors four plasmids, designated pSN35N-1, -2,
AB  - -3, and -4. Although four EPS-biosynthesizing genes, designated lpe1, lpe2, lpe3,
AB  - and lpe4, are present in the SN35N chromosomal DNA, another EPS gene cluster,
AB  - lpe5, is located in the pSN35N-3 plasmid, composed of 35425 bp. EPS low-producing
AB  - mutants, which were obtained by treating SN35N cells with novobiocin, lost the
AB  - lpe5 gene cluster in the plasmid-curing experiment, suggesting that the gene
AB  - cluster for the biosynthesis of acidic EPS is present in the plasmid. The present
AB  - study shows the chemical characterization of the acidic EPS and its inhibitory
AB  - effect to the hyaluronidase.
ER  -

TY  - JOUR
AU  - Noda, M.
AU  - Sugimoto, S.
AU  - Hayashi, I.
AU  - Danshiitsoodol, N.
AU  - Fukamachi, M.
AU  - Sugiyama, M.
TI  - A novel structure of exopolysaccharide produced by a plant-derived lactic acid bacterium Lactobacillus paracasei IJH-SONE68.
JO  - J. Biochem. (Tokyo)
PY  - 2018
SP  - 87
EP  - 92
VL  - 164
AB  - A lactic acid bacterium Lactobacillus paracasei IJH-SONE68, which was isolated
AB  - from a fig leaf by our group, was found to produce both acidic and neutral
AB  - exopolysaccharides (EPSs). The nuclear magnetic resonance analysis demonstrates
AB  - that the former EPS is composed primarily of mannose, and the latter one consists
AB  - of the alpha-1, 6-linked glycan chains made of N-acetylglucosamine (GlcNAc). The
AB  - presence of alpha-1, 6-linked GlcNAc polysaccharide is first reported in
AB  - prokaryotes. Furthermore, to reveal the EPS-biosynthetic gene organization in the
AB  - IJH-SONE68 strain, in the present study, we determined the whole-genome sequence.
ER  -

TY  - JOUR
AU  - Noda, S.
AU  - Aihara, C.
AU  - Yuki, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Lactococcus sp. Strain NtB2 (JCM 32569), Isolated from the Gut of the Higher Termite Nasutitermes takasagoensis.
JO  - Genome Announcements
PY  - 2018
SP  - e00445
EP  - e00418
VL  - 6
AB  - Lactic acid bacteria are widely distributed in the termite gut. Here, we report the draft
AB  - genome sequence of Lactococcus sp. strain NtB2, which was isolated from
AB  - the gut of a wood-feeding higher termite.
ER  -

TY  - JOUR
AU  - Noel, A.J.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - DNA recognition by the homing endonuclease PI-SceI involves a divalent metal ion cofactor-induced conformational change.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 6794
EP  - 6804
VL  - 279
AB  - PI-SceI, a homing endonuclease of the IAGLIDADG family, consists of two domains involved in
AB  - DNA cleavage and protein splicing, respectively.
AB  - Both domains cooperate in binding the recognition sequence. Comparison
AB  - of the structures of PI-SceI in the absence and presence of substrate
AB  - reveals major conformational changes in both the protein and DNA.
AB  - Notably, in the protein-splicing domain the loop comprising residues
AB  - 53-70 and adopts a "closed" conformation, thus enabling it to interact
AB  - with the DNA. We have studied the dynamics of DNA binding and
AB  - subsequent loop movement by fluorescence techniques. Six amino acids in
AB  - loop53-70 were individually replaced by cysteine and modified by
AB  - fluorescein. The interaction of the modified PI-SceI variants with the
AB  - substrate, unlabeled or labeled with tetramethylrhodamine, was analyzed
AB  - in equilibrium and stopped-flow experiments. A kinetic scheme was
AB  - established describing the interaction between PI-SceI and DNA. It is
AB  - noteworthy that the apparent hinge-flap motion of loop53-70 is only
AB  - observed in the presence of a divalent metal ion cofactor. Substitution
AB  - of the major Mg2+-binding ligands in PI-SceI, Asp-218 and Asp-326, by
AB  - Asn or "nicking" PI-SceI with trypsin at Arg-277, which interferes with
AB  - formation of an active enzyme-substrate complex, both prevent the
AB  - conformational change of loop53-70. Deletion of the loop inactivates
AB  - the enzyme. We conclude that loop53-70 is an important structural
AB  - element that couples DNA recognition by the splicing domain with DNA
AB  - cleavage by the catalytic domain and as such "communicates" with the
AB  - Mg2+ binding sites at the catalytic centers.
ER  -

TY  - JOUR
AU  - Noel, S.J.
AU  - Hojberg, O.
AU  - Urich, T.
AU  - Poulsen, M.
TI  - Draft Genome Sequence of 'Candidatus Methanomethylophilus' sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the  Methanomassiliicoccales Order.
JO  - Genome Announcements
PY  - 2016
SP  - e01734
EP  - e01715
VL  - 4
AB  - Here, we present the draft genome of 'Candidatus Methanomethylophilus' sp. 1R26,  a member
AB  - of the newly described Methanomassiliicoccales order of Euryarcheaota.
AB  - The enrichment culture was established from bovine rumen contents and produced
AB  - methane from trimethylamine and methanol. The draft genome contains genes for
AB  - methanogenesis from methylated compounds.
ER  -

TY  - JOUR
AU  - Nogami, S.
AU  - Fukuda, T.
AU  - Nagai, Y.
AU  - Yabe, S.
AU  - Sugiura, M.
AU  - Mizutani, R.
AU  - Satow, Y.
AU  - Anraku, Y.
AU  - Ohya, Y.
TI  - Homing at an extragenic locus mediated by VDE (PI-Scel) in  Saccharomyces cerevisiae.
JO  - Yeast
PY  - 2002
SP  - 773
EP  - 782
VL  - 19
AB  - PI-SceI (VDE), a homing endonuclease with protein splicing activity,  is a genomic parasite in
AB  - the VMA1 gene of Saccharomyces cerevisiae. In a
AB  - heterozygous diploid of the VDE-less VMA1 allele and a VDE-containing VMA1
AB  - allele, VDE specifically cleaves its recognition sequence (VRS) in the
AB  - VDE-less VMA1 allele at meiosis, followed by 'homing', i.e. a conversion
AB  - to a VDE-containing allele. We found that upon VDE expression, homing of a
AB  - marker gene at an extragenic locus occurs only when a 45 bp element
AB  - containing the VRS is inserted at its allelic site, while mutants of VDE
AB  - with no endonuclease activity lack authentic extragenic homing activity.
AB  - Thus, both the VRS and VDE are required for homing. Insertion of the VRS
AB  - in a homozygous diploid significantly lowered the spore germination
AB  - ability, indicating that a template for gene repair at its allelic locus
AB  - is essential for efficient homing and survival of yeast cells. Copyright
AB  - (C) 2002 John Wiley Sons, Ltd.
ER  -

TY  - JOUR
AU  - Noh, Y.
AU  - Kim, S.Y.
AU  - Lee, Y.S.
AU  - Kim, D.W.
AU  - Kwon, T.
AU  - Hwang, K.J.
TI  - Whole-Genome Sequence of Borrelia garinii Strain 935T Isolated from Ixodes persulcatus in South Korea.
JO  - Genome Announcements
PY  - 2014
SP  - e01298
EP  - e01214
VL  - 2
AB  - We report here the genome sequence of Borrelia garinii strain 935T isolated from  Ixodes
AB  - persulcatus in South Korea. The 1,176,739 bp (G+C content, 27.73%) genome
AB  - consists of 1,194 coding regions, 4 rRNA genes, and 33 aminoacyl-tRNA synthetase
AB  - genes. This is the first whole-genome report of a Korean Borrelia species
AB  - isolate.
ER  -

TY  - JOUR
AU  - Nolan, M. et al.
TI  - Complete genome sequence of Rhodothermus marinus type strain (R-10).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 283
EP  - 290
VL  - 1
AB  - Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and  is of
AB  - phylogenetic interest because the Rhodothermaceae represent the deepest
AB  - lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative,
AB  - non-motile, non-spore-forming bacterium isolated from marine hot springs off the
AB  - coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly
AB  - halophilic conditions for growth. Here we describe the features of this organism,
AB  - together with the complete genome sequence, and annotation. This is the first
AB  - complete genome sequence of the genus Rhodothermus, and only the second sequence
AB  - from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a
AB  - 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Nolan, M. et al.
TI  - Complete genome sequence of Streptosporangium roseum type strain (NI 9100).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 29
EP  - 37
VL  - 2
AB  - Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type
AB  - species of the genus Streptosporangium. The 'pinkish coiled
AB  - Streptomyces-like organism with a spore case' was isolated from vegetable garden
AB  - soil in 1955. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. This is the first completed genome
AB  - sequence of a member of the family Streptosporangiaceae, and the second largest
AB  - microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its
AB  - 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Nolan, M. et al.
TI  - Complete genome sequence of Streptobacillus moniliformis type strain (9901).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 300
EP  - 307
VL  - 1
AB  - Streptobacillus moniliformis Levaditi et al. 1925 is the type and sole species of the genus
AB  - Streptobacillus, and is of phylogenetic interest because of its
AB  - isolated location in the sparsely populated and neither taxonomically nor
AB  - genomically much accessed family 'Leptotrichiaceae' within the phylum
AB  - Fusobacteria. The 'Leptotrichiaceae' have not been well characterized,
AB  - genomically or taxonomically. S. moniliformis,is a Gram-negative, non-motile,
AB  - pleomorphic bacterium and is the etiologic agent of rat bite fever and Haverhill
AB  - fever. Strain 9901(T), the type strain of the species, was isolated from a
AB  - patient with rat bite fever. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is only the
AB  - second completed genome sequence of the order Fusobacteriales and no more than
AB  - the third sequence from the phylum Fusobacteria. The 1,662,578 bp long chromosome
AB  - and the 10,702 bp plasmid with a total of 1511 protein-coding and 55 RNA genes
AB  - are part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Nolan, M. et al.
TI  - Complete genome sequence of Ferrimonas balearica type strain (PAT).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 174
EP  - 182
VL  - 3
AB  - Ferrimonas balearica Rossello-Mora et al. 1996 is the type species of the genus Ferrimonas,
AB  - which belongs to the family Ferrimonadaceae within the
AB  - Gammaproteobacteria. The species is a Gram-negative, motile, facultatively
AB  - anaerobic, non spore-forming bacterium, which is of special interest because it
AB  - is a chemoorganotroph and has a strictly respiratory metabolism with oxygen,
AB  - nitrate, Fe(III)-oxyhydroxide, Fe(III)-citrate, MnO(2), selenate, selenite and
AB  - thiosulfate as electron acceptors. This is the first completed genome sequence of
AB  - a member of the genus Ferrimonas and also the first sequence from a member of the
AB  - family Ferrimonadaceae. The 4,279,159 bp long genome with its 3,803
AB  - protein-coding and 144 RNA genes is a part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Noll, L.W.
AU  - Worley, J.N.
AU  - Yang, X.
AU  - Shridhar, P.B.
AU  - Bai, J.
AU  - Meng, J.
AU  - Caragea, D.
AU  - Nagaraja, T.G.
TI  - Draft Genome Sequences of Enterohemorrhagic Escherichia coli O103:H2 Strains Isolated from Feces of Feedlot Cattle.
JO  - Genome Announcements
PY  - 2017
SP  - e00094
EP  - e00017
VL  - 5
AB  - The enterohemorrhagic pathotype represents a minor proportion of the Escherichia  coli O103
AB  - strains shed in the feces of cattle. We report here the genome
AB  - sequences of 43 strains of enterohemorrhagic E. coli (EHEC) O103:H2 isolated from
AB  - feedlot cattle feces. The genomic analysis will provide information on the
AB  - genetic diversity and virulence potential of bovine EHEC O103.
ER  -

TY  - JOUR
AU  - Noll, L.W.
AU  - Worley, J.N.
AU  - Yang, X.
AU  - Shridhar, P.B.
AU  - Bai, J.
AU  - Meng, J.
AU  - Caragea, D.
AU  - Nagaraja, T.G.
TI  - Draft Genome Sequences of Enteropathogenic Escherichia coli O103 Strains Isolated from Feces of Feedlot Cattle.
JO  - Genome Announcements
PY  - 2017
SP  - e00387
EP  - e00317
VL  - 5
AB  - Enteropathogenic Escherichia coli (EPEC) pathotype represents a minor proportion  of E. coli
AB  - O103 strains shed in the feces of feedlot cattle. The draft genome
AB  - sequences of 13 strains of EPEC O103 are reported here. The availability of the
AB  - genome sequences will help in the assessment of genetic diversity and virulence
AB  - potential of bovine EPEC O103.
ER  -

TY  - JOUR
AU  - Nolling, J. et al.
TI  - Genome sequencing and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum.
JO  - J. Bacteriol.
PY  - 2001
SP  - 4823
EP  - 4838
VL  - 183
AB  - The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has
AB  - been determined by the shotgun approach.  The genome consists of a 3.94-Mb chromosome and a
AB  - 192-kb megaplasmid that contains the majority of genes responsible for solvent production.
AB  - Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of
AB  - gene order, which has not been seen in comparisons of other genomes with similar, or, in some
AB  - cases closer, phylogenetic proximity.  This conservation allows the prediction of many
AB  - previously undetected operons in both bacteria.  However, the C. acetobutylicum genome also
AB  - contains a significant number of predicted operons that are shared with distantly related
AB  - bacteria and archaea but not with B. subtilis.  Phylogenetic analysis is compatible with the
AB  - dissemination of such operons by horizontal transfer.  The enzymes of the solventogenesis
AB  - pathway and of the cellulosome of C. acetobutylicum comprise a new set of metabolic capacities
AB  - not previously represented in the collection of complete genomes.  These enzymes show a
AB  - complex pattern of evolutionary affinities, emphasizing the role of lateral gene exchange in
AB  - the evolution of the unique metabolic profile of the bacterium.  Many of the sporulation genes
AB  - identified in B. subtilis are missing in C. acetobutylicum, which suggests major differences
AB  - in the sporulation process.  Thus, comparative analysis reveals both significant conservation
AB  - of the genome organization and pronounced differences in many systems that reflect unique
AB  - adaptive strategies of the two gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Nolling, J.
AU  - de Vos, W.M.
TI  - Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: Homology to the bacterial NgoPII system from Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1992
SP  - 5719
EP  - 5726
VL  - 174
AB  - A restriction-modification system, designated MthTI, was localized on plasmid pFV1 from the
AB  - thermophilic archaeon Methanobacterium thermoformicicum THF. The MthTI system is a new member
AB  - of the family of GGCC-recognizing restriction-modification systems. Functional expression of
AB  - the archaeal MthTI genes was obtained in Escherichia coli. The mthTIR and mthTIM genes are 843
AB  - and 990 bp in size and code for proteins of 281 (32,102 Da) and 330 (37,360 Da) amino acids,
AB  - respectively. The deduced amino acids sequences of M.MthTI showed high similarity with that of
AB  - the isospecific methyltransferases M.NgoPII and M.HaeIII. In addition, extensive sequence
AB  - similarity on the amino acid level was observed for the endonucleases R.MthTI and R.NgoPII.
AB  - Moreover, the endonuclease and methyltransferase genes of the thermophilic MthTI system and
AB  - those of Neisseria gonorrhoeae NgoPII system show identical organizations and high (54.5%)
AB  - nucleotide identity. This finding suggests horizontal transfer of restriction-modification
AB  - systems between members of the domains Bacteria and Archaea.
ER  -

TY  - JOUR
AU  - Nolling, J.
AU  - de Vos, W.M.
TI  - Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5047
EP  - 5052
VL  - 20
AB  - Two CTAG-recognizing restriction and modification (R/M) systems, designated MthZI and MthFI,
AB  - were identified in the thermophilic archaeon Methanobacterium thermoformicicum strains Z-245
AB  - and FTF, respectively. Further analysis revealed that the methyltransferase (MTase) genes are
AB  - plasmid-located in both strains. The plasmid pFZ1-encoded mthZIM gene of strain Z-245 was
AB  - further characterized by subcloning and expression studies in Escherichia coli followed by
AB  - nucleotide sequence analysis. The mthZIM gene is 1065 bp in size and may code for a protein of
AB  - 355 amino acids (Mr 42,476 Da). The deduced amino acid sequence of the M.MthZI enzyme shares
AB  - substantial similarity with four distinct regions from several m4C and m6A-MTases, and
AB  - contains the TSPPY motif that is so far only found in m4C-MTases. Partially overlapping with
AB  - the mthZIM gene and in reverse orientation, an additional ORF was identified with a size of
AB  - 606 bp potentially coding for a protein of 202 amino acids (mr 23.710 Da). This ORF is
AB  - suggested to encode the corresponding endonuclease R.MthZI.
ER  -

TY  - JOUR
AU  - Nolling, J.
AU  - Groffen, A.
AU  - De Vos, W.M.
TI  - PhiF1 and PhiF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium.
JO  - J. Gen. Microbiol.
PY  - 1993
SP  - 2511
EP  - 2516
VL  - 139
AB  - Two virulent archaeal phages, PhiF1 and PhiF3, were isolated that were capable of infecting
AB  - different thermophilic members of the genus Methanobacterium. Both phages exhibited a similar
AB  - morphology consisting of a polyhedral head and tail, but differed considerably in their host
AB  - specificities and the size and topology of their genomes. Phage PhiF1 contained a linear,
AB  - double-stranded DNA genome of 85+/-5 kb in size and showed a broad host range including M.
AB  - thermoformicicum strains Z-245, FTF FF1, FF3 and CSM3, and M. thermoautotrophicum strain H. In
AB  - contrast, PhiF3 phage particles contained a circular or terminally redundant linear genome,
AB  - comprising approximately 36+/-2 kb double-stranded DNA, and could only be propagated on M.
AB  - thermoformicicum strain FF3. Hybridization experiments did not reveal similarity between the
AB  - genomes of PhiF1 and PhiF3 nor between both phages and genomic DNA from different thermophilic
AB  - members of the genus Methanobacterium or DNA from phage M1 of M. thermoautotrophicum Marburg.
AB  - A physical map of both phage genomes was constructed. The DNA of phage phiF1 was found to
AB  - contain multiple GGCC sites which form the target for the restriction-modification (R/M)
AB  - system MthTI of M. thermoformicicum THF. In contrast, the DNA of PhiF1 contained only a single
AB  - CTAG site recognized by the R/M systems MthZI and MthFI of M. thermoformicicum Z-245 and FTF,
AB  - respectively. The distribution of these sites correlates well with the capacity of PhiF1 to
AB  - infect M. thermoformicicum strains Z-245 and FTF but not strain THF.
ER  -

TY  - JOUR
AU  - Nolling, J.
AU  - Van Eeden, J.M.
AU  - Eggen, R.I.L.
AU  - de Vos, W.M.
TI  - Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6501
EP  - 6507
VL  - 20
AB  - Nucleotide sequence comparison of the related 13513-bp plasmid pFV1 and the 11014-bp plasmid
AB  - pFZ1 from the thermophilic Archaeon Methanobacterium thermoformicicum THF and Z-245,
AB  - respectively, revealed a homologous, approximately 8.2 kb backbone structure that is
AB  - interrupted by plasmid-specific elements. Various highly conserved palindromic structures and
AB  - an ORF that could code for an NTP-binding protein were identified within the backbone
AB  - structure and may be involved in plasmid maintenance and replication. Each plasmid contains at
AB  - comparable locations a module which specifies components of different restriction-modificaton
AB  - (R/M) systems. The R/M module of pFV1 contained, in addition to the genes of the
AB  - GGCC-recognizing R/M system MthTI, an ORF which may be involved in repair of G-T mismatches
AB  - generated by deamination of m5C at high temperatures.
ER  -

TY  - JOUR
AU  - Nomura, N.
AU  - Morinaga, Y.
AU  - Shirai, N.
AU  - Sako, Y.
TI  - I-Apel: A novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 5017
EP  - 5017
VL  - 33
AB  - Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests
AB  - putative homing endonuclease (HEase) genes. Here, we report the identification and
AB  - characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeI, encoded by the ApeK1.S908
AB  - intron within the 16S rDNA of Aeropyrum pernix K1. I-ApeI consists of 222 amino acids and
AB  - harbors two LAGLIDADG-like sequences. It recognizes the 20 bp non-palindromic sequence
AB  - 5'-GCAAGGCTGAAAC TTAAAGG and cleaves target DNA to produce protruding tetranucleotide 3'
AB  - ends. Either Mn2+ or Co2+ can be substituted for Mg2+ as a cofactor in the cleavage reaction.
AB  - Of the 20 bases within the minimal recognition site, 7 are essential for cleavage and are
AB  - located at positions proximal to the cleavage sites.
ER  -

TY  - JOUR
AU  - Nomura, N.
AU  - Nomura, Y.
AU  - Sussman, D.
AU  - Klein, D.
AU  - Stoddard, B.L.
TI  - Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 6988
EP  - 6998
VL  - 36
AB  - The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers
AB  - the entire element with the ability to invade
AB  - genomic targets. The persistence of a homing endonuclease lineage
AB  - depends in part on conservation of its DNA target site. One such rDNA
AB  - sequence has been invaded both in archaea and in eukarya, by LAGLIDADG
AB  - and His-Cys box homing endonucleases, respectively. The bases encoded
AB  - by this target include a universally conserved ribosomal structure,
AB  - termed helix 69 (H69) in the large ribosomal subunit. This region forms
AB  - the 'B2a' intersubunit bridge to the small ribosomal subunit, contacts
AB  - bound tRNA in the A-and P-sites, and acts as a trigger for ribosome
AB  - disassembly through its interactions with ribosome recycling factor. We
AB  - have determined the DNA-bound structure and specificity profile of an
AB  - archaeal LAGLIDADG homing endonuclease (I-Vdi141I) that recognizes this
AB  - target site, and compared its specificity with the analogous eukaryal
AB  - His-Cys box endonuclease I-PpoI. These homodimeric endonuclease
AB  - scaffolds have arrived at similar specificity profiles across their
AB  - common biological target and analogous solutions to the problem of
AB  - accommodating conserved asymmetries within the DNA sequence, but with
AB  - differences at individual base pairs that are fine-tuned to the
AB  - sequence conservation of archaeal versus eukaryal ribosomes.
ER  -

TY  - JOUR
AU  - Nomura, W.
AU  - Barbas, C.F. III
TI  - In Vivo Site-Specific DNA Methylation with a Designed Sequence-Enabled DNA Methylase.
JO  - J. Am. Chem. Soc.
PY  - 2007
SP  - 8676
EP  - 8677
VL  - 129
AB  - As an alternative to the continual expression of transcriptional repressors to turn off genes
AB  - after they have served their purpose, nature has developed epigenetic strategies that result
AB  - in the covalent modification of DNA itself to induce heritable gene silencing.  Mounting
AB  - evidence supports the notion that once a genomic region has been targeted for silencing by
AB  - acquisition of one or more covalent epigenetic marks, mark can be propagated and may influence
AB  - acquisition of others.  If epigenetic modifications can be made specifically by the addition
AB  - of targeted exogenous agents, new approaches to transcriptional therapy should result.
ER  -

TY  - JOUR
AU  - Nomura, W.
AU  - Masuda, A.
AU  - Tamamura, H.
TI  - Development of site-specific DNA methylase for epigenetic regulation of gene expression.
JO  - Seikagaku
PY  - 2010
SP  - 393
EP  - 397
VL  - 82
ER  -

TY  - JOUR
AU  - Nomura, W.
AU  - Tamamura, H.
AU  - Barbas, C.F. III
TI  - Site-selective cytosine methylation by a split DNA methylase.
JO  - Pept. Sci.
PY  - 2009
SP  - 491
EP  - 492
VL  - 45
AB  - Cytosine methylation plays pivotal roles in gene expression.  Methylation pattern in genome is
AB  - heritable, then the effect of methylation is largely influenced across generation.  Truly
AB  - specific methylation has been a challenging problem because fusion methylases with zinc finger
AB  - domain still methylate the native sites as background.  To avoid this, split methylase domains
AB  - were constructed.  These domains were designed to assemble only on the zinc finger target site
AB  - with high specificity.  The split methylase showed it works as specific methylase to the
AB  - target sites.
ER  -

TY  - JOUR
AU  - Nomura, Y.
AU  - Ishino, Y.
AU  - Kimizuka, F.
AU  - Kato, I.
TI  - A novel Streptomyces restriction endonuclease, Sse1825I, cleaving at 5'-GG/GWCCC-3'.
JO  - Gene
PY  - 1995
SP  - 323
EP  - 324
VL  - 157
AB  - We isolated and characterized from a Streptomyces species a new class-II restriction
AB  - endonuclease, which recognizes the palindromic heptanucleotide sequence: 5'-GG/GWCCC
AB  - 3'-CCCWG/GG (where W=A or T) and cleaves double-stranded DNA after the second G in this
AB  - sequence.  This Sse1825I enzyme cleaves phage lambda DNA at one site, adenovirus type 2 DNA at
AB  - eight sites, but does not cleave pBR322, SV40, ColE1, pUC18 and pUC19, and replicative forms
AB  - of M13mp18 and M13mp19, and PhiX174 DNAs.
ER  -

TY  - JOUR
AU  - Nomura, Y.
AU  - Kotani, H.
AU  - Kita, K.
AU  - Sadaoka, A.
AU  - Hiraoka, N.
AU  - Nakamura, T.
AU  - Abe, N.
AU  - Izaki, K.
TI  - Purification and properties of a new restriction endonuclease, MxaI, from Myxococcus xanthus F18E.
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 3011
EP  - 3012
VL  - 54
AB  - Gliding bacteria have an unusual cell cycle, which consists of vegetative
AB  - growth, the formation of a swarm, and the development of fruiting bodies and
AB  - microcysts.  Only one restriction endonuclease of these bacteria has been
AB  - reported.  Here, we screened 103 strains of Myxococcus species isolated from
AB  - soil and detected endonuclease activity in nine strains.  One strain,
AB  - Myxococcus xanthus F18E, produced a restriction endonuclease, MxaI, that is a
AB  - new isoschizomer of SacI.  We identified the recognition and cleavage sites of
AB  - MxaI and compared the properties of this enzyme with those of SacI.
ER  -

TY  - JOUR
AU  - Nonaka, H.
AU  - Keresztes, G.
AU  - Shinoda, Y.
AU  - Ikenaga, Y.
AU  - Abe, M.
AU  - Naito, K.
AU  - Inatomi, K.F.K.
AU  - Inui, M.
AU  - Yukawa, H.
TI  - Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195 - bacterium genomic comparison and genome sequencing for use in bioremediation.
JO  - J. Bacteriol.
PY  - 2006
SP  - 2262
EP  - 2274
VL  - 188
AB  - AUTHOR ABSTRACT - Desulfitobacterium strains have the ability to dechlorinate halogenated
AB  - compounds under anaerobic conditions by
AB  - dehalorespiration. The complete genome of the tetrachloroethene
AB  - (PCE)-dechlorinating strain Desulfitobacterium hafniense Y51 is a
AB  - 5,727,534-bp circular chromosome harboring 5,060 predicted protein
AB  - coding sequences. This genome contains only two reductive dehalogenase
AB  - genes, a lower number than reported in most other dehalorespiring
AB  - strains. More than 50 members of the dimethyl sulfoxide reductase
AB  - superfamily and 30 paralogs of the flavoprotein subunit of the fumarate
AB  - reductase are encoded as well. A remarkable feature of the genome is
AB  - the large number of O-demethylase paralogs, which allow utilization of
AB  - lignin-derived phenyl methyl ethers as electron donors. The large
AB  - genome reveals a more versatile microorganism that can utilize a larger
AB  - set of specialized electron donors and acceptors than previously
AB  - thought. This is in sharp contrast to the PCE-dechlorinating strain
AB  - Dehalococcoides ethenogenes 195, which has a relatively small genome
AB  - with a narrow metabolic repertoire. A genomic comparison of these two
AB  - very different strains allowed us to narrow down the potential
AB  - candidates implicated in the dechlorination process. Our results
AB  - provide further impetus to the use of desulfitobacteria as tools for
AB  - bioremediation.
ER  -

TY  - JOUR
AU  - Noom, M.C.
AU  - van den Broek, B.
AU  - Wuite, G.J.L.
TI  - Direct observation of the searching mechanism of restriction enzymes using multiple optical traps.
JO  - Biophys. J.
PY  - 2003
SP  - 304a
EP  - 304a
VL  - 84
AB  - Restriction enzymes recognize specific sequences in dsDNA.  Once they find their target
AB  - sequence, they cut the DNA at that site.  This cutting is evolved in bacteria to protect
AB  - itself against foreign DNA.  The searching mechanism for finding the target sequence is
AB  - important, because the number of non-specific sites is usually larger than the number of
AB  - specific sites.  Therefore, it's unlikely that the initial encounter of the enzyme with the
AB  - DNA will be at the target sequence.  To visualize the possible sliding, hopping and jumping of
AB  - a restriction enzyme during the searching process, the translocation of EcoRI enzymes is
AB  - analyzed using a three-bead-assay created with multiple optical traps.  In this assay
AB  - biotinylated EcoRI enzymes are bound to streptavidin-coated beads.  Such coated beads are
AB  - offered to a DNA molecule held between two beads kept in optical tweezers.  Movement of a
AB  - coated bead is tracked with video microscopy and the forces exerted by the enzyme on the DNA
AB  - are measured using the traps.  Here we report our first results on the movement by EcoRI
AB  - during the searching process for the target sequence.  Such direct observation of restriction
AB  - enzymes during the searching for and recognition of the target sequence provides us with new
AB  - insights into the dynamics of these enzyme-DNA interactions.
ER  -

TY  - JOUR
AU  - Noor, Y.M.
AU  - Samsulrizal, N.H.
AU  - Jema'on, N.A.
AU  - Low, K.O.
AU  - Ramli, A.N.
AU  - Alias, N.I.
AU  - Damis, S.I.
AU  - Fuzi, S.F.
AU  - Isa, M.N.
AU  - Murad, A.M.
AU  - Raih, M.F.
AU  - Bakar, F.D.
AU  - Najimudin, N.
AU  - Mahadi, N.M.
AU  - Illias, R.M.
TI  - A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1.
JO  - Gene
PY  - 2014
SP  - 253
EP  - 261
VL  - 545
AB  - Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium
AB  - isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase
AB  - (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in
AB  - foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1
AB  - consists of a single circular 3.99Mb chromosome containing 4017 protein-coding
AB  - sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936
AB  - (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no
AB  - match with any protein database. Bacillus clausii KSM-K16 was established as the
AB  - closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA
AB  - phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to
AB  - have orthologues in B. clausii, including sodium-proton antiporters, transport
AB  - proteins, and proteins involved in ATP synthesis. A comparative analysis of these
AB  - proteins and those in B. clausii and other alkaliphilic Bacillus species was
AB  - carried out to investigate their contributions towards the alkalitolerance of the
AB  - microorganism. The similarities and differences in alkalitolerance-related genes
AB  - among alkalitolerant/alkaliphilic Bacillus species highlight the complex
AB  - mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for
AB  - proteins and enzymes with potential viability for industrial and commercial
AB  - purposes.
ER  -

TY  - JOUR
AU  - Noorian, P.
AU  - Sun, S.
AU  - McDougald, D.
TI  - Complete Genome Sequence of Oyster Isolate Vibrio vulnificus Env1.
JO  - Genome Announcements
PY  - 2018
SP  - e00421
EP  - e00418
VL  - 6
AB  - Vibrio vulnificus, a ubiquitous inhabitant of coastal marine environments, has been isolated
AB  - from a variety of sources. It is an opportunistic pathogen of both
AB  - marine animals and humans. Here, the genome sequence of V. vulnificus Env1, an
AB  - environmental isolate resistant to predation by the ciliate Tetrahymena
AB  - pyriformis, is reported.
ER  -

TY  - JOUR
AU  - Nord, D.
AU  - Sjoberg, B.M.
TI  - Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 300
EP  - 310
VL  - 36
AB  - Several group I introns have been previously found in strains of the Bacillus cereus group at
AB  - three different insertion sites in the nrdE gene
AB  - of the essential nrdIEF operon coding for ribonucleotide reductase. Here,
AB  - we identify an uncharacterized group IA intron in the nrdF gene in 12
AB  - strains of the B. cereus group and show that the pre-mRNA is efficiently
AB  - spliced. The Bacillus thuringiensis ssp. pakistani nrdF intron encodes a
AB  - homing endonuclease, denoted I-BthII, with an unconventional GIY-(X)8-YIG
AB  - motif that cleaves an intronless nrdF gene 7 nt upstream of the intron
AB  - insertion site, producing 2-nt 3' extensions. We also found four
AB  - additional occurrences of two of the previously reported group I introns
AB  - in the nrdE gene of 25 sequenced B. thuringiensis and one B. cereus
AB  - strains, and one non-annotated group I intron at a fourth nrdE insertion
AB  - site in the B. thuringiensis ssp. Al Hakam sequenced genome. Two strains
AB  - contain introns in both the nrdE and the nrdF genes. Phylogenetic studies
AB  - of the nrdIEF operon from 39 strains of the B. cereus group suggest
AB  - several events of horizontal gene transfer for two of the introns found in
AB  - this operon.
ER  -

TY  - JOUR
AU  - Nord, D.
AU  - Torrents, E.
AU  - Sjoberg, B.M.
TI  - A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron.
JO  - J. Bacteriol.
PY  - 2007
SP  - 5293
EP  - 5301
VL  - 189
AB  - The essential Bacillus anthracis nrdE gene carries a self-splicing group I intron with a
AB  - putative homing endonuclease belonging to the GIY-YIG
AB  - family. Here, we show that the nrdE pre-mRNA is spliced and that the
AB  - homing endonuclease cleaves an intronless nrdE gene 5 nucleotides (nt)
AB  - upstream of the intron insertion site, producing 2-nt 3' extensions. We
AB  - also show that the sequence required for efficient cleavage spans at least
AB  - 4 bp upstream and 31 bp downstream of the cleaved coding strand. The
AB  - position of the recognition sequence in relation to the cleavage position
AB  - is as expected for a GIY-YIG homing endonuclease. Interestingly, nrdE
AB  - genes from several other Bacillaceae were also susceptible to cleavage,
AB  - with those of Bacillus cereus, Staphylococcus epidermidis (nrdE1), B.
AB  - anthracis, and Bacillus thuringiensis serovar konkukian being better
AB  - substrates than those of Bacillus subtilis, Bacillus lichenformis, and S.
AB  - epidermidis (nrdE2). On the other hand, nrdE genes from Lactococcus
AB  - lactis, Escherichia coli, Salmonella enterica serovar Typhimurium, and
AB  - Corynebacterium ammoniagenes were not cleaved. Intervening sequences
AB  - (IVSs) residing in protein-coding genes are often found in enzymes
AB  - involved in DNA metabolism, and the ribonucleotide reductase nrdE gene is
AB  - a frequent target for self-splicing IVSs. A comparison of nrdE genes from
AB  - seven gram-positive low-G+C bacteria, two bacteriophages, and Nocardia
AB  - farcinica showed five different insertion sites for self-splicing IVSs
AB  - within the coding region of the nrdE gene.
ER  -

TY  - JOUR
AU  - Nordlund, T.M.
AU  - Andersson, S.
AU  - Nilsson, L.
AU  - Rigler, R.
TI  - Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies.
JO  - Biochemistry
PY  - 1989
SP  - 9095
EP  - 9103
VL  - 28
AB  - The self-complementary DNA decamer duplex d(CTGAATTCAG)2 and its modified counterpart
AB  - d(CTGA[2AP]TTCAG)2, where the innermost adenine (6-aminopurine) has been replaced with the
AB  - fluorescent analogue 2-aminopurine (2AP), have been studied by fluorescence and NMR
AB  - spectroscopy and simulated by molecular dynamics.  Both decamers are recognized and cleaved by
AB  - the EcoRI restriction endonuclease.  2D NMR results show that both decamers have a standard
AB  - B-type conformation below 20oC, though a disturbance exists to the 5' side of the 2AP site
AB  - which may originate from increased local mobility.  The fluorescence and fluorescence
AB  - anisotropy decays of both decamers, as well as the one containing 2AP in only one chain, were
AB  - studied as a function of temperature.  The data show that the 2AP base exists in a
AB  - temperature-dependent distribution of states and shows rapid motions, suggesting
AB  - interconversion among these states on a time scale of about 10^-10s.  The integrated
AB  - fluorescence of the decamer with 2AP in both chains shows a large increase around the helix
AB  - melting temperature whereas the decamer with one 2AP shows only a mild increase, showing that
AB  - the mixed helix has a different structural transition as sensed by the 2AP base.  The data
AB  - suggest a model of conformational states which have distinct fluorescence decay times.  The
AB  - various states may differ in the degree of base stacking.  Fluctuations in the degree of
AB  - stacking of the A or 2AP base are supported by molecular dynamics simulations, which
AB  - additionally show that the 2AP-T or A-T base pair hydrogen bonds remain intact during these
AB  - large motions.
ER  -

TY  - JOUR
AU  - Norlander, L.
AU  - Davies, J.K.
AU  - Hagblom, P.
AU  - Normark, S.
TI  - Deoxyribonucleic acid modifications and restriction endonuclease production in Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1981
SP  - 788
EP  - 795
VL  - 145
AB  - Modification of gonococcal deoxyribonucleic acid (DNA) was investigated, and the relationship
AB  - with endonuclease production was explored.  Both chromosomal and plasmid DNA from different
AB  - gonococcal strains, irrespective of their plasmid content, was poorly cleaved by the
AB  - restriction endonucleases HaeII, HaeIII, SacII, and BamHI.  The fragment pattern of the Tn3
AB  - segment present on the 7.2-kilobase gonococcal resistance plasmid, when compared to its known
AB  - DNA sequence, allowed us to conclude that the HaeIII and BamHI resistance was due to
AB  - modification of these sites.  A comparison of the fragment pattern of the resistance plasmid,
AB  - when isolated from Escherichia coli or Neisseria gonorrhoeae, revealed that the resistance of
AB  - HaeII must also be due to modification of its recognition sequence.  Isoschizomers of HaeII
AB  - and HaeIII can be found in isolates of N. gonorrhoeae (NgoI and NgoII, respectively).  A new
AB  - restriction endonuclease in gonococci, NgoIII, with a specificity similar to SacII, is
AB  - reported here.  High-pressure liquid chromatography of gonococcal DNA showed the presence of
AB  - 5-methylcytosine.  It is suggested that the methylation of cytosine residues in the HaeII
AB  - (NgoI), HaeIII (NgoII), and SacII (NgoIII) recognition sites is the basis for the resistance
AB  - of gonococcal DNA to cleavage by these enzymes.  This methylation may be part of a
AB  - host-restriction modification system.  In two out of five gonococcal strains the sequence
AB  - -GATC- was modified.  One strain unable to modify this sequence was a spontaneous mutant of a
AB  - strain carrying such a modifying function. [ The enzyme called NgoI in this abstract has been
AB  - renamed NgoHI, Jan/1998. ] [ The enzyme called NgoII in this abstract has been renamed NgoHII,
AB  - Jan/1998. ] [ The enzyme called NgoIII in this abstract has been renamed NgoKIII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Norman, A.
AU  - Ciofu, O.
AU  - Amador, C.I.
AU  - Hoiby, N.
AU  - Jelsbak, L.
TI  - Genome Sequence of Pseudomonas aeruginosa Strain DK1-NH57388A, a Stable Mucoid Cystic Fibrosis Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00008
EP  - e00016
VL  - 4
AB  - Pseudomonas aeruginosa is an important opportunistic pathogen associated with chronic
AB  - pulmonary infections and mortality in cystic fibrosis (CF) patients.
AB  - Here, we present the complete genome sequence of stable mucoid P. aeruginosa
AB  - strain DK1-NH57388A, a CF isolate which has previously been used to establish
AB  - chronic lung infections in an animal model.
ER  -

TY  - JOUR
AU  - Normand, P.
AU  - Gury, J.
AU  - Pujic, P.
AU  - Chouaia, B.
AU  - Crotti, E.
AU  - Brusetti, L.
AU  - Daffonchio, D.
AU  - Vacherie, B.
AU  - Barbe, V.
AU  - Medigue, C.
AU  - Calteau, A.
AU  - Ghodhbane-Gtari, F.
AU  - Essoussi, I.
AU  - Nouioui, I.
AU  - Abbassi-Ghozzi, I.
AU  - Gtari, M.
TI  - Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4773
EP  - 4774
VL  - 194
AB  - Here we report the full genome sequence of Modestobacter marinus strain BC501, an
AB  - actinobacterial isolate that thrives on stone surfaces. The generated chromosome
AB  - is circular, with a length of 5.57 Mb and a G+C content of 74.13%, containing
AB  - 5,445 protein-coding genes, 48 tRNAs, and 3 ribosomal operons.
ER  -

TY  - JOUR
AU  - Norton Hughes, C.A.
AU  - Johnson, R.C.
TI  - Identification of a DNA methylase gene homologue in Borrelia burgdorferi.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 125
EP  - 125
VL  - 94
AB  - DNA methylation may play an important role in DNA mismatch repair, DNA replication and
AB  - recombination, and gene expression. DNA methylases are enzymes that transfer methyl groups
AB  - from donor S-adenosylmethionine to the adenine or cytosine residues within a recognizable DNA
AB  - sequence, thereby preventing digestion at the site and protecting host DNA. The dcm gene
AB  - product of Escherichia coli methylates the C5 position (m5C) of the internal cytosine in the
AB  - sequence CC(A/T)GG. Cytosine (dcm) methylation is prevalent in Borrelia burgdorferi. In this
AB  - study, we examine the B. burgdorferi, 297 genome for the presence of the dcm gene homologue.
AB  - 
AB  - An oligonucleotide (21 nucleotides) was synthesized to target a consensus sequence for the
AB  - prokaryotic cytosine methyltransferases. The oligonucleotide was labeled at the 3' end by the
AB  - addition of digoxigenin-11-ddUTP using terminal transferase. The labeled oligonucleotide was
AB  - used to probe genome B. burgdorferi, 297 DNA. The probe hybridized strongly to chromosomal DNA
AB  - in addition to the ospA/ospB plasmid and a 28.4-kb plasmid. These results suggest that a dcm
AB  - homologue is present in B. burgdorferi.
AB  - 
ER  -

TY  - JOUR
AU  - Nosikov, V.V.
AU  - Braga, E.A.
AU  - Karlishev, A.V.
AU  - Zhuze, A.L.
AU  - Polyanovsky, O.L.
TI  - Protection of particular cleavage sites of restriction endonucleases by distamycin A and actinomycin D.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 2293
EP  - 2301
VL  - 3
AB  - It is shown here that distamycin A and actinomycin D can protect the
AB  - recognition sites of endo R.EcoRI, EcoRII, HindII, HindIII, HpaI and HpaII from
AB  - the attack of these restriction endonucleases.  At proper distamycin
AB  - concentrations only two endo R.EcoRI sites of phage lambda DNA are available
AB  - for the restriction enzyme - sRI1 and sRI4.  This phenomenon results in the
AB  - appearance of large DNA fragments comprising several consecutive fragments of
AB  - endo R.EcoRI complete cleavage.  The distamycin fragments isolated from the
AB  - agarose gels can be subsequently cleaved by endo R.EcoRI with the yield of the
AB  - fragments of complete digestion.  We have compared the effect of distamycin A
AB  - and actinomycin D on a number of restriction endonucleases having different
AB  - nucleotide sequences in the recogniton sites and established that antibiotic
AB  - action depends on the nucleotide sequences of the recognition sites and their
AB  - closest environment.
ER  -

TY  - JOUR
AU  - Nosikov, V.V.
AU  - Sain, B.
TI  - Protection of particular endonuclease R.HindIII cleavage sites by distamycin A, propyl-distamycin and netropsin.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 2263
EP  - 2273
VL  - 4
AB  - It is shown that three related antibiotics, distamycin A, propyl-distamycin and netropsin, can
AB  - protect certain endo R.HindIII cleavage sites from attack by endonuclease, giving rise, after
AB  - endo R.HindIII digestion, to larger DNA fragments.  Bacteriophage lambda DNA has six
AB  - recognition sites for HindIII enzyme.  Three of these sites: shindIII 2, 3 and 6 can be
AB  - protected from nuclease action by all the antibiotics used.  Propyl-distamycin protects partly
AB  - shindIII 5, too.  Netropsin protects partly sites shindIII5 and 4, while distamycin A protects
AB  - all the sites but shindIII 1 so the HindII digestion produces only two large fragments of
AB  - lambda DNA.
ER  -

TY  - JOUR
AU  - Notani, N.K.
AU  - Setlow, J.K.
TI  - Molecular events accompanying the fixation of genetic information in Haemophilus heterospecific transformation.
JO  - J. Bacteriol.
PY  - 1972
SP  - 751
EP  - 760
VL  - 112
AB  - Heterospecific transformation between Haemophilus influenzae and H.
AB  - parainfluenzae was investigated by isopycnic analysis of deoxyribonucleic acid
AB  - (DNA) extracts of 3H-labeled transforming cells that had been exposed to
AB  - 32P-labeled, heavy transforming DNA.  The density distribution of genetic
AB  - markers from the resident DNA and from the donor DNA was determined by
AB  - transformation assay of fractions from CsCl gradients, both species being used
AB  - as recipients.  About 50% of the 32P atoms in H. parainfluenzae donor DNA taken
AB  - up by H. influenzae cells were transferred to resident DNA, and only a small
AB  - amount of the label was lost under conditions of little cell growth.  There was
AB  - less transfer in the reciprocal cross, and almost half of the donor label was
AB  - lost.  In both crosses,the transferred donor material transformed for the donor
AB  - marker considerably more efficiently when assayed on the donor species than on
AB  - the recipient species, indicating that at least some of the associated 32P
AB  - atoms are contained in relatively long stretches of donor DNA.  When the
AB  - transformed cultures were incubated under growth conditions, the donor marker
AB  - associated with recipient DNA transformed the donor species with progressively
AB  - decreasing efficiency.  The data indicate that the low heterospecific
AB  - transformation between H. influenzae and H. parainfluenzae  may be due partly
AB  - to events occurring before association of donor and resident DNA but results
AB  - mostly from events that occur after the association of the two DNA
AB  - preparations.
ER  -

TY  - JOUR
AU  - Noto, J.M.
AU  - Chopra, A.
AU  - Loh, J.T.
AU  - Romero-Gallo, J.
AU  - Piazuelo, M.B.
AU  - Watson, M.
AU  - Leary, S.
AU  - Beckett, A.C.
AU  - Wilson, K.T.
AU  - Cover, T.L.
AU  - Mallal, S.
AU  - Israel, D.A.
AU  - Peek, R.M.
TI  - Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments.
JO  - Gut
PY  - 2017
SP  - 1793
EP  - 1804
VL  - 67
AB  - OBJECTIVE: Helicobacter pylori is the strongest risk factor for gastric cancer;
AB  - however, the majority of infected individuals do not develop disease.
AB  - Pathological outcomes are mediated by complex interactions among bacterial, host
AB  - and environmental constituents, and two dietary factors linked with gastric
AB  - cancer risk are iron deficiency and high salt. We hypothesised that prolonged
AB  - adaptation of H. pylori to in vivo carcinogenic microenvironments results in
AB  - genetic modification important for disease. DESIGN: Whole genome sequencing of
AB  - genetically related H. pylori strains that differ in virulence and targeted H.
AB  - pylori sequencing following prolonged exposure of bacteria to in vitro
AB  - carcinogenic conditions were performed. RESULTS: A total of 180 unique single
AB  - nucleotide polymorphisms (SNPs) were identified among the collective genomes when
AB  - compared with a reference H. pylori genome. Importantly, common SNPs were
AB  - identified in isolates harvested from iron-depleted and high salt carcinogenic
AB  - microenvironments, including an SNP within fur (FurR88H). To investigate the
AB  - direct role of low iron and/or high salt, H. pylori was continuously cultured in
AB  - vitro under low iron or high salt conditions to assess fur genetic variation.
AB  - Exposure to low iron or high salt selected for the FurR88H variant after only 5
AB  - days. To extend these results, fur was sequenced in 339 clinical H. pylori
AB  - strains. Among the isolates examined, 17% (40/232) of strains isolated from
AB  - patients with premalignant lesions harboured the FurR88H variant, compared with
AB  - only 6% (6/107) of strains from patients with non-atrophic gastritis alone
AB  - (p=0.0034). CONCLUSION: These results indicate that specific genetic variation
AB  - arises within H. pylori strains during in vivo adaptation to conditions conducive
AB  - for gastric carcinogenesis.
ER  -

TY  - JOUR
AU  - Noto, M.J.
AU  - Kreiswirth, B.N.
AU  - Monk, A.B.
AU  - Archer, G.L.
TI  - Gene acquisition at the insertion site for SCCmec, the genomic island conferring methicillin resistance in Staphylococcus aureus.
JO  - J. Bacteriol.
PY  - 2008
SP  - 1276
EP  - 1283
VL  - 190
AB  - Staphylococcus aureus becomes resistant to methicillin by acquiring a
AB  - genomic island, known as staphylococcal chromosome cassette mec (SCCmec),
AB  - which contains the methicillin resistance determinant, mecA. SCCmec is
AB  - site-specifically integrated into the staphylococcal chromosome at a locus
AB  - known as the SCCmec attachment site (attB). In an effort to gain a better
AB  - understanding of the potential that methicillin-sensitive S. aureus (MSSA)
AB  - isolates have for acquiring SCCmec, the nucleotide sequences of attB and
AB  - surrounding DNA regions were examined in a diverse collection of 42 MSSA
AB  - isolates. The chromosomal region surrounding attB varied among the
AB  - isolates studied and appears to be a common insertion point for acquired
AB  - foreign DNA. Insertions of up to 15.1 kb were found containing open
AB  - reading frames with homology to enterotoxin genes,
AB  - restriction-modification systems, transposases, and several sequences that
AB  - have not been previously described in staphylococci. Two groups,
AB  - containing eight and four isolates, had sequences found in known SCCmec
AB  - elements, suggesting SCCmec elements may have evolved through repeated DNA
AB  - insertions at this locus. In addition, the attB sequences of the majority
AB  - of MSSA isolates in this collection differ from the attB sequences of
AB  - strains for which integrase-mediated SCCmec insertion or excision has been
AB  - demonstrated, suggesting that some S. aureus isolates may lack the ability
AB  - to site-specifically integrate SCCmec into their chromosomes.
ER  -

TY  - JOUR
AU  - Nou, X.
AU  - Skinner, B.
AU  - Braaten, B.
AU  - Blyn, L.
AU  - Hirsch, D.
AU  - Low, D.
TI  - Regulation of pyelonephritis-associated pili phase-variation in Excherichia coli: binding of the PapI and the Lrp regulatory proteins is controlled by DNA methylation.
JO  - Mol. Microbiol.
PY  - 1993
SP  - 545
EP  - 553
VL  - 7
AB  - Expression of pyelonephritis-associated pili (Pap) in Escherichia coli is under a
AB  - phase-variation control mechanism in which individual cells alternate between pili+ (ON) and
AB  - pili- (OFF) states through a process involving DNA methylation by deoxyadenosine methylase
AB  - (Dam). Methylation of two GATC sites (GATC1028 and GATC1130) within the pap regulatory region
AB  - is differentially inhibited in phase ON and phase OFF cells. The GATC1028 site of phase ON
AB  - cells is non-methylated and the GATC1130 site is fully methylated. Conversely, in phase OFF
AB  - cells the GATC1028 site is fully methylated whereas the GATC1130 site is non-methylated. Two
AB  - transcriptional activators, PapI and Lrp (leucine-responsive regulatory protein), are required
AB  - for this specific methylation inhibition. DNA footprint analysis using non-methylated pap DNAs
AB  - indicates that Lrp binds to a region surrounding the GATC1130 site, whereas PapI does not
AB  - appear to bind to pap regulatory DNA. However, addition of Lrp and PapI together results in an
AB  - additional DNaseI footprint around the GATC1028 site. Moreover, Dam methylation inhibits
AB  - binding of Lrp/PapI near the GATC1028 site and alters binding of Lrp at the GATC1130 site. Our
AB  - results support a model in which Dam and Lrp/PapI compete for binding near the GATC1028 site,
AB  - regulating the methylation state of this GATC site and consequently, the pap transcription
AB  - state.
ER  -

TY  - JOUR
AU  - Nouioui, I. et al.
TI  - Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils.
JO  - Genome Announcements
PY  - 2013
SP  - e00468
EP  - e00413
VL  - 1
AB  - Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different
AB  - families of actinorhizal plants. We report a draft genome sequence for
AB  - Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from
AB  - Tunisian soils with the ability to infect Elaeagnus angustifolia and Myrica gale.
ER  -

TY  - JOUR
AU  - Nouioui, I.
AU  - Goker, M.
AU  - Carro, L.
AU  - Montero-Calasanz, M.D.
AU  - Rohde, M.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Klenk, H.P.
TI  - High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 4
EP  - 4
VL  - 12
AB  - Nakamurella lactea DLS-10T, isolated from rock in Korea, is one of the four type  strains of
AB  - the genus Nakamurella. In this study, we describe the high quality
AB  - draft genome of N. lactea DLS-10T and its annotation. A summary of phenotypic
AB  - data collected from previously published studies was also included. The genome of
AB  - strain DLS-10T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C +
AB  - G content of 68.9%. Based on the genome analysis, emended description of N.
AB  - lactea in terms of G + C content was also proposed.
ER  -

TY  - JOUR
AU  - Nouioui, I.
AU  - Gtari, M.
AU  - Goker, M.
AU  - Ghodhbane-Gtari, F.
AU  - Tisa, L.S.
AU  - Fernandez, M.P.
AU  - Normand, P.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Varghese, N.
AU  - Reddy, T.B.
AU  - Ivanova, N.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Klenk, H.P.
TI  - Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of  the Order Rhamnales.
JO  - Genome Announcements
PY  - 2016
SP  - e00437
EP  - e00416
VL  - 4
AB  - Frankia sp. strain G2 was originally isolated from Casuarina equisetifolia and is
AB  - characterized by its ability to nodulate actinorhizal plants of the Rhamnales
AB  - order, but not its original host. It represents one of the largest Frankia
AB  - genomes so far sequenced (9.5 Mbp).
ER  -

TY  - JOUR
AU  - Novakova, E.
AU  - Hypsa, V.
AU  - Nguyen, P.
AU  - Husnik, F.
AU  - Darby, A.C.
TI  - Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 72
EP  - 72
VL  - 11
AB  - Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate
AB  - intracellular symbiont of the blood feeding deer ked, Lipoptena cervi
AB  - (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from
AB  - host gut epithelia (bacteriocytes) forming a compact symbiotic organ
AB  - (bacteriome). Compared to the closely related complex symbiotic system in the
AB  - sheep ked, involving four bacterial species, Lipoptena cervi appears to maintain
AB  - its symbiosis exclusively with Ca. Arsenophonus lipopteni. The genome of 836,724
AB  - bp and 24.8 % GC content codes for 667 predicted functional genes and bears the
AB  - common characteristics of sequence economization coupled with obligate
AB  - host-dependent lifestyle, e.g. reduced number of RNA genes along with the rRNA
AB  - operon split, and strongly reduced metabolic capacity. Particularly, biosynthetic
AB  - capacity for B vitamins possibly supplementing the host diet is highly
AB  - compromised in Ca. Arsenophonus lipopteni. The gene sets are complete only for
AB  - riboflavin (B2), pyridoxine (B6) and biotin (B7) implying the content of some B
AB  - vitamins, e.g. thiamin, in the deer blood might be sufficient for the insect
AB  - metabolic needs. The phylogenetic position within the spectrum of known
AB  - Arsenophonus genomes and fundamental genomic features of Ca. Arsenophonus
AB  - lipopteni indicate the obligate character of this symbiosis and its independent
AB  - origin within Hippoboscidae.
ER  -

TY  - JOUR
AU  - Novikov, A.D.
AU  - Lavrov, K.V.
AU  - Kasianov, A.S.
AU  - Gerasimova, T.V.
AU  - Yanenko, A.S.
TI  - Draft Genome Sequence of Rhodococcus sp. Strain M8, Which Can Degrade a Broad Range of Nitriles.
JO  - Genome Announcements
PY  - 2018
SP  - e01526
EP  - e01517
VL  - 6
AB  - Rhodococcus sp. strain M8 is a nitrile-degrading bacterium isolated from
AB  - acrylonitrile-contaminated sites. This strain produces the enzymes for sequential
AB  - nitrile degradation, cobalt-type nitrile hydratase, and amidase in large amounts.
AB  - Its draft genome sequence, announced here, has an estimated size of 6.3 Mbp.
ER  -

TY  - JOUR
AU  - Novinscak, A.
AU  - Gadkar, V.J.
AU  - Joly, D.L.
AU  - Filion, M.
TI  - Complete Genome Sequence of Pseudomonas brassicacearum LBUM300, a Disease-Suppressive Bacterium with Antagonistic Activity toward Fungal, Oomycete,  and Bacterial Plant Pathogens.
JO  - Genome Announcements
PY  - 2016
SP  - e01623
EP  - e01615
VL  - 4
AB  - Pseudomonas brassicacearum LBUM300, a plant rhizosphere-inhabiting bacterium, produces
AB  - 2,4-diacetylphloroglucinol and hydrogen cyanide and has shown
AB  - antagonistic activity against the plant pathogens Verticillium dahliae,
AB  - Phytophthora cactorum, and Clavibacter michiganensis subsp. michiganensis. Here,
AB  - we report the complete genome sequence of P. brassicacearum LBUM300.
ER  -

TY  - JOUR
AU  - Nowak, A.
AU  - Kur, J.
AU  - Gospodarek, E.
AU  - Bielawski, K.
TI  - Characterization of restriction endonuclease AjoI from Acinetobacter johnsonii.
JO  - FEMS Microbiol. Lett.
PY  - 1994
SP  - 97
EP  - 102
VL  - 117
AB  - A new type II restriction endonuclease, named AjoI, was detected in Acinetobacter johnsonii.
AB  - The enzyme AjoI, an isoschizomer of PstI, recognized the hexanucleotide sequence
AB  - [5'-CTGCA/G-3'], with a cleavage site generating fragments of DNA with protruding cohesive
AB  - 3' termini.
ER  -

TY  - JOUR
AU  - Nowrousian, M.
AU  - Stajich, J.E.
AU  - Chu, M.
AU  - Engh, I.
AU  - Espagne, E.
AU  - Halliday, K.
AU  - Kamerewerd, J.
AU  - Kempken, F.
AU  - Knab, B.
AU  - Kuo, H.C.
AU  - Osiewacz, H.D.
AU  - Poggeler, S.
AU  - Read, N.D.
AU  - Seiler, S.
AU  - Smith, K.M.
AU  - Zickler, D.
AU  - Kuck, U.
AU  - Freitag, M.
TI  - De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
JO  - PLoS Genet.
PY  - 2010
SP  - E1000891
EP  - E1000891
VL  - 6
AB  - Filamentous fungi are of great importance in ecology, agriculture, medicine, and
AB  - biotechnology. Thus, it is not surprising that genomes for more than 100
AB  - filamentous fungi have been sequenced, most of them by Sanger sequencing. While
AB  - next-generation sequencing techniques have revolutionized genome resequencing,
AB  - e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses,
AB  - de novo assembly of eukaryotic genomes still presents significant hurdles,
AB  - because of their large size and stretches of repetitive sequences. Filamentous
AB  - fungi contain few repetitive regions in their 30-90 Mb genomes and thus are
AB  - suitable candidates to test de novo genome assembly from short sequence reads.
AB  - Here, we present a high-quality draft sequence of the Sordaria macrospora genome
AB  - that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing.
AB  - Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional
AB  - 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of
AB  - DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with
AB  - the Velvet assembler. Comparative analysis with Neurospora genomes increased the
AB  - N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than
AB  - its closest sequenced relative, Neurospora crassa. Comparison with genomes of
AB  - other fungi showed that S. macrospora, a model organism for morphogenesis and
AB  - meiosis, harbors duplications of several genes involved in
AB  - self/nonself-recognition. Furthermore, S. macrospora contains more polyketide
AB  - biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of
AB  - these genes may have been acquired by horizontal gene transfer from a distantly
AB  - related ascomycete group. Our study shows that, for typical filamentous fungi, de
AB  - novo assembly of genomes from short sequence reads alone is feasible, that a
AB  - mixture of Solexa and 454 sequencing substantially improves the assembly, and
AB  - that the resulting data can be used for comparative studies to address basic
AB  - questions of fungal biology.
ER  -

TY  - JOUR
AU  - Noy-Malka, C.
AU  - Yaari, R.
AU  - Itzhaki, R.
AU  - Mosquna, A.
AU  - Gershovitz, N.A.
AU  - Katz, A.
AU  - Ohad, N.
TI  - A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens.
JO  - Plant Mol. Biol.
PY  - 2014
SP  - 719
EP  - 735
VL  - 84
AB  - C-5 DNA methylation is an essential mechanism controlling gene expression and developmental
AB  - programs in a variety of organisms. Though the role of DNA methylation has been intensively
AB  - studied in mammals and Arabidopsis, little is known about the evolution of this mechanism. The
AB  - chromomethylase (CMT) methyltransferase family is unique to plants and was found to be
AB  - involved in DNA methylation in Arabidopsis, maize and tobacco. The moss Physcomitrella patens,
AB  - a model for early terrestrial plants, harbors a single homolog of the CMT protein family
AB  - designated as PpCMT. Our phylogenetic analysis suggested that the CMT family is unique to
AB  - embryophytes and its earliest known member PpCMT belongs to the CMT3 subfamily. Thus, P.
AB  - patens may serve as a model to study the ancient functions of the CMT3 family. We have
AB  - generated a Delta Ppcmt deletion mutant which demonstrated that PpCMT is essential for P.
AB  - patens protonema and gametophore development and is involved in CHG methylation as
AB  - demonstrated at four distinct genomic loci. PpCMT protein accumulation pattern correlated with
AB  - proliferating cells and was sub-localized to the nucleus as predicted from its function. Taken
AB  - together, our results suggested that CHG DNA methylation mediated by CMT has been employed
AB  - early in land plant evolution to control developmental programs during both the vegetative and
AB  - reproductive haploid phases along the plant life cycle.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
TI  - A novel mcrB-based Escherichia coli K-12 vector system and its use in analyzing the genetic determinants for the McrB nuclease.
JO  - Gene
PY  - 1988
SP  - 177
EP  - 178
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Diaz, R.
AU  - Reiners, L.
TI  - Cytosine-specific DNA modification interferes with plasmid establishement in Escherichia coli K12:  Involvement of rgl B.
JO  - Mol. Gen. Genet.
PY  - 1986
SP  - 469
EP  - 475
VL  - 205
AB  - Several chimeric pBR322/328 derivatives containing genes for cytosine-specific
AB  - DNA methyltransferases (Mtases) can be transformed into the Escherichia coli
AB  - K12/E. coli B hybrid strains HB101 and RR1 but not into other commonly used E.
AB  - coli K12 strains.  In vitro methylation of cytosine residues in pBR328 and
AB  - other unrelated plasmids also reduces their potential to transform such
AB  - methylation sensitive strains, albeit to a lesser degree than observed with
AB  - plasmids containing Mtase genes.  The extent of reduced transformability
AB  - depends on the target specificity of the enzyme used for in vitro modification.
AB  - The role of a host function in the discrimination against methylated plasmids
AB  - was verified by the isolation of K12 mutants which tolerate cytosine methylated
AB  - DNA.  The mutations map in the vicinity of the serB locus.  This and other data
AB  - indicate that the host rg/B function is involved in the discrimination against
AB  - modified DNA.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Jentsch, S.
AU  - Kupsch, J.
AU  - Bergbauer, M.
AU  - Trautner, T.A.
TI  - DNA methyltransferase genes of Bacillus subtilis phages: structural relatedness and gene expression.
JO  - Gene
PY  - 1985
SP  - 143
EP  - 150
VL  - 35
AB  - The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages
AB  - Phi3T, Rho11 and SPbeta were cloned and expressed in Escherichia coli.  Each
AB  - gene specifies a 47-kDal protein, which modifies BsuR (GGCC) and Fnu4HI (GCNGC)
AB  - target sequences.  Transcription is controlled by phage promoters located on
AB  - the cloned fragments.  The direction of transcription and the approximate
AB  - position of the Mtase genes were determined.  DNA/DNA hybridization experiments
AB  - revealed close structural relatedness of the Phi3T, Rho11 and SPbeta genes.  A
AB  - significant degree of homology was also found among these genes and the Mtase
AB  - gene of related phage SPR, which codes for an enzyme with different
AB  - modification specificity.  These results suggest a common ancestor of the
AB  - different phage Mtase genes.  Phage Z, the only BsuR-sensitive member of this
AB  - phage group, lacks a modification gene, but contains regions homologous to
AB  - sequences flanking the SPR, Phi3T, Rho11 and SPbeta Mtase genes.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Jentsch, S.
AU  - Pawlek, B.
AU  - Gunthert, U.
AU  - Trautner, T.A.
TI  - Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SPbeta, Phi3T, and Rho11.
JO  - J. Virol.
PY  - 1983
SP  - 446
EP  - 453
VL  - 46
AB  - The DNA methylation capacity and some other properties of the related temperate
AB  - Bacillus subtilis phages Z, SPR, SPbeta, Phi3T, and Rho11 are compared.  With
AB  - phage mutants affected in their methylation potential, we show that phage-coded
AB  - methyltransferase genes are interchangeable among the phages studied.  DNA/DNA
AB  - hybridization experiments indicate that phage methyltransferase genes are
AB  - structurally related, whereas no such relationship is observed to a bacterial
AB  - gene, specifying a methyltransferase with the same specificity.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Pawlek, B.
AU  - Jentsch, S.
AU  - Gunthert, U.
AU  - Trautner, T.A.
TI  - Restriction and modification in Bacillus subtilis: gene coding for a BsuR-specific modification methyltransferase in the temperate bacteriophage Phi3T.
JO  - J. Virol.
PY  - 1981
SP  - 1077
EP  - 1080
VL  - 38
AB  - The resistance of Phi3T DNA to degradation by the restriction enzyme BsuR or
AB  - its isoschizomer HaeIII is due to obligatory modification of such DNA.
AB  - Biochemical and genetical experiments indicate that Phi3T codes for a
AB  - methyltransferase, which methylates Phi3T DNA itself or heterologous DNA at
AB  - target sites 5'-GG*CC.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Reiners-Schramm, L.
TI  - Highly efficient positive selection of recombinant plasmids using a novel rglB-based Escherichia coli K-12 vector system.
JO  - Gene
PY  - 1988
SP  - 269
EP  - 278
VL  - 66
AB  - We have developed pBR328-derived vectors which allow highly efficient positive
AB  - selection of recombinant plasmids.  The system is based on the rglB-coded
AB  - restriction activity of Escherichia coli K-12 directed against 5-methylcytosine
AB  - (5mC)-containing DNA.  The vectors code for cytosine-specific,
AB  - temperature-sensitive DNA methyltransferases (ts-Mtases), whose specificity
AB  - elicits RglB restriction.  5mC-free vector DNA - a prerequisite to allow
AB  - establishment of such plasmids in cells expressing the RglB nuclease activity -
AB  - can be prepared from cultures grown at 42C.  At 30C the vector plasmids are
AB  - vulnerable to RglB restriction due to the expression of suicidal Mtase
AB  - activity.  Cloning a DNA fragment into the ts-Mtase-coding gene disrupts the
AB  - lethal methylation and thus permits selection of such recombinant plasmids at
AB  - 30C.  The standard vector used, pBN73, contains unique recognition sites for
AB  - nine restriction enzymes within the ts-Mtase-coding gene, which can be used
AB  - independently or in combination for the construction of recombinant plasmids
AB  - selectable by the rglB-coded activity.  Plasmid pBN74, which carries the
AB  - determinants for both the ts-Mtase and the RglB nuclease, contains seven unique
AB  - sites within the ts-Mtase-coding gene.  While selection of recombinant plasmids
AB  - derived from pBN73 obligatorily requires the employment of rglB+ strains,
AB  - selection of pBN74 derivatives can be performed independent of the E. coli host
AB  - genotype.  It remains to be elucidated whether positive selection of
AB  - pBN74-derived recombinant plasmids can also be achieved in hosts other than E.
AB  - coli.  Plasmids pBN73, pBN74 and the recombinants are structurally stable.
AB  - Generally applicable procedures, as developed during the establishment of this
AB  - vector system, are described; they allow the isolation of ts-Mtases and
AB  - facilitate the cloning of genes coding for nucleases directed against
AB  - 5mC-containing DNA.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Trautner, T.A.
TI  - Methylation of DNA in prokaryotes.
JO  - DNA Methylation: Molecular Biology and Biological Significance
PY  - 1993
SP  - 39
EP  - 108
VL  - 0
AB  - A much wider variety of biological functions of postreplicative DNA methylation is observed in
AB  - prokaryotes than in eukaryotes. In eukaryotes DNA methylation is primarily a means of the
AB  - control of gene expression. Many chapters of this book are devoted to various aspects of this
AB  - function. In prokaryotes, DNA methylation affects such diverse phenomena as determination of
AB  - accessiblity of DNA to digestion by endonucleases, control of initiation of DNA replication,
AB  - and the definition of origins of packaging in the maturation of phage DNA, which will be dealt
AB  - with in this article. We shall also be concerned with enzymes which facilitate methylation,
AB  - the DNA methyltransferases. In the eukaryotes, as far as we know at this time, the various DNA
AB  - methyltransferases encountered represent a rather homogenous group, whereas in prokaryotes, we
AB  - find a very diverse set of DNA methyltransferases. Beyond their biological significance, DNA
AB  - methyltransferases represent a remarkable class of enzyme in their own right. Not only are
AB  - they paradigms for sequence specific DNA binding proteins, but they also show specificity in
AB  - their catalytic interaction with defined DNA sequences. Furthermore, their universal
AB  - distribution, the multitude of enzymes with different or identical specificities observed
AB  - among prokaryotes and the obligatory coexistence of isospecific restriction and methylating
AB  - enzymes in restriction/modification systems make DNA methyltransferases choice candidates for
AB  - evolutionary studies.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Walter, J.
AU  - Terschuren, P.-A.
AU  - Chai, S.
AU  - Trautner, T.A.
TI  - M.Phi3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 4066
EP  - 4072
VL  - 22
AB  - The temperate B.subtilis phages Phi3T and Rho11s code, in addition to the multispecific DNA
AB  - (cytosine-C5) methyltransferases (C5-MTases) M.Phi3TI and M.Rho11sI, which were previously
AB  - characterized, for the identical monospecific C5-MTases M.Phi3TII and M.Rho11s.II. These
AB  - enzymes modify the C of TCGA sites, a novel target specificity among C5-MTases. The primary
AB  - sequence of M.Phi3TII (326 amino acids) shows all conserved motifs typical of the building
AB  - plan of C5-MTases. The degree of relatedness between M.Phi3TII and all other mono- or
AB  - multispecific C5-MTases ranges from 30-40% amino acid identity. Particularly M.Phi3TII does
AB  - not show pronounced similarity to M.Phi3TI indicating that both MTase genes were not generated
AB  - from one another but were acquired independently by the phage. The amino terminal part of the
AB  - M.Phi3TII (preceding the variable region 'V'), which predominantly constitutes the catalytic
AB  - domain of the enzyme, exhibits pronounced sequence similarity to the amino termini of a family
AB  - of A-N6-MTases, which -- like M. TaqI -- recognize the general sequence TNNA. This suggests
AB  - that recently described similarities in the general three dimensional organization of C5- and
AB  - A-N6-MTases imply divergent evolution of these enzymes originating from a common molecular
AB  - ancestor.
ER  -

TY  - JOUR
AU  - Noyer-Weidner, M.
AU  - Walter, J.
AU  - Terschuren, P.-A.
AU  - Chai, S.
AU  - Trautner, T.A.
TI  - M.Phi3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 5517
EP  - 5523
VL  - 22
AB  - The temperate B.subtilis phages Phi3T and Rho11S code, in addition to the multispecific DNA
AB  - (cytosine-C5) methyltransferases (C5-MTases) M.Phi3TI and M.Rho11SI, which were previously
AB  - characterized, for the identical monospecific C5-MTases M.Phi3TII and M.Rho11SII. These
AB  - enzymes modify the C of TCGA sites, a novel target specificity among C5-MTases. The primary
AB  - sequence of M.Phi3TII (326 amino acids) shows all conserved motifs typical of the building
AB  - plan of C5-MTases. The degree of relatedness between M.Phi3TII and all other mono- or
AB  - multispecific C5-MTases ranges from 30-40% amino acid identity. Particularly M.Phi3TII does
AB  - not show pronounced similarity to M.Phi3TI indicating that both Mtase genes were not generated
AB  - from one another but were acquired independently by the phage. The amino terminal part of the
AB  - M.Phi3TII (preceding the variable region 'V'), which predominantly constitutes the catalytic
AB  - domain of the enzyme, exhibits pronounced sequence similarity to the amino termini of a family
AB  - of A-N6-MTases, which -- like M. TaqI -- recognize the general sequence TNNA. This suggests
AB  - that recently described similarities in the general three dimensional organization of C5- and
AB  - A-N6-MTases imply divergent evolution of these enzymes originating from a common molecular
AB  - ancestor.
ER  -

TY  - JOUR
AU  - Ntougias, S.
AU  - Lapidus, A.
AU  - Copeland, A.
AU  - Reddy, T.B.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Markowitz, V.M.
AU  - Klenk, H.P.
AU  - Woyke, T.
AU  - Fasseas, C.
AU  - Kyrpides, N.C.
AU  - Zervakis, G.I.
TI  - High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 52
EP  - 52
VL  - 10
AB  - Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can
AB  - tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and
AB  - are involved in the degradation of industrial effluents. Here, the characteristics and the
AB  - permanent-draft genome sequence and  annotation of Halotalea alkalilenta AW-7(T) are
AB  - described. The microorganism was  sequenced as a part of the Genomic Encyclopedia of Type
AB  - Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome
AB  - Institute, and it is the only strain within the genus Halotalea having its genome sequenced.
AB  - The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC  content.
AB  - A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes.
AB  - Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea
AB  - alkalilenta AW-7(T) encodes the catechol and protocatechuate degradation to beta-ketoadipate
AB  - via the beta-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it
AB  - possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. An emended
AB  - description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe
AB  - the delayed fermentation ability of the type strain.
ER  -

TY  - JOUR
AU  - Ntougias, S.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Mavromatis, K.
AU  - Pati, A.
AU  - Chen, A.
AU  - Klenk, H.P.
AU  - Woyke, T.
AU  - Fasseas, C.
AU  - Kyrpides, N.C.
AU  - Zervakis, G.I.
TI  - High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 783
EP  - 793
VL  - 9
AB  - Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae,
AB  - phylum Bacteroidetes. Members of the genus Olivibacter are
AB  - phylogenetically diverse and of significant interest. They occur in diverse
AB  - habitats, such as rhizosphere and contaminated soils, viscous wastes, composts,
AB  - biofilter clean-up facilities on contaminated sites and cave environments, and
AB  - they are involved in the degradation of complex and toxic compounds. Here we
AB  - describe the features of O. sitiensis AW-6(T), together with the permanent-draft
AB  - genome sequence and annotation. The organism was sequenced under the Genomic
AB  - Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome
AB  - Institute and is the first genome sequence of a species within the genus
AB  - Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds
AB  - with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were
AB  - protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%)
AB  - were assigned to a putative function. The identification of 2-keto-4-pentenoate
AB  - hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates
AB  - involvement of this organism in the catechol catabolic pathway. In addition,
AB  - genes encoding for beta-1,4-xylanases and beta-1,4-xylosidases reveal the
AB  - xylanolytic action of O. sitiensis.
ER  -

TY  - JOUR
AU  - Nunes, A.
AU  - Rocha, R.
AU  - Vale, F.F.
AU  - Vieira, L.
AU  - Sampaio, D.A.
AU  - Dias, R.
AU  - Gomes, J.P.
AU  - Oleastro, M.
TI  - Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with  Nonulcer Dyspepsia and Peptic Ulcer Disease.
JO  - Genome Announcements
PY  - 2015
SP  - e01488
EP  - e01414
VL  - 3
AB  - We present draft genome sequences of 10 Helicobacter pylori clinical strains isolated from
AB  - children. This will be important for future studies of comparative
AB  - genomics in order to better understand the virulence determinants underlying
AB  - peptic ulcer disease.
ER  -

TY  - JOUR
AU  - Nunoura, T.
AU  - Takaki, Y.
AU  - Kakuta, J.
AU  - Nishi, S.
AU  - Sugahara, J.
AU  - Kazama, H.
AU  - Chee, G.J.
AU  - Hattori, M.
AU  - Kanai, A.
AU  - Atomi, H.
AU  - Takai, K.
AU  - Takami, H.
TI  - Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 3204
EP  - 3223
VL  - 39
AB  - The domain Archaea has historically been divided into two phyla, the Crenarchaeota and
AB  - Euryarchaeota. Although regarded as members of the
AB  - Crenarchaeota based on small subunit rRNA phylogeny, environmental
AB  - genomics and efforts for cultivation have recently revealed two novel
AB  - phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'.
AB  - Here, we show the genome sequence of Candidatus 'Caldiarchaeum
AB  - subterraneum' that represents an uncultivated crenarchaeotic group. A
AB  - composite genome was reconstructed from a metagenomic library previously
AB  - prepared from a microbial mat at a geothermal water stream of a
AB  - sub-surface gold mine. The genome was found to be clearly distinct from
AB  - those of the known phyla/divisions, Crenarchaeota (hyperthermophiles),
AB  - Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest
AB  - that this crenarchaeotic group can be considered as a novel archaeal
AB  - phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like
AB  - protein modifier system consisting of Ub, E1, E2 and small Zn RING finger
AB  - family protein with structural motifs specific to eukaryotic system
AB  - proteins, a system clearly distinct from the prokaryote-type system
AB  - recently identified in Haloferax and Mycobacterium. The presence of such a
AB  - eukaryote-type system is unprecedented in prokaryotes, and indicates that
AB  - a prototype of the eukaryotic protein modifier system is present in the
AB  - Archaea.
ER  -

TY  - JOUR
AU  - Nunvar, J.
AU  - Elhottova, D.
AU  - Chronakova, A.
AU  - Schneider, B.
AU  - Licha, I.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage.
JO  - Genome Announcements
PY  - 2014
SP  - e00134
EP  - e00114
VL  - 2
AB  - Stenotrophomonas maltophilia is an omnipresent environmental bacterium emerging as an
AB  - opportunistic human pathogen and exhibiting multidrug resistance. Here, we
AB  - report the draft genome sequence of S. maltophilia strain 5BA-I-2, a soil isolate
AB  - and a member of a phylogenetically basal lineage.
ER  -

TY  - JOUR
AU  - Nur, I.
AU  - Szyf, M.
AU  - Razin, A.
AU  - Glaser, G.
AU  - Rottem, S.
AU  - Razin, S.
TI  - Procaryotic and Eucaryotic Traits of DNA Methylation in Spiroplasmas (Mycoplasmas).
JO  - J. Bacteriol.
PY  - 1985
SP  - 19
EP  - 24
VL  - 164
AB  - Differences in the type of base methylated (cytosine or adenine) and in the
AB  - extent of methylation were detected by high-pressure liquid chromatography in
AB  - the DNAs of five spiroplasmas.  Nearest neighbor analysis and digestion by
AB  - restriction enzyme isoschizomers also revealed differences in methylation
AB  - sequence specificity.  Whereas in Spiroplasma floricola and Spiroplasma sp.
AB  - strain PPS-1 5-methylcytosine was found on the 5' side of each of the four
AB  - major bases, the cytosine in Spiroplasma apis DNA was methylated only when its
AB  - 3' neighboring base was adenine or thymine.  In Spiroplasma sp. strain MQ-1
AB  - over 95% of the methylated cytosine was in C-G sequences.  Essentially all of
AB  - the C-G sequences in the MQ-1 DNA were methylated.  Partially purified extracts
AB  - of S. apis and Spiroplasma sp. strain MQ-1 were used to study substrate and
AB  - sequence specificity of the methylase activity.  Methylation by the MQ-1 enzyme
AB  - was exclusively at C-G sequences, resembling in this respect eucaryotic DNA
AB  - methylases.  However, the MQ-1 emthylase differed from eucaryotic methylases by
AB  - showing high activity on nonmethylated DNA duplexes, low activity with
AB  - hemimethylated DNA duplexes, and no activity on single-stranded DNA.
ER  -

TY  - JOUR
AU  - Nurjadi, D.
AU  - Boutin, S.
AU  - Dalpke, A.
AU  - Heeg, K.
AU  - Zanger, P.
TI  - Draft Genome Sequence of Staphylococcus aureus Strain HD1410, Isolated from a Persistent Nasal Carrier.
JO  - Genome Announcements
PY  - 2018
SP  - e00411
EP  - e00418
VL  - 6
AB  - We report here the draft genome sequence of a Staphylococcus aureus strain isolated from the
AB  - nares of an 18-year-old female healthy persistent-carrier
AB  - individual, and it was used to investigate S. aureus-specific immune responses in
AB  - colonized and noncolonized individuals.
ER  -

TY  - JOUR
AU  - Nurminsky, D.I.
AU  - Hartl, D.L.
TI  - Design of compact multiple cloning sites.
JO  - Biotechniques
PY  - 1993
SP  - 209
EP  - 213
VL  - 15
AB  - Cloning procedures in molecular biology are usually enhanced by the availability of desired
AB  - restriction sites in vectors engineering for cloning or expression purposes. In the absence of
AB  - such sites, cloning required blunt ends or the addition of linkers, which requires more
AB  - manipulation, both being less efficient. During the past decade, many vectors have been
AB  - developed that have a multiple cloning site (MCS) containing many restriction sites found only
AB  - once within each vector. An ideal MCS would be one that has many unique restriction sites that
AB  - would satisfy general cloning needs. The upper limit to the number of restriction sites that
AB  - can be placed in an MCS is usually determined by the absence of identical recognition
AB  - specificities in the rest of the vector and the functional length available for the MCS. Here
AB  - we present a simple method to design compact MCSs which are 50% shorter than presently
AB  - available MCSs as a result of the presence of restriction sites that overlap each other.
ER  -

TY  - JOUR
AU  - Nutter, R.L.
AU  - Bullas, L.R.
AU  - Siapco, B.J.
AU  - Pearson, C.
TI  - The role of methylation in host-induced modification of Salmonella bacteriophage P3.
JO  - Bacteriol. Proc.
PY  - 1971
SP  - 196
EP  - 196
VL  - 71
AB  - The temperate Salmonella potsdam bacteriophage P3 lyses E. coli K with high
AB  - efficiency.  It is modified in this passage and subsequently restricted by S.
AB  - potsdam.  Studies with P-32 tagged phage showed that the E. coli passed P3
AB  - phage were adsorbing to S. potsdam, however, and infecting their DNA.  When a
AB  - methionine requiring mutant of S. potsdam was deprived of methionine and
AB  - infected with restricted P3 phage, the restriction was reduced to less than
AB  - half of its former value.  Experiments employing adenine-2-H3 revealed that the
AB  - unrestricted phage DNA from S. potsdam has about 1.2% as many MAP groups as
AB  - adenine whereas the restricted phage DNA from E. coli has about 0.6%.
ER  -

TY  - JOUR
AU  - Nutter, R.L.
AU  - Bullas, L.R.
AU  - Siapco, B.S.
AU  - Pearson, C.A.
TI  - Change in methylation of Salmonella bacteriophage P3 deoxyribonucleic acid with host-controlled modification by Escherichia coli.
JO  - J. Virol.
PY  - 1972
SP  - 560
EP  - 562
VL  - 10
AB  - Modification of bacteriophage P3 by passage through Escherichia coli K was
AB  - correlated with a 54% decrease in the content of 6-methylaminopurine in the
AB  - phage deoxyribonucleic acid.
ER  -

TY  - JOUR
AU  - Nwaiwu, O.
AU  - Moura, A.
AU  - Thouvenot, P.
AU  - Rees, C.
AU  - Leclercq, A.
AU  - Lecuit, M.
TI  - Draft Genome Sequences of Listeria monocytogenes, Isolated from Fresh Leaf Vegetables in Owerri City, Nigeria.
JO  - Genome Announcements
PY  - 2017
SP  - e00354
EP  - e00317
VL  - 5
AB  - Here, we report the draft genome sequences of three Listeria monocytogenes isolates from fresh
AB  - leaves collected in Nigeria, belonging to sequence types ST5
AB  - and ST155 (sublineages SL5 and SL155, respectively).
ER  -

TY  - JOUR
AU  - Nwankwo, D.
AU  - Wilson, G.
TI  - Cloning of two type II methylase genes that recognise asymmetric nucleotide sequences:  FokI and HgaI.
JO  - Mol. Gen. Genet.
PY  - 1987
SP  - 570
EP  - 574
VL  - 209
AB  - The modification genes of Flavobacterium okeanokoites and Haemophilus
AB  - gallinarum have been cloned into the vector of pBR322 and expressed in
AB  - Escherichia coli cells.  FokI methylase gene is contained on a 3.80 kb piece of
AB  - F. okeanokoites DNA.  Plasmid constructs carrying this fragment of DNA are
AB  - resistant to digestion by FokI restriction endonuclease but are sensitive to
AB  - cleavage by HindIII, EcoRI and PstI.  Unmodified lambda DNA molecules, exposed
AB  - in vitro to cell extracts prepared from cells harbouring this plasmid, became
AB  - resistant to digestion by FokI.  The smallest HgaI methylase clone carries the
AB  - pBR322 plasmid containing a 3.50 kb piece of H. gallinarum DNA.  This plasmid
AB  - is resistant to digestion by HgaI.  Neither the FokI nor the HgaI restriction
AB  - endonuclease was detected in either clone.  This is the first report of cloning
AB  - modification genes whose protein products recognise asymmetric nucleotide
AB  - sequences.
ER  -

TY  - JOUR
AU  - Nwankwo, D.O.
TI  - Cloning of a pair of genes encoding isoschizomeric restriction endonucleases from Bacillus species: the BspEI and BspMII restriction and modification systems.
JO  - Gene
PY  - 1995
SP  - 31
EP  - 35
VL  - 157
AB  - The respective genes (R-M) encoding restriction and modification systems from two Bacillus
AB  - species which recognize the same nucleotide sequence, 5'TCCGGA, have been cloned and
AB  - expressed in Escherichia coli.  The BspEI R-M genes were cloned on a 3.6-kb HindIII fragment,
AB  - whereas the BspMII R-M genes were cloned on three contiguous HindIII fragments totalling 9.8
AB  - kb.  Upon thermal induction, E. coli carrying the bspEIR clones under the control of the phage
AB  - lambda PL promoter, express high levels of R.BspEI (106 units/g wet cell paste).  The
AB  - bspMIIR  gene, on the other hand, is only poorly expressed (about 4 x 10/3 units/g wet cell
AB  - paste) following induction.  Although the enzymes of both R-M systems recognize the same
AB  - sequence and  the restriction endonucleases (ENases) cleave DNA at the same position, the
AB  - modification specified by the methyltransferases (MTases) differ.  The internal cytosine is
AB  - the site for M.BspMII modification (TCmeCGGA), whereas the external cytosine is modified by
AB  - M.BspEI.
ER  -

TY  - JOUR
AU  - Nwankwo, D.O.
AU  - Lynch, J.J.
AU  - Moran, L.S.
AU  - Fomenkov, A.
AU  - Slatko, B.E.
TI  - The XmnI restriction-modification system: cloning, expression, sequence organization and similarity between the R and M genes.
JO  - Gene
PY  - 1996
SP  - 121
EP  - 127
VL  - 173
AB  - The xmn1RM genes from Xanthomonas manihotis 7AS1 have been cloned and expressed in Escherichia
AB  - coli.  The nucleotide (nt) sequences of both genes were determined.  The XmnI
AB  - methyltransferase (Mtase)-encoding gene is 1861 bp in length and codes for 620 amino acids
AB  - (aa) (68,660 Da).  The restriction endonuclease (Enase)-encoding gene is 969 bp long and
AB  - therefore codes for a 319-aa protein (35,275 Da).  The two genes are aligned tail to tail and
AB  - they overlap at their respective stop codons.  About 4 x 10^4 units/g wet cell paste of R.XmnI
AB  - was obtained following IPTG induction in a suitable E. coli host.  The xmnIR gene is expressed
AB  - from the T7 promoter.  M.XmnI probably modifies the first A in the sequence, GAA(N)4TTC.  The
AB  - xmnIR and M genes contain regions of conserved similarity and probably evolved from a common
AB  - ancestor.  M.XmnI is losely related to M.EcoRI.  The XmnI R-M system and the type-I R-M
AB  - systems probably derived from a common ancestor.
ER  -

TY  - JOUR
AU  - Nwankwo, D.O.
AU  - Maunus, R.E.
AU  - Xu, S.-Y.
TI  - Cloning and expression of AatII restriction-modification system.
JO  - Gene
PY  - 1997
SP  - 105
EP  - 109
VL  - 185
AB  - The genes encoding the AatII restriction endonuclease and methylase from Acetobacter aceti
AB  - have been cloned and expressed in Escherichia coli.  The nucleotide sequences of aatIIM and
AB  - aatIIR genes were determined.  The aatIIM and aatIIR genes are 996 bp and 1038 bp,
AB  - respectively, encoding the 331-aa methylase with a predicted molecular mass of 36.9 kDa, and
AB  - the 345-aa AatII restriction endonuclease with a predicted molecular mass of 38.9 kDa.  The
AB  - two genes overlap by 4 base pairs and are transcribed in the same orientation.  The aatIIRM
AB  - genes are located next to a putative gene for plasmid mobilization.  A stable overproducing
AB  - strain was constructed, in which the aatIIM gene was expressed from a pSC101-derived plasmid.
AB  - The aatIIR gene was inserted into a modified T7 expression vector that carries transcription
AB  - terminators upstream from the T7 promoter.  The recombinant AatII restriction endonuclease was
AB  - purified to near homogeneity by chromatography through DEAE Sepharose, Heparin Sepharose, and
AB  - phosphocellulose columns.
ER  -

TY  - JOUR
AU  - Nwankwo, D.O.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Waite-Rees, P.A.
AU  - Dorner, L.F.
AU  - Benner, J.S.
AU  - Wilson, G.G.
TI  - Cloning, analysis and expression of the HindIII R-M-encoding genes.
JO  - Gene
PY  - 1994
SP  - 75
EP  - 80
VL  - 150
AB  - The genes encoding the HindIII restriction endonuclease (R.HindIII ENase) and
AB  - methyltransferase (M.HindIII MTase) from Haemophilus influenzae Rd were cloned and expressed
AB  - in Escherichia coli and their nucleotide (nt) sequences were determined. The genes are
AB  - transcribed in the same orientation, with the ENase-encoding gene (hindIIIR) preceding the
AB  - MTase-encoding gene (hindIIIM). The two genes overlap by several nt. The ENase is predicted to
AB  - be 300 amino acids (aa) in length (34950 Da); the MTase is predicted to be 309 aa (35550 Da).
AB  - The HindIII ENase and MTase activities increased approx. 20-fold when the genes were brought
AB  - under the control of an inducible lambda pL promoter. Highly purified HindIII ENase and MTase
AB  - proteins were prepared and their N-terminal aa sequences determined. In H. influenzae Rd, the
AB  - HindIII R-M genes are located between the holC and valS genes; they are not closely linked to
AB  - the HindII R-M genes.
ER  -

TY  - JOUR
AU  - Nwankwo, D.O.
AU  - Wilson, G.G.
TI  - Cloning and expression of the MspI restriction and modification genes.
JO  - Gene
PY  - 1988
SP  - 1
EP  - 8
VL  - 64
AB  - The genes for the MspI restriction (R) and modification enzymes (recognition
AB  - sequence CCGG) have been cloned into Escherichia coli using the vector pBR322.
AB  - Clones carrying both genes have been isolated from libraries prepared with
AB  - EcoRI, HindIII and BamHI.  The smallest fragment that encodes both activities
AB  - is a 3.6-kb HindIII fragment.  Plasmids purified from the clones are fully
AB  - resistant to digestion by MspI, indicating that the modification gene is
AB  - functional in E. coli.  The clones remain sensitive to phage infection,
AB  - however, indicating that the endonuclease is dysfunctional.  When the R gene is
AB  - brought under the control of the inducible leftward promoter from phage lambda,
AB  - the level of endonuclease increases and the level of methylase decreases,
AB  - suggesting that the genes are transcribed in opposite directions.
ER  -

TY  - JOUR
AU  - Nwosu, V.U.
TI  - Overexpression of the wild-type gene coding for Escherichia coli DNA adenine methylase (dam).
JO  - Biochem. J.
PY  - 1992
SP  - 745
EP  - 750
VL  - 283
AB  - The gene coding for Escherichia coli dam methylase was isolated from a dam+ K12 strain by the
AB  - PCR method. The gene was subcloned into an overexpression vector under the control of the
AB  - strong lambdaPL promoter. The resultant construct produced the dam methylase at about 20% of
AB  - total cellular protein. Purification of the protein was achieved with two chromatography
AB  - columns and yielded 6 mg of pure methylase per gram cell paste. The methylase readily
AB  - methylates the synthetic dodecamer GACTGATCAGTC containing its recognition sequence. It also
AB  - methylates a synthetic dodecamer containing the EcoRV recognition sequence GATATC. However,
AB  - methyl transfer is to the second adenine in the EcoRV sequence.
ER  -

TY  - JOUR
AU  - Nwosu, V.U.
AU  - Connolly, B.A.
AU  - Halford, S.E.
AU  - Garnett, J.
TI  - The cloning, purification and characterization of the EcoRV modification methylase.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 3705
EP  - 3720
VL  - 16
AB  - The gene for the EcoRV methylase has been cloned into a plasmid under control
AB  - of the strong lambda PL promoter and overexpressed in E. coli.  This plasmid,
AB  - pVIC1, gives reliable overexpression of the methylase at levels of about 20% of
AB  - total protein.  Maximum yields of soluble protein are achieved after about 6
AB  - hours of induction.  If the cells are harvested later than this much of the
AB  - enzyme is found in the pellet fraction following centrifugation.  A two column
AB  - purification scheme using phosphocellulose and Blue-Sepharose chromatography
AB  - has been developed.  This yielded pure methylase in amounts of 5mg per gram E.
AB  - coli cell paste.  The enzyme is monomeric and methylates the first
AB  - deoxyadenosine residue in its recognition sequence GATATC.
ER  -

TY  - JOUR
AU  - Nyarko, E.
AU  - Tabata, M.
AU  - Watanabe, K.
TI  - Enhanced DNA cleavage by mercury(II) porphyrin at a low concentration of HaeIII restriction enzyme.
JO  - Chem. Lett.
PY  - 2001
SP  - 932
EP  - 933
VL  - 0
AB  - Mercury(II) porphyrin enhanced DNA cleavage in the presence of 0.2 units per microL of HaeIII
AB  - at which concentration the restriction enzyme
AB  - could not cleave DNA in the absence of the porphyrin. This was ascribed
AB  - to the synergistic effect of the bound Hg2+ ions to DNA and the
AB  - intercalated free base porphyrin, released from the mercury(II)
AB  - porphyrin complex upon binding to DNA, which was confirmed by
AB  - UV-visible and CD spectroscopic measurements.
ER  -

TY  - JOUR
AU  - Nye, T.M.
AU  - Schroeder, J.W.
AU  - Kearns, D.B.
AU  - Simmons, L.A.
TI  - Complete Genome Sequence of Undomesticated Bacillus subtilis Strain NCIB 3610.
JO  - Genome Announcements
PY  - 2017
SP  - e00364
EP  - e00317
VL  - 5
AB  - Bacillus subtilis is a Gram-positive bacterium that serves as an important experimental
AB  - system. B. subtilis NCIB 3610 is an undomesticated strain that
AB  - exhibits phenotypes lost from the more common domesticated laboratory strains.
AB  - Here, we announce the complete genome sequence of DK1042, a genetically competent
AB  - derivative of NCIB 3610.
ER  -

TY  - JOUR
AU  - Nyengaard, N.
AU  - Vogensen, F.K.
AU  - Josephsen, J.
TI  - Restriction-modification systems in Lactococcus lactis.
JO  - Gene
PY  - 1995
SP  - 13
EP  - 18
VL  - 157
AB  - Several restriction-modification (R-M) systems have been identified in Lactococcus lactis.
AB  - Most of the systems have been plasmid encoded and function as phage-resistance mechanisms. At
AB  - least five different type-II R-M systems, LlaAI, LlaBI, LlaCI, LlaDI and LlaEI, were
AB  - identified in isolates from a mixed Cheddar starter culture. LlaAI and LlaBI recognized the
AB  - DNA sequences 5'-/GATC-3' and 5'-C/TRYAG-3', respectively. The genes coding for the LlaAI
AB  - and LlaBI R-M systems have been cloned and sequenced. The LlaAI R-M system had two genes
AB  - coding for methyltransferases (MTases) and one gene coding for a restriction endonuclease
AB  - (ENase). The MTases showed high homology to the MTases from DpnII. The LlaBI R-M system had
AB  - one gene coding for a MTase and one gene coding for an ENase.
ER  -

TY  - JOUR
AU  - Nyengaard, N.
AU  - Vogensen, F.K.
AU  - Josephsen, J.
TI  - LlaAI and LlaBI, two type-II restriction endonucleases from Lactococcus lactis subsp. cremoris W9 and W56 recognizing, respectively, 5'-/GATC-3' and 5'-C/TRYAG-3'.
JO  - Gene
PY  - 1993
SP  - 371
EP  - 372
VL  - 136
AB  - Two type-II restriction endonucleases have been purified from Lactococus lactis subsp.
AB  - cremoris W9 and W56, the strains isolated from a mixed Cheddar starter. Their characterization
AB  - showed that LlaAI was an isoschizomer of MboI from Moraxella bovis with the cleaving sequence
AB  - 5'-/GATC-3' being sensitive to methylation of the adenine residue; LlaBI was an isoschizomer
AB  - to SfcI from Streptococcus faecium with the cleaving sequence 5'C/TRYAG-3'. Both LlaAI and
AB  - LlaBI restriction-modification (R-M) systems are encoded by the plasmids, respectively, pFW094
AB  - and pJW563, protecting the harboring strain against phage attack.
ER  -

TY  - JOUR
AU  - Nyengaard, N.R.
AU  - Falkenberg-Klok, J.
AU  - Josephsen, J.
TI  - Cloning and analysis of the restriction-modification system LlaBI, a bacteriophage resistance system from Lactococcus lactis subsp. cremoris W56.
JO  - Appl. Environ. Microbiol.
PY  - 1996
SP  - 3494
EP  - 3498
VL  - 62
AB  - The genes coding for the type II restriction-modification (R/M) system LlaBI, which recognized
AB  - the sequence 5'-C/TRYAG-3', have been cloned from a plasmid in Lactococcus lactis subsp.
AB  - cremoris W56 and sequenced.  The DNA sequence predicts an endonuclease of 299 amino acids (33
AB  - kDa) and a methylase of 580 amino acids (65 kDa).  A 4.0-kb HindIII fragment in pSA3 was able
AB  - to restrict bacteriophages, showing that the cloned R/M system can function as a phage defense
AB  - mechanism in L. lactis.
ER  -

TY  - JOUR
AU  - Nyyssonen, M.
AU  - Tran, H.M.
AU  - Karaoz, U.
AU  - Weihe, C.
AU  - Hadi, M.Z.
AU  - Martiny, J.B.
AU  - Martiny, A.C.
AU  - Brodie, E.L.
TI  - Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries.
JO  - Front. Microbiol.
PY  - 2013
SP  - 282
EP  - 282
VL  - 4
AB  - Recent advances in sequencing technologies generate new predictions and
AB  - hypotheses about the functional roles of environmental microorganisms. Yet, until
AB  - we can test these predictions at a scale that matches our ability to generate
AB  - them, most of them will remain as hypotheses. Function-based mining of
AB  - metagenomic libraries can provide direct linkages between genes, metabolic traits
AB  - and microbial taxa and thus bridge this gap between sequence data generation and
AB  - functional predictions. Here we developed high-throughput screening assays for
AB  - function-based characterization of activities involved in plant polymer
AB  - decomposition from environmental metagenomic libraries. The multiplexed assays
AB  - use fluorogenic and chromogenic substrates, combine automated liquid handling and
AB  - use a genetically modified expression host to enable simultaneous screening of
AB  - 12,160 clones for 14 activities in a total of 170,240 reactions. Using this
AB  - platform we identified 374 (0.26%) cellulose, hemicellulose, chitin, starch,
AB  - phosphate and protein hydrolyzing clones from fosmid libraries prepared from
AB  - decomposing leaf litter. Sequencing on the Illumina MiSeq platform, followed by
AB  - assembly and gene prediction of a subset of 95 fosmid clones, identified a broad
AB  - range of bacterial phyla, including Actinobacteria, Bacteroidetes, multiple
AB  - Proteobacteria sub-phyla in addition to some Fungi. Carbohydrate-active enzyme
AB  - genes from 20 different glycoside hydrolase (GH) families were detected. Using
AB  - tetranucleotide frequency (TNF) binning of fosmid sequences, multiple enzyme
AB  - activities from distinct fosmids were linked, demonstrating how
AB  - biochemically-confirmed functional traits in environmental metagenomes may be
AB  - attributed to groups of specific organisms. Overall, our results demonstrate how
AB  - functional screening of metagenomic libraries can be used to connect microbial
AB  - functionality to community composition and, as a result, complement large-scale
AB  - metagenomic sequencing efforts.
ER  -

TY  - JOUR
AU  - O'Brien, K.
AU  - Perron, G.G.
AU  - Jude, B.A.
TI  - Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed.
JO  - Genome Announcements
PY  - 2018
SP  - e01429
EP  - e01417
VL  - 6
AB  - Water samples from the Hudson Valley watershed indicate that the area is host to  many
AB  - violacein-producing bacterial isolates. Here, we report the draft
AB  - whole-genome sequence of Janthinobacterium sp. strain BJB412, an isolate lacking
AB  - violacein production yet containing genes responsible for prodigiosin, biofilm
AB  - production, and quorum sensing, like its purple-pigmented counterparts.
ER  -

TY  - JOUR
AU  - O'Callaghan, A.
AU  - Bottacini, F.
AU  - O'Connell-Motherway, M.
AU  - van Sinderen, D.
TI  - Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.
JO  - BMC Genomics
PY  - 2015
SP  - 832
EP  - 832
VL  - 16
AB  - BACKGROUND: Bifidobacterial genome analysis has provided insights as to how these
AB  - gut commensals adapt to and persist in the human GIT, while also revealing
AB  - genetic diversity among members of a given bifidobacterial (sub)species.
AB  - Bifidobacteria are notoriously recalcitrant to genetic modification, which
AB  - prevents exploration of their genomic functions, including those that convey
AB  - (human) health benefits. METHODS: PacBio SMRT sequencing was used to determine
AB  - the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum
AB  - pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree
AB  - was constructed using a maximum-likelihood based approach in PhyML v3.0.
AB  - M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned
AB  - into pORI19 for insertion mutagenesis. RESULTS: In this study we present the
AB  - complete genome sequences of two Bifidobacterium longum subsp. longum strains.
AB  - Comparative analysis with thirty one publicly available B. longum genomes allowed
AB  - the definition of the B. longum core and dispensable genomes. This analysis also
AB  - highlighted differences in particular metabolic abilities between members of the
AB  - B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic
AB  - analysis of the B. longum core genome indicated the existence of a novel
AB  - subspecies. Methylome data, coupled to the analysis of restriction-modification
AB  - systems, allowed us to substantially increase the genetic accessibility of B.
AB  - longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed
AB  - mutagenesis. CONCLUSIONS: Comparative genomic analysis of thirty three B. longum
AB  - representatives revealed a closed pan-genome for this bifidobacterial species.
AB  - Phylogenetic analysis of the B. longum core genome also provides evidence for a
AB  - novel fifth B. longum subspecies. Finally, we improved genetic accessibility for
AB  - the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a
AB  - mutant of this strain.
ER  -

TY  - JOUR
AU  - O'Callaghan, A.
AU  - Hilliard, A.
AU  - Morgan, C.A.
AU  - Culligan, E.P.
AU  - Leong, D.
AU  - DeLappe, N.
AU  - Hill, C.
AU  - Jordan, K.
AU  - Cormican, M.
AU  - Gahan, C.G.M.
TI  - Draft Genome Sequences of 25 Listeria monocytogenes Isolates Associated with Human Clinical Listeriosis in Ireland.
JO  - Genome Announcements
PY  - 2017
SP  - e00184
EP  - e00117
VL  - 5
AB  - Listeria monocytogenes is a Gram-positive opportunistic pathogen that is the causative agent
AB  - of listeriosis. Here, we report the draft genome sequences of 25
AB  - L. monocytogenes strains isolated from patients with clinical listeriosis in the
AB  - Republic of Ireland between 2013 and 2015.
ER  -

TY  - JOUR
AU  - O'Connell-Motherway, M. et al.
TI  - Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 11217
EP  - 11222
VL  - 108
AB  - Development of the human gut microbiota commences at birth, with bifidobacteria being among
AB  - the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis
AB  - of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome
AB  - analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model
AB  - revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene
AB  - cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene
AB  - cluster is essential for efficient in vivo murine gut colonization, and immunogold
AB  - transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve
AB  - UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and
AB  - among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host
AB  - colonization and persistence mechanism for bifidobacteria.
ER  -

TY  - JOUR
AU  - O'Connell-Motherway, M.
AU  - O'Driscoll, J.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
TI  - Overcoming the restriction barrier to plasmid transformation and targeted mutagenesis in Bifidobacterium breve UCC2003.
JO  - Micro. Biotech.
PY  - 2009
SP  - 321
EP  - 332
VL  - 2
AB  - In silico analysis of the Bifidobacterium breve UCC2003 genome predicted two distinct loci,
AB  - which encode three different restriction/modification systems, each comprising a modification
AB  - methylase and a restriction endonuclease.  Based on sequence homology and observed protection
AB  - against restriction we conclude that the first restriction endonuclease, designated BbrI, is
AB  - an isoschizomer of BbeI, the second, BbrII, is a neoschizomer of SalI, while the third,
AB  - BbrIII, is an isoschizomer of PstI.  Expression of each of the B. breve UCC2003
AB  - methylase-encoding genes in B. breve JCM 7017 established that BbrII and BbrIII are active and
AB  - restrict incoming DNA.  By exploiting knowledge on restriction/modification in B. breve
AB  - UCC2003 we successfully increased the transformation efficiency to a level that allows the
AB  - reliable generation of mutants by homologous recombination using a non-replicative plasmid.
ER  -

TY  - JOUR
AU  - O'Connell-Motherway, M.
AU  - Watson, D.
AU  - Bottacini, F.
AU  - Clark, T.A.
AU  - Roberts, R.J.
AU  - Korlach, J.
AU  - Garault, P.
AU  - Chervaux, C.
AU  - van-Hylckama-Vlieg, J.E.
AU  - Smokvina, T.
AU  - van-Sinderen, D.
TI  - Identification of Restriction-Modification Systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT Sequencing and Associated Methylome Analysis.
JO  - PLoS ONE
PY  - 2014
SP  - e94875
EP  - e94875
VL  - 9
AB  - Bifidobacterium animalis subsp. lactis CNCM I-2494 is a component of a commercialized
AB  - fermented dairy product for which beneficial effects on health has
AB  - been studied by clinical and preclinical trials. To date little is known about
AB  - the molecular mechanisms that could explain the beneficial effects that
AB  - bifidobacteria impart to the host. Restriction-modification (R-M) systems have
AB  - been identified as key obstacles in the genetic accessibility of bifidobacteria,
AB  - and circumventing these is a prerequisite to attaining a fundamental
AB  - understanding of bifidobacterial attributes, including the genes that are
AB  - responsible for health-promoting properties of this clinically and industrially
AB  - important group of bacteria. The complete genome sequence of B. animalis subsp.
AB  - lactis CNCM I-2494 is predicted to harbour the genetic determinants for two type
AB  - II R-M systems, designated BanLI and BanLII. In order to investigate the
AB  - functionality and specificity of these two putative R-M systems in B. animalis
AB  - subsp. lactis CNCM I-2494, we employed PacBio SMRT sequencing with associated
AB  - methylome analysis. In addition, the contribution of the identified R-M systems
AB  - to the genetic accessibility of this strain was assessed.
ER  -

TY  - JOUR
AU  - O'Connor, B.R.
AU  - Perry, B.J.
AU  - Yost, C.K.
TI  - Draft Genome Sequence of Rheinheimera sp. KL1, Isolated from a Freshwater Lake in Southern Saskatchewan, Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e01177
EP  - e01115
VL  - 3
AB  - Rheinheimera sp. KL1 was isolated from an algal bloom in Katepwa Lake, Saskatchewan, Canada.
AB  - The isolate shares genetic and physiological similarities with Rheinheimera tangshanensis. The
AB  - genome is estimated to be 4,295,060 bp in length with a GC content of 46.37%. Sequence
AB  - analysis suggests the strain carries a previously uncharacterized prophage.
ER  -

TY  - JOUR
AU  - O'Connor, C.D.
AU  - Humphreys, G.O.
TI  - Expression of the EcoRI restriction-modification system and the construction of positive-selection cloning vectors.
JO  - Gene
PY  - 1982
SP  - 219
EP  - 229
VL  - 20
AB  - The genes encoding the EcoRI restriction-modification (R/M) system have been
AB  - separately cloned onto compatible plasmids.  We have shown that the EcoRI
AB  - restriction gene is expressed in the total absence of methylase enzyme and
AB  - confirmed that a temperature-sensitive mutant is defective in EcoRI
AB  - modification activity at higher temperatures.  Insertion of transcriptional
AB  - terminators into the restriction gene had no detectable effect on EcoRI
AB  - modification activity.  This strongly suggests that a separate promoter exists
AB  - for the methylase gene.  Analysis of the published sequence shows that the
AB  - methylase gene promoter may overlap with the COOH-terminal region of the
AB  - endonuclease structural gene.  The temperature-sensitive EcoRI system has been
AB  - exploited in the construction of two plasmid cloning vectors, pLV57 and pLV59,
AB  - which can be used to select positively for transformants bearing recombinant
AB  - plasmids; cloning of a DNA fragment into pLV57 or pLV59 at the unique HindIII,
AB  - BglII, or PstI sites inactivates the EcoRI restriction gene and permits the
AB  - hybrid plasmid to survive at 37C.  The temperature-sensitive modification
AB  - activity of these vectors should also facilitate the introduction of EcoRI
AB  - linkers into DNA cloned in this way.
ER  -

TY  - JOUR
AU  - O'Connor, C.D.
AU  - Metcalf, E.
AU  - Wrighton, C.J.
AU  - Harris, T.J.R.
AU  - Saunders, J.R.
TI  - RsrII - a novel restriction endonuclease with a heptanucleotide recognition site.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 6701
EP  - 6708
VL  - 12
AB  - A sequence-specific endonuclease present in extracts of Rhodopseudomonas
AB  - sphaeroides 630 has been purified and characterized.  The enzyme, RsrII,
AB  - recognises and cleaves the palindromic heptanucleotide sequence:  5' -
AB  - CG^G(A/T)CCG - 3' By virtue of its unusual specificity, RsrII cuts most DNA
AB  - molecules very infrequently which should facilitate the physical mapping of
AB  - large genomes.
ER  -

TY  - JOUR
AU  - O'Connor, C.D.
AU  - Timmis, K.N.
TI  - Highly repressible expression system for cloning genes that specify potentially toxic proteins.
JO  - J. Bacteriol.
PY  - 1987
SP  - 4457
EP  - 4462
VL  - 169
AB  - A highly repressible expression vector system that allows the cloning of potentially
AB  - deleterious genes has been constructed.  Undesired expression of a cloned gene was prevented
AB  - (I) at the level of initiation of transcription, by the presence of the strong but highly
AB  - repressible leftward promoter of bacteriophage lambda, lambda PL, and (ii) at the level of
AB  - transcript elongation or translation, through synthesis of antisense RNA complementary to the
AB  - mRNA of the cloned gene.  The system was tested by measuring the inhibition of expression of
AB  - traT, the gene for the TraT major outer membrane lipoprotein.  Direct detection and functional
AB  - assays indicated that an essentially complete inhibition of traT expression was obtained.  As
AB  - a further test of the system, the gene encoding the EcoRI restriction endonuclease was cloned
AB  - in the absence of the gene of the corresponding protective EcoRI modification methylase.
AB  - Transformants harboring this construct were only viable when both repression controls were
AB  - operational.
ER  -

TY  - JOUR
AU  - O'Connor, C.D.
AU  - Walker, J.N.B.
AU  - Saunders, J.R.
TI  - RsrII:  a restriction endonuclease with a heptanucleotide recognition sequence.
JO  - Methods Enzymol.
PY  - 1987
SP  - 11
EP  - 15
VL  - 155
AB  - The purple nonsulfur photosynthetic bacterium Rhodopseudomonas sphaeroides 630
AB  - produces two restriction endonucleases, RsrI and RsrII, that can be isolated
AB  - free of contaminating endonucleases and exonucleases.  Although RsrI is an
AB  - isoschizomer of the well-characterized Escherichia coli restriction enzyme
AB  - EcoRI, RsrII is the only enzyme described to date that recognizes and cleaves a
AB  - palindromic heptanucleotide sequence.  We describe here an improved procedure
AB  - for the purification of RsrII and discuss some uses of the enzymes.
ER  -

TY  - JOUR
AU  - O'Connor, T.J.
AU  - Adepoju, Y.
AU  - Boyd, D.
AU  - Isberg, R.R.
TI  - Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 14733
EP  - 14740
VL  - 108
AB  - Legionella pneumophila is a bacterial pathogen of amoebae and humans.
AB  - Intracellular growth requires a type IVB secretion system that
AB  - translocates at least 200 different proteins into host cells. To
AB  - distinguish between proteins necessary for growth in culture and those
AB  - specifically required for intracellular replication, a screen was
AB  - performed to identify genes necessary for optimal growth in nutrient-rich
AB  - medium. Mapping of these genes revealed that the L. pneumophila chromosome
AB  - has a modular architecture consisting of several large genomic islands
AB  - that are dispensable for growth in bacteriological culture. Strains
AB  - lacking six of these regions, and thus 18.5% of the genome, were viable
AB  - but required secondary point mutations for optimal growth. The
AB  - simultaneous deletion of five of these genomic loci had no adverse effect
AB  - on growth of the bacterium in nutrient-rich media. Remarkably, this
AB  - minimal genome strain, which lacked 31% of the known substrates of the
AB  - type IVB system, caused only marginal defects in intracellular growth
AB  - within mouse macrophages. In contrast, deletion of single regions reduced
AB  - growth within amoebae. The importance of individual islands, however,
AB  - differed among amoebal species. The host-specific requirements of these
AB  - genomic islands support a model in which the acquisition of foreign DNA
AB  - has broadened the L. pneumophila host range.
ER  -

TY  - JOUR
AU  - O'Cuiv, P.
AU  - Klaassens, E.S.
AU  - Smith, W.J.
AU  - Mondot, S.
AU  - Durkin, A.S.
AU  - Harkins, D.M.
AU  - Foster, L.
AU  - McCorrison, J.
AU  - Torralba, M.
AU  - Nelson, K.E.
AU  - Morrison, M.
TI  - Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.
JO  - Genome Announcements
PY  - 2013
SP  - e00160
EP  - e00112
VL  - 1
AB  - is commonly isolated from the gastrointestinal tract of healthy infants and adults, where it
AB  - contributes to host health and well-being. We describe here the
AB  - draft genome sequence of PC1.1, a candidate probiotic strain isolated from human
AB  - feces.
ER  -

TY  - JOUR
AU  - O'Cuiv, P.
AU  - Klaassens, E.S.
AU  - Smith, W.J.
AU  - Mondot, S.
AU  - Durkin, A.S.
AU  - Harkins, D.M.
AU  - Foster, L.
AU  - McCorrison, J.
AU  - Torralba, M.
AU  - Nelson, K.E.
AU  - Morrison, M.
TI  - Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces.
JO  - Genome Announcements
PY  - 2014
SP  - e00022
EP  - e00014
VL  - 2
AB  - Enterococcus faecium is commonly isolated from the human gastrointestinal tract;  however,
AB  - important intraspecies variations exist with relevance for host health
AB  - and well-being. Here, we describe the draft genome sequence of E. faecium PC4.1,
AB  - a clade B strain isolated from human feces.
ER  -

TY  - JOUR
AU  - O'Dell, K.B.
AU  - Woo, H.L.
AU  - Utturkar, S.
AU  - Klingeman, D.
AU  - Brown, S.D.
AU  - Hazen, T.C.
TI  - Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm.
JO  - Genome Announcements
PY  - 2015
SP  - e00402
EP  - e00415
VL  - 3
AB  - Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water
AB  - enriched with insoluble organosolv lignin. It was further screened for
AB  - growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic
AB  - liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is
AB  - presented in this report.
ER  -

TY  - JOUR
AU  - O'Donnell, M.M.
AU  - Harris, H.M.
AU  - O'Toole, P.W.
AU  - Ross, R.P.
TI  - The Genome of the Predominant Equine Lactobacillus Species, Lactobacillus equi, Is Reflective of Its Lifestyle Adaptations to an Herbivorous Host.
JO  - Genome Announcements
PY  - 2014
SP  - e01155
EP  - e01113
VL  - 2
AB  - We report the draft genome sequence of Lactobacillus equi strain DPC6820, isolated from equine
AB  - feces. L. equi is a predominant Lactobacillus species in the
AB  - horse hindgut microbiota. An examination of the genome identified genes and
AB  - enzymes highlighting L. equi adaptations to the herbivorous gastrointestinal
AB  - tract of the horse, including fructan hydrolases. This genome sequence may help
AB  - us further understand the microbial ecology of the equine hindgut and the
AB  - influence lactobacilli have on it.
ER  -

TY  - JOUR
AU  - O'Driscoll, J.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
TI  - A dichotomous epigenetic mechanism governs expression of the LlaJI restriction/modification system.
JO  - Mol. Microbiol.
PY  - 2005
SP  - 1532
EP  - 1544
VL  - 57
AB  - The LlaJI restriction/modification (R/M) system is comprised of two 5mC MTase-encoding genes,
AB  - llaJIM1 and llaJIM2, and two genes required for
AB  - restriction activity, llaJIR1 and llaJIR2. Here, we report the
AB  - molecular mechanism by which this R/M system is transcriptionally
AB  - regulated. The recognition sequence for the LlaJI MTases was deduced to
AB  - be 5'GACGC'3 for M1.LlaJI and 5'GCGTC'3 for M2.LlaJI, thus together
AB  - constituting an asymmetric complementary recognition site. Two
AB  - recognition sequences for both LlaJI MTases are present within the
AB  - LlaJI promoter region, indicative of an epigenetic role. Following in
AB  - vivo analysis of expression of the LlaJI promoter, we established that
AB  - both LlaJI MTases were required for complete transcriptional
AB  - repression. A mutational analysis and DNA binding studies of this
AB  - promoter revealed that the methylation of two specific cytosines by
AB  - M2.LlaJI within this region was required to trigger the specific and
AB  - high affinity binding of M1.LlaJI, which serves to regulate expression
AB  - of the LlaJI operon. This regulatory system therefore represents the
AB  - amalgamation of an epigenetic stimulation coupled to the formation of a
AB  - MTase/repressor:promoter complex.
ER  -

TY  - JOUR
AU  - O'Driscoll, J.
AU  - Glynn, F.
AU  - Cahalane, O.
AU  - O'Connell-Motherway, M.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
TI  - Lactococcal plasmid pNP40 encodes a novel, temperature-sensitive restriction-modification system.
JO  - Appl. Environ. Microbiol.
PY  - 2004
SP  - 5546
EP  - 5556
VL  - 70
AB  - A novel restriction-modification system, designated LlaJI, was identified on pNP40, a
AB  - naturally occurring 65-kb plasmid from Lactococcus lactis. The system comprises four adjacent
AB  - similarly oriented genes that are predicted to encode two m(5)C methylases and two restriction
AB  - endonucleases. The LlaJI system, when cloned into a low-copy-number vector, was shown to
AB  - confer resistance against representatives of the three most common lactococcal phage species.
AB  - This phage resistance phenotype was found to be strongly temperature dependent, being most
AB  - effective at 19 degrees C. A functional analysis confirmed that the predicted
AB  - methylase-encoding genes, llaJIM1 and llaJIM2, were both required to mediate complete
AB  - methylation, while the assumed restriction enzymes, specified by llaJIR1 and llaJIR2, were
AB  - both necessary for the complete restriction phenotype. A Northern blot analysis revealed that
AB  - the four LlaJI genes are part of a 6-kb operon and that the relative abundance of the
AB  - LlaJI-specific mRNA in the cells does not appear to contribute to the observed
AB  - temperature-sensitive profile. This was substantiated by use of a LlaJI promoter-lacZ fusion,
AB  - which further revealed that the LlaJI operon appears to be subject to transcriptional
AB  - regulation by an as yet unidentified element(s) encoded by pNP40.
ER  -

TY  - JOUR
AU  - O'Driscoll, J.
AU  - Glynn, F.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
TI  - Sequence Analysis of the Lactococcal Plasmid pNP40: a Mobile Replicon for Coping with Environmental Hazards.
JO  - J. Bacteriol.
PY  - 2006
SP  - 6629
EP  - 6639
VL  - 188
AB  - The conjugative lactococcal plasmid pNP40, identified in Lactococcus lactis subsp.
AB  - diacetylactis DRC3, possesses a potent complement of bacteriophage resistance systems, which
AB  - has stimulated its application as a fitness-improving, food-grade genetic element for
AB  - industrial starter cultures. The complete sequence of this plasmid allowed the mapping of
AB  - previously known functions including replication, conjugation, bacteriocin resistance, heavy
AB  - metal tolerance, and bacteriophage resistance. In addition, functions for cold shock
AB  - adaptation and DNA damage repair were identified, further confirming pNP40's contribution to
AB  - environmental stress protection. A plasmid cointegration event appears to have been part of
AB  - the evolution of pNP40, resulting in a "stockpiling" of bacteriophage resistance systems.
ER  -

TY  - JOUR
AU  - O'Driscoll, J.
AU  - Heiter, D.F.
AU  - Wilson, G.G.
AU  - Fitzgerald, G.F.
AU  - Roberts, R.
AU  - van Sinderen, D.
TI  - A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system.
JO  - BMC Microbiol.
PY  - 2006
SP  - 40
EP  - 40
VL  - 6
AB  - ABSTRACT: BACKGROUND: Restriction/modification systems provide the dual function of protecting
AB  - host DNA against restriction by methylation of appropriate bases within their recognition
AB  - sequences, and restriction of foreign invading un-methylated DNA, such as promiscuous plasmids
AB  - or infecting bacteriphage. The plasmid-encoded LlaJI restriction/modification system from
AB  - Lactococcus lactis recognizes an asymmetric, complementary DNA sequence, consisting of
AB  - 5-GACGC-3 in one strand and 5-GCGTC-3 in the other and provides a prodigious barrier to
AB  - bacteriophage infection. LlaJI is comprised of four similarly oriented genes, encoding two
AB  - 5mC-MTases (M1.LlaJI and M2.LlaJI) and two subunits responsible for restriction activity
AB  - (R1.LlaJI and R2.LlaJI). Here we employ a detailed genetic analysis of the LlaJI restriction
AB  - determinants in an attempt to characterize mechanistic features of this unusual
AB  - hetero-oligomeric endonuclease. RESULTS: Detailed bioinformatic analysis confirmed the
AB  - presence of a conserved GTP binding and hydrolysis domain within the C-terminal half of the
AB  - R1.LlaJI amino acid sequence whilst the N-terminal half appeared to be entirely unique. This
AB  - domain architecture was homologous with that of the B subunit of the GTP-dependent,
AB  - methyl-specific McrBC endonuclease from E.coli K-12. R1.LlaJI did not appear to contain a
AB  - catalytic centre, whereas this conserved motif; PD...D/EXK, was clearly identified within the
AB  - amino acid sequence for R2.LlaJI. Both R1.LlaJI and R2.LlaJI were found to be absolutely
AB  - required for detectable LlaJI activity in vivo. The LlaJI restriction subunits were purified
AB  - and examined in vitro, which allowed the assignment of R1.LlaJI as the sole specificity
AB  - determining subunit, whilst R2.LlaJI is believed to mediate DNA cleavage. CONCLUSIONS: The
AB  - hetero-subunit structure of LlaJI, wherein one subunit mediates DNA binding whilst the other
AB  - subunit is predicted to catalyze strand hydrolysis distinguishes LlaJI from previously
AB  - characterized restriction-modification systems. Furthermore, this distinction is accentuated
AB  - by the fact that whilst LlaJI behaves as a conventional Type IIA system in vivo, in that it
AB  - restricts un-methylated DNA, it resembles the Type IV McrBC endonuclease, an enzyme specific
AB  - for methylated DNA. A number of similar restriction determinants were identified in the
AB  - database and it is likely LlaJI together with these homologous systems, comprise a new subtype
AB  - of the Type II class incorporating features of Type II and Type IV systems.
ER  -

TY  - JOUR
AU  - O'Gara, M.
AU  - Adams, G.M.
AU  - Gong, W.
AU  - Kobayashi, R.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
JO  - Eur. J. Biochem.
PY  - 1997
SP  - 1009
EP  - 1018
VL  - 247
AB  - The type II DNA-methyltransferase (cytosine N4-specific) M.PvuII was overexpressed in
AB  - Escherichia coli, starting from the internal translation initiator at Met14.  Selenomethionine
AB  - was efficiently incorporated into this short form of M.PvuII by a strain prototrophic for
AB  - methionine.  Both native and selenomethionyl M.PvuII were purified to apparent homogeneity by
AB  - a two-column chromatography procedure.  The yield of purified protein was approximately 1.8
AB  - mg/g bacterial paste.  Mass spectrometry analysis of selenomethionyl M.PvuII revealed three
AB  - major forms that probably differ in the degree of selenomethionine incorporation and the
AB  - extent of selenomethionine oxidation.  Amino acid sequencing and mass spectrometry analysis of
AB  - selenomethionine-containing peptides suggests that Met30, Met51, and Met261 were only
AB  - partially replaced by selenomethionine.  Furthermore, amino acid 261 may be preferentially
AB  - oxidized in both native and selenomethionyl form.  Selenomethionyl and native M.PvuII were
AB  - crystallized separately as binary complexes of the methyl donor S-adenosyl-L-methionine in the
AB  - monoclinic space group P21.  Two complexes were present per asymmetric unit.  Six out of nine
AB  - selenium positions (per molecule), including the three that were found to be partially
AB  - substituted, were identified crystallographically.
ER  -

TY  - JOUR
AU  - O'Gara, M.
AU  - Horton, J.R.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
JO  - Nat. Struct. Biol.
PY  - 1998
SP  - 872
EP  - 877
VL  - 5
AB  - Three structures have been determined for complexes between HhaI methyltransferase (M.HhaI)
AB  - and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic)
AB  - mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all
AB  - flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the
AB  - same conformation as in the flipped-out normal substrate. These results, particularly the
AB  - flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If
AB  - the process involves the protein pushing the base out of the helix, then the push must take
AB  - place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA
AB  - backbone is probably the key to base flipping.
ER  -

TY  - JOUR
AU  - O'Gara, M.
AU  - Klimasauskas, S.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 634
EP  - 645
VL  - 261
AB  - The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated
AB  - or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved
AB  - binary and covalent ternary structures, offer a detailed picture of the active site at
AB  - individual stages throughout the reaction cycle.  This picture supports and extends a proposed
AB  - mechanism for C5-cytosine methylation that may be general for the whole family of C5-cytosine
AB  - methyltransferases.  The structures of the two new complexes have been refined to
AB  - crystallographic R-factors of 0.189 and 0.178, respectively, at 2.7 A resolution.  We observe
AB  - that both unmethylated 2'-deoxycytidine and 5-methyl-2'-deoxycytidine flip out of the DNA
AB  - helix and fit into the active site of the enzyme.  The catalytic sulfur atom of Cys81
AB  - interacts strongly with C6.  The C5 methyl group of the flipped 5-methyl-2'-deoxycytidine is
AB  - bent ~50o out of the plane of the cytosine ring and towards the sulfur atom of
AB  - S-adenosyl-L-homocysteine.  This unusual position is probably due to partial sp3 character at
AB  - C5 and C6 and to steric effects of the conserved amino acid residues Pro80 and Cys81.  Two
AB  - water molecules are held near the hydrophobic edge (C5 and C6) of the flipped cytosine by two
AB  - conserved amino acid residues (Gln82 and Asn304) and the phosphoryl oxygen atom of the
AB  - phosphate group 3' to the flipped nucleotide, and one of them may serve as the general base
AB  - for eliminating the proton from C5.  Protonation of the cytosine N3 during the methylation
AB  - reaction may involve Glu119, which itself might be protonated via a water-mediated interaction
AB  - between the terminal carboxyl group of Glu119 and the amino group of the methionine moiety of
AB  - S-adenosyl-L-methionine.  The cofactor thus plays two key roles in the reaction.
ER  -

TY  - JOUR
AU  - O'Gara, M.
AU  - McCloy, K.
AU  - Malone, T.
AU  - Cheng, X.
TI  - Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases.
JO  - Gene
PY  - 1995
SP  - 135
EP  - 138
VL  - 157
AB  - M.HhaI, M.TaqI and COMT are DNA methyltransferases (MTases) which catalyze the transfer of a
AB  - methyl group from the cofactor AdoMet to C5 of cytosine, to N6 of adenine and to a hydroxyl
AB  - group of catechol, respectively.  The larger catalytic domains of the bilobal proteins, M.HhaI
AB  - and M.TaqI, and the entire single domain of COMT have an alpha/beta structure containing a
AB  - mixed central beta-sheet.  These domains have very similar folding.  By allowing appropriate
AB  - 'insertions' or 'deletions' in the bakbones of the three structures, it was possible to
AB  - find more conserved motifs in M.TaqI and COMT.  The similarity in protein folding and the
AB  - equivalence of amino-acid sequences revealed by the structural alignment indicate that many
AB  - AdoMet-dependent MTases may share a common catalytic domain structure.
ER  -

TY  - JOUR
AU  - O'Gara, M.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 597
EP  - 606
VL  - 263
AB  - The crystal structure of HhaI methyltransferase complexed with non-palindromic duplex DNA,
AB  - containing a hemimethylated recognition sequence, and with the cofactor analog
AB  - S-adenosyl-L-homocysteine (AdoHcy), has been determined.  The structure provides an
AB  - explanation for the stronger affinities of DNA methyltransferases for hemimethylated DNA than
AB  - for unmethylated or fully methylated DNA in the presence of AdoHcy.  The unmethylated target
AB  - 2'-deoxycytidine flips out of the DNA helix and the CH group at position 5 makes van der
AB  - Waals' contacts with the sulfur atom of AdoHcy.  Selectivity/preference for hemimethylated
AB  - over fully methylated DNA may thus reflect interactions among the chemical substituent (H or
AB  - CH3) at the C5 position of the flipped cytosine, protein and the bound AdoHcy.  The
AB  - 5-methyl-2'-deoxycytidine on the complementary strand remains in the DNA helix, with the
AB  - methyl group almost perpendicular to the carboxylate group of Glu239, which is part of the
AB  - sequence recognition loop.  Thus, selectivity/preference for hemimethylated over unmethylated
AB  - DNA appears to result largely from van der Waals' contacts between the planar Glu239
AB  - carboxylate and the methyl group of the 5-methyl-2'-deoxycytidine.  Furthermore, the positive
AB  - electrostatic potential originating from the bound AdoHcy extends to the DNA phosphate groups
AB  - flanking the flipped cytosine.  The increased binding to DNA by long-range electrostatic
AB  - interactions should also occur with the methyl donor S-adenosyl-L-methionine.
ER  -

TY  - JOUR
AU  - O'Gara, M.
AU  - Zhang, X.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 201
EP  - 209
VL  - 287
AB  - We have determined a structure for a complex formed between HhaI methyltransferase and
AB  - S-adenosyl-L-methionine in the presence of a non-specific short oligonucleotide.  M.HhaI binds
AB  - to the non-specific short oligonucleotides in solution.  Although no DNA is incorporated in
AB  - the crystal, AdoMet binds in a primed orientation, identical with that observed in the ternary
AB  - complex of the enzyme, cognate DNA, and AdoMet or S-adenosyl-L-homocysteine.  This orientation
AB  - differs from the previously observed unprimed orientation in the M.HhaI-AdoMet binary complex,
AB  - where the S+-CH3 unit of AdoMet is protected by a favorable cation-pi interaction with Trp41.
AB  - The structure suggests that the presence of DNA can guide AdoMet into the primed orientation.
AB  - These results shed new light on the proposed ordered mechanism of binding and explains the
AB  - stable association between Ado-Met and M.HhaI.
ER  -

TY  - JOUR
AU  - O'Hair, J.A.
AU  - Li, H.
AU  - Thapa, S.
AU  - Scholz, M.
AU  - Zhou, S.
TI  - Draft Genome Sequences of Three Cellulolytic Bacillus licheniformis Strains Isolated from Imperial Geyser, Amphitheater Springs, and Whiterock Springs inside  Yellowstone National Park.
JO  - Genome Announcements
PY  - 2017
SP  - e00065
EP  - e00017
VL  - 5
AB  - Novel cellulolytic microorganisms are becoming more important for rapidly growing biofuel
AB  - industries. This paper reports the draft genome sequences of Bacillus licheniformis strains
AB  - YNP2-TSU, YNP3-TSU, and YNP5-TSU. These cellulolytic isolates were collected from several
AB  - hydrothermal features inside Yellowstone National Park.
ER  -

TY  - JOUR
AU  - O'Hair, J.A.
AU  - Li, H.
AU  - Thapa, S.
AU  - Scholz, M.B.
AU  - Zhou, S.
TI  - Draft Genome Sequence of Bacillus licheniformis Strain YNP1-TSU Isolated from Whiterock Springs in Yellowstone National Park.
JO  - Genome Announcements
PY  - 2017
SP  - e01496
EP  - e01416
VL  - 5
AB  - Novel cellulolytic microorganisms can potentially influence second-generation biofuel
AB  - production. This paper reports the draft genome sequence of Bacillus
AB  - licheniformis strain YNP1-TSU, isolated from hydrothermal-vegetative microbiomes
AB  - inside Yellowstone National Park. The assembled sequence contigs predicted 4,230
AB  - coding genes, 66 tRNAs, and 10 rRNAs through automated annotation.
ER  -

TY  - JOUR
AU  - O'Hara-Hanley, K.
AU  - Harrison, A.
AU  - Soby, S.D.
TI  - Draft Genomic Sequences of Chromobacterium sp. nov. Strains MWU13-2610 and MWU14-2602, Isolated from Wild Cranberry Bogs in Massachusetts.
JO  - Genome Announcements
PY  - 2018
SP  - e00332
EP  - e00318
VL  - 6
AB  - Chromobacterium sp. nov. strains MWU13-2610 and MWU14-2602 were isolated from cranberry bogs
AB  - in the Cape Cod National Seashore. These nonpigmented bacteria
AB  - represent two new presumptive species of the rapidly growing genus
AB  - Chromobacterium Gene homologs are present for multiple antibiotic resistance,
AB  - virulence functions, and prophages.
ER  -

TY  - JOUR
AU  - O'Loughlin, J.L.
AU  - Eucker, T.P.
AU  - Chavez, J.D.
AU  - Samuelson, D.R.
AU  - Neal-McKinney, J.
AU  - Gourley, C.R.
AU  - Bruce, J.E.
AU  - Konkel, M.E.
TI  - Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.
JO  - PLoS ONE
PY  - 2015
SP  - e0118533
EP  - e0118533
VL  - 10
AB  - Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. The goal of this
AB  - study was to analyze the C. jejuni F38011 strain, recovered from an
AB  - individual with severe enteritis, at a genomic and proteomic level to gain
AB  - insight into microbial processes. The C. jejuni F38011 genome is comprised of
AB  - 1,691,939 bp, with a mol.% (G+C) content of 30.5%. PacBio sequencing coupled with
AB  - REBASE analysis was used to predict C. jejuni F38011 genomic sites and enzymes
AB  - that may be involved in DNA restriction-modification. A total of five putative
AB  - methylation motifs were identified as well as the C. jejuni enzymes that could be
AB  - responsible for the modifications. Peptides corresponding to the deduced amino
AB  - acid sequence of the C. jejuni enzymes were identified using proteomics. This
AB  - work sets the stage for studies to dissect the precise functions of the C. jejuni
AB  - putative restriction-modification enzymes. Taken together, the data generated in
AB  - this study contributes to our knowledge of the genomic content, methylation
AB  - profile, and encoding capacity of C. jejuni.
ER  -

TY  - JOUR
AU  - O'Loughlin, T.J.
AU  - Xu, Q.
AU  - Kucera, R.B.
AU  - Dorner, L.F.
AU  - Sweeney, S.
AU  - Schildkraut, I.
AU  - Guo, H.-C.
TI  - Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2000
SP  - 1652
EP  - 1655
VL  - 56
AB  - The MspI restriction endonuclease is a type II restriction enzyme. Unlike all other
AB  - restriction enzymes with known structures, MspI recognizes the palindromic tetranucleotide
AB  - sequence 5'-C/CGG and cleaves it as indicated by the '/' to produce DNA products with 5'
AB  - two-base overhangs. Owing to the nature of its cleavage pattern, it is likely that MspI would
AB  - represent a new structural class of restriction endonucleases.  Crystals of the dimeric MspI
AB  - restriction enzyme bound to a duplex DNA molecule containing the specific recognition sequence
AB  - have been obtained by vapor-diffusion techniques in the presence of polyethylene glycol as
AB  - precipitant. The crystals belong to the monoclinic space group P2(1), with unit-cell
AB  - parameters a = 50.2, b = 131.6, c = 59.3 Angstroms, beta = 109.7 degrees. The crystals contain
AB  - one dimeric complex in the asymmetric unit.  A complete native data set has been collected to
AB  - a resolution of 2.05 Angstroms by cryo-crystallographic methods, with an R(merge) of 4.0%.
ER  -

TY  - JOUR
AU  - O'Neill, M.
AU  - Chen, A.
AU  - Murray, N.E.
TI  - The restriction-modification genes of Escherichia coli K-12 may not be selfish: They do not resist loss and are readily replaced by alleles conferring different specificities.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 14596
EP  - 14601
VL  - 94
AB  - Type II restriction and modification genes have been described as selfish because they have
AB  - been shown to impose selection for the maintenance of the plasmid that encodes them. In our
AB  - experiments, the type I R-M system EcoKI does not behave in the same way.  The genes
AB  - specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses
AB  - were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector.
AB  - If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss
AB  - of the relevant chromosomal genes by mutation of recombination should lead to cell death
AB  - because the cell would become deficient in modification enzyme and the bacterial chromosome
AB  - would be vulnerable to the restriction endonuclease.  Our data contradict this prediction;
AB  - they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant
AB  - alleles and by alleles encoding a type I R-M system of different specificity.  The acquisition
AB  - of allelic genes conferring a new sequence specificity, but not the loss of the resident
AB  - genes, is dependent on the product of an unlinked gene, one predicted to be relevant to
AB  - control of expression of the genes that encode EcoKI.  Our evidence suggests that not all R-M
AB  - systems are evolving as "selfish" units; rather, the diversity and distribution of the family
AB  - of type I enzymes we have investigated require an alternative selective pressure.
ER  -

TY  - JOUR
AU  - O'Neill, M.
AU  - Dryden, D.T.F.
AU  - Murray, N.E.
TI  - Localization of a protein-DNA interface by random mutagenesis.
JO  - EMBO J.
PY  - 1998
SP  - 7118
EP  - 7127
VL  - 17
AB  - The type I restriction and modification enzymes do not possess obvious DNA-binding motifs
AB  - within their target recognition domains of 150-180 amino acids.  To identify residues involved
AB  - in DNA recognition, changes were made in the amino-TRD of EcoKI by random mutagenesis.  Most
AB  - of the 101 substitutions affecting 79 residues had no effect on the phenotype.  Changes at
AB  - only seven positions caused the loss of restriction and modification activities.  The seven
AB  - residues identified by mutation are not randomly distributed throughout the primary sequence
AB  - of the TRD: five are within the interval between residues 80 and 110.  Sequence analyses have
AB  - led to the suggestion that the TRDs of type I restriction enzymes include a tertiary structure
AB  - similar to the TRD of the HhaI methyltransferase, and to a model for a DNA-protein interface
AB  - in EcoKI.  In this model, the residues within the interval identified by the five mutations
AB  - are close to the protein-DNA interface.  Three additional residues close to the DNA in the
AB  - model were changed; each substitution impaired both activities.  Proteins from twelve mutants
AB  - were purified: six from mutants with partial or wild-type activity and six from mutants
AB  - lacking activity.  There is a strong correlation between phenotype and DNA-binding affinity,
AB  - as determined by fluorescence anisotropy.
ER  -

TY  - JOUR
AU  - O'Neill, M.
AU  - Powell, L.M.
AU  - Murray, N.E.
TI  - Target recognition by EcoKI: the recognition domain is robust and restriction-deficiency commonly results from the proteolytic control of enzyme activity.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 951
EP  - 963
VL  - 307
AB  - We report a genetic and biochemical analysis of a target recognition domain (TRD) of EcoKI, a
AB  - type I restriction and modification enzyme. The TRDs of type I R-M systems are within the
AB  - specificity subunit (HsdS) and HsdS confers sequence specificity to a complex endowed with
AB  - both restriction and modification activities. Random mutagenesis has revealed that most
AB  - substitutions within the amino TRD of EcoKI, a region comprising 157 amino acid residues, have
AB  - no detectable effect on the phenotype of the bacterium, even when the substitutions are non-
AB  - conservative. The structure of the TRD appears to be robust. All but one of the six
AB  - substitutions that confer a restriction-deficient, modification-deficient (r(-)m(-)) phenotype
AB  - were found to be in the interval between residues 80 and 110, a region predicted by sequence
AB  - comparisons to form part of the protein-DNA interface. Additional site-directed mutations
AB  - affecting this interval commonly impair both restriction and modification. However, we show
AB  - that an r(-) phenotype cannot be taken as evidence that the EcoKI complex lacks endonuclease
AB  - activity; in response to even a slightly impaired modification efficiency, the endonuclease
AB  - activity of EcoKI is destroyed by a process dependent upon the ClpXP protease. Enzymes from
AB  - mutants with an r(-)m(-) phenotype commonly retain some sequence-specific activity; methylase
AB  - activity can be detected on hemimethylated DNA substrates and residual endonuclease activity
AB  - is implied whenever the viability of the r(-)m(-) bacterium is dependent on ClpXP. Conversely,
AB  - the viability of ClpX(-) r(-)m(-) bacteria can be used as evidence for little, or no,
AB  - endonuclease activity. Of 14 mutants with an r(-)m(-) phenotype, only six are viable in the
AB  - absence of ClpXP. The significance of four of the six residues (G91, G105, F107 and G141) is
AB  - enhanced by the finding that even conservative substitutions for these residues impair
AB  - modification, thereby conferring an r(-)m(-) phenotype.
ER  -

TY  - JOUR
AU  - O'Sullivan, D.
AU  - Coffey, A.
AU  - Fitzgerald, G.F.
AU  - Hill, C.
AU  - Ross, R.P.
TI  - Design of a phage-insensitive lactococcal dairy starter via sequential transfer of naturally occurring conjugative plasmids.
JO  - Appl. Environ. Microbiol.
PY  - 1998
SP  - 4618
EP  - 4622
VL  - 64
AB  - The plasmid-free Lactococcus lactis subsp. cremoris MG1614 is highly phage sensitive and lacks
AB  - lactose fermenting ability (Lac) and primary casein degrading ability (Prt). Food grade gene
AB  - transfer systems were used to sequentially superimpose different phage defense systems on this
AB  - background, resulting in a gradual increase in resistance to bacteriophage in the derivatives.
AB  - pLP712, encoding Lac and Prt, was then transferred to one of these hosts, into which plasmids
AB  - encoding adsorption inhibition, restriction modification, and abortive infection had already
AB  - been introduced. This resulted in a phage-resistant strain which was successfully used as a
AB  - single-strain starter for cheddar cheese manufacture under industrial conditions.
ER  -

TY  - JOUR
AU  - O'Sullivan, D.
AU  - Ross, R.P.
AU  - Twomey, D.P.
AU  - Fitzgerald, G.F.
AU  - Hill, C.
AU  - Coffey, A.
TI  - Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable markerpotential use to impart phage resistance to dairy fermentation starter culture.
JO  - Appl. Environ. Microbiol.
PY  - 2001
SP  - 929
EP  - 937
VL  - 67
AB  - Phage resistance plasmid pAH90 (26,490 bp) of Lactococcus lactis subsp. lactis biovar.
AB  - diacetylactis DPC721 is a natural cointegrate plasmid
AB  - formed by homologous recombination between the type I
AB  - restriction-modification specificity determinants (hsdS) of plasmid
AB  - pAH33 (6,159 bp) and plasmid pAH82 (20,331 bp), giving rise to a
AB  - phage-sensitive mutant following phage challenge. The recombinant event
AB  - is favored by phage infection. The nucleotide sequence of pAH90 was
AB  - determined, identifying 24 open reading frames responsible for
AB  - restriction-modification, phage adsorption inhibition, plasmid
AB  - replication, cadmium resistance, cobalt transport and conjugative
AB  - mobilization phenotypes. The cadmium resistance property, encoded by
AB  - the cadA gene, facilitated the selection of pAH90 in other
AB  - phage-sensitive lactococci after electroporation. The fortuitous
AB  - association of multiple phage resistance systems, which acted at
AB  - different stages in the phage lytic cycle, with a food-grade selectable
AB  - marker on a mobilizable plasmid makes pAH90 an ideal candidate for use
AB  - in food-grade starter culture improvement in industrial dairy
AB  - fermentations.
ER  -

TY  - JOUR
AU  - O'Sullivan, D.
AU  - Twomey, D.P.
AU  - Coffey, A.
AU  - Hill, C.
AU  - Fitzgerald, G.F.
AU  - Ross, R.P.
TI  - Novel type I restriction specificities through domain shuffling of HsdS subunits in lactococcus lactis.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 866
EP  - 875
VL  - 36
AB  - This study identifies a natural system in Lactococcus lactis, in which a restriction
AB  - modification specificity subunit resident on a 6159 bp plasmid (pAH33) alters the specificity
AB  - of a functional R/M mechanism encoded by a 20.3 kb plasmid, pAH82. The new specificity was
AB  - identified after phenotypic and molecular analysis of a 26.5 kb co-integrate plasmid (pAH90),
AB  - which was detected after bacteriophage challenge of the parent strain. Analysis of the regions
AB  - involved in the co-integration revealed that two novel hybrid hsdS genes had been formed
AB  - during the co-integration event. The HsdS chimeras had interchanged the C- and N-terminal
AB  - variable domains of the parent subunits, generating two new restriction specificities.
AB  - Comparison of the parent hsdS genes with other type I specificity determinants revealed that
AB  - the region of the hsdS genes responsible for the co-integration event is highly conserved
AB  - among lactococcal type I hsdS determinants. Thus, as hsdS determinants are widespread in the
AB  - genus Lactococcus, new restriction specificities may evolve rapidly after homologous
AB  - recombination between these genes. This study demonstrates that, similar to previous
AB  - observations in Gram-negative bacteria, a Gram-positive bacterium can acquire novel
AB  - restriction specificities naturally through domain shuffling of resident HsdS subunits.
ER  -

TY  - JOUR
AU  - O'Sullivan, D.J.
AU  - Klaenhammer, T.R.
TI  - C.LlaI is a bifunctional regulatory protein of the LlaI restriction modification operon from Lactococcus lactis.
JO  - Dev. Biol. Stand.
PY  - 1995
SP  - 591
EP  - 595
VL  - 85
AB  - Strains of Lactococcus lactis are used commercially as starter bacteria in dairy
AB  - fermentations.  Bacteriophage attack of these bacteria represents a major problem in the
AB  - industry.  Plasmid-borne phage resistance traits have been found naturally in some strains and
AB  - the mobilization of these plasmids into desired industrial starter strains has provided a
AB  - dynamic new source of cultures in the industry.  One of these plasmids, pTR2030, has been
AB  - studied extensively in this laboratory and shown to encode two phage-resistance determinants;
AB  - the AbiA abortive infection mechanism and the LlaI restriction modification system.  The LlaI
AB  - methylase is a bifunctional type IIS methylase with 39% identity to M.FokI and is encoded by
AB  - 1.9 kb on pTR2030, ~5 kb upstream from the abiA gene.  The LlaI restriction component is
AB  - encoded by three genes, llaI.1, llaI.2, llaI.3, positioned downstream from llaIM. A
AB  - GTP-binding site on the deduced protein from llaI.2 suggests that LlaI restriction is probably
AB  - energy-dependent.  Data bank searches did not reveal any significant homologies with these
AB  - deduced proteins, except for the GTP-binding motif on LlaI.2 with a corresponding motif on the
AB  - Escherichia coli McrB protein, which is part of a GTP-dependent, multi-subunit restriction
AB  - enzyme.  From the molecular studies on the LlaI R/M system, it is suggested that the LlaI
AB  - restriction enzyme is a novel type with properties reminiscent of both type IIS and type I
AB  - enzymes.
ER  -

TY  - JOUR
AU  - O'Sullivan, D.J.
AU  - Klaenhammer, T.R.
TI  - Control of expression of LlaI restriction in Lactococcus lactis.
JO  - Mol. Microbiol.
PY  - 1998
SP  - 1009
EP  - 1020
VL  - 27
AB  - The plasmid encoded LlaI R/M sytem from Lactococcus lactis ssp. lactis consists of a bidomain
AB  - methylase, with close evolutionary ties to type IIS methylases, and a tri-subunit restriction
AB  - complex.  Both the methylase and restriction subunits are encoded on a polycistronic 6.9 kb
AB  - operon.  In this study, the 5' end of the llaI 6.9 kb transcript was determined by primer
AB  - extension analysis to be 254 bp upstream from the first R/M gene on the operon, llaIM.
AB  - Deletion of this promoter region abolished LlaI restriction in L. lactis.  Analysis of the
AB  - intervening sequence revealed a 72-amino-acid open reading frame, designated llaIC, with a
AB  - conserved ribosome binding site and helix-turn-helix domain.  Overexpression of llaIC in
AB  - Escherichia coli with a T7 expression vector produced the predicted protein of 8.2 kDa.
AB  - Mutation and in trans complementation analysis indicated that C.LlaI positively enhanced LlaI
AB  - restriction activity in vivo.  Northern analysis and transcriptional fusions of the llaI
AB  - promoter to a lacZ reporter gene indicated that C.LlaI did not enhance transcription of the
AB  - llaI operon.  Databank searches with the deduced protein sequence for llaIC revealed
AB  - significant homologies to the E. coli Rop regulatory and mRNA stabilizer protein.
AB  - Investigation of the effect of C.LlaI on enhancement of LlaI restriction in L. lactis revealed
AB  - that growth at elevated temperatures (40oC) completely abolished any enhancement of
AB  - restriction activity.  These data provide molecular evidence for a mechanism on how the
AB  - expression of a restriction system in a prokaryote can be drastically reduced during elevated
AB  - growth temperatures, by a small regulatory protein.
ER  -

TY  - JOUR
AU  - O'Sullivan, D.J.
AU  - Zagula, K.
AU  - Klaenhammer, T.R.
TI  - In vivo restriction by LlaI is encoded by three genes, arranged in an operon with llaIM, on the conjugative Lactococcus plasmid pTR2030.
JO  - J. Bacteriol.
PY  - 1995
SP  - 134
EP  - 143
VL  - 177
AB  - The LlaI restriction and modification (R/M) system is encoded on pTR2030, a 46.2-kb
AB  - conjugative plasmid from Lactococcus lactis. The llaI methylase gene, sequenced previously,
AB  - encodes a functional type IIS methylase and is located approximately 5 kb upstream from the
AB  - abiA gene, encoding abortive phage resistance. In this study, the sequence of the region
AB  - between llaIM and abiA was determined and revealed four consecutive open reading frames
AB  - (ORFs). Northern (RNA) analysis showed that the four ORFs were part of a 7-kb operon with llaM
AB  - and the downstream abiA gene on a separate transcriptional unit. The deduced protein sequence
AB  - of ORF2 revealed a P-loop consensus motif for ATP/GTP-binding sites and a three-part consensus
AB  - motif for GTP-binding proteins. Data bank searches with the deduced protein sequences for all
AB  - four ORFs revealed no homology except for ORF2 with McrB, in three regions that coincided with
AB  - the GTP-binding motifs in both proteins. To phenotypically analyze the llaI operon, a 9.0-kb
AB  - fragment was cloned into a high-copy-number lactococcal shuttle vector, pTRKH2. The resulting
AB  - construct, pTRK370, exhibited a significantly higher level of in vivo restriction and
AB  - modification in L. lactis NCK203 than the low-copy-number parental plasmid, pTR2030. A
AB  - combination of deletion constructions and frameshift mutations indicated that the first three
AB  - ORFs were involved in LlaI restriction, and they were therefore designated llaI.1, llaI.2, and
AB  - llaI.3. Mutating llaI.1 completely abolished restriction, while disrupting llaI.2 or llaI.3
AB  - allowed an inefficient restriction of phage DNA to occur, manifested primarily by a variable
AB  - plaque phenotype. ORF4 had no discernible effect on in vivo restriction. A frameshift mutation
AB  - in llaIM proved lethal to L. lactis NCK203, implying that the restriction component was active
AB  - without the modification subunit. These results suggested that the LlaI R/M system is unlike
AB  - any other R/M system studied to date and has diverged from the type IIS class of restriction
AB  - enzymes by acquiring some characteristics reminiscent of type I enzymes.
ER  -

TY  - JOUR
AU  - O'Sullivan, O.
AU  - O'Callaghan, J.
AU  - Sangrador-Vegas, A.
AU  - McAuliffe, O.
AU  - Slattery, L.
AU  - Kaleta, P.
AU  - Callanan, M.
AU  - Fitzgerald, G.F.
AU  - Ross, R.P.
AU  - Beresford, T.
TI  - Comparative genomics of lactic acid bacteria reveals a niche-specific gene set.
JO  - BMC Microbiol.
PY  - 2009
SP  - 50
EP  - 50
VL  - 9
AB  - Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 [1] revealed a
AB  - dairy organism with significant homology (75% of
AB  - genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM [2].
AB  - This led us to hypothesise that a group of genes could be determined
AB  - which could define an organism's niche.
AB  - Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as
AB  - our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we
AB  - demonstrated that the presence or absence of certain genes involved in
AB  - sugar metabolism, the proteolytic system, and restriction modification
AB  - enzymes were pivotal in suggesting the niche of a strain. We identified
AB  - 9 niche specific genes, of which 6 are dairy specific and 3 are gut
AB  - specific. The dairy specific genes identified in Lactobacillus
AB  - helveticus DPC4571 were lhv 1161 and lhv 1171, encoding components of
AB  - the proteolytic system, lhv 1031 lhv 1152, lhv 1978 and lhv 0028
AB  - encoding restriction endonuclease genes, while bile salt hydrolase
AB  - genes lba 0892 and lba 1078, and the sugar metabolism gene lba 1689
AB  - from Lb. acidophilus NCFM were identified as gut specific genes.
AB  - Conclusion: Comparative analysis revealed that if an organism had
AB  - homologs to the dairy specific geneset, it probably came from a dairy
AB  - environment, whilst if it had homologs to gut specific genes, it was
AB  - highly likely to be of intestinal origin.
AB  - We propose that this "barcode" of 9 genes will be a useful initial
AB  - guide to researchers in the LAB field to indicate an organism's ability
AB  - to occupy a specific niche.
ER  -

TY  - JOUR
AU  - O'Sullivan, T.
AU  - van Sinderen, D.
AU  - Fitzgerald, G.
TI  - Structural and functional analysis of pCI65st, a 6.5 kb plasmid from Streptococcus thermophilus NDI-6.
JO  - Microbiology
PY  - 1999
SP  - 127
EP  - 134
VL  - 145
AB  - The 6.5 kb cryptic plasmid pCI65st from Streptococcus thermophilus NDI-6, a strain isolated
AB  - from the Indian fermented milk dahi, was subcloned and sequenced. Five putative ORFs were
AB  - identified. ORF1 could encode a 315 aa polypeptide almost identical to the RepA protein of
AB  - previously sequenced S. thermophilus plasmids, indicating that pCI65st is one of the pC194
AB  - group of small gram-positive rolling-circle plasmids. ORFs 2 and 4 were virtually identical
AB  - and could specify proteins of approximately 150 aa with significant similarity to the small
AB  - heat-shock proteins described from a variety of gram-positive bacteria. ORF3 could encode a
AB  - 415 aa protein similar to enolase, an enzyme involved in glycolysis and gluconeogenesis. ORF5
AB  - could encode a 412 aa protein which had high similarity to the HsdS (specificity) proteins of
AB  - type I restriction-modification systems. Variants of strain NDI-6 which lacked pCI65st were
AB  - readily isolated after subculture of the parent strain at 32 degrees C. The plasmid-bearing
AB  - parent culture was significantly more resistant to a temperature shift from 42 degrees C to 62
AB  - degrees C than its plasmid-free variant and expressed proteins which corresponded with the
AB  - predicted translation products from ORF2 and ORF4. In addition, plasmid-free mutants were
AB  - lysed in broth by bacteriophages to which the parent culture was resistant.
ER  -

TY  - JOUR
AU  - O'Toole, R.F.
AU  - Johari, B.M.
AU  - Mac, A.M.
AU  - Rogers, T.R.
AU  - Bower, J.E.
AU  - Basu, I.
AU  - Freeman, J.T.
TI  - Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in New Zealand.
JO  - Genome Announcements
PY  - 2014
SP  - e00319
EP  - e00314
VL  - 2
AB  - Extensively drug-resistant (XDR) tuberculosis has now been described in >90 countries
AB  - worldwide. The first case of XDR tuberculosis (XDR-TB) in New Zealand
AB  - was recorded in 2010. We report the draft whole-genome sequence of the New
AB  - Zealand isolate, NZXDR1, and describe a number of single-nucleotide polymorphisms
AB  - that relate to drug resistance.
ER  -

TY  - JOUR
AU  - O-Cuiv, P.
AU  - Klaassens, E.S.
AU  - Durkin, A.S.
AU  - Harkins, D.M.
AU  - Foster, L.
AU  - McCorrison, J.
AU  - Torralba, M.
AU  - Nelson, K.E.
AU  - Morrison, M.
TI  - Draft genome sequence of Bacteroides vulgatus PC510, a strain isolated from human feces.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4025
EP  - 4026
VL  - 193
AB  - Although Bacteroides vulgatus is one of the most prevalent microorganisms in the human
AB  - gastrointestinal tract little is known about the genetic
AB  - potential of this species. Here we describe the annotated draft genome
AB  - sequence of B. vulgatus PC510 isolated from human faeces.
ER  -

TY  - JOUR
AU  - Oakeley, E.J.
TI  - DNA methylation analysis: a review of current methodologies.
JO  - Pharmacol. Ther.
PY  - 1999
SP  - 389
EP  - 400
VL  - 84
AB  - The relationship between levels of DNA methylation and gene activity has been known for some
AB  - time. Many of the early procedures developed gave only
AB  - somewhat limited information about methylation patterns, for example, the total level of
AB  - 5-methyl cytosine in the genome or the frequency of methylation of cytosines within
AB  - certain restriction sites. However, in the last few years, there has been an explosion of
AB  - interest in DNA methylation, and with it, many new and powerful techniques have
AB  - been developed to facilitate its study. In this paper, the key techniques currently available
AB  - are reviewed and the advantages, disadvantages, and potential artifacts of each are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Oakeley, E.J.
AU  - Schmitt, F.
AU  - Jost, J.P.
TI  - Quantification of 5-methylcytosine in DNA by the chloroacetaldehyde reaction.
JO  - Biotechniques
PY  - 1999
SP  - 744
EP  - 746
VL  - 27
AB  - The study of changes in genome-wide levels of DNA methylation has become a key focus for
AB  - understanding the epigenetic regulation of gene expression. Many procedures exist to study DNA
AB  - methylation, falling into two categories: gene-specific and genome-wide. Genome-wide
AB  - methylation analysis is best performed by DNA hydrolysis followed by HPLC; however, it
AB  - requires access to an HPLC machine, which is not always available. Alternative procedures,
AB  - such as the radioactive labeling of CpG sites using SssI DNA methyltransferase, have been
AB  - developed to address this problem, but it can only monitor CpG methylation changes, and CpNpG
AB  - methylation is not detected. Here, we present a method for the analysis of DNA methylation in
AB  - any sequence context by fluorescent labeling. We present control analyses using synthetic
AB  - oligonucleotides of known methylation levels and a comparison of genomic DNA from two
AB  - transgenic tobacco lines known to differ in their methylation levels. The results indicate
AB  - that hygromycin-induced hypermethylation acts equally on all classes of methylatable cytosine,
AB  - perhaps indicating a common mechanism.
ER  -

TY  - JOUR
AU  - Oakeson, K.F.
AU  - Gil, R.
AU  - Clayton, A.L.
AU  - Dunn, D.M.
AU  - von Niederhausern, A.C.
AU  - Hamil, C.
AU  - Aoyagi, A.
AU  - Duval, B.
AU  - Baca, A.
AU  - Silva, F.J.
AU  - Vallier, A.
AU  - Jackson, D.G.
AU  - Latorre, A.
AU  - Weiss, R.B.
AU  - Heddi, A.
AU  - Moya, A.
AU  - Dale, C.
TI  - Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 76
EP  - 93
VL  - 6
AB  - Symbiotic associations between animals and microbes are ubiquitous in nature, with an
AB  - estimated15%of all insect species harboring
AB  - intracellular bacterial symbionts. Most bacterial symbionts sharemany genomic features
AB  - including small genomes, nucleotide composition
AB  - bias, high coding density, and a paucity ofmobileDNA, consistent with long-term host
AB  - association. In this study,wefocus on
AB  - the early stages of genome degeneration in a recently derived insect-bacterial mutualistic
AB  - intracellular association. We present the
AB  - completegenomesequenceandannotationof Sitophilusoryzae primary endosymbiont (SOPE).We
AB  - alsopresent the finishedgenome
AB  - sequence and annotation of strainHS, a close free-living relative of SOPEand other insect
AB  - symbionts of the Sodalis-allied clade,whose
AB  - gene inventory is expected to closely resemble the putative ancestor of this group.
AB  - Structural, functional, and evolutionary analyses
AB  - indicate that SOPE has undergone extensive adaptation toward an insect-associated lifestyle in
AB  - a very short timeperiod. The genome
AB  - of SOPE is large in sizewhen compared withmany ancient bacterial symbionts; however, almost
AB  - half of the protein-coding genes in
AB  - SOPE are pseudogenes. There is also evidence for relaxed selection on the remaining intact
AB  - protein-coding genes. Comparative
AB  - analyses of the whole-genome sequence of strain HS and SOPE highlight numerous genomic
AB  - rearrangements, duplications, and
AB  - deletions facilitated by a recent expansion of insertions sequence elements, some of which
AB  - appear to have catalyzed adaptive
AB  - changes. Functional metabolic predictions suggest that SOPE has lost the ability to synthesize
AB  - several essential amino acids and
AB  - vitamins. Analyses of the bacterial cell envelope and genes encoding secretion systems suggest
AB  - that these structures and elements
AB  - have become simplified in the transition to a mutualistic association.
ER  -

TY  - JOUR
AU  - Oakeson, K.F.
AU  - Miller, A.
AU  - Dale, C.
AU  - Dearing, D.
TI  - Draft Genome Sequence of an Oxalate-Degrading Strain of Clostridium sporogenes from the Gastrointestinal Tract of the White-Throated Woodrat (Neotoma albigula).
JO  - Genome Announcements
PY  - 2016
SP  - e00392
EP  - e00316
VL  - 4
AB  - The gastrointestinal tract of the white-throated woodrat Neotoma albigula harbors a diverse
AB  - microbial population that functions in the degradation of ingested
AB  - plant secondary compounds. Here, we present the draft genome sequence and
AB  - annotation of Clostridium sporogenes strain 8-O, a novel oxalate-degrading
AB  - bacterium isolated from the feces of N. albigula.
ER  -

TY  - JOUR
AU  - Oakey, H.J.
AU  - Cullen, B.R.
AU  - Owens, L.
TI  - The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML.
JO  - J. Appl. Microbiol.
PY  - 2002
SP  - 1089
EP  - 1098
VL  - 93
AB  - Aims: To determine the complete nucleotide sequence of the bacteriophage VHML and establish a
AB  - hypothesis for the virulence conversion caused by
AB  - VHML infection of Vibrio harveyi. Methods and Results: The complete
AB  - nucleotide sequence of VHML was determined (43 193 bp) and used to
AB  - identify putative genes. The translated products of these genes were
AB  - compared with reported sequences to assign hypothetical functions. All
AB  - anticipated structural genes and putative genes for lysogeny were
AB  - identified. In addition, we found a complete N6-adenine methyltransferase
AB  - (Dam) gene that appeared to have an essential site for ADP-ribosylating
AB  - toxins at the C-terminal of the translated product. Conclusions: Virulence
AB  - conversion of V. harveyi by VHML may be associated with Dam
AB  - transcriptional regulation. The Dam gene may also encode for a toxin
AB  - component similar to ADP-ribosylating toxins. Significance and Impact of
AB  - Study: This manuscript lays the foundation for understanding the virulence
AB  - of toxin-producing V. harveyi. Further research into aspects discussed
AB  - here will lead to a greater comprehension regarding the invertebrate
AB  - disease vibriosis and its control in the farming of these animals.
ER  -

TY  - JOUR
AU  - Oana, H.
AU  - Tsumoto, K.
AU  - Yoshikawa, Y.
AU  - Yoshikawa, K.
TI  - Folding transition of large DNA completely inhibits the action of a restriction endonuclease as revealed by single-chain observation.
JO  - FEBS Lett.
PY  - 2002
SP  - 143
EP  - 146
VL  - 530
AB  - The biochemical characteristics of lambda DNA chains in folded/unfolded states upon cleavage
AB  - by the restriction enzyme ApaLI were investigated in the presence of spermine. These
AB  - characteristics of DNA chains depending on their higher-order structure were studied at the
AB  - single-molecule level using fluorescence microscopy. With a low concentration of spermine,
AB  - lambda DNA takes a random coiled conformation and allows digestion by the enzyme, while under
AB  - a high concentration of spermine, lambda DNA takes a compact folded structure and inhibits
AB  - such attack. Together with comparative experiments on short oligomeric DNA, our results
AB  - suggest that the transition in the higher-order structure causes on/off-type switching of
AB  - sensitivity to the enzyme.
ER  -

TY  - JOUR
AU  - Obarska, A.
AU  - Blundell, A.
AU  - Feder, M.
AU  - Vejsadova, S.
AU  - Sisakova, E.
AU  - Weiserova, M.
AU  - Bujnicki, J.M.
AU  - Firman, K.
TI  - Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 1992
EP  - 2005
VL  - 34
AB  - Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the
AB  - functionally uncharacterized Type I
AB  - restriction-modification (R-M) enzymes MjaXIP and MgeORF438 have provided
AB  - a convenient structural template for analysis of the more extensively
AB  - characterized members of this interesting family of multisubunit molecular
AB  - motors. Here, we present a structural model of the Type IC M.EcoR124I DNA
AB  - methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits,
AB  - the cofactor AdoMet and the substrate DNA molecule. The structure was
AB  - obtained by docking models of individual subunits generated by
AB  - fold-recognition and comparative modelling, followed by optimization of
AB  - inter-subunit contacts by energy minimization. The model of M.EcoR124I has
AB  - allowed identification of a number of functionally important residues that
AB  - appear to be involved in DNA-binding. In addition, we have mapped onto the
AB  - model the location of several new mutations of the hsdS gene of M.EcoR124I
AB  - that were produced by misincorporation mutagenesis within the central
AB  - conserved region of hsdS, we have mapped all previously identified
AB  - DNA-binding mutants of TRD2 and produced a detailed analysis of the
AB  - location of surface-modifiable lysines. The model structure, together with
AB  - location of the mutant residues, provides a better background on which to
AB  - study protein-protein and protein-DNA interactions in Type I R-M systems.
ER  -

TY  - JOUR
AU  - Obarska-Kosinska, A.
AU  - Taylor, J.E.
AU  - Callow, P.
AU  - Orlowski, J.
AU  - Bujnicki, J.M.
AU  - Kneale, G.G.
TI  - HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 438
EP  - 452
VL  - 376
AB  - Type I restriction-modification (RM) systems are large, multifunctional enzymes composed of
AB  - three different subunits. HsdS and HsdM form a complex
AB  - in which HsdS recognizes the target DNA sequence, and HsdM carries out
AB  - methylation of adenosine residues. The HsdR subunit, when associated with
AB  - the HsdS-HsdM complex, translocates DNA in an ATP-dependent process and
AB  - cleaves unmethylated DNA at a distance of several thousand base-pairs from
AB  - the recognition site. The molecular mechanism by which these enzymes
AB  - translocate the DNA is not fully understood, in part because of the
AB  - absence of crystal structures. To date, crystal structures have been
AB  - determined for the individual HsdS and HsdM subunits and models have been
AB  - built for the HsdM-HsdS complex with the DNA. However, no structure is
AB  - available for the HsdR subunit. In this work, the gene coding for the HsdR
AB  - subunit of EcoR124I was re-sequenced, which showed that there was an error
AB  - in the published sequence. This changed the position of the stop codon and
AB  - altered the last 17 amino acid residues of the protein sequence. An
AB  - improved purification procedure was developed to enable HsdR to be
AB  - purified efficiently for biophysical and structural analysis. Analytical
AB  - ultracentrifugation shows that HsdR is monomeric in solution, and the
AB  - frictional ratio of 1.21 indicates that the subunit is globular and fairly
AB  - compact. Small angle neutron-scattering of the HsdR subunit indicates a
AB  - radius of gyration of 3.4 nm and a maximum dimension of 10 nm. We
AB  - constructed a model of the HsdR using protein fold-recognition and
AB  - homology modelling to model individual domains, and small-angle neutron
AB  - scattering data as restraints to combine them into a single molecule. The
AB  - model reveals an ellipsoidal shape of the enzymatic core comprising the
AB  - N-terminal and central domains, and suggests conformational heterogeneity
AB  - of the C-terminal region implicated in binding of HsdR to the HsdS-HsdM
AB  - complex.
ER  -

TY  - JOUR
AU  - Oberto, J.
AU  - Gaudin, M.
AU  - Cossu, M.
AU  - Gorlas, A.
AU  - Slesarev, A.
AU  - Marguet, E.
AU  - Forterre, P.
TI  - Genome Sequence of a Hyperthermophilic Archaeon, Thermococcus nautili 30-1, That  Produces Viral Vesicles.
JO  - Genome Announcements
PY  - 2014
SP  - e00243
EP  - e00214
VL  - 2
AB  - Thermococcus nautili 30-1 (formerly Thermococcus nautilus), an anaerobic hyperthermophilic
AB  - marine archaeon, was isolated in 1999 from a deep-sea
AB  - hydrothermal vent during the Amistad campaign. Here, we present the complete
AB  - sequence of T. nautili, which is able to produce membrane vesicles containing
AB  - plasmid DNA. This property makes T. nautili a model organism to study horizontal
AB  - gene transfer.
ER  -

TY  - JOUR
AU  - Obregon, V.
AU  - Garcia, P.
AU  - Lopez, R.
AU  - Garcia, J.L.
TI  - VO1, a temperate bacteriophage of the type 19A multiresistant epidemic 8249 strain of Streptococcus pneumoniae: Analysis of variability of  lytic and putative C5 methyltransferase genes.
JO  - Microb. Drug Resist.
PY  - 2003
SP  - 7
EP  - 15
VL  - 9
AB  - A temperate bacteriophage (VO1) has been isolated from the Streptococcus pneumoniae type 19F
AB  - multiresistant epidemic 8249 strain (South African
AB  - strain). Structural analysis of the specific integration site, protein
AB  - composition, restriction patterns, and molecular dissection of the lytic
AB  - system of this phage revealed high sequence similarity with MM1, a
AB  - temperate phage from the Spain23F-1 strain of pneumococcus, another
AB  - multiresistant epidemic clone. The different pneumococcal strains
AB  - sequenced so far exhibit an identical and single attB located in the same
AB  - site of the genome. Remarkably, the LytA amidase coded by VO1 showed clear
AB  - differences with that of the host bacterium in contrast with the situation
AB  - previously documented for bacterial- and phage-coded amidases of
AB  - pneumococcus. In addition, a new gene (orfmet) putatively coding for a C5
AB  - methyltransferase has been identified. A noticeable variability affecting
AB  - the presence (or absence) of this supernumerary gene(s) in the same region
AB  - of the genomes of three otherwise highly similar phages (i.e., VO1, MM1,
AB  - and HB-3) suggests frequent recombinational events leading to introduce
AB  - variability in this genome region. The peculiarities of genes like lytA
AB  - and orfmet in VO1 provide interesting insights on mechanisms of horizontal
AB  - transfer and lysogenic state co-evolution.
ER  -

TY  - JOUR
AU  - Ocampo-Sosa, A.A.
AU  - Fernandez-Martinez, M.
AU  - Cabot, G.
AU  - Pena, C.
AU  - Tubau, F.
AU  - Oliver, A.
AU  - Martinez-Martinez, L.
TI  - Draft Genome Sequence of the Quorum-Sensing and Biofilm-Producing Pseudomonas aeruginosa Strain Pae221, Belonging to the Epidemic High-Risk Clone Sequence Type  274.
JO  - Genome Announcements
PY  - 2015
SP  - e01343
EP  - e01314
VL  - 3
AB  - Pseudomonas aeruginosa Pae221 is a clinical isolate from blood culture. Pae221 was found to be
AB  - a strong quorum-sensing and biofilm-producing strain and also
AB  - demonstrates a notable production of phenazines. This strain belongs to sequence
AB  - type 274 (ST274), an epidemic high-risk clone. Here, we report the draft genome
AB  - sequence of P. aeruginosa Pae221.
ER  -

TY  - JOUR
AU  - Ochiai, H.
AU  - Inoue, Y.
AU  - Takeya, M.
AU  - Sasaki, A.
AU  - Kaku, H.
TI  - Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity.
JO  - Japan Agricultural Research Quarterly
PY  - 2005
SP  - 275
EP  - 287
VL  - 39
AB  - The plant-pathogenic prokaryote Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight,
AB  - one of the most important diseases of rice.  The bacterium is a model organism for the
AB  - analysis of plant-pathogen interaction, because more than 30 races differing in virulence and
AB  - 25 resistance genes in rice have been reported to date.  We present here the complete genome
AB  - sequence of Xoo strain MAFF 311018.  The size of the genome was 4,940,217 bp, in a single
AB  - circular chromosome.  The genome structure of Xoo MAFF 311018 was characterized by large
AB  - numbers of effector (avr) genes of the avrBs3/pth family and insertion sequences (Iss).  RFLP
AB  - analysis of diverse strains using ISxo1 as a probe suggests that the prevalence of mobile
AB  - elements in this species, which can bring about genome inversions and rearrangement, may have
AB  - played a major role in generating the high degree of genetic diversity and race
AB  - differentiation characteristic of this pathogen.  The Xoo MAFF 311018 sequence was also highly
AB  - similar to those of X. axonopodis pv. citri and X. campestris pv. campestris with the
AB  - exception of the large number of effectors and IS elements, and numerous inversions and
AB  - rearrangements.
ER  -

TY  - JOUR
AU  - Ochiai, H.
AU  - Shibata, H.
AU  - Sawa, Y.
AU  - Ashida, N.
TI  - Restriction endonucleases from Phormidium lapideum, a strain of filamentous and thermophilic Cyanobacteria.
JO  - Bull. Fac. Agr. Shimane Univ.
PY  - 1989
SP  - 184
EP  - 191
VL  - 23
AB  - A couple of restriction endonucleases, PlaI and PlaII, have been purified from
AB  - a filamentous and thermophilic cyanobacterium, Phormidium lapideum.  PlaI
AB  - proved to be an isoschizomer of HaeIII and cleaved the site GG^CC and was a
AB  - monomeric protein that had a molecular weight of about 40 kilodaltons.  PlaII
AB  - was an isoschizomer of Nsp(7524)V and recognized the site TTCGAA and was
AB  - estimated as a heterotetrameric protein (alpha2,beta2).  PlaII has an apparent
AB  - molecular mass of 176 kilodaltons and that of the alpha subunit was 63
AB  - kilodaltons, beta subunit 31 kilodaltons.  Characteristics of PlaI and PlaII
AB  - were investigated in comparison with that of the respective isoschizomers,
AB  - HaeIII and Nsp(7524)V.
ER  -

TY  - JOUR
AU  - Oda, K.
AU  - Marmur, J.
TI  - Purification and properties of deoxyribonucleic acid methylase from Bacillus subtilis.
JO  - Biochemistry
PY  - 1966
SP  - 761
EP  - 773
VL  - 5
AB  - DNA methylase was purified about 100-fold from Bacillus subtilis strain 6633.
AB  - The novel features of this enzyme are as follows: (1) During growth of
AB  - bacteria, enzyme activity was detected principally in the early exponential
AB  - phase.  (2) The enzyme catalyzes the methylation of both native and
AB  - heat-denatured DNA.  (3) The product of the enzymatic methylation of DNA was
AB  - 5-methylcytosine (5MC) only.  (4) The extent of the methylation of both native
AB  - and heat-denatured bacterial DNA is approximately proportional to its GC
AB  - (guanine plus cytosine) content.  The higher the per cent GC in DNA, the
AB  - greater the extent of methylation that takes place, even if the ratio of 5MC to
AB  - total cytosine residues in DNA is considered.  The possibility of the selective
AB  - methylation of one strand of DNA was also examined by using B. subtilis
AB  - bacteriophage 2C DNA, whose strands, after denaturation, can be fractionated
AB  - because of a bias in base composition.  The H and L strands of phage 2C DNA
AB  - were separated by MAK column chromatography or by centrifugation in alkaline
AB  - CsCl density gradients, and it was found that both strands were equally
AB  - methylated in vivo and in vitro.
ER  -

TY  - JOUR
AU  - Oda, M.
AU  - Tanaka, S.
AU  - Shiota, K.
TI  - DNA methyltransferase 1 is essential for establishment of trophoblast stem cells in culture.
JO  - Biol. Reprod.
PY  - 2001
SP  - 175
EP  - 176
VL  - 64
AB  - DNA methylation patterns in mammals are stage- and tissue-specific.  This suggests that
AB  - methylation patterns contribute to proper cell differentiation and/or to the maintenance of
AB  - cellular characteristics.  Several different DNA methyltransferases exist that both establish
AB  - and maintain proper methylation patterns.  Dnmt1 is largely a maintenance methyltransferase
AB  - that ensures an established methylation pattern is inherited by daughter cells.  Disruption of
AB  - Dnmt1 causes growth delay at gastrulation and homozygous mutants are embryonic lethal.  To
AB  - evaluate the role of Dnmt1 in placental development, we attempted to establish trophoblast
AB  - stem cells from homozygous Dnmt1 hypomorphic mutant embryos.  TS cells exclusively contribute
AB  - to the trophoblast lineage in vivo in chimeras.  At the blastocyst stage, TS cells appear in
AB  - the polar trophectoderm, which is adjacent to the inner cell mass.  TS cells can be maintained
AB  - in culture with media supplemented with FGF-4, and differentiate into several subtypes of
AB  - trophoblast cells.  To establish homozygous mutant TS cells, we used blastocysts from
AB  - heterozygous matings.  The 39 blastocysts from 6 female mice were incubated in FGF4-contained
AB  - medium with feeder cells.  Of 39 blastocysts, 28 generated stem cell colonies; 3 were
AB  - homozygous, 10 were wild type, 13 were heterozygous clones, and 2 could not be genotyped, but
AB  - were probably also homozygous.  All clones were passed two more times and most (70-80%) of
AB  - wild type and heterozygous clones survived.  However, no homozygous clone survived beyond the
AB  - second passage.  Some autonomous differentiation was observed in the homozygous TS cells.  Our
AB  - results indicate that Dnmt1-hypomorphic TS cells cannot be established in cell culture, as
AB  - normal and heterozygous TS cells can.  This is in contrast to Dnmt1-hypomorphic embryonic stem
AB  - cells, which can be maintained in culture.  These data suggest that the trophoblast lineage is
AB  - more dependent on Dnmt1 than the embryo proper.
ER  -

TY  - JOUR
AU  - Odom, O.W.
AU  - Holloway, S.P.
AU  - Deshpande, N.N.
AU  - Lee, J.
AU  - Herrin, D.L.
TI  - Mobile self-splicing Group I introns from the psbA gene of Chlamydomonas reinhardtii: highly efficient homing of an exogenous intron containing its own promoter.
JO  - Mol. Cell. Biol.
PY  - 2001
SP  - 3472
EP  - 3481
VL  - 21
AB  - Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 and
AB  - Cr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used
AB  - transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing.
AB  - Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in
AB  - both orientations and then cotransformed into IL along with a spectinomycin resistance marker
AB  - (16S rrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron
AB  - whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both
AB  - orientations produced highly efficient cointegration of the intron. Efficient cointegration of
AB  - Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any
AB  - known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron,
AB  - consistent with homing. The Cr.psbA4 constructs also contained a
AB  - 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present
AB  - when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary
AB  - selection for this marker gave >100-fold more transformants (>10,000/?g of DNA) than did the
AB  - spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the
AB  - ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay
AB  - was used to identify an intronic region between bp -88 and -194 (relative to the ORF) that
AB  - stimulated homing and contained a possible bacterial (-10, -35)-type promoter. Primer
AB  - extension analysis detected a transcript that could originate from this promoter. Thus, this
AB  - mobile, self-splicing intron also contains its own promoter for ORF expression. The
AB  - implications of these results for horizontal intron transfer and organelle transformation are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Oehlerking, J.
AU  - Kube, M.
AU  - Felder, K.M.
AU  - Matter, D.
AU  - Wittenbrink, M.M.
AU  - Schwarzenbach, S.
AU  - Kramer, M.M.
AU  - Hoelzle, K.
AU  - Hoelzle, L.E.
TI  - The complete genome sequence of the hemotrophic Mycoplasma suis_KI3806.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2369
EP  - 2370
VL  - 193
AB  - Mycoplasma suis, a member of the hemotrophic mycoplasma (HM) group, parasitize erythrocytes of
AB  - pigs. Increasing evidences suggest that M. suis is also a zoonotic agent. Highly pathogenic
AB  - strains of M. suis (e.g. M. suis_KI3806) have been demonstrated to invade erythrocytes. This
AB  - complete sequenced and manually annotated genome of M. suis_KI3806 is the first available from
AB  - this species and from all HM. The DNA was isolated from blood-samples of experimentally
AB  - infected pigs due to the lack of an in vitro cultivation system. The small circular chromosome
AB  - of 709270 bp with an unexpected-high number of hypothetical proteins and limited transport and
AB  - metabolic capacities could reflect the unique life-style of HM on the surface of erythrocytes.
ER  -

TY  - JOUR
AU  - Oelgeschlager, T.
AU  - Geiger, R.
AU  - Ruter, T.
AU  - Alves, J.
AU  - Fliess, A.
AU  - Pingoud, A.
TI  - Probing the function of individual amino acid residues in the DNA binding site of the EcoRI restriction endonuclease by analysing the toxicity of genetically engineered mutants.
JO  - Gene
PY  - 1990
SP  - 19
EP  - 27
VL  - 89
AB  - We have developed an assay that allows analysis of the activity of EcoRI
AB  - restriction endonuclease (ENase) and its mutants in vivo.  This assay is based
AB  - on the fact that wild type (wt) EcoRI ENase is toxic for Escherichia coli cells
AB  - not expressing the EcoRI methyltransferase (MTase).  The viability factor
AB  - defined by the ratio of the viable counts of E. coli cultures having or not
AB  - having expressed the ecoRIR gene for a defined time is 10-6 for wt EcoRI ENase
AB  - and close to one for a totally inactive EcoRI ENase mutant.  While the EcoRI
AB  - MTase (M.EcoRI) provides substantial protection against the toxic effects of
AB  - the wt EcoRI ENase and several of the mutants, some mutants become more toxic
AB  - in the presence of M.EcoRI.  Twenty-four different DNA-binding-site mutants of
AB  - EcoRI ENase were characterized in their activity in vivo with this assay.  The
AB  - results obtained allow us to conclude that the structural integrity of the
AB  - region at and around aa 200 seems to be very critical for the enzymatic
AB  - function of EcoRI ENase: nonconservative replacements there lead to viability
AB  - factors of 1-10/2.  While our results indicate that the region around aa 144
AB  - and 145 is also involved in the EcoRI ENase-catalyzed reaction, it is also
AB  - evident that the effects of mutation there are not as large:  viability factors
AB  - of approx. 10-3 are obtained even for drastic replacements.  These results are
AB  - discussed in the light of the x-ray structure analysis of an EcoRI ENase-DNA
AB  - recognition complex.
ER  -

TY  - JOUR
AU  - Ofir, G.
AU  - Melamed, S.
AU  - Sberro, H.
AU  - Mukamel, Z.
AU  - Silverman, S.
AU  - Yaakov, G.
AU  - Doron, S.
AU  - Sorek, R.
TI  - DISARM is a widespread bacterial defence system with broad anti-phage activities.
JO  - Nature Microbiology
PY  - 2018
SP  - 90
EP  - 98
VL  - 3
AB  - The evolutionary pressure imposed by phage predation on bacteria and archaea has  resulted in
AB  - the development of effective anti-phage defence mechanisms, including
AB  - restriction-modification and CRISPR-Cas systems. Here, we report on a new defence
AB  - system, DISARM (defence island system associated with restriction-modification),
AB  - which is widespread in bacteria and archaea. DISARM is composed of five genes,
AB  - including a DNA methylase and four other genes annotated as a helicase domain, a
AB  - phospholipase D (PLD) domain, a DUF1998 domain and a gene of unknown function.
AB  - Engineering the Bacillus paralicheniformis 9945a DISARM system into Bacillus
AB  - subtilis has rendered the engineered bacteria protected against phages from all
AB  - three major families of tailed double-stranded DNA phages. Using a series of gene
AB  - deletions, we show that four of the five genes are essential for DISARM-mediated
AB  - defence, with the fifth (PLD) being redundant for defence against some of the
AB  - phages. We further show that DISARM restricts incoming phage DNA and that the B.
AB  - paralicheniformis DISARM methylase modifies host CCWGG motifs as a marker of self
AB  - DNA akin to restriction-modification systems. Our results suggest that DISARM is
AB  - a new type of multi-gene restriction-modification module, expanding the arsenal
AB  - of defence systems known to be at the disposal of prokaryotes against their
AB  - viruses.
ER  -

TY  - JOUR
AU  - Ogasawara, Y.
AU  - Torrez-Martinez, N.
AU  - Aragon, A.D.
AU  - Yackley, B.J.
AU  - Weber, J.A.
AU  - Sundararajan, A.
AU  - Ramaraj, T.
AU  - Edwards, J.S.
AU  - Melancon, C.E.I.I.I.
TI  - High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio   Technologies.
JO  - Genome Announcements
PY  - 2015
SP  - e00114
EP  - e00115
VL  - 3
AB  - Here, we report the high-quality draft genome sequence of actinobacterium Kibdelosporangium
AB  - sp. MJ126-NF4, producer of the type II polyketide azicemicins,
AB  - obtained using Illumina and PacBio sequencing technologies. The 11.75-Mbp genome
AB  - contains >11,000 genes and 22 polyketide and nonribosomal peptide natural product
AB  - gene clusters.
ER  -

TY  - JOUR
AU  - Ogata, H.
AU  - Audic, S.
AU  - Renesto-Audiffren, P.
AU  - Fournier, P.-E.
AU  - Barbe, V.
AU  - Samson, D.
AU  - Roux, V.
AU  - Cossart, P.
AU  - Weissenbach, J.
AU  - Claverie, J.-M.
AU  - Raoult, D.
TI  - Mechanisms of evolution in Rickettsia conorii and R. prowazekii.
JO  - Science
PY  - 2001
SP  - 2093
EP  - 2098
VL  - 293
AB  - Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted
AB  - fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R.
AB  - conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the
AB  - previously determined R. prowazekii genome plus 552 supplementary open reading frames and a
AB  - 10-fold increase in the number of repetitive elements. Despite these differences, the two
AB  - genomes exhibit a nearly perfect colinearity that allowed the clear identification of
AB  - different stages of gene alterations with gene remnants and 37 genes split in 105 fragments,
AB  - of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the
AB  - divergence of the genus.
ER  -

TY  - JOUR
AU  - Ogata, H.
AU  - La Scola, B.
AU  - Audic, S.
AU  - Renesto, P.
AU  - Blanc, G.
AU  - Robert, C.
AU  - Fournier, P.E.
AU  - Claverie, J.M.
AU  - Raoult, D.
TI  - Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens.
JO  - PLoS Genet.
PY  - 2006
SP  - e76
EP  - e76
VL  - 2
AB  - The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several
AB  - genes usually associated with DNA transfer,
AB  - suggesting that ancestral rickettsiae might have been endowed with a
AB  - conjugation apparatus. Here we present the genome sequence of Rickettsia
AB  - bellii, the earliest diverging species of known rickettsiae. The 1,552,076
AB  - base pair-long chromosome does not exhibit the colinearity observed
AB  - between other rickettsia genomes, and encodes a complete set of putative
AB  - conjugal DNA transfer genes most similar to homologues found in
AB  - Protochlamydia amoebophila UWE25, an obligate symbiont of amoebae. The
AB  - genome exhibits many other genes highly similar to homologues in
AB  - intracellular bacteria of amoebae. We sought and observed sex pili-like
AB  - cell surface appendages for R. bellii. We also found that R. bellii very
AB  - efficiently multiplies in the nucleus of eukaryotic cells and survives in
AB  - the phagocytic amoeba, Acanthamoeba polyphaga. These results suggest that
AB  - amoeba-like ancestral protozoa could have served as a genetic "melting
AB  - pot" where the ancestors of rickettsiae and other bacteria promiscuously
AB  - exchanged genes, eventually leading to their adaptation to the
AB  - intracellular lifestyle within eukaryotic cells.
ER  -

TY  - JOUR
AU  - Ogata, H.
AU  - Renesto, P.
AU  - Audic, S.
AU  - Robert, C.
AU  - Blanc, G.
AU  - Fournier, P.E.
AU  - Parinello, H.
AU  - Claverie, J.M.
AU  - Raoult, D.
TI  - The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite.
JO  - PLoS Biology
PY  - 2005
SP  - e248
EP  - e248
VL  - 3
AB  - We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular
AB  - alpha-proteobacterium causing spotted fever in humans.
AB  - Besides a circular chromosome of 1,485,148 bp, R. felis exhibits the first
AB  - putative conjugative plasmid identified among obligate intracellular
AB  - bacteria. This plasmid is found in a short (39,263 bp) and a long (62,829
AB  - bp) form. R. felis contrasts with previously sequenced Rickettsia in terms
AB  - of many other features, including a number of transposases, several
AB  - chromosomal toxin-antitoxin genes, many more spoT genes, and a very large
AB  - number of ankyrin- and tetratricopeptide-motif-containing genes.
AB  - Host-invasion-related genes for patatin and RickA were found. Several
AB  - phenotypes predicted from genome analysis were experimentally tested:
AB  - conjugative pili and mating were observed, as well as beta-lactamase
AB  - activity, actin-polymerization-driven mobility, and hemolytic properties.
AB  - Our study demonstrates that complete genome sequencing is the fastest
AB  - approach to reveal phenotypic characters of recently cultured obligate
AB  - intracellular bacteria.
ER  -

TY  - JOUR
AU  - Ogawa, S.
AU  - Matsuo, K.
AU  - Angata, K.
AU  - Yanagisawa, K.
AU  - Tanaka, Y.
TI  - Group-I introns in the cytochrome c oxidase genes of Dictyostelium discoideum: two related ORFs in one loop of a group-I intron, a cox1/2 hybrid gene and an unusually large cox3 gene.
JO  - Curr. Genet.
PY  - 1997
SP  - 80
EP  - 88
VL  - 31
AB  - The DNA sequences of cytochrome oxidase (subunits 1, 2 and 3) genes of the cellular slime mold
AB  - Dictyostelium discoideum mitochondria were determined.  The genes for subunits 1 and 2 have a
AB  - single continuous ORF (COX1/2) which contains four group-I introns.  The insertion sites of
AB  - the two group-I introns (DdOX1/2.2 and DdOX1/2.3) coincide with those of fungal and algal
AB  - group-I introns, as well as a liverwort group-I intron, in the cytochrome oxidase subunit 1.
AB  - Interestingly, intron DdOX1/2.2 has two free-standing ORFs in a loop (L8) which have similar
AB  - amino-acid sequences and are homologous to ai4 DNA endonuclease (I-Sce II) and bi4 RNA
AB  - maturase found in group-I introns of Saccharomyces cerevisiae mitochondrial DNA.  Two group-I
AB  - introns (DdOX1/2.3 and DdOX1/2.4) also have a free-standing ORF in loop 1 and loop 2,
AB  - respectively.  These results show that these group-I introns and the intronic ORFs have
AB  - evolved from the same ancestral origin, but that these ORFs have been propagated
AB  - independently.
ER  -

TY  - JOUR
AU  - Ogawa, S.
AU  - Naito, K.
AU  - Angata, K.
AU  - Morio, T.
AU  - Urushihara, H.
AU  - Tanaka, Y.
TI  - A site-specific DNA endonuclease specified by one of two ORFs encoded by a group I intron in Dictyostelium discoideum mitochondrial DNA.
JO  - Gene
PY  - 1997
SP  - 115
EP  - 121
VL  - 191
AB  - The second intron (DdOX1/2.2) of Dictyostelium discoideum cytochrome oxidase subunit 1/2 fused
AB  - gene has two free-standing ORF genes (Dd ai2a and Dd ai2b) in a loop, which have similar amino
AB  - acid sequences and are homologous to aI4 DNA endonuclease (I-SceII) of Saccharomyces
AB  - cerevisiae.  To elucidate the functions of these ORFs, we cloned the ORFs into an expression
AB  - vector and introduced the composite vectors into E. coli.  The expression of Dd ai2a in E.
AB  - coli caused growth inhibition and degradation of the E. coli genomic DNA.  To determine
AB  - whether Dd ai2a protein is a homing type DNA endonuclease, the ability to cleave the homing
AB  - site of its intron in vivo was examined.  Dd ai2a cleaved only one strand of intronless DNA
AB  - sequence at the site which coincides with the I-SceII cleavage recognition site.  We suppose
AB  - that Dd ai2a functions actually as a homing type DNA endonuclease in D. discoideum
AB  - mitochondria by virtue of other factors.  To obtain further information about the relationship
AB  - between the existence of introns and the mating system, we carried out in vitro self-splicing
AB  - assay and polymerase chain reaction analysis using 13 strains of the cellular slime mold.
ER  -

TY  - JOUR
AU  - Ogawa, Y.
AU  - Ooka, T.
AU  - Shi, F.
AU  - Ogura, Y.
AU  - Nakayama, K.
AU  - Hayashi, T.
AU  - Shimoji, Y.
TI  - The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism's Intracellular Adaptations.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2959
EP  - 2971
VL  - 193
AB  - Erysipelothrix rhusiopathiae is a Gram-positive bacterium that represents
AB  - a new class, Erysipelotrichia, in the phylum Firmicutes. The organism is a
AB  - facultative intracellular pathogen that causes swine erysipelas, as well
AB  - as a variety of diseases in many animals. Here, we report the first
AB  - complete genome sequence analysis of a member of the class
AB  - Erysipelotrichia. The E. rhusiopathiae genome (1,787,941 bp) is one of the
AB  - smallest genomes in the phylum Firmicutes. Phylogenetic analyses based on
AB  - the 16S rRNA gene and 31 universal protein families suggest that E.
AB  - rhusiopathiae is phylogenetically close to Mollicutes, which comprises
AB  - Mycoplasma species. Genome analyses show that the overall features of the
AB  - E. rhusiopathiae genome are similar to those of other Gram-positive
AB  - bacteria; it possesses a complete set of peptidoglycan biosynthesis genes,
AB  - two-component regulatory systems, and various cell wall-associated
AB  - virulence factors, including a capsule and adhesins. However, it lacks
AB  - many orthologous genes for the biosynthesis of wall teichoic acids (WTA)
AB  - and lipoteichoic acids (LTA) and the dltABCD operon, which is responsible
AB  - for d-alanine incorporation into WTA and LTA, suggesting that the organism
AB  - has an atypical cell wall. In addition, like Mollicutes, its genome shows
AB  - a complete loss of fatty acid biosynthesis pathways and lacks the genes
AB  - for the biosynthesis of many amino acids, cofactors, and vitamins,
AB  - indicating reductive genome evolution. The genome encodes nine antioxidant
AB  - factors and nine phospholipases, which facilitate intracellular survival
AB  - in phagocytes. Thus, the E. rhusiopathiae genome represents evolutionary
AB  - traits of both Firmicutes and Mollicutes and provides new insights into
AB  - its evolutionary adaptations for intracellular survival.
ER  -

TY  - JOUR
AU  - Oger, P.
AU  - Sokolova, T.G.
AU  - Kozhevnikova, D.A.
AU  - Chernyh, N.A.
AU  - Bartlett, D.H.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Lebedinsky, A.V.
TI  - Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain AM4, Capable of Organotrophic Growth and Growth at the Expense  of Hydrogenogenic or Sulfidogenic Oxidation of Carbon Monoxide.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7019
EP  - 7020
VL  - 193
AB  - Analysis of the complete genome of Thermococcus sp. strain AM4, which was the first
AB  - lithotrophic Thermococcales isolate described and the first
AB  - archaeal isolate to exhibit a capacity for hydrogenogenic carboxydotrophy,
AB  - reveals a proximity with Thermococcus gammatolerans, corresponding to
AB  - close but distinct species that differ significantly in their lithotrophic
AB  - capacities.
ER  -

TY  - JOUR
AU  - Oger, P.
AU  - Sokolova, T.G.
AU  - Kozhevnikova, D.A.
AU  - Taranov, E.A.
AU  - Vannier, P.
AU  - Lee, H.S.
AU  - Kwon, K.K.
AU  - Kang, S.G.
AU  - Lee, J.H.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Lebedinsky, A.V.
TI  - Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus barophilus Ch5, Capable of Growth at the Expense of Hydrogenogenesis  from Carbon Monoxide and Formate.
JO  - Genome Announcements
PY  - 2016
SP  - e01534
EP  - e01515
VL  - 4
AB  - We report here the complete sequence and fully manually curated annotation of the genome of
AB  - strain Ch5, a new member of the piezophilic hyperthermophilic species
AB  - Thermococcus barophilus.
ER  -

TY  - JOUR
AU  - Oger, P.M.
TI  - Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea.
JO  - Genome Announcements
PY  - 2018
SP  - e00037
EP  - e00018
VL  - 6
AB  - We report here the genome sequences of the type strains of the species Thermococcus barossii,
AB  - T. celer, T. chitonophagus, T. gorgonarius, T. pacificus,
AB  - T. peptonophilus, T. profundus, T. radiotolerans, T. siculi, and T. thioreducens,
AB  - as well as the prototype of a possible type strain of a novel Thermococcus
AB  - species, strain P6.
ER  -

TY  - JOUR
AU  - Oger, P.M.
AU  - Callac, N.
AU  - Oger-Desfeux, C.
AU  - Hughes, S.
AU  - Gillet, B.
AU  - Jebbar, M.
AU  - Godfroy, A.
TI  - Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca's Roost Hydrothermal Vent in the  Guaymas Basin.
JO  - Genome Announcements
PY  - 2017
SP  - e01667
EP  - e01616
VL  - 5
AB  - Members of the order Thermococcales are common inhabitants of high-temperature hydrothermal
AB  - vent systems (black smokers) that are represented in clone libraries
AB  - mostly by isolates from the Thermococcus genus. We report the complete sequence
AB  - of a novel species from the Pyrococcus genus, P. kukulkanii strain NCB100, which
AB  - has been isolated from a flange fragment of the Rebecca's Roost hydrothermal vent
AB  - system in the Guaymas Basin.
ER  -

TY  - JOUR
AU  - Ogg, C.D.
AU  - Patel, B.K.
TI  - Draft Genome Sequence of Caloramator australicus strain RC3T a thermoanaerobe from the Great Artesian Basin of Australia.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2664
EP  - 2665
VL  - 193
AB  - Caloramator australicus strain RC3(T) (JCM 15081(T) = KCTC 5601(T)) is the type strain of a
AB  - newly identified thermophilic species, which was isolated from red-coloured microbial mats
AB  - that thrive at 66  degrees C in the runoff channel of a Great Artesian Basin bore (New Lorne
AB  - bore, registered number 17263) in outback Queensland, Australia. The ability of C. australicus
AB  - strain to use metals as terminal electron acceptors has led to concerns that it could colonise
AB  - and enhance corrosion of the metal casing of Great Artesian Basin bore-well pipes, and this
AB  - could subsequently lead to bore failure and loss of water availability for the community which
AB  - is so reliant on it. The genome of C. australicus strain has been sequenced, and annotation of
AB  - the  approximately  2.65 Mb sequence indicates that the attributes are consistent with
AB  - physiological and phenotypic traits.
ER  -

TY  - JOUR
AU  - Ogino, H.
AU  - Azuma, Y.
AU  - Hosoyama, A.
AU  - Nakazawa, H.
AU  - Matsutani, M.
AU  - Hasegawa, A.
AU  - Otsuyama, K.
AU  - Matsushita, K.
AU  - Fujita, N.
AU  - Shirai, M.
TI  - Complete Genome Sequence of NBRC 3288, a Unique Cellulose-Nonproducing Strain of Gluconacetobacter xylinus Isolated from Vinegar.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6997
EP  - 6998
VL  - 193
AB  - Gluconacetobacter xylinus is involved in the industrial production of cellulose. We have
AB  - determined the genome sequence of G. xylinus NBRC 3288,
AB  - a cellulose-nonproducing strain. Comparative analysis of genomes of G.
AB  - xylinus NBRC 3288 with those of the cellulose-producing strains clarified
AB  - the genes important for cellulose production in Gluconacetobacter.
ER  -

TY  - JOUR
AU  - Ogunremi, D.
AU  - Blais, B.
AU  - Huang, H.
AU  - Wang, L.
AU  - Elmufti, M.
AU  - Allain, R.
AU  - Hazelwood, J.
AU  - Grenier, C.
AU  - Amoako, K.
AU  - Savic, M.
AU  - Fattahi, G.N.
TI  - Draft Genome Sequences of Two Strains of Salmonella enterica Serovar Typhimurium  Displaying Different Virulence in an Experimental Chicken Model.
JO  - Genome Announcements
PY  - 2017
SP  - e01526
EP  - e01516
VL  - 5
AB  - Salmonella enterica serovar Typhimurium strains 22495 and 22792, obtained from wild birds,
AB  - were found to display different virulence attributes in an
AB  - experimental chicken model. Closed genome sequences were assembled after
AB  - sequencing with the Roche 454 and Illumina MiSeq platforms. An additional plasmid
AB  - was present in the more virulent strain 22495.
ER  -

TY  - JOUR
AU  - Ogunremi, D.
AU  - Devenish, J.
AU  - Amoako, K.
AU  - Kelly, H.
AU  - Dupras, A.A.
AU  - Belanger, S.
AU  - Wang, L.R.
TI  - High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis.
JO  - BMC Genomics
PY  - 2014
SP  - 713
EP  - 713
VL  - 15
AB  - BACKGROUND: There is a need to characterize genomes of the foodborne pathogen,
AB  - Salmonella enterica serovar Enteritidis (SE) and identify genetic information
AB  - that could be ultimately deployed for differentiating strains of the organism, a
AB  - need that is yet to be addressed mainly because of the high degree of clonality
AB  - of the organism. In an effort to achieve the first characterization of the
AB  - genomes of SE of Canadian origin, we carried out massively parallel sequencing of
AB  - the nucleotide sequence of 11 SE isolates obtained from poultry production
AB  - environments (n = 9), a clam and a chicken, assembled finished genomes and
AB  - investigated diversity of the SE genome. RESULTS: The median genome size was
AB  - 4,678,683 bp. A total of 4,833 chromosomal genes defined the pan genome of our
AB  - field SE isolates consisting of 4,600 genes present in all the genomes, i.e.,
AB  - core genome, and 233 genes absent in at least one genome (accessory genome).
AB  - Genome diversity was demonstrable by the presence of 1,360 loci showing single
AB  - nucleotide polymorphism (SNP) in the core genome which was used to portray the
AB  - genetic distances by means of a phylogenetic tree for the SE isolates. The
AB  - accessory genome consisted mostly of previously identified SE prophage sequences
AB  - as well as two, apparently full- sized, novel prophages namely a 28 kb sequence
AB  - provisionally designated as SE-OLF-10058 (3) prophage and a 43 kb sequence
AB  - provisionally designated as SE-OLF-10012 prophage. CONCLUSIONS: The number of
AB  - SNPs identified in the relatively large core genome of SE is a reflection of
AB  - substantial diversity that could be exploited for strain differentiation as shown
AB  - by the development of an informative phylogenetic tree. Prophage sequences can
AB  - also be exploited for SE strain differentiation and lineage tracking. This work
AB  - has laid the ground work for further studies to develop a readily adoptable
AB  - laboratory test for the subtyping of SE.
ER  -

TY  - JOUR
AU  - Oguntoyinbo, F.A.
AU  - Cho, G.S.
AU  - Brinks, E.
AU  - Fiedler, G.
AU  - Kabisch, J.
AU  - Koberg, S.
AU  - Bockelmann, W.
AU  - Neve, H.
AU  - Kang, Y.G.
AU  - Yun, D.
AU  - Kim, A.R.
AU  - Narbad, A.
AU  - Franz, C.M.
TI  - Draft Genome Sequence of Lactobacillus plantarum BFE 5092 Isolated from Maasai Fermented Milk.
JO  - Genome Announcements
PY  - 2016
SP  - e00481
EP  - e00416
VL  - 4
AB  - The draft genome of Lactobacillus plantarum BFE 5092 isolated from the Maasai traditional
AB  - fermented milk product kule naoto was sequenced, and sequence
AB  - analysis showed the assembled genome size to be 3,285,094 bp, containing a
AB  - predicted total of 3,111 protein-encoding genes, 17 rRNAs, and 70 tRNAs.
ER  -

TY  - JOUR
AU  - Oguro, K.
AU  - Tamura, K.
AU  - Yamane, J.
AU  - Shimizu, M.
AU  - Yamamoto, T.
AU  - Ikawa, T.
AU  - Ohnishi, K.
AU  - Oshima, S.
AU  - Imajoh, M.
TI  - Draft Genome Sequences of Two Genetic Variant Strains of Edwardsiella piscicida,  JF1305 and RSB1309, Isolated from Olive Flounder (Paralichythys olivaceus) and  Red Sea Bream (Pagrus major) Cultured in Japan, Respectively.
JO  - Genome Announcements
PY  - 2014
SP  - e00546
EP  - e00514
VL  - 2
AB  - Edwardsiella piscicida is a new species discovered within the group of organisms
AB  - traditionally classified as Edwardsiella tarda. We present draft genome sequences
AB  - of two variant strains of E. piscicida, JF1305 and RSB1309. Differences in
AB  - protein-coding sequence between these isolates are associated with virulence,
AB  - disease, and defense, suggesting differences in pathogenicity.
ER  -

TY  - JOUR
AU  - Oguro, K.
AU  - Yamane, J.
AU  - Yamamoto, T.
AU  - Ohnishi, K.
AU  - Oshima, S.
AU  - Imajoh, M.
TI  - Draft Genome Sequence of Streptococcus parauberis Strain SK-417, Isolated from Diseased Sebastes ventricosus in Kagoshima, Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e00453
EP  - e00414
VL  - 2
AB  - Streptococcus parauberis strain SK-417 was isolated from the brain of a diseased  Sebastes
AB  - ventricosus, collected from an aquaculture farm in April 2013 in
AB  - Kagoshima Prefecture, Japan. The draft genome sequence, obtained with a 454 GS
AB  - Junior sequencing system, consists of 33 large contigs of >500 bp, totaling
AB  - 1,958,836 bp, and has a G+C content of 35.4%.
ER  -

TY  - JOUR
AU  - Oh, C.
AU  - Heo, S.J.
AU  - De Zoysa, M.
AU  - Affan, A.
AU  - Jung, W.K.
AU  - Park, H.S.
AU  - Lee, Y.
AU  - Lee, J.
AU  - Yoon, K.T.
AU  - Kang, D.H.
TI  - Whole-Genome Sequence of the Xylanase-Producing Mesoflavibacter zeaxanthinifaciens Strain S86.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5557
EP  - 5557
VL  - 193
AB  - We isolated Mesoflavibacter zeaxanthinifaciens S86 as xylanase-producing bacteria from
AB  - seawater sampled in Micronesia. Analysis of the M.
AB  - zeaxanthinifaciens genome revealed that it contains a single circular
AB  - chromosome of 3,704,661 bp with 3,249 putative open reading frames.
ER  -

TY  - JOUR
AU  - Oh, C.
AU  - Kwon, Y.K.
AU  - Heo, S.J.
AU  - De Zoysa, M.
AU  - Affan, A.
AU  - Lee, Y.
AU  - Lee, J.
AU  - Choi, Y.U.
AU  - Park, H.S.
AU  - Jung, K.H.
AU  - Lee, H.Y.
AU  - Kang, D.H.
TI  - Complete genome sequence of strain s85, a novel member of the family flavobacteriaceae.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6107
EP  - 6107
VL  - 193
AB  - An agar-degrading marine bacterium identified as a novel member of the family
AB  - Flavobacteriaceae (strain S85) was isolated from seawater in
AB  - Micronesia. The sequenced strain S85 genome is composed of 3,384,629 bp in
AB  - a circular chromosome, which includes 2,883 complete open reading frames.
ER  -

TY  - JOUR
AU  - Oh, C.
AU  - Zoysa, M.D.
AU  - Kwon, Y.K.
AU  - Heo, S.J.
AU  - Affan, A.
AU  - Jung, W.K.
AU  - Park, H.S.
AU  - Lee, J.
AU  - Son, S.K.
AU  - Yoon, K.T.
AU  - Kang, D.H.
TI  - Complete genome sequence of the agarase-producing marine bacterium strain s89, representing a novel species of the genus alteromonas.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5538
EP  - 5538
VL  - 193
AB  - We report here the annotated genome sequence of the marine bacterium Alteromonas sp. S89 and
AB  - the identification of six genes coding for
AB  - agar-degrading enzymes. The sequenced Alteromonas sp. S89 genome is
AB  - composed of a 3,864,871-bp circular chromosome that includes 3,236
AB  - complete open reading frames.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Giovannoni, S.J.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Cho, J.C.
TI  - The Complete Genome Sequence of Erythrobacter litoralis HTCC2594.
JO  - J. Bacteriol.
PY  - 2009
SP  - 2419
EP  - 2420
VL  - 191
AB  - Erythrobacter litoralis has been known as a bacteriochlorophyll a-containing aerobic
AB  - anoxygenic phototrophic bacterium. Here we announce
AB  - the complete genome sequence of E. litoralis HTCC2594 that is devoid of
AB  - phototrophic potential. E. litoralis HTCC2594, isolated by
AB  - dilution-to-extinction culturing from seawater, could not carry out
AB  - aerobic anoxygenic phototrophy and lacked genes for bacteriochlorophyll a
AB  - biosynthesis and photosynthetic reaction center proteins.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Giovannoni, S.J.
AU  - Lee, K.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Cho, J.C.
TI  - Complete Genome Sequence of Robiginitalea biformata HTCC2501.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7144
EP  - 7145
VL  - 191
AB  - Robiginitalea biformata HTCC2501, isolated by dilution-to-extinction culturing from the
AB  - Sargasso Sea, has been known as an aerobic chemoheterotroph with carotenoid pigments and
AB  - dimorphic growth phases. Here we announce the complete genome sequence of R. biformata
AB  - HTCC2501 that contained genes for carotenoid biosynthesis and several macromolecule-degrading
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Kang, I.
AU  - Ferriera, S.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Genome Sequence of an Oligotrophic Marine Gammaproteobacterium HTCC2143 Isolated from Oregon Coast.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4530
EP  - 4531
VL  - 192
AB  - Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction
AB  - culturing. Here we present the genome of strain
AB  - HTCC2143 from BD1-7 clade of the oligotrophic marine Gammaproteobacteria
AB  - group (OMG). The genome of HTCC2143 encodes genes for carotenoid
AB  - biosynthesis, proteorhodopsin, and genes that have potential
AB  - biotechnological significance: epoxide hydrolases, Baeyer-Villiger
AB  - monooxygenases, and polyketide synthases.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Kang, I.
AU  - Lee, K.
AU  - Jang, Y.
AU  - Lim, S.I.
AU  - Cho, J.C.
TI  - Complete Genome Sequence of Strain IMCC9063 Belonging to SAR11 subgroup 3, Isolated from the Arctic Ocean.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3379
EP  - 3380
VL  - 193
AB  - Strain IMCC9063 is a novel isolate of the SAR11 clade and is distantly related to other
AB  - cultured representatives in this clade. The strain was
AB  - isolated off the coast of Svalbard, Norway by applying high-throughput
AB  - culturing methods based on dilution-to-extinction. Here we present the
AB  - finished genome sequence of strain IMCC9063.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Kang, I.
AU  - Vergin, K.L.
AU  - Kang, D.
AU  - Rhee, K.H.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Complete Genome Sequence of Parvularcula bermudensis HTCC2503T, the type species of the order 'Parvularculales' in the Alphaproteobacteria.
JO  - J. Bacteriol.
PY  - 2010
SP  - 305
EP  - 306
VL  - 193
AB  - The order 'Parvularculales' represents the seventh order in the class Alphaproteobacteria.
AB  - Parvularcula bermudensis, the type species of the order, was isolated from the Sargasso Sea
AB  - using dilution-to-extinction culturing. We present here the complete genome sequence of
AB  - Parvularcula bermudensis HTCC2503(T) that contains genes for carotenoid biosynthesis,
AB  - dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Kang, I.
AU  - Vergin, K.L.
AU  - Lee, K.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Genome Sequence of Oceanicaulis sp. HTCC2633, Isolated from the Western Sargasso Sea.
JO  - J. Bacteriol.
PY  - 2010
SP  - 317
EP  - 318
VL  - 193
AB  - The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine
AB  - dinoflagellate. Here we announce the genome sequence of Oceanicaulis sp. strain HTCC2633,
AB  - isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of
AB  - strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Kang, I.
AU  - Yang, S.J.
AU  - Jang, Y.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
AU  - Cho, J.C.
TI  - Complete Genome Sequence of strain HTCC2170, a Novel Member of the Genus Maribacter in the Family Flavobacteriaceae.
JO  - J. Bacteriol.
PY  - 2010
SP  - 303
EP  - 304
VL  - 193
AB  - Strain HTCC2170 was isolated from surface waters off the Oregon coast using
AB  - dilution-to-extinction culturing. Here we present the finished genome sequence of a marine
AB  - bacterium, Maribacter sp. HTCC2170. Maribacter sp. HTCC2170 is predicted to be a facultatively
AB  - aerobic chemoorganotroph that is capable of macromolecule degradation and anaerobic
AB  - respiration based on genomic sequence analysis.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Kwon, K.K.
AU  - Kang, I.
AU  - Kang, S.G.
AU  - Lee, J.H.
AU  - Kim, S.J.
AU  - Cho, J.C.
TI  - Complete genome sequence of 'Candidatus Puniceispirillum marinum' IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3240
EP  - 3241
VL  - 192
AB  - The complete genome sequence of 'Candidatus Puniceispirillum marinum' IMCC1322, the first
AB  - cultured representative of the SAR116 clade in the
AB  - Alphaproteobacteria, is reported here. The genome contains genes for
AB  - proteorhodopsin, aerobic-type carbon monoxide dehydrogenase,
AB  - dimethylsulfoniopropionate demethylase, and C(1) compound metabolism. The
AB  - genome information proposes the SAR116 group to be metabolic generalists
AB  - in ocean nutrient cycling.
ER  -

TY  - JOUR
AU  - Oh, H.M.
AU  - Lee, K.
AU  - Jang, Y.
AU  - Kang, I.
AU  - Kim, H.J.
AU  - Kang, T.W.
AU  - Kim, S.Y.
AU  - Cho, J.C.
TI  - Genome Sequence of Strain IMCC9480, a Xanthorhodopsin-bearing Betaproteobacterium Isolated from the Arctic Ocean.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3421
EP  - 3421
VL  - 193
AB  - Strain IMCC9480 is a novel member of the family Oxalobacteraceae of the Betaproteobacteria,
AB  - isolated from the Arctic Ocean by
AB  - dilution-to-extinction culturing. Here we present the draft genome
AB  - sequence of strain IMCC9480. The genome is predicted to contain genes for
AB  - xanthorhodopsin, retinoid biosynthesis, carbon monoxide dehydrogenase, and
AB  - C1 metabolism.
ER  -

TY  - JOUR
AU  - Oh, J.D.
AU  - Kling-Backhed, H.
AU  - Giannakis, M.
AU  - Xu, J.
AU  - Fulton, R.S.
AU  - Fulton, L.A.
AU  - Cordum, H.S.
AU  - Wang, C.
AU  - Elliott, G.
AU  - Edwards, J.
AU  - Mardis, E.R.
AU  - Engstrand, L.G.
AU  - Gordon, J.I.
TI  - The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 9999
EP  - 10004
VL  - 103
AB  - Helicobacter pylori produces acute superficial gastritis in nearly all of its human hosts.
AB  - However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition
AB  - characterized in part by diminished numbers of acid-producing parietal cells and increased
AB  - risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic
AB  - mouse model with an engineered ablation of parietal cells to show that loss of parietal cells
AB  - provides an opportunity for a H. pylori isolate from a patient with ChAG (HPAG1) to bind to,
AB  - enter, and persist within gastric stem cells. This finding raises the question of how ChAG
AB  - influences H. pylori genome evolution, physiology, and tumorigenesis. Here we describe the
AB  - 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its
AB  - predicted ORFs, were used for whole-genome genotyping of additional H. pylori ChAG isolates
AB  - obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as
AB  - ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric
AB  - adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as
AB  - genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome
AB  - transcriptional profiling of HPAG1's response to acid during in vitro growth indicates that
AB  - genes encoding components of metal uptake and utilization pathways, outer membrane proteins,
AB  - and virulence factors are among those associated with H. pylori's adaptation to ChAG.
ER  -

TY  - JOUR
AU  - Oh, S.
AU  - Zhang, R.
AU  - Wu, Q.L.
AU  - Liu, W.T.
TI  - Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake.
JO  - Genome Announcements
PY  - 2014
SP  - e01137
EP  - e01114
VL  - 2
AB  - SAR11 clade bacteria are abundant and play a key role in the nutrient cycles of marine and,
AB  - presumably, inland aquatic environments. We report here the draft
AB  - genome sequence of a novel species in the SAR11 cluster, reconstructed from a
AB  - metagenomic data set obtained from a Tibetan lake.
ER  -

TY  - JOUR
AU  - OHair, J.A.
AU  - Li, H.
AU  - Thapa, S.
AU  - Scholz, M.
AU  - Zhou, S.
TI  - Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park.
JO  - Genome Announcements
PY  - 2017
SP  - e00631
EP  - e00617
VL  - 5
AB  - Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel
AB  - cellulolytic thermophiles. We report here the draft genome sequence of
AB  - one of these isolates, Bacillus altitudinis YNP4-TSU.
ER  -

TY  - JOUR
AU  - Ohji, S.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Tsuchikane, K.
AU  - Ezaki, T.
AU  - Fujita, N.
TI  - The Complete Genome Sequence of Pseudomonas putida NBRC 14164T Confirms High Intraspecies Variation.
JO  - Genome Announcements
PY  - 2014
SP  - e00029
EP  - e00014
VL  - 2
AB  - Pseudomonas putida has attracted much interest for its environmental, industrial,
AB  - biotechnological, and clinical importance. Here, we report the complete genome
AB  - sequence of the type strain P. putida NBRC 14164. This genome sequence will
AB  - assist to further elucidate the molecular mechanisms of the characteristic traits
AB  - among strains belonging to the species P. putida.
ER  -

TY  - JOUR
AU  - Ohkuma, M.
AU  - Yuki, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Oshida, Y.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
TI  - Draft Genome Sequence of the Alkaliphilic and Xylanolytic Paenibacillus sp. Strain JCM 10914, Isolated from the Gut of a Soil-Feeding Termite.
JO  - Genome Announcements
PY  - 2014
SP  - e01144
EP  - e01113
VL  - 2
AB  - Panibacillus sp. strain JCM 10914 is a xylanolytic alkaliphile isolated from the  gut of a
AB  - soil-feeding termite. Its draft genome sequence revealed various genes
AB  - for hydrolytic enzymes and will facilitate studies on adaptation to the highly
AB  - alkaline gut environment and its role in digesting soil organic matter in the
AB  - gut.
ER  -

TY  - JOUR
AU  - Ohnishi, N.
AU  - Maruyama, F.
AU  - Ogawa, H.
AU  - Kachi, H.
AU  - Yamada, S.
AU  - Fujikura, D.
AU  - Nakagawa, I.
AU  - Hang'ombe, M.B.
AU  - Thomas, Y.
AU  - Mweene, A.S.
AU  - Higashi, H.
TI  - Genome Sequence of a Bacillus anthracis Outbreak Strain from Zambia, 2011.
JO  - Genome Announcements
PY  - 2014
SP  - e00116
EP  - e00114
VL  - 2
AB  - In August 2011, an anthrax outbreak occurred among Hippopotamus amphibius hippopotamuses and
AB  - humans in Zambia. Here, we report the draft genome sequence of
AB  - the Bacillus anthracis outbreak strain CZC5, isolated from tissues of H.
AB  - amphibius hippopotamuses that had died in the outbreak area.
ER  -

TY  - JOUR
AU  - Ohnishi, Y.
AU  - Ishikawa, J.
AU  - Hara, H.
AU  - Suzuki, H.
AU  - Ikenoya, M.
AU  - Ikeda, H.
AU  - Yamashita, A.
AU  - Hattori, M.
AU  - Horinouchi, S.
TI  - Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350.
JO  - J. Bacteriol.
PY  - 2008
SP  - 4050
EP  - 4060
VL  - 190
AB  - We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium
AB  - producing an antituberculosis agent, streptomycin, which is the first aminoglycoside
AB  - antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929
AB  - base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames,
AB  - six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted
AB  - repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary
AB  - structure, consisting of several palindromes with a loop sequence of 5'-GGA-3', are
AB  - different from those of typical telomeres conserved among other Streptomyces species. In
AB  - accordance with the difference, the chromosome has pseudogenes for a conserved terminal
AB  - protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap
AB  - proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species,
AB  - Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the
AB  - characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific
AB  - proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of
AB  - known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed
AB  - that at least four of these clusters, in addition to the streptomycin biosynthesis gene
AB  - cluster, were activated directly or indirectly by AdpA, which is a central transcriptional
AB  - activator for secondary metabolism and morphogenesis in the A-factor (a gamma-butyrolactone
AB  - signaling molecule) regulatory cascade in S. griseus.
ER  -

TY  - JOUR
AU  - Ohno, S.
AU  - Handa, N.
AU  - Watanabe-Matsui, M.
AU  - Takahashi, N.
AU  - Kobayashi, I.
TI  - Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity.
JO  - J. Bacteriol.
PY  - 2008
SP  - 2039
EP  - 2049
VL  - 190
AB  - Several type II restriction-modification gene complexes can force their maintenance on their
AB  - host bacteria by killing cells that have lost them
AB  - in a process called postsegregational killing or genetic addiction. It
AB  - is likely to proceed by dilution of the modification enzyme molecule
AB  - during rounds of cell division following the gene loss, which exposes
AB  - unmethylated recognition sites on the newly replicated chromosomes to
AB  - lethal attack by the remaining restriction enzyme molecules. This
AB  - process is in apparent contrast to the process of the classical types
AB  - of postsegregational killing systems, in which built-in metabolic
AB  - instability of the antitoxin allows release of the toxin for lethal
AB  - action after the gene loss. In the present study, we characterize a
AB  - mutant form of the EcoRII gene complex that shows stronger capacity in
AB  - such maintenance. This phenotype is conferred by an L80P amino acid
AB  - substitution (T239C nucleotide substitution) mutation in the
AB  - modification enzyme. This mutant enzyme showed decreased DNA
AB  - methyltransferase activity at a higher temperature in vivo and in vitro
AB  - than the nonmutated enzyme, although a deletion mutant lacking the
AB  - N-terminal 83 amino acids did not lose activity at either of the
AB  - temperatures tested. Under a condition of inhibited protein synthesis,
AB  - the activity of the L80P mutant was completely lost at a high
AB  - temperature. In parallel, the L80P mutant protein disappeared more
AB  - rapidly than the wild-type protein. These results demonstrate that the
AB  - capability of a restriction-modification system in forcing maintenance
AB  - on its host can be modulated by a region of its antitoxin, the
AB  - modification enzyme, as in the classical postsegregational killing
AB  - systems.
ER  -

TY  - JOUR
AU  - Ohsawa, K.
AU  - Imai, Y.
AU  - Ito, D.
AU  - Kohsaka, S.
TI  - Molecular cloning and characterization of annexin V-binding proteins with highly hydrophilic peptide structure.
JO  - J. Neurochem.
PY  - 1996
SP  - 89
EP  - 97
VL  - 67
AB  - We previously reported that annexin V promoted the survival of cultured rat neocortical
AB  - neurons.  In an effort to elucidate the mechanism underlying this neurotrophic activity of
AB  - annexin V, we have attempted to identify the target or binding proteins of annexin V in
AB  - neuronal cells.  Herein, we screened an embryonic day 17 rat brain cDNA library by western
AB  - blot using glutathione S-transferase-annexin V fusion protein as a probe and then isolated
AB  - four clones showing binding to annexin V in a ca2+ - and phospholipid-dependent manner.
AB  - Although these cDNAs encoded different polypeptides, all four polypeptides shared the unique
AB  - feature of containing highly hydrophilic stretches with high Lys, Glu, and Ser contents.
AB  - Deduced amino acid sequences of two clones showed high homology with human X-linked Helicase2
AB  - (XH2) and DNA (cytosine-5) methyltransferase (DMTase) sequences, whereas the other two were
AB  - not related to any known peptide sequence.  These results suggest that XH2 and DMTase are
AB  - candidates for annexin V-binding proteins and thus may mediate the biological activity of
AB  - annexin V.
ER  -

TY  - JOUR
AU  - Ohshima, H.
AU  - Matsuoka, S.
AU  - Asai, K.
AU  - Sadaie, Y.
TI  - Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg.
JO  - J. Bacteriol.
PY  - 2002
SP  - 381
EP  - 389
VL  - 184
AB  - Transcriptional analysis and disruption of five open reading frames (ORFs), ydiO, ydiP, ydiR,
AB  - ydiS, and ydjA, in the prophage 3 region of the chromosome of Bacillus subtilis Marburg
AB  - revealed that they are component genes of the intrinsic BsuM restriction and modification
AB  - system of this organism. The classical mutant strain RM125, which lacks the restriction and
AB  - modification system of B. subtilis Marburg, lacks the prophage 3 region carrying these five
AB  - ORFs. These ORFs constitute two operons, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon,
AB  - both of which are expressed during the logarithmic phase of growth. The predicted gene
AB  - products YdiO and YdiP are the orthologues of cytosine DNA methyltransferases. The predicted
AB  - YdiS product is an orthologue of restriction nucleases, while the predicted YdiR and YdjA
AB  - products have no apparent paralogues and orthologues whose functions are known. Disruption of
AB  - the ydiR-ydiS-ydjA operon resulted in enhanced transformation by plasmid DNA carrying multiple
AB  - BsuM target sequences. Disruption of ydiO or ydiP function requires disruption of at least one
AB  - of the following genes on the chromosome: ydiR, ydiS, and ydjA. The degrees of methylation of
AB  - the BsuM target sequences on chromosomal DNAs were estimated indirectly by determining the
AB  - susceptibility to digestion with XhoI (an isoschizomer of BsuM) of DNAs extracted from the
AB  - disruptant strains. Six XhoI (BsuM) sites were examined. XhoI digested at the XhoI sites in
AB  - the DNAs from disruptants with disruptions in both operons, while XhoI did not digest at the
AB  - XhoI sites in the DNAs from the wild-type strain or from the disruptants with disruptions in
AB  - the ydiR-ydiS-ydjA operon. Therefore, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon are
AB  - considered operons that are responsible for BsuM modification and BsuM restriction,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Ohta, K.
AU  - Keszenman-Pereyra, D.
AU  - Nicolas, A.
AU  - Shibata, T.
TI  - A novel meiosis-induced site-specific endonuclease activity in yeast mitochondria.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 174
EP  - 174
VL  - 17C
AB  - Sequence-specific endonucleases in eukaryotic cells have been shown to play a crucial role in
AB  - the initiation of genetic recombination. We have found a sequence-specific DNA endonuclease
AB  - activity that cuts DNAs of phage Phi105c and phage Phix174 in a cell-free extracts of a
AB  - synchronously-sporulating strain (SK1) of S. cerevisiae. The preparation from SK1 cells in
AB  - early meiotic phase had 40-fold higher activity than that in exponential growing phase.
AB  - Subcellular fractionation revealed that this activity is condensed in the crude mitochondrial
AB  - fraction. In addition, the activity to cut Phi105c DNA was not detected in the extract from
AB  - p-mutant (large deletion mutations that block all mitochondrial protein synthesis) of the SK1
AB  - strain. Furthermore, the ability to produce the endonuclease was able to be transferred into a
AB  - po strain by mitochondrial transfer through cytoduction. Comparison of nucleotide sequences
AB  - around the cutting sites in Phi 105c and Phix174 DNA suggests that the endonuclease recognizes
AB  - a -20 base pair sequence and generates ends with 4 base-5' overhang. The sequences around the
AB  - cutting sites are different from those by an other yeast mitochondrial endonucleases. As well
AB  - as other yeast mitochondrial sequence-specific endonucleases, the endonuclease in SK1 strain
AB  - is speculated to initiate gene conversion in the mitochondrial genome.
ER  -

TY  - JOUR
AU  - Ohta, K.
AU  - Nicolas, A.
AU  - Keszenman-Pereyra, D.
AU  - Shibata, T.
TI  - Endo.SK1: an inducible site-specific endonuclease from yeast mitochondria.
JO  - Mol. Gen. Genet.
PY  - 1996
SP  - 395
EP  - 404
VL  - 250
AB  - Site-specific endonucleases have been found in various eukaryotic organelles such
AB  - as mitochondria, chloroplasts and nuclei.  These endonucleases initiate site-specific or
AB  - homologous
AB  - gene conversion in mitochondrial and nuclear DNA.  Here, we report a new site-specific
AB  - endonuclease activity, Endo.SK1, identified in mitochondria of strain SK1, a homothallic
AB  - diploid
AB  - strain of Saccharomyces cerevisiae.  Nucleotide sequences around the Endo.SK1-cleavage sites
AB  - are
AB  - different from those of known yeast site-specific endonucleases.  The Endo.SK1 activity is, at
AB  - least partly, specified by a gene in the Sk1-derived mitochondria.  A novel feature of the
AB  - Endo.SK1 activity is its inducibility: the endonuclease activity was induced by ca. 40-fold by
AB  - transfer of cells from a glucose medium into an acetate medium, and was then repressed.  This
AB  - transient induction was independent of the ploidy level of the cells, and coincided with
AB  - induction of
AB  - fumarase, a mitochondrial enzyme involved in the TCA cycle.  Co-induction and co-repression of
AB  - the mitochondrial site-specific endonuclease activity and a respiration-related enzyme
AB  - indicate that
AB  - the endonuclease activity is regulated in response to physiological conditions, and suggest a
AB  - possible role for the endonuclease in mitochondrial DNA metabolism.
ER  -

TY  - JOUR
AU  - Ohta, Y.
AU  - Nishi, S.
AU  - Kobayashi, K.
AU  - Tsubouchi, T.
AU  - Iida, K.
AU  - Tanizaki, A.
AU  - Kurosawa, K.
AU  - Adachi, A.
AU  - Nishihara, M.
AU  - Sato, R.
AU  - Hasegawa, R.
AU  - Hatada, Y.
TI  - Draft Genome Sequence of Novosphingobium sp. Strain MBES04, Isolated from Sunken  Wood from Suruga Bay, Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e01373
EP  - e01314
VL  - 3
AB  - This report describes the draft genome sequence of Novosphingobium sp. strain MBES04, isolated
AB  - from sunken wood from Suruga Bay, Japan, which is capable of
AB  - degrading a wide range of lignin-related aromatic monomers. The draft genome
AB  - sequence contains 5,361,448 bp, with a G+C content of 65.4%.
ER  -

TY  - JOUR
AU  - Ohta, Y.
AU  - Shimane, Y.
AU  - Nishi, S.
AU  - Ichikawa, J.
AU  - Kurosawa, K.
AU  - Tsubouchi, T.
AU  - Ishii, S.
TI  - Complete Genome Sequence of Sphingobium sp. Strain YG1, a Lignin Model Dimer-Metabolizing Bacterium Isolated from Sediment in Kagoshima Bay, Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00267
EP  - e00218
VL  - 6
AB  - Sphingobium sp. strain YG1 is a lignin model dimer-metabolizing bacterium newly isolated from
AB  - sediment in Kagoshima, Japan, at a depth of 102 m. Here, we report
AB  - the complete genome nucleotide sequence of strain YG1.
ER  -

TY  - JOUR
AU  - Ohtani, N.
AU  - Sato, M.
AU  - Tomita, M.
AU  - Itaya, M.
TI  - Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2008
SP  - 2472
EP  - 2475
VL  - 72
AB  - Conjugational transfer of pLS20 in Bacillus subtilis Marburg 168 is restricted by the BsuM
AB  - restriction modification system. Restriction
AB  - efficiency was measured using pLS20 derivatives possessing various
AB  - numbers of XhoI sites, which are known to be recognized by BsuM. An
AB  - increase in XhoI sites clearly reduced the conjugational efficiency of
AB  - pLS20 as compared with that of pUB110 plasmid lacking XhoI.
ER  -

TY  - JOUR
AU  - Ohtani, N.
AU  - Tomita, M.
AU  - Itaya, M.
TI  - The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination.
JO  - Extremophiles
PY  - 2012
SP  - 237
EP  - 244
VL  - 16
AB  - The extremely thermophilic bacterium Thermus thermophilus is a model organism for structural
AB  - biology and systems biology, and the so-called "Structural and Functional Whole-Cell Project
AB  - for T. thermophilus HB8" is in progress. The released genomic sequence of the strain HB8 is
AB  - composed of chromosome, pTT27 megaplasmid, and pTT8 plasmid. In this paper, however, a third
AB  - plasmid was demonstrated and its sequence was determined. Although this plasmid pVV8 had been
AB  - reported before, limited information and an unfortunate dropout in the substrain, whose
AB  - genomic sequence was determined, would have prevented the plasmid from coming to public
AB  - attention. The intrinsic circular plasmid, which was estimated to be six to ten copies in a
AB  - cell, is 81151 bp and its G + C content is 68%. Among the identified 91 ORFs, a single gene
AB  - has been experimentally analyzed before and is known as xylose isomerase. The phnCDEGHIJKLMX
AB  - operon related to phosphonate metabolism, alkaline phosphatase, putative transcriptional
AB  - regulators, several sets of toxin-antitoxin system, and transposase-like ORFs are also encoded
AB  - on the pVV8 plasmid. Although association with cell aggregation was the one phenotypic
AB  - characteristic of the plasmid that had been reported, it was never confirmed. Comparison of T.
AB  - thermophilus HB8 strains suggests that the pVV8 is nonessential for growth.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Fujita, N.
AU  - Nagata, Y.
AU  - Tsuda, M.
AU  - Iwasaki, T.
AU  - Hatta, T.
TI  - Complete Genome Sequence of Ralstonia pickettii DTP0602, a 2,4,6-Trichlorophenol  Degrader.
JO  - Genome Announcements
PY  - 2013
SP  - e00903
EP  - e00913
VL  - 1
AB  - Ralstonia pickettii strain DTP0602 utilizes 2,4,6-trichlorophenol as its sole carbon and
AB  - energy source. Here, we report the complete genome sequence of strain
AB  - DTP0602, which comprises three chromosomes and no plasmids. We also found that
AB  - the two had gene clusters responsible for the degradation of
AB  - 2,4,6-trichlorophenol are located on the 2.9-Mb chromosome 2.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Kishida, K.
AU  - Sato, T.
AU  - Tabata, M.
AU  - Kawasumi, T.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Tsuda, M.
AU  - Nagata, Y.
TI  - Complete Genome Sequence of Pseudomonas sp. Strain TKP, Isolated from a gamma-Hexachlorocyclohexane-Degrading Mixed Culture.
JO  - Genome Announcements
PY  - 2014
SP  - e01241
EP  - e01213
VL  - 2
AB  - Pseudomonas sp. strain TKP does not degrade gamma-hexachlorocyclohexane (gamma-HCH), but it
AB  - persistently coexists with the gamma-HCH-degrading
AB  - Sphingobium sp. strain TKS in a mixed culture enriched by gamma-HCH. Here, we
AB  - report the complete genome sequence of strain TKP, which consists of one circular
AB  - chromosome with a size of 7 Mb.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Maruyama, F.
AU  - Mitsui, H.
AU  - Nagata, Y.
AU  - Tsuda, M.
TI  - Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6970
EP  - 6971
VL  - 194
AB  - We report the complete genome sequence of Acidovorax sp. strain KKS102, a
AB  - polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo.
AB  - The genome contains a single circular 5,196,935-bp chromosome and no plasmids.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Moriya, A.
AU  - Kato, H.
AU  - Ogawa, N.
AU  - Nagata, Y.
AU  - Tsuda, M.
TI  - Complete Genome Sequence of a Phenanthrene Degrader, Burkholderia sp. HB-1 (NBRC  110738).
JO  - Genome Announcements
PY  - 2015
SP  - e01283
EP  - e01215
VL  - 3
AB  - The phenanthrene-degrading Burkholderia sp. HB-1 was isolated from a phenanthrene-enrichment
AB  - culture seeded with a pristine farm soil sample. We
AB  - report the complete genome sequence of HB-1, which has been deposited to the
AB  - stock culture (NBRC 110738) at Biological Resource Center, National Institute of
AB  - Technology and Evaluation (NITE), Tokyo, Japan. The genome of strain HB-1
AB  - comprises two circular chromosomes of 4.1 Mb and 3.1 Mb. The finishing was
AB  - facilitated by the computational tools GenoFinisher, AceFileViewer, and
AB  - ShortReadManager.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Nagata, Y.
AU  - Numata, M.
AU  - Tsuchikane, K.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Tsuda, M.
AU  - Fujita, N.
AU  - Kawai, F.
TI  - Complete Genome Sequence of Polyvinyl Alcohol-Degrading Strain Sphingopyxis sp. 113P3 (NBRC 111507).
JO  - Genome Announcements
PY  - 2015
SP  - e01169
EP  - e01115
VL  - 3
AB  - Strain 113P3 was isolated from activated sludge and identified as a polyvinyl alcohol
AB  - (PVA)-degrading Pseudomonas species; it was later reidentified as Sphingopyxis species. Only
AB  - three genes are directly relevant to the metabolism of PVA and comprise the pva operon, which
AB  - was deposited as accession no. AB190228. Here, we report the complete genome sequence of
AB  - strain 113P3, which has been conserved as a stock culture (NBRC 111507) at the Biological
AB  - Resource Center, National Institute of Technology and Evaluation (NITE) (Tokyo, Japan). The
AB  - genome of strain 113P3 is composed of a 4.4-Mb circular chromosome and a 243-kb plasmid. The
AB  - whole finishing was conducted in silico except for four PCRs. The sequence corresponding to
AB  - AB190288 exists on the chromosome.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Nagata, Y.
AU  - Numata, M.
AU  - Tsuchikane, K.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Tsuda, M.
AU  - Fujita, N.
AU  - Kawai, F.
TI  - Complete Genome Sequence of Sphingopyxis macrogoltabida Type Strain NBRC 15033, Originally Isolated as a Polyethylene Glycol Degrader.
JO  - Genome Announcements
PY  - 2015
SP  - e01401
EP  - e01415
VL  - 3
AB  - Sphingopyxis macrogoltabida strain 203, the type strain of the species, grew on polyethylene
AB  - glycol (PEG) and has been deposited to the stock culture at the
AB  - Biological Resource Center, National Institute of Technology and Evaluation
AB  - (NITE), under the number NBRC 15033. Here, we report the complete genome sequence
AB  - of strain NBRC 15033. Unfortunately, genes for PEG degradation were missing.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Nagata, Y.
AU  - Numata, M.
AU  - Tsuchikane, K.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Tsuda, M.
AU  - Fujita, N.
AU  - Kawai, F.
TI  - Complete Genome Sequence of a Polypropylene Glycol-Degrading Strain, Microbacterium sp. No. 7.
JO  - Genome Announcements
PY  - 2015
SP  - e01400
EP  - e01415
VL  - 3
AB  - Microbacterium (formerly Corynebacterium) sp. No. 7 was isolated from activated sludge as a
AB  - polypropylene glycol (PPG)-assimilating bacterial strain. Its
AB  - oxidative PPG degradation has been proposed on the basis of PPG dehydrogenase
AB  - activity and the metabolic products. Here, we report the complete genome sequence
AB  - of Microbacterium sp. No. 7. The genome of the strain No. 7 is composed of a
AB  - 4,599,046-bp circular chromosome and two linear plasmids. The whole finishing was
AB  - conducted in silico with aids of the computational tools GenoFinisher and
AB  - AceFileViewer. Strain No. 7 is available from the Biological Resource Center,
AB  - National Institute of Technology and Evaluation (NITE) (Tokyo, Japan).
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Nagata, Y.
AU  - Numata, M.
AU  - Tsuchikane, K.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Tsuda, M.
AU  - Fujita, N.
AU  - Kawai, F.
TI  - Complete Genome Sequence of Polypropylene Glycol- and Polyethylene Glycol-Degrading Sphingopyxis macrogoltabida Strain EY-1.
JO  - Genome Announcements
PY  - 2015
SP  - e01399
EP  - e01315
VL  - 3
AB  - Strain EY-1 was isolated from a microbial consortium growing on a random polymer  of ethylene
AB  - oxide and propylene oxide. Strain EY-1 grew on polyethylene glycol
AB  - and polypropylene glycol and identified as Sphingopyxis macrogoltabida. Here, we
AB  - report the complete genome sequence of Sphingopyxis macrogoltabida EY-1. The
AB  - genome of strain EY-1 is comprised of a 4.76-Mb circular chromosome, and five
AB  - plasmids. The whole finishing was conducted in silico, with aids of computational
AB  - tools GenoFinisher and AceFileViewer. Strain EY-1 is available from Biological
AB  - Resource Center, National Institute of Technology and Evaluation (Tokyo, Japan)
AB  - (NITE).
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Nonoyama, S.
AU  - Nagata, Y.
AU  - Numata, M.
AU  - Tsuchikane, K.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Tsuda, M.
AU  - Fujita, N.
AU  - Kawai, F.
TI  - Complete Genome Sequence of Sphingopyxis terrae Strain 203-1 (NBRC 111660), a Polyethylene Glycol Degrader.
JO  - Genome Announcements
PY  - 2016
SP  - e00530
EP  - e00516
VL  - 4
AB  - The complete genome sequence of Sphingopyxis terrae strain 203-1, which is capable of growing
AB  - on polyethylene glycol, was determined. The genome consisted
AB  - of a chromosome with a size of 3.98 Mb and a plasmid with a size of 4,328 bp. The
AB  - strain was deposited to the National Institute of Technology and Evaluation
AB  - (Tokyo, Japan) under the number NBRC 111660.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Nonoyama, S.
AU  - Nagata, Y.
AU  - Numata, M.
AU  - Tsuchikane, K.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Tsuda, M.
AU  - Fujita, N.
AU  - Kawai, F.
TI  - Complete Genome Sequence of Sphingopyxis macrogoltabida Strain 203N (NBRC 111659), a Polyethylene Glycol Degrader.
JO  - Genome Announcements
PY  - 2016
SP  - e00529
EP  - e00516
VL  - 4
AB  - We determined the complete genome sequence of Sphingopyxis macrogoltabida strain  203N, a
AB  - polyethylene glycol degrader. Because the PacBio assembly (285x coverage)
AB  - seemed to be full of nucleotide-level mismatches, the Newbler assembly of MiSeq
AB  - mate-pair and paired-end data was used for finishing and the PacBio assembly was
AB  - used as a reference. The PacBio assembly carried 414 nucleotide mismatches over
AB  - 5,953,153 bases of the 203N genome.
ER  -

TY  - JOUR
AU  - Ohtsubo, Y.
AU  - Sato, T.
AU  - Kishida, K.
AU  - Tabata, M.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Tsuda, M.
AU  - Nagata, Y.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of  Hexachlorocyclohexane.
JO  - Genome Announcements
PY  - 2014
SP  - e01130
EP  - e01113
VL  - 2
AB  - Pseudomonas aeruginosa MTB-1 does not degrade gamma-hexachlorocyclohexane (gamma-HCH), but
AB  - this bacterium persistently coexists with a gamma-HCH-degrading
AB  - strain, Sphingomonas sp. MM-1, in a microbial community enriched by the technical
AB  - formulation of HCH. Here we report the complete MTB-1 genome sequence, with a
AB  - 6.6-Mb circular chromosome.
ER  -

TY  - JOUR
AU  - Ohtsuka, E.
AU  - Ishino, Y.
AU  - Ibaraki, K.
AU  - Ikehara, M.
TI  - Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties.
JO  - Eur. J. Biochem.
PY  - 1984
SP  - 447
EP  - 450
VL  - 139
AB  - The deoxyribooctanucleotide d(G-G-A-A-T-T-C-C), containing the recognition sequence for EcoRI,
AB  - d(G-A-A-T-T-C), and analogs containing modified sugar moieties were tested for their activity
AB  - in cleavage with EcoRI.  These analogs, with replacement in the third position from the 5'
AB  - end, were synthesized using 9-b-D-arabinosyladenine (aA), 2'-deoxy-2'-fluoroadenosine (Afl)
AB  - and adenosine (rA).  Duplex formation by the three analogs was confirmed by measurements of
AB  - ultraviolet/temperature profiles.  It was found that EcoRI cleaved these duplexes less
AB  - efficiently than d(G-G-A-A-T-T-C-C).  The adenosine-containing analog d(G-G)-rA-d(A-T-T-C-C)
AB  - was cleaved much more slowly than d(G-G)-aA-d(A-T-T-C-C) and d(G-G-Afl-A-T-T-C-C).  The
AB  - corresponding ribooctamer G-G-A-A-U-U-C-C showed a higher melting temperature than the
AB  - deoxyoctamers but its duplex was not cleaved by this enzyme.  An analog with
AB  - 2'-deoxy-2'-fluoroguanosine at the second position was cleaved by the endonuclease faster
AB  - than the natural deoxyoctamer.
ER  -

TY  - JOUR
AU  - Ohtsuka, E.
AU  - Morisawa, H.
AU  - Ikehara, M.
TI  - Studies on deoxynucleic acids and related compounds.  IV. Syntheses of an octanucleotide containing a recognition site for restriction enzyme EcoRI and of an arabinosyladenine analog.
JO  - Chem. Pharm. Bull. (Tokyo)
PY  - 1982
SP  - 874
EP  - 880
VL  - 30
AB  - An octanucleotide containing a recognition site for EcoRI and its
AB  - arabinosyladenine (araA) analog, dGGAATTCC and dGGaraAATTCC, were synthesized
AB  - by the phosphotriester approach with phosphoro-p-anisidate as the protecting
AB  - group for 3'-phosphodiesters.  araA was converted to
AB  - 5'-dimethoxytrityl-N,2'-O-O-benzoyl 3'-p-chlorophenyl phosphate and condensed
AB  - with N-benzoyldeoxyadenosine 3'-p-chlorophenyl phosphoro-p-anisidate to yield
AB  - the protected araAdAp.  Other deoxynucleotide blocks (dAAp, dGGp) were prepared
AB  - similarly and condensed with a 5'-deblocked dTTCC block having the 3'-O-benzoyl
AB  - group after removal of the p-anisidate group with isoamyl nitrite.
ER  -

TY  - JOUR
AU  - Ohtsuka, K.
AU  - Ohnishi, H.
AU  - Nozaki, E.
AU  - Pais, R.J.
AU  - Tortoli, E.
AU  - Yonetani, S.
AU  - Matsushima, S.
AU  - Tateishi, Y.
AU  - Matsumoto, S.
AU  - Watanabe, T.
TI  - Whole-Genome Sequence of Mycobacterium kyorinense.
JO  - Genome Announcements
PY  - 2014
SP  - e01062
EP  - e01014
VL  - 2
AB  - We report here the first draft genome sequence of Mycobacterium kyorinense, which was
AB  - described in 2009 and exhibits significant pathogenicity to humans.
ER  -

TY  - JOUR
AU  - Oinuma, K.I.
AU  - Suzuki, M.
AU  - Sato, K.
AU  - Nakaie, K.
AU  - Niki, M.
AU  - Takizawa, E.
AU  - Niki, M.
AU  - Shibayama, K.
AU  - Yamada, K.
AU  - Kakeya, H.
AU  - Kaneko, Y.
TI  - Genome Sequence of an Acinetobacter baumannii Strain Carrying Three Acquired Carbapenemase Genes.
JO  - Genome Announcements
PY  - 2016
SP  - e01290
EP  - e01216
VL  - 4
AB  - The emergence of multiple-carbapenemase-producing Acinetobacter strains has been  a serious
AB  - concern during the past decade. Here, we report the draft genome
AB  - sequence of an Acinetobacter baumannii strain isolated from a Japanese patient
AB  - with three acquired carbapenemase genes: blaNDM-1, blaTMB-1, and blaOXA-58.
ER  -

TY  - JOUR
AU  - Oishi, K.
AU  - Aoi, S.
AU  - Ehara, Y.
AU  - Otsuka, Y.
AU  - Shimamura, K.
AU  - Higuchi, Y.
AU  - Nomoto, M.
TI  - Inhibition of restriction endonucleases by commercial polysaccharides.
JO  - J. Ferment. Bioeng.
PY  - 1990
SP  - 360
EP  - 361
VL  - 69
AB  - Commercial polysaccharide preparations were investigated for their restriction
AB  - enzyme-inhibitory activities.  Dextran sulfate (S content 18.5%) and laminaran
AB  - from Eisenia arborea (0.88%) had marked inhibitory activity and haparin (13.1%)
AB  - and iota-, kappa-, and lambda-carrageenans (3.0, 3.8, and 4.3%) showed moderate
AB  - inhibition.  The effects of sulfation level and the structure of the
AB  - carbohydrate moiety on the inhibitory activity were discussed.
ER  -

TY  - JOUR
AU  - Ojala, T.
AU  - Kuparinen, V.
AU  - Koskinen, J.P.
AU  - Alatalo, E.
AU  - Holm, L.
AU  - Auvinen, P.
AU  - Edelman, S.
AU  - Westerlund-Wikstrom, B.
AU  - Korhonen, T.K.
AU  - Paulin, L.
AU  - Kankainen, M.
TI  - Genome Sequence of Lactobacillus crispatus ST1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3547
EP  - 3548
VL  - 192
AB  - Lactobacillus crispatus is a common member of the beneficial microbiota present in the
AB  - vertebrate gastrointestinal and human genitourinary tracts.
AB  - Here, we report the genome sequence of L. crispatus ST1, a chicken isolate
AB  - displaying strong adherence to vaginal epithelial cells.
ER  -

TY  - JOUR
AU  - Oka, M.
AU  - Meacham, A.M.
AU  - Hamazaki, T.
AU  - Rodic, N.
AU  - Chang, L.-J.
AU  - Terada, N.
TI  - De novo DNA methyltransferases Dnmt3a and Dnmt3b primarily mediate the cytotoxic effect of 5-aza-2'-deoxycytidine.
JO  - Oncogene
PY  - 2005
SP  - 3091
EP  - 3099
VL  - 24
AB  - The deoxycytidine analog 5-aza-2'-deoxycitidine (5-aza-dC) is a potent chemotherapeutic agent
AB  - effective against selective types of cancer. The molecular mechanism by which 5-aza-dC induces
AB  - cancer cell death, however, is not fully understood. It has been accepted that the mechanism
AB  - of toxicity is due to the covalent binding between the DNA methyltransferase (Dnmt) and
AB  - 5-aza-dC-substituted DNA. In order to define which member of the Dnmt family plays a dominant
AB  - role in the cytotoxicity, we examined the effect of 5-aza-dC on cell growth and apoptosis in
AB  - various Dnmt null mutant embryonic stem (ES) cells. Of interest, Dnmt3a-Dnmt3b double null ES
AB  - cells were highly resistant to 5-aza-dC when compared to wild type, Dnmt3a null, Dnmt3b null,
AB  - or Dnmt1 null ES cells. The cellular sensitivity to 5-aza-dC correlated well with the
AB  - expression status of Dnmt3 in both undifferentiated and differentiated ES cells. When
AB  - exogenous Dnmt3a or Dnmt3b was expressed in double null ES cells, the sensitivity to 5-aza-dC
AB  - was partially restored. These results suggest that the cytotoxic effect of 5-aza-dC may be
AB  - mediated primarily through Dnmt3a and Dnmt3b de novo DNA methyltransferases. Further, the
AB  - ability to form Dnmt-DNA adducts was similar in Dnmt1 and Dnmt3, and the expression level of
AB  - Dnmt3 was not higher than that of Dnmt1 in ES cells. Therefore, Dnmt3-DNA adducts may be more
AB  - effective for inducing apoptosis than Dnmt1-DNA adducts. These results imply a therapeutic
AB  - potential of 5-aza-dC to cancers expressing Dnmt3.
ER  -

TY  - JOUR
AU  - Okada, K.
AU  - Na-Ubol, M.
AU  - Natakuathung, W.
AU  - Roobthaisong, A.
AU  - Maruyama, F.
AU  - Nakagawa, I.
AU  - Chantaroj, S.
AU  - Hamada, S.
TI  - Comparative Genomic Characterization of a Thailand-Myanmar Isolate, MS6, of Vibrio cholerae O1 El Tor, Which Is Phylogenetically Related to a 'US Gulf Coast' Clone.
JO  - PLoS ONE
PY  - 2014
SP  - E98120
EP  - E98120
VL  - 9
AB  - BACKGROUND: The cholera outbreaks in Thailand during 2007-2010 were exclusively
AB  - caused by the Vibrio cholerae O1 El Tor variant carrying the cholera toxin gene
AB  - of the classical biotype. We previously isolated a V. cholerae O1 El Tor strain
AB  - from a patient with diarrhea and designated it MS6. Multilocus sequence-typing
AB  - analysis revealed that MS6 is most closely related to the U. S. Gulf Coast clone
AB  - with the exception of two novel housekeeping genes. METHODOLOGY/PRINCIPAL
AB  - FINDINGS: The nucleotide sequence of the genome of MS6 was determined and
AB  - compared with those of 26 V. cholerae strains isolated from clinical and
AB  - environmental sources worldwide. We show here that the MS6 isolate is distantly
AB  - related to the ongoing seventh pandemic V. cholerae O1 El Tor strains. These
AB  - strains differ with respect to polymorphisms in housekeeping genes, seventh
AB  - pandemic group-specific markers, CTX phages, two genes encoding predicted
AB  - transmembrane proteins, the presence of metY (MS6_A0927) or hchA/luxR in a highly
AB  - conserved region of the V. cholerae O1 serogroup, and a superintegron (SI). We
AB  - found that V. cholerae species carry either hchA/luxR or metY and that the V.
AB  - cholerae O1 clade commonly possesses hchA/luxR, except for MS6 and U. S. Gulf
AB  - Coast strains. These findings illuminate the evolutionary relationships among V.
AB  - cholerae O1 strains. Moreover, the MS6 SI carries a quinolone-resistance gene
AB  - cassette, which was closely related with those present in plasmid-borne integrons
AB  - of other gram-negative bacteria. CONCLUSIONS/SIGNIFICANCE: Phylogenetic analysis
AB  - reveals that MS6 is most closely related to a U. S. Gulf Coast clone, indicating
AB  - their divergence before that of the El Tor biotype strains from a common V.
AB  - cholerae O1 ancestor. We propose that MS6 serves as an environmental aquatic
AB  - reservoir of V. cholerae O1.
ER  -

TY  - JOUR
AU  - Okada, K.
AU  - Natakuathung, W.
AU  - Na-Ubol, M.
AU  - Roobthaisong, A.
AU  - Wongboot, W.
AU  - Maruyama, F.
AU  - Nakagawa, I.
AU  - Chantaroj, S.
AU  - Hamada, S.
TI  - Characterization of 3 Megabase-Sized Circular Replicons from Vibrio cholerae.
JO  - Emerg. Infect. Dis.
PY  - 2015
SP  - 1262
EP  - 1263
VL  - 21
AB  - To the Editor: Prokaryotes typically have a single circular chromosome.  However, some
AB  - bacteria have >1 chromosome.  Vibrio bacteria, for example, have 2 circular chromosomes: 1
AB  - (Ch1) and 2 (Ch2).  Most recognizable genes responsible for essential cell functions and
AB  - pathogenicity are located on Ch1.  Ch2 is also thought to encode some genes essential for
AB  - normal cell function and those associated with virulence.  Both chromosomes are controlled
AB  - coordinately in their replicon and segregation.  Evidence suggests that Ch2 was originally a
AB  - mega-plasmid captured by an ancestral Vibrio species.  We report the characterization of
AB  - recent isolates of V. cholera 01 from Thailand that carry a novel gigantic replicon (Rep.3) in
AB  - addition to Ch1 and Ch2.
ER  -

TY  - JOUR
AU  - Okada, K.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Abe, A.
AU  - Kuwae, A.
AU  - Horiguchi, Y.
AU  - Abe, H.
TI  - Complete Genome Sequence of Bordetella bronchiseptica S798, an Isolate from a Pig with Atrophic Rhinitis.
JO  - Genome Announcements
PY  - 2014
SP  - e00436
EP  - e00414
VL  - 2
AB  - Bordetella bronchiseptica colonizes the respiratory tracts of a wide variety of mammals and
AB  - causes a range of diseases, from lethal pneumonia to asymptomatic
AB  - chronic infection. We report the complete genome sequence of Bordetella
AB  - bronchiseptica strain S798, isolated from a pig with atrophic rhinitis in Japan.
ER  -

TY  - JOUR
AU  - Okada, M.
TI  - Host-controlled restriction and modification of Salmonella typhimurium.
JO  - Keio J. Med.
PY  - 1969
SP  - 81
EP  - 97
VL  - 18
AB  - Since the discovery of sexuality in bacteria, hybridization between Escherichia
AB  - coli and Salmonella strains has been intensively studied by a number of
AB  - workers.  Despite initial uniformal negative results, hybrids did occur at much
AB  - lower frequencies than those between E. coli strains.  In the mating of
AB  - Salmonella, Hfr strains of E. coli have been employed as donors.  The hybrids
AB  - were viable and more fertile as recipients than the parent Salmonella strains,
AB  - in the sense of the frequency of hybrid formation per donor cell.  It was not
AB  - known, however, whether this barrier in gene exchange between these species
AB  - might be poor mating capacity or poor integration capacity or both.  In the
AB  - present paper, I shall show that fertile mutants, which were selected for
AB  - abnormally increased recipient ability in the transmission of an R factor 222
AB  - from E. coli (R+), are simultaneously accompanied by acquisition of the
AB  - increased recipient ability for E. coli chromosome and some alteration of
AB  - host-controlled restriction and modification as to R factors and phage P22.
ER  -

TY  - JOUR
AU  - Okada, R.
AU  - Matsumoto, M.
AU  - Zhang, Y.
AU  - Isaka, M.
AU  - Tatsuno, I.
AU  - Hasegawa, T.
TI  - Emergence of type I restriction modification system-negative emm1 type Streptococcus pyogenes clinical isolates in Japan.
JO  - APMIS
PY  - 2014
SP  - 914
EP  - 921
VL  - 122
AB  - Streptococcus pyogenes emm1 type is the dominant cause of streptococcal toxic shock syndrome
AB  - (STSS) in Japan and many other developed countries. Recently, the number of STSS patients in
AB  - Japan was reported to be increasing. Hence, we analyzed the S. pyogenes clinical isolates
AB  - detected in Japan after 2005. We found that the regions encoding the Spy1908-1910
AB  - two-component regulatory system and the adjacent type I restriction modification system were
AB  - deleted in some emm1 type isolates. The isolates with the deletion were detected only in the
AB  - emm1 strains that were isolated between 2010 and 2013, but not before 2010. Twenty-six of 46
AB  - (56.5%) emm1 type isolates were isolated in 2010-2013, and among these isolates, five of seven
AB  - (71.4%) emm1 type STSS isolates were shown to have that deletion. PFGE and PCR analysis for
AB  - the presence of several pyrogenic exotoxin-related genes suggested that the emm1 isolates with
AB  - and without the deletion shared the same genetic background. The emm1 isolates with the
AB  - deletion could incorporate exogenous plasmids by experimental electroporation transformation
AB  - far more efficiently. These results suggested that the novel emm1 isolates have occupied a
AB  - fairly large part of total emm1 isolates.
ER  -

TY  - JOUR
AU  - Okai, M.
AU  - Watanabe, A.
AU  - Ishida, M.
AU  - Urano, N.
TI  - Draft Genome Sequence of a Benzo[a]pyrene-Degrading Bacterium, Olleya sp. Strain  ITB9.
JO  - Genome Announcements
PY  - 2015
SP  - e01328
EP  - e01315
VL  - 3
AB  - Olleya sp. ITB9 is a benzo[a]pyrene-degrading bacterium, isolated from surface water near a
AB  - waste treatment plant at Tokyo Bay, Japan. Here, we present the
AB  - draft genome sequence of this strain, which consists of 58 contigs corresponding
AB  - to 3.4 Mb and a G+C content of 31.2%.
ER  -

TY  - JOUR
AU  - Okamoto, A.
AU  - Lee, H.
AU  - Yabutani, M.
AU  - Yamada, K.
AU  - Ohta, M.
TI  - Draft Genome Sequence of a Legionella pneumophila Serogroup 4 Strain Causing Legionellosis.
JO  - Genome Announcements
PY  - 2014
SP  - e00602
EP  - e00614
VL  - 2
AB  - Here, we report the draft genome sequence of the Legionella pneumophila Nagoya-1  strain,
AB  - serogroup 4, which was isolated from a clinical sample from a patient
AB  - with legionellosis. Several virulence-associated genes, including those encoding
AB  - the type IV (Dot/Icm) secretion system and effector proteins, were highly
AB  - conserved.
ER  -

TY  - JOUR
AU  - Okamoto, A.
AU  - Tanabe, K.
AU  - Saito, I.
TI  - Site-specific discrimination of cytosine and 5-methylcytosine in duplex DNA by peptide nucleic acids.
JO  - J. Am. Chem. Soc.
PY  - 2002
SP  - 10262
EP  - 10263
VL  - 124
AB  - For site-specific discrimination of cytosine (C) and 5-methylcytosine ((m)C) in duplex DNA, we
AB  - developed a new method using peptide nucleic acids (PNAs). The combination of a PNA-assisted
AB  - DNA displacement complex and a fluorescein-labeled probe oligomer allowed the detection of
AB  - (m)C at the defined sites in target DNA using a restriction enzyme. After treatment of the
AB  - complex with a restriction enzyme, strong fluorescence emission was observed for the complex
AB  - containing C at the target site, whereas the fluorescence intensity for the complex containing
AB  - (m)C was extremely weak.
ER  -

TY  - JOUR
AU  - Okano, K.
AU  - Furuta, S.
AU  - Ichise, S.
AU  - Miyata, N.
TI  - Whole-Genome Sequences of Two Manganese(II)-Oxidizing Bacteria, Bosea sp. Strain  BIWAKO-01 and Alphaproteobacterium Strain U9-1i.
JO  - Genome Announcements
PY  - 2016
SP  - e01309
EP  - e01316
VL  - 4
AB  - This report describes the whole-genome sequences of two Mn(II)-oxidizing bacteria, filamentous
AB  - Mn oxide microparticle-forming Bosea sp. strain BIWAKO-01
AB  - and alphaproteobacterium strain U9-1i.
ER  -

TY  - JOUR
AU  - Okano, K.
AU  - Miyata, N.
AU  - Ozaki, Y.
TI  - Genome Sequence of Microcystis aeruginosa Strain NIES-44.
JO  - Genome Announcements
PY  - 2015
SP  - e00135
EP  - e00115
VL  - 3
AB  - Microcystis aeruginosa is a typical algal bloom-forming cyanobacterium. This report describes
AB  - the whole-genome sequence of a non-microcystin-producing strain
AB  - of Microcystis aeruginosa, NIES-44, which was isolated from a Japanese lake.
ER  -

TY  - JOUR
AU  - Okano, K.
AU  - Shimizu, K.
AU  - Maseda, H.
AU  - Kawauchi, Y.
AU  - Utsumi, M.
AU  - Itayama, T.
AU  - Zhang, Z.
AU  - Sugiura, N.
TI  - Whole-Genome Sequence of the Microcystin-Degrading Bacterium Sphingopyxis sp. Strain C-1.
JO  - Genome Announcements
PY  - 2015
SP  - e00838
EP  - e00815
VL  - 3
AB  - This report describes the whole-genome sequence of an alkalitolerant microcystin-degrading
AB  - bacterium, Sphingopyxis sp. strain C-1, isolated from a
AB  - lake in China.
ER  -

TY  - JOUR
AU  - Okano, M.
TI  - DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation in mouse early development.
JO  - Jikken Igaku
PY  - 2000
SP  - 468
EP  - 471
VL  - 18
ER  -

TY  - JOUR
AU  - Okano, M.
TI  - DNA methylation and DNA methyltransferases in mammals.
JO  - Saibo Kogaku
PY  - 2001
SP  - 381
EP  - 386
VL  - 20
ER  -

TY  - JOUR
AU  - Okano, M.
AU  - Bell, D.W.
AU  - Haber, D.A.
AU  - Li, E.
TI  - DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.
JO  - Cell
PY  - 1999
SP  - 247
EP  - 257
VL  - 99
AB  - The establishment of DNA methylation patterns requires de novo methylation that occurs
AB  - predominantly during early development and gametogenesis in mice.  Here we demonstrate that
AB  - two recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, are essential for de novo
AB  - methylation and for mouse development.  Inactivation of both genes by gene targeting blocks de
AB  - novo methylation in ES cells and early embryos, but it has no effect on maintenance of
AB  - imprinted methylation patterns.  Dnmt3a and Dnmt3b also exhibit nonoverlapping functions in
AB  - development, with Dnmt3b specifically required for methylation of centromeric minor satellite
AB  - repeats.  Mutations of human DNMT3B are found in ICF syndrome, a developmental defect
AB  - characterized by hypomethylation of pericentromeric repeats.  Our results indicate that both
AB  - Dnmt3a and Dnmt3b function as de novo methyltransferases that play important roles in normal
AB  - development and disease.
ER  -

TY  - JOUR
AU  - Okano, M.
AU  - Li, E.
TI  - Genetic analyses of DNA methyltransferase genes in mouse model system.
JO  - J. Nutr.
PY  - 2002
SP  - 2462S
EP  - 2465S
VL  - 132
AB  - DNA methylation regulates important biological processes and is involved in tumorigenesis and
AB  - several human diseases, such as Rett and immunodeficiency, centromeric instability and facial
AB  - anomalies (ICF). The major objective of our research is to investigate the roles of DNA
AB  - methylation in mammals through genetic analysis of DNA methyltransferase genes in mouse and
AB  - human. Previously, we found that Dnmt1 knockout embryonic stem (ES) cells are capable of
AB  - methylating retroviral DNA de novo. In search of enzymes responsible for de novo methylation,
AB  - we have cloned a novel family of mammalian DNA methyltransferase genes, Dnmt3a and Dnmt3b.
AB  - Although extensive sequence similarity was found between Dnmt3a and Dnmt3b, little homology
AB  - was observed between Dnmt1 and Dnmt3a/3b in the catalytic domain as well as in the N-terminal
AB  - domain. Additionally, biochemical analysis revealed that, unlike Dnmt1, neither Dnmt3a nor
AB  - Dnmt3b had a strong preference to hemimethylated DNA substrates. Genetic analysis demonstrated
AB  - that Dnmt3a and Dnmt3b were required for de novo methylation activities in ES cells and during
AB  - early embryogenesis and were essential for early development. Interestingly, phenotype
AB  - analyses of single homozygous mice for either Dnmt3a or Dnmt3b suggested that the functions of
AB  - Dnmt3a and Dnmt3b also were required at the late developmental stage and even at the adult
AB  - stage.
ER  -

TY  - JOUR
AU  - Okano, M.
AU  - Takebayashi, S.
AU  - Okumura, K.
AU  - Li, E.
TI  - Assignment of cytosine-5 DNA methyltransferases Dnmt3a and Dnmt3b to mouse chromosome bands 12A2-A3 and 2H1 by in situ hybridization.
JO  - Cytogenet. Cell Genet.
PY  - 1999
SP  - 333
EP  - 334
VL  - 86
AB  - Methylation of cytosine at the C-5 position is a major form of DNA modification in vertebrates
AB  - and plays important roles in regulation of gene expression and development.  Previously, only
AB  - one mammalian cytosine-5 methyltransferase (now termed Dnmt1) was known and shown to be
AB  - required for maintaining global DNA methylation levels.  Recently, we cloned a family of novel
AB  - cytosine-5 methyltransferase genes, termed Dnmt3a and Dnmt3b, which do not share sequence
AB  - similarities to any known eukaryotic cytosine-5 methyltransferase genes.  Expression pattern
AB  - and biological analysis suggest that Dnmt3a and Dnmt3b are probably responsible for de novo
AB  - methylation, a key process by which DNA methylation patterns are established during
AB  - development.  In this study we have mapped chromosome locations of Dnmt3a and Dnmt3b to
AB  - 12A2-A3 and 2H1, respectively, by FISH.
ER  -

TY  - JOUR
AU  - Okano, M.
AU  - Xie, S.
AU  - Li, E.
TI  - Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 2536
EP  - 2540
VL  - 26
AB  - We have shown previously that de novo methylation activities persist in mouse embryonic stem
AB  - cells homozygous for a null mutation of Dnmt1 that encodes the major DNA cytosine
AB  - methyltransferase.  In this study, we have cloned a putative mammalian DNA methyltransferase
AB  - gene, termed Dnmt2, that is homologous to pmt1 of fission yeast.  Different from pmt1 in which
AB  - the catalytic Pro-Pro-Cys motif is 'mutated' to Pro-Ser-Cys, Dnmt2 contains all the
AB  - conserved methyltransferase motifs, thus likely encoding a functional cytosine
AB  - methyltransferase.  However, baculovirus-expressed Dnmt2 protein failed to methylate DNA in
AB  - vitro.  To investigate whether Dnmt2 functions as a DNA methyltransferase in vivo, we
AB  - inactivated the Dnmt2 gene by targeted deletion of the putative catalytic PPC motif in ES
AB  - cells.  We showed that endogenous virus was fully methylated in Dnmt2-deficient mutant ES
AB  - cells.  Furthermore, newly integrated retrovirus DNA was methylated de novo in infected mutant
AB  - ES cells as efficiently as in wild-type cells.  These results indicate that Dnmt2 is not
AB  - essential for global de novo or maintenance methylation of DNA in ES cells.
ER  -

TY  - JOUR
AU  - Okano, M.
AU  - Xie, S.
AU  - Li, E.
TI  - Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases.
JO  - Nat. Genet.
PY  - 1998
SP  - 219
EP  - 220
VL  - 19
AB  - De novo methylation of genomic DNA is a developmentally regulated process that is believed to
AB  - play a pivotal role in regulation of genomic imprinting and X-chromosome inactivation in
AB  - mammals.  Aberrant de novo methylation of growth regulatory genes has been associated with
AB  - tumorigenesis in humans.  We have shown previously that de novo methylation persists in
AB  - embryonic stem cells lacking Dnmt1, which encodes the constitutive DNA methyltransferase Dnmt1
AB  - (or MT1), indicating the existence of independently encoded de novo methyltransferases.
ER  -

TY  - JOUR
AU  - Okhapkina, S.S.
AU  - Netesova, N.A.
AU  - Golikova, L.N.
AU  - Seregina, E.V.
AU  - Sosnovtsev, S.V.
AU  - Abdurashitov, M.A.
AU  - Degtyarev, S.K.
TI  - Comparison of the homologous SfeI and LlaBI restriction-modification  systems.
JO  - Mol. Biol. (Mosk)
PY  - 2002
SP  - 432
EP  - 437
VL  - 36
AB  - A fragment containing the SfeI restriction-modification system (RMS)  operon was cloned from a
AB  - Streptococcus faecalis SE72 plasmid. Nucleotide sequence analysis revealed its high (99.2%)
AB  - homology to the operon for Lactococcus lactis subsp. cremoris W56 LlaBI RMS recognizing the
AB  - same site, 5'-CTRYAG-3'. A substantial difference was that SfeI RMS operon had an additional
AB  - 198-bp fragment and a larger gene for the putative control protein. No homology was observed
AB  - between operon-flanking sequences of the two closely related species, suggesting horizontal
AB  - transfer of the operon.
ER  -

TY  - JOUR
AU  - Okinaka, R.T.
AU  - Challacombe, J.
AU  - Drees, K.
AU  - Birdsell, D.N.
AU  - Janke, N.
AU  - Naumann, A.
AU  - Seymour, M.
AU  - Hornstra, H.
AU  - Schupp, J.
AU  - Sahl, J.
AU  - Foster, J.T.
AU  - Pearson, T.
AU  - Turnbull, P.
AU  - Keim, P.
TI  - Genome Sequence of Bacillus anthracis STI, a Sterne-Like Georgian/Soviet Vaccine  Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00853
EP  - e00814
VL  - 2
AB  - The Bacillus anthracis strain STI is a Soviet vaccine strain that lacks the pXO2  plasmid.
AB  - Previous data indicate that this isolate forms a new branch within the
AB  - B. anthracis sub-group originally identified as A. Br.008/009.
ER  -

TY  - JOUR
AU  - Okrent, R.A.
AU  - Manning, V.A.
AU  - Trippe, K.M.
TI  - Draft Genome Sequences of Seven 4-Formylaminooxyvinylglycine Producers Belonging  to the Pseudomonas fluorescens Species Complex.
JO  - Genome Announcements
PY  - 2017
SP  - e00277
EP  - e00217
VL  - 5
AB  - Vinylglycines are nonproteinogenic amino acids that inhibit amino acid metabolism and ethylene
AB  - production. Here, we report the draft genome sequences of seven
AB  - isolates of Pseudomonas that produce 4-formylaminooxyvinylglycine, a compound
AB  - known to inhibit the germination of grasses and the growth of specific
AB  - plant-pathogenic bacteria.
ER  -

TY  - JOUR
AU  - Okshevsky, M.
AU  - Regina, V.R.
AU  - Marshall, I.P.
AU  - Schreiber, L.
AU  - Meyer, R.L.
TI  - Draft Genome Sequence of Bacillus sp. FMQ74, a Dairy-Contaminating Isolate from Raw Milk.
JO  - Genome Announcements
PY  - 2017
SP  - e01512
EP  - e01516
VL  - 5
AB  - Representatives of the genus Bacillus are common milk contaminants that cause spoilage and
AB  - flavor alterations of dairy products. Bacillus sp. FMQ74 was
AB  - isolated from raw milk on a Danish dairy farm. To elucidate the genomic basis of
AB  - this strain's survival in the dairy industry, a high-quality draft genome was
AB  - produced.
ER  -

TY  - JOUR
AU  - Okstad, O.A.
AU  - Hegna, I.
AU  - Lindback, T.
AU  - Rishovd, A.-L.
AU  - Kolsto, A.-B.
TI  - Genome organization is not conserved between Bacillus cereus and Bacillus subtilis.
JO  - Microbiology
PY  - 1999
SP  - 621
EP  - 631
VL  - 145
AB  - The opportunistic pathogen Bacillus cereus is the genetically stable member of a group of
AB  - closely related bacteria including the insect pathogen Bacillus thuringiensis and the
AB  - mammalian pathogen Bacillus anthracis. Physical maps of B. cereus and B. thuringiensis strains
AB  - show considerable variations in discrete parts of the chromosome, suggesting that certain
AB  - genome regions are more prone to rearrangements. B. cereus belongs to the same subgroup of
AB  - Bacillus species as Bacillus subtilis, by both phenotypic and rRNA sequence classification.
AB  - The analysis of 80 kb of genome sequence sampled from different regions of the B. cereus ATCC
AB  - 10987 chromosome is reported.  Analysis of the sequence and comparison of the localization of
AB  - the putative genes with that of B. subtilis orthologues show the following: (1) gene
AB  - organization is not conserved between B. cereus and B. subtilis; (2) several putative genes
AB  - are more closely related to genes from other bacteria and archaea than to B. subtilis, or may
AB  - be absent in B. subtilis 168; (3) B. cereus contains a 155 bp repetitive sequence that is not
AB  - present in B. subtilis. By hybridization, this repeat is present in all B. cereus and B.
AB  - thuringiensis strains so far investigated.
ER  -

TY  - JOUR
AU  - Oktavcovca, B.
AU  - Godany, A.
AU  - Pristas, P.
AU  - Stevcikova, B.
AU  - Farkasovska, J.
TI  - Isolation and characterization of the modification methylase M.SauLPI from Streptomyces aureofaciens B-96.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4843
EP  - 4843
VL  - 21
AB  - In our previous work we reported the presence of a GCC/GGC recognizing restriction system in
AB  - tetracycline producing strains of Streptomyces aureofaciens. In this paper we describe the
AB  - characterization of the cognate modification DNA methyltransferase M.SauLPI from
AB  - S.aureofaciens strain B-96.
ER  -

TY  - JOUR
AU  - Okubo, T. et al.
TI  - Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs.
JO  - Microbes Environ.
PY  - 2012
SP  - 306
EP  - 315
VL  - 27
AB  - Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil.
AB  - Although S23321 is
AB  - phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to
AB  - induce root nodules
AB  - in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of
AB  - S23321 is a single circular
AB  - chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains
AB  - 6,898 potential
AB  - protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome
AB  - structure between
AB  - S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in
AB  - USDA110 were absent
AB  - in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation
AB  - found in USDA110.
AB  - A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an
AB  - ancestral-type
AB  - genome that precedes the acquisition of a symbiosis island by horizontal gene transfer.
AB  - Although S23321 contains a
AB  - nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes
AB  - in this cluster were more
AB  - similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the
AB  - symbiosis island of USDA110.
AB  - In addition, we found genes encoding a complete photosynthetic system, many ABC transporters
AB  - for amino acids and
AB  - oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a
AB  - system for lignin monomer
AB  - catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide
AB  - range of environments,
AB  - probably including low-nutrient conditions, with multiple survival strategies in soil and
AB  - rhizosphere.
ER  -

TY  - JOUR
AU  - Okubo, T.
AU  - Fukushima, S.
AU  - Itakura, M.
AU  - Oshima, K.
AU  - Longtonglang, A.
AU  - Teaumroong, N.
AU  - Mitsui, H.
AU  - Hattori, M.
AU  - Hattori, R.
AU  - Hattori, T.
AU  - Minamisawa, K.
TI  - Soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica as suggested by genome analysis.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 2542
EP  - 2551
VL  - 79
AB  - Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58T is a nitrogen-fixing oligotrophic
AB  - bacterium isolated from paddy field soil that is able to grow in extra-low nutrient
AB  - environments.  Here, the complete genome sequence of S58 was determined.  The S58 genome was
AB  - found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1%
AB  - lacking nodABC genes and typical symbiosis island.  The genome showed a high level of
AB  - similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrizobium sp. BTAil including
AB  - nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant,
AB  - Aeschynomene indica, in a Nod factor-independent manner.  Although non-symbiotic
AB  - (brady)rhizobia are significant components of rhizobial populations in soil, we found that
AB  - most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and
AB  - fix) with A. indica were well conserved between the ORS278 and S58 genomes.  Therefore, we
AB  - performed inoculation experiments with five A. oligotrophica strians (S58, S42, S55, S72, and
AB  - S80).  Surpirsingly, all five strains of A. oligotrophica formed effective nitrogen-fixing
AB  - nodules on the roots and/or stems of A. indica with differentiated bacteroids.  Non-symbiotic
AB  - (brady)rhizobia are known to be significant components of rhizobial populations without
AB  - symbiosis isoland or symbiotic plasmids in soil, but the present results indicate that
AB  - soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A.
AB  - indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of
AB  - photosynthetic Bradyrhizobium clade including A. oligotrophica.
ER  -

TY  - JOUR
AU  - Okuda, Y.
AU  - Sasaki, D.
AU  - Nogami, S.
AU  - Kaneko, Y.
AU  - Ohya, Y.
AU  - Anraku, Y.
TI  - Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.
JO  - Yeast
PY  - 2003
SP  - 563
EP  - 573
VL  - 20
AB  - VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of
AB  - Saccharomyces cerevisiae. There have been two
AB  - independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and
AB  - the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they
AB  - share the identity of 96.3%. In order to search the occurrence,
AB  - intra/interspecies transfer and molecular degeneration of VDE, complete
AB  - sequences of VMA1 in 10 strains of S. cerevisiae, eight species of
AB  - saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were
AB  - determined. We found that six of 10 S. cerevisiae strains contain VDEs
AB  - 99.7-100% identical to that of the strain X2180-1A, one has no VDE,
AB  - whereas the other three harbour VDEs 100% identical to that of the strain
AB  - DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that
AB  - of the strain X2180-1A with VDE 100% identical to that of the strain
AB  - DH1-1A and the other containing the same VMA1 in S. pastorianus with no
AB  - VDE. This and other evidence indicates that intra/interspecies
AB  - transmissions of VDEs have occurred among saccharomycete yeasts.
AB  - Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs
AB  - had branched earlier than other VDEs from an ancestral VDE and had invaded
AB  - into the host loci as relatively late events. The two VDEs seemed to
AB  - degenerate in individual host loci, retaining their splicing capacity
AB  - intact. The degeneration of the endonuclease domains was distinct and, if
AB  - compared, its apparent rate was much faster than that of the
AB  - protein-splicing domains.
ER  -

TY  - JOUR
AU  - Okumura, K.
AU  - Arai, R.
AU  - Okura, M.
AU  - Kirikae, T.
AU  - Takamatsu, D.
AU  - Osaki, M.
AU  - Miyoshi-Akiyama, T.
TI  - Complete Genome Sequence of Melissococcus plutonius ATCC 35311.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4029
EP  - 4030
VL  - 193
AB  - We report the first completely annotated genome sequence of Melissococcus plutonius ATCC
AB  - 35311. M. plutonius is a one genus one species bacterium,
AB  - and the etiological agent of European foulbrood of the honey bee. The
AB  - genome sequence will provide new insights into the molecular mechanisms
AB  - underlying its pathogenicity.
ER  -

TY  - JOUR
AU  - Okura, M.
AU  - Takamatsu, D.
AU  - Maruyama, F.
AU  - Nozawa, T.
AU  - Nakagawa, I.
AU  - Osaki, M.
AU  - Sekizaki, T.
AU  - Gottschalk, M.
AU  - Kumagai, Y.
AU  - Hamada, S.
TI  - Genetic Analysis of Capsular Polysaccharide Synthesis Gene Clusters from All Serotypes of Streptococcus suis: Potential Mechanisms for the Generation of Capsular Variation.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 2796
EP  - 2806
VL  - 79
AB  - Streptococcus suis strains are classified into 35 serotypes on the basis of the
AB  - antigenicity of their capsular polysaccharides (CPs). CP synthesis genes are
AB  - known to be clustered on the chromosome (cps gene cluster). The entire cps gene
AB  - clusters of S. suis have so far been sequenced in 15 serotypes and found to be
AB  - located between orfZ and aroA. In this study, to provide comprehensive
AB  - information about S. suis CPs, we sequenced the entire cps gene clusters of the
AB  - remaining serotypes and analyzed the complete set of S. suis cps gene clusters.
AB  - Among the 35 cps gene clusters, 22 were located between orfZ and aroA, whereas
AB  - the other 13 were flanked by other gene(s) on the chromosomes, and the
AB  - chromosomal locus was classified into five patterns. By clustering analysis, the
AB  - predicted products of cps genes found in the 35 serotypes were assigned into 291
AB  - homology groups, and all serotypes possessed a serotype-specific gene, except for
AB  - serotypes 1, 2, 1/2 and 14. Because of the presence of genes encoding flippase
AB  - (wzx) and polymerase (wzy), CPs of all serotypes were thought to be synthesized
AB  - by the Wzx/Wzy pathway. Our data also implied the possibility of the transfer of
AB  - the entire or partial cps gene clusters among S. suis strains, as well as the
AB  - influence of spontaneous mutations in a single or a few genes on the antigenicity
AB  - of some serotypes. Accumulation of these gene transfers and small-scale mutations
AB  - may have generated the antigenic diversity of S. suis CPs.
ER  -

TY  - JOUR
AU  - Okutani, A.
AU  - Osaki, M.
AU  - Takamatsu, D.
AU  - Kaku, Y.
AU  - Inoue, S.
AU  - Morikawa, S.
TI  - Draft Genome Sequences of Bacillus anthracis Strains Stored for Several Decades in Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e00633
EP  - e00615
VL  - 3
AB  - We report the draft genome sequences of Bacillus anthracis strains Shikan-NIID, 52-40-NIAH,
AB  - and 44-NIAH stored in Japan and belonging to the A3 cluster.
ER  -

TY  - JOUR
AU  - Okutsu, N.
AU  - Morohoshi, T.
AU  - Ikeda, T.
TI  - Draft Genome Sequence of Alicycliphilus sp. B1, an N-Acylhomoserine Lactone-Producing Bacterium, Isolated from Activated Sludge.
JO  - Genome Announcements
PY  - 2015
SP  - e00424
EP  - e00415
VL  - 3
AB  - We report here the draft genome sequence of Alicycliphilus sp. B1, isolated from  activated
AB  - sludge in a wastewater treatment plant of an electronic component
AB  - factory as an N-acylhomoserine lactone-producing strain. The draft genome is
AB  - 7,465,959 bp in length, with 59 large contigs. About 7,391 protein-coding genes,
AB  - 82 tRNAs, and 13 rRNAs are predicted from this assembly.
ER  -

TY  - JOUR
AU  - Olano, C.
AU  - Cano-Prieto, C.
AU  - Losada, A.A.
AU  - Bull, A.T.
AU  - Goodfellow, M.
AU  - Fiedler, H.P.
AU  - Mendez, C.
AU  - Salas, J.A.
TI  - Draft Genome Sequence of Marine Actinomycete Streptomyces sp. Strain NTK 937, Producer of the Benzoxazole Antibiotic Caboxamycin.
JO  - Genome Announcements
PY  - 2014
SP  - e00534
EP  - e00514
VL  - 2
AB  - Streptomyces sp. strain NTK 937 is the producer of the benzoxazole antibiotic caboxamycin,
AB  - which has been shown to exert inhibitory activity against
AB  - Gram-positive bacteria, cytotoxic activity against several human tumor cell
AB  - lines, and inhibition of the enzyme phosphodiesterase. In this genome
AB  - announcement, we present a draft genome sequence of Streptomyces sp. NTK 937 in
AB  - which we identified at least 35 putative secondary metabolite biosynthetic gene
AB  - clusters.
ER  -

TY  - JOUR
AU  - Olasz, F.
AU  - Nagy, T.
AU  - Szabo, M.
AU  - Kiss, J.
AU  - Szmolka, A.
AU  - Barta, E.
AU  - van Tonder, A.
AU  - Thomson, N.
AU  - Barrow, P.
AU  - Nagy, B.
TI  - Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom.
JO  - Genome Announcements
PY  - 2015
SP  - e01468
EP  - e01414
VL  - 3
AB  - The genome sequences of three strains of Salmonella enterica subsp. enterica serovar Infantis
AB  - isolated from broiler chickens in 1994 and 2004 in Hungary and
AB  - in the 1980s in the United Kingdom are reported here. A sequence comparison
AB  - should improve our understanding of the evolution of the genome and spread of S.
AB  - Infantis in poultry.
ER  -

TY  - JOUR
AU  - Old, R.
AU  - Murray, K.
AU  - Roizes, G.
TI  - Recognition Sequence of Restriction Endonuclease III from Hemophilus influenzae.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 331
EP  - 339
VL  - 92
AB  - An endonuclease, R.HindIII, prepared from Hemophilus influenzae strain Rd,
AB  - degrades foreign DNA, but not homologous DNA.  Phage T7 DNA is also resistant
AB  - to the enzyme.  Fragments of phage lambda DNA produced by treatment with
AB  - R.HindIII have been labelled at their 5' termini and analysis of the
AB  - radioactive nucleotides in pancreatic DNAase digests of these fragments
AB  - revealed a single 5' terminal sequence.  From this and other data we conclude
AB  - that the enzyme recognizes and cleaves DNA at the following nucleotide
AB  - sequence, 3' -N-T-T-C-G-A-A-N- 5' 5' -N-A-A-G-C-T-T-N- 3' giving termini
AB  - bearing short cohesive ends.
ER  -

TY  - JOUR
AU  - Oleastro, M.
AU  - Monteiro, L.
AU  - Lehours, P.
AU  - Megraud, F.
AU  - Menard, A.
TI  - Identification of Markers for Helicobacter pylori Strains Isolated from Children with Peptic Ulcer Disease by Suppressive Subtractive Hybridization.
JO  - Infect. Immun.
PY  - 2006
SP  - 4064
EP  - 4074
VL  - 74
AB  - Peptic ulcer disease (PUD) occurs after a long-term Helicobacter pylori
AB  - infection. However, the disease can develop earlier, and rare cases have
AB  - been observed in children, suggesting that these H. pylori strains may be
AB  - more virulent. We used suppressive subtractive hybridization for
AB  - comparative genomics between H. pylori strains isolated from a 5-year-old
AB  - child with duodenal ulcer and from a sex- and age-matched child with
AB  - gastritis only. The prevalence of the 30 tester-specific subtracted
AB  - sequences was determined on a collection of H. pylori strains from
AB  - children (15 ulcers and 30 gastritis) and from adults (46 ulcers and 44
AB  - gastritis). Two of these sequences, jhp0562 (80.0% versus 33.3%, P =
AB  - 0.008) and jhp0870 (80.0% versus 36.7%, P = 0.015), were highly associated
AB  - with PUD in children and a third sequence, jhp0828, was less associated
AB  - (40.0% versus 10.0%, P = 0.048). Among adult strains, none of the 30
AB  - sequences was associated with PUD. However, both jhp0562 and jhp0870 were
AB  - less prevalent in adenocarcinoma strains than in PUD strains from children
AB  - and adults, the difference being statistically significant for jhp0870. In
AB  - conclusion, two H. pylori genes were identified as being strongly
AB  - associated with PUD in children, and their putative roles as an outer
AB  - membrane protein for jhp0870 and in lipopolysaccharide biosynthesis for
AB  - jhp0562, suggest that they may be novel virulence factors of H. pylori.
ER  -

TY  - JOUR
AU  - Olhoft, P.M.
TI  - Cloning and characterization of the 5-methylcytosine methyltransferase gene in maize plants and tissue cultures.
JO  - Diss. Abstr.
PY  - 1999
SP  - 4638
EP  - 4638
VL  - 59
AB  - The genomic sequence of maize containing the methyltransferase gene called Zmet1 was
AB  - successfully cloned and sequenced.  Seven clones were identified from a genomic library by
AB  - using a highly conserved region from an Arabidopsis EST homologous to the Met1
AB  - methyltransferase gene as a probe.  The assembled genomic sequence of four overlapping clones
AB  - covers both the 5' and 3' flanking regions of the maize methyltransferase gene totaling
AB  - 7,955 nucleotides.  Sequence alignments with the Arabidopsis Met1 cDNA revealed that the open
AB  - reading frame of Zmet1 encodes a putative protein of 1,525 amino acids, which is interrupted
AB  - in the genomic sequence by ten introns.  Northern analysis confirmed this result by the
AB  - identification of a single 4.6 kb RNA transcript.  The structure of the Zmet1 methylase is
AB  - similar to the other eukaryotic maintenance methylases; a large N-terminal domain of 1,054
AB  - amino  acids linked to a smaller C-terminal domain of 471 amino acids by a lysine-rich
AB  - sequence.  Zmet1 is highly expressed in actively dividing cells, namely in seedling tissue and
AB  - rapidly dividing callus tissue.  Restriction analysis suggests that there are at least two
AB  - Zmet1 loci in the maize genome, one of which maps to the short arm of chromosome 7 in bin 2.
AB  - The percent of 5-methylcytosine in maize DNA was shown to be dependent on the type of tissue
AB  - and the stage in development.  Although the amount of repetitive DNA remained stable in the
AB  - overall G/C to A/T ratio, methylation levels were found to significantly decrease from
AB  - 15-day-old embryos to one-week-old seedlings.  Remethylation occurs between the first and
AB  - second week of seedling growth.  These changes indicate that there are both de novo
AB  - methylation and demethylation activities in early development.  The methylation pattern at
AB  - four low-copy sequences remained unchanged throughout plant and callus development except for
AB  - a possible hypermethylation event in the third month of cell culture.  However, there was
AB  - significant demethylation in the repetitive sequences, rDNA and COS 12, throughout an eight
AB  - month period in tissue culture.  The identification of stages or tissues which are undergoing
AB  - demethylation and de novo methylation may be important in identifying undiscovered methylase
AB  - and demethylase enzymes, developmentally regulated genes, as well as interacting proteins that
AB  - may regulate methylase functions.
ER  -

TY  - JOUR
AU  - Oliveira, D.C.
AU  - Wu, S.W.
AU  - de Lencastre, H.
TI  - Genetic organization of the downstream region of the mecA element in methicillin-resistant Staphylococcus aureus isolates carrying different polymorphisms of this region.
JO  - Antimicrob. Agents Chemother.
PY  - 2000
SP  - 1906
EP  - 1910
VL  - 44
AB  - We describe here the genetic organization of the mec element downstream of
AB  - the mecA gene in 34 different methicillin-resistant Staphylococcus aureus
AB  - (MRSA) clinical isolates carrying 13 of the most frequent polymorphisms of
AB  - mecA and representing the major epidemic clones of MRSA. All polymorphisms
AB  - carried three common genetic elements: the hypervariable region, a copy of
AB  - IS431, and a unique 2-kb sequence (downstream constant segment, or dcs)
AB  - for which no homologous sequences are found in data banks. Polymorphisms
AB  - of the downstream region were shown to be caused by the presence of
AB  - linearized plasmids flanked by insertion sequences (pUB110, pT181, and
AB  - pI258) and the autonomous insertion sequence IS256.
ER  -

TY  - JOUR
AU  - Oliveira, L.C. et al.
TI  - Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e00980
EP  - e00914
VL  - 2
AB  - Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose
AB  - fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from
AB  - frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118,
AB  - a strain with probiotic potential activity.
ER  -

TY  - JOUR
AU  - Oliveira, L.M.
AU  - Resende, D.M.
AU  - Dorneles, E.M.
AU  - Horacio, E.C.
AU  - Alves, F.L.
AU  - Goncalves, L.O.
AU  - Tavares, G.S.
AU  - Stynen, A.P.
AU  - Lage, A.P.
AU  - Ruiz, J.C.
TI  - Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374.
JO  - Genome Announcements
PY  - 2016
SP  - e01344
EP  - e01316
VL  - 4
AB  - Campylobacter fetus subsp. fetus is a zoonotic bacterium important for animal and public
AB  - health. The complete sequencing and annotation of the genome of the type
AB  - strain C. fetus subsp. fetus ATCC 27374 are reported here.
ER  -

TY  - JOUR
AU  - Oliveira, M.
AU  - Barroco, C.
AU  - Mottola, C.
AU  - Santos, R.
AU  - Lemsaddek, A.
AU  - Tavares, L.
AU  - Semedo-Lemsaddek, T.
TI  - First report of Corynebacterium pseudotuberculosis from caseous lymphadenitis lesions in Black Alentejano pig (Sus scrofa domesticus).
JO  - BMC Vet. Res.
PY  - 2014
SP  - 218
EP  - 218
VL  - 10
AB  - BACKGROUND: Corynebacterium pseudotuberculosis is the etiologic agent of caseous
AB  - lymphadenitis, a common disease in small ruminant populations throughout the
AB  - world and responsible for a significant economic impact for producers. CASE
AB  - PRESENTATION: To our knowledge, this is the first characterization of C.
AB  - pseudotuberculosis from caseous lymphadenitis lesions in Black Alentejano pig
AB  - (Sus scrofa domesticus). In this study, phenotypic and genotypic identification
AB  - methods allocated the swine isolates in C. pseudotuberculosis biovar ovis. The
AB  - vast majority of the isolates were able to produce phospholipase D and were
AB  - susceptible to most of the antimicrobial compounds tested. Macrorestriction
AB  - patterns obtained by Pulsed Field Gel Electrophoresis (PFGE) grouped the C.
AB  - pseudotuberculosis in two clusters with a high similarity index, which reveals
AB  - their clonal relatedness. Furthermore, swine isolates were compared with C.
AB  - pseudotuberculosis from caprines and PFGE patterns also showed high similarity,
AB  - suggesting the prevalence of dominant clones and a potential cross-dissemination
AB  - between these two animal hosts. CONCLUSIONS: This work represents the first
AB  - report of Corynebacterium pseudotuberculosis from caseous lymphadenitis lesions
AB  - in Black Alentejano pig and alerts for the importance of the establishment of
AB  - suitable control and sanitary management practices to control the infection and
AB  - avoid further dissemination of this important pathogen to other animal hosts.
ER  -

TY  - JOUR
AU  - Oliveira, P.H.
AU  - Touchon, M.
AU  - Rocha, E.P.
TI  - The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 10618
EP  - 10631
VL  - 42
AB  - The roles of restriction-modification (R-M) systems in providing immunity against horizontal
AB  - gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs)
AB  - have been much debated. However, few studies have precisely addressed the
AB  - distribution of these systems in light of HGT, its mechanisms and its vectors. We
AB  - analyzed the distribution of R-M systems in 2261 prokaryote genomes and found
AB  - their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas
AB  - systems, integrons and natural transformation. Yet R-M systems are rare in
AB  - plasmids, in prophages and nearly absent from other phages. Their abundance
AB  - depends on genome size for small genomes where it relates with HGT but saturates
AB  - at two occurrences per genome. Chromosomal R-M systems might evolve under cycles
AB  - of purifying and relaxed selection, where sequence conservation depends on the
AB  - biochemical activity and complexity of the system and total gene loss is
AB  - frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M
AB  - genes rarely arise from the degradation of R-M systems. Solitary genes are
AB  - transferred by large MGEs, whereas complete systems are more frequently
AB  - transferred autonomously or in small MGEs. Our results suggest means of testing
AB  - the roles for R-M systems and their associations with MGEs.
ER  -

TY  - JOUR
AU  - Oliveira, P.H.
AU  - Touchon, M.
AU  - Rocha, E.P.
TI  - Regulation of genetic flux between bacteria by restriction-modification systems.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2016
SP  - 5658
EP  - 5663
VL  - 113
AB  - Restriction-modification (R-M) systems are often regarded as bacteria's innate immune
AB  - systems, protecting cells from infection by mobile genetic elements
AB  - (MGEs). Their diversification has been recently associated with the emergence of
AB  - particularly virulent lineages. However, we have previously found more R-M
AB  - systems in genomes carrying more MGEs. Furthermore, it has been suggested that
AB  - R-M systems might favor genetic transfer by producing recombinogenic
AB  - double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic
AB  - exchanges, we analyzed their frequency with respect to the inferred events of
AB  - homologous recombination and horizontal gene transfer within 79 bacterial
AB  - species. Genetic exchanges were more frequent in bacteria with larger genomes and
AB  - in those encoding more R-M systems. We created a recognition target motif
AB  - predictor for Type II R-M systems that identifies genomes encoding systems with
AB  - similar restriction sites. We found more genetic exchanges between these genomes,
AB  - independently of their evolutionary distance. Our results reconcile previous
AB  - studies by showing that R-M systems are more abundant in promiscuous species,
AB  - wherein they establish preferential paths of genetic exchange within and between
AB  - lineages with cognate R-M systems. Because the repertoire and/or specificity of
AB  - R-M systems in bacterial lineages vary quickly, the preferential fluxes of
AB  - genetic transfer within species are expected to constantly change, producing
AB  - time-dependent networks of gene transfer.
ER  -

TY  - JOUR
AU  - Oliynyk, M.
AU  - Samborskyy, M.
AU  - Lester, J.B.
AU  - Mironenko, T.
AU  - Scott, N.
AU  - Dickens, S.
AU  - Haydock, S.F.
AU  - Leadlay, P.F.
TI  - Complete genome sequence of the erythromycinproducing bacterium Saccharopolyspora erythraea NRRL23338.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 447
EP  - 453
VL  - 25
AB  - Saccharopolyspora erythraea is used for the industrial-scale production of the antibiotic
AB  - erythromycin A, derivatives of which play a vital role in medicine. The sequenced chromosome
AB  - of this soil bacterium comprises 8,212,805 base pairs, predicted to encode 7,264 genes. It is
AB  - circular, like those of the pathogenic actinomycetes Mycobacterium tuberculosis and
AB  - Corynebacterium diphtheriae, but unlike the linear chromosomes of the model actinomycete
AB  - Streptomyces coelicolor A3(2) and the closely related Streptomyces avermitilis. The S.
AB  - erythraea genome contains at least 25 gene clusters for production of known or predicted
AB  - secondary metabolites, at least 72 genes predicted to confer resistance to a range of common
AB  - antibiotic classes and many sets of duplicated genes to support its saprophytic lifestyle. The
AB  - availability of the genome sequence of S. erythraea will improve insight into its biology and
AB  - facilitate rational development of strains to generate high-titer producers of clinically
AB  - important antibiotics.
ER  -

TY  - JOUR
AU  - Oller, A.R.
AU  - Vanden Broek, W.
AU  - Conrad, M.
AU  - Topal, M.D.
TI  - Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species.
JO  - Biochemistry
PY  - 1991
SP  - 2543
EP  - 2549
VL  - 30
AB  - Previous work has described the novel ability to modulate in vitro the activity
AB  - of restriction endonuclease NaeI from Nocardia aerocoligenes by using cleavable
AB  - DNA and spermidine [Conrad & Topal (1989) Proc. Natl. Acad. Sci. 86,
AB  - 9707-9711].  In this paper we report the results of a study of 49 type II
AB  - restriction enzymes from a variety of bacterial species.  On the basis of the
AB  - rates of cleavage observed, we found that in addition to expected cleavable
AB  - sites a number of enzymes had slow and resistant cognate recognition sites.
AB  - Resistant sites were identified for BspMI, NaeI, and NarI; slow sites were
AB  - identified for HpaII, NaeI, and SacII.  Cleavage of these sites was found to be
AB  - signficantly enhanced by the addition of cleavable DNA or spermidine.  We
AB  - demonstrate that for BspMI, as for NaeI, activator DNAs increased Vmax without
AB  - altering Km, whereas for HpaII, NarI, and SacII activator DNAs decreased Km
AB  - without changing Vmax.  Comparison among the Kms for NaeI cleavage of several
AB  - different substrates demonstrated that distant DNA sequences can affect DNA
AB  - recognition by the activated enzyme.  Our observations extend DNA activation of
AB  - the Nocardia NaeI endonuclease to restriction endonucleases from Nocardia
AB  - argentinensis (NarI), Bacillus species M (BspMI), Haemophilus parainfluenza
AB  - (HpaII), and Streptomyces achromogenes (SacII).  In addition, activation has
AB  - now been found to affect slow as well as resistant recognition sites.
ER  -

TY  - JOUR
AU  - Olmos, A.
AU  - Henriquez-Piskulich, P.
AU  - Sanchez, C.
AU  - Rojas-Herrera, M.
AU  - Moreno-Pino, M.
AU  - Gomez, M.
AU  - Rodriguez, Da.S.R.
AU  - Maracaja-Coutinho, V.
AU  - Aldea, P.
AU  - Trombert, A.N.
TI  - Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2.
JO  - Genome Announcements
PY  - 2014
SP  - e01013
EP  - e01014
VL  - 2
AB  - Here, we report the first draft genome sequence of Lactobacillus kunkeei strain MP2, isolated
AB  - from a Chilean honeybee gut. The sequenced genome has a total size
AB  - of 1.58 Mb distributed into 44 contigs and 1,356 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Olonade, I.
AU  - van Zyl, L.J.
AU  - Trindade, M.
TI  - Draft Genome Sequences of Marine Isolates of Thalassomonas viridans and Thalassomonas actiniarum.
JO  - Genome Announcements
PY  - 2015
SP  - e00297
EP  - e00215
VL  - 3
AB  - Thalassomonas viridans and Thalassomonas actiniarum are aerobic Gram-negative bacilli which
AB  - belong to a genus that has not received much attention, even
AB  - though, as demonstrated here by the sequencing of their genomes, they are quite
AB  - different from their closest relatives in current databases. Their genomes are
AB  - relatively large at 7.7 and 7.4 Mb, respectively. This brief report describes the
AB  - first draft genomes for any Thalassomonas species.
ER  -

TY  - JOUR
AU  - Olsen, D.B.
AU  - Kotzorek, G.
AU  - Eckstein, F.
TI  - Investigation of the inhibitory role of phosphorothioate internucleotidic linkages on the catalytic activity of the restriction endonuclease EcoRV.
JO  - Biochemistry
PY  - 1990
SP  - 9546
EP  - 9551
VL  - 29
AB  - The inhibitory effect of phosphorothioate residues, located within one strand
AB  - of double-stranded DNA, on the hydrolytic activity of the restriction
AB  - endonuclease EcoRV was investigated.  Specific incorporation of a
AB  - phosphorothioate group at the site of cleavage yielded the sequence
AB  - 5'-GATsATC-3'.  This modified sequence was cleaved at a relative rate of 0.1
AB  - compared to the unmodified substrate.  Substrates 5'-GATsAsTC-3' and
AB  - 5'-GsATsATC-3', both containing one additional phosphorothioate substitution,
AB  - were linearized at a rate of 0.04 relative to unmodified DNA.  However, under
AB  - the same conditions, fully dAMPS-substituted DNA was found to be virtually
AB  - resistant to the hydrolytic activity of EcoRV.  Further experiments showed that
AB  - double-stranded DNA fragments generated by PCR containing phosphorothioate
AB  - groups within both strands are potent inhibitors of EcoRV catalysis.  The
AB  - inhibition was independent of whether the inhibitor fragment contained an EcoRV
AB  - recognition site.  We concluded that substitution of the phosphate group at the
AB  - site of cleavage by a phosphorothioate residue decreases the rate of
AB  - EcoRV-catalyzed hydrolysis most significantly.  Substitution of other phosphate
AB  - groups within the recognition sequence plays a limited role in enzyme
AB  - inhibition.  The presence of multiple dNMPS residues at regions of the DNA
AB  - removed from the EcoRV recognition site may decrease the amount of enzyme
AB  - available for catalysis by nonspecific binding to EcoRV.
ER  -

TY  - JOUR
AU  - Olsen, D.B.
AU  - Kotzorek, G.
AU  - Sayers, J.R.
AU  - Eckstein, F.
TI  - Inhibition of the restriction endonuclease BanII using modified DNA substrates.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 14389
EP  - 14394
VL  - 265
AB  - The restriction endonuclease BanII catalyzes the cleavage of double-stranded
AB  - DNA and recognizes the degenerate sequence 5'-GPuGCPyC-3'.  The polylinker of
AB  - M13mp18 contains one such sequence, 5'-GAGCTC-3'.  The three other possible
AB  - sites recognized by the enzyme were prepared by site-directed mutagenesis.  The
AB  - substitution of phosphate groups by phosphorothioate residues at some positions
AB  - within the various recognition sites had relatively little effect on the rate
AB  - of cleavage of the DNA.  However, when the DNA contained a phosphorothioate
AB  - group at the site of cleavage the rate of linearization of the DNA was
AB  - decreased by a factor of 9.  Interestingly, DNA which contained an additional
AB  - phosphorothioate internucleotidic linkage immediately 3'-outside the
AB  - recognition site could not be linearized by the enzyme.  The results indicate
AB  - that an important contact between enzyme and substrate is perturbed by the
AB  - presence of the sulfur atom at this position.
ER  -

TY  - JOUR
AU  - Olsen, D.B.
AU  - Sayers, J.R.
AU  - Kotzorek, G.
AU  - Eckstein, F.
TI  - Interaction of restriction endonucleases with phosphorothioate-containing DNA.
JO  - Nucleosides and Nucleotides
PY  - 1991
SP  - 665
EP  - 667
VL  - 10
AB  - The requirements for inhibition of cleavage of phosporothioate-containing DNA
AB  - by the restriction enzymes BanII and EcoRV with respect to number and position
AB  - of these groups was determined.
ER  -

TY  - JOUR
AU  - Olsen, R.H.
AU  - Thofner, I.C.
AU  - Pors, S.E.
AU  - Christensen, H.
AU  - Bisgaard, M.
AU  - Christensen, J.P.
TI  - Draft Genome Sequences of Three Escherichia coli Strains with Different In Vivo Pathogenicities in an Avian (Ascending) Infection Model of the Oviduct.
JO  - Genome Announcements
PY  - 2015
SP  - e00399
EP  - e00315
VL  - 3
AB  - Here, we present three draft genome sequences of Escherichia coli strains that experimentally
AB  - were proven to possess low (strain D2-2), intermediate
AB  - (Chronic_salp), or high virulence (Cp6salp3) in an avian (ascending) infection
AB  - model of the oviduct.
ER  -

TY  - JOUR
AU  - Olsson, B.E.
AU  - Korsakova, E.S.
AU  - Anan'ina, L.N.
AU  - Pyankova, A.A.
AU  - Mavrodi, O.V.
AU  - Plotnikova, E.G.
AU  - Mavrodi, D.V.
TI  - Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region  of Russia.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 39
EP  - 39
VL  - 12
AB  - Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic
AB  - osmoadaptation and sources of enzymes and chemicals for
AB  - biotechnological applications. Despite the progress in understanding the
AB  - diversity of these organisms, our ability to explain ecological, metabolic, and
AB  - biochemical traits of halomonads at the genomic sequence level remains limited.
AB  - This study addresses this gap by presenting draft genomes of Salinicola socius
AB  - SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were
AB  - isolated from potash mine tailings in the Verkhnekamsk salt deposit area of
AB  - Russia. The analysis of these genomes confirmed the importance of ectoines and
AB  - quaternary amines to the capacity of halomonads to tolerate osmotic stress and
AB  - adapt to hypersaline environments. The study also revealed that Chromohalobacter
AB  - and Salinicola share 75-90% of the predicted proteome, but also harbor a set of
AB  - genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp.
AB  - These genus-specific genome segments may contribute to the phenotypic diversity
AB  - of the Halomonadaceae and the ability of these organisms to adapt to changing
AB  - environmental conditions and colonize new ecological niches.
ER  -

TY  - JOUR
AU  - Olszewski, J.
AU  - Wasserman, B.P.
TI  - Effect of glutaraldehyde on the activity of some DNA restriction endonucleases.
JO  - Appl. Biochem. Biotechnol.
PY  - 1986
SP  - 29
EP  - 35
VL  - 13
AB  - The effect of the bifunctional crosslinking reagent glutaraldehyde on the
AB  - activity of the restriction enzymes BamHI, HindIII, EcoRI, and Tth111I was
AB  - investigated.  The four enzymes exhibited differential sensitivity to
AB  - inactivation.  Tth111I was the most sensitive, with activity losses occurring
AB  - at levels of 0.0025% and above.  HindIII was the most stable of the four and
AB  - remained fully active at concentrations as high as 0.075%.  Addition of BSA to
AB  - incubation mixtures generally had a stabilizing effect.  Implications of these
AB  - results for the design of glutaraldehyde-based methods for the immobilization
AB  - of restriction endonucleases are discussed.
ER  -

TY  - JOUR
AU  - Olvera, C.
AU  - Santamaria, R.I.
AU  - Bustos, P.
AU  - Vallejo, C.
AU  - Montor, J.J.
AU  - Wacher, C.
AU  - Lopez, M.A.
TI  - Draft Genome Sequence of Leuconostoc citreum CW28 Isolated from Pozol, a Pre-Hispanic Fermented Corn Beverage.
JO  - Genome Announcements
PY  - 2017
SP  - e01283
EP  - e01217
VL  - 5
AB  - Leuconostoc citreum CW28 was isolated from pozol, a Mayan fermented corn beverage. This strain
AB  - produces a cell-associated inulosucrase, the first
AB  - described in bacteria. Its draft genome sequence, announced here, has an
AB  - estimated size of 1.98 Mb and harbors 1,915 coding genes, 12 rRNAs, 68 tRNAs, 17
AB  - putative pseudogenes, and 1 putative phage.
ER  -

TY  - JOUR
AU  - Olvera-Garcia, M.
AU  - Fontes-Perez, H.
AU  - Chavez-Martinez, A.
AU  - Ruiz, B.O.
AU  - Rodriguez-Almeida, F.A.
AU  - Sanchez-Flores, A.
AU  - Corral-Luna, A.
TI  - Draft Genome Sequences for Five Strains of Trabulsiella odontotermitis, Isolated  from Heterotermes sp. Termite Gut.
JO  - Genome Announcements
PY  - 2015
SP  - e01289
EP  - e01215
VL  - 3
AB  - Trabulsiella odontotermitis represents a novel species in the genus Trabulsiella  with no
AB  - complete genome reported yet. Here, we describe the draft genome
AB  - sequences of five isolates from termites present in the north of Mexico, which
AB  - have an interesting pool of genes related to cellulose degradation with
AB  - biotechnological application.
ER  -

TY  - JOUR
AU  - Omar, S.V.
AU  - Allam, M.
AU  - Joseph, L.
AU  - Mtshali, S.
AU  - Ismail, N.A.
AU  - Ismail, A.
TI  - Draft Genome Sequence of Mycobacterium peregrinum Isolated from an HIV-Positive Patient in South Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e00759
EP  - e00717
VL  - 5
AB  - Here, we report a draft genome sequence of Mycobacterium peregrinum obtained from a sputum
AB  - sample of a South African HIV-infected patient with suspected pulmonary
AB  - tuberculosis. The genome described here comprises 6,931,852 bp, revealing 66.2%
AB  - G+C content, 6,808 coding sequences, and 81 RNA genes.
ER  -

TY  - JOUR
AU  - Ong, K.S.
AU  - Aw, Y.K.
AU  - Gan, H.M.
AU  - Yule, C.M.
AU  - Lee, S.M.
TI  - Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e01032
EP  - e01014
VL  - 2
AB  - We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp.
AB  - strains MSh1 and MSh2, which were isolated from tropical peat
AB  - swamp forest soil. Putative genes related to different antimicrobial production
AB  - have been annotated in both genome sequences.
ER  -

TY  - JOUR
AU  - Ong, S.Y.
AU  - Pratap, C.B.
AU  - Wan, X.
AU  - Hou, S.
AU  - Abdul, R.A.Y.
AU  - Saito, J.A.
AU  - Nath, G.
AU  - Alam, M.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi P-stx-12.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2115
EP  - 2116
VL  - 194
AB  - We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar
AB  - Typhi P-stx-12, a clinical isolate obtained from a typhoid
AB  - carrier in India.
ER  -

TY  - JOUR
AU  - Ong, S.Y.
AU  - Pratap, C.B.
AU  - Wan, X.
AU  - Hou, S.
AU  - Rahman, A.Y.
AU  - Saito, J.A.
AU  - Nath, G.
AU  - Alam, M.
TI  - The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 483
EP  - 496
VL  - 7
AB  - Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative,
AB  - facultatively anaerobic bacterium. It belongs to the family
AB  - Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of
AB  - residing in the human gallbladder by forming a biofilm and hence causing the
AB  - person to become a typhoid carrier. Here we present the complete genome of
AB  - Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was
AB  - isolated from a chronic carrier in Varanasi, India. The complete genome comprises
AB  - a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding
AB  - genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is
AB  - closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella
AB  - enterica serovar Typhi strain CT18, although their genome structure is slightly
AB  - different.
ER  -

TY  - JOUR
AU  - Onkendi, E.M.
AU  - Ramesh, A.M.
AU  - Kwenda, S.
AU  - Naidoo, S.
AU  - Moleleki, L.
TI  - Draft Genome Sequence of a Virulent Pectobacterium carotovorum subsp. brasiliense Isolate Causing Soft Rot of Cucumber.
JO  - Genome Announcements
PY  - 2016
SP  - e01530
EP  - e01515
VL  - 4
AB  - Pectobacterium carotovorum subsp. brasiliense causes soft rot and blackleg diseases on
AB  - potatoes, ornamentals, and other crops of economic importance. Here,
AB  - we report a draft genome sequence of a highly virulent P. carotovorum subsp.
AB  - brasiliense strain, PcbHPI01, isolated from a cucumber in South Africa.
ER  -

TY  - JOUR
AU  - Ono, A.
AU  - Matsuo, Y.
AU  - Matsuda, A.
AU  - Ueda, T.
TI  - Nucleosides and nucleotides. CXIX. Inhibition of DNA-cytosine methylase HhaI by a self-complementary oligonucleotide containing 5-fluorocytosine.
JO  - Biol. Pharm. Bull.
PY  - 1993
SP  - 529
EP  - 533
VL  - 16
AB  - A self-complementary decadeoxyribonucleotide, 5'd(GAAGFGCTTC)3', containing 5-fluorocytosine
AB  - (F) in substitution for cytosine at the methylation site of DNA-cytosine methylase HhaI
AB  - (mHhaI) has been synthesized M.HhaI was inhibited by the pre-incubation of the enzyme with
AB  - d(GAAGFGCTTC).
ER  -

TY  - JOUR
AU  - Ono, A.
AU  - Ohtani, Y.
AU  - Sato, M.
AU  - Ueda, T.
TI  - Oligodeoxynucleotides containing 7-deazaadenine: synthesis and recognition by restriction.
JO  - Nucleic Acids Symp. Ser.
PY  - 1983
SP  - 67
EP  - 70
VL  - 12
AB  - Deoxydecanucleotides containing a recognition sequence of BglII and Sau3AI, and their
AB  - 7-deazaadenine analogs were synthesized by the phosphotriester method.  The decanucleotides
AB  - containing 7-deazaadenine in place of adenine were partially or strongly resistant to the
AB  - hydrolysis by these restriction endonucleases.
ER  -

TY  - JOUR
AU  - Ono, A.
AU  - Sato, M.
AU  - Ohtani, Y.
AU  - Ueda, T.
TI  - Synthesis of deoxyoligonucleotides containing 7-deazaadenine: recognition and cleavage by restriction endonuclease BglII and Sau3AI.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 8939
EP  - 8949
VL  - 12
AB  - Deoxydecanucleotides having a recognition sequence of BglII and Sau3AI, and
AB  - their 7-deazaadenine analogs were synthesized.  The decanucleotides containing
AB  - 7-deazaadenine in place of adenine were partially resistant to the hydrolysis
AB  - by Sau3AI and strongly resistant to that by BglII.  A new hypothesis on the
AB  - mode of recognition and cleavage of specific nucleotide sequences by BglII,
AB  - recognizing one strand and cleaving the other strand, is presented.
ER  -

TY  - JOUR
AU  - Ono, A.
AU  - Ueda, T.
TI  - Synthesis of decadeoxyribonucleotides containing N6-methyladenine, N4-methylcytosine, and 5-methylcytosine: recognition and cleavage by restriction endonucleases (nucleosides and nucleotides part 74).
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 219
EP  - 232
VL  - 15
AB  - The naturally-occurring modified bases, N6-methyladenine, N4-methylcytosine,
AB  - and 5-methylcytosine were chemically introduced in place of the adenine or
AB  - cytosine in the decadeoxyribonucleotides containing recognition sequences of
AB  - BglII, Sau3AI, MboI and MflI.  The modified oligomers bind to the enzymes but
AB  - the rates of cleavage by the enzymes are variable.
ER  -

TY  - JOUR
AU  - Ono, A.
AU  - Ueda, T.
TI  - Minor-groove-modified oligonucleotides: synthesis of decadeoxynucleotides containing hypoxanthine, N2-methylguanine and 3-deazaadenine, and their interactions with restriction endonucleases BglII, Sau3AI, and MboI.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3059
EP  - 3072
VL  - 15
AB  - Decadeoxynucleotides containing hypoxanthine, N2-methylguanine, 3-deazaadenine in the
AB  - recognition sequences of restriction endonucleases BglII, Sau3AI, and MboI were synthesized.
AB  - These decanucleotides modified in the base moieties facing into the minor groove were strongly
AB  - resistant to hydrolysis by BglII and partially resistant to that of Sau3AI and MboI.  The
AB  - decadeoxynucleotide containing 3-deazaadenine in place of adenine was bound to BglII strongly,
AB  - whereas the nucleotides containing hypoxanthine and N2-methylguanine were bound less tightly.
ER  -

TY  - JOUR
AU  - Onodera, N.T.
AU  - Ryu, J.
AU  - Durbic, T.
AU  - Nislow, C.
AU  - Archibald, J.M.
AU  - Rohde, J.R.
TI  - Genome Sequence of Shigella flexneri Serotype 5a Strain M90T Sm.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3022
EP  - 3022
VL  - 194
AB  - Bacteria of the genus Shigella are a major cause of death worldwide (L. von Seidlein et al.,
AB  - PLoS Med. 3:e353, 2006). We sequenced the genome of Shigella flexneri strain M90T Sm (serotype
AB  - 5a) and compared it to the published genome sequence of S. flexneri strain 8401 (serotype 5b).
ER  -

TY  - JOUR
AU  - Onyango, M.
AU  - Wang, Y.
AU  - Nickel, O.
AU  - Zhao, C.
AU  - Zhang, X.
AU  - Hartke, A.
AU  - Hemberger, J.
AU  - Cemic, F.
TI  - First Genome Sequence of Potential Mycotoxin-Degrading Bacterium Devosia nanyangense DDB001.
JO  - Genome Announcements
PY  - 2014
SP  - e00922
EP  - e00914
VL  - 2
AB  - Devosia sp. nov. DDB001, isolated from mycotoxin-contaminated soil, is a potential
AB  - mycotoxin-degrading alphaproteobacterium. To our knowledge, this is the
AB  - first draft genome announcement of a Devosia species.
ER  -

TY  - JOUR
AU  - Ooi, S.K.
AU  - Qiu, C.
AU  - Bernstein, E.
AU  - Li, K.
AU  - Jia, D.
AU  - Yang, Z.
AU  - Erdjument-Bromage, H.
AU  - Tempst, P.
AU  - Lin, S.P.
AU  - Allis, C.D.
AU  - Cheng, X.
AU  - Bestor, T.H.
TI  - DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
JO  - Nature
PY  - 2007
SP  - 714
EP  - 717
VL  - 448
AB  - Mammals use DNA methylation for the heritable silencing of retrotransposons and imprinted
AB  - genes and for the inactivation of the X
AB  - chromosome in females. The establishment of patterns of DNA methylation
AB  - during gametogenesis depends in part on DNMT3L, an enzymatically inactive
AB  - regulatory factor that is related in sequence to the DNA
AB  - methyltransferases DNMT3A and DNMT3B. The main proteins that interact in
AB  - vivo with the product of an epitope-tagged allele of the endogenous Dnmt3L
AB  - gene were identified by mass spectrometry as DNMT3A2, DNMT3B and the four
AB  - core histones. Peptide interaction assays showed that DNMT3L specifically
AB  - interacts with the extreme amino terminus of histone H3; this interaction
AB  - was strongly inhibited by methylation at lysine 4 of histone H3 but was
AB  - insensitive to modifications at other positions. Crystallographic studies
AB  - of human DNMT3L showed that the protein has a carboxy-terminal
AB  - methyltransferase-like domain and an N-terminal cysteine-rich domain.
AB  - Cocrystallization of DNMT3L with the tail of histone H3 revealed that the
AB  - tail bound to the cysteine-rich domain of DNMT3L, and substitution of key
AB  - residues in the binding site eliminated the H3 tail-DNMT3L interaction.
AB  - These data indicate that DNMT3L recognizes histone H3 tails that are
AB  - unmethylated at lysine 4 and induces de novo DNA methylation by
AB  - recruitment or activation of DNMT3A2.
ER  -

TY  - JOUR
AU  - Ooka, T.
AU  - Ogura, Y.
AU  - Katsura, K.
AU  - Seto, K.
AU  - Kobayashi, H.
AU  - Kawano, K.
AU  - Tokuoka, E.
AU  - Furukawa, M.
AU  - Harada, S.
AU  - Yoshino, S.
AU  - Seto, J.
AU  - Ikeda, T.
AU  - Yamaguchi, K.
AU  - Murase, K.
AU  - Gotoh, Y.
AU  - Imuta, N.
AU  - Nishi, J.
AU  - Gomes, T.A.
AU  - Beutin, L.
AU  - Hayashi, T.
TI  - Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli.
JO  - Genome Biol. Evol.
PY  - 2015
SP  - 3170
EP  - 3179
VL  - 7
AB  - Escherichia albertii is a recently recognized close relative of E. coli. This
AB  - emerging enteropathogen possesses a type III secretion system (T3SS) encoded by
AB  - the locus of enterocyte effacement (LEE), similar to enteropathogenic and
AB  - enterohemorrhagic E. coli (EPEC and EHEC). Shiga toxin-producing strains have
AB  - also been identified. The genomic features of E. albertii, particularly
AB  - differences from other Escherichia species, have not yet been well clarified.
AB  - Here, we sequenced the genome of 29 E. albertii strains (3 complete and 26 draft
AB  - sequences) isolated from multiple sources and performed intra-species and
AB  - intra-genus genomic comparisons. The sizes of the E. albertii genomes range from
AB  - 4.5 Mb to 5.1 Mb, smaller than those of E. coli strains. Intra-species genomic
AB  - comparisons identified five phylogroups of E. albertii. Intra-genus genomic
AB  - comparison revealed that the possible core genome of E. albertii comprises 3,250
AB  - genes, whereas that of the genus Escherichia comprises 1,345 genes. Our analysis
AB  - further revealed several unique or notable genetic features of E. albertii,
AB  - including those responsible for known biochemical features and virulence factors
AB  - and a possibly active second T3SS known as ETT2 (E. coli T3SS 2) that is
AB  - inactivated in E. coli. Although this organism has been observed to be non-motile
AB  - in vitro, genes for flagellar biosynthesis are fully conserved;
AB  - chemotaxis-related genes have been selectively deleted. Based on these results,
AB  - we have developed a nested PCR system to directly detect E. albertii. Our data
AB  - define the genomic features of E. albertii and provide a valuable basis for
AB  - future studies of this important emerging enteropathogen.
ER  -

TY  - JOUR
AU  - Oosterkamp, M.J. et al.
TI  - Genome sequences of Alicycliphilus denitrificans strains BC and K601T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5028
EP  - 5029
VL  - 193
AB  - Alicycliphilus denitrificans strain BC and A. denitrificans strain K601(T) degrade cyclic
AB  - hydrocarbons. These strains have been isolated from a
AB  - mixture of wastewater treatment plant material and benzene polluted soil
AB  - and from a wastewater treatment plant, respectively, suggesting their role
AB  - in bioremediation of soil and water. Although the strains are
AB  - phylogenetically closely related, there are some clear physiological
AB  - differences. The hydrocarbon cyclohexanol, for example, can be degraded by
AB  - strain K601(T), but not by strain BC. Furthermore, both strains can use
AB  - nitrate and oxygen as an electron acceptor, but only strain BC can use
AB  - chlorate as electron acceptor. To better understand nitrate and chlorate
AB  - reduction mechanisms coupled to the oxidation of cyclic compounds, the
AB  - genomes of A. denitrificans strain BC and K601(T) were sequenced. Here, we
AB  - report the complete genome sequences of A. denitrificans strain BC and
AB  - K601(T).
ER  -

TY  - JOUR
AU  - Ootsuka, M.
AU  - Nishizawa, T.
AU  - Ohta, H.
TI  - Complete Genome Sequence of the Nonylphenol-Degrading Bacterium Sphingobium cloacae JCM 10874T.
JO  - Genome Announcements
PY  - 2016
SP  - e01358
EP  - e01316
VL  - 4
AB  - Sphingobium cloacae JCM 10874T can degrade phenolic endocrine-disrupting chemicals,
AB  - nonylphenol, and octylphenol. Here, we report the complete genome
AB  - sequence of the JCM 10874T strain.
ER  -

TY  - JOUR
AU  - Opazo, A.
AU  - Lopes, B.S.
AU  - Garcia, P.
AU  - Dominguez, Y.M.
AU  - Lima, C.
AU  - Bello-Toledo, H.
AU  - Gonzalez-Rocha, G.
AU  - Amyes, S.G.
TI  - Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii Strain from Chile.
JO  - Genome Announcements
PY  - 2015
SP  - e00687
EP  - e00615
VL  - 3
AB  - Acinetobacter baumannii strain Ab5 was isolated in the year 2007 in Chile, being  one of the
AB  - first multidrug-resistant (MDR) cases reported in the country. Here,
AB  - we present the very first draft genome sequence of an MDR Chilean strain, which
AB  - shows the presence of diverse resistance and acquired virulence genes.
ER  -

TY  - JOUR
AU  - Opazo, R.
AU  - Gajardo, F.
AU  - Ruiz, M.
AU  - Romero, J.
TI  - Genome Sequence of a Lactococcus lactis Strain Isolated from Salmonid Intestinal  Microbiota.
JO  - Genome Announcements
PY  - 2016
SP  - e00881
EP  - e00816
VL  - 4
AB  - Lactococcus lactis is a common inhabitant of the intestinal microbiota of salmonids,
AB  - especially those in aquaculture systems. Here, we present a genome
AB  - sequence of a Lactococcus lactis strain isolated from the intestinal contents of
AB  - rainbow trout reared in Chile.
ER  -

TY  - JOUR
AU  - Orata, F.D.
AU  - Kits, K.D.
AU  - Stein, L.Y.
TI  - Complete Genome Sequence of Methylomonas denitrificans Strain FJG1, an Obligate Aerobic Methanotroph That Can Couple Methane Oxidation with Denitrification.
JO  - Genome Announcements
PY  - 2018
SP  - e00276
EP  - e00218
VL  - 6
AB  - Methylomonas denitrificans strain FJG1 is a member of the gammaproteobacterial methanotrophs.
AB  - The sequenced genome of FJG1 reveals the presence of genes that
AB  - encode methane, methanol, formaldehyde, and formate oxidation. It also contains
AB  - genes that encode enzymes for nitrate reduction to nitrous oxide, consistent with
AB  - the ability of FJG1 to couple denitrification with methane oxidation.
ER  -

TY  - JOUR
AU  - Orata, F.D.
AU  - Rosana, A.R.
AU  - Xu, Y.
AU  - Simkus, D.N.
AU  - Bramucci, A.R.
AU  - Boucher, Y.
AU  - Case, R.J.
TI  - Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type) Emiliania huxleyi CCMP1516.
JO  - Genome Announcements
PY  - 2016
SP  - e00674
EP  - e00616
VL  - 4
AB  - Strains of Sulfitobacter spp., Erythrobacter sp., and Marinobacter sp. were isolated from a
AB  - polymicrobial culture of the naked (N-type) haptophyte Emiliania
AB  - huxleyi strain CCMP1516. The genomes encode genes for the production of
AB  - phytohormones, vitamins, and the consumption of their hosts' metabolic
AB  - by-products, suggesting symbiotic interactions within this polymicrobial culture.
ER  -

TY  - JOUR
AU  - Ordinario, D.D.
AU  - Burke, A.M.
AU  - Long, P.
AU  - Jocson, J.-M.
AU  - Wang, H.
AU  - Dickson, M.N.
AU  - Gorodetsky, A.A.
TI  - Sequence Specific Detection of Restriction Enzymes at DNA-Modified Carbon Nanotube Field Effect Transistors.
JO  - Anal. Chem.
PY  - 2014
SP  - 8628
EP  - 8633
VL  - 86
AB  - Protein-DNA interactions play a central role in many cellular processes, and their
AB  - misregulation has been implicated in a number of human diseases. Thus, there is a pressing
AB  - need for the development of analytical strategies for interrogating the binding of proteins to
AB  - DNA. Herein, we report the electrical monitoring of a prototypical DNA-binding protein, the
AB  - PvuII restriction enzyme, at microfluidic-encapsulated, DNA-modified carbon nanotube field
AB  - effect transistors. Our integrated platform enables the sensitive, sequence specific detection
AB  - of PvuII at concentrations as low as 0.5 pM in a volume of 0.025 mu L (corresponding to
AB  - similar to 7500 proteins). These figures of merit compare favorably to state of the art values
AB  - reported for alternative fluorescent and electrical assays. The overall detection strategy
AB  - represents a step toward the massively parallel electrical monitoring, identification, and
AB  - quantification of protein DNA interactions at arrayed nanoscale devices.
ER  -

TY  - JOUR
AU  - Ordogh, L.
AU  - Hunyadkurti, J.
AU  - Voros, A.
AU  - Horvath, B.
AU  - Szucs, A.
AU  - Urban, E.
AU  - Kereszt, A.
AU  - Kondorosi, E.
AU  - Nagy, I.
TI  - Complete Genome Sequence of Propionibacterium avidum Strain 44067, Isolated from  a Human Skin Abscess.
JO  - Genome Announcements
PY  - 2013
SP  - e00337
EP  - e00313
VL  - 1
AB  - Propionibacterium avidum is an anaerobic Gram-positive bacterium that forms part  of the
AB  - normal human cutaneous microbiota, colonizing moist areas such as the
AB  - vestibule of the nose, axilla, and perineum. Here we present the complete genome
AB  - sequence of P. avidum strain 44067, which was isolated from a carbuncle of the
AB  - trunk.
ER  -

TY  - JOUR
AU  - Ordonez, O.F.
AU  - Lanzarotti, E.
AU  - Kurth, D.
AU  - Gorriti, M.F.
AU  - Revale, S.
AU  - Cortez, N.
AU  - Vazquez, M.P.
AU  - Farias, M.E.
AU  - Turjanski, A.G.
TI  - Draft Genome Sequence of the Polyextremophilic Exiguobacterium sp. Strain S17, Isolated from Hyperarsenic Lakes in the Argentinian Puna.
JO  - Genome Announcements
PY  - 2013
SP  - e00480
EP  - e00413
VL  - 1
AB  - Exiguobacterium sp. strain S17 is a moderately halotolerant, arsenic-resistant bacterium that
AB  - was isolated from Laguna Socompa stromatolites in the Argentinian
AB  - Puna. The draft genome sequence suggests potent enzyme candidates that are
AB  - essential for survival under multiple environmental extreme conditions, such as
AB  - high levels of UV radiation, elevated salinity, and the presence of critical
AB  - arsenic concentrations.
ER  -

TY  - JOUR
AU  - Orduna, P.
AU  - Cevallos, M.A.
AU  - de Leon, S.P.
AU  - Arvizu, A.
AU  - Hernandez-Gonzalez, I.L.
AU  - Mendoza-Hernandez, G.
AU  - Lopez-Vidal, Y.
TI  - Genomic and proteomic analyses of Mycobacterium bovis BCG Mexico 1931 reveal a diverse immunogenic repertoire against tuberculosis infection.
JO  - BMC Genomics
PY  - 2011
SP  - 493
EP  - 493
VL  - 12
AB  - BACKGROUND: Studies of Mycobacterium bovis BCG strains used in different
AB  - countries and vaccination programs show clear variations in the genomes
AB  - and immune protective properties of BCG strains. The aim of this study was
AB  - to characterise the genomic and immune proteomic profile of the BCG 1931
AB  - strain used in Mexico. RESULTS: BCG Mexico 1931 has a circular chromosome
AB  - of 4,350,386 bp with a G+C content and numbers of genes and pseudogenes
AB  - similar to those of BCG Tokyo and BCG Pasteur. BCG Mexico 1931 lacks
AB  - Region of Difference 1 (RD1), RD2 and N-RD18 and one copy of IS6110,
AB  - indicating that BCG Mexico 1931 belongs to DU2 group IV within the BCG
AB  - vaccine genealogy. In addition, this strain contains three new RDs, which
AB  - are 53 (RDMex01), 655 (RDMex02) and 2,847 bp (REDMex03) long, and 55
AB  - single-nucleotide polymorphisms representing non-synonymous mutations
AB  - compared to BCG Pasteur and BCG Tokyo. In a comparative proteomic
AB  - analysis, the BCG Mexico 1931, Danish, Phipps and Tokyo strains showed
AB  - 812, 794, 791 and 701 protein spots, respectively. The same analysis
AB  - showed that BCG Mexico 1931 shares 62% of its protein spots with the BCG
AB  - Danish strain, 61% with the BCG Phipps strain and only 48% with the BCG
AB  - Tokyo strain. Thirty-nine reactive spots were detected in BCG Mexico 1931
AB  - using sera from subjects with active tuberculosis infections and positive
AB  - tuberculin skin tests. CONCLUSIONS: BCG Mexico 1931 has a smaller genome
AB  - than the BCG Pasteur and BCG Tokyo strains. Two specific deletions in BCG
AB  - Mexico 1931 are described (RDMex02 and RDMex03). The loss of RDMex02
AB  - (fadD23) is associated with enhanced macrophage binding and RDMex03
AB  - contains genes that may be involved in regulatory pathways. We also
AB  - describe new antigenic proteins for the first time.
ER  -

TY  - JOUR
AU  - Ordway, J.M.
AU  - Bedell, J.A.
AU  - Citek, R.W.
AU  - Nunberg, A.N.
AU  - Jeddeloh, J.A.
TI  - MethylIMapper: a method for high-throughput, multilocus bisulfite sequence analysis and reporting.
JO  - Biotechniques
PY  - 2005
SP  - 464
EP  - 468
VL  - 39
AB  - Understanding the phenotypic contribution of epigenetic components is making DNA methylation
AB  - pattern analysis more important in higher eukaryotic genomes as well as human disease.
AB  - Bisulfite sequencing protocols report DNA methylation occupancy information as a positive
AB  - assay output that allows methylation patterns to be elucidated from particular developmental
AB  - or disease states.  Reported here is a new method for bisulfite sequencing project management,
AB  - data analysis, and site-specific methylation test development that is designed for integration
AB  - in high-throughput genomic and bioinformatics analyses.
ER  -

TY  - JOUR
AU  - Orekhov, A.V.
AU  - Rebentish, B.A.
AU  - Debabov, V.G.
TI  - A new site-specific endonuclease from Streptomyces -- SgrII.
JO  - Dokl. Akad. Nauk.
PY  - 1982
SP  - 217
EP  - 220
VL  - 263
AB  - At the present time 21 restriction enzymes have been isolated from various
AB  - species of Streptomyces.  According to the genetic data of T.A. Voeikova, the
AB  - same restriction-modification systems tested with the acid of actinophage Pg81,
AB  - have been detected in the strains S. griseus, Kr. 20 and Rcg 2, a recombinant
AB  - obtained in a cross of S. coelicolor A3/2 and S. griseus Kr. 15.  In this work
AB  - we describe the isolation and characterization of a new type of restriction
AB  - enzyme, called SgrII.  These enzymes have been subsequently renamed Sgr20I and
AB  - Scg2I.
ER  -

TY  - JOUR
AU  - Orekhov, A.V.
AU  - Strokina, I.V.
AU  - Foors, A.R.
TI  - Restriction of shuttle Escherichia coli - Streptomyces plasmids in Streptomyces Lividans 66.
JO  - Genetika
PY  - 1989
SP  - 614
EP  - 625
VL  - 25
AB  - The shuttle Escherichia coli - Streptomyces plasmids were used to transform S. lividans 66.
AB  - Plasmid DNAs isolated from this strain transform it 10-1000-fold more efficiently than DNAs
AB  - from E. coli. A rare transformant cured of the most restricted plasmid is a more efficient
AB  - recipient of plasmid DNA from E. coli and has the property of R+/-M+ mutant. Restriction in S.
AB  - lividans 66 correlates with the appearance in DNA from E. coli of the sites susceptible to
AB  - Scg2I restriction endonuclease. The latter was isolated earlier from recombinant strain Rcg2,
AB  - a hybrid between S. griseus Kr. 15 and S. coelicolor A3(2). Scg2I possesses the recognition
AB  - sequence CC(T/A)GG, like EcoRII, MvaI and Eco dcm methylase. The DNA resistant to Scg2I
AB  - cleavage retained this ability after in vitro modification by EcoRII methylase. So, the
AB  - resistance of DNA to Scg2I cleavage is not connected with methylation at 4th and 5th position
AB  - of second cytosine in the recognition sequence. Neither restriction of plasmid DNA in S.
AB  - lividans 66 is dependent on dcm modification in E. coli, though its dependence on dam
AB  - modification is not excluded. It is assumed that the restriction in S. lividans 66 is
AB  - specified by endonuclease analogous to Scg2I.
ER  -

TY  - JOUR
AU  - Orellana, P.
AU  - Pavon, A.
AU  - Cespedes, S.
AU  - Salazar, L.
AU  - Gutierrez, A.
AU  - Castillo, D.
AU  - Corsini, G.
TI  - Draft Genome Sequence of Chilean Antarctic Pseudomonas sp. Strain K2I15.
JO  - Genome Announcements
PY  - 2017
SP  - e00771
EP  - e00717
VL  - 5
AB  - We announce the draft genome sequence of Pseudomonas sp. strain K2I15, isolated from the
AB  - rhizosphere of Deschampsia antarctica Desv. The genome sequence had
AB  - 6,645,031 bp with a G+C content of 60.4%. This genome provides insights into the
AB  - niche adaptation, prophage carriage, and evolution of this specific Antarctic
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Orlowski, J.
AU  - Boniecki, M.
AU  - Bujnicki, J.M.
TI  - I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
JO  - Bioinformatics
PY  - 2007
SP  - 527
EP  - 530
VL  - 23
AB  - Motivation: Restriction endonucleases (REases) and homing endonucleases (HEases) are
AB  - biotechnologically important enzymes. Nearly all
AB  - structurally characterized REases belong to the PD-(D/E) XK superfamily
AB  - of nucleases, while most HEases belong to an unrelated LAGLIDADG
AB  - superfamily. These two protein folds are typically associated with very
AB  - different modes of protein-DNA recognition, consistent with the
AB  - different mechanisms of action required to achieve high specificity.
AB  - REases recognize short DNA sequences using multiple contacts per base
AB  - pair, while HEases recognize very long sites using a few contacts per
AB  - base pair, thereby allowing for partial degeneracy of the target
AB  - sequence. Thus far, neither REases with the LAGLIDADG fold, nor HEases
AB  - with the PD-(D/E) XK fold, have been found.Results: Using protein fold
AB  - recognition, we have identified the first member of the PD-(D/E) XK
AB  - superfamily among homing endonucleases, a cyanobacterial enzyme
AB  - I-Ssp6803I. We present a model of the I-Ssp6803I-DNA complex based on
AB  - the structure of Type II restriction endonuclease R. BglI and predict
AB  - the active site and residues involved in specific DNA sequence
AB  - recognition by I-Ssp6803I. Our finding reveals a new unexpected
AB  - evolutionary link between HEases and REases and suggests how PD-(D/E)
AB  - XK nucleases may develop a 'HEase-like' way of interacting with the
AB  - extended DNA sequence. This in turn may be exploited to study the
AB  - evolution of DNA sequence specificity and to engineer nucleases with
AB  - new substrate specificities.Contact: iamb@genesilico.pl.
ER  -

TY  - JOUR
AU  - Orlowski, J.
AU  - Bujnicki, J.M.
TI  - Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 3552
EP  - 3569
VL  - 36
AB  - For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans:
AB  - proteins with no detectable similarity to each other and to any other protein in the database,
AB  - despite common cellular and biochemical function. Crystallographic analyses published until
AB  - January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences
AB  - available in the Restriction Enzyme database (REBASE). Among these structures, all but two
AB  - possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are
AB  - unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a
AB  - new fold termed 'half-pipe'. Thus far, bioinformatic studies supported by site-directed
AB  - mutagenesis have extended the number of tentatively assigned REase folds to five (now
AB  - including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided
AB  - structural predictions for dozens of REase sequences without experimentally solved structures.
AB  - Here, we present a comprehensive study of all Type II REase sequences available in REBASE
AB  - together with their homologs detectable in the nonredundant and environmental samples
AB  - databases at the NCBI. We present the summary and critical evaluation of structural
AB  - assignments and predictions reported earlier, new classification of all REase sequences into
AB  - families, domain architecture analysis and new predictions of three-dimensional folds. Among
AB  - 289 experimentally characterized (not putative) Type II REases, whose apparently full-length
AB  - sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The
AB  - HNH domain is the second most common, with 24 (8%) members. When putative REases are taken
AB  - into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively.
AB  - Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase
AB  - folds identified so far, and may exhibit new architectures. These enzymes are proposed as the
AB  - most interesting targets for structure determination by high-resolution experimental methods.
AB  - Our analysis provides the first comprehensive map of sequence-structure relationships among
AB  - Type II REases and will help to focus the efforts of structural and functional genomics of
AB  - this large and biotechnologically important class of enzymes.
ER  -

TY  - JOUR
AU  - Orlowski, J.
AU  - Mebrhatu, M.T.
AU  - Michiels, C.W.
AU  - Bujnicki, J.M.
AU  - Aertsen, A.
TI  - Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2008
SP  - 862
EP  - 866
VL  - 377
AB  - The Mrr protein of Escherichia coli K12 is a cryptic Type IV restriction endonuclease whose
AB  - activity appears to be triggered by high
AB  - pressure stress. In this report We used high pressure to isolate and
AB  - analyze several Mrr mutants, and generated a new structural model of
AB  - the Mrr protein. The activity of a number of spontaneous and
AB  - Strategically Constructed Mrr mutants is discussed in the light of this
AB  - model, providing a first insight into the Structure-function
AB  - relationships of the Mrr enzyme.
ER  -

TY  - JOUR
AU  - Ormeno-Orrillo, E. et al.
TI  - Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.).
JO  - BMC Genomics
PY  - 2012
SP  - 735
EP  - 735
VL  - 13
AB  - ABSTRACT: BACKGROUND: Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are
AB  - alpha-Proteobacteria that establish nitrogen-fixing symbioses with a range of
AB  - legume hosts. These strains are broadly used in commercial inoculants for
AB  - application to common bean (Phaseolus vulgaris) in South America and Africa. Both
AB  - strains display intrinsic resistance to several abiotic stressful conditions such
AB  - as low soil pH and high temperatures, which are common in tropical environments,
AB  - and to several antimicrobials, including pesticides. The genetic determinants of
AB  - these interesting characteristics remain largely unknown. RESULTS: Genome
AB  - sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic
AB  - plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium
AB  - displaying a similar host range. This pSym seems to have arisen by a
AB  - co-integration event between two replicons. Remarkably, three distinct nodA genes
AB  - were found in the pSym, a characteristic that may contribute to the broad host
AB  - range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone
AB  - levels were also identified in the pSym. Analysis of genes involved in stress
AB  - response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH,
AB  - high temperatures and also with oxidative and osmotic stresses. Interestingly,
AB  - the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding
AB  - drug-efflux systems, which may explain their high resistance to antimicrobials.
AB  - Genome analysis also revealed a wide array of traits that may allow these strains
AB  - to be successful rhizosphere colonizers, including surface polysaccharides,
AB  - uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition
AB  - systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS
AB  - secreted adhesins. CONCLUSIONS: Availability of the complete genome sequences of
AB  - CIAT 899 and PRF 81 may be exploited in further efforts to understand the
AB  - interaction of tropical rhizobia with common bean and other legume hosts.
ER  -

TY  - JOUR
AU  - Ormeno-Orrillo, E.
AU  - Aguilar-Cuba, Y.
AU  - Zuniga-Davila, D.
TI  - Draft Genome Sequence of Rhizobium sophoriradicis H4, a Nitrogen-Fixing Bacterium Associated with the Leguminous Plant Phaseolus vulgaris on the Coast of Peru.
JO  - Genome Announcements
PY  - 2018
SP  - e00241
EP  - e00218
VL  - 6
AB  - The genome sequence of Rhizobium sophoriradicis H4, a nitrogen-fixing bacterium isolated from
AB  - the common bean (Phaseolus vulgaris) in Peru, is reported here. The
AB  - genome assembly revealed a 6.44-Mbp genome which was distributed into 95 contigs,
AB  - with N50 and L50 values of 293 kbp and 9, respectively. The genome contained
AB  - 6,312 coding sequence (CDS) genes and 52 RNA genes (49 tRNAs and 3 rRNAs).
ER  -

TY  - JOUR
AU  - Ormeno-Orrillo, E.
AU  - Rogel, M.A.
AU  - Chueire, L.M.
AU  - Tiedje, J.M.
AU  - Martinez-Romero, E.
AU  - Hungria, M.
TI  - Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6927
EP  - 6927
VL  - 194
AB  - The genome sequences of Burkholderia sp. strains CCGE1002 from Mexico and H160 from Brazil,
AB  - isolated from legume nodules, are reported. Their gene contents in
AB  - relation to plant-microbe interactions and xenobiotic degradation are discussed.
ER  -

TY  - JOUR
AU  - Ormeno-Orrillo, E.
AU  - Rogel, M.A.
AU  - Zuniga-Davila, D.
AU  - Martinez-Romero, E.
TI  - Complete Genome Sequence of the Symbiotic Strain Bradyrhizobium icense LMTR 13(T), Isolated from Lima Bean (Phaseolus lunatus) in Peru.
JO  - Genome Announcements
PY  - 2018
SP  - e00146
EP  - e00118
VL  - 6
AB  - The complete genome sequence of Bradyrhizobium icense LMTR 13(T), a root nodule bacterium
AB  - isolated from the legume Phaseolus lunatus, is reported here. The
AB  - genome consists of a circular 8,322,773-bp chromosome which codes for a large and
AB  - novel symbiotic island as well as genes putatively involved in soil and root
AB  - colonization.
ER  -

TY  - JOUR
AU  - Ormsby, M.J.
AU  - Johnson, S.A.
AU  - Wall, D.M.
TI  - Draft Genome Sequence of the Commensal Escherichia coli Strain F-18.
JO  - Genome Announcements
PY  - 2016
SP  - e01416
EP  - e01416
VL  - 4
AB  - Here, we report the draft genome sequence of Escherichia coli strain F-18, originally isolated
AB  - from the feces of a healthy individual in 1977. The draft genome is 5,246,829 bp, with a G+C
AB  - content of 50.50%, and it encodes 4,933 predicted coding sequences (CDSs), 10 rRNAs, and 84
AB  - tRNAs.
ER  -

TY  - JOUR
AU  - Oroguchi, T.
AU  - Hashimoto, H.
AU  - Shimizu, T.
AU  - Sato, M.
AU  - Ikeguchi, M.
TI  - Intrinsic Dynamics of Restriction Endonuclease EcoO109I Studied by Molecular Dynamics Simulations and X-Ray Scattering Data Analysis.
JO  - Biophys. J.
PY  - 2009
SP  - 2808
EP  - 2822
VL  - 96
AB  - EcoO109I is a type II restriction endonuclease that functions as a dimer in solution. Upon DNA
AB  - binding to the enzyme, the two subunits
AB  - rotate counterclockwise relative to each other, as the two catalytic
AB  - domains undergo structural changes to capture the cognate DNA. Using a
AB  - 150-ns molecular dynamics simulation, we investigated the intrinsic
AB  - dynamics of the DNA-free enzyme in solution to elucidate the
AB  - relationship between enzyme dynamics and structural changes. The
AB  - simulation revealed that the enzyme is considerably flexible, and thus
AB  - exhibits large fluctuations in the radius of gyration. The small-angle
AB  - x-ray scattering profile calculated from the simulation, including
AB  - scattering from explicit hydration water, was in agreement with the
AB  - experimentally observed profile. Principal component analysis revealed
AB  - that the major dynamics were represented by the open-close and
AB  - counterclockwise motions: the former is required for the enzyme to
AB  - access DNA, whereas the latter corresponds to structural changes upon
AB  - DNA binding. Furthermore, the intrinsic dynamics in the catalytic
AB  - domains were consistent with motions capturing the cognate DNA. These
AB  - results indicate that the structure of EcoO109I is intrinsically
AB  - flexible in the direction of its functional movement, to facilitate
AB  - effective structural changes for sequence-specific DNA recognition and
AB  - processing.
ER  -

TY  - JOUR
AU  - Orr, R.J.S.
AU  - Rombauts, S.
AU  - Van de Peer, Y.
AU  - Shalchian-Tabrizi, K.
TI  - Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples.
JO  - Genome Announcements
PY  - 2017
SP  - e00787
EP  - e00717
VL  - 5
AB  - We report here the draft genome sequences of two Chitinophagaceae bacteria, IBVUCB1 and
AB  - IBVUCB2, assembled from metagenomes of surface samples from
AB  - freshwater lakes. The genomes are >99% complete and may represent new genera
AB  - within the Chitinophagaceae family, indicating a larger diversity than currently
AB  - identified.
ER  -

TY  - JOUR
AU  - Orr, R.J.S.
AU  - Rombauts, S.
AU  - Van de Peer, Y.
AU  - Shalchian-Tabrizi, K.
TI  - Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples.
JO  - Genome Announcements
PY  - 2017
SP  - e00894
EP  - e00817
VL  - 5
AB  - We report here the draft genome sequences of Sphingomonas sp. IBVSS1 and IBVSS2,  two bacteria
AB  - assembled from the metagenomes of surface samples from freshwater
AB  - lakes. The genomes are >99% complete and may represent new species within the
AB  - Sphingomonas genus, indicating a larger diversity than currently identified.
ER  -

TY  - JOUR
AU  - Orr, R.J.S.
AU  - Rombauts, S.
AU  - Van de Peer, Y.
AU  - Shalchian-Tabrizi, K.
TI  - Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples.
JO  - Genome Announcements
PY  - 2017
SP  - e00884
EP  - e00817
VL  - 5
AB  - We report here the draft genome sequences of Hydrogenophaga sp. strains IBVHS1 and IBVHS2, two
AB  - bacteria assembled from the metagenomes of surface samples from
AB  - freshwater lakes. The genomes are >95% complete and may represent new species
AB  - within the Hydrogenophaga genus, indicating a larger diversity than currently
AB  - identified.
ER  -

TY  - JOUR
AU  - Orru, L.
AU  - Salvetti, E.
AU  - Cattivelli, L.
AU  - Lamontanara, A.
AU  - Michelotti, V.
AU  - Capozzi, V.
AU  - Spano, G.
AU  - Keller, D.
AU  - Cash, H.
AU  - Martina, A.
AU  - Torriani, S.
AU  - Felis, G.E.
TI  - Draft Genome Sequence of Bacillus coagulans GBI-30, 6086, a Widely Used Spore-Forming Probiotic Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e01080
EP  - e01014
VL  - 2
AB  - Bacillus coagulans GBI-30, 6086 is a safe strain, already available on the market, and
AB  - characterized by certified beneficial effects. The draft genome
AB  - sequence presented here constitutes the first pillar toward the identification of
AB  - the molecular mechanisms responsible for its positive features and safety.
ER  -

TY  - JOUR
AU  - Orsini, M.
AU  - Cornacchia, A.
AU  - Patavino, C.
AU  - Torresi, M.
AU  - Centorame, P.
AU  - Acciari, V.A.
AU  - Ruolo, A.
AU  - Marcacci, M.
AU  - Ancora, M.
AU  - Di Domenico, M.
AU  - Mangone, I.
AU  - Blasi, G.
AU  - Duranti, A.
AU  - Camma, C.
AU  - Pomilio, F.
AU  - Migliorati, G.
TI  - Whole-Genome Sequences of Two Listeria monocytogenes Serovar 1/2a Strains Responsible for a Severe Listeriosis Outbreak in Central Italy.
JO  - Genome Announcements
PY  - 2018
SP  - e00236
EP  - e00218
VL  - 6
AB  - We report the whole-genome sequences of two Listeria monocytogenes strains responsible for a
AB  - severe invasive listeriosis outbreak in central Italy that
AB  - occurred in 2015 and 2016. These two strains differ by a single band in their
AB  - pulsed-field gel electrophoresis (PFGE) profiles.
ER  -

TY  - JOUR
AU  - Orsini, M.
AU  - Krasteva, I.
AU  - Marcacci, M.
AU  - Ancora, M.
AU  - Ciammaruconi, A.
AU  - Gentile, B.
AU  - Lista, F.
AU  - Pini, A.
AU  - Scacchia, M.
AU  - Sacchini, F.
AU  - Camma, C.
TI  - Whole-Genome Sequencing of Mycoplasma mycoides subsp. mycoides Italian Strain 57/13, the Causative Agent of Contagious Bovine Pleuropneumonia.
JO  - Genome Announcements
PY  - 2015
SP  - e00197
EP  - e00115
VL  - 3
AB  - Mycoplasma mycoides subsp. mycoides is generally considered one of most pathogenic Mycoplasma
AB  - species, and it is the etiological agent of contagious
AB  - bovine pleuropneumonia (CBPP). Here, we present the annotated genome sequence of
AB  - M. mycoides subsp. mycoides Italian strain 57/13, isolated in 1992 during CBPP
AB  - outbreaks in Italy.
ER  -

TY  - JOUR
AU  - Orsini, M.
AU  - Mangone, I.
AU  - DiPasquale, A.
AU  - Perticara, S.
AU  - Sacchini, L.
AU  - Cito, F.
AU  - Iannetti, S.
AU  - Marcacci, M.
AU  - Ancora, M.
AU  - Calistri, P.
AU  - Di Giannatale, E.
AU  - Camma, C.
TI  - Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:-] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00911
EP  - e00915
VL  - 3
AB  - Here, we present the draft genome sequences of 19 Salmonella enterica serovar Typhimurium
AB  - monophasic variant [4,5:i:-] strains involved in a long-term
AB  - salmonellosis outbreak that occurred in central Italy in 2013 to 2014.
ER  -

TY  - JOUR
AU  - Ortega, D.B.
AU  - Costa, R.A.
AU  - Pires, A.S.
AU  - Araujo, T.F.
AU  - Araujo, J.F.
AU  - Kurokawa, A.S.
AU  - Magalhaes, B.S.
AU  - Reis, A.M.M.
AU  - Franco, O.L.
AU  - Kruger, R.H.
AU  - Pappas, G.J. Jr.
AU  - Barreto, C.C.
TI  - Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13.
JO  - Genome Announcements
PY  - 2018
SP  - e00573
EP  - e00518
VL  - 6
AB  - A Paenibacillus elgii strain isolated from soil samples from Cerrado, Brazil, showed
AB  - antimicrobial activity. Its genome sequence was acquired (GS20 FLX
AB  - Titanium 454 platform) and comprises 108 contigs (N50, 198,427 bp) and 6,810
AB  - predicted sequences. Here, we shed some light on the antimicrobial genes of the
AB  - strain, including a nonribosomal peptide synthetase (NRPS) module identified as
AB  - part of a pelgipeptin gene cluster.
ER  -

TY  - JOUR
AU  - Ortet, P.
AU  - Barakat, M.
AU  - Lalaouna, D.
AU  - Fochesato, S.
AU  - Barbe, V.
AU  - Vacherie, B.
AU  - Santaella, C.
AU  - Heulin, T.
AU  - Achouak, W.
TI  - Complete Genome Sequence of a beneficial plant root-associated bacterium Pseudomonas brassicacearum.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3146
EP  - 3146
VL  - 193
AB  - To shed light on the genetic equipment of the beneficial plant-associated bacterium
AB  - Pseudomonas brassicacearum, we sequenced the whole genome of the
AB  - strain NFM421. Its genome consists of one chromosome equipped with a
AB  - repertoire of plant growth beneficial factors. In addition a complete T3SS
AB  - and two complete T6SS were identified. We report here the first genome
AB  - sequence of this species.
ER  -

TY  - JOUR
AU  - Ortet, P.
AU  - Gallois, N.
AU  - Piette, L.
AU  - Long, J.
AU  - Berthomieu, C.
AU  - Armengaud, J.
AU  - Barakat, M.
AU  - Chapon, V.
TI  - Draft Genome Sequence of Microbacterium oleivorans Strain A9, a Bacterium Isolated from Chernobyl Radionuclide-Contaminated Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00092
EP  - e00017
VL  - 5
AB  - Here, we present the draft genome sequence of Microbacterium oleivorans strain A9, a
AB  - uranium-tolerant actinobacterium which has been isolated from
AB  - radionuclide-contaminated soil from the Chernobyl exclusion zone. It is composed
AB  - of 22 contigs totaling 2,954,335 bp and contains 2,813 coding DNA sequences, one
AB  - cluster of rRNA genes, and 45 tRNA genes.
ER  -

TY  - JOUR
AU  - Ortiz, E.M.
AU  - Berretta, M.F.
AU  - Navas, L.E.
AU  - Benintende, G.B.
AU  - Amadio, A.F.
AU  - Zandomeni, R.O.
TI  - Draft Genome Sequence of Geobacillus sp. Isolate T6, a Thermophilic Bacterium Collected from a Thermal Spring in Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e00743
EP  - e00715
VL  - 3
AB  - Geobacillus sp. isolate T6 was collected from a thermal spring in Salta, Argentina. The draft
AB  - genome sequence (3,767,773 bp) of this isolate is
AB  - represented by one major scaffold of 3,46 Mbp, a second one of 207 kbp, and 20
AB  - scaffolds of <13 kbp. The assembled sequences revealed 3,919 protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Osama, A.
AU  - Gan, H.M.
AU  - Teh, C.S.
AU  - Yap, K.P.
AU  - Thong, K.L.
TI  - Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain  Isolated from a Cholera Patient in Malaysia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6933
EP  - 6933
VL  - 194
AB  - The genome sequence analysis of a clinical Vibrio cholerae VC35 strain from an outbreak case
AB  - in Malaysia indicates multiple genes involved in host adaptation
AB  - and a novel Na(+)-driven multidrug efflux pump-coding gene in the genome of
AB  - Vibrio cholerae with the highest similarity to VMA_001754 of Vibrio mimicus
AB  - VMA223.
ER  -

TY  - JOUR
AU  - Osborne, A.J.
AU  - Jose, B.R.
AU  - Perry, J.
AU  - Smeele, Z.
AU  - Aitken, J.
AU  - Gardner, P.P.
AU  - Slow, S.
TI  - Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates.
JO  - Genome Announcements
PY  - 2017
SP  - e00436
EP  - e00417
VL  - 5
AB  - Legionella is a highly diverse genus of intracellular bacterial pathogens that cause
AB  - Legionnaire's disease (LD), an often severe form of pneumonia. Two L.
AB  - micdadei sp. clinical isolates, obtained from patients hospitalized with LD from
AB  - geographically distinct areas, were sequenced using PacBio SMRT cell technology,
AB  - identifying incomplete phage regions, which may impact virulence.
ER  -

TY  - JOUR
AU  - Osdaghi, E.
AU  - Forero, S.N.
AU  - Bolot, S.
AU  - Fischer-Le, S.M.
AU  - Jacques, M.A.
AU  - Portier, P.
AU  - Carrere, S.
AU  - Koebnik, R.
TI  - High-Quality Draft Genome Sequence of Curtobacterium sp. Strain Ferrero.
JO  - Genome Announcements
PY  - 2017
SP  - e01378
EP  - e01317
VL  - 5
AB  - Here, we present the high-quality draft genome sequence of Curtobacterium sp. strain Ferrero,
AB  - an actinobacterium belonging to a novel species isolated as an
AB  - environmental contaminant in a bacterial cell culture. The assembled genome of
AB  - 3,694,888 bp in 49 contigs has a G+C content of 71.6% and contains 3,516
AB  - predicted genes.
ER  -

TY  - JOUR
AU  - Osei-Sekyere, J.
AU  - Amoako, D.G.
TI  - Genomic and phenotypic characterisation of fluoroquinolone resistance mechanisms in Enterobacteriaceae in Durban, South Africa.
JO  - PLoS ONE
PY  - 2017
SP  - E0178888
EP  - E0178888
VL  - 12
AB  - Resistance to fluoroquinolones (FQ) is being increasingly reported and found to
AB  - be mediated by efflux pumps, plasmid-mediated quinolone resistance genes (PMQR)
AB  - and mutations in gyrA, gyrB, parC and parE. However, studies reporting on FQ
AB  - resistance mechanisms (FQRM), particularly in Africa, are focused mostly on
AB  - Salmonella. This study used a whole-genome-based approach to describe FQRM in
AB  - forty-eight clinical Enterobacteriaceae isolates comprising of Klebsiella
AB  - pneumoniae (n = 21), Serratia marcescens (n = 12), Enterobacter spp. (n = 10),
AB  - Citrobacter freundii (n = 3), Escherichia coli (n = 1), and Klebsiella
AB  - michiganensis (n = 1) with reduced susceptibility to FQ in Enterobacteriaceae.
AB  - All the isolates exhibited exceptionally high-level resistance (MIC of 4-512mg/L)
AB  - to all three FQs, which could not be reversed by carbonyl cyanide m-chlorophenyl
AB  - hydrazine (CCCP), verapamil (VRP) or reserpine (RSP). PMQR genes such as oqxAB (n
AB  - = 43), aac(6')-Ib-cr (n = 28), and qnr(S1, B1, B2, B9, B49, B66) (n = 23) were
AB  - identified without transposons or integrons in their immediate environments.
AB  - Multiple and diverse mutations were found in gyrA (including S83I/Y and
AB  - T/I83I/T), gyrB, parC and parE, which were clonally specific. There were vertical
AB  - and horizontal transmission of high-level FQ resistance in Enterobacteriaceae in
AB  - hospitals in Durban, South Africa, which are mediated by efflux, PMQR genes, and
AB  - gyrA, gyrB, parC and parE mutations.
ER  -

TY  - JOUR
AU  - Oshiki, M.
AU  - Fukushima, T.
AU  - Kawano, S.
AU  - Nakagawa, J.
TI  - Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation.
JO  - Genome Announcements
PY  - 2017
SP  - e00799
EP  - e00717
VL  - 5
AB  - A draft genome sequence of a neutrophilic halophile capable of thiocyanate degradation,
AB  - Thiohalobacter thiocyanaticus FOKN1, was determined using a PacBio
AB  - RSII sequencer. A 3.23-Mb circular genome sequence was assembled, in which 3,026
AB  - gene-coding sequences, 45 tRNAs, and 1 rrn operon were annotated.
ER  -

TY  - JOUR
AU  - Oshiki, M.
AU  - Shinyako-Hata, K.
AU  - Satoh, H.
AU  - Okabe, S.
TI  - Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, 'Candidatus Brocadia sinica'.
JO  - Genome Announcements
PY  - 2015
SP  - e00267
EP  - e00215
VL  - 3
AB  - A draft genome sequence of an anaerobic ammonium-oxidizing (anammox) bacterium, 'Candidatus
AB  - Brocadia sinica,' was determined by pyrosequencing and by screening a
AB  - fosmid library. A 4.07-Mb genome sequence comprising 3 contigs was assembled, in
AB  - which 3,912 gene-coding regions, 47 tRNAs, and a single rrn operon were
AB  - annotated.
ER  -

TY  - JOUR
AU  - Oshima, H.
AU  - Asai, K.
AU  - Sadaie, Y.
TI  - Restriction and modification system genes of Bacillus subtilis.
JO  - Genes Genet. Syst.
PY  - 2000
SP  - 380
EP  - 380
VL  - 75
AB  - We found a set of genes for DNA restriction and modification in the third prophage region of
AB  - the Bacillus subtilis chromosome, where only five orfs are found in the 12kb region.  Two orfs
AB  - code for proteins similar to DNA methylation enzymes and constitute an operon.  The other
AB  - three orfs make another operon and the middle orf codes for a protein similar to DNA
AB  - restriction enzyme.  They must be RM system genes which recognize XhoI site and are deleted in
AB  - a classical RM strain of Bacillus subtilis.  XhoI sites on the DNA extracted only from RM
AB  - knockout strain could be digested with XhoI, indicating they are involved in restriction and
AB  - modification of Bacillus subtilis chromosome.
ER  -

TY  - JOUR
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Shimizu, H.
AU  - Fukuda, K.
AU  - Nemoto, M.
AU  - Inagaki, K.
AU  - Tamura, T.
TI  - Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin.
JO  - Genome Announcements
PY  - 2015
SP  - e00715
EP  - e00715
VL  - 3
AB  - A draft genome sequence of Streptomyces incarnatus NRRL8089, which produces the nucleoside
AB  - antibiotic sinefungin, is described here. The genome contains
AB  - 8,897,465 bp in 76 contigs and 8,266 predicted genes. Interestingly, the genome
AB  - encodes an open reading frame for selenocysteine-containing formate
AB  - dehydrogenase-O and the selenoprotein biosynthetic gene cluster selABCD.
ER  -

TY  - JOUR
AU  - Oshima, K.
AU  - Hayashi, J.
AU  - Toh, H.
AU  - Nakano, A.
AU  - Omori, E.
AU  - Hattori, Y.
AU  - Morita, H.
AU  - Honda, K.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Scardovia inopinata JCM 12537T, Isolated from Human Dental Caries.
JO  - Genome Announcements
PY  - 2015
SP  - e00481
EP  - e00415
VL  - 3
AB  - Scardovia inopinata JCM 12537(T) was isolated from human dental caries. Here, we  report the
AB  - complete genome sequence of this organism. This paper is the first
AB  - report to demonstrate the fully sequenced and completely annotated genome of an
AB  - S. inopinata strain.
ER  -

TY  - JOUR
AU  - Oshima, K.
AU  - Hayashi, J.
AU  - Toh, H.
AU  - Nakano, A.
AU  - Shindo, C.
AU  - Komiya, K.
AU  - Morita, H.
AU  - Honda, K.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Parascardovia denticolens JCM 12538T, Isolated from Human Dental Caries.
JO  - Genome Announcements
PY  - 2015
SP  - e00485
EP  - e00415
VL  - 3
AB  - Parascardovia denticolens JCM 12538(T) was isolated from human dental caries. Here, we report
AB  - the complete genome sequence of this organism. This paper is the
AB  - first report demonstrating the completely sequenced and assembled genome of P.
AB  - denticolens.
ER  -

TY  - JOUR
AU  - Oshima, K.
AU  - Hisamatsu, S.
AU  - Toh, H.
AU  - Nakano, A.
AU  - Kiuchi, M.
AU  - Kuroyanagi, H.
AU  - Morita, H.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Gardnerella vaginalis Strain JCM 11026T, Isolated from Vaginal Tracts of Women.
JO  - Genome Announcements
PY  - 2015
SP  - e00286
EP  - e00215
VL  - 3
AB  - Gardnerella vaginalis strain JCM 11026(T) was isolated from vaginal tracts of women. Here, we
AB  - report the complete genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Oshima, T. et al.
TI  - A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map (supplement).
JO  - DNA Res.
PY  - 1996
SP  - 211
EP  - 223
VL  - 3
AB  - none
ER  -

TY  - JOUR
AU  - Oshima, T. et al.
TI  - A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min Region on the linkage map.
JO  - DNA Res.
PY  - 1996
SP  - 137
EP  - 155
VL  - 3
AB  - The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region
AB  - from 12.7 to 28.0 minutes on the genetic map is described.  This region contains at least 681
AB  - potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%)
AB  - are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical
AB  - genes registered in databases, and the remaining 118 (17%) do not show a significant
AB  - similarity to any other gene.  In this region, we assigned a cluster of cit genes encoding
AB  - multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes
AB  - encoding integrase, excisionase and repressor in the e14 genetic element.  In addition, a new
AB  - valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B
AB  - and -C, were found.
ER  -

TY  - JOUR
AU  - Oshima, T.
AU  - Wada, C.
AU  - Kawagoe, Y.
AU  - Ara, T.
AU  - Maeda, M.
AU  - Masuda, Y.
AU  - Hiraga, S.
AU  - Mori, H.
TI  - Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli.
JO  - Mol. Microbiol.
PY  - 2002
SP  - 673
EP  - 695
VL  - 45
AB  - Deoxyadenosine methyltransferase (Dam) methylates the deoxyadenine residues in 5'-GATC-3'
AB  - sequences and is important in many cellular processes in Escherichia coli. We performed a
AB  - computational analysis of the entire E. coli genome and confirmed that GATC sequences are
AB  - distributed unevenly in regulatory regions, which suggests that Dam might regulate gene
AB  - transcription. To test this, a high-density DNA microarray of 4097 E. coli genes was
AB  - constructed and used to assess the gene expression profiles of the wild type and the
AB  - dam-16::kam mutant strain grown under four different conditions. We also used two-dimensional
AB  - electrophoretic analysis of the proteome to assess the protein profiles. The expression of a
AB  - large number of genes was affected by the dam deficiency. Genes involved in aerobic
AB  - respiration, stress and SOS responses, amino acid metabolism and nucleotide metabolism were
AB  - expressed at higher levels in the mutant cells, especially in aerobic conditions. In contrast,
AB  - transcription of genes participating in anaerobic respiration, flagella biosynthesis,
AB  - chemotaxis and motility was decreased in the dam mutant strain under both aerobic and low
AB  - aerobic conditions. Thus, Dam-controlled genes are involved in adjusting the metabolic and
AB  - respiratory pathways and bacterial motility to suit particular environmental conditions. The
AB  - promoters of most of these Dam-controlled genes were also found to contain GATC sequences that
AB  - overlap with recognition sites for two global regulators, fumarate nitrate reduction (Fnr) and
AB  - catabolite activator protein (CRP). We propose that Dam-mediated methylation plays an
AB  - important role in the global regulation of genes, particularly those with Fnr and CRP binding
AB  - sites.
ER  -

TY  - JOUR
AU  - Oshkin, I.Y.
AU  - Miroshnikov, K.K.
AU  - Belova, S.E.
AU  - Korzhenkov, A.A.
AU  - Toshchakov, S.V.
AU  - Dedysh, S.N.
TI  - Draft Genome Sequence of Methylovulum psychrotolerans Sph1(T), an Obligate Methanotroph from Low-Temperature Environments.
JO  - Genome Announcements
PY  - 2018
SP  - e01488
EP  - e01417
VL  - 6
AB  - Methylovulum psychrotolerans Sph1(T) is an aerobic, obligate methanotroph, which  was isolated
AB  - from cold methane seeps in West Siberia. This bacterium possesses
AB  - only a particulate methane monooxygenase and is widely distributed in
AB  - low-temperature environments. Strain Sph1(T) has the genomic potential for
AB  - biosynthesis of hopanoids required for the maintenance of intracytoplasmic
AB  - membranes.
ER  -

TY  - JOUR
AU  - Oshone, R.
AU  - Hurst, S.G. IV
AU  - Abebe-Akele, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequences for Two Variants of Frankia sp. Strain CpI1, the First Frankia Strain Isolated from Root Nodules of Comptonia peregrina.
JO  - Genome Announcements
PY  - 2016
SP  - e01588
EP  - e01515
VL  - 4
AB  - Frankia stains CpI1-S and CpI1-P are members of Frankia lineage Ia that are able  to reinfect
AB  - plants of the Betulaceae and Myricaceae families. Here, we report two
AB  - 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding
AB  - genes for CpI1-S and CpI1-P, respectively.
ER  -

TY  - JOUR
AU  - Oshone, R.
AU  - Ngom, M.
AU  - Abebe-Akele, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Sy, M.O.
AU  - Champion, A.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain Allo2, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Allocasuarina.
JO  - Genome Announcements
PY  - 2016
SP  - e00388
EP  - e00316
VL  - 4
AB  - Frankia sp. strain Allo2 is a member of Frankia lineage Ib, which is able to reinfect plants
AB  - of the Casuarinaceae family, and exhibits a high level of salt
AB  - tolerance compared to other isolates. Here, we report the 5.3-Mbp draft genome
AB  - sequence of Frankia sp. strain Allo2 with a G+C content of 70.0% and 4,224
AB  - candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Osieka, V.
AU  - Grobbel, M.
AU  - Schmoger, S.
AU  - Szentiks, C.A.
AU  - Irrgang, A.
AU  - Kasbohrer, A.
AU  - Tenhagen, B.A.
AU  - Hammerl, J.A.
TI  - Complete Draft Genome Sequence of an Extended-Spectrum beta-Lactamase-Producing Citrobacter freundii Strain Recovered from the Intestine of a House Sparrow (Passer domesticus) in Germany, 2017.
JO  - Genome Announcements
PY  - 2018
SP  - e00599
EP  - e00518
VL  - 6
AB  - Here, we announce the genome of an extended-spectrum beta-lactamase-producing Citrobacter
AB  - freundii strain isolated from the cecum of a house sparrow that was
AB  - found dead in Berlin-Lichtenberg, Germany, in 2017. This isolate exhibits
AB  - increased MICs for several antimicrobials and a comprehensive set of acquired
AB  - resistance determinants potentially involved in horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Osipiuk, J.
AU  - Walsh, M.A.
AU  - Joachimiak, A.
TI  - Crystal structure of MboIIA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 5440
EP  - 5448
VL  - 31
AB  - DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group
AB  - from S-adenosyl-L-methionine (AdoMet) to the amino
AB  - group of either cytosine or adenine within a recognized DNA sequence.
AB  - Methylation of a base in a specific DNA sequence protects DNA from
AB  - nucleolytic cleavage by restriction enzymes recognizing the same DNA
AB  - sequence. We have determined at 1.74 A resolution the crystal structure of
AB  - a beta-class DNA MTase MboIIA (M.MboIIA) from the bacterium Moraxella
AB  - bovis, the smallest DNA MTase determined to date. M.MboIIA methylates the
AB  - 3' adenine of the pentanucleotide sequence 5'-GAAGA-3'. The protein
AB  - crystallizes with two molecules in the asymmetric unit which we propose to
AB  - resemble the dimer when M.MboIIA is not bound to DNA. The overall
AB  - structure of the enzyme closely resembles that of M.RsrI. However, the
AB  - cofactor-binding pocket in M.MboIIA forms a closed structure which is in
AB  - contrast to the open-form structures of other known MTases.
ER  -

TY  - JOUR
AU  - Oskam, L.
AU  - Hillenga, D.J.
AU  - Venema, G.
AU  - Bron, S.
TI  - The integrated state of the rolling-circle plasmid pTB913 in the composite Bacillus plasmid pTB19.
JO  - Mol. Gen. Genet.
PY  - 1992
SP  - 462
EP  - 468
VL  - 233
AB  - pTB19, a 27 kb plasmid originating from a thermophilic Bacillus species,
AB  - contains integrated copies of two rolling-circle type plasmids on a 10.6
AB  - kb DNA fragment. In the present study we analysed the part of pTB19 that
AB  - contains the rolling-circle plasmid pTB913 and the region in between the
AB  - two rolling-circle plasmids. We show that, in the integrated state, pTB913
AB  - was flanked by a 55 bp direct repeat that duplicated part of the
AB  - replication initiation gene repB. Since repB was interrupted, the
AB  - integrated pTB913 could not initiate rolling-circle replication.
AB  - Autonomously replicating pTB913 was produced from pTB19, probably through
AB  - recombination between the 55 bp direct repeats; this was a rare event.
AB  - Since the second integrated rolling-circle type plasmid also contained a
AB  - non-functional replication initiation gene, replication of pTB19 must be
AB  - controlled by the RepA determinant. Theta-type replication, controlled by
AB  - RepA is likely to account for the high stability of pTB19. In between the
AB  - two integrated rolling-circle plasmids was present an open reading frame
AB  - (447 codons) which could encode a protein of unknown function.
ER  -

TY  - JOUR
AU  - Osman, W.A.M.
AU  - van Berkum, P.
AU  - Leon-Barrios, M.
AU  - Velazquez, E.
AU  - Elia, P.
AU  - Tian, R.
AU  - Ardley, J.
AU  - Gollagher, M.
AU  - Seshadri, R.
AU  - Reddy, T.B.K.
AU  - Ivanova, N.
AU  - Woyke, T.
AU  - Pati, A.
AU  - Markowitz, V.
AU  - Baeshen, M.N.
AU  - Baeshen, N.N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 58
EP  - 58
VL  - 12
AB  - 10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that was isolated from an effective
AB  - nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample
AB  - collected near the town of Guatiza on the island of Lanzarote, the Canary
AB  - Islands, Spain. This strain nodulates and forms an effective symbiosis with the
AB  - highly specific host M. laciniata. This rhizobial genome was sequenced as part of
AB  - the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
AB  - Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of
AB  - 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft
AB  - genome sequence information and annotation. The 6,664,116 bp high-quality draft
AB  - genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding
AB  - genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to
AB  - 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T,
AB  - 10.1601/nm.1334 A 321T and 10.1601/nm.17831
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene
AB  - sequences. gANI values of >/=98.1% support the classification of strain Mlalz-1
AB  - as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele,
AB  - and the nodC gene of strain Mlalz-1 shares >/=98% sequence identity with nodC of
AB  - M. laciniata-nodulating 10.1601/nm.1328 strains, but </=93% with nodC of
AB  - 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is
AB  - unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding
AB  - components of a T2SS and in having two versions of the adaptive acid tolerance
AB  - response lpiA-acvB operon. In 10.1601/nm.1334 strain
AB  - 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing
AB  - survival in lethal acid conditions. The second copy of the lpiA-acvB operon of
AB  - strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334
AB  - strains, which suggests genetic recombination between strain Mlalz-1 and
AB  - 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
ER  -

TY  - JOUR
AU  - Ossandon, F.J.
AU  - Cardenas, J.P.
AU  - Corbett, M.
AU  - Quatrini, R.
AU  - Holmes, D.S.
AU  - Watkin, E.
TI  - Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant 'Thiobacillus prosperus' Type Strain DSM 5130.
JO  - Genome Announcements
PY  - 2014
SP  - e01042
EP  - e01014
VL  - 2
AB  - 'Thiobacillus prosperus' is a halotolerant mesophilic acidophile that gains energy through
AB  - iron and sulfur oxidation. Its physiology is poorly understood.
AB  - Here, we describe the principal genomic features of the type strain of T.
AB  - prosperus, DSM 5130. This is the first public genome sequence of an acidophilic
AB  - halotolerant bacterium.
ER  -

TY  - JOUR
AU  - Ostendorf, T.
AU  - Cherepanov, P.
AU  - deVries, J.
AU  - Wachernagel, W.
TI  - Characterization of a dam mutant of Serratia marcescens and nucleotide sequence of the dam region.
JO  - J. Bacteriol.
PY  - 1999
SP  - 3880
EP  - 3885
VL  - 181
AB  - The DNA of Serratia marcescens has N6-adenine methylation in GATC sequences. Among
AB  - 2-aminopurine-sensitive mutants isolated from S. marcescens Sr41, one was identified which
AB  - lacked GATC methylation. The mutant showed up to 30-fold increased spontaneous mutability and
AB  - enhanced mutability after treatment with 2-aminopurine, ethyl methanesulfonate, or UV light.
AB  - The gene (dam) coding for the adenine methyltransferase (Dam enzyme) of S. marcescens was
AB  - identified on a gene bank plasmid which alleviated the 2-aminopurine sensitivity and the
AB  - higher mutability of a dam-13::Tn9 mutant of Escherichia coli. Nucleotide sequencing revealed
AB  - that the deduced amino acid sequence of Dam (270 amino acids; molecular mass, 31.3 kDa) has
AB  - 72% identity to the Dam enzyme of E. coli. The dam gene is located between flanking genes
AB  - which are similar to those found to the sides of the E. coli dam gene. The results of
AB  - complementation studies indicated that like Dam of E. coli and unlike Dam of Vibrio cholerae,
AB  - the Dam enzyme of S. marcescens plays an important role in mutation avoidance by allowing the
AB  - mismatch repair enzymes to discriminate between the parental and newly synthesized strands
AB  - during correction of replication errors.
ER  -

TY  - JOUR
AU  - Osterlund, M.
AU  - Luthman, H.
AU  - Nilsson, S.V.
AU  - Magnusson, G.
TI  - Ethidium-bromide-inhibited restriction endonucleases cleave one strand of circular DNA.
JO  - Gene
PY  - 1982
SP  - 121
EP  - 125
VL  - 20
AB  - We analyzed the effect of ethidium bromide (EtBr) on the cleavage of closed
AB  - circular pBR322 DNA molecules by six restriction enzymes which make staggered
AB  - or flush cuts (EcoRI, HindIII, BglI, PstI, HincII, PvuII).  EtBr concentrations
AB  - and reaction temperatures were determined at which DNA molecules with
AB  - single-strand breaks were the major reaction product of digestion by all the
AB  - enzymes.  However, the amounts of intermediates which could be isolated
AB  - differed for various enzymes.  The results extend previous studies, showing
AB  - that sequential cleavage of the DNA strands probably is a general property of
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Osterman, D.G.
AU  - DePillis, G.D.
AU  - Wu, J.C.
AU  - Matsuda, A.
AU  - Santi, D.V.
TI  - 5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase.
JO  - Biochemistry
PY  - 1988
SP  - 5204
EP  - 5210
VL  - 27
AB  - 5-Fluorodeoxycytidine (FdCyd) was incorporated into a synthetic DNA polymer
AB  - containing the GCGC recognition sequence of HhaI methylase to give a polymer
AB  - with about 80% FdCyd.  In the absence of AdoMet, poly(FdC-dG) bound
AB  - competitively with respect to poly(dG-dC) (Ki=3nM).  In the presence of AdoMet,
AB  - the analogue caused a time-dependent, first-order (k=0.05 min-1) inactivation
AB  - of the enzyme.  There is an ordered mechanism of binding in which enzyme first
AB  - binds to poly(FdC-dG), then binds to AdoMet, and subsequently forms stable,
AB  - inactive complexes.  The complexes did not dissociate over the course of 3 days
AB  - and were stable to heat (95C) in the prsence of 1% SDS.  Gel filtration of a
AB  - complex formed with HhaI methylase, poly(FdC-dG), and [methyl-3H]AdoMet gave a
AB  - peak of radioactivity eluting near the void volume.  Digestion of the DNA in
AB  - the complex resulted in a reduction of the molecular weight to the size of the
AB  - methylase, and the radioactivity in this peak was shown to be associated with
AB  - protein.  These data indicate that the complexes contain covalently bound HhaI
AB  - methylase, poly(FdC-dG), and methyl groups and that 5-fluorodeoxycytidine is a
AB  - mechanism-based inactivator of the methylase.  By analogy with other
AB  - pyrimidine-modifying enzymes and recent studies on the mechanism of HhaI
AB  - methylase (Wu & Santi, 1987), these results suggest that an enzyme nucleophile
AB  - attacks FdCyd residues at C-6, activating the 5-position for one-carbon
AB  - transfer.  Subsequent transfer of the methyl group of AdoMet to the activated
AB  - FdCyd forms a stable complex in which the enzyme is covalently bound to the
AB  - 6-position of FdCyd in the polymer and a methyl group is attached to C-5.  The
AB  - effect of 5-fluorodeoxycytidine on the inhibition of DNA-cytosine
AB  - methyltransferases is thus due to irreversible, covalent inactivation.
ER  -

TY  - JOUR
AU  - Osterman, J.
AU  - Marsh, J.
AU  - Laine, P.
AU  - Zeng, Z.
AU  - Alatalo, E.
AU  - Sullivan, J.T.
AU  - Young, J.P.
AU  - Thomas-Oates, J.
AU  - Paulin, L.
AU  - Lindstrom, K.
TI  - Genome sequencing of two Neorhizobium galegae strains reveals a noeT gene responsible for the unusual acetylation of the nodulation factors.
JO  - BMC Genomics
PY  - 2014
SP  - 500
EP  - 500
VL  - 15
AB  - BACKGROUND: The species Neorhizobium galegae comprises two symbiovars that induce
AB  - nodules on Galega plants. Strains of both symbiovars, orientalis and officinalis,
AB  - induce nodules on the same plant species, but fix nitrogen only in their own host
AB  - species. The mechanism behind this strict host specificity is not yet known. In
AB  - this study, genome sequences of representatives of the two symbiovars were
AB  - produced, providing new material for studying properties of N. galegae, with a
AB  - special interest in genomic differences that may play a role in host specificity.
AB  - RESULTS: The genome sequences confirmed that the two representative strains are
AB  - much alike at a whole-genome level. Analysis of orthologous genes showed that N.
AB  - galegae has a higher number of orthologs shared with Rhizobium than with
AB  - Agrobacterium. The symbiosis plasmid of strain HAMBI 1141 was shown to transfer
AB  - by conjugation under optimal conditions. In addition, both sequenced strains have
AB  - an acetyltransferase gene which was shown to modify the Nod factor on the residue
AB  - adjacent to the non-reducing-terminal residue. The working hypothesis that this
AB  - gene is of major importance in directing host specificity of N. galegae could
AB  - not, however, be confirmed. CONCLUSIONS: Strains of N. galegae have many genes
AB  - differentiating them from strains of Agrobacterium, Rhizobium and Sinorhizobium.
AB  - However, the mechanism behind their ecological difference is not evident.
AB  - Although the final determinant for the strict host specificity of N. galegae
AB  - remains to be identified, the gene responsible for the species-specific
AB  - acetylation of the Nod factors was identified in this study. We propose the name
AB  - noeT for this gene to reflect its role in symbiosis.
ER  -

TY  - JOUR
AU  - Ostroff, G.R.
AU  - Pene, J.J.
TI  - Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis:  Isolation of a spontaneous mutant of Bacillus subtilis with enhanced transformability for Escherichia coli-propagated chimeric plasmid DNA.
JO  - J. Bacteriol.
PY  - 1983
SP  - 934
EP  - 936
VL  - 156
AB  - Hybrid plasmid DNA cloned in Escherichia coli undergoes deletions when returned
AB  - to competent Bacillus subtilis, even in defined restriction and modification
AB  - mutants of strain 168.  We have isolated a mutant of B. subtilis MI112 which is
AB  - stably transformed at high frequency by chimeric plasmid DNA propagated in E.
AB  - coli.
ER  -

TY  - JOUR
AU  - Ostroff, G.R.
AU  - Pene, J.J.
TI  - Molecular cloning with bifunctional plasmid vectors in Bacillus subtilis.  II.  Transfer of sequences propagated in Escherichia coli to B. subtilis.
JO  - Mol. Gen. Genet.
PY  - 1984
SP  - 306
EP  - 311
VL  - 193
AB  - Recombinant plasmid DNA cloned in E. coli via the bifunctional vector pDH5060
AB  - suffered deletions when returned to B. subtilis.  However, DNA preparations of
AB  - identical chimeras containing homologous or heterologous sequences stably
AB  - transformed B. subtilis at high efficiency when isolated from B. subtilis.  The
AB  - vector pDH5060, however, was not affected and could be stably shuttled between
AB  - E. coli and B. subtilis at high frequency.  These problems affected the
AB  - transfer of clone pools and individual chimeras, irrespective of the
AB  - restriction or recombination phenotype of B. subtilis recipients.  Deleted
AB  - chimeras lost at least one end of cloned inserts, and in most cases, flanking
AB  - plasmid sequences.  Single plasmid forms (intact or deleted) were isolated from
AB  - several hundred individual Cmr-transformants.  This suggests that events
AB  - leading to deletion of chimeric plasmid DNA occur during transformation by
AB  - restriction of unmodified insert sequences propagated in the intermediate host,
AB  - E. coli.  This conclusion is discussed with regard to the mechanism of plasmid
AB  - transformation in B. subtilis.
ER  -

TY  - JOUR
AU  - Ostrov, I.
AU  - Sela, N.
AU  - Freed, M.
AU  - Khateb, N.
AU  - Kott-Gutkowski, M.
AU  - Inbar, D.
AU  - Shemesh, M.
TI  - Draft Genome Sequence of Bacillus licheniformis S127, Isolated from a Sheep Udder Clinical Infection.
JO  - Genome Announcements
PY  - 2015
SP  - e00971
EP  - e00915
VL  - 3
AB  - Bacillus licheniformis is a Gram-positive biofilm- and endospore-forming bacterium, which
AB  - contaminates dairy products and can be pathogenic to humans. The draft genome sequencing for
AB  - B. licheniformis strain S127 is reported here, providing genetic data relevant to the ability
AB  - of this strain to sustain its survival in the dairy industry.
ER  -

TY  - JOUR
AU  - Osuna, J.
AU  - Flores, H.
AU  - Soberon, X.
TI  - Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities.
JO  - Gene
PY  - 1991
SP  - 7
EP  - 12
VL  - 106
AB  - A library of mutant ecoRIR genes encoding EcoRI restriction endonuclease was
AB  - generated using trinucleotide blocks and a combination of recombinant DNA
AB  - procedures, including primer extension and the polymerase chain reaction.
AB  - Codons corresponding to three amino acids (E144, R145 and R200), previously
AB  - implicated in the specific, recognition of the DNA substrate, were
AB  - combinatorially mutated so as to generate a library that potentially contains
AB  - all 8000 possible single, double and triple aa replacements, in a balanced
AB  - distribution.  Inspection of the phenotypes of Escherichia coli colonies
AB  - bearing the mutant genes showed that several of them retained activities that
AB  - were deleterious to the cells but were still protected by the EcoRI
AB  - methyltransferase.  These included new enzyme variants, including
AB  - non-conservative single (Thr or Val for Glu144) and double (Val for Glu144 and
AB  - Thr for Arg145) replacements.
ER  -

TY  - JOUR
AU  - Oswald, T.
AU  - Hornbostel, G.
AU  - Rinas, U.
AU  - Anspach, F.B.
TI  - Purification of (His)6EcoRV [recombinant restriction endonuclease EcoRV fused to a (His)6 affinity domain] by metal-chelate affinity chromatography.
JO  - Biotechnol. Appl. Biochem.
PY  - 1997
SP  - 109
EP  - 115
VL  - 25
AB  - The chromatographic purification of (His)6EcoRV, a fusion protein consisting of a
AB  - hexahistidine affinity domain and restriction endonuclease EcoRV produced from recombinant
AB  - Escherichia coli, led to high product concentrations (>-1 mg/ml) in the preparative mode.
AB  - Increasing the amount of applied crude cell homogenate caused competition with host-specific
AB  - proteins, leading to a decrease of recovery and purity of the fusion protein.  Reduction of
AB  - host-specific proteins was achieved by pre-adsorption on to a DEAE anion-exchange sorbent.
AB  - This, in combination with 0.5-1 M NaCl in the adsorption buffer, assured a purity >95% and a
AB  - total protein recovery of ~34% in the preparative mode.  Contamination of the product with
AB  - about 2 mol of Ni(II)/mol of (His)6EcoRV was found due to metal-ion transfer to the N-terminal
AB  - high affinity binding site at (His)6.  Tris(carboxymethyl)ethylenediamine (TED)-Sepharose was
AB  - employed as an Ni(II) adsorber.  One passage of Ni(II)-contaminated protein solutions through
AB  - the TED-Sepharose column resulted in a decrease in the Ni(II) content in the (His)6EcoRV
AB  - fractions below the detection limit (~0.02 mg/l) of the atomic-adsorption spectrophotometer.
ER  -

TY  - JOUR
AU  - Oswald, T.
AU  - Rinas, U.
TI  - Chloramphenicol resistance interferes with purification of histidine-tagged fusion proteins from recombinant Escherichia coli.
JO  - Anal. Biochem.
PY  - 1996
SP  - 357
EP  - 358
VL  - 236
AB  - The production of oligohistidine-tagged fusion proteins has become a widespread technique in
AB  - order to facilitate recombinant protein purification by using immobilized metal ion affinity
AB  - chromatography (IMAC).  In many cases a one-step purification procedure is sufficient to
AB  - obtain the protein of interest as 95% pure.  However, several host-specific proteins have been
AB  - identified which show a high affinity to the IMAC materials and are copurified with the
AB  - oligohistidine-tagged fusion protien.  Here we describe impaired purification of (His)6-tagged
AB  - fusion proteins by IMAC from chloramphenicol-resistant Escherichia coli cells.
ER  -

TY  - JOUR
AU  - Oswald, T.
AU  - Wende, W.
AU  - Pingoud, A.
AU  - Rinas, U.
TI  - Comparison of N-terminal affinity fusion domains: effect on expression level and product heterogeneity of recombinant restriction endonuclease EcoRV.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1994
SP  - 73
EP  - 77
VL  - 42
AB  - The influence of different N-terminal affinity fusion domains on the product heterogeneity of
AB  - recombinant proteins expressed in Escherichia coli was investigated. N-Terminal extended forms
AB  - of the restriction endonuclease EcoRV with either glutathione-S-transferase [GST], histidine
AB  - hexapeptide [(His)6], or a combination of GST and (His)6 [GST-(His)6] were compared to native
AB  - EcoRV with respect to expression level, susceptibility to inclusion body formation and protein
AB  - fragmentation. Fingerprinting of product heterogeneity was done by using two-dimensional (2-D)
AB  - non-equilibrium pH-gradient electrophoresis with subsequent immunoblotting. Fusion proteins
AB  - containing GST were poorly expressed compared to native EcoRV. In addition, GST fusion
AB  - proteins were highly susceptible to in vivo aggregation and fragmentation and displayed more
AB  - heterogeneity on 2-D immunoblots. However, the sole presence of oligohistidine at the
AB  - N-terminus of EcoRV proved to be advantageous. Fragmentation of (His)6-EcoRV was not observed
AB  - and 2-D immunoblots did not show heterogeneous forms of the recombinant protein. In addition,
AB  - fusion of the histidine-hexapeptide to the N-terminus of native EcoRV increased the expression
AB  - level of the recombinant protein twofold compared to native EcoRV. Inclusion body formation of
AB  - the (His)6-EcoRV fusion protein was intensive when cells were grown at 37oC but not at 30oC.
AB  - The advantage of oligohistidine fusion to EcoRV was finally demonstrated by purifying soluble
AB  - (His)6-EcoRV in a single-step procedure from crude cell lysates using immobilized metal
AB  - chelate affinity chromatography.
ER  -

TY  - JOUR
AU  - Otani, J.
AU  - Nankumo, T.
AU  - Arita, K.
AU  - Inamoto, S.
AU  - Ariyoshi, M.
AU  - Shirakawa, M.
TI  - Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.
JO  - EMBO Rep.
PY  - 2009
SP  - 1235
EP  - 1241
VL  - 10
AB  - DNMT3 proteins are de novo DNA methyltransferases that are responsible for the establishment
AB  - of DNA methylation patterns in mammalian genomes. Here,
AB  - we have determined the crystal structures of the ATRX-DNMT3-DNMT3L (ADD)
AB  - domain of DNMT3A in an unliganded form and in a complex with the
AB  - amino-terminal tail of histone H3. Combined with the results of
AB  - biochemical analysis, the complex structure indicates that DNMT3A
AB  - recognizes the unmethylated state of lysine 4 in histone H3. This finding
AB  - indicates that the recruitment of DNMT3A onto chromatin, and thereby de
AB  - novo DNA methylation, is mediated by recognition of the histone
AB  - modification state by its ADD domain. Furthermore, our biochemical and
AB  - nuclear magnetic resonance data show mutually exclusive binding of the ADD
AB  - domain of DNMT3A and the chromodomain of heterochromatin protein 1alpha to
AB  - the H3 tail. These results indicate that de novo DNA methylation by DNMT3A
AB  - requires the alteration of chromatin structure.
ER  -

TY  - JOUR
AU  - Ott, B.M.
AU  - Beka, L.
AU  - Graf, J.
AU  - Rio, R.V.
TI  - Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings.
JO  - Genome Announcements
PY  - 2015
SP  - e01469
EP  - e01415
VL  - 3
AB  - The Pedobacter sp. Hv1 strain was isolated from the medicinal leech, Hirudo verbana, mucosal
AB  - castings. These mucosal sheds have been demonstrated to play a
AB  - role in horizontal symbiont transmission. Here, we report the draft 4.9 Mbp
AB  - genome sequence of Pedobacter sp. strain Hv1.
ER  -

TY  - JOUR
AU  - Ott, J.
AU  - Eckstein, F.
TI  - 31P NMR spectral analysis of the dodecamer d(CGCGAATTCGCG).
JO  - Biochemistry
PY  - 1985
SP  - 2530
EP  - 2535
VL  - 24
AB  - The resonances in the 31P NMR spectrum of the dodecamer d(CGCGAATTCGCG) have
AB  - been assigned by use of regiospecific labeling with oxygen-17.  At 19C the
AB  - resonsances of 9 of the 11 dinucleoside phosphates are resolved.  Most
AB  - noticeably, different chemical shifts are observed for the phosphates of d(GpC)
AB  - at positions 2 and 10 as well as for d(CpG) at positions 1,3,9, and 11,
AB  - indicating that the position in an oligonucleotide influences the chemical
AB  - shift.  For the central d(GAATTC) portion of this dodecamer, a close
AB  - relationship between the chemical shift of the phosphate groups and their
AB  - position in the sequence of the oligonucleotide exists, in that the more
AB  - central the phosphate residue is the more the signal appears at higher field.
AB  - This finding parallels that found for the octamer d(GGAATTCC) [Connolly, B.A. &
AB  - Eckstein, F. (1984) Biochemistry 23,5523-5527].  The signals of the phosphate
AB  - residues at positions 3 and 9, however, are found at lower field strength than
AB  - expected from their position in the sequence, indicating a break in
AB  - conformation at these two locations.  A discontinuity of structure is also
AB  - observed at these positions in the X-ray structure of this dodecamer
AB  - [Dickerson, R.F., & Drew, H.R. (1981) J. Mol. Biol. 149, 761-786] as shown by
AB  - the anomalous twist angles between the third and fourth as well as the ninth
AB  - and tenth base pairs.  The dependence of the chemical shift on temperature
AB  - indicates different mobilities for each of the 11 phosphate groups.  There
AB  - seems to be no fraying at the ends but conformational changes particularly at
AB  - the central A-T base pairs at the center of the molecule, consistent with the
AB  - data obtained by H NMR spectroscopy [Patel, D.J., Kozlowski, S.A., Marky, L.A.,
AB  - Broka, C., Rice, J.A., Itakura, K., & Breslauer, K.J. (1982) Biochemistry 21,
AB  - 428-436].
ER  -

TY  - JOUR
AU  - Ou, H.Y.
AU  - He, X.
AU  - Shao, Y.
AU  - Tai, C.
AU  - Rajakumar, K.
AU  - Deng, Z.
TI  - dndDB: a database focused on phosphorothioation of the DNA backbone.
JO  - PLoS ONE
PY  - 2009
SP  - e5132
EP  - e5132
VL  - 4
AB  - BACKGROUND: The Dnd DNA degradation phenotype was first observed during electrophoresis of
AB  - genomic DNA from Streptomyces lividans more than 20
AB  - years ago. It was subsequently shown to be governed by the five-gene dnd
AB  - cluster. Similar gene clusters have now been found to be widespread among
AB  - many other distantly related bacteria. Recently the dnd cluster was shown
AB  - to mediate the incorporation of sulphur into the DNA backbone via a
AB  - sequence-selective, stereo-specific phosphorothioate modification in
AB  - Escherichia coli B7A. Intriguingly, to date all identified dnd clusters
AB  - lie within mobile genetic elements, the vast majority in laterally
AB  - transferred genomic islands. METHODOLOGY: We organized available data from
AB  - experimental and bioinformatics analyses about the DNA phosphorothioation
AB  - phenomenon and associated documentation as a dndDB database. It contains
AB  - the following detailed information: (i) Dnd phenotype; (ii) dnd gene
AB  - clusters; (iii) genomic islands harbouring dnd genes; (iv) Dnd proteins
AB  - and conserved domains. As of 25 December 2008, dndDB contained data
AB  - corresponding to 24 bacterial species exhibiting the Dnd phenotype
AB  - reported in the scientific literature. In addition, via in silico
AB  - analysis, dndDB identified 26 syntenic dnd clusters from 25 species of
AB  - Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid
AB  - containing 114 dnd genes. A further 397 other genes coding for proteins
AB  - with varying levels of similarity to Dnd proteins were also included in
AB  - dndDB. A broad range of similarity search, sequence alignment and
AB  - phylogenetic tools are readily accessible to allow for to individualized
AB  - directions of research focused on dnd genes. CONCLUSION: dndDB can
AB  - facilitate efficient investigation of a wide range of aspects relating to
AB  - dnd DNA modification and other island-encoded functions in host organisms.
AB  - dndDB version 1.0 is freely available at http://mml.sjtu.edu.cn/dndDB/.
ER  -

TY  - JOUR
AU  - Oude Essink, B.B.
AU  - Berkhout, B.
TI  - The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 108
EP  - 108
VL  - 22
AB  - We constructed a synthetic tRNAlys,3 gene that was cloned into pUC9. A BanI site was
AB  - introduced at the 3' end to allow run-off transcription by T7 RNA polymerase. Surprisingly,
AB  - we were unable to digest this BanI site, while three BanI sites in the pUC9 plasmid were
AB  - efficiently cleaved (Figure 1, lane 7). Similar results were obtained upon prolonged
AB  - incubation at either 37 degrees C or 50 degrees C which is the optimal temperature for BanI
AB  - (results not shown). Since BanI recognizes different sequences (G/GPyPuCC), this could be due
AB  - to site-preference. However, the BanI site in the tRNA gene was identical to one of the pUC9
AB  - sites (GGCGCC). Inspection of the downstream sequences indicated the presence of an
AB  - overlapping dcm-methylation site (GGCGCCAGG). Because the plasmid was grown in a dcm+ host
AB  - (DH5), this will result in C5-methylation of the final C of the BanI site (GGCGCm5C). Next, we
AB  - grew pUC-tRNAlys3 in a dcm-host (GM48), which resulted in complete digestion of the plasmid
AB  - (lane 3). These results indicate that the BanI enzyme is not active on GGCGCm5C sites.
ER  -

TY  - JOUR
AU  - Ouellette, M.
AU  - Gogarten, J.P.
AU  - Lajoie, J.
AU  - Makkay, A.M.
AU  - Papke, R.T.
TI  - Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.
JO  - Genes (Basel)
PY  - 2018
SP  - E129
EP  - E129
VL  - 9
AB  - DNA methyltransferases (MTases), which catalyze the methylation of adenine and cytosine bases
AB  - in DNA, can occur in bacteria and archaea alongside cognate
AB  - restriction endonucleases (REases) in restriction-modification (RM) systems or
AB  - independently as orphan MTases. Although DNA methylation and MTases have been
AB  - well-characterized in bacteria, research into archaeal MTases has been limited. A
AB  - previous study examined the genomic DNA methylation patterns (methylome) of the
AB  - halophilic archaeon Haloferax volcanii, a model archaeal system which can be
AB  - easily manipulated in laboratory settings, via single-molecule real-time (SMRT)
AB  - sequencing and deletion of a putative MTase gene (HVO_A0006). In this follow-up
AB  - study, we deleted other putative MTase genes in H. volcanii and sequenced the
AB  - methylomes of the resulting deletion mutants via SMRT sequencing to characterize
AB  - the genes responsible for DNA methylation. The results indicate that deletion of
AB  - putative RM genes HVO_0794, HVO_A0006, and HVO_A0237 in a single strain abolished
AB  - methylation of the sole cytosine motif in the genome (C(m4)TAG). Amino acid
AB  - alignments demonstrated that HVO_0794 shares homology with characterized cytosine
AB  - CTAG MTases in other organisms, indicating that this MTase is responsible for
AB  - C(m4)TAG methylation in H. volcanii. The CTAG motif has high density at only one
AB  - of the origins of replication, and there is no relative increase in CTAG motif
AB  - frequency in the genome of H. volcanii, indicating that CTAG methylation might
AB  - not have effectively taken over the role of regulating DNA replication and
AB  - mismatch repair in the organism as previously predicted. Deletion of the putative
AB  - Type I RM operon rmeRMS (HVO_2269-2271) resulted in abolished methylation of the
AB  - adenine motif in the genome (GCA(m6)BN(6)VTGC). Alignments of the MTase
AB  - (HVO_2270) and site specificity subunit (HVO_2271) demonstrate homology with
AB  - other characterized Type I MTases and site specificity subunits, indicating that
AB  - the rmeRMS operon is responsible for adenine methylation in H. volcanii. Together
AB  - with HVO_0794, these genes appear to be responsible for all detected methylation
AB  - in H. volcanii, even though other putative MTases (HVO_C0040, HVO_A0079) share
AB  - homology with characterized MTases in other organisms. We also report the
AB  - construction of a multi-RM deletion mutant (DeltaRM), with multiple RM genes
AB  - deleted and with no methylation detected via SMRT sequencing, which we anticipate
AB  - will be useful for future studies on DNA methylation in H. volcanii.
ER  -

TY  - JOUR
AU  - Ouellette, M.
AU  - Jackson, L.
AU  - Chimileski, S.
AU  - Papke, R.T.
TI  - Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006.
JO  - Front. Microbiol.
PY  - 2015
SP  - 251
EP  - 251
VL  - 6
AB  - Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and
AB  - are composed of two enzymes: a DNA methyltransferase and a
AB  - restriction endonuclease. Although RM systems are present in both archaeal and
AB  - bacterial genomes, DNA methylation in archaea has not been well defined. In order
AB  - to characterize the function of RM systems in archaeal species, we have made use
AB  - of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis
AB  - of H. volcanii strain H26 was performed using PacBio single molecule real-time
AB  - (SMRT) sequencing. This analysis was also performed on a strain of H. volcanii in
AB  - which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the
AB  - genome. Sequence analysis of H26 revealed two motifs which are modified in the
AB  - genome: C(m4)TAG and GCA(m6)BN6VTGC. Analysis of the DeltaHVO_A0006 strain
AB  - indicated that it exhibited reduced adenine methylation compared to the parental
AB  - strain and altered the detected adenine motif. However, protein domain
AB  - architecture analysis and amino acid alignments revealed that HVO_A0006 is
AB  - homologous only to the N-terminal endonuclease region of Type IIG RM proteins and
AB  - contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK
AB  - nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene
AB  - demonstrated that the gene is rare among the Halobacteria. It is surrounded by
AB  - two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM
AB  - gene, which has likely been acquired through gene transfer, and affects
AB  - restriction-modification activity by interacting with another RM system
AB  - component(s). Here, we present the first genome-wide characterization of DNA
AB  - methylation in an archaeal species and examine the function of a DNA
AB  - methyltransferase related gene HVO_A0006.
ER  -

TY  - JOUR
AU  - Ouwerkerk, J.P.
AU  - Koehorst, J.J.
AU  - Schaap, P.J.
AU  - Ritari, J.
AU  - Paulin, L.
AU  - Belzer, C.
AU  - de Vos, W.M.
TI  - Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.
JO  - Genome Announcements
PY  - 2017
SP  - e01098
EP  - e01016
VL  - 5
AB  - Akkermansia glycaniphila is a novel Akkermansia species that was isolated from the intestine
AB  - of the reticulated python and shares the capacity to degrade mucin
AB  - with the human strain Akkermansia muciniphila MucT Here, we report the complete
AB  - genome sequence of strain PytT of 3,074,121 bp. The genomic analysis reveals
AB  - genes for mucin degradation and aerobic respiration.
ER  -

TY  - JOUR
AU  - Ovechkina, L.G.
AU  - Zinoviev, V.V.
AU  - Gorbunov, Y.A.
AU  - Malygin, E.G.
TI  - The oligomerization of phage T4 DNA-(adenine-N-6)-methyltransferase and its effect on the catalytic characteristics of the enzyme.
JO  - Bioorg. Khim.
PY  - 2000
SP  - 940
EP  - 943
VL  - 26
AB  - The structural and catalytic properties of the phage T4 DNA-(adenine-N-6)-methyltransferase
AB  - (EC 2.1;1.72) were studied at
AB  - different enzyme-substrate concentration ratios by chemical
AB  - cross-linking of the protein subunits and by measuring the presteady
AB  - state kinetics of the reactions. Various structural states of the
AB  - methyltransferase were correlated with its catalytic activity, and it
AB  - was shown that the oligomeric forms of the enzyme are catalytically
AB  - active but are characterized by the reaction parameters different from
AB  - those of the monomer.
ER  -

TY  - JOUR
AU  - Overballe-Petersen, S.
AU  - Roer, L.
AU  - Ng, K.
AU  - Hansen, F.
AU  - Justesen, U.S.
AU  - Andersen, L.P.
AU  - Stegger, M.
AU  - Hammerum, A.M.
AU  - Hasman, H.
TI  - Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying blaNDM-5 on an IncF Multidrug Resistance Plasmid and blaOXA-181 on an  IncX3 Plasmid.
JO  - Genome Announcements
PY  - 2018
SP  - e01542
EP  - e01517
VL  - 6
AB  - Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli
AB  - sequence type 410 (ST410) strain with five closed plasmids. A large 111-kb
AB  - incompatibility group F (IncF) plasmid harbored blaNDM-5 and 16 other resistance
AB  - genes. A 51-kb IncX3 plasmid carried QnrS1 and blaOXA-181E. coli isolates with
AB  - both blaNDM-5 and blaOXA-181 carbapenemases are rare.
ER  -

TY  - JOUR
AU  - Overholt, W.A.
AU  - Green, S.J.
AU  - Marks, K.P.
AU  - Venkatraman, R.
AU  - Prakash, O.
AU  - Kostka, J.E.
TI  - Draft genome sequences for oil-degrading bacterial strains from beach sands impacted by the deepwater horizon oil spill.
JO  - Genome Announcements
PY  - 2013
SP  - e01015
EP  - e01013
VL  - 1
AB  - We report the draft genome sequences of 10 proteobacterial strains isolated from  beach sands
AB  - contaminated with crude oil discharged from the Deepwater Horizon
AB  - spill, which were cultivated under aerobic and anaerobic conditions with crude
AB  - oil as the sole carbon source. All strains contain multiple putative genes
AB  - belonging to hydrocarbon degradation pathways.
ER  -

TY  - JOUR
AU  - Ozdemir, O.
TI  - The construction of a mammalian transfection vector for expression of cytosine-5 specific DNA methyltransferase gene M.MspI in cultured cells.
JO  - Turkish J. Biol.
PY  - 1998
SP  - 161
EP  - 170
VL  - 22
AB  - The expression vectors are designed for expression and purification of normal or recombinant
AB  - genes of interest.  There is a wide variety of stable and transferable selectable mammalian
AB  - expression vectors.  The vector pCDM8 and its derivatives, pcDNAI/Ampicillin are widely used
AB  - for cloning and analyzing of genes in higher eukaryotic cells.  The vectors pRC/CMV, pcDNA3
AB  - and pRC/RSV are designed for high-level expression of recombinant genes in mammalian cells.
AB  - In the present study, we have been able to transfect and express the monospecific bacterial
AB  - (Moraxella sp.) cytosine-5 DNA methyltransferase M.MspI gene in cultured cells within a newly
AB  - constructed mammalian transfection vector.  We have constructed a very efficient, stable or
AB  - transferable eukaryotic expression vector analogous to the well-known expression system in COS
AB  - cells.  A bacterial cytosine-5 MTase gene with a vertebrate nuclear targeting signal SV40 VP1
AB  - and marker enzyme glutathione-S-transferase genes were transferred into the eukaryotic shuttle
AB  - vector pcDNA3 using a PCR based method.  This novel plasmid which contains a strong
AB  - cytomegalovirus and T7 promoters and the SV40 origin of replication for autonomous replication
AB  - in mammalian cells was called pOZT4.  Human kidney epithelial 293 and CHO cells were
AB  - transfected with pOZT4 which was encoding the fusion gene and it was established that the
AB  - genomic DNA of both cells were methylated at the CCCG sites by the active enzyme.
ER  -

TY  - JOUR
AU  - Ozdemir, O.
AU  - Hornby, D.
TI  - In vivo DNA methylation of Escherichia coli DH5a and top10F' strains by bacterial cytosine-5 methyltransferase M.MspI.
JO  - Turkish J. Biol.
PY  - 1998
SP  - 143
EP  - 151
VL  - 22
AB  - At the chromatin level, methylated CpG dinucleotides are R.MspI resistant compared with
AB  - nonmethylated counterparts.  The DNA of two E. coli strains was analyzed following
AB  - transformation with bacterial cytosine-5-methyltransferase gene M.MspI in the mammalian
AB  - transfection vector pcDNA3.  Expression of the M.MspI was tested by R.MspI digestion.  The
AB  - results suggest that the DNA of both strains was fully methylated at the CCGG sequences, by
AB  - the active enzyme under the control of T7 and cytomegalovirus promoters.  Methylated DNA
AB  - cannot be digested and it exhibits higher fragment sizes in 1% agarose gel in contrast to the
AB  - untransformed cell DNAs in vivo.
ER  -

TY  - JOUR
AU  - Ozer, E.A.
AU  - Allen, J.P.
AU  - Hauser, A.R.
TI  - Draft Genome Sequence of the Pseudomonas aeruginosa Bloodstream Isolate PABL056.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5999
EP  - 5999
VL  - 194
AB  - Pseudomonas aeruginosa is an important cause of disease in hospitalized and immunocompromised
AB  - patients. The genome of P. aeruginosa is among the largest of
AB  - bacteria pathogenic to humans. We present the draft genome sequence of P.
AB  - aeruginosa strain PABL056, a human bloodstream isolate with the largest genome
AB  - yet reported in P. aeruginosa.
ER  -

TY  - JOUR
AU  - Ozer, E.A.
AU  - Fitzpatrick, M.A.
AU  - Hauser, A.R.
TI  - Draft Genome Sequence of Acinetobacter baumannii Strain ABBL099, a Multidrug-Resistant Clinical Outbreak Isolate with a Novel Multilocus Sequence  Type.
JO  - Genome Announcements
PY  - 2014
SP  - e00738
EP  - e00714
VL  - 2
AB  - Acinetobacter baumannii is associated with hospital-acquired infections and can cause
AB  - persistent outbreaks. Here we report the draft genome sequence of ABBL099,
AB  - a multidrug-resistant clinical isolate of A. baumannii belonging to a novel
AB  - sequence type and representative of clonal isolates cultured from patients at one
AB  - institution over a 4-year time period.
ER  -

TY  - JOUR
AU  - Ozer, E.A.
AU  - Hauser, A.R.
AU  - Gerding, D.N.
AU  - Espinosa, R.O.
AU  - Hecht, D.W.
AU  - Kociolek, L.K.
TI  - Complete Genome Sequence of Clostridioides difficile Epidemic Strain DH/NAP11/106/ST-42, Isolated from Stool from a Pediatric Patient with Diarrhea.
JO  - Genome Announcements
PY  - 2017
SP  - e00923
EP  - e00917
VL  - 5
AB  - We report here the complete genome sequence of Clostridioides difficile strain
AB  - DH/NAP11/106/ST-42, which is now the most common strain causing C. difficile
AB  - infection among U.S. adults. This strain was isolated from the stool from a
AB  - hospitalized pediatric patient with frequent relapses of C. difficile infection.
ER  -

TY  - JOUR
AU  - Ozer, E.A.
AU  - Morris, A.R.
AU  - Krapp, F.
AU  - Henry, C.S.
AU  - Tyo, K.E.
AU  - Lathem, W.W.
AU  - Hauser, A.R.
TI  - Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp.  similipneumoniae Isolate from a Clinical Source.
JO  - Genome Announcements
PY  - 2016
SP  - e00422
EP  - e00416
VL  - 4
AB  - We report here the draft genome sequence of a multidrug-resistant clinical isolate of
AB  - Klebsiella quasipneumoniae subsp. similipneumoniae, KP_Z4175. This
AB  - strain, isolated as part of a hospital infection-control screening program, is
AB  - resistant to multiple beta-lactam antibiotics, aminoglycosides, and
AB  - trimethoprim-sulfamethoxazole.
ER  -

TY  - JOUR
AU  - Pabo, C.O.
TI  - Specificity by design - The specificity of a homing endonuclease has been altered using computational modeling of the protein-DNA interface.
JO  - Nat. Biotechnol.
PY  - 2006
SP  - 954
EP  - 955
VL  - 24
AB  - Endonucleases that cleave DNA with high specificity have been exploited in biotechnology for
AB  - gene cloning and for nuclease-induced recombination.  As methods are developed that can
AB  - retarget such proteins to recognize any endogenous DNA site of interest, they should become
AB  - powerful tools that facilitate new approaches in gene therapy and genome editing.  In this
AB  - context, a recent Nature paper by David Baker and colleagues marks an important milestone.
AB  - The work builds on Barry Stoddard's long-standing interest in the study of homing
AB  - endonucleases and on recent studies from the Baker laboratory in which a computational model
AB  - of the protein-DNA interface was tested and optimized.  Using this model, Baker and colleagues
AB  - have now designed a variant of the I-MsoI homing endonuclease that binds and cleaves DNA at a
AB  - new site.  Their experiment had a relatively modest goal -- only one base pair was changed in
AB  - each recognition half-site -- but it nonetheless represents a critical conceptual and
AB  - methodological advance for the field.
ER  -

TY  - JOUR
AU  - Pace, L.A.
AU  - Hemp, J.
AU  - Ward, L.M.
AU  - Fischer, W.W.
TI  - Draft Genome of Thermanaerothrix daxensis GNS-1, a Thermophilic Facultative Anaerobe from the Chloroflexi Class Anaerolineae.
JO  - Genome Announcements
PY  - 2015
SP  - e01354
EP  - e01315
VL  - 3
AB  - We present the draft genome of Thermanaerothrix daxensis GNS-1, a thermophilic member of the
AB  - Chloroflexi phylum. This organism was initially characterized as a
AB  - nonmotile, strictly anaerobic fermenter; however, genome analysis demonstrates
AB  - that it encodes genes for a flagellum and multiple pathways for aerobic and
AB  - anaerobic respiration.
ER  -

TY  - JOUR
AU  - Pachebat, J.A.
AU  - van Keulen, G.
AU  - Whitten, M.M.
AU  - Girdwood, S.
AU  - Del Sol, R.
AU  - Dyson, P.J.
AU  - Facey, P.D.
TI  - Draft Genome Sequence of Rhodococcus rhodnii Strain LMG5362, a Symbiont of Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae), the Principle Vector of  Trypanosoma cruzi.
JO  - Genome Announcements
PY  - 2013
SP  - e00329
EP  - e00313
VL  - 1
AB  - We report the 4,385,577-bp high-quality draft assembly of the bacterial symbiont  Rhodococcus
AB  - rhodnii strain LMG5362, isolated from the gut of Rhodnius prolixus
AB  - (Hemiptera, Reduviidae, Triatominae), the principle vector of the protozoan
AB  - Trypanosoma cruzi, the etiological agent of Chagas disease. This sequence might
AB  - provide useful information for subsequent studies of the symbiotic relationship
AB  - between Rd. prolixus and Rc. rhodnii, while also providing a starting point for
AB  - the development of biotechnological applications for the control of Rd. prolixus.
ER  -

TY  - JOUR
AU  - Pacheco, L.G.
AU  - Castro, T.L.
AU  - Carvalho, R.D.
AU  - Moraes, P.M.
AU  - Dorella, F.A.
AU  - Carvalho, N.B.
AU  - Slade, S.E.
AU  - Scrivens, J.H.
AU  - Feelisch, M.
AU  - Meyer, R.
AU  - Miyoshi, A.
AU  - Oliveira, S.C.
AU  - Dowson, C.G.
AU  - Azevedo, V.
TI  - A Role for Sigma Factor sigma(E) in Corynebacterium pseudotuberculosis Resistance to Nitric Oxide/Peroxide Stress.
JO  - Front. Microbiol.
PY  - 2012
SP  - 126
EP  - 126
VL  - 3
AB  - Pathogenic intracellular bacteria can respond to antimicrobial mechanisms of the
AB  - host cell through transient activation of stress-responsive genes by alternative
AB  - sigma (sigma) factors of the RNA polymerase. We evaluated the contribution of the
AB  - extracytoplasmic function sigma factor sigma(E) for Corynebacterium
AB  - pseudotuberculosis resistance to stress conditions resembling those found
AB  - intracellularly during infection. A sigE-null mutant strain (DeltasigE) of this
AB  - bacterium was more susceptible in vitro to acidic pH, cell surface stressors, and
AB  - biologically relevant concentrations of nitric oxide (NO). The same mutant strain
AB  - was unable to persist in C57BL/6 mice but remained infective in mice lacking
AB  - inducible nitric oxide synthase (iNOS), confirming the significance of sigma(E)
AB  - for resistance to nitric oxide/peroxide stress in vivo. High-throughput proteomic
AB  - analysis identified NO-responsive extracellular proteins of C. pseudotuberculosis
AB  - and demonstrated the participation of sigma(E) in composition of this bacterium's
AB  - exoproteome.
ER  -

TY  - JOUR
AU  - Pacheco-Montealegre, M.
AU  - Patino, R.E.
AU  - Torres, L.
AU  - Jimenez, S.
AU  - Rodriguez, J.L.
AU  - Caro-Quintero, A.
TI  - The draft genome of Brucella abortus strain Ba col-B012, isolated from a dairy farm in Narino, Colombia, bring new insights into the epidemiology of biovar 4  strains.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 89
EP  - 89
VL  - 12
ER  -

TY  - JOUR
AU  - Pachkunov, D.M.
AU  - Kramarov, B.M.
AU  - Dobritsa, A.P.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease BmeI from Bacillus Megaterium 216.
JO  - Bioorg. Khim.
PY  - 1983
SP  - 127
EP  - 129
VL  - 9
AB  - A site-specific endonuclease BmeI has been isolated from Bacillus megaterium
AB  - 216 by gel filtration on ultragel AcA-44 with a subsequent chromatography on
AB  - heparin-sepharose 6B.  On the double-stranded DNA the endonuclease recognizes
AB  - the pentanucleotide sequence 5' - GG (A) CC - 3' 3' - CC (T) GG - 5' and
AB  - hydrolyzes it in the points shown by arrows.  At gel filtration the
AB  - endonuclease is eluted in the volume corresponding to a molecular mass of
AB  - 60,000.
ER  -

TY  - JOUR
AU  - Pack, S.P.
AU  - Doi, A.
AU  - Choi, Y.S.
AU  - Kodaki, T.
AU  - Makino, K.
TI  - Biomolecular response of oxanine in DNA strands to T4 polynucleotide kinase, T4 DNA ligase, and restriction enzymes.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2010
SP  - 118
EP  - 122
VL  - 391
AB  - Oxanine (Oxa) generated from guanine (Gua) by NO- or HNO2-induced nitrosative oxidation, has
AB  - been thought to cause mutagenic problems in
AB  - cellular systems. In this study, the response of Oxa to different
AB  - enzymatic functions was explored to understand how similarly it can
AB  - participate in biomolecular reactions compared to the natural base,
AB  - Gua. The phosphorylation efficiency of the T4 polynucleotide kinase was
AB  - highest when Oxa was located on the 5'-end of single stranded DNAs
AB  - compared to when other nucleobases were in this position. The order of
AB  - phosphorylation efficiency was as follows, Oxa > Gua > adenine (Ade)
AB  - similar to thymine (Thy) > cylosine (Cyt) Base-pairing of Oxa and Cyt
AB  - (Oxa Cyt) between the ligation fragment and template was found to
AB  - influence the ligation performance of the T4 DNA ligase to a lesser
AB  - degree compared to Gua:Cyt. In addition, EcoRl and BglII showed higher
AB  - cleavage activities on DNA substrates containing Oxa:Cyt than those
AB  - containing Gua:Cyt, while BamHl, HindIII and EcoRV showed lower
AB  - cleavage activity; however, this decrease in activity was relatively
AB  - small.
ER  -

TY  - JOUR
AU  - Padegimiene, E.
AU  - Maneliene, Z.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - OliI, a unique restriction endonuclease that recognizes the discontinuous sequence 5'-CACNN/NNGTG-3'.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - e30
EP  - e30
VL  - 29
AB  - A new type II restriction endonuclease designated OliI has been partially purified from the
AB  - halophilic bacterium Oceanospirillum linum 4-5D. OliI recognizes the interrupted
AB  - hexanucleotide palindrome 5'-CACNNNNGTG-3' and cleaves it in the center generating
AB  - blunt-ended DNA fragments.
ER  -

TY  - JOUR
AU  - Padhy, R.N.
AU  - Hottat, F.G.
AU  - Coene, M.M.
AU  - Hoet, P.P.
TI  - Restriction analysis and quantitative estimation of methylated bases of filamentous and unicellular cyanobacterial DNAs.
JO  - J. Bacteriol.
PY  - 1988
SP  - 1934
EP  - 1939
VL  - 170
AB  - The DNAs of strains of three cyanobacterial genera (Anabaena, Plectonema, and Synechococcus)
AB  - were found to be partially or fully resistant to many restriction endonucleases. This could be
AB  - due to the absence of specific sequences or to modifications, rendering given sequences
AB  - resistant to cleavage. The latter explanation is substantiated by the content of
AB  - N6-methyladenine and 5-methylcytosine in these genomes, which is high in comparison with that
AB  - in other bacterial genomes. dcm- and dam-like methylases are present in the three strains
AB  - (based on the restriction patterns obtained with the appropriate isoschizomeric enzymes).
AB  - Their contribution to the overall content of methyladenine and methylcytosine in the genomes
AB  - was calculated. Partial methylation of GATC sequences was observed in Anabaena DNA. In
AB  - addition, the GATC methylation patterns might not have been random in the three cyanobacterial
AB  - DNA preparations, as revealed by the appearance of discrete fragments (possibly of plasmid
AB  - origin) withstanding cleavage by DpnI (which requires the presence of methyladenine in the
AB  - GATC sequence).
ER  -

TY  - JOUR
AU  - Padilla, J.C.
AU  - Bustos, P.
AU  - Castro-Escarpulli, G.
AU  - Sanchez-Varela, A.
AU  - Palma-Martinez, I.
AU  - Arzate-Barbosa, P.
AU  - Garcia-Perez, C.A.
AU  - Lopez-Lopez, M.J.
AU  - Gonzalez, V.
AU  - Guo, X.
TI  - Draft Genome Sequence of Aeromonas caviae Strain 429865 INP, Isolated from a Mexican Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e01240
EP  - e01215
VL  - 3
AB  - Aeromonas caviae is an emerging human pathogen. Here, we report the draft genome  sequence of
AB  - Aeromonas caviae strain 429865 INP which shows the presence of various putative
AB  - virulence-related genes.
ER  -

TY  - JOUR
AU  - Padmanabhan, R.
AU  - Dubourg, G.
AU  - Lagier, J.C.
AU  - Couderc, C.
AU  - Michelle, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome sequence and description of Corynebacterium ihumii sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1128
EP  - 1143
VL  - 9
AB  - Corynebacterium ihumii strain GD7(T) sp. nov. is proposed as the type strain of a new species,
AB  - which belongs to the family Corynebacteriaceae of the class
AB  - Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old
AB  - male patient, as a part of the culturomics study. Corynebacterium ihumii is a
AB  - Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe
AB  - the features of this organism, together with the high quality draft genome
AB  - sequence, annotation and the comparison with other member of the genus
AB  - Corynebacteria. C. ihumii genome is 2,232,265 bp long (one chromosome but no
AB  - plasmid) containing 2,125 protein-coding and 53 RNA genes, including 4 rRNA
AB  - genes. The whole-genome shotgun sequence of Corynebacterium ihumii strain GD7(T)
AB  - sp. nov has been deposited in EMBL under accession number GCA_000403725.
ER  -

TY  - JOUR
AU  - Padmanabhan, R.
AU  - Dubourg, G.
AU  - Nguyen, T.T.
AU  - Couderc, C.
AU  - Rossi-Tamisier, M.
AU  - Caputo, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1144
EP  - 1158
VL  - 9
AB  - Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp.
AB  - nov., a new species within the genus Collinsella. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of a
AB  - 53-year-old French Caucasoid woman who had been admitted to intensive care unit
AB  - for Guillain-Barre syndrome. Collinsella massiliensis is a Gram-positive,
AB  - obligate anaerobic, non motile and non sporulating bacillus. Here, we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits
AB  - a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes,
AB  - including 1 rRNA operon.
ER  -

TY  - JOUR
AU  - Padmanabhan, R.
AU  - Lagier, J.C.
AU  - Dangui, N.P.
AU  - Michelle, C.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 525
EP  - 538
VL  - 8
AB  - Megasphaera massiliensis strain NP3(T) sp. nov. is the type strain of Megasphaera massiliensis
AB  - sp. nov., a new species within the genus Megasphaera. This strain,
AB  - whose genome is described here, was isolated from the fecal flora of an
AB  - HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic
AB  - coccobacillus. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 2,661,757 bp long genome (1
AB  - chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes,
AB  - including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Padmanabhan, R.
AU  - Robert, C.
AU  - Fenollar, F.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Necropsobacter rosorum Strain P709T.
JO  - Genome Announcements
PY  - 2014
SP  - e00913
EP  - e00914
VL  - 2
AB  - Necropsobacter is a recently described genus that contains a single species, N. rosorum, and
AB  - belongs to the family Pasteurellaceae. Here, we present the draft
AB  - genome of N. rosorum strain P709(T), which is the first genome sequence from this
AB  - species.
ER  -

TY  - JOUR
AU  - Pagani, I. et al.
TI  - Complete genome sequence of Desulfobulbus propionicus type strain (1pr3).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 100
EP  - 110
VL  - 4
AB  - Desulfobulbus propionicus Widdel 1981 is the type species of the genus Desulfobulbus, which
AB  - belongs to the family Desulfobulbaceae. The species is of
AB  - interest because of its great implication in the sulfur cycle in aquatic
AB  - sediments, its large substrate spectrum and a broad versatility in using various
AB  - fermentation pathways. The species was the first example of a pure culture known
AB  - to disproportionate elemental sulfur to sulfate and sulfide. This is the first
AB  - completed genome sequence of a member of the genus Desulfobulbus and the third
AB  - published genome sequence from a member of the family Desulfobulbaceae. The
AB  - 3,851,869 bp long genome with its 3,351 protein-coding and 57 RNA genes is a part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pagani, I. et al.
TI  - Complete genome sequence of Marivirga tractuosa type strain (H-43).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 154
EP  - 162
VL  - 4
AB  - Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus
AB  - Marivirga, which belongs to the family Flammeovirgaceae. Members of
AB  - this genus are of interest because of their gliding motility. The species is of
AB  - interest because representative strains show resistance to several antibiotics,
AB  - including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is
AB  - the first complete genome sequence of a member of the family Flammeovirgaceae.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp
AB  - plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pagie, L.
AU  - Hogeweg, P.
TI  - Individual- and population-based diversity in restriction-modification systems.
JO  - Bull. Math. Biol.
PY  - 2000
SP  - 759
EP  - 774
VL  - 62
AB  - Restriction-modification (RM) systems are cognate gene complexes that code for an endonuclease
AB  - and a methylase. They are often thought to have developed in bacteria as protection against
AB  - invading genetic material, e.g., phage DNA. The high diversity of RM systems, as observed in
AB  - nature, is often ascribed to the coevolution of RM systems (which 'invent' novel types) and
AB  - phages. However, the extent to which phages are insensitive to RM systems casts doubts on the
AB  - effectiveness of RM systems as protection against infection and thereby on the reason for the
AB  - diversity of RM systems. We present an eco-evolutionary model in order to study the evolution
AB  - of the diversity of RM systems. The model predicts that in general diversity of RM systems is
AB  - high. More importantly, the diversity of the RM systems is expressed either at the individual
AB  - level or at the population level. In the first case all individuals carry RM systems of all
AB  - sequence specificities, whereas in the second case they carry only one RM system or no RM
AB  - systems at all. Nevertheless, in the second case the same number of sequence specificities are
AB  - present in the population.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Boughalmi, M.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Genome Sequence of Legionella tunisiensis Strain LegMT, a New Legionella Species  Isolated from Hypersaline Lake Water.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5978
EP  - 5978
VL  - 194
AB  - Legionella tunisiensis is a gammaproteobacterium from the class Legionellaceae, growing in
AB  - amoebae. We sequenced the genome from strain LegM(T). It is composed
AB  - of 3,508,121 bp and contains 4,747 protein-coding genes and 38 RNA genes,
AB  - including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 548
EP  - 560
VL  - 8
AB  - Anaerococcus pacaensis strain 9403502(T), is the type strain of Anaerococcus pacaensis sp.
AB  - nov., a new species within a new genus Anaerococcus. This strain,
AB  - whose genome is described here, was isolated from a blood sample. A. pacaensis
AB  - strain 9403502(T) is an obligate anaerobic Gram-positive coccus. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 2.36 Mbp long genome exhibits a G+C content of 35.05% and
AB  - contains 2,186 protein-coding and 72 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Genome Sequence of Legionella anisa, Isolated from a Respiratory Sample, Using an Amoebal Coculture Procedure.
JO  - Genome Announcements
PY  - 2014
SP  - e00031
EP  - e00014
VL  - 2
AB  - Legionella anisa is a gammaproteobacterium from the class Legionellaceae, which is responsible
AB  - for nosocomial pneumonia. We sequenced the genome from the L.
AB  - anisa strain Linanisette, which was recovered from a clinical sample using an
AB  - amoebal coculture procedure but not with standard culture methods.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1198
EP  - 1210
VL  - 9
AB  - Anaerococcus provenciensis strain 9402080(T) sp. nov. is the type strain of A. provenciensis
AB  - sp. nov., a new species within the genus Anaerococcus. This strain
AB  - was isolated from a cervical abscess sample. A. provenciensis is a Gram-positive
AB  - anaerobic cocci. Here, we describe the features of this organism, together with
AB  - the complete genome sequence and annotation. The 2.26 Mbp long genome contains
AB  - 2099 protein-coding and 57 RNA genes including 8 rRNA genes and exhibits a G+C
AB  - content of 33.48%.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 704
EP  - 717
VL  - 9
AB  - Fenollaria massiliensis strain 9401234(T), is the type strain of Fenollaria massiliensis gen.
AB  - nov., sp. nov., a new species within a new genus Fenollaria.
AB  - This strain, whose genome is described here, was isolated from an osteoarticular
AB  - sample. F. massiliensis strain 9401234(T) is an obligate anaerobic Gram-negative
AB  - bacillus. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C
AB  - content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3
AB  - rRNA genes.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Genome Sequence of Reyranella massiliensis, a Bacterium Associated with Amoebae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5698
EP  - 5698
VL  - 194
AB  - Reyranella massiliensis is an Alphaproteobacterium member of the class Rhodospirillaceae,
AB  - growing in amoebae. We sequenced the genome of type strain
AB  - 521(T). It is composed of a 5,792,218-bp chromosome and encodes 5,675
AB  - protein-coding genes and 53 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Genome Sequence of Afipia birgiae, a Rare Bacterium Associated with Amoebae.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7018
EP  - 7018
VL  - 194
AB  - Afipia birgiae is an alphaproteobacterium from the family Bradyrhizobiaceae, growing in
AB  - amoebae, and a potential human pathogen. We sequenced the genome of
AB  - type strain 34632(T). It is composed of 5,325,467 bp and contains 5,160
AB  - protein-coding genes and 53 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Pagnier, I.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - La Scola, B.
TI  - Genome Sequence of Legionella massiliensis, Isolated from a Cooling Tower Water Sample.
JO  - Genome Announcements
PY  - 2014
SP  - e01068
EP  - e01014
VL  - 2
AB  - We present the draft genome sequence of Legionella massiliensis strain LegA(T), recovered from
AB  - a cooling tower water sample, using an amoebal coculture
AB  - procedure. The strain described here is composed of 4,387,007 bp, with a G+C
AB  - content of 41.19%, and its genome has 3,767 protein-coding genes and 60 predicted
AB  - RNA genes.
ER  -

TY  - JOUR
AU  - Pai, S.-H.
AU  - Chuang, J.-Z.
AU  - Kou, M.-C.
AU  - Hsu, T.-T.
TI  - Purification of EcoRI endonuclease on heparin sepharose-4B column chromatography.
JO  - Proc. Natl. Sci. Counc. Repub. China B
PY  - 1984
SP  - 41
EP  - 45
VL  - 8
AB  - Restriction endonucleases play a very important role in genetic engineering and
AB  - DNA mapping.  Among hundreds of restriction endonucleases, the EcoRI enzyme is
AB  - the most useful and widely investigated enzyme.  After sonication and
AB  - ultracentrifugation, crude extracts of E. coli RY 13 were purified by employing
AB  - the polyethyleneimine precipitate, ammonium sulfate precipitate and heparin
AB  - Sepharose-4B affinity column chromatography.  The EcoRI enzyme were purified at
AB  - about 42 fold and the specific activity was about 100,000 U/mg of protein.  The
AB  - whole purification procedure was finished within two days.  The recovery was
AB  - about 42%.  The enzyme was sufficiently concentrated for direct specific DNA
AB  - hydrolysis.
ER  -

TY  - JOUR
AU  - Paigen, K.
AU  - Weinfeld, H.
TI  - Cooperative infection by host-modified lambda phage.
JO  - Virology
PY  - 1963
SP  - 565
EP  - 572
VL  - 19
AB  - Host-modified lambda which arises by phage growth in Escherichia coli strain C
AB  - plates with an efficiency of 10-3 to 10-4 on E. coli strain K when infection is
AB  - performed at a low multiplicity.  The occasional infection which results arises
AB  - from the presence in K populations of rare cells in which lambda.C is capable
AB  - of multiplying.  When several lambda.C phage particles infect a single K cell,
AB  - a form of cooperative infection, analogous to multiplicity reactivation,
AB  - occurs, such that at high multiplicities more than 10% of the infected cells
AB  - yield progeny.  The latent period and burst size are normal when lambda.C
AB  - infects strain K either singly or multiply.  In both cases all the progeny that
AB  - are formed in a single cycle of growth are of the unrestricted or lambda.K
AB  - type.  The occurrence of cooperative infection is explained by assuming that
AB  - the restriction present in host modification is applied independently to
AB  - genetic structures smaller than the entire phage chromosome.  Each susceptible
AB  - site has a small chance of escaping restriction, and undamaged sites in
AB  - separate phage chromosomes can complement each other to produce an infection.
AB  - The quantitative dependence of the number of successful infections upon the
AB  - multiplicity of infection suggests that approximately 10 independent phage
AB  - sites are involved, each with approximately a 15% change of surviving.
ER  -

TY  - JOUR
AU  - Paim, T.G.
AU  - Pieta, L.
AU  - Prichula, J.
AU  - Sambrano, G.E.
AU  - Soares, R.
AU  - Bello, A.D.
AU  - Frazzon, J.
AU  - d'Azevedo, P.A.
TI  - Draft Genome Sequence of Enterococcus faecalis Strain F165 Isolated from a Urinary Tract Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e01084
EP  - e01016
VL  - 4
AB  - We report here a draft genome sequence of Enterococcus faecalis strain F165 isolated from a
AB  - urine specimen in South Brazil. The genome size was 3,049,734 bp,
AB  - with a G+C content of 37.38%, and genes related to antimicrobial resistance and
AB  - adherence were found in the strain. These findings are consistent with
AB  - pathogenesis of E. faecalis species.
ER  -

TY  - JOUR
AU  - Paim, T.G.
AU  - Pieta, L.
AU  - Prichula, J.
AU  - Sambrano, G.E.
AU  - Soares, R.
AU  - Caierao, J.
AU  - Frazzon, J.
AU  - d'Azevedo, P.A.
TI  - Draft Genome Sequence of Brazilian Escherichia coli Uropathogenic Strain E2.
JO  - Genome Announcements
PY  - 2016
SP  - e01085
EP  - e01016
VL  - 4
AB  - Escherichia coli is a common pathogen recovered from cystitis infections. In this report, we
AB  - announce the draft genome sequence of strain E2 isolated from the
AB  - urine specimen from a female patient in South Brazil. The genome assembly has
AB  - 5,081,209 bp, a G+C content of 50.57%, and virulence factors associated with both
AB  - enteroaggregative and uropathogenic E. coli strains.
ER  -

TY  - JOUR
AU  - Paixao, T.A.
AU  - Coura, F.M.
AU  - Malta, M.C.
AU  - Tinoco, H.P.
AU  - Pessanha, A.T.
AU  - Pereira, F.L.
AU  - Leal, C.A.
AU  - Heinemann, M.B.
AU  - Figueiredo, H.C.
AU  - Santos, R.L.
TI  - Draft Genome Sequences of Two Salmonella enterica Serotype Infantis Strains Isolated from a Captive Western Lowland Gorilla (Gorilla gorilla gorilla) and a  Cohabitant Black and White Tegu (Tupinambis merianae) in Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01590
EP  - e01515
VL  - 4
AB  - The draft genome sequences of two Salmonella enterica serotype Infantis isolates  are reported
AB  - here. One of the strains was isolated from a western lowland gorilla
AB  - (Gorilla gorilla gorilla) with colitis. The second strain was isolated from a
AB  - reptile that inhabited the same premises. Whole-genome sequencing demonstrated
AB  - that these isolates were not clonal.
ER  -

TY  - JOUR
AU  - Pajunen, M.I.
AU  - Elizondo, M.R.
AU  - Skurnik, M.
AU  - Kieleczawa, J.
AU  - Molineux, I.J.
TI  - Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 1115
EP  - 1132
VL  - 319
AB  - We report the complete genome sequence (38,208 bp) of bacteriophage T3 and
AB  - provide a bioinformatic comparative analysis with other completely
AB  - sequenced members of the T7 group of phages. This comparison suggests that
AB  - T3 has evolved from a recombinant between a T7-like coliphage and a
AB  - yersiniophage. To assess this, recombination between T7 and the Yersinia
AB  - enterocolitica serotype O:3 phage phiYeO3-12 was accomplished in vivo;
AB  - coliphage progeny from this cross were selected that had many biological
AB  - properties of T3. This represents the first experimentally observed
AB  - recombination between lytic phages whose normal hosts are different
AB  - bacterial genera.
ER  -

TY  - JOUR
AU  - Pak, C.M.
AU  - Kim, U.Y.
AU  - Ra, S.R.
TI  - Study on recognization and cleavage characteristics of restriction enzyme Bci528I.
JO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
PY  - 2009
SP  - 50
EP  - 51
VL  - 98
AB  - We find that restriction enzyme Bci528I isolated Bacillus circulans 528 recognizes
AB  - pallindromic hexanucleotide sequence.
ER  -

TY  - JOUR
AU  - Pak, T.R.
AU  - Altman, D.R.
AU  - Attie, O.
AU  - Sebra, R.
AU  - Hamula, C.L.
AU  - Lewis, M.
AU  - Deikus, G.
AU  - Newman, L.C.
AU  - Fang, G.
AU  - Hand, J.
AU  - Patel, G.
AU  - Wallach, F.
AU  - Schadt, E.E.
AU  - Huprikar, S.
AU  - van Bakel, H.
AU  - Kasarskis, A.
AU  - Bashir, A.
TI  - Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia.
JO  - Antimicrob. Agents Chemother.
PY  - 2015
SP  - 7117
EP  - 7120
VL  - 59
AB  - Whole-genome sequences for Stenotrophomonas maltophilia serial isolates from a bacteremic
AB  - patient before and after development of levofloxacin resistance were
AB  - assembled de novo and differed by one single-nucleotide variant in smeT, a
AB  - repressor for multidrug efflux operon smeDEF. Along with sequenced isolates from
AB  - five contemporaneous cases, they displayed considerable diversity compared
AB  - against all published complete genomes. Whole-genome sequencing and complete
AB  - assembly can conclusively identify resistance mechanisms emerging in S.
AB  - maltophilia strains during clinical therapy.
ER  -

TY  - JOUR
AU  - Pal, K.K.
AU  - Dey, R.
AU  - Sherathia, D.
AU  - Dalsania, T.
AU  - Savsani, K.
AU  - Patel, I.
AU  - Thomas, M.
AU  - Ghorai, S.
AU  - Vanpariya, S.
AU  - Rupapara, R.
AU  - Acharya, N.
AU  - Rawal, P.
AU  - Joshi, P.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Saxena, A.K.
TI  - Draft Genome Sequence of Salinibacillus aidingensis Strain MSP4, an Obligate Halophilic Bacterium Isolated from a Salt Crystallizer of the Rann of Kutch,  India.
JO  - Genome Announcements
PY  - 2013
SP  - e00253
EP  - e00213
VL  - 1
AB  - We report the 7.42-Mbp draft whole genome sequence of Salinibacillus aidingensis  strain MSP4,
AB  - an obligate halophilic bacterium, isolated from a salt crystallizer
AB  - of the Rann of Kutch in India. Analysis of the genome of this organism will lead
AB  - to a better understanding of the genes and metabolic pathways involved in
AB  - imparting osmotolerance.
ER  -

TY  - JOUR
AU  - Pal, K.K.
AU  - Dey, R.
AU  - Sherathia, D.
AU  - Sukhadiya, B.
AU  - Dalsania, T.
AU  - Patel, I.
AU  - Savsani, K.
AU  - Thomas, M.
AU  - Vanpariya, S.
AU  - Mandaliya, M.
AU  - Rupapara, R.
AU  - Rawal, P.
AU  - Ghorai, S.
AU  - Bhayani, S.
AU  - Shah, A.
AU  - Saxena, A.K.
TI  - Draft Genome Sequence of an Obligate and Moderately Halophilic Bacterium, Thalassobacillus devorans Strain MSP14, the First Draft Genome of the Genus  Thalassobacillus.
JO  - Genome Announcements
PY  - 2013
SP  - e01103
EP  - e01113
VL  - 1
AB  - We report the 3.93-Mbp first draft genome sequence of a species of the genus Thalassobacillus,
AB  - Thalassobacillus devorans strain MSP14, a moderate but obligate
AB  - halophile, isolated from a salt crystallizer of the Little Rann of Kutch, India.
AB  - Exploring the genome of this organism will facilitate understanding the
AB  - mechanism(s) of its obligate halophilism.
ER  -

TY  - JOUR
AU  - Pal, K.K.
AU  - Dey, R.
AU  - Sherathia, D.
AU  - Vanpariya, S.
AU  - Patel, I.
AU  - Dalsania, T.
AU  - Savsani, K.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Thomas, M.
AU  - Ghorai, S.
AU  - Rupapara, R.
AU  - Rawal, P.
AU  - Shah, A.
AU  - Bhayani, S.
TI  - Draft Genome Sequence of a Moderately Halophilic Bacillus megaterium Strain, MSP20.1, Isolated from a Saltern of the Little Rann of Kutch, India.
JO  - Genome Announcements
PY  - 2014
SP  - e01134
EP  - e01113
VL  - 2
AB  - The 4.37-Mbp draft genome of a moderately halophilic Bacillus megaterium strain,  MSP20.1,
AB  - isolated from a saltern of the Little Rann of Kutch, India, is reported
AB  - here. To understand the mechanism(s) of moderate halophilism and to isolate the
AB  - gene(s) involved in osmotolerance and adaptation, the genome of MSP20.1 was
AB  - sequenced.
ER  -

TY  - JOUR
AU  - Pal, K.K.
AU  - Dey, R.
AU  - Thomas, M.
AU  - Sherathia, D.
AU  - Dalsania, T.
AU  - Patel, I.
AU  - Savsani, K.
AU  - Ghorai, S.
AU  - Vanpariya, S.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Rupapara, R.
AU  - Rawal, P.
TI  - Draft Genome Sequence of the Extremely Halophilic Bacillus sp. Strain SB49, Isolated from a Salt Crystallizer Pond of the Little Rann of Kutch, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00869
EP  - e00813
VL  - 1
AB  - Here we report the draft whole-genome sequence (3.72 Mbp) of Bacillus sp. strain  SB49, an
AB  - extremely halophilic bacterium isolated from a salt crystallizer pond of
AB  - the Little Rann of Kutch in India. Unraveling the genome of this organism will
AB  - facilitate understanding and isolation of the genes involved in imparting extreme
AB  - osmotolerance.
ER  -

TY  - JOUR
AU  - Pal, K.K.
AU  - Dey, R.
AU  - Thomas, M.
AU  - Sherathia, D.
AU  - Dalsania, T.
AU  - Patel, I.
AU  - Savsani, K.
AU  - Ghorai, S.
AU  - Vanpariya, S.
AU  - Sukhadiya, B.
AU  - Mandaliya, M.
AU  - Rupapara, R.
AU  - Rawal, P.
AU  - Saxena, A.K.
TI  - Draft Genome Sequence of Bacillus sp. Strain SB47, an Obligate Extreme Halophile  Isolated from a Salt Pan of the Little Rann of Kutch, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00816
EP  - e00813
VL  - 1
AB  - Here, we report the 4.46-Mbp draft genome sequence of Bacillus sp. strain SB47, an extreme
AB  - halophile isolated from a salt pan of the Little Rann of Kutch, India.
AB  - Exploring the genome of this organism will facilitate the understanding and
AB  - isolation of the gene(s) involved in its extreme osmotolerance.
ER  -

TY  - JOUR
AU  - Pal, M.
AU  - Swarnkar, M.K.
AU  - Thakur, R.
AU  - Kiran, S.
AU  - Chhibber, S.
AU  - Singh, A.K.
AU  - Gulati, A.
TI  - Complete Genome Sequence of Paenibacillus sp. Strain IHBB 10380 Using PacBio Single-Molecule Real-Time Sequencing Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e00356
EP  - e00315
VL  - 3
AB  - The complete genome sequence of 5.77 Mb is reported for Paenibacillus sp. strain  IHBB 10380,
AB  - isolated from the cold desert area of the northwestern Himalayas and
AB  - exhibiting amylase and cellulase activities. The gene-coding clusters predicted
AB  - the presence of genes for hydrolytic enzymes in the genome.
ER  -

TY  - JOUR
AU  - Pal, S.
AU  - Das Banerjee, T.
AU  - Roy, A.
AU  - Sar, P.
AU  - Kazy, S.K.
TI  - Genome Sequence of Hydrocarbon-Degrading Cronobacter sp. Strain DJ34 Isolated from Crude Oil-Containing Sludge from the Duliajan Oil Fields, Assam, India.
JO  - Genome Announcements
PY  - 2015
SP  - e01321
EP  - e01315
VL  - 3
AB  - We report here the 4,856,096-bp draft genome sequence of hydrocarbon-degrading Cronobacter sp.
AB  - strain DJ34 isolated from crude oil-containing sludge from the
AB  - Duliajan oil fields, India. DJ34 contains genes that mediate hydrocarbon
AB  - degradation, metal resistance, and biosurfactant production. This is the first
AB  - report of the genome sequence of Cronobacter sp. inhabiting an oil-contaminated
AB  - environment.
ER  -

TY  - JOUR
AU  - Palakawong, Na.A.S.
AU  - Hornung, B.
AU  - Ravikumar, V.A.
AU  - Plugge, W.
AU  - Plugge, C.M.
TI  - Draft Genome Sequence of Actinomycessucciniciruminis Strain Am4T, Isolated from Cow Rumen Fluid.
JO  - Genome Announcements
PY  - 2017
SP  - e01587
EP  - e01516
VL  - 5
AB  - Actinomyces succiniciruminis strain Am4T, isolated from cow rumen fluid, can metabolize a
AB  - range of substrates including complex carbohydrates to organic
AB  - acids. Here, we report a 3.33-Mbp draft genome of Actinomyces succiniciruminis.
ER  -

TY  - JOUR
AU  - Palakawong, Na.A.S.
AU  - Strepis, N.
AU  - Pristas, P.
AU  - Plugge, C.M.
TI  - Draft Genome Sequence of Actinomyces glycerinitolerans Strain G10T, Isolated from Sheep Rumen Fluid.
JO  - Genome Announcements
PY  - 2017
SP  - e01589
EP  - e01516
VL  - 5
AB  - Actinomyces glycerinitolerans strain G10T, which was isolated from sheep rumen fluid, can
AB  - metabolize a range of substrates, including complex carbohydrates to
AB  - organic acids (OAs). Here, we report a 3.69-Mbp draft genome of Actinomyces
AB  - glycerinitolerans.
ER  -

TY  - JOUR
AU  - Palakawong-Na-Ayudthaya, S.
AU  - Marshall, I.P.G.
AU  - Schreiber, L.
AU  - Plugge, C.M.
TI  - Draft Genome Sequence of Streptococcus caviae Strain Cavy grass 6T, Isolated from Domesticated Guinea Pig Fecal Samples.
JO  - Genome Announcements
PY  - 2017
SP  - e00080
EP  - e00017
VL  - 5
AB  - Streptococcus caviae strain Cavy grass 6T, isolated from fecal samples of pet guinea pigs, can
AB  - metabolize a range of plant mono- and disaccharides, as well as polymeric carbohydrates. Here,
AB  - we report the draft genome sequence of this strain, which comprises 2.11 Mb.
ER  -

TY  - JOUR
AU  - Palaniappan, K. et al.
TI  - Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the  genus Thermanaerovibrio.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 57
EP  - 70
VL  - 9
AB  - Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae,  a family in
AB  - the phylum Synergistetes that is already well-characterized at the
AB  - genome level. Members of this phylum were described as Gram-negative staining
AB  - anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical
AB  - outer cell envelope. They inhabit a large variety of anaerobic environments
AB  - including soil, oil wells, wastewater treatment plants and animal
AB  - gastrointestinal tracts. They are also found to be linked to sites of human
AB  - diseases such as cysts, abscesses, and areas of periodontal disease. The
AB  - moderately thermophilic and organotrophic T. velox shares most of its morphologic
AB  - and physiologic features with the closely related species, T. acidaminovorans. In
AB  - addition to Su883(T), the type strain of T. acidaminovorans, stain Z-9701(T) is
AB  - the second type strain in the genus Thermanaerovibrio to have its genome sequence
AB  - published. Here we describe the features of this organism, together with the
AB  - non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome
AB  - (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes
AB  - is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Palau, M.
AU  - Boujida, N.
AU  - Manresa, A.
AU  - Minana-Galbis, D.
TI  - Complete Genome Sequence of Marinobacter flavimaris LMG 23834(T), Which Is Potentially Useful in Bioremediation.
JO  - Genome Announcements
PY  - 2018
SP  - e00273
EP  - e00218
VL  - 6
AB  - The complete genome sequence of the halophilic strain Marinobacter flavimaris LMG 23834(T) is
AB  - presented here. The genomic information of this type strain will be
AB  - useful for taxonomic purposes and for its potential use in bioremediation
AB  - studies.
ER  -

TY  - JOUR
AU  - Palecek, E.
AU  - Boublikova, P.
AU  - Galazka, G.
AU  - Klysik, J.
TI  - Inhibition of restriction endonuclease cleavage due to site-specific chemical modification of the B-Z junction in supercoiled DNA.
JO  - Gen. Physiol. Biophys.
PY  - 1987
SP  - 327
EP  - 341
VL  - 6
AB  - Structural distortions on the boundary between right-handed B and left-handed Z
AB  - DNA segments in plasmid pRW751 (a derivative of pBR322 containing (dC-dG)13 and
AB  - (dC-dG)16 segments) were studied by means of chemical probes.  Samples of
AB  - supercoiled DNA were treated with the respective chemical probe, linearized
AB  - with EcoRI and inhibition of BamHI (whose recognition sequence GGATCC lies on
AB  - the boundary between the (dC-dG)n segments and the pBR322 nucleotide sequence)
AB  - cleavage was tested.  Treatment with osmium tetroxide in the presence of
AB  - pyridine or 2,2'-bipyridine, respectively, resulted in a strong inhibition of
AB  - the BamHI cleavage at both restriction sites, provided the (dC-dG)n segments
AB  - were in the left-handed form.  In the presence of 2,2'-bipyridine submillimolar
AB  - concentrations of OsO4 (at 26C) were sufficient to induce the inhibition of
AB  - BamHI.  Chloroacetaldehyde was used as a probe reacting selectively with atoms
AB  - involved in the Watson-Crick hydrogen bonding.  Similarly as in the case of
AB  - osmium tetroxide treatment of pRW751 with this agent resulted in the inhibition
AB  - of BamHI cleavage.  It was concluded that the B-Z junction regions in pRW751
AB  - contain few solitary bases with disturbed hydrogen bonding or non-Watson-Crick
AB  - base pairs.
ER  -

TY  - JOUR
AU  - Palenik, B.
AU  - Brahamsha, B.
AU  - Larimer, F.W.
AU  - Land, M.
AU  - Hauser, L.
AU  - Chain, P.
AU  - Lamerdin, J.
AU  - Regala, W.
AU  - Allen, E.E.
AU  - McCarren, J.
AU  - Paulsen, I.
AU  - Dufresne, A.
AU  - Partensky, F.
AU  - Webb, E.A.
AU  - Waterbury, J.
TI  - The genome of a motile marine Synechococcus.
JO  - Nature
PY  - 2003
SP  - 1037
EP  - 1037
VL  - 424
AB  - Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll
AB  - biomass and carbon fixation in the oceans. Here we have
AB  - sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain
AB  - WH8102, revealing some of the ways that these organisms have adapted to
AB  - their largely oligotrophic environment. WH8102 uses organic nitrogen and
AB  - phosphorus sources and more sodium-dependent transporters than a model
AB  - freshwater cyanobacterium. Furthermore, it seems to have adopted
AB  - strategies for conserving limited iron stores by using nickel and cobalt
AB  - in some enzymes, has reduced its regulatory machinery (consistent with the
AB  - fact that the open ocean constitutes a far more constant and buffered
AB  - environment than fresh water), and has evolved a unique type of swimming
AB  - motility. The genome of WH8102 seems to have been greatly influenced by
AB  - horizontal gene transfer, partially through phages. The genetic material
AB  - contributed by horizontal gene transfer includes genes involved in the
AB  - modification of the cell surface and in swimming motility. On the basis of
AB  - its genome, WH8102 is more of a generalist than two related marine
AB  - cyanobacteria.
ER  -

TY  - JOUR
AU  - Palenik, B.
AU  - Ren, Q.
AU  - Dupont, C.L.
AU  - Myers, G.S.
AU  - Heidelberg, J.F.
AU  - Badger, J.H.
AU  - Madupu, R.
AU  - Nelson, W.C.
AU  - Brinkac, L.M.
AU  - Dodson, R.J.
AU  - Durkin, A.S.
AU  - Daugherty, S.C.
AU  - Sullivan, S.A.
AU  - Khouri, H.
AU  - Mohamoud, Y.
AU  - Halpin, R.
AU  - Paulsen, I.T.
TI  - Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 13555
EP  - 13559
VL  - 103
AB  - Coastal aquatic environments are typically more highly productive and dynamic than open ocean
AB  - ones. Despite these differences, cyanobacteria
AB  - from the genus Synechococcus are important primary producers in both types
AB  - of ecosystems. We have found that the genome of a coastal cyanobacterium,
AB  - Synechococcus sp. strain CC9311, has significant differences from an open
AB  - ocean strain, Synechococcus sp. strain WH8102, and these are consistent
AB  - with the differences between their respective environments. CC9311 has a
AB  - greater capacity to sense and respond to changes in its (coastal)
AB  - environment. It has a much larger capacity to transport, store, use, or
AB  - export metals, especially iron and copper. In contrast, phosphate
AB  - acquisition seems less important, consistent with the higher concentration
AB  - of phosphate in coastal environments. CC9311 is predicted to have
AB  - differences in its outer membrane lipopolysaccharide, and this may be
AB  - characteristic of the speciation of some cyanobacterial groups. In
AB  - addition, the types of potentially horizontally transferred genes are
AB  - markedly different between the coastal and open ocean genomes and suggest
AB  - a more prominent role for phages in horizontal gene transfer in
AB  - oligotrophic environments.
ER  -

TY  - JOUR
AU  - Palevich, N.
AU  - Kelly, W.J.
AU  - Leahy, S.C.
AU  - Altermann, E.
AU  - Rakonjac, J.
AU  - Attwood, G.T.
TI  - The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 72
EP  - 72
VL  - 12
AB  - Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents
AB  - from a pasture-grazed New Zealand dairy cow, and was selected for
AB  - genome sequencing in order to examine its ability to degrade plant
AB  - polysaccharides. The genome of MB2003 is 3.39 Mb and consists of four replicons;
AB  - a chromosome, a secondary chromosome or chromid, a megaplasmid and a small
AB  - plasmid. The genome has an average G + C content of 39.7%, and encodes 2983
AB  - putative protein-coding genes. MB2003 is able to use a variety of monosaccharide
AB  - substrates for growth, with acetate, butyrate and formate as the principal
AB  - fermentation end-products, and the genes encoding these metabolic pathways have
AB  - been identified. MB2003 is predicted to encode an extensive repertoire of CAZymes
AB  - with 78 GHs, 7 CEs, 1 PL and 78 GTs. MB2003 is unable to grow on xylan or pectin,
AB  - and its role in the rumen appears to be as a utilizer of monosaccharides,
AB  - disaccharides and oligosaccharides made available by the degradative activities
AB  - of other bacterial species.
ER  -

TY  - JOUR
AU  - Palkova, L.
AU  - Minarik, G.
AU  - Soltys, K.
TI  - Draft Genome Sequencing of an Acinetobacter ursingii Isolate from Healthy Human Skin, Carrying Multidrug Resistance Genes.
JO  - Genome Announcements
PY  - 2018
SP  - e00394
EP  - e00318
VL  - 6
AB  - In this paper, we report the data from whole-genome shotgun sequencing of an Acinetobacter
AB  - ursingii isolate from healthy human skin of the forearm. The
AB  - bacterial genome includes 3,473 genes and carries beta-lactamase resistance genes
AB  - as well as resistance genes for several heavy metals.
ER  -

TY  - JOUR
AU  - Palma, L.
AU  - Del Valle, E.E.
AU  - Frizzo, L.
AU  - Berry, C.
AU  - Caballero, P.
TI  - Draft Genome Sequence of Photorhabdus luminescens Strain DSPV002N Isolated from Santa Fe, Argentina.
JO  - Genome Announcements
PY  - 2016
SP  - e00744
EP  - e00716
VL  - 4
AB  - Here, we report the draft genome sequence of Photorhabdus luminescens strain DSPV002N, which
AB  - consists of 177 contig sequences accounting for 5,518,143 bp,
AB  - with a G+C content of 42.3% and 4,701 predicted protein-coding genes (CDSs). From
AB  - these, 27 CDSs exhibited significant similarity with insecticidal toxin proteins
AB  - from Photorhabdus luminescens subsp. laumondii TT01.
ER  -

TY  - JOUR
AU  - Palma, L.
AU  - Munoz, D.
AU  - Murillo, J.
AU  - Caballero, P.
TI  - Draft Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Na205-3, an Isolate Toxic for Helicoverpa armigera.
JO  - Genome Announcements
PY  - 2014
SP  - e00187
EP  - e00114
VL  - 2
AB  - We report here the complete annotated 6,510,053-bp draft genome sequence of Bacillus
AB  - thuringiensis serovar tolworthi strain Na205-3, which is toxic for
AB  - Helicoverpa armigera. This strain potentially contains nine insecticidal toxin
AB  - genes homologous to cry1Aa12, cry1Ab1, cry1Ab8, cry1Ba1, cry1Af1, cry1Ia10,
AB  - vip1Bb1, vip2Ba2, and vip3Aa6.
ER  -

TY  - JOUR
AU  - Palmer, B.R.
AU  - Marinus, M.G.
TI  - The dam and dcm strains of Escherichia coli--a review.
JO  - Gene
PY  - 1994
SP  - 1
EP  - 12
VL  - 143
AB  - The construction of a variety of strains deficient in the methylation of adenine and cytosine
AB  - residues in DNA by the methyltransferases (MTases) Dam and Dcm has allowed the study of the
AB  - role of these enzymes in the biology of Escherichia coli. Dam methylation has been shown to
AB  - play a role in coordinating DNA replication initiation. DNA mismatch repair and the regulation
AB  - of expression of some genes. The regulation of expression of dam has been found to be complex
AB  - and influenced by five promoters. A role for Dcm methylation in the cell remains elusive and
AB  - dcm- cells have no obvious phenotype, dam- and dcm- strains have a range of uses in molecular
AB  - biology and bacterial genetics, including preparation of DNA for restriction by some
AB  - restriction endonucleases, for transformation into other bacterial species, nucleotide
AB  - sequencing and site-directed mutagenesis. A variety of assays are available for rapid
AB  - detection of both the Dam and Dcm phenotypes. A number of restriction systems in E. coli have
AB  - been described which recognise foreign DNA methylation, but ignore Dam and Dcm methylation.
AB  - Here, we describe the most commonly used mutant alleles of dam and dcm and the characteristics
AB  - of a variety of the strains that carry these genes. A description of several plasmids that
AB  - carry dam gene constructs is also included.
ER  -

TY  - JOUR
AU  - Palmer, K.L.
AU  - Carniol, K.
AU  - Manson, J.M.
AU  - Heiman, D.
AU  - Shea, T.
AU  - Young, S.
AU  - Zeng, Q.
AU  - Gevers, D.
AU  - Feldgarden, M.
AU  - Birren, B.
AU  - Gilmore, M.S.
TI  - High-quality draft genome sequences of 28 Enterococcus sp. isolates.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2469
EP  - 2470
VL  - 192
AB  - The enterococci are low-GC Gram-positive bacteria that have emerged as leading causes of
AB  - hospital-acquired infection. They are also commensals of
AB  - the gastrointestinal tract of healthy humans and most other animals with
AB  - gastrointestinal flora and are important for food fermentations. Here we
AB  - report the availability of draft genome sequences for 28 enterococcal
AB  - strains of diverse origin, including the species Enterococcus faecalis, E.
AB  - faecium, E. casseliflavus, and E. gallinarum.
ER  -

TY  - JOUR
AU  - Palmer, M.
AU  - de Maayer, P.
AU  - Poulsen, M.
AU  - Steenkamp, E.T.
AU  - van Zyl, E.
AU  - Coutinho, T.A.
AU  - Venter, S.N.
TI  - Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 23
EP  - 23
VL  - 11
AB  - The genus Pantoea incorporates many economically and clinically important species. The
AB  - plant-associated species, Pantoea agglomerans and Pantoea vagans,
AB  - are closely related and are often isolated from similar environments. Plasmids
AB  - conferring certain metabolic capabilities are also shared amongst these two
AB  - species. The genomes of two isolates obtained from fungus-growing termites in
AB  - South Africa were sequenced, assembled and annotated. A high number of
AB  - orthologous genes are conserved within and between these species. The difference
AB  - in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7
AB  - (4,598,703 bp) can largely be attributed to the differences in plasmid content.
AB  - The genome sequences of these isolates may shed light on the common traits that
AB  - enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated
AB  - niches.
ER  -

TY  - JOUR
AU  - Palmer, M.E.
AU  - Lipsitch, M.
AU  - Moxon, E.R.
AU  - Bayliss, C.D.
TI  - Broad Conditions Favor the Evolution of Phase-Variable Loci.
JO  - MBio
PY  - 2013
SP  - e00430
EP  - e00412
VL  - 4
AB  - Simple sequence repeat (SSR) tracts produce stochastic on-off switching, or phase variation,
AB  - in the expression of a panoply of
AB  - surface molecules in many bacterial commensals and pathogens. A change
AB  - to the number of repeats in a tract may alter the phase of the
AB  - translational reading frame, which toggles the on-off state of the
AB  - switch. Here, we construct an in silico SSR locus with mutational
AB  - dynamics calibrated to those of the Haemophilus influenzae mod locus.
AB  - We simulate its evolution in a regimen of two alternating environments,
AB  - simultaneously varying the selection coefficient, s, and the epoch
AB  - length, T. Some recent work in a simpler (two-locus) model suggested
AB  - that stochastic switching in a regimen of two alternating environments
AB  - may be evolutionarily favored only if the selection coefficients in the
AB  - two environments are nearly equal ('symmetric') or selection is very
AB  - strong. This finding was puzzling, as it greatly restricted the
AB  - conditions under which stochastic switching might evolve. Instead, we
AB  - find agreement with other recent theoretical work, observing selective
AB  - utility for stochastic switching if the product sT is large enough for
AB  - the favored state to nearly fix in both environments. Symmetry is
AB  - required neither in s nor in sT. Because we simulate finite populations
AB  - and use a detailed model of the SSR locus, we are also able to examine
AB  - the impact of population size and of several SSR locus parameters. Our
AB  - results indicate that conditions favoring evolution and maintenance of
AB  - SSR loci in bacteria are quite broad.
AB  - IMPORTANCE Bacteria experience frequent changes of environment
AB  - during the infection cycle. One means to rapidly adapt is stochastic
AB  - switching: a bacterial lineage will stochastically produce a variety of
AB  - genotypes, so that some descendants will survive if the environment
AB  - changes. Stochastic switching mediated by simple sequence repeat (SSR)
AB  - loci is widespread among bacterial commensals and pathogens and
AB  - influences critical interactions with host surfaces or immune
AB  - effectors, thereby affecting host persistence, transmission, and
AB  - virulence. Here, we use the most detailed in silico model of an SSR
AB  - locus to date, with its phase variation calibrated to match the mod
AB  - locus of Haemophilus influenzae. The type III restriction-modification
AB  - system encoded by mod participates in the regulation of multiple other
AB  - genes; thus, SSR-mediated phase variation of mod has far-reaching
AB  - cis-regulatory effects. This coupling of phase-variable switching to
AB  - complex phenotypic effects has been described as the 'phasevarion' and
AB  - is central to understanding the infection cycle of bacterial commensals
AB  - and pathogens.
ER  -

TY  - JOUR
AU  - Palomino, M.M.
AU  - Allievi, M.C.
AU  - Fina, M.J.
AU  - Waehner, P.M.
AU  - Prado, A.M.
AU  - Sanchez, R.C.
AU  - Ruzal, S.M.
TI  - Draft Genome Sequence of the Probiotic Strain Lactobacillus acidophilus ATCC 4356.
JO  - Genome Announcements
PY  - 2015
SP  - e01421
EP  - e01414
VL  - 3
AB  - We present the 1,956,699-bp draft genome sequence of Lactobacillus acidophilus strain ATCC
AB  - 4356. Comparative genomic analysis revealed 99.96% similarity with L.
AB  - acidophilus NCFM NC_006814.3 and 99.97% with La-14 NC_021181.2 genomes.
ER  -

TY  - JOUR
AU  - Palomino, M.M.
AU  - Burguener, G.F.
AU  - Campos, J.
AU  - Allievi, M.
AU  - Fina-Martin, J.
AU  - Prado, A.M.
AU  - Fernandez, Do.P.D.A.
AU  - Ruzal, S.M.
TI  - Draft Genome Sequence of Lactobacillus helveticus ATCC 12046.
JO  - Genome Announcements
PY  - 2018
SP  - e01595
EP  - e01517
VL  - 6
AB  - Lactobacillus helveticus is a lactic acid bacterium used traditionally in the dairy industry,
AB  - especially in the manufacture of cheeses. We present here the
AB  - 2,141,841-bp draft genome sequence of L. helveticus strain ATCC 12046, a
AB  - potential starter strain for improving cheese production.
ER  -

TY  - JOUR
AU  - Paludo, C.R.
AU  - Ruzzini, A.C.
AU  - Silva-Junior, E.A.
AU  - Pishchany, G.
AU  - Currie, C.R.
AU  - Nascimento, F.S.
AU  - Kolter, R.G.
AU  - Clardy, J.
AU  - Pupo, M.T.
TI  - Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis.
JO  - Genome Announcements
PY  - 2016
SP  - e00174
EP  - e00116
VL  - 4
AB  - We announce the complete genome sequence ofBacillussp. strain SDLI1, isolated from larval gut
AB  - of the stingless beeScaptotrigona depilis The 4.13-Mb circular
AB  - chromosome harbors biosynthetic gene clusters for the production of antimicrobial
AB  - compounds.
ER  -

TY  - JOUR
AU  - Pan, L.
AU  - Zhou, H.
AU  - Li, J.
AU  - Huang, B.
AU  - Guo, J.
AU  - Zhang, X.L.
AU  - Gao, L.C.
AU  - Xu, C.
AU  - Liu, C.T.
TI  - Draft genome sequence of Sphingomonas paucimobilis strain LCT-SP1 isolated from the Shenzhou X spacecraft of China.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 18
EP  - 18
VL  - 11
AB  - Sphingomonas paucimobilis strain LCT-SP1 is a glucose-nonfermenting Gram-negative,
AB  - chemoheterotrophic, strictly aerobic bacterium. The major feature
AB  - of strain LCT-SP1, isolated from the Chinese spacecraft Shenzhou X, together with
AB  - the genome draft and annotation are described in this paper. The total size of
AB  - strain LCT-SP1 is 4,302,226 bp with 3,864 protein-coding and 50 RNA genes. The
AB  - information gained from its sequence is potentially relevant to the elucidation
AB  - of microbially mediated corrosion of various materials.
ER  -

TY  - JOUR
AU  - Pan, X.
AU  - Lin, L.
AU  - Xu, Y.
AU  - Yuan, X.
AU  - Yao, J.
AU  - Yin, W.
AU  - Hao, G.
AU  - Shen, J.
TI  - Draft Genome Sequence of Aeromonas hydrophila Strain BSK-10 (Serotype O97), Isolated from Carassius carassius with Motile Aeromonad Septicemia in China.
JO  - Genome Announcements
PY  - 2017
SP  - e00497
EP  - e00417
VL  - 5
AB  - We report here a draft genome sequence of Aeromonas hydrophila strain BSK-10, belonging to
AB  - serotype O97, isolated from crucian carp (Carassius carassius) with
AB  - motile aeromonad septicemia in Zhejiang, China. The assembly resulted in 34
AB  - scaffolds totaling approximately 4.97 Mb, with an average G+C content of 60.97%
AB  - and 4,594 predicted coding genes.
ER  -

TY  - JOUR
AU  - Pan, X.S.
AU  - Chen, Z.F.
TI  - A new Type II restriction endonuclease, BsaOI, from Bacillus stearothermophilus.
JO  - Chinese Sci. Bull.
PY  - 1991
SP  - 1231
EP  - 1232
VL  - 36
AB  - A new Type II restriction endonuclease, BsaOI, has been isolated from the thermophile Bacillus
AB  - stearothermophilus O-122. This enzyme cleaves pBR322 DNA at 7 sites, pUC19 DNA at 5 sites and
AB  - PhiX174 DNA at one site.
ER  -

TY  - JOUR
AU  - Pan, Y.
AU  - Kong, K.F.
AU  - Tsang, J.S.
TI  - Complete genome sequence and characterization of the haloacid-degrading Burkholderia caribensis MBA4.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 114
EP  - 114
VL  - 10
AB  - Burkholderia caribensis MBA4 was isolated from soil for its capability to grow on haloacids.
AB  - This bacterium has a genome size of 9,482,704 bp. Here we report the
AB  - genome sequences and annotation, together with characteristics of the genome. The
AB  - complete genome sequence consists of three replicons, comprising 9056
AB  - protein-coding genes and 80 RNA genes. Genes responsible for dehalogenation and
AB  - uptake of haloacids were arranged as an operon. While dehalogenation of
AB  - haloacetate would produce glycolate, three glycolate operons were identified. Two
AB  - of these operons contain an upstream glcC regulator gene. It is likely that the
AB  - expression of one of these operons is responsive to haloacetate. Genes
AB  - responsible for the metabolism of dehalogenation product of halopropionate were
AB  - also identified.
ER  -

TY  - JOUR
AU  - Pan, Y.
AU  - Kong, K.F.
AU  - Tsang, J.S.
TI  - Complete Genome Sequence of the Exopolysaccharide-Producing Burkholderia caribensis Type Strain MWAP64.
JO  - Genome Announcements
PY  - 2016
SP  - e01636
EP  - e01615
VL  - 4
AB  - We report the complete genome sequence of Burkholderia caribensis MWAP64 (LMG 18531), which
AB  - was isolated from soil for its proficiency in producing large
AB  - amounts of exopolysaccharide that help form microaggregates in a vertisol. There
AB  - are four replicons with a total size of 9,032,119 bp.
ER  -

TY  - JOUR
AU  - Pan, Y.
AU  - Wang, Y.
AU  - Yan, X.
AU  - Mazumder, A.
AU  - Liang, Y.
TI  - Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation.
JO  - Genome Announcements
PY  - 2016
SP  - e00724
EP  - e00716
VL  - 4
AB  - We present here the draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a
AB  - bacterium possessing potential quorum-sensing regulatory activity. This
AB  - strain was isolated from water from the South China Sea, People's Republic of
AB  - China. The assembly consists of 4,252,538 bp and contains 144 contigs, with a G+C
AB  - content of 41.85%.
ER  -

TY  - JOUR
AU  - Pan, Y.
AU  - Yang, X.
AU  - Duan, J.
AU  - Lu, N.
AU  - Leung, A.S.
AU  - Tran, V.
AU  - Hu, Y.
AU  - Wu, N.
AU  - Liu, D.
AU  - Wang, Z.
AU  - Yu, X.
AU  - Chen, C.
AU  - Zhang, Y.
AU  - Wan, K.
AU  - Liu, J.
AU  - Zhu, B.
TI  - Whole-genome sequences of four Mycobacterium bovis BCG vaccine strains.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3152
EP  - 3153
VL  - 193
AB  - Bacille Calmette-Guerin (BCG) is the only vaccine available against tuberculosis (TB).
AB  - Currently there are a number of BCG strains that are in
AB  - use, which exhibit biochemical and genetic differences. We report the
AB  - genome sequences of four BCG strains representing different lineages,
AB  - which will help to design more effective TB vaccines.
ER  -

TY  - JOUR
AU  - Pan, Y.
AU  - Yang, X.
AU  - Li, J.
AU  - Zhang, R.
AU  - Hu, Y.
AU  - Zhou, Y.
AU  - Wang, J.
AU  - Zhu, B.
TI  - The genome sequence of spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3150
EP  - 3151
VL  - 193
AB  - Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known
AB  - biodegradable insecticide used for agricultural
AB  - pests control and has an excellent environmental and mammalian
AB  - toxicological profile. Here, we present the first draft genome sequence of
AB  - the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22
AB  - scaffolds.
ER  -

TY  - JOUR
AU  - Pan, Y.J.
AU  - Lin, T.L.
AU  - Lin, Y.T.
AU  - Su, P.A.
AU  - Chen, C.T.
AU  - Hsieh, P.F.
AU  - Hsu, C.R.
AU  - Chen, C.C.
AU  - Hsieh, Y.C.
AU  - Wang, J.T.
TI  - Identification of capsular types in carbapenem-resistant Klebsiella pneumoniae strains by wzc sequencing and implications in capsule depolymerase treatment.
JO  - Antimicrob. Agents Chemother.
PY  - 2015
SP  - 1038
EP  - 1047
VL  - 59
AB  - Klebsiella pneumoniae is an important human pathogen associated with a variety of
AB  - diseases and the prevalence of multiple drug resistant K. pneumoniae (MDRKP) was
AB  - rapidly increasing. Here we determined the capsular types of 85
AB  - carbapenem-resistant K. pneumoniae (CRKP) by wzc sequencing and investigated the
AB  - presence of carbapenemases and integrons among CRKP. Ten strains (12%) of the
AB  - CRKP was positive for carbapenemase (IMP: 6/85, KPC: 3/85, and VIM: 1/85).
AB  - Capsular type K64 accounted for 32 (38%) of CRKP, followed by K62 (13%), K24
AB  - (8%), KN2 (7%) and K28 (6%). Sequence types (STs) were determined by multilocus
AB  - sequence typing (MLST) and the results indicated that ST11 which accounted for
AB  - 47% (40/85) of these CRKP was the major ST. We further isolated a K64 specific
AB  - capsule depolymerase (K64dep) which can enhance serum and neutrophil killing in
AB  - vitro and increase survival rate in K64 K. pneumoniae inoculated mice. The
AB  - toxicity study demonstrated that mice treated with K64dep showed normal
AB  - biochemical parameters and no significant histopathological changes of liver,
AB  - kidney and spleen, indicating enzyme treatment did not cause toxicity in mice.
AB  - Therefore, the findings of capsular type clustering among CRKP and an effective
AB  - treatment of capsule depolymerase for MDRKP infections are important for
AB  - capsule-based vaccine development and therapy.
ER  -

TY  - JOUR
AU  - Panayotatos, N.
TI  - Practical consequences of restriction site symmetry.
JO  - Gene
PY  - 1984
SP  - 291
EP  - 294
VL  - 31
AB  - Because of the palindromic character of most 6-bp restriction sites, filling-in
AB  - and ligation of the protruding ends create symmetric sequences which include
AB  - new 6-bp restriction sites.  The old site is, in most cases, lost.  After
AB  - cleavage at the new palindromic site and removal of the protruding ends, a new
AB  - center of symmetry is created which is often part of yet another 6-bp
AB  - restriction site.  A compilation of potential and available sites as presented
AB  - should prove useful in genetic engineering.
ER  -

TY  - JOUR
AU  - Panda, A.
AU  - Nagaraj, S.
AU  - Zhao, X.
AU  - Tettelin, H.
AU  - DeTolla, L.J.
TI  - Complete Genome Sequences of Mycobacterium kansasii Strains Isolated from Rhesus  Macaques.
JO  - Genome Announcements
PY  - 2017
SP  - e00187
EP  - e00117
VL  - 5
AB  - Mycobacterium kansasii is a nontuberculous mycobacterium. It causes opportunistic infections
AB  - with pulmonary and extrapulmonary manifestations. We report here the
AB  - complete genome sequences of two M. kansasii strains isolated from rhesus
AB  - macaques. We performed genome comparisons with human and environmental isolates
AB  - of M. kansasii to assess the genomic diversity of this species.
ER  -

TY  - JOUR
AU  - Panda, A.N.
AU  - Mishra, S.R.
AU  - Ray, L.
AU  - Sahu, N.
AU  - Acharya, A.
AU  - Jadhao, S.
AU  - Suar, M.
AU  - Adhya, T.K.
AU  - Rastogi, G.
AU  - Pattnaik, A.K.
AU  - Raina, V.
TI  - Draft Genome Sequence of Halobacillus sp. Strain KGW1, a Moderately Halophilic and Alkaline Protease-Producing Bacterium Isolated from the Rhizospheric Region of Phragmites karka from Chilika Lake, Odisha, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00361
EP  - e00316
VL  - 4
AB  - Halobacillus sp. strain KGW1 is a moderately halophilic, rod shaped, Gram-positive, yellow
AB  - pigmented, alkaline protease-producing bacterium isolated from a water sample from Chilika
AB  - Lake, Odisha, India. Sequencing of bacterial DNA assembled a 3.68-Mb draft genome. The genome
AB  - annotation analysis showed various gene clusters for tolerance to stress, such as elevated pH,
AB  - salt concentration, and toxic metals.
ER  -

TY  - JOUR
AU  - Panda, P.
AU  - Fiers, M.W.
AU  - Lu, A.
AU  - Armstrong, K.F.
AU  - Pitman, A.R.
TI  - Draft Genome Sequences of Three Pectobacterium Strains Causing Blackleg of Potato: P. carotovorum subsp. brasiliensis ICMP 19477, P. atrosepticum ICMP 1526,  and P. carotovorum subsp. carotovorum UGC32.
JO  - Genome Announcements
PY  - 2015
SP  - e00874
EP  - e00815
VL  - 3
AB  - Blackleg is a disease caused by several species of Pectobacterium that results in losses to
AB  - potato crops worldwide. Here, we report the draft genomes of three
AB  - taxonomically and geographically distinct blackleg-causing strains of
AB  - Pectobacterium: P. carotovorum subsp. brasiliensis ICMP 19477, P. atrosepticum
AB  - ICMP 1526, and P. carotovorum subsp. carotovorum UGC32. Comparison of these
AB  - genomes will support the identification of common traits associated with their
AB  - capacity to cause blackleg.
ER  -

TY  - JOUR
AU  - Panda, P.
AU  - Lu, A.
AU  - Armstrong, K.F.
AU  - Pitman, A.R.
TI  - Draft Genome Sequence for ICMP 5702, the Type Strain of Pectobacterium carotovorum subsp. carotovorum That Causes Soft Rot Disease on Potato.
JO  - Genome Announcements
PY  - 2015
SP  - e00875
EP  - e00815
VL  - 3
AB  - Pectobacterium species are economically important bacteria that cause soft rotting of potato
AB  - tubers in the field and in storage. Here, we report the draft
AB  - genome sequence of the type strain for P. carotovorum subsp. carotovorum, ICMP
AB  - 5702 (ATCC 15713). The genome sequence of ICMP 5702 will provide an important
AB  - reference for future phylogenomic and taxonomic studies of the phytopathogenic
AB  - Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Panda, S.
AU  - Singh, D.V.
TI  - Whole-Genome Sequences of Staphylococcus haemolyticus Isolated from Infected Eyes and Healthy Conjunctiva in Bhubaneswar, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00099
EP  - e00016
VL  - 4
AB  - Staphylococcus haemolyticus, an opportunistic pathogen, is known to exhibit multidrug
AB  - resistance and produce biofilm. We sequenced the genome of four
AB  - multidrug resistant, biofilm forming isolates from infected eyes and asymptomatic
AB  - healthy conjunctiva.
ER  -

TY  - JOUR
AU  - Pandey, A.K.
AU  - Cleary, D.W.
AU  - Laver, J.R.
AU  - Maiden, M.C.J.
AU  - Didelot, X.
AU  - Gorringe, A.
AU  - Read, R.C.
TI  - Neisseria lactamica Y92-1009 complete genome sequence.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 41
EP  - 41
VL  - 12
AB  - We present the high quality, complete genome assembly of Neisseria lactamica Y92-1009 used to
AB  - manufacture an outer membrane vesicle (OMV)-based vaccine, and a
AB  - member of the Neisseria genus. The strain is available on request from the Public
AB  - Health England Meningococcal Reference Unit. This Gram negative, dipplococcoid
AB  - bacterium is an organism of worldwide clinical interest because human
AB  - nasopharyngeal carriage is related inversely to the incidence of meningococcal
AB  - disease, caused by Neisseria meningitidis. The organism sequenced was isolated
AB  - during a school carriage survey in Northern Ireland in 1992 and has been the
AB  - subject of a variety of laboratory and clinical studies. Four SMRT cells on a
AB  - RSII machine by Pacific Biosystems were used to produce a complete, closed genome
AB  - assembly. Sequence data were obtained for a total of 30,180,391 bases from 2621
AB  - reads and assembled using the HGAP algorithm. The assembly was corrected using
AB  - short reads obtained from an Illumina HiSeq 2000instrument. This resulted in a
AB  - 2,146,723 bp assembly with approximately 460 fold mean coverage depth and a GC
AB  - ratio of 52.3%.
ER  -

TY  - JOUR
AU  - Pandin, C.
AU  - Le Coq, D.
AU  - Deschamps, J.
AU  - Vedie, R.
AU  - Rousseau, T.
AU  - Aymerich, S.
AU  - Briandet, R.
TI  - Complete genome sequence of Bacillus velezensis QST713: A biocontrol agent that protects Agaricus bisporus crops against the green mould disease.
JO  - J. Biotechnol.
PY  - 2018
SP  - 10
EP  - 19
VL  - 278
AB  - Bacillus subtilis QST713 is extensively used as a biological control agent in agricultural
AB  - fields including in the button mushroom culture, Agaricus bisporus.
AB  - This last use exploits its inhibitory activity against microbial pathogens such
AB  - as Trichoderma aggressivum f. europaeum, the main button mushroom green mould
AB  - competitor. Here, we report the complete genome sequence of this bacterium with a
AB  - genome size of 4 233 757bp, 4263 predicted genes and an average GC content of
AB  - 45.9%. Based on phylogenomic analyses, strain QST713 is finally designated as
AB  - Bacillus velezensis. Genomic analyses revealed two clusters encoding potential
AB  - new antimicrobials with NRPS and TransATPKS synthetase. B. velezensis QST713
AB  - genome also harbours several genes previously described as being involved in
AB  - surface colonization and biofilm formation. This strain shows a strong ability to
AB  - form in vitro spatially organized biofilm and to antagonize T. aggressivum. The
AB  - availability of this genome sequence could bring new elements to understand the
AB  - interactions with micro or/and macroorganisms in crops.
ER  -

TY  - JOUR
AU  - Pandiyan, A.
AU  - Ray, M.K.
TI  - Draft Genome Sequence of the Antarctic Psychrophilic Bacterium Pseudomonas syringae Strain Lz4W.
JO  - Genome Announcements
PY  - 2013
SP  - e00377
EP  - e00313
VL  - 1
AB  - The psychrophilic bacterium Pseudomonas syringae strain Lz4W was isolated from soil samples
AB  - from Antarctica to decipher the mechanisms of low-temperature
AB  - adaptation. We report here the 4.982-Mb draft genome sequence of P. syringae
AB  - Lz4W. This sequence will provide insights into the genomic basis of the
AB  - psychrophilicity of this bacterium.
ER  -

TY  - JOUR
AU  - Panescu, J.
AU  - Daly, R.A.
AU  - Wrighton, K.C.
AU  - Mouser, P.J.
TI  - Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales.
JO  - Genome Announcements
PY  - 2018
SP  - e00159
EP  - e00118
VL  - 6
AB  - Genome sequences were obtained for two isolates of the genus Arcobacter from saline fluids
AB  - produced from hydraulically fractured shale gas wells in the
AB  - Marcellus and Utica formations. These genomes provide insight into microbial
AB  - sulfur cycles occurring in a high-salt deep terrestrial shale environment.
ER  -

TY  - JOUR
AU  - Panesso, D. et al.
TI  - Methicillin-Susceptible, Vancomycin-Resistant Staphylococcus aureus, Brazil.
JO  - Emerg. Infect. Dis.
PY  - 2015
SP  - 1844
EP  - 1848
VL  - 21
AB  - We report characterization of a methicillin-susceptible,
AB  - vancomycin-resistant bloodstream isolate of Staphylococcus aureus recovered from a patient in
AB  - Brazil. Emergence of vancomycin resistance in methicillin-susceptible S. aureus would indicate
AB  - that this resistance trait might be poised to disseminate more rapidly among S. aureus and
AB  - represents a major public health threat.
ER  -

TY  - JOUR
AU  - Pang, J.
AU  - Dong, M.
AU  - Li, N.
AU  - Zhao, Y.
AU  - Liu, B.
TI  - Functional characterization of a rice de novo DNA methyltransferase, OsDRM2, expressed in Escherichia coli and yeast.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2013
SP  - 157
EP  - 162
VL  - 432
AB  - DNA methylation of cytosine nucleotides is an important epigenetic modification that occurs in
AB  - most eukaryotic organisms and is established and maintained by various DNA methyltransferases
AB  - together with their co-factors. There are two major categories of DNA methyltransferases: de
AB  - novo and maintenance. Here, we report the isolation and functional characterization of a de
AB  - novo methyltransferase, named OsDRM2, from rice (Oryza sativa L.). The full-length coding
AB  - region of OsDRM2 was cloned and transformed into Escherichia coil and Saccharomyces
AB  - cerevisiae. Both of these organisms expressed the OsDRM2 protein, which exhibited stochastic
AB  - de novo methylation activity in vitro at CG, CHG, and CHH di- and tri-nucleotide patterns. Two
AB  - lines of evidence demonstrated the de novo activity of OsDRM2: (1) a 5'-CCGG-3' containing
AB  - DNA fragment that had been pre-treated with OsDRM2 protein expressed in E. coli was protected
AB  - from digestion by the CG-methylation-sensitive isoschizomer HpaII; (2) methylation-sensitive
AB  - amplified polymorphism (MSAP) analysis of S. cerevisiae genomic DNA from transformants that
AB  - had been introduced with OsDRM2 revealed CG and CHG methylation levels of 3.92-9.12%, and
AB  - 2.88-6.93%, respectively, whereas the mock control S. cerevisiae DNA did not exhibit cytosine
AB  - methylation. These results were further supported by bisulfite sequencing of the 18S rRNA and
AB  - EAF5 genes of the transformed S. cerevisiae, which exhibited different DNA methylation
AB  - patterns, which were observed in the genomic DNA. Our findings establish that OsDRM2 is an
AB  - active de novo DNA methyltransferase gene with conserved activity in both prokaryotic and
AB  - eukaryotic non-host species. (C) 2013 Elsevier Inc. All rights reserved.
ER  -

TY  - JOUR
AU  - Pang, M.
AU  - Jiang, J.
AU  - Xie, X.
AU  - Wu, Y.
AU  - Dong, Y.
AU  - Kwok, A.H.
AU  - Zhang, W.
AU  - Yao, H.
AU  - Lu, C.
AU  - Leung, F.C.
AU  - Liu, Y.
TI  - Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics.
JO  - Sci. Rep.
PY  - 2015
SP  - 9833
EP  - 9833
VL  - 5
AB  - Outbreaks in fish of motile Aeromonad septicemia (MAS) caused by Aeromonas
AB  - hydrophila have caused a great concern worldwide. Here, for the first time, we
AB  - provide two complete genomes of epidemic A. hydrophila strains isolated in China.
AB  - To gain an insight into the pathogenicity of epidemic A. hydrophila, we performed
AB  - comparative genomic analyses of five epidemic strains belonging to sequence type
AB  - (ST) 251, together with the environmental strain ATCC 7966(T). We found that the
AB  - known virulence factors, including a type III secretion system, a type VI
AB  - secretion system and lateral flagella, are not required for the high virulence of
AB  - the ST251 clonal group. Additionally, our work identifies three utilization
AB  - pathways for myo-inositol, sialic acid and L-fucose providing clues regarding the
AB  - factors that underlie the epidemic and virulent nature of ST251 A. hydrophila.
AB  - Based on the geographical distribution and biological resources of the ST251
AB  - clonal group, we conclude that ST251 is a high-risk clonal group of A. hydrophila
AB  - which may be responsible for the MAS outbreaks in China and the southeastern
AB  - United States.
ER  -

TY  - JOUR
AU  - Pang, S.
AU  - Renvoise, A.
AU  - Perret, C.
AU  - Guinier, M.
AU  - Chelghoum, N.
AU  - Brossier, F.
AU  - Capton, E.
AU  - Jarlier, V.
AU  - Sougakoff, W.
TI  - Whole-Genome Sequence of Mycobacterium abscessus Clinical Strain V06705.
JO  - Genome Announcements
PY  - 2013
SP  - e00690
EP  - e00613
VL  - 1
AB  - Infection caused by Mycobacterium abscessus strains is a growing cause of concern in both
AB  - community-acquired and health care-associated diseases, as these
AB  - organisms naturally display multiple drug resistances. We report an annotated
AB  - draft genome sequence of M. abscessus strain V06705 obtained from a patient in
AB  - France.
ER  -

TY  - JOUR
AU  - Panina, E.M.
AU  - Mironov, A.A.
AU  - Gelfand, M.S.
TI  - Statistical analysis of complete bacterial genomes: Avoidance of palindromes and restriction-modification systems.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 246
EP  - 252
VL  - 34
AB  - Absence of 4, 5, and 6-letter palindromes is observed in genome sequences of a broad spectrum
AB  - of bacteria. Recognition sites of
AB  - restrictases of a particular species (or of a species closely related
AB  - to it) comprise a significant portion of such palindromes. A
AB  - significant role is played by the horizontal transfer of genes that
AB  - encode the restriction-modification systems (R-M systems). In organisms
AB  - that are practically isolated from the effects of such systems (for
AB  - example, in Mycoplasma), such phenomenon is not observed. Common trends
AB  - to preference and "avoidance" of nucleotides were studied in
AB  - representatives of 33 bacterial families on the basis available
AB  - bacterial genomes. The results of the study present additional data on
AB  - intra- and interrelationships in established taxonomic groups.
ER  -

TY  - JOUR
AU  - Panis, G.
AU  - Lambert, C.
AU  - Viollier, P.H.
TI  - Complete genome sequence of Caulobacter crescentus bacteriophage phiCbK.
JO  - J. Virol.
PY  - 2012
SP  - 10234
EP  - 10235
VL  - 86
AB  - phiCbK is a B3 morphotype bacteriophage of the Siphoviridae family that infects Caulobacter
AB  - crescentus, the preeminent model system for bacterial cell cycle studies. The last 4 decades
AB  - of research with phiCbK as a genetic and cytological tool to study the biology of the host
AB  - warrant an investigation of the phage genome composition. Herein, we report the complete
AB  - genome sequence of phiCbK and highlight unusual features that emerged from its annotation. The
AB  - complete genome analysis of the phiCbK phage provides new insight into its characteristics and
AB  - potential interactions with its Caulobacter crescentus host, setting the stage for future
AB  - functional studies with phiCbK.
ER  -

TY  - JOUR
AU  - Panne, D.
AU  - Muller, S.A.
AU  - Wirtz, S.
AU  - Engel, A.
AU  - Bickle, T.A.
TI  - The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides.
JO  - EMBO J.
PY  - 2001
SP  - 3210
EP  - 3217
VL  - 20
AB  - McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+)
AB  - proteins and cuts DNA containing modified cytosines. Two proteins are expressed from the mcrB
AB  - gene: a full-length version, McrB(L), and a short version, McrB(S). McrB(L) binds specifically
AB  - to the methylated recognition site and is, therefore, the DNA-binding moiety of the McrBC
AB  - endonuclease. McrB(S) is devoid of DNA-binding activity. We observed that the quaternary
AB  - structure of the endonuclease depends on binding of the cofactors. In gel filtration
AB  - experiments, McrB(L) and McrB(S) form high molecular weight oligomers in the presence of
AB  - Mg(2+) and GTP, GDP or GTP-gamma-S. Oligomerization did not require the presence of DNA and
AB  - was independent of GTP hydrolysis. Electron micrographs of negatively stained McrB(L) and
AB  - McrB(S) revealed ring-shaped particles with a central channel. Mass analysis by scanning
AB  - transmission electron microscopy indicates that McrB(L) and McrB(S) form single heptameric
AB  - rings as well as tetradecamers. In the presence of McrC, a subunit that is essential for DNA
AB  - cleavage, the tetradecameric species was the major form of the endonuclease.
ER  -

TY  - JOUR
AU  - Panne, D.
AU  - Raleigh, E.A.
AU  - Bickle, T.A.
TI  - McrBS, a modulator peptide for McrBC activity.
JO  - EMBO J.
PY  - 1998
SP  - 5477
EP  - 5483
VL  - 17
AB  - McrBC is a methylation-dependent endonuclease from Escherichia coli K-12.  The enzyme
AB  - recognizes DNA with modified cytosine preceded by a purine.  McrBC restricts DNA that contains
AB  - at least two methylated recognition sites separated by 40-80 bp.  Two gene products, McrBL and
AB  - McrBS, are produced from the mcrB gene and one, McrC, from the mcrC gene.  DNA cleavage in
AB  - vitro requires McrBL, McrC, GTP and Mg2+.  We found that DNA cleavage was optimal at a ratio
AB  - of 3-5 McrBL per molecule of McrC, suggesting that formation of a multisubunit complex with
AB  - several molecules of McrBL is required for cleavage.  To understand the role of McrBS, we have
AB  - purified the protein and analyzed its role in vitro.  At the optimal ratio of 3-5 McrBL per
AB  - molecule of McrC, McrBS acted as an inhibitor of DNA cleavage.  Inhibition was due to
AB  - sequestration of McrC and required the presence of GTP, suggesting that the interaction is GTP
AB  - dependent.  If McrC was in excess, a condition resulting in suboptimal DNA cleavage, addition
AB  - of McrBS enhanced DNA cleavage, presumably due to sequestration of excess McrC.  We suggest
AB  - that the role of McrBS is to modulate McrBC activity by binding to McrC.
ER  -

TY  - JOUR
AU  - Panne, D.
AU  - Raleigh, E.A.
AU  - Bickle, T.A.
TI  - The McrBC endonuclease translocates DNA in a reaction dependent on GTP hydrolysis.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 49
EP  - 60
VL  - 290
AB  - McrBC specifically recognizes and cleaves methylated DNA in a reaction dependent on GTP
AB  - hydrolysis. DNA cleavage requires at least two recognition sites that are optimally separated
AB  - by 40-80 bp, but can be spaced as far as 3 kb apart. The nature of the communication between
AB  - two recognition sites was analyzed on DNA substrates containing one or two recognition sites.
AB  - DNA cleavage of circular DNA required only one methylated recognition site, whereas the
AB  - linearized form of this substrate was not cleaved. However, the linearized substrate was
AB  - cleaved if a Lac repressor was bound adjacent to the recognition site. These results suggest a
AB  - model in which communication between two remote sites is accomplished by DNA translocation
AB  - rather than looping. A mutant protein with defective GTPase activity cleaved substrates with
AB  - closely spaced recognition sites, but not substrates where the sites were further apart. This
AB  - indicates that McrBC translocates DNA in a reaction dependent on GTP hydrolysis. We suggest
AB  - that DNA cleavage occurs by the encounter of two DNA-translocating McrBC complexes, or can be
AB  - triggered by non-specific physical obstacles like the Lac repressor bound on the enzyme's
AB  - path along DNA. Our results indicate that McrBC belongs to the general class of DNA "motor
AB  - proteins", which use the free energy associated with nucleoside 5'-triphosphate hydrolysis to
AB  - translocate along DNA.
ER  -

TY  - JOUR
AU  - Panschin, I. et al.
TI  - Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae  UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola  Nedashkovskaya et al. 2005 emend.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 37
EP  - 37
VL  - 11
AB  - Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated
AB  - from marine habitats such as tidal flat sediments, coastal surface
AB  - seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the
AB  - decomposition of plant and algal polysaccharides. However, the potential to
AB  - decompose polysaccharides may differ tremendously even between species of the
AB  - same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella
AB  - portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths,
AB  - similar numbers of protein coding genes and RNA genes. Both genomes encode for a
AB  - greater number of peptidases compared to 'G. forsetii'. In contrast to the genome
AB  - of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven
AB  - polysaccharide utilization loci were identified in the genomes of DSM 19838(T)
AB  - and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan,
AB  - arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose
AB  - (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas
AB  - strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose.
AB  - Conclusively, both Gramella type strains exhibit characteristic physiological,
AB  - morphological and genomic differences that might be linked to their habitat.
AB  - Furthermore, the identified enzymes mediating polysaccharide decomposition, are
AB  - of biotechnological interest.
ER  -

TY  - JOUR
AU  - Panthee, S.
AU  - Paudel, A.
AU  - Hamamoto, H.
AU  - Sekimizu, K.
TI  - Draft Genome Sequence of the Vancomycin-Resistant Clinical Isolate Staphylococcus aureus VRS3b.
JO  - Genome Announcements
PY  - 2017
SP  - e00452
EP  - e00417
VL  - 5
AB  - We report here the draft genome sequence of the vancomycin-resistant strain Staphylococcus
AB  - aureus VRS3b. The 2.8-Mb genome, assembled into 46 contigs,
AB  - harbored 2,915 putative coding sequences. The G+C content of the genome was
AB  - 32.7%.
ER  -

TY  - JOUR
AU  - Panzenhagen, P.H.N.
AU  - Cabral, C.C.
AU  - Suffys, P.N.
AU  - Aquino, M.H.C.
AU  - Franco, R.M.
AU  - Pereira, V.L.A.
AU  - Rodrigues, D.P.
AU  - Conte-Junior, C.A.
TI  - Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Chicken and Swine Carcasses in Two Distinct Geographical  Regions from Rio de Janeiro State, Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00197
EP  - e00117
VL  - 5
AB  - Salmonella enterica subsp. enterica serovar Typhimurium is a surveyed worldwide serotype with
AB  - well-characterized genomes for several different strains. In
AB  - Brazil, very few studies have submitted whole-genome sequences to GenBank. This
AB  - genome may be useful to analyze the genetic mechanisms comparable to those of
AB  - other related studies conducted in Brazil and globally.
ER  -

TY  - JOUR
AU  - Panzenhagen, P.H.N.
AU  - Paul, N.C.
AU  - Conte, J.C.A.
AU  - Costa, R.G.
AU  - Rodrigues, D.P.
AU  - Shah, D.H.
TI  - Draft Genome Sequences of 11 Salmonella enterica Serovar Typhimurium Strains Isolated from Human Systemic and Nonsystemic Sites in Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e01223
EP  - e01217
VL  - 6
AB  - Salmonella enterica serovar Typhimurium strains isolated from systemic sites outside
AB  - sub-Saharan Africa have been rarely sequenced. Here, we report the draft
AB  - genome sequences of S Typhimurium sequence type 19 (ST19) (n = 9), ST1649 (n =
AB  - 1), and ST313 (n = 1) strains isolated from human systemic (e.g., blood) and
AB  - nonsystemic (e.g., stool and wounds) sites in Brazil.
ER  -

TY  - JOUR
AU  - Paoli, G.C.
AU  - Wijey, C.
AU  - Nguyen, L.H.
AU  - Chen, C.Y.
AU  - Yan, X.
AU  - Irwin, P.L.
TI  - Complete Genome Sequences of Two Strains of the Meat Spoilage Bacterium Brochothrix thermosphacta Isolated from Ground Chicken.
JO  - Genome Announcements
PY  - 2017
SP  - e01357
EP  - e01317
VL  - 5
AB  - Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome
AB  - sequences of two strains of B. thermosphacta isolated from ground
AB  - chicken. The genome sequences were determined using long-read PacBio
AB  - single-molecule real-time (SMRT) technology and are the first complete genome
AB  - sequences reported for B. thermosphacta.
ER  -

TY  - JOUR
AU  - Papa, C.M.
AU  - Springer, N.M.
AU  - Muszynski, M.G.
AU  - Meeley, R.
AU  - Kaeppler, S.M.
TI  - Maize chromomethylase Zea methyltransferase2 is required for CpNpG methyl ation.
JO  - Plant Cell
PY  - 2001
SP  - 1919
EP  - 1928
VL  - 13
AB  - A cytosine DNA methyltransferase containing a chromodomain, Zea methyltransferase2 (Zmet2),
AB  - was cloned from maize. The sequence of ZMET2 is similar to that of the Arabidopsis
AB  - chromomethylases CMT1 and CMT3, with C-terminal motifs characteristic of eukaryotic and
AB  - prokaryotic DNA methyltransferases. We used a reverse genetics approach to determine the
AB  - function of the Zmet2 gene. Plants homozygous for a Mutator transposable element insertion
AB  - into motif IX had a 13% reduction in methylated cytosines. DNA gel blot analysis of these
AB  - plants with methylation-sensitive restriction enzymes and bisulfite sequencing of a 180-bp
AB  - knob sequence showed reduced methylation only at CpNpG sites. No reductions in methylation
AB  - were observed at CpG or asymmetric sites in heterozygous or homozygous mutant plants. Our
AB  - research shows that chromomethylase Zmet2 is required for in vivo methylation of CpNpG
AB  - sequences.
ER  -

TY  - JOUR
AU  - Papadakos, G.A.
TI  - The effect of active site mutations on the homodimeric behavior of the PvuII restriction endonuclease.
JO  - Ph.D. Thesis, University of Missouri
PY  - 2008
SP  - 1
EP  - 233
AB  - The PvuII restriction endonuclease, a homodimer of two 18 kDa subunits, belongs to the type II
AB  - family of restriction enzymes. As a part of the Proteus vulgaris RM system, it specifically
AB  - cleaves the 5'-CAG|CTG-3' sequence in the presence of Mg2+ ions. Located in the active site
AB  - of PvuII, Tyrosine 94 has previously been shown to be involved in the metal ion binding by the
AB  - enzyme. The profile of the Ca2+ dependence of the DNA binding to the Y94F variant is shown to
AB  - be clearly biphasic. The application of a sequential binding model yielded two weak binding
AB  - constants in the upper phase with a coupling energy (delta G degrees coop) at -0.3, while two
AB  - tight binding constants are shown for the lower phase with -1.4 kcal/mole interaction energy.
AB  - The similar metal binding pattern between the Y94F and the WT PvuII for Mg2+, Ca2+, Tb3+ and
AB  - Eu3+ in the absence of DNA is also shown. The application of 1H-15N HSQC spectroscopy in the
AB  - presence of Ca2+ and DNA and the chemical denaturation of the Y94F variant confirm the
AB  - conformational impact of Tyr94. It is concluded that the removal of the aromatic iii hydroxyl
AB  - group of Tyr94 slightly repositions the metal ions in the active site of PvuII affecting the
AB  - intra and/or inter-subunit interactions among the metal binding sites. The single chain (SC)
AB  - PvuII bearing a covalent linker between the two subunits is utilized in the exploration of the
AB  - modes of cooperativity among the metal binding sites. The heterodimeric WT|E68A-SC PvuII was
AB  - prepared and studied in parallel to the WTSC homodimer. Global analysis of DNA binding
AB  - isotherms at different Ca2+ concentrations for the WT|E68A-SC variant returned an
AB  - intra-subunit delta G degrees coop at +1.6 and +1.0 kcal/mole in the absence and presence of
AB  - DNA, respectively. Combined with similar analysis for the WT-SC variant, the corresponding
AB  - values for the inter-subunit delta G degrees coop are shown at -2.8 and -1.1 kcal/mole for the
AB  - occupation of two sites simultaneously. The sequential binding of metal ions in the absence
AB  - and presence of DNA is overall unfavorable with significant negative interaction being
AB  - observed between the metal sites. It is shown that the effect of Ca2+ ions on DNA binding is
AB  - greater than the effect of the DNA on the affinity for metal ions. The cleavage of plasmid DNA
AB  - under single turnover conditions reveals a similar dependence of the nicking and linearization
AB  - rates on the concentration of Mg2+ ions for the WT-SC and the WT|E68A-SC PvuII. The series of
AB  - events leading to the linear product (DNA association, nicking, release of the intermediate,
AB  - re-association and linearization) in the presence of metal ions in one PvuII subunit is not
AB  - significantly slower than the synchronized double strand cleavage in the presence of metal
AB  - ions in both PvuII subunits.
ER  -

TY  - JOUR
AU  - Papadimitriou, K.
AU  - Ferreira, S.
AU  - Papandreou, N.C.
AU  - Mavrogonatou, E.
AU  - Supply, P.
AU  - Pot, B.
AU  - Tsakalidou, E.
TI  - Complete Genome Sequence of the Dairy Isolate Streptococcus macedonicus ACA-DC 198.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1838
EP  - 1839
VL  - 194
AB  - The species Streptococcus macedonicus is associated with the food environment, especially with
AB  - fermented dairy products. Here we present the complete 2.1-Mb
AB  - genome sequence of strain ACA-DC 198, which was isolated from naturally fermented
AB  - Greek kasseri cheese.
ER  -

TY  - JOUR
AU  - Papadimitriou, K.
AU  - Mavrogonatou, E.
AU  - Bolotin, A.
AU  - Tsakalidou, E.
AU  - Renault, P.
TI  - Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679.
JO  - Genome Announcements
PY  - 2016
SP  - e01025
EP  - e01016
VL  - 4
AB  - It is well recognized that Streptococcus macedonicus can populate artisanal fermented foods,
AB  - especially those of dairy origin. However, the safety of S.
AB  - macedonicus remains to be established. Here, we present the whole-genome sequence
AB  - of strain 679, which was isolated from a French uncooked semihard cheese made
AB  - with cow milk.
ER  -

TY  - JOUR
AU  - Papagiannitsis, C.C.
AU  - Miriagou, V.
AU  - Giakkoupi, P.
AU  - Tzouvelekis, L.S.
AU  - Vatopoulos, A.C.
TI  - Characterization of pKP1433, a Novel KPC-2-Encoding Plasmid from Klebsiella pneumoniae ST340.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 3427
EP  - 3429
VL  - 57
AB  - The nucleotide sequence of pKP1433 (55417 bp), a blaKPC-2-carrying plasmid from
AB  - Klebsiella pneumoniae sequence type 340 was determined. pKP1433 displayed
AB  - extensive sequence and structural similarities with the IncN plasmids possessing
AB  - the KPC-2-encoding Tn4401b isoform. However, replication, partitioning, and
AB  - stability of pKP1433 were determined by sequences related to diverse non-IncN
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Papagiannitsis, C.C.
AU  - Tzouvelekis, L.S.
AU  - Kotsakis, S.D.
AU  - Tzelepi, E.
AU  - Miriagou, V.
TI  - Sequence of pR3521, an IncB Plasmid from Escherichia coli Encoding ACC-4, SCO-1, and TEM-1 {beta}-Lactamases.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 376
EP  - 381
VL  - 55
AB  - The sequence of pR3521, a self-transmissible plasmid from Escherichia
AB  - coli, was determined. pR3521 (110,416 bp) comprised a contiguous IncB
AB  - sequence (84,034 bp) sharing extensive similarities with IncI replicons
AB  - and an acquired region (26,382 bp) carrying sequences of diverse origin,
AB  - containing bla(ACC-4), bla(SCO-1), bla(TEM-1b) (two copies), strA, strB,
AB  - sul2, and aacC2.
ER  -

TY  - JOUR
AU  - Papapanagiotou, I.
AU  - Streeter, S.D.
AU  - Cary, P.D.
AU  - Kneale, G.G.
TI  - DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2643
EP  - 2650
VL  - 35
AB  - Controller proteins such as C.AhdI regulate the expression of bacterial
AB  - restriction-modification genes, and ensure that methylation of the host DNA precedes
AB  - restriction by delaying transcription of the endonuclease. The operator DNA sequence to which
AB  - C.AhdI binds consists of two adjacent binding sites, O(L) and O(R). Binding of C.AhdI to O(L)
AB  - and to O(L) + O(R) has been investigated by circular permutation DNA-bending assays and by
AB  - circular dichroism (CD) spectroscopy. CD indicates considerable distortion to the DNA when
AB  - bound by C.AhdI. Binding to one or two sites to form dimeric and tetrameric complexes
AB  - increases the CD signal at 278 nm by 40 and 80% respectively, showing identical local
AB  - distortion at both sites. In contrast, DNA-bending assays gave similar bend angles for both
AB  - dimeric and tetrameric complexes (47 and 38 degrees , respectively). The relative orientation
AB  - of C.AhdI dimers in the tetrameric complex and the structural role of the conserved Py-A-T
AB  - sequences found at the centre of C-protein-binding sites are discussed.
ER  -

TY  - JOUR
AU  - Papke, R.T.
AU  - de la Haba, R.R.
AU  - Infante-Dominguez, C.
AU  - Perez, D.
AU  - Sanchez-Porro, C.
AU  - Lapierre, P.
AU  - Ventosa, A.
TI  - Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19.
JO  - Genome Announcements
PY  - 2013
SP  - e00379
EP  - e00313
VL  - 1
AB  - Marinobacter lipolyticus strain SM19, isolated from saline soil in Spain, is a moderately
AB  - halophilic bacterium belonging to the class Gammaproteobacteria. Here,
AB  - we report the draft genome sequence of this strain, which consists of a 4.0-Mb
AB  - chromosome and which is able to produce the halophilic enzyme lipase LipBL.
ER  -

TY  - JOUR
AU  - Pappas, K.M.
AU  - Kouvelis, V.N.
AU  - Saunders, E.
AU  - Brettin, T.S.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Balakireva, M.
AU  - Han, C.
AU  - Savvakis, G.
AU  - Kyrpides, N.C.
AU  - Typas, M.A.
TI  - Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5051
EP  - 5052
VL  - 193
AB  - Zymomonas mobilis ATCC 10988 is the type strain of the Z. mobilis subsp. mobilis taxon,
AB  - members of which are some of the most rigorous
AB  - ethanol-producing bacteria. Isolated from Agave cactus fermentations in
AB  - Mexico, ATCC 10988 is of the first Z. mobilis strains to be described and
AB  - studied. Its robustness in sucrose-substrate fermentations, physiological
AB  - characteristics, large number of plasmids and overall genomic plasticity
AB  - render this strain important to the study of the species. Here we report
AB  - the finishing and annotation of the ATCC 10988 chromosomal and plasmid
AB  - genome.
ER  -

TY  - JOUR
AU  - Paques, F.
AU  - Duchateau, P.
TI  - Meganucleases and DNA double-strand break-induced recombination: Perspectives for gene therapy.
JO  - Curr. Gene Ther.
PY  - 2007
SP  - 49
EP  - 66
VL  - 7
AB  - Meganucleases are sequence-specific endonucleases recognizing large (> 12 bp) sequence sites
AB  - and several laboratories have used these proteins
AB  - to induce highly efficient gene targeting in mammalian cells. The
AB  - recent development of artificial endonucleases with tailored
AB  - specificities has opened the door for a wide range of new applications,
AB  - including therapeutic ones: redesigned endonucleases cleaving chosen
AB  - sequences could be used to in gene therapy to correct mutated genes or
AB  - introduce transgenes in chosen loci. Such "targeted" approaches
AB  - markedly differ from current gene therapy strategies based on the
AB  - random insertion of a complementing virus-borne transgene. As a
AB  - consequence, they should bypass the odds of random insertion.
AB  - Artificial fusion proteins including Zinc-Finger binding domains have
AB  - provided important proofs of concept, however the toxicity of these
AB  - proteins is still an issue. Today custom-designed homing endonucleases,
AB  - the natural meganucleases, could represent an efficient alternative.
AB  - After a brief description of the origin of the technology, current
AB  - systems based on redesigned endonucleases will be presented, with a
AB  - special emphasis on the recent advances in homing endonuclease
AB  - engineering. Finally, we will discuss the main issues that will need to
AB  - be addressed in order to bring this promising technology to the
AB  - patient.
ER  -

TY  - JOUR
AU  - Paquin, B.
AU  - Laforest, M.-J.
AU  - Lang, B.F.
TI  - Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 11807
EP  - 11810
VL  - 91
AB  - In eukaryotes, horizontal gene transfer is a rare event.  Here we show that the mitochondrial
AB  - genome of a lower fungus, Allomyces macrogynus, has an extra DNA segment not present in a
AB  - close relative, Allomyces arbusculus.  This insert consists of the C terminus of a foreign
AB  - gene encoding a subunit of the ATP synthetase complex (atp6) plus an open reading frame
AB  - encoding an endonuclease.  The inserted atp6 portion is fused in phase to the resident gene,
AB  - resulting in expression of a hybrid atp6 gene and the displacement of the original C-terminal
AB  - atp6 region.  We present evidence that this insertion may have been acquired by interspecific
AB  - transfer and we discuss the possible role of the endonuclease in this process.
ER  -

TY  - JOUR
AU  - Paquin, B.
AU  - Lang, B.F.
TI  - The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 688
EP  - 701
VL  - 255
AB  - We have determined the complete nucleotide sequence of the circular mitochondrial DNA (mtDNA)
AB  - of the chytridiomycete fungus, Allomyces macrogynus (57,473 bp; A + T content 60.5%).  The
AB  - identified genes that are typical for most fungal mitochondria include those for the large
AB  - (rnl) and small subunit (rns) ribosomal RNAs, a complete set of 25 tRNAs, three ATPase
AB  - subunits (atp6, atp8 and atp9), apocytochrome b (cob), three subunits of the cytochrome
AB  - oxidase complex (cox1, cox2 and cox3), and seven subunits of the NADH dehydrogenase complex
AB  - (nad1, nad2, nad3, nad4, nad4L, nad5 and nad6).  A total of 28 introns of both groups are
AB  - found, some of which contain open reading frames (ORFs) coding for potential endonucleases
AB  - (group I) or reverse-transcriptases (group II).  All  mitochondrial genes are transcribed from
AB  - the same DNA strand, as is the case in many other eufungi.  Particular features of the A.
AB  - macrogynus mtDNA include: (1) the first documented case of a fungal mitochondrial ribosomal
AB  - protein gene (rps3) that is clearly identified by similarity with bacterial homologues; (2)
AB  - four unique ORFs; (3) the presence of an insert in the atp6 gene that may have been acquired
AB  - by interspecific transfer; (4) more than 67 short, highly structured and conserved DNA
AB  - elements inserted in intergenic spacers, introns, and variable regions of the rnl and rns
AB  - genes: these elements are unusually G + C rich; (5) rRNA structures that resemble more closely
AB  - those of eubacteria than their counterparts in other fungal mitochondria.  The high degree of
AB  - conservation of the A. macrogynus mitochondrial rRNA secondary structures, the existence of a
AB  - mitochondrial rps3 gene (common to protist but unique in fungal mtDNAs), and phylogenetic
AB  - relationships inferred from highly conserved protein genes, demonstrate consistently the
AB  - ancestral character of this fungal mitochondrial genome.
ER  -

TY  - JOUR
AU  - Paquin, B.
AU  - O'Kelly, C.J.
AU  - Lang, B.F.
TI  - Intron-encoded open reaading frame of the GIY-YIG subclass in a plastid gene.
JO  - Curr. Genet.
PY  - 1995
SP  - 97
EP  - 99
VL  - 28
AB  - Group-I introns, containing open reading frames that code for homing endonucleases, are widely
AB  - distributed amongst eukaryotic organellar genomes.  However, endonucleases of the GIY-YIG
AB  - subclass have a restricted distribution in mitochondria and bacteriophages, and have never
AB  - been observed in plastids.  We have found the GIY-YIG motif in an intronic ORF within the
AB  - previously published psbA gene sequence from Chlamydomonas reinhardtii chloroplasts.  Based on
AB  - phylogenetic analysis and an evaluation of amino-acid substitutions, this ORF is not closely
AB  - related to any of the other GIY-YIG ORFs.  These results suggest that GIY-YIG ORFs have a
AB  - longer evolutionary history than previously assumed.
ER  -

TY  - JOUR
AU  - Paradiso, R.
AU  - Orsini, M.
AU  - Criscuolo, D.
AU  - Borrelli, R.
AU  - Valvini, O.
AU  - Camma, C.
AU  - Chiusano, M.L.
AU  - Galiero, G.
AU  - Borriello, G.
TI  - Complete Genome Sequencing of 10 Brucella abortus Biovar 3 Strains Isolated from  Water Buffalo.
JO  - Genome Announcements
PY  - 2018
SP  - e00180
EP  - e00118
VL  - 6
AB  - Brucellosis is a zoonotic disease that affects both humans and animals. Its distribution is
AB  - global, concentrated in the Mediterranean area, India, Central
AB  - Asia, and Latin America. Here, we present a complete genome assembly of 10
AB  - Brucella abortus strains isolated from water buffaloes farmed in the Campania
AB  - region of Italy.
ER  -

TY  - JOUR
AU  - Paradiso, R.
AU  - Orsini, M.
AU  - Riccardi, M.G.
AU  - Cecere, B.
AU  - Cerrone, A.
AU  - Camma, C.
AU  - Chiusano, M.L.
AU  - Galiero, G.
AU  - Borriello, G.
TI  - Complete Genome Sequencing of Eight Brucella abortus Biovar 1 Strains Isolated from Water Buffalo.
JO  - Genome Announcements
PY  - 2018
SP  - e00179
EP  - e00118
VL  - 6
AB  - Brucellosis is a zoonotic disease caused by bacteria of the genus Brucella The disease is
AB  - endemic in many areas, causing chronic infections responsible for
AB  - reproductive disorders in infected animals. Here, we present eight complete
AB  - genome assemblies of eight Brucella abortus strains isolated from water buffaloes
AB  - farmed in the Campania region.
ER  -

TY  - JOUR
AU  - Parajuli, P.
AU  - Adamski, M.
AU  - Verma, N.K.
TI  - Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis.
JO  - BMC Genomics
PY  - 2017
SP  - 722
EP  - 722
VL  - 18
AB  - BACKGROUND: Shigella flexneri is the primary cause of bacillary dysentery in the
AB  - developing countries. S. flexneri serotype 1c is a novel serotype, which is found
AB  - to be endemic in many developing countries, but little is known about its genomic
AB  - architecture and virulence signatures. We have sequenced for the first time, the
AB  - complete genome of S. flexneri serotype 1c strain Y394, to provide insights into
AB  - its diversity and evolution. RESULTS: We generated a high-quality reference
AB  - genome of S. flexneri serotype 1c using the hybrid methods of long-read
AB  - single-molecule real-time (SMRT) sequencing technology and short-read MiSeq
AB  - (Illumina) sequencing technology. The Y394 chromosome is 4.58 Mb in size and
AB  - shares the basic genomic features with other S. flexneri complete genomes.
AB  - However, it possesses unique and highly modified O-antigen structure comprising
AB  - of three distinct O-antigen modifying gene clusters that potentially came from
AB  - three different bacteriophages. It also possesses a large number of hypothetical
AB  - unique genes compared to other S. flexneri genomes. CONCLUSIONS: Despite a high
AB  - level of structural and functional similarities of Y394 genome with other S.
AB  - flexneri genomes, there are marked differences in the pathogenic islands. The
AB  - diversity in the pathogenic islands suggests that these bacterial pathogens are
AB  - well adapted to respond to the selection pressures during their evolution, which
AB  - might contribute to the differences in their virulence potential.
ER  -

TY  - JOUR
AU  - Parales, R.E.
AU  - Navara, R.
AU  - Gettys, R.
AU  - Huang, J.J.
TI  - Genome Sequence of Pseudomonas putida Strain ASAD, an Acetylsalicylic Acid-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01169
EP  - e01117
VL  - 5
AB  - Pseudomonas putida strain ASAD was isolated from compost because of its ability to utilize
AB  - aspirin (acetylsalicylic acid) as a carbon and energy source. We
AB  - report the draft genome sequence of strain ASAD, with an estimated length of 6.9
AB  - Mb. Study of this isolate will provide insight into the aspirin biodegradation
AB  - pathway.
ER  -

TY  - JOUR
AU  - Parashar, V.
AU  - Capalash, N.
AU  - Sharma, P.
TI  - Demonstration of REBASE-assisted restriction mapping to determine the recognition site of unknown restriction endonucleases.
JO  - Biochem. Mol. Biol. Educ.
PY  - 2007
SP  - 337
EP  - 341
VL  - 35
AB  - An important step in the characterization of a new restriction enzyme involves determination
AB  - of its recognition site. Comparison of its DNA
AB  - substrate digestion fragment patterns with those obtained using enzymes
AB  - of known specificity indicates whether the enzyme recognizes a novel
AB  - sequence or is an isoschizomer of already existing prototype. REBASE
AB  - (Restriction Enzyme dataBASE: hftp://www.neb.com/rebase)-assisted
AB  - restriction mapping is described in this paper for a rare cutter [TspMI
AB  - (REBASE No. 7191)] and a frequent cutter [Bfll (REBASE No. 4910)] as a
AB  - practical exercise for undergraduate students to understand how to
AB  - determine recognition sequence of a REase.
ER  -

TY  - JOUR
AU  - Parashar, V.
AU  - Capalash, N.
AU  - Xu, S.Y.
AU  - Sako, Y.
AU  - Sharma, P.
TI  - TspMI, a thermostable isoschizomer of XmaI (5' C/CCGGG 3'): characterization and single molecule imaging with DNA - involving vector-mediated gene transfer and expression in host cell with restriction endonuclease activity.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2006
SP  - 917
EP  - 923
VL  - 72
AB  - AUTHOR ABSTRACT - TspMI, a thermostable isoschizomer of XmaI from a Thermus sp., has been
AB  - characterized. The enzyme was purified to homogeneity using Cibacron-Blue 3GA agarose, Heparin
AB  - agarose, SP sephadex C50, and Mono-Q fast protein liquid chromatography and was found to be a
AB  - homodimer of 40 kDa. Restriction mapping and run-off sequencing of TspMI-cleaved DNA ends
AB  - depicted that it cleaved at 5'C/CCGGG3' to generate a four-base, 5'-CCGG overhang. The
AB  - enzyme was sensitive to methylation of second and third cytosines in its recognition sequence.
AB  - TspMI worked optimally at 60 degrees C with 6 mM Mg2+, no Na+/K+, and showed no star activity
AB  - in the presence of 25% glycerol. The enzyme could efficiently digest the DNA labeled with a
AB  - higher concentration of YOYO-I (one dye molecule to one nucleotide), making it a useful
AB  - candidate for real-time imaging experiments. Single molecule interaction between TspMI and
AB  - lambda DNA was studied using total internal reflection fluorescence microscopy. The enzyme
AB  - survived 30 polymerase chain reaction (PCR) cycles in the presence of 10% glycerol and 0.5 M
AB  - trehalose without any activity loss and, hence, is suitable for incorporation in
AB  - restriction-endonuclease-mediated selective-PCR for various applications.
ER  -

TY  - JOUR
AU  - Pardo, C.E.
AU  - Carr, I.M.
AU  - Hoffman, C.J.
AU  - Darst, R.P.
AU  - Markham, A.F.
AU  - Bonthron, D.T.
AU  - Kladde, M.P.
TI  - MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual  templates (MAPit) projects.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - e5
EP  - e5
VL  - 39
AB  - Bisulfite sequencing is a widely-used technique for examining cytosine DNA methylation at
AB  - nucleotide resolution along single DNA strands.
AB  - Probing with cytosine DNA methyltransferases followed by bisulfite
AB  - sequencing (MAPit) is an effective technique for mapping protein-DNA
AB  - interactions. Here, MAPit methylation footprinting with M.CviPI, a GC
AB  - methyltransferase we previously cloned and characterized, was used to
AB  - probe hMLH1 chromatin in HCT116 and RKO colorectal cancer cells.
AB  - Because M. CviPI-probed samples contain both CG and GC methylation, we
AB  - developed a versatile, visually-intuitive program, called MethylViewer,
AB  - for evaluating the bisulfite sequencing results. Uniquely, MethylViewer
AB  - can simultaneously query cytosine methylation status in
AB  - bisulfite-converted sequences at as many as four different user-defined
AB  - motifs, e.g. CG, GC, etc., including motifs with degenerate bases. Data
AB  - can also be exported for statistical analysis and as
AB  - publication-quality images. Analysis of hMLH1 MAPit data with
AB  - MethylViewer showed that endogenous CG methylation and accessible GC
AB  - sites were both mapped on single molecules at high resolution.
AB  - Disruption of positioned nucleosomes on single molecules of the PHO5
AB  - promoter was detected in budding yeast using M.CviPII, increasing the
AB  - number of enzymes available for probing protein-DNA interactions.
AB  - MethylViewer provides an integrated solution for primer design and
AB  - rapid, accurate and detailed analysis of bisulfite sequencing or MAPit
AB  - datasets from virtually any biological or biochemical system.
ER  -

TY  - JOUR
AU  - Parini, C.
AU  - Fortina, M.G.
TI  - Site-specific restriction endonucleases in Bacillus licheniformis.
JO  - FEMS Microbiol. Lett.
PY  - 1995
SP  - 285
EP  - 289
VL  - 132
AB  - We systematically studied site-specific restriction endonucleases in Bacillus licheniformis
AB  - strains and detected endonuclease activity in 25 of 217 strains tested.  Three different
AB  - activities were obtained.  One of these activities detected in 21 strains was the most
AB  - representative within the species and produced a banding pattern, after digestion of lambda
AB  - DNA, identical to that seen with ClaI.  Two other strains isolated from soil samples from
AB  - China and USA were found to produce a DNA-cleaving enzyme with the same recognition sequence
AB  - as BsaI.  One producer strain, isolated from a Peruvian soil sample, possessed a mixture of
AB  - two isoschizomers, ClaI and BsaI.  Finally, one strain produced an endonuclease activity, not
AB  - previously described in B. licheniformis, that showed the same recognition sites as Bsu36I.
ER  -

TY  - JOUR
AU  - Parise, D.
AU  - Parise, M.T.D.
AU  - Viana, M.V.C.
AU  - Munoz-Bucio, A.V.
AU  - Cortes-Perez, Y.A.
AU  - Arellano-Reynoso, B.
AU  - Diaz-Aparicio, E.
AU  - Dorella, F.A.
AU  - Pereira, F.L.
AU  - Carvalho, A.F.
AU  - Figueiredo, H.C.P.
AU  - Ghosh, P.
AU  - Barh, D.
AU  - Gomide, A.C.P.
AU  - Azevedo, V.A.C.
TI  - First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 21
EP  - 21
VL  - 13
AB  - Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading
AB  - all over the world, causing economic losses in the agricultural
AB  - sector and sporadically infecting humans. Six C. pseudotuberculosis strains were
AB  - isolated from goats, sheep, and horses with distinct abscess locations. For the
AB  - first time, Mexican genomes of this bacterium were sequenced and studied in
AB  - silico. All strains were sequenced using Ion Personal Genome Machine sequencer,
AB  - assembled using Newbler and SPAdes software. The automatic genome annotation was
AB  - done using the software RAST and in-house scripts for transference, followed by
AB  - manual curation using Artemis software and BLAST against NCBI and UniProt
AB  - databases. The six genomes are publicly available in NCBI database. The analysis
AB  - of nucleotide sequence similarity and the generated phylogenetic tree led to the
AB  - observation that the Mexican strains are more similar between strains from the
AB  - same host, but the genetic structure is probably more influenced by
AB  - transportation of animals between farms than host preference. Also, a putative
AB  - drug target was predicted and in silico analysis of 46 strains showed two gene
AB  - clusters capable of differentiating the biovars equi and ovis: Restriction
AB  - Modification system and CRISPR-Cas cluster.
ER  -

TY  - JOUR
AU  - Parizzi, L.P.
AU  - Grassi, M.C.
AU  - Llerena, L.A.
AU  - Carazzolle, M.F.
AU  - Queiroz, V.L.
AU  - Lunardi, I.
AU  - Zeidler, A.F.
AU  - Teixeira, P.J.
AU  - Mieczkowski, P.
AU  - Rincones, J.
AU  - Pereira, G.A.
TI  - The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential.
JO  - BMC Genomics
PY  - 2012
SP  - 562
EP  - 562
VL  - 13
AB  - ABSTRACT: BACKGROUND: Synthetic biology allows the development of new biochemical
AB  - pathways for the production of chemicals from renewable sources. One major
AB  - challenge is the identification of suitable microorganisms to hold these pathways
AB  - with sufficient robustness and high yield. In this work we analyzed the genome of
AB  - the propionic acid producer Actinobacteria Propionibacterium acidipropionici
AB  - (ATCC 4875). RESULTS: The assembled P. acidipropionici genome has 3,656,170 base
AB  - pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We
AB  - identified 3,336 protein coding genes, approximately 1000 more than P.
AB  - freudenreichii and P. acnes, with an increase in the number of genes putatively
AB  - involved in maintenance of genome integrity, as well as the presence of an
AB  - invertase and genes putatively involved in carbon catabolite repression. In
AB  - addition, we made an experimental confirmation of the ability of P.
AB  - acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene
AB  - was found in the genome. Instead, we identified the pyruvate carboxylase gene and
AB  - confirmed the presence of the corresponding enzyme in proteome analysis as a
AB  - potential candidate for this activity. Similarly, the phosphate acetyltransferase
AB  - and acetate kinase genes, which are considered responsible for acetate formation,
AB  - were not present in the genome. In P. acidipropionici, a similar function seems
AB  - to be performed by an ADP forming acetate-CoA ligase gene and its corresponding
AB  - enzyme was confirmed in the proteome analysis. CONCLUSIONS: Our data shows that
AB  - P. acidipropionici has several of the desired features that are required to
AB  - become a platform for the production of chemical commodities: multiple pathways
AB  - for efficient feedstock utilization, ability to fix CO2, robustness, and
AB  - efficient production of propionic acid, a potential precursor for valuable
AB  - 3-carbon compounds.
ER  -

TY  - JOUR
AU  - Park, B.S.
AU  - Han, J.
AU  - Shin, D.J.
AU  - Jeong, Y.J.
AU  - Lee, N.
TI  - Complete Genome Sequence of Actinobacillus pleuropneumoniae Strain KL 16 (Serotype 1).
JO  - Genome Announcements
PY  - 2017
SP  - e01025
EP  - e01017
VL  - 5
AB  - Actinobacillus pleuropneumoniae is a bacterial pathogen causing highly contagious porcine
AB  - pleuropneumonia. Due to limited information on this species, it is
AB  - difficult to study the biology of A. pleuropneumoniae at the genome level. Here,
AB  - we report the fully annotated genome sequence of A. pleuropneumoniae strain KL
AB  - 16.
ER  -

TY  - JOUR
AU  - Park, C.
AU  - Shin, H.H.
AU  - Kwon, E.Y.
AU  - Choi, S.M.
AU  - Kim, S.H.
AU  - Park, S.H.
AU  - Choi, J.H.
AU  - Yoo, J.H.
AU  - Lee, D.G.
AU  - Shin, W.S.
TI  - Two variants of staphylococcal cassette chromosome mec type IVA in community-associated meticillin-resistant Staphylococcus aureus strains in South Korea.
JO  - J. Med. Microbiol.
PY  - 2009
SP  - 1314
EP  - 1321
VL  - 58
AB  - Meticillin-resistant Staphylococcus aureus (MRSA) strains harbouring staphylococcal cassette
AB  - chromosome mec (SCCmec) type IVA are known to be more prevalent in South Korea than in other
AB  - countries. Variations in the SCCmec IVA structure have been identified, including in sequence
AB  - type (ST)
AB  - 1 and ST72 strains. This study compared and investigated the genetic characteristics of two
AB  - subtypes common in South Korea. Type IVA SCCmec of
AB  - ST1 strains was characterized by type IV features with the linearized pUB110 at the junkyard
AB  - (J) 3 region. However, that of ST72 strains carried a variant class B mec complex, ccrA2, with
AB  - an identity of approximately 96 % and the linearized pUB110 at the J3 region. In SCCmec of
AB  - ST72 strains, the organization of the class B variant and the J3 region may be more similar to
AB  - that of type IA than to other types, but the ccr type and other J regions seemed to be derived
AB  - from type IV. These genetic characteristics showed that type IVA appears to result from the
AB  - dynamic genetic exchange and recombination of SCC DNA.
ER  -

TY  - JOUR
AU  - Park, C.K.
AU  - Joshi, H.K.
AU  - Agrawal, A.
AU  - Ghare, M.I.
AU  - Little, E.J.
AU  - Dunten, P.W.
AU  - Bitinaite, J.
AU  - Horton, N.C.
TI  - Domain swapping in allosteric modulation of DNA specificity.
JO  - PLoS Biology
PY  - 2010
SP  - e1000554
EP  - e1000554
VL  - 8
AB  - SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence
AB  - and exhibits allosteric self-modulation of cleavage
AB  - activity and sequence specificity. Previous studies have shown that DNA
AB  - bound dimers of SgrAI oligomerize into an activated form with higher DNA
AB  - cleavage rates, although previously determined crystal structures of SgrAI
AB  - bound to DNA show only the DNA bound dimer. A new crystal structure of the
AB  - type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now
AB  - presented, which shows the close association of two DNA bound SgrAI
AB  - dimers. This tetrameric form is unlike those of the homologous enzymes
AB  - Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24
AB  - amino acid residues. Two mutations predicted to destabilize the swapped
AB  - form of SgrAI, P27W and P27G, have been made and shown to eliminate both
AB  - the oligomerization of the DNA bound SgrAI dimers as well as the
AB  - allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving
AB  - domain swapping is proposed to explain the unusual allosteric properties
AB  - of SgrAI via association of the domain swapped tetramer of SgrAI bound to
AB  - DNA into higher order oligomers.
ER  -

TY  - JOUR
AU  - Park, D.H.
AU  - Thapa, S.P.
AU  - Choi, B.S.
AU  - Kim, W.S.
AU  - Hur, J.H.
AU  - Cho, J.M.
AU  - Lim, J.S.
AU  - Choi, I.Y.
AU  - Lim, C.K.
TI  - Complete Genome Sequence of Japanese Erwinia Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear.
JO  - J. Bacteriol.
PY  - 2010
SP  - 586
EP  - 587
VL  - 193
AB  - The Japanese Erwinia strain Ejp617 is a plant pathogen that causes bacterial shoot blight of
AB  - pear (BSBP) in Japan. Here, we report the
AB  - complete genome sequence of strain Ejp617 isolated from Nashi pears in
AB  - Japan to provide for further valuable insight among related Erwinia
AB  - species.
ER  -

TY  - JOUR
AU  - Park, D.S.
AU  - Bae, K.S.
AU  - Kim, H.
AU  - Shin, K.S.
AU  - Choi, S.H.
AU  - Kim, D.S.
AU  - Kim, B.W.
AU  - Oh, H.W.
TI  - Draft Genome Sequence of the Novel Enteric Bacterium Galloisinimonas intestini B14T KCTC 32180, Isolated from the Gut of a Galloisiana Species (Notoptera:  Grylloblattidae) Fossil Insect.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6648
EP  - 6648
VL  - 194
AB  - We report the 3.74-Mb genome sequence of Galloisinimonas intestini B14(T), isolated from the
AB  - gut of one of the world's rarest insect species, Galloisiana
AB  - sp., collected at a Mosan cave, Moonkyung, Gyungsangbook-do, South Korea. Strain
AB  - B14(T) is a novel genus candidate of the family Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Park, G.S.
AU  - Hong, S.J.
AU  - Lee, C.H.
AU  - Khan, A.R.
AU  - Ullah, I.
AU  - Jung, B.K.
AU  - Choi, J.
AU  - Kwak, Y.
AU  - Back, C.G.
AU  - Jung, H.Y.
AU  - Shin, J.H.
TI  - Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.
JO  - Genome Announcements
PY  - 2014
SP  - e01237
EP  - e01214
VL  - 2
AB  - Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been
AB  - isolated from poultry waste. Here, we report the 4.6-Mbp draft
AB  - genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and
AB  - 4,087 protein-coding genes.
ER  -

TY  - JOUR
AU  - Park, G.S.
AU  - Khan, A.R.
AU  - Hong, S.J.
AU  - Jang, E.K.
AU  - Ullah, I.
AU  - Jung, B.K.
AU  - Choi, J.
AU  - Yoo, N.K.
AU  - Park, K.J.
AU  - Shin, J.H.
TI  - Draft Genome Sequence of Entomopathogenic Bacterium Photorhabdus temperata Strain M1021, Isolated from Nematodes.
JO  - Genome Announcements
PY  - 2013
SP  - e00747
EP  - e00713
VL  - 1
AB  - Photorhabdus temperata strain M1021 is an entomopathogenic bacterium belonging to the family
AB  - Enterobacteriaceae and is symbiotically associated with nematodes. The
AB  - draft genome sequence of P. temperata strain M1021 consists of 5,598,253 bp with
AB  - a G+C content of 43.7%, and it has 6,120 protein-coding genes.
ER  -

TY  - JOUR
AU  - Park, H.
AU  - Park, B.
AU  - Kim, H.J.
AU  - Park, W.
AU  - Choi, I.G.
TI  - Draft Genome Sequences of Two Ureolytic Bacteria Isolated from Concrete Block Waste.
JO  - Genome Announcements
PY  - 2016
SP  - e00762
EP  - e00716
VL  - 4
AB  - We sequenced genomes of two ureolytic bacteria, Bacillus sp. JH7 and Sporosarcina sp. HYO08,
AB  - which were isolated from concrete waste and have a potential for
AB  - biocementation applications.
ER  -

TY  - JOUR
AU  - Park, H.J.
AU  - Kim, D.
TI  - Draft Genome Sequence of a Humic Substance-Degrading Paenibacillus sp. Isolated from the Subarctic Grasslands at Low Temperature.
JO  - Genome Announcements
PY  - 2013
SP  - e00170
EP  - e00112
VL  - 1
AB  - The Paenibacillus sp. strain PAMC 26794 was isolated from the tundra grasslands in Alaska for
AB  - its high ability to degrade humic acids. We sequenced the PAMC
AB  - 26794 genome to discover the degradative genes for natural humic substances and
AB  - we propose the degradation pathway(s) of an abundant bacterial group (genus
AB  - Paenibacillus) that inhabits cold environments.
ER  -

TY  - JOUR
AU  - Park, H.J.
AU  - Shin, S.C.
AU  - Kim, D.
TI  - Draft Genome Sequence of Arctic Marine Bacterium Pseudoalteromonas issachenkonii  PAMC 22718.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4140
EP  - 4140
VL  - 194
AB  - The psychrotolerant Pseudoalteromonas issachenkonii PAMC 22718 was isolated for its higher
AB  - chitinase and protease activities from cold seawater in the Kara Sea,
AB  - Arctic. Here, we present the draft genome sequence of PAMC 22718 to provide
AB  - further information for the ecological function of the genus Pseudoalteromonas in
AB  - a cold marine environment.
ER  -

TY  - JOUR
AU  - Park, H.J.
AU  - Shin, S.C.
AU  - Kim, D.
TI  - Draft genome sequence of a subarctic humic substance-degrading pseudomonad.
JO  - Genome Announcements
PY  - 2013
SP  - e00070
EP  - e00012
VL  - 1
AB  - The Pseudomonas sp. PAMC 26793 was isolated because of its high ability to degrade humic acids
AB  - from a subarctic grassland in Alaska. We sequenced the PAMC 26793 genome to discover the genes
AB  - for degradation of natural humic substances and to provide further information for the
AB  - degradation process of soil bacteria in a low-temperature environment.
ER  -

TY  - JOUR
AU  - Park, I.H.
AU  - Baek, J.Y.
AU  - Song, J.H.
AU  - Ko, K.S.
AU  - Kim, K.H.
TI  - Draft Genome Sequences of Clinical Isolates of Serotype 6E Streptococcus pneumoniae from Five Asian Countries.
JO  - Genome Announcements
PY  - 2017
SP  - e01728
EP  - e01716
VL  - 5
AB  - Although serotype 6E Streptococcus pneumoniae consistently expresses capsules of  either
AB  - vaccine-serotype 6A or 6B, certain genetic variants of serotype 6E may
AB  - evade vaccine induced immunity. Thus, draft genome sequences from five clinical
AB  - isolates of serotype 6E from each of five different Asian countries have been
AB  - generated to provide insight into the genomic diversity in serotype 6E strains.
ER  -

TY  - JOUR
AU  - Park, J.
AU  - Zhang, Y.
AU  - Buboltz, A.M.
AU  - Zhang, X.
AU  - Schuster, S.C.
AU  - Ahuja, U.
AU  - Liu, M.
AU  - Miller, J.F.
AU  - Sebaihia, M.
AU  - Bentley, S.D.
AU  - Parkhill, J.
AU  - Harvill, E.T.
TI  - Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens.
JO  - BMC Genomics
PY  - 2012
SP  - 545
EP  - 545
VL  - 13
AB  - ABSTRACT: BACKGROUND: The classical Bordetella subspecies are phylogenetically
AB  - closely related, yet differ in some of the most interesting and important
AB  - characteristics of pathogens, such as host range, virulence and persistence. The
AB  - compelling picture from previous comparisons of the three sequenced genomes was
AB  - of genome degradation, with substantial loss of genome content (up to 24%)
AB  - associated with adaptation to humans. RESULTS: For a more comprehensive picture
AB  - of lineage evolution, we employed comparative genomic and phylogenomic analyses
AB  - using seven additional diverse, newly sequenced Bordetella isolates. Genome-wide
AB  - single nucleotide polymorphism (SNP) analysis supports a reevaluation of the
AB  - phylogenetic relationships between the classical Bordetella subspecies, and
AB  - suggests a closer link between ovine and human B. parapertussis lineages than has
AB  - been previously proposed. Comparative analyses of genome content revealed that
AB  - only 50% of the pan-genome is conserved in all strains, reflecting substantial
AB  - diversity of genome content in these closely related pathogens that may relate to
AB  - their different host ranges, virulence and persistence characteristics.
AB  - Strikingly, these analyses suggest possible horizontal gene transfer (HGT) events
AB  - in multiple loci encoding virulence factors, including O-antigen and pertussis
AB  - toxin (Ptx). Segments of the pertussis toxin locus (ptx) and its secretion system
AB  - locus (ptl) appear to have been acquired by the classical Bordetella subspecies
AB  - and are divergent in different lineages, suggesting functional divergence in the
AB  - classical Bordetellae. CONCLUSIONS: Together, these observations, especially in
AB  - key virulence factors, reveal that multiple mechanisms, such as point mutations,
AB  - gain or loss of genes, as well as HGTs, contribute to the substantial phenotypic
AB  - diversity of these versatile subspecies in various hosts.
ER  -

TY  - JOUR
AU  - Park, J.H.
AU  - Cho, Y.J.
AU  - Chun, J.
AU  - Seok, Y.J.
AU  - Lee, J.K.
AU  - Kim, K.S.
AU  - Lee, K.H.
AU  - Park, S.J.
AU  - Choi, S.H.
TI  - Complete Genome Sequence of Vibrio vulnificus MO6-24/O.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2062
EP  - 2063
VL  - 193
AB  - Vibrio vulnificus is the causative agent of life-threatening septicemia and severe wound
AB  - infections. Here, we announce the complete annotated
AB  - genome sequence of V. vulnificus MO6-24/O, isolated from a patient with
AB  - septicemia. When it is compared with previously known V. vulnificus
AB  - genomes, the genome of this bacterium shows a unique genetic makeup,
AB  - including phagelike elements, carbohydrate metabolism-related genes, and
AB  - the superintegron.
ER  -

TY  - JOUR
AU  - Park, J.Y.
AU  - Han, S.H.
AU  - Lee, J.H.
AU  - Han, Y.S.
AU  - Lee, Y.S.
AU  - Rong, X.
AU  - McSpadden, G.B.B.
AU  - Park, H.S.
AU  - Kim, Y.C.
TI  - Draft Genome Sequence of the Biocontrol Bacterium Pseudomonas putida B001, an Oligotrophic Bacterium That Induces Systemic Resistance to Plant  Diseases.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6795
EP  - 6796
VL  - 193
AB  - Pseudomonas putida B001 is a rhizobacterium that was isolated on the basis of its abilities to
AB  - grow under low-nutrient conditions and induce systemic
AB  - resistance against bacterial, fungal, and viral diseases of plants. Here
AB  - we report the draft genome sequence and automatic annotation of strain
AB  - B001. Comparison of this sequence to the sequenced genome of P. putida
AB  - KT2440 points to a subset of gene functions that may be related to the
AB  - defense-inducing functions of B001.
ER  -

TY  - JOUR
AU  - Park, J.Y.
AU  - Kim, S.
AU  - Kim, S.M.
AU  - Cha, S.H.
AU  - Lim, S.K.
AU  - Kim, J.
TI  - Complete Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain 1656-2, Which Forms Sturdy Biofilm.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6393
EP  - 6394
VL  - 193
AB  - Acinetobacter baumannii is a Gram-negative bacterium causing nosocomial infections worldwide.
AB  - To gain quick insight into the molecular basis of
AB  - biofilm formation in A. baumannii, we determined the complete genome
AB  - sequence of A. baumannii strain 1656-2, which forms sturdy biofilm and is
AB  - resistant to multiple drugs.
ER  -

TY  - JOUR
AU  - Park, M.A.
AU  - Kwon, M.G.
AU  - Hwang, J.Y.
AU  - Jung, S.H.
AU  - Kim, D.W.
AU  - Park, J.Y.
AU  - Kim, J.S.
AU  - Na, Y.J.
AU  - Kim, M.Y.
AU  - Kim, D.S.
AU  - Chae, S.H.
AU  - Seo, J.S.
TI  - Genome Sequence of Streptococcus parauberis Strain KCTC11980, Isolated from Diseased Paralichthys olivaceus.
JO  - Genome Announcements
PY  - 2013
SP  - e00780
EP  - e00713
VL  - 1
AB  - Streptococcus parauberis is a coccoid, nonmotile, alpha-hemolytic, Gram-positive  bacterium of
AB  - the Streptococcaceae family. Streptococcus parauberis strain
AB  - KCTC11980 was isolated from the kidney of a diseased olive flounder collected
AB  - from an aquaculture farm on Jeju Island in 2010. The 2.12-Mb genome sequence
AB  - consists of 44 large contigs in 16 scaffolds and contains 2,214 predicted
AB  - protein-coding genes, with a G+C content of 35.4%.
ER  -

TY  - JOUR
AU  - Park, S.
AU  - Ji, Y.
AU  - Jung, H.Y.
AU  - Park, H.
AU  - Kang, J.
AU  - Choi, S.H.
AU  - Shin, H.
AU  - Hyun, C.K.
AU  - Kim, K.T.
AU  - Holzapfel, W.H.
TI  - Lactobacillus plantarum HAC01 regulates gut microbiota and adipose tissue accumulation in a diet-induced obesity murine model.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2017
SP  - 1605
EP  - 1614
VL  - 101
AB  - The functional features of Lactobacillus plantarum HAC01 (HAC01), isolated from
AB  - fermented Korean kimchi, were studied with regard to the fat mass,
AB  - immunometabolic biomarkers and dysbiosis in a diet-induced obesity (DIO) murine
AB  - model. L. rhamnosus GG (LGG) served as reference strain and a PBS-treated group
AB  - as control. The administration of L. plantarum HAC01 resulted in reduction of the
AB  - mesenteric adipose depot, the conjunctive tissue closely associated with the
AB  - gastrointestinal tract, where lipid oxidative gene expression was upregulated
AB  - compared to the control group. Metagenome analysis of intestinal microbiota
AB  - showed that both strains HAC01 and LGG influenced specific bacterial families
AB  - such as the Lachnospiraceae and Ruminococcaceae rather than the phyla Firmicutes
AB  - and Bacteroidetes as a whole. The relative abundance of the Lachnospiraceae
AB  - (phylum Firmicutes) was significantly higher in both LAB-treated groups than in
AB  - the control. Comparing the impact of the two Lactobacillus strains on microbial
AB  - composition in the gut also suggests strain-specific effects. The study
AB  - emphasises the need for deeper studies into functional specificity of a probiotic
AB  - organism at the strain level. Alleviation of obesity-associated dysbiosis by
AB  - modulation of the gut microbiota appears to be associated with "indicator"
AB  - bacterial taxa such as the family Lachnospiraceae. This may provide further
AB  - insight into mechanisms basic to the mode of probiotic action against obesity and
AB  - associated dysbiosis.
ER  -

TY  - JOUR
AU  - Park, S.-Y.
AU  - Lee, H.-J.
AU  - Song, J.-M.
AU  - Sun, J.
AU  - Hwang, H.-J.
AU  - Nishi, K.
AU  - Kim, J.-S.
TI  - Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2012
SP  - 1570
EP  - 1577
VL  - 68
AB  - In multifunctional type I restriction enzymes, active methyl-transferases (MTases) are
AB  - constituted of methylation (HsdM) and
AB  - specificity (HsdS) subunits. In this study, the crystal structure of a
AB  - putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was
AB  - elucidated at a resolution of 1.80 angstrom. A cofactor-binding site
AB  - for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed
AB  - within the C-terminal domain of an alpha/beta-fold, in which a number
AB  - of residues are conserved, including the GxGG and (N/D) PP(F/Y) motifs,
AB  - which are likely to interact with several functional moieties of the
AB  - SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus
AB  - aquaticus and other HsdM structures suggests that two aromatic rings
AB  - (Phe199 and Phe312) in the motifs that are conserved among the HsdMs
AB  - may sandwich both sides of the adenine ring of the recognition sequence
AB  - so that a conserved Asn residue (Asn309) can interact with the N6 atom
AB  - of the target adenine base (a methyl-group acceptor) and locate the
AB  - target adenine base close to the transferred SAM methyl group.
ER  -

TY  - JOUR
AU  - Park, S.H.
AU  - Kim, H.U.
AU  - Kim, T.Y.
AU  - Park, J.S.
AU  - Kim, S.S.
AU  - Lee, S.Y.
TI  - Metabolic engineering of Corynebacterium glutamicum for L-arginine production.
JO  - Nat. Commun.
PY  - 2014
SP  - 4618
EP  - 4618
VL  - 5
AB  - L-Arginine is an important amino acid for diverse industrial and health product
AB  - applications. Here we report the development of metabolically engineered
AB  - Corynebacterium glutamicum ATCC 21831 for the production of L-arginine. Random
AB  - mutagenesis is first performed to increase the tolerance of C. glutamicum to
AB  - L-arginine analogues, followed by systems metabolic engineering for further
AB  - strain improvement, involving removal of regulatory repressors of arginine
AB  - operon, optimization of NADPH level, disruption of L-glutamate exporter to
AB  - increase L-arginine precursor and flux optimization of rate-limiting L-arginine
AB  - biosynthetic reactions. Fed-batch fermentation of the final strain in 5 l and
AB  - large-scale 1,500 l bioreactors allows production of 92.5 and 81.2 g l(-1) of
AB  - L-arginine with the yields of 0.40 and 0.35 g L-arginine per gram carbon source
AB  - (glucose plus sucrose), respectively. The systems metabolic engineering strategy
AB  - described here will be useful for engineering Corynebacteria strains for the
AB  - industrial production of L-arginine and related products.
ER  -

TY  - JOUR
AU  - Park, S.J.
AU  - Ghai, R.
AU  - Martin-Cuadrado, A.B.
AU  - Rodriguez-Valera, F.
AU  - Jung, M.Y.
AU  - Kim, J.G.
AU  - Rhee, S.K.
TI  - Draft Genome Sequence of the Sulfur-Oxidizing Bacterium 'Candidatus Sulfurovum sediminum' AR, Which Belongs to the Epsilonproteobacteria.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4128
EP  - 4129
VL  - 194
AB  - Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich
AB  - environments. They play important roles in the global sulfur cycle on earth.
AB  - Here, we present a high-quality draft genome sequence of a sulfur-oxidizing
AB  - bacterium, 'Candidatus Sulfurovum sediminum' strain AR, which belongs to the
AB  - class Epsilonproteobacteria and dominated an enrichment culture from a marine
AB  - sediment collected off Svalbard, within the Arctic Circle. Its genome contains
AB  - genes for sulfur oxidation and carbon fixation. The size of the draft genome is
AB  - 2.12 Mb, and the G+C content is 39.4%.
ER  -

TY  - JOUR
AU  - Park, S.J.
AU  - Kim, J.G.
AU  - Jung, M.Y.
AU  - Kim, S.J.
AU  - Cha, I.T.
AU  - Ghai, R.
AU  - Martin-Cuadrado, A.B.
AU  - Rodriguez-Valera, F.
AU  - Rhee, S.K.
TI  - Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, 'Candidatus Nitrosopumilus sediminis' AR2, from Svalbard in the Arctic Circle.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6948
EP  - 6949
VL  - 194
AB  - Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in
AB  - marine sediments. We herein present the draft genome sequence of an
AB  - ammonia-oxidizing archaeon, 'Candidatus Nitrosopumilus sediminis' AR2, which was
AB  - enriched in culture from a marine sediment obtained off Svalbard, within the
AB  - Arctic Circle. The typical genes involved in archaeal ammonia oxidation and
AB  - carbon fixation necessary for chemolithoautotrophic growth were observed.
AB  - Interestingly, the AR2 genome sequence was revealed to possess, uniquely among
AB  - cultivated AOA from marine environments, a capability for urea utilization.
ER  -

TY  - JOUR
AU  - Park, S.J.
AU  - Kim, J.G.
AU  - Jung, M.Y.
AU  - Kim, S.J.
AU  - Cha, I.T.
AU  - Kwon, K.
AU  - Lee, J.H.
AU  - Rhee, S.K.
TI  - Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, 'Candidatus Nitrosopumilus koreensis' AR1, from Marine Sediment.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6940
EP  - 6941
VL  - 194
AB  - Ammonia-oxidizing archaea (AOA) are ubiquitous in various marine environments and play
AB  - important roles in the global nitrogen and carbon cycles. We here present a
AB  - high-quality draft genome sequence of an ammonia-oxidizing archaeon, 'Candidatus
AB  - Nitrosopumilus koreensis' AR1, which was found to dominate an ammonia-oxidizing
AB  - enrichment culture in marine sediment off Svalbard, the Arctic Circle. Despite a
AB  - significant number of nonoverlapping genes (ca. 30%), similarities of this strain
AB  - to 'Candidatus Nitrosopumilus maritimus' were revealed by core genes for archaeal
AB  - ammonia oxidation and carbon fixation, G+C content, and extensive synteny
AB  - conservation.
ER  -

TY  - JOUR
AU  - Park, S.K.
AU  - Roh, S.W.
AU  - Whon, T.W.
AU  - Bae, J.W.
TI  - Genome Sequence of Brachybacterium squillarum M-6-3T, Isolated from Salt-Fermented Seafood.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6416
EP  - 6417
VL  - 193
AB  - Brachybacterium squillarum M-6-3(T) was isolated from salt-fermented seafood in Korea and
AB  - belongs to the Dermabacteraceae, a rather isolated
AB  - family within the actinobacterial suborder Micrococcineae. Here, we
AB  - present the draft genome sequence of the type strain Brachybacterium
AB  - squillarum M-6-3(T) (3,191,479 bp), a Gram-positive bacterium with high
AB  - (72.8%) G+C content.
ER  -

TY  - JOUR
AU  - Park, S.N.
AU  - Cho, E.
AU  - Kim, H.S.
AU  - Kim, D.S.
AU  - Jung, J.
AU  - Baek, J.H.
AU  - Kyong, L.Y.
AU  - Jo, E.
AU  - Chang, Y.H.
AU  - Hwan, S.J.
AU  - Choi, S.H.
AU  - Kang, J.
AU  - Choi, Y.
AU  - Kong, S.W.
AU  - Han, S.E.
AU  - Park, H.S.
AU  - Kim, H.
AU  - Kook, J.K.
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. animalis ChDC F324, Isolated from a Human Subgingival Plaque in the Republic of Korea.
JO  - Genome Announcements
PY  - 2013
SP  - e01042
EP  - e01013
VL  - 1
AB  - Five subspecies of Fusobacterium nucleatum have been classified: animalis, nucleatum,
AB  - polymorphum, vincentii, and fusiforme. F. nucleatum subsp. animalis
AB  - ChDC F324 (KCOM 1325) was isolated from a human subgingival plaque in the
AB  - Republic of Korea. Here, we report the draft genome sequence of the strain.
ER  -

TY  - JOUR
AU  - Park, S.N.
AU  - Cho, E.
AU  - Kim, H.S.
AU  - Kim, D.S.
AU  - Jung, J.
AU  - Baek, J.H.
AU  - Kyong, L.Y.
AU  - Jo, E.
AU  - Chang, Y.H.
AU  - Hwan, S.J.
AU  - Choi, S.H.
AU  - Kang, J.
AU  - Choi, Y.
AU  - Park, H.S.
AU  - Kim, H.
AU  - Kook, J.K.
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. nucleatum ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea.
JO  - Genome Announcements
PY  - 2013
SP  - e01041
EP  - e01013
VL  - 1
AB  - Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of
AB  - periodontal diseases, including peri-implantitis. Fusobacterium
AB  - nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human
AB  - peri-implantitis lesion. Here, we report the draft genome sequence of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Park, S.N.
AU  - Cho, E.
AU  - Kim, H.S.
AU  - Kim, D.S.
AU  - Jung, J.
AU  - Baek, J.H.
AU  - Kyong, L.Y.
AU  - Jo, E.
AU  - Chang, Y.H.
AU  - Hwan, S.J.
AU  - Kim, J.
AU  - Choi, S.H.
AU  - Kang, J.
AU  - Choi, Y.
AU  - Park, H.S.
AU  - Kim, H.
AU  - Kook, J.K.
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. vincentii ChDC F8, Isolated from a Human Subgingival Plaque in the Republic of Korea.
JO  - Genome Announcements
PY  - 2013
SP  - e01040
EP  - e01013
VL  - 1
AB  - Fusobacterium nucleatum is a Gram-negative, nonmotile, obligately anaerobic rod bacterium
AB  - which might play an important role in the initiation and progression of
AB  - periodontal diseases. F. nucleatum subsp. vincentii ChDC F8 (KCOM 1231) was
AB  - isolated from a human gingivitis lesion. Here, we report the draft genome
AB  - sequence of the strain.
ER  -

TY  - JOUR
AU  - Park, S.N.
AU  - Cho, E.
AU  - Lim, Y.K.
AU  - Kim, H.S.
AU  - Kim, D.S.
AU  - Jung, J.
AU  - Baek, J.H.
AU  - Jo, E.
AU  - Chang, Y.H.
AU  - Shin, J.H.
AU  - Choi, S.H.
AU  - Kang, J.
AU  - Choi, Y.
AU  - Park, H.S.
AU  - Kim, H.
AU  - Kook, J.K.
TI  - Draft Genome Sequences of Fusobacterium nucleatum ChDC F145, ChDC F174, ChDC F206, and ChDC F300, Isolated from Human Subgingival Plaques in the Republic of  Korea.
JO  - Genome Announcements
PY  - 2014
SP  - e01233
EP  - e01213
VL  - 2
AB  - Recently, five strains were isolated from human subgingival plaques and were proposed as a
AB  - novel subspecies of Fusobacterium nucleatum. Here, we report the
AB  - draft genome sequences of the strains, except one for which the draft sequence
AB  - was already introduced.
ER  -

TY  - JOUR
AU  - Park, S.N.
AU  - Kong, S.W.
AU  - Kim, H.S.
AU  - Park, M.S.
AU  - Lee, J.W.
AU  - Cho, E.
AU  - Lim, Y.K.
AU  - Choi, M.H.
AU  - Chang, Y.H.
AU  - Shin, J.H.
AU  - Park, H.S.
AU  - Choi, S.H.
AU  - Kook, J.K.
TI  - Draft Genome Sequence of Fusobacterium nucleatum ChDC F128, Isolated from a Periodontitis Lesion.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6322
EP  - 6323
VL  - 194
AB  - Fusobacterium nucleatum is classified into five subspecies. F. nucleatum ChDC F128 was
AB  - isolated from a periodontitis lesion and proposed as a new subspecies
AB  - based on the comparison of the nucleotide sequences of the RNA polymerase beta
AB  - subunit and zinc protease genes. Here, we report the draft genome sequence of the
AB  - strain.
ER  -

TY  - JOUR
AU  - Park, S.N.
AU  - Kong, S.W.
AU  - Park, M.S.
AU  - Lee, J.W.
AU  - Cho, E.
AU  - Lim, Y.K.
AU  - Choi, M.H.
AU  - Kim, H.S.
AU  - Chang, Y.H.
AU  - Shin, J.H.
AU  - Park, H.S.
AU  - Choi, S.H.
AU  - Kook, J.K.
TI  - Draft Genome Sequence of Fusobacterium nucleatum subsp. fusiforme ATCC 51190T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5445
EP  - 5446
VL  - 194
AB  - Fusobacterium nucleatum, one of the major causative bacteria of periodontitis, is classified
AB  - into five subspecies (nucleatum, polymorphum, vincentii, animalis, and
AB  - fusiforme) on the basis of the several phenotypic characteristics and DNA
AB  - homology. This is the first report of the draft genome sequence of F. nucleatum
AB  - subsp. fusiforme ATCC 51190(T).
ER  -

TY  - JOUR
AU  - Park, T.H.
AU  - Choi, B.S.
AU  - Choi, A.Y.
AU  - Choi, I.Y.
AU  - Heu, S.
AU  - Park, B.S.
TI  - Genome Sequence of Pectobacterium carotovorum subsp. carotovorum Strain PCC21, a  Pathogen Causing Soft Rot in Chinese Cabbage.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6345
EP  - 6346
VL  - 194
AB  - Pectobacterium carotovorum is a plant-pathogenic enterobacterium responsible for  soft rot in
AB  - various commercially important plants. Here we report the complete
AB  - genome sequence and automatic annotation of strain PCC21.
ER  -

TY  - JOUR
AU  - Park, Y.
AU  - Kim, G.-D.
AU  - Choi, T.-J.
TI  - Molecular cloning and characterization of the DNA adenine methyltransferase gene in Feldmannia sp virus.
JO  - Virus Genes
PY  - 2007
SP  - 177
EP  - 183
VL  - 34
AB  - The genome of Feldmannia sp. virus (FsV), a marine brown alga virus, contains a putative DNA
AB  - adenine methyltransferase (dam) gene of 1,245
AB  - bp that encodes a polypeptide of 45.8 kDa. A BLAST search with the FsV
AB  - dam gene showed high amino acid identity to two putative
AB  - methyltransferase genes, ORF B29 of Feldmannia irregularis virus
AB  - (FirrV, 54%) and ORF129 of Ectocarpus siliculosus virus (EsV, 36%); and
AB  - a PSI BLAST search revealed similarity to the N-6-adenine
AB  - methyltransferases (MTases) of other species. Most conserved motifs of
AB  - beta-class MTases were observed in the FsV dam gene. However, neither
AB  - of the highly conserved sequences in motifs I (FxGxG) or IV
AB  - [(S/N/D)PP(Y/F/W)] perfectly matched those in the FsV dam gene. The
AB  - highly conserved DPPY consensus sequence in motif IV was NTPW in the
AB  - FsV dam gene, perfectly matching the sequences in ORF B29 of FirrV and
AB  - ORF129 of EsV. Therefore, the dam genes in brown algae viruses may
AB  - belong to a yet undiscovered group. The FsV Dam protein expressed from
AB  - the cloned FsV dam gene methylated E. coli chromosomal DNA. This is the
AB  - first report showing that a virus infecting marine filamentous brown
AB  - algae encodes a functional Dam protein.
ER  -

TY  - JOUR
AU  - Park, Y.K.
AU  - Kang, H.
AU  - Yoo, H.
AU  - Lee, S.H.
AU  - Roh, H.
AU  - Kim, H.J.
AU  - Ryoo, S.
TI  - Whole-Genome Sequence of Mycobacterium tuberculosis Korean Strain KIT87190.
JO  - Genome Announcements
PY  - 2014
SP  - e01103
EP  - e01114
VL  - 2
AB  - Mycobacterium tuberculosis is a contagious agent that causes tuberculosis. A specific type
AB  - (called the K cluster) of M. tuberculosis with 10 copies of IS6110
AB  - in restriction fragment length polymorphism (RFLP) has been found in about 4% of
AB  - M. tuberculosis isolates in Korea. Here, we report the complete genome sequence
AB  - of M. tuberculosis Korean strain KIT87190 belonging to the K cluster.
ER  -

TY  - JOUR
AU  - Park, Y.K.
AU  - Lee, K.M.
AU  - Lee, W.K.
AU  - Cho, M.J.
AU  - Lee, H.S.
AU  - Cho, Y.G.
AU  - Lee, Y.C.
AU  - Lee, W.K.
AU  - Seong, W.K.
AU  - Hwang, K.J.
TI  - Dermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2016
SP  - 2573
EP  - 2577
VL  - 66
AB  - A Gram-stain-positive, catalase-positive, facultatively anaerobic, non-motile,
AB  - coryneform bacterium, designated strain 32(T), was isolated from a closed pus
AB  - sample from a patient having finger necrosis in Korea. Strain 32(T) was
AB  - considered as representing a novel species according to its initial
AB  - identification by matrix-assisted laser desorption/ionization-time-of-flight MS.
AB  - Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 32(T)
AB  - belonged to the genus Dermabacter and was closely related to Dermabacter hominis
AB  - DSM 7083(T) (=ATCC 49369(T)) (98.34 % similarity). Optimal growth was observed at
AB  - 30-40 degrees C and pH 7. Growth occurred in the presence of 0-6 % (w/v) NaCl.
AB  - Menaquinones MK-8, MK-7 and MK-9 were the major respiratory quinones. The major
AB  - polar lipids were phosphatidylethanolamine, phosphatidylcholine, glycolipid and
AB  - two unknown lipids. The major cellular fatty acids were anteiso-C17 : 0,
AB  - anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. The DNA G+C content of strain 32(T)
AB  - was 62.58 mol%, and the mean level of DNA-DNA relatedness between strain 32(T)
AB  - and D. hominis ATCC 49369(T) was 49+/-1.6 %. Based on the phenotypic and
AB  - genotypic characteristics, strain 32(T) is confirmed to represent a novel species
AB  - of the genus Dermabacter, for which the name Dermabacter jinjuensis sp. nov. is
AB  - proposed. The type strain is 32(T) (=NCCP 16133(T)=DSM 101003(T)).
ER  -

TY  - JOUR
AU  - Parker, B.
AU  - Marinus, M.G.
TI  - A simple and rapid method to obtain substitution mutations in Escherichia coli:  isolation of a dam deletion/insertion mutation.
JO  - Gene
PY  - 1988
SP  - 531
EP  - 535
VL  - 73
AB  - We describe the isolation of a strain of Escherichia coli bearing a deletion/insertion (i.e.,
AB  - a substitution mutation) in the dam gene (dam-16). The mutagenesis protocol used should be
AB  - applicable to any cloned non-essential gene of E. coli. The substitution mutation confers
AB  - resistance to kanamycin and can easily be transferred to other strains by standard genetic
AB  - techniques. The amount of Dam methyltransferase (MTase) in dam-16 strains as determined either
AB  - in vitro or in vivo is below the level of detection. We conclude that the Dam MTase is not
AB  - required for viability of E. coli.
ER  -

TY  - JOUR
AU  - Parker, C.T.
AU  - Gorski, L.
AU  - Huynh, S.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Thompson  Strain RM6836.
JO  - Genome Announcements
PY  - 2013
SP  - e00900
EP  - e00913
VL  - 1
AB  - Salmonella enterica subsp. enterica serovar Thompson strain RM6836 was isolated from lettuce
AB  - in 2002. We report here the complete sequence and annotation of the
AB  - genome of S. Thompson RM6836. This is the first reported complete genome sequence
AB  - for S. Thompson and it will enhance our understanding of this serovar and provide
AB  - another point for comparative studies between Salmonella enterica strains.
ER  -

TY  - JOUR
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - Gorski, L.
AU  - Cooper, K.K.
AU  - Miller, W.G.
TI  - Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp. enterica Serovar Thompson Associated with Cilantro.
JO  - Genome Announcements
PY  - 2015
SP  - e01365
EP  - e01315
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986
AB  - (CADPH-99A2345) are associated with a 1999 outbreak in
AB  - contaminated cilantro. We report here the complete genome sequences and
AB  - annotation of these two S. Thompson strains. These genomes are distinct and
AB  - provide additional data for our understanding of S. enterica.
ER  -

TY  - JOUR
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - Heikema, A.P.
TI  - Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Penner Serotype Reference Strain RM3420.
JO  - Genome Announcements
PY  - 2017
SP  - e01701
EP  - e01716
VL  - 5
AB  - Campylobacter jejuni subsp. jejuni infections are a leading cause of foodborne gastroenteritis
AB  - and the most prevalent antecedent to Guillain-Barre syndrome
AB  - (GBS). Penner serotype HS:19 is among several capsular types shown to be markers
AB  - for GBS. This study describes the genome of C. jejuni subsp. jejuni HS:19 Penner
AB  - reference strain RM3420.
ER  -

TY  - JOUR
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - Heikema, A.P.
TI  - Complete Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Strain RM1285 Isolated from Packaged Chicken.
JO  - Genome Announcements
PY  - 2016
SP  - e01100
EP  - e01116
VL  - 4
AB  - Poultry products serve as the main source of Campylobacter jejuni subsp. jejuni infections in
AB  - humans. C. jejuni subsp. jejuni infections are a leading cause of
AB  - foodborne gastroenteritis and are a prevalent antecedent to Guillain-Barre
AB  - syndrome. This study describes the genome of C. jejuni subsp. jejuni HS:19 strain
AB  - RM1285, isolated from packaged chicken in California.
ER  -

TY  - JOUR
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - Heikema, A.P.
AU  - Cooper, K.K.
AU  - Miller, W.G.
TI  - Complete Genome Sequences of Campylobacter jejuni Strains RM3196 (233.94) and RM3197 (308.95) Isolated from Patients with Guillain-Barre Syndrome.
JO  - Genome Announcements
PY  - 2015
SP  - e01312
EP  - e01315
VL  - 3
AB  - Infections with Campylobacter jejuni subsp. jejuni are a leading cause of foodborne
AB  - gastroenteritis and the most prevalent infection preceding
AB  - Guillain-Barre syndrome (GBS). This study describes the genomes of C. jejuni
AB  - subsp. jejuni HS:41 strains RM3196 (233.94) and RM3197 (308.95) that were
AB  - isolated from patients with GBS in Cape Town, South Africa.
ER  -

TY  - JOUR
AU  - Parker, D.
AU  - Narechania, A.
AU  - Sebra, R.
AU  - Deikus, G.
AU  - Larussa, S.
AU  - Ryan, C.
AU  - Smith, H.
AU  - Prince, A.
AU  - Mathema, B.
AU  - Ratner, A.J.
AU  - Kreiswirth, B.
AU  - Planet, P.J.
TI  - Genome Sequence of Bacterial Interference Strain Staphylococcus aureus 502A.
JO  - Genome Announcements
PY  - 2014
SP  - e00284
EP  - e00214
VL  - 2
AB  - Staphylococcus aureus 502A was a strain used in bacterial interference programs
AB  - during the 1960s and early 1970s. Infants were deliberately colonized with 502A
AB  - with the goal of preventing colonization with more invasive strains. We present
AB  - the completed genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Parker, M.M.
AU  - Belisle, M.
AU  - Belfort, M.
TI  - Intron homing with limited exon homology. Illegitimate double-strand-break repair in intron acquisition by phage t4.
JO  - Genetics
PY  - 1999
SP  - 1513
EP  - 1523
VL  - 153
AB  - The td intron of bacteriophage T4 encodes a DNA endonuclease that initiates intron homing to
AB  - cognate intronless alleles by a double-strand-break (DSB) repair process. A genetic assay was
AB  - developed to analyze the relationship between exon homology and homing efficiency. Because
AB  - models predict exonucleolytic processing of the cleaved recipient leading to homologous strand
AB  - invasion of the donor allele, the assay was performed in wild-type and exonuclease-deficient
AB  - (rnh or dexA) phage. Efficient homing was supported by exon lengths of 50 bp or greater,
AB  - whereas more limited exon lengths led to a precipitous decline in homing levels. However,
AB  - extensive homology in one exon still supported elevated homing levels when the other exon was
AB  - completely absent. Analysis of these "one-sided" events revealed recombination junctions at
AB  - ectopic sites of microhomology and implicated nucleolytic degradation in illegitimate DSB
AB  - repair in T4. Interestingly, homing efficiency with extremely limiting exon homology was
AB  - greatly elevated in phage deficient in the 3'-5' exonuclease, DexA, suggesting that the
AB  - length of 3' tails is a major determinant of the efficiency of DSB repair. Together, these
AB  - results suggest that illegitimate DSB repair may provide a means by which introns can invade
AB  - ectopic sites.
ER  -

TY  - JOUR
AU  - Parkhill, J. et al.
TI  - The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.
JO  - Nature
PY  - 2000
SP  - 665
EP  - 668
VL  - 403
AB  - Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic,
AB  - Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric
AB  - pathogen Helicobacter pylori.  It is the leading cause of bacterial food-borne diarrhoeal
AB  - disease throughout the world.  In addition, infection with C. jejuni is the most frequent
AB  - antecedent to a form of neuromuscular paralysis known as Guillain-Barre syndrome.  Here we
AB  - report the genome sequence of C. jejuni NCTC11168.  C. jejuni has a circular chromosome of
AB  - 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA
AB  - species.  The genome is unusual in that there are virtually no insertion sequences or
AB  - phage-associated sequences and very few repeat sequences.  One of the most striking findings
AB  - in the genome was the presence of hypervariable sequences.  These short homopolymeric runs of
AB  - nucleotides were commonly found in genes encoding the biosynthesis or modification of surface
AB  - structures, or in closely linked genes of unknown function.  The apparently high rate of
AB  - variation of these homopolymeric tracts may be important in the survival strategy of C.
AB  - jejuni.
ER  -

TY  - JOUR
AU  - Parkhill, J. et al.
TI  - Genome sequence of Yersinia pestis, the causative agent of plague.
JO  - Nature
PY  - 2001
SP  - 523
EP  - 527
VL  - 413
AB  - The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive
AB  - infectious disease classically referred to as plague, and has been responsible for three human
AB  - pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to
AB  - nineteenth centuries) and modern plague (nineteenth century to the present day). The recent
AB  - identification of strains resistant to multiple drugs and the potential use of Y. pestis as an
AB  - agent of biological warfare mean that plague still poses a threat to human health. Here we
AB  - report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase
AB  - (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is
AB  - unusually rich in insertion sequences and displays anomalies in GC base-composition bias,
AB  - indicating frequent intragenomic recombination. Many genes seem to have been acquired from
AB  - other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins).
AB  - The genome contains around 150 pseudogenes, many of which are remnants of a redundant
AB  - enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay
AB  - suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a
AB  - unique insight into the ways in which new and highly virulent pathogens evolve.
ER  -

TY  - JOUR
AU  - Parkhill, J. et al.
TI  - Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.
JO  - Nature
PY  - 2000
SP  - 502
EP  - 506
VL  - 404
AB  - Neisseria meningitidis causes bacterial meningitis and is therefore responsible for
AB  - considerable morbidity and mortality in both the developed and the developing world.
AB  - Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of
AB  - asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain
AB  - access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and
AB  - meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of
AB  - the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for
AB  - major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity
AB  - and mortality associated with this disease. Here we have determined the complete genome
AB  - sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406
AB  - base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted
AB  - coding sequences. The most notable feature of the genome is the presence of many hundreds of
AB  - repetitive elements, ranging from short repeats, positioned either singly or in large multiple
AB  - arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these
AB  - repeats appear to be involved in genome fluidity and antigenic variation in this important
AB  - human pathogen.
ER  -

TY  - JOUR
AU  - Parkhill, J. et al.
TI  - Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
JO  - Nature
PY  - 2001
SP  - 848
EP  - 852
VL  - 413
AB  - Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a
AB  - serious invasive bacterial disease of humans with an annual global burden of approximately 16
AB  - million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the
AB  - mucosal surface of the intestine but are normally contained in healthy individuals by the
AB  - local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the
AB  - deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the
AB  - 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs,
AB  - revealing the presence of hundreds of insertions and deletions compared with the Escherichia
AB  - coli genome, ranging in size from single genes to large islands. Notably, the genome sequence
AB  - identifies over two hundred pseudogenes, several corresponding to genes that are known to
AB  - contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to
AB  - the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp
AB  - multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2),
AB  - which shows recent common ancestry with a virulence plasmid of Yersinia pestis.
ER  -

TY  - JOUR
AU  - Parmeciano, Di.N.G.
AU  - Vazquez, S.C.
AU  - MacCormack, W.P.
AU  - Iriarte, A.
AU  - Quiroga, C.
TI  - Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica.
JO  - Genome Announcements
PY  - 2016
SP  - e00289
EP  - e00216
VL  - 4
AB  - We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King
AB  - George Island, Antarctica, which encodes the carbapenemase
AB  - SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain
AB  - harbors several mobile genetic elements that provide insight into lateral gene
AB  - transfer and bacterial plasticity and evolution.
ER  -

TY  - JOUR
AU  - Parraga, A.
AU  - Portugal, J.
TI  - Detection of elsamicin-DNA binding specificity by restriction enzyme cleavage.
JO  - FEBS Lett.
PY  - 1992
SP  - 25
EP  - 29
VL  - 300
AB  - The sequence specificity of elsamicin A, an anti-tumour antibotic, binding to
AB  - DNA was elucidated considering the inhibition of the rate of digestion of
AB  - linearised pBR322 DNA by AatII, ClaI, EcoRI, HindIII and NruI restriction
AB  - enzymes.  Elsamicin A inhibits the rate of digestion by NruI (recognition
AB  - sequence TCG/CGA) to a greater extent than it does for the other enzymes, thus
AB  - evidencing the sequence-selective binding of elsamicin to CGC regions in DNA.
AB  - Our results also show the important role of the neighbouring sequences in the
AB  - elsamicin A-DNA interactions and their effects on the cleavage by restriction
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Parreira, V.R.
AU  - Costa, M.
AU  - Eikmeyer, F.
AU  - Blom, J.
AU  - Prescott, J.F.
TI  - Sequence of Two Plasmids from Clostridium perfringens Chicken Necrotic Enteritis Isolates and Comparison with C. perfringens Conjugative Plasmids.
JO  - PLoS ONE
PY  - 2012
SP  - E49753
EP  - E49753
VL  - 7
AB  - Twenty-six isolates of Clostridium perfringens of different MLST types from
AB  - chickens with necrotic enteritis (NE) (15 netB-positive) or from healthy chickens
AB  - (6 netB-positive, 5 netB-negative) were found to contain 1-4 large plasmids, with
AB  - most netB-positive isolates containing 3 large and variably sized plasmids which
AB  - were more numerous and larger than plasmids in netB-negative isolates. NetB and
AB  - cpb2 were found on different plasmids consistent with previous studies. The
AB  - pathogenicity locus NELoc1, which includes netB, was largely conserved in these
AB  - plasmids whereas NeLoc3, present in the cpb2 containing plasmids, was less well
AB  - conserved. A netB-positive and a cpb2-positive plasmid were likely to be
AB  - conjugative, and the plasmids were completely sequenced. Both plasmids possessed
AB  - the intact tcp conjugative region characteristic of C. perfringens conjugative
AB  - plasmids. Comparative genomic analysis of nine CpCPs, including the two plasmids
AB  - described here, showed extensive gene rearrangements including pathogenicity
AB  - locus and accessory gene insertions around rather than within the backbone
AB  - region. The pattern that emerges from this analysis is that the major
AB  - toxin-containing regions of the variety of virulence-associated CpCPs are
AB  - organized as complex pathogenicity loci. How these different but related CpCPs
AB  - can co-exist in the same host has been an unanswered question. Analysis of the
AB  - replication-partition region of these plasmids suggests that this region controls
AB  - plasmid incompatibility, and that CpCPs can be grouped into at least four
AB  - incompatibility groups.
ER  -

TY  - JOUR
AU  - Parro, V.
AU  - Moreno-Paz, M.
AU  - Gonzalez-Toril, E.
TI  - Analysis of environmental transcriptomes by DNA microarrays.
JO  - Environ. Microbiol.
PY  - 2007
SP  - 453
EP  - 464
VL  - 9
AB  - In this work we investigated the correlations between global gene expression patterns and
AB  - environmental parameters in natural ecosystems. We
AB  - studied the preferential gene expression of the iron oxidizer bacterium
AB  - Leptospirillum ferrooxidans to adapt its physiology to changes in the
AB  - physicochemical parameters in its natural medium. Transcriptome analysis
AB  - by DNA microarrays can proportionate an instant picture about the
AB  - preferential gene expression between two different environmental samples.
AB  - However, this type of analysis is very difficult and complex in natural
AB  - ecosystems, mainly because of the broad biodiversity and multiple
AB  - environmental parameters that may affect gene expression. The necessity of
AB  - high-quality RNA preparations as well as complicated data analysis are
AB  - also technological limitations. The low prokaryotic diversity of the
AB  - extremely acidic and iron-rich waters of the Tinto River (Spain)
AB  - ecosystem, where L. ferrooxidans is abundant, allows the opportunity to
AB  - achieve global gene expression studies and to associate gene function with
AB  - environmental parameters. We applied a total RNA amplification protocol
AB  - validated previously for the amplification of the environmental
AB  - transcriptome (meta-transcriptome). The meta-transcriptome of two sites
AB  - from the Tinto River mainly differing in the salt and oxygen contents were
AB  - amplified and analysed by a L. ferrooxidans DNA microarray. The results
AB  - showed a clear preferential induction of genes involved in certain
AB  - physicochemical parameters like: high salinity (ectAB, otsAB), low oxygen
AB  - concentration (cydAB), iron uptake (fecA-exbBD-tonB), oxidative stress
AB  - (carotenoid synthesis, oxyR, recG), potassium (kdpBAC) or phosphate
AB  - concentrations (pstSCAB), etc. We conclude that specific gene expression
AB  - patterns can be useful indicators for the physiological conditions in a
AB  - defined ecosystem. Also, the upregulation of certain genes and operons
AB  - reveals information about the environmental conditions (nutrient
AB  - limitations, stresses, etc.).
ER  -

TY  - JOUR
AU  - Parry, D.
AU  - Moon, S.A.
AU  - Liu, H.H.
AU  - Heslop, P.
AU  - Connolly, B.A.
TI  - DNA Recognition by the EcoRV Restriction Endonuclease Probed using Base Analogues.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 1005
EP  - 1016
VL  - 331
AB  - The EcoRV restriction endonuclease recognises palindromic GATATC sequences and cuts between
AB  - the central T and dA bases in a reaction that has an
AB  - absolute requirement for a divalent metal ion, physiologically Mg(2+). Use
AB  - has been made of base analogues, which delete hydrogen bonds between the
AB  - protein and DNA (or hydrophobic interactions in the case of the 5-CH(3)
AB  - group of thymine), to evaluate the roles of the outer two base-pairs
AB  - (GATATC) in DNA recognition. Selectivity arises at both the binding steps
AB  - leading to the formation of the enzyme-DNA-metal ion ternary complex
AB  - (assayed by measuring the dissociation constant in the presence of the
AB  - non-reactive metal Ca(2+)) and the catalytic step (evaluated using
AB  - single-turnover hydrolysis in the presence of Mg(2+)), with each
AB  - protein-DNA contact contributing to recognition. With the A:T base-pair,
AB  - binding was reduced by the amount expected for the simple loss of a single
AB  - contact; much more severe effects were observed with the G:C base-pair,
AB  - suggesting additional conformational perturbation. Most of the modified
AB  - bases lowered the rate of hydrolysis; furthermore, the presence of an
AB  - analogue in one strand of the duplex diminished cutting at the second,
AB  - unmodified strand, indicative of communication between DNA binding and the
AB  - active site. The essential metal ion Mg(2+) plays a key role in mediating
AB  - interactions between the DNA binding site and active centre and in many
AB  - instances rescue of hydrolysis was seen with Mn(2+). It is suggested that
AB  - contacts between the GATATC site are required for tight binding and for
AB  - the correct assembly of metal ions and bound water at the catalytic site,
AB  - functions important in providing acid/base catalysis and transition state
AB  - stabilisation.
ER  -

TY  - JOUR
AU  - Parsa, Y.L.
AU  - Azarbaijani, R.
AU  - Sarikhan, S.
AU  - Mousavi, H.
AU  - Ramezani, M.
AU  - Amoozegar, M.A.
AU  - Shahzadeh, F.A.
AU  - Salekdeh, G.H.
TI  - Complete Genome Sequence of Oceanimonas sp. GK1, a Halotolerant Bacterium from Gavkhouni Wetland in Iran.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2123
EP  - 2124
VL  - 194
AB  - Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium  which was
AB  - characterized as producing large amounts of poly-beta-hydroxybutyrate.
AB  - Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists
AB  - of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245
AB  - bp in length.
ER  -

TY  - JOUR
AU  - Parschat, K.
AU  - Hauer, B.
AU  - Kappl, R.
AU  - Kraft, R.
AU  - Huttermann, J.
AU  - Fetzner, S.
TI  - Gene cluster of Arthrobacter ilicis Ru61a involved in the degradation of quinaldine to anthranilate: characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 27483
EP  - 27494
VL  - 278
AB  - A genetic analysis of the anthranilate pathway of quinaldine degradation was
AB  - performed. A 23-kb region of DNA from Arthrobacter ilicis Ru61a was cloned into
AB  - the cosmid pVK100. Although Escherichia coli clones containing the recombinant
AB  - cosmid did not transform quinaldine, cosmids harboring the 23-kb region, or a
AB  - 10.8-kb stretch of this region, conferred to Pseudomonas putida KT2440 the
AB  - ability to cometabolically convert quinaldine to anthranilate. The 10.8-kb
AB  - fragment thus contains the genes coding for quinaldine 4-oxidase (Qox),
AB  - 1H-4-oxoquinaldine 3-monooxygenase, 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase,
AB  - and N-acetylanthranilate amidase. The qoxLMS genes coding for the molybdopterin
AB  - cytosine dinucleotide-(MCD-), FeSI-, FeSII-, and FAD-containing Qox were inserted
AB  - into the expression vector pJB653, generating pKP1. Qox is the first
AB  - MCD-containing enzyme to be synthesized in a catalytically fully competent form
AB  - by a heterologous host, P. putida KT2440 pKP1; the catalytic properties and the
AB  - UV-visible and EPR spectra of Qox purified from P. putida KT2440 pKP1 were
AB  - essentially like those of wild-type Qox. This provides a starting point for the
AB  - construction of protein variants of Qox by site-directed mutagenesis. Downstream
AB  - of the qoxLMS genes, a putative gene whose deduced amino acid sequence showed 37%
AB  - similarity to the cofactor-inserting chaperone XdhC was located. Additional open
AB  - reading frames identified on the 23-kb segment may encode further enzymes (a
AB  - glutamyl tRNA synthetase, an esterase, two short-chain dehydrogenases/reductases,
AB  - an ATPase belonging to the AAA family, a 2-hydroxyhepta-2,4-diene-1,7-dioate
AB  - isomerase/5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase-like protein, and an
AB  - enzyme of the mandelate racemase group) and hypothetical proteins involved in
AB  - transcriptional regulation, and metabolite transport.
ER  -

TY  - JOUR
AU  - Parschat, K.
AU  - Overhage, J.
AU  - Strittmatter, A.W.
AU  - Henne, A.
AU  - Gottschalk, G.
AU  - Fetzner, S.
TI  - Complete Nucleotide Sequence of the 113-Kilobase Linear Catabolic Plasmid pAL1 of Arthrobacter nitroguajacolicus Ru61a and Transcriptional Analysis of Genes Involved in Quinaldine Degradation.
JO  - J. Bacteriol.
PY  - 2007
SP  - 3855
EP  - 3867
VL  - 189
AB  - The nucleotide sequence of the linear catabolic plasmid pAL1 from the 2-methylquinoline
AB  - (quinaldine)-degrading strain Arthrobacter nitroguajacolicus Ru61a comprises 112,992 bp. A
AB  - total of 103 open reading frames (ORFs) were identified on pAL1, 49 of which had no
AB  - annotatable function. The ORFs were assigned to the following functional groups: (i)
AB  - catabolism of quinaldine and anthranilate, (ii) conjugation, and (iii) plasmid maintenance and
AB  - DNA replication and repair. The genes for conversion of quinaldine to anthranilate are
AB  - organized in two operons that include ORFs presumed to code for proteins involved in assembly
AB  - of the quinaldine-4-oxidase holoenzyme, namely, a MobA-like putative molybdopterin cytosine
AB  - dinucleotide synthase and an XdhC-like protein that could be required for insertion of the
AB  - molybdenum cofactor. Genes possibly coding for enzymes involved in anthranilate degradation
AB  - via 2-aminobenzoyl coenzyme A form another operon. These operons were expressed when cells
AB  - were grown on quinaldine or on aromatic compounds downstream in the catabolic pathway.
AB  - Single-stranded 3' overhangs of putative replication intermediates of pAL1 were predicted to
AB  - form elaborate secondary structures due to palindromic and superpalindromic terminal
AB  - sequences; however, the two telomeres appear to form different structures. Sequence analysis
AB  - of ORFs 101 to 103 suggested that pAL1 codes for one or two putative terminal proteins,
AB  - presumed to be covalently bound to the 5' termini, and a multidomain telomere-associated
AB  - protein (Tap) comprising 1,707 amino acids. Even if the putative proteins encoded by ORFs 101
AB  - to 103 share motifs with the Tap and terminal proteins involved in telomere patching of
AB  - Streptomyces linear replicons, their overall sequences and domain structures differ
AB  - significantly.
ER  -

TY  - JOUR
AU  - Parthasarathy, S.
AU  - Azam, S.
AU  - Lakshman-Sagar, A.
AU  - Narasimha-Rao, V.
AU  - Gudla, R.
AU  - Parapatla, H.
AU  - Yakkala, H.
AU  - Ghanta-Vemuri, S.
AU  - Siddavattam, D.
TI  - Genome-Guided Insights Reveal Organophosphate-Degrading Brevundimonas diminuta as Sphingopyxis wildii and Define Its Versatile Metabolic Capabilities and Environmental Adaptations.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 77
EP  - 81
VL  - 9
AB  - The complete genome sequence of Brevundimonas diminuta represented a chromosome (
AB  - approximately 4.15 Mb) and two plasmids (pCMS1 and pCMS2) with sizes of 65,908
AB  - and 30,654 bp, respectively. The sequence of the genome showed no significant
AB  - similarity with the known bacterial genome sequences, instead showed weak
AB  - similarity with the members of different genera of family, Sphingomonadaceae.
AB  - Contradicting existing taxonomic position, the core genome-guided phylogenetic
AB  - tree placed B. diminuta in the genus Sphingopyxis and showed sufficient
AB  - genome-to-genome distance warranting a new species name. Reflecting the strains
AB  - ability to grow in harsh environments, the genome-contained genetic repertoire
AB  - required for mineralization of several recalcitrant man-made aromatic compounds.
ER  -

TY  - JOUR
AU  - Partridge, S.R.
AU  - Ginn, A.N.
AU  - Paulsen, I.T.
AU  - Iredell, J.R.
TI  - pEl1573 carrying blaIMP-4 from Sydney, Australia, is closely related to other IncL/M plasmids.
JO  - Antimicrob. Agents Chemother.
PY  - 2012
SP  - 6029
EP  - 6032
VL  - 56
AB  - Complete sequencing of pEl1573, a representative IncL/M plasmid carrying blaIMP-4 from Sydney,
AB  - Australia, revealed a ~60 kb backbone almost identical to those of IncL/M plasmids
AB  - pCTX-M3,from Poland, and pCTX-M360, from China, and less closely related to pNDM-HK, pOXA-48a
AB  - and pEL60, suggesting different lineages. The ~28 kb Tn2-derived multiresistance region in
AB  - pEl1573 is inserted in the same location as those in pCTX-M3 and pNDM-HK and shares some of
AB  - the same components, but has undergone rearrangements.
ER  -

TY  - JOUR
AU  - Partridge, S.R.
AU  - Zong, Z.
AU  - Iredell, J.R.
TI  - Recombination in IS26 and Tn2 in the Evolution of Multiresistance Regions Carrying blaCTX-M-15 on Conjugative IncF Plasmids from Escherichia coli.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 4971
EP  - 4978
VL  - 55
AB  - CTX-M-15 now appears to be the dominant extended-spectrum beta-lactamase
AB  - worldwide, and a number of different factors may contribute to this
AB  - success. These include associations between bla(CTX-M-15) and particular
AB  - plasmids (IncF) and/or strains, such as Escherichia coli ST131, as well as
AB  - the genetic contexts in which this gene is found. We previously identified
AB  - bla(CTX-M-15) as the dominant ESBL gene in the western Sydney area,
AB  - Australia, and found that it was carried mainly on IncF or IncI1 plasmids.
AB  - Here, we have mapped the multiresistance regions of the 11 conjugative
AB  - plasmids with one or more IncF replicons obtained from that survey and
AB  - conducted a limited comparison of plasmid backbones. Two plasmids with
AB  - only an IncFII replicon appear to be very similar to the published
AB  - plasmids pC15-1a and pEK516. The remaining nine plasmids, with multiple
AB  - IncF replicons, have multiresistance regions related to those of pC15-1a
AB  - and pEK516, but eight contain additional modules previously found in
AB  - resistance plasmids from different geographic locations that carry a
AB  - variety of different resistance genes. Differences between the
AB  - multiresistance regions are largely due to IS26-mediated deletions,
AB  - insertions, and/or rearrangements, which can explain the observed variable
AB  - associations between bla(CTX-M-15) and certain other resistance genes. We
AB  - found no evidence of independent movement of bla(CTX-M-15) or of a large
AB  - multiresistance region between different plasmid backbones. Instead,
AB  - homologous recombination between common components, such as IS26 and Tn2,
AB  - appeared to be more important in creating new multiresistance regions, and
AB  - this may be coupled with recombination in plasmid backbones to reassort
AB  - multiple IncF replicons as well as components of multiresistance regions.
ER  -

TY  - JOUR
AU  - Parvataneni, S.
AU  - Mijalis, E.M.
AU  - Kuty, E.G.F.
AU  - Rasche, E.S.
AU  - Liu, M.
AU  - Gill, J.J.
TI  - Complete Genome Sequence of Citrobacter freundii Myophage Mijalis.
JO  - Genome Announcements
PY  - 2017
SP  - e00228
EP  - e00217
VL  - 5
AB  - Citrobacter freundii is responsible for various opportunistic nosocomial infections. Phage
AB  - therapies against C. freundii may prove useful in human
AB  - medicine for treatment of infections caused by the ubiquitous bacteria. Here, we
AB  - announce the complete genome sequence of the C. freundii Felix O1-like myophage
AB  - Mijalis and present its features.
ER  -

TY  - JOUR
AU  - Pascopella, L.
AU  - Raupach, B.
AU  - Ghori, N.
AU  - Monack, D.
AU  - Falkow, S.
AU  - Small, P.L.C.
TI  - Host restriction phenotypes of Salmonella typhi and Salmonella gallinarum.
JO  - Infect. Immun.
PY  - 1995
SP  - 4329
EP  - 4335
VL  - 63
AB  - Salmonella typhi and Salmonella gallinarum phenotypes correlated with mouse host restriction
AB  - have been identified by using in vitro and in vivo systems. S. typhi is capable of entering
AB  - the murine intestinal epithelium via M cells, as is Salmonella typhimurium, which causes
AB  - systemic infection in the mouse.  But, unlike S. typhimurium, S. typhi does not destroy the
AB  - epithelium and is cleared from the Peyer's patches soon after M-cell entry, S. gallinarum
AB  - appears to be incapable of entering the murine Peyer's patch epithelium.  Our in vitro
AB  - evidence suggests that S. gallinarum is taken up in murine phagocytic cells by a mechanism
AB  - different from that of S. typhimurium.  S. typhimurium is taken up at a higher frequency and
AB  - is maintained at higher viable counts throughout a 24-h time course in a murine
AB  - macrophage-like cell line than are S. gallinarum and S. typhi.
ER  -

TY  - JOUR
AU  - Pascual, J.
AU  - Udaondo, Z.
AU  - Molina, L.
AU  - Segura, A.
AU  - Esteve-Nunez, A.
AU  - Caballero, A.
AU  - Duque, E.
AU  - Ramos, J.L.
AU  - van Dillewijn, P.
TI  - Draft Genome Sequence of Pseudomonas putida JLR11, a Facultative Anaerobic 2,4,6-Trinitrotoluene Biotransforming Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00904
EP  - e00915
VL  - 3
AB  - We report the draft genome sequence of Pseudomonas putida JLR11, a facultative anaerobic
AB  - bacterium that has been studied in detail for its capacity to use the explosive
AB  - 2,4,6-trinitrotoluene (TNT) as a nitrogen source. The sequence confirms the mechanisms used by
AB  - this versatile strain to reduce and assimilate nitrogen from TNT.
ER  -

TY  - JOUR
AU  - Pashenkov, A.L.
AU  - Nikolskaya, I.I.
AU  - Nigmatullin, T.G.
AU  - Debov, S.S.
TI  - Search for DNA host specificity system in Salmonella typhi.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1985
SP  - 3
EP  - 6
VL  - 4
AB  - Seventeen pure lines of S. typhi bacteriophages have been obtained from mother races O and Vi;
AB  - of these, three were used to study 152 S. typhi strains with a view to detecting their DNA
AB  - host specificity systems.  10 S. typhi strains having the DNA host specificity system have
AB  - been detected by the rough determination of the lytic spectrum and the cross titration of
AB  - phage Vi IX.
ER  -

TY  - JOUR
AU  - Pashkova, T.M.
AU  - Vasilchenko, A.S.
AU  - Khlopko, Y.A.
AU  - Kochkina, E.E.
AU  - Kartashova, O.L.
AU  - Sycheva, M.V.
TI  - Genome Sequence of Enterococcus faecium Strain ICIS 96 Demonstrating Intermicrobial Antagonism Associated with Bacteriocin Production.
JO  - Genome Announcements
PY  - 2018
SP  - e00126
EP  - e00118
VL  - 6
AB  - We report here the complete genome sequence of Enterococcus faecium strain ICIS 96, which was
AB  - isolated from the feces of a horse. Bacteriological
AB  - characterization of strain ICIS 96 revealed the absence of pathogenicity factors,
AB  - while its spectrum of antagonistic activity was found to be broad, having
AB  - activities associated with both Gram-positive and Gram-negative bacteria.
AB  - Analysis of the E. faecium ICIS 96 genome revealed five genes associated with
AB  - antimicrobial activity (enterocin [ent] A, ent B, lactobin A/cerein 7b, and ent
AB  - L50 A/B). No genes that correlate with human pathogenicity were identified.
ER  -

TY  - JOUR
AU  - Passerini, D.
AU  - Vuillemin, M.
AU  - Laguerre, S.
AU  - Amari, M.
AU  - Loux, V.
AU  - Gabriel, V.
AU  - Robert, H.
AU  - Morel, S.
AU  - Monsan, P.
AU  - Gabriel, B.
AU  - Fontagne-Faucher, C.
AU  - Remaud-Simeon, M.
AU  - Moulis, C.
TI  - Complete Genome Sequence of Leuconostoc citreum Strain NRRL B-742.
JO  - Genome Announcements
PY  - 2014
SP  - e01179
EP  - e01114
VL  - 2
AB  - Leuconostoc citreum belongs to the group of lactic acid bacteria and plays an important role
AB  - in fermented foods of plant origin. Here, we report the complete
AB  - genome of the Leuconostoc citreum strain NRRL B-742, isolated in 1954 for its
AB  - capacity to produce dextran.
ER  -

TY  - JOUR
AU  - Passos-da-Silva, D.
AU  - Devescovi, G.
AU  - Paszkiewicz, K.
AU  - Moretti, C.
AU  - Buonaurio, R.
AU  - Studholme, D.J.
AU  - Venturi, V.
TI  - Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.
JO  - Genome Announcements
PY  - 2013
SP  - e00205
EP  - e00213
VL  - 1
AB  - Erwinia toletana was first reported in 2004 as a bacterial species isolated from  olive knots
AB  - caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi.
AB  - Recent studies have shown that the presence of this bacterium in the olive knot
AB  - environment increases the virulence of the disease, indicating possible
AB  - interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft
AB  - genome sequence of an E. toletana strain.
ER  -

TY  - JOUR
AU  - Pasternak, Z.
AU  - Pietrokovski, S.
AU  - Rotem, O.
AU  - Gophna, U.
AU  - Lurie-Weinberger, M.N.
AU  - Jurkevitch, E.
TI  - By their genes ye shall know them: genomic signatures of predatory bacteria.
JO  - ISME J.
PY  - 2013
SP  - 756
EP  - 769
VL  - 7
AB  - Predatory bacteria are taxonomically disparate, exhibit diverse predatory
AB  - strategies and are widely distributed in varied environments. To date, their
AB  - predatory phenotypes cannot be discerned in genome sequence data thereby limiting
AB  - our understanding of bacterial predation, and of its impact in nature. Here, we
AB  - define the 'predatome,' that is, sets of protein families that reflect the
AB  - phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory
AB  - bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria
AB  - from across the phylogenetic and ecological landscapes were compared. Protein
AB  - families discriminating between the two groups were identified and quantified,
AB  - demonstrating that differences in the proteomes of predatory and non-predatory
AB  - bacteria are large and significant. This analysis allows predictions to be made,
AB  - as we show by confirming from genome data an over-looked bacterial predator. The
AB  - predatome exhibits deficiencies in riboflavin and amino acids biosynthesis,
AB  - suggesting that predators obtain them from their prey. In contrast, these genomes
AB  - are highly enriched in adhesins, proteases and particular metabolic proteins,
AB  - used for binding to, processing and consuming prey, respectively. Strikingly,
AB  - predators and non-predators differ in isoprenoid biosynthesis: predators use the
AB  - mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP
AB  - pathway. By defining predatory signatures in bacterial genomes, the predatory
AB  - potential they encode can be uncovered, filling an essential gap for measuring
AB  - bacterial predation in nature. Moreover, we suggest that full-genome proteomic
AB  - comparisons are applicable to other ecological interactions between microbes, and
AB  - provide a convenient and rational tool for the functional classification of
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Patel, B.K.
TI  - Draft Genome Sequence of Fervidicella metallireducens Strain AeBT, an Iron-Reducing Thermoanaerobe from the Great Artesian Basin.
JO  - Genome Announcements
PY  - 2014
SP  - e00345
EP  - e00314
VL  - 2
AB  - The genome sequence of Fervidicella metallireducens strain AeB(T), a curved, heterotrophic,
AB  - thermoanaerobic, and iron-reducing bacterium isolated from a gray
AB  - microbial mat colonizing the free-flowing waters of a Great Artesian Basin (GAB)
AB  - bore well located in outback Queensland, Australia, is reported here. The
AB  - analysis of the 2.9-Mb sequence indicates that the attributes of the genome are
AB  - consistent with its physiological and phenotypic traits.
ER  -

TY  - JOUR
AU  - Patel, B.K.
TI  - Draft Genome Sequence of Anoxybacillus Strain BCO1, Isolated from a Thermophilic  Microbial Mat Colonizing the Outflow of a Bore Well of the Great Artesian Basin  of Australia.
JO  - Genome Announcements
PY  - 2015
SP  - e01547
EP  - e01514
VL  - 3
AB  - Anoxybacillus strain BCO1, isolated from a thermophilic (50 degrees C) microbial  mat
AB  - colonizing an outflow of a Great Artesian bore well of Australia, possessed a
AB  - genome of ~2.8 Mb, with a G+C content of 41.7 mol%, and encoded 3,205 genes.
ER  -

TY  - JOUR
AU  - Patel, B.K.
AU  - Te'o, V.S.
TI  - Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin.
JO  - Genome Announcements
PY  - 2016
SP  - e01578
EP  - e01515
VL  - 4
AB  - The genome sequence of Caloramator mitchellensis strain VF08, a rod-shaped, heterotrophic,
AB  - strictly anaerobic bacterium isolated from the free-flowing waters
AB  - of a Great Artesian Basin (GAB) bore well located in Mitchell, an outback
AB  - Queensland town in Australia, is reported here. The analysis of the 2.42-Mb
AB  - genome sequence indicates that the attributes of the genome are consistent with
AB  - its physiological and phenotypic traits.
ER  -

TY  - JOUR
AU  - Patel, D.J.
TI  - A molecular handshake.
JO  - Nature
PY  - 1994
SP  - 688
EP  - 690
VL  - 367
AB  - Review of the M.HhaI/DNA crystal structure paper.
ER  -

TY  - JOUR
AU  - Patel, H.K.
AU  - Passos-da-Silva, D.
AU  - Devescovi, G.
AU  - Maraite, H.
AU  - Paszkiewicz, K.
AU  - Studholme, D.J.
AU  - Venturi, V.
TI  - Draft Genome Sequence of Pseudomonas fuscovaginae, a Broad-Host-Range Pathogen of Plants.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2765
EP  - 2766
VL  - 194
AB  - Pseudomonas fuscovaginae was first reported as a pathogen of rice causing sheath  rot in
AB  - plants grown at high altitudes. P. fuscovaginae is now considered a
AB  - broad-host-range plant pathogen causing disease in several economically important
AB  - plants. We report what is, to our knowledge, the first draft genome sequence of a
AB  - P. fuscovaginae strain.
ER  -

TY  - JOUR
AU  - Patel, J.
AU  - Firman, K.
TI  - The domain structure of the DNA specificity subunit of type I restriction endonucleases. I. Cloning, mutagenesis and over-production of the EcoR124 DNA methyltransferase.
JO  - Proc. Eur. Meet. Genet. Transform.
PY  - 1993
SP  - 179
EP  - 187
VL  - 0
AB  - Type I restriction endonucleases consist of three subunits encoded by the genes hsdR, hsdM and
AB  - hsdS.  The hsdS gene product is responsible for DNA specificity and together with the hsdM
AB  - gene product is sufficient for modification (methylation) of the DNA recognition sequence;
AB  - hsdR is required for endonuclease activity.  The endonuclease requires ATP, SAM and Mg2+ as
AB  - cofactors while the DNA methyltransferase requires only SAM and Mg2+.  Evidence has been
AB  - presented to support the hypothesis that the HsdS protein has two domains responsible for DNA
AB  - recognition, separated by a spacer region.  The EcoR124 R-M system is of particular interest
AB  - in that an alternative DNA specificity (EcoR124/3) has been identified which differs from the
AB  - EcoR124 DNA specificity by the presence of an extra non-specific nucleotide:  EcoR124 -
AB  - GAANNNNNNRTCG (or GAAN6RTCG), EcoR124/3 - GAANNNNNNNRTCG (or GAAN7RTCG).  EcoR124 and its
AB  - variant form EcoR124/3 have been cloned producing the recombinant plasmids pCP1005 and pUNG31
AB  - respectively, their transcripts mapped, the genes sequenced and low levels of the endonuclease
AB  - have been purified.  These data show that they are members of a new sub-class of type I R-M
AB  - systems: type IC.  The only difference between EcoR124 and EcoR124/3 lies within their hsdS
AB  - genes.  The EcoR124/3 hsdS gene has an extra copy of a 12-bp repeat within the predicted
AB  - spacer region (repeated twice in EcoR124 and three times in EcoR124/3).
ER  -

TY  - JOUR
AU  - Patel, J.
AU  - Taylor, I.
AU  - Dutta, C.F.
AU  - Kneale, G.
AU  - Firman, K.
TI  - High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124.
JO  - Gene
PY  - 1992
SP  - 21
EP  - 27
VL  - 112
AB  - We have cloned the genes coding for the two subunits (HsdM and HsdS) of the
AB  - type-I DNA methyltransferase (MTase), M.EcoR124, into the specially constructed
AB  - expression vector, pJ119.  These subunit have been synthesized together as an
AB  - intact MTase.  WE have also cloned the individual subunit-encoding genes under
AB  - the control of the T7 gene 10 promoter or the lacUV5 promoter.  High levels of
AB  - expression have been obtained in all cases.  While HsdM was found to be
AB  - soluble, HsdS was insoluble.  However, in the presence of the co-produced HsdM
AB  - subunit, HsdS was found in the soluble fraction as part of an active MTase.  We
AB  - have partially purified the cloned multi-subunit enzyme and shown that it is
AB  - capable of DNA methylation both in vivo and in vitro.
ER  -

TY  - JOUR
AU  - Patel, N.
AU  - Graslund, A.
AU  - Berglund, H.
AU  - Nilsson, L.
AU  - Rigler, R.
AU  - McLaughlin, L.W.
TI  - Interaction of a minor groove binder with a fluorescent DNA oligomer containing the EcoRI recognition sequence.
JO  - Nucleosides and Nucleotides
PY  - 1991
SP  - 547
EP  - 548
VL  - 10
AB  - The minor groove binding drug netropsin quenches the 2-aminopurine (2AP)
AB  - fluorescence in the duplex d(CTGA(2AP)TTCAG)2.  Drug binding constants, K
AB  - approx.10/5 M-1 were established between 5-25C.  A preliminary evaluation of
AB  - the thermodynamic data indicated a predominantly entropy driven interaction.
ER  -

TY  - JOUR
AU  - Patel, P.A.
AU  - Kothari, V.V.
AU  - Kothari, C.R.
AU  - Faldu, P.R.
AU  - Domadia, K.K.
AU  - Rawal, C.M.
AU  - Bhimani, H.D.
AU  - Parmar, N.R.
AU  - Nathani, N.M.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Kothari, R.K.
TI  - Draft Genome Sequence of Petroleum Hydrocarbon-Degrading Pseudomonas aeruginosa Strain PK6, Isolated from the Saurashtra Region of Gujarat, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00002
EP  - e00014
VL  - 2
AB  - Pseudomonas aeruginosa strain PK6, a potential petroleum hydrocarbon-degrading soil bacterium,
AB  - was isolated from a site contaminated by a petroleum hydrocarbon
AB  - spill from an automobile service station in Junagadh, Gujarat, India. Here, we
AB  - provide the 6.04-Mb draft genome sequence of strain PK6, which has genes encoding
AB  - enzymes for potential and related metabolic pathways of the strain.
ER  -

TY  - JOUR
AU  - Patel, P.H.
AU  - Suzuki, M.
AU  - Adman, E.
AU  - Shinkai, A.
AU  - Loeb, L.A.
TI  - Prokaryotic DNA polymerase I: evolution, structure, and "base flipping" mechanism for nucleotide selection.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 823
EP  - 837
VL  - 308
AB  - Accurate transmission of DNA material from one generation to the next is crucial for prolonged
AB  - cell survival. Following the discovery of DNA polymerse I in Escherichia coli, the DNA
AB  - polymerase I class of enzymes has served as the prototype for studies on structural and
AB  - biochemical mechanisms of DNA replication. Recently, a series of genomic, mutagenesis and
AB  - structural investigations have provided key insights into how Pol I class of enzymes function
AB  - and evolve. X-ray crystal structures of at least three Pol I class of enzymes have been solved
AB  - in the presence of DNA and dNTP, thus allowing a detailed description of a productive
AB  - replication complex. Rapid-quench stop-flow studies have helped define individual steps during
AB  - nucleotide incorporation and conformational changes that are rate limiting during catalysis.
AB  - Studies in our laboratory have generated large libraries of active mutant enzymes (8000)
AB  - containing a variety of substitutions within the active site, some of which exhibit altered
AB  - biochemical properties. Extensive genomic information of Pol I has recently become available,
AB  - as over 50 polA genes from different prokaryotic species have been sequenced. In light of
AB  - these advancements, we review here the structure-function relationships of Pol I, and we
AB  - highlight those interactions that are responsible for the high fidelity of DNA synthesis. We
AB  - present a mechanism for "flipping" of the complementary template base to enhance interactions
AB  - with the incoming nucleotide substrate during DNA synthesis.
ER  -

TY  - JOUR
AU  - Patel, P.N.
AU  - Lindsey, R.L.
AU  - Garcia-Toledo, L.
AU  - Rowe, L.A.
AU  - Batra, D.
AU  - Whitley, S.W.
AU  - Drapeau, D.
AU  - Stoneburg, D.
AU  - Martin, H.
AU  - Juieng, P.
AU  - Loparev, V.N.
AU  - Strockbine, N.
TI  - High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing.
JO  - Genome Announcements
PY  - 2018
SP  - e00391
EP  - e00318
VL  - 6
AB  - Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause
AB  - mild to severe illness. Here, we report the availability of
AB  - high-quality whole-genome sequences for 77 STEC strains generated using the
AB  - PacBio sequencing platform.
ER  -

TY  - JOUR
AU  - Patel, S.
AU  - Fletcher, B.
AU  - Scott, D.C.
AU  - Ely, B.
TI  - Genome sequence and phenotypic characterization of Caulobacter segnis.
JO  - Curr. Microbiol.
PY  - 2015
SP  - 355
EP  - 363
VL  - 70
AB  - Caulobacter segnis is a unique species of Caulobacter that was initially deemed
AB  - Mycoplana segnis because it was isolated from soil and appeared to share a number
AB  - of features with other Mycoplana. After a 16S rDNA analysis showed that it was
AB  - closely related to Caulobacter crescentus, it was reclassified C. segnis. Because
AB  - the C. segnis genome sequence available in GenBank contained 126 pseudogenes, we
AB  - compared the original sequencing data to the GenBank sequence and determined that
AB  - many of the pseudogenes were due to sequence errors in the GenBank sequence.
AB  - Consequently, we used multiple approaches to correct and reannotate the C. segnis
AB  - genome sequence. In total, we deleted 247 bp, added 14 bp, and changed 8 bp
AB  - resulting in 233 fewer bases in our corrected sequence. The corrected sequence
AB  - contains only 15 pseudogenes compared to 126 in the original annotation.
AB  - Furthermore, we found that unlike Mycoplana, C. segnis divides by fission,
AB  - producing swarmer cells that have a single, polar flagellum.
ER  -

TY  - JOUR
AU  - Patel, Y.
AU  - Nelson, M.
AU  - McClelland, M.
TI  - Methylation at overlapping dam (Gm6ATC) sites does not block cleavage by the NruI (TCGCGA) isoschizomer restriction endonucleases AmaI, SalDI and Sbo13I.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 3613
EP  - 3613
VL  - 17
AB  - AmaI, NruI, SalDI and Sbo13I endonucleases were tested for sensitivity to TCGCGm6A at an
AB  - overlapping dam site in Ad2 DNA (pos 7723). NruI cleavage was blocked by m6A modification, but
AB  - the other endonucleases were not.
ER  -

TY  - JOUR
AU  - Patel, Y.
AU  - Van Cott, E.
AU  - Wilson, G.G.
AU  - McClelland, M.
TI  - Cleavage at the twelve-base-pair sequence 5'-TCTAGATCTAGA-3' using M.XbaI (TCTAGm6A) methylation and DpnI (Gm6A/TC) cleavage .
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1603
EP  - 1607
VL  - 18
AB  - The DNA methylase M.XbaI was isolated from an E. coli recombinant clone.  We
AB  - deduce that the enzyme methylates at the sequence 5'-TCTAGm6A-3'.  In
AB  - combination with the methylation-dependent restriction endonuclease, DpnI
AB  - (5'-Gm6A/TC-3'), DNA cleavage occurs at the sequence 5'-TCTAGA/TCTAGA-3'.  This
AB  - twelve-base-pair site should occur once every 16,000,000 base pairs in a random
AB  - sequence of DNA.  The exceptional rarity of the M.XbaI/DpnI sequence makes it
AB  - an ideal candidate for transpositional integration of a unique cleavage site
AB  - into bacterial genomes.  Retrotransposition into mammalian genomes is also an
AB  - attractive possibility.
ER  -

TY  - JOUR
AU  - Paterson, J.
AU  - Gross, H.
TI  - Draft Genome Sequence and Annotation of the Phytopathogenic Ralstonia pickettii (Previously Burkholderia glumae) Strain ICMP-8657.
JO  - Genome Announcements
PY  - 2018
SP  - e00128
EP  - e00118
VL  - 6
AB  - Strain ICMP-8657 was formerly taxonomically classified as Burkholderia glumae and reported to
AB  - be the producer of an antibacterial pyrazole derivative. Here, we
AB  - report the draft genome sequence of ICMP-8657, which failed to demonstrate the
AB  - biosynthetic capacity to produce the stated antibacterial compound, leading to
AB  - its taxonomic reclassification as Ralstonia pickettii ICMP-8657.
ER  -

TY  - JOUR
AU  - Pathak, A.
AU  - Green, S.J.
AU  - Ogram, A.
AU  - Chauhan, A.
TI  - Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential.
JO  - Genome Announcements
PY  - 2013
SP  - e00144
EP  - e00112
VL  - 1
AB  - Soil-borne Gram-positive bacteria from the genus Rhodococcus metabolize a range of aromatic
AB  - hydrocarbons and also produce a variety of value-added products, such
AB  - as triacylglycerols and steroids. We report the draft genome sequence of
AB  - Rhodococcus opacus strain M213 (9,193,504 bp with a G+C content of 66.99%),
AB  - providing a comprehensive understanding of the repertoire of metabolic genes of
AB  - this strain.
ER  -

TY  - JOUR
AU  - Pathak, A.
AU  - Jaswal, R.
AU  - Stothard, P.
AU  - Brooks, S.
AU  - Chauhan, A.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated  Sediment.
JO  - Genome Announcements
PY  - 2018
SP  - e00518
EP  - e00518
VL  - 6
AB  - The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is
AB  - reported. The genome comprises 6,706,934 bases, 6,059
AB  - coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of
AB  - biodegradative genes, many located on genomic islands, were identified from
AB  - strain B1, further enhancing our understanding of the versatile pseudomonads.
ER  -

TY  - JOUR
AU  - Pathak, A.
AU  - Jaswal, R.
AU  - Xu, X.
AU  - Chauhan, A.
TI  - Draft Genome Sequence of Serratia sp. Strain S1B, Isolated from Mercury-Contaminated Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e00534
EP  - e00518
VL  - 6
AB  - We report here the draft genome sequence of Serratia sp. strain S1B, comprising 7,710,841
AB  - bases, 7,075 coding sequences, a G+C content of 45.9%, and 138 RNAs.
AB  - Notably, a repertoire of biodegradative genes, several occurring on genomic
AB  - islands, was also identified, which enhances our understanding of the
AB  - environmental relevance of Serratia spp.
ER  -

TY  - JOUR
AU  - Pathania, R.
AU  - Ahmad, A.
AU  - Srivastava, S.
TI  - Draft Genome Sequence of an Indian Marine Cyanobacterial Strain with Fast Growth  and High Polyglucan Content.
JO  - Genome Announcements
PY  - 2017
SP  - e01334
EP  - e01317
VL  - 5
AB  - Marine cyanobacteria play an important role in global carbon cycling and are a potential
AB  - source of polyglucans for biotechnological purposes. This report
AB  - provides the draft sequence of an Indian marine cyanobacterium, Synechococcus
AB  - elongatus BDU 130192, which shows fast growth and high polyglucan content. The
AB  - genome sequence will help in understanding the unique properties of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 41
EP  - 49
VL  - 5
AB  - Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella,
AB  - which belongs to the family Prevotellaceae. The species is of
AB  - medical interest because its members are able to cause diseases in the human oral
AB  - cavity such as periodontitis, root caries and others. Although 77 Prevotella
AB  - genomes have already been sequenced or are targeted for sequencing, this is only
AB  - the second completed genome sequence of a type strain of a species within the
AB  - genus Prevotella to be published. The 3,388,644 bp long genome is assembled in
AB  - three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and
AB  - is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Saccharomonospora viridis type strain (P101).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 141
EP  - 149
VL  - 1
AB  - Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type
AB  - species of the genus Saccharomonospora which belongs to the family
AB  - Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative
AB  - organism classified among the usually Gram-positive actinomycetes. Members of the
AB  - species are frequently found in hot compost and hay, and its spores can cause
AB  - farmer's lung disease, bagassosis, and humidifier fever. Strains of the species
AB  - S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP).
AB  - The strain described in this study has been isolated from peat-bog in Ireland.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence, and annotation. This is the first complete genome sequence of the
AB  - family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with
AB  - its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 49
EP  - 56
VL  - 2
AB  - Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of  the genus
AB  - Sphaerobacter, which is the type genus of the family
AB  - Sphaerobacteraceae, the order Sphaerobacterales and the subclass
AB  - Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied
AB  - class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome
AB  - of strain S 6022(T) is described which is an obligate aerobe that was originally
AB  - isolated from an aerated laboratory-scale fermentor that was pulse fed with
AB  - municipal sewage sludge. We describe the features of this organism, together with
AB  - the complete genome and annotation. This is the first complete genome sequence of
AB  - the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the
AB  - chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525
AB  - protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Brachyspira murdochii type strain (56-150).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 260
EP  - 269
VL  - 2
AB  - Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of
AB  - the family Brachyspiraceae. Initially isolated from the intestinal
AB  - content of a healthy swine, the 'group B spirochaetes' were first described as
AB  - Serpulina murdochii. Members of the family Brachyspiraceae are of great
AB  - phylogenetic interest because of the extremely isolated location of this family
AB  - within the phylum 'Spirochaetes'. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is the first
AB  - completed genome sequence of a type strain of a member of the family
AB  - Brachyspiraceae and only the second genome sequence from a member of the genus
AB  - Brachyspira. The 3,241,804 bp long genome with its 2,893 protein-coding and 40
AB  - RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Arcobacter nitrofigilis type strain (CI).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 300
EP  - 308
VL  - 2
AB  - Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991 is the type species of the
AB  - genus Arcobacter in the family Campylobacteraceae within the
AB  - Epsilonproteobacteria. The species was first described in 1983 as Campylobacter
AB  - nitrofigilis [1] after its detection as a free-living, nitrogen-fixing
AB  - Campylobacter species associated with Spartina alterniflora Loisel roots [2]. It
AB  - is of phylogenetic interest because of its lifestyle as a symbiotic organism in a
AB  - marine environment in contrast to many other Arcobacter species which are
AB  - associated with warm-blooded animals and tend to be pathogenic. Here we describe
AB  - the features of this organism, together with the complete genome sequence, and
AB  - annotation. This is the first complete genome sequence of a type stain of the
AB  - genus Arcobacter. The 3,192,235 bp genome with its 3,154 protein-coding and 70
AB  - RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Bacteroides helcogenes type strain (P 36-108).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 45
EP  - 53
VL  - 4
AB  - Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic
AB  - location and, although it has been found in pig feces and is known
AB  - to be pathogenic for pigs, occurrence of this bacterium is rare and it does not
AB  - cause significant damage in intensive animal husbandry. The genome of B.
AB  - helcogenes P 36-108(T) is already the fifth completed and published type strain
AB  - genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp
AB  - long genome with its 3,353 protein-coding and 83 RNA genes consists of one
AB  - circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and
AB  - Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Oceanithermus profundus type strain (506).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 210
EP  - 220
VL  - 4
AB  - Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus
AB  - Oceanithermus, which belongs to the family Thermaceae. The genus currently
AB  - comprises two species whose members are thermophilic and are able to reduce
AB  - sulfur compounds and nitrite. The organism is adapted to the salinity of sea
AB  - water, is able to utilize a broad range of carbohydrates, some proteinaceous
AB  - substrates, organic acids and alcohols. This is the first completed genome
AB  - sequence of a member of the genus Oceanithermus and the fourth sequence from the
AB  - family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and
AB  - 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a
AB  - part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pati, A. et al.
TI  - Complete genome sequence of Cellulophaga lytica type strain (LIM-21).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 221
EP  - 232
VL  - 4
AB  - Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 is the type species of the  genus
AB  - Cellulophaga, which belongs to the family Flavobacteriaceae within the
AB  - phylum 'Bacteroidetes' and was isolated from marine beach mud in Limon, Costa
AB  - Rica. The species is of biotechnological interest because its members produce a
AB  - wide range of extracellular enzymes capable of degrading proteins and
AB  - polysaccharides. After the genome sequence of Cellulophaga algicola this is the
AB  - second completed genome sequence of a member of the genus Cellulophaga. The
AB  - 3,765,936 bp long genome with its 3,303 protein-coding and 55 RNA genes consists
AB  - of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Patil, Y.
AU  - Muller, N.
AU  - Schink, B.
AU  - Whitman, W.B.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Palaniappan, K.
AU  - Varghese, N.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.B.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Junghare, M.
TI  - High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698).
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 24
EP  - 24
VL  - 12
AB  - Anaerobium acetethylicum strain GluBS11T belongs to the family Lachnospiraceae within the
AB  - order Clostridiales. It is a Gram-positive, non-motile and strictly
AB  - anaerobic bacterium isolated from biogas slurry that was originally enriched with
AB  - gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol
AB  - 65:3289-3296, 2015). Here we describe the draft genome sequence of strain
AB  - GluBS11T and provide a detailed insight into its physiological and metabolic
AB  - features. The draft genome sequence generated 4,609,043 bp, distributed among 105
AB  - scaffolds assembled using the SPAdes genome assembler method. It comprises in
AB  - total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124
AB  - RNA genes and 867 pseudogenes. The G + C content was 43.51 mol %. The annotated
AB  - genome of strain GluBS11T contains putative genes coding for the pentose
AB  - phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff
AB  - pathway and the tricarboxylic acid cycle. The genome revealed the presence of
AB  - most of the necessary genes required for the fermentation of glucose and
AB  - gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for
AB  - production of formate was not identified.
ER  -

TY  - JOUR
AU  - Patole, S.
AU  - Mishra, M.
AU  - Mohapatra, H.
TI  - Draft Genome Sequences of Clinical and Nonclinical Isolates of Klebsiella spp. Exhibiting Nonheritable Tolerance toward Antimicrobial Compounds.
JO  - Genome Announcements
PY  - 2017
SP  - e01217
EP  - e01217
VL  - 5
AB  - A clinical isolate and a nonclinical isolate of Klebsiella pneumoniae were found  to exhibit
AB  - nonheritable tolerance in response to antimicrobial compounds. The
AB  - draft genome sequences of both isolates are presented here.
ER  -

TY  - JOUR
AU  - Patrick, S.
AU  - Blakely, G.W.
AU  - Houston, S.
AU  - Moore, J.
AU  - Abratt, V.R.
AU  - Bertalan, M.
AU  - Cerdeno-Tarraga, A.M.
AU  - Quail, M.A.
AU  - Corton, N.
AU  - Corton, C.
AU  - Bignell, A.
AU  - Barron, A.
AU  - Clark, L.
AU  - Bentley, S.D.
AU  - Parkhill, J.
TI  - Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.
JO  - Microbiology
PY  - 2010
SP  - 3255
EP  - 3269
VL  - 156
AB  - Comparison of the complete genome sequence of Bacteroides fragilis 638R, originally isolated
AB  - in the USA, was made with two previously
AB  - sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The
AB  - presence of 10 loci containing genes associated with polysaccharide
AB  - (PS) biosynthesis, each including a putative Wzx flippase and Wzy
AB  - polymerase, was confirmed in all three strains, despite a lack of
AB  - cross-reactivity between NCTC 9343 and 638R surface PS-specific
AB  - antibodies by immunolabelling and microscopy. Genomic comparisons
AB  - revealed an exceptional level of PS biosynthesis locus diversity. Of
AB  - the 10 divergent PS-associated loci apparent in each strain, none is
AB  - similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC
AB  - 9343, confirmed by mAb labelling, and a second different locus with
AB  - 638R, making a total of 28 divergent PS biosynthesis loci amongst the
AB  - three strains. The lack of expression of the phase-variable large
AB  - capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due
AB  - to a point mutation that generates a stop codon within a putative
AB  - initiating glycosyltransferase, necessary for the expression of the LC
AB  - in NCTC 9343. Other major sequence differences were observed to arise
AB  - from different numbers and variety of inserted extra-chromosomal
AB  - elements, in particular prophages. Extensive horizontal gene transfer
AB  - has occurred within these strains, despite the presence of a
AB  - significant number of divergent DNA restriction and modification
AB  - systems that act to prevent acquisition of foreign DNA. The level of
AB  - amongst-strain diversity in PS biosynthesis loci is unprecedented.
ER  -

TY  - JOUR
AU  - Pattabiraman, V.
AU  - Bopp, C.A.
TI  - Draft Whole-Genome Sequences of 10 Serogroup O6 Enterotoxigenic Escherichia coli  Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e01274
EP  - e01214
VL  - 2
AB  - Entertotoxigenic Escherichia coli (ETEC) is a major cause of global diarrhea, resulting in
AB  - approximately 200 million occurrences and 300,000 to 400,000 deaths
AB  - annually, primarily in children under the age of five. Here, we announce the
AB  - release of the draft genomes of 10 ETEC isolates belonging to serogroup O6.
ER  -

TY  - JOUR
AU  - Pattabiraman, V.
AU  - Bopp, C.A.
TI  - Draft Whole-Genome Sequences of Nine Enterotoxigenic Escherichia coli Serogroup O6 Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e00564
EP  - e00515
VL  - 3
AB  - Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children under
AB  - the age of 5 years and in adults living in developing countries, as well as in travelers to
AB  - these countries. In this announcement, we release the draft whole-genome sequences of 10 ETEC
AB  - serogroup O6 strains.
ER  -

TY  - JOUR
AU  - Patten, C.L.
AU  - Jeong, H.
AU  - Blakney, A.J.
AU  - Wallace, N.
TI  - Draft Genome Sequence of a Diazotrophic, Plant Growth-Promoting Rhizobacterium of the Pseudomonas syringae Complex.
JO  - Genome Announcements
PY  - 2016
SP  - e01023
EP  - e01016
VL  - 4
AB  - We report here the draft genome sequence of Pseudomonas syringae GR12-2, a nitrogen-fixing,
AB  - plant growth-promoting bacterium, isolated from the rhizosphere
AB  - of an Arctic grass. The 6.6-Mbp genome contains 5,676 protein-coding genes,
AB  - including a nitrogen-fixation island similar to that in P. stutzeri.
ER  -

TY  - JOUR
AU  - Patterson, N.H.
AU  - Pauling, C.
TI  - Evidence for two restriction-modification systems in Halobacterium cutirubrum.
JO  - J. Bacteriol.
PY  - 1985
SP  - 783
EP  - 784
VL  - 163
AB  - Data from plating experiments indicated that Halobacterium cutirubrum NRC34001
AB  - has at least two separate restriction-modifiction systems.  A spontaneous or
AB  - induced loss of one or both systems resulted in four restriction-modification
AB  - phenotypes.  There was a positive correlation between changes in gas
AB  - vacuolation phenotypes and either restriction-modifiction system.
ER  -

TY  - JOUR
AU  - Paul, D.
AU  - Austin, F.W.
AU  - Arick, T.
AU  - Bridges, S.M.
AU  - Burgess, S.C.
AU  - Dandass, Y.S.
AU  - Lawrence, M.L.
TI  - Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5554
EP  - 5555
VL  - 192
AB  - Clostridium carboxidivorans strain P7(T) is a strictly anaerobic acetogenic bacterium that
AB  - produces acetate, ethanol, butanol, and
AB  - butyrate. The C. carboxidivorans genome contains all the genes for the
AB  - carbonyl branch of the Wood-Ljungdahl pathway for CO(2) fixation, and it
AB  - encodes enzymes for conversion of acetyl coenzyme A into butanol and
AB  - butyrate.
ER  -

TY  - JOUR
AU  - Paul, D.
AU  - Bridges, S.
AU  - Burgess, S.C.
AU  - Dandass, Y.
AU  - Lawrence, M.L.
TI  - Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T.
JO  - J. Bacteriol.
PY  - 2008
SP  - 5531
EP  - 5532
VL  - 190
AB  - Oligotropha carboxidovorans OM5(T) (DSM 1227, ATCC 49405) is a
AB  - chemolithoautotrophic bacterium with the capability to utilize carbon
AB  - monoxide, carbon dioxide, and hydrogen. It is also capable of
AB  - heterotrophic growth under appropriate environmental conditions. Here we
AB  - report the annotated genome sequence of the circular chromosome of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Paul, R.
AU  - Jinkerson, R.E.
AU  - Buss, K.
AU  - Steel, J.
AU  - Mohr, R.
AU  - Hess, W.R.
AU  - Chen, M.
AU  - Fromme, P.
TI  - Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation.
JO  - Genome Announcements
PY  - 2014
SP  - e01166
EP  - e01113
VL  - 2
AB  - Leptolyngbya sp. strain Heron Island is a cyanobacterium exhibiting chromatic acclimation.
AB  - However, this strain has strong interactions with other bacteria,
AB  - making it impossible to obtain axenic cultures for sequencing. A protocol
AB  - involving an analysis of tetranucleotide frequencies, G+C content, and BLAST
AB  - searches has been described for separating the cyanobacterial scaffolds from
AB  - those of its cooccurring bacteria.
ER  -

TY  - JOUR
AU  - Paulsen, I. et al.
TI  - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 13148
EP  - 13153
VL  - 99
AB  - The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent,
AB  - Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a
AB  - finite set of differences that could be responsible for the differences in virulence and host
AB  - preference between these organisms, and indicates that phage have played a significant role in
AB  - their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities
AB  - akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1
AB  - and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this
AB  - animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to
AB  - known bacterial virulence factors were identified.
ER  -

TY  - JOUR
AU  - Paulsen, I.T. et al.
TI  - Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.
JO  - Science
PY  - 2003
SP  - 2071
EP  - 2074
VL  - 299
AB  - The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical
AB  - isolate, revealed that more than a quarter
AB  - of the genome consists of probable mobile or foreign DNA. One of the
AB  - predicted mobile elements is a previously unknown vanB
AB  - vancomycin-resistance conjugative transposon. Three plasmids were
AB  - identified, including two pheromone-sensing conjugative plasmids, one
AB  - encoding a previously undescribed pheromone inhibitor. The apparent
AB  - propensity for the incorporation of mobile elements probably contributed
AB  - to the rapid acquisition and dissemination of drug resistance in the
AB  - enterococci.
ER  -

TY  - JOUR
AU  - Paulsen, I.T. et al.
TI  - Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.
JO  - Nat. Biotechnol.
PY  - 2005
SP  - 873
EP  - 878
VL  - 23
AB  - Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and
AB  - produces secondary metabolites that suppress soilborne
AB  - plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was
AB  - determined. We analyzed repeat sequences to identify genomic islands that,
AB  - together with other approaches, suggested P. fluorescens Pf-5's recent
AB  - lateral acquisitions include six secondary metabolite gene clusters, seven
AB  - phage regions and a mobile genomic island. We identified various features
AB  - that contribute to its commensal lifestyle on plants, including broad
AB  - catabolic and transport capabilities for utilizing plant-derived
AB  - compounds, the apparent ability to use a diversity of iron siderophores,
AB  - detoxification systems to protect from oxidative stress, and the lack of a
AB  - type III secretion system and toxins found in related pathogens. In
AB  - addition to six known secondary metabolites produced by P. fluorescens
AB  - Pf-5, three novel secondary metabolite biosynthesis gene clusters were
AB  - also identified that may contribute to the biocontrol properties of P.
AB  - fluorescens Pf-5.
ER  -

TY  - JOUR
AU  - Pavan, M.E.
AU  - Pavan, E.E.
AU  - Lopez, N.I.
AU  - Levin, L.
AU  - Pettinari, M.J.
TI  - Genome Sequence of the Melanin-Producing Extremophile Aeromonas salmonicida subsp. pectinolytica Strain 34melT.
JO  - Genome Announcements
PY  - 2013
SP  - e00675
EP  - e00613
VL  - 1
AB  - The genome of Aeromonas salmonicida subsp. pectinolytica strain 34mel(T), isolated from a
AB  - heavily polluted river, contains several genomic islands and
AB  - putative virulence genes. The identification of genes involved in resistance to
AB  - different kinds of stress sheds light on the mechanisms used by this strain to
AB  - thrive in an extreme environment.
ER  -

TY  - JOUR
AU  - Pavco, P.A.
AU  - Steege, D.A.
TI  - A DNA binding protein acts as a transcriptional roadblock.
JO  - J. Cell Biochem. Suppl.
PY  - 1988
SP  - 145
EP  - 145
VL  - 12D
AB  - What results when an elongating RNA polymerase encounters DNA-bound protein is
AB  - of general interest.  To ask if a protein bound tightly to a specific sequence
AB  - blocks further elongation by E. coli RNA polymerase, transcription on templates
AB  - associated with a mutant of the EcoRI endonuclease has been studied in vitro.
AB  - This protein (E111G) binds to the wild type recognition sequence with high
AB  - affinity yet carries out no appreciable cleavage.  When a DNA template
AB  - containing one EcoRI site is transcribed in the presence of E111G and
AB  - rifampicin, two RNA products are seen:  a full-length runoff transcript and a
AB  - truncated RNA species whose 3' endpoint is immediately upstream of the EcoRI
AB  - recognition sequence.  Under conditions of complete binding by E111G, the
AB  - shorter transcript is the major RNA species appearing.  Blockage appears
AB  - long-lived and not dependent on the DNA sequence context upstream of the EcoRI
AB  - site.  During steady state transcription an additional RNA 3' endpoint, due to
AB  - a second RNA polymerase stalled behind the first, is seen.  From analysis of
AB  - the RNA 3' ends, the position of the 3' terminal ribonucleotide with respect to
AB  - the leading edge of the RNA polymerase ternary complex has been located.
ER  -

TY  - JOUR
AU  - Pavlopoulou, A.
AU  - Kossida, S.
TI  - Plant cytosine-5 DNA methyltransferases: Structure, function, and molecular evolution.
JO  - Genomics
PY  - 2007
SP  - 530
EP  - 541
VL  - 90
AB  - A detailed analysis of the structure and function, along with evolutionary aspects, of the
AB  - main plant cytosine-5 DNA
AB  - methyltransferases (C5-MTases) is presented. The evolutionary
AB  - relationships between the already known and four candidate plant
AB  - C5-MTases identified in this work were investigated using the distance,
AB  - maximum-parsimony, and maximum-likelihood approaches. The topologies of
AB  - the trees were overall congruent: four monophyletic groups
AB  - corresponding to the four plant C5-MTase families were clearly
AB  - distinguished. In addition, sequence analyses of the plant C5-MTase
AB  - target recognition domain sequences were performed and phylogenetic
AB  - trees were reconstructed showing that there is good conservation among
AB  - but not within the plant C5-MTase families. Furthermore, a conserved
AB  - dipeptide that plays an important role in flipping the target base into
AB  - the catalytic site of the C5-MTases was identified in all plant
AB  - C5-MTases under study.
ER  -

TY  - JOUR
AU  - Pavlopoulou, A.
AU  - Kossida, S.
TI  - Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases.
JO  - Genomics
PY  - 2009
SP  - 350
EP  - 357
VL  - 93
AB  - RNA (cytosine-5)-methyltransferases (RCMTs) have been characterized both in prokaryotic and
AB  - eukaryotic organisms. The RCMT family, however, remains largely uncharacterized, as opposed to
AB  - the family of DNA (cytosine-5)-methyltransferases which has been studied in depth. In the
AB  - present study, an in silico identification of the putative 5-methylcytosine RNA-generating
AB  - enzymes in the eukaryotic genomes was performed. A comprehensive phylogenetic analysis of the
AB  - putative eukaryotic RCMT-related proteins has been performed in order to redefine subfamilies
AB  - within the RCMT family. Five distinct eukaryotic subfamilies were identified, including the
AB  - three already known (NOP2, NCL1 and YNL022c), one novel subfamily (RCMT9) and a fifth one
AB  - which hitherto was considered to exist exclusively in prokaryotes (Fmu). The potential
AB  - evolutionary relationships among the different eukaryotic RCMT subfamilies were also
AB  - investigated.  Furthermore, the results of this study add further support to a previous
AB  - hypothesis that RCMTs represent evolutionary intermediates of RNA
AB  - (uridine-5)-methyltransferases and DNA (cytosine-5)-methyltransferases.
ER  -

TY  - JOUR
AU  - Pavlov, M.S.
AU  - Lira, F.
AU  - Martinez, J.L.
AU  - Olivares, J.
AU  - Marshall, S.H.
TI  - Draft Genome Sequence of Antarctic Pseudomonas sp. Strain KG01 with Full Potential for Biotechnological Applications.
JO  - Genome Announcements
PY  - 2015
SP  - e00906
EP  - e00915
VL  - 3
AB  - We report here the draft genome sequence of a free-living psychrotolerant, Pseudomonas sp.
AB  - strain KG01, isolated from an Antarctic soil sample and
AB  - displaying interesting antimicrobial and surfactant activities. The sequence is
AB  - 6.3 Mb long and includes 5,648 predicted-coding sequences.
ER  -

TY  - JOUR
AU  - Pavlovic, G.
AU  - Burrus, V.
AU  - Gintz, B.
AU  - Decaris, B.
AU  - Guedon, G.
TI  - Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus.
JO  - Microbiology
PY  - 2004
SP  - 759
EP  - 774
VL  - 150
AB  - The 34 734-bp integrative and potentially conjugative element (putative ICE)
AB  - ICESt1 has been previously found to be site-specifically integrated in the 3' end
AB  - of the fda locus of Streptococcus thermophilus CNRZ368. Four types of genomic
AB  - islands related to ICESt1 are integrated in the same position in seven other
AB  - strains of S. thermophilus. One of these elements, ICESt3, harbours conjugation
AB  - and recombination modules closely related to those of ICESt1 and excises by
AB  - site-specific recombination. Two other types of elements, CIME19258 and CIME302,
AB  - are flanked by site-specific attachment sites closely related to attL and attR of
AB  - ICESt1 and ICESt3, whereas Delta CIME308 only possesses a putative attR site;
AB  - none of these three elements carry complete conjugation and recombination
AB  - modules. ICESt1 contains a functional internal recombination site, attL', that is
AB  - almost identical to attL of CIME19258. The recombination between attL' and attR
AB  - of ICESt1 leads to the excision of the expected circular molecule (putative ICE);
AB  - a cis-mobilizable element (CIME) flanked by an attL site and an attB' site
AB  - remains integrated into the 3' end of fda. Furthermore, sequences that could be
AB  - truncated att sites were found within ICESt1, ICESt3 and CIME302. All together,
AB  - these data suggest that these genomic islands evolved by deletion and tandem
AB  - accretion of ICEs and CIMEs resulting from site-specific recombination. A model
AB  - for this evolution is proposed and its application to other genomic islands is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Pavlovic, G.
AU  - Burrus, V.
AU  - Toulmay, A.
AU  - Choulet, F.
AU  - Decaris, B.
AU  - Guedon, G.
TI  - Characterization and evolution of a family of integrative and potentially conjugative or mobilizable elements from Streptococcus  thermophilus.
JO  - Lait
PY  - 2004
SP  - 7
EP  - 14
VL  - 84
AB  - The integrative and conjugative elements (ICEs) excise by site-specific recombination.
AB  - self-transfer the resulting circular form by conjugation
AB  - and integrate into the genome of the recipient bacterium. The 34.7-kb
AB  - element from Streptococcus thermophilus CNRZ368, ICEStl, excises and
AB  - integrates by site-specific recombination. This element also possesses
AB  - a conjugation module distantly related to that of the conjugative
AB  - transposon Tn9l6 from Enterococcus faecalis. Therefore, ICEStl is
AB  - probably an ICE. Four types of elements related to ICEStl are
AB  - integrated into the same location as ICEStl in seven other strains of
AB  - S. thermophilus. One of these elements, ICESt3, is probably an ICE
AB  - whereas the three others (CIMEs) would have arisen from ICEs by
AB  - deletion of the conjugation and recombination modules. These elements
AB  - also encode functions that are not involved in element maintenance or
AB  - transfer, Such as restriction-modification systems. Each of these
AB  - elements has a chimerical Structure resulting from the acquisition of
AB  - modules from different origins. Sequence analyses indicate that these
AB  - elements are involved in horizontal transfers with various species of
AB  - dairy or pathogenic lactic acid bacteria. DeltaCIME308 has exchanged
AB  - restriction-modification and cadmium resistance modules with plasmids.
AB  - CIME19258 has acquired a cadmium resistance module by the integration
AB  - of an ICE related to Tn9l6 within the CIME. The site-specific
AB  - recombination between an internal anL-related site and attR of ICEStl
AB  - leads to the excision of a circular molecule which could be another
AB  - ICE, ICEt2, suggesting that ICEStl has arisen by accretion of a CIME
AB  - and ICEt2. CIME302, ICESt2 and ICESt3 would also have arisen by
AB  - site-specific accretion of CIMEs and ICEs and/or mobilization of CIMEs
AB  - by ICEs. An ICE would integrate by site-specific recombination in the
AB  - attR site of a CIME; then the CIME-ICE would excise by site-specific
AB  - recombination and transfer by conjugation.
ER  -

TY  - JOUR
AU  - Pavon, A.
AU  - Orellana, P.
AU  - Salazar, L.
AU  - Cespedes, S.
AU  - Muino, L.
AU  - Gutierrez, A.
AU  - Castillo, D.
AU  - Corsini, G.
TI  - Draft Genome Sequence of Bacillus sp. Strain K2I17, Isolated from the Rhizosphere of Deschampsia antarctica Desv.
JO  - Genome Announcements
PY  - 2017
SP  - e00786
EP  - e00717
VL  - 5
AB  - We present here the draft genome sequence of Bacillus sp. strain K2I17, which was isolated
AB  - from the rhizosphere of Deschampsia antarctica Desv. The genomic
AB  - sequence contained 6,113,341 bp. This genome provides insights into the possible
AB  - new biomedical and biotechnical applications of this specific Antarctic
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Pawar, S.P.
AU  - Dhotre, D.P.
AU  - Shetty, S.A.
AU  - Chowdhury, S.P.
AU  - Chaudhari, B.L.
AU  - Shouche, Y.S.
TI  - Genome Sequence of Janibacter hoylei MTCC8307, Isolated from the Stratospheric Air.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6629
EP  - 6630
VL  - 194
AB  - Janibacter hoylei MTCC8307 was isolated from stratospheric air at an altitude of  41.4 km over
AB  - Hyderabad, India. Here, we present the draft genome of Janibacter
AB  - hoylei MTCC8307, which contains 3,139,099 bp with a G+C content of 72.8 mol%,
AB  - 2,972 protein-coding genes, and 57 structural RNAs.
ER  -

TY  - JOUR
AU  - Pawitwar, S.S.
AU  - Utturkar, S.M.
AU  - Brown, S.D.
AU  - Yoshinaga, M.
AU  - Rosen, B.P.
TI  - Draft Genome Sequence of Burkholderia sp. MR1, a Methylarsenate-Reducing Bacterial Isolate from Florida Golf Course Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00608
EP  - e00615
VL  - 3
AB  - To elucidate the environmental organoarsenical biocycle, we isolated a soil organism,
AB  - Burkholderia sp. MR1, which reduces relatively nontoxic pentavalent
AB  - methylarsenate to the more toxic trivalent methylarsenite, with the goal of
AB  - identifying the gene for the reductase. Here, we report the draft genome sequence
AB  - of Burkholderia sp. MR1.
ER  -

TY  - JOUR
AU  - Pawlak, S.D.
AU  - Radlinska, M.
AU  - Chmiel, A.A.
AU  - Bujnicki, J.M.
AU  - Skowronek, K.J.
TI  - Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study   of restriction endonucleases Bsp6I and PvuII.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 661
EP  - 671
VL  - 33
AB  - Thus far, identification of functionally important residues in Type II restriction
AB  - endonucleases (REases) has been difficult using conventional
AB  - methods. Even though known REase structures share a fold and marginally
AB  - recognizable active site, the overall sequence similarities are
AB  - statistically insignificant, unless compared among proteins that recognize
AB  - identical or very similar sequences. Bsp6I is a Type II REase, which
AB  - recognizes the palindromic DNA sequence 5'GCNGC and cleaves between the
AB  - cytosine and the unspecified nucleotide in both strands, generating a
AB  - double-strand break with 5'-protruding single nucleotides. There are no
AB  - solved structures of REases that recognize similar DNA targets or generate
AB  - cleavage products with similar characteristics. In straightforward
AB  - comparisons, the Bsp6I sequence shows no significant similarity to REases
AB  - with known structures. However, using a fold-recognition approach, we have
AB  - identified a remote relationship between Bsp6I and the structure of PvuII.
AB  - Starting from the sequence-structure alignment between Bsp6I and PvuII, we
AB  - constructed a homology model of Bsp6I and used it to predict functionally
AB  - significant regions in Bsp6I. The homology model was supported by
AB  - site-directed mutagenesis of residues predicted to be important for
AB  - dimerization, DNA binding and catalysis. Completing the picture of
AB  - sequence-structure-function relationships in protein superfamilies becomes
AB  - an essential task in the age of structural genomics and our study may
AB  - serve as a paradigm for future analyses of superfamilies comprising
AB  - strongly diverged members with little or no sequence similarity.
ER  -

TY  - JOUR
AU  - Pawlak, S.D.
AU  - Skowronek, K.
AU  - Radlinska, M.
AU  - Bujnicki, J.M.
TI  - Fold-recognition, homology modeling and mutagenesis of restriction enzyme Bsp6I.
JO  - FEBS J.
PY  - 2005
SP  - 95
EP  - 95
VL  - 272
AB  - Identification of functionally important residues in type II restriction enzymes (REases) has
AB  - been difficult using conventional methods. Even though known REase structures share a common
AB  - fold and marginally recognizable active site, the overall sequence similarities are
AB  - statistically insignificant, unless compared among proteins that recognize identical or very
AB  - similar sequences. Bsp6I is a Type II REase, which recognizes the palindromic DNA sequence
AB  - 5'GCNGC and cleaves between the cytosine and the unspecified nucleotide in both strands,
AB  - generating a double strand break with 5'-protruding single nucleotides. There are no solved
AB  - structures of REases that recognize similar DNA targets or generate cleavage products with
AB  - similar characteristics. The Bsp6I sequence shows no significant similarity to REases with
AB  - known structures. However, using a protein fold-recognition approach, we have identified a
AB  - remote relationship between Bsp6I and the structure of PvuII, which allowed us to construct a
AB  - homology model of Bsp6I and use it to predict functionally important regions and residues in
AB  - Bsp6I. The model of the Bsp6I structure was built using the "Frankenstein's monster" method
AB  - and tested by the characterization of the effects of single amino acid substitutions of
AB  - residues predicted to be directly involved in involved in cleavage, DNA-binding and
AB  - dimerization. The endonuclease activity of an extensive panel of mutants was tested in vivo
AB  - using the bacteriophage lambda-plating assay. All mutations in residues predicted as
AB  - catalytic, involved in DNA binding dimerization decreased the restriction level to less than
AB  - 1% of the wild type (wt) activity. A subset of mutants exhibiting different levels of
AB  - reduction of the in vivo activity was recloned into an expression vector, overexpressed,
AB  - purified and tested in an in vitro cleavage assay. The results agreed with the in vivo
AB  - analyses, thus corroborating the model-based predictions. Our study represents an example of
AB  - how the computational protein fold-recognition followed by model-based identification and
AB  - experimental validation of functionally important residues can be used to reduce the "white
AB  - spaces" on the structural map of a protein superfamily by providing links between known
AB  - structures and the sequences of their remote homologs. Confident identification of a protein
AB  - fold, which is very difficult in the case of restriction enzymes, is important for the
AB  - selection of targets for high-resolution studies. Completing the picture of
AB  - sequence-structure-function relationships in protein superfamilies becomes an essential task
AB  - in the age of structural genomics and our study may serve as a paradigm for future analyses.
ER  -

TY  - JOUR
AU  - Pazos, A.
AU  - Kodaman, N.
AU  - Piazuelo, M.B.
AU  - Romero-Gallo, J.
AU  - Sobota, R.S.
AU  - Israel, D.A.
AU  - Bravo, L.E.
AU  - Morgan, D.R.
AU  - Wilson, K.T.
AU  - Correa, P.
AU  - Peek, R.M. Jr.
AU  - Williams, S.M.
AU  - Schneider, B.G.
TI  - Draft Genome Sequences of 13 Colombian Helicobacter pylori Strains Isolated from  Pacific Coast and Andean Residents.
JO  - Genome Announcements
PY  - 2017
SP  - e00113
EP  - e00117
VL  - 5
AB  - We present here the draft genomes of 13 Helicobacter pylori strains isolated from Colombian
AB  - residents on the Pacific coast (n = 6) and in the Andes mountains (n =
AB  - 7), locations that differ in gastric cancer risk. These 13 strains were obtained
AB  - from individuals with diagnosed gastric lesions.
ER  -

TY  - JOUR
AU  - Peakman, L.J.
AU  - Antognozzi, M.
AU  - Bickle, T.A.
AU  - Janscak, P.
AU  - Szczelkun, M.D.
TI  - S-Adenosyl Methionine Prevents Promiscuous DNA Cleavage by the EcoP1I type III Restriction Enzyme.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 321
EP  - 335
VL  - 333
AB  - DNA cleavage by the type III restriction endonuclease EcoP1I was analysed on circular and
AB  - catenane DNA in a variety of buffers with different salts.
AB  - In the presence of the cofactor S-adenosyl methionine (AdoMet), and
AB  - irrespective of buffer, only substrates with two EcoP1I sites in inverted
AB  - repeat were susceptible to cleavage. Maximal activity was achieved at a
AB  - Res2Mod2 to site ratio of approximately 1:1 yet resulted in cleavage at
AB  - only one of the two sites. In contrast, the outcome of reactions in the
AB  - absence of AdoMet was dependent upon the identity of the monovalent buffer
AB  - components, in particular the identity of the cation. With Na+, cleavage
AB  - was observed only on substrates with two sites in inverted repeat at
AB  - elevated enzyme to site ratios (>15:1). However, with K+ every substrate
AB  - tested was susceptible to cleavage above an enzyme to site ratio of
AB  - approximately 3:1, including a DNA molecule with two directly repeated
AB  - sites and even a DNA molecule with a single site. Above an enzyme to site
AB  - ratio of 2:1, substrates with two sites in inverted repeat were cleaved at
AB  - both cognate sites. The rates of cleavage suggested two separate events: a
AB  - fast primary reaction for the first cleavage of a pair of inverted sites;
AB  - and an order-of-magnitude slower secondary reaction for the second
AB  - cleavage of the pair or for the first cleavage of all other site
AB  - combinations. EcoP1I enzymes mutated in either the ATPase or nuclease
AB  - motifs did not produce the secondary cleavage reactions. Thus, AdoMet
AB  - appears to play a dual role in type III endonuclease reactions: Firstly,
AB  - as an allosteric activator, promoting DNA association; and secondly, as a
AB  - "specificity factor", ensuring that cleavage occurs only when two
AB  - endonucleases bind two recognition sites in a designated orientation.
AB  - However, given the right conditions, AdoMet is not strictly required for
AB  - DNA cleavage by a type III enzyme.
ER  -

TY  - JOUR
AU  - Peakman, L.J.
AU  - Szczelkun, M.D.
TI  - DNA communications by Type III restriction endonucleases - confirmation of 1D translocation over 3D looping.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 4166
EP  - 4174
VL  - 32
AB  - DNA cleavage by Type III restriction enzymes is governed strictly by the relative arrangement
AB  - of recognition sites on a DNA substrate.  Xendonuclease activity is usually only triggered by
AB  - sequences in head-to-head orientation. Tens to thousands of base pairs can separate these
AB  - sites. Long distance communication over such distances could occur by either one-dimensional
AB  - (1D) DNA translocation or 3D DNA looping. To distinguish between these alternatives, we
AB  - analysed the activity of EcoPI and EcoP15I on DNA catenanes in which the recognition sites
AB  - were either on the same or separate rings. While substrates with a pair of sites located on
AB  - the same ring were cleaved efficiently, catenanes with sites on separate rings were not
AB  - cleaved. These results exclude a simple 3D DNA-looping activity. To characterize the
AB  - interactions further, EcoPI was incubated with plasmids carrying two recognition sites
AB  - interspersed with two 21res sites for site-specific recombination by Tn21 resolvase;
AB  - inhibition of recombination would indicate the formation of stable DNA loops. No inhibition
AB  - was observed, even under conditions where EcoPI translocation could also occur.
ER  -

TY  - JOUR
AU  - Peakman, L.J.
AU  - Szczelkun, M.D.
TI  - S-Adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3934
EP  - 3945
VL  - 37
AB  - In the absence of the methyl donor S-adenosyl methionine and under certain permissive reaction
AB  - conditions, EcoPI shows non-specific endonuclease
AB  - activity. We show here that the cofactor analogue S-adenosyl homocysteine
AB  - promotes this promiscuous DNA cleavage. Additionally, an extensive
AB  - exonuclease-like processing of the DNA is also observed that can even
AB  - result in digestion of non-specific DNA in trans. We suggest a model for
AB  - how DNA communication events initiating from non-specific sites, and in
AB  - particular free DNA ends, could produce the observed cleavage patterns.
ER  -

TY  - JOUR
AU  - Pearce, S.L.
AU  - Pandey, R.
AU  - Dorrian, S.J.
AU  - Russell, R.J.
AU  - Oakeshott, J.G.
AU  - Pandey, G.
TI  - Genome sequence of the newly isolated chemolithoautotrophic Bradyrhizobiaceae strain SG-6C.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5057
EP  - 5057
VL  - 193
AB  - Strain SG-6C (DSM 23264, CCM 7827) is a chemolithoautotrophic bacterium, of the family
AB  - Bradyrhizobiaceae. It can also grow heterotrophically under
AB  - appropriate environmental conditions. Here we report the annotated genome
AB  - sequence of this strain in a single 4.3-Mb circular scaffold.
ER  -

TY  - JOUR
AU  - Pearce, S.L.
AU  - Pushiri, H.
AU  - Oakeshott, J.G.
AU  - Russell, R.J.
AU  - Pandey, G.
TI  - Draft Genome Sequence of Ralstonia sp. Strain GA3-3, Isolated from Australian Suburban Soil.
JO  - Genome Announcements
PY  - 2013
SP  - e00414
EP  - e00413
VL  - 1
AB  - Ralstonia sp. strain GA3-3 is a hexachlorocyclohexane (HCH)-degrading bacterial strain
AB  - isolated from suburban soil in Canberra, Australia. The genome of strain
AB  - GA3-3 was sequenced to investigate its ability to degrade alpha-HCH. Here, we
AB  - report the annotated genome sequence of this strain.
ER  -

TY  - JOUR
AU  - Pearson, B.M.
AU  - Gaskin, D.J.
AU  - Segers, R.P.
AU  - Wells, J.M.
AU  - Nuijten, P.J.
AU  - Mvan, V.A.H.
TI  - The Complete Genome Sequence of Campylobacter jejuni Strain 81116 (NCTC11828).
JO  - J. Bacteriol.
PY  - 2007
SP  - 8402
EP  - 8403
VL  - 189
AB  - Campylobacter jejuni is a major human enteric pathogen that displays genetic variability via
AB  - genomic reorganization and phase variation. This
AB  - variability can adversely affect the outcomes and reproducibility of
AB  - experiments. C. jejuni strain 81116 (NCTC11828) has been suggested to be a
AB  - genetically stable strain (G. Manning, B. Duim, T. Wassenaar, J. A.
AB  - Wagenaar, A. Ridley, and D. G. Newell, Appl. Environ. Microbiol.
AB  - 67:1185-1189, 2001), is amenable to genetic manipulation, and is infective
AB  - for chickens. Here we report the finished annotated genome sequence of C.
AB  - jejuni strain 81116.
ER  -

TY  - JOUR
AU  - Pearson, B.M.
AU  - Rokney, A.
AU  - Crossman, L.C.
AU  - Miller, W.G.
AU  - Wain, J.
AU  - van Vliet, A.H.
TI  - Complete Genome Sequence of the Campylobacter coli Clinical Isolate 15-537360.
JO  - Genome Announcements
PY  - 2013
SP  - e01056
EP  - e01013
VL  - 1
AB  - Campylobacter coli strain 15-537360 was originally isolated in 2001 from a 42-year-old patient
AB  - with gastroenteritis. Here, we report its complete genome
AB  - sequence, which comprises a 1.7-Mbp chromosome and a 29-kbp conjugative cryptic
AB  - plasmid. This is the first complete genome sequence of a clinical isolate of C.
AB  - coli.
ER  -

TY  - JOUR
AU  - Pearson, M.D.
AU  - Noller, H.F.
TI  - The Draft Genome of Planococcus donghaensis MPA1U2 Reveals Nonsporulation Pathways Controlled by a Conserved Spo0A Regulon.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6106
EP  - 6106
VL  - 193
AB  - The Planococcaceae are extreme survivors, having been cultured from environments such as deep
AB  - sea sediments, marine solar salterns, glaciers,
AB  - permafrost, Antarctic deserts, and sea ice brine. The family contains both
AB  - sporulating and nonsporulating genera. Here we present the unclosed, draft
AB  - genome sequence of Planococcus donghaensis strain MPA1U2, a nonsporulating
AB  - psychrotrophic bacterium isolated from surface coastal water of the
AB  - Pacific Ocean.
ER  -

TY  - JOUR
AU  - Pearson, M.M. et al.
TI  - Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.
JO  - J. Bacteriol.
PY  - 2008
SP  - 4027
EP  - 4037
VL  - 190
AB  - The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract
AB  - infections in individuals with long-term indwelling
AB  - catheters or with complicated urinary tracts (e.g., due to spinal cord
AB  - injury or anatomic abnormality). P. mirabilis bacteriuria may lead to
AB  - acute pyelonephritis, fever, and bacteremia. Most notoriously, this
AB  - pathogen uses urease to catalyze the formation of kidney and bladder
AB  - stones or to encrust or obstruct indwelling urinary catheters. Here we
AB  - report the complete genome sequence of P. mirabilis HI4320, a
AB  - representative strain cultured in our laboratory from the urine of a
AB  - nursing home patient with a long-term (> or =30 days) indwelling urinary
AB  - catheter. The genome is 4.063 Mb long and has a G+C content of 38.88%.
AB  - There is a single plasmid consisting of 36,289 nucleotides. Annotation of
AB  - the genome identified 3,685 coding sequences and seven rRNA loci. Analysis
AB  - of the sequence confirmed the presence of previously identified virulence
AB  - determinants, as well as a contiguous 54-kb flagellar regulon and 17 types
AB  - of fimbriae. Genes encoding a potential type III secretion system were
AB  - identified on a low-G+C-content genomic island containing 24 intact genes
AB  - that appear to encode all components necessary to assemble a type III
AB  - secretion system needle complex. In addition, the P. mirabilis HI4320
AB  - genome possesses four tandem copies of the zapE metalloprotease gene,
AB  - genes encoding six putative autotransporters, an extension of the atf
AB  - fimbrial operon to six genes, including an mrpJ homolog, and genes
AB  - encoding at least five iron uptake mechanisms, two potential type IV
AB  - secretion systems, and 16 two-component regulators.
ER  -

TY  - JOUR
AU  - Pech, M.
AU  - Streeck, R.E.
AU  - Zachau, H.G.
TI  - Patchwork structure of a bovine satellite DNA.
JO  - Cell
PY  - 1979
SP  - 883
EP  - 893
VL  - 18
AB  - According to a previous restriction nuclease analysis, bovine 1.706 satellite
AB  - DNA (density 1.706 g/cm3 in CsCl) is organized in an unusual structure of
AB  - superimposed long- and short-range repeats (Streeck and Zachau, 1978).  We have
AB  - now determined the nucleotide sequence of this satellite DNA in both cloned
AB  - fragments and fragments from the total satellite DNA.  Each long-range repeat
AB  - unit (about 2350 bp) is divided into four segments.  Each segment consists of
AB  - different variants of a basic 23 bp sequence which is itself composed of a
AB  - dodecanucleotide and a related undecanucleotide.  A total of 2400 nucleotides
AB  - have been sequenced.  Detailed analysis of the sequence divergence reveals that
AB  - both the overall extent of divergence and the frequency of base changes at
AB  - individual positions of the 23 bp repeats are characteristically different in
AB  - the various segments.  Preferentially methylated sites and a high incidence of
AB  - symmetry elements are found.  In two of the four segments, 22 of 23 bp of the
AB  - prototype sequence are included in six overlapping elements of dyad symmetry
AB  - and in a palindrome.  A scheme for the evolution of the satellite DNA from a
AB  - basic dodecanucleotide is proposed which is based on the different degrees of
AB  - divergence for the various repeats superimposed in this satellite DNA.
ER  -

TY  - JOUR
AU  - Pechtl, A.
AU  - Ruckert, C.
AU  - Maus, I.
AU  - Koeck, D.E.
AU  - Trushina, N.
AU  - Kornberger, P.
AU  - Schwarz, W.H.
AU  - Schluter, A.
AU  - Liebl, W.
AU  - Zverlov, V.V.
TI  - Complete Genome Sequence of the Novel Cellulolytic, Anaerobic, Thermophilic Bacterium Herbivorax saccincola Type Strain GGR1, Isolated from a Lab Scale  Biogas Reactor as Established by Illumina and Nanopore MinION Sequencing.
JO  - Genome Announcements
PY  - 2018
SP  - e01493
EP  - e01417
VL  - 6
AB  - The cellulolytic bacterium Herbivorax saccincola strain GGR1, which represents the type strain
AB  - of this species, was isolated from the in vivo enriched
AB  - cellulose-binding community of a lab scale thermophilic biogas reactor. Here, we
AB  - report the complete genome sequence of H. saccincola GGR1(T), the first isolated
AB  - member of the genus Herbivorax.
ER  -

TY  - JOUR
AU  - Pedersen, K.
AU  - Bengtsson, A.
AU  - Edlund, J.
AU  - Rabe, L.
AU  - Hazen, T.
AU  - Chakraborty, R.
AU  - Goodwin, L.
AU  - Shapiro, N.
TI  - Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2.
JO  - Genome Announcements
PY  - 2014
SP  - e00509
EP  - e00514
VL  - 2
AB  - Desulfovibrio aespoeensis Aspo-2, DSM 10631(T), is a mesophilic, hydrogenotrophic
AB  - sulfate-reducing bacterium sampled from a 600-m-deep subsurface aquifer in hard
AB  - rock under the island of Aspo in southeastern Sweden. We report the genome
AB  - sequence of this bacterium, which is a 3,629,109-bp chromosome; plasmids were not
AB  - found.
ER  -

TY  - JOUR
AU  - Pedersen, T.B.
AU  - Kot, W.P.
AU  - Hansen, L.H.
AU  - Sorensen, S.J.
AU  - Broadbent, J.R.
AU  - Vogensen, F.K.
AU  - Ardo, Y.
TI  - Genome Sequence of Leuconostoc mesenteroides subsp. cremoris Strain T26, Isolated from Mesophilic Undefined Cheese Starter.
JO  - Genome Announcements
PY  - 2014
SP  - e00485
EP  - e00414
VL  - 2
AB  - Leuconostoc is the main group of heterofermentative bacteria found in mesophilic  dairy
AB  - starters. They grow in close symbiosis with the Lactococcus population and
AB  - are able to degrade citrate. Here we present a draft genome sequence of
AB  - Leuconostoc mesenteroides subsp. cremoris strain T26.
ER  -

TY  - JOUR
AU  - Pedersen, T.B.
AU  - Kot, W.P.
AU  - Hansen, L.H.
AU  - Sorensen, S.J.
AU  - Broadbent, J.R.
AU  - Vogensen, F.K.
AU  - Ardo, Y.
TI  - Genome Sequences of Two Leuconostoc pseudomesenteroides Strains Isolated from Danish Dairy Starter Cultures.
JO  - Genome Announcements
PY  - 2014
SP  - e00484
EP  - e00414
VL  - 2
AB  - The lactic acid bacterium Leuconostoc pseudomesenteroides can be found in mesophilic cheese
AB  - starters, where it produces aromatic compounds from, e.g.,
AB  - citrate. Here, we present the draft genome sequences of two L.
AB  - pseudomesenteroides strains isolated from traditional Danish cheese starters.
ER  -

TY  - JOUR
AU  - Pedulla, M.L. et al.
TI  - 
JO  - Cell
PY  - 2003
SP  - 171
EP  - 182
VL  - 113
AB  - Bacteriophages are the most abundant organisms in the biosphere and play major roles in the
AB  - ecological balance of microbial life. The genomic
AB  - sequences of ten newly isolated mycobacteriophages suggest that the
AB  - bacteriophage population as a whole is amazingly diverse and may represent
AB  - the largest unexplored reservoir of sequence information in the biosphere.
AB  - Genomic comparison of these mycobacteriophages contributes to our
AB  - understanding of the mechanisms of viral evolution and provides compelling
AB  - evidence for the role of illegitimate recombination in horizontal genetic
AB  - exchange. The promiscuity of these recombination events results in the
AB  - inclusion of many unexpected genes including those implicated in
AB  - mycobacterial latency, the cellular and immune responses to mycobacterial
AB  - infections, and autoimmune diseases such as human lupus. While the role of
AB  - phages as vehicles of toxin genes is well established, these observations
AB  - suggest a much broader involvement of phages in bacterial virulence and
AB  - the host response to bacterial infections.
ER  -

TY  - JOUR
AU  - Peek, R.M. Jr.
AU  - Thompson, S.A.
AU  - Atherton, J.C.
AU  - Blaser, M.J.
AU  - Miller, G.G.
TI  - Expression of ICEA, a novel ulcer-associated H. pylori gene, is induced by contact with gastric epithelial cells and is associated with enhanced mucosal IL-8.
JO  - Gut
PY  - 1996
SP  - A71
EP  - A71
VL  - 39
AB  - cagA+tox+ H. pylori strains are linked with peptic ulceration but most persons infected with
AB  - such isolates remain disease-free; thus, other unidentified virulence genes may be important
AB  - in pathogenesis.  For H. pylori, adherence to gastric epithelium may provide a stimulus for
AB  - induction of virulence gene expression.  iceA is a novel H. pylori gene that is selectively
AB  - up-regulated following contact with gastric epithelial cells.  The aims of this study were to
AB  - characterize iceA allellic diversity, correlate iceA genotypes with H. pylori virulence
AB  - determinants, peptic ulcer disease and in vivo IL-8 production, and examine expression of iceA
AB  - alleles following contact with gastric epithelial cells.
ER  -

TY  - JOUR
AU  - Peet, K.C.
AU  - Thompson, J.R.
TI  - Draft Genome Sequences of Supercritical CO2-Tolerant Bacteria Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214.
JO  - Genome Announcements
PY  - 2015
SP  - e00140
EP  - e00115
VL  - 3
AB  - We report draft genome sequences of Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214
AB  - isolated through enrichment of samples from geologic sequestration
AB  - sites in pressurized bioreactors containing a supercritical (sc) CO2 headspace.
AB  - Their genome sequences expand the phylogenetic range of sequenced bacilli and
AB  - allow characterization of molecular mechanisms of scCO2 tolerance.
ER  -

TY  - JOUR
AU  - Pei, D.
AU  - Hill-Clemons, C.
AU  - Carissimo, G.
AU  - Yu, W.
AU  - Vernick, K.D.
AU  - Xu, J.
TI  - Draft Genome Sequences of Two Strains of Serratia spp. from the Midgut of the Malaria Mosquito Anopheles gambiae.
JO  - Genome Announcements
PY  - 2015
SP  - e00090
EP  - e00015
VL  - 3
AB  - Here, we report the annotated draft genome sequences of two strains of Serratia spp., Ag1 and
AB  - Ag2, isolated from the midgut of two different strains of Anopheles
AB  - gambiae. The genomes of these two strains are almost identical.
ER  -

TY  - JOUR
AU  - Pei, D.
AU  - Nicholson, A.C.
AU  - Jiang, J.
AU  - Chen, H.
AU  - Whitney, A.M.
AU  - Villarma, A.
AU  - Bell, M.
AU  - Humrighouse, B.
AU  - Rowe, L.A.
AU  - Sheth, M.
AU  - Batra, D.
AU  - Juieng, P.
AU  - Loparev, V.N.
AU  - McQuiston, J.R.
AU  - Lan, Y.
AU  - Ma, Y.
AU  - Xu, J.
TI  - Complete Circularized Genome Sequences of Four Strains of Elizabethkingia anophelis, Including Two Novel Strains Isolated from Wild-Caught Anopheles  sinensis.
JO  - Genome Announcements
PY  - 2017
SP  - e01359
EP  - e01317
VL  - 5
AB  - We provide complete circularized genome sequences of two mosquito-derived Elizabethkingia
AB  - anophelis strains with draft sequences currently in the public
AB  - domain (R26 and Ag1), and two novel E. anophelis strains derived from a different
AB  - mosquito species, Anopheles sinensis (AR4-6 and AR6-8). The genetic similarity of
AB  - all four mosquito-derived strains is remarkable.
ER  -

TY  - JOUR
AU  - Pein, C.-D.
AU  - Reuter, M.
AU  - Cech, D.
AU  - Kruger, D.H.
TI  - Oligonucleotide duplexes containing CC(A/T)GG stimulate cleavage of refractory DNA by restriction endonuclease EcoRII.
JO  - FEBS Lett.
PY  - 1989
SP  - 141
EP  - 144
VL  - 245
AB  - Some DNA species are resistant towards the restriction endonuclease EcoRII
AB  - despite the presence of unmodified recognition sites.  We show that 14
AB  - base-pair oligonucleotide duplexes containing the EcoRII recognition site
AB  - 5'-CC(A/T)GG are cleaved by this enzyme and are able to stimulate EcoRII
AB  - cleavage of such resistant DNA molecules (e.g. DNA of bacterial virus T3).  A
AB  - direct correlation between the concentration of oligonucleotide duplex
AB  - molecules and the degree of EcoRII digestion of the primarily resistant DNA is
AB  - observed.  This indicates a stoichiometric rather than a catalytic mode of
AB  - enzyme activation.  An excess of DNA devoid of EcoRII sites (non-site DNA, e.g.
AB  - MvaI-digested T7 DNA) does not interfere with the activity of EcoRII.
ER  -

TY  - JOUR
AU  - Pein, C.-D.
AU  - Reuter, M.
AU  - Meisel, A.
AU  - Cech, D.
AU  - Kruger, D.H.
TI  - Activation of restriction endonuclease EcoRII does not depend on the cleavage of stimulator DNA.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 5139
EP  - 5142
VL  - 19
AB  - The restriction endonuclease EcoRII is unable to cleave DNA molecules when
AB  - recognition sites are very far apart.  The enzyme, however can be activated in
AB  - the presence of DNA molecules with a high frequency of EcoRII sites or by
AB  - oligonucleotides containing recognition sites:  Addition of the activator
AB  - molecules stimulates cleavage of the refractory substrate.  We now show that
AB  - endonucleolysis of the stimulator molecules is not a necessary prerequisite of
AB  - enzyme activation.  A total EcoRII digest of pBR322 DNA or oligonucleotide
AB  - duplexes with simulated EcoRII ends (containing the 5' phosphate group), as
AB  - well as oligonucleotide duplexes containing modified bases within the EcoRII
AB  - site, making them resistant to cleavage, are all capable of enzyme activation.
AB  - For activation EcoRII requires interaction with at least two recognition sites.
AB  - The two sites may be on the same DNA molecule, on different oligonucleotide
AB  - duplexes, or on one DNA molecule and one oligonucleotide duplex.  The
AB  - efficiency of functional intramolecular cooperation decreases with increasing
AB  - distance between the sites.  Intermolecular site interaction is inversely
AB  - related to the size of the stimulator oligonucleotide duplex.  The data are in
AB  - agreement with a model whereby EcoRII simultaneously interacts with two
AB  - recognition sites in the active complex, but cleavage of the site serving as an
AB  - allosteric activator is not necessary.
ER  -

TY  - JOUR
AU  - Pein, C.D.
AU  - Cech, D.
AU  - Gromova, E.S.
AU  - Orezkaya, T.S.
AU  - Shabarova, Z.A.
AU  - Kubareva, E.A.
TI  - Interaction of the MvaI restriction enzyme with synthetic DNA fragments.
JO  - Nucleic Acids Symp. Ser.
PY  - 1987
SP  - 225
EP  - 228
VL  - SS18
AB  - The cleavage of synthetic DNA duplexes by the restriction endonuclease MvaI has
AB  - been studied.  The main result of the cleavage experiments is that MvaI cleaves
AB  - unmodified duplexes in two single strand scissions in separate events and that
AB  - the two strands are cleaved at significantly different rates.  One strand nicks
AB  - within the recognition site do not affect the cleavage.  Furthermore, neither a
AB  - pyrophosphate internucleotide bond modification in one strand nor the absence
AB  - of one phosphate group at the central dA-residue of the recognition site
AB  - inhibits the cleavage of the second strand.
ER  -

TY  - JOUR
AU  - Pelaez, A.I.
AU  - Ribas-Aparicio, R.M.
AU  - Gomez, A.
AU  - Rodicio, M.R.
TI  - Establishment of a hybrid SalI-HgiDII type II restriction-modification system.
JO  - Biol. Chem.
PY  - 1998
SP  - 583
EP  - 584
VL  - 379
AB  - In the SalI system, endonuclease activity can be only achieved in the presence of a functional
AB  - modification gene.  Thus, the DNA methyltransferase is involved in the control of restriction.
AB  - By fusion of the restriction gene of the SalI system to the modification gene of the
AB  - isospecific HgiDII system a hybrid type II restriction-modification system was created.
AB  - Although in the hybrid situation the level of endonuclease activity was significantly lower
AB  - than in the natural system, the HgiDII modification enzyme clearly supports SalI restriction.
AB  - The mechanism by which the two isospecific methyltransferases control restriction is currently
AB  - under study.
ER  -

TY  - JOUR
AU  - Pellenz, S.
AU  - Dujon, B.
AU  - Schafer, B.
TI  - Target site cleavage by the homing endonuclease I-SpomI from fission yeast mitochondria.
JO  - Yeast
PY  - 2003
SP  - S47
EP  - S47
VL  - 20
AB  - Proteins encoded by mobile group I introns promote invasion into target DNAs.  The LAGLIDADG
AB  - homing endonuclease I-SpomI from the intron cox1Ilb of S. pombe mitochondria recognizes a
AB  - target DNA-sequence of 20bp.  As other representatives of this enzyme class I-SpomI generates
AB  - a 4nt 3' overhang.  Because of the length of the recognition sequence it can be employed for
AB  - the induction of specific double strand brakes in vitro and in vivo.  Since the recognition
AB  - site is almost palindromic, we changed it in such a way to give rise to a complete palindrome.
AB  - Since one of those variants was cut as well as the wild-type sequence, we assume that the
AB  - enzyme forms dimers and only one of the two LAGLIDADG-motifs is involved in the recognition of
AB  - the DNA-substrate.  An antibody against I-SpomI allows the determination of the active form in
AB  - mitochondrial extracts of the fission yeast.  Furthermore we introduced mutations into both
AB  - LADLIDADG-motifs: in motif P1 the aspartic residues were changed into alanine, in P2 the two
AB  - glutamic residues.  Inactivation of one of those motifs employed in the cutting mechanism was
AB  - supposed to result in a DNA single strand break actively of the mutant protein.  The
AB  - experiments were done in parallel with I-SceI from S. cerevisiae to have a direct comparison
AB  - between the different enzymes.  Enzymes with nicking activity can serve to study as well the
AB  - repair mechanisms of SSB and to give insights into the cutting mechanism of LAGLIDADG homing
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Pellenz, S.
AU  - Harington, A.
AU  - Dujon, B.
AU  - Wolf, K.
AU  - Schaefer, B.
TI  - Characterization of the I-SpomI endonuclease from fission yeast: Insights into the evolution of a group I intron-encoded homing  endonuclease.
JO  - J. Mol. Evol.
PY  - 2002
SP  - 302
EP  - 313
VL  - 55
AB  - The first group I intron in the cox1 gene (cox1I1b) of the mitochondrial genome of the fission
AB  - yeast Schizosaccharomyces pombe is
AB  - a mobile DNA element. The mobility is dependent on an endonuclease
AB  - protein that is encoded by an intronic open reading frame (ORF). The
AB  - intron-encoded endonuclease is a typical member of the LAGLIDADG
AB  - protein family of endonucleases with two consensus motifs. In addition
AB  - to this, analysis of several intron mutants revealed that this protein
AB  - is required for intron splicing. However, this protein is one of the
AB  - few group I intron-encoded proteins that functions in RNA splicing
AB  - simultaneously with its DNA endonuclease activity. We report here on
AB  - the biochemical characterization of the endonuclease activity of this
AB  - protein artificially expressed in Escherichia coli. Although the
AB  - intronic ORF is expressed as a fusion protein with the upstream exon in
AB  - vivo, the experiments showed that a truncated translation product
AB  - consisting of the C-terminal 304 codons of the cox1I1b ORF restricted
AB  - to loop 8 of the intron RNA secondary structure is sufficient for the
AB  - specific endonuclease activity in vitro. Based on the results, we
AB  - speculate on the evolution of site-specific homing endonucleases
AB  - encoded by group I introns in eukaryotes.
ER  -

TY  - JOUR
AU  - Pelletier, E.
AU  - Kreimeyer, A.
AU  - Bocs, S.
AU  - Rouy, Z.
AU  - Gyapay, G.
AU  - Chouari, R.
AU  - Riviere, D.
AU  - Ganesan, A.
AU  - Daegelen, P.
AU  - Sghir, A.
AU  - Cohen, G.N.
AU  - Medigue, C.
AU  - Weissenbach, J.
AU  - Le Paslier, D.
TI  - "Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.
JO  - J. Bacteriol.
PY  - 2008
SP  - 2572
EP  - 2579
VL  - 190
AB  - Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet
AB  - been cultivated. Here, we present, from a
AB  - metagenomic analysis of an anaerobic digester of a municipal wastewater
AB  - treatment plant, a reconstruction of the complete genome of a bacterium
AB  - belonging to the WWE1 candidate division. In silico proteome analysis
AB  - indicated that this bacterium might derive most of its carbon and energy
AB  - from the fermentation of amino acids, and hence, it was provisionally
AB  - classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus
AB  - Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is
AB  - present in many anaerobic digesters. This report highlights how
AB  - environmental sequence data might provide genomic and functional
AB  - information about a new bacterial clade whose members are involved in
AB  - anaerobic digestion.
ER  -

TY  - JOUR
AU  - Pelludat, C.
AU  - Mirold, S.
AU  - Hardt, W.D.
TI  - The SopEPhi Phage Integrates into the ssrA Gene of Salmonella enterica Serovar Typhimurium A36 and Is Closely Related to the Fels-2 Prophage.
JO  - J. Bacteriol.
PY  - 2003
SP  - 5182
EP  - 5191
VL  - 185
AB  - Salmonella spp. are enteropathogenic gram-negative bacteria that use a large array of
AB  - virulence factors to colonize the host, manipulate host
AB  - cells, and resist the host's defense mechanisms. Even closely related
AB  - Salmonella strains have different repertoires of virulence factors.
AB  - Bacteriophages contribute substantially to this diversity. There is
AB  - increasing evidence that the reassortment of virulence factor repertoires
AB  - by converting phages like the GIFSY phages and SopEPhi may represent an
AB  - important mechanism in the adaptation of Salmonella spp. to specific hosts
AB  - and to the emergence of new epidemic strains. Here, we have analyzed in
AB  - more detail SopEPhi, a P2-like phage from Salmonella enterica serovar
AB  - Typhimurium DT204 that encodes the virulence factor SopE. We have cloned
AB  - and characterized the attachment site (att) of SopEPhi and found that its
AB  - 47-bp core sequence overlaps the 3' terminus of the ssrA gene of serovar
AB  - Typhimurium. Furthermore, we have demonstrated integration of SopEPhi into
AB  - the cloned attB site of serovar Typhimurium A36. Sequence analysis of the
AB  - plasmid-borne prophage revealed that SopEPhi is closely related to (60 to
AB  - 100% identity over 80% of the genome) but clearly distinct from the Fels-2
AB  - prophage of serovar Typhimurium LT2 and from P2-like phages in the serovar
AB  - Typhi CT18 genome. Our results demonstrate that there is considerable
AB  - variation among the P2-like phages present in closely related Salmonella
AB  - spp.
ER  -

TY  - JOUR
AU  - Pembroke, J.T.
AU  - Piterina, A.V.
TI  - A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements.
JO  - FEMS Microbiol. Lett.
PY  - 2006
SP  - 80
EP  - 88
VL  - 264
AB  - A novel R391-like ICE (integrating conjugative element) has been detected in the  4.2 MB
AB  - genome of Shewanella putrefaciens W3-18-1 located on three different
AB  - contigs. Assembly of the ICE encoding contigs based on similarity with R391
AB  - revealed a mosaic element of plasmid, phage and transposon-like sequences typical
AB  - of SXT/R391 ICE-like elements. The element, which is 110 057 bp in length, was
AB  - highly similar to R391 sequences, with most related ORFs showing >96% amino acid
AB  - sequence identity. The element, designated ICESpuPO1, contained a number of
AB  - inserts determining resistance to copper and other heavy metals and a
AB  - broad-spectrum RND efflux pump similar to antibiotic efflux systems. The element
AB  - was integrated into the Shewanella prfC gene in a manner similar to related
AB  - ICE-like elements. The chromosomal element junctions contained a 17-bp
AB  - SXT/R391-like attL and attR site and an unannotated ORF between attL and the ICE
AB  - integrase encoding a putative recombinational directional factor necessary for
AB  - excision, with 100% amino acid identity to the R391 ORF4 product.
ER  -

TY  - JOUR
AU  - Pena, A.
AU  - Busquets, A.
AU  - Gomila, M.
AU  - Bosch, R.
AU  - Nogales, B.
AU  - Garcia-Valdes, E.
AU  - Lalucat, J.
AU  - Bennasar, A.
TI  - Draft Genome of Pseudomonas stutzeri Strain ZoBell (CCUG 16156), a Marine Isolate and Model Organism for Denitrification Studies.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1277
EP  - 1278
VL  - 194
AB  - Pseudomonas stutzeri strain ZoBell, formerly a strain of Pseudomonas perfectomarina (CCUG
AB  - 16156 = ATCC 14405), is a model organism for
AB  - denitrification. It was isolated by ZoBell in 1944 from a marine sample, and here
AB  - we report the first genome draft of a strain assigned to genomovar 2 of the
AB  - species P. stutzeri.
ER  -

TY  - JOUR
AU  - Pena, A.
AU  - Busquets, A.
AU  - Gomila, M.
AU  - Mayol, J.
AU  - Bosch, R.
AU  - Nogales, B.
AU  - Garcia-Valdes, E.
AU  - Bennasar, A.
AU  - Lalucat, J.
TI  - Draft Genome of Pseudomonas stutzeri Strain NF13, a Nitrogen Fixer Isolated from  the Galapagos Rift Hydrothermal Vent.
JO  - Genome Announcements
PY  - 2013
SP  - e0011313
EP  - e0011313
VL  - 1
AB  - Pseudomonas stutzeri strain NF13 was isolated from a water sample taken at a hydrothermal vent
AB  - in the Galapagos rift. It was selected for its ability to
AB  - metabolize sulfur compounds and to grow diazotrophically. Here, we report the
AB  - first draft genome of a member of genomovar 19 of the species.
ER  -

TY  - JOUR
AU  - Pena, A.
AU  - Busquets, A.
AU  - Gomila, M.
AU  - Mulet, M.
AU  - Gomila, R.M.
AU  - Reddy, T.B.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.
AU  - Markowitz, V.
AU  - Garcia-Valdes, E.
AU  - Goker, M.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.
AU  - Lalucat, J.
TI  - High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T)  type strains.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 55
EP  - 55
VL  - 11
AB  - Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and
AB  - is phylogenetically divided into several groups. The Pseudomonas
AB  - putida phylogenetic branch includes at least 13 species of environmental and
AB  - industrial interest, plant-associated bacteria, insect pathogens, and even some
AB  - members that have been found in clinical specimens. In the context of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project, we present the permanent,
AB  - high-quality draft genomes of the type strains of 3 taxonomically and
AB  - ecologically closely related species in the Pseudomonas putida phylogenetic
AB  - branch: Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and
AB  - Pseudomonas cremoricolorata DSM 17059(T). All three genomes are comparable in
AB  - size (4.6-4.9 Mb), with 4,119-4,459 protein-coding genes. Average nucleotide
AB  - identity based on BLAST comparisons and digital genome-to-genome distance
AB  - calculations are in good agreement with experimental DNA-DNA hybridization
AB  - results. The genome sequences presented here will be very helpful in elucidating
AB  - the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.
ER  -

TY  - JOUR
AU  - Pena-Gonzalez, A.
AU  - Marston, C.K.
AU  - Rodriguez-R, L.M.
AU  - Kolton, C.B.
AU  - Garcia-Diaz, J.
AU  - Theppote, A.
AU  - Frace, M.
AU  - Konstantinidis, K.T.
AU  - Hoffmaster, A.R.
TI  - Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids.
JO  - Genome Announcements
PY  - 2017
SP  - e00181
EP  - e00117
VL  - 5
AB  - We present the genome sequence of Bacillus cereus LA2007, a strain isolated in 2007 from a
AB  - fatal pneumonia case in Louisiana. Sequence-based genome analysis
AB  - revealed that LA2007 carries a plasmid highly similar to Bacillus anthracis pXO1,
AB  - including the genes responsible for the production and regulation of anthrax
AB  - toxin.
ER  -

TY  - JOUR
AU  - Pena-Montenegro, T.D.
AU  - Dussan, J.
TI  - Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 42
EP  - 56
VL  - 9
AB  - Lysinibacillus sphaericus strain OT4b.31 is a native Colombian strain having no larvicidal
AB  - activity against Culex quinquefasciatus and is widely applied in the
AB  - bioremediation of heavy-metal polluted environments. Strain OT4b.31 was placed
AB  - between DNA homology groups III and IV. By gap-filling and alignment steps, we
AB  - propose a 4,096,672 bp chromosomal scaffold. The whole genome (consisting of
AB  - 4,856,302 bp long, 94 contigs and 4,846 predicted protein-coding sequences)
AB  - revealed differences in comparison to the L. sphaericus C3-41 genome, such as
AB  - syntenial relationships, prophages and putative mosquitocidal toxins.
AB  - Sphaericolysin B354, the coleopteran toxin Sip1A and heavy metal resistance
AB  - clusters from nik, ars, czc, cop, chr, czr and cad operons were identified.
AB  - Lysinibacillus sphaericus OT4b.31 has applications not only in bioremediation
AB  - efforts, but also in the biological control of agricultural pests.
ER  -

TY  - JOUR
AU  - Pena-Montenegro, T.D.
AU  - Lozano, L.
AU  - Dussan, J.
TI  - Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 2
EP  - 2
VL  - 10
AB  - Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in
AB  - the Easter Planes of Colombia. This strain has potential in
AB  - bioremediation of heavy-metal polluted environments and biological control of
AB  - Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene
AB  - sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus
AB  - taxonomic group 1 that comprises mosquito pathogenic strains. After a combination
AB  - assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp
AB  - chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60
AB  - contigs and 5,209 predicted-coding sequences) revealed strong functional and
AB  - syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx),
AB  - binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik,
AB  - ars, czc, mnt, ter, cop, cad, and znu operons were identified.
ER  -

TY  - JOUR
AU  - Peng, J.
AU  - Yang, L.
AU  - Yang, F.
AU  - Yang, J.
AU  - Yan, Y.
AU  - Nie, H.
AU  - Zhang, X.
AU  - Xiong, Z.
AU  - Jiang, Y.
AU  - Cheng, F.
AU  - Xu, X.
AU  - Chen, S.
AU  - Sun, L.
AU  - Li, W.
AU  - Shen, Y.
AU  - Shao, Z.
AU  - Liang, X.
AU  - Xu, J.
AU  - Jin, Q.
TI  - Characterization of ST-4821 complex, a unique Neisseria meningitidis clone.
JO  - Genomics
PY  - 2008
SP  - 78
EP  - 87
VL  - 91
AB  - Ten outbreaks of a new serogroup C meningococcal disease emerged during
AB  - 2003-2005 in China. The multilocus sequence typing results indicated that
AB  - unique sequence type 4821 clone meningococci were responsible for these
AB  - outbreaks. Herein, we determined the entire genomic DNA sequence of
AB  - serogroup C isolate 053442, which belongs to ST-4821. Comparison of 053442
AB  - gene contents with other meningococcal genomes shows that they have
AB  - similar characteristics, including thousands of repetitive elements and
AB  - simple sequence repeats, numerous phase-variable genes, and similar
AB  - virulence-related factors. However, many strain-specific regions were
AB  - found in each genome. We also present the results of a genomic comparison
AB  - of 28 ST-4821 complex isolates that were isolated from different
AB  - serogroups using comparative genomic hybridization analysis. Genome
AB  - comparison between the newly emerged hyperinvasive isolates belonging to
AB  - different serogroups will further our understanding of their respective
AB  - pathogenetic mechanisms.
ER  -

TY  - JOUR
AU  - Peng, L.
AU  - Song, L.
AU  - Sun, L.
AU  - Cai, Y.
AU  - Wang, L.
AU  - Yu, B.
TI  - Genome Sequence of Bacillus coagulans P38, an Efficient Polymer-Grade l-Lactate Producer from Cellulosic Substrates.
JO  - Genome Announcements
PY  - 2015
SP  - e00495
EP  - e00415
VL  - 3
AB  - Bacillus coagulans P38 is an efficient polymer-grade l-lactic acid producer from  a cellulosic
AB  - carbon source. Here, the draft 3.37-Mb genome sequence of this
AB  - potential strain may provide useful information to further improve the strain
AB  - performance for higher titers and, importantly, to understand the mechanism of
AB  - its high tolerance for 2-furfural.
ER  -

TY  - JOUR
AU  - Peng, Q.
AU  - Yi, L.
AU  - Peng, Q.
AU  - Peng, Y.
TI  - Draft Genome Sequence of the Potassium Feldspar-Solubilizing Bacterium Ensifer adhaerens L18.
JO  - Genome Announcements
PY  - 2017
SP  - e00199
EP  - e00117
VL  - 5
AB  - Ensifer adhaerens L18, isolated from potassium feldspar mining area soil, was found to be
AB  - capable of solubilizing K from an insoluble K-bearing mineral source.
AB  - Here, we report the draft genome sequence and annotation of the
AB  - feldspar-solubilizing bacterium Ensifer adhaerens L18. These data provide the
AB  - basis to investigate the relative impact of bacteria in feldspar solubilizing and
AB  - the molecular mechanism of the potassium feldspar's dissolution.
ER  -

TY  - JOUR
AU  - Peng, Q.
AU  - Yi, L.
AU  - Zhou, L.
AU  - Peng, Q.
TI  - Draft Genome Sequence of the Vanadium-Leaching Bacterium Pseudomonas chlororaphis Strain L19.
JO  - Genome Announcements
PY  - 2018
SP  - e00966
EP  - e00917
VL  - 6
AB  - Pseudomonas chlororaphis strain L19, isolated from stone coal soil, has the ability to perform
AB  - bioleaching to release vanadium ions from mineral ore. Here,
AB  - we report the draft genome sequence and annotation of the vanadium-leaching
AB  - bacterium Pseudomonas chlororaphis L19. These data provide information for
AB  - understanding the genomic properties and mineral bioleaching mechanisms of strain
AB  - L19.
ER  -

TY  - JOUR
AU  - Peng, T.
AU  - Pan, S.
AU  - Christopher, L.
AU  - Sparling, R.
AU  - Levin, D.B.
TI  - Draft Genome Sequence of Thermoanaerobacter sp. Strain YS13, a Novel Thermophilic Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00584
EP  - e00515
VL  - 3
AB  - Here, we report the draft genome sequence of Thermoanerobacter sp. YS13, isolated from a
AB  - geothermal hot spring in Yellowstone National Park, which consists of
AB  - 2,713,030 bp with a mean G+C content of 34.05%. A total of 2,779 genes, including
AB  - 2,707 protein-coding genes, 12 rRNAs, and 59 tRNAs were identified.
ER  -

TY  - JOUR
AU  - Peng, X.
AU  - Adachi, K.
AU  - Chen, C.
AU  - Kasai, H.
AU  - Kanoh, K.
AU  - Shizuri, Y.
AU  - Misawa, N.
TI  - Discovery of a marine bacterium producing 4-hydroxybenzoate and its alkyl esters, parabens.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 5556
EP  - 5561
VL  - 72
AB  - Chemically synthesized 4-hydroxybenzoate (4HBA) is widely used in the chemical
AB  - and electrical industries as a material for producing polymers such as those of
AB  - the liquid crystal type. Its alkyl esters, called parabens, have been the most
AB  - widely used preservatives by the food and cosmetic industries. We report here for
AB  - the first time a microorganism, a marine bacterium, which biosynthesizes these
AB  - petrochemical products. The marine bacterial strain, A4B-17, which was found to
AB  - belong to the genus Microbulbifer on the basis of its rRNA and gyrB sequences,
AB  - was isolated from an ascidian in the coastal waters of Palau. Strain A4B-17 was,
AB  - surprisingly, found to produce 10 mg/liter of 4HBA, together with its butyl (24
AB  - mg/liter), heptyl (0.4 mg/liter), and nonyl (6 mg/liter) esters. We therefore
AB  - characterized 23 other marine bacteria belonging to the genus Microbulbifer,
AB  - which our institute had previously isolated from various marine environments, and
AB  - found that these bacteria also produced 4HBA, although with low production levels
AB  - (less than one-fifth of that produced by A4B-17). We also show that the alkyl
AB  - esters of 4HBA produced by strain A4B-17 were effective in preventing the growth
AB  - of yeasts, molds, and gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Peng, Z.
AU  - Liang, W.
AU  - Liu, W.
AU  - Wu, B.
AU  - Tang, B.
AU  - Tan, C.
AU  - Zhou, R.
AU  - Chen, H.
TI  - Genomic characterization of Pasteurella multocida HB01, a serotype A bovine isolate from China.
JO  - Gene
PY  - 2016
SP  - 85
EP  - 93
VL  - 581
AB  - Pasteurellamultocida infects various domestic and feral animals, generally causing clinical
AB  - disease. To investigate P. multocida disease in cattle, we sequenced the complete genome of P.
AB  - multocida HB01 (GenBank accession CP006976), a serotype A organism isolated from a cow in
AB  - China. The genome is composed of a single circular chromosome of 2,416,068 base pairs
AB  - containing 2212 protein-coding sequences, 6 ribosomal rRNA operons,
AB  - and 56 tRNA genes. The present study confirms that P. multocida HB01 possesses a more complete
AB  - metabolic pathway with an intact trichloroacetic acid cycle for anabolism compared with A.
AB  - pleuropneumoniae and Haemophilus parasuis. This is the first time that this metabolic
AB  - mechanism of P. multocida has been described. We also identified a full spectrum of genes
AB  - related to known virulence factors of P. multocida. The differences
AB  - in virulence factors between strains of different serotypes and origins were also compared.
AB  - This comprehensive comparative genome analysis will help in further studies of the metabolic
AB  - pathways, genetic basis of serotype, and virulence of P. multocida.
ER  -

TY  - JOUR
AU  - Peng, Z.
AU  - Wang, W.
AU  - Hu, Y.
AU  - Li, F.
TI  - Complete Genome Sequence of Enterococcus hirae R17, a Daptomycin-Resistant Bacterium Isolated from Retail Pork in China.
JO  - Genome Announcements
PY  - 2016
SP  - e00605
EP  - e00616
VL  - 4
AB  - Daptomycin-resistant Enterococcus hirae R17 was isolated from retail pork sold at a free-trade
AB  - market in Beijing, China. The complete genome sequence of R17
AB  - contains a circular 2,886,481-bp chromosome and a circular 73,574-bp plasmid.
AB  - Genes involved in cell envelope homeostasis of this bacterium were identified by
AB  - whole-genome analysis.
ER  -

TY  - JOUR
AU  - Penner, M.
AU  - Morad, I.
AU  - Snyder, L.
AU  - Kaufmann, G.
TI  - Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 857
EP  - 868
VL  - 249
AB  - The optional Escherichia coli prr locus encodes two physically associated restriction systems:
AB  - the type IC DNA restriction-modification enzyme EcoprrI and the tRNALys-specific anticodon
AB  - nuclease, specified by the PrrC polypeptide. Anticodon nuclease is kept latent as a result of
AB  - this interaction. The activation of anticodon nuclease, upon infection by phage T4, may cause
AB  - depletion of tRNALys and, consequently, abolition of T4 protein synthesis. However, this
AB  - effect is counteracted by the repair of tRNALys in consecutive reactions catalysed by the
AB  - phage enzymes polynucleotide kinase and RNA ligase. Stp, a short polypeptide encoded by phage
AB  - T4, has been implicated with activation of the anticodon nuclease. Here we confirm this notion
AB  - and also demonstrate a second function of Stp: inhibition of EcoprrI restriction. Both effects
AB  - depend, in general, on the same residues within the N-proximal 18 residue region of Stp. We
AB  - propose that Stp alters the conformation of EcoprrI and, consequently, of PrrC, allowing
AB  - activation of the latent anticodon nuclease. Presumably, Stp evolved to offset a DNA
AB  - restriction system of the host cell but was turned, eventually, against the phage as an
AB  - activator of the appended tRNA restriction enzyme.
ER  -

TY  - JOUR
AU  - Penton, P.K.
AU  - Tyagi, E.
AU  - Humrighouse, B.W.
AU  - McQuiston, J.R.
TI  - Complete Genome Sequence of Corynebacterium minutissimum, an Opportunistic Pathogen and the Causative Agent of Erythrasma.
JO  - Genome Announcements
PY  - 2015
SP  - e00139
EP  - e00115
VL  - 3
AB  - Corynebacterium minutissimum was first isolated in 1961 from infection sites of patients
AB  - presenting with erythrasma, a common cutaneous infection characterized
AB  - by a rash. Since its discovery, C. minutissimum has been identified as an
AB  - opportunistic pathogen in immunosuppressed cancer and HIV patients. Here, we
AB  - report the whole-genome sequence of C. minutissimum.
ER  -

TY  - JOUR
AU  - Perea, J.
AU  - Desdouets, C.
AU  - Schapira, M.
AU  - Jacq, C.
TI  - I-SceIII: A novel group I intron-encoded endonuclease from the yeast mitochondria.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 358
EP  - 358
VL  - 21
AB  - Re-engineered gene with "good" codons and expressed in E. coli. Cleavage site determined.
ER  -

TY  - JOUR
AU  - Pereira, J.Q.
AU  - Ambrosini, A.
AU  - Sant'Anna, F.H.
AU  - Tadra-Sfeir, M.
AU  - Faoro, H.
AU  - Pedrosa, F.O.
AU  - Souza, E.M.
AU  - Brandelli, A.
AU  - Passaglia, L.M.
TI  - Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03,  Isolated from the Antarctic Environment.
JO  - Genome Announcements
PY  - 2015
SP  - e00246
EP  - e00215
VL  - 3
AB  - Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin
AB  - feathers collected in the Antarctic environment. This strain
AB  - has the ability to degrade keratin at low temperatures. The A03 genome sequence
AB  - provides the possibility of finding new genes with biotechnological potential to
AB  - better understand its cold-adaptation mechanism and survival in cold
AB  - environments.
ER  -

TY  - JOUR
AU  - Pereira, M.F.
AU  - Rossi, C.C.
AU  - de Carvalho, F.M.
AU  - de Almeida, L.G.
AU  - Souza, R.C.
AU  - de Vasconcelos, A.T.
AU  - Bazzolli, D.M.
TI  - Draft Genome Sequences of Six Actinobacillus pleuropneumoniae Serotype 8 Brazilian Clinical Isolates: Insight into New Applications.
JO  - Genome Announcements
PY  - 2015
SP  - e01585
EP  - e01514
VL  - 3
AB  - Actinobacillus pleuropneumoniae is the causative agent of swine pleuropneumonia,  a highly
AB  - contagious disease associated with pigs of all ages that results in
AB  - severe economic losses to the industry. Here, we report for the first time six
AB  - genome sequences of A. pleuropneumoniae clinical isolates of serotype 8, found
AB  - worldwide.
ER  -

TY  - JOUR
AU  - Pereira, U.P.
AU  - Gouran, H.
AU  - Nascimento, R.
AU  - Adaskaveg, J.E.
AU  - Goulart, L.R.
AU  - Dandekar, A.M.
TI  - Complete Genome Sequence of Xanthomonas arboricola pv. juglandis 417, a Copper-Resistant Strain Isolated from Juglans regia L.
JO  - Genome Announcements
PY  - 2015
SP  - e01126
EP  - e01115
VL  - 3
AB  - Here, we report the complete genome sequence of Xanthomonas arboricola pv. juglandis 417, a
AB  - copper-resistant strain isolated from a blighted walnut fruit (Juglans regia L. cv. Chandler).
AB  - The genome consists of a single chromosome (5,218 kb).
ER  -

TY  - JOUR
AU  - Perelman, E.V.
AU  - Shtanchaeva, S.M.
AU  - Bulk, V.F.
AU  - Tarasov, A.P.
AU  - Bakh, N.L.
AU  - Semina, I.S.
TI  - Use of different media for growing the producers of restricting enzyme XbaI.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1984
SP  - 48
EP  - 50
VL  - 12
AB  - The possibility of using culture media prepared from local ingredients and
AB  - intended for growing the producers of restricting enzyme XbaI has been
AB  - demonstrated.  The yield of restricting enzyme XbaI per g of crude biomass,
AB  - obtained with the use of peptone-yeast medium prepared from ingredients
AB  - supplied by Difco Laboratories (USA), has proved to be 4 times greater than
AB  - that obtained with the use of peptone-yeast medium prepared from local
AB  - ingredients.  At the same time the use of casein-saline medium ensures the
AB  - yield of the enzyme, similar to that obtained with the use of peptone-yeast
AB  - medium prepared from ingredients supplied by Difco Laboratories, but with a
AB  - greater content of nonspecific nucleases.
ER  -

TY  - JOUR
AU  - Perevyazova, T.A.
AU  - Rogulin, E.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Cloning and sequencing of the gene of site-specific nickase N.BspD6I.
JO  - Biokhimiia
PY  - 2003
SP  - 1203
EP  - 1207
VL  - 68
AB  - A fragment of chromosomal DNA from Bacillus species D6 containing the gene of nickase N.BspD6I
AB  - and the regions adjacent to its 5;- and 3;-ends was cloned and sequenced. The nucleotide
AB  - sequence of the nickase gene, except of one neutral change, is homologous to the nicking
AB  - endonuclease N.BstNBI gene sequenced by Higgens et al. (2001). After integration of a PCR-copy
AB  - of the nickase gene into an expression vector pET28b under the control of the phage T7
AB  - promoter, specific nicking activity was detected in the lysates of transformed E. coli cells.
ER  -

TY  - JOUR
AU  - Perez-de-la-Rosa, D.
AU  - Perez-de-la-Rosa, J.J.
AU  - Cossio-Bayugar, R.
AU  - Miranda-Miranda, E.
AU  - Lozano, L.
AU  - Bravo-Diaz, M.A.
AU  - Rocha-Martinez, M.K.
AU  - Sachman-Ruiz, B.
TI  - Complete Genome Sequence of Paenibacillus larvae MEX14, Isolated from Honey Bee Larvae from the Xochimilco Quarter in Mexico City.
JO  - Genome Announcements
PY  - 2015
SP  - e00968
EP  - e00915
VL  - 3
AB  - Paenibacillus larvae strain MEX14 is a facultative anaerobic endospore-forming bacterium that
AB  - infects Apis mellifera larvae. Strain MEX14 was isolated from domestic bee larvae collected in
AB  - a backyard in Mexico City. The estimated genome  size was determined to be 4.18 Mb, and it
AB  - harbors 4,806 protein coding genes (CDSs).
ER  -

TY  - JOUR
AU  - Perez-Maya, A.A.
AU  - Hinojosa-Robles, R.M.
AU  - Barcenas-Walls, J.R.
AU  - Rojas-Martinez, A.
AU  - Barrera-Saldana, H.A.
AU  - Ortiz-Lopez, R.
TI  - Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Serotype  19A Isolated from Cerebrospinal Fluid.
JO  - Genome Announcements
PY  - 2016
SP  - e00277
EP  - e00216
VL  - 4
AB  - We present here the draft genome sequence of ITALIC! Streptococcus pneumoniaestrain
AB  - MTY32702340SN814 isolated in Monterrey, Mexico, from a girl with
AB  - bacterial meningitis. The strain belongs to the atypical and multidrug-resistant
AB  - serogroup 19A. This is the first report in the literature of sequence type 3936
AB  - (ST3936) in ITALIC! S. pneumoniaeserotype 19A.
ER  -

TY  - JOUR
AU  - Perez-Maya, A.A.
AU  - Hinojosa-Robles, R.M.
AU  - Barcenas-Walls, J.R.
AU  - Vignau-Cantu, A.
AU  - Barrera-Saldana, H.A.
AU  - Ortiz-Lopez, R.
TI  - Complete Genome Sequence of Streptococcus pneumoniae Serotype 19A, a Blood Clinical Isolate from Northeast Mexico.
JO  - Genome Announcements
PY  - 2016
SP  - e00195
EP  - e00116
VL  - 4
AB  - We report here the draft genome sequence of aStreptococcus pneumoniaestrain isolated in
AB  - Monterrey, Mexico, MTY1662SN214, from a man with purpura fulminans.
AB  - The strain belongs to the invasive and multidrug-resistant serogroup 19A,
AB  - sequence type 320 (ST320). The draft genome sequence consists of 60 large
AB  - contigs, a total of 2,069,474 bp, and has a G+C content of 39.7%.
ER  -

TY  - JOUR
AU  - Perez-Oseguera, A.
AU  - Castro-Jaimes, S.
AU  - Salgado-Camargo, A.D.
AU  - Silva-Sanchez, J.
AU  - Garza-Gonzalez, E.
AU  - Castillo-Ramirez, S.
AU  - Cevallos, M.A.
TI  - Complete Genome Sequence of a blaOXA-58-Producing Acinetobacter baumannii Strain  Isolated from a Mexican Hospital.
JO  - Genome Announcements
PY  - 2017
SP  - e00949
EP  - e00917
VL  - 5
AB  - In this study, we present the complete genome sequence of a blaOXA-58-producing Acinetobacter
AB  - baumannii strain, sampled from a Mexican hospital and not related
AB  - to the international clones.
ER  -

TY  - JOUR
AU  - Perez-Ramos, A.
AU  - Mohedano, M.L.
AU  - Puertas, A.
AU  - Lamontanara, A.
AU  - Orru, L.
AU  - Spano, G.
AU  - Capozzi, V.
AU  - Duenas, M.T.
AU  - Lopez, P.
TI  - Draft Genome Sequence of Pediococcus parvulus 2.6, a Probiotic beta-Glucan Producer Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01381
EP  - e01316
VL  - 4
AB  - We report here the draft genome sequence of the probiotic Pediococcus parvulus 2.6, a lactic
AB  - acid bacterial strain isolated from ropy cider. The bacterium
AB  - produces a prebiotic and immunomodulatory exopolysaccharide, and this is the
AB  - first strain of the P. parvulus species whose genome has been characterized.
ER  -

TY  - JOUR
AU  - Pericone, C.D.
AU  - Bae, D.
AU  - Shchepetov, M.
AU  - McCool, T.
AU  - Weiser, J.N.
TI  - Short-sequence tandem and nontandem DNA repeats and endogenous hydrogen peroxide production contribute to genetic instability of Streptococcus   pneumoniae.
JO  - J. Bacteriol.
PY  - 2002
SP  - 4392
EP  - 4399
VL  - 184
AB  - Loss-of-function mutations in the following seven pneumococcal genes were detected and
AB  - analyzed: pspA, spxB, xba, licD2, lytA, nanA, and atpC.
AB  - Factors associated with these mutations included (i) frameshifts caused by
AB  - reversible gain and loss of single bases within homopolymeric repeats as
AB  - short as 6 bases, (ii) deletions caused by recombinational events between
AB  - nontandem direct repeats as short as 8 bases, and (iii) substitutions of
AB  - guanine residues caused at an increased frequency by the high levels of
AB  - hydrogen peroxide (>2 mM) typically generated by this species under
AB  - aerobic growth conditions. The latter accounted for a frequency as high as
AB  - 2.8 x 10(-6) for spontaneous mutation to resistance to optochin and was
AB  - 10- to 200-fold lower in the absence of detectable levels of H2O2. Some of
AB  - these mutations appear to have been selected for in vivo during
AB  - pneumococcal infection, perhaps as a consequence of immune pressure or
AB  - oxidative stress.
ER  -

TY  - JOUR
AU  - Peris-Bondia, F.
AU  - Muraille, E.
AU  - Van Melderen, L.
TI  - Complete Genome Sequence of the Escherichia coli PMV-1 Strain, a Model Extraintestinal Pathogenic E. coli Strain Used for Host-Pathogen Interaction  Studies.
JO  - Genome Announcements
PY  - 2013
SP  - e00913
EP  - e00913
VL  - 1
AB  - Escherichia coli is a highly versatile species, causing diverse intestinal and extraintestinal
AB  - infections. Here, we present the complete genome sequence of
AB  - PMV-1, an O18:K1 extraintestinal pathogenic E. coli (ExPEC) strain that is used
AB  - as a model for peritonitis in mice and was useful for deciphering the innate
AB  - immune response triggered by ExPEC infections.
ER  -

TY  - JOUR
AU  - Perler, F.B.
TI  - Inteins - A historical perspective.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 193
EP  - 210
VL  - 16
AB  - Protein splicing elements, termed inteins, were first identified in 1990.  Since then,
AB  - post-translational protein splicing has been demonstrated and the self-catalytic mechanism
AB  - deciphered.  The robust nature of these single turnover enzymes is evidenced by the expanding
AB  - list of naturally occurring variations in the protein splicing mechanism.  Protein splicing
AB  - must be efficient and neutral, and must not cause detrimental effects to the spliced extein;
AB  - otherwise, selective pressure would lead to intein loss.  Inteins are probably ancient
AB  - elements, but their original function can only be speculated upon, because invasion by homing
AB  - endonucleases mobilized them into new locations and converted them into selfish DNA.  To date,
AB  - there is no evidence of regulation of protein splicing in native systems.  The sporadic
AB  - distribution of inteins may relate more to the types of genes found in mobile elements capable
AB  - of spreading inteins, than to the function of those genes.  Inteins tend to be found in
AB  - conserved host protein motifs, which may be due to conservation of homing endonuclease
AB  - recognition sites, difficulty in removing inteins from essential regions or the ease of
AB  - accepting an insertion sequence in a conserved substrate or cofactor binding site designed to
AB  - interact with the environment.  The ability to cleave peptide bonds, to ligate protein
AB  - fragments and to generate carboxy-terminal alpha-thioesters have made inteins the fastest
AB  - growing tool for protein engineering and biotechnology.
ER  -

TY  - JOUR
AU  - Perler, F.B.
TI  - Hyperthermophilic inteins.
JO  - Methods Enzymol.
PY  - 2001
SP  - 270
EP  - 280
VL  - 334
AB  - Inteins are intervening sequences that are posttranslationally excised from protein
AB  - precursors.  They are the protein equivalent of introns, which are intervening sequences that
AB  - splice from precursor RNAs.  The sequences flanking both sides of the intein are called
AB  - exteins.  During protein splicing, the intein is excised from a precursor protein and the
AB  - flanking exteins are joined by a peptide bond.  This ligation of exteins differentiates
AB  - protein splicing from other forms of proteolytic processing.  The self-catalytic protein
AB  - splicing reaction is mediated by the intein plus the first carboxy-extein amino acid, which
AB  - are capable of splicing in heterologous exteins.  However, each intein has its own "substrate"
AB  - specificity that dictates allowable proximal extein residues.  As of December 31, 1999, there
AB  - were 100 putative inteins listed in the Intein Registry, representing all three domains of
AB  - life (see InBase2 at http://www.neb.com/neb/intins.html); 74% of these inteins are found in
AB  - thermophilic organisms, mainly Archaea.  Thermophilic inteins were among the first inteins
AB  - discovered and played a key role in establishing protein splicing as a fundamental method of
AB  - protein biosynthesis.  The proof that inteins were spliced from precursor proteins rather than
AB  - from precursor RNAs and the mechanism of protein splicing were initially demonstrated using
AB  - archaeal inteins.  Since their discovery in 1990, inteins have been harnessed to perform
AB  - numerous protein engineering processes.
ER  -

TY  - JOUR
AU  - Perler, F.B.
TI  - InBase, the New England Biolabs Intein Database.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 346
EP  - 347
VL  - 27
AB  - Inteins are intervening sequences that splice as proteins, not RNA.  InBase, the New England
AB  - Biolabs Intein Database (http://www.neb.com/neb.inteins.html), is a comprehensive on-line
AB  - database that includes the Intein Registry, along with detailed information about each intein
AB  - and its host protein, tabulated comparisons and a comprehensive bibliography including papers
AB  - in press.
ER  -

TY  - JOUR
AU  - Perler, F.B.
AU  - Comb, D.G.
AU  - Jack, W.E.
AU  - Moran, L.S.
AU  - Qiang, B.
AU  - Kucera, R.B.
AU  - Benner, J.
AU  - Slatko, B.E.
AU  - Nwankwo, D.O.
AU  - Hempstead, S.K.
AU  - Carlow, C.K.S.
AU  - Jannasch, H.
TI  - Intervening sequences in an Archaea DNA polymerase gene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 5577
EP  - 5581
VL  - 89
AB  - The DNA polymerase gene from the Archaea Thermococcus litoralis has been cloned and expressed
AB  - in Escherichia coli. It is split by two intervening sequences (IVSs) that form one continuous
AB  - open reading frame with three polymerase exons. To our knowledge, neither IVS is similar to
AB  - previously described introns. However, the deduced amino acid sequences of both IVSs are
AB  - similar to open reading frames present in mobile group I introns. The second IVS (IVS2)
AB  - encodes an endonuclease, I-TliI, that cleaves at the exon 2-exon 3 junction after IVS2 has
AB  - been deleted. IVS2 self-splices in E. coli to yield active polymerase, but processing is
AB  - abolished if the IVS2 reading frame is disrupted. Silent changes in the DNA sequence at the
AB  - exon 2-IVS2 junction that maintain the original protein sequence do not inhibit splicing.
AB  - These data suggest that protein rather than mRNA splicing may be responsible for production of
AB  - the mature polymerase.
ER  -

TY  - JOUR
AU  - Perler, F.B.
AU  - Davis, E.O.
AU  - Dean, G.E.
AU  - Gimble, F.S.
AU  - Jack, W.E.
AU  - Neff, N.
AU  - Noren, C.J.
AU  - Thorner, J.
AU  - Belfort, M.
TI  - Protein splicing elements: inteins and exteins--a definition of terms and recommended nomenclature.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 1125
EP  - 1127
VL  - 22
AB  - Several archaeal, eubacterial and eucaryotic genes have been identified with in-frame
AB  - insertions that are excised at the protein level, not at the RNA level. This process is termed
AB  - protein splicing. Initially, a single precursor polypeptide is synthesized. The intervening
AB  - protein sequences is then excised from within the precursor, and the flanking protein
AB  - sequences are joined. Thus, protein splicing results in the production of two proteins from a
AB  - single primary translation product, the internal protein and the protein formed by the joining
AB  - of the external sequences. The removal of the internal segment, concomitant with the formation
AB  - of a normal peptide bond joining the external polypeptide sequences, distinguishes protein
AB  - splicing from simple autoproteolysis. The rapid production of the mature products suggests
AB  - that protein splicing is very efficient. The protein precursor rarely accumulates, even when
AB  - the native gene is expressed in heterologous systems, both in vivo and in vitro. Evidence to
AB  - date suggests that protein splicing is autocatalytic.
ER  -

TY  - JOUR
AU  - Perlloni, A.
AU  - Brown, E.W.
AU  - LeClerc, J.E.
AU  - Cebula, T.A.
TI  - Phylogenetic evidence for horizontal gene transfer of type I restriction and modification (hsd) genes among highly homogenous Salmonella strains.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2005
SP  - 284
EP  - 284
VL  - 105
AB  - Previous studies from our laboratory have documented the prevalence of horizontal gene
AB  - transfer (HGT) among strains of Salmonella enterica subspecies I. In comparing subspecies, a
AB  - recombination gradient was noted wherein the incidence of HGT is inversely correlated with the
AB  - genetic diversity separating individual strains. These findings suggested that there are
AB  - barriers, either genetic or ecological, that restrict exchange between disparate serovars of
AB  - Salmonella. The compatibility of restriction-modification (R-M) systems among strains has been
AB  - proposed as one explanation to account for the contrasting recombination rates. To explore
AB  - this possibility, 40 closely-related strains of the highly homogenous Typhimurium complex were
AB  - compared by cladistic analysis of the hsd genes, R, M, and S, which compose the type I R-M
AB  - system in Salmonella enterica subspecies I. The resultant trees revealed a prominent role for
AB  - HGT in the evolution of the hsd operon. Several Salmonella strains were found to be
AB  - evolutionarily discordant when hsd gene trees were compared to known markers of S. enterica
AB  - chromosome evolution (e.g., mdh). Additionally, several distinct clusters of mdh and mutS
AB  - alleles were coalesced into single hsd clades for the three type I R-M loci. Analyses of
AB  - congruence among hsd genes showed nearly unanimous discordance, the only exception being the
AB  - hsdM/S2 comparison (p = 1.0). This finding would suggest that the type I R-M operon is
AB  - anevolutionary mosaic, subject to numerous HGT events. This conclusion is further supported by
AB  - the identification of unique cassettes of sequence at two sites in hsdS. The hsdS2 segment
AB  - comprised two distinct sequences while the hsdS3 segment contained one of three unique
AB  - alleles. One of the hsdS3 alleles showed high homology to an E. coli hsd insert, suggesting a
AB  - recent cross-species transfer of this sequence. These data demonstrate that HGT has been a
AB  - common occurrence in hsd gene evolution and indicate an overall genetic compatibility among
AB  - closely-related salmonellae. This may explain in part why Salmonella known to share homologous
AB  - genomes and common niches are permitted to exchange DNA more freely.
ER  -

TY  - JOUR
AU  - Permala, R.R.
AU  - Glady-Croue, J.
AU  - Watkin, E.L.J.
AU  - Ramsay, J.P.
AU  - Croue, J.P.
TI  - Complete Genome Sequence of Stenotrophomonas maltophilia AB550, an Environmental  Solar Radiation- and Multidrug-Resistant Strain Isolated in Western Australia.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00914
EP  - e00918
VL  - 7
AB  - We report here the complete genome sequence of Stenotrophomonas maltophilia AB550, a
AB  - multidrug- and solar radiation-resistant strain isolated from the
AB  - effluents of an urban wastewater treatment plant in Western Australia. The genome
AB  - consists of a single 4.9-Mb chromosome.
ER  -

TY  - JOUR
AU  - Perna, N.T. et al.
TI  - Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.
JO  - Nature
PY  - 2001
SP  - 529
EP  - 533
VL  - 409
AB  - The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been
AB  - implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused
AB  - by haemolytic uraemic syndrome.  Close to 75,000 cases of O157:H7 infection are now estimated
AB  - to occur annually in the United States.  The severity of disease, the lack of effective
AB  - treatment and the potential for large-scale outbreaks from contaminated food supplies have
AB  - propelled intensive research on the pathogenesis and detection of E. coli O157:H7.  Here we
AB  - have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for
AB  - pathogenesis, to develop better methods of strain detection and to advance our understanding
AB  - of the evolution of E. coli, through comparison with the genome of the non-pathogenic
AB  - laboratory strain E. coli K-12.  We find that lateral gene transfer is far more extensive than
AB  - previously anticipated.  In fact, 1,387 new genes encoded in strain-specific clusters of
AB  - diverse sizes were found in O157:H7.  These include candidate virulence factors, alternative
AB  - metabolic capacities, several prophages and other new functions - all of which could be
AB  - targets for surveillance.
ER  -

TY  - JOUR
AU  - Pernstich, C.
AU  - Halford, S.E.
TI  - Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 1203
EP  - 1213
VL  - 40
AB  - The FokI restriction endonuclease is a monomeric protein that recognizes an asymmetric
AB  - sequence and cleaves both DNA strands at fixed loci downstream of the
AB  - site. Its single active site is positioned initially near the recognition
AB  - sequence, distant from its downstream target 13 nucleotides away. Moreover, to
AB  - cut both strands, it has to recruit a second monomer to give an assembly with two
AB  - active sites. Here, the individual steps in the FokI reaction pathway were
AB  - examined by fluorescence resonance energy transfer (FRET). To monitor DNA binding
AB  - and domain motion, a fluorescence donor was attached to the DNA, either
AB  - downstream or upstream of the recognition site, and an acceptor placed on the
AB  - catalytic domain of the protein. A FokI variant incapable of dimerization was
AB  - also employed, to disentangle the signal due to domain motion from that due to
AB  - protein association. Dimerization was monitored separately by using two samples
AB  - of FokI labelled with donor and acceptor, respectively. The stopped-flow studies
AB  - revealed a complete reaction pathway for FokI, both the sequence of events and
AB  - the kinetics of each individual step.
ER  -

TY  - JOUR
AU  - Pero, J.
AU  - Hannett, N.M.
AU  - Talkington, C.
TI  - Restriction cleavage map of SP01 DNA: general location of early, middle, and late genes.
JO  - J. Virol.
PY  - 1979
SP  - 156
EP  - 171
VL  - 31
AB  - A detailed restriction endonuclease map for the genome of Bacillus subtilis phage SP01 is
AB  - presented. Sites of cleavage for the restriction
AB  - enzymes BglII, EcoRI, HaeIII, and SalI were determined. This physical map
AB  - showed that SP01 DNA was 140 kilobases in length and contained a repeated
AB  - sequence of 12.4 kilobases at its termini. Combined with previously
AB  - published information, we were also able to identify the general locations
AB  - of genes expressed at early, middle, or late times in the phage lytic
AB  - cycle. In particular, early genes were largely clustered in the terminal
AB  - repeats, whereas a major cluster of late genes was located in the
AB  - left-central portion of the genome.
ER  -

TY  - JOUR
AU  - Perona, J.J.
TI  - Type II restriction endonucleases.
JO  - Methods
PY  - 2002
SP  - 353
EP  - 364
VL  - 28
AB  - Type II restriction endonucleases have emerged as important paradigms for the study of
AB  - protein-nucleic acid interactions. This is due to their ability to catalyse phosphodiester
AB  - bond cleavage with very large rate enhancements while also maintaining exquisite sequence
AB  - selectivities. The principles and methods developed to analyze site-specific binding and
AB  - catalysis for restriction endonucleases can be applied to other enzymes which also operate on
AB  - nucleic acids. This paper reviews biochemical and structural approaches to characterization of
AB  - these enzymes, with particular attention to the multiple crucial roles of divalent metal ions,
AB  - the possibilities for use of alternative substrates in binding and catalytic experiments, the
AB  - strategies for exploring the detailed chemistry of phosphoryl transfer, and the use of X-ray
AB  - crystallography to provide descriptions of conformational pathways at specific, nonspecific,
AB  - and noncognate DNA sites.
ER  -

TY  - JOUR
AU  - Perona, J.J.
TI  - Structural pathways of phosphoryl transfer in type II restriction endonucleases.
JO  - ACS Abstracts
PY  - 2002
SP  - C
EP  - 38-C-39
VL  - 223
AB  - Crystal structures of EcoRV endonuclease bound to DNA and divalent metal
AB  - ions have elucidated important aspects of the structural pathway of DNA
AB  - bending, the stereochemical mechanism of catalysis, and the coupling of
AB  - sequence selectivity to phosphoryl transfer. Three distinct divalent metal
AB  - ion binding sites have been located in the vicinity of the scissile DNA
AB  - phosphates, while a fourth site specific to manganese is found at the
AB  - interface of the enzyme with the DNA flanks. Mutational analysis of
AB  - active-site residues places important constraints on the reaction mechanism,
AB  - and suggests that moderate-range electrostatic effects play an important
AB  - role in facilitating rate enhancement. Measurements of the pH and
AB  - metal-dependence of the chemical step, by rapid-quench kinetics, lend
AB  - support to a detailed model of the reaction pathway derived from the crystal
AB  - structures. Comparisons of the EcoRV mechanism with those of other
AB  - restriction endonucleases offer further insight into the origins of
AB  - catalytic power.
ER  -

TY  - JOUR
AU  - Perona, J.J.
AU  - Horton, N.C.
AU  - Sam, M.D.
TI  - Catalytic mechanism of EcoRV endonuclease derived from crystal structures and transient kinetics.
JO  - Transactions ACA
PY  - 2000
SP  - 9
EP  - 17
VL  - 35
AB  - High-resolution cocrystal structures of wild-type and mutant forms of EcoRV endonuclease bound
AB  - to duplex DNA and divalent metal ions allow construction of a detailed model for the
AB  - pre-transition state configuration.  Three distinct metal-ion binding sites have been revealed
AB  - in different structural analyses.  In particular, a new site (site I) was recently found in a
AB  - ternary complex of the T93A mutant bound to cognate DNA and Ca2+ ions.  The same site is
AB  - occupied by Ca2+, Mg2+ or Mn2+ in three high-resolution structures of EcoRV bound to duplex
AB  - DNA containing 3'S-phosphorothiolate linkages (3'-PS) at the scissile phosphates.  Each of
AB  - these four structures traps a pre-transition state conformation in which the DNA is not
AB  - cleaved.  The new site I metal is ligated through an inner-sphere water molecule to the
AB  - phosphate group located 3' to the scissile phosphate.  A second inner-sphere water on this
AB  - metal is positioned approximately in-line for attack on the scissile phosphate.  These
AB  - structures corroborate the observation that the pro-SP phosphoryl oxygen on the adjacent
AB  - 3'-phosphate cannot be modified without severe loss of catalytic efficiency.  Together with
AB  - previous cocrystal structures, these data allow construction of a detailed model for the
AB  - pre-transition state configuration in EcoRV.  This model features three divalent metal ions
AB  - per active site, and invokes assistance in the bond-making step by a conserved lysine, which
AB  - stabilizes the attacking hydroxide ion nucleophile.  The model is supported by pre-steady
AB  - state and single-turnover kinetic data, in which the metal and pH-dependencies of the
AB  - phosphoryl transfer step are directly evaluated.  The structural equivalence of key groups,
AB  - conserved in the active sites of many type II restriction endonucleases, suggests that
AB  - ligation of a catalytic divalent metal ion to the adjacent 3'-phosphate may occur in many
AB  - type II restriction enzymes.
ER  -

TY  - JOUR
AU  - Perona, J.J.
AU  - Martin, A.M.
TI  - Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 207
EP  - 225
VL  - 273
AB  - The structures of wild-type and mutant forms of the unliganded EcoRV endonuclease dimer have
AB  - been determined at 2.4 angstroms resolution in a new crystal lattice.  Comparison of these
AB  - structures with that of the free enzyme determined with different packing constraints shows
AB  - that the conformations of the domain interfaces are not conserved between crystal forms.  The
AB  - unliganded enzyme and the enzyme-DNA complex delineate two distinct quaternary states
AB  - separated by a 25 degree intersubunit rotation, but considerable conformational heterogeneity,
AB  - of the order of 10^6 domain rotations, exists within each of these states.  Comparison of the
AB  - free enzyme structure between the two crystal forms further reveals that the C-terminal 28
AB  - amino acid residues are disordered and undergo an extensive local folding transition upon DNA
AB  - binding.  Introduction of the mutation T93A at the DNA-binding cleft causes large-scale
AB  - effects on the protein conformation.  Structural changes in the mutated unliganded enzyme
AB  - propagate some 20 to 25 angstroms to the dimerization interface and lead to a rearrangement of
AB  - monomer subunits.  Comparative analysis of these structures, a new structure of the enzyme
AB  - cocrystallized with DNA and calcium ions, and previously determined cocrystal structures
AB  - suggests important roles for a number of amino acid residues in facilitating the intersubunit
AB  - motions and local folding transitions.  In particular, the T93A structure reveals a pathway
AB  - through the protein, by which DNA-binding may cause the domain movements required for proper
AB  - alignment of catalytic groups.  The key active-site residue Glu45 is located on a flexible
AB  - helix inside the pathway, and this provides a direct means by which essential catalytic
AB  - functions are coupled to the protein conformational change.  It appears that indirect
AB  - perturbation of the Glu45 conformation via an altered quaternary structure may be a
AB  - contributing factor to the decreased catalytic efficiency of T93A, and this mechanism may also
AB  - explain the diminished activities of other active site variants of EcoRV.
ER  -

TY  - JOUR
AU  - Perotto, S.
AU  - Nepote-Fus, P.
AU  - Saletta, L.
AU  - Bandi, C.
AU  - Young, J.P.W.
TI  - A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes.
JO  - Mol. Biol. Evol.
PY  - 2000
SP  - 44
EP  - 59
VL  - 17
AB  - Ericoid mycorrhizal fungi form symbioses with the roots of members of the Ericales. Although
AB  - only two genera have been identified in culture,
AB  - the taxonomic diversity of ericoid symbionts is certainly wider.
AB  - Genetic variation among 40 ericoid fungal isolates was investigated in
AB  - this study. PCR amplification of the nuclear small-subunit ribosomal
AB  - DNA (SSU rDNA) and of the internal transcribed spacer (ITS), followed
AB  - by sequencing, led to the discovery of DNA insertions of various sizes
AB  - in the SSU rDNA of most isolates. They reached sizes of almost 1,800 bp
AB  - and occurred in up to five different insertion sites. Their positions
AB  - and sizes were generally correlated with morphological and ITS-RFLP
AB  - grouping of the isolates, although some insertions were found to be
AB  - optional among isolates of the same species, and insertions were not
AB  - always present in all SSU rDNA repeats within an isolate. Most
AB  - insertions were identified as typical group I introns, possessing the
AB  - conserved motifs characteristic of this group. However, other
AB  - insertions lack these motifs and form a distinct group that includes
AB  - other fungal ribosomal introns. Alignments with almost 70 additional
AB  - sequences from fungal nuclear SSU rDNA introns indicate that introns
AB  - inserted at the same site along the rDNA gene are generally homologous,
AB  - but they also suggest the possibility of some horizontal transfers. Two
AB  - of the ericoid fungal introns showed strong homology with a conserved
AB  - motif found in endonuclease genes from nuclear rDNA introns.
ER  -

TY  - JOUR
AU  - Perreten, V.
AU  - Chanchaithong, P.
AU  - Prapasarakul, N.
AU  - Rossano, A.
AU  - Blum, S.E.
AU  - Elad, D.
AU  - Schwendener, S.
TI  - Novel Pseudo-Staphylococcal Cassette Chromosome mec Element ({Psi}SCCmec57395) in Methicillin-Resistant Staphylococcus pseudintermedius CC45.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 5509
EP  - 5515
VL  - 57
AB  - Genetic characterization of methicillin-resistant Staphylococcus pseudintermedius
AB  - (MRSP) from Thailand and Israel revealed the presence of a predominant atypical
AB  - clonal lineage which was not typeable by SmaI-PFGE and SCCmec typing. All the
AB  - atypical isolates (n = 34) belonged to CC45 (30 ST45 and 2 ST179 isolates, 1 ST57
AB  - isolate, and 1 ST85 isolate). The isolates originated from healthy and diseased
AB  - dogs and cats, as well as from the environment of one clinic. Cfr9I-pulsed-field
AB  - gel electrophoresis (Cfr9I-PFGE) and dru typing permitted the further distinction
AB  - of CC45 isolates from the two different countries. Microarray analysis identified
AB  - genes that confer resistance to beta-lactams (mecA; blaZ), aminoglycosides
AB  - [aac(6')-Ie-aph(2')-Ia; aph(3')-III; ant(6)-Ia], macrolides and lincosamides
AB  - [erm(B)], tetracyclines [tet(M)], trimethoprim [dfr(G)], streptothricin (sat4),
AB  - and chloramphenicol (catpC221). Fluoroquinolone resistance was attributed to
AB  - specific amino acid substitutions, i.e., Ser84Leu in GyrA and Ser80Ile and
AB  - Asp84Asn in GrlA. A novel pseudo-staphylococcal cassette chromosome
AB  - (PsiSCCmec57395) element was identified in MRSP strain 57395 (sequence type ST45)
AB  - by whole-genome sequencing. The 12,282-bp PsiSCCmec57395 element contained a
AB  - class C1 mec gene complex but no ccr genes. In addition to the methicillin
AB  - resistance gene mecA, PsiSCCmec57395 also carried determinants of resistance to
AB  - heavy metals, such as arsenic, cadmium, and copper. Bsu36I restriction analysis
AB  - of the PsiSCCmec57395 element amplified by long-range PCR revealed the presence
AB  - of PsiSCCmec57395 in the 33 additional isolates of MRSP CC45. The PsiSCCmec57395
AB  - element represents a new class of SCCmec and has been identified in MRSP of CC45,
AB  - which is a predominant clonal lineage in Israel and Thailand.
ER  -

TY  - JOUR
AU  - Perrin, A.
AU  - Buckle, M.
AU  - Dujon, B.
TI  - Asymmetrical recognition and activity of the I-SceI endonuclease on its site and on intron-exon junctions.
JO  - EMBO J.
PY  - 1993
SP  - 2939
EP  - 2947
VL  - 12
AB  - Group I intron-encoded endonucleases represent a new class of double strand cutting
AB  - endonucleases whose function is to initiate the homing of introns by generating double strand
AB  - breaks in site-specific sequences. We have studied the mechanism of interaction of the I-SceI
AB  - endonuclease with different DNA substrates derived from its natural site in the intron-less
AB  - gene or from intron-exon junctions in the gene with an intron. We show that the enzyme
AB  - recognizes it asymmetrical site with high affinity binding to the sequence corresponding to
AB  - the downstream exon followed by binding to the upstream exon and catalysis of phosphodiester
AB  - bond hydrolysis. Asymmetrical nicking activity is observed as an intermediate of the cleavage
AB  - reaction. In the intron-containing gene, the enzyme recognizes the downstream intron-exon
AB  - junction without any cleavage activity. This binding raises the possibility of a specific
AB  - function of homing endonucleases in either gene expression or intron homing steps subsequent
AB  - to DNA cleavage.
ER  -

TY  - JOUR
AU  - Perrody, E.
AU  - Cirinesi, A.M.
AU  - Desplats, C.
AU  - Keppel, F.
AU  - Schwager, F.
AU  - Tranier, S.
AU  - Georgopoulos, C.
AU  - Genevaux, P.
TI  - A Bacteriophage-Encoded J-Domain Protein Interacts with the DnaK/Hsp70 Chaperone and Stabilizes the Heat-Shock Factor sigma(32) of Escherichia coli.
JO  - PLoS Genet.
PY  - 2012
SP  - E1003037
EP  - E1003037
VL  - 8
AB  - The universally conserved J-domain proteins (JDPs) are obligate cochaperone
AB  - partners of the Hsp70 (DnaK) chaperone. They stimulate Hsp70's ATPase activity,
AB  - facilitate substrate delivery, and confer specific cellular localization to
AB  - Hsp70. In this work, we have identified and characterized the first functional
AB  - JDP protein encoded by a bacteriophage. Specifically, we show that the ORFan gene
AB  - 057w of the T4-related enterobacteriophage RB43 encodes a bona fide JDP protein,
AB  - named Rki, which specifically interacts with the Escherichia coli host
AB  - multifunctional DnaK chaperone. However, in sharp contrast with the three known
AB  - host JDP cochaperones of DnaK encoded by E. coli, Rki does not act as a generic
AB  - cochaperone in vivo or in vitro. Expression of Rki alone is highly toxic for
AB  - wild-type E. coli, but toxicity is abolished in the absence of endogenous DnaK or
AB  - when the conserved J-domain of Rki is mutated. Further in vivo analyses revealed
AB  - that Rki is expressed early after infection by RB43 and that deletion of the rki
AB  - gene significantly impairs RB43 proliferation. Furthermore, we show that
AB  - mutations in the host dnaK gene efficiently suppress the growth phenotype of the
AB  - RB43 rki deletion mutant, thus indicating that Rki specifically interferes with
AB  - DnaK cellular function. Finally, we show that the interaction of Rki with the
AB  - host DnaK chaperone rapidly results in the stabilization of the heat-shock factor
AB  - sigma(32), which is normally targeted for degradation by DnaK. The mechanism by
AB  - which the Rki-dependent stabilization of sigma(32) facilitates RB43 bacteriophage
AB  - proliferation is discussed.
ER  -

TY  - JOUR
AU  - Perry, B.J.
AU  - Bergsveinson, J.
AU  - Tambalo, D.D.
AU  - Yost, C.K.
AU  - Khan, N.H.
AU  - Whiting, M.
TI  - Complete Genome Sequence of Delftia acidovorans RAY209, a Plant Growth-Promoting  Rhizobacterium for Canola and Soybean.
JO  - Genome Announcements
PY  - 2017
SP  - e01224
EP  - e01217
VL  - 5
AB  - Herein, we report the genome sequence of Delftia acidovorans strain RAY209, a plant
AB  - growth-promoting rhizobacterium that is used in commercial inoculants for
AB  - canola and soybean. The genome of RAY209 has a consensus of 6,528,879 bp and an
AB  - estimated 5,721 coding sequences.
ER  -

TY  - JOUR
AU  - Persicke, M.
AU  - Albersmeier, A.
AU  - Bednarz, H.
AU  - Niehaus, K.
AU  - Kalinowski, J.
AU  - Ruckert, C.
TI  - Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 5
EP  - 5
VL  - 10
AB  - Corynebacterium callunae DSM 20147(T) is a member of the genus Corynebacterium which contains
AB  - Gram-positive and non-spore forming bacteria with a high G + C
AB  - content. C. callunae was isolated during a screening for l-glutamic acid
AB  - producing bacteria and belongs to the aerobic and non-haemolytic corynebacteria.
AB  - As this is a type strain in a subgroup of industrial relevant bacteria for many
AB  - of which there are also complete genome sequence available, knowledge of the
AB  - complete genome sequence might enable genome comparisons to identify production
AB  - relevant genetic loci. This project, describing the 2.84 Mbp long chromosome and
AB  - the two plasmids, pCC1 (4.11 kbp) and pCC2 (85.02 kbp), with their 2,647
AB  - protein-coding and 82 RNA genes, will aid the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Persinoti, G.F.
AU  - Paixao, D.A.A.
AU  - Bugg, T.D.H.
AU  - Squina, F.M.
TI  - Genome Sequence of Lysinibacillus sphaericus, a Lignin-Degrading Bacterium Isolated from Municipal Solid Waste Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e00353
EP  - e00318
VL  - 6
AB  - We report here the draft genome sequence of Lysinibacillus sphaericus strain A1,  a potential
AB  - lignin-degrading bacterium isolated from municipal solid waste (MSW)
AB  - soil and capable of enhancing gas release from lignocellulose-containing soil.
ER  -

TY  - JOUR
AU  - Persson, T. et al.
TI  - Genome Sequence of 'Candidatus Frankia datiscae' Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot Datisca  glomerata.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7017
EP  - 7018
VL  - 193
AB  - Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal
AB  - species from the orders Cucurbitales and
AB  - Rosales. We report the genome sequence of a member of this clade
AB  - originally from Pakistan but obtained from root nodules of the American
AB  - plant Datisca glomerata without isolation in culture.
ER  -

TY  - JOUR
AU  - Pertry, I.
AU  - Vaclavikova, K.
AU  - Depuydt, S.
AU  - Galuszka, P.
AU  - Spichal, L.
AU  - Temmerman, W.
AU  - Stes, E.
AU  - Schmulling, T.
AU  - Kakimoto, T.
AU  - Van Montagu, M.C.
AU  - Strnad, M.
AU  - Holsters, M.
AU  - Tarkowski, P.
AU  - Vereecke, D.
TI  - Identification of Rhodococcus fascians cytokinins and their modus operandi to reshape the plant.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 929
EP  - 934
VL  - 106
AB  - Decades ago, the importance of cytokinins (CKs) during Rhodococcus
AB  - fascians pathology had been acknowledged, and an isopentenyltransferase
AB  - gene had been characterized in the fas operon of the linear virulence
AB  - plasmid, but hitherto, no specific CK(s) could be associated with
AB  - virulence. We show that the CK receptors AHK3 and AHK4 of Arabidopsis
AB  - thaliana are essential for symptom development, and that the CK perception
AB  - machinery is induced upon infection, underlining its central role in the
AB  - symptomatology. Three classical CKs [isopentenyladenine, trans-zeatin, and
AB  - cis-zeatin (cZ)] and their 2-methylthio (2MeS)-derivatives were identified
AB  - by CK profiling of both the pathogenic R. fascians strain D188 and its
AB  - nonpathogenic derivative D188-5. However, the much higher CK levels in
AB  - strain D188 suggest that the linear plasmid is responsible for the
AB  - virulence-associated production. All R. fascians CKs were recognized by
AB  - AHK3 and AHK4, and, although they individually provoked typical CK
AB  - responses in several bioassays, the mixture of bacterial CKs exhibited
AB  - clear synergistic effects. The cis- and 2MeS-derivatives were poor
AB  - substrates of the apoplastic CK oxidase/dehydrogenase enzymes and the
AB  - latter were not cytotoxic at high concentrations. Consequently, the
AB  - accumulating 2MeScZ (and cZ) in infected Arabidopsis tissue contribute to
AB  - the continuous stimulation of tissue proliferation. Based on these
AB  - results, we postulate that the R. fascians pathology is based on the local
AB  - and persistent secretion of an array of CKs.
ER  -

TY  - JOUR
AU  - Pertsev, A.V.
AU  - Denmukhametov, M.M.
AU  - Anoshkin, A.G.
AU  - Ariskina, E.V.
AU  - Berezin, I.A.
AU  - Solonin, A.S.
AU  - Kuzmin, N.P.
TI  - Restriction endonucleases from various bacterial strains displaying an ice-nucleating activity.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 2000
SP  - 13
EP  - 16
VL  - 36
AB  - Six strains containing Type II site-specific endonucleases were selected from a collection of
AB  - 45
AB  - ice-nucleating bacterial strains isolated from the
AB  - rhizosphere of plants growing in various geographical regions.
AB  - Endonucleases Pfl21I, Psp8I, and Psp23I were isolated and purified
AB  - from two Pseudomonas sp. strains and a Pseudomonas fluorescens strain.
AB  - Restriction endonucleases Pfl21I and Psp23I were shown to recognize and
AB  - cleave the DNA nucleotide sequence 5'-CTGCA^G-3'.
AB  - Endonuclease Psp8I recognized and cleaved the DNA nucleotide sequence
AB  - 5'-G^GATCC-3'. These endonucleases were found to be true
AB  - isoschizomers of PstI and BamHI, respectively.
ER  -

TY  - JOUR
AU  - Pertzev, A.V.
AU  - Kravetz, A.N.
AU  - Mayorov, S.G.
AU  - Zakharova, M.V.
AU  - Solonin, A.S.
TI  - Isolation of a strain overproducing endonuclease Eco29kI: Purification and characterization of the homogeneous enzyme.
JO  - Biokhimiia
PY  - 1997
SP  - 858
EP  - 867
VL  - 62
AB  - The physical map of the plasmid pSACII1 carrying the genes of the restriction-modification
AB  - system Eco29kI (isoschizomer of SacII) was determined.  The cloning of the Eco29kI
AB  - endonuclease methylase genes into the plasmid vector pUC129 produced recombinant strain
AB  - Escherichia coli K802 [pECO29A15] with Eco29kI synthesis level about 100 times higher than in
AB  - the parent strain.  The restriction endonuclease was purified from Escherichia coli K802
AB  - [pECO29A15] cells to near homogeneity using column chromatography sequentially on
AB  - phosphocellulose, hydroxyapatite, and heparin-Sepharose and rechromatography on
AB  - phosphocellulose.  Biochemical characterization of the homogeneous R.Eco29kI is given.  The
AB  - enzyme has molecular mass 24.5 kD and is present in the solution as a monomer.
ER  -

TY  - JOUR
AU  - Pertzev, A.V.
AU  - Ruban, N.M.
AU  - Zakharova, M.V.
AU  - Beletzkaja, I.V.
AU  - Petrov, S.I.
AU  - Kravetz, A.N.
AU  - Solonin, A.S.
TI  - Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1991
EP  - 1991
VL  - 20
AB  - Eco29kI is a type II restriction endonuclease from clinical strain Escherichia coli 29
AB  - isolated in Kiev. The genes for the Eco29kI restriction modification system were located on
AB  - one of its plasmids, namely pSACII1 about 4.0 kb in size as was determined by plasmid
AB  - transformation of E. coli K802 (Figure 1) according to (1) except that the phage Phi 80 vir
AB  - was used for selection of clones.
ER  -

TY  - JOUR
AU  - Pesce, C.
AU  - Bolot, S.
AU  - Berthelot, E.
AU  - Bragard, C.
AU  - Cunnac, S.
AU  - Fischer-Le, S.M.
AU  - Portier, P.
AU  - Arlat, M.
AU  - Gagnevin, L.
AU  - Jacques, M.A.
AU  - Noel, L.D.
AU  - Carrere, S.
AU  - Koebnik, R.
TI  - Draft Genome Sequence of Xanthomonas translucens pv. graminis Pathotype Strain CFBP 2053.
JO  - Genome Announcements
PY  - 2015
SP  - e01174
EP  - e01115
VL  - 3
AB  - Strains of Xanthomonas translucens pv. graminis cause bacterial wilt on several forage
AB  - grasses. A draft genome sequence of pathotype strain CFBP 2053 was generated to facilitate the
AB  - discovery of new pathogenicity factors and to develop diagnostic tools for the species X.
AB  - translucens.
ER  -

TY  - JOUR
AU  - Pesce, C.
AU  - Bolot, S.
AU  - Cunnac, S.
AU  - Portier, P.
AU  - Fischer-Le, S.M.
AU  - Jacques, M.A.
AU  - Gagnevin, L.
AU  - Arlat, M.
AU  - Noel, L.D.
AU  - Carrere, S.
AU  - Bragard, C.
AU  - Koebnik, R.
TI  - High-Quality Draft Genome Sequence of the Xanthomonas translucens pv. cerealis Pathotype Strain CFBP 2541.
JO  - Genome Announcements
PY  - 2015
SP  - e01574
EP  - e01514
VL  - 3
AB  - Xanthomonas translucens pv. cerealis is the causal agent of bacterial leaf streak on true
AB  - grasses. The genome of the pathotype strain CFBP 2541 was sequenced in
AB  - order to decipher mechanisms that provoke disease and to elucidate the role of
AB  - transcription activator-like (TAL) type III effectors in pathogenicity.
ER  -

TY  - JOUR
AU  - Pester, M. et al.
TI  - Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and  Desulfosporosinus acidiphilus DSM22704T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6300
EP  - 6301
VL  - 194
AB  - Desulfosporosinus species are sulfate-reducing bacteria belonging to the Firmicutes. Their
AB  - genomes will give insights into the genetic repertoire and
AB  - evolution of sulfate reducers typically thriving in terrestrial environments and
AB  - able to degrade toluene (Desulfosporosinus youngiae), to reduce Fe(III)
AB  - (Desulfosporosinus meridiei, Desulfosporosinus orientis), and to grow under
AB  - acidic conditions (Desulfosporosinus acidiphilus).
ER  -

TY  - JOUR
AU  - Pestova, E.V.
AU  - Morrison, D.A.
TI  - Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector.
JO  - J. Bacteriol.
PY  - 1998
SP  - 2701
EP  - 2710
VL  - 180
AB  - Although more than a dozen new proteins are produced when Streptococcus pneumoniae cells
AB  - become competent for genetic transformation, only a few of the corresponding genes have been
AB  - identified to date.  To find genes responsible for the production of competence-specific
AB  - proteins, a random lacZ transcriptional fusion library was constructed in S. pneumoniae by
AB  - using the insertional lacZ reporter vector pEVP3.  Screening the library for clones with
AB  - competence-specific B-galactosidase production yielded three insertion mutants with induced
AB  - beta-Gal levels of about 4, 10, and 40 Miller units.  In all three clones, activation of the
AB  - lacZ reporter correlated with competence and depended on competence-stimulating peptide.
AB  - Chromosomal loci adjacent to the integrated vector were subcloned from the insertion mutants,
AB  - and their nucleotide sequences were determined.  Genes at two of the loci exhibited strong
AB  - similarity to parts of Bacillus subtilis com operons.  One locus contained open reading frames
AB  - homologous to the comEA and comEC genes in B. subtilis but lacked a comEB homolog.  A second
AB  - locus contained four ORFs with homology to the B. subtilis comG gene ORFs 1 to 4, but comG
AB  - gene ORFs 5 to 7 were replaced in S. pneumoniae with an ORF encoding a protein homologous to
AB  - transport ATP-binding proteins.  Genes at all three loci were confirmed to be required for
AB  - transformation by mutagenesis using pEVP3 for insertion duplications or an erm cassette for
AB  - gene disruptions.
ER  -

TY  - JOUR
AU  - Petering, H.
AU  - Hammerschmidt, S.
AU  - Frosch, M.
AU  - van Putten, J.P.M.
AU  - Ison, C.A.
AU  - Robertson, B.D.
TI  - Genes associated with the meningococcal capsule complex are also found in Neisseria gonorrhoeae.
JO  - J. Bacteriol.
PY  - 1996
SP  - 3342
EP  - 3345
VL  - 178
AB  - A homolog of the meningococcal cps locus region E has been identified in Neisseria gonorrhoeae
AB  - immediately upstream of the gonococcal region D locus.  Region E has no detectable function in
AB  - capsule biosynthesis in Neisseria meningitidis or in lipopolysaccharide biosynthesis in either
AB  - organism.  The open reading frame is homologous to proteins of unknown function in Escherichia
AB  - coli and Haemophilus influenzae.  Further analysis of the N. meningitidis cps cluster has
AB  - identified a second copy of region D encoding three additional open reading frames, including
AB  - homologs of DNA methyltransferases.  The organization of the region D and E genes in N.
AB  - gonorrhoeae and N. meningitidis in relation to the cps genes provides some insight into the
AB  - evolutionary origin of encapsulation in N. meningitidis.
ER  -

TY  - JOUR
AU  - Peters, I.
TI  - Changing the sequence specificity of the restriction endonuclease EcoRI.
JO  - Ph.D. Thesis, Germany
PY  - 2003
SP  - 1
EP  - 167
AB  - EcoRI is one of the best studied restriction endonucleases of type II.  It recognizes the
AB  - palindromic DNA sequence GAATTC with high specificity and cleaves it between G and A in the
AB  - presence of Mg2+ ions.  This specific recognition is due to a highly complex and redundant
AB  - network of hydrogen bonds, ionic and hydrophobic contacts.  In order to change the sequence
AB  - specificity of the enzyme concerning the GC base pair at the end of the recognition sequence
AB  - three amino acid residues (Met137, Arg200 and Arg203) were mutated.  Met137 was replaced by
AB  - Asn, Cys, Gln, Leu and Lys, Arg200 by Lys and Tyr and Arg203 by Lys.  Already the single
AB  - mutation M137Q results in an obvious change of specificity, because of its preference for
AB  - 5-methyl cytosine instead of cytosine during cleavage experiments with both
AB  - oligodeoxynucleotide and plasmid substrates depending on the sequence context within the DNA.
AB  - All other mutants at amino acid Met137 revealed a strong reduction of cleavage activity.  Thus
AB  - only the single mutant M137Q was used as a starting point for further mutations within one
AB  - protein.  The four mutations M137Q, R200K, R200Y and R203K were combined with each other to
AB  - form any variation possible in order to generate multiple mutants.  Except for M137Q/R203K all
AB  - mutants showed heavy loss of cleavage activity.  The mutant M137Q/R203K revealed an increased
AB  - ability to cleave star sites.  In this case the stringent coupling of specific DNA recognition
AB  - and catalysis is relaxed and the cleavage of DNA also takes place even if there are more
AB  - interrupted DNA contacts than those to the GC base pair.  By combining the double mutation
AB  - M137Q/R203K with R200Y an enzyme was created, that despite very low activity was able to
AB  - cleave all four palindromic hexamer variations with a central AATT sequence at star
AB  - conditions, whereas the sequence CAATTG was obviously preferred.  Thus an alteration of
AB  - sequence specificity was obtained for the triple mutant M137Q/R200Y/R203K.
ER  -

TY  - JOUR
AU  - Peters, W.
TI  - New applications of (S)-adenosyl-L-methionine analogues with protein methyltransferases and click chemistry for sequence specific protein labelling.
JO  - Ph.D. Thesis, Germany
PY  - 2007
SP  - 1
EP  - 126
ER  -

TY  - JOUR
AU  - Petersen, R.
AU  - Lomholt, H.B.
AU  - Scholz, C.F.
AU  - Bruggemann, H.
TI  - Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin.
JO  - Genome Announcements
PY  - 2015
SP  - e01250
EP  - e01215
VL  - 3
AB  - Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has
AB  - been associated with skin disorders such as acne vulgaris and
AB  - progressive macular hypomelanosis (PMH). Here, we report draft genome sequences
AB  - of two type III P. acnes strains, PMH5 and PMH7, isolated from PMH skin lesions.
ER  -

TY  - JOUR
AU  - Peterson, K.R.
AU  - Mount, D.W.
TI  - Analysis of the genetic requirements for viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants.
JO  - J. Bacteriol.
PY  - 1993
SP  - 7505
EP  - 7508
VL  - 175
AB  - RecBCD protein, necessary for Escherichia coli dam mutant viability, is directly required for
AB  - DNA repair. Recombination genes recF+, recN+, recO+, and recQ+ are not essential for dam
AB  - mutant viability; they are required for recBC sbcBC dam mutant survival, mutH, mutL, or mutS
AB  - mutations do not suppress subinduction of SOS genes in dam mutants.
ER  -

TY  - JOUR
AU  - Peterson, K.R.
AU  - Wertman, K.F.
AU  - Mount, D.W.
AU  - Marinus, M.G.
TI  - Viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants requires increased expression of specific genes in the SOS regulon.
JO  - Mol. Gen. Genet.
PY  - 1985
SP  - 14
EP  - 19
VL  - 201
AB  - We have examined the level of expression of the SOS regulon in cells lacking DNA adenine
AB  - methylase activity (dam-). Mud (Ap,lac) fusions to several SOS operons (recA, lexA, uvrA,
AB  - uvrB,uvrD, sulA, dinD and dinF) were found to express higher levels of beta-galactosidase in
AB  - dam- strains than in isogenic dam+ strains. The attempted construction of dam- strains that
AB  - were also mutant in one of several SOS genes indicated that the viability of
AB  - methylase-deficient strains correlates with the inactivation of the SOS repressor (LexA
AB  - protein). Consistent with this, the wild-type functions of two LexA-repressed genes (recA and
AB  - ruv) appear to be required for dam- strain viability.
ER  -

TY  - JOUR
AU  - Peterson, R.C.
TI  - Prediction of restriction endonuclease site distribution based on dinucleotide frequency.
JO  - Fed. Proc.
PY  - 1986
SP  - 1850
EP  - 1850
VL  - 45
AB  - Most analyses of the frequency of restriction endonuclease recognition sites
AB  - have assumed a random distribution of nucleotides.  Nearest neighbor analysis
AB  - and the sequence of nucleic acids indicate that the distribution of nucleotides
AB  - is nonrandom at least at the dinucleotide level.  Recent analyses have made use
AB  - of the nonrandom dinucleotide distribution observed in sequenced nucleic acids
AB  - to predict the frequency of restriction endonuclease sites.  The frequency of
AB  - sites in DNAs which have not been extensively sequenced can also be predicted
AB  - using the dinucleotide frequencies measured by nearest neighbor analysis.
AB  - Taking into account the dinucleotide bias, the site frequencies for a large
AB  - number of restriction endonucleases have been calculated for the DNAs from
AB  - several organisms.  Some restriction endonucleases which have the same base
AB  - composition in their recognition sites [e.g. EcoRV (GATATC) and HindIII
AB  - (AAGCTT)] have widely different site frequencies in the DNA from some
AB  - organisms.  The observed distribution of DNA fragments generated by selected
AB  - restriction endonucleases correlates with the predicted frequency of the
AB  - recognition site.  This type of analysis should be useful in the selection of
AB  - suitable restriction endonucleases for mapping genomic DNAs, for generating DNA
AB  - fragments for subcloning, and for screening for restriction fragment length
AB  - polymorphisms.
ER  -

TY  - JOUR
AU  - Peterson, R.C.
TI  - Prediction of the frequencies of restriction endonuclease recognition sequences using di- and mononucleotide frequencies.
JO  - Biotechniques
PY  - 1988
SP  - 34
EP  - 39
VL  - 6
AB  - The calculation of probabilities of nucleotide sequences from the freqeuencies
AB  - of dinucleotides is described.  The dinucleotide and mononucleotide frequencies
AB  - used can be obtained from nearest neighbor analysis or from databank sequences.
AB  - If dinucleotide and mononucleotide frequencies from nearest neighbor analysis
AB  - are used, probabilities for oligonucleotides can be calculated for genomes in
AB  - which there is little or no sequence data.  Within a given genome, a broad
AB  - range of probabilities for hexanucleotide palindromes with the same base
AB  - composition is predicted and shown.
ER  -

TY  - JOUR
AU  - Peterson, S.N.
AU  - Reich, N.O.
TI  - GATC flanking sequences regulate Dam activity: evidence for how Dam specificity may influence pap expression.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 459
EP  - 472
VL  - 355
AB  - Escherichia coli DNA adenine methyltransferase (Dam) plays essential roles in DNA replication,
AB  - mismatch repair and gene regulation. The differential methylation by Dam of the two GATC
AB  - sequences in the pap promoter regulates the expression of pili genes necessary for
AB  - uropathogenic E.coli cellular adhesion. Dam processively methylates GATC sites in various DNA
AB  - substrates, yet the two pap GATC sites are not processively methylated. We previously proposed
AB  - that the flanking sequences surrounding the two pap GATC sites contribute to the enzyme's
AB  - distributive methylation. We show here that replacement of the poorly methylated pap GATC
AB  - sites with sites predicted to be processively methylated indeed results in an increase in Dam
AB  - processivity. The increased processivity is due to a change in the methyltransfer kinetics and
AB  - not the binding efficiency of Dam. A competition experiment in which the flanking sequences of
AB  - only one pap GATC site were altered demonstrates that the GATC flanking sequences directly
AB  - regulate the enzyme's catalytic efficiency. The GATC flanking sequences in Dam-regulated
AB  - promoters in E.coli and other bacteria are similar to those in the pap promoter. Gene
AB  - regulation from some of these promoters involves mechanisms and proteins that are quite
AB  - different from those in the pap operon. Further, GATC sequences previously identified to
AB  - remain unmethylated within the E.coli genome, but whose function remains largely unassigned,
AB  - are flanked by sequences predicted to be poorly methylated. We conclude that the GATC flanking
AB  - sequences may be critical for expression of pap and other Dam-regulated genes by affecting the
AB  - activity of Dam at such sites and, thus, its processivity. A model is proposed, illustrating
AB  - how the sequences flanking the GATC sites in Dam-regulated promoters may contribute to this
AB  - epigenetic mechanism of gene expression, and how flanking sequences contribute to the diverse
AB  - biological roles of Dam.
ER  -

TY  - JOUR
AU  - Peterson, S.N.
AU  - Reich, N.O.
TI  - Competitive Lrp and Dam assembly at the pap regulatory region: implications for mechanisms of epigenetic regulation.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 92
EP  - 105
VL  - 383
AB  - Escherichia coli DNA adenine methyltransferase (Dam) and Leucine-responsive regulatory protein
AB  - (Lrp) are key regulators of the pap operon, which codes for
AB  - the pilus proteins necessary for uropathogenic E. coli cellular adhesion. The pap
AB  - operon is regulated by a phase variation mechanism in which the methylation
AB  - states of two GATC sites in the pap regulatory region and the binding position of
AB  - Lrp determine whether the pilus genes are expressed. The post-replicative
AB  - reassembly of Dam, Lrp, and the local regulator PapI onto a hemimethylated pap
AB  - intermediate is a critical step of the phase variation switching mechanism and is
AB  - not well understood. We show that Lrp, in the presence and in the absence of PapI
AB  - and nonspecific DNA, specifically protects pap regulatory GATC sites from Dam
AB  - methylation when allowed to compete with Dam for assembly on unmethylated and
AB  - hemimethylated pap DNA. The methylation protection is dependent upon the
AB  - concentration of Lrp and does not occur with non-regulatory GATC sites. Our data
AB  - suggest that only at low Lrp concentrations will Dam compete effectively for
AB  - binding and methylation of the proximal GATC site, leading to a phase switch
AB  - resulting in the expression of pili.
ER  -

TY  - JOUR
AU  - Pethick, F.E. et al.
TI  - Complete Genome Sequences of Corynebacterium pseudotuberculosis Strains 3/99-5 and 42/02-A, Isolated from Sheep in Scotland and Australia, Respectively.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4736
EP  - 4737
VL  - 194
AB  - Here, we report the whole-genome sequences of two ovine-pathogenic Corynebacterium
AB  - pseudotuberculosis isolates: strain 3/99-5, which represents the
AB  - first C. pseudotuberculosis genome originating from the United Kingdom, and
AB  - 42/02-A, the second from Australia. These genome sequences will contribute to the
AB  - objective of determining the global pan-genome of this bacterium.
ER  -

TY  - JOUR
AU  - Pethick, F.E.
AU  - Macfadyen, A.C.
AU  - Tang, Z.
AU  - Sangal, V.
AU  - Liu, T.T.
AU  - Chu, J.
AU  - Kosec, G.
AU  - Petkovic, H.
AU  - Guo, M.
AU  - Kirby, R.
AU  - Hoskisson, P.A.
AU  - Herron, P.R.
AU  - Hunter, I.S.
TI  - Draft Genome Sequence of the Oxytetracycline-Producing Bacterium Streptomyces rimosus ATCC 10970.
JO  - Genome Announcements
PY  - 2013
SP  - e0006313
EP  - e0006313
VL  - 1
AB  - We report the draft genome of Streptomyces rimosus (ATCC 10970), a soil isolate that produces
AB  - oxytetracycline, a commercially important and clinically useful
AB  - antibiotic.
ER  -

TY  - JOUR
AU  - Petranovic, M.
AU  - Petranovic, D.
AU  - Dohet, C.
AU  - Brooks, P.
AU  - Radman, M.
TI  - Some restriction endonucleases tolerate single mismatches of the pyrimidine-purine type.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 2159
EP  - 2162
VL  - 18
AB  - DNAs from phage mutants M13mp18 and M13mp18/MP-1 were used to construct two
AB  - closed circular heteroduplexes.  One of them carried the sequence 5'-CCTGGG-3'
AB  - 3'-GGGCCC-5' with a T-G mismatch at the position 6248.  The other carried the
AB  - sequence  5'-CCCGGG-3' 3'-GGACCC-5' with a C-A mismatch at the same position.
AB  - Heteroduplexes were exposed to 7 restriction endonucleases having recognition
AB  - sites within the sequence  5'-CCCGGG-3'  3'-GGGCCC-5' and to 1 restriction
AB  - endonuclease having a recognition site within the sequence  5'-CCTGGG-3'
AB  - 3'-GGACCC-5'.  All tested enzymes cleaved at least one mismatch-containing
AB  - sequence although with reduced efficiency.  SmaI and XmaI tolerated both
AB  - mismatch-containing sequences.  AvaI, HpaII, MspI, NciI and NspIII were able to
AB  - tolerate only the T-G containing sequence while BstNI was able to tolerate only
AB  - the C-A containing sequence.  It is inferred that the tolerance displayed by
AB  - SmaI and XmaI depends on the presence of either the original purines or the
AB  - original pyrimidines in mismatches of both the T-G and C-A type and that all
AB  - other tested enzymes require the presence of the original purines in mismatches
AB  - of both types.
ER  -

TY  - JOUR
AU  - Petrauskene, O.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
TI  - A spectrophotometric method for studying the cleavage of DNA duplexes by restriction endonucleases.
JO  - Mol. Biol. (Mosk)
PY  - 1991
SP  - 1424
EP  - 1426
VL  - 25
AB  - A spectrophotometric method for continuously monitoring the cleavage of DNA duplexes by type
AB  - II restriction endonucleases was proposed.  The time course of cleavage of a 14-membered DNA
AB  - duplex by MvaI endonuclease was obtained.  The spectrophotometric method is characterized by
AB  - rapidity and high precision in determining the kinetic parameters of the reaction.  It can be
AB  - recommended for testing preparations for the presence of restriction endonucleases, rapid
AB  - determination of the activity of any restriction endonucleases, highly precise quantitative
AB  - analysis of the restriction enzyme catalysed reactions.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Babkina, O.V.
AU  - Tashlitsky, V.N.
AU  - Kazankov, G.M.
AU  - Gromova, E.S.
TI  - EcoRII endonuclease has two identical DNA-binding sites and cleaves one of two co-ordinated recognition sites in one catalytic event.
JO  - FEBS Lett.
PY  - 1998
SP  - 29
EP  - 34
VL  - 425
AB  - EcoRII is a typical restriction enzyme that cleaves DNA using a two-site mechanism.  EcoRII
AB  - endonuclease is unable to cleave DNA which contains a small number of EcoRII recognition sites
AB  - but the enzyme activity can be stimulated in the presence of DNA with a high frequency of
AB  - EcoRII sites.  To investigate the mechanism of activation, the kinetics of stimulated EcoRII
AB  - cleavage has been studied.  A 14 bp substrate activated the cleavage of the 71 bp substrate,
AB  - containing one EcoRII recognition site (trans-activation) by a competitive mechanism: the
AB  - activator increased substrate binding but not catalysis.  The activation increased if the
AB  - substrate concentration decreased and if the activator had a lower affinity for the enzyme
AB  - than the substrate.  The introduction of the second recognition site into the 71 bp duplex
AB  - also enabled cleavage of this substrate (cis-activation).  Pyrophosphate bonds were
AB  - incorporated into one of two recognition sites to switch off the cleavage of the
AB  - phosphodiester bonds.  Analysis of cleavage products of these modified substrates showed that
AB  - EcoRII cuts one of two coordinated recognition sites in one catalytic event.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Gromova, E.S.
AU  - Romanova, E.A.
AU  - Volkov, E.M.
AU  - Oretskaya, T.S.
AU  - Shabarova, Z.A.
TI  - DNA duplexes containing methylated bases or non-nucleotide inserts in the recognition site are cleaved by restriction endonuclease R.EcoRII in presence of canonical substrate.
JO  - Gene
PY  - 1995
SP  - 173
EP  - 176
VL  - 157
AB  - DNA duplexes containing the natural methylated bases N6-methyladenine (m6Ade),
AB  - N4-methylcytosine (m4Cyt) or C5-methylcytosine (m5Cyt) in one strand of the recognition
AB  - sequence are resistant to EcoRII restriction endonuclease (R.EcoRII).  Hydrolysis of these
AB  - modified duplexes was observed in the presence of the canonical substrate.  Incorporation of
AB  - m4Cyt or m5Cyt into both strands of the recognition sequence precludes such activation by a
AB  - canonical substrate.  R.EcoRII also fails to cleave substrate analogs in which one of the
AB  - nucleosides in the recognition site is replaced by the 1,2-dideoxyribose (D) or by
AB  - 1,3-propanediol (Prd) (modeling DNA with an abasic site).  The hydrolysis of DNA duplexes with
AB  - non-nucleotide inserts is also activated in the presence of canonical substrate.  Thus, the
AB  - two-substrate mechanism of EcoRII-DNA interaction allows hydrolysis of apurinic/apyrimidinic
AB  - and hemimethylated DNA.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Karpova, E.A.
AU  - Gromova, E.S.
AU  - Guschlbauer, W.
TI  - Two subunits of EcoRII restriction endonuclease interact with two DNA recognition sites.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1994
SP  - 885
EP  - 890
VL  - 198
AB  - The cleavage of a 14 base pair DNA duplex containing one EcoRII recognition site by EcoRII
AB  - restriction endonuclease (R.EcoRII) was studied in single turnover experiments with varying
AB  - enzyme concentrations in the micromolar range. The reaction rate increased with enzyme
AB  - concentration until a ratio of one dimeric R.EcoRII enzyme to two double stranded
AB  - olionucleotide molecules. Excess of R.EcoRII lead to inhibition of cleavage. Maximum cleavage
AB  - was also found with pBR322 DNA containing six EcoRII recognition sites at a ratio of one
AB  - dimeric enzyme to two EcoRII recognition sites of the plasmid DNA. At higher ratios inhibition
AB  - was observed. These observations indicate that the active enzyme complex is formed when two
AB  - subunits of the enzyme interact with two R. EcoRII recognition sites.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Krynetskaya, N.F.
AU  - Tashlitsky, V.N.
AU  - Belkov, V.M.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Guschlbauer, W.
AU  - Shabarova, Z.A.
TI  - Use of UV spectroscopy for the study of nucleic acid cleavage by E.coli RNase H and restriction endonucleases.
JO  - Biochem. Mol. Biol. Int.
PY  - 1995
SP  - 1127
EP  - 1135
VL  - 37
AB  - A one-step spectrophotometric method for monitoring of nucleic acid cleavage by ribonuclease H
AB  - from E.coli and type II restriction endonucleases has been proposed.  It is based on recording
AB  - the increase in the UV absorbance at 260 nm during the course of enzymatic reaction.  Duplexes
AB  - stable under the reaction conditions were chosen as substrates for the enzymes being studied.
AB  - In order to obtain duplex dissociation following their cleavage by the enzyme appropriate
AB  - temperature conditions were selected.  The spectrophotometric method may be applied for rapid
AB  - testing of the nuclease activity in protein preparations as well as for precise quantitative
AB  - analysis of nucleic acid degradation by enzymes.  This method may be successfully employed in
AB  - kinetic studies of nucleic acid - protein interactions.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Pein, C.-D.
AU  - Cech, D.
AU  - Shabarova, Z.A.
TI  - Synthetic DNA duplexes as a tool in studying the mechanism of EcoRII activation.
JO  - Mol. Biol. (Mosk)
PY  - 1993
SP  - 507
EP  - 518
VL  - 27
AB  - The efficiency of EcoRII cleavage of synthetic DNA duplexes with one EcoRII recognition site
AB  - decreases with increasing substrate length. This enzyme virtually fails to cleave DNA duplexes
AB  - longer than 215 bp. However, EcoRII cleaves long DNA duplexes with one recognition site in the
AB  - presence of 11-14 bp substrates. The extent of hydrolysis activation depends on the length and
AB  - concentration of the added substrate. A model system is suggested for studying the molecular
AB  - and kinetic mechanism of EcoRII activation. This system includes a 30-bp substrate with one
AB  - EcoRII recognition site, and DNA duplexes as activating substrates that contain modified
AB  - heterocyclic bases and internucleotide phosphate groups. DNA duplexes with a modified EcoRII
AB  - recognition site may activate hydrolysis of the 30-bp substrate and of phage T3 DNA. Their
AB  - catalytic effect on the cleavage of extended duplexes depends on the type of modification and
AB  - its localization in the recognition site. Cooperative interaction of EcoRII with two
AB  - recognition sites in DNA has been shown to be essential for the functioning of the enzyme.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Mechanism of the interaction of EcoRII restriction endonuclease with two recognition sites - probing of modified DNA duplexes as activators of the enzyme.
JO  - Eur. J. Biochem.
PY  - 1992
SP  - 617
EP  - 622
VL  - 208
AB  - The efficiency of cleavage of DNA duplexes with single EcoRII recognition sites by the EcoRII
AB  - restriction endonuclease decreases with increasing substrate length. DNA duplexes of more than
AB  - 215 bp are not effectively cleaved by this enzyme. Acceleration of the hydrolysis of long
AB  - single-site substrates by EcoRII is observed in the presence of 11-14 bp substrates. The
AB  - stimulation of hydrolysis depends on the length and concentration of the second substrate. To
AB  - study the mechanism of EcoRII endonuclease stimulation, DNA duplexes with base analogs and
AB  - modified internucleotide phosphate groups in the EcoRII site have been investigated as
AB  - activators. These modified duplexes are cleaved by EcoRII enzyme with different efficiences or
AB  - are not cleaved at all. It has been discovered that the resistance of some of them can be
AB  - overcome by incubation with a susceptible canonical substrate. The acceleration of cleavage of
AB  - long single-site substrates depends on the type of modification of the activator. The modified
AB  - DNA duplexes can activate EcoRII catalyzed hydrolysis if they can be cleaved by EcoRII
AB  - themselves or in the presence of the second canonical substrate. It has been demonstrated that
AB  - EcoRII endonuclease interacts in a cooperative way with two recognition sites in DNA. The
AB  - cleavage of one of the recognition sites depends on the cleavage of the other. We suggest that
AB  - the activator is not an allosteric effector but acts as a second substrate.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Schmidt, S.
AU  - Karyagina, A.S.
AU  - Nikolskaya, I.I.
AU  - Gromova, E.S.
AU  - Cech, D.
TI  - The interaction of DNA duplexes containing 2-aminopurine with restriction endonucleases EcoRII and SsoII.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 2192
EP  - 2197
VL  - 23
AB  - Oligonucleotides containing 2-aminopurine (2-AP) in place of G or A in the recognition site of
AB  - EcoRII (CCT/AGG) or SsoII (CCNGG) restriction endonucleases have been synthesized in order to
AB  - investigate the specific interaction of DNA with these enzymes. Physicochemical properties (CD
AB  - spectra and melting behaviour) have shown that DNA duplexes containing 2-aminopurine exist
AB  - largely in a stable B-like form. 2-Aminopurine base paired with cytidine, however, essentially
AB  - influences the helix structure. The presence of a 2-AP.C mismatch strongly reduces the
AB  - stability of the duplexes in comparison with the natural double strand, indicated by a
AB  - biphasic melting behaviour. SsoII restriction endonuclease recognizes and cleaves the modified
AB  - substrate with a 2-AP.T mismatch in the centre of the recognition site, but it does not cleave
AB  - the duplexes containing 2-aminopurine in place of inner and outer G, or both. EcoRII
AB  - restriction endonuclease does not cleave duplexes containing 2-aminopurine at all. The
AB  - two-substrate mechanism of EcoRII-DNA interaction, however, allows hydrolysis of the duplex
AB  - containing 2-aminopurine in place of adenine in the presence of the canonical substrate.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Tashlitsky, V.N.
AU  - Brevnov, M.G.
AU  - Bakman, Y.
AU  - Gromova, E.S.
TI  - Kinetic modeling of allosteric interaction of EcoRII restriction endonuclease with two DNA sites.
JO  - Biokhimiia
PY  - 1996
SP  - 1257
EP  - 1269
VL  - 61
AB  - The effect of correlations between kinetic parameters of two inducible substrates on
AB  - allosteric activation of EcoRII endonuclease hydrolysis of one substrate was studied.  The
AB  - pairs of DNA duplexes were constructed that were the substrates of EcoRII restriction
AB  - endonuclease or their analogs and had different kinetic constants of interaction with the
AB  - enzyme; the effects of their concentrations on mutual hydrolysis induction were studied.  A
AB  - kinetic mechanism is suggested considering the allosteric effects of two DNA recognition sites
AB  - on a dimeric molecule of EcoRII.  Mathematic modelling was used to analyze the kinetic
AB  - mechanism and evaluate optimal characteristics of the inductor.  Thus, activation increases
AB  - when substrate concentration decreases, enzyme binding of two inductor or substrate molecules
AB  - decreases, binding of one substrate molecule increases versus binding of one inductor
AB  - molecule, and kcat of the enzyme-substrate complex including one substrate and one inductor
AB  - increases.
ER  -

TY  - JOUR
AU  - Petrauskene, O.V.
AU  - Yakovleva, J.N.
AU  - Alekseev, Y.I.
AU  - Subach, F.V.
AU  - Babkina, O.V.
AU  - Gromova, E.S.
TI  - DNA duplexes containing altered sugar residues as probes of EcoRII and MvaI endonuclease interactions with sugar-phosphate backbone.
JO  - J. Biomol. Struct. Dyn.
PY  - 2000
SP  - 857
EP  - 870
VL  - 17
AB  - Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or
AB  - 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the
AB  - EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific
AB  - recognition of the DNA sugar-phosphate backbone by EcoRII and MvaI restriction endonucleases.
AB  - In 2'-deoxyxylosyl moieties of dCx and dTx, 3'-hydroxyl groups were inverted, which perturbs
AB  - the related individual phosphates. Introduction of a single 2'-deoxyxylosyl moiety into a dC
AB  - x dG pair resulted in a minor destabilization of double-stranded DNA structure. In the case of
AB  - a dA x dT pair the effect of a 2'-deoxyxylose incorporation was much more pronounced.
AB  - Multiple dCx modifications and their combination with dTx did not enhance the destabilization
AB  - effect. Hydrolysis of dCx-containing DNA duplexes by EcoRII endonuclease was blocked and
AB  - binding affinity was strongly dependent on the location of an altered sugar. A DNA duplex
AB  - containing a dTx residue was cleaved by the enzyme, but kcat/K(M) was slightly reduced. In
AB  - contrast, MvaI endonuclease efficiently cleaved both types of sugar-altered substrate analogs.
AB  - However it did not cleave conformationally perturbed scissile bonds, when the corresponding
AB  - unmodified bonds were perfectly hydrolyzed in the same DNA duplexes. Based on these data the
AB  - possible contributions of individual phosphates in the recognition site to substrate
AB  - recognition and catalysis by EcoRII were proposed. We observed strikingly non-equivalent
AB  - inputs for different phosphates with respect to their effect on EcoRII-DNA complex formation.
ER  -

TY  - JOUR
AU  - Petrauskiene, L.J.
AU  - Klimasauskas, S.J.
AU  - Butkus, V.V.
AU  - Janulaitis, A.
TI  - Synthesis of oligodeoxynucleotides containing N4-methylcytosine.
JO  - Bioorg. Khim.
PY  - 1986
SP  - 1597
EP  - 1603
VL  - 12
AB  - With deoxyuridine as starting material, N4-methyldeoxycytidine and its fully protected
AB  - mononucleotide, suitable for oligonucleotide synthesis, have been prepared.  By means of the
AB  - phosphotriester approach, the fully protected mononucleotide was used for the synthesis of
AB  - seven dodecadeoxynucleotides containing either m4C or m5C in various positions of the CCCGGG
AB  - sequence, the recognition site of some restriction endonucleases.
ER  -

TY  - JOUR
AU  - Petronella, N.
AU  - Kenwell, R.
AU  - Pagotto, F.
AU  - Pightling, A.W.
TI  - Draft Genome Sequences of Two Clostridium botulinum Group II (Nonproteolytic) Type B Strains (DB-2 and KAPB-3).
JO  - Genome Announcements
PY  - 2014
SP  - e01111
EP  - e01114
VL  - 2
AB  - Clostridium botulinum is important for food safety and studies of neurotoxins associated with
AB  - human botulism. We present the draft genome sequences of two
AB  - strains belonging to group II type B: one collected from Pacific Ocean sediments
AB  - (DB-2) and another obtained during a botulism outbreak (KAPB-3).
ER  -

TY  - JOUR
AU  - Petroni, E.A.
AU  - Bocca, S.N.
AU  - Ielpi, L.
TI  - Sequence-specific DNA modification in Acetobacter xylinum.
JO  - Cell. Mol. Biol. (Noisy-le-grand)
PY  - 1996
SP  - 759
EP  - 767
VL  - 42
AB  - Two cryptic plasmids have been discovered in Acetobacter xylinum B42 and in its derivative
AB  - PEA-1, a cellulose defective mutant.  These two plasmids were designated pAX1 and pAX2 (50 and
AB  - 105 in size, respectively).  A restriction map was constructed for pAX1.  Attempts to cure
AB  - these plasmids were unsuccessful.  Enzyme restriction analysis showed that these plasmids
AB  - contain protected EcoRI and ApoI sites.  Using Southern blot and hybridization techniques, the
AB  - protection was extended to chromosomal DNA.  Enzyme restriction analysis of several plasmids,
AB  - from different origins and containing different incompatibility groups, isolated from strain
AB  - PEA-1 also showed EcoRI and ApoI protection.  The presence of modifications on specific
AB  - sequences was not found in A. xylinum 8747.  These results strongly suggest the presence of a
AB  - modification system in A. xylinum B42 that recognizes the tetranucleotide 5'-AATT.
ER  -

TY  - JOUR
AU  - Petronzio, T.
AU  - Schildkraut, I.
TI  - Altered specificity of restriction endonucleases HinfI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3666
EP  - 3666
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Petrosino, J.F.
AU  - Xiang, Q.
AU  - Karpathy, S.E.
AU  - Jiang, H.
AU  - Yerrapragada, S.
AU  - Liu, Y.
AU  - Gioia, J.
AU  - Hemphill, L.
AU  - Gonzalez, A.
AU  - Raghavan, T.M.
AU  - Uzman, A.
AU  - Fox, G.E.
AU  - Highlander, S.
AU  - Reichard, M.
AU  - Morton, R.J.
AU  - Clinkenbeard, K.D.
AU  - Weinstock, G.M.
TI  - Chromosome Rearrangement and Diversification of Francisella tularensis Revealed by the Type B (OSU18) Genome Sequence.
JO  - J. Bacteriol.
PY  - 2006
SP  - 6977
EP  - 6985
VL  - 188
AB  - The gamma-proteobacterium Francisella tularensis is one of the most
AB  - infectious human pathogens, and the highly virulent organism F. tularensis
AB  - subsp. tularensis (type A) and less virulent organism F. tularensis subsp.
AB  - holarctica (type B) are most commonly associated with significant disease
AB  - in humans and animals. Here we report the complete genome sequence and
AB  - annotation for a low-passage type B strain (OSU18) isolated from a dead
AB  - beaver found near Red Rock, Okla., in 1978. A comparison of the F.
AB  - tularensis subsp. holarctica sequence with that of F. tularensis subsp.
AB  - tularensis strain Schu4 (P. Larsson et al., Nat. Genet. 37:153-159, 2005)
AB  - highlighted genetic differences that may underlie different pathogenicity
AB  - phenotypes and the evolutionary relationship between type A and type B
AB  - strains. Despite extensive DNA sequence identity, the most significant
AB  - difference between type A and type B isolates is the striking amount of
AB  - genomic rearrangement that exists between the strains. All but two
AB  - rearrangements can be attributed to homologous recombination occurring
AB  - between two prominent insertion elements, ISFtu1 and ISFtu2. Numerous
AB  - pseudogenes have been found in the genomes and are likely contributors to
AB  - the difference in virulence between the strains. In contrast, no
AB  - rearrangements have been observed between the OSU18 genome and the genome
AB  - of the type B live vaccine strain (LVS), and only 448 polymorphisms have
AB  - been found within non-transposase-coding sequences whose homologs are
AB  - intact in OSU18. Nonconservative differences between the two strains
AB  - likely include the LVS attenuating mutation(s).
ER  -

TY  - JOUR
AU  - Petrosova, H.
AU  - Zobanikova, M.
AU  - Cejkova, D.
AU  - Mikalova, L.
AU  - Pospisilova, P.
AU  - Strouhal, M.
AU  - Chen, L.
AU  - Qin, X.
AU  - Muzny, D.M.
AU  - Weinstock, G.M.
AU  - Smajs, D.
TI  - Whole Genome Sequence of Treponema pallidum ssp. pallidum, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains.
JO  - PLoS Neglected Trop. Dis.
PY  - 2012
SP  - E1832
EP  - E1832
VL  - 6
AB  - BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of
AB  - syphilis, and Treponema pallidum ssp. pertenue (TPE), the causative agent of
AB  - yaws, are closely related spirochetes causing diseases with distinct clinical
AB  - manifestations. The TPA Mexico A strain was isolated in 1953 from male, with
AB  - primary syphilis, living in Mexico. Attempts to cultivate TPA Mexico A strain
AB  - under in vitro conditions have revealed lower growth potential compared to other
AB  - tested TPA strains. METHODOLOGY/PRINCIPAL FINDINGS: The complete genome sequence
AB  - of the TPA Mexico A strain was determined using the Illumina sequencing
AB  - technique. The genome sequence assembly was verified using the whole genome
AB  - fingerprinting technique and the final sequence was annotated. The genome size of
AB  - the Mexico A strain was determined to be 1,140,038 bp with 1,035 predicted ORFs.
AB  - The Mexico A genome sequence was compared to the whole genome sequences of three
AB  - TPA (Nichols, SS14 and Chicago) and three TPE (CDC-2, Samoa D and Gauthier)
AB  - strains. No large rearrangements in the Mexico A genome were found and the
AB  - identified nucleotide changes occurred most frequently in genes encoding putative
AB  - virulence factors. Nevertheless, the genome of the Mexico A strain, revealed two
AB  - genes (TPAMA_0326 (tp92) and TPAMA_0488 (mcp2-1)) which combine TPA- and TPE-
AB  - specific nucleotide sequences. Both genes were found to be under positive
AB  - selection within TPA strains and also between TPA and TPE strains.
AB  - CONCLUSIONS/SIGNIFICANCE: The observed mosaic character of the TPAMA_0326 and
AB  - TPAMA_0488 loci is likely a result of inter-strain recombination between TPA and
AB  - TPE strains during simultaneous infection of a single host suggesting horizontal
AB  - gene transfer between treponemal subspecies.
ER  -

TY  - JOUR
AU  - Petrossian, T.
AU  - Clarke, S.
TI  - Bioinformatic identification of novel methyltransferases.
JO  - Epigenomics
PY  - 2009
SP  - 163
EP  - 175
VL  - 1
AB  - Methylation of DNA, protein and even RNA species are integral processes in epigenesis. Enzymes
AB  - that catalyze these reactions using the donor S-adenosylmethionine fall into several
AB  - structurally distinct classes. The members in each class share sequence similarity that can be
AB  - used to identify additional methyltransferases. Here, we characterize these classes and in
AB  - silico approaches to infer protein function. Computational methods, such as hidden Markov
AB  - model profiling and the Multiple Motif Scanning program, can be used to analyze known
AB  - methyltransferases and relay information into the prediction of new ones. In some cases, the
AB  - substrate of methylation can be inferred from hidden Markov model sequence similarity
AB  - networks. Functional identification of these candidate species is much more difficult; we
AB  - discuss one biochemical approach.
ER  -

TY  - JOUR
AU  - Petrossian, T.C.
AU  - Clarke, S.G.
TI  - Computational methods to identify novel methyltransferases.
JO  - BMC Bioinformatics
PY  - 2009
SP  - 7
EP  - 7
VL  - 10
AB  - 1.2% of the yeast genes are estimated to encode enzymes that catalyze the transfer of a methyl
AB  - group from S-adenosylmethionine to protein, nucleic acid, lipid, and small molecule
AB  - substrates.  These enzymes function in biosynthesis, regulating metabolic pathways and
AB  - controlling gene expressiopn, including writing the histone code.  BLAST and MEM/MAST analysis
AB  - using the amino acid sequence of motifs have previously generated a list of putative Class I
AB  - methyltransferases.  Recently we have used a combination of a new search algorithm and
AB  - structural information to refine this analysis.  This study utilizes these updated methods of
AB  - identifying motifs and scanning the proteome to predict new members of the different families
AB  - of methyltransferases in different organisms.  These new members may function in novel
AB  - pathways or new modes of regulation.
ER  -

TY  - JOUR
AU  - Petrosyan, V.
AU  - Holder, M.
AU  - Ajami, N.J.
AU  - Petrosino, J.F.
AU  - Sahasrabhojane, P.
AU  - Thompson, E.J.
AU  - Kalia, A.
AU  - Shelburne, S.A.
TI  - Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome.
JO  - Genome Announcements
PY  - 2016
SP  - e00259
EP  - e00216
VL  - 4
AB  - Streptococcus mitisfrequently causes invasive infections in neutropenic cancer patients, with
AB  - a subset of patients developing viridans group streptococcal (VGS)
AB  - shock syndrome. We report here the first complete genome sequence ofS.
AB  - mitisstrain SVGS_061, which caused VGS shock syndrome, to help elucidate the
AB  - pathogenesis of severe VGS infection.
ER  -

TY  - JOUR
AU  - Petrov, N.A.
AU  - Gorbunov, Y.A.
AU  - Malygin, E.G.
TI  - Interaction of T4 phage DNA-[N6-adenine]-methyltransferase with substrates containing defective recognition sites.
JO  - Mol. Biol. (Mosk)
PY  - 1997
SP  - 973
EP  - 977
VL  - 31
AB  - The effect of the structure of the recognition site GATC in a substrate duplex on its complex
AB  - form ation with DNA-[N6-adenine]-methyltransferase of T4 phage was studied.  The gel
AB  - retardation method was employed to reveal the complexes.  As compared with the native
AB  - duplexes, the majority of defective duplexes had the same or even better affinity to T4 MTase;
AB  - however, no correlation was found between the complex stability and effectiveness of the
AB  - duplexes as substrates for methylation.  Apparently, formation of a stale enzyme-DNA complex
AB  - does not require continuity of the two strands of the duplex and perfect base pairing in the
AB  - recognition site.  A half of the constituents of the recognition site suffices for stable
AB  - complexes with T4 MTase to form.  Deoxyguanosine residues in both strands of the modified GATC
AB  - are shown to be indispensable for complex formation.
ER  -

TY  - JOUR
AU  - Petrov, N.A.
AU  - Gorbunov, Y.A.
AU  - Naumochkin, A.N.
AU  - Malygin, E.G.
TI  - Substrate complexes of DNA-[N6-adenine]-methyltransferases of T-even phages registered by the gel retardation method.
JO  - Mol. Biol. (Mosk)
PY  - 1997
SP  - 966
EP  - 972
VL  - 31
AB  - DNA-[N6-adenine]-methyltransferases of T4 and T2 phages (T4 and T2 Mtases) recognize, in
AB  - double-stranded DNA, the palindrome GATC and catalyze the transfer of the methyl group from
AB  - S-adenosyl-L-methionine (SAM) to position N6 of the adenine residue.  The gel retardation
AB  - method was used to study the relative effectiveness of complex formation of T4 and T2 MTases
AB  - with oligonucleotide substrates of varying length containing GATC in the middle of the duplex.
AB  - It is shown that T4 MTase forms stable complexes with 20-mer duplexes bearing a nonmodified or
AB  - hemimethylated GATC site.  The binding of the duplex to T4 MTase is enhanced in the presence
AB  - of SAM.  Parameters of the interaction of SAM with MTase not bound and bound with the 20-mer
AB  - duplex are determined.  T2 MTase, which has a higher catalytic activity than the T4 enzyme,
AB  - forms less stable complexes with oligonucleotides.  Thus, there is no direct relation between
AB  - the stability of the enzyme-substrate complexes and the catalytic activity.
ER  -

TY  - JOUR
AU  - Petrov, V.M.
AU  - Ratnayaka, S.
AU  - Nolan, J.M.
AU  - Miller, E.S.
AU  - Karam, J.D.
TI  - Genomes of the T4-related bacteriophages as windows on microbial genome evolution.
JO  - Virol. J.
PY  - 2010
SP  - 292
EP  - 292
VL  - 7
AB  - ABSTRACT: The T4-related bacteriophages are a group of bacterial viruses
AB  - that share morphological similarities and genetic homologies with the
AB  - well-studied Escherichia coli phage T4, but that diverge from T4 and each
AB  - other by a number of genetically determined characteristics including the
AB  - bacterial hosts they infect, the sizes of their linear double-stranded
AB  - (ds) DNA genomes and the predicted compositions of their proteomes. The
AB  - genomes of about 40 of these phages have been sequenced and annotated over
AB  - the last several years and are compared here in the context of the factors
AB  - that have determined their diversity and the diversity of other microbial
AB  - genomes in evolution. The genomes of the T4 relatives analyzed so far
AB  - range in size between ~160,000 and ~250,000 base pairs (bp) and are
AB  - mosaics of one another, consisting of clusters of homology between them
AB  - that are interspersed with segments that vary considerably in genetic
AB  - composition between the different phage lineages. Based on the known
AB  - biological and biochemical properties of phage T4 and the proteins encoded
AB  - by the T4 genome, the T4 relatives reviewed here are predicted to share a
AB  - genetic core, or "Core Genome" that determines the structural design of
AB  - their dsDNA chromosomes, their distinctive morphology and the process of
AB  - their assembly into infectious agents (phage morphogenesis). The Core
AB  - Genome appears to be the most ancient genetic component of this phage
AB  - group and constitutes a mere 12-15% of the total protein encoding
AB  - potential of the typical T4-related phage genome. The high degree of
AB  - genetic heterogeneity that exists outside of this shared core suggests
AB  - that horizontal DNA transfer involving many genetic sources has played a
AB  - major role in diversification of the T4-related phages and their spread to
AB  - a wide spectrum of bacterial species domains in evolution. We discuss some
AB  - of the factors and pathways that might have shaped the evolution of these
AB  - phages and point out several parallels between their diversity and the
AB  - diversity generally observed within all groups of interrelated dsDNA
AB  - microbial genomes in nature.
ER  -

TY  - JOUR
AU  - Petrovski, S.
AU  - Seviour, R.J.
AU  - Tillett, D.
TI  - Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 7864
EP  - 7867
VL  - 77
AB  - Most activated sludge treatment plants suffer from the presence of foams
AB  - on the surfaces of their aeration reactors. These are often stabilized by
AB  - hydrophobic mycolic acid-synthesizing actinobacterial species. A
AB  - polyvalent Siphoviridae phage, GTE7, which lysed several Gordonia and
AB  - Nocardia species, is described here. Its genome has a modular structure
AB  - similar to that described for Rhodococcus phage ReqiDocB7. In
AB  - laboratory-scale experiments, we showed that GTE7 prevents stabilization
AB  - of foams by these Gordonia and Nocardia species.
ER  -

TY  - JOUR
AU  - Petruska, J.
AU  - Horn, D.
TI  - Sequence-specific responses of restriction endonucleases to bromodeoxyuridine substitution in mammalian DNA.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 2495
EP  - 2510
VL  - 11
AB  - Substitution of BrdU for dT in mammalian DNA alters the rates of DNA cleavage
AB  - by restriction endonucleases in a manner that can be related to the specificity
AB  - of cleavage.  A formula is proposed that describes inhibitory and stimulatory
AB  - contributions arising from the substitution of a Br atom for the CH3 group on
AB  - T.  The larger Br atom is postulated to sterically hinder the nuclease from
AB  - binding to adjacent groups in the DNA cleavage site, while allowing a tighter
AB  - binding to itself.  The inhibition caused by steric hindrance is predicted to
AB  - vary inversely with distance from the point of cleavage, whereas the
AB  - stimulation caused by tighter binding is predicted to be independent of
AB  - distance.  The resultant formula gives a good fit to the data obtained for
AB  - thirteen different restriction nucleases of known specificity.  The parameters
AB  - in the formula appear to be simple functions of ionic strength.  This formula
AB  - can be used to predict the effect of BrdU substitution on any endonuclease
AB  - whose specificity of cleavage is known.
ER  -

TY  - JOUR
AU  - Petrusyte, M.
AU  - Bitinaite, J.
AU  - Menkevicius, S.
AU  - Klimasauskas, S.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Restriction endonucleases of a new type.
JO  - Gene
PY  - 1988
SP  - 89
EP  - 91
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Petrusyte, M.
AU  - Rudokas, K.
AU  - Maneliene, Z.
AU  - Kiuduliene, E.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Bsp1407I, a restriction endonuclease from Bacillus stearothermophilus, which recognizes novel palindromic sequence 5'-T^GTACA-3'.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2514
EP  - 2514
VL  - 21
AB  - A new type II restriction endonuclease, Bsp1407I, has been isolated from Bacillus
AB  - stearothermophilus RFL1407. Bsp1407I recognizes the palindromic hexanucleotide 5'- TGTACA-3'
AB  - generating 5'-protruding tetranucleotide. Bsp1407I cuts lambda DNA at five sites, SV40 at two
AB  - sites and does not cleave phiX174 and pBR322 DNA. We found that the computer calculated number
AB  - of fragments that would be generated at the sequences 5'-TGTACA, correlated with the observed
AB  - cleavage frequency of the above mentioned substrates. Double digestion with Bsp1407I and
AB  - Bsp1201 (ApaI), Pfl23II(SplI), Eco81I(SauI) and XhoI were used to map the Bsp1407I sites on
AB  - lambda DNA. The mapped positions matched those predicted by cleavage at the sequence
AB  - 5'-TGTACA. The cleavage site of Bsp1407I was determined using a synthetic oligonucleotide
AB  - duplex which contains the Bsp1407I recognition sequence:
AB  - 5'-GAGTGTACACTC-3'
AB  - 3'-CTCACATGTGAG-5'.
ER  -

TY  - JOUR
AU  - Petrusyte, M.P.
AU  - Bitinaite, J.B.
AU  - Kersulyte, D.R.
AU  - Menkevicius, S.J.
AU  - Butkus, V.V.
AU  - Janulaitis, A.
TI  - New types of restriction endonucleases.
JO  - Dokl. Akad. Nauk.
PY  - 1987
SP  - 1250
EP  - 1253
VL  - 295
AB  - The restriction enzymes GsuI and Eco57I are described.  The cleavage sites were
AB  - characterized as CTGGAG (16/14) for GsuI and CTGAAG (16/14) for Eco57I.  Both
AB  - enzymes are activated by SAM.  Complete fragmentation was not possible!
AB  - Endonuclease and methylase activities could not be separated for Eco57I.  For
AB  - GsuI no methylase activity was detected.
ER  -

TY  - JOUR
AU  - Petrusyte, M.P.
AU  - Janulaitis, A.
TI  - Isolation and some properties of the restriction endonuclease BcnI from Bacillus centrosporus.
JO  - Eur. J. Biochem.
PY  - 1982
SP  - 377
EP  - 381
VL  - 121
AB  - A specific type-II restriction endonuclease BcnI from Bacillus centrosporus has
AB  - been purified to electrophoretic homogeneity in three chromatographic steps.
AB  - Around 15 micrograms of such a preparation can be isolated from 1g of the cell
AB  - paste.  The yield of the enzyme is higher than that of any type-II restriction
AB  - endonuclease so far reported.The molecular weight of the enzyme determined by
AB  - gel filtration and polyacrylamide gel electrophoresis in the presence of sodium
AB  - dodecyl sulphate equals 27500 and 28000 respectively.  The activity of the
AB  - restriction endonuclease is maximal at pH 9.2 and 40-45C.  The optimal
AB  - magnesium concentration was estimated to be 7.5mM.  The activity of BcnI may
AB  - also be observed in the presence of Co2+, Mn2+, Ni2+ and Zn2+ but it is
AB  - markedly less than in the presence of Mg2+.
ER  -

TY  - JOUR
AU  - Petrusyte, M.P.
AU  - Janulaitis, A.
TI  - Specific methylase from Bacillus centrosporus.
JO  - Bioorg. Khim.
PY  - 1981
SP  - 1885
EP  - 1887
VL  - 7
AB  - A new site-specific methylase, BcnI, has been isolated from the Bacillus centrosporus strain.
AB  - The enzyme recognizes the sequence 5'CmC (C/G)GG in double-stranded DNA and methylating the
AB  - underlined cytosine residue.
ER  -

TY  - JOUR
AU  - Pettengill, E.A.
AU  - Hoffmann, M.
AU  - Binet, R.
AU  - Roberts, R.J.
AU  - Payne, J.
AU  - Allard, M.
AU  - Michelacci, V.
AU  - Minelli, F.
AU  - Morabito, S.
TI  - Complete Genome Sequence of Enteroinvasive Escherichia coli O96:H19 Associated with a Severe Foodborne Outbreak.
JO  - Genome Announcements
PY  - 2015
SP  - e00883
EP  - e00815
VL  - 3
AB  - We present here the complete genome sequence of a strain of enteroinvasive Escherichia coli
AB  - O96:H19 from a severe foodborne outbreak in a canteen in Italy
AB  - in 2014. The complete genome may provide important information about the acquired
AB  - pathogenicity of this strain and the transition between commensal and pathogenic
AB  - E. coli.
ER  -

TY  - JOUR
AU  - Pettersson, B.M.
AU  - Behra, P.R.
AU  - Manduva, S.
AU  - Das, S.
AU  - Dasgupta, S.
AU  - Bhattacharya, A.
AU  - Kirsebom, L.A.
TI  - Draft Genome Sequence of Saccharopolyspora rectivirgula.
JO  - Genome Announcements
PY  - 2014
SP  - e01117
EP  - e01113
VL  - 2
AB  - We have sequenced the genome of Saccharopolyspora rectivirgula, the causative agent of
AB  - farmer's lung disease. The draft genome consists of 182 contigs totaling
AB  - 3,977,051 bp, with a GC content of 68.9%.
ER  -

TY  - JOUR
AU  - Petty, N.K.
AU  - Bulgin, R.
AU  - Crepin, V.F.
AU  - Cerdeno-Tarraga, A.M.
AU  - Schroeder, G.N.
AU  - Quail, M.A.
AU  - Lennard, N.
AU  - Corton, C.
AU  - Barron, A.
AU  - Clark, L.
AU  - Toribio, A.L.
AU  - Parkhill, J.
AU  - Dougan, G.
AU  - Frankel, G.
AU  - Thomson, N.R.
TI  - The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.
JO  - J. Bacteriol.
PY  - 2010
SP  - 525
EP  - 538
VL  - 192
AB  - Citrobacter rodentium (formally Citrobacter freundii biotype 4280) is a
AB  - highly infectious pathogen that causes colitis and transmissible colonic
AB  - hyperplasia in mice. In common with enteropathogenic and enterohemorrhagic
AB  - Escherichia coli (EPEC and EHEC, respectively), C. rodentium exploits a
AB  - type III secretion system (T3SS) to induce attaching and effacing (A/E)
AB  - lesions that are essential for virulence. Here, we report the fully
AB  - annotated genome sequence of the 5.3-Mb chromosome and four plasmids
AB  - harbored by C. rodentium strain ICC168. The genome sequence revealed key
AB  - information about the phylogeny of C. rodentium and identified 1,585 C.
AB  - rodentium-specific (without orthologues in EPEC or EHEC) coding sequences,
AB  - 10 prophage-like regions, and 17 genomic islands, including the locus for
AB  - enterocyte effacement (LEE) region, which encodes a T3SS and effector
AB  - proteins. Among the 29 T3SS effectors found in C. rodentium are all 22 of
AB  - the core effectors of EPEC strain E2348/69. In addition, we identified a
AB  - novel C. rodentium effector, named EspS. C. rodentium harbors two type VI
AB  - secretion systems (T6SS) (CTS1 and CTS2), while EHEC contains only one
AB  - T6SS (EHS). Our analysis suggests that C. rodentium and EPEC/EHEC have
AB  - converged on a common host infection strategy through access to a common
AB  - pool of mobile DNA and that C. rodentium has lost gene functions
AB  - associated with a previous pathogenic niche.
ER  -

TY  - JOUR
AU  - Petzsch, P.
AU  - Poehlein, A.
AU  - Johnson, D.B.
AU  - Daniel, R.
AU  - Schlomann, M.
AU  - Muhling, M.
TI  - Genome Sequence of the Acidophilic Sulfate-Reducing Peptococcaceae Strain CEB3.
JO  - Genome Announcements
PY  - 2015
SP  - e00886
EP  - e00815
VL  - 3
AB  - We report the draft genome of the Peptococcaceae strain CEB3 that originated from an acidic
AB  - (pH 2.5) stream draining an abandoned copper mine. Strain CEB3 is one
AB  - of the very few reported acidophilic sulfate-reducing isolates. The 5.04-Mb draft
AB  - genome harbors 5,069 predicted protein-encoding and 66 RNA genes.
ER  -

TY  - JOUR
AU  - Petzsch, P.
AU  - Poehlein, A.
AU  - Johnson, D.B.
AU  - Daniel, R.
AU  - Schlomann, M.
AU  - Muhling, M.
TI  - Genome Sequence of the Moderately Acidophilic Sulfate-Reducing Firmicute Desulfosporosinus acididurans (Strain M1T).
JO  - Genome Announcements
PY  - 2015
SP  - e00881
EP  - e00815
VL  - 3
AB  - Microbial dissimilatory sulfate reduction is commonplace in many anaerobic environments,
AB  - though few acidophilic bacteria are known to mediate this process.
AB  - We report the 4.64-Mb draft genome of the type strain of the moderate acidophile
AB  - Desulfosporosinus acididurans, which was isolated from acidic sediment in a river
AB  - draining the Soufriere volcano, Montserrat.
ER  -

TY  - JOUR
AU  - Pfaller, S.
AU  - Tokarev, V.
AU  - Kessler, C.
AU  - McLimans, C.
AU  - Gomez-Alvarez, V.
AU  - Wright, J.
AU  - King, D.
AU  - Lamendella, R.
TI  - Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169.
JO  - Genome Announcements
PY  - 2017
SP  - e01620
EP  - e01616
VL  - 5
AB  - We report here the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169, a
AB  - member of the Mycobacterium avium complex (MAC). M. chimaera
AB  - Fl-0169T was isolated from a patient in Italy and is highly similar to strains of
AB  - M. chimaera isolated in Ireland, although Fl-0169T possesses unique virulence
AB  - genes.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of the Cyanobacterium Anabaena sp. 33047.
JO  - Genome Announcements
PY  - 2016
SP  - e00809
EP  - e00816
VL  - 4
AB  - This study presents the complete nucleotide sequence of Anabaena sp. ATCC 33047 (Anabaena CA),
AB  - a filamentous, nitrogen-fixing marine cyanobacterium, which under
AB  - salt stress conditions accumulates sucrose internally. The elucidation of the
AB  - genome will contribute to the understanding of cyanobacterial diversity.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Mehta, K.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of a Gluconacetobacter hansenii ATCC 23769 Isolate, AY201, Producer of Bacterial Cellulose and Important Model Organism for the Study  of Cellulose Biosynthesis.
JO  - Genome Announcements
PY  - 2016
SP  - e00808
EP  - e00816
VL  - 4
AB  - The cellulose producer and model organism used for the study of cellulose biosynthesis,
AB  - Gluconacetobacter hansenii AY201, is a variant of G. hansenii ATCC
AB  - 23769. We report here the complete nucleotide sequence of G. hansenii AY201,
AB  - information which may be utilized to further the research into understanding the
AB  - genes necessary for cellulose biosynthesis.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Mehta, K.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of Gluconacetobacter hansenii Strain NQ5 (ATCC 53582), an Efficient Producer of Bacterial Cellulose.
JO  - Genome Announcements
PY  - 2016
SP  - e00785
EP  - e00716
VL  - 4
AB  - This study reports the release of the complete nucleotide sequence of Gluconacetobacter
AB  - hansenii strain NQ5 (ATCC 53582). This strain was isolated by
AB  - R. Malcolm Brown, Jr. in a sugar mill in North Queensland, Australia, and is an
AB  - efficient producer of bacterial cellulose. The elucidation of the genome will
AB  - contribute to the study of the molecular mechanisms necessary for cellulose
AB  - biosynthesis.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Santos, R.
AU  - Ebels, M.
AU  - Bordbar, D.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of Komagataeibacter hansenii Strain SC-3B.
JO  - Genome Announcements
PY  - 2017
SP  - e00169
EP  - e00117
VL  - 5
AB  - This study reports the release of the complete nucleotide sequence of Komagataeibacter
AB  - hansenii SC-3B, a new efficient producer of cellulose.
AB  - Elucidation of the genome may provide more information to aid in understanding
AB  - the genes necessary for cellulose biosynthesis.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Santos, R.
AU  - Ebels, M.
AU  - Bordbar, D.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of Komagataeibacter hansenii LMG 23726T.
JO  - Genome Announcements
PY  - 2017
SP  - e00168
EP  - e00117
VL  - 5
AB  - This study reports the release of the complete nucleotide sequence of Komagataeibacter
AB  - hansenii LMG 23726T This organism is a cellulose producer, and
AB  - its genome may provide more information to aid in the understanding of the genes
AB  - necessary for cellulose biosynthesis.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Santos, R.
AU  - Ebels, M.
AU  - Bordbar, D.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of Komagataeibacter hansenii Strain HUM-1.
JO  - Genome Announcements
PY  - 2017
SP  - e00167
EP  - e00117
VL  - 5
AB  - This study reports the release of the complete nucleotide sequence of Komagataeibacter
AB  - hansenii HUM-1, a new efficient producer of cellulose.
AB  - Elucidation of the genome may provide more information to aid in understanding
AB  - the genes necessary for cellulose biosynthesis.
ER  -

TY  - JOUR
AU  - Pfeffer, S.
AU  - Sowa, S.
AU  - Brown, R.M. Jr.
TI  - Complete Genome Sequence of a Novel Strain of Cyanobacterium, Anabaena sp. 4-3.
JO  - Genome Announcements
PY  - 2016
SP  - e00842
EP  - e00816
VL  - 4
AB  - We report the complete nucleotide sequence of Anabaena sp. 4-3, an efficient producer of
AB  - sucrose. It was isolated from salt flats near the University of Texas
AB  - Marine Science Institute in Port Aransas, Texas. The genome may provide insight
AB  - into the utilization of cyanobacteria as a source for biofuels.
ER  -

TY  - JOUR
AU  - Pfeifer, G.P.
AU  - Kohlmaier, L.
AU  - Tomassetti, A.
AU  - Schleicher, R.
AU  - Follmann, H.
AU  - Pfohl-Leszkowicz, A.
AU  - Dirheimer, G.
AU  - Drahovsky, D.
TI  - Polypeptide composition and an immunological analysis of DNA methyltransferases from different species.
JO  - Arch. Biochem. Biophys.
PY  - 1989
SP  - 388
EP  - 392
VL  - 268
AB  - The cross-reactivity of the monoclonal anti-human placental DNA
AB  - methyltransferase antibody M2B10 with DNA methyltransferases isolated from
AB  - other species was investigated.  This antibody immunoprecipitates DNA
AB  - methyltransferases from mammalian cells, i.e., human placenta, mouse P815
AB  - cells, and rat liver cells.  No cross-reactivity is observed with DNA
AB  - methyltransferases from wheat germ and with bacterial DNA methyltransferases
AB  - HpaII and EcoRI.  The mammalian enzymes are characterized by polypeptides of
AB  - molecular mass 150-190 kDa.  Polypeptides smaller than 190 kDa are presumably
AB  - generated by proteolysis of the native 190-kDa DNA methyltransferase.  Trypsin
AB  - digestion of the 190-kDa polypeptide isolated from mouse cells results in
AB  - progressive appearance of DNA methyltransferase polypeptides of 150-190, 110,
AB  - 100, and 52-60 kDa.
ER  -

TY  - JOUR
AU  - Pfeiffer, F.
AU  - Schuster, S.C.
AU  - Broicher, A.
AU  - Falb, M.
AU  - Palm, P.
AU  - Rodewald, K.
AU  - Ruepp, A.
AU  - Soppa, J.
AU  - Tittor, J.
AU  - Oesterhelt, D.
TI  - Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1.
JO  - Genomics
PY  - 2008
SP  - 335
EP  - 346
VL  - 91
AB  - We report the sequence of the Halobacterium salinarum strain R1 chromosome and its four
AB  - megaplasmids. Our set of protein-coding genes is supported by
AB  - extensive proteomic and sequence homology data. The structures of the
AB  - plasmids, which show three large-scale duplications (adding up to 100 kb),
AB  - were unequivocally confirmed by cosmid analysis. The chromosome of strain
AB  - R1 is completely colinear and virtually identical to that of strain NRC-1.
AB  - Correlation of the plasmid sequences revealed 210 kb of sequence that
AB  - occurs only in strain R1. The remaining 350 kb shows virtual sequence
AB  - identity in the two strains. Nevertheless, the number and overall
AB  - structure of the plasmids are largely incompatible. Also, 20% of the
AB  - protein sequences differ despite the near identity at the DNA sequence
AB  - level. Finally, we report genome-wide mobility data for insertion
AB  - sequences from which we conclude that strains R1 and NRC-1 originate from
AB  - the same natural isolate. This exemplifies evolution in the laboratory.
ER  -

TY  - JOUR
AU  - Pfleiderer, A.
AU  - Mishra, A.K.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Caputo, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1221
EP  - 1235
VL  - 9
AB  - Alistipes ihumii strain AP11(T) sp. nov. is the type strain of A. ihumii sp. nov., a new
AB  - species within the genus Alistipes. This strain, whose genome is
AB  - described here, was isolated from the fecal flora of a 21-year-old French
AB  - Caucasian female, suffering from a severe restrictive form of anorexia nervosa
AB  - since the age of 12 years. A. ihumii is a Gram-negative anaerobic bacillus. Here
AB  - we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 2,753,264 bp long genome (one chromosome but no
AB  - plasmid) contains 2,254 protein-coding and 47 RNA genes, including 3 rRNA genes.
ER  -

TY  - JOUR
AU  - Pfreundt, U.
AU  - Stal, L.J.
AU  - Voss, B.
AU  - Hess, W.R.
TI  - Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium.
JO  - ISME J.
PY  - 2012
SP  - 1367
EP  - 1377
VL  - 6
AB  - Marine cyanobacteria of the genus Acaryochloris are the only known organisms that
AB  - use chlorophyll d as a photosynthetic pigment. However, based on chemical
AB  - sediment analyses, chlorophyll d has been recognized to be widespread in oceanic
AB  - and lacustrine environments. Therefore it is highly relevant to understand the
AB  - genetic basis for different physiologies and possible niche adaptation in this
AB  - genus. Here we show that unlike all other known isolates of Acaryochloris, the
AB  - strain HICR111A, isolated from waters around Heron Island, Great Barrier Reef,
AB  - possesses a unique genomic region containing all the genes for the structural and
AB  - enzymatically active proteins of nitrogen fixation and cofactor biosynthesis.
AB  - Their phylogenetic analysis suggests a close relation to nitrogen fixation genes
AB  - from certain other marine cyanobacteria. We show that nitrogen fixation in
AB  - Acaryochloris sp. HICR111A is regulated in a light-dark-dependent fashion. We
AB  - conclude that nitrogen fixation, one of the most complex physiological traits
AB  - known in bacteria, might be transferred among oceanic microbes by horizontal gene
AB  - transfer more often than anticipated so far. Our data show that the two powerful
AB  - processes of oxygenic photosynthesis and nitrogen fixation co-occur in one and
AB  - the same cell also in this branch of marine microbes and characterize
AB  - Acaryochloris as a physiologically versatile inhabitant of an ecological niche,
AB  - which is primarily driven by the absorption of far-red light.
ER  -

TY  - JOUR
AU  - Phale, P.S.
AU  - Paliwal, V.
AU  - Raju, S.C.
AU  - Modak, A.
AU  - Purohit, H.J.
TI  - Genome Sequence of Naphthalene-Degrading Soil Bacterium Pseudomonas putida CSV86.
JO  - Genome Announcements
PY  - 2013
SP  - e00234
EP  - e00212
VL  - 1
AB  - CSV86, a soil isolate, preferentially utilizes naphthalene over glucose as a source of carbon
AB  - and energy. We present the draft genome sequence, which is 6.4
AB  - Mb in size; analysis suggests the chromosomal localization of genes coding for
AB  - naphthalene utilization. The operons coding for glucose and other aromatic
AB  - compounds might also be annotated in another study.
ER  -

TY  - JOUR
AU  - Phalke, S.
AU  - Nickel, O.
AU  - Walluscheck, D.
AU  - Hortig, F.
AU  - Onorati, M.C.
AU  - Reuter, G.
TI  - Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2.
JO  - Nat. Genet.
PY  - 2009
SP  - 696
EP  - 702
VL  - 41
AB  - Here we show that the cytosine-5 methyltransferase DNMT2 controls retrotransposon silencing in
AB  - Drosophila somatic cells. In Drosophila,
AB  - significant DNMT2-dependent DNA methylation occurs during early
AB  - embryogenesis. Suppression of white gene silencing by Mt2 (Dnmt2) null
AB  - mutations in variegated P[w(+)] element insertions identified functional
AB  - targets of DNMT2. The enzyme controls DNA methylation at retrotransposons
AB  - in early embryos and initiates histone H4K20 trimethylation catalyzed by
AB  - the SUV4-20 methyltransferase. In somatic cells, loss of DNMT2 eliminates
AB  - H4K20 trimethylation at retrotransposons and impairs maintenance of
AB  - retrotransposon silencing. In Dnmt2 and Suv4-20 null genotypes,
AB  - retrotransposons are strongly overexpressed in somatic but not germline
AB  - cells, where retrotransposon silencing depends on an RNAi mechanism. DNMT2
AB  - also controls integrity of chromosome 2R and 3R telomeres. In Dnmt2 null
AB  - strains, we found stable loss of the subtelomeric clusters of defective
AB  - Invader4 elements. Together, these results demonstrate a previously
AB  - unappreciated role of DNA methylation in retrotransposon silencing and
AB  - telomere integrity in Drosophila.
ER  -

TY  - JOUR
AU  - Pham, T.T.
AU  - Jacobs-Sera, D.
AU  - Pedulla, M.L.
AU  - Hendrix, R.W.
AU  - Hatfull, G.F.
TI  - Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria.
JO  - Microbiology
PY  - 2007
SP  - 2711
EP  - 2723
VL  - 153
AB  - Mycobacteriophage Tweety is a newly isolated phage of Mycobacterium
AB  - smegmatis. It has a viral morphology with an isometric head and a long
AB  - flexible tail, and forms turbid plaques from which stable lysogens can
AB  - be
AB  - isolated. The Tweety genome is 58 692 bp in length, contains 109
AB  - protein-coding genes, and shows significant but interrupted nucleotide
AB  - sequence similarity with the previously described mycobacteriophages
AB  - Llij,
AB  - PMC and Che8. However, overall the genome possesses mosaic architecture,
AB  - with gene products being related to other mycobacteriophages such as
AB  - Che9d, Omega and Corndog. A gene encoding an integrase of the
AB  - tyrosine-recombinase family is located close to the centre of the
AB  - genome,
AB  - and a putative attP site has been identified within a short intergenic
AB  - region immediately upstream of int. This Tweety attP-int cassette was
AB  - used
AB  - to construct a new set of integration-proficient plasmid vectors that
AB  - efficiently transform both fast- and slow-growing mycobacteria through
AB  - plasmid integration at a chromosomal locus containing a tRNA(Lys) gene.
AB  - These vectors are maintained well in the absence of selection and are
AB  - completely compatible with integration vectors derived from
AB  - mycobacteriophage L5, enabling the simple construction of complex
AB  - recombinants with genes integrated simultaneously at different
AB  - chromosomal
AB  - positions.
ER  -

TY  - JOUR
AU  - Phelan, J.
AU  - de Sessions, P.F.
AU  - Tientcheu, L.
AU  - Perdigao, J.
AU  - Machado, D.
AU  - Hasan, R.
AU  - Hasan, Z.
AU  - Bergval, I.L.
AU  - Anthony, R.
AU  - McNerney, R.
AU  - Antonio, M.
AU  - Portugal, I.
AU  - Viveiros, M.
AU  - Campino, S.
AU  - Hibberd, M.L.
AU  - Clark, T.G.
TI  - Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally.
JO  - Sci. Rep.
PY  - 2018
SP  - 160
EP  - 160
VL  - 8
AB  - DNA methylation is an epigenetic modification of the genome involved in regulating crucial
AB  - cellular processes, including transcription and chromosome
AB  - stability. Advances in PacBio sequencing technologies can be used to robustly
AB  - reveal methylation sites. The methylome of the Mycobacterium tuberculosis complex
AB  - is poorly understood but may be involved in virulence, hypoxic survival and the
AB  - emergence of drug resistance. In the most extensive study to date, we
AB  - characterise the methylome across the 4 major lineages of M. tuberculosis and 2
AB  - lineages of M. africanum, the leading causes of tuberculosis disease in humans.
AB  - We reveal lineage-specific methylated motifs and strain-specific mutations that
AB  - are abundant globally and likely to explain loss of function in the respective
AB  - methyltransferases. Our work provides a set of sixteen new complete reference
AB  - genomes for the Mycobacterium tuberculosis complex, including complete lineage 5
AB  - genomes. Insights into lineage-specific methylomes will further elucidate
AB  - underlying biological mechanisms and other important phenotypes of the
AB  - epi-genome.
ER  -

TY  - JOUR
AU  - Phelippeau, M.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491.
JO  - Genome Announcements
PY  - 2015
SP  - e00817
EP  - e00815
VL  - 3
AB  - We announce the draft genome sequence of Mycobacterium lentiflavum strain CSUR P1491, a
AB  - nontuberculous mycobacterium responsible for opportunistic potentially
AB  - life-threatening infections in immunocompromised patients. The genome described
AB  - here comprises a 6,818,507-bp chromosome exhibiting a 65.75% G+C content, 6,354
AB  - protein-coding genes, and 75 RNA genes.
ER  -

TY  - JOUR
AU  - Phelippeau, M.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium europaeum Strain CSUR P1344.
JO  - Genome Announcements
PY  - 2015
SP  - e00816
EP  - e00815
VL  - 3
AB  - We report the draft genome sequence of Mycobacterium europaeum strain CSUR P1344, a slowly
AB  - growing mycobacterium of the Mycobacterium simiae complex and
AB  - opportunistic respiratory tract colonizer and pathogen. This genome of 6,152,523
AB  - bp exhibits a 68.18% G+C content, encoding 5,814 predicted proteins and 74 RNAs.
ER  -

TY  - JOUR
AU  - Phelippeau, M.
AU  - Robert, C.
AU  - Croce, O.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium neoaurum Strain DSM 44074T.
JO  - Genome Announcements
PY  - 2014
SP  - e00699
EP  - e00614
VL  - 2
AB  - We report the draft genome sequence of Mycobacterium neoaurum strain DSM 44074(T), a
AB  - nontuberculosis species responsible for opportunistic infections in
AB  - immunocompromised patients. The strain described here is composed of 5,536,033
AB  - bp, with a G+C content of 66.24%, and carries 5,274 protein-coding genes and 72
AB  - RNA genes.
ER  -

TY  - JOUR
AU  - Philippe, N.
AU  - Legendre, M.
AU  - Doutre, G.
AU  - Coute, Y.
AU  - Poirot, O.
AU  - Lescot, M.
AU  - Arslan, D.
AU  - Seltzer, V.
AU  - Bertaux, L.
AU  - Bruley, C.
AU  - Garin, J.
AU  - Claverie, J.M.
AU  - Abergel, C.
TI  - Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.
JO  - Science
PY  - 2013
SP  - 281
EP  - 286
VL  - 341
AB  - Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba,
AB  - initiated a reappraisal of the upper limits of the viral world, both in terms of
AB  - particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions
AB  - typical of parasitic bacteria. The diversity of these giant viruses (the
AB  - Megaviridae) was assessed by sampling a variety of aquatic environments and their
AB  - associated sediments worldwide. We report the isolation of two giant viruses, one
AB  - off the coast of central Chile, the other from a freshwater pond near Melbourne
AB  - (Australia), without morphological or genomic resemblance to any previously
AB  - defined virus families. Their micrometer-sized ovoid particles contain DNA
AB  - genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the
AB  - first members of the proposed "Pandoravirus" genus, a term reflecting their lack
AB  - of similarity with previously described microorganisms and the surprises expected
AB  - from their future study.
ER  -

TY  - JOUR
AU  - Philippe, N.
AU  - Maigre, L.
AU  - Santini, S.
AU  - Pinet, E.
AU  - Claverie, J.M.
AU  - Davin-Regli, A.V.
AU  - Pages, J.M.
AU  - Masi, M.
TI  - In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem.
JO  - PLoS ONE
PY  - 2015
SP  - E0138828
EP  - E0138828
VL  - 10
AB  - Infections caused by multidrug resistant (MDR) bacteria are a major concern
AB  - worldwide. Changes in membrane permeability, including decreased influx and/or
AB  - increased efflux of antibiotics, are known as key contributors of bacterial MDR.
AB  - Therefore, it is of critical importance to understand molecular mechanisms that
AB  - link membrane permeability to MDR in order to design new antimicrobial
AB  - strategies. In this work, we describe genotype-phenotype correlations in
AB  - Enterobacter aerogenes, a clinically problematic and antibiotic resistant
AB  - bacterium. To do this, series of clinical isolates have been periodically
AB  - collected from two patients during chemotherapy with imipenem. The isolates
AB  - exhibited different levels of resistance towards multiple classes of antibiotics,
AB  - consistently with the presence or the absence of porins and efflux pumps.
AB  - Transport assays were used to characterize membrane permeability defects.
AB  - Simultaneous genome-wide analysis allowed the identification of putative
AB  - mutations responsible for MDR. The genome of the imipenem-susceptible isolate G7
AB  - was sequenced to closure and used as a reference for comparative genomics. This
AB  - approach uncovered several loci that were specifically mutated in MDR isolates
AB  - and whose products are known to control membrane permeability. These were omp35
AB  - and omp36, encoding the two major porins; rob, encoding a global AraC-type
AB  - transcriptional activator; cpxA, phoQ and pmrB, encoding sensor kinases of the
AB  - CpxRA, PhoPQ and PmrAB two-component regulatory systems, respectively. This
AB  - report provides a comprehensive analysis of membrane alterations relative to
AB  - mutational steps in the evolution of MDR of a recognized nosocomial pathogen.
ER  -

TY  - JOUR
AU  - Phillips, K.E.
AU  - Schipma, M.J.
AU  - Satchell, K.J.
TI  - Draft Genome Sequences of Four Closely Linked Vibrio vulnificus Isolates from the Biotype 1 Environmental Genotype.
JO  - Genome Announcements
PY  - 2015
SP  - e01317
EP  - e01314
VL  - 3
AB  - Biotype 1 of Vibrio vulnificus, which causes severe invasive intestinal and wound infections,
AB  - is split into two genotypes with all previously sequenced clinical
AB  - isolates from the C genotypes. We report here the whole-genome sequencing of two
AB  - clinical isolates and two closely linked oyster isolates from the E genotype for
AB  - comparative studies.
ER  -

TY  - JOUR
AU  - Phillips, K.E.
AU  - Schipma, M.J.
AU  - Satchell, K.J.
TI  - Draft Genome Sequence of Israeli Outbreak-Associated Vibrio vulnificus Biotype 3  Clinical Isolate BAA87.
JO  - Genome Announcements
PY  - 2014
SP  - e00032
EP  - e00014
VL  - 2
AB  - Vibrio vulnificus is a seafood-associated pathogen that causes severe wound and intestinal
AB  - infections. Biotype 3 of V. vulnificus emerged in 1996 as the cause of
AB  - an Israeli outbreak associated with the handling of infected tilapia. Here, we
AB  - describe the whole-genome sequence of the ATCC biotype 3 clinical isolate BAA87
AB  - (CDC9530-96).
ER  -

TY  - JOUR
AU  - Phillips, P.L.
TI  - Cloning and characterization of a methyl-dependent restriction endonuclease and a cell cycle regulating DNA methyltransferase from Zymomonas mobilis subspecies mobilis CP4.
JO  - Ph.D. Thesis, Univ. of Florida, Gainesville
PY  - 2005
SP  - 1
EP  - 220
AB  - A Zymomonas mobilis CP4 genomic library was screened using the E. coli indicator strains
AB  - AP1-200-9 and ER1992 to isolate clones of enzymes that cause DNA damage.  Sequence analysis of
AB  - positive clones identified two open reaading frames encoding DNA modification enzymes: (a) a
AB  - 924 base pair open reading frame with sequence similarity to mrr, a methyl-dependant
AB  - restriction endonuclease, which was designated ZmCP4mrr, and (2) a 1149 bp open reading frame
AB  - with amino acid sequence similarity to ccrM, a cell cycle regulating DNA methyltransferase,
AB  - which was designated ZmCP4ccM.  Sequence analysis indicates that ZmCP4mrr is a solitary
AB  - methyl-dependent restriction endonuclease without a cognate DNA methyltransferase.
AB  - Transformation of Eschichia coli K12 strains with various DNA methyltransferase backgrounds
AB  - demonstrated that a plasmid borne ZmCP4mrr gene readily transforms E. coli strains that
AB  - experess dcm, hsdM, and EcoKccrM DNA methyltransferases, indicating that ZmCP4Mrr does not
AB  - recognize and restrict sites methylated by these DNA methyltransferases.  E. coli strains that
AB  - express the dam DNA methyltransferase could only be transformed if expression of plasmid borne
AB  - ZmCP4mrr was repressed.  Subsequent induction of ZmCP4mrr expression in these cells resulted
AB  - in inhibition of growth and cell death, indicating that ZmCP4Mrr specifically restricts Dam
AB  - N6-adenine methylated DNA (5'-GmATC-3').  Plasmid DNA originating from dam deficient E. coli
AB  - strains did not improve transformation efficiency, indicating that Z. mobilis CP4 has a
AB  - restriction system in addition to ZmCP4Mrr contributing to low frequency of gene transfer from
AB  - foreign DNA.  Sequence analysis indicates that AmCP4ccrM is a solitary DNA methyltransferase
AB  - with two possible in-frame translation initiation sites.  A ribosomal binding site containing
AB  - a sequence, 5'-AGGA-3', conserved in Z. mobilis promoters of highly expressed genes is
AB  - located adjacent to the first possible translation initiation site and not the second,
AB  - suggesting that ZmCP4ccrM is being expressed from the first translational initiation site. The
AB  - specificity for ZmCP4CcrM methylation was directly determined to be the N6-adenine of its
AB  - recognition site 5'-GANTC-3'.  Z. mobilis CP4 cells overexpressing ZmCP4ccrM exhibited a
AB  - subpopulation of filamentous cells, ranging from 10-90 uM in length, with multiple
AB  - chromosomes.  Overexpression of ZmCP4ccrM caused disruption of normal cell division and
AB  - chromosomal segregation, suggesting that ZmCP4CcrM is involved in cell cycle regulation.
ER  -

TY  - JOUR
AU  - Phillips, S.E.V.
TI  - Induced flip.
JO  - Nat. Struct. Biol.
PY  - 1994
SP  - 76
EP  - 77
VL  - 1
AB  - Hhal methyltransferase, caught in the act of methylating a cytosine on a DNA substrate,
AB  - reveals how the enzyme overcomes the problem of chemically modifying bases in the relatively
AB  - inaccessible environment of the DNA duplex.
ER  -

TY  - JOUR
AU  - Photolo, M.M.
AU  - Mavumengwana, V.
AU  - Serepa-Dlamini, M.H.
AU  - Tlou, M.G.
TI  - Draft Genome Sequence of Methylobacterium radiotolerans Strain MAMP 4754, a Bacterial Endophyte Isolated from Combretum erythrophyllum in South Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e00976
EP  - e00917
VL  - 5
AB  - We announce here the draft genome sequence of Methylobacterium radiotolerans strain MAMP 4754,
AB  - isolated from the roots of the medicinal plant Combretum
AB  - erythrophyllumM. radiotolerans has a genome size of 7,389,282 bp with 7,166 genes
AB  - and a G+C content of 70.5%.
ER  -

TY  - JOUR
AU  - Phung, L.T.
AU  - Silver, S.
AU  - Trimble, W.L.
AU  - Gilbert, J.A.
TI  - Draft Genome of Halomonas Species Strain GFAJ-1 (ATCC BAA-2256).
JO  - J. Bacteriol.
PY  - 2012
SP  - 1835
EP  - 1836
VL  - 194
AB  - Halomonas strain GFAJ-1 was reported in Science magazine to be a remarkable microbe for which
AB  - there was 'arsenate in macromolecules that normally contain phosphate, most notably nucleic
AB  - acids.' The draft genome of the bacterium was determined (NCBI accession numbers AHBC01000001
AB  - through AHBC01000103). It appears to be a typical gamma proteobacterium.
ER  -

TY  - JOUR
AU  - Phung, L.T.
AU  - Trimble, W.L.
AU  - Meyer, F.
AU  - Gilbert, J.A.
AU  - Silver, S.
TI  - Draft Genome Sequence of Alcaligenes faecalis subsp. faecalis NCIB 8687 (CCUG 2071).
JO  - J. Bacteriol.
PY  - 2012
SP  - 5153
EP  - 5153
VL  - 194
AB  - Alcaligenes faecalis subsp. faecalis NCIB 8687, the betaproteobacterium from which arsenite
AB  - oxidase had its structure solved and the first 'arsenate gene
AB  - island' identified, provided a draft genome of 3.9 Mb in 186 contigs (with the
AB  - largest 15 comprising 90% of the total) for this opportunistic pathogen species.
ER  -

TY  - JOUR
AU  - Picardeau, M. et al.
TI  - Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis.
JO  - PLoS ONE
PY  - 2008
SP  - e1607
EP  - e1607
VL  - 3
AB  - Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We
AB  - determined the genome sequence of L. biflexa,
AB  - making it the first saprophytic Leptospira to be sequenced. The L. biflexa
AB  - genome has 3,590 protein-coding genes distributed across three circular
AB  - replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also
AB  - carries essential genes, and a third 74-kb replicon. Comparative sequence
AB  - analysis provides evidence that L. biflexa is an excellent model for the
AB  - study of Leptospira evolution; we conclude that 2052 genes (61%) represent
AB  - a progenitor genome that existed before divergence of pathogenic and
AB  - saprophytic Leptospira species. Comparisons of the L. biflexa genome with
AB  - two pathogenic Leptospira species reveal several major findings. Nearly
AB  - one-third of the L. biflexa genes are absent in pathogenic Leptospira. We
AB  - suggest that once incorporated into the L. biflexa genome, laterally
AB  - transferred DNA undergoes minimal rearrangement due to physical
AB  - restrictions imposed by high gene density and limited presence of
AB  - transposable elements. In contrast, the genomes of pathogenic Leptospira
AB  - species undergo frequent rearrangements, often involving recombination
AB  - between insertion sequences. Identification of genes common to the two
AB  - pathogenic species, L. borgpetersenii and L. interrogans, but absent in L.
AB  - biflexa, is consistent with a role for these genes in pathogenesis.
AB  - Differences in environmental sensing capacities of L. biflexa, L.
AB  - borgpetersenii, and L. interrogans suggest a model which postulates that
AB  - loss of signal transduction functions in L. borgpetersenii has impaired
AB  - its survival outside a mammalian host, whereas L. interrogans has retained
AB  - environmental sensory functions that facilitate disease transmission
AB  - through water.
ER  -

TY  - JOUR
AU  - Picchi, S.C.
AU  - Vilas-Boas, L.A.
AU  - Ceresini, P.C.
AU  - de Macedo-Lemos, E.G.
AU  - Lemos, M.V.
TI  - Strain variability in the DNA immigration control region (ICR) of Xylella fastidiosa.
JO  - Res. Microbiol.
PY  - 2006
SP  - 254
EP  - 262
VL  - 157
AB  - The genome of the bacterium Xylella fastidiosa contains four ORFs (XF2721, XF2725, XF2739 and
AB  - XF0295) related to the restriction
AB  - modification type I system, ordinarily named R-M. This system belongs
AB  - to the DNA immigration control region (ICR). Each CIRF is related to
AB  - different operon structures, which are homologues among themselves and
AB  - with subunit Hsd R from the endonuclease coding genes. In addition,
AB  - these ORFs are highly homologous to genes in Pseudomonas aeruginosa,
AB  - Methylococcus capsulatus str. Bath, Legionella pneumophila,
AB  - Helicobacter pylori, Xanthomonas oryzae pv. Oryzae and Silicibacter
AB  - pomeroyi, as well as to genes from X. fastidiosa strains that infect
AB  - grapevine, almond and oleander plants. This study was carried out on
AB  - R-M ORFs from forty-three X. fastidiosa strains isolated from citrus,
AB  - coffee, grapevine, periwinkle, almond and plum trees, in order to
AB  - assess the genetic diversity of these loci through PCR-RFLP. PCR-RFLP
AB  - analysis of the four ORFs related to the R-M system from these strains
AB  - enabled the detection of haplotypes for these loci. When the haplotypes
AB  - were defined, wide genetic diversity and a large range of similar
AB  - strains originating from different hosts were observed. This analysis
AB  - also provided information indicating differences in population genetic
AB  - structures, which led to detection of different levels of gene transfer
AB  - among the groups of strains.
ER  -

TY  - JOUR
AU  - Piccinni, F.
AU  - Murua, Y.
AU  - Ghio, S.
AU  - Talia, P.
AU  - Rivarola, M.
AU  - Campos, E.
TI  - Draft Genome Sequence of Cellulolytic and Xylanolytic Cellulomonas sp. Strain B6  Isolated from Subtropical Forest Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00891
EP  - e00816
VL  - 4
AB  - Cellulomonas sp. strain B6 was isolated from a subtropical forest soil sample and presented
AB  - (hemi)cellulose-degrading activity. We report here its draft genome
AB  - sequence, with an estimated genome size of 4 Mb, a G+C content of 75.1%, and
AB  - 3,443 predicted protein-coding sequences, 92 of which are glycosyl hydrolases
AB  - involved in polysaccharide degradation.
ER  -

TY  - JOUR
AU  - Piechaczyk, M.
AU  - Jeanteur, P.
AU  - Louarn, J.-M.
TI  - An easy method for the selection of restriction- and modification-deficient mutants of Escherichia coli K-12.
JO  - Gene
PY  - 1980
SP  - 173
EP  - 175
VL  - 11
AB  - An easy and rapid method for selecting restriction- and modification-
AB  - defective mutants of
AB  - Escherichia coli K-12 is described. This method employs selection of tetracycline-resistant
AB  - lysogens after
AB  - infection with lambda::Tn10 phage and results in a high yield of spontaneous rk-mk- and
AB  - rk-mk- mutants.
ER  -

TY  - JOUR
AU  - Piechula, S.
AU  - Kim, S.C.
AU  - Podhajska, A.J.
TI  - PamI and PamII restriction endonucleases from Phormidium ambiguum.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 619
EP  - 619
VL  - 20
AB  - PamI and PamII are type II restriction endonucleases from the Cyanobacterial
AB  - strain Phormidium ambiguum GOM (CCALA Hindak 1965/117).  PamI and PamII are
AB  - isoschizomers of MstI and AcyI respectively.  The enzymes were purified using
AB  - two chromatographic steps: 1) phosphocellulose, 2) DEAE-sephadex G-25.  The
AB  - enzymes were free of contaminating nuclease activity.  All digestions were
AB  - performed at 37C in a buffer containing 50 mM NaCl, 10 mM Tris-HCl (pH 7.5), 10
AB  - mM MgCl2.
ER  -

TY  - JOUR
AU  - Piechula, S.
AU  - Kur, J.
AU  - Bielawski, K.
AU  - Podhajska, A.J.
TI  - Isolation and identification of the restriction endonuclease PtaI from Phormidium tadzschicicum, an isoschizomer of BspMII.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6738
EP  - 6738
VL  - 20
AB  - PtaI is a type II restriction endonuclease from the cyanobacterial strain Phormidium
AB  - tadzschicicum. PtaI recognizes the sequence TCCGGA and cleaves between T and C. It is an
AB  - isoschizomer of BspMII.
ER  -

TY  - JOUR
AU  - Piechula, S.
AU  - Kur, J.
AU  - Woszczyk, J.
AU  - Podhajska, A.J.
TI  - Purification and characterization of two restriction endonucleases isolated from Phormidium inundatum.
JO  - Gene
PY  - 1995
SP  - 315
EP  - 316
VL  - 157
AB  - We have isolated two restriction endonucleases, PinBI and PinBII, from the cyanobacterial
AB  - strain Phormidium inundatum, and identified them as isoschizomers of AvaIII and BspMII,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Piechula, S.
AU  - Piosik, J.
AU  - Bielawski, K.
AU  - Podhajska, A.J.
TI  - Isolation and characterization of the restriction endonuclease PpeI from Phormidium persicinum.
JO  - Mol. Biotechnol.
PY  - 1996
SP  - 97
EP  - 99
VL  - 5
AB  - PpeI is a type II restriction endonuclease isolated from cyanobacterial strain
AB  - Phormidium persicinum.  The endonuclease PpeI, an isoschizomer of ApaI, recognizes the
AB  - hexanucleotide sequence (5'-GGGCC/C-3') and cleaves, after the second C, producing
AB  - four nucleotide 3'-cohesive ends.
ER  -

TY  - JOUR
AU  - Piechula, S.
AU  - Skowron, P.M.
AU  - Piatyszek, M.
AU  - Podhajska, A.J.
TI  - Isolation and identification of two new Synechococcus-derived restriction endonucleases, SleI and SspAI isoschizomers of EcoRII.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2782
EP  - 2782
VL  - 19
AB  - Two new type-II restriction endonucleases, SleI and SspAI, have been isolated
AB  - from Synechococcus leopoliensis.  Strain 1402-1 was obtained from the Institut
AB  - Pasteur Culture Collection of Cyanobacterial Strains.  Synechococcus sp. AN6301
AB  - was obtained from Pflanzenphysiologisches Institut, Universitat Gottingen,
AB  - Nikolausberg, FRG.  Both strains were grown aerobically at 30C in BG medium
AB  - under fluorescent light.  The cells were harvested and stored in liquid
AB  - nitrogen.  Frozen cells were disrupted by sonication.  Purification of the
AB  - enzymes was carried out by the following steps: (I) DEAE-cellulose
AB  - chromatography (II) DNA-cellulose chromatography, (III) QAE-Sephadex
AB  - chromatography.  The digestion pattern of pBR322 DNA with BstNI was identical
AB  - to the patterns obtained with SleI and SspAI, indicating that SleI and SspAI
AB  - are isoschizomers of BstNI, and therefore, of its isoschizomer EcoRII.  It was
AB  - found that SleI and SspAI enzymes generate 5 nucleotide (nt) cohesive ends, as
AB  - assessed by digestion of lambda DNA and fill-in reaction with T7 DNA
AB  - polymerase, [alpha-35S]dATP and the other dNTPs.  EcoRII and BstNI recognize
AB  - the same sequence, but cut between different nt generating 5-nt and 1-nt
AB  - cohesive ends, respectively.  Generally following the approach described by
AB  - Brown et al., we have directly determined the sequence of the cleavage site of
AB  - SleI and SspAI in M13mp18 double stranded DNA.  The first restriction site
AB  - recognized by EcoRII is located 167 nt from the first nt of the 17-mer
AB  - sequencing primer, and thus can easily be sequenced.  We found that the SleI
AB  - and SspAI cut sites (represented by arrows) are shifted by two nt (Fig. 2)
AB  - within the recognition site with respect to the BstNI cuts (represented by
AB  - dots), and thus are identical to the EcoRII cuts.
ER  -

TY  - JOUR
AU  - Piechula, S.
AU  - Waleron, K.
AU  - Swiatek, W.
AU  - Biedrzycka, I.
AU  - Podhajska, A.J.
TI  - Mesophilic cyanobacteria producing thermophilic restriction endonucleases.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 135
EP  - 140
VL  - 198
AB  - When searching for the site-specific endonucleases in several strains of Phormidium we made
AB  - the following observations. Among the 16 strains
AB  - that originated from 15 species of Phormidium. 12 produced one or more
AB  - restriction enzymes, of which two produced the highly thermophilic
AB  - restriction endonucleases PtaI and PpaAII with their optimum activity
AB  - at 65-80 C, which is far above the lethal temperature for the
AB  - host microorganism (40 C). These two temperature-resistant
AB  - enzymes are isoschizomers of known BspMII and TaqI endonucleases,
AB  - respectively. The presence of the thermophilic TaqI isoschizomer does
AB  - not seem to play any role in the mesophilic host microorganism, which
AB  - does not even contain an active cognate methyltransferase. Among the
AB  - remaining 10 strains, six produced isoschizomers of endonucleases which
AB  - we first described in cyanobacteria, namely: PfuAII (NdeI), PinBII and
AB  - PtaI(BspMII). PlaAII (RsaI), PpaAII PpeI (ApaI). Two enzymes, PauAII
AB  - (AhaIII) and PfaAII (NdeI), belong to a group of a very rarely
AB  - occurring isoschizomers. Out of 21 cyanobacterial endonucleases
AB  - investigated by us, Four were active in a wide range of temperatures
AB  - (from 15 to 60 C) which also extended the optimal growth
AB  - temperature of the hosts. We assume that our observation on the
AB  - presence of temperature-resistant restriction enzymes in mesophilic
AB  - hosts supports the idea of horizontal gene transfer. Restriction
AB  - modification systems may be an excellent tool for investigation of that
AB  - phenomenon.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
TI  - HineI is an isoschizomer of HinfIII restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1982
SP  - 373
EP  - 381
VL  - 157
AB  - HineI is a restriction enzyme isolated from Haemophilus influenzae strain Re.
AB  - Like other type III restriction endonucleases it requires ATP for cleavage and
AB  - S-adenosyl-methionine for methylation of DNA.  This enzyme recognises the same
AB  - sequence as HinfIII (Piekarowicz et al., 1981) and cleaves and methylates DNA
AB  - in a manner similar to all type III restriction enzymes.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
TI  - The influence of methionine deprivation on restriction properties of Haemophilus influenzae Rd and Ra strains.
JO  - Acta Microbiol. Pol. A
PY  - 1974
SP  - 71
EP  - 74
VL  - 6
AB  - The influence of methionine starvation on the restriction properties of H.
AB  - influenzae Rd and Ra has been examined.  It was shown that the methionine
AB  - deprivation of Rd and Ra cells does not change their capacity to restrict HPlcl
AB  - phage.  These results suggest that S-adenosylmethionine may not be required for
AB  - the action of H. influenzae Rd and Ra restriction endonucleases.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
TI  - Preferential cleavage by restriction endonuclease HinfIII.
JO  - Acta Biochim. Pol.
PY  - 1984
SP  - 453
EP  - 464
VL  - 31
AB  - The efficiency of endonucleolytic scission by restriction endonuclease HinfIII
AB  - varies markedly for different recognition sites.  The relative frequencies of
AB  - cleavage at these sites have been determined on the basis of analysis of
AB  - specific unit length linear molecules formed.  The efficiency of restriction
AB  - reaction depends also on the number of recognition sites in the DNA substrate.
AB  - Cleavage by HinfIII in the absence or presence of S-adenosylmethionine is
AB  - observed only when at least three recognition sites are present.  HinfIII also
AB  - shows preferential methylation of certain sites observable even for a substrate
AB  - with one recognition site.  The nucleotide sequences at sites cleaved or
AB  - methylated at high frequency have been compared.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
TI  - Identification of a new restriction endonuclease R.NciII, from Neisseria cinerea.
JO  - Acta Microbiol. Pol.
PY  - 1994
SP  - 103
EP  - 105
VL  - 43
AB  - Site-specific restriction endonuclease R.NciII has been purified from Neisseria cinerea strain
AB  - 32615. The enzyme recognizes the sequence 5'GATC3' and its activity is inhibited by the
AB  - presence of methylated adenine residue within the recognition sequence.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
TI  - DNA methyltransferases of Neisseria gonorrhoeae.
JO  - Acta Microbiol. Pol.
PY  - 1994
SP  - 269
EP  - 277
VL  - 43
AB  - The DNA of both prokaryotic and eukaryotic organisms can undergo postreplicative modification.
AB  - The most widely known type of modification is the addition of the methyl groups to either
AB  - cytosine or adenine residues.  This process is carried out by the enzymes called DNA
AB  - methyltransferases or MTases.  Methylation by all types of MTases requires
AB  - S-adenosylmethionine (SAM).  The function of SAM is in most of the cases limited to serving as
AB  - a methyl group donor.  In the case of Escherichia coli Dam MTase, however, it also affects
AB  - binding of the enzyme to the target site.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Baj, J.
TI  - Host specificity of DNA in Haemophilus influenzae:  The physiological and genetical bases of instability of restriction and modification of DNA in strain RD.
JO  - Acta Microbiol. Pol. A
PY  - 1975
SP  - 119
EP  - 130
VL  - 8
AB  - Further investigations of the instability of restriction and modification
AB  - properties of H. influenzae Rd strain were carried out.  It has been shown that
AB  - the instable properties of hsd HindI system are maintained even after transfer
AB  - of this system to another H. influenzae strain.  The expression of hsd HindI
AB  - system is very sensitive to various physiological changes which do not
AB  - influence the other hsd systems present in the same Rd strain.  The instability
AB  - of hsd HindI system is postulated to be connected with some regulator gene(s).
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Bickle, T.A.
AU  - Shepherd, J.C.W.
AU  - Ineichen, K.
TI  - The DNA sequence recognised by the HinfIII restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1981
SP  - 167
EP  - 172
VL  - 146
AB  - HinfIII is a type III restriction enzyme (Kaue & Piekarowicz, 1978) isolated
AB  - from Haemophilus influenzae Rf.  Like other type III restriction endonucleases,
AB  - the enzyme also catalyses the modification of susceptible DNA.  It requires ATP
AB  - for DNA cleavage and S-adenosyl methionine for DNA methylation.  We have
AB  - determined the DNA sequence recognised by HinfIII to be: 5'-C-G-A-A-T-3'
AB  - 3'-G-C-T-T-A-5' In restriction, the enzyme cleaves the DNA about 25 base-pairs
AB  - to the right of this sequence.  In the modification reaction only one of the
AB  - strands is methylated, that containing the 5'-C-G-A-A-T-3' sequence.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Brzezinski, R.
TI  - Cleavage and methylation of DNA by the restriction endonuclease HinfIII isolated from Haemophilus influenzae Rf.
JO  - J. Mol. Biol.
PY  - 1980
SP  - 415
EP  - 429
VL  - 144
AB  - HinfIII is a restriction enzyme isolated from Haemophilus influenzae strain Rf. It requires
AB  - ATP for cleavage and S-adenosyl-methionine for methylation of DNA. This enzyme can be present
AB  - in two forms: one with AdoMet bound to it, and a second form free of this cofactor.  In the
AB  - presence of AdoMet and ATP the enzyme cleaves ColE1 DNA molecules once, to produce unit-length
AB  - linear molecules.  The HinfIII endonuclease cleaves at unique sites, though not every site on
AB  - every molecule is cut.  The five HinfIII cleavage sites were mapped relative to the EcoRI
AB  - restriction endonuclease cleavage site.  If AdoMet is omitted from the enzyme reaction
AB  - mixture, the second form of HinfIII enzyme cleaves ColE1 DNA into several fragments.  An
AB  - average of 6.2 +/- 1 methyl groups are transferred to ColE1 DNA from AdoMet.  The methyl
AB  - groups were mapped relative to the HaeIII restriction endonuclease fragments.  The position of
AB  - methylation sites correlates well with the cleavage sites. The restriction activity of the
AB  - HinfIII enzyme shows some dependence upon the structure of the substrate DNA.  The linear
AB  - molecule of ColE1 DNA is a poorer substrate than the supercoiled molecules.  Lambda DNA
AB  - fragments with molecular weights smaller than approximately 2,000,000 are not cleaved by
AB  - HinfIII enzyme, but since they can be methylated the enzyme is able to recognize the specific
AB  - sequences on these fragments.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Brzezinski, R.
AU  - Kauc, L.
TI  - Host specificity of DNA in Haemophilus influenzae: DNA restriction enzyme from H. Influenzae Rf232.
JO  - Acta Microbiol. Pol.
PY  - 1976
SP  - 307
EP  - 312
VL  - 25
AB  - A restriction endonuclease has been partially purified from Haemophilus
AB  - influenzae Rf232 containing the genetically determined system of restriction
AB  - and modification of DNA.  The enzyme requires ATP for the degradation of
AB  - transfecting phage DNA.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Brzezinski, R.
AU  - Kauc, L.
TI  - Host Specificity of DNA in Haemophilus influenzae:  The in vivo Action of the Restriction Endonucleases on Phage and Bacterial DNA.
JO  - Acta Microbiol. Pol. A
PY  - 1975
SP  - 51
EP  - 65
VL  - 7
AB  - In Haemophilus influenzae strains only the type 1 of the restriction
AB  - endonucleases have an in vivo effect on phage and bacterial transforming DNA.
AB  - The type 2 of restriction endonucleases which act very efficiently in vitro are
AB  - completely inactive in vivo.  The reasons for this inactivity is unknown.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Bujnicki, J.
TI  - Cloning of the Dam methyltransferase gene from Haemophilus influenzae bacteriophage HP1.
JO  - Acta Microbiol. Pol.
PY  - 1999
SP  - 123
EP  - 129
VL  - 48
AB  - The putative product of orf13 from the genome of Haemophilus influenzae HP1 bacteriophage
AB  - shows homology only to bacteriophage T1 Dam methyltransferase, and a weak similarity to the
AB  - conserved amino acids sequence motifs characteristic of m6A-methyltransferases.  Especially
AB  - interesting is the lack of characteristic motif I responsible for binding of
AB  - S-adenosylmethionine.  Despite this fact, a DNA sequence of HP1 bacteriophage of Haemophilus
AB  - influenzae encoding methyltransferase activity was cloned and expressed in Escherichia coli
AB  - using pMPMT4omega expression vector.  The cloned methyltransferase recognizes the sequence
AB  - 5'-GATC-3' and methylates an adenine residue.  The enzyme methylates both double- and
AB  - single-stranded DNA substrates.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Glover, S.W.
TI  - Host specificity of DNA in Haemophilus influenzae:  the two restriction and modification systems in strain Ra.
JO  - Mol. Gen. Genet.
PY  - 1972
SP  - 11
EP  - 25
VL  - 116
AB  - Rough R strains of Haemophilus influenzae derived from the smooth (S) serotypes
AB  - Sa, Sb, Sd, Se and Sf each carry DNA restriction and modification systems.  The
AB  - DNA host specificity determined by Re and Rf may be the same but is different
AB  - from that for Ra, Rb and Rd all of which can be distinguished from one another.
AB  - Strain Ra carries two genetically distinct host specificity systems Al and A2
AB  - each of which is able to restrict Haemophilus phage HP1, and each of which
AB  - confers a specific modification on phage grown in strain Ra.  Among
AB  - restriction-deficient mutants isolated from strain Ra, seven of the eight
AB  - possible phenotypes for these two systems were obtained after either one or two
AB  - mutational steps.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Goguen, J.D.
TI  - The DNA sequence recognized by the EcoDXXI restriction endonuclease.
JO  - Eur. J. Biochem.
PY  - 1986
SP  - 295
EP  - 298
VL  - 154
AB  - EcoDXXI is a type-I restriction enzyme coded for by the plasmid pDXX1.  Like
AB  - other type-I restriction endonucleases, the enzyme catalyses the modification
AB  - of susceptible DNA.  We have determined the DNA sequence recognised by EcoDXXI
AB  - to be:5'-TCANNNNNNNATTC-3' 3'-AGTNNNNNNNTAAG-5'where N can be any nucleotide.
AB  - This sequence has an overall structure very similar to previously determined
AB  - type-I sequences.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Goguen, J.D.
AU  - Skrzypek, E.
TI  - The EcoDXXI restriction and modification system of Escherichia coli ET7.  Purification, subunit structure and properties of the restriction endonuclease.
JO  - Eur. J. Biochem.
PY  - 1985
SP  - 387
EP  - 393
VL  - 152
AB  - The Escherichia coli plasmid pDXX1 codes for a new restriction-modification system. The
AB  - specific restriction endonuclease coded by this system has been purified by a procedure that
AB  - includes phosphocellulose and heparin-agarose chromatography. Sedimentation on glycerol
AB  - gradients showed one peak of activity with a value of about 12S. The highly purified enzyme
AB  - require ATP and Mg2+ for activity as well as S-adenosylmethionine, although some
AB  - S-adenosylmethionine molecules are probably bound to the enzyme. The enzyme does not cleave
AB  - lambda DNA at well-defined sites and has a strong non-modified DNA-dependent ATPase activity.
AB  - The enzyme has also methylase activity acting against non-modified DNA. te is repeated in
AB  - inverse orientation. The additional base pair in the non-specific spacer of the mutant
AB  - recognition sequence maintains the proper spacing between the two methylatable adenine groups.
AB  - Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion
AB  - occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire
AB  - carboxyl-terminal DNA binding domain which recognizes the 3' half of the EcoDXXI binding
AB  - site. The truncated hsdS gene still encodes both the amino-terminal DNA binding domain and the
AB  - conserved repeated sequence that defines the length of the recognition site spacer region. We
AB  - propose that the EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize
AB  - its binding site. The implications of this finding in terms of subunit interactions and the
AB  - malleability of the type I R-M systems will be discussed.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Golaszewska, M.
AU  - Sunday, A.O.
AU  - Siwinska, M.
AU  - Stein, D.C.
TI  - The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1055
EP  - 1065
VL  - 293
AB  - The HaeIV restriction endonuclease (ENase) belongs to a distinct class of ENases,
AB  - characterized by its ability to cleave double-stranded DNA on both sides of its recognition
AB  - sequence, excising a short DNA fragment that includes the recognition sequence. The gene
AB  - encoding the HaeIV ENase was cloned from Haemophilus aegyptius into pUC19 using a previously
AB  - described system that does not need the knowledge that a particular ENase is produced by a
AB  - bacterial strain. DNA sequence analysis of the insert contained on this plasmid identified a
AB  - single open reading frame (ORF), with the predicted protein having an apparent molecular mass
AB  - of approximately 110 kDa. The protein encoded by this ORF was purified to homogeneity from
AB  - Escherichia coli strain ER1944 carrying the haeIVRM gene on a recombinant plasmid under the
AB  - control of the inducible ara promoter. The protein possessed both ENase and methyltransferase
AB  - (MTase) activities. Amino acid sequence analysis was able to identify several conserved motifs
AB  - found in DNA MTases, located in the middle of the protein. The enzyme recognizes the
AB  - interrupted palindromic sequence 5' GAPyNNNNNPuTC 3', cleaving double-stranded DNA on both
AB  - strands upstream and downstream of the recognition sequence, releasing an approximately 33 bp
AB  - fragment. The ENase possessed an absolute requirement only for Mg(+2). ATP had no influence on
AB  - ENase or MTase activities. The ENase made the first strand cleavage randomly on either side of
AB  - the recognition sequence, but the second cleavage occurred more slowly. The MTase activity
AB  - modified symmetrically located adenine residues on both strands within the recognition
AB  - sequence yielding N6-methyl adenine. Furthermore, the MTase was active as a dimer.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Kalinowska, J.
TI  - Host specificity of DNA in Haemophilus influenzae: Similarity between host-specificity types of Haemophilus influenzae Re and Rf.
JO  - J. Gen. Microbiol.
PY  - 1974
SP  - 405
EP  - 411
VL  - 81
AB  - Strain Re of Haemophilus influenzae carries two genetically distinct
AB  - host-specificity systems EI and E2 each of which is able to restrict
AB  - Haemophilus phage HPIcI and each of which confers a specific modification upon
AB  - phage grown in strain Re.  These two systems are apparently identical to the
AB  - host-specificity systems of H. influenzae Rf F1 and F2.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Kauc, L.
AU  - Glover, S.W.
TI  - Host specificity of DNA in Haemophilus influenzae: The restriction and modification systems in strains Rb and Rf.
JO  - J. Gen. Microbiol.
PY  - 1974
SP  - 391
EP  - 403
VL  - 81
AB  - Haemophilus influenzae Rf possesses two distinct host specificity systems FI
AB  - and F2 each of which is able to restrict and modify Haemophilus phage HPICI,
AB  - while strain Rb posseses only one system, B.  Among restriction-deficient
AB  - mutants isolated from strain Rf, the r-m+ as well as r-m- phenotypes for these
AB  - two systems were obtained after either one or two mutational steps.  The FI
AB  - system was introduced into H. influenzae Rd by genetic transformation to show
AB  - that the DI and FI systems are not allelic.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Klyz, A.
AU  - Kwiatek, A.
AU  - Stein, D.C.
TI  - Analysis of type I restriction modification systems in the Neisseriaceae: Genetic organization and properties of the gene products.
JO  - Mol. Microbiol.
PY  - 2001
SP  - 1199
EP  - 1210
VL  - 41
AB  - The hsd locus (host specificity of DNA) was identified in the Neisseria gonorrhoeae genome.
AB  - The DNA fragment encoding this locus produced an active restriction and modification (R/M)
AB  - system when cloned into Escherichia coli. This R/M system was designated NgoAV. The cloned
AB  - genomic fragment (7800 bp) has the potential to encode seven open reading frames (ORFs).
AB  - Several of these ORFs had significant homology with other proteins found in the databases:
AB  - ORF1, the hsdM, a methylase subunit (HsdM); ORF2, a homologue of dinD; ORF3, a homologue of
AB  - hsdS; ORF4, a homologue of hsdS; and ORF5, an endonuclease subunit hsdR. The endonuclease and
AB  - methylase subunits possessed strongest protein sequence homology to the EcoR124II R/M system,
AB  - indicating that NgoAV belongs to the type IC R/M family. Deletion analysis showed that only
AB  - ORF3 imparted the sequence specificity of the RM.NgoAV system, which recognizes an interrupted
AB  - palindrome sequence (GCAN8TGC). The genetic structure of ORF3 (208 amino acids) is almost
AB  - identical to the structure of the 5' truncated hsdS genes of EcoDXXI or EcoR124II R/M systems
AB  - obtained by in vitro manipulation. Genomic sequence analysis allowed us to identify hsd loci
AB  - with a very high homology to RM.NgoAV in two strains of Neisseria meningitidis. However,
AB  - significant differences in the organization and structure of the hsdS genes in both these
AB  - systems suggests that, if functional, they would possess recognition sites that differ from
AB  - the gonococcus and from themselves.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Radlinska, M.
TI  - Sensitivity of the restriction endonucleases HaeIII, BsrI, EaeI and CfrI to cytosine N4-methylation.
JO  - Acta Microbiol. Pol.
PY  - 1998
SP  - 405
EP  - 407
VL  - 47
AB  - HaeIII, BsrI and NgoII are isochizomers that recognize the sequence GGCC while EaeI and CfrI
AB  - recognize the overlapping sequence YGGCCR. It has previously been shown that all these enzymes
AB  - are inhibited by cytosine C5-methylation within the recognition sequence. The methylation
AB  - sensitivities of these enzymes to cytosine N4-methylation have not been previously reported.
AB  - In this paper we present data demonstrating that all these enzymes, except NgoII, are
AB  - inhibited by cytosine N4-methylation of the second 5' cytosine residue within the recognition
AB  - sequence.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Radlinska, M.
AU  - Wiernicka-Gnas, M.
TI  - DNA methyltransferases of Neisseria gonorrhoeae.
JO  - Bull. Acad. Pol. Sci. [Biol]
PY  - 1996
SP  - 205
EP  - 210
VL  - 44
AB  - An individual strain of Neisseria gonorrhoeae may produce up to 16 different DNA
AB  - methyltransferases.  We have used a novel cloning system that is able to detect MTase clones
AB  - in the absence of direct selection to identify different MTase clones.  The characterization
AB  - of six of these clones showed that MTase genes are linked to restriction endonuclease systems
AB  - but none of these six R-M systems are genetically linked on the chromosome.  The initial
AB  - characterization of four other clones indicates that none of the encoded MTase genes are
AB  - linked to the restriction endonuclease systems.  On the other hand, several of these MTases
AB  - show genetical linkage on the chromosome.  Four of these MTase clones have been characterized
AB  - by DNA sequence analysis, and the open reading frames encoding each of these MTases have been
AB  - identified.  These MTases belong either to the 5mC or N4mC group of MTases.  Some of the 5mC
AB  - MTases show the presence of typical MTase conserved motifs.  However, some other cloned 5mC
AB  - MTase show the lack of these motifs.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Skowronek, K.
TI  - Identification of a new restriction endonuclease R.BcrAI from Bacillus cremoris.
JO  - Acta Microbiol. Pol.
PY  - 1995
SP  - 315
EP  - 316
VL  - 44
AB  - Site specific restriction endonuclease R.BcrAI has been purified from Bacillus cremoris.  The
AB  - enzyme recognizes the sequence 5' CTCTTC 3'.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Stasiak, A.
AU  - Stanczak, J.
TI  - Specific restriction endonucleases from Haemophilus influenzae JC9.
JO  - Acta Microbiol. Pol.
PY  - 1980
SP  - 151
EP  - 156
VL  - 29
AB  - Two types of restriction endonucleases have been isolated from Haemophilus
AB  - influenzae.  The presence of type III restriction enzymes is in vivo correlated
AB  - with the activity against Haemophilus phages HP1, S2 and N3 (Piekarowicz,
AB  - Brzezinski and Kauc, 1975, Kauc and Piekarowicz, 1978).
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Stein, D.C.
TI  - Purification and characterization of a new DNA methyltransferase from Neisseria gonorrhoeae.
JO  - Gene
PY  - 1995
SP  - 101
EP  - 102
VL  - 157
AB  - A new DNA methyltransferase, M.NgoBVII, was isolated from Neisseria gonorrhoeae strain WR302.
AB  - M.NgoVII recognizes the sequence 5'-GCNGC-3'.
AB  - [ The enzyme called NgoBVII in this abstract has been renamed NgoBXII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Weglenska, A.
TI  - Improvement of the strain for the rapid identification of genes encoding restriction and modification enzymes.
JO  - Acta Microbiol. Pol.
PY  - 1994
SP  - 229
EP  - 231
VL  - 43
AB  - The E. coli AP1-200-9 strain used for rapid identification of genes encoding restriction and
AB  - modification enzymes carries a temperature sensitive lacZ gene fused to the damage-inducible
AB  - dinD locus. A derivative of this strain was constructed that has a wild-type form of this
AB  - locus which allows for a more efficient identification of recombinant plasmids encoding
AB  - restriction and modification enzymes.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - Identification of a new restriction endonuclease, R.NgoBI, from Neisseria gonorrhoeae.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 9868
EP  - 9868
VL  - 16
AB  - As a species, Neisseria gonorrhoeae produces five restriction endonucleases, and several other
AB  - DNA methyltransferases.  We have purified a methyltransferase that recognizes the sequence 5'
AB  - TCACC 3' and report here the purification from N. gonorrhoeae WR302 of a restriction
AB  - endonuclease, R.NgoBI, that also recognizes this sequence.  Purification scheme:  The
AB  - purification scheme employed was as previously described (2) except the (NH4)2SO4 precipitate
AB  - was dissolved in buffer A (20 mM KPO4, 1 mM EDTA, 10% glycerol, 10 mM 2-mercaptoethanol, pH
AB  - 7.5) before being purified by chromatography through a 2x20 cm phosphocellulose column.  The
AB  - enzyme activity eluted at 0.15 M NaCl. Active fractions were further purified through an Accel
AB  - QMA column and active fractions eluted at 0.1 M NaCl.  The recognition sequence for R.NgoBI
AB  - was determined by digesting lambda DNA with it and comparing the banding pattern obtained with
AB  - computer generated patterns obtained with all known enzymes.  The data indicated that this
AB  - enzyme cleaved lambda DNA at the same sequence as HphI.  Figure 1 is a comparison of the
AB  - fragments obtained after digesting pUC8 with NgoBI and HphI.  The restriction enzyme was most
AB  - active in a buffer containing 25 mM Tris-HCl, 25 mM KCl, 10 mM MgCl2, 2 mM 2-mercaptoethanol,
AB  - pH 7.8.
AB  - [ The enzyme called NgoBI in this abstract has been renamed NgoBVIII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - Purification and characterization of DNA methyltransferases from Neisseria gonorrhoeae.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 5957
EP  - 5972
VL  - 16
AB  - Three DNA methyltransferases, M.NgoAI, and M.NgoBI and M.NgoBII, free of any nuclease
AB  - activities were isolated from Neisseria gonorrhoeae strains WR220 and MUG116 respectively.
AB  - M.NgoAI recognizes the sequence 5' GGCC 3' and methylates the first 5' cytosine on both
AB  - strands.  M.NgoBI and M.NgoBII recognize 5' TCACC 3' and 5' GTANNNNNCTC 3' respectively.
AB  - M.NgoBII 5' GTANNNNNmCTC 3'.
AB  - [ The enzyme called NgoAI in this abstract has been renamed NgoGII, Jan/1998. ]
AB  - [ The enzyme called NgoBI in this abstract has been renamed NgoBVIII, Jan/1998. ]
AB  - [ The enzyme called NgoBII in this abstract has been renamed NgoBIX, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - Construction of a temperature-sensitive mutation for the direct identification of plasmids encoding DNA methyltransferases.
JO  - Gene
PY  - 1988
SP  - 233
EP  - 235
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - Neisseria gonorrhoeae M.NgoAI DNA methyltransferase:  physical and catalytic properties of the homogeneous enzyme.
JO  - Gene
PY  - 1988
SP  - 93
EP  - 97
VL  - 74
AB  - A DNA methyltransferase, M.NgoAI, was purified to homogeneity from Neisseria
AB  - gonorrhoeae strain WR220 by successive column chromatography.  Its Mr is 25000,
AB  - as determined by both gel filtration and denaturing polyacrylamide gel
AB  - electrophoresis.  Maximal enzymatic activity was obtained in 50 mM Tris.HCl (pH
AB  - 7.4), 10 mM EDTA, with incubation at 37C.  An apparent Km value for
AB  - S-adenosylmethionine and 5'-GGCC sites was determined to be 1.25 microM and
AB  - 89.6 nM, respectively.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - Cleavage of DNA by HaeII is inhibited by the presence of 5-methylcytosine at the second cytosine within the recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 10132
EP  - 10132
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - A new method for the rapid identification of genes encoding restriction and modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 1831
EP  - 1835
VL  - 19
AB  - We have constructed derivatives of Escherichia coli that can be used for the
AB  - rapid identification of recombinant plasmids encoding DNA restriction enzymes
AB  - and methyltransferases.  The induction of the DNA-damage inducible SOS response
AB  - by the Mcr and Mrr systems, in the presence of methylated DNA, is used to
AB  - select plasmids encoding DNA methyltransferases.  The strains of E. coli that
AB  - we have constructed are temperature-sensitive for the Mcr and Mrr systems and
AB  - have been further modified to include a lacZ gene fused to the damage-inducible
AB  - dinD locus of E. coli.  The detection of recombinant plasmids encoding DNA
AB  - methyltransferases and restriction enzymes is a simple, one step procedure that
AB  - is based on the induction at the restrictive temperature of the lacZ gene.
AB  - Transformants encoding DNA methyltransferase genes are detected on LB agar
AB  - plates supplemented with X-gal as blue colonies.  Using this method, we have
AB  - cloned a variety of DNA methyltransferase genes from diverse species such as
AB  - Neisseria, Haemophilus, Treponema, Pseudomonas, Xanthomonas and
AB  - Saccharopolyspora.
ER  -

TY  - JOUR
AU  - Piekarowicz, A.
AU  - Yuan, R.
AU  - Stein, D.C.
TI  - Isolation of temperature-sensitive McrA and McrB mutations and complementation analysis of the McrBC region of Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1991
SP  - 150
EP  - 155
VL  - 173
AB  - We isolated temperature-sensitive mcrA and mcrBC mutants of Escherichia coli.
AB  - At 42C, they were unable to restrict the T-even bacteriophages T6gt and Tegt or
AB  - plasmids encoding cloned DNA methylase genes whose specificities confer
AB  - sensitivity to the McrA and McrBC nucleases.  Complementation analysis of the
AB  - McrBC region (mcrB251) with the complete cloned McrBC system or a derivative
AB  - with mcrB alone indicated that the mutation shows an absolute defect for the
AB  - restriction of DNA containing hydroxymethylcytosine and a thermosensitive
AB  - defect for the restriction of DNA containing methylcytosine.  The properties of
AB  - the McrA temperature-sensitive mutants suggest that some of these mutations can
AB  - also influence the restriction of DNA containing hydroxymethylcytosine or
AB  - methylcytosine residues.
ER  -

TY  - JOUR
AU  - Pieper, U.
AU  - Brinkmann, T.
AU  - Kruger, T.
AU  - Noyer-Weidner, M.
AU  - Pingoud, A.
TI  - Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 190
EP  - 199
VL  - 272
AB  - McrBC, a GTP-dependent restriction enzyme from E. coli K-12, cleaves DNA containing methylated
AB  - cytosine residues 40 to 80 residues apart and 3'-adjacent to a purine residue
AB  - (pumCN40-80PumC).  The presence of the three consensus sequences characteristic for guanine
AB  - nucleotide binding proteins in one of the two subunits of McrBC suggests that this subunit is
AB  - responsible for GTP binding and hydrolysis.  We show here that (i) McrB binds GTP with an
AB  - affinity of 106 M^-1 and that GTP binding stabilizes McrB against thermal denaturation.  (ii)
AB  - McrB binds GDP about 50-fold and ATP at least three orders of magnitude more weakly than GTP.
AB  - (iii) McrB hydrolyzes GTP in the presence of Mg2+ with a steady-state rate of approximately
AB  - 0.5 min^-1.  (iv) McrC stimulates GTP hydrolysis 30-fold, but substrate DNA has no detectable
AB  - effect on the GTPase activity of McrB, neither by itself nor in the presence of McrC.  (v)
AB  - Substitution of N339 and N376 with alanine allowed us to identify NTAD (339 to 342) rather
AB  - than NKKA (376 to 379) as the equivalent of the third consensus sequence motif characteristic
AB  - for guanine nucleotide binding proteins, NKXD.
ER  -

TY  - JOUR
AU  - Pieper, U.
AU  - Groll, D.H.
AU  - Wunsch, S.
AU  - Gast, F.U.
AU  - Speck, C.
AU  - Mucke, N.
AU  - Pingoud, A.
TI  - The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat.
JO  - Biochemistry
PY  - 2002
SP  - 5245
EP  - 5254
VL  - 41
AB  - The GTP-dependent restriction enzyme McrBC consists of two polypeptides: one (McrB) that is
AB  - responsible for GTP binding and hydrolysis as well as DNA binding and another (McrC) that is
AB  - responsible for DNA cleavage. It recognizes two methylated or hemimethylated RC sites (R(m)C)
AB  - at a distance of approximately 30 to more than 2000 base pairs and cleaves the DNA close to
AB  - one of the two R(m)C sites. This process is strictly coupled to GTP hydrolysis and involves
AB  - the formation of high-molecular mass complexes. We show here using footprinting techniques,
AB  - surface plasmon resonance, and scanning force microscopy experiments that in the absence of
AB  - McrC, McrB binds to a single R(m)C site. If a second R(m)C site is present on the DNA, it is
AB  - occupied independently by McrB. Whereas the DNA-binding domain of McrB forms 1:1 complexes
AB  - with each R(m)C site and shows a clear footprint on both R(m)C sites, full-length McrB forms
AB  - complexes with a stoichiometry of at least 4:1 at each R(m)C site, resulting in a slightly
AB  - more extended footprint. In the presence of McrC, McrB forms high-molecular mass complexes of
AB  - unknown stoichiometry, which are considerably larger than the complexes formed with McrB
AB  - alone. In these complexes and when GTP is present, the DNA is cleaved next to one of the R(m)C
AB  - sites at distances differing by one to five helical turns, suggesting that in the McrBC-DNA
AB  - complex only a few topologically well-defined phosphodiester bonds of the DNA are accessible
AB  - for the nucleolytic center of McrC.
ER  -

TY  - JOUR
AU  - Pieper, U.
AU  - Pingoud, A.
TI  - A mutational analysis of the PD...D/EXK motif suggests that McrC harbors the catalytic center for DNA cleavage by the GTP-dependent restriction enzyme McrBC from Escherichia coli.
JO  - Biochemistry
PY  - 2002
SP  - 5236
EP  - 5244
VL  - 41
AB  - McrBC is a unique restriction enzyme which binds specifically to the bipartite recognition
AB  - sequence RmCNa~30-2000RmC and in the
AB  - presence of GTP translocates the DNA and cleaves both strands at
AB  - multiple positions within the two RmC "half-sites". It is known that
AB  - McrBC is composed of two subunits: McrB which binds and hydrolyzes GTP
AB  - and specifically interacts with DNA and McrC whose function is not
AB  - clear but which has been suspected to harbor the catalytic center for
AB  - DNA cleavage. A multiple-sequence alignment of the amino acid sequence
AB  - of Escherichia coli McrC and of six presumably homologous open reading
AB  - frames from various bacterial species shows that a sequence motif found
AB  - in many restriction enzymes, but also in other nucleases, the
AB  - PD....D/EXK motif, is conserved among these sequences. A mutational
AB  - analysis, in which the carboxylates (aspartic acid in McrC) of this
AB  - motif were substituted with alanine or asparagine and lysine was
AB  - substituted with alanine or arginine, strongly suggests that Asp244,
AB  - Asp257, and Lys259 represent the catalytic center of E. coli McrC.
AB  - Whereas the variants D244A (or -N), D257A (or -N), and K259A are
AB  - inactive in DNA cleavage (K259R has residual DNA cleavage activity),
AB  - they interact with McrB like wild-type McrC, as can be deduced from the
AB  - finding that they stimulate the McrB-catalyzed GTP hydrolysis to the
AB  - same extent as wild-type McrC. Thus, whereas McrC variants defective in
AB  - DNA cleavage can stimulate the GTPase activity of McrB, the DNase
AB  - activity of McrC is not supported by McrB variants defective in GTP
AB  - hydrolysis.
ER  -

TY  - JOUR
AU  - Pieper, U.
AU  - Schweitzer, T.
AU  - Groll, D.H.
AU  - Gast, F.-U.
AU  - Pingoud, A.
TI  - The GTP-binding domain of McrB: More than just a variation on common theme?
JO  - J. Mol. Biol.
PY  - 1999
SP  - 547
EP  - 556
VL  - 292
AB  - The methylation-dependent restriction endonuclease McrBC from Escherichia coli K12 cleaves DNA
AB  - containing two R(m)C dinucleotides separated by about 40 to 2000 base-pairs. McrBC is unique
AB  - in that cleavage is totally dependent on GTP hydrolysis. McrB is the GTP binding and
AB  - hydrolyzing subunit, whereas MrC stimulates its GTP hydrolysis. The C-terminal part of McrB
AB  - contains the sequences characteristic for GTP-binding proteins, consisting of the GxxxxGK(S/T)
AB  - motif (position 201-208), followed by the DxxG motif (position 300-303). The third motif
AB  - (NKxD) is present only in a non-canonical form (NTAD 333-336). Here we report a mutational
AB  - analysis of the putative GTP-binding domain of McrB. Amino acid substitutions were initially
AB  - performed in the three proposed GTP-binding motifs. Whereas substitutions in motif 1 (P203V)
AB  - and 2 (D300N) show the expected, albeit modest effects, mutation in the motif 3 is at variance
AB  - with the expectations. Unlike the corresponding EF-Tu and ras -p21 variants, the D336N
AB  - mutation in McrB does not change the nucleotide specificity from GTP to XTP, but results in a
AB  - lack of GTPase stimulation by McrC. The finding that McrB is not a typical G protein motivated
AB  - us to perform a search for similar sequences in DNA databases. Eight microbial sequences were
AB  - found, mainly from unfinished sequencing projects, with highly conserved sequence blocks
AB  - within a presumptive GTP-binding domain. From the five sequences showing the highest homology,
AB  - 17 invariant charged or polar residues outside the classical three GTP-binding motifs were
AB  - identified and subsequently exchanged to alanine. Several mutations specifically affect GTP
AB  - affinity and/or GTPase activity. Our data allow us to conclude that McrB is not a typical
AB  - member of the superfamily of GTP-binding proteins, but defines a new subfamily within the
AB  - superfamily of GTP-binding proteins, together with similar prokaryotic proteins of as yet
AB  - unidentified function.
ER  -

TY  - JOUR
AU  - Pieper, U.
AU  - Schweitzer, T.
AU  - Groll, D.H.
AU  - Pingoud, A.
TI  - Defining the location and function of domains of McrB by deletion mutagenesis.
JO  - Biol. Chem.
PY  - 1999
SP  - 1225
EP  - 1230
VL  - 380
AB  - The GTP-dependent restriction endonuclease McrBC of E. coli K12, which recognizes
AB  - cytosine-methylated DNA, consists of two protein subunits, McrB and McrC. We have investigated
AB  - the structural assignment and interdependence of the McrB subunit functions, namely (i)
AB  - specific DNA recognition and (ii) GTP binding and hydrolysis. Extending earlier work, we have
AB  - produced McrB variants comprising N- and C-terminal fragments. The variants McrB1-162 and
AB  - McrB1-170 are still capable of specific DNA binding. McrB169-465 shows GTP binding and
AB  - hydrolysis characteristics indistinguishable from full-length McrB as well as wild-type like
AB  - interaction with McrC. Thus, DNA and GTP binding are spatially separated on the McrB molecule,
AB  - and the respective domains function quite independently.
ER  -

TY  - JOUR
AU  - Pierce, J.V.
AU  - Bernstein, H.D.
TI  - Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis.
JO  - PLoS ONE
PY  - 2016
SP  - e0158171
EP  - e0158171
VL  - 11
AB  - Enterotoxigenic (ETBF) strains of Bacteroides fragilis are the subset of strains  that secrete
AB  - a toxin called fragilysin (Bft). Although ETBF strains are known to
AB  - cause diarrheal disease and have recently been associated with colorectal cancer,
AB  - they have not been well characterized. By sequencing the complete genome of four
AB  - ETBF strains, we found that these strains exhibit considerable variation at the
AB  - genomic level. Only a small number of genes that are located primarily in the Bft
AB  - pathogenicity island (BFT PAI) and the flanking CTn86 conjugative transposon are
AB  - conserved in all four strains and a fifth strain whose genome was previously
AB  - sequenced. Interestingly, phylogenetic analysis strongly suggests that the BFT
AB  - PAI was acquired by non-toxigenic (NTBF) strains multiple times during the course
AB  - of evolution. At the phenotypic level, we found that the ETBF strains were less
AB  - fit than the NTBF strain NCTC 9343 and were susceptible to a growth-inhibitory
AB  - protein that it produces. The ETBF strains also showed a greater tendency to form
AB  - biofilms, which may promote tumor formation, than NTBF strains. Although the
AB  - genomic diversity of ETBF strains raises the possibility that they vary in their
AB  - pathogenicity, our experimental results also suggest that they share common
AB  - properties that are conferred by different combinations of non-universal genetic
AB  - elements.
ER  -

TY  - JOUR
AU  - Pieretti, I.
AU  - Bolot, S.
AU  - Carrere, S.
AU  - Barbe, V.
AU  - Cociancich, S.
AU  - Rott, P.
AU  - Royer, M.
TI  - Draft Genome Sequence of Xanthomonas sacchari Strain LMG 476.
JO  - Genome Announcements
PY  - 2015
SP  - e00146
EP  - e00115
VL  - 3
AB  - We report the high-quality draft genome sequence of Xanthomonas sacchari strain LMG 476,
AB  - isolated from sugarcane. The genome comparison of this strain with a
AB  - previously sequenced X. sacchari strain isolated from a distinct environmental
AB  - source should provide further insights into the adaptation of this species to
AB  - different habitats and its evolution.
ER  -

TY  - JOUR
AU  - Pieretti, I.
AU  - Royer, M.
AU  - Barbe, V.
AU  - Carrere, S.
AU  - Koebnik, R.
AU  - Cociancich, S.
AU  - Couloux, A.
AU  - Darrasse, A.
AU  - Gouzy, J.
AU  - Jacques, M.A.
AU  - Lauber, E.
AU  - Manceau, C.
AU  - Mangenot, S.
AU  - Poussier, S.
AU  - Segurens, B.
AU  - Szurek, B.
AU  - Verdier, V.
AU  - Arlat, M.
AU  - Rott, P.
TI  - The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae.
JO  - BMC Genomics
PY  - 2009
SP  - 616
EP  - 616
VL  - 10
AB  - BACKGROUND: The Xanthomonadaceae family contains two xylem-limited plant
AB  - pathogenic bacterial species, Xanthomonas albilineans and Xylella
AB  - fastidiosa. X. fastidiosa was the first completely sequenced plant
AB  - pathogen. It is insect-vectored, has a reduced genome and does not possess
AB  - hrp genes which encode a Type III secretion system found in most plant
AB  - pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group
AB  - based on phylogenetic analyses with rRNA sequences. RESULTS: The complete
AB  - genome of X. albilineans was sequenced and annotated. X. albilineans,
AB  - which is not known to be insect-vectored, also has a reduced genome and
AB  - does not possess hrp genes. Phylogenetic analysis using X. albilineans
AB  - genomic sequences showed that X. fastidiosa belongs to the Xanthomonas
AB  - group. Order of divergence of the Xanthomonadaceae revealed that X.
AB  - albilineans and X. fastidiosa experienced a convergent reductive genome
AB  - evolution during their descent from the progenitor of the Xanthomonas
AB  - genus. Reductive genome evolutions of the two xylem-limited
AB  - Xanthomonadaceae were compared in light of their genome characteristics
AB  - and those of obligate animal symbionts and pathogens. CONCLUSION: The two
AB  - xylem-limited Xanthomonadaceae, during their descent from a common
AB  - ancestral parent, experienced a convergent reductive genome evolution.
AB  - Adaptation to the nutrient-poor xylem elements and to the cloistered
AB  - environmental niche of xylem vessels probably favoured this convergent
AB  - evolution. However, genome characteristics of X. albilineans differ from
AB  - those of X. fastidiosa and obligate animal symbionts and pathogens,
AB  - indicating that a distinctive process was responsible for the reductive
AB  - genome evolution in this pathogen. The possible role in genome reduction
AB  - of the unique toxin albicidin, produced by X. albilineans, is discussed.
ER  -

TY  - JOUR
AU  - Piet, J.R.
AU  - Huis, I.V.R.A.
AU  - van Schaik, B.D.
AU  - van Kampen, A.H.
AU  - Baas, F.
AU  - van de Beek, D.
AU  - Pannekoek, Y.
AU  - van der Ende, A.
TI  - Genome Sequence of Neisseria meningitidis serogroup B strain H44/76.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2371
EP  - 2372
VL  - 193
AB  - Neisseria meningitidis is an obligate human pathogen. While it is a frequent commensal of the
AB  - upper respiratory tract, in some individuals the bacterium spreads to the bloodstream causing
AB  - meningitis and/or sepsis, serious conditions with high morbidity and mortality. Here we report
AB  - the availability of the genome sequence of the widely used serogroup B laboratory strain
AB  - H44/76.
ER  -

TY  - JOUR
AU  - Pieta, L.
AU  - Campos, F.S.
AU  - Mariot, R.F.
AU  - Prichula, J.
AU  - de Moura, T.M.
AU  - Frazzon, A.P.
AU  - Frazzon, J.
TI  - Complete Genome Sequences of Two Listeria monocytogenes Serovars, 1/2a and 4b, Isolated from Dairy Products in Brazil.
JO  - Genome Announcements
PY  - 2015
SP  - e01494
EP  - e01415
VL  - 3
AB  - Listeria monocytogenes is the foodborne pathogen responsible for a bacterial infection called
AB  - listeriosis. Here, we present the whole-genome sequences of two
AB  - L. monocytogenes serovars, 1/2a and 4b, which are considered the most prevalent
AB  - in food processing plants and listeriosis outbreaks, respectively.
ER  -

TY  - JOUR
AU  - Pietila, M.K.
AU  - Laurinmaki, P.
AU  - Russell, D.A.
AU  - Ko, C.C.
AU  - Jacobs-Sera, D.
AU  - Hendrix, R.W.
AU  - Bamford, D.H.
AU  - Butcher, S.J.
TI  - Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2013
SP  - 10604
EP  - 10609
VL  - 110
AB  - It has been proposed that viruses can be divided into a small number of
AB  - structure-based viral lineages. One of these lineages is exemplified by bacterial
AB  - virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages.
AB  - Seemingly similar viruses also infect archaea. Here we demonstrate using genomic
AB  - analysis, electron cryomicroscopy, and image reconstruction that the major coat
AB  - protein fold of newly isolated archaeal Haloarcula sinaiiensis tailed virus 1 has
AB  - the canonical coat protein fold of HK97. Although it has been anticipated
AB  - previously, this is physical evidence that bacterial and archaeal head-tailed
AB  - viruses share a common architectural principle. The HK97-like fold has previously
AB  - been recognized also in herpesviruses, and this study expands the HK97-like
AB  - lineage to viruses from all three domains of life. This is only the second
AB  - established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus,
AB  - our findings support the hypothesis that the last common universal ancestor of
AB  - cellular organisms was infected by a number of different viruses.
ER  -

TY  - JOUR
AU  - Pietrokovski, S.
TI  - Modular organization of inteins and C-terminal autocatalytic domains.
JO  - Protein Sci.
PY  - 1998
SP  - 64
EP  - 71
VL  - 7
AB  - Analysis of the conserved sequence features of inteins (protein "introns") reveals that they
AB  - are composed of three distinct modular domains.  The N-terminal and C-terminal domains are
AB  - predicted to perform different parts of the autocatalytic protein splicing reaction.  An
AB  - optional endonuclease domain is shown to correspond to different types of homing endonucleases
AB  - in different inteins.  The N domain contains motifs predicted to catalyze the first steps of
AB  - protein splicing, leading to the cleavage of the intein N terminus from its protein host.
AB  - Intein N domain motifs are also found in C-terminal autocatalytic domains present in hedgehog
AB  - and other protein families.  Specific residues in the N domain of intein and CADs are proposed
AB  - to form a charge relay system involved in cleaving their N-termini.  The intein C domain is
AB  - apparently unique to inteins and contains motifs that catalyze the final protein splicing
AB  - steps: ligation of the intein flanks and cleavage of its C terminus to release the free intein
AB  - and spliced host protein.  All intein EN domains known thus far have dodecapeptide (DOD,
AB  - LAGLI-DADG) type homing endonuclease motifs.  This work identifies an EN domain with an HNH
AB  - homing-endonuclease motif and two new small inteins with no EN domains.  One of these small
AB  - inteins might be inactive or a "pseudo intein".  The results suggest a modular architecture
AB  - for inteins, clarify their origin and relationship to other protein families, and extend
AB  - recent experimental findings on the functional roles of intein N, C and EN motifs.
ER  -

TY  - JOUR
AU  - Pietrokovski, S.
TI  - Intein spread and extinction in evolution.
JO  - Trends Genet.
PY  - 2001
SP  - 465
EP  - 472
VL  - 17
AB  - Inteins are selfish DNA elements found within coding regions. They are translated with their
AB  - host protein, but then catalyze their own
AB  - excision and the formation of a peptide bond between their flanking
AB  - protein regions. Understanding what drives and selects inteins is
AB  - relevant for assessing whether they have unidentified biological
AB  - functions and whether they can invade and become established in new
AB  - genes and organisms. Inteins are suggested to have been present and
AB  - more common in the progenitors of eukaryotes and prokaryotes. In these
AB  - cells, inteins had some beneficial function or had evolved from an
AB  - unknown beneficial protein. Since then, this putative benefit has been
AB  - lost and inteins are gradually becoming extinct. The proteins in which
AB  - inteins are currently found are proposed to be proteins vital for the
AB  - survival of the organism, where intein removal is most difficult.
ER  -

TY  - JOUR
AU  - Pietrokovski, S.
TI  - Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins.
JO  - Protein Sci.
PY  - 1994
SP  - 2340
EP  - 2350
VL  - 3
AB  - Inteins (protein introns) are internal portions of protein sequences that are
AB  - posttranslationally excised while the flanking regions are spliced together, making an
AB  - additional protein product.  Inteins have been found in a number of homologous genes in
AB  - yeast, mycobacteria, and extreme thermophile archaebacteria.  The inteins are probably
AB  - multifunctional, autocatalyzing their own splicing, and some were also shown to be DNA
AB  - endonucleases.  The splice junction regions and two regions similar to homing
AB  - endonucleases were thought to be the only common sequence features of inteins.  This
AB  - work analyzed all published intein sequences with recently developed methods for detecting
AB  - weak, conserved sequence features.  The methods complemented each other in the
AB  - identification and assessment of several patterns characterizing the intein sequences.  New
AB  - intein conserved features are discovered and the known ones are quantitatively described
AB  - and localized.  The general sequence description of all the known inteins is derived from
AB  - the motifs and their relative positions.  The intein sequence description is used to search
AB  - the
AB  - sequence databases for intein-like proteins.  A sequence region in a mycobacterial open
AB  - reading frame possessing all of the intein motifs and absent from sequences homologous to
AB  - both of its flanking sequences is identified as an intein.  A newly discovered putative intein
AB  - in red algae chloroplasts is found not to contain the endonuclease motifs present in all other
AB  - inteins.  The yeast HO endonuclease is found to have an overall intein-like structure and a
AB  - few viral polyprotein cleavage sites are found to be significantly similar to the inteins
AB  - amino-end splice junction motif.  The intein features described may serve for detection of
AB  - intein sequences.
ER  -

TY  - JOUR
AU  - Pietrokovski, S.
TI  - A new intein in cyanobacteria and its significance for the spread of inteins.
JO  - Trends Genet.
PY  - 1996
SP  - 287
EP  - 288
VL  - 12
AB  - Inteins are protein 'introns' encoded inside the polypeptide sequence of
AB  - other proteins.  The inteins splice out post-translationally by a proteolytic cleavage and
AB  - ligation process.  Inteins appear to autocatalyze their own excision and some are site-
AB  - specific endonucleases.  Inteins are mobile genetic elements and at least one can home, that
AB  - is, insert a copy of its DNA into its integration site in an intein-less allele.  Fifteen
AB  - inteins
AB  - have been found in various organisms, including mycobacteria, thermophilic
AB  - archaebacteria, yeast and chloroplast of red alga.  Inteins are not very similar to one
AB  - another, but homologous sites in archaebacterial DNA polymerases and in mycobacterial
AB  - gyrase-A proteins contain homologous inteins.  However, the mycobacterial RecA proteins
AB  - and DNA polymerases also contain different inteins in different integration sites.
ER  -

TY  - JOUR
AU  - Pightling, A.W.
AU  - Lin, M.
AU  - Pagotto, F.
TI  - Draft Genome Sequence of Listeria monocytogenes Strain LI0521 (syn. HPB7171), Isolated in 1983 during an Outbreak in Massachusetts Caused by Contaminated  Cheese.
JO  - Genome Announcements
PY  - 2014
SP  - e00729
EP  - e00714
VL  - 2
AB  - Listeria monocytogenes, a pathogenic food-borne bacterium, is the causative agent of both
AB  - sporadic and outbreak cases of human listeriosis. Here, we present the
AB  - genome sequence of L. monocytogenes reference strain LI0521, isolated during an
AB  - outbreak involving contaminated cheese, which has been used as the model during
AB  - several proteomic studies.
ER  -

TY  - JOUR
AU  - Pightling, A.W.
AU  - Pagotto, F.
TI  - Genome Sequence of Listeria monocytogenes Strain HPB5415, Collected during a 2008 Listeriosis Outbreak in Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e00637
EP  - e00615
VL  - 3
AB  - Listeria monocytogenes strain HPB5415-isolated from deli meat-was found in 2008 to have the
AB  - same pulsed-field gel electrophoresis patterns as a clinical strain
AB  - (08-5923). However, whether nucleotide differences (single nucleotide
AB  - polymorphisms [SNPs]) exist between their genomes was not determined. We
AB  - sequenced the L. monocytogenes strain HPB5415 genome and identified 52 SNPs
AB  - relative to strain 08-5923.
ER  -

TY  - JOUR
AU  - Pightling, A.W.
AU  - Pagotto, F.
TI  - Draft Genome Sequence of Cronobacter sakazakii Clonal Complex 45 Strain HPB5174,  Isolated from a Powdered Infant Formula Facility in Ireland.
JO  - Genome Announcements
PY  - 2014
SP  - e00778
EP  - e00714
VL  - 2
AB  - Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe  illness in
AB  - neonates and the elderly. We present the genome sequence of a rare
AB  - strain (ST40, CC45), commonly found in multiple food processing facilities and in
AB  - powdered infant formula and only indicted in a single clinical case.
ER  -

TY  - JOUR
AU  - Pightling, A.W.
AU  - Rand, H.
AU  - Strain, E.
AU  - Pagotto, F.
TI  - Genome Sequence of the Listeria monocytogenes Food Isolate HPB913, Collected in Canada in 1993.
JO  - Genome Announcements
PY  - 2016
SP  - e00911
EP  - e00916
VL  - 4
AB  - Listeria monocytogenes is a pathogenic bacterium of importance to public health and food
AB  - safety agencies. We present the genome sequence of the serotype 1/2a L.
AB  - monocytogenes food isolate HPB913, which was collected in Canada in 1993 as part
AB  - of an investigation into a sporadic case of foodborne illness.
ER  -

TY  - JOUR
AU  - Pightling, A.W.
AU  - Rand, H.
AU  - Strain, E.
AU  - Pagotto, F.
TI  - Genome Sequence of Listeria monocytogenes Strain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994.
JO  - Genome Announcements
PY  - 2016
SP  - e00760
EP  - e00716
VL  - 4
AB  - Listeria monocytogenes is a foodborne pathogen that causes severe illness. Thus,  ongoing
AB  - efforts at real-time whole-genome sequencing are of utmost importance.
AB  - However, it is also important that retrospective analyses that place these data
AB  - into context be performed. Here, we present the genome sequence of strain
AB  - HPB2088, which was collected in 1994.
ER  -

TY  - JOUR
AU  - Pignot, M.
AU  - Pljevaljcic, G.
AU  - Weinhold, E.
TI  - Efficient synthesis of S-adenosyl-L-homocysteine natural product analogues and their use to elucidate the structural determinant for cofactor binding of the DNA methyltransferase M.HhaI.
JO  - Eur. J. Org. Chem.
PY  - 2000
SP  - 549
EP  - 555
VL  - 2000
AB  - 5'-Acetylthio-5'-deoxy-2',3'-O-isopropylideneadenosine was directly prepared from
AB  - commercially available 2',3'-O-isopropylideneadenosine and thioacetic acid under Mitsunobu
AB  - conditions in almost quantitative yield.  In situ cleavage of the acetylthio function of
AB  - 5'-Acetylthio-5'-deoxy-2',3'-O-isopropylideneadenosine followed by coupling with different
AB  - alkyl bromides proceeded with high yields.  Deprotection of the obtained 5'-thionucleosides
AB  - yielded the S-adenosyl-L-homocysteine analogues decarboxylated AdHcy, deaminated AdoHcy and
AB  - 5'-[3-(cyano)propylthio]-5'-deoxyadenosine in good overall yields.  Direct deprotection of
AB  - the thionucleoside 5'-Acetylthio-5'-deoxy-2',3'-O-isopropylideneadenosine delivered
AB  - 5'-thio-5'-deoxyadenosine in excellent yield.  In addition, binding constants of these
AB  - AdoHcy analogues and the DNA methyltransferase M.HhaI were determined in a fluorescence assay.
ER  -

TY  - JOUR
AU  - Pignot, M.
AU  - Siethoff, C.
AU  - Linscheid, M.
AU  - Weinhold, E.
TI  - Coupling of a nucleoside with DNA by a methyltransferase.
JO  - Angew. Chem. Int. Ed. Engl.
PY  - 1998
SP  - 2888
EP  - 2891
VL  - 37
AB  - S-Adenosyl-L-methionine-dependent methyltransferases catalyze the transfer of the activated
AB  - methyl group from the cofactor S-adenosyl-L-methionine to sulfur, nitrogen, oxygen, and carbon
AB  - acceptors (Scheme 1) of small molecules, phospholipids, proteins, RNA and DNA with high
AB  - specificity.  The transfer of larger chemical entities in a Mtase-catalyzed reaction has not
AB  - been reported and thus represents an interesting challenge for bioorganic chemists.  In
AB  - principal, covalent linking of the activated methyl group with the gamma-C atom of 1 would
AB  - yield a three-membered thiiranium compound, which could lead to a coupling of the whole
AB  - cofactor to the target substrate.  Since thiiranium compounds are known to be unstable in
AB  - nucleophilic solvents, we concentrated on the more stable aziridine analogues, which can be
AB  - activated as alkylating reagents upon protonation of their ring nitrogen atom.
AB  - N-adenosylaziridine was synthesized by nucleophilic substitution of the tosylate group of
AB  - 5'-deoxy-5'-tosyladenosine (tosyl=Ts=toluene-4-sulfonyl) with aziridine (Scheme 2).
ER  -

TY  - JOUR
AU  - Pikin, S.A.
TI  - On the distinction of the mechanisms of DNA cleavage by restriction enzymes - The I-, II-, and III-type molecular motors.
JO  - Crystallogr. Rep.
PY  - 2008
SP  - 858
EP  - 867
VL  - 53
AB  - A comparative physical description is given for the functioning of various restriction enzymes
AB  - and for their processes of DNA cleavage.
AB  - The previously proposed model system of kinetic equations is applied to
AB  - the I- and III-type enzymes, which use ATP molecules as an energy
AB  - source, while the II-type enzymes work thanks to catalytic reactions
AB  - with participation of an electric field. All the enzymes achieved
AB  - bending and twisting DNA, providing for either the linear motion of the
AB  - II-type enzyme along the DNA chain or the DNA translocation by the
AB  - I-and III-type enzymes due to moving chiral kinks. A comparative
AB  - estimation of the considered linear and angular velocities is
AB  - performed. The role of stalling forces for enzyme-DNA complexes, which
AB  - induce the observed cutting of the DNA either inside the enzyme (II) or
AB  - in some "weak" places outside enzymes I and III, which results in the
AB  - supercoiling of the DNA, is shown. The role of ionic screening for the
AB  - described processes is discussed.
ER  -

TY  - JOUR
AU  - Pikin, S.A.
TI  - On the DNA cleavage by restriction enzymes - molecular motors with polarization properties.
JO  - Mol. Cryst. Liq. Cryst.
PY  - 2009
SP  - 403
EP  - 413
VL  - 508
AB  - In the paper, on the general physical basis, the attempt was done to explain the operation of
AB  - restriction enzymes of different types.  The physical model lies in the DNA deformation in the
AB  - protein zone which is caused by catalytic processes taking place here.  It is shown that some
AB  - phenomena are similar to liquid-crystalline effects.  The DNA molecule either forms locally a
AB  - chiral kink moving together with a protein (the II type enzymes) or realizes the translocation
AB  - through protein (the I and III type enzymes).  The velocity of linear motion of the enzymes
AB  - was estimated on the basis of proper kinetic equations which include the action of a
AB  - longitudinal stalling force, the role of this force in DNA cleavage being different for
AB  - different enzymes.  The supercoiling of DNA during tis translocation is discussed.
ER  -

TY  - JOUR
AU  - Pikin, S.A.
TI  - Physical aspects of the structure and function of helicases as rotary molecular motors.
JO  - Crystallogr. Rep.
PY  - 2009
SP  - 929
EP  - 936
VL  - 54
AB  - Helicases were shown to have common physical properties with rotary molecular motors, such as
AB  - F (0) F (1)-ATP synthase and type I
AB  - restriction-modification (RM) enzymes. The necessary conditions for
AB  - action of molecular motors are chirality, the presence of the C (2) (or
AB  - lower) symmetry axis within rather large atomic groups, and
AB  - polarization properties. The estimates were made for the material
AB  - parameters of helicases, which translocate DNA due to moving chiral
AB  - kinks without DNA cleavage and are characterized by higher viscosity,
AB  - low mobility, and smaller chiral kinetic coefficients than type II RM
AB  - enzymes. This paper discusses the efficiency of helicases with opposite
AB  - polarities that drive DNA translocation in opposite directions.
ER  -

TY  - JOUR
AU  - Piknova, M.
AU  - Filova, M.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - Different restriction and modification phenotypes in ruminal lactate-utilizing bacteria.
JO  - FEMS Microbiol. Lett.
PY  - 2004
SP  - 91
EP  - 95
VL  - 236
AB  - Analysis of restriction and modification activities in lactate-utilizing bacteria belonging to
AB  - the Megasphaera elsdenii and Mitsuokella multiacida species revealed the presence of
AB  - GATC-specific, MboI isospecific, restriction-modification (R-M) systems in all strains tested.
AB  - While restriction endonucleases isolated from M. elsdenii strains were found to be sensitive
AB  - to Dam methylation, enzymes from M. multiacida cleaved DNA irrespective of Dam methylation.
AB  - The comparison of type 11 R-M systems specificities in three closely related lactate-utilizing
AB  - ruminal bacterial species indicated complete lack of restriction and/or modification enzymes
AB  - previously characterized from Selenomonas ruminantium in tested M. elsdenii and M. multiacida
AB  - strains. R-M systems are believed to represent the main defense tool against phage infection.
AB  - Based on the results of our experiments it could be assumed that M. elsdenii and M. multiacida
AB  - use the different strategy for bacteriophage protection compared to S. ruminantium.
ER  -

TY  - JOUR
AU  - Piknova, M.
AU  - Filova, M.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - A Unique Pair of GATC Specific DNA Methyltransferases in Mitsuokella multiacida.
JO  - Mol. Biol. Rep.
PY  - 2005
SP  - 281
EP  - 284
VL  - 32
AB  - Two GATC specific methylases together with Sau3AI isoschizomeric restriction endonuclease were
AB  - partially characterized in Mitsuokella
AB  - multiacida 46/5. This is the first report on the presence of solitary Dam
AB  - methyltransferase alongside GATC specific restriction-modification system
AB  - resulting in the unusual two-fold methylation of the GATC motifs.
ER  -

TY  - JOUR
AU  - Piknova, M.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - Multiple restriction-modification systems are present in rumen treponemes.
JO  - FEMS Microbiol. Lett.
PY  - 2005
SP  - 99
EP  - 99
VL  - 251
AB  - Type II restriction endonucleases were purified by heparin-sepharose followed by ion
AB  - chromatography from Treponema strains. The results
AB  - indicate that in addition to frequently cutting GATC-specific
AB  - restriction enzymes, the tested strains also possess rarely cutting
AB  - endonucleases. The purified restriction endonucleases represent four
AB  - different sequence specificities, comprising isoschizomers of Drdl,
AB  - AflII, Tth111II and NdeI. The data presented show that three rumen
AB  - Treponema strains possess altogether seven type II
AB  - restriction-modification systems. Thus, individual Treponema strains
AB  - may be considered an interesting source of multiple type II restriction
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Piknova, M.
AU  - Pristas, P.
AU  - Javorsky, P.
TI  - GATC-specific restriction-modification systems in ruminal bacteria.
JO  - Folia Microbiol. (Praha)
PY  - 2004
SP  - 191
EP  - 193
VL  - 49
AB  - The GATC-specific restriction and modification activities were analyzed in 11 major bacterial
AB  - representatives of ruminal microflora.
AB  - Modification phenotype was observed in 13 out of 40 ruminal strains.
AB  - MboI isoschizomeric restriction endonucleases were detected in 10
AB  - bacterial strains tested; three strains lacked any detectable
AB  - corresponding endonuclease activity. The only examined strain of
AB  - Mitsuokella multiacida was found to possess a different type of
AB  - endonuclease activity. This is the first report on restriction activity
AB  - in ruminal treponemes M. multiacida and Megasphaera elsdenii.
ER  -

TY  - JOUR
AU  - Piknova, M.
AU  - Pristas, P.
AU  - Javorsky, P.
TI  - Some evolutionary aspects of biology of the type II restriction-modification systems.
JO  - Biol. Listy
PY  - 2004
SP  - 15
EP  - 28
VL  - 69
AB  - Restriction-modification (R-M) systems occur exclusively among prokaryotic organisms, mainly
AB  - bacteria, and they represent the main protection mechanism against bacteriophage infections.
AB  - R-M systems comprise two enzymatic activities: a restriction endonuclease activity that
AB  - specifically cleaves DNA; and a corresponding methyltransferase activity that specifically
AB  - methylates the DNA, thereby protecting the genome of the host bacterium from cleavage by a
AB  - partner's restriction enzyme.  There are three main groups of R-M systems called Types I, II
AB  - and III and recently a new Type IV has been added to accommodate a class of methyl-dependent
AB  - restriction enzymes.  R-M systems are widely distributed among bacteria and more than 3500
AB  - restriction enzymes and 600 methyltransferases have been identified to date.  The most
AB  - abundant are type II R-M systems, which form a very large family of enzymes of similar
AB  - function.  Considering the dissimilarities in amino acid sequences and, paradoxically,
AB  - structural resemblances of restriction enzymes, it is very hard to decide whether restriction
AB  - endonucleases are the outcome of divergent evolution from a very distant ancestor or whether
AB  - they evolved independently.  While generally accepted that R-M systems act as barrier against
AB  - genetic exchanges, there is increasing evidence for their behavior as mobile genetic elements.
ER  -

TY  - JOUR
AU  - Piknova, M.
AU  - Pristas, P.
AU  - Javorsky, P.
AU  - Kasperowic, A.
AU  - Michalowski, T.
TI  - GATC-specific restriction and modification systems in treponemes.
JO  - Lett. Appl. Microbiol.
PY  - 2004
SP  - 311
EP  - 314
VL  - 38
AB  - Aims: To investigate the presence of GATC-specific modification and restriction activities in
AB  - rumen isolates of Treponema sp.
AB  - Methods: The presence of N-6-methyladenine within GATC (Dam)
AB  - sequences was analysed using isoschizomeric restriction endonucleases
AB  - having different sensitivities to the methylation of the target
AB  - sequence. A fast screening method was used for testing of site-specific
AB  - endonuclease activities directly in crude cell extracts. Three out of
AB  - six rumen isolates of Treponema sp. showed restriction activities.
AB  - Restriction endonucleases were further purified by Heparin-Sepharose
AB  - chromatography. Using PCR and specific primers, no sequence homologous
AB  - to the T. pallidum dam gene was found.
AB  - Conclusions: Three rumen treponemal strains were documented to
AB  - possess MboI isoschizomeric restriction- modification systems.
AB  - Significance: This is the first report on restriction activity in
AB  - rumen treponemes.
ER  -

TY  - JOUR
AU  - Pillay, A.
AU  - Katz, S.S.
AU  - Abrams, A.J.
AU  - Ballard, R.C.
AU  - Simpson, S.V.
AU  - Taleo, F.
AU  - Lahra, M.M.
AU  - Batra, D.
AU  - Rowe, L.
AU  - Trees, D.L.
AU  - Asiedu, K.
AU  - Chen, C.Y.
TI  - Complete Genome Sequences of 11 Haemophilus ducreyi Isolates from Children with Cutaneous Lesions in Vanuatu and Ghana.
JO  - Genome Announcements
PY  - 2016
SP  - e00459
EP  - e00416
VL  - 4
AB  - Haemophilus ducreyi causes chancroid and has recently been shown to be a significant cause of
AB  - cutaneous lesions in tropical or subtropical regions where
AB  - yaws is endemic. Here, we report the draft genome assemblies for 11 cutaneous
AB  - strains of Haemophilus ducreyi, isolated from children in Vanuatu and Ghana.
ER  -

TY  - JOUR
AU  - Pinarbasi, E.
AU  - Elliott, J.
AU  - Hornby, D.P.
TI  - Activation of a yeast pseudo DNA methyltransferase by deletion of a single amino acid.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 804
EP  - 813
VL  - 257
AB  - The biological methylation of cytosine bases in DNA is central to such diverse phenomena as
AB  - restriction and modification in bacteria, repeat induced point-mutation (RIPing) in fungi and
AB  - for programming gene expression patterns in vertebrates.  Structural studies on HhaI DNA
AB  - methyltransferase, together with the sequence comparisons of around 40 cytosine-specific DNA
AB  - methyltransferases, have recently provided a molecular framework for understanding the
AB  - mechanism of action of the related group of enzymes that catalyse this base modification.
AB  - There are, however, a number of organisms, including Saccharomyces cerevisiae,
AB  - Schizosaccharomyces pombe and Drosophila melanogaster, which have no detectable DNA
AB  - methylation.  Here we report that the product of the pmt1 gene recently identified in S.
AB  - pombe, which contains most of the primary structure elements of a typical cytosine-specific
AB  - DNA methyltransferase, is catalytically inert owing to the insertion of a Ser residue between
AB  - the Pro-Cys motif found at the active site of all such DNA methyltransferases.  Following
AB  - deletion of this Ser residue, catalytic activity is restored and, using a range of DNA binding
AB  - experiments, it is shown that the enzyme recognises and methylates the sequence CC(A/T)GG, the
AB  - same sequence that is modified by the product of the Escherichia coli dcm gene.  The pmt gene
AB  - of S. pombe therefore encodes a pseudo DNA methyltransferase, which we have called psiM.SpoI.
ER  -

TY  - JOUR
AU  - Pinarbasi, E.
AU  - Kan, M.S.
AU  - Duran, C.
AU  - Ford, G.C.
AU  - Hornby, D.P.
TI  - Substitution of the conserved phenylalanine in the S-adenosyl-L-methionine binding site of M.MspI with tyrosine modifies the kinetic properties of the enzyme.
JO  - Biol. Chem.
PY  - 1998
SP  - 591
EP  - 594
VL  - 379
AB  - Cytosine (C-5)-specific DNA methyltransferases share a set of ten conserved motifs distributed
AB  - evenly throughout the entire polypeptide chain.  The first conserved motif contains a Phe,
AB  - which is intimately associated with cofactor recognition.  In the pseudo-DNA methyltransferase
AB  - M.SpoI, encoded by the pmt1 gene in Schizosaccharomyces pombe, a Tyr replaces this Phe
AB  - residue.  We describe the properties of a mutant form of M.MspI, a typical cytosine
AB  - (C-5)-specific DNA methyltransferase, in which Tyr replaces the conserved Phe.  This mutant
AB  - shows differences in ternary complex formation and in the pattern of covalent complex
AB  - formation with an inhibitory, fluorinated DNA duplex which may be due to anomalous hydrogen
AB  - bonding between the mutant Tyr hydroxyl group and the catalytic loop of the enzyme or through
AB  - interference with cofactor binding.
ER  -

TY  - JOUR
AU  - Pinarbasi, E.
AU  - Pinarbasi, H.
AU  - Hornby, D.P.
TI  - Subcloning and expression of a cDNA encoding a Schizosaccharomyces pombe putative C-5 DNA methyltransferase.
JO  - Turkish J. Biol.
PY  - 1996
SP  - 325
EP  - 331
VL  - 20
AB  - The pmt1+ gene, which shows a striking similarity to bacterial C-5 DNA methyltransferases, has
AB  - recently been isolated from Schizosaccharomyces pombe.  In this study, we have subcloned pmt1+
AB  - cDNA into the bacterial expression vector pET14b, which contains a sequence coding six
AB  - histidine residues upstream of the coding site so that the recombinant protein possesses a
AB  - histidine tag (Hig-Tag) at its N-terminus.  The constructed vector, which we have called
AB  - pETSPO1, encoding the pmt1+ cDNA, was then introduced into E. coli BL21 (DE3)pLysS cells and
AB  - the expressed recombinant protein was purified to homogeneity by nickel-chelate-affinity
AB  - chromatography.  Approximately 5 mg of His-Tag-pmt1+ fusion protein was purified from one
AB  - liter of induced culture.
ER  -

TY  - JOUR
AU  - Pinarbasi, H.
AU  - Pinarbasi, E.
AU  - Hornby, D.
TI  - Recombinant alpha and beta subunits of M.AquI constitute an active DNA methyltransferase.
JO  - J. Biochem. Mol. Biol.
PY  - 2002
SP  - 348
EP  - 351
VL  - 35
AB  - AquI DNA methyltransferase, M.AquI, catalyses the transfer of a methyl group from
AB  - S-adenosyl-L-methionine to the C5 position of the outermost
AB  - deoxycytidine base in the DNA sequence 5'CYCGRG3'. M.AquI is encoded by
AB  - two overlapping ORFs (termed a and P) instead of the single ORF that is
AB  - customary for Class II methyltransferase genes. The structural
AB  - organization of the M.AquI protein sequence is quite similar to that of
AB  - other bacteria] C5-DNA methyltransferases. Ten conserved motifs are
AB  - also present in the correct order, but only on two polypeptides. We
AB  - separately subcloned the genes that encode the alpha and beta subunits
AB  - of M.AquI into expression vectors. The overexpressed His-fusion alpha
AB  - and beta subunits of the enzyme were purified to homogeneity in a
AB  - single step by Nickel-chelate affinity chromatography. The purified
AB  - recombinant proteins were assayed for biological activity by an in
AB  - vitro DNA tritium transfer assay. The alpha and beta subunits of M.AquI
AB  - alone have no DNA methyltransferase activity, but when both subunits
AB  - are included in the assay, an active enzyme that catalyses the transfer
AB  - of the methyl group from S-adenosyl-L-methionine to DNA is
AB  - reconstituted. We also showed that the beta subunit alone contains all
AB  - of the information that is required to generate recognition of specific
AB  - DNA duplexes in the absence of the alpha subunit.
ER  -

TY  - JOUR
AU  - Pinarbasi, H.
AU  - Pinarbasi, E.
AU  - Hornby, D.P.
TI  - The small subunit of M.AquI is responsible for sequence-specific DNA recognition and binding in the absence of the catalytic domain.
JO  - J. Bacteriol.
PY  - 2003
SP  - 1284
EP  - 1288
VL  - 185
AB  - AquI DNA methyltransferase (M. AquI) catalyzes the transfer of a methyl group from
AB  - S-adenosyl-L-methionine to the C5 position of the outermost
AB  - deoxycytidine base in the DNA sequence 5'-CCCGGG-3'. M. AquI is a
AB  - heterodimer in which the polypeptide chain is separated at the junction
AB  - between the two equivalent structural domains in the related enzyme M.
AB  - HhaI. Recently, we reported the subcloning, overexpression, and
AB  - purification of the subunits (alpha and beta) of M. AquI separately. Here
AB  - we describe the DNA binding properties of M. AquI. The results presented
AB  - here indicate that the beta subunit alone contains all of the information
AB  - for sequence-specific DNA recognition and binding. The first step in the
AB  - sequence-specific recognition of DNA by M. AquI involves the formation of
AB  - binary complex with the target recognition domain in conjunction with
AB  - conserved sequence motifs IX and X, found in all known C5 DNA
AB  - methyltransferases, contained in the beta subunit. The alpha subunit
AB  - enhances the binding of the beta subunit to DNA specifically and
AB  - nonspecifically. It is likely that the addition of the alpha subunit to
AB  - the beta subunit stabilizes the conformation of the beta subunit and
AB  - thereby enhances its affinity for DNA indirectly. Addition of
AB  - S-adenosyl-L-methionine and its analogues S-adenosyl-L-homocysteine and
AB  - sinefungin enhances binding, but only in the presence of the alpha
AB  - subunit. These compounds did not have any effect on DNA binding by the
AB  - beta subunit alone. Using a 30-mer oligodeoxynucleotide substrate
AB  - containing 5-fluorodeoxycytidine (5-FdC), it was found that the beta
AB  - subunit alone did not form a covalent complex with its specific sequence
AB  - in the absence or presence of S-adenosyl-L-methionine. However, the
AB  - addition of the alpha subunit to the beta subunit led to the formation of
AB  - a covalent complex with specific DNA sequence containing 5-FdC.
ER  -

TY  - JOUR
AU  - Pinarbasi, H.
AU  - Pinarbasi, E.
AU  - Hornby, D.P.
TI  - Substitution of the conserved cysteine with glycine (Cys82Gly) of Agmenellum quadruplicatum methylase AquI (M.AquI) is not cytotoxic to  E. coli.
JO  - Turkish J. Biol.
PY  - 2001
SP  - 177
EP  - 184
VL  - 25
AB  - Cytosine 5 DNA methyltransferases share ten conserved motifs. Motif IV contains an absolutely
AB  - conserved proline-cysteine dipeptide. The
AB  - cysteine residue of this motif is involved in catalysis by forming a
AB  - covalent bond with the 6-position of cytosine prior to methyl group
AB  - transfer. AquI DNA methyltransferase recognising the sequence CCCGGG is
AB  - a heterodimer unlike other C5 DNA methyltransferases. We changed the
AB  - conserved cysteine (Cys82) of M.AquI to serine and glycine. The
AB  - presence of mutations was confirmed by automated DNA sequencing.
AB  - Mutants were tested by in vivo plasmid protection assay and also by
AB  - transformation into mcrA+BC+ strain of E. coli. Replacement of the
AB  - conserved cysteine with serine led to an apparent loss of the
AB  - methyltransferring ability of the enzyme. Interestingly, it was found
AB  - that substitution of cysteine with glycine is not cytotoxic to E. coli
AB  - in the case of M.AquI.
ER  -

TY  - JOUR
AU  - Pinard, M.
TI  - Multitiered regulation of 5-cytosine DNA methyltransferase expression.
JO  - Diss. Abstr.
PY  - 2000
SP  - 5938
EP  - 5938
VL  - 60
AB  - The methylation of DNA at the 5 position of the cytosine moiety within CpG dinucleotides
AB  - sequences forms a complex pattern which delimits non-expressed genes.  For many years,
AB  - especially through studies of the correlation between methylation and gene silencing,
AB  - researchers have tried to decipher this genomic subtext.  Probably, a better way to achieve an
AB  - understanding of DNA methylation is by first elucidating what regulates the apparatus
AB  - responsible for its establishment.  The DNA MeTase is the enzyme responsible for the catalysis
AB  - of the DNA methylation reaction.  It was therefore the objective of this thesis to define some
AB  - of the factors that regulate the expression of this enzyme.  Preceding work had described a
AB  - promoter for the gene encoding the DNA MeTase.  Recent data has prompted some to put in doubt
AB  - the validity of this promoter.  In the first part of this thesis I present a report which
AB  - describes a selection between two possible promoters for the DNA MeTase gene effected by
AB  - methylation in P19 cells.  This data not only revalidates the previous description of the
AB  - promoter, but adds a new level of possible control.  In the second part, I elucidated the
AB  - elements within the minimal region of the aforementioned promoter which are necessary for
AB  - activity.  The results illustrate that most of the sequence plays a role in the promoter
AB  - function, and pRb is found to be able to modulate the activity in a novel cooperation between
AB  - AP1 and Sp1 which is absolutely necessary for the promoter to fulfil its purpose.  The third
AB  - part of the thesis is based on an effort to investigate the generality of oncogenic control of
AB  - DNA MeTase expression.  The promoter was previously demonstrated to be responsive to the
AB  - Ras/AP1 pathway leading to oncogenesis.  Therefore, another oncogene, the SV40 large T
AB  - antigen, known to act through a separate pathway from Ras and AP1, was transfected into BALB/c
AB  - 3T3 cells in order to see how the expression of the DNA MeTase would be affected during this
AB  - transformation.  It was found that T antigen, through its actions on pRb, can induce DNA
AB  - MeTase expression by stabilizing its mRNA.  These studies establish that the DNA MeTase is a
AB  - nodal point of control by oncogenes and tumor suppressors which may need this enzyme in order
AB  - to execute their effects on the cell.
ER  -

TY  - JOUR
AU  - Pinard, M.
AU  - Szyf, M.
TI  - Regulation of cytosine DNA methyltransferase expression by tumor suppressors.
JO  - Mol. Biol. Cell
PY  - 1996
SP  - 174a
EP  - 174a
VL  - 7
AB  - In mammalian genomes, 60-80% of CpG dinucleotide sequences are methylated on the cytosine 5'
AB  - position.  These methylated sequences are distributed in a tissue specific pattern which is
AB  - correlated with gene silencing.  Recent data suggest a critical role for DNA MeTase in
AB  - oncogenesis.  The DNA methyltransferase gene expression has previously been shown to respond
AB  - to the oncogenic Ras pathway via AP-1 sites found in its promoter.  The effective silencing of
AB  - certain tumor suppressors by DNA methylation has also been demonstrated.  We hypothesize that
AB  - DNA MeTase acts as a pivotal point in the cross-talk between oncogenes and tumor suppressors.
AB  - In order to elucidate the effect of tumor suppressors on DNA MeTase expression, the SV40 T
AB  - antigen was stably transfected into BalbC3T3 cells to inhibit pRb activity.  We demonstrate
AB  - that expression of T antigen includes expression of DNA MeTase RNA as determined by RNAase
AB  - protection, of DNA MeTase protein as shown by Western blot analysis and of DNA MeTase activity
AB  - as assessed by an enzymatic activity assay.  DNA MeTase induction is at least partly
AB  - transcriptional as shown by nuclear Run-off assays.  By Southern blot assays we have observed
AB  - differences in the levels of methylation in several CpG island genes although not all to the
AB  - same extent.  Therefore, we clearly show that T antigen affects the regulation of DNA MeTase
AB  - and, in consequence, affects the methylation of specific genes.  These results may be the
AB  - first to show a feedback regulation of DNA MeTase by tumor suppressors which may mean that the
AB  - DNA MeTase is a center point in growth regulation by both oncogenes and tumor suppressors.
ER  -

TY  - JOUR
AU  - Pingoud, A.
TI  - Spermidine increases the accuracy of type II restriction endonucleases.  Suppression of cleavage at degenerate, non-symmetrical sites.
JO  - Eur. J. Biochem.
PY  - 1985
SP  - 105
EP  - 109
VL  - 147
AB  - The non-specific cleavage of DNA by type II restriction endonucleases (BamHI,
AB  - BsuRI, EcoRI, EcoRV, HindIII, PstI and SalI) can be effectively suppressed by
AB  - spermidine in millimolar concentrations, regardless of whether the non-specific
AB  - cleavage is induced by high concentrations of enzyme under optimal buffer
AB  - conditions or by high pH, low ionic strength, organic solvents and Mn2+ ions.
AB  - The increased specificity of restriction endonucleases in the presence of
AB  - spermidine is due to an enhancement of the cleavage rate at the canonical site
AB  - and a slowing down of the cleavage rate at related sites.  It is argued that
AB  - spermidine is essential for the high accuracy of restriction endonucleases in
AB  - vivo.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Alves, J.
AU  - Fliess, A.
AU  - Geiger, R.
AU  - Rueter, T.
AU  - Wolfes, H.
TI  - Site-directed mutagenesis of the EcoRI restriction endonuclease.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1987
SP  - 1093
EP  - 1093
VL  - 368
AB  - EcoRI is the only restriction endonuclease for which detailed structural
AB  - information is available.  Based on this information we have begun to study the
AB  - involvement of individual amino acid residues in the recognition process and in
AB  - catalysis by site directed mutagenesis.  In an effort to identify the essential
AB  - Glu and His residues of EcoRI we have replaced Glu 96, Glu 111, Glu 144 by Gln
AB  - and His 14, His 31 and His 114 by Asn.  All these single point mutations
AB  - drastically lower the catalytic effectivity of EcoRI, mainly by affecting the
AB  - kcat-value.  The Glu 96 mutant, furthermore, shows reduced specificity towards
AB  - its DNA substrate.  At present these results can only in part be explained by
AB  - the 3D structure of the EcoRI recognition complex as deduced from the x-ray
AB  - analysis of an EcoRI oligodeoxynucleotide complex crystallized in the absence
AB  - of Mg2+.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Alves, J.
AU  - Geiger, R.
TI  - Restriction Enzymes.
JO  - Methods Mol. Biol.
PY  - 1993
SP  - 107
EP  - 200
VL  - 16
AB  - A review focussing on the practical aspects of the use of these enzymes.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Fuxreiter, M.
AU  - Pingoud, V.
AU  - Wende, W.
TI  - Type II restriction endonucleases: structure and mechanism.
JO  - Cell. Mol. Life Sci.
PY  - 2005
SP  - 685
EP  - 707
VL  - 62
AB  - Type II restriction endonucleases are components of restriction modification systems that
AB  - protect bacteria and archaea against invading
AB  - foreign DNA. Most are homodimeric or tetrameric enzymes that cleave DNA
AB  - at defined sites of 4 - 8 bp in length and require Mg2+ ions for
AB  - catalysis. They differ in the details of the recognition process and
AB  - the mode of cleavage, indicators that these enzymes are more diverse
AB  - than originally thought. Still, most of them have a similar structural
AB  - core and seem to share a common mechanism of DNA cleavage, suggesting
AB  - that they evolved from a common ancestor. Only a few restriction
AB  - endonucleases discovered thus far do not belong to the PD...D/ExK
AB  - family of enzymes, but rather have active sites typical of other
AB  - endonuclease families. The present review deals with new developments
AB  - in the field of Type II restriction endonucleases. One of the more
AB  - interesting aspects is the increasing awareness of the diversity of
AB  - Type II restriction enzymes. Nevertheless, structural studies
AB  - summarized herein deal with the more common subtypes. A major emphasis
AB  - of this review will be on target site location and the mechanism of
AB  - catalysis, two problems currently being addressed in the literature.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Geiger, R.
AU  - Alves, J.
AU  - Oelgeschlager, T.
AU  - Ruter, T.
TI  - Functional sites of the EcoRI restriction endonuclease probed by site directed mutagenesis.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1989
SP  - 943
EP  - 944
VL  - 370
AB  - The EcoRI restriction endonuclease recognizes with high specificity the double
AB  - stranded DNA sequence G^AATTC/CTTAA^G and in the presence of Mg2+ cleaves the
AB  - DNA as indicated.  A 3 Angstrom X-ray structure analysis of an EcoRI-DNA
AB  - complex, crystallized in the absence of Mg2+, indicates that the amino acid
AB  - residues in positions 144 and 145 as well as 200 are involved in DNA binding.
AB  - Site directed mutagenesis experiments have shown that their involvement in the
AB  - recognition process, however, is more intricate than proposed by the authors of
AB  - the X-ray structure analysis.  To define more precisely the role of these and
AB  - adjacent amino acids we have produced single and double mutants of EcoRI with
AB  - amino acid replacements in position 144, 145, 147 as well as 199, 200, 203 and
AB  - analyzed their activity in vivo and in vitro after purification to homogeneity.
AB  - The results of the in vivo assay allows us to conclude that the structural
AB  - integrity of the region at and around position 200 is very critical for the
AB  - enzymatic function of EcoRI:  nonconservative mutations lead to a dramatic
AB  - decrease in activity.  In contrast, the region around position 144 and 145
AB  - seems to be of minor importance for the enzymatic activity:  non-conservative
AB  - mutations in this region have similar moderate effects as conservative
AB  - mutations.  The analysis of the purified EcoRI mutants confirms these results.
AB  - In addition, they demonstrate that some mutants which have a very low activity
AB  - are still specific for the EcoRI site (Arg200->Gly), while others show a
AB  - relaxed specificity (Arg200->Glu or Gln and Asn199->Asp).  The Asn199->Asp
AB  - mutant, furthermore, attacks preferentially the central phosphodiester bond in
AB  - its degenerate hexanucleotide recognition sequence.  Taken together our results
AB  - suggest that not only Glu144, Arg145 and Arg200 are involved in specificity
AB  - determining interactions but other amino acids as well.  The recognition
AB  - process, furthermore, does not only depend on hydrogen bonds but also on the
AB  - overall complementarity of charge dipoles, and presumably is highly redundant.
AB  - We have begun to locate the catalytic center and the Mg2+ binding site of
AB  - EcoRI.  Two candidate regions were analyzed:
AB  - 1.  92GGIVEVKD - DYGEWR
AB  - 2. 126LLVGKRGDQDLMAAG
AB  - which show a homology to a consensus sequence proposed to be involved in Mg2+
AB  - binding in a variety of polymerases.  Preliminary results demonstrate that the
AB  - second region is more critical than the first one for the catalytic action of
AB  - EcoRI.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Jeltsch, A.
TI  - Structure and function of type II restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3705
EP  - 3727
VL  - 29
AB  - More than 3000 type II restriction endonucleases have been discovered. They recognize short,
AB  - usually palindromic, sequences of 4-8 bp and, in the presence of Mg(2+), cleave the DNA within
AB  - or in close proximity to the recognition sequence. The orthodox type II enzymes are homodimers
AB  - which recognize palindromic sites. Depending on particular features subtypes are classified.
AB  - All structures of restriction enzymes show a common structural core comprising four
AB  - beta-strands and one alpha-helix. Furthermore, two families of enzymes can be distinguished
AB  - which are structurally very similar (EcoRI-like enzymes and EcoRV-like enzymes). Like other
AB  - DNA binding proteins, restriction enzymes are capable of non-specific DNA binding, which is
AB  - the prerequisite for efficient target site location by facilitated diffusion. Non-specific
AB  - binding usually does not involve interactions with the bases but only with the DNA backbone.
AB  - In contrast, specific binding is characterized by an intimate interplay between direct
AB  - (interaction with the bases) and indirect (interaction with the backbone) readout. Typically
AB  - approximately 15-20 hydrogen bonds are formed between a dimeric restriction enzyme and the
AB  - bases of the recognition sequence, in addition to numerous van der Waals contacts to the bases
AB  - and hydrogen bonds to the backbone, which may also be water mediated. The recognition process
AB  - triggers large conformational changes of the enzyme and the DNA, which lead to the activation
AB  - of the catalytic centers. In many restriction enzymes the catalytic centers, one in each
AB  - subunit, are represented by the PD...D/EXK motif, in which the two carboxylates are
AB  - responsible for Mg(2+) binding, the essential cofactor for the great majority of enzymes. The
AB  - precise mechanism of cleavage has not yet been established for any enzyme, the main
AB  - uncertainty concerns the number of Mg(2+) ions directly involved in cleavage. Cleavage in the
AB  - two strands usually occurs in a concerted fashion and leads to inversion of configuration at
AB  - the phosphorus. The products of the reaction are DNA fragments with a 3'-OH and a
AB  - 5'-phosphate.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Jeltsch, A.
TI  - Recognition and cleavage of DNA by type-II restriction endonucleases.
JO  - Eur. J. Biochem.
PY  - 1997
SP  - 1
EP  - 22
VL  - 246
AB  - Restriction endonucleases are enzymes which recognize short DNA sequences and cleave the DNA
AB  - in both strands.  Depending on the enzymological properties different types are distinguished.
AB  - Type II restriction endonucleases are homodimers which recognize short palindromic sequences
AB  - 4-8 bp in length and, in the presence of Mg2+, cleave the DNA within or next to the
AB  - recognition site.  They are capable of non-specific binding to DNA and make use of linear
AB  - diffusion to locate their target site.  Binding and recognition of the specific site involves
AB  - contacts to the bases of the recognition sequence and the phosphodiester backbone over
AB  - approximately 10-12 bp.  In general, recognition is highly redundant which explains the
AB  - extreme specificity of these enzymes.  Specific binding is accompanied by conformational
AB  - changes over both the protein and the DNA.  This mutual induced fit leads to the activation of
AB  - the catalytic centers.  The precise mechanism of cleavage has not yet been established for any
AB  - restriction endonuclease.  Currently two models are discussed: the substrate-assisted
AB  - catalysis mechanism and the two-metal-ion mechanism.  Structural similarities identified
AB  - between EcoRI, EcoRV, BamHI, PvuII and Cfr10I suggest that many type II restriction
AB  - endonucleases are not only functionally but also evolutionarily related.  A review.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Jeltsch, A.
AU  - Lanio, T.
AU  - Schulze, C.
AU  - Selent, U.
AU  - Stahl, F.
AU  - Wende, W.
AU  - Wenz, C.
TI  - Mechanism of DNA recognition and cleavage by restriction enzymes.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S138
EP  - S138
VL  - 376
AB  - The crystal structure analyses of specific DNA complexes of EcoRI, EcoRV and PvuII have
AB  - greatly aided in our understanding of how these enzymes recognize and cleave their DNA
AB  - substrate.  Many questions, however, remain, in particular, how is the target site located,
AB  - what is the relative contribution of direct and indirect readout for the recognition process,
AB  - how do the two subunits of the homodimeric restriction enzymes cooperate in recognition as
AB  - well as cleavage, and, what is the precise mechanism of phosphodiester bond hydrolysis.  Using
AB  - EcoRV as a model restriction enzyme we have tried to answer some of these questions.  It is
AB  - apparent from our studies that EcoRV makes use of facilitated diffusion along the DNA to
AB  - locate its target site and that Mg ions are required for specific binding which leads to a
AB  - pronounced DNA bending.  During recognition, contacts are formed to the bases and the
AB  - backbone: base contacts are in general more important than phosphate contacts, the latter,
AB  - however, are needed for binding, linear diffusion and to make sites with different flanking
AB  - sequences equally accessible for EcoRV,  Mutants of EcoRV have been constructed that exhibit
AB  - preferences for sites containing a modified base or backbone as well as for certain flanking
AB  - sequences.  We have shown that the two identical subnits of EcoRV communicate with each other
AB  - in DNA recognition, not, however, in catalysis per se.  Accordingly, artifical heterodimers
AB  - could be produced that exhibit a pronounced nicking activity.  While the catalytic amino acid
AB  - residues and the stereochemical course for the reaction have been identfied for EcoRV, it is
AB  - still not clear how the attacking hydroxide ion is generated and how many metal ions are
AB  - involved in the catalytic mechanism.  Based on the current experimental evidence, we believe
AB  - that a water molecule is activated by the phosphate residue 3' to the scissile phosphodiester
AB  - bond, that only one Mg ion is needed to polarize the P-O bond, to stabilize the transition
AB  - state and to supply a water molecule for protonation of the leaving group.  It is becoming
AB  - increasingly clear that restriction enzymes, which in general do not share significant
AB  - sequence homology, have structural and mechanistic features in common.  Indeed, using a
AB  - genotypic and phenotypic analysis it has been possible to demonstrate a common evolutionary
AB  - history for these enzymes.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Jeltsch, A.
AU  - Maxwell, A.
AU  - Sherratt, D.
TI  - Enzymes that keep DNA under control.
JO  - EMBO Rep.
PY  - 2001
SP  - 271
EP  - 276
VL  - 2
AB  - Life demands not only the faithful and controlled replication of DNA but, in addition, many
AB  - other enzymatic processes involving DNA, including topoisomerase action, recombination,
AB  - repair, restriction and modification.  These topics and their interrelationships were
AB  - discussed at the IUBMB symposium in Bangalore (India) on DNA enzymes: structures and
AB  - mechanisms (December 1-3, 2000), which was organized by V. Nagaraja and D.N. Rao (Bangalore,
AB  - India) and brought together about 200 scientists from all over the world.  Whereas most
AB  - presentations focused on detailed biochemical and genetic mechanisms, several reminded us that
AB  - enzymes and DNA are components of complex living organisms that live, die and evolve.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Pingoud, V.
AU  - Wende, W.
TI  - Homing endonucleases - multifaceted tools for genome engineering.
JO  - BIOspektrum
PY  - 2003
SP  - 592
EP  - 595
VL  - 9
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Silva, G.H.
TI  - Precision genome surgery.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 743
EP  - 744
VL  - 25
AB  - Zinc finger nucleases hold great potential for gene therapy as they allow one to cleave DNA at
AB  - a chosen target sequence.  Unfortunately, however, they also cleave prolifically at off-target
AB  - sites, resulting in unacceptable toxicity.  Two papers in this issue, by Miller et al. and
AB  - Szczepek et al., show that off-target cleavage can be greatly reduced by rationally
AB  - redesigning the ZFN dimer interface to inhibit homodimerization.  The goal of gene therapy is
AB  - to repair genetic defects without othewise modifying the genome.  One of the most promising
AB  - strategies for gene correction is homologous recombination.  In this approach, the correct DNA
AB  - sequence is saupplied in trans and is integrated into the genome by an endogenous mechanism of
AB  - site-specific recombination.  Ideally, the deficient gene is replaced with a functional copy
AB  - in its natural context while leaving the rest of the genome untouched.  Homologous
AB  - recombination can also be used for gene inactivation, insertion or deletion.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Thielking, V.
AU  - Selent, U.
AU  - Kohler, E.
AU  - Liedtke, M.
AU  - Wolfes, H.
AU  - Pieper, U.
AU  - Geiger, R.
AU  - Winkler, F.K.
TI  - Identification of functional sites in the EcoRV restriction endonuclease by site-directed mutagenesis.
JO  - J. Biomol. Struct. Dyn.
PY  - 1991
SP  - A165
EP  - A165
VL  - 8
AB  - Guided by the X-ray structure analysis of a crystalline EcoRV d(GGGATATCCC)
AB  - complex (Winkler, unpublished) we have replaced various amino acid residues in
AB  - EcoRV by site-directed mutagenesis in order to identify those amino acids which
AB  - participate in the binding and cleavage of DNA.  Mutant enzymes were isolated
AB  - and characterized physico-chemically and biochemically.  Our results show that
AB  - three regions are of importance for DNA binding: region I around Ser183,
AB  - Asn185, Thr186 and Asn188, region II around Gln69 and Asn70 and region III
AB  - comprising the C-terminus.  The conservative substitution of these amino acids
AB  - leads to mutant enzymes of no or considerably reduced activity but unaltered
AB  - specificity, indicating that the process of recognition is tightly coupled to
AB  - catalysis and highly redundant.  Region I contains a sequence motif
AB  - (-SerGlyXXXAsnIIeXSer-) which is also found in other restriction enzymes
AB  - recognizing the sequence G--/--C or G-/-C, the dashes representing A or T.
AB  - Region III is homologous to a sequence found in SmaI.  Presumably the catalytic
AB  - center is formed by Asp74 and Asp90, which may serve to bind Mg2+ and activate
AB  - water for a nucleophilic attack, and Lys92 which may hold the scissile
AB  - phosphodiester bond in place.  The mutation of Asp74 to Gln leads to a nearly
AB  - inactive enzyme.  Other mutations are currently being characterized.  It is
AB  - noteworthy that in EcoRI a similar sequence motif (-ProAsp...Glu(Asp)XLys-) is
AB  - found in the vicinity of the scissile phosphodiester bond.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Urbanke, C.
AU  - Alves, J.
AU  - Ehbrecht, H.-J.
AU  - Zabeau, M.
AU  - Gualerzi, C.
TI  - Effect of polyamines and basic proteins on cleavage DNA by restriction endonucleases.
JO  - Biochemistry
PY  - 1984
SP  - 5697
EP  - 5703
VL  - 23
AB  - We have investigated the effect of the polyamines spermine, spermidine, and
AB  - putrescine and the prokaryotic histone-like proteins NS1 and NS2 on the
AB  - restriction endonuclease EcoRI catalyzed cleavage of plasmid and bacteriophage
AB  - DNAs.  At low concentrations of spermine and spermidine, the rate of DNA
AB  - cleavage by EcoRI is increased, while high concentrations of spermine as well
AB  - as of spermidine are inhibitory.  These phenomena are also observed with other
AB  - restriction endonucleases.  They are, therefore, probably due to the
AB  - interaction of the polyamines with the DNA.  Putrescine does not have such an
AB  - effect within the concentration range investigated.  Remarkably, low
AB  - concentrations of spermine and spermidine very efficiently suppress EcoRI
AB  - activity.  An inhibition of the EcoRI-catalyzed cleavage of DNA is also
AB  - observed with NS1 and NS2, an effect that can be mimicked with other basic
AB  - proteins that interact with DNA.  The results are discussed in terms of the
AB  - mechanism of restriction in vivo.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Wende, W.
TI  - A sliding restriction enzyme pauses.
JO  - Structure
PY  - 2007
SP  - 391
EP  - 393
VL  - 15
AB  - In this issue of Structure, Aggarwal and colleagues (Townson et al., 2007) present the crystal
AB  - structure of the restriction endonuclease BstYI in
AB  - complex with a near-cognate substrate. This structure most likely reflects
AB  - the conformation BstYI adopts as it scans DNA and pauses upon encountering
AB  - a site similar to its recognition sequence.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Wende, W.
TI  - Generation of Novel Nucleases with Extended Specificity by Rational and Combinatorial Strategies.
JO  - Chembiochem
PY  - 2011
SP  - 1495
EP  - 1500
VL  - 12
AB  - After the discovery of DNA as the molecule carrying the hereditary information of all living
AB  - organisms, DNA processing enzymes, in particular restriction endonucleases, led to the
AB  - development of recombinant DNA technology. Today, in the postgenomic era, a steadily growing
AB  - number of entire genome sequences is available.  The emerging genome-engineering technology
AB  - requires more sophisticated nucleases with very high specificity, that ideally target a unique
AB  - sequence in a complex genome.  The design and control of these rare-cutting endonucleases by
AB  - using rational and evolutionary strategies is the focus of this Minireview.
ER  -

TY  - JOUR
AU  - Pingoud, A.
AU  - Wilson, G.G.
AU  - Wende, W.
TI  - Type II restriction endonucleases-a historical perspective and more.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 7489
EP  - 7527
VL  - 42
AB  - This article continues the series of Surveys and Summaries on restriction endonucleases
AB  - (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the
AB  - kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what
AB  - they do, and how they do it. Type II REases are produced by prokaryotes to combat
AB  - bacteriophages. With extreme accuracy, each recognizes a particular sequence in
AB  - double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these
AB  - enzymes in the 1970s, and of the uses to which they could be put, have since impacted every
AB  - corner of the life sciences. They became the enabling tools of molecular biology, genetics and
AB  - biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different
AB  - REases have been discovered and are available commercially. Their genes have been cloned,
AB  - sequenced and overexpressed. Most have been characterized to some extent, but few have been
AB  - studied in depth. Here, we describe the original discoveries in this field, and the properties
AB  - of the first Type II REases investigated. We discuss the mechanisms of sequence recognition
AB  - and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the
AB  - surprising heterogeneity revealed by comparisons of their sequences and structures.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Conzelmann, C.
AU  - Kinzebach, S.
AU  - Sudina, A.
AU  - Metelev, V.
AU  - Kubareva, E.
AU  - Bujnicki, J.M.
AU  - Lurz, R.
AU  - Luder, G.
AU  - Xu, S.Y.
AU  - Pingoud, A.
TI  - PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 913
EP  - 929
VL  - 329
AB  - We present here the first detailed biochemical analysis of an archaeal restriction enzyme.
AB  - PspGI shows sequence similarity to SsoII, EcoRII,
AB  - NgoMIV and Cfr10I, which recognize related DNA sequences. We demonstrate
AB  - here that PspGI, like SsoII and unlike EcoRII or NgoMIV and Cfr10I,
AB  - interacts with and cleaves DNA as a homodimer and is not stimulated by
AB  - simultaneous binding to two recognition sites. PspGI and SsoII differ in
AB  - their basic biochemical properties, viz. stability against chemical
AB  - denaturation and proteolytic digestion, DNA binding and the pH, MgCl(2)
AB  - and salt-dependence of their DNA cleavage activity. In contrast, the
AB  - results of mutational analyses and cross-link experiments show that PspGI
AB  - and SsoII have a very similar DNA binding site and catalytic center as
AB  - NgoMIV and Cfr10I (whose crystal structures are known), and presumably
AB  - also as EcoRII, in spite of the fact that these enzymes, which all
AB  - recognize variants of the sequence -/CC-GG- (/ denotes the site of
AB  - cleavage), are representatives of different subgroups of type II
AB  - restriction endonucleases. A sequence comparison of all known restriction
AB  - endonuclease sequences, furthermore, suggests that several enzymes
AB  - recognizing other DNA sequences also share amino acid sequence
AB  - similarities with PspGI, SsoII and EcoRII in the region of the presumptive
AB  - active site. These results are discussed in an evolutionary context.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Geyer, H.
AU  - Geyer, R.
AU  - Kubareva, E.
AU  - Bujnicki, J.M.
AU  - Pingoud, A.
TI  - Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: A case study using the  restriction endonuclease SsoII.
JO  - Mol. BioSyst.
PY  - 2005
SP  - 135
EP  - 141
VL  - 1
AB  - Specific protein-nucleic acid interactions are of paramount importance for the propagation,
AB  - maintenance and expression of genetic information.  Restriction endonucleases serve as model
AB  - systems to study the mechanisms of DNA recognition by proteins.  SsoII is a Type II
AB  - restriction endonuclease that recognizes the double stranded sequence / CCNGG and cleaves it
AB  - in the presence of Mg2+-ions, as indicated.  SsoII shows sequence similarity over a stretch of
AB  - ~70 amino acid residues with several other restriction endonucleases that recognize a similar
AB  - sequence as SsoII (Cfr10I, EcoRII, NgoMIV, PspGI).  In the NgoMIV this stretch is involved in
AB  - DNA recognition and cleavage, as shown by the crystal structure analysis of an enzyme-product
AB  - complex.  To find out whether the presumptive DNA recognition region in SsoII is indeed in
AB  - contact with DNA we have photocrosslinked SsoII with an oligodeoxyribonucleotide in which the
AB  - first guanine of the recognition sequence was replaced by 5-iodouracil.  Following digestion
AB  - by trypsin, the peptide-oligodeoxyribonucleotide conjugate was purified by Fe3+-IMAC and then
AB  - incubated with hydrogen fluoride, which hydrolyzes the oligodeoxyribonucleotide to yield the
AB  - peptide-deoxyuridine conjugate.  The site of photocrosslinking was identified by MALDI-TOF-MS
AB  - and MALDI-TOF-MS/MS to be Trp189, adjacent to Arg188, which aligns with Arg194 in NgoMIV,
AB  - involved in recognition of the second guanine in the NgoMIV recognition sequence G/CCGGC.
AB  - This result confirms previously published conclusions drawn on the basis of a mutational
AB  - analysis of SsoII.  The methodology that was employed here can be used in principle to
AB  - identify the DNA binding site of any protein.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Grindl, W.
AU  - Wende, W.
AU  - Thole, H.
AU  - Pingoud, A.
TI  - Structural and functional analysis of the homing endonuclease PI-SceI by limited proteolytic cleavage and molecular cloning of partial digestion products.
JO  - Biochemistry
PY  - 1998
SP  - 8233
EP  - 8243
VL  - 37
AB  - PI-SceI is a member of an unusual class of rare cutting homing endonucleases produced by an
AB  - autocatalytic protein splicing from a precursor.  To analyze the structural and functional
AB  - domain organization of the endonuclease PI-SceI and to examine whether the DNA binding
AB  - activity can be structurally separated from the catalytic activity, we performed limited
AB  - proteolytic digestion experiments with various proteases.  Two protease-resistant fragments
AB  - spanning the N- and C-terminal halves of the nuclease were identified using different
AB  - proteases which cleave the protein in the same region. Each fragment contains one of the two
AB  - conserved LAGLIDADG motifs.  The products of the limited proteolytic digests were shown to
AB  - remain associated and to exhibit specific DNA binding but to be inactive in DNA cleavage.
AB  - Different from what is observed with native PI-SceI, only one complex is formed as shown in an
AB  - electrophoretic mobility shift assay.  Expression clones for the N- and C-terminal protein
AB  - fragments obtained by tryptic digestion were constructed, and the proteins PI-SceI-N and
AB  - PI-SceI-C were purified.  Only PI-SceI-N exhibits DNA binding activity.  Bending experiments
AB  - with PI-SceI-N, a mixture of PI-SceI-N and PI-SceI-C, as well as the products of the limited
AB  - tryptic digest show that a DNA substrate with the full length recognition sequence is bent by
AB  - 45 degrees.  This degree of bending is also observed with a DNA containing only the right side
AB  - of the recognition sequence, corresponding to one of the DNA cleavage products of PI-SceI.
AB  - Our results demonstrate that the N-terminal half of PI-SceI which lacks one of the two
AB  - LAGLDADG motifs is able to bind to DNA specifically and to induce one of the distortions
AB  - observed to occur in the process of DNA binding by PI-SceI.  These results are discussed in
AB  - light of the recently solve crystal structure of PI-SceI and used to refine a model for the
AB  - mechanism of DNA binding and cleavage by PI-SceI.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Kubareva, E.
AU  - Stengel, G.
AU  - Friedhoff, P.
AU  - Bujnicki, J.M.
AU  - Urbanke, C.
AU  - Sudina, A.
AU  - Pingoud, A.
TI  - Evolutionary relationship between different subgroups of restriction endonucleases.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 14306
EP  - 14314
VL  - 277
AB  - The type II restriction endonuclease SsoII shows sequence similarity with 10 other restriction
AB  - endonucleases, among them the type IIE
AB  - restriction endonuclease EcoRII, which requires binding to an effector
AB  - site for efficient DNA cleavage, and the type IIF restriction
AB  - endonuclease NgoMIV, which is active as a homotetramer and cleaves DNA
AB  - with two recognition sites in a concerted reaction. We show here that
AB  - SsoII is an orthodox type II enzyme, which is active as a homodimer and
AB  - does not require activation by binding to an effector site.
AB  - Nevertheless, it shares with EcoRII and NgoMIV a very similar
AB  - DNA-binding site and catalytic center as shown here by a mutational
AB  - analysis, indicative of an evolutionary relationship between these
AB  - three enzymes. We suggest that a similar relationship exists between
AB  - other orthodox type II, type IIE, and type IIF restriction
AB  - endonucleases. This may explain why similarities may be more pronounced
AB  - between members of different subtypes of restriction enzymes than among
AB  - the members of a given subtype.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Sudina, A.
AU  - Geyer, H.
AU  - Bujnicki, J.M.
AU  - Lurz, R.
AU  - Luder, G.
AU  - Morgan, R.
AU  - Kubareva, E.
AU  - Pingoud, A.
TI  - Specificity changes in the evolution of Type II restriction endonucleases - A biochemical and bioinformatic analysis of restriction  enzymes that recognize unrelated sequences.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 4289
EP  - 4298
VL  - 280
AB  - How restriction enzymes with their different specificities and mode of cleavage evolved has
AB  - been a long standing question in evolutionary
AB  - biology. We have recently shown that several Type II restriction
AB  - endonucleases, namely SsoII (down arrow CCNGG), PspGI (^CCWGG), Eco-RII (^CCWGG), NgoMIV
AB  - (G^CCGGC), and Cfr10I (R^CCGGY), which recognize similar DNA sequences (as indicated, where ^
AB  - denotes cleavage position), share limited
AB  - sequence similarity over an interrupted stretch of approximately 70 amino
AB  - acid residues with MboI, a Type II restriction endonuclease from
AB  - Moraxella bovis (Pingoud, V., Conzelmann, C., Kinzebach, S., Sudina,
AB  - A., Metelev, V., Kubareva, E., Bujnicki, J.M., Lurz, R., Luder, G., Xu,
AB  - S. Y., and Pingoud, A. (2003) J. Mol. Biol 329, 913-929). Nevertheless,
AB  - MboI has a dissimilar DNA specificity (^GATC) compared with
AB  - these enzymes. In this study, we characterize MboI in detail to
AB  - determine whether it utilizes a mechanism of DNA recognition similar to
AB  - SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. Mutational analyses and
AB  - photocross-linking experiments demonstrate that MboI exploits the
AB  - stretch of approximately 70 amino acids for DNA recognition and cleavage.
AB  - It is therefore likely that MboI shares a common evolutionary origin
AB  - with SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. This is the first
AB  - example of a relatively close evolutionary link between Type
AB  - II restriction enzymes of widely different specificities.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Thole, H.
AU  - Christ, F.
AU  - Grindl, W.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - Photocross-linking of the homing endonuclease PI-SceI to its recognition sequence.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 10235
EP  - 10243
VL  - 274
AB  - PI-SceI is an intein-encoded protein that belongs to the LAGLIDADG family of homing
AB  - endonucleases.  According to the crystal structure and mutational studies, this endonuclease
AB  - consists of two domains, one responsible for protein splicing, the other for DNA cleavage, and
AB  - both presumably for DNA binding.  To define the DNA binding site of PI-SceI,
AB  - photocross-linking was used to identify amino acid residues in contact with DNA.  Sixty-three
AB  - double-stranded oligodeoxynucleotides comprising the minimal recognition sequence and
AB  - containing single 5-iodopyrimidine substitutions in almost all positions of the recognition
AB  - sequence were synthesized and irradiated in the presence of PI-SceI with a helium/cadmium
AB  - laser (325 nm).  The best cross-linking yield (approximately 30%) was obtained with an
AB  - oligodeoxynucleotide with a 5-iododeoxyuridine at position +9 in the bottom strand.  The
AB  - subsequent analysis showed that cross-linking had occurred with amino acid His-333, 6 amino
AB  - acids after the second LAGLIDADG motif.  With the H333A variant of PI-SceI or in the presence
AB  - of excess unmodified oligodeoxynucleotide, no cross-linking was observed, indicating the
AB  - specificity of the cross-linking reaction.  Chemical modification of His residues in PI-SceI
AB  - by diethylpyrocarbonate leads to a substantial reduction in the binding and cleavage activity
AB  - of PI-SceI.  This inactivation can be suppressed by substrate binding.  This result further
AB  - supports the finding that at least one His residue is in close contact to the DNA.  Based on
AB  - these and published results, conclusions are drawn regarding the DNA binding site of PI-SceI.
ER  -

TY  - JOUR
AU  - Pingoud, V.
AU  - Wende, W.
AU  - Friedhoff, P.
AU  - Reuter, M.
AU  - Alves, J.
AU  - Jeltsch, A.
AU  - Mones, L.
AU  - Fuxreiter, M.
AU  - Pingoud, A.
TI  - On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family.
JO  - J. Mol. Biol.
PY  - 2009
SP  - 140
EP  - 160
VL  - 393
AB  - Restriction endonucleases of the PD...D/EXK family need Mg(2+) for DNA cleavage. Whereas
AB  - Mg(2+) (or Mn(2+)) promotes catalysis, Ca(2+) (without
AB  - Mg(2+)) only supports DNA binding. The role of Mg(2+) in DNA cleavage by
AB  - restriction endonucleases has elicited many hypotheses, differing mainly
AB  - in the number of Mg(2+) involved in catalysis. To address this problem, we
AB  - measured the Mg(2+) and Mn(2+) concentration dependence of DNA cleavage by
AB  - BamHI, BglII, Cfr10I, EcoRI, EcoRII (catalytic domain), MboI, NgoMIV,
AB  - PspGI, and SsoII, which were reported in co-crystal structure analyses to
AB  - bind one (BglII and EcoRI) or two (BamHI and NgoMIV) Me(2+) per active
AB  - site. DNA cleavage experiments were carried out at various Mg(2+) and
AB  - Mn(2+) concentrations at constant ionic strength. All enzymes show a
AB  - qualitatively similar Mg(2+) and Mn(2+) concentration dependence. In
AB  - general, the Mg(2+) concentration optimum (between approximately 1 and 10
AB  - mM) is higher than the Mn(2+) concentration optimum (between approximately
AB  - 0.1 and 1 mM). At still higher Mg(2+) or Mn(2+) concentrations, the
AB  - activities of all enzymes tested are reduced but can be reactivated by
AB  - Ca(2+). Based on these results, we propose that one Mg(2+) or Mn(2+) is
AB  - critical for restriction enzyme activation, and binding of a second Me(2+)
AB  - plays a role in modulating the activity. Steady-state kinetics carried out
AB  - with EcoRI and BamHI suggest that binding of a second Mg(2+) or Mn(2+)
AB  - mainly leads to an increase in K(m), such that the inhibitory effect of
AB  - excess Mg(2+) or Mn(2+) can be overcome by increasing the substrate
AB  - concentration. Our conclusions are supported by molecular dynamics
AB  - simulations and are consistent with the structural observations of both
AB  - one and two Me(2+) binding to these enzymes.
ER  -

TY  - JOUR
AU  - Pinto, A.J.
AU  - Sharp, J.O.
AU  - Yoder, M.J.
AU  - Almstrand, R.
TI  - Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome.
JO  - Genome Announcements
PY  - 2016
SP  - e01563
EP  - e01515
VL  - 4
AB  - Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in  heavy
AB  - metal-contaminated acidic environments. However, their phylogenetic and
AB  - metabolic diversity is poorly resolved. We present draft genome sequences of two
AB  - novel and phylogenetically distinct Acidimicrobiaceae members assembled from an
AB  - acid mine drainage biofilm metagenome.
ER  -

TY  - JOUR
AU  - Pinto, C.
AU  - Sousa, S.
AU  - Froufe, H.
AU  - Egas, C.
AU  - Clement, C.
AU  - Fontaine, F.
AU  - Gomes, A.C.
TI  - Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 30
EP  - 30
VL  - 13
AB  - Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321 is a naturally occurring strain
AB  - in vineyard, with the ability to colonise grapevine and which
AB  - unveils a naturally antagonistic potential against phytopathogens of grapevine,
AB  - including those responsible for the Botryosphaeria dieback, a GTD disease. Herein
AB  - we report the draft genome sequence of B. amyloliquefaciens subsp. plantarum
AB  - Fito_F321, isolated from the leaf of Vitis vinifera cv. Merlot at Bairrada
AB  - appellation (Cantanhede, Portugal). The genome size is 3,856,229 bp, with a GC
AB  - content of 46.54% that contains 3697 protein-coding genes, 86 tRNA coding genes
AB  - and 5 rRNA genes. The draft genome of strain Fito_F321 allowed to predict a set
AB  - of bioactive compounds as bacillaene, difficidin, macrolactin, surfactin and
AB  - fengycin that due to their antimicrobial activity are hypothesized to be of
AB  - utmost importance for biocontrol of grapevine diseases.
ER  -

TY  - JOUR
AU  - Pinto, F.
AU  - Tett, A.
AU  - Armanini, F.
AU  - Asnicar, F.
AU  - Boscaini, A.
AU  - Pasolli, E.
AU  - Zolfo, M.
AU  - Donati, C.
AU  - Salmaso, N.
AU  - Segata, N.
TI  - Draft Genome Sequence of the Planktic Cyanobacterium Tychonema bourrellyi, Isolated from Alpine Lentic Freshwater.
JO  - Genome Announcements
PY  - 2017
SP  - e01294
EP  - e01217
VL  - 5
AB  - We describe here the draft genome sequence of the cyanobacterium Tychonema bourrellyi,
AB  - assembled from a metagenome of a nonaxenic culture. The strain
AB  - (FEM_GT703) was isolated from a freshwater sample taken from Lake Garda, Italy.
AB  - The draft genome sequence represents the first assembled T. bourrellyi strain.
ER  -

TY  - JOUR
AU  - Pinto, F.
AU  - Tett, A.
AU  - Armanini, F.
AU  - Asnicar, F.
AU  - Boscaini, A.
AU  - Pasolli, E.
AU  - Zolfo, M.
AU  - Donati, C.
AU  - Salmaso, N.
AU  - Segata, N.
TI  - Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem.
JO  - Genome Announcements
PY  - 2018
SP  - e00009
EP  - e00018
VL  - 6
AB  - Freshwater ecosystems represent 0.01% of the water on Earth, but they support 6%  of global
AB  - biodiversity that is still mostly uncharacterized. Here, we describe
AB  - the genome sequences of three strains belonging to novel species in the
AB  - Pseudomonas, Flavobacterium, and Sediminibacterium genera recovered from a water
AB  - sample of Lake Garda, Italy.
ER  -

TY  - JOUR
AU  - Pinto, S.B.
AU  - Stainton, K.
AU  - Harris, S.
AU  - Kambris, Z.
AU  - Sutton, E.R.
AU  - Bonsall, M.B.
AU  - Parkhill, J.
AU  - Sinkins, S.P.
TI  - Transcriptional Regulation of Culex pipiens Mosquitoes by Wolbachia Influences Cytoplasmic Incompatibility.
JO  - PLoS Pathog.
PY  - 2013
SP  - E1003647
EP  - E1003647
VL  - 9
AB  - Cytoplasmic incompatibility (CI) induced by the endosymbiont Wolbachia pipientis
AB  - causes complex patterns of crossing sterility between populations of the Culex
AB  - pipiens group of mosquitoes. The molecular basis of the phenotype is yet to be
AB  - defined. In order to investigate what host changes may underlie CI at the
AB  - molecular level, we examined the transcription of a homolog of the Drosophila
AB  - melanogaster gene grauzone that encodes a zinc finger protein and acts as a
AB  - regulator of female meiosis, in which mutations can cause sterility. Upregulation
AB  - was observed in Wolbachia-infected C. pipiens group individuals relative to
AB  - Wolbachia-cured lines and the level of upregulation differed between lines that
AB  - were reproductively incompatible. Knockdown analysis of this gene using RNAi
AB  - showed an effect on hatch rates in a Wolbachia infected Culex molestus line.
AB  - Furthermore, in later stages of development an effect on developmental
AB  - progression in CI embryos occurs in bidirectionally incompatible crosses. The
AB  - genome of a wPip Wolbachia strain variant from Culex molestus was sequenced and
AB  - compared with the genome of a wPip variant with which it was incompatible. Three
AB  - genes in inserted or deleted regions were newly identified in the C. molestus
AB  - wPip genome, one of which is a transcriptional regulator labelled wtrM. When this
AB  - gene was transfected into adult Culex mosquitoes, upregulation of the grauzone
AB  - homolog was observed. These data suggest that Wolbachia-mediated regulation of
AB  - host gene expression is a component of the mechanism of cytoplasmic
AB  - incompatibility.
ER  -

TY  - JOUR
AU  - Pintor-Toro, J.A.
TI  - Adenine methylation in zein genes.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1987
SP  - 1082
EP  - 1087
VL  - 147
AB  - This paper reports the novel finding of adenine methylation in higher plants. Comparison of
AB  - restriction patterns of genomic maize DNA digested with enzymes MboI and Sau3AI enabled us to
AB  - detect the existence of adenine methylation in zein genes. Adenine methylation within or
AB  - around zein genes turned out to be similar in endosperm (where zeins are actively synthesized)
AB  - and in seedling tissue (where zein genes are not expressed). Furthermore, adenine methylation
AB  - patterns were found to be similar both in wild-type and opaque-2 mutant plants. These lines of
AB  - evidence suggest that adenine methylation is unrelated to the regulation of gene expression.
ER  -

TY  - JOUR
AU  - Pique, N.
AU  - Aquilini, E.
AU  - Alioto, T.
AU  - Minana-Galbis, D.
AU  - Tomas, J.M.
TI  - Genome Sequence of Plesiomonas shigelloides Strain 302-73 (Serotype O1).
JO  - Genome Announcements
PY  - 2013
SP  - e00404
EP  - e00413
VL  - 1
AB  - Plesiomonas shigelloides, the only species of the genus, is an emergent pathogenic bacterium
AB  - associated with human diarrheal and extraintestinal disease.
AB  - We present the whole-genome sequence analysis of the representative strain for
AB  - the O1 serotype (strain 302-73), providing a tool for studying bacterial
AB  - outbreaks, virulence factors, and accurate diagnostic methods.
ER  -

TY  - JOUR
AU  - Pires, D.P.
AU  - Sillankorva, S.
AU  - Kropinski, A.M.
AU  - Lu, T.K.
AU  - Azeredo, J.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1.
JO  - Genome Announcements
PY  - 2015
SP  - e00918
EP  - e00915
VL  - 3
AB  - vB_PaeM_CEB_DP1 is a Pseudomonas aeruginosa bacteriophage (phage) belonging to the
AB  - Pbunalikevirus genus of the Myoviridae family of phages. It was isolated from hospital sewage.
AB  - vB_PaeM_CEB_DP1 is a double-stranded DNA (dsDNA) phage, with a genome of 66,158 bp, containing
AB  - 89 predicted open reading frames.
ER  -

TY  - JOUR
AU  - Pirone-Davies, C.
AU  - Hoffmann, M.
AU  - Roberts, R.J.
AU  - Muruvanda, T.
AU  - Timme, R.E.
AU  - Strain, E.
AU  - Luo, Y.
AU  - Payne, J.
AU  - Luong, K.
AU  - Song, Y.
AU  - Tsai, Y.C.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Evans, P.S.
AU  - Allard, M.W.
TI  - Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars.
JO  - PLoS ONE
PY  - 2015
SP  - e0123639
EP  - e0123639
VL  - 10
AB  - The methylation of DNA bases plays an important role in numerous biological processes
AB  - including development, gene expression, and DNA replication. Salmonella
AB  - is an important foodborne pathogen, and methylation in Salmonella is implicated
AB  - in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced
AB  - and assembled the complete genomes of eleven Salmonella enterica isolates from
AB  - nine different serovars, and analysed the whole-genome methylation patterns of
AB  - each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs,
AB  - one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these
AB  - motifs are novel, i.e., they have not been previously described. We also
AB  - identified the methyltransferases (MTases) associated with 13 of the motifs. Some
AB  - motifs are conserved across all Salmonella serovars tested, while others were
AB  - found only in a subset of serovars. Eight of the nine serovars contained a unique
AB  - methylated motif that was not found in any other serovar (most of these motifs
AB  - were part of Type I restriction modification systems), indicating the high
AB  - diversity of methylation patterns present in Salmonella.
ER  -

TY  - JOUR
AU  - Pirrotta, V.
TI  - Two restriction endonucleases from Bacillus globigii.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 1747
EP  - 1760
VL  - 3
AB  - The sites of action of the restriction enzyme BglII on lambda DNA are mapped. This enzyme
AB  - recognises the sequence 5'...AGATCT...3' and makes staggered cuts producing sticky ends. In
AB  - lambda DNA, the second A in this sequence is methylated about 50% of the time by a bacterial
AB  - methylase absent in E. coli dam-. In contrast to BglII, BglI makes many cuts in lambda DNA and
AB  - produces 5' terminals which are not substrates for polynucleotide kinase.
ER  -

TY  - JOUR
AU  - Pirrotta, V.
AU  - Bickle, T.A.
TI  - General purification schemes for restriction endonucleases.
JO  - Methods Enzymol.
PY  - 1980
SP  - 89
EP  - 95
VL  - 65
AB  - The range of organisms used for the production of restriction enzymes and the
AB  - various properties of these enzymes is such that it is difficult to devise a
AB  - purification scheme of general application.  the combination of
AB  - polyethyleneimine precipitation and chromatography on heparin-agarose discussed
AB  - in this article has a sufficiently wide applicability and a number of
AB  - advantages to recommend it as the backbone of a general purification scheme or
AB  - as a first approach in the isolation of new restriction endonuclease
AB  - activities.  In individual cases, however, additions or modifications of this
AB  - procedure are necessary to optimize the results.  In this article we will first
AB  - present the basic procedure and then discuss alternatives or modifications
AB  - suitable to certain particular cases.
ER  -

TY  - JOUR
AU  - Pitluck, S. et al.
TI  - Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 108
EP  - 116
VL  - 3
AB  - Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus
AB  - Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic,
AB  - barophilic, chemoorganotrophic thermophile is characterized by straight to curved
AB  - Gram-negative rods. The strain described in this study was isolated from a core
AB  - sample of deep sea sediments of the Peruvian high productivity upwelling system.
AB  - This is the first completed genome sequence of a member of the genus
AB  - Thermosediminibacter and the seventh genome sequence in the family
AB  - Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285
AB  - protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Pitluck, S. et al.
TI  - Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 285
EP  - 293
VL  - 3
AB  - Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which
AB  - belongs to the family Synergistaceae. The species is of
AB  - interest because it is an asaccharolytic chemoorganotrophic bacterium which
AB  - ferments quite a number of amino acids. This is the first finished genome
AB  - sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and
AB  - the third sequence from the family Synergistaceae. The 2,630,120 bp long genome
AB  - with its 2,433 protein-coding and 61 RNA genes is a part of the
AB  - GenomicEncyclopedia ofBacteria andArchaea project.
ER  -

TY  - JOUR
AU  - Pitluck, S. et al.
TI  - Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 54
EP  - 62
VL  - 4
AB  - Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus
AB  - Calditerrivibrio. The species is of interest because of its important role in the
AB  - nitrate cycle as nitrate reducer and for its isolated phylogenetic position in
AB  - the Tree of Life. Here we describe the features of this organism, together with
AB  - the complete genome sequence and annotation. This is the third complete genome
AB  - sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long
AB  - genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pitsikas, P.
AU  - Cupples, C.
TI  - Effects of increasing DCM expression on Vsr repair of site specific and related sequences.
JO  - FASEB J.
PY  - 1997
SP  - A1369
EP  - A1369
VL  - 11
AB  - DCM, the only cytosine methylase in Escherichia coli, methylates the second cytosine of this
AB  - specific site: CCAGG.  However, overexpression of dcm leads to methylation of other related
AB  - sequences as well.  5-methylcytosine spontaneously deaminates to thymine.  Vsr repairs T/G
AB  - mismatches, and restores the cytosine both at CTAGG sites and at related sequences.  Our
AB  - experiments aim to demonstrate what sequences are methylated by Dcm and which ones are
AB  - repaired by Vsr, and show if there is overlap between the two.  We have regulated the
AB  - expression of Dcm by placing dcm under the PBAD promoter and by varying the concentration of
AB  - arabinose from 0% to 0.2%.  The results showed variation over 3 orders of magnitude in Dcm
AB  - expression.  Further work will be done to analyze Vsr repair.
ER  -

TY  - JOUR
AU  - Pitsikas, P.
AU  - Cupples, C.G.
TI  - Fate of Dcm cytosine methylase after treatment of Escherichia coli with 5-Azacytidine.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1999
SP  - 334
EP  - 334
VL  - 99
AB  - 5-azacytidine is a chemotherapeutic agent used in the treatment of leukemia.  When
AB  - incorporated into DNA as 5-azacytosine, it causes C-to-G transversion mutations.  In addition,
AB  - when it replaces cytosine in methylase recognition sites, transfer of the methyl group cannot
AB  - take place, and the enzyme remains covalently bound to the DNA.  The resulting inactivation of
AB  - the methyltransferase leads to DNA demethylation.  We are interested in determining how the
AB  - DNA-methylase complexes are removed, how the DNA is repaired, and what becomes of the enzyme.
AB  - As a first step, we have made an antibody to Dcm, the sole cytosine methylase in Escherichia
AB  - coli, and used it to quantify the levels of free protein present in the cells after treatment
AB  - with 5-azacytidine.  We find that levels of analog which are sufficient to cause an increase
AB  - in C-to-G mutations result in a large reduction in the amount of Dcm.  The levels of an
AB  - enzymatically inactive mutant are unaffected.  Transcription of the dcm gene is apparently not
AB  - autoregulated.  We are currently combining western analysis with Southern analysis to
AB  - determine the fate of the DNA/protein complexes.
ER  -

TY  - JOUR
AU  - Pitt, M.E.
AU  - Elliott, A.G.
AU  - Cao, M.D.
AU  - Ganesamoorthy, D.
AU  - Karaiskos, I.
AU  - Giamarellou, H.
AU  - Abboud, C.S.
AU  - Blaskovich, M.A.
AU  - Cooper, M.A.
AU  - Coin, L.J.
TI  - Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae.
JO  - Microbial Genomics
PY  - 2018
SP  - 0
EP  - 0
VL  - 0
AB  - Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high
AB  - mortality and are disseminating globally. Identifying the genetic basis
AB  - underpinning resistance allows for rapid diagnosis and treatment. XDR isolates
AB  - sourced from Greece and Brazil, including 19 polymyxin-resistant and five
AB  - polymyxin-susceptible strains, were subjected to whole genome sequencing.
AB  - Seventeen of the 19 polymyxin-resistant isolates harboured variations upstream or
AB  - within mgrB. The most common mutation identified was an insertion at nucleotide
AB  - position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13
AB  - in one ST11 isolate. Three strains acquired an IS1 element upstream of mgrB and
AB  - another strain had an ISKpn25 insertion at 133 bp. Other isolates had truncations
AB  - (C28STOP, Q30STOP) or a missense mutation (D29E) affecting mgrB. Complementation
AB  - assays revealed all mgrB perturbations contributed to resistance. Missense
AB  - mutations in phoQ (T281M, G385C) were also found to facilitate resistance.
AB  - Several variants in phoPQ co-segregating with the ISKpn26-like insertion were
AB  - identified as potential partial suppressor mutations. Three ST258 samples were
AB  - found to contain subpopulations with different resistance-conferring mutations,
AB  - including the ISKpn26-like insertion colonizing with a novel mutation in pmrB
AB  - (P158R), both confirmed via complementation assays. These findings highlight the
AB  - broad spectrum of chromosomal modifications which can facilitate and regulate
AB  - resistance against polymyxins in K. pneumoniae.
ER  -

TY  - JOUR
AU  - Pittard, J.
TI  - Effect of phage-controlled restriction on genetic links in bacterial crosses.
JO  - J. Bacteriol.
PY  - 1964
SP  - 1256
EP  - 1257
VL  - 87
AB  - Arber and Dussoix (J. Mol. Biol. 5:18, 1962) demonstrated that
AB  - lambda-bacteriophage, when grown on Escherichia coli K-12, plates with an
AB  - efficiency of 1 on E. coli K-12 but with an efficiency of only 2 X 10-5 on E.
AB  - coli K-12 (P1) which is lysogenic for bacteriophage Pl.  They showed that the
AB  - low efficiency of plating is a result of the breakdown of the
AB  - lambda-deoxyribonucleic acid (DNA) injected into the Pl lysogenic host. The
AB  - present paper reports some studies of recombination between a P1 sensitive Hfr,
AB  - AB2229, and a P1 lysogenic recipient, AB2147, in which two effects of
AB  - restriction on the recovery of recombinants were observed.
ER  -

TY  - JOUR
AU  - Pittet, V.
AU  - Abegunde, T.
AU  - Marfleet, T.
AU  - Haakensen, M.
AU  - Morrow, K.
AU  - Jayaprakash, T.
AU  - Schroeder, K.
AU  - Trost, B.
AU  - Byrns, S.
AU  - Bergsveinson, J.
AU  - Kusalik, A.
AU  - Ziola, B.
TI  - Complete Genome Sequence of the Beer Spoilage Organism Pediococcus claussenii ATCC BAA-344T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1271
EP  - 1272
VL  - 194
AB  - Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and
AB  - plasmids of the type strain P. claussenii ATCC BAA-344. A ropy
AB  - variant was chosen for sequencing to obtain genetic information related to growth
AB  - in beer, as well as exopolysaccharide and possibly biofilm formation by this
AB  - organism.
ER  -

TY  - JOUR
AU  - Pittet, V.
AU  - Ewen, E.
AU  - Bushell, B.R.
AU  - Ziola, B.
TI  - Genome Sequence of Lactobacillus rhamnosus ATCC 8530.
JO  - J. Bacteriol.
PY  - 2012
SP  - 726
EP  - 726
VL  - 194
AB  - Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for
AB  - probiotics. We became interested in L. rhamnosus isolate
AB  - ATCC 8530 in relation to beer spoilage and hops resistance. We report here
AB  - the genome sequence of this isolate, along with a brief comparison to
AB  - other available L. rhamnosus genome sequences.
ER  -

TY  - JOUR
AU  - Piya, D.
AU  - Vara, L.
AU  - Russell, W.K.
AU  - Young, R.
AU  - Gill, J.J.
TI  - The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis.
JO  - Mol. Microbiol.
PY  - 2017
SP  - 399
EP  - 412
VL  - 105
AB  - Bacterial Type I restriction-modification (R-M) systems present a major barrier to foreign DNA
AB  - entering the bacterial cell. The temperate phage P1 packages
AB  - several proteins into the virion that protect the phage DNA from host
AB  - restriction. Isogenic P1 deletion mutants were used to reconstitute the
AB  - previously described restriction phenotypes associated with darA and darB. While
AB  - P1DeltadarA and P1DeltadarB produced the expected phenotypes, deletions of
AB  - adjacent genes hdf and ddrA also produced darA-like phenotypes and deletion of
AB  - ulx produced a darB-like phenotype, implicating several new proteins of
AB  - previously unknown function in the P1 dar antirestriction system. Interestingly,
AB  - disruption of ddrB decreased P1's sensitivity to EcoB and EcoK restriction.
AB  - Proteomic analysis of purified virions suggests that packaging of antirestriction
AB  - components into P1 virions follows a distinct pathway that begins with the
AB  - incorporation of DarA and Hdf and concludes with DarB and Ulx. Electron
AB  - microscopy analysis showed that hdf and darA mutants also produce abnormally high
AB  - proportions of virions with aberrant small heads, which suggests Hdf and DarA
AB  - play a role in capsid morphogenesis. The P1 antirestriction system is more
AB  - complex than previously realized and is comprised of multiple proteins including
AB  - DdrA, DdrB, Hdf, and Ulx in addition to DarA and DarB.
ER  -

TY  - JOUR
AU  - Planet, P.J. et al.
TI  - Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.
JO  - J. Infect. Dis.
PY  - 2015
SP  - 1874
EP  - 1882
VL  - 212
AB  - BACKGROUND: The community-associated methicillin-resistant Staphylococcus aureus
AB  - (CA-MRSA) epidemic in the United States is attributed to the spread of the USA300
AB  - clone. An epidemic of CA-MRSA closely related to USA300 has occurred in northern
AB  - South America (USA300 Latin-American variant, USA300-LV). Using phylogenomic
AB  - analysis, we aimed to understand the relationships between these 2 epidemics.
AB  - METHODS: We sequenced the genomes of 51 MRSA clinical isolates collected between
AB  - 1999 and 2012 from the United States, Colombia, Venezuela, and Ecuador.
AB  - Phylogenetic analysis was used to infer the relationships and times since the
AB  - divergence of the major clades. RESULTS: Phylogenetic analyses revealed 2
AB  - dominant clades that segregated by geographical region, had a putative common
AB  - ancestor in 1975, and originated in 1989, in North America, and in 1985, in South
AB  - America. Emergence of these parallel epidemics coincides with the independent
AB  - acquisition of the arginine catabolic mobile element (ACME) in North American
AB  - isolates and a novel copper and mercury resistance (COMER) mobile element in
AB  - South American isolates. CONCLUSIONS: Our results reveal the existence of 2
AB  - parallel USA300 epidemics that shared a recent common ancestor. The simultaneous
AB  - rapid dissemination of these 2 epidemic clades suggests the presence of shared,
AB  - potentially convergent adaptations that enhance fitness and ability to spread.
ER  -

TY  - JOUR
AU  - Planet, P.J.
AU  - Rampersaud, R.
AU  - Hymes, S.R.
AU  - Whittier, S.
AU  - Della-Latta, P.A.
AU  - Narechania, A.
AU  - Daugherty, S.C.
AU  - Santana-Cruz, I.
AU  - Desalle, R.
AU  - Ravel, J.
AU  - Ratner, A.J.
TI  - Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1.
JO  - Genome Announcements
PY  - 2013
SP  - e00117
EP  - e00112
VL  - 1
AB  - Streptococcus intermedius is a human pathogen with a propensity for abscess formation. We
AB  - report a high-quality draft genome sequence of S. intermedius strain BA1, an isolate from a
AB  - human epidural abscess. This sequence provides insight into the biology of S. intermedius and
AB  - will aid investigations of pathogenicity.
ER  -

TY  - JOUR
AU  - Platonov, M.E.
AU  - Blouin, Y.
AU  - Evseeva, V.V.
AU  - Afanas'ev, M.V.
AU  - Pourcel, C.
AU  - Balakhonov, S.V.
AU  - Vergnaud, G.
AU  - Anisimov, A.P.
TI  - Draft Genome Sequences of Five Yersinia pseudotuberculosis ST19 Isolates and One  Isolate Variant.
JO  - Genome Announcements
PY  - 2013
SP  - e00122
EP  - e00113
VL  - 1
AB  - We report the first draft genome sequences of five Yersinia pseudotuberculosis isolates of
AB  - sequence type (ST) 19 and of a variant from one of the five isolates.
AB  - The total length of assemblies ranged from 4,226,485 bp to 4,274,148 bp,
AB  - including between 3,808 and 3,843 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Pleska, M.
AU  - Qian, L.
AU  - Okura, R.
AU  - Bergmiller, T.
AU  - Wakamoto, Y.
AU  - Kussell, E.
AU  - Guet, C.C.
TI  - Bacterial Autoimmunity Due to a Restriction-Modification System.
JO  - Curr. Biol.
PY  - 2016
SP  - 404
EP  - 409
VL  - 26
AB  - Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of
AB  - self/non-self discrimination in prokaryotes [1], which
AB  - protects hosts from exogenous DNA [2]. The mechanism is based on the balance
AB  - between methyltransferase (M) and cognate restriction endonuclease (R). M tags
AB  - endogenous DNA as self by methylating short specific DNA sequences called
AB  - restriction sites, whereas R recognizes unmethylated restriction sites as
AB  - non-self and introduces a double-stranded DNA break [3]. Restriction sites are
AB  - significantly underrepresented in prokaryotic genomes [4-7], suggesting that the
AB  - discrimination mechanism is imperfect and occasionally leads to autoimmunity due
AB  - to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote
AB  - DNA recombination [9] and contribute to genetic variation in microbial
AB  - populations, thus facilitating adaptive evolution [10]. However, cleavage of
AB  - self-DNA by RM systems as elements shaping prokaryotic genomes has not been
AB  - directly detected, and its cause, frequency, and outcome are unknown. We quantify
AB  - self-restriction caused by two RM systems of Escherichia coli and find that, in
AB  - agreement with levels of restriction site avoidance, EcoRI, but not EcoRV,
AB  - cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process,
AB  - which temporarily induces the SOS response, and is followed by DNA repair,
AB  - maintaining cell viability. We find that RM systems with higher restriction
AB  - efficiency against bacteriophage infections exhibit a higher rate of
AB  - self-restriction, and that this rate can be further increased by stochastic
AB  - imbalance between R and M. Our results identify molecular noise in RM systems as
AB  - a factor shaping prokaryotic genomes.
ER  -

TY  - JOUR
AU  - Plessis, A.
AU  - Perrin, A.
AU  - Haber, J.E.
AU  - Dujon, B.
TI  - Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus.
JO  - Genetics
PY  - 1992
SP  - 451
EP  - 460
VL  - 130
AB  - The Saccharomyces cerevisiae mitochondrial endonuclease I-SceI creates a double-strand break
AB  - as the initiating step in the gene conversional transfer of the omega+ intron to omega- DNA.
AB  - We have expressed a glactose-inducible synthetic I-SceI gene in the nucleus of yeast that also
AB  - carries the I-SceI recognition site on a plasmid substrate.  We find that the
AB  - galactose-induced I-SceI protein can be active in the nucleus and efficiently catalyze
AB  - recombination.  With a target plasmid containing direct repeats of the Escherichia coli lacZ
AB  - gene, one copy of which is interrupted by a 24-bp cutting site, galactose induction produces
AB  - both deletions and gene conversions.  Both the kinetics and the proportion of deletions and
AB  - gene conversions are very similar to analogous events initiated by a galactose-inducible HO
AB  - endonuclease gene.  We also find that, in a rad52 mutant strain, the repair of double-strand
AB  - breaks initiated by I-SceI and by HO are similarly affected: the formation of deletions is
AB  - reduced, but not eliminated.  Altogether, these results suggest either that the two
AB  - endonucleases act in the same way after double-strand break formation or that the two
AB  - endonucleases are not involved in subsequent steps.
ER  -

TY  - JOUR
AU  - Pljevaljcic, G.
AU  - Pignot, M.
AU  - Weinhold, E.
TI  - Design of a new fluorescent cofactor for DNA methyltransferases and sequence-specific labeling of DNA.
JO  - J. Am. Chem. Soc.
PY  - 2003
SP  - 3486
EP  - 3492
VL  - 125
AB  - Sequence-specific labeling of DNA is of immense interest for analytical and functional studies
AB  - of DNA. We present a novel approach for
AB  - sequence-specific labeling of DNA using a newly designed fluorescent
AB  - cofactor for the DNA methyltransferase from Thermus aquaticus (M.TaqI).
AB  - Naturally, M.TaqI catalyzes the nucleophilic attack of the exocyclic amino
AB  - group of adenine within the double-stranded 5'-TCGA-3' DNA sequence onto
AB  - the methyl group of the cofactor S-adenosyl-L-methionine (AdoMet) leading
AB  - to methyl group transfer. The design of a new fluorescent cofactor for
AB  - covalent labeling of DNA was based on three criteria: (1) Replacement of
AB  - the methionine side chain of the natural cofactor AdoMet by an aziridinyl
AB  - residue leads to M.TaqI-catalyzed nucleophilic ring opening and coupling
AB  - of the whole nucleoside to DNA. (2) The adenosyl moiety is the molecular
AB  - anchor for cofactor binding. (3) Attachment of a fluorophore via a
AB  - flexible linker to the 8-position of the adenosyl moiety does not block
AB  - cofactor binding. According to these criteria the new fluorescent cofactor
AB  - 8-amino[1'-(N'-dansyl)-4'-aminobutyl]-5'-(1-aziridinyl)-5'-deoxyadenosi
AB  - ne (3) was synthesized. 3 binds about 4-fold better than the natural
AB  - cofactor AdoMet to M.TaqI and is coupled with a short duplex
AB  - oligodeoxynucleotide by M.TaqI. The identity of the expected modified
AB  - nucleoside was verified by electrospray ionization mass spectrometry after
AB  - enzymatic fragmentation of the product duplex. In addition, the new
AB  - cofactor 3 was used to sequence-specifically label plasmid DNA in a
AB  - M.TaqI-catalyzed reaction.
ER  -

TY  - JOUR
AU  - Pljevaljcic, G.
AU  - Schmidt, F.
AU  - Peschlow, A.
AU  - Weinhold, E.
TI  - Sequence-specific DNA labeling using methyltransferases.
JO  - Methods Mol. Biol.
PY  - 2004
SP  - 145
EP  - 161
VL  - 283
AB  - Sequence-specific labeling of native deoxyribonucleic acid (DNA) still represents a
AB  - more-or-less unsolved problem. Difficulties mainly arise from
AB  - the necessity to combine two different functions: sequence-specific
AB  - recognition of DNA and covalent bond formation between the label and DNA.
AB  - DNA methyltransferases (MTases) naturally possess these two functions and
AB  - transfer a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet)
AB  - to adenine or cytosine residues within specific DNA sequences, typically
AB  - ranging from two to eight base pairs. Unfortunately, the methyl group
AB  - itself is a very limited reporter group and it would be desirable to
AB  - transfer larger chemical entities with DNA MTases. Replacement of the
AB  - methionine side chain of the natural cofactor AdoMet by an aziridinyl
AB  - residue leads to the synthetic cofactor N-adenosylaziridine, which is
AB  - quantitatively, base- and sequence-specifically coupled with DNA in a DNA
AB  - MTase-catalyzed reaction. By attaching interesting reporter groups to a
AB  - suitable position of N-adenosylaziridine a large variety of new synthetic
AB  - cofactors are obtained for sequence-specific labeling of DNA. This method
AB  - is illustrated by coupling primary amino groups and biotin to short duplex
AB  - oligodeoxynucleotides or plasmid DNA using the DNA MTase M.TaqI.
ER  -

TY  - JOUR
AU  - Pljevaljcic, G.
AU  - Schmidt, F.
AU  - Scheidig, A.J.
AU  - Lurz, R.
AU  - Weinhold, E.
TI  - Quantitative labeling of long plasmid DNA with nanometer precision.
JO  - Chembiochem
PY  - 2007
SP  - 1516
EP  - 1519
VL  - 8
ER  -

TY  - JOUR
AU  - Pljevaljcic, G.
AU  - Schmidt, F.
AU  - Weinhold, E.
TI  - Sequence-specific methyltransferase-induced labeling of DNA (SMILing DNA).
JO  - Chembiochem
PY  - 2004
SP  - 265
EP  - 269
VL  - 5
AB  - A new concept for sequence-specific labeling of DNA by using chemically modified cofactors for
AB  - DNA methyltransferases is presented. Replacement
AB  - of the amino acid side chain of the natural cofactor
AB  - S-adenosyl-L-methionine with an aziridine group leads to a cofactor
AB  - suitable for DNA methyltransferase-catalyzed sequence-specific coupling
AB  - with DNA. Sequence-specifically fluorescently labeled plasmid DNA was
AB  - obtained by using the DNA methyltransferase from Thermus aquaticus
AB  - (M.TaqI) as catalyst and attaching a fluorophore to the aziridine
AB  - cofactor. First results suggest that all classes of DNA
AB  - methyltransferases with different recognition sequences can be used. In
AB  - addition, this novel method for DNA labeling should be applicable to a
AB  - wide variety of reporter groups.
ER  -

TY  - JOUR
AU  - Plugge, C.M.
AU  - Henstra, A.M.
AU  - Worm, P.
AU  - Swarts, D.C.
AU  - Paulitsch-Fuchs, A.H.
AU  - Scholten, J.C.
AU  - Lykidis, A.
AU  - Lapidus, A.L.
AU  - Goltsman, E.
AU  - Kim, E.
AU  - McDonald, E.
AU  - Rohlin, L.
AU  - Crable, B.R.
AU  - Gunsalus, R.P.
AU  - Stams, A.J.
AU  - McInerney, M.J.
TI  - Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 91
EP  - 106
VL  - 7
AB  - strain MPOB is the best-studied species of the genus . The species is of interest because of
AB  - its anaerobic syntrophic lifestyle, its involvement in the conversion
AB  - of propionate to acetate, H and CO during the overall degradation of organic
AB  - matter, and its release of products that serve as substrates for other
AB  - microorganisms. The strain is able to ferment fumarate in pure culture to CO and
AB  - succinate, and is also able to grow as a sulfate reducer with propionate as an
AB  - electron donor. This is the first complete genome sequence of a member of the
AB  - genus and a member genus in the family . Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 4,990,251 bp long genome with its 4,098 protein-coding and 81 RNA genes is a part
AB  - of the Microbial Genome Program (MGP) and the Genomes to Life (GTL) Program
AB  - project.
ER  -

TY  - JOUR
AU  - Plumbridge, J.
TI  - The role of dam methylation in controlling gene expression.
JO  - Biochimie
PY  - 1987
SP  - 439
EP  - 443
VL  - 69
AB  - The E. coli gene dam encodes an adenine-specific methylase which converts all adenine residues
AB  - in the sequence GATC into 6-methyl adenine. dam type methylases seem to be ubiquitous in
AB  - Enterobacteriaceae and Haemophilus, since DNA from these strains cross hybridizes with the
AB  - cloned dam gene and they contain DNA resistant to MboI cleavage, which only cleaves
AB  - non-methylated DNA. However, dam methylation is absent from most species of eubacteria not
AB  - phylogenetically related to E. coli and presumably evolved late in prokaryotic evolution. At
AB  - least, one reason why people have become more aware of dam (and dcm) methylation in the last
AB  - decade is because certain restriction enzymes are sensitive to DNA methylation and hence
AB  - overlapping dam and restriction sites are not cleaved. A third phenotype for the dam mutations
AB  - has been described in the literature: that of controlling the level of expression of a
AB  - miscellaneous selection of genes with GATC sequences in their promoter regions. It is this
AB  - third phenotype which is the subject of this paper, but initially it is worth summarizing the
AB  - evidence for the dam methylation affecting other phenotypes of the E. coli bacteria.
ER  -

TY  - JOUR
AU  - Plumed-Ferrer, C.
AU  - Gazzola, S.
AU  - Fontana, C.
AU  - Bassi, D.
AU  - Cocconcelli, P.S.
AU  - von Wright, A.
TI  - Genome Sequence of Lactococcus lactis subsp. cremoris Mast36, a Strain Isolated from Bovine Mastitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00449
EP  - e00415
VL  - 3
AB  - The genome sequence of Lactococcus lactis subsp. cremoris Mast36, isolated from bovine
AB  - mastitis, is reported here. This strain was shown to be able to grow in
AB  - milk and still possess genes of vegetable origin. The genome also contains a
AB  - cluster of genes associated with pathogenicity.
ER  -

TY  - JOUR
AU  - Plunkett, G. III
AU  - Rose, D.J.
AU  - Durfee, T.J.
AU  - Blattner, F.R.
TI  - Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product.
JO  - J. Bacteriol.
PY  - 1999
SP  - 1767
EP  - 1778
VL  - 181
AB  - Lysogenic bacteriophages are major vehicles for the transfer of genetic
AB  - information between bacteria, including pathogenicity and/or virulence
AB  - determinants. In the enteric pathogen Escherichia coli O157:H7, which
AB  - causes hemorrhagic colitis and hemolytic-uremic syndrome, Shiga toxins 1
AB  - and 2 (Stx1 and Stx2) are phage encoded. The sequence and analysis of the
AB  - Stx2 phage 933W is presented here. We find evidence that the toxin genes
AB  - are part of a late-phage transcript, suggesting that toxin production may
AB  - be coupled with, if not dependent upon, phage release during lytic growth.
AB  - Another phage gene, stk, encodes a product resembling eukaryotic
AB  - serine/threonine protein kinases. Based on its position in the sequence,
AB  - Stk may be produced by the prophage in the lysogenic state, and, like the
AB  - YpkA protein of Yersinia species, it may interfere with the signal
AB  - transduction pathway of the mammalian host. Three novel tRNA genes present
AB  - in the phage genome may serve to increase the availability of rare tRNA
AB  - species associated with efficient expression of pathogenicity
AB  - determinants: both the Shiga toxin and serine/threonine kinase genes
AB  - contain rare isoleucine and arginine codons. 933W also has homology to
AB  - lom, encoding a member of a family of outer membrane proteins associated
AB  - with virulence by conferring the ability to survive in macrophages, and
AB  - bor, implicated in serum resistance.
ER  -

TY  - JOUR
AU  - Poch, M.T.
AU  - Somkuti, G.A.
TI  - Detection of restriction endonuclease activity in Streptococcus thermophilus ST132.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1993
SP  - 330
EP  - 330
VL  - 93
AB  - Genetic development of Streptococcus thermophilus (ST), an important industrial bacterium in
AB  - dairy fermentations, requires the understanding of enzymes that influence the survival and
AB  - replication of transforming DNAs. We have detected a new restriction endonuclease (R-ENase),
AB  - designated as Sth132I, in sonically disrupted cell extracts of strain ST132. Ion exchange
AB  - chromatography (DEAE-cellulose) of crude extracts with a continuous salt gradient resolved
AB  - Sth132I (50-100mM Kcl) and nonspecific exonucleases which coprecipitated by ammonium sulfate
AB  - fractionation. Sth132I had several recognition sites on PhiX174 (5.38 kbp), a single site each
AB  - on pVA736 (7.6 kbp) and pERB (2.2 kbp) but failed to digest pBR322 (4.36 kbp) and lambda DNA.
AB  - Single, double and triple digestions performed on the model pER8 (a native plasmid of ST108)
AB  - allowed tentative positioning of the Sth132I recognition sie at coordinate 0.22 kbp but the
AB  - enzyme was not identifiable as one of the known single-restriction R-NEses. Sth132I required
AB  - Mg++ and retained activity up to 55oC.
ER  -

TY  - JOUR
AU  - Poch, M.T.
AU  - Somkuti, G.A.
TI  - Isolation of SagI, a new HaeIII isoschizomer from Streptococcus agalactiae.
JO  - Appl. Microbiol. Biotechnol.
PY  - 1995
SP  - 282
EP  - 284
VL  - 43
AB  - A new HaeIII isoschizomer from Streptococcus agalactiae was isolated by a single-step
AB  - purification method. The highly active restriction endonuclease, SagI, was free of nonspecific
AB  - nuclease activity and was suitable for use in molecular biology procedures. The rapid
AB  - isolation procedure may be applicable for the recovery of other restriction endonucleases from
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Poch, M.T.
AU  - Somkuti, G.A.
TI  - Rapid isolation of restriction endonucleases from Streptococci.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 385
EP  - 385
VL  - 94
AB  - Streptococcus thermophilus can be genetically-engineered to favorably alter characteristics of
AB  - fermented dairy products.  However, endogeneous restriction-modification systems in these
AB  - bacteria can influence the survival and replication of transforming DNAs. A rapid, microscale
AB  - Heparin Sepharose CL-6B affinity gel procedure was developed for detection of restriction
AB  - endonucleases (RE-Nases) in S. thermophilus and other Streptococcus species.
AB  - RE-Nase-containing extracts free of DNA, RNA and nonspecific nuclease activity were produced
AB  - for forty or more strains daily. RE-Nase activity was detected in 10 of 44 strains of
AB  - Streptococci assayed.        	SagI, a new isoschizomer of HaeIII was purified using this
AB  - single-step method from S. agalactiae. This highly active isoschizomer (12,000 U/g of dry
AB  - cells) was free of nonspecific nuclease activity and was suitable for use in molecular biology
AB  - procedures. The isolation procedures was applicable for the rapid isolation of RE-Nases from
AB  - other lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Poch, M.T.
AU  - Somkuti, G.A.
TI  - Rapid screening of lactic acid bacteria for restriction endonuclease activity.
JO  - Biotechnol. Tech.
PY  - 1993
SP  - 781
EP  - 784
VL  - 7
AB  - A rapid microscale heparin Sepharose CL-6B affinity gel procedure was developed for detecting
AB  - restriction endonuclease (RE-Nase) activity in a variety of lactic acid bacteria.
AB  - Re-Nase-containing extracts free of DNA, RNA and nonspecific nuclease activity can be produced
AB  - for forty or more strains daily and only 10-12 ml of each log phase culture as required for
AB  - screening. RE-Nase activity was tested in several streptococci and lactobacilli. With
AB  - appropriate modifications, this procedure should allow rapid detection of RE-Nase activity in
AB  - other bacterial species.
ER  -

TY  - JOUR
AU  - Poch, M.T.
AU  - Somkuti, G.A.
AU  - Solaiman, D.K.Y.
TI  - Sth132I, a novel class-IIS restriction endonuclease of Streptococcus thermophilus ST132.
JO  - Gene
PY  - 1997
SP  - 201
EP  - 206
VL  - 195
AB  - The Sth132I restriction endonuclease (R.Sth132I) was detected in Streptococcus thermophilus
AB  - ST132 and purified to near homogeneity by heparin Sepharose CL-6B affinity chromatography.
AB  - Fragments from Sth132I digestion of plasmid DNA were subcloned into pUC19 in Escherichia coli
AB  - DH5a and sequenced.  Sequence analysis of inserts and their ligation junction sites revealed
AB  - that Sth132I is a novel class-IIS restriction endonuclease, which recognizes the
AB  - non-palindromic sequence 5'-CCCG(N)4-3' 3'-GGGC(N)8-5'.
ER  -

TY  - JOUR
AU  - Poddar, A.
AU  - Lepcha, R.T.
AU  - Whitman, W.B.
AU  - Das, S.K.
TI  - Draft Genome Sequence of Tepidiphilus thermophilus Strain JHK30T (JCM 19170T) Isolated from a Terrestrial Hot Spring in India.
JO  - Genome Announcements
PY  - 2016
SP  - e00832
EP  - e00816
VL  - 4
AB  - Tepidiphilus thermophilus strain JHK30(T) was isolated from a hot spring at Surajkund,
AB  - Jharkhand, India. It is a Gram-negative rod, nonsporulating, aerobic,
AB  - and motile. The estimated genome is 2.3 Mb, with 2,186 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Podgorska, B.
AU  - Kujawska, G.
AU  - Skurzewski, M.
AU  - Batsko, O.
AU  - Kaczorowski, T.
TI  - A rapid and simple method for detection of type II restriction endonucleases in cells of bacteria with high activity of nonspecific nucleases.
JO  - Acta Biochim. Pol.
PY  - 2012
SP  - 669
EP  - 672
VL  - 59
AB  - In this work we describe a novel, rapid and simple microscale procedure for identification of
AB  - restriction endonuclease activity in bacteria
AB  - lysates, which contain high levels of non-specific DNA nucleases.
ER  -

TY  - JOUR
AU  - Podhajska, A.J.
AU  - Kim, S.C.
AU  - Szybalski, W.
TI  - Conferring new specificities on restriction enzymes: cleavage at any predetermined site by combining adapter oligodeoxynucleotide and Class-IIS enzyme.
JO  - Methods Enzymol.
PY  - 1992
SP  - 303
EP  - 309
VL  - 216
ER  -

TY  - JOUR
AU  - Podhajska, A.J.
AU  - Szybalski, W.
TI  - Conversion of the FokI endonuclease to a universal restriction enzyme:  cleavage of phage M13mp7 DNA at predetermined sites.
JO  - Gene
PY  - 1985
SP  - 175
EP  - 182
VL  - 40
AB  - Endonuclease FokI belongs to class IIS of restriction enzymes, for which the
AB  - DNA cut points lie outside the enzyme-recognition sites.  This permitted
AB  - conferring new cleavage specificities by combining FokI with tailored
AB  - oligodeoxynucleotide adapters.  Such adapters carry a single-stranded (ss)
AB  - target-recognition domain, complementary to the selected ss target DNA, and a
AB  - double-stranded (ds) enzyme-recognition site.  Neither enzyme nor adapter alone
AB  - has endonucleolytic activity toward phage M13mp7 ss DNA, whereas the
AB  - enzyme-adapter complex cleaves this ss target DNA at the particular sites fore
AB  - ordained by the sequence of the ss domain of the adapter.  Two kinds of
AB  - adapters (32 and 34 nucleotides long), with opposing orientations of the
AB  - asymmetric FokI recognition site, were constructed and shown to direct specific
AB  - cleavage under a variety of conditions.  In addition to FokI, other class IIS
AB  - enzymes, HphI, MboII and BbvI, which alone do not cleave ss DNA, are suitable
AB  - for construction of tailored enzyme-adapter complexes with predictable cleavage
AB  - specificities.  This report provides a preliminary experimental confirmation
AB  - for the proposal of Szybalski [Gene 40 (1985) 169-173] for the design of
AB  - adapter-enzyme complexes with novel and predictable specificities.
AB  - Theoretically, using this approach any sequence could be precisely cleaved at a
AB  - predetermined point.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Alghaithi, H.S.
AU  - Chandran, L.
AU  - Chibani, C.M.
AU  - Davydova, E.
AU  - Dhamotharan, K.
AU  - Ge, W.
AU  - Gutierrez-Gutierrez, D.A.
AU  - Jagirdar, A.
AU  - Khonsari, B.
AU  - Nair, K.P.
AU  - Daniel, R.
TI  - First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388.
JO  - Genome Announcements
PY  - 2014
SP  - e00754
EP  - e00714
VL  - 2
AB  - Clostridium litorale is a Gram-positive, rod-shaped, and spore-forming bacterium, which is
AB  - able to use amino acids such as glycine, sarcosine, proline, and betaine
AB  - as single carbon and energy sources via Stickland reactions. The genome consists
AB  - of a circular chromosome (3.41 Mb) and a circular plasmid (27 kb).
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Anbalagan, A.
AU  - Nagel, A.
AU  - Daniel, R.
TI  - First Insight into the Genome Sequence of Clostridium thermobutyricum DSM 4928, a Butyrate-Producing Moderate Thermophile.
JO  - Genome Announcements
PY  - 2017
SP  - e00367
EP  - e00317
VL  - 5
AB  - The moderately thermophilic and Gram-positive bacterium Clostridium thermobutyricum is
AB  - strictly anaerobic and forms subterminally located endospores.
AB  - It was isolated from horse manure compost. C. thermobutyricum produces butyrate
AB  - as the main fermentation product. The draft genome consists of one circular
AB  - chromosome (3.425 Mb) and contains 3,201 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Andreesen, J.R.
AU  - Daniel, R.
TI  - Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953).
JO  - Genome Announcements
PY  - 2014
SP  - e00573
EP  - e00514
VL  - 2
AB  - Eubacterium acidaminophilum is a strictly anaerobic, Gram-positive, rod-shaped
AB  - bacterium which belongs to cluster XI of the Clostridia. It ferments amino acids
AB  - by a Stickland reaction. The genome harbors a chromosome (2.25 Mb) and a
AB  - megaplasmid (0.8 Mb). It contains several gene clusters coding for
AB  - selenocysteine-containing, glycine-derived, and amino acid-degrading reductases.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bandera, A.
AU  - Horne, D.
AU  - Maier, J.
AU  - Pawlowicz, D.
AU  - Siebert, V.
AU  - Daniel, R.
TI  - First Insights into the Genome of the N-Methylhydantoin-Degrading Clostridium sp. Strain FS41 (DSM 6877).
JO  - Genome Announcements
PY  - 2015
SP  - e00394
EP  - e00315
VL  - 3
AB  - Clostridium sp. strain FS41 (DSM 6877) is a strictly anaerobic and Gram-positive
AB  - spindle-shaped rod. This spore-forming bacterium is able to degrade
AB  - N-methylhydantoin, with N-carbamoylsarcosine and sarcosine as intermediates. The
AB  - genome consists of one replicon (6.28 Mb) and harbors 5,735 predicted
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Esser, C.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella  thermoacetica DSM 521T.
JO  - Genome Announcements
PY  - 2015
SP  - e01159
EP  - e01115
VL  - 3
AB  - Here we report the closed genome sequence of the type strain Moorella thermoacetica DSM
AB  - 521(T), an acetogenic bacterium, which is able to grow autotrophically on H2 + CO2 and/or CO,
AB  - using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.53 Mb).
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911T.
JO  - Genome Announcements
PY  - 2016
SP  - e01430
EP  - e01416
VL  - 4
AB  - Here, we report the draft genome sequence of Acetobacterium wieringae DSM 1911T,  an
AB  - anaerobic, autotrophic, acetogenic, d,l-lactate-utilizing bacterium. The genome consists of a
AB  - chromosome (3.88 Mb) and 3,620 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Draft Genome Sequence of Purine-Degrading Gottschalkia purinilyticum (Formerly Clostridium purinilyticum) WA1 (DSM 1384).
JO  - Genome Announcements
PY  - 2015
SP  - e01088
EP  - e01015
VL  - 3
AB  - Here, we report the draft genome sequence of Gottschalkia purinilyticum (formerly Clostridium
AB  - purinilyticum) WA1, an anaerobic bacterium specialized on degradation of purines (including
AB  - adenine) and glycine, which uses the selenoprotein glycine  reductase for substrate
AB  - degradation. The genome consists of a single chromosome (3.40 Mb).
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bengelsdorf, F.R.
AU  - Schiel-Bengelsdorf, B.
AU  - Gottschalk, G.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Complete Genome Sequence of Rnf- and Cytochrome-Containing Autotrophic Acetogen Clostridium aceticum DSM 1496.
JO  - Genome Announcements
PY  - 2015
SP  - e00786
EP  - e00715
VL  - 3
AB  - Here, we report the closed genome sequence of Clostridium aceticum, an Rnf- and
AB  - cytochrome-containing autotrophic acetogen that is able to convert CO2 and H2 to
AB  - acetate using the Wood-Ljungdahl pathway. The genome consists of a circular
AB  - chromosome (4.2 Mbp) and a small circular plasmid (5.7 kbp).
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Berg, A.
AU  - Welsing, G.
AU  - Daniel, R.
TI  - First Insights into the Genome Sequence of the Alkaliphilic Thermotolerant Bacterium Clostridium thermoalcaliphilum JW/YL23-2T.
JO  - Genome Announcements
PY  - 2017
SP  - e00368
EP  - e00317
VL  - 5
AB  - Clostridium thermoalcaliphilum is an obligate anaerobic and rod-shaped bacterium  isolated
AB  - from sewage sludge. It is an alkaliphilic thermotolerant organism and
AB  - utilizes sucrose, glucose, fructose, maltose, cellobiose, amino acids, and
AB  - Casamino Acids as substrates. The draft genome comprises 2.031 Mbp and 2,027
AB  - predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Boer, T.
AU  - Steensen, K.
AU  - Daniel, R.
TI  - Draft Genome Sequence of the Hydrogenogenic Carboxydotroph Moorella stamsii DSM 26271.
JO  - Genome Announcements
PY  - 2018
SP  - e00345
EP  - e00318
VL  - 6
AB  - The spore-forming, thermophilic, and obligate anaerobic bacterium Moorella stamsii was
AB  - isolated from digester sludge. Apart from its ability to use carbon
AB  - monoxide for growth, M. stamsii harbors several enzymes for the use of different
AB  - sugars. The draft genome has a size of 3,329 Mb and contains 3,306 predicted
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bolz, S.
AU  - Fischer, B.
AU  - Daniel, R.
TI  - First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica.
JO  - Genome Announcements
PY  - 2018
SP  - e00334
EP  - e00318
VL  - 6
AB  - Clostridium vincentii is an obligate anaerobic, saccharophilic, psychrophilic, Gram-positive,
AB  - motile, and rod-shaped bacterium. It was isolated from a pond
AB  - sediment of the McMurdo Ice Shelf, Antarctica. C. vincentii produces acetate and
AB  - formate as main fermentation products. The draft genome consists of one
AB  - chromosome (3.506 Mb) with 3,379 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Bremekamp, R.
AU  - Lutz, V.T.
AU  - Schulz, L.M.
AU  - Daniel, R.
TI  - Draft Genome Sequence of the Butanoic Acid-Producing Bacterium Clostridium luticellarii DSM 29923, Used for Strong Aromatic Chinese Liquor Production.
JO  - Genome Announcements
PY  - 2018
SP  - e00377
EP  - e00318
VL  - 6
AB  - The strictly anaerobic, Gram-positive bacterium Clostridium luticellarii, which has straight
AB  - or slightly curved rod-shaped cells, polar endospores, and
AB  - peritrichous flagella, is used for the production of strong aromatic Chinese
AB  - liquors. C. luticellarii is able to produce butanoic acid. The draft genome
AB  - sequence consists of 3.757 Mbp, including 3,632 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Daniel, R.
AU  - Simeonova, D.D.
TI  - Draft Genome Sequence of Desulfotignum phosphitoxidans DSM 13687 Strain FiPS-3.
JO  - Genome Announcements
PY  - 2013
SP  - e00227
EP  - e00213
VL  - 1
AB  - We report the 5.008-Mbp assembled draft genome sequence of Desulfotignum phosphitoxidans
AB  - strain FiPS-3 (DSM 13687), which gains metabolic energy from the
AB  - oxidation of phosphite to phosphate. Its genome provides insights into the
AB  - composition and architecture of the phosphite-utilizing and energy-transducing
AB  - systems required to live with phosphite as electron donor.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Daniel, R.
AU  - Simeonova, D.D.
TI  - Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 100
EP  - 100
VL  - 10
AB  - The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of
AB  - the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft
AB  - genome is arranged into 93 contigs containing 3311 predicted protein-coding and
AB  - 41 RNA-encoding genes. This genome report presents the specific properties and
AB  - common features of P. glucosidilyticus DD6b genome in comparison with the genomes
AB  - of P. glucosidilyticus type strain DSM 23,534, and another five Pedobacter type
AB  - strains with publicly available completely sequenced genomes. Here, we present
AB  - the first journal report on P. glucosidilyticus genome sequence and provide
AB  - information on a new specific physiological determinant of P. glucosidilyticus
AB  - species.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Daniel, R.
AU  - Thurmer, A.
AU  - Bollinger, A.
AU  - Thies, S.
AU  - Katzke, N.
AU  - Jaeger, K.E.
TI  - First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045.<jour_book>Genome Announc.
JO  - 
PY  - 2017
SP  - e00774
EP  - e00717
VL  - 5
AB  - The Gram-negative proteobacterium Pseudomonas oleovorans DSM 1045 is considered a promising
AB  - source for enzymes of biotechnological interest, e.g., hydrolases and
AB  - transaminases. Here, we present a draft sequence of its 4.86-Mb genome, enabling
AB  - the identification of novel biocatalysts.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Deutzmann, J.S.
AU  - Daniel, R.
AU  - Simeonova, D.D.
TI  - Draft Genome Sequence of the Methanotrophic Gammaproteobacterium Methyloglobulus  morosus DSM 22980 Strain KoM1.
JO  - Genome Announcements
PY  - 2013
SP  - e01078
EP  - e01013
VL  - 1
AB  - Here, we report the draft genome sequence of the methanotrophic gammaproteobacterium
AB  - Methyloglobulus morosus DSM 22980 strain KoM1, which is
AB  - proposed to be the type species for the novel genus Methyloglobulus. The genome
AB  - (4.143 Mb) consists of a single circular chromosome and harbors genes for
AB  - 2-aminoethylphosphonate (ciliatine) biosynthesis.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Freese, H.
AU  - Daniel, R.
AU  - Simeonova, D.D.
TI  - Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 14
EP  - 14
VL  - 11
AB  - Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from
AB  - homogenized guts of 4 days starved zooplankton Daphnia magna. Here
AB  - we report the draft genome of this bacterium, which comprises 7,677,812 bp and
AB  - 7505 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Freese, H.M.
AU  - Daniel, R.
AU  - Simeonova, D.D.
TI  - Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna.
JO  - Genome Announcements
PY  - 2014
SP  - e00903
EP  - e00914
VL  - 2
AB  - We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from
AB  - the family Enterobacteriaceae. It was isolated from
AB  - homogenized guts of Daphnia magna. The genome size is 5,274 Mb.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Friedrich, I.
AU  - Kruger, L.
AU  - Daniel, R.
TI  - First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.
JO  - Genome Announcements
PY  - 2016
SP  - e00379
EP  - e00316
VL  - 4
AB  - The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs
AB  - to clostridial cluster I. It was isolated from a hydrothermal vent
AB  - chimney. Substrates utilized by C. tepidiprofundi include casein, peptone,
AB  - tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome
AB  - consists of one replicon (3.06 Mb).
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Funkner, K.
AU  - Schuler, M.A.
AU  - Daniel, R.
TI  - First Insights into the Genome Sequence of the Cellulolytic Bacterium Clostridium hungatei DSM 14427.
JO  - Genome Announcements
PY  - 2017
SP  - e00363
EP  - e00317
VL  - 5
AB  - Clostridium hungatei is an obligate anaerobic and spore-forming bacterium, which  was isolated
AB  - from soil. It ferments carbohydrates, such as cellulose or
AB  - d-glucose. C. hungatei is able to fix nitrogen. The draft genome consists of 1
AB  - chromosome (4.902 Mb) with 4,246 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Galperin, M.Y.
AU  - Andreesen, J.R.
AU  - Daniel, R.
TI  - Genome Sequence of Uric Acid-Fermenting Eubacterium angustum DSM 1989T (MK-1).
JO  - Genome Announcements
PY  - 2017
SP  - e01439
EP  - e01416
VL  - 5
AB  - Eubacterium angustum DSM 1989T (MK-1) is a strictly anaerobic and uric acid-, xanthine-, and
AB  - guanine-fermenting organism isolated from sewage sludge. The draft
AB  - genome consists of one circular chromosome (2.4 Mb) and harbors 2,397 predicted
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Gippert, A.L.
AU  - Bierenbroodspot, M.J.
AU  - Daniel, R.
TI  - First Insights into the Genome Sequence of Clostridium oryzae DSM 28571, Isolated from the Soil of a Japanese Rice Field.
JO  - Genome Announcements
PY  - 2017
SP  - e00539
EP  - e00517
VL  - 5
AB  - Clostridium oryzae was originally isolated from the soil of a Japanese rice field. C. oryzae
AB  - represents a novel species within the genus Clostridium and is
AB  - associated with anaerobic rice straw degradation. Here, we present the draft
AB  - genome sequence of C. oryzae DSM 28571 (5.076 Mbp), containing 4,590 predicted
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Gottschalk, G.
AU  - Daniel, R.
TI  - First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662.
JO  - Genome Announcements
PY  - 2013
SP  - e00734
EP  - e00713
VL  - 1
AB  - The genome of Sporomusa ovata strain H1 DSM 2662, an anaerobic, Gram-negative
AB  - endospore-forming bacterium, was sequenced. S. ovata uses N-methyl compounds,
AB  - primary alcohols, fatty acids, and H2 and CO2 as energy and carbon sources to
AB  - produce acetate. The genome harbors one chromosome, which encodes proteins
AB  - typical for sporulation.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Grosse-Honebrink, A.
AU  - Zhang, Y.
AU  - Minton, N.P.
AU  - Daniel, R.
TI  - Complete Genome Sequence of the Nitrogen-Fixing and Solvent-Producing Clostridium pasteurianum DSM 525.
JO  - Genome Announcements
PY  - 2015
SP  - e01591
EP  - e01514
VL  - 3
AB  - Here, we report on the closed genome sequence of Clostridium pasteurianum DSM 525, which is an
AB  - anaerobic, Gram-positive and endospore-forming organism. C. pasteurianum can fix N2 and
AB  - produce solvents such as butanol and 1,3-propanediol  from carbohydrates. The genome consists
AB  - of a single 4,350,673-bp replicon.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Hartwich, K.
AU  - Krabben, P.
AU  - Ehrenreich, A.
AU  - Liebl, W.
AU  - Durre, P.
AU  - Gottschalk, G.
AU  - Daniel, R.
TI  - Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864).
JO  - Genome Announcements
PY  - 2013
SP  - e00997
EP  - e00913
VL  - 1
AB  - Clostridium saccharobutylicum was employed for the production of acetone and butanol in South
AB  - Africa until the 1970s. The genome comprises a single replicon
AB  - (5,107,814 bp) harboring all the genes necessary for solvent production and the
AB  - degradation of various organic compounds, such as fructose, cellobiose, sucrose,
AB  - and mannose.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Hettwer, E.
AU  - Mohnike, L.
AU  - Daniel, R.
TI  - First Insights into the Genome Sequence of Clostridium thermopalmarium DSM 5974,  a Butyrate-Producing Bacterium Isolated from Palm Wine.
JO  - Genome Announcements
PY  - 2018
SP  - e00338
EP  - e00318
VL  - 6
AB  - Clostridium thermopalmarium is a moderate thermophilic, rod-shaped, and endospore-forming
AB  - bacterium, which was isolated from palm wine in Senegal.
AB  - Butyrate is produced from a broad variety of sugar substrates. Here, we present
AB  - the draft genome sequence of C. thermopalmarium DSM 5974 (2.822 Mb) containing
AB  - 2,665 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Heym, D.
AU  - Quitzke, V.
AU  - Fersch, J.
AU  - Daniel, R.
AU  - Rother, M.
TI  - Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea.
JO  - Genome Announcements
PY  - 2018
SP  - e00237
EP  - e00218
VL  - 6
AB  - Methanococcus maripaludis type strain JJ (DSM 2067) is an important organism because it serves
AB  - as a model for primary energy metabolism and hydrogenotrophic
AB  - methanogenesis and is amenable to genetic manipulation. The complete genome (1.7
AB  - Mb) harbors 1,815 predicted protein-encoding genes, including 9 encoding
AB  - selenoproteins.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Hoche, N.
AU  - Mehr, A.
AU  - Daniel, R.
TI  - First Insights into the Genome of the Cr(VI)-Reducing Bacterium Clostridium chromiireducens DSM 23318.
JO  - Genome Announcements
PY  - 2017
SP  - e00420
EP  - e00417
VL  - 5
AB  - Clostridium chromiireducens is an obligate, anaerobic, Gram-positive, rod-shaped, and
AB  - spore-forming bacterium that is able to reduce Cr(VI). The draft genome
AB  - consists of one chromosome (5,448 Mb) and contains 4,773 predicted
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Hollensteiner, J.
AU  - Granzow, S.
AU  - Wemheuer, B.
AU  - Vidal, S.
AU  - Wemheuer, F.
TI  - First Insights into the Draft Genome Sequence of the Endophyte Paenibacillus amylolyticus Strain GM1FR, Isolated from Festuca rubra L.
JO  - Genome Announcements
PY  - 2018
SP  - e01516
EP  - e01517
VL  - 6
AB  - Paenibacillus amylolyticus strain GM1FR is an endophyte isolated from aerial plant tissues of
AB  - Festuca rubra L. Here, we report the draft genome sequence (7.3
AB  - Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially
AB  - involved in plant growth promotion and biocontrol.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Keyl, A.
AU  - Milsch, J.C.
AU  - Daniel, R.
TI  - Draft Genome Sequence of the Thermophilic Acetogen Moorella humiferrea DSM 23265.
JO  - Genome Announcements
PY  - 2018
SP  - e00357
EP  - e00318
VL  - 6
AB  - Moorella humiferrea is an endospore-forming, anaerobic, and thermophilic bacterium which was
AB  - isolated from a terrestrial hydrothermal spring. M.
AB  - humiferrea is able to use humic acid or 10-anthraquinone-2,6-disulfonate as an
AB  - electron-shuttling compound for growth and Fe(III) reduction. The genome has a
AB  - size of 2.629 Mb and contains 2,668 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Krabben, P.
AU  - Durre, P.
AU  - Daniel, R.
TI  - Complete Genome Sequence of the Solvent Producer Clostridium saccharoperbutylacetonicum Strain DSM 14923.
JO  - Genome Announcements
PY  - 2014
SP  - e01056
EP  - e01014
VL  - 2
AB  - Clostridium saccharoperbutylacetonicum strain DSM 14923 is known as a butanol-producing
AB  - bacterium. Various organic compounds such as glucose, fructose,
AB  - sucrose, mannose, and cellobiose are fermented. The genome consists of one
AB  - chromosome and one circular megaplasmid. C. saccharoperbutylacetonicum was used
AB  - in industrial fermentation processes to produce the solvents acetone, butanol,
AB  - and ethanol.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Kusian, B.
AU  - Friedrich, B.
AU  - Daniel, R.
AU  - Bowien, B.
TI  - Complete genome sequence of the type strain Cupriavidus necator N-1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5017
EP  - 5017
VL  - 193
AB  - Here we announce the complete genome sequence of the copper-resistant bacterium Cupriavidus
AB  - necator N-1, the type strain of the genus
AB  - Cupriavidus. The genome consists of two chromosomes and two circular
AB  - plasmids. Based on genome comparison the chromosomes of C. necator N-1
AB  - share a high degree of similarity with the two chromosomal replicons of
AB  - the bioplastic-producing hydrogen bacterium Ralstonia eutropha H16. The
AB  - two strains differ in their plasmids and the presence of hydrogenase
AB  - genes, which are absent in strain N-1.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Montoya, S.J.D.
AU  - Bengelsdorf, F.R.
AU  - Schiel-Bengelsdorf, B.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Draft Genome Sequence of Purine-Degrading Clostridium cylindrosporum HC-1 (DSM 605).
JO  - Genome Announcements
PY  - 2015
SP  - e00917
EP  - e00915
VL  - 3
AB  - Here, we report the draft genome sequence of Clostridium cylindrosporum HC-1, a purine- and
AB  - glycine-fermenting anaerobe, which uses selenoprotein glycine
AB  - reductase for substrate degradation. The genome consists of a single chromosome
AB  - (2.72 Mb) and a circular plasmid (14.4 kb).
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Mucek, K.
AU  - Enders, M.
AU  - Pankok, F.
AU  - Daniel, R.
TI  - First Insights into the Genome Sequence of the Halophilic Archaeon Halalkalicoccus paucihalophilus (DSM 24557).
JO  - Genome Announcements
PY  - 2016
SP  - e00382
EP  - e00316
VL  - 4
AB  - Halalkalicoccus paucihalophilus is an extremely halophilic, Gram-negative, and nonmotile
AB  - coccus-like archaeon, which was originally isolated from the Lop Nur
AB  - region in the northwest of China. The genome consists of a single replicon (3.98
AB  - Mbp). H. paucihalophilus is able to utilize mannose, which is unique for members
AB  - of this genus.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Najdenski, H.
AU  - Simeonova, D.D.
TI  - Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae ATCC 9621.
JO  - Genome Announcements
PY  - 2017
SP  - e01718
EP  - e01716
VL  - 5
AB  - We present here the 5.561-Mbp assembled draft genome sequence of Klebsiella pneumoniae subsp.
AB  - pneumoniae ATCC 9621, a phosphite- and
AB  - organophosphonate-assimilating Gammaproteobacterium. The genome harbors 5,179
AB  - predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Najdenski, H.
AU  - Simeonova, D.D.
TI  - Draft Genome Sequence of Flavobacterium succinicans Strain DD5b.
JO  - Genome Announcements
PY  - 2017
SP  - e01492
EP  - e01416
VL  - 5
AB  - We present the first 3.315-Mbp assembled draft genome sequence of Flavobacterium  succinicans
AB  - strain DD5b. This bacterium is a phosphite-assimilating
AB  - representative of the genus Flavobacterium isolated from guts of the zooplankton
AB  - Daphnia magna.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Neubauer, H.
AU  - Niemeyer, P.
AU  - Daniel, R.
TI  - First Insight into the Genome Sequence of Clostridium liquoris DSM 100320, a Butyrate- and Ethanol-Producing Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00376
EP  - e00318
VL  - 6
AB  - Clostridium liquoris is a strictly anaerobic, Gram-positive, nonmotile, spore-forming,
AB  - rod-shaped bacterium. The major fermentation products from glucose
AB  - are ethanol and butyrate. C. liquoris was isolated from a 20-year-old liquor
AB  - fermentation pit. The draft genome sequence consists of a chromosome (2.892 Mb)
AB  - harboring 2,788 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Riegel, K.
AU  - Konig, S.M.
AU  - Leimbach, A.
AU  - Daniel, R.
AU  - Durre, P.
TI  - Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 40
EP  - 40
VL  - 10
AB  - Clostridium sporogenes DSM 795 is the type strain of the species Clostridium sporogenes, first
AB  - described by Metchnikoff in 1908. It is a Gram-positive,
AB  - rod-shaped, anaerobic bacterium isolated from human faeces and belongs to the
AB  - proteolytic branch of clostridia. C. sporogenes attracts special interest because
AB  - of its potential use in a bacterial therapy for certain cancer types. Genome
AB  - sequencing and annotation revealed several gene clusters coding for proteins
AB  - involved in anaerobic degradation of amino acids, such as glycine and betaine via
AB  - Stickland reaction. Genome comparison showed that C. sporogenes is closely
AB  - related to C. botulinum. The genome of C. sporogenes DSM 795 consists of a
AB  - circular chromosome of 4.1 Mb with an overall GC content of 27.81 mol% harboring
AB  - 3,744 protein-coding genes, and 80 RNAs.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Schilling, T.
AU  - Bhaskar, S.N.U.
AU  - Daniel, R.
TI  - First Insights into the Draft Genome of Clostridium colicanis DSM 13634, Isolated from Canine Feces.
JO  - Genome Announcements
PY  - 2016
SP  - e00385
EP  - e00316
VL  - 4
AB  - Clostridium colicanis DSM 13634 is a strictly anaerobic, rod-shaped, and spore-forming
AB  - bacterium. It produces acids from common sugars such as glucose and
AB  - fructose. The draft genome consists of one chromosome (2.6 Mbp) and contains
AB  - 2,159 predicted protein-encoding genes.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Schlien, K.
AU  - Chowdhury, N.P.
AU  - Gottschalk, G.
AU  - Buckel, W.
AU  - Daniel, R.
TI  - Complete Genome Sequence of the Amino Acid-Fermenting Clostridium propionicum X2  (DSM 1682).
JO  - Genome Announcements
PY  - 2016
SP  - e00294
EP  - e00216
VL  - 4
AB  - Clostridium propionicumis a strict anaerobic, Gram positive, rod-shaped bacterium that belongs
AB  - to the clostridial cluster XIVb. The genome consists of one replicon
AB  - (3.1 Mb) and harbors 2,936 predicted protein-encoding genes. The genome encodes
AB  - all enzymes required for fermentation of the amino acids alpha-alanine,
AB  - beta-alanine, serine, threonine, and methionine.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Seedorf, H.
TI  - Draft Genome Sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501,   and Methanobrevibacter oralis DSM7256.
JO  - Genome Announcements
PY  - 2016
SP  - e00617
EP  - e00616
VL  - 4
AB  - Here, the draft genome sequences of four different Methanobrevibacter species are presented.
AB  - Three of the Methanobrevibacter species (M. curvatus, M. cuticularis,
AB  - and M. filiformis) have been isolated from the termite hindgut, while M. oralis
AB  - was isolated from human subgingival plaque.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Wubbeler, J.H.
AU  - Daniel, R.
AU  - Steinbuchel, A.
TI  - Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029.
JO  - Genome Announcements
PY  - 2017
SP  - e00889
EP  - e00817
VL  - 5
AB  - Sphingomonas mucosissima and Sphingomonas dokdonensis are Gram-negative chemoheterotrophic
AB  - strictly aerobic rods or cocci. The genomes (3.453 Mb and
AB  - 3.587 Mb, respectively) contain 3,279 and 3,329 predicted protein-encoding genes,
AB  - respectively. The genome of S. dokdonensis harbors a 90-kb plasmid.
ER  -

TY  - JOUR
AU  - Poehlein, A.
AU  - Zverlov, V.V.
AU  - Daniel, R.
AU  - Schwarz, W.H.
AU  - Liebl, W.
TI  - Complete Genome Sequence of Clostridium stercorarium subsp. stercorarium Strain DSM 8532, a Thermophilic Degrader of Plant Cell Wall Fibers.
JO  - Genome Announcements
PY  - 2013
SP  - e0007313
EP  - e0007313
VL  - 1
AB  - Clostridium stercorarium strain DSM 8532 is a thermophilic bacterium capable of efficiently
AB  - degrading polysaccharides in plant biomass and converting the
AB  - resulting sugars to ethanol and acetate. The complete genome sequence of 2.96 Mbp
AB  - reveals a multitude of genes for hydrolytic enzymes and enables further study of
AB  - the organism and its enzymes, and their exploitation for biotechnological
AB  - processes.
ER  -

TY  - JOUR
AU  - Pogge von Strandmann, R.
AU  - Stadtler, R.
AU  - Walter, T.
AU  - Frey, B.
AU  - Kaluza, K.
AU  - Hengstenberg, W.
AU  - Schmitz, G.
TI  - BpuAI, a novel BbsI and BbvII isoschizomer from Bacillus pumilus recognizing 5'-GAAGAC-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4664
EP  - 4664
VL  - 20
AB  - We have isolated BpuAI, a novel class-IIs restriction endonuclease from Bacillus pumilus
AB  - recognizing the sequence 5'-GAAGAC-3', cutting at N2-3' and N6-5'. High amounts of
AB  - activity can be purified due to a fast protocol and the presence of high amounts of specific
AB  - activity in the crude extract.
ER  -

TY  - JOUR
AU  - Pogolotti, A.L.
AU  - Ono, A.
AU  - Subramaniam, R.
AU  - Santi, D.V.
TI  - On the mechanism of DNA-adenine methylase.
JO  - J. Biol. Chem.
PY  - 1988
SP  - 7461
EP  - 7464
VL  - 263
AB  - Experiments were performed to determine whether EcoRI methylase catalyzes the
AB  - transfer of the methyl group of S-adenosylmethionine (a) directly to the N6 of
AB  - adenine in DNA or (b) initially to N1 to give N1-methyladenine followed by
AB  - isomerization of the N1-methylamino and 6-NH2 to give N6-methyladenine (Dimroth
AB  - rearrangement).  A facile synthesis of highly enriched [6-15N]deoxyadenosine
AB  - and a dodecamer substrate of EcoRI methylase with [6-15N]adenine in the
AB  - methylation site are reported.  In the product of EcoRI enzymatic methylation,
AB  - all of the isotope remains at the N6 position of the N6-methyladenine product.
AB  - It is concluded that, contrary to existing chemical precedent, the methylation
AB  - occurs by direct transfer from S-adenosylmethionine to the N6 of adenine in
AB  - DNA.
ER  -

TY  - JOUR
AU  - Pohl, F.M.
AU  - Thomae, R.
AU  - Karst, A.
TI  - Temperature dependence of the activity of DNA-modifying enzymes: endonucleases and DNA ligase.
JO  - Eur. J. Biochem.
PY  - 1982
SP  - 141
EP  - 152
VL  - 123
AB  - The activities of 17 endonucleases: the restriction endonucleases AvaI, BamHI,
AB  - EcoRI, HindIII, PstI and SalI, which cleave pBR322 DNA once: AluI, AvaII, CfoI,
AB  - HaeIII, HhaI, HinfI, HpaII and TaqI, which cut pBR322 DNA several times, and
AB  - three "unspecific" nucleases (S1 nuclease, staphylococcal nuclease and DNase I
AB  - from bovine pancreas) were determined between 0C and 65C.  The reaction was
AB  - followed by the disappearance of covalently closed circular pBR322 DNA, using
AB  - the alkaline ethidium fluorescence assay of Morgan et al. [Nucl. Acids Res.
AB  - (1979) 7, 547-594]; the activity of T4 DNA ligase was similarly measured by the
AB  - conversion of nicked circular DNA to closed circular DNA.  For each enzyme,
AB  - small aliquots of the same solution were incubated at different temperatures
AB  - simultaneously in a temperature gradient device, resulting in a high relative
AB  - precision.  The experimental results are summarized by the simplest possible
AB  - theoretical description, using linear or exponential kinetics and apparent
AB  - activation energies Ea for the enzymatic reaction, Ei for the enzyme
AB  - inactivation and Ti for the inactivation temperature.  To a good approximation
AB  - these three parameters suffice for describing the temperature dependence of the
AB  - activity of most of the enzymes.
ER  -

TY  - JOUR
AU  - Pohlner, M.
AU  - Marshall, I.
AU  - Schreiber, L.
AU  - Cypionka, H.
AU  - Engelen, B.
TI  - Draft Genome Sequence of Pseudoruegeria sp. SK021, a Representative of the Marine Roseobacter Group, Isolated from North Sea Sediment.
JO  - Genome Announcements
PY  - 2017
SP  - e00541
EP  - e00517
VL  - 5
AB  - Pseudoruegeria sp. SK021 is a member of the Roseobacter group, isolated under aerobic
AB  - conditions from North Sea sediment. The draft genome comprises 3.95 Mb
AB  - and contains 3,747 protein-coding sequences. Although the strain is nonmotile
AB  - under laboratory conditions, the entire set of genes for the formation of a
AB  - flagellar apparatus was found.
ER  -

TY  - JOUR
AU  - Poirier, S.
AU  - Coeuret, G.
AU  - Champomier-Verges, M.C.
AU  - Chaillou, S.
TI  - Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis,  Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas  lundensis, and Weissella viridesc.
JO  - Genome Announcements
PY  - 2018
SP  - e00479
EP  - e00418
VL  - 6
AB  - In this study, we present the draft genome sequences of nine strains from various
AB  - psychrotrophic species identified in meat products and being recognized as
AB  - important emerging food spoilers. Many of these species have only one or few
AB  - strains being sequenced, and this work will contribute to the improvement of the
AB  - overall genomic knowledge about them.
ER  -

TY  - JOUR
AU  - Poland, B.W.
AU  - Xu, M.Q.
AU  - Quiocho, F.A.
TI  - Structural Insights into the Protein Splicing Mechanism of PI-SceI.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 16408
EP  - 16413
VL  - 275
AB  - PI-SceI is a member of a class of proteins (inteins) that excise themselves from a precursor
AB  - protein and in the process ligate the flanking protein sequences (exteins). We report here the
AB  - 2.1-A resolution crystal structure of a PI-SceI miniprecursor (VMA29) containing 10 N-terminal
AB  - extein residues and 4 C-terminal extein residues. Mutations at the N- and C-terminal splicing
AB  - junctions, blocking in vivo protein splicing, allowed the miniprecursor to be purified and
AB  - crystallized. The structure reveals both the N- and C-terminal scissile peptide bonds to be in
AB  - distorted trans conformations (tau approximately 100 degrees ). Modeling of the wild-type
AB  - PI-SceI based on the VMA29 structure indicates a large conformational change (movement of >9
AB  - A) must occur to allow transesterification to be completed. A zinc atom was discovered at the
AB  - C-terminal splicing junction. Residues Cys(455), His(453), and Glu(80) along with a water
AB  - molecule (Wat(53)) chelate the zinc atom. The crystal structure of VMA29 has captured the
AB  - intein in its pre-spliced state.
ER  -

TY  - JOUR
AU  - Pold, G.
AU  - Conlon, E.M.
AU  - Huntemann, M.
AU  - Pillay, M.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.B.K.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - DeAngelis, K.M.
TI  - Genome Sequence of Verrucomicrobium sp. Strain GAS474, a Novel Bacterium Isolated from Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e01451
EP  - e01417
VL  - 6
AB  - Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous
AB  - forest in central Massachusetts. Here, we present the
AB  - complete genome sequence of this phylogenetically novel organism, which consists
AB  - of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and
AB  - 3,273 predicted open reading frames.
ER  -

TY  - JOUR
AU  - Pold, G.
AU  - Huntemann, M.
AU  - Pillay, M.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.B.K.
AU  - Daum, C.
AU  - Shapiro, N.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - DeAngelis, K.M.
TI  - Draft Genome Sequences of Three Strains of a Novel Rhizobiales Species Isolated from Forest Soil.
JO  - Genome Announcements
PY  - 2018
SP  - e01452
EP  - e01417
VL  - 6
AB  - Three strains of a novel Rhizobiales species were isolated from temperate deciduous forest
AB  - soil in central Massachusetts. Their genomes consist of 9.09 to
AB  - 10.29 Mb over 3 to 4 scaffolds each and indicate that diverse nitrogenous
AB  - compounds are used by these organisms.
ER  -

TY  - JOUR
AU  - Poli, A.
AU  - Nicolaus, B.
AU  - Chan, K.G.
AU  - Kahar, U.M.
AU  - Chan, C.S.
AU  - Goh, K.M.
TI  - Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy.
JO  - Genome Announcements
PY  - 2015
SP  - e00490
EP  - e00415
VL  - 3
AB  - Anoxybacillus thermarum AF/04(T) was isolated from the Euganean hot springs in Abano Terme,
AB  - Italy. The present work reports a high-quality draft genome sequence
AB  - of strain AF/04(T). This work also provides useful insights into glycoside
AB  - hydrolases, glycoside transferases, and sugar transporters that may be involved
AB  - in cellular carbohydrate metabolism.
ER  -

TY  - JOUR
AU  - Polishchuk, L.V.
AU  - Lukyanchuk, V.V.
AU  - Matselyuch, B.P.
TI  - Site-specific endonucleases of Streptomycetes.
JO  - Actinomycetes
PY  - 2000
SP  - 13
EP  - 15
VL  - 10
AB  - Production of restriction enzymes is widespread among soil streptomycetes. More than 15% of
AB  - fresh soil isolates showed this ability. Of eight strains showing enzyme activity, seven
AB  - formed isoschizomers of AsuII. Enzymes with such specificity were not previously found amongst
AB  - streptomycetes.  Enzymes of restriction-modification (RM} systems are present in large amounts
AB  - in streptomycetes and some strains are strong producers of endonucleases (e.g., SacI, SacII,
AB  - SalGI). Streptomycetes also produce isoschizomers of EcoRI, PstI and others. Studies on these
AB  - enzymes are valuable for understanding regulation and functioning of RM systems, actual
AB  - production of the enzymes themselves and for pharmaceutical and other biotechnological
AB  - applications (Rodicio & Chater, 1988}. The aim of the present study was to investigate the
AB  - amount of restrictases among fresh soil isolates.
ER  -

TY  - JOUR
AU  - Polisky, B.
AU  - Greene, P.
AU  - Garfin, D.E.
AU  - McCarthy, B.J.
AU  - Goodman, H.M.
AU  - Boyer, H.W.
TI  - Specificity of substrate recognition by the EcoRI restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1975
SP  - 3310
EP  - 3314
VL  - 72
AB  - The substrate specificity of the EcoRI restriction endonuclease can be varied
AB  - in vitro by changing the pH and the ionic environment of the reaction.
AB  - Phosphodiester bond cleavage occurs at a DNA hexanucleotide sequence
AB  - d(N-G-A-A-T-T-C-N) d(N-C-T-T-A-A-G-N)	when the ionic strength is high, 100mM
AB  - Tris-HCl, 50 mM NaCl, 5 mM MgCl2, and the pH is approximately 7.3.  Lowering
AB  - the ionic strength to 25 mM Tris-HCl, 2 mM MgCl2, and adjusting the pH to 8.5
AB  - reduces the recognition specificity of the EcoRI endonuclease to the
AB  - tetranucleotide sequence, d(N-A-A-T-T-N) d(N-T-T-A-A-N)	The enzymatic activity
AB  - responsible for this substrate recognition is referred to as EcoRI*.  Cleavage
AB  - of pVH51 plasmid DNA under EcoRI* conditions results in a number of partial
AB  - digest fragments, some of which disappear slowly over a prolonged digestion
AB  - period.  This suggests that different recognition sites are cleaved at
AB  - different rates.  Comparison of DNA fragment patterns of modified and
AB  - unmodified pVH51 DNA indicates that the canonical EcoRI sequence is the most
AB  - rapidly cleaved site under EcoRI* conditions.  DNA modified in vivo by the
AB  - EcoRI methylase is not cleaved by the EcoRI endonuclease under standard
AB  - conditions, but is cleaved under EcoRI* conditions at sites other than the
AB  - standard EcoRI substrate.
ER  -

TY  - JOUR
AU  - Polisson, C.
TI  - MscI, a type II restriction endonuclease from Micrococcus species which recognizes 5' TGGCCA 3' .
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 5858
EP  - 5858
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Polisson, C.
AU  - Morgan, R.D.
TI  - AseI, a restriction endonuclease from Aquaspirillum serpens which recognizes 5'ATTAAT3'.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 10365
EP  - 10365
VL  - 16
AB  - AseI and AseII, type II restriction endonucleases, have been isolated from
AB  - Aquaspirillum serpens (NEB#448).  AseI, an isoschizomer of VspI, recognizes the
AB  - six base palindromic sequence 5'ATTAAT3', and cleaves 3' of the 5' T, to
AB  - generate a two base 5' overhang, 5' AT^TAAT3'.  AseII is an isoschizomer of
AB  - NciI (data not shown).
ER  -

TY  - JOUR
AU  - Polisson, C.
AU  - Morgan, R.D.
TI  - BsrI, a unique restriction endonuclease from Bacillus stearothermophilus which recognizes 5'ACTGG3'.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 5205
EP  - 5205
VL  - 16
AB  - A new type II restriction endonuclease, BsrI, has been isolated from Bacillus
AB  - stearothermophilus (NEB#447).  BsrI recognizes the five base non-palindromic
AB  - sequence 5' ACTGG 3'.  It cleaves one nucleotide outside of the recognition
AB  - sequence on one strand, and within the recognition sequence on the opposite
AB  - strand, to generate a two base 3' overhang.
ER  -

TY  - JOUR
AU  - Polisson, C.
AU  - Morgan, R.D.
TI  - AciI, a unique restriction endonuclease from Arthrobacter citreus which recognizes 5' CCGC3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 5911
EP  - 5911
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Polisson, C.
AU  - Morgan, R.D.
TI  - DrdI, a unique restriction endonuclease from Deinococcus radiodurans which recognizes 5'GACN6GTC3'.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 3316
EP  - 3316
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Polisson, C.
AU  - Morgan, R.D.
TI  - EarI, a restriction endonuclease from Enterobacter aerogenes which recognizes 5'CTCTTC3'.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 9872
EP  - 9872
VL  - 16
AB  - EarI, a TypeII restriction endonuclease, has been isolated from Enterobacter aerogenes
AB  - (NEB#450).  EarI, an isoschizomer of Ksp632I, recognizes the six base non-palindromic sequence
AB  - 5'CTCTTC3', and cleaves one nucleotide 3' of the 3' cytosine on one strand, and four
AB  - nucleotides 5' of the 5' guanine on the opposite strand, to generate a three base 5'
AB  - overhang.  The single cleavage site of EarI on SV40 DNA was mapped to approximately position
AB  - 4450 by analysis against BglI, EcoRI and TaqI cleaved SV40 DNA (figure 1, lanes B-E).  The
AB  - sequence 5'CTCTTC3' occurs at position 4437.  The number and sizes of the fragments
AB  - generated by digestion with EarI on eight DNA molecules (119 sites) match the computer
AB  - predicted number and sizes of the fragments that would be generated by cleavage at the
AB  - sequence 5'CTCTTC3'.  EarI has the following number of recognition sites on these commonly
AB  - used DNAs:  pUC19, 3; pBR322, 2; phiX174, 2; M13mp18, 2; SV40, 1; Adeno2, 29; T7, 46; and
AB  - Lambda, 34 (fig. 1, lanes F-l).  From these data we conclude that EarI recognizes the sequence
AB  - 5'CTCTTC3'.  The crude extract contained approximately 8,000 units EarI per gram of cells.
AB  - The cleavage site of EarI was determined by cleavage of a primed synthesis reaction.  Using
AB  - M13mp18 DNA as template with an appropriate primer, the four standard dideoxy DNA sequencing
AB  - reactions were performed and a fifth reaction containing no dideoxy terminations was extended
AB  - through the EarI site.  The fifth reaction was terminated by heat treatment.  EarI was added
AB  - to the fifth reaction.  The cleaved product resulted in a single band (fig. II, lane -) which
AB  - comigrates with the first 3'nucleotide outside of the recognition sequence.  The addition of
AB  - Klenow subsequent to EarI digestion resulted in a single band, three nucleotides longer,
AB  - comigrating with the fourth 3' nucleotide outside of the recognition sequence (fig. II, lane
AB  - +).  These results indicate that EarI cleaves one nucleotide 3' of the recognition sequence
AB  - on the 5'CTCTTC3' strand, and four nucleotides 5' of the 5' G on the opposite strand
AB  - sequence 5'GAAGAG3', generating a three base 5' overhang.
AB  - 5'CTCTTCN3'
AB  - 3'GAGAAGNNNN5'.
ER  -

TY  - JOUR
AU  - Polisson, C.
AU  - Robinson, D.
TI  - ApoI, a unique restriction endonuclease from Arthrobacter protophormiae which recognizes 5' RAATTY-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2888
EP  - 2888
VL  - 20
AB  - ApoI, a novel type II restriction endonuclease, has been isolated from Arthrobacter
AB  - protophormiae (NEB#723). ApoI recognizes the six base palindromic sequence 5' R|AATTY 3',
AB  - and cleaves after the first base pair, as indicated by the arrow, to create a four base 5'
AB  - extension.
ER  -

TY  - JOUR
AU  - Pollak, A.J.
AU  - Reich, N.O.
TI  - Proximal Recognition Sites Facilitate Intrasite Hopping by DNA Adenine Methyltransferase MECHANISTIC EXPLORATION OF EPIGENETIC GENE REGULATION.
JO  - J. Biol. Chem.
PY  - 2012
SP  - 22873
EP  - 22881
VL  - 287
AB  - The methylation of adenine in palindromic 5'-GATC-3' sites by Escherichia coli Dam supports
AB  - diverse roles, including the essential
AB  - regulation of virulence genes in several human pathogens. As a result
AB  - of a unique hopping mechanism, Dam methylates both strands of the same
AB  - site prior to fully dissociating from the DNA, a process referred to as
AB  - intrasite processivity. The application of a DpnI restriction
AB  - endonuclease-based assay allowed the direct interrogation of this
AB  - mechanism with a variety of DNA substrates. Intrasite processivity is
AB  - disrupted when the DNA flanking a single GATC site is longer than 400
AB  - bp on either side. Interestingly, the introduction of a second GATC
AB  - site within this flanking DNA reinstates intrasite methylation of both
AB  - sites. Our results show that intrasite methylation occurs only when
AB  - GATC sites are clustered, as is found in gene segments both known and
AB  - postulated to undergo in vivo epigenetic regulation by Dam methylation.
AB  - We propose a model for intrasite methylation in which Dam bound to
AB  - flanking DNA is an obligate intermediate. Our results provide insights
AB  - into how intrasite processivity, which appears to be context-dependent,
AB  - may contribute to the diverse biological roles that are carried out by
AB  - Dam.
ER  -

TY  - JOUR
AU  - Pollo, S.M.
AU  - Charchuk, R.
AU  - Nesbo, C.L.
TI  - Draft Genome Sequences of Kosmotoga sp. Strain DU53 and Kosmotoga arenicorallina  S304.
JO  - Genome Announcements
PY  - 2016
SP  - e00570
EP  - e00516
VL  - 4
AB  - Here, we announce the draft genome sequences of two thermophilic Thermotogae bacteria:
AB  - Kosmotoga sp. strain DU53, isolated from a continental oil reservoir,
AB  - and Kosmotoga arenicorallina, isolated from hydrothermal sediments. The sequences
AB  - will provide further insight into evolution of the Kosmotogales.
ER  -

TY  - JOUR
AU  - Polosina, Y.Y.
AU  - Mui, J.
AU  - Pitsikas, P.
AU  - Cupples, C.G.
TI  - The Escherichia coli Mismatch Repair Protein MutL Recruits the Vsr and MutH Endonucleases in Response to DNA Damage.
JO  - J. Bacteriol.
PY  - 2009
SP  - 4041
EP  - 4043
VL  - 191
AB  - The activities of the Vsr and MutH endonucleases of Escherichia coli are stimulated by MutL.
AB  - The interaction of MutL with each enzyme is enhanced
AB  - in vivo by 2-aminopurine treatment and by inactivation of the mutY gene.
AB  - We hypothesize that MutL recruits the endonucleases to sites of DNA
AB  - damage.
ER  -

TY  - JOUR
AU  - Poltaraus, A.B.
AU  - Sokolova, D.S.
AU  - Grouzdev, D.S.
AU  - Ivanov, T.M.
AU  - Malakho, S.G.
AU  - Korshunova, A.V.
AU  - Rozanov, A.S.
AU  - Tourova, T.P.
AU  - Nazina, T.N.
TI  - Draft Genome Sequence of Aeribacillus pallidus Strain 8m3, a Thermophilic Hydrocarbon-Oxidizing Bacterium Isolated from the Dagang Oil Field (China).
JO  - Genome Announcements
PY  - 2016
SP  - e00500
EP  - e00516
VL  - 4
AB  - The draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic aerobic
AB  - oil-oxidizing bacterium isolated from production water from the Dagang
AB  - high-temperature oil field, China, is presented here. The genome is annotated to
AB  - provide insights into the genomic and phenotypic diversity of the genus
AB  - Aeribacillus.
ER  -

TY  - JOUR
AU  - Poltaraus, A.B.
AU  - Sokolova, D.S.
AU  - Grouzdev, D.S.
AU  - Ivanov, T.M.
AU  - Malakho, S.G.
AU  - Korshunova, A.V.
AU  - Tourova, T.P.
AU  - Nazina, T.N.
TI  - Draft Genome Sequence of Geobacillus subterraneus Strain K, a Hydrocarbon-Oxidizing Thermophilic Bacterium Isolated from a Petroleum Reservoir   in Kazakhstan.
JO  - Genome Announcements
PY  - 2016
SP  - e00782
EP  - e00716
VL  - 4
AB  - The draft genome sequence of Geobacillus subterraneus strain K, a thermophilic aerobic
AB  - oil-oxidizing bacterium isolated from production water of the Uzen
AB  - high-temperature oil field in Kazakhstan, is presented here. The genome is
AB  - annotated for elucidation of the genomic and phenotypic diversity of thermophilic
AB  - alkane-oxidizing bacteria.
ER  -

TY  - JOUR
AU  - Polter, S.J.
AU  - Caraballo, A.A.
AU  - Lee, Y.P.
AU  - Eng, W.W.
AU  - Gan, H.M.
AU  - Wheatley, M.S.
AU  - Savka, M.A.
AU  - Thomas, B.N.
AU  - Hudson, A.O.
TI  - Isolation, Identification, Whole-Genome Sequencing, and Annotation of Four Bacillus Species, B. anthracis RIT375, B. circulans RIT379, B. altitudinis  RIT380, and B. megaterium RIT381, from Internal Stem Tissue of the Insulin Plant   Costus igneus.
JO  - Genome Announcements
PY  - 2015
SP  - e00847
EP  - e00815
VL  - 3
AB  - Here, we report the isolation, identification, whole-genome sequencing, and annotation of four
AB  - Bacillus species from internal stem tissue of the insulin
AB  - plant Costus igneus, grown in Puerto Rico. The plant is of medicinal importance,
AB  - as extracts from its leaves have been shown to lower blood sugar levels of
AB  - hyperglycemic rats.
ER  -

TY  - JOUR
AU  - Poly, F.
AU  - Read, T.
AU  - Tribble, D.R.
AU  - Baqar, S.
AU  - Lorenzo, M.
AU  - Guerry, P.
TI  - Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand.
JO  - Infect. Immun.
PY  - 2007
SP  - 3425
EP  - 3433
VL  - 75
AB  - Campylobacter jejuni CG8486, which belongs to the HS4 complex, was isolated from a patient
AB  - with inflammatory diarrhea in Thailand.  This strain caused a diarrheal disease in ferrets
AB  - comparable to that caused by C. jejuni strain 81-176, but it was much less invasive for
AB  - epithelial cells in vitro than 81-176.  Complete genome sequencing of CG8486 revealed a
AB  - 1.65-Mb genome that was very similar to the other two published genomes of clinical isolates
AB  - of C. jejuni, the genomes of 81-176 and NCTC 11168, with a limited number of CG8486-specific
AB  - genes mapping outside the hypervariable carbohydrate biosynthesis loci.  These data suggest
AB  - that the genes required for induction of inflammatory diarrhea are among the genes shared by
AB  - CG8486 and 81-176 but that either major changes in the carbohydrate loci and/or more subtle
AB  - changes in other genes may modulate virulence.
ER  -

TY  - JOUR
AU  - Poly, F.
AU  - Read, T.D.
AU  - Chen, Y.H.
AU  - Monteiro, M.A.
AU  - Serichantalergs, O.
AU  - Pootong, P.
AU  - Bodhidatta, L.
AU  - Mason, C.J.
AU  - Rockabrand, D.
AU  - Baqar, S.
AU  - Porter, C.K.
AU  - Tribble, D.
AU  - Darsley, M.
AU  - Guerry, P.
TI  - Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies.
JO  - Infect. Immun.
PY  - 2008
SP  - 5655
EP  - 5667
VL  - 76
AB  - The development of vaccines against Campylobacter jejuni would be facilitated by
AB  - the ability to perform phase II challenge studies. However, molecular mimicry of
AB  - the lipooligosaccharide (LOS) of most C. jejuni strains with human gangliosides
AB  - presents safety concerns about the development of Guillain-Barre syndrome.
AB  - Clinical isolates of C. jejuni that appeared to lack genes for the synthesis of
AB  - ganglioside mimics were identified by DNA probe analyses. Two clinical isolates
AB  - from Southeast Asia (strains BH-01-0142 and CG8421) were determined to express
AB  - the LOS type containing N-acetyl quinovosamine. No ganglioside structures were
AB  - observed to be present in the LOSs of these strains, and pyrosequence analyses of
AB  - the genomes of both strains confirmed the absence of genes involved in
AB  - ganglioside mimicry. The capsule polysaccharide (CPS) of BH-01-0142 was
AB  - determined to be composed of galactose (Gal), 6-deoxy-ido-heptose, and, in
AB  - smaller amounts, D-glycero-D-ido-heptose, and the CPS of CG8421 was observed to
AB  - contain Gal, 6-deoxy-altro-heptose, N-acetyl-glucosamine, and minor amounts of
AB  - 6-deoxy-3-O-Me-altro-heptose. Both CPSs were shown to carry
AB  - O-methyl-phosphoramidate. The two genomes contained strain-specific zones, some
AB  - of which could be traced to a plasmid origin, and both contained a large
AB  - chromosomal insertion related to the CJEI3 element of C. jejuni RM1221. The
AB  - genomes of both strains shared a high degree of similarity to each other and,
AB  - with the exception of the capsule locus of CG8421, to the type strain of the HS3
AB  - serotype, TGH9011.
ER  -

TY  - JOUR
AU  - Poly, F.
AU  - Threadgill, D.
AU  - Stintzi, A.
TI  - Genomic diversity in Campylobacter jejuni: Identification of C-jejuni 81-176-specific genes.
JO  - J. Clin. Microbiol.
PY  - 2005
SP  - 2330
EP  - 2338
VL  - 43
AB  - Since the publication of the complete genomic sequence of Campylobacter jejuni NCTC 11168 in
AB  - February 2000, evidence has been compiling that
AB  - suggests C. jejuni strains exhibit high genomic diversity. In order to
AB  - investigate this diversity, the unique genomic DNA sequences from a
AB  - nonsequenced Campylobacter strain, C. jejuni 81-176, were identified by
AB  - comparison with C. jejuni NCTC 11168 by using a shotgun DNA microarray
AB  - approach. Up to 63 kb of new chromosomal DNA sequences unique to this
AB  - pathogen were obtained. Eighty-six open reading frames were identified
AB  - by the presence of uninterrupted coding regions encoding a minimum of
AB  - 40 amino acids. In addition, this study shows that the whole-plasmid
AB  - shotgun microarray approach is effective and provides a comprehensive
AB  - coverage of DNA regions that differ between two closely related
AB  - genomes. The two plasmids harbored by this Campylobacter strain, pTet
AB  - and pVir, were also sequenced, with coverages of 2.5- and 2.9-fold,
AB  - respectively, representing 72 and 92% of their complete nucleotide
AB  - sequences. The unique chromosomal genes encode proteins involved in
AB  - capsule and lipooligosaccharide biosynthesis, restriction and
AB  - modification systems, and respiratory metabolism. Several of these
AB  - unique genes are likely associated with C. jejuni 81-176 fitness and
AB  - virulence. Interestingly, the comparison of C. jejuni 81-176 unique
AB  - genes with those of C. jejuni ATCC 43431 revealed a single gene which
AB  - encodes a probable TraG-like protein. The product of this gene might be
AB  - associated with the mechanism of C. jejuni invasion into epithelial
AB  - cells. In conclusion, this study extends the repertoire of C. jejuni
AB  - genes and thus will permit the construction of a composite and more
AB  - comprehensive microarray of C. jejuni.
ER  -

TY  - JOUR
AU  - Poly, F.
AU  - Threadgill, D.
AU  - Stintzi, A.
TI  - Identification of Campylobacter jejuni ATCC 43431-specific genes by whole microbial genome comparisons.
JO  - J. Bacteriol.
PY  - 2004
SP  - 4781
EP  - 4795
VL  - 186
AB  - This study describes a novel approach to identify unique genomic DNA sequences from the
AB  - unsequenced strain C. jejuni ATCC 43431 by comparison with the sequenced strain C. jejuni NCTC
AB  - 11168. A shotgun DNA microarray was constructed by arraying 9,600 individual DNA fragments
AB  - from a C. jejuni ATCC 43431 genomic library onto a glass slide. DNA fragments unique to C.
AB  - jejuni ATCC 43431 were identified by competitive hybridization to the array with genomic DNA
AB  - of C. jejuni NCTC 11168. The plasmids containing unique DNA fragments were sequenced, allowing
AB  - the identification of up to 130 complete and incomplete genes. Potential biological roles were
AB  - assigned to 66% of the unique open reading frames. The mean G+C content of these unique genes
AB  - (26%) differs significantly from the G+C content of the entire C. jejuni genome (30.6%). This
AB  - suggests that they may have been acquired through horizontal gene transfer from an organism
AB  - with a G+C content lower than that of C. jejuni. Because the two C. jejuni strains differ by
AB  - Penner serotype, a large proportion of the unique ATCC 43431 genes encode proteins involved in
AB  - lipooligosaccharide and capsular biosynthesis, as expected. Several unique open reading frames
AB  - encode enzymes which may contribute to genetic variability, i.e., restriction-modification
AB  - systems and integrases. Interestingly, many of the unique C. jejuni ATCC 43431 genes show
AB  - identity with a possible pathogenicity island from Helicobacter hepaticus and components of a
AB  - potential type IV secretion system. In conclusion, this study provides a valuable resource to
AB  - further investigate Campylobacter diversity and pathogenesis.
ER  -

TY  - JOUR
AU  - Polyachenko, V.M.
AU  - Melnikova, V.A.
AU  - Gruber, I.M.
AU  - Smirnova, G.A.
AU  - Raskin, B.M.
TI  - Development of a culture medium for bacteria of the genus Haemophilus, producing restriction endonucleases.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1989
SP  - 3
EP  - 8
VL  - 3
AB  - A culture medium for the cultivation of hemophilic bacteria, containing acidic
AB  - casein hydrolysate, aminopeptide and fodder yeast extract, has been proposed.
AB  - The growth-stimulating properties of this medium have been studied on 5 strains
AB  - producing restrictases differing in their specificity.  In growing these
AB  - producer strains in a model AHKYM-2 fermenter with the supply of carbohydrate
AB  - substrates (glucose, sucrose, glycerin) the yield of biomass, considered to be
AB  - high for hemophilic bacteria (10-14 g wet weight from 1 liter of the medium),
AB  - has been achieved.  As shown on H. influenzae Rc B-2297 used as an example, an
AB  - increase in the yield of microbial biomass leads to a decrease in restrictase
AB  - specific activity.
ER  -

TY  - JOUR
AU  - Polyanovsky, O.L.
AU  - Nosikov, V.V.
AU  - Zhuze, A.L.
AU  - Braga, E.A.
AU  - Karlyshev, A.V.
TI  - Regulation of restriction endonuclease activity with antibiotics.
JO  - Adv. Enzyme Regul.
PY  - 1979
SP  - 307
EP  - 321
VL  - 17
AB  - Restriction-modification systems were made known in the early 1960's.  Active investigation,
AB  - however, has begun in the last years.  These systems serve to protect the bacterial cell from
AB  - invasion by foreign DNA.  Simultaneously, restriction enzymes are widely used as a tool for
AB  - specific DNA cleavage and obtaining of recombinant DNA molecules in vitro.
ER  -

TY  - JOUR
AU  - Ponger, L.
AU  - Li, W.H.
TI  - Evolutionary diversification of DNA methyltransferases in eukaryotic Genomes.
JO  - Mol. Biol. Evol.
PY  - 2005
SP  - 1119
EP  - 1128
VL  - 22
AB  - In eukaryotes, C5-cytosine methylation is a common mechanism associated with a variety of
AB  - functions such as gene regulation or control of
AB  - genomic stability. Different subfamilies of eukaryotic
AB  - methyltransferases (MTases) have been identified, mainly in metazoa,
AB  - plants, and fungi. In this paper, we used hidden Markov models to
AB  - detect MTases in completed or almost completed eukaryotic genomes,
AB  - including different species of Protozoa. A phylogenetic analysis of
AB  - MTases enabled us to define six subfamilies of MTases, including two
AB  - new subfamilies. The dnmt1 subfamily that includes all the known MTases
AB  - with a maintenance activity seems to be absent in the Protozoa. The
AB  - dnmt2 subfamily seems to be the most widespread, being present even in
AB  - the nonmethylated Dictyostelium discoideum. We also found two dnmt2
AB  - members in the bacterial genus Geobacter, suggesting that horizontal
AB  - transfers of MTases occurred between eukaryotes and prokaryotes. Even
AB  - if the direction of transfer cannot be determined, this relationship
AB  - might be useful for understanding the function of this enigmatic
AB  - subfamily of MTases. Globally, our analysis reveals a great diversity
AB  - of MTases in eukaryotes, suggesting the existence of different
AB  - methylation systems. Our results also suggest acquisitions and losses
AB  - of different MTases in every eukaryotic lineage studied and that some
AB  - eukaryotes appear to be devoid of methylation.
ER  -

TY  - JOUR
AU  - Ponnudurai, R.
AU  - Sayavedra, L.
AU  - Kleiner, M.
AU  - Heiden, S.E.
AU  - Thurmer, A.
AU  - Felbeck, H.
AU  - Schluter, R.
AU  - Sievert, S.M.
AU  - Daniel, R.
AU  - Schweder, T.
AU  - Markert, S.
TI  - Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 50
EP  - 50
VL  - 12
AB  - Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the
AB  - East Pacific Rise, lives in symbiosis with chemosynthetic
AB  - Gammaproteobacteria within its gills. The intracellular symbiont population
AB  - synthesizes nutrients for the bivalve host using the reduced sulfur compounds
AB  - emanating from the vents as energy source. As the symbiont is uncultured,
AB  - comprehensive and detailed insights into its metabolism and its interactions with
AB  - the host can only be obtained from culture-independent approaches such as
AB  - genomics and proteomics. In this study, we report the first draft genome sequence
AB  - of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named
AB  - Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045
AB  - protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate
AB  - as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation.
AB  - Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates
AB  - oxaloacetate and succinate were absent, suggesting that these intermediates may
AB  - be substituted by metabolites from external sources. We also detected a
AB  - repertoire of genes associated with cell surface adhesion, bacteriotoxicity and
AB  - phage immunity, which may perform symbiosis-specific roles in the B. thermophilus
AB  - symbiosis.
ER  -

TY  - JOUR
AU  - Pope, W.H. et al.
TI  - Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.
JO  - PLoS ONE
PY  - 2011
SP  - E16329
EP  - E16329
VL  - 6
AB  - Mycobacteriophages are viruses that infect mycobacterial hosts such as
AB  - Mycobacterium smegmatis and Mycobacterium tuberculosis. All
AB  - mycobacteriophages characterized to date are dsDNA tailed phages, and have
AB  - either siphoviral or myoviral morphotypes. However, their genetic
AB  - diversity is considerable, and although sixty-two genomes have been
AB  - sequenced and comparatively analyzed, these likely represent only a small
AB  - portion of the diversity of the mycobacteriophage population at large.
AB  - Here we report the isolation, sequencing and comparative genomic analysis
AB  - of 18 new mycobacteriophages isolated from geographically distinct
AB  - locations within the United States. Although no clear correlation between
AB  - location and genome type can be discerned, these genomes expand our
AB  - knowledge of mycobacteriophage diversity and enhance our understanding of
AB  - the roles of mobile elements in viral evolution. Expansion of the number
AB  - of mycobacteriophages grouped within Cluster A provides insights into the
AB  - basis of immune specificity in these temperate phages, and we also
AB  - describe a novel example of apparent immunity theft. The isolation and
AB  - genomic analysis of bacteriophages by freshman college students provides
AB  - an example of an authentic research experience for novice scientists.
ER  -

TY  - JOUR
AU  - Pope, W.H. et al.
TI  - Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha.
JO  - Genome Announcements
PY  - 2016
SP  - e00578
EP  - e00516
VL  - 4
AB  - Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia
AB  - terrae 3612. Both have siphoviral morphologies with isometric heads and
AB  - long tails (500 nm). The genomes are 75,380 bp long and closely related, and the
AB  - tape measure genes (9 kbp) are among the largest to be identified.
ER  -

TY  - JOUR
AU  - Popin, R.V.
AU  - Rigonato, J.
AU  - Abreu, V.A.
AU  - Andreote, A.P.
AU  - Silveira, S.B.
AU  - Odebrecht, C.
AU  - Fiore, M.F.
TI  - Draft Genome Assembly of the Bloom-Forming Cyanobacterium Nodularia spumigena Strain CENA596 in Shrimp Production Ponds.
JO  - Genome Announcements
PY  - 2016
SP  - e00466
EP  - e00416
VL  - 4
AB  - We report here the draft genome assembly of the brackish cyanobacterium Nodularia spumigena
AB  - strain CENA596 isolated from a shrimp production pond in Rio Grande do
AB  - Sul, Brazil. The draft genome consists of 291 contigs with a total size of
AB  - 5,189,679 bp. Secondary metabolite annotations resulted in several predicted gene
AB  - clusters, including those responsible for encoding the hepatotoxin nodularin.
ER  -

TY  - JOUR
AU  - Popovski, B.
TI  - The location of genes coding the specific modification and restriction system in the recombinant E. coli strain tF.
JO  - Vet. Med. Nauki
PY  - 1987
SP  - 9
EP  - 12
VL  - 24
AB  - The recombinant Escherichia coli tF strain has been shown to have its own specific
AB  - modification and restriction system.  In order to establish the location of genes, coding this
AB  - system a plasmid has been isolated from the investigated strain, which substantiates the
AB  - resistance to streptomycin.  The plasmid DNA has been transformed into a recipient strain, E.
AB  - coli O, which has no modification and restriction system of its own.  The newly obtained E.
AB  - coli O (ptF) transformants also have proved negative with regard to their testing for the
AB  - presence of a specific modification and restriction system.  The conclusion follows that the
AB  - genes, coding the modification and restriction system of the E. coli tF strain are not located
AB  - in the plasmid isolated from it.
ER  -

TY  - JOUR
AU  - Popovski, B.
TI  - Structure and mechanisms of action of restrictional endonucleases.
JO  - Vet. Med. Nauki
PY  - 1986
SP  - 13
EP  - 17
VL  - 23
AB  - The structure and the mode of restrictional endonucleases are dealt with in
AB  - detail.  Described are some more important representatives of the three types
AB  - of endonucleases.  Stated are their role and place in present-day molecular
AB  - biology.
ER  -

TY  - JOUR
AU  - Popovski, B.
TI  - Phenotypic characteristics of a new modificational and restriction system in Escherichia coli.
JO  - Vet. Med. Nauki
PY  - 1987
SP  - 19
EP  - 24
VL  - 24
AB  - It has been demonstrated phenotypically that there exists a new
AB  - modification-and-restrictional system as synthesized by the recombinant
AB  - Escherichia coli tF strain.  A series of passages of the T3 and T7 phages and
AB  - their mutants in E. coli tF has made it possible to ascertain a specific
AB  - modification of the phage DNA, which was shown to be induced by the host
AB  - strain.  The high level of adsorption of these phages on the cell surface of E.
AB  - coli tF has ruled out the possibility of the existance of a nonclassical
AB  - modification and restriction of DNA.  In view of the further characterizing of
AB  - this modificational-and-restrictional system of E. coli tF it has been
AB  - comparatively studied with the already known modification-and-restrictional
AB  - systems isolated from various Escherichia coli strains.  Results have shown
AB  - that no identity exists between the tested systems and the one in E. coli tF.
AB  - It is stated that the new modificational-and-restrictional system of E. coli tF
AB  - belongs to none of the three known types of restrictional endonucleases.
ER  -

TY  - JOUR
AU  - Poratti, G.W.
AU  - Yaakop, A.S.
AU  - Chan, C.S.
AU  - Urbieta, M.S.
AU  - Chan, K.G.
AU  - Ee, R.
AU  - Tan-Guan-Sheng, A.
AU  - Goh, K.M.
AU  - Donati, E.R.
TI  - Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquen, Argentina.
JO  - Genome Announcements
PY  - 2016
SP  - e00870
EP  - e00816
VL  - 4
AB  - Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing
AB  - bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome
AB  - in which we found genes related with the anaerobic respiration of sulfur compounds similar to
AB  - those present in the Copahue environment.
ER  -

TY  - JOUR
AU  - Porcellato, D.
AU  - Frantzen, C.
AU  - Rangberg, A.
AU  - Umu, O.C.
AU  - Gabrielsen, C.
AU  - Nes, I.F.
AU  - Amdam, G.V.
AU  - Diep, D.B.
TI  - Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut.
JO  - Genome Announcements
PY  - 2015
SP  - e00144
EP  - e00115
VL  - 3
AB  - Lactobacillus kunkeei is a common inhabitant in honey bee gut, being present in several parts
AB  - of the world. Here, we describe the draft genome of L. kunkeei
AB  - AR114, an isolate from late foraging season in Norway.
ER  -

TY  - JOUR
AU  - Porcellato, D.
AU  - Ostlie, H.M.
AU  - Skeie, S.B.
TI  - Draft Genome Sequence of Enterococcus hirae Strain INF E1 Isolated from Cultured  Milk.
JO  - Genome Announcements
PY  - 2014
SP  - e00498
EP  - e00414
VL  - 2
AB  - Here, we present the draft genome of Enterococcus hirae INF E1, found as a contaminant in
AB  - cultured milk and studied for its ability to metabolize milk fat
AB  - globule membrane glycoconjugates.
ER  -

TY  - JOUR
AU  - Pore, S.D.
AU  - Arora, P.
AU  - Dhakephalkar, P.K.
TI  - Draft Genome Sequence of Geobacillus sp. Strain FW23, Isolated from a Formation Water Sample.
JO  - Genome Announcements
PY  - 2014
SP  - e00352
EP  - e00314
VL  - 2
AB  - The thermophilic Geobacillus sp. strain FW23 was isolated from the Mehsana oil wells in
AB  - Gujrat, India, during a screening for oil-degrading bacteria. Here, we
AB  - report the draft genome sequence of Geobacillus sp. FW23, which may help reveal
AB  - the genomic differences between this strain and the earlier reported species of
AB  - the genus Geobacillus.
ER  -

TY  - JOUR
AU  - Poret-Peterson, A.T.
AU  - Bhatnagar, S.
AU  - McClean, A.E.
AU  - Kluepfel, D.A.
TI  - Draft Genome Sequence of Agrobacterium tumefaciens Biovar 1 Strain 186, Isolated  from Walnut.
JO  - Genome Announcements
PY  - 2017
SP  - e01232
EP  - e01217
VL  - 5
AB  - Agrobacterium tumefaciens biovar 1 strain 186 was isolated from a walnut tree expressing crown
AB  - gall symptoms. The draft genome sequence of this strain harbored
AB  - genes for crown gall formation and will be useful for understanding its virulence
AB  - on Paradox, the predominant hybrid rootstock used for the cultivation of English
AB  - walnut in California.
ER  -

TY  - JOUR
AU  - Port, G.C.
AU  - Paluscio, E.
AU  - Caparon, M.G.
TI  - Complete Genome Sequence of emm Type 14 Streptococcus pyogenes Strain HSC5.
JO  - Genome Announcements
PY  - 2013
SP  - e00612
EP  - e00613
VL  - 1
AB  - Streptococcus pyogenes causes a greater diversity of human disease than any other bacterial
AB  - pathogen. Here, we present the complete genome sequence of the emm type
AB  - 14 S. pyogenes strain HSC5. This strain is a robust producer of the cysteine
AB  - protease SpeB and is capable of producing infection in several different animal
AB  - models.
ER  -

TY  - JOUR
AU  - Port, G.C.
AU  - Paluscio, E.
AU  - Caparon, M.G.
TI  - Complete Genome Sequences of emm6 Streptococcus pyogenes JRS4 and Parental Strain D471.
JO  - Genome Announcements
PY  - 2015
SP  - e00725
EP  - e00715
VL  - 3
AB  - We report the complete genome assemblies of the group A Streptococcus pyogenes serotype emm6
AB  - strain D471 and its streptomycin-resistant derivative JRS4. Both of
AB  - these well-studied laboratory strains have been extensively characterized over
AB  - the past three decades and have been instrumental in the discovery of multiple
AB  - aspects of streptococcal pathogenesis.
ER  -

TY  - JOUR
AU  - Porter, S.L.
AU  - Wilkinson, D.A.
AU  - Byles, E.D.
AU  - Wadhams, G.H.
AU  - Taylor, S.
AU  - Saunders, N.J.
AU  - Armitage, J.P.
TI  - Genome Sequence of Rhodobacter sphaeroides strain WS8N.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4027
EP  - 4028
VL  - 193
AB  - R. sphaeroides is a metabolically diverse photosynthetic alpha-proteobacterium found
AB  - ubiquitously in soil and in fresh water
AB  - habitats. Here we present the annotated genome sequence of Rhodobacter
AB  - sphaeroides WS8N.
ER  -

TY  - JOUR
AU  - Portillo, F.G.D.
AU  - Pucciarelli, M.G.
AU  - Casadesus, J.
TI  - DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 11578
EP  - 11583
VL  - 96
AB  - Mutants of Salmonella typhimurium lacking DNA adenine methylase are attenuated for virulence
AB  - in BALB/c mice.  LD(50) values of a DNA adenine methylation (Dam)(-) mutant are at least
AB  - 10(3)- to 10(4)-fold higher than those of the parental strain when administrated by oral or
AB  - intraperitoneal routes. Dam(-) mutants are unable to proliferate in target organs but persist
AB  - in low numbers in these locations. Efficient protection to challenge with the virulent
AB  - parental strain is observed in mice infected with a Dam(-) mutant. Use of the ileal loop assay
AB  - shows that Dam(-) mutants are less cytotoxic to M cells and fail to invade enterocytes. In the
AB  - tissue culture model, lack of DNA adenine methylation causes reduced ability to invade
AB  - nonphagocytic cells. In contrast, no effect is observed either in intracellular proliferation
AB  - within nonphagocytic cells or in survival within macrophages. The invasion defect of Dam(-)
AB  - mutants is correlated with a distinct pattern of secreted proteins, which is observed in both
AB  - PhoP(+) and PhoP(-) backgrounds. Altogether, our observations suggest a multifactorial role of
AB  - Dam methylation in Salmonella virulence.
ER  -

TY  - JOUR
AU  - Portmann, A.C.
AU  - Fournier, C.
AU  - Gimonet, J.
AU  - Ngom-Bru, C.
AU  - Barretto, C.
AU  - Baert, L.
TI  - A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica.
JO  - Front. Microbiol.
PY  - 2018
SP  - 446
EP  - 446
VL  - 9
AB  - Whole genome sequencing (WGS), using high throughput sequencing technology,
AB  - reveals the complete sequence of the bacterial genome in a few days. WGS is
AB  - increasingly being used for source tracking, pathogen surveillance and outbreak
AB  - investigation due to its high discriminatory power. In the food industry, WGS
AB  - used for source tracking is beneficial to support contamination investigations.
AB  - Despite its increased use, no standards or guidelines are available today for the
AB  - use of WGS in outbreak and/or trace-back investigations. Here we present a
AB  - validation of our complete (end-to-end) WGS workflow for Listeria monocytogenes
AB  - and Salmonella enterica including: subculture of isolates, DNA extraction,
AB  - sequencing and bioinformatics analysis. This end-to-end WGS workflow was
AB  - evaluated according to the following performance criteria: stability,
AB  - repeatability, reproducibility, discriminatory power, and epidemiological
AB  - concordance. The current study showed that few single nucleotide polymorphism
AB  - (SNPs) were observed for L. monocytogenes and S. enterica when comparing genome
AB  - sequences from five independent colonies from the first subculture and five
AB  - independent colonies after the tenth subculture. Consequently, the stability of
AB  - the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite
AB  - the few genomic variations that can occur during subculturing steps.
AB  - Repeatability and reproducibility were also demonstrated. The WGS workflow was
AB  - shown to have a high discriminatory power and has the ability to show genetic
AB  - relatedness. Additionally, the WGS workflow was able to reproduce published
AB  - outbreak investigation results, illustrating its capability of showing
AB  - epidemiological concordance. The current study proposes a validation approach
AB  - comprising all steps of a WGS workflow and demonstrates that the workflow can be
AB  - applied to L. monocytogenes or S. enterica.
ER  -

TY  - JOUR
AU  - Posey, K.L.
AU  - Gimble, F.S.
TI  - Insertion of a reversible redox switch into a rare-cutting DNA endonuclease.
JO  - Biochemistry
PY  - 2002
SP  - 2184
EP  - 2190
VL  - 41
AB  - Target sites for homing endonucleases occur infrequently in complex genomes. As a consequence,
AB  - these enzymes can be used in mammalian systems to introduce double-strand breaks at
AB  - recognition sites inserted within defined loci to study DNA repair by homologous and
AB  - nonhomologous recombination. Using homing endonucleases for gene targeting in vivo would be
AB  - more feasible if temporal or spatial regulation of their enzymatic activity were possible.
AB  - Here, we show that the DNA cleavage activity of the yeast PI-SceI homing endonuclease can be
AB  - turned on and off using a redox switch. Two cysteine pairs (Cys-64/Cys-344 and Cys-67/Cys-365)
AB  - were separately inserted into flexible DNA binding loop(s) to create disulfide bonds that lock
AB  - the endonuclease into a nonproductive conformation. The cleavage activities of the reduced
AB  - Cys-64/Cys-344 and Cys-67/Cys-365 variants are similar or slightly lower than that of the
AB  - control protein, but the activities of the proteins in the oxidized state are decreased more
AB  - than 30-fold. Modulating the activity of the proteins is easily accomplished by adding or
AB  - removing the reducing agent. We show that defects in DNA binding account for the decreased DNA
AB  - cleavage activities of the proteins containing disulfide bonds. Interestingly, the
AB  - Cys-67/Cys-365 variant toggles between two different DNA binding conformations under reducing
AB  - and oxidizing conditions, which may permit the identification of structural differences
AB  - between the two states. These studies demonstrate that homing endonuclease activity can be
AB  - controlled using a molecular switch.
ER  -

TY  - JOUR
AU  - Posey, K.L.
AU  - Koufopanou, V.
AU  - Burt, A.
AU  - Gimble, F.S.
TI  - Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3947
EP  - 3956
VL  - 32
AB  - Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit
AB  - to their host. They encode site-specific DNA endonucleases that perpetuate the element within
AB  - a species population by homing and disseminate it between species by horizontal transfer.
AB  - Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived
AB  - endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying
AB  - their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces
AB  - bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition
AB  - sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six
AB  - nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae
AB  - substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI
AB  - between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to
AB  - a single base-pair substitution (A/T+5  T/A+5). Structural modeling of the PI-ZbaI/DNA complex
AB  - suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity
AB  - observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data
AB  - illustrate that homing endonucleases evolve altered specificity as they adapt to recognize
AB  - alternative target sites.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Baldauf, F.
AU  - Erdei, S.
AU  - Posfai, J.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Structure of the gene coding for the sequence-specific DNA-methyltransferase of the B. subtilis phage SPR.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 9039
EP  - 9049
VL  - 12
AB  - The nucleotide sequence of the gene coding for the 5'GGCC and 5'CCGG specific
AB  - DNA methyltransferase of the Bacillus subtilis phage SPR was determined by the
AB  - Maxam-Gilbert procedure.  Transcriptional and translational signals of the
AB  - sequence were assigned with the help of S1 mapping and translation in E. coli
AB  - minicells.  The gene codes for a 49 kd polypeptide.  The amino acid sequence of
AB  - the SPR methylase shows regions of homology with the sequence of the
AB  - 5'-GGCC-specific BspRI modification methylase.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Kim, S.C.
AU  - Szilak, L.
AU  - Kovacs, A.
AU  - Venetianer, P.
TI  - Complementation by detached parts of GGCC-specific DNA methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4843
EP  - 4847
VL  - 19
AB  - Individually inactive N- and C-terminal fragments of the m5C-methyltransferase
AB  - M.BspRI can complement each other resulting in specific, in vivo methylation of
AB  - the DNA.  This was shown by cloning the coding regions for N- and C-terminal
AB  - parts of the enzyme in compatible plasmids and co-transforming them into E.
AB  - coli cells.  The enzyme could be detached at several different sites, producing
AB  - either non-overlapping or partially overlapping fragments capable of
AB  - complementation.  Reconstitution of the active methyltransferase from inactive
AB  - fragments was demonstrated in vitro, as well.  Another GGCC-specific
AB  - methyltransferase, M.BsuRI, showed a similar complementation phenomenon.
AB  - Moreover, interspecies complmentation was observed between appropriate
AB  - fragments of the two closely related enzymes M.BspRI and M.BsuRI.  Fragments of
AB  - structurally and functionally more different methyltransferases were unable to
AB  - complement each other.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Kiss, A.
AU  - Erdei, S.
AU  - Posfai, J.
AU  - Venetianer, P.
TI  - Structure of the Bacillus sphaericus R modification methylase gene.
JO  - J. Mol. Biol.
PY  - 1983
SP  - 597
EP  - 610
VL  - 170
AB  - A 2500 base-pair segment of Bacillus sphaericus R DNA cloned in Escherichia
AB  - coli has previously been shown to carry the functional BspRI modification
AB  - methylase gene.  The approximate location of the gene on this DNA segment and
AB  - its direction of transcription were established by subcloning experiments.  The
AB  - nucleotide sequence of the relevant region was determined by the Maxam-Gilbert
AB  - procedure.  An open reading frame that can code for a 424 amino acid protein
AB  - was found.  The calculated molecular weight (48,264) of this protein is in fair
AB  - agreement with previous estimates (50,000 to 52,000).  The synthesis of this
AB  - protein was demonstrated in E. coli minicells.  The initiation point of
AB  - transcription by E. coli RNA polymerase was localized by in vitro transcription
AB  - experiments.  The open reading frame starts 29 base-pairs downstream from the
AB  - transcription initiation site and it is preceded by a sequence showing
AB  - extensive Shine-Dalgarno complementarity.  Subcloning experiments and
AB  - translation in minicells suggest that after removal of this translational
AB  - initiation site, a secondary start site 29 amino acids downstream can also
AB  - start translation in E. coli and this shorter protein retains the methylase
AB  - activity.  The overall base composition of the gene and the codon usage
AB  - indicate a strong preference for A.T base-pairs.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Kiss, A.
AU  - Venetianer, P.
TI  - Overproduction of the Bacillus sphaericus R modification methylase in Escherichia coli and its purification to homogeneity.
JO  - Gene
PY  - 1986
SP  - 63
EP  - 67
VL  - 50
AB  - A DNA fragment containing the information coding for the GGCC-specific Bacillus
AB  - sphaericus R modification methylase, BspR, was inserted into plasmid vector
AB  - pKK223-3 under the control of the strong and inducible tac promoter, and
AB  - transformed into Escherichia coli HB101.  Upon induction this strain
AB  - accumulated the methylase enzyme (while cell growth was inhibited) up to
AB  - several percent of total cellular protein.  Homogeneous methylase could be
AB  - prepared in three purification steps.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Szybalski, W.
TI  - Increasing the FokI cleavage specificity from 5 to 7 base pairs by two-step methylation.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 6245
EP  - 6245
VL  - 16
AB  - Non-cognate methylation of specific nucleotides of the recognition sequence
AB  - could inhibit the methylase but not the endonuclease of the same
AB  - restriction-modification system.  This permits an increase in the cleavage
AB  - specificity of the restriction enzyme by two-step methylation of the DNA, as
AB  - shown here for the three-component M.MspI-M.FokI-FokI combination, changing
AB  - FokI specificity from 5 to 7 bp.  The cleavage specificity of FokI is
AB  - 5'-GGATG(N)9/13.  M.FokI methylates only one strand of the recognition site
AB  - resulting in GGmATG sequence.  MspI and FokI sites can overlap in the 7-bp
AB  - sequence CCGGATG or in the 8-bp sequence CCGGGATG.  Methylation of such sites
AB  - by M.MspI (methylation specificity:  mCCGG) produces non-cognate methylation of
AB  - the overlapping FokI sites, resulting in  (a)G GATG    CmCTAC or (b)GGATG
AB  - mCCTAC sequences, respectively.  We show here that in case (a), M.FokI is
AB  - inhibited and FokI is unaffected (Fig. 2, lanes 3 and 2, respectively), while
AB  - in case (b), M.FokI is unaffected and FokI is partially inhibited (Fig. 2,
AB  - lanes 6 and 5, respectively, where M.HpaII was used to produce the (b) type
AB  - non-cognate methylation of FokI sites on the same 7-bp sequences).  As a
AB  - result, when the DNA is premethylated by M.MspI, M.FokI cannot methylate those
AB  - 7-bp CCGGATG sequences (which thus remain susceptible to FokI), whereas all
AB  - other FokI sites would be methylated and thus protected from FokI cleavage.
AB  - However, cleavage by FokI at the CCGGATG sites may not be complete (max 90%),
AB  - because M.FokI has some residual affinity to the sites premethylated by M.MspI,
AB  - especially when excess M.FokI is used (data not shown).  Nevertheless, in many
AB  - cases this does not affect the applicability of the system.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Szybalski, W.
TI  - A simple method for locating methylated bases in DNA, as applied to detect asymmetric methylation by M.FokIA.
JO  - Gene
PY  - 1988
SP  - 147
EP  - 151
VL  - 69
AB  - Class-IIS restriction enzymes, which cut the DNA outside their recognition sequence, could be
AB  - used for locating the bases methylated by a DNA-modification methylase.  This is possible
AB  - because methylation of the class-IIS cut sites does not interfere with the cleavage.  The
AB  - method consists of (i) selection of a nucleotide sequence with appropriate overlap between the
AB  - methylase recognition site and the class-IIS enzyme cut site, (ii) methylation using
AB  - S-adenosylmethionine as [3H]methyl donor, (iii) cleavage of the methylated sequence with the
AB  - class-IIS enzyme, (iv) separation of the cleavage products and identification of the
AB  - 3H-labelled fragment.  Using this simple and straightforward method, we have shown that
AB  - M.FokIA is an adenine methylase and methylates asymmetrically one strand of the FokI
AB  - recognition site, resulting in the
AB  - 5'-GGmATG(N)9
AB  - CC TAC(N)13
AB  - sequence.  In addition, it was observed that another class-IIS restriction enzyme, SfaNI, is
AB  - completely inhibited by methylation of its recognition site,  5'-GCA TC/CGTmAG, by M.FokIA.
ER  -

TY  - JOUR
AU  - Posfai, G.
AU  - Szybalski, W.
TI  - A simple method for locating methylated bases in DNA using class-IIS restriction enzymes.
JO  - Gene
PY  - 1988
SP  - 179
EP  - 181
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Posfai, J.
AU  - Bhagwat, A.S.
AU  - Posfai, G.
AU  - Roberts, R.J.
TI  - Predictive motifs derived from cytosine methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 2421
EP  - 2435
VL  - 17
AB  - Thirteen bacterial DNA methyltransferases that catalyze the formation of
AB  - 5-methylcytosine within specific DNA sequences possess related structures.
AB  - Similar building blocks (motifs), containing invariant positions, can be found
AB  - in the same order in all thirteen sequences.  Five of these blocks are highly
AB  - conserved while a further five contain weaker similarities.  One block, which
AB  - has the most invariant residues, contains the proline-cysteine dipeptide of the
AB  - proposed catalytic site.  A region in the second half of each sequence is
AB  - unusually variable both in length and sequence composition.  Those
AB  - methyltransferases that exhibit significant homology in this region share
AB  - common specificity in DNA recognition.  The five highly conserved motifs can be
AB  - used to discriminate the known 5-methylcytosine forming methyltransferases from
AB  - all other methyltransferases of known sequence, and from all other identified
AB  - proteins in the PIR, GenBank and EMBL databases.  These five motifs occur in a
AB  - mammalian methyltransferase responsible for the formation of 5-methylcytosine
AB  - within CG dinucleotides.  By searching the unidentified open reading frames
AB  - present in the GenBank and EMBL databases, two potential 5-methylcytosine
AB  - forming methyltransferases have been found.
ER  -

TY  - JOUR
AU  - Posfai, J.
AU  - Bhagwat, A.S.
AU  - Roberts, R.J.
TI  - Sequence motifs specific for cytosine methyltransferases.
JO  - Gene
PY  - 1988
SP  - 261
EP  - 265
VL  - 74
AB  - Using a new alignment method, the sequences of 13 m5C methyltransferases
AB  - (MTases) have been examined.  Five extremely well-conserved blocks of sequence
AB  - have been detected and have been used as fixed points for the alignment of the
AB  - 13 sequences.  Following this initial alignment, five further blocks of
AB  - similarity have been identified to give a total of ten recognizable blocks of
AB  - sequence homology that are all arranged in a common order.  The structures of
AB  - these MTases consist of a variable-length N-terminal arm followed by eight
AB  - well-conserved blocks each separated by small variable-length regions.  A large
AB  - variable-length segment of 90 to 270 amino acids (aa) then follows.  After this
AB  - are two blocks, and a variable-length C-terminal segment completes the
AB  - sequence.  Within the final alignment, 20 aa in the protein sequences, and 86
AB  - nucleotides in the nucleotide sequences are invariant.  The strongest
AB  - conservation is found in proximity to a suspected functional site that contains
AB  - the dipeptide proline-cysteine.  Consensus patterns can be defined for the five
AB  - best conserved blocks and, when used as search motifs, are able to clearly
AB  - distinguish between the m5C MTases and all other identified proteins in the PIR
AB  - database.  This suggests they may be of use in identifying putative MTases
AB  - among protein sequences of unknown function.
ER  -

TY  - JOUR
AU  - Posfai, J.
AU  - Roberts, R.J.
TI  - Predictive motifs of cytosine methylases.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 213
EP  - 213
VL  - 13D
AB  - Fourteen bacterial DNA methyltransferases that catalyze the formation of
AB  - 5-methylcytosine within specific DNA sequences possess related structures.
AB  - Similar building blocks (motifs), containing invariant positions, can be found
AB  - in the same order in all fourteen sequences.  Five of these blocks are highly
AB  - conserved while a further five contain weaker similarities.  One block which
AB  - has the most invariant residues, contains the proline-cysteine dipeptide of the
AB  - proposed catalytic site.  A region in the second half of each sequence is
AB  - unusually variable both in length and sequence composition.  Those
AB  - methyltransferases that exhibit significant homology in this region share
AB  - common specificity in DNA recognition.  The five highly conserved motifs can be
AB  - used to discriminate the known 5-methylcytosine forming methyltransferases from
AB  - all other methyltransferases of known sequence and from all other identified
AB  - proteins in the PIR, GenBank and EMBL databases.  These five motifs occur in
AB  - the eukaryotic mammalian methyltransferase.  By searching the unidentified open
AB  - reading frames present in the GenBank and EMBL databases two potential cytosine
AB  - methyltransferases have been found that were not recognized previously.
ER  -

TY  - JOUR
AU  - Potnis, N.
AU  - Krasileva, K.
AU  - Chow, V.
AU  - Almeida, N.F.
AU  - Patil, P.B.
AU  - Ryan, R.P.
AU  - Sharlach, M.
AU  - Behlau, F.
AU  - Dow, J.M.
AU  - Momol, M.
AU  - White, F.F.
AU  - Preston, J.F.
AU  - Vinatzer, B.A.
AU  - Koebnik, R.
AU  - Setubal, J.C.
AU  - Norman, D.J.
AU  - Staskawicz, B.J.
AU  - Jones, J.B.
TI  - Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper.
JO  - BMC Genomics
PY  - 2011
SP  - 146
EP  - 146
VL  - 12
AB  - BACKGROUND: Bacterial spot of tomato and pepper is caused by four Xanthomonas
AB  - species and is a major plant disease in warm humid climates. The four species are
AB  - distinct from each other based on physiological and molecular characteristics.
AB  - The genome sequence of strain 85-10, a member of one of the species, Xanthomonas
AB  - euvesicatoria (Xcv) has been previously reported. To determine the relationship
AB  - of the four species at the genome level and to investigate the molecular basis of
AB  - their virulence and differing host ranges, draft genomic sequences of members of
AB  - the other three species were determined and compared to strain 85-10. RESULTS: We
AB  - sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X.
AB  - perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The
AB  - genomes were compared with each other and with the previously sequenced Xcv
AB  - strain 85-10. In addition, the molecular features were predicted that may be
AB  - required for pathogenicity including the type III secretion apparatus, type III
AB  - effectors, other secretion systems, quorum sensing systems, adhesins,
AB  - extracellular polysaccharide, and lipopolysaccharide determinants. Several novel
AB  - type III effectors from Xg strain 101 and Xv strain 1111 genomes were
AB  - computationally identified and their translocation was validated using a reporter
AB  - gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice,
AB  - and a functional Ax21 sulfation system were identified in Xcv. Genes encoding
AB  - proteins with functions mediated by type II and type IV secretion systems have
AB  - also been compared, including enzymes involved in cell wall deconstruction, as
AB  - contributors to pathogenicity. CONCLUSIONS: Comparative genomic analyses revealed
AB  - considerable diversity among bacterial spot pathogens, providing new insights
AB  - into differences and similarities that may explain the diverse nature of these
AB  - strains. Genes specific to pepper pathogens, such as the O-antigen of the
AB  - lipopolysaccharide cluster, and genes unique to individual strains, such as novel
AB  - type III effectors and bacteriocin genes, have been identified providing new
AB  - clues for our understanding of pathogen virulence, aggressiveness, and host
AB  - preference. These analyses will aid in efforts towards breeding for broad and
AB  - durable resistance in economically important tomato and pepper cultivars.
ER  -

TY  - JOUR
AU  - Potshangbam, M.
AU  - Sahoo, D.
AU  - Verma, P.
AU  - Verma, S.
AU  - Kalita, M.C.
AU  - Indira, D.S.
TI  - Draft Genome Sequence of Bacillus altitudinis Lc5, a Biocontrol and Plant Growth-Promoting Endophyte Strain Isolated from Indigenous Black Rice of Manipur.
JO  - Genome Announcements
PY  - 2018
SP  - e00601
EP  - e00618
VL  - 6
AB  - We report here the 3.6-Mb draft genome of Bacillus altitudinis Lc5, a potential plant growth
AB  - promoter and an active antagonistic endophyte of black rice. This
AB  - genome study will provide better insights into the strain's mechanisms for plant
AB  - growth promotion and biocontrol, thus facilitating its application in organic
AB  - agriculture.
ER  -

TY  - JOUR
AU  - Potter, A.A.
AU  - Loutit, J.S.
TI  - Exonuclease activity from Pseudomonas aeruginosa which is missing in phenotypically restrictionless mutants.
JO  - J. Bacteriol.
PY  - 1982
SP  - 1204
EP  - 1209
VL  - 151
AB  - A phenotypically restrictionless strain of Pseudomonas aeruginosa was found to
AB  - lack a deoxyribonuclease specific for linear duplex DNA.  The purified enzyme
AB  - had an optimum pH of 8.5, required MgCl2 (10 mM) for maximum activity, and did
AB  - not require ATP.  Neither the degradation of heat-denatured DNA nor the
AB  - degradation of bacteriophage F116 DNA was detected.  The genome of
AB  - bacteriophage F116 was shown to possess single-stranded terminal regions, which
AB  - account for the resistance to degradation and for the ability of the phage to
AB  - transfect restriction-proficient strains.
ER  -

TY  - JOUR
AU  - Potter, B.V.L.
AU  - Eckstein, F.
TI  - Cleavage of phosphorothioate-substituted DNA by restriction endonucleases.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 14243
EP  - 14248
VL  - 259
AB  - M13 RF DNA was synthesized in vitro in the presence of various single
AB  - deoxynucleoside 5'-O-(1-thiotriphosphate) phosphorothioate analogues, and the
AB  - three other appropriate deoxynucleoside triphosphates using a M13
AB  - (+)-single-stranded template, Escherichia coli DNA polymerase I and T4 DNA
AB  - ligase.  The resulting DNAs contained various restriction endonuclease
AB  - recognition sequences which had been modified at their cleavage points in the
AB  - (-)-strand by phosphorothioate substitution.  The behavior of the restriction
AB  - enzymes AvaI, BamHI, EcoRI, HindIII, and SalI towards these substituted DNAs
AB  - was investigated.  EcoRI, BamHI, and HindIII were found to cleave appropriate
AB  - phosphorothioate-substituted DNA at a reduced rate compared to normal M13 RF
AB  - DNA, and by a two-step process in which all of the DNA is converted to an
AB  - isolable intermediate nicked molecule containing a specific discontinuity at
AB  - the respective recognition site presumably in the (+)-strand.  By contrast,
AB  - SalI cleaved substituted DNA effectively without the intermediacy of a nicked
AB  - form.  AvaI, however, is only capable of cleaving the unsubstituted (+)-strand
AB  - in appropriately modified DNA.
ER  -

TY  - JOUR
AU  - Potter, R.F.
AU  - D'Souza, A.W.
AU  - Wallace, M.A.
AU  - Shupe, A.
AU  - Patel, S.
AU  - Gul, D.
AU  - Kwon, J.H.
AU  - Andleeb, S.
AU  - Burnham, C.A.
AU  - Dantas, G.
TI  - Draft Genome Sequence of the blaOXA-436- and blaNDM-1-Harboring Shewanella putrefaciens SA70 Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00644
EP  - e00617
VL  - 5
AB  - We sequenced a carbapenem-resistant Shewanella putrefaciens isolate cultured from the sink
AB  - handle of a Pakistan hospital room. Assembly annotation indicates that
AB  - the isolate has a chromosomal blaOXA-436 carbapenemase and a plasmid-borne
AB  - blaNDM-1 gene. To our knowledge, this is the first report of a Shewanella species
AB  - harboring blaNDM.
ER  -

TY  - JOUR
AU  - Potter, S.S.
AU  - Bott, K.F.
AU  - Newbold, J.E.
TI  - Two-dimensional restriction analysis of the Bacillus subtilis genome: gene purification and ribosomal ribonucleic acid gene organization.
JO  - J. Bacteriol.
PY  - 1977
SP  - 492
EP  - 500
VL  - 129
AB  - With two-dimensional restriction enzyme analysis we have been able to cleave
AB  - the Bacillus subtilis genome and resolve the resulting deoxyribonucleic acid
AB  - (DNA) segments into discrete bands on agarose gels.  A general procedure for
AB  - gene purification has been developed by coupling multidimensional restriction
AB  - analysis with a biological assay for gene detection.  The organization of
AB  - ribosomal ribonucleic acid (rRNA) genes was studied by hybridizing 16S and 23S
AB  - rRNA probes to the two-dimensional DNA banding patterns.
ER  -

TY  - JOUR
AU  - Pouillot, F.
AU  - Fayolle, C.
AU  - Carniel, E.
TI  - A putative DNA adenine methyltransferase is involved in Yersinia pseudo tuberculosis pathogenicity.
JO  - Microbiology
PY  - 2007
SP  - 2426
EP  - 2434
VL  - 153
AB  - Some adenine methyltransferases have been shown not only to protect specific DNA restriction
AB  - sites from cleavage by a restriction
AB  - endonuclease, but also to play a role in various bacterial processes
AB  - and sometimes in bacterial virulence. This study focused on a type I
AB  - restriction-modification system (designated yrml) of Y.
AB  - pseudotuberculosis. This system is composed of three adjacent genes
AB  - which could potentially encode an N-6-adenine DNA methylase (YamA), an
AB  - enzyme involved in site-specific recognition (YrsA) and a restriction
AB  - endonuclease (YreA). Screening of 85 isolates of Y. pestis and Y.
AB  - pseudotuberculosis indicated that the yrml system has been lost by Y.
AB  - pestis and that yamA (but not yrsA or yreA) is present in all Y
AB  - pseudotuberculosis strains tested, suggesting that it may be important
AB  - at some stages of the epidemiological cycle of this species. To further
AB  - investigate the role of yamA in Y pseudo tuberculosis survival,
AB  - multiplication or virulence, a Delta yamA mutant of Y
AB  - pseudotuberculosis IP32953 was constructed by allelic exchange with a
AB  - kanamycin cassette. The fact that Delta yamA mutants were obtained
AB  - indicated that this gene is not essential for Y pseudotuberculosis
AB  - viability. The IP32953 Delta yamA mutant strain grew as well as the
AB  - wild-type in a rich medium at both 28 degrees C and 37 degrees C. It
AB  - also grew normally in a chemically defined medium at 28 degrees C, but
AB  - exhibited a growth defect at 37 degrees C. In contrast to the Dam
AB  - adenine methyltransferase, a mutation in yamA did not impair the
AB  - functions of DNA repair or resistance to detergents. However, the Delta
AB  - yamA mutant exhibited a virulence defect in a mouse model of
AB  - intragastric infection. The in silico analysis indicated that the
AB  - chromosomal region carrying the Y pseudotuberculosis yrml locus has
AB  - been replaced in Y. pestis by a horizontally acquired region which
AB  - potentially encodes another methyltransferase. YamA might thus be
AB  - dispensable for Y. pestis growth and virulence because this species has
AB  - acquired another gene fulfilling the same functions.
ER  -

TY  - JOUR
AU  - Poulter, R.
AU  - Taiaroa, G.
AU  - Sumpter, N.
AU  - Stockwell, P.
AU  - Butler, M.
TI  - Complete Genome Sequence of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Biovar 5, Originating from Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01409
EP  - e01417
VL  - 5
AB  - We present the first complete genome sequence of a copper-resistant biovar 5 strain of a
AB  - bacterial pathogen of kiwifruit, Pseudomonas syringae pv. actinidiae.
AB  - Comparison with the genome sequence of a copper-sensitive biovar 5 isolate
AB  - indicates that copper resistance is encoded on a plasmid.
ER  -

TY  - JOUR
AU  - Poulter, R.T.M.
AU  - Goodwin, T.J.D.
AU  - Butler, M.I.
TI  - The nuclear-encoded inteins of fungi.
JO  - Fungal Genet. Biol.
PY  - 2007
SP  - 153
EP  - 179
VL  - 44
AB  - An intein is a protein sequence embedded within a precursor protein that is excised during
AB  - protein maturation. Inteins were first found
AB  - encoded in the VMA gene of Saccharomyces cerevisiae. Subsequently, they
AB  - have been found in diverse organisms (eukaryotes, archaea, eubacteria
AB  - and viruses). The VMA intein has been found in various saccharomycete
AB  - yeasts but not in other fungi. Different inteins have now been found
AB  - widely in the fungi (ascomycetes, basidiomycetes, zygomycetes and
AB  - chytrids) and in diverse proteins. A protein distantly related to
AB  - inteins, but closely related to metazoan hedgehog proteins, has been
AB  - described from Glomeromycota. Many of the newly described inteins
AB  - contain homing endonucleases and some of these are apparently active.
AB  - The enlarged fungal intein data set permits insight into the evolution
AB  - of inteins, including the role of horizontal transfer in their
AB  - persistence. The diverse fungal inteins provide a resource for
AB  - biotechnology using their protein splicing or homing endonuclease
AB  - capabilities.
ER  -

TY  - JOUR
AU  - Povilionis, P.I.
AU  - Lubys, A.A.
AU  - Janulaitis, A.
TI  - Cloning of the restriction-modification genes of Bacillus centrosporus in Escherichia coli.
JO  - Genetika
PY  - 1988
SP  - 210
EP  - 215
VL  - 24
AB  - Using the pBR327 vector we have produced a genomic library of Bacillus
AB  - centrosporus.  The total plasmid DNA of the library was cleaved by the
AB  - restriction endonuclease BcnI and then transformed in Escherichia coli RR1.
AB  - Among the transformants obtained we identified two clones possessing
AB  - restriction and DNA modification profiles of BcnI and containing 13.3 kb and
AB  - 9.05 kb plasmids, respectively.  Restriction mapping of both plasmids showed
AB  - that they contained two sites for HindIII, one site for Eco31I, and one site
AB  - for Eco47III located at equal distances.  Deletion mapping of the recombinant
AB  - plasmids confirmed that this was the region of the location of the BcnI
AB  - restriction-modification genes.  On the basis of the results obtained we
AB  - discuss the special features of cloning of the restriction-modification genes.
ER  -

TY  - JOUR
AU  - Povilionis, P.I.
AU  - Lubys, A.A.
AU  - Vaisvila, R.I.
AU  - Kulakauskas, S.T.
AU  - Janulaitis, A.
TI  - Investigation of methyl-cytosine specific restriction in Escherichia coli K-12.
JO  - Genetika
PY  - 1989
SP  - 753
EP  - 755
VL  - 25
AB  - Experiments on transformation of Escherichia coli K-12 cells by plasmids
AB  - carrying RM systems with different recognition sites containing
AB  - 5-methylcytosine have shown that the gene mcrB dtermines the function of
AB  - restriction.  The data obtained made it possible to believe that E. coli
AB  - possesses no restriction system recognizing specifically cytosine methylated in
AB  - position 4.
ER  -

TY  - JOUR
AU  - Powell, I.B.
AU  - Davidson, B.E.
TI  - Resistance to in vitro restriction of DNA from lactic streptococcal bacteriophage c6A.
JO  - Appl. Environ. Microbiol.
PY  - 1986
SP  - 1358
EP  - 1360
VL  - 51
AB  - DNA isolated from streptococcal bacteriophage c6A was cut only infrequently by
AB  - many restriction endonucleases.  Fragments of c6A DNA cloned in Escherichia
AB  - coli plasmids were similarly resistant to cleavage.  We conclude that the low
AB  - frequency of cleavage is due to an unusually low number of restriction enzyme
AB  - recognition sequences in c6A DNA.
ER  -

TY  - JOUR
AU  - Powell, L.M.
AU  - Connolly, B.A.
AU  - Dryden, D.T.F.
TI  - The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarization and DNA footprint.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 947
EP  - 961
VL  - 283
AB  - The type I DNA restriction and modification systems of enteric bacteria display several
AB  - enzymatic activities due to their oligomeric structure.  Partially assembled forms of the
AB  - EcoKI enzyme from E. coli K12 can display specific DNA binding properties and modification
AB  - methyltransferase activity.  The heterodimer of one specificity (S) subunit and one
AB  - modification (M) subunit can only bind DNA whereas  the addition of a second modification
AB  - subunit to form M2S1 also confers methyltransferase activity.  We have examined the DNA
AB  - binding specificity of M1S1 and M2S1 using the change in fluorescence anisotropy which occurs
AB  - on binding of a DNA probe labelled with a hexachlorofluorescein fluorophore.  The dimer has
AB  - much weaker affinity for the EcoKI target sequence than the trimer and slightly less ability
AB  - to discriminate against other DNA sequences.  Binding of both proteins is strongly dependent
AB  - on salt concentration.  The fluorescence results compare favorably with those obtained with
AB  - the gel retardation method.  DNA footprinting using exonucleaseIII and DNaseI, and methylation
AB  - interference show no asymmetry, with both DNA strands being protected by the dimer and the
AB  - trimer.  This indicates that the dimer is a mixture of the two possible forms, M1S1 and S1M1.
AB  - The dimer has a footprint on the DNA substrate of the same length as the trimer implying that
AB  - the modification subunits are located on either side of the DNA helical axis rather than lying
AB  - along the helical axis.
ER  -

TY  - JOUR
AU  - Powell, L.M.
AU  - Dryden, D.T.F.
AU  - Murray, N.E.
TI  - Sequence-specific DNA binding by EcoKI, a type IA DNA restriction enzyme.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 963
EP  - 976
VL  - 283
AB  - The type I DNA restriction and modification enzymes of prokaryotes are multimeric enzymes that
AB  - cleave unmethylated, foreign DNA in a complex process involving recognition of the methylation
AB  - status of a DNA target sequence, extensive translocation of DNA in both directions towards the
AB  - enzyme bound at the target sequence, ATP hydrolysis, which is believed to drive the
AB  - translocation possibly via a helicase mechanism, and eventual endonucleolytic cleavage of the
AB  - DNA.  We have examined the DNA binding affinity and exonuclease III footprint of the EcoKI
AB  - type IA restriction enzyme on oligonucleotide duplexes that either contain or lack the target
AB  - sequence.  The influence of the cofactors, S-adenosyl methionine and ATP, on binding to DNA of
AB  - different methylation states has been assessed.  EcoKI in the absence of ATP, with or without
AB  - S-adenosyl methionine, binds tightly even to DNA lacking the target site and the exonuclease
AB  - footprint is large, approximately 45 base-pairs.  The protection is weaker on DNA lacking the
AB  - target site.  Partially assembled EcoKI lacking one or both of the subunits essential for DNA
AB  - cleavage, is unable to bind tightly to DNA lacking the target site but can bind tightly to the
AB  - recognition site.  The addition of ATP to EcoKI, in the presence of AdoMet, allows tight
AB  - binding only to the target site and the footprint shrinks to 30 base pairs, almost identical
AB  - to that of the modification enzyme which makes up the core of EcoKI.  The same effect occurs
AB  - when S-adenosyl homocysteine or sinefungin are substituted for S-adenosyl methionine, and ADP
AB  - or ATPgammaS are substituted for ATP.  It is proposed that the DNA binding surface of EcoKI
AB  - comprises three regions: a "core" region which recognizes the target sequence and which is
AB  - present on the modification enzyme, and a region on each DNA cleavage subunit.  The cleavage
AB  - subunits make tight contacts to any DNA molecule in the absence of cofactors, but this contact
AB  - is weakened in the presence of cofactors to allow the protein conformational changes required
AB  - for DNA translocation when a target site is recognized by the core modification enzyme.  This
AB  - weakening of the interaction between the DNA cleavage subunits and the DNA could allow more
AB  - access of exonuclease III to DNA and account for the shorter footprint.
ER  -

TY  - JOUR
AU  - Powell, L.M.
AU  - Dryden, D.T.F.
AU  - Willcock, D.F.
AU  - Pain, R.H.
AU  - Murray, N.E.
TI  - DNA recognition by the EcoK methyltransferase. The influence of DNA methylation and the cofactor S-adenosyl-L-methionine.
JO  - J. Mol. Biol.
PY  - 1993
SP  - 60
EP  - 71
VL  - 234
AB  - The methyltransferase of the EcoK type I restriction/modification system is trimeric, M2S1,
AB  - where the S subunit determines the sequence specificity of the enzyme. The methyltransferase
AB  - has a strong preference for hemimethylated substrate DNA and therefore, we have investigated
AB  - the effect of the methylation state of DNA on binding by the enzyme, together with the effects
AB  - on binding of the cofactor S-adenosyl-L-methionine. Our results indicate that the
AB  - methyltransferase has two non-interacting S-adenosyl-L-methionine binding sites, each with a
AB  - dissociation constant of 3.60 (+-0.42)uM determined by equilibrium dialysis, or 2.21 (+-0.29)
AB  - uM determined by the displacement of a fluorescent probe. Ultraviolet light-induced
AB  - crosslinking showed that S-adenosyl-L-methionine binds strongly only to the modification (M)
AB  - subunits. Changes in the sedimentation velocity of the methyltransferases imply a protein
AB  - conformational change due to S-adenosyl-L-methionine binding. Gel retardation results show
AB  - that the binding of S-adenosyl-L-methionine to the methyltransferase enhances binding to both
AB  - specific and non-specific DNAs, but the enhancement is greater for the specific DNA.
AB  - Differences in binding affinities contribute to the recognition of the specific nucleotide
AB  - sequence AAC(N)6GTGC by the methyltransferase in preference to a non-specific sequence. In
AB  - contrast, although the complexes of unmodified and hemimethylated DNAs with the
AB  - methyltransferase have different mobilities in non-denaturing gels, there appears to be no
AB  - contribution of binding affinity to the distinction between these two substrates. Therefore,
AB  - the preference for the hemimethylated substrate must be due to a difference in catalysis.
ER  -

TY  - JOUR
AU  - Powell, L.M.
AU  - Lejeune, E.
AU  - Hussain, F.S.
AU  - Cronshaw, A.D.
AU  - Kelly, S.M.
AU  - Price, N.C.
AU  - Dryden, D.T.
TI  - Assembly of EcoKI DNA methyltransferase requires the C-terminal region of the HsdM modification subunit.
JO  - Biophys. Chem.
PY  - 2003
SP  - 129
EP  - 137
VL  - 103
AB  - The methyltransferase component of type I DNA restriction and modification systems comprises
AB  - three subunits, one DNA sequence specificity subunit and
AB  - two DNA modification subunits. Limited proteolysis of the EcoKI
AB  - methyltransferase shows that a 55-kDa N-terminal fragment of the 59-kDa
AB  - modification subunit is resistant to degradation. We have purified this
AB  - fragment and determined by mass spectrometry that proteolysis removes 43
AB  - or 44 amino acids from the C-terminus. The fragment fails to interact with
AB  - the other subunits even though it still possesses secondary and tertiary
AB  - structure and the ability to bind the S-adenosylmethionine cofactor. We
AB  - conclude that the C-terminal region of the modification subunit of EcoKI
AB  - is essential for the assembly of the EcoKI methyltransferase.
ER  -

TY  - JOUR
AU  - Powell, L.M.
AU  - Murray, N.E.
TI  - S-adenosyl methionine alters the DNA contacts of the EcoKI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 967
EP  - 974
VL  - 23
AB  - The EcoKI methyltransferase methylates two adenines on opposite strands of its bipartite DNA
AB  - recognition sequence AAC(N6)GTGC. The enzyme has a strong preference for hemimethylated DNA
AB  - substrates, but the methylation state of the DNA does not influence its binding affinity.
AB  - Methylation interference was used to compare the contacts made by the EcoKI methyltransferase
AB  - with unmodified, hemimethylated or fully modified DNAs. Contacts were seen at or near the N7
AB  - position of guanine, in the major groove, for all of the guanines in the EcoKI recognition
AB  - sequence, and at two guanines on the edge of the intervening spacer sequence. The presence of
AB  - the cofactor and methyl donor S-adenosyl methionine had a striking effect on the interference
AB  - pattern for unmodified DNA which could not be mimicked by the presence of the cofactor
AB  - analogue S-adenosyl homocysteine. In contrast, S-adenosyl methionine had no effect on the
AB  - interference patterns for either kind of hemimethylated DNA, or for fully modified DNA.
AB  - Differences between the interference patterns for the unmodified DNA provide evidence that
AB  - methylation of the target sequence influences the conformation of the protein-DNA interface,
AB  - and illustrate the importance of S-adenosyl methionine in the distinction between unmodified
AB  - and methylated DNA by the methyltransferase.
ER  -

TY  - JOUR
AU  - Powell, R.J.
AU  - Bachvaroff, T.R.
AU  - Hill, R.T.
TI  - Draft Genome Sequence of the Alga-Aggregating Bacterium Bacillus sp. Strain RP1137.
JO  - Genome Announcements
PY  - 2014
SP  - e00973
EP  - e00913
VL  - 2
AB  - Bacillus sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate
AB  - biofuel-producing microalgae. By 16S rRNA gene sequencing, it was found
AB  - to be related to the industrially important Bacillus megaterium. Here, we report
AB  - the draft genome sequence of Bacillus sp. strain RP1137.
ER  -

TY  - JOUR
AU  - Power, K.A.
AU  - Yan, Q.
AU  - Fox, E.M.
AU  - Cooney, S.
AU  - Fanning, S.
TI  - Genome Sequence of Cronobacter sakazakii SP291, a Persistent Thermotolerant Isolate Derived from a Factory Producing Powdered Infant Formula.
JO  - Genome Announcements
PY  - 2013
SP  - e0008213
EP  - e0008213
VL  - 1
AB  - Cronobacter is an opportunistic pathogen associated with meningitis in neonates.  Based on
AB  - long-term surveillance of a powdered infant formula production facility,
AB  - a persistent and thermotolerant isolate, denoted Cronobacter sakazakii SP291, was
AB  - detected. Here we report the complete genome along with the sequences of three
AB  - plasmids identified in this organism.
ER  -

TY  - JOUR
AU  - Power, S.E.
AU  - Harris, H.M.
AU  - Bottacini, F.
AU  - Ross, R.P.
AU  - O'Toole, P.W.
AU  - Fitzgerald, G.F.
TI  - Draft Genome Sequence of Lactobacillus crispatus EM-LC1, an Isolate with Antimicrobial Activity Cultured from an Elderly Subject.
JO  - Genome Announcements
PY  - 2013
SP  - e01070
EP  - e01013
VL  - 1
AB  - Here we report the 1.86-Mb draft genome sequence of Lactobacillus crispatus EM-LC1, a fecal
AB  - isolate with antimicrobial activity. This genome sequence is
AB  - expected to provide insights into the antimicrobial activity of L. crispatus and
AB  - improve our knowledge of its potential probiotic traits.
ER  -

TY  - JOUR
AU  - Powers, J.G.
AU  - Weigman, V.J.
AU  - Shu, J.
AU  - Pufky, J.M.
AU  - Cox, D.
AU  - Hurban, P.
TI  - Efficient and accurate whole genome assembly and methylome profiling of E. coli.
JO  - BMC Genomics
PY  - 2013
SP  - 675
EP  - 675
VL  - 14
AB  - BACKGROUND: With the price of next generation sequencing steadily decreasing, bacterial genome
AB  - assembly is now accessible to a wide range of researchers. It is
AB  - therefore necessary to understand the best methods for generating a genome
AB  - assembly, specifically, which combination of sequencing and bioinformatics
AB  - strategies result in the most accurate assemblies. Here, we sequence three E.
AB  - coli strains on the Illumina MiSeq, Life Technologies Ion Torrent PGM, and
AB  - Pacific Biosciences RS. We then perform genome assemblies on all three datasets
AB  - alone or in combination to determine the best methods for the assembly of
AB  - bacterial genomes. RESULTS: Three E. coli strains - BL21(DE3), Bal225, and
AB  - DH5alpha - were sequenced to a depth of 100x on the MiSeq and Ion Torrent
AB  - machines and to at least 125x on the PacBio RS. Four assembly methods were
AB  - examined and compared. The previously published BL21(DE3) genome
AB  - [GenBank:AM946981.2], allowed us to evaluate the accuracy of each of the
AB  - BL21(DE3) assemblies. BL21(DE3) PacBio-only assemblies resulted in a 90%
AB  - reduction in contigs versus short read only assemblies, while N50 numbers
AB  - increased by over 7-fold. Strikingly, the number of SNPs in PacBio-only
AB  - assemblies were less than half that seen with short read assemblies (~20 SNPs vs.
AB  - ~50 SNPs) and indels also saw dramatic reductions (~2 indel >5 bp in PacBio-only
AB  - assemblies vs. ~12 for short-read only assemblies). Assemblies that used a
AB  - mixture of PacBio and short read data generally fell in between these two
AB  - extremes. Use of PacBio sequencing reads also allowed us to call covalent base
AB  - modifications for the three strains. Each of the strains used here had a known
AB  - covalent base modification genotype, which was confirmed by PacBio sequencing.
AB  - CONCLUSION: Using data generated solely from the Pacific Biosciences RS, we were
AB  - able to generate the most complete and accurate de novo assemblies of E. coli
AB  - strains. We found that the addition of other sequencing technology data offered
AB  - no improvements over use of PacBio data alone. In addition, the sequencing data
AB  - from the PacBio RS allowed for sensitive and specific calling of covalent base
AB  - modifications.
ER  -

TY  - JOUR
AU  - Powney, R.
AU  - Smits, T.H.
AU  - Sawbridge, T.
AU  - Frey, B.
AU  - Blom, J.
AU  - Frey, J.E.
AU  - Plummer, K.M.
AU  - Beer, S.V.
AU  - Luck, J.
AU  - Duffy, B.
AU  - Rodoni, B.
TI  - Genome Sequence of an Erwinia amylovora Strain with Restricted Pathogenicity to Rubus Plants.
JO  - J. Bacteriol.
PY  - 2010
SP  - 785
EP  - 786
VL  - 193
AB  - Here we present the genome of a strain of Erwinia amylovora, the fire blight pathogen, with
AB  - restricted pathogenicity to Rubus spp. Comparative
AB  - genomics of ATCC BAA-2158 with E. amylovora strains from non-Rubus hosts
AB  - identified significant genetic differences but supports the inclusion of
AB  - this strain within the species E. amylovora.
ER  -

TY  - JOUR
AU  - Pozidis, C.
AU  - Vlatakis, G.
AU  - Bouriotis, V.
TI  - Sequence-specific DNA affinity chromatography: Application of a group specific adsorbent for the isolation of restriction endonucleases.
JO  - Prog. Biotechnol.
PY  - 1994
SP  - 543
EP  - 546
VL  - 9
AB  - Several rapid and effective methods have been described to obtain restriction endonucleases
AB  - suitable for commercial exploitation. However lengthy and laborious protocols have been
AB  - necessary to obtain homogeneous enzymes. The use of sequence-specific DNA affinity
AB  - chromatography to purify restriction endonucleases EcoRI and SphI to near homogeneity in a two
AB  - step procedure has been recently reported. However, the high cost of these adsorbents is a
AB  - limiting factor for their wider application. The application of a sequence-specific DNA
AB  - affinity ligand containing recognition sequences for 34 restriction endonucleases as
AB  - group-specific ligand for the isolation of restriction endonucleases is now reported. Crude
AB  - samples of six restriction endonucleases namely BshFI, BamHI, SmaI, SacII, PvuII and SalI were
AB  - shown to bind to this adsorbent and could be eluted at different Kcl concentrations with
AB  - purification factors obtained varying from 8 to greater than 300 fold and recoveries from
AB  - 75-94%. Furthermore, restriction endonuclease BshFI, an isoschizomer of HaeIII from the
AB  - microorganism Bacillus sphaericus was purified to near homogeneity employing a two step
AB  - procedure which involves DNA cellulose chromatography and oligonucleotide ligand affinity
AB  - chromatography.
ER  -

TY  - JOUR
AU  - Pozidis, C.
AU  - Vlatakis, G.
AU  - Bouriotis, V.
TI  - Sequence-specific DNA affinity chromatography: application of a group-specific adsorbent for the isolation of restriction endonucleases.
JO  - J. Chromatogr.
PY  - 1993
SP  - 151
EP  - 157
VL  - 630
AB  - The use of sequence-specific DNA affinity adsorbents for the isolation of restriction
AB  - endonuclease EcoRI and SphI to near homogeneity has been reported. However, the high cost of
AB  - these adsorbents is a limiting factor for their wider application. This paper reports the
AB  - application of sequence-specific DNA affinity ligands containing recognition sequences for 34
AB  - restriction endonucleases as group specific ligands in the isolation of restriction
AB  - endonuclease. Crude samples of six restriction endonucleases, namely BshFI, BamHI, SmaI,
AB  - SacII, PvuII and SalI, were shown to bind to these adsorbents and could be eluted at different
AB  - KCl concentrations. High purification factors and recoveries were obtained. Restriction
AB  - endonuclease BshFI, an isoschizomer of HaeIII, from the microorganism Bacillus sphaericus was
AB  - purified to near homogeneity employing a two-step procedure which involves DNA-cellulose
AB  - chromatography and oligonucleotide-ligand affinity chromatography. The enzyme exists as a
AB  - monomer with an apparent relative molecular mass of 34000 as determined by both sodium dodecyl
AB  - sulphate-polyacrylamide gel electrophoresis and size exclusion chromatography.
ER  -

TY  - JOUR
AU  - Prabhakara, S.
AU  - Khedkar, S.
AU  - Loganathan, R.M.
AU  - Chandana, S.
AU  - Gowda, M.
AU  - Arakere, G.
AU  - Seshasayee, A.S.
TI  - Draft Genome Sequence of Staphylococcus aureus 118 (ST772), a Major Disease Clone from India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3727
EP  - 3728
VL  - 194
AB  - We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying
AB  - staphylococcal cassette chromosome mec (SCCmec) type V from a
AB  - pyomyositis patient. Our de novo short read assembly is approximately 2.8 Mb and
AB  - encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes
AB  - similar to those of varphi7247PVL and novel lysogenic genes at the N termini.
ER  -

TY  - JOUR
AU  - Prabhakaran, D.M.
AU  - Chowdhury, G.
AU  - Pazhani, G.P.
AU  - Ramamurthy, T.
AU  - Thomas, S.
TI  - Draft Genome Sequence of an Environmental trh+ Vibrio parahaemolyticus K23 Strain Isolated from Kerala, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00282
EP  - e00216
VL  - 4
AB  - Vibrio parahaemolyticusis the leading cause of seafood-related gastroenteritis. Here, we
AB  - report the draft genome sequence of atrh(+)strain,V.
AB  - parahaemolyticusK23, isolated from seafood. The sequence will be useful for
AB  - comparative analysis between environmental and clinical isolates ofV.
AB  - parahaemolyticus.
ER  -

TY  - JOUR
AU  - Prabhakaran, M.
AU  - Couger, M.B.
AU  - Jackson, C.A.
AU  - Weirick, T.
AU  - Fathepure, B.Z.
TI  - Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood.
JO  - Genome Announcements
PY  - 2015
SP  - e00019
EP  - e00015
VL  - 3
AB  - Pseudomonas sp. strain YS-1p and Rhizobium sp. strain YS-1r were isolated from a
AB  - lignin-degrading enrichment culture. The isolates degraded lignin-derived
AB  - monomers, dimers, alkali lignin, and, to a smaller extent (3% to 5%), lignin in
AB  - switch grass and alfalfa. Genome analysis revealed the presence of a variety of
AB  - lignin-degrading genes.
ER  -

TY  - JOUR
AU  - Pradeep, B.E.
AU  - Mahalingam, N.
AU  - Manivannan, B.
AU  - Padmanabhan, K.
AU  - Nilawe, P.
AU  - Gurung, G.
AU  - Chhabra, A.
AU  - Nagaraja, V.
TI  - Draft Genome Sequence of Elizabethkingia meningoseptica, Isolated from a Postoperative Endophthalmitis Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e01335
EP  - e01314
VL  - 2
AB  - We present the draft genome assembly of an Elizabethkingia meningoseptica strain  isolated
AB  - from a 67-year-old postoperative endophthalmitis patient who suffered
AB  - loss of vision in the right eye. The draft genome assembly has 167 contigs with a
AB  - total size of 4,019,665 bp encoding multiple drug-resistant genes.
ER  -

TY  - JOUR
AU  - Pradel, N.
AU  - Ji, B.
AU  - Gimenez, G.
AU  - Talla, E.
AU  - Lenoble, P.
AU  - Garel, M.
AU  - Tamburini, C.
AU  - Fourquet, P.
AU  - Lebrun, R.
AU  - Bertin, P.
AU  - Denis, Y.
AU  - Pophillat, M.
AU  - Barbe, V.
AU  - Ollivier, B.
AU  - Dolla, A.
TI  - The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus.
JO  - PLoS ONE
PY  - 2013
SP  - E55130
EP  - E55130
VL  - 8
AB  - Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was
AB  - isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents
AB  - a unique model for studying the adaptation of sulfate-reducing bacteria to
AB  - hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this
AB  - piezophilic bacterium. An analysis of the genome revealed the presence of seven
AB  - genomic islands as well as gene clusters that are most likely linked to life at a
AB  - high hydrostatic pressure. Comparative genomics and differential proteomics
AB  - identified the transport of solutes and amino acids as well as amino acid
AB  - metabolism as major cellular processes for the adaptation of this bacterium to
AB  - hydrostatic pressure. In addition, the proteome profiles showed that the
AB  - abundance of key enzymes that are involved in sulfate reduction was dependent on
AB  - hydrostatic pressure. A comparative analysis of orthologs from the
AB  - non-piezophilic marine bacterium D. salexigens and D. piezophilus identified
AB  - aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the
AB  - amino acids preferentially replaced by arginine, histidine, alanine and threonine
AB  - in the piezophilic strain. This work reveals the adaptation strategies developed
AB  - by a sulfate reducer to a deep-sea lifestyle.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Adams, R.L.P.
TI  - DNA methylation in plants: involvement of two different methyltransferases.
JO  - Biochem. Soc. Trans.
PY  - 1994
SP  - 297S
EP  - 297S
VL  - 22
AB  - The DNA of higher eukaryotes is methylated at carbon 5 of some cytosine residues. In
AB  - vertebrates, 3 to 8% of cytosine residues are methylated, whereas in plants as many as 30% of
AB  - the total cytosines are methylated. The higher content of methylated cytosine in the DNA of
AB  - some plants could be partly attributed to their large genome with many repetitive sequences.
AB  - However, in the vertebrate genome 5-methylcytosine (5mC) is largely confined to CG
AB  - dinucleotides, whereas in higher plants both CG dinucleotides and CNG trinucleotides are
AB  - methylated. In non-vascular plants, methylation appears to occur only at CNG trinucleotides.
AB  - Methylation of DNA in plants, as in vertebrates, is implicated in the regulation of gene
AB  - expression; an effect that may be direct, through DNA:transcription factor interaction, or
AB  - indirect via an alteration in chromatin structure.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Adams, R.L.P.
TI  - Distinct CG and CNG DNA methyltransferases in Pisum sativum.
JO  - Plant J.
PY  - 1995
SP  - 471
EP  - 481
VL  - 7
AB  - DNA methyltransferase activity, present in low salt extracts of nuclei from young pea shoot
AB  - apices, has been fractionated into two different species by assaying with model substrates.
AB  - The CG methyltransferase (an unstable enzyme believed to be of 140 kDa) methylates cytosine
AB  - only in oligonucleotides with CG and CI dinucleotide targets while an enzyme of 110 kDa (the
AB  - CNG methyltransferase) methylates the cytosines in 5'-CAG-3' and 5'-CTG-3' target
AB  - sequences, especially when hemimethylated, but not in 5'-CCG-3' nor in 5'-CGG-3' target
AB  - sequences present in oligonucleotides.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Bacolla, A.
AU  - Wells, R.D.
AU  - Roberts, R.J.
TI  - Recombinant human DNA (cytosine-5) methyltransferase.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 33002
EP  - 33010
VL  - 274
AB  - A method is described to express and purify human DNA (cytosine-5) methyltransferase (human
AB  - DNMT1) using a protein splicing (intein) fusion partner in a baculovirus expression vector.
AB  - The system produces ~1 mg of intact recombinant enzyme >95% pure per 1.5 x 10^9 insect cells.
AB  - The protein lacks any affinity tag and is identical to the native enzyme except for the two
AB  - C-terminal amino acids, proline and glycine, that were substituted for lysine and aspartic
AB  - acid for optimal cleavage from the intein affinity tag. Human DNMT1 was used for steady-state
AB  - kinetic analysis with poly(dI-dC).poly(dI-dC) and unmethylated and hemimethylated 36- and
AB  - 75-mer oligonucleotides. The turnover number (k(cat)) was 131-237 h(-1) on
AB  - poly(dI-dC).poly(dI-dC), 1.2-2.3 h(-1) on unmethylated DNA, and 8.3-49 h(-1) on hemimethylated
AB  - DNA. The Michaelis constants for DNA (K(m)(CG)) and S-adenosyl-L-methionine (AdoMet)
AB  - (K(m)(AdoMet)) ranged from 0.33-1.32 and 2.6-7.2 muM, respectively, whereas the ratio of
AB  - k(cat)/K(m)(CG) ranged from 3.9 to 44 (237-336 for poly(dI-dC).poly(dI-dC)) x 10(6) M(-1)
AB  - h(-1). The preference of the enzyme for hemimethylated, over unmethylated, DNA was 7-21-fold.
AB  - The values of k(cat) on hemimethylated DNAs showed a 2-3-fold difference, depending upon which
AB  - strand was pre-methylated. Furthermore, human DNMT1 formed covalent complexes with substrates
AB  - containing 5-fluoro-CNG, indicating that substrate specificity extended beyond the canonical
AB  - CG dinucleotide. These results show that, in addition to maintenance methylation, human DNMT1
AB  - may also carry out de novo and non-CG methyltransferase activities in vivo.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Cummings, M.
AU  - Roberts, R.J.
AU  - Adams, R.L.P.
TI  - Isolation, characterization and baculovirus-mediated expression of cDNA encoding cytosine DNA methyltransferase from Pisum sativum.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1214
EP  - 1222
VL  - 26
AB  - A series of overlapping clones complementy to the Arabidopsis cytosine-5 DNA methyltransferase
AB  - has been isolated from pea cDNA libraries.  The assembled nucleic acid sequence contains an
AB  - open reading frame of 4761 bp encoding a protein of 1554 amino acids.  Like other eukaryotic
AB  - C-5 MTases, the inferred protein has a presumed regulatory N-terminal region linked to a
AB  - catalytic C-terminal domain, which has eight of the ten conserved motifs found in prokaryotic
AB  - C-5 MTases.  The pea C-5 MTase has 65% identity at the nucleotide level and 61% identity at
AB  - the protein level, with the Arabidopsis C-5 MTase.  The catalytic domain of the pea enzyme
AB  - shares 78% identity with Arabidopsis and ~52% identity with murine and human C-5 MTases,
AB  - including the relative position of the proline-cysteine dipeptides of the catalytic center.
AB  - Using the conserved region of the cDNA as a probe, we have identified a transcript of 5 kb.
AB  - Southern blot analysis of pea genomic DNA with the above probe indicates the presence of a
AB  - single gene.  Using poly(A)+ RNA from different developmental stages and different tissues, we
AB  - have observed that expression is confined mostly to the rapidly dividing tissues of the plant.
AB  - Expression of this assembled cDNA in a baculovirus system gives a protein of ~174 kDa.  The
AB  - expressed protein can be cross-linked, in an AdoMet-dependent manner, to duplex
AB  - oligonucleotide substrates containing FdC in place of target cytosines in either CG or CAG/CTG
AB  - sequences.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Esteve, P.O.
TI  - Allosteric activator domain of maintenance human DNA (cytosine-5) methyltransferase and its role in methylation spreading.
JO  - Biochemistry
PY  - 2003
SP  - 5321
EP  - 5332
VL  - 42
AB  - The human maintenance DNA (cytosine-5) methyltransferase (hDNMT1) consists of a large
AB  - N-terminal regulatory domain fused to a catalytic C-terminal
AB  - domain by randomly repeated Gly-Lys dipeptides. Several N-terminal
AB  - deletion mutants of hDNMT1 were made, purified, and tested for substrate
AB  - specificity. Deletion mutants lacking 121, 501, 540, or 580 amino acids
AB  - from the N-terminus still functioned as DNA methyltransferases, methylated
AB  - CG sequences, and preferred hemimethylated to unmethylated DNA, as did the
AB  - full-length hDNMT1. Methylated DNA stimulated methylation spreading on
AB  - unmethylated CpG sequences for the full-length and the 121 amino acid
AB  - deletion hDNMT1 equally well but not for the mutants lacking 501, 540, or
AB  - 580 amino acids, indicating the presence of an allosteric activation
AB  - determinant between amino acids 121 and 501. Peptides from the N- and
AB  - C-termini bound methylated DNA independently. Point mutation analysis
AB  - within the allosteric region revealed that amino acids 284-287 (KKHR) were
AB  - involved in methylated DNA-mediated allosteric activation. Allosteric
AB  - activation was reduced in the double point mutant enzymes D25 (K284A and
AB  - K285A) and D12 (H286A and R287A). Retinoblastoma gene product (Rb), a
AB  - negative regulator of DNA methylation, bound to the allosteric site of
AB  - hDNMT1 and inhibited methylation, suggesting Rb may regulate methylation
AB  - spreading.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Esteve, P.O.
TI  - Mammalian DNA (cytosine-5) methyltransferases and their expression.
JO  - Clin. Immunol.
PY  - 2003
SP  - 6
EP  - 16
VL  - 109
AB  - Two classes of functional DNA (cytosine-5) methyltransferases have been discovered in mammals
AB  - to date. One class methylates the unmodified DNA and
AB  - is designated as the de novo enzyme, whereas the other maintains the
AB  - methylation status of the daughter strand during DNA replication and thus
AB  - is referred to as a maintenance DNA methyltransferase. Each enzyme
AB  - catalyzes methyl group transfer from S-adenosyl-L-methionine to cytosine
AB  - bases in DNA. During methylation the enzyme flips its target base out of
AB  - the DNA duplex into a typically concave catalytic pocket. This flipped
AB  - cytosine base is then a substrate for the enzyme-catalyzed reaction. The
AB  - newly formed 5-methylcytosine confers epigenetic information on the
AB  - parental genome without altering nucleotide sequences. This epigenetic
AB  - information is inherited during DNA replication and cell division. In
AB  - mammals, DNA methylation participates in gene expression, protection of
AB  - the genome against selfish DNA, parental imprinting, mammalian X
AB  - chromosome inactivation, developmental regulation, T cell development, and
AB  - various diseases.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Houlston, C.
AU  - Cummings, M.
AU  - Adams, R.L.P.
TI  - CG and CNG methyltransferases in plants.
JO  - Gene
PY  - 1995
SP  - 289
EP  - 291
VL  - 157
AB  - We have purified two distinct DNA methyltransferases from pea shoot tips and analyzed their
AB  - sequence specificity using synthetic oligodeoxyribonucleotide substrates and chemical
AB  - sequencing methods.  One methylates only CG target sequences, whereas the other methylates
AB  - only CAG or CTG target sequences.  We have found no evidence for methylation of the 5'
AB  - cytosine in CCG target sequences either in vivo or in vitro.  Using amino-acid sequence data,
AB  - PCR-amplified fragments from conserved sequences and heterologous probes, we have isolated
AB  - several cDNA clones that react with mRNA molecules of different sizes.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Kim, G.D.
TI  - The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity.
JO  - EMBO J.
PY  - 2002
SP  - 779
EP  - 788
VL  - 21
AB  - The mammalian DNA (cytosine-5) methyltransferase (Dnmt1) is involved in the maintenance of
AB  - methylation patterns in the genome during DNA replication and development.  The retinoblastoma
AB  - gene product, Rb, is a cell cycle regulator protein that represses transcription by recruiting
AB  - histone deacetylase (HDAC1).  In vivo, histone deacetylase associates with Dnmt1.  Here we
AB  - show that Rb itself associates with human Dnmt1 (hDnmt1) independently of its own
AB  - phosphorylation status.  Methyltransferase activity was co-purified with Rb.  The regulatory
AB  - domain of hDnmt1 binds strongly to the B and C pockets of Rb (amino acids 701-872) and
AB  - inhibits methyltransferase activity by disruption of the hDnmt1-DNA binary complex.  Weak
AB  - interaction of Rb pockets A and B with Dnmt1 was also observed.  Overexpression of Rb leads to
AB  - hypomethylation of the cellular DNA, suggesting that Rb may modulate Dnmt1 activity during DNA
AB  - replication in the cell cycle.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Roberts, R.J.
TI  - Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain.
JO  - EMBO J.
PY  - 2000
SP  - 2103
EP  - 2114
VL  - 19
AB  - The mouse (cytosine-5) DNA methyltransferase (Dnmt1) consists of a regulatory N-terminal and a
AB  - catalytic C-terminal domain, which are fused by a stretch of Gly-Lys dipeptide repeats. The
AB  - C-terminal region contains all of the conserved motifs found in other cytosine-5 DNA
AB  - methyltransferases including the relative position of the catalytic Pro-Cys dipeptide. In
AB  - prokaryotes, the methyltransferases are simpler and lack the regulatory N-terminal domain. We
AB  - constructed three hybrid methyltransferases, containing the intact N-terminus of the murine
AB  - Dnmt1 and most of the coding sequences from M.HhaI (GCGC), M.HpaII (CCGG) or M.SssI (CG).
AB  - These hybrids are biologically active when expressed in a baculovirus system and show the
AB  - specificity of the parental C-terminal domain. Expression of these recombinant constructs
AB  - leads to de novo methylation of both host and viral genomes in a sequence-specific manner.
AB  - Steady-state kinetic analyses were performed on the murine Dnmt1-HhaI hybrid using
AB  - poly(dG-dC).poly (dG-dC), unmethylated and hemimethylated oligonucleotides as substrates. The
AB  - enzyme has a slow catalytic turnover number of 4.38 h(-1) for poly(dG-dC). poly(dG-dC), and
AB  - exhibits 3-fold higher catalytic efficiency for hemimethylated substrates.
ER  -

TY  - JOUR
AU  - Pradhan, S.
AU  - Talbot, D.
AU  - Sha, M.
AU  - Benner, J.
AU  - Hornstra, L.
AU  - Li, E.
AU  - Jaenisch, R.
AU  - Roberts, R.J.
TI  - Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4666
EP  - 4673
VL  - 25
AB  - The original cDNA sequence reported for the murine DNA methyltransferase was not full length.
AB  - Recently, additional cDNA sequences have been reported that lie upstream of the original and
AB  - contain an extended open reading frame with three additional ATGs in frame with the coding
AB  - region.  Genomic DNA upstream of this ATG contains two more ATGs in frame and no obvious
AB  - splice site.  We have constructed, and expressed in baculovirus, MTase clones that begin at
AB  - each of these four ATGs and examined their properties.  Constructs beginning with any of the
AB  - first three ATGs as their initiator methionines give a predominant DNA MTase band of ~185 kDa
AB  - on SDS-PAGE corresponding to translational initiation at the third ATG.  The fourth ATG
AB  - construct gives a much smaller protein band of 173 kDa.  The 185 kDa protein was purified by
AB  - HPLC, characterized by mass spectrometry and has a measured molecular mass of 184+/- 0.5 kDa.
AB  - All of these MTases were functional in vitro and steady state kinetic analysis showed that the
AB  - recombinant proteins exhibit similar kinetic properties irrespective of their length.  The
AB  - homogeneous recombinant enzyme from the fourth ATG construct shows a 2.5-fold preference for a
AB  - hemi-methylated DNA substrate as compared to an unmethylated substrate, whereas the 185 kDa
AB  - protein is equally active on both substrates.  The kinetic properties of the recombinant
AB  - enzyme are similar to those reported for the native MTase derived from murine erythroleukemia
AB  - cells.  The new clones are capable of yielding large quantities of intact MTases for further
AB  - structural and functional studies.
ER  -

TY  - JOUR
AU  - Pragasam, A.K.
AU  - Yesurajan, F.
AU  - Doss, C.G.P.
AU  - George, B.
AU  - Devanga, R.N.K.
AU  - Walia, K.
AU  - Veeraraghavan, B.
TI  - Draft Genome Sequence of Extremely Drug-Resistant Pseudomonas aeruginosa (ST357)  Strain CMC_VB_PA_B22862 Isolated from a Community-Acquired Bloodstream Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e01092
EP  - e01016
VL  - 4
AB  - Extremely drug-resistant Pseudomonas aeruginosa strains causing severe infections have become
AB  - a serious concern across the world. Here, we report draft genome
AB  - sequence of P. aeruginosa with an extremely drug-resistant profile isolated from
AB  - a patient with community-acquired bloodstream infection in India.
ER  -

TY  - JOUR
AU  - Prajapati, J.B.
AU  - Khedkar, C.D.
AU  - Chitra, J.
AU  - Suja, S.
AU  - Mishra, V.
AU  - Sreeja, V.
AU  - Patel, R.K.
AU  - Ahir, V.B.
AU  - Bhatt, V.D.
AU  - Sajnani, M.R.
AU  - Jakhesara, S.J.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
TI  - Whole-Genome Shotgun Sequencing of Lactobacillus rhamnosus MTCC 5462, a Strain with Probiotic Potential.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1264
EP  - 1265
VL  - 194
AB  - Lactobacillus rhamnosus MTCC 5462 was isolated from infant gastrointestinal flora. The strain
AB  - exhibited an ability to reduce cholesterol and stimulate
AB  - immunity. The strain has exhibited positive results in alleviating
AB  - gastrointestinal discomfort and good potential as a probiotic. We sequenced the
AB  - whole genome of the strain and compared it to the published genome sequence of
AB  - Lactobacillus rhamnosus GG (ATCC 53103).
ER  -

TY  - JOUR
AU  - Prajapati, J.B.
AU  - Khedkar, C.D.
AU  - Chitra, J.
AU  - Suja, S.
AU  - Mishra, V.
AU  - Sreeja, V.
AU  - Patel, R.K.
AU  - Ahir, V.B.
AU  - Bhatt, V.D.
AU  - Sajnani, M.R.
AU  - Jakhesara, S.J.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
TI  - Whole-Genome Shotgun Sequencing of an Indian-Origin Lactobacillus helveticus Strain, MTCC 5463, with Probiotic Potential.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4282
EP  - 4283
VL  - 193
AB  - Lactobacillus helveticus MTCC 5463 was isolated from a vaginal swab from a healthy adult
AB  - female. The strain exhibited potential probiotic properties,
AB  - with their beneficial role in the gastrointestinal tract and their ability
AB  - to reduce cholesterol and stimulate immunity. We sequenced the whole
AB  - genome and compared it with the published genome sequence of Lactobacillus
AB  - helveticus DPC4571.
ER  -

TY  - JOUR
AU  - Prakash, A.
AU  - Chung, S.
AU  - Ryu, J.-I.
TI  - Study of the expression of hsd genes of E. coli K-12 after conjugal transfer.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - 165
EP  - 165
VL  - 91
AB  - The enzyme for DNA restriction and modification in E. coli K-12 is encoded by
AB  - three contiguous genes: hsdRK (restriction), hsdMK (modification) and hsdSK
AB  - (specificity).  Two promoters are known pres upstream of hsdRK, and pmod
AB  - upstream of hsdMK and hsdSK.  F plasmids carrying the wild-type hsd genes can
AB  - be transferred to a non-K modified recipient (e.g., E. coli) without killing
AB  - the recipient strain.  Thus there must be control at either the
AB  - transcriptional, translational or post-translational level which allows the
AB  - modification of the recipient's chromosome, thereby preventing its restriction.
AB  - F plasmids carrying various hsd-lacZ operon fusions were constructed and
AB  - subsequent F transfer experiments showed simultaneous expression of both pres
AB  - and pmod promoters, and thus no control at the transcriptional level was
AB  - indicated.  Further we have isolated a mutant of E. coli C which is killed
AB  - (efficiency of transfer <10/4) upon conjugal transfer of the wild type hsd
AB  - genes, suggesting a genetic basis for this control phenomenon.  A plasmid
AB  - expressing the R subunit was then introduced into this mutant as well as into
AB  - wild type E. coli C.  Subsequent conjugal transfer of an F plasmid carrying the
AB  - hsdRK hsdM+K hsdS+K genes into this mutant resulted in complementation between
AB  - the incoming M and S subunits with the pre-existing R subunit, as evidenced by
AB  - the killing of the mutant recipient.  However, in the case of the wild type
AB  - recipient strain harboring the plasmid expressing the R subunit, modification
AB  - of the recipient DNA occurred, resulting in successful conjugation.  This
AB  - suggests that there is control of the incoming hsd gene expression in the
AB  - recipient at the post-translational level.
ER  -

TY  - JOUR
AU  - Prakash, A.
AU  - Valinluck, B.
AU  - Ryu, J.-I.
TI  - Genomic hsd-Mu(lac) operon fusion mutants of Escherichia coli K-12.
JO  - Gene
PY  - 1991
SP  - 9
EP  - 14
VL  - 99
AB  - Genomic (chromosomal) hsd-Mu(lac) operon fusions have been constructed in two
AB  - strains of Escherichia coli K-12 for the three hsd genes, hsdRK, hsdMK and
AB  - hsdSK, using MudX and lambda placMu53.  Expression of hsdK mutants ranged from
AB  - 16 to 74 units (u) (with a mean of 52 u) for fusions to promoter Pres and
AB  - ranged from 26-75 u (also with a mean of 52 u) for fusions to promoter Pmod.
AB  - The expression of the two hsdK promoters was measured in different stages of
AB  - growth.  The Pres fusion mutant showed a lag in Beta-galactosidase (BetaGal)
AB  - production, as compared to the Pmod fusion mutant.  One rK-mK mutant (JR205)
AB  - showed more than ten times the BetaGal activity of other insertion mutants.
AB  - The activity of this mutant decreased by 20-fold upon the transfer of F101-102,
AB  - which includes the wild-type hsd region.  Positive gene-dosage effect was
AB  - observed using F' plasmids containing the hsd-lacZ region.
ER  -

TY  - JOUR
AU  - Prakash, O.
AU  - Muduli, S.
AU  - Kumar, R.
AU  - Kumari, C.
AU  - Nimonkar, Y.
AU  - Shouche, Y.S.
AU  - Sharma, R.
TI  - Description of Auricoccucs indicus gen. nov., sp. nov., isolated from skin of human ear.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2017
SP  - 1212
EP  - 1218
VL  - 67
AB  - In present study, a Gram-stain-positive, non-motile, non-spore-forming, small
AB  - spherical bacterium, strain S31T was isolated from skin surface (external ear
AB  - lobe) of a healthy human subject and characterized using polyphasic approach of
AB  - bacterial taxonomy. Based on 1507 bp 16S rRNA gene sequence comparison, strain
AB  - S31T showed highest (92.8%, AY119686) sequence similarity with Macrococcus
AB  - brunensis CCUG 47200T followed by Macrococcus caseolyticus DSM 20597T (92.7%
AB  - AP009484) and formed a separate clade with 65% bootstrap support. The DNA G+C
AB  - content was found to be 34 mol%. Anteiso C15:0, Anteiso C17:0 and iso C16:0 are
AB  - the predominant fatty acids in fatty acid methyl ester (FAME) profile of strain
AB  - S31T. It contained A3alpha type peptidoglycan with L-Lys- Gly3-L-Ala peptide.
AB  - Comparative study of morphological and physiological traits indicated that strain
AB  - S31T phenetically diverged from its closest relatives. Based on morphological,
AB  - chemotaxonomic and genotypic data, strain S31T showed sufficient delineations
AB  - from its closest relatives of family Staphylococcaceae and is proposed as a new
AB  - genus Auricoccus with Auricoccus indicus as type species of the genus. Strain
AB  - S31T (CCUG 69858T = KCTC 33611T = MCC 3027T) is the type strain of the species.
ER  -

TY  - JOUR
AU  - Prakash, T.
AU  - Oshima, K.
AU  - Morita, H.
AU  - Fukuda, S.
AU  - Imaoka, A.
AU  - Kumar, N.
AU  - Sharma, V.K.
AU  - Kim, S.-W.
AU  - Takahashi, M.
AU  - Saitou, N.
AU  - Taylor, T.D.
AU  - Ohno, H.
AU  - Umesaki, Y.
AU  - Hattori, M.
TI  - Complete Genome Sequences of Rat and Mouse Segmented Filamentous Bacteria, a Potent Inducer of Th17 Cell Differentiation.
JO  - Cell Host Microbe
PY  - 2011
SP  - 273
EP  - 284
VL  - 10
AB  - Segmented filamentous bacteria (SFB) are noncultivable
AB  - commensals inhabiting the gut of various vertebrate
AB  - species and have been shown to induce Th17
AB  - cells in mice. We present the complete genome
AB  - sequences of both rat and mouse SFB isolated from
AB  - SFB-monocolonized hosts. The rat and mouse SFB
AB  - genomes each harbor a single circular chromosome
AB  - of 1.52 and 1.59 Mb encoding 1346 and 1420
AB  - protein-coding genes, respectively. The overall nucleotide
AB  - identity between the two genomes is 86%, and
AB  - the substitution rate was estimated to be similar to
AB  - that of the free-living E. coli. SFB genomes encode
AB  - typical genes for anaerobic fermentation and spore
AB  - and flagella formation, but lack most of the amino
AB  - acid biosynthesis enzymes, reminiscent ofpathogenic
AB  - Clostridia, exhibiting large dependency on the host.
AB  - However, SFB lack most of the clostridial virulencerelated
AB  - genes. Comparative analysis with clostridial
AB  - genomes suggested possible mechanisms for host
AB  - responses and specific adaptations in the intestine.
ER  -

TY  - JOUR
AU  - Prakash-Cheng, A.
AU  - Chung, S.S.
AU  - Ryu, J.-I.
TI  - The expression and regulation of hsdK genes after conjugative transfer.
JO  - Mol. Gen. Genet.
PY  - 1993
SP  - 491
EP  - 496
VL  - 241
AB  - The type I restriction and modification genes of Escherichia coli can be transferred to other
AB  - non-modified strains by conjugation without killing the recipient, implying that the
AB  - restriction function must be regulated. In this study, two isogenic F plasmids (r+k and r-K)
AB  - served as donors in quantitative conjugation experiments with various restriction-deficient
AB  - strains of E. coli and Salmonella typhimurium. Conjugation studies with hsd:lacZ operon
AB  - fusions in F' plasmids indicate that both the hsdK promoters, Pres and Pmod, express
AB  - simultaneously following conjugative transfer. Thus these genes do not appear to be regulated
AB  - at the transcriptional level. A spontaneous mutant of E. coli C was discovered that is
AB  - presumably killed upon conjugative transfer of the hsdK genes (defined as a Crc- phenotype).
AB  - The gene that is defective in the mutant was tentatively designated hsdC (control). Hfr gene
AB  - replacement studies led to the localization of the putative hsdC gene between 6 and 16 min on
AB  - the E. coli genetic map.
ER  -

TY  - JOUR
AU  - Prakash-Cheng, A.
AU  - Ryu, J.
TI  - Delayed expression of in vivo restriction activity following conjugal transfer of Escherichia coli hsdk (restriction-modification) genes.
JO  - J. Bacteriol.
PY  - 1993
SP  - 4905
EP  - 4906
VL  - 175
AB  - Following conjugal transfer of the hsdk genes (hsdRK, hsdMk, and hsdSk) of Escherichia coli
AB  - K-12, restriction activity was first detected only after approximately 15 generations, whereas
AB  - modification activity was observed immediately. This sequential expression explains the
AB  - establishment of hsdk genes in a nonmodified host and suggests regulation of restriction
AB  - activity after conjugal transfer.
ER  -

TY  - JOUR
AU  - Pramono, A.K.
AU  - Kuwahara, H.
AU  - Itoh, T.
AU  - Toyoda, A.
AU  - Yamada, A.
AU  - Hongoh, Y.
TI  - Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut.
JO  - Microbes Environ.
PY  - 2017
SP  - 112
EP  - 117
VL  - 32
AB  - Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal
AB  - gut communities have been extensively studied.  However, limited information is available on
AB  - viruses in the termite gut.  We herein report the complete genome sequence (99,517 bp) of a
AB  - phage obtained during a genome analysis of "Candidatus Azobacteroides pseudotrichonymphae"
AB  - phylotype ProJPt-1, which is an obligate intracellular symbiont of the cellulolytic protest
AB  - Pseudotrichonympha sp. in the gut of the termite Prorhinotermes japonicas.  The genome of the
AB  - phage, designated ProJPt-Bp1, was circular or circularly permuted, and was not integrated into
AB  - the two circular chromosomes or five circular plasmids composing the host ProJPt-1 genome.
AB  - The phage was putatively affiliated with the order Caudovirales based on sequence similarities
AB  - with several phage-related genes; however, most of the 52 protein-coding sequences had no
AB  - significant homology to sequences in the databases.  The phage genome contained a tRNA-Gln
AB  - (CAG) gene, which showed the highest sequence similarity to the tRNA-Gln (CAG) gene, the phage
AB  - tRNA gene may compensate for differences in codon usage bias between the phage and host
AB  - genomes.  The phage genome also contained a non-coding region with high nucleotide sequence
AB  - similarity to a region in one of the host plasmids.  No other phage-related sequences were
AB  - found in the host ProJPt-1 genome.  To the best of our knowledge, this is the first report of
AB  - a phage from an obligate, mutualistic endosymbiont permanently associated with eukaryotic
AB  - cells.
ER  -

TY  - JOUR
AU  - Prangishvili, D.A.
AU  - Chinchaladze, D.Z.
AU  - Chelidze, M.G.
TI  - Thermostability of nucleic acid and restriction endonuclease template synthesis enzymes from extremely thermophilic archebacteria.
JO  - Biotekhnologiya
PY  - 1987
SP  - 440
EP  - 446
VL  - 3
AB  - A study has been made of the thermostability of DNA-dependent RNA polymerases, DNA-dependent
AB  - DNA polymerases, and restriction endonucleases from extremely thermophilic archebacteria. The
AB  - optimum temperature for enzyme catalytic activity (T opt) lay in the optimum temperature
AB  - region for growth of the organisms involved: at 85C for RNA polymerases from Thermoproteus
AB  - tenax and Desulfurococcus mucosus, at 55-65C and 70-75C for three DNA polymerases and
AB  - restrictase SuaI from Sulfolobus acidocaldarius, respectively, and at 55-60C for DNA
AB  - polymerase and restrictase ThaI from Thermoplasma acidophilum. All the enzymes investigated
AB  - were highly stable at temperatures up to T opt.
ER  -

TY  - JOUR
AU  - Prangishvili, D.A.
AU  - Vashakidze, R.P.
AU  - Chelidze, M.G.
AU  - Chinchaladze, D.Z.
AU  - Tsalkalamanidze, N.V.
TI  - Isolation and properties of a restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.
JO  - Biokhimiia
PY  - 1987
SP  - 1043
EP  - 1050
VL  - 52
AB  - A new restriction endonuclease SuaI was isolated from the thermoacidophilic
AB  - archaebacterium Sulfolobus acidocaldarius.  The enzyme is an isoschizomer of
AB  - BspRI; it recognizes the tetranucleotide GGCC and cleaves DNA in the center of
AB  - this sequence.  SuaI requires Mg2+, the optimal concentration being 6 mM.  KCl
AB  - at concentrations above 25 mM significantly inhibits the enzyme activity.  The
AB  - pH optimum lies within the range of 6-7 at 70C, the temperature optimum is at
AB  - 70-75C.  the enzyme is highly stable at temperatures up to 80C.  DNA of S.
AB  - acidocaldarius is not cleaved by the enzyme.
ER  -

TY  - JOUR
AU  - Prangishvili, D.A.
AU  - Vashakidze, R.P.
AU  - Chelidze, M.G.
AU  - Gabriadze, I.Y.
TI  - A restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius.
JO  - FEBS Lett.
PY  - 1985
SP  - 57
EP  - 60
VL  - 192
AB  - A type II restriction endonuclase (SuaI) has been isolated from the
AB  - thermoacidophilic archaebacterium Sulfolobus acidocaldarius.  The enzyme is an
AB  - isoschizomer of BspRI.  It does not cut S. acidocaldarius DNA, as the
AB  - recognition sequence GGCC in this DNA contains modified nucleotide(s).  The
AB  - enzyme is most active at 60-70C and is highly thermostable.
ER  -

TY  - JOUR
AU  - Prasad, B.J.
AU  - Sabnis, K.
AU  - Deobagkar, D.D.
AU  - Deobagkar, D.N.
TI  - Deinococcus radiodurans strain R1 contains N6-methyladenine in its genome.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2005
SP  - 412
EP  - 416
VL  - 335
AB  - Methylation of DNA is known to be involved in DNA repair mechanisms in bacteria. Deinococcus
AB  - radiodurans strain R1 on exposure to high
AB  - radiation undergoes significant DNA damage, which is repaired without
AB  - mutations. However, the presence of modified nucleotides has not been
AB  - reported in its genome. We report here the detection of
AB  - N6-methyladenine in the genome of D. radiodurans strain R1 using
AB  - immunochemical techniques. This N6-methyladenine is not a part of GATC
AB  - restriction-modification system. D. radiodurans cell extract also
AB  - exhibited a DNA adenine methyltransferase activity which was reduced in
AB  - the early post-irradiation recovery phase.
ER  -

TY  - JOUR
AU  - Prasanna, L.
AU  - Moharana, T.R.
AU  - Sheikh, N.
AU  - Arravapalli, V.R.
AU  - Kumaraswamy, T.
AU  - Eijsink, V.G.H.
AU  - Nalam, M.R.
TI  - Draft Genome Sequence of Entomopathogenic Brevibacillus laterosporus Strain Lak 1210, an Alkaliphilic Chitin Degrader.
JO  - Genome Announcements
PY  - 2017
SP  - e01251
EP  - e01217
VL  - 5
AB  - We announce here the draft genome sequence of Brevibacillus laterosporus strain Lak 1210,
AB  - isolated from mangrove soil. This alkaliphilic strain is an efficient
AB  - chitin degrader and has the ability to control insects and inhibit
AB  - phytopathogenic fungi. The assembly consists of 5,082,926 bp, with 4,321
AB  - protein-coding sequences and a GC content of 41.15%.
ER  -

TY  - JOUR
AU  - Prasannan, C.B.
TI  - Modulation of restriction enzyme PvuII activity by metal ion cofactors.
JO  - Ph.D. Thesis, University of Missouri
PY  - 2009
AB  - Many nucleases require cofactors (usually Mg2+) for activity. Metal ions like Ca2+, Mn2+,
AB  - Tb3+, Eu3+ etc., can bind at the active site and have varying effects on the enzymatic
AB  - activity. In a crystal structure with DNA, two Ca2+ ions were bound to the active site of each
AB  - PvuII monomer, and the metals share the ligands. Ca2+ ions promote DNA binding and not
AB  - cleavage in many nucleases. We explored the role of Mg2+ and Ca2+ binding at the metal binding
AB  - sites of PvuII to elucidate the role of each metal site. Ca2+ binding at the catalytic metal
AB  - site would inhibit the cleavage activity,
AB  - whereas its binding at the regulatory site can have varied effects. In EcoRV enzyme, it was
AB  - seen that Ca2+ at the regulatory site increases the activity of the enzyme. We monitored the
AB  - cleavage kinetics of PvuII in presence of mixed metals. The cleavage kinetics data for Ca2+
AB  - and Mg2+ set were modeled using parameters from previous studies on PvuII. Our global analysis
AB  - on single turnover cleavage kinetics datasets show best fit to a model in which mixed metal
AB  - species are formed and active. The cleavage rate constants for the mixed metal species ranged
AB  - from 0.01-0.08 sec-1, which is similar to the rate when only one metal is bound. From earlier
AB  - work in our lab, Tb3+ was shown to have a tight (2 iM) binding site and a weak binding site in
AB  - PvuII. The difference in affinity allows one site to be filled with Tb3+ and the other with
AB  - another metal. Indirect Tb3+ luminescence spectroscopy of the Tb3+ bound to enzyme in presence
AB  - of other metals indicates that Ca2+ and Mn2+ displace Tb3+ from the enzyme. This was observed
AB  - by the decrease in the luminescence intensity of E-Tb3+ complex with the addition of Ca2+/Mn2+
AB  - ions. Under similar conditions, the addition of Mg2+ ions to the E-Tb3+ complex results in an
AB  - increase in the signal observed. This indicates the formation of the mixed species
AB  - E-Tb3+-Mg2+. No enzymatic activity was detected for the enzyme with the addition of Mg2+ to
AB  - the E-Tb3+ complex, whereas with the addition of Mn2+ ions there was detectable activity.
AB  - The observed activity with Mn2+ ion was due to the displacement of Tb3+ ions from the active
AB  - site, forming the active EMn2+Mn2+ species. Although the E-Mg2+-Tb3+ species is catalytically
AB  - inactive, it does bind the DNA as confirmed by fluorescence anisotropy using nonhydrolyzable
AB  - phosphoramidate DNA.
ER  -

TY  - JOUR
AU  - Premkrishnan, B.N.V. et al.
TI  - Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252.
JO  - Genome Announcements
PY  - 2018
SP  - e00229
EP  - e00218
VL  - 6
AB  - Staphylococcus haemolyticus is a coagulase-negative staphylococcal species that is part of the
AB  - skin microbiome and an opportunistic human pathogen. The strain
AB  - SGAir0252 was isolated from tropical air samples collected in Singapore, and its
AB  - complete genome comprises one chromosome of 2.63 Mb and one plasmid of 41.6 kb.
ER  -

TY  - JOUR
AU  - Prere, M.F.
AU  - Fayet, O.
TI  - DNA methylase activities in a Neisseria gonorrhoeae extract.
JO  - FEMS Microbiol. Lett.
PY  - 1986
SP  - 37
EP  - 41
VL  - 33
AB  - Resistance of Neisseria gonorrhoeae DNA to cleavage by various restriction endonucleases
AB  - suggests the existence of modification enzymes which protect the corresponding recognition
AB  - sequences. We indeed found methylase activities in N. gonorrhoeae extracts. These activities
AB  - lead to the methylation of adenine and cytosine residues in bacteriophage lambda DNA and DNA
AB  - from an Escherichia coli Dam- strain. They also result in partial protection of lambda DNA to
AB  - cleavage by the restriction endonucleases HaeII, HaeIII, BamHI and SacII.
ER  -

TY  - JOUR
AU  - Prere, M.F.
AU  - Fayet, O.
TI  - Susceptibility of Neisseria Gonorrhoeae DNA to Cleavage by Restriction Endonuclease KpnI.
JO  - Ann. Inst. Pasteur Microbiol.
PY  - 1985
SP  - 329
EP  - 338
VL  - 136A
AB  - We compared the susceptibility of Escherichia coli and Neisseria gonorrhoeae
AB  - DNA to cleavage by KpnI and found that KpnI has a lower affinity for gonococcal
AB  - DNA.  Site-specific methylation is suggested as the cause of this altered
AB  - affinity.
ER  -

TY  - JOUR
AU  - Prere, M.F.
AU  - Fayet, O.
TI  - DNA modification in Neisseria gonorrhoeae: Resistance of DNA of 19 strains to cleavage by restriction enzymes.
JO  - Ann. Inst. Pasteur Microbiol.
PY  - 1985
SP  - 323
EP  - 328
VL  - 136A
AB  - Site-specific modification is frequently encountered in the DNA of bacteria.  It is generally
AB  - due to the methylation of either a cytosine or an adenine in short sequences 4- to
AB  - 6-base-pairs long.  One way to reveal the presence of site-specific methylation in a DNA
AB  - sample is to demonstrate its resistance to cleavage by a restriction endonuclease.  In
AB  - Neisseria gonorrhoeae, studies performed in a limited number of strains revealed that their
AB  - DNA is resistant to digestion by several restriction enzymes.  Those included HaeII, HaeIII,
AB  - SacII, BamHI, NarI and KpnI.  In order to determine whether this pattern of resistance is a
AB  - general property, or if there is variation from strain to strain, we have analyzed the DNA of
AB  - a collection of 19 gonococcal strains for resistance to various restriction endonucleases.  We
AB  - have also investigated the plasmid content of these strains to determine whether this
AB  - correlates with a given resistance pattern.
ER  -

TY  - JOUR
AU  - Presta, L.
AU  - Bosi, E.
AU  - Fondi, M.
AU  - Maida, I.
AU  - Perrin, E.
AU  - Miceli, E.
AU  - Maggini, V.
AU  - Bogani, P.
AU  - Firenzuoli, F.
AU  - Di Pilato, V.
AU  - Rossolini, G.M.
AU  - Mengoni, A.
AU  - Fani, R.
TI  - Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds.
JO  - Genome Announcements
PY  - 2016
SP  - e00346
EP  - e00316
VL  - 4
AB  - We announce here the draft genome sequence of Pseudomonas sp. strain EpS/L25, isolated from
AB  - the stem/leaves of the medicinal plant Echinacea purpurea This
AB  - genome will allow for comparative genomics in order to identify genes associated
AB  - with the production of bioactive compounds and antibiotic resistance.
ER  -

TY  - JOUR
AU  - Presta, L.
AU  - Inzucchi, I.
AU  - Bosi, E.
AU  - Fondi, M.
AU  - Perrin, E.
AU  - Maida, I.
AU  - Miceli, E.
AU  - Tutino, M.L.
AU  - Lo, G.A.
AU  - de Pascale, D.
AU  - Fani, R.
TI  - Draft Genome Sequences of the Antimicrobial Producers Pseudomonas sp. TAA207 and  Pseudomonas sp. TAD18 Isolated from Antarctic Sediments.
JO  - Genome Announcements
PY  - 2016
SP  - e00728
EP  - e00716
VL  - 4
AB  - We report here the draft genome sequence of the Pseudomonas sp. TAA207 and Pseudomonas sp.
AB  - TAD18 strains, isolated from Antarctic sediments during a summer
AB  - campaign near coastal areas of Terra Nova Bay (Antarctica). Genome sequence
AB  - knowledge allowed the identification of genes associated with the production of
AB  - bioactive compounds and antibiotic resistance. Furthermore, it will be
AB  - instrumental for comparative genomics and the fulfillment of both basic and
AB  - application-oriented investigations.
ER  -

TY  - JOUR
AU  - Presta, L.
AU  - Inzucchi, I.
AU  - Bosi, E.
AU  - Fondi, M.
AU  - Perrin, E.
AU  - Miceli, E.
AU  - Tutino, M.L.
AU  - Lo, G.A.
AU  - de Pascale, D.
AU  - Fani, R.
TI  - Draft Genome Sequence of Flavobacterium sp. Strain TAB 87, Able To Inhibit the Growth of Cystic Fibrosis Bacterial Pathogens Belonging to the Burkholderia  cepacia Complex.
JO  - Genome Announcements
PY  - 2016
SP  - e00410
EP  - e00416
VL  - 4
AB  - We report here the draft genome sequence of the Flavobacterium sp. TAB 87 strain, isolated
AB  - from Antarctic seawater during a summer campaign near the French
AB  - Antarctic station Dumont d'Urville (60 degrees 40'S, 40 degrees 01'E). It will
AB  - allow for comparative genomics and the fulfillment of both fundamental and
AB  - application-oriented investigations. It allowed the recognition of genes
AB  - associated with the production of bioactive compounds and antibiotic resistance.
ER  -

TY  - JOUR
AU  - Price, C.
AU  - Bickle, T.A.
TI  - A possible role for DNA restriction in bacterial evolution.
JO  - Microbiol. Sci.
PY  - 1986
SP  - 296
EP  - 299
VL  - 3
AB  - The phenomena of restriction and modification (R-M) were first described more
AB  - than 30 years ago and it is now more than 20 years since Arber & Dussoix
AB  - proposed, rightly, that R-M was due to the action of endonucleases and
AB  - methylases acting at the same DNA sequences.  Briefly, the endonuclease (or
AB  - restriction enzyme) recognizes a specific DNA sequence as a signal to cleave
AB  - the DNA unless the sequence has previously been methylated by a modification
AB  - methylase of the same sequence specificity.  The DNA of a cell carrying a R-M
AB  - system will normally be modified and is therefore not a substrate for the
AB  - restriction enzyme.  The only natural substrate for a restriction enzyme is
AB  - invasive foreign DNA containing unmethylated recognition sequences.
AB  - Restriction is independent of the mode of introduction of the DNA into the
AB  - cell, and phage infection, plasmid conjugation or transformation all lead to
AB  - restriction.
ER  -

TY  - JOUR
AU  - Price, C.
AU  - Bickle, T.A.
TI  - Evolution of DNA sequence specificity in type I restriction enzymes.
JO  - Biochem. Soc. Trans.
PY  - 1988
SP  - 942
EP  - 943
VL  - 16
AB  - None
ER  -

TY  - JOUR
AU  - Price, C.
AU  - Gubler, M.
AU  - Braguglia, D.
AU  - Meister, J.
AU  - Tyndall, C.
AU  - Piekarowicz, A.
AU  - Bickle, T.A.
TI  - Evolution of DNA sequence specificity in type 1C restriction and modification systems.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 151
EP  - 151
VL  - 17C
AB  - The type I restriction-modification (R-M) systems of the Enterobacteriaceae form three
AB  - genetically complementing families, one of which is the type 1C family. All type I R-M systems
AB  - recognize DNA sequences that are asymmetric and split into two by a spacer that can have any
AB  - sequence but which, for a given R-M system, has fixed length. The specific DNA-binding
AB  - components of both restriction and modification enzymes are the products of the hsdS genes,
AB  - which form complexes with the hsdM and hsdR gene products. Within a family of type I systems
AB  - the hsdS genes have a characteristic structure with two variable regions, each coding a
AB  - protein domain (called Target Recognition Domains, TRD) that recognizes one half of the
AB  - recognition sequence, and two (three in one case) conserved regions that are thought to code
AB  - regions of the protein that are important for protein-protein interactions. The type IA and IC
AB  - R-M systems are so far the only DNA binding protein that have been show to alter their binding
AB  - specificity by natural means. Type IA enzymes can reassort their TRDs by recombination within
AB  - a conserved region of the hsdS gene, leading to the production of enzymes that have new,
AB  - hybrid recognition sequences. Type IC systems (and, presumable, type IB systems, although it
AB  - has not yet been demonstrated) can also change their specificity in this way. In addition type
AB  - IC systems can change the length of the central conserved region of the hsdS gene by unequal
AB  - crossing over at a 12 bp long repeated sequence. This leads to enzymes that recognize the same
AB  - specific sequence but with different lengths of non-specific spacer. We have discovered yet a
AB  - third way in which type IC enzymes can change their specificity. We have recovered a mutant
AB  - that has a transposon inserted in the middle of the hsdS gene and which nevertheless produces
AB  - an active R-M system with altered sequence specificity. The structure of the mutant enzymes
AB  - and the sequence that it recognizes with be presented. The sequence is the only known type I
AB  - recognition sequence that is palindromic. Finally, we will present data on a type IC R-M
AB  - system of as yet unknown DNA specificity that appears to be on a transposable element. This
AB  - system is particulary interesting because it is closely integrated, both genetically and
AB  - physically, with an RNA restriction system that is specific for cells infected by T even
AB  - phages.
ER  -

TY  - JOUR
AU  - Price, C.
AU  - Lingner, J.
AU  - Bickle, T.A.
AU  - Firman, K.
AU  - Glover, S.W.
TI  - Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 Type I DNA restriction and modification enzymes.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 115
EP  - 125
VL  - 205
AB  - EcoR124I and EcoR124/3I are type I DNA restriction and modification systems.
AB  - The EcoR124/3I system arose from the EcoR124I system some 15 years ago and at
AB  - the electron microscopic DNA heteroduplex level the genes for both systems are
AB  - still apparently identical.  We have shown that the DNA sequences recognized by
AB  - the two systems are GAA(N6)RTCG for EcoR124I and GAA(N7)RTCG for EcoR124/3I.
AB  - The sequences thus differ only in the length of the non-specific spacer.  This
AB  - difference nevertheless places the two specific domains of the EcoR124/3I
AB  - recognition sequence 0.34 nm further apart and rotates them 36C with respect to
AB  - those of EcoR124I, which implies major structural differences in the proteins
AB  - recognizing these sequences.  We have now determined the nucleotide sequences
AB  - of the hsdS and hsdM genes of both systems and of the hsdR gene of EcoR124/3I.
AB  - The hsdS gene products provide DNA sequence specificity in both restriction and
AB  - modification, the hsdM gene products are necessary for modification and all
AB  - three hsd gene products are required for restriction.  The only difference that
AB  - we have detected between the two systems is that a 12 base-pair sequence
AB  - towards the middle of the hsdS gene is repeated twice in the EcoR124I gene and
AB  - three times in the EcoR124/3I gene.  We have deleted one of the repeats in the
AB  - EcoR124/3I gene and shown that this changes the specificity to that of
AB  - EcoR124I.  Thus, the extra four amino acids in the middle of the EcoR124/3I
AB  - hsdS gene product, which in an alpha-helical configuration would extend 0.6 nm,
AB  - are sufficient to explain the differences in sequence recognition.  We suggest
AB  - that this kind of specificity change should not be rare in Nature.
ER  -

TY  - JOUR
AU  - Price, C.
AU  - Pripfl, T.
AU  - Bickle, T.A.
TI  - EcoR124 and EcoR124/3:  the first members of a new family of type I restriction and modification systems.
JO  - Eur. J. Biochem.
PY  - 1987
SP  - 111
EP  - 115
VL  - 167
AB  - We have purified the EcoR124 and EcoR124/3 restriction enzymes and shown that
AB  - they are type I enzymes by several criteria:  subunit composition, DNA and
AB  - S-adenosylmethionine-dependent ATPase activity, and site-specific DNA methylase
AB  - activity.  By immunochemical criteria these enzymes are related to each other
AB  - but are unrelated to the two previously investigated families of type I
AB  - restriction enzymes.  They form therefore a new family which we call type IC.
AB  - The arrangement of the structural genes coding for these enzymes and their
AB  - transcriptional organisation have been determined.  These are different from
AB  - the common arrangement found for the other two families of type I enzymes.
ER  -

TY  - JOUR
AU  - Price, C.
AU  - Shepherd, J.C.W.
AU  - Bickle, T.A.
TI  - DNA recognition by a new family of type I restriction enzymes:  a unique relationship between two different DNA specificities.
JO  - EMBO J.
PY  - 1987
SP  - 1493
EP  - 1497
VL  - 6
AB  - The DNA sequences recognized by the allelic type I restriction enzymes EcoR124
AB  - and EcoR124/3 were determined.  EcoR124 recognizes 5'-GAA(N6)RTCG-3' and
AB  - EcoR124/3 recognizes 5'-GAA(N7)RTCG-3'.  These are typical of sequences
AB  - recognized by type I recognition enzymes in that they consist of two specific
AB  - domains separated by a non-specific spacer sequence.  For these two enzymes,
AB  - the specific sequences are identical but the length of the non-specific spacer
AB  - is different.  The specific domains of EcoR124/3 are thus 3.4 angstroms further
AB  - apart than those of EcoR124 and rotated with respect to each other through a
AB  - further 36 degrees.
ER  -

TY  - JOUR
AU  - Price, E.P.
AU  - Smith, M.L.
AU  - Paxinos, E.E.
AU  - Tallon, L.J.
AU  - Sadzewicz, L.
AU  - Sengamalay, N.
AU  - Baird, R.W.
AU  - Currie, B.J.
AU  - Sarovich, D.S.
TI  - Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility.
JO  - Genome Announcements
PY  - 2017
SP  - e00053
EP  - e00017
VL  - 5
AB  - We report here paired isogenic Burkholderia pseudomallei genomes obtained from three patients
AB  - receiving intravenous meropenem for melioidosis treatment, with
AB  - post-meropenem isolates developing decreased susceptibility. Two genomes were
AB  - finished, and four were drafted to improved high-quality standard. These genomes
AB  - will be used to identify meropenem resistance mechanisms in B. pseudomallei.
ER  -

TY  - JOUR
AU  - Price, M.N. et al.
TI  - Mutant phenotypes for thousands of bacterial genes of unknown function.
JO  - Nature
PY  - 2018
SP  - 503
EP  - 509
VL  - 557
AB  - One-third of all protein-coding genes from bacterial genomes cannot be annotated  with a
AB  - function. Here, to investigate the functions of these genes, we present
AB  - genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth
AB  - conditions. We identified mutant phenotypes for 11,779 protein-coding genes that
AB  - had not been annotated with a specific function. Many genes could be associated
AB  - with a specific condition because the gene affected fitness only in that
AB  - condition, or with another gene in the same bacterium because they had similar
AB  - mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that
AB  - have high confidence because they are conserved in other bacteria. By combining
AB  - these conserved associations with comparative genomics, we identified putative
AB  - DNA repair proteins; in addition, we propose specific functions for poorly
AB  - annotated enzymes and transporters and for uncharacterized protein families. Our
AB  - study demonstrates the scalability of microbial genetics and its utility for
AB  - improving gene annotations.
ER  -

TY  - JOUR
AU  - Price, T.K.
AU  - Mehrtash, A.
AU  - Kalesinskas, L.
AU  - Malki, K.
AU  - Hilt, E.E.
AU  - Putonti, C.
AU  - Wolfe, A.J.
TI  - Genome sequences and annotation of two urinary isolates of E. coli.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 79
EP  - 79
VL  - 11
AB  - The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result
AB  - most often from colonization of the bladder by uropathogenic E.
AB  - coli strains. In contrast, a poorly defined condition called asymptomatic
AB  - bacteriuria results from colonization of the bladder with E. coli strains without
AB  - symptoms. As part of an on-going attempt to identify and characterize the newly
AB  - discovered female urinary microbiota, we report the genome sequences and
AB  - annotation of two urinary isolates of E. coli: one (E78) was isolated from a
AB  - female patient who self-reported cystitis; the other (E75) was isolated from a
AB  - female patient who reported that she did not have symptoms of cystitis. Whereas
AB  - strain E75 is most closely related to an avian extraintestinal pathogen, strain
AB  - E78 is a member of a clade that includes extraintestinal strains often found in
AB  - the human bladder. Both genomes are uncommonly rich in prophages.
ER  -

TY  - JOUR
AU  - Price, T.K.
AU  - Shaheen, M.
AU  - Kalesinskas, L.
AU  - Malki, K.
AU  - Hilt, E.E.
AU  - Putonti, C.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus.
JO  - Genome Announcements
PY  - 2016
SP  - e01278
EP  - e01216
VL  - 4
AB  - While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its
AB  - role in urinary health remains unclear. As part of an on-going
AB  - attempt to characterize the female urinary microbiota, we report the genome
AB  - sequence of an L. crispatus strain isolated from a woman displaying no lower
AB  - urinary tract symptoms.
ER  -

TY  - JOUR
AU  - Price, V.J.
AU  - Huo, W.
AU  - Sharifi, A.
AU  - Palmer, K.L.
TI  - CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.
JO  - 
PY  - 2016
SP  - e00064
EP  - e00016
VL  - 1
AB  - Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial
AB  - infections. Conjugative pheromone-responsive plasmids are
AB  - narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of
AB  - antibiotic resistance in the faecalis species. Clustered regularly interspaced
AB  - short palindromic repeat (CRISPR)-Cas and restriction-modification confer
AB  - acquired and innate immunity, respectively, against MGE acquisition in bacteria.
AB  - Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an
AB  - orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is
AB  - known about restriction-modification defense in E. faecalis. Here, we explore the
AB  - hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We
AB  - assessed MGE acquisition by E. faecalis T11, a strain closely related to the
AB  - multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of
AB  - horizontally acquired genome content that characterizes V583. T11 possesses the
AB  - E. faecalis CRISPR3-cas locus and a predicted restriction-modification system,
AB  - neither of which occurs in V583. We demonstrate that CRISPR-Cas and
AB  - restriction-modification together confer a 4-log reduction in acquisition of the
AB  - pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show
AB  - that the orphan CRISPR2 locus is functional for genome defense against another
AB  - pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from
AB  - the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis
AB  - isolates lack. Overall, our work demonstrated that the loss of only two loci led
AB  - to a dramatic reduction in genome defense against a clinically relevant MGE,
AB  - highlighting the critical importance of the E. faecalis accessory genome in
AB  - modulating horizontal gene transfer. Our results rationalize the development of
AB  - antimicrobial strategies that capitalize upon the immunocompromised status of
AB  - multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium
AB  - that normally inhabits the gastrointestinal tracts of humans and other animals.
AB  - Although these bacteria are members of our native gut flora, they can cause
AB  - life-threatening infections in hospitalized patients. Antibiotic resistance genes
AB  - appear to be readily shared among high-risk E. faecalis strains, and multidrug
AB  - resistance in these bacteria limits treatment options for infections. Here, we
AB  - find that CRISPR-Cas and restriction-modification systems, which function as
AB  - adaptive and innate immune systems in bacteria, significantly impact the spread
AB  - of antibiotic resistance genes in E. faecalis populations. The loss of these
AB  - systems in high-risk E. faecalis suggests that they are immunocompromised, a
AB  - tradeoff that allows them to readily acquire new genes and adapt to new
AB  - antibiotics.
ER  -

TY  - JOUR
AU  - Prichodko, E.A.
AU  - Rechnukova, N.I.
AU  - Degtyarev, S.K.
TI  - Determination of substrate specificity of restriction endonuclease Tru9I.
JO  - Sib. Biol. J.
PY  - 1991
SP  - 57
EP  - 59
VL  - 1
AB  - Tru9I, type II restriction endonuclease, has been isolated from Thermus ruber
AB  - 9.  The recognition sequence and cleavage point of restriction endonuclease
AB  - Tru9I have been determined as 5'T^TAA.  Tru9I is an isoschizomer of MseI.
ER  -

TY  - JOUR
AU  - Prichodko, G.G.
AU  - Degtyarev, S.K.
AU  - Rechkunova, N.I.
AU  - Sosnovsev, S.V.
AU  - Tchigikov, V.E.
TI  - General method for determining the sites of DNA cleavage by restriction endonucleases.
JO  - Biotekhnologiya
PY  - 1990
SP  - 12
EP  - 16
VL  - 1
AB  - A method for determining substrate specificity of large block cleaving restrictases is
AB  - suggested. Plasmid vectors pUBS18 and pUBS19, that permit labelling at one end of a Bse21I
AB  - site for rapid DNA sequencing were constructed. Restriction endonuclease BimI recognizing the
AB  - sequence TT^CGAA was isolated from the bacterial strain Brevibacterium immotum.
ER  -

TY  - JOUR
AU  - Prichodko, G.G.
AU  - Petrov, N.A.
AU  - Chizhikov, V.E.
AU  - Degtyarev, S.K.
TI  - A modified method for determining the sites of DNA cleavage by restriction endonucleases.
JO  - Biotekhnologiya
PY  - 1988
SP  - 618
EP  - 620
VL  - 4
AB  - The modification merely involves labelling the 3' end of restriction fragments
AB  - using Klenow so as to avoid problems of the extra phosphate group which arise
AB  - when kinase-labelled fragments are compared with chemically degraded fragments.
ER  -

TY  - JOUR
AU  - Prichodko, G.G.
AU  - Petrov, N.A.
AU  - Repin, V.E.
AU  - Degtyarev, S.K.
TI  - Establishing the substrate specificity of restriction endonuclease Bsu15I.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1988
SP  - 108
EP  - 109
VL  - 14
AB  - The recognition sequence and cleavage point of restriction endonuclease Bsu15I has been
AB  - determined as 5'AT^CGAT.
ER  -

TY  - JOUR
AU  - Prichodko, G.G.
AU  - Rechnukova, N.I.
AU  - Repin, V.E.
AU  - Degtyarev, S.K.
TI  - Determination of substrate specificity of restriction endonuclease Acc65I.
JO  - Sib. Biol. J.
PY  - 1991
SP  - 59
EP  - 60
VL  - 1
AB  - The recognition sequence and cleavage point of restriction endonuclease Acc65I
AB  - have been determined as 5'G^GTACC.
ER  -

TY  - JOUR
AU  - Prichula, J.
AU  - Campos, F.S.
AU  - Pereira, R.I.
AU  - Cardoso, L.A.
AU  - Wachholz, G.R.
AU  - Pieta, L.
AU  - Mariot, R.F.
AU  - de Moura, T.M.
AU  - Tavares, M.
AU  - d'Azevedo, P.A.
AU  - Frazzon, J.
AU  - Frazzon, A.P.
TI  - Complete Genome Sequence of Enterococcus faecalis Strain P8-1 Isolated from Wild  Magellanic Penguin (Spheniscus magellanicus) Feces on the South Coast of Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01531
EP  - e01515
VL  - 4
AB  - Enterococcus faecalis strains have a ubiquitous nature that allows them to survive in
AB  - different niches. Studies involving enterococci isolated from marine
AB  - animals are scarce. Therefore, in this study, we report the complete genome
AB  - sequence of E. faecalis strain P8-1 isolated from feces of a Magellanic penguin
AB  - on the south coast of Brazil.
ER  -

TY  - JOUR
AU  - Pride, D.T.
AU  - Blaser, M.J.
TI  - Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis.
JO  - Genome Lett.
PY  - 2002
SP  - 2
EP  - 15
VL  - 1
AB  - The Helicobacter pylori genome contains genetic elements believed to have been horizontally
AB  - acquired. We compared a Markov chain method dependent on genomic oligonucleotide frequencies
AB  - with
AB  - methods based upon G + C content to identify potential horizontally acquired gene clusters.
AB  - Compared with G +
AB  - C content analysis, oligonucleotide difference analysis (ODA) identified a unique set of
AB  - genes, with a few genes
AB  - shared by the two methods. However, each method identified a large number of cag island and
AB  - plasticity zone
AB  - genes, with 12-18% identified by both. ODA also was applicable to other prokaryotes,
AB  - identifying as foreign
AB  - prophages in Bacillus subtilis, insertion elements in Campylobacter jejuni, genes with
AB  - repetitive elements in
AB  - Mycobacterium tuberculosis, and the integron island in Vibrio cholerae. GATC, the cognate
AB  - sequence for the
AB  - hpyIII restriction-modification system in H. pylori, is substantially underrepresented in the
AB  - plasticity zone,
AB  - suggesting a role for that R-M system in limiting horizontal transfer events. That GATC is not
AB  - substantially
AB  - underrepresented in the cag island suggests that the two islands likely have different
AB  - origins. The information
AB  - provided by ODA is complementary to G + C content for identifying horizontal acquisitions in
AB  - prokaryotes.
ER  -

TY  - JOUR
AU  - Pridgeon, J.W.
AU  - Zhang, D.
AU  - Zhang, L.
TI  - Complete Genome Sequence of a Moderately Virulent Aeromonas hydrophila Strain, pc104A, Isolated from Soil of a Catfish Pond in West Alabama.
JO  - Genome Announcements
PY  - 2014
SP  - e00554
EP  - e00514
VL  - 2
AB  - Aeromonas hydrophila pc104A is a moderately virulent strain isolated from the soil of a
AB  - catfish pond in west Alabama in 2010. Its full genome is 5,023,829 bp.
AB  - The availability of this genome will allow comparative genomics to identify the
AB  - virulence genes that are important for pathogenesis or immunogens for the purpose
AB  - of vaccine development.
ER  -

TY  - JOUR
AU  - Pridgeon, J.W.
AU  - Zhang, D.
AU  - Zhang, L.
TI  - Complete Genome Sequence of a Virulent Strain, Streptococcus iniae ISET0901, Isolated from Diseased Tilapia.
JO  - Genome Announcements
PY  - 2014
SP  - e00553
EP  - e00514
VL  - 2
AB  - Streptococcus iniae ISET0901 is a virulent strain isolated in 2007 from diseased  tilapia. Its
AB  - full genome is 2,070,856 bp. The availability of this genome will
AB  - allow comparative genomics to identify virulence genes important for the
AB  - pathogenesis of streptococcosis caused by S. iniae, as well as possible
AB  - immunogens for vaccine development.
ER  -

TY  - JOUR
AU  - Pridgeon, J.W.
AU  - Zhang, D.
AU  - Zhang, L.
TI  - Complete Genome Sequence of the Attenuated Novobiocin-Resistant Streptococcus iniae Vaccine Strain ISNO.
JO  - Genome Announcements
PY  - 2014
SP  - e00510
EP  - e00514
VL  - 2
AB  - Streptococcus iniae ISNO is an attenuated novobiocin-resistant vaccine strain. Its full genome
AB  - is 2,070,182 bp in length. The availability of this genome will
AB  - allow comparative genomics to identify potential virulence genes important for
AB  - pathogenesis of S. iniae and potential mechanisms associated with novobiocin
AB  - resistance in this strain.
ER  -

TY  - JOUR
AU  - Pridgeon, J.W.
AU  - Zhang, D.
AU  - Zhang, L.
TI  - Complete Genome Sequence of the Highly Virulent Aeromonas hydrophila AL09-71 Isolated from Diseased Channel Catfish in West Alabama.
JO  - Genome Announcements
PY  - 2014
SP  - e00450
EP  - e00414
VL  - 2
AB  - Aeromonas hydrophila AL09-71 was isolated from diseased channel catfish in west Alabama during
AB  - a 2009 disease outbreak. The full genome of A. hydrophila AL09-71
AB  - is 5,023,861 bp. The availability of this genome will allow comparative genomics
AB  - to identify genes involved in pathogenesis or immunogens for the purpose of
AB  - vaccine development.
ER  -

TY  - JOUR
AU  - Pridmore, R.D.
AU  - Berger, B.
AU  - Desiere, F.
AU  - Vilanova, D.
AU  - Barretto, C.
AU  - Pittet, A.-C.
AU  - Zwahlen, M.-C.
AU  - Rouvet, M.
AU  - Altermann, E.
AU  - Barrangou, R.
AU  - Mollet, B.
AU  - Mercenier, A.
AU  - Klaenhammer, T.
AU  - Arigoni, F.
AU  - Schell, M.A.
TI  - The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2004
SP  - 2512
EP  - 2517
VL  - 101
AB  - Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal
AB  - lactobacilli that has been extensively studied for their "probiotic" activities that include,
AB  - pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into
AB  - its physiology and identify genes potentially involved in interactions with the host, we
AB  - sequenced and analyzed the 1.99-Mb genome of L. johnsonii NCC 533. Strikingly, the organism
AB  - completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides,
AB  - and most cofactors. In apparent compensation, a remarkable number of uncommon and often
AB  - duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were
AB  - discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes
AB  - to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of
AB  - large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in
AB  - adhesion to glycoproteins or other components of mucin, a characteristic expected to affect
AB  - persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid
AB  - transporters, proteins apparently critical for GIT survival, were also detected. In silico
AB  - genome comparisons with the >95% complete genome sequence of the closely related Lactobacillus
AB  - gasseri revealed extensive synteny punctuated by clear-cut insertions or deletions of single
AB  - genes or operons. Many of these regions of difference appear to encode metabolic or structural
AB  - components that could affect the organisms competitiveness or interactions with the GIT
AB  - ecosystem.
ER  -

TY  - JOUR
AU  - Prieto, J.
AU  - Epinat, J.C.
AU  - Redondo, P.
AU  - Ramos, E.
AU  - Padro, D.
AU  - Cedrone, F.
AU  - Montoya, G.
AU  - Paques, F.
AU  - Blanco, F.J.
TI  - Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease.
JO  - J. Biol. Chem.
PY  - 2008
SP  - 4364
EP  - 4374
VL  - 283
AB  - The hyperthermophilic archaeon Desulfurococcus mobilis I-DmoI protein belongs to the family of
AB  - proteins known as homing endonucleases (HEs).
AB  - HEs are highly specific DNA-cleaving enzymes that recognize long
AB  - stretches of DNA and are powerful tools for genome engineering. Because
AB  - of its monomeric nature, I-DmoI is an ideal scaffold for generating
AB  - mutant enzymes with novel DNA specificities, similarly reported for
AB  - homodimeric HEs, but providing single chain endonucleases instead of
AB  - dimers. However, this would require the use of a mesophilic variant
AB  - cleaving its substrate at temperatures of 37 C and below. We have
AB  - generated mesophilic mutants of I-DmoI, using a single round of
AB  - directed evolution that relies on a functional assay in yeast. The
AB  - effect of mutations identified in the novel proteins has been
AB  - investigated. These mutations are located distant to the DNA-binding
AB  - site and cause changes in the size and polarity of buried residues,
AB  - suggesting that they act by destabilizing the protein. Two of the novel
AB  - proteins have been produced and analyzed in vitro. Their overall
AB  - structures are similar to that of the parent protein, but they are
AB  - destabilized against thermal and chemical denaturation. The
AB  - temperature-dependent activity profiles for the mutants shifted toward
AB  - lower temperatures with respect to the wild-type activity profile.
AB  - However, the most destabilized mutant was not the most active at low
AB  - temperatures, suggesting that other effects, like local structural
AB  - distortions and/or changes in the protein dynamics, also influence
AB  - their activity. These mesophilic I-DmoI mutants form the basis for
AB  - generating new variants with tailored DNA specificities.
ER  -

TY  - JOUR
AU  - Prieto, J.
AU  - Molina, R.
AU  - Montoya, G.
TI  - Molecular scissors for in situ cellular repair.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 2012
SP  - 207
EP  - 221
VL  - 47
AB  - The engineering of protein-DNA interactions in different protein scaffolds may provide
AB  - 'toolkits' to modify the genome. Homing
AB  - endonucleases are powerful tools for genome manipulation through
AB  - homologous recombination, as these enzymes possess a very low frequency
AB  - of DNA cleavage in eukaryotic genomes due to their high specificity.
AB  - Therefore, the combination of a precise 'cutter' with the presence of a
AB  - natural or modified homologous DNA donor provides a potentially useful
AB  - means to modify the genome. However, the basis of protein-DNA
AB  - recognition must be understood to generate tailored enzymes that target
AB  - the DNA at sites of interest. The engineering of homing endonucleases
AB  - and alternative scaffolds, such as zinc fingers or transcription
AB  - activator-like effector domains, has demonstrated the potential of
AB  - these approaches to create new specific instruments to target genes for
AB  - inactivation or repair. Customized homing endonucleases targeting
AB  - selected human genes can excise or correct regions of genes implicated
AB  - in monogenic diseases, thereby representing important tools for
AB  - intervention in eukaryotic genomes.
ER  -

TY  - JOUR
AU  - Prieto, J.
AU  - Redondo, P.
AU  - Merino, N.
AU  - Villate, M.
AU  - Montoya, G.
AU  - Blanco, F.J.
AU  - Molina, R.
TI  - Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2016
SP  - 473
EP  - 479
VL  - 72
AB  - Homing endonucleases are highly specific DNA-cleaving enzymes that recognize and  cleave long
AB  - stretches of DNA. The engineering of these enzymes provides
AB  - instruments for genome modification in a wide range of fields, including gene
AB  - targeting. The homing endonuclease I-SceI from the yeast Saccharomyces cerevisiae
AB  - has been purified after overexpression in Escherichia coli and its crystal
AB  - structure has been determined in complex with its target DNA. In order to
AB  - evaluate the number of ions that are involved in the cleavage process, thus
AB  - determining the catalytic mechanism, crystallization experiments were performed
AB  - in the presence of Mn(2+), yielding crystals that were suitable for X-ray
AB  - diffraction analysis. The crystals belonged to the orthorhombic space group
AB  - P212121, with unit-cell parameters a = 80.11, b = 80.57, c = 130.87 A, alpha =
AB  - beta = gamma = 90 degrees . The self-rotation function and the Matthews
AB  - coefficient suggested the presence of two protein-DNA complexes in the asymmetric
AB  - unit. The crystals diffracted to a resolution limit of 2.9 A using synchrotron
AB  - radiation. From the anomalous data, it was determined that three cations are
AB  - involved in catalysis and it was confirmed that I-SceI follows a two-metal-ion
AB  - DNA-strand cleavage mechanism.
ER  -

TY  - JOUR
AU  - Prieto, J.
AU  - Redondo, P.
AU  - Padro, D.
AU  - Arnould, S.
AU  - Epinat, J.C.
AU  - Paques, F.
AU  - Blanco, F.J.
AU  - Montoya, G.
TI  - The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage1.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 3262
EP  - 3271
VL  - 35
AB  - Meganucleases are sequence-specific endonucleases with large cleavage sites that can be used
AB  - to induce efficient homologous gene targeting in
AB  - cultured cells and plants. These enzymes open novel perspectives for
AB  - genome engineering in a wide range of fields, including gene therapy. A
AB  - new crystal structure of the I-CreI dimer without DNA has allowed the
AB  - comparison with the DNA-bound protein. The C-terminal loop displays a
AB  - different conformation, which suggests its implication in DNA binding. A
AB  - site-directed mutagenesis study in this region demonstrates that whereas
AB  - the C-terminal helix is negligible for DNA binding, the final C-terminal
AB  - loop is essential in DNA binding and cleavage. We have identified two
AB  - regions that comprise the Ser138-Lys139 and Lys142-Thr143 pairs whose
AB  - double mutation affect DNA binding in vitro and abolish cleavage in vivo.
AB  - However, the mutation of only one residue in these sites allows DNA
AB  - binding in vitro and cleavage in vivo. These findings demonstrate that the
AB  - C-terminal loop of I-CreI endonuclease plays a fundamental role in its
AB  - catalytic mechanism and suggest this novel site as a region to take into
AB  - account for engineering new endonucleases with tailored specificity.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Fliegerova, K.
AU  - Javorsky, P.
TI  - Two restriction endonucleases in Selenomonas ruminantium subsp. lactilytica.
JO  - Lett. Appl. Microbiol.
PY  - 1998
SP  - 83
EP  - 85
VL  - 27
AB  - Crude protein extract from a recently isolated ruminal bacterium identified as Selenomonas
AB  - ruminantium subsp. lactilytica specifically cleaved DNA.  This ability was due to the presence
AB  - of two site-specific restriction endonucleases.  SrlI, a NaeI isoschizomer, recognizes the
AB  - 5'-GCCGGC-3' sequence.  SrlII, an NsiI isoschizomer, recognizes 5'-ATGCAT-3'.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Godany, A.
AU  - Sevcikova, B.
AU  - Oktavcova, B.
AU  - Farkasovska, J.
TI  - Characterization of restriction endonuclease activities in tetracycline producing strains of Streptomyces aureofaciens.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 4364
EP  - 4364
VL  - 20
AB  - We have tested several strains of streptomyces aureofaciens from different sources for
AB  - restriction endonuclease. In all tested tetracycline producing strains (B-96, NMU, 16, R8/26)
AB  - restriction endonuclease was isolated and characterized (SauLPI, SauNI, SauSI, SauHPI
AB  - respectively). Previously described restriction endonuclease from strain S.aureofaciens R8/26I
AB  - (1) was renamed for SauHPI in this report. Endonucleases were purified from cell extracts by
AB  - phosphocellulose and heparin-sepharose chromatography according to (2) with minor
AB  - modifications. The restriction endonucleases were free of contaminating nucleases activity.
AB  - All isolated restriction endonucleases produced the same cleavage pattern on tested DNA
AB  - substrates. Computer-derived mapping data predict the sequence 5'-GCCGCC-3'. The comparison
AB  - of cleavage patterns of pBR322 by S.aureofaciens restrictases to NaeI confirmed the
AB  - recognition sequence (Figure 1).
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Javorsky, P.
TI  - Restriction-modification systems in ruminal bacteria: occurrence and some evolutionary implications.
JO  - Reprod. Nutr. Dev.
PY  - 1997
SP  - 74
EP  - 75
VL  - 37
AB  - Type II restriction modification systems involve a DNA methyltransferase and an endonuclease
AB  - of the same recognition sequence specificity.  It is generally accepted that these systems act
AB  - primarily to protect bacteria from foreign DNA, particularly from infection by bacteriophages.
AB  - The study of the biology of restriction-modification systems has revealed some general
AB  - features and it has been shown that the composition of the bacterial chromosome and the
AB  - restriction-modification systems present within cells are evolutionarily linked.  Restriction
AB  - endonucleases have been found in bacteria from all taxonomic and ecological groups.  Ruminal
AB  - bacteria have been shown to be a promising source of these enzymes.  Up to now ten restriction
AB  - endonucleases have been isolated from bacteria of this ecological group.  Our studies on
AB  - variability of endonucleolytic activity in S. ruminantium have demonstrated a high frequency
AB  - and diversity of restriction endonucleases in this species, and at least ten different
AB  - specificities have been characterized.  In addition the observed frequency of restriction
AB  - endonucleases, which were present in more than one-third of strains tested, is higher than
AB  - observed in bacteria from other ecological groups.  A high frequency of restriction
AB  - endonucleases in S. ruminantium can also be inferred from the analysis of DNA.  Using the
AB  - method of Karlin et al., it was shown that average counts of perfect 4- and 6- base pairs
AB  - palindromes observed within S. ruminantium DNA are lower than in other bacteria, and even
AB  - lower than those observed among phage DNAs.  The observed low frequency of short palindromes
AB  - is therefore in good agreement with the high frequency of restriction endonucleases observed
AB  - in this genus.  Similarly other ruminal bacteria show lower counts of palindromes than would
AB  - be predicted from a random distribution.  We suppose that the consistently low frequencies of
AB  - 4-bp and 6-bp palindromes observed within the DNA of ruminal bacteria is probably a result of
AB  - the variety and multiplicity of restriction systems found in bacteria from this ecological
AB  - group.  Possibly, there is a correlation between bacterial population density and the
AB  - frequency of restriction endonucleases.  Bacterial counts in the rumen are higher than in any
AB  - other environment.  Together with the high bacterial counts, there are also unusually high
AB  - concentrations of bacteriophages.  If the protection of cells from bacteriophage infection is
AB  - a primary role of restriction-modification systems, these systems should be more frequent in
AB  - the rumen than in environments with lower populations of bacteriophages.  In such a strongly
AB  - competitive ecosystem as the rumen of herbivorous animals the possession of restriction
AB  - activity can provide a selective advantage for survival of both the individual bacterial clone
AB  - and the species as a whole.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Molnarova, V.
AU  - Javorsky, P.
TI  - Diversity of restriction and modification phenotypes in local population of rumen bacterium Selenomonas ruminantium.
JO  - Biologia (Bratisl)
PY  - 2002
SP  - 777
EP  - 782
VL  - 57
AB  - Type II restriction endonuclease activities detected in various strains of Selenomonas
AB  - ruminantium species, coming from genetically homogenous
AB  - local population, were characterised. The recognition sequence of
AB  - Srl55DI was determined to be 5'-G/AATTC-3', identical to that of EcoRI.
AB  - Srl5DI restriction endonuclease recognises 5'-CTGCA/G-3' sequence and
AB  - is true isoschizomer of PstI. The Srl56DI restriction endonuclease was
AB  - found to recognise and cleave 5-C/TRYAG-3' sequence and is true
AB  - isoschizomer of SfcI. All other restriction activities characterised
AB  - were duplicates of restriction endonucleases, which have previously
AB  - been detected in bacteria of S. ruminantium species. In total, 9
AB  - different restriction endonucleases were found in the tested bacteria.
AB  - Much higher variability of modification phenotypes was observed, when
AB  - totally 13 types of modification profiles were found in the studied S.
AB  - ruminantium strains. Chromosomal DNA isolated from S. ruminantium
AB  - strains was found to be refractive to cleavage by various restriction
AB  - enzymes, implying the presence of methylase activities additional to
AB  - those required for protection against the cellular endonucleases. While
AB  - extremely diverse in restriction and modification phenotypes the tested
AB  - strains showed very low genetic diversity, when all but one strain
AB  - produced identical profiles in ARDREA analysis. Based on close
AB  - similarity of the tested strains the lateral gene transfer is proposed
AB  - as a source of the observed diversity of restriction and modification
AB  - phenotypes in S. ruminantium.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Molnarova, V.
AU  - Javorsky, P.
TI  - Restriction and modification systems of ruminal bacteria.
JO  - Folia Microbiol. (Praha)
PY  - 2001
SP  - 71
EP  - 72
VL  - 46
AB  - A high frequency of type II restriction endonuclease activities was detected in Selenomonas
AB  - ruminantium but not in other rumen bacteria tested. Eight different restriction endonucleases
AB  - were characterized in 17 strains coming from genetically homogeneous local populations.
AB  - Chromosomal DNA isolated from S. ruminantium strains was found to be refractory to cleavage by
AB  - various restriction enzymes, implying the presence of methylase activities additional to those
AB  - required for protection against the cellular endonucleases. The presence of Dam methylation
AB  - was detected in S. ruminantium strains as well as in several other species belonging to the
AB  - Sporomusa sub-branch of low G + C Gram-positive bacteria (Megasphaera elsdenii, Mitsuokella
AB  - multiacidus).
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Molnarova, V.
AU  - Javorsky, P.
TI  - Detection of N6-methyladenine in GATC sequences of Selenomonas ruminantium.
JO  - J. Basic Microbiol.
PY  - 1998
SP  - 283
EP  - 287
VL  - 38
AB  - The presence of N6-methyladenine in GATC sequences in DNA of Selenomonas ruminantium was
AB  - investigated using sensitive methylation discriminating isoschizomeric restriction enzyme
AB  - analysis.  Methylated adenine was detected in 8 out of 18 tested strains belonging to the
AB  - subsp. lactilytica of S. ruminantium.  No corresponding restriction activity was detected in
AB  - three tested strains.  No GATC methylation was detected in 3 analyzed S. ruminantium subsp.
AB  - ruminantium strains.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Piknova, M.
TI  - Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and  modification systems?
JO  - Can. J. Microbiol.
PY  - 2005
SP  - 315
EP  - 318
VL  - 51
AB  - Molecular analysis of isolates of the rumen bacterium Selenomonas ruminantium revealed a high
AB  - variety and frequency of site-specific
AB  - (restriction) endonucleases. While all known S. ruminantium restriction
AB  - and modification systems recognize hexanucleotide sequences only,
AB  - consistently low counts of both 6-bp and 4-bp palindromes were found in
AB  - DNA sequences of S. ruminantium. Statistical analysis indicated that
AB  - there is some correlation between the degree of underrepresentation of
AB  - tetranucleotide words and the number of known restriction endonucleases
AB  - for a given sequence. Control analysis showed the same correlation in
AB  - lambda DNA but not in human adenovirus DNA. Based on the data
AB  - presented, it could be proposed that there is a much higher historical
AB  - occurrence of restriction and modification systems in S. ruminantium
AB  - and (or) frequent horizontal gene transfer of restriction and
AB  - modification gene complexes.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Vanat, I.
AU  - Godany, A.
AU  - Javorsky, P.
TI  - Restriction endonucleases from Selenomonas ruminantium which recognize and cleave 5'-AT/TAAT-3'.
JO  - Arch. Microbiol.
PY  - 1994
SP  - 439
EP  - 441
VL  - 161
AB  - Two natural isolates from fallow-deer rumen identified as Selenomonas ruminantium were found
AB  - to produce a restriction endonuclease which we called Sru4DI. This enzyme was isolated from
AB  - cell extracts by phosphocellulose chromatography. Analysis of the Sru4DI recognition site
AB  - showed that Sru4DI recognizes the hexanucleotide sequence 5'-AT/TAAT-3' generating 5'
AB  - dinucleotide protruding ends upon cleavage and thus is a true isoschizomer of VspI, a
AB  - restriction enzyme isolated from Vibrio sp.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Vanat, I.
AU  - Javorsky, P.
TI  - Isolation and characterization of a new restriction endonuclease, Sru30DI, from Selenomonas ruminantium.
JO  - Gene
PY  - 1995
SP  - 139
EP  - 140
VL  - 158
AB  - The restriction endonuclease (ENase) Sru30DI, an isoschizomer of StuI, which recognizes the
AB  - sequence 5'-AGG/CCT-3', was purified from a natural isolate of Selenomonas ruminantium. The
AB  - ENase was isolated from cell extracts using single-step purification by phosphocellulose
AB  - column chromatography. Activity of Sru30DI is inhibited by overlapping Dcm methylation. The
AB  - ENase is extremely stable at 37oC and is active over a wide range of pH, temperature and salt
AB  - concentrations.
ER  -

TY  - JOUR
AU  - Pristas, P.
AU  - Vanat, I.
AU  - Javorsky, P.
TI  - Variability of endonucleolytic activity indicates high genetic diversity within the natural population of Selenomonas ruminantium.
JO  - Folia Microbiol. (Praha)
PY  - 1997
SP  - 121
EP  - 124
VL  - 42
AB  - The population of bacteria of Selenomonas ruminantium species in the rumen of fallow-deer was
AB  - analyzed using endonucleolytic activity assay and plasmid profiles, indicating the presence of
AB  - the different specificity nucleases, have been observed.  Site-specific endonucleases were
AB  - detected in 17 out of 45 strains tested.  In other strains a various level of non-specific
AB  - activity was detected.  Plasmid DNAs ranging in size from 0.9 to more than 25 kbp were
AB  - detected in 60% of strains analyzed.  No or little correlation was observed between the
AB  - endonuclease activity and the plasmid content.  The presence of different specificity
AB  - endonucleases, as well as differences of plasmid profiles of isolates possessing identical
AB  - specific activity indicate that the population of S. ruminantium in the rumen of an individual
AB  - animal consists of at least 10 different clones.
ER  -

TY  - JOUR
AU  - Pritchard, L.
AU  - Humphris, S.
AU  - Baeyen, S.
AU  - Maes, M.
AU  - Van Vaerenbergh, J.
AU  - Elphinstone, J.
AU  - Saddler, G.
AU  - Toth, I.
TI  - Draft Genome Sequences of Four Dickeya dianthicola and Four Dickeya solani Strains.
JO  - Genome Announcements
PY  - 2013
SP  - e00087
EP  - e00012
VL  - 1
AB  - Dickeya dianthicola and 'Dickeya solani' are currently the dominant bacterial pathogens of
AB  - potatoes in Europe. Here, we present the draft genome sequences of
AB  - four strains of each pathogen.
ER  -

TY  - JOUR
AU  - Pritchard, L.
AU  - Humphris, S.
AU  - Saddler, G.S.
AU  - Elphinstone, J.G.
AU  - Pirhonen, M.
AU  - Toth, I.K.
TI  - Draft Genome Sequences of 17 Isolates of the Plant Pathogenic Bacterium Dickeya.
JO  - Genome Announcements
PY  - 2013
SP  - e00978
EP  - e00913
VL  - 1
AB  - Dickeya (formerly Erwinia chrysanthemi) species cause diseases on a wide range of crops and
AB  - ornamental plants worldwide. Here we present the draft sequences of 17
AB  - Dickeya isolates spanning four Dickeya species, including five isolates that are
AB  - currently unassigned to a species.
ER  -

TY  - JOUR
AU  - Privman, E.
TI  - Bioinformatic Identification of Homing Endonucleases and Their Target Sites.
JO  - Methods Mol. Biol.
PY  - 2014
SP  - 27
EP  - 35
VL  - 1123
AB  - Homing endonuclease genes (HEGs) are a large, phylogenetically diverse superfamily of enzymes
AB  - with high specificity for especially long target sites. The public genomic sequence databases
AB  - contain thousands of HEGs. This is a large and diverse arsenal of potential genome editing
AB  - tools. To make use of this natural resource, one needs to identify candidate HEGs. Due to
AB  - their special relationship with a host gene, it is also possible to predict their cognate
AB  - target sequences. Here I describe the HomeBase algorithm that was developed to this end. A
AB  - detailed description of the computational pipeline is provided with emphasis on technical and
AB  - methodological caveats of the approach.
ER  -

TY  - JOUR
AU  - Probst, M.
AU  - Aeschimann, W.
AU  - Chau, T.T.
AU  - Langenegger, S.M.
AU  - Stocker, A.
AU  - Haner, R.
TI  - Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI  endonuclease.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 7079
EP  - 7089
VL  - 44
AB  - The use of the DNA duplex as a supramolecular scaffold is an established approach for the
AB  - assembly of chromophore aggregates. In the absence of detailed structural
AB  - insight, the characterization of thus assembled oligochromophores is, today,
AB  - largely based on solution-phase spectroscopy. Here, we describe the crystal
AB  - structures of three DNA-organized chromophore aggregates. DNA hybrids containing
AB  - non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with
AB  - the recently described binding domain of the restriction enzyme BpuJI. Crystal
AB  - structures of these complexes were determined at 2.7, 1.9 and 1.6 A resolutions.
AB  - The structures reveal aromatic stacking interactions between pyrene and/or
AB  - phenanthrene units within the framework of the B-DNA duplex. In hybrids
AB  - containing a single modification in each DNA strand near the end of the duplex,
AB  - the two polyaromatic hydrocarbons are engaged in a face-to-face stacking
AB  - orientation. Due to crystal packing and steric effects, the terminal GC base pair
AB  - is disrupted in all three crystal structures, which results in a non-perfect
AB  - stacking arrangement of the aromatic chromophores in two of the structures. In a
AB  - hybrid containing a total of three pyrenes, crystal lattice induced end-to-end
AB  - stacking of individual DNA duplexes leads to the formation of an extended
AB  - aromatic pi-stack containing four co-axially arranged pyrenes. The aromatic
AB  - planes of the stacked pyrenes are oriented in a parallel way. The study
AB  - demonstrates the value of co-crystallization of chemically modified DNA with the
AB  - recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed
AB  - structural insight into DNA-assembled oligochromophores.
ER  -

TY  - JOUR
AU  - Prochazka, B.
AU  - Indra, A.
AU  - Hasenberger, P.
AU  - Blaschitz, M.
AU  - Wagner, L.
AU  - Wewalka, G.
AU  - Sorschag, S.
AU  - Schmid, D.
AU  - Ruppitsch, W.
TI  - Draft Genome Sequence of Legionella jamestowniensis Isolated from a Patient with  Chronic Respiratory Disease.
JO  - Genome Announcements
PY  - 2016
SP  - e01007
EP  - e01016
VL  - 4
AB  - Legionella jamestowniensis can be found in the environment in various water samples, in wet
AB  - soil, and in compost facilities, but evidence of its human
AB  - pathogenicity has not yet been demonstrated. Here, we report the first draft
AB  - genome sequence of an L. jamestowniensis isolate, derived from a patient
AB  - suffering from a chronic respiratory disease.
ER  -

TY  - JOUR
AU  - Proenca, D.N.
AU  - Espirito, S.C.
AU  - Grass, G.
AU  - Morais, P.V.
TI  - Draft Genome Sequence of Serratia sp. Strain M24T3, Isolated from Pinewood Disease Nematode Bursaphelenchus xylophilus.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3764
EP  - 3764
VL  - 194
AB  - Here we report the draft genome sequence of Serratia sp. strain M24T3, which is associated
AB  - with pinewood nematode Bursaphelenchus xylophilus, the causative agent
AB  - of pine wilt disease. Serratia sp. strain M24T3 has been identified as a
AB  - bionematocide for B. xylophilus in vitro, and multiple genes potentially involved
AB  - in virulence and nematotoxity were identified.
ER  -

TY  - JOUR
AU  - Proenca, D.N.
AU  - Espirito, S.C.
AU  - Grass, G.
AU  - Morais, P.V.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain M47T1, Carried by Bursaphelenchus xylophilus Isolated from Pinus pinaster.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4789
EP  - 4790
VL  - 194
AB  - The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus
AB  - xylophilus pinewood nematode, the causative agent of pine wilt
AB  - disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a
AB  - plant growth-promoting bacterium, as well as genes potentially involved in
AB  - nematotoxicity, were identified.
ER  -

TY  - JOUR
AU  - Proenca, D.N.
AU  - Whitman, W.B.
AU  - Shapiro, N.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Morais, P.V.
TI  - Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 53
EP  - 53
VL  - 12
AB  - Here we report the draft genome sequence of Chitinophaga costai A37T2T (=CIP 110584T, =LMG
AB  - 27458T), which was isolated from the endophytic community of Pinus
AB  - pinaster tree. The total genome size of C. costaii A37T2T is 5.07 Mbp, containing
AB  - 4204 coding sequences. Strain A37T2T encoded multiple genes likely involved in
AB  - cellulolytic, chitinolytic and lipolytic activities. This genome showed 1145
AB  - unique genes assigned into 109 Cluster of Orthologous Groups in comparison with
AB  - the complete genome of C. pinensis DSM 2588T. The genomic information suggests
AB  - the potential of the strain A37T2T to interact with the plant metabolism. As
AB  - there are only a few bacterial genomes related to Pine Wilt Disease, this work
AB  - provides a contribution to the field.
ER  -

TY  - JOUR
AU  - Proffitt, J.H.
AU  - Davie, J.R.
AU  - Swinton, D.
AU  - Hattman, S.
TI  - 5-methylcytosine is not detectable in Saccharomyces cerevisiae.
JO  - Mol. Cell. Biol.
PY  - 1984
SP  - 985
EP  - 988
VL  - 4
AB  - We examined the DNA of Saccharomyces cerevisiae by both HpaII-MspI restriction enzyme
AB  - digestion and high-performance liquid chromatography analysis for the possible presence of
AB  - 5-methylcytosine.  Both of these methods failed to detect cytosine methylation within this
AB  - yeast DNA; i.e. there is <1 5-methylcytosine per 3,100 to 6,000 cytosine residues.
ER  -

TY  - JOUR
AU  - Protozanova, E.
AU  - Demidov, V.V.
AU  - Nielsen, P.E.
AU  - Frank-Kamenetskii, M.D.
TI  - Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 3929
EP  - 3935
VL  - 31
AB  - This study evaluates the potential of pseudocomplementary peptide nucleic acids (pcPNAs) for
AB  - sequence-specific modification of enzyme activity
AB  - towards double-stranded DNA (dsDNA). To this end, we analyze the ability
AB  - of pcPNA-dsDNA complexes to site-selectively interfere with the action of
AB  - four type IIs restriction enzymes. We have found that pcPNA-dsDNA
AB  - complexes exhibit a different degree of DNA protection against
AB  - cleaving/nicking activity of various isoschizomeric endonucleases under
AB  - investigation (PleI, MlyI and N.BstNBI) depending on their type and mutual
AB  - arrangement of PNA-binding and enzyme recognition/cleavage sites. We have
AB  - also found that the pcPNA targeting to closely located PleI or BbsI
AB  - recognition sites on dsDNA generates in some cases the nicking activity of
AB  - these DNA cutters. At the same time, MlyI endonuclease, a PleI
AB  - isoschizomer, does not exhibit any DNA nicking/cleavage activity, being
AB  - completely blocked by the nearby pcPNA binding. Our results have general
AB  - implications for effective pcPNA interference with the performance of
AB  - DNA-processing proteins, thus being important for prospective applications
AB  - of pcPNAs.
ER  -

TY  - JOUR
AU  - Protozanova, E.
AU  - Demidov, V.V.
AU  - Soldatenkov, V.
AU  - Chasovskikh, S.
AU  - Frank-Kamenetskii, M.D.
TI  - Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping.
JO  - EMBO Rep.
PY  - 2002
SP  - 956
EP  - 961
VL  - 3
AB  - DNA looping is one of the key factors allowing proteins bound to different DNA sites to signal
AB  - one another via direct contacts. We demonstrate that DNA looping can be generated in an
AB  - arbitrary chosen site by sequence-directed targeting of double-stranded DNA with
AB  - pseudocomplementary peptide-nucleic acids (pcPNAs). We designed pcPNAs to mask the DNA from
AB  - cleavage by type IIs restriction enzyme PleI while not preventing the enzyme from binding to
AB  - its primary DNA recognition site. Direct interaction between two protein molecules (one bound
AB  - to the original recognition site and the other to a sequence-degenerated site) results in a
AB  - totally new activity of PleI: it produces a nick near the degenerate site. The PNA-induced
AB  - nicking efficiency varies with the distance between the two protein-binding sites in a phase
AB  - with the DNA helical periodicity. Our findings imply a general approach for the fine-tuning of
AB  - proteins bound to DNA sites well separated along the DNA chain.
ER  -

TY  - JOUR
AU  - Protsenko, A.
AU  - Zakharova, M.
AU  - Nagornykh, M.
AU  - Solonin, A.
AU  - Severinov, K.
TI  - Transcription regulation of restriction-modification system Ecl18kI.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 5322
EP  - 5330
VL  - 37
AB  - Restriction-modification (R-M) system Ecl18kI is representative of R-M systems whose
AB  - coordinated transcription is achieved through a separate
AB  - DNA-binding domain of the methyltransferase. M.Ecl18kI recognizes an
AB  - operator sequence located in the noncoding region that separates the
AB  - divergently transcribed R and M genes. Here we show that, contrary to
AB  - previous predictions, the two ecl18kI promoters are not divergent, but
AB  - actually face one another. The binding of M.Ecl18kI to its operator
AB  - prevents RNA polymerase (RNAP) binding to the M promoter by steric
AB  - exclusion, but has no direct effect on RNAP interaction with the R
AB  - promoter. The start point for R transcription is located outside of the
AB  - intergenic region, opposite the initiation codon of the M gene. Regulated
AB  - transcription of the potentially toxic ecl18kI R gene is accomplished (i)
AB  - at the stage of promoter complex formation, through direct competition
AB  - from complexes formed at the M promoter, and (ii) at the stage of promoter
AB  - clearance, since R promoter-bound RNAP escapes the promoter more slowly
AB  - than RNAP bound to the M promoter.
ER  -

TY  - JOUR
AU  - Proust, L.
AU  - Loux, V.
AU  - Martin, V.
AU  - Magnabosco, C.
AU  - Pedersen, M.
AU  - Monnet, V.
AU  - Juillard, V.
TI  - Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01029
EP  - e01018
VL  - 7
AB  - Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt
AB  - and cheese. We report here the complete genome sequence of
AB  - the industrial strain S. thermophilus N4L, which is used in dairy technology for
AB  - its fast-acidifying phenotype.
ER  -

TY  - JOUR
AU  - Proux, C.
AU  - Van Sinderen, D.
AU  - Suarez, J.
AU  - Garcia, P.
AU  - Ladero, V.
AU  - Fitzgerald, G.F.
AU  - Desiere, F.
AU  - Brussow, H.
TI  - The dilemma of phage taxonomy illustrated by comparative genomics of sfi21-like siphoviridae in lactic acid bacteria.
JO  - J. Bacteriol.
PY  - 2002
SP  - 6026
EP  - 6036
VL  - 184
AB  - The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and
AB  - Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are
AB  - members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage
AB  - type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving
AB  - biological systems, was observed when different Sfi21-like phages were compared. Across the
AB  - structural module, the graded relatedness was represented by a high level of DNA sequence
AB  - similarity or protein sequence similarity, or a shared gene map in the absence of sequence
AB  - relatedness. This varying range of relatedness was found within Sfi21-like phages from a
AB  - single species as demonstrated by the different prophages harbored by Lactococcus lactis
AB  - strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome
AB  - sequences revealed a clear separation of all temperate phages from two classes of virulent
AB  - phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion
AB  - over the nonstructural gene cluster. With respect to structural genes, four DNA homology
AB  - groups could be defined within temperate L. lactis phages. Closely related structural modules
AB  - for all four DNA homology groups were detected in phages from Streptococcus or Listeria,
AB  - suggesting that they represent distinct evolutionary lineages that have not uniquely evolved
AB  - in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics.
AB  - However, the peculiar modular nature of phage evolution creates ambiguities in the definition
AB  - of phage taxa by comparative genomics. For example, depending on the module on which the
AB  - classification is based, temperate lactococcal phages can be classified as a single phage
AB  - species, as four distinct phage species, or as two if not three different phage genera. We
AB  - propose to base phage taxonomy on comparative genomics of a single structural gene module
AB  - (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some
AB  - aspects of the current International Committee on Taxonomy in Virology classification system.
AB  - In this system the currently sequenced lactococcal phages would be grouped into five genera:
AB  - c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.
ER  -

TY  - JOUR
AU  - Prozorov, A.A.
AU  - Belova, T.S.
AU  - Surikov, N.N.
TI  - Transformation and transduction of Bacillus subtilis strains with the BsuR restriction-modification system by means of modified and unmodified DNA of pUB110 plasmid.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 135
EP  - 138
VL  - 180
AB  - During transformation of B. subtilis cells with the BsuR restriction-modification system by
AB  - means of pUB110 plasmid, restriction and modification of the plasmid DNA occurs.  The effect
AB  - of restriction on the transformation frequency is relatively weak, bringing about a 20-fold
AB  - decrease only.  When using cells of a modifying recipient, the frequency of AR9 phage-mediated
AB  - transduction of unmodified plasmid DNA is also relatively little decreased.  The frequency of
AB  - transduction by chromosomal markers, under the same conditions, falls much lower.
ER  -

TY  - JOUR
AU  - Pryshliak, M.
AU  - Hammerl, J.A.
AU  - Reetz, J.
AU  - Strauch, E.
AU  - Hertwig, S.
TI  - Vibrio vulnificus Phage PV94 Is Closely Related to Temperate Phages of V. cholerae and Other Vibrio Species.
JO  - PLoS ONE
PY  - 2014
SP  - E94707
EP  - E94707
VL  - 9
AB  - BACKGROUND: Vibrio vulnificus is an important pathogen which can cause serious
AB  - infections in humans. Yet, there is limited knowledge on its virulence factors
AB  - and the question whether temperate phages might be involved in pathogenicity, as
AB  - is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1)
AB  - infecting V. vulnificus have been genetically characterized. These phages were
AB  - isolated from the environment and are not related to Vibrio cholerae phages. The
AB  - lack of information on temperate V. vulnificus phages prompted us to isolate
AB  - those phages from lysogenic strains and to compare them with phages of other
AB  - Vibrio species. RESULTS: In this study the temperate phage PV94 was isolated from
AB  - a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus
AB  - whose genome is a linear double-stranded DNA of 33,828 bp with 5'-protruding
AB  - ends. Sequence analysis of PV94 revealed a modular organization of the genome.
AB  - The left half of the genome comprising the immunity region and genes for the
AB  - integrase, terminase and replication proteins shows similarites to V. cholerae
AB  - kappa phages whereas the right half containing genes for structural proteins is
AB  - closely related to a prophage residing in V. furnissii NCTC 11218. CONCLUSION: We
AB  - present the first genomic sequence of a temperate phage isolated from a human V.
AB  - vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the
AB  - wide distribution of closely related prophages in various Vibrio species.
AB  - Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal
AB  - genetic exchange within the genus Vibrio, by which V. vulnificus might acquire
AB  - virulence-associated genes from other species.
ER  -

TY  - JOUR
AU  - Ptashne, M.
TI  - Replication and host modification of DNA transferred during bacterial mating.
JO  - J. Mol. Biol.
PY  - 1965
SP  - 829
EP  - 838
VL  - 11
AB  - An experiment is presented which shows that during the course of bacterial
AB  - mating between Escherichia coli F-prime (lambda) male and an E. coli (lambda)
AB  - female, the transferred lambda prophages all replicate.  This strongly suggests
AB  - that all the transferred F-prime factors carrying the lambda prophage replicate
AB  - during the mating.  A separate experiment, employing host-induced modification,
AB  - shows that at least 20% of the strands injected into the female are synthesized
AB  - in the male just prior to injection.  It is argued that all the injected DNA
AB  - replicates in the male just prior to injection, and that most of the newly made
AB  - strands are not endowed with the host-induced modification properties normally
AB  - associated with DNA synthesized in the male.
ER  -

TY  - JOUR
AU  - Pu, A.T.
AU  - Radany, E.H.
TI  - Regulated expression of restriction endonuclease activity in mammalian cells.
JO  - J. Cell. Biochem.
PY  - 1995
SP  - 327
EP  - 327
VL  - S21
AB  - DNA double-strand breaks (dsbs) are the primary lethal lesion in cells exposed to ionizing
AB  - radiation (IR).  Detecting cellular responses specific to the dsbs formed by IR is hampered by
AB  - a broad spectrum of damage.  Transfer of restriction enzymes (REs) into mammalian cells
AB  - affords access to dsbs in the absence of other lesions; however, this approach is not
AB  - quantitatively radiomimetic due to the variable introduction of REs into cells in quantities
AB  - ranging from none to much greater than average.  While this effect might be eliminated by
AB  - regulated, homogeneous RE gene expression in mammalian cells, such a strategy has been limited
AB  - by leaky transcriptional control.  Braselman et al. reported stringent regulation by estrogen
AB  - of a chimeric transcription factor::estrogen receptor (ER) fusion protein activity in
AB  - mammalian cells in an effort to create a radiomimetic dsb model system tightly controlled by
AB  - estrogen.  PCR was used to modify a RE gene (PvuII) to allow efficient translation in
AB  - eucaryotic cells; expression of the modified gene in E. coli verified function by phage
AB  - restriction.  This gene was installed in a mammalian expression system expected to afford
AB  - estrogen-dependent regulation; the resulting construct has been transferred into rodent cells.
AB  - Recovery of robust G418-resistant stable transfectants at similar frequencies of RE
AB  - gene-containing and control constructs (in the absence of estrogen) indicates that any basal
AB  - PvuII expression in the former case occurs at a level tolerated by the cells.  Preliminary
AB  - results suggest cytotoxicity associated with estrogenic steroid exposure in the former, but
AB  - not the latter, cells.  The dependence of killing on estrogen exposure duration is currently
AB  - under investigation, as is the ability of putative RE-induced dsb to function as sublethal
AB  - damage with respect to subsequent IR exposure.  Direct measurement of dsb yields will be
AB  - performed using pulse field gels.  The PvuII gene has been engineered for regulated mammalian
AB  - cell expression.  This system apparently affords tight control of intracellular RE activity by
AB  - estrogen, providing a means to study quantitative DNA dsb effects in the absence of other
AB  - changes generated in X-irradiated cells.  Current results will be presented.
ER  -

TY  - JOUR
AU  - Pucciarelli, M.G.
AU  - Prieto, A.I.
AU  - Casadesus, J.
AU  - Portillo, F.G.D.
TI  - Envelope instability in DNA adenine methylase mutants of Salmonella  enterica.
JO  - Microbiology
PY  - 2002
SP  - 1171
EP  - 1182
VL  - 148
AB  - Mutants of Salmonella enterica serovar Typhimurium lacking DNA
AB  - adenine (Dam) methylase show reduced secretion of invasion effectors
AB  - encoded in the Salmonella-pathogenicity island 1 (SPI-1). Concomitant with
AB  - this alteration, a high number and quantity of extracellular proteins are
AB  - detected in cultures of Dam(-) mutants. This study shows by subcellular
AB  - fractionation analysis that the presence of numerous extracellular proteins
AB  - in cultures of Dam(-) mutants is linked to an exacerbated release of
AB  - membrane particulate material. The membrane 'leaky' phenotype and the
AB  - impaired functionality of type III secretion systems were, however,
AB  - unrelated since exacerbated release of proteins to the medium was evident
AB  - in Dam(-) strains carrying mutations in either SPI-1 (invA, invJ) or
AB  - flagellar (flhD) genes. This result supports the view that Dam methylation
AB  - controls a plethora of cellular processes. Electron microscopy analysis
AB  - demonstrated that the accumulation of membrane particulate material occurs
AB  - preferentially as vesicles in stationary cultures of Dam(-) strains. In
AB  - addition, a reduction in the relative amount of peptidoglycan-associated
AB  - lipoprotein (PAL), TolB, OmpA and murein lipoprotein (Lpp) bound to
AB  - peptidoglycan was observed in actively growing Dam(-) mutants. The
AB  - existence of an envelope defect was further confirmed by the increased
AB  - sensitivity to deoxycholate exhibited by Dam(-) mutants, mostly during
AB  - exponential growth. Unexpectedly, lack of Dam methylation neither increased
AB  - envelope instability nor impaired the association of PAL-Tol-Lpp proteins
AB  - to the peptidoglycan in Escherichia coli. Accordingly, E. coli Dam(-)
AB  - mutants did not show sensitivity to deoxycholate. Altogether, these results
AB  - indicate that, besides its role in modulating the secretion of effectors by
AB  - the SPI-1-encoded type III apparatus, Dam methylation controls cell
AB  - envelope integrity in S. enterica.
ER  -

TY  - JOUR
AU  - Puchkova, L.I.
AU  - Kalmykova, G.V.
AU  - Burtseva, L.I.
AU  - Repin, V.E.
TI  - Entomapathogenic bacteria Bacillus thuringiensis as producers of restriction endonucleases.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 2002
SP  - 140
EP  - 144
VL  - 38
AB  - A total of 115 collection strains of Bacillus thuringiensis, belonging to various subspecies,
AB  - have been studied for the presence of DNA restriction-modification systems.  Restriction
AB  - endonucleases of 13 strains have been isolated and characterized.  No considerable
AB  - correlations between the taxonomic positions of the bacteria and the specificities of the
AB  - endonucleases isolated have been detected.  It is concluded that the enzymes with identical
AB  - specificities are present in both the crystalliferous and acrystalliferous strains of the same
AB  - subspecies.
ER  -

TY  - JOUR
AU  - Puchkova, L.I.
AU  - Krivopalova, G.N.
AU  - Andreeva, I.S.
AU  - Selina, A.V.
AU  - Serov, G.D.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
TI  - Streptomyces fradiae is the producer of the restriction endonuclease Sfr274I.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1990
SP  - 32
EP  - 34
VL  - 1
AB  - Experiments were carried out to assay for restrictase producers in
AB  - microorganisms from the Streptomyces genus.  Streptomyces fradiae Ac 149 was
AB  - found to be a producer of the restriction endonuclease Sfr274I - an
AB  - isoschizomer of the restrictase XhoI (recognition site CTCGAG).
ER  -

TY  - JOUR
AU  - Puchkova, L.I.
AU  - Ushakova, T.A.
AU  - Mikhailova, V.K.
AU  - Serov, G.D.
AU  - Krivopalova, G.N.
AU  - Repin, V.E.
TI  - Testing and isolation of high-purity restriction endonucleases.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 2002
SP  - 20
EP  - 24
VL  - 38
AB  - A new method of testing restriction nucleases is proposed.  This method is based on
AB  - high-temperature treatment of crude cell extracts.  Disrupted cells were heated at 50-60 C,
AB  - centrifuged, and assayed for restrictases.  This method provides the opportunity for screening
AB  - new enzymes in microbial strains enriched with nonspecific restrictases.  High-temperature
AB  - treatment of cell extracts of certain producers reduces the number of steps of the procedure
AB  - used for isolating high-purity restrictases; the resulting preparations are capable of
AB  - maintaining high enzymatic activity during long-term storage.  It was shown that
AB  - high-temperature treatment can be applied not only to thermophilic but also to mesophilic
AB  - strains of microorganisms of different taxa.
ER  -

TY  - JOUR
AU  - Puchta, H.
AU  - Dujon, B.
AU  - Hohn, B.
TI  - Homologous recombination in plant cells in enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 5034
EP  - 5040
VL  - 21
AB  - Induction of double strand breaks (DSBs) is coupled to meiotic and mitotic recombination in
AB  - yeast. We show that also in a higher eukaryote induction of DSBs is directly correlated with a
AB  - strong enhancement of recombination frequencies. We cotransfected Nicotiana plumbaginifolia
AB  - protopasts with a plasmid carrying a synthetic I-SceI gene, coding for a highly sequence
AB  - specific endonuclease, together with recombination substrates carrying an I-SceI-site adjacent
AB  - to their homologous sequences. We measured efficiencies of extrachromosomal recombination,
AB  - using a well established transient B-glucuronidase (GUS) assay. GUS enzyme activities were
AB  - strongly increased when a plasmid carrying the I-SceI gene in sense but not in antisense
AB  - orientation with respect to the promoter was included in the transfections. The in vivo
AB  - induced DSBs were detected in the recombination substrates by Southern blotting, demonstrating
AB  - that the yeast enzyme is functional in plant cells. At high ratios of transfected I-SceI-genes
AB  - to I-SceI-sites the majority of the I-SceI-sites in the recombination substrates are cleaved,
AB  - indicating that the induction of the DSBs is the rate limiting step in the described
AB  - recombination reaction. These results imply that in vivo induction of transient breaks at
AB  - specific sites in the plant genome could allow foreign DNA to be targeted to these sites via
AB  - homologous recombination.
ER  -

TY  - JOUR
AU  - Puente-Sanchez, F.
AU  - Gonzalez-Silva, C.
AU  - Parro, V.
AU  - Tamames, J.
AU  - Azua-Bustos, A.
TI  - Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1.
JO  - Genome Announcements
PY  - 2018
SP  - e00216
EP  - e00218
VL  - 6
AB  - Gloeocapsopsis sp. strain AAB1 is an extremely desiccation-tolerant cyanobacterium isolated
AB  - from translucent quartz stones from the Atacama Desert
AB  - (Chile). Here, we report its draft genome sequence, which consists of 137 contigs
AB  - with an approximately 5.4-Mb genome size. The annotation revealed 5,641 coding
AB  - DNA sequences, 38 tRNA genes, and 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Puente-Sanchez, F.
AU  - Pieper, D.H.
AU  - Arce-Rodriguez, A.
TI  - Draft Genome Sequence of the Deep-Subsurface Actinobacterium Tessaracoccus lapidicaptus IPBSL-7T.
JO  - Genome Announcements
PY  - 2016
SP  - e01078
EP  - e01016
VL  - 4
AB  - The type strain of Tessaracoccus lapidicaptus was isolated from the deep subsurface of the
AB  - Iberian Pyrite Belt (southwest Spain). Here, we report its
AB  - draft genome, consisting of 27 contigs with a ~3.1-Mb genome size. The annotation
AB  - revealed 2,905 coding DNA sequences, 45 tRNA genes, and three rRNA genes.
ER  -

TY  - JOUR
AU  - Puertas, A.I.
AU  - Capozzi, V.
AU  - Llamas, M.G.
AU  - Lopez, P.
AU  - Lamontanara, A.
AU  - Orru, L.
AU  - Russo, P.
AU  - Spano, G.
AU  - Duenas, M.T.
TI  - Draft Genome Sequence of Lactobacillus collinoides CUPV237, an Exopolysaccharide  and Riboflavin Producer Isolated from Cider.
JO  - Genome Announcements
PY  - 2016
SP  - e00506
EP  - e00516
VL  - 4
AB  - Lactobacillus collinoides CUPV237 is a strain isolated from a Basque cider. Lactobacillus
AB  - collinoides is one of the most frequent species found in cider from
AB  - Spain, France, or England. A notable feature of the L. collinoides CUPV237 strain
AB  - is its ability to produce exopolysaccharides.
ER  -

TY  - JOUR
AU  - Pues, H.
AU  - Bleimling, N.
AU  - Holz, B.
AU  - Wolcke, J.
AU  - Weinhold, E.
TI  - Functional roles of the conserved aromatic amino acid residues at position 108 (Motif IV) and position 196 (Motif VIII) in base flipping and catalysis by the N6-adenine DNA methyltransferase from Thermus aquaticus.
JO  - Biochemistry
PY  - 1999
SP  - 1426
EP  - 1434
VL  - 38
AB  - The DNA methyltransferase from Thermus aquaticus catalyzes the transfer of the activated
AB  - methyl group of S-adenosyl-L-methionine to the N6 position of adenine within the
AB  - double-stranded DNA sequence 5'-TCGA-3'.  To achieve catalysis M.TaqI flips the target
AB  - adenine out of the DNA helix.  On the basis of the three-dimensional structure of M.TaqI in
AB  - complex with the cofactor and its structural homology to the C5-cytosine DNA Mtase from
AB  - Haemophilus haemolyticus, Tyr108 and Phe196 were suggested to interact with the extrahelical
AB  - adenine.  The functional roles of these two aromatic amino acid residues in M.TaqI were
AB  - investigated by mutational analysis.  The obtained mutant Mtases were analyzed in an improved
AB  - kinetic assay, and their ability to flip the target base was studied in a fluorescence-based
AB  - assay using a duplex oligodeoxynucleotide containing the fluorescent base analogue
AB  - 2-aminopurine at the target position.  While the mutant Mtases containing the aromatic amino
AB  - acid Trp at position 108 or 196 (Y108W and F196W) showed almost wild-type catalytic activity,
AB  - the mutant Mtases with the nonaromatic amino acid Ala (Y108A and F196A) had a strongly reduced
AB  - catalytic constant.  Y108A was still able to flip the target base, whereas F196A was strongly
AB  - impaired in base flipping.  These results indicate that Phe196 is important for stabilizing
AB  - the extrahelical target adenine and suggest that Tyr108 is involved in placing the
AB  - extrahelical target base in an optimal position for methyl group transfer.  Since both
AB  - aromatic amino acids belong to the conserved motifs IV and XIII found in N6-adenine and
AB  - N4-cytosine DNA Mtases as well as in N6-adenine RNA Mtases, a similar function of aromatic
AB  - amino acid residues within these motifs is expected for the different Mtases.
ER  -

TY  - JOUR
AU  - Pugatsch, T.
AU  - Weber, H.
TI  - A thermostable, sequence-specific restriction endonuclease from Bacillus stearothermophilus: BstPI.
JO  - Nucleic Acids Res.
PY  - 1979
SP  - 1429
EP  - 1444
VL  - 7
AB  - A restriction endonuclease, BstPI, was purified from a strain of B.
AB  - stearothermophilus, and its cleavage specificity was determined.  The enzyme
AB  - cleaves at palindromic sites of the general structure: 5' -G^-G-T-N-A-C-C- 3'
AB  - 3' -C-C-A-N-T-G^-G- 5' where N-N' can be any base pair.  It produces
AB  - phosphorylated 5'-termini which are single stranded over a length of 5
AB  - nucleotides.  Ends generated by cleavage with BstPI can be rejoined by DNA
AB  - ligase.
ER  -

TY  - JOUR
AU  - Puglisi, E.
AU  - Mattarelli, P.
AU  - Modesto, M.
AU  - Bonetti, A.
AU  - Spiezio, C.
AU  - Sandri, C.
AU  - Morelli, L.
TI  - Draft Genome Sequences of Strains TRE 1, TRE D, TRE H, and TRI 7, Isolated from Tamarins and Belonging to Four Putative Novel Bifidobacterium Species.
JO  - Genome Announcements
PY  - 2018
SP  - e01449
EP  - e01417
VL  - 6
AB  - Bifidobacterium sp. strains TRE 1, TRE D, TRE H, and TRI 7 were isolated from two tamarins
AB  - housed in Parco Natura Viva, Garda Zoological Park S.r.l. (Bussolengo,
AB  - Verona, Italy). These strains belong to four putative novel species of the genus
AB  - Bifidobacterium The genome sizes were 2.7 Mb for TRE 1, 2.7 Mb for TRE D, 2.4 Mb
AB  - for TRE H, and 2.7 Mb for TRI 7. The average GC contents were 63.18% for TRE 1,
AB  - 58.27% for TRE D, 57.11% for TRE H, and 63.79% for TRI 7.
ER  -

TY  - JOUR
AU  - Puiu, D.
AU  - Salzberg, S.L.
TI  - Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.
JO  - PLoS ONE
PY  - 2008
SP  - E3427
EP  - E3427
VL  - 3
AB  - Francisella tularensis is a highly infectious human intracellular pathogen
AB  - that is the causative agent of tularemia. It occurs in several major
AB  - subtypes, including the live vaccine strain holarctica (type B). F.
AB  - tularensis is classified as category A biodefense agent in part because a
AB  - relatively small number of organisms can cause severe illness. Three
AB  - complete genomes of subspecies holarctica have been sequenced and
AB  - deposited in public archives, of which OSU18 was the first and the only
AB  - strain for which a scientific publication has appeared. We re-assembled
AB  - the OSU18 strain using both de novo and comparative assembly techniques,
AB  - and found that the published sequence has two large inversion
AB  - mis-assemblies. We generated a corrected assembly of the entire genome
AB  - along with detailed information on the placement of individual reads
AB  - within the assembly. This assembly will provide a more accurate basis for
AB  - future comparative studies of this pathogen.
ER  -

TY  - JOUR
AU  - Pujic, P.
AU  - Bolotin, A.
AU  - Fournier, P.
AU  - Sorokin, A.
AU  - Lapidus, A.
AU  - Richau, K.H.
AU  - Briolay, J.
AU  - Mebarki, F.
AU  - Normand, P.
AU  - Sellstedt, A.
TI  - Genome Sequence of the Atypical Symbiotic Frankia R43 Strain, a Nitrogen-Fixing and Hydrogen-Producing Actinobacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01387
EP  - e01315
VL  - 3
AB  - Frankia strain R43 is a nitrogen-fixing and hydrogen-producing symbiotic actinobacterium that
AB  - was isolated from nodules of Casuarina cunninghamiana but
AB  - infects only Elaeagnaceae. This communication reports the genome of the strain
AB  - R43 and provides insights into the microbe genomics and physiological potentials.
ER  -

TY  - JOUR
AU  - Pukall, R. et al.
TI  - Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 234
EP  - 241
VL  - 1
AB  - Slackia heliotrinireducens (Lanigan 1983) Wade et al. 1999 is of phylogenetic interest because
AB  - of its location in a genomically yet uncharted section of the
AB  - family Coriobacteriaceae, within the deep branching Actinobacteria. Strain RHS
AB  - 1(T) was originally isolated from the ruminal flora of a sheep. It is a
AB  - proteolytic anaerobic coccus, able to reductively cleave pyrrolizidine alkaloids.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence, and annotation. This is the first complete genome sequence of the genus
AB  - Slackia, and the 3,165,038 bp long single replicon genome with its 2798
AB  - protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Pukall, R. et al.
TI  - Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 262
EP  - 269
VL  - 1
AB  - Jonesia denitrificans (Prevot 1961) Rocourt et al. 1987 is the type species of the genus
AB  - Jonesia, and is of phylogenetic interest because of its isolated
AB  - location in the actinobacterial suborder Micrococcineae. J. denitrificans is
AB  - characterized by a typical coryneform morphology and is able to form irregular
AB  - nonsporulating rods showing branched and club-like forms. Coccoid cells occur in
AB  - older cultures. J. denitrificans is classified as a pathogenic organism for
AB  - animals (vertebrates). The type strain whose genome is described here was
AB  - originally isolated from cooked ox blood. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. This is the
AB  - first completed genome sequence of a member of the genus for which a complete
AB  - genome sequence is described. The 2,749,646 bp long genome with its 2558
AB  - protein-coding and 71 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Pukall, R. et al.
TI  - Complete genome sequence of Kribbella flavida type strain (IFO 14399).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 186
EP  - 193
VL  - 2
AB  - The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the
AB  - type species. The name Kribbella was formed from the acronym of the
AB  - Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the
AB  - various Kribbella species were originally isolated from soil, potato, alum slate
AB  - mine, patinas of catacombs or from horse racecourses. Here we describe the
AB  - features of K. flavida together with the complete genome sequence and annotation.
AB  - In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the
AB  - second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp
AB  - long genome with its 7,086 protein-coding and 60 RNA genes and is part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pukall, R. et al.
TI  - Complete genome sequence of Conexibacter woesei type strain (ID131577).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 212
EP  - 219
VL  - 2
AB  - The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family
AB  - Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with
AB  - Conexibacter woesei as the type species of the genus. C. woesei is a
AB  - representative of a deep evolutionary line of descent within the class
AB  - Actinobacteria. Strain ID131577(T) was originally isolated from temperate forest
AB  - soil in Gerenzano (Italy). Cells are small, short rods that are motile by
AB  - peritrichous flagella. They may form aggregates after a longer period of growth
AB  - and, then as a typical characteristic, an undulate structure is formed by
AB  - self-aggregation of flagella with entangled bacterial cells. Here we describe the
AB  - features of the organism, together with the complete sequence and annotation. The
AB  - 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA
AB  - genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pukall, R. et al.
TI  - Complete genome sequence of Deinococcus maricopensis type strain (LB-34).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 163
EP  - 172
VL  - 4
AB  - Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus,
AB  - which is comprised of 44 validly named species and is located within
AB  - the deeply branching bacterial phylum Deinococcus-Thermus. Strain LB-34(T) was
AB  - isolated from a soil sample from the Sonoran Desert in Arizona. Various species
AB  - of the genus Deinococcus are characterized by extreme radiation resistance, with
AB  - D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of
AB  - three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have
AB  - already been published, no special physiological characteristic is currently
AB  - known that is unique to this group. It is therefore of special interest to
AB  - analyze the genomes of additional species of the genus Deinococcus to better
AB  - understand how these species adapted to gamma- or UV ionizing-radiation. The
AB  - 3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66
AB  - RNA genes consists of one circular chromosome and is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Pukkila, P.J.
AU  - Peterson, J.
AU  - Herman, G.
AU  - Modrich, P.
AU  - Meselson, M.
TI  - Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli.
JO  - Genetics
PY  - 1983
SP  - 571
EP  - 582
VL  - 104
AB  - Two methods were used in an attempt to increase the efficiency and strand
AB  - selectivity of methyl-directed mismatch repair of bacteriophage lambda
AB  - heteroduplexes in E. coli.  Previous studies of such repair used lambda DNA
AB  - that was only partially methylated as the source of methylated chains.  Also,
AB  - transfection was carried out in methylating strains.  Either of these factors
AB  - might have been responsible for the incompleteness of the strand selectivity
AB  - observed previously.  In the first approach to increasing strand selectivity,
AB  - heteroduplexes were transfected into a host deficient in methylation, but no
AB  - changes in repair frequencies were observed.  In the second approach,
AB  - heteroduplexes were prepared using DNA that had been highly methylated in vitro
AB  - with purified DNA adenine methylase as the source of methylated chains.  In
AB  - heteroduplexes having a repairable cI/+ mismatch, strand selectivity was indeed
AB  - enhanced.  In heteroduplexes with one chain highly methylated and the
AB  - complementary chain unmethylated, the frequency of repair on the unmethylated
AB  - chain increased to nearly 100%.  Heteroduplexes with both chains highly
AB  - methylated were not repaired at a detectable frequency.  Thus, chains highly
AB  - methylated by DNA adenine methylase were refractory to mismatch repair by this
AB  - system, regardless of the methylation of the complementary chain.  These
AB  - results support the hypothesis that methyl-directed mismatch repair acts to
AB  - correct errors of replication, thus lowering the mutation rate.
ER  -

TY  - JOUR
AU  - Pullan, S.T.
AU  - Chandra, G.
AU  - Bibb, M.J.
AU  - Merrick, M.
TI  - Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes.
JO  - BMC Genomics
PY  - 2011
SP  - 175
EP  - 175
VL  - 12
AB  - ABSTRACT: BACKGROUND: GlnR is an atypical response regulator found in
AB  - actinomycetes that modulates the transcription of genes in response to
AB  - changes in nitrogen availability. We applied a global in vivo approach to
AB  - identify the GlnR regulon of Streptomyces venezuelae, which, unlike many
AB  - actinomycetes, grows in a diffuse manner that is suitable for
AB  - physiological studies. Conditions were defined that facilitated analysis
AB  - of GlnR-dependent induction of gene expression in response to rapid
AB  - nitrogen starvation. Microarray analysis identified global transcriptional
AB  - differences between glnR+ and glnR mutant strains under varying nitrogen
AB  - conditions. To differentiate between direct and indirect regulatory
AB  - effects of GlnR, chromatin immuno-precipitation (ChIP) using antibodies
AB  - specific to a FLAG-tagged GlnR protein, coupled with microarray analysis
AB  - (ChIP-chip), was used to identify GlnR binding sites throughout the S.
AB  - venezuelae genome. RESULTS: GlnR bound to its target sites in both
AB  - transcriptionally active and apparently inactive forms. Thirty-six GlnR
AB  - binding sites were identified by ChIP-chip analysis allowing derivation of
AB  - a consensus GlnR-binding site for S. venezuelae. GlnR-binding regions were
AB  - associated with genes involved in primary nitrogen metabolism, secondary
AB  - metabolism, the synthesis of catabolic enzymes and a number of
AB  - transport-related functions. CONCLUSIONS: The GlnR regulon of S.
AB  - venezuelae is extensive and impacts on many facets of the organism's
AB  - biology. GlnR can apparently bind to its target sites in both
AB  - transcriptionally active and inactive forms.
ER  -

TY  - JOUR
AU  - Pullan, S.T.
AU  - Miles, R.W.
AU  - Lewandowski, K.
AU  - Vipond, R.
TI  - Closed genome sequence using hybrid Nanopore/Illumina assembly of a Bacillus anthracis isolate from an animal-skin-drum-associated anthrax case in the UK.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00802
EP  - e00818
VL  - 7
AB  - Hybrid de novo assembly of Illumina/Nanopore reads produced a complete genome sequence of the
AB  - chromosome and two virulence plasmids of a
AB  - Bacillus anthracis isolate from a fatal anthrax case in the United Kingdom linked to imported
AB  - animal skins/drums; this provides a high-quality representative sequence for this lineage.
ER  -

TY  - JOUR
AU  - Pullinger, G.D.
AU  - Bevir, T.
AU  - Lax, A.J.
TI  - The Pasteurella multocida toxin is encoded within a lysogenic bacteriophage.
JO  - Mol. Microbiol.
PY  - 2004
SP  - 255
EP  - 269
VL  - 51
AB  - Toxigenic strains of Pasteurella multocida produce a 146 kDa toxin (PMT)
AB  - that acts as a potent mitogen. Sequence analysis of the structural gene
AB  - for PMT, toxA, previously suggested it was horizontally acquired, because
AB  - it had a low G + C content relative to the P. multocida genome. To address
AB  - this, the sequence of DNA flanking toxA was determined. The sequence
AB  - analysis showed the presence of homologues to bacteriophage tail protein
AB  - genes and a bacteriophage antirepressor, suggesting that the toxin gene
AB  - resides within a prophage. In addition to phage genes, the toxA flanking
AB  - DNA contained a homologue of a restriction/modification system that was
AB  - shown to be functional. The presence of a bacteriophage was demonstrated
AB  - in spent medium from toxigenic P. multocida isolates. Its production was
AB  - increased by mitomycin C addition, a treatment that is known to induce the
AB  - lytic cycle of many temperate bacteriophages. The genomes of
AB  - bacteriophages from three different toxigenic P. multocida strains had
AB  - similar but not identical restriction profiles, and were approximately
AB  - 45-50 kb in length. The prophages from two of these had integrated at the
AB  - same site in the chromosome, in a tRNA gene. Southern blot analysis
AB  - confirmed that these bacteriophages contained the toxA gene.
ER  -

TY  - JOUR
AU  - Pullinger, G.D.
AU  - Dziva, F.
AU  - Charleston, B.
AU  - Wallis, T.S.
AU  - Stevens, M.P.
TI  - Identification of Salmonella enterica serovar Dublin-specific sequences by subtractive hybridization and analysis of their role in intestinal colonization and systemic translocation in cattle.
JO  - Infect. Immun.
PY  - 2008
SP  - 5310
EP  - 5321
VL  - 76
AB  - Salmonella enterica serovar Dublin is a host-restricted serovar associated
AB  - with typhoidal disease in cattle. In contrast, the fowl-associated serovar
AB  - S. enterica serovar Gallinarum is avirulent in calves, yet it invades
AB  - ileal mucosa and induces enteritis at levels comparable to those induced
AB  - by S. enterica serovar Dublin. Suppression subtractive hybridization was
AB  - employed to identify S. enterica serovar Dublin strain SD3246 genes absent
AB  - from S. enterica serovar Gallinarum strain SG9. Forty-one S. enterica
AB  - serovar Dublin fragments were cloned and sequenced. Among these, 24
AB  - mobile-element-associated genes were identified, and 12 clones exhibited
AB  - similarity with sequences of known or predicted function in other
AB  - serovars. Three S. enterica serovar Dublin-specific regions were
AB  - homologous to regions from the genome of Enterobacter sp. strain 638.
AB  - Sequencing of fragments adjacent to these three sequences revealed the
AB  - presence of a 21-kb genomic island, designated S. enterica serovar Dublin
AB  - island 1 (SDI-1). PCR analysis and Southern blotting showed that SDI-1 is
AB  - highly conserved within S. enterica serovar Dublin isolates but rarely
AB  - found in other serovars. To probe the role of genes identified by
AB  - subtractive hybridization in vivo, 24 signature-tagged S. enterica serovar
AB  - Dublin SD3246 mutants lacking loci not present in Salmonella serovar
AB  - Gallinarum SG9 were created and screened by oral challenge of cattle.
AB  - Though attenuation of tagged SG9 and SD3246 Salmonella pathogenicity
AB  - island-1 (SPI-1) and SPI-2 mutant strains was detected, no obvious defects
AB  - of these 24 mutants were detected. Subsequently, a DeltaSDI-1 mutant was
AB  - found to exhibit weak but significant attenuation compared with the parent
AB  - strain in coinfection of calves. SDI-1 mutation did not impair invasion,
AB  - intramacrophage survival, or virulence in mice, implying that SDI-1 does
AB  - not influence fitness per se and may act in a host-specific manner.
ER  -

TY  - JOUR
AU  - Puopolo, G.
AU  - Sonego, P.
AU  - Engelen, K.
AU  - Pertot, I.
TI  - Draft Genome Sequence of Lysobacter capsici AZ78, a Bacterium Antagonistic to Plant-Pathogenic Oomycetes.
JO  - Genome Announcements
PY  - 2014
SP  - e00325
EP  - e00314
VL  - 2
AB  - Lysobacter capsici AZ78, isolated from tobacco rhizosphere, effectively controls  Phytophthora
AB  - infestans and Plasmopara viticola on tomato and grapevine plants, respectively. We report the
AB  - first draft genome sequence of the L. capsici species.
ER  -

TY  - JOUR
AU  - Pupo, E.
AU  - Perez, E.
AU  - Trujillo, L.E.
AU  - Miranda, F.
AU  - Gonzalez, E.
AU  - Brito, J.
TI  - Validation of radioactive methods in the quality control of DNA restriction enzymes.
JO  - Biotecnol. Apl.
PY  - 1996
SP  - 197
EP  - 200
VL  - 13
AB  - In this paper two radioactive substrates obtained from lambda DNA digested with the
AB  - restriction enzyme HpaII were evaluated for the detection of 5' to 3', 3' to 5' single and
AB  - double stranded-DNA dependent exonuclease and phosphatase activities found in DNA restriction
AB  - and modifying enzyme preparations.  A cloning simulation assay was performed using the same
AB  - conditions established for the radioactive assay taking into account enzyme units and pmols of
AB  - DNA ends used as substrate.  As a result, it was found that for degradation of the radioactive
AB  - DNA substrate per enzyme unit below 0.5%, the false positives in the cloning simulation assay
AB  - became less than 5%.  Finally, the use of the radiolabeled [gamma 32P] ATP lambda HpaII DNA
AB  - substrate to detect 5' to 3' single stranded-DNA dependent exonuclease and phosphatase
AB  - contaminating activities is described at certain critical steps of the purification process of
AB  - the restriction enzyme KpnI.
ER  -

TY  - JOUR
AU  - Puranik, R.
AU  - Quan, G.
AU  - Werner, J.
AU  - Zhou, R.
AU  - Xu, Z.
TI  - A pipeline for completing bacterial genomes using in silico and wet lab approaches.
JO  - BMC Genomics
PY  - 2015
SP  - S7
EP  - S7
VL  - 16
AB  - Despite the large volume of genome sequencing data produced by next-generation sequencing
AB  - technologies and the highly sophisticated software dedicated to handling these types of data,
AB  - gaps are commonly found in draft genome assemblies. The existence of gaps compromises our
AB  - ability to take full advantage of the genome data. This study aims to identify a practical
AB  - approach for biologists to complete their own genome assemblies using commonly available tools
AB  - and resources. A pipeline was developed to assemble complete genomes primarily from the next
AB  - generation sequencing
AB  - (NGS) data. The input of the pipeline is paired-end Illumina sequence reads, and the output is
AB  - a high quality complete genome sequence. The pipeline alternates the employment of
AB  - computational and biological methods in
AB  - seven steps. It combines the strengths of de novo assembly, reference-based assembly,
AB  - customized programming, public databases utilization, and wet lab experimentation. The
AB  - application of the pipeline is demonstrated by the
AB  - completion of a bacterial genome, Thermotoga sp. strain RQ7, a hydrogen-producing strain. The
AB  - developed pipeline provides an example of effective integration of computational and
AB  - biological principles. It highlights the complementary roles that in silico and wet lab
AB  - methodologies play in bioinformatical studies. The constituting principles and methods are
AB  - applicable to similar studies on both prokaryotic and eukaryotic genomes.
ER  -

TY  - JOUR
AU  - Puranik, S.
AU  - Talkal, R.
AU  - Qureshi, A.
AU  - Khardenavis, A.
AU  - Kapley, A.
AU  - Purohit, H.J.
TI  - Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans, Isolated from Loktak Lake.
JO  - Genome Announcements
PY  - 2013
SP  - e01115
EP  - e01113
VL  - 1
AB  - The whole genome of a pigment-producing isolate from a lake in northern India,
AB  - Pseudogulbenkiania ferrooxidans strain EGD-HP2, has been sequenced to study the
AB  - spectrum of biosynthesis of secondary metabolites. The genome annotation data
AB  - revealed an operon for violacein, which showed homology with the reported operon
AB  - of a Chromobacterium sp., and also a quinone cofactor.
ER  -

TY  - JOUR
AU  - Purdy, D.
AU  - O'Keeffe, T.A.
AU  - Elmore, M.
AU  - Herbert, M.
AU  - McLeod, A.
AU  - Bokori-Brown, M.
AU  - Ostrowski, A.
AU  - Minton, N.P.
TI  - Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction  barrier.
JO  - Mol. Microbiol.
PY  - 2002
SP  - 439
EP  - 452
VL  - 46
AB  - Progress towards understanding the molecular basis of virulence in Clostridium difficile has
AB  - been hindered by the lack of effective gene transfer systems. We have now, for the first time,
AB  - developed procedures that may be used to introduce autonomously replicating vectors into this
AB  - organism through their conjugative, oriT-based mobilization from Escherichia coli donors.
AB  - Successful transfer was achieved through the use of a plasmid replicon isolated from an
AB  - indigenous C. difficile plasmid, pCD6, and through the characterization and subsequent
AB  - circumvention of host restriction/modification (RM) systems. The characterized replicon is the
AB  - first C. difficile plasmid replicon to be sequenced and encodes a large replication protein
AB  - (RepA) and a repetitive region composed of a 35 bp iteron sequence repeated seven times.
AB  - Strain CD6 has two RM systems, CdiCD6I/M.CdiCD6I and CdiCD6II/M.CdiCD6II, with equivalent
AB  - specificities to Sau96I/M. Sau96I (5'-GGNmCC-3') and Mbol/M. Mbol (5'-GmATC-3')
AB  - respectively. A second strain (CD3) possesses a type IIs restriction enzyme, CdiI, which
AB  - cleaves the sequence 5'-CATCG-3' between the fourth and fifth nucleotide to give a
AB  - blunt-ended fragment. This is the first time that an enzyme with this specificity has been
AB  - reported. The sequential addition of this site to vectors showed that each site caused between
AB  - a five- and 16-fold reduction in transfer efficiency. The transfer efficiencies achieved with
AB  - both strains equated to between 1.0x10^-6 and 5.5x10^-5 transconjugants per donor.
ER  -

TY  - JOUR
AU  - Purdy, M.M.
AU  - Holz-Schietinger, C.
AU  - Reich, N.O.
TI  - Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion.
JO  - Arch. Biochem. Biophys.
PY  - 2010
SP  - 13
EP  - 22
VL  - 498
AB  - The human DNA methyltransferase 3A (DNMT3A) is essential for establishing DNA methylation
AB  - patterns. Knowing the key factors involved
AB  - in the regulation of mammalian DNA methylation is critical to
AB  - furthering understanding of embryonic development and designing
AB  - therapeutic approaches targeting epigenetic mechanisms. We observe
AB  - substrate inhibition for the full length DNMT3A but not for its
AB  - isolated catalytic domain, demonstrating that DNMT3A has a second
AB  - binding site for DNA. Deletion of recognized domains of DNMT3A reveals
AB  - that the conserved PWWP domain is necessary for substrate inhibition
AB  - and forms at least part of the allosteric DNA binding site. The PWWP
AB  - domain is demonstrated here to bind DNA in a cooperative manner with mu
AB  - M affinity. No clear sequence preference was observed, similar to
AB  - previous observations with the isolated PWWP domain of Dnmt3b but with
AB  - one order of magnitude weaker affinity. Potential roles for a low
AB  - affinity, low specificity second DNA binding site are discussed.
ER  -

TY  - JOUR
AU  - Purdy, M.M.
AU  - Reich, N.O.
TI  - Modulation of mammalian DNA methyltransferase activity by RNA.
JO  - ACS Abstracts
PY  - 2006
SP  - 244
EP  - 244
VL  - 232
AB  - Recent studies indicate potential interactions between mammalian DNA methyltransferase enzymes
AB  - and RNA.  Transcriptional silencing by short or antisense RNA's directed to promoter regions
AB  - has been proposed to involve an RNA directed DNA methylation component, though this remains
AB  - controversial.  Binding of duplex RNA to the DNMT3 isoforms has been demonstrated, along with
AB  - inhibition of DNMT1 by single stranded DNA.  The present work shows that an ss RNA is a more
AB  - potent DNMT1 inhibitor than the corresponding ssDNA.  ssRNA, being more abundant than ssDNA,
AB  - may represent an endogenous DNMT1 inhibitor.  Preliminary results indicate that an RNA/DNA
AB  - hybrid duplex, suggested in some mechanisms for RNA directed DNA methylation, is a poor DNMT1
AB  - substrate.  Studies on interactions of the DNMT3 isoforms with ssRNA and RNA/DNA duplexes are
AB  - underway.
ER  -

TY  - JOUR
AU  - Purdy, M.M.
AU  - Reich, N.O.
TI  - DNA binding by HhaI DNA methyltransferase domain interface mutants.
JO  - FASEB J.
PY  - 2006
SP  - A901
EP  - A901
VL  - 20
AB  - The bacterial HhaI DNA methyltransferase (M.HhaI) is a structurally and mechanistically
AB  - characterized member of the cytosine C-5 DNA
AB  - methyltransferase family. A Statistical Coupling Analysis, which uses
AB  - genetic covariation to estimate energetic coupling between protein
AB  - residues, was performed on this enzyme family. This analysis identified
AB  - a network of co-evolving residues centered on two regions - the
AB  - catalytic loop and domain interface, both of which were previously
AB  - implicated by crystallography in large scale conformational changes
AB  - upon DNA binding. Mutation of several domain interface residues in
AB  - M.HhaI resulted in 6 - 100 fold decreases in DNA affinity, despite their 7 - 20 angstrom
AB  - distances from the DNA. The effects of these
AB  - mutations suggest a role of this network in positioning or moving the
AB  - two domains and the importance of proper domain positioning in DNA
AB  - binding. The crystal structure of the I308A mutant was solved to 2.2
AB  - angstrom resolution. It is unclear if this mutation alters the
AB  - structure enough to explain the 35 fold loss in DNA affinity,
AB  - suggesting that this mutation may perturb the domain - domain motions
AB  - necessary for DNA binding.
ER  -

TY  - JOUR
AU  - Purdy, M.M.
AU  - Reich, N.O.
TI  - DNA binding and hemimethylation preference of HhaI DNA methyltransferase domain interface mutants.
JO  - ACS Abstracts
PY  - 2005
SP  - U626
EP  - U626
VL  - 230
AB  - Recent studies indicate potential interactions between mammalian DNA methyltransferase (DNMT)
AB  - enzymes and RNA. Transcriptional silencing by short or antisense RNA's directed to promoter
AB  - regions has been proposed to involve an RNA directed DNA methylation component, though this
AB  - remains controversial. Binding of duplex RNA to the DNMT3 isoforms has been demonstrated,
AB  - along with inhibition of DNMT1 by single stranded (ss) DNA. The present work shows that an ss
AB  - RNA is a more potent DNMT1 inhibitor than the corresponding ss DNA. ss RNA, being more
AB  - abundant than ss DNA, may represent an endogenous DNMT1 inhibitor. Preliminary results
AB  - indicate that an RNA/DNA hybrid duplex, suggested in some mechanisms for RNA directed DNA
AB  - methylation, is a poor DNMT1 substrate. Studies on interactions of the DNMT3 isoforms with ss
AB  - RNA and RNA/DNA duplexes are underway.
ER  -

TY  - JOUR
AU  - Purmal, A.A.
AU  - Shabarova, Z.A.
AU  - Gumport, R.I.
TI  - A new affinity reagent for the site-specific, covalent attachment of DNA to active-site nucleophiles: application to the EcoRI and RsrI restriction and modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 3713
EP  - 3719
VL  - 20
AB  - A modified oligodeoxyribonucleotide duplex containing an unnatural internucleotide
AB  - trisubstituted 3' to 5' pyrophosphate bond in one strand
AB  - [5'(oligo1)3'-P(OCH3)P-5'(oligo2)3'] reacts with nucleophiles in aqueous media by acting
AB  - as a phosphorylating affinity reagent. When interacted with a protein, a portion of the
AB  - oligonucleotide [-P-5'(oligo2)3'] becomes attached to an amino acid nucleophilic group
AB  - through a phosphate of the O-methyl-modified pyrophosphate linkage. We demonstate the affinity
AB  - labeling of nucleophilic groups at the active sites of the EcoRI and RsrI restriction and
AB  - modification enzymes with an oligodeoxyribonucleotide duplex containg a modified scissile bond
AB  - in the EcoRI recognitin site. With the EcoRI and RsrI endonuclease in molar excess
AB  - approximately 1% of the oligonucleotide becomes attached to the protein and with the companion
AB  - methyltransferases the yield approaches 40% for the EcoRI enzyme and 30% for the RsrI
AB  - methyltransferase. Crosslinking proceeds only upon formation of a sequence-specific enzyme-DNA
AB  - complex and generates a covalent bond between the 3'-phosphate of the modified pyrophosphate
AB  - in the substrate and a nucleophilic group at the active site of the enzymes. The reaction
AB  - results in the elimination of an oligodeoxyribonucleotide remnant that contains the
AB  - 3'-O-methylphosphate [5'(oligo1)3'-P(OCH3)] derived from the modified phosphate of the
AB  - pyrophosphate linkage. Hydrolysis properties of the covalent protein-DNA adducts indicate that
AB  - phosphoamide (P-N) bonds are formed with the EcoRI endonuclease and methyltransferase.
ER  -

TY  - JOUR
AU  - Purmal, A.A.
AU  - Vinogradova, M.N.
AU  - Elov, A.A.
AU  - Gromova, E.S.
AU  - Drutsa, V.L.
TI  - Interaction of EcoRII restriction and modification enzymes with DNA duplexes containing pyrophosphate bonds.
JO  - Dokl. Akad. Nauk.
PY  - 1984
SP  - 992
EP  - 995
VL  - 276
ER  -

TY  - JOUR
AU  - Purswani, J.
AU  - Guisado, I.M.
AU  - Gonzalez-Lopez, J.
AU  - Pozo, C.
TI  - Draft Genome Sequence of Paenibacillus etheri sp. nov. SH7T, a Methyl Tert-Butyl  Ether Degrader.
JO  - Genome Announcements
PY  - 2016
SP  - e01696
EP  - e01615
VL  - 4
AB  - We report here the draft genome sequence of Paenibacillus etheri sp. nov. SH7(T)  (= CECT
AB  - 8558(T) = DSM 29760(T)), isolated from a hydrocarbon-contaminated soil
AB  - pilot plant in Granada, Spain. The bacterium was isolated and sequenced due to
AB  - its methyl tert-butyl ether (MTBE)-degrading properties.
ER  -

TY  - JOUR
AU  - Purvis, I.J.
AU  - Moseley, B.E.B.
TI  - Isolation and characterisation of DraI, a type II restriction endonuclease recognising a sequence containing only A:T basepairs, and inhibition of its activity by uv irradiation of substrate DNA.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 5467
EP  - 5474
VL  - 11
AB  - A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus
AB  - ATCC 27603 recognises the palindromic hexanucleotide sequence5'-T-T-T^A-A-A-3'
AB  - 3'-A-A-A^T-T-T-5'and cleaves it, as indicated by the arrows, to produce
AB  - blunt-ended fragments.  The yield of enzyme is 100 to 1000 times that of the
AB  - only other known type II restriction endonuclease that recognises a sequence
AB  - composed solely of A:T basepairs, the isoschizomer AhaIII.  Ultraviolet
AB  - irradiation of the DNA substrate at relatively low doses inhibits the activity
AB  - of DraI by "protecting" the recognition sequence and this may be exploited to
AB  - give control of partial digestion of DNA by DraI.
ER  -

TY  - JOUR
AU  - Pushiri, H.
AU  - Pearce, S.L.
AU  - Oakeshott, J.G.
AU  - Russell, R.J.
AU  - Pandey, G.
TI  - Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil.
JO  - Genome Announcements
PY  - 2013
SP  - e00415
EP  - e00413
VL  - 1
AB  - Pandoraea sp. strain SD6-2 is a delta-hexachlorocyclohexane-degrading bacterial strain
AB  - isolated from lindane-contaminated soil in Queensland, Australia. The
AB  - genome of SD6-2 was sequenced to investigate its ability to degrade
AB  - delta-hexachlorocyclohexane. Here we report the annotated genome sequence of this
AB  - strain.
ER  -

TY  - JOUR
AU  - Putonti, C.
AU  - Cudone, E.
AU  - Kalesinskas, L.
AU  - Engelbrecht, K.C.
AU  - Koenig, D.W.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698).
JO  - Genome Announcements
PY  - 2017
SP  - e00576
EP  - e00517
VL  - 5
AB  - The actinobacterium Micrococcus luteus can be found in a wide variety of habitats. Here, we
AB  - report the 2,411,958-bp draft genome sequence of the type
AB  - strain M. leuteus (Schroeter) Cohn (ATCC 12698). Characteristic of this taxa, the
AB  - genome sequence has a high G+C content, 73.14%.
ER  -

TY  - JOUR
AU  - Putonti, C.
AU  - Kalesinskas, L.
AU  - Cudone, E.
AU  - Engelbrecht, K.C.
AU  - Koenig, D.W.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128.
JO  - Genome Announcements
PY  - 2017
SP  - e00575
EP  - e00517
VL  - 5
AB  - While a part of the native gut microflora, the Gram-positive bacterium Enterococcus faecalis
AB  - can lead to serious infections elsewhere in the body. The
AB  - draft genome of E. faecalis strain ATCC BAA-2128, isolated from piglet feces, was
AB  - examined. This draft genome consists of 42 contigs, 12 of which exhibit homology
AB  - to annotated plasmids.
ER  -

TY  - JOUR
AU  - Putonti, C.
AU  - Kalesinskas, L.
AU  - Cudone, E.
AU  - Engelbrecht, K.C.
AU  - Koenig, D.W.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00618
EP  - e00617
VL  - 5
AB  - Draft genome sequences for Staphylococcus aureus subsp. aureus Rosenbach ATCC 14458 and ATCC
AB  - 27217 strains were investigated. The genome sizes were 2,880,761
AB  - bp and 2,759,100 bp, respectively. Strain ATCC 14458 was assembled into 39
AB  - contigs, including 3 plasmids, and strain ATCC 27217 was assembled into 25
AB  - contigs, including 2 plasmids.
ER  -

TY  - JOUR
AU  - Putonti, C.
AU  - Kalesinskas, L.
AU  - Cudone, E.
AU  - Engelbrecht, K.C.
AU  - Koenig, D.W.
AU  - Wolfe, A.J.
TI  - Draft Genome Sequence of Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990).
JO  - Genome Announcements
PY  - 2017
SP  - e00619
EP  - e00617
VL  - 5
AB  - Here, we report the draft genome sequence for the type strain Staphylococcus epidermidis
AB  - (Winslow and Winslow) Evans (ATCC 14990). The assembly consisted of
AB  - 2,457,519 bp with an observed G+C content of 32.04%. Thirty-seven contigs were
AB  - produced, including two putative plasmids, with a 296.8x coverage and an N50 of
AB  - 180,848 bp.
ER  -

TY  - JOUR
AU  - Putonti, C.
AU  - Polley, N.
AU  - Castignetti, D.
TI  - Draft Genome Sequence of an Active Heterotrophic Nitrifier-Denitrifier, Cupriavidus pauculus UM1.
JO  - Genome Announcements
PY  - 2018
SP  - e00028
EP  - e00018
VL  - 6
AB  - Here, we present the draft genome sequence of Cupriavidus pauculus UM1, a metal-resistant
AB  - heterotrophic nitrifier-denitrifier capable of synthesizing
AB  - nitrite from pyruvic oxime. The size of the genome is 7,402,815 bp with a GC
AB  - content of 64.8%. This draft assembly consists of 38 scaffolds.
ER  -

TY  - JOUR
AU  - Puvvada, M.S.
AU  - Hartley, J.A.
AU  - Jenkins, T.C.
AU  - Thurston, D.E.
TI  - A quantitative assay to measure the relative DNA-binding affinity of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) antitumor antibiotics based on the inhibition of restriction endonuclease BamHI.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3671
EP  - 3675
VL  - 21
AB  - An assay has been developed (restriction endonuclease digestion assay - RED100) based on
AB  - inhibition of the restriction endonuclease BamHI that is capable of quantitive evaluation of
AB  - the relative DNA-binding affinity of pyrrolo[2,1-c][1,4]benzodiazepine (PBD) antitumor
AB  - antibiotics. This method provides comparable results to those obtained from thermal
AB  - denaturation and ethidium bromide displacement assays but is much more sensitive,
AB  - discriminating between molecules of similar structure such as DC-81, iso-DC-81 and
AB  - neothramycin. The results reveal a trend between relative DNA-binding affinity and in vitro
AB  - cytotoxicity for the PBDs in two tumour cell lines studied.
ER  -

TY  - JOUR
AU  - Pylro, V.S.
AU  - Dias, A.C.F.
AU  - Andreote, F.D.
AU  - Morais, D.K.
AU  - Varani, A.M.
AU  - Andreote, C.C.F.
AU  - Bernardo, E.R.A.
AU  - Zucchi, T.
TI  - Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.
JO  - Genome Announcements
PY  - 2018
SP  - e00057
EP  - e00018
VL  - 6
AB  - We report here the closed and near-complete genome sequence and annotation of Bacillus
AB  - velezensis strain AGVL-005, a bacterium isolated from soybean seeds in
AB  - Brazil and used for phytopathogen biocontrol.
ER  -

TY  - JOUR
AU  - Pyne, M.E.
AU  - Moo-Young, M.
AU  - Chung, D.A.
AU  - Chou, C.P.
TI  - Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: chromosomal gene disruption of the endogenous CpaAI restriction  enzyme.
JO  - Biotechnol. Biofuels.
PY  - 2014
SP  - 163
EP  - 163
VL  - 7
AB  - BACKGROUND: Clostridium pasteurianum is one of the most promising biofuel producers within the
AB  - genus Clostridium owing to its unique metabolic ability to
AB  - ferment glycerol into butanol. Although an efficient means is available for
AB  - introducing foreign DNA to C. pasteurianum, major genetic tools, such as gene
AB  - knockout, knockdown, or genome editing, are lacking, preventing metabolic
AB  - engineering of C. pasteurianum. RESULTS: Here we present a methodology for
AB  - performing chromosomal gene disruption in C. pasteurianum using the programmable
AB  - lactococcus Ll.ltrB group II intron. Gene disruption was initially found to be
AB  - impeded by inefficient electrotransformation of Escherichia coli-C. pasteurianum
AB  - shuttle vectors, presumably due to host restriction. By assessing the ability of
AB  - various vector deletion derivatives to electrotransform C. pasteurianum and
AB  - probing the microorganism's methylome using next-generation sequence data, we
AB  - identified a new C. pasteurianum Type I restriction-methylation system, CpaAII,
AB  - with a predicted recognition sequence of 5'-AAGNNNNNCTCC-3' (N = A, C, G, or T).
AB  - Following rescue of high-level electrotransformation via mutation of the sole
AB  - CpaAII site within the shuttle vectors, we retargeted the intron to the cpaAIR
AB  - gene encoding the CpaAI Type II restriction endonuclease (recognition site of
AB  - 5'-CGCG-3'). Intron insertion was potentially hindered by low retrohoming
AB  - efficiency, yet this limitation could be overcome by a procedure for enrichment
AB  - of the intron insertion. The resulting DeltacpaAIR mutant strain was efficiently
AB  - electrotransformed with M.FnuDII-unmethylated plasmid DNA. CONCLUSIONS: The
AB  - markerless and plasmidless DeltacpaAIR mutant strain of C. pasteurianum developed
AB  - in this study can serve as a general host strain for future genetic and metabolic
AB  - manipulation. Further, the associated gene disruption protocol should not only
AB  - serve as a guide for chromosomal gene inactivation studies involving mobile group
AB  - II introns, but also prove invaluable for applying metabolic engineering
AB  - strategies to C. pasteurianum.
ER  -

TY  - JOUR
AU  - Pyne, M.E.
AU  - Moo-Young, M.
AU  - Chung, D.A.
AU  - Chou, C.P.
TI  - Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum.
JO  - Biotechnol. Biofuels.
PY  - 2013
SP  - 50
EP  - 50
VL  - 6
AB  - Background: Reducing the production cost of, and increasing revenues from, industrial biofuels
AB  - will greatly facilitate their proliferation
AB  - and co-integration with fossil fuels. The cost of feedstock is the
AB  - largest cost in most fermentation bioprocesses and therefore represents
AB  - an important target for cost reduction. Meanwhile, the biorefinery
AB  - concept advocates revenue growth through complete utilization of
AB  - by-products generated during biofuel production. Taken together, the
AB  - production of biofuels from low-cost crude glycerol, available in
AB  - oversupply as a by-product of bioethanol production, in the form of
AB  - thin stillage, and biodiesel production, embodies a remarkable
AB  - opportunity to advance affordable biofuel development. However, few
AB  - bacterial species possess the natural capacity to convert glycerol as a
AB  - sole source of carbon and energy into value-added bioproducts. Of
AB  - particular interest is the anaerobe Clostridium pasteurianum, the only
AB  - microorganism known to convert glycerol alone directly into butanol,
AB  - which currently holds immense promise as a high-energy biofuel and bulk
AB  - chemical. Unfortunately, genetic and metabolic engineering of C.
AB  - pasteurianum has been fundamentally impeded due to lack of an efficient
AB  - method for deoxyribonucleic acid (DNA) transfer.
AB  - Results: This work reports the development of an
AB  - electrotransformation protocol permitting high-level DNA transfer to C.
AB  - pasteurianum ATCC 6013 together with accompanying selection markers and
AB  - vector components. The CpaAI restriction-modification system was found
AB  - to be a major barrier to DNA delivery into C. pasteurianum which we
AB  - overcame by in vivo methylation of the recognition site (5'-CGCG-3')
AB  - using the M. FnuDII methyltransferase. With proper selection of the
AB  - replication origin and antibiotic-resistance marker, we initially
AB  - electroporated methylated DNA into C. pasteurianum at a low efficiency
AB  - of 2.4 x 10(1) transformants mu g(-1) DNA by utilizing conditions
AB  - common to other clostridial electroporations. Systematic investigation
AB  - of various parameters involved in the cell growth, washing and pulse
AB  - delivery, and outgrowth phases of the electrotransformation procedure
AB  - significantly elevated the electrotransformation efficiency, up to 7.5
AB  - x 10(4) transformants mu g(-1) DNA, an increase of approximately three
AB  - order of magnitude. Key factors affecting the electrotransformation
AB  - efficiency include cell-wall-weakening using glycine, ethanol-mediated
AB  - membrane solubilization, field strength of the electric pulse, and
AB  - sucrose osmoprotection.
AB  - Conclusions: C. pasteurianum ATCC 6013 can be electrotransformed at
AB  - a high efficiency using appropriately methylated plasmid DNA. The
AB  - electrotransformation method and tools reported here should promote
AB  - extensive genetic manipulation and metabolic engineering of this
AB  - biotechnologically important bacterium.
ER  -

TY  - JOUR
AU  - Pyne, M.E.
AU  - Utturkar, S.
AU  - Brown, S.D.
AU  - Moo-Young, M.
AU  - Chung, D.A.
AU  - Chou, C.P.
TI  - Improved Draft Genome Sequence of Clostridium pasteurianum Strain ATCC 6013 (DSM  525) Using a Hybrid Next-Generation Sequencing Approach.
JO  - Genome Announcements
PY  - 2014
SP  - e00790
EP  - e00714
VL  - 2
AB  - We present an improved draft genome sequence for Clostridium pasteurianum strain  ATCC 6013
AB  - (DSM 525), the type strain of the species and an important
AB  - solventogenic bacterium with industrial potential. Availability of a
AB  - near-complete genome sequence will enable strain engineering of this promising
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Qi, G.R.
AU  - Wong, P.
AU  - Cedergren, R.
TI  - Restriction of single-stranded M13 DNA using synthetic oligonucleotides:  the structural requirement of restriction enzymes.
JO  - Biochem. Cell Biol.
PY  - 1987
SP  - 50
EP  - 55
VL  - 65
AB  - A targeted ss (single stranded) DNA cleavage technique is reported which
AB  - involves the use of synthetic oligomers complementary to the ss M12 DNA
AB  - polylinker.  BamHI, SmaI, and KpnI restriction enzymes were tested with a
AB  - partial duplex DNA formed from ss M13 DNA and a nested series of fragments
AB  - derived from a synthetic 21-mer which were complementary to the polylinker
AB  - region.  These enzymes require up to two flanking nucleotides in addition to
AB  - the hexameric recognition site for efficient cleavage.  This technique could be
AB  - useful for effecting unique cleavages of DNA with enzymes which generally give
AB  - a large number of fragments and for strategies of ss DNA manipulation.
ER  -

TY  - JOUR
AU  - Qi, J.
AU  - Guo, A.
AU  - Cui, P.
AU  - Chen, Y.
AU  - Mustafa, R.
AU  - Ba, X.
AU  - Hu, C.
AU  - Bai, Z.
AU  - Chen, X.
AU  - Shi, L.
AU  - Chen, H.
TI  - Comparative Geno-Plasticity Analysis of Mycoplasma bovis HB0801 (Chinese Isolate).
JO  - PLoS ONE
PY  - 2012
SP  - E38239
EP  - E38239
VL  - 7
AB  - Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To
AB  - investigate M. bovis pathogenesis, we completed genome sequencing of strain
AB  - HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic
AB  - plasticity was determined by comparing HB0801 with M. bovis strain ATCC(R)
AB  - 25523/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung
AB  - tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of
AB  - HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb)
AB  - was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow
AB  - mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp)
AB  - gene cluster existed in HB0801, but contained less than half of the genes, and
AB  - had poor identity to that in PG45, but they had conserved structures. Further
AB  - inter-strain comparisons revealed other mechanisms of gene acquisition and loss
AB  - in HB0801 that primarily involved insertion sequence (IS) elements, integrative
AB  - conjugative element, restriction and modification systems, and some lipoproteins
AB  - and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was
AB  - compared. Results indicated that both strains were pathogenic to cattle. The
AB  - scores of gross pathological assessment for the control group, and the PG45- and
AB  - HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of
AB  - lung lesion for these three groups were 36, 70, and 69, respectively. In
AB  - addition, immunohistochemistry detection demonstrated that both strains were
AB  - similarly distributed in lungs and lymph nodes. Although PG45 showed slightly
AB  - higher virulence in calves than HB0801, there was no statistical difference
AB  - between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were
AB  - disclosed in HB0801. In conclusion, although genomic plasticity was thought to be
AB  - an evolutionary advantage, it did not apparently affect virulence of M. bovis
AB  - strains in cattle.
ER  -

TY  - JOUR
AU  - Qi, M.
AU  - Nelson, K.E.
AU  - Daugherty, S.C.
AU  - Nelson, W.C.
AU  - Hance, I.R.
AU  - Morrison, M.
AU  - Forsberg, C.W.
TI  - Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as  determined by suppressive subtractive hybridization.
JO  - J. Bacteriol.
PY  - 2005
SP  - 3739
EP  - 3751
VL  - 187
AB  - Suppressive subtractive hybridization was conducted to identify unique genes coding for plant
AB  - cell wall hydrolytic enzymes and other properties
AB  - of the gastrointestinal bacterium Fibrobacter intestinalis DR7 not shared
AB  - by Fibrobacter succinogenes S85. Subtractive clones from F. intestinalis
AB  - were sequenced and assembled to form 712 nonredundant contigs with an
AB  - average length of 525 bp. Of these, 55 sequences were unique to F.
AB  - intestinalis. The remaining contigs contained 764 genes with BLASTX
AB  - similarities to other proteins; of these, 80% had the highest similarities
AB  - to proteins in F. succinogenes, including 30 that coded for carbohydrate
AB  - active enzymes. The expression of 17 of these genes was verified by
AB  - Northern dot blot analysis. Of genes not exhibiting BLASTX similarity to
AB  - F. succinogenes, 30 encoded putative transposases, 6 encoded restriction
AB  - modification genes, and 45% had highest similarities to proteins in other
AB  - species of gastrointestinal bacteria, a finding suggestive of either
AB  - horizontal gene transfer to F. intestinalis or gene loss from F.
AB  - succinogenes. Analysis of contigs containing segments of two or more
AB  - adjacent genes revealed that only 35% exhibited BLASTX similarity and were
AB  - in the same orientation as those of F. succinogenes, indicating extensive
AB  - chromosomal rearrangement. The expression of eight transposases, and three
AB  - restriction-modification genes was confirmed by Northern dot blot
AB  - analysis. These data clearly document the maintenance of carbohydrate
AB  - active enzymes in F. intestinalis necessitated by the preponderance of
AB  - polysaccharide substrates available in the ruminal environment. It also
AB  - documents substantive changes in the genome from that of F. succinogenes,
AB  - which may be related to the introduction of the array of transposase and
AB  - restriction-modification genes.
ER  -

TY  - JOUR
AU  - Qi, M.
AU  - Wang, D.
AU  - Bradley, C.A.
AU  - Zhao, Y.
TI  - Genome Sequence Analyses of Pseudomonas savastanoi pv. glycinea and Subtractive Hybridization-Based Comparative Genomics with Nine Pseudomonads.
JO  - PLoS ONE
PY  - 2011
SP  - E16451
EP  - E16451
VL  - 6
AB  - Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a
AB  - common disease of soybean. In an effort to compare a current field isolate with
AB  - one isolated in the early 1960s, the genomes of two Psg strains, race 4 and B076,
AB  - were sequenced using 454 pyrosequencing. The genomes of both Psg strains share
AB  - more than 4,900 highly conserved genes, indicating very low genetic diversity
AB  - between Psg genomes. Though conserved, genome rearrangements and recombination
AB  - events occur commonly within the two Psg genomes. When compared to each other,
AB  - 437 and 163 specific genes were identified in B076 and race 4, respectively. Most
AB  - specific genes are plasmid-borne, indicating that acquisition and maintenance of
AB  - plasmids may represent a major mechanism to change the genetic composition of the
AB  - genome and even acquire new virulence factors. Type three secretion gene clusters
AB  - of Psg strains are near identical with that of P. savastanoi pv. phaseolicola
AB  - (Pph) strain 1448A and they shared 20 common effector genes. Furthermore, the
AB  - coronatine biosynthetic cluster is present on a large plasmid in strain B076, but
AB  - not in race 4. In silico subtractive hybridization-based comparative genomic
AB  - analyses with nine sequenced phytopathogenic pseudomonads identified dozens of
AB  - specific islands (SIs), and revealed that the genomes of Psg strains are more
AB  - similar to those belonging to the same genomospecies such as Pph 1448A than to
AB  - other phytopathogenic pseudomonads. The number of highly conserved genes (core
AB  - genome) among them decreased dramatically when more genomes were included in the
AB  - subtraction, suggesting the diversification of pseudomonads, and further
AB  - indicating the genome heterogeneity among pseudomonads. However, the number of
AB  - specific genes did not change significantly, suggesting these genes are indeed
AB  - specific in Psg genomes. These results reinforce the idea of a species complex of
AB  - P. syringae and support the reclassification of P. syringae into different
AB  - species.
ER  -

TY  - JOUR
AU  - Qi, Y.
AU  - D'Alessandro, J.M.
AU  - Blodgett, J.A.V.
TI  - Draft Genome Sequence of Streptomyces sp. Strain JV178, a Producer of Clifednamide-Type Polycyclic Tetramate Macrolactams.
JO  - Genome Announcements
PY  - 2018
SP  - e01401
EP  - e01417
VL  - 6
AB  - Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from
AB  - Connecticut (USA) garden soil. This strain produces the
AB  - polycyclic tetramate macrolactam compounds clifednamides A and B. The draft
AB  - genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several
AB  - natural product biosynthetic loci.
ER  -

TY  - JOUR
AU  - Qian, L.
AU  - Kussell, E.
TI  - Evolutionary Dynamics of Restriction Site Avoidance.
JO  - Phys. Rev. Lett.
PY  - 2012
SP  - 158105
EP  - 158105
VL  - 108
AB  - Molecular noise in bacterial restriction-modification systems can cause rare events of host
AB  - DNA cleavage at restriction sites. Such
AB  - noise-induced selective pressure may result in evolved sequences
AB  - exhibiting restriction site avoidance. We identify a two-state regime
AB  - of evolutionary dynamics, in which populations either develop avoidance
AB  - or go extinct. Using perturbation theory, we show that equilibrium
AB  - sequence statistics exhibit power-law scaling in the ratio of
AB  - restriction strength to mutation rate. Noise levels comparable to
AB  - mutation rates can be sufficient to evolve detectable avoidance.
ER  -

TY  - JOUR
AU  - Qian, Y.
AU  - Matsumoto, H.
AU  - Li, W.
AU  - Zhu, G.
AU  - Hashidoko, Y.
AU  - Hu, Y.
AU  - Wang, M.
TI  - Genome Sequence of Burkholderia plantarii ZJ171, a Tropolone-Producing Bacterial  Pathogen Responsible for Rice Seedling Blight.
JO  - Genome Announcements
PY  - 2016
SP  - e01318
EP  - e01316
VL  - 4
AB  - Burkholderia plantarii is the causal agent of rice seedling blight. Here, we report the draft
AB  - genome sequence of B. plantarii, which contains 8,020,831 bp,
AB  - with a G+C content of 68.66% and a predicted 7,688 coding sequences. The
AB  - annotated genome sequence will provide further insight into its pathogenicity.
ER  -

TY  - JOUR
AU  - Qian, Y.
AU  - Xi, Y.
AU  - Cheng, B.
AU  - Zhu, S.
TI  - Genome-wide identification and expression profiling of DNA methyltransferase gene family in maize.
JO  - Plant Cell
PY  - 2014
SP  - 1661
EP  - 1672
VL  - 33
AB  - In this study, we identified eight DNA MTase genes in maize and the diversity of expression
AB  - patterns of them was presented by EST mining, microarray and semi-quantitative expression
AB  - profile analyses.DNA methylation plays a pivotal role in promoting genomic stability through
AB  - diverse biological processes including regulation of gene expression during development and
AB  - chromatin organization. Although this important biological process is mainly regulated by
AB  - several conserved Cytosine-5 DNA methyltransferases encoded by a smaller multigene family in
AB  - plants, investigation of the plant C5-MTase-encoding gene family will serve to elucidate the
AB  - epigenetic mechanism diversity in plants. Recently, genome-wide identification and
AB  - evolutionary analyses of the C5-MTase-encoding gene family have been characterized in multiple
AB  - plant species including Arabidopsis, rice, carrot and wheat. However, little is known
AB  - regarding the C5-MTase-encoding genes in the entire maize genome. Here, genome-wide
AB  - identification and expression profile analyses of maize C5-MTase-encoding genes (ZmMETs) were
AB  - performed from the latest version of the maize (B73) genome. Phylogenetic analysis indicated
AB  - that the orthologs from the three species (maize, Arabidopsis and rice) were categorized into
AB  - four classes. Chromosomal location of these genes revealed that they are unevenly distributed
AB  - on 6 of all 10 chromosomes with three chromosomal/segmental duplication events, suggesting
AB  - that gene duplication played a key role in expansion of the maize C5-MTase-encoding gene
AB  - family. Furthermore, EST expression data mining, microarray data and semi-quantitative
AB  - expression profile analyses detected in the leaves by two different abiotic stress treatments
AB  - have demonstrated that these genes had temporal and spatial expression pattern and exhibited
AB  - different expression levels in stress treatments, suggesting that functional diversification
AB  - of ZmMET genes family. Overall, our study will serve to present signification insights to
AB  - explore the plant C5-MTase!
AB  - -encodin
AB  - g gene expression and function and also be beneficial for future experimental research to
AB  - further unravel the mechanisms of epigenetic regulation in plants.
ER  -

TY  - JOUR
AU  - Qiang, B.-Q.
AU  - McClelland, M.
AU  - Poddar, S.
AU  - Spokauskas, A.
AU  - Nelson, M.
TI  - The apparent specificity of NotI (5'-GCGGCCGC-3') is enhanced by M.FnuDII or M.BepI methyltransferases (5'-mCGCG-3'): cutting bacterial chromosomes into a few large pieces .
JO  - Gene
PY  - 1990
SP  - 101
EP  - 105
VL  - 88
AB  - The restriction endonuclease (ENase) NotI is blocked by methylation within its
AB  - recognition sequence at 5'GCGGCmCGC-3'.  This sensitivity to methylation can be
AB  - used to enhance the specificity of NotI in vivo and in vitro.  Modification by
AB  - M.FnuDII or M.BepI methyltransferases (MTase)(5'-mCGCG-3') will block NotI
AB  - (5'-GCGGCCGC-3') cleavage at overlapping MTase/ENase sites 5'-CGCGGCCGC-3'
AB  - (equivalent to 5'-GCGGCCGCG-3'), and increase the apparent cleavage specificity
AB  - of NotI about twofold.  This cross-protection procedure reduces the number of
AB  - NotI fragments in the genomes of Escherichia coli and Bacillus subtilis, as
AB  - resolved by pulsed field electrophoresis.  Application of this method to large
AB  - DNAs in vitro requires the preparation of highly purified DNA MTases.
ER  -

TY  - JOUR
AU  - Qiang, B.-Q.
AU  - Schildkraut, I.
TI  - A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 4507
EP  - 4515
VL  - 12
AB  - A new site-specific endonuclease, SfiI, has been isolated from Streptomyces
AB  - fimbriatus.  This is the first report of a type II restriction endonuclease
AB  - whose recognition specificity requires eight nucleotides.  SfiI cleaves the
AB  - sequence, GGCCNNNN^NGGCC, symmetrically to produce a three base, 3' extension.
ER  -

TY  - JOUR
AU  - Qiang, B.-Q.
AU  - Schildkraut, I.
TI  - Two unique restriction endonucleases from Neisseria lactamica.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 1991
EP  - 1999
VL  - 14
AB  - Two new site-specific endonucleases, NlaIII and NlaIV, have been isolated from
AB  - Neisseria lactamica.  NlaIII recognizes the sequence, CATG, and cleaves 3' of
AB  - the sequence to produce a four base 3' extension.  NlaIV recognizes the
AB  - sequence, GGNNCC, and cleaves between the two N's to produce blunt ended
AB  - fragments.
ER  -

TY  - JOUR
AU  - Qiang, B.-Q.
AU  - Schildkraut, I.
TI  - NotI and SfiI:  restriction endonucleases with octanucleotide recognition sequences.
JO  - Methods Enzymol.
PY  - 1987
SP  - 15
EP  - 21
VL  - 155
AB  - While there are over 500 reported Type II restriction endonucleases, only two,
AB  - NotI and SfiI, require an octanucleotide recognition sequence.  These two
AB  - endonucleases cleave DNA less frequently than conventional tetranucleotide-,
AB  - pentanucleotide-, and hexanucleotide-recognizing restriction endonucleases.  On
AB  - average, NotI and SfiI will cleave DNA only once every 64,000 nucleotides.
AB  - With the advent of physical methods that can separate very large DNA molecules,
AB  - NotI and SfiI have become useful analytical reagents for molecular biologists.
AB  - NotI is isolated from the bacterium Nocardia otitidis-caviarum ATCC 14630, and
AB  - recognizes the DNA sequence     5'...GC^GGCCGC...3'     3'...CGCCGG^CG...5'
AB  - cleaving the phosphodiester bonds in both strands as indicated.  SfiI is
AB  - isolated from the bacterium Streptomyces fimbriatus ATCC 25051 and recognizes
AB  - the DNA sequence     5'...GGCCNNNN^NGGCC...3'     3'...CCGGN^NNNNCCGG...5'
AB  - cleaving the phosphodiester bonds in both strands as indicated.
ER  -

TY  - JOUR
AU  - Qiao, J.
AU  - Chen, L.
AU  - Li, Y.
AU  - Wang, J.
AU  - Zhang, W.
AU  - Chen, S.
TI  - Whole-Genome Sequence of Nocardiopsis alba Strain ATCC BAA-2165, Associated with  Honeybees.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6358
EP  - 6359
VL  - 194
AB  - The actinomycete Nocardiopsis alba was reportedly associated with honeybees in separate
AB  - occurrences. We report the complete genome of Nocardiopsis alba ATCC
AB  - BAA-2165 isolated from honeybee guts. It will provide insights into the
AB  - metabolism and genetic regulatory networks of this genus of bacteria that enable
AB  - them to live in a range of environments.
ER  -

TY  - JOUR
AU  - Qiao, J.
AU  - Liu, Y.
AU  - Liang, X.
AU  - Hu, Y.
AU  - Du, Y.
TI  - Draft Genome Sequence of Root-Colonizing Bacterium Bacillus sp. Strain PTS-394.
JO  - Genome Announcements
PY  - 2014
SP  - e00038
EP  - e00014
VL  - 2
AB  - Here, we report the high-quality draft genome sequence of Bacillus sp. strain PTS-394,
AB  - isolated from the rhizosphere of tomatoes grown on Putuo Mountain
AB  - (Xiamen, Fujian province, China), which exhibited excellent colonization ability
AB  - on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root
AB  - colonization ability and may provide novel insights into plant-bacterium
AB  - interactions.
ER  -

TY  - JOUR
AU  - Qin, N.
AU  - Ding, W.
AU  - Yao, J.
AU  - Su, K.
AU  - Wu, L.
AU  - Li, L.
TI  - Genome Sequence of Staphylococcus capitis QN1, Which Causes Infective Endocarditis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4469
EP  - 4470
VL  - 194
AB  - Staphylococcus capitis is a subtype of coagulase-negative staphylococci (CoNS) which could
AB  - emerge as a significant pathogen causing infective endocarditis,
AB  - prosthetic valve endocarditis, and late-onset sepsis. We isolated S. capitis
AB  - strain QN1 from the skin swab sample of a female. Here we prepared a genome
AB  - sequence for this strain consisting of 30 contigs totaling 2,430,101 bases and a
AB  - GC content of 32.76%.
ER  -

TY  - JOUR
AU  - Qin, N.
AU  - Zheng, B.
AU  - Yang, F.
AU  - Chen, Y.
AU  - Guo, J.
AU  - Hu, X.
AU  - Li, L.
TI  - Genome Sequence of Aerococcus viridans LL1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4143
EP  - 4143
VL  - 194
AB  - Aerococcus viridans is a catalase-negative Gram-positive bacterium and has been described as
AB  - an airborne organism widely distributed in the hospital environment
AB  - or in clinical specimens. We isolated A. viridans strain LL1 from indoor dust
AB  - samples collected by a patient. Here, we prepared a genome sequence for this
AB  - strain consisting of 31 contigs totaling 1,994,039 bases and a GC content of
AB  - 39.42%.
ER  -

TY  - JOUR
AU  - Qin, Q.L.
AU  - Li, Y.
AU  - Zhang, Y.J.
AU  - Zhou, Z.M.
AU  - Zhang, W.X.
AU  - Chen, X.L.
AU  - Zhang, X.Y.
AU  - Zhou, B.C.
AU  - Wang, L.
AU  - Zhang, Y.Z.
TI  - Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913.
JO  - ISME J.
PY  - 2011
SP  - 274
EP  - 284
VL  - 5
AB  - Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well
AB  - characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on
AB  - the understanding of this ecosystem. In this study, the complete genome of deep-sea
AB  - sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with
AB  - that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis
AB  - TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible
AB  - sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913
AB  - was less tolerant of H(2)O(2) than TAC125. SM9913 has gene clusters related to both polar and
AB  - lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea
AB  - bacteria and absent in the related surface bacteria, are important for the survival of SM9913
AB  - in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and
AB  - swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate
AB  - organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the
AB  - deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may
AB  - confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal
AB  - resistance. Many signal transduction genes and a glycogen production operon were also present
AB  - in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy
AB  - in a deep-sea environment.
ER  -

TY  - JOUR
AU  - Qin, Q.L.
AU  - Xie, B.B.
AU  - Shu, Y.L.
AU  - Rong, J.C.
AU  - Zhao, D.L.
AU  - Zhang, X.Y.
AU  - Chen, X.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Genome Sequence of Proteorhodopsin-Containing Sea Ice Bacterium Glaciecola punicea ACAM 611T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3267
EP  - 3267
VL  - 194
AB  - Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea
AB  - ACAM 611(T), the type species of the genus Glaciecola. A
AB  - blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This
AB  - genome sequence can facilitate the study of the physiological metabolisms and
AB  - ecological roles of sea ice bacteria.
ER  -

TY  - JOUR
AU  - Qin, Q.L.
AU  - Zhang, X.Y.
AU  - Wang, X.M.
AU  - Liu, G.M.
AU  - Chen, X.L.
AU  - Xie, B.B.
AU  - Dang, H.Y.
AU  - Zhou, B.C.
AU  - Yu, J.
AU  - Zhang, Y.Z.
TI  - The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.
JO  - BMC Genomics
PY  - 2010
SP  - 247
EP  - 247
VL  - 11
AB  - BACKGROUND: Zunongwangia profunda SM-A87, which was isolated from deep-sea
AB  - sediment, is an aerobic, gram-negative bacterium that represents a new
AB  - genus of Flavobacteriaceae. This is the first sequenced genome of a
AB  - deep-sea bacterium from the phylum Bacteroidetes. RESULTS: The Z. profunda
AB  - SM-A87 genome has a single 5 128 187-bp circular chromosome with no
AB  - extrachromosomal elements and harbors 4 653 predicted protein-coding
AB  - genes. SM-A87 produces a large amount of capsular polysaccharides and
AB  - possesses two polysaccharide biosynthesis gene clusters. It has a total of
AB  - 130 peptidases, 61 of which have signal peptides. In addition to
AB  - extracellular peptidases, SM-A87 also has various extracellular enzymes
AB  - for carbohydrate, lipid and DNA degradation. These extracellular enzymes
AB  - suggest that the bacterium is able to hydrolyze organic materials in the
AB  - sediment, especially carbohydrates and proteinaceous organic nitrogen.
AB  - There are two clustered regularly interspaced short palindromic repeats in
AB  - the genome, but their spacers do not match any sequences in the public
AB  - sequence databases. SM-A87 is a moderate halophile. Our protein
AB  - isoelectric point analysis indicates that extracellular proteins have
AB  - lower predicted isoelectric points than intracellular proteins. SM-A87
AB  - accumulates organic osmolytes in the cell, so its extracelluar proteins
AB  - are more halophilic than its intracellular proteins. CONCLUSION: Here, we
AB  - present the first complete genome of a deep-sea sedimentary bacterium from
AB  - the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some
AB  - common features of deep-sea bacteria, as well as an important capacity to
AB  - hydrolyze sedimentary organic nitrogen.
ER  -

TY  - JOUR
AU  - Qin, S.
AU  - Zhang, H.
AU  - Li, F.
AU  - Zhu, B.
AU  - Zheng, H.
TI  - Draft Genome Sequence of Marine Streptomyces sp. Strain W007, Which Produces Angucyclinone Antibiotics with a Benz[a]anthracene Skeleton.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1628
EP  - 1629
VL  - 194
AB  - A series of angucyclinone antibiotics have been isolated from marine Streptomyces sp. strain
AB  - W007 and identified. Here, a draft genome sequence of Streptomyces sp.
AB  - W007 is presented. The genome contains an intact biosynthetic gene cluster for
AB  - angucyclinone antibiotics, which provides insight into the combinatorial
AB  - biosynthesis of angucyclinone antibiotics produced by marine streptomycetes.
ER  -

TY  - JOUR
AU  - Qin, T.
AU  - Cui, Y.
AU  - Cen, Z.
AU  - Liang, T.
AU  - Ren, H.
AU  - Yang, X.
AU  - Zhao, X.
AU  - Liu, Z.
AU  - Xu, L.
AU  - Li, D.
AU  - Song, Y.
AU  - Yang, R.
AU  - Shao, Z.
AU  - Song, Y.
TI  - Draft Genome Sequences of Two Legionella dumoffii Strains, TEX-KL and NY-23.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1251
EP  - 1252
VL  - 194
AB  - Legionella (Fluoribacter) dumoffii is one of the agents causing Legionnaires' disease. Here,
AB  - we used Illumina second-generation sequencing technology to
AB  - decipher for the first time the whole-genome sequences of two strains of this
AB  - species, TEX-KL and NY-23. The assembly results for both strains consist of one
AB  - chromosome and two plasmids.
ER  -

TY  - JOUR
AU  - Qin, W.
AU  - Yung, L.Y.L.
TI  - Efficient manipulation of nanoparticle-bound DNA by restriction endonuclease.
JO  - ACS Abstracts
PY  - 2005
SP  - U1077
EP  - U1077
VL  - 230
ER  -

TY  - JOUR
AU  - Qin, W.H.
AU  - Leonhardt, H.
AU  - Spada, F.
TI  - Usp7 and Uhrf1 Control Ubiquitination and Stability of the Maintenance DNA Methyltransferase Dnmt1.
JO  - J. Cell. Biochem.
PY  - 2011
SP  - 439
EP  - 444
VL  - 112
AB  - In mammals Dnmt1 is the DNA methyltransferase chiefly responsible for maintaining genomic
AB  - methylation patterns through DNA replication
AB  - cycles, but how its maintenance activity is controlled is still not
AB  - well understood. Interestingly, Uhrf1, a crucial cofactor for
AB  - maintenance of DNA methylation by Dnmt1, is endowed with E3 ubiquitin
AB  - ligase activity. Here, we show that both Dnmt1 and Uhrf1 coprecipitate
AB  - with ubiquitin specific peptidase 7 (Usp7), a de-ubiquitinating enzyme.
AB  - Overexpression of Uhrf1 and Usp7 resulted in opposite changes in the
AB  - ubiquitination status and stability of Dnmt1. Our findings suggest
AB  - that, by balancing Dnmt1 ubiquitination, Usp7 and Uhrf1 fine tune Dnmt1
AB  - stability.
ER  -

TY  - JOUR
AU  - Qin, W.J.
AU  - Yung, L.Y.L.
TI  - Efficient manipulation of nanoparticle-bound DNA via restriction endonuclease.
JO  - Biomacromolecules
PY  - 2006
SP  - 3047
EP  - 3051
VL  - 7
AB  - As a programmable biopolymer, DNA has shown great potential in the fabrication and
AB  - construction of nanometer-scale assemblies and devices.
AB  - In this report, we described a strategy for efficient manipulation of
AB  - gold nanoparticle-bound DNA using restriction endonuclease. The
AB  - digestion efficiency of this restriction enzyme was studied by varying
AB  - the surface coverage of stabilizer, the size of nanoparticles, as well
AB  - as the distance between the nanoparticle surface and the enzyme-cutting
AB  - site of particle-bound DNA. We found that the surface coverage of
AB  - stabilizer is crucial for achieving high digestion efficiency. In
AB  - addition, this stabilizer surface coverage can be tailored by varying
AB  - the ion strength of the system. Based on the results of polyacrylamide
AB  - gel electrophoresis and fluorescent study, a high digestion efficiency
AB  - of 90+% for particle-bound DNA was achieved for the first time. This
AB  - restriction enzyme manipulation can be considered as an additional
AB  - level of control of the particle-bound DNA and is expected to be
AB  - applied to manipulate more complicated nanostructures assembled by DNA.
ER  -

TY  - JOUR
AU  - Qin, X.
AU  - Evans, J.D.
AU  - Aronstein, K.A.
AU  - Murray, K.D.
AU  - Weinstock, G.M.
TI  - Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis.
JO  - Insect Mol. Biol.
PY  - 2006
SP  - 715
EP  - 718
VL  - 15
AB  - Genome sequences offer a broad view of host-pathogen interactions at the systems
AB  - biology level. With the completion of the sequence of the honey bee, interest in
AB  - the relevant pathogens is heightened. Here we report the genome sequences of two
AB  - of the major pathogens of honey bees, the bacterium Paenibacillus larvae
AB  - (causative agent for American foulbrood disease) and the fungus Ascosphaera apis.
AB  - (causative agent for chalkbrood disease). Ongoing efforts to characterize the
AB  - genomes of these species can be used to understand and mitigate the effects of
AB  - two important pathogens, and will provide a contrast with pathogenic, benign and
AB  - freeliving relatives.
ER  -

TY  - JOUR
AU  - Qin, Y.
AU  - Hasman, H.
AU  - Aarestrup, F.M.
AU  - Alwathnani, H.A.
AU  - Rensing, C.
TI  - Genome Sequences of Three Highly Copper-Resistant Salmonella enterica subsp. I Serovar Typhimurium Strains Isolated from Pigs in Denmark.
JO  - Genome Announcements
PY  - 2014
SP  - e01334
EP  - e01314
VL  - 2
AB  - Salmonella typhimurium is the causative agent of typhoid fever, which causes nearly 21.7
AB  - million illnesses and 217,000 deaths around the world each year.
AB  - Here, we describe the draft genome sequences of the Salmonella typhimurium
AB  - strains S7, S15, and S23, isolated from copper-fed pigs in Denmark and containing
AB  - additional putative determinants conferring resistances to copper and other
AB  - metals and metalloids.
ER  -

TY  - JOUR
AU  - Qin, Y.
AU  - Wang, D.
AU  - Brandt, K.K.
AU  - Rensing, C.
TI  - Two draft genome sequences of Pseudomonas jessenii strains isolated from a copper contaminated site in Denmark.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 86
EP  - 86
VL  - 11
AB  - Pseudomonas jessenii C2 and Pseudomonas jessenii H16 were isolated from low-Cu and high-Cu
AB  - industrially contaminated soil, respectively. P. jessenii H16
AB  - displayed significant resistance to copper when compared to P. jessenii C2. Here
AB  - we describe genome sequences and interesting features of these two strains. The
AB  - genome of P. jessenii C2 comprised 6,420,113 bp, with 5814 protein-coding genes
AB  - and 67 RNA genes. P. jessenii H16 comprised 6,807,788 bp, with 5995
AB  - protein-coding genes and 70 RNA genes. Of special interest was a specific
AB  - adaptation to this harsh copper-contaminated environment as P. jessenii H16
AB  - contained a novel putative copper resistance genomic island (GI) of around 50,000
AB  - bp.
ER  -

TY  - JOUR
AU  - Qin, Z.
AU  - Deng, Z.
AU  - Zhou, Q.
AU  - Chen, H.
TI  - Overcoming restriction of Streptomyces hygroscopicus 10-22 by the modification of S. fradiae -- An attempt to develop a transformation system for S. hygroscopicus 10-22.
JO  - I Chuan Hsueh Pao
PY  - 1993
SP  - 180
EP  - 184
VL  - 20
AB  - No transformant was obtained when pIJ702 (tsr, mel+) from S. lividans TK24 was used to
AB  - transform S. hygroscopicus 10-22. pIJ702 isolated from S. fradiae ATCC 10745, however, was
AB  - transformed into 10-22 at a frequency of 10/3-10/4 tranformants/ug DNA. Among the transformant
AB  - colonies, only 1/1000 of them were black in colour (mel+) while a great majority of them
AB  - remained white (mel-). The plasmid pIJ702 band was only visualized on agarose gels from the
AB  - black colonies but not from the white colonies. However, when pIJ702 isolated from both black
AB  - and white transformants were used to transform S. lividans TK24, the mel gene was expressed
AB  - normally in the recipients. The preparation was also successful in transforming S.
AB  - hygroscopicus 10-22, and again gave rise to 1/1000 of black colonies only. When the 10-22
AB  - (pIJ702) black colonies were plated on non-selective medium, among the majority of black
AB  - colonies grown, there were a few white colonies, which proved to be host mutants of 10-22.
AB  - These mutants were transformable by pIJ702 and homogeneous black colonies were obtained.
ER  -

TY  - JOUR
AU  - Qin, Z.
AU  - Peng, K.
AU  - Zhou, X.
AU  - Lliang, R.
AU  - Zhou, Q.
AU  - Chen, H.
AU  - Hopwood, D.A.
AU  - Kieser, T.
AU  - Deng, Z.
TI  - Development of a gene cloning system for Streptomyces hygroscopicus subsp. yingchengensis, a producer of three useful antifungal compounds, by elimination of three barriers to DNA transfer.
JO  - J. Bacteriol.
PY  - 1994
SP  - 2090
EP  - 2095
VL  - 176
AB  - Streptomyces hygroscopicus 10-22 could not be transformed with any of the commonly used
AB  - Streptomyces plasmid vectors and was resistant to plaque formation by the Streptomyces phages
AB  - C31 and R4. Repeated selection resulted in the isolation of derivatives of S. hygroscopicus
AB  - 10-22 that could be transformed with pIJ101- and pJV1-derived cloning vectors and of
AB  - restriction-deficient derivatives that could accept DNA propagated in Streptomyces lividans
AB  - 66. These new strains, which include three that still produce the original antibiotics, can be
AB  - used as hosts for gene cloning. Insertion of nonreplicating vectors by homologous
AB  - recombination and transposition of Tn4560 were demonstrated in S. hygroscopicus 10-22.
ER  -

TY  - JOUR
AU  - Qiu, C.
AU  - Sawada, K.
AU  - Zhang, X.
AU  - Cheng, X.
TI  - The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds.
JO  - Nat. Struct. Biol.
PY  - 2002
SP  - 217
EP  - 224
VL  - 9
AB  - The PWWP domain is a weakly conserved sequence motif found in >60 eukaryotic proteins,
AB  - including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain
AB  - other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids
AB  - 223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this
AB  - domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a
AB  - five-helix bundle. The two halves are packed against each other to form a single structural
AB  - module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds
AB  - DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2
AB  - protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and
AB  - Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated
AB  - CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds
AB  - DNA more strongly than Delta369, which lacks the PWWP domain.
ER  -

TY  - JOUR
AU  - Qiu, D.
AU  - Eisinger, V.M.
AU  - Head, N.E.
AU  - Pier, G.B.
AU  - Yu, H.D.
TI  - ClpXP proteases positively regulate alginate overexpression and mucoid conversion in Pseudomonas aeruginosa.
JO  - Microbiology
PY  - 2008
SP  - 2119
EP  - 2130
VL  - 154
AB  - Overproduction of the exopolysaccharide alginate and conversion to a mucoid
AB  - phenotype in Pseudomonas aeruginosa are markers for the onset of chronic lung
AB  - infection in cystic fibrosis (CF). Alginate production is regulated by the
AB  - extracytoplasmic function (ECF) sigma factor AlgU/T and the cognate anti-sigma
AB  - factor MucA. Many clinical mucoid isolates carry loss-of-function mutations in
AB  - mucA. These mutations, including the most common mucA22 allele, cause C-terminal
AB  - truncations in MucA, indicating that an inability to regulate AlgU activity by
AB  - MucA is associated with conversion to the mucoid phenotype. Here we report that a
AB  - mutation in a stable mucoid strain derived from the parental strain PAO1,
AB  - designated PAO581, that does not contain the mucA22 allele, was due to a
AB  - single-base deletion in mucA (DeltaT180), generating another type of C-terminal
AB  - truncation. A global mariner transposon screen in PAO581 for non-mucoid isolates
AB  - led to the identification of three regulators of alginate production, clpP
AB  - (PA1801), clpX (PA1802), and a clpP paralogue (PA3326, designated clpP2). The
AB  - PAO581 null mutants of clpP, clpX and clpP2 showed decreased AlgU transcriptional
AB  - activity and an accumulation of haemagglutinin (HA)-tagged N-terminal MucA
AB  - protein with an apparent molecular mass of 15 kDa. The clpP and clpX mutants of a
AB  - CF mucoid isolate revert to the non-mucoid phenotype. The ClpXP and ClpP2
AB  - proteins appear to be part of a proteolytic network that degrades the cytoplasmic
AB  - portion of truncated MucA proteins to release the sequestered AlgU, which drives
AB  - alginate biosynthesis.
ER  -

TY  - JOUR
AU  - Qiu, D.
AU  - Wei, H.
AU  - Tu, Q.
AU  - Yang, Y.
AU  - Xie, M.
AU  - Chen, J.
AU  - Pinkerton, M.H.
AU  - Liang, Y.
AU  - He, Z.
AU  - Zhou, J.
TI  - Combined Genomics and Experimental Analyses of Respiratory Characteristics of Shewanella putrefaciens W3-18-1.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 5250
EP  - 5257
VL  - 79
AB  - It has previously been shown that the Shewanella putrefaciens W3-18-1 strain produces
AB  - remarkably high current in microbial fuel cells (MFCs)
AB  - and can form magnetite at 0 degrees C. To explore the underlying
AB  - mechanisms, we developed a genetic manipulation method by deleting the
AB  - restriction-modification system genes of the SGI1 (Salmonella genome
AB  - island 1)-like prophage and analyzed the key genes involved in
AB  - bacterial respiration. W3-18-1 has less respiratory flexibility than
AB  - the well-characterized S. oneidensis MR-1 strain, as it possesses fewer
AB  - cytochrome c genes and lacks the ability to oxidize sulfite or reduce
AB  - dimethyl sulfoxide (DMSO) and timethylamine oxide (TMAO). W3-18-1 lacks
AB  - the hydrogen-producing Fe-only hydrogenase, and the hydrogen-oxidizing
AB  - Ni-Fe hydrogenase genes were split into two separate clusters. Two
AB  - periplasmic nitrate reductases (NapDAGHB and NapDABC) were functionally
AB  - redundant in anaerobic growth of W3-18-1 with nitrate as the electron
AB  - acceptor, though napDABC was not regulated by Crp. Moreover, nitrate
AB  - respiration started earlier in W3-18-1 than in MR-1 (with NapDAGHB
AB  - only) under microoxic conditions. These results indicate that
AB  - Shewanella putrefaciens W3-18-1 is well adapted to habitats with higher
AB  - oxygen levels. Taken together, the results of this study provide
AB  - valuable insights into bacterial genome evolution.
ER  -

TY  - JOUR
AU  - Qiu, J.
AU  - Ren, J.
TI  - Database management system for recognition sequences and sequences assembly of restriction endonuclease and methylase.
JO  - Zhongguo Yaoke Daxue Xuebao
PY  - 1989
SP  - 185
EP  - 187
VL  - 20
AB  - None
ER  -

TY  - JOUR
AU  - Qiu, T.
AU  - Zuo, Z.
AU  - Gao, J.
AU  - Gao, M.
AU  - Han, M.
AU  - Sun, L.
AU  - Zhang, L.
AU  - Wang, X.
TI  - Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2015
SP  - 2913
EP  - 2918
VL  - 65
AB  - A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain,
AB  - designated SL-205(T), was isolated from the biofilms of a denitrifying reactor
AB  - using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in
AB  - Beijing, PR China. A polyphasic taxonomic characterization was performed on the
AB  - novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed
AB  - that strain SL-205(T) is a member of the genus Diaphorobacter. High levels of 16S
AB  - rRNA gene sequence similarity were found between strain SL-205(T) and
AB  - Diaphorobacter nitroreducens NA10B(T) (99.4%) and Diaphorobacter oryzae RF3(T)
AB  - (98.5%), respectively. However, the DNA-DNA relatedness values between strain
AB  - SL-205(T) and D. nitroreducens NA10B(T) and D. oryzae RF3(T) were 57 +/- 1% and
AB  - 45 +/- 1.5%, respectively. The G+C content of the genomic DNA of strain SL-205(T)
AB  - was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16
AB  - : 1omega7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1omega7c. Ubiquinone Q-8
AB  - was the only respiratory quinone; the polar lipid profile comprised
AB  - phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one
AB  - uncharacterized phospholipid. We conclude that strain SL-205(T) represents a
AB  - novel species of the genus Diaphorobacter for which the name Diaphorobacter
AB  - polyhydroxybutyrativorans is proposed; the type strain is SL-205(T) ( = ACCC
AB  - 19739(T) = DSM 29460(T)).
ER  -

TY  - JOUR
AU  - Qiu, X.
AU  - Han, R.
AU  - Yan, X.
AU  - Liu, M.
AU  - Cao, L.
AU  - Yoshiga, T.
AU  - Kondo, E.
TI  - Identification and Characterization of a Novel Gene Involved in the trans-Specific Nematicidal Activity of Photorhabdus luminescens LN2.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 4221
EP  - 4223
VL  - 75
AB  - Photorhabdus luminescens subsp. akhurstii LN2 from Heterorhabditis indica
AB  - LN2 showed nematicidal activity against axenic Heterorhabditis
AB  - bacteriophora H06 infective juveniles (IJs). Transposon mutagenesis
AB  - identified an LN2 mutant that supports the growth of H06 nematodes. Tn5
AB  - disrupted the namA gene, encoding a novel 364-residue protein and
AB  - involving the nematicidal activity. The green fluorescent protein-labeled
AB  - namA mutant was unable to colonize the intestines of H06 IJs.
ER  -

TY  - JOUR
AU  - Qiu, X.
AU  - Zhan, Z.B.
AU  - Yan, X.
AU  - Han, R.
TI  - Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Photorhabdus luminescens LN2, Which Shows Nematicidal Activity against  Heterorhabditis bacteriophora H06 Nematodes.
JO  - Genome Announcements
PY  - 2014
SP  - e01268
EP  - e01214
VL  - 2
AB  - We present here the 5.6-Mb genome sequence of Photorhabdus luminescens strain LN2, a
AB  - Gram-negative bacterium that is a symbiont of Heterorhabditis indica LN2
AB  - and shows nematicidal activity against Heterorhabditis bacteriophora H06
AB  - nematodes.
ER  -

TY  - JOUR
AU  - Qiu, Y.L.
AU  - Tourlousse, D.M.
AU  - Matsuura, N.
AU  - Ohashi, A.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of Terrimicrobium sacchariphilum NM-5T, a Facultative Anaerobic Soil Bacterium of the Class Spartobacteria.
JO  - Genome Announcements
PY  - 2017
SP  - e00666
EP  - e00617
VL  - 5
AB  - We report here a high-quality draft genome sequence of Terrimicrobium sacchariphilum strain
AB  - NM-5T, a facultative anaerobic, mesophilic, fermentative
AB  - bacterium belonging to the class Spartobacteria of the phylum Verrucomicrobia The
AB  - genome comprises 4,751,807 bp in three contigs and has a G+C content of 60.19%.
AB  - Annotation predicted 4,175 protein-coding sequences and 54 RNAs.
ER  -

TY  - JOUR
AU  - Qiu, Y.L.
AU  - Tourlousse, D.M.
AU  - Matsuura, N.
AU  - Ohashi, A.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of Paludibacter jiangxiensis NM7T, a Propionate-Producing Fermentative Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00667
EP  - e00617
VL  - 5
AB  - We report here a high-quality draft genome sequence of Paludibacter jiangxiensis  strain NM7T,
AB  - a mesophilic, anaerobic, propionate-producing fermentative bacterium
AB  - within the family Porphyromonadaceae of the phylum Bacteroidetes The genome
AB  - comprises 3,664,884 bp in four contigs, has a G+C content of 42.92%, and contains
AB  - 2,949 protein-coding sequences and 62 RNAs.
ER  -

TY  - JOUR
AU  - Qu, G.
AU  - Kaushal, P.S.
AU  - Wang, J.
AU  - Shigematsu, H.
AU  - Piazza, C.L.
AU  - Agrawal, R.K.
AU  - Belfort, M.
AU  - Wang, H.W.
TI  - Structure of a group II intron in complex with its reverse transcriptase.
JO  - Nat. Struct. Mol. Biol.
PY  - 2016
SP  - 549
EP  - 557
VL  - 23
AB  - Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns
AB  - and eukaryotic retrotransposons. They self-splice, yielding
AB  - mature RNA, and integrate into DNA as retroelements. A fully active group II
AB  - intron forms a ribonucleoprotein complex comprising the intron ribozyme and an
AB  - intron-encoded protein that performs multiple activities including reverse
AB  - transcription, in which intron RNA is copied into the DNA target. Here we report
AB  - cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron
AB  - in its ribonucleoprotein complex form at 3.8-A resolution and in its
AB  - protein-depleted form at 4.5-A resolution, revealing functional coordination of
AB  - the intron RNA with the protein. Remarkably, the protein structure reveals a
AB  - close relationship between the reverse transcriptase catalytic domain and
AB  - telomerase, whereas the active splicing center resembles the spliceosomal Prp8
AB  - protein. These extraordinary similarities hint at intricate ancestral
AB  - relationships and provide new insights into splicing and retromobility.
ER  -

TY  - JOUR
AU  - Qu, J.
AU  - Miao, L.L.
AU  - Liu, Y.
AU  - Liu, Z.P.
TI  - Complete Genome Sequence of Rhodococcus sp. Strain IcdP1 Shows Diverse Catabolic  Potential.
JO  - Genome Announcements
PY  - 2015
SP  - e00711
EP  - e00715
VL  - 3
AB  - The complete genome sequence of Rhodococcus sp. strain IcdP1 is presented here. This organism
AB  - was shown to degrade a broad range of high-molecular-weight
AB  - polycyclic aromatic hydrocarbons and organochlorine pesticides. The sequence data
AB  - can be used to predict genes for xenobiotic biodegradation and metabolism.
ER  -

TY  - JOUR
AU  - Qu, Y.
AU  - Liu, Z.
AU  - Shen, W.
AU  - Li, S.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of an Indigoid-Producing Strain, Pseudomonas sp. PI1.
JO  - Genome Announcements
PY  - 2015
SP  - e00622
EP  - e00615
VL  - 3
AB  - Pseudomonas sp. strain PI1 can cometabolize indole in the presence of phenol to produce
AB  - various indigoids. Here, we present a 7.2-Mb draft genome sequence of
AB  - strain PI1, which may provide insight into the study of phenol-indole
AB  - cometabolism and its application in aromatic bioremediation and wastewater
AB  - treatment processes.
ER  -

TY  - JOUR
AU  - Qu, Y.
AU  - Zhang, X.
AU  - Yu, H.
AU  - Tang, H.
AU  - Shen, E.
AU  - Zhou, H.
AU  - Ma, Q.
AU  - Cao, X.
AU  - Zhou, J.
AU  - Xu, P.
TI  - Genome Sequence of Sphingomonas xenophaga QYY, an Anthraquinone-Degrading Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00031
EP  - e00012
VL  - 1
AB  - Sphingomonas xenophaga QYY is an efficient anthraquinone-degrading strain. Here,  we present a
AB  - 4.2-Mb assembly of the first genome sequence of S. xenophaga. We have annotated 36 coding
AB  - sequences (CDSs) encoding aromatic catabolism and 216 CDSs responsible for toxic resistance
AB  - and stress response, which may provide insights into the degradation of complex aromatics.
ER  -

TY  - JOUR
AU  - Quada, J.C.
AU  - Izbicka, E.
AU  - Rashidi, H.H.
TI  - Dual flipping and novel motifs of DNA methyltransferase.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 2000
SP  - 79
EP  - 79
VL  - 41
AB  - Structural superimposition of three resolved structures of DNA cytosine methyltransferase
AB  - (DCMTase) M.HhaI revealed the dual flipping feature of the enzyme and the cofactor
AB  - S-adenosyl-L-methionine (SAM) or its demethylated form, S-adenosyl-L-homocysteine (SAH).  In
AB  - the absence of DNA, enzyme-bound SAM is solvent exposed.  In the presence of DNA, SAM flips
AB  - from the surface of the enzyme into the catalytic site and complements the flipped out
AB  - cytosine methylation target in DNA.  Analysis of amino acid residues interacting with the
AB  - cofactor identified 16 contact amino acid residues for unflipped SAM and 24 residues for
AB  - flipped SAM/SAH in M.HhaI.  These contact residues are also conserved in higher eukaryotic
AB  - DCMTases.  Human Dnmt1 and M.HhaI bound to SAH and DNA and M.HhaI bound to flipped SAM reveals
AB  - that SAH and flipped SAM are coordinated in the same binding pocket.  Analysis of the
AB  - cofactor-interacting residues in M.HhaI, human Dnmt1 and other known DCMTases enabled us to
AB  - define two novel flipped SAM/SAH binding sequence motifs expressed in the same order in all
AB  - DCMTases, providing a specific tool for analysis of related proteins.  High sequence homology
AB  - of the cofactor interacting residues implies their conserved function and further underlines
AB  - the structural and functional similarity between bacterial M.HhaI and human Dnmt1 DCMTases.
AB  - Our findings also support the alternative binding mechanism in which SAM binding precedes DNA
AB  - binding in M.HhaI.
ER  -

TY  - JOUR
AU  - Quandt, E.M.
AU  - Summers, R.M.
AU  - Subramanian, M.V.
AU  - Barrick, J.E.
TI  - Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source.
JO  - Genome Announcements
PY  - 2015
SP  - e00640
EP  - e00615
VL  - 3
AB  - Pseudomonas putida CBB5 was isolated from soil by enriching for growth on caffeine
AB  - (1,3,7-trimethylxanthine). The draft genome of this strain is 6.9 Mb,
AB  - with 5,941 predicted coding sequences. It includes the previously studied Alx
AB  - gene cluster encoding alkylxanthine N-demethylase enzymes and other genes that
AB  - enable the degradation of purine alkaloids.
ER  -

TY  - JOUR
AU  - Quatrini, R.
AU  - Escudero, L.V.
AU  - Moya-Beltran, A.
AU  - Galleguillos, P.A.
AU  - Issotta, F.
AU  - Acosta, M.
AU  - Cardenas, J.P.
AU  - Nunez, H.
AU  - Salinas, K.
AU  - Holmes, D.S.
AU  - Demergasso, C.
TI  - Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 84
EP  - 84
VL  - 12
AB  - 10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from
AB  - the Gorbea salt flat, an acidic hypersaline environment in northern
AB  - Chile. This kind of environment is considered a terrestrial analog of ancient
AB  - Martian terrains and a source of new material for biotechnological applications.
AB  - 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity
AB  - of generating and maintaining acidic conditions by producing sulfuric acid and it
AB  - can also remove sulfur layers from the surface of minerals, which are detrimental
AB  - for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate
AB  - moderate chloride concentrations (up to 15 g L(-1) Cl(-)), a feature that is
AB  - quite unusual in extreme acidophilic microorganisms. Basic microbiological
AB  - features and genomic properties of this biotechnologically relevant strain are
AB  - described in this work. The 3,974,949 bp draft genome is arranged into 40
AB  - scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs
AB  - encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199
AB  - strain. The release of the genome sequence of this strain improves representation
AB  - of these extreme acidophilic Gram negative bacteria in public databases and
AB  - strengthens the framework for further investigation of the physiological
AB  - diversity and ecological function of 10.1601/nm.2199 populations.
ER  -

TY  - JOUR
AU  - Que, Q.
AU  - Zhang, Y.
AU  - Nelson, M.
AU  - Ropp, S.
AU  - Burbank, D.E.
AU  - Van Etten, J.L.
TI  - Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases.
JO  - Gene
PY  - 1997
SP  - 237
EP  - 244
VL  - 190
AB  - Chlorella virus SC-1A encodes at least six DNA methyltransferases: four N6-methyldeoxyadenine
AB  - (m6A) Mtases, M.CviSI (TGCmA), M.CviSII (CmATG), M.CviSIII (TCGmA) and M.CviSIV (GmATC), one
AB  - 5-methyldeoxycytosine (m5C) Mtase, M.CviSV (~RCmCG), and one nonfunctional m5C MTase,
AB  - M.CviSVI, which is homologous to the MTase M.CviJI [RGmC(T/C/G)] produced by another chlorella
AB  - virus IL-3A.  Genes encoding three of the SC-1A m6A MTases (M.CviSI, M.CviSII, and M.CviSIII)
AB  - and the nonfunctional m5C MTase were cloned and sequenced.  Neither M.CviSI nor M.CviSIII
AB  - genes hybridized to genes for their respective isomethylomers, M.CviRI and M.CviBIII, from
AB  - other chlorella viruses.  However, the M.CviSII gene hybridized strongly to its M.CviAII
AB  - isomethylomer gene from virus PBCV-1.  Like the prototype chlorella virus PBCV-1, the SC-1A
AB  - genome contains inverted terminal repeats, one of which is adjacent to the nonfunctional m5C
AB  - MTase.  The three cloned m6A MTase genes are distributed throughout the approx. 345 kb SC-1A
AB  - genome.
ER  -

TY  - JOUR
AU  - Quesada, J.M.
AU  - Aguilar, I.
AU  - de la Torre, J.
AU  - Wittich, R.M.
AU  - van Dillewijn, P.
TI  - Draft Genome Sequences of Isolates from Sediments of the River Elbe That Are Highly Tolerant to Diclofenac.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00849
EP  - e00818
VL  - 7
AB  - Here, we report the genome sequences of one Achromobacter and four Pseudomonas strains
AB  - isolated from sediments of the River Elbe which are highly tolerant
AB  - toward the xenobiotic target compound diclofenac, a nonsteroidal
AB  - anti-inflammatory drug (NSAID) and emerging contaminant.
ER  -

TY  - JOUR
AU  - Quick, J.
AU  - Constantinidou, C.
AU  - Pallen, M.J.
AU  - Oppenheim, B.
AU  - Loman, N.J.
TI  - Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound.
JO  - Genome Announcements
PY  - 2014
SP  - e00355
EP  - e00314
VL  - 2
AB  - We report the draft genome assembly of Elizabethkingia meningoseptica strain 502. The sample
AB  - was isolated from the wound of a repatriated military serviceperson
AB  - who suffered major trauma from an improvised explosive device (IED), resulting in
AB  - wounds with extensive environmental contamination. E. meningoseptica was isolated
AB  - from wounds in both legs. The draft genome assembly has 21 contigs with a total
AB  - size of 3,960,744 bases. The genome contains genes encoding 26 putative
AB  - beta-lactamases.
ER  -

TY  - JOUR
AU  - Quinones, B.
AU  - Yambao, J.C.
AU  - Lee, B.G.
TI  - Draft Genome Sequences of Escherichia coli O113:H21 Strains Recovered from a Major Produce Production Region in California.
JO  - Genome Announcements
PY  - 2017
SP  - e01203
EP  - e01217
VL  - 5
AB  - Shiga toxin-producing Escherichia coli is a foodborne and waterborne pathogen and is
AB  - responsible for outbreaks of human gastroenteritis. This report documents the
AB  - draft genome sequences of seven O113:H21 strains recovered from livestock,
AB  - wildlife, and soil samples recovered from a major agricultural region for leafy
AB  - greens in California, USA.
ER  -

TY  - JOUR
AU  - Quint, A.
AU  - Cedar, H.
TI  - In vitro methylation of DNA with HpaII methylase.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - 633
EP  - 646
VL  - 9
AB  - The enzyme HpaII methylase extracted and partially purified from Haemophilus
AB  - parainfluenza catalyzes the methylation of the tetranucleotide sequence CCGG at
AB  - the internal cytosine.  The enzyme will methylate this sequence if both DNA
AB  - strands are unmethylated or if only one strand is unmethylated.  Conditions
AB  - have been developed for producing fully methylated DNA from various sources.
AB  - In vitro methylation of this site protects the DNA against digestion by the
AB  - restriction enzyme HpaII as well as the enzyme SmaI which recognizes the
AB  - hexanucleotide sequence CCCGGG.  These properties make this enzyme a valuable
AB  - tool for analyzing methylation in eukaryotic DNA where the sequence CCGG is
AB  - highly methylated.  The activity of this methylase on such DNA indicates the
AB  - degree of undermethylation of the CCGG sequence.  Several examples show that
AB  - this technique can be used to detect small changes in the methylation state of
AB  - eukaryotic DNA.
ER  -

TY  - JOUR
AU  - Quirk, S.M.
AU  - Bell-Pedersen, D.
AU  - Belfort, M.
TI  - Intron mobility in the T-even phages:  high frequency inheritance of group I introns promoted by intron open reading frames.
JO  - Cell
PY  - 1989
SP  - 455
EP  - 465
VL  - 56
AB  - Intron mobility in the T-even phages has been demonstrated. Efficient nonreciprocal conversion
AB  - of intron minus (In-) alleles to intron plus (In+) occurred for the td and sunY genes, but not
AB  - for nrdB. Conversion to In+ was absolutely dependent on expression of the respective intron
AB  - open reading frame (ORF). Introns were inserted at their cognate sites in an intronless phage
AB  - genome via an RNA-independent, DNA-based, duplicative recombination event that was stimulated
AB  - by exon homology. The fd intron ORF product directs the endonucleolytic cleavage of DNA,
AB  - targeting the site of intron integration. A 21 nucleotide deletion of the integration site
AB  - abolished high frequency intron inheritance. These experiments provide a novel example of gene
AB  - conversion in prokaryotes, while suggesting a molecular rationale for the inconsistent
AB  - distribution of introns within highly conserved exon contexts of the T-even phage genomes.
ER  -

TY  - JOUR
AU  - Quiroz-Castaneda, R.E.
AU  - Martinez-Ocampo, F.
AU  - Dantan-Gonzalez, E.
TI  - Draft Genome Sequence of Mycoplasma wenyonii, a Second Hemotropic Mycoplasma Species Identified in Mexican Bovine Cattle.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00875
EP  - e00818
VL  - 7
AB  - The hemotropic mycoplasma (hemoplasma) Mycoplasma wenyonii is an animal pathogen  that affects
AB  - bovine cattle health. Here, we present the draft genome sequence of
AB  - the hemoplasma M. wenyonii strain INIFAP02 found in cattle from Mexico.
ER  -

TY  - JOUR
AU  - Qureshi, A.
AU  - Itankar, Y.
AU  - Ojha, R.
AU  - Mandal, M.
AU  - Khardenavis, A.
AU  - Kapley, A.
AU  - Purohit, H.J.
TI  - Genome Sequence of Lactobacillus plantarum EGD-AQ4, Isolated from Fermented Product of Northeast India.
JO  - Genome Announcements
PY  - 2014
SP  - e01122
EP  - e01113
VL  - 2
AB  - We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from
AB  - nonalcoholic fermented bamboo shoot products of Northeast India.
AB  - The size of the draft genome sequence is the largest among all the reported
AB  - genome sequences of Lactobacillus plantarum, thus enabling the exploration of new
AB  - gene clusters involved in various functional and probiotic attributes.
ER  -

TY  - JOUR
AU  - Ra, S.R.
AU  - Ri, D.C.
TI  - Isolation-purification of a new restriction endonuclease, CglI and its optimum reaction condition.
JO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
PY  - 2000
SP  - 36
EP  - 38
VL  - 0
AB  - A new restriction endonuclease CglI is isolated and purified from Corynebacterium glutamicum
AB  - 165 by a ultrasonication, Biogel filtered phosphocellulose and DEAE-cellulose column
AB  - chromatography.  We establish some reasonable reaction condition for the purified restriction
AB  - endonuclease, CglI.
ER  -

TY  - JOUR
AU  - Raaijmakers, H.
AU  - Toro, I.
AU  - Birkenbihl, R.
AU  - Kemper, B.
AU  - Suck, D.
TI  - Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 311
EP  - 323
VL  - 308
AB  - The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from
AB  - phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at
AB  - 2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two
AB  - different crystal environments reveals considerable conformational flexibility at the dimer
AB  - level affecting the substrate-binding cleft, the dimerization interface and the orientation of
AB  - the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the
AB  - C-terminal domains relative to the central dimerization domain as well as the relative
AB  - positioning of helices in the dimerization interface appear to be sensitive to the crystal
AB  - packing environment. The highly unexpected rearrangement within the extended hydrophobic
AB  - interface does change the contact surface area but keeps the number of hydrophobic contacts
AB  - about the same and will therefore not require significant energy input. The conformational
AB  - flexibility most likely is of functional significance for the broad substrate specificity of
AB  - EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the
AB  - active-site metal ions and residues known to be essential for catalysis allows us to propose a
AB  - possible catalytic mechanism. A comparison with the active-site geometries of other
AB  - magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia
AB  - endonuclease, shows common features, suggesting related catalytic mechanisms. Copyright 2001
AB  - Academic Press.
ER  -

TY  - JOUR
AU  - Rabinkova, E.V.
AU  - Torosyan, M.V.
AU  - Fradkin, G.E.
TI  - Restriction alleviation of phage lambda in Escherichia coli K-12 cells after gamma-irradiation.
JO  - Radiobiologiia
PY  - 1987
SP  - 563
EP  - 564
VL  - 27
AB  - In gamma-irradiated cells of Escherichia coli K-12 restriction alleviation of an unmodified
AB  - phage lambda is only observed in AB1157 strain.  No restriction alleviation by gamma-rays is
AB  - registered in AB1157 mutants (recA and ssb-1).
ER  -

TY  - JOUR
AU  - Rabsch, W.
AU  - Helm, R.A.
AU  - Eisenstark, A.
TI  - Diversity of phage types among archived cultures of the demerec collection of Salmonella enterica serovar Typhimurium strains.
JO  - Appl. Environ. Microbiol.
PY  - 2004
SP  - 664
EP  - 669
VL  - 70
AB  - The existence of several thousand Salmonella enterica serovar Typhimurium LT2 and LT7 cultures
AB  - originally collected by M. Demerec and
AB  - sealed in agar stab vials for 33 to 46 years is a resource for
AB  - evolutionary and mutational studies. Cultures from 74 of these vials,
AB  - descendants of cells sealed and stored in nutrient agar stabs several
AB  - decades ago, were phage typed by the Callow and Felix, Lilleengen, and
AB  - Anderson systems. Among 53 LT2 archived strains, 16 had the same phage
AB  - type as the nonarchival sequenced LT2 strain. The other 37 archived
AB  - cultures differed in phage typing pattern from the sequenced strain.
AB  - These 37 strains were divided into 10 different phage types. Among the
AB  - 19 LT7 strains, only one was similar to the parent by phage typing,
AB  - while 18 were different. These 18 strains fell into eight different
AB  - phage types. The typing systems were developed to track epidemics from
AB  - source to consumer, as well as geographic spread. The value of phage
AB  - typing is dependent upon the stability of the phage type of any given
AB  - strain throughout the course of the investigation. Thus, the variation
AB  - over time observed in these archived cultures is particularly
AB  - surprising. Possible mechanisms for such striking diversity may include
AB  - loss of prophages, prophage mosaics as a result of recombination
AB  - events, changes in phage receptor sites on the bacterial cell surface,
AB  - or mutations in restriction-modification systems.
ER  -

TY  - JOUR
AU  - Rabus, R.
AU  - Kube, M.
AU  - Heider, J.
AU  - Beck, A.
AU  - Heitmann, K.
AU  - Widdel, F.
AU  - Reinhardt, R.
TI  - The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1.
JO  - Arch. Microbiol.
PY  - 2005
SP  - 27
EP  - 36
VL  - 183
AB  - Recent research on microbial degradation of aromatic and other refractory compounds in anoxic
AB  - waters and soils has revealed that nitrate-reducing
AB  - bacteria belonging to the Betaproteobacteria contribute substantially to
AB  - this process. Here we present the first complete genome of a metabolically
AB  - versatile representative, strain EbN1, which metabolizes various aromatic
AB  - compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two
AB  - plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic
AB  - and four aerobic aromatic degradation pathways were recognized, with the
AB  - encoding genes mostly forming clusters. The presence of paralogous gene
AB  - clusters (e.g., for anaerobic phenylacetate oxidation), high sequence
AB  - similarities to orthologs from other strains (e.g., for anaerobic phenol
AB  - metabolism) and frequent mobile genetic elements (e.g., more than 200
AB  - genes for transposases) suggest high genome plasticity and extensive
AB  - lateral gene transfer during metabolic evolution of strain EbN1. Metabolic
AB  - versatility is also reflected by the presence of multiple respiratory
AB  - complexes. A large number of regulators, including more than 30
AB  - two-component and several FNR-type regulators, indicate a finely tuned
AB  - regulatory network able to respond to the fluctuating availability of
AB  - organic substrates and electron acceptors in the environment. The absence
AB  - of genes required for nitrogen fixation and specific interaction with
AB  - plants separates strain EbN1 ecophysiologically from the closely related
AB  - nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary
AB  - material on sequence and annotation are provided at the Web page
AB  - http://www.micro-genomes.mpg.de/ebn1/.
ER  -

TY  - JOUR
AU  - Rabus, R.
AU  - Ruepp, A.
AU  - Frickey, T.
AU  - Rattei, T.
AU  - Fartmann, B.
AU  - Stark, M.
AU  - Bauer, M.
AU  - Zibat, A.
AU  - Lombardot, T.
AU  - Becker, I.
AU  - Amann, J.
AU  - Gellner, K.
AU  - Teeling, H.
AU  - Leuschner, W.D.
AU  - Glockner, F.O.
AU  - Lupas, A.N.
AU  - Amann, R.
AU  - Klenk, H.P.
TI  - The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.
JO  - Environ. Microbiol.
PY  - 2004
SP  - 887
EP  - 902
VL  - 6
AB  - Summary Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is
AB  - able to grow at in situ temperatures below 0
AB  - degrees C. As abundant members of the microbial community in permanently
AB  - cold marine sediments, D. psychrophila-like bacteria contribute to the
AB  - global cycles of carbon and sulfur. Here, we describe the genome sequence
AB  - of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular
AB  - chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14
AB  - 663 bp. Analysis of the genome gave insight into the metabolic properties
AB  - of the organism, e.g. the presence of TRAP-T systems as a major route for
AB  - the uptake of C(4)-dicarboxylates, the unexpected presence of genes from
AB  - the TCA cycle, a TAT secretion system, the lack of a beta-oxidation
AB  - complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and
AB  - ncc. D. psychrophila encodes more than 30 two-component regulatory
AB  - systems, including a new Ntr subcluster of hybrid kinases, nine putative
AB  - cold shock proteins and nine potentially cold shock-inducible proteins. A
AB  - comparison of D. psychrophila's genome features with those of the only
AB  - other published genome from a sulfate reducer, the hyperthermophilic
AB  - archaeon Archaeoglobus fulgidus, revealed many striking differences, but
AB  - only a few shared features.
ER  -

TY  - JOUR
AU  - Rachinger, M.
AU  - Volland, S.
AU  - Meinhardt, F.
AU  - Daniel, R.
AU  - Liesegang, H.
TI  - First Insights into the Completely Annotated Genome Sequence of Bacillus licheniformis Strain 9945A.
JO  - Genome Announcements
PY  - 2013
SP  - e00525
EP  - e00513
VL  - 1
AB  - Strains of the species Bacillus licheniformis are widely used in biotechnology for the
AB  - production of enzymes and antibiotics (M. Schallmey, A. Singh, and O. P.
AB  - Ward, Can. J. Microbiol. 50:1-17, 2004). However, research and application of B.
AB  - licheniformis strains are adversely affected by poor genetic accessibility. Thus,
AB  - for a closer inspection of natural competence in B. licheniformis, the genome of
AB  - strain 9945A, of which derivatives are known to be naturally competent (C. B.
AB  - Thorne and H. B. Stull, J. Bacteriol. 91:1012-1020, 1966), was completely
AB  - sequenced and manually annotated.
ER  -

TY  - JOUR
AU  - Rachkevych, N.
AU  - Sybirna, K.
AU  - Boyko, S.
AU  - Boretsky, Y.
AU  - Sibirny, A.
TI  - Improving the efficiency of plasmid transformation in Shewanella oneidensis MR-1 by removing ClaI restriction site.
JO  - J. Microbiol. Methods
PY  - 2014
SP  - 35
EP  - 37
VL  - 99
AB  - Here we demonstrate that elimination of ClaI restriction site from the sequence of a plasmid
AB  - DNA increases the efficiency of transformation of Shewanella oneidensis MR-1 significantly. To
AB  - achieve reliable transformation of S. oneidensis MR-1 plasmids either lacking ClaI site or
AB  - isolated from primary transformants of S. oneidensis should be used. (C) 2014 Published by
AB  - Elsevier B.V.
ER  -

TY  - JOUR
AU  - Radford, D.R.
AU  - Leon-Velarde, C.G.
AU  - Chen, S.
AU  - Hamidi, O.A.M.
AU  - Balamurugan, S.
TI  - Draft Genome Sequences of Two Novel Salmonella enterica subsp. enterica Strains Isolated from Low-Moisture Foods with Applications in Food Safety Research.
JO  - Genome Announcements
PY  - 2018
SP  - e00183
EP  - e00118
VL  - 6
AB  - The genomes of two strains of Salmonella enterica subsp. enterica serovar Cubana  and serovar
AB  - Muenchen, isolated from dry hazelnuts and chia seeds, respectively,
AB  - were sequenced using the Illumina MiSeq platform, assembled de novo using the
AB  - overlap-layout-consensus method, and aligned to their respective most identical
AB  - sequence genome scaffolds using MUMMER and BLAST searches.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Bujnicki, J.M.
TI  - Cloning of enterohemorrhagic Escherichia coli Phage VT-2 Dam methyltransferase.
JO  - Acta Microbiol. Pol.
PY  - 2001
SP  - 161
EP  - 167
VL  - 50
AB  - Enterobacterial GATC-specific DNA adenine methyltransferase plays an essential role in
AB  - regulation of DNA replication, methyl-directed mismatch repair, transposition and gene
AB  - expression.  In Salmonella typhimurium it has been shown to directly control virulence.  In
AB  - this paper we report cloning and expression of the dam gene from the Shiga toxin-producing
AB  - VT2-Sa prophage of enterohemorrhagic Escherichia coli O157.  Comparisons of the predicted
AB  - amino acid sequence indicates that Dam methyltransferases of E. coli phages VT2-Sa, 933W, T1
AB  - and Haemophilus influenzae phage HP1 make up a separate subgroup of adenine-N6
AB  - methyltransferases.  These proteins are similar to the gamma subfamily of
AB  - amino-methyltransferases in respect to the linear order of sequence motifs and the presence of
AB  - the hallmark "NPPY" tetrapeptide.  However, they apparently lack an autonomous
AB  - target-recognizing domain at the C-terminus of the catalytic domain and therefore we propose
AB  - to dub them as a "mini-gamma" subfamily.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Bujnicki, J.M.
TI  - Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV.
JO  - Acta Microbiol. Pol.
PY  - 2001
SP  - 97
EP  - 105
VL  - 50
AB  - M.NgoMXV is one of the few atypical DNA:m4C methyltransferases that does not possess a serine
AB  - residue in its predicted active site.  We previously reported a homology model of M.NgoMXV and
AB  - argued that the aspartate side chain at a corresponding position, similarly to some
AB  - DNA:m6A-specific enzymes, is essential for the methyltransferase activity (Radlinska et al.
AB  - 1999).  Here we reported the corrected amino acid sequence of M.NgoMXV and the analysis of
AB  - substitution of D68 with alanine or serine, which both render the enzyme totally inactive.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Bujnicki, J.M.
AU  - Piekarowicz, A.
TI  - Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
JO  - Proteins
PY  - 1999
SP  - 717
EP  - 728
VL  - 37
AB  - Two adjacent genes encoding DNA methyltransferases (MTases) of Neisseria gonorrhoeae MS11, an
AB  - active N4-cytosine specific M. NgoMXV and an inactive 5-cytosine type M.NgoMorf2P, were cloned
AB  - into Escherichia coli and sequenced. We analyzed the deduced amino acid sequence of both gene
AB  - products and localized conserved regions characteristic for DNA MTases. Structure prediction,
AB  - threading-derived alignments, and comparison with the common fold for DNA MTases allowed for
AB  - construction of super-secondary and tertiary models for M.NgoMorf2P and M.NgoMXV,
AB  - respectively. These models helped in identification of amino acids and structural elements
AB  - essential for function of both enzymes. The implications of this putative structural model on
AB  - the catalytic mechanism of M.NgoMXV and its possible relation to the common ancestor of modern
AB  - DNA amino-MTases are also discussed.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Kondrzycka-Dada, A.
AU  - Piekarowicz, A.
AU  - Bujnicki, J.M.
TI  - Identification of amino acids important for target recognition by the DNA:m(5)C methyltransferase M.NgoPII by alanine-scanning mutagenesis  of residues at the protein-DNA interface.
JO  - Proteins
PY  - 2005
SP  - 263
EP  - 270
VL  - 58
AB  - DNA:m(5)C MTases comprise a catalytic domain with conserved residues of the active site and a
AB  - strongly diverged TRD with variable residues
AB  - involved in DNA recognition and binding. To date, crystal structures of
AB  - 2 DNA:m(5)C MTases complexed with the substrate DNA have been obtained;
AB  - however, for none of these enzymes has the importance of the whole set
AB  - of DNA-binding residues been comprehensively studied. We built a
AB  - comparative model of M.NgoPII, a close homologue and isomethylomer of
AB  - M.HaeIII, and systematically analyzed the effect of alanine
AB  - substitutions for the complete set of amino acid residues from its TRD
AB  - predicted to be important for DNA binding and target recognition. Our
AB  - data demonstrate that only 1 Arg residue is indispensable for the MTase
AB  - activity in vivo and in vitro, and that mutations of only a few other
AB  - residues cause significant reduction of the activity in vitro, with
AB  - little effect on the activity in vivo. The identification of
AB  - dispensable protein-DNA contacts in the wild-type MTase will serve as a
AB  - platform for exhaustive combinatorial mutagenesis aimed at the design
AB  - of new contacts, and thus construction of enzyme variants that retain
AB  - the activity but exhibit potentially new substrate preferences.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Piekarowicz, A.
TI  - Cloning and characterization of the gene encoding a new DNA methyltransferase from Neisseria gonorrhoeae.
JO  - Biol. Chem.
PY  - 1998
SP  - 1391
EP  - 1395
VL  - 379
AB  - A HindIII fragment of N. gonorrhoeae MS11 DNA coding for DNA methyltransferase activity was
AB  - cloned and expressed in E. coli AP1-200-9 cells.  The sequence of 4681 bp was determined, and
AB  - its analysis revealed two open reading frames sharing some similarity with known DNA MTases.
AB  - ORF1 encodes an active N4mC MTase (M.NgoMV).  The enzyme modifies only one strand of double
AB  - stranded DNA and preferentially recognizes the sequence GCCHR although it is able to methylate
AB  - other sites.  The exact recognition sequence cannot be precisely defined due to a relaxed
AB  - specificity.  The second ORF shows high homology to 5mC Mtases, but we were unable to
AB  - demonstrate DNA methylating activity of its product either in vivo or in vitro.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Piekarowicz, A.
AU  - Galimand, M.
AU  - Bujnicki, J.M.
TI  - Cloning and preliminary characterization of a GATC-specific beta(2)-class DNA:m(6)A methyltransferase encoded by transposon Tn1549  from Enterococcus spp.
JO  - Pol. J. Microbiol.
PY  - 2005
SP  - 249
EP  - 252
VL  - 54
AB  - A recent study revealed a subfamily of N6-adenine (m(6)A) methyltransferases that comprises a
AB  - few functionally studied eukaryotic
AB  - members acting on mRNA and prokaryotic members acting on DNA as well as
AB  - numerous uncharacterized open reading frames. Here, we report cloning
AB  - and functional characterization of a prokaryotic member of this family
AB  - encoded by transposon Tn1549 from Enterococcus spp.
ER  -

TY  - JOUR
AU  - Radlinska, M.
AU  - Skowronek, K.
TI  - Novel procedure for the detection of 5-methylcytosine.
JO  - Acta Microbiol. Pol.
PY  - 1998
SP  - 327
EP  - 334
VL  - 47
AB  - Bisulfite converts non-methylated cytosine in DNA to uracil leaving 5-methylcytosine
AB  - unaltered.  In this communication, we present a new approach omitting the conventional PCR
AB  - amplification step.  Bisulfite-converted methylated DNA is directly sequenced.  The
AB  - effectiveness of the new protocol is demonstrated by using it for the detection of
AB  - 5-methylation of cytosine residues introduced by three different DNA methyltransferases
AB  - (M.HaeIII, M.HpaII and M.HhaI).  A simple experimental system useful to determine the sequence
AB  - specificity of DNA methyltransferases is also presented.
ER  -

TY  - JOUR
AU  - Radnedge, L.
AU  - Pinney, R.J.
TI  - Ultraviolet light induction of lambda from dcm host strains alleviates EcoRII restriction of phage.
JO  - FEMS Microbiol. Lett.
PY  - 1991
SP  - 121
EP  - 126
VL  - 121-125
AB  - A new form of restriction alleviation is demonstrated for phage induced by ultraviolet light
AB  - from dcm strains of Escherichia coli K-12. EcoRII restriction of the induced phage is
AB  - alleviated, which is the first report of Type II restriction alleviation. Unlike previously
AB  - reported restriction alleviation, the increase in phage-plating efficiency is not dependent
AB  - upon irradiation of the plating host for its induction.
ER  -

TY  - JOUR
AU  - Raftis, E.J.
AU  - Forde, B.M.
AU  - Claesson, M.J.
AU  - O'Toole, P.W.
TI  - Unusual genome complexity in Lactobacillus salivarius JCM1046.
JO  - BMC Genomics
PY  - 2014
SP  - 771
EP  - 771
VL  - 15
AB  - BACKGROUND: Lactobacillus salivarius strains are increasingly being exploited for
AB  - their probiotic properties in humans and animals. Dissemination of antibiotic
AB  - resistance genes among species with food or probiotic-association is undesirable
AB  - and is often mediated by plasmids or integrative and conjugative elements. L.
AB  - salivarius strains typically have multireplicon genomes including circular
AB  - megaplasmids that encode strain-specific traits for intestinal survival and
AB  - probiotic activity. Linear plasmids are less common in lactobacilli and show a
AB  - very limited distribution in L. salivarius. Here we present experimental evidence
AB  - that supports an unusually complex multireplicon genome structure in the porcine
AB  - isolate L. salivarius JCM1046. RESULTS: JCM1046 harbours a 1.83 Mb chromosome,
AB  - and four plasmids which constitute 20% of the genome. In addition to the known
AB  - 219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated
AB  - the topology of three additional replicons, the circular pMP1046B (129 kb), a
AB  - linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative
AB  - transposon. pMP1046B harbours both plasmid-associated replication genes and
AB  - paralogues of chromosomally encoded housekeeping and information-processing
AB  - related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited
AB  - sequence homology or gene synteny with other L. salivarius plasmids, and its
AB  - putative replication-associated protein is homologous to the RepA/E proteins
AB  - found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046
AB  - harbours a single copy of an integrated conjugative transposon (Tn6224) which
AB  - appears to be functionally intact and includes the tetracycline resistance gene
AB  - tetM. CONCLUSION: Experimental validation of sequence assemblies and plasmid
AB  - topology resolved the complex genome architecture of L. salivarius JCM1046. A
AB  - high-coverage draft genome sequence would not have elucidated the genome
AB  - complexity in this strain. Given the expanding use of L. salivarius as a
AB  - probiotic, it is important to determine the genotypic and phenotypic organization
AB  - of L. salivarius strains. The identification of Tn6224-like elements in this
AB  - species has implications for strain selection for probiotic applications.
ER  -

TY  - JOUR
AU  - Raghavendra, N.K.
AU  - Bheemanaik, S.
AU  - Rao, D.N.
TI  - Mechanistic insights into type III restriction enzymes.
JO  - Front. Biosci.
PY  - 2012
SP  - 1094
EP  - 1107
VL  - 17
AB  - Type III restriction-modification (R-M) enzymes need to interact with two separate
AB  - unmethylated DNA sequences in indirectly repeated, head-to-head orientations for efficient
AB  - cleavage to occur at a defined location next to only one of the two sites. However, cleavage
AB  - of sites that are not in head-to-head orientation have been observed to occur under certain
AB  - reaction conditions in vitro. ATP hydrolysis is required for the long-distance communication
AB  - between the sites prior to cleavage. Type III R-M enzymes comprise two subunits, Res and Mod
AB  - that form a homodimeric Mod(2) and a heterotetrameric Res(2)Mod(2) complex. The Mod subunit in
AB  - M-2 or R2M2 complex recognizes and methylates DNA while the Res subunit in R2M2 complex is
AB  - responsible for ATP hydrolysis, DNA translocation and cleavage. A vast majority of biochemical
AB  - studies on Type III R-M enzymes have been undertaken using two closely related enzymes, EcoP1I
AB  - and EcoP15I. Divergent opinions about how the long-distance interaction between the
AB  - recognition sites exist and at least three mechanistic models based on 1D- diffusion and/or
AB  - 3D-DNA looping have been proposed.
ER  -

TY  - JOUR
AU  - Raghavendra, N.K.
AU  - Rao, D.N.
TI  - Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I-Usefulness in SAGE.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2005
SP  - 803
EP  - 811
VL  - 334
AB  - While it has been demonstrated that AdoMet is required for DNA cleavage by Type III
AB  - restriction enzymes, here we show that in the presence of
AB  - exogenous AdoMet, the head-to-head oriented recognition sites are cleaved
AB  - only on a supercoiled DNA. On a linear DNA, exogenous AdoMet strongly
AB  - drives methylation while inhibiting cleavage reaction. Strikingly, the AdoMet
AB  - analogue sinefungin results in cleavage at all recognition sites
AB  - irrespective of the topology of DNA. The cleavage reaction in the presence
AB  - of sinefungin is ATP dependent. The site of cleavage is comparable with
AB  - that in the presence of AdoMet. The use of EcoP15I restriction in presence
AB  - of sinefungin as an improved tool for serial analysis of gene expression
AB  - is discussed.
ER  -

TY  - JOUR
AU  - Raghavendra, N.K.
AU  - Rao, D.N.
TI  - Functional cooperation between exonucleases and endonucleases - basis for the evolution of restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 1888
EP  - 1896
VL  - 31
AB  - Many types of restriction enzymes cleave DNA away from their recognition site. Using the type
AB  - III restriction enzyme, EcoP15I, which cleaves DNA
AB  - 25-27 bp away from its recognition site, we provide evidence to show that
AB  - an intact recognition site on the cleaved DNA sequesters the restriction
AB  - enzyme and decreases the effective concentration of the enzyme. EcoP15I
AB  - restriction enzyme is shown here to perform only a single round of DNA
AB  - cleavage. Significantly, we show that an exonuclease activity is essential
AB  - for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage.
AB  - This observation may hold true for all restriction enzymes cleaving DNA
AB  - sufficiently far away from their recognition site. Our results highlight
AB  - the importance of functional cooperation in the modulation of enzyme
AB  - activity. Based on results presented here and other data on
AB  - well-characterised restriction enzymes, a functional evolutionary
AB  - hierarchy of restriction enzymes is discussed.
ER  -

TY  - JOUR
AU  - Raghavendra, N.K.
AU  - Rao, D.N.
TI  - Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 5703
EP  - 5711
VL  - 32
AB  - Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric
AB  - recognition sites oriented head-to-head to elicit
AB  - double-strand break 25-27 bp downstream of one of the two sites. The
AB  - proposed DNA cleavage mechanism involves ATP-dependent DNA translocation.
AB  - The sequence context of the recognition site was suggested to influence
AB  - the site of DNA cleavage by the enzyme. In this investigation, we
AB  - demonstrate that the cleavage site of the R.EcoP15I restriction enzyme
AB  - does not depend on the sequence context of the recognition site.
AB  - Strikingly, this study demonstrates that the enzyme can cleave linear DNA
AB  - having either recognition sites in the same orientation or a single
AB  - recognition site. Cleavage occurs predominantly at a site proximal to the
AB  - DNA end in the case of multiple site substrates. Such cleavage can be
AB  - abolished by the binding of Lac repressor downstream (3' side) but not
AB  - upstream (5' side) of the recognition site. Binding of HU protein has also
AB  - been observed to interfere with R.EcoP15I cleavage activity. In accordance
AB  - with a mechanism requiring two enzyme molecules cooperating to elicit
AB  - double-strand break on DNA, our results convincingly demonstrate that the
AB  - enzyme translocates on DNA in a 5' to 3' direction from its recognition
AB  - site and indicate a switch in the direction of enzyme motion at the DNA
AB  - ends. This study demonstrates a new facet in the mode of action of these
AB  - restriction enzymes.
ER  -

TY  - JOUR
AU  - Raghupathi, P.K.
AU  - Herschend, J.
AU  - Roder, H.L.
AU  - Sorensen, S.J.
AU  - Burmolle, M.
TI  - Genome Sequence of Psychrobacter cibarius Strain W1.
JO  - Genome Announcements
PY  - 2016
SP  - e00078
EP  - e00016
VL  - 4
AB  - Here, we report the draft genome sequence of Psychrobacter cibarius strain W1, which was
AB  - isolated at a slaughterhouse in Denmark. The 3.63-Mb genome sequence
AB  - was assembled into 241 contigs.
ER  -

TY  - JOUR
AU  - Raghupathi, P.K.
AU  - Herschend, J.
AU  - Roder, H.L.
AU  - Sorensen, S.J.
AU  - Burmolle, M.
TI  - Draft Genome Assembly of Two Pseudoclavibacter helvolus Strains, G8 and W3, Isolated from Slaughterhouse Environments.
JO  - Genome Announcements
PY  - 2016
SP  - e00077
EP  - e00016
VL  - 4
AB  - We report the draft genome sequences of twoPseudoclavibacter helvolusstrains. Strain G8 was
AB  - isolated from a meat chopper and strain W3 isolated from the wall
AB  - of a small slaughterhouse in Denmark. The two annotated genomes are 3.91 Mb and
AB  - 4.00 Mb in size, respectively.
ER  -

TY  - JOUR
AU  - Raghupathi, P.K.
AU  - Herschend, J.
AU  - Roder, H.L.
AU  - Sorensen, S.J.
AU  - Burmolle, M.
TI  - Genome Sequence of Kocuria varians G6 Isolated from a Slaughterhouse in Denmark.
JO  - Genome Announcements
PY  - 2016
SP  - e00076
EP  - e00016
VL  - 4
AB  - We report here the first draft genome sequence ofKocuria variansG6, which was isolated from a
AB  - meat chopper at a small slaughterhouse in Denmark. The 2.90-Mb
AB  - genome sequence consists of 95 contigs and contains 2,518 predicted
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Rahman, A.
AU  - Nahar, N.
AU  - Jass, J.
AU  - Olsson, B.
AU  - Mandal, A.
TI  - Complete Genome Sequence of Lysinibacillus sphaericus B1-CDA, a Bacterium That Accumulates Arsenic.
JO  - Genome Announcements
PY  - 2016
SP  - e00999
EP  - e00915
VL  - 4
AB  - Here, we report the genomic sequence and genetic composition of an arsenic-resistant
AB  - bacterium, Lysinibacillus sphaericus B1-CDA. Assembly of the
AB  - sequencing reads revealed that the genome size is ~4.5 Mb, encompassing ~80% of
AB  - the chromosomal DNA.
ER  -

TY  - JOUR
AU  - Rahman, A.
AU  - Nahar, N.
AU  - Olsson, B.
AU  - Mandal, A.
TI  - Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00483
EP  - e00416
VL  - 4
AB  - Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated
AB  - from the landfills of tannery industries in Bangladesh. Here, we
AB  - investigated its genetic composition using massively parallel sequencing and
AB  - comparative analysis with other known Enterobacter genomes. Assembly of the
AB  - sequencing reads revealed a genome of ~4.21 Mb in size.
ER  -

TY  - JOUR
AU  - Rahman, M.
AU  - Nguyen, S.V.
AU  - McCullor, K.A.
AU  - King, C.J.
AU  - Jorgensen, J.H.
AU  - McShan, W.M.
TI  - Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e01440
EP  - e01415
VL  - 3
AB  - Streptococcus anginosus is an opportunistic human pathogen that causes abscesses  of the
AB  - brain, liver, and other organs. Here, we announce the complete genome
AB  - sequence of a clinically isolated strain of S. anginosus J4211. The genome
AB  - sequence contains two prophages and multiple mobile genetic elements.
ER  -

TY  - JOUR
AU  - Rahman, M.A.
AU  - Mullany, P.
AU  - Roberts, A.P.
TI  - Draft Genome Sequence of Eggerthia catenaformis Strain MAR1 Isolated from Saliva  of Healthy Humans.
JO  - Genome Announcements
PY  - 2017
SP  - e00638
EP  - e00617
VL  - 5
AB  - Here, we report the draft genome sequence of Eggerthia catenaformis MAR1 isolated during a
AB  - screen for d-cycloserine-resistant bacteria from the saliva of healthy
AB  - humans. Analysis of the genome reveals that the strain has the potential to be a
AB  - human pathogen and carries genes related to virulence and antibiotic resistance.
ER  -

TY  - JOUR
AU  - Rai, K.
TI  - Roles of DNA and histone methyltransferases during zebrafish development.
JO  - Ph.D. Thesis, Univ. of Utah
PY  - 2006
SP  - 1
EP  - 160
AB  - The research work presented in this dissertation describes the roles of the major DNA
AB  - methyltransferases and histone methyltransferases in zebrafish development.  DNA and histone
AB  - methylation are two key processes that regulate transcription of genes in mammals.  Both of
AB  - these processes are essential for proper development of an organism and their misregulation
AB  - leads to multiple diseases including cancer.  A better understanding of these two processes
AB  - will help us understand how an organism develops and will also help in designing more
AB  - effective drugs against cancer.  Chapter 1 is an introduction on DNA and histone methylation
AB  - and the enzymes which catalyze these processes.  This chapter summarizes the literature on the
AB  - normal various organisms including zebrafish, how abnormalities in this process lead to
AB  - cancer, the protein structure and function of the known DNA methyltransferases and findings
AB  - about relationship between histone methylation and DNA methylation.  Chapter 2 describes the
AB  - function of DNA methyltransferase-1 during zebrafish development.  The focus of the studies
AB  - described in this chapter is on the function of this enzyme during later differentiation
AB  - during tissue-specific development.  Also, the epistatic relationship between Dnmt1 and
AB  - Suv39h1, the major H3K9 methyltransferase, is described in this chapter.  Chapter 3 shows our
AB  - findings about role of Dnmt3, a member of other sub-class of DNA methyltransferase family,
AB  - during zebrafish development.  Here I have shown novel roles of this enzyme during development
AB  - of vertebrate brain.  In Chapter 4, I have described our novel findings regarding the role of
AB  - Dnmt2, a mysterious DNA/RNA methyltransferase, during zebrafish development.  Here, I have
AB  - also described the importance of its function in the cytoplasm.  Chapter 5 is an attempt to
AB  - compare the phenotypes obtained by knocking-down protein levels of different DNA
AB  - methyltransferases.  This chapter is the crux of our studies which shows striking similarities
AB  - and differences of in vivo functions of different classes of DNA methyltransferases.  In
AB  - Chapter 6, the main conclusions of my work are summarized.  I have also discussed the
AB  - implications of our findings and the future approaches to unravel the mysteries of
AB  - developmental functions of DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Rai, R.
AU  - Swanson, E.
AU  - Sarkar, I.
AU  - Lama, D.
AU  - Abebe-Aleke, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Kar, P.
AU  - Gtari, M.
AU  - Sen, A.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of the French Bean Symbiont Rhizobium sp. Strain  RSm-3 Isolated from the Eastern Himalayan Region of India.
JO  - Genome Announcements
PY  - 2017
SP  - e00175
EP  - e00117
VL  - 5
AB  - The genus Rhizobium contains many species able to form nitrogen-fixing nodules on plants of
AB  - the legume family. Here, we report the 6.9-Mbp draft genome sequence of
AB  - Rhizobium sp. strain RSm-3, with a G+C content of 61.4% and 6,511 candidate
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Raiol, T.
AU  - De-Souza, M.T.
AU  - Oliveira, J.V.
AU  - Silva, H.S.
AU  - Orem, J.C.
AU  - Cavalcante, D.A.
AU  - Almeida, N.F.
AU  - Telles, G.P.
AU  - Setubal, J.C.
AU  - Brigido, M.M.
AU  - Torres, F.A.
AU  - Stadler, P.S.
AU  - Walter, M.E.
AU  - Moraes, L.M.
TI  - Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.
JO  - Genome Announcements
PY  - 2014
SP  - e01027
EP  - e01014
VL  - 2
AB  - A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had
AB  - its entire genome sequenced.
ER  -

TY  - JOUR
AU  - Raiol, T.
AU  - Ribeiro, G.M.
AU  - Maranhao, A.Q.
AU  - Bocca, A.L.
AU  - Silva-Pereira, I.
AU  - Junqueira-Kipnis, A.P.
AU  - Brigido, M.M.
AU  - Kipnis, A.
TI  - Complete Genome Sequence of Mycobacterium massiliense.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5455
EP  - 5455
VL  - 194
AB  - Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic
AB  - infections. The genome of a representative isolate (strain GO 06)
AB  - recovered from wound samples from patients who underwent arthroscopic or
AB  - laparoscopic surgery was sequenced. To the best of our knowledge, this is the
AB  - first announcement of the complete genome sequence of an M. massiliense strain.
ER  -

TY  - JOUR
AU  - Raizis, A.M.
AU  - Schmitt, F.
AU  - Jost, J.-P.
TI  - A bisulfite method of 5-methylcytosine mapping that minimizes template degradation.
JO  - Anal. Biochem.
PY  - 1995
SP  - 161
EP  - 166
VL  - 226
AB  - The bisulfite method is a highly sensitive approach to 5-methylcytosine mapping that utilizes
AB  - the capability of the polymerase chain reaction to exponentially amplify DNA. We have observed
AB  - that the bisulfite reaction results in a significant level of template degradation due to DNA
AB  - depurination.  Furthermore, our data suggest that the DNA fragmentation which occurs limits
AB  - the sensitivity of the method.  We describe a simple solution to limit degradation of the DNA
AB  - template.
ER  -

TY  - JOUR
AU  - Raja, M.C.
AU  - Dharmalingam, K.
TI  - Heat shock-induced relaxation of restriction enzyme specificity in Escherichia coli.
JO  - J. Genetics
PY  - 1991
SP  - 91
EP  - 101
VL  - 70
AB  - Methylated and hydroxymethylated cytosine containing DNA was restricted by
AB  - proteins encoded by the mcrBC (rglB) loci of E. coli.  In vivo, RglB proteins
AB  - recognize and cleave hmCT2 and hmCT4 DNAs at 30C and 42C but hmCT6 DNA was
AB  - unaffected at both temperatures.  However, cells carrying the rglB genes cloned
AB  - on pBR322 (pDSS17) did not restrict hmCT6 at 30C, but hmCT6 DNA was cleaved
AB  - efficiently at 42C.  Heat shock treatment for five minutes was enough to induce
AB  - this promiscuity in recognition specificity.  We call this activity RglB star.
AB  - A single copy of rglB located on the chromosome or cloned on a low copy vector
AB  - pMU575 failed to show RglB star activity.  De novo protein synthesis was not
AB  - required for the manifestation of RglB star activity.
ER  -

TY  - JOUR
AU  - Rajagopal, K.
TI  - Draft Genome Sequence of Enterococcus raffinosus Strain CFTRI 2200, Isolated from Infant Fecal Material.
JO  - Genome Announcements
PY  - 2013
SP  - e00932
EP  - e00913
VL  - 1
AB  - The complete genome sequence of Enterococcus raffinosus strain CFTRI 2200, isolated from the
AB  - fecal material of a 7-month-old infant, is reported. The
AB  - complete genome consists of 4.237 Mbp with a G+C content of 39.47% and 4,242
AB  - protein-coding genes, 54 tRNAs, and 46 rRNAs.
ER  -

TY  - JOUR
AU  - Rajanna, C.
AU  - Revazishvili, T.
AU  - Rashid, M.H.
AU  - Chubinidze, S.
AU  - Bakanidze, L.
AU  - Tsanava, S.
AU  - Imnadze, P.
AU  - Bishop-Lilly, K.A.
AU  - Sozhamannan, S.
AU  - Gibbons, H.S.
AU  - Morris, J.G.
AU  - Sulakvelidze, A.
TI  - Characterization of pPCP1 Plasmids in Yersinia pestis Strains Isolated from the Former Soviet Union.
JO  - Int. J. Microbiol.
PY  - 2010
SP  - 760
EP  - 819
VL  - 2010
AB  - Complete sequences of 9.5-kb pPCP1 plasmids in three Yersinia pestis strains from the former
AB  - Soviet Union (FSU) were determined and compared with those of pPCP1 plasmids in three
AB  - well-characterized, non-FSU Y.
AB  - pestis strains (KIM, CO92, and 91001). Two of the FSU plasmids were from strains C2614 and
AB  - C2944, isolated from plague foci in Russia, and one plasmid was from strain C790 from
AB  - Kyrgyzstan. Sequence analyses identified four sequence types among the six plasmids. The pPCP1
AB  - plasmids in the FSU strains were most genetically related to the pPCP1 plasmid in the KIM
AB  - strain and least related to the pPCP1 plasmid in Y. pestis 91001. The FSU strains generally
AB  - had larger pPCP1 plasmid copy numbers compared to strain CO92. Expression of the plasmid's
AB  - pla gene was significantly (P </= .05) higher in strain C2944 than in strain CO92. Given
AB  - pla's role in Y. pestis virulence, this difference may have important implications for the
AB  - strain's virulence.
ER  -

TY  - JOUR
AU  - Rajeshwari, K.
AU  - Uppal, B.
AU  - Singh, R.
AU  - Malakar, A.K.
AU  - Chikara, S.K.
TI  - Draft Genome of Escherichia coli O146 Isolate from Maulana Azad Medical College,  New Delhi, India.
JO  - Genome Announcements
PY  - 2015
SP  - e01515
EP  - e01514
VL  - 3
AB  - Here, we report the draft genome sequence of enteropathogenic Escherichia coli (EPEC) O146
AB  - strain isolated from a 1-year-old child with acute diarrhea in Delhi
AB  - who recovered completely. The multidrug transporter (mdtABCD) gene, responsible
AB  - for drug resistance, is present. The strain also contains the astA gene, an
AB  - additional virulence determinant.
ER  -

TY  - JOUR
AU  - Rajkumari, J.
AU  - Singha, L.P.
AU  - Pandey, P.
TI  - Draft Genome Sequence of Klebsiella pneumoniae AWD5.
JO  - Genome Announcements
PY  - 2017
SP  - e01531
EP  - e01516
VL  - 5
AB  - Here, we report the draft genome sequence of Klebsiella pneumoniae strain AWD5, isolated from
AB  - an automobile workshop in India. The de novo assembly resulted in a
AB  - 4,807,409 bp genome containing 25 rRNA genes, 81 tRNAs, and 4,636 coding
AB  - sequences (CDS). It carries important genes for polyaromatic hydrocarbon
AB  - degradation and benzoate degradation.
ER  -

TY  - JOUR
AU  - Rajoo, S.
AU  - Jeon, W.
AU  - Park, K.
AU  - Yoo, S.
AU  - Yoon, I.
AU  - Lee, H.
AU  - Ahn, J.
TI  - Complete Genome Sequence of Streptococcus iniae YSFST01-82, Isolated from Olive Flounder in Jeju, South Korea.
JO  - Genome Announcements
PY  - 2015
SP  - e00319
EP  - e00315
VL  - 3
AB  - Streptococcus iniae is associated with morbidity in commercial fish species, especially in
AB  - olive flounders (Paralichthys olivaceus), and was recently
AB  - identified as an emerging human pathogen. Here, we report the complete 2.09-Mb
AB  - genome sequence of S. iniae strain YSFST01-82, isolated from an olive flounder
AB  - with streptococcosis disease in Jeju, South Korea.
ER  -

TY  - JOUR
AU  - Rajski, S.R.
AU  - Kumar, S.
AU  - Roberts, R.J.
AU  - Barton, J.K.
TI  - Protein-modulated DNA electron transfer.
JO  - J. Am. Chem. Soc.
PY  - 1999
SP  - 5615
EP  - 5616
VL  - 121
AB  - Long-range oxidative damage to the 5'-guanine of 5'-GG-3' sequences in DNA readily occurs
AB  - as a result of electron migration through the pi-stack on long-range electron transfer, since
AB  - upon binding, the protein induces and stabilizes a pi-gap using a novel DNA base-flipping
AB  - mechanism.  Long-range oxidation of 5'-GG-3' sites was first shown with a rhodium
AB  - intercalator.  The rhodium photochemistry bound to DNA yields base photooxidation upon
AB  - irradiation at low energy (365nm), whereas irradiation at high energy (313 nm) leads to direct
AB  - strand scission, marking the sites of intercalation.  Other DNA-bound photooxidants also
AB  - promote DNA damage at long range.
ER  -

TY  - JOUR
AU  - Raleigh, E.
AU  - Dila, D.
AU  - Sutherland, E.
AU  - Kelleher, J.
AU  - Moran, L.
AU  - Slatko, B.
AU  - Briggs, P.
TI  - McrBC, a novel multisubunit GTP-dependent restriction endonuclease.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 152
EP  - 152
VL  - 17C
AB  - The McrBC system is one of four restriction systems used by E. coli K-12 to monitor the origin
AB  - of invading DNA and determine its fate. Like McrA and Mrr, the McrBC system is specific for
AB  - modified DNA. The system is encoded by two genes of low GC composition flanked by two similar
AB  - dyad symmetries, suggesting that the system may have been imported from elsewhere. Both genes
AB  - are required for restriction in vivo of a variety of modified targets, including those with
AB  - 5-methylcytosine, 5-hydroxymethylcytosine and N4-methylcytosine. A few modified targets are
AB  - sensitive to restriction mediated by mcrB in the absence of mcrC. Three proteins are expressed
AB  - from the two genes. Only two of the three are required for in vitro activity. The in vitro
AB  - cleavage activity reflects the in vivo properties of the system in its requirement for a
AB  - modified substrate and in the spectrum of site-specific modifications that are sensitive to
AB  - cleavage. GTP is required for cleavage. Non-hydrolysable analogues of GTP inhibit the
AB  - reaction, as does ATP. Our current model is that cleavage requires the sequence
AB  - RmC(N40-80)RmC, with multiple cleavage positions on both strands distributed within the spacer
AB  - region. The roles played by the two proteins are under investigation genetically. Twelve mcrB
AB  - mutants with dominant phenotypes have been isolated. These fall into three phenotypic classes.
AB  - All are defective in McrC-dependent restriction; they differ in their ability in vivo to
AB  - inhibit restriction by wild type genes in trans and in their ability to carry out
AB  - McrC-independent restriction. Sequence analysis reveals that each class corresponds to a
AB  - particular portion of the protein, one of which is the GTP-binding site motif identified in
AB  - the polypeptide sequence of McrB.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
TI  - Organization and function of the mcrBC genes of Escherichia coli K-12.
JO  - Mol. Microbiol.
PY  - 1992
SP  - 1079
EP  - 1086
VL  - 6
AB  - Many natural DNA sequences are restricted in Escherichia coli K-12, not only by the classic
AB  - Type I restriction system EcoK, but also by one of three modification-specific restriction
AB  - systems found in K-12. The McrBC system is the best studied of these. We infer from the base
AB  - composition of the mcrBC genes that they were imported from an evolutionarily distant source.
AB  - The genes are located in a hypervariable cluster of restriction genes that may play a
AB  - significant role in generation of species identity in enteric bacteria. Restriction activity
AB  - requires the products of two genes for activity both in vivo and in vitro. The mcrB gene
AB  - elaborates two protein products, only one of which is required for activity in vitro, but both
AB  - of which contain a conserved amino acid sequence motif identified as a possible GTP-binding
AB  - site. The mcrC gene product contains a leucine heptad repeat that could play a role in
AB  - protein-protein interactions. McrBC activity in vivo and in vitro depends on the presence of
AB  - modified cytosine in a specific sequence context; three different modifications are
AB  - recognized. The in vitro activity of this novel multi-subunit restriction enzyme displays an
AB  - absolute requirement for GTP as a cofactor.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
TI  - Restriction and modification in vivo by Escherichia coli K12.
JO  - Methods Enzymol.
PY  - 1987
SP  - 130
EP  - 141
VL  - 152
AB  - This chapter focuses on how restriction of newly introduced DNA by Escherichia coli can
AB  - interfere with cloning and subcloning work, and in particular on how the pattern of
AB  - methylation of the DNA influences this. A principal aim is to acquaint the reader with three
AB  - E. coli restriction systems that attack DNA only when it is appropriately methylated. The
AB  - second part of this chapter describes biological restriction and modification in general
AB  - terms. The third part discusses the particular restriction systems found in E. coli K12, first
AB  - briefly the familiar K and P1 restriction systems, and then in detail the methyl-specific
AB  - McrA, McrB and Mrr systems. Some common strains are discussed with special reference to their
AB  - restriction phenotypes. The fourth part briefly reviews the E. coli methylation functions, Dam
AB  - and Dcm, as they affect sensitivity to digestion of DNA in vitro.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
AU  - Benner, J.
AU  - Bloom, F.
AU  - Braymer, H.D.
AU  - DeCruz, E.
AU  - Dharmalingam, K.
AU  - Heitman, J.
AU  - Noyer-Weidner, M.
AU  - Piekarowicz, A.
AU  - Kretz, P.L.
AU  - Short, J.M.
AU  - Woodcock, D.
TI  - Nomenclature relating to restriction of modified DNA in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1991
SP  - 2707
EP  - 2709
VL  - 173
AB  - At least three restriction systems that attack DNA containing naturally
AB  - modified bases have been found in common Escherichia coli K-12 strains.  These
AB  - systems are McrA, McrBC, and Mrr.  A brief summary of the genetic and phenotype
AB  - properties so far observed in laboratory strains is set forth, together with a
AB  - proposed nomenclature for describing these properties.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
AU  - Brooks, J.E.
TI  - Restriction modification systems: where they are and what they do.
JO  - Bacterial Genomes
PY  - 1998
SP  - 78
EP  - 92
AB  - The review concentrates on restriction-modification in the context of bacterial genome
AB  - evolution and how the systems affect bacterial populations.  RM systems regulate the entry of
AB  - foreign DNA into cells.  A model of how the systems work is shown in Figure 8-1.  Foreign DNA
AB  - is restricted by a restriction endonuclease that recognizes a specific sequence and cleaves
AB  - the DNA unless the sequence is protected. Typically, a modification methyltransferase confers
AB  - protection, by methylating a particular base within the sequence recognized by the restriction
AB  - enzyme, thereby rendering it resistant to cleavage.  Alternatively, however, some restriction
AB  - enzymes recognize a sequence only when it is methylated.  In this case, methylation of a
AB  - suitable base confers sensitivity to restriction and protection arises from failure to
AB  - methylate the relevant sequence.  Both sorts of restriction can act to limit the transfer of
AB  - DNA into cells.  One key feature of RM is that the systems can be effective only if they are
AB  - variable and fluid within a bacterial population.  Modifications made to foreign DNA escaping
AB  - restriction are epigenetic, i.e., not heritable.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
AU  - Murray, N.E.
AU  - Revel, H.
AU  - Blumenthal, R.M.
AU  - Westaway, D.
AU  - Reith, A.D.
AU  - Rigby, P.W.J.
AU  - Elhai, J.
AU  - Hanahan, D.
TI  - McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 1563
EP  - 1575
VL  - 15
AB  - The McrA and McrB (modified cytosine restriction) systems of E. coli interfere
AB  - with incoming DNA containing methylcytosine.  DNA from many organisms,
AB  - including all mammalian and plant DNA, is expected to be sensitive, and this
AB  - could interfere with cloning experiments.  The McrA and B phenotypes of a few
AB  - strains have been reported previously.  The Mcr phenotypes of 94 strains,
AB  - primarily derived from E. coli K12, are tabulated here.  We briefly review some
AB  - evidence suggesting that McrB restriction of mouse-modified DNA does occur in
AB  - vivo and does in fact interfere with cloning of specific mouse sequences.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
AU  - Sutherland, E.
AU  - Dila, D.
AU  - Briggs, P.
AU  - Kelleher, J.
AU  - Coe, L.
AU  - Slatko, B.
AU  - Moran, L.
TI  - Molecular analysis of McrBC, a GTP-dependent restriction endonuclease from E. coli K-12.
JO  - J. Cell Biochem. Suppl.
PY  - 1992
SP  - 21
EP  - 21
VL  - 16B
AB  - The McrBC system is one of three modification-dependent restriction systems used by E. coli
AB  - K-12 to monitor the origin of invading DNA and determine its fate. The system is encoded by
AB  - two genes of low GC composition flanked by two similar dyad symmetries, suggesting that the
AB  - system may have been imported from elsewhere. Both genes are required for restriction in vivo
AB  - of a variety of modified targets, including those with 5-methylcytosine,
AB  - 5-hydroxymethylcytosine and N4-methylcytosine. Three proteins are expressed from the two
AB  - genes, two of which are required for in vitro activity. For each of these proteins (McrBL and
AB  - McrC), constructs that forced translation initiation at either of two potential start codons
AB  - yielded enzymatically active product. One of each was purified to >90% purity. The in vitro
AB  - cleavage activity reflected the in vivo properties of the system in its requirement for a
AB  - modified substrate and in the spectrum of site-specific modifications that were sensitive to
AB  - cleavage. GTP was required for cleavage. Non-hydrolysable analogues of GTP inhibited the
AB  - reaction, as did ATP. We are unaware of any other nuclease with an absolute requirement for a
AB  - guanosine nucleotide. The nature of the cleavage site was examined further by mapping sites on
AB  - natural substrates, delimiting the cleavage site by primer extension, and cleaving synthetic
AB  - oligonucleotide model substrates. Different sites are cleaved with differing efficiencies. Our
AB  - current model is that cleavage requires the sequence RmC(N40-70)RmC, with multiple cleavage
AB  - positions on both strands distributed within the spacer region.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
AU  - Trimarchi, R.
AU  - Revel, H.
TI  - Genetic and physical mapping of the mcrA (rglA) and mcrB (rglB) loci of Escherichia coli K-12.
JO  - Genetics
PY  - 1989
SP  - 279
EP  - 296
VL  - 122
AB  - We have genetically analyzed, cloned and physically mapped the modified
AB  - cytosine-specific restriction determinants mcrA (rglA) and mcrB (rglB) of
AB  - Escherichia coli K-12.  The independently discovered Rgl and Mcr restriction
AB  - systems are shown to be identical by three criteria:  1) mutants with the RglA-
AB  - or RglB- phenotypes display the corresponding McrA- or McrB- phenotypes, and
AB  - vice versa; 2) the gene(s) for RglA and McrA reside together at one locus,
AB  - while gene(s) for RglB and McrB are coincident at a different locus; and 3)
AB  - RglA+ and RglB+ recombinant clones complement for the corresponding
AB  - Mcr-deficient lesions.  The mcrA (rglA) gene(s) is on the excisable element
AB  - e14, just clockwise of purB at 25 min.  The mcrB (rglB) gene(s), at 99 min, is
AB  - in a cluster of restriction functions that includes hsd and mrr, determinants
AB  - of host-specific restriction (EcoK) and methyladenine-specific restriction
AB  - respectively.  Gene order is mcrB-hsdS-hsdM-hsdR-mrr-serB.  Possible models for
AB  - the acquisition of these restriction determinants by enteric bacteria are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Raleigh, E.A.
AU  - Wilson, G.
TI  - Escherichia coli K-12 restricts DNA containing 5-methylcytosine.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1986
SP  - 9070
EP  - 9074
VL  - 83
AB  - We have observed that plasmids containing certain cloned modification methylase genes of type
AB  - II restriction-modification systems cannot be transformed into many laboratory strains of
AB  - Escherichia coli K-12.  The investigation of this phenomenon, reported here, has revealed (i)
AB  - DNA containing 5-methylcytosine is biologically restricted by these strains, while DNA
AB  - containing 6-methyladenine is not; (ii) restriction is due to two genetically distinct systems
AB  - that differ in their sequence specificities, which we have named mcrA and mcrB (for modified
AB  - cytosine restriction).  Since 5-methylcytosine containing DNA is widespread in nature, the Mcr
AB  - systems probably have a broad biological role. Mcr restriction may seriously interfere with
AB  - molecular cloning of 5-methylcytosine-containing foreign DNAs.  The Mcr phenotypes of some
AB  - commonly used strains of E. coli K-12 are reported.
ER  -

TY  - JOUR
AU  - Ralph, D.
AU  - Que, Q.
AU  - Van Etten, J.L.
AU  - McClelland, M.
TI  - Leptospira genomes are modified at 5'-GTAC.
JO  - J. Bacteriol.
PY  - 1993
SP  - 3913
EP  - 3915
VL  - 175
AB  - Genomic DNAs of 14 strains from seven species of the spirochete Leptospira were resistant to
AB  - cleavage by the restriction endonuclease RsaI (5'-GTAC). A modified base comigrating with m4C
AB  - was detected by chromatography. Genomic DNAs from other spirochetes, Borrelia group VS461, and
AB  - Serpulina strains were not resistant to RsaI digestion. Modification at 5'-GTAm4C may occur
AB  - in most or all strains of all species of Leptospira but not in all genera of spirochetes.
AB  - Genus-wide DNA modification has rarely been observed in bacteria.
ER  -

TY  - JOUR
AU  - Ralston, D.J.
AU  - Baer, B.S.
TI  - A new property of phage group II Staphylococcus aureus strains:  Host restriction of phage K14.
JO  - J. Gen. Microbiol.
PY  - 1964
SP  - 1
EP  - 16
VL  - 36
AB  - Various strains of Staphylococcus aureus which type exclusively with phages of
AB  - lytic group II were found to modify phage K14 so that its ability to form
AB  - plaques on host K1N was lessened.  The restricted phage formed plaques with
AB  - high efficiency on all strains of lytic group II.  In general, it plated at
AB  - lower titres on strains of lytic groups I, II, IV, and on some strains of
AB  - miscellaneous typing characteristics; however, there were some variations among
AB  - separate cultures of the same strains.  For example, the restricted phage
AB  - plated at high titre on strains 52A/79a, 73, and 44A, but formed significantly
AB  - fewer numbers of plaques on strain 52A, 79b and on a second culture of 44A.
AB  - Strain K1N was found to dissociate into apt (K1H1) and non-apt (K1N2) forms.
AB  - The probability of plaque development by restricted phage on strain K1N was
AB  - dependent upon the nutritional state of the cocci and also upon the proportion
AB  - of apt and non-apt cells.  The restriction of phage K14 was eliminated during
AB  - its propagation on all strains other than lytic group II.  The unrestricted
AB  - progeny particles tended to assay at equal titre on all the indicator strains.
AB  - In all cases the genotype of the phage - susceptibility to
AB  - host-control-remained unchanged.  The observations add to existing data which
AB  - indicate that strains of phage group II form a genetically distinct group.  The
AB  - suggestion is made that this phenomenon might help in taxonomic classifiction
AB  - of strains of S. aureus.
ER  -

TY  - JOUR
AU  - Ralston, D.J.
AU  - Kruger, A.P.
TI  - Phage multiplication on two hosts, isolation and activity of variants of Staphylococcus phage P1.
JO  - Proc. Soc. Exp. Biol. Med.
PY  - 1952
SP  - 217
EP  - 220
VL  - 80
AB  - Analysis of phage activity by titration on two hosts has revealed the presence
AB  - of variants hitherto undetected in stock phage P1.  One isolate, Phage 14,
AB  - exhibits great changes in titration ratio on passage through the two hosts K1
AB  - and WF 145.  Produced on K1 cells, the ratio of free phage assayed on two hosts
AB  - is 1.3, whereas made on 145 cells,the free phage titrates in a ratio 145/K1 of
AB  - ca 40.  This occurs regardless of the host employed in previous passage and is
AB  - reproduced in the very first burst from infected cells.  Attempts to isolate
AB  - different strains from this phage by usual plaque isolation technics were not
AB  - successful.  The high ratio obtained with free phage made on 145 cells could
AB  - not be explained on the basis of differences in adsorption onto or latent
AB  - periods in the two hosts.  The difference was traced to the production of a
AB  - large number of particles from host 145 which adsorbed on K1 but formed no
AB  - plaques.  No evidence was found for an inhibitor of K1 activity associated with
AB  - phage 14 production on 145 cells.  Heat inactivation destroyed phage activity
AB  - for K1 cells much more rapidly than for 145 cells.  There was no interaction of
AB  - heat killed and active phage on exposure to 59C. Evidence has been accumulated
AB  - which indicates that the phage P14 is altered on passage through host 145.  The
AB  - fact that phage particles surviving a heat treatment which destroyed all
AB  - activity for K1 cells produce on strain 145 a mixture of two phages (one active
AB  - on K1 and on - or both - active on strain 145) points to an unusual host effect
AB  - on virus reproduction.
ER  -

TY  - JOUR
AU  - Ramaiah, A.
AU  - Dasch, G.A.
TI  - Genome Sequence of Coxiella-Like Endosymbiont Strain CLE-RmD, a Bacterial Agent in the Cattle Tick (Rhipicephalus microplus) Deutsch Strain.
JO  - Genome Announcements
PY  - 2018
SP  - e00003
EP  - e00018
VL  - 6
AB  - We report a partial genome sequence for the Coxiella-like endosymbiont strain CLE-RmD,
AB  - assembled from metagenomics data obtained from the southern cattle tick
AB  - (Rhipicephalus microplus) Deutsch strain.
ER  -

TY  - JOUR
AU  - Ramakrishna, J.
AU  - Mathee, K.
AU  - Plaut, A.G.
AU  - Wright, A.
TI  - Restriction enzyme systems of Helicobacter pylori.
JO  - Gastroenterology
PY  - 1995
SP  - A200
EP  - A200
VL  - 108
AB  - To date, the analysis of H. pylori using methods such as RFLP's, PCR and pulsed field gel
AB  - electrophoresis, has revealed considerable genetic diversity from strain to strain.  Due to
AB  - this diversity, there are as yet no methods for classifying this organism.  Also there are
AB  - considerable differences in the transformability of different clinical isolates, some being
AB  - easily transformable while others are not.  It has therefore been postulated that the organism
AB  - may have restriction-modification systems which differ among isolates.  Restriction enzymes
AB  - are produced by bacteria that cleave DNA at specific recognition sequences; these bacteria
AB  - therefore have a modification system to methylate their own DNA at the recognition sites to
AB  - protect it from cleavage.  No restriction enzymes have been described in H. pylori so far.
AB  - Since restriction-modification systems are highly conserved in a given strain of a pathogenic
AB  - organism, this can be a reliable method for classifying clinical isolates.  We cultured eleven
AB  - H. pylori isolates on Campylobacter agar Skirrow (Difco) plates supplemented with 10%
AB  - defibrinated sheep blood (Remel) in microaerobic chambers.  Cells were resuspended in a
AB  - suitable buffer and sonicated.  Protein extracts were prepared by precipitation with 60%
AB  - ammonium sulfate and subsequent dialysis, and these were used for restriction digests.
AB  - Preliminary digests were done using a standard DNA template, the plasmid pBR322, which has a
AB  - known restriction map and DNA sequence.  The patterns of these digests suggested the existence
AB  - of restriction enzymes.  The site specificity of the restriction enzymes was elucidated using
AB  - pBR322 that was linearized and labelled at one end with 32P.  Partial digests of the 32P
AB  - labelled DNA with Hp extracts were fractionated by electrophoresis on polyacrylamide and
AB  - agarose gels alongside appropriate radiolabelled markers.  By determining the sizes of the
AB  - fragments of DNA generated we were able to determine the restriction sites on pBR322.  The
AB  - various clinical isolates studied by us so far all have distinct restriction patterns.  Two
AB  - have so far been identified.  The enzyme present in Hp 32 has a specificity corresponding to
AB  - Sau96I while that in Hp 64 corresponds to DdeI.  Work is currently under way in our laboratory
AB  - to identify the restriction enzymes in other clinical isolates.  We anticipate that this will
AB  - yield a pattern that will form the bais for a classification system for H. pylori strains.
ER  -

TY  - JOUR
AU  - Ramalingam, R.
AU  - Prasad, R.
AU  - Shivapriya, R.
AU  - Dharmalingam, K.
TI  - Molecular cloning and sequencing of mcrA locus and identification of McrA protein in Escherichia coli.
JO  - J. Biosci.
PY  - 1992
SP  - 217
EP  - 232
VL  - 17
AB  - The Mcr systems (previously known as Rgl systems) of Escherichia coli recognize and cleave
AB  - specific sequences carrying methylated or hydroxymethylated cytosines.  We have cloned the
AB  - mcrA gene and determined its nucleotide sequence.  An 831 base pair sequence encodes the McrA
AB  - protein.  Analysis of the sequence data reveals that there are additional ORFs internal to the
AB  - above.  A phage T7 expression system was used to determine the protein products encoded by the
AB  - cloned mcrA gene.  The results clearly show that a 31 kDa polypeptide is responsible for McrA
AB  - activity.  This is in agreement with the molecular weight deduced from sequence data.  McrA
AB  - protein was found to be localized in the outer membrane of Escherichia coli.  To our knowledge
AB  - this is the first restriction enzyme localized in the outer membrane of Escherichia coli.
ER  -

TY  - JOUR
AU  - Ramalingam, S.
AU  - Kandavelou, K.
AU  - Rajenderan, R.
AU  - Chandrasegaran, S.
TI  - Creating Designed Zinc-Finger Nucleases with Minimal Cytotoxicity.
JO  - J. Mol. Biol.
PY  - 2011
SP  - 630
EP  - 641
VL  - 405
AB  - Zinc-finger nucleases (ZFNs) have emerged as powerful tools for delivering a targeted genomic
AB  - double-strand break (DSB) to either stimulate local
AB  - homologous recombination with investigator-provided donor DNA or induce
AB  - gene mutations at the site of cleavage in the absence of a donor by
AB  - nonhomologous end joining both in plant cells and in mammalian cells,
AB  - including human cells. ZFNs are formed by fusing zinc-finger proteins to
AB  - the nonspecific cleavage domain of the FokI restriction enzyme.
AB  - ZFN-mediated gene targeting yields high gene modification efficiencies
AB  - (>10%) in a variety of cells and cell types by delivering a recombinogenic
AB  - DSB to the targeted chromosomal locus, using two designed ZFNs. The
AB  - mechanism of DSB by ZFNs requires (1) two ZFN monomers to bind to their
AB  - adjacent cognate sites on DNA and (2) the FokI nuclease domains to
AB  - dimerize to form the active catalytic center for the induction of the DSB.
AB  - In the case of ZFNs fused to wild-type FokI cleavage domains, homodimers
AB  - may also form; this could limit the efficacy and safety of ZFNs by
AB  - inducing off-target cleavage. In this article, we report further
AB  - refinements to obligate heterodimer variants of the FokI cleavage domain
AB  - for the creation of custom ZFNs with minimal cellular toxicity. The
AB  - efficacy and efficiency of the reengineered obligate heterodimer variants
AB  - of the FokI cleavage domain were tested using the green fluorescent
AB  - protein gene targeting reporter system. The three-finger and four-finger
AB  - zinc-finger protein fusions to the REL_DKK pair among the newly generated
AB  - FokI nuclease domain variants appear to eliminate or greatly reduce the
AB  - toxicity of designer ZFNs to human cells.
ER  -

TY  - JOUR
AU  - Raman, G.
AU  - Sakthivel, N.
AU  - Park, S.
TI  - Draft Genome Sequence of a Novel Nicotine-Degrading Bacterium, Pseudomonas plecoglossicida TND35.
JO  - Genome Announcements
PY  - 2015
SP  - e01162
EP  - e01114
VL  - 3
AB  - Pseudomonas plecoglossicida TND35 is a potent nicotine-degrading bacterium. The draft genome
AB  - sequence of strain TND35 contains 6,209,227 bp, 5,511 coding genes,
AB  - and a G+C content of 62.3%. It encompasses genes related to catabolism of
AB  - nicotine, N-heterocyclic aromatic compounds, heavy metal degradation, and butanol
AB  - biosynthesis.
ER  -

TY  - JOUR
AU  - Ramanathan, S.P.
AU  - van Aelst, K.
AU  - Sears, A.
AU  - Peakman, L.J.
AU  - Diffin, F.M.
AU  - Szczelkun, M.D.
AU  - Seidel, R.
TI  - Type III restriction enzymes communicate in 1D without looping between their target sites.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 1748
EP  - 1753
VL  - 106
AB  - To cleave DNA, Type III restriction enzymes must communicate the relative orientation of two
AB  - asymmetric recognition sites over hundreds of base
AB  - pairs. The basis of this long-distance communication, for which ATP
AB  - hydrolysis by their helicase domains is required, is poorly understood.
AB  - Several conflicting DNA-looping mechanisms have been proposed, driven
AB  - either by active DNA translocation or passive 3D diffusion. Using
AB  - single-molecule DNA stretching in combination with bulk-solution assays,
AB  - we provide evidence that looping is both highly unlikely and unnecessary,
AB  - and that communication is strictly confined to a 1D route. Integrating our
AB  - results with previous data, a simple communication scheme is concluded
AB  - based on 1D diffusion along DNA.
ER  -

TY  - JOUR
AU  - Ramanujam, R.
AU  - Heaster, J.
AU  - Huang, C.
AU  - Jolly, J.
AU  - Koelbl, J.
AU  - Lively, C.
AU  - Ogutu, E.
AU  - Ting, E.
AU  - Treml, S.
AU  - Aldous, B.
AU  - Hatley, R.
AU  - Mathias, S.
AU  - Franks, F.
AU  - Burdick, B.
TI  - Ambient temperature-stable molecular biology reagents.
JO  - Biotechniques
PY  - 1993
SP  - 470
EP  - 474
VL  - 14
AB  - We have processed biological materials to generate several reagents that are ambient
AB  - temperature stable and ready to use. Stabilized biomolecules in a glassy matrix of
AB  - carbohydrate polymers offer water-soluble reagents for complex molecular biology applications.
AB  - This approach is particulary useful for reagent systems composed of enzymes, nucleotides and
AB  - other components dispensed in single-use aliquots. Reconstitution of the glassy matrix
AB  - delivers buffered enzymes and/or nucleotides for restriction, modification, sequencing and/or
AB  - amplification of nucleic acids. These ambient-temperature-stable reagents allow a high level
AB  - of reproducibility as they minimize the potential for pipetting errors. They also provide
AB  - advantages in shipping, storage and subsequent handling. Added convenience includes
AB  - elimination of setup time, cross contamination and refrigeration. Applications of
AB  - ambient-temperature-stable biological reagents for routine molecular biology methods are
AB  - presented.
ER  -

TY  - JOUR
AU  - Ramaraj, T.
AU  - Matyi, S.A.
AU  - Sundararajan, A.
AU  - Lindquist, I.E.
AU  - Devitt, N.P.
AU  - Schilkey, F.D.
AU  - Lamichhane-Khadka, R.
AU  - Hoyt, P.R.
AU  - Mudge, J.
AU  - Gustafson, J.E.
TI  - Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.
JO  - Genome Announcements
PY  - 2014
SP  - e01033
EP  - e01014
VL  - 2
AB  - We report the draft genome sequences of three vancomycin-susceptible methicillin-resistant
AB  - Staphylococcus aureus strains. S. aureus strain MV8 is a
AB  - sequence type 8 (ST-8) staphylococcal cassette chromosome mec element type IV
AB  - (SCCmec IV) derivative, while the other two strains (S. aureus MM25 and MM61) are
AB  - ST-5 SCCmec II strains. MM61 is also closely related to the heterogeneous
AB  - vancomycin-intermediate S. aureus strain MM66.
ER  -

TY  - JOUR
AU  - Ramaraj, T.
AU  - Sundararajan, A.
AU  - Schilkey, F.D.
AU  - Delvecchio, V.G.
AU  - Donlon, M.
AU  - Ziemer, C.
AU  - Mudge, J.
TI  - Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies.
JO  - Genome Announcements
PY  - 2014
SP  - e00237
EP  - e00214
VL  - 2
AB  - Bacteroides xlyanisolvens strains (SD_CC_1b, SD_CC_2a) isolated from human feces  were grown
AB  - on crystalline cellulose. Cellulolytic properties are not common in Bacteroides species. Here,
AB  - we report improved genome sequences of both of the B. xlyanisolvens strains.
ER  -

TY  - JOUR
AU  - Ramasamy, D.
AU  - Dubourg, G.
AU  - Robert, C.
AU  - Caputo, A.
AU  - Papazian, L.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Enorma timonensis sp.  nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 970
EP  - 986
VL  - 9
AB  - Enorma timonensis strain GD5(T) sp. nov., is the type strain of E. timonensis sp. nov., a new
AB  - member of the genus Enorma within the family Coriobacteriaceae. This
AB  - strain, whose genome is described here, was isolated from the fecal flora of a
AB  - 53-year-old woman hospitalized for 3 months in an intensive care unit. E.
AB  - timonensis is an obligate anaerobic rod. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060
AB  - protein-coding and 52 RNA genes, including 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Ramasamy, D.
AU  - Kokcha, S.
AU  - Lagier, J.C.
AU  - Nguyen, T.T.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome sequence and description of Aeromicrobium massiliense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 246
EP  - 257
VL  - 7
AB  - Aeromicrobium massiliense strain JC14(T)sp. nov. is the type strain of Aeromicrobium
AB  - massiliense sp. nov., a new species within the genus Aeromicrobium.
AB  - This strain, whose genome is described here, was isolated from the fecal
AB  - microbiota of an asymptomatic patient. Aeromicrobium massiliense is an aerobic
AB  - rod-shaped gram-positive bacterium. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 3,322,119 bp long genome contains 3,296 protein-coding and 51 RNA genes.
ER  -

TY  - JOUR
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Gorlas, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 264
EP  - 278
VL  - 8
AB  - Bacillus massiliosenegalensis strain JC6(T) sp. nov. is the type strain of Bacillus
AB  - massiliosenegalensis sp. nov., a new species within the genus Bacillus.
AB  - This strain was isolated from the fecal flora of a healthy Senegalese patient. B.
AB  - massiliosenegalensis is an aerobic Gram-positive rod-shaped bacterium. Here we
AB  - describe the features of this organism, together with the complete genome
AB  - sequence and annotation. The 4,981,278-bp long genome comprises a 4,957,301-bp
AB  - chromosome and a 23,977-bp plasmid. The chromosome contains 4,925 protein-coding
AB  - and 72 RNA genes, including 4 rRNA genes. The plasmid contains 29 protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Nguyen, T.T.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 336
EP  - 351
VL  - 8
AB  - Dielma fastidiosa strain JC13(T) gen. nov., sp. nov. is the type strain of D. fastidiosa gen.
AB  - nov., sp. nov., the type species of a new genus within the family
AB  - Erysipelotrichaceae. This strain, whose draft genome is described here, was
AB  - isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer.
AB  - D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of
AB  - this organism, together with the complete genome sequence and annotation. The
AB  - 3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp
AB  - plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including
AB  - 3 rRNA genes, whereas the plasmid contains 17 protein-coding genes.
ER  -

TY  - JOUR
AU  - Ramasamy, D.
AU  - Lagier, J.C.
AU  - Rossi-Tamisier, M.
AU  - Pfleiderer, A.
AU  - Michelle, C.
AU  - Couderc, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome sequence and description of Bacteroides timonensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1181
EP  - 1197
VL  - 9
AB  - Bacteroides timonensis strain AP1(T) (= CSUR P194 = DSM 26083) is the type strain of B.
AB  - timonensis sp. nov. This strain, whose genome is described here, was
AB  - isolated from the fecal flora of a 21-year-old French Caucasoid female who
AB  - suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative,
AB  - obligate anaerobic bacillus. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. The 7,130,768 bp long
AB  - genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains
AB  - 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.
ER  -

TY  - JOUR
AU  - Ramasubban, G.
AU  - Lakshmipathy, D.
AU  - Vetrivel, U.
AU  - Kulandai, L.T.
AU  - Madhavan, H.N.
AU  - Sridhar, R.
AU  - Meenakshi, N.
TI  - Whole-Genome Sequencing of Streptomycin-Resistant Mycobacterium tuberculosis Isolate VRFCWCF MRTB 180 Reveals Novel and Potential Mutations for Resistance.
JO  - Genome Announcements
PY  - 2014
SP  - e00919
EP  - e00914
VL  - 2
AB  - We announce the draft genome sequence of a streptomycin monoresistant Mycobacterium
AB  - tuberculosis strain (VRFCWCF MRTB 180) isolated from sputum of a
AB  - clinically suspected tuberculosis patient.
ER  -

TY  - JOUR
AU  - Ramazzotti, M.
AU  - Cimaglia, F.
AU  - Gallo, A.
AU  - Ranaldi, F.
AU  - Surico, G.
AU  - Mita, G.
AU  - Bleve, G.
AU  - Marchi, G.
TI  - Insights on a founder effect: the case of Xylella fastidiosa in the Salento area of Apulia, Italy.
JO  - Phytopathol. Mediterr.
PY  - 2018
SP  - 0
EP  - 0
VL  - 0
AB  - Summary. Xylella fastidiosa causing disease on different plant species has been reported in
AB  - several European countries, since 2013. Based on multilocus sequence typing (MLST) results,
AB  - there is evidence of repeated introductions of the pathogen in Spain and France. In contrast,
AB  - in the Salento area of Apulia (Puglia) in Southern Italy, the existence of a unique Apulian
AB  - MLST genotype of X. fastidiosa, causing the olive quick decline syndrome (OQDS; also referred
AB  - to as CoDiRO or ST53) was proven, and this was tentatively ascribed to X. fastidiosa subsp.
AB  - pauca. In order to acquire information on intra population diversity European Food Safety
AB  - Authority (EFSA) has strongly called for the characterization of X. fastidiosa isolates from
AB  - Apulia to produce the necessary data to better understand strain diversity and evolution. In
AB  - this work, for the first time the existence of sub-variants within a set of  14 ST53 isolates
AB  - of X. fastidiosa collected from different locations was searched using DNA typing methods
AB  - targeting the whole pathogen genome. Invariably, VNTR, RAPD and rep-PCR (ERIC and BOX motifs)
AB  - analyses indicated that all tested isolates possessed the same genomic fingerprint, supporting
AB  - the existence of predominant epidemiological strain in Apulia. To further explore the degree
AB  - of clonality within this population, two isolates from two different Salento areas (Taviano
AB  - and Ugento) were completely sequenced using PacBio SMRT technology. The whole genome map and
AB  - sequence comparisons revealed that both isolates are nearly identical, showing less than
AB  - 0.001% nucleotide diversity. However, the complete and circularized Salento-1 and Salento-2
AB  - genome sequences were different, in genome and plasmid size, from the reference strain 9a5c of
AB  - X. fastidiosa subsp. pauca (from citrus), and showed a PCR-proved large genome inversion of
AB  - about 1.7 Mb. Genome-wide indices ANIm and dDDH indicated that the three isolates of X.
AB  - fastidiosa from Salento (Apulia, Italy), namely Salento-1, Salento-2, and De Donno, whose
AB  - complete genome sequence has been recently released, share a very recent common ancestor. This
AB  - highlights the importance of continuous and extensive monitoring of molecular variation of
AB  - this invasive pathogen to understand evolution of adaptive traits, and the necessity for
AB  - adoption of all possible measures to reduce the risk of new introductions that may augment
AB  - pathogen diversity.
ER  -

TY  - JOUR
AU  - Rambach, A.
TI  - Purification and properties of the SstI endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 170
EP  - 173
VL  - 65
AB  - The SstI endonuclease is a restriction enzyme purified from a Streptomyces species which has
AB  - been named Streptomyces stanford and is available from the American Type Culture Collection as
AB  - ATCC No. 29415.  A crude lysate of these cells appears to cleave phage lambda DNA into two
AB  - large fragments and phage lambda plac5 DNA into three large fragments.  SstI endonuclease is
AB  - the major endonuclease which can be found in the lysate.  The enzyme produces cohesive ends
AB  - and seems to cut most DNAs tested at rare sites.
ER  -

TY  - JOUR
AU  - Ramchandani, S.
AU  - Bhattacharya, S.K.
AU  - Cervoni, N.
AU  - Szyf, M.
TI  - DNA methylation is a reversible biological signal.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 6107
EP  - 6112
VL  - 96
AB  - The pattern of DNA methylation plays an important role in regulating different genome
AB  - functions.  To test the hypothesis that DNA methylation is a reversible biochemical process,
AB  - we purified a DNA demethylase from human cells that catalyzes the cleavage of a methyl residue
AB  - from 5-methyl cytosine and its release as methanol.  We show that similar to DNA
AB  - methyltransferase, DNA demethylase shows CpG dinucleotide specificity, can demethylate mdCpdG
AB  - sites in different sequence contexts, and demethylates both fully methylated and
AB  - hemimethylated DNA.  Thus, contrary to the commonly accepted model, DNA methylation is a
AB  - reversible signal, similar to other physiological biochemical modifications.
ER  -

TY  - JOUR
AU  - Ramchandani, S.
AU  - Bigey, P.
AU  - Szyf, M.
TI  - Genomic structure of the human DNA methyltransferase gene.
JO  - Biol. Chem.
PY  - 1998
SP  - 535
EP  - 540
VL  - 379
AB  - We determined the genomic  structure of the gene encoding human DNA methyltransferase.  Six
AB  - overlapping human genomic DNA clones which include all of the known cDNA sequence were
AB  - isolated.  Analysis of these clones demonstrates that the human DNA MTase gene consists of at
AB  - least 40 exons and 39 introns spanning a distance of 60 kilobases.  Elucidation of the
AB  - chromosomal organization of the human DNA MTase gene provides the template for future
AB  - structure-function analysis of the properties of mammalian DNA MTase.
ER  -

TY  - JOUR
AU  - Ramchandani, S.
AU  - MacLeod, A.R.
AU  - Pinard, M.
AU  - von Hofe, E.
AU  - Szyf, M.
TI  - Inhibition of tumorigenesis by a cytosine-DNA, methyltransferase, antisense oligodeoxynucleotide.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 684
EP  - 689
VL  - 94
AB  - This paper tests the hypothesis that cytosine DNA methyltransferase (DNA MeTase) is a
AB  - candidate target for anticancer therapy.  Several observations have suggested recently that
AB  - hyperactivation of DNA MeTase plays a critical role in initiation and progression of cancer
AB  - and that its up-regulation is a component of the Ras oncogenic signaling pathway.  We show
AB  - that a phosphorothioate-modified, antisense oligodeoxynucleotide directed against the DNA
AB  - MeTase mRNA reduces the level of DNA MeTase mRNA, inhibits DNA MeTase activity, and inhibits
AB  - anchorage independent growth of Y1 adrenocortical carcinoma cells ex vivo in a dose-dependent
AB  - manner.  Injection of DNA MeTase antisense oligodeoxynucleotides i.p. inhibits the growth of
AB  - Y1 tumors in syngeneic LAF1 mice, reduces the level of DNA MeTase, and induces demethylation
AB  - of the adrenocortical-specific gene C21 and its expression in tumors in vivo.  These results
AB  - support the hypothesis that an increase in DNA MeTase activity is critical for tumorigenesis
AB  - and is reversible by pharmacological inhibition of DNA MeTase.
ER  -

TY  - JOUR
AU  - Ramchandani, S.
AU  - Szyf, M.
TI  - A novel RNA element mediates the cell cycle dependent posttranscriptional regulation of DNA methyltransferase.
JO  - Mol. Biol. Cell
PY  - 1996
SP  - 302a
EP  - 302a
VL  - 7
AB  - DNA methyltransferase is the enzyme responsible for methylation of DNA at CpG dinucleotide
AB  - sequences.  Patterns of methylation have been shown to be an important control over gene
AB  - regulation.  Recent evidence has linked the disregulation of the DNA MeTase to oncogenesis.
AB  - The only mechanism of regulation of DNA MeTase gene expression thoroughly studied has been
AB  - transcriptional.  However, in untransformed cells the regulation of DNA MeTase has been
AB  - described to be posttranscriptional and dependent on the cell cycle.  The stability of DNA
AB  - MeTase mRNA is dependent on protein synthesis as the stability of the message is enhanced at
AB  - G0 upon the addition of cycloheximide.  Differential mRNA stabilities can be conferred by the
AB  - make-up of a transcript's 3' untranslated region (3'UTR).  Homology comparison between the
AB  - 3' UTR's of the human, mouse, and chicken DNA MeTases have revealed two stretches of greater
AB  - than 90% homology between all three mRNAs and the AU content of these stretches is greater
AB  - than 85%.  To test the hypothesis that this sequence element regulates DNA MeTase mRNA it has
AB  - been inserted 3' to the rabbit-beta-globin gene and transfected into BALB/c 3T3 fibroblast
AB  - cells.  The chimeric globin-MeTase 3'UTR stability profile and its regulation with the cell
AB  - cycle recapitulates that of the endogenous DNA MeTase mRNA.  Our data suggests that a sequence
AB  - element in the DNA MeTase 3' UTR is a novel cell-cycle dependent regulator of mRNA stability.
ER  -

TY  - JOUR
AU  - Ramchandani, S.K.
AU  - Rouleau, J.
AU  - Szyf, M.
TI  - Cloning of the human DNA methyltransferase gene.
JO  - Am. J. Hum. Genet.
PY  - 1994
SP  - A137
EP  - A137
VL  - 55
AB  - During the process of carcinogenesis it has been observed that DNA methylation is deregulated.
AB  - Increasing levels of DNA methyltransferase (DNA MeTase) mRNA has been shown to parallel the
AB  - progression of cells through neoplasia to tumour cells. At least two levels of regulation of
AB  - the mouse DNA MeTase have been shown; at the transcriptional level, via its promoter, and at
AB  - the post transcriptional level in a cell cycle dependent fashion. Previously in our lab, the
AB  - mouse 5' region was identified and was shown to be regulated by known oncogenic pathways. The
AB  - sequence of the complete DNA MeTase gene has not yet been reported. Identifying the promoter
AB  - of the human gene along with its complete genomic sequence is essential for a thorough study
AB  - of the mechanisms involved in the multi-tiered regulation of DNA MeTase and to understand
AB  - it's deregulation in cancer. Using a probe generated by PCR of the human DNA MeTase cDNA
AB  - (position +156 to +507), a human genomic library was screened and a clone of approximately 22
AB  - kilobases (kb) was isolated. It was found that this clone contains the complete coding
AB  - sequence of the DNA MeTase enzyme. Sequence analysis along with restriction enzyme digests
AB  - have allowed us to construct a partial map of the physical structure of the human DNA MeTase
AB  - gene. This partial structure has already revealed some interesting aspects related to the
AB  - genetic evolution of the human DNA MeTase. First, the proposed catalytic domain of the human
AB  - DNA MeTase is extremely homologous to all other cytosine DNA MeTases, even to those that are
AB  - found in bacteria, and this catalytic domain is conserved within one complete exon in the
AB  - human gene. This is very different from the structure of the 5' region of the gene, which is
AB  - fragmented into numerous little introns and exons. Within one of the small introns that have
AB  - been identified, a trinucleotide repeat of ATG occurs (9 times in a row), and this repeat is
AB  - upstream of the proposed start site of translation. Trinucleotide repeat expansion has been
AB  - shown to be a genetic hot spot of mutation, but even more interesting is the nature of the
AB  - repeat, ATG, which is the translation start codon and this repeat appears to be in frame with
AB  - the "normal" coding sequence. The implications being that possible alternative
AB  - methyltransferases may be translated under certain conditions such as cancer.
ER  -

TY  - JOUR
AU  - Ramesh, R.
AU  - Gaitonde, S.
AU  - Achari, G.
AU  - Asolkar, T.
AU  - Singh, N.P.
AU  - Carrere, S.
AU  - Genin, S.
AU  - Peeters, N.
TI  - Genome Sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, Strains Rs-09-161 and Rs-10-244, Isolated from Eggplant and Chili in India.
JO  - Genome Announcements
PY  - 2014
SP  - e00323
EP  - e00314
VL  - 2
AB  - Ralstonia solanacearum Indian strains Rs-09-161 and Rs-10-244 were isolated from  the coastal
AB  - region of Goa and from the Andaman Islands. We report the draft
AB  - genome sequences of these representative isolates infecting solanaceous
AB  - vegetables in India.
ER  -

TY  - JOUR
AU  - Ramijan, K.
AU  - van Wezel, G.P.
AU  - Claessen, D.
TI  - Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens.
JO  - Genome Announcements
PY  - 2017
SP  - e01560
EP  - e01516
VL  - 5
AB  - The vast majority of antibiotics are produced by filamentous soil bacteria called
AB  - actinomycetes. We report here the genome sequence of the tetracycline producer
AB  - 'Streptomyces viridifaciens' DSM 40239. Given that this species has the hallmark
AB  - signatures characteristic of the Kitasatospora genus, we previously proposed to
AB  - rename this organism Kitasatospora viridifaciens.
ER  -

TY  - JOUR
AU  - Ramirez, M.S.
AU  - Adams, M.D.
AU  - Bonomo, R.A.
AU  - Centron, D.
AU  - Tolmasky, M.E.
TI  - Genomic Analysis of Acinetobacter baumannii A118 by Comparison of Optical Maps: Identification of Structures Related to its Susceptibility Phenotype.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 1520
EP  - 1526
VL  - 55
AB  - Acinetobacter baumannii A118, a naturally competent clinical isolate, is unusually susceptible
AB  - to several antibiotics. Comparison of the optical map of strain A118 with in silico-generated
AB  - restriction maps of sequenced genomes and sequence analyses showed that the AbaR region,
AB  - commonly found inserted within the comM gene in other isolates, is missing in strain A118,
AB  - which could in part explain the susceptible phenotype exhibited by this isolate. These
AB  - comparative studies also showed differences in regions where genes coding for functions that
AB  - may be involved in drug resistance or susceptibility are located. Further sequencing
AB  - demonstrated that cat and blaADC, named blaADC-55, are present but that a tet(A) gene usually
AB  - found in other strains is not. In addition, carO and pbp2, which may play a role in
AB  - susceptibility to carbapenems, are present in strain A118. These findings support the idea
AB  - that A. baumannii strains possess multiple mechanisms that contribute to antibiotic
AB  - resistance, and the presence of some of them is not sufficient for a resistant phenotype. The
AB  - results shown here indicate that optical mapping is a useful tool for preliminary comparative
AB  - genomic analysis.
ER  -

TY  - JOUR
AU  - Ramirez, M.S.
AU  - Xie, G.
AU  - Johnson, S.
AU  - Davenport, K.
AU  - van Duin, D.
AU  - Perez, F.
AU  - Bonomo, R.A.
AU  - Chain, P.
AU  - Tolmasky, M.E.
TI  - Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates.
JO  - Genome Announcements
PY  - 2014
SP  - e00558
EP  - e00514
VL  - 2
AB  - Klebsiella pneumoniae, an ESKAPE group (Enterococcus faecium, Staphylococcus aureus,
AB  - Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa,
AB  - and Enterobacter species) pathogen, has acquired multiple antibiotic resistance
AB  - genes and is becoming a serious public health threat. Here, we report the genome
AB  - sequences of two representative strains of K. pneumoniae from the emerging K.
AB  - pneumoniae carbapenemase (KPC) outbreak in northeast Ohio belonging to sequence
AB  - type 258 (ST258) (isolates Kb140 and Kb677, which were isolated from blood and
AB  - urine, respectively). Both isolates harbor a blaKPC gene, and strain Kb140
AB  - carries blaKPC-2, while Kb677 carries blaKPC-3.
ER  -

TY  - JOUR
AU  - Ramirez-Diaz, M.I.
AU  - Diaz-Magana, A.
AU  - Meza-Carmen, V.
AU  - Johnstone, L.
AU  - Cervantes, C.
AU  - Rensing, C.
TI  - Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes.
JO  - Plasmid
PY  - 2011
SP  - 7
EP  - 18
VL  - 66
AB  - We determined the complete nucleotide sequence of conjugative plasmid
AB  - pUM505 isolated from a clinical strain of Pseudomonas aeruginosa. The
AB  - plasmid had a length of 123,322bp and contained 138 complete coding
AB  - regions, including 46% open reading frames encoding hypothetical proteins.
AB  - pUM505 can be considered a hybrid plasmid because it presents two
AB  - well-defined regions. The first region corresponded to a larger DNA
AB  - segment with homology to a pathogenicity island from virulent Pseudomonas
AB  - strains; this island in pUM505 was comprised of genes probably involved in
AB  - virulence and genes encoding proteins implicated in replication,
AB  - maintenance and plasmid transfer. Sequence analysis identified pil genes
AB  - encoding a type IV secretion system, establishing pUM505 as a member of
AB  - the family of IncI1 plasmids. Plasmid pUM505 also contained virB4/virD4
AB  - homologues, which are linked to virulence in other plasmids. The second
AB  - region, smaller in length, contains inorganic mercury and chromate
AB  - resistance gene clusters both flanked by putative mobile elements.
AB  - Although no genes for antibiotic resistance were identified, when pUM505
AB  - was transferred to a recipient strain of P. aeruginosa it conferred
AB  - resistance to the fluoroquinolone ciprofloxacin. pUM505 also conferred
AB  - resistance to the superoxide radical generator paraquat. pUM505 could
AB  - provide Pseudomonas strains with a wide variety of adaptive traits such as
AB  - virulence, heavy-metal and antibiotic resistance and oxidative stress
AB  - tolerance which can be selective factors for the distribution and
AB  - prevalence of this plasmid in diverse environments, including hospitals
AB  - and heavy metal contaminated soils.
ER  -

TY  - JOUR
AU  - Ramirez-Paredes, J.G.
AU  - Larsson, P.
AU  - Wehner, S.
AU  - Bekaert, M.
AU  - Ohrman, C.
AU  - Metselaar, M.
AU  - Thompson, K.D.
AU  - Richards, R.H.
AU  - Penman, D.J.
AU  - Adams, A.
TI  - Draft Genome Sequence of Francisella noatunensis subsp. orientalis STIR-GUS-F2f7, a Highly Virulent Strain Recovered from Diseased Red Nile Tilapia Farmed in  Europe.
JO  - Genome Announcements
PY  - 2017
SP  - e01555
EP  - e01516
VL  - 5
AB  - A highly virulent strain of Francisella noatunensis subsp. orientalis, STIR-GUS-F2f7, was
AB  - isolated from moribund red Nile tilapia (Oreochromis
AB  - niloticus) farmed in Europe. In this communication, the complete genome
AB  - sequencing of this bacterium is reported.
ER  -

TY  - JOUR
AU  - Ramos, R.T. et al.
TI  - Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain, Isolated  from the Abscess of a Californian Horse.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6620
EP  - 6621
VL  - 194
AB  - The bacterium Corynebacterium pseudotuberculosis is of major veterinary importance because it
AB  - affects livestock, particularly sheep, goats, and horses,
AB  - in several countries, including Australia, Brazil, the United States, and Canada,
AB  - resulting in significant economic losses. In the present study, we describe the
AB  - complete genome of the Corynebacterium pseudotuberculosis Cp316 strain, biovar
AB  - equi, isolated from the abscess of a North American horse.
ER  -

TY  - JOUR
AU  - Ramos-Garcia, A.A.
AU  - Shankar, V.
AU  - Saski, C.A.
AU  - Hsiang, T.
AU  - Freedman, D.L.
TI  - Draft Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Pseudonocardia dioxanivorans BERK-1.
JO  - Genome Announcements
PY  - 2018
SP  - e00207
EP  - e00218
VL  - 6
AB  - Pseudonocardia dioxanivorans strain BERK-1 grows aerobically with 1,4-dioxane as  its sole
AB  - substrate. Reported here is its draft genome sequence, with a size of
AB  - 7.1 Mbp. Key genes are highlighted in this article. BERK-1 exhibits a reduced
AB  - level of cell aggregation and adherence to surfaces compared to those of P.
AB  - dioxanivorans CB1190, giving it an apparent advantage for movement through soil.
ER  -

TY  - JOUR
AU  - Ramos-Silva, P.
AU  - Brito, P.H.
AU  - Serrano, M.
AU  - Henriques, A.O.
AU  - Pereira-Leal, J.B.
TI  - Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice  Fields.
JO  - Genome Announcements
PY  - 2015
SP  - e00094
EP  - e00015
VL  - 3
AB  - Here, we report two genome sequences of endospore-forming bacteria isolated from  the rice
AB  - fields of Comporta, Portugal, identified as Bacillus aryabhattai C765
AB  - and Bacillus aerophilus C772. Both species were previously identified in air
AB  - samples from the upper atmosphere, but our findings suggest their presence in a
AB  - wider range of environmental niches.
ER  -

TY  - JOUR
AU  - Ramsahoye, B.H.
AU  - Biniszkiewicz, D.
AU  - Lyko, F.
AU  - Clark, V.
AU  - Bird, A.P.
AU  - Jaenisch, R.
TI  - Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 5237
EP  - 5242
VL  - 97
AB  - Current evidence indicates that methylation of cytosine in mammalian DNA is restricted to both
AB  - strands of the symmetrical sequence CpG, although there have been sporadic reports that
AB  - sequences other than CpG may also be methylated. We have used a dual-labeling nearest neighbor
AB  - technique and bisulphite genomic sequencing methods to investigate the nearest neighbors of
AB  - 5-methylcytosine residues in mammalian DNA. We find that embryonic stem cells, but not somatic
AB  - tissues, have significant cytosine-5 methylation at CpA and, to a lesser extent, at CpT. As
AB  - the expression of the de novo methyltransferase Dnmt3a correlates well with the presence of
AB  - non-CpG methylation, we asked whether Dnmt3a might be responsible for this modification.
AB  - Analysis of genomic methylation in transgenic Drosophila expressing Dnmt3a reveals that Dnmt3a
AB  - is predominantly a CpG methylase but also is able to induce methylation at CpA and at CpT.
ER  -

TY  - JOUR
AU  - Ramsahoye, B.H.
AU  - Burnett, A.K.
AU  - Taylor, C.
TI  - Restriction endonuclease isoschizomers ItaI, BsoFI and Fsp4HI are characterized by differences in their sensitivities to CpG methylation.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3196
EP  - 3198
VL  - 25
AB  - BsoFI, ItaI and Fsp4HI are isoschizomers of Fnu4HI (5'-GC/NGC-3').  Both Fnu4HI and BsoFI
AB  - have previously been shown to be inhibited by cytosine-specific methylation within the
AB  - recognition sequence.  Fnu4HI is inhibited if either the internal cytosine at position 2 or
AB  - the external cytosine at position 5 of the restriction sequence is methylated, but the precise
AB  - nature of the methylation sensitivity of BsoFI is unclear from the literature.  The
AB  - methylation sensitivities of ItaI and Fsp4HI have not previously been reported.  By
AB  - methylating the plasmid pUC18 with M.SssI (a DNA cytosine-5'-methyltransferase with a
AB  - specificity for CpG), we have determined that ItaI is sensitive only to methylation of
AB  - internal CpG sites within the restriction sequence.  The methylation sensitivity of Fsp4HI is
AB  - identical to that of Fnu4HI, being inhibited by methylation of either internal CpG sites or
AB  - overlapping CpG sites.  BsoFI, like the other isoschizomers tested, is sensitive to a
AB  - combination of internal and overlapping CpG methylation.  BsoFI is also sensitive to
AB  - overlapping CpG methylation (in the absence of internal CpG methylation) if CpG overlap with
AB  - both sides of the recognition sequence.  Sites containing one overlapping CpG (in the absence
AB  - of internal CpG) are cut when methylated but show marked individual variation in their rates
AB  - of cleavage.  Considerable variation in the rate of cleavage by BsoFI is also observed at
AB  - sites containing only internal methylated CpG.  Some sites are cut slowly, whilst others fail
AB  - to cut even after prolonged incubation with excess of enzyme.
ER  -

TY  - JOUR
AU  - Ramsay, B.D. et al.
TI  - High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from  Uranium(VI)-Contaminated Groundwater.
JO  - Genome Announcements
PY  - 2015
SP  - e00092
EP  - e00015
VL  - 3
AB  - Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic
AB  - acid/alcohol-oxidizing, sulfate-reducing delta-proteobacterium. FW-101-2B
AB  - was isolated from contaminated groundwater at The Field Research Center at Oak
AB  - Ridge National Lab after in situ stimulation for heavy metal-reducing conditions.
AB  - The genome will help elucidate the metabolic potential of sulfate-reducing
AB  - bacteria during uranium reduction.
ER  -

TY  - JOUR
AU  - Ramsden, J.J.
AU  - Dreier, J.
TI  - Kinetics of the interaction between DNA and the type IC restriction enzyme EcoR124II.
JO  - Biochemistry
PY  - 1996
SP  - 3746
EP  - 3753
VL  - 35
AB  - Optical waveguide mode spectroscopy was used to determine the binding constants characterizing
AB  - the interaction of EcoR124II, a type IC restriction modification enzyme from Salmonella
AB  - typhimurium, with DNA.  The DNA is immobilized on the surface of an optical waveguide, and the
AB  - enzyme is introduced in bulk solution flowing over the DNA under controlled hydrodynamic
AB  - conditions.  The binding kinetics of the protein to the DNA can be directly observed and the
AB  - number of bound protein molecules per base pair determined to a high accuracy.  Dissociation
AB  - of the protein was measured by switching flowing protein to protein-free buffer.  Binding to
AB  - two different kinds of DNA, with and without the specific sequence recognized by EcoR124II,
AB  - was investigated.  Protein binding and dissociation (M-RnonspecificM-S binding), quantified by
AB  - association and dissociation rate coefficients ka and kd, were the same for both types, but
AB  - the DNA carrying the recognition site showed an additional process, M-RirreversibleM-S
AB  - association (i.e. dissociation was not observed on the time scale of the experiments) of the
AB  - protein, quantified by a rate coefficient ks.  Some inferences regarding the mechanism of base
AB  - pair searching are made from the measured ka, kd and ks values.
ER  -

TY  - JOUR
AU  - Rand, A.C.
AU  - Jain, M.
AU  - Eizenga, J.M.
AU  - Musselman-Brown, A.
AU  - Olsen, H.E.
AU  - Akeson, M.
AU  - Paten, B.
TI  - Mapping DNA methylation with high-throughput nanopore sequencing.
JO  - Nat. Methods
PY  - 2017
SP  - 411
EP  - 413
VL  - 14
AB  - DNA chemical modifications regulate genomic function. We present a framework for  mapping
AB  - cytosine and adenosine methylation with the Oxford Nanopore Technologies
AB  - MinION using this nanopore sequencer's ionic current signal. We map three
AB  - cytosine variants and two adenine variants. The results show that our model is
AB  - sensitive enough to detect changes in genomic DNA methylation levels as a
AB  - function of growth phase in Escherichia coli.
ER  -

TY  - JOUR
AU  - Rand, K.N.
AU  - Young, G.P.
AU  - Ho, T.
AU  - Molloy, P.L.
TI  - Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - e15
EP  - e15
VL  - 41
AB  - We have developed a novel technique for specific amplification of rare methylated DNA
AB  - fragments in a high background of unmethylated sequences
AB  - that avoids the need of bisulphite conversion. The
AB  - methylation-dependent restriction enzyme GlaI is used to selectively
AB  - cut methylated DNA. Then targeted fragments are tagged using specially
AB  - designed 'helper' oligonucleotides that are also used to maintain
AB  - selection in subsequent amplification cycles in a process called
AB  - 'helper-dependent chain reaction'. The process uses disabled primers
AB  - called 'drivers' that can only prime on each cycle if the helpers
AB  - recognize specific sequences within the target amplicon. In this way,
AB  - selection for the sequence of interest is maintained throughout the
AB  - amplification, preventing amplification of unwanted sequences. Here we
AB  - show how the method can be applied to methylated Septin 9, a promising
AB  - biomarker for early diagnosis of colorectal cancer. The GlaI digestion
AB  - and subsequent amplification can all be done in a single tube. A
AB  - detection sensitivity of 0.1% methylated DNA in a background of
AB  - unmethylated DNA was achieved, which was similar to the
AB  - well-established Heavy Methyl method that requires bisulphite-treated
AB  - DNA.
ER  -

TY  - JOUR
AU  - Rangel, W.M.
AU  - Thijs, S.
AU  - Moreira, F.M.
AU  - Weyens, N.
AU  - Vangronsveld, J.
AU  - Van Hamme, J.D.
AU  - Bottos, E.M.
AU  - Rineau, F.
TI  - Draft Genome Sequence of Mesorhizobium sp. UFLA 01-765, a Multitolerant, Efficient Symbiont and Plant Growth-Promoting Strain Isolated from Zn-Mining Soil  Using Leucaena leucocephala as a Trap Plant.
JO  - Genome Announcements
PY  - 2016
SP  - e00050
EP  - e00016
VL  - 4
AB  - We report the 7.4-Mb draft genome sequence of Mesorhizobium sp. strain UFLA 01-765, a
AB  - Gram-negative bacterium of the Phyllobacteriaceae isolated from
AB  - Zn-mining soil in Minas Gerais, Brazil. This strain promotes plant growth,
AB  - efficiently fixes N2 in symbiosis with Leucaena leucocephala on multicontaminated
AB  - soil, and has potential for application in bioremediation of marginal lands.
ER  -

TY  - JOUR
AU  - Ranjan, V.K.
AU  - Saha, T.
AU  - Mukherjee, S.
AU  - Chakraborty, R.
TI  - Draft Genome Sequence of a Novel Bacterium, Pseudomonas sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West  Bengal, India.
JO  - Genome Announcements
PY  - 2018
SP  - e01443
EP  - e01417
VL  - 6
AB  - The draft genome sequence of a novel strain, Pseudomonas sp. MR 02, a pyomelanin-producing
AB  - bacterium isolated from the Mahananda River at Siliguri,
AB  - West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb,
AB  - with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean
AB  - gene length, 923 bp), among which 5,503 are protein-coding genes, including the
AB  - genes required for the catabolism of tyrosine or phenylalanine for the
AB  - characteristic production of homogentisic acid (HGA). Excess HGA, on excretion,
AB  - auto-oxidizes and polymerizes to form pyomelanin.
ER  -

TY  - JOUR
AU  - Ransom-Jones, E.
AU  - McDonald, J.E.
TI  - Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm.
JO  - Genome Announcements
PY  - 2016
SP  - e00985
EP  - e00916
VL  - 4
AB  - Here, we report the draft genome of Clostridium sp. strain W14A, isolated from the anaerobic,
AB  - cellulolytic biofilm of a cotton string sample incubated in a
AB  - landfill leachate microcosm. The draft genome comprises 131 contigs, 3,823,510
AB  - bp, 51.5% G+C content, and 4,119 predicted coding domain sequences.
ER  -

TY  - JOUR
AU  - Ranson, H.J.
AU  - LaPorte, J.
AU  - Spinard, E.
AU  - Chistoserdov, A.Y.
AU  - Gomez-Chiarri, M.
AU  - Nelson, D.R.
AU  - Rowley, D.C.
TI  - Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4.
JO  - Genome Announcements
PY  - 2018
SP  - e00313
EP  - e00318
VL  - 6
AB  - Aquimarina sp. strain I32.4 (formerly Aquimarina sp. 'homaria') is a putative pathogen
AB  - involved in epizootic shell disease in the American lobster (Homarus
AB  - americanus). We report here the draft genome sequence for Aquimarina sp. strain
AB  - I32.4 and describe virulence factors that may provide insight into its mechanism
AB  - of pathogenicity.
ER  -

TY  - JOUR
AU  - Ranson, H.J.
AU  - LaPorte, J.
AU  - Spinard, E.
AU  - Gomez-Chiarri, M.
AU  - Nelson, D.R.
AU  - Rowley, D.C.
TI  - Draft Genome Sequence of Loktanella maritima Strain YPC211, a Commensal Bacterium of the American Lobster (Homarus americanus).
JO  - Genome Announcements
PY  - 2018
SP  - e00314
EP  - e00318
VL  - 6
AB  - Loktanella maritima strain YPC211 was isolated from the American lobster (Homarus americanus).
AB  - We report here the draft genome sequence for L. maritima YPC211 and
AB  - identify genes of potential importance to its role within the microbial
AB  - community.
ER  -

TY  - JOUR
AU  - Rao, B.S.
AU  - Buckler-White, A.
TI  - Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 2505
EP  - 2507
VL  - 26
AB  - We report here a simple method of directly visualizing in automated DNA sequencing
AB  - chromatograms DNA methylations of different types including cytosine
AB  - methylations in Hpa II and dcm sites as well as adenine methylations in dam
AB  - sites. This is made possible by the observation that the extent of incorporation
AB  - of fluorescently labeled dideoxynucleotides is influenced by the methylated bases
AB  - in template DNA. This simple approach involves routine automated DNA sequencing
AB  - without any prior treatment of DNA specific for detecting DNA methylation.
ER  -

TY  - JOUR
AU  - Rao, C.
AU  - Guyard, C.
AU  - Pelaz, C.
AU  - Wasserscheid, J.
AU  - Bondy-Denomy, J.
AU  - Dewar, K.
AU  - Ensminger, A.W.
TI  - Active and Adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen.
JO  - Cell. Microbiol.
PY  - 2016
SP  - 1319
EP  - 1338
VL  - 18
AB  - CRISPR-Cas systems are widely recognized as critical genome defense systems that protect
AB  - microbes from external threats such as bacteriophage infection. Several isolates of the
AB  - intracellular pathogen Legionella pneumophila possess multiple CRISPR-Cas systems (Type I-C,
AB  - Type I-F, and Type II-B), yet the targets of these systems remain unknown. With the recent
AB  - observation that at least one of these systems (II-B) plays a non-canonical role in supporting
AB  - intracellular replication, the possibility remained that these systems are vestigial genome
AB  - defense systems co-opted for other purposes. Our data indicate this is not the case. Using an
AB  - established plasmid transformation assay, we demonstrate Type I-C, I-F, and II-B CRISPR-Cas
AB  - provide protection against spacer targets. We observe efficient laboratory acquisition of new
AB  - spacers under " priming" conditions, in which initially incomplete target elimination leads to
AB  - the generation of new spacers and ultimate loss of the invasive DNA. Critically, we identify
AB  - the first known target of L. pneumophila CRISPR-Cas: a 30 kilobase episome of unknown function
AB  - whose interbacterial transfer is guarded against by CRISPR-Cas. We provide evidence that the
AB  - element can subvert CRISPR-Cas by mutating its targeted sequences - but that primed spacer
AB  - acquisition may limit this mechanism of escape. Rather than generally impinging on bacterial
AB  - fitness, this element drives a host-specialization event - with improved fitness in
AB  - Acanthamoeba but a reduced ability to replicate in other hosts and conditions. These
AB  - observations add to a growing body of evidence that host-range restriction can serve as an
AB  - existential threat to L. pneumophila in the wild.
ER  -

TY  - JOUR
AU  - Rao, D.N.
AU  - Dryden, D.T.
AU  - Bheemanaik, S.
TI  - Type III restriction-modification enzymes: a historical perspective.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 45
EP  - 55
VL  - 42
AB  - Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA.
AB  - Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a
AB  - DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage
AB  - position and cofactor requirements, restriction-modification (R-M) systems are classified into
AB  - four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA
AB  - sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a
AB  - defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M
AB  - enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage.
AB  - ATP hydrolysis is required for the long-distance communication between the sites before
AB  - cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how
AB  - the long-distance interaction between the two recognition sites takes place. Type III R-M
AB  - systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria
AB  - also shows the presence of a number of phase-variable Type III R-M systems, which play a role
AB  - in virulence. A growing number of these enzymes are being subjected to biochemical and genetic
AB  - studies, which, when combined with ongoing structural analyses, promise to provide details for
AB  - mechanisms of DNA recognition and catalysis.
ER  -

TY  - JOUR
AU  - Rao, D.N.
AU  - Eberle, H.
AU  - Bickle, T.A.
TI  - Characterization of mutations of the bacteriophage P1 mod gene encoding the recognition subunit of the EcoPI restriction and modification system.
JO  - J. Bacteriol.
PY  - 1989
SP  - 2347
EP  - 2352
VL  - 171
AB  - This study characterized several mutations of the bacteriophage P1 mod gene.
AB  - This gene codes for the subunit of the EcoPI restriction enzyme that is
AB  - responsible for DNA sequence recognition and for modification methylation.  We
AB  - cloned the mutant mod genes into expression vectors and purified the mutant
AB  - proteins to near homogeneity.  Two of the mutant mod genes studied were the c2
AB  - clear-plaque mutants described by Scott (Virology 41:66-71, 1970).  These
AB  - mutant proteins can recognize EcoPI sites in DNA and direct restriction but are
AB  - unable to modify DNA.  Methylation assays as well as S-adenosylmethionine (SAM)
AB  - binding studies showed that the c2 mutants are methylation deficient because
AB  - they do not bind SAM, and we conclude that the mutations destroy the
AB  - SAM-binding site.  Both of the c2 mutations lie within a region of the EcoPI
AB  - mod gene that is not conserved when compared with the mod gene of the related
AB  - EcoPI5 system.  EcoPI5 and EcoPI recognize different DNA sequences, and we
AB  - believe that this region of the protein may code for the DNA-binding site of
AB  - the enzyme.  The other mutants characterized were made by site-directed
AB  - mutagenesis at codon 240.  Evidence is presented that one of them, Ser-240
AB  - ->Pro, simultaneously lost the capacity to bind SAM and may also have changed
AB  - its DNA sequence specificity.
ER  -

TY  - JOUR
AU  - Rao, D.N.
AU  - Page, M.G.P.
AU  - Bickle, T.A.
TI  - Cloning, over-expression and the catalytic properties of the EcoP15 modification methylase from Escherichia coli.
JO  - J. Mol. Biol.
PY  - 1989
SP  - 599
EP  - 606
VL  - 209
AB  - The EcoP15 modification methylase gene from the p15B plasmid of Escherichia
AB  - coli 15T- has been cloned and expressed at high levels in a plasmid vector
AB  - system.  We have purified the enzyme to near homogeneity in large amounts and
AB  - have studied some of its enzymatic properties.  Initial rates of methyl
AB  - transfer are first order in methylase concentration and, with a pUC19 DNA as
AB  - substrate, the reaction proceeds by a random mechanism in which either DNA or
AB  - S-adenosylmethionine can bind to the free enzyme.  After methyltransfer to DNA,
AB  - the methylated DNA and S-adenosylhomocysteine appear to dissociate in random
AB  - order.  As expected in such a mechanism, S-adenosylhomocysteine is a
AB  - non-competitive inhibitor with respect to both S-adenosylmethionine and DNA.
AB  - DNA-dependent substrate inhibition by S-adenosylmethionine at concentrations
AB  - not much above its KM suggests that release of methylated DNA may be the
AB  - rate-limiting step.  This suggestion is strengthened by the fact that a mutant
AB  - of the closely related EcoP1 does not show such substrate inhibition.
ER  -

TY  - JOUR
AU  - Rao, D.N.
AU  - Saha, S.
AU  - Krishnamurthy, V.
TI  - ATP-dependent restriction enzymes.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 2000
SP  - 1
EP  - 63
VL  - 64
AB  - The phenomenon of restriction and modification (R-M) was first observed in the course of
AB  - studies on bacteriophages in the early 1950s. It was only in the 1960s that work of Arber and
AB  - colleagues provided a molecular explanation for the host specificity. DNA restriction and
AB  - modification enzymes are responsible for the host-specific barriers to interstrain and
AB  - interspecies transfer of genetic information that have been observed in a variety of bacterial
AB  - cell types. R-M systems comprise an endonuclease and a methyltransferase activity. They serve
AB  - to protect bacterial cells against bacteriophage infection, because incoming foreign DNA is
AB  - specifically cleaved by the restriction enzyme if it contains the recognition sequence of the
AB  - endonuclease. The DNA is protected from cleavage by a specific methylation within the
AB  - recognition sequence, which is introduced by the methyltransferase. Classic R-M systems are
AB  - now divided into three types on the basis of enzyme complexity, cofactor requirements, and
AB  - position of DNA cleavage, although new systems are being discovered that do not fit readily
AB  - into this classification. This review concentrates on multisubunit, multifunctional
AB  - ATP-dependent restriction enzymes. A growing number of these enzymes are being subjected to
AB  - biochemical and genetic studies that, when combined with ongoing structural analyses, promise
AB  - to provide detailed models for mechanisms of DNA recognition and catalysis. It is now clear
AB  - that DNA cleavage by these enzymes involves highly unusual modes of interaction between the
AB  - enzymes and their substrates. These unique features of mechanism pose exciting questions and
AB  - in addition have led to the suggestion that these enzymes may have biological functions beyond
AB  - that of restriction and modification. The purpose of this review is to describe the exciting
AB  - developments in our understanding of how the ATP-dependent restriction enzymes recognize
AB  - specific DNA sequences and cleave or modify DNA.
ER  -

TY  - JOUR
AU  - Rao, M.
AU  - Suvarna, K.
AU  - Srinivasan, M.C.
AU  - Vasanti, D.
TI  - Development of Chainia as a host for xlanase gene cloning: evidence for occurrence of a restriction-modification system.
JO  - Biotechnol. Lett.
PY  - 1996
SP  - 327
EP  - 332
VL  - 18
AB  - Conditions for genetic transformation of the xylanase-negative (X-) strain of
AB  - Chainia with pIJ 702 were optimized.  The growth of Chainia at 30oC for 36-40h and addition of
AB  - gelatin (1%) to the medium resulted in the maximum yield of protoplasts and regeneration
AB  - efficiency.  Poor transformation efficiency of Chainia (X-) protoplasts by native pIJ 702
AB  - versus
AB  - improved efficiency (16 transformants/ug of plasmid DNA) by prior heating of protoplasts at
AB  - 42oC
AB  - for 10 min suggests the occurrence of a restriction system in Chainia.  Increased
AB  - transformation
AB  - efficiency by passage of the plasmid through Chainia together with the altered methylation
AB  - status of
AB  - the transformant plasmid presents evidence for the existence of an operative modification
AB  - system in
AB  - Chainia.  Development of thiostrepton resistance and formation of melamin pigment in Chainia
AB  - (X-
AB  - ) by transformation with pIJ 702 reveal that genes from Streptomyces can be functionally
AB  - expressed by Chainia (X-).
ER  -

TY  - JOUR
AU  - Rao, Q.
AU  - Wang, S.
AU  - Su, Y.L.
AU  - Bing, X.L.
AU  - Liu, S.S.
AU  - Wang, X.W.
TI  - Draft Genome Sequence of 'Candidatus Hamiltonella defensa,' an Endosymbiont of the Whitefly Bemisia tabaci.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3558
EP  - 3558
VL  - 194
AB  - 'Candidatus Hamiltonella defensa' is a facultative endosymbiont of the whitefly Bemisia
AB  - tabaci. Herein, we report the first draft genome sequence of 'Candidatus
AB  - Hamiltonella defensa' from the invasive Mediterranean cryptic species of the B.
AB  - tabaci complex. The 1.84-Mbp genome sequence comprises 404 contigs and contains
AB  - 1,806 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Rao, Q.
AU  - Wang, S.
AU  - Zhu, D.T.
AU  - Wang, X.W.
AU  - Liu, S.S.
TI  - Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly  Bemisia tabaci.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4741
EP  - 4742
VL  - 194
AB  - We report the draft genome sequence of the Rickettsia sp. strain MEAM1, which is  a
AB  - facultative symbiont from an invasive species of the whitefly Bemisia tabaci.
AB  - The total length of the assembled genome is approximately 1.24 Mb, with 335
AB  - scaffolds and 1,247 coding sequences predicted within the genome.
ER  -

TY  - JOUR
AU  - Rao, S.B.
AU  - Gupta, V.K.
AU  - Kumar, M.
AU  - Hegde, N.R.
AU  - Splitter, G.A.
AU  - Reddanna, P.
AU  - Radhakrishnan, G.K.
TI  - Draft Genome Sequence of the Field Isolate Brucella melitensis Strain Bm IND1 from India.
JO  - Genome Announcements
PY  - 2014
SP  - e00497
EP  - e00414
VL  - 2
AB  - Brucella spp. are facultative intracellular bacterial pathogens causing the zoonotic disease
AB  - brucellosis. Here, we report the draft genome sequence of the
AB  - Brucella melitensis strain from India designated Bm IND1, isolated from stomach
AB  - contents of an aborted goat fetus.
ER  -

TY  - JOUR
AU  - Rapa, R.A.
AU  - Islam, A.
AU  - Monahan, L.G.
AU  - Mutreja, A.
AU  - Thomson, N.
AU  - Charles, I.G.
AU  - Stokes, H.W.
AU  - Labbate, M.
TI  - A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.
JO  - Environ. Microbiol.
PY  - 2015
SP  - 1090
EP  - 1102
VL  - 17
AB  - Lateral gene transfer (LGT) has been crucial in the evolution of the cholera
AB  - pathogen, Vibrio cholerae. The two major virulence factors are present on two
AB  - different mobile genetic elements, a bacteriophage containing the cholera toxin
AB  - genes and a genomic island (GI) containing the intestinal adhesin genes.
AB  - Non-toxigenic V. cholerae in the aquatic environment are a major source of novel
AB  - DNA that allows the pathogen to morph via LGT. In this study, we report a novel
AB  - GI from a non-toxigenic V. cholerae strain containing multiple genes involved in
AB  - DNA repair including the recombination repair gene recA that is 23% divergent
AB  - from the indigenous recA and genes involved in the translesion synthesis pathway.
AB  - This is the first report of a GI containing the critical gene recA and the first
AB  - report of a GI that targets insertion into a specific site within recA. We show
AB  - that possession of the island in Escherichia coli is protective against DNA
AB  - damage induced by UV-irradiation and DNA targeting antibiotics. This study
AB  - highlights the importance of genetic elements such as GIs in the evolution of V.
AB  - cholerae and emphasizes the importance of environmental strains as a source of
AB  - novel DNA that can influence the pathogenicity of toxigenic strains.
ER  -

TY  - JOUR
AU  - Raphael, B.H.
AU  - Kozak-Muiznieks, N.A.
AU  - Morrison, S.S.
AU  - Mercante, J.W.
AU  - Winchell, J.M.
TI  - Complete Genome Sequences of Legionella pneumophila subsp. fraseri Strains Detroit-1 and Dallas 1E.
JO  - Genome Announcements
PY  - 2017
SP  - e01525
EP  - e01516
VL  - 5
AB  - We report here the complete genome sequences of two of the earliest known strains of
AB  - Legionella pneumophila subsp. fraseri Detroit-1 is serogroup 1 and was
AB  - isolated from a lung biopsy specimen in 1977. Dallas 1E is serogroup 5 and was
AB  - isolated in 1978 from a cooling tower.
ER  -

TY  - JOUR
AU  - Rappert, S.
AU  - Song, L.
AU  - Sabra, W.
AU  - Wang, W.
AU  - Zeng, A.P.
TI  - Draft Genome Sequence of Type Strain Clostridium pasteurianum DSM 525 (ATCC 6013), a Promising Producer of Chemicals and Fuels.
JO  - Genome Announcements
PY  - 2013
SP  - e00232
EP  - e00212
VL  - 1
AB  - Clostridium pasteurianum, an anaerobic bacterium able to utilize atmospheric free nitrogen for
AB  - biosynthesis, has recently been proven to be a promising producer of chemicals and fuels, such
AB  - as 1,3-propanediol and n-butanol. Here, we report the high-quality draft genome sequence of
AB  - DSM 525, a type strain of C. pasteurianum.
ER  -

TY  - JOUR
AU  - Raschke, E.
TI  - Comprehensive restriction enzyme lists to update to any DNA sequence computer program.
JO  - Genet. Anal. Tech. Appl.
PY  - 1993
SP  - 49
EP  - 60
VL  - 10
AB  - Restriction enzyme lists are presented for the practical working geneticist to update any DNA
AB  - computer program. These lists combine formerly scattered information and contain all presently
AB  - known restriction enzymes with a unique recognition sequence, a cut site, or methylation
AB  - (in)sensitivity. The lists are in the shortest possible form to also be functional with small
AB  - DNA computer programs, and will produce clear restriction maps without any redundancy or loss
AB  - of information. The lists discern between commercial and noncommercial enzymes, and prototype
AB  - enzymes and different isoschizomers are cross-referenced. Differences in general methylation
AB  - sensitivities and (in)sensitivities against Dam and Dcm methylases of Escherichia coli are
AB  - indicated. Commercial methylases and intron-encoded endonucleases are included. An address
AB  - list is presented to contact commercial suppliers. The lists are constantly updated and
AB  - available in electronic form as pure US ASCI filed, and in formats for the DNA computer
AB  - programs DNA-Strider for Apple Macintosh, and DNAsis for IBM personal computers or compatibles
AB  - via e-mail from the internet address: NETSERV@EMBLHEIDELBERG.DE by sending only the message
AB  - HELP RELIBRARY.
ER  -

TY  - JOUR
AU  - Rashid, S.R.
AU  - Clokie, M.R.
AU  - Millard, A.D.
TI  - Draft Genome Sequences of Three Novel Clostridium Isolates from Northern Iraq.
JO  - Genome Announcements
PY  - 2016
SP  - e00033
EP  - e00016
VL  - 4
AB  - Three Clostridium sp. strains were isolated from soil and sediment collected from the
AB  - Kurdistan region of Iraq. All three isolates were found to harbor putative
AB  - prophages, with a CRISPR-Cas system found in strains C105KSO13 and C105KSO14.
ER  -

TY  - JOUR
AU  - Rashmi, B.S.
AU  - Gayathri, D.
TI  - Draft Genome Sequence of the Gluten-Hydrolyzing Bacterium Bacillus subtilis GS 188, Isolated from Wheat Sourdough.
JO  - Genome Announcements
PY  - 2017
SP  - e00952
EP  - e00917
VL  - 5
AB  - The draft genome sequence of Bacillus subtilis GS 188, a novel spore-forming probiotic
AB  - bacterium with gluten-hydrolyzing potential, was isolated from wheat
AB  - sourdough and provides deep insights into the beneficial features of this strain
AB  - for its use in the preparation of gluten-reduced wheat foods for humans with
AB  - celiac disease.
ER  -

TY  - JOUR
AU  - Rasko, D.A. et al.
TI  - Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
JO  - N. Engl. J. Med.
PY  - 2011
SP  - 709
EP  - 717
VL  - 365
AB  - BACKGROUND: A large outbreak of diarrhea and the hemolytic-uremic syndrome
AB  - caused by an unusual serotype of Shiga-toxin-producing Escherichia coli
AB  - (O104:H4) began in Germany in May 2011. As of July 22, a large number of
AB  - cases of diarrhea caused by Shiga-toxin-producing E. coli have been
AB  - reported--3167 without the hemolytic-uremic syndrome (16 deaths) and 908
AB  - with the hemolytic-uremic syndrome (34 deaths)--indicating that this
AB  - strain is notably more virulent than most of the Shiga-toxin-producing E.
AB  - coli strains. Preliminary genetic characterization of the outbreak strain
AB  - suggested that, unlike most of these strains, it should be classified
AB  - within the enteroaggregative pathotype of E. coli. METHODS: We used
AB  - third-generation, single-molecule, real-time DNA sequencing to determine
AB  - the complete genome sequence of the German outbreak strain, as well as the
AB  - genome sequences of seven diarrhea-associated enteroaggregative E. coli
AB  - serotype O104:H4 strains from Africa and four enteroaggregative E. coli
AB  - reference strains belonging to other serotypes. Genomewide comparisons
AB  - were performed with the use of these enteroaggregative E. coli genomes, as
AB  - well as those of 40 previously sequenced E. coli isolates. RESULTS: The
AB  - enteroaggregative E. coli O104:H4 strains are closely related and form a
AB  - distinct clade among E. coli and enteroaggregative E. coli strains.
AB  - However, the genome of the German outbreak strain can be distinguished
AB  - from those of other O104:H4 strains because it contains a prophage
AB  - encoding Shiga toxin 2 and a distinct set of additional virulence and
AB  - antibiotic-resistance factors. CONCLUSIONS: Our findings suggest that
AB  - horizontal genetic exchange allowed for the emergence of the highly
AB  - virulent Shiga-toxin-producing enteroaggregative E. coli O104:H4 strain
AB  - that caused the German outbreak. More broadly, these findings highlight
AB  - the way in which the plasticity of bacterial genomes facilitates the
AB  - emergence of new pathogens.
ER  -

TY  - JOUR
AU  - Rasko, D.A.
AU  - Ravel, J.
AU  - Okstad, O.A.
AU  - Helgason, E.
AU  - Cer, R.Z.
AU  - Jiang, L.
AU  - Shores, K.A.
AU  - Fouts, D.E.
AU  - Tourasse, N.J.
AU  - Angiuoli, S.V.
AU  - Kolonay, J.
AU  - Nelson, W.C.
AU  - Kolsto, A.-B.
AU  - Fraser, C.M.
AU  - Read, T.D.
TI  - The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 977
EP  - 988
VL  - 32
AB  - We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in
AB  - the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated
AB  - that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while
AB  - containing a number of unique metabolic capabilities such as urease and xylose utilization and
AB  - lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for
AB  - variation of capsule carbohydrate and flagella surface structures were identified. Bacillus
AB  - cereus ATCC 10987 contains a single large plasmid (pBc10987, of  208 kb, that is similar in
AB  - gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated
AB  - island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity
AB  - of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large
AB  - pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and
AB  - regulatory cross-talk.
ER  -

TY  - JOUR
AU  - Rasko, T.
AU  - Der, A.
AU  - Klement, E.
AU  - Slaska-Kiss, K.
AU  - Posfai, E.
AU  - Medzihradszky, K.F.
AU  - Marshak, D.R.
AU  - Roberts, R.J.
AU  - Kiss, A.
TI  - BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 7155
EP  - 7166
VL  - 38
AB  - The GGCC-specific restriction endonuclease BspRI is one of the few Type IIP restriction
AB  - endonucleases, which were suggested to be a monomer. Amino
AB  - acid sequence information obtained by Edman sequencing and mass
AB  - spectrometry analysis was used to clone the gene encoding BspRI. The
AB  - bspRIR gene is located adjacently to the gene of the cognate modification
AB  - methyltransferase and encodes a 304 aa protein. Expression of the bspRIR
AB  - gene in Escherichia coli was dependent on the replacement of the native
AB  - TTG initiation codon with an ATG codon, explaining previous failures in
AB  - cloning the gene using functional selection. A plasmid containing a single
AB  - BspRI recognition site was used to analyze kinetically nicking and
AB  - second-strand cleavage under steady-state conditions. Cleavage of the
AB  - supercoiled plasmid went through a relaxed intermediate indicating
AB  - sequential hydrolysis of the two strands. Results of the kinetic analysis
AB  - of the first- and second-strand cleavage are consistent with cutting the
AB  - double-stranded substrate site in two independent binding events. A
AB  - database search identified eight putative restriction-modification systems
AB  - in which the predicted endonucleases as well as the methyltransferases
AB  - share high sequence similarity with the corresponding protein of the BspRI
AB  - system. BspRI and the related putative restriction endonucleases belong to
AB  - the PD-(D/E)XK nuclease superfamily.
ER  -

TY  - JOUR
AU  - Rasko, T.
AU  - Finta, C.
AU  - Kiss, A.
TI  - DNA bending induced by DNA (cytosine-5) methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3083
EP  - 3091
VL  - 28
AB  - DNA bending induced by six DNA (cytosine-5) methyltransferases was studied using circular
AB  - permutation gel mobility shift assay. The following bend angles were obtained: M.BspRI
AB  - (GG(m5)CC), 46-50 degrees; M.HaeIII (GG(m5)CC), 40-43 degrees; M.SinI (GGW(m5)CC), 34-37
AB  - degrees; M.Sau96I (GGN(m5)CC), 52-57 degrees; M.HpaII (C(m5)CGG), 30 degrees; and M.HhaI
AB  - (G(m5)CGC), 13 degrees. M.HaeIII was also tested with fragments carrying a methylated binding
AB  - site, and it was found to induce a 32 degrees bend. A phase-sensitive gel mobility shift
AB  - assay, using a set of DNA fragments with a sequence-directed bend and a single
AB  - methyltransferase binding site, indicated that M.HaeIII and M.BspRI bend DNA toward the
AB  - minor groove. The DNA curvature induced by M.HaeIII contrasts with the lack of DNA bend
AB  - observed for a covalent M.HaeIII-DNA complex in an earlier X-ray study. Our results and data
AB  - from other laboratories show a correlation between the bending properties and the recognition
AB  - specificities of (cytosine-5) methyltransferases: enzymes recognizing a cytosine 3' to the
AB  - target cytosine tend to induce greater bends than enzymes with guanine in this position. We
AB  - suggest that the observed differences indicate different mechanisms employed by (cytosine-5)
AB  - methyltransferases to stabilize the helix after the target base has flipped out.
ER  -

TY  - JOUR
AU  - Rasmussen, L.H.
AU  - Dargis, R.
AU  - Christensen, J.J.
AU  - Skovgaard, O.
AU  - Nielsen, X.C.
TI  - Draft Genome Sequence of Type Strain Streptococcus gordonii ATCC 10558.
JO  - Genome Announcements
PY  - 2016
SP  - e01745
EP  - e01715
VL  - 4
AB  - Streptococcus gordonii ATCC 10558(T) was isolated from a patient with infective endocarditis
AB  - in 1946 and announced as a type strain in 1989. Here, we report the
AB  - 2,154,510-bp draft genome sequence of S. gordonii ATCC 10558(T). This sequence
AB  - will contribute to knowledge about the pathogenesis of infective endocarditis.
ER  -

TY  - JOUR
AU  - Rasmussen, L.J.
AU  - Lobner-Olesen, A.
AU  - Marinus, M.G.
TI  - Growth-rate-dependent transcription initiation from the dam P2 promoter.
JO  - Gene
PY  - 1995
SP  - 213
EP  - 215
VL  - 157
AB  - Transcription of the dam gene in Escherichia coli is dependent on growth rate.  Using
AB  - single-copy promoter::lacZYA fusions we found that of the five promoter regions which affect
AB  - dam expression, only the P2 promoter shows growth-rate dependence.  The determinants for
AB  - growth-rate control must lie in the region -52 to +27 relative to the transcription start
AB  - point.
ER  -

TY  - JOUR
AU  - Rasmussen, L.J.
AU  - Marinus, M.G.
AU  - Lcbner-Olesen, A.
TI  - Regulation of expression of the dam methyltransferase gene (dam) from Escherichi coli.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 303
EP  - 303
VL  - 17E
AB  - The level of Dam protein (DNA adenine methyltransferase) in E. coli is critical for the
AB  - efficient action of Dam-directed mismatch repair and synchronous initiation of chromosome
AB  - replication from oriC. A drastic increase or decrease from the normal level of 130 molecules
AB  - per cell causes hypermutability and asynchronous initiation. The Dam methyltransferase is
AB  - encoded by the dam gene located at 74 min on the genetic map. The dam gene is part of a
AB  - transcriptional unit which includes five promoters and at least four genes: aroK (shikimic
AB  - acids kinase I), aroB (3-dehydroquinate synthase), urf74.3 (an unidentified open reading
AB  - frame) and dam (Dam methyltransferase). As a first step to elucidate the mechanism of
AB  - regulation we have found that the expression of the dam gene is growth rate regulated and
AB  - coordinated with cell growth. In order to determine the region responsible for this regulation
AB  - we have separated and characterized the promoters individually.
ER  -

TY  - JOUR
AU  - Rasmussen, L.J.
AU  - Marinus, M.G.
AU  - Lobner-Olesen, A.
TI  - Novel growth rate control of dam gene expression in Escherichia coli.
JO  - Mol. Microbiol.
PY  - 1994
SP  - 631
EP  - 638
VL  - 12
AB  - Transcription of the dam gene in Escherichia coli is growth rate regulated by a mechanism
AB  - distinct from that used for ribosomal RNA gene promoters.
AB  - Single-copy operon fusions to lacZ indicated that the major promoter, P2,
AB  - is responsible for most or all of the growth rate dependence. Promoter P2
AB  - is a typical sigma 70 promoter with 18 bp spacing between the -10 and -35
AB  - hexamers. Primer extension analysis was used to show that there was no
AB  - inhibition of transcription from promoter P2 in cells induced for the
AB  - stringent response. Beta-galactosidase specific activity from a
AB  - single-copy dam::lacZ fusion was unaffected by either excess rrnB RNA or
AB  - the level of Fis protein. Thus growth rate control of dam gene expression
AB  - differs from that of the rRNA and tRNA genes by its lack of response to
AB  - stringent control, ribosomal feedback and enhanced transcription by Fis
AB  - protein. We devised a procedure for selection of mutant cells in which dam
AB  - gene expression was unregulated. One such mutant (cde-4), obtained by
AB  - miniTn10 insertion, showed the same level of beta-galactosidase activity
AB  - at all growth rates tested. In contrast, growth rate-dependent expression
AB  - of the rrnB gene was unaffected by cde-4 confirming the different modes of
AB  - regulation. The cde-4::miniTn10 insertion is located close to kilobase 670
AB  - on the physical map in or near the lipB gene.
ER  -

TY  - JOUR
AU  - Rasmussen, L.J.
AU  - Samson, L.
AU  - Marinus, M.G.
TI  - Dam-directed DNA mismatch repair.
JO  - DNA Damage and Repair
PY  - 1998
SP  - 205
EP  - 228
VL  - 1
AB  - Base mismatches in duplex DNA are repaired by a variety of systems in Escherichia coli,
AB  - including: Very Short Patch repair; MutY-dependent repair; and DNA adenine
AB  - methyltransferase-directed DNA mismatch repair.  The first two systems have a restricted
AB  - substrate specificity (T.G and A.G mismatches, respectively), whereas the third system can
AB  - repair 11 out of the 12 possible base mispairs with only the C.C mismatch being refractory.
AB  - There is no known repair pathway for C.C mismatches in duplex DNA.  The DDMR pathway also acts
AB  - on insertions/deletions ("loops") of up to 4 bases.  In this chapter are reviewed the VSP
AB  - repair and DDMR systems with emphasis on the latter.  The MutY-pathway is discussed in Chapter
AB  - 6.
ER  -

TY  - JOUR
AU  - Rastorguev, S.M.
AU  - Zavilgelskii, G.B.
AU  - Suzuki, K.
AU  - Sakka, K.
TI  - Alleviation of type I restriction in Escherichia coli K12 in the presence of the arsR gene from pKW301 of Acidiphilium multivorum AIU 301.
JO  - Mol. Biol. (Mosk)
PY  - 2001
SP  - 79
EP  - 82
VL  - 35
AB  - A study was made of the antirestriction activity of Acidiphilium multivorum AIU 301 ArsR, a
AB  - repressor of the ars operon which confers resistance to arsenite and arsenate and is on
AB  - pKW301. In Escherichia coli, arsR cloned under the control of Plac in a multi-copy vector
AB  - alleviated restriction of nonmodified lambda DNA by a factor of 120, six times more
AB  - efficiently than its analogs of conjugal plasmids R64 (incI1) and R773 (incFI). Amino acid
AB  - sequence analysis showed that the three ArsR proteins have a homologous region of 38 residues,
AB  - including the antirestriction motif, in their N domains, whereas the motif is in the C domain
AB  - in the Ard proteins. The other regions are nonhomologous, and pKW301 ArsR is 33 residues
AB  - shorter than R64 and R773 ArsRs. The total charge is -4 in pKW301 ArsR and +2 in R64 and R733
AB  - ArsRs. A total negative charge was assumed to contribute to the antirestriction activity.
ER  -

TY  - JOUR
AU  - Rastorguev, S.M.
AU  - Zavilgelsky, G.B.
TI  - Role of "antirestriction" motif in functional activity of antirestriction protein ArdA pKM101 (IncN).
JO  - Genetika
PY  - 2003
SP  - 286
EP  - 292
VL  - 39
AB  - A number of mutant forms of the antirestriction protein ArdA encoded by the ardA gene located
AB  - in a transmissive IncN plasmid pKM101 have been
AB  - constructed. Proteins belonging to the Ard family are specific inhibitors
AB  - of type I restriction--modification enzymes. Single mutational
AB  - substitutions of negatively charged amino acid residues located in the
AB  - "antirestriction motif" with hydrophobic alanine, E134A, E137A, D144A, or
AB  - a double substitution E134A, E137A do not affect the antirestriction
AB  - activity (Ard) of ArdA but almost completely abolish the antimodification
AB  - activity (Amd). Mutational substitutions F107D and A110D in the assumed
AB  - interface ArdA, which determines contact between monomers in the active
AB  - dimer (Ard)2, cause an approximately 100-fold decrease in the
AB  - antirestriction protein activity. It is hypothesized that the ArdA protein
AB  - forms two complexes with the type I restriction--modification enzyme
AB  - (R2M2S): (1) with a specific region in the S subunit involved in contact
AB  - with the sK site in DNA; and (2) with a nonspecific region in the R
AB  - subunit involved in DNA translocation and degradation by restriction
AB  - endonucleases. The association of ArdA with the specific region inhibits
AB  - restriction endonuclease and methyltransferase activities simultaneously,
AB  - whereas the association of ArdA with a nonspecific region inhibits only
AB  - restriction endonuclease activity of the R2M2S enzyme.
ER  -

TY  - JOUR
AU  - Rastorguev, S.M.
AU  - Zavilgelsky, G.B.
AU  - Tchurikov, N.A.
TI  - IncI1 plasmid R64 encodes the ArsR protein that alleviates type I restriction.
JO  - FEBS Lett.
PY  - 1998
SP  - 21
EP  - 23
VL  - 426
AB  - The host-controlled EcoK restriction of unmodified phage lambda was five-fold alleviated in
AB  - the wild-type Escherichia coli strain K12 carrying the R64 plasmid of the incompatibility
AB  - group I1. The relevant gene was mapped between the origin of vegetative replication (rep,
AB  - oriV) and the tet(r) gene about 60 kbp downstream from the origin of transfer, oriT. We cloned
AB  - this gene inside the 613 bp long EcoRI-PstI fragment and sequenced it. Only one 351 bp long
AB  - open reading frame (ORF) starting at 124 bp from the beginning of the insert was found in the
AB  - sequence. Computer search in the current databases revealed that the putative protein is
AB  - identical to the ArsR protein specified by the IncFI plasmid R773. ArsR is a repressor of the
AB  - arsenical resistance (ars) operon, arsRDABC. There are no arsABC genes in the R64 plasmid
AB  - since plasmid R64- (or pSR8)-mediated resistance of E. coli K12 cells to the arsenicals
AB  - arsenate and arsenite was not detected. The gene arsR and the antirestriction genes ard (ardA
AB  - and ardB) are non-homologous. However, comparison of the deduced amino acid sequence of ArsR
AB  - with the ArdA and ArdB sequences revealed only one small region of similarity, a 9 amino acid
AB  - motif found in different antirestriction proteins that is hypothesized to be an interaction
AB  - site for antirestriction proteins with restriction endonucleases.
ER  -

TY  - JOUR
AU  - Rathert, P.
AU  - Rasko, T.
AU  - Roth, M.
AU  - Slaska-Kiss, K.
AU  - Pingoud, A.
AU  - Kiss, A.
AU  - Jeltsch, A.
TI  - Reversible inactivation of the CG specific Sssl DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group.
JO  - Chembiochem
PY  - 2007
SP  - 202
EP  - 207
VL  - 8
AB  - Caging of proteins by conjugation with a photocleavable group is a powerful approach for
AB  - reversibly blocking enzymatic activity. Here we
AB  - describe the covalent modification of the bacterial Sssl DNA
AB  - methyltransferase (M.Sssl) with the cysteine-specific reagent
AB  - 4,5-dimethoxy-2-nitrobenzyibromide (DMNBB). M.Sssl contains two
AB  - cysteine residues; replacement of the active-site Cys141 with Ser
AB  - resulted in an approximately 700-fold loss of enzymatic activity; this
AB  - indicates an important role for this residue in catalysis. However,
AB  - replacement of Cys368 with Ala did not affect methyltransferase
AB  - activity. Treatment of the Cys368Ala mutant enzyme with DMNBB led to an
AB  - almost complete loss of activity. Irradiation of the inactivated enzyme
AB  - with near-ultraviolet light (320400 nm) restored 60% of the catalytic
AB  - activity. This indicates that caging by DMNBB can be used for the
AB  - reversible inactivation of M.Sssl.
ER  -

TY  - JOUR
AU  - Raven, N.D.H.
AU  - Kelly, C.D.
AU  - Carter, N.D.
AU  - Eastlake, P.
AU  - Brown, C.
AU  - Williams, R.A.D.
TI  - A new restriction endonuclease, TspEI, from the genus Thermus that generates cohesive termini compatible with those of EcoRI.
JO  - Gene
PY  - 1993
SP  - 83
EP  - 86
VL  - 131
AB  - The detection, isolation and properties of the restriction endonuclease TspEI are described.
AB  - The canonical recognition sequence (AATT) is the same as the 4-bp core of the 6-bp sequence
AB  - (GAATTC) of EcoRI. Hydrolysis occurs 5' to the palindromic tetramer so that TspEI produces
AB  - the same cohesive termini as EcoRI. TspEI therefore has an obvious application in producing
AB  - partial digests of DNA for ligation to EcoRI-digested cloning vectors.
ER  -

TY  - JOUR
AU  - Raven, N.D.H.
AU  - Williams, R.A.D.
AU  - Smith, K.E.
AU  - Kelly, C.D.
AU  - Carter, N.D.
TI  - Tsp45I, a new thermostable site-specific endonuclease that cleaves the recognition sequence 5'-GTSAC-3'.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4397
EP  - 4397
VL  - 21
AB  - A site-specific nuclease from Thermus strain 45 was purified by ammonium sulphate
AB  - fractionation and then by chromatography on Phospho-Ultrogel, DEAE-Fractogel 650 M, and
AB  - Sephadex G200 columns. The Mr by gel filtration was 80 kD, and a single band on SDS-PAGE was
AB  - estimated as 38 kD. On the basis of the fragment pattern of digests of pBR322 and phiX174 RF
AB  - DNA< and by reference to reported fragment sizes for these substrates, it was concluded that
AB  - the recognition site was GTSAC. This was confirmed by the identity of Tsp45I patterns with
AB  - those predicted by computer simulations of substrate hydrolysis at this site (kindly provided
AB  - by R.Roberts), and by the agreement between observed and expected fragment sized for digests
AB  - of lambda DNA, M13mp18RF DNA, pHC624 and pUC18. The optimum activity was observed at 65oC in
AB  - 10 mM Tris chloride buffer, pH7.3 at 25oC containing no NaCl, l mM MgCl2, 2 mM dithiothreitol
AB  - and 100 mg/l albumin. The enzyme has a low requirement for inorganic ions, indeed activity was
AB  - detected even when magnesium ions were omitted from the assay buffer. The cleavage points were
AB  - determined by the primed synthesis method from the M13 -40 sequencing primer on a recognition
AB  - site provided by two complementary synthetic oligonucleotides 5'CCGTCGACGTGACGGATCCCC and 5'
AB  - GGGGATCCGTCACGTCGACGG that were annealed together and digested with SalI and BamHI. The
AB  - central fragment that contained the recognition site was ligated into M13mp8 digested with the
AB  - same enzymes and DNA was extracted and purified. The hydrolysis sites of Tsp45I (Figure 1) lie
AB  - outside the recognition site, 5' to the G residues in each strand: 5'^GTGAC-3', 3'-CACTG^5'.
ER  -

TY  - JOUR
AU  - Ravetch, J.V.
AU  - Horiuchi, K.
AU  - Zinder, N.D.
TI  - Nucleotide sequence of the recognition site for the restriction-modification enzyme of Escherichia coli B.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1978
SP  - 2266
EP  - 2270
VL  - 75
AB  - The nucleotide sequence of the recognition site for the restriction-modifiction
AB  - enzyme of Escherichia coli B (SB site) has been determined.  The recognition
AB  - site is a 15-nucleotide sequence consisting of the trimer 5'TGA3', followed by
AB  - an 8-nucleotide domain of variable sequence, which in turn is followed by the
AB  - tetramer 5'TGCT3'.  The sequence has no 2-fold rotational symmetry.  Single
AB  - base changes in the constant nucleotide domains result in the loss of
AB  - sensitivity to both restriction and modification.  Our data are also consistent
AB  - with modification occurring by methylation of two adenine residues per SB site:
AB  - one on the adenine of the trimer 5'TGA3' and the other on the complementary
AB  - strand on the adenine complementary to the first thymine of the tetramer
AB  - 5'TGCT3'.  All nine independently isolated spontaneous mutants at the SB1 site
AB  - of bacteriophage f1 are caused by a C-to-T transversion.  Mutations at the SB2
AB  - site are caused by various single base changes.
ER  -

TY  - JOUR
AU  - Ravi, R.S.
AU  - Sozhamannan, S.
AU  - Dharmalingam, K.
TI  - Transposon mutagenesis and genetic mapping of the rglA and rglB loci of Escherichia coli.
JO  - Mol. Gen. Genet.
PY  - 1985
SP  - 390
EP  - 392
VL  - 198
AB  - The rglA and rglB genes code for two different proteins which cleave the
AB  - hydroxymethylated cytosine residues of T-even phages.  We isolated Tn10 and Tn5
AB  - insertion mutants of the above genes and of the genes in and around the rglA
AB  - and rglB loci.  These insertions were used to cocnstruct a detailed genetic
AB  - map.  Our results show that the rglA gene maps at 25.24 min and the rglB gene
AB  - at 98.39 min on the standard Escherichia coli K12 genetic map.
ER  -

TY  - JOUR
AU  - Ravin, N.V.
AU  - Mardanov, A.V.
AU  - Beletsky, A.V.
AU  - Kublanov, I.V.
AU  - Kolganova, T.V.
AU  - Lebedinsky, A.V.
AU  - Chernyh, N.A.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Skryabin, K.G.
TI  - Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.
JO  - J. Bacteriol.
PY  - 2009
SP  - 2371
EP  - 2379
VL  - 191
AB  - Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon
AB  - isolated from a terrestrial hot spring. Its
AB  - genome consists of a single circular chromosome of 1365223 bp with no
AB  - extrachromosomal elements. A total of 1474 protein-coding genes were
AB  - annotated of which 205 are exclusive for D. kamchatkensis. The search for
AB  - a replication origin site revealed a single region coinciding with a
AB  - global extreme of the nucleotide composition disparity curve and
AB  - containing a set of crenarchaeal-type origin recognition boxes. Unlike in
AB  - most archaea, two genes encoding homologs of eukaryotic initiator proteins
AB  - Orc1/Cdc6 are located distantly from this site. A number of mobile
AB  - elements are present in the genome, including seven transposons
AB  - representing IS607 and IS200/IS605 families, and multiple copies of
AB  - miniature inverted repeat transposable elements. Two large clusters of
AB  - regularly interspaced repeats are present; none of the spacer sequences
AB  - matches with known archaeal extrachromosomal elements except that one
AB  - spacer matches the sequence of a resident gene of D. kamchatkensis. Many
AB  - of the predicted metabolic enzymes are associated with the fermentation of
AB  - peptides and sugars, including more than thirty peptidases with diverse
AB  - specificities, a number of polysaccharide degradation enzymes, and many
AB  - transporters. Consistently, the genome encodes both enzymes of the
AB  - modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes
AB  - needed for gluconeogenesis. The genome structure and content reflect the
AB  - organism's nutritionally diverse, competitive natural environment
AB  - periodically invaded by viruses and other mobile elements.
ER  -

TY  - JOUR
AU  - Ravin, V.
AU  - Raisanen, L.
AU  - Alatossava, T.
TI  - A conserved C-terminal region in Gp71 of the small isometric-head phage LL-H and ORF474 of the prolate-head phage JCL1032 is implicated in  specificity of adsorption of phage to its host, Lactobacillus  delbrueckii.
JO  - J. Bacteriol.
PY  - 2002
SP  - 2455
EP  - 2459
VL  - 184
AB  - Thirty-five phage-resistant mutants of Lactobacillus delbrueckii subsp. lactis ATCC 15808 were
AB  - selected. Thirty-three of these mutants were
AB  - assigned to the Bes group, while the remaining two were grouped under
AB  - the Ads designation. Bes group mutants adsorbed phage LL-H but did not
AB  - allow efficient phage development. Preliminary evidence suggests that
AB  - these strains exhibit a mutation that changes the DNA specificity of a
AB  - restriction-modification system. The Ads group mutants did not adsorb
AB  - the small isometric-head phage LL-H. The results suggest that there are
AB  - at least three different types of phage receptors in L. delbrueckii:
AB  - two that are specific for small isometric-head phages and one that is
AB  - specific for prolate-head phage JCL1032. Five LL-H host-range mutants
AB  - which could overcome the adsorption block (a-type mutants) were
AB  - selected and investigated by sequencing the genes g71 and g17, which
AB  - encode minor and major tail proteins, respectively. Each of the a-type
AB  - mutants carried a nucleotide change at the 3' end of gene g71. No
AB  - mutations were observed in gene g17. Comparison of the gene product of
AB  - g71 of phage LL-H with its homolog in JCL1032 (ORF474) showed that
AB  - these proteins had very similar C-terminal regions. No similarities
AB  - were found at the N-terminal part of the proteins. We conclude that the
AB  - C-terminal portion of the protein encoded by g71 of phage LL-H and its
AB  - homolog in phage JCL1032 determines the adsorption specificities of
AB  - these phages on L. delbrueckii.
ER  -

TY  - JOUR
AU  - Ravin, V.
AU  - Ravin, N.
AU  - Casjens, S.
AU  - Ford, M.E.
AU  - Hatfull, G.F.
AU  - Herdrix, R.W.
TI  - Genomic sequence and analysis of the atypical temperate bacteriophage N15.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 53
EP  - 73
VL  - 299
AB  - N15 is a temperate bacteriophage that forms stable lysogens in Escherichia coli. While its
AB  - virion is morphologically very similar to
AB  - phage lambda and its close relatives, it is unusual in that the
AB  - prophage form replicates autonomously as a linear DNA molecule with
AB  - closed hairpin telomeres. Here, we describe the genomic architecture of
AB  - N15, and its global pattern of gene expression, which reveal that N15
AB  - contains several plasmid-derived genes that are expressed in N15
AB  - lysogens. The tel site, at which processing occurs to form the prophage
AB  - ends is close to the center of the genome in a similar location to that
AB  - occupied by the attachment site, attP, in lambda and its relatives and
AB  - defines the boundary between the left and right arms. The left arm
AB  - contains a long cluster of structural genes that are closely related to
AB  - those of the lambda-like phages, but also includes homologs of umuD',
AB  - which encodes a DNA polymerase accessory protein, and the plasmid
AB  - partition genes, sopA and sopB. The right arm likewise contains a
AB  - mixture of apparently phage- and plasmid-derived genes including genes
AB  - encoding plasmid replication functions, a phage repressor, a
AB  - transcription antitermination system, as well as phage host cell lysis
AB  - genes and two putative DNA methylases. The unique structure of the N15
AB  - genome suggests that the large global population of bacteriophages may
AB  - exhibit a much greater diversity of genomic architectures than was
AB  - previously recognized.
ER  -

TY  - JOUR
AU  - Ravindran, A.
AU  - Jalan, N.
AU  - Yuan, J.S.
AU  - Wang, N.
AU  - Gross, D.C.
TI  - Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.
JO  - Microbiologyopen
PY  - 2015
SP  - 553
EP  - 573
VL  - 4
AB  - Pseudomonas syringae pv. syringae is a common plant-associated bacterium that
AB  - causes diseases of both monocot and dicot plants worldwide. To help delineate
AB  - traits critical to adaptation and survival in the plant environment, we generated
AB  - complete genome sequences of P. syringae pv. syringae strains B301D and HS191,
AB  - which represent dicot and monocot strains with distinct host specificities.
AB  - Intrapathovar comparisons of the B301D (6.09 Mb) and HS191 (5.95 Mb plus a 52 kb
AB  - pCG131 plasmid) genomes to the previously sequenced B728a genome demonstrated
AB  - that the shared genes encompass about 83% of each genome, and include genes for
AB  - siderophore biosynthesis, osmotolerance, and extracellular polysaccharide
AB  - production. Between 7% and 12% of the genes are unique among the genomes, and
AB  - most of the unique gene regions carry transposons, phage elements, or IS elements
AB  - associated with horizontal gene transfer. Differences are observed in the type
AB  - III effector composition for the three strains that likely influences host range.
AB  - The HS191 genome had the largest number at 25 of effector genes, and seven
AB  - effector genes are specific to this monocot strain. Toxin production is another
AB  - major trait associated with virulence of P. syringae pv. syringae, and HS191 is
AB  - distinguished by genes for production of syringopeptin SP25 and mangotoxin.
ER  -

TY  - JOUR
AU  - Rawal, C.M.
AU  - Raval, V.H.
AU  - Bhimani, H.D.
AU  - Bhensdadia, D.V.
AU  - Kothari, C.R.
AU  - Patel, A.B.
AU  - Bhatt, V.D.
AU  - Parmar, N.R.
AU  - Sajnani, M.R.
AU  - Koringa, P.G.
AU  - Joshi, C.G.
AU  - Kothari, R.K.
AU  - Singh, S.P.
TI  - Whole-Genome Shotgun Sequencing of the Extremophile Alkalibacillus haloalkaliphilus C-5, of Indian Origin.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4775
EP  - 4775
VL  - 194
AB  - Alkalibacillus haloalkaliphilus C-5 is a haloalkaliphilic bacterium that was isolated from a
AB  - soil sample from the salty Sambhar Lake, Rajasthan, India. The
AB  - organism is capable of alkaline protease production under conditions of pH 10 and
AB  - 10% (wt/vol) salt. We sequenced and have reported the whole genome of
AB  - Alkalibacillus haloalkaliphilus C-5, of Indian origin, for the first time.
ER  -

TY  - JOUR
AU  - Rawat, S.R.
AU  - Mannisto, M.K.
AU  - Starovoytov, V.
AU  - Goodwin, L.
AU  - Nolan, M.
AU  - Hauser, L.
AU  - Land, M.
AU  - Davenport, K.W.
AU  - Woyke, T.
AU  - Haggblom, M.M.
TI  - Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 59
EP  - 69
VL  - 7
AB  - SP1PR4 is a novel species of the genus . is of ecological interest because it is  a
AB  - representative of the phylum , which are dominant members of bacterial soil
AB  - microbiota in Arctic ecosystems. is a cold-adapted acidophile and a versatile
AB  - heterotroph utilizing a suite of simple sugars and complex polysaccharides. The
AB  - genome contained an abundance of genes assigned to metabolism and transport of
AB  - carbohydrates including gene modules encoding for carbohydrate-active enzyme
AB  - (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse
AB  - structural and storage polysaccharides. SP1PR4 represents the first member of
AB  - genus with a completed genome sequence, consisting of a single replicon of
AB  - 5,095,226 base pairs (bp), 54 RNA genes and 4,279 protein-coding genes. We infer
AB  - that the physiology and metabolic potential of is adapted to allow for resilience
AB  - to the nutrient-deficient conditions and fluctuating temperatures of Arctic
AB  - tundra soils.
ER  -

TY  - JOUR
AU  - Rawat, S.R.
AU  - Mannisto, M.K.
AU  - Starovoytov, V.
AU  - Goodwin, L.
AU  - Nolan, M.
AU  - Hauser, L.
AU  - Land, M.
AU  - Davenport, K.W.
AU  - Woyke, T.
AU  - Haggblom, M.M.
TI  - Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 449
EP  - 461
VL  - 9
AB  - Granulicella tundricola strain MP5ACTX9(T) is a novel species of the genus Granulicella in
AB  - subdivision 1 Acidobacteria. G. tundricola is a predominant
AB  - member of soil bacterial communities, active at low temperatures and nutrient
AB  - limiting conditions in Arctic alpine tundra. The organism is a cold-adapted
AB  - acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and
AB  - complex polysaccharides. Genome analysis revealed metabolic versatility with
AB  - genes involved in metabolism and transport of carbohydrates, including gene
AB  - modules encoding for the carbohydrate-active enzyme (CAZy) families for the
AB  - breakdown, utilization and biosynthesis of diverse structural and storage
AB  - polysaccharides such as plant based carbon polymers. The genome of G. tundricola
AB  - strain MP5ACTX9(T) consists of 4,309,151 bp of a circular chromosome and five
AB  - mega plasmids with a total genome content of 5,503,984 bp. The genome comprises
AB  - 4,705 protein-coding genes and 52 RNA genes.
ER  -

TY  - JOUR
AU  - Rawat, S.R.
AU  - Mannisto, M.K.
AU  - Starovoytov, V.
AU  - Goodwin, L.
AU  - Nolan, M.
AU  - Hauser, L.J.
AU  - Land, M.
AU  - Davenport, K.W.
AU  - Woyke, T.
AU  - Haggblom, M.M.
TI  - Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 71
EP  - 82
VL  - 9
AB  - Granulicella mallensis MP5ACTX8(T) is a novel species of the genus Granulicella in subdivision
AB  - 1of Acidobacteria. G. mallensis is of ecological interest being a
AB  - member of the dominant soil bacterial community active at low temperatures and
AB  - nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a
AB  - cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of
AB  - sugars and complex polysaccharides. Genome analysis revealed metabolic
AB  - versatility with genes involved in metabolism and transport of carbohydrates.
AB  - These include gene modules encoding the carbohydrate-active enzyme (CAZyme)
AB  - family involved in breakdown, utilization and biosynthesis of diverse structural
AB  - and storage polysaccharides including plant based carbon polymers. The genome of
AB  - Granulicella mallensis MP5ACTX8(T) consists of a single replicon of 6,237,577
AB  - base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes.
ER  -

TY  - JOUR
AU  - Ray, J.
AU  - Waters, R.J.
AU  - Skerker, J.M.
AU  - Kuehl, J.V.
AU  - Price, M.N.
AU  - Huang, J.
AU  - Chakraborty, R.
AU  - Arkin, A.P.
AU  - Deutschbauer, A.
TI  - Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.
JO  - Genome Announcements
PY  - 2015
SP  - e00322
EP  - e00315
VL  - 3
AB  - Cupriavidus basilensis 4G11 was isolated from groundwater at the Oak Ridge Field  Research
AB  - Center (FRC) site. Here, we report the complete genome sequence and
AB  - annotation of Cupriavidus basilensis 4G11. The genome contains 8,421,483 bp,
AB  - 7,661 predicted protein-coding genes, and a total GC content of 64.4%.
ER  -

TY  - JOUR
AU  - Raychaudhuri, S.
AU  - Saha, A.
AU  - Ghoshal, T.
AU  - Thakur, A.R.
TI  - Draft Genome Sequence of Ammonia-Producing Aeromonas sp. MDS8 Strain MCC2167 from Sludge of a Dairy Effluent Treatment Plant.
JO  - Genome Announcements
PY  - 2013
SP  - e00710
EP  - e00713
VL  - 1
AB  - The draft genome sequence of an amylase-, protease-, lipase-, oxidase-, and catalase-producing
AB  - Gram-negative bacillus (Aeromonas sp. MDS8 strain MCC2167)
AB  - with the ability to produce ammonia during 16 h of growth at 37 degrees C,
AB  - isolated from dairy sludge, with a size of 4,841,753 bp and a G+C content of
AB  - 63.1%, is reported here.
ER  -

TY  - JOUR
AU  - Raygoza-Garay, J.A.
AU  - Hughes, G.L.
AU  - Koundal, V.
AU  - Rasgon, J.L.
AU  - Mwangi, M.M.
TI  - Genome Sequence of Elizabethkingia anophelis Strain EaAs1, Isolated from the Asian Malaria Mosquito Anopheles stephensi.
JO  - Genome Announcements
PY  - 2016
SP  - e00084
EP  - e00016
VL  - 4
AB  - We sequenced the genome of a strain of the Gram-negative bacterial species Elizabethkingia
AB  - anophelis, which is an important component of the Anopheles mosquito microbiome. This genome
AB  - sequence will add to the list of resources used to examine host-microbe interactions in
AB  - mosquitoes.
ER  -

TY  - JOUR
AU  - Rayyan, A.A.
AU  - Meyer, T.E.
AU  - Kyndt, J.A.
TI  - Draft Genome Sequence and Brief History of Rhodovulum sp. Strain BSW8.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00983
EP  - e00918
VL  - 7
AB  - Rhodovulum is a marine Gram-negative purple photosynthetic bacterial genus that is a member of
AB  - the Alphaproteobacteria. Strain BSW8 is a variant that does not
AB  - appear to make a polysaccharide slime capsule, and its genome sequence further
AB  - contributes to the diversity of sequenced genomes belonging to this genus.
ER  -

TY  - JOUR
AU  - Razin, A.
TI  - Methylated bases in the single-stranded DNA phages.
JO  - The Single-Stranded DNA Phages
PY  - 1978
SP  - 165
EP  - 175
VL  - 0
AB  - The widespread occurrence of methylated bases in the DNA of living organisms and the
AB  - species-specific pattern of DNA methylation (Hall 1971) strongly suggest that these methyl
AB  - groups play an important biological role.  At the present time, however, few biological
AB  - processes can be correlated with methylated bases in DNA.  Most of the methylated bases in the
AB  - bacterial chromosome are not related to the modificatiton activity in these cells, since
AB  - bacteria that are devoid of a restriction-modification (R-M) system still methylate their own
AB  - DNA.  The function of these methyl groups, as well as of those found in eukaryotic cell DNA,
AB  - is obscure.  The single-stranded DNA bacteriophages, which possess a few methyl groups per
AB  - genome, are ideal tools for studying the role of DNA methylation.  Thus, the filamentous
AB  - bacteriophages f1, fd, and M13 have been investigated with respect to the function of the
AB  - methylated bases in the R-M phenomena (Arber 1968).  The isometric phage PhiX174, which is not
AB  - subject to R-M and is propagated in Escherichia coli C, a strain devoid of any known R-M
AB  - system, was chosen to study the role of methylated bases not related to R-M.  A single methyl
AB  - group has been found in the PhiX genome and it has been suggested that this group is essential
AB  - in the final stages of phage maturation.
ER  -

TY  - JOUR
AU  - Razin, A.
TI  - DNA methylases.
JO  - Genet. Eng. (N Y)
PY  - 1989
SP  - 1
EP  - 11
VL  - 11
AB  - A review.
ER  -

TY  - JOUR
AU  - Razin, A.
AU  - Friedman, J.
TI  - DNA methylation and its possible biological roles.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 1981
SP  - 33
EP  - 52
VL  - 25
AB  - Bases modified by methylation have been known to occur at a low frequency in DNA for more than
AB  - three decades.  This modification of DNA is carried out by specific methyltransferases (DNA
AB  - methylases) that transfer the chemically active methyl group from S-adenosylmethionine
AB  - (AdoMet) to either carbon 5 of cytosine residues or the exocyclic amino group attached to
AB  - carbon 6 of adenine residues of the DNA chain.
AB  - I. Introduction.
AB  - II.  Methylases and their specificity.
AB  - A. Substrate specificity.
AB  - B. Sequence specificity.
AB  - III. Distribution of methylated bases along the chromosome.
AB  - A. Distribution with respect to DNA sequences.
AB  - B. Distribution with respect to chromosomal proteins.
AB  - C. Distribution with respect to chromosome ultrastructure.
AB  - D. Methylated and unmethylated domains.
AB  - IV. The mode of methylation in vivo.
AB  - A. Semiconservative methylation.
AB  - B. DeNovo methylation.
AB  - C. "Origins" of methylation.
AB  - V. Possible functions of methylated bases in DNA.
AB  - A. Cell differentiation and gene activity.
AB  - B. Restriction and modification.
AB  - C. Interplay between DNA replication and methylation.
AB  - D. Mutation, recombination, and repair.
AB  - VI. Conclusions and prospects. References.
ER  -

TY  - JOUR
AU  - Razin, A.
AU  - Goren, D.
AU  - Friedman, J.
TI  - Studies on the biological role of DNA methylation:  inhibition of methylation and maturation of the bacteriophage PhiX174 by nicotinamide.
JO  - Nucleic Acids Res.
PY  - 1975
SP  - 1967
EP  - 1974
VL  - 2
AB  - Nicotinamide was found to be a potent inhibitor of DNA methylation in vivo without
AB  - interferring with protein or DNA synthesis.  The inhibition of DNA methylation in a
AB  - phage-infected cell resulted in a parallel decrease in the production of viable virus
AB  - particles.  In vitro experiments revealed that nicotinamide inhibits DNA methylase activity in
AB  - a competitive fashion with respect to S-adenosylmethionine and non-competitively with respect
AB  - to DNA. These results were interpreted to mean that DNA methylation is an essential step in
AB  - the process of maturation of the bacteriophage PhiChi174.
ER  -

TY  - JOUR
AU  - Razin, A.
AU  - Razin, S.
TI  - Methylated bases in mycoplasmal DNA.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 1383
EP  - 1390
VL  - 8
AB  - The DNAs of four Mycoplasma and one Acholeplasma species were found to contain methylated
AB  - bases.  All of the five species contained 6-methyladenine (m6Ade), the methylated base
AB  - characteristic of prokaryotic DNA.  The extent of methylation of adenine residues in the
AB  - mycoplasmal DNA ranged from 0.2% in Mycoplasma capricolum to about 2% in Mycoplasma arginini
AB  - and Mycoplasma hyorhinis with intermediate methylation values for Mycoplasma orale and
AB  - Acholeplasma laidlawii DNAs.  About 5.8% of the cytosine residues in M. hyorhinis DNA were
AB  - methylated also.  Analysis of cell culture DNA for the presence of m6Ade as a means for
AB  - detection of contamination by mycoplasmas, and the phylogenetic implications of the finding of
AB  - methylated bases in mycoplasmal DNAs are discussed.
ER  -

TY  - JOUR
AU  - Razin, A.
AU  - Riggs, D.
TI  - DNA methylation and gene function.
JO  - Science
PY  - 1980
SP  - 604
EP  - 610
VL  - 210
AB  - In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many
AB  - cytosine residues to 5-methylcytosine.  For several years, control of gene activity by DNA
AB  - methylation has been recognized as a logically attractive possibility, but experimental
AB  - support has proved elusive.  However, there is now reason to believe, from recent studies,
AB  - that DNA methylation is a key element in the hierarchy of control mechanisms that govern
AB  - vertebrate gene function and differentiation.
ER  -

TY  - JOUR
AU  - Razin, A.
AU  - Sedat, J.
TI  - Analysis of 5-methylcytosine in DNA.
JO  - Anal. Biochem.
PY  - 1977
SP  - 370
EP  - 377
VL  - 77
AB  - A method for analyzing 5-methylcytosine in DNA by gas chromatography is described.  The method
AB  - is based on degradation of the DNA to its free bases by treatment with trifluoroacetic acid
AB  - and gas chromatography of the trimethylsilyl derivatives of the free bases.  Chromatography of
AB  - microgram amounts of derivatized material is conducted at isothermal conditions using a 3%
AB  - SE-30 or 2% OV-225 column.  The peak areas corresponding to cytosine and 5-methylcytosine are
AB  - used to calculate the 5-methylcytosine/cytosine molar ratio in DNA.  The lower limit for
AB  - detection of 5-methylcytosine in DNA by this method is a 5-methylcytosine/cytosine molar ratio
AB  - of 0.001.
ER  -

TY  - JOUR
AU  - Razin, A.
AU  - Urieli, S.
AU  - Pollack, Y.
AU  - Gruenbaum, Y.
AU  - Glaser, G.
TI  - Studies on the biological role of DNA methylation; IV.  Mode of methylation of DNA in E. coli cells.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 1783
EP  - 1792
VL  - 8
AB  - Two pairs of restriction enzyme isoschizomers were used to study in vivo
AB  - methylation of E. coli and extrachromosomal DNA.  By use of the restriction
AB  - enzymes MboI (which cleaves only the unmethylated GATC sequence) and its
AB  - isoschizomer Sau3A (indifferent to a methylated adenine at this sequence), we
AB  - found that all the GATC sites in E. coli and in extrachromosomal DNAs are
AB  - symmetrically methylated on both strands.  The calculated number of GATC sites
AB  - in E. coli DNA can account for all its m6Ade residues.  Foreign DNA, like mouse
AB  - mtDNA, which is not methylated at GATC sites became fully methylated at these
AB  - sequences when introduced by transfection into E. coli cells.  This experiment
AB  - provides the first evidence for the operation of a de novo methylation
AB  - mechanism for E. coli methylases not involved in restriction modification.
AB  - When the two restriction enzyme isoschizomers, EcoRII and ApyI, were used to
AB  - analyze the methylation pattern of CCA/TGG sequences in E. coli C and PhiX174
AB  - DNA, it was found that all these sites are methylated.  The number of CCA/TGG
AB  - sites in E. coli C DNA does not account for all m5Cyt residues.
ER  -

TY  - JOUR
AU  - Read, T.D. et al.
TI  - Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 1397
EP  - 1406
VL  - 28
AB  - The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412
AB  - nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun
AB  - strategy. The MoPn genome exhibited a general conservation of gene order and content with the
AB  - previously sequenced C. trachomatis serovar D. Differences between C. trachomatis strains were
AB  - focused on an ~50 kb 'plasticity zone' near the termination origins. In this region MoPn
AB  - contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a
AB  - predicted toxin from Escherichia coli 0157:H7 but had apparently lost the tryptophan
AB  - biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was
AB  - >99.9% identical to the previously sequenced C. pneumoniae CWL029 genome, however, comparative
AB  - analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in
AB  - different orientations in the two genomes. AR39 also contained a novel 4524 nt circular
AB  - single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C.
AB  - pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing
AB  - differences in key nucleotide salvage pathways: C. pneumoniae has a uridine kinase gene for
AB  - dUTP production, MoPn has a uracil phosphororibosyl transferase, while C. trachomatis serovar
AB  - D contains neither gene. Chromosomal comparison revealed that there had been multiple large
AB  - inversion events since the species divergence of C. trachomatis and C. pneumoniae, apparently
AB  - oriented around the axis of the origin of replication and the termination region. The striking
AB  - synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of
AB  - minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological
AB  - isolation of the obligate intracellular parasites. In the absence of genetic analysis,
AB  - comparative genomics will continue to provide insight into the virulence mechanisms of these
AB  - important human pathogens.
ER  -

TY  - JOUR
AU  - Read, T.D. et al.
TI  - Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the   Chlamydiaceae.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 2134
EP  - 2147
VL  - 31
AB  - The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt
AB  - with a plasmid of 7966 nt) was determined,
AB  - representing the fourth species with a complete genome sequence from the
AB  - Chlamydiaceae family of obligate intracellular bacterial pathogens. Of
AB  - 1009 annotated genes, 798 were conserved in all three other completed
AB  - Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack
AB  - orthologs in any other completed chlamydial genomes, including tryptophan
AB  - and thiamine biosynthesis determinants and a ribose-phosphate
AB  - pyrophosphokinase, the product of the prsA gene. Notable amongst these was
AB  - a novel member of the virulence-associated invasin/intimin family (IIF) of
AB  - Gram-negative bacteria. Intriguingly, two authentic frameshift mutations
AB  - in the ORF indicate that this gene is not functional. Many of the unique
AB  - genes are found in the replication termination region (RTR or plasticity
AB  - zone), an area of frequent symmetrical inversion events around the
AB  - replication terminus shown to be a hotspot for genome variation in
AB  - previous genome sequencing studies. In C.caviae, the RTR includes several
AB  - loci of particular interest including a large toxin gene and evidence of
AB  - ancestral insertion(s) of a bacteriophage. This toxin gene, not present in
AB  - Chlamydia pneumoniae, is a member of the YopT effector family of type
AB  - III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR
AB  - is much more similar to orthologs in Chlamydia muridarum than those in the
AB  - phylogenetically closest species C.pneumoniae, suggesting the possibility
AB  - of horizontal transfer of genes between the rodent-associated Chlamydiae.
AB  - With most genes observed in the other chlamydial genomes represented,
AB  - C.caviae provides a good model for the Chlamydiaceae and a point of
AB  - comparison against the human atherosclerosis-associated C.pneumoniae. This
AB  - crucial addition to the set of completed Chlamydiaceae genome sequences is
AB  - enabling dissection of the roles played by niche-specific genes in these
AB  - important bacterial pathogens.
ER  -

TY  - JOUR
AU  - Read, T.D. et al.
TI  - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.
JO  - Nature
PY  - 2003
SP  - 81
EP  - 86
VL  - 423
AB  - Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key
AB  - virulence genes are found on plasmids
AB  - (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2)
AB  - and pXO2 (ref. 3). To identify additional genes that might contribute to
AB  - virulence, we analysed the complete sequence of the chromosome of B.
AB  - anthracis Ames (about 5.23 megabases). We found several chromosomally
AB  - encoded proteins that may contribute to pathogenicity--including
AB  - haemolysins, phospholipases and iron acquisition functions--and identified
AB  - numerous surface proteins that might be important targets for vaccines and
AB  - drugs. Almost all these putative chromosomal virulence and surface
AB  - proteins have homologues in Bacillus cereus, highlighting the similarity
AB  - of B. anthracis to near-neighbours that are not associated with anthrax.
AB  - By performing a comparative genome hybridization of 19 B. cereus and
AB  - Bacillus thuringiensis strains against a B. anthracis DNA microarray, we
AB  - confirmed the general similarity of chromosomal genes among this group of
AB  - close relatives. However, we found that the gene sequences of pXO1 and
AB  - pXO2 were more variable between strains, suggesting plasmid mobility in
AB  - the group. The complete sequence of B. anthracis is a step towards a
AB  - better understanding of anthrax pathogenesis.
ER  -

TY  - JOUR
AU  - Read, T.D.
AU  - Salzberg, S.L.
AU  - Pop, M.
AU  - Shumway, M.
AU  - Umayam, L.
AU  - Jiang, L.
AU  - Holtzapple, E.
AU  - Busch, J.D.
AU  - Smith, K.L.
AU  - Schupp, J.M.
AU  - Solomon, D.
AU  - Keim, P.
AU  - Fraser, C.M.
TI  - Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.
JO  - Science
PY  - 2002
SP  - 2028
EP  - 2033
VL  - 296
AB  - Comparison of the whole-genome sequence of Bacillus anthracis isolated from a victim of a
AB  - recent bioterrorist anthrax attack with a reference
AB  - reveals 60 new markers that include single nucleotide polymorphisms
AB  - (SNPs), inserted or deleted sequences, and tandem repeats. Genome
AB  - comparison detected four high-quality SNPs between the two sequenced B.
AB  - anthracis chromosomes and seven differences among different preparations
AB  - of the reference genome. These markers have been tested on a collection of
AB  - anthrax isolates and were found to divide these samples into distinct
AB  - families. These results demonstrate that genome-based analysis of
AB  - microbial pathogens will provide a powerful new tool for investigation of
AB  - infectious disease outbreaks.
ER  -

TY  - JOUR
AU  - Read, T.D.
AU  - Thomas, A.T.
AU  - Wilkins, B.M.
TI  - Evasion of type I and type II DNA restriction systems by IncI1 plasmid Collb-P9 during transfer by bacterial conjugation.
JO  - Mol. Microbiol.
PY  - 1992
SP  - 1933
EP  - 1941
VL  - 6
AB  - Transmission of unmodified plasmid CoIIb-P9 by bacterial conjugation is markedly resistant to
AB  - restriction compared with transfer by transformation. One process allowing evasion of type I
AB  - and II restriction systems involves conjugative transfer of multiple copies of the plasmid. A
AB  - more specialized evasion mechanism requires the Ard (alleviation of restriction of DNA) system
AB  - encoded by CoIIb. The ard gene is transferred early in conjugation and specifically alleviates
AB  - DNA restriction by all known families of type I enzyme, including EcoK.  CoIIb has no effect
AB  - on EcoK modification but this activity is impaired by multicopy recombinant plasmids
AB  - supporting overexpression of ard. Genetic evidence shows that Ard protects CoIIb from EcoK
AB  - restriction following conjugative transfer and that this protection requires expression of the
AB  - gene on the immigrant plasmid. It is proposed that carriage of ard facilitates transfer of
AB  - CoIIb between its natural enterobacterial hosts and that the route of DNA entry is important
AB  - to the restriction-evasion mechanism.
ER  -

TY  - JOUR
AU  - Reale, A.
AU  - Lindsay, H.
AU  - Saluz, H.P.
AU  - Pradhan, S.
AU  - Adams, R.L.P.
AU  - Jost, J.-P.
AU  - Strom, R.
TI  - DNA binding and methyl transfer catalysed by mouse DNA methyltransferase.
JO  - Biochem. J.
PY  - 1995
SP  - 855
EP  - 861
VL  - 312
AB  - By using a purified fraction of mouse DNA methyltransferase we have shown, by gel-retardation
AB  - analysis, that the enzyme forms a low-affinity complex preferentially with hemimethylated DNA;
AB  - the complexes formed with unmethylated or with fully methylated DNA are of even lower
AB  - affinity, and only very weak interaction occurs with DNA lacking CG dinucleotides.
AB  - Interaction is inhibited by N-ethylmaleimide.  Methyl transfer from S-adenosyl-methionine is
AB  - associated with the release of the fully methylated product from the complex.  Complexes
AB  - formed with the intact enzyme are extremely large, but limited trypsin treatment allows a
AB  - major complex to enter the gel.  DNA binding is not inhibited by this limited proteolysis of
AB  - the native enzyme.
ER  -

TY  - JOUR
AU  - Reaston, J.
AU  - Duyvesteyn, M.G.C.
AU  - de Waard, A.
TI  - Nostoc PCC7524, a cyanobacterium which contains five sequence-specific deoxyribonucleases.
JO  - Gene
PY  - 1982
SP  - 103
EP  - 110
VL  - 20
AB  - Five nucleotide sequence-specific deoxyribonucleases present in cell-free
AB  - extracts of the filamentous cyanobacterium Nostoc PCC7524 have been purified
AB  - and characterized.  One of these enzymes, designated Nsp(7524)I cleaves at a
AB  - new kind of nucleotide sequence, i.e. 5'-PuCATG^Py-3'.  The other four
AB  - restriction enzymes in this organism, designated Nsp(7524)II, Nsp(7524)III,
AB  - Nsp(7524)IV and Nsp(7524)V, are isoschizomers of enzymes which have been
AB  - previously described.  The cleavage site of Nsp(7524)II which is an
AB  - isoschizomer of SduI was determined.
ER  -

TY  - JOUR
AU  - Rebentish, B.A.
AU  - Bolotin, A.P.
AU  - Grachova, I.M.
AU  - Ren, L.S.
AU  - Uyan, J.M.
TI  - A new site-specific endodeoxyribonuclease FmuI from the strain Flavobacterium multivorum.
JO  - Biotekhnologiya
PY  - 1994
SP  - 15
EP  - 16
VL  - 3
AB  - A new site-specific endodeoxyribonuclease (restrictase) has been isolated from the strain
AB  - Flavobacterium multivorum and some of its characteristics were examined. It was named FmuI and
AB  - shown to determine the following nucleotide sequence: 5'-GGNC/C-3'. The new restrictase
AB  - turned out to be a false isoschizomer (or an alternative prototype) of the enzyme AsuI.
ER  -

TY  - JOUR
AU  - Rech, G.
AU  - Vilaplana, C.
AU  - Velasco, J.
AU  - Pluvinet, R.
AU  - Santin, S.
AU  - Prat, C.
AU  - Julian, E.
AU  - Alcaide, F.
AU  - Comas, I.
AU  - Sumoy, L.
AU  - Cardona, P.J.
TI  - Draft Genome Sequences of Mycobacterium setense Type Strain DSM-45070 and the Nonpathogenic Strain Manresensis, Isolated from the Bank of the Cardener River in  Manresa, Catalonia, Spain.
JO  - Genome Announcements
PY  - 2015
SP  - e01485
EP  - e01414
VL  - 3
AB  - We present here the draft genome sequences of two Mycobacterium setense strains.  One of them
AB  - corresponds to the M. setense type strain DSM-45070, originally
AB  - isolated from a patient with a posttraumatic chronic skin abscess. The other one
AB  - corresponds to the nonpathogenic M. setense strain Manresensis, isolated from the
AB  - Cardener River crossing Manresa, Catalonia, Spain. A comparative genomic analysis
AB  - shows a smaller genome size and fewer genes in M. setense strain Manresensis
AB  - relative to those of the type strain, and it shows the genome segments unique to
AB  - each strain.
ER  -

TY  - JOUR
AU  - Rechkunova, N.I.
AU  - Lokhov, S.G.
AU  - Gorbunov, Y.A.
AU  - Zinovev, V.V.
AU  - Buryanov, Y.I.
AU  - Malygin, E.G.
TI  - Stability of the secondary structure of the oligonucleotide substrates.  The effect of Ecodam DNA-methylase.
JO  - Biopol. Kletka
PY  - 1989
SP  - 43
EP  - 49
VL  - 5
AB  - Oligonucleotide complexes containing various defects in the Ecodam methylase recognition site
AB  - have been investigated for their stability. A partial duplex structure for the single-stranded
AB  - 20-base long oligonucleotide containing a self-complementary hexanucleotide sequence is
AB  - observed only below 5C. Other complexes melt within the narrow temperature range of 22-31C in
AB  - 30 mM of potassium-phosphate buffer, pH 7.8. The presence of the Ecodam methylase results in
AB  - an increase of the melting point of the complex at least by 5C.
ER  -

TY  - JOUR
AU  - Rechkunova, N.I.
AU  - Ovetchkina, L.G.
AU  - Jashina, L.N.
AU  - Vtorushina, I.A.
AU  - Gorbunov, J.A.
AU  - Zinoviev, V.V.
AU  - Malygin, E.G.
TI  - Effects of oligonucleotide structure on the kinetic values of the interaction with BamHI endonuclease.
JO  - Mol. Biol. (Mosk)
PY  - 1988
SP  - 217
EP  - 223
VL  - 22
AB  - Kinetic values of the BamHI endonuclease interaction with synthetic oligonucleotides,
AB  - containing some defects, have been determined.  These defects were: the absence of the one
AB  - internucleotide phosphate in the GGATCC sequence; substitution of a phosphate linkage by a
AB  - methylphosphonate one; 5'-protruding end of the double-stranded oligonucleotide substrate.
AB  - Some modifications resulted in the increase of the initial rates of cleavage due to higher
AB  - Vmax values for these substrates.  Several structural defects in the oligonucleotide
AB  - substrates have been shown to intensify the formation of productive complexes with the enzyme,
AB  - which can be explained by the significant role of the polynucleotide chain kinds in the
AB  - recognition process.  Studies on oligonucleotides with different defects made it possible to
AB  - reveal the phosphate groups essential for the interaction with BamHI endonuclease.
ER  -

TY  - JOUR
AU  - Rechkunova, N.I.
AU  - Zinovev, V.V.
AU  - Malygin, E.G.
AU  - Gorbunov, Y.A.
AU  - Popov, S.G.
AU  - Nesterenko, V.F.
AU  - Buryanov, Y.I.
TI  - Dimerization of Ecodam-methylase induced by the oligonucleotide substrate.
JO  - Biopol. Kletka
PY  - 1987
SP  - 152
EP  - 154
VL  - 3
AB  - The Ecodam-methylase has been investigated for its interaction with the 20-base
AB  - oligonucleotide duplex containing the enzyme recognition site. An increase of the enzyme
AB  - molecular weight was detected by the gel-filtration and sucrose density gradient
AB  - centrifugation methods. The maximal value of the complex molecular weight was observed when
AB  - concentrations of the enzyme and the substrate were equal. The results obtained prove the
AB  - formation of the dimeric enzyme form in the presence of the substrate.
ER  -

TY  - JOUR
AU  - Reckmann, B.
AU  - Krauss, G.
TI  - The cleavage of single-stranded DNA by the isoschizomeric restriction endonuclease HhaI and CfoI.
JO  - Biochim. Biophys. Acta
PY  - 1987
SP  - 90
EP  - 96
VL  - 908
AB  - The cleavage of single-stranded (ss) M13mp8(+) DNA by the isoschizomeric restriction
AB  - endonucleases HhaI and CfoI has been investigated.  The two enzymes differ considerably in
AB  - their ability to cleave ssDNA.  HhaI cleaves ssDNA about two orders of magnitude faster than
AB  - does CfoI, although both enzymes show the same activity when assayed on double-stranded DNA.
AB  - From the cleavage of oligonucleotides and of M13mp8(+) DNA fragments it is concluded that
AB  - cleavage of ssDNA occurs via transiently formed double-stranded hairpin structures.  A rough
AB  - correlation exists between the stability of the secondary structures and the cleavage
AB  - efficiency.
ER  -

TY  - JOUR
AU  - Recktenwald, J.
AU  - Schmidt, H.
TI  - The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is Conserved.
JO  - Infect. Immun.
PY  - 2002
SP  - 1896
EP  - 1908
VL  - 70
AB  - In this study we determined the complete nucleotide sequence of Shiga
AB  - toxin 2e-encoding bacteriophage phi P27, isolated from the Shiga
AB  - toxin-producing Escherichia coli patient isolate 2771/97. phi P27 is
AB  - integrated as a prophage in the chromosomal yecE gene. This integration
AB  - generates identity segments of attL and attR sites with lengths of 11
AB  - nucleotides. The integrated prophage genome has a size of 42,575 bp. We
AB  - identified 58 open reading frames (ORFs), each with a length of >150
AB  - nucleotides. The deduced proteins of 44 ORFs showed significant homologies
AB  - to other proteins present in sequence databases, whereas 14 putative
AB  - proteins did not. For 29 proteins, we could deduce a putative function.
AB  - Most of these are related to the basic phage propagation cycle. The phi
AB  - P27 genome represents a mosaic composed of genetic elements which are
AB  - obviously derived from related and unrelated phages. We identified five
AB  - short linker sequences of 22 to 151 bp in the phi P27 sequence which have
AB  - also been detected in a couple of other lambdoid phages. These linkers are
AB  - located between functional modules in the phage genome and are thought to
AB  - play a role in genetic recombination. Although the overall DNA sequence of
AB  - phi P27 is not highly related to other known phages, the data obtained
AB  - demonstrate a typical lambdoid genome structure.
ER  -

TY  - JOUR
AU  - Redaschi, N.
AU  - Bickle, T.A.
TI  - Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 790
EP  - 803
VL  - 257
AB  - Efficient establishment of a DNA restriction-modification (R-M) system in a non-modified cell
AB  - requires a tight control of the potentially lethal activity of the restriction enzyme.  The
AB  - type III R-M systems EcoP1I and EcoP15I can be transferred to non-modified Escherichia coli
AB  - cells by transfection, conjugation or transformation and become established without
AB  - difficulty.  Modification activity is expressed immediately after the R-M genes enter the
AB  - cell, whereas the expression of restriction activity is delayed until complete protection of
AB  - the cellular DNA is achievedby methylation.  We have shown by Western blot analysis that the
AB  - expression of the modification polypeptide subunit positively regulates the amount of
AB  - restriction subunit present in the cell.  The finding that ribosomal alterations affected the
AB  - expression of restriction activity pointed to additional control at the translational level.
AB  - The analysis of EcoP1I expression in E. coli strains mutated in either of the ribosomal
AB  - proteins S12 (rpsL) or S4 (rpsD) suggests that the level of in vivo restriction activity can
AB  - be modulated both by a decrease in the efficiency of translation and by varying ribosomal
AB  - accuracy conditions.  In addition, we have preliminary evidence from in vivo gene fusion
AB  - studies that the res gene may code for more than one gene product.
ER  -

TY  - JOUR
AU  - Redaschi, N.
AU  - Bickle, T.A.
TI  - DNA restriction and modification systems.
JO  - Escherichia coli and Salmonella: Cellular and Molecular Biology
PY  - 1996
SP  - 773
EP  - 781
VL  - 1
AB  - The phenomenon of restriction and modification was first observed in the course of studies on
AB  - bacterial viruses in the early 1950s.  Several authors reported that certain strains of
AB  - bacteria inhibited ("restricted") the growth of bacterial viruses previously propagated on a
AB  - different strain.  The molecular explanation for this effect was discovered in the early
AB  - 1960s: the restriction of viral growth was due to endonucleolytic cleavage of the viral DNA by
AB  - site-specific endonucleases.  Some of these restriction endonucleases were found to possess
AB  - very useful properties, and their subsequent exploitation in the 1970s was the key to the
AB  - development of genetic engineering technology.
ER  -

TY  - JOUR
AU  - Reddy, G.S.
AU  - Ara, S.
AU  - Singh, A.
AU  - Kumar, P.A.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of Psychrobacter aquaticus Strain CMS 56T, Isolated from a  Cyanobacterial Mat Sample Collected from Water Bodies in the McMurdo Dry Valley  Region of Antarctica.
JO  - Genome Announcements
PY  - 2013
SP  - e00918
EP  - e00913
VL  - 1
AB  - We report the 3.2-Mb draft genome sequence of Psychrobacter aquaticus strain CMS  56(T),
AB  - isolated from a cyanobacterial mat sample collected from a water body in
AB  - the McMurdo Dry Valley region of Antarctica.
ER  -

TY  - JOUR
AU  - Reddy, G.S.
AU  - Sreenivas, A.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of Cryobacterium roopkundensis Strain RuGl7, Isolated from  a Soil Sample in the Vicinity of Roopkund Lake, Himalayas, India.
JO  - Genome Announcements
PY  - 2014
SP  - e01206
EP  - e01214
VL  - 2
AB  - We report the 4.36-Mb genome of Cryobacterium roopkundensis strain RuGl7, isolated from a soil
AB  - sample collected in the periphery of Roopkund Lake, Himalayas, India. The draft genome
AB  - consists of 4,356,863 bp, 4,048 protein-coding sequences, and 50 RNAs, with 65.3% G+C DNA
AB  - content.
ER  -

TY  - JOUR
AU  - Reddy, Y.V.
AU  - Rao, D.N.
TI  - Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 597
EP  - 610
VL  - 298
AB  - EcoP15I DNA methyltransferase, a member of the type III restriction-modification system, binds
AB  - to the sequence 5'-CAGCAG-3' transferring a methyl group from S-adenosyl-l-methionine to the
AB  - second adenine base. We have investigated protein-DNA interactions in the methylase-DNA
AB  - complex by three methods. Determination of equilibrium dissociation constants indicated that
AB  - the enzyme had higher affinity for DNA containing mismatches at the target base within the
AB  - recognition sequence. Potassium permanganate footprinting studies revealed that there was a
AB  - hyper-reactive permanganate cleavage site coincident with adenine that is the target base for
AB  - methylation. More importantly, to detect DNA conformational alterations within the enzyme-DNA
AB  - complexes, we have used a fluorescence-based assay. When EcoP15I DNA methyltransferase bound
AB  - to DNA containing 2-aminopurine substitutions within the cognate sequence, an eight to tenfold
AB  - fluorescent enhancement resulting from enzymatic flipping of the target adenine base was
AB  - observed. Furthermore, fluorescence spectroscopy analysis showed that the changes attributable
AB  - to structural distortion were specific for only the bases within the recognition sequence.
AB  - More importantly, we observed that both the adenine bases in the recognition site appear to be
AB  - structurally distorted to the same extent. While the target adenine base is probably flipped
AB  - out of the DNA duplex, our results also suggest that fluorescent enhancements could be derived
AB  - from protein-DNA interactions other than base flipping. Taken together, our results support
AB  - the proposed base flipping mechanism for adenine methyltransferases.
ER  -

TY  - JOUR
AU  - Reddy, Y.V.R.
AU  - Rao, D.N.
TI  - Probing the role of cysteine residues in the EcoP15I DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 23866
EP  - 23876
VL  - 273
AB  - Chemical modification using thiol-directed agents and site-directed mutagenesis has been used
AB  - to investigate the role of cysteine residues of EcoP15I DNA methyltransferase.  Irreversible
AB  - inhibition of enzymatic activity was provoked by chemical modification of the enzyme by
AB  - N-ethylmaleimide and iodoacetamide.  5,5'-Dithiobis(2-nitrobenzoic acid) titration of the
AB  - enzyme under nondenaturing and denaturing conditions confirmed the presence of six cysteine
AB  - residues without any disulfides in the protein.  Aware that relatively bulky reagents
AB  - inactivate the methyltransferase by directly occluding the substrate-binding site or by
AB  - locking the methyltransferase in an inactive conformation, we used site-directed mutagenesis
AB  - to sequentially replace each of the six cysteines in the protein at positions 30, 213, 344,
AB  - 434, 553, and 577.  All the resultant mutation methylases except for the C344S and C344A
AB  - enzymes retained significant activity as assessed by in vivo and in vitro assays.  The effects
AB  - of the substitutions on the function of EcoP15I DNA methyltransferase were investigated by
AB  - substrate binding assays, activity measurements, and steady-state kinetic analysis of
AB  - catalysis.  Our results clearly indicate that the cysteines at positions other than 344 are
AB  - not essential for activity.  In contrast, the C344A enzyme showed a marked loss of enzymatic
AB  - activity.  More importantly, whereas the inactive C344A mutant enzyme bound
AB  - S-adenosyl-L-methionine, it failed to bind to DNA.  Furthermore, in double and triple mutants
AB  - where two or three cysteine residues were replaced by serine, all such mutants in which the
AB  - cysteine at position 344 was changed, were inactive.  Taken together, these results
AB  - convincingly demonstrate that the Cys-344 is necessary for enzyme activity and indicate an
AB  - essential role for it in DNA binding.
ER  -

TY  - JOUR
AU  - Redenbach, M.
AU  - Ikeda, K.
AU  - Yamasaki, M.
AU  - Kinashi, H.
TI  - Cloning and physical mapping of the EcoRI fragments of the giant linear plasmid SCP1.
JO  - J. Bacteriol.
PY  - 1998
SP  - 2796
EP  - 2799
VL  - 180
AB  - A cosmid library was constructed for the 350-kb giant linear plasmid SCP1
AB  - and aligned on a successive linear map. Only a 0.8-kb gap has remained
AB  - uncloned in the terminal inverted repeats close to both ends. Partial
AB  - digestion of the aligned cosmids with EcoRI and hybridization with the
AB  - flanking fragments of the vector enabled physical mapping of all of the
AB  - EcoRI fragments. On this map, the methylenomycin biosynthetic gene
AB  - cluster, the insertion sequence IS466, and the sapCDE genes coding for
AB  - spore-associated proteins were localized.
ER  -

TY  - JOUR
AU  - Redenbach, M.
AU  - Kieser, H.M.
AU  - Denapaite, D.
AU  - Eichner, A.
AU  - Cullum, J.
AU  - Kinashi, H.
AU  - Hopwood, D.A.
TI  - A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.
JO  - Mol. Microbiol.
PY  - 1996
SP  - 77
EP  - 96
VL  - 21
AB  - A Supercos-1 library carrying chromosomal DNA of a plasmid-free derivative of Streptomyces
AB  - coelicolor A3(2) was organized into an ordered encyclopaedia of overlapping clones by
AB  - hybridization. The minimum set of overlapping clones representing the entire chromosome (with
AB  - three short gaps) consists of 319 cosmids. The average insert size is 37.5 kb and the set of
AB  - clones therefore divides the chromosome into 637 alternating unique and overlapping segments
AB  - which have an average length of approx. 12.5 kb. More than 170 genes, gene clusters and other
AB  - genetic markers were mapped to their specific segment by hybridization to the encyclopaedia.
AB  - Genes could be cloned by direct transformation and complementation of S. coelicolor mutants
AB  - with cosmids isolated from Escherichia coli, selecting for insertion into the chromosome by
AB  - homologous recombination. As in other streptomycetes, the ends of the chromosome have long
AB  - terminal inverted repeats.
ER  -

TY  - JOUR
AU  - Redondo, P.
AU  - Merino, N.
AU  - Villate, M.
AU  - Blanco, F.J.
AU  - Montoya, G.
AU  - Molina, R.
TI  - Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2014
SP  - 256
EP  - 259
VL  - 70
AB  - Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of
AB  - DNA. The engineering of these enzymes provides novel instruments for genome modification in a
AB  - wide range of fields, including gene targeting, by inducing specific double-strand breaks.
AB  - I-CvuI is a homing endonuclease from the green alga Chlorella vulgaris. This enzyme was
AB  - purified after overexpression in Escherichia coli. Crystallization experiments of I-CvuI in
AB  - complex with its DNA target in the presence of Mg2+ yielded crystals suitable for X-ray
AB  - diffraction analysis. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1),
AB  - with unit-cell parameters a = 62.83, b = 83.56, c = 94.40 angstrom. The self-rotation function
AB  - and the Matthews coefficient suggested the presence of one protein-DNA complex per asymmetric
AB  - unit. The crystals diffracted to a resolution limit of 1.9 angstrom using synchrotron
AB  - radiation.
ER  -

TY  - JOUR
AU  - Redondo, P.
AU  - Prieto, J.
AU  - Munoz, I.G.
AU  - Alibes, A.
AU  - Stricher, F.
AU  - Serrano, L.
AU  - Cabaniols, J.P.
AU  - Daboussi, F.
AU  - Arnould, S.
AU  - Perez, C.
AU  - Duchateau, P.
AU  - Paques, F.
AU  - Blanco, F.J.
AU  - Montoya, G.
TI  - Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases.
JO  - Nature
PY  - 2008
SP  - 107
EP  - 111
VL  - 456
AB  - Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet
AB  - light. The cells of xeroderma pigmentosum
AB  - patients are defective in nucleotide excision repair, limiting their
AB  - capacity to eliminate ultraviolet-induced DNA damage, and resulting in a
AB  - strong predisposition to develop skin cancers. The use of rare cutting DNA
AB  - endonucleases-such as homing endonucleases, also known as
AB  - meganucleases-constitutes one possible strategy for repairing DNA lesions.
AB  - Homing endonucleases have emerged as highly specific molecular scalpels
AB  - that recognize and cleave DNA sites, promoting efficient homologous gene
AB  - targeting through double-strand-break-induced homologous recombination.
AB  - Here we describe two engineered heterodimeric derivatives of the homing
AB  - endonuclease I-CreI, produced by a semi-rational approach. These two
AB  - molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene
AB  - (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures
AB  - of the I-CreI variants complexed with intact and cleaved XPC target DNA
AB  - suggest that the mechanism of DNA recognition and cleavage by the
AB  - engineered homing endonucleases is similar to that of the wild-type
AB  - I-CreI. Furthermore, these derivatives induced high levels of specific
AB  - gene targeting in mammalian cells while displaying no obvious
AB  - genotoxicity. Thus, homing endonucleases can be designed to recognize and
AB  - cleave the DNA sequences of specific genes, opening up new possibilities
AB  - for genome engineering and gene therapy in xeroderma pigmentosum patients
AB  - whose illness can be treated ex vivo.
ER  -

TY  - JOUR
AU  - Redondo, P.
AU  - Prieto, J.
AU  - Ramos, E.
AU  - Blanco, F.J.
AU  - Montoya, G.
TI  - Crystallization and preliminary x-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2007
SP  - 1017
EP  - 1020
VL  - 63
AB  - Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of
AB  - base pairs. The availability of these
AB  - enzymes has opened novel perspectives for genome engineering in a wide
AB  - range of fields, including gene therapy, by taking advantage of the
AB  - homologous gene-targeting enhancement induced by a double-strand break.
AB  - I-Dmo-I is a well characterized homing endonuclease from the archaeon
AB  - Desulfurococcus mobilis. The enzyme was cloned and overexpressed in
AB  - Escherichia coli. Crystallization experiments of I-Dmo-I in complex
AB  - with its DNA target in the presence of Ca2+ and Mg2+ yielded crystals
AB  - that were suitable for X-ray diffraction analysis. The crystals
AB  - belonged to the monoclinic space group P2(1), with unit-cell parameters
AB  - a = 106.75, b = 70.18, c = 106.85 angstrom, alpha = gamma = 90, beta =
AB  - 119.93 degrees. The self-rotation function and the Matthews coefficient
AB  - suggested the presence of three protein-DNA complexes per asymmetric
AB  - unit. The crystals diffracted to a resolution limit of 2.6 angstrom
AB  - using synchrotron radiation at the Swiss Light Source (SLS) and the
AB  - European Synchrotron Radiation Facility (ESRF).
ER  -

TY  - JOUR
AU  - Redondo-Nieto, M. et al.
TI  - Genome Sequence of the Biocontrol Strain Pseudomonas fluorescens F113.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1273
EP  - 1274
VL  - 194
AB  - Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has
AB  - biocontrol activity against fungal plant pathogens and is a model for
AB  - rhizosphere colonization. Here, we present its complete genome sequence, which
AB  - shows that besides a core genome very similar to those of other strains sequenced
AB  - within this species, F113 possesses a wide array of genes encoding specialized
AB  - functions for thriving in the rhizosphere and interacting with eukaryotic
AB  - organisms.
ER  -

TY  - JOUR
AU  - Redzuan, R.A.
AU  - Bakar, N.A.
AU  - Rozano, L.
AU  - Badrun, R.
AU  - Amin, N.M.
AU  - Raih, M.F.M.
TI  - Draft Genome Sequence of Erwinia mallotivora BT-MARDI, Causative Agent of Papaya  Dieback Disease.
JO  - Genome Announcements
PY  - 2014
SP  - e00375
EP  - e00314
VL  - 2
AB  - Erwinia mallotivora was isolated from papaya trees infected with dieback disease, which were
AB  - planted at the Malaysian Agricultural Research and Development Institute (MARDI), Malaysia.
AB  - Here, we report a draft genome sequence of E. mallotivora BT-MARDI, which offers an important
AB  - source of information for understanding pathogen and host interaction during papaya dieback
AB  - development.
ER  -

TY  - JOUR
AU  - Reeben, M.
AU  - Prydz, H.
TI  - An improved method for detection of 5-methylcytosine by PCR-based genomic sequencing.
JO  - Biotechniques
PY  - 1994
SP  - 416
EP  - 417
VL  - 16
ER  -

TY  - JOUR
AU  - Rees, P.A.
AU  - Nwankwo, D.O.
AU  - Wilson, G.G.
AU  - Benner, J.S.
TI  - Cloning, purification and characterization of the HincII and HindII methyltransferases from Haemophilus influenzae.
JO  - Gene
PY  - 1988
SP  - 37
EP  - 37
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Reeve, J.N.
AU  - Amann, E.
AU  - Tailor, R.
AU  - Gunthert, U.
AU  - Scholz, K.
AU  - Trautner, T.A.
TI  - Unusual behaviour of SPO1 DNA with respect to restriction and modification enzymes recognizing the sequence 5'-G-G-C-C.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 229
EP  - 231
VL  - 178
AB  - SPO1 DNA contains only 5 cleavage sites for restriction enzymes which recognize
AB  - and cleave the sequence 5'-G-G-C-C (HaeIII or BsuR).  Fragments of SPO1 DNA
AB  - cloned in E. coli to substitute 5'-hydroxymethyluracil (HMU) by thymine (T)
AB  - remain resistant to HaeIII indicating that this unexpectedly small number of
AB  - cleavages by HaeIII is not correlated with the presence of HMU in the normal
AB  - phage DNA.  It was previously shown that SPO1 is neither subject to B. subtilis
AB  - R restriction (Trautner et al., 1974) nor modification in vivo (Gunthert et
AB  - al., 1975).  We now show that SPO1 DNA can however be restricted and modified
AB  - in vitro.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 410
EP  - 419
VL  - 9
AB  - Mesorhizobium australicum strain WSM2073(T) was isolated from root nodules on the pasture
AB  - legume Biserrula pelecinus growing in Australia in 2000. This aerobic,
AB  - motile, gram negative, non-spore-forming rod is poorly effective in N2 fixation
AB  - on B. pelecinus and has gained the ability to nodulate B. pelecinus following in
AB  - situ lateral transfer of a symbiosis island from the original inoculant strain
AB  - for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that
AB  - the genome size of M. australicum strain WSM2073(T) is 6,200,534 bp encoding
AB  - 6,013 protein-coding genes and 67 RNA-only encoding genes. This genome does not
AB  - contain any plasmids but has a 455.7 kb genomic island from Mesorhizobium ciceri
AB  - bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the Lebeckia ambigua-nodulating 'Burkholderia sprentiae' strain WSM5005(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 385
EP  - 394
VL  - 9
AB  - 'Burkholderia sprentiae' strain WSM5005(T) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that was isolated in Australia from an effective N2-fixing
AB  - root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South
AB  - Africa, in October 2007. Here we describe the features of 'Burkholderia
AB  - sprentiae' strain WSM5005(T), together with the genome sequence and its
AB  - annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds
AB  - of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding
AB  - genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint
AB  - Genome Institute 2010 Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 294
EP  - 303
VL  - 9
AB  - Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from
AB  - root nodules of the pasture legume Biserrula pelecinus that had been
AB  - inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic,
AB  - motile, Gram negative, non-spore-forming rod that has gained the ability to
AB  - nodulate B. pelecinus but is completely ineffective in N2 fixation with this
AB  - host. This report reveals that the genome of M. opportunistum strain WSM2075(T)
AB  - contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes
AB  - and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor
AB  - a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that
AB  - has been integrated into a phenylalanine-tRNA gene.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 283
EP  - 293
VL  - 9
AB  - Rhizobium leguminosarum bv. trifolii WSM2012 (syn. MAR1468) is an aerobic, motile,
AB  - Gram-negative, non-spore-forming rod that was isolated from an
AB  - ineffective root nodule recovered from the roots of the annual clover Trifolium
AB  - rueppellianum Fresen growing in Ethiopia. WSM2012 has a narrow, specialized host
AB  - range for N2-fixation. Here we describe the features of R. leguminosarum bv.
AB  - trifolii strain WSM2012, together with genome sequence information and
AB  - annotation. The 7,180,565 bp high-quality-draft genome is arranged into 6
AB  - scaffolds of 68 contigs, contains 7,080 protein-coding genes and 86 RNA-only
AB  - encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 273
EP  - 282
VL  - 9
AB  - Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod
AB  - that was isolated from an effective nitrogen (N2) fixing
AB  - root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this
AB  - microsymbiont is a poorly effective N2 fixer with the legume host Lupinus
AB  - angustifolius L.; a lupin species of considerable economic importance in both
AB  - Chile and Australia. The symbiosis formed with L. angustifolius produces less
AB  - than half of the dry matter achieved by the symbioses with commercial inoculant
AB  - strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an
AB  - important candidate strain with which to investigate the genetics of effective N2
AB  - fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of
AB  - Bradyrhizobium sp. strain WSM1417, together with genome sequence information and
AB  - annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single
AB  - scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only
AB  - encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 264
EP  - 272
VL  - 9
AB  - Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod isolated from a root nodule of the annual
AB  - clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembo,
AB  - Uruguay. This strain is generally ineffective for nitrogen (N2) fixation with
AB  - clovers of Mediterranean, North American and African origin, but is effective on
AB  - the South American perennial clover T. polymorphum Poir. Here we describe the
AB  - features of R. leguminosarum bv. trifolii strain WSM597, together with genome
AB  - sequence information and annotation. The 7,634,384 bp high-quality-draft genome
AB  - is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and
AB  - 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part
AB  - of the DOE Joint Genome Institute 2010 Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 254
EP  - 263
VL  - 9
AB  - Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod
AB  - that was isolated from an effective nitrogen- (N2) fixing
AB  - root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce
AB  - growing at Oyster Harbour, Albany district, Western Australia in 1982. This
AB  - strain is in commercial production as an inoculant for Lupinus and Ornithopus.
AB  - Here we describe the features of Bradyrhizobium sp. strain WSM471, together with
AB  - genome sequence information and annotation. The 7,784,016 bp high-quality-draft
AB  - genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding
AB  - genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes
AB  - sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing
AB  - Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 243
EP  - 253
VL  - 9
AB  - Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that is an effective nitrogen fixing
AB  - microsymbiont on the perennial clovers originating from Europe and the
AB  - Mediterranean basin. TA1 however is ineffective with many annual and perennial
AB  - clovers originating from Africa and America. Here we describe the features of R.
AB  - leguminosarum bv. trifolii strain TA1, together with genome sequence information
AB  - and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6
AB  - scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only
AB  - encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum.
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 66
EP  - 76
VL  - 2
AB  - Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a
AB  - diverse range of annual and perennial Trifolium (clover)
AB  - species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative
AB  - rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont
AB  - predominated in the perennial grasslands of Glencoe Research Station, in Uruguay,
AB  - to competitively nodulate its host, and fix atmospheric nitrogen. Here we
AB  - describe the basic features of WSM2304, together with the complete genome
AB  - sequence, and annotation. This is the first completed genome sequence for a
AB  - nitrogen fixing microsymbiont of a clover species from the American center of
AB  - origin. We reveal that its genome size is 6,872,702 bp encoding 6,643
AB  - protein-coding genes and 62 RNA only encoding genes. This multipartite genome was
AB  - found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four
AB  - circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419.
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 77
EP  - 86
VL  - 2
AB  - Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of  a diverse
AB  - range of annual Medicago (medic) species. Strain WSM419 is an aerobic,
AB  - motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule
AB  - collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in
AB  - Australia as an inoculant for annual medics during 1985 to 1993 due to its
AB  - nitrogen fixation, saprophytic competence and acid tolerance properties. Here we
AB  - describe the basic features of this organism, together with the complete genome
AB  - sequence, and annotation. This is the first report of a complete genome sequence
AB  - for a microsymbiont of the group of annual medic species adapted to acid soils.
AB  - We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding
AB  - genes and 81 RNA only encoding genes. The genome contains a chromosome of size
AB  - 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp.
AB  - The smallest plasmid is a feature unique to this medic microsymbiont.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 540
EP  - 550
VL  - 9
AB  - Microvirga lotononidis is a recently described species of root-nodule bacteria that is an
AB  - effective nitrogen- (N2) fixing microsymbiont of the symbiotically
AB  - specific African legume Listia angolensis (Welw. ex Bak.) B.-E. van Wyk & Boatwr.
AB  - M. lotononidis possesses several properties that are unusual in root-nodule
AB  - bacteria, including pigmentation and the ability to grow at temperatures of up to
AB  - 45 degrees C. Strain WSM3557(T) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod isolated from a L. angolensis root nodule collected in
AB  - Chipata, Zambia in 1963. This is the first report of a complete genome sequence
AB  - for the genus Microvirga. Here we describe the features of Microvirga lotononidis
AB  - strain WSM3557(T), together with genome sequence information and annotation. The
AB  - 7,082,538 high-quality-draft genome is arranged in 18 scaffolds of 104 contigs,
AB  - contains 6,956 protein-coding genes and 84 RNA-only encoding genes, and is one of
AB  - 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010
AB  - Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Reeve, W. et al.
TI  - Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325,  an effective microsymbiont of annual Mediterranean clovers.
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 347
EP  - 356
VL  - 2
AB  - Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that has the capacity to be
AB  - an effective nitrogen fixing microsymbiont of a diverse range of
AB  - annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile,
AB  - non-spore forming, Gram-negative rod isolated from root nodules collected in 1993
AB  - from the Greek Island of Serifos. WSM1325 is produced commercially in Australia
AB  - as an inoculant for a broad range of annual clovers of Mediterranean origin due
AB  - to its superior attributes of saprophytic competence, nitrogen fixation and
AB  - acid-tolerance. Here we describe the basic features of this organism, together
AB  - with the complete genome sequence, and annotation. This is the first completed
AB  - genome sequence for a microsymbiont of annual clovers. We reveal that its genome
AB  - size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding
AB  - genes. This multipartite genome contains 6 distinct replicons; a chromosome of
AB  - size 4,767,043 bp and 5 plasmids of size 828,924 bp, 660,973 bp, 516,088 bp,
AB  - 350,312 bp and 294,782 bp.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Ballard, R.
AU  - Drew, E.
AU  - Tian, R.
AU  - Brau, L.
AU  - Goodwin, L.
AU  - Huntemann, M.
AU  - Han, J.
AU  - Tatiparthi, R.
AU  - Chen, A.
AU  - Mavrommatis, K.
AU  - Markowitz, V.
AU  - Palaniappan, K.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Kyrpides, N.
TI  - Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant  strain RRI128.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 602
EP  - 613
VL  - 9
AB  - Ensifer meliloti strain RRI128 is an aerobic, motile, Gram-negative, non-spore-forming rod.
AB  - RRI128 was isolated from a nodule recovered from the roots
AB  - of barrel medic (Medicago truncatula) grown in the greenhouse and inoculated with
AB  - soil collected from Victoria, Australia. The strain is used in commercial
AB  - inoculants in Australia. RRI128 nodulates and forms an effective symbiosis with a
AB  - diverse range of lucerne cultivars (Medicago sativa) and several species of
AB  - annual medic (M. truncatula, Medicago littoralis and Medicago tornata), but forms
AB  - an ineffective symbiosis with Medicago polymorpha. Here we describe the features
AB  - of E. meliloti strain RRI128, together with genome sequence information and
AB  - annotation. The 6,900,273 bp draft genome is arranged into 156 scaffolds of 157
AB  - contigs, contains 6,683 protein-coding genes and 87 RNA-only encoding genes, and
AB  - is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome
AB  - Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
AB  - (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Ballard, R.
AU  - Howieson, J.
AU  - Drew, E.
AU  - Tian, R.
AU  - Brau, L.
AU  - Munk, C.
AU  - Davenport, K.
AU  - Chain, P.
AU  - Goodwin, L.
AU  - Pagani, I.
AU  - Huntemann, M.
AU  - Mavrommatis, K.
AU  - Pati, A.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Woyke, T.
AU  - Kyrpides, N.
TI  - Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 514
EP  - 526
VL  - 9
AB  - Ensifer medicae strain WSM1115 forms effective nitrogen fixing symbioses with a range of
AB  - annual Medicago species and is used in commercial inoculants in
AB  - Australia. WSM1115 is an aerobic, motile, Gram-negative, non-spore-forming rod.
AB  - It was isolated from a nodule recovered from the root of burr medic (Medicago
AB  - polymorpha) collected on the Greek Island of Samothraki. WSM1115 has a broad host
AB  - range for nodulation and N2 fixation capacity within the genus Medicago, although
AB  - this does not extend to all medic species. WSM1115 is considered saprophytically
AB  - competent in moderately acid soils (pH(CaCl2) 5.0), but it has failed to persist
AB  - at field sites where soil salinity exceeded 10 ECe (dS/m). Here we describe the
AB  - features of E. medicae strain WSM1115, together with genome sequence information
AB  - and its annotation. The 6,861,065 bp high-quality-draft genome is arranged into 7
AB  - scaffolds of 28 contigs, contains 6,789 protein-coding genes and 83 RNA-only
AB  - encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
AB  - Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Drew, E.
AU  - Ballard, R.
AU  - Melino, V.
AU  - Tian, R.
AU  - De Meyer, S.
AU  - Brau, L.
AU  - Ninawi, M.
AU  - Daligault, H.
AU  - Davenport, K.
AU  - Erkkila, T.
AU  - Goodwin, L.
AU  - Gu, W.
AU  - Munk, C.
AU  - Teshima, H.
AU  - Xu, Y.
AU  - Chain, P.
AU  - Kyrpides, N.
TI  - Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 232
EP  - 242
VL  - 9
AB  - Rhizobium leguminosarum bv. trifolii SRDI943 (strain syn. V2-2) is an aerobic, motile,
AB  - Gram-negative, non-spore-forming rod that was isolated from a root nodule
AB  - of Trifolium michelianum Savi cv. Paradana that had been grown in soil collected
AB  - from a mixed pasture in Victoria, Australia. This isolate was found to have a
AB  - broad clover host range but was sub-optimal for nitrogen fixation with T.
AB  - subterraneum (fixing 20-54% of reference inoculant strain WSM1325) and was found
AB  - to be totally ineffective with the clover species T. polymorphum and T. pratense.
AB  - Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943,
AB  - together with genome sequence information and annotation. The 7,412,387 bp
AB  - high-quality-draft genome is arranged into 5 scaffolds of 5 contigs, contains
AB  - 7,317 protein-coding genes and 89 RNA-only encoding genes, and is one of 100
AB  - rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010
AB  - Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB)
AB  - project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Drew, E.
AU  - Ballard, R.
AU  - Melino, V.
AU  - Tian, R.
AU  - De Meyer, S.
AU  - Brau, L.
AU  - Ninawi, M.
AU  - Teshima, H.
AU  - Goodwin, L.
AU  - Chain, P.
AU  - Liolios, K.
AU  - Pati, A.
AU  - Mavromatis, K.
AU  - Ivanova, N.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Kyrpides, N.
TI  - Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 220
EP  - 231
VL  - 9
AB  - Rhizobium leguminosarum bv. trifolii SRDI565 (syn. N8-J) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod. SRDI565 was isolated from a nodule
AB  - recovered from the roots of the annual clover Trifolium subterraneum subsp.
AB  - subterraneum grown in the greenhouse and inoculated with soil collected from New
AB  - South Wales, Australia. SRDI565 has a broad host range for nodulation within the
AB  - clover genus, however N2-fixation is sub-optimal with some Trifolium species and
AB  - ineffective with others. Here we describe the features of R. leguminosarum bv.
AB  - trifolii strain SRDI565, together with genome sequence information and
AB  - annotation. The 6,905,599 bp high-quality-draft genome is arranged into 7
AB  - scaffolds of 7 contigs, contains 6,750 protein-coding genes and 86 RNA-only
AB  - encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
AB  - Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Parker, M.
AU  - Tian, R.
AU  - Goodwin, L.
AU  - Teshima, H.
AU  - Tapia, R.
AU  - Han, C.
AU  - Han, J.
AU  - Liolios, K.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
TI  - Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1159
EP  - 1167
VL  - 9
AB  - Microvirga lupini LUT6(T) is an aerobic, non-motile, Gram-negative, non-spore-forming rod that
AB  - can exist as a soil saprophyte or as a legume
AB  - microsymbiont of Lupinus texensis. LUT6(T) was isolated in 2006 from a nodule
AB  - recovered from the roots of the annual L. texensis growing in Travis Co., Texas.
AB  - LUT6(T) forms a highly specific nitrogen-fixing symbiosis with endemic L.
AB  - texensis and no other Lupinus species can form an effective nitrogen-fixing
AB  - symbiosis with this isolate. Here we describe the features of M. lupini LUT6(T),
AB  - together with genome sequence information and its annotation. The 9,633,614 bp
AB  - improved high quality draft genome is arranged into 160 scaffolds of 1,366
AB  - contigs containing 10,864 protein-coding genes and 87 RNA-only encoding genes,
AB  - and is one of 20 rhizobial genomes sequenced as part of a DOE Joint Genome
AB  - Institute 2010 Community Sequencing Project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Sullivan, J.
AU  - Ronson, C.
AU  - Tian, R.
AU  - Brau, L.
AU  - Davenport, K.
AU  - Goodwin, L.
AU  - Chain, P.
AU  - Woyke, T.
AU  - Lobos, E.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
TI  - Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 3
EP  - 3
VL  - 9
AB  - Mesorhizobium loti strain R88B was isolated in 1993 in the Rocklands range in Otago, New
AB  - Zealand from a Lotus corniculatus root nodule. R88B is an aerobic,
AB  - Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti
AB  - strain R88B contains a single scaffold of size 7,195,110 bp which encodes 6,950
AB  - protein-coding genes and 66 RNA-only encoding genes. This genome does not harbor
AB  - any plasmids but contains the integrative and conjugative element ICEMlSym(R7A),
AB  - also known as the R7A symbiosis island, acquired by horizontal gene transfer in
AB  - the field environment from M. loti strain R7A. It also contains a mobilizable
AB  - genetic element ICEMladh(R88B), that encodes a likely adhesin gene which has
AB  - integrated downstream of ICEMlSym(R7A), and three acquired loci that together
AB  - allow the utilization of the siderophore ferrichrome. This rhizobial genome is
AB  - one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic
AB  - Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Sullivan, J.
AU  - Ronson, C.
AU  - Tian, R.
AU  - Munk, C.
AU  - Han, C.
AU  - Reddy, T.B.
AU  - Seshadri, R.
AU  - Woyke, T.
AU  - Pati, A.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
TI  - High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium  loti strain CJ3Sym.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 54
EP  - 54
VL  - 10
AB  - Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative
AB  - and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, in a laboratory
AB  - mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3.
AB  - Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in
AB  - 1994. CJ3Sym  is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the
AB  - genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. The
AB  - high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331
AB  - protein-coding genes and 70 RNA-only encoding genes, and  is part of the GEBA-RNB project
AB  - proposal.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - Tian, R.
AU  - Brau, L.
AU  - Goodwin, L.
AU  - Munk, C.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, C.
AU  - Liolios, K.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavrommatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Willems, A.
TI  - Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 473
EP  - 483
VL  - 9
AB  - Ensifer arboris LMG 14919(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that
AB  - can exist as a soil saprophyte or as a legume
AB  - microsymbiont of several species of legume trees. LMG 14919(T) was isolated in
AB  - 1987 from a nodule recovered from the roots of the tree Prosopis chilensis
AB  - growing in Kosti, Sudan. LMG 14919(T) is highly effective at fixing nitrogen with
AB  - P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum
AB  - acacia). LMG 14919(T) does not nodulate the tree Leucena leucocephala, nor the
AB  - herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago
AB  - sativa, Lotus corniculatus and Galega orientalis. Here we describe the features
AB  - of E. arboris LMG 14919(T), together with genome sequence information and its
AB  - annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7
AB  - scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only
AB  - encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
AB  - Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Reeve, W.
AU  - van Berkum, P.
AU  - Ardley, J.
AU  - Tian, R.
AU  - Gollagher, M.
AU  - Marinova, D.
AU  - Elia, P.
AU  - Reddy, T.B.
AU  - Pillay, M.
AU  - Varghese, N.
AU  - Seshadri, R.
AU  - Ivanova, N.
AU  - Woyke, T.
AU  - Baeshen, M.N.
AU  - Baeshen, N.A.
AU  - Kyrpides, N.
TI  - High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 26
EP  - 26
VL  - 12
AB  - Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium
AB  - elkanii, is an aerobic, motile, Gram-negative, non-spore-forming
AB  - rod that was isolated from an effective nitrogen-fixing root nodule of Glycine
AB  - max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of
AB  - this economically important legume, B. elkanii USDA 76T was selected as part of
AB  - the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
AB  - Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of
AB  - B. elkanii USDA 76T are described, together with its genome sequence information
AB  - and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2
AB  - scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only
AB  - encoding genes. The B. elkanii USDA 76T genome contains a low GC content region
AB  - with symbiotic nod and fix genes, indicating the presence of a symbiotic island
AB  - integration. A comparison of five B. elkanii genomes that formed a clique
AB  - revealed that 356 of the 9060 protein coding genes of USDA 76T were unique,
AB  - including 22 genes of an intact resident prophage. A conserved set of 7556 genes
AB  - were also identified for this species, including genes encoding a general
AB  - secretion pathway as well as type II, III, IV and VI secretion system proteins.
AB  - The type III secretion system has previously been characterized as a host
AB  - determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76T
AB  - genome contains genes encoding all the type III secretion system components,
AB  - including a translocon complex protein NopX required for the introduction of
AB  - effector proteins into host cells. While many bradyrhizobial strains are unable
AB  - to nodulate the soybean cultivar Clark (rj1), USDA 76T was able to elicit nodules
AB  - on Clark (rj1), although in reduced numbers, when plants were grown in Leonard
AB  - jars containing sand or vermiculite. In these conditions, we postulate that the
AB  - presence of NopX allows USDA 76T to introduce various effector molecules into
AB  - this host to enable nodulation.
ER  -

TY  - JOUR
AU  - Reeves, P.R.
AU  - Liu, B.
AU  - Zhou, Z.
AU  - Li, D.
AU  - Guo, D.
AU  - Ren, Y.
AU  - Clabots, C.
AU  - Lan, R.
AU  - Johnson, J.R.
AU  - Wang, L.
TI  - Rates of Mutation and Host Transmission for an Escherichia coli Clone over 3 Years.
JO  - PLoS ONE
PY  - 2011
SP  - E26907
EP  - E26907
VL  - 6
AB  - Although over 50 complete Escherichia coli/Shigella genome sequences are
AB  - available, it is only for closely related strains, for example the O55:H7
AB  - and O157:H7 clones of E. coli, that we can assign differences to
AB  - individual evolutionary events along specific lineages. Here we sequence
AB  - the genomes of 14 isolates of a uropathogenic E. coli clone that persisted
AB  - for 3 years within a household, including a dog, causing a urinary tract
AB  - infection (UTI) in the dog after 2 years. The 20 mutations observed fit a
AB  - single tree that allows us to estimate the mutation rate to be about 1.1
AB  - per genome per year, with minimal evidence for adaptive change, including
AB  - in relation to the UTI episode. The host data also imply at least 6 host
AB  - transfer events over the 3 years, with 2 lineages present over much of
AB  - that period. To our knowledge, these are the first direct measurements for
AB  - a clone in a well-defined host community that includes rates of mutation
AB  - and host transmission. There is a concentration of non-synonymous
AB  - mutations associated with 2 transfers to the dog, suggesting some
AB  - selection pressure from the change of host. However, there are no changes
AB  - to which we can attribute the UTI event in the dog, which suggests that
AB  - this occurrence after 2 years of the clone being in the household may have
AB  - been due to chance, or some unknown change in the host or environment. The
AB  - ability of a UTI strain to persist for 2 years and also to transfer
AB  - readily within a household has implications for epidemiology, diagnosis,
AB  - and clinical intervention.
ER  -

TY  - JOUR
AU  - Regar, R.K.
AU  - Gaur, V.K.
AU  - Mishra, G.
AU  - Jadhao, S.
AU  - Kamthan, M.
AU  - Manickam, N.
TI  - Draft Genome Sequence of Alcaligenes faecalis Strain IITR89, an Indole-Oxidizing  Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00067
EP  - e00016
VL  - 4
AB  - We report the draft genome sequence of Alcaligenes faecalis strain IITR89, a bacterium able to
AB  - form indigo by utilizing indole as the sole carbon source. The
AB  - Alcaligenes species is increasingly reported for biodegradation of diverse
AB  - toxicants and thus complete sequencing may provide insight into biodegradation
AB  - capabilities and other phenotypes.
ER  -

TY  - JOUR
AU  - Regar, R.K.
AU  - Gaur, V.K.
AU  - Mishra, G.
AU  - Jadhao, S.
AU  - Kamthan, M.
AU  - Manickam, N.
TI  - Draft Genome Sequence of Acinetobacter baumannii IITR88, a Bacterium Degrading Indoles and Other Aromatic Compounds.
JO  - Genome Announcements
PY  - 2016
SP  - e00065
EP  - e00016
VL  - 4
AB  - Here, we report the 4.16-Mb draft genome sequence of an indole-degrading bacterium,
AB  - Acinetobacter baumannii IITR88, isolated from the Bhagirathi river in
AB  - India. A total of 4,069 coding regions (CDSs), 3 rRNAs, and 52 tRNAs were
AB  - predicted. Genes for the degradation of indoles, phenylacetaldehyde,
AB  - anthranilate, and several other aromatic compounds were present.
ER  -

TY  - JOUR
AU  - Regenbogen, B.
AU  - Willmann, M.
AU  - Steglich, M.
AU  - Bunk, B.
AU  - Nubel, U.
AU  - Peter, S.
AU  - Neher, R.A.
TI  - Rapid and Consistent Evolution of Colistin Resistance in Extensively Drug-Resistant Pseudomonas aeruginosa during Morbidostat Culture.
JO  - Antimicrob. Agents Chemother.
PY  - 2017
SP  - e00043
EP  - e00017
VL  - 61
AB  - Colistin is a last resort antibiotic commonly used against multidrug-resistant strains of
AB  - Pseudomonas aeruginosa To investigate the potential for in-situ evolution of resistance
AB  - against colistin and to map the molecular targets of colistin resistance, we exposed two P.
AB  - aeruginosa isolates to colistin using a continuous culture device known as morbidostat. As a
AB  - result, colistin resistance reproducibly increased 10-fold within ten days, and 100-fold
AB  - within 20 days, along with highly stereotypic, yet strain specific mutation patterns. The
AB  - majority of mutations hit the pmrAB two component signaling system and genes involved in
AB  - lipopolysaccharide (LPS) synthesis, including lpxC, pmrE, and migA We tracked the frequencies
AB  - of all arising mutations by whole genome deep sequencing every 3-4 days to provide a detailed
AB  - picture of the dynamics of resistance evolution, including competition and displacement among
AB  - multiple resistant sub-populations. In seven out of 18 cultures, we observed mutations in mutS
AB  - along with a mutator phenotype that seemed to facilitate resistance evolution.
ER  -

TY  - JOUR
AU  - Register, K.B.
AU  - Ivanov, Y.V.
AU  - Harvill, E.T.
AU  - Brinkac, L.
AU  - Kim, M.
AU  - Losada, L.
TI  - Draft Genome Sequences of Six Bordetella hinzii Isolates Acquired from Avian and  Mammalian Hosts.
JO  - Genome Announcements
PY  - 2015
SP  - e00081
EP  - e00015
VL  - 3
AB  - Bordetella hinzii is a Gram-negative bacterium known to infect poultry, humans, rabbits, and
AB  - rodents. It is an opportunistic pathogen in immunocompromised
AB  - humans, and some strains cause mild to moderate respiratory disease in turkeys.
AB  - Little is known as to the degree of genetic diversity within the species or the
AB  - genetic basis for virulence. Here, we report the genome sequences of six isolates
AB  - of B. hinzii acquired from humans, rabbits, or turkeys. These data provide a
AB  - framework for refining the population structure of the genus, establishing
AB  - relationships among genetically distinct isolates, and developing an
AB  - understanding of the possible virulence mechanisms of the bacterium.
ER  -

TY  - JOUR
AU  - Register, K.B.
AU  - Ivanov, Y.V.
AU  - Jacobs, N.
AU  - Meyer, J.A.
AU  - Goodfield, L.L.
AU  - Muse, S.J.
AU  - Smallridge, W.E.
AU  - Brinkac, L.
AU  - Kim, M.
AU  - Sanka, R.
AU  - Harvill, E.T.
AU  - Losada, L.
TI  - Draft Genome Sequences of 53 Genetically Distinct Isolates of Bordetella bronchiseptica Representing 11 Terrestrial and Aquatic Hosts.
JO  - Genome Announcements
PY  - 2015
SP  - e00152
EP  - e00115
VL  - 3
AB  - Bordetella bronchiseptica infects a variety of mammalian and avian hosts. Here, we report the
AB  - genome sequences of 53 genetically distinct isolates acquired from
AB  - a broad range of terrestrial and aquatic animals. These data will greatly
AB  - facilitate ongoing efforts to better understand the evolution, host adaptation,
AB  - and virulence mechanisms of B. bronchiseptica.
ER  -

TY  - JOUR
AU  - Regmi, S.M.
AU  - Chaiprasert, A.
AU  - Coker, O.O.
AU  - Disratthakit, A.
AU  - Prammananan, T.
AU  - Suriyaphol, P.
AU  - Yik-Ying, T.
AU  - Twee, H.O.
TI  - Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Manu-Ancestor Spoligo-International Type 523 Isolate from Thailand.
JO  - Genome Announcements
PY  - 2015
SP  - e01589
EP  - e01514
VL  - 3
AB  - We present the draft genome sequence of DS-16780, with a rare spoligo-international type (SIT)
AB  - 523 (777777777777771) genotype, which reveals an extensively drug-resistant Mycobacterium
AB  - tuberculosis (XDR-TB) phenotype. The isolate is a representative of clonal XDR-TB from the
AB  - western part of Thailand.
ER  -

TY  - JOUR
AU  - Rego, R.O.M.
AU  - Bestor, A.
AU  - Rosa, P.A.
TI  - Defining the plasmid-encoded restriction-modification systems of the Lyme disease spirochete Borrelia burgdorferi.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1161
EP  - 1171
VL  - 193
AB  - The restriction-modification (R-M) systems of many bacteria present a barrier to the stable
AB  - introduction of foreign DNA. The Lyme disease spirochete Borrelia burgdorferi has two
AB  - plasmid-encoded putative R-M genes, bbe02 and bbq67, whose presence limits transformation by
AB  - shuttle vector DNA from E. coli. We show that both the bbe02 and bbq67 loci in recipient B.
AB  - burgdorferi limit transformation with shuttle vector DNA from E. coli, irrespective of its
AB  - dam, dcm, or hsd methylation status. However, plasmid DNA purified from B. burgdorferi
AB  - transformed naive B. burgdorferi much more efficiently than plasmid DNA from E. coli,
AB  - particularly when the bbe02 and bbq67 genotypes of the B. burgdorferi DNA source matched that
AB  - of the recipient. We detected adenine methylation of plasmid DNA prepared from B. burgdorferi
AB  - that carried bbe02 and bbq67. These results indicate that the bbe02 and bbq67 loci of B.
AB  - burgdorferi encode distinct R-M enzymes that methylate endogenous DNA and cleave foreign DNA
AB  - lacking the same sequence-specific modification. Our findings have basic implications for
AB  - horizontal gene transfer among B. burgdorferi strains with distinct plasmid contents. Further
AB  - characterization and identification of the nucleotide sequences recognized by BBE02 and BBQ67
AB  - will facilitate efficient genetic manipulation of this pathogenic spirochete.
ER  -

TY  - JOUR
AU  - Rehman, M.A.
AU  - Carrillo, C.
AU  - Malouin, F.
AU  - Diarra, M.S.
TI  - Draft Whole-Genome Sequences of Multidrug-Resistant Escherichia coli O157:H7 Strains Isolated from Feedlot Cattle Treated with Growth-Promoting Agents.
JO  - Genome Announcements
PY  - 2017
SP  - e00284
EP  - e00217
VL  - 5
AB  - Enterohemorrhagic Escherichia coli serotype O157:H7 is a major cause of foodborne outbreaks
AB  - and hemolytic-uremic syndrome. Here, we report the draft genome
AB  - sequences of three antibiotic-resistant E. coli O157:H7 strains isolated from
AB  - feedlot cattle. These draft genome sequences will aid in the development of
AB  - sequence-based tools for the detection of virulence and antimicrobial resistance
AB  - genotypes.
ER  -

TY  - JOUR
AU  - Rehman, M.A.
AU  - Labbe, G.
AU  - Ziebell, K.
AU  - Johnson, R.P.
AU  - Nash, J.H.
TI  - Complete Genome and Plasmid Sequences of Three Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis Belonging to Phage Types 8, 13, and  13a.
JO  - Genome Announcements
PY  - 2015
SP  - e01017
EP  - e01015
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is a prominent cause of human
AB  - salmonellosis frequently linked to poultry products. In Canada, S. Enteritidis phage types 8,
AB  - 13, and 13a predominate among both clinical and poultry isolates. Here, we report the complete
AB  - genome and plasmid sequences of poultry isolates of these three phage types.
ER  -

TY  - JOUR
AU  - Rehman, M.A.
AU  - Ziebell, K.
AU  - Nash, J.H.
AU  - Kropinski, A.M.
AU  - Ross, A.
AU  - Al-Lami, M.
AU  - Boerlin, P.
AU  - Chui, L.
AU  - Devenish, J.
AU  - Bekal, S.
AU  - Graham, M.
AU  - Amoako, K.K.
AU  - Johnson, R.P.
TI  - Complete Genome Sequences of 16 Canadian Strains of Salmonella enterica subsp. enterica Serovar Enteritidis.
JO  - Genome Announcements
PY  - 2014
SP  - e00330
EP  - e00314
VL  - 2
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is an important zoonotic food-borne
AB  - pathogen causing serious human illnesses frequently linked to poultry products. Here, we
AB  - report fully assembled genome sequences of 16 S. Enteritidis strains with common pulsed-field
AB  - gel electrophoresis (PFGE) and phage types (8, 13, 13a, and 14b) that predominate in North
AB  - America.
ER  -

TY  - JOUR
AU  - Rehman, M.A.
AU  - Ziebell, K.
AU  - Nash, J.H.
AU  - Kropinski, A.M.
AU  - Zong, Z.
AU  - Nafziger, E.
AU  - Boerlin, P.
AU  - Chui, L.
AU  - Devenish, J.
AU  - Bekal, S.
AU  - Graham, M.
AU  - Johnson, R.P.
TI  - High-Quality Draft Whole-Genome Sequences of 162 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Diverse Sources in Canada.
JO  - Genome Announcements
PY  - 2014
SP  - e00348
EP  - e00314
VL  - 2
AB  - We report the high-quality draft genome sequences of 162 strains of Salmonella enterica subsp.
AB  - enterica serovar Enteritidis representing diverse phage types and
AB  - pulsed-field gel electrophoresis (PFGE) profiles. The analysis of these genomes
AB  - will enable the identification of markers that are useful for differentiating
AB  - strains of this highly clonal serovar and will provide insights into the
AB  - evolution, virulence, and epidemiology of the strains.
ER  -

TY  - JOUR
AU  - Rehvathy, V.
AU  - Tan, M.H.
AU  - Gunaletchumy, S.P.
AU  - Teh, X.
AU  - Wang, S.
AU  - Baybayan, P.
AU  - Singh, S.
AU  - Ashby, M.
AU  - Kaakoush, N.O.
AU  - Mitchell, H.M.
AU  - Croft, L.J.
AU  - Goh, K.L.
AU  - Loke, M.F.
AU  - Vadivelu, J.
TI  - Multiple Genome Sequences of Helicobacter pylori Strains of Diverse Disease and Antibiotic Resistance Backgrounds from Malaysia.
JO  - Genome Announcements
PY  - 2013
SP  - e00687
EP  - e00613
VL  - 1
AB  - Helicobacter pylori causes human gastroduodenal diseases, including chronic gastritis and
AB  - peptic ulcer disease. It is also a major microbial risk factor for
AB  - the development of gastric adenocarcinoma and mucosa-associated lymphoid tissue
AB  - (MALT) lymphoma. Twenty-one strains with different ethnicity, disease, and
AB  - antimicrobial susceptibility backgrounds were sequenced by use of Illumina HiSeq
AB  - and PacBio RS platforms.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Danzitz, M.J.
TI  - High resolution mapping of the DNA-protein interface in the EcoRI DNA methylase system.
JO  - ACS Abstracts
PY  - 1987
SP  - 63
EP  - 63
VL  - 194
AB  - This monomeric, S-Adenosyl-Methionine (SAM) dependent enzyme recognizes the
AB  - palindromic double stranded DNA sequence 5' GAATTC 3' and methylates the
AB  - exocyclic amino of the second adenine.  As part of our effort to understand the
AB  - origins of sequence specific DNA binding we are characterizing the interactions
AB  - between the methylase and its DNA substrate.  The experimental methods include
AB  - the use of small, well defined oligonucleotides in conjunction with DNase I and
AB  - hydroxy radical (PNAS (1986) 83 5469) mapping.  Results with altered flanking
AB  - DNA sequences, hemimethylated recognition sequences, and modulation of binding
AB  - via SAM (and SAM analogs) will be presented.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Danzitz, M.J.
TI  - EcoRI DNA methyltransferase-DNA interactions.
JO  - Biochemistry
PY  - 1992
SP  - 1937
EP  - 1945
VL  - 31
AB  - We present a novel strategy with synthetic hemimethylated DNA substrates
AB  - containing uracil for thymine and inosine for guanosine replacements and EcoRI
AB  - DNA methyltransferase to characterize the importance of major groove
AB  - hydrophobic groups to the sequence-specific modification of DNA.  The bacterial
AB  - MTase uses S-adenosyl-L-methionine to methylate the double-stranded DNA site
AB  - 5'GAATTC3' at the N6 position of the central adenosine of each strand.  Uracil
AB  - substitution in either strand at the outer thymine (5'GAATUC3') causes 2.2- and
AB  - 1.7-fold improvements in specificity (kcat/KmDNA).  The fact that the
AB  - specificity constant for the substrate containing uracil in both strands is
AB  - identifical to the value expected for noninteracting substitutions suggests
AB  - that no significant methyltransferase-DNA interactions are altered beyond the
AB  - site of etiher substitution.  Similar analysis of the internal thymine
AB  - (5'GAAUTC3') also shows these methyl groups to make a negative contribution to
AB  - specificity, although the observed non-additivity with the doubly modified
AB  - substrate clearly shows methyltransferase-DNA interactions beyond the site of
AB  - substitution to be affected in this case.  To further probe the effect of
AB  - analogue incorporation on methyltransferase-DNA interactions beyond the site of
AB  - substitution, the relatively silent and additive uracil changes (5'GAATUC3')
AB  - were combined with inosine for guanosine substitutions (e.g., 5'IAATTC3') known
AB  - to have significant negative effects on specificity.  In contrast to the
AB  - additivity observed with the outer thymines, these studies show significant
AB  - changes in methyltransferase-DNA interactions caused by the removal of the
AB  - thymine methyls.  Our results implicate a complex and flexible
AB  - methyltransferase-DNA interface in which subtle structural changes in the
AB  - substrate are transmitted over the entire canonical site.  Thermal stability
AB  - analyses and determination of Delta H and Delta S for the double- to
AB  - single-stranded transition for single and doubly substituted substrates show no
AB  - additivity.  This suggests that structural changes in the DNA alone may occur
AB  - beyond the site of substitution.  Interestingly, substrates with widely varying
AB  - enthalpy and entropy terms show similar specificity with the Mtase, suggesting
AB  - the Mtase is insensitive to the underlying conformational differences.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Danzitz, M.J.
TI  - Non-additivity of sequence-specific enzyme-DNA interactions in the EcoRI DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6587
EP  - 6594
VL  - 19
AB  - We describe a novel strategy to characterize protein-DNA interactions involving
AB  - monomeric enzymes such as DNA methyltransferases (Mtases).  This strategy is
AB  - applied to our investigation of the EcoRI DNA Mtase, which binds its double
AB  - stranded recognition site 5'-G-AATTC-3' and methylates the central adenosine of
AB  - each strand using S-adenosyl-L-methionine as the methyl donor.  We show that
AB  - prior methylation of adenosine in either strand does not perturb catalysis.  In
AB  - contrast, substrates substituted with deoxyinosine at either guanosine position
AB  - (T-BM15 and T15-BM) show the minor groove residing N2 amino group of both
AB  - guanosines contribute to DNA recognition since specificity constants for the
AB  - modified substrates are reduced 13 and 39 fold.  Similar analysis of a
AB  - substrate containing deoxyinosine at both positions (T15-BM15) clearly shows
AB  - that some communication occurs between the sites.  To determine the extent to
AB  - which structural changes in the DNA alone contribute to this lack of
AB  - additivity, we performed DNA melting analysis of the singly and doubly
AB  - substituted substrates, and also found nonadditivity.  Although our functional
AB  - and structural analyses suggest that deoxyinosine incorporation causes long
AB  - range conformational effects, the similarity of Km(AdoMet) for all substrates
AB  - suggests that no large-scale structural changes occur in the Mtase-DNA-AdoMet
AB  - complex.  Our results support the following conclusions: 1) The non-additivity
AB  - shown in this system contrasts with the widespread demonstration of additivity
AB  - involving repressors (Lehming et al., 1990; Takeda et al., 1989; Ebright et
AB  - al., 1987), suggesting that sequence discrimination by enzymes may involve more
AB  - complex mechanisms.  Further, this non-additivity precludes quantitative
AB  - assignment of individual interactions and we suggest that future analyses of
AB  - this and related enzyme systems with base analogs include detailed information
AB  - about the long range structural consequences of individual substitutions.  2)
AB  - Although T15-BM and T-BM15 are shown to be radically different by thermodynamic
AB  - analysis, the similar specificity constants with the Mtase suggest that the
AB  - underlying structural differences (e.g., altered helical parameters of the DNA)
AB  - are not critical for sequence-recognition.  3) The significance of minor groove
AB  - Mtase-DNA interactions to specificity is confirmed.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Danzitz, M.J.
AU  - Osti, F.
TI  - Mechanisms of substrate discrimination in the EcoRI DNA methylase.
JO  - FASEB J.
PY  - 1990
SP  - A1793
EP  - A1793
VL  - 4
AB  - We have investigated how this prokaryotic Type II DNA methylase selectively
AB  - modifies the second adenine in the double stranded canonical site, 5' GAATTC
AB  - 3'.  Non-selfcomplementary 14 basepair DNA substrates have been submitted to
AB  - detailed functional analysis by comparisons of true steady-state kinetic
AB  - parameters.  Modifications within the recognition hexanucleotide include  i)
AB  - methylation of one strand, ii) removal of single sites of (potential)
AB  - methylase-DNA interaction (e.g. minor groove H-bond donor, major groove
AB  - thymidine-methyl) iii) substitution of basepairs within the recognition site.
AB  - Prior methylation of one strand does not effect kinetic parameters (Kcat, Km or
AB  - Kcat/Km).  A significant contribution toward specificity (kcat/Km)DNA derives
AB  - from minor groove interactions; this is largely a result of increases in KmDNA.
AB  - In contrast, discrimination against substrates related by single basepair
AB  - changes occur through decreases in kcat of up to one million fold.  No effects
AB  - on KmAdoMet were detected for any DNA substrate.  The structural integrity of
AB  - the modified DNA substrates was determined with melting temperature and second
AB  - site analyses.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - DiMichele, L.
TI  - Functional analysis of cysteines in the EcoRI DNA methylase.
JO  - ACS Abstracts
PY  - 1987
SP  - 64
EP  - 64
VL  - 194
AB  - This monomeric, S-adenosyl-methionine (SAM) dependent enzyme recognizes the
AB  - palindromic double stranded DNA sequence 5' GAATTC 3' and methylates the
AB  - exocyclic amino of the second adenine.  As part of our effort to understand the
AB  - origins of sequence specific DNA binding we are characterizing the functional
AB  - significance of the enzyme's seven cysteines (326 total amino acids).  Cysteine
AB  - labeling experiments with N-Ethyl-Maleimide (NEM) lead to inactivation of
AB  - enzyme activity.  Substrate and cofactor (SAM) protection are being used to
AB  - implicate specific cysteines.  Proteolytic digestion of 3H NEM labeled enzyme
AB  - followed by amino acid sequencing affords the assignment of specific
AB  - cysteine(s).
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Everett, E.A.
TI  - Identification of peptides involved in S-Adenosylmethionine binding in the EcoRI DNA methylase.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 8929
EP  - 8934
VL  - 265
AB  - The Mr 38,050 monomeric EcoRI DNA methylase is part of a bacterial
AB  - restriction-modification system.  The methylase transfers the methyl group from
AB  - S-adenosylmethionine (AdoMet) to the second adenine in the double-stranded DNA
AB  - sequence 5'-GAATTC-3'.  We have used the radiolabeled photoaffinity analog
AB  - 8-azido-S-adenosylmethionine (8-N3-AdoMet) to identify peptides at the AdoMet
AB  - binding site in the binary methylase-cofactor analog complex.  The dissociation
AB  - constants in the absence of DNA for the analog and AdoMet are 12.9 and 4.8
AB  - microM, respectively.  The apparent kcat and Km values, obtained with the
AB  - double-stranded DNA substrate 5'-CGCGAATTCGCG-3', are 5.0 s-1 and 0.710 microM
AB  - (8-N3-AdoMet) and 4.3 s-1 and 0.335 microM (AdoMet).  Photolabeling by
AB  - 8-N3-AdoMet occurs upon irradiation with ultraviolet light and is inhibited by
AB  - AdoMet.  Digestion of the adducted methylase with subtilisin generated several
AB  - radiolabeled peptides.  Peptide sequencing from independent photolabeling
AB  - experiments revealed two radiolabeled peptides containing amino acids 206-212
AB  - and 213-221.  Instability of the adducted peptides precluded assignment of
AB  - modified amino acids.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Maegley, K.A.
AU  - Shoemaker, D.D.
AU  - Everett, E.
TI  - Structural and functional analysis of EcoRI DNA methyltransferase by proteolysis.
JO  - Biochemistry
PY  - 1991
SP  - 2940
EP  - 2946
VL  - 30
AB  - Native EcoRI DNA methyltransferase (Mtase, Mr 38050) is proteolyzed by trypsin
AB  - to generate an intermediate 36-kDa fragment (p36) followed by the formation of
AB  - two polypeptides of Mr23000 and 13000 (p23 and p13, respectively).  Protein
AB  - sequence analysis of the tryptic fragments indicates that p36 results from
AB  - removal of the first 14 or 16 amino acids, p23 spans residues 15-216, and p13
AB  - spans residues 217-325.  The relative resistance to further degradation of p23
AB  - and p13 suggests stable domain structures.  This is further supported by the
AB  - generation of similar fragments with SV8 endoprotease which has entirely
AB  - different peptide specificities.  Our results suggest that Mtase is a
AB  - two-domain protein connected by a highly flexible interdomain hinge.  The
AB  - putative hinge region encompasses previously identified peptides implicated in
AB  - AdoMet binding [Reich, N.O. & Everett, E. (1990) J. Biol. Chem. 265, 8929-8934]
AB  - and catalysis [Everett et al. (1990) J. Biol. Chem. 265, 17713-17719].
AB  - Protection studies with DNA, S-adenosylmethionine (AdoMet),
AB  - S-adenosylhomocysteine (AdoHcy), and sinefungin (AdoMet analogue) show that the
AB  - Mtase undergoes significant conformational changes upon ligand binding.
AB  - Trypsinolysis of the AdoMet-bound form of the Mtase generates different
AB  - fragments, and the AdoMet-bound form is over 800 times more stable than unbound
AB  - Mtase.  The sequence-specific ternary complex (Mtase-DNA-sinefungin) is 2000
AB  - times more resistant to degradation by trypsin; cleavage eventually generates
AB  - 26- and 12-kDa fragments which span residues 104-325 and 1-103, respectively
AB  - (p26 and p12).  The first 14 or 16 amino acids of the Mtase are not essential
AB  - since p36 retains activity.  Activity analysis of the p26 and p12 mixture also
AB  - indicates retention of activity.  Therefore, either p26 is catalytically active
AB  - or the two fragments remain associated to create a functional enzyme.  The
AB  - former rationale is supported by the fact that for EcoRI Mtase, all peptide
AB  - regions implicated in DNA binding, AdoMet binding, and catalysis residue in the
AB  - p26 fragment.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Mashhoon, N.
TI  - Presteady state kinetics of an S-adenosylmethionine-dependent enzyme.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 9191
EP  - 9193
VL  - 268
AB  - We present the first presteady state kinetic analysis of an S-adenosylmethionine-dependent
AB  - enzyme. The target enzyme is the bacterial EcoRI DNA methyltransferase, which transfers the
AB  - methyl group to the second adenine in the DNA sequence GAATTC. The rate constant for
AB  - conversion of the central complex (enzyme-DNA-S-adenosylmethionine) to products
AB  - (enzyme-methylated DNA-S-adenosylhomocysteine) (41 +/- 7 s-1) is over 300-fold faster than
AB  - kcat, consistent with our demonstration that steps after methyltransfer are rate-limiting
AB  - (Reich, N.O., and Mashhoon, N. (1991) Biochemistry 30, 2933-2939). Methyltransfer at the N6
AB  - amino moiety of adenine on each strand requires a single binding orientation.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Mashhoon, N.
TI  - Inhibition of EcoRI DNA methylase with cofactor analogs.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 8966
EP  - 8970
VL  - 265
AB  - Four analogs of the natural cofactor S-adenosylmethionine (AdoMet) were tested
AB  - for their ability to bind and inhibit the prokaryotic enzyme, EcoRI adenine DNA
AB  - methylase.  The EcoRI methylase transfers the methyl group from AdoMet to the
AB  - second adenine in the double-stranded DNA sequence 5' GAATTC 3'.  Dissociation
AB  - constants (KD) of the binary methylase-analog complexes obtained in the absence
AB  - of DNA with S-adenosylhomocysteine (AdoHcy), sinefungin, N-methyl-AdoMet, and
AB  - N-ethylAdoMet are 225, 43, >1000, and >2000 microM, respectively.  In the
AB  - presence of a DNA substrate, all four analogs show simple competitive
AB  - inhibition with respect to AdoMet.  The product of the enzymic reaction,
AB  - AdoHcy, is a poor inhibitor of the enzyme (KI(AdoHcy)=9 microM; KM(AdoMet)=0.60
AB  - microM).  Two synthetic analogs, N-methyl-AdoMet and N-ethyl-AdoMet, were also
AB  - shown to be poor inhibitors with KI values of 50 and >1000 microM,
AB  - respectively.  In contrast, the naturally occurring analog sinefungin was shown
AB  - to be a highly potent inhibitor (KI=10 microM).  Gel retardation assays confirm
AB  - that the methylase-DNA-sinefungin complex is sequence-specific.  The ternary
AB  - complex is the first sequence-specific complex detected for any DNA methylase.
AB  - Potential applications to structural studies of methylase-DNA interations are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Mashhoon, N.
TI  - Kinetic mechanism of the EcoRI DNA methyltransferase.
JO  - Biochemistry
PY  - 1991
SP  - 2933
EP  - 2939
VL  - 30
AB  - We present kinetic analysis of the EcoRI DNA N6-adenosine methyltransferase
AB  - (Mtase).  The enzyme catalyzes the S-adenosylmethionine (AdoMet)-dependent
AB  - methylation of a short, synthetic 14 base pair DNA substrate and plasmid pBR322
AB  - DNA substrate with kcat/Km values of 0.51 x 10/8 and 4.1 x 10/8 S-1-M-1,
AB  - respectively.  The Mtase is thus one of the most efficient biocatalysts known.
AB  - Our data are consistent with an ordered bi-bi steady-state mechanism in which
AB  - AdoMet binds first, followed by DNA addition.  One of the reaction products,
AB  - S-adenosylhomocysteine (AdoHcy), is an uncompetitive inhibitor with respect to
AB  - DNA and a competititive inhibitor with respect to AdoMet.  Thus, initial DNA
AB  - binding followed by AdoHcy binding leads to formation of a ternary dead-end
AB  - complex (Mtase-DNA-AdoHcy).  We suggest that the product inhibition patterns
AB  - and apparent order of substrate binding can be reconciled by a mechanism in
AB  - which the Mtase binds AdoMet and noncanonical DNA randomly but that recognition
AB  - of the canonical site requires AdoMet to be bound.  Pre-steady-state and
AB  - isotope partitition analyses starting with the binary Mtase-AdoMet complex
AB  - confirm its catalytic competence.  Moreover, the methyl transfer step is at
AB  - least 10 times faster than catalytic turnover.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Mashhoon, N.
AU  - Everett, E.
AU  - Danzitz, M.
TI  - Structure-function analysis of enzyme-DNA interactions in the EcoRI DNA methylase.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 213
EP  - 213
VL  - 13D
AB  - Our goal is to understand the molecular basis of DNA sequence recognition and
AB  - the modulation of this process by the cofactor S-adenosylmethionine, [AdoMet]
AB  - in this prokaryotic system.  The kinetic mechanism and the rate determining
AB  - step[s] have been elucidated: AdoMet binds first, followed by the double
AB  - stranded DNA substrate [5'GAATTC3'].  Rapid transfer of the methyl group to the
AB  - DNA in the ternary methylase-AdoMet-DNA complex is followed by rate limiting
AB  - step[s].  One portion of the methylase involved in AdoMet binding has been
AB  - identified:  it is a flexible peptide connecting two stable domains.  This
AB  - flexible hinge region and the domains were characterized using photo affinity
AB  - analogs, in vitro proteolysis, and peptide sequencing.  Hydroxy radical
AB  - footprinting and synthetic oligonucleotides have been used to characterize the
AB  - methylase-DNA topology.  Moreover, DNA substrates with modified bases [uracil,
AB  - inosine, deaza-adenine, etc.] have been submitted to comparative specificity
AB  - analysis [kcat/KM].  Data from both analyses will be presented; the
AB  - contribution to overall specificity deriving from individual methylase-DNA
AB  - interactions has been elucidated.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Olsen, C.
AU  - Osti, F.
AU  - Murphy, J.
TI  - In vitro specificity of EcoRI DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 1992
SP  - 15802
EP  - 15807
VL  - 267
AB  - The sequence selectivity of enzyme-DNA interactions was analyzed by comparing discrimination
AB  - between synthetic oligonucleotides containing the canonical site GAATTC and altered DNA
AB  - sequences with the EcoRI DNA methyltransferase. The specificities (kcat/Km DNA) are decreased
AB  - from 5- to 23,000-fold relative to the unmodified site. For several substrates the decrease in
AB  - kcat makes a disproportionate contribution to the specificity difference, suggesting that
AB  - discrimination is mediated by the placement of critical catalytic residues rather than binding
AB  - interaction. This is supported by our observation that specificity changes are generally not
AB  - followed by changes in the stability of the methyltransferase-DNA complexes. Also, base pair
AB  - substitution near the site of methylation results in greater decreases in complex stability,
AB  - suggesting that recognition and catalytic mechanisms overlap.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Olsen, C.
AU  - Osti, F.
AU  - Murphy, J.
AU  - Smith, D.
AU  - Crowder, S.
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
JO  - ACS Abstracts
PY  - 1992
SP  - 113
EP  - BIOL
VL  - 203
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC using the
AB  - cofactor S-adenosylmethionine. We determined the in vitro sequence-selectivity with a family
AB  - of related hemimethylated 14mers (X=methyladenosine):
AB  - 5' GGCGGAATTCGCGG 3'
AB  - 3' CCGCCTTXAGCGCC 5'
AB  - Comparisons of true kcat, KmDNA, KmAdoMet and Kcat/KmDNA show specificity decreases from 5
AB  - (GAATCC) to 23,000 (GGATTC) fold (top strand shown). For several substrates the decrease in
AB  - kcat makes a disproportionate contribution toward specificity, suggesting that discrimination
AB  - is mediated by the placement of critical catalytic residues. Further evidence for this
AB  - conclusion is provided by our observation that the stability of the methyltransferase-DNA
AB  - complexes (determined by gel shift analysis) do not generally follow specificity changes. In
AB  - contrast, no methylation of noncanonical sites was detectable in vivo. We used three assays to
AB  - show that TAATTC, CAATTC, GTATTC, GGATTC and GAGTTC are not methylated in vivo under
AB  - conditions where the canonical site is protected. A possible reconciliation of these results
AB  - with our in vitro data is that noncanonical methylation does occur in vivo but is actively
AB  - repaired. The possible involvement of the recently identified mrr (methylated adenine
AB  - recognition and repair) locus in this capacity is being investigated.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Olsen, C.
AU  - Osti, F.
AU  - Murphy, J.
AU  - Smith, D.
AU  - Crowder, S.
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
JO  - FASEB J.
PY  - 1992
SP  - A217
EP  - A217
VL  - 6
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC
AB  - using the cofactor S-adenosylmethionine.  We determined the in vitro
AB  - sequence-selectivity with a family of related hemimethylated 14mers
AB  - X=methyladenosine):
AB  - 5' GGCCGGAATTCGCGG 3'
AB  - 3' CCGGCCTTXAGCGCC 5'
AB  - Comparisons of true kcat, KDNA, KmAdomet and kcat/KmDNA show specificity
AB  - decreases from 5(GAATCC) to 23,000 (GGATTC) fold (top strand shown).  For
AB  - several substrates the decrease in kcat makes a disproportionate contribution
AB  - toward specificity, suggesting that discrimination is mediated by the placement
AB  - of critical catalytic residues.  Further evidence for this conclusion is
AB  - provided by our observation that the stability of the methyltransferase-DNA
AB  - complexes (determined by gel shift analysis) do not generally follow
AB  - specificity changes.  In constrast, no methylation of noncanonical sites was
AB  - detectable in vivo.  We used three assays to show that TAATTC, CAATTC, GTATTC,
AB  - GGATTC and GAGTTC are not methylated in vivo under conditions where the
AB  - canonical site is protected.  A possible reconciliation of these results with
AB  - our in vitro data is that noncanonical methylation does occur in vivo but is
AB  - actively repaired.  The possible involvement of the recently identified mrr
AB  - (methylated adenine recognition and repair) locus in this capacity is being
AB  - investigated.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Olsen, C.
AU  - Osti, F.
AU  - Murphy, J.
AU  - Smith, D.
AU  - Crowder, S.
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
JO  - Biochemistry
PY  - 1992
SP  - 2208
EP  - 2208
VL  - 31
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC
AB  - using the cofactor S-adenosylmethionine.  We determined the in vitro sequence
AB  - selectivity with a family of related hemimethylated 14mers (X =
AB  - methyladenosine):
AB  - 5'GGCGGAATTCGCGG3'
AB  - 3'CCGCCTTXAGCGCC5'
AB  - Comparisons of true kcat, KmDNA, KmAdoMet, and kcat/Km DNA show specificity
AB  - decreases from 5-(GAATCC) to 23000-(GGATTC) fold (top strand shown).  For
AB  - several substrates the decrease in kcat makes a disproportionate contribution
AB  - toward specificity, suggesting that discrimination is mediated by the placement
AB  - of critical catalytic residues.  Further evidence for this conclusion is
AB  - provided by our observation that the stability of the methyltransferase-DNA
AB  - complexes (determined by gel shift analysis) do not generally follow
AB  - specificity changes.  In contrast, no methylation of noncanonical sites was
AB  - detectable in vivo.  We used three assays to show that TAATTC, CAATTC, GTATTC,
AB  - GGATTC, and GAGTTC are not methylated in vivo under conditions where the
AB  - canonical site is protected.  A possible reconciliation of these results with
AB  - our in vitro data is that noncanonical methylation does occur in vivo but is
AB  - actively repaired.  The possible involvement of the recently identified mrr
AB  - (methylated adenine recognition and repair locus in this capacity is being
AB  - investigated.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Olsen, C.
AU  - Osti, F.
AU  - Murphy, J.
AU  - Smith, D.
AU  - Crowder, S.
TI  - In vitro and in vivo specificity analysis of the EcoRI DNA methyltransferase.
JO  - Biophys. J.
PY  - 1992
SP  - A217
EP  - A217
VL  - 61
AB  - The EcoRI DNA methyltransferase modifies the second adenine in the site GAATTC
AB  - using the cofactor S-adenosylmethionine.  We determined the in vitro
AB  - sequence-selectivity with a family of related hemimethylated 14mers
AB  - (X-methyladenosine): top 5GGCGGAATTCGCGG3/5CCGCGAXTTCCGCC3' bottom.
AB  - Comparisons of the true kcat, KDNA, KmAdoMet and kcat/KmDNA show specificity
AB  - decreases from 5(GAATCC) to 23,000 (GGATTC) fold (top strand shown).  For
AB  - several substrates the decrease in kcat makes a disproportionate contribution
AB  - toward specificity, suggesting that discrimination is mediated by the placement
AB  - of critical catalytic residues.  Further evidence for this conclusion is
AB  - provided by our observation that the stability of the methyltransferase-DNA
AB  - complexes (determined by gel shift analysis) do not generally follow
AB  - specificity changes.  In contrast, no methylation of noncanonical sites was
AB  - detectable in vivo.  We used three assays to show that TAATTC, CAATTC, GTATTC,
AB  - GGATTC and GAGTTC are not methylated in vivo under conditions where the
AB  - canonical site is protected.  A possible reconciliation of these results with
AB  - our in vitro data is that noncanonical methylation does occur in vivo but is
AB  - actively repaired.  The possible involvement of the recently identified mrr
AB  - (methylated adenine recognition and repair) locus in this capacity is being
AB  - investigated.
ER  -

TY  - JOUR
AU  - Reich, N.O.
AU  - Svedruzic, Z.
AU  - Flynn, J.
AU  - Aubol, B.
TI  - The enzymology of epigenetics: Mechanism and inhibition of mammalian DNA cytosine methyltransferase.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 2000
SP  - 346
EP  - 347
VL  - 41
AB  - The major DNA cytosine methyltransferase in mammals, Dnmt1, is potently inhibited by a novel
AB  - allosteric inhibitor.  The inhibitor decreases DNA methylation in mammalian cells.  Other
AB  - compounds that decrease cellular DNA methylation levels have been shown to reverse
AB  - tumorigenesis in animals.  Thus, our inhibitor is being tested in tumor cell lines as a new
AB  - anticancer therapeutic.  The expression of newly integrated viral DNA is often stopped by DNA
AB  - methylation.  "DNA methylation spreading" results from the "activation" of the enzyme by
AB  - proximal 5-methylcytosine groups adjacent to the target CpG that undergoes methylation.  This
AB  - occurs primarily in single-stranded DNA, the 5-methylcytosine can be anywhere from 3 to 27
AB  - nucleotides removed from the CpG, and the effect is due to an increased affinity of the enzyme
AB  - for its substrate.  Our results have implications for the potential methylation-dependent
AB  - silencing of genes during gene therapy.  Dnmt1 prefers hemimethylated substrates; this occurs
AB  - during the initial attack at the C6 position of the target cytosine, rather than the
AB  - subsequent methyl transfer step.  Dnmt1 catalyzes the exchange of the C5 hydrogen of cytosine,
AB  - but only in the presence of the natural cofactor AdoMet, or certain cofactor analogs.  Similar
AB  - results were reported for the related deamination reaction catalyzed by bacterial enzymes,
AB  - suggesting that exchange and demamination occur through similar reaction intermediates.  Our
AB  - results suggest that Dnmt1 may not be mutagenic under the conditions previously demonstrated
AB  - for the bacterial enzyme.
ER  -

TY  - JOUR
AU  - Reich, S.
TI  - Reaction mechanism of type III restriction endonuclease EcoP151 and possible application in molecular diagnostics.
JO  - Ph.D. Thesis, Germany
PY  - 2003
SP  - 1
EP  - 100
AB  - EcoP15I is a multifunctional, hetero-oligomeric Type III restriction enzyme.  Type III
AB  - restriction enzymes are of general interest in medicine and functional genome analysis because
AB  - they cut DNA 25 bp downstream of their recognition site.  EcoP15I recognises the DNA sequence
AB  - 5'-CAGCAG and needs two inverse oriented recognition sites for effective DNA cleavage.
AB  - According to the present translocation collision model DNA cleavage was proposed to result
AB  - from ATP dependent DNA translocation, which is expected to induce DNA loop formation, and
AB  - collision of two enzyme-DNA complexes.  Experiments show that EcoP15 moves rather in a
AB  - three-dimensional than in a 'sliding' process in search for its recognition site.
AB  - Huntington's disease is a progressive neurodegenerative disorder with autosomal-dominant
AB  - inheritance.  The disease is caused by a CAG trinucleotide repeat expansion located in the
AB  - first exon of the HD gene.  To diagnose the illness the exact determination of the number of
AB  - CAG repeats is necessary.  This study shows that the number of CAG repeats in the HD gene can
AB  - be determined by restriction of the DNA with the endonuclease EcoP15I and subsequent
AB  - high-resolution analysis of the restriciton fragment pattern using the ALPexpress DNA Analysis
AB  - System.  Here, for the first time DNA translocation by the Type III restriction enzyme EcoP15I
AB  - is demonstrated.  The postulated EcoP15-DNA loops are visualised using scanning force
AB  - microscopy.  This confirms the translocation-collision model for DNA cleavage by EcoP15.
AB  - Similarities and differences between the DNA cleavage processes of the Type III restriciton
AB  - enzyme EcoP15I and other restriction enzymes are discussed.
ER  -

TY  - JOUR
AU  - Reich, S.
AU  - Gossl, D.
AU  - Reuter, M.
AU  - Rabe, J.P.
AU  - Kruger, D.H.
TI  - Scanning force microscopy of DNA translocation by the type III restriction enzyme EcoP15I.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 337
EP  - 343
VL  - 341
AB  - Type III restriction enzymes are multifunctional heterooligomeric enzymes that cleave DNA at a
AB  - fixed position downstream of a non-symmetric recognition site. For effective DNA cleavage
AB  - these restriction enzymes need the presence of two unmethylated, inversely oriented
AB  - recognition sites in the DNA molecule. DNA cleavage was proposed to result from ATP-dependent
AB  - DNA translocation, which is expected to induce DNA loop formation, and collision of two
AB  - enzyme-DNA complexes. We used scanning force microscopy to visualise the protein interaction
AB  - with linear DNA molecules containing two EcoP15I recognition sites in inverse orientation. In
AB  - the presence of the cofactors ATP and Mg2+, EcoP15I molecules were shown to bind specifically
AB  - to the recognition sites and to form DNA loop structures. One of the origins of the
AB  - protein-clipped DNA loops was shown to be located at an EcoP15I recognition site, the other
AB  - origin had an unspecific position in between the two EcoP15I recognition sites. The data
AB  - demonstrate for the first time DNA translocation by the Type III restriction enzyme EcoP15I
AB  - using scanning force microscopy. Moreover, our study revealed differences in the
AB  - DNA-translocation processes mediated by Type I and Type III restriction enzymes.
ER  -

TY  - JOUR
AU  - Reich, S.
AU  - Mucke, M.
AU  - Moncke-Buchner, E.
AU  - Reuter, M.
AU  - Kruger, D.H.
TI  - DNA cleavage by the restriction endonuclease EcoP15I.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A331
EP  - A331
VL  - 28
AB  - The type III restriction endonuclease EcoP15I recognizes the asymmetric DNA sequence
AB  - 5'-CAGCAG and cleaves it 25-27 bp downstream.  Two unmethylated, inversely oriented
AB  - recognition sites in head-to-head configuration (5'-CAGCAG...NNN...CTGCTG) are preferred
AB  - substrates in DNA cleavage.  An intrinsic ATPase activity is the potential driving force of
AB  - DNA translocation bringing two EcoP15I-DNA complexes together.  In this work we investigated
AB  - EcoP15I cleavage efficiency in dependence on distance of two inversely oriented recognition
AB  - sites.  We showed that EcoP15I proceeds to cleave DNA efficiently even in the case of two
AB  - adjacent head-to-head oriented recognition sites, but cleavage rate rapidly diminished with
AB  - increasing distance of two tail-to-tail oriented recognition sites.  EcoP15I cleavage was
AB  - abolished in the presence of non-hydrolysable ATP analogs instead of ATP, even on substrates
AB  - with recognition sites in close vicinity.  This confirmed a role of ATP hydrolysis for the
AB  - phosphodiester bond cleavage.  Furthermore, DNaseI footprint experiments were performed to get
AB  - insight into the spatial requirements of the enzyme on substrate DNA with one recognition site
AB  - and revealed a 36 base-footprint rather symmetrical in both strands.  It became evident that
AB  - the enzyme did not cover the region around the cleavage site.  Presence of ATP caused a change
AB  - in the footprint pattern.  Analyzing a DNA fragment with two head-to-head oriented recognition
AB  - sites, an additional region between the two cooperative cleavage sites was protected against
AB  - DNaseI digestion.  Our experimental data allow a refinement of the tracking-collision model
AB  - discussed for type III enzymes and give suggestions on the spatial organization of the
AB  - collision complex.
ER  -

TY  - JOUR
AU  - Reichley, S.R.
AU  - Waldbieser, G.C.
AU  - Lawrence, M.L.
AU  - Griffin, M.J.
TI  - Complete Genome Sequence of Edwardsiella hoshinae ATCC 35051.
JO  - Genome Announcements
PY  - 2017
SP  - e01605
EP  - e01616
VL  - 5
AB  - Edwardsiella hoshinae is a Gram-negative facultative anaerobe that has primarily  been
AB  - isolated from avians and reptiles. We report here the complete and annotated
AB  - genome sequence of an isolate from a monitor lizard (Varanus sp.), which contains
AB  - a chromosome of 3,811,650 bp and no plasmids.
ER  -

TY  - JOUR
AU  - Reichley, S.R.
AU  - Waldbieser, G.C.
AU  - Lawrence, M.L.
AU  - Griffin, M.J.
TI  - Complete Genome Sequence of an Edwardsiella piscicida-Like Species, Recovered from Tilapia in the United States.
JO  - Genome Announcements
PY  - 2015
SP  - e01004
EP  - e01015
VL  - 3
AB  - An Edwardsiella piscicida-like species is a Gram-negative facultative anaerobe that causes
AB  - disease in some fish species. In this report, we present the complete and annotated genome of
AB  - isolate LADL05-105, recovered from cultured tilapia reared in Louisiana, which contains a
AB  - chromosome of 4,142,037 bp and no plasmids.
ER  -

TY  - JOUR
AU  - Reichley, S.R.
AU  - Waldbieser, G.C.
AU  - Soto, E.
AU  - Lawrence, M.L.
AU  - Griffin, M.J.
TI  - Complete Genome Sequence of Edwardsiella ictaluri Isolate RUSVM-1 Recovered from  Nile Tilapia (Oreochromis niloticus) in the Western Hemisphere.
JO  - Genome Announcements
PY  - 2017
SP  - e00390
EP  - e00317
VL  - 5
AB  - Edwardsiella ictaluri is a Gram-negative bacillus that has recently been implicated in disease
AB  - outbreaks in tilapia and zebrafish. We report here the
AB  - complete and annotated genome sequence of an isolate from a Nile tilapia
AB  - (Oreochromis niloticus), which contains a chromosome of 3,630,639 bp and two
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Reichley, S.R.
AU  - Waldbieser, G.C.
AU  - Tekedar, H.C.
AU  - Lawrence, M.L.
AU  - Griffin, M.J.
TI  - Complete Genome Sequence of Edwardsiella tarda Isolate FL95-01, Recovered from Channel Catfish.
JO  - Genome Announcements
PY  - 2015
SP  - e00682
EP  - e00615
VL  - 3
AB  - Edwardsiella tarda is a Gram-negative facultative anaerobe that has been isolated from fish,
AB  - reptiles, amphibians, and mammals, including humans. This is a report
AB  - of the complete and annotated genome of isolate FL95-01, recovered from channel
AB  - catfish (Ictalurus punctatus).
ER  -

TY  - JOUR
AU  - Reichley, S.R.
AU  - Waldbieser, G.C.
AU  - Tekedar, H.C.
AU  - Lawrence, M.L.
AU  - Griffin, M.J.
TI  - Complete Genome Sequence of Edwardsiella piscicida Isolate S11-285 Recovered from Channel Catfish (Ictalurus punctatus) in Mississippi, USA.
JO  - Genome Announcements
PY  - 2016
SP  - e01259
EP  - e01216
VL  - 4
AB  - Edwardsiella piscicida is a recently described Gram-negative facultative anaerobe and an
AB  - important pathogen to many wild and cultured fish species worldwide. Here,
AB  - we report the complete and annotated genome of E. piscicida isolate S11-285
AB  - recovered from channel catfish (Ictalurus punctatus), consisting of a chromosome
AB  - of 3,923,603 bp and 1 plasmid.
ER  -

TY  - JOUR
AU  - Reichley, S.R.
AU  - Waldbieser, G.C.
AU  - Ucko, M.
AU  - Colorni, A.
AU  - Dubytska, L.
AU  - Thune, R.L.
AU  - Lawrence, M.L.
AU  - Griffin, M.J.
TI  - Complete Genome Sequence of an Edwardsiella piscicida-Like Species Isolated from  Diseased Grouper in Israel.
JO  - Genome Announcements
PY  - 2015
SP  - e00829
EP  - e00815
VL  - 3
AB  - The Edwardsiella piscicida-like sp. is a Gram-negative facultative anaerobe that  causes
AB  - disease in some fish species. We report here the complete genome sequence
AB  - of a virulent isolate from a diseased white grouper (Epinephelus aeneus) raised
AB  - on the Red Sea in Israel, which contains a chromosome of 3,934,167 bp and no
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Reid, S.L.
AU  - Parry, D.
AU  - Liu, H.-H.
AU  - Connolly, B.A.
TI  - Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: A study using fluorescent oligonucleotides and fluorescence polarization.
JO  - Biochemistry
PY  - 2001
SP  - 2484
EP  - 2494
VL  - 40
AB  - Oligonucleotides labeled with hexachlorofluorescein (hex) have enabled the interaction of the
AB  - restriction endonuclease EcoRV with DNA to be
AB  - evaluated using fluorescence anisotropy. The sensitivity of hex allowed
AB  - measurements at oligonucleotide concentrations as low as 1 nM, enabling
AB  - KD values in the low nanomolar range to be measured. Both direct
AB  - titration, i.e., addition of increasing amounts of the endonuclease to
AB  - hex-labeled oligonucleotides, and displacement titration, i.e.,
AB  - addition of unlabeled oligonucleotide to preformed
AB  - hex-oligonucleotide/EcoRV endonuclease complexes, have been used for KD
AB  - determination. Displacement titration is the method of choice;
AB  - artifacts due to any direct interaction of the enzyme with the dye are
AB  - eliminated, and higher fluorescent-labeled oligonucleotide
AB  - concentrations may be used, improving signal-to-noise ratio. Using this
AB  - approach (with three different oligonucleotides) we found that the
AB  - EcoRV restriction endonuclease showed a preference of between 1.5 and
AB  - 6.5 for its GATATC target sequence at pH 7.5 and 100 mM NaCl, when the
AB  - divalent cation Ca2+ is absent. As expected, both the presence of Ca2+
AB  - and a decrease in pH value stimulated the binding of specific sequences
AB  - but had much less effect on nonspecific ones.
ER  -

TY  - JOUR
AU  - Reik, W.
AU  - Allen, N.D.
TI  - Imprinting with and without methylation.
JO  - Curr. Biol.
PY  - 1994
SP  - 145
EP  - 147
VL  - 4
AB  - Methyltransferase-deficient mice reveal that DNA methylation is required for the somatic-cell
AB  - maintenance of parental imprinting, which alters the expression of a gene according to the
AB  - parent from which it was inherited.
ER  -

TY  - JOUR
AU  - Reik, W.
AU  - Kelsey, G.
AU  - Walter, J.
TI  - Dissecting de novo methylation.
JO  - Nat. Genet.
PY  - 1999
SP  - 380
EP  - 382
VL  - 23
AB  - The methylation of DNA is fundamental to mammalian development.  This is vividly illustrated
AB  - by the fact that mouse embryos deficient in Dnmt1, a DNA methyltransferase that methylates
AB  - cytosine groups, die as a result of genome-wide demethylation.  Dnmt1 seems to be the main
AB  - enzyme responsible for maintaining methylation after each round of DNA replication.  But
AB  - studies of Dnmt1-deficient embryonic stem cells have revealed that other enzymes must exist to
AB  - methylate the genome de novo after the wave of global demethylation that occurs during early
AB  - embryonic development.  Okano et al. recently reported that murine Dnmt3a and Dnmt3b are the
AB  - long-sought mammalian de novo methyltransferases.  Their findings, as well as those of Xu et
AB  - al. and Hansen et al., also show that mutations of DNMT3B cause a disorder associated with
AB  - immunodeficiency, centromere instability and facial anomalies (ICF syndrome).  This disorder
AB  - is the only known human condition with constitutive abnormalities in DNA methylation.
ER  -

TY  - JOUR
AU  - Reik, W.
AU  - Walter, J.
TI  - Imprinting mechanisms in mammals.
JO  - Current Opinion in Genetics
PY  - 1998
SP  - 154
EP  - 164
VL  - 8
AB  - Imprinting is a genetic mechanism that determines expression or repression of genes according
AB  - to their parental origin.  Some imprinted genes occur in clusters in the genome.  Recent work
AB  - using transgenic mice shows that multiple cis-acting sequences are needed for correct
AB  - imprinting.  Mutation analysis in a normal chromosomal context reveals the importance of
AB  - imprinting centers for regional establishment or maintenance of imprinting in a cluster.
AB  - Elements that contribute to the function of imprinting centers and regional propagation of the
AB  - imprints are CpG-rich differentially methylated regions (that during development retain
AB  - germline imposed methylation or demethylation), direct repeat clusters, and unusual RNA's
AB  - (antisense, non-translated etc.).  The interaction of these cis elements with transacting
AB  - factors such as methylase and chromatin factors establishes a hierarchical control system with
AB  - local and regional effects.
ER  -

TY  - JOUR
AU  - Reimundo, P.
AU  - Rivas, A.J.
AU  - Osorio, C.R.
AU  - Mendez, J.
AU  - Perez-Pascual, D.
AU  - Navais, R.
AU  - Gomez, E.
AU  - Sotelo, M.
AU  - Lemos, M.L.
AU  - Guijarro, J.A.
TI  - Application of suppressive subtractive hybridization to the identification of genetic differences between two Lactococcus garvieae strains showing distinct differences in virulence for rainbow trout and mouse.
JO  - Microbiology
PY  - 2011
SP  - 2106
EP  - 2119
VL  - 157
AB  - Lactococcus garvieae is the causative microbial agent of lactococcosis, an important and
AB  - damaging fish disease in aquaculture. This bacterium has also been isolated from vegetables,
AB  - milk, cheese, meat and sausages, from cow and buffalo as a mastitis agent, and even from
AB  - humans, as an opportunistic infectious agent. In this work pathogenicity experiments were
AB  - performed in rainbow trout and mouse models with strains isolated from human (L. garvieae HF)
AB  - and rainbow trout (L. garvieae UNIUDO74; henceforth referred to as 074). The mean LD(50) value
AB  - in rainbow trout obtained for strain 074 was 2.1x10(2)+/-84 per fish. High doses of the
AB  - bacteria caused specific signs of disease as well as histological alterations in mice. In
AB  - contrast, strain HF did not prove to be pathogenic either for rainbow trout or for mice. Based
AB  - on these virulence differences, two suppressive subtractive hybridizations were carried out to
AB  - identify unique genetic sequences present in L. garvieae HF (SSHI) and L. garvieae 074
AB  - (SSHII). Differential dot-blot screening of the subtracted libraries allowed the
AB  - identification of 26 and 13 putative ORFs specific for L. garvieae HF and L. garvieae 074,
AB  - respectively. Additionally, a PCR-based screening of 12 of the 26 HF-specific putative ORFs
AB  - and the 13 074-specific ones was conducted to identify their presence/absence in 25 L.
AB  - garvieae strains isolated from different origins and geographical areas. This study
AB  - demonstrates the existence of genetic heterogeneity within L. garvieae isolates and provides a
AB  - more complete picture of the genetic background of this bacterium.
ER  -

TY  - JOUR
AU  - Rein, T.
AU  - DePamphilis, M.L.
AU  - Zorbas, H.
TI  - Identifying 5-methylcytosine and related modifications in DNA genomes.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 2255
EP  - 2264
VL  - 26
AB  - Intense interest in the biological roles of DNA methylation, particularly in eukaryotes, has
AB  - produced at least eight different methods for identifying 5-methylcytosine and related
AB  - modifications in DNA genomes.  However, the utility of each method depends not only on its
AB  - simplicity but on its specificity, resolution, sensitivity and potential artifacts.  Since
AB  - these parameters affect the interpretation of data, they should be considered in any
AB  - application.  Therefore, we have outlined the principles and applications of each method,
AB  - quantitatively evaluated their specificity, resolution and sensitivity, identified potential
AB  - artifacts and suggested solutions, and discussed a paradox in the distribution of m5C in
AB  - mammalian genomes that illustrates how methodological limitations can affect interpretation of
AB  - data.  Hopefully, the information and analysis provided here will guide new investigators
AB  - entering this exciting field.
ER  -

TY  - JOUR
AU  - Reinecke, S.N.
AU  - Morgan, R.D.
TI  - BfaI, a new MaeI isoschizomer from Bacteroides fragilis, recognizes the sequence 5' C^TAG 3'.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 1152
EP  - 1152
VL  - 19
AB  - A new type II restriction endonuclease, BfaI, has been isolated from
AB  - Bacteroides fragilis (NEB #668).  BfaI recognizes the four base sequence 5'
AB  - CTAG 3' and cleaves between the C and the T residues to produce a 2 base 5'
AB  - extension; C/TAG.
ER  -

TY  - JOUR
AU  - Reiner, J.E.
AU  - Lapp, C.J.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Overmann, J.
AU  - Gescher, J.
TI  - Complete Genome Sequence of Kyrpidia sp. Strain EA-1, a Thermophilic Knallgas Bacterium, Isolated from the Azores.
JO  - Genome Announcements
PY  - 2018
SP  - e01505
EP  - e01517
VL  - 6
AB  - Kyrpidia sp. strain EA-1 is a thermophilic hydrogen-oxidizing bacterium isolated  from
AB  - hydrothermal systems at Sao Miguel Island, Portugal. Here, we present the
AB  - complete genome sequence of the strain assembled to a single circular chromosome.
AB  - The genome spans 3,352,175 bp, with a GC content of 58.7%.
ER  -

TY  - JOUR
AU  - Reinhard, B.M.
AU  - Sheikholeslami, S.
AU  - Mastroianni, A.
AU  - Alivisatos, A.P.
AU  - Liphardt, J.
TI  - Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 2667
EP  - 2672
VL  - 104
AB  - Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the
AB  - dependence of their light scattering on the interparticle distance. Preliminary work has
AB  - suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over
AB  - the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be
AB  - used to measure dynamical biophysical processes by applying the ruler to a system that has
AB  - been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by
AB  - the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the
AB  - end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously
AB  - monitored for hours. The kinetic parameters extracted from our single-molecule cleavage
AB  - trajectories agree well with values obtained in bulk through other methods and confirm well
AB  - known features of the cleavage process, such as DNA bending before cleavage. Previously
AB  - unreported dynamical information is revealed as well, for instance, the degree of softening of
AB  - the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high
AB  - signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies
AB  - and conformational changes at the single-molecule level.
ER  -

TY  - JOUR
AU  - Reinhardt, M.
AU  - Hammerl, J.A.
AU  - Hertwig, S.
TI  - Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany.
JO  - Genome Announcements
PY  - 2018
SP  - e00266
EP  - e00218
VL  - 6
AB  - We report here the draft genome sequences of 10 Yersinia pseudotuberculosis isolates recovered
AB  - from tonsils of wild boars hunted between 2015 and 2016 in
AB  - Germany. Whole-genome sequencing and bioinformatic analyses were performed to
AB  - assess the diversity of Y. pseudotuberculosis, which may result in human
AB  - infections caused by the consumption of game meat.
ER  -

TY  - JOUR
AU  - Reinisch, K.M.
TI  - The crystal structure of HaeIII methylase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing.
JO  - Diss. Abstr.
PY  - 1996
SP  - 3746B
EP  - 3746B
VL  - 56
AB  - Many organisms expand the information content of their genome through enzymatic methylation of
AB  - cytosine residues.  The structure of M.HaeIII, a bacterial DNA (cytosine-5) methyltransferase
AB  - (DCMtase), bound covalently to DNA, is presented here.  The structure has been solved by X-ray
AB  - diffraction using the multiple isomorphous replacement method.  It has been refined to 2.8 A
AB  - with a crystallographic Rfree-value of 32.6% (R-value of 22.6%) and root mean square
AB  - deviations from ideal values of 0.012 Angstroms and 2.3 degrees for bond lengths and angles,
AB  - respectively.  In the M.HaeIII-DNA complex, the substrate cytosine is extruded from the DNA
AB  - helix and inserted into the active site of the enzyme, as was observed for another DCMtase,
AB  - M.HhaI.  The DNA is bound in a cleft between the two domains of the protein and is distorted
AB  - from the characteristic B-form conformation at its recognition sequence.  A comparison of
AB  - structures shows that the M.HaeIII complex differs from that of M.HhaI in that the remaining
AB  - bases in the M.HaeIII recognition sequence undergo an extensive rearrangement in their
AB  - pairing.  In this process, the bases are unstacked, and a gap 8 Angstroms long opens in the
AB  - DNA.
ER  -

TY  - JOUR
AU  - Reinisch, K.M.
AU  - Chen, L.
AU  - Verdine, G.L.
AU  - Lipscomb, W.N.
TI  - Crystallization and preliminary crystallographic anlaysis of a DNA (cytosine-5)-methyltransferase from Haemophilus aegyptius bound covalently to DNA.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 626
EP  - 629
VL  - 238
AB  - A DNA (cytosine)-5-methyltransferase from Haemophilus aegyptius (M.HaeIII), which catalyzes
AB  - methyl transfer from S-adenosyl-L-methionine to DNA, has been crystallized as a covalent
AB  - complex with a suicide oliogonucleotide substrate. Crystals of the co-complex were grown by
AB  - vapor diffusion with hanging droplets, using polyethylene glycol 3500 as the precipitant. The
AB  - crystals belong to the orthorhombic space group P212121; the unit cell parameters are a=57.6A,
AB  - b=108.0A, c=155.8A with two protein-DNA complexes in the asymmetric unit. Complete sets of
AB  - native and derivative data have been collected to 2.7A using a laboratory source.
ER  -

TY  - JOUR
AU  - Reinisch, K.M.
AU  - Chen, L.
AU  - Verdine, G.L.
AU  - Lipscomb, W.N.
TI  - The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
JO  - Cell
PY  - 1995
SP  - 143
EP  - 153
VL  - 82
AB  - Many organisms expand the information content of their genome through enzymatic methylation of
AB  - cytosine residues.  Here we report the 2.8 A crystal structure of a bacterial DNA
AB  - (cytosine-5)-methyltransferase (DCMtase), M. HaeIII, bound covalently to DNA.  In this
AB  - complex, the substrate cytosine is extruded from the DNA helix and inserted into the active
AB  - site of the enzyme, as has been observed for another DCMtase, M.HhaI.  The DNA is bound in a
AB  - cleft between the two domains of the protein and is distorted from the characteristic B-form
AB  - conformation at its recognition sequence.  A comparison of structures shows a variation in the
AB  - mode of DNA recognition: M.HaeIII differs from M.HhaI in that the remaining bases in its
AB  - recognition sequence undergo an extensive rearrangement in their pairing.  In this process,
AB  - the bases are unstacked, and a gap 8 A long opens in the DNA.
ER  -

TY  - JOUR
AU  - Reis, A.C.
AU  - Kroll, K.
AU  - Gomila, M.
AU  - Kolvenbach, B.A.
AU  - Corvini, P.F.X.
AU  - Nunes, O.C.
TI  - Complete Genome Sequence of Achromobacter denitrificans PR1.
JO  - Genome Announcements
PY  - 2017
SP  - e00762
EP  - e00717
VL  - 5
AB  - Achromobacter denitrificans strain PR1 was isolated from an enrichment culture able to use
AB  - sulfamethoxazole as an energy source. Here, we describe the complete
AB  - genome of this strain sequenced by Illumina MiSeq and Oxford Nanopore MinION.
ER  -

TY  - JOUR
AU  - Reisenauer, A.
AU  - Kahng, L.S.
AU  - McCollum, S.
AU  - Shapiro, L.
TI  - Bacterial DNA Methylation: a Cell Cycle Regulator?
JO  - J. Bacteriol.
PY  - 1999
SP  - 5135
EP  - 5139
VL  - 181
AB  - A MiniReview of the role of CcrM (M.CcrMI) and Dam (M.EcoDam) methylases in regulating various
AB  - cellular processes such as DNA replication, cell-cycle and others.
ER  -

TY  - JOUR
AU  - Reisenauer, A.
AU  - Shapiro, L.
TI  - DNA methylation affects the cell cycle transcription of the CtrA global regulator in Caulobacter.
JO  - EMBO J.
PY  - 2002
SP  - 4969
EP  - 4977
VL  - 21
AB  - The Caulobacter chromosome changes progressively from the fully methylated to the
AB  - hemimethylated state during DNA replication. These changes in DNA methylation could signal
AB  - differential binding of regulatory proteins to activate or repress transcription. The gene
AB  - encoding CtrA, a key cell cycle regulatory protein, is transcribed from two promoters. The P1
AB  - promoter fires early in S phase and contains a GAnTC sequence that is recognized by the CcrM
AB  - DNA methyltransferase. Using analysis of CcrM mutant strains, transcriptional reporters
AB  - integrated at different sites on the chromosome, and a ctrA P1 mutant, we demonstrate that
AB  - transcription of the P1 promoter is repressed by DNA methylation. Moreover moving the native
AB  - ctrA gene to a position near the chromosomal terminus, which delays the conversion of the ctrA
AB  - promoter from the fully to the hemimethylated state until late in the cell cycle, inhibited
AB  - ctrA P1 transcription, and altered the time of accumulation of the CtrA protein and the size
AB  - distribution of swarmer cells. Together, these results show that CcrM-catalyzed methylation
AB  - adds another layer of control to the regulation of ctrA expression.
ER  -

TY  - JOUR
AU  - Reiser, J.
AU  - Yuan, R.
TI  - Purification and properties of the P15 specific restriction endonuclease from Escherichia coli.
JO  - J. Biol. Chem.
PY  - 1977
SP  - 451
EP  - 456
VL  - 252
AB  - The specific restriction endonuclease of the Escherichia coli plasmid, P15, has
AB  - been purified to apparent homogeneity by a procedure that includes
AB  - DNA-cellulose chromatography as well as a new endonuclease assay.
AB  - Sedimentation on glycerol gradients showed two peaks of activity with values of
AB  - 11.3 S and 15.7 S.  The highly purified enzyme requires ATP and Mg2+ for
AB  - activity and is stimulated by S-adenosylmethionine.  A methylase activity is
AB  - observed in the course of the endonucleolytic reaction which protects some of
AB  - the DNA sites from cleavage.
ER  -

TY  - JOUR
AU  - Reiser, J.
AU  - Yuan, R.
TI  - A new cleavage assay for restriction endonucleases.
JO  - Experientia
PY  - 1975
SP  - 745
EP  - 745
VL  - 31
AB  - Four different assays have recently been used for restriction enzymes.  Both
AB  - sucrose gradient and gel electrophoresis assays do not give quantitative values
AB  - whereas transfection is very time consuming.  The standard filter-binding assay
AB  - is based on the formation of an enzyme-DNA complex which can then be trapped on
AB  - nitrocellulose filters.  However, the restriction endonucleases from E. coli
AB  - (P1) and E. coli (15) do not show such binding, and a new cleavage assay that
AB  - was quick and quantitative had to be developed.  The basis for the assay is the
AB  - observation of Saucier and Wang (Biochem. 12, 2755, 1973) that circular lambda
AB  - DNA binds to nitrocellulose filters under specified conditions, whereas linear
AB  - lambda DNA will pass through.  For the cleavage assay linear lambda DNA is
AB  - circularized to form hydrogen-bonded circles (Hershey circles).  The circles
AB  - are then exposed to the enzyme in a complete reaction mixture; the reaction is
AB  - stopped by SDS and filtered rapidly through nitrocellulose filters without any
AB  - subsequent washing.  The filters are dried and counted in a liquid
AB  - scintillation counter.  The assay is specific (as checked with modified DNA and
AB  - dependence on cofactors), linear and quantitative.  It has been used
AB  - successfully in the purification of the restriction endonucleases from E. coli
AB  - (P1) and E. coli (15).
ER  -

TY  - JOUR
AU  - Reith, M.
AU  - Munholland, J.
TI  - Complete nucleotide sequence of the Porphyra purpurea chloroplast genome.
JO  - Plant Mol. Biol. Rep.
PY  - 1995
SP  - 333
EP  - 335
VL  - 13
AB  - The complete nucleotide sequence of the chloroplast genome of the red alga Porphyra purpurea
AB  - has been determined (accession number = U38804).  The circular genome is 191,028 bp in length
AB  - and encodes approximately 250 genes.
ER  -

TY  - JOUR
AU  - Reither, S.
AU  - Li, F.
AU  - Gowher, H.
AU  - Jeltsch, A.
TI  - Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 675
EP  - 684
VL  - 329
AB  - Co-transfections of reporter plasmids and plasmids encoding the catalytic domain of the murine
AB  - Dnmt3a DNA methyltransferase lead to inhibition of
AB  - reporter gene expression. As Dnmt3a mutants with C-->A and E-->A exchanges
AB  - in the conserved PCQ and ENV motifs in the catalytic center of the enzyme
AB  - also cause repression, we checked for their catalytic activity in vitro.
AB  - Surprisingly, the activity of the cysteine variant and of the
AB  - corresponding full-length Dnmt3a variant is only two to sixfold reduced
AB  - with respect to wild-type Dnmt3a. In contrast, enzyme variants carrying
AB  - E-->A, E-->D or E-->Q exchanges of the ENV glutamate are catalytically
AB  - almost inactive, demonstrating that this residue has a central function in
AB  - catalysis. Since the glutamic acid residue contacts the flipped base, its
AB  - main function could be to hold the target base at a position that supports
AB  - methyl group transfer. Whereas wild-type Dnmt3a and the ENV variants form
AB  - covalent complexes with 5-fluorocytidine modified DNA, the PCN variant
AB  - does not. Therefore, covalent complex formation is not essential in the
AB  - reaction mechanism of Dnmt3a. We propose that correct positioning of the
AB  - flipped base and the cofactor and binding to the transition state of
AB  - methyl group transfer are the most important roles of the Dnmt3a enzyme in
AB  - the catalytic cycle of methyl group transfer.
ER  -

TY  - JOUR
AU  - Remenant, B.
AU  - Babujee, L.
AU  - Lajus, A.
AU  - Medigue, C.
AU  - Prior, P.
AU  - Allen, C.
TI  - Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2742
EP  - 2743
VL  - 194
AB  - Ralstonia solanacearum is a widespread and destructive plant pathogen. We present the genome
AB  - of the type strain, K60 (phylotype IIA, sequevar 7). Sequevar 7
AB  - strains cause ongoing tomato bacterial wilt outbreaks in the southeastern United
AB  - States. K60 generally resembles R. solanacearum CFBP2957, a Caribbean tomato
AB  - isolate, but has almost 360 unique genes.
ER  -

TY  - JOUR
AU  - Remenant, B.
AU  - Borges, F.
AU  - Cailliez-Grimal, C.
AU  - Revol-Junelles, A.M.
AU  - Marche, L.
AU  - Lajus, A.
AU  - Medigue, C.
AU  - Pilet, M.F.
AU  - Prevost, H.
AU  - Zagorec, M.
TI  - Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01109
EP  - e01116
VL  - 4
AB  - In this study, we present the draft genome sequence of Carnobacterium divergens V41. This
AB  - strain was previously reported as producing divercin V41, a bacteriocin
AB  - of interest for food biopreservation. Its genome revealed also the presence of a
AB  - gene cluster putatively involved in polyketide production, which is unique in
AB  - lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Remenant, B.
AU  - Coupat-Goutaland, B.
AU  - Guidot, A.
AU  - Cellier, G.
AU  - Wicker, E.
AU  - Allen, C.
AU  - Fegan, M.
AU  - Pruvost, O.
AU  - Elbaz, M.
AU  - Calteau, A.
AU  - Salvignol, G.
AU  - Mornico, D.
AU  - Mangenot, S.
AU  - Barbe, V.
AU  - Medigue, C.
AU  - Prior, P.
TI  - Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence.
JO  - BMC Genomics
PY  - 2010
SP  - 379
EP  - 379
VL  - 11
AB  - ABSTRACT: BACKGROUND: The Ralstonia solanacearum species complex includes
AB  - thousands of strains pathogenic to an unusually wide range of plant
AB  - species. These globally dispersed and heterogeneous strains cause
AB  - bacterial wilt diseases, which have major socio-economic impacts.
AB  - Pathogenicity is an ancestral trait in R. solanacearum and strains with
AB  - high genetic variation can be subdivided into four phylotypes, correlating
AB  - to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB),
AB  - Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome
AB  - sequences strains representative of this phylogenetic diversity can help
AB  - determine which traits allow this bacterium to be such a pathogen of so
AB  - many different plant species and how the bacteria survive in many
AB  - different habitats. RESULTS: The genomes of three tomato bacterial wilt
AB  - pathogens, CFBP2957 (Phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were
AB  - sequenced and manually annotated. These genomes were compared with those
AB  - of three previously sequenced R. solanacearum strains: GMI1000 (tomato,
AB  - phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The
AB  - major genomic features (size, G+C content, number of genes) were conserved
AB  - across all of the six sequenced strains. Despite relatively high genetic
AB  - distances (calculated from average nucleotide identity) and many genomic
AB  - rearrangements, more than 60% of the genes of the megaplasmid and 70% of
AB  - those on the chromosome are syntenic. The three new genomic sequences
AB  - revealed the presence of several previously unknown traits, probably
AB  - acquired by horizontal transfers, within the genomes of R. solanacearum,
AB  - including a type IV secretion system, a rhi-type anti-mitotic toxin and
AB  - two small plasmids. Genes involved in virulence appear to be evolving at a
AB  - faster rate than the genome as a whole. CONCLUSIONS: Comparative analysis
AB  - of genome sequences and gene content confirmed the differentiation of R.
AB  - solanacearum species complex strains into four phylotypes. Genetic
AB  - distances between strains, in conjunction with CGH analysis of a larger
AB  - set of strains, revealed differences great enough to consider
AB  - reclassification of the R. solanacearum species complex into three
AB  - species. The data are still too fragmentary to link genomic classification
AB  - and phenotypes, but these new genome sequences identify a pan-genome more
AB  - representative of the diversity in the R. solanancearum species complex.
ER  -

TY  - JOUR
AU  - Remenant, B.
AU  - de Cambiaire, J.C.
AU  - Cellier, G.
AU  - Jacobs, J.M.
AU  - Mangenot, S.
AU  - Barbe, V.
AU  - Lajus, A.
AU  - Vallenet, D.
AU  - Medigue, C.
AU  - Fegan, M.
AU  - Allen, C.
AU  - Prior, P.
TI  - Phylotype IV strains of Ralstonia solanacearum, R. syzygii and the blood disease bacterium form a single genomic species despite their divergent life-styles.
JO  - PLoS ONE
PY  - 2011
SP  - e24356
EP  - e24356
VL  - 6
ER  -

TY  - JOUR
AU  - Remus-Emsermann, M.N.
AU  - Kim, E.B.
AU  - Marco, M.L.
AU  - Tecon, R.
AU  - Leveau, J.H.
TI  - Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R.
JO  - Genome Announcements
PY  - 2013
SP  - e00036
EP  - e00013
VL  - 1
AB  - Bacteria belonging to the genus are common colonizers of plant leaf surfaces. Here, we present
AB  - the draft genome sequence of 299R, a phyllosphere isolate that
AB  - has become a model strain for studying the ecology of plant leaf-associated
AB  - bacterial commensals.
ER  -

TY  - JOUR
AU  - Remus-Emsermann, M.N.
AU  - Schmid, M.
AU  - Gekenidis, M.T.
AU  - Pelludat, C.
AU  - Frey, J.E.
AU  - Ahrens, C.H.
AU  - Drissner, D.
TI  - Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 75
EP  - 75
VL  - 11
AB  - Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the
AB  - order Pseudomonadales and the family Pseudomonadaceae. We
AB  - isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.).
AB  - Here we describe the physiology of this microorganism, its full genome sequence,
AB  - and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein
AB  - coding sequences and 96 RNA coding sequences. P. citronellolis has been the
AB  - subject of many studies including the investigation of long-chain aliphatic
AB  - compounds and terpene degradation. Plant leaves are covered by long-chain
AB  - aliphates making up a waxy layer that is associated with the leaf cuticle. In
AB  - addition, basil leaves are known to contain high amounts of terpenoid substances,
AB  - hinting to a potential nutrient niche that might be exploited by P.
AB  - citronellolis. Furthermore, the isolated strain exhibited resistance to several
AB  - antibiotics. To evaluate the potential of this strain as source of transferable
AB  - antibiotic resistance genes on raw consumed herbs we therefore investigated if
AB  - those resistances are encoded on mobile genetic elements. The availability of the
AB  - genome will be helpful for comparative genomics of the phylogenetically broad
AB  - pseudomonads, in particular with the sequence of the P. citronellolis type strain
AB  - PRJDB205 not yet publicly available. The genome is discussed with respect to a
AB  - phyllosphere related lifestyle, aliphate and terpenoid degradation, and
AB  - antibiotic resistance.
ER  -

TY  - JOUR
AU  - Ren, L.
AU  - Shi, Y.
AU  - Jia, Y.
AU  - Yan, Y.
TI  - Genome Sequence of Arthrobacter sp. YC-RL1, an Aromatic Compound-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00749
EP  - e00715
VL  - 3
AB  - We report the 4.04-Mb draft genome sequence of Arthrobacter sp. YC-RL1, an aromatic
AB  - compound-degrading bacterium. YC-RL1 could degrade a wide range of
AB  - aromatic compounds, including naphthaline, 1,2,3,4-tetrachlorobenzene, fluorene,
AB  - 4-nitrophenol, bisphenol A, biphenyl, and p-xylene. The genome sequence of YC-RL1
AB  - will promote the investigation of the biodegradation of aromatic compounds.
ER  -

TY  - JOUR
AU  - Ren, L.S.
AU  - Oreshkin, E.N.
AU  - Grachyov, Y.P.
TI  - Biosynthesis of restriction endonuclease SalGI and optimal conditions of its purification.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1986
SP  - 736
EP  - 741
VL  - 22
AB  - The effect of the growing phase of Streptomyces albus G. and the components of
AB  - the culture medium on the biosynthesis of restriction endonuclease SalGI was
AB  - studied.  The conditions of DNA sedimentation with streptomycin sulfate and
AB  - polyethylenimine and separation of proteins with ammonium sulfate were
AB  - investigated as well.  A maximal quantity of the enzyme was observed in the
AB  - cells in 18-20 h of cultivation in flasks on a shaker.  The optimal
AB  - concentrations of the medium components (g/l) were found by mathematical
AB  - methods of the experiment planning:  glucose - 19,0; peptone - 5.2;
AB  - K2HPO4.3H2O-5.0.  The optimal concentrations for DNA sedimentation with
AB  - streptomycin sulfate and polyethylenimine were found to be 1.8-2.0% and
AB  - 0.2-0.3%, respectively.  The optimal concentration of ammonium sulfate for
AB  - protein separation is 70% of saturation.
ER  -

TY  - JOUR
AU  - Ren, S.-X. et al.
TI  - Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing.
JO  - Nature
PY  - 2003
SP  - 888
EP  - 888
VL  - 422
AB  - Leptospirosis is a widely spread disease of global concern. Infection causes flu-like episodes
AB  - with frequent severe renal and hepatic damage,
AB  - such as haemorrhage and jaundice. In more severe cases, massive pulmonary
AB  - haemorrhages, including fatal sudden haemoptysis, can occur. Here we
AB  - report the complete genomic sequence of a representative virulent serovar
AB  - type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae
AB  - consisting of a 4.33-megabase large chromosome and a 359-kilobase small
AB  - chromosome, with a total of 4,768 predicted genes. In terms of the genetic
AB  - determinants of physiological characteristics, the facultatively parasitic
AB  - L. interrogans differs extensively from two other strictly parasitic
AB  - pathogenic spirochaetes, Treponema pallidum and Borrelia burgdorferi,
AB  - although similarities exist in the genes that govern their unique
AB  - morphological features. A comprehensive analysis of the L. interrogans
AB  - genes for chemotaxis/motility and lipopolysaccharide synthesis provides a
AB  - basis for in-depth studies of virulence and pathogenesis. The discovery of
AB  - a series of genes possibly related to adhesion, invasion and the
AB  - haematological changes that characterize leptospirosis has provided clues
AB  - about how an environmental organism might evolve into an important human
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Ren, W.
AU  - Liu, G.
AU  - Yin, J.
AU  - Chen, S.
AU  - Li, T.
AU  - Kong, X.
AU  - Peng, Y.
AU  - Yin, Y.
AU  - Hardwidge, P.R.
TI  - Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain W25K.
JO  - Genome Announcements
PY  - 2014
SP  - e00593
EP  - e00514
VL  - 2
AB  - Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in  humans and
AB  - newly weaned pigs. Here, we report the draft genome sequence of ETEC
AB  - strain W25K, which causes diarrhea in piglets.
ER  -

TY  - JOUR
AU  - Ren, Y.
AU  - Ren, Y.
AU  - Zhou, Z.
AU  - Guo, X.
AU  - Li, Y.
AU  - Feng, L.
AU  - Wang, L.
TI  - Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2463
EP  - 2464
VL  - 192
AB  - Enterobacter cloacae is an important nosocomial pathogen. Here, we report the completion of
AB  - the genome sequence of E. cloacae ATCC 13047, the type
AB  - strain of E. cloacae subsp. cloacae. Multiple sets of virulence
AB  - determinant and heavy-metal resistance genes have been found in the
AB  - genome. To the best of our knowledge, this is the first complete genome
AB  - sequence of the E. cloacae species.
ER  -

TY  - JOUR
AU  - Renbaum, P.
AU  - Abrahamove, D.
AU  - Fainsod, A.
AU  - Wilson, G.G.
AU  - Rottem, S.
AU  - Razin, A.
TI  - Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI) .
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1145
EP  - 1152
VL  - 18
AB  - We describe here the cloning, characterization and expression in E. coli of the
AB  - gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI).  This
AB  - enzyme methylates completely and exclusively CpG sequences.  The Spiroplasma
AB  - gene was transcribed in E. coli using its own promoter.  Translation of the
AB  - entire message required the use of an opal suppressor, suggesting that UGA
AB  - triplets code for tryptophan in Spiroplasma.  Sequence analysis of the gene
AB  - revealed several UGA triplets, in a 1158 bp long open reading frame.  The
AB  - deduced amino acid sequence revealed in M.SssI all common domains
AB  - characteristic of bacterial cytosine DNA methylases.  The putative sequence
AB  - recognition domain of M.SssI showed no obvious similarities with that of the
AB  - mouse DNA methylase, in spite of their common sequence specificity.  The cloned
AB  - enzyme methylated exclusively CpG sequences both in vivo and in vitro.  In
AB  - contrast to the mammalian enzyme which is primarily a maintenance methylase,
AB  - M.SssI displayed de novo methylase activity, characteristic of prokaryotic
AB  - cytosine DNA methylases.
ER  -

TY  - JOUR
AU  - Renbaum, P.
AU  - Razin, A.
TI  - Footprint analysis of M.SssI and M.HhaI methyltransferases reveals extensive interactions with the substrate DNA backbone.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 19
EP  - 26
VL  - 248
AB  - The interactions of the CpG methyltransferases M.SssI and M.HhaI (GCGC) with substrate DNA
AB  - were investigated using three different footprinting techniques. The two structurally related
AB  - enzymes displayed similar specific and non-specific contacts with DNA while bound to their
AB  - target sequences. DNase I footprinting implicated a region of 18 to 21 base-pairs with which
AB  - these enzymes interact. Dimethylsulfate protection experiments mostly revealed specific base
AB  - interactions; each enzyme was shown to interact predominantly with bases at its recognition
AB  - site in the major groove. However, hydroxyl radical footprints demonstrated extensive
AB  - interactions with the sugar-phosphate backbone on both strands of the DNA substrate. Both
AB  - enzymes protected a 16 nucleotide region, in a staggered fashion, covering 9 to 10 nucleotides
AB  - on each strand. The protected regions, extending for almost a full turn of DNA on each strand,
AB  - were offset by 6 to 7 nucleotides in the 5' direction, placing both regions on the same face
AB  - of the double helix, bracketing the major groove. The results suggest that these
AB  - methyltransferases straddle the major groove from the backbone, but protrude into the groove
AB  - only to specifically interact with their recognition sites. The sequence-independent
AB  - interactions observed on the sugar-phosphate backbone may explain the ability of the enzymes
AB  - to recognize a small sequence, as well as their processive mode of action.
ER  -

TY  - JOUR
AU  - Renbaum, P.
AU  - Razin, A.
TI  - Mode of action of the Spiroplasma CpG methylase M.SssI.
JO  - FEBS Lett.
PY  - 1992
SP  - 243
EP  - 247
VL  - 313
AB  - The cytosine DNA methylase from the wall-less prokaryote, Spiroplasma strain MQ1 (M.SssI)
AB  - methylates completely and exclusively CpG-containing sequences, thus showing sequence
AB  - specificity which is similar to that of mammalian DNA methylases. M.SssI is shown here to
AB  - methylate duplex DNA processively as judged by kinetic analysis of methylated intermediates.
AB  - The cytosine DNA methylases. M.HpaII and M.HhaI from other prokaryotic organisms, appear to
AB  - methylate in a non-processive manner or with a very low degree of processivity. The
AB  - Spiroplasma enzyme interacts with duplex DNA irrespective of the presence of CpG sequences in
AB  - the substrate DNA. The enzyme proceeds along a CpG-containing DNA substrate molecule
AB  - methylating one strand of DNA at a time.
ER  -

TY  - JOUR
AU  - Renbaum, P.
AU  - Razin, A.
TI  - Interaction of M.SssI and M.HhaI with single-base mismatched oligodeoxynucleotide duplexes.
JO  - Gene
PY  - 1995
SP  - 177
EP  - 179
VL  - 157
AB  - As part of an attempt to elucidate the mode of interaction of the CpG methyltransferase M.SssI
AB  - with its substrate, we have prepared a series of double-stranded oligodeoxyribonucleotides
AB  - containing one mismatch in the CpG recognition site.  The mismatched duplexes were used to
AB  - analyze the binding capabilities and enzymatic activity of M.SssI and M.HhaI (recognizes
AB  - GCGC).  We demonstrate here that M.SssI binds specifically to substrates containing either a
AB  - C/A or G/T mismatch in the recognition sequence, i.e., 5'-GCGC/CACG-5' or 5'-GCGC/CGTG-5',
AB  - respectively.  The enzyme also shows significant enzymatic activity with these mismatched
AB  - substrates.  These results suggest that site recognition and methylation of M.SssI take place
AB  - on the same strand.  M.HhaI bound and methylated the C/A mismatch very efficiently, but
AB  - recognition of the G/T mismatch was scarcely detectable.
ER  -

TY  - JOUR
AU  - Rendulic, S.
AU  - Jagtap, P.
AU  - Rosinus, A.
AU  - Eppinger, M.
AU  - Baar, C.
AU  - Lanz, C.
AU  - Keller, H.
AU  - Lambert, C.
AU  - Evans, K.J.
AU  - Goesmann, A.
AU  - Meyer, F.
AU  - Sockett, R.E.
AU  - Schuster, S.C.
TI  - A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective.
JO  - Science
PY  - 2004
SP  - 689
EP  - 692
VL  - 303
AB  - Predatory bacteria remain molecularly enigmatic, despite their presence in
AB  - many microbial communities. Here we report the complete genome of
AB  - Bdellovibrio bacteriovorus HD100, a predatory Gram-negative bacterium that
AB  - invades and consumes other Gram-negative bacteria. Its surprisingly large
AB  - genome shows no evidence of recent gene transfer from its prey. A plethora
AB  - of paralogous gene families coding for enzymes, such as hydrolases and
AB  - transporters, are used throughout the life cycle of B. bacteriovorus for
AB  - prey entry, prey killing, and the uptake of complex molecules.
ER  -

TY  - JOUR
AU  - Rensing, S.A. et al.
TI  - The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
JO  - Science
PY  - 2008
SP  - 64
EP  - 69
VL  - 319
AB  - We report the draft genome sequence of the model moss Physcomitrella patens and compare its
AB  - features with those of flowering plants, from which it is separated
AB  - by more than 400 million years, and unicellular aquatic algae. This comparison
AB  - reveals genomic changes concomitant with the evolutionary movement to land,
AB  - including a general increase in gene family complexity; loss of genes associated
AB  - with aquatic environments (e.g., flagellar arms); acquisition of genes for
AB  - tolerating terrestrial stresses (e.g., variation in temperature and water
AB  - availability); and the development of the auxin and abscisic acid signaling
AB  - pathways for coordinating multicellular growth and dehydration response. The
AB  - Physcomitrella genome provides a resource for phylogenetic inferences about gene
AB  - function and for experimental analysis of plant processes through this plant's
AB  - unique facility for reverse genetics.
ER  -

TY  - JOUR
AU  - Renvoise, A.
AU  - Pang, S.
AU  - Bernard, C.
AU  - Brossier, F.
AU  - Veziris, N.
AU  - Capton, E.
AU  - Jarlier, V.
AU  - Sougakoff, W.
TI  - First Whole-Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium bovis BCG.
JO  - Genome Announcements
PY  - 2014
SP  - e00611
EP  - e00614
VL  - 2
AB  - The attenuated BCG strain of Mycobacterium bovis is widely used as a vaccine against
AB  - tuberculosis. However, in rare cases, it can be pathogenic to humans.
AB  - Here, we report the first draft of a whole-genome sequence of a
AB  - multidrug-resistant clinical isolate of M. bovis BCG.
ER  -

TY  - JOUR
AU  - Renye, J.A. Jr.
AU  - Needleman, D.S.
AU  - Somkuti, G.A.
AU  - Steinberg, D.H.
TI  - Complete Genome Sequence of Streptococcus thermophilus Strain B59671, Which Naturally Produces the Broad-Spectrum Bacteriocin Thermophilin 110.
JO  - Genome Announcements
PY  - 2017
SP  - e01213
EP  - e01217
VL  - 5
AB  - Streptococcus thermophilus strain B59671 is a Gram-positive lactic acid bacterium that
AB  - naturally produces a broad-spectrum bacteriocin, thermophilin 110, and is
AB  - capable of producing gamma-aminobutyric acid (GABA). The complete genome sequence
AB  - for this strain contains 1,821,173 nucleotides, 1,936 predicted genes, and an
AB  - average G+C content of 39.1%.
ER  -

TY  - JOUR
AU  - Repik, A.V.
TI  - Structural and functional organization of the genes of the EcoRII restriction-modification system.
JO  - Ph.D. Thesis, Russian Academy of Sciences
PY  - 1994
SP  - 1
EP  - 22
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Andreeva, I.S.
AU  - Kileva, E.V.
AU  - Shevchenko, A.V.
AU  - Abdurashitov, M.A.
AU  - Repin, M.V.
AU  - Degtyarev, S.K.
TI  - MspR91, a new isoschizomer of ScrFI restriction endonuclease from Micrococcus species.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1997
SP  - 284
EP  - 286
VL  - 33
AB  - MspR91 restriction endonuclease was isolated from Micrococcus species identified by screening
AB  - soil bacteria for site-specific endonucleases.  The enzyme recognizes and cleaves the
AB  - palindromic sequence 5'-CC/NGG-3'.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Babkin, I.V.
AU  - Tereshchenko, T.A.
TI  - Bse118I, an isoschizomer of the Cfr10I restriction endonuclease from Bacillus coagulans.
JO  - Bioorg. Khim.
PY  - 1993
SP  - 406
EP  - 409
VL  - 19
AB  - The recognition sequence and cleavage point for Bse118I restriction endonuclease have been
AB  - determined as (5') R^CCGGY.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Burtseva, L.I.
AU  - Burlak, V.A.
AU  - Trusova, S.I.
TI  - Search of restriction endonuclease producers with required specificity.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1991
SP  - 20
EP  - 22
VL  - 11
AB  - Six site-specific restriction endonucleases were isolated from Bacillus
AB  - thuringiensis strains chosen from 58 strains sought purposefully for the
AB  - production of restriction enzymes.  All six strains produce isoschizomers of
AB  - Sau3AI.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Chizhikov, V.E.
AU  - Tereshchenko, T.A.
AU  - Lebedev, L.R.
TI  - Bco116I, An isoschizomer of Ksp632I from Bacillus coagulans.
JO  - Bioorg. Khim.
PY  - 1993
SP  - 410
EP  - 413
VL  - 4
AB  - The recognition sequence and cleavage point of restriction endonuclease Bco116I have been
AB  - determined as (5') CTCTTC (1/4).
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Degtyarev, S.K.
TI  - Comparison of express-methods used for the detection of restriction endonucleases in microorganisms.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1992
SP  - 152
EP  - 155
VL  - 28
AB  - The sensitivity of several express-methods used for the detection of bacterial endonucleases
AB  - was compared. The most sensitive method is that employing Triton X-100.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Lebedev, L.R.
AU  - Andreeva, I.S.
AU  - Puchkova, L.I.
AU  - Zernov, Y.P.
AU  - Serov, G.D.
AU  - Tereshchenko, T.A.
AU  - Aphinogenova, G.N.
AU  - Pustoshilova, N.M.
TI  - The producers of restriction endonucleases from natural microbe isolates and the development on this basis of enzyme production technologies.
JO  - Biotekhnologiya
PY  - 1998
SP  - 18
EP  - 27
VL  - 0
AB  - The screening of natural bacterial strains isolated from various ecological niches in order to
AB  - discover site specific nucleases has been carried out using different modifications of the
AB  - express method for detection of restriction endonucleases in bacterial colonies.  More than 60
AB  - easy to grow strains belonging to different bacterial taxa and promising for practical use
AB  - were obtained.  Some approaches to increase the strain efficiency as well as the purification
AB  - schemes to produce highly pure preparations of restriction endonuclease were suggested.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Lebedev, L.R.
AU  - Puchkova, L.
AU  - Serov, G.D.
AU  - Tereschenko, T.
AU  - Chizikov, V.E.
AU  - Andreeva, I.
TI  - New restriction endonucleases from thermophilic soil bacteria.
JO  - Gene
PY  - 1995
SP  - 321
EP  - 322
VL  - 157
AB  - Using the most effective rapid method for the detection of restriction endonucleases (ENases)
AB  - in microorganisms, 32 thermophilic producers have been isolated.  All strains belong to the
AB  - genus Bacillus.  Thermostable isoschizomers of ENases, such as AvaI, BbvI, BbvII, BclI, BsaBI,
AB  - BsiYI, BsrI, BstEII, BstNI, Cfr10I, ClaI, FspI, HaeIII, HpaII, Ksp632I and SfeI, were
AB  - isolated.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Polshina, S.V.
AU  - Bozhko, N.A.
AU  - Degtyarev, S.K.
TI  - The cultivation of Bacillus species 21, producer of restriction endonuclease Bse21I.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1989
SP  - 108
EP  - 111
VL  - 15
AB  - The effect of the components of the culture medium, temperature of cultivation
AB  - and the growing phase of Bacillus species 21 on the yield of the restrictase
AB  - activity of this microorganism was studied.  A maximal quantity of the enzyme
AB  - per 1 g cells was observed at the beginning of the stationary phase of growth.
AB  - Using mathematical methods for planning experiments allowed us to raise the
AB  - Bse21I yield more than 8-fold.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Prichodko, E.A.
AU  - Degtyarev, S.K.
TI  - Search of soil microorganisms for production of restriction endonucleases.
JO  - Izv. Sib. Otd. Akad. Nauk SSSR
PY  - 1988
SP  - 110
EP  - 113
VL  - 14
AB  - A search of soil microorganisms for the production of restriction endonucleases
AB  - was carried out.  Three strains belonging to species of Bacillus subtilis,
AB  - Bacillus megaterium and Aeromonas punctata were found and identified.  The
AB  - strains' restrictases were shown to be isoschizomers of ClaI and Sau3AI.  The
AB  - optimal conditions for cultivation of Bacillus subtilis 15 to increase enzyme
AB  - outcome were established.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Puchkova, L.I.
AU  - Ananko, G.G.
AU  - Reshetnikov, O.V.
AU  - Kurilovich, S.A.
TI  - HpyNI is the first restriction endonuclease isolated from Helicobacter pylori.
JO  - Gut
PY  - 1999
SP  - A6
EP  - A6
VL  - 45
AB  - Restriction-modification systems serve as a biological tool to ensure relative stability of
AB  - genetic material of the microbe, degrading alien DNA penetrated into bacterial cell.  The aim
AB  - of the study was to isolate and characterize restriction endonucleases of H. pylori.  H.
AB  - pylori strain was isolated from the gastric mucosa of duodenal ulcer patient.  The strain had
AB  - typical morphological and biochemical properties of H. pylori and was highly resistant to
AB  - metronidazole.  To study site-specificity viral and plasmid DNA's were used: T7, lambda, and
AB  - pBR322.  MsrR9I and Bst38I restrictases were utilized as standard.  The given strain of H.
AB  - pylori showed nuclease activity, and endonuclease obtained was called HpyNI according to the
AB  - generally accepted nomenclature.  The enzyme restricted standard substrate DNAs with the site
AB  - specific to base sequence 5'-CCNGG-3'.  Additional hydrolysis with Bst38I could not yield
AB  - novel fragments.  However, hydrolysis with HpyNI and MsrR9I showed complete homogeneity.  Thus
AB  - HpyNI proved to be an isoschizomer of ScrFI, in which this recognition site was first
AB  - described. Similar site specific endonucleases are widely represented in various microbial
AB  - taxons.  Horizontal transfer occurs between genomes of various bacteria, and restriction may
AB  - play a part in this process.  H. pylori is evolutionarily close to Escherichia coli and the
AB  - latter showed the greatest number of ScrFI isoschizomers, thus one could not exclude the
AB  - exchange of genes between these two bacteria.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Puchkova, L.I.
AU  - Rodicheva, E.K.
AU  - Vydryakova, G.A.
TI  - Luminescent bacteria as producers of specific restriction endonucleases.
JO  - Microbiology
PY  - 1995
SP  - 751
EP  - 755
VL  - 64
AB  - Luminescent bacteria isolated from the waters of the Black Sea and the Indian and Pacific
AB  - Oceans were tested for the presence of restriction endonucleases.  Restriction sites were
AB  - determined for 12 of the 19 restriction enzyme producers revealed.  The enzymes were
AB  - identified as isoschizomers of AflII, BanI, HaeIII, PstI, Sau3AI, and Sau96I.  Possible
AB  - participation of the restriction and modification enzymes in the interaction of bacterial
AB  - symbionts with the animal macrosymbiont is discussed.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Puchkova, L.I.
AU  - Rodicheva, E.K.
AU  - Vydryakova, G.A.
TI  - Restriction endonucleases from symbiotic luminous bacteria.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1997
SP  - 152
EP  - 155
VL  - 33
AB  - Marine luminous bacteria from the Black Sea and the Indian and Pacific Oceans were assayed for
AB  - restriction endonucleases.  Nineteen producers of restriction endonucleases were found; the
AB  - recognition sites were determined for 13 identified restriction endonucleases.  The identified
AB  - enzymes were isoschizomers of AflII, BanI, HaeIII, NarI, PstI, Sau3AI, or Sau96I restriction
AB  - endonucleases.  The role of restriction-modification enzymes in the symbiotic relationships
AB  - between bacteria and their hosts was suggested.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Rechkunova, N.I.
AU  - Degtyarev, S.K.
AU  - Hachaturyan, A.A.
AU  - Afrikyan, E.K.
TI  - Aerobic spore-forming bacteria as producers of restriction endonucleases.
JO  - Biol. J. Armenia
PY  - 1989
SP  - 969
EP  - 972
VL  - 42
AB  - From 58 strains of aerobic sporeforming bacteria studied, including
AB  - their thermophilic forms, 5 strains have restrictase activity.  All
AB  - restrictases
AB  - produced by these strains are isoschizomers of known restrictases
AB  - characteristic
AB  - of bacilli.  For the forst time specific restrictase producers have been
AB  - indicated, which reveal the order of hexanucleotides.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Serov, G.D.
AU  - Puchkova, L.I.
AU  - Tereshenko, T.A.
AU  - Lebedev, L.R.
AU  - Chigikov, V.E.
TI  - New restriction endonucleases from thermophilic bacteria of the genus Bacillus.
JO  - Bioorg. Khim.
PY  - 1993
SP  - 583
EP  - 585
VL  - 19
AB  - Restriction endonucleases have been isolated from 26 thermophilic strains of the Bacillus
AB  - genus, their recognition sequences were determined, and for 15 of them cleavage sites
AB  - identified. The enzymes proved to be isoschizomers of known endonucleases BstNI, EarI, HaeIII,
AB  - HpaII, Cfr10I, BsiYI, BclI, BbvII, BbvI, BstEII, BsaBI, BsrI, FspI, ClaI, SfeI.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Shelkunov, S.N.
TI  - Occurrence and function of restriction endonucleases (A Review).
JO  - Usp. Sovrem. Biol.
PY  - 1990
SP  - 34
EP  - 47
VL  - 110
AB  - Modern nomenclature and classification of restriction endonucleases and related
AB  - topics are discussed.  Particular emphasis is placed on the distribution of
AB  - restriction enzymes among various taxons of microorganisms.  The possible
AB  - functional role of restriction enzymes in vivo and their evolution within
AB  - bacteria is discussed.  Basic methods for screening for type II enzymes are
AB  - described with a rationale for the use of rapid methods for analyzing large
AB  - numbers of bacterial strains.  Research perspectives in this branch of
AB  - molecular biology are presented.
ER  -

TY  - JOUR
AU  - Repin, V.E.
AU  - Shilyayeva, O.H.
TI  - Screening microorganisms isolated from air for restriction endonuclease producers.
JO  - Microbiological investigations in Western Siberia
PY  - 1989
SP  - 14
EP  - 17
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Resch, G.
AU  - Kulik, E.M.
AU  - Dietrich, F.S.
AU  - Meyer, E.
TI  - Complete genomic nucleotide sequence of the temperate bacteriophage Aaphi23 of Actinobacillus actinomycetemcomitans.
JO  - J. Bacteriol.
PY  - 2004
SP  - 5523
EP  - 5528
VL  - 186
AB  - The entire double-stranded DNA genome of the Actinobacillus actinomycetemcomitans
AB  - bacteriophage AaPhi23 was sequenced. Linear DNA
AB  - contained in the phage particles is circularly permuted and terminally
AB  - redundant. Therefore, the physical map of the phage genome is circular.
AB  - Its size is 43,033 bp with an overall molar G+C content of 42.5 mol%.
AB  - Sixty-six potential open reading frames (ORFs) were identified,
AB  - including an ORF resulting from a translational frameshift. A putative
AB  - function could be assigned to 23 of them. Twenty-three other ORFs share
AB  - homologies only with hypothetical proteins present in several bacteria
AB  - or bacteriophages, and 20 ORFs seem to be specific for phage AaPhi23.
AB  - The organization of the phage genome and several genetic functions
AB  - share extensive similarities to that of the lambdoid phages. However,
AB  - AaPhi23 encodes a DNA adenine methylase, and the DNA packaging strategy
AB  - is more closely related to the P22 system. The attachment sites of
AB  - AaPhi23 (attP) and several A. actinomycetemcomitans hosts (attB) are 49
AB  - bp long.
ER  -

TY  - JOUR
AU  - Retamales, J.
AU  - Segovia, C.
AU  - Alvarado, R.
AU  - Nunez, P.
AU  - Santander, J.
TI  - Draft Genome Sequence of Xanthomonas arboricola pv. juglandis J303, Isolated from Infected Walnut Trees in Southern Chile.
JO  - Genome Announcements
PY  - 2017
SP  - e01085
EP  - e01017
VL  - 5
AB  - Here, we report the draft genome sequence of Xanthomonas arboricola pv. juglandis J303,
AB  - isolated from infected walnut trees in southern Chile. The size of the
AB  - genome is 5,066,424 bp with a G+C content of 65.4%. X. arboricola pv. juglandis
AB  - J303 has several genes related to virulence, antibiotic resistance, and copper
AB  - resistance.
ER  -

TY  - JOUR
AU  - Retamales, J.
AU  - Vasquez, I.
AU  - Santos, L.
AU  - Segovia, C.
AU  - Ayala, M.
AU  - Alvarado, R.
AU  - Nunez, P.
AU  - Santander, J.
TI  - Complete Genome Sequences of Lytic Bacteriophages of Xanthomonas arboricola pv. juglandis.
JO  - Genome Announcements
PY  - 2016
SP  - e00336
EP  - e00316
VL  - 4
AB  - Three bacteriophages, f20-Xaj, f29-Xaj, and f30-Xaj, with lytic activity against  Xanthomonas
AB  - arboricola pv. juglandis were isolated from walnut trees (VIII Bio
AB  - Bio Region, Chile). These lytic bacteriophages have double-stranded DNA (dsDNA)
AB  - genomes of 43,851 bp, 41,865 bp, and 44,262 bp, respectively. These are the first
AB  - described bacteriophages with lytic activity against X. arboricola pv. juglandis
AB  - that can be utilized as biocontrol agents.
ER  -

TY  - JOUR
AU  - Reuss, D.R.
AU  - Schuldes, J.
AU  - Daniel, R.
AU  - Altenbuchner, J.
TI  - Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain 3NA.
JO  - Genome Announcements
PY  - 2015
SP  - e00084
EP  - e00015
VL  - 3
AB  - Bacillus subtilis 3NA reaches high cell densities during fed-batch fermentation and is an
AB  - interesting target for further optimization as a production strain.
AB  - Here, we announce the full genome of B. subtilis 3NA. The presence of specific
AB  - Bacillus subtilis 168 and W23 genetic features suggests that 3NA is a hybrid of
AB  - these strains.
ER  -

TY  - JOUR
AU  - Reuss, D.R.
AU  - Thurmer, A.
AU  - Daniel, R.
AU  - Quax, W.J.
AU  - Stulke, J.
TI  - Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain 6.
JO  - Genome Announcements
PY  - 2016
SP  - e00759
EP  - e00716
VL  - 4
AB  - Bacillus subtilis 6 is a genome-reduced strain that was cured from six prophages  and AT-rich
AB  - islands. This strain is of great interest for biotechnological
AB  - applications. Here, we announce the full-genome sequence of this strain.
AB  - Interestingly, the conjugative element ICEBs1 has most likely undergone
AB  - self-excision in B. subtilis 6.
ER  -

TY  - JOUR
AU  - Reuter, M.
AU  - Kruger, D.H.
AU  - Scholz, D.
AU  - Rosenthal, H.A.
TI  - Protection of foreign DNA against host-controlled restriction in bacterial cells.  II. Protection of pSF2124 plasmid by the gene function of bacteriophages T3 and T7.
JO  - Z. Allg. Mikrobiol.
PY  - 1980
SP  - 345
EP  - 354
VL  - 20
AB  - When restriction-active Escherichia coli cells (r+p1m+p1) are transformed
AB  - with the pSF2124 plasmid, a common vector in experimental gene transfer, the efficiency
AB  - of transformation (e.o.t.) is lowered by 2 orders of magnitude compared with restriction-
AB  - negative (r-p1m-p1 or r-p1m+p1) recipient cells due to restriction of the pSF2124 DNA by
AB  - endoR.EcoP1.  Preinfection of r+p1m+p1 recipient cells with pSF2124 attains the same
AB  - high value as that of r-m- cells.  The specific role of the ocr+ gene function was
AB  - demonstrated by the use of ocr- mutants (T3/R7, T7/D111): Preinfection with such phage
AB  - mutants does not increase the e.o.t. of r+p1m+p1 cells.  An unspecific e.o.t. alteration of
AB  - restriction-negative (r-m-) recipient cells by ocr+ or ocr- phages was excluded.  The ocr+
AB  - gene function can be exploited to protect pSF2124 against DNA restriction.  The recipient
AB  - cells survive the process of phage preinfection and transformation and stably replicate
AB  - themselves as well as the plasmid DNA.
ER  -

TY  - JOUR
AU  - Reuter, M.
AU  - Kupper, D.
AU  - Meisel, A.
AU  - Schroeder, C.
AU  - Kruger, D.H.
TI  - Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 8294
EP  - 8300
VL  - 273
AB  - EcoRII is a member of the expanding group of type IIe restriction endonucleases that share the
AB  - distinguishing feature of requiring cooperativity between two recognition sites in their
AB  - substrate DNA.  To determine the stoichiometry of the active NDA-enzyme complex and the mode
AB  - of cooperative interaction, we have investigated the dependence of EcoRII cleavage on the
AB  - concentration of EcoRII dimers.  Maximal restriction was observed at dimer/site ratios of 0.25
AB  - and 0.5.  The molecular weight of the DNA-enzyme complex eluted from a gel filtration column
AB  - also corresponds to a dimeric enzyme structure bound to two substrate sites.  We conclude that
AB  - one EcoRII dimer is sufficient to interact cooperatively with two DNA recognition sites.  A
AB  - Lac repressor "barrier" bound between two normally reactive EcoRII sites did not inhibit
AB  - restriction endonuclease activity, indicating that cooperativity between EcoRII sites is
AB  - achieved by bending or looping of the intervening DNA stretch.  Comparative cleavage of linear
AB  - substrates with differently spaced interacting sites revealed an inverse correlation between
AB  - cleavage rate and site distance.  At the optimal distance of one helical turn, EcoRII cleavage
AB  - is independent of the orientation of the recognition sequence in the DNA double strand.
ER  -

TY  - JOUR
AU  - Reuter, M.
AU  - Kupper, D.
AU  - Pein, C.D.
AU  - Petrusyte, M.
AU  - Siksnys, V.
AU  - Frey, B.
AU  - Kruger, D.H.
TI  - Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases.
JO  - Anal. Biochem.
PY  - 1993
SP  - 232
EP  - 237
VL  - 209
AB  - There are numerous restriction endonuclease (ENases) which are known never to achieve total
AB  - cleavage of certain unmethylated target DNAs. In addition to EcoRII we found seven ENasese
AB  - (AtuBI, Cfr9I, Eco57I, Ksp6321, NaeI, NarI, and SauBMKI) that were stimulated by
AB  - oligodeoxyribonucleotide (oligo) duplexes containing enzyme-specific recognition sequences to
AB  - cut the target DNAs much more efficiently and in most cases even to completion. These enzymes
AB  - are class-II and class-IIS ENases isolated from different bacterial species and possess a
AB  - varying number of specific sites in the refractory DNA substrates. For DNA analysis and
AB  - large-scale preparation of certain restriction fragments where complete digestions are
AB  - essential we recommend taking into account the fact that various ENases can be activiated by
AB  - specific oligo duplexes to drive restriction digestions to completion.
ER  -

TY  - JOUR
AU  - Reuter, M.
AU  - Muecke, M.
AU  - Krueger, D.H.
TI  - Structure and function of Type IIE restriction endonucleases or: From a plasmid that restricts phage replication to a new molecular DNA recognition mechanism.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 261
EP  - 295
VL  - 14
AB  - Restriction endonucleases and DNA methyltransferases are encoded by chromosomal, plasmid, or
AB  - viral genes.  In eubacteria as well as in archaea, they often form biologically active DNA
AB  - restriction-modification systems.  The first R-M systems, discovered by reversible growth
AB  - reduction of bacterial viruses, were found to be encoded by chromosomal genes in Escherichia
AB  - coli K-12, Escherichia coli B, and Salmonella typhimurium.  Besides the prophage P1 and the
AB  - related plasmid p15 also naturally occurring drug resistance plasmids (R factors) of the fi-
AB  - (fertility inhibition-minus) type have been shown to restrict and modify infecting
AB  - bacteriophage or trans-conjugated plasmid DNAs in vivo.  The first R-factor controlled R-M
AB  - systems, called EcoRI and EcoRII today, have been defined by those phenotypical properties.
AB  - Endonucleolysis and cytosine methylation, respectively, have been proposed as the molecular
AB  - mechanisms of EcoRII-specific restriction and modification.  EcoRII was among the very first
AB  - R-M enzymes for which the DNA substrate site was identified.  The REase EcoRII recognizes the
AB  - sequence 5'-CC(A/T)GG which exhibits a twofold rotational symmetry with a dyad axis
AB  - corresponding to the central A-T pair.  EcoRII cleaves the phosphodiester bond at the 5' end
AB  - of the first cytosine of the unmethylated sequence.
ER  -

TY  - JOUR
AU  - Reuter, M.
AU  - Pein, C.-D.
AU  - Butkus, V.
AU  - Kruger, D.H.
TI  - An improved method for the detection of Dcm methylation in DNA molecules.
JO  - Gene
PY  - 1990
SP  - 161
EP  - 162
VL  - 95
AB  - The intrinsic insensitivity of EcoRII recognition sites in RF DNAs of phage M13 and vector
AB  - M13mp18 towards this restriction endonuclease can be overcome by adding site-specific
AB  - oligodeoxyribonucleotide duplexes to the restriction sample. Since Dcm- DNA but not Dcm+
AB  - -methylated DNA becomes susceptible under these conditions, this procedure constitutes an
AB  - improvement of the Dcm methylation assay.
ER  -

TY  - JOUR
AU  - Reuter, M.
AU  - Schneider-Mergener, J.
AU  - Kupper, D.
AU  - Meisel, A.
AU  - Mackeldanz, P.
AU  - Kruger, D.H.
AU  - Schroeder, C.
TI  - Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 5213
EP  - 5221
VL  - 274
AB  - Target sequence-specific DNA binding regions of the restriction endonuclease EcoRII were
AB  - identified by screening a membrane-bound EcoRII-derived peptide scan with an EcoRII
AB  - recognition site (CCWGG) oligonucleotide duplex.  Dodecapeptides overlapping by nine amino
AB  - acids and representing the complete protein were prepared by spot synthesis.  Two separate DNA
AB  - binding regions, amino acids 88-102 and amino acids 256-273, which share the consensus motif
AB  - KXRXXK, emerged.  Screening 570 single substitution analogues obtained by exchanging every
AB  - residue of both binding sites for all other amino acids demonstrated that replacing basic
AB  - residues in the consensus motifs significantly reduced DNA binding.  EcoRII mutant enzymes
AB  - generated by substituting alanine or glutamic acid for the consensus lysine residues in DNA
AB  - binding site I expressed attentuated DNA binding, whereas corresponding substitutions in DNA
AB  - binding site II caused impaired cleavage, but enzyme secondary structure was unaffected.
AB  - Furthermore, Glu96, which is part of a potential catalytic motif and also locates to DNA
AB  - binding site I, was demonstrated to be critical for DNA cleavage and binding.  Homology
AB  - studies of DNA binding site II revealed strong local homology to SsoII (recognition sequence,
AB  - CCNGG) and patterns of sequence conservation, suggesting the existence of functionally related
AB  - DNA binding sites in diverse restriction endonucleases with recognition sequences containing
AB  - terminal C:G or G:C pairs.
ER  -

TY  - JOUR
AU  - Reuter, V.M.
AU  - Bogdarina, I.G.
AU  - Kruger, D.H.
TI  - Evidence for a specific inhibitor protein of DNA methyltransferases.
JO  - Biol. Rundsch.
PY  - 1986
SP  - 323
EP  - 325
VL  - 24
AB  - The ocr protein encoded by the bacterial virus T7 is the first known inhibitor protein which
AB  - blocks DNA methyltransferases specifically. It inhibits the methyl transfer to DNA conferred
AB  - by the methylase M.EcoK, however, it is not active against the methylases M.dam and M.EcoRII.
ER  -

TY  - JOUR
AU  - Reva, O.M.
AU  - Lukyanchuk, V.V.
AU  - Polishchuk, L.V.
TI  - Bsu5044I - Isoschisomer of endonuclease restriction AsuI.
JO  - Mikrobiol. Zh.
PY  - 2002
SP  - 57
EP  - 59
VL  - 64
AB  - Endonuclease of restriction of type II has been found in Bacillus subtilis B-5044 during
AB  - testing of endophytic strains of cotton plants bacilli.  The restrictase Bsu5044I hydrolysed
AB  - DNA of M13mp18 phage in 4 sites; pUC19 DNA in 5 sites; pBR322 in 15 sites.  There were a lot
AB  - of sites restriction in DNAs of phages T7 and lambda.  A comparison of electrophoretical
AB  - divisions of Bsu5044I and Cfr13I fragments of phages and plasmid DNAs showed their identity.
AB  - Thus, the found restrictase Bsu5044I is an isoschisomer of AsuI.
ER  -

TY  - JOUR
AU  - Revel, H.R.
TI  - DNA Modification:  Glucosylation.
JO  - Bacteriophage T4
PY  - 1983
SP  - 156
EP  - 165
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Revel, H.R.
TI  - Restriction of nonglucosylated T-even bacteriophage: properties of permissive mutants of Escherichia coli B and K12.
JO  - Virology
PY  - 1967
SP  - 688
EP  - 701
VL  - 31
AB  - Mutants of Escherichia coli B and K12 which are permissive for either nonglucosylated
AB  - T6 alone or for all the nonglucosylated T-even bacteriophages have been isolated
AB  - after mutagenesis with nitrosoguanidine. The fully permissive mutants of B, derived
AB  - in a single step, require vitamin Bl, whereas those of K12, obtained in two steps, have
AB  - no novel nutritional requirements. Extracts of related permissive and reskicting
AB  - bacteria show no differences in the levels or specificities of their endonuclease I and
AB  - exonuclease III activities. Strain KlZ-1100, an endonuclease-deficient strain, restricts
AB  - all nonglucosylated T-even bacteriophages. Spheroplasts of restrict.ing bacteria
AB  - restrict ?r particles of the nonglucosylated T-even phages.
ER  -

TY  - JOUR
AU  - Revel, H.R.
AU  - Georgopoulos, C.P.
TI  - Restriction of nonglucosylated T-even bacteriophages by prophage P1.
JO  - Virology
PY  - 1969
SP  - 1
EP  - 17
VL  - 39
AB  - Glucosyl transferase (gt) mutants of all the T-even bacteriophages, with less
AB  - than 3% of the normal complement of glucose on their DNA, fall into two groups
AB  - with respect to restriction by prophage P1.  Mutants of the first group, called
AB  - rp1, are restricted by P1 prophage irrespective of the nature of the hosts on
AB  - which the phage has grown; mutants of the second group, called rcp1, are
AB  - restricted by P1 only if they have grown on a permissive host lacking
AB  - UDPG-PPase.  Mutant prophages P1 r-m+ and P1 r-m-, which do not restrict
AB  - unmodified lambda phage, also fail to restrict gt rp1 or rcp1 phage.  The gt
AB  - mutants grown on P1 r-m+ lysogens are not modified.  Single-step mutants of gt
AB  - phage, called up1, which are insensitive to P1 restriction have been isolated
AB  - from T1gt rp1 and T4gt rp1, but not from T6gt rp1.  The up1 mutation does not
AB  - arise from loss or gain of a diffusible function and probably represents an
AB  - alteration in a site on the DNA recognized by the P1 restricting enzyme.  The
AB  - rp1 site maps outside the gt genes.  Both gt rp1 and gt up1 phages are
AB  - restricted by the resistance transfer factor N1.
ER  -

TY  - JOUR
AU  - Revel, H.R.
AU  - Hattman, S.M.
TI  - Mutants of T2gt with altered DNA methylase activity:  relation to restriction by prophage P1.
JO  - Virology
PY  - 1971
SP  - 484
EP  - 495
VL  - 45
AB  - Glucosyl transferase (gt) mutants of T-even phages of a class called rp1 are restricted by
AB  - prophage P1. Unrestricted mutants up1, derived from T2gt rp1, have hypermethylated DNA. From
AB  - up1 one obtains in turn uRp1 mutants, which lack methyl groups on their DNA. Phage up1 is
AB  - dominant to either rp1 or uRp1 phage in mixed infections. The uRp1 mutations map close to and
AB  - on either side of the up1 mutation suggesting that both classes of mutation affect a single
AB  - gene. Analysis of DNA methylase activity in crude extracts of Sh infected with T2 or its
AB  - various gt derivatives reveals that the phage methylase induced by up1 phage differs in
AB  - specificity from the methylase of wild-type phage. The uRp1 phage fail to induce any methylase
AB  - activity.
ER  -

TY  - JOUR
AU  - Revel, H.R.
AU  - Luria, S.E.
TI  - DNA-glucosylation in T-even phage:  Genetic determination and role in phage-host interaction.
JO  - Annu. Rev. Genet.
PY  - 1970
SP  - 177
EP  - 192
VL  - 4
AB  - Host-controlled modification phenomena.  The term "host-controlled
AB  - modification" covers a number of phenomena, first discovered in work on
AB  - bacteriophage:  a phage may become unable to infect successfully a given host
AB  - strain because of having previously grown in a different host.  Analysis of
AB  - this phenomenon in its most common form, especially with Escherichia coli and
AB  - phages lambda and fd, has revealed that these "restrictions" in host range are
AB  - due to changes in the DNA molecules that made them susceptible to a limited
AB  - endonucleolytic attack upon entering the "restricting" bacterial host.  The
AB  - attack occurs at specific "sites," presumably specific nucleotide sequences, in
AB  - the DNA molecules, and is accompanied in vivo by partial exonucleolytic
AB  - solubilization of the DNA fragments.  The term "modification" refers to the
AB  - fact that DNA produced in a given host strain is not restricted when it enters
AB  - cells of that same strain.  Modification consists of a specific methylation of
AB  - some base(s), adenine or cytosine, which renders the sites insensitive to the
AB  - specific restriction.  Because restriction can affect sites in the bacterial
AB  - DNA, it is not surprising that ability to restrict and ability to modify a
AB  - given site are usually associated in a given strain.  In fact, the restriction
AB  - and modification activities in a given E. coli strain are determined by a group
AB  - of three adjacent genes, r,m, and s, which together constitute the hs (host
AB  - specificity) system.  The r and m genes specify the restricting and modifying
AB  - functions.  The s gene determines the specificity of the phenomenon, presumably
AB  - by specifying a component common to a restricting and a modifying enzyme, which
AB  - recognizes the target sequence in the DNA: the m enzyme methylates the target
AB  - sequence if it is inside the cell; the r enzyme breaks it if it enters
AB  - unmethylated from the outside.  Both hs modification and restriction require
AB  - S-adenosyl methionine (SAM), as a methyl donor in modification  and also as a
AB  - cofactor in restriction.  Methylation of DNA generates 6-methyl-aminopurine
AB  - (6-MAP) from adenine residues and 5-methylcytosine (MC) from cytosine.  Mutants
AB  - r- do not restrict; mutants s- neither restrict nor modify.  Mutations m- are
AB  - found only together with r- mutations; it has been suggested that in an r+m-
AB  - bacterium there would be a suicidal attack on the bacterial DNA by the r+
AB  - function.  Besides its own hs system, which may be present or absent in a given
AB  - strain, a bacterium may exhibit other restriction systems due to episomes or
AB  - plasmids such as prophages or "resistance" factors.
ER  -

TY  - JOUR
AU  - Revez, J.
AU  - Schott, T.
AU  - Rossi, M.
AU  - Hanninen, M.L.
TI  - Complete Genome Sequence of a Variant of Campylobacter jejuni NCTC 11168.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6298
EP  - 6299
VL  - 194
AB  - Campylobacter jejuni NCTC 11168 is widely used in research, but at least two variants have
AB  - been reported. The available genome was sequenced from a variant
AB  - which later showed a different phenotype and gene expression profile. Here we
AB  - present the complete genome sequence of a second variant of C. jejuni NCTC 11168.
ER  -

TY  - JOUR
AU  - Rexer, B.U.
AU  - Jarsch, M.
AU  - Sagmeister, C.
AU  - Gluck, B.
AU  - Berger, G.
AU  - Kessler, C.
TI  - AsnI:  a novel class II restriction endonuclease from Arthrobacter sp., strain N-CM, recognizing 5'-AT/TAAT-3'.
JO  - FEBS Lett.
PY  - 1988
SP  - 241
EP  - 246
VL  - 235
AB  - A new class II restriction endonuclease, AsnI, with a novel sequence
AB  - specificity was isolated from the Gram-positive eubacterium Arthrobacter
AB  - species, strain N-CM.  AsnI recognizes the unambiguously defined palindromic
AB  - hexanucleotide  5'-AT^TAAT-3' 3'-TAAT^TA-5' consisting of A- and T-residues.
AB  - The novel enzyme in the presence of Mg2+ cleaves specifically both strands as
AB  - indicated by the arrows.  The staggered cuts generate 5'-protruding ends with
AB  - single-stranded 5'-TA-3' dinucleotide extensions.  The novel enzyme may be a
AB  - useful tool for cloning experiments by complementation of the few enzymes such
AB  - as PstI and PvuI cutting only once in the Ampr-gene of plasmids pBR322 and
AB  - pBR328.
ER  -

TY  - JOUR
AU  - Rey, A.
AU  - Silva-Quintero, L.
AU  - Dussan, J.
TI  - Complete Genome Sequence of the Larvicidal Bacterium Lysinibacillus sphaericus Strain OT4b.25.
JO  - Genome Announcements
PY  - 2016
SP  - e00257
EP  - e00216
VL  - 4
AB  - Lysinibacillus sphaericus OT4b.25 is a native Colombian strain isolated from coleopteran
AB  - larvae in an oak forest near Bogota D.C.; this strain has shown high
AB  - levels of pathogenic activity against Culex quinquefasciatus larvae in laboratory
AB  - assays compared to that of other members of the same species. Using Pacific
AB  - Biosciences sequencing technology, we propose a chromosomal contig of 4,665,775
AB  - bp that, according to comparative analysis, is highly similar to that of
AB  - reference strain L. sphaericus C3-41.
ER  -

TY  - JOUR
AU  - Rey, M.W. et al.
TI  - Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species.
JO  - Genome Biology
PY  - 2004
SP  - R77
EP  - R77
VL  - 5
AB  - Bacillus licheniformis is a Gram-positive, spore-forming soil
AB  - bacterium that is used in the biotechnology industry to manufacture
AB  - enzymes, antibiotics, biochemicals and consumer products. This species is
AB  - closely related to the well studied model organism Bacillus subtilis, and
AB  - produces an assortment of extracellular enzymes that may contribute to
AB  - nutrient cycling in nature.  We determined the complete nucleotide sequence
AB  - of the B. licheniformis ATCC 14580 genome which comprises a circular
AB  - chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted
AB  - protein-coding genes with an average size of 873 bp, seven rRNA operons,
AB  - and 72 tRNA genes. The B. licheniformis chromosome contains large regions
AB  - that are colinear with the genomes of B. subtilis and Bacillus halodurans,
AB  - and approximately 80% of the predicted B. licheniformis coding sequences
AB  - have B. subtilis orthologs.  Despite the unmistakable organizational
AB  - similarities between the B. licheniformis and B. subtilis genomes, there
AB  - are notable differences in the numbers and locations of prophages,
AB  - transposable elements and a number of extracellular enzymes and secondary
AB  - metabolic pathway operons that distinguish these species. Differences
AB  - include a region of more than 80 kilobases (kb) that comprises a cluster of
AB  - polyketide synthase genes and a second operon of 38 kb encoding plipastatin
AB  - synthase enzymes that are absent in the B. licheniformis genome. The
AB  - availability of a completed genome sequence for B. licheniformis should
AB  - facilitate the design and construction of improved industrial strains and
AB  - allow for comparative genomics and evolutionary studies within this group
AB  - of Bacillaceae.
ER  -

TY  - JOUR
AU  - Reyna-Flores, F.
AU  - Barrios-Camacho, H.
AU  - Dantan-Gonzalez, E.
AU  - Ramirez-Trujillo, J.A.
AU  - Lozano, A.B.L.F.
AU  - Rodriguez-Medina, N.
AU  - Garza-Ramos, U.
AU  - Suarez-Rodriguez, R.
TI  - Draft Genome Sequences of Endophytic Isolates of Klebsiella variicola and Klebsiella pneumoniae Obtained from the Same Sugarcane Plant.
JO  - Genome Announcements
PY  - 2018
SP  - e00147
EP  - e00118
VL  - 6
AB  - Endophytic Klebsiella variicola KvMx2 and Klebsiella pneumoniae KpMx1 isolates obtained from
AB  - the same sugarcane stem were used for whole-genome sequencing. The
AB  - genomes revealed clear differences in essential genes for plant growth,
AB  - development, and detoxification, as well as nitrogen fixation, catalases,
AB  - cellulases, and shared virulence factors described in the K. pneumoniae pathogen.
ER  -

TY  - JOUR
AU  - Reysenbach, A.-L.
AU  - Flores, G.E.
TI  - Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei.
JO  - Geobiology
PY  - 2008
SP  - 331
EP  - 336
VL  - 6
AB  - Terry Beveridge's enthusiasm about the ingenuity of microorganisms has stimulated many new
AB  - avenues of microbial research. One example where Terry's observations helped direct the
AB  - scientific process was in the analysis of the draft genome of the thermoacidophilic archaeum,
AB  - Aciduliprofundum boonei. This deep-sea vent heterotroph ferments peptides as its primary
AB  - metabolic pathway, using numerous enzymes encoding for proteolytic or peptidolytic activities.
AB  - An almost complete modified Embden-Meyerhof-Parnas pathway operates in the gluconeogenic
AB  - direction. Terry was particularly intrigued by the S-layer and flagellum of A. boonei.
AB  - Although only putative genes for the S-layer protein could be identified, several genes
AB  - encoding for glycosyl transferases were located in the draft genome that could glycosylate the
AB  - S-layer proteins and protect the proteins from the acidic environment. Furthermore, A. boonei
AB  - possesses a unique organization to its flagellum genes and may represent a third
AB  - organizational type within the Archaea.
ER  -

TY  - JOUR
AU  - Reysenbach, A.L.
AU  - Donaho, J.A.
AU  - Hinsch, T.M.
AU  - Kelley, J.F.
AU  - Kouba, K.
AU  - Podar, M.
AU  - Stott, M.B.
TI  - Draft Genome Sequence of a Novel Thermofilum sp. Strain from a New Zealand Hot Spring Enrichment Culture.
JO  - Genome Announcements
PY  - 2018
SP  - e00005
EP  - e00018
VL  - 6
AB  - A draft genome of a new Thermofilum sp. strain was obtained from an enrichment culture
AB  - metagenome. Like its relatives, Thermofilum sp. strain NZ13 is adapted to
AB  - organic-rich thermal environments and has to depend on other organisms and the
AB  - environment for some key amino acids, purines, and cofactors.
ER  -

TY  - JOUR
AU  - Reysenbach, A.L.
AU  - Donaho, J.A.
AU  - Kelley, J.F.
AU  - St. John, E.
AU  - Turner, C.
AU  - Podar, M.
AU  - Stott, M.B.
TI  - Draft Genome Sequence of a Dictyoglomus sp. from an Enrichment Culture of a New Zealand Geothermal Spring.
JO  - Genome Announcements
PY  - 2018
SP  - e00150
EP  - e00118
VL  - 6
AB  - A draft genome of a novel Dictyoglomus sp., NZ13-RE01, was obtained from a New Zealand hot
AB  - spring enrichment culture. The 1,927,012-bp genome is similar in both
AB  - size and G+C content to other Dictyoglomus spp. Like its relatives, Dictyoglomus
AB  - sp. NZ13-RE01 encodes many genes involved in complex carbohydrate metabolism.
ER  -

TY  - JOUR
AU  - Reysenbach, A.L.
AU  - Hamamura, N.
AU  - Podar, M.
AU  - Griffiths, E.
AU  - Ferreira, S.
AU  - Hochstein, R.
AU  - Heidelberg, J.
AU  - Johnson, J.
AU  - Mead, D.
AU  - Pohorille, A.
AU  - Sarmiento, M.
AU  - Schweighofer, K.
AU  - Seshadri, R.
AU  - Voytek, M.A.
TI  - Complete and draft genome sequences of six members of the Aquificales.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1992
EP  - 1993
VL  - 191
AB  - The Aquificales are widespread in marine and terrestrial hydrothermal
AB  - environments. Here, we report the complete and draft genome sequences of
AB  - six new members of the Aquificales: two marine species, Persephonella
AB  - marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East
AB  - Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau
AB  - Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively),
AB  - and four terrestrial isolates, Sulfurihydrogenibium azorense strain
AB  - Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and
AB  - Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and
AB  - Calcite Springs and Obsidian Pool in Yellowstone National Park, United
AB  - States, respectively), and the only thermoacidophilic isolate,
AB  - Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool).
AB  - Significant differences among the different species exist that include
AB  - nitrogen metabolism, hydrogen utilization, chemotaxis, and signal
AB  - transduction, providing insights into their ecological niche adaptations.
ER  -

TY  - JOUR
AU  - Reznicek, O.
AU  - Facey, S.J.
AU  - Hauer, B.
TI  - Draft Genome Sequence of a Papaverine-Degrading, Gram-positive Arthrobacter sp.,  Isolated from Soil Near Hohenheim, Germany.
JO  - Genome Announcements
PY  - 2015
SP  - e00422
EP  - e00415
VL  - 3
AB  - We present the 4.8-Mb draft genome of a soil bacterium identified as Arthrobacter sp. This
AB  - Gram-positive soil bacterium is able to use the aromatic compound
AB  - papaverine as sole carbon source and will be examined for novel oxygenases.
ER  -

TY  - JOUR
AU  - Reznicek, O.
AU  - Luesken, F.
AU  - Facey, S.J.
AU  - Hauer, B.
TI  - Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated  from Uncontaminated Soil in Ecuador.
JO  - Genome Announcements
PY  - 2015
SP  - e00420
EP  - e00415
VL  - 3
AB  - We report the draft genome sequence of 3.3 Mb and the sequence (19.2 kb) of a natural plasmid
AB  - isolated from Phenylobacterium immobile strain E (DSM 1986), able
AB  - to degrade xenobiotic compounds as the sole carbon source. The sequences reveal a
AB  - large number of novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases
AB  - (RHOs).
ER  -

TY  - JOUR
AU  - Rezulak, M.
AU  - Borsuk, I.
AU  - Mruk, I.
TI  - Natural C-independent expression of restriction endonuclease in a C protein-associated restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 2646
EP  - 2660
VL  - 44
AB  - Restriction-modification (R-M) systems are highly prevalent among bacteria and archaea, and
AB  - appear to play crucial roles in modulating horizontal gene transfer and protection against
AB  - phage. There is much to learn about these diverse enzymes systems, especially their
AB  - regulation. Type II R-M systems specify two independent enzymes: a restriction endonuclease
AB  - (REase) and protective DNA methyltransferase (MTase). Their activities need to be finely
AB  - balanced in vivo. Some R-M systems rely on specialized transcription factors called C
AB  - (controller) proteins. These proteins play a vital role in the temporal regulation of R-M gene
AB  - expression, and function to indirectly modulate the horizontal transfer of their genes across
AB  - the species. We report novel regulation of a C-responsive R-M system that involves a C protein
AB  - of a poorly-studied structural class - C.Csp231I. Here, the C and REase genes share a
AB  - bicistronic transcript, and some of the transcriptional auto-control features seen in other
AB  - C-regulated R-M systems are conserved. However, separate tandem promoters drive most
AB  - transcription of the REase gene, a distinctive property not seen in other tested C-linked R-M
AB  - systems. Further, C protein only partially controls REase expression, yet plays a role in
AB  - system stability and propagation. Consequently, high REase activity was observed after
AB  - deletion of the entire C gene, and cells bearing the DeltaC R-M system were outcompeted in
AB  - mixed culture assays by those with the WT R-M system. Overall, our data reveal unexpected
AB  - regulatory variation among R-M systems.
ER  -

TY  - JOUR
AU  - Rezvani, M.
AU  - Mendoza, M.
AU  - Koci, M.D.
AU  - Daron, C.
AU  - Levy, J.
AU  - Hassan, H.M.
TI  - Draft Genome Sequences of Lactobacillus animalis Strain P38 and Lactobacillus reuteri Strain P43 Isolated from Chicken Cecum.
JO  - Genome Announcements
PY  - 2016
SP  - e01229
EP  - e01216
VL  - 4
AB  - Here, we present the genome sequence of Lactobacillus animalis strain P38 and Lactobacillus
AB  - reuteri strain P43, both isolated from the cecum content of a
AB  - 4-week old chicken fed a diet supplemented with the prebiotic
AB  - beta(1-4)galacto-oligosaccharide (GOS). These indigenous Lactobacillus isolates
AB  - are potential probiotic organisms for poultry.
ER  -

TY  - JOUR
AU  - Rezvani, M.
AU  - Mendoza, M.
AU  - Koci, M.D.
AU  - Daron, C.
AU  - Levy, J.
AU  - Hassan, H.M.
TI  - Draft Genome Sequence of Lactobacillus crispatus C25 Isolated from Chicken Cecum.
JO  - Genome Announcements
PY  - 2016
SP  - e01223
EP  - e01216
VL  - 4
AB  - Lactic acid bacteria are important members of the gut microbiota of humans and animals. Here,
AB  - we present the genome sequence of Lactobacillus crispatus strain
AB  - C25, originally isolated from the cecum of 4-week-old chicken fed a standard
AB  - diet. This isolate represents a potential probiotic strain for poultry.
ER  -

TY  - JOUR
AU  - Rheaume, B.A.
AU  - Mithoefer, S.
AU  - MacLea, K.S.
TI  - Genome Sequence of the Deep-Sea Bacterium Idiomarina abyssalis KMM 227T.
JO  - Genome Announcements
PY  - 2015
SP  - e01256
EP  - e01215
VL  - 3
AB  - Idiomarina abyssalis KMM 227(T) is an aerobic flagellar gammaproteobacterium found at a depth
AB  - of 4,000 to 5,000 m below sea level in the Pacific Ocean. This
AB  - paper presents a draft genome sequence for I. abyssalis KMM 227(T), with a
AB  - predicted composition of 2,684,812 bp (47.15% G+C content) and 2,611 genes, of
AB  - which 2,508 were predicted coding sequences.
ER  -

TY  - JOUR
AU  - Rhee, I.
AU  - Bachman, K.E.
AU  - Park, B.H.
AU  - Jair, K.-W.
AU  - Yen, R.-W.C.
AU  - Schuebel, K.E.
AU  - Cui, H.
AU  - Feinberg, A.P.
AU  - Lengauer, C.
AU  - Kinzler, K.W.
AU  - Baylin, S.B.
AU  - Vogelstein, B.
TI  - DNMT1 and DNMT3b cooperate to silence genes in human cancer cells.
JO  - Nature
PY  - 2002
SP  - 552
EP  - 556
VL  - 416
AB  - Inactivation of tumour suppressor genes is central to the development of all common forms of
AB  - human cancer. This inactivation often results from epigenetic silencing associated with
AB  - hypermethylation rather than intragenic mutations. In human cells, the mechanisms underlying
AB  - locus-specific or global methylation patterns remain unclear. The prototypic DNA
AB  - methyltransferase, Dnmt1, accounts for most methylation in mouse cells, but human cancer cells
AB  - lacking DNMT1 retain significant genomic methylation and associated gene silencing. We
AB  - disrupted the human DNMT3b gene in a colorectal cancer cell line. This deletion reduced global
AB  - DNA methylation by less than 3%. Surprisingly, however, genetic disruption of both DNMT1 and
AB  - DNMT3b nearly eliminated methyltransferase activity, and reduced genomic DNA methylation by
AB  - greater than 95%. These marked changes resulted in demethylation of repeated sequences, loss
AB  - of insulin-like growth factor II (IGF2) imprinting, abrogation of silencing of the tumour
AB  - suppressor gene p16INK4a, and growth suppression. Here we demonstrate that two enzymes
AB  - cooperatively maintain DNA methylation and gene silencing in human cancer cells, and provide
AB  - compelling evidence that such methylation is essential for optimal neoplastic proliferation.
ER  -

TY  - JOUR
AU  - Rhee, I.
AU  - Jair, K.W.
AU  - Yen, R.W.
AU  - Lengauer, C.
AU  - Herman, J.G.
AU  - Kinzler, K.W.
AU  - Vogelstein, B.
AU  - Baylin, S.B.
AU  - Schuebel, K.E.
TI  - CpG methylation is maintained in human cancer cells lacking DNMT1.
JO  - Nature
PY  - 2000
SP  - 1003
EP  - 1007
VL  - 404
AB  - Hypermethylation is associated with the silencing of tumour susceptibility genes in several
AB  - forms of cancer; however, the mechanisms responsible for this aberrant methylation are poorly
AB  - understood. The prototypic DNA methyltransferase, DNMT1, has been widely assumed to be
AB  - responsible for most of the methylation of the human genome, including the abnormal
AB  - methylation found in cancers. To test this hypothesis, we disrupted the DNMT1 gene through
AB  - homologous recombination in human colorectal carcinoma cells. Here we show that cells lacking
AB  - DNMT1 exhibited markedly decreased cellular DNA methyltransferase activity, but there was only
AB  - a 20% decrease in overall genomic methylation. Although juxtacentromeric satellites became
AB  - significantly demethylated, most of the loci that we analysed, including the tumour suppressor
AB  - gene p16INK4a, remained fully methylated and silenced. These results indicate that DNMT1 has
AB  - an unsuspected degree of regional specificity in human cells and that methylating activities
AB  - other than DNMT1 can maintain the methylation of most of the genome.
ER  -

TY  - JOUR
AU  - Rhee, J.I.
AU  - Bode, J.
AU  - Diaz-Ricci, J.C.
AU  - Poock, D.
AU  - Weigel, B.
AU  - Kretzmer, G.
AU  - Schugerl, K.
TI  - Influence of the medium composition and plasmid combination on the growth of recombinant Escherichia coli JM109 and on the production of the fusion protein EcoRI::SPA.
JO  - J. Biotechnol.
PY  - 1997
SP  - 69
EP  - 83
VL  - 55
AB  - Plasmid-free and plasmid-harboring E. coli JM109 strains were investigated in shaken flasks,
AB  - stirred tanks in batch and continuous operation.  The shaken flask cultivations were performed
AB  - in M9 minimal medium and in media with various protein supplements.  The host hardly grows on
AB  - M9 minimal medium as opposed to the plasmid-harboring cells, which grow well on this medium.
AB  - All of the investigated cells propagate well on protein-containing media.  The influence of
AB  - the combinations of repressor plasmid pRK248cI, the protection plasmid EcoR4 and the
AB  - production plasmid pMTC48 were determined on the initial specific growth rate of the E. coli
AB  - JM109 without gene expression, on the yield coefficient of cell growth, acetate concentration
AB  - and acetate yield coefficient in the yeast extract-containing (HM) medium.  The influence of
AB  - various media on the induction of the gene expression were evaluated.  In cultivation media
AB  - with protein supplement, the growth rate and yield coefficient increased.  The variation of
AB  - the volumetric and specific beta-lactamase activities with the cultivation time were
AB  - determined in a stirred tank reactor in HM medium.  With increasing dilution rate the process
AB  - performance decreased.  Simple relationships exist between the substrate uptake rate and the
AB  - specific growth rate of the continuous cultivated cells in M9 and HM media.  The influence of
AB  - the dilution rate on the cell mass concentration, colony forming units, acetate formation,
AB  - yield coefficients of growth and acetate formation, substrate uptake rate, CO2 production
AB  - rate, ammonium formation rate and beta-lactamase activity in M9 and HM media were determined
AB  - as well.  Carbon balances of the batch and continuous cultivations indicated high carbon
AB  - recoveries.  On account of the higher growth rate of plasmid-harboring cells than that of the
AB  - plasmid-free cells, the behavior of the investigated plasmid-free and plasmid-harboring E.
AB  - coli JM109 cells deviates from the published properties of other plasmid-free and
AB  - plasmid-harboring E. coli cells.
ER  -

TY  - JOUR
AU  - Rhee, J.I.
AU  - Schuegerl, K.
TI  - Mathematical simulation of the growth of a three plasmid harboring Escherichia coli JM109 strain and the production of the fusion protein EcoRI::SPA with a four-compartment model.
JO  - Bioprocess Eng.
PY  - 1998
SP  - 261
EP  - 267
VL  - 19
AB  - In the previous papers the process variables of plasmid-free, one-, two- and three-plasmid
AB  - harboring E. coli JM109 cells were investigated in batch and continuous cultivation as a
AB  - function of the medium composition, plasmid content, dilution rate and cultivation
AB  - (generation) time.  In the present paper the growth of the recombinant E. coli JM109 [pEcoR4,
AB  - pRK248cI, pMTC48] and the production of the fusion protein EcoRI::SPA are simulated by using a
AB  - four-compartment model, consisting of the active cell components (ribosomes, mRNA, tRNA, and
AB  - others) (A), the structure forming materials and chromosomal DNA (Z), the plasmid-DNA (G) and
AB  - the recombinant enzyme protein (E).  At the first time, all of the three plasmids: the
AB  - production plasmid (Gp), the repressor plasmid (Gr) and the protection plasmid (Gs) are taken
AB  - into account in the plasmid DNA-compartment of the model.  The calculated and measured courses
AB  - of the cell mass, the concentrations of glucose and acetate, and the products as well as the
AB  - particular plasmids agree well.
ER  -

TY  - JOUR
AU  - Rhee, M.S.
AU  - Moritz, B.E.
AU  - Xie, G.
AU  - Glavina-del-Rio, T.
AU  - Dalin, E.
AU  - Tice, H.
AU  - Bruce, D.
AU  - Goodwin, L.
AU  - Chertkov, O.
AU  - Brettin, T.
AU  - Han, C.
AU  - Detter, C.
AU  - Pitluck, S.
AU  - Land, M.L.
AU  - Patel, M.
AU  - Ou, M.
AU  - Harbrucker, R.
AU  - Ingram, L.O.
AU  - Shanmugam, K.T.
TI  - Complete genome sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 331
EP  - 340
VL  - 5
AB  - Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 oC and pH 5.0 and
AB  - fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of
AB  - this spo-rogenic lactic acid bacterium to grow at 50-55 oC and pH 5.0 makes this organism an
AB  - attrac-tive microbial biocatalyst for production of optically pure lactic acid at industrial
AB  - scale not only from glucose derived from cellulose but also from xylose, a major constituent
AB  - of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome
AB  - se-quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.
ER  -

TY  - JOUR
AU  - Ri, S.
AU  - Ra, S.R.
TI  - Determination of cleavage sites of restriction endonuclease FmuI to plasmid pUB110 DNA.
JO  - Choson Minjujuui Inmin Konghwaguk Kwahagwon Tongbo
PY  - 2002
SP  - 50
EP  - 53
VL  - 0
AB  - We cleave the plasmid pUB110 DNA with FmuI and some restriction endonucleases and map the
AB  - restriction sites according to the cleavage fragments.  The restriction endonuclease, FmuI
AB  - acts on 6 cleavage sites in the plasmid pUB110 DNA.
ER  -

TY  - JOUR
AU  - Riazuddin, S.
AU  - Athar, A.
AU  - Sohail, A.
AU  - Ahmed, Z.
TI  - Molecular mechanism of host controlled restriction and modification in Haemophilus influenzae 1.  Isolation of a restriction positive mutant.
JO  - Pak. J. Zool.
PY  - 1987
SP  - 393
EP  - 405
VL  - 19
AB  - Wild type Haemophilus influenzae strain Rd has been mutagenized by acridine
AB  - orange treatment to produce a mutant MB69 which has cell division time,
AB  - transforming ability and radiosensitivity similar to that of the parent, but
AB  - does not allow normal growth of Haemophilus phage.  The mutant is sensitive to
AB  - adsorption of phage HP1c1 at similar levels as the parent strain.  However,
AB  - after entry into the host, phage HP1c1 DNA is specifically degraded into
AB  - discrete fragments of molecular sizes about one fifth of the parent phage DNA
AB  - estimated at 4.5 x 10/6 daltons.  Evidence is presented to support the
AB  - suggestion that the isolated mutant is restriction positive.
ER  -

TY  - JOUR
AU  - Riazuddin, S.
AU  - Sohail, A.
AU  - Maqbool, T.
AU  - Khan, E.
AU  - Mushtaq, R.
TI  - Presence of new TypeII specificity restriction enzymes in local bacteria.
JO  - Pak. J. Sci. Ind. Res.
PY  - 1987
SP  - 819
EP  - 824
VL  - 30
AB  - Eight bacterial strains isolated from local environments have been screened for
AB  - the presence of new Type II restriction enzymes by analyzing lambda DNA
AB  - fragments resulting from protein DNA interactions.  Partially purified protein
AB  - extracts of two of these strains, namely Pseudomonas aeruginosa A and
AB  - Citrobacter freundii A4 contain endonuclease activities which have been highly
AB  - purified by a combination of gel filtration, ion exchange and affinity
AB  - chromatography.  The identity of the new enzymes, designated as PaeAI and
AB  - CfrA4I, have been confirmed by analyses of incised lambda, PhiX174RFI, pBR322,
AB  - adeno-2 and M13 mp 19 RFI DNA substrates as truly Type II restriction enzymes.
AB  - The isolated enzymes, by analogy with known enzymes, seem to recognize CCGCGG
AB  - and CTGCAG base sequences respectively.
ER  -

TY  - JOUR
AU  - Ribeiro, F.J.
AU  - Przybylski, D.
AU  - Yin, S.
AU  - Sharpe, T.
AU  - Gnerre, S.
AU  - Abouelleil, A.
AU  - Berlin, A.M.
AU  - Montmayeur, A.
AU  - Shea, T.P.
AU  - Walker, B.J.
AU  - Young, S.K.
AU  - Russ, C.
AU  - Nusbaum, C.
AU  - Maccallum, I.
AU  - Jaffe, D.B.
TI  - Finished bacterial genomes from shotgun sequence data.
JO  - Genome Res.
PY  - 2012
SP  - 2270
EP  - 2277
VL  - 22
AB  - Exceptionally accurate genome reference sequences have proven to be of great
AB  - value to microbial researchers. Thus, to date, about 1800 bacterial genome
AB  - assemblies have been "finished" at great expense with the aid of manual
AB  - laboratory and computational processes that typically iterate over a period of
AB  - months or even years. By applying a new laboratory design and new assembly
AB  - algorithm to 16 samples, we demonstrate that assemblies exceeding finished
AB  - quality can be obtained from whole-genome shotgun data and automated computation.
AB  - Cost and time requirements are thus dramatically reduced.
ER  -

TY  - JOUR
AU  - Ribeiro, R.A.
AU  - Delamuta, J.R.
AU  - Gomes, D.F.
AU  - Souza, R.C.
AU  - Chueire, L.M.
AU  - Hungria, M.
TI  - Genome Sequence of Rhizobium ecuadorense Strain CNPSo 671T, an Indigenous N2-Fixing Symbiont of the Ecuadorian Common Bean (Phaseolus vulgaris L.) Genetic  Pool.
JO  - Genome Announcements
PY  - 2015
SP  - e01058
EP  - e01015
VL  - 3
AB  - Rhizobium ecuadorense CNPSo 671(T) was isolated from a common bean nodule in Ecuador. The
AB  - draft genome brings novelty about indigenous rhizobial species in centers of genetic diversity
AB  - of the legume.
ER  -

TY  - JOUR
AU  - Ribeiro, R.A.
AU  - Helene, L.C.F.
AU  - Delamuta, J.R.M.
AU  - Hungria, M.
TI  - Genome Sequence of Bradyrhizobium mercantei Strain SEMIA 6399T, Isolated from Nodules of Deguelia costata in Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e00943
EP  - e00917
VL  - 5
AB  - SEMIA 6399T is the type strain of Bradyrhizobium mercantei, a nitrogen-fixing symbiont of
AB  - Deguelia costata Its draft genome contains 8,842,857 bp with 8,246
AB  - predicted coding sequences (CDS), several related to amino acids and derivatives
AB  - and to stress tolerance, with an emphasis on oxidative stress, in addition to
AB  - symbiotic genes.
ER  -

TY  - JOUR
AU  - Ricaboni, D.
AU  - Mailhe, M.
AU  - Labas, N.
AU  - Vitton, V.
AU  - Raoult, D.
AU  - Million, M.
TI  - Draft Genome Sequence of Blautia faecis Strain Marseille-P328, Isolated from the  Human Ascending Colon.
JO  - Genome Announcements
PY  - 2016
SP  - e01383
EP  - e01316
VL  - 4
AB  - Blautia faecis strain Marseille P328 was isolated from the ascending colon of a French
AB  - patient. We sequenced the 4.45-Mb genome of the strain and compared it
AB  - with that of other species of the Blautia genus.
ER  -

TY  - JOUR
AU  - Riccelli, P.V.
AU  - Vallone, P.M.
AU  - Kashin, I.
AU  - Faldasz, B.D.
AU  - Lane, M.J.
AU  - Benight, A.S.
TI  - Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in six 22-base pair deoxyoligonucleotides.
JO  - Biochemistry
PY  - 1999
SP  - 11197
EP  - 11208
VL  - 38
AB  - Effects of different end sequences on stability, circular dichroism spectra (CD), and enzyme
AB  - binding properties were investigated for six 22-base pair, non-self-complementary duplex DNA
AB  - oligomers. The center sequences of these deoxyoligonucleotides have 8-14 base pairs in common
AB  - and are flanked on both sides by sequences differing in context and A-T content.
AB  - Temperature-induced melting transitions monitored by differential scanning calorimetry (DSC)
AB  - and ultraviolet absorbance were measured for the six duplexes in buffered 115 mM Na(+)
AB  - solutions. Values of the melting transition enthalpy, DeltaH(cal), and entropy, DeltaS(cal),
AB  - were obtained directly from DSC experiments. Melting transition parameters, DeltaH(vH) and
AB  - DeltaS(vH), were also estimated from van't Hoff analysis of optical melting curves collected
AB  - as a function of DNA concentration, assuming a two-state melting transition. Melting free
AB  - energies (20 degrees C) of the six DNAs evaluated from DSC experiments ranged from -18.7 to
AB  - -32.7 kcal/mol. van't Hoff estimates of the free energies ranged from -18.5 to -48.0
AB  - kcal/mol. With either method, the trends in free energy as a function of sequence were
AB  - identical. Equilibrium binding by BamHI restriction endonuclease to the 22-base pair DNAs was
AB  - also investigated. The central eight base pairs of all six molecules, 5'-A-GGATCC-A-3',
AB  - contained a BamHI recognition sequence bounded by A-T base pairs. Magnesium free binding
AB  - assays were performed by titering BamHI against a constant concentration of each of the
AB  - deoxyoligonucleotide substrates and analyzing reaction products by gel retardation. Binding
AB  - isotherms of the total amount of bound DNA versus protein concentration were constructed which
AB  - provided semiquantitative estimates of the equilibrium dissociation constants for dissociation
AB  - of BamHI from the six DNA oligomers. Dissociation constants ranged from 0.5 x 10(-)(9) to 12.0
AB  - x 10(-)(9) M with corresponding binding free energies of -12.5 to -10.6 (+/-0. 1) kcal/mol. An
AB  - inverse relationship is found when binding and stability are compared.
ER  -

TY  - JOUR
AU  - Riccelli, P.V.
AU  - Vallone, P.M.
AU  - Lane, M.J.
AU  - Benight, A.S.
TI  - Investigations of DNA context effects: influences of flanking sequence stability on site specific binding of BamHI restriction enzyme to duplex DNA oligomers.
JO  - J. Biophys.
PY  - 1997
SP  - A95
EP  - A95
VL  - 72
AB  - Binding of BamHI restriction enzyme was investigated for short DNA duplex oligomer substrates
AB  - containing the cognate site 5'-GGATCC-3' flanked on both sides by sequences of different A-T
AB  - or G-C composition.  Binding reactions were conducted in buffer containing 10 mM CaCl2 and
AB  - analyzed by gel-shift assays.  While cleavage activity of the enzyme was eliminated under
AB  - these conditions, site specific binding was retained.  For each DNA substrate, binding
AB  - isotherms were constructed and equilibrium binding constants evaluated.  Binding constants
AB  - greater than 10^9 M-1 were observed and found to vary at least 10-fold as a function of
AB  - flanking sequence.  Significantly higher binding of BamHI was observed for duplex substrates
AB  - containing A-T flanking sequences.  Optical melting curves of the DNAs were also measured in
AB  - the binding buffer.  From these results, the thermodynamic stabilities of the DNA substrates
AB  - were evaluated.  Comparisons of the results of the binding assays with those of the melting
AB  - analysis revealed an inverse correlation between flanking sequence stability and binding
AB  - affinity of BamHI suggesting stability of flanking DNA context may comprise a significant
AB  - component of DNA recognition by site-specific binding agents.
ER  -

TY  - JOUR
AU  - Ricci, G.
AU  - Ferrario, C.
AU  - Borgo, F.
AU  - Eraclio, G.
AU  - Fortina, M.G.
TI  - Genome Sequences of Two Lactococcus garvieae Strains Isolated from Meat.
JO  - Genome Announcements
PY  - 2013
SP  - e00018
EP  - e00012
VL  - 1
AB  - Lactococcus garvieae is an important fish pathogen and an emerging opportunistic  human
AB  - pathogen, as well as a component of natural microbiota in dairy and meat products. We present
AB  - the first report of genome sequences of L. garvieae I113 and Tac2 strains isolated from a meat
AB  - source.
ER  -

TY  - JOUR
AU  - Ricci, G.
AU  - Ferrario, C.
AU  - Borgo, F.
AU  - Rollando, A.
AU  - Fortina, M.G.
TI  - Genome Sequences of Lactococcus garvieae TB25, Isolated from Italian Cheese, and  Lactococcus garvieae LG9, Isolated from Italian Rainbow Trout.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1249
EP  - 1250
VL  - 194
AB  - Lactococcus garvieae is a fish pathogen and an emerging zoonotic opportunistic pathogen as
AB  - well as a component of natural microbiota in dairy products. Here, we
AB  - present the first report of a genome sequence of L. garvieae TB25, isolated from
AB  - a dairy source, and that of L. garvieae LG9, isolated from rainbow trout.
ER  -

TY  - JOUR
AU  - Riccobono, E.
AU  - Di Pilato, V.
AU  - Della, M.N.
AU  - Meini, S.
AU  - Ciraolo, F.
AU  - Torricelli, F.
AU  - Rossolini, G.M.
TI  - Draft Genome Sequence of Clostridium difficile Belonging to Ribotype 018 and Sequence Type 17.
JO  - Genome Announcements
PY  - 2016
SP  - e00907
EP  - e00916
VL  - 4
AB  - Clostridium difficile, belonging to ribotype 018 (RT018), is one of the most prevalent
AB  - genotypes circulating in hospital settings in Italy. Here, we report
AB  - the draft genome of C. difficile CD8-15 belonging to RT018, isolated from a
AB  - patient with fatal C. difficile-associated infection.
ER  -

TY  - JOUR
AU  - Rice, M.C. et al.
TI  - Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 46
EP  - 46
VL  - 11
AB  - Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid
AB  - agricultural soil. N. briensis C-128 was sequenced with PacBio RS
AB  - technologies at the DOE-Joint Genome Institute through their Community Science
AB  - Program (2010). The high-quality finished genome contains one chromosome of 3.21
AB  - Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein
AB  - coding. The two-way average nucleotide identity between the chromosomes of
AB  - Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to
AB  - be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were
AB  - identified in their genomic context. The gene inventory supports
AB  - chemolithotrophic metabolism with implications for function in soil environments.
ER  -

TY  - JOUR
AU  - Rice, M.C. et al.
TI  - Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic  Waters.
JO  - Genome Announcements
PY  - 2017
SP  - e00011
EP  - e00017
VL  - 5
AB  - Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing  bacterium
AB  - isolated from seawater collected in the Gulf of Alaska. The
AB  - high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp
AB  - plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2
AB  - fixation were identified.
ER  -

TY  - JOUR
AU  - Rice, M.R.
AU  - Blumenthal, R.M.
TI  - Recognition of native DNA methylation by the PvuII restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3143
EP  - 3150
VL  - 28
AB  - Recognizing the methylation status of specific DNA sequences is central to the function of
AB  - many systems in eukaryotes and prokaryotes. Restriction-modification systems have to
AB  - distinguish between 'self' and 'non-self' DNA and depend on the inability of restriction
AB  - endonucleases to cleave their DNA substrates when the DNA is appropriately methylated. These
AB  - endonucleases thus provide a model system for studying the recognition of DNA methylation by
AB  - proteins. We have characterized the interaction of R.PvuII with DNA containing the
AB  - physiologically relevant N4-methylcytosine modification. R.PvuII binds (N4m)C-modified DNA
AB  - and cleaves it very slowly. Methylated strands in hemimethylated duplexes were cleaved at a
AB  - higher rate than in fully methylated duplexes, in parallel with a higher binding affinity for
AB  - hemimethylated DNA. The co-crystal structures of R.PvuII-DNA, together with a mutagenesis
AB  - study, have implicated specific amino acids in recognition of the methylatable base; one of
AB  - these is His84. We report that replacing His84 with Ala reduced the rate of cleavage of
AB  - unmodified DNA but, in contrast, slightly increased the cleavage of (N4m)C-modified DNA.
ER  -

TY  - JOUR
AU  - Rice, M.R.
AU  - Calvin-Koons, M.D.
AU  - Blumenthal, R.M.
TI  - The PvuII (CAGCTG) endonuclease binds to and cleaves CAG5mCTG sites.
JO  - FASEB J.
PY  - 1995
SP  - A1400
EP  - A1400
VL  - 9
AB  - The PvuII restriction modification system recognizes the sequence CAGCTG. Cleavage by the
AB  - restriction endonuclease (R.PvuII) occurs between the central bases, leaving blunt ends. The
AB  - PvuII methylase modifies the internal cytosine residue at the N4 position, but the sequence
AB  - CAG5mCTG has also been reported to be protected from cleavage by R.PvuII. Our evidence
AB  - suggests that cleavage of this sequence does in fact occur. This conclusion is based on the
AB  - following criteria. First, a cell expressing M.AluI, which generates AG5mCT, cannot be stably
AB  - transformed with R.PvuII, indicating that the protection provided by M.AluI is incomplete.
AB  - Second, a synthetic oligonucleotide with 5-methylcytosine substituted from the internal
AB  - cytosine is bound by R.PvuII in gel mobility shift assays. Third, the same methylated
AB  - oligonucleotide is slowly cleaved by R.PvuII (but not at all by R.AluI). These results are
AB  - consistent with the recently-determined structure of R.PvuII-DNA cocrystals.
ER  -

TY  - JOUR
AU  - Rice, M.R.
AU  - Koons, M.D.
AU  - Blumenthal, R.M.
TI  - Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG sites.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 1032
EP  - 1038
VL  - 27
AB  - The PvuII restriction endonuclease (R.PvuII) cleaves CAG/CTG sequences as indicated, leaving
AB  - blunt ends.  Its cognate methyltransferase generates N4-methylcytosine, yielding CAGN4mCTG,
AB  - though the mechanism by which this prevents cleavage by R.PvuII is unknown.  The heterologous
AB  - 5-methylcytosine methylation CAG5mCTG has also been reported to prevent cleavage by R.PvuII
AB  - and this has been used in some cloning methods.  Since this heterologous methylation occurs at
AB  - the native methylated base, it can provide insights into the detection of DNA methylation by
AB  - R.PvuII.  We found that the cloned gene for R.PvuII could not stably transform cells protected
AB  - only by M.AluI (AG5mCT) and then determined that R.PvuII cleaves CAG5mCTG in vitro, even when
AB  - both strands are methylated.  DNase I footprint analysis and competition experiments reveal
AB  - that R.PvuII binds to CAG5mCTG specifically, though with reduced affinity relative to the
AB  - unmethylated sequence.  These results provide biochemical support for the published structures
AB  - of R.PvuII complexed with DNA containing CAGCTG and CAG5-iodoCTG and support a model for how
AB  - methylation interferes with DNA cleavage by this enzyme.
ER  -

TY  - JOUR
AU  - Richard, D.
AU  - Boyer, C.
AU  - Lefeuvre, P.
AU  - Canteros, B.I.
AU  - Beni-Madhu, S.
AU  - Portier, P.
AU  - Pruvost, O.
TI  - Complete Genome Sequences of Six Copper-Resistant Xanthomonas Strains Causing Bacterial Spot of Solaneous Plants, Belonging to X. gardneri, X. euvesicatoria,  and X. vesicatoria, Using Long-Read Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e01693
EP  - e01616
VL  - 5
AB  - Xanthomonas vesicatoria, Xanthomonas euvesicatoria, and Xanthomonas gardneri cause bacterial
AB  - spot disease. Copper has been applied since the 1920s as part of
AB  - integrated management programs. The first copper-resistant strains were reported
AB  - some decades later. Here, we fully sequenced six Xanthomonas strains pathogenic
AB  - to tomato and/or pepper and having a copper-resistant phenotype.
ER  -

TY  - JOUR
AU  - Richard, D.
AU  - Boyer, C.
AU  - Lefeuvre, P.
AU  - Pruvost, O.
TI  - Complete Genome Sequence of a Copper-Resistant Bacterium from the Citrus Phyllosphere, Stenotrophomonas sp. Strain LM091, Obtained Using Long-Read  Technology.
JO  - Genome Announcements
PY  - 2016
SP  - e01327
EP  - e01316
VL  - 4
AB  - The Stenotrophomonas genus shows great adaptive potential including resistance to multiple
AB  - antimicrobials, opportunistic pathogenicity, and production of numerous
AB  - secondary metabolites. Using long-read technology, we report the sequence of a
AB  - plant-associated Stenotrophomonas strain originating from the citrus phyllosphere
AB  - that displays a copper resistance phenotype.
ER  -

TY  - JOUR
AU  - Richard, D.
AU  - Boyer, C.
AU  - Verniere, C.
AU  - Canteros, B.I.
AU  - Lefeuvre, P.
AU  - Pruvost, O.
TI  - Complete Genome Sequences of Six Copper-Resistant Xanthomonas citri pv. citri Strains Causing Asiatic Citrus Canker, Obtained Using Long-Read Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e00010
EP  - e00017
VL  - 5
AB  - The gammaproteobacterium Xanthomonas citri pv. citri causes Asiatic citrus canker. Pathotype A
AB  - strains have a broad host range, which includes most
AB  - commercial citrus species, and they cause important economic losses worldwide.
AB  - Control often relies on frequent copper sprays. We present here the complete
AB  - genomes of six X. citri pv. citri copper-resistant strains.
ER  -

TY  - JOUR
AU  - Richards, D.F.
AU  - Linnett, P.E.
AU  - Oultram, J.D.
AU  - Young, M.
TI  - Restriction endonucleases in Clostridium pasteurianum ATCC 6013 and Clostridium thermohydrosulfuricum DSM568.
JO  - J. Gen. Microbiol.
PY  - 1988
SP  - 3151
EP  - 3157
VL  - 134
AB  - A small collection of Clostridia were surveyed for type II restriction endonucleases. Enzymes
AB  - were detected in two organisms. Clostridium pasteurianum ATCC 6013 contains an isoschizomer of
AB  - ThaI (FnuDII) [5'-CGCG-3'] and preliminary evidence suggests that cleavage generates
AB  - blunt-ended fragments. Clostridium thermohydrosulfuricum DSM568 contains an isoschizomer of
AB  - MboI (Sau3A) [5'-GATC-3'], that is inactive on dam methylated substrates. The DNA of this
AB  - latter organism shows dam methylation.
ER  -

TY  - JOUR
AU  - Richards, G.P.
AU  - Bono, J.L.
AU  - Watson, M.A.
AU  - Needleman, D.S.
TI  - Complete Genome Sequence for the Shellfish Pathogen Vibrio coralliilyticus RE98 Isolated from a Shellfish Hatchery.
JO  - Genome Announcements
PY  - 2014
SP  - e01253
EP  - e01214
VL  - 2
AB  - Vibrio coralliilyticus is a pathogen of corals and larval shellfish. Publications on strain
AB  - RE98 list it as a Vibrio tubiashii; however, whole genome sequencing
AB  - confirms RE98 as V. coralliilyticus containing a total of 6,037,824 bp consisting
AB  - of two chromosomes (3,420,228 and 1,917,482 bp) and two megaplasmids (380,714 and
AB  - 319,400 bp).
ER  -

TY  - JOUR
AU  - Richards, G.P.
AU  - Needleman, D.S.
AU  - Watson, M.A.
TI  - Complete Genome Sequence of Pseudoalteromonas piscicida Strain DE2-B, a Bacterium with Broad Inhibitory Activity toward Human and Fish Pathogens.
JO  - Genome Announcements
PY  - 2017
SP  - e00752
EP  - e00717
VL  - 5
AB  - Pseudoalteromonas piscicida strain DE2-B is a halophilic bacterium which has broad inhibitory
AB  - activity toward vibrios and other human and fish pathogens. We
AB  - report the first closed genome sequence for this species, which consists of two
AB  - chromosomes (4,128,210 and 1,188,838 bp). Annotation revealed multiple genes
AB  - encoding proteases with potential antibacterial properties.
ER  -

TY  - JOUR
AU  - Richards, G.P.
AU  - Needleman, D.S.
AU  - Watson, M.A.
AU  - Bono, J.L.
TI  - Complete Genome Sequence of the Larval Shellfish Pathogen Vibrio tubiashii Type Strain ATCC 19109.
JO  - Genome Announcements
PY  - 2014
SP  - e01252
EP  - e01214
VL  - 2
AB  - Vibrio tubiashii is a larval shellfish pathogen. Here, we report the first closed genome
AB  - sequence for this species (ATCC type strain 19109), which consists of two
AB  - chromosomes (3,294,490 and 1,766,582 bp), two megaplasmids (251,408 and 122,808
AB  - bp), and two plasmids (57,076 and 47,973 bp).
ER  -

TY  - JOUR
AU  - Richards, V.P.
AU  - Lang, P.
AU  - Pavinski-Bitar, P.D.
AU  - Lefebure, T.
AU  - Schukken, Y.H.
AU  - Zadoks, R.N.
AU  - Stanhope, M.J.
TI  - Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae.
JO  - Infect. Genet. Evol.
PY  - 2011
SP  - 1263
EP  - 1275
VL  - 11
AB  - In addition to causing severe invasive infections in humans, Streptococcus
AB  - agalactiae, or group B Streptococcus (GBS), is also a major cause of bovine
AB  - mastitis. Here we provide the first genome sequence for S. agalactiae isolated
AB  - from a cow diagnosed with clinical mastitis (strain FSL S3-026). Comparison to
AB  - eight S. agalactiae genomes obtained from human disease isolates revealed 183
AB  - genes specific to the bovine strain. Subsequent polymerase chain reaction (PCR)
AB  - screening for the presence/absence of a subset of these loci in additional bovine
AB  - and human strains revealed strong differentiation between the two groups (Fisher
AB  - exact test: p<0.0001). The majority of the bovine strain-specific genes (
AB  - approximately 85%) clustered tightly into eight genomic islands, suggesting these
AB  - genes were acquired through lateral gene transfer (LGT). This bovine GBS also
AB  - contained an unusually high proportion of insertion sequences (4.3% of the total
AB  - genome), suggesting frequent genomic rearrangement. Comparison to other
AB  - mastitis-causing species of bacteria provided strong evidence for two cases of
AB  - interspecies LGT within the shared bovine environment: bovine S. agalactiae with
AB  - Streptococcus uberis (nisin U operon) and Streptococcus dysgalactiae subsp.
AB  - dysgalactiae (lactose operon). We also found evidence for LGT, involving the
AB  - salivaricin operon, between the bovine S. agalactiae strain and either
AB  - Streptococcus pyogenes or Streptococcus salivarius. Our findings provide insight
AB  - into mechanisms facilitating environmental adaptation and acquisition of
AB  - potential virulence factors, while highlighting both the key role LGT has played
AB  - in the recent evolution of the bovine S. agalactiae strain, and the importance of
AB  - LGT among pathogens within a shared environment.
ER  -

TY  - JOUR
AU  - Richardson, B.
AU  - Yung, R.
TI  - Role of DNA methylation in the regulation of cell function.
JO  - J. Lab. Clin. Med.
PY  - 1999
SP  - 333
EP  - 340
VL  - 134
AB  - The methylation of DNA helps stabilize chromatin in an inactive configuration and inhibits
AB  - gene transcription. This mechanism of gene regulation is involved in essential genetic events
AB  - including differentiation, genomic imprinting, and X chromosome inactivation. The alteration
AB  - of methylation patterns can result in abnormal gene expression, with significant pathologic
AB  - effects including carcinogenesis, autoimmunity, and some of the changes in gene expression
AB  - associated with aging. The mechanisms establishing, maintaining, and modifying methylation
AB  - patterns in normal and pathologic states are only now becoming understood, as are the
AB  - mechanisms relating DNA methylation to gene expression and chromosome inactivation. Further
AB  - characterization of these mechanisms holds promise for delaying or preventing the changes in
AB  - methylation patterns that contribute to cancer, autoimmunity, and aging.
ER  -

TY  - JOUR
AU  - Richardson, C.
AU  - Elliott, B.
AU  - Jasin, M.
TI  - Chromosomal double strand breaks induced in mammalian cells by expression of I-SceI endonuclease.
JO  - Methods Mol. Biol.
PY  - 1999
SP  - 453
EP  - 463
VL  - 113
AB  - Until recently, investigators interested in analyzing the repair of chromosomal double-strand
AB  - breaks in mammalian cells have been limited by the inability to introduce defined DSBs within
AB  - the genome.  Traditional methods of introducing breaks have included irradiation or the
AB  - introduction of restriction enzymes; however, both of these methods cause multiple lesions at
AB  - different chromosomal loci.  Many of these types of studies have relied on cytogenetics for
AB  - the detection of gross genomic changes owing to misrepair at these damaged sites.
ER  -

TY  - JOUR
AU  - Richardson, E.J.
AU  - Limaye, B.
AU  - Inamdar, H.
AU  - Datta, A.
AU  - Manjari, K.S.
AU  - Pullinger, G.D.
AU  - Thomson, N.R.
AU  - Joshi, R.R.
AU  - Watson, M.
AU  - Stevens, M.P.
TI  - Genome sequences of Salmonella enterica serovar Typhimurium, Choleraesuis, Dublin and Gallinarum strains of highly defined virulence in  food-producing animals.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3162
EP  - 3163
VL  - 193
AB  - Salmonella enterica is an animal and zoonotic pathogen of worldwide importance and may be
AB  - classified into serovars differing in virulence and
AB  - host range. We sequenced and annotated the genomes of serovar Typhimurium,
AB  - Choleraesuis, Dublin and Gallinarum strains of defined virulence in each
AB  - of three food-producing animal hosts. This provides valuable measures of
AB  - intra-serovar diversity and opportunities to formally link genotypes to
AB  - phenotypes in target animals.
ER  -

TY  - JOUR
AU  - Richardson, F.C.
AU  - Richardson, K.K.
TI  - Alterations in DNA-restriction enzyme interactions by O4-alkyldeoxythymidines.
JO  - Mol. Carcinog.
PY  - 1991
SP  - 162
EP  - 168
VL  - 4
AB  - O4-Alkyldeoxythymidines have been extensively studied for their ability to cause mutations and
AB  - to induce cancer.  Since these adducts can change DNA conformation, they may also have a more
AB  - immediate effect of altering DNA-protein interactions.  To address this issue, the effects of
AB  - these adducts on restriction enzyme activity were examined.  Oligodeoxyribonucleosides
AB  - containing O4-ethyldeoxythymidine (O4-EtdT) or O4-methyldeoxythymidine (O4-MedT) at a unique
AB  - site within the sequence 5'-GAATGGATCCTAATGAGATC-3' were constructed by automated DNA
AB  - synthesis.  This sequence contains the recognition site for various restriction enzymes.
AB  - These oligomers were annealed to various complementary strands and digested with restriction
AB  - enzymes:  BamHI or BstI (GGATCC); Sau3A, NdeII, or MboI (GATC); DpnI (GmATC); and BstYI, MflI,
AB  - or XhoII (PuGATCPy).  Analysis of the digests demonstrated that the presence of either O4-EtdT
AB  - or O4-MedT abolished the ability of XhoII, MboI, MflI, or NdeII to cut at the restriction
AB  - site.  DpnI failed to cut any of the oligomers.  BamHI, Sau3A, BstI, and BstYI exhibited
AB  - alterations in cutting specificity depending upon the oligomers used.  These results
AB  - demonstrated that O4-alkyldeoxythymidine adducts alter DNA-restriction enzyme interactions in
AB  - a protein- and sequence-dependent manner.  Because of the importance of natural methylation in
AB  - genetic regulation it is possible that aberrant methylation in the form of DNA adducts could
AB  - also alter protein-DNA interactions in cells exposed to DNA-modifying agents.
ER  -

TY  - JOUR
AU  - Richardson, F.C.
AU  - Richardson, K.K.
AU  - Kroin, J.S.
AU  - Hertel, L.W.
TI  - Synthesis and restriction enzyme analysis of oligodeoxyribonucleotides containing the anti-cancer drug 2', 2'-difluoro-2'-deoxycytidine.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1763
EP  - 1768
VL  - 20
AB  - The anti-cancer drug 2',2'-difluoro-2'-deoxycytidine (dFdC) is internally incorporated into
AB  - DNA in vitro. To determine the effects of this incorporation on DNA structure and function,
AB  - the beta-cyanoethyl phosphoramidite of dFdC was synthesized and oligodeoxyribonucleotides
AB  - containing dFdC were made using automated solid phase DNA synthesis techniques. Extension of
AB  - the coupling time was required to achieve high coupling efficiency, suggesting a significant
AB  - reduction in the rate of phosphotriester formation. Insertion of dFdC 5' into the recognition
AB  - sequence of restriction enzymes HpaII and KpnI reduced the rate of cutting by 4% and 14% over
AB  - 60 minutes. This reduction is similar to the effects seen with arabinofuranosylcytidine
AB  - (ara-C) but small compared to the reductions caused by base analogues and phosphothioates.
AB  - Insertion of dFdC into the BamHI recognition sequence, but not 5' to the cut site, did not
AB  - alter the rate of cutting/recognition. The presence of a single dFdC reduced the Tm's of
AB  - oligomers by 2-4C, depending on sequence and location. These results demonstrate that, once
AB  - incorporated into DNA, dFdC does not greatly alter recognition between DNA and restriction
AB  - enzymes; however, it does significantly alter duplex stability.
ER  -

TY  - JOUR
AU  - Richter, M.
AU  - Kube, M.
AU  - Bazylinski, D.A.
AU  - Lombardot, T.
AU  - Glockner, F.O.
AU  - Reinhardt, R.
AU  - Schuler, D.
TI  - Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.
JO  - J. Bacteriol.
PY  - 2007
SP  - 4899
EP  - 4910
VL  - 189
AB  - Magnetotactic bacteria (MTB) are a heterogeneous group of aquatic
AB  - prokaryotes with a unique intracellular organelle, the magnetosome, which
AB  - orients the cell along magnetic field lines. Magnetotaxis is a complex
AB  - phenotype, which depends on the coordinate synthesis of magnetosomes and
AB  - the ability to swim and orient along the direction caused by the
AB  - interaction with the Earth's magnetic field. Although a number of putative
AB  - magnetotaxis genes were recently identified within a conserved genomic
AB  - magnetosome island (MAI) of several MTB, their functions have remained
AB  - mostly unknown, and it was speculated that additional genes located
AB  - outside the MAI might be involved in magnetosome formation and
AB  - magnetotaxis. In order to identify genes specifically associated with the
AB  - magnetotactic phenotype, we conducted comparisons between four sequenced
AB  - magnetotactic Alphaproteobacteria including the nearly complete genome of
AB  - Magnetospirillum gryphiswaldense strain MSR-1, the complete genome of
AB  - Magnetospirillum magneticum strain AMB-1, the complete genome of the
AB  - magnetic coccus MC-1, and the comparative-ready preliminary genome
AB  - assembly of Magnetospirillum magnetotacticum strain MS-1 against an
AB  - in-house database comprising 426 complete bacterial and archaeal genome
AB  - sequences. A magnetobacterial core genome of about 891 genes was found
AB  - shared by all four MTB. In addition to a set of approximately 152
AB  - genus-specific genes shared by the three Magnetospirillum strains, we
AB  - identified 28 genes as group specific, i.e., which occur in all four
AB  - analyzed MTB but exhibit no (MTB-specific genes) or only remote
AB  - (MTB-related genes) similarity to any genes from nonmagnetotactic
AB  - organisms and which besides various novel genes include nearly all mam and
AB  - mms genes previously shown to control magnetosome formation. The
AB  - MTB-specific and MTB-related genes to a large extent display synteny,
AB  - partially encode previously unrecognized magnetosome membrane proteins,
AB  - and are either located within (18 genes) or outside (10 genes) the MAI of
AB  - M. gryphiswaldense. These genes, which represent less than 1% of the 4,268
AB  - open reading frames of the MSR-1 genome, as yet are mostly of unknown
AB  - functions but are likely to be specifically involved in magnetotaxis and,
AB  - thus, represent prime targets for future experimental analysis.
ER  -

TY  - JOUR
AU  - Ricker, N.
AU  - Shen, S.Y.
AU  - Goordial, J.
AU  - Jin, S.
AU  - Fulthorpe, R.R.
TI  - PacBio SMRT assembly of a complex multi-replicon genome reveals chlorocatechol degradative operon in a region of genome plasticity.
JO  - Gene
PY  - 2016
SP  - 239
EP  - 247
VL  - 586
AB  - We have sequenced a Burkholderia genome that contains multiple replicons and large repetitive
AB  - elements that would make it inherently difficult to assemble by short read sequencing
AB  - technologies. We illustrate how the integrated long read correction algorithms implemented
AB  - through the PacBio Single Molecule Real-Time (SMRT) sequencing technology successfully
AB  - provided a de novo assembly that is a reasonable estimate of both the gene content and genome
AB  - organization without making any further modifications. This assembly is comparable to related
AB  - organisms assembled by more labour intensive methods. Our assembled genome revealed regions of
AB  - genome plasticity for further investigation, one of which harbours a chlorocatechol
AB  - degradative operon highly homologous to those previously identified on globally ubiquitous
AB  - plasmids. In an ideal world, this assembly would still require experimental validation to
AB  - confirm gene order and copy number of repeated elements. However, we submit that particularly
AB  - in instances where a polished genome is not the primary goal of the sequencing project, PacBio
AB  - SMRT sequencing provides a financially viable option for generating a biologically relevant
AB  - genome estimate that can be utilized by other researchers for comparative studies.
ER  -

TY  - JOUR
AU  - Ricks, N.J.
AU  - Carroll, C.
AU  - Walters, A.
AU  - Newell, P.D.
AU  - Chaston, J.M.
TI  - Genome Sequence of Weissella cibaria DmW_103, Isolated from Wild Drosophila.
JO  - Genome Announcements
PY  - 2017
SP  - e00512
EP  - e00517
VL  - 5
AB  - Lactic acid bacteria are commonly associated with Drosophila spp. Here, we report on the
AB  - isolation of a strain of Weissella cibaria and the sequencing, assembly,
AB  - and annotation of its genome. A total of 35 contigs were generated, with 2,349
AB  - coding sequences found.
ER  -

TY  - JOUR
AU  - Riddihough, G.
TI  - No limits on restriction.
JO  - Nature
PY  - 1994
SP  - 78
EP  - 78
VL  - 370
AB  - The structure of the endonuclease R.PvuII in the absence and presence of its recognition site
AB  - indicates how the interaction with DNA might proceed.
ER  -

TY  - JOUR
AU  - Ridl, J.
AU  - Suman, J.
AU  - Fraraccio, S.
AU  - Hradilova, M.
AU  - Strejcek, M.
AU  - Cajthaml, T.
AU  - Zubrova, A.
AU  - Macek, T.
AU  - Strnad, H.
AU  - Uhlik, O.
TI  - Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 3
EP  - 3
VL  - 13
AB  - In this study, following its isolation from contaminated soil, the genomic sequence of
AB  - Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a
AB  - biphenyl-degrading bacterium, is reported and analyzed in relation to its
AB  - extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank
AB  - accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC
AB  - content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes.
AB  - The genome harbors a bph gene cluster, permitting degradation of biphenyl and
AB  - many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling
AB  - benzoate and its derivatives to be degraded, and phe gene cluster, which permits
AB  - phenol degradation. In addition, P. alcaliphila JAB1 is capable of
AB  - cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol.
AB  - The strain carries both catechol and protocatechuate branches of the
AB  - beta-ketoadipate pathway, which is used to funnel the pollutants to the central
AB  - metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with
AB  - closest phylogenetic relatives should be used when taxonomically classifying the
AB  - isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic
AB  - data analyses, enables more precise identification of the culture at the species
AB  - level.
ER  -

TY  - JOUR
AU  - Riedel, T. et al.
TI  - Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 389
EP  - 402
VL  - 8
AB  - Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically  well
AB  - characterized Roseobacter clade within the family Rhodobacteraceae.
AB  - Representatives of the marine Roseobacter clade are metabolically versatile and
AB  - involved in carbon fixation and biogeochemical processes. They form a
AB  - physiologically heterogeneous group, found predominantly in coastal or polar
AB  - waters, especially in symbiosis with algae, in microbial mats, in sediments or
AB  - associated with invertebrates. Here we describe the features of L. aquimarina DSM
AB  - 24565(T) together with the permanent-draft genome sequence and annotation. The
AB  - 5,344,253 bp long genome consists of one chromosome and an unusually high number
AB  - of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA
AB  - genes. It was sequenced as part of the DOE Joint Genome Institute Community
AB  - Sequencing Program 2010 and of the activities of the Transregional Collaborative
AB  - Research Centre 51 funded by the German Research Foundation (DFG).
ER  -

TY  - JOUR
AU  - Riedel, T. et al.
TI  - Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 120
EP  - 130
VL  - 7
AB  - Lau . 2005 is the sole member of the monospecific genus in the family a poorly characterized
AB  - family at the genome level thus far. This family comprises seven
AB  - genera within the class . Family members are known to be psychrotolerant,
AB  - rod-shaped and orange pigmented (beta-carotene), typical for . For growth,
AB  - seawater and complex organic nutrients are necessary. The genome of UST20020801
AB  - is only the second genome of a member of the family whose sequence has been
AB  - deciphered. Here we describe the features of this organism, together with the
AB  - complete genome sequence and annotation. The 4,000,057 bp long chromosome with
AB  - its 3,518 protein-coding and 45 RNA genes is a part of the project.
ER  -

TY  - JOUR
AU  - Riedel, T. et al.
TI  - Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 107
EP  - 119
VL  - 7
AB  - Van Trappen et al. 2004 is the type species of the genus , which is a member of the well
AB  - characterized family . The genome of R-8282 is the first sequenced
AB  - genome (permanent draft) from a type strain of the genus . Here we describe the
AB  - features of this organism, together with the permanent-draft genome sequence and
AB  - annotation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569
AB  - protein-coding and 51 RNA genes is a part of the of and project.
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Bunk, B.
AU  - Thurmer, A.
AU  - Sproer, C.
AU  - Brzuszkiewicz, E.
AU  - Abt, B.
AU  - Gronow, S.
AU  - Liesegang, H.
AU  - Daniel, R.
AU  - Overmann, J.
TI  - Genome Resequencing of the Virulent and Multidrug-Resistant Reference Strain Clostridium difficile 630.
JO  - Genome Announcements
PY  - 2015
SP  - e00276
EP  - e00215
VL  - 3
AB  - We resequenced the complete genome of the virulent and multidrug-resistant pathogen
AB  - Clostridium difficile strain 630. A combination of single-molecule
AB  - real-time and Illumina sequencing technology revealed the presence of an
AB  - additional rRNA gene cluster, additional tRNAs, and the absence of a transposon
AB  - in comparison to the published and reannotated genome sequence.
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Bunk, B.
AU  - Wittmann, J.
AU  - Thurmer, A.
AU  - Sproer, C.
AU  - Gronow, S.
AU  - Liesegang, H.
AU  - Daniel, R.
AU  - Overmann, J.
TI  - Complete Genome Sequence of the Clostridium difficile Type Strain DSM 1296T.
JO  - Genome Announcements
PY  - 2015
SP  - e01186
EP  - e01115
VL  - 3
AB  - In this study, we sequenced the complete genome of the Clostridium difficile type strain DSM
AB  - 1296(T). A combination of single-molecule real-time (SMRT) and Illumina sequencing technology
AB  - revealed the presence of one chromosome and two extrachromosomal elements, the bacteriophage
AB  - phiCDIF1296T and a putative plasmid-like structure harboring genes of another bacteriophage.
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Fiebig, A.
AU  - Goker, M.
AU  - Klenk, H.P.
TI  - Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group  isolated from Australian coast sand.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 840
EP  - 854
VL  - 9
AB  - Roseibacterium elongatum Suzuki et al. 2006 is a pink-pigmented and bacteriochlorophyll
AB  - a-producing representative of the Roseobacter group within
AB  - the alphaproteobacterial family Rhodobacteraceae. Representatives of the marine
AB  - 'Roseobacter group' were found to be abundant in the ocean and play an important
AB  - role in global and biogeochemical processes. In the present study we describe the
AB  - features of R. elongatum strain OCh 323(T) together with its genome sequence and
AB  - annotation. The 3,555,102 bp long genome consists of one circular chromosome with
AB  - no extrachromosomal elements and is one of the smallest known Roseobacter
AB  - genomes. It contains 3,540 protein-coding genes and 59 RNA genes. Genome analysis
AB  - revealed the presence of a photosynthetic gene cluster, which putatively enables
AB  - a photoheterotrophic lifestyle. Gene sequences associated with quorum sensing,
AB  - motility, surface attachment, and thiosulfate and carbon monoxide oxidation could
AB  - be detected. The genome was sequenced as part of the activities of the
AB  - Transregional Collaborative Research Centre 51 (TRR51) funded by the German
AB  - Research Foundation (DFG).
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Fiebig, A.
AU  - Han, J.
AU  - Huntemann, M.
AU  - Spring, S.
AU  - Petersen, J.
AU  - Ivanova, N.N.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Goker, M.
AU  - Kyrpides, N.C.
AU  - Klenk, H.P.
TI  - Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 855
EP  - 865
VL  - 9
AB  - Wenxinia marina Ying et al. 2007 is the type species of the genus Wenxinia, a representative
AB  - of the Roseobacter group within the alphaproteobacterial family
AB  - Rhodobacteraceae, isolated from oilfield sediments of the South China Sea. This
AB  - family was shown to harbor the most abundant bacteria especially from coastal and
AB  - polar waters, but was also found in microbial mats, sediments and attached to
AB  - different kind of surfaces. Here we describe the features of W. marina strain
AB  - HY34(T) together with the genome sequence and annotation of strain DSM 24838(T)
AB  - and novel aspects of its phenotype. The 4,181,754 bp containing genome sequence
AB  - encodes 4,047 protein-coding genes and 59 RNA genes. The genome of W. marina DSM
AB  - 24838(T) was sequenced as part of the activities of the Genomic Encyclopedia of
AB  - Type Strains, Phase I: the one thousand microbial genomes (KMG) project funded by
AB  - the DoE and the Transregional Collaborative Research Centre 51 (TRR51) funded by
AB  - the German Research Foundation (DFG).
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Fiebig, A.
AU  - Petersen, J.
AU  - Gronow, S.
AU  - Kyrpides, N.C.
AU  - Goker, M.
AU  - Klenk, H.P.
TI  - Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member  of the Roseobacter clade isolated from sea sand.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 117
EP  - 127
VL  - 9
AB  - Litoreibacter arenae Kim et al. 2012 is a member of the genomically well-characterized
AB  - Rhodobacteraceae clade within the Roseobacter clade.
AB  - Representatives of this clade are known to be metabolically versatile and
AB  - involved in marine carbon-producing and biogeochemical processes. They form a
AB  - physiologically heterogeneous group of Alphaproteobacteria and were mostly found
AB  - in coastal or polar waters, especially in symbiosis with algae, in microbial
AB  - mats, in sediments or together with invertebrates and vertebrates. Here we
AB  - describe the features of L. arenae DSM 19593(T), including novel aspects of its
AB  - phenotype, together with the draft genome sequence and annotation. The 3,690,113
AB  - bp long genome consists of 17 scaffolds with 3,601 protein-coding and 56 RNA
AB  - genes. This genome was sequenced as part of the activities of the Transregional
AB  - Collaborative Research Centre 51 funded by the German Research Foundation (DFG).
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Spring, S.
AU  - Fiebig, A.
AU  - Petersen, J.
AU  - Goker, M.
AU  - Klenk, H.P.
TI  - Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group   isolated from soil, and emended description of the species.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 902
EP  - 913
VL  - 9
AB  - Rubellimicrobium mesophilum Dastager et al. 2008 is a mesophilic and light reddish-pigmented
AB  - representative of the Roseobacter group within the
AB  - alphaproteobacterial family Rhodobacteraceae. Representatives of the Roseobacter
AB  - group play an important role in the marine biogeochemical cycles and were found
AB  - in a broad variety of marine environments associated with algal blooms, different
AB  - kinds of sediments, and surfaces of invertebrates and vertebrates. Roseobacters
AB  - were shown to be widely distributed, especially within the total bacterial
AB  - community found in coastal waters, as well as in mixed water layers of the open
AB  - ocean. Here we describe the features of R. mesophilum strain MSL-20(T) together
AB  - with its genome sequence and annotation generated from a culture of DSM 19309(T).
AB  - The 4,927,676 bp genome sequence consists of one chromosome and probably one
AB  - extrachromosomal element. It contains 5,082 protein-coding genes and 56 RNA
AB  - genes. As previously reported, the G+C content is significantly different from
AB  - the actual genome sequence-based G+C content and as the type strain tests
AB  - positively for oxidase, the species description is emended accordingly. The
AB  - genome was sequenced as part of the activities of the Transregional Collaborative
AB  - Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Spring, S.
AU  - Fiebig, A.
AU  - Petersen, J.
AU  - Kyrpides, N.C.
AU  - Goker, M.
AU  - Klenk, H.P.
TI  - Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain  (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1333
EP  - 1345
VL  - 9
AB  - Salipiger mucosus Martinez-Canovas et al. 2004 is the type species of the genus Salipiger, a
AB  - moderately halophilic and exopolysaccharide-producing representative
AB  - of the Roseobacter lineage within the alphaproteobacterial family
AB  - Rhodobacteraceae. Members of this family were shown to be the most abundant
AB  - bacteria especially in coastal and polar waters, but were also found in microbial
AB  - mats and sediments. Here we describe the features of the S. mucosus strain DSM
AB  - 16094(T) together with its genome sequence and annotation. The 5,689,389-bp
AB  - genome sequence consists of one chromosome and several extrachromosomal elements.
AB  - It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus
AB  - DSM 16094(T) was sequenced as part of the activities of the Transregional
AB  - Collaborative Research Center 51 (TRR51) funded by the German Research Foundation
AB  - (DFG).
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Spring, S.
AU  - Fiebig, A.
AU  - Scheuner, C.
AU  - Petersen, J.
AU  - Goker, M.
AU  - Klenk, H.P.
TI  - Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group  isolated from the dinoflagellate Alexandrium ostenfeldii.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 17
EP  - 17
VL  - 10
AB  - Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of
AB  - the marine Roseobacter group within the alphaproteobacterial
AB  - family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium
AB  - ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean
AB  - and plays an important role for global and biogeochemical processes. Here we
AB  - describe the features of the R. mucosus strain DFL-24(T) together with its genome
AB  - sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724
AB  - bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA
AB  - genes. In addition to the presence of four plasmids, genome analysis revealed the
AB  - presence of genes associated with host colonization, DMSP utilization,
AB  - cytotoxins, and quorum sensing that could play a role in the interrelationship of
AB  - R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms.
AB  - Furthermore, the genome encodes genes associated with mixotrophic growth, where
AB  - both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic
AB  - lifestyle using light as additional energy source could be used.
ER  -

TY  - JOUR
AU  - Riedel, T.
AU  - Wetzel, D.
AU  - Hofmann, J.D.
AU  - Plorin, S.P.
AU  - Dannheim, H.
AU  - Berges, M.
AU  - Zimmermann, O.
AU  - Bunk, B.
AU  - Schober, I.
AU  - Sproer, C.
AU  - Liesegang, H.
AU  - Jahn, D.
AU  - Overmann, J.
AU  - Gross, U.
AU  - Neumann-Schaal, M.
TI  - High metabolic versatility of different toxigenic and non-toxigenic Clostridioides difficile isolates.
JO  - Int. J. Med. Microbiol.
PY  - 2017
SP  - 311
EP  - 320
VL  - 307
AB  - Clostridioides difficile (formerly Clostridium difficile) is a major nosocomial
AB  - pathogen with an increasing number of community-acquired infections causing
AB  - symptoms from mild diarrhea to life-threatening colitis. The pathogenicity of C.
AB  - difficile is considered to be mainly associated with the production of
AB  - genome-encoded toxins A and B. In addition, some strains also encode and express
AB  - the binary toxin CDT. However; a large number of non-toxigenic C. difficile
AB  - strains have been isolated from the human gut and the environment. In this study,
AB  - we characterized the growth behavior, motility and fermentation product formation
AB  - of 17 different C. difficile isolates comprising five different major genomic
AB  - clades and five different toxin inventories in relation to the C. difficile model
AB  - strains 630Deltaerm and R20291. Within 33 determined fermentation products, we
AB  - identified two yet undescribed products (5-methylhexanoate and
AB  - 4-(methylthio)-butanoate) of C. difficile. Our data revealed major differences in
AB  - the fermentation products obtained after growth in a medium containing casamino
AB  - acids and glucose as carbon and energy source. While the metabolism of branched
AB  - chain amino acids remained comparable in all isolates, the aromatic amino acid
AB  - uptake and metabolism and the central carbon metabolism-associated fermentation
AB  - pathways varied strongly between the isolates. The patterns obtained followed
AB  - neither the classification of the clades nor the ribotyping patterns nor the
AB  - toxin distribution. As the toxin formation is strongly connected to the
AB  - metabolism, our data allow an improved differentiation of C. difficile strains.
AB  - The observed metabolic flexibility provides the optimal basis for the adaption in
AB  - the course of infection and to changing conditions in different environments
AB  - including the human gut.
ER  -

TY  - JOUR
AU  - Rieger, A.
AU  - Nassal, M.
TI  - Restriction endonuclease AlwNI is blocked by overlapping Dcm methylation.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4148
EP  - 4148
VL  - 21
AB  - Many restriction enzymes are unable to cleave DNA if their recognition sequence contains
AB  - methylated residues. The two sequence-specific methylases present in most laboratory strains
AB  - of Escherichia coli are the Dam methylase, which methylates the N6 position of A within the
AB  - sequence GATC, and the Dcm methylase, which methylates the C5 position of the internal C
AB  - residue with the sequence CC(A/T)GG. During the construction of derivatives of plasmid
AB  - pCHG-3122, which contains three recognition sites for the restriction endonuclease AlwNI, we
AB  - observed that one of the sites was only poorly cleaved when the plasmid DNA was isolated from
AB  - E. coli strain DH5-alpha. Inspection of the sequences flanking the three AlwNI recognition
AB  - sites showed that one of them located inside the LacZ fragment (ant position 2145) overlapped
AB  - with a recognition site for Dcm Methylase (see Table 1).
ER  -

TY  - JOUR
AU  - Rieger, M.
AU  - Denapaite, D.
AU  - Bruckner, R.
AU  - Maurer, P.
AU  - Hakenbeck, R.
TI  - Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19A Sequence Type 226 Clinical Isolates from Hungary, Hu17 with High-Level Beta-Lactam Resistance and Hu15 of a Penicillin-Sensitive Phenotype.
JO  - Genome Announcements
PY  - 2017
SP  - e00401
EP  - e00417
VL  - 5
AB  - The draft genome sequences of two multiple-antibiotic-resistant Streptococcus pneumoniae
AB  - isolates from Hungary, Hu15 and Hu17, are reported here. Strain Hu15
AB  - is penicillin susceptible, whereas Hu17 is a high-level-penicillin-resistant
AB  - strain. Both isolates belong to the serotype 19A sequence type 226, a
AB  - single-locus variant (in the ddl locus) of the Hungary19A-6 clone.
ER  -

TY  - JOUR
AU  - Rifat, D.
AU  - Wright, N.T.
AU  - Varney, K.M.
AU  - Weber, D.J.
AU  - Black, L.W.
TI  - Restriction Endonuclease Inhibitor IPI* of Bacteriophage T4: A Novel Structure for a Dedicated Target.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 720
EP  - 734
VL  - 375
AB  - Phage T4 protects its DNA from the two-gene-encoded gmrS/gmrD (glucose-modified
AB  - hydroxymethylcytosine restriction endonuclease) CT of
AB  - pathogenic Escherichia coli, CT596, by injecting several hundred copies of
AB  - the 76-amino-acid-residue nuclease inhibitor, IPI*, into the infected
AB  - host. Here, the three-dimensional solution structure of mature IPI* is
AB  - reported as determined by nuclear magnetic resonance techniques using 1290
AB  - experimental nuclear Overhauser effect and dipolar coupling constraints (
AB  - approximately 17 constraints per residue). Close examination of this
AB  - oblate-shaped protein structure reveals a novel fold consisting of two
AB  - small beta-sheets (beta1: B1 and B2; beta2: B3-B5) flanked at the N- and
AB  - C-termini by alpha-helices (H1 and H2). Such a fold is very compact in
AB  - shape and allows ejection of IPI* through the narrow 30-A portal and tail
AB  - tube apertures of the virion without unfolding. Structural and dynamic
AB  - measurements identify an exposed hydrophobic knob that is a putative
AB  - gmrS/gmrD-binding site. A single gene from the uropathogenic E. coli
AB  - UT189, which codes for a gmrS/gmrD-like UT fusion enzyme (with
AB  - approximately 90% identity to the heterodimeric CT enzyme), has evolved
AB  - IPI* inhibitor immunity. Analysis of the gmrS/gmrD restriction
AB  - endonuclease enzyme family and its IPI* family phage antagonists reveals
AB  - an evolutionary pathway that has elaborated a surprisingly diverse and
AB  - specifically fitted set of coevolving attack and defense structures.
ER  -

TY  - JOUR
AU  - Riggs, A.D.
TI  - X chromosome inactivation, differentiation, and DNA methylation revisited, with a tribute to Susumu Ohno.
JO  - Cytogenet. Genome Res.
PY  - 2002
SP  - 17
EP  - 24
VL  - 99
AB  - X chromosome inactivation and DNA methylation are reviewed, with emphasis on the contributions
AB  - of Susumu Ohno and the predictions made
AB  - in my 1975 paper (Riggs, 1975) in which I proposed the "maintenance
AB  - methylase" model for somatic inheritance of methylation patterns and
AB  - suggested that DNA methylation would be involved in mammalian X
AB  - chromosome inactivation and development. The maintenance methylase
AB  - model is discussed and updated to consider methylation patterns in cell
AB  - populations that have occasional, stochastic methylation changes by de
AB  - novo methylation or demethylation, either active or passive. The "way
AB  - station" model for the spread of X inactivation by LINE- 1 elements is
AB  - also considered, and some recent results from my laboratory are briefly
AB  - reviewed.
ER  -

TY  - JOUR
AU  - Rigonato, J.
AU  - Alvarenga, D.O.
AU  - Branco, L.H.
AU  - Varani, A.M.
AU  - Brandini, F.P.
AU  - Fiore, M.F.
TI  - Draft genome sequence of a novel culturable marine chroococcalean cyanobacterium  from the South atlantic ocean.
JO  - Genome Announcements
PY  - 2015
SP  - e00384
EP  - e00315
VL  - 3
AB  - The novel chroococcalean cyanobacterium strain CENA595 was isolated from the deep chlorophyll
AB  - maximum layer of the continental shelf of the South Atlantic Ocean.
AB  - Here, we report the draft genome sequence for this strain, consisting of 60
AB  - contigs containing a total of 5,265,703 bp and 3,276 putative protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Rihova, J.
AU  - Novakova, E.
AU  - Husnik, F.
AU  - Hypsa, V.
TI  - Legionella becoming a mutualist: adaptive processes shaping the genome of symbiont in the louse Polyplax serrata.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 2946
EP  - 2957
VL  - 9
AB  - Legionellaceae are intracellular bacteria known as important human pathogens. In
AB  - the environment, they are mainly found in biofilms associated with amoebas. In
AB  - contrast to the gammaproteobacterial family Enterobacteriaceae, which established
AB  - a broad spectrum of symbioses with many insect taxa, the only instance of
AB  - legionella-like symbiont has been reported from lice of the genus Polyplax. Here,
AB  - we sequenced the complete genome of this symbiont and compared its main
AB  - characteristics to other Legionella species and insect symbionts. Based on
AB  - rigorous multigene phylogenetic analyses, we confirm this bacterium as a member
AB  - of the genus Legionella and propose the name Candidatus Legionella polyplacis,
AB  - sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive
AB  - degeneration, including considerable size reduction (529.746 bp, 484 protein
AB  - coding genes) and a severe decrease in GC content (23%). We identify several
AB  - possible constraints underlying the evolution of this bacterium. On one hand, Ca.
AB  - Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced
AB  - convergent evolution, perhaps due to adaptation to similar hosts. On the other
AB  - hand, some metabolic differences are likely to reflect different phylogenetic
AB  - positions of the symbionts and hence availability of particular metabolic
AB  - function in the ancestor. This is exemplified by different arrangements of
AB  - thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal
AB  - gene transfer is shown to play a significant role in the adaptive and
AB  - diversification process. Particularly, we show that Ca. L. polyplacis
AB  - horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted
AB  - this bacterium when becoming an obligate mutualist.
ER  -

TY  - JOUR
AU  - Riipinen, K.A.
AU  - Forsman, P.
AU  - Alatossava, T.
TI  - The genomes and comparative genomics of Lactobacillus delbrueckii phages.
JO  - Arch. Virol.
PY  - 2011
SP  - 1217
EP  - 1233
VL  - 156
AB  - Lactobacillus delbrueckii phages are a great source of genetic diversity.
AB  - Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032
AB  - were analyzed in detail, and the genetic diversity of Lb. delbrueckii
AB  - phages belonging to different taxonomic groups was explored. The lytic
AB  - isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a
AB  - minimum nucleotide sequence identity of 90% over about three-fourths of
AB  - their genomes. The genomic locations of their lysis modules were unique,
AB  - and the genomes featured several putative overlapping transcription units
AB  - of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity
AB  - associated with a ~36-kDa protein similar in size to the endolysin.
AB  - Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032
AB  - (temperate, group c) revealed a conserved gene order within its structural
AB  - genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and
AB  - c possessed only limited protein sequence homology. Genomic comparison of
AB  - LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is
AB  - mainly due to insertions, deletions and recombination. For the first time,
AB  - the complete genome sequences of group b and c Lb. delbrueckii phages are
AB  - reported.
ER  -

TY  - JOUR
AU  - Riley, A.B.
AU  - Kim, D.
AU  - Hansen, A.K.
TI  - Genome Sequence of 'Candidatus Carsonella ruddii' Strain BC, a Nutritional Endosymbiont of Bactericera cockerelli.
JO  - Genome Announcements
PY  - 2017
SP  - e00236
EP  - e00217
VL  - 5
AB  - Here, we report the genome of 'Candidatus Carsonella ruddii' strain BC, a nutritional
AB  - endosymbiont of the tomato psyllid Bactericera cockerelli The
AB  - 173,802-bp genome contains 198 protein-coding genes, with a G+C content of 14.8%.
ER  -

TY  - JOUR
AU  - Riley, M.C.
AU  - Perreten, V.
AU  - Bemis, D.A.
AU  - Kania, S.A.
TI  - Complete Genome Sequences of Three Important Methicillin-Resistant Clinical Isolates of Staphylococcus pseudintermedius.
JO  - Genome Announcements
PY  - 2016
SP  - e01194
EP  - e01116
VL  - 4
AB  - We report the first complete genome sequences of three predominant clones (ST68,  ST71, and
AB  - ST84) of methicillin-resistant Staphylococcus pseudintermedius in North
AB  - America. All strains were isolated from canine infections and have different
AB  - SCCmec elements and antibiotic resistance gene patterns.
ER  -

TY  - JOUR
AU  - Rimbara, E.
AU  - Matsui, M.
AU  - Mori, S.
AU  - Suzuki, S.
AU  - Suzuki, M.
AU  - Kim, H.
AU  - Sekizuka, T.
AU  - Kuroda, M.
AU  - Shibayama, K.
TI  - Draft Genome Sequence of Helicobacter fennelliae Strain MRY12-0050, Isolated from a Bacteremia Patient.
JO  - Genome Announcements
PY  - 2013
SP  - e00512
EP  - e00513
VL  - 1
AB  - Helicobacter fennelliae, a human enterohepatic pathogen, causes bacteremia and colitis. We
AB  - isolated H. fennelliae strain MRY12-0050 from a female patient; this
AB  - strain was isolated from 2 other patients from the same hospital during the same
AB  - period, suggesting human-to-human transmission. This is the first report of an H.
AB  - fennelliae genome sequence.
ER  -

TY  - JOUR
AU  - Rimseliene, R.
AU  - Janulaitis, A.
TI  - Mutational analysis of two putative catalytic motifs of the Type IV restriction endonuclease Eco57I.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 10492
EP  - 10497
VL  - 276
AB  - The role of two sequence motifs (SM) as putative cleavage catalytic centers (77)PD(X13)EAK (SM
AB  - I) and (811)PD(X20)DQK (SM II) of type IV restriction endonuclease Eco57I was studied by
AB  - site-directed mutational analysis. Substitutions within SM I; D78N, D78A, D78K, and E92Q
AB  - reduced cleavage activity of Eco57I to a level undetectable both in vivo and in vitro.
AB  - Residual endonucleolytic activity of the E92Q mutant was detected only when the Mg(2+) in the
AB  - standard reaction mixture was replaced with Mn(2+). The mutants D78N and E92Q retained the
AB  - ability to interact with DNA specifically. The mutants also retained DNA methylation activity
AB  - of Eco57I. The properties of the SM I mutants indicate that Asp(78) and Glu(92) residues are
AB  - essential for cleavage activity of the Eco57I, suggesting that the sequence motif
AB  - (77)PD(X13)EAK represents the cleavage active site of this endonuclease. Eco57I mutants
AB  - containing single amino acid substitutions within SM II (D812A, D833N, D833A) revealed only a
AB  - small or moderate decrease of cleavage activity as compared with wild-type Eco57I, indicating
AB  - that the SM II motif does not represent the catalytic center of Eco57I. The results, taken
AB  - together, allow us to conclude that the Eco57I restriction endonuclease has one catalytic
AB  - center for cleavage of DNA.
ER  -

TY  - JOUR
AU  - Rimseliene, R.
AU  - Janulaitis, A.
TI  - Saturation mutagenesis of Thr862, the amino acid essential for substrate specificity of Eco57I restriction endonuclease.
JO  - Biologija
PY  - 2005
SP  - 11
EP  - 14
VL  - 1
AB  - Type IIG restriction endonuclease Eco57I cleaves DNA 16/14 nucleotides away from the
AB  - asymmetric recognition sequence 5'-CTGAAG.  The enzyme also possesses methyltransferase
AB  - activity that modifies the second A base within the 5'-CTGAAG strand of the target duplex
AB  - (underlined).  In previous studies, Eco57I mutants with altered substrate specificity
AB  - 5'-CTGRAG were isolated.  These mutant enzymes have Asn or Ser instead of Thr in the 862th
AB  - position of the protein.  In order to evaluate the impact of T862 on the substrate
AB  - specificity, it was changed to the other 17 amino acids.  The in vivo cleavage activity and
AB  - substrate specificity of the resulting mutant enzymes was examined (i) by testing lethality of
AB  - the mutants to the host cells in the absence or presence of Eco57I (specificity 5'-CTGAAG) and
AB  - GsuI (specificity 5'-CTGGAG) methyltransferases, and (ii) by testing the ability of the
AB  - mutants to induce SOS DNA repair response in the absence or presence of protecting
AB  - methyltransferases.  The results indicate that mutants T862G, T862C and, probably, T862A and
AB  - T862D could display altered substrate specificity.  The recognition sequence of T862F, H, K,
AB  - L, Q, M and Y mutants was the same as that of the wild type enzyme.  The remaining
AB  - substitutions rendered the enzyme catalytically inactive.
ER  -

TY  - JOUR
AU  - Rimseliene, R.
AU  - Maneliene, Z.
AU  - Lubys, A.
AU  - Janulaitis, A.
TI  - Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco571 to select the mutant with a novel sequence specificity.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 383
EP  - 391
VL  - 327
AB  - Type II restriction endonucleases (REs) are widely used tools in molecular biology,
AB  - biotechnology and diagnostics. Efforts to generate new
AB  - specificities by structure-guided design and random mutagenesis have been
AB  - unsuccessful so far. We have developed a new procedure called the
AB  - methylation activity-based selection (MABS) for generating REs with a new
AB  - specificity. MABS uses a unique property of bifunctional type II REs to
AB  - methylate DNA targets they recognize. The procedure includes three steps:
AB  - (1) conversion of a bifunctional RE into a monofunctional DNA-modifying
AB  - enzyme by cleavage center disruption; (2) mutagenesis and selection of
AB  - mutants with altered DNA modification specificity based on their ability
AB  - to protect predetermined DNA targets; (3) reconstitution of the cleavage
AB  - center's wild-type structure. The efficiency of the MABS technique was
AB  - demonstrated by altering the sequence specificity of the bifunctional RE
AB  - Eco57I from 5'-CTGAAG to 5'-CTGRAG, and thus generating the mutant
AB  - restriction endonuclease (and DNA methyltransferase) of a specificity not
AB  - known before. This study provides evidence that MABS is a promising
AB  - technique for generation of REs with new specificities.
ER  -

TY  - JOUR
AU  - Rimseliene, R.
AU  - Timinskas, A.
TI  - Site-directed mutagenesis of type IV restriction endonuclease Eco57I.
JO  - Biologija
PY  - 1997
SP  - 31
EP  - 33
VL  - 1
AB  - Amino acid sequence analysis of type IV restriction endonuclease Eco57I revealed two sequence
AB  - motifs 77PDX13EXK and 811PDX20 DXK as putative catalytic sites.  We have used a site-directed
AB  - mutational analysis of these regions in order, to determine their role in catalysis.
AB  - Catalytic properties of the mutants were studied in vivo and in vitro.  The replacement of D78
AB  - and E92, respectively, by mutations N78, A78, K78, Q92, resulted in the complete loss of
AB  - cleavage activity.  The D833N mutant cleaves DNA with reduced rate.  The activity of the D812A
AB  - mutant seems to be the same as that of the wild type R. Eco57I.  The results suggest that
AB  - amino acids D87 and E92 are essential for cleavage activity of the Eco57I restriction
AB  - endonuclease, and the sequence motif 77PDX13EXK is a catalytic center of the enzyme.
ER  -

TY  - JOUR
AU  - Rimseliene, R.
AU  - Vaisvila, R.
TI  - Cloning the PaeI restriction-modification system in Escherichia coli.
JO  - Biologija
PY  - 1998
SP  - 77
EP  - 78
VL  - 2
AB  - PaeI, type II restriction-modification system from bacterium Pseudomonas aeruginosa,
AB  - recognizes DNA sequence 5'-CGATCG-3'.  The PaeI methyltransferase (Mtase)-encoding gene,
AB  - paeIM, was cloned into Escherichia coli using biochemical Mtase selection method.  According
AB  - to the results of Southern-blot analysis, chromosomal map of Pseudomonas aeruginosa was
AB  - generated localizing the paeIM gene and flanking regions.  The paeIR gene was cloned as a 2.1
AB  - kb Eco47III DNA fragment into pBR322 vector.  In order to increase the PaeI restriction
AB  - endonuclease expression and yield in E. coli, the paeIR gene was subcloned into multicopy
AB  - plasmid pIC-19H.  80000 units of R.PaeI per gram of wet-weight cells were produced, approx. 20
AB  - times more than were produced by P. aeruginosa.
ER  -

TY  - JOUR
AU  - Rimseliene, R.
AU  - Vaisvila, R.
AU  - Janulaitis, A.
TI  - The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco72I restriction-modification system.
JO  - Gene
PY  - 1995
SP  - 217
EP  - 219
VL  - 157
AB  - Eco72I from Escherichia coli RFL72 is a type-II restriction-modification (R-M) system
AB  - recognizing and cleaving the sequence 5'-CAC/GTG-3'.  The R-M genes are transcribed
AB  - divergently and between the two genes is a small open reading frame codirectional to the R
AB  - gene.  This small ORF acts both to stimulate ENase expression and to depress DNA
AB  - methyltransferase synthesis.  The activity of beta-Gal produced from the eco72IM::lacZ
AB  - translational fusion increased ten-fold, and eco72IR::lacZ translational fusion beta-Gal
AB  - activity decreased 130-fold when eco72IC was inactivated by a frameshift mutation.  Analysis
AB  - of nucleotide sequences of R-M systems, containing C genes, revealed a 5'-ACCTTATAGTC-3'
AB  - consensus sequence upstream from the regulatory genes in all six analysed R-M systems.  This
AB  - sequence, named the C-box, may play the role of an operator sequence.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Bouriotis, V.
TI  - Cloning, purification and characterization of the BseCI DNA methyltransferase from Bacillus stearothermophilus.
JO  - Gene
PY  - 1993
SP  - 91
EP  - 94
VL  - 133
AB  - The gene (bseCIM) encoding the BseCI DNA methyltransferase (MTase; M.BseCI) from a Bacillus
AB  - stearothermophilus species was cloned and expressed in Escherichia coli using plasmid vector
AB  - pBR322. Selection of transformants carrying bseCIM was based on resistance of the modified
AB  - plasmid to cleavage by BseCI. The MTase was purified to homogeneity and further characterized.
AB  - Its size as determined by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis and size
AB  - exclusion chromatography was 68 kDa, suggesting that the MTase exists as a monomer. When phage
AB  - lambda DNA was used as a substrate, the optimum temperature for MTase activity was determined
AB  - to be 50-55 degrees C and optimum pH approx 7.4. M.BseCI is inhibited by concentrations of
AB  - NaCl and KCl greater than 50 mM, and it does not require Mg2+ for activity. Finally, M.BseCI
AB  - methylates the 3' adenine residue in the sequence, 5'ATCGAT 3', similarly to its
AB  - isoschizomer M.ClaI.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BsiSI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1654
EP  - 1654
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Caufrier, F.
AU  - Markaki, M.
AU  - Mavromatis, K.
AU  - Kokkinidis, M.
AU  - Bouriotis, V.
TI  - Cloning and characterization of the gene encoding PspPI methyltransferase from the Antarctic psychrotroph Psychrobacter sp. strain TA137.
JO  - Gene
PY  - 1997
SP  - 353
EP  - 360
VL  - 197
AB  - The gene (pspPIM) encoding the PspPI DNA methyltransferase (MTase) associated with the PspPI
AB  - restriction-modification system (5'-GGNCC-3') of Psychrobacter species TA137 has been cloned
AB  - and expressed in E. coli, and its nucleotide sequence has been determined.  The coding region
AB  - was 1248 nt in length and capable of specifying a 46,826-Da protein of 416 amino acids.  The
AB  - predicted sequence of the MTase protein displays ten sequence motifs characteristic of all
AB  - prokaryotic m5C-MTases and shows the highest similarity to other MTases that methylate the
AB  - GGNCC sequence, namely M.Eco47II and M.Sau96I.  All three MTases methylate the internal
AB  - cytosine within their recognition sequence.  Sequence similarities between M.PspPI and its
AB  - isospecific M.Eco47II and M.Sau96I as well as with four other m5C-MTases that methylate the
AB  - related GGWCC sequence, namely M.SinI, M.HgiCII, M.HgiBI, M.HgiEI have been also found within
AB  - the variable region of these proteins.  On the basis of structural information from M.HhaI and
AB  - M.HaeIII, several M.PspPI residues that are expected to interact with DNA can be predicted.
AB  - Furthermore, an organization of the variable region of m5C-MTases into two segments exhibiting
AB  - a pattern of conserved residues and a considerable degree of structural homologies is
AB  - described.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Clark, D.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BsiKI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1655
EP  - 1655
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Dialektakis, D.
AU  - Clark, D.
AU  - Pagomenou, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BseCl.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1807
EP  - 1807
VL  - 20
AB  - BseCI, an isoschizomer of ClaI has been purified from Bacillus species. BseCI recognizes the
AB  - sequence 5' ...ATCGAT ...3' and cleaves between T and C. The enzyme was purified using the
AB  - following chromatographic steps: 1. Phosphocellulose, 2. Heparin-Sepharose, 3. DEAE-cellulose.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Karagouni, A.
AU  - Pagomenou, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease SgrBI.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6342
EP  - 6342
VL  - 19
AB  - SgrBI, an isoschizomer of SacII has been purified from Streptomyces griseus.
AB  - SgrBI recognises the palindromic sequence 5'...CCGCGG...3' generating
AB  - 3'-protruding GC-dinucleotides.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Karagouni, A.
AU  - Pagomenou, M.
AU  - Tsigos, I.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease SseAI.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6341
EP  - 6341
VL  - 19
AB  - SseAI, an isoschizomer of NarI, has been purified from Streptomyces species.
AB  - SseAI recognises the palindromic sequence 5'...GGCGCC...3' and cleaves between
AB  - the second G and C.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Markaki, M.
AU  - Bouriotis, V.
TI  - Sequence of the cloned bseCIM gene: M.BseCI reveals high homology to M.BanIII.
JO  - Gene
PY  - 1994
SP  - 71
EP  - 73
VL  - 150
AB  - The bseCIM gene, encoding M.BseCI methyltransferase (MTase) from a Bacillus stearothermophilus
AB  - strain, has been previously cloned and expressed in Escherichia coli. The nucleotide (nt)
AB  - sequence of a 2357-bp BspMII-EcoRI fragment encoding bseCIM has now been determined. The
AB  - sequence predicts a MTase of 579 amino acids (aa), 66.7 kDa. Comparison of the deduced aa
AB  - sequence of M.BseCI with sequences of various MTases revealed a significant homology to
AB  - m6A-MTases, especially to its isoschizomer M.BanIII from Bacillus aneurinolyticus.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Stratidakis, I.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BssAI.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6161
EP  - 6161
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Tsigos, I.
AU  - Karagouni, A.
AU  - Pagomenou, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BseBI.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4776
EP  - 4776
VL  - 19
AB  - BseBI, an isoschizomer of BstNI has been purified from Bacillus
AB  - stearothermophilus species.  BseBI recognises the sequence 5'...CCWGG...3' (W=A
AB  - or T) and cleaves between C and W.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Tzanodaskalaki, M.
AU  - Karagouni, A.
AU  - Pagomenou, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease SseBI.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1808
EP  - 1808
VL  - 20
AB  - SseBI, an isoschizomer of StuI has been purified from Streptomyces species. SseBI recognizes
AB  - the sequence 5' ... AGGCCT ...3' and cleaves between G and C. The enzyme was purified using
AB  - the following chromatographic steps: 1. Blue Sepharose F3GA, 2. Heparin-Sepharose.
ER  -

TY  - JOUR
AU  - Rina, M.
AU  - Tzanodaskalaki, M.
AU  - Karagouni, A.
AU  - Pagomenou, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease MspCI.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1806
EP  - 1806
VL  - 20
AB  - MspCI, an isoschizomer of AflII, has been purified from Micrococcus species. MspCI recognizes
AB  - the sequence 5' ...CTTAAG ...3' and cleaves between C and T. The enzyme was purified using
AB  - the following chromatographic steps: 1. Blue Sepharose F3GA; 2. Heparin-Sepharose; 3. DEAE
AB  - Sepharose.
ER  -

TY  - JOUR
AU  - Rine, J.
AU  - Barnes, G.
TI  - Entry of a procaryotic endonuclease into the nucleus of Saccharomyces cerevisiae.
JO  - Yeast Cell Biology
PY  - 1986
SP  - 395
EP  - 413
VL  - 0
AB  - Recent experiment have documented the existence of amino acid sequences, acting
AB  - as nuclear signal sequences, that result in the accumulation of proteins in the
AB  - nucleus.  In this paper, the issue of whether or not a protein must possess a
AB  - nuclear signal in order to enter the nucleus is examined.  For these
AB  - experiments, a plasmid capable of expressing EcoRI endonuclease in the yeast
AB  - Saccharomyces cerevisiae has been constructed and transformed into several
AB  - yeast strains.  Two results demonstrate that this bacterial protein can enter
AB  - the yeast nucleus:  First, yeast cells expressing the endonuclease gene die
AB  - with kinetics that are proportional to the capacity of the strain to repair
AB  - double stranded breaks in nuclear DNA.  Secondly, the nuclear DNA contains
AB  - extensive double stranded breaks at EcoRI sites and only at EcoRI sites.
AB  - Therefore, there is no apparent requirement for a protein to contain a complex
AB  - nuclear localization signal in order to enter the nucleus.  Additional
AB  - experiments demonstrate that in-frame fusion of an open reading frame to the 5'
AB  - end of the endonuclease structural gene results in synthesis of a hybrid
AB  - protein that retains endonucleolytic activity.  Mutants of the endonuclease are
AB  - described that allow the activity of the enzyme to be modulated independently
AB  - of its synthesis.
ER  -

TY  - JOUR
AU  - Ring, N.
AU  - Abrahams, J.
AU  - Jain, M.
AU  - Olsen, H.
AU  - Preston, A.
AU  - Bagby, S.
TI  - Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing.
JO  - bioRxiv
PY  - 2018
SP  - 0
EP  - 0
VL  - 381640
AB  - The genome of Bordetella pertussis is complex, with high GC content and many repeats, each
AB  - longer than 1,000 bp. Short-read DNA sequencing is unable to resolve the structure of the
AB  - genome; however, long-read sequencing offers the opportunity to produce single-contig B.
AB  - pertussis assemblies using sequencing reads which are longer than the repetitive sections. We
AB  - used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single
AB  - sequencing run. We then trialled combinations of the many nanopore-user-community-built
AB  - long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis
AB  - genome sequences. Our best long-read-only assemblies were produced by Canu read correction
AB  - followed by assembly with Flye and polishing with Nanopolish, whilst the best hybrids (using
AB  - nanopore and Illumina reads together) were produced by Canu correction followed by Unicycler.
AB  - This pipeline produced closed genome sequences for four strains, revealing inter-strain
AB  - genomic rearrangement. However, read mapping to the Tohama I reference genome suggests that
AB  - the remaining strain contains an ultra-long duplicated region (over 100 kbp), which was not
AB  - resolved by our pipeline. We have therefore demonstrated the ability to resolve the structure
AB  - of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with
AB  - highest complexity (e.g. very large duplicated regions) remain only partially resolved using
AB  - the standard library preparation and will require an alternative library preparation method.
AB  - For full strain characterisation, we recommend hybrid assembly of long and short reads
AB  - together; for comparison of genome arrangement, assembly using long reads alone is sufficient.
ER  -

TY  - JOUR
AU  - Ringquist, S.
AU  - Smith, C.L.
TI  - The Escherichia coli chromosome contains specific, unmethylated dam and dcm sites.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 4539
EP  - 4543
VL  - 89
AB  - The Escherichia coli chromosome encodes two methylases, dam and dcm, which recognize the
AB  - sequences GATC and CC(A/T)GG, respectively. Specific dam and dcm sites on the E. coli
AB  - chromosome were found to be unmethylated in vivo by using pulsed-field gel electrophoresis
AB  - experiments scanning megabase regions of DNA. Some sites were totally unmethylated. The dam
AB  - sites display variable methylation depending on the local sequence, and, in general, their
AB  - methylation shows complex modulation by growth conditions and growth rate, suggesting multiple
AB  - protection mechanisms. Sites resistant to complete dam or dcm methylation appear to be
AB  - distributed throughout the chromosome. These unusual sites may identify regions of the
AB  - chromosome with interesting biological functions.
ER  -

TY  - JOUR
AU  - Rinke, C. et al.
TI  - Insights into the phylogeny and coding potential of microbial dark matter.
JO  - Nature
PY  - 2013
SP  - 431
EP  - 437
VL  - 499
AB  - Genome sequencing enhances our understanding of the biological world by providing
AB  - blueprints for the evolutionary and functional diversity that shapes the
AB  - biosphere. However, microbial genomes that are currently available are of limited
AB  - phylogenetic breadth, owing to our historical inability to cultivate most
AB  - microorganisms in the laboratory. We apply single-cell genomics to target and
AB  - sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats
AB  - belonging to 29 major mostly uncharted branches of the tree of life, so-called
AB  - 'microbial dark matter'. With this additional genomic information, we are able to
AB  - resolve many intra- and inter-phylum-level relationships and to propose two new
AB  - superphyla. We uncover unexpected metabolic features that extend our
AB  - understanding of biology and challenge established boundaries between the three
AB  - domains of life. These include a novel amino acid use for the opal stop codon, an
AB  - archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea
AB  - similar to those in Bacteria. The single-cell genomes also served to
AB  - phylogenetically anchor up to 20% of metagenomic reads in some habitats,
AB  - facilitating organism-level interpretation of ecosystem function. This study
AB  - greatly expands the genomic representation of the tree of life and provides a
AB  - systematic step towards a better understanding of biological evolution on our
AB  - planet.
ER  -

TY  - JOUR
AU  - Rinkel, L.J.
AU  - van der Marel, G.A.
AU  - van Boom, J.H.
AU  - Altona, C.
TI  - Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy 1. The duplex form.
JO  - Eur. J. Biochem.
PY  - 1987
SP  - 275
EP  - 286
VL  - 163
AB  - One- and two-dimensional NMR studies at 300 MHz and 500 MHz were carried out on
AB  - the two oligonucleotides d(C-C-G-A-A-T-T-C-G-G) and d(C-C-G-A-m6A-T-T-C-G-G) in
AB  - aqueous solution.  NMR spectra was observed at 10 mM sample concentration over
AB  - the temperature range 273-368 K.  Assignments are given of the base, H1', H2',
AB  - H2", H3' and of some H4' resonances, based upon a combination of
AB  - two-dimensional correlation spectra (COSY) and two-dimensional nuclear
AB  - Overhauser effect spectra (NOESY); imino-proton resonances were assigned with
AB  - the aid of a two-dimensional NOE experiment.  Chemical shift vs temperature
AB  - profiles were constructed in order to gain insight into the influence of
AB  - N6-methylation of residue A(5) on the temperature-dependent conformational
AB  - behaviour of the decamer and to determine thermodynamic parameters for the
AB  - duplex-to-coil tranasition.  The NOESY spectra, the imino-proton spectra and
AB  - the shift profiles of the two compounds, under conditions where each forms a
AB  - B-DNA-type duplex, are very similar.  This is taken to indicate that the
AB  - influence of N6-methylation of residue A(5) on the local structure of the
AB  - duplex must be small.  However, the temperature dependence of the
AB  - (non-)exchangeable proton resonances of the two compounds reveals that
AB  - methylation slows down the duplex- single-strand exchange.  Furthermore, a
AB  - thermodynamic analysis of the two compounds indicates that N6-methylation
AB  - slightly decreases the stability of the duplex relative to the monomeric forms
AB  - (Tm is reduced from 332 K down to 325 K at 10 mM sample concentration).
AB  - Proton-proton couplings were obtained by means of one-dimensional and
AB  - two-dimensional NMR experiments and were used in a conformational analysis of
AB  - the sugar ring of each residue of the two compounds in the duplex form.  The
AB  - analysis indicated that all sugar rings display conformational flexibility in
AB  - the intact duplex:  population S-type sugar conformation ranges from 70% to
AB  - 100%. A more refined analysis of the sugar rings of the parent compound
AB  - revealed a sequence-dependent variation of the sugar geometry.  This variation
AB  - does not follow well the trend predicted by the Calladine/Dickerson Sigma3-sum
AB  - rule [Dickerson, R.E.(1983).  J. Mol. Biol. 166, 419-441; Calladine, C.R.
AB  - (1982) J. Mol. Biol. 161, 343-352}; moreover the actual variations appear to be
AB  - smaller in solution than those expected on the basis of known X-ray structures.
ER  -

TY  - JOUR
AU  - Rischer, M.
AU  - Klassen, J.L.
AU  - Wolf, T.
AU  - Guo, H.
AU  - Shelest, E.
AU  - Clardy, J.
AU  - Beemelmanns, C.
TI  - Draft Genome Sequence of Shewanella sp. Strain P1-14-1, a Bacterial Inducer of Settlement and Morphogenesis in Larvae of the Marine Hydroid Hydractinia  echinata.
JO  - Genome Announcements
PY  - 2016
SP  - e00003
EP  - e00016
VL  - 4
AB  - The assembly and annotation of the draft genome sequence of Shewanella sp. strain P1-14-1 are
AB  - reported here to investigate the genes responsible for interkingdom
AB  - interactions, secondary metabolite production, and microbial electrogenesis.
ER  -

TY  - JOUR
AU  - Risser, R.
AU  - Hopkins, N.
AU  - Davis, R.W.
AU  - Delius, H.
AU  - Mulder, C.
TI  - Action of Escherichia coli P1 restriction endonuclease on Simian Virus 40 DNA.
JO  - J. Mol. Biol.
PY  - 1974
SP  - 517
EP  - 544
VL  - 89
AB  - The P1 restriction endonuclease prepared from a P1 lysogen of Escherichia coli makes one
AB  - double-strand break in simian virus (SV40) DNA.  In the presence of cofactors
AB  - S-adenosylmethionine and ATP the enzyme cleaves 70% of the closed circular SV40 DNA molecules
AB  - once to produce unit-length linear molecules and renders the remaining 30% resistant to
AB  - further cleavage.  No molecules were found by electron microscopy or by gel electrophoresis
AB  - that were cleaved more than once.  It would appear that the double-strand break is made by two
AB  - nearly simultaneous single-strand breaks, since no circular DNA molecules containing one
AB  - single-strand break were found as intermediates during the cleavage reaction.  The EcoP1
AB  - endonuclease-cleaved linear SV40 DNA molecules are not cleaved at a unique site, as shown by
AB  - the generation of about 65% circular molecules after denaturation and renaturation.  These
AB  - EcoP1 endonuclease-cleaved, renatured circular molecules are resistant to further cleavage by
AB  - EcoP1 endonuclease.  The EcoP1 endonuclease cleavage sites on SV40 DNA were mapped relative to
AB  - the partial denaturation map and to the EcoRI and HpaII restriction endonuclease cleavage
AB  - sites.  These maps suggest there are a minimum of four unique but widely space cleavage sites
AB  - at 0.09, 0.19, 0.52, and 0.66 SV40 units relative to the EcoRI site.  The frequency of
AB  - cleavage at any particular site differs from that at another site.  If S-adenosylmethionine is
AB  - omitted from the enzyme reaction mix, SV40 DNA is cleaved into several fragments.  An average
AB  - of 4.6 +/- 1 methyl groups are transferred to SV40 DNA from S-adenosylmethionine during the
AB  - course of a normal reaction containing the cofactors.  Under conditions which optimize this
AB  - methylation, 7 +/- 1 methyl groups can be transferred to DNA.  This methylation protects most
AB  - of the molecules from further cleavage.  he methyl groups were mapped relative to the
AB  - Hemophilus influenzae restriction endonuclease fragments.  The A fragment receives three to
AB  - four methyl groups and the B and G fragments each receive one to two methyl groups.  These
AB  - fragments correspond to those in which cleavage sites are located.
ER  -

TY  - JOUR
AU  - Ritchie, L.
AU  - Podger, D.M.
AU  - Hall, R.M.
TI  - A mutation in the DNA adenine methylase gene (dam) of Salmonella typhimurium decreases susceptibility to 9-aminoacridine-induced frameshift mutagenesis.
JO  - Mutat. Res.
PY  - 1988
SP  - 131
EP  - 141
VL  - 194
AB  - A mutant of Salmonella typhimurium with a reduced response to mutation
AB  - induction by 9-aminoacridine (9AA) has been isolated.  The mutation (dam-2) is
AB  - located in the DNA adenine methylase gene.  The dam-2 mutant strain exhibits a
AB  - level of sensitivity to 2-aminopurine (2AP) intermediate between that of the
AB  - dam+ and the DNA adenine methylation-deficit dam-1 strain, and 2AP sensitivity
AB  - was reversed by introduction of a mutH mutation or of the plasmid pMQ148 (which
AB  - carries a functional Escherichia coli dam+ gene).  However, the dam-2 strain is
AB  - not grossly defective in DNA adenine methylase activity.  Whole cell DNA
AB  - appears full methylated at -GATC- sites.  The levels of 9AA required to induce
AB  - equivalent levels of frameshift mutagenesis in the dam-2 strain were
AB  - approximately 2-fold higher than for the dam+ strain.  Introduction of pMQ148
AB  - dam+ reduced the level of 9AA required for induction of frameshift mutations
AB  - 4-fold in the dam-2 strain and 2-fold in the dam+ strain.  The dam-2 mutation
AB  - had no effect on the levels of ICR191 required for induction of frameshift
AB  - mutations, but introduction of pMQ148 reduced the ICR191-induced mutagenesis
AB  - 2-fold.  The dam+/pMQ148, dam-2/pMQ148 and dam-1/pMQ148 strains showed
AB  - identical dose-response curves for both 9AA and ICR191.  These results are
AB  - consistent with a slightly reduced (dam-2) or increased (pMQ148) rate of
AB  - methylation at the replication fork.  The 2AP sensitivity of the dam-2 strain
AB  - cannot be simply explained.  Furthermore, addition of methionine to the assay
AB  - medium reverses the 2AP sensitivity of the dam-2 strain, but has no effect on
AB  - 9AA mutagenesis.
ER  -

TY  - JOUR
AU  - Ritchie, L.J.
AU  - Hall, R.M.
AU  - Podger, D.M.
TI  - Mutant of Salmonella typhimurium LT2 deficient in DNA adenine methylation.
JO  - J. Bacteriol.
PY  - 1986
SP  - 420
EP  - 422
VL  - 167
AB  - A mutant of Salmonella typhimurium LT2 deficient in methylation of the adenine residues in the
AB  - sequence 5'-GATC-3' was isolated.  The mutation (dam-1) was linked to the cysG locus, and
AB  - the properties of the mutant were similar to those of Escherichia coli dam mutants.  Reversion
AB  - of the hisC3076 frameshift marker by 9-aminoacridine was substantially enhanced by the dam-1
AB  - mutation, implying a direct role for adenine methylation in the prevention of frameshift
AB  - mutation induction.
ER  -

TY  - JOUR
AU  - Ritchot, N.
AU  - Roy, P.H.
TI  - DNA methylation in Neisseria gonorrhoeae and other Neisseriae.
JO  - Gene
PY  - 1990
SP  - 103
EP  - 106
VL  - 86
AB  - It has been reported in the literature that Neisseria gonorrhoeae DNA is modified by the
AB  - methyltransferases (MTases) M.NgoI, M.NgoII, and M.NgoIII, as well as three other cytosine
AB  - MTases and one adenine MTase, even if the corresponding restriction endonucleases are not
AB  - present.  We envisioned the possibility of cloning one of the N. gonorrhoeae MTase-encoding
AB  - genes for use as a species-specific DNA probe.  We therefore undertook a survey of methylation
AB  - patterns of several clinical isolates of N. gonorrhoeae and N. meningitidis as well as ATCC
AB  - strains of other Neisseriae.  We found, from digestion patterns with isoschizomers, one N.
AB  - gonorrhoeae strain that lacked M.NgoII and two that lacked M.NgoIII.  All N. meningitidis
AB  - strains (save one) were resistant to digestion with NlaIV thus possessing an MTase like NgoV,
AB  - and one was resistant to SstII, thus having an NgoIII-like MTase.  None were resistant to
AB  - isoschizomers of NgoI, NgoIII and NgoIV.  Some other Neisseriae had an MTase with NlaIV (NgoV)
AB  - specificity, but none had NgoI, NgoIV, NgoII or NgoIII specificity, except for the
AB  - Branhamella-like N. caviae-ovis group and N. lactamica where these specificities were present
AB  - in at least one strain of this group.  Therefore, among the Neisseriae other than N. caviae
AB  - only M.NgoI is N. gonorrhoeae-specific.
AB  - [ The enzyme called NgoI in this abstract has been renamed NgoWI, Jan/1998. ]
AB  - [ The enzyme called NgoII in this abstract has been renamed NgoCII, Jan/1998. ]
AB  - [ The enzyme called NgoIII in this abstract has been renamed NgoKIII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Rival, A.
AU  - Jaligot, E.
AU  - Beule, T.
AU  - Finnegan, E.J.
TI  - Isolation and expression analysis of genes encoding MET, CMT, and DRM methyltransferases in oil palm (Elaeis guineensis Jacq.) in relation to the mantled somaclonal variation.
JO  - J. Exp. Bot.
PY  - 2008
SP  - 3271
EP  - 3281
VL  - 59
AB  - In oil palm (Elaeis guineensis Jacq.), 5% of somatic embryo-derived regenerants show homeotic
AB  - changes during floral development, involving
AB  - an apparent feminization of male parts in flowers of both sexes, called
AB  - the 'mantled' phenotype. This variant phenotype is associated with a
AB  - reduction in the level of global DNA methylation. To explore possible
AB  - relationships between DNA methylation level and accumulation of
AB  - DNA-(cytosine-5) methyltransferase (DNMT) transcripts, the full-length
AB  - coding sequences corresponding to three different DNMT families in oil
AB  - palm, namely the MET, CMT, and DRM classes, have been isolated and
AB  - characterized. The corresponding genes were designated as EgMET1,
AB  - EgCMT1, and EgDRM1, and encode predicted polypeptides of 1543, 925, and
AB  - 591 amino acid residues, respectively. Expression of oil palm DNMTs was
AB  - compared between normal and variant calli and in florescence tissues
AB  - using quantitative reverse-transcription PCR. A consistent increase in
AB  - transcript levels of EgMET1 and EgCMT1 was found in variant
AB  - fast-growing calli relative to nodular-compact calli. Nodular-compact
AB  - calli give rise to about 5% of abnormal regenerants whereas
AB  - fast-growing calli generate 95% of 'mantled' palms in their clonal
AB  - offspring and were previously demonstrated as having markedly
AB  - hypomethylated DNA. In immature abnormal in florescences only EgMET1
AB  - transcript levels were increased, while no changes in relative
AB  - abundance of the EgCMT1 or EgDRM1 transcripts were observed.
ER  -

TY  - JOUR
AU  - Rivera, D.
AU  - Revale, S.
AU  - Molina, R.
AU  - Gualpa, J.
AU  - Puente, M.
AU  - Maroniche, G.
AU  - Paris, G.
AU  - Baker, D.
AU  - Clavijo, B.
AU  - McLay, K.
AU  - Spaepen, S.
AU  - Perticari, A.
AU  - Vazquez, M.
AU  - Wisniewski-Dye, F.
AU  - Watkins, C.
AU  - Martinez-Abarca, F.
AU  - Vanderleyden, J.
AU  - Cassan, F.
TI  - Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense  Az39, Successfully Applied in Agriculture.
JO  - Genome Announcements
PY  - 2014
SP  - e00683
EP  - e00614
VL  - 2
AB  - We present the complete genome sequence of Azospirillum brasilense Az39, isolated from wheat
AB  - roots in the central region of Argentina and used as inoculant in
AB  - extensive and intensive agriculture during the last four decades. The genome
AB  - consists of 7.39 Mb, distributed in six replicons: one chromosome, three
AB  - chromids, and two plasmids.
ER  -

TY  - JOUR
AU  - Riveros-Mckay, F.
AU  - Campos, I.
AU  - Giles-Gomez, M.
AU  - Bolivar, F.
AU  - Escalante, A.
TI  - Draft Genome Sequence of Leuconostoc mesenteroides P45 Isolated from Pulque, a Traditional Mexican Alcoholic Fermented Beverage.
JO  - Genome Announcements
PY  - 2014
SP  - e01130
EP  - e01114
VL  - 2
AB  - Leuconostoc mesenteroides P45 was isolated from the traditional Mexican pulque beverage. We
AB  - report its draft genome sequence, assembled in 6 contigs consisting
AB  - of 1,874,188 bp and no plasmids. Genome annotation predicted a total of 1,800
AB  - genes, 1,687 coding sequences, 52 pseudogenes, 9 rRNAs, 51 tRNAs, 1 noncoding
AB  - RNA, and 44 frameshifted genes.
ER  -

TY  - JOUR
AU  - Rivers, A.R.
AU  - Smith, C.B.
AU  - Moran, M.A.
TI  - An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 11
EP  - 11
VL  - 9
AB  - When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented  the first
AB  - sequence from a heterotrophic marine bacterium. Over the last ten
AB  - years, the strain has become a valuable model for understanding the cycling of
AB  - sulfur and carbon in the ocean. To ensure that this genome remains useful, we
AB  - have updated 69 genes to incorporate functional annotations based on new
AB  - experimental data, and improved the identification of 120 protein-coding regions
AB  - based on proteomic and transcriptomic data. We review the progress made in
AB  - understanding the biology of R. pomeroyi DSS-3 and list the changes made to the
AB  - genome.
ER  -

TY  - JOUR
AU  - Roa, M.B.
AU  - Liles, V.R.
AU  - Torres, B.C.
AU  - Klinzing, D.C.
AU  - Lagamayo, E.
AU  - Navoa-Ng, J.
AU  - Daroy, M.L.G.
TI  - Draft Whole-Genome Assemblies of Drug-Resistant Clinical Isolates of Klebsiella pneumoniae from the Philippines.
JO  - Genome Announcements
PY  - 2017
SP  - e00475
EP  - e00417
VL  - 5
AB  - Here, we report the draft assemblies of 11 clinical isolates of Klebsiella pneumoniae that are
AB  - resistant to cephalosporins, carbapenems, and/or colistin.
AB  - The assemblies ranged from 5.37 Mbp to 5.70 Mbp in size. Several plasmid
AB  - sequences were present, and resistance genes spanning multiple classes of
AB  - antibiotics were predicted.
ER  -

TY  - JOUR
AU  - Robbins, J.B.
AU  - Smith, D.
AU  - Belfort, M.
TI  - Redox-Responsive Zinc Finger Fidelity Switch in Homing Endonuclease and  Intron Promiscuity in Oxidative Stress.
JO  - Curr. Biol.
PY  - 2011
SP  - 243
EP  - 248
VL  - 21
AB  - It is well understood how mobile introns home to allelic sites, but how
AB  - they are stimulated to transpose to ectopic locations on an
AB  - evolutionary timescale is unclear [1]. Here we show that a group I
AB  - intron can move to degenerate sites under oxidizing conditions. The
AB  - phage T4 td intron endonuclease, I-Tevl, is responsible for this
AB  - infidelity. We demonstrate that I-Tevl, which promotes mobility and is
AB  - subject to autorepression [2] and translational control [3], is also
AB  - regulated posttranslationally by a redox mechanism. Redox regulation is
AB  - exercised by a zinc finger (ZF) in a linker that connects the catalytic
AB  - domain of I-Tevl to the DNA binding domain. Four cysteines coordinate
AB  - Zn2+ in the ZF, which ensures that I-Tevl cleaves its DNA substrate at
AB  - a fixed distance, 23-25 nucleotides upstream of the intron insertion
AB  - site [4]. We show that the fidelity of I-Tevl cleavage is controlled by
AB  - redox-responsive Zn2+ cycling. When the ZF is mutated, or after
AB  - exposure of the wild-type I-Tevl to H2O2, intron homing to degenerate
AB  - sites is increased, likely because of indiscriminate DNA cleavage.
AB  - These results suggest a mechanism for rapid intron dispersal, joining
AB  - recent descriptions of the activation of biomolecular processes by
AB  - oxidative stress through cysteine chemistry [5, 6].
ER  -

TY  - JOUR
AU  - Robbins, J.B.
AU  - Stapleton, M.
AU  - Stanger, M.J.
AU  - Smith, D.
AU  - Dansereau, J.T.
AU  - Derbyshire, V.
AU  - Belfort, M.
TI  - Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 1589
EP  - 1600
VL  - 35
AB  - Homing endonucleases are unusual enzymes, capable of recognizing lengthy DNA sequences and
AB  - cleaving site-specifically within genomes. Many homing
AB  - endonucleases are encoded within group I introns, and such enzymes promote
AB  - the mobility reactions of these introns. Phage T4 has three group I
AB  - introns, within the td, nrdB and nrdD genes. The td and nrdD introns are
AB  - mobile, whereas the nrdB intron is not. Phage RB3 is a close relative of
AB  - T4 and has a lengthier nrdB intron. Here, we describe I-TevIII, the H-N-H
AB  - endonuclease encoded by the RB3 nrdB intron. In contrast to previous
AB  - reports, we demonstrate that this intron is mobile, and that this mobility
AB  - is dependent on I-TevIII, which generates 2-nt 3' extensions. The enzyme
AB  - has a distinct catalytic domain, which contains the H-N-H motif, and
AB  - DNA-binding domain, which contains two zinc fingers required for
AB  - interaction with the DNA substrate. Most importantly, I-TevIII, unlike the
AB  - H-N-H endonucleases described so far, makes a double-strand break on the
AB  - DNA homing site by acting as a dimer. Through deletion analysis, the
AB  - dimerization interface was mapped to the DNA-binding domain. The unusual
AB  - propensity of I-TevIII to dimerize to achieve cleavage of both DNA strands
AB  - underscores the versatility of the H-N-H enzyme family.
ER  -

TY  - JOUR
AU  - Robene, I.
AU  - Bolot, S.
AU  - Pruvost, O.
AU  - Arlat, M.
AU  - Noel, L.D.
AU  - Carrere, S.
AU  - Jacques, M.A.
AU  - Koebnik, R.
AU  - Gagnevin, L.
TI  - High-Quality Draft Genome Sequences of Two Xanthomonas Pathotype Strains Infecting Aroid Plants.
JO  - Genome Announcements
PY  - 2016
SP  - e00902
EP  - e00916
VL  - 4
AB  - We present here the draft genome sequences of bacterial pathogens of the Araceae  family,
AB  - Xanthomonas axonopodis pv. dieffenbachiae LMG 695 and Xanthomonas
AB  - campestris pv. syngonii LMG 9055, differing in host range. A comparison between
AB  - genome sequences will help understand the mechanisms involved in tissue
AB  - specificity and adaptation to host plants.
ER  -

TY  - JOUR
AU  - Roberts, C.H.
AU  - Shaw, H.A.
AU  - Ferguson, N.
AU  - Holland, M.
AU  - Wren, B.W.
AU  - Stabler, R.A.
TI  - Draft Genome Sequence of Robinsoniella peoriensis 6600698, a Confounder of Clostridium difficile Diagnosis.
JO  - Genome Announcements
PY  - 2016
SP  - e01275
EP  - e01216
VL  - 4
AB  - Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped
AB  - organism. Here, we report the draft genome of R. peoriensis 6600698,
AB  - initially classified as Clostridium difficile due to growth on selective agar, a
AB  - fecal gdh PCR-positive result, and clinical symptoms. R. peoriensis is a
AB  - potential confounder of C. difficile diagnosis.
ER  -

TY  - JOUR
AU  - Roberts, D.
AU  - Hoopes, B.C.
AU  - McClure, W.R.
AU  - Kleckner, N.
TI  - IS10 transposition is regulated by DNA adenine methylation.
JO  - Cell
PY  - 1985
SP  - 117
EP  - 130
VL  - 43
AB  - We show that dam- mutants are a major class of E. coli mutants with increased IS10 activity.
AB  - IS10 has two dam methylation sites, one within the transposase
AB  - promoter and one within the inner terminus where transposase presumably binds.
AB  - Absence of methylation results in increased activity of both promoter and
AB  - terminus, and completely accounts for increased transposition in dam- strains.
AB  - Transposition of Tn903 and Tn5 are also increased in dam- strains, probably for
AB  - analogous reasons. Transposition is also increased when IS10 is hemimethylated.
AB  - One hemimethylated species is much more active than the other and is estimated to
AB  - be at least 1000 times more active than a fully methylated element. Evidence is
AB  - presented that the promoter and inner terminus of IS10 are coordinately activated
AB  - in a dam-dependent fashion, presumably because they are hemimethylated at the
AB  - same time. Thus, in dam+ strains, IS10 will transpose preferentially when DNA is
AB  - hemimethylated. We suggest specifically that IS10 transposition may
AB  - preferentially occur immediately after passage of a chromosomal replication fork.
ER  -

TY  - JOUR
AU  - Roberts, G.A.
AU  - Chen, K.
AU  - Bower, E.K.M.
AU  - Madrzak, J.
AU  - Woods, A.
AU  - Barker, A.M.
AU  - Cooper, L.P.
AU  - White, J.H.
AU  - Blakely, G.W.
AU  - Manfield, I.
AU  - Dryden, D.T.F.
TI  - Mutations of the domain forming the dimeric interface of the ArdA protein affect dimerization and antimodification activity but not antirestriction activity.
JO  - FEBS J.
PY  - 2013
SP  - 4903
EP  - 4914
VL  - 280
AB  - ArdA antirestriction proteins are encoded by genes present in many conjugative plasmids and
AB  - transposons within bacterial genomes. Antirestriction is the ability to prevent cleavage of
AB  - foreign incoming DNA by restriction-modification (RM) systems. Antimodification, the ability
AB  - to inhibit modification by the RM system, can also be observed with some antirestriction
AB  - proteins. As these mobile genetic elements can transfer antibiotic resistance genes, the ArdA
AB  - proteins assist their spread. The consequenc of antirestriction is therefore the enhanced
AB  - dissemination of mobile genetic elements. ArdA proteins cause antirestriction by mimicking the
AB  - DNA structure bound by TypeI RM enzymes. The crystal structure of ArdA showed it to be a
AB  - dimeric protein with a highly elongated curved cylindrical shape [McMahon SA etal. (2009)
AB  - Nucleic Acids Res 37, 4887-4897]. Each monomer has three domains covered with negatively
AB  - charged side chains and a very small interface with the other monomer. We investigated the
AB  - role of the domain forming the dimer interface for ArdA activity via site-directed
AB  - mutagenesis. The antirestriction activity of ArdA was maintained when up to seven mutations
AB  - per monomer were made or the interface was disrupted such that the protein could only exist as
AB  - a monomer. The antimodification activity of ArdA was lost upon mutation of this domain. The
AB  - ability of the monomeric form of ArdA to function in antirestriction suggests, first, that it
AB  - can bind independently to the restriction subunit or the modificat ion subunits of the RM
AB  - enzyme, and second, that the many ArdA homologues with long amino acid extensions, present in
AB  - sequence databases, may be active in antirestriction.Structured digital abstract ArdA and ArdA
AB  - bind by molecular sieving (1, 2) ArdA and ArdA bind by cosedimentation in solution (1, 2)
ER  -

TY  - JOUR
AU  - Roberts, G.A.
AU  - Chen, K.
AU  - Cooper, L.P.
AU  - White, J.H.
AU  - Blakely, G.W.
AU  - Dryden, D.T.
TI  - Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA  restriction and modification system produces a new type of system and links the  different families of Type I systems.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 10916
EP  - 10924
VL  - 40
AB  - The EcoKI DNA methyltransferase is a trimeric protein comprised of two modification subunits
AB  - (M) and one sequence specificity subunit (S). This enzyme
AB  - forms the core of the EcoKI restriction/modification (RM) enzyme. The 3' end of
AB  - the gene encoding the M subunit overlaps by 1 nt the start of the gene for the S
AB  - subunit. Translation from the two different open reading frames is
AB  - translationally coupled. Mutagenesis to remove the frameshift and fuse the two
AB  - subunits together produces a functional RM enzyme in vivo with the same
AB  - properties as the natural EcoKI system. The fusion protein can be purified and
AB  - forms an active restriction enzyme upon addition of restriction subunits and of
AB  - additional M subunit. The Type I RM systems are grouped into families, IA to IE,
AB  - defined by complementation, hybridization and sequence similarity. The fusion
AB  - protein forms an evolutionary intermediate form lying between the Type IA family
AB  - of RM enzymes and the Type IB family of RM enzymes which have the frameshift
AB  - located at a different part of the gene sequence.
ER  -

TY  - JOUR
AU  - Roberts, G.A.
AU  - Cooper, L.P.
AU  - White, J.H.
AU  - Su, T.J.
AU  - Zipprich, J.T.
AU  - Geary, P.
AU  - Kennedy, C.
AU  - Dryden, D.T.
TI  - An investigation of the structural requirements for ATP hydrolysis and DNA cleavage by the EcoKI Type I DNA restriction and modification enzyme.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 7667
EP  - 7676
VL  - 39
AB  - Type I DNA restriction/modification systems are oligomeric enzymes capable of switching
AB  - between a methyltransferase function on hemimethylated host
AB  - DNA and an endonuclease function on unmethylated foreign DNA. They have
AB  - long been believed to not turnover as endonucleases with the enzyme
AB  - becoming inactive after cleavage. Cleavage is preceded and followed by
AB  - extensive ATP hydrolysis and DNA translocation. A role for dissociation of
AB  - subunits to allow their reuse has been proposed for the EcoR124I enzyme.
AB  - The EcoKI enzyme is a stable assembly in the absence of DNA, so recycling
AB  - was thought impossible. Here, we demonstrate that EcoKI becomes unstable
AB  - on long unmethylated DNA; reuse of the methyltransferase subunits is
AB  - possible so that restriction proceeds until the restriction subunits have
AB  - been depleted. We observed that RecBCD exonuclease halts restriction and
AB  - does not assist recycling. We examined the DNA structure required to
AB  - initiate ATP hydrolysis by EcoKI and find that a 21-bp duplex with
AB  - single-stranded extensions of 12 bases on either side of the target
AB  - sequence is sufficient to support hydrolysis. Lastly, we discuss whether
AB  - turnover is an evolutionary requirement for restriction, show that the ATP
AB  - hydrolysis is not deleterious to the host cell and discuss how foreign DNA
AB  - occasionally becomes fully methylated by these systems.
ER  -

TY  - JOUR
AU  - Roberts, G.A.
AU  - Houston, P.J.
AU  - White, J.H.
AU  - Chen, K.
AU  - Stephanou, A.S.
AU  - Cooper, L.P.
AU  - Dryden, D.T.
AU  - Lindsay, J.A.
TI  - Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 7472
EP  - 7484
VL  - 41
AB  - A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible
AB  - for MRSA infections worldwide, and those of different lineages carry
AB  - unique Type I restriction-modification (RM) variants. We have identified the
AB  - specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and
AB  - ST239. We experimentally demonstrate that this RM system is sufficient to block
AB  - horizontal gene transfer between clinically important MRSA, confirming the
AB  - bioinformatic evidence that each lineage is evolving independently. Target sites
AB  - are distributed randomly in S. aureus genomes, except in a set of large
AB  - conjugative plasmids encoding resistance genes that show evidence of spreading
AB  - between two successful MRSA lineages. This analysis of the identification and
AB  - distribution of target sites explains evolutionary patterns in a pathogenic
AB  - bacterium. We show that a lack of specific target sites enables plasmids to evade
AB  - the Type I RM system thereby contributing to the evolution of increasingly
AB  - resistant community and hospital MRSA.
ER  -

TY  - JOUR
AU  - Roberts, G.A.
AU  - Stephanou, A.S.
AU  - Kanwar, N.
AU  - Dawson, A.
AU  - Cooper, L.P.
AU  - Chen, K.
AU  - Nutley, M.
AU  - Cooper, A.
AU  - Blakely, G.W.
AU  - Dryden, D.T.
TI  - Exploring the DNA mimicry of the Ocr protein of phage T7.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 8129
EP  - 8143
VL  - 40
AB  - DNA mimic proteins have evolved to control DNA-binding proteins by competing with the target
AB  - DNA for binding to the protein. The Ocr protein of bacteriophage T7 is
AB  - the most studied DNA mimic and functions to block the DNA-binding groove of Type
AB  - I DNA restriction/modification enzymes. This binding prevents the enzyme from
AB  - cleaving invading phage DNA. Each 116 amino acid monomer of the Ocr dimer has an
AB  - unusual amino acid composition with 34 negatively charged side chains but only 6
AB  - positively charged side chains. Extensive mutagenesis of the charges of Ocr
AB  - revealed a regression of Ocr activity from wild-type activity to partial activity
AB  - then to variants inactive in antirestriction but deleterious for cell viability
AB  - and lastly to totally inactive variants with no deleterious effect on cell
AB  - viability. Throughout the mutagenesis the Ocr mutant proteins retained their
AB  - folding. Our results show that the extreme bias in charged amino acids is not
AB  - necessary for antirestriction activity but that less charged variants can affect
AB  - cell viability by leading to restriction proficient but modification deficient
AB  - cell phenotypes.
ER  -

TY  - JOUR
AU  - Roberts, M.D.
AU  - Martin, N.L.
AU  - Kropinski, A.M.
TI  - The genome and proteome of coliphage T1.
JO  - Virology
PY  - 2004
SP  - 245
EP  - 266
VL  - 318
AB  - The genome of enterobacterial phage T1 has been sequenced, revealing that
AB  - its 50.7-kb terminally redundant, circularly permuted sequence contains
AB  - 48,836 bp of nonredundant nucleotides. Seventy-seven open reading frames
AB  - (ORFs) were identified, with a high percentage of small genes located at
AB  - the termini of the genomes displaying no homology to existing phage or
AB  - prophage proteins. Of the genes showing homologs (47%), we identified
AB  - those involved in host DNA degradation (three endonucleases) and T1
AB  - replication (DNA helicase, primase, and single-stranded DNA-binding
AB  - proteins) and recombination (RecE and Erf homologs). While the tail genes
AB  - showed homology to those from temperate coliphage N15, the capsid
AB  - biosynthetic genes were unique. Phage proteins were resolved by 2D gel
AB  - electrophoresis, and mass spectrometry was used to identify several of the
AB  - spots including the major head, portal, and tail proteins, thus verifying
AB  - the annotation.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Life Illuminated
PY  - 2008
SP  - 215
EP  - 216
VL  - 0
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes.
JO  - Molecular Genetic Analysis of Populations: A Practical Approach
PY  - 1998
SP  - 379
EP  - 397
AB  - A summary of the properties of the commercially available Type II restriction enzymes,
AB  - including digestion conditions. The information in this list is taken from Roberts, R.J. and
AB  - Macelis, D. (1996) 24, 223-235 plus updates from REBASE, the restriction enzyme database (URL
AB  - - http://www.neb.com/rebase).
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes.
JO  - Nucleic Acid Hybridisation: A Practical Approach
PY  - 1985
SP  - 203
EP  - 210
VL  - 0
AB  - Restriction enzymes are endodeoxyribonucleases that recognise short, specific
AB  - sequences within DNA molecules and then catalyse double-strand cleavage of the
AB  - DNA.  Three distinct classes of restriction enzymes are known:  Type I, Type
AB  - II, Type III.  In this Appendix, restriction enzymes and their isoschizomers
AB  - are listed alphabetically by prototype.  Their availability from three major
AB  - commercial sources is indicated, as are the buffer conditions recommended by
AB  - the manufacturer.  It should be noted that for most restriction enzymes, their
AB  - activity varies little over a wide range of ionic strength and pH, and the
AB  - values listed in general have not rigorously been shown to be optimal.  The
AB  - information in this list is taken from Roberts, R.J. Nucleic Acids Res. (1984)
AB  - 12, r167-r204, and the New England Biolabs catalogue (1984 edition).
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes.
JO  - Molecular Genetic Analysis of Populations: A Practical Approach
PY  - 1992
SP  - 281
EP  - 296
VL  - 0
AB  - Restriction enzymes are endodeoxyribonucleases that recognize short, specific
AB  - sequences within DNA molecules and then catalyse double-strand cleavage of the
AB  - DNA.  Three distinct classes of restriction enzymes are known: (a) Type I
AB  - enzymes (b) Type II enzymes (c) Type III enzymes.  In this Appendix restriction
AB  - enzymes and their isoschizomers are listed alphabetically by prototype.  Their
AB  - availability from three major commercial sources is indicated, as are the
AB  - buffer conditions recommended by the manufacturer.  It should be noted that for
AB  - most restriction enzymes, their activity varies little over a wide range of
AB  - ionic strength and pH, and the values listed in general have not rigorously
AB  - been shown to be optimal.  The information in this list is taken from Roberts,
AB  - R.J., Nucleic Acids Res. (1984), 12, r167=t204, and the New England Biolabs
AB  - catalogue (1991 edition).
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction endonucleases.
JO  - Microbiology-1982
PY  - 1978
SP  - 5
EP  - 9
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction endonucleases, DNA sequencing and computers.
JO  - In Physics and Contemporary Needs
PY  - 1984
SP  - 305
EP  - 316
VL  - 6
AB  - Among the 250 TypeII restriction endonucleases now characterized, there are
AB  - more than 70 different specificities and yet there is no indication that the
AB  - range of specificities is exhausted.  Indeed, there is good reason to believe
AB  - that hundreds, if not thousands, of different specificities would be found if a
AB  - diligent search were carried out.  One reason for this speculation is
AB  - illustrated in Table 1, which shows the range of sequence patterns with which
AB  - different Type II restriction endonucleases interact.  Among the simple
AB  - symmetric hexanucleotide sequences designated here as Class A, almost half of
AB  - the possible sequence patterns are already represented by well-characterized
AB  - enzymes.  There is no reason to believe that a similar number of enzymes will
AB  - not be found for the other patterns in Classes B through F.  Similarly, it
AB  - seems likely that enzymes recognizing degenerate patterns, like HgiAI and AccI,
AB  - are not the sole representatives of the class.  Within the last year alone,
AB  - five new classes (C,D,F,N., and O) were added to this list.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction endonucleases.
JO  - Nucleases
PY  - 1982
SP  - 311
EP  - 340
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - The role of restriction endonucleases in genetic engineering.
JO  - In: Recombinant Molecules: Impact on Science Society
PY  - 1977
SP  - 21
EP  - 32
VL  - 0
AB  - The class II restriction endonucleases have played a key role in the
AB  - development of recombinant DNA technology although, of the many enzymes now
AB  - available, only EcoRI and HindIII have been used extensively.  This chapter
AB  - describes some of the newly discovered restriction endonucleases which seem to
AB  - provide alternative possibilities for genetic engineering and suggests schemes
AB  - whereby the specificity of the nucleases can be exploited in the creation of
AB  - new recombinant genomes.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - In Handbook of Biochemistry and Molecular Biology
PY  - 1976
SP  - 532
EP  - 534
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - DNA Insertion Elements, Plasmids, and Episomes.
PY  - 1977
SP  - 757
EP  - 768
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - How restriction enzymes became the workhorses of molecular biology.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 5905
EP  - 5908
VL  - 102
AB  - Restriction enzymes have proved to be invaluable for the physical mapping of DNA. They offer
AB  - unparalleled opportunities for diagnosing DNA sequence content and are used in fields as
AB  - disparate as criminal forensics and basic research. In fact, without restriction enzymes, the
AB  - biotechnology industry would certainly not have flourished as it has. The first experiments
AB  - demonstrating the utility of restriction enzymes were carried out by Danna and Nathans and
AB  - reported in 1971. This pioneering study set the stage for the modern practice of molecular
AB  - biology in which restriction enzymes are ubiquitous tools, although they are often taken for
AB  - granted.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - An amazing distortion in DNA induced by a methyltransferase.
JO  - Biosci. Rep.
PY  - 1994
SP  - 103
EP  - 117
VL  - 14
AB  - republication of the Nobel lecture
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - An amazing distortion in DNA induced by a methyltransferase (Nobel lecture).
JO  - Angew. Chem. Int. Ed. Engl.
PY  - 1994
SP  - 1222
EP  - 1228
VL  - 33
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Analysis of Restriction Modification systems from whole genome sequences.
JO  - Abstracts AAAS Ann. Mtg.
PY  - 2000
SP  - A37
EP  - A37
VL  - 166
AB  - Until recently all of the 3200 restriction enzymes known to man had been found by obtaining
AB  - bacteria from culture collections or environ-mental samples and assaying them biochemically
AB  - and genetically.  During the last 15 years, many of these Restriction-Modification (RM)
AB  - systems have been cloned and sequenced and it is now possible to use quite so-phisticated
AB  - search algorithms to screen new DNA sequences for the presence of DNA methyltransferase genes.
AB  - Experience among known systems has shown that restriction enzyme genes always lie close to
AB  - their cognate methyltransferase genes.  Analysis of the bacterial and archaeal genome
AB  - sequences shows that methyltransferase genes are more common than one would have expected on
AB  - the basis of previous biochemical screening.  Frequently, they clearly form part of an RM
AB  - system, because the adjacent open reading frames show similarity to known restriction enzyme
AB  - genes.  Very often, though, the adjacent open reading frames have no homologs in GenBank and
AB  - become candidates either for restriction enzymes with novel specificities or for new examples
AB  - of previously uncloned specificities. We are developing methods to allow these candidate genes
AB  - quickly to be tested biochemically. Initial results are promising and it seems clear that
AB  - screening DNA sequence databases and websites will be a very productive method to find
AB  - restriction enzymes with new specificities.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Directory of restriction endonucleases.
JO  - Methods Enzymol.
PY  - 1980
SP  - 1
EP  - 15
VL  - 65
AB  - This article is intended to serve as a directory to the restriction endonucleases which have
AB  - not been characterized.  All endonucleases which cleave DNA at a specific sequence have been
AB  - considered to be restriction enzymes, although in most cases there is no direct genetic
AB  - evidence for the presence of a host-controlled restriction-modification system.  Certain
AB  - strains are omitted from the table to save space.  Thus the many different Staphylococcus
AB  - aureus isolates which contain an isoschizomer of Sau3A are not listed individually.  Similarly
AB  - the many strains of gliding bacteria (orders: Myxobacterales and Cytophagales) which showed
AB  - evidence of specific endonucleases during a large-scale screening are still rather poorly
AB  - characterized.  Within the table the source of each microorganism is given either as an
AB  - individual or a National Culture Collection.  The enzymes are named in accordance with the
AB  - proposal of Smith and Nathans.  When two enzymes recognize the same sequence (i.e., are
AB  - isoschizomers), the prototype (i.e., the first example isolated) is indicated in parentheses
AB  - in column 3 of the table.  The recognition sequences (column 4 of the table) are abbreviated
AB  - so that only one strand, reading 5'-3', is indicated and the point of cleavage, when known,
AB  - is indicated by an arrow.  When two bases appear in parentheses, either one may appear at that
AB  - position within the recognition sequence.  Where known, the base modified by the corresponding
AB  - methylase is indicated by an asterisk.  A* is N6-methyladenosine; C* is 5-methylcytosine.  The
AB  - frequency of cleavage (columns five to eight) is experimentally determined for bacteriophage
AB  - lambda and adenovirus-2 DNAs, but represents the computer-derived values from the published
AB  - sequences of SV40 and PhiX174 DNAs.  When more than one reference appears (column 9 of the
AB  - table), the first contains the purification procedure for the restriction enzyme, the second
AB  - concerns its recognition sequence, the third contains the purification procedure for the
AB  - methylase, and the fourth describes its recognition sequence.  In some cases two references
AB  - appear in one of these categories when two independent groups have reached similar
AB  - conclusions.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Directory of restriction endonucleases.
JO  - Methods Enzymol.
PY  - 1979
SP  - 27
EP  - 41
VL  - 68
AB  - Table I is intended to serve as a directory to the restriction endonucleases
AB  - that have now been characterized.  In forming the list, all endonucleases that
AB  - cleave DNA at a specific sequence have been considered restriction enzymes,
AB  - although in most cases there is no direct genetic evidence for the presence of
AB  - a host-controlled restriction-modification system.  Certain strains have been
AB  - omitted from this list to save space.  Thus the many different Staphylococcus
AB  - aureus isolates containing an isoschizomer of Sau3A are not listed
AB  - individually.  Similarly the numerous strains of gliding bacteria (orders
AB  - Myxobacterales and Cytophagales) that showed evidence of specific endonucleases
AB  - during a large-scale screening are still rather poorly characterized.  Within
AB  - Table I the source of each microorganism is given either as an individual or a
AB  - national culture collection.  The enzymes are named in accordance with the
AB  - proposal of Smith and Nathans.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction endonucleases:  a new role in vivo?
JO  - Nature
PY  - 1978
SP  - 502
EP  - 502
VL  - 271
AB  - Few enzymes have been exploited as thoroughly as the bacterial restriction
AB  - enzymes.  In recent years they have been instrumental in dramatic advances in
AB  - DNA sequence analysis, genetic engineering, and studies of gene structure.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - The Nobel Prizewinners 1978: Medicine.
JO  - Nature
PY  - 1978
SP  - 689
EP  - 690
VL  - 275
AB  - The restriction endonucleases, which have become so familiar to the molecular
AB  - biologist, have finally come of age with the award of this year's Nobel Prize
AB  - in Physiology and Medicine to Dr. Werner Arber of the University of Basel and
AB  - to Drs. Daniel Nathans and Hamilton O. Smith of Johns Hopkins University.  They
AB  - each played a critical but separate role in drawing attention to these
AB  - bacterial enzymes which dominate so much present research.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - r117
EP  - r144
VL  - 10
AB  - Since the last compilation of restriction endonucleases, 97 new entries have been added,
AB  - including 17 new specificities. Most notable among the new specificities is AhaIII (TTTAAA),
AB  - which is the first restriction enzyme to recognize only A/T base pairs. Other valuable new
AB  - specificities are ApaI (GGGCCC), AflII (CTTAAG), CfrI (PYGGCCPu), EcoRV (GATATC), FokI
AB  - (GGATG), HgiJII (GPuGCPyC), MluI (ACGCGT), NdeI (CATATG), NaeI (GCCGGC), NarI (GGCGCC), NcoI
AB  - (CCATGG), NruI (TCGCGA), NspBII (GCC/GGC), NspCI (PuCATGPy), ScrFI (CCNGG) and XmnI
AB  - (GAA[N]4TTC). Two entries have been removed, RruI and RruII, because the strain producing them
AB  - has been lost. Fortunately an isoschizomer of RruI has been found. This is ScaI (AGTACT).
AB  - Among the 355 enzymes listed, there are a minimum of 85 different specificities.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Hans Krebs Lecture Bacterial methylomes.
JO  - FEBS J.
PY  - 2013
SP  - 0
EP  - 0
VL  - 280
AB  - Bacterial DNA methyltransferases are best known as orphan enzymes such as the Dam methylase of
AB  - E. coli or as components of restriction-modification systems.  Until recently, rigorously
AB  - determining the specificity of MTases has been a tedious process.  When they were components
AB  - of Type II restriction systems it has been assumed that the MTases would have the same
AB  - specificity as the cognate restriction enzyme.  For Type I and Type III RM systems specificity
AB  - determination was rarely attempted.  With the advent of SMRT sequencing from Pacific
AB  - Biosciences this situation has changed dramatically.  Now it has become very simple to
AB  - determine MTase recognition sequences both for individual MTases cloned in plasmids and also
AB  - for whole bacterial genomes.  This offers new insights into the functioning of bacteria and
AB  - has led to the discovery of several novel MTases with unexpected properties.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - r63
EP  - r80
VL  - 8
AB  - Since the last compilation of restriction endonucleases, more than 30 Type II
AB  - restriction endonucleases have been discovered, including some valuable new
AB  - specificities.  These include AcyI (GPuCGPyC), DdeI (CTNAG), Fnu4HI (GCNGC),
AB  - RsaI (GTAC), SphI (GCAGTC), and XmaIII (CGGCCG).  In addition, a number of new
AB  - isoschizomers have been discovered and further information about the
AB  - recognition sequences of some old entries is now available.  AvaX is renamed
AB  - AvaIII.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes and their isoschizomers.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 2331
EP  - 2365
VL  - 18
AB  - A review
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - r167
EP  - r204
VL  - 12
AB  - Since the last compilation of restriction endonucleases, 80 new entries have
AB  - been added, including 12 new specificities.  These are Cfr101 (PuCCGGPy),
AB  - Eco47III (AGCGCT), EcoA (GAG(N)7GTCA), MaeI (CTAG), MaeII (ACGT), MaeIII
AB  - (GTNAC), NlaIII (CATG), NlaIV (GGNNCC), NotI (GCGGCCGC), SnaBI (TACGTA), ScaI
AB  - (AGTACT) and SfiI (GGCCNNNNNGGCC).  NotI and SfiI are the first example of Type
AB  - II enzymes that recognize octanucleotide sequences.  In addition to these two
AB  - new sequence patterns, one additional new sequence pattern is recognized by
AB  - NlaIV.  The first example of unusual methylation is provided in the BcnI system
AB  - where the methylase protects by the formation of N4-methylcytosine.  Among the
AB  - 475 enzymes listed, there are a minimum of 103 different specificities.  New
AB  - entries, together with new information about recognition sequences, are
AB  - indicated (@).  In forming this list, all endonucleases cleaving DNA at a
AB  - specific sequence have been considered to be restriction enzymes, although in
AB  - most cases there is no direct genetic evidence for the presence of a
AB  - restriction-modification system.  These endonucleases are named in accordance
AB  - with the proposal of Smith and Nathans.  Within the table, the source of each
AB  - microorganism is given either as an individual or a National Culture
AB  - Collection.  If further information is required, it can be found either in the
AB  - first reference which, in each case, refer to the purification procedure for
AB  - the restriction enzyme, or from the individuals who have provided their
AB  - unpublished results.  Where more than one reference appears, the second
AB  - concerns the recognition sequence for the restriction enzyme, the third
AB  - describes the purification procedure for the methylase and the fourth describes
AB  - the recognition sequence of the methylase.  In some cases, several references
AB  - appear in one of these categories when independent groups have reached similar
AB  - conclusions.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction endonucleases, DNA sequencing, and computers.
JO  - Developmental Biology Using Purified Genes
PY  - 1981
SP  - 621
EP  - 634
VL  - 0
AB  - Among the 250 Type II restriction endonucleases now characterized, there are
AB  - more than 70 different specificities and yet there is no indication that the
AB  - range of specificities is exhausted.  Indeed, there is good reason to believe
AB  - that hundreds, if not thousands, of different specificities would be found if a
AB  - diligent search were carried out.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Gene
PY  - 1980
SP  - 329
EP  - 343
VL  - 8
AB  - Since the last compilation of restriction endonucleases, more than 30 type II
AB  - restriction endonucleases have been discovered, including some with valuable
AB  - new specificities.  These include AcyI (GPuCGPyC), AsuII (TTCGAA), DdeI
AB  - (CTNAG), Fnu4HI (GCNGC), RsaI (GTAC), SphI (GCATGC) and XmaIII (CGGCCG).  In
AB  - addition, a number of new isoschizomers have been discovered and further
AB  - information about the recognition sequences of some old entries is now
AB  - available.  AvaX is renamed AvaIII.  In forming this list, all endonucleases
AB  - cleaving DNA at a specific sequence have been considered to be restriction
AB  - enzymes although, in most cases, there is no direct genetic evidence for the
AB  - presence of a restriction modification system.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1981
SP  - r75
EP  - r96
VL  - 9
AB  - Since the last compilation of Type II restriction endonucleases, more than 45 new enzymes have
AB  - been discovered. Among the valuable new specificities are GdiI and its isoschizomer StuI
AB  - (AGGCCT), GdiII (PyGGCCG), HgiEII (ACC[N]6GGT), RruI (AGTACT), Tth111I and its isoschizomers
AB  - TtrI and TteI (GACNNNGTC), and Tth111II (CAAPuCA). The new enzyme NciI (CC[G/C]GG) turns out
AB  - to be an isoschizomer of CauII whose recognition has recently been determined. The recognition
AB  - sequences of SnaI (GTATAC) and SauI (CDTNAGG) have also been newly determined. Among the 258
AB  - enzymes listed, there are at least 69 different specificities. New entries, together with new
AB  - information about recognition sequences, are indicated. .
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Gene
PY  - 1978
SP  - 183
EP  - 193
VL  - 4
AB  - During the last few years many bacterial strains have been examined for the
AB  - presence of Type II restriction endonucleases and a large number of these
AB  - enzymes have now been characterized.  Much of the information available has
AB  - never been formally published.  While this reflects the lengthy time which can
AB  - elapse between discovery and publication, increasingly it results from the fact
AB  - that a newly discovered endonuclease is an isoschizomer of a more familiar one.
AB  - Thtus, unless the new source offers some advantage, there is a natural trend
AB  - to avoid formal publication.  To some extent, review articles fill this gap;
AB  - however, they quickly become outdated.  The present compilation is an attempt
AB  - to extend current awareness of the enzymes now available.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes and their isoschizomers.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - r189
EP  - r217
VL  - 15
AB  - Since the last compilation of restriction enzymes, 251 new entries have been
AB  - added including 21 new specificities.  With the growing size of this database
AB  - and the recognition that the most widespread use of the information is as a
AB  - database for computer programs predicting restriction enzyme cleavage patterns,
AB  - a new format has been adopted.  This new format is intended to contain the
AB  - minimal amount of information required by a computer program.  It should be
AB  - noted that only enzymes for which the recognition sequence is known are
AB  - included.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequence.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 1
EP  - 49
VL  - 5
AB  - Since the last published compilation of restriction endonucleases 130 new
AB  - enzymes have been discovered, including many new specificities.  Especially
AB  - noteworthy are the enzymes NotI (GCGGGCCGC) and SfiI (GGCCNNNNNGGCC) which are
AB  - the first Type II enzymes to recognize octanucleotide sequences.  They have the
AB  - useful property of cutting DNA sufficiently infrequently so that their sites
AB  - provide useful landmarks for mapping bacterial genomes and eukaryotic
AB  - chromosomes.  Among the 645 enzymes listed there are now a minimum of 137
AB  - different specificities.  In forming this list all endonucleases cleaving DNA
AB  - at a specific sequence have been considered to be restriction enzymes, although
AB  - in most cases there is no direct genetic evidence for the presenece of a
AB  - restriction-modification system.  These endonucleases are named in accordance
AB  - with the proposal of Smith and Nathans.  Within the table the source of each
AB  - microorganism is given either as an individual or a national culture
AB  - collection.  If further information is required it can be found either in the
AB  - first reference which in each case refers to the purification procedure for the
AB  - restriction enzyme, or from the individuals who have provided their unpublished
AB  - results.  Where more than one reference appears, the second concerns the
AB  - recognition sequence for the restriction enzyme, the third describes the
AB  - purification procedure for the methylase and the fourth describes the
AB  - recognition sequence of the methylase.  In some cases, several references
AB  - appear in one of these categories when independent groups have reached similar
AB  - conclusions.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes and their isoschizomers.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - r347
EP  - r387
VL  - 17
AB  - Since the last compilation of restriction enzymes (1), 156 new entries have
AB  - been added including 12 new specificities.  With the growing size of this
AB  - database and the recognition that the most widespread use of the information is
AB  - as a database for computer programs predicting restriction enzyme cleavage
AB  - patterns, the new format has been continued.  This format is intended to
AB  - contain the minimal amount of information required by a computer program.  It
AB  - should be noted that only enzymes for which the recognition sequence is known
AB  - are included.  This new list is shown in the first Table, while an alphabetical
AB  - listing of all Type II enzymes is presented in the second Table.  A copy of the
AB  - restriction enzyme data base in its previous format (2), including enzymes of
AB  - unknown recognition sequence, will be available upon request.  It should also
AB  - be noted that an alternative compilation of these enzymes has recently been
AB  - produced (3).
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - r135
EP  - r167
VL  - 11
AB  - Since the last compilation of restriction endonucleases, 43 new entries have
AB  - been added, including 6 new specificities.  These are AatII (GACGTC), AflIII
AB  - (ACPuPyGT), BinI (GGATC), EcopDXI (ATCA(N)^ATTC), NspBII (C(A/C)GC(T/G)G and
AB  - SduI (G(G/A/T)GC(C/A/T)C).  EcopDXI is the first example of a Type I enzyme
AB  - that recognizes an octanucleotide sequence.  Both NspBII and SduI recognize
AB  - sequence patterns that have not been described before.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction and modification enzymes and their recognition sequences.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - r165
EP  - r200
VL  - 13
AB  - Since the last compilation of restriction endonucleases forty-nine new entries
AB  - have been added, including nine new specificities, these are DraII (PuGGNCCPy),
AB  - DraIII (CACNNNGTG), EcoD (TTA(N)7GTCPy), EspI (GCTNAGC), NheI (GCTAGC), RsrII
AB  - (CGG(A/T)CCG), StyI (CC(A/T)(A/T)GG), SspI (AATATT) and SpeI (ACTAGT).  In
AB  - addition, the enzyme Asp718 is an interesting isoschizomer of KpnI.  It cleaves
AB  - the recognition sequence to leave a 5' terminal extension instead of the 3'
AB  - terminal extension left by KpnI.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction enzymes and their isoschizomers.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - r271
EP  - r313
VL  - 16
AB  - Since the last compilation of restriction enzymes, 156 new entries have been
AB  - added including 12 new specificities.  With the growing size of this database
AB  - and the recognition that the most widespread use of the information is as a
AB  - database for computer programs predicting restriction enzyme cleavage patterns,
AB  - the new format has been continued.  This format is intended to contain the
AB  - minimal amount of information required by a computer program.  It should be
AB  - noted that only enzymes for which the recognition sequence is known are
AB  - included.  This new list is shown in the first Table, while an alphabetical
AB  - listing of all Type II enzymes is presented in the second Table.  A copy of the
AB  - restriction enzyme data base in its previous format, including enzymes of
AB  - unknown recognition sequence, will be available upon request.  It should also
AB  - be noted that an alternative compilation of these enzymes has recently been
AB  - produced.  The database shown in these Tables is available online through the
AB  - BIONET computer resource.  A version corresponding to the printed text is
AB  - located in the file <ROBERTS>RESTRICT.NAR several alternative versions are
AB  - available and are documented in <ROBERTS>RESTRICT.DOC  In forming this list,
AB  - all endonucleases cleaving DNA at a specific sequence have been considered to
AB  - be restriction enzymes, although in most cases there is no direct genetic
AB  - evidence for the presence of a restriction-modification system.  The
AB  - endonucleases are named in accordance with the proposal of Smith and Nathans.
AB  - Several enzymes appear in this list with revised names.  These revisions were
AB  - made to avoid confusion with existing enzymes or to increase the uniformity of
AB  - the names.  In each case the name changes were made with the approval of the
AB  - appropriate authors.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
TI  - Restriction endonucleases.
JO  - CRC Crit. Rev. Biochem.
PY  - 1976
SP  - 123
EP  - 164
VL  - 4
AB  - This review provides a comprehensive account of the current status of the biology and
AB  - biochemistry of restriction endonucleases. Both Class I and Class II restriction endonucleases
AB  - will be considered. However, emphasis will be placed on the Class II group, which recognizes
AB  - and cleaves a specific duplex DNA sequence. Their occurrence, purification, and
AB  - characterization is discussed in detail. The characterization includes physical mapping
AB  - information and determination of recognition sequences. In addition to detailed discussions of
AB  - the biochemical properties of the enzymes, considerable attention is paid to the uses of these
AB  - enzymes as tools for research in molecular biology. These uses include physical mapping of
AB  - genomes and their transcripts, genetic analysis (marker rescue, etc.), DNA sequence analysis,
AB  - analysis of complex genomes, and genetic engineering. Specific examples of each use are
AB  - outlined. Practical aspects of both the isolation and use of the restriction endonucleases
AB  - form the major theme of this review.
ER  -

TY  - JOUR
AU  - Roberts, R.J. et al.
TI  - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 1
EP  - 18
VL  - 14
AB  - There are three main groups of restriction endonucleases (REases) called Types I, II, and III.
AB  - Since 1973, REases and DNA methyltransferases (MTases) have been named based on an original
AB  - suggestion by Smith and Nathans.  They proposed that the enzyme names should begin with a
AB  - three-letter acronym in which the first letter was the first letter of the genus from which
AB  - the enzyme was isolated and the next two letters were the first two letters of the species
AB  - name.  Extra letters or numbers could be added to indicate individual strains or serotypes.
AB  - Thus, the enzyme HindII was one of four enzymes isolated from Haemophilus influenzae serotype
AB  - d.  The first three letters of the name were italicized.  Later, a formal proposition for
AB  - naming the genes encoding REases and MTases was adopted.  When there were only a handful of
AB  - enzymes known, these schemes were very useful, but as more enzymes have been found, often from
AB  - different genera and species with names whose three-letter acronyms would be identical,
AB  - considerable laxity in naming conventions has appeared.  In addition, we now know that each
AB  - major type of enzyme can contain subtypes.  This especially applies to the Type II enzymes, of
AB  - which more than 3500 have been characterized.  In this paper we revisit the naming conventions
AB  - and outline an updated scheme that incorporates current knowledge about the complexities of
AB  - these enzymes.  We describe a set of naming conventions for REases and their associated
AB  - MTases.  Since the homing endonucleases have been named in an analogous fashion, we proposed
AB  - that similar guidelines be applied to that group of enzymes.  Finally, it is important to
AB  - realize that the aim of this document is to provide a nomenclature for these enzymes, not to
AB  - provide a rigorous classification.
ER  -

TY  - JOUR
AU  - Roberts, R.J. et al.
TI  - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 1805
EP  - 1812
VL  - 31
AB  - A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing
AB  - endonucleases and related genes and gene
AB  - products. It provides explicit categories for the many different Type II
AB  - enzymes now identified and provides a system for naming the putative genes
AB  - found by sequence analysis of microbial genomes.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Breitmeyer, J.B.
AU  - Tabachnik, N.F.
AU  - Myers, P.A.
TI  - A second specific endonuclease from Haemophilus aegyptius.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 121
EP  - 123
VL  - 91
AB  - A second restriction-like endonuclease has been partially purified from
AB  - Haemophilus aegyptius.  This enzyme cleaves bacteriophage lambda DNA and
AB  - adenovirus 2 DNA at many sites, but cleaves simian virus 40 DNA at only one
AB  - site.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - Base flipping.
JO  - Annu. Rev. Biochem.
PY  - 1998
SP  - 181
EP  - 198
VL  - 67
AB  - Base flipping is the phenomenon whereby a base in normal B-DNA is swung completely out of the
AB  - helix into an extrahelical position.  It was discovered in 1994 when the first co-crystal
AB  - structure was reported for a cytosine-5 DNA methyltransferase binding to DNA.  Since then it
AB  - has been shown to occur in many systems where enzymes need access to a DNA base to perform
AB  - chemistry on it.  Many DNA glycosylases that remove abnormal bases from DNA use this
AB  - mechanism.  This review describes systems known to use base flipping as well as many systems
AB  - where it is likely to occur but has not yet been rigorously demonstrated.  The mechanism and
AB  - evolution of base flipping are also discussed.  A review.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Halford, S.E.
TI  - Type II restriction enzymes.
JO  - Nucleases
PY  - 1993
SP  - 35
EP  - 88
VL  - 0
AB  - 
AB  -     I. Introduction and history
AB  -    II. Recognition sequences and cleavage properties
AB  -             A. Type IIs enzymes
AB  -             B. Degenerate recognition sequences
AB  -             C. Unusual type II enzymes
AB  -             D. Determination of cleavage sites
AB  -             E. Effects of methylation
AB  -             F. Single-stranded DNA cleavage
AB  -   III. Genes and their organization
AB  -             A. Cloning
AB  -             B. Genetic location
AB  -             C. Sequences
AB  -    IV. DNA Binding
AB  -             A. Enzymes that bind specifically to their recognition sites
AB  -             B. Enzymes that fail to bind specifically to their recognition sites
AB  -             C. Transfer to recognition sites
AB  -     V. DNA Cleavage
AB  -             A. Plasmid substrates
AB  -             B. Oligonucleotide substrates
AB  -             C. Specificity
AB  -    VI. Crystallography
AB  -             A. Protein structures
AB  -             B. DNA structures
AB  -             C. DNA-protein interfaces
AB  -   VII. Phosphodiester hydrolysis
AB  -  VIII. DNA recognition functions
AB  -             A. Altered enzymes
AB  -             B. Altered substrates
AB  -             C. Coupling recognition to catalysis
AB  -    IX. Evolution
AB  -     X. Conclusions and future prospects
AB  - 
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - The restriction enzymes.
JO  - Nucleases
PY  - 1993
SP  - 439
EP  - 444
VL  - 0
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - Restriction enzymes and their isoschizomers.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2167
EP  - 2180
VL  - 20
AB  - The restriction enzyme database, REBASE, contains information about restriction enzymes and
AB  - their associated methylases. Since the last description of the contents of REBASE, 204 new
AB  - entries have been added including 5 new Type II enzymes and 4 new Type I enzymes. A complete
AB  - list of these new enzymes can be found in Table I. A total of 2103 restriction enzymes are now
AB  - known and include 17 different Type I specificities, 179 different Type II specificities and 4
AB  - different Type III specificities. Table II contains a listing of all prototype restriction
AB  - enzymes (Types I, II and III), together with their commercially available isoschizomers and
AB  - neoschizomers that cleave at a position different from their prototype.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE-restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3125
EP  - 3137
VL  - 21
AB  - The restriction enzyme database, REBASE, is a collection of information about restriction
AB  - enzymes and methylases. Since the last description of the contents of REBASE (1), 265 new
AB  - entries have been added including 8 new Type II enzymes: AclI, AA^CGTT; Bce83I, CTTGAG
AB  - (16/14); BscGI, CCCGT; BseRI, GAGGAG (10/8); Bsp1407I, T^GTACA; BspLU11I, A^CATGT; BsrDI,
AB  - GCAATG (2/0) and SexAI A^CCWGGT. A complete list of these new enzymes can be found in Table I.
AB  - A total of 2393 restriction enzymes is now known including 17 different Type I specificities,
AB  - 188 different Type II specificities and 4 different Type II specificities. Table II contains a
AB  - listing of all prototype restriction enzymes (Types I, II and III), together with their
AB  - commercially available isoschizomers and neoschizomers that cleave at a position different
AB  - from their prototype.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE - restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 3628
EP  - 3639
VL  - 22
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
AB  - associated methylases, including their recognition and cleavage sites and their commercial
AB  - availability. Information from REBASE is available via monthly electronic mailings as well as
AB  - via WAIS and anonymous ftp. Specialized files are available that can be used directly by many
AB  - software packages.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE--restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 223
EP  - 235
VL  - 24
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
AB  - associated methylases, including their recognition and cleavage sites and their commercial
AB  - availability.  Information from REBASE is available via monthly electronic mailings as well as
AB  - via WAIS, anonymouse ftp and through the World Wide Web (htp://www.neb.com/rebase).
AB  - Specialized files are available that can be used directly by many software packages.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE - restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 338
EP  - 350
VL  - 26
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
AB  - associated methylases, including their recognition and cleavage sites and their commercial
AB  - availability. Also included is a listing of homing endonucleases. Information from REBASE is
AB  - available via monthly electronic mailings as well as via anonymous ftp and through the World
AB  - Wide Web. The REBASE web site, http://www.neb.com/rebase , is where we maintain a web page for
AB  - every enzyme, reference and supplier. Additionally, there is a search facility, help and NEWS
AB  - pages, and a complete description of our various services. Specialized files are available
AB  - that can be used directly by many software packages.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE-restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 268
EP  - 269
VL  - 29
AB  - REBASE contains comprehensive information about restriction enzymes, DNA methylases and
AB  - related proteins such as nicking enzymes, specificity subunits and control proteins.
AB  - It contains published and unpublished references, recognition and cleavage sites,
AB  - isoschizomers, commercial availability, methylation sensitivity, crystal data and
AB  - sequence data. Homing endonucleases are also included. Most recently, extensive
AB  - information about the methylation sensitivity of restriction enzymes has been added
AB  - and a new feature contains complete analyses of the putative restriction systems in
AB  - the sequenced bacterial and archaeal genomes. The data is distributed via email,
AB  - ftp (ftp.neb.com) and the Web (http://rebase.neb.com).
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE - restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 306
EP  - 307
VL  - 28
AB  - REBASE is a comprehensive database of information about restriction enzymes and related
AB  - proteins. It contains published and unpublished references, recognition and cleavage sites,
AB  - isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.
AB  - DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and
AB  - control proteins are also included. Most recently, putative DNA methyltransferases and
AB  - restriction enzymes, as predicted from analysis of genomic sequences, are also listed. The
AB  - data is distributed via Email, ftp (ftp.neb.com), and the Web (http://rebase.neb.com).
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - Restriction enzymes and their isoschizomers.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2077
EP  - 2109
VL  - 19
AB  - A review of all known restriction enzymes and a description of the REBASE
AB  - database.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE-restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 248
EP  - 262
VL  - 25
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
AB  - associated methylases, including their recognition and cleavage sites and their commercial
AB  - availability.  Information from REBASE is available via monthly electronic mailings as well as
AB  - via anonymous ftp, WAIS/gopher and through the World Wide Web (http://www.neb.com/rebase).
AB  - Specialized files are available that can be used directly by many software packages.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Macelis, D.
TI  - REBASE-restriction enzymes and methylases.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 312
EP  - 313
VL  - 27
AB  - REBASE is a comprehensive database of information about restriction enzymes and their
AB  - associated methylases, including their recognition and cleavage sites and their commercial
AB  - availability.  Also included is a listing of homing endonucleases.  Information from REBASE is
AB  - distributed via monthly electronic mailings as well as through anonymous ftp and the World
AB  - Wide Web.  The REBASE web site (http://www.neb.com/rebase) contains a web page for every
AB  - enzyme, reference and supplier.  Additionally, there is a search facility, help and NEWS
AB  - pages, and a complete description of our various services.  Specialized files are available
AB  - that can be used directly by many software packages.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Myers, P.A.
AU  - Morrison, A.
AU  - Murray, K.
TI  - A specific endonuclease from Haemophilus haemolyticus.
JO  - J. Mol. Biol.
PY  - 1976
SP  - 199
EP  - 208
VL  - 103
AB  - A restriction-like endonuclease, HhaI, has been partially purified from
AB  - Haemophilus haemolyticus.  This enzyme cleaves bacteriophage lambda DNA and
AB  - adenovirus-2 DNA at many sites, and cleaves simian virus 40 DNA at only two
AB  - sites.  It recognizes the sequence 5'-G-C-G-^C-3' 3'-C-^G-C-G-5' and cuts at
AB  - the sites indicated by the arrows.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Myers, P.A.
AU  - Morrison, A.
AU  - Murray, K.
TI  - A specific endonuclease from Arthrobacter luteus.
JO  - J. Mol. Biol.
PY  - 1976
SP  - 157
EP  - 165
VL  - 102
AB  - A new restriction-like endonuclease, AluI, has been partially purified from Arthrobacter
AB  - luteus. This enzyme cleaves bacteriophage lambda DNA, adenovirus-2 DNA and simian virus 40 DNA
AB  - at may sites including all sites cleaved by the endonuclease HindIII from Haemophilus
AB  - influenzae serotype d. Radioactive oligonucleotides in pancreatic DNAase digests of
AB  - (5'-32P)-labelled fragments of phage lambda DNA relased by the action of AluI had the 5'
AB  - terminal sequence pC-T-N-. The enzyme recognizes the tetranucleotide sequence
AB  - 3'-T-C-^-G-A-5' 5'-A-G-^C-T-3' and cleaves it at the position marked by the arrows.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Vincze, T.
AU  - Posfai, J.
AU  - Macelis, D.
TI  - REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - D234
EP  - D236
VL  - 38
AB  - REBASE is a comprehensive database of information about restriction enzymes, DNA
AB  - methyltransferases and related proteins involved in the
AB  - biological process of restriction-modification (R-M). It contains fully
AB  - referenced information about recognition and cleavage sites,
AB  - isoschizomers, neoschizomers, commercial availability, methylation
AB  - sensitivity, crystal and sequence data. Experimentally characterized
AB  - homing endonucleases are also included. The fastest growing segment of
AB  - REBASE contains the putative R-M systems found in the sequence databases.
AB  - Comprehensive descriptions of the R-M content of all fully sequenced
AB  - genomes are available including summary schematics. The contents of REBASE
AB  - may be browsed from the web (http://rebase.neb.com) and selected
AB  - compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly
AB  - updates can be requested via email.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Vincze, T.
AU  - Posfai, J.
AU  - Macelis, D.
TI  - REBASE - Restriction enzymes and DNA methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - D230
EP  - D232
VL  - 33
AB  - REBASE is a comprehensive database of information about restriction enzymes, DNA
AB  - methyltransferases and related proteins involved in restriction-modification.  It contains
AB  - both published and unpublished work with information about recognition and cleavage sites,
AB  - isoschizomers, commercial availability, crystal and sequence data.  Experimentally
AB  - characterized homing endonucleases are also included.  Additionally, REBASE contains complete
AB  - and up-to-date information about the methylation sensitivity of restriction endonucleases.  An
AB  - extensive analysis is included of the restriction-modification systems that are predicted to
AB  - be present in the sequenced bacterial and archaeal genomes from GenBank.  The contents of
AB  - REBASE are available by browsing from the web (http://rebase.neb.com/rebase/rebase.html) and
AB  - through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be
AB  - requested via email.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Vincze, T.
AU  - Posfai, J.
AU  - Macelis, D.
TI  - REBASE--enzymes and genes for DNA restriction and modification.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - D269
EP  - D270
VL  - 35
AB  - REBASE is a comprehensive database of information about restriction enzymes, DNA
AB  - methyltransferases and related proteins involved in the biological process of
AB  - restriction-modification. It contains fully referenced information about recognition and
AB  - cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation
AB  - sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are
AB  - also included. All newly sequenced genomes are analyzed for the presence of putative
AB  - restriction systems and these data are included within the REBASE. The contents or REBASE may
AB  - be browsed from the web (http://rebase.neb.com/rebase/rebase.ftp.html) and selected
AB  - compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be
AB  - requested via email.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Vincze, T.
AU  - Posfai, J.
AU  - Macelis, D.
TI  - REBASE-a database for DNA restriction and modification: enzymes, genes and genomes.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - D298
EP  - D299
VL  - 43
AB  - REBASE is a comprehensive and fully curated database of information about the components of
AB  - restriction-modification (RM) systems. It contains fully referenced
AB  - information about recognition and cleavage sites for both restriction enzymes and
AB  - methyltransferases as well as commercial availability, methylation sensitivity,
AB  - crystal and sequence data. All genomes that are completely sequenced are analyzed
AB  - for RM system components, and with the advent of PacBio sequencing, the
AB  - recognition sequences of DNA methyltransferases (MTases) are appearing rapidly.
AB  - Thus, Type I and Type III systems can now be characterized in terms of
AB  - recognition specificity merely by DNA sequencing. The contents of REBASE may be
AB  - browsed from the web http://rebase.neb.com and selected compilations can be
AB  - downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Vincze, T.
AU  - Posfai, J.
AU  - Macelis, D.
TI  - REBASE: restriction enzymes and methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 418
EP  - 420
VL  - 31
AB  - REBASE contains comprehensive information about restriction enzymes, DNA methyltransferases
AB  - and related proteins such as nicking enzymes,
AB  - specificity subunits and control proteins. It contains published and
AB  - unpublished references, recognition and cleavage sites, isoschizomers,
AB  - commercial availability, crystal and sequence data. Homing endonucleases
AB  - are also included. REBASE contains the most complete and up-to-date
AB  - information about the methylation sensitivity of restriction
AB  - endonucleases. In addition, there is extensive information about the known
AB  - and putative restriction-modification (R-M) systems in more than 100
AB  - sequenced bacterial and archaeal genomes. The data is available on the web
AB  - (http://rebase.neb.com/rebase/rebase.html), through ftp (ftp.neb.com) and
AB  - as monthly updates via email.
ER  -

TY  - JOUR
AU  - Roberts, R.J.
AU  - Wilson, G.A.
AU  - Young, F.E.
TI  - Recognition sequence of specific endonuclease BamHI from Bacillus amyloliquefaciens H.
JO  - Nature
PY  - 1977
SP  - 82
EP  - 84
VL  - 265
AB  - Many specific endonucleases (restriction endonucleases) have been isolated and
AB  - recognition sequences have been determined for a number of them.  The isolation
AB  - of a new specific endonuclease, BamHI, from Bacillus amyloliquefaciens H has
AB  - recently been described.  We have determined the recognition sequence of BamHI
AB  - and find that it cleaves the two-fold rotationallly symmetric sequence
AB  - 5'-G-^G-A-T-C-C-3' 3'-C-C-T-A-G-^G-5' at the positions indicated by the arrows
AB  - generating fragments with cohesive termini.
ER  -

TY  - JOUR
AU  - Robertson, A.K.
AU  - Geiman, T.M.
AU  - Sankpal, U.T.
AU  - Hager, G.L.
AU  - Robertson, K.D.
TI  - Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2004
SP  - 110
EP  - 118
VL  - 322
AB  - DNA methylation is an epigenetic modification of the genome critical for numerous processes,
AB  - including transcriptional repression and
AB  - maintenance of chromatin structure. Recent studies have revealed
AB  - connections between DNA methylation and other epigenetic modifications
AB  - such as ATP-dependent chromatin remodeling. It remains unclear,
AB  - however, exactly how chromatin and epigenetic chromatin modifications
AB  - affect the biological properties of the DNA methyltransferases (DNMT1,
AB  - DNMT3A, and DNMT3B). Using a highly purified system and the 5S rDNA
AB  - gene as free DNA or assembled into a mononucleosome, we have compared
AB  - the effects of chromatin structure on DNMT1 and Dnmt3a. The catalytic
AB  - efficiency for both enzymes decreased on the mononucleosome, similar
AB  - to8-fold for DNMT1 and 17-fold for Dnmt3a. DNMT1 and Dnmt3a bound to
AB  - DNA and mononucleosomal substrates in gel shift experiments with
AB  - approximately equal affinity and in a cooperative manner. We also show
AB  - that DNMT1 interacts with hSNF2H chromatin remodeling enzyme and that
AB  - DNMT1 binds mononucleosomes with higher affinity in the presence of
AB  - hSNF2H. These findings raise interesting implications about the
AB  - interactions of mammalian DNA methyltransferases with chromatin and
AB  - provide the first evidence that a chromatin remodeling enzyme can alter
AB  - the biological properties of a DNMT.
ER  -

TY  - JOUR
AU  - Robertson, G.T.
AU  - Reisenauer, A.
AU  - Wright, R.
AU  - Jensen, R.B.
AU  - Jensen, A.
AU  - Shapiro, L.
AU  - Roop, R.M.
TI  - The Brucella abortus CcrM DNA methyltransferase is essential for viability, and its overexpression attenuates intracellular replication in murine macrophages.
JO  - J. Bacteriol.
PY  - 2000
SP  - 3482
EP  - 3489
VL  - 182
AB  - The CcrM DNA methyltransferase of the alpha-proteobacteria catalyzes the methylation of the
AB  - adenine in the sequence GAnTC.  Like Dam in the enterobacteria, CcrM plays a regulatory role
AB  - in Caulobacter crescentus and Rhizobium meliloti.  CcrM is essential for viability in both of
AB  - these organisms, and we show here that it is also essential in Brucella abortus.  Further,
AB  - increased copy number of the ccrM gene results in striking changes in B. abortus morphology,
AB  - DNA replication, and growth in murine macrophages.  We generated strains that carry ccrM
AB  - either on a low-copy-number plasmid (strain GR131) or on a moderate-copy-number plasmid
AB  - (strain GR132).  Strain GR131 has wild-type morphology and chromosome number, as assessed by
AB  - flow cytometry.  In contrast, strain GR132 has abnormal branched morphology, suggesting
AB  - aberrant cell division, and increased chromosome number.  Although these strains exhibit
AB  - different morphologies and DNA content, the replication of both strains in macrophages is
AB  - attenuated.  These data imply that the reduction in survival in host cells is not due solely
AB  - to a cell division defect but is due to additional functions of CcrM.  Because CcrM is
AB  - essential in B. abortus and increased ccrM copy number attentuates survival in host cells, we
AB  - propose that CcrM is an appropriate target for new antibiotics.
ER  -

TY  - JOUR
AU  - Robertson, J.
AU  - Lin, J.
AU  - Levett, P.N.
AU  - Nadon, C.
AU  - Nash, J.
AU  - Berry, C.
TI  - Complete Genome Sequence of an Escherichia coli O121:H19 Strain from an Outbreak  in Canada Associated with Flour.
JO  - Genome Announcements
PY  - 2018
SP  - e01561
EP  - e01517
VL  - 6
AB  - Here, we present the first complete genome sequence of an Escherichia coli non-O157
AB  - Shiga-toxin producing isolate, 16-9255, from serotype O121:H19. This
AB  - strain is notable as a clinical case recovered from a recent Canadian
AB  - flour-associated outbreak event.
ER  -

TY  - JOUR
AU  - Robertson, J.
AU  - Yoshida, C.
AU  - Gurnik, S.
AU  - Nash, J.H.E.
TI  - Completed Genome Sequences of Strains from 36 Serotypes of Salmonella.
JO  - Genome Announcements
PY  - 2018
SP  - e01472
EP  - e01417
VL  - 6
AB  - We report here the completed closed genome sequences of strains representing 36 serotypes of
AB  - Salmonella These genome sequences will provide useful references for
AB  - understanding the genetic variation between serotypes, particularly as references
AB  - for mapping of raw reads or to create assemblies of higher quality, as well as to
AB  - aid in studies of comparative genomics of Salmonella.
ER  -

TY  - JOUR
AU  - Robertson, K.
TI  - DNA methyltransferase function and regulation.
JO  - J. Nutr.
PY  - 2003
SP  - 3845S
EP  - 3845S
VL  - 133
AB  - DNA methylation is an epigenetic modification of the genome catalyzed by a group of 3 DNA
AB  - methyltransferases: DNMT1, 3A, and 3B.  Methyl groups are not randomly distributed in
AB  - mammalian cells but rather are compartmentalized in repetitive DNA, heterochromatic regions,
AB  - and parasitic elements.  Other regions of the genome, such as CpG island promoters, are almost
AB  - always unmethylated.  Given the minimal sequence requirements of the DNMTs (CpG), it is likely
AB  - that they are directed to sequences that are to be methylated by interactions with other
AB  - proteins, particularly chromatin-associated factors.  This compartmentalization is essential
AB  - because genetic knockouts of the DNMTs lead to embryonic lethality, and reversal of the normal
AB  - DNA methylation patterns is a hallmark of the most transformed cells.
ER  -

TY  - JOUR
AU  - Robertson, K.D.
TI  - DNA methylation, methyltransferases, and cancer.
JO  - Oncogene
PY  - 2001
SP  - 3139
EP  - 3155
VL  - 20
AB  - The field of epigenetics has recently moved to the forefront of studies relating to diverse
AB  - processes such as transcriptional regulation, chromatin structure, genome integrity, and
AB  - tumorigenesis. Recent work has revealed how DNA methylation and chromatin structure are linked
AB  - at the molecular level and how methylation anomalies play a direct causal role in
AB  - tumorigenesis and genetic disease. Much new information has also come to light regarding the
AB  - cellular methylation machinery, known as the DNA methyltransferases, in terms of their roles
AB  - in mammalian development and the types of proteins they are known to interact with. This
AB  - information has forced a new view for the role of DNA methyltransferases. Rather than enzymes
AB  - that act in isolation to copy methylation patterns after replication, the types of
AB  - interactions discovered thus far indicate that DNA methyltransferases may be components of
AB  - larger complexes actively involved in transcriptional control and chromatin structure
AB  - modulation. These new findings will likely enhance our understanding of the myriad roles of
AB  - DNA methylation in disease as well as point the way to novel therapies to prevent or repair
AB  - these defects.
ER  -

TY  - JOUR
AU  - Robertson, K.D.
AU  - Ait-Si-Ali, S.
AU  - Yokochi, T.
AU  - Wade, P.A.
AU  - Jones, P.L.
AU  - Wolffe, A.P.
TI  - DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters.
JO  - Nat. Genet.
PY  - 2000
SP  - 338
EP  - 342
VL  - 25
AB  - Methylation of CpG islands is associated with transcriptional silencing and the formation of
AB  - nuclease-resistant chromatin structures enriched in hypoacetylated histones.
AB  - Methyl-CpG-binding proteins, such as MeCP2, provide a link between methylated DNA and
AB  - hypoacetylated histones by recruiting histone deacetylase, but the mechanisms establishing the
AB  - methylation patterns themselves are unknown. Whether DNA methylation is always causal for the
AB  - assembly of repressive chromatin or whether features of transcriptionally silent chromatin
AB  - might target methyltransferase remains unresolved. Mammalian DNA methyltransferases show
AB  - little sequence specificity in vitro, yet methylation can be targeted in vivo within
AB  - chromosomes to repetitive elements, centromeres and imprinted loci. This targeting is
AB  - frequently disrupted in tumour cells, resulting in the improper silencing of tumour-suppressor
AB  - genes associated with CpG islands. Here we show that the predominant mammalian DNA
AB  - methyltransferase, DNMT1, co-purifies with the retinoblastoma (Rb) tumour suppressor gene
AB  - product, E2F1, and HDAC1 and that DNMT1 cooperates with Rb to repress transcription from
AB  - promoters containing E2F-binding sites. These results establish a link between DNA
AB  - methylation, histone deacetylase and sequence-specific DNA binding activity, as well as a
AB  - growth-regulatory pathway that is disrupted in nearly all cancer cells.
ER  -

TY  - JOUR
AU  - Robertson, K.D.
AU  - Jones, P.A.
TI  - DNA methylation: past, present and future directions.
JO  - Carcinogenesis
PY  - 2000
SP  - 461
EP  - 467
VL  - 21
AB  - DNA methylation, or the covalent addition of a methyl group to cytosine within the context of
AB  - the CpG dinucleotide, has profound effects on the mammalian genome. These effects include
AB  - transcriptional repression via inhibition of transcription factor binding or the recruitment
AB  - of
AB  - methyl-binding proteins and their associated chromatin remodeling factors, X chromosome
AB  - activation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also
AB  - essential for proper embryonic development; however, its presence can add an additional burden
AB  - to the genome. Normal methylation patterns are frequently disrupted in tumor cells with global
AB  - hypomethylation accompanying region-specific hypermethylation. When these hypermethylation
AB  - events occur within the promoter of a tumor suppressor gene they will silence the gene and
AB  - provide the cell with a growth advantage in a manner akin to deletions or mutations. Recent
AB  - work indicating that DNA methylation is an important player in both DNA repair and genome
AB  - stability as well as the discovery of a new family of DNA methyltransferases makes now a very
AB  - exciting period for the methylation field. This review will highlight the major findings in
AB  - the methylation field over the past 20 years then summarize the most important and interesting
AB  - future directions the field is likely to take in the next millennium.
ER  -

TY  - JOUR
AU  - Robertson, K.D.
AU  - Keyomarsi, K.
AU  - Gonzales, F.A.
AU  - Velicescu, M.
AU  - Jones, P.A.
TI  - Differential mRNA expression of the human DNA methyltransferases (DNMTs) 1, 3a and 3b during the G0/G1 to S phase transition in normal and tumor cells.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 2108
EP  - 2113
VL  - 28
AB  - DNA methylation is essential for mammalian development, X-chromosome inactivation, and
AB  - imprinting yet aberrant methylation patterns are one of the most common features of
AB  - transformed cells. One of the proposed causes for these defects in the methylation machinery
AB  - is overexpression of one or more of the three known catalytically active DNA
AB  - methyltransferases (DNMTs) 1, 3a and 3b, yet there are clearly examples in which
AB  - overexpression is minimal or non-existent but global methylation anomalies persist. An
AB  - alternative mechanism which could give rise to global methylation errors is the improper
AB  - expression of one or more of the DNMTs during the cell cycle. To begin to study the latter
AB  - possibility we examined the expression of the mRNAs for DNMT1, 3a and 3b during the cell cycle
AB  - of normal and transformed cells. We found that DNMT1 and 3b levels were significantly
AB  - downregulated in G0/G1 while DNMT3a mRNA levels were less sensitive to cell cycle
AB  - alterations and were maintained at a slightly higher level in tumor lines compared to normal
AB  - cell strains. Enzymatic activity assays revealed a similar decrease in the overall methylation
AB  - capacity of the cells during G0/G1 arrest and again revealed that a tumor cell line
AB  - maintained a higher methylation capacity during arrest than a normal cell strain. These
AB  - results reveal a new level of control exerted over the cellular DNA methylation machinery, the
AB  - loss of which provides an alternative mechanism for the genesis of the aberrant methylation
AB  - patterns observed in tumor cells.
ER  -

TY  - JOUR
AU  - Robertson, K.D.
AU  - Uzvolgyi, E.
AU  - Liang, G.
AU  - Talmadge, C.
AU  - Sumegi, J.
AU  - Gonzales, F.A.
AU  - Jones, P.A.
TI  - The human DNA methyltransferases 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 2291
EP  - 2298
VL  - 27
AB  - DNA methylation in mammals is required for embryonic development, X chromosome inactivation
AB  - and imprinting.  Previous studies have shown that methylation patterns become abnormal in
AB  - malignant cells and may contribute to tumorigenesis by improper de novo methylation and
AB  - silencing of the promoters for growth-regulatory genes.  RNA and protein levels of the DNA
AB  - methyltransferase DNMT1 have been shown to be elevated in tumors, however murine stem cells
AB  - lacking Dnmt1 are still able to de novo methylate viral DNA.  The recent cloning of a new
AB  - family of DNA methyltransferases (Dmnt3a and Dmnt3b) in mouse which methylate hemimethylated
AB  - and unmethylated templates with equal efficiencies make them candidates for the long sought de
AB  - novo methyltransferases.  We have investigated the expression of human DNMT1, 3a and 3b and
AB  - found widespread, coordinate expression of all three transcripts in most normal tissues.
AB  - Chromosomal mapping placed DNMT3a on chromosome 2p23 and DNMT3b on chromosome 20q11.2.
AB  - Significant overexpression of DNMT3b was seen in tumors while DNMT1 and DNMT3a were only
AB  - modestly overexpressed and with lower frequency.  Lastly, several novel alternatively spliced
AB  - forms of DNMT3b, which may have altered enzymatic activity, were found to be expressed in a
AB  - tissue-specific manner.
ER  -

TY  - JOUR
AU  - Robertson, K.D.
AU  - Wolffe, A.P.
TI  - DNA methylation in health and disease.
JO  - Genetics
PY  - 2000
SP  - 11
EP  - 19
VL  - 1
AB  - DNA methylation has recently moved to centre stage in the aetiology of human
AB  - neurodevelopmental syndromes such as the fragile X, ICF and Rett syndromes.  These diseases
AB  - result from the misregulation of genes that occurs with the loss of appropriate epigenetic
AB  - controls during neuronal development.  Recent advances have connected DNA methylation to
AB  - chromatin-remodelling enzymes, and understanding this link will be central to the design of
AB  - new therapeutic tools.
ER  -

TY  - JOUR
AU  - Robinson, C.R.
AU  - Sligar, S.G.
TI  - Mediation of molecular recognition in protein-DNA complexes by bound water: a mechanism for "star activity" of restriction endonucleases.
JO  - Biophys. J.
PY  - 1994
SP  - A34
EP  - A34
VL  - 66
AB  - For many restriction endonucleases such as EcoRI, accurate protein-DNA recognition is
AB  - disrupted by changes in buffer composition, leading to an unexplained loss of specificity
AB  - termed "star activity". We have found that the extent of cleavage by EcoRI at non-canonical
AB  - sites is strongly correlated with the osmotic pressure in the reaction. This relationship is
AB  - unique to osmotic pressure, and is independent of other physical or chemical properties of the
AB  - osmolyte. An analogous correlation between osmotic pressure and star activity is observed for
AB  - other restriction enzymes including PvuII and BamHI. Specificity for cleavage at canonical
AB  - sites is restored by the application of hydrostatic pressure to counteract the effects of
AB  - osmotic pressure. Elevated osmotic pressures induce a fundamental change in the selectivity of
AB  - EcoRI -- at 100 atm osmotic pressure the rate of cleavage at the canonical site actually
AB  - decreases, whereas the rate of cleavage at "star" sites increases. The alteration of
AB  - specificity accompanying release of water clearly implicates one or more water molecules in
AB  - mediating accurate recognition of specific sequences of DNA by the enzyme. The change in
AB  - selectivity is manifested in both the association and catalytic steps of the reaction. Under
AB  - standard conditions, water may participate as a general mediator for sequence specific
AB  - recognition of DNA by restriction enzymes and other DNA-binding proteins.
ER  -

TY  - JOUR
AU  - Robinson, C.R.
AU  - Sligar, S.G.
TI  - Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 2186
EP  - 2191
VL  - 95
AB  - Restriction endonucleases such as EcoRI bind and cleave DNA with great specificity and
AB  - represent a paradigm for protein-DNA interactions and molecular recognition.  Using osmotic
AB  - pressure to induce water release, we demonstrate the participation of bound waters in the
AB  - sequence discrimination of substrate DNA by EcoRI.  Changes in solvation can play a critical
AB  - role in directing sequence-specific DNA binding by EcoRI and are also crucial in assisting
AB  - site discrimination during catalysis.  By measuring the volume change for complex formation,
AB  - we show that at the cognate sequence (GAATTC) EcoRI binding releases about 70 fewer water
AB  - molecules than binding at an alternate DNA sequence (TAATTC), which differs by a single base
AB  - pair.  EcoRI complexation with nonspecific DNA releases substantially less water than either
AB  - of these specific complexes.  In cognate substrates (GAATTC) kcat decreases as osmotic
AB  - pressure is increased, indicating that binding of about 30 water molecules accompanies the
AB  - cleavage reaction.  For the alternate substrate (TAATTC), release of about 40 water molecules
AB  - accompanies the reaction, indicated by a dramatic acceleration of the rate when osmotic
AB  - pressure is raised.  These large differences in solvation effects demonstrate that water
AB  - molecules can be key players in the molecular recognition process during both association and
AB  - catalytic phases of the EcoRI reaction, acting to change the specificity of the enzyme.  For
AB  - both the protein-DNA complex and the transition state, there may be substantial conformational
AB  - differences between cognate and alternate sites, accompanied by significant alterations in
AB  - hydration and solvent accessibility.
ER  -

TY  - JOUR
AU  - Robinson, C.R.
AU  - Sligar, S.G.
TI  - Mediation of molecular recognition in protein-DNA complexes by bound water: a mechanism for "star activity" of restriction endonucleases.
JO  - J. Cell Biochem. Suppl.
PY  - 1994
SP  - 138
EP  - 138
VL  - 18C
AB  - For many restriction endonucleases such as EcoRI, accurate protein-DNA recognition is
AB  - disrupted by changes in buffer composition, leading to an unexplained loss of specificity
AB  - termed "star activity". We have found that the extent of cleavage by EcoRI at non-canonical
AB  - sites is strongly correlated with the osmotic pressure in the reaction. This relationship is
AB  - unique to osmotic pressure, and is independent of other physical or chemical properties of the
AB  - osmolyte. An analogous correlation between osmotic pressure and star activity is observed for
AB  - other restriction enzymes including PvuII and BamHI. For EcoRI, specificity for cleavage at
AB  - the canonical site is restored by the application of hydrostatic pressure to counteract the
AB  - effects of osmotic pressure. Elevated osmotic pressures induce a fundamental change in the
AB  - selectivity of EcoRI -- at 100 atm osmotic pressure the rate of cleavage at the canonical sie
AB  - actually decreases, whereas the rate of cleavage at "star" sites increases. The alteration of
AB  - specificity accompanying release of water clearly implicates one or more water molecules in
AB  - mediating accurate recognition of specific sequences of DNA by the enzyme. The change in
AB  - selectivity is manifested in both the association and catalytic steps of the reaction. Under
AB  - standard conditions, water may participate as a general mediator for sequence specific
AB  - recognition of DNA by restriction enzymes and other DNA-binding proteins.
ER  -

TY  - JOUR
AU  - Robinson, C.R.
AU  - Sligar, S.G.
TI  - Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI.
JO  - J. Mol. Biol.
PY  - 1993
SP  - 302
EP  - 306
VL  - 234
AB  - Many restriction endonucleases such as EcoRI lose some specificity for their recognition
AB  - sequence under certain buffer conditions. The cause of this disruption of accurate protein-DNA
AB  - recognition has never been explained. By cleaving DNA with EcoRI in the presence of several
AB  - osmolytes, we show that the extent of this EcoRI "star activity" depends strongly upon osmotic
AB  - pressure. The loss of specificity accompanying decreased water activity implies a role for one
AB  - or more water molecules in recognition of specific sequences of DNA. Water mediation may
AB  - constitute a general motif for sequence-specific DNA recognition by restriction enzymes and
AB  - other DNA-binding proteins.
ER  -

TY  - JOUR
AU  - Robinson, C.R.
AU  - Sligar, S.G.
TI  - Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions.
JO  - Biochemistry
PY  - 1994
SP  - 3787
EP  - 3793
VL  - 33
AB  - To characterize the role of water in protein-DNA interactions, we have studied the specificity
AB  - of the EcoRI restriction endonuclease as a function of osmotic and hydrostatic pressure. The
AB  - extent of cleavage by the enzyme at noncanonical ("star") sites is shown to depend uniquely
AB  - upon the osmotic pressure in the reaction as controlled by the addition of a wide variety of
AB  - neutral solutes. Alteration of cleavage specificity ("EcoRI* activity") is not uniformly
AB  - correlated with any other colligative solvent property such as dielectric constant, viscosity,
AB  - or water concentration. The application of hydrostatic pressure reverses the effects of
AB  - osmotic pressure, restoring the natural selectivity of the enzyme for its canonical site
AB  - GAATTC. This combination of observations provides compelling evidence that the site-specific
AB  - recognition of canonical site DNA by EcoRI is mediated by discretely bound water molecules and
AB  - that the release of these waters induces a fundamental change in the specificity of the
AB  - interaction, leading to cleavage at alternative sites. This comprehensive analysis of solvent
AB  - effects facilitates the unambiguous identification of structurally and functionally specific
AB  - waters involved in macromolecular recognition events.
ER  -

TY  - JOUR
AU  - Robinson, C.R.
AU  - Sligar, S.G.
TI  - Heterogeneity in molecular recognition by restriction endonucleases: Osmotic and hydrostatic pressure effects on BamHI, PvuII, and EcoRV specificity.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1995
SP  - 3444
EP  - 3448
VL  - 92
AB  - The cleavage specificity of the PvuII and BamHI restriction endonucleases is found to be
AB  - dramatically reduced at elevated osmotic pressure. Relaxation in specificity of these
AB  - otherwise highly accurate and specific enzymes, previously termed "star activity", is uniquely
AB  - correlated with osmotic pressure between 0 and 100 atmospheres. No other colligative solvent
AB  - property exhibits a uniform correlation with star activity for all of the compounds tested.
AB  - Application of hydrostatic pressure counteracts the effects of osmotic pressure and restores
AB  - the natural selectivity of the enzymes for their canonical recognition sequences. These
AB  - results indicate that water solvation plays an important role in the site-specific recognition
AB  - of DNA by many restriction enzymes. Osmotic pressure did not induce an analogous effect on the
AB  - specificity of the EcoRV endonuclease, implying that selective hydration effects do not
AB  - participate in DNA recognition in this system. Hydrostatic pressure was found to have little
AB  - effect on the star activity induced by changes in ionic strength, pH, or divalent cation,
AB  - suggesting that distinct mechanisms may exist for these observed alterations in specificity.
AB  - Recent evidence has indicated that BamHI and EcoRI share similar structural motifs, while
AB  - PvuII and EcoRV belong to a different structural family. Evidently, the use of hydration water
AB  - to assist in site-specific recognition is a motif neither limited to nor defined by structural
AB  - families.
ER  -

TY  - JOUR
AU  - Robinson, D.
AU  - Walsh, P.R.
AU  - Bonventre, J.A.
TI  - Restriction endonucleases.
JO  - Molecular biology problem solver.
PY  - 2001
SP  - 225
EP  - 266
AB  - Molecular biologists routinely use restriction enzymes as key reagents for a variety of
AB  - applications including genomic mapping, restriction fragment length polymorphism (RFLP)
AB  - analysis, DNA sequencing, and a host of recombinant DNA methodologies.  Few would argue that
AB  - these enzymes are not indispensable tools for the variety of techniques used in the
AB  - manipulation of DNA, but like many common tools that are easy to use, they are not always
AB  - applied as efficiently and effectively as possible.  This chapter focuses on the biochemical
AB  - attributes and requirements of restriction enzymes and delivers strategies to optimize their
AB  - use in simple and complex reactions.
ER  -

TY  - JOUR
AU  - Robinson, L.S.
AU  - Perry, J.
AU  - Lek, S.
AU  - Wollam, A.
AU  - Sodergren, E.
AU  - Weinstock, G.
AU  - Lewis, W.G.
AU  - Lewis, A.L.
TI  - Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis.
JO  - Genome Announcements
PY  - 2016
SP  - e00879
EP  - e00816
VL  - 4
AB  - Gardnerella vaginalis is a predominant species in bacterial vaginosis, a dysbiosis of the
AB  - vagina that is associated with adverse health outcomes,
AB  - including preterm birth. Here, we present the draft genome sequences of 15
AB  - Gardnerella vaginalis strains (now available through BEI Resources) isolated from
AB  - women with and without bacterial vaginosis.
ER  -

TY  - JOUR
AU  - Robinson, V.L.
AU  - Oyston, P.C.
AU  - Titball, R.W.
TI  - A dam mutant of Yersinia pestis is attenuated and induces protection against plague.
JO  - FEMS Microbiol. Lett.
PY  - 2005
SP  - 251
EP  - 256
VL  - 252
AB  - We have constructed a dam mutant of Yersinia pestis GB. In BALB/c mice inoculated
AB  - subcutaneously, the median lethal dose of the mutant was at least 2000-fold
AB  - higher than the wild type. Mice inoculated with sub-lethal doses of the mutant
AB  - were protected against a subsequent challenge with virulent Y. pestis. The effect
AB  - of dam inactivation on gene expression was examined using a DNA microarray, which
AB  - revealed increased expression of a number of genes associated with the SOS
AB  - response. These results confirm the key role of Dam in the regulation of
AB  - virulence, and its potential role as a target for the generation of attenuated
AB  - strains of pathogenic bacteria.
ER  -

TY  - JOUR
AU  - Robson, R.L.
AU  - Jones, R.
AU  - Robson, R.M.
AU  - Schwartz, A.
AU  - Richardson, T.H.
TI  - Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412).
JO  - PLoS ONE
PY  - 2015
SP  - E0127997
EP  - E0127997
VL  - 10
AB  - The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium
AB  - Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It
AB  - consists of 7 circular replicons totalling 5,192,291 bp comprising a circular
AB  - chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp,
AB  - 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has
AB  - a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3,
AB  - 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined
AB  - and 5 methylation motifs have been identified. The genome also contains a very
AB  - high number of transposase/inactivated transposase genes from at least 12 of the
AB  - 17 recognised insertion sequence families. The Ac-8003 genome has been compared
AB  - with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain
AB  - O, the only other member of the Azotobacteraceae determined so far which has a
AB  - single chromosome of 5,365,318 bp and no plasmids. The chromosomes show
AB  - significant stretches of synteny throughout but also reveal a history of many
AB  - deletion/insertion events. The Ac-8003 genome encodes 4628 predicted
AB  - protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of
AB  - these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ,
AB  - and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways
AB  - and macromolecular architectures and machineries of these organisms appear
AB  - largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and
AB  - a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic
AB  - differences reported for these organisms have also been identified. Also many
AB  - other potential phenotypic differences have been uncovered. Properties endowed by
AB  - the plasmids are described including the presence of an entire aerobic corrin
AB  - synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in
AB  - pAcX50c. All these findings are related to the potentially different
AB  - environmental niches from which these organisms were isolated and to emerging
AB  - theories about how microbes contribute to their communities.
ER  -

TY  - JOUR
AU  - Rocap, G. et al.
TI  - Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.
JO  - Nature
PY  - 2003
SP  - 1042
EP  - 1047
VL  - 424
AB  - The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving
AB  - autotroph. It numerically dominates the
AB  - phytoplankton in the tropical and subtropical oceans, and is responsible
AB  - for a significant fraction of global photosynthesis. Here we compare the
AB  - genomes of two Prochlorococcus strains that span the largest evolutionary
AB  - distance within the Prochlorococcus lineage and that have different
AB  - minimum, maximum and optimal light intensities for growth. The
AB  - high-light-adapted ecotype has the smallest genome (1,657,990 base pairs,
AB  - 1,716 genes) of any known oxygenic phototroph, whereas the genome of its
AB  - low-light-adapted counterpart is significantly larger, at 2,410,873 base
AB  - pairs (2,275 genes). The comparative architectures of these two strains
AB  - reveal dynamic genomes that are constantly changing in response to myriad
AB  - selection pressures. Although the two strains have 1,350 genes in common,
AB  - a significant number are not shared, and these have been differentially
AB  - retained from the common ancestor, or acquired through duplication or
AB  - lateral transfer. Some of these genes have obvious roles in determining
AB  - the relative fitness of the ecotypes in response to key environmental
AB  - variables, and hence in regulating their distribution and abundance in the
AB  - oceans.
ER  -

TY  - JOUR
AU  - Rocha, E.P.
AU  - Danchin, A.
AU  - Viari, A.
TI  - Evolutionary role of restriction/modification systems as revealed by comparative genome analysis.
JO  - Genome Res.
PY  - 2001
SP  - 946
EP  - 958
VL  - 11
AB  - Type II restriction modification systems (RMSs) have been regarded either as defense tools or
AB  - as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the
AB  - study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of
AB  - palindrome avoidance. This analysis reveals that palindrome avoidance is not universally
AB  - spread among bacterial species and that it does not correlate with taxonomic proximity.
AB  - Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for
AB  - RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome
AB  - avoidance is intimately correlated with the infective behavior of the phage. We observe that
AB  - the degree of palindrome and restriction site avoidance is significantly and consistently less
AB  - important in phages than in their bacterial hosts. This result brings to the fore a larger
AB  - selective load for palindrome and restriction site avoidance on the bacterial hosts than on
AB  - their infecting phages. It is then consistent with a view where type II RMSs are considered as
AB  - parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial
AB  - third player in the host-parasite relationship between bacteria and phages.
ER  -

TY  - JOUR
AU  - Rocha, E.P.C.
AU  - Blanchard, A.
TI  - Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 2031
EP  - 2042
VL  - 30
AB  - Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous
AB  - repeated sequences with important roles in their evolution. We have established a
AB  - bioinformatic strategy to detect the major recombination hot-spots in the genomes of
AB  - Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis.
AB  - This allowed the identification of large numbers of potentially variable regions, as well as a
AB  - comparison of the relative recombination potentials of different genomic regions. Different
AB  - trends are perceptible among mycoplasmas, probably due to different functional and structural
AB  - constraints. The largest potential for illegitimate recombination in M. pulmonis is found at
AB  - the vsa locus and its comparison in two different strains reveals numerous changes since
AB  - divergence. On the other hand, the main M. pneumoniae and M. genitalium adhesins rely on large
AB  - distant repeats and, hence, homologous recombination for variation. However, the relation
AB  - between the existence of repeats and antigenic variation is not necessarily straightforward,
AB  - since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by
AB  - patient antibodies. These different strategies have important consequences for the structures
AB  - of genomes, since large distant repeats correlate well with the major chromosomal
AB  - rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in
AB  - comparison to co-oriented repeats.
ER  -

TY  - JOUR
AU  - Rocha, T.S.
AU  - Bertolotti, L.
AU  - Catania, S.
AU  - Pourquier, P.
AU  - Rosati, S.
TI  - Genome Sequence of a Mycoplasma meleagridis Field Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00017
EP  - e00016
VL  - 4
AB  - Mycoplasma meleagridis is a major cause of disease and economic loss in turkeys.  Here, we
AB  - report the genome sequence of an M. meleagridis field strain, which
AB  - enlarges the knowledge about this bacterium and helps the identification of
AB  - possible coding sequences for drug resistance genes and specific antigens.
ER  -

TY  - JOUR
AU  - Rochaix, J.D.
AU  - Rahire, M.
AU  - Michel, F.
TI  - The chloroplast ribosomal intron of Chlamydomonas reinhardii codes for a polypeptide related to mitochondrial maturases.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 975
EP  - 984
VL  - 13
AB  - The sequences of the 888bp chloroplast ribosomal intron and of the flanking 23S rRNA gene
AB  - regions of Chlamydomonas reinhardii have been established. The intron can be folded with a
AB  - secondary structure which is typical of group I introns of fungal mitochondrial genes. It
AB  - contains a 489bp open reading frame encoding a potential polypeptide that is related to
AB  - mitochondrial maturases.
ER  -

TY  - JOUR
AU  - Rochat, T.
AU  - Barbier, P.
AU  - Nicolas, P.
AU  - Loux, V.
AU  - Perez-Pascual, D.
AU  - Guijarro, J.A.
AU  - Bernardet, J.F.
AU  - Duchaud, E.
TI  - Complete Genome Sequence of Flavobacteriumpsychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis.
JO  - Genome Announcements
PY  - 2017
SP  - e01665
EP  - e01616
VL  - 5
AB  - We report here the complete annotated genome sequence of Flavobacterium psychrophilum OSU
AB  - THCO2-90, isolated from Coho salmon (Oncorhynchus kisutch) in
AB  - Oregon. The genome consists of a circular chromosome with 2,343 predicted open
AB  - reading frames. This strain has proved to be a valuable tool for functional
AB  - genomics.
ER  -

TY  - JOUR
AU  - Rochefort, A.
AU  - Boukthir, S.
AU  - Moullec, S.
AU  - Meygret, A.
AU  - Adnani, Y.
AU  - Lavenier, D.
AU  - Faili, A.
AU  - Kayal, S.
TI  - Full Sequencing and Genomic Analysis of Three emm75 Group A Streptococcus Strains Recovered in the Course of an Epidemiological Shift in French Brittany.
JO  - Genome Announcements
PY  - 2017
SP  - e00957
EP  - e00917
VL  - 5
AB  - While the incidence and invasiveness of type emm75 group A Streptococcus (GAS) infections
AB  - increased in French Brittany during 2013, we sequenced and analyzed
AB  - the genomes of three independent strains isolated in 2009, 2012, and 2014,
AB  - respectively. In this short-term evolution, genomic analysis evidenced mainly the
AB  - integration of new phages encoding virulence factors.
ER  -

TY  - JOUR
AU  - Rochepeau, P.
AU  - Selinger, L.B.
AU  - Hynes, M.F.
TI  - Transposon-like structure of a new plasmid-encoded restriction-modification system in Rhizobium leguminosarum VF39SM.
JO  - Mol. Gen. Genet.
PY  - 1997
SP  - 387
EP  - 396
VL  - 256
AB  - Total DNA isolated from Rhizobium leguminosarum VF39SM cells is resistant to cleavage by the
AB  - restriction endonuclease PstI.  Plasmid curing and transfer studies localized this phenotype
AB  - to pRleVF39b, the second smallest of six plasmids found in this bacterium.  In vitro selection
AB  - for vector modification was employed to isolate a presumptive methylase gene (M.Rle39BI) from
AB  - a plasmid gene library.  Total and plasmid DNAs isolated from E. coli containing M.RleBI were
AB  - resistant to digestion by PstI.  Sequence data suggested that a putative restriction
AB  - endonuclease (R.Rle39BI) was also encoded on the same fragment.  The two genes were flanked by
AB  - identical copies of a putative insertion sequence, which was also present in several copies
AB  - elsewhere in the VF39SM genome.  The presence of this element in other strains examined
AB  - suggested that this element is indeed an insertion sequence.  The differences in G/C content
AB  - between the DNA coding for the R/M system and that of the IS element suggest that this DNA
AB  - region may have been acquired by horizontal transfer.
ER  -

TY  - JOUR
AU  - Rockah-Shmuel, L.
AU  - Tawfik, D.S.
TI  - Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 11627
EP  - 11637
VL  - 40
AB  - DNA-binding and modifying proteins show high specificity but also exhibit a certain level of
AB  - promiscuity. Such latent promiscuous activities comprise the
AB  - starting points for new protein functions, but this hypothesis presents a
AB  - paradox: a new activity can only evolve if it already exists. How then, do novel
AB  - activities evolve? DNA methyltransferases, for example, are highly divergent in
AB  - their target sites, but how transitions toward novel sites occur remains unknown.
AB  - We performed laboratory evolution of the DNA methyltransferase M.HaeIII. We found
AB  - that new target sites emerged primarily through expansion of the original site,
AB  - GGCC, and the subsequent shrinkage of evolved expanded sites. Variants evolved
AB  - for sites that are promiscuously methylated by M.HaeIII [GG((A)/(T))CC and
AB  - GGCGCC] carried mutations in 'gate-keeper' residues. They could thereby methylate
AB  - novel target sites such as GCGC and GGATCC that were neither selected for nor
AB  - present in M.HaeIII. These 'generalist' intermediates were further evolved to
AB  - obtain variants with novel target specificities. Our results demonstrate the ease
AB  - by which new DNA-binding and modifying specificities evolve and the mechanism by
AB  - which they occur at both the protein and DNA levels.
ER  -

TY  - JOUR
AU  - Rockah-Shmuel, L.
AU  - Toth-Petroczy, A.
AU  - Tawfik, D.S.
TI  - Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.
JO  - PLOS Comp. Biol.
PY  - 2015
SP  - e1004421
EP  - e1004421
VL  - 11
AB  - Systematic mappings of the effects of protein mutations are becoming increasingly popular.
AB  - Unexpectedly, these experiments often find that proteins are tolerant to
AB  - most amino acid substitutions, including substitutions in positions that are
AB  - highly conserved in nature. To obtain a more realistic distribution of the
AB  - effects of protein mutations, we applied a laboratory drift comprising 17 rounds
AB  - of random mutagenesis and selection of M.HaeIII, a DNA methyltransferase. During
AB  - this drift, multiple mutations gradually accumulated. Deep sequencing of the
AB  - drifted gene ensembles allowed determination of the relative effects of all
AB  - possible single nucleotide mutations. Despite being averaged across many
AB  - different genetic backgrounds, about 67% of all nonsynonymous, missense mutations
AB  - were evidently deleterious, and an additional 16% were likely to be deleterious.
AB  - In the early generations, the frequency of most deleterious mutations remained
AB  - high. However, by the 17th generation, their frequency was consistently reduced,
AB  - and those remaining were accepted alongside compensatory mutations. The tolerance
AB  - to mutations measured in this laboratory drift correlated with sequence exchanges
AB  - seen in M.HaeIII's natural orthologs. The biophysical constraints dictating
AB  - purging in nature and in this laboratory drift also seemed to overlap. Our
AB  - experiment therefore provides an improved method for measuring the effects of
AB  - protein mutations that more closely replicates the natural evolutionary forces,
AB  - and thereby a more realistic view of the mutational space of proteins.
ER  -

TY  - JOUR
AU  - Roddy, E.S.
AU  - Price, M.
AU  - Ewing, A.G.
TI  - Continuous monitoring of a restriction enzyme digest of DNA on a microchip with automated capillary sample introduction.
JO  - Anal. Chem.
PY  - 2003
SP  - 3704
EP  - 3711
VL  - 75
AB  - Continuous analysis of a DNA restriction enzyme digest on a microfabricated device is
AB  - demonstrated with minimal intervention and
AB  - enhanced time resolution. A 62-base-pair fragment of dsDNA containing a
AB  - KpnI site was used to demonstrate this process. A capillary was used to
AB  - transfer sample from a single reaction mix to a microfabricated chip with
AB  - parallel separation lanes. The 6-carboxyfluorescein-labeled DNA fragments
AB  - were detected with a CCD camera as they separated in the lanes, which were
AB  - filled with linear polyacrylamide. The products of the restriction enzyme
AB  - digest were monitored for up to 60 min at an average sampling rate of 1
AB  - injection/46 s, with consecutive injections as short as 1 injection/14 s.
AB  - The digest was injected directly into the chip, eliminating the need for
AB  - any sample-handling steps after addition of the enzyme to the reaction
AB  - mix. The effects of temperature and restriction enzyme concentration were
AB  - briefly examined, as well. This work shows the potential of this method to
AB  - provide valuable information about the process of restriction enzyme
AB  - cleavage.
ER  -

TY  - JOUR
AU  - Rodicio, M.R.
AU  - Alvarez, M.A.
AU  - Chater, K.F.
TI  - Isolation and genetic structure of IS112, an insertion sequence responsible for the inactivation of the SalI restriction-modification system of Streptomyces albus G.
JO  - Mol. Gen. Genet.
PY  - 1991
SP  - 142
EP  - 147
VL  - 225
AB  - IS112 is a transposable element identified in Streptomyces albus G by its
AB  - frequent mutagenic insertion into the genes for the SalI
AB  - restriction-modification system.  IS112 is present in several copies in the
AB  - genome of S. albus G.  Homologous sequences were detected in other Streptomyces
AB  - strains.  Sequence analysis revealed that IS112 has a length of 883 bp with a
AB  - GC content of 67.4%.  The copy that was isolated contained imperfect inverted
AB  - repeats (16/20 match) at its ends and was flanked by a 2 bp duplication at the
AB  - target site, which was located within the gene (salIR) for the SalI
AB  - endonuclease.  A long open reading frame (ORF) encoding a putative polypeptide
AB  - of 256-253 amino acids spans almost the entire sequence.  Significant homology
AB  - was detected between this polypeptide and that corresponding to ORFB of IS493,
AB  - an insertion sequence recently isolated from Streptomyces lividans 66.
ER  -

TY  - JOUR
AU  - Rodicio, M.R.
AU  - Chater, K.F.
TI  - Cloning and expression of the SalI restriction-modification genes of Streptomyces albus G.
JO  - Mol. Gen. Genet.
PY  - 1988
SP  - 346
EP  - 353
VL  - 213
AB  - The Streptomyces albus G genes (salR and salM) for the class II restriction
AB  - enzyme SalI (SalGI) and its cognate modification enzyme were cloned in
AB  - Streptomyces lividans 66.  Selection was initially for the salR gene.  From a
AB  - library of S. albus G DNA in the high copy number plasmid pIJ486 several clones
AB  - of S. lividans were obtained that were resistant to phage PhiC31 unmodified at
AB  - the many SalI sites in its DNA, but were sensitive to modified phages last
AB  - propagated on a restriction-deficient, modification- proficient mutant of S.
AB  - albus G.  SalI activity was detected in cell-free extracts of the clones,
AB  - though only at levels comparable with that in S. albus G.  Five different
AB  - recombinant plasmids were isolated, with inserts of 5.6, 5.7, 8.9, 10 and 18.9
AB  - kb that contained a common region of 4.5 kb.  These plasmids could not be
AB  - digested by SalI, although the vector has four recognition sites for this
AB  - enzyme, indicating that the salM gene was also cloned and expressed.
AB  - Subcloning experiments in S. lividans indicated the approximate location of
AB  - salR and salM, and in Escherichia coli led to detectable expression of salM but
AB  - not of salR.  A variety of previously isolated S. albus G mutants affected in
AB  - aspects of SalI-specific restriction and modification were complemented by the
AB  - cloned DNA; they included a mutant temperature-sensitive for growth apparently
AB  - because of a mutation in salM.  Southern blotting showed that DNA homologous to
AB  - the cloned sal genes was present in Xanthomonas and Rhodococcus strains, but
AB  - not detectably in Herpetosiphon strains, all of which produce SalI
AB  - isoschizomers.
ER  -

TY  - JOUR
AU  - Rodicio, M.R.
AU  - Chater, K.F.
TI  - The SalI (SalGI) restriction-modification system of Streptomyces albus G.
JO  - Gene
PY  - 1988
SP  - 39
EP  - 42
VL  - 74
AB  - The salIR and salM genes of Streptomyces albus G specify the SalGI (SalI)
AB  - restriction enzyme and its cognate methyltransferase, respectively.  These
AB  - enzymes are responsible for restriction and modification of bacteriophages.
AB  - Some phages carry genes that interfere with SalI-specific modification.  The
AB  - sal genes have been cloned in a Streptomyces host-vector system.  Use of the
AB  - cloned DNA as a hybridization probe reveals that sal mutants frequently arise
AB  - from transposition of a DNA segment of approx. 1 kb into the sal genes.  Some,
AB  - but not all, other bacteria that produce SalGI isoschizomers contain nucleotide
AB  - sequences that hybridize with sal DNA.
ER  -

TY  - JOUR
AU  - Rodicio, M.R.
AU  - Quinton-Jager, T.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Wilson, G.G.
TI  - Organization and sequence of the SalI restriction-modification system.
JO  - Gene
PY  - 1994
SP  - 167
EP  - 172
VL  - 151
AB  - The organization and nucleotide (nt) sequences were determined for the genes encoding the SalI
AB  - restriction and modification (R-M) system (recognition sequence 5'-GTCGAC-3') from
AB  - Streptomyces albus G. The system comprises two genes, salIR, coding for the restriction
AB  - endonuclease (ENase, R.SalI; probably 315 amino acids (aa), a predicted Mr of 35,305; product,
AB  - GTCGAC) and salIM, coding for the methyltransferase (MTase, M.SalI; probably 587 aa, a
AB  - predicted Mr of 64,943; product, GRCGm6AC). The genes are adjacent, they have the same
AB  - orientation, and they occur in the order salIR then SalIM. R.SalI contains a putative
AB  - magnesium-binding motif similar to those at the active sites of R.EcoRI and R.EcoRV, but
AB  - otherwise it bears little aa sequence similarity to other ENases. M.SalI is a member of the
AB  - m6A-gamma class of MTases. In aa sequence it resembles M.AccI, another m5A-gamma-MTase whose
AB  - recognition sequence includes the SalI recognition sequence as a subset.
ER  -

TY  - JOUR
AU  - Rodrigues, C.
AU  - Kapil, A.
AU  - Sharma, A.
AU  - Devanga, R.N.K.
AU  - Inbanathan, F.Y.
AU  - Veeraraghavan, B.
AU  - Kang, G.
TI  - Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Salmonella enterica Serovar Typhi.
JO  - Genome Announcements
PY  - 2017
SP  - e01639
EP  - e01616
VL  - 5
AB  - Typhoid is one of the leading causes of mortality in developing countries. Here,  we report
AB  - the draft genome sequences of four Salmonella enterica serovar Typhi
AB  - strains isolated from bloodstream infections in a tertiary care hospital. The
AB  - sequence data indicate genomes of ~4.5 Mb for all isolates, with one plasmid in
AB  - each.
ER  -

TY  - JOUR
AU  - Rodrigues, E.M.
AU  - Pylro, V.S.
AU  - Dobbler, P.T.
AU  - Victoria, F.
AU  - Roesch, L.F.
AU  - Totola, M.R.
TI  - Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01707
EP  - e01715
VL  - 4
AB  - Here, we present a draft genome and annotation of Rhodococcus rhodochrous TRN7, isolated from
AB  - Trindade Island, Brazil, which will provide genetic data to benefit
AB  - the understanding of its metabolism.
ER  -

TY  - JOUR
AU  - Rodrigues, G.N.
AU  - Lago-Leston, A.
AU  - Costa, R.
AU  - Keller-Costa, T.
TI  - Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong  Halogen Degradation Potential.
JO  - Genome Announcements
PY  - 2018
SP  - e00132
EP  - e00118
VL  - 6
AB  - We report here the genome sequence of Labrenzia sp. EL143, an alphaproteobacterium isolated
AB  - from the gorgonian coral Eunicella labiata that
AB  - possesses various genes involved in halogen and aromatic compound degradation, as
AB  - well as polyketide synthesis. The strain also maintains multiple genes that
AB  - confer resistance to toxic compounds such as heavy metals and antibiotics.
ER  -

TY  - JOUR
AU  - Rodriguez, A.
AU  - Lleonart, R.
AU  - Martinez, A.S.
AU  - Ryes, G.
AU  - Gonzalez, E.
AU  - Brito, J.E.
TI  - Cloning and expression of genes coding for Haemophilus influenzae Rf restriction and modification enzymes.  Purification of the recombinant endonuclease.
JO  - Biotecnol. Apl.
PY  - 1995
SP  - 156
EP  - 159
VL  - 12
AB  - The genes coding for HinfI restriction and modification enzymes were cloned from the
AB  - Haemophilus influenzae Rf strain using pUC18 plasmid as vector.  To select the genes from the
AB  - library, the classical modification phenotype selection was used.  When introduced into
AB  - Escherichia coli HB101 strain, the recombinant plasmid pERHinf4 was able to direct the
AB  - expression of the restriction phenotype.  The crude extracts from the transformed E. coli
AB  - contained roughly twice the amount of restrictase expressed by the natural source.  A
AB  - purification procedure for the restrictase is described which when applied to the recombinant
AB  - enzyme, renders a preparation free of contaminant exonucleases and phosphatases.  The overall
AB  - recovery of the purification procedure was about 33% of the total activity.
ER  -

TY  - JOUR
AU  - Rodriguez, J.G.
AU  - Pino, C.
AU  - Tauch, A.
AU  - Murcia, M.I.
TI  - Complete Genome Sequence of the Clinical Beijing-Like Strain Mycobacterium tuberculosis 323 Using the PacBio Real-Time Sequencing Platform.
JO  - Genome Announcements
PY  - 2015
SP  - e00371
EP  - e00315
VL  - 3
AB  - We report here the whole-genome sequence of the multidrug-resistant Beijing-like  strain
AB  - Mycobacterium tuberculosis 323, isolated from a 15-year-old female patient
AB  - who died shortly after the initiation of second-line drug treatment. This strain
AB  - is representative of the Beijing-like isolates from Colombia, where this lineage
AB  - is becoming a public health concern.
ER  -

TY  - JOUR
AU  - Rodriguez, R.J.
TI  - Polyphosphate present in DNA preparations from Filamentous fungal species of Colletotrichum inhibits restriction endonucleases and other enzymes.
JO  - Anal. Biochem.
PY  - 1993
SP  - 291
EP  - 297
VL  - 209
AB  - During the development of a procedure for the isolation of total genomic DNA from filamentous
AB  - fungi (Rodriguez, R.J., and Yoder, O.C., Exp. Myco. 15, 232-242, 1991) a cell fraction was
AB  - isolated which inhibited the digestion of DNA by restriction enzymes. After elimination of
AB  - DNA, RNA, proteins, and lipids, the active compund was purified by gel filtration to yield a
AB  - single fraction capable of complete inhibition of restriction enzyme activity. The inhibitor
AB  - did not absorb uv light above 220 nm, and was resistant to alkali and acid at 25 degrees C and
AB  - to temperatures as high as 100 degrees C. More extensive analyses demonstrated that the
AB  - inhibitor was also capable of inhibiting T4 DNA ligase and TaqI DNA polymerase, but not DNase
AB  - or RNase. Chemical analyses indicated that the inhibitor was devoid of carbohydrates, protein,
AB  - lipids and nucleic acids but rich in phosphorus. A combination of nuclear magnetic resonance,
AB  - metachromatic shift of toluidine blue, and gel filtration indicated that the inhibitor was a
AB  - polyphosphate (polyP) containing approximately 60 phosphate molecules. The mechanism of
AB  - inhibition appeared to involve complexing of polyP to the enzymatic proteins. All species of
AB  - Colletotrichum analyzed produced polyP equivalent in chain length and concentration. A
AB  - modification to the original DNA extraction procedure is described which eliminates polyP and
AB  - reduces the time necessary to obtain DNA of sufficient purity for restriction enzyme digestion
AB  - and TaqI polymerase amplification.
ER  -

TY  - JOUR
AU  - Rodriguez-Osorio, N.
AU  - Wang, H.F.
AU  - Rupinski, J.
AU  - Bridges, S.M.
AU  - Memili, E.
TI  - Comparative functional genomics of mammalian DNA methyltransferases.
JO  - Reprod. Biomed. Online
PY  - 2010
SP  - 243
EP  - 255
VL  - 20
AB  - DNA methylation involves biochemical modification of DNA by addition of methyl groups onto CpG
AB  - dinucleotides, and this epigenetic mechanism
AB  - regulates gene expression in disease and development. Mammalian DNA
AB  - methyltransferases, DNMT (DNMT1, DNMT3A and DNMT3B), together with the
AB  - accessory protein DNMT3L establish specific DNA methylation patterns in
AB  - the genome during gametogenesis, embryogenesis and somatic tissue
AB  - development. The present study addresses the structural and functional
AB  - conservation of the DNMT in humans, mice and cattle and the patterns of
AB  - mRNA abundance of the different enzymes during embryogenesis to improve
AB  - understanding of epigenetic regulation in early development. The
AB  - findings showed a high degree of structural and functional conservation
AB  - among the human, mouse, and bovine DNMT. The results also showed
AB  - similar patterns of transcript abundance for all of the proteins at
AB  - different stages of early embryo development. Remarkably, all of the
AB  - DNMT with an important role in DNA methylation (DNMT1, DNMT3A, DNMT3B,
AB  - and DNMT3L) show a greater degree of structural similarity between
AB  - human and bovine than that between human and mouse. These results have
AB  - important implications for the selection of an appropriate model for
AB  - study of DNA methylation during early development in humans.
ER  -

TY  - JOUR
AU  - Rodriguez-Palenzuela, P. et al.
TI  - Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts.
JO  - Environ. Microbiol.
PY  - 2010
SP  - 1604
EP  - 1620
VL  - 12
AB  - Pseudomonas savastanoi pv. savastanoi is a tumour-inducing pathogen of Olea
AB  - europaea L. causing olive knot disease. Bioinformatic analysis of the draft
AB  - genome sequence of strain NCPPB 3335, which encodes 5232 predicted coding genes
AB  - on a total length of 5856 998 bp and a 57.12% G + C, revealed a large degree of
AB  - conservation with Pseudomonas syringae pv. phaseolicola 1448A and P. syringae pv.
AB  - tabaci 11528. However, NCPPB 3335 contains twelve variable genomic regions, which
AB  - are absent in all previously sequenced P. syringae strains. Various features that
AB  - could contribute to the ability of this strain to survive in a woody host were
AB  - identified, including broad catabolic and transport capabilities for degrading
AB  - plant-derived aromatic compounds, the duplication of sequences related to the
AB  - biosynthesis of the phytohormone indoleacetic acid (iaaM, iaaH) and its amino
AB  - acid conjugate indoleacetic acid-lysine (iaaL gene), and the repertoire of
AB  - strain-specific putative type III secretion system effectors. Access to this
AB  - seventh genome sequence belonging to the 'P. syringae complex' allowed us to
AB  - identify 73 predicted coding genes that are NCPPB 3335-specific. Results shown
AB  - here provide the basis for detailed functional analysis of a tumour-inducing
AB  - pathogen of woody hosts and for the study of specific adaptations of a P.
AB  - savastanoi pathovar.
ER  -

TY  - JOUR
AU  - Roer, L.
AU  - Aarestrup, F.M.
AU  - Hasman, H.
TI  - EcoKI Type I Restriction-Modification System in Escherichia coli Affect, but is Not an Absolute Barrier for, Conjugation.
JO  - J. Bacteriol.
PY  - 2014
SP  - 337
EP  - 342
VL  - 197
AB  - The rapid evolution of bacteria is crucial to their survival, and is among other  things
AB  - caused by exchange, transfer and uptake of DNA. Conjugation is one of the
AB  - main mechanisms by which bacteria share their DNA, and is thought to be
AB  - controlled by varied bacterial immune systems. Contradictory results, based on
AB  - phenotypical studies, have been presented on Restriction-Modification systems as
AB  - a barrier for conjugation and other means of uptake of exogenous DNA. In this
AB  - study, we show that inactivation of the R.EcoKI restriction enzyme in strain
AB  - Escherichia coli K-12 strain MG1655 increases the conjugational transfer of
AB  - plasmid pOLA52, which carriers two EcoKI recognition sites. Interestingly, the
AB  - results were not absolute, and uptake of un-methylated pOLA52 was still observed
AB  - in the wild-type strain (with intact hsdR gene), but with a reduction of 85%
AB  - compared to the mutant recipient having a disrupted hsdR gene. This leads to the
AB  - conclusion that EcoKI Restriction-Modification affects the uptake of DNA by
AB  - conjugation, but is not a major barrier for plasmid transfer.
ER  -

TY  - JOUR
AU  - Roer, L.
AU  - Hendriksen, R.S.
AU  - Leekitcharoenphon, P.
AU  - Lukjancenko, O.
AU  - Kaas, R.S.
AU  - Hasman, H.
AU  - Aarestrup, F.M.
TI  - Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?
JO  - mSystems
PY  - 2016
SP  - e00009
EP  - e00016
VL  - 1
AB  - Salmonella enterica subsp. enterica bacteria are highly diverse foodborne pathogens that are
AB  - subdivided into more than 1,500 serovars. The diversity is
AB  - believed to result from mutational evolution, as well as intra- and interspecies
AB  - recombination that potentially could be influenced by restriction-modification
AB  - (RM) systems. The aim of this study was to investigate whether RM systems were
AB  - linked to the evolution of Salmonella enterica subsp. enterica. The study
AB  - included 221 Salmonella enterica genomes, of which 68 were de novo sequenced and
AB  - 153 were public available genomes from ENA. The data set covered 97 different
AB  - serovars of Salmonella enterica subsp. enterica and an additional five genomes
AB  - from four other Salmonella subspecies as an outgroup for constructing the
AB  - phylogenetic trees. The phylogenetic trees were constructed based on multiple
AB  - alignment of core genes, as well as the presence or absence of pangenes. The
AB  - topology of the trees was compared to the presence of RM systems, antimicrobial
AB  - resistance (AMR) genes, Salmonella pathogenicity islands (SPIs), and plasmid
AB  - replicons. We did not observe any correlation between evolution and the RM
AB  - systems in S. enterica subsp. enterica. However, sublineage correlations and
AB  - serovar-specific patterns were observed. Additionally, we conclude that plasmid
AB  - replicons, SPIs, and AMR were all better correlated to serovars than to RM
AB  - systems. This study suggests a limited influence of RM systems on the evolution
AB  - of Salmonella enterica subsp. enterica, which could be due to the conjugational
AB  - mode of horizontal gene transfer in Salmonella. Thus, we conclude that other
AB  - factors must be involved in shaping the evolution of bacteria. IMPORTANCE The
AB  - evolution of bacterial pathogens, their plasticity and ability to rapidly change
AB  - and adapt to new surroundings are crucial for understanding the epidemiology and
AB  - public health. With the application of genomics, it became clear that horizontal
AB  - gene transfer played a key role in evolution. To understand the evolution and
AB  - diversification of pathogens, we need to understand the processes that drive the
AB  - horizontal gene transfer. Restriction-modification systems are thought to cause
AB  - rearrangements within the chromosome, as well as act as a barrier to horizontal
AB  - gene transfer. However, here we show that the correlation between
AB  - restriction-modification systems and evolution in other bacterial species does
AB  - not apply to Salmonella enterica subsp. enterica. In summary, from this work, we
AB  - conclude that other mechanisms might be involved in controlling and shaping the
AB  - evolution of Salmonella enterica subsp. enterica.
ER  -

TY  - JOUR
AU  - Rogel-Hernandez, M.A.
AU  - Guerrero, G.
AU  - Rincon-Molina, C.I.
AU  - Ruiz-Valdiviezo, V.M.
AU  - Cisneros-Perez, C.
AU  - Castanon-Gonzalez, J.H.
AU  - Lopez-Lopez, A.
AU  - Martinez-Romero, E.
AU  - Rincon-Rosales, R.
TI  - Genome Sequence of Acinetobacter lactucae OTEC-02, Isolated from Hydrocarbon-Contaminated Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00400
EP  - e00417
VL  - 5
AB  - Acinetobacter lactucae OTEC-02 was isolated from hydrocarbon-contaminated soils.  Whole-genome
AB  - sequence analysis was performed to learn more about the strain's
AB  - ability to degrade different types of recalcitrant toxic monoaromatic
AB  - hydrocarbons. The genome of this bacterium revealed its genomic properties and
AB  - versatile metabolic features, as well as a complete prophage.
ER  -

TY  - JOUR
AU  - Rogulin, E.A.
AU  - Perevyazova, T.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Plasmid pRARE as a vector for cloning to construct a superproducer of the site-specific nickase N.BspD6I.
JO  - Biokhimiia
PY  - 2004
SP  - 1123
EP  - 1127
VL  - 69
AB  - The gene of methylase M.SccL1I that protects DNA against hydrolysis with the nickase N.BspD6I
AB  - was inserted into plasmid pRARE carrying
AB  - genes of tRNA, which are rare in E. coli. The insertion of the gene
AB  - sscML1I into pRARE was reasoned by incompatibility of pRARE and the
AB  - plasmid carrying the gene sscML1I, because both plasmids contained the
AB  - same ori-site. Upon transformation of E. coli TOP10F' cells with both
AB  - the recombinant plasmid pRARE/MSsc and the expression vector pET28b
AB  - containing the nickase gene bspD6IN under the phage T7 promoter, a
AB  - strain of E. coli was obtained which produced 7(.)10(5) units of the
AB  - nickase N.BspD6I per 1 g wet biomass, and this yield was two orders of
AB  - magnitude higher than the yield of the enzyme from the strain free of
AB  - pRARE/MSsc.
ER  -

TY  - JOUR
AU  - Roh, H.
AU  - Ko, H.J.
AU  - Kim, D.
AU  - Choi, D.G.
AU  - Park, S.
AU  - Kim, S.
AU  - Chang, I.S.
AU  - Choi, I.G.
TI  - Complete Genome Sequencing of A Carbon Monooxide Utilizing Acetogen, Eubacterium limosum KIST612.
JO  - J. Bacteriol.
PY  - 2010
SP  - 307
EP  - 308
VL  - 193
AB  - Eubacterium limosum KIST612 is an anaerobic acetogenic bacterium that uses CO as a sole
AB  - carbon/energy source and produces acetate, butyrate and
AB  - ethanol. To evaluate its potential as a syngas microbial catalyst, we have
AB  - sequenced the complete 4.3 Mb genome of E. limosum KIST612.
ER  -

TY  - JOUR
AU  - Roh, H.
AU  - Uguru, G.C.
AU  - Ko, H.J.
AU  - Kim, S.
AU  - Kim, B.Y.
AU  - Goodfellow, M.
AU  - Bull, A.T.
AU  - Kim, K.H.
AU  - Bibb, M.J.
AU  - Choi, I.G.
AU  - Stach, J.E.
TI  - Genome Sequence of the Abyssomicin- and Proximicin-Producing Marine Actinomycete Verrucosispora maris AB-18-032.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3391
EP  - 3392
VL  - 193
AB  - Verrucosispora maris AB-18-032 is a marine actinomycete that produces atrop-abyssomicin C and
AB  - proximicin A, both of which have novel structures
AB  - and modes of action. In order to understand the biosynthesis of these
AB  - compounds, to identify further biosynthetic potential and to facilitate
AB  - rational improvement of secondary metabolite titers, we have sequenced the
AB  - complete 6.7 Mb genome of Verrucosispora maris AB-18-032.
ER  -

TY  - JOUR
AU  - Roh, H.
AU  - Yun, E.J.
AU  - Lee, S.
AU  - Ko, H.J.
AU  - Kim, S.
AU  - Kim, B.Y.
AU  - Song, H.
AU  - Lim, K.I.
AU  - Kim, K.H.
AU  - Choi, I.G.
TI  - Genome Sequence of Vibrio sp. Strain EJY3, an Agarolytic Marine Bacterium Metabolizing 3,6-Anhydro-L-Galactose as a Sole Carbon Source.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2773
EP  - 2774
VL  - 194
AB  - The metabolic fate of 3,6-anhydro-l-galactose (l-AHG) is unknown in the global marine carbon
AB  - cycle. Vibrio sp. strain EJY3 is an agarolytic marine bacterium
AB  - that can utilize l-AHG as a sole carbon source. To elucidate the metabolic
AB  - pathways of l-AHG, we have sequenced the complete genome of Vibrio sp. strain
AB  - EJY3.
ER  -

TY  - JOUR
AU  - Roh, S.W.
AU  - Nam, Y.D.
AU  - Nam, S.H.
AU  - Choi, S.H.
AU  - Park, H.S.
AU  - Bae, J.W.
TI  - Complete Genome Sequence of Halalkalicoccus jeotgali B3T, an Extremely Halophilic Archaeon.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4528
EP  - 4529
VL  - 192
AB  - Halalkalicoccus jeotgali B3(T), isolated from salt-fermented seafood from Korea, is an
AB  - extremely halophilic archaeon belonging to the family
AB  - Halobacteriaceae. Here, we present the complete genome sequence of the
AB  - type strain Hac. jeotgali B3(T) (3,698,650 bp, with a G+C content of
AB  - 62.5%), which consists of one chromosome and six plasmids. This is the
AB  - first complete genome sequence of the Halalkalicoccus species.
ER  -

TY  - JOUR
AU  - Rohit, A.
AU  - Kumar, B.K.
AU  - Deekshit, V.K.
AU  - Rai, P.
AU  - Kumar, R.V.
AU  - Jayaprakash, J.
AU  - Madhushankara, B.
AU  - Karunasagar, I.
AU  - Karunasagar, I.
TI  - Draft Genome Sequence of Campylobacter fetus MMM01, Isolated from a Chronic Kidney Disease Patient with Sepsis.
JO  - Genome Announcements
PY  - 2015
SP  - e01055
EP  - e01015
VL  - 3
AB  - Campylobacter fetus is a Gram-negative bacterium that has caused several cases of human and
AB  - animal disease. Here, we report the draft genome sequence of C. fetus MMM01, isolated from the
AB  - blood of a 60-year-old patient with type II diabetes and chronic kidney disease. The sequence
AB  - has a total length of 1,740,393 bp and an average G+C content of 33.1%. The availability of
AB  - the draft genome sequence of C. fetus MMM01 isolated from a case of chronic kidney disease
AB  - will contribute to a better understanding of the pathophysiological mechanisms of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Rohmer, L.
AU  - Brittnacher, M.
AU  - Svensson, K.
AU  - Buckley, D.
AU  - Haugen, E.
AU  - Zhou, Y.
AU  - Chang, J.
AU  - Levy, R.
AU  - Hayden, H.
AU  - Forsman, M.
AU  - Olson, M.
AU  - Johansson, A.
AU  - Kaul, R.
AU  - Miller, S.I.
TI  - Potential source of Francisella tularensis live vaccine strain attenuation determined by genome comparison.
JO  - Infect. Immun.
PY  - 2006
SP  - 6895
EP  - 6906
VL  - 74
AB  - Francisella tularensis is a bacterial pathogen that causes the zoonotic
AB  - disease tularemia and is important to biodefense. Currently, the only
AB  - vaccine known to confer protection against tularemia is a specific live
AB  - vaccine strain (designated LVS) derived from a virulent isolate of
AB  - Francisella tularensis subsp. holarctica. The origin and source of
AB  - attenuation of this strain are not known. To assist with the design of a
AB  - defined live vaccine strain, we sought to determine the genetic basis of
AB  - the attenuation of LVS. This analysis relied primarily on the comparison
AB  - between the genome of LVS and Francisella tularensis holarctica strain
AB  - FSC200, which differ by only 0.08% of their nucleotide sequences. Under
AB  - the assumption that the attenuation was due to a loss of function(s), only
AB  - coding regions were examined in this comparison. To complement this
AB  - analysis, the coding regions of two slightly more distantly related
AB  - Francisella tularensis strains were also compared against the LVS coding
AB  - regions. Thirty-five genes show unique sequence variations predicted to
AB  - alter the protein sequence in LVS compared to the other Francisella
AB  - tularensis strains. Due to these polymorphisms, the functions of 15 of
AB  - these genes are very likely lost or impaired. Seven of these genes were
AB  - demonstrated to be under stronger selective constraints, suggesting that
AB  - they are the most probable to be the source of LVS attenuation and useful
AB  - for a newly defined vaccine.
ER  -

TY  - JOUR
AU  - Roizes, G.
AU  - Charlieu, J.-P.
AU  - Marcais, B.
AU  - Bellis, M.
TI  - Use of the DNA fragments generated by a restriction enzyme (Bcg I) for the construction of overlapping clone libraries.
JO  - DNA Seq.
PY  - 1991
SP  - 65
EP  - 67
VL  - 2
AB  - The human genome contains at intervals the sequence recognized by the
AB  - restriction endonuclease BcgI.  We propose to take advantage of the presence of
AB  - this sequence for the construction of overlapping clone libraries.  The
AB  - proposal holds for any other genome in which there are similar projects of
AB  - physical mapping and sequencing.
ER  -

TY  - JOUR
AU  - Roizes, G.
AU  - Nardeux, P.C.
AU  - Monier, R.
TI  - A new specific endonuclease from Anabaena variabilis.
JO  - FEBS Lett.
PY  - 1979
SP  - 39
EP  - 44
VL  - 104
AB  - A large number of site-specific endonucleases have been isolated from Anabaena
AB  - variabilis and we now describe a third from this organism, AvaIII, which cuts
AB  - SV40 DNA three times.  From the positions of these breaks on the physical map
AB  - of SV40, the DNA sequence recognised by the enzyme can be deduced.  It has not
AB  - yet been possible to separate this enzyme from AvaI.
ER  -

TY  - JOUR
AU  - Roizes, G.
AU  - Pages, M.
AU  - Lecou, C.
AU  - Patillon, M.
AU  - Kovoor, A.
TI  - A new site-specific endonuclease showing phenotypical crypticity in a tumorigenic strain of Agrobacterium tumefaciens.
JO  - Gene
PY  - 1979
SP  - 43
EP  - 50
VL  - 6
AB  - AtuBVI, an endonuclease showing new site-specificity, has been isolated from
AB  - the tumorigenic strain IIBV7 of Agrobacterium tumefaciens, and is undetectable
AB  - in the non-tumorigenic sister strain IIBNV6.  AtuBVI degrades IIBV7 DNA in
AB  - vitro and should, therefore, be regarded as being phenotypically cryptic in the
AB  - bacterial cell; it also shows anomalous behavior under certain incubation
AB  - conditions.  These properties point to a possible role for this enzyme in the
AB  - insertion of exogenous Ti-plasmid DNA into plant tissues during tumorigenesis.
ER  -

TY  - JOUR
AU  - Roizes, G.
AU  - Patillon, M.
AU  - Kovoor, A.
TI  - A restriction endonuclease from Agrobacterium tumefaciens.
JO  - FEBS Lett.
PY  - 1977
SP  - 69
EP  - 70
VL  - 82
AB  - The tumorous growth of plant tissues known as Crowngall is induced by certain
AB  - strains of Agrobacterium tumefaciens (Smith and Townsend, Conn.) and there is
AB  - considerable evidence that foreign DNA is integrated in the genome of the
AB  - transformed host cell.  A specific endonuclease of the bacterium could then
AB  - conceivably play a role in the insertion process.  In this letter we describe
AB  - the isolation of a sequence-specific endonuclease from a tumorigenic strain,
AB  - B6, of Agrobacterium tumefaciens.  The recognition site as well as the
AB  - modification specificity of this enzyme, named AtuI, are shown to be identical
AB  - to those of a known restriction enzyme, EcoRI.
ER  -

TY  - JOUR
AU  - Rojas, J.D.
AU  - Starcevic, A.
AU  - Baranasic, D.
AU  - Ferreira-Torres, M.A.
AU  - Contreras, C.A.
AU  - Garrido, L.M.
AU  - Araujo, W.L.
AU  - de Souza, R.F.
AU  - Zucko, J.
AU  - Hranueli, D.
AU  - Long, P.F.
AU  - Cullum, J.
AU  - Padilla, G.
TI  - Genome Sequence of Streptomyces olindensis DAUFPE 5622, Producer of the Antitumoral Anthracycline Cosmomycin D.
JO  - Genome Announcements
PY  - 2014
SP  - e00541
EP  - e00514
VL  - 2
AB  - Streptomyces olindensis DAUFPE 5622, which was isolated from a Brazilian soil sample, produces
AB  - the antitumor anthracycline cosmomycin D. The genome sequence is
AB  - 9.4 Mb in length, with a G+C content of 71%. Thirty-four putative secondary
AB  - metabolite biosynthetic gene clusters were identified, including the cosmomycin D
AB  - cluster.
ER  -

TY  - JOUR
AU  - Rojas, R.
AU  - Miranda, C.D.
AU  - Romero, J.
AU  - Asenjo, F.
AU  - Valderrama, K.
AU  - Segovia, C.
AU  - Ugalde, J.A.
AU  - Santander, J.
TI  - Genome Sequence of Vibrio VPAP30, Isolated from an Episode of Massive Mortality of Reared Larvae of the Scallop Argopecten purpuratus.
JO  - Genome Announcements
PY  - 2015
SP  - e00745
EP  - e00715
VL  - 3
AB  - We report here the 5.167-Mbp draft genome sequence of Vibrio VPAP30, isolated from an
AB  - Argopecten purpuratus larval culture. Vibrio VPAP30 is the etiological
AB  - agent of a vibriosis outbreak causing a complete collapse of a larval culture of
AB  - the scallop A. purpuratus, which occurred in a commercial hatchery in Chile.
ER  -

TY  - JOUR
AU  - Rojas, T.C.
AU  - Maluta, R.P.
AU  - Parizzi, L.P.
AU  - Koenigkan, L.V.
AU  - Yang, J.
AU  - Yu, J.
AU  - Pereira, G.A.
AU  - Dias-da-Silveira, W.
TI  - Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry.
JO  - Genome Announcements
PY  - 2013
SP  - e0011013
EP  - e0011013
VL  - 1
AB  - Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in
AB  - the poultry industry worldwide. The disease might present
AB  - as different local infections or as septicemia. Here, we present the draft genome
AB  - sequences of three Brazilian APEC strains isolated from different kinds of
AB  - infections. The availability of these APEC genome sequences is important for
AB  - gaining a thorough understanding of the genomic features of E. coli, particularly
AB  - those of this pathotype.
ER  -

TY  - JOUR
AU  - Rojas, T.C.
AU  - Parizzi, L.P.
AU  - Tiba, M.R.
AU  - Chen, L.
AU  - Pereira, G.A.
AU  - Sangal, V.
AU  - Yang, J.
AU  - Yu, J.
AU  - Dias-da-Silveira, W.
TI  - Draft Genome of a Brazilian Avian-Pathogenic Escherichia coli Strain and In Silico Characterization of Virulence-Related Genes.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3023
EP  - 3023
VL  - 194
AB  - Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian
AB  - species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was
AB  - isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying
AB  - hen with swollen head syndrome.
ER  -

TY  - JOUR
AU  - Rojas-Rojas, F.U. et al.
TI  - Draft genome of Paraburkholderia caballeronis TNe-841(T), a free-living, nitrogen-fixing, tomato plant-associated bacterium.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 80
EP  - 80
VL  - 12
AB  - 10.1601/nm.26956 caballeronis is a plant-associated bacterium. Strain TNe-841(T)  was isolated
AB  - from the rhizosphere of tomato (Solanum lycopersicum L. var.
AB  - lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was
AB  - found to effectively nodulate Phaseolus vulgaris L. However, from an analysis of
AB  - the genome of strain TNe-841(T) and from repeat inoculation experiments, we found
AB  - that this strain did not nodulate bean and also lacked nodulation genes,
AB  - suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G
AB  - + C content of 67.01%. The sequence includes 6251 protein-coding genes and 87 RNA
AB  - genes.
ER  -

TY  - JOUR
AU  - Rojas-Rojas, F.U.
AU  - Huntemann, M.
AU  - Clum, A.
AU  - Pillay, M.
AU  - Palaniappan, K.
AU  - Varghese, N.
AU  - Mikhailova, N.
AU  - Stamatis, D.
AU  - Reddy, T.B.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Shapiro, N.
AU  - Ibarra, J.A.
AU  - Estrada-de, L.S.P.
TI  - Draft Genome Sequence of Heavy Metal-Resistant Cupriavidus alkaliphilus ASC-732T, Isolated from Agave Rhizosphere in the Northeast of Mexico.
JO  - Genome Announcements
PY  - 2016
SP  - e01013
EP  - e01016
VL  - 4
AB  - Cupriavidus alkaliphilus ASC-732(T) was isolated from the rhizosphere of agave plant growing
AB  - in alkaline soils in San Carlos, Tamaulipas, Mexico. The species is
AB  - able to grow in the presence of arsenic, zinc, and copper. The genome sequence of
AB  - strain ASC-732(T) is 6,125,055 bp with 5,586 genes and an average G+C content of
AB  - 67.81%.
ER  -

TY  - JOUR
AU  - Rolain, J.M.
AU  - Vayssier-Taussat, M.
AU  - Gimenez, G.
AU  - Robert, C.
AU  - Fournier, P.E.
AU  - Raoult, D.
TI  - Genome Sequence of Bartonella birtlesii, a Bacterium Isolated from Small Rodents  of the Genus Apodemus.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4779
EP  - 4779
VL  - 194
AB  - Bartonella birtlesii is a facultative intracellular bacterium isolated from the blood of small
AB  - mammals of the genus Apodemus. The present study reports the draft
AB  - genome of Bartonella birtlesii strain IBS 135(T) (CIP 106691(T)).
ER  -

TY  - JOUR
AU  - Romanenko, E.B.
AU  - Pushkareva, M.Y.
AU  - Alessenko, A.V.
AU  - Vanyushin, B.F.
TI  - Effects of Sphingomyelin and its enzymatic hydrolysis products on heterologous methylation of calf thymus DNA by cytosine-DNA methyltransferase EcoRII.
JO  - Biokhimiia
PY  - 1991
SP  - 295
EP  - 300
VL  - 56
AB  - It was found that sphingomyelin and its enzymatic hydrolysis products, choline
AB  - and sphingosine, influence the degree of DNA methylation in the reaction of
AB  - heterologous methylation by methylase EcoRII in vitro.  Sphingomyelin was found
AB  - to be able to activate (by 20%), sphingosine and choline inhibit methylation.
AB  - Phosphatidylcholine had no effect on DNA methylation in an in vitro system.
AB  - The role of lipids in the regulation of gene expression during enzymatic
AB  - modification (methylation) of DNA is discussed.
ER  -

TY  - JOUR
AU  - Romanenkov, A.S.
AU  - Kisil, O.V.
AU  - Zatsepin, T.S.
AU  - Yamskova, O.V.
AU  - Karyagina, A.S.
AU  - Metelev, V.G.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - DNA-methyltransferase SsoII as a bifunctional protein: Features of the interaction with the promoter region of SsoII restriction-modification genes.
JO  - Biokhimiia
PY  - 2006
SP  - 1341
EP  - 1349
VL  - 71
AB  - DNA duplexes bearing an aldehyde group at the 2'-position of the sugar moiety were used for
AB  - affinity modification of (cytosine-5)-DNA
AB  - methyltransferase SsoII. It is shown that lysine residues of M.SsoII
AB  - N-terminal region are located in proximity to DNA sugar-phosphate
AB  - backbone of a regulatory sequence of promoter region of SsoII
AB  - restriction-modification enzyme coding genes. The ability of the two
AB  - M.SsoII subunits to interact with DNA regulatory sequence has been
AB  - demonstrated by affinity modification using DNA duplexes with two
AB  - 2'-aldehyde groups. Changes in nucleotide sequence of one half of the
AB  - regulatory region prevented cross-linking of the second M.SsoII
AB  - subunit. The results on sequential affinity modification of M.SsoII by
AB  - two types of modified DNA ligands (i.e. by 2'-aldehyde-containing and
AB  - phosphoryldisulfide-containing) have demonstrated the possibility of
AB  - covalent attachment of the protein to two different DNA recognition
AB  - sites: regulatory sequence and methylation site.
ER  -

TY  - JOUR
AU  - Romano, A.
AU  - Bellio, A.
AU  - Macori, G.
AU  - Cotter, P.D.
AU  - Bianchi, D.M.
AU  - Gallina, S.
AU  - Decastelli, L.
TI  - Whole-Genome Shotgun Sequence of Salmonella bongori, First Isolated in Northwestern Italy.
JO  - Genome Announcements
PY  - 2017
SP  - e00560
EP  - e00517
VL  - 5
AB  - This study describes the whole-genome shotgun sequence of Salmonella bongori 48:z35:-,
AB  - originally isolated from a 1-year-old symptomatic patient in northwest
AB  - Italy, a typically nonendemic area. The draft genome sequence contained 4.56 Mbp
AB  - and the G+C content was 51.27%.
ER  -

TY  - JOUR
AU  - Romano, A.
AU  - Trip, H.
AU  - Campbell-Sills, H.
AU  - Bouchez, O.
AU  - Sherman, D.
AU  - Lolkema, J.S.
AU  - Lucas, P.M.
TI  - Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines.
JO  - Genome Announcements
PY  - 2013
SP  - e00097
EP  - e00012
VL  - 1
AB  - Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines
AB  - histamine, putrescine, and cadaverine by decarboxylating their amino acid
AB  - precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C
AB  - content) and the principal findings from its annotation, which might shed light
AB  - onto the enzymatic machineries that are involved in its production of biogenic
AB  - amines.
ER  -

TY  - JOUR
AU  - Romanovskaya, V.A.
AU  - Alexeyev, M.F.
AU  - Gunkovskaya, N.V.
AU  - Stolyar, S.M.
AU  - Shatohina, E.S.
AU  - Malashenko, Y.R.
TI  - Screening for restriction endonucleases in methane-oxidizing bacteria.
JO  - Mikrobiol. Zh.
PY  - 1992
SP  - 32
EP  - 39
VL  - 54
AB  - 51 methane-oxidizing bacterial strains such as Methylomonas methanica, M.rubra, Methylococcus
AB  - capsulatus, M. thermophilus, M. luteus, M. ucrainicus, M. whittenburyi, Methylosinus
AB  - trichosporium, M. sporium, Methylocystis parvus isolated from various ecological niches and
AB  - geographical regions of the Ukraine and also the strains received from R. Whittenbury and Y.
AB  - Heyer were screened for restriction endonucleases. Type II restriction endonucleases were
AB  - detected in IMV B-3112 (=12 b), IMV B-3027 (=26), IMV B-3019 (=9 c), IMV B-3017 (=17 c). IMV
AB  - B-3226 (=26 v). IMV B-3033 (=Y), IMV B-3100 (=100) and IMV B-3494 (=IE494). The results
AB  - obtained were indicative of a relatively high frequency of occurrence of restriction enzymes
AB  - in methane-oxidizing bacteria. There were KpnI (Asp718I) restriction endonuclease
AB  - isoschizomers in crude extracts of IMV B-3112, B-3017, B-3019, B-3027 isolated from
AB  - fresh-water silt as well as in IMV B-3226 strain isolated from waste-water silt. Although
AB  - these isolates had been previously considered as atypical strains of M. ucrainicus, more
AB  - detailed study of their properties allowed placing them with Methylovarius luteus
AB  - (=Methylococcus luteus). IMV B-3494 strain was identified as Methylococcus capsulatus. Strain
AB  - IMV B-3033 had earlier been allocated to Methylovarius whittenburyi (=Methylococcus
AB  - whittenburyi). Specificity of restriction endonucleases of this strain was not tested.
AB  - Therefore, for the first time restriction endonucleases were detected in methane-oxidizing
AB  - bacteria. 8 strains (3 species) among 51 strains (13 species) were found to produce
AB  - restriction endonucleases displaying three different types of specificity at least. Producers
AB  - of restriction endonucleases having KpnI (Asp718I) specificity were isolated from different
AB  - water and silt samples of the Dnieper flood-land more than 20 years ago.
ER  -

TY  - JOUR
AU  - Romao, F.T.
AU  - Hernandes, R.T.
AU  - Ooka, T.
AU  - Hayashi, T.
AU  - Sperandio, V.
AU  - Gomes, T.A.T.
TI  - Complete Genome Sequence of Escherichia albertii Strain 1551-2, a Potential Extracellular and Intracellular Pathogen.
JO  - Genome Announcements
PY  - 2018
SP  - e00075
EP  - e00018
VL  - 6
AB  - Escherichia albertii has recently been recognized as an emerging human and bird enteric
AB  - pathogen. Here, we report the complete chromosome sequence of a clinical
AB  - isolate of E. albertii strain 1551-2, which may provide information about the
AB  - pathogenic potential of this new species and the mechanisms of evolution of
AB  - Escherichia species.
ER  -

TY  - JOUR
AU  - Romero, D.A.
AU  - Klaenhammer, T.R.
TI  - Abortive phage infection and restriction/modification activities directed by pTR2030 determinants are enhanced by recombination with conjugal elements in lactococci.
JO  - J. Gen. Microbiol.
PY  - 1990
SP  - 1817
EP  - 1824
VL  - 136
AB  - The recombinant plasmid pTK6 is composed of a 13.6 kb fragment from pTR2030
AB  - encoding phage resistance determinants for restriction/modification (R+/M+) and
AB  - abortive phage infection (Hsp+) cloned into shuttle vector pSA3 (erythromycin
AB  - resistance, Emr).  Conjugal matings were performed to mobilize pTK6-encoded
AB  - markers from Lactococcus lactis subsp. lactis MMS362 and MG1363.  Emr
AB  - transconjugants were recovered at 10-6 per input donor and harboured pTK6 or
AB  - recombinant plasmids not found in either parental strain.  The recombinant
AB  - plasmids (pTRK78 and pTRK79) encoded Emr, Hsp+ and R+/M+, and transferred at
AB  - high frequency in second-round matings.  Mobilization of pTK6 from the
AB  - otherwise plasmid-free donor, L. lactis MG1363, confirmed the presence of a
AB  - conjugal element in this strain.  Phage resistance in transconjugants
AB  - containing pTRK78 and pTRK79 was markedly enhanced over a pTK6-directed Hsp+
AB  - and R+/M+.  In L. lactis LM2345 transconjugants, a reduction in plaque size was
AB  - accompanied by a significant decrease in the efficiency of plaquing for phages
AB  - c2 (10-2 to 10-6) and p2(<10-9).  L. lactis NCK203 transconjugants containing
AB  - pTRK78 or pTRK79 exhibited an additional 100-1000-fold reduction in the
AB  - plaquing efficiency of Phi48 (10-4 to 10-5) over pTK6 imposed restriction
AB  - (10-2).  Increased resistance to phage was a consequence of the physical
AB  - interaction of pTR2030-derived sequences on pTK6 with a conjugal element
AB  - resident in the donor strains.
ER  -

TY  - JOUR
AU  - Romine, M.F.
AU  - Stillwell, L.C.
AU  - Wong, K.-K.
AU  - Thurston, S.J.
AU  - Sisk, E.C.
AU  - Sensen, C.
AU  - Gaasterland, T.
AU  - Fredrickson, J.K.
AU  - Saffer, J.D.
TI  - Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199.
JO  - J. Bacteriol.
PY  - 1999
SP  - 1585
EP  - 1602
VL  - 181
AB  - The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1,
AB  - from Sphingomonas aromaticivorans F199 has been determined.  A total of 186 open
AB  - reading frames are predicted to encode proteins, of which 79 are likely directly
AB  - associated with catabolism or transport of aromatic compounds.  Genes that encode
AB  - enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-
AB  - cresol are predicted to be distributed among 15 gene clusters.  The unusual coclustering
AB  - of genes associated with different pathways appears to have evolved in response to
AB  - similarities in biochemical mechanisms required for the degradation of intermediates in
AB  - different pathways.  A putative efflux pump and several hypothetical membrane-
AB  - associated proteins were identified and predicted to be involved in the transport of
AB  - aromatic compounds and/or intermediates in catabolism across the cell wall.  Several
AB  - genes associated with integration and recombination, including two group II intron-
AB  - associated maturases, were identified in the replication region, suggesting that pNL1 is
AB  - able to undergo integration and excision events with the chromosome and/or other
AB  - portions of the plasmid.  Conjugative transfer of pNL1 to another Sphingomonas sp. was
AB  - demonstrated, and genes associated with this function were found in two large clusters.
AB  - Approximately one-third of the ORFs (59 of them) have no obvious homology to known
AB  - genes.
ER  -

TY  - JOUR
AU  - Ronca, S.
AU  - Frossard, A.
AU  - Guerrero, L.D.
AU  - Makhalanyane, T.P.
AU  - Aislabie, J.M.
AU  - Cowan, D.A.
TI  - Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica.
JO  - Genome Announcements
PY  - 2015
SP  - e01309
EP  - e01314
VL  - 3
AB  - Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted
AB  - soil near Scott Base, Ross Island, Antarctica. The genome of this
AB  - aromatic hydrocarbon-degrading bacterium provides valuable information on the
AB  - microbially mediated biodegradation of aromatic compounds in cold-climate
AB  - systems.
ER  -

TY  - JOUR
AU  - Ronco, T.
AU  - Stegger, M.
AU  - Andersen, P.S.
AU  - Pedersen, K.
AU  - Li, L.
AU  - Thofner, I.C.
AU  - Olsen, R.H.
TI  - Draft Genome Sequences of Two Avian Pathogenic Escherichia coli Strains of Clinical Importance, E44 and E51.
JO  - Genome Announcements
PY  - 2016
SP  - e00768
EP  - e00716
VL  - 4
AB  - Avian pathogenic Escherichia coli strains have remarkable impacts on animal welfare and the
AB  - production economy in the poultry industry worldwide. Here, we
AB  - present the draft genomes of two isolates from chickens (E44 and E51) obtained
AB  - from field outbreaks and subsequently investigated for their potential for use in
AB  - autogenous vaccines for broiler breeders.
ER  -

TY  - JOUR
AU  - Ronco, T.
AU  - Stegger, M.
AU  - Pedersen, K.
TI  - Draft Genome Sequence of a Sequence Type 398 Methicillin-Resistant Staphylococcus aureus Isolate from a Danish Dairy Cow with Mastitis.
JO  - Genome Announcements
PY  - 2017
SP  - e00492
EP  - e00417
VL  - 5
AB  - Livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) strains of
AB  - sequence type 398 (ST398) colonize both humans and various livestock
AB  - species. In 2016, an ST398 LA-MRSA isolate (Sa52) was collected from a Danish
AB  - dairy cow with mastitis, and here, we report the draft genome sequence of strain
AB  - Sa52.
ER  -

TY  - JOUR
AU  - Rondelet, G.
AU  - Dal Maso, T.
AU  - Willems, L.
AU  - Wouters, J.
TI  - Structural basis for recognition of histone H3K36me3 nucleosome by human de novo  DNA methyltransferases 3A and 3B.
JO  - J. Struct. Biol.
PY  - 2016
SP  - 357
EP  - 367
VL  - 194
AB  - DNA methylation is an important epigenetic modification involved in chromatin organization and
AB  - gene expression. The function of DNA methylation depends on cell
AB  - context and is correlated with histone modification patterns. In particular,
AB  - trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA
AB  - methylation and elongation phase of transcription. PWWP domains of the de novo
AB  - DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA
AB  - methylation. Here we report the first crystal structure of the DNMT3B PWWP
AB  - domain-H3K36me3 complex. Based on this structure, we propose a model of the
AB  - DNMT3A PWWP domain-H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in
AB  - a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is
AB  - inserted into an aromatic cage similar to the 'Royal' superfamily domains known
AB  - to bind methylated histones. A key interaction between trimethylated Lys36 and a
AB  - conserved water molecule stabilized by Ser270 explains the lack of affinity of
AB  - mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF
AB  - (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome.
AB  - The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome
AB  - highlights the mechanism for recognition of nucleosome by DNMT3s and explains the
AB  - periodicity of de novo DNA methylation.
ER  -

TY  - JOUR
AU  - Rondelet, G.
AU  - Fleury, L.
AU  - Faux, C.
AU  - Masson, V.
AU  - Dubois, J.
AU  - Arimondo, P.B.
AU  - Willems, L.
AU  - Wouters, J.
TI  - Inhibition studies of DNA methyltransferases by maleimide derivatives of RG108 as non-nucleoside inhibitors.
JO  - Future Med Chem
PY  - 2017
SP  - 1465
EP  - 1481
VL  - 9
AB  - AIM: DNA methyltransferases (DNMTs) are important drug targets for epigenetic therapy of
AB  - cancer. Nowadays, non-nucleoside DNMT inhibitors are in development to
AB  - address high toxicity of nucleoside analogs. However, these compounds still have
AB  - low activity in cancer cells and mode of action of these compounds remains
AB  - unclear. MATERIALS and METHODS: In this work, we studied maleimide derivatives of
AB  - RG108 by biochemical, structural and computational approaches to highlight their
AB  - inhibition mechanism on DNMTs. RESULTS: Findings demonstrated a correlation
AB  - between cytotoxicity on mesothelioma cells of these compounds and their
AB  - inhibitory potency against DNMTs. Noncovalent and covalent docking studies,
AB  - supported by crystallographic (apo structure of M.HhaI) and differential scanning
AB  - fluorimetry assays, provided detailed insights into their mode of action and
AB  - revealed essential residues for the stabilization of such compounds inside DNMTs.
AB  - [Formula: see text].
ER  -

TY  - JOUR
AU  - Rong, X.
AU  - Baysal, G.F.
AU  - Meulia, T.
AU  - McSpadden, G.B.B.
TI  - Draft Genome Sequences of the Pseudomonas fluorescens Biocontrol Strains Wayne1R and Wood1R.
JO  - J. Bacteriol.
PY  - 2012
SP  - 724
EP  - 725
VL  - 194
AB  - Pseudomonas fluorescens strains Wayne1R and Wood1R have proven capacities to improve plant
AB  - health. Here we report the draft genome sequences and
AB  - automatic annotations of both strains. Genome comparisons reveal
AB  - similarities with P. fluorescens strain Pf-5, reveal the novelty of
AB  - Wood1R, and indicate some genes that may be related to biocontrol.
ER  -

TY  - JOUR
AU  - Rong, X.
AU  - Gurel, F.B.
AU  - Meulia, T.
AU  - McSpadden, G.B.B.
TI  - Draft Genome Sequences of the Biocontrol Bacterium Mitsuaria sp. Strain H24L5A.
JO  - J. Bacteriol.
PY  - 2012
SP  - 734
EP  - 735
VL  - 194
AB  - Mitsuaria sp. strain H24L5A is a plant-associated bacterium with proven capacities to suppress
AB  - plant pathogens. Here, we report the draft genome
AB  - sequences and automatic annotation of H24L5A. Comparative genomic analysis
AB  - indicates H24L5A's similarity to the Leptothrix and Methylibium species,
AB  - as well as several genes potentially contributing to its biocontrol
AB  - activities.
ER  -

TY  - JOUR
AU  - Ronholm, J.
AU  - Petronella, N.
AU  - Kenwell, R.
AU  - Banerjee, S.
TI  - Draft Whole-Genome Sequences of 14 Vibrio parahaemolyticus Clinical Isolates with an Ambiguous K Serogroup.
JO  - Genome Announcements
PY  - 2015
SP  - e00217
EP  - e00215
VL  - 3
AB  - Vibrio parahaemolyticus is a bacterial pathogen responsible for mild to severe
AB  - gastroenteritis, wound infections, and septicemia resulting from the ingestion or
AB  - handling of raw or undercooked contaminated seafood. Here, we report the draft
AB  - whole-genome sequences and annotations of 14 Canadian V. parahaemolyticus
AB  - clinical isolates that were serologically identified as K group II using
AB  - polyvalent antisera but were not specifically K serogrouped using monovalent
AB  - antisera.
ER  -

TY  - JOUR
AU  - Ronholm, J.
AU  - Petronella, N.
AU  - Tamber, S.
TI  - Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted  Chia and Flax Seed Powders.
JO  - Genome Announcements
PY  - 2016
SP  - e00963
EP  - e00916
VL  - 4
AB  - A 2014 foodborne salmonellosis outbreak in Canada and the United States implicated, for the
AB  - first time, sprouted chia seed powder as the vehicle of
AB  - transmission. Here, we report the draft whole genome sequences of two Salmonella
AB  - enterica strains isolated from sprouted powders related to the aforementioned
AB  - outbreak.
ER  -

TY  - JOUR
AU  - Ronholm, J.
AU  - Petronella, N.
AU  - Tamber, S.
TI  - Draft Genome Sequences of 11 Salmonella enterica Strains with Variable Levels of  Barotolerance.
JO  - Genome Announcements
PY  - 2016
SP  - e00952
EP  - e00916
VL  - 4
AB  - The diversity of the genus Salmonella is reflected in the physiological adaptations used by
AB  - its members in response to stressors such as high pressure.
AB  - Here we report the draft whole genome sequences of 11 Salmonella enterica
AB  - strains, five sensitive strains and six demonstrating high levels of pressure
AB  - resistance.
ER  -

TY  - JOUR
AU  - Ronka, J.
AU  - Hjorleifsdottir, S.
AU  - Tenkanen, T.
AU  - Pitkanen, K.
AU  - Mattila, P.
AU  - Kristjansson, J.K.
TI  - RmaI, a type II restriction endonuclease from Rhodothermus marinus which recognizes 5' CTAG 3'.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2789
EP  - 2789
VL  - 19
AB  - RmaI, an isoschizomer of MaeI has been isolated from Rhodothermus marinus. RmaI recognizes the
AB  - palindromic sequence 5'-CTAG-3'.  Like its isoschizomer RmaI cleaves the sequence, C/TAG,
AB  - generating 5'-protruding TA-dinucleotides. The recognition sequence of RmaI was determined
AB  - using double digestions on pBR322- and phiX174 DNAs (figure 1, lanes 2-6 and 8-12).  The
AB  - cleavage patterns obtained were compared with computer-derived mapping data.  The data
AB  - predicts the sequence 5'-CTAG-3'.  The sequence was also tested by digesting Lambda- and
AB  - M13mp18 DNAs with RmaI (figure 1, lanes 13 and 14).  The fragments obtained matched the
AB  - computer predicted fragments that would be produced when cleaving at 5'-CTAG-3'.  RmaI has
AB  - the following number of recognition sites on these commonly used DNAs: pUC19, pBR322, phiX174,
AB  - SV40, M13mp18, T7, Lambda and Adeno2.  The cleavage site of RmaI was determined by cleavage of
AB  - primed synthesis reaction.  M13mp19 DNA containing the recognition site of RmaI was used as a
AB  - template.  Using an M13 sequencing primer the DNA was sequenced according to Sanger et al.  In
AB  - addition to the four standard reactions a fifth reaction was performed which was extended
AB  - through the RmaI recognition site. The reaction was terminated by heat treatment and the
AB  - product was cleaved with RmaI.  The cleaved product was divided in two.  The addition of
AB  - Klenow to one part resulted in a band migrating with the A-band (figure 2, lane +).  The
AB  - cleaved product (figure 2, lane -) migrated with the C-band.  Thus, the cleavage site for RmaI
AB  - is:
AB  - 5'-C/TA-G-3'
AB  - 3'-G-AT/C-5'.
ER  -

TY  - JOUR
AU  - Ronneseth, A.
AU  - Castillo, D.
AU  - D'Alvise, P.
AU  - Tonnesen, O.
AU  - Haugland, G.
AU  - Grotkjaer, T.
AU  - Engell-Sorensen, K.
AU  - Norremark, L.
AU  - Bergh, O.
AU  - Wergeland, H.I.
AU  - Gram, L.
TI  - Comparative assessment of Vibrio virulence in marine fish larvae.
JO  - J. Fish Dis.
PY  - 2017
SP  - 1373
EP  - 1385
VL  - 40
AB  - Vibrionaceae infections are a major obstacle for marine larviculture; however,
AB  - little is known about virulence differences of Vibrio strains. The virulence of
AB  - Vibrio strains, mostly isolated from vibriosis outbreaks in farmed fish, was
AB  - tested in larval challenge trials with cod (Gadus morhua), turbot (Scophthalmus
AB  - maximus) and halibut (Hippoglossus hippoglossus) using a multiwell dish assays
AB  - with single-egg/larvae cultures. The strains differed significantly in virulence
AB  - as some caused a high mortality of larva reaching 100% mortality after a few
AB  - days, while others had no or only marginal effects on survival. Some Vibrio
AB  - strains were pathogenic in all of the larva species, while some caused disease
AB  - only in one of the species. Twenty-nine of the Vibrio anguillarum strains
AB  - increased the mortality of larvae from at least one fish species; however,
AB  - pathogenicity of the strains differed markedly. Other Vibrio species had no or
AB  - less pronounced effects on larval mortalities. Iron uptake has been related to V.
AB  - anguillarum virulence; however, the presence or absence of the plasmid pJM1
AB  - encoding anguibactin did not correlate with virulence. The genomes of V.
AB  - anguillarum were compared (D. Castillo, P.W. D'Alvise, M. Middelboe and L. Gram,
AB  - unpublished data) and most of the high-virulent strains had acquired virulence
AB  - genes from other pathogenic Vibrio.
ER  -

TY  - JOUR
AU  - Rooney, E.A. et al.
TI  - Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a.
JO  - Genome Announcements
PY  - 2015
SP  - e00797
EP  - e00715
VL  - 3
AB  - Clostridium clariflavum strain 4-2a, a novel strain isolated from a thermophilic  biocompost
AB  - pile, has demonstrated an extensive capability to utilize both
AB  - cellulose and hemicellulose under thermophilic anaerobic conditions. Here, we
AB  - report the draft genome of this strain.
ER  -

TY  - JOUR
AU  - Roquigny, R.
AU  - Arseneault, T.
AU  - Gadkar, V.J.
AU  - Novinscak, A.
AU  - Joly, D.L.
AU  - Filion, M.
TI  - Complete Genome Sequence of Biocontrol Strain Pseudomonas fluorescens LBUM223.
JO  - Genome Announcements
PY  - 2015
SP  - e00443
EP  - e00415
VL  - 3
AB  - Pseudomonas fluorescens LBUM223 is a plant growth-promoting rhizobacterium (PGPR) with
AB  - biocontrol activity against various plant pathogens. It produces the
AB  - antimicrobial metabolite phenazine-1-carboxylic acid, which is involved in the
AB  - biocontrol of Streptomyces scabies, the causal agent of common scab of potato.
AB  - Here, we report the complete genome sequence of P. fluorescens LBUM223.
ER  -

TY  - JOUR
AU  - Rosa, B.A.
AU  - Hallsworth-Pepin, K.
AU  - Martin, J.
AU  - Wollam, A.
AU  - Mitreva, M.
TI  - Genome Sequence of Christensenella minuta DSM 22607T.
JO  - Genome Announcements
PY  - 2017
SP  - e01451
EP  - e01416
VL  - 5
AB  - Obesity influences and is influenced by the human gut microbiome. Here, we present the genome
AB  - of Christensenella minuta, a highly heritable bacterial
AB  - species which has been found to be strongly associated with obesity through an
AB  - unknown biological mechanism. This novel genome provides a valuable resource for
AB  - future obesity therapeutic studies.
ER  -

TY  - JOUR
AU  - Rosamond, J.
AU  - Endlich, B.
AU  - Linn, S.
TI  - Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 619
EP  - 635
VL  - 129
AB  - Reaction intermediates and products formed by the restriction endonuclease of Escherichia coli
AB  - B with fd replicative form DNA substrates containing recognition sites in known positions and
AB  - orientations have been characterized by electron microscopy.  After exposure of these
AB  - substrates to enzyme, loops of duplex DNA were frequently observed, usually at or near the
AB  - termini.  Analysis of the size and structure of the loops observed with various DNA substrates
AB  - suggests that the enzyme binds initially to the recognition site then remains bound to the DNA
AB  - in the region of this site while tracking towards a site of cleavage.  Tracking appears to
AB  - occur only on the 5' side of the asymmetric recognition sequence, 5' . . .
AB  - T-G-A-(N)8-T-G-C-T . . . 3'; however, the location of the cleavage sites appears to be
AB  - random, at least within certain limits of distance from the recognition site.  Enzyme-DNA
AB  - complexes remain intact even after the double-strand cleavage is completed, and this complex
AB  - acts as a potent ATPase with no obvious function.  This latter reaction might represent an
AB  - artifactual uncoupling of ATP hydrolysis from the tracking of the enzyme along the DNA;
AB  - alternatively, it might indicate an in vivo function for the enzyme of which we are unaware.
ER  -

TY  - JOUR
AU  - Rosana, A.R.
AU  - Orata, F.D.
AU  - Xu, Y.
AU  - Simkus, D.N.
AU  - Bramucci, A.R.
AU  - Boucher, Y.
AU  - Case, R.J.
TI  - Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217.
JO  - Genome Announcements
PY  - 2016
SP  - e00673
EP  - e00616
VL  - 4
AB  - Strains of Rhodobacteraceae, Sphingomonadales, Alteromonadales, and Bacteroidetes were
AB  - isolated from a polymicrobial culture of the coccolith-forming (C-type)
AB  - haptophyte Emiliania huxleyi strain M217. The genomes encode genes for the
AB  - production of algal growth factors and the consumption of their hosts' metabolic
AB  - by-products, suggesting that the polymicrobial culture harbors many symbiotic
AB  - interactions.
ER  -

TY  - JOUR
AU  - Rosas-Morales, J.P.
AU  - Perez-Mancilla, X.
AU  - Lopez-Kleine, L.
AU  - Montoya, C.D.
AU  - Riano-Pachon, D.M.
TI  - Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents.
JO  - Genome Announcements
PY  - 2015
SP  - e00486
EP  - e00415
VL  - 3
AB  - Genomes from four Clostridium sp. strains considered to be mesophilic anaerobic bacteria,
AB  - isolated from crop soil in Colombia, with a strong potential to produce
AB  - alcohols like 1,3-propanediol, were analyzed. We present the draft genome of
AB  - these strains, which will be useful for developing genetic engineering
AB  - strategies.
ER  -

TY  - JOUR
AU  - Rosati, O.
AU  - Srivastava, T.K.
AU  - Katti, S.B.
AU  - Alves, J.
TI  - Importance of phosphate contacts for sequence recognition by EcoRI restriction enzyme.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2002
SP  - 198
EP  - 205
VL  - 295
AB  - We have studied the importance of charge and hydrogen-bonding potential of the phosphodiester
AB  - backbone for binding and cleavage by EcoRI restriction endonuclease.  We used 12-mer
AB  - oligodeoxynucleotide substrates with single substitutions of phosphates by chiral
AB  - methylphosphonates at each position of the recognition sequence -pGpApApTpTpCp-.  Binding was
AB  - moderately reduced between 4- and 400-fold more or less equally for the RP and SP-analogues
AB  - mainly caused by missing charge interaction.  The range of cleavage effects was much wider.
AB  - Four substrates were not cleaved at all.  At both flanking positions and in the purine half of
AB  - the sequence up to the central position, cleavage was more impaired than binding and
AB  - differences between RP and SP diastereomers were more pronounced.  These effects are easily
AB  - interpreted by direct phosphate contacts seen in the crystal structure.  For the effects of
AB  - substitutions in the pyrimidine half of the recognition sequence, more indirect effects have
AB  - to be discussed.
ER  -

TY  - JOUR
AU  - Rose, T.M.
AU  - Schultz, E.R.
AU  - Henikoff, J.G.
AU  - Pietrokovski, S.
AU  - McCallum, C.M.
AU  - Henikoff, S.
TI  - Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1628
EP  - 1635
VL  - 26
AB  - We describe a new primer design strategy for PCR amplification of unknown targets that are
AB  - related to multiply-aligned protein sequences.  Each primer consists of a short 3' degenerate
AB  - core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid
AB  - residues are necessary for design of the core, which is stabilized by the clamp during
AB  - annealing to template molecules.  During later rounds of amplification, the non-degenerate
AB  - clamp permits stable annealing to product molecules.  We demonstrate the practical utility of
AB  - this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human
AB  - genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs.  In each
AB  - case, amplified products were sufficiently pure to be cloned without gel fractionation.  This
AB  - Consensus-Degenerate Hybrid Oligonucleotide Primer strategy has been implemented as a computer
AB  - program that is accessible over the World Wide Web (http://blocks.fhcrc.org/codehop.html) and
AB  - is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer
AB  - prediction beginning with a set of related protein sequences.
ER  -

TY  - JOUR
AU  - Rosen, L.E.
AU  - Morrison, H.A.
AU  - Masri, S.
AU  - Brown, M.J.
AU  - Springstubb, B.
AU  - Sussman, D.
AU  - Stoddard, B.L.
AU  - Seligman, L.M.
TI  - Homing endonuclease I-CreI derivatives with novel DNA target specificities - mutant homing enzyme via mutagenesis for DNA cleavage and gene therapy.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 4791
EP  - 4800
VL  - 34
AB  - Homing endonucleases are highly specific enzymes, capable of recognizing and cleaving unique
AB  - DNA sequences in complex genomes. Since such DNA
AB  - cleavage events can result in targeted allele-inactivation and/or
AB  - allele-replacement in vivo, the ability to engineer homing endonucleases
AB  - matched to specific DNA sequences of interest would enable powerful and
AB  - precise genome manipulations. We have taken a step-wise genetic approach
AB  - in analyzing individual homing endonuclease I-CreI protein/DNA contacts,
AB  - and describe here novel interactions at four distinct target site
AB  - positions. Crystal structures of two mutant endonucleases reveal the
AB  - molecular interactions responsible for their altered DNA target
AB  - specificities. We also combine novel contacts to create an endonuclease
AB  - with the predicted target specificity. These studies provide important
AB  - insights into engineering homing endonucleases with novel target
AB  - specificities, as well as into the evolution of DNA recognition by this
AB  - fascinating family of proteins.
ER  -

TY  - JOUR
AU  - Rosenberg, A.H.
AU  - Simon, M.N.
AU  - Studier, F.W.
AU  - Roberts, R.J.
TI  - Survey and mapping of restriction endonuclease cleavage sites in bacteriophage T7 DNA.
JO  - J. Mol. Biol.
PY  - 1979
SP  - 907
EP  - 915
VL  - 135
AB  - A survey of restriction endonucleases having different cleavage specificities
AB  - has identified 10 that do not cut wild-type bacteriophage T7 DNA, 11 that cut
AB  - at six or fewer sites, four that cut at 18 to 45 sites, and 12 that cut at more
AB  - than 50 sites.  All the cleavage sites for the 13 enzymes that cut a 26 or
AB  - fewer sites have been mapped.  Cleavage sites for each of the 10 enzymes that
AB  - do not cut T7 DNA would be expected to occur an average of 9 to 10 times in a
AB  - random nucleotide sequence the length of T7 DNA.  A possible explanation for
AB  - the lack of any cleavage sites for these enzymes might be that T7 encounters
AB  - enzymes having these specificities in natural hosts, and that the sites have
AB  - been eliminated from T7 DNA by natural selection.  Five restriction
AB  - endonucleases were found to cut within the terminal repetition of T7 DNA; one
AB  - of these, KpnI, cuts at only three additional sites in the T7 DNA molecule.
AB  - The length of the terminal repetition was estimated by two independent means to
AB  - be approximately 155 to 160 base-pairs.
ER  -

TY  - JOUR
AU  - Rosenberg, J.
AU  - Wang, B.
AU  - Frederick, C.
AU  - Reich, N.
AU  - Greene, P.
AU  - Grable, J.
AU  - McClarin, J.
TI  - Development of a Protein Design Strategy for EcoRI Endonuclease.
JO  - Protein Eng.
PY  - 1987
SP  - 237
EP  - 250
VL  - 0
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
AB  - endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved.
AB  - Each subunit of the endonuclease is organized into a domain with a/b
AB  - architecture.  The b-sheet consists of anti-parallel and parallel motifs.  The
AB  - amino acid residues which interact directly with the DNA to perform the
AB  - hydrolysis are located primarily in the anti-parallel motif, while those which
AB  - form sequence specific hydrogen bonds with the bases are found in the parallel
AB  - motif.  The hydrolytic active site is located in a cleft which is not fully
AB  - assembled in this structure (which was obtained in the absence of magnesium).
AB  - The DNA conformation departs significantly from those which have been observed
AB  - in crystals containing pure DNA; suggesting that the altered conformation has
AB  - been stabilized by the enzyme.  The conformations seen only upon protein
AB  - binding are termed neo-conformations to distinguish them from those which are
AB  - intrinsically stable in the absence of protein.  The determinants of sequence
AB  - specificity include "modular" interactions based on the crossover
AB  - alpha-helices, i.e., those which connect the b-strands of the parallel segment
AB  - of the principal B-sheet.  They are pointing into the major groove of the DNA
AB  - and amino acid side chains at the amino ends of these helices form bidentate
AB  - hydrogen bonding interactions with the bases.  The inner recognition module
AB  - consists of two symmetry-related alpha-helices which recognize the inner
AB  - tetranucleotide (AATT), while the two symmetry-equivalent outer recognition
AB  - modules are single alpha-helices which recognize the GC base pairs.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
TI  - Structure and function of restriction endonucleases.
JO  - Curr. Opin. Struct. Biol.
PY  - 1991
SP  - 104
EP  - 113
VL  - 1
AB  - The past year has seen significant advances in our understanding of the
AB  - structure and function of restriction endonucleases.  The highlights include a
AB  - revised chain tracing for EcoRI endonuclease from Escherichia coli, structures
AB  - soon to be reported for E. coli EcoRV endonuclease and significant advances in
AB  - the biochemistry and molecular genetics of both enzymes.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - Boyer, H.W.
AU  - Greene, P.
TI  - The structure and function of the EcoRI restriction endonuclease.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 131
EP  - 164
VL  - 1
AB  - *
AB  -   I. DNA mapping
AB  -  II. X-ray diffraction analysis of EcoRI endonuclease crystals
AB  - III. DNA binding properties of EcoRI methylase and endonuclease
AB  -  IV. Degeneracies in restriction recognition sequences
AB  - 
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - Dickerson, R.E.
AU  - Greene, P.J.
AU  - Boyer, H.W.
TI  - Preliminary X-ray diffraction analysis of crystalline EcoRI endonuclease.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 241
EP  - 245
VL  - 122
AB  - EcoRI endonuclease crystallizes in space group C2 with unit cell parameters a =
AB  - 209 angstroms, b = 129 angstroms, c = 50 angstroms and B = 98.4o.  Four 29,000
AB  - molecular weight subunits per asymmetric unit would give a reasonable Vm value
AB  - of 2.87 cubic angstroms/dalton.  EcoRI endonuclease is the first protein which
AB  - recognizes a specific sequence of bases in DNA to be crystallized in a form
AB  - suitable for high resolution structure analysis.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - Greene, P.
TI  - EcoRI* specificity and hydrogen bonding.
JO  - DNA
PY  - 1982
SP  - 117
EP  - 124
VL  - 1
AB  - Under standard conditions, EcoRI endonuclease uniquely recognizes the inverted
AB  - repeat GAATTC.  However, this specificity breaks down under non-standard
AB  - conditions into what has been termed EcoRI* specificity, wherein many other
AB  - sequences are recognized.  We show here that the hydrolysis rates at all known
AB  - EcoRI* sites can be summarized by the hierarchies: G > > A > T > > C at the
AB  - first position, A > > [G,C] > > T at the second and third position, and the
AB  - corresponding complements at the last three positions.  This is consistent with
AB  - a recognition model which assumes that there are two specific hydrogen bonds
AB  - per base pair under standard conditions.  One or more of these are randomly
AB  - replaced by water under EcoRI* conditions and the position of a sequence within
AB  - the appropriate bonds are common recognition features that can be identified by
AB  - examining the DNA.  The recognition points thereby identified for EcoRI all
AB  - fall within the major groove of the DNA.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - McClarin, J.
AU  - Grable, J.
AU  - Frederick, C.
AU  - Samudzi, C.
AU  - Jen-Jacobson, L.
TI  - Structure of DNA-EcoRI endonuclease complex at 3 angstroms resolution.
JO  - J. Cell Biochem. Suppl.
PY  - 1985
SP  - 101
EP  - 101
VL  - 9B
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
AB  - endonuclease and the oligonucleotide TCGCGAATTCGCG will be reported.  The DNA
AB  - and the protein share a common (crystallographic) two-fold axis of rotational
AB  - symmetry, as expected from the intrinsic symmetry of the recognition site
AB  - (GAATTC).  The DNA conformation within the complex is different from that found
AB  - in the absence of protein suggesting that the set of conformational states
AB  - which are accessable to protein-free DNA is expanded by the binding of sequence
AB  - specific proteins.  These include the torsional neo-1 kink which widens the
AB  - major groove by unwinding the DNA by approximately 25o thereby facilitating
AB  - contact between the edges of the purine bases and amino acid side chains.  A
AB  - second (neo-2) kink is located three base-pairs away which also facilitates
AB  - access of protein to DNA and/or has a role in the hydrolytic mechanism of this
AB  - enzyme.  A five stranded a/b structure forms the foundation of each
AB  - endonuclease subunit with the strands of beta-sheet and the alpha-helices
AB  - oriented approximately perpendicular to the average DNA helix axis.
AB  - Polypeptide loops at the carboxy edge of the beta-sheet form a cleft which
AB  - contains the segment of DNA backbone spanning the scissile bond.  (DNA
AB  - hydrolysis was inhibited via omission of Mg+2).  The cleft is complementary to
AB  - one strand of double helical DNA and its shape determined by the intrinsic
AB  - twist of b-sheet.  This novel feature suggests that DNA and protein are
AB  - intrinsically complementary at fundamental level.  Sequence specificity is
AB  - determined by "modular" interactions.  One large symmetric module recognizes
AB  - the inner tetranucleotide (AATT while two additional symmetry-equivalent
AB  - modules recognizes the outer base pairs.  The inner module consists of two
AB  - symmetry equivalent alpha-helices which project from the a/b units.  Lysine and
AB  - glutamic acid side chains at the ends of the alpha-helices hydrogen bond to the
AB  - adenine residues thereby determining the specificity for the inner
AB  - tetranucleotide.  The outer module is formed by a separate segment of the
AB  - polypeptide chain containing an arginine side chain which hydrogen bonds to
AB  - guanine.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Grable, J.
AU  - Boyer, H.W.
AU  - Greene, P.J.
TI  - Structure and function of the EcoRI restriction endonuclease.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 119
EP  - 145
VL  - 5
AB  - The highly specific recognition of the double-stranded sequence d(GAATTC) by
AB  - EcoRI endonuclease offers compelling advantages as a system for investigating
AB  - sequence specific recognition of DNA.  It is a small protein (31,065 daltons,
AB  - 276 amino acids) of known sequence which forms highly stable catalytically
AB  - active dimers in solution.  The enzyme hydrolyzes the phosphodiester bond
AB  - between the guanylic and adenylic acid residues resulting in a 5'-phosphate.
AB  - The reaction proceeds with inversion of configuration at the reactive
AB  - phosphorus, implying that there is an odd number of chemical events during the
AB  - hydrolysis.  The simplest interpretation of this observation is that the enzyme
AB  - does not form a covalent intermediate with the DNA.  Although EcoRI
AB  - endonuclease requires Mg2+ for phosphodiester bond hydrolysis, it binds
AB  - specifically to its cognate hexanucleotide in the absence of Mg2+ with a
AB  - dissociation constant on the order of 10-11 M-1.  The enzyme also binds DNA in
AB  - a nonspecific manner ie., at sites other than GAATTC; this does not result in
AB  - hydrolysis of the DNA.  It has been postulated that the nonspecific complex
AB  - enhances the rate of formation of formation of the specific complex by
AB  - facilitated diffusion along the DNA.  Both the EcoRI endonuclease and the EcoRI
AB  - methylase recognize the same hexanucleotide; however, the latter methylates the
AB  - central adenine residues of both strands at the exocyclic N-6 amino group.
AB  - When either one or both groups is methtylated the endonuclease no longer
AB  - cleaves the DNA.  Thus, EcoRI endonuclease not only discriminates between its
AB  - hexanucleotide and all other hexanucleotides, it also discriminates between
AB  - different methtylation states of the same hexanucleotide.  Cocrystals of DNA
AB  - and protein that diffract to high resolution are required for a full
AB  - understanding of sequence specificity in the EcoRI system.  We have obtained
AB  - cocrystals and determined their structure.  Here we report the structure of the
AB  - recognition complex including interactions involved in sequence specificity.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Wang, B.-C.
AU  - Boyer, H.W.
AU  - Grable, J.
AU  - Greene, P.
TI  - The structure and function of EcoRI endonuclease.
JO  - Biological Organization: Macromolecular Interactions at High Resolution.
PY  - 1987
SP  - 11
EP  - 43
VL  - 0
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
AB  - endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved by
AB  - the ISIR method using a platinum isomorphous derivative.  Each subunit of the
AB  - endonuclease is organized into an a/b domain based on a five stranded
AB  - beta-sheet and an extension, called the "arm" which wraps around the DNA.  The
AB  - primary beta-sheet consists of anti-parallel and parallel motifs which contain
AB  - the sites of DNA strand scission and sequence specific recognition,
AB  - respectively.  The hydrolytic active site is located in a cleft which binds the
AB  - DNA backbone in the vicinity of the scissile bond.  The DNA conformation
AB  - departs significantly from those which have been observed in crystals
AB  - containing pure DNA; suggesting that the altered conformation has been
AB  - stabilized by the enzyme.  The conformations seen only upon protein binding are
AB  - termed neo-conformations to distinguish them from those which are intrinsically
AB  - stable in the absence of protein.  Sequence specificity is determined by
AB  - "modular" interactions based on the crossover alpha-helices, i.e., those which
AB  - connect the beta-strands of the parallel segment of the principal beta-sheet.
AB  - They are pointing into the major groove of the DNA and amino acid side chains
AB  - at the amino ends of these helices form bidentate interactions with the bases.
AB  - The inner recognition module consists of two symmetry-related alpha-helices
AB  - which recognize the inner tetranucleotide (AATT), while the two
AB  - symmetry-equivalent outer recognition modules are single alpha-helices wihch
AB  - recognize the GC base pairs.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Wang, B.-C.
AU  - Boyer, H.W.
AU  - Greene, P.
TI  - The 3 angstrom structure of a DNA-EcoRI endonuclease recognition complex.
JO  - Chem. Scr.
PY  - 1986
SP  - 147
EP  - 157
VL  - 26B
AB  - The 3 angstrom structure of a co-crystalline recognition complex between EcoRI
AB  - endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved by
AB  - the ISIR method using a platinum isomorphous derivative.  Each subunit of the
AB  - endonuclease is organized into an a/b domain based on a five stranded
AB  - beta-sheet and an extension, called the "arm", which wraps around the DNA.  The
AB  - primary beta-sheet consists of anti-parallel and parallel sub-domains which
AB  - contain the sites of DNA strand scission and sequence specific recognition,
AB  - respectively.  The hydrolytic active site is located in a cleft which binds the
AB  - DNA backbone in the vicinity of the scissile bond.  The DNA conformation
AB  - departs significantly from those which have been observed in crystals
AB  - containing pure DNA; suggesting that the altered conformation has been
AB  - stabilized by the enzyme.  The conformations seen only upon protein binding are
AB  - termed neo-conformations to distinguish them from those which are intrinsically
AB  - stable in the absence of protein.  Sequence specificity is determined by
AB  - "modular" interactions based on the crossover alpha-helices, i.e., those which
AB  - connect the beta-strands of the parallel segment of the principal beta-sheet.
AB  - They are pointing into the major groove of the DNA and amino acid side chains
AB  - at the amino ends of these helices form bidentate interactions with the bases.
AB  - The inner recognition module consists of two symmetry-related alpha-helices
AB  - which recognize the inner tetranucleotide (AATT), while the two
AB  - symmetry-equivalent outer recognition modules are single alpha-helices which
AB  - recognize the GC base pairs.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Wang, B.-C.
AU  - Grable, J.
AU  - Boyer, H.W.
AU  - Greene, P.
TI  - Structure of the DNA-EcoRI endonuclease recognition complex.
JO  - Structure, Dynamics and Function of Biomolecules
PY  - 1987
SP  - 255
EP  - 259
VL  - 0
AB  - The 3 angstrom structure of the co-crystalline recognition complex between
AB  - EcoRI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been
AB  - solved by the ISIR method using a platinum isomorphous derivative.  Refinement
AB  - is in progress.  The endonuclease-DNA recognition complex consists of a
AB  - distorted double helix and a protein dimer composed of identical subunits
AB  - related by a two-fold axis of rotational symmetry.  The distortions of the DNA
AB  - are induced by the binding of the protein.  They are concentrated into separate
AB  - features which are localized disruptions of the double helical symmetry.  These
AB  - disruptions appear to have structural consequences which propagate over long
AB  - distances through the DNA via twisting and perhaps bending effects.  They are
AB  - therefore referred to as neo-kinks.  The Type-I neo-kink spans the central
AB  - two-fold symmetry axis of the complex and it introduces a net unwinding of 25
AB  - degrees into the DNA.  This increases the separation of the DNA backbones
AB  - across the major groove thereby facilitating access by the protein to the base
AB  - edges, which are at the floor of the groove.  The Type-I neo-kink also realigns
AB  - adjacent adenine residues within the central AATT tetranucleotide so as to
AB  - create the detailed geometry necessary for amino acid side chains to bridge
AB  - across these purines.
ER  -

TY  - JOUR
AU  - Rosenberg, J.M.
AU  - McClarin, J.A.
AU  - Frederick, C.A.
AU  - Wang, B.-C.
AU  - Grable, J.
AU  - Boyer, H.W.
AU  - Greene, P.
TI  - Structure and recognition mechanism of EcoRI endonuclease.
JO  - Trends Biochem. Sci.
PY  - 1987
SP  - 395
EP  - 398
VL  - 12
AB  - The structure of a complex between EcoRI endonuclease and a cognate
AB  - oligonucleotide shows that sequence specificity is mediated by 12 protein-DNA
AB  - hydrogen bonds.  These interactions discriminate the EcoRI recognition site
AB  - from all other sequences because any base substitution would rupture at least
AB  - one of these hydrogen bonds.
ER  -

TY  - JOUR
AU  - Rosenberg, S.M.
TI  - EcoK restriction during in vitro packaging of coliphage lambda DNA.
JO  - Gene
PY  - 1985
SP  - 313
EP  - 315
VL  - 39
AB  - The K restriction system of Escherichia coli works in vitro [Meselson and Yuan,
AB  - Nature 217 (1968) 1110-1114].  E. coli C lacks the K restriction system.  I
AB  - show that in vitro packaging in standard E. coli K-12-derived systems effects a
AB  - loss of plaque-former output from K-unmodified lambda DNA relative to
AB  - K-modified lambda DNA when compared with packaging in the E. coli C-derived
AB  - system of Rosenberg et al. [Gene 38 (1985) 165-175].  I conclude that the EcoK
AB  - restriction system is active in standard in vitro packaging systems.  EcoK
AB  - restriction during in vitro packaging could specifically depress recovery of
AB  - some lambdaand cosmid clones of eukaryotic DNA or any other DNA not modified
AB  - for EcoK restriction.
ER  -

TY  - JOUR
AU  - Rosenstein, R.
AU  - Nerz, C.
AU  - Biswas, L.
AU  - Resch, A.
AU  - Raddatz, G.
AU  - Schuster, S.C.
AU  - Gotz, F.
TI  - Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 811
EP  - 822
VL  - 75
AB  - The Staphylococcus carnosus genome has the highest GC content of all
AB  - sequenced staphylococcal genomes, with 34.6%, and therefore represents a
AB  - species that is set apart from S. aureus, S. epidermidis, S.
AB  - saprophyticus, and S. haemolyticus. With only 2.56 Mbp, the genome belongs
AB  - to a family of smaller staphylococcal genomes, and the ori and ter regions
AB  - are asymmetrically arranged with the replichores I (1.05 Mbp) and II (1.5
AB  - Mbp). The events leading up to this asymmetry probably occurred not that
AB  - long ago in evolution, as there was not enough time to approach the
AB  - natural tendency of a physical balance. Unlike the genomes of pathogenic
AB  - species, the TM300 genome does not contain mobile elements such as
AB  - plasmids, insertion sequences, transposons, or STAR elements; also, the
AB  - number of repeat sequences is markedly decreased, suggesting a
AB  - comparatively high stability of the genome. While most S. aureus genomes
AB  - contain several prophages and genomic islands, the TM300 genome contains
AB  - only one prophage, PhiTM300, and one genomic island, nuSCA1, which is
AB  - characterized by a mosaic structure mainly composed of species-specific
AB  - genes. Most of the metabolic core pathways are present in the genome. Some
AB  - open reading frames are truncated, which reflects the nutrient-rich
AB  - environment of the meat starter culture, making some functions
AB  - dispensable. The genome is well equipped with all functions necessary for
AB  - the starter culture, such as nitrate/nitrite reduction, various sugar
AB  - degradation pathways, two catalases, and nine osmoprotection systems. The
AB  - genome lacks most of the toxins typical of S. aureus as well as genes
AB  - involved in biofilm formation, underscoring the nonpathogenic status.
ER  -

TY  - JOUR
AU  - Rosenthal, A.Z.
AU  - Matson, E.G.
AU  - Eldar, A.
AU  - Leadbetter, J.R.
TI  - RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture.
JO  - ISME J.
PY  - 2011
SP  - 1133
EP  - 1142
VL  - 5
AB  - The hindguts of wood-feeding termites typically contain hundreds of
AB  - microbial species. Together with their insect host, these gut microbes
AB  - degrade lignocellulose into usable catabolites. Although past research
AB  - revealed many facets of the stepwise flow of metabolites in this scheme,
AB  - not much is known about the breadth of interactions occurring between
AB  - termite-gut microbes. Most of these microbes are thought to depend on, and
AB  - to have co-speciated with, their host and each other for millions of
AB  - years. In this study, we explored the interactions of two spirochetes
AB  - previously isolated from the very same termite species. As hydrogen (H(2))
AB  - is the central free intermediate in termite-gut lignocellulose digestion,
AB  - we focused on interactions between two closely related termite-gut
AB  - spirochetes possessing complementary H(2) physiologies: one produces H(2),
AB  - while the other consumes it. In vitro, these two Treponema species
AB  - markedly enhanced each other's growth. RNA sequencing resolved the
AB  - transcriptomes of these two closely related organisms, revealing that
AB  - co-cultivation causes comprehensive changes in global gene expression. The
AB  - expression of well over a 100 genes in each species was changed >twofold,
AB  - with over a dozen changed >10-fold. Several changes implicating
AB  - synergistic cross-feeding of known metabolites were validated in vitro.
AB  - Additionally, certain activities beneficial to the host were
AB  - preferentially expressed during consortial growth. However, the majority
AB  - of changes in gene expression are not yet understandable, but indicate a
AB  - broad, comprehensive and mutualistic interaction between these closely
AB  - related, co-resident gut symbionts. The results suggest that staggeringly
AB  - intricate networks of metabolic and gene interactions drive lignocellulose
AB  - degradation and co-evolution of termite gut microbiota.
ER  -

TY  - JOUR
AU  - Rosewarne, C.P.
AU  - Cheung, J.L.
AU  - Smith, W.J.
AU  - Evans, P.N.
AU  - Tomkins, N.W.
AU  - Denman, S.E.
AU  - O'Cuiv, P.
AU  - Morrison, M.
TI  - Draft Genome Sequence of Treponema sp. Strain JC4, a Novel Spirochete Isolated from the Bovine Rumen.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4130
EP  - 4130
VL  - 194
AB  - Morphologically and biochemically diverse members of the Treponema genus are present in the
AB  - gastrointestinal tract of ruminants, yet very little is understood
AB  - about their functional importance to this microbiome. Here we describe the
AB  - annotated draft genome sequence of Treponema sp. strain JC4, a novel spirochete
AB  - isolated from a bovine rumen sample.
ER  -

TY  - JOUR
AU  - Rosewarne, C.P.
AU  - Greenfield, P.
AU  - Li, D.
AU  - Tran-Dinh, N.
AU  - Bradbury, M.I.
AU  - Midgley, D.J.
AU  - Hendry, P.
TI  - Draft Genome Sequence of Clostridium sp. Maddingley, Isolated from Coal-Seam Gas  Formation Water.
JO  - Genome Announcements
PY  - 2013
SP  - e00081
EP  - e00012
VL  - 1
AB  - Clostridium sp. Maddingley was isolated as an axenic culture from a brown coal-seam formation
AB  - water sample collected from Victoria, Australia. It lacks the solventogenesis genes found in
AB  - closely related clostridial strains. Metabolic reconstructions suggest that volatile fatty
AB  - acids are the main fermentation end products.
ER  -

TY  - JOUR
AU  - Rosewarne, C.P.
AU  - Greenfield, P.
AU  - Li, D.
AU  - Tran-Dinh, N.
AU  - Midgley, D.J.
AU  - Hendry, P.
TI  - Draft Genome Sequence of Methanobacterium sp. Maddingley, Reconstructed from Metagenomic Sequencing of a Methanogenic Microbial Consortium Enriched from  Coal-Seam Gas Formation Water.
JO  - Genome Announcements
PY  - 2013
SP  - e00082
EP  - e00012
VL  - 1
AB  - The draft genome of Methanobacterium sp. Maddingley was reconstructed from metagenomic
AB  - sequencing of a methanogenic microbial consortium enriched from coal-seam gas formation water.
AB  - It is a hydrogenotrophic methanogen predicted to grow using hydrogen and carbon dioxide.
ER  -

TY  - JOUR
AU  - Rosinski-Chupin, I.
AU  - Sauvage, E.
AU  - Mairey, B.
AU  - Mangenot, S.
AU  - Ma, L.
AU  - Da Cunha, V.
AU  - Rusniok, C.
AU  - Bouchier, C.
AU  - Barbe, V.
AU  - Glaser, P.
TI  - Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage.
JO  - BMC Genomics
PY  - 2013
SP  - 252
EP  - 252
VL  - 14
AB  - BACKGROUND: During host specialization, inactivation of genes whose function is
AB  - no more required is favored by changes in selective constraints and evolutionary
AB  - bottlenecks. The Gram positive bacteria Streptococcus agalactiae (also called
AB  - GBS), responsible for septicemia and meningitis in neonates also emerged during
AB  - the seventies as a cause of severe epidemics in fish farms. To decipher the
AB  - genetic basis for the emergence of these highly virulent GBS strains and of their
AB  - adaptation to fish, we have analyzed the genomic sequence of seven strains
AB  - isolated from fish and other poikilotherms. RESULTS: Comparative analysis shows
AB  - that the two groups of GBS strains responsible for fish epidemic diseases are
AB  - only distantly related. While strains belonging to the clonal complex 7 cannot be
AB  - distinguished from their human CC7 counterparts according to their gene content,
AB  - strains belonging to the ST260-261 types probably diverged a long time ago. In
AB  - this lineage, specialization to the fish host was correlated with a massive gene
AB  - inactivation and broad changes in gene expression. We took advantage of the low
AB  - level of sequence divergence between GBS strains and of the emergence of
AB  - sublineages to reconstruct the different steps involved in this process.
AB  - Non-homologous recombination was found to have played a major role in the genome
AB  - erosion. CONCLUSIONS: Our results show that the early phase of genome reduction
AB  - during host specialization mostly involves accumulation of small and likely
AB  - reversible indels, followed by a second evolutionary step marked by a higher
AB  - frequency of large deletions.
ER  -

TY  - JOUR
AU  - Roske, K.
AU  - Calcutt, M.J.
AU  - Wise, K.S.
TI  - The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein.
JO  - Mol. Microbiol.
PY  - 2004
SP  - 1703
EP  - 1720
VL  - 52
AB  - The approximately 16 kb genome of the Mycoplasma fermentans phiMFV1 prophage is described, and
AB  - its mobility, replication and effect on the
AB  - mycoplasma surface phenotype are demonstrated. In various M. fermentans
AB  - strains, phiMFV1 was either absent or integrated at diverse (and sometimes
AB  - multiple) chromosomal sites, each marked by a conserved TTTTTA target
AB  - sequence that is duplicated upon integration. Precise excision,
AB  - replication of an extrachromosomal form and loss of phiMFV1 from the
AB  - mycoplasmal genome were documented in a series of clonal derivatives of M.
AB  - fermentans propagated in culture. Of 18 open reading frames (ORFs) encoded
AB  - by phiMFV1, most can be ascribed functions related to phage biology,
AB  - whereas one encodes a unique coiled-coil membrane surface protein, Mem,
AB  - that was confirmed to be expressed in propagating populations of M.
AB  - fermentans. With the exception of Mem and other minor ORFs, the striking
AB  - similarity between the deduced proteomes of phiMFV1 and the recently
AB  - described phiMAV1 of arthritogenic strains of Mycoplasma arthritidis,
AB  - along with the prominent gene synteny between these elements, provides the
AB  - taxonomic basis for a new family of prophage. Their coding features are
AB  - consistent with long-term residence in mycoplasma genomes and the
AB  - divergence of species within a phylogenetic clade of mycoplasmas. The
AB  - unique Mem protein expressed from phiMFV1 and the unique hypothetical
AB  - surface lipoproteins encoded by phiMAV1 and phiMFV1 also suggest that
AB  - prophage-associated genes may provide specific, selectable phenotypic
AB  - traits during co-evolution of mycoplasma species with their respective
AB  - mammalian hosts. Retention of these labile prophage elements in organisms
AB  - with such drastically reduced genome sizes implies a significant role in
AB  - adaptation and survival.
ER  -

TY  - JOUR
AU  - Roslan, N.N.
AU  - Sabri, S.
AU  - Oslan, S.N.
AU  - Baharum, S.N.
AU  - Leow, T.C.
TI  - Complete Genome Sequence of Photobacterium sp. Strain J15, Isolated from Seawater of Southwestern Johor, Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00739
EP  - e00716
VL  - 4
AB  - Here, we report the genome sequences of Photobacterium sp. strain J15, isolated from seawater
AB  - in Johor, Malaysia, with the ability to produce lipase and
AB  - asparaginase. The PacBio genome sequence analysis of Photobacterium sp. strain
AB  - J15 generated revealed its potential in producing enzymes with different
AB  - catalytic functions.
ER  -

TY  - JOUR
AU  - Roslan, N.S.
AU  - Jabeen, S.
AU  - Mat, I.N.
AU  - Omar, A.R.
AU  - Bejo, M.H.
AU  - Ideris, A.
TI  - Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium  Strain UPM 260, Isolated from a Broiler Chicken in Perak, Malaysia.
JO  - Genome Announcements
PY  - 2017
SP  - e01272
EP  - e01217
VL  - 5
AB  - Salmonella enterica subsp. enterica serovar Typhimurium is one of several well-categorized
AB  - Salmonella serotypes recognized globally. Here, we report the
AB  - whole-genome sequence of S Typhimurium strain UPM 260, isolated from a broiler
AB  - chicken.
ER  -

TY  - JOUR
AU  - Rosner, J.L.
TI  - Modification-deficient mutants of bacteriophage Pl.  I. Restriction by Pl cryptic lysogens.
JO  - Virology
PY  - 1973
SP  - 213
EP  - 222
VL  - 52
AB  - The Pl restriction-modification system is responsible for the inefficient
AB  - plating of c2 and c3 mutants of bacteriophage Pl on Pl cryptic lysogens.  Pl
AB  - cryptic is a defective prophage which does not express Pl immunity but which
AB  - does express Pl modification and restriction.  The rare c2 or c3 phage which do
AB  - grow on the Pl cryptic lysogens [abbreviated (Plcry)], lose their ability to do
AB  - so after growth on a nonlysogenic host.  Temperature-sensitive c2 mutants grown
AB  - on a nonlysogenic host at the permissive temperature plate efficiently on
AB  - (Plcry).  If grown at a nonpermissive temperature, however, the c2 ts mutants
AB  - plate inefficiently on (Plcry).  Plr-m+, a nonrestricting P1 phage, plates
AB  - efficiently on (Plcry), but Plr-m-, which neither restricts nor modifies,
AB  - plates inefficiently on (Plcry).  These results are explained as follows:  Pl
AB  - DNA is itself a substrate for the Pl directed modification-restriction system.
AB  - Normally, during lytic growth, Pl DNA is modified.  However, Plr-m-, c2, and c3
AB  - mutants are modification-defective.  Thus, when their unmodified DNA enters
AB  - (Plcry), it is subject to Pl restriction.  Direct evidence for this hypothesis
AB  - was obtained from experiments in which the abilitiy of Pl phage to modify
AB  - lambda was studied.  Plr-m-, c2 and c3 mutants cannot modify lambda whereas Pl
AB  - wild type and Plr-m+ are able to do so.  Furthermore, c2 and c3 mutants can
AB  - complement each other to express Pl modification.  Plr-m- is not complemented
AB  - by either c2 or c3 mutants.  It is concluded that c2 and c3 are two cistrons
AB  - required for P1 modification.  Plr-m- may be missing, or unable to transcribe,
AB  - the c2 and c3 genes.
ER  -

TY  - JOUR
AU  - Ross, D.E.
AU  - Gulliver, D.
TI  - Metagenome-Assembled Genome Sequence of Pseudomonas stutzeri Strain CO183 Isolated from a Coalbed Methane Well.
JO  - Genome Announcements
PY  - 2016
SP  - e01237
EP  - e01216
VL  - 4
AB  - A near-complete Pseudomonas stutzeri draft genome was extracted from a coalbed metagenome. The
AB  - draft genome described herein provides insight into the
AB  - functional pathways encoded by this bacterium and its potential role in coalbed
AB  - methane environments.
ER  -

TY  - JOUR
AU  - Ross, D.E.
AU  - Gulliver, D.
TI  - Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome.
JO  - Genome Announcements
PY  - 2016
SP  - e01024
EP  - e01016
VL  - 4
AB  - The draft genome sequence of Pseudomonas stutzeri strain K35 was separated from a metagenome
AB  - derived from a produced water microbial community of a coalbed methane
AB  - well. The genome encodes a complete nitrogen fixation pathway and the upper and
AB  - lower naphthalene degradation pathways.
ER  -

TY  - JOUR
AU  - Ross, D.E.
AU  - Marshall, C.W.
AU  - May, H.D.
AU  - Norman, R.S.
TI  - Metagenome-Assembled Genome Sequences of Acetobacterium sp. Strain MES1 and Desulfovibrio sp. Strain MES5 from a Cathode-Associated Acetogenic Microbial  Community.
JO  - Genome Announcements
PY  - 2017
SP  - e00938
EP  - e00917
VL  - 5
AB  - Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5
AB  - were obtained from the metagenome of a cathode-associated community
AB  - enriched within a microbial electrosynthesis system (MES). The draft genome
AB  - sequences provide insight into the functional potential of these microorganisms
AB  - within an MES and a foundation for future comparative analyses.
ER  -

TY  - JOUR
AU  - Ross, D.E.
AU  - Marshall, C.W.
AU  - May, H.D.
AU  - Norman, R.S.
TI  - Draft Genome Sequence of Sulfurospirillum sp. Strain MES, Reconstructed from the  Metagenome of a Microbial Electrosynthesis System.
JO  - Genome Announcements
PY  - 2015
SP  - e01336
EP  - e01314
VL  - 3
AB  - A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic  binning of a
AB  - metagenome sequenced from a microbial electrosynthesis system (MES)
AB  - actively producing acetate and hydrogen. The genome contains the nosZDFLY genes,
AB  - which are involved in nitrous oxide reduction, suggesting the potential role of
AB  - this strain in denitrification.
ER  -

TY  - JOUR
AU  - Ross, D.W.
TI  - Restriction enzymes.
JO  - Arch. Pathol. Lab. Med.
PY  - 1990
SP  - 906
EP  - 906
VL  - 114
AB  - None
ER  -

TY  - JOUR
AU  - Ross, T.K.
AU  - Achberger, E.C.
AU  - Braymer, H.D.
TI  - Characterization of the Escherichia coli modified cytosine restriction (mcrB) gene.
JO  - Gene
PY  - 1987
SP  - 277
EP  - 289
VL  - 61
AB  - The McrB restriction system of Escherichia coli K-12 is responsible for the
AB  - inactivation of 5-methylcytosine-containing DNA.  The mcrB mutation of E. coli
AB  - strain K802 was complemented by hybrid plasmid pUC9-14 which consists of a
AB  - 5.5-kb BglII-EcoRI fragment from the E. coli K-12 chromosome cloned in pUC9
AB  - (Ross and Braymer, 1987).  The limits of the mcrB gene within the 5.5-kb insert
AB  - were defined by deletion portions of the fragment and assaying for McrB
AB  - restriction of M. AluI-methylated DNA.   A 51-kDa polypeptide was identified as
AB  - the mcrB gene product based on an analysis of maxicell-labeled polypeptides
AB  - from pUC9-14 and deletion derivatives of this plasmid.  Deletion analyses and
AB  - transcription initiation assays enabled us to determine the direction of
AB  - transcription and translation of mcrB.  Transcription initiates approx. 710 bp
AB  - beyond the end of the hsdS gene, and proceeds in the same direction as the
AB  - transcription of the hsdR, hsdM, and hsdS genes, which is clockwise on the
AB  - conventional E. coli map.
ER  -

TY  - JOUR
AU  - Ross, T.K.
AU  - Achberger, E.C.
AU  - Braymer, H.D.
TI  - Nucleotide sequence of the McrB region of Escherichia coli K-12 and evidence for two independent translational initiation sites at the mcrB locus.
JO  - J. Bacteriol.
PY  - 1989
SP  - 1974
EP  - 1981
VL  - 171
AB  - The McrB restriction system of Escherichia coli K-12 is responsible for the
AB  - biological inactivation of foreign DNA that contains 5-methylcytosine residues.
AB  - Within the McrB region of the chromosome is the mcrB gene, which encodes a
AB  - protein of 51 kilodaltons (kDa), and the mcrC gene, the product of which is 39
AB  - kDa.  The nucleotide sequence of a 2695-base-pair segment encompassing the McrB
AB  - region was determined.  The deduced amino acid sequence was used to identify
AB  - two open reading frames specifying peptides of 455 and 348 amino acids,
AB  - corresponding to the products of the mcrB and mcrC genes, respectively.  A
AB  - single-nucleotide overlap was found to exist between the termination codon of
AB  - the mcrB gene and the proposed initiation codon of the mcrC gene.  The presence
AB  - of an additional peptide of 33 kDa in strains containing various recombinant
AB  - plasmids with portions of the McrB region has been reported by Ross et al.  The
AB  - analysis of frameshift and deletion mutants of one such hybrid plasmid,
AB  - pRAB-13, provided evidence for a second translational initiation site within
AB  - the McrB open reading frame.  The proposed start codon for translation of the
AB  - 33-kDa peptide lies 481 nucleotides downstream from the initation codon for the
AB  - 51-kDa mcrB gene product.  The 33-kDa peptide may play a regulatory role in the
AB  - McrB restriction of DNA containing 5-methylcytosine.
ER  -

TY  - JOUR
AU  - Ross, T.K.
AU  - Achberger, E.C.
AU  - Braymer, H.D.
TI  - Identification of a second polypeptide required for McrB restriction of 5-methylcytosine-containing DNA in Escherichia coli K12.
JO  - Mol. Gen. Genet.
PY  - 1989
SP  - 402
EP  - 407
VL  - 216
AB  - The McrB restriction system in Escherichia coli K12 causes sequence-specific
AB  - recognition and inactivation of DNA containing 5-methylcytosine residues.  We
AB  - have previously located the mcrB gene near hsdS at 99 min on the E. coli
AB  - chromosome and demonstrated that it encodes a 51 kDa polypeptide required for
AB  - restriction of M.AluI methylated (A-G-5mC-T) DNA.  We show here, by analysis of
AB  - maxicell protein synthesis of various cloned fragments from the mcrB region,
AB  - that a second protein of approximately 39 kDa is also required for
AB  - McrB-directed restriction.  The new gene, designated mcrC, is adjacent to mcrB
AB  - and located distally to hsdS.  The McrB phenotype has been correlated
AB  - previously with restriction of 5-hydroxy-methylcytosine (HMC)-containing T-even
AB  - phage DNA that lacks the normal glucose modification of HMC, formally
AB  - designated RglB (for restriction of glucoseless phage).  This report reveals a
AB  - difference between the previously correlated McrB and RglB restriction systems:
AB  - while both require the mcrB gene product only the McrB system requires the
AB  - newly identified mcrC-encoded 39-kDa polypeptide.
ER  -

TY  - JOUR
AU  - Ross, T.K.
AU  - Braymer, H.D.
TI  - Localization of a genetic region involved in McrB restriction by Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1987
SP  - 1757
EP  - 1759
VL  - 169
AB  - A 5,500-base-pairs BglII-EcoRI fragment proximal to the hsd genes of
AB  - Escherichia coli K-12 has been cloned in the plasmid vector pUC9.  The
AB  - resultant hybrid plasmid was shown to complement the mcrR mutation of E. coli
AB  - K802.  The presence of the hybrid plasmid in strain K802 caused an 18.3-fold
AB  - drop in transformation efficiency with AluI-methylated pACYC184 relative to
AB  - unmethylated pACYC184.  These results indicate that the cloned DNA is involved
AB  - in the McrB system of restriction of 5-methylcytosine DNA.
ER  -

TY  - JOUR
AU  - Rossi, S.
AU  - Buera, M.P.
AU  - Moreno, S.
AU  - Chirife, J.
TI  - Stabilization of the restriction enzyme EcoRI dried with Trehalose and other selected glass-forming solutes.
JO  - Biotechnol. Prog.
PY  - 1997
SP  - 609
EP  - 616
VL  - 13
AB  - The stabilization of the restriction enzyme EcoRI by its incorporation into aqueous
AB  - glass-forming carbohydrate or polymer solutions, followed by vacuum-drying to low moisture,
AB  - has been studied.  Glass-forming solutes included trehalose, sucrose, lactose, maltose,
AB  - raffinose, maltodextrin, DE 10, and poly(vinylpyrrolidone) (molecular weight 40,000, PVP).
AB  - Among the solutes examined, trehalose and sucrose protected the enzyme most effectively during
AB  - storage at 37 and 45 C.  The restriction enzyme dried with trehalose or sucrose maintained its
AB  - activity without detectable loss for at least 20 days at 37 C and 12 days at 45 C.  In
AB  - contrast, the activity of the enzyme dried with maltodextrin or PVP was reduced during vacuum
AB  - desiccation and also it decreased remarkably during storage at the same temperatures.  Stored
AB  - (37/45 C) vacuum-dried trehalose and sucrose systems were either a dense paste or a very
AB  - viscous syrup, and this indicated that they were not glassy.  Moreover, no relationship was
AB  - found between the glass transition temperatures (Tg) of the pure added solute and enzyme
AB  - protection during storage, since, e.g., sucrose which has significantly lower Tg values
AB  - protected the enzyme much better than either maltose, lactose, maltodextrin, or PVP.  The
AB  - trisaccharide raffinose offered good protection of enzyme activity, and its role as a novel
AB  - excipient matrix for labile enzyme stabilization deserves further investigation.  The
AB  - stability of enzyme EcoRI was rapidly lost when the vacuum-dried trehalose and sucrose systems
AB  - were humidified to 58% relative humidity and stored at 45 C, and this was attributed to
AB  - disaccharide crystallization.
ER  -

TY  - JOUR
AU  - Rossino, R.
AU  - Gosalvez, J.
AU  - Mezzanotte, R.
TI  - The effects of enzyme inactivation and incubation buffer on digestion in situ with restriction endonucleases.
JO  - Biotech. Histochem.
PY  - 1998
SP  - 325
EP  - 328
VL  - 73
AB  - Previous studies have shown that components of the incubation reaction other than the
AB  - restriction endonucleases in an in situ restriction enzyme digest of chromosomes may induce
AB  - G-like banding patterns.  To determine whether factors other than DNA base composition play a
AB  - role in determining restriction enzyme induced bands, we investigated the effect of reaction
AB  - buffers alone or in the presence of heat inactivated enzymes.  Our results show that enzymes
AB  - such as AluI, RsaI and MspI become inactivated during 3-24 hr incubations at 37 C and that
AB  - reaction buffers alone failed to produce G-like bands when inactive endonucleases were
AB  - included.
ER  -

TY  - JOUR
AU  - Roszczyk, E.
AU  - Goodgal, S.
TI  - Methylase Activities from Haemophilus influenzae that protect Haemophilus parainfluenzae Transforming Deoxyribonucleic Acid from Inactivation by Haemophilus influenzae Endonuclease R.
JO  - J. Bacteriol.
PY  - 1975
SP  - 287
EP  - 293
VL  - 123
AB  - Specific methylases that have the properties of deoxyribonucleic acid (DNA)
AB  - modification enzymes have been isolated from Haemophilus influenzae strain Rd.
AB  - Two activities (methylase IIa and methylase III) were found to protect
AB  - transforming DNA of H. parainfluenzae from the action of H. influenzae
AB  - restriction enzymes.  To determine the specificity of the protection, a
AB  - procedure based on biological activity was developed for the separation and
AB  - purification of the restriction endonucleases from H. influenzae strain Rd.
AB  - Two endonuclease R activities presumably corresponding to HindII and HindIII
AB  - (P.H. Roy and H.O. Smith, 1973; H.O. Smith and K.W. Wilcox, 1970) were
AB  - characterized by differences in their chromatographic properties, ability to
AB  - attack T7 DNA, and inactivation of the transforming activity of different
AB  - markers of H. parainfluenzae DNA.  One endonuclease R enzyme (HindII) attacked
AB  - T7 DNA and was found to inactivate the dalacin resistance marker (<0.01%
AB  - activity remaining) with only a slight effect on the streptomycin resistance
AB  - marker (83% activity remaining).  Methylase IIa treatment protected 40% of the
AB  - dalacin resistance marker of H. parainfluenzae DNA from inactivation by HindII.
AB  - The other restriction activity (HindIII) was inert towards T7 DNA and
AB  - inactivated the streptomycin resistance marker of H. parainfluenzae DNA (<0.01%
AB  - activity remaining) without any effect on the dalacin resistance marker.  The
AB  - methylation of H. parainfluenzae DNA accomplished by methylase III protected
AB  - 60% of the transforming activity of the streptomycin resistance marker of H.
AB  - parainfluenzae DNA from the action of HindIII.
ER  -

TY  - JOUR
AU  - Roth, M.
AU  - Helm-Kruse, S.
AU  - Friedrich, T.
AU  - Jeltsch, A.
TI  - Functional roles of conserved amino acid residues in DNA methyltransferases investigated by site-directed mutagenesis of the EcoRV adenine-M6-methyltransferase.
JO  - J. Biol. Chem.
PY  - 1998
SP  - 17333
EP  - 17342
VL  - 273
AB  - All DNA methyltransferases have similar catalytic domains containing nine blocks of conserved
AB  - amino acid residues.  We have investigated by site-directed mutagenesis the function of 17
AB  - conserved residues in the EcoRV alpha-adenine-N6-DNA methyltransferase.  The structure of this
AB  - class of MTases has been predicted recently.  The variants were characterized with respect to
AB  - their catalytic activities and their abilities to bind to DNA and the S-adenosylmethionine
AB  - cofactor.  Amino acids located in motifs X, I, and II are shown to be involved in AdoMet
AB  - binding (Lys16, Glu37, Phe39, and Asp58).  Some of the mutants defective in AdoMet binding are
AB  - also impaired in DNA binding, suggesting allosteric interactions between the AdoMet and DNA
AB  - binding site.  Asp78 (motif III), which was supposed to form a hydrogen bond to the AdoMet on
AB  - the basis of the structure predictions, turned out not to be important for AdoMet binding,
AB  - suggesting that motif III has not been identified correctly.  R128A and N130A, having
AB  - mutations in the putative DNA binding domain, are unable to bind to DNA.  Residues located in
AB  - motifs IV, V, VI, and VIII are involved in catalysis (Asp193, Tyr196, Asp211, Ser229, Trp231,
AB  - and Tyr258), some of them presumably in binding the flipped target base, because mutations at
AB  - these residues fail to significantly interfere with DNA and AdoMet binding but strongly reduce
AB  - catalysis. Our results are in substantial agreement with the structure prediction for EcoRV
AB  - alpha-adenine-N6-methyltransferase and x-ray structures of other MTases.
ER  -

TY  - JOUR
AU  - Roth, M.
AU  - Jeltsch, A.
TI  - Biotin-Avidin microplate assay for the quantitative analysis of enzymatic methylation of DNA by DNA methyltransferases.
JO  - Biol. Chem.
PY  - 2000
SP  - 269
EP  - 272
VL  - 381
AB  - An assay is described to measure methylation of biotinylated oligonucleotide substrates by DNA
AB  - methyltransferases using [methyl-3H]-AdoMet.  After the methylation reaction the
AB  - oligonucleotides are immobilized on an avidin-coated microplate.  The incorporation of [3H]
AB  - into the DNA is quenched by addition of unlabeled AdoMet to the binding buffer.  Unreacted
AB  - AdoMet and enzyme are removed by washing.  To release the radioactivity incorporated into the
AB  - DNA, the wells are incubated with a non-specific endonuclease and the radioactivity determined
AB  - by liquid scintillation counting.  As an example, we have studied methylation of DNA by the
AB  - EcoRV DNA methyltransferase.  The reaction progress curves measured with this assay are linear
AB  - with respect to time.  Methylation rates linearly increase with enzyme concentration.  The
AB  - rates are comparable to results obtained with the same enzyme using a different assay.  The
AB  - biotin-avidin assay is inexpensive, convenient, quantitative, fast and well suited to process
AB  - many samples in parallel.  The accuracy of the assay is high, allowing to reproduce results
AB  - within +-10%. The assay is very sensitive as demonstrated by the detection of incorporation of
AB  - 0.8 fmol methyl groups into the DNA. Under the experimental conditions, this corresponds to
AB  - methylation of only 0.03% of all target sites of the substrate.  Using this assay, the DNA
AB  - methylation activity of some M.EcoRV variants could be detected that was not visible by other
AB  - in vitro methylation assays.
ER  -

TY  - JOUR
AU  - Roth, M.
AU  - Jeltsch, A.
TI  - Changing the target base specificity of the EcoRV DNA methyltransferase by rational de novo protein-design.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3137
EP  - 3144
VL  - 29
AB  - The EcoRV DNA-(adenine-N(6))-methyltransferase (M.EcoRV) specifically modifies the first
AB  - adenine residue within GATATC sequences. During catalysis, the enzyme flips its target base
AB  - out of the DNA helix and binds it into a target base-binding pocket, which is formed in part
AB  - by Lys16 and Tyr196. A cytosine residue is accepted by wild-type M.EcoRV as a substrate at a
AB  - 31-fold reduced efficiency with respect to the k(cat)/K(M) values if it is located in a CT
AB  - mismatch substrate (GCTATC/GATATC). Cytosine residues positioned in a CG base pair
AB  - (GCTATC/GATAGC) are modified at much more reduced rates, because flipping out the target base
AB  - is much more difficult in this case. We intended to change the target base specificity of
AB  - M.EcoRV from adenine-N(6) to cytosine-N(4). To this end we generated, purified and
AB  - characterized 15 variants of the enzyme, containing single, double and triple amino acid
AB  - exchanges following different design approaches. One concept was to reduce the size of the
AB  - target base-binding pocket by site-directed mutagenesis. The K16R variant showed an altered
AB  - specificity, with a 22-fold preference for cytosine as the target base in a mismatch
AB  - substrate. This corresponds to a 680-fold change in specificity, which was accompanied by only
AB  - a small loss in catalytic activity with the cytosine substrate. The K16R/Y196W variant no
AB  - longer methylated adenine residues at all and its activity towards cytosine was reduced only
AB  - 17-fold. Therefore, we have changed the target base specificity of M.EcoRV from adenine to
AB  - cytosine by rational protein design. Because there are no natural paragons for the variants
AB  - described here, a change of the target base specificity of a DNA interacting enzyme was
AB  - possible by rational de novo design of its active site.
ER  -

TY  - JOUR
AU  - Rothen, J.
AU  - Schindler, T.
AU  - Pothier, J.F.
AU  - Younan, M.
AU  - Certa, U.
AU  - Daubenberger, C.
AU  - Pfluger, V.
AU  - Jores, J.
TI  - Draft Genome Sequences of Seven Streptococcus agalactiae Strains Isolated from Camelus dromedarius at the Horn of Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e00525
EP  - e00517
VL  - 5
AB  - We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated
AB  - from Camelus dromedarius in Kenya and Somalia. These data are an
AB  - extension to the group B Streptococcus (GBS) pangenome and might provide more
AB  - insight into the underlying mechanisms of pathogenicity and antibiotic resistance
AB  - of camel GBS.
ER  -

TY  - JOUR
AU  - Rothrock, M.J. Jr.
AU  - Fan, P.
AU  - Jeong, K.C.
AU  - Kim, S.A.
AU  - Ricke, S.C.
AU  - Park, S.H.
TI  - Complete Genome Sequence of Listeria monocytogenes Strain MR310, Isolated from a  Pastured-Flock Poultry Farm System.
JO  - Genome Announcements
PY  - 2018
SP  - e00171
EP  - e00118
VL  - 6
AB  - Investigation of Listeria monocytogenes transmission from environmental sources associated
AB  - with pasture-raised chickens to poultry products is needed to
AB  - determine ways to prevent potential foodborne illness. Here, we report the
AB  - complete genome sequence of Listeria monocytogenes MR310, one of the isolates
AB  - from a pastured-flock poultry management system.
ER  -

TY  - JOUR
AU  - Rotman, E.
AU  - Kouzminova, E.
AU  - Plunkett, G. III
AU  - Kuzminov, A.
TI  - Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6802
EP  - 6817
VL  - 194
AB  - The novel temperate bacteriophage Lula, contaminating laboratory Escherichia coli
AB  - strains, turned out to be the well-known lambdoid phage phi80. Our previous
AB  - studies revealed that two characteristics of Lula/phi80 facilitate its spread in
AB  - the laboratory environment: cryptic lysogen productivity and stealthy
AB  - infectivity. To understand the genetics/genomics behind these traits, we
AB  - sequenced and annotated the Lula/phi80 genome, encountering an E. coli-toxic gene
AB  - revealed as a gap in the sequencing contig and analyzing a few genes in more
AB  - detail. Lula/phi80's genome layout copies that of lambda, yet homology with other
AB  - lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is
AB  - resistant to cutting with several restriction enzymes, suggesting DNA
AB  - modification, but deletion of the phage's damL gene, coding for DNA adenine
AB  - methylase, did not make DNA cuttable. The damL mutation of Lula/phi80 also did
AB  - not change the phage titer in lysogen cultures, whereas the host dam mutation did
AB  - increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80
AB  - lysogens is apparently in response to endogenous DNA damage, we deleted the only
AB  - Lula/phi80 SOS-controlled gene, dinL. We found that dinL mutant lysogens release
AB  - fewer phage in response to endogenous DNA damage but are unchanged in their
AB  - response to external DNA damage. The toxic gene of Lula/phi80, gamL, encodes an
AB  - inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own
AB  - antidote, agt, apparently encoding a modifier protein, was found nearby.
AB  - Interestingly, Lula/phi80 lysogens are recD and sbcCD phenocopies, so GamL and
AB  - Agt are part of lysogenic conversion.
ER  -

TY  - JOUR
AU  - Rotta, C.
AU  - Poehlein, A.
AU  - Schwarz, K.
AU  - McClure, P.
AU  - Daniel, R.
AU  - Minton, N.P.
TI  - Closed Genome Sequence of Clostridium pasteurianum ATCC 6013.
JO  - Genome Announcements
PY  - 2015
SP  - e01596
EP  - e01514
VL  - 3
AB  - We report here the closed genome of Clostridium pasteurianum ATCC 6013, a saccharolytic,
AB  - nitrogen-fixing, and spore-forming Gram-positive obligate anaerobe. The organism is of
AB  - biotechnological interest due to the production of solvents (butanol and 1,3-propanediol) but
AB  - can be associated with food spoilage.  The genome comprises a total of 4,351,223 bp.
ER  -

TY  - JOUR
AU  - Rouet, P.
AU  - Smih, F.
AU  - Jasin, M.
TI  - Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease.
JO  - Mol. Cell. Biol.
PY  - 1994
SP  - 8096
EP  - 8106
VL  - 14
AB  - To maintain genomic integrity, double-strand breaks (DSBs) in chromosomal DNA must be
AB  - repaired. In mammalian systems, the analysis of the repair of chromosomal DSBs has been
AB  - limited by the inability to introduce well-defined DSBs in genomic DNA. In this study, we
AB  - created specific DSBs in mouse chromosomes for the first time, using an expression system for
AB  - a rare-cutting endonuclease, I-SceI. A genetic assay has been devised to monitor the repair of
AB  - DSBs, whereby cleavage sites for I-SceI have been integrated into the mouse genome in two
AB  - tandem neomycin phosphotransferase genes. We find that cleavage of the I-SceI sites is very
AB  - efficient, with at least 12% of stably transfected cells having at least one cleavage event
AB  - and, of these, more than 70% have undergone cleavage at both I-SceI sites. Cleavage of both
AB  - sites in a fraction of clones deletes 3.8 kb of intervening chromosomal sequences. We find
AB  - that the DSBs are repaired by both homologous and nonhomologous mechanisms. Nonhomologous
AB  - repair events frequently result in small deletions after rejoining of the two DNA ends. Some
AB  - of these appear to occur by simple blunt-ended ligation, whereas several others may occur
AB  - through annealing of short regions of terminal homology. The DSBs are apparently
AB  - recombinogenic, stimulating gene targeting of a homologous fragment by more than 2 orders of
AB  - magnitude. Whereas gene-targeted clones are nearly undetectable without endonuclease
AB  - expression, they represent approximately 10% of cells transfected with the I-SceI expression
AB  - vector. Gene targeted clones are of two major types, those that occur by two-sided homologous
AB  - recombination with the homologous fragment and those that occur by one-sided homologous
AB  - recombination. Our results are expected to impact a number of areas in the study of mammalian
AB  - genome dynamics, including the analysis of the repair of DSBs and homologous recombination
AB  - and, potentially, molecular genetic analyses of mammalian genomes.
ER  -

TY  - JOUR
AU  - Rouet, P.
AU  - Smith, F.
AU  - Jasin, M.
TI  - Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 6064
EP  - 6068
VL  - 91
AB  - Double-strand breaks introduced into DNA in vivo have been shown to enhance homologous
AB  - recombination in a variety of chromosomal and extrachromosomal loci in Saccharomyces
AB  - cerevisiae. To introduce double-strand breaks in DNA at defined locations in mammalian cells,
AB  - we have constructed a mammalian expression vector for a modified form of I-SceI, a yeast
AB  - mitochondrial intron-encoded endonuclease with an 18-bp recognition sequence. Expression of
AB  - the modified I-SceI endonuclease in COS1 cells results in cleavage of model recombination
AB  - substrates and enhanced extrachromosomal recombination, as assayed by chloramphenicol
AB  - acetyltransferase activity and Southern blot analysis. Constitutive expression of the
AB  - endonuclease in mouse 3T3 cells is not lethal, possibly due to either the lack of I-SceI sites
AB  - in the genome or sufficient repair of them. Expression of an endonuclease with such a long
AB  - recognition sequence will provide a powerful approach to studying a number of molecular
AB  - processes in mammalian cells, including homologous recombination.
ER  -

TY  - JOUR
AU  - Rouleau, J.
AU  - MacLeod, A.R.
AU  - Szyf, M.
TI  - Regulation of the DNA methyltransferase by the Ras-AP-1 signaling pathway.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 1595
EP  - 1601
VL  - 270
AB  - Using deletion analysis and site-specific mutagenesis to map the 5' regulatory region of the
AB  - DNA methyltransferase (MeTase) gene, we show that a 106-bp sequence (at -1744 to -1650)
AB  - bearing three AP-1 sites is responsible for induction of DNA MeTase promoter activity. Using
AB  - transient cotransfection chloramphenicol acetyltransferase assays in P19 cells, we show that
AB  - the DNA MeTase promoter is induced by c-Jun or Ha-Ras but not by a dominant negative mutant of
AB  - Jun, 99. The activation of the DNA MeTase promoter by Jun is inhibited in a ligand dependent
AB  - manner by the glucocorticoid receptor. Stable expression of Ha-Ras in P19 cells results in
AB  - induction of transcription of the DNA MeTase mRNA as determined by nuclear run-on assays and
AB  - the steady state levels of DNA MeTase mRNA as determined by an RNase protection assay. These
AB  - experiments establish a potential molecular link between nodal cellular signaling pathways and
AB  - the control of expression of the DNA MeTase gene. This provides us with a possible molecular
AB  - explanation for the hyperactivation of DNA MeTase in many cancer cells and suggests that DNA
AB  - MeTase is one possible downstream effector of Ras.
ER  -

TY  - JOUR
AU  - Rouleau, J.
AU  - Szyf, M.
TI  - Regulation of the mouse DNA methyltransferase by signal transduction pathways.
JO  - Mol. Biol. Cell
PY  - 1992
SP  - A25
EP  - A25
VL  - 3
AB  - A hallmark of DNA methylation in vertebrates is the fact that only a fraction of the CpG
AB  - sequences is methylated (60-80%) and that nonmethylated cytosines are distributed in a
AB  - nonrandom fashion, generating a pattern of methylation that is gene and tissue specific. DNA
AB  - methylation is catalyzed by the DNA methyltransferase enzyme (DNA MeTase). We have previously
AB  - hypothesized that regulated changes in the level of DNA MeTase gene expression might be an
AB  - important mechanism through which DNA methylation patterns are generated(Szyf et al., J. Biol.
AB  - Chem. 266, 10027-10030, 1991). If this is true the DNA MeTase gene should be responsive to
AB  - cellular signal transduction pathways that are involved in cellular differentiation. Sequence
AB  - analysis of the promoter region revealed several potential binding sites for transcript factor
AB  - complexes (AP-1, GRE and E-boxes) that might be involved in the regulation of the DNA MeTase
AB  - gene expression by different signal transduction pathways (Rouleau et al., J. Biol. Chem.,
AB  - 267, 7368-7377. 1992). To test this hypothesis we cotransfected P19 cells with a chimeric
AB  - construct containing 2.3 kb sequences from the 5' region of the DNA MeTase fused to
AB  - CAT(pMetCAT+) with fos and jun. DNA MeTase gene promoter activity was induced 60-fold by fos
AB  - and jun but not by a mutant of jun lacking the DNA binding domain. This induction was
AB  - inhibited by deletion of the 7 AP-1 sites in the 5' region of the DNA MeTase. Gel retardation
AB  - assays demonstated the formation of an AP-1 complex with an AP-1 binding site in the promoter
AB  - region. Induction of DNA MeTase transcripton by fos and jun was inhibited by the human
AB  - glucocorticoid receptor while expression of the receptor per se had no effect on DNA MeTase
AB  - activity. The DNA MeTase is responsive also to the myogenesis regulator MyoD which expression
AB  - results in a 20 fold induction of the DNA MeTase gene. This work suggests for the first time a
AB  - molecular link between extracellular signals and possible changes in the covalent structure of
AB  - the genome.
ER  -

TY  - JOUR
AU  - Rouleau, J.
AU  - Tanigawa, G.
AU  - Szyf, M.
TI  - The mouse DNA methyltransferase 5'-region .
JO  - J. Biol. Chem.
PY  - 1992
SP  - 7368
EP  - 7377
VL  - 267
AB  - We have cloned and characterized 5'-flanking sequences of the DNA methyltransferase (MeTase)
AB  - gene. DNA MeTase gene transcription is initiated at a few discrete sites: 343 and 90 base
AB  - pairs upstream of the translation initiation site as determined by RNase protection and primer
AB  - extension assays. The promoter sequences that regulate expression of DNA MeTase, as defined by
AB  - chloramphenicol acetyltransferase assays, reside between position - 171 and the transcription
AB  - start site. The promoter of DNA MeTase does not contain TATAA or CAAT boxes and is unusual
AB  - because it does not contain the CG-rich elements characteristic of TATAA-less housekeeping
AB  - genes. The 5'-flanking region of DNA MeTase contains AP-1, AP-2 and glucocorticoid response
AB  - elements, suggesting possible regulation by cellular transduction pathways. The base
AB  - composition of the DNA MeTase promoter is markedly different from that of other housekeeping
AB  - genes. Whereas most housekeeping genes are characterized by CG-rich areas in their
AB  - 5'-flanking regions, the TG dinucleotide is over-represented in DNA MeTase 5'-flanking
AB  - sequences, including a perfect tandem repeat of T/G between positions -685 and -650. DNA
AB  - methylation patterns play an important role in the developmental regulation of gene expression
AB  - in vertebrates. DNA MeTase activity is probably regulated to maintain this pattern of
AB  - methylation. We suggest that the DNA MeTase promoter represents a new class of housekeeping
AB  - gene promoters that was designed to ensure high fidelity regulation of gene expression.
ER  -

TY  - JOUR
AU  - Rouli, L.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Yagupsky, P.
TI  - Kingella kingae KK247, an Atypical Pulsed-Field Gel Electrophoresis Clone A Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e01228
EP  - e01214
VL  - 2
AB  - Kingella kingae strain KK247 was isolated from an adult Israeli patient with endocarditis. It
AB  - belongs to pulsed-field gel electrophoresis clone A, has a
AB  - 2,113,021-bp genome, a 15,507-bp plasmid that carries genes encoding
AB  - beta-lactamases, and possesses 45 transposases, compared to the 5 detected in
AB  - other K. kingae strains.
ER  -

TY  - JOUR
AU  - Rouli, L.
AU  - Rolain, J.M.
AU  - El Filali, A.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Genome Sequence of Coxiella burnetii 109, a Doxycycline-Resistant Clinical Isolate.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6939
EP  - 6939
VL  - 194
AB  - Coxiella burnetii 109, with a 2.03-Mb genome, is a doxycycline-resistant human isolate that
AB  - was isolated from the cardiac valve of a German male patient with Q
AB  - fever endocarditis who died during the course of the treatment due to the
AB  - bacterium's resistance to doxycycline. This new genome can be useful for future
AB  - comparative genomic or Q fever studies.
ER  -

TY  - JOUR
AU  - Roulland-Dussoix, D.
AU  - Boyer, H.W.
TI  - The Escherichia coli B restriction endonuclease.
JO  - Biochim. Biophys. Acta
PY  - 1969
SP  - 219
EP  - 229
VL  - 195
AB  - 1.  The restriction endonuclease of Escherichia coli B has been purified
AB  - 1000-fold from crude extracts. 2.  It has been found to be similar to the K12
AB  - and PI restriction endonucleases, i.e., it requires ATP,
AB  - S-adenosyl-L-methionine and Mg2+ and unmodified DNA for enzymatic activity and
AB  - has an estimated large molecular weight (approx. 300,000 daltons). 3.  It
AB  - introduces a limited number of double strand scissions in unmodified lambda vir
AB  - DNA, Escherichia coli chromosomal DNA and probably one double strand scission
AB  - per fd replicative form DNA.  The double strand scission in the unmodified fd
AB  - replicative form DNA occurs by a two-step mechanism. 4.  Replicative form DNA
AB  - generated from an fd mutant which is only restricted by Escherichia coli B by a
AB  - factor of 1.10-2 (versus 1.10-4 for wild type fd) is also a substrate for the B
AB  - restriction endonuclease.  Cosedimentation of the endonuclease-treated wild
AB  - type and mutant replicative form DNA results in qualitatively identical
AB  - patterns of DNA distribution.
ER  -

TY  - JOUR
AU  - Roulland-Dussoix, D.
AU  - Boyer, H.W.
TI  - B Restriction endonuclease of Escherichia coli.
JO  - Bacteriol. Proc.
PY  - 1969
SP  - 46
EP  - 46
VL  - 69
AB  - We have purified the B restriction endonuclease by a factor of 1,500 from a
AB  - crude extract of E. coli.  The enzyme preparation is free of detectable
AB  - exonuclease and nonspecific endonuclease activities under conditions optimum
AB  - for the restriction endonuclease activity.  The B restriction endonuclease
AB  - activity has an absolute requirement for SAM, ATP, Mg++ and unmodified duplex
AB  - DNA (i.e. DNA originating in a strain without B modification).  The enzyme
AB  - produces a limited number of double strand scissions in unmodified lambda++,
AB  - lambda vir,  fd RF, colE1 and E. coli DNA.  The double strand scission is made
AB  - by two proximal single strand scissions.  The molecular weight of the enzyme
AB  - has been estimated at about 140,000 daltlons.  With the exception of substrate
AB  - specificity, the B restriction endonuclease appears to be similar to the K
AB  - restriction endonuclease.  We have found that the B restriction endonuclease
AB  - produces a linear molecule from the fd RF with an estimated molecular weight of
AB  - 2.8 x 10/6 daltons and sediments a little slower than the nicked RF molecules
AB  - (ratio =  1.14).  We conclude that there is one double strand scission per RF
AB  - molecule and have used this as a substrate to study the kinetics of the
AB  - reaction.  RF, prepared from a mutant fd which is restricted in vivo 100-fold
AB  - less than WT fd, is attacked at a rate less than one-half that of the WT RF.
ER  -

TY  - JOUR
AU  - Roulland-Dussoix, D.
AU  - Yoshimori, R.
AU  - Greene, P.
AU  - Betlach, M.
AU  - Goodman, H.M.
AU  - Boyer, H.W.
TI  - R Factor-Controlled Restriction and Modification of Deoxyribonucleic Acid.
JO  - Microbiology-1974
PY  - 1975
SP  - 187
EP  - 198
VL  - 0
AB  - The restriction and modification of deoxyribonucleic acid (DNA) appear to be
AB  - quite prevalent in bacteria although by no means ubiquitous.  In Escherichia
AB  - coli strains alone, there appear to be over six different restriction and
AB  - modification systems in terms of enzymatic specificity.  In E. coli strains,
AB  - the enzymes responsible for the restriction and modification of DNA are
AB  - genetically controlled by chromosomal, plasmid, or viral genes.  At least in
AB  - some cases, it is clear that the restriction endonuclease and modification
AB  - methylase of a given "host specificity" interact with the same substrate, a
AB  - specific sequence of nucleotide base pairs.  This sequence defines the host
AB  - specificity of a bacterial cell which possesses a set of restriction and
AB  - modification enzymes. Naturally occurring bacterial strains or strains
AB  - constructed in the laboratory can be demonstrated to have several sets of
AB  - restriction and modification enzymes.
ER  -

TY  - JOUR
AU  - Rountree, M.R.
AU  - Bachman, K.E.
AU  - Baylin, S.B.
TI  - DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci.
JO  - Nat. Genet.
PY  - 2000
SP  - 269
EP  - 277
VL  - 25
AB  - DNA methylation can contribute to transcriptional silencing through several transcriptionally
AB  - repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone
AB  - deacetylases (HDACs).  We show here that the chief enzyme that maintains mammalian DNA
AB  - methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic
AB  - amino terminus of DNMT1 binds to HDAC2 and a new protein, DMAP1 (for DNMT1 associated
AB  - protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription
AB  - repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted
AB  - to replication foci through interaction with the far N terminus of DNMT1 throughout S phase,
AB  - whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how
AB  - histones may become deacetylated in heterochromatin following replication. Thus, DNMT1 not
AB  - only maintains DNA methylation, but also may directly target, in a heritable manner,
AB  - transcriptionally repressive chromatin to the genome during DNA replication.
ER  -

TY  - JOUR
AU  - Rountree, P.M.
TI  - Variations in a related series of staphylococcal bacteriophages.
JO  - J. Gen. Microbiol.
PY  - 1956
SP  - 266
EP  - 279
VL  - 15
AB  - Stocks of staphylococcal phage 47C (serological group A) contained some group B
AB  - phage.  This was found to have originated in a lysogenic staphylococcus
AB  - previously used to propagate phage 47C and which had subsequently lost its
AB  - lysogenicity.  The lysogenic phage was thus perpetuated in the phage stocks as
AB  - a lytic phage.  The characters of the two phages are described.  When they
AB  - lysogenized five different strains of staphylococci changes in typing pattern
AB  - were produced.  There was evidence which indicated that, in the prophage state,
AB  - the two phages occupy different sites and that there is no cross-immunity
AB  - between them.  The propagation of the phages in different hosts resulted in
AB  - changes in their host range.  A virulent mutant of the B prophage was induced
AB  - by the application of a variety of phages to the strain carrying it.
ER  -

TY  - JOUR
AU  - Roustan-Espinosa, I.
AU  - Guerrero, D.
AU  - Flores, E.
AU  - Huete-Perez, J.
TI  - Restriction enzymes in native bacteria of Nicaragua.
JO  - Revista Univ. Centroamer.
PY  - 2000
SP  - 10
EP  - 18
VL  - 52
AB  - Advances in genetic engineering and molecular biology have led to the utilization of bacteria
AB  - in the biotechnology industry.  In this study, restriction enzymes present in bacteria
AB  - collected from aqueous medium in Nicaragua have been identified and classified.  Restriction
AB  - activity was found in 25% of the total of bacteria analyzed.  The process of purification of
AB  - bacterial protein extracts with Sau96I and PvuII activities is discussed.  This work is a
AB  - result of an effort to implement modern biotechnological methods of research in Nicaragua.
ER  -

TY  - JOUR
AU  - Rout, S.P.
AU  - Rai, A.
AU  - Humphreys, P.N.
TI  - Draft Genome Sequence of Alkaliphilic Exiguobacterium sp. Strain HUD, Isolated from a Polymicrobial Consortia.
JO  - Genome Announcements
PY  - 2015
SP  - e01451
EP  - e01414
VL  - 3
AB  - An alkaliphilic microorganism from the genus Exiguobacterium, Exiguobacterium sp. strain HUD
AB  - was isolated from a fermentative, methanogenic polymicrobial microcosm
AB  - operating at pH 10. The draft genome shows the presence of genes encoding for the
AB  - metabolism of a range of carbohydrates under both aerobic and anaerobic
AB  - conditions.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - El Karkouri, K.
AU  - Lagier, J.C.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 221
EP  - 232
VL  - 7
AB  - Kurthia massiliensis strain JC30(T) sp. nov. is the type strain of K. massiliensis sp. nov., a
AB  - new species within the genus Kurthia. This strain, whose
AB  - genome is described here, was isolated from the fecal flora of a healthy patient.
AB  - K. massiliensis is a Gram-positive aerobic rod. Here we describe the features of
AB  - this organism, together with the complete genome sequence and annotation. The
AB  - 3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes,
AB  - including between 3 and 4 rRNA genes.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Lagier, J.C.
AU  - Gorlas, A.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1321
EP  - 1332
VL  - 9
AB  - Kurthia senegalensis strain JC8E(T) sp. nov. is the type strain of K. senegalensis sp. nov., a
AB  - new species within the genus Kurthia. This strain, whose
AB  - genome is described here, was isolated from the fecal flora of a healthy patient.
AB  - K. senegalensis is an aerobic rod. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 2,975,103 bp long genome contains 2,889 protein-coding genes and 83 RNA genes,
AB  - including between 4 and 6 rRNA genes.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Million, M.
AU  - Robert, C.
AU  - Magne, A.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 370
EP  - 384
VL  - 9
AB  - Oceanobacillus massiliensis strain N'Diop(T) sp. nov. is the type strain of O. massiliensis
AB  - sp. nov., a new species within the genus Oceanobacillus. This
AB  - strain, whose genome is described here, was isolated from the fecal flora of a
AB  - healthy patient. O. massiliensis is an aerobic rod. Here we describe the features
AB  - of this organism, together with the complete genome sequence and annotation. The
AB  - 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes,
AB  - including between 6 and 8 rRNA operons.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Robert, C.
AU  - Gimenez, G.
AU  - Gharbi, R.
AU  - Raoult, D.
TI  - Draft Genome Sequence of Actinomyces massiliensis Strain 4401292T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5121
EP  - 5121
VL  - 194
AB  - A draft genome sequence of Actinomyces massiliensis, an anaerobic bacterium isolated from a
AB  - patient's blood culture, is described here. CRISPR-associated
AB  - proteins, insertion sequences, and toxin-antitoxin loci were found on the genome.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Robert, C.
AU  - Gimenez, G.
AU  - Raoult, D.
TI  - Draft Genome Sequence of Brevibacterium massiliense Strain 541308T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5151
EP  - 5152
VL  - 194
AB  - A draft genome sequence of Brevibacterium massiliense, an aerobic bacterium isolated from a
AB  - human ankle discharge, is described here. CRISPR-associated
AB  - proteins were found to be encoded in the genome, and analysis of transport
AB  - proteins was performed.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Robert, C.
AU  - Gimenez, G.
AU  - Raoult, D.
TI  - Draft Genome Sequence of Staphylococcus massiliensis Strain 5402776T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6984
EP  - 6985
VL  - 194
AB  - A draft genome sequence of Staphylococcus massiliensis, Gram-positive cocci isolated from a
AB  - human brain abscess sample, is described here. One clustered
AB  - regularly interspaced short palindromic repeat, three transposases, six putative
AB  - transposases, and one potential provirus were characterized.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence of Phocaeicola abscessus type strain 7401987(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 351
EP  - 358
VL  - 9
AB  - Phocaeicola abscessus strain 7401987(T) is the sole member of the genus Phocaeicola. This
AB  - bacterium is Gram-negative, non-spore-forming, coccoid to
AB  - rod-shaped and motile by lophotrichous flagella. It was isolated from a human
AB  - brain abscess sample. In this work, we describe a set of features of this
AB  - organism, together with the complete genome sequence and annotation. The
AB  - 2,530,616 bp long genome contains 2,090 protein-coding genes and 54 RNA genes,
AB  - including 4 rRNA operons.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1346
EP  - 1353
VL  - 9
AB  - Prevotella timonensis strain 4401737(T) is a member of the genus Prevotella, which contains
AB  - anaerobic Gram-negative bacteria. It was isolated from a human
AB  - breast abscess. In this work, we describe a set of features of this organism,
AB  - together with the complete genome sequence and annotation. The 3,169,464 bp long
AB  - genome contains 2,746 protein-coding genes and 56 RNA genes, including 3 or 4
AB  - rRNA operons.
ER  -

TY  - JOUR
AU  - Roux, V.
AU  - Robert, C.
AU  - Raoult, D.
TI  - Non-contiguous finished genome sequence of Corynebacterium timonense type strain  5401744(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 948
EP  - 955
VL  - 9
AB  - Corynebacterium timonense strain 5401744(T) is a member of the genus Corynebacterium which
AB  - contains Gram-positive bacteria with a high G+C content. It
AB  - was isolated from the blood of a patient with endocarditis. In this work, we
AB  - describe a set of features of this organism, together with the complete genome
AB  - sequence and annotation. The 2,553,575 bp long genome contains 2,401
AB  - protein-coding genes and 55 RNA genes, including between 5 and 6 rRNA operons.
ER  -

TY  - JOUR
AU  - Rowland, G.C.
AU  - Lim, P.P.
AU  - Glass, R.E.
TI  - 'Stop-codon-specific' restriction endonucleases: their use in mapping and gene manipulation.
JO  - Gene
PY  - 1992
SP  - 21
EP  - 26
VL  - 116
AB  - Certain restriction endonucleases recognize target sequences that contain the stop triplet TAG
AB  - and are commonly either 4 or 6 bp in length. Interestingly, these restriction targets do not
AB  - occur at the frequency expected on the basis of base composition and size. For example, the
AB  - tetranucleotide MaeI recognition sequence (CTAG) occurs considerably less commonly (5-8 fold)
AB  - in the genome of Escherichia coli (and many other eubacteria) than expected from
AB  - mononucleotide frequencies. This surprising rarity is particularly evident in protein-encoding
AB  - genes and is largely dictated by codon usage. Thus, amber (TAG) nonsense mutations frequently
AB  - give rise to novel MaeI (CTAG) sites which are unique within a translated region. Such
AB  - amber/MaeI sites, whether arising spontaneously or created in vitro by site-directed
AB  - mutagensis, act as a useful physical marker for the presence of the nonsense mutation and are
AB  - a convenient startpoint for a range of diverse procedures. These features provide a useful
AB  - supplement to protein engineering methods which use nonsense suppression to mediate amino acid
AB  - replacements.
ER  -

TY  - JOUR
AU  - Roy, A.C.
AU  - Wilson, G.G.
AU  - Edgell, D.R.
TI  - Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 7350
EP  - 7359
VL  - 44
AB  - Homing endonucleases are sequence-tolerant DNA endonucleases that act as mobile genetic
AB  - elements. The ability of homing endonucleases to cleave substrates with
AB  - multiple nucleotide substitutions suggests a high degree of adaptability in that
AB  - changing or modulating cleavage preference would require relatively few amino
AB  - acid substitutions. Here, using directed evolution experiments with the GIY-YIG
AB  - homing endonuclease I-TevI that targets the thymidylate synthase gene of phage
AB  - T4, we readily isolated variants that dramatically broadened I-TevI cleavage
AB  - preference, as well as variants that fine-tuned cleavage preference. By combining
AB  - substitutions, we observed an approximately 10 000-fold improvement in cleavage
AB  - on some substrates not cleaved by the wild-type enzyme, correlating with a
AB  - decrease in readout of information content at the cleavage site. Strikingly, we
AB  - were able to change the cleavage preference of I-TevI to that of the isoschizomer
AB  - I-BmoI which targets a different cleavage site in the thymidylate synthase gene,
AB  - recapitulating the evolution of cleavage preference in this family of homing
AB  - endonucleases. Our results define a strategy to isolate GIY-YIG nuclease domains
AB  - with distinct cleavage preferences, and provide insight into how homing
AB  - endonucleases may escape a dead-end life cycle in a population of saturated
AB  - target sites by promoting transposition to different target sites.
ER  -

TY  - JOUR
AU  - Roy, A.S.
AU  - Baruah, R.
AU  - Gogoi, D.
AU  - Borah, M.
AU  - Singh, A.K.
AU  - Deka, B.H.P.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain N002, Isolated from Crude  Oil-Contaminated Soil from Geleky, Assam, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00104
EP  - e00112
VL  - 1
AB  - Here, we report the draft genome sequence of crude oil-degrading Pseudomonas aeruginosa strain
AB  - N002, isolated from a crude oil-polluted soil sample from
AB  - Geleky, Assam, India. Multiple genes potentially involved in crude oil
AB  - degradation were identified.
ER  -

TY  - JOUR
AU  - Roy, K.B.
AU  - Vrushank, D.
TI  - Bam HI cleaves the self complementary dodecamer d-CGCGGAGCCGCG, before the two G's and possibly binds in the DNA major groove.
JO  - Biochem. Mol. Biol. Int.
PY  - 1995
SP  - 759
EP  - 770
VL  - 36
AB  - Oligodeoxynucleotides with GT or GA mispairs within the Bam HI recognition sequence (GGATCC),
AB  - have been prepared. Binding and cleavage of the native
AB  - vis a vis the mismatch substrates by Bam HI are analysed. UV melting
AB  - curves and CD spectra of the oligomers suggest a double stranded B-DNA
AB  - conformation. The enzyme Bam HI binds with varying affinities to the
AB  - oligomers except the one with the GT wobble base pair. Bam HI cleaves the
AB  - cognate sequence, GGATCC, between the two Guanines but cleaves GGAGCC
AB  - before the guanines. The unusual cleavage is due to a local distortion in
AB  - the DNA structure. Kinetic analysis of the cleavage reactions using the
AB  - 35S labeled hexadecamers, d-ATGGCGGATCCGCCAT and d-ATGGCGGAGCCGCCAT, as
AB  - substrates gives Km values 11.08 nM and 1.16 nM with corresponding Kcat of
AB  - 11.04 and 0.62 min-1 respectively. The results are consistent with the
AB  - binding of Bam HI in the major groove.
ER  -

TY  - JOUR
AU  - Roy, K.B.
AU  - Vrushank, D.
AU  - Jayaram, B.
TI  - Use of isotope-dilution phenomenon to advantage in the determination of kinetic constants Km and Kcat for BamHI restriction endonuclease: an empirical and interative approach.
JO  - Anal. Biochem.
PY  - 1994
SP  - 160
EP  - 164
VL  - 220
AB  - An assay using a very small amount of 35S-labeled deoxyoligonucleotide as a substrate for the
AB  - determination of Km and Kcat for the restriction enzyme BamHI is described. Two synthetic
AB  - deoxyoligonucleotides, ATGGCGGATCCGC and ATGGCGGAGCCGC, containing the cognate and a mismatch
AB  - BamHI sequence, respectively, were labeled by an end-filling reaction using the Klenow
AB  - fragment of DNA polymerase and [35S]dATP to generate the labeled self-complementary
AB  - substrates. The dependence of BamHI hydrolysis on substrate concentration was investigated
AB  - using mixtures of a fixed amount of radiolabeled substrate and varying amounts of cold-labeled
AB  - substrate over a wide range. The apparent competitive inhibition observed due to the
AB  - phenomenon of carrier dilution was analytically corrected by an empirical as well as an
AB  - iterative approach to give Km values comparable to those reported in the literature. We have
AB  - found that the values obtained using the empirical formula are very close to the precise
AB  - values obtained through iteration. Our procedure has used isotopic dilution to advantage to
AB  - make the assay less expensive and can be applied effectively to any enzyme-substrate reaction
AB  - in which the substrate and the product have radioactive labels. The method would be especially
AB  - useful for a rapid analysis and comparison of kinetic constants of various mutant enzymes or
AB  - substrates.
ER  -

TY  - JOUR
AU  - Roy, P.H.
AU  - Smith, H.O.
TI  - DNA methylases of Hemophilus influenzae Rd.  II. Partial recognition site base sequences.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 445
EP  - 459
VL  - 81
AB  - A small percentage of the adenine bases in Hemophilus influenzae strain Rd DNA
AB  - are methylated in the 6-amino position.  The methyl groups are introduced
AB  - specifically by at least four different DNA methylases (I, II, III and IV).  A
AB  - method is described for determining the 3' and 5' nearest-neighbor bases to
AB  - methylated adenine so as to reveal the specificity of each methylase.
AB  - Tritium-labeled methyl groups are introduced into the DNA.  The DNA is then
AB  - digested to dinucleotides using the Bacillus subtilis phage SP3 DNase, followed
AB  - by removal of the terminal 5'-phosphoryl group with phosphatase to produce
AB  - dinucleoside monophosphates.  These are analyzed by Aminex A25 (Bio-Rad)
AB  - chromatography.  Dinucleoside monophosphate species containing the 3' neighbor
AB  - or the 5' neighbor are resolved so that a trinucleotide is determined that
AB  - contains the centrally placed methylated adenine.  H. influenzae Rd DNA
AB  - contains seven dinucleoside monophosphate species, about 80% representing GpmA
AB  - and mApT in approximately equal amount.  DNA methylases I, II, III and IV
AB  - introduce methyl groups into sequences containing the trinucleotides CpmApC,
AB  - PupmApC, NpmApA and GpmApT, respectively.  The sequence methylated by DNA
AB  - methylase II is consistent with the recognition site determined by Kelly &
AB  - Smith (1970) for the H. influenzae restriction enzyme, endonuclease R.
ER  -

TY  - JOUR
AU  - Roy, P.H.
AU  - Smith, H.O.
TI  - DNA methylases of Hemophilus influenzae Rd I.  Purification and properties.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 427
EP  - 444
VL  - 81
AB  - Hemophilus influenzae strain Rd DNA contains small amounts of 5-methylcytosine
AB  - (0.012%) and significantly greater amounts of N-6-methyladenine (0.34%).  Four
AB  - DNA adenine methylases have been identified and purified from crude extracts of
AB  - H. influenzae Rd by means of phosphocellulose chromatography.  Each of the four
AB  - enzymes requires S-adenosyl-L-methionine as a methyl group donor and each
AB  - differs in its ability to methylate various DNAs in vitro.  DNA methylase I is
AB  - related to the genetically described modification-restriction system in H.
AB  - influenzae Rd, and is presumably the modification enzyme for that system.  DNA
AB  - methylase II introduces approximately 130 methyl groups into a phage T7 DNA
AB  - molecule and protects T7 DNA from the H. influenzae Rd restriction enzyme,
AB  - endonuclease R, described by Smith & Wilcox (1970).  These findings indicate
AB  - that DNA methylase II is the modification enzyme corresponding to endonuclease
AB  - R.  A third modification-restriction system, which does not affect T7 DNA, has
AB  - been detected in H. influenzae Rd.  DNA methylase III is apparently the
AB  - modification enzyme for this system.  The biological function of DNA methylase
AB  - IV remains unknown.
ER  -

TY  - JOUR
AU  - Roy, P.H.
AU  - Tetu, S.G.
AU  - Larouche, A.
AU  - Elbourne, L.
AU  - Tremblay, S.
AU  - Ren, Q.
AU  - Dodson, R.
AU  - Harkins, D.
AU  - Shay, R.
AU  - Watkins, K.
AU  - Mahamoud, Y.
AU  - Paulsen, I.T.
TI  - Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7.
JO  - PLoS ONE
PY  - 2010
SP  - e8842
EP  - e8842
VL  - 5
AB  - Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is
AB  - multiresistant to antibiotics. We first sequenced gyrA,
AB  - gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found
AB  - that PA7 is a taxonomic outlier. We report here the complete sequence of
AB  - the 6,588,339 bp genome, which has only about 95% overall identity to
AB  - other strains. PA7 has multiple novel genomic islands and a total of 51
AB  - occupied regions of genomic plasticity. These islands include antibiotic
AB  - resistance genes, parts of transposons, prophages, and a pKLC102-related
AB  - island. Several PA7 genes not present in PAO1 or PA14 are putative
AB  - orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7
AB  - appears to be closely related to the known taxonomic outlier DSM1128
AB  - (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS
AB  - region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor
AB  - exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin
AB  - type II. Preliminary proteomic studies indicate numerous differences with
AB  - PAO1, some of which are probably a consequence of a frameshift mutation in
AB  - the mvfR quorum sensing regulatory gene.
ER  -

TY  - JOUR
AU  - Roycroft, E.
AU  - Mac, A.M.
AU  - O'Toole, R.F.
AU  - Fitzgibbon, M.
AU  - Rogers, T.R.
TI  - Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in Ireland.
JO  - Genome Announcements
PY  - 2014
SP  - e01002
EP  - e01014
VL  - 2
AB  - Extensive drug resistance is an emerging threat to the control of tuberculosis (TB) worldwide,
AB  - even in countries with low TB incidence. We report the draft
AB  - whole-genome sequence of the first reported extensively drug-resistant TB
AB  - (XDR-TB) strain isolated in Ireland (a low-incidence setting) and describe a
AB  - number of single-nucleotide variations that correlate with its XDR phenotype.
ER  -

TY  - JOUR
AU  - Rozanov, A.S.
AU  - Bryanskaya, A.V.
AU  - Kotenko, A.V.
AU  - Malup, T.K.
AU  - Peltek, S.E.
TI  - Draft Genome Sequence of Anoxybacillus flavithermus Strain 25, Isolated from the  Garga Hot Spring in the Barguzin Valley, Baikal Region, Russian Federation.
JO  - Genome Announcements
PY  - 2014
SP  - e01258
EP  - e01214
VL  - 2
AB  - Anoxybacillus flavithermus strain 25 was isolated from a sediment sample from the Garga hot
AB  - spring in the Barguzin Valley, Baikal Region, Russian Federation (54
AB  - degrees 19'3.72'N, 110 degrees 59'38.4'E). The sequenced and annotated genome
AB  - is 2,838,680 bp and encodes 3,009 genes.
ER  -

TY  - JOUR
AU  - Rozanov, A.S.
AU  - Bryanskaya, A.V.
AU  - Malup, T.K.
AU  - Kotenko, A.V.
AU  - Peltek, S.E.
TI  - Draft genome sequence of a halorubrum h3 strain isolated from the burlinskoye salt lake (altai krai, Russia).
JO  - Genome Announcements
PY  - 2015
SP  - e00566
EP  - e00515
VL  - 3
AB  - A Halorubrum H3 strain was isolated from a water and silt sample from Burlinskoye Lake (Altai
AB  - Krai, Russia, 53 degrees 8'19'N 78 degrees 24'27'E). According to
AB  - 16S rRNA sequences, this strain is most closely related to Halorubrum
AB  - saccharovorum. The completely sequenced and annotated genome is 3,282,373 bp and
AB  - contains 3,237 genes.
ER  -

TY  - JOUR
AU  - Rozanov, A.S.
AU  - Korzhuk, A.V.
AU  - Shipova, A.A.
AU  - Bryanskaya, A.V.
AU  - Peltek, S.E.
TI  - Draft Genome Sequence of Bacillus altitudinis Strain KU-skv2(2), Isolated from a  Microbial Mat on an Anthropogenic Pipe from Caldera Uzon (Kamchatka, Russia).
JO  - Genome Announcements
PY  - 2018
SP  - e01572
EP  - e01517
VL  - 6
AB  - Bacillus altitudinis strain KU-skv2(2) was isolated from a microbial mat on an anthropogenic
AB  - pipe from Caldera Uzon (Kamchatka, Russia, 54 degrees 30'0.23'N,
AB  - 160 degrees 0'15.18'E). The sequenced and annotated genome is 3,739,340 bp in
AB  - size and encodes 3,929 genes.
ER  -

TY  - JOUR
AU  - Rozanov, A.S.
AU  - Logacheva, M.D.
AU  - Peltek, S.E.
TI  - Draft Genome Sequences of Geobacillus stearothermophilus Strains 22 and 53, Isolated from the Garga Hot Spring in the Barguzin River Valley of the Russian  Federation.
JO  - Genome Announcements
PY  - 2014
SP  - e01205
EP  - e01214
VL  - 2
AB  - Geobacillus stearothermophilus strains 22 and 53 were isolated from sediment samples isolated
AB  - from the Garga hot spring (72 degrees C) located in the valley
AB  - of the river Barguzin (the Baikal region, Russian Federation) (54 degrees
AB  - 19'3.72'N, 110 degrees 59'38.4'E).
ER  -

TY  - JOUR
AU  - Rozanov, A.S.
AU  - Shipova, A.A.
AU  - Bryanskaya, A.V.
AU  - Tekutieva, L.A.
AU  - Son, O.M.
AU  - Peltek, S.E.
TI  - Draft Genome Sequence of Bacillus altitudinis Strain KL4, Isolated from Bottom Sediments in Lake Krotovaya Lyaga (Novosibirsk Region, Russia).
JO  - Genome Announcements
PY  - 2018
SP  - e01494
EP  - e01417
VL  - 6
AB  - The Bacillus altitudinis strain KL4 was isolated from bottom sediments in Lake Krotovaya Lyaga
AB  - (Novosibirsk Region, Russia, 53.7 degrees N, 77.9 degrees E). The
AB  - sequenced and annotated genome is 3,738,419 bp long and carries 3,909 genes.
ER  -

TY  - JOUR
AU  - Ruan, H.
AU  - Lunnen, K.D.
AU  - Pelletier, J.J.
AU  - Xu, S.-Y.
TI  - Overexpression of BsoBI restriction endonuclease in E. coli, purification of the recombinant BsoBI, and identification of catalytic residues of BsoBI by random mutagenesis.
JO  - Gene
PY  - 1997
SP  - 35
EP  - 39
VL  - 188
AB  - BsoBI is a type II restriction enzyme found in Bacillus stearothermophilus JN209 that
AB  - recognizes the symmetric sequence 5'-CYCGRG-3' (Y=C or T; R=A or G) and cleaves between the
AB  - first and second base to generate a four-base 5' extension.  The cloning and sequencing of
AB  - BsoBI restriction-modification system has been described by Ruan et al.  Here we report the
AB  - overexpression of the BsoBI restriction endonuclease gene in E. coli by insertion of the
AB  - endonuclease gene into an expression vector pRRS.  The recombinant BsoBI was purified to
AB  - homogeneity and its N-terminus sequence was determined.  It has the same N-terminal aa
AB  - sequence as the native enzyme.  The constitutive expression of BsoBI from pRRS is lethal to E.
AB  - coli in the absence of the cognate methylase.  The BsoBIR gene was mutagenized with either
AB  - hydroxylamine or by error-prone polymerase chain reaction in vitro and transferred into E.
AB  - coli via plasmid vectors in the absence of the cognate methylase.  Surviving transformants
AB  - were selected that carry BsoBI variants which lost endonuclease activity.  DNA sequencing of
AB  - the mutant alleles revealed that G123, D124, D212, D246, E252 and H253 are important residues
AB  - for enzymatic activity.  An electrophoretic mobility shift assay was used to identify
AB  - binding-proficient and cleavage-deficient variants.  Seven variants I95M&D124Y, G123R, D212N,
AB  - K207R&D212V, D246N, D246G and E252K can still bind DNA despite the loss of cleavage activity.
AB  - Thus, residues D124, D212, D246 and E252 may be located near or within the catalytic center,
AB  - and are likely involved in metal ion binding.
ER  -

TY  - JOUR
AU  - Ruan, H.
AU  - Lunnen, K.D.
AU  - Scott, M.E.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Pelletier, J.J.
AU  - Hess, E.J.
AU  - Benner, J.
AU  - Wilson, G.G.
AU  - Xu, S.-Y.
TI  - Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems.
JO  - Mol. Gen. Genet.
PY  - 1996
SP  - 695
EP  - 699
VL  - 252
AB  - AvaI and BsoBI restriction endonucleases are isoschizomers which recognize the symmetric
AB  - sequence 5'CYCGRG3' and cleave between the first C and second Y to generate a four-base 5'
AB  - extension.  The AvaI restriction endonuclease gene (avaIR) and methylase gene (avaIM) were
AB  - cloned into Escherichia coli by the methylase selection method.  The BsoBI restriction
AB  - endonuclease gene (bsoBIM) were cloned by the "endo-blue" method (SOS induction assay), and
AB  - the remainder of bsoBIM was cloned by inverse PCR.  The nucleotide sequences of the two
AB  - restriction-modification (RM) systems were determined.  Comparisons of the predicted amino
AB  - acid sequences indicated that AvaI and BsoBI endonucleases share 55% identity, whereas the two
AB  - methylases share 41% identity.  Although the two systems show similarity in protein sequence,
AB  - their gene organization differs.  The avaIM gene precedes avaIR in the AvaI RM system, while
AB  - the bsoBIR gene is located upstream of bsoBIM in the BsoBI RM system.  Both AvaI and BsoBI
AB  - methylases contain  motifs conserved among the N4 cytosine methylases.
ER  -

TY  - JOUR
AU  - Ruan, L.
AU  - Xu, X.
TI  - Sequence analysis and characterizations of two novel plasmids isolated from Thermus sp. 4C.
JO  - Plasmid
PY  - 2007
SP  - 84
EP  - 87
VL  - 58
AB  - Two novel plasmids, named pS4C and pL4C, were isolated from the thermophilic bacterium Thermus
AB  - sp. 4C. The pS4C with a length of 5015bp
AB  - and 58.25% of G+C content, contains 9 putative open reading frames (ORFs).
AB  - The larger plasmid, pL4C, consisting of 21,248bp, has a G+C content of
AB  - 68.60% and 34 putative ORFs. Both plasmids encode their own replication
AB  - protein. The ORF 22 of pL4C and the ORF 4 of pS4C encode proteins with
AB  - high sequence similarities to integrase (97%) and transposase (97%),
AB  - respectively, which are both involved in DNA rearrangement and exchange.
AB  - Furthermore, sequence analysis of pL4C also showed that several
AB  - plasmid-encoded genes may be involved in DNA modification and repair, such
AB  - as DNA G:T-mismatch repair endonuclease and micrococcal nuclease-like
AB  - protein. These proteins may be involved in raising the repair efficiency
AB  - and other minor editing needs. Interestingly, the elimination of plasmids
AB  - significantly lowered the growth temperature of Thermus sp. 4C. Few
AB  - reports dealing with the DNA repair enzymes on the plasmid from Thermus
AB  - strains were published so far.
ER  -

TY  - JOUR
AU  - Ruan, Z.
AU  - Wang, Y.
AU  - Song, J.
AU  - Zhai, Y.
AU  - Zhang, C.
AU  - Chen, C.
AU  - Li, Y.
AU  - Zhao, B.
AU  - Zhao, B.
TI  - Draft Genome Sequence of Kurthia huakuii LAM0618T, an Organic-Pollutant-Degrading Strain Isolated from Biogas Slurry.
JO  - Genome Announcements
PY  - 2014
SP  - e01158
EP  - e01113
VL  - 2
AB  - Kurthia huakuii LAM0618(T) is a facultative anaerobic pollutant-degrading bacterium isolated
AB  - from biogas slurry. An analysis of the draft genome sequence
AB  - of LAM0618(T) reveals a genome size of 3,585,165 bp, with a mean G+C content of
AB  - 39.1%. The genome contains 3,560 coding sequences and 112 tRNA and 33 rRNA genes.
ER  -

TY  - JOUR
AU  - Ruben, G.
AU  - Spielman, P.
AU  - Tu, C.-P.D.
AU  - Jay, E.
AU  - Siegel, B.
AU  - Wu, R.
TI  - Relaxed circular SV40 DNA as cleavage intermediate of two restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 1977
SP  - 1803
EP  - 1813
VL  - 4
AB  - We have determined the mode of cleavage of superhelical SV40 DNA (Form I) by
AB  - restriction endonucleases EcoRI and HpaII at 37C.  By analysis with agarose gel
AB  - electrophoresis and direct examination with dark field electron microscopy, we
AB  - found that a large amount of the single-nicked circular DNA (FormII) was
AB  - produced before the linear SV40 DNA (Form III) appeared.  Thus, both
AB  - restriction enzymes cleave only one strand of the superhelical DNA first.  The
AB  - second cleavage on the complementary strand occurred after a lag period.  The
AB  - first order rate constant for the second cleavage by EcoRI endonuclease was
AB  - determined and a kinetic reaction scheme for both enzymes is proposed.
ER  -

TY  - JOUR
AU  - Rubin, R.A.
AU  - Modrich, P.
TI  - Substrate dependence of the mechanism of EcoRI endonuclease.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 2991
EP  - 2997
VL  - 5
AB  - The mechanism of EcoRI endonuclease is substrate dependent.  At 37C,
AB  - dissociation of the enzyme-Form II DNA intermediates of ColE1 ENA and
AB  - bacteriophage G4 RFI DNA is negligible.  Therefore, both DNA strands within the
AB  - EcoRI sequence are cleaved during a single binding event.  However, double
AB  - strand cleavage of SV40 DNA occurs without dissociation of the enzyme in only
AB  - 75% of the catalytic events.  This mechanistic difference presumably reflects
AB  - sequence differences about the EcoRI sites of these DNA's.
ER  -

TY  - JOUR
AU  - Rubin, R.A.
AU  - Modrich, P.
TI  - EcoRI methylase physical and catalytic properties of the homogeneous enzyme.
JO  - J. Biol. Chem.
PY  - 1977
SP  - 7265
EP  - 7272
VL  - 252
AB  - Escherichia coli RI methylase has been isolated by a procedure which is suitable for large
AB  - scale use and which yields enzyme with a specific activity 10-fold higher than previous
AB  - methods.  The purified methylase is homogeneous as judged by polyacrylamide gel
AB  - electrophoresis, isoelectric focusing, and analytical sedimentation.  The methylase is a basic
AB  - protein composed of a single polypeptide chain of molecular weight 39,000, the stable form in
AB  - solution being a 3.0 S monomer.  No aggregation has been observed at concentrations up to 0.3
AB  - mg/ml in the temperature range of 4-30C, and the presence of S-adenosyl-L-methionine is
AB  - without effect.  Catalytic studies have demonstrated that the enzyme functions as a monomer.
AB  - Initial rates of methyl transfer are first order in methylase concentration, and the enzyme
AB  - obeys Michaelis-Menten kinetics with respect to both substrates.  At 37C, the Km for the EcoRI
AB  - site of ColE1 DNA is 1.3 nM, that for S-adenosyl-L-methionine is 0.26 microm, and the turnover
AB  - number is three methyl transfers per min.  The mechanism of methyl transfer to unmodified DNA
AB  - is also consistent with the functional form of the enzyme being a monomer.  The enzyme
AB  - transfers methyl groups to the EcoRI sequence one at a time and dissociates from the DNA prior
AB  - to any subsequent catalytic events.  Furthermore, the kinetic parameters for addition of a
AB  - second methyl group to a site which is already methylated on one strand are not more favorable
AB  - than those for addition of the first.  These properties of the methylase are in marked
AB  - contrast to those of the endonuclease (Modrich, P., and Zabel, D. (1976) J. Biol. Chem. 251,
AB  - 5866-5874).  Thus, we suggest that the two proteins interact with their common recognition
AB  - sequence in different ways.
ER  -

TY  - JOUR
AU  - Rubin, R.A.
AU  - Modrich, P.
TI  - Purification and properties of EcoRI endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 96
EP  - 104
VL  - 65
AB  - The Escherichia coli RI (EcoRI) DNA restriction and modification enzymes
AB  - recognize a common twofold symmetrical hexanucleotide sequence in duplex DNA.
AB  - d(pG^pApA*pTpTpCp) d(pCpTpTpA*pAp^Gp) EcoRI restriction endonuclease cleaves
AB  - the DNA duplex within this sequence (see arrows in above sequence), while the
AB  - modification enzyme methylates the two adenine residues adjacent to the axis of
AB  - symmetry (asterisks) to yield 6-methylaminopurine.  The presence of one
AB  - 6-methylaminopurine residue within this sequence is sufficient to block single-
AB  - or double-stranded cleavage by the endonuclease.  EcoRI endonuclease has been
AB  - extensively used as a reagent for the preparation of recombinant molecules.  In
AB  - addition, the EcoRI enzymes are biochemically simple and hence provide an ideal
AB  - system for study of sequence-specific DNA-protein interaction.  We describe
AB  - here a convenient method for isolation of large quantities of the endonuclease,
AB  - a rapid assay procedure for quantitation of specific endonucleolytic activity,
AB  - as well as physical and catalytic properties of the homogeneous protein.
ER  -

TY  - JOUR
AU  - Rubin, R.A.
AU  - Modrich, P.
AU  - Vanaman, T.C.
TI  - Partial NH2- and C00H-Terminal Sequence Analyses of EcoRI DNA Restriction and Modification Enzymes.
JO  - J. Biol. Chem.
PY  - 1981
SP  - 2140
EP  - 2142
VL  - 256
AB  - NH2- and C00H-terminal amino acid sequences of the EcoRI restriction and modification enzymes
AB  - have been determined.  The results allow localization of the coding regions within the DNA
AB  - segment which controls activity of both enzymes.  Processing of the endonuclease is limited to
AB  - removal of NH2-terminal formylmethionine whereas, in the case of the methylase, formylMet-Ala
AB  - is removed.
ER  -

TY  - JOUR
AU  - Ruby, E.G.
AU  - Urbanowski, M.
AU  - Campbell, J.
AU  - Dunn, A.
AU  - Faini, M.
AU  - Gunsalus, R.
AU  - Lostroh, P.
AU  - Lupp, C.
AU  - McCann, J.
AU  - Millikan, D.
AU  - Schaefer, A.
AU  - Stabb, E.
AU  - Stevens, A.
AU  - Visick, K.
AU  - Whistler, C.
AU  - Greenberg, E.P.
TI  - Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 3004
EP  - 3009
VL  - 102
AB  - Vibrio fischeri belongs to the Vibrionaceae, a large family of marine gamma-proteobacteria
AB  - that includes several dozen species known to engage in a diversity of beneficial or pathogenic
AB  - interactions with animal tissue. Among the small number of pathogenic Vibrio species that
AB  - cause human diseases are Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus, the
AB  - only members of the Vibrionaceae that have had their genome sequences reported. Nonpathogenic
AB  - members of the genus Vibrio, including a number of beneficial symbionts, make up the majority
AB  - of the Vibrionaceae, but none of these species has been similarly examined. Here we report the
AB  - genome sequence of V. fischeri ES114, which enters into a mutualistic symbiosis in the light
AB  - organ of the bobtail squid, Euprymna scolopes. Analysis of this sequence has revealed
AB  - surprising parallels with V. cholerae and other pathogens.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Albersmeier, A.
AU  - Al-Dilaimi, A.
AU  - Bednarz, H.
AU  - Niehaus, K.
AU  - Szczepanowski, R.
AU  - Kalinowski, J.
TI  - Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 505
EP  - 513
VL  - 9
AB  - Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium,
AB  - which contains Gram-positive and non-spore forming bacteria with
AB  - a high G+C content. C. terpenotabidum was isolated from soil based on its ability
AB  - to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria.
AB  - It displays tolerance to salts (up to 8%) and is related to Corynebacterium
AB  - variabile involved in cheese ripening. As this is a type strain of
AB  - Corynebacterium, this project describing the 2.75 Mbp long chromosome with its
AB  - 2,369 protein-coding and 72 RNA genes will aid the G enomic E ncyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Albersmeier, A.
AU  - Al-Dilaimi, A.
AU  - Niehaus, K.
AU  - Szczepanowski, R.
AU  - Kalinowski, J.
TI  - Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 284
EP  - 293
VL  - 7
AB  - Corynebacterium halotolerans Chen et al. 2004 is a member of the genus
AB  - Corynebacterium which contains Gram-positive bacteria with a high G+C content. C.
AB  - halotolerans, isolated from a saline soil, belongs to the non-lipophilic,
AB  - non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%)
AB  - and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As
AB  - this is a type strain in a subgroup of Corynebacterium without complete genome
AB  - sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp
AB  - plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the
AB  - Genomic Encyclopedia ofBacteria andArchaea project.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Albersmeier, A.
AU  - Winkler, A.
AU  - Tauch, A.
TI  - Complete Genome Sequence of Corynebacterium camporealensis DSM 44610, Isolated from the Milk of a Manchega Sheep with Subclinical Mastitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00572
EP  - e00515
VL  - 3
AB  - Corynebacterium camporealensis has been isolated in pure culture from milk samples of dairy
AB  - sheep affected by subclinical mastitis. The complete genome
AB  - sequence of the type strain DSM 44610, recovered from milk of a Manchega sheep,
AB  - comprises 2,451,810 bp with a mean G+C content of 59.41% and 2,249 protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Albersmeier, A.
AU  - Winkler, A.
AU  - Tauch, A.
TI  - Complete Genome Sequence of Corynebacterium kutscheri DSM 20755, a Corynebacterial Type Strain with Remarkably Low G+C Content of Chromosomal DNA.
JO  - Genome Announcements
PY  - 2015
SP  - e00571
EP  - e00515
VL  - 3
AB  - The complete genome sequence of the type strain Corynebacterium kutscheri DSM 20755 comprises
AB  - 2,354,065 bp and 2,047 protein-coding genes. The mean G+C content
AB  - of the chromosomal DNA is 46.46%, which is the lowest value detected so far in a
AB  - member of the genus Corynebacterium.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Eimer, J.
AU  - Winkler, A.
AU  - Tauch, A.
TI  - Complete Genome Sequence of the Type Strain Corynebacterium epidermidicanis DSM 45586, Isolated from the Skin of a Dog Suffering from Pruritus.
JO  - Genome Announcements
PY  - 2015
SP  - e00959
EP  - e00915
VL  - 3
AB  - The complete genome sequence of Corynebacterium epidermidicanis DSM 45586 comprises 2,692,072
AB  - bp with 58.06% G+C content. The annotation revealed 2,466
AB  - protein-coding regions, including genes for surface-anchored proteins with Cna
AB  - B-type or bacterial Ig-like domains and for an adhesive SpaABC-type pilus with
AB  - similarity to fimbrial subunits of Corynebacterium resistens DSM 45100.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Eimer, J.
AU  - Winkler, A.
AU  - Tauch, A.
TI  - Complete Genome Sequence of the Type Strain Corynebacterium mustelae DSM 45274, Isolated from Various Tissues of a Male Ferret with Lethal Sepsis.
JO  - Genome Announcements
PY  - 2015
SP  - e01012
EP  - e01015
VL  - 3
AB  - The complete genome of Corynebacterium mustelae DSM 45274 comprises 3,474,226 bp  and 3,188
AB  - genes. Prominent niche and virulence factors are SpaBCA- and SpaDEF-type pili with similarity
AB  - to pilus proteins of Corynebacterium resistens and Corynebacterium urealyticum and an
AB  - immunomodulatory EndoS-like endoglycosidase probably catalyzing the removal of distinct
AB  - glycans from IgG antibodies.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Kalinowski, J.
AU  - Heide, L.
AU  - Apel, A.K.
TI  - Draft Genome Sequence of Streptomyces roseochromogenes subsp. oscitans DS 12.976, Producer of the Aminocoumarin Antibiotic Clorobiocin.
JO  - Genome Announcements
PY  - 2014
SP  - e01147
EP  - e01113
VL  - 2
AB  - Streptomyces roseochromogenes subsp. oscitans DS 12.976 is the producer of the
AB  - gyrase-inhibiting aminocoumarin antibiotic clorobiocin. Here, we present a draft
AB  - genome sequence of this strain, in which we identified the clorobiocin gene
AB  - cluster as well as an unusually high number (43) of further putative secondary
AB  - metabolite clusters.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Kriete, M.
AU  - Jaenicke, S.
AU  - Winkler, A.
AU  - Tauch, A.
TI  - Complete Genome Sequence of the Type Strain Corynebacterium testudinoris DSM 44614, Recovered from Necrotic Lesions in the Mouth of a Tortoise.
JO  - Genome Announcements
PY  - 2015
SP  - e00784
EP  - e00715
VL  - 3
AB  - The complete genome sequence of the type strain Corynebacterium testudinoris DSM  44614 from
AB  - the mouth of a tortoise comprises 2,721,226 bp with a mean G+C content
AB  - of 63.14%. The automatic annotation of the genome sequence revealed 4 rRNA
AB  - operons, 51 tRNA genes, 7 other RNA genes, and 2,561 protein-coding regions.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Kriete, M.
AU  - Jaenicke, S.
AU  - Winkler, A.
AU  - Tauch, A.
TI  - Virulence Factor Genes Detected in the Complete Genome Sequence of Corynebacterium uterequi DSM 45634, Isolated from the Uterus of a Maiden Mare.
JO  - Genome Announcements
PY  - 2015
SP  - e00783
EP  - e00715
VL  - 3
AB  - The complete genome sequence of the type strain Corynebacterium uterequi DSM 45634 from an
AB  - equine urogenital tract specimen comprises 2,419,437 bp and 2,163
AB  - protein-coding genes. Candidate virulence factors are homologs of DIP0733,
AB  - DIP1281, and DIP1621 from Corynebacterium diphtheriae and of sialidase precursors
AB  - from Trueperella pyogenes and Chlamydia trachomatis.
ER  -

TY  - JOUR
AU  - Ruckert, C.
AU  - Licht, K.
AU  - Kalinowski, J.
AU  - Espirito, S.C.
AU  - Antwerpen, M.
AU  - Hanczaruk, M.
AU  - Reischl, U.
AU  - Holzmann, T.
AU  - Gessner, A.
AU  - Tiemann, C.
AU  - Grass, G.
TI  - Draft Genome Sequence of Bacillus anthracis UR-1, Isolated from a German Heroin User.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5997
EP  - 5998
VL  - 194
AB  - We report the draft genome sequence of Bacillus anthracis UR-1, isolated from a fatal case of
AB  - injectional anthrax in a German heroin user. Analysis of the genome
AB  - sequence of strain UR-1 may aid in describing phylogenetic relationships between
AB  - virulent heroin-associated isolates of B. anthracis isolated in the United
AB  - Kingdom, Germany, and other European countries.
ER  -

TY  - JOUR
AU  - Rueckert, C.
AU  - Blom, J.
AU  - Chen, X.H.
AU  - Reva, O.
AU  - Borriss, R.
TI  - Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42.
JO  - J. Biotechnol.
PY  - 2011
SP  - 78
EP  - 85
VL  - 155
AB  - The complete genome sequence of Bacillus amyloliquefaciens type strain DSM7T is presented. A
AB  - comparative
AB  - analysis between the genome sequences of the plant associated strain FZB42 (Chen et al., 2007)
AB  - with the genome of B. amyloliquefaciens DSM7T revealed obvious differences in the variable
AB  - part of the
AB  - genomes, whilst the core genomes were found to be very similar. The strains FZB42 and DSM7T
AB  - have in
AB  - common 3345 genes (CDS) in their core genomes; whilst 547 and 344 CDS were found to be unique
AB  - in
AB  - DSM7T and FZB42, respectively. The core genome shared by both strains exhibited 97.89%
AB  - identity on
AB  - amino acid level. The number of genes representing the core genome of the strains FZB42,
AB  - DSM7T, and
AB  - Bacillus subtilis DSM10T was calculated as being 3098 and their identity was 92.25%. The
AB  - 3,980,199 bp
AB  - genome of DSM7T contains numerous genomic islands (GI) detected by different methods. Many of
AB  - them
AB  - were located in vicinity of tRNA, glnA, and glmS gene copies. In contrast to FZB42, but
AB  - similar to B. subtilis
AB  - DSM10T, the GI were enriched in prophage sequences and often harbored transposases, integrases
AB  - and recombinases. Compared to FZB42, B. amyloliquefaciens DSM7T possessed a reduced potential
AB  - to
AB  - non-ribosomally synthesize secondary metabolites with antibacterial and/or antifungal action.
AB  - B. amyloliquefaciens
AB  - DSM7T did not produce the polyketides difficidin and macrolactin and was impaired in its
AB  - ability to produce lipopeptides other than surfactin. Differences established within the
AB  - variable part of
AB  - the genomes, justify our proposal to discriminate the plant-associated ecotype represented by
AB  - FZB42
AB  - from the group of type strain related B. amyloliquefaciens soil bacteria.
ER  -

TY  - JOUR
AU  - Ruepp, A.
AU  - Graml, W.
AU  - Santos-Martinez, M.-L.
AU  - Koretke, K.K.
AU  - Volker, C.
AU  - Mewes, H.W.
AU  - Frishman, D.
AU  - Stocker, S.
AU  - Lupas, A.N.
AU  - Baumeister, W.
TI  - The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.
JO  - Nature
PY  - 2000
SP  - 508
EP  - 513
VL  - 407
AB  - Thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 C and pH2, which
AB  - was isolated from self-heating coal refuse piles and solfatara fields.  Species of the genus
AB  - Thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane.
AB  - Many macromolecular assemblies from Thermoplasma, primarily proteases and chaperones, have
AB  - been pivotal in elucidating the structure and function of their more complex eukaryotic
AB  - homologues.  Our interest in protein folding and degradation led us to seek a more complete
AB  - representation of the proteins involved in these pathways by determining the genome sequence
AB  - of the organism.  Here we have sequenced the 1,564,905-base-pair genome in just 7,855
AB  - sequencing reactions by using a new strategy.  The 1,509 open reading frames identify
AB  - Thermoplasma as a typical euryarchaeon with a substantial complement of bacteria-related
AB  - genes; however, evidence indicates that there has been much lateral gene transfer between
AB  - Thermoplasma and Sulfolobus solfataricus, a phylogenetically distance crenarchaeon inhabiting
AB  - the same environment.  At least 252 open reading frames, including a complete protein
AB  - degradation pathway and various transport proteins, resemble Sulfolobus proteins most closely.
ER  -

TY  - JOUR
AU  - Ruffing, A.M.
AU  - Castro-Melchor, M.
AU  - Hu, W.S.
AU  - Chen, R.R.
TI  - Genome Sequence of the Curdlan-Producing Agrobacterium sp. Strain ATCC 31749.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4294
EP  - 4295
VL  - 193
AB  - Agrobacterium sp. ATCC 31749 is an industrial strain for the commercial production of curdlan,
AB  - an important exopolysaccharide with food and
AB  - medical applications. Here we report the genome sequence of the
AB  - curdlan-producing strain ATCC 31749. Genome sequencing is the first step
AB  - toward the understanding of regulation of curdlan biosynthesis.
ER  -

TY  - JOUR
AU  - Ruh, M.
AU  - Briand, M.
AU  - Bonneau, S.
AU  - Jacques, M.A.
AU  - Chen, N.W.G.
TI  - Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors.
JO  - BMC Genomics
PY  - 2017
SP  - 670
EP  - 670
VL  - 18
AB  - BACKGROUND: Common bacterial blight is a devastating bacterial disease of common
AB  - bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas
AB  - phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause
AB  - similar symptoms on common bean, suggesting that they have acquired common
AB  - genetic determinants of adaptation to common bean. Transcription Activator-Like
AB  - (TAL) effectors are bacterial type III effectors that are able to induce the
AB  - expression of host genes to promote infection or resistance. Their capacity to
AB  - bind to a specific host DNA sequence suggests that they are potential candidates
AB  - for host adaption. RESULTS: To study the diversity of tal genes from Xanthomonas
AB  - strains responsible for common bacterial blight of bean, whole genome sequences
AB  - of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli
AB  - pv. phaseoli were obtained by single molecule real time sequencing. Analysis of
AB  - these genomes revealed the existence of four tal genes named tal23A, tal20F,
AB  - tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A
AB  - and tal18H were carried on plasmids and shared between phylogenetically distant
AB  - strains, therefore suggesting recent horizontal transfers of these genes between
AB  - X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was
AB  - present in all strains studied, suggesting that it played an important role in
AB  - adaptation to common bean. In silico predictions of TAL effectors targets in the
AB  - common bean genome suggested that TAL effectors shared by X. citri pv. fuscans
AB  - and X. phaseoli pv. phaseoli strains target the promoters of genes of similar
AB  - functions. This could be a trace of convergent evolution among TAL effectors from
AB  - different phylogenetic groups, and comforts the hypothesis that TAL effectors
AB  - have been implied in the adaptation to common bean. CONCLUSIONS: Altogether, our
AB  - results favour a model where plasmidic TAL effectors are able to contribute to
AB  - host adaptation by being horizontally transferred between distant lineages.
ER  -

TY  - JOUR
AU  - Ruh, M.
AU  - Briand, M.
AU  - Bonneau, S.
AU  - Jacques, M.A.
AU  - Chen, N.W.G.
TI  - First Complete Genome Sequences of Xanthomonas citri pv. vignicola Strains CFBP7111, CFBP7112, and CFBP7113 Obtained Using Long-Read Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e00813
EP  - e00817
VL  - 5
AB  - Xanthomonas citri pv. vignicola strains cause bacterial blight of the legume crop cowpea. We
AB  - report whole-genome sequences of three X. citri pv. vignicola strains
AB  - obtained using PacBio single-molecule real-time sequencing. Such genomic data
AB  - provide new information on pathogenicity factors, such as transcription
AB  - activator-like effectors.
ER  -

TY  - JOUR
AU  - Ruinelli, M.
AU  - Blom, J.
AU  - Pothier, J.F.
TI  - Complete Genome Sequence of Pseudomonas viridiflava CFBP 1590, Isolated from Diseased Cherry in France.
JO  - Genome Announcements
PY  - 2017
SP  - e00662
EP  - e00617
VL  - 5
AB  - Pseudomonas viridiflava causes foliar and stem necrosis, as well as stem and root rot on a
AB  - wide range of plants. We report here the first complete genome of a P.
AB  - viridiflava strain, isolated from diseased tissue of a cherry tree.
ER  -

TY  - JOUR
AU  - Ruiz, O.N.
AU  - Brown, L.M.
AU  - Striebich, R.C.
AU  - Mueller, S.S.
AU  - Gunasekera, T.S.
TI  - Draft Genome Sequence of Pseudomonas frederiksbergensis SI8, a Psychrotrophic Aromatic-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00811
EP  - e00815
VL  - 3
AB  - Pseudomonas frederiksbergensis strain SI8 is a psychrotrophic bacterium capable of efficient
AB  - aerobic degradation of aromatic hydrocarbons. The draft genome of P.
AB  - frederiksbergensis SI8 is 6.57 Mb in size, with 5,904 coding sequences and 60.5%
AB  - G+C content. The isopropylbenzene (cumene) degradation pathway is predicted to be
AB  - present in P. frederiksbergensis SI8.
ER  -

TY  - JOUR
AU  - Ruiz, S.M.
AU  - Letourneau, S.
AU  - Cupples, C.G.
TI  - Isolation and characterization of an Escherichia coli strain with a high frequency of C-to-T mutations at 5-methylcytosines.
JO  - J. Bacteriol.
PY  - 1993
SP  - 4985
EP  - 4989
VL  - 175
AB  - We used a genetic selection system to isolate a strain of Escherichia coli with a high
AB  - frequency of C-to-T transition mutations at the second C of the sequence CCAGG. Cytosines in
AB  - other sequences do not mutate to thymine at a high frequency in this strain, and the
AB  - frequencies of other base substitution mutations are not increased to the same extent. The
AB  - gene responsible for the mutator phenotype has been mapped to 43 min on the E. coli
AB  - chromosome. Several lines of evidence indicate that this gene is distinct from the very short
AB  - patch repair gene vsr.
ER  -

TY  - JOUR
AU  - Ruiz-Herrera, J.
AU  - Ruiz-Medrano, R.
AU  - Dominguez, A.
TI  - Selective inhibition of cytosine-DNA methylases by polyamines.
JO  - FEBS Lett.
PY  - 1995
SP  - 192
EP  - 196
VL  - 357
AB  - We have advanced the hypothesis that polyamines affect DNA methylation and thus promote the
AB  - expression of developmentally controlled genes. We demonstrate that the activity of
AB  - cytosine-DNA methyltransferases HpaII, HhaI, HaeIII and SssI is inhibited by physiological
AB  - concentrations of polyamines. On the other hand, activity of the adenine-DNA methyltransferase
AB  - EcoRI, and restriction enzymes HpaII, HhaI, HaeIII and EcoRI, is insensitive to polyamine
AB  - concentrations up to 40 mM. Our results indicate that the effect of polyamines on cytosine-DNA
AB  - methyltransferases is rather selective and suggest a possible mode of action in vivo.
ER  -

TY  - JOUR
AU  - Ruiz-Valdiviezo, V.M.
AU  - Rogel-Hernandez, M.A.
AU  - Guerrero, G.
AU  - Rincon-Molina, C.I.
AU  - Garcia-Perez, L.G.
AU  - Gutierrez-Miceli, F.A.
AU  - Villalobos-Maldonado, J.J.
AU  - Lopez-Lopez, A.
AU  - Martinez-Romero, E.
AU  - Rincon-Rosales, R.
TI  - Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e01280
EP  - e01217
VL  - 5
AB  - We report here the complete genome sequence of Rhizobium sp. strain ACO-34A, isolated from
AB  - Agave americana L. rhizosphere. No common nod genes were found, but
AB  - there were nif genes for nitrogen fixing. A low average nucleotide identity to
AB  - reported species supports its designation as a novel Rhizobium species that has a
AB  - complete ribosomal operon in a plasmid.
ER  -

TY  - JOUR
AU  - Rume, F.I.
AU  - Antwerpen, M.
AU  - Braun, P.
AU  - Biswas, P.K.
AU  - Yasmin, M.
AU  - Grass, G.
AU  - Ahsan, C.R.
AU  - Hanczaruk, M.
TI  - Genome Sequence of Bacillus anthracis Strain Tangail-1 from Bangladesh.
JO  - Genome Announcements
PY  - 2016
SP  - e00748
EP  - e00716
VL  - 4
AB  - Soil was collected in July 2013 at a site where a cow infected with anthrax had been the month
AB  - before. Selective culturing yielded Bacillus anthracis strain
AB  - Tangail-1. Here, we report the draft genome sequence of this Bacillus anthracis
AB  - isolate that belongs to the canonical A.Br.001/002 clade.
ER  -

TY  - JOUR
AU  - Rump, L.V.
AU  - Strain, E.A.
AU  - Cao, G.
AU  - Allard, M.W.
AU  - Fischer, M.
AU  - Brown, E.W.
AU  - Gonzalez-Escalona, N.
TI  - Draft Genome Sequences of Six Escherichia coli Isolates from the Stepwise Model of Emergence of Escherichia coli O157:H7.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2058
EP  - 2059
VL  - 193
AB  - Enterohemorrhagic Escherichia coli (EHEC) of serotype O157:H7 has been implicated in
AB  - food-borne illnesses worldwide. An evolutionary model was
AB  - proposed in which the highly pathogenic EHEC O157:H7 serotype arose from
AB  - its ancestor, enteropathogenic E. coli (EPEC) O55:H7 (sorbitol fermenting
AB  - [SOR(+)] and beta-glucuronidase positive [GUD(+)]), through sequential
AB  - gain of virulence, phenotypic traits, and serotype change. Here we report
AB  - six draft genomes of strains belonging to this evolutionary model: two
AB  - EPEC O55:H7 (SOR(+) GUD(+)) strains, two nonmotile EHEC O157:H(-) strains
AB  - (SOR(+) GUD(+)) containing plasmid pSFO157, one EHEC O157:H7 (SOR(-)
AB  - GUD(+)) strain, and one O157:H7 strain containing plasmid pSFO157 (SOR(+)
AB  - GUD(+)).
ER  -

TY  - JOUR
AU  - Ruoff, B.
AU  - Johansen, S.
AU  - Vogt, V.M.
TI  - Characterization of the self-splicing products of a mobile intron from the nuclear rDNA of Physarum polycephalum.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5899
EP  - 5906
VL  - 20
AB  - We have characterized the splicing products formed in vitro from RNA derived from the mobile
AB  - group I intron in the nuclear rDNA of Physarum polycephalum, Pp LSU 3. This intron is a close
AB  - relative of the well known Tetrahymena intron Tt LSU 1, being inserted at exactly the same
AB  - position in the rDNA and sharing about 90% sequence identity with Tt LSU 1 in the conserved
AB  - elements characteristic of the catalytic core of all group I introns. However, Pp LSU 3
AB  - differs from Tt LSU 1 in that it encodes a site-specific endonuclease, which mediates the
AB  - homing of the intron to unoccupied target sites. The endonuclease, I-Ppo, would appear to be a
AB  - unique example of a protein encoded by an RNA polymerase I transcript. To gain clues to the
AB  - splicing products formed in vivo, and to the nature of the messenger RNA for I-Ppo, we
AB  - subjected Pp LSU 3 RNA to standard self-splicing conditions in vitro, and then analyzed the
AB  - products by size, by northern blotting, and by primer extension. The results show two novel
AB  - features. First, in addition to the expected 5' splice site, there is an alternative 5'
AB  - splice site in the upstream exon, just preceding the first codon of the I-Ppo open reading
AB  - frame. Second, at the position corresponding to the major circularization site in Tt LSU 1
AB  - there is an internal processing site, leading to the efficient separation of two halves of the
AB  - excised intron, the 5' half encoding I-Ppo and 3' half containing the ribozyme.
AB  - Surprisingly, this cleavage appears not to be due to circularization followed by the
AB  - hydrolytic opening of the circle, but rather to G addition. The formation of these products in
AB  - vitro suggests how the messenger RNA for the I-Ppo endonuclease may be generated in vivo.
ER  -

TY  - JOUR
AU  - Ruppe, E.
AU  - Olearo, F.
AU  - Pires, D.
AU  - Baud, D.
AU  - Renzi, G.
AU  - Cherkaoui, A.
AU  - Goldenberger, D.
AU  - Huttner, A.
AU  - Francois, P.
AU  - Harbarth, S.
AU  - Schrenzel, J.
TI  - Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing.
JO  - Clin. Microbiol. Infect.
PY  - 2017
SP  - 470475
EP  - 470475
VL  - 23
AB  - OBJECTIVES: Whole-genome sequencing (WGS) is a promising tool for identifying
AB  - transmission pathways in outbreaks caused by multidrug-resistant bacteria.
AB  - However, it is uncertain how the data produced by WGS can be best integrated into
AB  - epidemiologic investigations. METHODS: We tested various genomic analyses to
AB  - identify clonal groups in two distinct outbreaks of Klebsiella pneumoniae
AB  - carbapenemase-producing K. pneumoniae that occurred in Switzerland in 2013 and
AB  - 2015. In blinded fashion, we sequenced 12 strains involved in the two outbreaks,
AB  - respectively, and six that were epidemiologically unrelated. We analysed genomic
AB  - commonalities from conserved genes to plasmid-borne antibiotic resistance genes
AB  - (ARGs) and contrasted these results with available epidemiologic evidence.
AB  - RESULTS: Using WGS, blinded analysts correctly identified the two clusters of
AB  - strains from the two outbreaks. Nonetheless, the 2015 index strain was found to
AB  - be slightly different (1-3 single nucleotide variants) from the strains recovered
AB  - from secondary cases, likely because prior long-term carriage (3 years) by the
AB  - index patient allowed for genetic mutations over time. Also, we observed
AB  - occasional loss of ARG-bearing plasmidic fragments in outbreak-causing strains.
AB  - CONCLUSIONS: Retrospective WGS analysis was successful in identifying clonal
AB  - groups in both outbreaks. Still, data should be analysed with caution in cases of
AB  - previous long-term carriage of the studied bacteria.
ER  -

TY  - JOUR
AU  - Rusch, D.B. et al.
TI  - The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific.
JO  - PLoS Biology
PY  - 2007
SP  - e77
EP  - e77
VL  - 5
AB  - The world's oceans contain a complex mixture of micro-organisms that are for the most part,
AB  - uncharacterized both genetically and biochemically. We report here a metagenomic study of the
AB  - marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as
AB  - part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a
AB  - several-thousand km transect from the North Atlantic through the Panama Canal and ending in
AB  - the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3
AB  - billion bp). Though a few major microbial clades dominate the planktonic marine niche, the
AB  - dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled
AB  - data being unique at a 98% sequence identity cutoff. Using the metadata associated with each
AB  - sample and sequencing library, we developed new comparative genomic and assembly methods. One
AB  - comparative genomic method, termed "fragment recruitment," addressed questions of genome
AB  - structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical
AB  - diversity of genes and gene families. A second method, termed "extreme assembly," made
AB  - possible the assembly and reconstruction of large segments of abundant but clearly nonclonal
AB  - organisms. Within all abundant populations analyzed, we found extensive intra-ribotype
AB  - diversity in several forms: (1) extensive sequence variation within orthologous regions
AB  - throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most
AB  - individual sequencing reads are unique; (2) numerous changes in gene content some with direct
AB  - adaptive implications; and (3) hypervariable genomic islands that are too variable to
AB  - assemble. The intra-ribotype diversity is organized into genetically isolated populations that
AB  - have overlapping but independent distributions, implying distinct environmental preference. We
AB  - present novel methods for measuring the genomic similarity between metagenomic samples and
AB  - show how they may be grouped into several community types. Specific functional adaptations can
AB  - be identified both within individual ribotypes and across the entire community, including
AB  - proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene
AB  - PstS.
ER  -

TY  - JOUR
AU  - Rusch, D.B.
AU  - Lombardo, M.J.
AU  - Yee-Greenbaum, J.
AU  - Novotny, M.
AU  - Brinkac, L.M.
AU  - Lasken, R.S.
AU  - Dupont, C.L.
TI  - Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa.
JO  - Genome Announcements
PY  - 2013
SP  - e00030
EP  - e00012
VL  - 1
AB  - SAR86 denotes a 16S clade of gammaproteobacteria that are ubiquitous in ocean surface waters.
AB  - So far, SAR86 is resistant to cultivation; thus, little is known about the genome contents or
AB  - physiology of this clade. Recently, four partial genome sequences for SAR86 subclades I and II
AB  - were published. Here, we present the draft genome sequence of a single cell from SAR86
AB  - subgroup IIIa isolated from coastal waters in San Diego, CA.
ER  -

TY  - JOUR
AU  - Rusch, D.B.
AU  - Rowe-Magnus, D.A.
TI  - Complete Genome Sequence of the Pathogenic Vibrio vulnificus Type Strain ATCC 27562.
JO  - Genome Announcements
PY  - 2017
SP  - e00907
EP  - e00917
VL  - 5
AB  - Vibrio vulnificus has the highest death rate and economic burden per case of any  foodborne
AB  - pathogen in the United States. A complete genome sequence of the type
AB  - strain promotes comparative analyses with other clinical and environmental
AB  - isolates, improving our understanding of this important human pathogen and
AB  - successful environmental organism.
ER  -

TY  - JOUR
AU  - Ruscher, K.
AU  - Reuter, M.
AU  - Kupper, D.
AU  - Trendelenburg, G.
AU  - Dirnagl, U.
AU  - Meisel, A.
TI  - A fluorescence based non-radioactive electrophoretic mobility shift assay.
JO  - J. Biotechnol.
PY  - 2000
SP  - 163
EP  - 170
VL  - 78
AB  - Electrophoretic mobility shift assay (EMSA) or gel shift assay is one of the most powerful
AB  - methods for studying protein-DNA interactions. Typically,
AB  - 32P-labeled DNA probes containing the sequence bound by the protein of interest are used in
AB  - EMSA (rEMSA). Although rEMSA is sensitive and practicable, it relies on the
AB  - handling of hazardous radioisotopes, and does not easily allow quantification. We developed a
AB  - non-radioactive procedure using fluorescence (Cyano dye Cy5) labeled
AB  - oligodeoxynucleotide duplexes as specific probes (fEMSA) and an automatic DNA sequencer for
AB  - analysis. Testing different DNA-binding proteins (restriction endonuclease
AB  - EcoRII, transcription factor NFkappaB and it's subunit p50) the results in fEMSA and rEMSA
AB  - are similar in regard to quality, reproducibility, and sensitivity. fEMSA allows
AB  - a semiquantitative screening of large amounts of samples for specific DNA binding activities
AB  - and is, therefore, a high throughput technology for semiquantitative analysis of
AB  - DNA-protein interaction.
ER  -

TY  - JOUR
AU  - Rusconi, B.
AU  - Chen, Y.
AU  - Koenig, S.S.
AU  - El-Helow, E.R.
AU  - Eppinger, M.
TI  - Genome Sequence of Bacillus thuringiensis Strain Btm27, an Egyptian Isolate Highly Toxic to Cotton Leafworm.
JO  - Genome Announcements
PY  - 2015
SP  - e00446
EP  - e00415
VL  - 3
AB  - Bacillus thuringiensis is a potent microbial control agent against insect pests.  Here, we
AB  - present the draft genome of the Egyptian strain Btm27 that shows high
AB  - toxicity toward the cotton leafworm. The genome contains three insecticidal genes
AB  - cry1Ac9, cry2Ab1, and vip3V that have been implicated in conferring toxicity
AB  - toward lepidoptera.
ER  -

TY  - JOUR
AU  - Rushizky, G.W.
TI  - Purification of the sequence-specific endonuclease PalI.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 239
EP  - 242
VL  - 1
AB  - *
AB  -   I. Growth of cells
AB  -  II. Purification of PalI
AB  - III. Physical and chemical properties of the enzyme
AB  -  IV. Purification of other enzymes
AB  - 
ER  -

TY  - JOUR
AU  - Rusinov, I.
AU  - Ershova, A.
AU  - Karyagina, A.
AU  - Spirin, S.
AU  - Alexeevski, A.
TI  - Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.
JO  - BMC Genomics
PY  - 2015
SP  - 1084
EP  - 1084
VL  - 16
AB  - BACKGROUND: Avoidance of palindromic recognition sites of Type II restriction-modification
AB  - (R-M) systems was shown for many R-M systems in dozens
AB  - of prokaryotic genomes. However the phenomenon has not been investigated
AB  - systematically for all presently available genomes and annotated R-M systems. We
AB  - have studied all known recognition sites in thousands of prokaryotic genomes and
AB  - found factors that influence their avoidance. RESULTS: Only Type II R-M systems
AB  - consisting of independently acting endonuclease and methyltransferase (called
AB  - 'orthodox' here) cause avoidance of their sites, both palindromic and asymmetric,
AB  - in corresponding prokaryotic genomes; the avoidance takes place for ~ 50 % of
AB  - 1774 studied cases. It is known that prokaryotes can acquire and lose R-M
AB  - systems. Thus it is possible to talk about the lifespan of an R-M system in a
AB  - genome. We have shown that the recognition site avoidance correlates with the
AB  - lifespan of R-M systems. The sites of orthodox R-M systems that are encoded in
AB  - host genomes for a long time are avoided more often (up to 100 % in certain
AB  - cohorts) than the sites of recently acquired ones. We also found cases of site
AB  - avoidance in absence of the corresponding R-M systems in the genome. An analysis
AB  - of closely related bacteria shows that such avoidance can be a trace of lost R-M
AB  - systems. Sites of Type I, IIcapital ES, Cyrillic/G, IIM, III, and IV R-M systems
AB  - are not avoided in vast majority of cases. CONCLUSIONS: The avoidance of orthodox
AB  - Type II R-M system recognition sites in prokaryotic genomes is a widespread
AB  - phenomenon. Presence of an R-M system without an underrepresentation of its site
AB  - may indicate that the R-M system was acquired recently. At the same time, a
AB  - significant underrepresentation of a site may be a sign of presence of the
AB  - corresponding R-M system in this organism or in its ancestors for a long time.
AB  - The drastic difference between site avoidance for orthodox Type II R-M systems
AB  - and R-M systems of other types can be explained by a higher rate of specificity
AB  - changes or a less self-toxicity of the latter.
ER  -

TY  - JOUR
AU  - Rusling, D.A.
AU  - Laurens, N.
AU  - Pernstich, C.
AU  - Wuite, G.J.
AU  - Halford, S.E.
TI  - DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 4977
EP  - 4987
VL  - 40
AB  - Most restriction endonucleases, including FokI, interact with two copies of their recognition
AB  - sequence before cutting DNA. On DNA with two sites they act in cis
AB  - looping out the intervening DNA. While many restriction enzymes operate
AB  - symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic
AB  - site. The directionality of its sequence means that two FokI sites can be bridged
AB  - in either parallel or anti-parallel alignments. Here we show by biochemical and
AB  - single-molecule biophysical methods that FokI aligns two recognition sites on
AB  - separate DNA molecules in parallel and that the parallel arrangement holds for
AB  - sites in the same DNA regardless of whether they are in inverted or repeated
AB  - orientations. The parallel arrangement dictates the topology of the loop trapped
AB  - between sites in cis: the loop from inverted sites has a simple 180 degrees bend,
AB  - while that with repeated sites has a convoluted 360 degrees turn. The ability of
AB  - FokI to act at asymmetric sites thus enabled us to identify the synapse geometry
AB  - for sites in trans and in cis, which in turn revealed the relationship between
AB  - synapse geometry and loop topology.
ER  -

TY  - JOUR
AU  - Rusmintratip, V.
AU  - Riggs, A.D.
AU  - Sowers, L.C.
TI  - Examination of the DNA substrate selectivity of DNA cytosine methyltransferases using mass tagging.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3594
EP  - 3599
VL  - 28
AB  - The biological significance of cytosine methylation is as yet incompletely understood, but
AB  - substantial and growing evidence strongly suggests that perturbation of methylation patterns,
AB  - resulting from the infidelity of DNA cytosine methyltransferase, is an important component of
AB  - the development of human cancer. We have developed a novel in vitro assay that allows us to
AB  - quantitatively determine the DNA substrate preferences of cytosine methylases. This approach,
AB  - which we call mass tagging, involves the labeling of target cytosine residues in synthetic DNA
AB  - duplexes with stable isotopes, such as (15)N. Methylation is then measured by the formation of
AB  - 5-methylcytosine (5mC) by gas chromatography/mass spectrometry. The DNA substrate selectivity
AB  - is determined from the mass spectrum of the product 5mC. With the non-symmetrical duplex DNA
AB  - substrate examined in this study we find that the bacterial methyltransferase HpaII (duplex
AB  - DNA recognition sequence CCGG) methylates the one methylatable cytosine of each strand
AB  - similarly. Introduction of an A-C mispair at the methylation site shifts methylation
AB  - exclusively to the mispaired cytosine residue. In direct competition assays with HpaII
AB  - methylase we observe that the mispaired substrate is methylated more extensively than the
AB  - fully complementary, normal substrate, although both have one HpaII methylation site. Through
AB  - the use of this approach we will be able to learn more about the mechanisms by which
AB  - methylation patterns can become altered.
ER  -

TY  - JOUR
AU  - Rusniok, C.
AU  - Couve, E.
AU  - Da Cunha, V.
AU  - El Gana, R.
AU  - Zidane, N.
AU  - Bouchier, C.
AU  - Poyart, C.
AU  - Leclercq, R.
AU  - Trieu-Cuot, P.
AU  - Glaser, P.
TI  - Genome Sequence of Streptococcus gallolyticus: Insights into Its Adaptation to the Bovine Rumen and Its Ability To Cause Endocarditis.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2266
EP  - 2276
VL  - 192
AB  - Streptococcus gallolyticus (formerly known as Streptococcus bovis biotype I) is an increasing
AB  - cause of endocarditis among streptococci and
AB  - frequently associated with colon cancer. S. gallolyticus is part of the
AB  - rumen flora but also a cause of disease in ruminants as well as in birds.
AB  - Here we report the complete nucleotide sequence of strain UCN34,
AB  - responsible for endocarditis in a patient also suffering from colon
AB  - cancer. Analysis of the 2,239 proteins encoded by its 2,350-kb-long genome
AB  - revealed unique features among streptococci, probably related to its
AB  - adaptation to the rumen environment and its capacity to cause
AB  - endocarditis. S. gallolyticus has the capacity to use a broad range of
AB  - carbohydrates of plant origin, in particular to degrade polysaccharides
AB  - derived from the plant cell wall. Its genome encodes a large repertoire of
AB  - transporters and catalytic activities, like tannase, phenolic compounds
AB  - decarboxylase, and bile salt hydrolase, that should contribute to the
AB  - detoxification of the gut environment. Furthermore, S. gallolyticus
AB  - synthesizes all 20 amino acids and more vitamins than any other sequenced
AB  - Streptococcus species. Many of the genes encoding these specific functions
AB  - were likely acquired by lateral gene transfer from other bacterial species
AB  - present in the rumen. The surface properties of strain UCN34 may also
AB  - contribute to its virulence. A polysaccharide capsule might be implicated
AB  - in resistance to innate immunity defenses, and glucan mucopolysaccharides,
AB  - three types of pili, and collagen binding proteins may play a role in
AB  - adhesion to tissues in the course of endocarditis.
ER  -

TY  - JOUR
AU  - Russell, D.A.
AU  - Bowman, C.A.
AU  - Hatfull, G.F.
TI  - Genome Sequence of Salmonella enterica subsp. enterica Strain Durban.
JO  - Genome Announcements
PY  - 2014
SP  - e00399
EP  - e00314
VL  - 2
AB  - We report the genome sequence of Salmonella enterica subsp. enterica strain Durban, isolated
AB  - from a patient with salmonellosis and typhoid fever. The strain
AB  - is closely related to S. enterica subsp. enterica strain P125109 but differs in
AB  - loss of the SE20 prophage and acquisition of a prophage similar to ELPhiS.
ER  -

TY  - JOUR
AU  - Russell, D.A.
AU  - Guerrero, B.C.A.
AU  - Garlena, R.A.
AU  - Hatfull, G.F.
TI  - Complete Genome Sequence of Gordonia terrae 3612.
JO  - Genome Announcements
PY  - 2016
SP  - e01058
EP  - e01016
VL  - 4
AB  - Here, we report the complete genome sequence of Gordonia terrae 3612, also known  by the
AB  - strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome
AB  - sequence reveals it to be free of prophage and clustered regularly interspaced
AB  - short palindromic repeats (CRISPRs), and it is an effective host for the
AB  - isolation and characterization of Gordonia bacteriophages.
ER  -

TY  - JOUR
AU  - Russell, D.A.
AU  - Hatfull, G.F.
TI  - Complete Genome Sequence of Arthrobacter sp. ATCC 21022, a Host for Bacteriophage Discovery.
JO  - Genome Announcements
PY  - 2016
SP  - e00168
EP  - e00116
VL  - 4
AB  - We report the complete genome sequence ofArthrobactersp. ATCC 21022, a strain maintained by
AB  - ATCC and a commonly used host for bacteriophage isolation and
AB  - genomic analysis. The strain is prophage-free and CRISPR-free but codes for two
AB  - predicted restriction-modification systems.
ER  -

TY  - JOUR
AU  - Russell, D.F.
AU  - Betts, D.H.
TI  - Alternative splicing and expression analysis of bovine DNA methyltransferase 1.
JO  - Dev. Dyn.
PY  - 2008
SP  - 1051
EP  - 1059
VL  - 237
AB  - Methylation of specific CG residues in the mammalian genome results in tissue-specific
AB  - patterns of gene expression, which are critical for
AB  - cell differentiation. Embryos that fail to establish and maintain
AB  - proper DNA methylation patterns show severe developmental abnormalities
AB  - as is the case of DNA methyltransferase 1 (Dnmt1) -deficient embryos.
AB  - Dnmt1 is the main maintenance methyltransferase in the mouse and its
AB  - expression is regulated by a splicing mechanism that dictates the
AB  - expression of stage-specific isoforms. Little is known about Dnmt1
AB  - expression in the cow and isoforms of Dnmt1 are yet unknown in this
AB  - species. Here we demonstrate that the previously described bovine Dnmt1
AB  - transcript is ubiquitously expressed in embryos and fetal tissue. In
AB  - addition, we report the identification of a splice variant of the
AB  - bovine Dnmt1, which shows a ubiquitous expression pattern. This new
AB  - transcript was detected using 5'RACE and genomic mapping and its
AB  - expression pattern was shown to be consistent with a tissue-specific
AB  - mode of regulation. Furthermore, our analysis shows that the expression
AB  - of an oocyte-specific isoform of Dnmt1 is unlikely to occur in cattle.
AB  - The newly reported isoform of Dnmt1 was demonstrated to be, similarly
AB  - to Dnmt1a, polyadenylated and if translated possess the functional
AB  - domains necessary for maintenance and de novo methyltransferase
AB  - activity.
ER  -

TY  - JOUR
AU  - Russell, D.W.
AU  - Hirata, R.K.
TI  - The detection of extremely rare DNA modifications.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 10787
EP  - 10794
VL  - 264
AB  - DNA methylation in Escherichia coli plays a role in many key cellular processes, including DNA
AB  - replication, repair, restriction, and transcription. However, several mutant bacterial strains
AB  - exist which are deficient in DNA methylase activities. Thus, it has been suggested that
AB  - methylation produced by the dam (DNA adenine methylase) gene is required for the viability of
AB  - E. coli and that dam- strains still produce low levels of methylation. Current experimental
AB  - methods are not sensitive enough to detect a few potentially essential methylated sites per
AB  - genome. Here we describe a method for the detection of N6-methyladenine at specific sites with
AB  - a sensitivity of one site in more than 10 megabases. We show that methylation produced by both
AB  - the dam and hsd (EcoK) genes is not required for the growth of E. coli and identify the site
AB  - of EcoK modification. Minor adaptations of the technique should enable the identification of
AB  - other rare DNA modifications.
ER  -

TY  - JOUR
AU  - Russell, D.W.
AU  - Zinder, N.D.
TI  - Hemimethylation prevents DNA replication in E. coli.
JO  - Cell
PY  - 1987
SP  - 1071
EP  - 1079
VL  - 50
AB  - The DNA adenine methylase of E. coli methylates adenines at GATC sequences. Strains deficient
AB  - in this methylase are transformed poorly by methylated plasmids that depend on either the
AB  - pBR322 or the chromosomal origins for replication. We show here that hemimethylated plasmids
AB  - also transform dam- bacteria poorly but that unmethylated plasmids transform them at high
AB  - frequencies. Hemimethylated daughter molecules accumulate after the transformation of dam-
AB  - strains by fully methylated plasmids, suggesting that hemimethylation prevents DNA
AB  - replication. We also show that plasmids purified from dam+ bacteria are hemimethylated at
AB  - certain sites. These results can explain why newly formed daughter molecules are not
AB  - substrates for an immediate reinitiation of DNA replication in wild-type E. coli.
ER  -

TY  - JOUR
AU  - Russo, T.A.
AU  - Gill, S.R.
TI  - Draft Genome Sequence of the Hypervirulent Klebsiella pneumoniae Strain hvKP1, Isolated in Buffalo, New York.
JO  - Genome Announcements
PY  - 2013
SP  - e0006513
EP  - e0006513
VL  - 1
AB  - Hypervirulent variants of Klebsiella pneumoniae have been primarily reported in the Asian
AB  - Pacific Rim, but they are spreading across the globe. We report the
AB  - sequence of K. pneumoniae strain hvKP1, which caused liver-splenic abscesses in
AB  - an otherwise healthy 24-year-old from Buffalo, NY, which will assist in
AB  - determining why these variants are more pathogenic than 'classic' K. pneumoniae
AB  - strains.
ER  -

TY  - JOUR
AU  - Rusu, V.
AU  - Dorobat-Baron, O.
AU  - Cosman, M.
AU  - Lazaroae, D.
TI  - Restriction and modification of typing phages by an R factor in S. typhi.
JO  - Zentralbl. Bakteriol. [Orig. A]
PY  - 1976
SP  - 491
EP  - 501
VL  - 234
AB  - We have investigated the qualities of one R factor 552 discovered on a strain of S. typhi
AB  - resistant to A, C, S, T, non-typable, isolated from stool cultures; from the same patient,
AB  - before starting the treatment we isolated, from his blood sample, the strain S. typhi 221,
AB  - sensitive to A, C, T, degraded phage-type Vi A.  Factor R 552 fi- when infecting strains of S.
AB  - typhi Vi A and of A degraded 221- leads to the conversion of the respective phage-types into
AB  - non-typable ones, as a result of the restricting and modifying effect on phage ViA and on the
AB  - derivatives resulting from it.  Derivative R 552-1 as a resistance marker to ampicillin has a
AB  - restrictive effect on the phage of S. panama A 47 too.  Not taking into account possible
AB  - causes such as spontaneous mutation, lysogeny, and adsorption of phages, we reach the
AB  - conclusion that R factor 552, through its restrictive effect, is the only cause responsible
AB  - for the existence in the same patient of two strains of S. typhi different from the point of
AB  - view of phage-type antibiotype.
ER  -

TY  - JOUR
AU  - Rutebuka, O.B.
TI  - Molecular studies of restriction genes in enteric bacteria.
JO  - Diss. Abstr.
PY  - 1997
SP  - 4210
EP  - 4210
VL  - 57
AB  - Bacterial cells contain various restriction-modification systems to protect themselves from
AB  - incoming foreign DNA.  Most bacteria have at least one such system.  In this study, the
AB  - restriction genes and the location of the genes on the chromosome were examined in three
AB  - enteric bacteria, Salmonella typhimurium LT2, Klebsiella pneumoniae GM 236, and Klebsiella
AB  - pneumoniae M5a1.  The 98 minute region of the Salmonella typhimurium LT2 chromosome comprises
AB  - at least two R-M systems.  From genetic data this region was previously thought to be only one
AB  - minute in length but was found to be larger than two minutes using a physical mapping
AB  - technique, pulsed field gel electrophoresis.  The KpnAI and KpnBI R-M systems were recognized
AB  - in K. pneumoniae strain M5a1 and GM236, respectively.  A macro-restriction map of Klebsiella
AB  - pneumoniae GM236 was constructed in this study using PFGE and Southern hybridization.  The
AB  - genome was digested with three rare cutting restriction enzymes (BlnI, I-CeuI, and XbaI).  The
AB  - estimated size of the GM236 genome was 4,582 (+/-80) kb, in accordance with the range of other
AB  - enteric bacteria.  The partial digest of I-CeuI allowed a tentative ordering of the eight
AB  - fragments on a circular map.  The map was remarkably similar to the map of Escherichia coli
AB  - and S. typhimurium with the exception of two fragments.  I-CeuI cuts the GM236 chromosome in
AB  - eight fragments whereas it cuts E. coli and Salmonella genomes in seven.  This suggests a
AB  - possible duplication of the ribosomal cluster in the GM236 strain.  The constructed map,
AB  - although tentative, has permitted the mapping of hsdRKpnBI, a restriction gene located on a
AB  - 322 kb BlnI fragment and also on a 40 kb XbaI fragment.  In this study, hsdRKpnAI, another
AB  - restriction gene recognized in K. pneumoniae M5a1, was subcloned and sequenced.  The DNA
AB  - sequence of 4.5 kb was determined and only one open reading frame of 3,305 base pairs was
AB  - considered as the coding region for the HsdRKpnAI polypeptide.  The nucleotide sequence of the
AB  - hsdRKpnAI gene showed no significant similarity to any other sequences in the GenBank
AB  - database.  However, the deduced amino acid sequence showed a moderate degree of homology (26%)
AB  - with EcoR124II (former EcoR124/3I), a type IC restriction enzyme and KpnBI.  After alignment
AB  - of the three proteins, seven helicase motifs, typical of type I and III restriction enzymes,
AB  - were found.  This similarity between the three proteins and other current evidence show that
AB  - KpnAI and KpnBI are probably the first type I restriction endonucleases recognized in K.
AB  - pneumoniae.
ER  -

TY  - JOUR
AU  - Rutebuka, O.B.
AU  - Lee, N.S.
AU  - Ryu, J.
TI  - DNA sequence analysis of the KpnAI restriction gene of Klebsiella pneumoniae M5a1.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1995
SP  - 522
EP  - 522
VL  - 95
AB  - We have recently cloned the restriction genes of the KpnAI and KpnBI restriction-modification
AB  - systems of K. pneumoniae strains M5aI and GM236 and have reported the nucleotide and deduced
AB  - amino acid sequence of the KpnBI gene.  We have now sequenced and analyzed a 4.5 kb
AB  - Sau3AI/BamHI restriction fragment of the KpnAI clone, pNLA2, which expresses restriction
AB  - activity in r-KpnAI m+KpnAI mutants.  From the DNA sequence, we deduce an open reading frame
AB  - (ORF) of 3.3 kb (nucleotides 1156 to 4458) that appears to encode an HsdR polypeptide.
AB  - However, the ORF does not show any nucleotide sequence similarity with other genes that are
AB  - available from the PC/Gene GenBank.  In spite of the lack of nucleotide sequence similarity,
AB  - the deduced amino acid sequence shows a high degree of homology with EcoR124/3, a type IC
AB  - restriction enzyme, and the KpnBI polypeptide.  The KpnAI restriction endonuclease, like other
AB  - type I and type III endonuclease, also contains sequence motifs characteristic of
AB  - superfamily-II helicases which may be involved in DNA unwinding at the cleavage site.  Our
AB  - data suggests that the KpnAI system is most likely to be a type I restriction-modification
AB  - system.
ER  -

TY  - JOUR
AU  - Rutkauskas, D.
AU  - Petkelyte, M.
AU  - Naujalis, P.
AU  - Sasnauskas, G.
AU  - Tamulaitis, G.
AU  - Zaremba, M.
AU  - Siksnys, V.
TI  - Restriction Enzyme Ecl18kI-Induced DNA Looping Dynamics by Single-Molecule FRET.
JO  - J. Phys. Chem. B
PY  - 2014
SP  - 8575
EP  - 8582
VL  - 118
AB  - Many type II restriction endonucleases require binding of two copies of a recognition site for
AB  - efficient DNA cleavage. Simultaneous interaction of the enzyme with two DNA sites results in
AB  - DNA loop formation. It was demonstrated with the tethered particle motion technique that such
AB  - looping is a dynamic process where a DNA loop is repeatedly formed and disrupted. Here we use
AB  - a better and in the context of protein-induced DNA looping virtually unexploited strategy of
AB  - single-molecule Forster resonance energy transfer of surface immobilized biomolecules to
AB  - quantitatively study the dynamics of Ecl18kI endonuclease-induced DNA looping and determine
AB  - the rate constants of loop formation and disruption. We show that two DNA-bound Ecl18kI dimers
AB  - efficiently form a bridging tetramer looping out intervening DNA with a rate that is only a
AB  - few orders of magnitude lower than the diffusion limited rate. On the other hand, the
AB  - existence of Ecl18kI tetramer is only transient, and the loop is rapidly disrupted within
AB  - about 1 s.
ER  -

TY  - JOUR
AU  - Rutkowska, S.M.
AU  - Skowron, P.M.
AU  - Bielawski, K.
AU  - Podhajska, A.J.
TI  - SacNI, an isoschizomer of BanII isolated from Streptomyces achromogenes recognizes the 5'-GRGCY/C sequence.
JO  - Gene
PY  - 1995
SP  - 319
EP  - 320
VL  - 157
AB  - SacNI, an isoschizomer of the restriction endonuclease, BanII, has been isolated from
AB  - Streptomyces achromogenes N-J-H.  SacNI recognizes the palindromic sequence, 5'-GRGCY/C, and
AB  - cleaves within the recognition sequence, generating a 3' protruding RGCY end (where R=A or G,
AB  - and Y=C or G).
ER  -

TY  - JOUR
AU  - Rutkowska, S.M.
AU  - Skowron, P.M.
AU  - Podhajska, A.J.
TI  - Purification and characterization of the restriction endonuclease AvcI from Actinomyces cristalomycini.
JO  - Gene
PY  - 1995
SP  - 317
EP  - 318
VL  - 157
AB  - The restriction endonuclease AvcI, an isoschizomer of Sau96I was purified from Actinomyces
AB  - cristalomycini.  AvcI recognizes a 5-bp palindromic sequence, 5'-G/GNCC and cleaves it after
AB  - the first G residue producing a 3-nucleotide 5'-overhang.
ER  -

TY  - JOUR
AU  - Rutter, J.M.
TI  - Recent Advances in Microbial Genetics.
JO  - Br. Vet. J.
PY  - 1975
SP  - 284
EP  - 289
VL  - 131
AB  - Evolution depends on genetic diversity, and the genetic information contained
AB  - within double-stranded deoxyribonucleic acid (DNA) of bacterial cells can be
AB  - altered by mutation or by recombination.  Mutations include changes in genes
AB  - that occur naturally or are brought about experimentally by agents such as
AB  - chemicals or by ionizing radiation.  In contrast, recombination results from an
AB  - interaction between one micro-organism with another distinct and separate
AB  - micro-organism.  Recombination provides a rapid method for producing changes in
AB  - genotype and is generally confined to a sexual process in higher animals.  The
AB  - prokaryotic unicellular bacterium differs from eukaryotic animal and plant
AB  - cells in that it possesses a single, circular, closed chromosome.  A variety of
AB  - different recombination mechanisms have been discovered in bacteria; these
AB  - include the entry of naked DNA into bacterial cells (a process called
AB  - transformation), the transfer of genetic information incorporated in
AB  - bacteriophages (termed transduction), and a sexual process involving transfer
AB  - of genetic material between bacterial cells in close apposition (called
AB  - conjugation).  Studies of these mechanisms have led to a deeper understanding
AB  - of the molecular basis of gene action and are well described (see Hayes, 1968).
AB  - Recent advances in our knowledge of nucleic acids have led to the creation in
AB  - the laboratory of new combinations of genetic material.  This has been achieved
AB  - by splicing together DNA from entirely different sources to form hybrid
AB  - molecules that are less likely to occur during evolutionary processes.  This
AB  - review is confined to a discussion of these techniques which have caused so
AB  - much public disquiet.
ER  -

TY  - JOUR
AU  - Ryan, K.A.
AU  - Lo, Y.C.
TI  - Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 1505
EP  - 1511
VL  - 27
AB  - In a previous study, a recombinant plasmid that contains a CACAG pentanucleotide repeat was
AB  - isolated from a Pasteurella haemolytica A1 library.  Southern hybridization analysis using a
AB  - (CACAG)5 probe indicated the presence of two loci that contain the pentanucleotide repeats on
AB  - the genome of P. haemolytica A1. Additional hybridization analyses against genomic DNA from
AB  - related microorganisms indicated that the repeats are only present in P. haemolytica and
AB  - Pasteurella trehalosi T3.  The various serotypes of P. haemolytica were found to have either
AB  - one or two of the CACAG repeat-containing loci.  Examination of the locus designated Rpt2 by
AB  - PCR and sequence analysis indicated that the number of CACAG repeats could change upon serial
AB  - subculture which most likely occurs as a result of DNA slipped-strand mispairing.  A plasmid
AB  - carrying the Rpt2 locus was isolated and characterized.  Sequence analysis indicated that the
AB  - CACAG repeats are contained within the 5'-end of a gene that showed homology to mod genes of
AB  - type III restriction-modification systems.  A second open reading frame downstream was
AB  - identified which showed homology to res genes of type III restriction-modification systems.
AB  - Both the modification and restriction proteins could be expressed and polypeptides of the
AB  - expected sizes were detected by SDS-PAGE.  Restriction activity could also be detected in
AB  - crude cytoplasmic extracts of Escherichia coli strains carrying the mod and res genes on
AB  - recombinant plasmids.
ER  -

TY  - JOUR
AU  - Ryan, P.M.
AU  - Guinane, C.M.
AU  - London, L.E.
AU  - Kelleher, P.R.
AU  - Fitzgerald, G.F.
AU  - Caplice, N.M.
AU  - Ross, R.P.
AU  - Stanton, C.
TI  - Genome Sequence of the Heteropolysaccharide-Producing Strain Lactobacillus mucosae DPC 6426.
JO  - Genome Announcements
PY  - 2015
SP  - e01350
EP  - e01314
VL  - 3
AB  - Exopolysaccharide-synthesizing Lactobacillus mucosae DPC 6426 is a heterofermentative strain,
AB  - which has demonstrated cholesterol-lowering properties
AB  - in an animal model of lipid-driven atherosclerosis. The genome revealed a
AB  - plethora of homologues linked to carbohydrate metabolism and mucin binding.
ER  -

TY  - JOUR
AU  - Ryazanova, A.
AU  - Migur, A.
AU  - Norkin, M.
AU  - Timofeyeva, N.
AU  - Fedorova, O.
AU  - Kubareva, E.
TI  - DNA methyltransferase SsoII: a balance between DNA methylation and transcription repression.
JO  - FEBS J.
PY  - 2013
SP  - 127
EP  - 127
VL  - 280
AB  - Restriction-modification systems serve as primitive immune systems protecting bacterial cells
AB  - from phage infection.  R-M system SsoII from Shigella sonnei consists of a DNA
AB  - methyltransferase and a restriction endonuclease.  M.SsoII methylates C5 atom of the second
AB  - cytosine in the sequence 5'-CCNGG-3' (N=A, C, G or T) in dsDNA while R.SsoII cleaves this
AB  - site in case it remains unmethylated.  Since phage DNA is not methylated, R.SsoII hydrolyzes
AB  - it and protects the host cell.  In case the endonuclease activity exceeds the
AB  - methyltransferase activity, the host cell DNA can be cleaved as well.  Therefore, M. SsoII and
AB  - R.SsoII expression should be strictly coordinated.  This coordination is provided by M.SsoII
AB  - itself: it represses transcription of its own gene and stimulates transcription of the R.SsoII
AB  - gene via binding to the regulatory site which is located in the promoter region of the R-M
AB  - system SsoII.  Surpringly, M.SsoII forms a much more stable complex with the regulatory site
AB  - than with the methylation site.  Moreover, M.SsoII binding with the former one prevents its
AB  - binding with the latter one.  Does M.SsoII still methylate DNA?  We show that (i) M.SsoII
AB  - association rate with the methylation site is higher than that for the regulatory site; (ii)
AB  - amount of the methylation sites in a bacterial cell is on average 10,000 times higher than
AB  - amount of the regulatory sites.  Both these factors direct M.SsoII to the DNA methylation.
AB  - M.SsoII has an extremely high affinity to the regulatory site (Kd < nM, i.e. effective binding
AB  - even when there are only two regulatory sites per cell).  We conclude that the plasmid-encoded
AB  - R-M system SsoII is naturally adjusted for acting at low concentrations.  Therefore, this
AB  - system is not a great burden for a cell and has spread among different species and genders of
AB  - Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Ryazanova, A.Y.
AU  - Abrosimova, L.A.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - Diverse domains of (cytosine-5)-DNA methyltransferases: Structural and functional characterization.
JO  - Methylation - from DNA, RNa and histones to diseases and treatment
PY  - 2012
SP  - 29
EP  - 69
VL  - 0
AB  - (Cytosine-5)-DNA methyltransferases (C5-DNA MTases) are enzymes which catalyze methyl group
AB  - transfer from S-adenosyl-L-methionine to C5 atom of cytosine residue in DNA.  As a result,
AB  - AdoMet is converted into S-adenosyl-L-homocysteine.  The recognition sites of C5-DNA MTases
AB  - are usually short palindromic sequences (2-6 bp) in double-stranded DNA.  One or both DNA
AB  - strands can be methylated.  The introduced methyl group is localized in the major groove of
AB  - the DNA double helix and thus does not disrupt Watson-Crick interactions.
ER  -

TY  - JOUR
AU  - Ryazanova, A.Y.
AU  - Kubareva, E.A.
AU  - Grman, I.
AU  - Lavrova, N.V.
AU  - Ryazanova, E.M.
AU  - Oretskaya, T.S.
AU  - Hianik, T.
TI  - The study of the interaction of (cytosine-5)-DNA methyltransferase SsoII with DNA by acoustic method.
JO  - Analyst
PY  - 2011
SP  - 1227
EP  - 1233
VL  - 136
AB  - The interaction of (cytosine-5)-DNA methyltransferase SsoII (M. SsoII) with double-stranded
AB  - DNA was studied by means of thickness shear mode
AB  - acoustic method (TSM) and gel electrophoresis. M. SsoII recognizes in
AB  - double-stranded DNA the methylation site 5'-CCNGG-3' (N = A, C, G, T)
AB  - and methylates the inner cytosine residue. M. SsoII also acts as a
AB  - transcription factor via binding to the regulatory site
AB  - 5'-AGGACAAATTGTCCT-3' in the promoter region of SsoII
AB  - restriction-modification system. We designed three 60-mer biotinylated
AB  - DNA duplexes: with the methylation site (60met), with the regulatory
AB  - site (60reg), and without a specific binding site (60oct). A strong
AB  - binding of M. SsoII with each one of the studied DNA immobilized on the
AB  - TSM transducer has been shown. The equilibrium dissociation constants,
AB  - K-D, of the M. SsoII-DNA complexes decreased in the order 60oct > 60reg
AB  - > 60met, suggesting a higher stability of M. SsoII-60met complex in
AB  - comparison with the others. The association rate constant, k(a), was
AB  - also higher for 60met, while similar values were obtained for 60reg and
AB  - 60oct. The difference in the kinetic parameters for 60met and 60reg
AB  - suggested a possible way of coordination between the two M. SsoII
AB  - functions in a cell.
ER  -

TY  - JOUR
AU  - Ryazanova, A.Y.
AU  - Molochkov, N.V.
AU  - Abrosimova, L.A.
AU  - Alexeevsky, A.V.
AU  - Karyagina, A.S.
AU  - Protsenko, A.S.
AU  - Friedhoff, P.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - Secondary structure of SsoII-like (Cytosine-5)-DNA methyltransferases N-terminal region determined by Circular dichroism spectroscopy.
JO  - Mol. Biol. (Mosk)
PY  - 2010
SP  - 911
EP  - 921
VL  - 44
AB  - (Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) has a long N-terminal region (1-71
AB  - residues) preceding the sequence with conservative motifs, which are characteristic for all
AB  - DNA methyltrans-ferases of such kind. The presence of this region provides M.SsoII capability
AB  - to act as a transcription regulator in SsoII restriction-modification system. To perform its
AB  - regulatory function, M.SsoII binds specifically to a 15-mer inverted repeat in the promoter
AB  - region of SsoII restriction-modification system genes. In the present work, properties of the
AB  - protein Delta(72-379)M.Ecl18kI are studied, which is a deletion mutant of the SsoII-like
AB  - DNA-methyltransferase M.Ecl18kI and is homologous to M.SsoII N-terminal region.
AB  - Delta(72-379)M.Ecl18kI capability to bind specifically a DNA duplex containing the regulatory
AB  - site is demonstrated. However, such a binding takes place only in the presence of high protein
AB  - excess relative to DNA, which could indicate an altered structure in the deletion mutant in
AB  - comparison with the full-length M.SsoII. Circular dichroism spectroscopy demonstrated that
AB  - Delta(72-379)M.Ecl18kI has a strongly pronounced secondary structure and contains 32%
AB  - alpha-helices and 20% beta-strands. Amino acid sequences alignment of M.SsoII N-terminal
AB  - region and transcription factors of known spatial structure is made. An assumption is made how
AB  - alpha-helices and beta-strands are arranged in M.SsoII N-terminal region.
ER  -

TY  - JOUR
AU  - Ryazanova, A.Y.
AU  - Winkler, I.
AU  - Friedhoff, P.
AU  - Viryasov, M.B.
AU  - Oretskaya, T.S.
AU  - Kubareval, E.A.
TI  - Crosslinking of (cytosine-5)-DNA methyltransferase SsoII and its complexes with specific DNA duplexes provides an insight into their structures.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2011
SP  - 632
EP  - 650
VL  - 30
AB  - (Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) functions as a methyltransferase and also
AB  - as a transcription factor Chemical and photochemical crosslinking was used for exploring the
AB  - structure of M.SsoII-DNA complexes and M.SsoII in the absence of DNA. Photocrosslinking with
AB  - 4-(N-maleimido)benzophenone demonstrated that in the M.SsoII complex with DNA containing the
AB  - regulatory site, the M.SsoII region responsible for methylation was bound to DNA flanking the
AB  - regulatory site, which contained no methylation sequence. This required high flexibility of
AB  - the linker connecting the M.SsoII N-terminal domain and the M.SsoII region responsible for
AB  - methylation. The flexibility was demonstrated by crosslinking with bis-maleimidoethane and
AB  - 1,11-bis-maleimidotetraethyleneglycol.
ER  -

TY  - JOUR
AU  - Rybakova, D.
AU  - Wetzlinger, U.
AU  - Muller, H.
AU  - Berg, G.
TI  - Complete Genome Sequence of Paenibacillus polymyxa Strain Sb3-1, a Soilborne Bacterium with Antagonistic Activity toward Plant Pathogens.
JO  - Genome Announcements
PY  - 2015
SP  - e00052
EP  - e00015
VL  - 3
AB  - The genome of Paenibacillus polymyxa Sb3-1, a strain that shows antagonistic activities
AB  - against pathogenic fungi and bacteria, consists of one 5.6-Mb circular
AB  - chromosome and two plasmids of 223 kb and 8 kb. The genome reveals several genes
AB  - that potentially contribute to its antagonistic and plant growth promotion
AB  - activity.
ER  -

TY  - JOUR
AU  - Rye, P.T.
TI  - Biochemical characterization of the Escherichia coli very short patch repair pathway and its coordination with methyltransferase repair of  O6-methylguanine.
JO  - Ph.D. Thesis, MIT, USA
PY  - 2006
SP  - 1
EP  - 273
AB  - The E. coli Very Short Patch Repair (VSPR) system corrects T:G mismatches that arise through
AB  - Dcm-mediated methylation and subsequent deamination of the underlined cytosine residue in the
AB  - palindromic sequence 5'-CCWGG-3' (W is an adenine or thymine). Vsr initiates VSPR by
AB  - producing a single stranded nick on the 5' side of the mismatched T. The MutS and MutL
AB  - mismatch recognition proteins stimulate this activity, as cells lacking either of these
AB  - proteins display diminished VSPR. Genetic studies also indicate that Pol I is responsible for
AB  - removing and replacing a short tract of nucleotides downstream of the incision site and that
AB  - DNA Ligase seals the nick to complete the repair event. However, until now, biochemical
AB  - investigation of the repair steps downstream of Vsr incision have been lacking.  Herein, we
AB  - describe two novel in vitro assays used to probe the biochemical events of VSPR. The first was
AB  - used to verify the reconstitution of VSPR using purified E. coli Vsr, Pol I, and DNA Ligase
AB  - enzymes, while the second was used to measure the distribution of VSPR patch sizes in whole
AB  - cell extracts. By monitoring the loss of radiosignal from a series of substrates that
AB  - contained the label at prescribed distances downstream of the T:G mismatch, we were able to
AB  - determine that VSPR patches are distributed around 2 to 4 deoxynucleotides in length.
AB  - Interestingly, under certain reaction conditions, the addition of DNA Ligase improved the
AB  - efficiency of repair initiation by Vsr, suggesting that VSPR may be optimal in the context of
AB  - a multi-protein complex.  Lastly, we investigated the effect of VSPR proteins on
AB  - methyltransferase (MTase) repair of O6-methylguanine (6mG). MTase repair of O6mG opposite T
AB  - results in a G:T mismatch that must be further processed to yield the native G:C base pairing.
AB  - The G:T mismatch is therefore an intersection of the two pathways and led us to hypothesize
AB  - that MTase and VSPR proteins might interact. Indeed, cells lacking the functions of MutS,
AB  - MutL, or Vsr proteins displayed decreased MTase repair in vivo, revealing a previously unknown
AB  - interaction. The cooperation between proteins of these two repair systems may shed light on
AB  - the biological significance of the VSPR system.
ER  -

TY  - JOUR
AU  - Ryu, C.J.
AU  - Lee, C.H.
AU  - Yoo, O.J.
TI  - A new restriction endonuclease, Bsp1894I, from Bacillus sphaericus 1894.
JO  - Korean Biochem. J.
PY  - 1989
SP  - 444
EP  - 447
VL  - 22
AB  - A new restriction endonuclease, Bsp1894I, has been isolated from Bacillus
AB  - sphaericus 1894 (KCTC 1188), and its catalytic properties have been studied.
AB  - This enzyme recognizes the DNA sequence 5'-G^GNCC-3' and cleaves at the site as
AB  - indicated by the arrow.  Bsp1894I is an isoschizomer of AsuI, Sau96I, and
AB  - Cfr13I.  It shows maximum activity at a pH range between 6 and 7 in the
AB  - presence of 10 mM MgCl2.  The optimum reaction temperature for Bsp1894I is 42C.
AB  - Unlike its isoschizomers, Bsp1894I does not require NaCl for optimum activity.
ER  -

TY  - JOUR
AU  - Ryu, J.
TI  - Establishment of the KpnAI R-M system of Klebsiella pneumoniae requires prior host modification.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1998
SP  - 288
EP  - 288
VL  - 0
AB  - Type I restriction-modification systems have been classified into 4 families: IA, IB, IC and
AB  - newly identified ID.  They consist of 3 consecutive genes, hsdR, hsdM and hsdS which encode
AB  - for subunits R(restriction), M(modification) and S(specificity), respectively.  When entire
AB  - R-M genes were transferred to bacteria, without corresponding modification, through either
AB  - conjugation, transduction or transformation, the expression of restriction enzymes are somehow
AB  - regulated that the R-M genes can be established without degrading recipient DNA.  The basis of
AB  - the mechanism of "establishment" still remains to be elucidated.  We have recently cloned R
AB  - and MS genes separately for Klebsiella pneumoniae KpnAI R-M system.  In the present project,
AB  - the "establishment" of the KpnAI system was studied by using plasmid transformation as a gene
AB  - transfer system.  All the three (R, M and S) genes were combined and cloned into pUC18.  When
AB  - the entire system was transferred into recipient (E. coli DH5a), no Amp-resistant
AB  - transformants were obtained.  However, when the recipient cells were modified with a
AB  - modification proficient plasmid, many transformants were obtained.  This result is in sharp
AB  - contrast with other known type I enzymes where the entire system is transferred without
AB  - killing the recipient.  Thus, the KpnAI R-M enzymes seems to be the first example of the type
AB  - I R-M system which requires prior methylation of the chromosome before their establishments.
ER  -

TY  - JOUR
AU  - Ryu, J.
TI  - The restriction enzyme KpnAI of Klebsiella pneumoniae is a new member of the type ID family.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1997
SP  - 285
EP  - 285
VL  - 97
AB  - We have described the KpnAI restriction and modification system in Klebsiella pneumoniae M5a1.
AB  - The restriction gene (hsdR, 3.3 kb) was cloned into pBR322 and the DNA was sequenced.  In this
AB  - project, the corresponding modification genes were identified in the 5' flanking region of
AB  - the hsdR gene and cloned into pUC19.  The DNA sequence reveals two open reading frames that
AB  - are designated hsdM (1.6kb) and hsdS (1.3kb).  These two genes form a single transcriptional
AB  - unit and their coding sequences overlap by five nucleotides.  Thus the KpnAI R-M system
AB  - consists of three genes in the order of hsdM, hsdS and hsdR and organized into two
AB  - transcriptional units.  These features are typical to the type I restriction enzymes. Homology
AB  - studies reveal that the predicted R, M and S peptides share 97%, 98% and 58% homology,
AB  - respectively, with the corresponding peptides of the StySBLI restriction enzyme, a prototype
AB  - of the type ID family recently identified in Salmonella blegdam.  These high homologies
AB  - indicate that the KpnAI restriction enzyme is another member of the type ID family. The KpnAI
AB  - enzyme is the first type I restriction enzyme identified in Klebsiella species.
ER  -

TY  - JOUR
AU  - Ryu, J.
AU  - Rowsell, E.
TI  - Quick identification of Type I restriction enzyme isoschizomers using newly developed pTypeI and reference plasmids.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - e81
EP  - e81
VL  - 36
AB  - Although DNA-recognition sequences are among the most important characteristics of restriction
AB  - enzymes and their corresponding methylases,
AB  - determination of the recognition sequence of a Type-I restriction enzyme
AB  - is a complicated procedure. To facilitate this process we have previously
AB  - developed plasmid R-M tests and the computer program RM search. To
AB  - specifically identify Type-I isoschizomers, we engineered a pUC19
AB  - derivative plasmid, pTypeI, which contains all of the 27 Type-I
AB  - recognition sequences in a 248-bp DNA fragment. Furthermore, a series of
AB  - 27 plasmids (designated 'reference plasmids'), each containing a unique
AB  - Type-I recognition sequence, were also constructed using pMECA, a
AB  - derivative of pUC vectors. In this study, we tried those vectors on 108
AB  - clinical E. coli strains and found that 48 strains produced isoschizomers
AB  - of Type I enzymes. A detailed study of 26 strains using these 'reference
AB  - plasmids' revealed that they produce seven different isoschizomers of the
AB  - prototypes: EcoAI, EcoBI, EcoKI, Eco377I, Eco646I, Eco777I and Eco826I.
AB  - One strain EC1344 produces two Type I enzymes (EcoKI and Eco377I).
ER  -

TY  - JOUR
AU  - Ryu, J.-I.
AU  - Rajadas, P.T.
AU  - Bullas, L.R.
TI  - Complementation and hybridization evidence for additional families of Type I DNA restriction and modification genes in Salmonella serotypes.
JO  - J. Bacteriol.
PY  - 1988
SP  - 5785
EP  - 5788
VL  - 170
AB  - Of eight Salmonella, serB-linked hsd genes for the restriction and modification
AB  - of DNA transferred to Escherichia coli/Salmonella hybrids, only two-those with
AB  - SM and ST (S. muenchen and S. thompson, respectively) specificities - may have
AB  - weakly complemented rSB- and non complemented rK-.  An A-specific DNA probe
AB  - failed to hybridize to HindIII-restricted fragments of each of the hybrids, but
AB  - an SB (S. typhimurium)-specific probe hybridized to DNA from the hybrid with ST
AB  - specificity.  These results indicate that additional families of the type I hsd
AB  - genes may exist.
ER  -

TY  - JOUR
AU  - Saad, J.
AU  - Levasseur, A.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium parafortuitum Strain P7335.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00950
EP  - e00918
VL  - 7
AB  - Mycobacterium parafortuitum is a rapidly growing nontuberculous mycobacterium, initially
AB  - isolated from soil in Japan. The 6,175,772-bp draft genome sequence of
AB  - M. parafortuitum strain P7335 exhibits a G+C content of 68.4%, 5,783
AB  - protein-coding genes, and 66 predicted RNA genes, including 59 tRNA genes, 6 rRNA
AB  - operons, and 1 transfer-messenger RNA.
ER  -

TY  - JOUR
AU  - Saavedra, C.
AU  - Gonzalez, E.
AU  - Vasquez, C.
TI  - Studies on the heterologous expression of BstVI restriction endonuclease in Escherichia coli.
JO  - Biochem. Mol. Biol. Int.
PY  - 1998
SP  - 391
EP  - 397
VL  - 44
AB  - Bacterial restriction and modification systems must be regulated to avoid self-restriction.
AB  - It is generally accepted that cognate DNA methyltransferases normally protect both, the
AB  - host's chromosome and extrachromosomal elements from the activity of their endonuclease
AB  - counterparts.  When the bstVIRm genes from Bacillus stearothermophilusV were subcloned into
AB  - Escherichia coli, several clones exhibiting a r+m- phenotype were found.  The present work was
AB  - undertaken to analyze the possibility that mechanisms other than DNA methylation could account
AB  - for the viability of these cells.  No evidence was found for an inhibitory agent or
AB  - endonuclease compartmentation.  In vivo experiments showed that lambda phage multiplication
AB  - was poorly restricted by the heterologous enzyme.  The restricting activity against the
AB  - incoming phage increased however when phage adsortion was performed at higher temperatures.
AB  - Analogous experiments in which a DNA-repair deficient strain was used as a host for the
AB  - thermophilic R-M system suggested, to some extent, the participation of the repair machinery
AB  - in the viability of r-m- clones.
ER  -

TY  - JOUR
AU  - Saavedra, C.
AU  - Vasquez, C.
AU  - Encinas, M.V.
TI  - Structural studies of the BstVI restriction-modification proteins by fluorescence spectroscopy.
JO  - Eur. J. Biochem.
PY  - 1999
SP  - 65
EP  - 70
VL  - 263
AB  - Structural studies of the proteins of the BstVI restriction-modification system of Bacillus
AB  - stearothermophilus V were carried out using intrinsic fluorescence techniques. The exposure
AB  - and environments of their tryptophanyl residues were determined using collisional quenchers.
AB  - Quenching of BstVI endonuclease by iodide suggested a heterogeneous class of tryptophan
AB  - residues, while the results obtained with M.BstVI methylase were consistent with a rather
AB  - exposed tryptophan population. A comparison of the quenching efficiencies at 20 degrees C and
AB  - 55 or 60 degrees C showed that their structures are more flexible and open at the temperature
AB  - at which they exhibit maximal activity. The endonuclease reached its active conformation only
AB  - after 1 h of incubation at 60 degrees C. Fluorescence changes were observed upon Mn2+ and Mg2+
AB  - binding, with Kd values in the range 3-5 microM.  The binding of S-adenosyl-L-methionine to
AB  - the methylase produced conformational changes, which were consistent with binding to a single
AB  - site of Kd 550 and 680 microM at 20 degrees C and 55 degrees C, respectively. Quenching
AB  - experiments with iodide showed that the presence of S-adenosyl-L-methionine leads to different
AB  - conformational states at 20 degrees C and 55 degrees C.  These results were interpreted in
AB  - terms of differences in the structural characteristics of these restriction-modification
AB  - proteins as well as in terms of differences in the conformational states that these enzymes
AB  - exhibit at 20 degrees C and at the temperature at which they are most active.
ER  -

TY  - JOUR
AU  - Saavedra, L.
AU  - Hebert, E.M.
AU  - Albarracin, L.
AU  - Salva, S.
AU  - Alvarez, S.
AU  - Kitazawa, H.
AU  - Villena, J.
TI  - Draft Genome Sequence of Lactobacillus plantarum CRL1506, an Immunomodulatory Strain Isolated from Goat Milk.
JO  - Genome Announcements
PY  - 2016
SP  - e00108
EP  - e00116
VL  - 4
AB  - This report describes a draft genome sequence of Lactobacillus plantarum CRL1506, a probiotic
AB  - strain with immunomodulatory properties isolated from goat milk. The
AB  - reads generated by a whole-genome shotgun (WGS) strategy on an Illumina MiSeq
AB  - sequencer were assembled into contigs with a total size of 3,228,096 bp. The
AB  - draft genome sequence of L. plantarum CRL1506 will be useful for further studies
AB  - of specific genetic features of this strain and for understanding the mechanisms
AB  - of its immunobiotic properties.
ER  -

TY  - JOUR
AU  - Saavedra, S.Y.
AU  - Prada-Cardozo, D.
AU  - Rincon, V.
AU  - Perez-Cardona, H.
AU  - Hidalgo, A.M.
AU  - Gonzalez, M.N.
AU  - Reguero, M.T.
AU  - Valenzuela-de-Silva, E.M.
AU  - Mantilla, J.R.
AU  - Falquet, L.
AU  - Barreto-Hernandez, E.
AU  - Duarte, C.
TI  - Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases.
JO  - Genome Announcements
PY  - 2017
SP  - e01558
EP  - e01516
VL  - 5
AB  - Colombian Acinetobacter baumannii strain ST920 was isolated from the sputum of a  68-year-old
AB  - male patient. This isolate possessed blaOXA-72 and blaOXA-255-like
AB  - genes. The assembled genome contained 4,104,098 pb and 38.79% G+C content. This
AB  - is the first case reported of the coproduction (blaOXA-72 and blaOXA-255-like) of
AB  - carbapenem-hydrolyzing class D beta-lactamases (CHDLs) in Acinetobacter
AB  - baumannii.
ER  -

TY  - JOUR
AU  - Sabat, A.J.
AU  - Hermelijn, S.M.
AU  - Akkerboom, V.
AU  - Juliana, A.
AU  - Degener, J.E.
AU  - Grundmann, H.
AU  - Friedrich, A.W.
TI  - Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.
JO  - Sci. Rep.
PY  - 2017
SP  - 41050
EP  - 41050
VL  - 7
AB  - We report the investigation of an outbreak situation of methicillin-resistant
AB  - Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo
AB  - (AZP) in the Republic of Suriname from April to May 2013. We performed whole
AB  - genome sequencing with complete gap closure for chromosomes and plasmids on all
AB  - isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the
AB  - AZP. In total 24 isolates were investigated. spa typing, genome-wide single
AB  - nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence
AB  - typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to
AB  - determine phylogenetic relatedness and to identify transmission. Whole-genome
AB  - sequencing (WGS) showed that all isolates were members of genomic variants of the
AB  - North American USA300 clone. However, WGS revealed a heterogeneous population
AB  - structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5
AB  - alleles of difference by wgMLST when the isolates were recovered from different
AB  - body sites of the same patient or if direct transmission between patients was
AB  - most likely. This work describes the usefulness of complete genome sequencing of
AB  - bacterial chromosomes and plasmids providing an unprecedented level of detail
AB  - during outbreak investigations not being visible by using conventional typing
AB  - methods.
ER  -

TY  - JOUR
AU  - Sabat, A.J.
AU  - Kock, R.
AU  - Akkerboom, V.
AU  - Hendrix, R.
AU  - Skov, R.L.
AU  - Becker, K.
AU  - Friedrich, A.W.
TI  - Novel Organization of the Arginine Catabolic Mobile Element and Staphylococcal Cassette Chromosome mec Composite Island and Its Horizontal Transfer between Distinct Staphylococcus aureus Genotypes.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 5774
EP  - 5777
VL  - 57
AB  - In this study, 425 methicillin-resistant Staphylococcus aureus (MRSA) isolates
AB  - recovered in the Dutch-German Euregio were investigated for the presence of the
AB  - arginine catabolic mobile element (ACME). Sequence analysis by whole-genome
AB  - sequencing revealed an entirely new organization of the ACME-staphylococcal
AB  - cassette chromosome mec composite island (SCCmec-CI), with truncated ACME type II
AB  - located downstream of SCCmec. An identical nucleotide sequence of ACME-SCCmec-CI
AB  - was found in two distinct MRSA lineages (t064-ST8 and t002-ST5), which has not
AB  - been reported previously in S. aureus.
ER  -

TY  - JOUR
AU  - Sabat, A.J.
AU  - Pournaras, S.
AU  - Akkerboom, V.
AU  - Tsakris, A.
AU  - Grundmann, H.
AU  - Friedrich, A.W.
TI  - Whole-genome analysis of an oxacillin-susceptible CC80 mecA-positive Staphylococcus aureus clinical isolate: insights into the mechanisms of cryptic methicillin resistance.
JO  - J. Antimicrob. Chemother.
PY  - 2015
SP  - 2956
EP  - 2964
VL  - 70
AB  - OBJECTIVES: The mec and bla systems, among other genetic factors, are critical in regulating
AB  - the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a
AB  - naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the
AB  - mechanism conferring oxacillin susceptibility.
AB  - METHODS: The mecA-positive oxacillin-susceptible S. aureus isolate GR2 (penicillin and
AB  - oxacillin MICs 0.094 and 1 mg/L, respectively), belonging to clonal complex 80, was
AB  - characterized. DNA fragment libraries were sequenced on Roche 454 and Illumina MiSeq
AB  - sequencers and de novo assembly of the genome was generated using SeqMan NGen software.
AB  - Plasmid curing was conducted by SDS treatment. Expression of mecA was quantified without/with
AB  - beta-lactam pressure.
AB  - RESULTS: The genome of GR2 consisted of a 2 792 802 bp chromosome and plasmids pGR2A (28 895
AB  - bp) and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a truncated/non-functional mecR1
AB  - gene and no mecI. A single copy of the bla system, with an organization unique for S. aureus,
AB  - was found, harboured by plasmid pGR2A. Particularly, the blaZ gene was orientated like its
AB  - regulatory genes, blaI and blaR1, and a gene encoding transposase IS66 was integrated between
AB  - blaZ and the regulatory genes deleting the 5'-end of blaR1; blaI, encoding blaZ/mecA
AB  - repressor, was intact. After plasmid loss, GR2 became penicillin and oxacillin resistant (MICs
AB  - 0.5 and 6 mg/L, respectively).
AB  - CONCLUSIONS: We can conclude that after exposure to beta-lactams, the non-functional BlaR1
AB  - does not cleave the mecA repressor BlaI, derepression does not occur and mecA is not
AB  - efficiently expressed. Removal of the bla system after curing of pGR2A allows constitutive
AB  - expression of mecA, resulting in oxacillin and penicillin resistance.
ER  -

TY  - JOUR
AU  - Sabehi, G.
AU  - Beja, O.
AU  - Suzuki, M.T.
AU  - Preston, C.M.
AU  - DeLong, E.F.
TI  - Different SAR86 subgroups harbour divergent proteorhodopsins.
JO  - Environ. Microbiol.
PY  - 2004
SP  - 903
EP  - 910
VL  - 6
AB  - Proteorhodopsins (PRs), bacterial photoactive proton pumps, were originally detected in the
AB  - uncultured marine gamma-proteobacterial SAR86
AB  - group. PRs are now known to occur in both the gamma and alpha marine
AB  - proteobacterial lineages. Recent environmental shotgun sequence analysis
AB  - in the Sargasso Sea has added yet more diversity, and a potentially
AB  - broader taxonomic distribution, to the PR family. Much remains to be
AB  - learned, however, about within-taxon PR variability and the broader
AB  - organismal distribution of different PR types. We report here genomic
AB  - analyses of large genome fragments from different subgroups of the SAR86
AB  - lineage, recovered from naturally occurring bacterioplankton populations
AB  - in coastal Red Sea and open ocean Pacific waters. Sequence comparisons
AB  - were performed on large bacterial artificial chromosomes (BACs) bearing
AB  - both rRNA and PR genes, derived from different SAR86 subgroups. Our
AB  - analyses indicated the presence of different PR sequence types within the
AB  - same SAR86 rRNA subgroup. The data suggested that the distribution of
AB  - particular PR types does not necessarily parallel the phylogenetic
AB  - relationship inferred from highly conserved genes such as rRNA. Further
AB  - analyses of the genomic regions flanking PR also revealed a potential
AB  - pathway for the biosynthesis of retinal, the PR chromophore that is
AB  - required to generate the functionally active photoprotein. Finally,
AB  - comparison of our results with recently reported Sargasso Sea
AB  - environmental shotgun sequence assemblies demonstrated the utility of BAC
AB  - clones for interpreting environmental shotgun sequence data, much of which
AB  - is represented in short contigs that have an overall low depth of
AB  - coverage.
ER  -

TY  - JOUR
AU  - Sabelnikov, A.G.
AU  - Greenberg, B.
AU  - Lacks, S.A.
TI  - An extended -10 promoter alone directs transcription of the DpnII operon of Streptococcus pneumoniae.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 144
EP  - 155
VL  - 250
AB  - The genetic cassette encoding the DpnII restriction-modification system of Streptococcus
AB  - pneumoniae gave transcription products of approximately 2.7 and 1.8 kilobases. The larger,
AB  - mRNA1, covered both of the methylase genes, dpnM and dpnA, and the endonuclease gene dpnB; the
AB  - smaller, mRNA2, covered only the dpnA and dpnB genes. Transcription of mRNA1 was shown to
AB  - begin at the translation start site for dpnM, thereby producing an mRNA without any apparent
AB  - ribosome-binding site for translation of the DpnM methylase. The promoter for mRNA1 was shown
AB  - by base substitution and deletion analysis to consist of an extended -10 site, TaTGgTATAAT,
AB  - with no required -35 site. A possible promoter further upstream with close matches to a -35
AB  - site and a nonextended -10 site was not used. A survey of 36 proven and putative promoters
AB  - used by S. pneumoniae revealed that 61% of them contained the full -10 extension, although,
AB  - other than the dpmM promoter, they matched at a -35 site, as well. It appears that, unlike
AB  - those found in Escherchia coli, S. pneumoniae promoters frequently require an extended -10
AB  - site, and such a site can function naturally without a -35 site.
ER  -

TY  - JOUR
AU  - Sabharwal, A.
AU  - Liao, Y.C.
AU  - Lin, H.H.
AU  - Haase, E.M.
AU  - Scannapieco, F.A.
TI  - Draft genome sequences of 18 oral streptococcus strains that encode amylase-binding proteins.
JO  - Genome Announcements
PY  - 2015
SP  - e00510
EP  - e00515
VL  - 3
AB  - A number of commensal oral streptococcal species produce a heterogeneous group of proteins
AB  - that mediate binding of salivary alpha-amylase. This interaction likely
AB  - influences streptococcal colonization of the oral cavity. Here, we present draft
AB  - genome sequences of several strains of oral streptococcal species that bind human
AB  - salivary amylase.
ER  -

TY  - JOUR
AU  - Sabirova, J.S.
AU  - Xavier, B.B.
AU  - Coppens, J.
AU  - Zarkotou, O.
AU  - Lammens, C.
AU  - Janssens, L.
AU  - Burggrave, R.
AU  - Wagner, T.
AU  - Goossens, H.
AU  - Malhotra-Kumar, S.
TI  - Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS.
JO  - J. Antimicrob. Chemother.
PY  - 2016
SP  - 1501
EP  - 1509
VL  - 71
AB  - OBJECTIVES: We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical
AB  - carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). METHODS: All strains were
AB  - screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII)
AB  - (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and
AB  - annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned
AB  - directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen;
AB  - BioNumerics, Applied Maths). RESULTS: All 12 strains were ST383. Of the 12 strains, 11 were
AB  - carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters
AB  - for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE
AB  - types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned
AB  - all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or >/=10
AB  - unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a
AB  - difference of three or more bands between PFGE profiles, the Simpson's diversity indices
AB  - (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife
AB  - pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of
AB  - WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of
AB  - PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values
AB  - CI: 0.212-0.849) (P = 0.007). CONCLUSIONS: This study demonstrates the application of WGM to
AB  - understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination
AB  - of WGM and WGS, we also present here the first longitudinal genomic characterization of the
AB  - highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining
AB  - importance in Europe.
ER  -

TY  - JOUR
AU  - Sabirova, J.S.
AU  - Xavier, B.B.
AU  - Hernalsteens, J.P.
AU  - De Greve, H.
AU  - Ieven, M.
AU  - Goossens, H.
AU  - Malhotra-Kumar, S.
TI  - Complete Genome Sequences of Two Prolific Biofilm-Forming Staphylococcus aureus Isolates Belonging to USA300 and EMRSA-15 Clonal Lineages.
JO  - Genome Announcements
PY  - 2014
SP  - e00610
EP  - e00614
VL  - 2
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) causes serious infections that are even
AB  - more difficult to treat when associated with a biofilm phenotype that
AB  - facilitates evasion of the host immune system and antibiotics. As a first step
AB  - toward understanding the mechanisms underlying biofilm formation, we sequenced
AB  - the genomes of two prolific biofilm-forming strains belonging to the two most
AB  - important globally disseminated clonal lineages, USA300 and EMRSA-15.
ER  -

TY  - JOUR
AU  - Sacher, J.C.
AU  - Yee, E.
AU  - Szymanski, C.M.
AU  - Miller, W.G.
TI  - Complete Genome Sequences of Three Campylobacter jejuni Phage-Propagating Strains.
JO  - Genome Announcements
PY  - 2018
SP  - e00514
EP  - e00518
VL  - 6
AB  - Bacteriophage therapy can potentially reduce Campylobacter jejuni numbers in livestock, but it
AB  - requires a detailed understanding of phage-host interactions.
AB  - C. jejuni strains readily infected by certain phages are designated as
AB  - phage-propagating strains. Here, we report the complete genome sequences of three
AB  - such strains, NCTC 12660, NCTC 12661, and NCTC 12664.
ER  -

TY  - JOUR
AU  - Sacher, J.C.
AU  - Yee, E.
AU  - Szymanski, C.M.
AU  - Miller, W.G.
TI  - Complete Genome Sequence of Campylobacter jejuni Strain 12567, a Livestock-Associated Clade Representative.
JO  - Genome Announcements
PY  - 2018
SP  - e00513
EP  - e00518
VL  - 6
AB  - We report here the complete genome sequence of Campylobacter jejuni strain 12567, a member of
AB  - a C. jejuni livestock-associated clade that expresses glycoconjugates
AB  - associated with improved gastrointestinal tract persistence.
ER  -

TY  - JOUR
AU  - Sack, G.H. Jr.
AU  - Nathans, D.
TI  - Studies of SV40 DNA. IV.  Cleavage of SV40 DNA by restriction endonuclease from Hemophilus parainfluenzae.
JO  - Virology
PY  - 1973
SP  - 517
EP  - 520
VL  - 51
AB  - None
ER  -

TY  - JOUR
AU  - Sadri, R.
AU  - Hornsby, P.J.
TI  - Rapid analysis of DNA methylation using new restriction enzyme sites created by bisulfite modification.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 5058
EP  - 5059
VL  - 24
AB  - Bisulfite converts non-methylated cytosine in DNA to uracil leaving 5-methylcytosine
AB  - unaltered.  Here, predicted changes in restriction enzyme sites following reaction of genomic
AB  - DNA with bisulfite and amplification of the product by the polymerase chain reaction (PCR)
AB  - were used to assess the methylation of CpG sites.  This procedure differs from conventional
AB  - DNA methylation analysis by methylation-sensitive restriction enzymes because it does not rely
AB  - on an absence of cleavage to detect methylated sites, the two strands of DNA produce different
AB  - restriction enzyme sites and may be differentially analyzed, and closely related sequences may
AB  - be separately analyzed by using specific PCR primers.
ER  -

TY  - JOUR
AU  - Sadykov, M.
AU  - Asami, Y.
AU  - Niki, H.
AU  - Handa, N.
AU  - Itaya, M.
AU  - Tanokura, M.
AU  - Kobayashi, I.
TI  - Multiplication of a restriction-modification gene complex.
JO  - Mol. Microbiol.
PY  - 2003
SP  - 417
EP  - 427
VL  - 48
AB  - Previous works have suggested that some gene complexes encoding a restriction (R) enzyme and a
AB  - cognate modification (M) enzyme may behave as
AB  - selfish mobile genetic elements. RM gene complexes, which destroy
AB  - 'non-self' elements marked by the absence of proper methylation, are often
AB  - associated with mobile genetic elements and are involved in various genome
AB  - rearrangements. Here, we found amplification of a restriction-modification
AB  - gene complex. BamHI gene complex inserted into the Bacillus chromosome
AB  - showed resistance to replacement by a homologous stretch of DNA. Some
AB  - cells became transformed with the donor without losing BamHI. In most of
AB  - these transformants, multiple copies of BamHI and the donor allele were
AB  - arranged as tandem repeats. When a clone carrying one copy of each allele
AB  - was propagated, extensive amplification of BamHI and the donor unit was
AB  - observed in a manner dependent on restriction enzyme gene. This suggests
AB  - that restriction cutting of the genome participates in the amplification.
AB  - Visualization by fluorescent in situ hybridization revealed that the
AB  - amplification occurred in single cells in a burst-like fashion that is
AB  - reminiscent of induction of provirus replication. The multiplication
AB  - ability in a bacterium with natural capacity for DNA release, uptake and
AB  - transformation will be discussed in relation to spreading of RM gene
AB  - -complexes.
ER  -

TY  - JOUR
AU  - Sadykov, M.
AU  - Handa, N.
AU  - Asami, Y.
AU  - Tanokura, M.
AU  - Itaya, M.
AU  - Kobayashi, I.
TI  - Selfish maintenance and amplification of BamHI restriction modification gene complex on Bacillus subtilis chromosome.
JO  - Mutat. Res.
PY  - 2001
SP  - S159
EP  - S159
VL  - 483
AB  - It has been shown that some type II RM (restriction modification) gene complexes on a plasmid
AB  - resist replacement by an incompatible plasmid through post-segregational host killing.  Here
AB  - we present experimental evidence for selfish maintenance of BamHI RM gene complex on Bacillus
AB  - subtilis chromosome.  pBR322 derivatives carrying BamHI restriction +/- modification gene
AB  - complex and neomycin resistance gene were inserted into B. subtilis chromosome.  We then tried
AB  - to replace them by a homologous stretch of DNA that contains spectinomycin resistance gene by
AB  - natural transformation.  The efficiency of apparent replacement was several fold less, and the
AB  - resulting transformant colonies were smaller in the r+ cells than in the r- cells.  Moreover,
AB  - some of these clones were able to grow on media containing both spectinomycin and neomycin.
AB  - By PCR, we found that some of these clones retained the recipient RM gene complex and neomycin
AB  - phosphotransferase gene as well as the donor spectinomycin resistance gene.  Southern analysis
AB  - of chromosomal DNA provided supporting evidence.  Moreover, by Southern analyses and DNA
AB  - sequencing we found genome rearrangements, i.e. "amplicon" structures with different level of
AB  - amplification.  Possible mechanisms of gene amplification will be discussed.
ER  -

TY  - JOUR
AU  - Saelens, J.W.
AU  - Lau-Bonilla, D.
AU  - Moller, A.
AU  - Xet-Mull, A.M.
AU  - Medina, N.
AU  - Guzman, B.
AU  - Calderon, M.
AU  - Herrera, R.
AU  - Stout, J.E.
AU  - Arathoon, E.
AU  - Samayoa, B.
AU  - Tobin, D.M.
TI  - Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala.
JO  - Genome Announcements
PY  - 2018
SP  - e00024
EP  - e00018
VL  - 6
AB  - Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium
AB  - tuberculosis However, only limited genomic data are available from
AB  - M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of
AB  - clinical strains belonging to the Euro-American lineage 4, the most common
AB  - lineage found in Guatemala and Central America.
ER  -

TY  - JOUR
AU  - Saenz, H.L.
AU  - Engel, P.
AU  - Stoeckli, M.C.
AU  - Lanz, C.
AU  - Raddatz, G.
AU  - Vayssier-Taussat, M.
AU  - Birtles, R.
AU  - Schuster, S.C.
AU  - Dehio, C.
TI  - Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors.
JO  - Nat. Genet.
PY  - 2007
SP  - 1469
EP  - 1476
VL  - 39
AB  - The bacterial genus Bartonella comprises 21 pathogens causing characteristic intraerythrocytic
AB  - infections. Bartonella bacilliformis is a
AB  - severe pathogen representing an ancestral lineage, whereas the other
AB  - species are benign pathogens that evolved by radial speciation. Here, we
AB  - have used comparative and functional genomics to infer pathogenicity genes
AB  - specific to the radiating lineage, and we suggest that these genes may
AB  - have facilitated adaptation to the host environment. We determined the
AB  - complete genome sequence of Bartonella tribocorum by shotgun sequencing
AB  - and functionally identified 97 pathogenicity genes by signature-tagged
AB  - mutagenesis. Eighty-one pathogenicity genes belong to the core genome
AB  - (1,097 genes) of the radiating lineage inferred from genome comparison of
AB  - B. tribocorum, Bartonella henselae and Bartonella quintana. Sixty-six
AB  - pathogenicity genes are present in B. bacilliformis, and one has been lost
AB  - by deletion. The 14 pathogenicity genes specific for the radiating lineage
AB  - encode two laterally acquired type IV secretion systems, suggesting that
AB  - these systems have a role in host adaptability.
ER  -

TY  - JOUR
AU  - Saffarian, A.
AU  - Mulet, C.
AU  - Naito, T.
AU  - Bouchier, C.
AU  - Tichit, M.
AU  - Ma, L.
AU  - Grompone, G.
AU  - Sansonetti, P.J.
AU  - Pedron, T.
TI  - Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue.
JO  - Genome Announcements
PY  - 2015
SP  - e01089
EP  - e01015
VL  - 3
AB  - Here, we report three genome sequences of bacteria isolated from murine proximal  colonic
AB  - tissue and identified as Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and
AB  - Stenotrophomonas maltophilia BR12.
ER  -

TY  - JOUR
AU  - Saffarian, A.
AU  - Mulet, C.
AU  - Tournebize, R.
AU  - Naito, T.
AU  - Sansonetti, P.J.
AU  - Pedron, T.
TI  - Complete Genome Sequence of Delftia tsuruhatensis CM13 Isolated from Murine Proximal Colonic Tissue.
JO  - Genome Announcements
PY  - 2016
SP  - e01398
EP  - e01316
VL  - 4
AB  - We report here the complete genome sequence of Delftia tsuruhatensis CM13, isolated from
AB  - murine proximal colonic tissue. The genome assembly using PacBio
AB  - single-molecule real-time sequencing resulted in a single scaffold of 7.19 Mb.
ER  -

TY  - JOUR
AU  - Sagarkar, S.
AU  - Bhardwaj, P.
AU  - Yadav, T.C.
AU  - Qureshi, A.
AU  - Khardenavis, A.
AU  - Purohit, H.J.
AU  - Kapley, A.
TI  - Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil.
JO  - Genome Announcements
PY  - 2014
SP  - e01149
EP  - e01113
VL  - 2
AB  - We report the draft genome sequences of two tropical bacterial isolates capable of degrading
AB  - the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and
AB  - Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in
AB  - which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has
AB  - the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine
AB  - degradation.
ER  -

TY  - JOUR
AU  - Sagawa, H.
AU  - Ohshima, A.
AU  - Kato, I.
TI  - Sse8387I, a useful eight base cutter for mammalian genome analysis (influence of methylation on the activity of Sse8387I).
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 2367
EP  - 2370
VL  - 23
AB  - To develop restriction enzymes that are useful for genome analysis, we previously performed
AB  - screening and isolated Sse8387I from Streptomyces sp. strain 8387. Sse8387I is a restriction
AB  - enzyme that recognizes 5'-CCTGCA/GG-3' and cleaves DNA at the site shown by the diagonal.
AB  - The present study evaluated the effects of methylation that is important when Sse8387I is used
AB  - for genome analysis. Sse8387I lost cleavage activity after methylation of adenine or
AB  - methylation of cytosine at any site in the recognition sequence. However, the recognition
AB  - sequence of Sse8387I contains no CG sequence, which is the mammalian methylation sequence. In
AB  - addition, we evaluated the effects of methylation of CG at sites other than the recognition
AB  - sequence. The cleavage activity of Sse8387I was maintained even when CG sequences were present
AB  - immediately before or after, or near the recognition sequence, and cytosine was methylated.
AB  - These results suggest that CG methylation does not affect the cleavage activity of Sse8387I.
AB  - Therefore, Sse8387I seems to be very useful for mammalian genome analysis.
ER  -

TY  - JOUR
AU  - Sagawa, H.
AU  - Takagi, M.
AU  - Nomura, Y.
AU  - Inagaki, K.
AU  - Tano, T.
AU  - Kishimato, N.
AU  - Kotani, H.
AU  - Nakajima, K.
TI  - Isolation and identification of restriction endonuclease Aor51HI from Acidiphilium organovorum 51H.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 365
EP  - 365
VL  - 20
AB  - Aor5HI, a type II restriction endonuclease, has been isolated from Acidiphilium
AB  - organovorum 51H, an isoschizomer of Eco47III, recognizes the palindromic six
AB  - base sequence 5'-AGCGCT-3', and cleaves the center of recognition sequence
AB  - giving the blunted end.
ER  -

TY  - JOUR
AU  - Sager, R.
AU  - Kitchin, R.
TI  - Selective Silencing of eukaryotic DNA.
JO  - Science
PY  - 1975
SP  - 426
EP  - 433
VL  - 189
AB  - A molecular basis is proposed for programmed inactivation or loss of eukaryotic
AB  - DNA.
ER  -

TY  - JOUR
AU  - Sager, R.
AU  - Lane, D.
TI  - Molecular basis of maternal inheritance.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1972
SP  - 2410
EP  - 2413
VL  - 69
AB  - The mechanism of preferential transmission (i.e., maternal inheritance) of
AB  - cytoplasmic genes was investigated with chloroplast DNA of Chlamydomonas as a
AB  - model system.  The behavior of nuclear and chloroplast DNAs were compared in
AB  - the sexual cycle; DNAs from male and female parents were distinguished by
AB  - labeling with 14N- or 15NH4Cl and then by making the crosses: 14N (female) X
AB  - 15N (male) and the reciprocal.  Chloroplast DNAs from the two parents followed
AB  - different paths in the zygote, but nuclear DNAs showed no differences.
AB  - Chloroplast DNA from the female parent persists in the zygote, but undergoes a
AB  - density shift of 0.003-0.005 g/cm3 to a lighter buoyant density, whereas that
AB  - from the male disappears soon after zygote formation.  The possibility is
AB  - discussed that a modification-restriction system may be involved.
ER  -

TY  - JOUR
AU  - Saghatelyan, A.
AU  - Poghosyan, L.
AU  - Panosyan, H.
AU  - Birkeland, N.K.
TI  - Draft Genome Sequence of Thermus scotoductus Strain K1, Isolated from a Geothermal Spring in Karvachar, Nagorno Karabakh.
JO  - Genome Announcements
PY  - 2015
SP  - e01346
EP  - e01315
VL  - 3
AB  - The 2,379,636-bp draft genome sequence of Thermus scotoductus strain K1, isolated from
AB  - geothermal spring outlet located in the Karvachar region in Nagorno Karabakh
AB  - is presented. Strain K1 shares about 80% genome sequence similarity with T.
AB  - scotoductus strain SA-01, recovered from a deep gold mine in South Africa.
ER  -

TY  - JOUR
AU  - Sagitov, V.R.
AU  - Aleksandrov, A.A.
TI  - Selectivity of DNA methylase BspRI.
JO  - Dokl. Akad. Nauk.
PY  - 1988
SP  - 1266
EP  - 1268
VL  - 298
AB  - None
ER  -

TY  - JOUR
AU  - Sagredo-Beltran, J.
AU  - De La Cruz-Rodriguez, Y.
AU  - Alvarado-Rodriguez, M.
AU  - Vega-Arreguin, J.
AU  - Rodriguez-Guerra, R.
AU  - Alvarado-Gutierrez, A.
AU  - Fraire-Velazquez, S.
TI  - Genome Sequence of Bacillus halotolerans Strain MS50-18A with Antifungal Activity against Phytopathogens, Isolated from Saline Soil in San Luis Potosi, Mexico.
JO  - Genome Announcements
PY  - 2018
SP  - e00135
EP  - e00118
VL  - 6
AB  - Bacillus halotolerans strain MS50-18A, isolated from saline soil, possesses antifungal
AB  - activity toward root rot causal phytopathogens and has friendly
AB  - interactions with the chili pepper plant. The draft genome sequence is 4.06 Mb in
AB  - length and contains 4,215 genes. Genes related to glycine/betaine uptake and
AB  - bacilysin biosynthesis are present, supporting its saline stress tolerance and
AB  - antifungal activity.
ER  -

TY  - JOUR
AU  - Saguez, C.
AU  - Lecellier, G.
AU  - Koll, F.
TI  - Intronic GIY-YIUG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 1299
EP  - 1306
VL  - 28
AB  - Endonuclease genes encoded in invasive introns are themselves supposed to be mobile elements
AB  - which, during evolution, have colonized pre-existing introns converting them into invasive
AB  - elements.  This hypothesis is supported by numerous data concerning the LAGLI-DADG subclass of
AB  - intronic endonucleases. Less is known about the GIY-YIG ORFs which constitute another family
AB  - of endonucleases. In this paper we describe the presence of one optional GIY-YIG ORF in the
AB  - second intron of the mitochondrial cytochrome b gene in the fungus Podospora curvicolla. We
AB  - show that this GIY-YIG ORF is efficiently transferred from an ORF-containing intron to an
AB  - ORF-less allele. We also show that the products of both the GIY-YIG ORF and the non-canonical
AB  - LAGLI-DADG-GIY-YIG ORF, which is generated by its integration, have endonuclease activities
AB  - which recognize and cut the insertion site of the optional sequence. This constitutes the
AB  - first direct evidence for potential mobility of an intronic GIY-YIG endonuclease. We discuss
AB  - the role that such a mobile sequence could have played during evolution.
ER  -

TY  - JOUR
AU  - Saha, S. et al.
TI  - Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007.
JO  - Genome Announcements
PY  - 2017
SP  - e01123
EP  - e01117
VL  - 5
AB  - We report here the genome sequences of three newly isolated phages that infect Mycobacterium
AB  - smegmatis mc(2)155. Phages Findley, Hurricane, and TBond007 were
AB  - discovered in geographically distinct locations and are related to cluster K
AB  - mycobacteriophages, with Findley being similar to subcluster K2 phages and
AB  - Hurricane and TBond007 being similar to subcluster K3 phages.
ER  -

TY  - JOUR
AU  - Saha, S.
AU  - Ahmad, I.
AU  - Reddy, Y.V.R.
AU  - Krishnamurthy, V.
AU  - Rao, D.N.
TI  - Functional analysis of conserved motifs in type III restriction-modification enzymes.
JO  - Biol. Chem.
PY  - 1998
SP  - 511
EP  - 517
VL  - 379
AB  - EcoP1I and EcoP15I are members of type III restriction-modification enzymes.  EcoPI and
AB  - EcoP15I DNA methyltransferases transfer a methyl group from S-adenosyl-L-methionine to the N6
AB  - position of the second adenine residues in their recognition sequences, 5'-AGACC-3' and
AB  - 5'-CAGCAG-3' respectively.  We have altered various residues in two highly conserved
AB  - sequences, FxGxG (motif I) and DPPY (motif IV) in these proteins by site-directed mutagenesis.
AB  - Using a mixture of in vivo and in vitro assays, our results on the mutational analysis of
AB  - these methyltransferases demonstrate the universal role of motif I in AdoMet binding and a
AB  - role for motif IV in catalysis.  All six cysteine residues in EcoP15I DNA methyltransferase
AB  - have been substituted with serine and the role of cysteine residues in EcoP15I DNA
AB  - methyltransferase catalyzed reaction assessed.  The Res subunits of type III restriction
AB  - enzymes share a distant sequence similarity with and contain the motifs characteristic of the
AB  - DEAD box proteins.  We have carried out site-directed mutagenesis of the conserved residues in
AB  - two of the helicase motifs of the EcoP1I restriction enzyme in order to investigate the role
AB  - of motifs in DNA cleavage by this enzyme.  Our findings indicate that certain conserved
AB  - residues in these motifs are involved in ATP hydrolysis while the other residues are involved
AB  - in coupling restriction of DNA to ATP hydrolysis.  Taken collectively, these results form the
AB  - basis for a detailed structure-function analysis of EcoP1I and EcoP15I restriction enzymes.
ER  -

TY  - JOUR
AU  - Saha, S.
AU  - Rao, D.N.
TI  - ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 559
EP  - 567
VL  - 247
AB  - The type III restriction endonuclease EcoPI, coded by bacteriophage P1, cleaves unmodified DNA
AB  - in the presence of ATP and magnesium ions. We show that purified EcoPI restriction enzyme
AB  - fails to cleave DNA in the presence of non-hydrolyzable ATP analogs. More importantly, this
AB  - study demonstrates that EcoPI restriction enzyme has an inherent ATPase activity, and ATP
AB  - hydrolysis is necessary for DNA cleavage. Furthermore, we show that the progress curve of the
AB  - reaction with EcoPI restriction enzyme exhibits a lag which is dependent on the enzyme
AB  - concentration. Kinetic analysis of the progress curves of the reaction suggest slow
AB  - transitions that can occur during the reaction, characteristic of hysteretic enzymes. The role
AB  - of ATP in the cleavage mechanism of type III restriction enzymes is discussed.
ER  -

TY  - JOUR
AU  - Saha, S.
AU  - Rao, D.N.
TI  - Mutations in the Res subunit of the EcoPI restriction enzyme that affect ATP-dependent reactions.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 342
EP  - 354
VL  - 269
AB  - The Res subunits of the type III restriction-modification enzymes share a statistically
AB  - significant amino acid sequence similarity with several RNA and DNA helicases of the so-called
AB  - DEAD family.  It was postulated that in type III restriction enzymes a DNA helicase activity
AB  - may be required for local unwinding at the cleavage site.  The members of this family share
AB  - seven conserved motifs, all of which are found in the Res subunit of the type III restriction
AB  - enzymes.  To determine the contribution, if any, of these motifs in DNA cleavage by EcoPI, a
AB  - type III restriction enzyme, we have made changes in motifs I and II.  While mutations in
AB  - motif I (GTGKT) clearly affected ATP hydrolysis and resulted in loss of DNA cleavage activity,
AB  - mutation in motif II (DEPH) significantly decreased ATP hydrolysis but had no effect on DNA
AB  - cleavage.  The double mutant R.EcoPIK90R-H229K showed no significant ATPase or DNA restriction
AB  - activity though ATP binding was not affected.  These results imply that there are at least two
AB  - ATPase reaction centers in EcoPI restriction enzyme.  Motif I appears to be involved in
AB  - coupling DNA restriction to ATP hydrolysis.  Our results indicate that EcoPI restriction
AB  - enzyme does not have a strand separation activity.  We suggest that these motifs play a role
AB  - in the ATP-dependent translocation that has been proposed to occur in the type III restriction
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Sahl, J.W.
AU  - Mayo, M.
AU  - Price, E.P.
AU  - Sarovich, D.S.
AU  - Kaestli, M.
AU  - Pearson, T.
AU  - Williamson, C.H.D.
AU  - Nottingham, R.
AU  - Sheridan, K.
AU  - Wagner, D.M.
AU  - Currie, B.J.
AU  - Keim, P.
TI  - Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence  Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection.
JO  - Genome Announcements
PY  - 2018
SP  - e00072
EP  - e00018
VL  - 6
AB  - The Burkholderia pseudomallei isolate MSHR1435 is a fully virulent environmental  sequence
AB  - type 131 (ST131) isolate that is epidemiologically associated with a
AB  - 17.5-year chronic melioidosis infection. The completed genome will serve as a
AB  - reference for studies of environmental ecology, virulence, and chronic B.
AB  - pseudomallei infections.
ER  -

TY  - JOUR
AU  - Sahl, J.W.
AU  - Stone, J.K.
AU  - Gelhaus, H.C.
AU  - Warren, R.L.
AU  - Cruttwell, C.J.
AU  - Funnell, S.G.
AU  - Keim, P.
AU  - Tuanyok, A.
TI  - Genome Sequence of Burkholderia pseudomallei NCTC 13392.
JO  - Genome Announcements
PY  - 2013
SP  - e00183
EP  - e00113
VL  - 1
AB  - Here, we describe the draft genome sequence of Burkholderia pseudomallei NCTC 13392. This
AB  - isolate has been distributed as K96243, but distinct genomic
AB  - differences have been identified. The genomic sequence of this isolate will
AB  - provide the genomic context for previously conducted functional studies.
ER  -

TY  - JOUR
AU  - Sahni, R.D.
AU  - Amalanathan, R.
AU  - Devanga, R.N.K.
AU  - Mathai, J.
AU  - Veeraraghavan, B.
AU  - Biswas, I.
TI  - Complete Genome Sequence of Serratia marcescens U36365, a Green Pigment-Producing Strain Isolated from a Patient with Urinary Tract Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e00837
EP  - e00816
VL  - 4
AB  - Serratia marcescens is an emerging nosocomial pathogen associated with urinary and respiratory
AB  - tract infections. In this study, we determined the genome of a
AB  - green pigment-producing clinical strain, U36365, isolated from a hospital in
AB  - Southern India. De novo assembly of PacBio long-read sequencing indicates that
AB  - the U36365 genome consists of a chromosome of 5.12 Mbps and no plasmids.
ER  -

TY  - JOUR
AU  - Saikawa, Y.
AU  - Kubota, T.
AU  - Maeda, S.
AU  - Otani, Y.
AU  - Kumai, K.
AU  - Kitajima, M.
TI  - Inhibition of DNA methyltransferase by antisense oligodeoxynucleotide modifies cell characteristics in gastric cancer cell lines.
JO  - Oncol. Rep.
PY  - 2004
SP  - 527
EP  - 531
VL  - 12
AB  - DNA (cytosine-5-)-methyltransferase 1 (DNMT1) plays an important role in the maintenance of
AB  - DNA methylation patterns via complicated networks
AB  - including signaling pathways and transcriptional factors, relating to
AB  - cell differentiation or carcinogenesis. In the present study, we
AB  - designed an antisense oligodeoxynucleotide of DNMT1 (AS/MT: 5'-CGGTAC
AB  - GCGCCGGCATCT-3') and demonstrated successful inhibition of DNMT1
AB  - expression by AS/MT at the protein level, using gastric cancer cell
AB  - lines in vitro. E-cadherin protein expression was increased, and both
AB  - cyclin D1 and PCNA were decreased by AS/MT treatment. AS/MT also
AB  - induced suppression of cell growth as determined by BrDU uptake
AB  - incorporation, in a dose-dependent manner, suggesting specificity of
AB  - AS/MT. Simultaneously, morphological alterations were observed in both
AB  - TMK-1 and MKN-45 cells after 24 h incubation with 2 muM of AS/MT. The
AB  - cells changed shape from their original forms to dispersed,
AB  - fibroblast-like cells with neurite-like processes, accompanied by an
AB  - increased adhesive potential of the cells. An in vivo model of
AB  - peritoneal dissemination using the nude mouse system showed an
AB  - increased malignant potential of AS/MT treated TMK-1 cells as
AB  - demonstrated by a greater number of peritoneal tumor nodules in the
AB  - AS/MT as compared to the NS/MT treated group, 34.8+/-4.3 vs. 22.4+/-3.0
AB  - nodules, respectively (p=0.0039). The total wet tumor weight in the
AB  - AS/MT group (350+/-47.4 g) was significantly greater than that in the
AB  - NS/MT group (248+/-41.5 g) (p=0.0065). In conclusion, the inhibition of
AB  - DNA methylation by DNMT1 by an antisense oligodeoxynucleotide
AB  - influences cell morphology and adhesion, as well as cell growth in
AB  - gastric cancer cells in vitro. Moreover, these alterations in the
AB  - characteristics of cancer cells resulted in an increased ability to
AB  - attach onto the peritoneum in the nude mouse system in vivo, suggesting
AB  - that strict clinical guidelines will be necessary to utilize such a DNA
AB  - methylation inhibitor, since it does not always mean a therapeutic
AB  - antitumor strategy.
ER  -

TY  - JOUR
AU  - Saile, N.
AU  - Schwarz, L.
AU  - Eissenberger, K.
AU  - Klumpp, J.
AU  - Fricke, F.W.
AU  - Schmidt, H.
TI  - Growth advantage of Escherichia coli O104:H4 strains on 5-N-acetyl-9-O-acetyl neuraminic acid as a carbon source is dependent on heterogeneous phage-Borne nanS-p esterases.
JO  - Int. J. Med. Microbiol.
PY  - 2018
SP  - 459
EP  - 468
VL  - 308
AB  - Enterohemorrhagic E. coli (EHEC) are serious bacterial pathogens which are able
AB  - to cause a hemorrhagic colitis or the life-threatening hemolytic-uremic syndrome
AB  - (HUS) in humans. EHEC strains can carry different numbers of phage-borne nanS-p
AB  - alleles that are responsible for acetic acid release from mucin from bovine
AB  - submaxillary gland and 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac2), a
AB  - carbohydrate present in mucin. Thus, Neu5,9Ac2 can be transformed to 5-N-acetyl
AB  - neuraminic acid, an energy source used by E. coli strains. We hypothesize that
AB  - these NanS-p proteins are involved in competitive growth of EHEC in the
AB  - gastrointestinal tract of humans and animals. The aim of the current study was to
AB  - demonstrate and characterize the nanS-p alleles of the 2011 E. coli O104:H4
AB  - outbreak strain LB226692 and analyze whether the presence of multiple nanS-p
AB  - alleles in the LB226692 genome causes a competitive growth advantage over a
AB  - commensal E. coli strain. We detected and characterized five heterogeneous
AB  - phage-borne nanS-p alleles in the genome of E. coli O104:H4 outbreak strain
AB  - LB226692 by in silico analysis of its genome. Furthermore, successive deletion of
AB  - all nanS-p alleles, subsequent complementation with recombinant NanS-p13-His, and
AB  - in vitro co-culturing experiments with the commensal E. coli strain AMC 198 were
AB  - conducted. We could show that nanS-p genes of E. coli O104:H4 are responsible for
AB  - growth inhibition of strain AMC 198, when Neu5,9Ac2 was used as sole carbon
AB  - source in co-culture. The results of this study let us suggest that multiple
AB  - nanS-p alleles may confer a growth advantage by outcompeting other E. coli
AB  - strains in Neu5,9Ac2 rich environments, such as mucus in animal and human gut.
ER  -

TY  - JOUR
AU  - Saile, N.
AU  - Voigt, A.
AU  - Kessler, S.
AU  - Stressler, T.
AU  - Klumpp, J.
AU  - Fischer, L.
AU  - Schmidt, H.
TI  - In Silico and Functional Analysis of Prophage-Encoded 5-N-Acetyl-9-O-Acetyl Neuraminic Acid Esterases of E. coli O157:H7 Strain EDL933.
JO  - Appl. Environ. Microbiol.
PY  - 2016
SP  - 5940
EP  - 5950
VL  - 82
AB  - (ORFs) in its genome which are highly homologous to the chromosomal nanS gene. The latter is
AB  - part of the nanCMS operon,
AB  - which is present in most E. coli strains and encodes an esterase which is responsible for the
AB  - monodeacetylation of 5-N-acetyl-9-
AB  - O-acetyl neuraminic acid (Neu5,9Ac2). Whereas one prophage-borne ORF (z1466) has been
AB  - characterized in previous studies,
AB  - the functions of the other nanS-homologous ORFs are unknown. In the current study, the
AB  - nanS-homologous ORFs of EDL933
AB  - were initially studied in silico. Due to their homology to the chromosomal nanS gene and their
AB  - location in prophage genomes,
AB  - we designated them nanS-p and numbered the different nanS-p alleles consecutively from 1 to
AB  - 10. The two alleles nanS-p2 and
AB  - nanS-p4 were selected for production of recombinant proteins, their enzymatic activities were
AB  - investigated, and differences in
AB  - their temperature optima were found. Furthermore, a function of these enzymes in substrate
AB  - utilization could be demonstrated
AB  - using an E. coli C600nanS mutant in a growth medium with Neu5,9Ac2 as the carbon source and
AB  - supplementation with the
AB  - different recombinant NanS-p proteins. Moreover, generation of sequential deletions of all
AB  - nanS-p alleles in strain EDL933 and
AB  - subsequent growth experiments demonstrated a gene dose effect on the utilization of Neu5,9Ac2.
AB  - Since Neu5,9Ac2 is an important
AB  - component of human and animal gut mucus and since the nutrient availability in the large
AB  - intestine is limited, we hypothesize
AB  - that the presence of multiple Neu5,9Ac2 esterases provides them a nutrient supply under
AB  - certain conditions in the large intestine,
AB  - even if particular prophages are lost.
ER  -

TY  - JOUR
AU  - Sain, B.
AU  - Murray, N.E.
TI  - The hsd (host specificity) genes of E. coli K12.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 35
EP  - 46
VL  - 180
AB  - The hsd genes of E. coli K12 have been cloned in phage lambda by a combination
AB  - of in vitro and in vivo techniques.  Three genes, whose products are required
AB  - for K-specific restriction and modification, have been identified by
AB  - complementation tests as hsdR, M, and S.  The order of these closely linked
AB  - genes was established as R, M, S by analysis of the DNA of genetically
AB  - characterised deletion derivatives of lambda hsd phages.  The three genes are
AB  - transcribed in the same direction but not necessarily as a single operon.
AB  - Genetic evidence identifies two promoters, one from which transcription of hsdM
AB  - and S is initiated and a second for the hsdR gene.  The hsdR gene codes for a
AB  - polypeptide of molecular weight ~130,000; hsdM for one of 62-65,000 and the
AB  - hsdS gene was associated with two polypeptides of approximately 50000.
AB  - Circumstantial evidence suggest that one of these two polypeptides may be a
AB  - degradation, or processed, derivative of the other.  The hsdS polypeptide of E.
AB  - coli B has a slightly higher mobility in an SDS-polyacrylamide gel than does
AB  - that of E. coli K12.  A probe comprising most of the hsdR gene and all of the
AB  - hsdM and S genes of E. coli K12 shares extensive homology with the DNA of E.
AB  - coli B but none with that of E. coli C.
ER  -

TY  - JOUR
AU  - Sainz, F.
AU  - Mas, A.
AU  - Torija, M.J.
TI  - Draft Genome Sequence of Acetobacter malorum CECT 7742, a Strain Isolated from Strawberry Vinegar.
JO  - Genome Announcements
PY  - 2016
SP  - e00620
EP  - e00616
VL  - 4
AB  - The present article reports the draft genome sequence of the strain Acetobacter malorum CECT
AB  - 7742, an acetic acid bacterium isolated from strawberry vinegar.
AB  - This species is characterized by the production of d-gluconic acid from
AB  - d-glucose, which it further metabolizes to keto-d-gluconic acids.
ER  -

TY  - JOUR
AU  - Sainz, F.
AU  - Mas, A.
AU  - Torija, M.J.
TI  - Draft Genome Sequences of Gluconobacter cerinus CECT 9110 and Gluconobacter japonicus CECT 8443, Acetic Acid Bacteria Isolated from Grape Must.
JO  - Genome Announcements
PY  - 2016
SP  - e00621
EP  - e00616
VL  - 4
AB  - We report here the draft genome sequences of Gluconobacter cerinus strain CECT9110 and
AB  - Gluconobacter japonicus CECT8443, acetic acid bacteria isolated from grape must. Gluconobacter
AB  - species are well known for their ability to oxidize sugar alcohols into the corresponding
AB  - acids. Our objective was to select strains  to oxidize effectively d-glucose.
ER  -

TY  - JOUR
AU  - Sait, M.
AU  - Aitchison, K.
AU  - Wheelhouse, N.
AU  - Wilson, K.
AU  - Lainson, F.A.
AU  - Longbottom, D.
AU  - Smith, D.G.
TI  - Genome Sequence of Lawsonia intracellularis Strain N343, Isolated from a Sow with Hemorrhagic Proliferative Enteropathy.
JO  - Genome Announcements
PY  - 2013
SP  - e00027
EP  - e00013
VL  - 1
AB  - is the etiological agent of proliferative enteropathy (PE), causing mild or acute hemorrhagic
AB  - diarrhea in infected animals. Here we report the genome sequence of
AB  - strain N343, isolated from a sow that died of hemorrhagic PE. N343 contains 24
AB  - single nucleotide polymorphisms and 90 indels compared to the reference strain
AB  - PHE/MN1-00.
ER  -

TY  - JOUR
AU  - Saito, H.
AU  - Shibata, T.
AU  - Ando, T.
TI  - Mapping of genes determining nonpermissiveness and host-specific restriction to bacteriophages in Bacillus subtilis Marburg.
JO  - Mol. Gen. Genet.
PY  - 1979
SP  - 117
EP  - 122
VL  - 170
AB  - Bacillus subtilis Marburg is nonpermissive for the multiplication of
AB  - bacteriophages SP10 and uNR2.  A permissive mutant was derived from the Marburg
AB  - strain, and the genetic determinants of nonpermissiveness were analyzed by PBS1
AB  - transduction.  The simultaneous presence of two genes as mutant alleles, nonA
AB  - and nonB, was necessary for permissiveness.  The gene nonA is linked very
AB  - closely to rfm (cotransfer: 90%); nonB is located between dal and purB
AB  - (cotransfer of nonB and purB6: 48%).  The genetic determinant of host-specific
AB  - restriction intrinsic to the Marburg strain (hsrM) was found to be identical or
AB  - very closely linked to nonB.  The segregation of nonB and hsrM has never been
AB  - observed in the course of transduction analysis.  The mutation, hsrM1,
AB  - diminishes the restriction activity, but not the host-controlled modifiction.
ER  -

TY  - JOUR
AU  - Saito, M.
AU  - Hirasawa, M.
AU  - Kuwahara, N.
AU  - Okada, T.
AU  - Umezawa, K.
AU  - Kobayashi, T.
AU  - Okamoto, M.
AU  - Naito, M.
AU  - Hirasawa, M.
AU  - Takada, K.
TI  - Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Serotype g Strain NUM4039 (JCM 30399).
JO  - Genome Announcements
PY  - 2016
SP  - e00158
EP  - e00116
VL  - 4
AB  - Aggregatibacter actinomycetemcomitans is considered to be a major etiological agent of
AB  - aggressive periodontitis and includes serotype a to g strains. We herein
AB  - report the first complete genome sequence of A. actinomycetemcomitans serotype g
AB  - strain NUM4039. The genome is 2,382,853 bp in length with a G+C content of
AB  - 44.34%.
ER  -

TY  - JOUR
AU  - Sakaguchi, Y.
AU  - Hayashi, T.
AU  - Kurokawa, K.
AU  - Nakayama, K.
AU  - Oshima, K.
AU  - Fujinaga, Y.
AU  - Ohnishi, M.
AU  - Ohtsubo, E.
AU  - Hattori, M.
AU  - Oguma, K.
TI  - The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 17472
EP  - 17477
VL  - 102
AB  - Botulinum neurotoxins (BoNTXs) produced by Clostridium botulinum are among
AB  - the most poisonous substances known. Of the seven types of BoNTXs, genes
AB  - for type C1 and D toxins (BoNTX/C1 and D) are carried by bacteriophages.
AB  - The gene for exoenzyme C3 also resides on these phages. Here, we present
AB  - the complete genome sequence of c-st, a representative of
AB  - BoNTX/C1-converting phages. The genome is a linear double-stranded DNA of
AB  - 185,682 bp with 404-bp terminal direct repeats, the largest known
AB  - temperate phage genome. We identified 198 potential protein-coding
AB  - regions, including the genes for production of BoNTX/C1 and exoenzyme C3.
AB  - Very exceptionally, as a viable bacteriophage, a number of insertion
AB  - sequences were found on the c-st genome. By analyzing the molecular
AB  - structure of the c-st genome in lysogens, we also found that it exists as
AB  - a circular plasmid prophage. These features account for the unstable
AB  - lysogeny of BoNTX phages, which has historically been called
AB  - "pseudolysogeny." The PCR scanning analysis of other BoNTX/C1 and D phages
AB  - based on the c-st sequence further revealed that BoNTX phages comprise a
AB  - divergent phage family, probably generated by exchanging genomic segments
AB  - among BoNTX phages and their relatives.
ER  -

TY  - JOUR
AU  - Sakaguchi, Y.
AU  - Hosomi, K.
AU  - Uchiyama, J.
AU  - Ogura, Y.
AU  - Umeda, K.
AU  - Sakaguchi, M.
AU  - Kohda, T.
AU  - Mukamoto, M.
AU  - Misawa, N.
AU  - Matsuzaki, S.
AU  - Hayashi, T.
AU  - Kozaki, S.
TI  - Draft Genome Sequence of Clostridium botulinum Type B Strain Osaka05, Isolated from an Infant Patient with Botulism in Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e01010
EP  - e01013
VL  - 2
AB  - Clostridium botulinum strain Osaka05, which has been isolated from an infant patient with
AB  - botulism in Japan, is the first strain producing botulinum
AB  - neurotoxin subtype B6. Here, we report the draft genome sequence of C. botulinum
AB  - Osaka05.
ER  -

TY  - JOUR
AU  - Sakai-Kawada, F.E.
AU  - Yakym, C.J.
AU  - Helmkampf, M.
AU  - Hagiwara, K.
AU  - Ip, C.G.
AU  - Antonio, B.J.
AU  - Armstrong, E.
AU  - Ulloa, W.J.
AU  - Awaya, J.D.
TI  - Draft Genome Sequence of Marine Sponge Symbiont Pseudoalteromonas luteoviolacea IPB1, Isolated from Hilo, Hawaii.
JO  - Genome Announcements
PY  - 2016
SP  - e01002
EP  - e01016
VL  - 4
AB  - We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain IPB1
AB  - that was isolated from the Hawaiian marine sponge
AB  - Iotrochota protea Genome mining complemented with bioassay studies will elucidate
AB  - secondary metabolite biosynthetic pathways and will help explain the ecological
AB  - interaction between host sponge and microorganism.
ER  -

TY  - JOUR
AU  - Sakamoto, M.
AU  - Ikeyama, N.
AU  - Yuki, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Lawsonibacter asaccharolyticus JCM 32166(T), a Butyrate-Producing Bacterium, Isolated from Human Feces.
JO  - Genome Announcements
PY  - 2018
SP  - e00563
EP  - e00518
VL  - 6
AB  - Here, we report the draft genome sequence of Lawsonibacter asaccharolyticus JCM 32166(T), a
AB  - butyrate-producing bacterium, isolated from human feces. The genomic
AB  - analysis reveals genes for butyrate synthesis and will facilitate the study on
AB  - the role of this strain in the human gut.
ER  -

TY  - JOUR
AU  - Sakamoto, M.
AU  - Ikeyama, N.
AU  - Yuki, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Faecalimonas umbilicata JCM 30896(T), an Acetate-Producing Bacterium Isolated from Human Feces.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e01091
EP  - e01018
VL  - 7
AB  - Here, we report the draft genome sequence of Faecalimonas umbilicata JCM 30896(T), an
AB  - acetate-producing bacterium isolated from human feces. The genomic
AB  - analysis reveals genes for acetate and vitamin B12 synthesis and will facilitate
AB  - the study of the role of this strain in the human gut.
ER  -

TY  - JOUR
AU  - Sakamoto, M.
AU  - Lapidus, A.L.
AU  - Han, J.
AU  - Trong, S.
AU  - Haynes, M.
AU  - Reddy, T.B.
AU  - Mikhailova, N.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Pukall, R.
AU  - Markowitz, V.M.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Ohkuma, M.
TI  - High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 48
EP  - 48
VL  - 10
AB  - Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to
AB  - the family Bacteroidaceae. Strain BL2(T) is of interest because  it was isolated from the gut
AB  - of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of
AB  - benefit for the host and may impact poultry farming. The 3,621,509 bp long genome with its
AB  - 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains,
AB  - Phase I: the  one thousand microbial genomes (KMG) project.
ER  -

TY  - JOUR
AU  - Sakamoto, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine.
JO  - Genome Announcements
PY  - 2014
SP  - e01242
EP  - e01213
VL  - 2
AB  - Here, we report the draft genome sequences of Bacteroides pyogenes JCM 6294(T), JCM 6292, and
AB  - JCM 10003, which were isolated from a cat and swine and were
AB  - recently classified into a single species, B. pyogenes. Comparative analyses of
AB  - these genomes revealed the diversification of B. pyogenes strains isolated from
AB  - different animals.
ER  -

TY  - JOUR
AU  - Sakamoto, M.
AU  - Tanaka, N.
AU  - Shiwa, Y.
AU  - Yoshikawa, H.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Porphyromonas crevioricanis JCM 15906T and Porphyromonas cansulci JCM 13913T Isolated from a Canine Oral Cavity.
JO  - Genome Announcements
PY  - 2013
SP  - e00483
EP  - e00413
VL  - 1
AB  - Here, we report the draft genome sequences of Porphyromonas crevioricanis JCM 15906(T) and
AB  - Porphyromonas cansulci JCM 13913(T), which were isolated from a
AB  - canine oral cavity and were recently united under the single species P.
AB  - crevioricanis. These two genome sequences are very similar, and yet a high degree
AB  - of genome rearrangements is observed.
ER  -

TY  - JOUR
AU  - Sakata, T.
AU  - Kanesaki, Y.
AU  - Yoshikawa, H.
AU  - Tsurumaru, H.
AU  - Yamakawa, T.
TI  - Draft Genome Sequence of Bradyrhizobium japonicum Is-1, Which Is Incompatible with Rj2 Genotype Soybeans.
JO  - Genome Announcements
PY  - 2015
SP  - e01219
EP  - e01215
VL  - 3
AB  - We report the draft genome sequence of Bradyrhizobium japonicum Is-1, which is incompatible
AB  - with Rj2 genotype soybeans. The estimated genome size of this strain is 8.9 Mb. Genome
AB  - sequence information of this strain will help to identify a causal gene for this
AB  - incompatibility.
ER  -

TY  - JOUR
AU  - Sakihara, K.
AU  - Maeda, J.
AU  - Tashiro, K.
AU  - Fujino, Y.
AU  - Kuhara, S.
AU  - Ohshima, T.
AU  - Ogata, S.
AU  - Doi, K.
TI  - Draft Genome Sequence of Thiostrepton-Producing Streptomyces azureus ATCC 14921.
JO  - Genome Announcements
PY  - 2015
SP  - e01183
EP  - e01115
VL  - 3
AB  - Streptomyces azureus ATCC 14921 belongs to the Streptomyces cyaneus cluster and is known to be
AB  - a thiostrepton producer. Here, we report a draft genome sequence for this strain, consisting
AB  - of 350 contigs containing a total of 8,790,525 bp, 8,164 predicted coding sequences, and a G+C
AB  - content of 70.9%.
ER  -

TY  - JOUR
AU  - Sakoula, D.
AU  - Nowka, B.
AU  - Spieck, E.
AU  - Daims, H.
AU  - Lucker, S.
TI  - The draft genome sequence of 'Nitrospira lenta' strain BS10, a nitrite oxidizing  bacterium isolated from activated sludge.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 32
EP  - 32
VL  - 13
AB  - The genus Nitrospira is considered to be the most widespread and abundant group of
AB  - nitrite-oxidizing bacteria in many natural and man-made ecosystems. However,
AB  - the ecophysiological versatility within this phylogenetic group remains highly
AB  - understudied, mainly due to the lack of pure cultures and genomic data. To
AB  - further expand our understanding of this biotechnologically important genus, we
AB  - analyzed the high quality draft genome of 'Nitrospira lenta' strain BS10, a
AB  - sublineage II Nitrospira that was isolated from a municipal wastewater treatment
AB  - plant in Hamburg, Germany. The genome of 'N. lenta' has a size of 3,756,190 bp
AB  - and contains 3968 genomic objects, of which 3907 are predicted protein-coding
AB  - sequences. Thorough genome annotation allowed the reconstruction of the 'N.
AB  - lenta' core metabolism for energy conservation and carbon fixation. Comparative
AB  - analyses indicated that most metabolic features are shared with N. moscoviensis
AB  - and 'N. defluvii', despite their ecological niche differentiation and
AB  - phylogenetic distance. In conclusion, the genome of 'N. lenta' provides important
AB  - insights into the genomic diversity of the genus Nitrospira and provides a
AB  - foundation for future comparative genomic studies that will generate a better
AB  - understanding of the nitrification process.
ER  -

TY  - JOUR
AU  - Salah, Z.B.
AU  - Rout, S.P.
AU  - Humphreys, P.N.
TI  - Draft Whole-Genome Sequence of the Alkaliphilic Alishewanella aestuarii Strain HH-ZS, Isolated from Historical Lime Kiln Waste-Contaminated Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01447
EP  - e01416
VL  - 4
AB  - Here, we present the whole-genome sequence of an environmental Gram-negative Alishewanella
AB  - aestuarii strain (HH-ZS), isolated from the hyperalkaline
AB  - contaminated soil of a historical lime kiln in Buxton, United Kingdom.
ER  -

TY  - JOUR
AU  - Salaj-Smic, E.
AU  - Donjerkovic, D.
AU  - Trgovcevic, Z.
TI  - In vivo modulation of the EcoK restriction endonuclease.
JO  - Periodicum Biologorum
PY  - 1994
SP  - 357
EP  - 358
VL  - 96
AB  - Recently, we have found a novel type of restriction alleviation (RA) which occurs in strains
AB  - carrying recB alone or recB in combination with additional mutations (recBC sbcBC, recBC sbcBC
AB  - recJ, recBC sbcBC recF, recBC sucBC recA).  It occurs in the absence of UV irraditation and
AB  - depends on the presence of the commonly used plasmids (such as pACYC184).  It is, however,
AB  - independent of the host and phage recombination systems.  The mechanism of this type of RA is
AB  - unknown.  Therefore, it was interesting to see whether UV-induced RA and plasmid-mediated RA
AB  - have a common mechanism.  For this purpose, we measured the efficiency of plating of
AB  - unmodified lambda on three sets of UV-irradiated bacteria: 1. E. coli JC7623 recB21 recC22
AB  - sbcB15 sbcC201 carrying the plasmid pACYC184 and, as a control, plasmid-free derivative; 2. E.
AB  - coli N2281 rec B21 recC22 sbcB15 sbcC201 recA13 carrying pACYC184 and its plasmid-free
AB  - derivative.  3. E. coli AB1157 (wild type) carrying pACYC184 and its plasmid-free derivative.
ER  -

TY  - JOUR
AU  - Salaj-Smic, E.
AU  - Marsic, N.
AU  - Trgovcevic, Z.
AU  - Lloyd, R.G.
TI  - Modulation of EcoKI restriction in vivo: Role of the lambda gam protein and plasmid metabolism.
JO  - J. Bacteriol.
PY  - 1997
SP  - 1852
EP  - 1856
VL  - 179
AB  - Two novel types of alleviation of DNA restriction by the EcoKI restriction endonuclease are
AB  - described.  The first type depends on the presence of the gam gene product (Gam protein) of
AB  - bacteriophage lambda.  The efficiency of plating of unmodified phage lambda is greatly
AB  - increased when the restricting Escherichia coli K-12 host carries a gam+ plasmid.  The effect
AB  - is particularly striking in wild-type strains and, to a lesser extent, in the presence of sbcC
AB  - and recA mutations.  In all cases, Gam-dependent alleviation of restriction requires active
AB  - recBCD genes of the host and recombination (red) genes of the infecting phage.  The enhanced
AB  - capacity of Gam-expressing cells to repair DNA strand breaks might account for this
AB  - phenomenon.  The second type is caused by the presence of a plasmid in a restricting host
AB  - lacking RecBCD enzyme.  Commonly used plasmids such as the cloning vector pACYC184  can
AB  - produce such an effect in strains carrying recB single mutations or in recBC sbcBC strains.
AB  - Plasmid-mediated restriction alleviation in recBC sbcBC strains is independent of the host
AB  - RecF, RecJ, and RecA proteins and phage recombination functions.  The presence of plasmids can
AB  - also relieve restriction in recD strains.  This effect depends, however, on the RecA function
AB  - in the host.  The molecular mechanism of the plasmid-mediated restriction alleviation remains
AB  - unclear.
ER  -

TY  - JOUR
AU  - Salama, N.
AU  - Guillemin, K.
AU  - McDaniel, T.K.
AU  - Sherlock, G.
AU  - Tompkins, L.
AU  - Falkow, S.
TI  - A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 14668
EP  - 14673
VL  - 97
AB  - Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide
AB  - spectrum of disease ranging from
AB  - asymptomatic gastritis to ulcers to gastric cancer. Although the basis
AB  - for these diverse clinical outcomes is not understood, more severe
AB  - disease is associated with strains harboring a pathogenicity island. To
AB  - characterize the genetic diversity of more and less virulent strains,
AB  - we examined the genomic content of 15 H. pylori clinical isolates by
AB  - using a whole genome H. pylori DNA microarray. We found that a full 22%
AB  - of H. pylori genes are dispensable in one or more strains, thus
AB  - defining a minimal functional core of 1281 H. pylori genes. While the
AB  - core genes encode most metabolic and cellular processes, the
AB  - strain-specific genes include genes unique to H. pylori, restriction
AB  - modification genes, transposases, and genes encoding cell surface
AB  - proteins, which may aid the bacteria under specific circumstances
AB  - during their long-term infection of genetically diverse hosts. We
AB  - observed distinct patterns of the strain-specific gene distribution
AB  - along the chromosome, which may result from different mechanisms of
AB  - gene acquisition and loss. Among the strain-specific genes, we have
AB  - found a class of candidate virulence genes identified by their
AB  - coinheritance with the pathogenicity island.
ER  -

TY  - JOUR
AU  - Salama, N.R.
AU  - Gonzalez-Valencia, G.
AU  - Deatherage, B.
AU  - Aviles-Jimenez, F.
AU  - Atherton, J.C.
AU  - Graham, D.Y.
AU  - Torres, J.
TI  - Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection.
JO  - J. Bacteriol.
PY  - 2007
SP  - 3834
EP  - 3845
VL  - 189
AB  - Genetic diversity of the human gastric pathogen Helicobacter pylori in an
AB  - individual host has been observed; whether this diversity represents
AB  - diversification of a founding strain or a mixed infection with distinct
AB  - strain populations is not clear. To examine this issue, we analyzed
AB  - multiple single-colony isolates from two to four separate stomach biopsies
AB  - of eight adult and four pediatric patients from a high-incidence Mexican
AB  - population. Eleven of the 12 patients contained isolates with identical
AB  - random amplified polymorphic DNA, amplified fragment length polymorphism,
AB  - and vacA allele molecular footprints, whereas a single adult patient had
AB  - two distinct profiles. Comparative genomic hybridization using
AB  - whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes
AB  - in isolates from patients with similar molecular footprints. The one
AB  - patient with distinct profiles contained two strain populations differing
AB  - at 113 gene loci, including the cag pathogenicity island virulence genes.
AB  - The two strain populations in this single host had different spatial
AB  - distributions in the stomach and exhibited very limited genetic exchange.
AB  - The total genetic divergence and pairwise genetic divergence between
AB  - isolates from adults and isolates from children were not statistically
AB  - different. We also analyzed isolates obtained 15 and 90 days after
AB  - experimental infection of humans and found no evidence of genetic
AB  - divergence, indicating that transmission to a new host does not induce
AB  - rapid genetic changes in the bacterial population in the human stomach.
AB  - Our data suggest that humans are infected with a population of closely
AB  - related strains that vary at a small number of gene loci, that this
AB  - population of strains may already be present when an infection is
AB  - acquired, and that even during superinfection genetic exchange among
AB  - distinct strains is rare.
ER  -

TY  - JOUR
AU  - Salanoubat, M. et al.
TI  - Genome sequence of the plant pathogen Ralstonia solanacearum.
JO  - Nature
PY  - 2002
SP  - 497
EP  - 502
VL  - 415
AB  - Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution
AB  - and an unusually wide host range. It is a model system for the dissection of molecular
AB  - determinants governing pathogenicity. We present here the complete genome sequence and its
AB  - analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a
AB  - 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing
AB  - evidence for the acquisition of genes through horizontal gene transfer. Regions containing
AB  - genetically mobile elements associated with the percentage of G+C bias may have an important
AB  - function in genome evolution. The genome encodes many proteins potentially associated with a
AB  - role in pathogenicity. In particular, many putative attachment factors were identified. The
AB  - complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates
AB  - were identified. Comparison with other genomes suggests that bacterial plant pathogens and
AB  - animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
ER  -

TY  - JOUR
AU  - Salauen, L.
AU  - Linz, B.
AU  - Suerbaum, S.
AU  - Saunders, N.J.
TI  - The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori.
JO  - Microbiology
PY  - 2004
SP  - 817
EP  - 830
VL  - 150
AB  - Phase variation is a common mechanism used by pathogenic bacteria to generate intra-strain
AB  - diversity that is important in niche adaptation and is strongly associated with virulence
AB  - determinants.  Previous analyses of the complete sequences of the Helicobacter pylori strains
AB  - 26695 and J99 have identified 36 putative phase-variable genes among the two genomes through
AB  - their association with homopolymeric tracts and dinucleotide repeats.  Here a comparative
AB  - analysis of the two genomes is reported and an updated and expanded list of 46 candidate
AB  - phase-variable genes in H. pylori is described.  These have been systematically investigated
AB  - by PCR and sequencing for the presence of the genes, and the presence and variability in
AB  - length of the repeats in strains 26695 and J99 and in a collection of unrelated H. pylori
AB  - strains representative of the main global subdivisions recently suggested.  This provides
AB  - supportive evidence for the phase variability of 30 of the 46 candidates.  Other differences
AB  - in this subset of genes were observed (i) in the repeats, which can be present or absent among
AB  - the strains, or stabilized in different strains and (ii) in the gene-complements of the
AB  - strains.  Differences between genes were not consistently correlated with the geographic
AB  - population distribution of the strains.  This study extends and provides new evidence for
AB  - variation of this type in H. pylori, and of the high degree of diversity of the repertoire of
AB  - genes which display phase-variable switching within individual strains.
ER  -

TY  - JOUR
AU  - Salazar, J.K.
AU  - Gonsalves, L.J.
AU  - Schill, K.M.
AU  - Sanchez, L.M.
AU  - Anderson, N.
AU  - Keller, S.E.
TI  - Complete Genome Sequence of Listeria monocytogenes DFPST0073, Isolated from Imported Mexican Soft Cheese.
JO  - Genome Announcements
PY  - 2018
SP  - e00496
EP  - e00418
VL  - 6
AB  - The genome of Listeria monocytogenes strain DFPST0073, isolated from imported fresh Mexican
AB  - soft cheese in 2003, was sequenced using the Illumina MiSeq
AB  - platform. Reads were assembled using SPAdes, and genome annotation was performed
AB  - using the NCBI Prokaryotic Genome Annotation Pipeline.
ER  -

TY  - JOUR
AU  - Saldana-Ahuactzi, Z.
AU  - Cruz-Cordova, A.
AU  - Rodea, G.E.
AU  - Porta, H.
AU  - Navarro-Ocana, A.
AU  - Eslava-Campos, C.
AU  - Cevallos, M.A.
AU  - Xicohtencatl-Cortes, J.
TI  - Genome Sequence of Enterotoxigenic Escherichia coli Strain FMU073332.
JO  - Genome Announcements
PY  - 2017
SP  - e01600
EP  - e01616
VL  - 5
AB  - Enterotoxigenic Escherichia coli (ETEC) is an important cause of bacterial diarrheal illness,
AB  - affecting practically every population worldwide, and was
AB  - estimated to cause 120,800 deaths in 2010. Here, we report the genome sequence of
AB  - ETEC strain FMU073332, isolated from a 25-month-old girl from Tlaltizapan,
AB  - Morelos, Mexico.
ER  -

TY  - JOUR
AU  - Saldanha, R.
AU  - Chen, B.
AU  - Wank, H.
AU  - Matsuura, M.
AU  - Edwards, J.
AU  - Lambowitz, A.M.
TI  - RNA and protein catalysis in group II intron splicing and mobility reactions using purified components.
JO  - Biochemistry
PY  - 1999
SP  - 9069
EP  - 9083
VL  - 38
AB  - Group II introns encode proteins with reverse transcriptase activity. These proteins also
AB  - promote RNA splicing (maturase activity) and then, with the excised intron, form a
AB  - site-specific DNA endonuclease that promotes intron mobility by reverse splicing into DNA
AB  - followed by target DNA-primed reverse transcription. Here, we used an Escherichia coli
AB  - expression system for the Lactococcus lactis group II intron Ll.LtrB to show that the
AB  - intron-encoded protein (LtrA) alone is sufficient for maturase activity, and that RNP
AB  - particles containing only the LtrA protein and excised intron RNA have site-specific DNA
AB  - endonuclease and target DNA-primed reverse transcriptase activity. Detailed analysis of the
AB  - splicing reaction indicates that LtrA is an intron-specific splicing factor that binds to
AB  - unspliced precursor RNA with a K(d) of </=0.12 pM at 30 degrees C. This binding occurs in a
AB  - rapid bimolecular reaction, which is followed by a slower step, presumably an RNA
AB  - conformational change, required for splicing to occur. Our results constitute the first
AB  - biochemical analysis of protein-dependent splicing of a group II intron and demonstrate that a
AB  - single intron-encoded protein can interact with the intron RNA to carry out a coordinated
AB  - series of reactions leading to splicing and mobility.
ER  -

TY  - JOUR
AU  - Sales, A.I.L.
AU  - Milanez, G.P.
AU  - Nascimento, L.C.
AU  - do Carmo, C.P.
AU  - da Costa, F.L.P.
AU  - Pereira, G.A.G.
AU  - Martinez, R.
AU  - Brocchi, M.
TI  - Draft Genome Sequences of Three Salmonella enterica Serovar 4,[5],12:i:- Strains  and One S. enterica Serovar Typhimurium Strain, Isolated in Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00488
EP  - e00418
VL  - 6
AB  - Draft genomes of three Salmonella enterica 4,[5],12:i:- (STi) strains isolated from human
AB  - infections were obtained using Illumina sequencing. They were negative
AB  - for the fljBA operon but positive for hin, and k-mer analyses revealed their
AB  - identity as S. enterica 4,[5],12:i:- 08-1736 and S Typhimurium. A draft S
AB  - Typhimurium sequence is described for comparison.
ER  -

TY  - JOUR
AU  - Sales, C.M.
AU  - Mahendra, S.
AU  - Grostern, A.
AU  - Parales, R.E.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Nolan, M.
AU  - Lapidus, A.
AU  - Chertkov, O.
AU  - Ovchinnikova, G.
AU  - Szcyrba, A.
AU  - Alvarez-Cohen, L.
TI  - Genome sequence of 1,4-dioxane degrading Pseudonocardia dioxanivorans strain CB1190.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4549
EP  - 4550
VL  - 193
AB  - Pseudonocardia dioxanivorans CB1190 is the first bacterium reported to be capable of growth on
AB  - the environmental contaminant 1,4-dioxane, and the
AB  - first member of the genus Pseudonocardia for which there is an annotated
AB  - genome sequence. Preliminary analysis of the genome (chromosome and three
AB  - plasmids) indicates that strain CB1190 possesses several multicomponent
AB  - monooxygenases that could be involved in the aerobic degradation of
AB  - 1,4-dioxane and other environmental contaminants.
ER  -

TY  - JOUR
AU  - Salgado-Morales, R.
AU  - Rivera-Gomez, N.
AU  - Lozano-Aguirre, B.L.F.
AU  - Hernandez-Mendoza, A.
AU  - Dantan-Gonzalez, E.
TI  - Draft Genome Sequence of a Pseudomonas aeruginosa NA04 Bacterium Isolated from an Entomopathogenic Nematode.
JO  - Genome Announcements
PY  - 2017
SP  - e00746
EP  - e00717
VL  - 5
AB  - We report the draft genome sequence of Gram-negative bacterium Pseudomonas aeruginosa NA04,
AB  - isolated from the entomopathogenic nematode Heterorhabditis
AB  - indica MOR03. The draft genome consists of 54 contigs, a length of 6.37 Mb, and a
AB  - G+C content 66.49%.
ER  -

TY  - JOUR
AU  - Salgado-Morales, R.
AU  - Rivera-Gomez, N.
AU  - Martinez-Ocampo, F.
AU  - Lozano-Aguirre, B.L.F.
AU  - Hernandez-Mendoza, A.
AU  - Dantan-Gonzalez, E.
TI  - Draft Genome Sequence of Photorhabdus luminescens HIM3 Isolated from an Entomopathogenic Nematode in Agricultural Soils.
JO  - Genome Announcements
PY  - 2017
SP  - e00745
EP  - e00717
VL  - 5
AB  - In this work, we report the draft genome sequence of Photorhabdus luminescens strain HIM3, a
AB  - symbiotic bacterium associated with the entomopathogenic nematode
AB  - Heterorhabditis indica MOR03, isolated from soil sugarcane in Yautepec, Morelos,
AB  - Mexico. These bacteria have a G+C content of 42.6% and genome size of 5.47 Mb.
ER  -

TY  - JOUR
AU  - Salipante, S.J.
AU  - Roach, D.J.
AU  - Kitzman, J.O.
AU  - Snyder, M.W.
AU  - Stackhouse, B.
AU  - Butler-Wu, S.M.
AU  - Lee, C.
AU  - Cookson, B.T.
AU  - Shendure, J.
TI  - Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains.
JO  - Genome Res.
PY  - 2014
SP  - 119
EP  - 128
VL  - 25
AB  - Large-scale bacterial genome sequencing efforts to date have provided limited information on
AB  - the most prevalent category of disease: sporadically acquired infections caused by common
AB  - pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312
AB  - blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a
AB  - common agent of sepsis and community-acquired urinary tract infections, obtained during the
AB  - course of routine clinical care at a single institution. We find that ExPEC E. coli are highly
AB  - genomically heterogeneous, consistent with pan-genome analyses encompassing the larger
AB  - species. Investigation of differential virulence factor content and antibiotic resistance
AB  - phenotypes reveals markedly different profiles among lineages and among strains infecting
AB  - different body sites. We use high-resolution molecular epidemiology to explore the dynamics of
AB  - infections at the level of individual patients, including identification of possible
AB  - person-to-person transmission. Notably, a limited number of discrete lineages caused the
AB  - majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of
AB  - bacteremic E. coli infections over a 3-yr period. We additionally use a microbial
AB  - genome-wide-association study (GWAS) approach to identify individual genes responsible for
AB  - antibiotic resistance, successfully recovering known genes but notably not identifying any
AB  - novel factors. We anticipate that in the near future, whole-genome sequencing of
AB  - microorganisms associated with clinical disease will become routine. Our study reveals what
AB  - kind of information can be obtained from sequencing clinical isolates on a large scale, even
AB  - well-characterized organisms such as E. coli, and provides insight into how this information
AB  - might be utilized in a healthcare setting.
ER  -

TY  - JOUR
AU  - Salka, I.
AU  - Srivastava, A.
AU  - Allgaier, M.
AU  - Grossart, H.P.
TI  - The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for  Humic Matter Degradation.
JO  - Genome Announcements
PY  - 2014
SP  - e01183
EP  - e01114
VL  - 2
AB  - Sphingomonas spp. are Alphaproteobacteria considered to be versatile bacteria that can utilize
AB  - a variety of natural substrates available in terrestrial and
AB  - aquatic systems. Sphingomonas sp. strain FukuSWIS1 was isolated from the
AB  - eutrophic and acidic freshwater Lake Grosse Fuchskuhle in northeastern Germany.
AB  - The strain has a genome size of 3.89 Mb, possesses a set of photosynthetic genes,
AB  - and expresses photopigment BChl a under oxic conditions. Thus, this strain
AB  - belongs to the aerobic anoxygenic phototrophic (AAP) bacteria, which are most
AB  - likely involved in humic matter degradation as indicated by the presence of
AB  - organic compound mineralizing genes.
ER  -

TY  - JOUR
AU  - Salman, V.
AU  - Berben, T.
AU  - Bowers, R.M.
AU  - Woyke, T.
AU  - Teske, A.
AU  - Angert, E.R.
TI  - Insights into the single cell draft genome of 'Candidatus Achromatium palustre'.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 28
EP  - 28
VL  - 11
AB  - 'Candidatus Achromatium palustre' was recently described as the first marine representative
AB  - of the Achromatium spp. in the Thiotrichaceae - a sister lineage
AB  - to the Chromatiaceae in the Gammaproteobacteria. Achromatium spp. belong to the
AB  - group of large sulfur bacteria as they can grow to nearly 100 mum in size and
AB  - store elemental sulfur (S(0)) intracellularly. As a unique feature, Achromatium
AB  - spp. can accumulate colloidal calcite (CaCO3) inclusions in great amounts.
AB  - Currently, both process and function of calcite accumulation in bacteria is
AB  - unknown, and all Achromatium spp. are uncultured. Recently, three single-cell
AB  - draft genomes of Achromatium spp. from a brackish mineral spring were published,
AB  - and here we present the first draft genome of a single 'Candidatus Achromatium
AB  - palustre' cell collected in the sediments of the Sippewissett Salt Marsh, Cape
AB  - Cod, MA. Our draft dataset consists of 3.6 Mbp, has a G + C content of 38.1 % and
AB  - is nearly complete (83 %). The next closest relative to the Achromatium spp.
AB  - genomes is Thiorhodovibrio sp. 907 of the family Chromatiaceae, containing
AB  - phototrophic sulfide-oxidizing bacteria.
ER  -

TY  - JOUR
AU  - Salmon-Divon, M.
AU  - Banai, M.
AU  - Bardenstein, S.
AU  - Blum, S.E.
AU  - Kornspan, D.
TI  - Complete Genome Sequence of the Live Attenuated Vaccine Strain Brucella melitensis Rev.1.
JO  - Genome Announcements
PY  - 2018
SP  - e00175
EP  - e00118
VL  - 6
AB  - Live attenuated vaccines are essential elements in control programs for the prevention of
AB  - brucellosis. Here, we report the whole-genome sequence of the
AB  - original Elberg Brucella melitensis Rev.1 vaccine strain, passage 101 (1970).
AB  - Commercial lines of the original strain have been successfully used in small
AB  - ruminants worldwide.
ER  -

TY  - JOUR
AU  - Salva-Serra, F.
AU  - Jakobsson, H.E.
AU  - Busquets, A.
AU  - Gomila, M.
AU  - Jaen-Luchoro, D.
AU  - Segui, C.
AU  - Aliaga-Lozano, F.
AU  - Garcia-Valdes, E.
AU  - Lalucat, J.
AU  - Moore, E.R.
AU  - Bennasar-Figueras, A.
TI  - Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site.
JO  - Genome Announcements
PY  - 2017
SP  - e00116
EP  - e00117
VL  - 5
AB  - The genome sequences of Pseudomonas balearica strains LS401 (CCUG 66666) and st101 (CCUG
AB  - 66667) have been determined. The strains were isolated as naphthalene
AB  - degraders from polluted marine sediment and from a sample from an oil refinery
AB  - site, respectively. These genomes provide essential data about the biodegradation
AB  - capabilities and the ecological implications of P. balearica.
ER  -

TY  - JOUR
AU  - Salva-Serra, F.
AU  - Jakobsson, H.E.
AU  - Thorell, K.
AU  - Gonzales-Siles, L.
AU  - Hallback, E.T.
AU  - Jaen-Luchoro, D.
AU  - Boulund, F.
AU  - Sikora, P.
AU  - Karlsson, R.
AU  - Svensson, L.
AU  - Bennasar, A.
AU  - Engstrand, L.
AU  - Kristiansson, E.
AU  - Moore, E.R.
TI  - Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.
JO  - Genome Announcements
PY  - 2016
SP  - e00175
EP  - e00116
VL  - 4
AB  - Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup,
AB  - isolated from a case of subacute bacterial endocarditis. Here, we
AB  - report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41
AB  - contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.
ER  -

TY  - JOUR
AU  - Salwan, R.
AU  - Swarnkar, M.K.
AU  - Singh, A.K.
AU  - Kasana, R.C.
TI  - First draft genome sequence of a member of the genus planomicrobium, isolated from the chandra river, India.
JO  - Genome Announcements
PY  - 2014
SP  - e01259
EP  - e01213
VL  - 2
AB  - We report the first draft genome sequence of a member of the genus Planomicrobium, isolated
AB  - from a soil sample from the Chandra River, located in
AB  - the cold deserts of Himachal Pradesh, India. The draft genome assembly for
AB  - Planomicrobium glaciei strain CHR43 has a size of 3,900,800 bp with a G+C content
AB  - of 46.97%.
ER  -

TY  - JOUR
AU  - Salzberg, S.L. et al.
TI  - Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
JO  - BMC Genomics
PY  - 2008
SP  - 204
EP  - 204
VL  - 9
AB  - BACKGROUND: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a
AB  - major disease that constrains production of this
AB  - staple crop in many parts of the world. We report here on the complete
AB  - genome sequence of strain PXO99A and its comparison to two previously
AB  - sequenced strains, KACC10331 and MAFF311018, which are highly similar to
AB  - one another. RESULTS: The PXO99A genome is a single circular chromosome of
AB  - 5,240,075 bp, considerably longer than the genomes of the other strains
AB  - (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083
AB  - protein-coding genes, including 87 not found in KACC10331 or MAFF311018.
AB  - PXO99A contains a greater number of virulence-associated transcription
AB  - activator-like effector genes and has at least ten major chromosomal
AB  - rearrangements relative to KACC10331 and MAFF311018. PXO99A contains
AB  - numerous copies of diverse insertion sequence elements, members of which
AB  - are associated with 7 out of 10 of the major rearrangements. A
AB  - rapidly-evolving CRISPR (clustered regularly interspersed short
AB  - palindromic repeats) region contains evidence of dozens of phage
AB  - infections unique to the PXO99A lineage. PXO99A also contains a unique,
AB  - near-perfect tandem repeat of 212 kilobases close to the replication
AB  - terminus. CONCLUSION: Our results provide striking evidence of genome
AB  - plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The
AB  - comparisons point to sources of genomic variation and candidates for
AB  - strain-specific adaptations of this pathogen that help to explain the
AB  - extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and
AB  - races that have been isolated from around the world.
ER  -

TY  - JOUR
AU  - Sam, K.K.
AU  - Lau, N.S.
AU  - Furusawa, G.
AU  - Amirul, A.A.
TI  - Draft Genome Sequence of Halophilic Hahella sp. Strain CCB-MM4, Isolated from Matang Mangrove Forest in Perak, Malaysia.
JO  - Genome Announcements
PY  - 2017
SP  - e01147
EP  - e01117
VL  - 5
AB  - Hahella sp. strain CCB-MM4 is a halophilic bacterium isolated from estuarine mangrove
AB  - sediment. The genome sequence of Hahella sp. CCB-MM4 provides insights
AB  - into exopolysaccharide biosynthesis and the lifestyle of the bacterium thriving
AB  - in a saline mangrove environment.
ER  -

TY  - JOUR
AU  - Sam, M.D.
AU  - Horton, N.C.
AU  - Nissan, T.A.
AU  - Perona, J.J.
TI  - Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 851
EP  - 861
VL  - 306
AB  - Crystal structures of EcoRV endonuclease bound in a ternary complex with cognate duplex DNA
AB  - and manganese ions have previously revealed an Mn2+-binding site located between the enzyme
AB  - and the DNA outside of the dyad-symmetric GATATC recognition sequence. In each of the two
AB  - enzyme subunits, this metal ion bridges between a distal phosphate group of the DNA and the
AB  - imidazole ring of His71. The new metal-binding site is specific to Mn2+ and is not occupied in
AB  - ternary cocrystal structures with either Mg2+ or Ca2+. Characterization of the H71A and H71Q
AB  - mutants of EcoRV now demonstrates that these distal Mn2+ sites significantly modulate activity
AB  - toward both cognate and non-cognate DNA substrates. Single-turnover and steady-state kinetic
AB  - analyses show that removal of the distal site in the mutant enzymes increases Mn2+-dependent
AB  - cleavage rates of specific substrates by tenfold. Conversely, the enhancement of non-cognate
AB  - cleavage at GTTATC sequences by Mn2+ is significantly attenuated in the mutants. As a
AB  - consequence, under Mn2+ conditions Eco RV-H71A and EcoRV-H71Q are 100 to 700-fold more
AB  - specific than the wild-type enzyme for cognate DNA relative to the GTTATC non-cognate site.
AB  - These data reveal a strong dependence of DNA cleavage efficiency upon metal ion-mediated
AB  - interactions located some 20 ? distant from the scissile phosphodiester linkages.  They also
AB  - show that discrimination of cognate versus non-cognate DNA sequences by EcoRV depends in part
AB  - on contacts with the sugar-phosphate backbone outside of the target site.
ER  -

TY  - JOUR
AU  - Sam, M.D.
AU  - Perona, J.J.
TI  - Mn2+-dependent catalysis by restriction enzymes: Pre-steady-state analysis of EcoRV endonuclease reveals burst kinetics and the origins of reduced activity.
JO  - J. Am. Chem. Soc.
PY  - 1999
SP  - 1444
EP  - 1447
VL  - 121
AB  - The origins of divalent metal-dependent catalytic properties in phosphoryl transfer by EcoRV
AB  - endonuclease have been investigated by transient kinetic methods.  Pre-steady-state
AB  - measurements on short oligodeoxynucleotide substrates reveal a burst of product formation for
AB  - both Mg2+- and Mn2+-catalyzed DNA cleavage reactions, indicating that for each metal ion the
AB  - product release step is partially or completely rate-limiting.  However, the steepness of the
AB  - burst is far greater for Mn2+ reactions, and analysis of the steady-state portions of the
AB  - reaction profiles shows that the overall rate is 6-fold slower in the presence of this
AB  - cofactor.  The strongly rate-limiting product release step in Mn2+ reactions may arise from
AB  - the higher intrinsic affinity of this metal ion for phosphates.  Single-turnover experiments
AB  - carried out with enzyme in molar excess over DNA were also used to isolate the chemical step
AB  - of the reaction.  In contrast to the slower steady-state rates, both these measurements and
AB  - the pre-steady-state reaction bursts show that the bond-breaking and bond-making steps are
AB  - significantly better catalyzed by Mn2+.  This supports models for catalysis deduced from X-ray
AB  - crystal structures of the enzyme-substrate DNA complex, in which a divalent metal ion is
AB  - directly ligated to the pro-Sp oxygen of the scissile group.
ER  -

TY  - JOUR
AU  - Sam, M.D.
AU  - Perona, J.J.
TI  - Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.
JO  - Biochemistry
PY  - 1999
SP  - 6576
EP  - 6586
VL  - 38
AB  - The rate constant for the phosphoryl transfer step in site-specific DNA cleavage by EcoRV
AB  - endonuclease has been determined as a function of pH and identity of the required divalent
AB  - metal ion cofactor, for both wild-type and T93A mutant enzymes. These measurements show
AB  - bell-shaped pH-rate curves for each enzyme in the presence of Mg2+ as a cofactor, indicating
AB  - general base catalysis for the nucleophilic attack of hydroxide ion on the scissile phosphate,
AB  - and general acid catalysis for protonation of the leaving 3'-O anion. The kinetic data
AB  - support a model for phosphoryl transfer based on wild-type and T93A cocrystal structures, in
AB  - which the ionizations of two distinct metal-ligated waters respectively generate the attacking
AB  - hydroxide ion and the proton for donation to the leaving group. The model concurs with recent
AB  - observations of two metal ions bound in the active sites of the type II restriction
AB  - endonucleases BamHI and BglI, suggesting the possibility of a similar catalytic mechanism
AB  - functioning in many or all members of this enzyme family.
ER  -

TY  - JOUR
AU  - Samad, A.
AU  - Trognitz, F.
AU  - Antonielli, L.
AU  - Compant, S.
AU  - Sessitsch, A.
TI  - High-Quality Draft Genome Sequence of an Endophytic Pseudomonas viridiflava Strain with Herbicidal Properties against Its Host, the Weed Lepidium draba L.
JO  - Genome Announcements
PY  - 2016
SP  - e01170
EP  - e01116
VL  - 4
AB  - Here, we report the draft genome sequence of Pseudomonas viridiflava strain CDRTc14 a
AB  - pectinolytic bacterium showing herbicidal activity, isolated from the
AB  - root of Lepidium draba L. growing as a weed in an Austrian vineyard. The
AB  - availability of this genome sequence allows us to investigate the genetic basis
AB  - of plant-microbe interactions.
ER  -

TY  - JOUR
AU  - Sambles, C.M.
AU  - White, D.A.
TI  - Genome Sequence of Rhodococcus sp. Strain PML026, a Trehalolipid Biosurfactant Producer and Biodegrader of Oil and Alkanes.
JO  - Genome Announcements
PY  - 2015
SP  - e00433
EP  - e00415
VL  - 3
AB  - Rhodococcus sp. strain PML026 produces an array of trehalolipid biosurfactant compounds in
AB  - order to utilize hydrophobic carbon sources, such as oils and
AB  - alkanes. Here, we report the high-quality draft genome sequence of this strain,
AB  - which has a total length of 5,168,404 bp containing 4,835 protein-coding
AB  - sequences, 12 rRNAs, and 45 tRNAs.
ER  -

TY  - JOUR
AU  - Samko, O.T.
AU  - Kalugin, A.A.
AU  - Eldarov, M.A.
AU  - Karpychev, I.V.
AU  - Anikeitcheva, N.V.
AU  - Khoroshutina, E.B.
AU  - Skryabin, K.G.
AU  - Librik, G.I.
AU  - Sokolov, N.N.
TI  - Isolation, purification and characterization of new site-specific endonucleases BciBI and BciBII produced by Bacillus circulans.
JO  - Bioorg. Khim.
PY  - 1994
SP  - 1327
EP  - 1333
VL  - 20
AB  - New site-specific endonucleases BciBI and BciBII have been detected in Bacillus circulans. The
AB  - enzymes were purified by fractionation of cell-free extract with polyethylene imine and
AB  - ammonium sulphate (40-80% of saturation) followed by chromatography on DEAE-sepharose,
AB  - blue-sepharose and phosphocellulose. The endonucleases BciBI and BciBII were separated only at
AB  - the final step of the purification -- by chromatography on the phosphocellulose column. The
AB  - yields of BciBI and BciBII were 600 and 10,000 U/g of cells. It was found that restriction
AB  - endonucleases BciBI and BciBII are isoschizomers of ClaI and BstNI, respectively.
ER  -

TY  - JOUR
AU  - Sampaio, J.L.
AU  - Ribeiro, V.B.
AU  - Campos, J.C.
AU  - Rozales, F.P.
AU  - Magagnin, C.M.
AU  - Falci, D.R.
AU  - da Silva, R.C.
AU  - Dalarosa, M.G.
AU  - Luz, D.I.
AU  - Vieira, F.J.
AU  - Antochevis, L.C.
AU  - Barth, A.L.
AU  - Zavascki, A.P.
TI  - Detection of OXA-370, an OXA-48-Related Class D beta-Lactamase, in Enterobacter hormaechei from Brazil.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 3566
EP  - 3567
VL  - 58
AB  - The class D B-lactamase OXA-48 (1) and its variants have emerged as important determinants of
AB  - carbapenem resistance in Enterobacteriaceae, representing a public health concern in some
AB  - countries (2-4). The objective of this study was to report a new OXA-48 variant.
ER  -

TY  - JOUR
AU  - Sampath, J.
AU  - Vijayakumar, M.N.
TI  - A DNA cytosine methyltransferase-like gene in Streptococcal conjugative transposon, Tn5252.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1995
SP  - 511
EP  - 511
VL  - 95
AB  - Tn5252, a 47 kb element, belongs to a distinct class of conjugative transposons mediating
AB  - multiple antibiotic resistance in Streptococci.  To determine the physical structure of the
AB  - element, fragments of transposon DNA were cloned into Escherichia coli.  However, a 3.27 kb
AB  - EcoRI segment of DNA carrying the right junction region could not be cloned on several of the
AB  - commonly used high copy E. coli plasmid vectors, even though portions of this DNA segment
AB  - could be independently cloned.  Using these the DNA sequence of this region was obtained and
AB  - was found to carry an open reading frame (ORF6).  Genbank analysis of the predicted amino acid
AB  - sequence of ORF6 detected extensive homology to a number of prokaryotic cytosine
AB  - methyltransferases.  To investigate the possible role of the cytosine methyltransferase-like
AB  - gene in the conjugative transposition of Tn5252, insertion mutagenesis of this locus was
AB  - carried out using the E. coli plasmid, pVA891.  Blot hybridization experiments confirmed the
AB  - intended insertion mutation.  The newly created strain would be used as a donor in
AB  - filter-mating experiments to determine the transferability of the element carrying the
AB  - mutation.  Also we have cloned the 3.27 kb EcoRI fragment carrying the ORF6 in a Streptococcal
AB  - plasmid, pLS1, which would be used in complementation experiments.
ER  -

TY  - JOUR
AU  - Sampath, J.
AU  - Vijayakumar, M.N.
TI  - Identification of a DNA cytosine methyltransferase gene in conjugative transposon Tn5252.
JO  - Plasmid
PY  - 1998
SP  - 63
EP  - 76
VL  - 39
AB  - The nucleotide sequence of the 3.5-kb right junction fragment of the streptococcal conjugative
AB  - transposon Tn5252 was obtained.  The DNA fragment was found to carry four putative genes one
AB  - of which displayed a high degree of similarity to prokaryotic 5C-cytosine methyltransferases
AB  - carrying multiple sequence specificities.  No cognate endonuclease gene was detected in the
AB  - sequenced DNA.  Purified methylase polypeptide synthesized in a T7 promoter-controlled
AB  - overexpression system was found to lack methylase activity while the cell extracts of host
AB  - cells containing the recombinant plasmid carrying the methylase gene were active.  In vivo
AB  - mutations in the methylase gene did not seem to affect the transferability of the element.
ER  -

TY  - JOUR
AU  - Samrakandi, M.M.
AU  - Cirillo, S.L.G.
AU  - Ridenour, D.A.
AU  - Bermudez, L.E.
AU  - Cirillo, J.D.
TI  - Genetic and phenotypic differences between Legionella pneumophila strains.
JO  - J. Clin. Microbiol.
PY  - 2002
SP  - 1352
EP  - 1362
VL  - 40
AB  - Legionnaires' disease is a potentially lethal pneumonia that is primarily due to infection by
AB  - the species Legionella pneumophila, although more than 40 other species are known. Certain L.
AB  - pneumophila subgroups, particularly serogroup 1, are associated with the majority of the
AB  - epidemics. The genetic bases for these differences in virulence have not been determined.
AB  - Three strains, AA100, JR32, and Lp01, have been used in many molecular pathogenesis studies of
AB  - L. pneumophila. We found genetic differences between these strains by PCR and Southern
AB  - analyses that may be related to their ability to cause disease. We also examined the
AB  - distribution of these genetic loci in clinical and environmental isolates of Legionella and
AB  - found a correlation between the presence of two of these loci, rtxA and lvh, and the ability
AB  - to cause disease in humans. Examination of the interactions of these strains with host cells
AB  - suggested that they differ in important phenotypic characteristics including adherence, entry,
AB  - and intracellular replication. Furthermore, in the mouse model of infection they display
AB  - differing levels of replication in lungs. These studies emphasize the importance of further
AB  - investigation into the genetic makeup of these strains, which is likely to lead to the
AB  - identification of additional factors involved in Legionella pathogenesis.
ER  -

TY  - JOUR
AU  - Samson, J.E.
AU  - Belanger, M.
AU  - Moineau, S.
TI  - Effect of the abortive infection mechanism and type III toxin/antitoxin system AbiQ on the lytic cycle of Lactococcus lactis phages.
JO  - J. Bacteriol.
PY  - 2013
SP  - 3947
EP  - 3956
VL  - 195
AB  - To survive in phage-containing environments, bacteria have evolved an array of
AB  - anti-phage systems. Similarly, phages have overcome these hurdles through various
AB  - means. Here, we investigated how phages are able to circumvent the Lactococcus
AB  - lactis AbiQ system, a type III toxin-antitoxin with antiviral activities.
AB  - Lactococcal phage-escaping mutants were obtained in the laboratory and their
AB  - genome sequenced. Three unrelated genes of unknown function were mutated in
AB  - derivatives of three distinct lactococcal siphophages: orf38 of phage P008, m1 of
AB  - phage bIL170, and e19 of phage c2. One-step growth curve experiments revealed
AB  - that the phage mutations had a fitness cost while transcriptional analyses showed
AB  - that AbiQ modified the early-expressed phage mRNAs profile. The L. lactis AbiQ
AB  - system was also transferred into E. coli MG1655 and tested against several
AB  - coliphages. While AbiQ was efficient against phages T4 (Myoviridae) and T5
AB  - (Siphoviridae), escaping mutants of only phage 2 (Myoviridae) could be isolated.
AB  - Genome sequencing revealed a mutation in gene orf210, a putative DNA polymerase.
AB  - Taken altogether, different phages genes or genes products are targeted or
AB  - involved in AbiQ phenotype. Moreover, this antiviral system is active against
AB  - various phages families infecting Gram-positive and Gram-negative bacteria. A
AB  - model for the mode of action of AbiQ is proposed.
ER  -

TY  - JOUR
AU  - Samson, J.E.
AU  - Magadan, A.H.
AU  - Sabri, M.
AU  - Moineau, S.
TI  - Revenge of the phages: defeating bacterial defences.
JO  - Nat. Rev. Microbiol.
PY  - 2013
SP  - 675
EP  - 687
VL  - 11
AB  - Bacteria and their viral predators (bacteriophages) are locked in a constant battle. In order
AB  - to proliferate in phage-rich environments, bacteria have an impressive arsenal of defence
AB  - mechanisms, and in response, phages have evolved counter-strategies to evade these antiviral
AB  - systems. In this Review, we describe the various tactics that are used by phages to overcome
AB  - bacterial resistance mechanisms, including adsorption inhibition, restriction-modification,
AB  - CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated
AB  - proteins) systems and abortive infection. Furthermore, we consider how these observations have
AB  - enhanced our knowledge of phage biology, evolution and phage-host interactions.
ER  -

TY  - JOUR
AU  - Samson, J.E.
AU  - Moineau, S.
TI  - Characterization of Lactococcus lactis phage 949 and comparison with other lactococcal phages.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 6843
EP  - 6852
VL  - 76
AB  - The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese
AB  - whey in New Zealand. This phage is a member of the Siphoviridae family and
AB  - of a rare lactococcal phage group that bears its name (949 group). It has
AB  - an icosahedral capsid (79-nm diameter) and a very long noncontractile tail
AB  - (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis
AB  - strains, a somewhat expanded host range for a rare lactococcal phage. The
AB  - abortive phage infection defense mechanisms AbiQ and AbiT strongly
AB  - inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its
AB  - double-stranded DNA (dsDNA) genome of 114,768 bp is, to date, the largest
AB  - among lactococcal phages. Its GC content was calculated at 32.7%, which is
AB  - the lowest reported for a lactococcal phage. Its 154 open reading frames
AB  - (ORFs) share limited identity with database sequences. In addition,
AB  - terminal redundancy was observed as well as the presence of six tRNAs, one
AB  - group I intron, and putative recombinases. SDS-PAGE coupled with mass
AB  - spectrometry identified 13 structural proteins. The genomes of the members
AB  - of the 10 currently known L. lactis phage groups were used to construct a
AB  - proteomic tree. Each L. lactis phage group separated into distinct genetic
AB  - clusters, validating the current classification scheme. Of note, members
AB  - of the polythetic P335 groups were clearly separated into subgroups.
ER  -

TY  - JOUR
AU  - Samuel, B.S.
AU  - Hansen, E.E.
AU  - Manchester, J.K.
AU  - Coutinho, P.M.
AU  - Henrissat, B.
AU  - Fulton, R.
AU  - Latreille, P.
AU  - Kim, K.
AU  - Wilson, R.K.
AU  - Gordon, J.I.
TI  - Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 10643
EP  - 10648
VL  - 104
AB  - The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as
AB  - hydrogen-consuming methanogenic archaea. Studies in
AB  - gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant
AB  - archaeon in the human gut ecosystem, affects the specificity and
AB  - efficiency of bacterial digestion of dietary polysaccharides, thereby
AB  - influencing host calorie harvest and adiposity. Metagenomic studies of the
AB  - gut microbial communities of genetically obese mice and their lean
AB  - littermates have shown that the former contain an enhanced representation
AB  - of genes involved in polysaccharide degradation, possess more archaea, and
AB  - exhibit a greater capacity to promote adiposity when transplanted into
AB  - germ-free recipients. These findings have led to the hypothesis that M.
AB  - smithii may be a therapeutic target for reducing energy harvest in obese
AB  - humans. To explore this possibility, we have sequenced its 1,853,160-bp
AB  - genome and compared it to other human gut-associated M. smithii strains
AB  - and other Archaea. We have also examined M. smithii's transcriptome and
AB  - metabolome in gnotobiotic mice that do or do not harbor Bacteroides
AB  - thetaiotaomicron, a prominent saccharolytic bacterial member of our gut
AB  - microbiota. Our results indicate that M. smithii is well equipped to
AB  - persist in the distal intestine through (i) production of surface glycans
AB  - resembling those found in the gut mucosa, (ii) regulated expression of
AB  - adhesin-like proteins, (iii) consumption of a variety of fermentation
AB  - products produced by saccharolytic bacteria, and (iv) effective
AB  - competition for nitrogenous nutrient pools. These findings provide a
AB  - framework for designing strategies to change the representation and/or
AB  - properties of M. smithii in the human gut microbiota.
ER  -

TY  - JOUR
AU  - Samuelson, J.C.
AU  - Morgan, R.D.
AU  - Benner, J.S.
AU  - Claus, T.E.
AU  - Packard, S.L.
AU  - Xu, S.Y.
TI  - Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 796
EP  - 805
VL  - 34
AB  - Restriction endonucleases (REases) with 8-base specificity are rare specimens in nature. NotI
AB  - from Nocardia otitidis-caviarum (recognition
AB  - sequence 5'-GCGGCCGC-3') has been cloned, thus allowing for mutagenesis
AB  - and screening for enzymes with altered 8-base recognition and cleavage
AB  - activity. Variants possessing altered specificity have been isolated by
AB  - the application of two genetic methods. In step 1, variant E156K was
AB  - isolated by its ability to induce DNA-damage in an indicator strain
AB  - expressing M.EagI (to protect 5'-NCGGCCGN-3' sites). In step 2, the E156K
AB  - allele was mutagenized with the objective of increasing enzyme activity
AB  - towards the alternative substrate site: 5'-GCTGCCGC-3'. In this procedure,
AB  - clones of interest were selected by their ability to eliminate a
AB  - conditionally toxic substrate vector and induce the SOS response. Thus,
AB  - specific DNA cleavage was linked to cell survival. The secondary
AB  - substitutions M91V, F157C and V348M were each found to have a positive
AB  - effect on specific activity when paired with E156K. For example, variant
AB  - M91V/E156K cleaves 5'-GCTGCCGC-3' with a specific activity of 8.2 x 10(4)
AB  - U/mg, a 32-fold increase over variant E156K. A comprehensive analysis
AB  - indicates that the cleavage specificity of M91V/E156K is relaxed to a
AB  - small set of 8 bp substrates while retaining activity towards the NotI
AB  - sequence.
ER  -

TY  - JOUR
AU  - Samuelson, J.C.
AU  - Xu, S.-Y.
TI  - Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 673
EP  - 683
VL  - 319
AB  - Restriction endonucleases have proven to be especially resistant to engineering altered
AB  - substrate specificity, in part, due to the requirement of a cognate DNA methyltransferase for
AB  - cellular DNA protection. The thermophilic restriction endonuclease BstYI recognizes and
AB  - cleaves all hexanucleotide sequences described by 5'-RGATCY-3' (where R=A or G and Y=C or
AB  - T). The recognition of a degenerate sequence is a relatively common feature of the more than
AB  - 3000 characterized restriction endonucleases. However, very little is known concerning
AB  - substrate recognition by such an enzyme. Our objective was to investigate the substrate
AB  - specificity of BstYI by attempting to increase the specificity to recognition of only AGATCT.
AB  - By a novel genetic selection/screening process, two BstYI variants were isolated with a
AB  - preference for AGATCT cleavage. A fundamental element of the selection process is modification
AB  - of the Escherichia coli host genomic DNA by the BglII N4-cytosine methyltransferase to protect
AB  - AGATCT sites. The amino acid substitutions resulting in a partial change of specificity were
AB  - identified and combined into one superior variant designated NN1. BstYI variant NN1 displays a
AB  - 12-fold preference for cleavage of AGATCT over AGATCC or GGATCT. Moreover, cleavage of the
AB  - GGATCC sequence is no longer detected. This study provides further evidence that laboratory
AB  - evolution strategies offer a powerful alternative to structure-guided protein design.
ER  -

TY  - JOUR
AU  - Samuelson, J.C.
AU  - Zhu, Z.
AU  - Xu, S.-y.
TI  - The isolation of strand-specific nicking endonucleases from a randomized SapI expression library.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3661
EP  - 3671
VL  - 32
AB  - The Type IIS restriction endonuclease SapI recognizes the DNA sequence 5'-GCTCTTC-3' (top
AB  - strand by convention) and cleaves downstream (N1/N4) indicating top- and bottom-strand
AB  - spacing, respectively. The asymmetric nature of DNA recognition presented the possibility that
AB  - one, if not two, nicking variants might be created from SapI. To explore this possibility, two
AB  - parallel selection procedures were designed to isolate either top-strand nicking or
AB  - bottom-strand nicking variants from a randomly mutated SapI expression library. These
AB  - procedures take advantage of a SapI substrate site designed into the expression plasmid, which
AB  - allows for in vitro selection of plasmid clones possessing a site-specific and strand-specific
AB  - nick. A procedure designed to isolate bottom-strand nicking enzymes yielded Nb.SapI-1
AB  - containing a critical R420I substitution near the end of the protein. The top-strand procedure
AB  - yielded several SapI variants with a distinct preference for top-strand cleavage. Mutations
AB  - present within the selected clones were segregated to confirm a top-strand nicking phenotype
AB  - for single variants Q240R, E250K, G271R or K273R. The nature of the amino acid substitutions
AB  - found in the selected variants provides evidence that SapI may possess two active sites per
AB  - monomer. This work presents a framework for establishing the mechanism of SapI DNA cleavage.
ER  -

TY  - JOUR
AU  - San Martin-Uriz, P.
AU  - Gomez, M.J.
AU  - Arcas, A.
AU  - Bargiela, R.
AU  - Amils, R.
TI  - Draft Genome Sequence of the Electricigen Acidiphilium sp. Strain PM (DSM 24941).
JO  - J. Bacteriol.
PY  - 2011
SP  - 5585
EP  - 5586
VL  - 193
AB  - Acidiphilium sp. strain PM (DSM 24941) was isolated from Rio Tinto's acidic, heavy metal-rich
AB  - waters. Voltammetry experiments revealed that
AB  - this strain is capable of electricity production even under aerobic
AB  - conditions. Here we report the draft genome sequence of Acidiphilium sp.
AB  - PM and a preliminary genome analysis that reveals a versatile respiratory
AB  - metabolism.
ER  -

TY  - JOUR
AU  - Sanabria, L.
AU  - Lagrave, L.
AU  - Nishibe, C.
AU  - Ribas, A.C.A.
AU  - Zumarraga, M.J.
AU  - Almeida, N.F.
AU  - Araujo, F.R.
TI  - Draft Genome Sequences of Two Mycobacterium bovis Strains Isolated from Beef Cattle in Paraguay.
JO  - Genome Announcements
PY  - 2017
SP  - e00616
EP  - e00617
VL  - 5
AB  - This work reports the draft genome sequences of the Mycobacterium bovis strains M1009 and
AB  - M1010, isolated from the lymph nodes of two infected cows on a beef
AB  - farm in Paraguay. Comparative genomics between these strains and other regional
AB  - strains may provide more insights regarding M. bovis epidemiology in South
AB  - America.
ER  -

TY  - JOUR
AU  - Sanchez, D.O.
AU  - Zandomeni, R.O.
AU  - Cravero, S.
AU  - Verdun, R.E.
AU  - Pierrou, E.
AU  - Faccio, P.
AU  - Diaz, G.
AU  - Lanzavecchia, S.
AU  - Aguero, F.
AU  - Frasch, A.C.C.
AU  - Andersson, S.G.E.
AU  - Rosetti, O.L.
AU  - Grau, O.
AU  - Ugalde, R.A.
TI  - Gene discovery through genomic sequencing of Brucella abortus.
JO  - Infect. Immun.
PY  - 2001
SP  - 865
EP  - 868
VL  - 69
AB  - Brucella abortus is the etiological agent of brucellosis, a disease that
AB  - affects bovines and human. We generated DNA random sequences from the
AB  - genome of B. abortus strain 2308 in order to characterize molecular
AB  - targets that might be useful for developing immunological or
AB  - chemotherapeutic strategies against this pathogen. The partial sequencing
AB  - of 1,899 clones allowed the identification of 1,199 genomic sequence
AB  - surveys (GSSs) with high homology (BLAST expect value < 10(-5)) to
AB  - sequences deposited in the GenBank databases. Among them, 925 represent
AB  - putative novel genes for the Brucella genus. Out of 925 nonredundant GSSs,
AB  - 470 were classified in 15 categories based on cellular function. Seven
AB  - hundred GSSs showed no significant database matches and remain available
AB  - for further studies in order to identify their function. A high number of
AB  - GSSs with homology to Agrobacterium tumefaciens and Rhizobium meliloti
AB  - proteins were observed, thus confirming their close phylogenetic
AB  - relationship. Among them, several GSSs showed high similarity with genes
AB  - related to nodule nitrogen fixation, synthesis of nod factors, nodulation
AB  - protein symbiotic plasmid, and nodule bacteroid differentiation. We have
AB  - also identified several B. abortus homologs of virulence and pathogenesis
AB  - genes from other pathogens, including a homolog to both the Shda gene from
AB  - Salmonella enterica serovar Typhimurium and the AidA-1 gene from
AB  - Escherichia coli. Other GSSs displayed significant homologies to genes
AB  - encoding components of the type III and type IV secretion machineries,
AB  - suggesting that Brucella might also have an active type III secretion
AB  - machinery.
ER  -

TY  - JOUR
AU  - Sanchez, J.
AU  - Barbes, C.
AU  - Hernandez, A.
AU  - de los Reyes-Gavilan, C.G.
AU  - Hardisson, C.
TI  - Restriction-modification systems in Streptomyces antibioticus.
JO  - Can. J. Microbiol.
PY  - 1985
SP  - 942
EP  - 946
VL  - 31
AB  - Several restriction systems were detected in different strains of Streptomyces
AB  - antibioticus by using actinophages as biological indicators. Adsorption of
AB  - phages to the bacteria, together with the study of the efficiency of plating
AB  - gave an initial indication of restriction in three strains. The alternation of
AB  - efficiency of plating values obtained from restricting and nonrestricting
AB  - hosts, detected among the different strains tested. Two specific endonucleases
AB  - with a possible role in restriction were detected in strains ATCC 11891 and ETH
AB  - 7451, respectively.
ER  -

TY  - JOUR
AU  - Sanchez-Canizares, C.
AU  - Jorrin, B.
AU  - Duran, D.
AU  - Nadendla, S.
AU  - Albareda, M.
AU  - Rubio-Sanz, L.
AU  - Lanza, M.
AU  - Gonzalez-Guerrero, M.
AU  - Prieto, R.
AU  - Brito, B.
AU  - Giglio, M.
AU  - Rey, L.
AU  - Ruiz-Argueso, T.
AU  - Palacios, J.M.
AU  - Imperial, J.
TI  - Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum.
JO  - Genes (Basel)
PY  - 2018
SP  - E60
EP  - E60
VL  - 9
AB  - Rhizobium leguminosarum bv. viciae is a soil -proteobacterium that establishes a diazotrophic
AB  - symbiosis with different legumes of the Fabeae tribe. The number of genome sequences from
AB  - rhizobial strains available in public databases is constantly increasing, although complete,
AB  - fully annotated
AB  - genome structures from rhizobial genomes are scarce. In this work, we report and analyse the
AB  - complete genome of R. leguminosarum bv. viciae UPM791. Whole genome sequencing can provide new
AB  - insights into the genetic features contributing to symbiotically relevant processes such as
AB  - bacterial
AB  - adaptation to the rhizosphere, mechanisms for efficient competition with other bacteria, and
AB  - the ability to establish a complex signalling dialogue with legumes, to enter the root without
AB  - triggering plant defenses, and, ultimately, to fix nitrogen within the host. Comparison of the
AB  - complete genome sequences of two strains of R. leguminosarum bv. viciae, 3841 and UPM791,
AB  - highlights the existence of different symbiotic plasmids and a common core chromosome.
AB  - Specific genomic traits, such as plasmid content or a distinctive regulation, define
AB  - differential physiological capabilities of these endosymbionts. Among them, strain UPM791
AB  - presents unique adaptations for recycling the hydrogen generated in the nitrogen fixation
AB  - process.
ER  -

TY  - JOUR
AU  - Sanchez-Castro, I.
AU  - Bakkali, M.
AU  - Merroun, M.L.
TI  - Draft Genome Sequence of Stenotrophomonas bentonitica BII-R7T, a Selenite-Reducing Bacterium Isolated from Spanish Bentonites.
JO  - Genome Announcements
PY  - 2017
SP  - e00719
EP  - e00717
VL  - 5
AB  - The Gram-negative bacterium Stenotrophomonas bentonitica BII-R7T was isolated from bentonite
AB  - formations. Like other species within the genus Stenotrophomonas,
AB  - strain BII-R7T possesses high tolerance to numerous heavy metals, suggesting
AB  - potential for bioremediation purposes. The draft genome sequence reported here
AB  - comprises 4.37 Mb with a G+C content of 66.5% and 3,796 predicted protein-coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Sanchez-Leon, M.
AU  - Fashae, K.
AU  - Kastanis, G.
AU  - Allard, M.
TI  - Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in  Ibadan, Nigeria, Representing 21 Salmonella Serovars.
JO  - Genome Announcements
PY  - 2017
SP  - e01128
EP  - e01117
VL  - 5
AB  - To provide a better understanding of the diversity of Salmonella enterica, we report the
AB  - assembled genome sequences of 23 Salmonella enterica strains isolated from fecal samples of
AB  - cattle in Nigeria comprising 21 different Salmonella serovars.
ER  -

TY  - JOUR
AU  - Sanchez-Porro, C.
AU  - de la Haba, R.R.
AU  - Cruz-Hernandez, N.
AU  - Gonzalez, J.M.
AU  - Reyes-Guirao, C.
AU  - Navarro-Sampedro, L.
AU  - Carballo, M.
AU  - Ventosa, A.
TI  - Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae.
JO  - Genome Announcements
PY  - 2013
SP  - e0008313
EP  - e0008313
VL  - 1
AB  - Halomonas titanicae strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated
AB  - from rusticles of the RMS Titanic wreck. Here we report the draft
AB  - genome sequence of this halophilic gammaproteobacterium.
ER  -

TY  - JOUR
AU  - Sanchez-Romero, M.A.
AU  - Cota, I.
AU  - Casadesus, J.
TI  - DNA methylation in bacteria: from the methyl group to the methylome.
JO  - Curr. Opin. Microbiol.
PY  - 2015
SP  - 9
EP  - 16
VL  - 25
AB  - Formation of C(5)-methyl-cytosine, N(4)-methyl-cytosine, and N(6)-methyl-adenine  in bacterial
AB  - genomes is postreplicative, and occurs at specific targets. Base methylation can modulate the
AB  - interaction of DNA-binding proteins with their cognate sites, and controls chromosome
AB  - replication, correction of DNA mismatches, cell cycle-coupled transcription, and formation of
AB  - epigenetic lineages by phase variation. During four decades, the roles of DNA methylation in
AB  - bacterial physiology have been investigated by analyzing the contribution of individual methyl
AB  - groups or small methyl group clusters to the control of DNA-protein interactions. Nowadays,
AB  - single-molecule real-time sequencing can analyze the DNA methylation of the entire genome (the
AB  - 'methylome'). Bacterial methylomes provide a wealth of information on the methylation marks
AB  - present in bacterial genomes, and may open a new era in bacterial epigenomics.
ER  -

TY  - JOUR
AU  - Sanchez-Vizuete, P.
AU  - Tanaka, K.
AU  - Bridier, A.
AU  - Shirae, Y.
AU  - Yoshida, K.
AU  - Bouchez, T.
AU  - Aymerich, S.
AU  - Briandet, R.
AU  - Le Coq, D.
TI  - Genome Sequences of Two Nondomesticated Bacillus subtilis Strains Able To Form Thick Biofilms on Submerged Surfaces.
JO  - Genome Announcements
PY  - 2014
SP  - e00946
EP  - e00914
VL  - 2
AB  - Genomes of two nondomesticated strains of Bacillus subtilis subspecies subtilis,  NDmed and
AB  - NDfood, have been sequenced. Both strains form very thick and spatially
AB  - complex biofilms on submerged surfaces. Moreover, biofilms of the NDmed isolate
AB  - were shown to be highly resistant to antimicrobials action.
ER  -

TY  - JOUR
AU  - Sandal, I.
AU  - Seleem, M.N.
AU  - Elswaifi, S.F.
AU  - Sriranganathan, N.
AU  - Inzana, T.J.
TI  - Construction of a high-efficiency shuttle vector for Histophilus somni.
JO  - J. Microbiol. Methods
PY  - 2008
SP  - 106
EP  - 109
VL  - 74
AB  - The genetic manipulation of Histophilus somni is limited due to its high-fidelity
AB  - restriction-modification system. The broad host-range
AB  - shuttle plasmid pLS88 is capable of transforming some strains of H.
AB  - somni, but is an inefficient vector. We have constructed an improved
AB  - version of pLS88, pNS3K, that transforms H. somni strain 2336 100-fold
AB  - more efficiently than its predecessor. The transformation efficiency
AB  - was further increased when pNS3K was isolated from H. somni and
AB  - retransformed into the same strain. As proof of principle, the
AB  - lipooligosaccharide biosynthesis gene lob-2A was cloned into pNS3K and
AB  - expressed in H. somni strain 129Pt, which lacks this gene. Thus, pNS3K
AB  - is a useful shuttle vector for H. somni and a potential vector for
AB  - genetic manipulation of this bacterium.
ER  -

TY  - JOUR
AU  - Sandegren, L.
AU  - Linkevicius, M.
AU  - Lytsy, B.
AU  - Melhus, A.
AU  - Andersson, D.I.
TI  - Transfer of an Escherichia coli ST131 multiresistance cassette has created a Klebsiella pneumoniae-specific plasmid associated with a major nosocomial outbreak.
JO  - J. Antimicrob. Chemother.
PY  - 2012
SP  - 74
EP  - 83
VL  - 67
AB  - ObjectivesTo characterize the complete sequence, horizontal spread and
AB  - stability of the CTX-M-15-encoding multiresistance plasmid of a Klebsiella
AB  - pneumoniae strain involved in a large nosocomial outbreak.MethodsThe 220
AB  - kbp plasmid pUUH239.2 was completely sequenced using 454 technology. The
AB  - conjugational host range, conjugation frequencies, plasmid stability and
AB  - fitness cost of plasmid carriage were studied in vitro. Conjugational
AB  - spread during the outbreak was assessed retrospectively by multiplex PCR
AB  - screening, restriction fragment length polymorphism and
AB  - PFGE.ResultsPlasmid pUUH239.2 encodes resistance to beta-lactams
AB  - (bla(CTX-M-15), bla(TEM-1) and bla(OXA-1)), aminoglycosides
AB  - [aac-(6')-1b-cr and aadA2], tetracyclines [tet(A) and tetR], trimethoprim
AB  - (dhfrXII), sulphonamides (sul1), quaternary ammonium compounds
AB  - (qacEDelta1), macrolides [mph(A)-mxr-mphR(A)] and heavy metal ions
AB  - (silver, copper and arsenic). The plasmid consists of a backbone, highly
AB  - similar to the K. pneumoniae plasmid pKPN3, and a 41 kbp resistance
AB  - region, highly similar to the resistance regions of plasmids pEK499 and
AB  - pC15-1a previously isolated from Escherichia coli strains belonging to the
AB  - outbreak lineage ST131 (where ST stands for sequence type). The pUUH239.2
AB  - plasmid is stable in K. pneumoniae but unstable in E. coli and confers a
AB  - fitness cost when introduced into a naive host cell. Transfer of pUUH239.2
AB  - from the outbreak K. pneumoniae clone to the E. coli of the patients'
AB  - intestinal floras has occurred on multiple occasions during the
AB  - outbreak.ConclusionsThe plasmid pUUH239.2 is a composite of the pKPN3 K.
AB  - pneumoniae plasmid backbone and the bla(CTX-M-15)-encoding multiresistance
AB  - cassette associated with the internationally recognized outbreak strain E.
AB  - coli ST131. The resulting plasmid differs in stability between K.
AB  - pneumoniae and E. coli, and this has probably limited the spread of this
AB  - plasmid during the outbreak.
ER  -

TY  - JOUR
AU  - Sandegren, L.
AU  - Nord, D.
AU  - Sjoberg, B.M.
TI  - SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 6203
EP  - 6213
VL  - 33
AB  - T4 contains two groups of genes with similarity to homing endonucleases, the seg-genes ((s)
AB  - over bar imilarity to (e) over bar
AB  - ndonucleases encoded by (g) over bar roup I introns) containing GIY-YIG
AB  - motifs and the mob-genes (similarity to mobile endonucleases)
AB  - containing H-N-H motifs. The four seg-genes characterized to date
AB  - encode homing endonucleases with cleavage sites close to their
AB  - respective gene loci while none of the mob-genes have been shown to
AB  - cleave DNA. Of 18 phages screened, only T4 was found to have mobC while
AB  - mobE genes were found in five additional phages. Interestingly, three
AB  - phages encoded a seg-like gene (hereby called segH) with a GIY-YIG
AB  - motif in place of mobC. An additional phage has an unrelated gene
AB  - called hef ((h) over bar oming (e) over bar ndonuclease-like (f) over
AB  - bar unction) in place of the mobE gene. The gene products of both novel
AB  - genes displayed homing endonuclease activity with cleavage site
AB  - specificity close to their respective genes. In contrast to intron
AB  - encoded homing endonucleases, both SegH and Hef can cleave their own
AB  - DNA as well as DNA from phages without the genes. Both segH and mobE
AB  - (and most likely hef) can home between phages in mixed infections. We
AB  - discuss why it might be a selective advantage for phage freestanding
AB  - homing endonucleases to cleave both HEG-containing and HEG-less
AB  - genomes.
ER  -

TY  - JOUR
AU  - Sandegren, L.
AU  - Sjoberg, B.M.
TI  - Distribution, sequence homology, and homing of group I introns among T-even-like bacteriophages: evidence for recent transfer of old introns.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 22218
EP  - 22227
VL  - 279
AB  - Self-splicing group I introns are being found in an increasing number of bacteriophages. Most
AB  - introns contain an open reading frame coding for a homing endonuclease that confers mobility
AB  - to both the intron and the homing endonuclease gene (HEG). The frequent occurrence of
AB  - intron/HEG has raised questions whether group I introns are spread via horizontal transfer
AB  - between phage populations. We have determined complete sequences for the known group I introns
AB  - among T-even-like bacteriophages together with sequences of the intron-containing genes td,
AB  - nrdB, and nrdD from phages with and without introns. A previously uncharacterized phage
AB  - isolate, U5, is shown to contain all three introns, the only phage besides T4 found with a
AB  - "full set" of these introns. Sequence analysis of td and nrdB genes from intron-containing and
AB  - intronless phages provides evidence that recent horizontal transmission of introns has
AB  - occurred among the phages. The fact that several of the HEGs have suffered deletions rendering
AB  - them non-functional implies that the homing endonucleases are of no selective advantage to the
AB  - phage and are rapidly degenerating and probably dependent upon frequent horizontal
AB  - transmissions for maintenance within the phage populations. Several of the introns can home to
AB  - closely related intronless phages during mixed infections. However, the efficiency of homing
AB  - varies and is dependent on homology in regions flanking the intron insertion site. The
AB  - occurrence of optional genes flanking the respective intron-containing gene can strongly
AB  - affect the efficiency of homing. These findings give further insight into the mechanisms of
AB  - propagation and evolution of group I introns among the T-even-like bacteriophages.
ER  -

TY  - JOUR
AU  - Sanders, K.L.
AU  - Catto, L.E.
AU  - Bellamy, S.R.
AU  - Halford, S.E.
TI  - Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 2105
EP  - 2115
VL  - 37
AB  - Many restriction endonucleases are dimers that act symmetrically at palindromic DNA sequences,
AB  - with each active site cutting one strand. In
AB  - contrast, FokI acts asymmetrically at a non-palindromic sequence, cutting
AB  - 'top' and 'bottom' strands 9 and 13 nucleotides downstream of the site.
AB  - FokI is a monomeric protein with one active site and a single monomer
AB  - covers the entire recognition sequence. To cut both strands, the monomer
AB  - at the site recruits a second monomer from solution, but it is not yet
AB  - known which DNA strand is cut by the monomer bound to the site and which
AB  - by the recruited monomer. In this work, mutants of FokI were used to show
AB  - that the monomer bound to the site made the distal cut in the bottom
AB  - strand, whilst the recruited monomer made in parallel the proximal cut in
AB  - the top strand. Procedures were also established to direct FokI activity,
AB  - either preferentially to the bottom strand or exclusively to the top
AB  - strand. The latter extends the range of enzymes for nicking specified
AB  - strands at specific sequences, and may facilitate further applications of
AB  - FokI in gene targeting.
ER  -

TY  - JOUR
AU  - Sanders, M.E.
TI  - Phage resistance in lactic acid bacteria.
JO  - Biochimie
PY  - 1988
SP  - 411
EP  - 422
VL  - 70
AB  - The interactions between lactic acid bacteria and their phages are commercially
AB  - significant.  Current research has focused on the elucidation of the mechanisms
AB  - and genetics of phage resistance.  Phage resistance genes have been linked to
AB  - plasmid DNA for Streptococcus lactis and Streptococcus cremoris, and
AB  - preliminary studies suggest the operation of mechanisms such as the prevention
AB  - of phage adsorption, restriction/modification, and abortive infection.  Some
AB  - phage resistance plasmids can be conjugally transferred, providing a means of
AB  - dissemination among phage-sensitive strains for the construction of
AB  - phage-resistant starter cultures.
ER  -

TY  - JOUR
AU  - Sanders, M.E.
AU  - Klaenhammer, T.R.
TI  - Evidence for plasmid linkage of restriction and modification in Streptococcus cremoris KH.
JO  - Appl. Environ. Microbiol.
PY  - 1981
SP  - 944
EP  - 950
VL  - 42
AB  - Restriction and modification have been demonstrated in Streptococcus cremoris
AB  - KH cells when infected by Streptococcus lactis C2 phage (designated c2) at an
AB  - efficiency of plating of 2 X 10-7.  The growth of c2 phage through KH cells
AB  - produces modified progeny phage capable of unrestricted growth on KH cells.
AB  - The ability of single-colony isolates of S. cremoris KH cultures to restrict
AB  - and modify c2 phage was found to be variable.  From 2 to 6.5% of colonies
AB  - isolated were partially deficient in restrictive capacity, permitting a greater
AB  - plaquing ability by c2 phage of 1.8 to 2.9 log cycles.  No completely
AB  - restrictionless mutants were isolated from 1,000 colonies examined.  Mutants
AB  - were shown to be deficient in both restriction and modification capabilities of
AB  - the same specificity.  The frequent occurrence of a genotypic change that
AB  - resulted in the loss of both restriction and modification capacities indicated
AB  - the involvement of plasmid deoxyribonucleic acid in genetically determining
AB  - this specific restriction and modification system.  S. cremoris KH was found to
AB  - harbor 11 plasmid molecules, with molecular weights (X10-6) estimated to be 50,
AB  - 41, 24, 18, 10, 7.4, 3.3, 3.0, 2.8, 2.5, and 1.5.  Of the 27 mutants examined,
AB  - 25 were missing the 10-megadalton plasmid.  This consistent plasmid difference
AB  - among the majority of mutants isolated supports the involvement of this plasmid
AB  - in restriction and modification.  Plasmid linkage of restriction and
AB  - modification systems provides a genetic mechanism for the rapid development of
AB  - phage-sensitive starter cultures due to the inherent instability of
AB  - extrachromosomal elements.
ER  -

TY  - JOUR
AU  - Sanders, M.E.
AU  - Klaenhammer, T.R.
TI  - Phage resistance in a phage-insensitive strain of Streptococcus lactis:  temperature-dependent phage development and host-controlled phage replication.
JO  - Appl. Environ. Microbiol.
PY  - 1984
SP  - 979
EP  - 985
VL  - 47
AB  - Streptococcus lactis ME2 is a dairy starter strain that is insensitive to a
AB  - variety of phage, including Phi18.  The efficiency of plating of Phi18 on ME2
AB  - and N1 could be increased from <1 X 10-9 to 5.0 X 10-2 and from 7.6 X 10-7 to
AB  - 2.1 X 10-2, respectively, when the host strains were subcultured at 40C before
AB  - plating the phage and the phage assay plates were incubated at 40C.
AB  - Host-dependent replication was demonstrated in N1 at 30C and in N1 and ME2 at
AB  - 40C, suggesting the operation of a temperature-sensitive restriction and
AB  - modification system in MER2 and N1.  The increased sensitivity of ME2 and N1 to
AB  - Phi18 at 40C was also demonstrated by lysis of broth cultures and increased
AB  - plaque size.  ME2 grown at 40C showed an increased ability to adsorb Phi18,
AB  - indicating a second target for temperature-dependent phage sensitivity in ME2.
AB  - Challenge of N1 with a Phi18 preparation that had been previously modified for
AB  - growth on N1 indicated that at 40C phage development was characterized by a
AB  - shorter latent period and larger burst size than at 30C.  The evidence
AB  - presented suggests that the high degree of phage insensitivity expressed by ME2
AB  - consists of a variety of temperature-sensitive mechanisms, including (i) the
AB  - prevention of phage adsorption, (ii) host-controlled restriction of phage, and
AB  - (iii) suppression of phage development.  At 30C these factors appear to act
AB  - cooperatively to prevent the successful emergence of lytic phage active against
AB  - S. lactis ME2.
ER  -

TY  - JOUR
AU  - Sanders, M.E.
AU  - Klaenhammer, T.R.
TI  - Restriction and modification in group N streptococci: Effect of heat on development of modified lytic bacteriophage.
JO  - Appl. Environ. Microbiol.
PY  - 1980
SP  - 500
EP  - 506
VL  - 40
AB  - The appearance of lytic bacteriophage against newly introduced starter strains used during
AB  - commercial cheese manufacture occurs rapidly, and their origin is not well understood.  In
AB  - this study, members of the group N streptococci were examined for the presence of
AB  - bacteriophage restriction and modification systems.  Two streptococcal phages from
AB  - Streptococcus cremoris TR and Streptococcus lactis C2 (phage designations tr and c2) showed
AB  - restricted lytic development on S. cremoris 799 and KH, respectively.  Efficiency of plaquing
AB  - was 1.9 x 10^-7 for tr plaqued on 799 and 2.1 x 10^-7 for c2 plaqued on KH.  After passage
AB  - through the restrictive hosts, these phages demonstrated high  lytic ability for formerly
AB  - restrictive hosts.  Stress of the restrictive host strains at temperatures of 40 to 50oC
AB  - resulted in a significant increase in the efficiency of plaquing of restricted bacteriophages.
AB  - Elevated temperatures are encountered during commercial cheese manufacture.  The results
AB  - suggested that the temporary loss of host restriction activity with the resulting modification
AB  - of nonspecific bacteriophage may contribute directly to the appearance of lytic phage against
AB  - new starter strains.
ER  -

TY  - JOUR
AU  - Sanders, M.E.
AU  - Klaenhammer, T.R.
TI  - Characterization of phage-sensitive mutants from a phage-insensitive strain of Streptococcus lactis: Evidence for a plasmid determinant that prevents phage adsorption.
JO  - Appl. Environ. Microbiol.
PY  - 1983
SP  - 1125
EP  - 1133
VL  - 46
AB  - A phage-insensitive strain of Streptococcus lactis, designated ME2, was used as a prototype
AB  - strain for the study of mechanisms and genetics of phage resistance in the lactic
AB  - streptococci.  Mutants sensitive to a Streptococcus cremoris phage, Phi18, were isolated at a
AB  - level of 17% from cultures of ME2 after sequential transfer at 30oC.  Phage-sensitive mutants
AB  - of ME2 were not fully permissive to Phi18.  The efficiency of plating of Phi18 on the mutants
AB  - was 5 x 10^-7 as compared with <10^-0 for Phi18 on ME2.  Further characterization of the
AB  - mutants showed that they efficiently adsorbed Phi18 at levels of >99.8%, whereas ME2 adsorbed
AB  - only 20 to 40% of Phi18.  These results suggest that increased phage susceptibility of the
AB  - mutants may result from the loss of a mechanism that inhibits phage adsorption.  Moreover, the
AB  - high frequency of spontaneous mutation in ME2 indicates the involvement of an unstable genetic
AB  - determinant in this phage defense mechanism.  ME2 was shown to possess 13 plasmids ranging in
AB  - size from 1.6 to 34 megadaltons.  Of 40 mutants examined that had increased efficiencies of
AB  - plating, all were missing a 30-megadalton plasmid, pME0030.  These data suggest that pME0030
AB  - codes for a function that prevents phage adsorption.  Further phenotypic characterization of
AB  - the phage-sensitive mutants showed that some mutants were deficient in the ability to ferment
AB  - lactose and hydrolyze milk proteins.  However, the Lac+ and Prt+ phenotype segregated
AB  - independently of the phage-sensitivity phenotype.  One phage-sensitive adsorption mutant,
AB  - designated N1, was tested for susceptibility to 14 different phages.  N1 showed increased
AB  - capacity to adsorb 4 and to replicate 2 of these 14 phages, thereby indicating a phage
AB  - resistance mechanism in ME2 that generalizes to phage interactions other than the specific
AB  - o18-ME2 phage-host interaction.  These data provide evidence for a unique plasmid-linked phage
AB  - defense mechanism in phage-insensitive strains of lactic streptococci.
ER  -

TY  - JOUR
AU  - Sanders, M.E.
AU  - Shultz, J.W.
TI  - Cloning of phage resistance genes from Lactococcus lactis ssp. cremoris KH.
JO  - J. Dairy Sci.
PY  - 1990
SP  - 2044
EP  - 2053
VL  - 73
AB  - A 17.5-kb plasmid conferring restriction and modification-type phage resistance
AB  - in Lactococcus lactis ssp. cremoris KH was transformed into Lactococcus lactis
AB  - LM0230 and cloned onto an origin of replication-deficient vector directly into
AB  - L. lactis.  Expression of phage resistance was seen in L. lactis but not in E.
AB  - coli.  A restriction map was generated of the cloned plasmid, and the region
AB  - encoding phage resistance was localized by insertional inactivation and
AB  - deletion analysis.
ER  -

TY  - JOUR
AU  - Sandner-Miranda, L.
AU  - Vinuesa, P.
AU  - Soberon-Chavez, G.
AU  - Morales-Espinosa, R.
TI  - Complete Genome Sequence of Serratia marcescens SmUNAM836, a Nonpigmented Multidrug-Resistant Strain Isolated from a Mexican Patient with Obstructive  Pulmonary Disease.
JO  - Genome Announcements
PY  - 2016
SP  - e01417
EP  - e01415
VL  - 4
AB  - Serratia marcescens SmUNAM836 is a multidrug-resistant clinical strain isolated in Mexico City
AB  - from a patient with chronic obstructive pulmonary disease. Its
AB  - complete genome sequence was determined using PacBio RS II SMRT technology,
AB  - consisting of a 5.2-Mb chromosome and a 26.3-kb plasmid, encoding multiple
AB  - resistance determinants and virulence factors.
ER  -

TY  - JOUR
AU  - Sandoval, N.R.
AU  - Venkataramanan, K.P.
AU  - Groth, T.S.
AU  - Papoutsakis, E.T.
TI  - Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth.
JO  - Biotechnol. Biofuels.
PY  - 2015
SP  - 227
EP  - 227
VL  - 8
AB  - BACKGROUND: Biodiesel production results in crude glycerol waste from the transesterification
AB  - of fatty acids (10 % w/w). The solventogenic Clostridium
AB  - pasteurianum, an anaerobic Firmicute, can produce butanol from glycerol as the
AB  - sole carbon source. Coupling butanol fermentation with biodiesel production can
AB  - improve the overall economic viability of biofuels. However, crude glycerol
AB  - contains growth-inhibiting byproducts which reduce feedstock consumption and
AB  - solvent production. RESULTS: To obtain a strain with improved characteristics, a
AB  - random mutagenesis and directed evolution selection technique was used. A
AB  - wild-type C. pasteurianum (ATCC 6013) culture was chemically mutagenized, and the
AB  - resulting population underwent 10 days of selection in increasing concentrations
AB  - of crude glycerol (80-150 g/L). The best-performing mutant (M150B) showed a 91 %
AB  - increase in butanol production in 100 g/L crude glycerol compared to the
AB  - wild-type strain, as well as increased growth rate, a higher final optical
AB  - density, and less production of the side product PDO (1,3-propanediol). Wild-type
AB  - and M150B strains were sequenced via Single Molecule Real-Time (SMRT) sequencing.
AB  - Mutations introduced to the M150B genome were identified by sequence comparison
AB  - to the wild-type and published closed sequences. A major mutation (a deletion) in
AB  - the gene of the master transcriptional regulator of sporulation, Spo0A, was
AB  - identified. A spo0A single gene knockout strain was constructed using a
AB  - double--crossover genome-editing method. The Spo0A-deficient strain showed
AB  - similar tolerance to crude glycerol as the evolved mutant strain M150B.
AB  - Methylation patterns on genomic DNA identified by SMRT sequencing were used to
AB  - transform plasmid DNA to overcome the native C. pasteurianum restriction
AB  - endonuclease. CONCLUSIONS: Solvent production in the absence of Spo0A shows C.
AB  - pasteurianum differs in solvent-production regulation compared to other
AB  - solventogenic Clostridium. Growth-associated butanol production shows C.
AB  - pasteurianum to be an attractive option for further engineering as it may prove a
AB  - better candidate for butanol production through continuous fermentation.
ER  -

TY  - JOUR
AU  - Sands, T.W.
AU  - Petras, M.L.
AU  - Van Wijngaarden, J.
TI  - A computer program to assist in the choice of restriction endonucleases for use in DNA analysis.
JO  - Int. J. Biomed. Comput.
PY  - 1990
SP  - 39
EP  - 52
VL  - 26
AB  - Type II restriction endonucleases cleave double stranded DNA molecules at sites characterized
AB  - by one or more sets of nucleotide pairs sequences. These digestions are essential in such
AB  - procedures as DNA cloning, DNA sequencing and restriction fragment length polymorphism (RFLP)
AB  - analyses. A large number of enzymes with different sequence specificities are available. To
AB  - date, most choices of restriction endonucleases have been made by trial and error. A computer
AB  - program, REDI, has been developed that predicts the ability of a particular restriction enzyme
AB  - to detect mutations. Characteristics of both the restriction endonuclease used and the DNA
AB  - being cut are incorporated as variables in the program. The program was tested using mouse
AB  - mitochondrial DNA (mtDNA) and bacteriophage lambda DNA because these have been sequenced and
AB  - are well characterized. REDI was strongly correlated (rs = +0.862, n = 11, P less than 0.001)
AB  - with mouse mtDNA RFLP detected by Ferris et al. [1] (Genetics, 105 (1983) 681-721). Even
AB  - though predictions may be altered by a non-random association of nucleotides, which varies
AB  - among DNA molecules, the predictions increase the probability of selecting the most efficient
AB  - enzymes for use in the analysis of a particular DNA molecule.
ER  -

TY  - JOUR
AU  - Sangal, V.
AU  - Blom, J.
AU  - Sutcliffe, I.C.
AU  - von Hunolstein, C.
AU  - Burkovski, A.
AU  - Hoskisson, P.A.
TI  - Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome.
JO  - BMC Genomics
PY  - 2015
SP  - 765
EP  - 765
VL  - 16
AB  - BACKGROUND: Non-toxigenic Corynebacterium diphtheriae strains are emerging as a
AB  - major cause of severe pharyngitis and tonsillitis as well as invasive diseases
AB  - such as endocarditis, septic arthritis, splenic abscesses and osteomyelitis. C.
AB  - diphtheriae strains have been reported to vary in their ability to adhere and
AB  - invade different cell lines. To identify the genetic basis of variation in the
AB  - degrees of pathogenicity, we sequenced the genomes of four strains of C.
AB  - diphtheriae (ISS 3319, ISS 4060, ISS 4746 and ISS 4749) that are well
AB  - characterised in terms of their ability to adhere and invade mammalian cells.
AB  - RESULTS: Comparative analyses of 20 C. diphtheriae genome sequences, including 16
AB  - publicly available genomes, revealed a pan-genome comprising 3,989 protein coding
AB  - sequences that include 1,625 core genes and 2,364 accessory genes. Most of the
AB  - genomic variation between these strains relates to uncharacterised genes encoding
AB  - hypothetical proteins or transposases. Further analyses of protein sequences
AB  - using an array of bioinformatic tools predicted most of the accessory proteome to
AB  - be located in the cytoplasm. The membrane-associated and secreted proteins are
AB  - generally involved in adhesion and virulence characteristics. The genes encoding
AB  - membrane-associated proteins, especially the number and organisation of the pilus
AB  - gene clusters (spa) including the number of genes encoding surface proteins with
AB  - LPXTG motifs differed between different strains. Other variations were among the
AB  - genes encoding extracellular proteins, especially substrate binding proteins of
AB  - different functional classes of ABC transport systems and 'non-classical'
AB  - secreted proteins. CONCLUSIONS: The structure and organisation of the spa gene
AB  - clusters correlates with differences in the ability of C. diphtheriae strains to
AB  - adhere and invade the host cells. Furthermore, differences in the number of genes
AB  - encoding membrane-associated proteins, e.g., additional proteins with LPXTG
AB  - motifs could also result in variation in the adhesive properties between
AB  - different strains. The variation in the secreted proteome may be associated with
AB  - the degree of pathogenesis. While the role of the 'non-classical' secretome in
AB  - virulence remains unclear, differences in the substrate binding proteins of
AB  - various ABC transport systems and cytoplasmic proteins potentially suggest strain
AB  - variation in nutritional requirements or a differential ability to utilize
AB  - various carbon sources.
ER  -

TY  - JOUR
AU  - Sangal, V.
AU  - Burkovski, A.
AU  - Hunt, A.C.
AU  - Edwards, B.
AU  - Blom, J.
AU  - Hoskisson, P.A.
TI  - A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing.
JO  - Infect. Genet. Evol.
PY  - 2014
SP  - 54
EP  - 57
VL  - 21
AB  - The differentiation of clinically important Corynebacterium diphtheriae into
AB  - specific biovars is complex and phylogenetically unclear. Comparative genomic
AB  - analyses of 17 strains indicate that the division of C. diphtheriae into
AB  - different biovars does not correlate with the variation in the gene content in
AB  - the relevant metabolic categories that are potentially involved in the biovar
AB  - discrimination. The biochemical separation is also not supported by phylogenetic
AB  - analyses, suggesting molecular methods of typing C. diphtheriae strains should be
AB  - adopted much more widely.
ER  -

TY  - JOUR
AU  - Sangal, V.
AU  - Tucker, N.P.
AU  - Burkovski, A.
AU  - Hoskisson, P.A.
TI  - Draft Genome Sequence of Corynebacterium diphtheriae Biovar Intermedius NCTC 5011.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4738
EP  - 4738
VL  - 194
AB  - We report an annotated draft genome of the human pathogen Corynebacterium diphtheriae bv.
AB  - intermedius NCTC 5011. This strain is the first C. diphtheriae
AB  - bv. intermedius strain to be sequenced, and our results provide a useful
AB  - comparison to the other primary disease-causing biovars, C. diphtheriae bv.
AB  - gravis and C. diphtheriae bv. mitis. The sequence has been deposited at
AB  - DDBJ/EMBL/GenBank with the accession number AJVH01000000.
ER  -

TY  - JOUR
AU  - Sangal, V.
AU  - Tucker, N.P.
AU  - Burkovski, A.
AU  - Hoskisson, P.A.
TI  - The Draft Genome Sequence of Corynebacterium diphtheriae bv. mitis NCTC 3529 Reveals Significant Diversity between the Primary Disease-Causing Biovars.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3269
EP  - 3269
VL  - 194
AB  - We report the draft genome of the human pathogen Corynebacterium diphtheriae bv.  mitis NCTC
AB  - 3529. This is the first C. diphtheriae bv. mitis strain to be
AB  - sequenced and reveals significant differences from the other primary biovar, C.
AB  - diphtheriae bv. gravis.
ER  -

TY  - JOUR
AU  - Sanjar, F. et al.
TI  - Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States.
JO  - Genome Announcements
PY  - 2014
SP  - e01120
EP  - e01113
VL  - 2
AB  - First identified in 1982 as a human pathogen, enterohemorrhagic Escherichia coli  of the
AB  - O157:H7 serotype is a major cause of food-borne acquired human infections.
AB  - Here, we report the genome sequence of the first known strain of this serotype
AB  - isolated in the United States.
ER  -

TY  - JOUR
AU  - Sanjar, F.
AU  - Karna, S.L.
AU  - Chen, T.
AU  - Chen, P.
AU  - Abercrombie, J.J.
AU  - Leung, K.P.
TI  - Whole-Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain BAMCPA07-48, Isolated from a Combat Injury Wound.
JO  - Genome Announcements
PY  - 2016
SP  - e00547
EP  - e00516
VL  - 4
AB  - We report here the complete genome sequence of Pseudomonas aeruginosa strain BAMCPA07-48,
AB  - isolated from a combat injury wound. The closed genome sequence of
AB  - this isolate is a valuable resource for pathogenome characterization of P.
AB  - aeruginosa associated with wounds, which will aid in the development of a
AB  - higher-resolution phylogenomic framework for molecular-guided
AB  - pathogen-surveillance.
ER  -

TY  - JOUR
AU  - Sanko, T.J.
AU  - Kraemer, A.S.
AU  - Niemann, N.
AU  - Gupta, A.K.
AU  - Flett, B.C.
AU  - Mienie, C.
AU  - Bezuidenhout, C.C.
TI  - Draft Genome Assemblages of 10 Xanthomonas vasicola pv. zeae Strains, Pathogens Causing Leaf Streak Disease of Maize in South Africa.
JO  - Genome Announcements
PY  - 2018
SP  - e00532
EP  - e00518
VL  - 6
AB  - Maize bacterial leaf streak disease has spread across maize crops in South Africa and
AB  - therefore potentially poses a threat to maize production and food security.
AB  - Until recently, this pathogen was identified as a Xanthomonas campestris
AB  - pathovar, whereas our South African genomes seem to be more divergent and create
AB  - their own subclade.
ER  -

TY  - JOUR
AU  - Sankpal, U.T.
AU  - Rao, D.N.
TI  - Mutational analysis of conserved residues in HhaI DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 2628
EP  - 2638
VL  - 30
AB  - HhaI DNA methyltransferase belongs to the C5-cytosine methyltransferase family, which is
AB  - characterized by the presence of a set of highly conserved amino acids and motifs present in
AB  - an invariant order. HhaI DNA methyltransferase has been subjected to a lot of biochemical and
AB  - crystallographic studies. A number of issues, especially the role of the conserved amino acids
AB  - in the methyltransferase activity, have not been addressed. Using sequence comparison and
AB  - structural data, a structure-guided mutagenesis approach was undertaken, to assess the role of
AB  - conserved amino acids in catalysis. Site-directed mutagenesis was performed on amino acids
AB  - involved in cofactor S-adenosyl-L-methionine (AdoMet) binding (Phe18, Trp41, Asp60 and
AB  - Leu100). Characterization of these mutants, by in vitro /in vivo restriction assays and
AB  - DNA/AdoMet binding studies, indicated that most of the residues present in the AdoMet-binding
AB  - pocket were not absolutely essential. This study implies plasticity in the recognition of
AB  - cofactor by HhaI DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Sankpal, U.T.
AU  - Rao, D.N.
TI  - Structure, function, and mechanism of HhaI DNA methyltransferases.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 2002
SP  - 167
EP  - 197
VL  - 37
AB  - A vast amount of literature has accumulated on the characterization of DNA methyltransferases.
AB  - The HhaI DNA methyltransferase, a C5-cytosine methyltransferase, has been the subject of
AB  - investigation for the last 2 decades. Biochemical and kinetic characterization have led to an
AB  - understanding of the catalytic and kinetic mechanism of the methyltransfer reaction. The HhaI
AB  - methyltransferase has also been subjected to extensive structural analysis, with the
AB  - availability of 12 structures with or without a cofactor and a variety of DNA substrates. The
AB  - mechanism of base flipping, first described for the HhaI methyltransferase, is conserved among
AB  - all DNA methyltransferases and is also found to occur in numerous DNA repair enzymes. Studies
AB  - with other methyltransferase reveal a significant structural and functional similarity among
AB  - different types of methyltransferases. This review aims to summarize the available information
AB  - on the HhaI DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Sannazzaro, A.I.
AU  - Torres, T.G.A.
AU  - Caballero, M.
AU  - Dip, D.
AU  - Pistorio, M.
AU  - Estrella, M.J.
TI  - Genome Sequence of the Symbiotic Type Strain Mesorhizobium helmanticense CSLC115N Isolated from Lotus corniculatus Nodules.
JO  - Genome Announcements
PY  - 2018
SP  - e00412
EP  - e00418
VL  - 6
AB  - Mesorhizobium helmanticense is a novel species that was isolated from root nodules of Lotus
AB  - corniculatus grown in an alfisol soil from Carbajosa de la
AB  - Sagrada, a Mediterranean region in the province of Salamanca in northwest Spain.
AB  - The whole-genome sequence of the type strain M. helmanticense CSLC115N is
AB  - reported in this study.
ER  -

TY  - JOUR
AU  - Sannino, D.
AU  - Angert, E.R.
TI  - Genomic insights into the thiamin metabolism of Paenibacillus thiaminolyticus NRRL B-4156 and P. apiarius NRRL B-23460.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 59
EP  - 59
VL  - 12
AB  - Paenibacillus thiaminolyticus is the model organism for studying thiaminase I, an enigmatic
AB  - extracellular enzyme. Originally isolated from the feces of clinical
AB  - patients suffering from thiamin deficiency, P. thiaminolyticus has been
AB  - implicated in thiamin deficiencies in humans and other animals due to its ability
AB  - to produce this thiamin-degrading enzyme. Its close relative, P. apiarius, also
AB  - produces thiaminase I and was originally isolated from dead honeybee larvae,
AB  - though it has not been reported to be a honeybee pathogen. We generated draft
AB  - genomes of the type strains of both species, P. thiaminolyticus NRRL B-4156 and
AB  - P. apiarius NRRL B-23460, to deeply explore potential routes of thiamin
AB  - metabolism. We discovered that the thiaminase I gene is located in a highly
AB  - conserved operon with thiamin biosynthesis and salvage genes, as well as genes
AB  - involved in the biosynthesis of the antibiotic bacimethrin. Based on metabolic
AB  - pathway predictions, P. apiarius NRRL B-23460 has the genomic capacity to
AB  - synthesize thiamin de novo using a pathway that is rarely seen in bacteria, but
AB  - P. thiaminolyticus NRRL B-4156 is a thiamin auxotroph. Both genomes encode
AB  - importers for thiamin and the pyrimidine moiety of thiamin, as well as enzymes to
AB  - synthesize thiamin from pyrimidine and thiazole.
ER  -

TY  - JOUR
AU  - Sano, H.
AU  - Sager, R.
TI  - Deoxyribonucleic acid methyltransferase from the eukaryote, Chlamydomonas reinhardi.
JO  - Eur. J. Biochem.
PY  - 1980
SP  - 471
EP  - 480
VL  - 105
AB  - DNA methyltransferase was purified 310-fold from a green alga. Chlamydomonas reinhardi
AB  - vegetative cells. The native enzyme of molecular weight 55000-58000 catalyzed the transfer of
AB  - methyl groups from S-adenosylmethionine to the 5 position of cytosine in DNA. Native DNA
AB  - accepted methyl groups 10-fold more than did denatured DNA. The sequence specificity analysis
AB  - of methylated deoxycytidine in vitro revealed that the enzyme introduces methyl groups
AB  - preferentially into sequences containing 5'd(T-mC-R)3'. Kinetic anlaysis of the reaction
AB  - indicated that the enzyme obeys a random sequential mechanism. The extent of saturation with
AB  - methyl groups depends upon the species from which the DNA was obtained. Kinetic analysis of
AB  - the reaction catalyzes by RNA polymerase II has indicated that DNA methylation decreases the
AB  - rate of initiation of RNA synthesis, but does not affect the rate of RNA chain elongation.
ER  -

TY  - JOUR
AU  - Sano, K.I.
AU  - Anraku, A.
TI  - Draft Genome Sequence of Brevibacillusreuszeri Strain NIT02, Isolated from a Laundered Rental Cloth Hot Towel.
JO  - Genome Announcements
PY  - 2018
SP  - e01353
EP  - e01317
VL  - 6
AB  - Brevibacillus reuszeri is a Gram-positive spore-forming bacterium. Here, we present the draft
AB  - genome sequence of Brevibacillus reuszeri strain NIT02, which
AB  - was isolated from a laundered rental cloth hot towel.
ER  -

TY  - JOUR
AU  - Sansom, C.E.
AU  - Biro, J.C.
AU  - Benyo, B.
AU  - Benyo, Z.
TI  - Codes in the codons: codon-amino acid complementarity revealed in the structures of restriction enzyme - DNA complexes.
JO  - FEBS J.
PY  - 2005
SP  - 100
EP  - 100
VL  - 272
AB  - In the early years after the elucidation of the DNA structure, there was controversy about
AB  - whether there was any chemical rationale underlying the genetic code. In 1967, Carl Woese
AB  - proposed that there was stereochemical affinity between amino acids and the base sequences
AB  - that code for them. The alternative hypothesis proposed by Crick among others, that the exact
AB  - genetic code was largely accidental, became largely accepted by the molecular biology
AB  - community. We have now constructed a "periodic table" linking the chemical properties of the
AB  - amino acids and the sequences of their associated codons. The amino acid table showed
AB  - significant periodicity and indicated the importance of the central base in determining the
AB  - chemical properties of amino acids. This adds support to Woese' original hypothesis. If this
AB  - stereochemical and structural affinity were true, we would expect interactions between amino
AB  - acids and their associated codons to be favoured in DNA-protein complexes. We originally
AB  - tested this hypothesis using known structures of restriction enzyme - DNA complexes. We found
AB  - that, not only were cleavage-site like base sequences found disproportionately often in the
AB  - DNA sequences of restriction enzymes, but that, in the complex structures, the amino acids
AB  - coded by those site-like sequences were found close to the restriction sites themselves. The
AB  - average distance between the closest atoms in the codon and amino acid was significantly
AB  - lowest when the amino acid involved was positively charged. We now update this work to include
AB  - restriction enzyme - DNA complexes that have entered the PDB since December 2003.
ER  -

TY  - JOUR
AU  - Santagati, M.
AU  - Iannelli, F.
AU  - Cascone, C.
AU  - Campanile, F.
AU  - Oggioni, M.R.
AU  - Stefani, S.
AU  - Pozzi, G.
TI  - The novel conjugative transposon tn1207.3 carries the macrolide efflux gene mef(A) in Streptococcus pyogenes.
JO  - Microb. Drug Resist.
PY  - 2003
SP  - 243
EP  - 247
VL  - 9
AB  - The macrolide efflux gene mef(A) of the Streptococcus pyogenes clinical strain 2812A was found
AB  - to be carried by a 52-kb chromosomal genetic
AB  - element that could be transferred by conjugation to the chromosome of
AB  - other streptococcal species. The characteristics of this genetic element
AB  - are typical of conjugative transposons and was named Tn1207.3. The size of
AB  - Tn1207.3 was established by pulsed-field gel electrophoresis (PFGE), and
AB  - DNA sequencing analysis showed that the 7,244 bp at the left end of
AB  - Tn1207.3 were identical to those of the pneumococcal Tn1207.1 element.
AB  - Tn1207.3-like genetic elements were found to be inserted at a single
AB  - specific chromosomal site in 12 different clinical isolates S. pyogenes
AB  - exhibiting the M phenotype of resistance to macrolides and carrying the
AB  - mef(A) gene. Tn1207.3 was transferred from S. pyogenes 2812A to
AB  - Streptococcus pneumoniae, and sequence analysis carried out on six
AB  - independent transconjugants showed that insertion of Tn1207.3 in the
AB  - pneumococcal genome always occurred at a single specific site as in
AB  - Tn1207.1. Using MF2, a representative S. pneumoniae transconjugant, as a
AB  - donor, Tn1207.3 was transferred again by conjugation to S. pyogenes and
AB  - Streptococcus gordonii. The previously described nonconjugative element
AB  - Tn1207.1 of S. pneumoniae appears to be a defective element, part of a
AB  - longer conjugative transposon that carries mef(A) and is found in clinical
AB  - isolates of S. pyogenes.
ER  -

TY  - JOUR
AU  - Santamaria, R.I.
AU  - Bustos, P.
AU  - Perez-Carrascal, O.M.
AU  - Miranda-Sanchez, F.
AU  - Vinuesa, P.
AU  - Martinez-Flores, I.
AU  - Juarez, S.
AU  - Lozano, L.
AU  - Martinez-Romero, E.
AU  - Cevallos, M.A.
AU  - Romero, D.
AU  - Davila, G.
AU  - Ormeno-Orrillo, E.
AU  - Gonzalez, V.
TI  - Complete Genome Sequences of Eight Rhizobium Symbionts Associated with Common Bean (Phaseolus vulgaris).
JO  - Genome Announcements
PY  - 2017
SP  - e00645
EP  - e00617
VL  - 5
AB  - We present here the high-quality complete genome sequences of eight strains of
AB  - Rhizobium-nodulating Phaseolus vulgaris Comparative analyses showed that some of
AB  - them belonged to different genomic and evolutionary lineages with common
AB  - symbiotic properties. Two novel symbiotic plasmids (pSyms) with P. vulgaris
AB  - specificity are reported here.
ER  -

TY  - JOUR
AU  - SantAnna, B.M.
AU  - Marbach, P.P.
AU  - Rojas-Herrera, M.
AU  - De Souza, J.T.
AU  - Roque, M.R.
AU  - Queiroz, A.T.
TI  - High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao.
JO  - Genome Announcements
PY  - 2015
SP  - e01325
EP  - e01315
VL  - 3
AB  - Bacillus amyloliquefaciens strain 629 is an endophyte isolated from Theobroma cacao L. Here,
AB  - we report the draft genome sequence (3.9 Mb) of B.
AB  - amyloliquefaciens strain 629 containing 16 contigs (3,903,367 bp), 3,912 coding
AB  - sequences, and an average 46.5% G+C content.
ER  -

TY  - JOUR
AU  - Santhoshkumar, P.
AU  - Sharma, K.K.
TI  - Analysis of alpha-crystallin chaperone function using restriction enzymes and citrate synthase.
JO  - Mol. Vis.
PY  - 2001
SP  - 172
EP  - 177
VL  - 7
AB  - PURPOSE: To compare the abilities of [alpha]A-crystallin, [alpha]B-crystallin, and
AB  - mini-[alpha]A-crystallin (a synthetic peptide
AB  - chaperone representing the functional unit of [alpha]A-crystallin) to
AB  - protect against heat-induced inactivation of citrate synthase (CS) and
AB  - restriction enzymes, SmaI and NdeI. METHODS: Restriction enzymes, SmaI and
AB  - NdeI were heated at different temperatures in the presence of various
AB  - amounts of molecular chaperones and tested for their ability to cleave
AB  - plasmid DNA. The aggregation of CS was measured at 43 degrees C while the
AB  - loss in activity was monitored at 37 degrees C in the presence of various
AB  - crystallins. RESULTS: Restriction enzyme activities were protected by the
AB  - crystallin subunits up to 37 degrees C for SmaI and 43 degrees C for NdeI.
AB  - However, the mini-[alpha]A-crystallin was unable to protect endonuclease
AB  - activity. The crystallin subunits and the peptide chaperone were able to
AB  - suppress thermal aggregation of CS at 43 degrees C, but failed to
AB  - stabilize its activity at 37 degrees C. CONCLUSIONS: The ability of
AB  - [alpha]-crystallin subunits to stabilize denaturing proteins varies from
AB  - enzyme to enzyme as evidenced by the inactivation of CS and protection of
AB  - SmaI and NdeI activity in the presence of [alpha]-crystallin subunits.
AB  - Additionally, our results show that there could be more than one site in
AB  - [alpha]A-crystallin responsible for its chaperone-like action. By addition
AB  - of crystallin subunits to restriction enzymes prior to or during storage,
AB  - transport, or assay would maintain or improve their activity thereby
AB  - decreasing their cost.
ER  -

TY  - JOUR
AU  - Santi, D.V.
AU  - Garrett, C.E.
AU  - Barr, P.J.
TI  - On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs.
JO  - Cell
PY  - 1983
SP  - 9
EP  - 10
VL  - 33
AB  - In recent years 5-methylcytosine residues in DNA have been implicated to have an important
AB  - role in the control of eucaryotic gene expression (see Razin and Riggs, Science 210, 604-610,
AB  - 1980). Consequently, there has been much interest in cytosine analogs such as 5-azacytosine
AB  - (5-azaC) and 5-fluorocytosine (5-fluoro-C), which, when incorporated into DNA, inhibit
AB  - methylation and profoundly affect gene expression and differentiation (see Taylor and Jones,
AB  - JBM 162, 679-692, 1982). The degree of hypomethylation far exceeds the levels of such analogs
AB  - in DNA and is not simply a result of their inability to serve as methyl acceptors. It is now
AB  - clear that DNAs containing low levels of these analogs are potent inhibitors of DNA-cytosine
AB  - methyltansferase (DCMT), but the mechanism of inhibition is unresolved. In this report, we
AB  - review pertinent literature and formulate a proposal for the molecular mechanism by which DCMT
AB  - is inhibited bly DNA containing 5-aza-C or 5-fluoro-C. A similar mechanism explains how small
AB  - amounts of 5-aza-C or 5-fluoro-C in tRNA cause specific loss of tRNA-cytosine
AB  - methyltransferase activity (Lu et al., Biochem. Pharmacol. 28, 489-495, 1979; Lu and
AB  - Randerath, Cancer Res. 40, 2701-2705, 1980).
ER  -

TY  - JOUR
AU  - Santi, D.V.
AU  - Norment, A.
AU  - Garrett, C.E.
TI  - Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 6993
EP  - 6997
VL  - 81
AB  - DNA containing 5-azacytosine (azaC) has previously been shown to be a
AB  - potent inhibitor of DNA-cytosine methyltransferases.  In this report, we describe
AB  - experiments which demonstrate that azaC-DNA forms a covalent complex with HpaII
AB  - methylase, a bacterial enzyme that methylates the internal C of C-C-G-G sequences.  The
AB  - complex does not undergo detectable dissociation over at least 3 days and is stable to
AB  - denaturation with NaDodSO4.  After extensive digestion of the complex with DNase and
AB  - phosphodiesterase, gel filtration gave the methylase bound to approximately one equivalent
AB  - of azaC; the digested complex had an apparent molecular weight similar to that of the native
AB  - enzyme.  Although prior treatment of azaC-DNA with HpaII endonuclease had only a slight
AB  - effect on binding of the methylase, treatment with MspI endonuclease, which also cleaves
AB  - at C-C-G-G sequences, resulted in a significant reduction in binding; this indicates that
AB  - azaC residues in the recognition sequence of HpaII are an important component in the
AB  - covalent interaction of the methylase.  However, since there was residual binding it is
AB  - possible that azaC residues elsewhere in DNA also covalently bind to the methylase.  These
AB  - results provide an explanation of why azaC-DNA is such a potent inhibitor of cytosine
AB  - methyltransferases and how the incorporation of such low levels of azaC into DNA can
AB  - result in dramatic decreases in the methylation of cytosine.  Finally, consideration of the
AB  - probable catalytic mechanism of cytosine methylases and the chemical properties of azaC
AB  - suggests that the inhibition is, at least in part, an active-site directed process and permits
AB  - a
AB  - proposal for the structure of the covalent complex.
ER  -

TY  - JOUR
AU  - Santini, S.
AU  - Jeudi, S.
AU  - Bartoli, J.
AU  - Poirot, O.
AU  - Lescot-David, M.
AU  - Barbe, V.
AU  - Wommack, E.K.
AU  - Abergel, C.
AU  - Brussaard, C.
AU  - Claverie, J.-M.
TI  - The genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2013
SP  - 10800
EP  - 10805
VL  - 110
AB  - Large dsDNA viruses are involved in the population control of many
AB  - globally distributed species of eukaryotic phytoplankton and have
AB  - a prominent role in bloomtermination. The genus Phaeocystis (Haptophyta,
AB  - Prymnesiophyceae) includes several high-biomass-forming
AB  - phytoplankton species, such as Phaeocystis globosa, the blooms of
AB  - which occur mostly in the coastal zone of the North Atlantic and the
AB  - North Sea. Here,we report the 459,984-bp-long genomesequence of
AB  - P. globosa virus strain PgV-16T, encoding 434 proteins and eight
AB  - tRNAs and, thus, the largest fully sequenced genome to date among
AB  - viruses infecting algae. Surprisingly, PgV-16T exhibits no phylogenetic
AB  - affinity with other viruses infecting microalgae (e.g., phycodnaviruses),
AB  - including those infecting Emiliania huxleyi, another
AB  - ubiquitous bloom-forming haptophyte. Rather, PgV-16T belongs to
AB  - anemerging clade (theMegaviridae) clustering the viruses endowed
AB  - with the largest known genomes, including Megavirus, Mimivirus
AB  - (both infecting acanthamoeba), and a virus infecting the marine
AB  - microflagellate grazer Cafeteria roenbergensis. Seventy-five percent
AB  - of the best matches of PgV-16T-predicted proteins correspond to
AB  - two viruses [Organic Lake phycodnavirus (OLPV)1 and OLPV2] from
AB  - a hypersaline lake in Antarctica (Organic Lake), the hosts of which
AB  - are unknown. As for OLPVs and other Megaviridae, the PgV-16T
AB  - sequence data revealed the presence of a virophage-like genome.
AB  - However, no virophage particle was detected in infected P. globosa
AB  - cultures. The presence of many genes found only in Megaviridae in
AB  - its genome and the presence of an associated virophage strongly
AB  - suggest that PgV-16T shares a common ancestry with the largest
AB  - known dsDNA viruses, the host range ofwhich already encompasses
AB  - the earliest diverging branches of domain Eukarya.
ER  -

TY  - JOUR
AU  - Santopolo, L.
AU  - Marchi, E.
AU  - Decorosi, F.
AU  - Galardini, M.
AU  - Brilli, M.
AU  - Giovannetti, L.
AU  - Viti, C.
TI  - Draft Genome Sequence of Chromate-Resistant and Biofilm-Producing Strain Pseudomonas alcaliphila 34.
JO  - Genome Announcements
PY  - 2013
SP  - e00125
EP  - e00112
VL  - 1
AB  - We report the draft genome sequence of 34, a Cr(VI)-hyperresistant and biofilm-producing
AB  - bacterium that might be used for the bioremediation of
AB  - chromate-polluted soils. The genome sequence might be helpful in exploring the
AB  - mechanisms involved in chromium resistance and biofilm formation.
ER  -

TY  - JOUR
AU  - Santoro, A.E.
AU  - Dupont, C.L.
AU  - Richter, R.A.
AU  - Craig, M.T.
AU  - Carini, P.
AU  - McIlvin, M.R.
AU  - Yang, Y.
AU  - Orsi, W.
AU  - Moran, D.
AU  - Saito, M.
TI  - Genomic and proteomic characterization of Candidatus Nitrosopelagicus brevis: an ammonia-oxidizing archaeon from the open ocean.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2015
SP  - 1173
EP  - 1178
VL  - 112
AB  - Thaumarchaeota are among the most abundant microbial cells in the
AB  - ocean, but difficulty in cultivating marine Thaumarchaeota has
AB  - hindered investigation into the physiological and evolutionary basis
AB  - of their success. We report here a closed genome assembled from
AB  - a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon
AB  - CN25, originating from the open ocean. The CN25
AB  - genome exhibits strong evidence of genome streamlining, including
AB  - a 1.23-Mbp genome, a high coding density, and a low number of
AB  - paralogous genes. Proteomic analysis recovered nearly 70% of the
AB  - predicted proteins encoded by the genome, demonstrating that
AB  - a high fraction of the genome is translated. In contrast to other
AB  - minimal marine microbes that acquire, rather than synthesize,
AB  - cofactors, CN25 encodes and expresses near-complete biosynthetic
AB  - pathways for multiple vitamins. Metagenomic fragment recruitment
AB  - indicated the presence of DNA sequences >90% identical to the CN25
AB  - genome throughout the oligotrophic ocean. We propose the provisional
AB  - name "Candidatus Nitrosopelagicus brevis" str. CN25 for this
AB  - minimalist marine thaumarchaeon and suggest it as a potentialmodel
AB  - system for understanding archaeal adaptation to the open ocean.
ER  -

TY  - JOUR
AU  - Santos, A.P.
AU  - Guimaraes, A.M.S.
AU  - do Nascimento, N.C.
AU  - SanMiguel, P.J.
AU  - Martin, S.W.
AU  - Messick, J.B.
TI  - Genome of Mycoplasma haemofelis, unraveling its strategies for survival and persistence.
JO  - Vet. Res.
PY  - 2011
SP  - 102
EP  - 102
VL  - 42
AB  - Mycoplasma haemofelis is a mycoplasmal pathogen (hemoplasma) that attaches to the host's
AB  - erythrocytes. Distributed worldwide, it has a
AB  - significant impact on the health of cats causing acute disease and,
AB  - despite treatment, establishing chronic infection. It might also have a
AB  - role as a zoonotic agent, especially in immunocompromised patients.
AB  - Whole genome sequencing and analyses of M. haemofelis strain Ohio2 was
AB  - undertaken as a step toward understanding its survival and persistence.
AB  - Metabolic pathways are reduced, relying on the host to supply many of
AB  - the nutrients and metabolites needed for survival. M. haemofelis must
AB  - import glucose for ATP generation and ribose derivates for RNA/DNA
AB  - synthesis. Hypoxanthine, adenine, guanine, uracil and CMP are scavenged
AB  - from the environment to support purine and pyrimidine synthesis. In
AB  - addition, nicotinamide, amino acids and any vitamins needed for growth,
AB  - must be acquired from its environment. The core proteome of M.
AB  - haemofelis contains an abundance of paralogous gene families,
AB  - corresponding to 70.6% of all the CDSs. This 'paralog pool' is a rich
AB  - source of different antigenic epitopes that can be varied to elude the
AB  - host's immune system and establish chronic infection. M. haemofelis
AB  - also appears to be capable of phase variation, which is particularly
AB  - relevant to the cyclic bacteremia and persistence, characteristics of
AB  - the infection in the cat. The data generated herein should be of great
AB  - use for understanding the mechanisms of M. haemofelis infection.
AB  - Further, it will provide new insights into its pathogenicity and clues
AB  - needed to formulate media to support the in vitro cultivation of M.
AB  - haemofelis.
ER  -

TY  - JOUR
AU  - Santos, F.
AU  - Yarza, P.
AU  - Parro, V.
AU  - Briones, C.
AU  - Anton, J.
TI  - The metavirome of a hypersaline environment.
JO  - Environ. Microbiol.
PY  - 2010
SP  - 2965
EP  - 2976
VL  - 12
AB  - Hypersaline environments harbour the highest number of virus-like
AB  - particles reported for planktonic systems. However, very little is known
AB  - about the genomic diversity of these virus assemblages since most of the
AB  - knowledge on halophages is based on the analysis of a few isolates
AB  - infecting strains of hyperhalophilic Archaea that may not be
AB  - representatives of the natural microbiota. Here, we report the
AB  - characterization, through a metagenomic approach, of the viral assemblage
AB  - inhabiting a crystallizer pond (CR30) from a multi-pond solar saltern in
AB  - Santa Pola (SE Spain). A total of 1.35 Mbp were cloned that yielded a
AB  - total of 620 kb sequenced viral DNA. The metavirome was highly diverse and
AB  - different from virus communities of marine and other aquatic environments
AB  - although it showed some similarities with metaviromes from high-salt ponds
AB  - in solar salterns in San Diego (SW USA), indicating some common traits
AB  - between high-salt viromes. A high degree of diversity was found in the
AB  - halophages as revealed by the presence of 2479 polymorphic nucleotides.
AB  - Dinucleotide frequency analysis of the CR30 metavirome showed a good
AB  - correlation with GC content and enabled the establishment of different
AB  - groups, and even the assignment of their putative hosts: the archaeon
AB  - Haloquadratum walsbyi and the bacterium Salinibacter ruber.
ER  -

TY  - JOUR
AU  - Santos, O.C.
AU  - Duarte, A.F.
AU  - Albano, R.M.
AU  - Bastos, M.C.
TI  - Draft Genome Sequence of the Aureocin A53-Producing Strain Staphylococcus aureus  A53.
JO  - Genome Announcements
PY  - 2016
SP  - e00858
EP  - e00816
VL  - 4
AB  - Here, we present the 2,658,363-bp draft genome sequence of the aureocin A53-producing strain
AB  - Staphylococcus aureus A53. This genome information may
AB  - contribute to the optimal and rational exploitation of aureocin A53 as an
AB  - antimicrobial agent and to its production in large scale.
ER  -

TY  - JOUR
AU  - Santos, S.N.
AU  - Gacesa, R.
AU  - Taketani, R.G.
AU  - Long, P.F.
AU  - Melo, I.S.
TI  - Genome Sequence of Streptomyces caatingaensis CMAA 1322, a New Abiotic Stress-Tolerant Actinomycete Isolated from Dried Lake Bed Sediment in the Brazilian Caatinga Biome.
JO  - Genome Announcements
PY  - 2015
SP  - e01020
EP  - e01015
VL  - 3
AB  - The genome sequence of the first Streptomyces species isolated from the Brazilian Caatinga is
AB  - reported here. Genes related to environmental stress tolerance were prevalent and included
AB  - many secondary metabolic gene clusters.
ER  -

TY  - JOUR
AU  - Santos, S.N.
AU  - Kavamura, V.N.
AU  - Taketani, R.G.
AU  - Vasconcellos, R.L.
AU  - Zucchi, T.D.
AU  - Melo, I.S.
TI  - Draft Genome Sequence of Bacillus sp. Strain CMAA 1185, a Cellullolytic Bacterium Isolated from Stain House Lake, Antarctic Peninsula.
JO  - Genome Announcements
PY  - 2015
SP  - e00436
EP  - e00415
VL  - 3
AB  - The aim of this study was to report the genome sequence of the cellulolytic Bacillus sp.
AB  - strain CMAA 1185, isolated from Stain House Lake, Antarctica.
ER  -

TY  - JOUR
AU  - Santos, T.
AU  - Cruz, A.
AU  - Caetano, T.
AU  - Covas, C.
AU  - Mendo, S.
TI  - Draft Genome Sequence of Pedobacter sp. Strain NL19, a Producer of Potent Antibacterial Compounds.
JO  - Genome Announcements
PY  - 2015
SP  - e00184
EP  - e00115
VL  - 3
AB  - Here, we report the draft genome sequence of Pedobacter sp. strain NL19. The genome has 5.99
AB  - Mbp and a G+C content of 39.0%. NL19 was isolated from sludge
AB  - from an abandoned uranium mine in the north of Portugal, and it produces potent
AB  - antibacterials against Gram-positive and Gram-negative bacteria.
ER  -

TY  - JOUR
AU  - Santos-Garcia, D.
AU  - Farnier, P.A.
AU  - Beitia, F.
AU  - Zchori-Fein, E.
AU  - Vavre, F.
AU  - Mouton, L.
AU  - Moya, A.
AU  - Latorre, A.
AU  - Silva, F.J.
TI  - Complete Genome Sequence of 'Candidatus Portiera aleyrodidarum' BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6654
EP  - 6655
VL  - 194
AB  - The genome of 'Candidatus Portiera aleyrodidarum,' the primary endosymbiont of the whitefly
AB  - Bemisia tabaci (Mediterranean species), is reported. It presents a
AB  - reduced genome (357 kb) encoding the capability to synthetize, or participate in
AB  - the synthesis of, several amino acids and carotenoids, being the first insect
AB  - endosymbiont capable of supplying carotenoids.
ER  -

TY  - JOUR
AU  - Santourlidis, S.
AU  - Schulz, W.A.
TI  - The cytotoxic effect of DNA methyltransferase I over-expression is mediated by the N-terminal.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A182
EP  - A182
VL  - 28
AB  - DNA methyltransferase 1, the essential enzyme maintaining DNA methylation patterns in
AB  - mammalian cells, contains a 500 amino acid catalytic domain and an N-terminal 1200 amino acid
AB  - complex regulatory domain determining specificity and intracellular localization.
AB  - Overexpression of the enzyme in somatic cells is very difficult, even more of the
AB  - oocyte-specific form lacking the first 120 amino acids.  To elucidate the underlying causes,
AB  - the mouse and human cDNAs encoding this form were transfected into mouse F9 cells and various
AB  - human cell lines.  Few cell clones were obtained which contained rearranged cDNAs after two
AB  - weeks, but the number of transfected cells was not notably diminished up to 3 days.
AB  - Surprisingly, deletion of the catalytic domain did not obliterate cytotoxicity; rather a 150
AB  - amino acid subdomain containing the PCNA-binding site and an NLS was found to be sufficient.
AB  - Mutation of the PCNA-binding sequence abolished cytotoxicity.  Thus, DNMT1 overexpression
AB  - causes a slow-acting cytotoxic effect via binding to PCNA, possibly by interfering with DNA
AB  - replication.  DNMT1 may be a multifunctional enzyme important beyond DNA methylation.
ER  -

TY  - JOUR
AU  - Sanudo, A.I.
AU  - Olivares, M.M.
AU  - Banuelos, O.
TI  - Draft Genome Sequence of Lactobacillus reuteri CECT8605.
JO  - Genome Announcements
PY  - 2017
SP  - e00297
EP  - e00217
VL  - 5
AB  - Lactobacillus reuteri CECT8605 has shown potential probiotic properties in both in vitro and
AB  - in vivo assays. Besides its beneficial characteristics, general
AB  - aspects concerning genetic stability and safety for human consumption have been
AB  - studied. Its genome sequence has been a useful tool to support preliminary
AB  - conclusions based on empirical observations.
ER  -

TY  - JOUR
AU  - Sapienza, P.
AU  - Kurpiewski, M.
AU  - Jen-Jacobson, L.
TI  - Thermodynamic and kinetic basis of promiscuity in mutant EcoRI endonucleases.
JO  - Biophys. J.
PY  - 2003
SP  - 367a
EP  - 367a
VL  - 84
AB  - We have used fluorescence-quenching measurements to characterize the partitioning of a variety
AB  - of indolyl-labeled phospho- and sphingolipids
AB  - between gel or liquid-ordered and liquid-disordered lipid domains in
AB  - several types of lipid bilayers where such domains coexist. In both
AB  - cholesterol-free and cholesterol-containing lipid mixtures, sphingolipids
AB  - with diverse polar headgroups (ranging from sphingomyelin and
AB  - monoglycosylceramides to ganglioside GM1) show a net preference for
AB  - partitioning into ordered domains, which varies modestly in magnitude with
AB  - varying headgroup structure. The affinities of different sphingolipids for
AB  - ordered lipid domains do not vary in a consistent manner with the size or
AB  - other simple structural properties of the polar headgroup, such that for
AB  - example ganglioside GM1 partitions between ordered and disordered lipid
AB  - domains in a manner very similar to sphingomyelin. Ceramide exhibits a
AB  - dramatically higher affinity for ordered lipid domains in both
AB  - cholesterol-free and cholesterol-containing bilayers than do other
AB  - sphingolipids. Our findings suggest that sphingolipids with a variety of
AB  - headgroup structures will be enriched by substantial factors in
AB  - liquid-ordered versus liquid-disordered regions of membranes, in a manner
AB  - that is only modestly dependent on the nature of the polar headgroup.
AB  - Ceramide is predicted to show a very strong enrichment in such domains,
AB  - supporting previous suggestions that ceramide-mediated signaling may be
AB  - compartmentalized to liquid-ordered (raft and raft-related) domains in the
AB  - plasma membrane.
ER  -

TY  - JOUR
AU  - Sapienza, P.J.
AU  - Dela-Torre, C.A.
AU  - McCoy, W.H.
AU  - Jana, S.V.
AU  - Jen-Jacobson, L.
TI  - Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 307
EP  - 324
VL  - 348
AB  - Promiscuous mutant EcoRI endonucleases produce lethal to sublethal effects because they cleave
AB  - Escherichia coli DNA despite the presence of the EcoRI methylase. Three promiscuous mutant
AB  - forms, Ala138Thr, Glu192Lys and His114Tyr, have been characterized with respect to their
AB  - binding affinities and first-order cleavage rate constants towards the three classes of DNA
AB  - sites: specific, miscognate (EcoRI*) and non-specific. We have made the unanticipated and
AB  - counterintuitive observations that the mutant restriction endonucleases that exhibit relaxed
AB  - specificity in vivo nevertheless bind more tightly than the wild-type enzyme to the specific
AB  - recognition sequence in vitro, and show even greater preference for binding to the cognate
AB  - GAATTC site over miscognate sites. Binding preference for EcoRI* over non-specific DNA is also
AB  - improved. The first-order cleavage rate constants of the mutant enzymes are normal for the
AB  - cognate site GAATTC, but are greater than those of the wild-type enzyme at EcoRI* sites. Thus,
AB  - the mutant enzymes use two mechanisms to partially bypass the multiple fail-safe mechanisms
AB  - that protect against cleavage of genomic DNA in cells carrying the wild-type EcoRI
AB  - restriction-modification system: (a) binding to EcoRI* sites is more probable than for
AB  - wild-type enzyme because non-specific DNA is less effective as a competitive inhibitor; (b)
AB  - the combination of increased affinity and elevated cleavage rate constants at EcoRI* sites
AB  - makes double-strand cleavage of these sites a more probable outcome than it is for the
AB  - wild-type enzyme. Semi-quantitative estimates of rates of EcoRI* site cleavage in vivo,
AB  - predicted using the binding and cleavage constants measured in vitro, are in accord with the
AB  - observed lethal phenotypes associated with the three mutations.
ER  -

TY  - JOUR
AU  - Sapienza, P.J.
AU  - Rosenberg, J.M.
AU  - Jen-Jacobson, L.
TI  - Structural and Thermodynamic Basis for Enhanced DNA Binding by a Promiscuous Mutant EcoRI Endonuclease.
JO  - Structure
PY  - 2007
SP  - 1368
EP  - 1382
VL  - 15
AB  - Promiscuous mutant EcoRI endonucleases bind to the canonical site GAATTC more tightly than
AB  - does the wild-type endonuclease, yet cleave variant
AB  - (EcoRI( *)) sites more rapidly than does wild-type. The crystal structure
AB  - of the A138T promiscuous mutant homodimer in complex with a GAATTC site is
AB  - nearly identical to that of the wild-type complex, except that the Thr138
AB  - side chains make packing interactions with bases in the 5'-flanking
AB  - regions outside the recognition hexanucleotide while excluding two bound
AB  - water molecules seen in the wild-type complex. Molecular dynamics
AB  - simulations confirm exclusion of these waters. The structure and
AB  - simulations suggest possible reasons why binding of the A138T protein to
AB  - the GAATTC site has DeltaS degrees more favorable and DeltaH degrees less
AB  - favorable than for wild-type endonuclease binding. The interactions of
AB  - Thr138 with flanking bases may permit A138T, unlike wild-type enzyme, to
AB  - form complexes with EcoRI( *) sites that structurally resemble the
AB  - specific wild-type complex with GAATTC.
ER  -

TY  - JOUR
AU  - Sapp, A.
AU  - Huguet-Tapia, J.C.
AU  - Sanchez-Lamas, M.
AU  - Antelo, G.T.
AU  - Primo, E.D.
AU  - Rinaldi, J.
AU  - Klinke, S.
AU  - Goldbaum, F.A.
AU  - Bonomi, H.R.
AU  - Christner, B.C.
AU  - Otero, L.H.
TI  - Draft Genome Sequence of Methylobacterium sp. Strain V23, Isolated from Accretion Ice of the Antarctic Subglacial Lake Vostok.
JO  - Genome Announcements
PY  - 2018
SP  - e00145
EP  - e00118
VL  - 6
AB  - Here, we report the draft genome sequence of Methylobacterium sp. strain V23, a bacterium
AB  - isolated from accretion ice of the subglacial Lake Vostok (3,592 meters
AB  - below the surface). This genome makes possible the study of ancient and
AB  - psychrophilic genes and proteins from a subglacial environment isolated from the
AB  - surface for at least 15 million years.
ER  -

TY  - JOUR
AU  - Sapranauskas, R.
TI  - Investigation of type IIS restriction endonuclease BfiI domain organization by using a new random gene dissection approach.
JO  - Ph.D. Thesis, Vilnius University
PY  - 2008
SP  - 1
EP  - 42
AB  - Conclusions
AB  - 1. The genes of BfiI restriction-modification system were cloned. The system
AB  - comprises two cytosine-N4-methyltransferases and a restriction endonuclease.
AB  - 2. A new method for investigation of protein domain organization, Random
AB  - Gene Dissection, was proposed. The interdomain region of the chosen model protein, FokI REase,
AB  - was determined using the new method, and it was in perfect agreement with the linker region
AB  - predicted from the tertiary structure of FokI.
AB  - 3. Interdomain region of BfiI REase was determined by Random Gene
AB  - Dissection method.
AB  - 4. Indirect data (induction of SOS response, toxicity) indicate that the
AB  - N-terminal domain of BfiI acts as a nuclease.
AB  - 5. The DNA binding assay using purified C-terminal domain of BfiI indicates
AB  - that it is responsible for target recognition.
AB  - 6. The complementary fragments of FokI and BfiI were isolated using Random
AB  - Gene Dissection. Therefore the Random Gene Dissection method can be
AB  - used not only for identification of interdomain regions, but also for isolation of
AB  - complementing fragments of proteins.
ER  -

TY  - JOUR
AU  - Sapranauskas, R.
AU  - Lubys, A.
TI  - Random gene dissection: a tool for the investigation of protein structural organization.
JO  - Biotechniques
PY  - 2005
SP  - 395
EP  - 402
VL  - 39
AB  - To investigate the domain structure of proteins and the function of individual domains,
AB  - proteins are usually subjected to limited proteolysis, followed by isolation of protein
AB  - fragments and determination of their functions.  We have developed an approach we call random
AB  - gene dissection for the identification of functional protein domains and their interdomain
AB  - regions as well as their in vivo complementing fragments.  The approach was tested on a
AB  - two-domain protein, the type IIS restriction endonuclease BfiI.  The collection of BfiI
AB  - insertional mutants was screened for those that are endonucleolytically active and thus induce
AB  - the SOS DNA repair response.  Sixteen isolated mutants of the wild-type specificity contained
AB  - insertions that were dispersed in a relatively large region of the target recognition domain.
AB  - They split the gene into two complementing parts that separately were unable to induce the SOS
AB  - DNA repair response.  In contrast, all 19 mutants of relaxed specificity contained the
AB  - cassette inserted into a very narrow interdomain region that connects BfiI domains responsible
AB  - for DNA recognition and for cleavage.  As expected, only the N-terminal fragment of BfiI was
AB  - required to induce SOS response.  Our results demonstrate that RGD can be used as a general
AB  - method to identify complementing fragments and functional domains in enzymes.
ER  -

TY  - JOUR
AU  - Sapranauskas, R.
AU  - Sasnauskas, G.
AU  - Lagunavicius, A.
AU  - Vilkaitis, G.
AU  - Lubys, A.
AU  - Siksnys, V.
TI  - Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 30878
EP  - 30885
VL  - 275
AB  - The type IIs restriction enzyme BfiI recognizes the non-palindromic nucleotide sequence
AB  - 5'-ACTGGG-3' and cleaves complementary DNA strands 5/4 nucleotides downstream of the
AB  - recognition sequence. The genes coding for the BfiI restriction-modification (R-M) system were
AB  - cloned/sequenced and biochemical characterization of the BfiI restriction enzyme was
AB  - performed. The BfiI R-M system contained three proteins: two N4-methylcytosine
AB  - methyltransferases and a restriction enzyme. Sequencing of bisulfite-treated methylated DNA
AB  - indicated that each methyltransferase modifies cytosines on opposite strands of the
AB  - recognition sequence.  The N-terminal part of the BfiI restriction enzyme amino acid sequence
AB  - revealed intriguing similarities to an EDTA-resistant nuclease of Salmonella typhimurium.
AB  - Biochemical analyses demonstrated that BfiI, like the nuclease of S. typhimurium, cleaves DNA
AB  - in the absence of Mg(2+) ions and hydrolyzes an artificial substrate bis(p-nitrophenyl)
AB  - phosphate. However, unlike the nonspecific S. typhimurium nuclease, BfiI restriction enzyme
AB  - cleaves DNA specifically. We propose that the DNA-binding specificity of BfiI stems from the
AB  - C-terminal part of the protein. The catalytic N-terminal subdomain of BfiI radically differs
AB  - from that of type II restriction enzymes and is presumably similar to the EDTA-resistant
AB  - nonspecific nuclease of S. typhimurium; therefore, BfiI did not require metal ions for
AB  - catalysis. We suggest that BfiI represents a novel subclass of type IIs restriction enzymes
AB  - that differs from the archetypal FokI endonuclease by the fold of its cleavage domain, the
AB  - domain location, and reaction mechanism.
ER  -

TY  - JOUR
AU  - Saranathan, R.
AU  - Tomar, A.
AU  - Sudhakar, P.
AU  - Arunkumar, K.P.
AU  - Prashanth, K.
TI  - Draft Genome Sequence of a Multidrug-Resistant Acinetobacter baumannii PKAB07 Clinical Strain from India Belonging to Sequence Type 195.
JO  - Genome Announcements
PY  - 2014
SP  - e00184
EP  - e00114
VL  - 2
AB  - Acinetobacter baumannii has emerged as one of the most common nosocomial pathogens and is
AB  - considered to be a significant threat to public health
AB  - worldwide. Here, we present the draft genome sequence of a multidrug-resistant
AB  - clinical strain of A. baumannii PKAB07 isolated from a wound infection in India
AB  - during 2011 to 2012.
ER  -

TY  - JOUR
AU  - Saravanan, M.
AU  - Bujnicki, J.M.
AU  - Cymerman, I.A.
AU  - Rao, D.N.
AU  - Nagaraja, V.
TI  - Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 6129
EP  - 6135
VL  - 32
AB  - The restriction endonuclease (REase) R.KpnI is an orthodox Type IIP enzyme, which binds to DNA
AB  - in the absence of metal ions and cleaves the DNA sequence 5'-GGTAC^C-3' in the presence of
AB  - Mg2+ as shown generating 3' four base overhangs. Bioinformatics analysis reveals that R.KpnI
AB  - contains a beta-beta-alpha-Me-finger fold, which is characteristic of many HNH-superfamily
AB  - endonucleases, including homing endonuclease I-HmuI, structure-specific T4 endonuclease VII,
AB  - colicin E9, sequence non-specific Serratia nuclease and sequence-specific homing endonuclease
AB  - I-PpoI. According to our homology model of R.KpnI, D148, H149 and Q175 correspond to the
AB  - critical D, H and N or H residues of the HNH nucleases. Substitutions of these three conserved
AB  - residues lead to the loss of the DNA cleavage activity by R.KpnI, confirming their importance.
AB  - The mutant Q175E fails to bind DNA at the standard conditions, although the DNA binding and
AB  - cleavage can be rescued at pH 6.0, indicating a role for Q175 in DNA binding and cleavage. Our
AB  - study provides the first experimental evidence for a Type IIP REase that does not belong to
AB  - the PD...D/EXK superfamily of nucleases, instead is a member of the HNH superfamily.
ER  -

TY  - JOUR
AU  - Saravanan, M.
AU  - Elango, K.
AU  - Chandrashekaran, S.
AU  - Anand, N.
AU  - Nagaraja, V.
TI  - A new type II restriction endonuclease, OfoI from nonheterocystous cynobacterium Oscillatoria foreaui.
JO  - Curr. Sci.
PY  - 2003
SP  - 188
EP  - 190
VL  - 85
AB  - Although restriction enzymes are widely distributed in nature, many bacterial genera are yet
AB  - to be explored for the presence of this important class of enzymes.  We have purified and
AB  - characterized a new type II restriction endonuclease, OfoI from a nonheterocyst cyanobacterium
AB  - Oscillatoria foreaui.  The recognition sequence has been determined by primer extension
AB  - analysis.  The purified enzyme OfoI recognizes and cleaves the palindromic hexanucleotide
AB  - 5'-C/YCGRG-3', generating 5'-protruding ends.
ER  -

TY  - JOUR
AU  - Saravanan, M.
AU  - Vasu, K.
AU  - Ghosh, S.
AU  - Nagaraja, V.
TI  - Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease.
JO  - J. Biol. Chem.
PY  - 2007
SP  - 32320
EP  - 32326
VL  - 282
AB  - We describe two uncommon roles for Zn2+ in enzyme KpnI restriction endonuclease (REase). Among
AB  - all of the REases studied, KpnI REase is unique in its DNA binding and cleavage
AB  - characteristics. The enzyme is a poor discriminator of DNA sequences, cleaving DNA in a
AB  - promiscuous manner in the presence of Mg2+. Unlike most Type II REases, the active site of the
AB  - enzyme comprises an HNH motif, which can accommodate Mg2+, Mn2+, or Ca2+. Among these metal
AB  - ions, Mg2+ and Mn2+ induce promiscuous cleavage by the enzyme, whereas Ca2+-bound enzyme
AB  - exhibits site-specific cleavage. Examination of the sequence of the protein revealed the
AB  - presence of a zinc finger CCCH motif rarely found in proteins of prokaryotic origin. The zinc
AB  - binding motif tightly coordinates zinc to provide a rigid structural framework for the enzyme
AB  - needed for its function. In addition to this structural scaffold, another atom of zinc binds
AB  - to the active site to induce high fidelity cleavage and suppress the Mg2+- and Mn2+-mediated
AB  - promiscuous behavior of the enzyme. This is the first demonstration of distinct structural and
AB  - catalytic roles for zinc in an enzyme, suggesting the distinct origin of KpnI REase.
ER  -

TY  - JOUR
AU  - Saravanan, M.
AU  - Vasu, K.
AU  - Kanakaraj, R.
AU  - Rao, D.N.
AU  - Nagaraja, V.
TI  - R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2777
EP  - 2786
VL  - 35
AB  - KpnI REase recognizes palindromic sequence, GGTAC downward arrowC, and forms complex in the
AB  - absence of divalent metal ions, but requires the ions for DNA cleavage. Unlike most other
AB  - REases, R.KpnI shows promiscuous DNA cleavage in the presence of Mg(2+). Surprisingly, Ca(2+)
AB  - suppresses the Mg(2+)-mediated promiscuous activity and induces high fidelity cleavage. To
AB  - further analyze these unique features of the enzyme, we have carried out DNA binding and
AB  - kinetic analysis. The metal ions which exhibit disparate pattern of DNA cleavage have no role
AB  - in DNA recognition. The enzyme binds to both canonical and non-canonical DNA with comparable
AB  - affinity irrespective of the metal ions used. Further, Ca(2+)-imparted exquisite specificity
AB  - of the enzyme is at the level of DNA cleavage and not at the binding step. With the canonical
AB  - oligonucleotides, the cleavage rate of the enzyme was comparable for both Mg(2+)- and
AB  - Mn(2+)-mediated reactions and was about three times slower with Ca(2+). The enzyme
AB  - discriminates non-canonical sequences poorly from the canonical sequence in Mg(2+)-mediated
AB  - reactions unlike any other Type II REases, accounting for the promiscuous behavior. R.KpnI,
AB  - thus displays properties akin to that of typical Type II REases and also endonucleases with
AB  - degenerate specificity in its DNA recognition and cleavage properties.
ER  -

TY  - JOUR
AU  - Saravanan, M.
AU  - Vasu, K.
AU  - Nagaraja, V.
TI  - Evolution of sequence specificity in a restriction endonuclease by a point mutation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 10344
EP  - 10347
VL  - 105
AB  - Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed
AB  - with exquisite sequence specificity. REases have
AB  - originated from the ancestral proteins and evolved new sequence
AB  - specificities by genetic recombination, gene duplication, replication
AB  - slippage, and transpositional events. They are also speculated to have
AB  - evolved from nonspecific endonucleases, attaining a high degree of
AB  - sequence specificity through point mutations. We describe here an example
AB  - of generation of exquisitely site-specific REase from a highly-promiscuous
AB  - one by a single point mutation.
ER  -

TY  - JOUR
AU  - Sargueil, B.
AU  - Delahodde, A.
AU  - Hatat, D.
AU  - Tian, G.L.
AU  - Lazowska, J.
AU  - Jacq, C.
TI  - A new specific DNA endonuclease activity in yeast mitochondria.
JO  - Mol. Gen. Genet.
PY  - 1991
SP  - 340
EP  - 341
VL  - 225
AB  - Two group I intron-encoded proteins from the yeast mitochondrial genome have already been
AB  - shown to have a specific DNA endonuclease activity. This activity mediates intron insertion by
AB  - cleaving the DNA sequence corresponding to the splice junction of an intronless strain. We
AB  - have discovered in mitochondrial extracts from the yeast strain 777-3A a new DNA endonuclease
AB  - activity which cleaves the fused exon A3-exon A4 junction sequence of the COXI gene.
ER  -

TY  - JOUR
AU  - Sargueil, B.
AU  - Hatat, D.
AU  - Delahodde, A.
AU  - Jacq, C.
TI  - In vivo and in vitro analyses of an intron-encoded DNA endonuclease from yeast mitochondria.  Recognition site by site-directed mutagenesis.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 5659
EP  - 5665
VL  - 18
AB  - The pal 4 nuclease (termed I-Sce II) is encoded in the group I aI 4 intron of the COX I gene
AB  - of Saccharomyces cerevisiae. It introduces a specific double-strand break at the junction of
AB  - the two exons A4-A5 and thus mediates the insertion of the intron into an intronless strain.
AB  - To define the sequence recognized by pal 4 we introduced 35 single mutations in its target
AB  - sequence and examined their cleavage properties either in vivo in E. coli (when different
AB  - forms of the paI 4 proteins were artificially produced) or in vitro with mitochondrial
AB  - extracts of a mutant yeast strain blocked in the splicing of the aI 4 intron. We also detected
AB  - the pal 4 DNA endonuclease activity in extracts of the wild type strain. The results suggest
AB  - that 6 to 9 noncontiguous bases in the 17 base-pair region examined are necessary for pal 4
AB  - nuclease to bind and cleave its recognition site. We observed that the pal 4 nuclease
AB  - specificity can be significantly different with the different forms of the protein thus
AB  - explaining why only some forms are highly toxic in E. coli. This study shows that pal 4
AB  - recognition site is a complex phenomenon and this might have evolutionary implications on the
AB  - transfer properties of the intron.
ER  -

TY  - JOUR
AU  - Saridaki, A.
AU  - Sapountzis, P.
AU  - Harris, H.L.
AU  - Batista, P.D.
AU  - Biliske, J.A.
AU  - Pavlikaki, H.
AU  - Oehler, S.
AU  - Savakis, C.
AU  - Braig, H.R.
AU  - Bourtzis, K.
TI  - Wolbachia Prophage DNA Adenine Methyltransferase Genes in Different Drosophila-Wolbachia Associations.
JO  - PLoS ONE
PY  - 2011
SP  - e19708
EP  - e19708
VL  - 6
AB  - Wolbachia is an obligatory intracellular bacterium which often manipulates the reproduction of
AB  - its insect and isopod hosts. In
AB  - contrast, Wolbachia is an essential symbiont in filarial nematodes.
AB  - Lately, Wolbachia has been implicated in genomic imprinting of host DNA
AB  - through cytosine methylation. The importance of DNA methylation in cell
AB  - fate and biology calls for in depth studing of putative
AB  - methylation-related genes. We present a molecular and phylogenetic
AB  - analysis of a putative DNA adenine methyltransferase encoded by a
AB  - prophage in the Wolbachia genome. Two slightly different copies of the
AB  - gene, met1 and met2, exhibit a different distribution over various
AB  - Wolbachia strains. The met2 gene is present in the majority of strains,
AB  - in wAu, however, it contains a frameshift caused by a 2 bp deletion.
AB  - Phylogenetic analysis of the met2 DNA sequences suggests a long
AB  - association of the gene with the Wolbachia host strains. In addition,
AB  - our analysis provides evidence for previously unnoticed multiple
AB  - infections, the detection of which is critical for the molecular
AB  - elucidation of modification and/or rescue mechanism of cytoplasmic
AB  - incompatibility.
ER  -

TY  - JOUR
AU  - Sarikhan, S.
AU  - Azarbaijani, R.
AU  - Yeganeh, L.P.
AU  - Fazeli, A.S.
AU  - Amoozegar, M.A.
AU  - Salekdeh, G.H.
TI  - Draft Genome Sequence of Nesterenkonia sp. Strain F, Isolated From Aran-Bidgol Salt Lake in Iran.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5580
EP  - 5580
VL  - 193
AB  - The draft genome of the aerobic, Gram-positive, halophilic chemoorganotroph Nesterenkonia sp.
AB  - strain F consists of a 2,812,133-bp
AB  - chromosome. This study is the first to report the shotgun-sequenced draft
AB  - genome of a member of the genus Nesterenkonia.
ER  -

TY  - JOUR
AU  - Sarker, M.S.A.
AU  - Rahman, M.T.
AU  - Mahmud, M.M.
AU  - Tagliamonte, M.S.
AU  - Chowdhury, S.M.Z.H.
AU  - Islam, M.R.
AU  - Rahman, M.B.
AU  - El Zowalaty, M.E.
AU  - Nazir, K.H.M.N.H.
TI  - First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00901
EP  - e00918
VL  - 7
AB  - Here, we report the first genome sequence of Pasteurella multocida BAUTB2 isolated from a
AB  - buffalo that died from hemorrhagic septicemia in Rajshahi,
AB  - Bangladesh. Using Illumina HiSeq technology, the BAUTB2 genome length was
AB  - determined to be 2,439,149 bp, with 40.8% GC content, 2,307 coding sequences
AB  - (CDS), 6 rRNAs, 51 tRNAs, and 4 noncoding RNAs (ncRNAs).
ER  -

TY  - JOUR
AU  - Sarma, M.H.
AU  - Dhingra, M.M.
AU  - Gupta, G.
AU  - Sarma, R.H.
TI  - Conformational Microheterogeniety in a DNA Double Helix:  Structure of Restriction Endonuclease BamHI Recognition Site.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1985
SP  - 269
EP  - 276
VL  - 131
AB  - Structural studies using 500 MHz 1H NMR spectroscopy on BamHI recognition site
AB  - d(GGATCC)2 in solution at 19C is reported.  The resonances from the sugar ring
AB  - and base protons have been assigned from the 2D-COSY and NOESY spectra.
AB  - Analyses of the NOESY cross-peaks between the base protons H8/H6 and sugar
AB  - protons H2'/H2", H3' reveal that the nucleotide units G2, A3 and C6 adopt
AB  - (C3'-endo, x = 200o-220o) conformation while G1, T4 and C5 exhibit (C2'-endo,
AB  - x= 240o-260o) conformation.  NMR data clearly suggest that the two strands of
AB  - d(GGATCC)2 are conformationally equivalent and there is a structural two-fold
AB  - between the two A-T pairs.  The above information and the NOESY data are used
AB  - to generate a structural model of d(GGATCC)2.  The important features are: (i)
AB  - G1-G2 stack, the site of cleavage, shows an alternation in sugar pucker i.e.
AB  - C2'-endo, C3'-endo as in a B-A junction, (ii) G2-A3 stack adopts a mini A-DNA,
AB  - both the sugars being C3'-endo, (iii) A3-T4 stack, the site of two-fold,
AB  - displays an A-B junction with alternation in sugar pucker as C3'-endo,
AB  - C2'-endo, (iv) T4-C5 stack adopts a mini B-DNA both the sugars being C2'-endo
AB  - and (v) C5-C6 stack exhibits a B-A junction with C2'-endo, C3'-endo sugar
AB  - puckers.  Thus, our studies demonstrate that conformational microheterogeniety
AB  - with a structural two fold, is present in the BamHI recognition site.
ER  -

TY  - JOUR
AU  - Sarnacki, S.H.
AU  - Marolda, C.L.
AU  - Noto, L.M.
AU  - Giacomodonato, M.N.
AU  - Valvano, M.A.
AU  - Cerquetti, M.C.
TI  - Dam methylation controls O-antigen chain length in Salmonella enterica serovar enteritidis by regulating the expression of Wzz protein.
JO  - J. Bacteriol.
PY  - 2009
SP  - 6694
EP  - 6700
VL  - 191
AB  - We reported previously that a Salmonella enterica serovar Enteritidis dam mutant  expressing a
AB  - truncated Dam protein does not agglutinate in the presence of
AB  - specific antibodies against O9 polysaccharide. Here we investigate the
AB  - participation of Dam in lipopolysaccharide (LPS) synthesis in Salmonella. The LPS
AB  - O-antigen profiles of a dam null mutant (SEDeltadam) and the Salmonella serovar
AB  - Enteritidis parental strain were examined by using electrophoresis and silver
AB  - staining. Compared to the parental strain, SEDeltadam produced LPS with shorter
AB  - O-antigen polysaccharide chains. Since Wzz is responsible for the chain length
AB  - distribution of the O antigen, we investigated whether Dam methylation is
AB  - involved in regulating wzz expression. Densitometry analysis showed that the
AB  - amount of Wzz produced by SEDeltadam is threefold lower than the amount of Wzz
AB  - produced by the parental strain. Concomitantly, the activity of the wzz promoter
AB  - in SEDeltadam was reduced nearly 50% in logarithmic phase and 25% in stationary
AB  - phase. These results were further confirmed by reverse transcription-PCR showing
AB  - that wzz gene expression was threefold lower in the dam mutant than in the
AB  - parental strain. Our results demonstrate that wzz gene expression is
AB  - downregulated in a dam mutant, indicating that Dam methylation activates
AB  - expression of this gene. This work indicates that wzz is a new target regulated
AB  - by Dam methylation and demonstrates that DNA methylation not only affects the
AB  - production of bacterial surface proteins but also the production of surface
AB  - polysaccharides.
ER  -

TY  - JOUR
AU  - Sarrade-Loucheur, A.
AU  - Xu, S.Y.
AU  - Chan, S.H.
TI  - The Role of the Methyltransferase Domain of Bifunctional Restriction Enzyme RM.BpuSI in Cleavage Activity.
JO  - PLoS ONE
PY  - 2013
SP  - e80967
EP  - e80967
VL  - 8
AB  - Restriction enzyme (REase) RM.BpuSI can be described as a Type IIS/C/G REase for its cleavage
AB  - site outside of the recognition sequence (Type IIS), bifunctional polypeptide possessing both
AB  - methyltransferase (MTase) and endonuclease activities (Type IIC) and endonuclease activity
AB  - stimulated by S-adenosyl-L-methionine (SAM) (Type IIG). The stimulatory effect of SAM on
AB  - cleavage activity presents a major paradox: a co-factor of the MTase activity that renders the
AB  - substrate unsusceptible to cleavage enhan es the cleavage activity. Here we show that the RM.
AB  - BpuSI MTase activity modifies both cleavage substrate and product only when they are
AB  - unmethylated. The MTase activity is, however, much lower than that of M1. BpuSI and is thought
AB  - not to be the major MTase for host DNA protection. SAM and sinefungin (SIN) increase the V-max
AB  - of the RM. BpuSI cleavage activity with a proportional change in Km, suggesting the presence
AB  - of an energetically more favorable pathway is taken. We further showed that RM. BpuSI under
AB  - goes substantial conformational changes in the presence of Ca2+, SIN, cleavage substrate
AB  - and/or product. Distinct conformers are inferred as the pre-cleavage/cleavage state (in the
AB  - presence of Ca2+, substrate or both) and MTase state (in the presence of SIN and substrate,
AB  - SIN and product or product alone). Interestingly, RM. BpuSI adopts a unique conformation when
AB  - only SIN is present. This SIN-bound state is inferred as a branch point for cleavage and MTase
AB  - activity and an intermediate to an energetically  favorable pathway for cleavage, probably
AB  - through increasing the binding affinity of the substrate to the enzyme under cleavage
AB  - conditions. Mutation of a SAM-binding residue resulted in altered conformational changes in
AB  - the presence of substrate or Ca2+ and eliminated cleavage activity. The present study
AB  - underscores the role of the MTase domain as facilitator of efficient cleavage activity for RM.
AB  - BpuSI.
ER  -

TY  - JOUR
AU  - Sarver, J.
AU  - Stone, K.
AU  - Townsend, J.
AU  - Sapienza, P.
AU  - Jen-Jacobson, L.
AU  - Saxena, S.
TI  - In the Arms of EcoRI - probing the Binding Specificity of the Restriction Endonuclease Using Electron Spin Resonance.
JO  - Biophys. J.
PY  - 2011
SP  - 144a
EP  - 145a
VL  - 100
AB  - Pulsed electron spin resonance (ESR) was used to probe the binding specificity of EcoRI, a
AB  - restriction endonuclease that binds to and cleaves a six base pair sequence of DNA. EcoRI
AB  - binds to the specific sequence GAATTC with an affinity that is 50,000-90,000-fold greater than
AB  - that of a miscognate site that differs by only one base pair. Low binding affinity is also
AB  - exhibited at non-specific binding sites which differ from the specific sequence by two or more
AB  - base pairs.  Distance measurements were performed on several spin labeled EcoRI mutants when
AB  - bound to specific, miscognate, and non-specific sequences of DNA using Double
AB  - Electron-Electron Resonance. These distances demonstrated that on average the arms of EcoRI,
AB  - thought to play a major role in binding specificity, are similarly positioned. Additionally,
AB  - noncognate (miscognate and non-specific) complexes demonstrated broader distance distributions
AB  - indicating that the flexibility
AB  - of the arms is greater in these complexes. Room temperature continuous
AB  - wave (CW) experiments were also performed on the EcoRI mutant complexes at both X-band and
AB  - W-band to probe the arm region dynamics. Higher sensitivity
AB  - to the fast motional dynamics of the spin label at W-band resolved differences in two of the
AB  - EcoRI complexes that were not apparent in the X-band CW spectra. Molecular dynamics (MD)
AB  - simulations were performed on the
AB  - spin-label-modified specific EcoRI-DNA crystal structure to model the average
AB  - nitroxide orientation. Disparity in average distance as well as distribution indicates a need
AB  - for further sampling of the spin label in silico. This work is supported by NSF.
ER  -

TY  - JOUR
AU  - Sasaki, H.
AU  - Ishikawa, H.
AU  - Asano, R.
AU  - Ueshiba, H.
AU  - Matsumoto, T.
AU  - Boot, R.
AU  - Kawamoto, E.
TI  - Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149T.
JO  - Genome Announcements
PY  - 2014
SP  - e00771
EP  - e00714
VL  - 2
AB  - Pasteurella pneumotropica is an opportunistic pathogen in rodents that is commonly isolated
AB  - from upper respiratory tracts in laboratory rodents. Here, we
AB  - report the draft genome sequence of the P. pneumotropica type strain ATCC 35149,
AB  - which was first isolated and characterized as biotype Jawetz.
ER  -

TY  - JOUR
AU  - Sasaki, J.
AU  - Murakami, M.
AU  - Yamada, Y.
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from Gluconobacter cerinus IFO 3285.
JO  - Agric. Biol. Chem.
PY  - 1985
SP  - 3017
EP  - 3022
VL  - 49
AB  - A type II restriction endonuclease designated as GceCLI, was purified from
AB  - cells of Gluconobacter cerinus IFO 3285.  The purified enzyme was found to be
AB  - homogeneous on polyacrylamide gel disc electrophoresis.  The enzyme worked best
AB  - at 37C and pH 7.5 and required 7mm MgCl2 and 100 mm NaCl.  The purified enzyme
AB  - was stable when preincubated over a pH range of 7.5 to 9.5 for 12 hr at 4C and
AB  - a temperature range of 37 to 40C for 5 min at pH 7.5.  The enzyme was shown to
AB  - cleave lambda, PhiX174 RF, SV40, pBR322, M13 mp7 RF and Ad2 DNAs at 4, 1,0,0,0
AB  - and 25 or more sites, respectively, and to recognize the DNA sequence of
AB  - 5'-C-C-G-G-3' and to cut between C and G on the right side of the sequence,
AB  - being an isoschizomer of SacII of Streptomyces achromogenes ATCC 12767.
ER  -

TY  - JOUR
AU  - Sasaki, J.
AU  - Yamada, Y.
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from Acetobacter liquefaciens AJ 2881.
JO  - Agric. Biol. Chem.
PY  - 1984
SP  - 3027
EP  - 3034
VL  - 48
AB  - A type II restriction endonuclease, designated as AliAJI, was purified from
AB  - cells of Acetobacter liquefaciens AJ 2881 by combined column chromatography on
AB  - heparin-Sepharose CL-6B, DEAE-Sepharose CL-6B and blue Sepharose CL-6B.  The
AB  - purified enzyme was homogeneous on polyacrylamide gel disc electrophoresis, and
AB  - the enzyme preparation was free from other nuclease activities, as judged by
AB  - constancy of lambda DNA-digest electrophoretic patterns after prolonged
AB  - incubation fro 24 hr.  The enzyme was optimally active at 37C at pH 7.5,
AB  - required neither sodium chloride nor ammonium sulfate, both of which rather
AB  - inhibited enzyme activity at high concentration (100 and 75 mM, respectively),
AB  - and cleaved lambda, PhiX174 RF, SV40, pBR322, M13 mp7RF and Ad2 DNAs at 18, 1,
AB  - 2, 1, 1 and 25 more sites, respectively.  The recognition sequence of the
AB  - enzyme on DNA molecules was determined to be 5'-C-T-G-C-A-G-3', and the enzyme
AB  - was found to cut between A and G in the sequence, being an isoschizomer of the
AB  - endonuclease of Providencia stuartii 164 (PstI).
ER  -

TY  - JOUR
AU  - Sasaki, M.
AU  - Akahira, A.
AU  - Oshiman, K.
AU  - Tsuchido, T.
AU  - Matsumura, Y.
TI  - Purification of cytochrome P450 and ferredoxin, involved in bisphenol A degradation, from Sphingomonas sp. strain AO1.
JO  - Appl. Environ. Microbiol.
PY  - 2005
SP  - 8024
EP  - 8030
VL  - 71
AB  - In a previous study (M. Sasaki, J. Maki, K. Oshiman, Y. Matsumura, and T.
AB  - Tsuchido, Biodegradation 16:449-459, 2005), the cytochrome P450 monooxygenase
AB  - system was shown to be involved in bisphenol A (BPA) degradation by Sphingomonas
AB  - sp. strain AO1. In the present investigation, we purified the components of this
AB  - monooxygenase, cytochrome P450 (P450bisd), ferredoxin (Fd(bisd)), and ferredoxin
AB  - reductase (Red(bisd)). We demonstrated that P450bisd and Fd(bisd) are homodimeric
AB  - proteins with molecular masses of 102.3 and 19.1 kDa, respectively, by gel
AB  - filtration chromatography analysis. Spectroscopic analysis of Fd(bisd) revealed
AB  - the presence of a putidaredoxin-type [2Fe-2S] cluster. P450(bisd), in the
AB  - presence of Fd(bisd), Red(bisd), and NADH, was able to convert BPA. The K(m) and
AB  - kcat values for BPA degradation were 85 +/- 4.7 microM and 3.9 +/- 0.04 min(-1),
AB  - respectively. NADPH, spinach ferredoxin, and spinach ferredoxin reductase
AB  - resulted in weak monooxygenase activity. These results indicated that the
AB  - electron transport system of P450bisd might exhibit strict specificity. Two BPA
AB  - degradation products of the P450(bisd) system were detected by high-performance
AB  - liquid chromatography analysis and were thought to be
AB  - 1,2-bis(4-hydroxyphenyl)-2-propanol and 2,2-bis(4-hydroxyphenyl)-1-propanol based
AB  - on mass spectrometry-mass spectrometry analysis. This is the first report
AB  - demonstrating that the cytochrome P450 monooxygenase system in bacteria is
AB  - involved in BPA degradation.
ER  -

TY  - JOUR
AU  - Sasaki, T.
AU  - Tsubakishita, S.
AU  - Kuwahara-Arai, K.
AU  - Matsuo, M.
AU  - Lu, Y.J.
AU  - Tanaka, Y.
AU  - Hiramatsu, K.
TI  - Complete Genome Sequence of Methicillin-Resistant Staphylococcus schleiferi Strain TSCC54 of Canine Origin.
JO  - Genome Announcements
PY  - 2015
SP  - e01268
EP  - e01215
VL  - 3
AB  - We report a complete genome sequence of the methicillin-resistant Staphylococcus  schleiferi
AB  - strain TSCC54, isolated from the skin of a dog in Tokyo, Japan.
ER  -

TY  - JOUR
AU  - Sasaki, Y.
AU  - Ishikawa, J.
AU  - Yamashita, A.
AU  - Oshima, K.
AU  - Kenri, T.
AU  - Furuya, K.
AU  - Yoshino, C.
AU  - Horino, A.
AU  - Shiba, T.
AU  - Sasaki, T.
AU  - Hattori, M.
TI  - The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 5293
EP  - 5300
VL  - 30
AB  - The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans
AB  - HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular
AB  - chromosome containing 1038 predicted coding sequences (CDSs), one set of rRNA genes and 30
AB  - tRNA genes. Among the 1038 CDSs, 264 predicted proteins are common to the Mycoplasmataceae
AB  - sequenced thus far and 463 are M.penetrans specific. The genome contains the two-component
AB  - system but lacks the essential cellular gene, uridine kinase. The relatively large genome of
AB  - M.penetrans HF-2 among mycoplasma species may be accounted for by both its rich core proteome
AB  - and the presence of a number of paralog families corresponding to 25.4% of all CDSs. The
AB  - largest paralog family is the p35 family, which encodes surface lipoproteins including the
AB  - major antigen, P35. A total of 44 genes for p35 and p35 homologs were identified and 30 of
AB  - them form one large cluster in the chromosome. The genetic tree of p35 paralogs suggests the
AB  - occurrence of dynamic chromosomal rearrangement in paralog formation during evolution. Thus,
AB  - M.penetrans HF-2 may have acquired diverse repertoires of antigenic variation-related genes to
AB  - allow its persistent infection in humans.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Connolly, B.A.
AU  - Halford, S.E.
AU  - Siksnys, V.
TI  - Site-specific DNA transesterification catalyzed by a restriction enzyme.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2007
SP  - 2115
EP  - 2120
VL  - 104
AB  - Most restriction endonucleases use Mg2+ to hydrolyze phosphodiester bonds at specific DNA
AB  - sites. We show here that Bfil, a
AB  - metal-independent restriction enzyme from the phospholipase D
AB  - superfamily, catalyzes both DNA hydrolysis and transesterification
AB  - reactions at its recognition site. In the presence of alcohols such as
AB  - ethanol or glycerol, it attaches the alcohol covalently to the 5'
AB  - terminus of the cleaved DNA. Under certain conditions, the terminal
AB  - 3'-OH of one DNA strand can attack the target phosphodiester bond in
AB  - the other strand to create a DNA hairpin. Transesterification reactions
AB  - on DNA with phosphorothioate linkages at the target bond proceed with
AB  - retention of stereoconfiguration at the phosphorus, indicating,
AB  - uniquely for a restriction enzyme, a two-step mechanism. We propose
AB  - that Bfil first makes a covalent enzyme-DNA intermediate, and then it
AB  - resolves it by a nucleophilic attack of water or an alcohol, to yield
AB  - hydrolysis or transesterification products, respectively.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Connolly, B.A.
AU  - Halford, S.E.
AU  - Siksnys, V.
TI  - Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 3969
EP  - 3977
VL  - 36
AB  - Restriction endonucleases catalyse DNA cleavage at specific sites. The BfiI endonuclease cuts
AB  - DNA to give staggered ends with 1-nt 3'-extensions.
AB  - We show here that BfiI can also fill in the staggered ends: while cleaving
AB  - DNA, it can add a 2'-deoxynucleoside to the reaction product to yield
AB  - directly a blunt-ended DNA. We propose that nucleoside incorporation
AB  - proceeds through a two-step reaction, in which BfiI first cleaves the DNA
AB  - to make a covalent enzyme-DNA intermediate and then resolves it by a
AB  - nucleophilic attack of the 3'-hydroxyl group of the incoming nucleoside,
AB  - to yield a transesterification product. We demonstrate that base pairing
AB  - of the incoming nucleoside with the protruding DNA end serves as a
AB  - template for the incorporation and governs the yield of the elongated
AB  - product. The efficiency of the template-directed process has been
AB  - exploited by using BfiI for the site-specific modification of DNA
AB  - 5'-termini with an amino group using a 5'-amino-5'-deoxythymidine.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Halford, S.E.
AU  - Siksnys, V.
TI  - How the BfiI restriction enzyme uses one active site to cut two DNA strands.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 6410
EP  - 6415
VL  - 100
AB  - Unlike other restriction enzymes, BfiI functions without metal ions. It recognizes an
AB  - asymmetric DNA sequence, 5'-ACTGGG-3', and cuts top and
AB  - bottom strands at fixed positions downstream of this sequence. Many
AB  - restriction enzymes are dimers of identical subunits, with one active site
AB  - for each DNA strand. Others, like FokI, dimerize transiently during
AB  - catalysis. BfiI is also a dimer but it has only one active site, at the
AB  - dimer interface. We show here that BfiI remains a dimer as it makes
AB  - double-strand breaks in DNA and that its single active site acts
AB  - sequentially, first on the bottom and then the top strand. Hence, after
AB  - cutting the bottom strand, a rearrangement of either the protein and/or
AB  - the DNA in the BfiI-DNA complex must switch the active site to the top
AB  - strand. Low pH values selectively block top-strand cleavage, converting
AB  - BfiI into a nicking enzyme that cleaves only the bottom strand. The switch
AB  - to the top strand may depend on the ionization of the cleaved 5' phosphate
AB  - in the bottom strand. BfiI thus uses a mechanism for making double-strand
AB  - breaks that is novel among restriction enzymes.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Jeltsch, A.
AU  - Pingoud, A.
AU  - Siksnys, V.
TI  - Plasmid DNA cleavage by MunI restriction enzyme: Single-turnover and steady-state kinetic analysis.
JO  - Biochemistry
PY  - 1999
SP  - 4028
EP  - 4036
VL  - 38
AB  - Mutational analysis has previously indicated that D83 and E98 residues are essential for DNA
AB  - cleavage activity and presumably chelate a Mg2+ ion at the active site of MunI restriction
AB  - enzyme. In the absence of metal ions, protonation of an ionizable residue with a pKa > 7.0,
AB  - most likely one of the active site carboxylates, controls the DNA binding specificity of MunI.
AB  - Thus, competition between H+ and Mg2+ binding at the active site of MunI presumably plays an
AB  - important role in catalysis/binding. In the present study we have identified elementary steps
AB  - and intermediates in the reaction pathway of plasmid DNA cleavage by MunI and elucidated the
AB  - effect of pH and Mg2+ ions on the individual steps of the DNA cleavage reaction. The kinetic
AB  - analysis indicated that the multiple-turnover rate of plasmid cleavage by MunI is limited by
AB  - product release     throughout the pH range 6.0-9.3. Quenched-flow experiments revealed that
AB  - open circle DNA is an obligatory intermediate in the reaction pathway. Under optimal reaction
AB  - conditions, open circle DNA remains bound to the MunI; however it is released into the
AB  - solution at low [MgCl2]. Rate constants for the phosphodiester bond hydrolysis of the first
AB  - (k1) and second (k2) strand of plasmid DNA at pH 7.0 and 10 mM MgCl2 more than 100-fold exceed
AB  - the kcat value which is limited by product dissociation. The analysis of the pH and [Mg2+]
AB  - dependences of k1 and k2 revealed that both H+ and Mg2+ ions compete for the binding to the
AB  - same residue at the active site of MunI. Thus, the decreased rate of phosphodiester hydrolysis
AB  - by MunI at pH < 7.0 may be due to the reduction of affinity for the Mg2+ binding at the active
AB  - site. Kinetic analysis of DNA cleavage by MunI yielded estimates for the
AB  - association-dissociation rate constants of enzyme-substrate complex and demonstrated the
AB  - decreased stability of the MunI-DNA complex at pH values above 8.0.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Kostiuk, G.
AU  - Tamulaitis, G.
AU  - Siksnys, V.
TI  - Target site cleavage by the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 8844
EP  - 8856
VL  - 39
AB  - Endonucleases that generate double-strand breaks in DNA often possess two identical subunits
AB  - related by rotational symmetry, arranged so that the
AB  - active sites from each subunit act on opposite DNA strands. In contrast to
AB  - many endonucleases, Type IIP restriction enzyme BcnI, which recognizes the
AB  - pseudopalindromic sequence 5'-CCSGG-3' (where S stands for C or G) and
AB  - cuts both DNA strands after the second C, is a monomer and possesses a
AB  - single catalytic center. We show here that to generate a double-strand
AB  - break BcnI nicks one DNA strand, switches its orientation on DNA to match
AB  - the polarity of the second strand and then cuts the phosphodiester bond on
AB  - the second DNA strand. Surprisingly, we find that an enzyme flip required
AB  - for the second DNA strand cleavage occurs without an excursion into bulk
AB  - solution, as the same BcnI molecule acts processively on both DNA strands.
AB  - We provide evidence that after cleavage of the first DNA strand, BcnI
AB  - remains associated with the nicked intermediate and relocates to the
AB  - opposite strand by a short range diffusive hopping on DNA.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Tamulaitiene, G.
AU  - Tamulaitis, G.
AU  - Calyseva, J.
AU  - Laime, M.
AU  - Rimseliene, R.
AU  - Lubys, A.
AU  - Siksnys, V.
TI  - UbaLAI is a monomeric Type IIE restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 9583
EP  - 9594
VL  - 45
AB  - Type II restriction endonucleases (REases) form a large and highly diverse group  of enzymes.
AB  - Even REases specific for a common recognition site often vary in
AB  - their oligomeric structure, domain organization and DNA cleavage mechanisms. Here
AB  - we report biochemical and structural characterization of the monomeric
AB  - restriction endonuclease UbaLAI, specific for the pseudosymmetric DNA sequence
AB  - 5'-CC/WGG-3' (where W = A/T, and '/' marks the cleavage position). We present a
AB  - 1.6 A co-crystal structure of UbaLAI N-terminal domain (UbaLAI-N) and show that
AB  - it resembles the B3-family domain of EcoRII specific for the 5'-CCWGG-3'
AB  - sequence. We also find that UbaLAI C-terminal domain (UbaLAI-C) is closely
AB  - related to the monomeric REase MvaI, another enzyme specific for the 5'-CCWGG-3'
AB  - sequence. Kinetic studies of UbaLAI revealed that it requires two recognition
AB  - sites for optimal activity, and, like other type IIE enzymes, uses one copy of a
AB  - recognition site to stimulate cleavage of a second copy. We propose that during
AB  - the reaction UbaLAI-N acts as a handle that tethers the monomeric UbaLAI-C domain
AB  - to the DNA, thereby helping UbaLAI-C to perform two sequential DNA nicking
AB  - reactions on the second recognition site during a single DNA-binding event. A
AB  - similar reaction mechanism may be characteristic to other monomeric two-domain
AB  - REases.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Zagorskaite, E.
AU  - Kauneckaite, K.
AU  - Tamulaitiene, G.
AU  - Siksnys, V.
TI  - Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 6144
EP  - 6155
VL  - 43
AB  - The eukaryotic Set and Ring Associated (SRA) domains and structurally similar DNA recognition
AB  - domains of prokaryotic cytosine modification-dependent restriction
AB  - endonucleases recognize methylated, hydroxymethylated or glucosylated cytosine in
AB  - various sequence contexts. Here, we report the apo-structure of the N-terminal
AB  - SRA-like domain of the cytosine modification-dependent restriction enzyme LpnPI
AB  - that recognizes modified cytosine in the 5'-C(mC)DG-3' target sequence (where mC
AB  - is 5-methylcytosine or 5-hydroxymethylcytosine and D = A/T/G). Structure-guided
AB  - mutational analysis revealed LpnPI residues involved in base-specific
AB  - interactions and demonstrated binding site plasticity that allowed limited target
AB  - sequence degeneracy. Furthermore, modular exchange of the LpnPI specificity loops
AB  - by structural equivalents of related enzymes AspBHI and SgrTI altered sequence
AB  - specificity of LpnPI. Taken together, our results pave the way for specificity
AB  - engineering of the cytosine modification-dependent restriction enzymes.
ER  -

TY  - JOUR
AU  - Sasnauskas, G.
AU  - Zakrys, L.
AU  - Zaremba, M.
AU  - Cosstick, R.
AU  - Gaynor, J.W.
AU  - Halford, S.E.
AU  - Siksnys, V.
TI  - A novel mechanism for the scission of double-stranded DNA: BfiI cuts both 3'-5' and 5'-3' strands by rotating a single active site.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 2399
EP  - 2410
VL  - 38
AB  - Metal-dependent nucleases that generate double-strand breaks in DNA often possess two
AB  - symmetrically-equivalent subunits, arranged so that the active
AB  - sites from each subunit act on opposite DNA strands. Restriction
AB  - endonuclease BfiI belongs to the phospholipase D (PLD) superfamily and
AB  - does not require metal ions for DNA cleavage. It exists as a dimer but has
AB  - at its subunit interface a single active site that acts sequentially on
AB  - both DNA strands. The active site contains two identical histidines
AB  - related by 2-fold symmetry, one from each subunit. This symmetrical
AB  - arrangement raises two questions: first, what is the role and the
AB  - contribution to catalysis of each His residue; secondly, how does a
AB  - nuclease with a single active site cut two DNA strands of opposite
AB  - polarities to generate a double-strand break. In this study, the roles of
AB  - active-site histidines in catalysis were dissected by analysing
AB  - heterodimeric variants of BfiI lacking the histidine in one subunit. These
AB  - variants revealed a novel mechanism for the scission of double-stranded
AB  - DNA, one that requires a single active site to not only switch between
AB  - strands but also to switch its orientation on the DNA.
ER  -

TY  - JOUR
AU  - Sass, P.
AU  - Berscheid, A.
AU  - Jansen, A.
AU  - Oedenkoven, M.
AU  - Szekat, C.
AU  - Strittmatter, A.
AU  - Gottschalk, G.
AU  - Bierbaum, G.
TI  - Genome Sequence of Staphylococcus aureus VC40, a Vancomycin- and Daptomycin-Resistant Strain, To Study the Genetics of Development of Resistance  to Currently Applied Last-Resort Antibiotics.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2107
EP  - 2108
VL  - 194
AB  - The increasing emergence of multidrug-resistant Staphylococcus aureus is a problem of global
AB  - importance. Here, we report the genome of S. aureus VC40, which
AB  - is resistant to the last-resort antibiotics vancomycin and daptomycin. Its genome
AB  - sequence will allow insights into the mechanisms that convey full resistance to
AB  - these compounds.
ER  -

TY  - JOUR
AU  - Sassera, D.
AU  - Gaiarsa, S.
AU  - Scaltriti, E.
AU  - Morganti, M.
AU  - Bandi, C.
AU  - Casadei, G.
AU  - Pongolini, S.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Manhattan Strain 111113, from an Outbreak of Human Infections in Northern Italy.
JO  - Genome Announcements
PY  - 2013
SP  - e00632
EP  - e00613
VL  - 1
AB  - We announce the draft genome sequence of Salmonella enterica subsp. enterica serovar Manhattan
AB  - strain 111113, isolated from a patient during an outbreak in
AB  - northern Italy. The genome, which was obtained with Illumina MiSeq technology, is
AB  - composed of 21 contigs for a total of 4,684,342 bp, with a G+C content of 52.17%.
ER  -

TY  - JOUR
AU  - Sassera, D.
AU  - Leardini, I.
AU  - Villa, L.
AU  - Comandatore, F.
AU  - Carta, C.
AU  - Almeida, A.
AU  - do Ceu, S.M.
AU  - Gaiarsa, S.
AU  - Marone, P.
AU  - Pozio, E.
AU  - Caccio, S.M.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain EPM1, Found in Association with a Culture of the Human Parasite Giardia duodenalis.
JO  - Genome Announcements
PY  - 2013
SP  - e00182
EP  - e00113
VL  - 1
AB  - We report the draft genome sequence of the Stenotrophomonas maltophilia strain EPM1, found in
AB  - association with a culture of Giardia duodenalis. The draft genome
AB  - sequence of S. maltophilia strain EPM1, obtained with Roche 454 GS-FLX Titanium
AB  - technology, is composed of 19 contigs totaling 4,785,869 bp, with a G+C content
AB  - of 66.37%.
ER  -

TY  - JOUR
AU  - Sassera, D.
AU  - Lo, N.
AU  - Epis, S.
AU  - D'Auria, G.
AU  - Montagna, M.
AU  - Comandatore, F.
AU  - Horner, D.
AU  - Pereto, J.
AU  - Luciano, A.M.
AU  - Franciosi, F.
AU  - Ferri, E.
AU  - Crotti, E.
AU  - Bazzocchi, C.
AU  - Daffonchio, D.
AU  - Sacchi, L.
AU  - Moya, A.
AU  - Latorre, A.
AU  - Bandi, C.
TI  - Phylogenomic evidence for the presence of a flagellum and cbb3 oxidase in the free-living mitochondrial ancestor.
JO  - Mol. Biol. Evol.
PY  - 2011
SP  - 3285
EP  - 3296
VL  - 28
AB  - The initiation of the intracellular symbiosis that would give rise to
AB  - mitochondria and eukaryotes was a major event in the history of life on
AB  - earth. Hypotheses to explain eukaryogenesis fall into two broad and
AB  - competing categories: those proposing that the host was a phagocytotic
AB  - proto-eukaryote that preyed upon the free-living mitochondrial ancestor
AB  - (hereafter FMA) and those proposing that the host was an archaebacterium
AB  - that engaged in syntrophy with the FMA. Of key importance to these
AB  - hypotheses are whether the FMA was motile or non-motile, and the
AB  - atmospheric conditions under which the FMA thrived. Reconstructions of the
AB  - FMA based on genome content of Rickettsiales representatives - generally
AB  - considered to be the closest living relatives of mitochondria - indicate
AB  - that it was non-motile and aerobic. We have sequenced the genome of
AB  - Candidatus Midichloria mitochondrii, a novel and phylogenetically
AB  - divergent member of the Rickettsiales. We found that it possesses unique
AB  - gene sets found in no other Rickettsiales, including 26 genes associated
AB  - with flagellar assembly, and a cbb(3)-type cytochrome oxidase.
AB  - Phylogenomic analyses show that these genes were inherited in a vertical
AB  - fashion from an ancestral alpha-proteobacterium, and indicate that the FMA
AB  - possessed a flagellum, and could undergo oxidative phosphorylation under
AB  - both aerobic and microoxic conditions. These results indicate that the FMA
AB  - played a more active and potentially parasitic role in eukaryogenesis than
AB  - currently appreciated, and provide an explanation for how the symbiosis
AB  - could have evolved under low levels of oxygen.
ER  -

TY  - JOUR
AU  - Sassi, M.
AU  - Croce, O.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Draft Genome Sequence of Mycobacterium triplex DSM 44626.
JO  - Genome Announcements
PY  - 2014
SP  - e00499
EP  - e00414
VL  - 2
AB  - We announce the draft genome sequence of Mycobacterium triplex strain DSM 44626,  a
AB  - nontuberculosis species responsible for opportunistic infections. The genome
AB  - described here is composed of 6,382,840 bp, with a G+C content of 66.57%, and
AB  - contains 5,988 protein-coding genes and 81 RNA genes.
ER  -

TY  - JOUR
AU  - Sassi, M.
AU  - Felden, B.
AU  - Augagneur, Y.
TI  - Draft Genome Sequence of Staphylococcus aureus subsp. aureus Strain HG003, an NCTC8325 Derivative.
JO  - Genome Announcements
PY  - 2014
SP  - e00855
EP  - e00814
VL  - 2
AB  - We report the draft genome sequence of a Staphylococcus aureus NCTC8325 derivative, strain
AB  - HG003. HG003 contains functional global regulators rsbU and
AB  - tcaR and is therefore considered as a reference for studies of regulation and
AB  - virulence. The genome is composed of 2,797,898 bp and will be essential for
AB  - subsequent RNAseq analysis.
ER  -

TY  - JOUR
AU  - Sassi, M.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Noncontiguous Genome Sequence of Mycobacterium septicum Strain DSM 44393T.
JO  - Genome Announcements
PY  - 2013
SP  - e00574
EP  - e00513
VL  - 1
AB  - The rapidly growing Mycobacterium septicum rarely causes pulmonary infections. We report here
AB  - the draft genome sequence of M. septicum strain DSM 44393(T),
AB  - isolated from catheter-related bacteremia and initially identified as a member of
AB  - Mycobacterium fortuitum.
ER  -

TY  - JOUR
AU  - Sassi, M.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Drancourt, M.
TI  - Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 306
EP  - 317
VL  - 8
AB  - Mycobacterium simiae is a non-tuberculosis mycobacterium causing pulmonary infections in both
AB  - immunocompetent and imunocompromized patients. We announce the
AB  - draft genome sequence of M. simiae DSM 44165(T). The 5,782,968-bp long genome
AB  - with 65.15% GC content (one chromosome, no plasmid) contains 5,727 open reading
AB  - frames (33% with unknown function and 11 ORFs sizing more than 5000 -bp), three
AB  - rRNA operons, 52 tRNA, one 66-bp tmRNA matching with tmRNA tags from
AB  - Mycobacterium avium, Mycobacterium tuberculosis, Mycobacterium bovis,
AB  - Mycobacterium microti, Mycobacterium marinum, and Mycobacterium africanum and 389
AB  - DNA repetitive sequences. Comparing ORFs and size distribution between M. simiae
AB  - and five other Mycobacterium species M. simiae clustered with M. abscessus and M.
AB  - smegmatis. A 40-kb prophage was predicted in addition to two prophage-like
AB  - elements, 7-kb and 18-kb in size, but no mycobacteriophage was seen after the
AB  - observation of 10(6) M. simiae cells. Fifteen putative CRISPRs were found. Three
AB  - genes were predicted to encode resistance to aminoglycosides, betalactams and
AB  - macrolide-lincosamide-streptogramin B. A total of 163 CAZYmes were annotated. M.
AB  - simiae contains ESX-1 to ESX-5 genes encoding for a type-VII secretion system.
AB  - Availability of the genome sequence may help depict the unique properties of this
AB  - environmental, opportunistic pathogen.
ER  -

TY  - JOUR
AU  - Sassi, M.
AU  - Sharma, D.
AU  - Brinsmade, S.R.
AU  - Felden, B.
AU  - Augagneur, Y.
TI  - Genome Sequence of the Clinical Isolate Staphylococcus aureus subsp. aureus Strain UAMS-1.
JO  - Genome Announcements
PY  - 2015
SP  - e01584
EP  - e01514
VL  - 3
AB  - We report here the draft genome sequence of Staphylococcus aureus subsp. aureus strain UAMS-1.
AB  - UAMS-1 is a virulent oxacillin-susceptible clinical isolate. Its
AB  - genome is composed of 2,763,963 bp and will be useful for further gene expression
AB  - analysis using RNA sequencing (RNA-seq) technology.
ER  -

TY  - JOUR
AU  - Sastre, D.E.
AU  - Santos, L.P.
AU  - Kagohara, E.
AU  - Andrade, L.H.
TI  - Draft Whole-Genome Sequence of Psychrotrophic Arthrobacter sp. Strain 7749, Isolated from Antarctic Marine Sediments with Applications in Enantioselective  Alcohol Oxidation.
JO  - Genome Announcements
PY  - 2017
SP  - e01197
EP  - e01117
VL  - 5
AB  - Here, we report the 4.12-Mb draft genome sequence of Arthrobacter sp. strain 7749, isolated
AB  - from marine sediment samples of the Antarctic Peninsula, using
AB  - enriched medium with (RS)-1-(4-phenyl)-ethanol as a carbon source. This genome
AB  - sequence will provide relevant information for applications in enantioselective
AB  - alcohol oxidation to improve industrial catalytic processes.
ER  -

TY  - JOUR
AU  - Sater, M.R.
AU  - Lamelas, A.
AU  - Wang, G.
AU  - Clark, T.A.
AU  - Roltgen, K.
AU  - Mane, S.
AU  - Korlach, J.
AU  - Pluschke, G.
AU  - Schmid, C.D.
TI  - DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates.
JO  - PLoS ONE
PY  - 2015
SP  - e0144612
EP  - e0144612
VL  - 10
AB  - The Gram-negative bacterium Neisseria meningitidis features extensive genetic variability. To
AB  - present, proposed virulence genotypes are also detected in
AB  - isolates from asymptomatic carriers, indicating more complex mechanisms
AB  - underlying variable colonization modes of N. meningitidis. We applied the Single
AB  - Molecule, Real-Time (SMRT) sequencing method from Pacific Biosciences to assess
AB  - the genome-wide DNA modification profiles of two genetically related N.
AB  - meningitidis strains, both of serogroup A. The resulting DNA methylomes revealed
AB  - clear divergences, represented by the detection of shared and of strain-specific
AB  - DNA methylation target motifs. The positional distribution of these methylated
AB  - target sites within the genomic sequences displayed clear biases, which suggest a
AB  - functional role of DNA methylation related to the regulation of genes. DNA
AB  - methylation in N. meningitidis has a likely underestimated potential for
AB  - variability, as evidenced by a careful analysis of the ORF status of a panel of
AB  - confirmed and predicted DNA methyltransferase genes in an extended collection of
AB  - N. meningitidis strains of serogroup A. Based on high coverage short sequence
AB  - reads, we find phase variability as a major contributor to the variability in DNA
AB  - methylation. Taking into account the phase variable loci, the inferred functional
AB  - status of DNA methyltransferase genes matched the observed methylation profiles.
AB  - Towards an elucidation of presently incompletely characterized functional
AB  - consequences of DNA methylation in N. meningitidis, we reveal a prominent
AB  - colocalization of methylated bases with Single Nucleotide Polymorphisms (SNPs)
AB  - detected within our genomic sequence collection. As a novel observation we report
AB  - increased mutability also at 6mA methylated nucleotides, complementing mutational
AB  - hotspots previously described at 5mC methylated nucleotides. These findings
AB  - suggest a more diverse role of DNA methylation and Restriction-Modification (RM)
AB  - systems in the evolution of prokaryotic genomes.
ER  -

TY  - JOUR
AU  - Sato'o, Y.
AU  - Hisatsune, J.
AU  - Hirakawa, H.
AU  - Ono, H.K.
AU  - Omoe, K.
AU  - Sugai, M.
TI  - Complete Sequence of a Staphylococcus aureus Clonal Complex 81 Strain, the Dominant Lineage in Food Poisoning Outbreaks in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e00853
EP  - e00817
VL  - 5
AB  - Staphylococcus aureus No. 10 is an isolate from a staphylococcal food poisoning outbreak in
AB  - Japan, classified as clonal complex 81 subtype 1. It preferentially
AB  - produces larger quantities of staphylococcal enterotoxin A (SEA) and
AB  - staphylococcal enterotoxin H (SEH) in foods and media. Here, we report the
AB  - complete annotated genome sequence of the chromosome and a plasmid.
ER  -

TY  - JOUR
AU  - Sato, H.
AU  - Suzuki, T.
AU  - Yamada, Y.
TI  - Purification of restriction endonuclease from Acetobacter aceti IFO 3281 (AatII) and its properties.
JO  - Agric. Biol. Chem.
PY  - 1990
SP  - 3319
EP  - 3325
VL  - 54
AB  - The restriction endonuclease AatII was purified from cell-free extracts of
AB  - Acetobacter aceti IFO 3281 by streptomycin treatment, ammonium sulfate
AB  - fractionation, combined column chromatographies on DEAE-Toyopearl 650S,
AB  - heparin-Sepharose CL-6B and DEAE-Sepharose CL-6B and FPLC on Mono Q and on
AB  - Superose 12 (gel filtration).  The purified enzyme was homogeneous on
AB  - SDS-polyacrylamide gel disk electrophoresis.  The relative molecular mass of
AB  - the purified enzyme was 190,000 daltons by gel filtration.  The
AB  - SDS-polyacrylamide gel disk electrophoresis gave the relative molecular mass of
AB  - 47,500 daltons.  These data indicated that the purified, native enzyme is a
AB  - tetramer (190,000 daltons) composed of four 47,500-dalton subunits.  The
AB  - isoelectric point of the enzyme was 6.0.  The purified enzyme was intensely
AB  - activated by manganese ion (50-fold increase or more when compared with
AB  - magnesium ion).  The enzyme worked best at 37C and pH 8.5 in a reaction mixture
AB  - (50 microliters) containing 1.0 micrograms lambda DNA, 10 mM Tris-HCI, 7 mM
AB  - 2-mercaptoethanol, 7 mM MnCl2 and 50 mM NaCl.  The enzyme recognizes the same
AB  - palindromic hexanucleotide sequence 5'-GACGTC-3', cuts between T and C and
AB  - produces a 3'-tetranucleotide extension in the presence of MnCl2, as it does in
AB  - the presence of MgCl2.
ER  -

TY  - JOUR
AU  - Sato, H.
AU  - Yamada, Y.
TI  - The restriction endonuclease AatI from Acetobacter aceti IFO 3281, an isoschizomer of StuI, has a dimeric structure.
JO  - J. Gen. Appl. Microbiol.
PY  - 1990
SP  - 273
EP  - 277
VL  - 36
AB  - The restriction endonuclease AatI, an isoschizomer of the StuI endonuclease,
AB  - was first reported in Acetobacter aceti IFO 3281 by Sugisaki et al.  However, a
AB  - detailed enzymatic study has not been done as yet regarding the AatI
AB  - endonuclease.  During the course of our studies on acetic acid bacteria, we
AB  - purified the AatI endonuclease to a homogeneous state and found that the enzyme
AB  - has a dimeric structure.  This paper describes the purification and properties
AB  - of the AatI endonuclease.
ER  -

TY  - JOUR
AU  - Sato, S.
AU  - Hutchison, C.A. III
AU  - Harris, J.I.
TI  - A thermostable sequence-specific endonuclease from Thermus aquaticus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1977
SP  - 542
EP  - 546
VL  - 74
AB  - A sequence-specific endonuclease, TaqI, of novel specificity has been partially purified from
AB  - an extreme thermophile, Thermus aquaticus.  The enzyme cleaves bacteriophage lambda DNA at
AB  - many (>30) sites and bacteriophage PhiX174 RF DNA at 10 sites.  The enzyme is active at
AB  - temperatures up to 79C.  The cleavage sites on PhiX174 RF DNA have been mapped.  The sequence
AB  - recognized and cleaved by TaqI has been shown to be the symmetrical tetranucleotide:
AB  - 5' T-^C-G-A 3'
AB  - 3' A-G-C-^T 5'.
ER  -

TY  - JOUR
AU  - Sato, S.
AU  - Nakazawa, K.
AU  - Shinomiya, T.
TI  - A DNA methylase from Thermus thermophilus HB8.
JO  - J. Biochem. (Tokyo)
PY  - 1980
SP  - 737
EP  - 747
VL  - 88
AB  - A DNA methylase was purified in a homogeneous state from an extremely
AB  - thermophilic bacterium, Thermus thermophilus HB8, by chromatography on,
AB  - successively, phosphocellulose, CM-cellulose, and haparin-Sepharose.  The
AB  - molecular weight of the enzyme was determined to be about 44,000 by gel
AB  - filtration on a Sephadex G-100 column and 41,000 by SDS-polyacrylamide gel
AB  - electrophoresis, and these findings suggest a single polypeptide enzyme.  The
AB  - enzyme develops maximum activity around pH 7.4 and at 70C.  Enzymatic activity
AB  - is completely inhibited by 0.2M NaCl or 2 mM HgCl2.  The enzyme transfers
AB  - methyl groups from S-adenosyl-L-methionine to a double stranded DNA.  The sole
AB  - product of the reaction was identified as N-6-methyl adenine after hydrolysis
AB  - of the DNA with formic acid.  The enzyme kinetics obey the Michaelis-Menten
AB  - equation and Km values for S-adenosylmethionine and lambda phage DNA were
AB  - determined to be 0.8 microM and 10 microgram/ml, respectively.  The enzyme does
AB  - not transfer methyl groups to TthHB8I endonuclease digested DNA as well as the
AB  - host (T. thermophilus HB8) DNA.  The number of methyl groups of the fully
AB  - methylated PhiX174 RF DNA was about twice as many as TthHB8I endonuclease sites
AB  - on the DNA.  The distribution of the methyl groups of PhiX174 RF DNA among the
AB  - HaeIII  fragments was the same as that of TthHB8I endonuclease sites,
AB  - suggesting that this DNA methylase is the other component of the
AB  - modification-restriction system including TthHB8I endonuclease.  The enzyme
AB  - probably recognizes the sequence, 5'-TCGA-3', in a double stranded DNA and
AB  - probably methylates adenine in the above sequence.
ER  -

TY  - JOUR
AU  - Sato, S.
AU  - Shinomiya, T.
TI  - An isoschizomer of TaqI from Thermus thermophilus HB8.
JO  - J. Biochem. (Tokyo)
PY  - 1978
SP  - 1319
EP  - 1321
VL  - 84
AB  - A site-specific endonuclease has been isolated from Thermus thermophilus HB8
AB  - and named TthHB81.  It recognizes the same sequences as TaqI from Thermus
AB  - aquaticus TY-1 does.  The amount of Tth HB81 in the cells was comparable to
AB  - that of TaqI.  T. thermophilus HB8 has an advantage over T. aquaticus YT-1 for
AB  - preparation of a TaqI-like enzyme since it is easier to obtain T. thermophilus
AB  - HB8 cells in quantity.
ER  -

TY  - JOUR
AU  - Sato, S.
AU  - Umemura, M.
AU  - Koike, H.
AU  - Habe, H.
TI  - Draft Genome Sequence of Gluconobacter frateurii NBRC 103465, a Glyceric Acid-Producing Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00369
EP  - e00313
VL  - 1
AB  - Gluconobacter frateurii strain NBRC 103465 can efficiently produce glyceric acid  (GA) from
AB  - raw glycerol feedstock derived from biodiesel fuel production
AB  - processes. Here, we report the 3.4-Mb draft genome sequence of G. frateurii NBRC
AB  - 103465. The draft genome sequence can be applied to examine the enzymes and
AB  - electron transport system involved in GA production.
ER  -

TY  - JOUR
AU  - Sato, T.
AU  - Ohkoshi, Y.
AU  - Wada, T.
AU  - Fukushima, Y.
AU  - Murabayashi, H.
AU  - Takakuwa, Y.
AU  - Nishiyama, K.
AU  - Shiraishi, T.
AU  - Nakajima, C.
AU  - Suzuki, Y.
AU  - Yokota, S.I.
TI  - Complete Genome Sequence of Multidrug-Resistant Streptococcus pneumoniae Serotype 19F Isolated from an Invasive Infection in Sapporo, Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01239
EP  - e01217
VL  - 5
AB  - Invasive infection of multidrug-resistant Streptococcus pneumoniae is a serious clinical
AB  - concern. Here, we report the complete genome sequence of a
AB  - multidrug-resistant S. pneumoniae serotype 19F strain isolated from a patient
AB  - with an invasive infection in Sapporo, Japan.
ER  -

TY  - JOUR
AU  - Sato, T.
AU  - Shimizu, T.
AU  - Watarai, M.
AU  - Kobayashi, M.
AU  - Kano, S.
AU  - Hamabata, T.
AU  - Takeda, Y.
AU  - Yamasaki, S.
TI  - Genome analysis of a novel Shiga toxin 1 (Stx1)-converting phage which is closely related to Stx2-converting phages but not to other Stx1-converting phages.
JO  - J. Bacteriol.
PY  - 2003
SP  - 3966
EP  - 3971
VL  - 185
AB  - Two Stx-converting phages, designated Stx1 phi and Stx2 phi-II, were isolated from an
AB  - Escherichia coli O157:H7 strain, Morioka V526, and their
AB  - entire nucleotide sequences were determined. The genomes of both phages
AB  - were similar except for the stx gene-flanking regions. Comparing these
AB  - phages to other known Stx-converting phages, we concluded that Stx1 phi is
AB  - a novel Stx1-converting phage closely related to Stx2-converting phages so
AB  - far reported.
ER  -

TY  - JOUR
AU  - Sato, Y.
AU  - Koike, H.
AU  - Kondo, S.
AU  - Hori, T.
AU  - Kanno, M.
AU  - Kimura, N.
AU  - Morita, T.
AU  - Kirimura, K.
AU  - Habe, H.
TI  - Draft Genome Sequence of Burkholderia stabilis LA20W, a Trehalose Producer That Uses Levulinic Acid as a Substrate.
JO  - Genome Announcements
PY  - 2016
SP  - e00795
EP  - e00716
VL  - 4
AB  - Burkholderia stabilis LA20W produces trehalose using levulinic acid (LA) as a substrate. Here,
AB  - we report the 7.97-Mb draft genome sequence of B. stabilis
AB  - LA20W, which will be useful in investigations of the enzymes involved in LA
AB  - metabolism and the mechanism of LA-induced trehalose production.
ER  -

TY  - JOUR
AU  - Satoh, K.
AU  - Arai, H.
AU  - Sanzen, T.
AU  - Kawaguchi, Y.
AU  - Hayashi, H.
AU  - Yokobori, S.I.
AU  - Yamagishi, A.
AU  - Oono, Y.
AU  - Narumi, I.
TI  - Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125,  Isolated from the High Atmosphere above Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00080
EP  - e00018
VL  - 6
AB  - Deinococcus aerius strain TR0125 is a bacterium isolated from the high atmosphere above Japan
AB  - that shows strong resistance to desiccation, UV-C, and gamma
AB  - radiation. Here, we report the draft genome sequence of D. aerius (4.5 Mb), which
AB  - may provide useful genetic information supporting its biochemical features.
ER  -

TY  - JOUR
AU  - Satoh, K.
AU  - Onodera, T.
AU  - Omoso, K.
AU  - Takeda-Yano, K.
AU  - Katayama, T.
AU  - Oono, Y.
AU  - Narumi, I.
TI  - Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e01631
EP  - e01615
VL  - 4
AB  - Deinococcus grandis is a radioresistant bacterium isolated from freshwater fish in Japan. Here
AB  - we reported the draft genome sequence of D. grandis (4.1 Mb),
AB  - which will be useful for elucidating the common principles of radioresistance in
AB  - Deinococcus species through the comparative analysis of genomic sequences.
ER  -

TY  - JOUR
AU  - Satou, K.
AU  - Shimoji, M.
AU  - Tamotsu, H.
AU  - Juan, A.
AU  - Ashimine, N.
AU  - Shinzato, M.
AU  - Toma, C.
AU  - Nohara, T.
AU  - Shiroma, A.
AU  - Nakano, K.
AU  - Teruya, K.
AU  - Terabayashi, Y.
AU  - Ohki, S.
AU  - Koizumi, N.
AU  - Okano, S.
AU  - Suzuki, T.
AU  - Hirano, T.
TI  - Complete Genome Sequences of Low-Passage Virulent and High-Passage Avirulent Variants of Pathogenic Leptospira interrogans Serovar Manilae Strain UP-MMC-NIID,  Originally Isolated from a Patient with Severe Leptospirosis, Determined Using  PacBio Single-.
JO  - Genome Announcements
PY  - 2015
SP  - e00882
EP  - e00815
VL  - 3
AB  - Here, we report the complete genome sequences of low-passage virulent and high-passage
AB  - avirulent variants of pathogenic Leptospira interrogans serovar
AB  - Manilae strain UP-MMC-NIID, a major causative agent of leptospirosis. While there
AB  - were no major differences between the genome sequences, the levels of base
AB  - modifications were higher in the avirulent variant.
ER  -

TY  - JOUR
AU  - Satou, K.
AU  - Shiroma, A.
AU  - Teruya, K.
AU  - Shimoji, M.
AU  - Nakano, K.
AU  - Juan, A.
AU  - Tamotsu, H.
AU  - Terabayashi, Y.
AU  - Aoyama, M.
AU  - Teruya, M.
AU  - Suzuki, R.
AU  - Matsuda, M.
AU  - Sekine, A.
AU  - Kinjo, N.
AU  - Kinjo, F.
AU  - Yamaoka, Y.
AU  - Hirano, T.
TI  - Complete Genome Sequences of Eight Helicobacter pylori Strains with Different Virulence Factor Genotypes and Methylation Profiles, Isolated from Patients with Diverse Gastrointestinal Diseases on Okinawa Island, Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e00286
EP  - e00214
VL  - 2
AB  - We report the complete genome sequences of eight Helicobacter pylori strains isolated from
AB  - patients with gastrointestinal diseases in Okinawa, Japan.
AB  - Whole-genome sequencing and DNA methylation detection were performed using the PacBio
AB  - platform. De novo assembly determined a single, complete contig for each strain. Furthermore,
AB  - methylation analysis identified virulence factor genotype-dependent motifs.
ER  -

TY  - JOUR
AU  - Saunders, E. et al.
TI  - Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 174
EP  - 182
VL  - 1
AB  - Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended Wurdemann et al. 2009  is the type
AB  - species of the genus Eggerthella, which belongs to the
AB  - actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive,
AB  - non-motile, non-sporulating pathogenic bacterium that can cause severe
AB  - bacteremia. The strain described in this study has been isolated from a rectal
AB  - tumor in 1935. Here we describe the features of this organism, together with the
AB  - complete genome sequence, and annotation. This is the first complete genome
AB  - sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon
AB  - genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Saunders, E. et al.
TI  - Complete genome sequence of Haloterrigena turkmenica type strain (4k).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 107
EP  - 116
VL  - 2
AB  - Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is
AB  - the type species of the genus Haloterrigena in the euryarchaeal
AB  - family Halobacteriaceae. It is of phylogenetic interest because of the yet
AB  - unclear position of the genera Haloterrigena and Natrinema within the
AB  - Halobacteriaceae, which created some taxonomic problems historically. H.
AB  - turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a
AB  - relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme
AB  - halophile, requiring at least 2 M NaCl for growth. Here we describe the features
AB  - of this organism, together with the complete genome sequence, and annotation.
AB  - This is the first complete genome sequence of the genus Haloterrigena, but the
AB  - eighth genome sequence from a member of the family Halobacteriaceae. The
AB  - 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63
AB  - RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Saunders, N.
AU  - Snyder, L.
TI  - The minimal mobile element.
JO  - Microbiology
PY  - 2002
SP  - 3756
EP  - 3760
VL  - 148
AB  - Horizontal transfer of genes is an integral component of bacterial evolution and is
AB  - particularly associated with processes related to environmental adaptation and virulence.  The
AB  - association of many host adaptive and virulence genes with mobile genetic elements such as
AB  - transposases and bacteriophages rejects this.  Presumably the association of the gene
AB  - conferring some competitive advantage for the recipient strain facilitates the dissemination
AB  - of the mobile element.  The presence of larger elements such as pathogenicity islands or
AB  - islands of horizontal transfer is also characteristic of some bacterial species.  However,
AB  - analysis of complete bacterial genomes suggests a previously unrecognized mechanism of
AB  - mobilization that utilizes natural transformation and homologous recombination, and that is
AB  - independent of transposases and other mobilization mechanisms.
ER  -

TY  - JOUR
AU  - Saunders, N.J.
AU  - Jeffries, A.C.
AU  - Peden, P.F.
AU  - Hood, D.W.
AU  - Tettelin, H.
AU  - Rappuoli, R.
AU  - Moxon, E.R.
TI  - Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58.
JO  - Mol. Microbiol.
PY  - 2000
SP  - 207
EP  - 215
VL  - 37
AB  - Phase variation, mediated through variation in the length of simple sequence repeats, is
AB  - recognized as an important mechanism for
AB  - controlling the expression of factors involved in bacterial virulence.
AB  - Phase variation is associated with most of the currently recognized
AB  - virulence determinants of Neisseria meningitidis. Based upon the
AB  - complete genome sequence of the N. meningitidis serogroup B strain
AB  - MC58, we have identified tracts of potentially unstable simple sequence
AB  - repeats and their potential functional significance determined on the
AB  - basis of sequence context. Of the 65 potentially phase variable genes
AB  - identified, only 13 were previously recognized. Comparison with the
AB  - sequences from the other two pathogenic Neisseria sequencing projects
AB  - shows differences in the length of the repeats in 36 of the 65 genes
AB  - identified, including 25 of those not previously known to be phase
AB  - variable. Six genes that did not have differences in the length of the
AB  - repeat instead had polymorphisms such that the gene would not be
AB  - expected to be phase variable in at least one of the other strains. A
AB  - further 12 candidates did not have homologues in either of the other
AB  - two genome sequences. The large proportion of these genes that are
AB  - associated with frameshifts and with differences in repeat length
AB  - between the neisserial genome sequences is further corroborative
AB  - evidence that they are phase variable. The number of potentially phase
AB  - variable genes is substantially greater than for any other species
AB  - studied to date, and would allow N. meningitidis to generate a very
AB  - large repertoire of phenotypes through expression of these genes in
AB  - different combinations. Novel phase variable candidates identified in
AB  - the strain MC58 genome sequence include a spectrum of genes encoding
AB  - glycosyltransferases, toxin related products, and metabolic activities
AB  - as well as several restriction/modification and bacteriocin-related
AB  - genes and a number of open reading frames (ORFs) for which the function
AB  - is currently unknown. This suggests that the potential role of phase
AB  - variation in mediating bacterium-host interactions is much greater than
AB  - has been appreciated to date. Analysis of the distribution of
AB  - homopolymeric tract lengths indicates that this species has
AB  - sequence-specific mutational biases that favour the instability of
AB  - sequences associated with phase variation.
ER  -

TY  - JOUR
AU  - Saunders, N.J.
AU  - Peden, J.F.
AU  - Hood, D.W.
AU  - Moxon, E.R.
TI  - Simple sequence repeats in the Helicobacter pylori genome.
JO  - Mol. Microbiol.
PY  - 1998
SP  - 1091
EP  - 1098
VL  - 27
AB  - We describe an integrated system for the analysis of DNA sequence motifs within complete
AB  - bacterial genome sequences.  This system is based around ACeDB, a genome database with an
AB  - integrated graphical user interface; we identify and display motifs in the context of genetic,
AB  - sequence and bibliographic data.  Tomb et al. (1997) previously reported the identification of
AB  - contingency genes in Helicobacter pylori through their association with homopolymeric tracts
AB  - and dinucleotide repeats.  With this as a starting point, we validated the system by a search
AB  - for this type of repeat and used the contextual information to assess the likelihood that they
AB  - mediate phase variation in the associated open reading frames.  We found all of the repeats
AB  - previously described, and identified 27 putative phase-variable genes (including 17 previously
AB  - described).  These could be divided into three groups: lipopolysaccharide biosynthesis,
AB  - cell-surface-associated proteins and DNA restriction/modification systems.  Five of the
AB  - putative genes did not have obvious homologues in any of the public domain sequence databases.
AB  - The reading frame of some ORFs was disrupted by the presence of the repeats, including the
AB  - alpha(1-2) fucosyltransferase gene, necessary for the synthesis of the Lewis Y epitope.  An
AB  - additional benefit of this approach is that the results of each search can be analyzed further
AB  - and compared with those from other genomes.  This revealed that H. pylori has an unusually
AB  - high frequency of homopurine:homopyrimidine repeats suggesting mechanistic biases that favor
AB  - their presence and instability.
ER  -

TY  - JOUR
AU  - Saves, I.
AU  - Eleaume, H.
AU  - Dietrich, J.
AU  - Masson, J.-M.
TI  - The Thy Pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 4391
EP  - 4396
VL  - 28
AB  - Thy Pol-2 intein, from Thermococcus hydrothermalis, belongs to the same allelic family as
AB  - TliPol-2 (PI-TliI), Tfu Pol-2 (PI-TfuII) and TspTY Pol-3 mini-intein, all inserted at the
AB  - pol-c site of archaeal DNA polymerase genes. This new intein was cloned, expressed in
AB  - Escherichia coli and purified. The intein is a specific endonuclease (PI-ThyI) which cleaves
AB  - the inteinless sequence of the ThyDNA pol gene.  Moreover, PI-TliI, PI-TfuII and PI-ThyI are
AB  - very similar endonucleases which cleave DNA in the same optimal conditions at 70 degrees C
AB  - yielding similar 3'-hydroxyl overhangs of 4 bp and the reaction is subject to product
AB  - inhibition. The three enzymes are able to cleave the three DNA sequences spanning the pol-c
AB  - site and a 24 bp consensus cleavage site was defined for the three isoschizomers. However, the
AB  - exact size of the minimal cleavage site depends both on the substrate sequence and the
AB  - endonuclease. The inability of the isoschizomers to cleave the inteinless DNA polymerase gene
AB  - from Pyrococcus spp. KOD is due to point substitutions on the 5' side of the pol-c site,
AB  - suggesting that the absence of inteins of this allelic family in DNA polymerase genes from
AB  - Pyrococcus spp. can be linked to small differences in the target site sequence.
ER  -

TY  - JOUR
AU  - Saves, I.
AU  - Morlot, C.
AU  - Thion, L.
AU  - Rolland, J.-L.
AU  - Dietrich, J.
AU  - Masson, J.-M.
TI  - Investigating the endonuclease activity of four Pyrococcus abyssi inteins.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 4158
EP  - 4165
VL  - 30
AB  - Among the 14 inteins of the Pyrococcus abyssi genome, 10 harbour the LAGLIDADG motifs of
AB  - dodecapeptide endonucleases.  Four of these were cloned, expressed in Escherichia coli and
AB  - purified to assay their potential endonuclease activity.  PabRIR1-2 and PabRIR1-3 are specific
AB  - endonucleases, named PI-PabI and PI-PabII, respectively, cleaving the sequence spanning their
AB  - homing site.  This is consistent with their size and with the relative positions and sequences
AB  - of their endonuclease motifs.  However, PI-PabI is 10-fold more active than PI-PabII and a
AB  - discrepancy of the DNA recognition and cleavage mechanisms was observed between the two
AB  - inteins.  In particular, analysis of the DNA cleavage reactions by MALDI-TOF highlighted that
AB  - while the cleavage of DNA by PI-PabI consists of two steps corresponding to the cleavage of
AB  - each DNA strand, PI-PabII processes the two DNA strands simultaneously.  Furthermore, the two
AB  - inteins interact differently with DNA.  In addition, we did not detect any endonuclease
AB  - activity for PabLon and PabRIR1-1.  deletions in the intein sequences and mutations in the
AB  - putative endonuclease motifs probably abolish this activity.  Hence, inteins from the same
AB  - archaebacteria, even if contained in the same host protein, did not evolve uniformly and are
AB  - presumably at different stages of the invasion cycle.
ER  -

TY  - JOUR
AU  - Saves, I.
AU  - Ozanne, V.
AU  - Dietrich, J.
AU  - Masson, J.M.
TI  - Inteins of Thermococcus fumicolans DNA Polymerase Are Endonucleases with Distinct Enzymatic Behaviors.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 2335
EP  - 2341
VL  - 275
AB  - The DNA polymerase gene of Thermococcus fumicolans harbors two intein genes. Both inteins have
AB  - been produced in Escherichia coli and purified either as naturally spliced products from the
AB  - expression of the complete DNA polymerase gene or directly from the cloned inteins genes. Both
AB  - recombinant inteins exhibit endonuclease activity, with an optimal temperature of 70 degrees
AB  - C. The Tfu pol-1 intein, which belongs to the Psp KOD pol-1 allelic family, recognizes and
AB  - cleaves a minimal sequence of 16 base pairs (bp) on supercoiled DNA with either Mn(2+) or
AB  - Mg(2+) as cofactor. It cleaves linear DNA only with Mn(2+) and requires a 19-bp minimal
AB  - recognition sequence. The Tfu pol-2 intein, which belongs to the Tli pol-2 allelic family, is
AB  - a highly active homing endonuclease using Mg(2+) as cofactor. Its minimal recognition and
AB  - cleavage site is 21 bp long either on linear or circular DNA substrates. Its endonuclease
AB  - activity is strongly inhibited by the 3' digestion product, which remains bound to the enzyme
AB  - after the cleavage reaction. According to current nomenclature, these endonucleases were named
AB  - PI-TfuI and PI-TfuII. These two inteins thus exhibit different requirements for metal cofactor
AB  - and substrate topology as well as different mechanism of action.
ER  -

TY  - JOUR
AU  - Saves, I.
AU  - Westrelin, F.
AU  - Daffe, M.
AU  - Masson, J.-M.
TI  - Identification of the first eubacterial endonuclease coded by an intein allele in the pps1 gene of mycobacteria.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 4310
EP  - 4318
VL  - 29
AB  - A survey of a vast range of mycobacterial strains led us to discover a new Pps1 intein allele
AB  - in Mycobacterium gastri which differs from those of Mycobacterium tuberculosis and
AB  - Mycobacterium leprae in both its sequence and insertion site. While little is known about
AB  - Pps1, except that it belongs to the YC24 family of ABC transporters, we show that, unlike the
AB  - other inteins described so far from Eubacteria, the MgaPps1 intein possesses a specific
AB  - endonuclease activity. The intein is the first eubacterial intein to be characterised as an
AB  - endonuclease. Like other intein endonucleases, its minimal sequence for recognition and
AB  - cleavage is quite large, with 22 bp spanning the Pps1-c site. The fact that an active
AB  - endonuclease is found among the mycobacterial inteins supports the concept of a cyclical model
AB  - of invasion by horizontal transfer of these genes, followed by degeneration and loss until a
AB  - new invasion event, thus explaining their long-term persistence in closely related eubacterial
AB  - species.
ER  -

TY  - JOUR
AU  - Savin, C.
AU  - Frangeul, L.
AU  - Ma, L.
AU  - Bouchier, C.
AU  - Moszer, I.
AU  - Carniel, E.
TI  - Draft Genome Sequence of a Clinical Strain of Yersinia enterocolitica (IP10393) of Bioserotype 4/O:3 from France.
JO  - Genome Announcements
PY  - 2013
SP  - e00150
EP  - e00112
VL  - 1
AB  - We sequenced the genome of a clinical isolate of (IP10393) from France. This strain belongs to
AB  - bioserotype 4/O:3, which is the most common pathogenic subgroup
AB  - worldwide. The draft genome has a size of 4,463,212 bp and a G+C content of
AB  - 47.0%, and it is predicted to contain 4,181 coding sequences.
ER  -

TY  - JOUR
AU  - Saw, J.H.
AU  - Yuryev, A.
AU  - Kanbe, M.
AU  - Hou, S.
AU  - Young, A.G.
AU  - Aizawa, S.
AU  - Alam, M.
TI  - Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 84
EP  - 93
VL  - 6
AB  - Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine
AB  - bacteria using a mechanism known as 'ixotrophy'. Here, we present
AB  - the complete genome sequence of Saprospira grandis str. Lewin isolated from La
AB  - Jolla beach in San Diego, California. The complete genome sequence comprises a
AB  - chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed
AB  - incomplete pathways for the biosynthesis of nine essential amino acids but
AB  - presence of a large number of peptidases. The genome encodes multiple copies of
AB  - sensor globin-coupled rsbR genes thought to be essential for stress response and
AB  - the presence of such sensor globins in Bacteroidetes is unprecedented. A total of
AB  - 429 spacer sequences within the three CRISPR repeat regions were identified in
AB  - the genome and this number is the largest among all the Bacteroidetes sequenced
AB  - to date.
ER  -

TY  - JOUR
AU  - Saw, J.H.W.
AU  - Schatz, M.
AU  - Brown, M.V.
AU  - Kunkel, D.D.
AU  - Foster, J.S.
AU  - Shick, H.
AU  - Christensen, S.
AU  - Hou, S.
AU  - Wan, X.
AU  - Donachie, S.P.
TI  - Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kilauea Caldera, Hawai'i.
JO  - PLoS ONE
PY  - 2013
SP  - e76376
EP  - e76376
VL  - 8
AB  - The ancestor of Gloeobacter violaceus PCC 7421T is believed to have diverged from that of all
AB  - known cyanobacteria before
AB  - the evolution of thylakoid membranes and plant plastids. The long and largely independent
AB  - evolutionary history of G.
AB  - violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs,
AB  - and in whom cyanobacteria
AB  - evolution can be investigated. No other Gloeobacter species has been described since the genus
AB  - was established in 1974
AB  - (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have
AB  - been reported in
AB  - environmental DNA libraries, but only the type strain's genome has been sequenced. However,
AB  - we report here the
AB  - cultivation of a new Gloeobacter species, G. kilaueensis JS1T, from an epilithic biofilm in a
AB  - lava cave in Ky'lauea Caldera,
AB  - Hawai'i. The strain's genome was sequenced from an enriched culture resembling a
AB  - low-complexity metagenomic sample,
AB  - using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1T and G.
AB  - violaceus PCC 7421T
AB  - genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes
AB  - shows they do not
AB  - belong to the same species. Our results support establishing a new species to accommodate
AB  - JS1T, for which we propose the
AB  - name Gloeobacter kilaueensis sp. nov. Strain JS1T has been deposited in the American Type
AB  - Culture Collection (BAA-2537),
AB  - the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and
AB  - the Belgian Coordinated
AB  - Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the
AB  - Algal Collection of the US
AB  - National Herbarium (US# 217948). The JS1T genome sequence has been deposited in GenBank under
AB  - accession number
AB  - CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G.
AB  - kilaueensis JS1T may
AB  - further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic
AB  - photosynthesis.
ER  -

TY  - JOUR
AU  - Sawaya, M.R.
AU  - Zhu, Z.
AU  - Mersha, F.
AU  - Chan, S.-h.
AU  - Dabur, R.
AU  - Xu, S.-y.
AU  - Balendiran, G.K.
TI  - Crystal structure of the restriction-modification system control element C.BclI and mapping of its binding site.
JO  - Structure
PY  - 2005
SP  - 1837
EP  - 1847
VL  - 13
AB  - Protection from DNA invasion is afforded by restriction-modification systems in many bacteria.
AB  - The efficiency of protection depends crucially on the relative expression levels of
AB  - restriction versus methytransferase genes. This regulation is provided by a controller
AB  - protein, named C protein. Studies of the Bcll system in E. coli suggest that C.Bcll functions
AB  - as a negative regulator for M.Bcll expression, implying that it plays a role in defense
AB  - against foreign DNA during virus infection. C.Bcll binds (Kd = 14.3 nM) to a 2-fold symmetric
AB  - C box DNA sequence that overlaps with the putative -35 promoter region upstream of the bcllM
AB  - and bcllC genes. The C.Bcll fold comprises five alpha helices: two helices form a
AB  - helix-turn-helix motif, and the remaining three helices form the extensive dimer interface.
AB  - The C.Bcll-DNA model proposed suggests that DNA bending might play an important role in gene
AB  - regulation, and that Glu27 and Asp31 in C.Bcll might function critically in the regulation.
ER  -

TY  - JOUR
AU  - Saxena, A.
AU  - Kumari, R.
AU  - Mukherjee, U.
AU  - Singh, P.
AU  - Lal, R.
TI  - Draft Genome Sequence of the Rifamycin Producer Amycolatopsis rifamycinica DSM 46095.
JO  - Genome Announcements
PY  - 2014
SP  - e00662
EP  - e00614
VL  - 2
AB  - Amycolatopsis rifamycinica DSM 46095 is an actinobacterium that produces rifamycin SV, an
AB  - antibiotic used against Mycobacterium tuberculosis. Here, we
AB  - present the draft genome of DSM 46095, which harbors a novel rifamycin polyketide
AB  - biosynthetic gene cluster (rif PKS) that differed by 10% in nucleotide sequence
AB  - from the already reported rif PKS cluster of Amycolatopsis mediterranei S699.
ER  -

TY  - JOUR
AU  - Saxena, A.
AU  - Nayyar, N.
AU  - Sangwan, N.
AU  - Kumari, R.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite.
JO  - Genome Announcements
PY  - 2013
SP  - e00715
EP  - e00713
VL  - 1
AB  - Novosphingobium lindaniclasticum LE124(T) is a hexachlorocyclohexane (HCH)-degrading bacterium
AB  - isolated from a high-dosage-point HCH dumpsite (450 mg
AB  - HCH/g soil) located in Lucknow, India (27 degrees 00'N and 81 degrees 09'E).
AB  - Here, we present the annotated draft genome sequence of strain LE124(T), which
AB  - has an estimated size of 4.86 Mb and is comprised of 4,566 coding sequences.
ER  -

TY  - JOUR
AU  - Saxena, D.
AU  - Caufield, P.W.
AU  - Li, Y.
AU  - Brown, S.
AU  - Song, J.
AU  - Norman, R.
TI  - Genetic Classification of Severe Early Childhood Caries Using Subtracted DNA Fragments from Streptococcus mutans.
JO  - J. Clin. Microbiol.
PY  - 2008
SP  - 2868
EP  - 2873
VL  - 46
AB  - Streptococcus mutans is one of several members of the oral indigenous
AB  - biota linked with severe early childhood caries (S-ECC). Because most
AB  - humans harbor S. mutans, but not all manifest disease, it has been
AB  - proposed that the strains of S. mutans associated with S-ECC are
AB  - genetically distinct from those found in caries-free (CF) children. The
AB  - objective of this study was to identify common DNA fragments from S.
AB  - mutans present in S-ECC but not in CF children. Using suppressive
AB  - subtractive hybridization, we found a number of DNA fragments (biomarkers)
AB  - present in 88 to 95% of the S-ECC S. mutans strains but not in CF S.
AB  - mutans strains. We then applied machine learning techniques including
AB  - support vector machines and neural networks to identify the biomarkers
AB  - with the most predictive power for disease status, achieving a 92%
AB  - accurate classification of the strains as either S-ECC or CF associated.
AB  - The presence of these gene fragments in 90 to 100% of the 26 S-ECC
AB  - isolates tested suggested their possible functional role in the
AB  - pathogenesis of S. mutans associated with dental caries.
ER  -

TY  - JOUR
AU  - Saxena, R.
AU  - Chaudhary, N.
AU  - Dhakan, D.B.
AU  - Sharma, V.K.
TI  - Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India.
JO  - Genome Announcements
PY  - 2015
SP  - e01295
EP  - e01215
VL  - 3
AB  - This paper reports the draft genome sequence of the proteobacterium Gulbenkiania  mobilis
AB  - strain MB1, a sulfur-metabolizing thermophile isolated from a hot spring
AB  - located in Pachmarhi, India. This study reports the first draft genome sequence
AB  - of any species from the genus Gulbenkiania.
ER  -

TY  - JOUR
AU  - Sayed, M.
AU  - Sayed, W.F.
AU  - Hatti-Kaul, R.
AU  - Pyo, S.H.
TI  - Complete Genome Sequence of Mycobacterium sp. MS1601, a Bacterium Performing Selective Oxidation of Polyols.
JO  - Genome Announcements
PY  - 2017
SP  - e00156
EP  - e00117
VL  - 5
AB  - Corynebacterium sp. (ATCC 21245) is reclassified here as Mycobacterium sp. MS1601 based on 16S
AB  - rRNA gene and complete-genome sequence analysis. It is able to
AB  - oxidize branched polyols to corresponding hydroxycarboxylic acids. The total size
AB  - of the genome sequence was 6,829,132 bp, including one circular chromosome of
AB  - 6,407,860 bp.
ER  -

TY  - JOUR
AU  - Sayers, J.R.
AU  - Olsen, D.B.
AU  - Eckstein, F.
TI  - Inhibition of restriction endonuclease hydrolysis by phosphorothioate-containing DNA.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9495
EP  - 9495
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Sayers, J.R.
AU  - Schmidt, W.
AU  - Wendeler, A.
AU  - Eckstein, F.
TI  - Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 803
EP  - 813
VL  - 16
AB  - A method for achieving strand specific nicking of DNA has been developed.
AB  - Phosphorothioate groups were incorporated enzymatically into the (-) strand of
AB  - M13 RF IV DNA.  When such DNA is reacted with restriction endonucleases in the
AB  - presence of ethidium bromide, nicked DNA (RF II) is produced.  All of the
AB  - restriction enzymes tested linearised phosphorothioate-containing DNA in the
AB  - absence of this dye.  The strand specificity of the reaction was investigated
AB  - by employing the ethidium bromide mediated nicking reaction in the
AB  - phosphorothioate-based oligonucleotide-directed mutagenesis method.  The
AB  - mutational efficiences obtained were in the region of 64-89%, indicating that
AB  - these restriction enzymes hydrolyse the phosphodiester bond at the cleavage
AB  - site of the unsubstituted (+) strand.
ER  -

TY  - JOUR
AU  - Scales, B.S.
AU  - Erb-Downward, J.R.
AU  - Falkowski, N.R.
AU  - LiPuma, J.J.
AU  - Huffnagle, G.B.
TI  - Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans.
JO  - Genome Announcements
PY  - 2018
SP  - e01461
EP  - e01417
VL  - 6
AB  - We report here the first complete genome sequence of a human Pseudomonas lundensis isolate,
AB  - strain AU1044, and the draft genomes of 11 other clinical P.
AB  - lundensis strains, isolated from the lungs of cystic fibrosis patients. The
AB  - genome of strain AU1044 is 4.81 Mb and encodes seven 16S rRNAs.
ER  -

TY  - JOUR
AU  - Scales, B.S.
AU  - Erb-Downward, J.R.
AU  - Huffnagle, I.M.
AU  - LiPuma, J.J.
AU  - Huffnagle, G.B.
TI  - Draft Genome Sequences of Seven Pseudomonas fluorescens Subclade III Strains Isolated from Cystic Fibrosis Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e01285
EP  - e01214
VL  - 3
AB  - We report here the first draft genome sequences of Pseudomonas fluorescens strains that have
AB  - been isolated from humans. The seven assembled draft genomes
AB  - contained an average of 60.1% G+C content, were an average genomic size of 6.3
AB  - Mbp, and mapped by multilocus sequence analysis to subclade III.
ER  -

TY  - JOUR
AU  - Scales, B.S.
AU  - Erb-Downward, J.R.
AU  - LiPuma, J.J.
AU  - Huffnagle, G.B.
TI  - Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e00837
EP  - e00815
VL  - 3
AB  - We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical
AB  - samples. Phylogenetic analysis places three in subclade I and two
AB  - in subclade II of the P. fluorescens species complex. The average G+C content and
AB  - genomic size are 63% and 7.1 Mbp (subclade I) and 59.6% and 6.14 Mbp (subclade
AB  - II), respectively.
ER  -

TY  - JOUR
AU  - Scalley-Kim, M.
AU  - McConnell-Smith, A.
AU  - Stoddard, B.L.
TI  - Coevolution of a Homing Endonuclease and Its Host Target Sequence.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 1305
EP  - 1319
VL  - 372
AB  - We have determined the specificity profile of the homing endonuclease I-AniI and compared it
AB  - to the conservation of its host gene. Homing
AB  - endonucleases are encoded within intervening sequences such as group I
AB  - introns. They initiate the transfer of such elements by cleaving cognate
AB  - alleles lacking the intron, leading to their transfer via homologous
AB  - recombination. Each structural homing endonuclease family has arrived at
AB  - an appropriate balance of specificity and fidelity that avoids toxicity
AB  - while maximizing target recognition and invasiveness. I-AniI recognizes a
AB  - strongly conserved target sequence in a host gene encoding apocytochrome B
AB  - and has fine-tuned its specificity to correlate with wobble versus
AB  - nonwobble positions across that sequence and to the amount of degeneracy
AB  - inherent in individual codons. The physiological target site in the host
AB  - gene is not the optimal substrate for recognition and cleavage: at least
AB  - one target variant identified during a screen is bound more tightly and
AB  - cleaved more rapidly. This is a result of the periodic cycle of intron
AB  - homing, which at any time can present nonoptimal combinations of
AB  - endonuclease specificity and insertion site sequences in a biological
AB  - host.
ER  -

TY  - JOUR
AU  - Scarpelis, G.
AU  - Moissidou, A.
AU  - Rina, M.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BshGI.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8883
EP  - 8883
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Scavetta, R.D.
AU  - Thomas, C.B.
AU  - Walsh, M.A.
AU  - Szegedi, S.
AU  - Joachimiak, A.
AU  - Gumport, R.I.
AU  - Churchill, M.E.A.
TI  - Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3950
EP  - 3961
VL  - 28
AB  - DNA methylation is important in cellular, developmental and disease processes, as well as in
AB  - bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine
AB  - and adenine is a common mode of protection against restriction endonucleases afforded by the
AB  - bacterial methyltransferases.  The first structure of an N6-adenine methyltransferase
AB  - belonging to the beta class of bacterial methyltransferases is described here. The structure
AB  - of M.RsrI from Rhodobacter sphaeroides, which methylates the second adenine of the GAATTC
AB  - sequence, was determined to 1.75 A resolution using X-ray crystallography. Like other
AB  - methyltransferases, the enzyme contains the methylase fold and has well-defined substrate
AB  - binding pockets. The catalytic core most closely resembles the PvuII methyltransferase, a
AB  - cytosine amino methyltransferase of the same beta group. The larger nucleotide binding pocket
AB  - observed in M.RsrI is expected because it methylates adenine. However, the most striking
AB  - difference between the RsrI methyltransferase and the other bacterial enzymes is the structure
AB  - of the putative DNA target recognition domain, which is formed in part by two helices on an
AB  - extended arm of the protein on the face of the enzyme opposite the active site. This
AB  - observation suggests that a dramatic conformational change or oligomerization may take place
AB  - during DNA binding and methylation.
ER  -

TY  - JOUR
AU  - Schaefer, B.
AU  - Wilde, B.
AU  - Massardo, D.R.
AU  - Manna, F.
AU  - Del Giudice, L.
AU  - Wolf, K.
TI  - A mitochondrial group-I intron in fission yeast encodes a maturase and is mobile in crosses.
JO  - Curr. Genet.
PY  - 1994
SP  - 336
EP  - 341
VL  - 25
AB  - The open reading frame in the first intron of the mitochondrial gene encoding subunit I of
AB  - cytochrome c oxidase encodes a maturase and stimulates homologous recombination in Escherichia
AB  - coli.  In this paper, we demonstrate that this intron is mobile in crosses, indicating that it
AB  - also encodes an endonuclease.  This is the first report on an intron which possesses mobility
AB  - and acts as a maturase.
ER  -

TY  - JOUR
AU  - Schaeffer, C.J.
AU  - Huang, B.
AU  - Tsai, M.-D.
TI  - A new class IIS zinc finger restriction enzyme with specificity for SP1 binding sites.
JO  - FASEB J.
PY  - 1996
SP  - A1241
EP  - A1241
VL  - 10
AB  - A new restriction endonuclease (Sp1ase) was constructed by fusing the DNA-cleavage domain of
AB  - the restriction endonuclease FokI in frame with the zinc-finger DNA-binding domain of the
AB  - transcription factor Sp1.  This construct was shown to selectively digest plasmid DNA carrying
AB  - consensus Sp1 sites.  Splase was also shown to selectively digest plasmid DNA carrying the
AB  - HIV-1 LTR.  Sp1ase is a genetically engineered restriction enzyme conveying specificity for
AB  - Sp1 binding sites.  The site-specific phosphodiesterase activity of Sp1ase has been
AB  - characterized and shown to have more specific cleavage of one strand of DNA than the other.
AB  - Sp1ase recognizes a ten base-pair DNA sequence and hydrolyzes phosphodiester bonds upstream of
AB  - the binding sequence.  The binding specificity of Sp1ase makes this a rare cutter
AB  - restriction enzyme which could be valuable in creating large DNA fragments for genome
AB  - sequencing projects.  This result presents the opportunity to creat other restriction enzymes
AB  - by altering the binding specificity of the zinc finger recognition helix.
ER  -

TY  - JOUR
AU  - Schaefler, S.
TI  - Staphylococcus epidermidis BV:  Antibiotic resistance patterns, physiological characteristics, and bacteriophage susceptibility.
JO  - Appl. Microbiol.
PY  - 1971
SP  - 693
EP  - 699
VL  - 22
AB  - Staphylococcus epidermidis BV is a group of mannitol-fermenting
AB  - coagulase-negative staphylococci characterized by multiple antibiotic
AB  - resistance, very similar biochemical characteristics, and phage susceptibility.
AB  - Clinical isolates belonging to this group are resistant to most antibiotics
AB  - tested, including oxacillin, lincomycin, and novobiocin.  The only antibiotic
AB  - to which all tested strains are sensitive is vancomycin.  Common biochemical
AB  - traits of the tested S. epidermidis BV strains include fermentation of
AB  - trehalose and ribose, phospho-b-glucosidase activity, growth on synthetic
AB  - medium with amino acids as carbon source, and lack of deoxyribonuclease,
AB  - phosphatase, lipase, and gelatinase activity.  Some of these characteristics
AB  - appear more frequently in mannitol-positive control strains than in
AB  - mannitol-negative strains.  S. epidermidis  BV strains carry lysogenic phages
AB  - with a host range restricted to this group.  These phages allow the
AB  - differentiation of individual strains.
ER  -

TY  - JOUR
AU  - Schafer, A.
AU  - Schwarzer, A.
AU  - Kalinowski, J.
AU  - Puhler, A.
TI  - Cloning and characterization of a DNA region encoding a stress-sensitive restriction system from Corynebacterium glutamicum ATCC 13032 and analysis of its role in intergeneric conjugation with Escherichia coli.
JO  - J. Bacteriol.
PY  - 1994
SP  - 7309
EP  - 7319
VL  - 176
AB  - RP4-mediated transfer of mobilizable plasmids in intergeneric conjugation of Escherichia coli
AB  - donors with Corynebacterium glutamicum ATCC 13032 is severely affected by a restriction system
AB  - in the recipient that can be inactivated by a variety of exogenous stress factors. In this
AB  - study a rapid test procedure based on intergeneric conjugal plasmid transfer that permitted
AB  - the distinction between restriction-negative and restriction-positive C. glutamicum clones was
AB  - developed. By using this procedure, clones of the restriction-deficient mutant strain C.
AB  - glutamicum RM3 harboring a plasmid library of the wild-type chromosome were checked for their
AB  - restriction properties. A complemented clone with a restriction-positive phenotype was
AB  - isolated and found to contain a plasmid with a 7-kb insertion originating from the wild-type
AB  - chromosome. This plasmid, termed pRES806, is able to complement the restriction-deficient
AB  - phenotype of different C. glutamicum mutants. Sequence analysis revealed the presence of two
AB  - open reading frames (orf1 and orf2) on the complementing DNA fragment. The region comprising
AB  - orf1 and orf2 displayed a strikingly low G+C content and was present exclusively in C.
AB  - glutamicum strains. Gene disruption experiments with the wild type proved that orf1 is
AB  - essential for complementation, but inactivation of orf2 also resulted in a small but
AB  - significant increase in fertility. These results were confirmed by infection assays with the
AB  - bacteriophage CL31 from Corynebacterium lilium ATCC 15990.
ER  -

TY  - JOUR
AU  - Schafer, A.
AU  - Tauch, A.
AU  - Droste, N.
AU  - Puhler, A.
AU  - Kalinowski, J.
TI  - The Corynebacterium glutamicum cglIM gene encoding a 5-cytosine methyltransferase enzyme confers a specific DNA methylation pattern in an McrBC-deficient Escherichia coli strain.
JO  - Gene
PY  - 1997
SP  - 95
EP  - 101
VL  - 203
AB  - The cglIM gene of the coryneform soil bacterium Corynebacterium glutamicum ATCC 13032 has been
AB  - cloned and characterized.  The coding region comprises 1092 nucleotides and specifies a
AB  - protein of 363 amino acid residues with a deduced Mr of 40,700.  The amino acid sequence
AB  - showed striking similarities to methyltransferase enzymes generating 5-methylcytosine
AB  - residues, especially to M.NgoVII from Neisseria gonorrhoeae recognizing the sequence GCSGC.
AB  - The cglIM gene is organized in an unusual operon which contains, in addition, two genes
AB  - encoding stress-sensitive restriction enzymes.  Using PCR techniques the entire gene including
AB  - the promoter region was amplified from the wild-type chromosome and cloned in Escherichia
AB  - coli.  Expression of the cglIM gene in E. coli under the control of its own promoter conferred
AB  - the C. glutamicum-specific methylation pattern to co-resident shuttle plasmids and led to a
AB  - 260-fold increase in the transformation rate of C. glutamicum.  In addition, the methylation
AB  - pattern produced by this methyltransferase enzyme is responsible for the sensitivity of DNA
AB  - from C. glutamicum to the modified cytosine restriction system of E. coli.
ER  -

TY  - JOUR
AU  - Schafer, B.
AU  - Kaulich, K.
AU  - Wolf, K.
TI  - Mosaic structure of the cox2 gene in the petite negative yeast Schizosaccharomyces pombe: a group II intron is inserted at the same location as the otherwise unrelated group II introns in the mitochondria of higher plants.
JO  - Gene
PY  - 1998
SP  - 101
EP  - 112
VL  - 214
AB  - In contrast to homologous genes in other fungal mitochondrial genomes, the gene encoding
AB  - subunit 2 of cytochrome oxidase (cox2) in several Schizosaccharomyces pombe strains contains a
AB  - large group II intron. Its 2436 nucleotides can be folded into a typical group II intron
AB  - secondary structure, possessing all the expected sequence motifs for subgroup IIA1 (Michel et
AB  - al., 1989).  This intron is remarkable for the following reasons: (i) Five nucleotide changes
AB  - were observed compared with the continuous form of the cox2 gene in the reference strain 50 at
AB  - the 3'-exon sequence, but not in the 5'-exon. (ii) One of these changes occurred at the
AB  - splice point leading to a serine instead of a threonine residue in the deduced cox2
AB  - polypeptide. In all cases, the alterations resulted in the replacement of more frequently used
AB  - codons by rare ones. (iii) Although the intron is able to undergo splicing, the sequence
AB  - motifs thought to be necessary for interaction between the 5'-exon and the intron during the
AB  - splicing process (the EBS1/IBS1 as well as the EBS2/IBS2 pairings) are unusual. (iv) The
AB  - intron is inserted at the same location in the cox2 gene as the otherwise unrelated intron
AB  - from higher plants.
ER  -

TY  - JOUR
AU  - Schafers, C.
AU  - Blank, S.
AU  - Wiebusch, S.
AU  - Elleuche, S.
AU  - Antranikian, G.
TI  - Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 22
EP  - 22
VL  - 12
AB  - Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile
AB  - bacterium that was isolated from the Geysir geothermal area, Iceland.
AB  - Like other thermophiles, Thermus species are often used as model organisms to
AB  - understand the mechanism of action of extremozymes, especially focusing on their
AB  - heat-activity and thermostability. Genome-specific features of T. brockianus GE-1
AB  - and their properties further help to explain processes of the adaption of
AB  - extremophiles at elevated temperatures. Here we analyze the first whole genome
AB  - sequence of T. brockianus strain GE-1. Insights of the genome sequence and the
AB  - methodologies that were applied during de novo assembly and annotation are given
AB  - in detail. The finished genome shows a phred quality value of QV50. The complete
AB  - genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid
AB  - pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction
AB  - revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and
AB  - 66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified
AB  - encoding key enzymes for xylan depolymerization and xylose metabolism. This is in
AB  - agreement with the growth experiments in which xylan is utilized as sole source
AB  - of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an
AB  - endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding
AB  - protein XylF, the xylose isomerase XylA catalyzing the first step of xylose
AB  - metabolism and the xylulokinase XylB, responsible for the second step of xylose
AB  - metabolism. Our data indicate that an ancestor of T. brockianus obtained the
AB  - ability to use xylose as alternative carbon source by horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Schaffert, L.
AU  - Albersmeier, A.
AU  - Bednarz, H.
AU  - Niehaus, K.
AU  - Kalinowski, J.
AU  - Ruckert, C.
TI  - Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 516
EP  - 524
VL  - 8
AB  - Corynebacterium maris Coryn-1(T) Ben-Dov et al. 2009 is a member of the genus Corynebacterium
AB  - which contains Gram-positive, non-spore forming bacteria with a
AB  - high G+C content. C. maris was isolated from the mucus of the Scleractinian coral
AB  - Fungia granulosa and belongs to the aerobic and non-haemolytic corynebacteria. It
AB  - displays tolerance to salts (up to 10%) and is related to the soil bacterium
AB  - Corynebacterium halotolerans. As this is a type strain in a subgroup of
AB  - Corynebacterium without complete genome sequences, this project, describing the
AB  - 2.78 Mbp long chromosome and the 45.97 kbp plasmid pCmaris1, with their 2,584
AB  - protein-coding and 67 RNA genes, will aid the G enomic E ncyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Schaffert, L.
AU  - Albersmeier, A.
AU  - Winkler, A.
AU  - Kalinowski, J.
AU  - Zotchev, S.B.
AU  - Ruckert, C.
TI  - Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 91
EP  - 91
VL  - 11
AB  - Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment
AB  - producing and spore-forming actinomycete, which forms branching
AB  - vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis.
AB  - Actinomycete bacteria are prolific producers of secondary metabolites, some of
AB  - which have been developed into anti-microbial, anti-tumor and immunosuppressive
AB  - drugs currently used in human therapy. Considering this and the growing interest
AB  - in natural products as sources of new drugs, actinomycete bacteria from the
AB  - hitherto poorly explored marine environments may represent promising sources for
AB  - drug discovery. As A. hymeniacidonis, isolated from the marine sponge, is a type
AB  - strain of the recently described and rare genus Actinoalloteichus, knowledge of
AB  - the complete genome sequence enables genome analyses to identify genetic loci for
AB  - novel bioactive compounds. This project, describing the 6.31 Mbp long chromosome,
AB  - with its 5346 protein-coding and 73 RNA genes, will aid the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Schapira, M.
AU  - Desdouets, C.
AU  - Jacq, C.
AU  - Perea, J.
TI  - I-SceIII an intron-encoded DNA endonuclease from yeast mitochondria. Asymmetrical DNA binding properties and cleavage reaction.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3683
EP  - 3689
VL  - 21
AB  - We have previously discovered the new intron-encoded endonuclease I-SceIII by expressing, in
AB  - E.coli, the ORF contained in the third intron of the yeast mitochondrial COX I gene. In this
AB  - work, we analyzed the in vitro properties of partially purified I-SceIII and found that it is
AB  - a very specific DNA endonuclease, tolerating relatively few base changes in its 20 base pair
AB  - long target site. I-SceIII should be a useful molecular tool to analyze the structure of large
AB  - genomes. Interestingly, I-SceIII is the first P1-P2 DNA endonuclease for which DNA binding
AB  - properties could be analyzed by band-shift experiments. Clearly, the cleavage products
AB  - corresponding to the upstream A3 exon and to the downstream A4 exon could compete with the
AB  - substrate A3-A4 in forming a DNA-protein complex. However, the A3 exon competes more
AB  - efficiently than the downstream A4 product. The cleavage of the two DNA strands is also
AB  - asymmetric; the top strand (non-transcribed strand) is cleaved faster than the bottom strand,
AB  - a property found under various experimental conditions. These findings sugest that this
AB  - intron-encoded DNA endonuclease may have a role in the RNA splicing process of the intron.
ER  -

TY  - JOUR
AU  - Scharnagl, M.
AU  - Richter, S.
AU  - Hagemann, M.
TI  - The cyanobacterium Synechocystis sp. strain PCC 6803 expresses a DNA methyltransferase specific for the recognition sequence of the restriction endonuclease PvuI.
JO  - J. Bacteriol.
PY  - 1998
SP  - 4116
EP  - 4122
VL  - 180
AB  - By use of restriction endonucleases, the DNA of the cyanobacterium Synechocystis sp. strain
AB  - PCC 6803 was analyzed for DNA-specific methylation.  Three different recognition sites of
AB  - methyltransferases, a dam-like site including N6-methyladenosine and two other sites with
AB  - methylcytosine, were identified, whereas no activities of restriction endonucleases could be
AB  - detected in this strain.  Slr0214, a Synechocystis gene encoding a putative methyltransferase
AB  - that shows significant similarities to C5-methylcytosine-synthesizing enzymes, was amplified
AB  - by PCR and cloned for further characterization.  Mutations in slr0214 were generated by the
AB  - insertion of an aphII gene cassette.  Analyses of chromosomal DNAs of such mutants
AB  - demonstrated that the methylation pattern was changed.  The recognition sequence of the
AB  - methyltransferase was identified as 5'-CGATCG-3', corresponding to the recognition sequence
AB  - of PvuI.  The specific methyltransferase activity was significantly reduced in protein
AB  - extracts obtained from mutant cells.  Mutation of slr0214 also led to changed growth
AB  - characteristics of the cells compared to wild-type cells.  These alterations led to the
AB  - conclusion that the methyltransferase Slr0214 might play a regulatory role in Synechocystis.
AB  - The Slr0214 protein was also overexpressed in Escherichia coli, and the purified protein
AB  - demonstrated methyltransferase activity and specificity for PvuI recognition sequences in
AB  - vitro.  We propose the designation SynMI (Synechocystis methyltransferase I) for the
AB  - slr0214-encoded enzyme.
ER  -

TY  - JOUR
AU  - Scheidt, G.
AU  - Graessmann, A.
AU  - Weber, H.
TI  - Cloning of the methyltransferase gene from Arabidopsis thaliana.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1991
SP  - 742
EP  - 743
VL  - 372
AB  - DNA methylation is a widespread modification in eucaryotic cells and thought to be envolved in
AB  - gene regulation.  Recently we showed that in vitro methylation of transgenes was inherited in
AB  - tobacco plants and led to gene inactivation.  In plants DNA methylation differs from that in
AB  - animal cells in respect to a much higher amount of 5-methylcytosine content of the DNA and to
AB  - an altered sequence specificity of the methyltransferase (Mtase).  Cytosines in CpG and CpNpG
AB  - sequences were methylated in plant DNA whereas only 5mCpG can be found in animal DNA.
AB  - Furthermore it was shown that wheat Mtase had a preference for endogenous double stranded DNA
AB  - as substrate and a lower molecular mass distinguishes it from the mammalian enzyme.  Little is
AB  - known about the structure and regulation of eucaryotic Mtases, especially from plants and only
AB  - from mouse cells the corresponding cDNA had been cloned and sequenced.  To characterize the
AB  - Mtase gene from Arabidopsis a genomic library from nuclear DNA was established in EMBL3 and
AB  - screened with heterologous probes encoding the cDNA of mouse Mtase (gift from T. Bestor).
AB  - Several clones which hybridized under low stringent conditions were isolated and part of the
AB  - DNA sequence was determined.  We found significant homology to the mouse Mtase cDNA on
AB  - nucleotide and on amino acid level.  Furthermore this region is part of a conserved domain of
AB  - cytosine Mtases not only from eucaryotic but also from bacterial and phage origin.  Using the
AB  - cloned fragments as probes for hybridization experiments to each other and to total
AB  - Arabidopsis DNA we identified at least 3 different sequences which are related but not totally
AB  - homologous.  However they all hybridize to the mouse Mtase cDNA.  We conclude therefore that
AB  - Arabidopsis Mtase is encoded by a gene family.
ER  -

TY  - JOUR
AU  - Scheidt, G.
AU  - Weber, H.
AU  - Graessmann, M.
AU  - Graessmann, A.
TI  - Are there two DNA methyltransferase gene families in plant cells?  A new potential methyltransferase gene isolated from an Arabidopsis thaliana genomic library.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 953
EP  - 958
VL  - 22
AB  - Using the 1kb 3' terminal DNA fragment of the mouse methyltransferase cDNA as a probe and low
AB  - stringent hybridisation conditions, a new potential methyltransferase (MTase) gene family was
AB  - isolated from an Arabidopsis thaliana genomic DNA library. One clone (MTase-11), which gave
AB  - the strongest signal at the Northern blot, was entirely sequenced (11483 bp) and further
AB  - characterised. Under consideration of the likely open reading frames and our preliminary cDNA
AB  - experiments we propose that the clone 11 gene encodes for an ~90 kD protein. As deduced from
AB  - the DNA sequence this protein contains all conserved sequence motifs specific for the 5m
AB  - cytosine MTases. MTase-11 gene expression was demonstrable in callus and during germination
AB  - but not in one month old plants or in leaves.
ER  -

TY  - JOUR
AU  - Scheinbart, L.S.
AU  - Johnson, M.A.
AU  - Gross, L.A.
AU  - Edelstein, S.R.
AU  - Richardson, B.C.
TI  - Procainamide inhibits DNA methyltransferase in a human T cell line.
JO  - J. Rheumatol.
PY  - 1991
SP  - 530
EP  - 534
VL  - 18
AB  - Procainamide, a widely used antiarrythmic, causes DNA hypomethylation in the
AB  - human T cell line Jurkat, but the mechanism is unknown.  We report that
AB  - procainamide inhibits the DNA methyltransferase catalyzed transfer of methyl
AB  - groups from S-adenosylmethionine to DNA, but has no effect on other known
AB  - regulators of DNA methylation.  Our results suggest that procainamide could
AB  - inhibit cellular DNA methylation by inhibiting DNA methyltransferase activity.
ER  -

TY  - JOUR
AU  - Schell, J.
TI  - The mechanism of restriction of bacteriophage lambda in Escherichia coli strains: Demonstration of an in vivo requirement for S-adenosylmethionine.
JO  - Virology
PY  - 1969
SP  - 66
EP  - 73
VL  - 39
AB  - Restriction of phage lambda by certain Escherichia coli strains involves the degradation of
AB  - the phage DNA in strains with a host-controlled modification system different from the one
AB  - carried by the restricted phage.  By infecting the restricting host strain with phage T3,
AB  - prior to infection with phage lambda, it was possible to inactivate the capacity of host cells
AB  - to restrict phage lambda.  We have shown that this inactivation is specifically due to the
AB  - production, in these T3-infected host cells, of an enzyme which cleaves S-adenosylmethionine.
AB  - Since SAM is necessary for methylation reactions, it follows from these observations that
AB  - methylation of the restricted lambda DNA might be required to make it susceptible to the
AB  - host-controlled restriction system.  Several E. coli strains have a host-controlled
AB  - restriction system, e.g., E. coli K12 and E. coli B, but also prophage P1 controls such a
AB  - system.  Our results show that both the E. coli K12 and B restriction systems require SAM for
AB  - activity.  The P1 restriction system, however, does not appear to have such a requirement.
ER  -

TY  - JOUR
AU  - Schell, J.
AU  - Glover, S.W.
TI  - The effect of heat on host-controlled restriction of phage lambda in Escherichia coli K(P1).
JO  - J. Gen. Microbiol.
PY  - 1966
SP  - 61
EP  - 72
VL  - 45
AB  - The growth of phage lambda.C (i.e. phage lambda grown in Escherichia coli C) in
AB  - E. coli K lysogenized by phage P1 is normally restricted so that the efficiency
AB  - of plating of phage lambda.C on K(P1) compared to C is about 10-7.  When K(P1)
AB  - bacteria are heated before infection with phage lambda.C this restriction may
AB  - be decreased as much as a million-fold.  The time of exposure to elevated
AB  - temperature (49C and above) required to achieve this increase in e.o.p. of
AB  - phage lambda.C decreased with increasing temperature up to temperatures which
AB  - began to inhibit the capacity of bacteria to grow phage.  Heated K(P1) bacteria
AB  - recovered their ability to restrict phage lambda.C following the resumption of
AB  - growth at 37C.  Part of this recovery can be inhibited by chloramphenicol.  A
AB  - more dramatic recovery of restriction is observed when heated K(P1) bacteria
AB  - are resuspended in hypertonic media.  Experiments are described which indicate
AB  - that phage lambda.C is restricted at an early step after adsorption and that,
AB  - if phage escapes this restriction, it can grow in heated bacteria subsequently
AB  - converted into restricting hosts by resuspension in hypertonic media.
ER  -

TY  - JOUR
AU  - Schell, J.
AU  - Glover, S.W.
TI  - The effect of various physiological conditions on host-controlled restriction in Escherichia coli K (P1).
JO  - Genet. Res.
PY  - 1966
SP  - 273
EP  - 276
VL  - 7
AB  - Growth of K(P1) bacteria under conditions which lead to a reduction in the level of nucleases
AB  - also leads to a reduction in their ability to restrict the growth of lambda.C.  Experiments
AB  - designed to estimate the time after adsorption at which restriction takes place indicate that
AB  - phage DNA is probably restricted by a nuclease while passing through the periplasm.
ER  -

TY  - JOUR
AU  - Schell, J.
AU  - Glover, S.W.
TI  - On the localization of a factor responsible for host-controlled restriction in Escherichia coli K(P1).
JO  - Genet. Res.
PY  - 1966
SP  - 277
EP  - 279
VL  - 7
AB  - Recent experiments indicate that an essential step in the restriction of phage lambda.C by E.
AB  - coli K(P1) bacteria may involve an enzyme located on the surface of the cells, and a
AB  - surface-localized nuclease has been implicated in the restriction of non-glucosylated T4 DNA
AB  - by E. coli B.  Neu & Heppel have shown that several enzymes, alkaline phosphatase, latent
AB  - RNase, 5'-nucleotidase, acid phosphatase, cyclic phosphodiesterase and an RNA inhibited DNase
AB  - can be partly or completely released by E. coli cells during spheroplast formation.  These
AB  - authors also reported that surface-localized enzymes can also be released by EDTA treatment
AB  - followed by washing at 4 C.  The results reported in this paper show that the restriction of
AB  - phage lambda.C by K(P1) cells is markedly reduced when the cells are treated with EDTA and
AB  - washed several times with cold distilled water.
ER  -

TY  - JOUR
AU  - Schell, J.
AU  - Glover, S.W.
AU  - Stacey, K.A.
AU  - Broda, P.M.A.
AU  - Symonds, N.
TI  - The restriction of phage T3 by certain strains of Escherichia coli.
JO  - Genet. Res.
PY  - 1963
SP  - 483
EP  - 484
VL  - 4
AB  - The efficiency of plating (e.o.p.) of phage T3 is equal on the E. coli strains
AB  - B and C, and also on most F- strains of K12 (afterwards called K).  However, in
AB  - strains of K which carry the F episome its e.o.p. is greatly reduced.  On most
AB  - F+ strains of K its e.o.p. is about 10-5.  The phages which do multiply in the
AB  - F+ bacteria are not modified; they still have an e.o.p. of 10-5 when replated
AB  - on the same host.  The actual fraction of cells which accept T3 phages is
AB  - approximately 10-2, and these cells yield a small burst of unmodified T3.  It
AB  - seems to be this combination of restriction coupled with a small burst which
AB  - defines the level of the e.o.p. and produces the typical small plaques which
AB  - are observed on F+ strains.  As a result of screening a large number of male
AB  - and female strains of K two striking exceptions were found to the observation
AB  - stated above.  The F+ strain W1485 was found to plate efficiently, while some
AB  - F- derivatives of 58-161 plate T3 with a low e.o.p.  In an effort to elucidate
AB  - this situation a series of conjugation experiments was performed to establish
AB  - the relationship between F and T3 restriction.  The results of these
AB  - experiments are presented in Table 1.
ER  -

TY  - JOUR
AU  - Schell, M.A.
AU  - Karmirantzou, M.
AU  - Snel, B.
AU  - Vilanova, D.
AU  - Berger, B.
AU  - Pessi, G.
AU  - Zwahlen, M.C.
AU  - Desiere, F.
AU  - Bork, P.
AU  - Delley, M.
AU  - Prodmore, R.D.
AU  - Arigoni, F.
TI  - The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 14422
EP  - 14427
VL  - 99
AB  - Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human
AB  - gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex
AB  - intestinal microflora, they are considered as key commensals that promote a healthy GIT. We
AB  - determined the 2.26-Mb genome sequence of an infant-derived strain of Bifidobacterium longum,
AB  - and identified 1,730 possible coding sequences organized in a 60%-GC circular chromosome.
AB  - Bioinformatic analysis revealed several physiological traits that could partially explain the
AB  - successful adaptation of this bacteria to the colon. An unexpectedly large number of the
AB  - predicted proteins appeared to be specialized for catabolism of a variety of oligosaccharides,
AB  - some possibly released by rare or novel glycosyl hydrolases acting on "nondigestible" plant
AB  - polymers or host-derived glycoproteins and glycoconjugates. This ability to scavenge from a
AB  - large variety of nutrients likely contributes to the competitiveness and persistence of
AB  - bifidobacteria in the colon. Many genes for oligosaccharide metabolism were found in
AB  - self-regulated modules that appear to have arisen in part from gene duplication or horizontal
AB  - acquisition. Complete pathways for all amino acids, nucleotides, and some key vitamins were
AB  - identified; however, routes for Asp and Cys were atypical. More importantly, genome analysis
AB  - provided insights into the reciprocal interactions of bifidobacteria with their hosts. We
AB  - identified polypeptides that showed homology to most major proteins needed for production of
AB  - glycoprotein-binding fimbriae, structures that could possibly be important for adhesion and
AB  - persistence in the GIT. We also found a eukaryotic-type serine protease inhibitor (serpin)
AB  - possibly involved in the reported immunomodulatory activity of bifidobacteria.
ER  -

TY  - JOUR
AU  - Schenk, J.A.
AU  - Heymann, S.
AU  - Micheel, B.
TI  - The accessibility of thiophosphorylated groups in DNA fragments to the enzymatic activity of ligases and restriction endonuclease BbsI.
JO  - Biochem. Mol. Biol. Int.
PY  - 1995
SP  - 1037
EP  - 1043
VL  - 36
AB  - The aim of this paper was to test the possibility to ligate and hydrolyse DNA
AB  - sequences containing thiomodified ends and bonds.  T4 DNA ligase was shown to ligate DNA
AB  - fragments regardless of whether it contains phosphorylated or thiophosphorylated 5'-ends.  But
AB  - the cleavage of an internally thiomodified phosphodiester bond was found to be totally
AB  - inhibited
AB  - when using the nonpalindromic restrictase BbsI.  The special properties of this restriction
AB  - endonuclease should allow the development of an oriented cloning strategy when combined with
AB  - T4 ligase and a thiophosphorylation of DNA fragments.
ER  -

TY  - JOUR
AU  - Schermelleh, L.
AU  - Haemmer, A.
AU  - Spada, F.
AU  - Rosing, N.
AU  - Meilinger, D.
AU  - Rothbauer, U.
AU  - Cristina, C.M.
AU  - Leonhardt, H.
TI  - Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 4301
EP  - 4312
VL  - 35
AB  - Postreplicative maintenance of genomic methylation patterns was proposed to depend largely on
AB  - the binding of DNA methyltransferase 1 (Dnmt1) to PCNA, a core component of the replication
AB  - machinery. We investigated how
AB  - the slow and discontinuous DNA methylation could be mechanistically linked
AB  - with fast and processive DNA replication. Using photobleaching and
AB  - quantitative live cell imaging we show that Dnmt1 binding to PCNA is
AB  - highly dynamic. Activity measurements of a PCNA-binding-deficient mutant
AB  - with an enzyme-trapping assay in living cells showed that this interaction
AB  - accounts for a 2-fold increase in methylation efficiency. Expression of
AB  - this mutant in mouse dnmt1(-/-) embryonic stem (ES) cells restored CpG
AB  - island methylation. Thus association of Dnmt1 with the replication
AB  - machinery enhances methylation efficiency, but is not strictly required
AB  - for maintaining global methylation. The transient nature of this
AB  - interaction accommodates the different kinetics of DNA replication and
AB  - methylation while contributing to faithful propagation of epigenetic
AB  - information.
ER  -

TY  - JOUR
AU  - Schermelleh, L.
AU  - Spada, F.
AU  - Easwaran, H.P.
AU  - Zolghadr, K.
AU  - Margot, J.B.
AU  - Cardoso, M.C.
AU  - Leonhardt, H.
TI  - Trapped in action: direct visualization of DNA methyltransferase activity in living cells.
JO  - Nat. Methods
PY  - 2005
SP  - 751
EP  - 756
VL  - 2
AB  - DNA methyltransferases have a central role in the complex regulatory network of epigenetic
AB  - modifications controlling gene expression in
AB  - mammalian cells. To study the regulation of DNA methylation in living
AB  - cells, we developed a trapping assay using transiently expressed
AB  - fluorescent DNA methyltransferase 1 (Dnmt1) fusions and mechanism-based
AB  - inhibitors 5-azacytidine (5-aza-C) or 5-aza-2'-deoxycytidine (5-aza-dC).
AB  - These nucleotide analogs are incorporated into the newly synthesized DNA
AB  - at nuclear replication sites and cause irreversible immobilization, that
AB  - is, trapping of Dnmt1 fusions at these sites. We measured trapping by
AB  - either fluorescence bleaching assays or photoactivation of
AB  - photoactivatable green fluorescent protein fused to Dnmt1 (paGFP-Dnmt1) in
AB  - mouse and human cells; mutations affecting the catalytic center of Dnmt1
AB  - prevented trapping. This trapping assay monitors kinetic properties and
AB  - activity-dependent immobilization of DNA methyltransferases in their
AB  - native environment, and makes it possible to directly compare mutations
AB  - and inhibitors that affect regulation and catalytic activity of DNA
AB  - methyltransferases in single living cells.
ER  -

TY  - JOUR
AU  - Scherr, M.
AU  - Reed, M.
AU  - Huang, C.F.
AU  - Riggs, A.D.
AU  - Rossi, J.J.
TI  - Oligonucleotide scanning of native mRNAs in extracts predicts intracellular ribozyme efficiency: ribozyme-mediated reduction of the murine DNA methyltransferase.
JO  - Mol. Ther.
PY  - 2000
SP  - 26
EP  - 38
VL  - 2
AB  - Modulation of gene expression by catalytic RNA requires accessible ribozyme cleavage sites in
AB  - the target mRNA, and accessibility is determined by the secondary and tertiary structure of
AB  - the target RNA, as affected by its interactions with cellular proteins. As we previously
AB  - reported, an oligonucleotide-scanning approach using antisense oligonucleotides can be used to
AB  - determine RNA accessibility in cell extracts. To test whether this method can be used to
AB  - improve selection of ribozyme target sites, we designed ribozymes corresponding to the sites
AB  - identified by oligonucleotide scanning and have evaluated their catalytic activities, first in
AB  - cell extracts and then in transduced cell lines. As a target we used the mRNA of murine DNA
AB  - (cytosine-5)-methyltransferase 1 (MTase). For intracellular studies, the ribozyme genes were
AB  - inserted downstream of a Pol III tRNAVAL promoter, which in turn was cloned in the U3 region
AB  - of a retroviral vector. We find that the efficiency of the ribozymes both in cell extracts and
AB  - in vivo corresponds with the relative effectiveness predicted by the oligonucleotide-scanning
AB  - assay. The best ribozyme causes a 70-80% reduction in the MTase mRNA levels in NIH 3T3 cells
AB  - that are stably transduced with the retroviral constructs. This reduction in mRNA levels is
AB  - accompanied by a small decrease in the methylation of repetitive intercisternal A particle DNA
AB  - elements. Ribozyme expression also increased several-fold the reactivation frequency of a
AB  - methylation-silenced green fluorescent protein (GFP) transgene. Both the reduction in
AB  - methylation and reactivation of GFP were roughly equivalent to the effects obtained by
AB  - treating NIH 3T3 cells with 2.5 mM 5-azacytidine, which gives an effect of about 10% of
AB  - maximum. These results confirm the validity of the cell extract approach for ribozyme site
AB  - selection and provide a potentially useful ribozyme for future study of DNA methyltransferase
AB  - function.
ER  -

TY  - JOUR
AU  - Scherzer, E.
AU  - Auer, B.
AU  - Schweiger, M.
TI  - Identification, purification and characterization of Escherichia coli virus T1 DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 1987
SP  - 15225
EP  - 15231
VL  - 262
AB  - An Escherichia coli virus T1-induced DNA methyltransferase was identified by
AB  - activity gel analysis in homogenates of infected E. coli
AB  - DNA-adenine-methylation-deficient strains.  Although the Mr of this protein
AB  - (31,000) is in the same range as that of the E. coli DNA adenine
AB  - methyltransferase, the two proteins are not closely related; the E. coli dam
AB  - gene does not hybridize with T1 DNA. Selective conditions for measurement of
AB  - the T1 activity were developed, and the enzyme was purified to functional
AB  - homogeneity, as shown by activity analysis in polyacrylamide gels.
AB  - Requirements for optimal activity of the viral enzyme were determined to be pH
AB  - 6.9, ionic strengths below 0.1 M KCl, and a temperature between 40 and 43C.
AB  - The Km for S-adenosyl-L-methionine is 4.9 microM.  The purified T1 DNA
AB  - methyltransferase is capable of methylating adenine in 5'-GATC-3' sites in
AB  - vitro.
ER  -

TY  - JOUR
AU  - Scheuner, C. et al.
TI  - Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)),  phylogenomic analysis and reclassification of Planctomycetes including the  descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen.   nov. and emen.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 10
EP  - 10
VL  - 9
AB  - Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs
AB  - from other bacterial taxa by several distinctive features such as
AB  - internal cell compartmentalization, multiplication by forming buds directly from
AB  - the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a
AB  - proteinaceous layer rather than a peptidoglycan layer. The first strains of P.
AB  - brasiliensis, including the type strain IFAM 1448(T), were isolated from a water
AB  - sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the
AB  - second completed genome sequence of a type strain of the genus Planctomyces to be
AB  - published and the sixth type strain genome sequence from the family
AB  - Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and
AB  - 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea
AB  - project. Phylogenomic analyses indicate that the classification within the
AB  - Planctomycetaceae is partially in conflict with its evolutionary history, as the
AB  - positioning of Schlesneria renders the genus Planctomyces paraphyletic. A
AB  - re-analysis of published fatty-acid measurements also does not support the
AB  - current arrangement of the two genera. A quantitative comparison of phylogenetic
AB  - and phenotypic aspects indicates that the three Planctomyces species with type
AB  - strains available in public culture collections should be placed in separate
AB  - genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to
AB  - accommodate P. maris, P. limnophilus and P. brasiliensis, respectively.
AB  - Pronounced differences between the reported G + C content of Gemmata
AB  - obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C
AB  - content calculated from their genome sequences call for emendation of their
AB  - species descriptions. In addition to other features, the range of G + C values
AB  - reported for the genera within the Planctomycetaceae indicates that the
AB  - descriptions of the family and the order should be emended.
ER  -

TY  - JOUR
AU  - Scheuring-Vanamee, E.
AU  - Viadiu, H.
AU  - Lukacs, C.M.
AU  - Aggarwal, A.K.
TI  - Two of a kind: BamHI and BglII.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 215
EP  - 236
VL  - 14
AB  - Among the more than 3500 Type II restriction endonucleases identified to date, fourteen have
AB  - been structurally characterized so far, including EcoRI, EcoRV, BamHI, PvuII, FokI, Cfr10I,
AB  - BglI, BglII, BsoBI, NaeI, NgoMIV, Bse634I (an isoschizomer of Cfr10I), MunI, and HincII.  All
AB  - except Cfr10I and Bse634I have been found to be bound to their cognate DNA sites.  Despite the
AB  - lack of sequence homology, all REases consist of a central beta-sheet that is flanked by
AB  - alpha-helices on both sides.  Interestingly, a similar alpha/beta core is also present in
AB  - other DNA-acting enzymes such as lambda-exonuclease, MutH, Vsr endonuclease, and TnsA from the
AB  - Tn7 transposase.  In the common core only three beta-strands are absolutely conserved, two of
AB  - these strands contain the amino acid residues directly involved in catalysis.  The similarity
AB  - at the tertiary structure level is strongest between endonucleases that share a similar
AB  - cleavatge pattern, such as between BamHI and EcoRI which cleave DNA to leave four-base 5'
AB  - overhangs, or between EcoRV and PvuII which cleave DNA to produce blunt ends.  An exception is
AB  - BglI that has a similar fold as EcoRV and PvuII but cleaves DNA to leave 3' overhangs.
AB  - Overall, the similarity reflects constraints in positioning of the active sites: 17-19 A apart
AB  - to produce four-base 5' overhangs and ~2A apart to produce blunt ends.  The active sites
AB  - occur at one end of the central beta-sheet and contain at least three superimposable residues
AB  - that are critical for catalysis.  Two of these residues are acidic, while the third residue is
AB  - usually a lysine, except in BamHI, which has a glutamate and in BglII which has a glutamine.
ER  -

TY  - JOUR
AU  - Schicklberger, M.
AU  - Shapiro, N.
AU  - Loque, D.
AU  - Woyke, T.
AU  - Chakraborty, R.
TI  - Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte.
JO  - Genome Announcements
PY  - 2015
SP  - e00607
EP  - e00615
VL  - 3
AB  - Raoultella terrigena R1Gly is a diazotrophic endophyte isolated from surface-sterilized roots
AB  - of Nicotiana tabacum. The whole-genome sequence was
AB  - obtained to investigate the endophytic characteristics of this organism at the
AB  - genetic level, as well as to compare this strain with its close relatives. To our
AB  - knowledge, this is the first genome obtained from the Raoultella terrigena
AB  - species and only the third genome from the Raoultella genus, after Raoultella
AB  - ornitholytic and Raoultella planticola. This genome will provide a foundation for
AB  - further comparative genomic, metagenomic, and functional studies of this genus.
ER  -

TY  - JOUR
AU  - Schierling, B.
AU  - Dannemann, N.
AU  - Gabsalilow, L.
AU  - Wende, W.
AU  - Cathomen, T.
AU  - Pingoud, A.
TI  - A novel zinc-finger nuclease platform with a sequence-specific cleavage module.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 2623
EP  - 2638
VL  - 40
AB  - Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the
AB  - non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration,
AB  - the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new
AB  - binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts
AB  - have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in
AB  - ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate
AB  - an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs,
AB  - ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites
AB  - are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter
AB  - K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at
AB  - addressed sites with a >1000-fold preference over unaddressed PvuII sites in vitro as well as
AB  - in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over
AB  - substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results
AB  - present the ZF-PvuII platform as a valid alternative to conventional ZFNs.
ER  -

TY  - JOUR
AU  - Schierling, B.
AU  - Noel, A.J.
AU  - Thi, L.H.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - Development of a 'photoswitchable' restriction endonuclease.
JO  - FEBS J.
PY  - 2009
SP  - 291
EP  - 291
VL  - 276
AB  - The engineering of proteins in order to obtain light-responsive characteristics is in focus of
AB  - photochemical research, because of the possibility to regulate protein function quickly and
AB  - reversibly, which is difficult to achieve by other means. As a proof of principle for
AB  - promising applications in future, we tried to generate a restriction endonuclease that can be
AB  - turned on and off by irradiation with light, using the single chain (sc) variant of the
AB  - restriction enzyme PvuII. 'Photoswitchable' proteins have been produced using azobenzene
AB  - crosslinkers that can be isomerized between the trans- and cis-state and vice versa by
AB  - illumination at specific wavelengths or by thermal relaxation from the cis- to the more stable
AB  - trans-state. Up to now, a 7-fold higher activity could be obtained with a variant of scPvuII
AB  - modified by two intramolecular crosslinks with 4,4'- azobenzene-dimaleimide in the cis
AB  - configuration than in the trans configuration. Switching was shown to be fully reversible. The
AB  - higher activity of the scPvuII variant with the azobenzene group in the cis state was shown to
AB  - be due to an increase mainly in Vmax.
ER  -

TY  - JOUR
AU  - Schierling, B.
AU  - Noel, A.J.
AU  - Wende, W.
AU  - Hien, L.T.
AU  - Volkov, E.
AU  - Kubareva, E.
AU  - Oretskaya, T.
AU  - Kokkinidis, M.
AU  - Rompp, A.
AU  - Spengler, B.
AU  - Pingoud, A.
TI  - Controlling the enzymatic activity of a restriction enzyme by light.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 1361
EP  - 1366
VL  - 107
AB  - For many applications it would be desirable to be able to control the activity of proteins by
AB  - using an external signal. In the present study, we have explored the possibility of modulating
AB  - the activity of a restriction
AB  - enzyme with light. By cross-linking two suitably located cysteine residues
AB  - with a bifunctional azobenzene derivative, which can adopt a cis- or
AB  - trans-configuration when illuminated by UV or blue light, respectively,
AB  - enzymatic activity can be controlled in a reversible manner. To determine
AB  - which residues when cross-linked show the largest 'photoswitch effect,'
AB  - i.e., difference in activity when illuminated with UV vs. blue light, > 30
AB  - variants of a single-chain version of the restriction endonuclease PvuII
AB  - were produced, modified with azobenzene, and tested for DNA cleavage
AB  - activity. In general, introducing single cross-links in the enzyme leads
AB  - to only small effects, whereas with multiple cross-links and additional
AB  - mutations larger effects are observed. Some of the modified variants,
AB  - which carry the cross-links close to the catalytic center, can be
AB  - modulated in their DNA cleavage activity by a factor of up to 16 by
AB  - illumination with UV (azobenzene in cis) and blue light (azobenzene in
AB  - trans), respectively. The change in activity is achieved in seconds, is
AB  - fully reversible, and, in the case analyzed, is due to a change in V(max)
AB  - rather than K(m).
ER  -

TY  - JOUR
AU  - Schierling, B.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - Redesigning the single-chain variant of the restriction endonuclease PvuII by circular permutation.
JO  - FEBS Lett.
PY  - 2012
SP  - 1736
EP  - 1741
VL  - 586
AB  - The restriction endonuclease PvuII has been introduced as a sequence-specific cleavage module
AB  - in highly-specific nucleases for gene
AB  - targeting. Here, a structural reorganization of the single-chain
AB  - variant of PvuII (scPvuII) was performed by circular permutation as a
AB  - proof-of-concept in order to find out whether the relocated, new
AB  - termini next to structural elements important for DNA recognition and
AB  - catalysis could be used for the fusion with other regulatory protein
AB  - domains. Three circularly permuted variants of scPvuII were obtained
AB  - that all maintain the specific endonucleolytic activity of scPvuII.
ER  -

TY  - JOUR
AU  - Schiestl, R.H.
AU  - Petes, T.D.
TI  - Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1991
SP  - 7585
EP  - 7589
VL  - 88
AB  - DNA fragments (generated by BamHI treatment) with no homology to the yeast genome were
AB  - transformed into Saccharomyces cerevisiae. When the fragments were transformed in the presence
AB  - of the BamHI enzyme, they integrated into genomic BamHI sites. When the fragments were
AB  - transformed in the absence of the enzyme, they integrated into genomic G-A-T-C sites. Since
AB  - the G-A-T-C sequence is present at the ends of BamHI fragments, this result indicates that
AB  - four base pairs of homology are sufficient for some types of mitotic recombination.
ER  -

TY  - JOUR
AU  - Schijffelen, M.J.
AU  - Boel, C.H.
AU  - van Strijp, J.A.
AU  - Fluit, A.C.
TI  - Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis.
JO  - BMC Genomics
PY  - 2010
SP  - 376
EP  - 376
VL  - 11
AB  - BACKGROUND: Recently, a new livestock-associated methicillin-resistant Staphylococcus aureus
AB  - (MRSA) Sequence Type 398 (ST398) isolate has emerged
AB  - worldwide. Although there have been reports of invasive disease in humans, MRSA
AB  - ST398 colonization is much more common in livestock and demonstrates especially
AB  - high prevalence rates in pigs and calves. The aim of this study was to compare
AB  - the genome sequence of an ST398 MRSA isolate with other S. aureus genomes in
AB  - order to identify genetic traits that may explain the success of this particular
AB  - lineage. Therefore, we determined the whole genome sequence of S0385, an MRSA
AB  - ST398 isolate from a human case of endocarditis. RESULTS: The entire genome
AB  - sequence of S0385 demonstrated considerable accessory genome content differences
AB  - relative to other S. aureus genomes. Several mobile genetic elements that confer
AB  - antibiotic resistance were identified, including a novel composite of an type V
ER  -

TY  - JOUR
AU  - Schildkraut, I.
TI  - Screening for and characterizing restriction endonucleases.
JO  - Genet. Eng. (N Y)
PY  - 1984
SP  - 117
EP  - 140
VL  - 6
AB  - The ability to cleave DNA at specific sequences is the fundamental technology
AB  - which was responsible for the rapid development of genetic engineering.  The
AB  - type II restriction endonucleases are the enzymes which enable scientists to
AB  - cleave DNA at specific sequences.  In 1974, Richard Roberts distributed a list
AB  - of 30 restriction endonucleases.  Eighteen of these recognized unique
AB  - sequences; the remainder were isoschizomers, enzymes from different bacterial
AB  - sources that recognize the same sequence.  Presently the list contains 398
AB  - restriction endonucleases, 91 of which are unique.  The increased number of
AB  - restriction endonucleases available now has allowed greater flexibility and
AB  - versatility in experimental strategies and design.  Continuing the search for
AB  - and identifying new restriction endonucleases will further reduce the
AB  - limitations and permit more precision in genetic engineering.  This chapter
AB  - describes a method for screening bacterial cells for the presence of type II
AB  - restriction endonucleases, and procedures for characterizing these restriction
AB  - endonucleases with respect to recognition sequence and site of cleavage.  The
AB  - recognition sequence is defined here as the nucleotide sequence which is
AB  - required for cleavage.  The site of cleavage is defined as the position of the
AB  - cleavage with relation to the recognition sequence.  For example, the
AB  - recognition sequence for EcoRI is GAATTC.  The site of cleavage is between the
AB  - G and A residues which produces a four base 5' extension (GAATTC).
ER  -

TY  - JOUR
AU  - Schildkraut, I.
AU  - Banner, C.D.B.
AU  - Rhodes, C.S.
AU  - Parekh, S.
TI  - The cleavage site for the restriction endonuclease EcoRV is 5'-GAT^ATC-3'.
JO  - Gene
PY  - 1984
SP  - 327
EP  - 329
VL  - 27
AB  - The cleavage site for the restriction endonuclease EcoRV has been found to be
AB  - 5'-GAT^ATC-3', rather than 5'-GATAT^C-3' as reported earlier by Kholmina et al.
AB  - (Dokl. Akad. Nauk. SSSR 253 (1980) 495-497).
ER  -

TY  - JOUR
AU  - Schildkraut, I.
AU  - Lynch, J.
AU  - Morgan, R.
TI  - The cleavage site for the restriction endonucleases BanI and HgiCI is 5' ...G^GPyPuCC ...3'.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 5492
EP  - 5492
VL  - 15
AB  - We have determined the cleavage site for the restriction endonucleases BanI and
AB  - HgiC 1 to be identical.  Both cleaving the sequence 5'... G^GPyPuCC ...3'
AB  - leaving a 4 base 5' extension.  This is in contrast to Kroger et al, who
AB  - reported the cleavage for HgiCI as 5' ...^GGPyPuCC...3' leaving a 6 base 5'
AB  - extension.
ER  -

TY  - JOUR
AU  - Schink, A.K.
AU  - Kadlec, K.
AU  - Schwarz, S.
TI  - Detection of qnr genes among Escherichia coli isolates of animal origin and complete sequence of the conjugative qnrB19-carrying plasmid pQNR2078.
JO  - J. Antimicrob. Chemother.
PY  - 2012
SP  - 1099
EP  - 1102
VL  - 67
AB  - OBJECTIVES: The aims of this study were to identify qnr genes among
AB  - quinolone-resistant Escherichia coli isolates from defined disease conditions of
AB  - companion and farm animals obtained in the BfT-GermVet study, and to gain insight
AB  - into their localization and the organization of the qnr gene regions. METHODS:
AB  - The qnr genes were detected by PCR and confirmed by sequencing. qnr-positive
AB  - isolates were checked for mutations in DNA gyrase and topoisomerase IV genes by
AB  - PCR and sequencing of the quinolone resistance-determining regions. Multilocus
AB  - sequence typing (MLST) was performed for the qnr-positive E. coli isolates.
AB  - Plasmids harbouring qnr genes were transferred by conjugation into E. coli
AB  - recipients, subjected to PCR-based replicon typing and plasmid-MLST, and one
AB  - qnrB19-carrying plasmid was sequenced completely. RESULTS: Only 2 of 417 E. coli
AB  - isolates investigated carried qnr genes. Both isolates originated from horses and
AB  - showed MLST type ST86. They harboured conjugative qnrB19-carrying plasmids, which
AB  - proved to be indistinguishable by restriction analysis, belonged to
AB  - incompatibility group IncN, showed plasmid-MLST type ST8 and did not carry other
AB  - resistance genes. The qnrB19 gene was flanked by copies of the insertion sequence
AB  - IS26. One of these plasmids, pQNR2078, was sequenced completely and had a size of
AB  - 42 379 bp. Except for the resistance gene region, plasmid pQNR2078 closely
AB  - resembled the bla(CTX-M-65)-carrying plasmid pKC396 from E. coli. CONCLUSIONS:
AB  - qnr genes were rarely detected among E. coli from animals in the BfT-GermVet
AB  - study. The qnrB19 gene was detected on conjugative plasmids, with IS26 being
AB  - likely involved in the mobility of qnrB19.
ER  -

TY  - JOUR
AU  - Schinzel, R.
AU  - Burger, K.J.
TI  - A site-specific endonuclease activity in Halobacterium halobium.
JO  - FEMS Microbiol. Lett.
PY  - 1986
SP  - 325
EP  - 329
VL  - 37
AB  - In Halobacterium halobium and some related strains, a site-specific
AB  - endonuclease activity was found.  This activity requires 3 M NaCl and 5-10 mM
AB  - Mg2+ ions for function.  The 3 cleavage sites in plasmid pBR322 were mapped,
AB  - but no homology between these sites was found.  H. halobium DNA is resistant to
AB  - cleavage, which may be due to a modification of the DNA.  The behaviour of the
AB  - endonuclease can be explained by the presence of a Type I or Type III-like
AB  - restriction-modification system.
ER  -

TY  - JOUR
AU  - Schirawski, J.
AU  - van Sinderen, D.
AU  - Fitzgerald, G.
TI  - Bacteriophage resistance in Streptococcus thermophilus.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 476
EP  - 476
VL  - 101
AB  - Thermophilic lactic acid bacteria are frequently used as starter cultures for the industrial
AB  - preparation of yoghurt or cheese.
AB  - Bacteriophage attack of these starter cultures has been described as
AB  - the main reason for fermentation failures. Natural phage resistance
AB  - mechanisms of bacteria include restriction/modification (R/M) systems,
AB  - enzyme complexes, that modify host DNA by methylation and degrade
AB  - unmodified incoming DNA. Type 1 R/M systems are encoded by three genes,
AB  - named hsdR, hsdM and hsdS. A complex of all three proteins, R, M and S,
AB  - is needed for degradation of unmodified DNA, whereas DNA modification
AB  - only requires the M and S subunits. The hsdM and hsdS genes are located
AB  - on the same operon, whereas the hsdR gene is usually transcribed from
AB  - its own promoter. A type I R/M system was identified on the genome of
AB  - S. thermophilus 4134, a phage resistant industrial strain used for the
AB  - production of yoghurt. The organization of the three genes is unusual,
AB  - in that they appear to be located on the same operon. The hsdR and hsdM
AB  - genes show high sequence identity to the corresponding genes of plasmid
AB  - located type 1 R/M systems from Lactococcos lactis or S. thermophilus,
AB  - suggesting a gene transfer event from a mobile genetic element into the
AB  - genome of S. thermophilus 4134.
ER  -

TY  - JOUR
AU  - Schirrmacher, E.
AU  - Beck, C.
AU  - Brueckner, B.
AU  - Schmitges, F.
AU  - Siedlecki, P.
AU  - Bartenstein, P.
AU  - Lyko, F.
AU  - Schirrmacher, R.
TI  - Synthesis and in vitro evaluation of biotinylated RG108: a high affinity compound for studying binding interactions with human DNA  methyltransferases.
JO  - Bioconjugate Chem.
PY  - 2006
SP  - 261
EP  - 266
VL  - 17
AB  - Small-molecule inhibitors of DNA methyltransferases such as RG108 represent promising
AB  - candidates for cancer drug development. We report the
AB  - synthesis and in vitro analysis of a biotinylated RG108 conjugate,
AB  - 2-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-3-(5-[3-[5-(2-oxo-hexahydro-thieno
AB  - [3,4-d]imidazol-4-yl)pentanoylamino]propoxy]-1H-indol-3-yl)propionic acid
AB  - (bio-RG108), for the evaluation of interactions with DNA methyltransferase
AB  - enzymes. The structural design of the chemically modified inhibitor was
AB  - aided by molecular modeling, which suggested the possibility for extensive
AB  - chemical modifications at the 5-position of the tryptophan moiety in
AB  - RG108. The inhibitory activity of the corresponding derivative was
AB  - confirmed in a cell-free biochemical assay, where bio-RG108 showed an
AB  - undiminished inhibition of DNA methyltransferase activity (IC50 = 40 nM).
AB  - Bio-RG108 therefore represents a suitable bioconjugate for the elucidation
AB  - of inhibitory mechanisms and for the affinity purification of
AB  - RG108-associated proteins.
ER  -

TY  - JOUR
AU  - Schirwitz, K.
AU  - Lundin, A.
AU  - Skoglund, A.
AU  - Krabbe, M.
AU  - Engstrand, L.
AU  - Enroth, C.
TI  - Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of HP1352, a putative DNA methyltransferase  in Helicobacter pylori.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2003
SP  - 719
EP  - 720
VL  - 59
AB  - The putative methyltransferase gene HP1352 from Helicobacter pylori strain 26695 was
AB  - heterologously expressed in Escherichia coli. The 359-amino-acid
AB  - gene product was purified and crystallized. The crystals belong to space
AB  - group I2(1)2(1)2(1) and show diffraction to at least 2.5 A resolution. The
AB  - unit-cell parameters are a = 69.6, b = 86.6, c = 140.0 A. A greater than
AB  - 90% complete native data set has been collected and structure
AB  - determination using the molecular-replacement method is ongoing.
ER  -

TY  - JOUR
AU  - Schlagman, S.
AU  - Hattman, S.
TI  - Mutants of the N-3 R-Factor conditionally defective in hspII modification and deoxyribonucleic acid-cytosine methylase activity.
JO  - J. Bacteriol.
PY  - 1974
SP  - 234
EP  - 239
VL  - 120
AB  - The N-3 resistance (R) factor specifies a deoxyribonucleic acid (DNA)-cytosine
AB  - methylase and a DNA restriction-modification (hspII) system.  We have isolated
AB  - three independent mutants that are conditionally defective in their ability to
AB  - modify bacteriophage lambda and to methylate DNA-cytosine residues.  The ratio
AB  - of 5-methylcytosine to N6-methyladenine in bacterial DNA and in the DNA of
AB  - phages lambda and fd was determined after labeling with [methyl-3H]methionine
AB  - at various growth temperatures.  Although the ability of the wild-type N-3
AB  - factor to modify phage lambda and to methylate DNA-cytosine residues was
AB  - unaffected with increasing temperature, two of the mutants exhibited a parallel
AB  - loss in modification and cytosine methylation ability.  The ability of the
AB  - third mutant to carry out these functions was dependent on the presence or
AB  - absence of an amber suppressor mutation in the host genome.  These results
AB  - offer further support for the notion that hspII modification is mediated by a
AB  - DNA-cytosine methylase.  Evidence is also presented that the modification
AB  - methylase is responsible for the in vivo methylation of phage fd DNA (which is
AB  - not subject to hspII restriction in vivo).
ER  -

TY  - JOUR
AU  - Schlagman, S.
AU  - Hattman, S.
AU  - May, M.S.
AU  - Berger, L.
TI  - In vivo methylation by Escherichia coli K-12 mec+ Deoxyribonucleic Acid-cytosine methylase protects against in vitro cleavage by the RII restriction endonuclease (R.EcoRII).
JO  - J. Bacteriol.
PY  - 1976
SP  - 990
EP  - 996
VL  - 126
AB  - We have analyzed the susceptibility of the deoxyribonucleic acid (DNA) of phage
AB  - fd replicative form (RF) and of Escherichia coli to in vitro cleavage by
AB  - purified RII restriction endonuclease (R.EcoRII).  The results are summarized
AB  - as follows:  (i) fd.mec- RFI, isolated from infected E. coli K-12 mec- bacteria
AB  - (a mutant strain lacking DNA-cytosine methylase activity), is cleaved into at
AB  - least two fragments, whereas fd.mec+ RFI, isolated from the parental mec+
AB  - strain, is not cleaved.  (ii) E. coli mec- DNA is extensively degraded, whereas
AB  - E. coli mec+ DNA is resistant to cleavage.  We conclude that the E. coli mec+
AB  - DNA-cytosine methylase acts as an RII modification enzyme.
ER  -

TY  - JOUR
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9101
EP  - 9112
VL  - 17
AB  - Bacteriophages T2 and T4 encode DNA-[N6-adenine] methyltransferases (Dam) which differ from
AB  - each other by only three amino acids. The canonical recognition sequence for these enzymes in
AB  - both cytosine and 5-hydroxymethylcytosine-containing DNA is GATC; at a lower efficiency they
AB  - also recognize some non-canonical sites in sequences derived from GAY (where Y is cytosine or
AB  - thymine). We found that T4 Dam fails to methylate certain GATA and GATT sequences which are
AB  - methylated by T2 Dam. This indicates that T2 Dam and T4 Dam do not have identical sequence
AB  - specificities. We analyzed DNA sequence data files obtained from GenBank, containing bout 30%
AB  - of the T4 genome, to estimate the overall frequency of occurrence of GATC, as well as
AB  - non-canonical sites derived from GAY. The observed N6methyladenine (m6A) content of T4 DNA,
AB  - methylated exclusively at GATC (by Escherichia coli Dam), was found to be in good agreeement
AB  - with this estimate. Although GATC is fully methylated in virion DNA, only a small percentage
AB  - of the non-canonical sequences are methylated.
ER  -

TY  - JOUR
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Molecular cloning of a functional dam+ gene coding for phage T4 DNA adenine methylase.
JO  - Gene
PY  - 1983
SP  - 139
EP  - 156
VL  - 22
AB  - Phages T2 and T4 induce synthesis of a DNA-adenine methylase which is coded for
AB  - by a phage gene, dam+. These enzymes methylate adenine residues in specific
AB  - sequences which include G-A-T-C, the methylation site of the host Escherichia
AB  - coli dam+ methylase.  Methylation of G-A-T-C to G-m6A-T-C protects the site
AB  - against cleavage by the MboI restriction nuclease.  We have taken advantage of
AB  - this property to enrich and screen for transformants which contain a cloned,
AB  - functional T4 dam+ gene.  These recombinant molecules consist of a 1.85-kb
AB  - HindIII fragment inserted into the plasmid pBR322; both orientations of the
AB  - fragment express the methylase gene, suggesting that transcription is from a T4
AB  - promoter.  We have tested the 1.85-kb insert for sensitivity to a variety of
AB  - restriction nucleases and have found single sites for EcoRI, BalI, XbaI, and at
AB  - least two sites for BstNI (EcoRII).  The relative positions of these
AB  - restriction sites have also been determined.  Physical mapping was carried out
AB  - by Southern blot hybridization with 32P-labeled (nick-translated clone) probe.
AB  - These experiments showed that the insert corresponds to a HindIII fragment
AB  - located on the physical map of T4 between positions 16.2 and 18.1 kb from the
AB  - T4rIIA-rIIB junction.  E. coli dam- possesses several phenotypic differences
AB  - from the wild-type dam+ parent, including an increased sensitivity to
AB  - 2-aminopurine (2-AP).  We found that T4 dam+ clones could relieve dam- cells of
AB  - their increased sensitivity to 2-AP.
ER  -

TY  - JOUR
AU  - Schlagman, S.L.
AU  - Hattman, S.
AU  - Marinus, M.G.
TI  - Direct role of the Escherichia coli Dam DNA methyltransferase in methylation-directed mismatch repair.
JO  - J. Bacteriol.
PY  - 1986
SP  - 896
EP  - 900
VL  - 165
AB  - The T4 dam+ gene has been cloned (S. L. Schlagman and S. Hattman, Gene 22:139-156, 1983) and
AB  - transferred into an Escherichia coli dam-host. In this host, the T4 Dam DNA methyltransferase
AB  - methylates mainly, if not exclusively, the sequence 5'-GATC-3'; this sequence specificity is
AB  - the same as that of the E. coli Dam enzyme. Expression of the cloned T4 dam+ gene suppresses
AB  - almost all the phenotypic traits associated with E. coli dam mutants, with the exception of
AB  - hypermutability. In wild-type hosts, 20- to 500-fold overproduction of the E. coli Dam
AB  - methylase by plasmids containing the cloned E. coli dam+ gene results in a hypermutability
AB  - phenotype (G.E. Herman and P. Modrich, J. Bacteriol. 145:644-646, 1981; M.G. Marinus, A.
AB  - Poteete, and J.A. Arraj, Gene 28:123-125, 1984). In contrast, the same high level of T4 Dam
AB  - methylase activity, produced by plasmids containing the cloned T4 dam+ gene, does not result
AB  - in hypermutability. To account for these results we propose that the E. coli Dam methylase may
AB  - be directly involved in the process of methylation-instructed mismatch repair and that the T4
AB  - Dam methylase is unable to substitute for the E. coli enzyme.
ER  -

TY  - JOUR
AU  - Schlagman, S.L.
AU  - Miner, Z.
AU  - Feher, Z.
AU  - Hattman, S.
TI  - The DNA [adenine-N6]methyltransferase (Dam) of bacteriophage T4.
JO  - Gene
PY  - 1988
SP  - 517
EP  - 530
VL  - 73
AB  - A functional bacteriophage T4 dam+ gene, which specifies a DNA [adenine-N6]
AB  - methyltransferase (Dam), was cloned on a 1.8-kb HindIII fragment [Schlagman and
AB  - Hattman, Gene 22 (1983) 139-156].  Sequence analysis [McDonald and Mosig, EMBO
AB  - J. 3(1984) 2863-2871] revealed two overlapping in-phase open reading frames
AB  - (ORFs).  The 5' proximal ORF initiates translation at an AUG and encodes a
AB  - 30-kDA polypeptide, whereas the downstream ORF initiates translation at a GUG
AB  - and encodes a 26-kDa polypeptide.  Analysis of BAL 31 deletions in our original
AB  - dam+ clone has verified that at least one of these overlapping ORFs, in fact,
AB  - encodes T4 Dam.  To investigate where T4 Dam translation is initiated, we have
AB  - constructed plasmids in which a tac or lambda pL promoter is placed 5' to
AB  - either the longer ORF or just the shorter ORF.  Only clones which contain a
AB  - promoter in front of the longer ORF produce active T4 Dam.  This indicates that
AB  - the 26-kDa polypeptide alone cannot be T4 Dam.  Additional experiments suggest
AB  - that only the 30-kDa polypeptide is required for enzyme activity and that the
AB  - shorter ORF is not translated in plasmid-carrying cells.  We also present
AB  - evidence that T4 Dam is capable of methylating 5'-GATC-3', GATm5C, and GAThmC
AB  - sequences; non-canonical sites (e.g., GACC) are also methylated, but much less
AB  - efficiently.
ER  -

TY  - JOUR
AU  - Schleheck, D.
AU  - Weiss, M.
AU  - Pitluck, S.
AU  - Bruce, D.
AU  - Land, M.L.
AU  - Han, S.
AU  - Saunders, E.
AU  - Tapia, R.
AU  - Detter, C.
AU  - Brettin, T.
AU  - Han, J.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Pennacchio, L.
AU  - Nolan, M.
AU  - Cook, A.M.
AU  - Kjelleberg, S.
AU  - Thomas, T.
TI  - Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 298
EP  - 310
VL  - 5
AB  - Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in
AB  - the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of
AB  - the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented,
AB  - aerobic, heterotrophic bacterium and represents the first tier member of
AB  - environmentally important bacterial communities that catalyze the complete
AB  - degradation of synthetic laundry surfactants. Here we describe the features of
AB  - this organism, together with the complete genome sequence and annotation. The
AB  - 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the
AB  - first completed genome sequence of the genus Parvibaculum, and the first genome
AB  - sequence of a representative of the family Rhodobiaceae.
ER  -

TY  - JOUR
AU  - Schleif, R.
TI  - Assaying of organisms for the presence of restriction endonucleases.
JO  - Methods Enzymol.
PY  - 1980
SP  - 19
EP  - 23
VL  - 65
AB  - The utility of sequence-specific endonucleases recommends their use in a wide variety of
AB  - applications.  Typically a potential user is faced with the problem of determining which of
AB  - the large number of enzymes already known will cleave in acceptable locations.  Thus an easy,
AB  - uniform, and rapid scheme for partial purification of these enzymes would greatly assist the
AB  - initial screening.  A purification step fulfilling these requirements could also be of value
AB  - as a first step when pure enzyme is required or of use in searching for new varieties of
AB  - endonuclease.  Dextran-polyethylene glycol phase partition meets the requirements of speed and
AB  - convenience.  Here it is shown that adjustment of the salt concentration during the phase
AB  - partition step allows separation of most of the interfering nuclease activities in the crude
AB  - extracts of many strains containing site-specific nucleases.
ER  -

TY  - JOUR
AU  - Schleper, C.
TI  - Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group.
JO  - Front. Microbiol.
PY  - 2012
SP  - 208
EP  - 208
VL  - 3
AB  - Ammonia-oxidising archaea (AOA) have recently been recognized as a significant component of
AB  - many microbial communities and represent one of the most abundant prokaryotic groups in the
AB  - biosphere. However, only few AOA have been successfully cultivated so far and information on
AB  - the physiology and genomic content remains scarce. We have performed a metagenomic analysis to
AB  - extend the knowledge of the AOA affiliated with group I.1b that is widespread in terrestrial
AB  - habitats and of which no genome sequences has been described yet. A fosmid library was
AB  - generated from samples of a radioactive thermal cave (46oC) in the Austrian Central Alps in
AB  - which AOA had been found as a major part of the microbial community. Out of sixteen fosmids
AB  - that possessed either an amoA or 16S rRNA gene affiliating with AOA, five were fully
AB  - sequenced, four of which grouped with the soil/I.1b (Nitrososphaera-) lineage and one with
AB  - marine/I.1a (Nitrosopumilus-) lineage. Phylogenetic analyses of amoBC and an associated
AB  - conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and
AB  - supported the separation of the soil and marine group. Several putative genes that did not
AB  - have homologues in  currently available marine thaumarchaeota genomes indicated that AOA of
AB  - the soil group contain specific genes that are distinct from their marine relatives. Potential
AB  - cis regulatory elements around conserved promoter motifs found upstream of the amo genes in
AB  - sequenced (meta-) genomes differed in marine and soil group AOA. On one fosmid, a group of
AB  - genes including amoA and amoB were flanked by identical transposable insertion sequences,
AB  - indicating that amoAB could potentially be co-mobilized in the form of a composite transposon.
AB  - This might be one of the mechanisms that caused the greater variation in gene order compared
AB  - to genomes in the marine counterparts. Our findings highlight the genetic diversity within the
AB  - two major and widespread lineages of thaumarchaeota.
ER  -

TY  - JOUR
AU  - Schleper, C.
AU  - DeLong, E.F.
AU  - Preston, C.M.
AU  - Feldman, R.A.
AU  - Wu, K.-Y.
AU  - Swanson, R.V.
TI  - Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum.
JO  - J. Bacteriol.
PY  - 1998
SP  - 5003
EP  - 5009
VL  - 180
AB  - Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal
AB  - group that inhabits cold and temperate terrestrial and marine environments.  To date these
AB  - organisms have resisted isolation in pure culture, and so their phenotypic and genotypic
AB  - characteristics remain largely unknown.  To characterize these archaea, and to extend
AB  - methodological approaches for characterizing uncultivated microorganisms, we initiated genomic
AB  - analyses of the nonthermophilic crenarchaeote Cenarchaeum symbiosum found living in
AB  - association with a marine sponge, Axinella mexicana.  Complex DNA libraries derived from the
AB  - host-symbiont population yielded several large clones containing the ribosomal operon from C.
AB  - symbiosum.  Unexpectedly, cloning and sequence analysis revealed the presence of two closely
AB  - related variants that were consistently found in the majority of host individuals analyzed.
AB  - Homologous regions from the two variants were sequenced and compared in detail.  The variants
AB  - exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain
AB  - homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping
AB  - region.  Our study not only indicates the potential for characterizing uncultivated
AB  - prokaryotes by genome sequencing but also identifies the primary complication inherent in the
AB  - approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic
AB  - populations.
ER  -

TY  - JOUR
AU  - Schlesinger, D.J.
AU  - Shoemaker, N.B.
AU  - Salyers, A.A.
TI  - Possible Origins of CTnBST, a Conjugative Transposon Found Recently in a Human Colonic Bacteroides Strain.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 4226
EP  - 4233
VL  - 73
AB  - A previous survey of Bacteroides isolates suggested that the ermB gene
AB  - entered Bacteroides spp. recently. Previously, ermB had been found almost
AB  - exclusively in gram-positive bacteria. In one Bacteroides strain, ermB was
AB  - located on 100-kb conjugative transposon (CTn) CTnBST. To assess the
AB  - possible origin of this CTn, we obtained the full DNA sequence of CTnBST
AB  - and used this information to investigate its possible origins. Over
AB  - one-half of CTnBST had high sequence identity to a putative CTn found in
AB  - the genome of Bacteroides fragilis YCH46. This included the ends of the
AB  - CTn and genes involved in integration, transfer, and excision. However,
AB  - the region around the ermB gene contained genes that appeared to originate
AB  - from gram-positive organisms. In particular, a 7-kb segment containing the
AB  - ermB gene was 100% identical to an ermB region found in the genome of the
AB  - gram-positive bacterium Arcanobacterium pyogenes. A screen of Bacteroides
AB  - isolates whose DNA cross-hybridized with a CTnBST probe revealed that
AB  - several isolates did not carry the 7-kb region, implying that the
AB  - acquisition of this region may be more recent than the acquisition of the
AB  - entire CTnBST element by Bacteroides spp. We have also identified other
AB  - Bacteroides isolates that carry a slightly modified 7-kb region but have
AB  - no other traces of CTnBST. Thus, it is possible that this 7-kb region
AB  - could itself be part of a mobile element that has inserted in a
AB  - Bacteroides CTn. Our results show that CTnBST is a hybrid element which
AB  - has acquired a portion of its coding region from gram-positive bacteria
AB  - but which may originally have come from Bacteroides spp. or some related
AB  - species.
ER  -

TY  - JOUR
AU  - Schlickenrieder, M.
TI  - Structure, localization/regulation and interaction-partners of the Dam-Methyltransferase of Escherichia coli.
JO  - Ph.D. Thesis, Germany
PY  - 2006
SP  - 1
EP  - 161
ER  -

TY  - JOUR
AU  - Schluckebier, G.
AU  - Kozak, M.
AU  - Bleimling, N.
AU  - Weinhold, E.
AU  - Saenger, W.
TI  - Differential binding of S-adenosylmethionine, S-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M.TaqI.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 56
EP  - 67
VL  - 265
AB  - The crystal structures of the binary complexes of the DNA methyltransferase M.TaqI with the
AB  - inhibitor Sinefungin and the reaction product S-adenosyl-L-homocysteine were determined, both
AB  - at 2.6 A resolution.  Structural comparison of these binary complexes with the complex formed
AB  - by M.TaqI and the cofactor S-adenosyl-L-methionine suggests that the key element for molecular
AB  - recognition of these ligands is the binding of their adenosine part in a pocket, and
AB  - discrimination between cofactor, reaction product and inhibitor is mediated by different
AB  - conformations of these molecules; the methionine part of S-adenosyl-L-methionine is located in
AB  - the binding cleft, whereas the amino acid moieties of Sinefungin and S-adenosyl-l-homocysteine
AB  - are in a different orientation and interact with the active site amino acid residues
AB  - 105NPPY108.  Dissociation constants for the complexes of M.TaqI with the three ligands were
AB  - determined spectrofluorometrically.  Sinefungin binds more strongly than
AB  - S-adenosyl-L-homocysteine or S-adenosyl-L-methionine, with KD=0.34 microM, 2.4 microM and 2.0
AB  - microM, respectively.
ER  -

TY  - JOUR
AU  - Schluckebier, G.
AU  - Labahn, J.
AU  - Granzin, J.
AU  - Saenger, W.
TI  - Structure and function of the adenine specific DNA methyltransferase M.TaqI.
JO  - J. Biomol. Struct. Dyn.
PY  - 1995
SP  - A206
EP  - A206
VL  - 12
AB  - Methylation of DNA bases is frequently employed by most living organisms to enhance the
AB  - informational content of DNA.  DNA methyltransferases (MTases) transfer a methyl group from
AB  - the cofactor S-adenosyl-methionine (AdoMet) to either adenine N6, cytosine N4 (N-MTases) or
AB  - cytosine C5 (C-MTases) in a specific DNA sequence.  AdoMet is thereby converted to
AB  - S-adenosyl-homocysteine (AdoHcy), and a proton is released.  In procaryotes, DNA MTases are
AB  - usually part of restriction/modification systems (R/M system), which consist typically of an
AB  - endonuclease (ENase) and a DNA MTase with the same recognition sequence.  The ENase cleaves
AB  - unmethylated double stranded DNA, e.g. of invading viruses.  The cognate MTase methylates the
AB  - host's DNA making it insusceptable against cleavage.  In eucaryotes DNA methylation plays a
AB  - role in such different phenomena as cell differentiation, genomic imprinting and
AB  - carcinogenesis.  We determined the first crystal structure of an N-MTase from the R/M system I
AB  - of Thermus aquaticus (M.TaqI) in complex with its cofactor AdoMet at a resolution of 2.4
AB  - Angstroms.  It shows alpha/beta-folding of the enzyme into two domains of roughly equal size.
AB  - Both domains are oriented towards each other such that they form a cleft which is studded
AB  - with positively charged amino acid residues and is sufficiently wide to accommodate B-DNA.
AB  - The N-terminal domain binds AdoMet and contains all amino acid residues which are conserved
AB  - throughout all DNA MTases.  As with probably all AdoMet dependent MTases the cofactor is bound
AB  - at an alpha-beta-alpha-fold which resembles the Rossmann-fold of dinucleotide binding
AB  - proteins.  The C-terminal domain functions in DNA binding and molecular recognition of the DNA
AB  - substrate.  Additionally, crystals of the enzyme complexed with the reaction product AdoHcy
AB  - and the competitive inhibitor Sinefungin were grown.  The X-Ray structures show the same
AB  - overall folding of the polypeptide chain as with the M.TaqI-AdoMet complex.  Small, but
AB  - distinctive differences in the binding of the small molecules provide insight into the
AB  - molecular recognition of the cofactor.
ER  -

TY  - JOUR
AU  - Schluckebier, G.
AU  - Labahn, J.
AU  - Granzin, J.
AU  - Saenger, W.
TI  - M.TaqI: Possible catalysis via cation-pi interactions in N-specific DNA methyltransferases.
JO  - Biol. Chem.
PY  - 1998
SP  - 389
EP  - 400
VL  - 379
AB  - The adenine-specific DNA methyltransferase M.TaqI transfers a methyl group from
AB  - S-adenosylmethionine to N6 of the adenine residue in the DNA sequence 5'-TCGA-3'.  In the
AB  - crystal structure of M.TaqI in complex with S-adenosylmethionine the enzyme is folded into two
AB  - domains: An N-terminal catalytic domain, whose fold is conserved among S-adenosylmethionine
AB  - dependent methyltransferases, and a DNA recognition domain which possesses a unique fold.  In
AB  - the active site, two aromatic residues, Tyr 108 and Phe 196, are postulated to bind the
AB  - flipped-out target DNA adenine which becomes methylated.  By lowering the energy of the
AB  - positively charged transition state via cationic-pi interactions, these two residues probably
AB  - hold a key role in catalysis.
ER  -

TY  - JOUR
AU  - Schluckebier, G.
AU  - Labahn, J.
AU  - Granzin, J.
AU  - Schildkraut, I.
AU  - Saenger, W.
TI  - A model for DNA binding and enzyme action derived from crystallographic studies of the TaqI N6-adenine-methyltransferase.
JO  - Gene
PY  - 1995
SP  - 131
EP  - 134
VL  - 157
AB  - The crystal structures of the DNA-N6-adenine-methyltransferase M.TaqI, in complexes with the
AB  - cofactor S-adenosyl-L-methionine (AdoMet) and the competitive inhibitor sinefungin (Sf) show
AB  - identical folding of the polypeptide chains into two domains.  The N-terminal domain carries
AB  - the cofactor-binding site, the C-terminal domain is thought to be implicated in
AB  - sequence-specific DNA binding.  Model building of the M.TaqI-DNA complex suggests that the
AB  - adenine to be methylated swings out of the double helix as found previously in the
AB  - cytosine-C5-MTase HhaI DNA co-crystal structure.  A torsion of the methionine moiety of the
AB  - cofactor is required to bring the methyl group within reach of the swung-out base and allow
AB  - methyl group transfer.
ER  -

TY  - JOUR
AU  - Schluckebier, G.
AU  - O'Gara, M.
AU  - Saenger, W.
AU  - Cheng, X.
TI  - Universal catalytic domain structure of AdoMet-dependent methyltransferases.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 16
EP  - 20
VL  - 247
AB  - The DNA methyltransferases, M.HhaI and M.TaqI, and catechol O-methyl-transferase (COMT)
AB  - catalyze the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to
AB  - carbon-5 of cytosine, to nitrogen-6 of adenine, and to a hydroxyl group of catechol,
AB  - respectively. The catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire
AB  - single domain of COMT have similar folding with an alpha/beta structure containing a mixed
AB  - central beta-sheet. The functional residues are located in equivalent regions at the carboxyl
AB  - ends of the parallel beta-strands. The cofactor binding sites are almost identical and the
AB  - essential catalytic amino acids coincide. The comparable protein folding and the existence of
AB  - equivalent amino acids in similar secondary and tertiary positions indicate that many (if not
AB  - all) AdoMet-dependent methyltransferases have a common catalytic domain structure. This
AB  - permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule
AB  - AdoMet-dependent methyltransferases from their amino acid sequences.
ER  -

TY  - JOUR
AU  - Schluter, A.
AU  - Heuer, H.
AU  - Szczepanowski, R.
AU  - Poler, S.M.
AU  - Schneiker, S.
AU  - Puhler, A.
AU  - Top, E.M.
TI  - Plasmid pB8 is closely related to the prototype IncP-1beta plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein.
JO  - Plasmid
PY  - 2005
SP  - 135
EP  - 148
VL  - 54
AB  - The IncP-1beta plasmid pB8, which confers resistance to amoxicillin,
AB  - spectinomycin, streptomycin, and sulfonamides, was previously isolated
AB  - from a sewage treatment plant. It was found to possess abnormal
AB  - conjugative transfer properties, i.e., transfer to Escherichia coli by
AB  - conjugation or electroporation could not be detected. We showed in this
AB  - study that plasmid pB8 is transferable to E. coli by conjugation, but only
AB  - at low frequencies and under specific experimental conditions, a
AB  - phenomenon that is very unusual for IncP-1 plasmids. Determination of the
AB  - complete 57,198bp pB8 nucleotide sequence revealed that the backbone of
AB  - the plasmid consists of a complete set of IncP-1beta-specific genes for
AB  - replication initiation, conjugative plasmid transfer, stable inheritance,
AB  - and plasmid control with an organisation identical to that of the
AB  - prototype IncP-1beta plasmid R751. All of the minor differences in the pB8
AB  - backbone sequence compared to that of R751 were also found in other
AB  - IncP-1beta plasmids known to transfer to and replicate in E. coli.
AB  - Plasmids pB8 and R751 can be distinguished with respect to their accessory
AB  - genetic elements. First, the pB8 region downstream of the replication
AB  - initiation gene trfA contains two transposable elements one of which is
AB  - similar to Tn5501. The latter transposon encodes a putative
AB  - post-segregational-killing system and the small multidrug resistance (SMR)
AB  - protein QacF, mediating quaternary ammonium compound resistance. The
AB  - accessory genes in this region are not responsible for the poor plasmid
AB  - transfer to E. coli since a pB8 deletion derivative devoid of all genes in
AB  - that region showed the same conjugative transfer properties as pB8. A
AB  - Tn5090/Tn402 derivative carrying a class 1 integron is located between the
AB  - conjugative transfer modules. The Tn5090/Tn402 integration-sites are
AB  - exactly identical on pB8 and R751 but in contrast to R751 the pB8 element
AB  - carries the resistance gene cassettes oxa-2 for amoxicillin resistance and
AB  - aadA4 for streptomycin/spectinomycin resistance, the integron-specific
AB  - conserved segment consisting of the genes qacEDelta1, sul1, and orf5, and
AB  - a truncated tni transposition module (tniAB). Although future work will
AB  - have to determine the molecular basis for the poor transfer of pB8 to E.
AB  - coli, our findings demonstrate that the host-range of typical IncP-1
AB  - plasmids may be less broad than expected.
ER  -

TY  - JOUR
AU  - Schmeisser, C. et al.
TI  - Rhizobium sp. NGR234 possesses a remarkable number of secretion systems.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 4035
EP  - 4045
VL  - 75
AB  - Rhizobium sp. NGR234 is a unique alpha-proteobacterium (Order -
AB  - Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any
AB  - other micro-symbiont. Here we report that the 3.93 Mbp chromosome
AB  - (cNGR234) encodes most functions required for cellular growth. Few
AB  - essential functions are encoded on the 2.43 Mbp mega-plasmid (pNGR234b)
AB  - and none are present on the second 0.54 Mbp symbiotic plasmid (pNGR234a).
AB  - Amongst many striking features, the 6.9 Mbp genome encodes more different
AB  - secretion systems than any other known rhizobia and probably most known
AB  - bacteria. Altogether 132 genes and proteins are linked to secretory
AB  - processes. Secretion systems identified include general and export
AB  - pathways (GSP
ER  -

TY  - JOUR
AU  - Schmid, E.N.
AU  - von Recklinghausen, G.
AU  - Ansorg, R.
TI  - Bacteriophages in Helicobacter (Campylobacter) pylori.
JO  - J. Med. Microbiol.
PY  - 1990
SP  - 101
EP  - 104
VL  - 32
AB  - Bacteriophages in different stages of maturation were found in thin sections of a clinical
AB  - isolate of Helicobacter (Campylobacter) pylori. Mature phage heads measured 70 x 60 nm and the
AB  - tail at least 120 nm. Lysogeny was maintained during subculture on blood agar for more than 3
AB  - months after isolation from a gastric biopsy.
ER  -

TY  - JOUR
AU  - Schmid, J.
AU  - Huptas, C.
AU  - Wenning, M.
TI  - Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031.
JO  - Genome Announcements
PY  - 2016
SP  - e01069
EP  - e01016
VL  - 4
AB  - Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly
AB  - no genetic information is available, despite its good
AB  - xanthan-producing properties. We performed an Illumina-based sequencing approach
AB  - of LMG 8031. The genome revealed a 5.0-Mb chromosome having 4,434 coding
AB  - sequences and a G+C content of 65%.
ER  -

TY  - JOUR
AU  - Schmid, J.
AU  - Koenig, S.
AU  - Pick, A.
AU  - Steffler, F.
AU  - Yoshida, S.
AU  - Miyamoto, K.
AU  - Sieber, V.
TI  - Draft Genome Sequence of Kozakia baliensis SR-745, the First Sequenced Kozakia Strain from the Family Acetobacteraceae.
JO  - Genome Announcements
PY  - 2014
SP  - e00594
EP  - e00514
VL  - 2
AB  - Kozakia baliensis belongs to the family Acetobacteraceae and was described for the first time
AB  - in 2002. These acetic acid bacteria are able to produce acetic
AB  - acid from various carbon sources and 2- and 5-keto-d-gluconate from glucose. The
AB  - novel K. baliensis strain SR-745 was isolated from a pineapple fruit bought in a
AB  - German supermarket. The strain produces large amounts of organic acids when grown
AB  - on glucose-containing medium and accepts also glycerol, fructose, mannitol, and
AB  - sucrose as a C source. When grown under light and high-oxygen conditions in
AB  - submerged culture, the production of a pink pigment is observed after 72 h.
ER  -

TY  - JOUR
AU  - Schmid, K.
AU  - Thomm, M.
AU  - Laminet, A.
AU  - Laue, F.G.
AU  - Kessler, C.
AU  - Stetter, K.O.
AU  - Schmitt, R.
TI  - Three new restriction endonucleases MaeI, MaeII and MaeIII from Methanococcus aeolicus.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 2619
EP  - 2628
VL  - 12
AB  - Three type II restriction endonucleases, MaeI, MaeII and MaeIII, with novel
AB  - site specificities have been isolated and purified form the archaebacterium
AB  - Methanococcus aeolicus PL-15/H.  The recognition sequences of these enzymes are
AB  - C^T A G   (MaeI)  A^C G T   (MaeII) ^G T N A C  (MaeIII)  with the sites of
AB  - cleavage as indicated by the arrows.  The sequences were confirmed by
AB  - restriction and computer analyses on sequenced DNA's of plasmid pBR322,
AB  - bacteriophage lambda and PhiX174 and virus SV40.
ER  -

TY  - JOUR
AU  - Schmidt, A.
AU  - Reinert, H.
AU  - Venner, H.
AU  - Bieber, J.
TI  - Studies on the substrate specificity of the DNA methylase activity from Escherichia coli K-12.
JO  - Z. Allg. Mikrobiol.
PY  - 1979
SP  - 489
EP  - 495
VL  - 19
AB  - A partially purified extract of DNA methylases from E. coli K-12 containing DNA-adenine as
AB  - well as DNA-cytosine methylase activities has been examined with respect to different DNA
AB  - species as substrates.  The results show that the natural content of 6-MAP in the applied DNA
AB  - represses the DNA-adenine methylase activity.  On the other hand, 5-MC, already present in the
AB  - substrate does not influence the activity of the DNA-cytosine methylase.  DNA from Micrococcus
AB  - radiodurans, which is completely free of methylated bases served as a comparison.  Since
AB  - netropsin preferentially binds to AT-rich regions of DNA, the influence of this oligopeptide
AB  - antibiotic on the methylation of DNA was investigated.  As expected the antibiotic
AB  - predominantly inhibits adenine methylation of DNA.  The degree of inhibition depends on the
AB  - molar ratio of netropsin to DNA phosphate.
ER  -

TY  - JOUR
AU  - Schmidt, F.H.-G.
AU  - Hueben, M.
AU  - Gider, B.
AU  - Renault, F.
AU  - Teulade-Fichou, M.-P.
AU  - Weinhold, E.
TI  - Sequence-specific methyltransferase-induced labelling (SMILing) of plasmid DNA for studying cell transfection.
JO  - Bioorg. Med. Chem.
PY  - 2008
SP  - 40
EP  - 48
VL  - 16
AB  - Plasmid DNA (pUC19 and pBR322) was sequence-specifically, covalently labelled with Cy3
AB  - fluorophores using a newly synthesised
AB  - N-adenosylaziridine cofactor and the DNA methyltransferase M.TaqI. The
AB  - fluorescently labelled plasmids were used for transfection of mammalian
AB  - cells and their intracellular distribution was visualised by
AB  - epifluorescence and confocal fluorescence microscopy. Although these
AB  - prokaryotic plasmids do not contain nuclear import sequences,
AB  - translocation into the nuclei was observed.
ER  -

TY  - JOUR
AU  - Schmidt, I.
AU  - Riedel, T.
AU  - Schober, I.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Bierbrodt, A.
AU  - Lehnherr, H.
AU  - Wittmann, J.
TI  - Genome Sequence of Escherichia coli E28, a Multidrug-Resistant Strain Isolated from a Chicken Carcass, and Its Spontaneously Inducible Prophage.
JO  - Genome Announcements
PY  - 2017
SP  - e00348
EP  - e00317
VL  - 5
AB  - In this study, we sequenced the complete genome of the multidrug-resistant Escherichia coli
AB  - strain E28, which was used as an indicator strain for phage
AB  - therapy in vivo We used a combination of single-molecule real-time and Illumina
AB  - sequencing technology to reveal the presence of a spontaneously inducible
AB  - prophage.
ER  -

TY  - JOUR
AU  - Schmidt, S.
AU  - Cech, D.
AU  - Fritz, H.-J.
TI  - Enzyme - substrate investigation of dcm methylase.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1991
SP  - 748
EP  - 748
VL  - 372
AB  - To investigate the enzyme-substrate complex of the dcm methylase we synthesized
AB  - 5-fluoro-2'-deoxycytidine as a substrate analogue. The synthesis was successful by selective
AB  - amination of 5-fluoro-2'-deoxyuridine. 5-fluoro-2'-deoxycytidine has not been incorporated
AB  - into oligonucleotides chemically. The direct usage of 5-fluoro-2'-deoxycytidine for
AB  - oligonucleotide synthesis is made difficult due to the increased acid and alkaline sensitivity
AB  - of this monomer. As an alternative we investigated the incorporation of
AB  - 4-methylmercapto-5-fluoro-2'-deoxyuridine and the subsequently amination of the 4' position.
AB  - In principal it is possible to incorporate the 4' methylmercapto derivative into
AB  - oligonucleotides using the phosporamidite method. However, during the oxidation step we
AB  - observed a partial conversion into 5-fluoro-2'deoxyuridine. Under the assumption that only
AB  - the 5-fluoro-2'-deoxycytidine-containing oligonucleotide will be recognized as a substrate we
AB  - used the oligonucleotide mixture for our first experiments.
ER  -

TY  - JOUR
AU  - Schmitz-Esser, S.
AU  - Gram, L.
AU  - Wagner, M.
TI  - Complete Genome Sequence of the Persistent Listeria monocytogenes Strain R479a.
JO  - Genome Announcements
PY  - 2015
SP  - e00150
EP  - e00115
VL  - 3
AB  - The complete genome sequence of the persistent Listeria monocytogenes strain R479a isolated
AB  - from smoked salmon in Denmark and belonging to lineage II, serovar
AB  - 1/2a, and multilocus sequence type 8 (ST8) is presented here.
ER  -

TY  - JOUR
AU  - Schmutte, C.
AU  - Jones, P.A.
TI  - Involvement of DNA methylation in human carcinogenesis.
JO  - Biol. Chem.
PY  - 1998
SP  - 377
EP  - 388
VL  - 379
AB  - It is now generally accepted that the presence of 5-methylcytosine in human DNA has both a
AB  - genetic and an epigenetic effect on cellular development, differentiation and transformation.
AB  - First, 5mC is more unstable than its unmethylated counterpart cytosine.  Hydrolytic
AB  - deamination of 5mC leads to a G/T mismatch and subsequently, if unrepaired, to a C-T
AB  - transition mutation.  Sites of DNA methylation are mutational hotspots in many human tumors.
AB  - Second, DNA methylation of promoter regions is often correlated with the down regulation of
AB  - the corresponding gene.  Both of these effects have fundamental consequences for basic
AB  - functions of the cell like cellular differentiation, the development of cancer and possibly
AB  - other diseases, and on the evolutionary process.  Recent hypotheses also propose a role for
AB  - methylation in the process of aging.  In this review we will describe recent findings and
AB  - hypotheses about the function of 5mC in DNA with the focus on its involvement in human
AB  - carcinogenesis.
ER  -

TY  - JOUR
AU  - Schmutz, J. et al.
TI  - Genome sequence of the palaeopolyploid soybean.
JO  - Nature
PY  - 2010
SP  - 178
EP  - 183
VL  - 463
AB  - Soybean (Glycine max) is one of the most important crop plants for seed protein and oil
AB  - content, and for its capacity to fix atmospheric nitrogen through
AB  - symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by
AB  - a whole-genome shotgun approach and integrated it with physical and high-density
AB  - genetic maps to create a chromosome-scale draft sequence assembly. We predict
AB  - 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar
AB  - genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78%
AB  - of the predicted genes occur in chromosome ends, which comprise less than
AB  - one-half of the genome but account for nearly all of the genetic recombination.
AB  - Genome duplications occurred at approximately 59 and 13 million years ago,
AB  - resulting in a highly duplicated genome with nearly 75% of the genes present in
AB  - multiple copies. The two duplication events were followed by gene diversification
AB  - and loss, and numerous chromosome rearrangements. An accurate soybean genome
AB  - sequence will facilitate the identification of the genetic basis of many soybean
AB  - traits, and accelerate the creation of improved soybean varieties.
ER  -

TY  - JOUR
AU  - Schnegg, B.
AU  - Hofschneider, P.H.
TI  - Mutant of PhiX174 accessible to host-controlled modification.
JO  - J. Virol.
PY  - 1969
SP  - 541
EP  - 542
VL  - 3
AB  - Host-controlled modification has been shown to occur with several bacteriophage
AB  - strains carrying their genetic information on a single-stranded
AB  - deoxyribonucleic acid (DNA) molecule.  All these bacteriophage strains (fd, fl,
AB  - M13, F12) are related inasmuch as their particles are rod shaped, contain
AB  - single-stranded DNA molecules of comparable size, and infect only male
AB  - bacteria.  Other single-stranded DNA phages unrelated to this group, such as
AB  - PhiX174 and S13, are unable to infect cells of Escherichia coli K-12 and B, so
AB  - that their sensitivity to K- and B- host specificity cannot be investigated
AB  - directly.  However, using spheroplasts of E. coli and infecting them with
AB  - PhiX174 DNA molecules, Benzinger showed that PhiX174 DNA is not restricted by
AB  - B- or Pl host specificity.  Lack of restriction of PhiX174 and the related
AB  - phage S13 by P1-host specificity has also been shown by Eskridge, Weinfeld, and
AB  - Paigen by using the host pair E. coli C and C (P1).  In the experiments
AB  - presented here, hybrids were selected from crosses with E. coli C and B (rB+
AB  - mB+), and C and K-12 (rK+ mK+), sensitive to infection by PhiX174 and carrying
AB  - the genes responsible for B- and K-host specificity, respectively.  With these
AB  - hybrids, E. coli BC and KC, respectively, it is shown that wild-type PhiX174 is
AB  - not susceptible to modification and restriction controlled by the genes
AB  - responsible for lambda DNA modification and restriction.  The findings
AB  - concerning B-host specificity thus confirm the results of Benzinger.  However,
AB  - a PhiX174 mutant was isolated which is accessible to restriction and
AB  - modification in the hybrid E. coli BC.
ER  -

TY  - JOUR
AU  - Schneider-Scherzer, E.
AU  - Auer, B.
AU  - de Groot, E.J.
AU  - Schweiger, M.
TI  - Primary structure of a DNA (N6-Adenine)-methyltransferase from Escherichia coli virus T1.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 6086
EP  - 6091
VL  - 265
AB  - Escherichia coli virus T1 encodes a DNA (N6-adenine)-methyltransferase (M.T1)
AB  - with the same sequence specificity as the E. coli DNA
AB  - (N6-adenine)-methyltransferase (M.Eco dam).  This enzyme was purified to
AB  - homogeneity and a partial amino acid sequence determined.  Oligonucleotides
AB  - were constructed and used not only as probes to map the gene on the T1 genome,
AB  - but also as primers in sequencing reactions to establish the nucleotide
AB  - sequence of the M.T1 locus by primer extension.  These data represent the first
AB  - analysis of the genomic organization of bacterial virus T1 on a molecular
AB  - level.  Significant homology to E. coli consensus transcription and
AB  - translation-initiation signals suggest that the gene for M.T1 is most probably
AB  - under control of its own promoter.  It may be transcribed as a polycistronic
AB  - mRNA, together with a downstream open reading frame which codes for a
AB  - polypeptide containing 83 amino acids (HP 83).  Both the deduced primary and
AB  - the secondary structure of the M.T1 were compared to those of other known DNA
AB  - methyltransferases, especially those recognizing the sequence, GATC; there is
AB  - little similarity of the T1 enzyme to the other members of this family.
ER  -

TY  - JOUR
AU  - Schneider-Scherzer, E.
AU  - Auer, B.
AU  - Schweiger, M.
TI  - Identification, purification, characterization and sequencing of DNA-methyltransferase from E. coli virus T1.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1988
SP  - 910
EP  - 910
VL  - 369
AB  - Immediately after infection E. coli virus T1 induces a DNA-methyltransferase,
AB  - which methylates the GATC-sites at adenine in vivo and in vitro.  The activity
AB  - is associated with a protein of MW 31,000 and can be visualized by activity
AB  - analysis in polyacrylamide gels.  Assay conditions were developed which permit
AB  - selective measurement of the T1 activity in the presence of E. coli
AB  - DNA-methyltransferases.
ER  -

TY  - JOUR
AU  - Schneiker, S. et al.
TI  - Complete genome sequence of the myxobacterium Sorangium cellulosum.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 1281
EP  - 1289
VL  - 25
AB  - The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from
AB  - myxobacteria, including the anti-cancer
AB  - metabolite epothilone. We report the complete genome sequence of the model
AB  - Sorangium strain S. cellulosum So ce56, which produces several natural
AB  - products and has morphological and physiological properties typical of the
AB  - genus. The circular genome, comprising 13,033,779 base pairs, is the
AB  - largest bacterial genome sequenced to date. No global synteny with the
AB  - genome of Myxococcus xanthus is apparent, revealing an unanticipated level
AB  - of divergence between these myxobacteria. A large percentage of the genome
AB  - is devoted to regulation, particularly post-translational phosphorylation,
AB  - which probably supports the strain's complex, social lifestyle. This
AB  - regulatory network includes the highest number of eukaryotic protein
AB  - kinase-like kinases discovered in any organism. Seventeen secondary
AB  - metabolite loci are encoded in the genome, as well as many enzymes with
AB  - potential utility in industry.
ER  -

TY  - JOUR
AU  - Schneiker-Bekel, S.
AU  - Wibberg, D.
AU  - Bekel, T.
AU  - Blom, J.
AU  - Linke, B.
AU  - Neuweger, H.
AU  - Stiens, M.
AU  - Vorholter, F.J.
AU  - Weidner, S.
AU  - Goesmann, A.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome.
JO  - J. Biotechnol.
PY  - 2011
SP  - 20
EP  - 33
VL  - 155
AB  - Isolates of the symbiotic nitrogen-fixing species Sinorhizobium meliloti usually contain a
AB  - chromosome and two large megaplasmids encoding functions that are absolutely required for the
AB  - specific interaction of the microsymbiont with corresponding host plants leading to an
AB  - effective symbiosis. The complete genome sequence, including the megaplasmids pSmeSM11c
AB  - (related to pSymA) and pSmeSM11d (related to pSymB), was established for the dominant,
AB  - indigenous S. meliloti strain SM11 that had been isolated during a long-term field release
AB  - experiment with genetically modified S. meliloti strains. The chromosome, the largest replicon
AB  - of S. meliloti SM11, is 3,908,022bp in size and codes for 3785 predicted protein coding
AB  - sequences. The size of megaplasmid pSmeSM11c is 1,633,319bp and it contains 1760 predicted
AB  - protein coding sequences whereas megaplasmid pSmeSM11d is 1,632,395bp in size and comprises
AB  - 1548 predicted coding sequences. The gene content of the SM11 chromosome is quite similar to
AB  - that of the reference strain S. meliloti Rm1021. Comparison of pSmeSM11c to pSymA of the
AB  - reference strain revealed that many gene regions of these replicons are variable, supporting
AB  - the assessment that pSymA is a major hot-spot for intra-specific differentiation. Plasmids
AB  - pSymA and pSmeSM11c both encode unique genes. Large gene regions of pSmeSM11c are closely
AB  - related to corresponding parts of Sinorhizobium medicae WSM419 plasmids. Moreover, pSmeSM11c
AB  - encodes further novel gene regions, e.g. additional plasmid survival genes (partition,
AB  - mobilisation and conjugative transfer genes), acdS encoding 1-aminocyclopropane-1-carboxylate
AB  - deaminase involved in modulation of the phytohormone ethylene level and genes having predicted
AB  - functions in degradative capabilities, stress response, amino acid metabolism and associated
AB  - pathways. In contrast to Rm1021 pSymA and pSmeSM11c, megaplasmid pSymB of strain Rm1021 and
AB  - pSmeSM11d are highly conserved showing extensive synteny with only few rearrangements. Most
AB  - remarkably, pSmeSM11b contains a new gene cluster predicted to be involved in polysaccharide
AB  - biosynthesis. Compilation of the S. meliloti SM11 genome sequence contributes to an extension
AB  - of the S. meliloti pan-genome.
ER  -

TY  - JOUR
AU  - Schnetz, K.
AU  - Rak, B.
TI  - Cleavage by EcoO109I and DraII is inhibited by overlapping dcm methylation.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 1623
EP  - 1623
VL  - 16
AB  - We have recently determined the nucleotide sequence of the bgl operon of E. coli. Sequence
AB  - analysis revealed the presence of two recognition sites for restriction endonuclease EcoO109I
AB  - and its isoschizomer DraII. Both enzymes recognize and cut the sequence RG'GNCCY. However,
AB  - digestion of plasmid pFDX733 containing the entire operon with either enzyme resulted in only
AB  - linearization (Fig. 1, lanes 1 and 3). We noted that the resistant site overlaps with a dcm
AB  - methylation site (CmCT/AGG). The sequence at this site is GGGGCCTGG. When we isolated plasmid
AB  - pFDX733 from a Dcm- host, the DNA was efficiently cut with both enzymes at both positions
AB  - (Fig. 1, lanes 2 and 4). We conclude that enzymes EcoO109I and DraII are sensitive to
AB  - overlapping dcm methylation at their recognition sites.
ER  -

TY  - JOUR
AU  - Schniete, J.K.
AU  - Salih, T.S.
AU  - Algora-Gallardo, L.
AU  - Santos, T.
AU  - Filgueira-Martinez, S.
AU  - Herron, P.R.
TI  - Draft Genome Sequence of Streptomyces phaeoluteigriseus DSM41896.
JO  - Genome Announcements
PY  - 2017
SP  - e00371
EP  - e00317
VL  - 5
AB  - The draft genome for the type strain Streptomyces phaeoluteigriseus DSM41896 (ISP 5182) is
AB  - reported. It was classified as a member of the Streptomyces
AB  - violaceusniger clade; however, a polyphasic study showed it was a separate
AB  - species based on its distinct spore morphology and 16S rRNA sequence. The genome
AB  - sequence confirms it as a separate species.
ER  -

TY  - JOUR
AU  - Schoen, C.
AU  - Weber-Lehmann, J.
AU  - Blom, J.
AU  - Joseph, B.
AU  - Goesmann, A.
AU  - Strittmatter, A.
AU  - Frosch, M.
TI  - Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2064
EP  - 2065
VL  - 193
AB  - Serogroup A meningococci are a leading cause of bacterial meningitis in children and young
AB  - adults worldwide. However, the genetic basis of
AB  - serogroup A strains' virulence and their epidemiological properties remain
AB  - poorly understood. Therefore, we sequenced the complete genome of the
AB  - transformable Neisseria meningitidis serogroup A strain WUE2594.
ER  -

TY  - JOUR
AU  - Schoenfeld, T.
TI  - A Practical Guide to DNA Methylation.
JO  - Promega Notes
PY  - 1993
SP  - 22
EP  - 27
VL  - 42
AB  - Most problems attributable to DNA methylation fall into one of two categories: inability to
AB  - cut DNA with restriction enzymes; inability to obtain transformants. This article contains
AB  - background information that explains why these problems ocur in cloning, followed by
AB  - troubleshooting tips that will help you determine if methylation is the problem and if so, how
AB  - to solve it. A final Section describes common eukaryotic methylation patterns and how to use
AB  - this information to your advantage. DNA methylation refers to the covalent modification of DNA
AB  - by transfer of a methyl group from S-adenosylmethionine to one of a few possible sites on
AB  - cyosine or adenine. The molecular biologist will primarily encounter m5C methylation of
AB  - cytosine and m6N methylation of adenine (Figure 1). The guidelines in this article, however,
AB  - also apply to other types of methylation such as m4C methylation of cytosine and m4C
AB  - hydroxymethylation of cytosine (1).
ER  -

TY  - JOUR
AU  - Schoenfeld, T.
TI  - Bca77I: A restriction enzyme from Bacillus caldolyticus cleaving the novel hexanucleotide (A/T)^CCGG(A/T) .
JO  - FASEB J.
PY  - 1992
SP  - A77
EP  - A77
VL  - 6
AB  - I describe a restriction enzyme, Bca77I, derived from the intermediate
AB  - thermophile, Bacillus caldolyticus (Promega strain 77).  The cognate sequence
AB  - for this restriction enzyme is the degenerate hexanucleotide, (A/T)CCGG(A/T)
AB  - and the cleavage site is 5' of the external cytosine.  The methylation
AB  - sensitivity of the endonuclease was examined.  Methylation of the external
AB  - cytosine (m5C) completely blocks restriction by Bca77I; methylation of the
AB  - internal cytosine (5mC) only decreases marginally the rate of cleavage.  It is
AB  - expected that Bca77I will be a valuable tool for the molecular biologist.
ER  -

TY  - JOUR
AU  - Schoenfeld, T.
TI  - Bca77I: A restriction enzyme from Bacillus caldolyticus cleaving the novel hexanucleotide (A/T)^CCGG(A/T) .
JO  - Biophys. J.
PY  - 1992
SP  - A77
EP  - A77
VL  - 61
AB  - I describe a restriction enzyme, Bca77I, derived from the intermediate
AB  - thermophile, Bacillus caldolyticus (Promega strain 77).  The cognate sequence
AB  - for this restriction enzyme is the degenerate hexanucleotide, (A/T)CCGG(A/T)
AB  - and the cleavage site is 5' of the external cytosine.  The methylation
AB  - sensitivity of the endonuclease was examined.  Methylation of the external
AB  - cytosine (5mC) completely blocks restriction by Bca77I; methylation of the
AB  - internal cytosine (5mC) only decreases marginally the rate of cleavage.  It is
AB  - expected that Bca77I will be a valuable tool for the molecular biologist.
ER  -

TY  - JOUR
AU  - Schoenfeld, T.
AU  - Fiandt, M.
AU  - Schink, M.
TI  - Bst71I: an isoschizomer of the type-IIS restriction enzyme, BbvI, recognizing the GCAGC(8/12) site.
JO  - Gene
PY  - 1992
SP  - 141
EP  - 142
VL  - 111
AB  - A new type-IIS restriction enzyme, Bst71I, with the specificity 5'-GCAGC(N)8
AB  - CGTCG(N)12
AB  - was isolated from Bacillus stearothermophilus (Promega No. 71).  This enzyme
AB  - is an isoschizomer of BbvI with somewhat improved characteristics for use by
AB  - molecular biologists.
ER  -

TY  - JOUR
AU  - Schoenfeld, T.
AU  - King, K.B.
AU  - Schink, M.
TI  - Bca771: a new type-II restriction endonuclease from Bacillus caldolyticus cutting at the (A/T)^CCGG(A/T) site.
JO  - Gene
PY  - 1992
SP  - 99
EP  - 101
VL  - 117
AB  - We describe a new restriction enzyme recognizing a degenerate hexanucleotide sequence and
AB  - cleaving the 5'-W^CCGGW site (W = A or T). This enzyme cuts with high efficiency all four
AB  - permutations of this sequence; ACCGGA (TCCGGT on the opposite stand), ACCGGT and TCCGGA.
AB  - Methylation of the external cytosine completely blocks restriction while methylation of the
AB  - internal cytosine only decreases the rate of restriction activity.
ER  -

TY  - JOUR
AU  - Schoenfeld, T.
AU  - Mead, D.A.
AU  - Fiandt, M.
TI  - Purification and characterization of an isoschizomer of AsuII from Clostridium sporogenes.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 4417
EP  - 4417
VL  - 17
AB  - A new type II restriction enzyme, Csp45I, was isolated from Clostridium
AB  - sporogenes and characterized.  Digestion of a standard substrate and sequencing
AB  - confirmed that both the recognition sequence and the cut site, TT/CGAA, were
AB  - the same as those of AsuII and BstBI.
ER  -

TY  - JOUR
AU  - Schoenfeld, T.W.
AU  - Murugapiran, S.
AU  - Dodsworth, J.A.
AU  - Floyd, S.
AU  - Lodes, M.
AU  - Mead, D.A.
AU  - Hedlund, B.P.
TI  - Lateral gene transfer of Family A DNA polymerases between thermophilic viruses, Aquificae, and Apicomplexa.
JO  - Mol. Biol. Evol.
PY  - 2013
SP  - 1653
EP  - 1664
VL  - 30
AB  - Bioinformatics and functional screens identified a group of Family A-type DNA
AB  - Polymerase (polA) genes encoded by viruses inhabiting circumneutral and alkaline
AB  - hot springs in Yellowstone National Park and the US Great Basin. The proteins
AB  - encoded by these viral polA genes (PolAs) shared no significant sequence
AB  - similarity with any known viral proteins but were remarkably similar to PolAs
AB  - encoded by two of three families of the bacterial phylum Aquificae and by several
AB  - apicoplast-targeted PolA-like proteins found in the eukaryotic phylum
AB  - Apicomplexa, which includes the obligate parasites Plasmodium, Babesia, and
AB  - Toxoplasma. The viral gene products share signature elements previously
AB  - associated only with Aquificae and Apicomplexa PolA-like proteins and were
AB  - similar to proteins encoded by prophage elements of a variety of otherwise
AB  - unrelated Bacteria, each of which additionally encoded a prototypical bacterial
AB  - PolA. Unique among known viral DNA polymerases, the viral PolA proteins of this
AB  - study share with the Apicomplexa proteins large amino-terminal domains with
AB  - putative helicase/primase elements but low primary sequence similarity. The
AB  - genomic context and distribution, phylogeny, and biochemistry of these PolA
AB  - proteins suggest that thermophilic viruses transferred polA genes to the
AB  - Apicomplexa, likely through secondary endosymbiosis of a virus-infected
AB  - proto-apicoplast, and to the common ancestor of two of three Aquificae families,
AB  - where they displaced the orthologous cellular polA gene. On the basis of
AB  - biochemical activity, gene structure, and sequence similarity, we speculate that
AB  - the xenologous viral-type polA genes may have functions associated with
AB  - diversity-generating recombination in both Bacteria and Apicomplexa.
ER  -

TY  - JOUR
AU  - Schoettler, S.
AU  - Christ, F.
AU  - Pingoud, V.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - Identification of the catalytic centres of the homing endonuclease PI-SceI by site-directed mutagenesis.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A332
EP  - A332
VL  - 28
AB  - The homing endonuclease PI-SceI from Saccharomyces cerevisiae is composed of two domains:
AB  - Domain I is responsible for protein splicing and specific DNA binding and domain II harbours
AB  - the endonuclease function which mediates the mobility of the gene of PI-SceI by introducing a
AB  - double strand break into an allele that lacks it.  Cellular repair leads to the integration of
AB  - the sequence into this allele.  It was unknown whether the DNA cleavage is due to one
AB  - catalytic centre cleaving both DNA strands or two active sites each cleaving one strand.  To
AB  - solve this problem we exchanged amino acids in the vicinity of D218 and D326 of the
AB  - characteristic LAGLIDADG motifs which were already shown to be essential.  The amino acids
AB  - chosen for mutagenesis were selected based on a structural comparison with the homodimeric
AB  - enzyme I-CreI.  Results of experiments with substrates with a nick in the cleavage position
AB  - are taken as evidence for the existence of two catalytic sites: The variant D229N cleaves a
AB  - substrate with a nick in the top strand whereas a substrate with a nick in the bottom strand
AB  - is hardly cleaved.  T341N displays an opposite behavior, i.e. prefers to cleave a DNA
AB  - substrate nicked in the bottom strand.  Taking together all our results, including
AB  - characterization of PI-SceI with respect to DNA binding and cleavage, leads to this model of
AB  - DNA strand cleavage: PI-SceI contains two catalytic centres.  In catalytic centre I D218 and
AB  - D229 coordinate the metal ion and induce the cleavage of the top strand.  This is the rate
AB  - limiting step of cleavage.  The cleavage of the bottom strand is done by active site II
AB  - containing D326 as metal ion binding site.  Intriguingly, the mutants D229N and T341N which
AB  - are almost inactive in cleaving double stranded DNA can do so when crosslinked to the
AB  - substrate.  This could be interpreted to mean that crosslinking fixes the enzyme-substrate
AB  - complex in a conformation resembling the transition state, similarly as observed with EcoRV.
ER  -

TY  - JOUR
AU  - Schoettler, S.
AU  - Wende, W.
AU  - Pingoud, V.
AU  - Pingoud, A.
TI  - Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.
JO  - Biochemistry
PY  - 2000
SP  - 15895
EP  - 15900
VL  - 39
AB  - The monomeric homing endonuclease PI-SceI harbors two catalytic centers which cooperate in the
AB  - cleavage of the two strands of its extended
AB  - recognition sequence. Structural and biochemical data suggest that
AB  - catalytic center I contains Asp218, Asp229, and Lys403, while catalytic
AB  - center II contains Asp326, Thr341, and Lys301. The analogy with I-CreI,
AB  - for which the cocrystal structure with the DNA substrate has been
AB  - determined, suggests that Asp218 and Asp229 in catalytic center I and
AB  - Asp326 and Thr341 in catalytic center II serve as ligands for Mg2+, the
AB  - essential divalent metal ion cofactor which can be replaced by Mn2+ in
AB  - vitro. We have carried out a mutational analysis of these presumptive
AB  - Mg2+ ligands. The variants carrying an alanine or asparagine
AB  - substitution bind DNA, but (with the exception of the D229N variant)
AB  - are inactive in DNA cleavage in the presence of Mg2+, demonstrating
AB  - that these residues are important for cleavage. Our finding that the
AB  - PI-SceI variants carrying single cysteine substitutions at these
AB  - positions are inactive in the presence of the oxophilic Mg2+ but active
AB  - in the presence of the thiophilic Mn2+ suggests that the amino acid
AB  - residues at these positions are involved in cofactor binding. From the
AB  - fact that in the presence of Mn2+ the D218C and D326C variants are even
AB  - more active than the wild-type enzyme, it is concluded that Asp218 and
AB  - Asp326 are the principal Mg2+ ligands of PI-SceI. On the basis of these
AB  - findings and the available structural information, a model for the
AB  - composition of the two Mg2+ binding sites of PI-SceI is proposed.
ER  -

TY  - JOUR
AU  - Schofield, B.J.
AU  - Skarshewski, A.
AU  - Lachner, N.
AU  - Ouwerkerk, D.
AU  - Klieve, A.V.
AU  - Dart, P.
AU  - Hugenholtz, P.
TI  - Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 60
EP  - 60
VL  - 11
AB  - Bacillus amyloliquefaciens H57 is a bacterium isolated from lucerne for its ability to prevent
AB  - feed spoilage. Further interest developed when ruminants fed
AB  - with H57-inoculated hay showed increased weight gain and nitrogen retention
AB  - relative to controls, suggesting a probiotic effect. The near complete genome of
AB  - H57 is ~3.96 Mb comprising 16 contigs. Within the genome there are 3,836 protein
AB  - coding genes, an estimated sixteen rRNA genes and 69 tRNA genes. H57 has the
AB  - potential to synthesise four different lipopeptides and four polyketide
AB  - compounds, which are known antimicrobials. This antimicrobial capacity may
AB  - facilitate the observed probiotic effect.
ER  -

TY  - JOUR
AU  - Scholl, D.
AU  - Merril, C.
TI  - The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli.
JO  - J. Bacteriol.
PY  - 2005
SP  - 8499
EP  - 8503
VL  - 187
AB  - Bacteriophage K1F specifically infects Escherichia coli strains that
AB  - produce the K1 polysaccharide capsule. Like several other K1
AB  - capsule-specific phages, K1F encodes an endo-neuraminidase (endosialidase)
AB  - that is part of the tail structure which allows the phage to recognize and
AB  - degrade the polysaccharide capsule. The complete nucleotide sequence of
AB  - the K1F genome reveals that it is closely related to bacteriophage T7 in
AB  - both genome organization and sequence similarity. The most striking
AB  - difference between the two phages is that K1F encodes the endosialidase in
AB  - the analogous position to the T7 tail fiber gene. This is in contrast with
AB  - bacteriophage K1-5, another K1-specific phage, which encodes a very
AB  - similar endosialidase which is part of a tail gene \"module\" at the end of
AB  - the phage genome. It appears that diverse phages have acquired
AB  - endosialidase genes by horizontal gene transfer and that these genes or
AB  - gene products have adapted to different genome and virion architectures.
ER  -

TY  - JOUR
AU  - Scholl, D.R.
AU  - Patterson, R.B. Jr.
AU  - Jollick, J.D.
TI  - Modification of EcoRI restriction sites by Cauloacter vibrioides.
JO  - Gene
PY  - 1982
SP  - 163
EP  - 166
VL  - 17
AB  - A comparison of EcoRI digestion profiles of plasmid RP1 isolated from
AB  - Caulobacter vibrioides WS48 and Escherichia coli CSH29 demonstrated that EcoRI
AB  - sites were modified by WS48.
ER  -

TY  - JOUR
AU  - Scholtissek, S.
AU  - Pingoud, A.
AU  - Maass, G.
AU  - Zabeau, M.
TI  - Polypeptide sequences involved in the cleavage of DNA by the restriction endonuclease EcoRI.
JO  - J. Biol. Chem.
PY  - 1986
SP  - 2228
EP  - 2234
VL  - 261
AB  - We have prepared a variety of fragments of the restriction endonuclease EcoRI
AB  - by partial or total CNBr or acid cleavage of the protein.  These fragments were
AB  - isolated by preparatvie polyacrylamide gel electrophoresis in the presence of
AB  - sodium dodecyl sulfate.  They were analyzed in a qualitative manner for
AB  - phosphodiesterase activity.  Antibodies against these fragments were elicited
AB  - in rats and tested for binding to native EcoRI in an enzyme-linked immunoassay.
AB  - We conclude from these experiments that the DNA binding site of EcoRI is
AB  - located in the COOH-terminal half of the molecule, close to and probably
AB  - comprising amino acid residues 137 to 157.  This conclusion is reinforced by
AB  - the observation that this sequence shows homology to the sequences of the
AB  - recognition helix of other gene-regulatory proteins.
ER  -

TY  - JOUR
AU  - Schoner, B.
AU  - Kelly, S.
AU  - Smith, H.O.
TI  - The nucleotide sequence of the HhaII restriction and modification genes from Haemophilus haemolyticus.
JO  - Gene
PY  - 1983
SP  - 227
EP  - 236
VL  - 24
AB  - We have determined the nucleotide squence of a cloned 1710-bp segment of Haemophilus
AB  - haemolyticus DNA which contains the HhaII restriction (r) and modification (m) genes. The m
AB  - gene is 513 bp in length and the r gene is 681 bp in length. Both are in the same reading
AB  - frame, being separated by a 21-bp region. A ribosome-binding site is identified in front of
AB  - each gene, but no Haemophilus promoter is apparent on the cloned fragment. Transcription
AB  - originates from a plasmid promoter and proceeds in the direction m to r.
ER  -

TY  - JOUR
AU  - Schopf, S.
AU  - Ullrich, S.R.
AU  - Heine, T.
AU  - Schlomann, M.
TI  - Draft Genome of the Heterotrophic Iron-Oxidizing Bacterium 'Acidibacillus ferroxidans' Huett2, Isolated from a Mine Drainage Ditch in Freiberg, Germany.
JO  - Genome Announcements
PY  - 2017
SP  - e00323
EP  - e00317
VL  - 5
AB  - Here, we communicate the draft genome of 'Acidibacillus ferrooxidans' Huett2, a novel strain
AB  - of an acidophilic, heterotrophic, iron-oxidizing bacterium belonging
AB  - to the phylum Firmicutes It was isolated from a water drainage system of a former
AB  - minefield in Freiberg, Germany.
ER  -

TY  - JOUR
AU  - Schork, S.
AU  - Schluter, A.
AU  - Blom, J.
AU  - Schneiker-Bekel, S.
AU  - Puhler, A.
AU  - Goesmann, A.
AU  - Frosch, M.
AU  - Schoen, C.
TI  - Genome Sequence of a Neisseria meningitidis Capsule Null Locus Strain from the Clonal Complex of Sequence Type 198.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5144
EP  - 5145
VL  - 194
AB  - Neisseria meningitidis is a commensal and accidental pathogen exclusively of humans. Although
AB  - the production of polysaccharide capsules is considered to be
AB  - essential for meningococcal virulence, there have been reports of constitutively
AB  - unencapsulated strains causing invasive meningococcal disease (IMD). Here we
AB  - report the genome sequence of a capsule null locus (cnl) strain of sequence type
AB  - 198 (ST-198), which is found in half of the reported cases of IMD caused by cnl
AB  - meningococcal strains.
ER  -

TY  - JOUR
AU  - Schott, T.
AU  - Rossi, M.
AU  - Hanninen, M.L.
TI  - Genome sequence of Helicobacter bizzozeronii strain CIII-1, an isolate from human gastric mucosa.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4565
EP  - 4566
VL  - 193
AB  - The canine-adapted Helicobacter bizzozeronii is the only non-pylori Helicobacter species
AB  - isolated from human gastric biopsies. Here we present
AB  - the genome sequence of the strain CIII-1 isolated from a 45 year-old
AB  - female patient with severe gastric symptoms. This is the first genome
AB  - sequence of non-pylori gastric Helicobacter isolated from human gastritis.
ER  -

TY  - JOUR
AU  - Schottler, S.
AU  - Wenz, C.
AU  - Lanio, T.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Protein engineering of the restriction endonuclease EcoRV: structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site.
JO  - Eur. J. Biochem.
PY  - 1998
SP  - 184
EP  - 191
VL  - 258
AB  - We generated variants of the restriction endonuclease EcoRV that discriminate between
AB  - recognition sites with different flanking sequences.  This was achieved by designing new
AB  - contacts to the bases in the major groove of the DNA preceding and following the EcoRV
AB  - recognition site.  We selected Ala181 as the starting point for the extension of the site
AB  - specificity of EcoRV because, according to the structure of the specific EcoRV DNA complex,
AB  - this residue is involved in a water mediated contact with the bases flanking the recognition
AB  - sequence on the 5' side.  A substitution of this alanine residue by other amino acid residues
AB  - changes the protein-DNA interface in this region and potentially creates new contacts, such
AB  - that EcoRV variants could have an extended specificity, i.e. a greater selectivity for EcoRV
AB  - sites within a particular sequence context.  EcoRV variants with naturally occurring amino
AB  - acid residues at position 181 were produced and their selectivity analyzed with
AB  - oligodeoxynucleotide and plasmid substrates that differ only in the base pairs immediately
AB  - flanking the EcoRV site.  Some variants, having amino acid residues with long or bulky side
AB  - chains at position 181 showed altered preferences for the base pairs flanking the recognition
AB  - sequence with oligodeoxynucleotide substrates without losing their catalytic efficiency.  One
AB  - variant, A181K, is able to discriminate between purine and pyrimidine bases on the 5' side of
AB  - the recognition sequence, probably by means of a new hydrogen bond to the N7 of the purine
AB  - base.  Another variant, A181E, strongly prefers a thymine base on the 5' side of the
AB  - recognition sequence, presumably due to a hydrogen bond formed between the protonated glutamic
AB  - acid residue and the 04 of thymine.
ER  -

TY  - JOUR
AU  - Schouler, C.
AU  - Clier, F.
AU  - Luisa, A.
AU  - Lerayer, L.
AU  - Ehrlich, S.D.
AU  - Chopin, M.-C.
TI  - A type IC restriction-modification system in Lactococcus lactis.
JO  - J. Bacteriol.
PY  - 1998
SP  - 407
EP  - 411
VL  - 180
AB  - Three genes coding for the endonuclease, methylase, and specificity subunits of a type I
AB  - restriction-modification (RM) system in the Lactococcus lactis plasmid pIL2614 have been
AB  - characterized.  Plasmid location, sequence homologies, and inactivation studies indicated that
AB  - this R-M system is most probably of type IC.
ER  -

TY  - JOUR
AU  - Schouler, C.
AU  - Gautier, M.
AU  - Ehrlich, S.D.
AU  - Chopin, M.-C.
TI  - Combinational variation of restriction modification specificities in Lactococcus lactis.
JO  - Mol. Microbiol.
PY  - 1998
SP  - 169
EP  - 178
VL  - 28
AB  - Three genes coding for a type I R-M system related to the class C enzymes have been identified
AB  - on the chromosome of Lactococcus lactis strain IL1403.  In addition, plasmids were found that
AB  - encode only the HsdS subunit that directs R-M specificity.  The presence of these plasmids in
AB  - IL1403 conferred a new R-M phenotype on the host, indicating that the plasmid-encoded HsdS is
AB  - able to interact with the chromosomally encoded HsdR and hsdM subunits.  Such combinational
AB  - variation of type I R-M systems may facilitate the evolution of their specificity and thus
AB  - reinforce bacterial resistance against invasive foreign unmethylated DNA.
ER  -

TY  - JOUR
AU  - Schreier, H.J.
AU  - Schott, E.J.
TI  - Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain  OY15.
JO  - Genome Announcements
PY  - 2014
SP  - e01006
EP  - e01014
VL  - 2
AB  - We report the draft genome sequence of Vibrio sp. strain OY15, a Gram-negative marine
AB  - bacterium isolated from an oyster (Crassostrea virginica) digestive tract
AB  - and shown to possess probiotic activity. The availability of this genome sequence
AB  - will facilitate the study of the mechanisms of probiotic activity as well as
AB  - virulence capacity.
ER  -

TY  - JOUR
AU  - Schreier, H.J.
AU  - Schott, E.J.
TI  - Draft Genome Sequence of the Shellfish Bacterial Pathogen Vibrio sp. Strain B183.
JO  - Genome Announcements
PY  - 2014
SP  - e00914
EP  - e00914
VL  - 2
AB  - We report the draft genome sequence of Vibrio sp. strain B183, a Gram-negative marine
AB  - bacterium isolated from shellfish that causes mortality in larval
AB  - mariculture. The availability of this genome sequence will facilitate the study
AB  - of its virulence mechanisms and add to our knowledge of Vibrio sp. diversity and
AB  - evolution.
ER  -

TY  - JOUR
AU  - Schroder, J.
AU  - Braun, B.
AU  - Liere, K.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of Rheinheimera sp. Strain SA_1 Isolated from Iron Backwash Sludge in Germany.
JO  - Genome Announcements
PY  - 2016
SP  - e00853
EP  - e00816
VL  - 4
AB  - Rheinheimera sp. strain SA_1 is an iron-depositing bacterium for which we report  a draft
AB  - genome sequence. Strain SA_1 was isolated from iron backwash sludge of a
AB  - waterworks in Germany. The Illumina MiSeq technique was used to sequence the
AB  - genome of the strain.
ER  -

TY  - JOUR
AU  - Schroder, J.
AU  - Glaub, A.
AU  - Schneider, J.
AU  - Trost, E.
AU  - Tauch, A.
TI  - Draft Genome Sequence of Corynebacterium bovis DSM 20582, Which Causes Clinical Mastitis in Dairy Cows.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4437
EP  - 4437
VL  - 194
AB  - Bovine mastitis represents the most economically important disease in dairy cows  and can be
AB  - caused by Corynebacterium bovis, a commensal in the bovine udder. The
AB  - draft genome sequence provides insights into the adaptation of this bacterium to
AB  - the bovine habitat and its lipolytic capabilities to utilize components of cow's
AB  - milk.
ER  -

TY  - JOUR
AU  - Schroder, J.
AU  - Maus, I.
AU  - Meyer, K.
AU  - Wordemann, S.
AU  - Blom, J.
AU  - Jaenicke, S.
AU  - Schneider, J.
AU  - Trost, E.
AU  - Tauch, A.
TI  - Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.
JO  - BMC Genomics
PY  - 2012
SP  - 141
EP  - 141
VL  - 13
AB  - BACKGROUND: Corynebacterium resistens was initially recovered from human
AB  - infections and recognized as a new coryneform species that is highly resistant to
AB  - antimicrobial agents. Bacteremia associated with this organism in
AB  - immunocompromised patients was rapidly fatal as standard minocycline therapies
AB  - failed. C. resistens DSM 45100 was isolated from a blood culture of samples taken
AB  - from a patient with acute myelocytic leukemia. The complete genome sequence of C.
AB  - resistens DSM 45100 was determined by pyrosequencing to identify genes
AB  - contributing to multi-drug resistance, virulence, and the lipophilic lifestyle of
AB  - this newly described human pathogen. RESULTS: The genome of C. resistens DSM
AB  - 45100 consists of a circular chromosome of 2,601,311 bp in size and the 28,312-bp
AB  - plasmid pJA144188. Metabolic analysis showed that the genome of C. resistens DSM
AB  - 45100 lacks genes for typical sugar uptake systems, anaplerotic functions, and a
AB  - fatty acid synthase, explaining the strict lipophilic lifestyle of this species.
AB  - The genome encodes a broad spectrum of enzymes ensuring the availability of
AB  - exogenous fatty acids for growth, including predicted virulence factors that
AB  - probably contribute to fatty acid metabolism by damaging host tissue. C.
AB  - resistens DSM 45100 is able to use external L-histidine as a combined carbon and
AB  - nitrogen source, presumably as a result of adaptation to the hitherto unknown
AB  - habitat on the human skin. Plasmid pJA144188 harbors several genes contributing
AB  - to antibiotic resistance of C. resistens DSM 45100, including a tetracycline
AB  - resistance region of the Tet W type known from Lactobacillus reuteri and
AB  - Streptococcus suis. The tet(W) gene of pJA144188 was cloned in Corynebacterium
AB  - glutamicum and was shown to confer high levels of resistance to tetracycline,
AB  - doxycycline, and minocycline in vitro. CONCLUSIONS: The detected gene repertoire
AB  - of C. resistens DSM 45100 provides insights into the lipophilic lifestyle and
AB  - virulence functions of this newly recognized pathogen. Plasmid pJA144188 revealed
AB  - a modular architecture of gene regions that contribute to the multi-drug
AB  - resistance of C. resistens DSM 45100. The tet(W) gene encoding a ribosomal
AB  - protection protein is reported here for the first time in corynebacteria. Cloning
AB  - of the tet(W) gene mediated resistance to second generation tetracyclines in C.
AB  - glutamicum, indicating that it might be responsible for the failure of
AB  - minocycline therapies in patients with C. resistens bacteremia.
ER  -

TY  - JOUR
AU  - Schroeder, C.
AU  - Jurkschat, H.
AU  - Meisel, A.
AU  - Reich, J.G.
AU  - Kruger, D.
TI  - Unusual occurrence of EcoP1 and EcoP15 recognition sites and counterselection of type II methylation and restriction sequences in bacteriophage T7 DNA.
JO  - Gene
PY  - 1986
SP  - 77
EP  - 86
VL  - 45
AB  - Selected and counterselected oligodeoxynucleotide sequences were identified in the total
AB  - sequence of bacteriophage T7 DNA using a statistical criterion derived for a probability model
AB  - of the Markov chain type. All extremely rare tetra- and pentadeoxynucleotides are (or contain)
AB  - recognition sequences for the Escherichia coli DNA methylases dam or dcm. Most of the 37
AB  - hexadeoxynucleotides absent from T7 DNA are recognition sequences for type II
AB  - modification/restriction enzymes of E. coli or related species.  In contrast
AB  - to most restriction sites counterselected during evolution, the EcoP1 site GGTCT
AB  - occurs 126 times in the T7 genome, and phage T7 replication is severly repressed in
AB  - P1-lysogenic host cells. We demonstrate that the frequency of the EcoP1 site is determined by
AB  - that of the overlapping recognition sites for T7 primase, an essential phage enzyme. The
AB  - recognition site of a type III enzyme, EcoP15, is also not counterselected. In T7 DNA all 36
AB  - EcoP15 sites are arranged in such a manner that the sequence CAGCAG is confined to the H
AB  - strand, the complementary sequence CTGCTG to the L strand. This "strand bias" is highly
AB  - significant and, therefore, very probably selected. A functional relational between this
AB  - strand bias and the refractive behaviour of phage T7 to EcoP15 restriction is suspected.
ER  -

TY  - JOUR
AU  - Schroeder, C.
AU  - Reuter, M.
AU  - Kruger, D.H.
TI  - DNA methylation of T3 virus ocr+ and ocr- strains in Escherichia coli cells harbouring the EcoK DNA host specificity system.
JO  - Biomed. Biochim. Acta
PY  - 1984
SP  - K1
EP  - K5
VL  - 43
AB  - The influence of the T3 gene functions ocr+ and sam+ on the extent of phage DNA
AB  - methylation in Escherichia coli K12 cells was studied by determining the
AB  - proportion of 6-methylaminopurine to adenine in the purified DNA of T3
AB  - wild-type, sam- and ocr-sam phage strains.  We demonstrate that the DNA of T3
AB  - ocr-sam- mutants carries 12 methyl groups as a result of the action of the
AB  - host-specificity methylase EcoK.  In contrast to this the DNA of ocr+ strains
AB  - is not EcoK-specifically methylated.
ER  -

TY  - JOUR
AU  - Schroeder, D.C.
AU  - Park, Y.
AU  - Yoon, H.M.
AU  - Lee, Y.S.
AU  - Kang, S.W.
AU  - Meints, R.H.
AU  - Ivey, R.G.
AU  - Choi, T.J.
TI  - Genomic analysis of the smallest giant virus--Feldmannia sp. virus 158.
JO  - Virology
PY  - 2009
SP  - 223
EP  - 232
VL  - 384
AB  - Genomic analysis of Feldmannia sp. virus 158, the second phaeovirus to be sequenced in hits
AB  - entirety, provides further evidence that large double-stranded DNA viruses share similar
AB  - evolutionary pressures as cellular organisms.  Reductive evolution is clearly evident within
AB  - the phaeoviruses which occurred via several routes: the loss of genes from an ancestral virus
AB  - core genome most likely through genetic drift; and as a result of relatively large
AB  - recombination events that caused wholesale loss of genes.  The entire genome is 154,641 bp in
AB  - lenth and has 150 predicted coding sequences of which 87% have amino acid sequence
AB  - similarities to other algal virus coding sequences within the family Phycodnavirdae.
AB  - Significant similarities were found, for thirty eight coding sequences (25%), to genes in gene
AB  - databanks that are known to be involved in processes that include DNA replication, DNA
AB  - methylation, signal transduction, viral integration and transposition, and protein-protein
AB  - interactions.  Unsurprisingly, the greatest similarity was observed between the two known
AB  - viruses that infect Feldmannia, indicating the taxonomic linkage of these two viruses with
AB  - their hosts.  Moreover, comparative analysis of phycodnaviral genomic sequences revealed the
AB  - smallest set of core genes (10 out of a possible 31) required to make a functional
AB  - nucleocytoplasmic large dsDNA virus.
ER  -

TY  - JOUR
AU  - Schroeder, J.W.
AU  - Simmons, L.A.
TI  - Complete Genome Sequence of Bacillus subtilis Strain PY79.
JO  - Genome Announcements
PY  - 2013
SP  - e01085
EP  - e01013
VL  - 1
AB  - Bacillus subtilis is a Gram-positive soil-dwelling and endospore-forming bacterium in the
AB  - phylum Firmicutes. B. subtilis strain PY79 is a prototrophic
AB  - laboratory strain that has been highly used for studying a wide variety of
AB  - cellular pathways. Here, we announce the complete whole-genome sequence of B.
AB  - subtilis PY79.
ER  -

TY  - JOUR
AU  - Schroeder, S.G.
TI  - Structure-function studies of lima bean trypsin inhibitor and EcoRII methyltransferase.
JO  - Diss. Abstr.
PY  - 2000
SP  - 3052
EP  - 305B
VL  - 61
AB  - Lima bean trypsin inhibitor studies.  The crystal structure of a stable trypsin inhibitor from
AB  - lima bean was determined to 2.5 Angstrom resolution.  The space group is cubic, I213 with
AB  - a=110.67 A.  Native Lima Bean Trypsin Inhibitor (LBTI) crystals diffract x-rays to 1.65
AB  - Angstrom resolution and yield data that are 93.99% complete.  LBTI has a unique property in
AB  - that it is thermally stable to the extent that it can be boiled for ten minutes without
AB  - destroying its activity.  This protein also shows a high degree of homology with protease
AB  - inhibitors of the Bowman-Birk class: it contains 79 amino acid residues, including 14
AB  - cysteines.  Thus, the structure was determined by first building a homology model of LBTI
AB  - using adzuki bean trypsin inhibitor and of the molecular replacement method using the
AB  - homology-modeled LBTI as a search model.  In this study, the three-dimensional structure of
AB  - LBTI is presented and discussed.  Methyltransferase studies.  DNA methylation is believed to
AB  - be an important mechanism for DNA recognition, transcription regulation and DNA replication in
AB  - bacteria, plants and animals.  EcoRII methyltransferase (M.EcoRII) is a cytosine-C5 DNA
AB  - methylating enzyme.  A model of its three-dimensional structure is proposed on the basis of
AB  - homology modeling.  Crystal structures of two members of the same family of enzymes, HaeIII
AB  - and HhaI methyltransferases (M.HaeIII and M.HhaI respectively), were used as template
AB  - molecules.  Molecular dynamics calculations were used to ensure sampling of conformationally
AB  - stable structures.  The final model has good geometry.  The DNA and cofactor binding residues
AB  - are in expected positions to form proper interactions.  M.EcoRIII is 147 amino acids longer
AB  - than the template molecules, and hence the model contains several loops that are significantly
AB  - longer than those in M.HaeIII and M.HhaI.  The model provides a framework for interpretation
AB  - and designing site-directed mutants that have a potential to improve crystallization
AB  - experiments of this enzyme, and other similar enzymes.
ER  -

TY  - JOUR
AU  - Schroeder, S.G.
AU  - Samudzi, C.T.
TI  - Structural studies of EcoRII methylase: exploring similarities among methylases.
JO  - Protein Eng.
PY  - 1997
SP  - 1385
EP  - 1393
VL  - 10
AB  - EcoRII methyltransferase is a cytosine-C5 DNA methylating enzyme.  A model of its
AB  - three-dimensional structure is proposed on the basis of homology modeling.  Crystal structures
AB  - of two members of the same family of enzymes, HaeIII and HhaI methyltransferases (M.HaeIII and
AB  - M.HhaI respectively), were used as template molecules.  Molecular dynamics was used to ensure
AB  - sampling of conformationally stable structures.  The final model has good geometry.  The DNA
AB  - and cofactor binding residues are in expected positions and form proper interactions.
AB  - M.EcoRII is 147 amino acids longer than the template molecules, and hence the model contains
AB  - several loops that are significantly longer than those in M.HaeIII and M.HhaI.  The model
AB  - provides a framework for interpretation and designing site-directed mutants that have a
AB  - potential to improve crystallization experiments of this enzyme, and possibly other similar
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Schubert, H.L.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases.
JO  - Enzymes
PY  - 2006
SP  - 3
EP  - 28
VL  - 24
AB  - S-adenosyl-L-methionine (AdoMet) dependent methyltransferases (MTases) are involved in
AB  - biosynthesis, signal transduction, protein repair,
AB  - chromatin regulation, and gene silencing. Five different structural
AB  - folds (designated I through V) have been described that bind AdoMet and
AB  - catalyze methyltransfer to diverse substrates, although the great
AB  - majority of known MTases have the Class I fold. Even within a
AB  - particular MTase class the amino-acid sequence similarity can be as low
AB  - as 10%. Thus, the structural and catalytic requirements for
AB  - methyltransfer from AdoMet appear to be remarkably flexible. MTases
AB  - that act on protein substrates have been found to date among three of
AB  - the five structural classes (I, the classical fold; III, the corrin
AB  - MTase fold; and V, the SET fold).'There are many paths to the top of
AB  - the mountain, but the view is always the same.'-Chinese proverb The
AB  - Columbia World of Quotations, New York, Columbia University Press, 1996
ER  -

TY  - JOUR
AU  - Schubert, H.L.
AU  - Blumenthal, R.M.
AU  - Cheng, X.
TI  - Many paths to methyltransfer: a chronicle of convergence.
JO  - Trends Biochem. Sci.
PY  - 2003
SP  - 329
EP  - 335
VL  - 28
AB  - S-adenosyl-L-methionine (AdoMet) dependent methyltransferases (MTases) are involved in
AB  - biosynthesis, signal transduction, protein repair, chromatin
AB  - regulation and gene silencing. Five different structural folds (I-V) have
AB  - been described that bind AdoMet and catalyze methyltransfer to diverse
AB  - substrates, although the great majority of known MTases have the Class I
AB  - fold. Even within a particular MTase class the amino-acid sequence
AB  - similarity can be as low as 10%. Thus, the structural and catalytic
AB  - requirements for methyltransfer from AdoMet appear to be remarkably
AB  - flexible.
ER  -

TY  - JOUR
AU  - Schubert, H.L.
AU  - Phillips, J.D.
AU  - Hill, C.P.
TI  - Structures along the catalytic pathway of PrmC/HemK, an N(5)-glutamine AdoMet-dependent methyltransferase.
JO  - Biochemistry
PY  - 2003
SP  - 5592
EP  - 5599
VL  - 42
AB  - Posttranslational methylation of release factors on the glutamine residue of a conserved GGQ
AB  - motif is required for efficient termination of protein
AB  - synthesis. This methylation is performed by an N(5)-glutamine
AB  - methyltransferase called PrmC/HemK, whose crystal structure we report here
AB  - at 2.2 A resolution. The electron density at the active site appears to
AB  - contain a mixture of the substrates, S-adenosyl-L-methionine (AdoMet) and
AB  - glutamine, and the products, S-adenosyl-L-homocysteine (AdoHcy) and
AB  - N(5)-methylglutamine. The C-terminal domain of PrmC adopts the canonical
AB  - AdoMet-dependent methyltransferase fold and shares structural similarity
AB  - with the nucleotide N-methyltransferases in the active site, including use
AB  - of a conserved (D/N)PPY motif to select and position the glutamine
AB  - substrate. Residues of the PrmC (197)NPPY(200) motif form hydrogen bonds
AB  - that position the planar Gln side chain such that the lone-pair electrons
AB  - on the nitrogen nucleophile are oriented toward the methyl group of
AB  - AdoMet. In the product complex, the methyl group remains pointing toward
AB  - the sulfur, consistent with either an sp(3)-hybridized, positively charged
AB  - Gln nitrogen, or a neutral sp(2)-hybridized nitrogen in a strained
AB  - conformation. Due to steric overlap within the active site, proton loss
AB  - and formation of the neutral planar methylamide product are likely to
AB  - occur during or after product release. These structures, therefore,
AB  - represent intermediates along the catalytic pathway of PrmC and show how
AB  - the (D/N)PPY motif can be used to select a wide variety substrates.
ER  -

TY  - JOUR
AU  - Schuch, R.
AU  - Pelzek, A.J.
AU  - Fazzini, M.M.
AU  - Nelson, D.C.
AU  - Fischetti, V.A.
TI  - Complete Genome Sequence of Bacillus cereus Sensu Lato Bacteriophage Bcp1.
JO  - Genome Announcements
PY  - 2014
SP  - e00334
EP  - e00314
VL  - 2
AB  - Bacillus cereus sensu lato organisms are an ecologically diverse group that includes etiologic
AB  - agents of food poisoning, periodontal disease, and anthrax.
AB  - The recently identified Bcp1 bacteriophage infects B. cereus sensu lato and is
AB  - being developed as a therapeutic decontamination agent and diagnostic
AB  - countermeasure. We announce the complete genome sequence of Bcp1.
ER  -

TY  - JOUR
AU  - Schugerl, K.
TI  - Comparison of different reactor designs and performances.
JO  - Proc. Ninth Int. Biotech. Symp. Expo.
PY  - 1992
SP  - 232
EP  - 235
VL  - 0
AB  - *
AB  - In the chemical industry, the production costs are mainly influenced by chemical and other
AB  - running expenditures. The same holds true for the manufacturing of biotechnological bulk
AB  - products. In contrast to the high-added-value products, the costs of product separation and
AB  - purification are low compared to the product formation costs.
AB  - 	
AB  - In the case of production with aerobic microorganisms, the key factors are the costs for
AB  - chemicals (mainly substrate) and energy (including aeration and cooling). The reactor costs
AB  - are relatively unimportant. Therefore, for the selection of suitable reactors, not only their
AB  - volumetric peformance (e.g., volumetric productivity), but their specific performance with
AB  - respect to the key parameters (chemicals, energy) are decisive.
AB  - 
AB  - According to industrial practice, the medium composition has a much larger effect on the
AB  - process performance than on the reactor type, upon which, however, the optimal medium
AB  - composition depends, at least for filamentous molds.
AB  - 
AB  - Comparison of reactors and their performances can be carried out on different levels, i.e.,
AB  - with regard to
AB  -    - the oxygen transfer rate and efficiency,
AB  -    - the cell mass productivity and efficiency,
AB  -    - the metabolite or enzyme productivity.
AB  - 
AB  - The efficiency can be related to the substrate or energy consumption.
AB  - 
ER  -

TY  - JOUR
AU  - Schuldes, J.
AU  - Rodriguez, O.M.
AU  - Schmeisser, C.
AU  - Krishnan, H.B.
AU  - Daniel, R.
AU  - Streit, W.R.
TI  - Complete Genome Sequence of the Broad-Host-Range Strain Sinorhizobium fredii USDA257.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4483
EP  - 4483
VL  - 194
AB  - Here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium
AB  - Sinorhizobium fredii USDA257. The genome shares a high
AB  - degree of sequence similarity with the closely related broad-host-range strains
AB  - S. fredii NGR234 and HH103. Most strikingly, the USDA257 genome encodes a wealth
AB  - of secretory systems.
ER  -

TY  - JOUR
AU  - Schuler, W.
AU  - Bunikis, I.
AU  - Weber-Lehman, J.
AU  - Comstedt, P.
AU  - Kutschan-Bunikis, S.
AU  - Stanek, G.
AU  - Huber, J.
AU  - Meinke, A.
AU  - Bergstrom, S.
AU  - Lundberg, U.
TI  - Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis.
JO  - PLoS ONE
PY  - 2015
SP  - E0120548
EP  - E0120548
VL  - 10
AB  - The main Borrelia species causing Lyme borreliosis in Europe and Asia are
AB  - Borrelia afzelii, B. garinii, B. burgdorferi and B. bavariensis. This is in
AB  - contrast to the United States, where infections are exclusively caused by B.
AB  - burgdorferi. Until to date the genome sequences of four B. afzelii strains, of
AB  - which only two include the numerous plasmids, are available. In order to further
AB  - assess the genetic diversity of B. afzelii, the most common species in Europe,
AB  - responsible for the large variety of clinical manifestations of Lyme borreliosis,
AB  - we have determined the full genome sequence of the B. afzelii strain K78, a
AB  - clinical isolate from Austria. The K78 genome contains a linear chromosome
AB  - (905,949 bp) and 13 plasmids (8 linear and 5 circular) together presenting 1,309
AB  - open reading frames of which 496 are located on plasmids. With the exception of
AB  - lp28-8, all linear replicons in their full length including their telomeres have
AB  - been sequenced. The comparison with the genomes of the four other B. afzelii
AB  - strains, ACA-1, PKo, HLJ01 and Tom3107, as well as the one of B. burgdorferi
AB  - strain B31, confirmed a high degree of conservation within the linear chromosome
AB  - of B. afzelii, whereas plasmid encoded genes showed a much larger diversity.
AB  - Since some plasmids present in B. burgdorferi are missing in the B. afzelii
AB  - genomes, the corresponding virulence factors of B. burgdorferi are found in B.
AB  - afzelii on other unrelated plasmids. In addition, we have identified a species
AB  - specific region in the circular plasmid, cp26, which could be used for species
AB  - determination. Different non-coding RNAs have been located on the B. afzelii K78
AB  - genome, which have not previously been annotated in any of the published Borrelia
AB  - genomes.
ER  -

TY  - JOUR
AU  - Schultz, J.
AU  - de Souza, Y.A.P.
AU  - Mansur, M.C.P.P.R.
AU  - Vermelho, A.B.
AU  - da Mota, F.F.
AU  - Rosado, A.S.
TI  - Draft Genome Sequence of Microbacterium sp. Strain LEMMJ01, Isolated from Antarctic Ornithogenic Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00672
EP  - e00617
VL  - 5
AB  - We report here the 3,637,012-bp draft genome sequence of Microbacterium sp. strain LEMMJ01,
AB  - isolated from ornithogenic soil from King George Island,
AB  - Antarctica. The total number of genes presented in the draft genome sequence was
AB  - 3,553, and the total number of coding sequences was 3,497. In addition, genes
AB  - related to the production of terpene and carotenoids were revealed.
ER  -

TY  - JOUR
AU  - Schultz, P.G.
TI  - The interplay between chemistry and biology in the design of enzymatic catalysts.
JO  - Science
PY  - 1988
SP  - 426
EP  - 433
VL  - 240
AB  - Chemists and biologist are focusing considerable effort on the development of
AB  - efficient, highly selective catalysts for the synthesis or modification of
AB  - complex molecules.  Two approaches are described here, the generation of
AB  - catalytic antibodies and hybrid enzymes, which exploit the binding and
AB  - catalytic machinery of nature in catalyst design.  Characterization of these
AB  - systems is providing additional insight into the mechanisms of molecular
AB  - recognition and catalysis which may, in turn, lead to the design of tailor-made
AB  - catalysts for applications in chemistry, biology and medicine.
ER  -

TY  - JOUR
AU  - Schultz, P.G.
AU  - Dervan, P.B.
TI  - Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA.Fe(II).
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1983
SP  - 6834
EP  - 6837
VL  - 80
AB  - In the presence of O2 and 5 mM dithiothreitol,
AB  - penta-N-methylpyrrolecarboxamide-EDTA.Fe(II) [P5E.Fe(II)] at 0.5 microM cleaves
AB  - pBR322 plasmid DNA (50 microM in base pairs) on opposite strands to afford
AB  - discrete DNA fragments as analyzed by agarose gel electrophoresis.
AB  - High-resolution denaturing gel electrophoresis of a 32P-end-labeled
AB  - 517-base-pair restriction fragment containing a major cleavage site reveals
AB  - that P5E.Fe(II) cleaves 3-5 base pairs contiguous to a 6-base-pair sequence,
AB  - 5'-T-T-T-T-T-A-3' (4,323-4,328 base pairs).  The major binding orientation of
AB  - the pentapeptide occurs with the amino terminus at the adenine side of this
AB  - sequence.  In the presence of 5 mM dithiothreitol, 0.01 microM P5E.Fe(II)
AB  - converts form I pBR322 DNA at 022 microM plasmid (1.0 mM in base pairs) to 40%
AB  - form II, indicating the cleavage reaction is catalytic, turning over a minimum
AB  - of nine times.  This synthetic molecule achieves double-strand cleavage of DNA
AB  - (pH 7.9, 25C) at the 6-base-pair recognition level and may provide an approach
AB  - to the design of "artificial restriction enzymes".
ER  -

TY  - JOUR
AU  - Schultz-Johansen, M.
AU  - Glaring, M.A.
AU  - Bech, P.K.
AU  - Stougaard, P.
TI  - Draft Genome Sequence of a Novel Marine Bacterium, Paraglaciecola sp. Strain S66, with Hydrolytic Activity against Seaweed Polysaccharides.
JO  - Genome Announcements
PY  - 2016
SP  - e00304
EP  - e00316
VL  - 4
AB  - A novel agarolytic gammaproteobacterium, ITALIC! Paraglaciecolasp. S66, was isolated from
AB  - marine samples of eelgrass ( ITALIC! Zosterasp.) and sequenced. The
AB  - draft genome contains a large number of enzyme-encoding genes with predicted
AB  - function against several complex polysaccharides found in the cell walls of
AB  - algae.
ER  -

TY  - JOUR
AU  - Schulze, C.
AU  - Jeltsch, A.
AU  - Franke, I.
AU  - Urbanke, C.
AU  - Pingoud, A.
TI  - Crosslinking the EcoRV restriction endonuclease across the DNA-binding site reveals transient intermediates and conformational changes of the enzyme during DNA binding and catalytic turnover.
JO  - EMBO J.
PY  - 1998
SP  - 6757
EP  - 6766
VL  - 17
AB  - EcoRV completely encircles bound DNA with two loops, forming the entry and exit gate for the
AB  - DNA substrate.  These loops were crosslinked generating CL-EcoRV which binds and releases
AB  - linear DNA only slowly, because threading linear DNA into and out of the DNA-binding
AB  - 'tunnel' of CL-EcoRV is not very effective.  If the crosslinking reaction is carried out
AB  - with a circular bound DNA, CL-EcoRV is hyperactive towards the trapped substrate which is
AB  - cleaved very quickly but not very accurately.  CL-EcoRV also binds to, but does not cleave,
AB  - circular DNA when added from the outside, because it cannot enter the active site.  Based on
AB  - these results a two-step binding model is proposed for EcoRV: initial DNMA binding occurs at
AB  - the outer side of the loops before the gate opens and then the DNA is transferred to the
AB  - catalytic center.
ER  -

TY  - JOUR
AU  - Schumann, J.
AU  - Walter, J.
AU  - Willert, J.
AU  - Wild, C.
AU  - Koch, D.
AU  - Trautner, T.A.
TI  - M.BssHII, a multispecific cytosine-C5-DNA-methyltransferase with unusual target recognizing properties.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 949
EP  - 959
VL  - 257
AB  - A new multispecific cytosine-C5-DNA-methyltransferase (C5-MTase), M.BssHII,
AB  - was identified in Bacillus stearothermophilus H3.  The M.BssHII gene was cloned and sequenced.
AB  - The amino acid sequence deduced shows the characteristic building plan of a C5-MTase.  By
AB  - sequencing bisulfite-treated DNA methylated by M.BssHII and by restriction enzyme analysis, we
AB  - defined the following methylation targets of M.BssHII: ACGCGT/CCGCGG (Mlu/SacII),
AB  - PuGCGCPy (HaeII), PuCCGGPy (Cfr10I) and GCGCGC (BssHII).  The relative location of the
AB  - specificity determinants in the C5-MTase was derived from the analysis of M.BssHII derivatives
AB  - carrying deletions within the variable region V and chimeric C5-MTases constructed between
AB  - M.BssHII and the related monospecific enzyme M.Phi3TII.  Four of the M.BssHII specificities
AB  - (MluI, SacII, Cfr10I and BssHII) could be associated with amino acid segments within the
AB  - variable region V.  The determinant for HaeII activity had to be assigned to sequences
AB  - defining
AB  - the enzyme core, the first example of a C5-MTase in which a sequence-specific methylation
AB  - potential is mediated by structures outside of the variable region.  Another intriguing result
AB  - came
AB  - from the analysis of one particular chimera made between M.BssHII and M.Phi3TII.  This
AB  - construct showed a relaxation of the methylation capacity, both with respect to the target
AB  - recognized and the targeting of methylation within this sequence.
ER  -

TY  - JOUR
AU  - Schumann, J.
AU  - Willert, J.
AU  - Wild, C.
AU  - Waler, J.
AU  - Trautner, T.A.
TI  - M.BssHII: a new multispecific C5-DNA-methyltransferase.
JO  - Gene
PY  - 1995
SP  - 103
EP  - 104
VL  - 157
AB  - M.BssHII is a new multispecific C5-DNA-methyltransferase recognizing five different targets.
AB  - As the enzyme has been isolated from a thermophilic Bacillus, the protein should show enhanced
AB  - intrinsic thermostability and therefore be a promising candidate for crystallizing a
AB  - multispecific MTase.
ER  -

TY  - JOUR
AU  - Schuster, A.K.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of Rheinheimera sp. F8, a Biofilm-Forming Strain Which Produces Large Amounts of Extracellular DNA.
JO  - Genome Announcements
PY  - 2016
SP  - e00082
EP  - e00016
VL  - 4
AB  - Rheinheimera sp. strain F8 is a biofilm-forming gammaproteobacterium that has been found to
AB  - produce large amounts of filamentous extracellular DNA. Here, we
AB  - announce the de novo assembly of its genome. It is estimated to be 4,464,511 bp
AB  - in length, with 3,970 protein-coding sequences and 92 RNA-coding sequences.
ER  -

TY  - JOUR
AU  - Schuster, A.M.
AU  - Burbank, D.E.
AU  - Meister, B.
AU  - Skrdla, M.P.
AU  - Meints, R.H.
AU  - Hattman, S.
AU  - Swinton, D.
AU  - Van Etten, J.L.
TI  - Characterization of viruses infecting a eukaryotic chlorella-like green alga.
JO  - Virology
PY  - 1986
SP  - 170
EP  - 177
VL  - 150
AB  - Nineteen plaque-forming viruses of the unicellular, eukaryotic Chlorella-like
AB  - green alga, strain NC64A, were isolated from the various geographic regions in
AB  - the United States and characterized.  Like the previously described virus,
AB  - PBCV-1, all of the new viruses were large polyhedrons, sensitive to chloroform,
AB  - and contained large dsDNA genomes of ca.  300 kbp.  All of the viral DNAs
AB  - contained 5-methyldeoxycytidine which varied from 0.1 to 47% of the
AB  - deoxycytidine.  In addition, 10 of the viral DNAs contained
AB  - N6-methyldeoxyadenosine which varied from 8.1 to 37% of the deoxyadenosine.
AB  - These viruses, along with 11 previously described viruses which replicate in
AB  - the same Chlorella host, were grouped into 11 classes based on at least one of
AB  - the following properties:  plaque size, reaction with PBCV-1 antiserum, or the
AB  - nature and abundance of methylated bases in their genomic DNA.
ER  -

TY  - JOUR
AU  - Schutzer, S.E.
AU  - Fraser-Liggett, C.M.
AU  - Casjens, S.R.
AU  - Qiu, W.G.
AU  - Dunn, J.J.
AU  - Mongodin, E.F.
AU  - Luft, B.J.
TI  - Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1018
EP  - 1020
VL  - 193
AB  - Borrelia burgdorferi is a causative agent of Lyme disease in North America and Eurasia. The
AB  - first complete genome sequence of B. burgdorferi strain 31, available for more than a decade,
AB  - has assisted research on the
AB  - pathogenesis of Lyme disease. Because a single genome sequence is not
AB  - sufficient to understand the relationship between genotypic and geographic
AB  - variation and disease phenotype, we determined the whole-genome sequences
AB  - of 13 additional B. burgdorferi isolates that span the range of natural
AB  - variation. These sequences should allow improved understanding of
AB  - pathogenesis and provide a foundation for novel detection, diagnosis, and
AB  - prevention strategies.
ER  -

TY  - JOUR
AU  - Schutzer, S.E.
AU  - Fraser-Liggett, C.M.
AU  - Qiu, W.G.
AU  - Kraiczy, P.
AU  - Mongodin, E.F.
AU  - Dunn, J.J.
AU  - Luft, B.J.
AU  - Casjens, S.R.
TI  - Whole-Genome Sequences of Borrelia bissettii, Borrelia valaisiana, and Borrelia spielmanii.
JO  - J. Bacteriol.
PY  - 2012
SP  - 545
EP  - 546
VL  - 194
AB  - It has been known for decades that human Lyme disease is caused by the three spirochete
AB  - species Borrelia burgdorferi, Borrelia afzelii, and
AB  - Borrelia garinii. Recently, Borrelia valaisiana, Borrelia spielmanii, and
AB  - Borrelia bissettii have been associated with Lyme disease. We report the
AB  - complete genome sequences of B. valaisiana VS116, B. spielmanii A14S, and
AB  - B. bissettii DN127.
ER  -

TY  - JOUR
AU  - Schuyler, J.A.
AU  - Chadwick, S.G.
AU  - Mordechai, E.
AU  - Adelson, M.E.
AU  - Gygax, S.E.
AU  - Hilbert, D.W.
TI  - Draft Genome Sequence of a Metronidazole-Resistant Gardnerella vaginalis Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00992
EP  - e00915
VL  - 3
AB  - We report the draft genome sequence of a Gardnerella vaginalis strain (3549624) isolated from
AB  - a vaginal specimen. G. vaginalis is associated with bacterial vaginosis, the most common cause
AB  - of vaginal discharge, which is often treated with metronidazole. This isolate is highly
AB  - resistant to metronidazole (MIC, 500 microg/ml) and may be useful for comparative genomic
AB  - studies to determine the molecular basis of metronidazole resistance in this species.
ER  -

TY  - JOUR
AU  - Schuyler, J.A.
AU  - Mordechai, E.
AU  - Adelson, M.E.
AU  - Gygax, S.E.
AU  - Hilbert, D.W.
TI  - Draft Genome Sequence of a Metronidazole-Resistant Derivative of Gardnerella vaginalis Strain ATCC 14019.
JO  - Genome Announcements
PY  - 2015
SP  - e01345
EP  - e01315
VL  - 3
AB  - We report the genome sequence of a metronidazole-resistant derivative of Gardnerella vaginalis
AB  - ATCC 14019. This strain was obtained after serial selection
AB  - to increase the MIC from 4 to >/=500 microg/ml. Two coding changes, in genes
AB  - encoding a response regulator and an NAD(+) synthetase, arose during selection.
ER  -

TY  - JOUR
AU  - Schuyler, J.A.
AU  - Mordechai, E.
AU  - Adelson, M.E.
AU  - Gygax, S.E.
AU  - Hilbert, D.W.
TI  - Draft Genome Sequence of a Metronidazole-Susceptible Atopobium vaginae Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00991
EP  - e00915
VL  - 3
AB  - We report the draft genome sequence of a vaginal isolate of Atopobium vaginae vaginae (strain
AB  - 44061), an organism linked to bacterial vaginosis (BV), the most  common gynecological
AB  - infection in the United States. This species is often highly resistant to metronidazole, which
AB  - is a front-line therapy for BV. Strain 44061 is a metronidazole-susceptible isolate (MIC, 16
AB  - microg/ml), and its genome sequence  will be useful for comparative studies to elucidate the
AB  - molecular basis of metronidazole resistance in this species.
ER  -

TY  - JOUR
AU  - Schwabe, G.
AU  - Posseckert, G.
AU  - Klingmuller, W.
TI  - Restriction endonucleases in Azospirillum.
JO  - Gene
PY  - 1985
SP  - 113
EP  - 116
VL  - 39
AB  - Azospirillum brasilense, A. amazonense, and A. lipoferum strains were screened
AB  - for restriction endonucleases using phage lambda DNA.  The extract of A.
AB  - brasilense 29711 cleaved lambda DNA into specific fragments.  It was concluded
AB  - that this strain possesses a class II restriction endonuclease which was named
AB  - AbrI.  AbrI has a single recognition site on lambda DNA at position of approx.
AB  - 33500 bp. AbrI was characterized as an isoschizomer of XhoI, which cuts lambda
AB  - DNA at 33498 bp and cleaves double-stranded DNA at the sequence 5'-C^TCGAG-3'.
AB  - From other Azospirilla strains only A. amazonense QRZ42 extracts (AamI
AB  - activity) cleaved DNA into specific fragments under certain conditions.
ER  -

TY  - JOUR
AU  - Schwartz, E.
AU  - Henne, A.
AU  - Cramm, R.
AU  - Eitinger, T.
AU  - Friedrich, B.
AU  - Gottschalk, G.
TI  - Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 369
EP  - 383
VL  - 332
AB  - The self-transmissible megaplasmid pHG1 carries essential genetic information for the
AB  - facultatively lithoautotrophic and facultatively
AB  - anaerobic lifestyles of its host, the Gram-negative soil bacterium
AB  - Ralstonia eutropha H16. We have determined the complete nucleotide
AB  - sequence of pHG1. This megaplasmid is 452,156 bp in size and carries 429
AB  - potential genes. Groups of functionally related genes form loose clusters
AB  - flanked by mobile elements. The largest functional group consists of
AB  - lithoautotrophy-related genes. These include a set of 41 genes for the
AB  - biosynthesis of the three previously identified hydrogenases and of a
AB  - fourth, novel hydrogenase. Another large cluster carries the genetic
AB  - information for denitrification. In addition to a dissimilatory nitrate
AB  - reductase, both specific and global regulators were identified. Also
AB  - located in the denitrification region is a set of genes for cytochrome c
AB  - biosynthesis. Determinants for several enzymes involved in the
AB  - mineralization of aromatic compounds were found. The genes for conjugative
AB  - plasmid transfer predict that R.eutropha forms two types of pili. One of
AB  - them is related to the type IV pili of pathogenic enterobacteria. pHG1
AB  - also carries an extensive "junkyard" region encompassing 17 remnants of
AB  - mobile elements and 22 partial or intact genes for phage-type integrase.
AB  - Among the mobile elements is a novel member of the IS5 family, in which
AB  - the transposase gene is interrupted by a group II intron.
ER  -

TY  - JOUR
AU  - Schwarz, F.W.
AU  - Toth, J.
AU  - van Aelst, K.
AU  - Cui, G.
AU  - Clausing, S.
AU  - Szczelkun, M.D.
AU  - Seidel, R.
TI  - The helicase-like domains of type III restriction enzymes trigger long-range diffusion along DNA.
JO  - Science
PY  - 2013
SP  - 353
EP  - 356
VL  - 340
AB  - Helicases are ubiquitous adenosine triphosphatases (ATPases) with widespread roles in genome
AB  - metabolism.  Here, we report a previously undescribed functionality for ATPases with
AB  - helicase-like domains; namely, that ATP hydrolysis can trigger ATP-independent long-range
AB  - protein diffusion on DNA in one dimension (1D).  Specifically, using single-molecule
AB  - fluorescence microscopy we show that the Type III restriction enzyme EcoP15I uses its ATPase
AB  - to switch into a distinct structural state that diffuses on DNA over long distances and long
AB  - times.  The switching occurs only upon binding to the target site and requires hydrolysis of
AB  - ~30 ATPs.  We define the mechanism for these enzymes and show how ATPase activity is involved
AB  - in DNA target site verification and 1D signaling, roles that are common in DNA metabolism: for
AB  - example, in nucleotide excision and mismatch repair.
ER  -

TY  - JOUR
AU  - Schwarz, F.W.
AU  - Toth, J.
AU  - van Aelst, K.
AU  - Cui, G.
AU  - Szczelkun, M.D.
AU  - Seidel, R.
TI  - Type III Restriction Enzymes Use 1D Diffusion to Communicate the Relative Orientation of their Distant Target Sites.
JO  - Biophys. J.
PY  - 2011
SP  - 191
EP  - 191
VL  - 100
AB  - Type III restriction enzymes sense that relative orientation of their distant target sites and
AB  - cleave DNA only if at least two of them are situated in an inverted repeat.  The communication
AB  - process is strictly dependent on ATP hydrolysis catalyzed by their superfamily 2 helicase
AB  - domains.  Given the similarity to Type I restriction enzymes, which couple ATP hydrolysis to
AB  - directed motion on DNA, unidirectional loop translocation that may partially be accommpanied
AB  - by 3D diffusive looping has  been the suggested communication mechanism for Type III enzymes.
AB  - Based on magnetic tweezers single-molecule cleavage experiments and ATPase measurements we
AB  - suggest an alternative inter-site communication mechanism using 1D diffusion along the DNA
AB  - contour.  In order to verify this hypothesis we directly visualize the motion of quantum-dot
AB  - labeled Type III restriction enzymes along DNA.  For this we use a setup that combines
AB  - magnetic tweezers with total internal reflection fluorescence microscopy.  The enzymes undergo
AB  - a fast diffusive motion along DNA capable of scanning kbp distances per second.  We also find
AB  - that the affinity of the enzymes to non-specific and specific DNA is regulated by the presence
AB  - of ATP suggesting that ATP hydrolysis acts as a trigger for diffusion.  Thus, Type III
AB  - restricotn enzymes are the first DNa-mopdifying enzymes which communicate target site
AB  - orientations over long distances via 1D diffusion.
ER  -

TY  - JOUR
AU  - Schwarz, F.W.
AU  - van Aelst, K.
AU  - Toth, J.
AU  - Seidel, R.
AU  - Szczelkun, M.D.
TI  - DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 8042
EP  - 8051
VL  - 39
AB  - DNA cleavage by the Type III Restriction-Modification enzymes requires communication in 1D
AB  - between two distant indirectly-repeated recognitions
AB  - sites, yet results in non-specific dsDNA cleavage close to only one of the
AB  - two sites. To test a recently proposed ATP-triggered DNA sliding model, we
AB  - addressed why one site is selected over another during cleavage. We
AB  - examined the relative cleavage of a pair of identical sites on DNA
AB  - substrates with different distances to a free or protein blocked end, and
AB  - on a DNA substrate using different relative concentrations of protein.
AB  - Under these conditions a bias can be induced in the cleavage of one site
AB  - over the other. Monte-Carlo simulations based on the sliding model
AB  - reproduce the experimentally observed behaviour. This suggests that
AB  - cleavage site selection simply reflects the dynamics of the preceding
AB  - stochastic enzyme events that are consistent with bidirectional motion in
AB  - 1D and DNA cleavage following head-on protein collision.
ER  -

TY  - JOUR
AU  - Schwarzhans, J.P.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Kalinowski, J.
AU  - Friehs, K.
TI  - Complete Draft Genome Sequence of Escherichia coli KRX, a Strain for Efficient Cloning and High-Yield Expression of Proteins under Control of the T7 RNA  Polymerase.
JO  - Genome Announcements
PY  - 2017
SP  - e00933
EP  - e00917
VL  - 5
AB  - Escherichia coli KRX is a strain offering both a high transformation efficiency and the
AB  - possibility to produce the target protein to high yields in one host,
AB  - avoiding additional cloning steps. Here, the draft genome sequence of E. coli KRX
AB  - is presented and provides the genetic basis for additional biotechnological
AB  - applications.
ER  -

TY  - JOUR
AU  - Schweikart, K.M.
AU  - Ribeiro, E.
AU  - Larcom, L.L.
TI  - Analysis of the inhibition of restriction endonuclease cleavage by UV damage.
JO  - Photochem. Photobiol.
PY  - 1987
SP  - 76s
EP  - 76s
VL  - 45
AB  - It has been shown that thymine dimers in the recognition sequence of a
AB  - restriction endonuclease inhibit cleavage of the substrate.  Quantitative gel
AB  - electrophoresis analysis allows evaluation of the extent to which cleavage is
AB  - inhibited at different sites in the same DNA.  Since the recognition sequence
AB  - is the same at all sites, any differences in sensitivity to cleavage must
AB  - result from differences in the base sequences near the recognition sites.  We
AB  - have observed different amounts of cleavage inhibition for the EcoRI sites in
AB  - lambda DNA.  The amount of inhibition is correlated with the probability of
AB  - dimer formation within 10 bases on either side of the cleavage site.
AB  - Endonucleases BamHI, EcoRI and HaeII were found to be insensitive to damage by
AB  - 254 nm UV.  DNA complexed with EcoRI was protected from UV damage by the bound
AB  - protein.
ER  -

TY  - JOUR
AU  - Schwendener, S.
AU  - Cotting, K.
AU  - Perreten, V.
TI  - Novel methicillin resistance gene mecD in clinical Macrococcus caseolyticus strains from bovine and canine sources.
JO  - Sci. Rep.
PY  - 2017
SP  - 43797
EP  - 43797
VL  - 7
AB  - Methicillin-resistant Macrococcus caseolyticus strains from bovine and canine
AB  - origins were found to carry a novel mecD gene conferring resistance to all
AB  - classes of beta-lactams including anti-MRSA cephalosporins. Association of
AB  - beta-lactam resistance with mecD was demonstrated by gene expression in S. aureus
AB  - and deletion of the mecD-containing island in M. caseolyticus. The mecD gene was
AB  - located either on an 18,134-bp M. caseolyticus resistance island (McRImecD-1) or
AB  - a 16,188-bp McRImecD-2. Both islands were integrated at the 3' end of the rpsI
AB  - gene, carried the mecD operon (mecD-mecR1m-mecIm), and genes for an integrase of
AB  - the tyrosine recombinase family and a putative virulence-associated protein
AB  - (virE). Apart from the mecD operon, that shared 66% overall nucleotide identity
AB  - with the mecB operon, McRImecD islands were unrelated to any mecB-carrying
AB  - elements or staphylococcal cassette chromosome mec. Only McRImecD-1 that is
AB  - delimitated at both ends by direct repeats was capable of circular excision. The
AB  - recombined excision pattern suggests site-specific activity of the integrase and
AB  - allowed identification of a putative core attachment site. Detection of
AB  - rpsI-associated integrases in Bacillus and S. aureus reveals a potential for
AB  - broad-host range dissemination of the novel methicillin resistance gene mecD.
ER  -

TY  - JOUR
AU  - Schwibbert, K.
AU  - Marin-Sanguino, A.
AU  - Bagyan, I.
AU  - Heidrich, G.
AU  - Lentzen, G.
AU  - Seitz, H.
AU  - Rampp, M.
AU  - Schuster, S.C.
AU  - Klenk, H.-P.
AU  - Pfeiffer, F.
AU  - Oesterhelt, D.
AU  - Kunte, H.J.
TI  - A blueprint of ectoine metabolism from the genome of the Industrial producer Halomonas elongata DSM 2581(T).
JO  - Environ. Microbiol.
PY  - 2011
SP  - 1973
EP  - 1994
VL  - 13
AB  - The halophilic g-proteobacterium Halomonas elongata DSM 2581T thrives at high salinity by
AB  - synthesizing and accumulating the compatible solute ectoine.  Ectoine levels are highly
AB  - regulated according to external salt levels but the overall picture of its metabolism and
AB  - control is not well understood. Apart from its critical role in cell adaptation to halophilic
AB  - environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin
AB  - and health care applications and is thus produced annually on a scale of tons in an industrial
AB  - process using H. elongata as producer strain. This paper presents the complete genome sequence
AB  - of H. elongata (4 061 296 bp) and includes experiments and analysis identifying and
AB  - characterizing the entire ectoine metabolism, including a newly discovered pathway for ectoine
AB  - degradation and its cyclic connection to ectoine synthesis.  The degradation of ectoine (doe)
AB  - proceeds via hydrolysis of ectoine (DoeA) to Na-acetyl-L-2,4-diaminobutyric acid, followed by
AB  - deacetylation to diaminobutyric acid (DoeB). In H. elongata, diaminobutyric acid can either
AB  - flow off to aspartate or re-enter the ectoine synthesis pathway, forming a cycle of ectoine
AB  - synthesis and degradation. Genome comparison revealed that the ectoine degradation pathway
AB  - exists predominantly in non-halophilic bacteria unable to synthesize ectoine. Based on the
AB  - resulting genetic and biochemical data, a metabolic flux model of ectoine metabolism was
AB  - derived that can be used to understand the way H. elongata survives under varying salt
AB  - stresses and that provides a basis for a model-driven improvement of industrial ectoine
AB  - production.
ER  -

TY  - JOUR
AU  - Schwinghamer, E.A.
TI  - Host-controlled modification of Rhizobium bacteriophage.
JO  - Aust. J. Biol. Sci.
PY  - 1964
SP  - 333
EP  - 343
VL  - 18
AB  - Host-controlled phenotypic variation of host specificity was observed with two
AB  - rhizobiophage strains, OL1 and OL5, following growth on six strains of
AB  - Rhizobium leguminosarum and R. trifolii.  The six hosts could be assigned to
AB  - four groups, each group representing a different pattern of host specificity.
AB  - Initial adaptation of OL5 to hosts L2, L7, and L25 appeared to involve
AB  - mutation, although replication in cells of these hosts generally involved
AB  - additional phenotypic restriction.  Restricted and unrestricted forms of a
AB  - phage did not differ significantly in their ability to adsorb to several hosts.
AB  - One-step analysis of the L25-specific form of OL5 grown in L25 cells indicated
AB  - a low average burst size of approximately one unrestricted plaque-forming unit
AB  - in a small proportion of cells which were able to produce infective centres on
AB  - L4.  One-cycle analysis of L4-specific OL5 modified by growth in L25 confirmed
AB  - the phenotypic nature of phage variation in this phage-host system, and
AB  - indicated that specificity for L4 was not replicated in L25.
ER  -

TY  - JOUR
AU  - Schwudke, D.
AU  - Ergin, A.
AU  - Michael, K.
AU  - Volkmar, S.
AU  - Appel, B.
AU  - Knabner, D.
AU  - Konietzny, A.
AU  - Strauch, E.
TI  - Broad-host-range Yersinia phage PY100: genome sequence, proteome analysis of virions, and DNA packaging strategy.
JO  - J. Bacteriol.
PY  - 2008
SP  - 332
EP  - 342
VL  - 190
AB  - PY100 is a lytic bacteriophage with a broad host range within the genus
AB  - Yersinia. The phage forms plaques on strains of the three human pathogenic
AB  - species Yersinia enterocolitica, Y. pseudotuberculosis, and Y. pestis at
AB  - 37 degrees C. PY100 was isolated from farm manure and intended to be used
AB  - in phage therapy trials. PY100 has an icosahedral capsid containing
AB  - double-stranded DNA and a contractile tail. The genome consists of 50,291
AB  - bp and is predicted to contain 93 open reading frames (ORFs). PY100 gene
AB  - products were found to be homologous to the capsid proteins and proteins
AB  - involved in DNA metabolism of the enterobacterial phage T1; PY100 tail
AB  - proteins possess homologies to putative tail proteins of phage AaPhi23 of
AB  - Actinobacillus actinomycetemcomitans. In a proteome analysis of virion
AB  - particles, 15 proteins of the head and tail structures were identified by
AB  - mass spectrometry. The putative gene product of ORF2 of PY100 shows
AB  - significant homology to the gene 3 product (small terminase subunit) of
AB  - Salmonella phage P22 that is involved in packaging of the concatemeric
AB  - phage DNA. The packaging mechanism of PY100 was analyzed by hybridization
AB  - and sequence analysis of DNA isolated from virion particles. Newly
AB  - replicated PY100 DNA is cut initially at a pac recognition site, which is
AB  - located in the coding region of ORF2.
ER  -

TY  - JOUR
AU  - Schyns, G.
AU  - Serra, C.R.
AU  - Lapointe, T.
AU  - Pereira-Leal, J.B.
AU  - Potot, S.
AU  - Fickers, P.
AU  - Perkins, J.B.
AU  - Wyss, M.
AU  - Henriques, A.O.
TI  - Genome of a Gut Strain of Bacillus subtilis.
JO  - Genome Announcements
PY  - 2013
SP  - e00184
EP  - e00112
VL  - 1
AB  - Bacillus subtilis is a Gram-positive, rod-shaped, spore-forming bacterium. We present the
AB  - genome sequence of an undomesticated strain, BSP1, isolated from
AB  - poultry. The sequence of the BSP1 genome supports the view that B. subtilis has a
AB  - biphasic lifestyle, cycling between the soil and the animal gastrointestinal
AB  - tract, and it provides molecular-level insight into the adaptation of B. subtilis
AB  - to life under laboratory conditions.
ER  -

TY  - JOUR
AU  - Sclair, M.
AU  - Edgell, M.H.
AU  - Hutchison, C.A.
TI  - Mapping of new Escherichia coli K and 15 restriction sites on specific fragments of bacteriophage PhiX174 DNA.
JO  - J. Virol.
PY  - 1973
SP  - 378
EP  - 385
VL  - 11
AB  - We have isolated several new PhiX174 mutants which contain sites sensitive to
AB  - restriction by Escherichia coli.  One contains an E. coli 15 restriction site
AB  - and three are double mutants containing an E. coli K site as well as the E.
AB  - coli 15 site.  The replicative form (RF) DNA of one of the mutants containing a
AB  - K site has been shown to be restricted in spheroplasts of a K-12 strain.  The
AB  - infectivity of this RF, but not wild-type RF, has also been shown to be
AB  - inactivated by an E. coli K extract and by purified K restriction enzyme in
AB  - vitro.  The product of the RF treated with purified K restriction enzyme in
AB  - vitro is a full length linear molecule.  The mutant sites have also been
AB  - localized to specific regions of the PhiX174 genome by a fragment mapping
AB  - technique, making use of specific fragments of PhiX174 RF DNA obtained by
AB  - digestion with a specific endonuclease.
ER  -

TY  - JOUR
AU  - Scott, A.
AU  - Song, J.
AU  - Ewing, R.
AU  - Wang, Z.
TI  - Regulation of protein stability of DNA methyltransferase 1 by post-translational modifications.
JO  - Acta Biochim. Biophys. Sin.
PY  - 2014
SP  - 199
EP  - 203
VL  - 46
AB  - DNA methylation is an important epigenetic mechanism that ensures correct gene expression and
AB  - maintains genetic stability. DNA methyltransferase 1 (DNMT1) is the primary enzyme that
AB  - maintains DNA methylation during replication. Dysregulation of DNMT1 is implicated in a
AB  - variety of diseases. DNMT1 protein stability is regulated via various post-translational
AB  - modifications, such as acetylation and ubiquitination, but also through protein-protein
AB  - interactions. These mechanisms ensure DNMT1 is properly activated during the correct time of
AB  - the cell cycle and at correct genomic loci, as well as in response to appropriate
AB  - extracellular cues. Further understanding of these regulatory mechanisms may help to design
AB  - novel therapeutic approaches for human diseases.
ER  -

TY  - JOUR
AU  - Scott, K.M. et al.
TI  - The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2.
JO  - PLoS Biology
PY  - 2006
SP  - e383
EP  - e383
VL  - 4
AB  - Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2,
AB  - representative of ubiquitous chemolithoautotrophic sulfur-oxidizing
AB  - bacteria isolated from deep-sea hydrothermal vents. This
AB  - gammaproteobacterium has a single chromosome (2,427,734 base pairs), and
AB  - its genome illustrates many of the adaptations that have enabled it to
AB  - thrive at vents globally. It has 14 methyl-accepting chemotaxis protein
AB  - genes, including four that may assist in positioning it in the redoxcline.
AB  - A relative abundance of coding sequences (CDSs) encoding regulatory
AB  - proteins likely control the expression of genes encoding carboxysomes,
AB  - multiple dissolved inorganic nitrogen and phosphate transporters, as well
AB  - as a phosphonate operon, which provide this species with a variety of
AB  - options for acquiring these substrates from the environment. Thiom.
AB  - crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in
AB  - relying on the Sox system for the oxidation of reduced sulfur compounds.
AB  - The genome has characteristics consistent with an obligately
AB  - chemolithoautotrophic lifestyle, including few transporters predicted to
AB  - have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered
AB  - throughout the genome.
ER  -

TY  - JOUR
AU  - Sczesnak, A.
AU  - Segata, N.
AU  - Qin, X.
AU  - Gevers, D.
AU  - Petrosino, J.F.
AU  - Huttenhower, C.
AU  - Littman, D.R.
AU  - Ivanov, I.I.
TI  - The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.
JO  - Cell Host Microbe
PY  - 2011
SP  - 260
EP  - 272
VL  - 10
AB  - Perturbations of the composition of the symbiotic intestinal microbiota can have
AB  - profound consequences for host metabolism and immunity. In mice, segmented
AB  - filamentous bacteria (SFB) direct the accumulation of potentially proinflammatory
AB  - Th17 cells in the intestinal lamina propria. We present the genome sequence of
AB  - SFB isolated from monocolonized mice, which classifies SFB phylogenetically as a
AB  - unique member of Clostridiales with a highly reduced genome. Annotation analysis
AB  - demonstrates that SFB depend on their environment for amino acids and essential
AB  - nutrients and may utilize host and dietary glycans for carbon, nitrogen, and
AB  - energy. Comparative analyses reveal that SFB are functionally related to members
AB  - of the genus Clostridium and several pathogenic or commensal "minimal" genera,
AB  - including Finegoldia, Mycoplasma, Borrelia, and Phytoplasma. However, SFB are
AB  - functionally distinct from all 1200 examined genomes, indicating a gene
AB  - complement representing biology relatively unique to their role as a gut
AB  - commensal closely tied to host metabolism and immunity.
ER  -

TY  - JOUR
AU  - Sears, A.
AU  - Peakman, L.J.
AU  - Wilson, G.G.
AU  - Szczelkun, M.D.
TI  - Characterization of the Type III restriction endonuclease PstII from Providencia stuartii.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 4775
EP  - 4787
VL  - 33
AB  - A new Type III restriction endonuclease designated PstII has been purified from Providencia
AB  - stuartii. PstII recognizes the hexanucleotide sequence 5'-CTGATG(N)(25-26/27-28)-3'.
AB  - Endonuclease activity requires a substrate with two copies of the recognition site in
AB  - head-to-head repeat and is dependent on a low level of ATP hydrolysis ( approximately 40
AB  - ATP/site/min). Cleavage occurs at just one of the two sites and results in a staggered cut
AB  - 25-26 nt downstream of the top strand sequence to generate a two base 5'-protruding end.
AB  - Methylation of the site occurs on one strand only at the first adenine of 5'-CATCAG-3'.
AB  - Therefore, PstII has characteristic Type III restriction enzyme activity as exemplified by
AB  - EcoPI or EcoP15I. Moreover, sequence asymmetry of the PstII recognition site in the T7 genome
AB  - acts as an historical imprint of Type III restriction activity in vivo. In contrast to other
AB  - Type I and III enzymes, PstII has a more relaxed nucleotide specificity and can cut DNA with
AB  - GTP and CTP (but not UTP). We also demonstrate that PstII and EcoP15I cannot interact and
AB  - cleave a DNA substrate suggesting that Type III enzymes must make specific protein-protein
AB  - contacts to activate endonuclease activity.
ER  -

TY  - JOUR
AU  - Sears, A.
AU  - Szczelkun, M.D.
TI  - Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitro.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 4788
EP  - 4796
VL  - 33
AB  - We demonstrate that, like other Type III restriction endonuclease, PstII does not turnover
AB  - such that a DNA substrate is only fully cleaved at a
AB  - Res2Mod2-to-site ratio of approximately 1:1. However, unlike other Type
AB  - III enzymes, the cleavage rate profiles varied with protein concentration:
AB  - using 5 nM DNA and 25 nM PstII, approximately half of the DNA was cut at a
AB  - fast rate while the remainder was cut 24 times more slowly; in comparison,
AB  - with 100 nM PstII cleavage occurs at a single fast rate. The inclusion of
AB  - the methyl donor S-adenosyl methionine does not alter the rates with 100
AB  - nM PstII but with 25 nM PstII the reaction stopped after completion of the
AB  - initial fast cleavage phase owing to methylation. Concentration-dependent
AB  - rates were also observed in methylation assays: at 100 nM PstII, a single
AB  - slow rate was measured while at lower PstII concentrations both fast and
AB  - slow rates were measured. We propose a model in which the intact Res2Mod2
AB  - complex favoured at high PstII concentrations is a fast endonuclease/slow
AB  - methyltransferase while the various subassemblies which coexist at lower
AB  - concentrations are fast methyltransferases. A potential role for
AB  - disassembly in control of restriction activity in vivo is discussed.
ER  -

TY  - JOUR
AU  - Sears, L.E.
AU  - Zhou, B.
AU  - Aliotta, J.M.
AU  - Morgan, R.D.
AU  - Kong, H.
TI  - BaeI, another unusual BcgI-like restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 3590
EP  - 3592
VL  - 24
AB  - BcgI and BcgI-like restriction endonucleases have a very distinct characteristic which causes
AB  - them to differ from the other classified restriction enzymes; they all cleave double-stranded
AB  - DNA specifically on both sides of the recognition sites.  Here we report a new BcgI-like
AB  - restriction endonuclease, BaeI, isolated from Bacillus sphaericus.  Like BcgI, BaeI also
AB  - cleaves double-stranded DNA on both strands upstream and downstream of its recognition
AB  - sequence (10/15)ACNNNNGTAYC(12/7).  There are two dominant polypeptides in the final
AB  - preparation of BaeI with molecular masses of ~80 and 55 kDa.  Both are slightly larger than
AB  - the two BcgI subunits.  BaeI requires both Mg2+ and AdoMet to cleave DNA.  Accompanying
AB  - bilateral cleavage activity, the heteromeric BaeI also has an N6-adenine methyltransferase
AB  - activity which modifies the symmetrically located adenines within its recognition sequence.
ER  -

TY  - JOUR
AU  - Sebaihia, M. et al.
TI  - The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.
JO  - Nat. Genet.
PY  - 2006
SP  - 779
EP  - 786
VL  - 38
AB  - We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and
AB  - multidrug-resistant strain. Our analysis indicates
AB  - that a large proportion (11%) of the genome consists of mobile genetic
AB  - elements, mainly in the form of conjugative transposons. These mobile
AB  - elements are putatively responsible for the acquisition by C. difficile of
AB  - an extensive array of genes involved in antimicrobial resistance,
AB  - virulence, host interaction and the production of surface structures. The
AB  - metabolic capabilities encoded in the genome show multiple adaptations for
AB  - survival and growth within the gut environment. The extreme genome
AB  - variability was confirmed by whole-genome microarray analysis; it may
AB  - reflect the organism's niche in the gut and should provide information on
AB  - the evolution of virulence in this organism.
ER  -

TY  - JOUR
AU  - Sebaihia, M. et al.
TI  - Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction.
JO  - J. Bacteriol.
PY  - 2006
SP  - 6002
EP  - 6015
VL  - 188
AB  - Bordetella avium is a pathogen of poultry and is phylogenetically distinct from Bordetella
AB  - bronchiseptica, Bordetella pertussis, and Bordetella parapertussis, which are other species in
AB  - the Bordetella genus that infect mammals. In order to understand the evolutionary relatedness
AB  - of Bordetella species and further the understanding of pathogenesis, we obtained the complete
AB  - genome sequence of B. avium strain 197N, a pathogenic strain that has been extensively
AB  - studied. With 3,732,255 base pairs of DNA and 3,417 predicted coding sequences, it has the
AB  - smallest genome and gene complement of the sequenced bordetellae. In this study, the presence
AB  - or absence of previously reported virulence factors from B. avium was confirmed, and the
AB  - genetic bases for growth characteristics were elucidated. Over 1,100 genes present in B. avium
AB  - but not in B. bronchiseptica were identified, and most were predicted to encode surface or
AB  - secreted proteins that are likely to define an organism adapted to the avian rather than the
AB  - mammalian respiratory tracts. These include genes coding for the synthesis of a polysaccharide
AB  - capsule, hemagglutinins, a type I secretion system adjacent to two very large genes for
AB  - secreted proteins, and unique genes for both lipopolysaccharide and fimbrial biogenesis. Three
AB  - apparently complete prophages are also present. The BvgAS virulence regulatory system appears
AB  - to have polymorphisms at a poly(C) tract that is involved in phase variation in other
AB  - bordetellae. A number of putative iron-regulated outer membrane proteins were predicted from
AB  - the sequence, and this regulation was confirmed experimentally for five of these.
ER  -

TY  - JOUR
AU  - Sebaihia, M. et al.
TI  - Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.
JO  - Genome Res.
PY  - 2007
SP  - 1082
EP  - 1092
VL  - 17
AB  - Clostridium botulinum is a heterogeneous Gram-positive species that comprises four genetically
AB  - and physiologically distinct groups of bacteria that share the
AB  - ability to produce botulinum neurotoxin, the most poisonous toxin known to man,
AB  - and the causative agent of botulism, a severe disease of humans and animals. We
AB  - report here the complete genome sequence of a representative of Group I
AB  - (proteolytic) C. botulinum (strain Hall A, ATCC 3502). The genome consists of a
AB  - chromosome (3,886,916 bp) and a plasmid (16,344 bp), which carry 3650 and 19
AB  - predicted genes, respectively. Consistent with the proteolytic phenotype of this
AB  - strain, the genome harbors a large number of genes encoding secreted proteases
AB  - and enzymes involved in uptake and metabolism of amino acids. The genome also
AB  - reveals a hitherto unknown ability of C. botulinum to degrade chitin. There is a
AB  - significant lack of recently acquired DNA, indicating a stable genomic content,
AB  - in strong contrast to the fluid genome of Clostridium difficile, which can form
AB  - longer-term relationships with its host. Overall, the genome indicates that C.
AB  - botulinum is adapted to a saprophytic lifestyle both in soil and aquatic
AB  - environments. This pathogen relies on its toxin to rapidly kill a wide range of
AB  - prey species, and to gain access to nutrient sources, it releases a large number
AB  - of extracellular enzymes to soften and destroy rotting or decayed tissues.
ER  -

TY  - JOUR
AU  - Sebaihia, M.
AU  - Bocsanczy, A.M.
AU  - Biehl, B.S.
AU  - Quail, M.A.
AU  - Perna, N.T.
AU  - Glasner, J.D.
AU  - Declerck, G.A.
AU  - Cartinhour, S.
AU  - Schneider, D.J.
AU  - Bentley, S.D.
AU  - Parkhill, J.
AU  - Beer, S.V.
TI  - Complete Genome Sequence Of The Plant Pathogen Erwinia amylovora Strain ATCC 49946.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2020
EP  - 2021
VL  - 192
AB  - Erwinia amylovora causes the economically important disease fire blight that affects rosaceous
AB  - plants, especially pear and apple. Here we report the complete genome sequence and annotation
AB  - of strain ATCC 49946. The analysis of the sequence and its comparison with sequenced genomes
AB  - of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts.
ER  -

TY  - JOUR
AU  - Sebastiani, H.
AU  - Jager, H.
TI  - Bacteriophages of Streptococcus-salivarius ssp thermophilus: Characterization of hereditary relationships and determination of virus-host interaction.
JO  - Milchwissenschaft
PY  - 1992
SP  - 25
EP  - 29
VL  - 48
AB  - Problems due to bacteriophage infection are widespread in all dairy fermentations. Since the
AB  - pioneering work of Whitehead and Cox, numerous studies in the past 50 years have led to a
AB  - higher degree in the control of starter activity. However, most of the research in this area
AB  - focussed on bacteriophages of mesophilic streptococci, which are now characterized quite well
AB  - down to the genomic level. On the other hand very little is known about the phages of
AB  - thermophilic streptococci. Up to now these viruses were mainly characterized on the basis of
AB  - ultrastructure and their host range. Problems like the frequency of temperate phages and the
AB  - risk of lysogenic strains in fermentation, as well as the spontaneous change of some host
AB  - strains in their sensitivity to bacteriophages or phage-defense mechanisms of Streptococcus
AB  - salivarius ssp. thermophilus are as poorly understood as the genome of the bacteriophage, but
AB  - demand a solution in order to isolate or construct stable phage-resistant starter cultures for
AB  - the dairy industry.
ER  -

TY  - JOUR
AU  - Sechler, J.M.G.
AU  - Clouse, K.A.
AU  - Strebel, K.
AU  - Weih, K.A.
AU  - Rosenberg, A.S.
TI  - Effect of restriction endonucleases on HIV infection.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 76
EP  - 76
VL  - 17D
AB  - HIV RNA undergoes obligatory reverse transcription to a dsDNA form in the cytoplasm of
AB  - infected cells. This step is critical for the establishment of infection. However, no
AB  - treatment has yet been devised to target the dsDNA. If the dsDNA form of the virus could be
AB  - destroyed before translocating to the nucleus and integrating into the host genome, then
AB  - perhaps amplifiation of the virus within the organism might be prevented and disease
AB  - progression halted. Bacterial cells possess DNA site-specific restriction-modification systems
AB  - that provide protection from viral infections. The type II restriction endonucleases recognize
AB  - a particular sequence in DNA and cleave the DNA in the vicinity of that sequence. We
AB  - investigated whether the type II restriction endonucleases could modify the course of HIV
AB  - infection in human PBL. Studies performed to date indicate that enzymes known to cleave the
AB  - dsDNA form of the virus inhibit the development of RT activity in cultures of infected human
AB  - PBL whereas a control enzyme which lacks a restriction site on HIV dsDNA fails to inhibit
AB  - virus replication. The replication kinetics were delayed and the absolute RT level achieved in
AB  - the treated cultures was reduced. Additionally, morphologic changes associated with infection,
AB  - such as syncytia formation, were significantly delayed. Of critical importance, the
AB  - restriction endonucleases do not appear to damage host cell DNA as shown by their failure to
AB  - inhibit proliferation of activated human PBL in vitro. Thus, type II restriction endonucleases
AB  - may prove useful in the study and treatment of HIV infection.
ER  -

TY  - JOUR
AU  - See-Too, W.S.
AU  - Ee, R.
AU  - Lim, Y.L.
AU  - Convey, P.
AU  - Pearce, D.A.
AU  - Mohidin, T.B.M.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 52
EP  - 52
VL  - 12
AB  - Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample
AB  - obtained at Rothera Point, Adelaide Island, close to the Antarctic
AB  - Peninsula. Strain R3.8 was sequenced in order to help discover potential cold
AB  - active enzymes with biotechnological applications. Genome analysis identified
AB  - various cold adaptation genes including some coding for anti-freeze proteins and
AB  - cold-shock proteins, genes involved in bioremediation of xenobiotic compounds
AB  - including naphthalene, and genes with chitinolytic and N-acetylglucosamine
AB  - utilization properties and also plant-growth-influencing properties. In this
AB  - genome report, we present a complete genome sequence of A. alpinus strain R3.8
AB  - and its annotation data, which will facilitate exploitation of potential novel
AB  - cold-active enzymes.
ER  -

TY  - JOUR
AU  - Seeber, S.
AU  - Kessler, C.
AU  - Gotz, F.
TI  - Cloning, expression and characterization of the Sau3AI restriction and modification genes in Staphylococcus carnosus TM300.
JO  - Gene
PY  - 1990
SP  - 37
EP  - 43
VL  - 94
AB  - The genes encoding the restriction enzyme (ENase) and modification enzyme
AB  - (MTase) of Staphylococcus aureus 3A (recognition sequence 5'-GATC-3') have been
AB  - cloned in Staphylococcus carnosus TM300 using the vector pCA44.  Clones
AB  - carrying both genes were isolated from DNA libraries prepared with MboI +
AB  - BamHI.  The DNA region encoding M.Sau3AI was subcloned on a 3.66-kb EcoRV
AB  - fragment in vector pT181mcs.  Plasmids purified from the clones were resistant
AB  - to digestion with Sau3AI, indicating that the sau3AIM gene was expressed and
AB  - the product was functional in S. carnosus.  Cell lysates of clones with both
AB  - activities encoded on plasmid pSEM7, cut DNA with the same pattern as Sau3AI,
AB  - showing that the sau3AIR gene was also expressed and the ENase was functional
AB  - in S. carnosus.  Sequence analysis shows that both genes are transcribed in the
AB  - same direction and encode polypeptides with calculated Mrs of 56477 for
AB  - R.Sau3AI and 47300 for M.Sau3AI.  Efforts to clone one or both genes in
AB  - Escherichia coli have so far failed.
ER  -

TY  - JOUR
AU  - Seed, K.D.
AU  - Bodi, K.L.
AU  - Kropinski, A.M.
AU  - Ackermann, H.W.
AU  - Calderwood, S.B.
AU  - Qadri, F.
AU  - Camilli, A.
TI  - Evidence of a Dominant Lineage of Vibrio cholerae-Specific Lytic Bacteriophages Shed by Cholera Patients over a 10-Year Period in Dhaka, Bangladesh.
JO  - MBio
PY  - 2011
SP  - e00334
EP  - e00310
VL  - 2
AB  - ABSTRACT Lytic bacteriophages are hypothesized to contribute to the seasonality and duration
AB  - of cholera epidemics in Bangladesh. However, the bacteriophages contributing to this
AB  - phenomenon have yet to be characterized at a molecular genetic level. In this study, we
AB  - isolated and sequenced the genomes of 15 bacteriophages from stool samples from cholera
AB  - patients spanning a 10-year surveillance period in Dhaka, Bangladesh. Our results indicate
AB  - that a single novel bacteriophage type, designated ICP1 (for the International Centre for
AB  - Diarrhoeal Disease Research, Bangladesh cholera phage 1) is present in all stool samples from
AB  - cholera patients, while two other bacteriophage types, one novel (ICP2) and one T7-like
AB  - (ICP3), are transient. ICP1 is a member of the Myoviridae family and has a 126-kilobase genome
AB  - comprising 230 open reading frames. Comparative sequence analysis of ICP1 and related isolates
AB  - from this time period indicates a high level of genetic conservation. The ubiquitous presence
AB  - of ICP1 in cholera patients and the finding that the O1 antigen of lipopolysaccharide (LPS)
AB  - serves as the ICP1 receptor suggest that ICP1 is extremely well adapted to predation of
AB  - human-pathogenic V. cholerae O1. IMPORTANCE The severe diarrheal disease cholera is caused by
AB  - the bacterium Vibrio cholerae, which can be transmitted to humans from the aquatic
AB  - environment. Factors that affect V. cholerae in the environment can impact the occurrence of
AB  - cholera outbreaks; one of these factors is thought to be the presence of bacterial viruses, or
AB  - bacteriophages. Bacteriophages that prey on V. cholerae in the environment, and potentially in
AB  - humans, have not been extensively genetically characterized. Here, we isolated and sequenced
AB  - the genomes of bacteriophages from cholera patient stool samples collected over a 10-year
AB  - period in Dhaka, Bangladesh, a region that suffers from regular cholera outbreaks. We describe
AB  - a unique bacteriophage present in all samples, infer its evolution by sequencing multiple
AB  - isolates from different patients over time, and identify the host receptor that shows that the
AB  - bacteriophage specifically predates the serogroup of V. cholerae responsible for the majority
AB  - of disease occurrences.
ER  -

TY  - JOUR
AU  - Seed, K.D.
AU  - Dennis, J.J.
TI  - Isolation and characterization of bacteriophages of the Burkholderia cepacia complex.
JO  - FEMS Microbiol. Lett.
PY  - 2005
SP  - 273
EP  - 280
VL  - 251
AB  - The Burkholderia cepacia complex consists of nine phenotypically similar
AB  - but genotypically distinct beta-proteobacteria that are metabolically
AB  - diverse and highly antibiotic resistant. Because of this exceptional
AB  - intrinsic antibiotic resistance, infections with B. cepacia complex
AB  - members are difficult to treat clinically and new alternative therapies
AB  - are required. One strategy that holds some promise is the use of naturally
AB  - occurring antibacterial bacteriophages that could potentially bind to and
AB  - lyse B. cepacia complex cells in vivo. Towards that end, we used
AB  - enrichment techniques to isolate lytic and lysogenic bacteriophages
AB  - specific to the B. cepacia complex. The newly isolated bacteriophages were
AB  - characterized by host range analysis, electron microscopy, genome
AB  - restriction analysis, and partial DNA sequencing. These isolates include a
AB  - bacteriophage with one of the broadest host ranges yet identified for any
AB  - bacteriophage specific to the B. cepacia complex, and the first
AB  - description of bacteriophages capable of lysing B. ambifaria.
ER  -

TY  - JOUR
AU  - Seedorf, H.
AU  - Fricke, W.F.
AU  - Veith, B.
AU  - Bruggemann, H.
AU  - Liesegang, H.
AU  - Strittmatter, A.
AU  - Miethke, M.
AU  - Buckel, W.
AU  - Hinderberger, J.
AU  - Li, F.
AU  - Hagemeier, C.
AU  - Thauer, R.K.
AU  - Gottschalk, G.
TI  - The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 2128
EP  - 2133
VL  - 105
AB  - Clostridium kluyveri is unique among the clostridia; it grows anaerobically on ethanol and
AB  - acetate as sole energy sources. Fermentation products are butyrate, caproate, and H(2). We
AB  - report here the genome sequence of C. kluyveri, which revealed new insights into the metabolic
AB  - capabilities of this well studied organism. A membrane-bound energy-converting NADH:ferredoxin
AB  - oxidoreductase (RnfCDGEAB) and a cytoplasmic butyryl-CoA dehydrogenase complex (Bcd/EtfAB)
AB  - coupling the reduction of crotonyl-CoA to butyryl-CoA with the reduction of ferredoxin
AB  - represent a new energy-conserving module in anaerobes. The genes for NAD-dependent ethanol
AB  - dehydrogenase and NAD(P)-dependent acetaldehyde dehydrogenase are located next to genes for
AB  - microcompartment proteins, suggesting that the two enzymes, which are isolated together in a
AB  - macromolecular complex, form a carboxysome-like structure. Unique for a strict anaerobe, C.
AB  - kluyveri harbors three sets of genes predicted to encode for polyketide/nonribosomal peptide
AB  - synthetase hybrides and one set for a nonribosomal peptide synthetase. The latter is predicted
AB  - to catalyze the synthesis of a new siderophore, which is formed under iron-deficient growth
AB  - conditions.
ER  -

TY  - JOUR
AU  - Seegers, J.F.M.L.
AU  - van Sinderen, D.
AU  - Fitzgerald, G.F.
TI  - Molecular characterization of the lactococcal plasmid pCIS3: natural stacking of specificity subunits of a type I restriction/modification system in a single lactococcal strain.
JO  - Microbiology
PY  - 2000
SP  - 435
EP  - 443
VL  - 146
AB  - A 6.1 kb plasmid from the Lactococcus lactis subsp. cremoris strain UC509.9. named pCIS3, was
AB  - found to mediate a restriction/modification
AB  - (RIM) phenotype, Nucleotide sequence analysis of pCIS3 revealed the
AB  - presence of an hsdS gene, typical of type I R/M systems, The presence
AB  - of this plasmid resulted in a 10(4)-fold reduction in the efficiency of
AB  - plating (e.o.p.) of unmodified phage. In addition to the hsdS gene of
AB  - pCIS3, two more hsd5 genes were identified in strain UC509.9, one
AB  - located on the chromosome downstream of a gene highly homologous to
AB  - hsdM genes and a third on the smallest (4 kb) plasmid, named pCIS1. The
AB  - replication region of pCIS3 was highly similar to that of a large
AB  - family of lactococcal theta replicons, In addition, pCIS3 was found to
AB  - encode a member of the CorA family of magnesium transporters.
ER  -

TY  - JOUR
AU  - Seela, F.
AU  - Driller, H.
TI  - Palindromic oligonucleotides containing 7-deaza-2'-deoxyguanosine: solid-phase synthesis of d[(p)GG*AATTCC] octamers and recognition by the endodeoxyribonuclease EcoRI.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 2319
EP  - 2332
VL  - 14
AB  - Octadeoxynucleotides with the sequence d[(p)GG*AATTCC] have been prepared by
AB  - solid-phase synthesis employing regular and base-modified phosphoramidites.
AB  - These oligomers which contain an isosterically altred recognition sequence of
AB  - the endodeoxyribonuclease EcoRI form duplexes under appropriate salt
AB  - conditions.  Since G* can represent 7-deaza-2'-deoxyguanosine the oligomers
AB  - were used as probes to study their cleavage by the endodeoxyribonuclease EcoRI.
AB  - The enzymatic hydrolysis of the modified octamer was strongly decreased
AB  - compared to the regular DNA-fragment.  This shows that quanine N-7 located at
AB  - the cleavage site is important for the recognition process by the enzyme.  The
AB  - residual enzymatic activity is discussed on the basis of reduced specificity
AB  - towards the recognition fragment.  The fact that this cleavage occurs already
AB  - under regular conditions indicates that the process described here bases on an
AB  - intrinsic property of the oligomer and is different from the star activity.
ER  -

TY  - JOUR
AU  - Seela, F.
AU  - Kehne, A.
TI  - Palindromic  octa-  and  dodecanucleotides containing 2'-deoxytubercidin: synthesis,  hairpin formation, and recognition by the endodeoxyribonuclease EcoRI.
JO  - Biochemistry
PY  - 1987
SP  - 2232
EP  - 2238
VL  - 26
AB  - Octa- and dodecanucleotides containing 2'-deoxytubericidin within the
AB  - endodeoxyribonuclease   EcoRI  recognition  fragment  d(GAATTC)  have  been
AB  - prepared  by  solid-phase synthesis. Whereas octamers as well as dodecamers
AB  - with  a  "random"  flanking region formed duplexes in aqueous solution, the
AB  - dodecamer  d(CGCGAATTCGCG)  and  isosterically  modified  oligomers thereof
AB  - showed  a  strong tendency of hairpin formation. Due to this, cleavage with the
AB  - endodeoxyribonuclease EcoRI was strongly decreased.  In contrast,
AB  - d(GTAGAATTCTAC) was easily cleaved by the enzyme. Single replacement of one of
AB  - the  dA  residues by 2'-deoxytubercidin within the recognition sequence
AB  - decreased   the   cleavage   velocity  but  retained  specificity.  Twofold
AB  - modification  prevents cleavage of the oligomer. This implies that both N-7
AB  - purine  nitrogens  are  proton acceptor sites for the endodeoxyribonuclease
AB  - EcoRI.
ER  -

TY  - JOUR
AU  - Seela, F.
AU  - Roling, A.
TI  - 7-Deazapurine containing DNA: efficiency of c7GdTP, c7AdTP and c7IdTP incorporation during PCR-amplification and protection from endodeoxyribonuclease hydrolysis.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 55
EP  - 61
VL  - 20
AB  - The enzymatic synthesis of 7-deazapurine nucleoside containing DNA (501 bp) is performed by
AB  - PCR-amplification (Taq polymerase) using a pUC18 plasmid DNA as template and the triphosphates
AB  - of 7-deaza-2'-deoxyguanosine (c7Gd), -adenosine (c7Ad) and -inosine (c7Id). c7GdTP can fully
AB  - replace dGTP resulting in a completely modified DNA-fragment of defined size and sequence. The
AB  - other two 7-deazapurine triphosphates (c7AdTP) and (c7IdTP) require the presence of the parent
AB  - purine 2-deoxyribonucleotides. In purine/7-deazapurine nucleotide mixtures Taq polymerase
AB  - prefers purine over 7-deazapurine nucleotides but accepts c7GdTP much better than c7AdTP or
AB  - c7IdTP. As incorporation of 7-deazapurine nucleotides represents a modification of the major
AB  - groove of DNA it can be used to probe DNA/protein interaction. Regioselective phosphodiester
AB  - hydrolysis of the modified DNA-fragments was studied with 28 endodeoxyribonucleases. c7Gd is
AB  - able to protect the DNA from the phosphodiester hydrolysis in more than 20 cases, only a few
AB  - enzymes (MaeIII, RsaI, HindIII, PvuII or TaqI) do still hydrolyze the modified DNA. c7Ad
AB  - protects DNA less efficiently, as this DNA could only be modified in part. The absence of N-7
AB  - as potential binding position or a geometric distortion of the recognition duplex caused by
AB  - the 7-deazapurine base can account for protection of hydrolysis.
ER  -

TY  - JOUR
AU  - Seeman, N.C.
AU  - Rosenberg, J.M.
AU  - Rich, A.
TI  - Sequence-specific recognition of double helical nucleic acids by proteins.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1976
SP  - 804
EP  - 808
VL  - 73
AB  - The base pairs in double helical nucleic acids have been compared to see how
AB  - they can be recognized by proteins.  We conclude that a single hydrogen bond is
AB  - inadequate for uniquely identifying any particular base pair, as this leads to
AB  - numerous degeneracies.  However, using two hydrogen bonds, fidelity of base
AB  - pair recognition may be achieved.  We propose specific amino-acid side chain
AB  - interactions involving two hydrogen bonds as a component of the recognition
AB  - system for base pairs.  In the major groove we suggest that asparagine or
AB  - glutamine binds to adenine of the base pair, or arginine binds to guanine.  In
AB  - the minor groove, we suggest an interaction between asparagine or glutamine
AB  - with guanine of the base pair.  We also discuss the role that ions and other
AB  - amino-acid side chains may play in recognition interactions.
ER  -

TY  - JOUR
AU  - Seemann, T.
AU  - Bulach, D.M.
AU  - Carter, G.
AU  - Albert, M.J.
TI  - Draft Genome Sequences of Two Strains of a Newly Described Species, Sphingobacterium cellulitidis.
JO  - Genome Announcements
PY  - 2017
SP  - e00956
EP  - e00917
VL  - 5
AB  - The draft genome sequences of two strains of a newly described species, Sphingobacterium
AB  - cellulitidis, have been determined. The type strain originated
AB  - from cellulitis of a toe of a patient and the other strain from the environment.
AB  - The sequences will provide the reference genomes of the new Sphingobacterium
AB  - species.
ER  -

TY  - JOUR
AU  - Seersholm, F.V.
AU  - Fischer, A.
AU  - Heller, M.
AU  - Jores, J.
AU  - Sachse, K.
AU  - Mourier, T.
AU  - Hansen, A.J.
TI  - Draft Genome Sequence of the First Human Isolate of the Ruminant Pathogen Mycoplasma capricolum subsp. capricolum.
JO  - Genome Announcements
PY  - 2015
SP  - e00583
EP  - e00515
VL  - 3
AB  - Mycoplasma capricolum subsp. capricolum is a well-known pathogen of small ruminants. A recent
AB  - human case of septicemia involving this agent raised the
AB  - question of its potential pathogenicity to humans. We present the first draft
AB  - genome sequence of a human Mycoplasma capricolum subsp. capricolum isolate.
ER  -

TY  - JOUR
AU  - Segata, N.
AU  - Ballarini, A.
AU  - Jousson, O.
TI  - Genome Sequence of Pseudomonas aeruginosa PA45, a Highly Virulent Strain Isolated from a Patient with Bloodstream Infection.
JO  - Genome Announcements
PY  - 2013
SP  - e00289
EP  - e00213
VL  - 1
AB  - Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen causing a broad range of
AB  - infections in humans. We provide the draft genome sequence of the
AB  - recently identified and highly virulent P. aeruginosa PA45 strain. Its 6.6-Mb
AB  - genome contains 6,822 genes, including an unparalleled number of virulence genes,
AB  - which might explain its aggressive phenotype.
ER  -

TY  - JOUR
AU  - Segura, A.
AU  - Auffret, P.
AU  - Klopp, C.
AU  - Bertin, Y.
AU  - Forano, E.
TI  - Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 61
EP  - 61
VL  - 12
AB  - Escherichia coli is the most abundant facultative anaerobic bacteria in the gastro-intestinal
AB  - tract of mammals but can be responsible for intestinal
AB  - infection due to acquisition of virulence factors. Genomes of pathogenic E. coli
AB  - strains are widely described whereas those of bovine commensal E. coli strains
AB  - are very scarce. Here, we report the genome sequence, annotation, and features of
AB  - the commensal E. coli BG1 isolated from the gastro-intestinal tract of cattle.
AB  - Whole genome sequencing analysis showed that BG1 has a chromosome of 4,782,107 bp
AB  - coding for 4465 proteins and 97 RNAs. E. coli BG1 belonged to the serotype
AB  - O159:H21, was classified in the phylogroup B1 and possessed the genetic
AB  - information encoding 'virulence factors' such as adherence systems, iron
AB  - acquisition and flagella synthesis. A total of 12 adherence systems were detected
AB  - reflecting the potential ability of BG1 to colonize different segments of the
AB  - bovine gastro-intestinal tract. E. coli BG1 is unable to assimilate ethanolamine
AB  - that confers a nutritional advantage to some pathogenic E. coli in the bovine
AB  - gastro-intestinal tract. Genome analysis revealed the presence of i) 34 amino
AB  - acids change due to non-synonymous SNPs among the genes encoding ethanolamine
AB  - transport and assimilation, and ii) an additional predicted alpha helix inserted
AB  - in cobalamin adenosyltransferase, a key enzyme required for ethanolamine
AB  - assimilation. These modifications could explain the incapacity of BG1 to use
AB  - ethanolamine. The BG1 genome can now be used as a reference (control strain) for
AB  - subsequent evolution and comparative studies.
ER  -

TY  - JOUR
AU  - Seib, K.L.
AU  - Jen, F.E.
AU  - Tan, A.
AU  - Scott, A.L.
AU  - Kumar, R.
AU  - Power, P.M.
AU  - Chen, L.T.
AU  - Wu, H.J.
AU  - Wang, A.H.
AU  - Hill, D.M.
AU  - Luyten, Y.A.
AU  - Morgan, R.D.
AU  - Roberts, R.J.
AU  - Maiden, M.C.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Rao, D.N.
AU  - Jennings, M.P.
TI  - Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 4150
EP  - 4162
VL  - 43
AB  - Phase variation (random ON/OFF switching) of gene expression is a common feature  of
AB  - host-adapted pathogenic bacteria. Phase variably expressed N(6)-adenine DNA
AB  - methyltransferases (Mod) alter global methylation patterns resulting in changes
AB  - in gene expression. These systems constitute phase variable regulons called
AB  - phasevarions. Neisseria meningitidis phasevarions regulate genes including
AB  - virulence factors and vaccine candidates, and alter phenotypes including
AB  - antibiotic resistance. The target site recognized by these Type III N(6)-adenine
AB  - DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome
AB  - analysis was used to identify the recognition site for three key N. meningitidis
AB  - methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY M6A: G-3'), ModA12
AB  - (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC M6A: CC-3') and ModD1
AB  - (exemplified by M.Nme579I) (5'-CC M6A: GC-3'). Restriction inhibition assays and
AB  - mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and
AB  - atypical and is dependent on the type of pyrimidine at the central position, in
AB  - combination with the bases flanking the core recognition sequence 5'-CGY M6A:
AB  - G-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome
AB  - ranged from 4.6% at 5'-GCGC M6A: GG-3' sites, to 100% at 5'-ACGT M6A: GG-3'
AB  - sites. Analysis of the distribution of modified sites in the respective genomes
AB  - shows many cases of association with intergenic regions of genes with altered
AB  - expression due to phasevarion switching.
ER  -

TY  - JOUR
AU  - Seib, K.L.
AU  - Peak, I.R.
AU  - Jennings, M.P.
TI  - Phase variable restriction-modification systems in Moraxella catarrhalis.
JO  - FEMS Immunol. Med. Microbiol.
PY  - 2002
SP  - 159
EP  - 165
VL  - 32
AB  - A repetitive DNA motif was used as a marker to identify novel genes in the mucosal pathogen
AB  - Moraxella catarrhalis. There is a high prevalence of such repetitive motifs in virulence genes
AB  - that display phase variable expression. Two repeat containing loci were identified using a
AB  - digoxigenin-labelled 5'-(CAAC)(6)-3' oligonucleotide probe. The repeats are located in the
AB  - methylase components of two distinct type III restriction-modification (R-M) systems. We
AB  - suggest that the phase variable nature of these R-M systems indicates that they have an
AB  - important role in the biology of M. catarrhalis.
ER  -

TY  - JOUR
AU  - Seib, K.L.
AU  - Pigozzi, E.
AU  - Muzzi, A.
AU  - Gawthorne, J.A.
AU  - Delany, I.
AU  - Jennings, M.P.
AU  - Rappuoli, R.
TI  - A novel epigenetic regulator associated with the hypervirulent Neisseria meningitidis clonal complex 41/44.
JO  - FASEB J.
PY  - 2011
SP  - 3622
EP  - 3633
VL  - 25
AB  - Neisseria meningitidis is a major cause of septicemia and meningitis. The hypervirulent clonal
AB  - complex 41/44 (cc41/44) has emerged as the predominant cause
AB  - of serogroup B meningococcal disease, having been responsible for recent
AB  - outbreaks and epidemics worldwide. However, the meningococcal factors that enable
AB  - transition from asymptomatic carriage to rapidly progressing disease are poorly
AB  - understood. Here we describe a novel phase-variable DNA methyltransferase, ModD,
AB  - which was identified in the genome sequence of a New Zealand epidemic isolate.
AB  - Investigation of the distribution of modD in the wider meningococcal population,
AB  - by PCR and sequence analysis of genetically diverse N. meningitidis strains,
AB  - revealed the presence of modD in 20/27 strains in cc41/44, but in only 2/47
AB  - strains from other clonal complexes, indicating a significant association of modD
AB  - with cc41/44 (Fisher's exact P value=3x10(-10)). The modD gene contains
AB  - 5'-ACCGA-3' repeats that mediate phase variation, leading to reversible on/off
AB  - switching of modD expression. Microarray analysis of modD-on/off variants
AB  - revealed that ModD regulates expression of multiple genes involved in
AB  - colonization, infection, and protection against host defenses, with increased
AB  - catalase expression in the modD-on variant conferring increased resistance to
AB  - oxidative stress. The modulation of gene expression via the ModD phase-variable
AB  - regulon (phasevarion), and its significant association with the cc41/44, suggest
AB  - a role in the fitness and/or pathogenesis of strains belonging to the cc41/44.
ER  -

TY  - JOUR
AU  - Seidel, R.
AU  - Bloom, J.G.
AU  - Dekker, C.
AU  - Szczelkun, M.D.
TI  - Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I.
JO  - EMBO J.
PY  - 2008
SP  - 1388
EP  - 1398
VL  - 27
AB  - The Type I restriction-modification enzyme EcoR124I is an archetypical helicase-based dsDNA
AB  - translocase that moves unidirectionally along the
AB  - 30-50 strand of intact duplex DNA. Using a combination of ensemble and
AB  - single-molecule measurements, we provide estimates of two
AB  - physicochemical constants that are fundamental to a full description of
AB  - motor protein activity-the ATP coupling efficiency (the number of ATP
AB  - consumed per base pair) and the step size (the number of base pairs
AB  - transported per motor step). Our data indicate that EcoR124I makes
AB  - small steps along the DNA of 1 bp in length with 1 ATP consumed per
AB  - step, but with some uncoupling of the ATPase and translocase cycles
AB  - occurring so that the average number of ATP consumed per base pair
AB  - slightly exceeds unity. Our observations form a framework for
AB  - understanding energy coupling in a great many other motors that
AB  - translocate along dsDNA rather than ssDNA.
ER  -

TY  - JOUR
AU  - Seidel, R.
AU  - Szczelkun, M.D.
TI  - Switching roles for a helicase.
JO  - Cell Cycle
PY  - 2013
SP  - 3125
EP  - 3126
VL  - 12
AB  - Helicases are widespread enzymes that share a core RecA fold and characteristic amino acid
AB  - motifs which together form an ATP binding/hydrolysis site.  For the classical helicases (i.e.,
AB  - those which confirm to the family name), ATP-binding provides energy to drive the separation
AB  - of polynucleotide duplexes into single strands.  There are also many enzymes which on the
AB  - basis of structure and motifs appear to be helicases, but which fulfill alternative functions
AB  - without the necessity for strand separation.  These include nucleo-protein remodeling,
AB  - long-range motion along dsDNA and molecular signaling.  The activities and mechanisms of these
AB  - enzymes, often termed "helicase-like" or "pseudo-helicases", are not well understood.  Recent
AB  - studies that try to elucidate the full repertoire of helicase activity provide more and more
AB  - surprises for their numerous roles in genome metabolism.
ER  -

TY  - JOUR
AU  - Seidel, R.
AU  - van der Scheer, C.
AU  - van Noort, J.
AU  - Firman, K.
AU  - Dekker, C.
TI  - Translocation of type I restriction endonuclease EcoR124I along DNA measured with magnetic tweezers.
JO  - Biophys. J.
PY  - 2004
SP  - 316a
EP  - 316a
VL  - 86
AB  - Type I restriction enzymes belong to the machinery of bacteria that protects them against
AB  - invasion by viruses. After sequence specific
AB  - binding to viral DNA they translocate up to several thousands of bp and
AB  - induce DNA cleavage remote from the recognition site. Using magnetic
AB  - tweezers, we measured the translocation process of this enzyme. A
AB  - magnetic particle is used to stretch DNA in an applied magnetic field.
AB  - By tracking the displacement of the particle, translocation activity
AB  - can be recorded in real time. We found that the enzyme is moving with a
AB  - constant speed as fast as 550+30 bp/s. By varying the applied force
AB  - the translocation velocity, the maximum translocated distance as well
AB  - as the time between translocation events, could be measured as a
AB  - function of the load exerted to the tethered DNA molecule.
ER  -

TY  - JOUR
AU  - Seidel, R.
AU  - van Noort, J.
AU  - van der Scheer, C.
AU  - Bloom, J.G.P.
AU  - Dekker, N.H.
AU  - Dutta, C.F.
AU  - Blundell, A.
AU  - Robinson, T.
AU  - Firman, K.
AU  - Dekker, C.
TI  - Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.
JO  - Nat. Struct. Mol. Biol.
PY  - 2004
SP  - 838
EP  - 843
VL  - 11
AB  - Type I restriction enzymes bind sequence-specifically to unmodified DNA and subsequently pull
AB  - the adjacent DNA toward themselves. Cleavage then
AB  - occurs remotely from the recognition site. The mechanism by which these
AB  - members of the superfamily 2 (SF2) of helicases translocate DNA is
AB  - largely unknown. We report the first single-molecule study of DNA
AB  - translocation by the type I restriction enzyme EcoR124I.
AB  - Mechanochemical parameters such as the translocation rate and
AB  - processivity, and their dependence on force and ATP concentration, are
AB  - presented. We show that the two motor subunits of EcoR124I work
AB  - independently. By using torsionally constrained DNA molecules, we found
AB  - that the enzyme tracks along the helical pitch of the DNA molecule.
AB  - This assay may be directly applicable to investigating the tracking of
AB  - other DNA-translocating motors along their DNA templates.
ER  -

TY  - JOUR
AU  - Seipke, R.F.
AU  - Crossman, L.
AU  - Drou, N.
AU  - Heavens, D.
AU  - Bibb, M.J.
AU  - Caccamo, M.
AU  - Hutchings, M.I.
TI  - Draft Genome Sequence of Streptomyces Strain S4, a Symbiont of the Leaf-Cutting Ant Acromyrmex octospinosus.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4270
EP  - 4271
VL  - 193
AB  - Streptomyces spp. are common symbionts of the leaf-cutting ant species Acromyrmex
AB  - octospinosus, which feeds on basidiomycete fungus leaf matter
AB  - and harvests the lipid- and carbohydrate-rich gongylidia as a food source.
AB  - A. octospinosus and other ant genera use antifungal compounds produced by
AB  - Streptomyces spp. and other actinomycetes in order to help defend their
AB  - fungal gardens from parasitic fungi. Herein, we report the draft genome
AB  - sequence of Streptomyces strain S4, an antifungal-producing symbiont of A.
AB  - octospinosus.
ER  -

TY  - JOUR
AU  - Sekiguchi, H.
AU  - Komiya, K.
AU  - Kiga, D.
AU  - Yamamura, M.
TI  - A design and feasibility study of reactions comprising DNA molecular machine that walks autonomously by using a restriction enzyme.
JO  - Nat. Comput.
PY  - 2008
SP  - 303
EP  - 315
VL  - 7
AB  - In this paper, we propose an autonomous molecular walking machine using DNA. This molecular
AB  - machine follows a track of DNA equipped with many single-strand DNA stators arranged in a
AB  - certain pattern. The molecular machine achieves autonomous walk by using a restriction enzyme
AB  - as source of power. With a proposed machine we can control its moving direction and we can
AB  - easily extend walking patterns in two or three dimensions. Combination of multiple legs and
AB  - ssDNA stators can control the walking pattern. We designed and performed a series of
AB  - feasibility study with computer simulation
AB  - and molecular biology experiments.
ER  -

TY  - JOUR
AU  - Sekine, M.
AU  - Tanikawa, S.
AU  - Omata, S.
AU  - Saito, M.
AU  - Fujisawa, T.
AU  - Tsukatani, N.
AU  - Tajima, T.
AU  - Sekigawa, T.
AU  - Kosugi, H.
AU  - Matsuo, Y.
AU  - Nishiko, R.
AU  - Imamura, K.
AU  - Ito, M.
AU  - Narita, H.
AU  - Tago, S.
AU  - Fujita, N.
AU  - Harayama, S.
TI  - Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4.
JO  - Environ. Microbiol.
PY  - 2006
SP  - 334
EP  - 346
VL  - 8
AB  - Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The
AB  - strain harbours one linear plasmid, pREL1
AB  - (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637
AB  - bp), all with some sequence similarities to other Rhodococcus plasmids.
AB  - For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames,
AB  - respectively, were predicted. Linear plasmid pREL1 has several regions
AB  - homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis
AB  - of pREL1 and pBD2 identified common metal-resistance genes on both, but
AB  - pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme
AB  - constituents some of which are quite different from those of other
AB  - organisms. The alkane hydroxylase consisted of a cytochrome P450
AB  - monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The
AB  - ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin
AB  - reductase) sequence. A zinc-containing alcohol dehydrogenase further
AB  - oxydizes alkanols, alkane oxidation products catalysed by alkane
AB  - hydroxylase. Of the circular plasmids, the pREC1 sequence is partially
AB  - similar to the sequence of pREAT701, the virulence plasmid found in
AB  - Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes
AB  - for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded
AB  - by pREL1 and pREC1 may enable efficient mineralization of alkanes.
ER  -

TY  - JOUR
AU  - Sekizaki, T.
AU  - Osaki, M.
AU  - Takamatsu, D.
AU  - Shimoji, Y.
TI  - Distribution of the SsuDAT1I restriction-modification system among different serotypes of Streptococcus suis.
JO  - J. Bacteriol.
PY  - 2001
SP  - 5436
EP  - 5440
VL  - 183
AB  - The SsuDAT1I restriction-modification (R-M) system, which contains two methyltransferases and
AB  - two restriction endonucleases with recognition sequence 5'-GATC-3', was first found in a
AB  - field isolate of Streptococcus suis serotype 2. Isoschizomers of the R-M system were found in
AB  - the same locus between purH and purD in a field isolate of serotype 1/2 and the reference
AB  - strains of serotypes 3, 7, 23, and 26 among 29 strains of different serotypes examined in this
AB  - study. The R-M gene sequences in serotypes 1/2, 3, 7, and 23 were very similar to those of
AB  - SsuDAT1I, whereas those in serotype 26 were less similar. These results indicate intraspecies
AB  - recombination among them and genetic divergence through their evolution.
ER  -

TY  - JOUR
AU  - Sekizaki, T.
AU  - Otani, Y.
AU  - Osaki, M.
AU  - Takamatsu, D.
AU  - Shimoji, Y.
TI  - Evidence for horizontal transfer of SsuDAT1I restriction-modification genes to the Streptococcus suis genome.
JO  - J. Bacteriol.
PY  - 2001
SP  - 500
EP  - 511
VL  - 183
AB  - Different strains of Streptococcus suis serotypes 1 and 2 isolated from pigs either contained
AB  - a restriction-modification (R-M) system or lacked it. The R-M system was an isoschizomer of
AB  - Streptococcus pneumoniae DpnII, which recognizes the nucleotide sequence 5'-GATC-3'. The
AB  - nucleotide sequencing of the genes encoding the R-M system in S. suis DAT1, designated
AB  - SsuDAT1I, showed that the SsuDAT1I gene region contained two methyltransferase genes,
AB  - designated ssuMA and ssuMB, as does the DpnII system. The deduced amino acid sequences of
AB  - M.SsuMA and M.SsuMB showed 70 and 90% identity to M.DpnII and M.DpnA, respectively. However,
AB  - the SsuDAT1I system contained two isoschizomeric restriction endonuclease genes, designated
AB  - ssuRA and ssuRB. The deduced amino acid sequence of R.SsuRA was 49% identical to that of
AB  - R.DpnII, and R.SsuRB was 72% identical to R.LlaDCHI of Lactococcus lactis subsp. cremoris
AB  - DCH-4. The four SsuDAT1I genes overlapped and were bounded by purine biosynthetic gene
AB  - clusters in the following gene order: purF-purM-purN-purH-ssuMA-ssuMB-ssuRA-ssuRB-purD-purE.
AB  - The G+C content of the SsuDAT1I gene region (34.1%) was lower than that of the pur region
AB  - (48.9%), suggesting horizontal transfer of the SsuDAT1I system. No transposable element or
AB  - long-repeat sequence was found in the flanking regions. The SsuDAT1I genes were functional by
AB  - themselves, as they were individually expressed in Escherichia coli. Comparison of the
AB  - sequences between strains with and without the R-M system showed that only the region from 53
AB  - bp upstream of ssuMA to 5 bp downstream of ssuRB was inserted in the intergenic sequence
AB  - between purH and purD and that the insertion target site was not the recognition site of
AB  - SsuDAT1I. No notable substitutions or insertions could be found, and the structures were
AB  - conserved among all the strains. These results suggest that the SsuDAT1I system could have
AB  - been integrated into the S. suis chromosome by an illegitimate recombination mechanism.
ER  -

TY  - JOUR
AU  - Sekizaki, T.
AU  - Takamatsu, D.
AU  - Osaki, M.
AU  - Shimoji, Y.
TI  - Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome.
JO  - J. Bacteriol.
PY  - 2005
SP  - 872
EP  - 883
VL  - 187
AB  - Some strains of Streptococcus suis possess a type II restriction-modification (RM) system,
AB  - whose genes are thought to be
AB  - inserted into the genome between purH and purD from a foreign source by
AB  - illegitimate recombination. In this study, we characterized the purHD
AB  - locus of the S. suis genomes of 28 serotype reference strains by DNA
AB  - sequencing. Four strains contained the RM genes in the locus, as
AB  - described before, whereas 11 strains possessed other genetic regions of
AB  - seven classes. The genetic regions contained a single gene or multiple
AB  - genes that were either unknown or similar to hypothetical genes of
AB  - other bacteria. The mutually exclusive localization of the genetic
AB  - regions with the atypical G+C contents indicated that these regions
AB  - were also acquired from foreign sources. No transposable element or
AB  - long-repeat sequence was found in the neighboring regions. An alignment
AB  - of the nucleotide sequences, including the RM gene regions, suggested
AB  - that the foreign regions were integrated by illegitimate recombination
AB  - via short stretches of nucleotide identity. By using a thermosensitive
AB  - suicide plasmid, the RM genes were experimentally introduced into an S.
AB  - suis strain that did not contain any foreign genes in that locus.
AB  - Integration of the plasmid into the S. suis genome did not occur in the
AB  - purHD locus but occurred at various chromosomal loci, where there were
AB  - 2 to 10 bp of nucleotide identity between the chromosome and the
AB  - plasmid. These results suggest that various foreign genes described
AB  - here were incidentally integrated into the same locus of the S. suis
AB  - genome.
ER  -

TY  - JOUR
AU  - Sekizuka, T.
AU  - Kai, M.
AU  - Nakanaga, K.
AU  - Nakata, N.
AU  - Kazumi, Y.
AU  - Maeda, S.
AU  - Makino, M.
AU  - Hoshino, Y.
AU  - Kuroda, M.
TI  - Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism.
JO  - PLoS ONE
PY  - 2014
SP  - e114848
EP  - e114848
VL  - 9
AB  - Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and
AB  - M. bolletii, are an environmental organism found in soil, water and other ecological niches,
AB  - and have been isolated from respiratory tract infection, skin and soft tissue infection,
AB  - postoperative infection of cosmetic surgery. To determine the unique genetic feature of M.
AB  - massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300
AB  - (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium
AB  - spp. and among M. abscessus group subspp., showing that additional sz-oxidation-related genes
AB  - and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M.
AB  - massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic
AB  - respiration system-related genes and additional mycolic acid cyclopropane synthetase-related
AB  - genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also
AB  - frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions
AB  - (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as
AB  - isolates of other countries (Malaysia, France, United Kingdom and United States). The
AB  - well-conserved genomic island MmGI-1 may play an important role in high growth potential with
AB  - additional lipid metabolism, extra factors for survival in the environment or synthesis of
AB  - complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of
AB  - phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or
AB  - genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.
ER  -

TY  - JOUR
AU  - Sekizuka, T.
AU  - Kawanishi, M.
AU  - Ohnishi, M.
AU  - Shima, A.
AU  - Kato, K.
AU  - Yamashita, A.
AU  - Matsui, M.
AU  - Suzuki, S.
AU  - Kuroda, M.
TI  - Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids.
JO  - Sci. Rep.
PY  - 2017
SP  - 928
EP  - 928
VL  - 7
AB  - A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2
AB  - plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin
AB  - pilus. The shufflon is one of the most difficult regions for de novo genome assembly because
AB  - of its structural diversity even in an isolated bacterial clone. We determined complete genome
AB  - sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains
AB  - using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences
AB  - assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid
AB  - analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that
AB  - the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the
AB  - abundance ratio of whole-shufflon structures could be determined by quantitative structural
AB  - variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of
AB  - whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that
AB  - remarkable rearrangement regions should be validated using both long-read and short-read
AB  - sequencing data and that the structural variation of PilV in the shufflon might be closely
AB  - related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in
AB  - horizontal gene transfer even in bacterial clonal populations.
ER  -

TY  - JOUR
AU  - Sekizuka, T.
AU  - Lee, K.
AU  - Kuroda, M.
AU  - Kusumoto, M.
AU  - Iwata, T.
AU  - Uchida, I.
AU  - Tanaka, K.
AU  - Tamamura, Y.
AU  - Akiba, M.
TI  - Whole-Genome Sequence of CMY-2 beta-Lactamase-Producing Salmonella enterica Serovar Typhimurium Strain L-3553.
JO  - Genome Announcements
PY  - 2014
SP  - e00711
EP  - e00714
VL  - 2
AB  - Salmonella enterica serovar Typhimurium pulsed-field gel electrophoresis cluster  VII has been
AB  - isolated from cattle populations in Japan since the mid-2000s. Some
AB  - cluster VII isolates exhibited extended-spectrum cephalosporin resistance defined
AB  - by the blaCMY-2 gene located in a chromosomal genomic island, GI-VII-6. We
AB  - determined the whole-genome sequence of strain L-3553 as the reference strain.
ER  -

TY  - JOUR
AU  - Sekizuka, T.
AU  - Matsui, M.
AU  - Yamane, K.
AU  - Takeuchi, F.
AU  - Ohnishi, M.
AU  - Hishinuma, A.
AU  - Arakawa, Y.
AU  - Kuroda, M.
TI  - Complete sequencing of the blaNDM-1-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens.
JO  - PLoS ONE
PY  - 2011
SP  - e25334
EP  - e25334
VL  - 6
AB  - The complete sequence of the plasmid pNDM-1_Dok01 carrying New Delhi metallo-b-lactamase
AB  - (NDM-1) was determined
AB  - by whole genome shotgun sequencing using Escherichia coli strain NDM-1_Dok01 (multilocus
AB  - sequence typing type: ST38)
AB  - and the transconjugant E. coli DH10B. The plasmid is an IncA/C incompatibility type composed
AB  - of 225 predicted coding
AB  - sequences in 195.5 kb and partially shares a sequence with blaCMY-2-positive IncA/C plasmids
AB  - such as E. coli AR060302
AB  - pAR060302 (166.5 kb) and Salmonella enterica serovar Newport pSN254 (176.4 kb). The blaNDM-1
AB  - gene in pNDM-1_Dok01 is
AB  - terminally flanked by two IS903 elements that are distinct from those of the other
AB  - characterized NDM-1 plasmids,
AB  - suggesting that the blaNDM-1 gene has been broadly transposed, together with various mobile
AB  - elements, as a cassette gene.
AB  - The chaperonin groES and groEL genes were identified in the blaNDM-1-related composite
AB  - transposon, and phylogenetic
AB  - analysis and guanine-cytosine content (GC) percentage showed similarities to the homologs of
AB  - plant pathogens such as
AB  - Pseudoxanthomonas and Xanthomonas spp., implying that plant pathogens are the potential source
AB  - of the blaNDM-1 gene.
AB  - The complete sequence of pNDM-1_Dok01 suggests that the blaNDM-1 gene was acquired by a novel
AB  - composite transposon
AB  - on an extensively disseminated IncA/C plasmid and transferred to the E. coli ST38 isolate.
ER  -

TY  - JOUR
AU  - Sekizuka, T.
AU  - Yamamoto, A.
AU  - Komiya, T.
AU  - Kenri, T.
AU  - Takeuchi, F.
AU  - Shibayama, K.
AU  - Takahashi, M.
AU  - Kuroda, M.
AU  - Iwaki, M.
TI  - Corynebacterium ulcerans 0102 carries the gene encoding diphtheria toxin on a prophage different from the C. diphtheriae NCTC 13129 prophage.
JO  - BMC Microbiol.
PY  - 2012
SP  - 72
EP  - 72
VL  - 12
AB  - ABSTRACT: BACKGROUND: Corynebacterium ulcerans can cause a diphtheria-like
AB  - illness, especially when the bacterium is lysogenized with a tox gene-carrying
AB  - bacteriophage that produces diphtheria toxin. Acquisition of toxigenicity upon
AB  - phage lysogenization is a common feature of C. ulcerans and C. diphtheriae.
AB  - However, because of a lack of C. ulcerans genome information, a detailed
AB  - comparison of prophages has not been possible between these two clinically
AB  - important and closely related bacterial species. RESULTS: We determined the whole
AB  - genome sequence of the toxigenic C. ulcerans 0102 isolated in Japan.The genomic
AB  - sequence showed a striking similarity with that of Corynebacterium
AB  - pseudotuberculosis and, to a lesser extent, with that of C. diphtheriae. The 0102
AB  - genome contained three distinct prophages. One of these, PhiCULC0102-I, was a
AB  - tox-positive prophage containing genes in the same structural order as for
AB  - tox-positive C. diphtheriae prophages. However, the primary structures of the
AB  - individual genes involved in the phage machinery showed little homology between
AB  - the two counterparts. CONCLUSION: Taken together, these results suggest that the
AB  - tox-positive prophage in this strain of C. ulcerans has a distinct origin from
AB  - that of C. diphtheriae NCTC 13129.
ER  -

TY  - JOUR
AU  - Sektas, M.
AU  - Kaczorowski, T.
AU  - Podhajska, A.J.
TI  - Purification and properties of the MboII, a class-IIS restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 433
EP  - 438
VL  - 20
AB  - After five purification steps a homogeneous preparation of endonuclease MboII was obtained,
AB  - and several properties of the enzyme were determined. MboII is a monomer, with Mr under native
AB  - and denaturing conditions being 47 - 49,000 Da. Endonuclease MboII is a basic protein (pl 8.3)
AB  - which remains active when Mg2+ is replaced by Mn2+, Co2+, Ca2+, or Fe2+. MboII exhibits a star
AB  - activity in the presence of some of the following reagents or ions: DMSO, glycerol, ethanol
AB  - (and Co2+ or Mn2+ at pH 6). MboII does not bend DNA and is heat sensitive, losing activity
AB  - after 15 min at 50C.
ER  -

TY  - JOUR
AU  - Sektas, M.
AU  - Kaczorowski, T.
AU  - Podhajska, A.J.
TI  - Interaction of the MboII restriction endonuclease with DNA.
JO  - Gene
PY  - 1995
SP  - 181
EP  - 185
VL  - 157
AB  - The binding of the MboII restriction endonuclease (R.MboII; ENase) to DNA containing its
AB  - recognition site was investigated using a mobility shift assay.  R.MboII forms specific,
AB  - stable and immunodetectable complexes with its canonical target sequence.  The association
AB  - constant (a) of R.MboII was calculated to be 2.89 x 10/9M, and is about 10/4-fold higher than
AB  - the Ka value for non-specific binding.  Based on results obtained after sedimentation of the
AB  - R.MboII-DNA complex in a glycerol gradient and measurement of the retardation of the complexes
AB  - in polyacrylamide gels, we conclude that specific binding to the canonical sequence involves
AB  - a monomer of R.MboII.  DNase I footprinting has shown that the enzyme covers 16 nucleotides of
AB  - DNA on the 5'-GAAGA-3' strand.
ER  -

TY  - JOUR
AU  - Sela, D.A.
AU  - Chapman, J.
AU  - Adeuya, A.
AU  - Kim, J.H.
AU  - Chen, F.
AU  - Whitehead, T.R.
AU  - Lapidus, A.
AU  - Rokhsar, D.S.
AU  - Lebrilla, C.B.
AU  - German, J.B.
AU  - Price, N.P.
AU  - Richardson, P.M.
AU  - Mills, D.A.
TI  - The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 18964
EP  - 18969
VL  - 105
AB  - Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a
AB  - microbial consortium often dominated by bifidobacteria.
AB  - Accordingly, the complete genome sequence of Bifidobacterium longum subsp.
AB  - infantis ATCC15697 reflects a competitive nutrient-utilization strategy
AB  - targeting milk-borne molecules which lack a nutritive value to the
AB  - neonate. Several chromosomal loci reflect potential adaptation to the
AB  - infant host including a 43 kbp cluster encoding catabolic genes,
AB  - extracellular solute binding proteins and permeases predicted to be active
AB  - on milk oligosaccharides. An examination of in vivo metabolism has
AB  - detected the hallmarks of milk oligosaccharide utilization via the central
AB  - fermentative pathway using metabolomic and proteomic approaches. Finally,
AB  - conservation of gene clusters in multiple isolates corroborates the
AB  - genomic mechanism underlying milk utilization for this infant-associated
AB  - phylotype.
ER  -

TY  - JOUR
AU  - Selent, U.
AU  - Pingoud, A.
TI  - Altering the substrate specificity of the restriction endonuclease EcoRV.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S152
EP  - S152
VL  - 376
AB  - The type II restriction endonuclease EcoRV recognizes and cleaves the DNA sequence GAT/ATC. By
AB  - simultaneous exchange of several amino acids of the DNA recognition loop we want to generate
AB  - mutant enzymes that no longer cleave the cognate site but related ones, preferably those for
AB  - which at present no restriction enzyme is described or even commercially available. In our
AB  - approach, a large pool of EcoRV-mutants is generated by random mutagenesis and after an in
AB  - vivo selection, mutants with the desired specificity are selected.  At present, the work
AB  - concentrates on establishing a suitable screening system: a catalytically inactive EcoRV
AB  - mutant is used as a repressor for a toxic gene product, i.e. the restriction endonuclease
AB  - EcoRI.  Cells expressing EcoRI that are not protected by the corresponding methyltransferase
AB  - have a probability for survival that is 1:10^6.  An exchange of the operator sequence upstream
AB  - of the toxic gene, i.e. from GATATC to TATATA, should allow for a positive screening for
AB  - EcoRV-mutants that bind to the new sequence and thereby repress the expression of the toxic
AB  - gene.  In a subsequent step, the catalytic activity of the EcoRV mutant has to be restored by
AB  - site-directed mutagenesis.  Alternatively, we try to identify EcoRV mutants with altered
AB  - specificity directly.  For this purpose, an E. coli strain is used that induces the lac operon
AB  - upon DNA damage.  After UV irradiation or expression of a restriction enzyme in the absence of
AB  - the corresponding methylase, these cells grow to blue colonies on X-Gal agar plates. If the
AB  - cells are protected against cleavage at GATATC sites by the EcoRV methylase, the colonies are
AB  - white.  In contrast, EcoRV mutants with an altered specificity can cleave DNA in vivo even in
AB  - the presence of the methylase, and cells expressing such a variant will give blue colonies on
AB  - X-Gal agar.
ER  -

TY  - JOUR
AU  - Selent, U.
AU  - Ruter, T.
AU  - Kohler, E.
AU  - Liedtke, M.
AU  - Thielking, V.
AU  - Alves, J.
AU  - Oelgeschlager, T.
AU  - Wolfes, H.
AU  - Peters, F.
AU  - Pingoud, A.
TI  - A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV.
JO  - Biochemistry
PY  - 1992
SP  - 4808
EP  - 4815
VL  - 31
AB  - We have used site-directed mutagenesis of the EcoRV restriction endonuclease to change amino
AB  - acid side chains that have been shown crystallographically to be in close proximity to the
AB  - scissile phosphodiester bond of the DNA substrate. DNA cleavage assays of the resulting mutant
AB  - proteins indicate that the larges effects on nucleolytic activity result from substitution of
AB  - Asp74, Asp90, and Lys92. We suggest on the basis of structural information, mutagenesis data,
AB  - and analogies with other nucleases that Asp74 and Asp90 might be involved in Mg2+ binding
AB  - and/or catalysis and that Lys92 probably stabilizes the pentacovalent phosphorus in the
AB  - transition state. These amino acids are part of a sequence motif, Pro-Asp...Asp/Glu-X-Lys,
AB  - which is also present in EcoRI. In both enzymes, it is located in a structurally similar
AB  - context near the scissile phosphodiester bond. A preliminary mutational analysis with EcoRI
AB  - indicates that this sequence motif is of similar functional importance for EcoRI and EcoRV. On
AB  - the basis of these results, a proposal is made for the mechanism of DNA cleavage by EcoRV and
AB  - EcoRI.
ER  -

TY  - JOUR
AU  - Seligman, L.M.
AU  - Chisholm, K.M.
AU  - Chevalier, B.S.
AU  - Chadsey, M.S.
AU  - Edwards, S.T.
AU  - Savage, J.H.
AU  - Veillet, A.L.
TI  - Mutations altering the cleavage specificity of a homing endonuclease.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3870
EP  - 3879
VL  - 30
AB  - The homing endonuclease I-CreI recognizes and cleaves a particular 22 bp DNA sequence. The
AB  - crystal structure of I-CreI bound to homing site DNA has previously been determined, leading
AB  - to a number of predictions about specific protein-DNA contacts. We test these predictions by
AB  - analyzing a set of endonuclease mutants and a complementary set of homing site mutants. We
AB  - find evidence that all structurally predicted I-CreI/DNA contacts contribute to DNA
AB  - recognition and show that these contacts differ greatly in terms of their relative importance.
AB  - We also describe the isolation of a collection of altered specificity I-CreI derivatives. The
AB  - in vitro DNA-binding and cleavage properties of two such endonucleases demonstrate that our
AB  - genetic approach is effective in identifying homing endonucleases that recognize and cleave
AB  - novel target sequences.
ER  -

TY  - JOUR
AU  - Selker, E.U.
AU  - Cambareri, E.B.
AU  - Garrett, P.W.
AU  - Haack, K.R.
AU  - Jensen, B.C.
AU  - Shabtach, E.
TI  - DNA methylation and control of genome organization in Neurospora crassa.
JO  - Gene
PY  - 1988
SP  - 109
EP  - 111
VL  - 74
AB  - Why are 5S rRNA genes dispersed in the genome of Neurospora, instead of tandemly arranged as
AB  - in most organisms? A likely answer to this question came from studying an exceptional pair of
AB  - adjacent Neurospora 5S genes, or pseudogenes, designated zeta and eta. The zeta-eta region
AB  - consists of a diverged direct tandem duplication of a 0.8-kb segment including a 5S rRNA gene.
AB  - Sequence comparisons of the zeta and eta 5S rRNA regions with each other and with other 5S
AB  - regions suggested that the approx. 15% divergence between the zeta and eta 'duplicate'
AB  - segments resulted exclusively from CG to TA mutations. Unlike other 5S rRNA regions examined,
AB  - the zeta-eta region is heavily methylated. Thus it seemed likely that these transition
AB  - mutations arose by deamination of mC residues. In the course of exploring the basis for the
AB  - extraordinarily heavy methylation in the zeta-eta region, we discovered a novel genetic
AB  - process that accounts for the methylation and provides a probable explanation for why 5S rRNA
AB  - genes are generally dispersed in Neurospora.
ER  -

TY  - JOUR
AU  - Selker, E.U.
AU  - Freitag, M.
AU  - Kothe, G.O.
AU  - Margolin, B.S.
AU  - Rountree, M.R.
AU  - Allis, C.D.
AU  - Tamaru, H.
TI  - Induction and maintenance of nonsymmetrical DNA methylation in Neurospora.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 16485
EP  - 16490
VL  - 99
AB  - One can imagine a variety of mechanisms that should result in self-perpetuating biological
AB  - states. It is generally assumed that cytosine methylation is propagated in eukaryotes by
AB  - enzymes that specifically methylate hemimethylated symmetrical sites (e.g., (5')CpG/GpC(5')
AB  - or (5')CpNpG/GpNpC(5')). Although there is wide support for this model, we and others have
AB  - found examples of methylation that must be propagated by a different mechanism. Most
AB  - methylated regions of the Neurospora genome that have been examined are products of
AB  - repeat-induced point mutation, a premeiotic genome defense system that litters duplicated
AB  - sequences with C.G to T.A mutations and typically leaves them methylated at remaining
AB  - cytosines. In general, such relics of repeat-induced point mutation are capable of triggering
AB  - methylation de novo. Nevertheless, some reflect a mechanism that can propagate heterogeneous
AB  - methylation at nonsymmetrical sites. We propose that de novo and maintenance methylation are
AB  - manifestations of a single mechanism in Neurospora, catalyzed by the DIM-2 DNA
AB  - methyltransferase. The action of DIM-2 is controlled by the DIM-5 histone H3 Lys-9
AB  - methyltransferase, which in turn is influenced by other modifications of histone H3. DNA
AB  - methylation indirectly recruits histone deacetylases, providing the framework of a
AB  - self-reinforcing system that could result in propagation of DNA methylation and the associated
AB  - silenced chromatin state.
ER  -

TY  - JOUR
AU  - Selker, E.U.
AU  - Fritz, D.Y.
AU  - Singer, M.J.
TI  - Dense nonsymmetrical DNA methylation resulting from repeat-induced point mutation in Neurospora.
JO  - Science
PY  - 1993
SP  - 1724
EP  - 1728
VL  - 262
AB  - Cytosine methylation has been implicated in epigenetic control of gene expression in animals,
AB  - plants and fungi. It has been assumed that all methylation in eukaryotes is at symmetrical
AB  - sequences such as CpG/GpC, because this can explain perpetuation of methylation states. Here
AB  - the bisulfite genomic sequencing method was used to examine methylation in DNA from a
AB  - Neurospora gene exposed to repeat-induced point mutation. 5-Methylcytosine was not limited to
AB  - symmetrical sites and individual molecules showed different patterns and amounts of
AB  - modification. The methylation extended beyond the mutated region and even beyond the edge of
AB  - the duplicated segment.
ER  -

TY  - JOUR
AU  - Selker, E.U.
AU  - Tountas, N.A.
AU  - Cross, S.H.
AU  - Margolin, B.S.
AU  - Murphy, J.G.
AU  - Bird, A.P.
AU  - Freitag, M.
TI  - The methylated component of the Neurospora crassa genome.
JO  - Nature
PY  - 2003
SP  - 893
EP  - 897
VL  - 422
AB  - Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals and the fungus
AB  - Neurospora crassa have about 2-3% of cytosines methylated.
AB  - In mammals, methylation is almost exclusively in the under-represented CpG
AB  - dinucleotides, and most CpGs are methylated whereas in Neurospora,
AB  - methylation is not preferentially in CpG dinucleotides and the bulk of the
AB  - genome is unmethylated. DNA methylation is essential in mammals but is
AB  - dispensable in Neurospora, making this simple eukaryote a favoured
AB  - organism in which to study methylation. Recent studies indicate that DNA
AB  - methylation in Neurospora depends on one DNA methyltransferase, DIM-2
AB  - (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but
AB  - little is known about its cellular and evolutionary functions. As only
AB  - four methylated sequences have been reported previously in N. crassa, we
AB  - used methyl-binding-domain agarose chromatography to isolate the
AB  - methylated component of the genome. DNA sequence analysis shows that the
AB  - methylated component of the genome consists almost exclusively of relics
AB  - of transposons that were subject to repeat-induced point mutation--a
AB  - genome defence system that mutates duplicated sequences.
ER  -

TY  - JOUR
AU  - Sellem, C.H.
AU  - Belcour, L.
TI  - Intron open reading frames as mobile elements and evolution of a group I intron.
JO  - Mol. Biol. Evol.
PY  - 1997
SP  - 518
EP  - 526
VL  - 14
AB  - Group I introns are proposed to have become mobile following the acquisition of open reading
AB  - frames (ORFs) that encode highly specific DNA endonucleases. This proposal implies that intron
AB  - ORFs could behave as autonomously mobile entities. This was supported by abundant
AB  - circumstantial evidence but no experiment of ORF transfer from an ORF-containing intron to its
AB  - ORF-less counterpart has been described. In this paper we present such experiments, which
AB  - demonstrate the efficient mobility of the mitochondrial nad1-i4-orf1 between two Podospora
AB  - strains. The homing of this mobile ORF was accompanied by a bidirectional co-conversion that
AB  - did not systematically involve the whole intron sequence. Orf1 acquisition would be the most
AB  - recent step in the evolution of the nad1-i4 intron, which has resulted in many strains of
AB  - Podospora having an intron with two ORFs (biorfic) and four splicing pathways. We show that
AB  - two of the splicing events that operate in this biorfic intron, as evidenced by PCR
AB  - experiments, are generated by a 5'-alternative splice site, which is most probably a remnant
AB  - of the monoorfic ancestral form of the intron. We propose a sequential evolution model that is
AB  - consistent with the four organizations of the corresponding nad1 locus that we found among
AB  - various species of the Pyrenomycete family; these organizations consist of no intron, an
AB  - intron alone, a monoorfic intron, and a biorfic intron.
ER  -

TY  - JOUR
AU  - Sellmann, E.
AU  - Knoblich, I.-M.
AU  - Kaluza, K.
AU  - Frey, B.
AU  - Schmitz, G.G.
AU  - Westermann, P.
TI  - Bsp423I, a novel isoschizomer of BbvI from Bacillus recognizing 5'-GCAGC-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2377
EP  - 2377
VL  - 20
AB  - We have isolated Bsp423I, a novel class-II restriction endonuclease from Bacillus species
AB  - recognizing the palindromic sequence 5'-GCAGC-3' generating 5'-protruding tetranucleotides
AB  - within the sequence complementary to 5'-GCAGC(N)8-3'. With respect to its isoschizomer BbvI
AB  - it can be isolated in higher purity and stability. From the mapping and sequencing data the
AB  - specificity of Bsp423I is concluded as: 5'-GCAGC(N)8/-3' 3'-CGTCG(N)12/-5'.
ER  -

TY  - JOUR
AU  - Selvakumar, K.S.
AU  - Shanmugasundaram, S.
TI  - Studies on DNA modification in Oscillatoria sp. MKU 178.
JO  - Curr. Sci.
PY  - 1993
SP  - 49
EP  - 50
VL  - 64
AB  - Cyanobacterial DNA are generally believed to be resistant to restriction by endonucleases due
AB  - to extensive modification of the DNA. We report here the absence of a dam-mediated
AB  - modification in a cyanobacterium, Oscillatoria sp. MKU 178.
ER  -

TY  - JOUR
AU  - Selvaraj, S.
AU  - Kono, H.
AU  - Sarai, A.
TI  - Specificity of Protein-DNA Recognition Revealed by Structure-based Potentials: Symmetric/Asymmetric and Cognate/Non-cognate Binding.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 907
EP  - 907
VL  - 322
AB  - Asymmetric binding of protein homodimers to DNA, which has been observed in a number of
AB  - protein-DNA complexes, leads to subtle structural differences between the two subunits. Such
AB  - structural differences are frequently observed when the subunits form cognate and non-cognate
AB  - protein-DNA complexes, respectively. Analysis of these structural effects on binding
AB  - specificity should provide insight into the mechanism of protein-DNA recognition. We
AB  - previously derived empirical potential functions for specific nucleotide base-amino acid
AB  - interactions from statistical analyses of the structures of many protein-DNA complexes and
AB  - used a combinatorial threading procedure to evaluate the fitness of the DNA sequences
AB  - involved. We then introduced Z-scores to measure the specificity with which proteins bind to
AB  - DNA within complexes, as compared to random DNA sequences. Here, we examined in detail the
AB  - structural effects of asymmetric and cognate/non-cognate binding on specificity. Marked
AB  - differences in the specificity of DNA binding were observed for the two subunits of lambda
AB  - repressor, the glucocorticoid receptor, and for transcription factors containing a Zn(2)Cys(6)
AB  - binuclear cluster domain, which are known to bind asymmetrically to DNA. Moreover, the
AB  - differences in the specificity with which BamHI and EcoRV endonucleases bind to their cognate
AB  - and non-cognate DNA sequences were clearly detected using this approach; indeed, analysis of
AB  - EcoRV binding enabled us to show the cooperative effect of sequence and structure on binding
AB  - specificity. The present results demonstrate the utility of this approach when examining the
AB  - structure-specificity relationship in protein-DNA recognition, as subtle structural
AB  - differences in symmetric/asymmetric and cognate/non-cognate binding were clearly shown to
AB  - cause marked differences in specificity. This method can also be used as a tool for checking
AB  - new structures of protein-DNA complexes for their specificity.
ER  -

TY  - JOUR
AU  - Semenova, E.
AU  - Minakhin, L.
AU  - Bogdanova, E.
AU  - Nagornykh, M.
AU  - Vasilov, A.
AU  - Heyduk, T.
AU  - Solonin, A.
AU  - Zakharova, M.
AU  - Severinov, K.
TI  - Transcription regulation of the EcoRV restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 6942
EP  - 6951
VL  - 33
AB  - When a plasmid containing restriction-modification (R-M) genes enters a naive host, unmodified
AB  - host DNA can be destroyed by restriction endonuclease. Therefore, expression of R-M genes must
AB  - be regulated to ensure that enough methyltransferase is produced and that host DNA is
AB  - methylated before the endonuclease synthesis begins. In several R-M systems, specialized
AB  - Control (C) proteins coordinate expression of the R and the M genes. C proteins bind to DNA
AB  - sequences called C-boxes and activate expression of their cognate R genes and inhibit the M
AB  - gene expression, however the mechanisms remain undefined. Here, we studied the regulation of
AB  - gene expression in the C protein-dependent EcoRV system. We map the divergent EcoRV M and R
AB  - gene promoters and we define the site of C protein-binding that is sufficient for activation
AB  - of the EcoRV R transcription.
ER  -

TY  - JOUR
AU  - Semmler, T.
AU  - Eichhorn, I.
AU  - Bethe, A.
AU  - Bauerfeind, R.
AU  - Pickard, D.
AU  - Kingsley, R.A.
AU  - Dougan, G.
AU  - Wieler, L.H.
TI  - Genome Sequence of Porcine Escherichia coli Strain IMT8073, an Atypical Enteropathogenic E. coli Strain Isolated from a Piglet with Diarrhea.
JO  - Genome Announcements
PY  - 2013
SP  - e00573
EP  - e00513
VL  - 1
AB  - Escherichia coli is a highly diverse bacterial species, with atypical enteropathogenic E. coli
AB  - (aEPEC) causing intestinal disease in both human and
AB  - animal hosts. Here, we report the first complete genome sequence of an aEPEC
AB  - strain of sequence type ST794 and serotype Ont:H7, isolated from a diseased
AB  - piglet.
ER  -

TY  - JOUR
AU  - Sen, A. et al.
TI  - Draft Genome Sequence of Frankia sp. Strain QA3, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodule of Alnus nitida.
JO  - Genome Announcements
PY  - 2013
SP  - e0010313
EP  - e0010313
VL  - 1
AB  - Members of the actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different
AB  - families of actinorhizal plants. We report a high-quality draft genome
AB  - sequence for Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated
AB  - from root nodules of Alnus nitida.
ER  -

TY  - JOUR
AU  - Sen, D.
AU  - Brown, C.J.
AU  - Top, E.M.
AU  - Sullivan, J.
TI  - Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees.
JO  - Mol. Biol. Evol.
PY  - 2012
SP  - 154
EP  - 166
VL  - 30
AB  - Plasmids of the incompatibility group IncP-1 can transfer and replicate in many
AB  - genera of the Proteobacteria. They are composed of backbone genes that encode a
AB  - variety of essential functions as well as accessory genes that have implications
AB  - for human health and environmental remediation. While it is well understood that
AB  - the accessory genes are transferred horizontally between plasmids, recent studies
AB  - have also provided examples of recombination in the backbone genes of IncP-1
AB  - plasmids. As a consequence, phylogeny estimation based on backbone genes is
AB  - expected to produce conflicting gene tree topologies. The main goal of this study
AB  - was therefore to infer the evolutionary history of IncP-1 plasmids in the
AB  - presence of both vertical and horizontal gene transfer. This was achieved by
AB  - quantifying the incongruence among gene trees and attributing it to known causes
AB  - such as, a) phylogenetic uncertainty, b) coalescent stochasticity, and c)
AB  - horizontal inheritance. Topologies of gene trees exhibited more incongruence than
AB  - could be attributed to phylogenetic uncertainty alone. Species-tree estimation
AB  - using a Bayesian framework that takes coalescent stochasticity into account was
AB  - well supported, but it differed slightly from the maximum likelihood tree
AB  - estimated by concatenation of backbone genes. After removal of the gene that
AB  - demonstrated a signal of intergroup recombination, the concatenated tree was
AB  - congruent with the species-tree estimate, which itself was robust to
AB  - inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene
AB  - exchange both within and among IncP-1 subgroups, the backbone genome of these
AB  - IncP-1 plasmids retains a detectable vertical evolutionary history.
ER  -

TY  - JOUR
AU  - Sen, D.
AU  - Chandrababunaidu, M.M.
AU  - Singh, D.
AU  - Sanghi, N.
AU  - Ghorai, A.
AU  - Mishra, G.P.
AU  - Madduluri, M.
AU  - Adhikary, S.P.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India.
JO  - Genome Announcements
PY  - 2015
SP  - e00009
EP  - e00015
VL  - 3
AB  - We report here the draft genome sequence of Scytonema millei VB511283, a cyanobacterium
AB  - isolated from biofilms on the exterior of stone monuments in
AB  - Santiniketan, eastern India. The draft genome is 11,627,246 bp long (11.63 Mb),
AB  - with 118 scaffolds. About 9,011 protein-coding genes, 117 tRNAs, and 12 rRNAs are
AB  - predicted from this assembly.
ER  -

TY  - JOUR
AU  - Sen, D.
AU  - Van der Auwera, G.A.
AU  - Rogers, L.M.
AU  - Thomas, C.M.
AU  - Brown, C.J.
AU  - Top, E.M.
TI  - Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 7975
EP  - 7983
VL  - 77
AB  - Broad-host-range plasmids are known to spread genes between distinct phylogenetic
AB  - groups of bacteria. These genes often code for resistances to antibiotics and
AB  - heavy metals or degradation of pollutants. Although some broad-host-range
AB  - plasmids have been extensively studied, their evolutionary history and genetic
AB  - diversity remain largely unknown. The goal of this study was to analyze and
AB  - compare the genomes of 12 broad-host-range plasmids that were previously isolated
AB  - from Norwegian soils by exogenous plasmid isolation and that encode mercury
AB  - resistance. Complete nucleotide sequencing followed by phylogenetic analyses
AB  - based on the relaxase gene traI showed that all the plasmids belong to one of two
AB  - subgroups (beta and epsilon) of the well-studied incompatibility group IncP-1. A
AB  - diverse array of accessory genes was found to be involved in resistance to
AB  - antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of
AB  - herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic
AB  - acid), and a putative new catabolic pathway. Intramolecular transposition of
AB  - insertion sequences followed by deletion was found to contribute to the diversity
AB  - of some of these plasmids. The previous observation that the insertion sites of a
AB  - Tn501-related element are identical in four IncP-1beta plasmids (pJP4, pB10,
AB  - R906, and R772) was further extended to three more IncP-1beta plasmids (pAKD15,
AB  - pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these
AB  - Tn501-bearing IncP-1beta plasmids that predicts recent diversification followed
AB  - by worldwide spread. Our study increases the available collection of complete
AB  - IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our
AB  - understanding of the evolution and function of this important plasmid family.
ER  -

TY  - JOUR
AU  - Sen, S.
AU  - Nilsson, L.
TI  - Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex.
JO  - Biophys. J.
PY  - 1999
SP  - 1801
EP  - 1810
VL  - 77
AB  - Molecular dynamics simulations and free energy calculations of the wild-type EcoRI-DNA complex
AB  - and several variants have been performed in aqueous solvent. In general, the theoretical
AB  - estimations of the free energy differences (DeltaDeltaA) qualitatively agree well with the
AB  - corresponding experimental data. The modifications which were experimentally found unfavorable
AB  - compared to the wild-type complex were also found to be so in theoretical estimates. The
AB  - mutant where the amino group of the base Ade(6) was replaced by a hydrogen atom eliminating
AB  - one H-bond between the DNA and the protein, was experimentally found to be more stable than
AB  - the wild-type complex. It was speculated that the modification also caused a structural
AB  - relaxation in the DNA making DeltaDeltaA favorable. Our theoretical estimate yields a positive
AB  - DeltaDeltaA in this case, but the difference is small, and no significant local structural
AB  - relaxation was observed. The major H-bonds between the DNA and the protein in the wild-type
AB  - complex are found to be maintained in the different mutants although the specific and
AB  - non-specific interaction energies between the interacting the DNA bases and the protein
AB  - residues are different in different mutants. The interaction pattern of the other nearby
AB  - nucleotides are significantly influenced by each modification. Thus, the alteration of the
AB  - non-specific interactions may also play an indirect role in determining the specificity of the
AB  - complex. The interaction of the Gua(4) of the DNA with the protein is found to be most
AB  - sensitive to any alteration in the recognition site. Because Gua(4) is the nucleotide closest
AB  - to the scissile bond, this extra sensitivity seems to play an important role in altering the
AB  - functional activity of the complex.
ER  -

TY  - JOUR
AU  - Sen, S.
AU  - Nilsson, L.
TI  - Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.
JO  - Biophys. J.
PY  - 1999
SP  - 1782
EP  - 1800
VL  - 77
AB  - A 0.7-ns molecular dynamics simulation of the DNA-EcoRI complex in a 7.0-A solvent shell
AB  - indicated a stable behavior of the system. No significant evaporation or smearing of the
AB  - solvent's outer boundary occurred. The structure and the intermolecular interactions were
AB  - found to be well maintained during the simulation. The interaction pattern in the simulation
AB  - was found to be very similar to that in the crystal structure. Most of the specific
AB  - interactions between the DNA and the protein were found to be enhanced in the simulation
AB  - compared to that in the crystal structure as a result of improved interaction geometry. The
AB  - nonspecific interactions were found to be stronger than the specific ones. The specific
AB  - interactions between the N7 atoms of Gua(4) or Ade(5) or Ade(6) and the protein were found to
AB  - be present over almost the entire time of the simulation, whereas hydrogen bonds involving the
AB  - amino groups of the Ade(5) and Ade(6) with the protein were found to be relatively weaker,
AB  - with lower probability and shorter lifetime. The time evolution of the root mean square
AB  - deviations of the DNA and the protein were highly correlated even at the later part of the
AB  - simulation, showing the tight binding between them. Several long-lived water bridges were
AB  - found between the DNA backbone atoms and the protein and also between the two protein
AB  - monomers, which increased the overall stability of the complex. The two protein monomers were
AB  - found to interact strongly with each other. The energy of the DNA kink deformation was
AB  - estimated as approximately 31 kcal/mol.
ER  -

TY  - JOUR
AU  - Sen, U.
AU  - Mukherjee, T.
AU  - Bose, S.
AU  - Roy, C.
AU  - Rameez, M.J.
AU  - Ghosh, W.
AU  - Mukhopadhyay, S.K.
TI  - Genome Sequence of the Arsenic-Resistant Haladaptatus sp. Strain R4 Isolated from Ramnagar, West Bengal, India.
JO  - Genome Announcements
PY  - 2016
SP  - e01017
EP  - e01016
VL  - 4
AB  - Here, we present the draft genome of Haladaptatus sp. strain R4, a halophilic archaea that
AB  - produces an orange-pink pigment and is capable of growing in a wide
AB  - salinity range. The genome assembly shows genes for arsenic resistance,
AB  - siderophore production, trehalose and glycine betaine biosynthesis, uptake and
AB  - transporters of sodium, potassium, and chloride ions.
ER  -

TY  - JOUR
AU  - Senejani, A.G.
AU  - Gogarten, J.P.
TI  - Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein.
JO  - Int. J. Biol. Sci.
PY  - 2007
SP  - 205
EP  - 211
VL  - 3
AB  - Homing endonucleases are site-specific and rare cutting endonucleases often encoded by intron
AB  - or intein containing genes. They lead to the
AB  - rapid spread of the genetic element that hosts them by a process termed
AB  - 'homing'; and ultimately the allele containing the element will be
AB  - fixed in the population.
AB  - PI-SceI, an endonuclease encoded as a protein insert or intein
AB  - within the yeast V-ATPase catalytic subunit encoding gene (vma1), is
AB  - among the best characterized homing endonucleases. The structures of
AB  - the Sce VMA1 intein and of the intein bound to its target site are
AB  - known. Extensive biochemical studies performed on the PI-SceI enzyme
AB  - provide information useful to recognize critical amino acids involved
AB  - in self-splicing and endonuclease functions of the protein. Here we
AB  - describe an insertion of the Green Fluorescence Protein (GFP) into a
AB  - loop which is located between the endonuclease and splicing domains of
AB  - the Sce VMA1 intein. The GFP is functional and the additional GFP
AB  - domain does not prevent intein excision and endonuclease activity.
AB  - However, the endonuclease activity of the newly engineered protein was
AB  - different from the wild-type protein in that it required the presence
AB  - of Mn2+ and not Mg2+ metal cations for activity.
ER  -

TY  - JOUR
AU  - Senesac, J.H.
AU  - Allen, J.R.
TI  - Oligonucleotide activation of the type IIe restriction enzyme NaeI for digestion of refractory sites.
JO  - Biotechniques
PY  - 1995
SP  - 990
EP  - 993
VL  - 19
AB  - Certain restriction endonucleases previously shown to exhibit DNA site preferences have a
AB  - two-site DNA cleavage mechanism.  These type IIe restriction endonucleases include NaeI, NarI,
AB  - EcoRII, HpaII and SacII.  Because of this two-site mechanism, it is often difficult or
AB  - impossible to achieve complete digestion of DNA subsrtrate.  Inasmuch as these enzymes are
AB  - commonly used in molecular biology, a method for enzyme activation to provide complete DNA
AB  - digestion is useful.  We have commercialized such a method for NaeI using a double-stranded
AB  - oligonucleotide containing a modified NaeI recognition sequence.  Cleavage of resistant sites
AB  - requires the presence of a DNA sequence that is more cleavable to bind the activator site.
AB  - The regions flanking the recognition site on our NaeI oligonucleotide cause it to serve as
AB  - this more cleavable sequence.  This activates the enzyme to cleave the resistant sequence in
AB  - the catalytic site, while the oligonucleotide modification does not allow the activator to be
AB  - depleted during the reaction.  Turbo NaeI provides for rapid digestion of sites previously
AB  - found difficult or impossible to completely cleave and does not interfere with subsequent
AB  - molecular biology techniques that might be performed downstream on the substrate DNA, such as
AB  - ligation, end-labeling or nick translation.
ER  -

TY  - JOUR
AU  - Senesac, J.H.
AU  - Romanin, J.K.
TI  - Application of oligonucleotide activation to restriction endonuclease NarI.
JO  - Biotechniques
PY  - 1997
SP  - 1166
EP  - 1168
VL  - 22
AB  - Restriction endonuclease NarI cleaves DNA using a two-site mechanism, placing it in the type
AB  - IIe class of restriction endonucleases.  Although these enzymes have very useful recognition
AB  - sequences, the two-site mechanism limits the practical application.  Site preferences often
AB  - cause incomplete substrate digestion.  Oligonucleotide activation of NarI eliminates
AB  - incomplete digestions, making it possible to use NarI restriction sites in many common
AB  - molecular biology techniques.  A modified oligonucleotide was chosen for optimal activation of
AB  - restriction endonuclease NarI.  This oligonucleotide was demonstrated to allow complete
AB  - digestion in many commonly used substrates.
ER  -

TY  - JOUR
AU  - Sengupta, S.
AU  - Pramanik, A.
AU  - Basak, P.
AU  - Bhattacharyya, M.
TI  - Draft Genome Sequence of Bioactive Strain Streptomyces sp. SMS_SU21, Isolated from Soil Sediment of the Sundarbans Mangrove Ecosystem.
JO  - Genome Announcements
PY  - 2018
SP  - e00614
EP  - e00618
VL  - 6
AB  - Streptomyces sp. SMS_SU21 possesses strong antimicrobial activity and antioxidant potential.
AB  - This strain was isolated from the Sundarbans mangrove ecosystem, and
AB  - its draft genome comprises 7,449,420 bp with 6,680 open reading frames. Genome
AB  - analysis of strain SMS_SU21 provides insight into its secondary metabolite
AB  - arsenal and reveals the gene clusters putatively responsible for its bioactive
AB  - potential.
ER  -

TY  - JOUR
AU  - Seni, J.
AU  - Mshana, S.E.
AU  - Msigwa, F.
AU  - Matee, M.
AU  - Mazigo, H.
AU  - Parkhill, J.
AU  - Holmes, M.A.
AU  - Paterson, G.K.
TI  - Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.
JO  - Genome Announcements
PY  - 2016
SP  - e01345
EP  - e01316
VL  - 4
AB  - We report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected
AB  - in Tanzania from a swab of healthy bovine perineum. The draft
AB  - genome sequence contained 2.72 Mbp and 2,750 coding sequences with a G+C content
AB  - of 31.7%.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - Abdad, M.Y.
AU  - Robert, C.
AU  - Stenos, J.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia gravesii, Isolated from Western Australian Ticks.
JO  - Genome Announcements
PY  - 2013
SP  - e00975
EP  - e00913
VL  - 1
AB  - Rickettsia gravesii is a new Rickettsia species closely related to the human pathogen
AB  - Rickettsia massiliae. Here, we describe the genome sequence of R.
AB  - gravesii strain BWI-1, isolated from Amblyomma triguttatum triguttatum ticks
AB  - collected from humans on Barrow Island, Western Australia.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Michelle, C.
AU  - Caputo, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia tamurae, a Recently Detected Human Pathogen in Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e00838
EP  - e00814
VL  - 2
AB  - Rickettsia tamurae is a member of the spotted fever group rickettsiae, which was  reported in
AB  - 2011 to cause human infections in Japan. We report the draft genome
AB  - sequence of R. tamurae strain AT-1(T), isolated from Amblyomma testudinarium
AB  - ticks.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Michelle, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Draft Genome Sequence of Rickettsia aeschlimannii, Associated with Hyalomma marginatum Ticks.
JO  - Genome Announcements
PY  - 2014
SP  - e00666
EP  - e00614
VL  - 2
AB  - Rickettsia aeschlimannii is a tick-associated human pathogen. We report here the  draft genome
AB  - of R. aeschlimannii strain MC16, isolated from Hyalomma marginatum
AB  - marginatum ticks collected in Morocco.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Nguyen, T.T.
AU  - Caputo, A.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01171
EP  - e01114
VL  - 2
AB  - Rickettsia hoogstraalii is a tick-associated member of the spotted fever group rickettsiae
AB  - that is geographically widely distributed. We report here the draft
AB  - genome of R. hoogstraalii strain Croatica(T) (=DSM 22243 = UTMB 00003), which was
AB  - isolated from Haemaphysalis sulcata ticks collected in Croatia.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia conorii subsp. caspia, the Agent of Astrakhan Fever.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4763
EP  - 4764
VL  - 194
AB  - Rickettsia conorii subsp. caspia is the agent of Astrakhan fever, a spotted fever group
AB  - rickettsiosis endemic to Astrakhan, Russia. The present study reports the
AB  - draft genome of Rickettsia conorii subsp. caspia strain A-167.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia conorii subsp. indica, the Agent of Indian Tick Typhus.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3288
EP  - 3289
VL  - 194
AB  - Rickettsia conorii subsp. indica is the agent of Indian tick typhus. The present  study
AB  - reports the draft genome of Rickettsia conorii subsp. indica strain ITTR
AB  - (ATCC VR-597).
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of Rickettsia conorii subsp. israelensis, the Agent of Israeli Spotted Fever.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5130
EP  - 5131
VL  - 194
AB  - Rickettsia conorii subsp. israelensis is the agent of Israeli spotted fever. The  present
AB  - study reports the draft genome of Rickettsia conorii subsp. israelensis
AB  - strain ISTT CDC1, isolated from a Rhipicephalus sanguineus tick collected in
AB  - Israel.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Sequence and Annotation of Rickettsia sibirica sibirica Genome.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2377
EP  - 2377
VL  - 194
AB  - Rickettsia sibirica sibirica is the causative agent of Siberian or North Asian tick typhus, a
AB  - tick-borne rickettsiosis known to exist in Siberia and eastern
AB  - China. Here we present the draft genome of Rickettsia sibirica sibirica strain
AB  - BJ-90 isolated from Dermacentor sinicus ticks collected in Beijing, China.
ER  -

TY  - JOUR
AU  - Sentausa, E.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genome Sequence of 'Rickettsia sibirica subsp. mongolitimonae'.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2389
EP  - 2390
VL  - 194
AB  - 'Rickettsia sibirica subsp. mongolitimonae' is the agent of lymphangitis-associated
AB  - rickettsiosis, an emerging human disease that has been
AB  - diagnosed in Europe and Africa. The present study reports the draft genome of
AB  - Rickettsia sibirica subsp. mongolitimonae strain HA-91.
ER  -

TY  - JOUR
AU  - Sentis, C.
AU  - Santos, J.
AU  - Fernandez-Piqueras, J.
TI  - In situ methylation of insect chromosomes with methylase HpaII.
JO  - Chromosoma
PY  - 1989
SP  - 105
EP  - 108
VL  - 98
AB  - A method of in situ DNA methylation with the prokaryotic methylase HpaII has
AB  - been developed on fixed mitotic and meiotic chromosomes of the insect species
AB  - Baetica ustulata.  Incorporation of methyl groups into the chromosomal DNA is
AB  - revealed by autoradiography using a laelled substrate and by its ability to
AB  - prevent endonuclease digestion.  The method allows direct visualization of
AB  - clusters of methylatable CCGG sites.  The distribution of these clusters in the
AB  - chromosome complement of Baetica shows two separate domains of heterochromatic
AB  - DNA which differ in their methylation patterns.  Each is distributed at
AB  - equivalent locations in both homologus and nonhomologus chromosomes.  The
AB  - existence of two compartments, one methylated and the other unmethylated, in
AB  - the heterochromatic DNA could be interpreted as a remnant of the ancestral
AB  - echinoderm-like pattern of methylation.
ER  -

TY  - JOUR
AU  - Seo, J.H.
AU  - Cho, Y.D.
TI  - Studies on the role of arginyl residue in EcoRI methylase.
JO  - Korean Biochem. J.
PY  - 1992
SP  - 54
EP  - 59
VL  - 25
AB  - Treatment of EcoRI methylase with phenylglyoxal resulted in time and concentration dependent
AB  - enzyme inactivation. The reaction followed pseudo first-order kinetics until 90 to 95% of the
AB  - enzyme had been inactivated, and prolonged incubation with phenylglyoxal resulted in complete
AB  - inactivation. Second order rate constant (K) for the inactivation of EcoRI methylase by
AB  - phenylglyoxal was 666 M-1 min-1. The slope determined from the plot of log (100/t1/2) against
AB  - log (phenylglyoxal) indicated that the reaction of 1 molecule of phenylglyoxal reagent in
AB  - necessary for inactivation of each active site in EcoRI methylase. Preincubation with pUC19 or
AB  - S-adenosylmethionine as substrates decreased significantly the rate of inactivation by
AB  - phenylglyoxal. By nitrocellulose binding assay, phenylglyoxal was observed to reduce DNA
AB  - binding capacity of the enzyme more rapidly than S-adenosylmethionine. Furthermore, DNA
AB  - binding capacity of the enzyme was preserved when the enzyme was preincubated with pUC19 DNA.
AB  - The cumulative results suggest that arginyl residue plays a very important role as a DNA
AB  - binding residue in EcoRI methylase.
ER  -

TY  - JOUR
AU  - Seo, J.H.
AU  - Cho, Y.D.
TI  - Studies on the role of cysteinyl residue in EcoRI methylase.
JO  - Korean Biochem. J.
PY  - 1991
SP  - 193
EP  - 199
VL  - 24
AB  - The chemical modification of cysteinyl residue of EcoRI methylase by NEM and
AB  - DACM resulted in the loss of the enzyme activity following pseudo first order
AB  - kinetics.  Second order rate constants (K) for the inactivation of EcoRI
AB  - methylase by NEM and DACM were 685 M-1.min-1 and  99960 M-1.min-1,
AB  - respectively.  The reaction orders with respect to NEM and DACM were determined
AB  - from plot of log (100/t1/2) against log (NEM) and log (DACM).  When the data
AB  - are plotted as indicated above, slopes of 0.95 and 1.25 are obtained,
AB  - suggesting that inactivation is the result of the reaction of one cysteinyl
AB  - residue per active site of EcoRI methylase.  The inactivation of EcoRI
AB  - methylase by DTNB was reversed upon addition of excess 2-mercaptoethanol.  When
AB  - the enzyme solution was preincubated with the substrates, the inactivation of
AB  - the enzyme by NEM and DACM was protected.  Furtheremore, loss of SAM binding
AB  - capacity of EcoRI methylase was detected by nitrocellulose filter binding
AB  - assay.  Based on the data, we suggest that cysteinyl residue of EcoRI methylase
AB  - plays a very important role as a SAM binding residue.
ER  -

TY  - JOUR
AU  - Seo, Y.S.
AU  - Lim, J.Y.
AU  - Choi, B.S.
AU  - Kim, H.
AU  - Goo, E.
AU  - Lee, B.
AU  - Lim, J.S.
AU  - Choi, I.Y.
AU  - Moon, J.S.
AU  - Kim, J.
AU  - Hwang, I.
TI  - Complete Genome Sequence of Burkholderia gladioli BSR3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3149
EP  - 3149
VL  - 193
AB  - We report the complete genome sequence of Burkholderia gladioli BSR3 isolated from a diseased
AB  - rice sheath in Korea.
ER  -

TY  - JOUR
AU  - Seo, Y.S.
AU  - Lim, J.Y.
AU  - Park, J.
AU  - Kim, S.
AU  - Lee, H.H.
AU  - Cheong, H.
AU  - Kim, S.M.
AU  - Moon, J.S.
AU  - Hwang, I.
TI  - Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts.
JO  - BMC Genomics
PY  - 2015
SP  - 349
EP  - 349
VL  - 16
AB  - BACKGROUND: In addition to human and animal diseases, bacteria of the genus
AB  - Burkholderia can cause plant diseases. The representative species of
AB  - rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B.
AB  - plantarii, which primarily cause grain rot, sheath rot, and seedling blight,
AB  - respectively, resulting in severe reductions in rice production. Though
AB  - Burkholderia rice pathogens cause problems in rice-growing countries,
AB  - comprehensive studies of these rice-pathogenic species aiming to control
AB  - Burkholderia-mediated diseases are only in the early stages. RESULTS: We first
AB  - sequenced the complete genome of B. plantarii ATCC 43733T. Second, we conducted
AB  - comparative analysis of the newly sequenced B. plantarii ATCC 43733T genome with
AB  - eleven complete or draft genomes of B. glumae and B. gladioli strains.
AB  - Furthermore, we compared the genome of three rice Burkholderia pathogens with
AB  - those of other Burkholderia species such as those found in environmental habitats
AB  - and those known as animal/human pathogens. These B. glumae, B. gladioli, and B.
AB  - plantarii strains have unique genes involved in toxoflavin or tropolone toxin
AB  - production and the clustered regularly interspaced short palindromic repeats
AB  - (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii
AB  - ATCC 43733T has many common features with those of B. glumae and B. gladioli,
AB  - this B. plantarii strain has several unique features, including quorum sensing
AB  - and CRISPR/CRISPR-associated protein (Cas) systems. CONCLUSIONS: The complete
AB  - genome sequence of B. plantarii ATCC 43733T and publicly available genomes of B.
AB  - glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome
AB  - analyses among three rice-pathogenic Burkholderia species responsible for tissue
AB  - rotting and seedling blight. Our results suggest that B. glumae has evolved
AB  - rapidly, or has undergone rapid genome rearrangements or deletions, in response
AB  - to the hosts. It also, clarifies the unique features of rice pathogenic
AB  - Burkholderia species relative to other animal and human Burkholderia species.
ER  -

TY  - JOUR
AU  - Seoane, A.
AU  - Sangari, F.J.
AU  - Lobo, J.M.
TI  - Complete nucleotide sequence of the fosfomycin resistance transposon Tn2921.
JO  - Int. J. Antimicrob. Agents
PY  - 2010
SP  - 413
EP  - 414
VL  - 35
AB  - Fosfomycin is a cell wall-active antibiotic introduced into clinical practice around 1970.
AB  - Despite its broad spectrum of activity and good pharmacological properties, its use has been
AB  - somewhat hampered by the high number of spontaneous resistant mutants isolated following
AB  - antibiotic challenge in many bacterial pathogens, most of them carrying chromosomal mutations
AB  - impairing drug transport.
ER  -

TY  - JOUR
AU  - Seong, H.J.
AU  - Park, H.J.
AU  - Hong, E.
AU  - Lee, S.C.
AU  - Sul, W.J.
AU  - Han, S.W.
TI  - Methylome Analysis of Two Xanthomonas spp. Using Single-Molecule Real-Time Sequencing.
JO  - Plant Pathol. J.
PY  - 2016
SP  - 500
EP  - 507
VL  - 32
AB  - Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and
AB  - methylation patterns/motifs at the genome level. Using SMRT
AB  - sequencing, diverse bacterial methylomes including those of Helicobacter pylori,
AB  - Lactobacillus spp., and Escherichia coli have been determined, and previously
AB  - unreported DNA methylation motifs have been identified. However, the methylomes
AB  - of Xanthomonas species, which belong to the most important plant pathogenic
AB  - bacterial genus, have not been documented. Here, we report the methylomes of
AB  - Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv.
AB  - vesicatoria (Xcv) strain 85-10. We identified N(6)-methyladenine (6mA) and
AB  - N(4)-methylcytosine (4mC) modification in both genomes. In addition, we assigned
AB  - putative DNA methylation motifs including previously unreported methylation
AB  - motifs via REBASE and MotifMaker, and compared methylation patterns in both
AB  - species. Although Xag and Xcv belong to the same genus, their methylation
AB  - patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682)
AB  - was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number
AB  - of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491).
AB  - Strikingly, there were no common or shared motifs in the 10 most frequently
AB  - methylated motifs of both strains, indicating they possess unique species- or
AB  - strain-specific methylation motifs. Among the 20 most frequent motifs from both
AB  - strains, for 9 motifs at least 1% of the methylated bases were located in
AB  - putative promoter regions. Methylome analysis by SMRT sequencing technology is
AB  - the first step toward understanding the biology and functions of DNA methylation
AB  - in this genus.
ER  -

TY  - JOUR
AU  - Seraphin, B.
AU  - Faye, G.
AU  - Hatat, D.
AU  - Jacq, C.
TI  - The yeast mitochondrial intron aI5a: associated endonuclease activity and in vivo mobility.
JO  - Gene
PY  - 1992
SP  - 1
EP  - 8
VL  - 113
AB  - By analyzing crosses between yeast strains carrying different combinations of mitochondrial
AB  - (mt) introns, we have shown that the aI5a intron is mobile in vivo. Furthermore, we have
AB  - observed that the mobility of intron aI5a is affected by both the nuclear and mt genotypes. We
AB  - have also detected a restriction endonuclease (ENase) activity that cleaves intronless mt
AB  - genomes close to the aI5a intron insertion site and thus might be involved in intron mobility.
AB  - Furthermore, similar to other ENases encoded by mobile mt introns of yeast, the ENase
AB  - generates a cut with a four-base 3'-OH overhang. Thus, intron aI5a represents a
AB  - characteristic member of the family of mobile group-I introns.
ER  -

TY  - JOUR
AU  - Seraphin, B.
AU  - Simon, M.
AU  - Faye, G.
TI  - A mitochondrial reading frame which may code for a maturase-like protein in Saccharomyces cerevisiae.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 3005
EP  - 3014
VL  - 13
AB  - In S. cerevisiae, the large oxi3/oli2 mitochondrial transcript contains
AB  - the products of the oxi3, aap1 and oli2 genes and an unassigned reading
AB  - frame, RF3. In the work presented here, we have completed the nucleotide
AB  - sequence of RF3. We have shown that RF3 is composed of four fairly large
AB  - ORFs which overlap within GC rich sequences. Furthermore, a shift of +1
AB  - base was found between each pair of consecutive reading frames. We discuss
AB  - how these frameshifts could be removed to produce a 500 aminoacid long
AB  - protein containing the two well conserved P1 and P2 oligopeptide sequences
AB  - featuring several mitochondrial intron reading frames, suggesting,
AB  - thereby, a RNA-maturase-like activity for the putative RF3 protein. In
AB  - addition, we suggest that the insertion of GC clusters in a gene could
AB  - provide a novel way of regulating its expression.
ER  -

TY  - JOUR
AU  - Serepa, M.H.
AU  - Gray, V.M.
TI  - Draft Whole-Genome Sequence of Serratia marcescens Strain MCB, Associated with Oscheius sp. MCB (Nematoda: Rhabditidae) Isolated from South Africa.
JO  - Genome Announcements
PY  - 2014
SP  - e00911
EP  - e00914
VL  - 2
AB  - Here we report on the draft genome sequence of Serratia marcescens strain MCB associated with
AB  - Oscheius sp. MCB (Nematoda: Rhabditidae) isolated from South
AB  - African soil. S. marcescens strain MCB has 5,304,212-bp genome size with 4,877
AB  - genes and a G+C content of 59.1%.
ER  -

TY  - JOUR
AU  - Serfiotis-Mitsa, D.
AU  - Herbert, A.P.
AU  - Roberts, G.A.
AU  - Soares, D.C.
AU  - White, J.H.
AU  - Blakely, G.W.
AU  - Uhrin, D.
AU  - Dryden, D.T.
TI  - The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo  but not in vitro.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 1723
EP  - 1737
VL  - 38
AB  - Plasmids, conjugative transposons and phage frequently encode anti-restriction proteins to
AB  - enhance their chances of entering a new
AB  - bacterial host that is highly likely to contain a Type I DNA restriction
AB  - and modification (RM) system. The RM system usually destroys the invading
AB  - DNA. Some of the anti-restriction proteins are DNA mimics and bind to the
AB  - RM enzyme to prevent it binding to DNA. In this article, we characterize
AB  - ArdB anti-restriction proteins and their close homologues, the KlcA
AB  - proteins from a range of mobile genetic elements; including an ArdB
AB  - encoded on a pathogenicity island from uropathogenic Escherichia coli and
AB  - a KlcA from an IncP-1b plasmid, pBP136 isolated from Bordetella pertussis.
AB  - We show that all the ArdB and KlcA act as anti-restriction proteins and
AB  - inhibit the four main families of Type I RM systems in vivo, but fail to
AB  - block the restriction endonuclease activity of the archetypal Type I RM
AB  - enzyme, EcoKI, in vitro indicating that the action of ArdB is indirect and
AB  - very different from that of the DNA mimics. We also present the structure
AB  - determined by NMR spectroscopy of the pBP136 KlcA protein. The structure
AB  - shows a novel protein fold and it is clearly not a DNA structural mimic.
ER  -

TY  - JOUR
AU  - Serfiotis-Mitsa, D.
AU  - Roberts, G.A.
AU  - Cooper, L.P.
AU  - White, J.H.
AU  - Nutley, M.
AU  - Cooper, A.
AU  - Blakely, G.W.
AU  - Dryden, D.T.
TI  - The Orf18 Gene Product from Conjugative Transposon Tn916 Is an ArdA Antirestriction Protein that Inhibits Type I DNA Restriction-Modification  Systems.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 970
EP  - 981
VL  - 383
AB  - Gene orf18, which is situated within the intercellular transposition region of the conjugative
AB  - transposon Tn916 from the bacterial pathogen Enterococcus faecalis, encodes a putative ArdA
AB  - (alleviation of restriction of DNA A) protein. Conjugative transposons are generally resistant
AB  - to DNA restriction upon transfer to a new host. ArdA from Tn916 may be responsible for the
AB  - apparent immunity of the transposon to DNA restriction and modification (R/M) systems and for
AB  - ensuring that the transposon has a broad host range. The orf18 gene was engineered for
AB  - overexpression in Escherichia coli, and the recombinant ArdA protein was purified to
AB  - homogeneity. The protein appears to exist as a dimer at nanomolar concentrations but can form
AB  - larger assemblies at micromolar concentrations. R/M assays revealed that ArdA can efficiently
AB  - inhibit R/M by all four major classes of Type I R/M enzymes both in vivo and in vitro. These
AB  - R/M systems are present in over 50% of sequenced prokaryotic genomes. Our results suggest that
AB  - ArdA can overcome the restriction barrier following conjugation and so helps increase the
AB  - spread of antibiotic resistance genes by horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Sergeev, V.N.
AU  - Chalov, S.E.
AU  - Drutsa, V.L.
AU  - Gromova, E.S.
TI  - A study of the Asp110-Glu112 region of EcoRII restriction endonuclease by site-directed mutagenesis.
JO  - Biochemistry
PY  - 2000
SP  - 1006
EP  - 1010
VL  - 65
AB  - Site-directed mutagenesis of the ecoRII gene has been used to search for the active site of
AB  - the EcoRII restriction endonuclease. Plasmids
AB  - with point mutations in ecoRII gene resulting in substitutions of amino
AB  - acid residues in the Asp110-Glu112 region of the EcoRII endonuclease
AB  - (Asp110 --> Lys, Asn, Thr, Val, or Ile; Pro111 --> Arg, His, Ala, or
AB  - Leu; Glu112 --> Lys, Gin, or Asp) have been constructed. When expressed
AB  - in E. coli, ail these plasmids displayed EcoRII endonuclease activity,
AB  - We also constructed a plasmid containing a mutant ecoRII gene with
AB  - deletion of the sequence coding the Gln109-Pro111 region of the
AB  - protein. This mutant protein had no EcoRII endonuclease activity. The
AB  - data suggest that Asp110, Pro111, and Glu112 residues do not
AB  - participate in the formation of the EcoRII active site. However, this
AB  - region seems to be relevant for the formation of the tertiary structure
AB  - of the EcoRII endonuclease.
ER  -

TY  - JOUR
AU  - Seribelli, A.A.
AU  - Frazao, M.R.
AU  - Gonzales, J.C.
AU  - Cao, G.
AU  - Leon, M.S.
AU  - Kich, J.D.
AU  - Allard, M.W.
AU  - Falcao, J.P.
TI  - Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e00232
EP  - e00218
VL  - 6
AB  - Salmonellosis is a disease with a high incidence worldwide, and Salmonella enterica subsp.
AB  - enterica serovar Typhimurium is one of the most clinically
AB  - important serovars. We report here the draft genome sequences of 20 S.
AB  - Typhimurium strains isolated from swine in Santa Catarina, Brazil. These draft
AB  - genomes will improve our understanding of S. Typhimurium in Brazil.
ER  -

TY  - JOUR
AU  - Serrano, A.E.
AU  - Escudero, L.V.
AU  - Tebes-Cayo, C.
AU  - Acosta, M.
AU  - Encalada, O.
AU  - Fernandez-Moroso, S.
AU  - Demergasso, C.
TI  - First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotan in Northern Chile.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 43
EP  - 43
VL  - 12
AB  - Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the
AB  - Firmicutes phylum, isolated from the Salar de Ascotan, a hypersaline
AB  - salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline
AB  - environment located at the bottom of a tectonic basin surrounded by mountain
AB  - range, including some active volcanoes. This landscape can be an advantageous
AB  - system to explore the effect of salinity on microorganisms that mediate
AB  - biogeochemical reactions. Since 2000, microbial reduction of arsenic has been
AB  - evidenced in the system, and the phylogenetic analysis of the original community
AB  - plus the culture enrichments has revealed the predominance of Firmicutes phylum.
AB  - Here, we describe the first whole draft genome sequence of an arsenic-reducing
AB  - strain belonging to the Fusibacter genus showing the highest 16S rRNA gene
AB  - sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome
AB  - consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%.
AB  - Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for
AB  - RNAs. Insights from the genome sequence and some microbiological features of the
AB  - strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample
AB  - SAMD00055724. The release of the genome sequence of this strain could contribute
AB  - to the understanding of the arsenic biogeochemistry in extreme environments.
ER  -

TY  - JOUR
AU  - Serrano, W.
AU  - Tarazona, U.I.
AU  - Olaechea, R.M.
AU  - Friedrich, M.W.
TI  - Draft Genome Sequence of Vibrio sp. Strain V1B Isolated from the Gut Microflora of the Scallop Argopecten purpuratus.
JO  - Genome Announcements
PY  - 2017
SP  - e01130
EP  - e01117
VL  - 5
AB  - A new Vibrio strain, V1B, was isolated from the intestinal tract of the scallop Argopecten
AB  - purpuratus Strain V1B is closely related to the species Vibrio
AB  - inhibens BFLP-10, which has been characterized as showing antagonistic activity
AB  - against pathogenic Vibrio sp. We report here the draft genome of the isolated
AB  - Vibrio sp. strain V1B.
ER  -

TY  - JOUR
AU  - Serrano, W.
AU  - Tarazona, U.I.
AU  - Olaechea, R.M.
AU  - Friedrich, M.W.
TI  - Draft Genome Sequence of a New Vibrio Strain with the Potential To Produce Bacteriocin-Like Inhibitory Substances, Isolated from the Gut Microflora of  Scallop (Argopecten purpuratus).
JO  - Genome Announcements
PY  - 2018
SP  - e00419
EP  - e00418
VL  - 6
AB  - A new Vibrio strain, V7A, was isolated from the intestinal tract of the Peruvian  scallop
AB  - (Argopecten purpuratus). Strain V7A clusters within the Mediterranei
AB  - clade of the genus Vibrio and has the potential to produce bacteriocin-like
AB  - inhibitory substances (BLIS). Here, we report the draft genome sequence of Vibrio
AB  - mediterranei strain V7A.
ER  -

TY  - JOUR
AU  - Serva, S.
AU  - Klimasauskas, S.
AU  - Weinhold, E.
TI  - Fluorescence studies of the DNA base flipping induced by a cytosine-5 methyltransferase.
JO  - Biologija
PY  - 1997
SP  - 9
EP  - 12
VL  - 1
AB  - A novel fluorescence-based method for detecting and studying DNA base flipping in enzyme-DNA
AB  - complexes is described.  The target cytosine for the DNA methyltransferase HhaI (GCGC) was
AB  - replaced by a fluorescent base, 2-aminopurine.  Constistent with the extrahelical trapping of
AB  - the target base, a 90-fold increase in the fluorescence intensity was observed upon binding of
AB  - M. HhaI to a 37-mer duplex substrate.  Similar substitutions of bases adjacent to the target
AB  - cytosine result in a relatively small change.  Stopped-flow fluorescence experiments under
AB  - non-catalytic conditions allowed to monitor the course of base-flipping directly.  Kinetic
AB  - analysis shows that the site-specific binding of the enzyme is a diffusion-controlled process,
AB  - while the subsequent flipping motion is achieved in 1 millisecond, or faster.  Other classes
AB  - of enzymes suspected to employ the base flipping in their mechanisms can be investigated with
AB  - this method.
ER  -

TY  - JOUR
AU  - Serva, S.
AU  - Velyvis, R.
AU  - Lazareviciute, L.
AU  - Klimasauskas, S.
TI  - High-level expression of MvaI DNA methyltransferase.
JO  - Biologija
PY  - 1996
SP  - 48
EP  - 50
VL  - 0
AB  - Construction of a high level expression system for the DNA-(cytosine-N4)-methyltransferase
AB  - M.MvaI is described.  The entire M.MvaI coding region was introduced as a 1511bp Alw44I-BpiI
AB  - fragment into the high expression vector pPR594E9.  The resultant plasmid (pPR-MvaIM7) was
AB  - expressed in the E. coli strain GM119 by induction with IPTG.  In the induced cells,
AB  - catalytically active M.MvaI was produced at a level of about 10% of their total protein.  The
AB  - enzyme was purified to apparent homogeneity by a four-column chromatographic procedure in a
AB  - yield of about 0.2 mg of pure enzyme per 1g of cell paste.  The molecular weight and the amino
AB  - terminal sequence of the protein agrees with that predicted from the DNA sequence.
ER  -

TY  - JOUR
AU  - Serva, S.
AU  - Weinhold, E.
AU  - Klimasauskas, S.
TI  - Stopped-flow fluorescence studies of DNA base flipping by HhaI methyltransferase.
JO  - Biochem. Soc. Trans.
PY  - 2000
SP  - A468
EP  - A468
VL  - 2000
AB  - Rotation of a nucleotide out of the DNA helix (base flipping) has been first observed for the
AB  - HhaI methyltransferase followed by numerous other DNA modification and repair enzymes.  M.HhaI
AB  - catalyzes transfer of a methyl group from cofactor S-adenosyl-L-methionine onto the C5
AB  - position of the first cytosine in the target sequence GCGC.  In this study, stopped-flow and
AB  - rapid-quench techniques were employed in combination with fluorescence detection for kinetic
AB  - characterization of individual steps on the reaction pathway of M.HhaI.  Selective labeling of
AB  - the DNA substrate was achieved by synthetic incorporation of 2-aminopurine at the target
AB  - position which showed a dramatic increase in fluorescence signal upon transition of the base
AB  - from the stacked to an extrahelical position.  Association, dissociation and single-turnover
AB  - experimental setups permitted the direct determination of microscopic rate constants for DNA
AB  - binding, flipping of the target base, methyl group transfer and release of methylated DNA.  We
AB  - demonstrate here that the target sites on short DNA duplexes are predominantly located via a
AB  - diffusion-collision pathway and the subsequent base flipping is nearly instantaneous (<1 ms)
AB  - for the G-2AP mismatch.  We show for the first time that the chemical methyl transfer step
AB  - (0.15 s-1) is faster than the steady-state turnover (0.02 s-1) and directly confirm that decay
AB  - of the ternary product complex (methylated DNA-M.HhaI-AdoHcy) is rate-limiting in the
AB  - catalytic cycle.  Global fitting and simulation analysis in conjunction with structural data
AB  - suggest detailed catalytic mechanisms for DNA base flipping and catalysis by DNA cytosine-5
AB  - methyltransferases.
ER  -

TY  - JOUR
AU  - Serva, S.
AU  - Weinhold, E.
AU  - Roberts, R.J.
AU  - Klimasauskas, S.
TI  - Chemical display of thymine residues flipped out by DNA methyltransferases.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 3473
EP  - 3479
VL  - 26
AB  - The DNA cytosine-C5 methyltransferase M.HhaI flips its target base out of the DNA helix during
AB  - interaction with the substrate sequence GCGC.  Binary and ternary complexes between M.HhaI and
AB  - hemimethylated DNA duplexes were used to examine the suitability of four chemical methods to
AB  - detect flipped-out bases in protein-DNA complexes.  These methods probe the structural
AB  - peculiarities of pyrimidine bases in DNA.  We find that in cases when the target cytosine is
AB  - replaced with thymine (GTGC), KMnO4 proved an efficient probe for positive display of
AB  - flipped-out thymines.  The generality of this procedure was further verified by examining a
AB  - DNA adenine-N6 methyltransferase, M.TaqI, in which case an enhanced reactivity of thymine
AB  - replacing the target adenine (TCGT) in the recognition sequence TCGA was also observed.  Our
AB  - results support the proposed base-flipping mechanism for adenine methyltransferases, and offer
AB  - a convenient laboratory tool for detection of flipped-out thymines in protein-DNA complexes.
ER  -

TY  - JOUR
AU  - Servin-Garciduenas, L.E.
AU  - Garrett, R.A.
AU  - Amils, R.
AU  - Martinez-Romero, E.
TI  - Genome Sequence of the Acidophilic Bacterium Acidocella sp. Strain MX-AZ02.
JO  - Genome Announcements
PY  - 2013
SP  - e00041
EP  - e00012
VL  - 1
AB  - Here, we report the draft genome sequence of Acidocella sp. strain MX-AZ02, an acidophilic and
AB  - heterotrophic alphaproteobacterium isolated from a geothermal lake in western Mexico.
ER  -

TY  - JOUR
AU  - Servin-Garciduenas, L.E.
AU  - Martinez-Romero, E.
TI  - Draft Genome Sequence of the Sulfolobales Archaeon AZ1, Obtained through Metagenomic Analysis of a Mexican Hot Spring.
JO  - Genome Announcements
PY  - 2014
SP  - e00164
EP  - e00114
VL  - 2
AB  - The Sulfolobales archaea have been found inhabiting acidic hot springs all over the world.
AB  - Here, we report the 1.798-Mbp draft genome sequence of the
AB  - thermoacidophilic Sulfolobales archaeon AZ1, reconstructed from the metagenome of
AB  - a Mexican hot spring. Sequence-based comparisons revealed that the Sulfolobales
AB  - archaeon AZ1 represents a novel candidate genus.
ER  -

TY  - JOUR
AU  - Servin-Garciduenas, L.E.
AU  - Peng, X.
AU  - Garrett, R.A.
AU  - Martinez-Romero, E.
TI  - Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a mexican hot spring.
JO  - Genome Announcements
PY  - 2013
SP  - e00164
EP  - e00113
VL  - 1
AB  - The consensus genome sequence of a new member of the family Fuselloviridae designated as SMF1
AB  - (Sulfolobales Mexican fusellovirus 1) is presented. The
AB  - complete circular genome was recovered from a metagenomic study of a Mexican hot
AB  - spring. SMF1 exhibits an exceptional coding strand bias and a reduced set of
AB  - fuselloviral core genes.
ER  -

TY  - JOUR
AU  - Servin-Garciduenas, L.E.
AU  - Rogel, M.A.
AU  - Ormeno-Orrillo, E.
AU  - Delgado-Salinas, A.
AU  - Martinez-Romero, J.
AU  - Sanchez, F.
AU  - Martinez-Romero, E.
TI  - Genome Sequence of Rhizobium sp. Strain CCGE510, a Symbiont Isolated from Nodules of the Endangered Wild Bean Phaseolus albescens.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6310
EP  - 6311
VL  - 194
AB  - We present the genome sequence of Rhizobium sp. strain CCGE510, a nitrogen fixing bacterium
AB  - taxonomically affiliated with the R. leguminosarum-R. etli group,
AB  - isolated from wild Phaseolus albescens nodules grown in native pine forests in
AB  - western Mexico. P. albescens is an endangered bean species phylogenetically
AB  - related to P. vulgaris. In spite of the close host relatedness, Rhizobium sp.
AB  - CCGE510 does not establish an efficient symbiosis with P. vulgaris. This is the
AB  - first genome of a Rhizobium symbiont from a Phaseolus species other than P.
AB  - vulgaris, and it will provide valuable new insights about symbiont-host
AB  - specificity.
ER  -

TY  - JOUR
AU  - Servin-Garciduenas, L.E.
AU  - Rogel, M.A.
AU  - Ormeno-Orrillo, E.
AU  - Zayas-Del, M.A.
AU  - Sanchez, F.
AU  - Martinez-Romero, E.
TI  - Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus.
JO  - Genome Announcements
PY  - 2016
SP  - e00126
EP  - e00116
VL  - 4
AB  - We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001,  a
AB  - nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus.
AB  - Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained
AB  - from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island.
ER  -

TY  - JOUR
AU  - Servin-Garciduenas, L.E.
AU  - Sanchez-Quinto, A.
AU  - Martinez-Romero, E.
TI  - Draft Genome Sequence of Commensalibacter papalotli MX01, a Symbiont Identified from the Guts of Overwintering Monarch Butterflies.
JO  - Genome Announcements
PY  - 2014
SP  - e00128
EP  - e00114
VL  - 2
AB  - We report the draft genome sequence of Commensalibacter papalotli strain MX01, isolated from
AB  - the intestines of an overwintering monarch butterfly. The
AB  - 2,332,652-bp AT-biased genome of C. papalotli MX01 is the smallest genome for a
AB  - member of the Acetobacteraceae family and provides the first evidence of plasmids
AB  - in Commensalibacter.
ER  -

TY  - JOUR
AU  - Servos, S.
AU  - Silva, C.
AU  - Dougan, G.
AU  - Charles, I.G.
TI  - The commercially available restriction enzyme BspHI is blocked by overlapping methylation.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 183
EP  - 183
VL  - 19
AB  - This report shows that BspHI is sensitive to dam methylation
ER  -

TY  - JOUR
AU  - Seshadri, R. et al.
TI  - Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.
JO  - Nat. Biotechnol.
PY  - 2018
SP  - 359
EP  - 367
VL  - 36
AB  - Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible
AB  - plant polysaccharides into nutrients used for growth. Understanding
AB  - the functions carried out by the rumen microbiota is important for reducing
AB  - greenhouse gas production by ruminants and for developing biofuels from
AB  - lignocellulose. We present 410 cultured bacteria and archaea, together with their
AB  - reference genomes, representing every cultivated rumen-associated archaeal and
AB  - bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid
AB  - production and methanogenesis pathways, and assign specific taxa to functions. A
AB  - total of 336 organisms were present in available rumen metagenomic data sets, and
AB  - 134 were present in human gut microbiome data sets. Comparison with the human
AB  - microbiome revealed rumen-specific enrichment for genes encoding de novo
AB  - synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical
AB  - inheritance of the rumen microbiome based on underrepresentation of markers of
AB  - environmental stress. We estimate that our Hungate genome resource represents
AB  - approximately 75% of the genus-level bacterial and archaeal taxa present in the
AB  - rumen.
ER  -

TY  - JOUR
AU  - Seshadri, R. et al.
TI  - Genome sequence of the PCE-Dechlorinating bacterium Dehalococcoides ethenogenes.
JO  - Science
PY  - 2005
SP  - 105
EP  - 108
VL  - 307
AB  - Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the
AB  - groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its
AB  - 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated
AB  - elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were
AB  - adjacent to genes for transcription regulators, and five hydrogenase complexes were
AB  - identified. These findings, plus a limited repertoire of other metabolic modes, indicate that
AB  - D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2.
AB  - Diversification of reductive dehalogenase functions appears to have been mediated by recent
AB  - genetic exchange and amplification. Genome analysis provides insights into the organism's
AB  - complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.
ER  -

TY  - JOUR
AU  - Seshadri, R.
AU  - Joseph, S.W.
AU  - Chopra, A.K.
AU  - Sha, J.
AU  - Shaw, J.
AU  - Graf, J.
AU  - Haft, D.
AU  - Wu, M.
AU  - Ren, Q.
AU  - Rosovitz, M.J.
AU  - Madupu, R.
AU  - Tallon, L.
AU  - Kim, M.
AU  - Jin, S.
AU  - Vuong, H.
AU  - Stine, O.C.
AU  - Ali, A.
AU  - Horneman, A.J.
AU  - Heidelberg, J.F.
TI  - Genome Sequence of Aeromonas hydrophila ATCC 7966T: Jack of All Trades.
JO  - J. Bacteriol.
PY  - 2006
SP  - 8272
EP  - 8282
VL  - 188
AB  - The complete genome of Aeromonas hydrophila ATCC 7966(T) was sequenced. Aeromonas, a
AB  - ubiquitous waterborne bacterium, has been placed by the
AB  - Environmental Protection Agency on the Contaminant Candidate List because
AB  - of its potential to cause human disease. The 4.7-Mb genome of this
AB  - emerging pathogen shows a physiologically adroit organism with broad
AB  - metabolic capabilities and considerable virulence potential. A large array
AB  - of virulence genes, including some identified in clinical isolates of
AB  - Aeromonas spp. or Vibrio spp., may confer upon this organism the ability
AB  - to infect a wide range of hosts. However, two recognized virulence
AB  - markers, a type III secretion system and a lateral flagellum, that are
AB  - reported in other A. hydrophila strains are not identified in the
AB  - sequenced isolate, ATCC 7966(T). Given the ubiquity and free-living
AB  - lifestyle of this organism, there is relatively little evidence of
AB  - fluidity in terms of mobile elements in the genome of this particular
AB  - strain. Notable aspects of the metabolic repertoire of A. hydrophila
AB  - include dissimilatory sulfate reduction and resistance mechanisms (such as
AB  - thiopurine reductase, arsenate reductase, and phosphonate degradation
AB  - enzymes) against toxic compounds encountered in polluted waters. These
AB  - enzymes may have bioremediative as well as industrial potential. Thus, the
AB  - A. hydrophila genome sequence provides valuable insights into its ability
AB  - to flourish in both aquatic and host environments.
ER  -

TY  - JOUR
AU  - Seshasayee, A.S.
TI  - An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli.
JO  - PLoS ONE
PY  - 2007
SP  - e273
EP  - e273
VL  - 2
AB  - N6-Adenine methylation is an important epigenetic signal, which regulates various processes,
AB  - such as DNA replication and repair and transcription. In gamma-proteobacteria, Dam is a
AB  - stand-alone enzyme that methylates GATC sites, which are non-randomly distributed in the
AB  - genome. Some of these overlap with transcription factor binding sites. This work describes a
AB  - global computational analysis of a published Dam knockout microarray alongside other publicly
AB  - available data to throw insights into the extent to which Dam regulates transcription by
AB  - interfering with protein binding. The results indicate that DNA methylation by DAM may not
AB  - globally affect gene transcription by physically blocking access of transcription factors to
AB  - binding sites. Down-regulation of Dam during stationary phase correlates with the activity of
AB  - TFs whose binding sites are enriched for GATC sites.
ER  -

TY  - JOUR
AU  - Seshasayee, A.S.
AU  - Singh, P.
AU  - Krishna, S.
TI  - Context-dependent conservation of DNA methyltransferases in bacteria.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 7066
EP  - 7073
VL  - 40
AB  - DNA methytransferases (MTs) in bacteria are best understood in the context of
AB  - restriction-modification (R-M) systems, which act as bacterial immune systems
AB  - against incoming DNA including phages, but have also been described as selfish
AB  - elements. But several orphan MTs, which are not associated with any restriction
AB  - enzyme, have also been characterized and may protect against parasitism by R-M
AB  - systems. The occurrence of MTs in these two contexts, namely as part of R-M
AB  - systems or as orphans, is poorly understood. Here we report the results of a
AB  - comparative genomic survey of DNA MTs across approximately 1000 bacterial
AB  - genomes. We show that orphan MTs overwhelm R-M systems in their occurrence. In
AB  - general, R-M MTs are poorly conserved, whereas orphans are nearly as conserved
AB  - within a genus as any average gene. However, oligonucleotide usage and
AB  - conservation patterns across genera suggest that both forms of MTs might have
AB  - been horizontally acquired. We suggest that many orphan MTs might be
AB  - 'degradation' products of R-M systems, based on the properties of orphan MTs
AB  - encoded adjacent to highly diverged REs. In addition, several fully degraded R-M
AB  - systems exist in which both the MT and the RE are highly divergent from their
AB  - corresponding reference R-M pair. Despite their sporadic occurrence, conserved
AB  - R-M systems are present in strength in two highly transformable genera, in which
AB  - they may contribute to selection against integration of foreign DNA.
ER  -

TY  - JOUR
AU  - Sethmann, S.
AU  - Ceglowski, P.
AU  - Willert, J.
AU  - Iwanicka-Nowicka, R.
AU  - Trautner, T.A.
AU  - Walter, J.
TI  - M.PhiBssHII, a novel cytosine-C5-DNA-methyltransferase with target-recognizing domains at separated locations of the enzyme.
JO  - EMBO J.
PY  - 1999
SP  - 3502
EP  - 3508
VL  - 18
AB  - In all cytosine-C5-DNA-methyltransferases (MTases) from prokaryotes and eukaryotes, remarkably
AB  - conserved amino acid sequence elements responsible for general enzymatic functions are
AB  - arranged in the same canonical order. In addition, one variable region, which includes the
AB  - target-recognizing domain(s) (TRDs) characteristic for each enzyme, has been localized in one
AB  - region between the same blocks of these conserved elements. This conservation in the order of
AB  - conserved and variable sequences suggests stringent structural constraints in the primary
AB  - structure to obtain the correct folding of the enzymes. Here we report the characterization of
AB  - a new type of a multispecific MTase, M.PhiBssHII, which is expressed as two isoforms. Isoform
AB  - I is an entirely novel type of MTase which has, in addition to the TRDs at the conventional
AB  - location, one TRD located at a non-canonical position at its N-terminus. Isoform II is
AB  - represented by the same MTase, but without the N-terminal TRD. The N-terminal TRD provides
AB  - HaeII methylation specificity to isoform I. The TRD is fully functional when engineered into
AB  - either the conventional variable region of M.PhiBssHII or the related monospecific M.Phi3TII
AB  - MTase. The implications of this structural plasticity with respect to the evolution of MTases
AB  - are discussed.
ER  -

TY  - JOUR
AU  - Sethuraman, J.
AU  - Majer, A.
AU  - Friedrich, N.C.
AU  - Edgell, D.R.
AU  - Hausner, G.
TI  - Genes within genes: multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within an rnl group I intron of  Ophiostoma and related taxa.
JO  - Mol. Biol. Evol.
PY  - 2009
SP  - 2299
EP  - 2315
VL  - 26
AB  - In some ascomycete fungi, ribosomal protein S3 (Rps3) is encoded within a group I intron
AB  - (mL2449) that is inserted in the U11 region of the
AB  - mitochondrial large subunit rDNA (rnl) gene. Previous characterization of
AB  - the mL2449 intron in strains of Ophiostoma novo-ulmi subspecies americana
AB  - (Dutch Elm Disease) revealed a complex genes-within-genes arrangement
AB  - whereby a LAGLIDADG homing endonuclease gene (HEG) is inserted into the
AB  - RPS3 gene near the 3' terminus, creating a hybrid Rps3-LAGLIDADG fusion
AB  - protein. Here, we examined 119 additional strains of Ophiostoma and
AB  - related taxa representing 85 different species by a polymerase chain
AB  - reaction- based survey and detected both short (approximately 1.6 kb) and
AB  - long (>2.2 kb) versions of the mL2449 intron in 88 and 31 strains,
AB  - respectively. Among the long versions encountered, 21 were sequenced,
AB  - revealing the presence of either intact or degenerated HEG-coding regions
AB  - inserted within the RPS3 gene. Surprisingly, we identified two new HEG
AB  - insertion sites in RPS3; one near the original C-terminal insertion site
AB  - and one near the N-terminus of RPS3. In all instances, the HEGs are fused
AB  - in-frame with the RPS3-coding sequences to create fusion proteins.
AB  - However, comparative sequence analysis showed that upon insertion, the
AB  - HEGs displaced a portion of the RPS3-coding region. Remarkably, the
AB  - displaced RPS3-coding segments are duplicated and fused in-frame to the 3'
AB  - end of RPS3, restoring a full-length RPS3 gene. We cloned and expressed
AB  - the LAGLIDADG portion of two Rps3-HEG fusions, and showed that I-OnuI and
AB  - I-LtrI generate 4 nucleotide (nt), 3' overhangs, and cleave at or 1 nt
AB  - upstream of the HEG insertion site, respectively. Collectively, our data
AB  - indicate that RPS3 genes are a refuge for distinct types of LAGLIDADG HEGs
AB  - that are defined by the presence of duplicated segments of the host gene
AB  - that restore the RPS3 gene, thus minimizing the impact of the HEG
AB  - insertion on Rps3 function.
ER  -

TY  - JOUR
AU  - Setubal, J.C. et al.
TI  - Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes.
JO  - J. Bacteriol.
PY  - 2009
SP  - 4534
EP  - 4545
VL  - 191
AB  - Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes
AB  - nitrogen under aerobic conditions while simultaneously
AB  - protecting nitrogenase from oxygen damage. In response to carbon
AB  - availability, this organism undergoes a simple differentiation process to
AB  - form cysts that are resistant to drought and other physical and chemical
AB  - agents. Here we report the complete genome sequence of A. vinelandii DJ,
AB  - which has a single circular genome of 5,365,318 bp. In order to reconcile
AB  - an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes,
AB  - A. vinelandii is specialized in terms of its complement of respiratory
AB  - proteins. It is able to produce alginate, a polymer that further protects
AB  - the organism from excess exogenous oxygen, and it has multiple
AB  - duplications of alginate modification genes, which may alter alginate
AB  - composition in response to oxygen availability. The genome analysis
AB  - identified the chromosomal locations of the genes coding for the three
AB  - known oxygen-sensitive nitrogenases, as well as genes coding for other
AB  - oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and
AB  - formate dehydrogenase. These findings offer new prospects for the wider
AB  - application of A. vinelandii as a host for the production and
AB  - characterization of oxygen-sensitive proteins.
ER  -

TY  - JOUR
AU  - Seurinck, J.
AU  - Van de Voorde, A.
AU  - Van Montagu, M.
TI  - A new restriction endonuclease from Acetobacter pasteurianus.
JO  - Nucleic Acids Res.
PY  - 1983
SP  - 4409
EP  - 4415
VL  - 11
AB  - A restriction endonuclease, ApaI, has been partially purified from Acetobacter
AB  - pasteurianus.  This enzyme cleaves bacteriophage lambda DNA and Simian virus 40
AB  - DNA at one site, adenovirus-2 DNA at more than nine sites, but it does not
AB  - cleave PhiX174 DNA nor plasmid pBR322 DNA.  This enzyme recognizes the
AB  - sequence5' GGGCC^C 3' 3' C^CGGG 5'and cuts at the sites indicated by the
AB  - arrows.
ER  -

TY  - JOUR
AU  - Seuylemezian, A.
AU  - Cooper, K.
AU  - Schubert, W.
AU  - Vaishampayan, P.
TI  - Draft Genome Sequences of 12 Dry-Heat-Resistant Bacillus Strains Isolated from the Cleanrooms Where the Viking Spacecraft Were Assembled.
JO  - Genome Announcements
PY  - 2018
SP  - e00094
EP  - e00018
VL  - 6
AB  - Spore-forming microorganisms are of concern for forward contamination because they can survive
AB  - harsh interplanetary travel. Here, we report the draft genome
AB  - sequences of 12 spore-forming strains isolated from the Manned Spacecraft
AB  - Operations Building (MSOB) and the Vehicle Assembly Building (VAB) in Cape
AB  - Canaveral, FL, where the Viking spacecraft were assembled.
ER  -

TY  - JOUR
AU  - Seuylemezian, A.
AU  - Singh, N.K.
AU  - Vaishampayan, P.
AU  - Venkateswaran, K.
TI  - Draft Genome Sequence of Solibacillus kalamii, Isolated from an Air Filter Aboard the International Space Station.
JO  - Genome Announcements
PY  - 2017
SP  - e00696
EP  - e00617
VL  - 5
AB  - We report here the draft genome of Solibacillus kalamii ISSFR-015, isolated from  a
AB  - high-energy particulate arrestance filter aboard the International Space
AB  - Station. The draft genome sequence of this strain contains 3,809,180 bp with an
AB  - estimated G+C content of 38.61%.
ER  -

TY  - JOUR
AU  - Seuylemezian, A.
AU  - Vaishampayan, P.
AU  - Cooper, K.
AU  - Venkateswaran, K.
TI  - Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces.
JO  - Genome Announcements
PY  - 2018
SP  - e01554
EP  - e01517
VL  - 6
AB  - We report here the draft genome sequences of four strains isolated from spacecraft-associated
AB  - surfaces exhibiting increased resistance to stressors such
AB  - as UV radiation and exposure to H2O2 The draft genomes of strains 1P01SC(T),
AB  - FO-92(T), 50v1, and 2P01AA had sizes of 5,500,894 bp, 4,699,376 bp, 3,174,402 bp,
AB  - and 4,328,804 bp, respectively.
ER  -

TY  - JOUR
AU  - Sevigny, J.L.
AU  - LaJoie, J.
AU  - Shehata, S.
AU  - Christensen, E.
AU  - Cornfield, S.
AU  - Koziol, L.
TI  - Whole-Genome Sequences of Two Pseudomonas fluorescens Strains Isolated from Roots of Tomato and Cucumber Plants.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00974
EP  - e00918
VL  - 7
AB  - Pseudomonas fluorescens strain EC1 was isolated from Cucumis sativus (cucumber) roots, and P.
AB  - fluorescens SC1 was isolated from Solanum lycopersicum (tomato)
AB  - roots. The P. fluorescens SC1 genome has a total sequence length of 6,157,842 bp,
AB  - and the P. fluorescens EC1 genome has a total sequence length of 6,125,428 bp.
ER  -

TY  - JOUR
AU  - Shabarova, Z.A.
AU  - Sheflyan, G.Y.
AU  - Kuznetsova, S.A.
AU  - Kubareva, E.A.
AU  - Sysoev, O.N.
AU  - Ivanovskaya, M.G.
AU  - Gromova, E.S.
TI  - Affinity modification of restriction-endonuclease EcoRII by DNA duplex containing a monosubstituted pyrophosphate internucleotide bond.
JO  - Bioorg. Khim.
PY  - 1994
SP  - 413
EP  - 419
VL  - 20
AB  - An oligonucleotide duplex with an active monosubstituted pyrophosphate bond within the
AB  - recognition site of the EcoRII restriction endonuclease was cross-linked to this enzyme with a
AB  - yield of 10-15%. The cross-linking specificity was proved by the absence of the cross-linking
AB  - to a DNA duplex with the same modification but without the EcoRII recognition site as well as
AB  - by unmodified EcoRII substrate's inhibition of the cross-linking.
ER  -

TY  - JOUR
AU  - Shafie, N.A.
AU  - Lau, N.S.
AU  - Ramachandran, H.
AU  - Amirul, A.A.
TI  - Complete Genome Sequences of Three Cupriavidus Strains Isolated from Various Malaysian Environments.
JO  - Genome Announcements
PY  - 2017
SP  - e01498
EP  - e01416
VL  - 5
AB  - Cupriavidus sp. USMAA1020, USMAA2-4, and USMAHM13 are capable of producing
AB  - polyhydroxyalkanoate (PHA). This biopolymer is an alternative solution to
AB  - synthetic plastics, whereby polyhydroxyalkanoate synthase is the key enzyme
AB  - involved in PHA biosynthesis. Here, we report the complete genomes of three
AB  - Cupriavidus sp. strains: USMAA1020, USMAA2-4, and USMAHM13.
ER  -

TY  - JOUR
AU  - Shah, B.
AU  - Jain, K.
AU  - Patel, N.
AU  - Pandit, R.
AU  - Patel, A.
AU  - Joshi, C.G.
AU  - Madamwar, D.
TI  - Draft Genome Sequence of Paenibacillus sp. Strain DMB20, Isolated from Alang Ship-Breaking Yard, Which Harbors Genes for Xenobiotic Degradation.
JO  - Genome Announcements
PY  - 2015
SP  - e00554
EP  - e00515
VL  - 3
AB  - Paenibacillus sp. strain DMB20, in cometabolism with other Proteobacteria and Firmicutes,
AB  - exhibits azoreduction of textile dyes. Here, we report the draft
AB  - genome sequence of this bacterium, consisting of 6,647,181 bp with 7,668 coding
AB  - sequences (CDSs). The data presented highlight multiple sets of functional genes
AB  - associated with xenobiotic compound degradation.
ER  -

TY  - JOUR
AU  - Shah, D.H.
AU  - Jones, L.P.
AU  - Paul, N.
AU  - Davis, M.A.
TI  - Draft Genome Sequences of 12 Clinical and Environmental Methicillin-Resistant Staphylococcus pseudintermedius Strains Isolated from a Veterinary Teaching  Hospital in Washington State.
JO  - Genome Announcements
PY  - 2018
SP  - e00290
EP  - e00218
VL  - 6
AB  - Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a globally emergent
AB  - multidrug-resistant pathogen of dogs associated with nosocomial
AB  - transmission in dogs and with potential zoonotic impacts. Here, we report the
AB  - draft whole-genome sequences of 12 hospital-associated MRSP strains and their
AB  - resistance genotypes and phenotypes.
ER  -

TY  - JOUR
AU  - Shah, D.H.
AU  - Paul, N.C.
AU  - Guard, J.
TI  - Complete Genome Sequence of a Ciprofloxacin-Resistant Salmonella enterica subsp.  enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State.
JO  - Genome Announcements
PY  - 2018
SP  - e00125
EP  - e00118
VL  - 6
AB  - Strains of the ciprofloxacin-resistant (Cip(r)) Salmonella enterica subsp. enterica serovar
AB  - Kentucky sequence type 198 (ST198) have rapidly and extensively
AB  - disseminated globally to become a major food safety and public health concern.
AB  - Here, we report the complete genome sequence of a Cip(r)S. Kentucky ST198 strain,
AB  - PU131, isolated from a human patient in Washington State (USA).
ER  -

TY  - JOUR
AU  - Shah, G.R.
AU  - Karunakaran, R.
AU  - Kumar, G.N.
TI  - In vivo restriction endonuclease activity of the Anabaena PCC 7120 XisA protein in Escherichia coli.
JO  - Res. Microbiol.
PY  - 2007
SP  - 679
EP  - 684
VL  - 158
AB  - Anabaena PCC 7120 genome contains three elements, which get excised out during late stages of
AB  - heterocyst differentiation by a site-specific
AB  - recombination process. The XisA protein, which excises the nifD
AB  - element, shows sequence homology with the integrase family of tyrosine
AB  - recombinase. The 11 by target site of XisA CGGAGTAATCC contains a 3 bp
AB  - inverted repeat. Here, we report restriction endonuclease activity of
AB  - XisA by specific loss of plasmids containing single or double target
AB  - sites. The pMX25 plasmid containing two tat-get sites demonstrated
AB  - endonuclease activity proportional to excision frequency. Different
AB  - plasmid substrates containing one base pair mutation in the inverted
AB  - repeat of the target site were monitored for endonuclease activity.
AB  - Mutation of A4C retained endonuclease activity, while other
AB  - modifications lost endonuclease activity. The presence of an additional
AB  - copy of the target site enhanced endonuclease activity. These results
AB  - suggest that the XisA protein could be an IIE type of restriction
AB  - endonuclease in addition to being a recombinase. (C) 2007 Elsevier
AB  - Masson SAS. All rights reserved.
ER  -

TY  - JOUR
AU  - Shah, M.R.
AU  - Ulyanova, V.
AU  - Malanin, S.
AU  - Dudkina, E.
AU  - Vershinina, V.
AU  - Ilinskaya, O.
TI  - Draft Whole-Genome Sequence of Bacillus altitudinis Strain B-388, a Producer of Extracellular RNase.
JO  - Genome Announcements
PY  - 2015
SP  - e01502
EP  - e01514
VL  - 3
AB  - Here, we present a draft genome sequence of Bacillus altitudinis strain B-388, including a
AB  - putative plasmid. The strain was isolated from the intestine of
AB  - Indian meal moth, a common pest of stored grains, and it is characterized by the
AB  - production of extracellular RNase, similar to binase, which is of interest for
AB  - comparative studies and biotechnology.
ER  -

TY  - JOUR
AU  - Shah, N.R.
AU  - Moksa, M.
AU  - Novikov, A.
AU  - Perry, M.B.
AU  - Hirst, M.
AU  - Caroff, M.
AU  - Fernandez, R.C.
TI  - Draft Genome Sequences of Bordetella hinzii and Bordetella trematum.
JO  - Genome Announcements
PY  - 2013
SP  - e00838
EP  - e00813
VL  - 1
AB  - Bordetella hinzii colonizes the respiratory tracts of poultry but can also infect
AB  - immunocompromised humans. Bordetella trematum, however, only infects humans,
AB  - causing ear and wound infections. Here, we present the first draft genome
AB  - sequences of strains B. hinzii ATCC 51730 and B. trematum CCUG 13902.
ER  -

TY  - JOUR
AU  - Shah, V.
AU  - Morris, R.M.
TI  - Genome Sequence of 'Candidatus Thioglobus autotrophica' Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e01156
EP  - e01115
VL  - 3
AB  - Chemoautotrophic marine bacteria from the SUP05 clade of marine gammaproteobacteria often
AB  - dominate low-oxygen waters in upwelling regions, fjords, and hydrothermal systems. Here, we
AB  - announce the complete genome sequence  of 'Candidatus Thioglobus autotrophica' strain EF1,
AB  - the first cultured chemoautotrophic representative from the SUP05 clade.
ER  -

TY  - JOUR
AU  - Shahinas, D.
AU  - Tamber, G.S.
AU  - Arya, G.
AU  - Wong, A.
AU  - Lau, R.
AU  - Jamieson, F.
AU  - Ma, J.H.
AU  - Alexander, D.C.
AU  - Low, D.E.
AU  - Pillai, D.R.
TI  - Whole-Genome Sequence of Streptococcus pseudopneumoniae Isolate IS7493.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6102
EP  - 6103
VL  - 193
AB  - Streptococcus pseudopneumoniae is a member of the viridans group streptococci (VGS) whose
AB  - pathogenic significance is unclear. We announce
AB  - the complete genome sequence of S. pseudopneumoniae IS7493. The genome
AB  - sequence will assist in the characterization of this new organism and
AB  - facilitate the development of accurate diagnostic assays to distinguish it
AB  - from Streptococcus pneumoniae and Streptococcus mitis.
ER  -

TY  - JOUR
AU  - Shajani, Z.
AU  - Varani, G.
TI  - C-13 relaxation studies of the DNA target sequence for HhaI methyltransferase reveal unique motional properties.
JO  - Biochemistry
PY  - 2008
SP  - 7617
EP  - 7625
VL  - 47
AB  - The goal of this work was to examine if sequence-dependent conformational flexibility in DNA
AB  - plays a role in base extrusion, a
AB  - common conformational change induced by many DNA-modifying enzymes. We
AB  - studied the dynamics of the double-stranded DNA target of the HhaI
AB  - methyltransferase by recording an extensive set of C-13 NMR relaxation
AB  - parameters. We observe that the cytidine furanose rings experience fast
AB  - (picosecond to nanosecond) motions that are not present in other
AB  - nucleotides; the methylation site experiences particularly high
AB  - mobility. We also observe that the bases of guanosine and cytidine
AB  - residues within the HhaI recognition sequence GCGC experience motions
AB  - on a much slower (1-100 mu s) time scale. We compare these observations
AB  - with previous solution and solid-state NMR studies of the EcoRI
AB  - nuclease target sequence, and solid-state NMR studies of a similar HhaI
AB  - target construct. While an increased mobility of cytidine furanose
AB  - rings compared to those of other nucleotides is observed for both
AB  - sequences, the slower motions are only observed in the HhaI target DNA.
AB  - We propose that this inherent flexibility lowers the energetic barriers
AB  - that must occur when the DNA binds to the HhaI methyltransferase and
AB  - for extrusion of the cytidine prior to its methylation.
ER  -

TY  - JOUR
AU  - Shambat, S.
AU  - Nadig, S.
AU  - Prabhakara, S.
AU  - Bes, M.
AU  - Etienne, J.
AU  - Arakere, G.
TI  - Clonal complexes and virulence factors of Staphylococcus aureus from several cities in India.
JO  - BMC Microbiol.
PY  - 2012
SP  - 64
EP  - 64
VL  - 12
AB  - BACKGROUND: Diseases from Staphylococcus aureus are a major problem in Indian
AB  - hospitals and recent studies point to infiltration of community associated
AB  - methicillin resistant S. aureus (CA-MRSA) into hospitals. Although CA-MRSA are
AB  - genetically different from nosocomial MRSA, the distinction between the two
AB  - groups is blurring as CA-MRSA are showing multidrug resistance and are endemic in
AB  - many hospitals. Our survey of samples collected from Indian hospitals between
AB  - 2004 and 2006 had shown mainly hospital associated methicillin resistant
AB  - Staphylococcus aureus (HA-MRSA) carrying staphylococcal cassette chromosome mec
AB  - (SCCmec) type III and IIIA. But S. aureus isolates collected from 2007 onwards
AB  - from community and hospital settings in India have shown SCCmec type IV and V
AB  - cassettes while several variations of type IV SCCmec cassettes from IVa to IVj
AB  - have been found in other parts of the world. In the present study, we have
AB  - collected nasal swabs from rural and urban healthy carriers and pus, blood etc
AB  - from in patients from hospitals to study the distribution of SCCmec elements and
AB  - sequence types (STs) in the community and hospital environment. We performed
AB  - molecular characterization of all the isolates to determine their lineage and
AB  - microarray of select isolates from each sequence type to analyze their toxins,
AB  - virulence and immune-evasion factors. RESULTS: Molecular analyses of 68 S. aureus
AB  - isolates from in and around Bengaluru and three other Indian cities have been
AB  - carried out. The chosen isolates fall into fifteen STs with all major clonal
AB  - complexes (CC) present along with some minor ones. The dominant MRSA clones are
AB  - ST22 and ST772 among healthy carriers and patients. We are reporting three novel
AB  - clones, two methicillin sensitive S. aureus (MSSA) isolates belonging to ST291
AB  - (related to ST398 which is live stock associated), and two MRSA clones, ST1208
AB  - (CC8), and ST672 as emerging clones in this study for the first time. Sixty nine
AB  - percent of isolates carry Panton- Valentine Leucocidin genes (PVL) along with
AB  - many other toxins. There is more diversity of STs among methicillin sensitive S.
AB  - aureus than resistant ones. Microarray analysis of isolates belonging to
AB  - different STs gives an insight into major toxins, virulence factors, adhesion and
AB  - immune evasion factors present among the isolates in various parts of India.
AB  - CONCLUSIONS: S. aureus isolates reported in this study belong to a highly diverse
AB  - group of STs and CC and we are reporting several new STs which have not been
AB  - reported earlier along with factors influencing virulence and host pathogen
AB  - interactions.
ER  -

TY  - JOUR
AU  - Shamseldin, A.
AU  - Nelson, M.S.
AU  - Staley, C.
AU  - Guhlin, J.
AU  - Sadowsky, M.J.
TI  - Draft Genome Sequences of Four Novel Thermal- and Alkaline-Tolerant Egyptian Rhizobium Strains Nodulating Berseem Clover.
JO  - Genome Announcements
PY  - 2016
SP  - e00988
EP  - e00916
VL  - 4
AB  - Four Rhizobium strains were isolated from berseem clover in Egypt. The symbiotically
AB  - effective, salt-tolerant, strain Rhiz950 was identified as new
AB  - species, Rhizobium aegypticaum sv. trifolii (USDA 7124(T)). The other three
AB  - thermal- and pH-tolerant strains were identified as Rhizobium bangladeshense sv.
AB  - trifolii, the type strain is USDA 7125(T).
ER  -

TY  - JOUR
AU  - Shan, D.
AU  - Li, X.
AU  - Gu, Z.
AU  - Wei, G.
AU  - Gao, Z.
AU  - Shao, Z.
TI  - Draft Genome Sequence of the Agar-Degrading Bacterium Catenovulum sp. Strain DS-2, Isolated from Intestines of Haliotis diversicolor.
JO  - Genome Announcements
PY  - 2014
SP  - e00144
EP  - e00114
VL  - 2
AB  - Catenovulum sp. strain DS-2, isolated from intestines of Haliotis diversicolor, is able to
AB  - degrade agar and produce agaro-oligosaccharides. Here, we report the
AB  - draft genome sequence of Catenovulum sp. strain DS-2.
ER  -

TY  - JOUR
AU  - Shan, D.
AU  - Ying, J.
AU  - Li, X.
AU  - Gao, Z.
AU  - Wei, G.
AU  - Shao, Z.
TI  - Draft Genome Sequence of the Carrageenan-Degrading Bacterium Cellulophaga sp. Strain KL-A, Isolated from Decaying Marine Algae.
JO  - Genome Announcements
PY  - 2014
SP  - e00145
EP  - e00114
VL  - 2
AB  - Cellulophaga sp. strain KL-A, isolated from decaying marine algae, is able to degrade
AB  - iota-carrageenan. Here, we report the draft genome sequence of
AB  - Cellulophaga sp. strain KL-A.
ER  -

TY  - JOUR
AU  - Shan, W.
AU  - Liu, H.
AU  - Zhou, Y.
AU  - Yu, X.
TI  - Draft Genome Sequence of Streptomyces sp. XY006, an Endophyte Isolated from Tea (Camellia sinensis).
JO  - Genome Announcements
PY  - 2017
SP  - e00971
EP  - e00917
VL  - 5
AB  - Streptomyces sp. XY006 is an endophytic bacterium isolated from the young leaf material of the
AB  - tea plant (Camellia sinensis). The draft genome consists of 8.2
AB  - Mb and encodes 7,415 putative open reading frames. This strain is found to
AB  - contain a high capacity for the production of natural products.
ER  -

TY  - JOUR
AU  - Shan, W.
AU  - Yang, X.
AU  - Ma, W.
AU  - Yang, Y.
AU  - Guo, X.
AU  - Guo, J.
AU  - Zheng, H.
AU  - Li, G.
AU  - Xie, B.
TI  - Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.
JO  - Genome Announcements
PY  - 2013
SP  - e00890
EP  - e00813
VL  - 1
AB  - Ralstonia solanacearum is an important etiological agent that can cause serious bacterial wilt
AB  - in a very wide range of potential host plants, including ginger.
AB  - Here, we report the complete genome sequence of R. solanacearum SD54, a race 4
AB  - biovar 4 (R4B4) strain from a diseased ginger plant in China.
ER  -

TY  - JOUR
AU  - Shanak, S.
AU  - Helms, V.
TI  - Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations.
JO  - J. Chem. Phys.
PY  - 2014
SP  - 22D512
EP  - 22D512
VL  - 141
AB  - Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences
AB  - at the levels of the genome and transcriptome. To characterize the differential roles of
AB  - methylating adenine or cytosine with respect to their hydration properties, we performed
AB  - conventional MD simulations and free energy perturbation calculations for two particular DNA
AB  - sequences, namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound
AB  - DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine,
AB  - respectively. We found that a single methylated cytosine has a clearly favorable hydration
AB  - free energy over cytosine since the attached methyl group has a slightly polar character. In
AB  - contrast, capping the strongly polar N6 of adenine with a methyl group gives a slightly
AB  - unfavorable contribution to its free energy of solvation. Performing the same demethylation in
AB  - the context of a DNA double-strand gave quite similar results for the more solvent-accessible
AB  - cytosine but much more unfavorable results for the rather buried adenine. Interestingly, the
AB  - same demethylation reactions are far more unfavorable when performed in the context of the
AB  - opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation
AB  - in a specific sequence context. In addition, free energy calculations for demethylating
AB  - adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z
AB  - transition of DNA transition is rather a property of cytosine methylated sequences but is not
AB  - preferable for the adenine-methylated sequences investigated here.
ER  -

TY  - JOUR
AU  - Shane, J.L.
AU  - Bongio, N.J.
AU  - Favia, G.
AU  - Lampe, D.J.
TI  - Draft Genome Sequence of Asaia sp. Strain SF2.1, an Important Member of the Microbiome of Anopheles Mosquitoes.
JO  - Genome Announcements
PY  - 2014
SP  - e01202
EP  - e01213
VL  - 2
AB  - Asaia spp. are abundant members of the microbiota of Anopheles mosquitoes, the principle
AB  - vectors of malaria. Here, we report the draft genome sequence of Asaia
AB  - sp. strain SF2.1. This strain is under development as a platform to deliver
AB  - antimalarial peptides and proteins to adult female Anopheles mosquitoes.
ER  -

TY  - JOUR
AU  - Shang, N.
AU  - Zhu, Q.
AU  - Dai, M.
AU  - Zhao, G.
TI  - Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of Salinicola tamaricis.
JO  - Genome Announcements
PY  - 2018
SP  - e00358
EP  - e00318
VL  - 6
AB  - The first complete genome sequence of a recently described Salinicola tamaricis species was
AB  - determined for the strain F01(T) (=CCTCC AB 2015304(T) =KCTC
AB  - 42855(T)). The strain was isolated from the leaves of wetland plant Tamarix
AB  - chinensis Lour and shows a high tolerance to heavy metals, such as manganese,
AB  - nickel, lead, and copper ions.
ER  -

TY  - JOUR
AU  - Shang, Y.
AU  - Zhang, N.
AU  - Zhu, P.
AU  - Luo, Y.
AU  - Huang, K.
AU  - Tian, W.
AU  - Xu, W.
TI  - Restriction enzyme cutting site distribution regularity for DNA looping technology.
JO  - Gene
PY  - 2014
SP  - 222
EP  - 228
VL  - 534
AB  - The restriction enzyme cutting site distribution regularity and looping conditions were
AB  - studied systematically. We obtained the restriction enzyme
AB  - cutting site distributions of 13 commonly used restriction enzymes in 5 model
AB  - organism genomes through two novel self-compiled software programs. All of the
AB  - average distances between two adjacent restriction sites fell sharply with
AB  - increasing statistic intervals, and most fragments were 0-499bp. A shorter DNA
AB  - fragment resulted in a lower looping rate, which was also directly proportional
AB  - to the DNA concentration. When the length was more than 500bp, the concentration
AB  - did not affect the looping rate. Therefore, the best known fragment length was
AB  - longer than 500bp, and did not contain the restriction enzyme cutting sites which
AB  - would be used for digestion. In order to make the looping efficiencies reach
AB  - nearly 100%, 4-5 single cohesive end systems were recommended to digest the
AB  - genome separately.
ER  -

TY  - JOUR
AU  - Shankar, C.
AU  - Nabarro, L.E.
AU  - Devanga, R.N.K.
AU  - Muthuirulandi, S.D.P.
AU  - Daniel, J.L.
AU  - Doss, C.G.P.
AU  - Veeraraghavan, B.
TI  - Draft Genome Sequences of Three Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Isolates from Bacteremia.
JO  - Genome Announcements
PY  - 2016
SP  - e01081
EP  - e01016
VL  - 4
AB  - Hypervirulent Klebsiella pneumoniae strains have been increasingly reported worldwide, and
AB  - there is emergence of carbapenem resistance among them. Here, we
AB  - report the genome sequences of three carbapenem-resistant hypervirulent K.
AB  - pneumoniae isolates isolated from bacteremic patients at a tertiary-care center
AB  - in South India.
ER  -

TY  - JOUR
AU  - Shankar, C.
AU  - Santhanam, S.
AU  - Kumar, M.
AU  - Gupta, V.
AU  - Devanga, R.N.K.
AU  - Veeraraghavan, B.
TI  - Draft Genome Sequence of an Extended-Spectrum-beta-Lactamase-Positive Hypervirulent Klebsiella pneumoniae Strain with Novel Sequence Type 2318 Isolated  from a Neonate.
JO  - Genome Announcements
PY  - 2016
SP  - e01273
EP  - e01216
VL  - 4
AB  - Antimicrobial resistance among hypervirulent Klebsiella pneumoniae is increasingly reported.
AB  - Here, we report the draft genome sequence of a
AB  - hypervirulent K. pneumoniae strain isolated from a neonate with sepsis belonging
AB  - to novel sequence type 2318 (ST2318).
ER  -

TY  - JOUR
AU  - Shankar, M.
AU  - Mageswari, A.
AU  - Suganthi, C.
AU  - Gunasekaran, P.
AU  - Gothandam, K.M.
AU  - Karthikeyan, S.
TI  - Genome Sequence of a Moderately Halophilic Bacillus cereus Strain, TS2, Isolated  from Saltern Sediments.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00873
EP  - e00818
VL  - 7
AB  - We report the 5.3-Mbp genome sequence of Bacillus cereus strain TS2, which was isolated from
AB  - the sediments of a solar saltern in southern India. Genome analysis
AB  - of B. cereus TS2, a salt-resistant strain, will improve our understanding of how
AB  - B. cereus, a food pathogen, responds to hyperosmotic stress.
ER  -

TY  - JOUR
AU  - Shankar, M.
AU  - Ponraj, P.
AU  - Ilakiam, D.
AU  - Rajendhran, J.
AU  - Gunasekaran, P.
TI  - Genome Sequence of the Plant Growth-Promoting Bacterium Enterobacter cloacae GS1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4479
EP  - 4479
VL  - 194
AB  - Here, we present the genome sequence of Enterobacter cloacae GS1. This strain proficiently
AB  - colonizes rice roots and promotes plant growth by improving plant
AB  - nutrition. Analyses of the E. cloacae GS1 genome will throw light on the genetic
AB  - factors involved in root colonization, growth promotion, and ecological success
AB  - of this rhizobacterium.
ER  -

TY  - JOUR
AU  - Shankar, S.
AU  - Tyagi, A.K.
TI  - Purification and characterization of restriction endonuclease MgoI from Mycobacterium gordonae.
JO  - Gene
PY  - 1993
SP  - 153
EP  - 154
VL  - 131
AB  - A restriction endonuclease, MgoI an isoschizomer of Sau3AI, was purified from Mycobacterium
AB  - gordonae TRC1318. As compared to Sau3AI, the yield of MgoI was seven-eight fold higher, the
AB  - enzyme was four times more stable at 37C, and in addition, had optimal activity over a much
AB  - broader range of salt concentrations.
ER  -

TY  - JOUR
AU  - Shankar, S.
AU  - Tyagi, A.K.
TI  - MchAI and MchAII, two class-II restriction endonucleases from Mycobacterium chelonei.
JO  - Gene
PY  - 1993
SP  - 119
EP  - 123
VL  - 132
AB  - We have purified and characterized two class-II restriction endonucleases from the saprophyte
AB  - Mycobacterium chelonei AMB 82. MchAI was an isoschizomer of NotI recognizing and cleaving at
AB  - 5'-GC/GGCCGC. MchAI did not require Triton X-100 for activity and was fully active at
AB  - concentrations over 10-200 mM KCl and MgCl2. MchAII was an isoschizomer of HaeIII recognizing
AB  - and cleaving at 5'-GG/CC. MchAII was active in 10 mM and was inactive at KCl concentrations
AB  - lower than 250 mM.
ER  -

TY  - JOUR
AU  - Shankar, S.
AU  - Tyagi, A.K.
TI  - MhaAI, a novel isoschizomer of PstI from Mycobacterium habana recognizing 5'-CTGCA/G-3'.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2891
EP  - 2891
VL  - 20
AB  - We have isolated a novel class II restriction endonuclease, MhaAI, from Mycobacterium habana
AB  - strain 206 which recognizes the sequence 5'-CTGCA/G-3' and generates 3' protruding
AB  - fragments. Unlike its isoschizomer PstI, MhaAI did not exhibit star activity even at glycerol
AB  - concentrations as high as 35% and at units/ug DNA ratios greater than 300. MhaAI was fully
AB  - active in low salt (10 mM Tris pH 8.0, 10 mM MgCl2) in comparison to PstI, which requires NaCl
AB  - at a concentration of 50-100 mM for optimal activity. MhaAI was also found equally active in
AB  - 10 to 200 mM concentration range of KCl as well as MgCl2. The enzyme, however, was inhibited
AB  - by NaCl concentrations greater than 50 mM.
ER  -

TY  - JOUR
AU  - Shankar, S.
AU  - Tyagi, A.K.
TI  - MfoAI, a novel isoschizomer of HaeIII from Mycobacterium fortuitum recognizing 5'-GG/CC-3' .
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2890
EP  - 2890
VL  - 20
AB  - We have isolated a novel class II restriction endonuclease, MfoAI, from Mycobacterium
AB  - fortuitum TMC 1529 which recognizes the sequence 5'-GG/CC-3' generating blunt ended
AB  - fragments. MfoAI was found to have a very high affinity for phosphocellulose and eluted late
AB  - at a concentration of 1.8 M KCl. This permitted very rapid purification of the enzyme
AB  - completely free from non-specific nucleases. In contrast to the situation in Haemophilus
AB  - aegyptius which has HaeIII and HaeII, MfoAI was found to be the only activity associated with
AB  - M. fortuitum TMC 1529, suggesting this organism to be a better source for this enzyme. In
AB  - addition, the activity of MfoAI was independent of salt concentration and purified MfoAI was
AB  - equally active in 10-200 mM concentrations of KCl, MgCl2 and NaCl and in the wide pH range of
AB  - 7.4-11.0.
ER  -

TY  - JOUR
AU  - Shankarappa, B.
AU  - Vijayananda, K.
AU  - Ehrlich, G.
TI  - Silmut: A Computer Program for the Identification of Regions Suitable for Silent Mutagenesis to Introduce Restriction Enzyme Recognition Sequences.
JO  - Biotechniques
PY  - 1992
SP  - 882
EP  - 884
VL  - 12
AB  - We describe a set of IBM-compatible computer programs designed to selectively identify the
AB  - potential sites for silent mutagenesis within a target DNA sequence. This program is based on
AB  - a novel strategy of identifying amino acid motifs compatible with each restriction site
AB  - (BioTechniques 12:382-384m 1991). The programs can be used to identify the suitability for the
AB  - introduction of any 6-base nucleic acid sequences, such as restriction enzyme sites in
AB  - cassette mutagenesis strategies. The Table program generates a table of multiple amino acid
AB  - motifs for each restriction enzyme, obtained by translating each unique recognition sequence
AB  - in all three reading frames. The Silmut program which utilizes the features of Table, will
AB  - further identify the presence of a match betwen any amino acid motif of each restriction
AB  - enzyme and the input target sequence. Minor manipulations of the database files will enable
AB  - the individual researcher to identify the potential for introduction of any 6-base sequences
AB  - by silent mutagenesis.
ER  -

TY  - JOUR
AU  - Shao, C.
AU  - Wang, C.
AU  - Zang, J.
TI  - Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2014
SP  - 2477
EP  - 2486
VL  - 70
AB  - 5-Hydroxymethylation is a curious modification of cytosine that was discovered some decades
AB  - ago, but its functional role in eukaryotes still awaits elucidation. 5-Hydroxymethylcytosine
AB  - is an epigenetic marker that is crucial for multiple biological processes. The profile is
AB  - altered under certain disease conditions such as cancer, Huntington's disease and
AB  - Alzheimer's disease. Using the DNA-modification-dependent restriction endonuclease AbaSI
AB  - coupled with sequencing (Aba-seq), the hydroxymethylome can be deciphered at the resolution of
AB  - individual bases. The method is based on the enzymatic properties of AbaSI, a member of the
AB  - PvuRts1I family of endonucleases. PvuRts1I is a modification-dependent endonuclease with high
AB  - selectivity for 5-hydroxymethylcytosine over 5-methylcytosine and cytosine. In this study, the
AB  - crystal structure of PvuRts1I was determined in order to understand and improve the substrate
AB  - selectivity. A nuclease domain and an SRA-like domain are located at the N- and C-termini,
AB  - respectively. Through comparison with other SRA-domain structures, the SRA-like domain was
AB  - proposed to be the 5-hmC recognition module. Several mutants of PvuRts1I with enzymatic
AB  - activity restricted to 5-hydroxymethylcytosine only were generated based on the structural
AB  - analysis, and these enzyme variants are appropriate for separating the hydroxymethylome from
AB  - the wider methylome.
ER  -

TY  - JOUR
AU  - Shao, Y.
AU  - Xu, M.-Q.
AU  - Paulus, H.
TI  - Protein splicing: Evidence for an N-O acyl rearrangement as the initial step in the splicing process.
JO  - Biochemistry
PY  - 1996
SP  - 3810
EP  - 3815
VL  - 35
AB  - Protein splicing involves the self-catalyzed formation of a branched
AB  - intermediate, which then resolves into the excised intervening sequence and the spliced
AB  - protein.  A possible mechanism for branched intemediate formation is an N-O
AB  - rearrangement of the peptide bond involving the amino group of the conserved
AB  - serine/cysteine residue at the upstream splice junction to yield a linear peptide ester
AB  - intermediate.  This possibility was examined using an in vitro splicing system involving the
AB  - intervening sequence from the DNA polymerase of the extremely thermophilic archeon,
AB  - Pyrococcus sp. GB-D.  Because thioesters react much more rapidly with nitrogen
AB  - nucleophiles at neutral pH than do oxygen esters, protein-splicing precursors in which the
AB  - serine residue of interest was replaced by cysteine were constructed and purified.  In the
AB  - presence of 0.25M hydroxylamine or 0.1M ethylene diamine at pH 6 or higher, these
AB  - constructs underwent rapid cleavage at the upstream splice junction, consistent with the
AB  - aminolysis of a thioester.  The site of hydroxylaminolysis was identified by analysis of the
AB  - C-terminus of the polypeptide cleavage products.  Comparison of the C-terminal peptide
AB  - hydroxamate with the synthetic peptide hydroxamates with respect to chromatographic
AB  - mobility, colorimetric assay, amino acid composition, and high-resolution mass
AB  - spectrometry showed that the hydroxylamine-sensitive site in the splicing precursor was the
AB  - peptide bond adjacent to the serine residue at the upstream splice junction.  These results
AB  - provide evidence that the peptide bond at the upstream splice junction can undergo a self-
AB  - catalyzed N-O or N-S acyl rearrangement to yield a linear polypeptide ester intermediate
AB  - and suggest that this kind of rearrangement constitutes the first step in protein splicing.
ER  -

TY  - JOUR
AU  - Shao, Y.
AU  - Xu, M.-Q.
AU  - Paulus, H.
TI  - Protein splicing: characterization of the aminosuccinimide residue at the carboxyl terminus of the excised intervening sequence.
JO  - Biochemistry
PY  - 1995
SP  - 10844
EP  - 10850
VL  - 34
AB  - Protein splicing is a self-catalyzed, posttranslational process which
AB  - converts a precursor polypeptide into two new proteins by the excision of an internal
AB  - polypeptide segment and the ligation of the flanking polypeptides.  Evidence has been
AB  - presented that protein splicing involves a branched intermediate, which is resolved into the
AB  - two protein products by the cyclization of an asparagine residue to aminosuccinimide.  This
AB  - report describes the chemical synthesis of a peptide with a C-terminal aminosuccinimide
AB  - residue, corresponding to the putative C-terminus of the excised intervening sequence
AB  - (intein) derived from the thermostable DNA polymerase of Pyrococcus species GB-D.  The
AB  - synthetic aminosuccinimide peptide was compared with the C-terminal cyanogen bromide
AB  - peptide of the excised intein and found to be indistinguishable in terms of its
AB  - chromatographic properties, high-resolution mass spectrum, and colorimetric assay
AB  - involving reaction with hydroxylamine.  This establishes definitively that protein splicing is
AB  - accompanied by the cyclization of asparagine to yield an aminosuccinimide residue at the C-
AB  - terminus of the excised intein and that this unusual residue is therefore a natural
AB  - constituent
AB  - of spliced proteins.  The effects of pH and temperature on the stability of the synthetic
AB  - aminosuccinimide peptide are described.  The stability of the C-terminal aminosuccinimide
AB  - decreased with increasing pH, similar to the internal aminosuccinimide residues that occur
AB  - in many proteins as intermediates in protein deamidation, but the C-terminal
AB  - aminosuccinimide was 5-10 times more stable than internal aminosuccinimides, with a half-
AB  - life of about 80 h at 25oC and pH 7.4, accounting for its relative ease of isolation.
ER  -

TY  - JOUR
AU  - Shapiro, L.R.
AU  - Scully, E.D.
AU  - Roberts, D.
AU  - Straub, T.J.
AU  - Geib, S.M.
AU  - Park, J.
AU  - Stephenson, A.G.
AU  - Salaau, R.E.
AU  - Liu, Q.
AU  - Beattie, G.
AU  - Gleason, M.
AU  - De Moraes, C.M.
AU  - Mescher, M.C.
AU  - Fleischer, S.G.
AU  - Kolter, R.
AU  - Pierce, N.
AU  - Zhaxybayeva, O.
TI  - Draft Genome Sequence of Erwinia tracheiphila, an Economically Important Bacterial Pathogen of Cucurbits.
JO  - Genome Announcements
PY  - 2015
SP  - e00482
EP  - e00415
VL  - 3
AB  - Erwinia tracheiphila is one of the most economically important pathogens of cucumbers, melons,
AB  - squashes, pumpkins, and gourds in the northeastern and
AB  - midwestern United States, yet its molecular pathology remains uninvestigated.
AB  - Here, we report the first draft genome sequence of an E. tracheiphila strain
AB  - isolated from an infected wild gourd (Cucurbita pepo subsp. texana) plant. The
AB  - genome assembly consists of 7 contigs and includes a putative plasmid and at
AB  - least 20 phage and prophage elements.
ER  -

TY  - JOUR
AU  - Shapovalova, N.I.
AU  - Ivanov, L.Y.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease BstM6I from the natural isolate Bacillus stearothermophilus M6.
JO  - Bioorg. Khim.
PY  - 1992
SP  - 1186
EP  - 1189
VL  - 18
AB  - A site-specific endonuclease activity was found in extracts of Bacillus stearothermophilus M6
AB  - isolated from molasses. The functionally pure enzyme designated as BstM6I was obtained by
AB  - consecutive chromatographies on blue sepharose, hydroxyapatite, and heparin-sepharose. The
AB  - endonuclease recognizes the nucleotide sequence CC^WGG in double-stranded DNA and cleaves it
AB  - as indicated by the arrow to give one-nucleotide 5'-protruding ends. Consequently, the
AB  - site-specific endonuclease BstM6I is an isoschizomer of BstNI.
ER  -

TY  - JOUR
AU  - Shapovalova, N.I.
AU  - Zheleznaja, L.A.
AU  - Matvienko, N.I.
TI  - BspKT6I, a new site-specific endonuclease which cleaves the GATC site producing two nucleotide 5'-protruding ends.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 5794
EP  - 5794
VL  - 21
AB  - A new class II restriction endonuclease BspKT6I was isolated from soil thermophilic bacteria
AB  - Bacillus species KT6. The enzyme was purified by chromatography on blue-agarose,
AB  - heparin-Sepharose and hydroxylapatite. Digestion of T7 DNA has revealed that the enzyme is an
AB  - isoschizomer of Sau3AI. Cleavage points were determined by the primed-synthesis reaction using
AB  - M13mp18 DNA. The cleavage product resulted in a band that comigrated with G (Fig 1). Upon
AB  - addition of the DNA-polymerase, a band appeared two nucleotides higher. These results indicate
AB  - that the enzyme recognizes the palindromic sequence G^ATC and cleaves it as indicated creating
AB  - two nucleotide 5'-extensions. It is the first isomer of Sau3AI producing such ends. The DNA
AB  - fragments produced by this enzyme can be ligated with PvuI-produced DNA fragments. BspKT6I is
AB  - sensitive to dam-methylation. It does not cleave pBR322 isolated from the E. coli dam+ strain
AB  - and results in almost complete digestion of pBR322 isolated from the dam-strain (Fig. 2). The
AB  - optimal reaction buffer is 10 mM Tris-HCl (ph 7.5), 10 mM MgCl2.
ER  -

TY  - JOUR
AU  - Shapovalova, N.I.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - New site-specific endonuclease and methylase from the thermophilic strain Bacillus species KT6.
JO  - Biokhimiia
PY  - 1994
SP  - 1730
EP  - 1738
VL  - 59
AB  - The site-specific endonuclease R.BspKT6I and the cognate site-specific methylase M.BspKT6I
AB  - were isolated to functionally pure state from the thermophilic strain Bacillus species KT6 by
AB  - Sephadex G-100 gel filtration followed by chromatography on heparin-Sepharose and
AB  - hydroxyapatite. Endonuclease BspKT6I is not an isoschizomer, but an isomer of Sau3AI and MboI.
AB  - It recognizes the GAT/C sequence and cleaves it as shown by arrow, and, in distinction to
AB  - Sau3AI and MboI, produces a protruding 3' dinucleotide. The cleavage of the site is inhibited
AB  - by dam methylation. The sticky ends resulting from BspKT6I cleavage are identical and
AB  - complementary to those formed after PvuI cleavage. The methylase isolated from B. species KT6
AB  - protects the DNA from subsequent cleavage by BspKT6I. The methylated base is adenine.
ER  -

TY  - JOUR
AU  - Shapovalova, N.I.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.N.
AU  - Matvienko, N.I.
TI  - A new site-specific endonuclease BspKT5I.
JO  - Biokhimiia
PY  - 1994
SP  - 485
EP  - 493
VL  - 59
AB  - A new site-specific endonuclease (BspKT5I) has been isolated from the thermophilic soil
AB  - bacterium Bacillus KT5 by chromatography on Blue agarose, hydroxyapatite, and
AB  - heparin-Sepharose; it is free from interfering impurities. On double-stranded DNA, BspKT5I
AB  - recognizes the sequence 5'-CTGAAG16N^/3'-GACTTC14N^ and cleaves the DNA at the recognition
AB  - site indicated by the arrows to form 3'-protruding dinucleotide termini. The isolated
AB  - endonuclease is an isoschizomer of Eco57I. However, unlike Eco57I, it is not stimulated by
AB  - S-adenosylmethionine (SAM) and thus belongs to subclass IIS and not to class IV, as Eco57I.
AB  - Furthermore, endonuclease BspKT5I, in contrast to Eco57I, has no methylase activity.
ER  -

TY  - JOUR
AU  - Sharath, A.N.
AU  - Weinhold, E.
AU  - Bhagwat, A.S.
TI  - Reviving a dead enzyme: cytosine deaminations promoted by an inactive DNA methyltransferase and an S-adenosylmethionine analogue.
JO  - Biochemistry
PY  - 2000
SP  - 14611
EP  - 14616
VL  - 39
AB  - The enzymes that transfer a methyl group to C5 of cytosine within specific sequences (C5
AB  - Mtases) deaminate the target cytosine to uracil if the methyl donor S-adenosylmethionine (SAM)
AB  - is omitted from the reaction.  Recently, it was shown that cytosine deamination caused by C5
AB  - Mtases M.HpaII, M.SssI and M.MspI is enhanced in the presence of several analogues of SAM, and
AB  - a mechanism for this analogue-promoted deamination was proposed. According to this mechanism,
AB  - the analogues protonate C5 of the target cytosine, creating a dihydrocytosine intermediate
AB  - that is susceptible to deamination. We show here that one of these analogues,
AB  - 5'-aminoadenosine (AA), enhances cytosine deamination by the Mtase M. EcoRII, but it does so
AB  - without enhancing protonation of C5. Further, we show that uracil is an intermediate in the
AB  - mutational pathway and propose an alternate mechanism for the analogue-promoted deamination.
AB  - The new mechanism involves a facilitated water attack at C4 but does not require attack at C6
AB  - by the enzyme. The latter feature of the mechanism was tested by using M.EcoRII mutants
AB  - defective in the nucleophilic attack at C6 in the deamination assay. We find that although
AB  - these proteins are defective in methyl transfer and cytosine deamination, they cause cytosine
AB  - deaminations in the presence of AA in the reaction. Our results point to a possible connection
AB  - between the catalytic mechanism of C5 Mtases and of enzymes that transfer methyl groups to
AB  - N(4) of cytosine. Further, they provide an unusual example where a coenzyme activates an
AB  - otherwise "dead" enzyme to perform catalysis by a new reaction pathway.
ER  -

TY  - JOUR
AU  - Sharko, F.S.
AU  - Shapovalova, A.A.
AU  - Tsygankova, S.V.
AU  - Komova, A.V.
AU  - Boulygina, E.S.
AU  - Teslyuk, A.B.
AU  - Gotovtsev, P.M.
AU  - Namsaraev, Z.B.
AU  - Khijniak, T.V.
AU  - Nedoluzhko, A.V.
AU  - Vasilov, R.G.
TI  - Draft Genome Sequence of 'Halomonas chromatireducens' Strain AGD 8-3, a Haloalkaliphilic Chromate- and Selenite-Reducing Gammaproteobacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00160
EP  - e00116
VL  - 4
AB  - Here, we report the complete genome sequence (3.97 Mb) of 'Halomonas chromatireducens' AGD
AB  - 8-3, a denitrifying bacterium capable of chromate and
AB  - selenite reduction under extreme haloalkaline conditions. This strain was
AB  - isolated from soda solonchak soils of the Kulunda steppe, Russian Federation.
ER  -

TY  - JOUR
AU  - Sharkova, E.V.
AU  - Nikolskaya, I.I.
AU  - Shomodi, P.
AU  - Feldesh, I.
AU  - Debov, S.S.
TI  - Effect of various conditions on stability of DNA-methylases from cells of Mycobacterium smegmatis butyricum.
JO  - Vopr. Med. Khim.
PY  - 1986
SP  - 125
EP  - 129
VL  - 32
AB  - DNA-methylases from M. sm. butyricum, produced by means of isoelectrofocusing, were
AB  - characterized by slow spontaneous variations in the activity with amplitude of 75-80% under
AB  - conditions of storage in glycerol at -10 C.  Effect of various conditions on stabilization of
AB  - activity of adenine methylases M.Mbu4,2 and M.Mbu7,2 was studied.  Alterations in the
AB  - enzymatic activity were not found in presence of substances applied usually to stabilize the
AB  - enzymes, blood serum albumin and cations of two valent metals as the values of the alterations
AB  - occurred in the ranges of the enzyme activity variations.
ER  -

TY  - JOUR
AU  - Sharkova, E.V.
AU  - Nikolskaya, I.I.
AU  - Shomodi, P.
AU  - Feldesh, I.
AU  - Debov, S.S.
TI  - Isolation and fractionation of DNA-methylases from Mycobacterium butyricum.
JO  - Vopr. Med. Khim.
PY  - 1984
SP  - 72
EP  - 76
VL  - 30
AB  - Properties of total preparation of methylases from M. butyricum strain were
AB  - studied using various methods of column chromatography.  Distinct heterogeneity
AB  - of the methylase preparation was demonstrated by gel filtration, anion exchange
AB  - chromatography on diethyl aminoethyl cellulose and affinity chromatography on
AB  - Sepharose blue.  Several methylases, dissimilar both in physico-chemical
AB  - properties and in their specificity to nitrogenous bases, were found in M.
AB  - butyricum cells.  In the strain studied methylases of adenine and cytosine were
AB  - found, which were responsible for biosynthesis of 6-methyladenine and
AB  - 5-methylcytosine in the acceptor DNA at the ratio 9:1.
ER  -

TY  - JOUR
AU  - Sharma, A.
AU  - Hira, P.
AU  - Shakarad, M.
AU  - Lal, R.
TI  - Draft Genome Sequence of Cellulosimicrobium sp. Strain MM, Isolated from Arsenic-Rich Microbial Mats of a Himalayan Hot Spring.
JO  - Genome Announcements
PY  - 2014
SP  - e01020
EP  - e01014
VL  - 2
AB  - Microbial mats situated at the Manikaran hot springs (>95 degrees C) are characterized by
AB  - their high arsenic content (140 ppb), qualifying as a stressed
AB  - niche. Here, we report the annotated draft genome (3.85 Mb) of Cellulosimicrobium
AB  - sp. strain MM, isolated from these microbial mats, consisting of 3,718 coding
AB  - sequences, with an average % G+C of 74.4%.
ER  -

TY  - JOUR
AU  - Sharma, G.
AU  - Khatri, I.
AU  - Subramanian, S.
TI  - Draft Genome Sequence of Kocuria palustris PEL.
JO  - Genome Announcements
PY  - 2014
SP  - e01261
EP  - e01213
VL  - 2
AB  - We report the 2.9-Mb draft genome sequence of an actinobacterium, Kocuria palustris PEL, of
AB  - the family Micrococcaceae.
ER  -

TY  - JOUR
AU  - Sharma, G.
AU  - Khatri, I.
AU  - Subramanian, S.
TI  - Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T.
JO  - Genome Biol. Evol.
PY  - 2016
SP  - 2520
EP  - 2529
VL  - 8
AB  - Myxobacteria are members of delta-proteobacteria and are typified by large genomes,
AB  - well-coordinated social behavior, gliding motility, and
AB  - starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole
AB  - genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T)
AB  - that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic
AB  - analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal
AB  - its divergence from other myxobacterial species and support its taxonomic
AB  - characterization into a separate family Sandaracinaceae, within the suborder
AB  - Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes
AB  - (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved
AB  - in starch, agar, chitin, and cellulose degradation. We identified 16
AB  - alpha-amylases and two gamma-amylases in the S. amylolyticus genome that likely
AB  - play a role in starch degradation. While many of the amylases are seen conserved
AB  - in other delta-proteobacteria, we notice several novel amylases acquired via
AB  - horizontal transfer from members belonging to phylum Deinococcus-Thermus,
AB  - Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in
AB  - the S. amylolyticus genome. Interestingly, several putative beta-glucosidases and
AB  - endoglucanases proteins involved in cellulose degradation were identified.
AB  - However, the absence of cellobiohydrolases/exoglucanases corroborates with the
AB  - lack of cellulose degradation by this bacteria.
ER  -

TY  - JOUR
AU  - Sharma, M.
AU  - Ellis, R.L.
AU  - Hinton, D.M.
TI  - Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 6658
EP  - 6662
VL  - 89
AB  - The bacteriophage T4 segA gene lies in a genetically unmapped region between the gene betagt
AB  - (beta-glucosyltransferase) and uvsX (recombination protein) and encodes a protein of 221 amino
AB  - acids. We have found that the first 100 amino acids of the SegA protein are highly similar to
AB  - the N termini of four other predicted T4 proteins, also of unknown function. Together these
AB  - five proteins, SegA-E (similar to endonucleases of group I introns), contain regions of
AB  - similarity to the endonuclease I-TevI, which is encoded by the mobile group I intron of the T4
AB  - td gene, and to putative endonucleases of group I introns present in the mitochondria of
AB  - Neurospora crassa, Podospora anserina, and Saccharomyces douglasii. Intron-encoded
AB  - endonucleases are required for the movement (homing) of the intron DNA into an intronless
AB  - gene, cutting at or near the site of intron insertion. Our in vitro assays indicate that SegA,
AB  - like I-TevI, is a Mg2+-dependent DNA endonuclease that has preferred sites for cutting. Unlike
AB  - the I-TevI gene, however, there is no evidence that segA (or the other seg genes) resides
AB  - within introns. Thus, it is possible that segA encodes an endonuclease that is involved in the
AB  - movement of the endonuclease-encoding DNA rather than in the homing of an intron.
ER  -

TY  - JOUR
AU  - Sharma, M.
AU  - Hinton, D.M.
TI  - Purification and characterization of the SegA protein of bacteriophage T4, an endonuclease related to proteins encoded by group I introns.
JO  - J. Bacteriol.
PY  - 1994
SP  - 6439
EP  - 6448
VL  - 176
AB  - Although not encoded by an intron, the bacteriophage T4 SegA protein shares common amino acid
AB  - motifs with a family of proteins found within mobile group I introns present in fungi and
AB  - phage.  Each of these intron-encoded proteins is thought to initiate the homing of its own
AB  - intron by cleaving the intronless DNA at or near the site of insertion.  Previously, we have
AB  - found that SegA also cleaves DNA.  In this report, we have purfied the SegA protein and
AB  - characterized this endonuclease activity extensively.  SegA protein cleaved circular and
AB  - linear plasmids, DNA containing unmodified cytosine, and wild-type T4 DNA containing
AB  - hydromethylated, glucosylated cytosines.  In all cases, certain sites on the DNA were highly
AB  - preferred for cleavage, but with increasing protein concentration or time of incubation,
AB  - cleavage occurred at many sites.  SegA cleaving activity was stimulated by the presence of ATP
AB  - or ATPgammaS.  Sequence analysis of three highly preferred cleavage sites did not reveal a
AB  - simple consensus sequence, suggesting that even among highly preferred sites, SegA tolerates
AB  - many different sequences.  A T4 segA amber mutant that we constructed had no phenotype, and
AB  - PCR analyses indicated that several T-even-related phages lack the segA gene.  Taken together,
AB  - our results show that SegA is an endonuclease with a hierarchy of site specificity, and these
AB  - results are consistent with the insertion of SegA DNA into the T4 genome some time after the
AB  - divergence of the closely related T-even phages.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - D'Souza, D.R.
AU  - Bhandari, D.
AU  - Parashar, V.
AU  - Capalash, N.
TI  - Demonstration of the principles of restriction endonuclease cleavage reactions using thermostable BflI from Anoxybacillus flavithermus.
JO  - Biochem. Mol. Biol. Educ.
PY  - 2003
SP  - 392
EP  - 396
VL  - 31
AB  - Restriction enzymes are basic tools in recombinant DNA technology. To shape the molecular
AB  - biology experiments, the students must know how to
AB  - work with these molecular scissors. Here, we describe an integrated set
AB  - of experiments, introduced in the "Advances in Molecular Biology and
AB  - Biotechnology" postgraduate course, which covers the important aspects
AB  - about restriction endonucleases: preparation of cell-lysate, one-column
AB  - partial-purification, assay, effect of temperature, buffers, Mg2+ ions
AB  - and glycerol on activity, and quality control of two-column partially
AB  - purified enzyme. Examples of study questions, which help students
AB  - understand the theoretical basis of the experiments, have been given.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - Diene, S.M.
AU  - Gimenez, G.
AU  - Robert, C.
AU  - Rolain, J.M.
TI  - Genome Sequence of Microbacterium yannicii, a Bacterium Isolated from a Cystic Fibrosis Patient.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4785
EP  - 4785
VL  - 194
AB  - Microbacterium yannicii is a Gram-positive, aerobic, yellow-pigmented, rod-shaped, nonmotile,
AB  - oxidase-negative, and catalase-positive bacterium isolated
AB  - on Columbia colistin-nalidixic acid (CNA) agar with 5% sheep blood from the
AB  - sputum of a cystic fibrosis patient. The present study reports the draft genome
AB  - of a Microbacterium yannicii strain.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - Gupta, S.K.
AU  - Adenipekun, E.O.
AU  - Barrett, J.B.
AU  - Hiott, L.M.
AU  - Woodley, T.A.
AU  - Iwalokun, B.A.
AU  - Oyedeji, K.S.
AU  - Oluwadun, A.
AU  - Ramadan, H.
AU  - Frye, J.G.
AU  - Jackson, C.R.
TI  - Draft Genome Sequence Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in 2013 from Humans and Chickens in Nigeria.
JO  - Genome Announcements
PY  - 2017
SP  - e01073
EP  - e01017
VL  - 5
AB  - Here, we present the draft genome sequences of nine multidrug-resistant Escherichia coli
AB  - strains isolated from humans (n = 6) and chicken carcasses (n =
AB  - 3) from Lagos, Nigeria, in 2013. Multiple extended-spectrum beta-lactamase (ESBL)
AB  - genes were identified in these isolates.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - Gupta, S.K.
AU  - Barrett, J.B.
AU  - Hiott, L.M.
AU  - House, S.L.
AU  - Woodley, T.A.
AU  - Frye, J.G.
AU  - Jackson, C.R.
TI  - Draft Genome Sequences of Eight Streptogramin-Resistant Enterococcus Species Isolated from Animal and Environmental Sources in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e01287
EP  - e01217
VL  - 5
AB  - Here, we present the draft genome sequences of eight streptogramin-resistant Enterococcus
AB  - species isolated from animals and an environmental source in the
AB  - United States from 2001 to 2004. Antimicrobial resistance genes were identified
AB  - conferring resistance to the macrolide-lincosamide-streptogramins,
AB  - aminoglycosides, tetracyclines, beta-lactams, and glycopeptides.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - Killmaster, L.F.
AU  - Volkening, J.D.
AU  - Cardenas-Garcia, S.
AU  - Shittu, I.
AU  - Meseko, C.A.
AU  - Sulaiman, L.K.
AU  - Joannis, T.M.
AU  - Miller, P.J.
AU  - Afonso, C.L.
TI  - Draft Genome Sequences of Five Novel Ochrobactrum spp. Isolated from Different Avian Hosts in Nigeria.
JO  - Genome Announcements
PY  - 2018
SP  - e00063
EP  - e00018
VL  - 6
AB  - Here, we present the draft genome sequences of five multidrug-resistant novel Ochrobactrum
AB  - species strains isolated from a pigeon, a duck, and chickens from
AB  - Nigeria in 2009.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - Killmaster, L.F.
AU  - Volkening, J.D.
AU  - Cardenas-Garcia, S.
AU  - Wajid, A.
AU  - Rehmani, S.F.
AU  - Basharat, A.
AU  - Miller, P.J.
AU  - Afonso, C.L.
TI  - Draft Genome Sequences of Three Ochrobactrum spp. Isolated from Different Avian Hosts in Pakistan.
JO  - Genome Announcements
PY  - 2018
SP  - e00269
EP  - e00218
VL  - 6
AB  - Here, we present the draft genome sequences of three Ochrobactrum sp. strains with
AB  - multidrug-resistant properties, isolated in 2015 from a pigeon and two
AB  - chickens in Pakistan.
ER  -

TY  - JOUR
AU  - Sharma, P.
AU  - Reddy, D.P.
AU  - Kumar, P.A.
AU  - Gadicherla, R.
AU  - George, N.
AU  - Bhandari, V.
TI  - Draft Genome Sequence of a Staphylococcus aureus Strain Isolated from a Cow with  Clinical Mastitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00914
EP  - e00915
VL  - 3
AB  - We report here the draft genome of Staphylococcus aureus causing clinical mastitis in a cow
AB  - from India. It is a major causative agent of mastitis and,
AB  - further, livestock-associated strains are emerging as a potential threat to
AB  - public health, thereby warranting studies to understand the genome of this deadly
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Sharma, P.K.
AU  - Fu, J.
AU  - Cicek, N.
AU  - Sparling, R.
AU  - Levin, D.B.
TI  - Kinetics of medium-chain-length polyhydroxyalkanoate production by a novel isolate of Pseudomonas putida LS46.
JO  - Can. J. Microbiol.
PY  - 2012
SP  - 982
EP  - 989
VL  - 58
AB  - Six bacteria that synthesize medium-chain-length polyhydroxyalkanoates (mcl-PHAs)
AB  - were isolated from sewage sludge and hog barn wash and identified as strains of
AB  - Pseudomonas and Comamonas by 16S rDNA gene sequencing. One isolate, Pseudomonas
AB  - putida LS46, showed good PHA production (22% of cell dry mass) in glucose medium,
AB  - and it was selected for further studies. While it is closely related to other P.
AB  - putida strains (F1, KT2440, BIRD-1, GB-1, S16, and W619), P. putida LS46 was
AB  - genetically distinct from these other strains on the basis of nucleotide sequence
AB  - analysis of the cpn60 gene hypervariable region. PHA production was detected as
AB  - early as 12 h in both nitrogen-limited and nitrogen-excess conditions. The
AB  - increase in PHA production after 48 h was higher in nitrogen-limited cultures
AB  - than in nitrogen-excess cultures. Pseudomonas putida LS46 produced mcl-PHAs when
AB  - cultured with glucose, glycerol, or C(6)-C(14) saturated fatty acids as carbon
AB  - sources, and mcl-PHAs accounted for 56% of the cell dry mass when cells were
AB  - batch cultured in medium containing 20 mmol/L octanoate. Although
AB  - 3-hydroxydecanoate was the major mcl-PHA monomer (58.1-68.8 mol%) in P. putida
AB  - LS46 cultured in glucose medium, 3-hydroxyoctanoate was the major monomer
AB  - produced in octanoate medium (88 mol%).
ER  -

TY  - JOUR
AU  - Sharma, P.K.
AU  - Fu, J.
AU  - Zhang, X.
AU  - Fristensky, B.W.
AU  - Davenport, K.
AU  - Chain, P.S.
AU  - Sparling, R.
AU  - Levin, D.B.
TI  - Draft Genome Sequence of Medium-Chain-Length Polyhydroxyalkanoate-Producing Pseudomonas putida Strain LS46.
JO  - Genome Announcements
PY  - 2013
SP  - e00151
EP  - e00113
VL  - 1
AB  - We describe the draft genome sequence of Pseudomonas putida strain LS46, a novel  isolate that
AB  - synthesizes medium-chain-length polyhydroxyalkanoates. The draft
AB  - genome of P. putida LS46 consists of approximately 5.86 million bp, with a G+C
AB  - content of 61.69%. A total of 5,316 annotated genes and 5,219 coding sequences
AB  - (CDS) were identified.
ER  -

TY  - JOUR
AU  - Sharma, R.
AU  - Singh, R.K.M.
AU  - Malik, G.
AU  - Deveshwar, P.
AU  - Tyagi, A.K.
AU  - Kapoor, S.
AU  - Kapoor, M.
TI  - Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress.
JO  - FEBS J.
PY  - 2009
SP  - 6301
EP  - 6311
VL  - 276
AB  - DNA methylation affects important developmental processes in both plants and animals. The
AB  - process of methylation of cytosines at C-5 is
AB  - catalysed by DNA methyltransferases (MTases), which are highly
AB  - conserved, both structurally and functionally, in eukaryotes. In this
AB  - study, we identified and characterized cytosine DNA MTase genes that
AB  - are activated with the onset of reproductive development in rice. The
AB  - rice genome (Oryza sativa L. subsp. japonica) encodes a total of 10
AB  - genes that contain the highly conserved MTase catalytic domain. These
AB  - genes have been categorized into subfamilies on the basis of
AB  - phylogenetic relationships. A microarray-based gene expression profile
AB  - of all 10 MTases during 22 stages/tissues that included 14 stages of
AB  - reproductive development and five vegetative tissues together with
AB  - three stresses, cold, salt and dehydration stress, revealed specific
AB  - windows of MTase activity during panicle and seed development. The
AB  - expression of six methylases was specifically/preferentially
AB  - upregulated with the initiation of floral organs. Significantly, one of
AB  - the MTases was also activated in young seedlings in response to cold
AB  - and salt stress. The molecular studies presented here suggest a greater
AB  - role for these proteins and the epigenetic process in affecting genome
AB  - activity during reproductive development and stress than was previously
AB  - anticipated.
ER  -

TY  - JOUR
AU  - Sharma, V.
AU  - Midha, S.
AU  - Ranjan, M.
AU  - Pinnaka, A.K.
AU  - Patil, P.B.
TI  - Genome Sequence of Xanthomonas axonopodis pv. punicae Strain LMG 859.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2395
EP  - 2395
VL  - 194
AB  - We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859,
AB  - the causal agent of bacterial leaf blight disease in pomegranate.
AB  - The draft genome will aid in comparative genomics, epidemiological studies, and
AB  - quarantine of this devastating phytopathogen.
ER  -

TY  - JOUR
AU  - Sharma, V.
AU  - Singh, P.K.
AU  - Midha, S.
AU  - Ranjan, M.
AU  - Korpole, S.
AU  - Patil, P.B.
TI  - Genome Sequence of Brevibacillus laterosporus Strain GI-9.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1279
EP  - 1279
VL  - 194
AB  - We report the 5.18-Mb genome sequence of Brevibacillus laterosporus strain GI-9,  isolated
AB  - from a subsurface soil sample during a screen for novel strains
AB  - producing antimicrobial compounds. The draft genome of this strain will aid in
AB  - biotechnological exploitation and comparative genomics of Brevibacillus
AB  - laterosporus strains.
ER  -

TY  - JOUR
AU  - Sharma, V.
AU  - Youngblood, B.
AU  - Reich, N.
TI  - Residues distal from the active site that alter enzyme function in M.HhaI DNA cytosine methyltransferase.
JO  - J. Biomol. Struct. Dyn.
PY  - 2005
SP  - 533
EP  - 543
VL  - 22
AB  - Ten M.HhaI residues were replaced with alanine to probe the importance of distal protein
AB  - elements to substrate/cofactor binding, methyl
AB  - transfer, and product release. The substitutions, ranging from 6-20 A
AB  - from the active site were evaluated by thermodynamic analysis, AdoMet
AB  - DNA pre-steady and steady-state kinetics, to obtain K-d(AdoMet),
AB  - K-d(DNA), k(cat)/K-m(DNA), k(cat), and k(methyltransfer) values. For
AB  - the wild-type M.Hhal, product release steps dominate catalytic turnover
AB  - while the 4-fold faster internal microscopic constant kmethyltransfer
AB  - presents an upper limit. The methyl transfer reaction has
AB  - Delta H and Delta S values of 10.3
AB  - kcal/mol and 29.4 cal/(mol K), respectively, consistent with a
AB  - compressed transition state similar to that observed in the gas phase.
AB  - Although the ten mutants remained largely unperturbed in methyl
AB  - transfer, long-range effects influencing substrate/cofactor binding and
AB  - product release were observed. Positive enhancements were seen in
AB  - Asp(73)Ala, which showed a 25-fold improvement in AdoMet affinity and
AB  - in Val(282)Ala, which showed a 4-fold improvement in catalytic
AB  - turnover. Based on an analysis of the positional probability within the
AB  - C-5-cytosine DNA methyltransferase family we propose that certain
AB  - conserved distal residues may be important in mediating long-range
AB  - effects.
ER  -

TY  - JOUR
AU  - Sharma, V.K.
AU  - Bayles, D.O.
AU  - Alt, D.P.
AU  - Looft, T.
TI  - Complete Genome Sequences of Curli-Negative and Curli-Positive Isolates of Foodborne Escherichia coli O157:H7 Strain 86-24.
JO  - Genome Announcements
PY  - 2016
SP  - e01323
EP  - e01316
VL  - 4
AB  - Escherichia coli O157:H7 strain 86-24 does not produce curli fimbriae, but gives  rise to
AB  - curli-positive isolates at a variable frequency. Here, we report the
AB  - complete genome sequences of curli-negative and curli-positive isolates of strain
AB  - 86-24.
ER  -

TY  - JOUR
AU  - Sharmin, D.
AU  - Guo, Y.
AU  - Nishizawa, T.
AU  - Ohshima, S.
AU  - Sato, Y.
AU  - Takashima, Y.
AU  - Narisawa, K.
AU  - Ohta, H.
TI  - Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica.
JO  - Microbes Environ.
PY  - 2018
SP  - 66
EP  - 76
VL  - 33
AB  - Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the
AB  - growth and metabolic potential of their hosts. To date, two EHB belonging to the
AB  - family Burkholderiaceae have been isolated and characterized as new taxa,
AB  - Burkholderia rhizoxinica (HKI 454(T)) and Mycoavidus cysteinexigens (B1-EB(T)),
AB  - in Japan. Metagenome sequencing was recently reported for Mortierella elongata
AB  - AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a
AB  - soil/litter sample in the USA. In the present study, we elucidated the complete
AB  - genome sequence of B1-EB(T) and compared it with those of Mc-AG77 and HKI 454(T).
AB  - The genomes of B1-EB(T) and Mc-AG77 contained a higher level of prophage
AB  - sequences and were markedly smaller than that of HKI 454(T). Although the
AB  - B1-EB(T) and Mc-AG77 genomes lacked the chitinolytic enzyme genes responsible for
AB  - invasion into fungal cells, they contained several predicted toxin-antitoxin
AB  - systems including an insecticidal toxin complex and PIN domain imposing an
AB  - addiction-like mechanism essential for endohyphal growth control during host
AB  - colonization. Despite the different host fungi, the alignment of amino acid
AB  - sequences showed that the HKI 454(T) genome consisted of 1,265 (32.6%) and 1,221
AB  - (31.5%) orthologous coding sequences (CDSs) with those of B1-EB(T) and Mc-AG77,
AB  - respectively. This comparative study of three phylogenetically associated
AB  - endosymbionts has provided insights into their origin and evolution, and suggests
AB  - the later bacterial invasion and adaptation of B1-EB(T) to its host metabolism.
ER  -

TY  - JOUR
AU  - Sharp, C.E. et al.
TI  - Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki.
JO  - Genome Announcements
PY  - 2015
SP  - e00644
EP  - e00615
VL  - 3
AB  - Methylohalobius crimeensis strain 10Ki is a moderately halophilic aerobic methanotroph
AB  - isolated from a hypersaline lake in the Crimean Peninsula, Ukraine.  This organism has the
AB  - highest salt tolerance of any cultured methanotroph. Here, we present a draft genome sequence
AB  - of this bacterium.
ER  -

TY  - JOUR
AU  - Sharp, P.A.
AU  - Sugden, B.
AU  - Sambrook, J.
TI  - Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose-ethidium bromide electrophoresis.
JO  - Biochemistry
PY  - 1973
SP  - 3055
EP  - 3063
VL  - 12
AB  - A rapid assay for restriction enzymes has been developed using electrophoresis
AB  - of DNA through 1.4% agarose gels in the presence of 0.5 microgram/ml of
AB  - ethidium bromide.  The method eliminates lengthy staining and destaining
AB  - procedures and resolves species of DNA which are less than 7 Mdaltons.  As
AB  - little as 0.05 microgram of DNA can easily be detected by direct examination of
AB  - the gels in ultraviolet light.  Using this technique, we have identified two
AB  - different restricting activities in extracts of Haemophilus parainfluenzae.
AB  - The two activities have different chromatographic properties on
AB  - phosphocellulose and Bio-Gel A-0.5m, and they attack SV40 DNA at different
AB  - sites.  One activity (HpaII) cleaves SV40 DNA at a single position situated
AB  - 0.38 fractional genome length from the insertion point of SV40 sequences into
AB  - the adenovirus SV40 hybrid Ad2++ND1.  The other activity (HpaI) cleaves SV40
AB  - DNA at three sites which appear to coincide with 3 of the 11 cleavage points
AB  - attacked by a restriction system isolated from H. influenzae strain Rd.
ER  -

TY  - JOUR
AU  - Sharp, P.M.
TI  - Molecular evolution of bacteriophages: Evidence of selection against the recognition sites of host restriction enzymes.
JO  - Mol. Biol. Evol.
PY  - 1986
SP  - 75
EP  - 83
VL  - 3
AB  - Restriction enzymes produced by bacteria serve as a defense against invading
AB  - bacteriophages, and so phages without other protection would be expected to
AB  - undergo selection to eliminate recognition sites for these enzymes from their
AB  - genomes.  The observed frequencies of all restriction sites in the genomes of
AB  - all completely sequenced DNA phages (T7, lambda, PhiX174, G4, M13, fl, fd, and
AB  - IKe) have been compared to expected frequencies derived from trinucleotide
AB  - frequencies.  Attention was focused on 6-base palindromes since they comprise
AB  - the typical recognition sites for type II restriction enzymes.  All of these
AB  - coliphages, with the exception of lambda and G4, exhibit significant avoidance
AB  - of the particular sequences that are enterobacterial restriction sites.  As
AB  - expected, the sequenced fraction of the genome of Phi29, a Bacillus subtilis
AB  - phage, lacks Bacillus restriction sites.  By contrast, the RNA phage MS2,
AB  - several viruses that infect eukaryotes (EBV, adenovirus, papilloma, and SV40),
AB  - and three mitochondrial genomes (human, mouse and cow) were found not to lack
AB  - restriction sites.  Because the particular palindromes avoided correspond
AB  - closely with the recognition sites for host enzymes and because other viruses
AB  - and small genomes do not show this avoidance, it is concluded that the effect
AB  - indeed results from natural selection.
ER  -

TY  - JOUR
AU  - Sharp, P.M.
AU  - Kelleher, J.E.
AU  - Daniel, A.S.
AU  - Cowan, G.M.
AU  - Murray, N.E.
TI  - Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 9836
EP  - 9840
VL  - 89
AB  - Restriction-modification systems can protect bacteria against viral infection. Sequences of
AB  - the hsdM gene, encoding one of the three subunits of type I restriction-modification systems,
AB  - have been determined for four strains of enterobacteria. Comparison with the known sequences
AB  - of EcoKI and EcoR124I indicated that all are homologous, though they fall into three families
AB  - (exemplified by EcoKI, EcoAI, and EcoR124I), the first two of which are apparently allelic.
AB  - The extent of amino acid sequence identity between EcoKI and EcoAI is so low that the genes
AB  - encoding them might be better termed pseudoalleles; this almost cerainly reflects genetic
AB  - exchange among highly divergent species. Within the EcoKI family the ratio of intra- to
AB  - interspecific divergence is very high. The extent of divergence between the genes from
AB  - Escherichia coli K-12 and Salmonella typhimurium LT2 is similar to that for other genes with
AB  - the same level of codon usage bias. In contrast, intraspecific divergence (between E. coli
AB  - strains B and K-12) is extremely high and may reflect the action of frequency-dependent
AB  - selection mediated by bacteriophages. There is also evidence of lateral transfer of a short
AB  - sequence between E. coli and S. typhimurium.
ER  -

TY  - JOUR
AU  - Sharpe, R.M.
AU  - Koepke, T.
AU  - Harper, A.
AU  - Grimes, J.
AU  - Galli, M.
AU  - Satoh-Cruz, M.
AU  - Kalyanaraman, A.
AU  - Evans, K.
AU  - Kramer, D.
AU  - Dhingra, A.
TI  - CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.
JO  - PLoS ONE
PY  - 2016
SP  - e0152404
EP  - e0152404
VL  - 11
AB  - High-throughput sequencing continues to produce an immense volume of information  that is
AB  - processed and assembled into mature sequence data. Data analysis tools
AB  - are urgently needed that leverage the embedded DNA sequence polymorphisms and
AB  - consequent changes to restriction sites or sequence motifs in a high-throughput
AB  - manner to enable biological experimentation. CisSERS was developed as a
AB  - standalone open source tool to analyze sequence datasets and provide biologists
AB  - with individual or comparative genome organization information in terms of
AB  - presence and frequency of patterns or motifs such as restriction enzymes.
AB  - Predicted agarose gel visualization of the custom analyses results was also
AB  - integrated to enhance the usefulness of the software. CisSERS offers several
AB  - novel functionalities, such as handling of large and multiple datasets in
AB  - parallel, multiple restriction enzyme site detection and custom motif detection
AB  - features, which are seamlessly integrated with real time agarose gel
AB  - visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the
AB  - REBASE enzyme database. Results from CisSERS enable the user to make decisions
AB  - for designing genotyping by sequencing experiments, reduced representation
AB  - sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS)
AB  - molecular markers for large sample sets. CisSERS is a java based graphical user
AB  - interface built around a perl backbone. Several of the applications of CisSERS
AB  - including CAPS molecular marker development were successfully validated using
AB  - wet-lab experimentation. Here, we present the tool CisSERS and results from
AB  - in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a
AB  - technology platform solution that facilitates efficient data utilization in
AB  - genomics and genetics studies.
ER  -

TY  - JOUR
AU  - Sharrocks, A.D.
AU  - Hornby, D.P.
TI  - Transcriptional analysis of the restriction and modification genes of bacteriophage P1.
JO  - Mol. Microbiol.
PY  - 1991
SP  - 685
EP  - 694
VL  - 5
AB  - Bacteriophage P1 res and mod genes encode the restriction and modification
AB  - polypeptides of the Type III restriction enzyme EcoPI.  Northern blot analysis
AB  - using res- and mod-specific probes revealed the presence of two separate
AB  - transcripts in strains harbouring the EcoPI restriction and modification genes.
AB  - Furthermore, by constructing a series of fusions with a promoterless lacZ
AB  - gene, we show that both the res and mod genes are transcribed from separate
AB  - promoters.  A more detailed investigation of the mod promoter region revealed
AB  - two promoters located some 70 and 140 bp upstream from the translational start
AB  - codon.  In addition, another pair of promoters and a further separate promoter
AB  - are located more than 500 bp upstream from this start codon.  Two short open
AB  - reading frames are located between these distal and proximal promoter clusters.
AB  - Transcription of the res gene is initiated from within the mod open reading
AB  - frame from two adjacent promoters.  In addition a functional promoter is
AB  - located on the antisense strand close to the res promoter region.  The
AB  - relationship between the transcription units of the res and mod genes is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Shaw, P.C.
AU  - Clark, D.R.
AU  - Kam, K.M.
AU  - Mok, Y.K.
TI  - Isolation and characterization of thermophilic restriction endonucleases.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - 199
EP  - 199
VL  - 91
AB  - Restriction endonucleases BsiBI, BsiEI, BsiGI, BsiUI and BsiYI were isolated from thermophilic
AB  - Bacillus spp. BsiBI, BsiEI and BsiUI were purified by using a DEAE sephacel column and a
AB  - heparin sepharose column, while BsiYI was followed by a FPLC mono Q column. Unpurified BsiGI
AB  - was used. Recognition sites of these enzymes were found by means of single and double
AB  - digestions on different DNA of known sequences. The cleavage sites were determined according
AB  - to FEMS Microbiol. Lett. 66:153-156 (1990). BsiGI and BsiUI were found to recognize TCCGGA and
AB  - CCWGG respectively. The recognition and cleavage sites of the other three enzymes are: BsiBI:
AB  - GATNN^NNATC; BsiEI: CGRY^CG and BsiYI: CCNNNNN^NNATC. These enzymes worked well at 55C. BsiBI
AB  - and BsiUI were sensitive to dam and dcm methylation respectively. The optimal ionic strength
AB  - for BsiEI and BsiYI was medium salt buffer, while that for BsiBI, BsiGI and BsiUI was high
AB  - salt buffer. During the characterization of BsiYI, we found that a G nucleotide is missed at
AB  - position 1227 of pACYC177 recorded in GenBank. This error also occurs in pACYC184 and p15A.
ER  -

TY  - JOUR
AU  - Shaw, P.C.
AU  - Mok, Y.K.
TI  - XcmI as a universal restriction enzyme for single-stranded DNA.
JO  - Gene
PY  - 1993
SP  - 85
EP  - 89
VL  - 133
AB  - Single-stranded DNA can be cleaved into defined fragments at any predetermined site by
AB  - interaction with a specially designed oligodeoxyribonucleotide (oligo) adaptor and the
AB  - class-IIN restriction endonuclease, XcmI. The oligo adaptor has the structure
AB  - (CCANNNNNNNNNTGG
AB  -  GGTNNNNNNNNNACC). Upon hybridization to the target DNA through the central 9-nucleotide
AB  - region and with the addition of XcmI, the template DNA is specifically cleaved to near
AB  - completion. Hairpin structures on the template close to the hybridization site reduce the
AB  - efficacy of cleavage.
ER  -

TY  - JOUR
AU  - Shaw, Y.J.
AU  - Chen, C.S.
TI  - Structure-activity relationship study of (-)-epicatechin analogues as DNA methyltransferase inhibitors.
JO  - ACS Abstracts
PY  - 2005
SP  - U186
EP  - U187
VL  - 229
AB  - Hypermethylation of DNA cPG islands is an important epigenetic mechanism for aberrant gene
AB  - silencing in cancer.  Although nucleoside analogue inhibitors of DNA methyltransferases can
AB  - reverse abnormal DNA hypermethylation in cancer cells, their clinical utility is limited due
AB  - to side effects.  The development of nonnucleoside DNMTs that lack systemic toxicity is a
AB  - promising approach to targeting epigenetic mechanisms for cancer therapy.  (-)-Epicatechin
AB  - analogues extracted from green tea inhibit DNMT.  Among them, EGCG and ECG exhibit inhibitory
AB  - activity with IC50 values of 20-30 uM.  Our objective is to synthesize (-)-epicatechin
AB  - scaffold, a series of derivaties have been synthesized and screened for activity in an in
AB  - vitro recombinant DNMT assay system.  Lead compounds with potent inhibitory activity will
AB  - subsequently be evaluated in cancer cell-based models of viability, apoptosis and DNA
AB  - methylation status.
ER  -

TY  - JOUR
AU  - She, Q. et al.
TI  - The complete genome of the crenarchaeon Sulfolobus solfataricus P2.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 7835
EP  - 7840
VL  - 98
AB  - The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single
AB  - chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no
AB  - detectable homologs in other sequenced genomes. Moreover, 40% appear to be archaeal-specific,
AB  - and only 12% and 2.3% are shared exclusively with bacteria and eukarya, respectively. The
AB  - genome shows a high level of plasticity with 200 diverse insertion sequence elements, many
AB  - putative nonautonomous mobile elements, and evidence of integrase-mediated insertion events.
AB  - There are also long clusters of regularly spaced tandem repeats. Different transfer systems
AB  - are used for the uptake of inorganic and organic solutes, and a wealth of intracellular and
AB  - extracellular proteases, sugar, and sulfur metabolizing enzymes are encoded, as well as
AB  - enzymes of the central metabolic pathways and motility proteins. The major metabolic electron
AB  - carrier is not NADH as in bacteria and eukarya but probably ferredoxin. The essential
AB  - components required for DNA replication, DNA repair and recombination, the cell cycle,
AB  - transcriptional initiation and translation, but not DNA folding, show a strong eukaryal
AB  - character with many archaeal-specific features. The results illustrate major differences
AB  - between crenarchaea and euryarchaea, especially for their DNA replication mechanism and cell
AB  - cycle processes and their translational apparatus.
ER  -

TY  - JOUR
AU  - She, X.
AU  - Tang, Y.
AU  - He, Z.
AU  - Lan, G.
TI  - Genome Sequencing of Ralstonia solanacearum Race 4, Biovar 4, and Phylotype I, Strain YC45, Isolated from Rhizoma kaempferiae in Southern China.
JO  - Genome Announcements
PY  - 2015
SP  - e01110
EP  - e01115
VL  - 3
AB  - Ralstonia solanacearum is an important phytopathogen that attacks over 400 plant  species,
AB  - including Zingiberaceae plants. Here, we report the complete genome sequence of strain YC45,
AB  - which was isolated from Rhizoma kaempferiae in southern  China.
ER  -

TY  - JOUR
AU  - Shearman, C.
AU  - Godon, J.-J.
AU  - Gasson, M.
TI  - Splicing of a group II intron in a functional transfer gene of Lactococcus lactis.
JO  - Mol. Microbiol.
PY  - 1996
SP  - 45
EP  - 53
VL  - 21
AB  - A chromosomally located sex factor that controls conjugation in Lactococcus lactis 712 has
AB  - been cloned and sequenced, leading to the discovery of an open reading frame with homology to
AB  - the maturases of group II self-splicing introns.  Reverse transcriptase polymerase chain
AB  - reaction amplification was used to demonstrate that the intron was spliced out of mRNA in
AB  - vivo, and sequence analysis revealed the site of splicing.  The intron was inserted within a
AB  - sex-factor gene which encodes a protein with homology to proteins involved in rolling-circle
AB  - DNA replication.  Gene-disruption experiments were used to demonstrate that this mobA gene was
AB  - essential for sex-factor transfer and this suggests that intron splicing is a necessary part
AB  - of the conjugation process.  The sequence of the intron was modelled to produce a secondary
AB  - structure that exhibited several features characteristic of the IIA subgroup.  Here we report
AB  - the characterization of a new group II intron in the Gram-positive bacterium L. lactis and
AB  - demonstrate for the first time in bacteria both splicing in vivo and an active role for the
AB  - gene carrying the intron.
ER  -

TY  - JOUR
AU  - Sheflyan, G.Y.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Conformational transition of restriction endonuclease MvaI-substrate complex under the influence of Mg2+ probed by DNA-protein linking studies.
JO  - Bioconjugate Chem.
PY  - 1998
SP  - 703
EP  - 707
VL  - 9
AB  - The method of protein affinity modification by DNA analogues was used to study the
AB  - characteristic features of restriction endonuclease MvaI interaction with DNA.
AB  - Oligonucleotide duplexes containing a monosubstituted pyrophosphate internucleotide bond were
AB  - used for cross-linking to the enzyme.  The conditions of the reaction of MvaI endonuclease
AB  - with these reagents were investigated.  On the basis of data obtained, the model of successive
AB  - inclusion of two Mg2+ ions into an MvaI endonuclease-substrate complex was proposed and
AB  - confirmed by the kinetic scheme of the process.
ER  -

TY  - JOUR
AU  - Sheflyan, G.Y.
AU  - Kubareva, E.A.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Hydrolysis of 5-fluorodeoxycytidine-containing DNA duplexes using restriction endonucleases.
JO  - Biokhimiia
PY  - 1993
SP  - 1806
EP  - 1811
VL  - 58
AB  - Cleavage by restriction endonucleases MvaI and EcoRII of DNA duplexes, in which the internal
AB  - deoxycytidine in one of the strands of the recognition site is substituted for
AB  - 5-fluorodeoxycytidine, has been studied. It has been found that the modified strands of these
AB  - duplexes are cleaved by endonuclease MvaI with a greater efficiency than the intact ones.
AB  - Endonuclease EcoRII does not practically cleave such substrate analogs. The UV absorbance
AB  - spectra of 5-fluorodeoxycytidine and the 14-member oligodeoxyribonucleotide with modification
AB  - in the middle of the strand have been measured. A hypothesis has been put forward about the
AB  - structural features of 5-fluorodeoxycytidine-containing DNA duplexes.
ER  -

TY  - JOUR
AU  - Sheflyan, G.Y.
AU  - Kubareva, E.A.
AU  - Kuznetsova, S.A.
AU  - Karyagina, A.S.
AU  - Nikolskaya, I.I.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Cross-linking of SsoII restriction endonuclease to cognate and non-cognate DNAs.
JO  - FEBS Lett.
PY  - 1996
SP  - 307
EP  - 310
VL  - 390
AB  - Specific and non-specific interactions of SsoII restriction endonuclease (R.SsoII) were probed
AB  - by the method of covalent attachment to modified DNA containing an active monosubstituted
AB  - pyrophosphate internucleotide bond instead of a phosphodiester one.  R.SsoII with six
AB  - N-terminal His residues was shown to be cross-linked to duplexes with this type of
AB  - modification, either containing or not the recognition sequence.  Competition experiments with
AB  - covalent attachment of R.SsoII to activated DNAs demonstrated the similar affinity of the
AB  - enzyme to cognate and noncognate DNAs in the absence of cofactor, Mg2+ ions.
ER  -

TY  - JOUR
AU  - Sheflyan, G.Y.
AU  - Kubareva, E.A.
AU  - Volkov, E.M.
AU  - Oretskaya, T.S.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Chemical cross-linking of MvaI and EcoRII enzymes to DNA duplexes containing monosubstituted pyrophosphate internucleotide bond.
JO  - Gene
PY  - 1995
SP  - 187
EP  - 190
VL  - 157
AB  - DNA duplexes containing a monosubstituted pyrophosphate internucleotide group, instead of a
AB  - phosphodiester bond, were used as cross-linking reagents for the affinity modification of the
AB  - restriction endonucleases EcoRII and MvaI (R.EcoRII and R.MvaI).  An active group was
AB  - introduced into the enzyme's recognition site or between the recognition site and flanking
AB  - sequence.  The substrate properties of such DNA duplexes were determined.  Cross-linking
AB  - specificity was demonstrated by competition experiments with unmodified substrate, as well as
AB  - by the absence of cross-linking to an active duplex lacking a recognition site.  It was shown
AB  - that the nucleophilicity of the buffer solution and the presence of the enzyme cofactor Mg2+
AB  - dramatically affected the cross-linking yield.
ER  -

TY  - JOUR
AU  - Sheflyan, G.Y.
AU  - Tashlitskii, V.N.
AU  - Kubareva, E.A.
TI  - Interaction of restriction endonuclease MvaI with synthetic DNA duplexes.
JO  - Vestn. Mosk. Univ.
PY  - 1993
SP  - 516
EP  - 520
VL  - 34
ER  -

TY  - JOUR
AU  - Sheh, A.
AU  - Piazuelo, M.B.
AU  - Wilson, K.T.
AU  - Correa, P.
AU  - Fox, J.G.
TI  - Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia.
JO  - Genome Announcements
PY  - 2013
SP  - e00736
EP  - e00713
VL  - 1
AB  - The draft genome sequences of six Colombian Helicobacter pylori strains are presented. These
AB  - strains were isolated from patients from regions of high and low
AB  - gastric cancer risk in Colombia and were characterized by multilocus sequence
AB  - typing. The data provide insights into differences between H. pylori strains of
AB  - different phylogeographic origins.
ER  -

TY  - JOUR
AU  - Sheh, A.
AU  - Shen, Z.
AU  - Fox, J.G.
TI  - Draft Genome Sequences of Eight Enterohepatic Helicobacter Species Isolated from  Both Laboratory and Wild Rodents.
JO  - Genome Announcements
PY  - 2014
SP  - e01218
EP  - e01214
VL  - 2
AB  - The draft genome sequences of eight enterohepatic Helicobacter species, H. muridarum, H.
AB  - trogontum, H. typhlonius, and five unnamed helicobacters, are
AB  - presented here. Using laboratory mice pervasively infected with helicobacters, we
AB  - characterized the presence of known virulence factors.
ER  -

TY  - JOUR
AU  - Sheik, C.S.
AU  - Sieber, J.R.
AU  - Badalamenti, J.P.
AU  - Carden, K.
AU  - Olson, A.
TI  - Complete Genome Sequence of Desulfovibrio desulfuricans Strain G11, a Model Sulfate-Reducing, Hydrogenotrophic, and Syntrophic Partner Organism.
JO  - Genome Announcements
PY  - 2017
SP  - e01207
EP  - e01217
VL  - 5
AB  - Here, we report the draft genome of the Gram-negative, sulfate-reducing bacterium
AB  - Desulfovibrio desulfuricans strain G11. Isolated from a rumen fluid enrichment,
AB  - this culture has been a model syntrophic partner due to its metabolic
AB  - flexibility. The assembly yielded a single circular chromosome of 3,414,943 bp
AB  - and a 57% G+C content.
ER  -

TY  - JOUR
AU  - Sheikhnejad, G.
AU  - Brank, A.
AU  - Christman, J.K.
AU  - Goddard, A.
AU  - Alvarez, E.
AU  - Ford, H. Jr.
AU  - Marquez, V.E.
AU  - Marasco, C.J.
AU  - Sufrin, J.R.
AU  - O'Gara, M.
AU  - Cheng, X.
TI  - Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 2021
EP  - 2034
VL  - 285
AB  - A key step in the predicted mechanism of enzymatic transfer of methyl groups from
AB  - S-adenosyl-L-methionine to cytosine residues in DNA is the transient formation of a
AB  - dihydrocytosine intermediate covalently linked to cysteine in the active site of a DNA
AB  - (cytosine C5)-methyltransferase.  Crystallographic analysis of complexes formed by HhaI
AB  - methyltransferase, AdoMet and a target oligodeoxyribonucleotide containing 5-fluorocytosine
AB  - confirmed the existence of this dihydrocytosine intermediate.  Based on the premise that
AB  - 5,6-dihydro-5-azacytosine, a cytosine analog with an sp3-hybridized carbon (CH2) at position 6
AB  - and an NH group at position 5, could mimic the non-aromatic character of the cytosine ring in
AB  - this transition state, we synthesized a series of synthetic substrates for DNA C5-MTase
AB  - containing DZCyt.  Substitution of DZCyt for target cytosines in C-G dinucleotides of
AB  - single-stranded or double-stranded oligodeoxyribonucleotide substrates led to complete
AB  - inhibition of methylation by murine DNA C5-MTase.  Substitution of DZCyt for the target
AB  - cytosine in G-C-G-C sites in double-stranded oligodeoxyribonucleotides had a similar effect on
AB  - methylation by M.HhaI.  Oligodeoxyribonucleotides containing DZCyt formed a tight but
AB  - reversible complex with M.HhaI, and were consistently more potent as inhibitors of DNA
AB  - methylation than oligodeoxyribonucleotides identical in sequence containing 5-fluorocytosine.
AB  - Crystallographic analysis of a ternary complex involving M.HhaI, S-adenosyl-L-homocysteine and
AB  - a double-stranded 13-mer oligodeoxyribonucleotide containing DZCyt at the target position
AB  - showed that the analog is flipped out of the DNA helix in the same manner as cytosine,
AB  - 5-methylcytosine, and 5-fluorocytosine.  However, no formation of a covalent bond was detected
AB  - between the sulfur atom of the catalytic site nucleophile, cysteine 81, and the pyrimidine C6
AB  - carbon.  These results indicate that DZCyt can occupy the active site of M.HhaI as a
AB  - transition state mimic and, because of the high degree of affinity of its interaction with the
AB  - enzyme, it can act as a potent inhibitor of methylation.
ER  -

TY  - JOUR
AU  - Sheikhnejad, G.
AU  - Marasco, C.
AU  - Sufrin, J.
AU  - Christman, J.K.
TI  - Comparison of substrate specificity of mammalian and bacterial CpG DNA methyltransferases (MTases).
JO  - Biomed. Pharmacother.
PY  - 1992
SP  - 24
EP  - 24
VL  - 46
AB  - Methylation of C residues at specific sites in DNA of higher eukaryotes appears to play a role
AB  - in regulating gene expression during development and diferentiation. Silencing genes by
AB  - methylation can in part explain genomic imprinting and alterations in patterns of methylation
AB  - during the early stages of carcinogenesis may account for some changes in gene expression in
AB  - tumor cells. Although the distribution of 5mC in mammalian DNA is tissue- and
AB  - species-specific, little is known about MTases role in establishing specific patterns of
AB  - methylation. Mammalian DNA (mDNA) MTase is most active in methylating C residues in
AB  - hemi-methylated CpG sites and prefers substrates with high GC content and multiple CpGs approx
AB  - 15 residues apart.  To more fully characterize the specificity of mDNA MTase, we analyzed
AB  - its activity with a variety of defined DNA substrates and compared it with a bacterial MTase,
AB  - SssI, which is reported to act on hemi-methylated CpG sites with equal efficency. Using
AB  - defined unmethylated single (ss)- and double stranded (ds)-DNAs as substrates, we find that:1)
AB  - the initial rate of methylation of both ss-and ds-DNA-by SssI and mDNA MTase is influenced by
AB  - sequence, often in opposite ways; 2) depending on sequence, SssI may be more active on ds-
AB  - than ss-DNA. Activity of mDNA MTase with ss-DNA is highly variable and dependent on sequence
AB  - but is always low with unmethylated ds-DNA. Using 5mC-substituted substrates, we find that
AB  - hemi-methylation either has no effect or inhibits activity of SssI but always activates mDNA
AB  - MTase. mDNA MTase is most active with hemi-methylated ds-DNA ans ss-DNA with 5mC near the
AB  - 5'-end. These results demonstrate that although both MTases catalyze the same reaction,
AB  - methylation of C residues in CpG dinucleotides, they have quite different specificities. This
AB  - should be considered when these enzymes are used to quantitate hypomethylation at CpG sites in
AB  - DNA resulting from exposure of mammalian cells or tissues to conditions or agents that affect
AB  - DNA methylation. Finally, our findings suggest that 5mC residues in specific sequences in
AB  - ss-DNA may serve to activate de novo methylation in mammalian cells allowing alteration of
AB  - existing methylation patterns.
ER  -

TY  - JOUR
AU  - Shell, S.S.
AU  - Prestwich, E.G.
AU  - Baek, S.H.
AU  - Shah, R.R.
AU  - Sassetti, C.M.
AU  - Dedon, P.C.
AU  - Fortune, S.M.
TI  - DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis.
JO  - PLoS Pathog.
PY  - 2013
SP  - e1003419
EP  - e1003419
VL  - 9
AB  - DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is
AB  - associated with gene repression, while it exerts both activating
AB  - and repressive effects in the Proteobacteria through largely locus-specific
AB  - mechanisms. Here, we identify a critical DNA methyltransferase in M.
AB  - tuberculosis, which we term MamA. MamA creates N(6)-methyladenine in a six base
AB  - pair recognition sequence present in approximately 2,000 copies on each strand of
AB  - the genome. Loss of MamA reduces the expression of a number of genes. Each has a
AB  - MamA site located at a conserved position relative to the sigma factor -10
AB  - binding site and transcriptional start site, suggesting that MamA modulates their
AB  - expression through a shared, not locus-specific, mechanism. While strains lacking
AB  - MamA grow normally in vitro, they are attenuated in hypoxic conditions,
AB  - suggesting that methylation promotes survival in discrete host microenvironments.
AB  - Interestingly, we demonstrate strikingly different patterns of DNA
AB  - methyltransferase activity in different lineages of M. tuberculosis, which have
AB  - been associated with preferences for distinct host environments and different
AB  - disease courses in humans. Thus, MamA is the major functional adenine
AB  - methyltransferase in M. tuberculosis strains of the Euro-American lineage while
AB  - strains of the Beijing lineage harbor a point mutation that largely inactivates
AB  - MamA but possess a second functional DNA methyltransferase. Our results indicate
AB  - that MamA influences gene expression in M. tuberculosis and plays an important
AB  - but strain-specific role in fitness during hypoxia.
ER  -

TY  - JOUR
AU  - Sheluho, D.
AU  - Khariwala, S.
AU  - Yebra, M.J.
AU  - Bhagwat, A.S.
TI  - Ability of cytosine methyltransferases to bind substrates containing mismatches is not sufficient for causing C to T mutations.
JO  - FASEB J.
PY  - 1996
SP  - A965
EP  - A965
VL  - 10
AB  - Hydrolytic deamination of cytosine to uracil and of 5-methylcytosine to thymine create
AB  - mismatches, which - if unrepaired - can cause C to T mutations.  It was found that cytosine
AB  - methyltransferases (C5 Mtases) M.HhaI and M.HpaII bind tightly to these mismatches suggesting
AB  - that the C5 Mtases may prevent repair of U:G and T:G mismatches by competing with mismatch
AB  - correction systems.  To test this, we studied the binding of WT M.EcoRII and its mutant in
AB  - which active site cysteine was replaced with serine (C186S) to oligonucleotide duplexes
AB  - containing U:G or T:G mismatches.  We found that C186S mutant binds more tightly to duplexes
AB  - containing mismatches than the wild type enzyme.  The tightness of binding to the mismatched
AB  - duplexes was generally comparable to that with the cognate sequence.  In contrast, when the
AB  - ability of the C186S mutant to promote C to T mutations was tested using a genetic reversion
AB  - system, we found that the magnitude of reversion caused by the WT M.EcoRII was about 50 fold
AB  - higher than that caused by the C186S mutant.  This shows that the ability of C5 Mtases to bind
AB  - U:G or T:G mismatch containing duplexes is not sufficient to promote C to T mutations.
ER  -

TY  - JOUR
AU  - Sheluho, D.
AU  - Yebra, M.J.
AU  - Shariwala, S.S.
AU  - Bhagwat, A.S.
TI  - Lack of correlation between binding of EcoRII methyltransferase to DNA duplexes containing mismatches and the promotion of C to T mutations.
JO  - Mol. Gen. Genet.
PY  - 1997
SP  - 54
EP  - 59
VL  - 255
AB  - The cytosine methyltransferases (MTases) M.HhaI and M.HpaII bind substrates in which the
AB  - target cytosine is replaced by uracil or thymine, i.e. DNA containing a U:G or a T:G mismatch.
AB  - We have extended this observation to the EcoRII MTase (M.EcoRII) and determined the apparent
AB  - Kd for binding.  Using a genetic assay we have also tested the possibility that MTase binding
AB  - to U:G mismatches may interfere with repair of the mismatches and promote C:G to T:A
AB  - mutations.  We have compared two mutants of M.EcoRII that are defective for catalysis by the
AB  - wild-type enzyme for their ability to bind DNA containing U:G or T:G mismatches and for their
AB  - ability to promote C to T mutations.  We find that although all three proteins are able to
AB  - bind DNAs with mismatches, only the wild-type enzyme promotes C:G to T:A mutations in vivo.
AB  - Therefore, the ability of M.EcoRII to bind U:G mismatched duplexes is not sufficient for their
AB  - mutagenic action in cells.
ER  -

TY  - JOUR
AU  - Shemer, R.
AU  - Birger, Y.
AU  - Riggs, A.D.
AU  - Razin, A.
TI  - Structure of the imprinted mouse Snrpn gene and establishment of its parental-specific methylation pattern.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1997
SP  - 10267
EP  - 10272
VL  - 94
AB  - The mouse Snrpn gene encodes the Smn protein, which is involved in RNA splicing.  The gene
AB  - maps to a region in the central part of chromosome 7 that is syntenic to the
AB  - Prader-Willi/Angelman syndromes region on human chromosome 15q11-q13.  The mouse gene, like
AB  - its human counterpart, is imprinted and paternally expressed, primarily in brain and heart.
AB  - We provide here a detailed description of the structural features and differential methylation
AB  - pattern of the gene.  We have identified a maternally methylated region at the 5' end (DMR1),
AB  - which correlates inversely with the Snrpn paternal expression.  We also describe a region at
AB  - the 3' end of the gene (DMR1), which correlates inversely with the Snrpn paternal expression.
AB  - We also describe a region at the 3' end of the gene (DMR2) that is preferentially methylated
AB  - on the paternal allele.  Analysis of Snrpn mRNA levels in a methylase-deficient mouse embryo
AB  - revealed that maternal methylation of DMR1 may play a role in silencing the maternal allele.
AB  - Yet both regions, DMR1 and DMR2, inherit the parental-specific methylation profile from the
AB  - gametes.  This methylation pattern is erased in 12.5 days postcoitum primordial germ cells and
AB  - reestablished during gametogenesis.  DMR1 is remethylated during oogenesis, whereas DMR2 is
AB  - remethylated during spermatogenesis.  Once established, these methylation patterns are
AB  - transmitted to the embryo and maintained, protected from methylation changes during
AB  - embryogenesis and cell differentiation.  Transfections of DMR1 and DMR2 into embryonic stem
AB  - cells and injection into pronuclei of fertilized eggs reveal that embryonic cells lack the
AB  - capacity to establish anew the differential methylation pattern of Snrpn.  That all PWS
AB  - patients lack DMR1, together with the overall high resemblance of the mouse gene to the human
AB  - SNRPN, offers an excellent experimental tool to study the regional control of this imprinted
AB  - chromosomal domain.
ER  -

TY  - JOUR
AU  - Shemer, R.
AU  - Razin, A.
TI  - Establishment of imprinted methylation patterns during development.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 215
EP  - 229
VL  - 0
AB  - Genomic imprinting is a classic example of epigenetic control of gene expression in mammals.
AB  - It represents a process that marks the parental origin of certain genes, resulting in their
AB  - allele-specific expression.  Imprinting, which is implicated in the inequality of the maternal
AB  - and paternal genomes in mammals, results in the developmental failure of isoparental embryos
AB  - to develop properly.  An imbalance of specific parental chromosomes in the embryo or aberrant
AB  - expression of the imprinted genes results in a number of genetic disorders in man and may also
AB  - contribute to tumor development.  Several model explanations have been proposed for the
AB  - evolutionary acquisition of genomic imprinting as a developmental control mechanism in
AB  - mammals.  One of these models suggests that imprinting might have evolved in mammals because
AB  - of the conflicting "interests" of maternal and paternal genes within the embryo.  This model
AB  - proposes that paternally expressed genes promote embryonic growth, whereas maternal genes act
AB  - to restrain the use of maternal resources.  A suitable example that corroborates this argument
AB  - is the paternally expressed Igf2 gene and its counterpart, maternally expressed receptor
AB  - (Igf2r).  The different contribution to the embryonic phenotype of paternal and maternal genes
AB  - had in fact been demonstrated in parthenogenetic and androgenetic embryos.  Although the
AB  - development of extraembryonic tissues in parthenogenetic embryos harboring two copies of the
AB  - maternal genome is impaired, the development of the embryo proper is normal.  In contrast, the
AB  - embryo proper in androgenones carrying two copies of the paternal genome does not develop
AB  - properly whereas extraembryonic tissues develop normally.
ER  -

TY  - JOUR
AU  - Shemesh, M.
AU  - Pasvolsky, R.
AU  - Sela, N.
AU  - Green, S.J.
AU  - Zakin, V.
TI  - Draft Genome Sequence of Alicyclobacillus acidoterrestris Strain ATCC 49025.
JO  - Genome Announcements
PY  - 2013
SP  - e00638
EP  - e00613
VL  - 1
AB  - Alicyclobacillus acidoterrestris is a spore-forming Gram-positive, thermo-acidophilic,
AB  - nonpathogenic bacterium which contaminates commercial
AB  - pasteurized fruit juices. The draft genome sequence for A. acidoterrestris strain
AB  - ATCC 49025 is reported here, providing genetic data relevant to the successful
AB  - adaptation and survival of this strain in its ecological niche.
ER  -

TY  - JOUR
AU  - Shen, B.W.
AU  - Heiter, D.F.
AU  - Chan, S.H.
AU  - Wang, H.
AU  - Xu, S.Y.
AU  - Morgan, R.D.
AU  - Wilson, G.G.
AU  - Stoddard, B.L.
TI  - Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
JO  - Structure
PY  - 2010
SP  - 734
EP  - 743
VL  - 18
AB  - The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with
AB  - its eightbase-pair target recognition sequence 50-TTAATT AA-30 has been determined to 1.9 Ao
AB  - resolution. The enzyme forms an extended homodimer, with each subunit containing two
AB  - zinc-bound motifs surrounding a bba-metal catalytic site. The latter is unusual in that a
AB  - tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target
AB  - sequence from Watson-Crick duplex DNA base pairing, with every base separated from its
AB  - original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A
AB  - and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners.
AB  - This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and
AB  - implies that initial recognition of the target site might involve significantly different
AB  - contacts from those visualized in the DNA-bound cocrystal structures.
ER  -

TY  - JOUR
AU  - Shen, B.W.
AU  - Lambert, A.
AU  - Walker, B.C.
AU  - Stoddard, B.L.
AU  - Kaiser, B.K.
TI  - The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.
JO  - J. Mol. Biol.
PY  - 2016
SP  - 206
EP  - 220
VL  - 428
AB  - LAGLIDADG homing endonucleases ('meganucleases') are highly specific DNA cleaving enzymes
AB  - that are used for genome engineering. Like other enzymes that act on DNA
AB  - targets, meganucleases often display binding affinities and cleavage activities
AB  - that are dominated by one protein domain. To decipher the underlying mechanism of
AB  - asymmetric DNA recognition and catalysis, we identified and characterized a new
AB  - monomeric meganuclease (I-SmaMI), which belongs to a superfamily of homologous
AB  - enzymes that recognize divergent DNA sequences. We solved a series of crystal
AB  - structures of the enzyme-DNA complex representing a progression of sequential
AB  - reaction states, and we compared the structural rearrangements and surface
AB  - potential distributions within each protein domain against their relative
AB  - contribution to binding affinity. We then determined the effects of equivalent
AB  - point mutations in each of the two enzyme active sites to determine whether
AB  - asymmetry in DNA recognition is translated into corresponding asymmetry in DNA
AB  - cleavage activity. These experiments demonstrate the structural basis for
AB  - 'dominance' by one protein domain over the other and provide insights into this
AB  - enzyme's conformational switch from a nonspecific search mode to a more specific
AB  - recognition mode.
ER  -

TY  - JOUR
AU  - Shen, B.W.
AU  - Landthaler, M.
AU  - Shub, D.A.
AU  - Stoddard, B.L.
TI  - DNA binding and cleavage by the HNH homing endonuclease I-HmuI.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 43
EP  - 56
VL  - 342
AB  - The structure of I-HmuI, which represents the last family of homing endonucleases without a
AB  - defining crystallographic structure, has been
AB  - determined in complex with its DNA target. A series of diverse protein
AB  - structural domains and motifs, contacting sequential stretches of
AB  - nucleotide bases, are distributed along the DNA target. I-HmuI contains
AB  - an N-terminal domain with a DNA-binding surface found in the I-PpoI
AB  - homing endonuclease and an associated HNH/N active site found in the
AB  - bacterial colicins, and a C-terminal DNA-binding domain previously
AB  - observed in the I-TevI homing endonuclease. The combination and
AB  - exchange of these features between protein families indicates that the
AB  - genetic mobility associated with homing endonucleases extends to the
AB  - level of independent structural domains. I-HmuI provides an unambiguous
AB  - structural connection between the His-Cys box endonucleases and the
AB  - bacterial colicins, supporting the hypothesis that these enzymes
AB  - diverged from a common ancestral nuclease.
ER  -

TY  - JOUR
AU  - Shen, B.W.
AU  - Xu, D.
AU  - Chan, S.H.
AU  - Zheng, Y.
AU  - Zhu, Z.
AU  - Xu, S.Y.
AU  - Stoddard, B.L.
TI  - Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 8223
EP  - 8236
VL  - 39
AB  - A type IIG restriction endonuclease, RM.BpuSI from Bacillus pumilus, has been characterized
AB  - and its X-ray crystal structure determined at 2.35A
AB  - resolution. The enzyme is comprised of an array of 5-folded domains that
AB  - couple the enzyme's N-terminal endonuclease domain to its C-terminal
AB  - target recognition and methylation activities. The REase domain contains a
AB  - PD-x(15)-ExK motif, is closely superimposable against the FokI
AB  - endonuclease domain, and coordinates a single metal ion. A helical bundle
AB  - domain connects the endonuclease and methyltransferase (MTase) domains.
AB  - The MTase domain is similar to the N6-adenine MTase M.TaqI, while the
AB  - target recognition domain (TRD or specificity domain) resembles a
AB  - truncated S subunit of Type I R-M system. A final structural domain, that
AB  - may form additional DNA contacts, interrupts the TRD. DNA binding and
AB  - cleavage must involve large movements of the endonuclease and TRD domains,
AB  - that are probably tightly coordinated and coupled to target site
AB  - methylation status.
ER  -

TY  - JOUR
AU  - Shen, J.
AU  - Rideout, W.M. III
AU  - Jones, P.A.
TI  - High frequency mutagenesis by a DNA methyltransferase.
JO  - Cell
PY  - 1992
SP  - 1073
EP  - 1080
VL  - 71
AB  - HpaII methylase (M. HpaII), an example of a DNA(cytosine-5)-methyltransferase, was found to
AB  - induce directly a high frequency of C to U transition mutations in double-stranded DNA. A
AB  - mutant pSV2-neo plasmid, constructed with an inactivating T to C transition mutation creating
AB  - a CCGG site, was incubated with M.HpaII in the absence of S-adenosylmethionine (SAM). This
AB  - caused an approximately 104-fold increase in the rate of reversion when the mutant neo plasmid
AB  - was transformed into bacteria lacking uracil-DNA glycosylase. The mutation frequency was very
AB  - sensitive to SAM concentration and was reduced to background when the concentration of the
AB  - methyl donor exceeded 300 nM. The data support current models for the formation of a covalent
AB  - complex between the methyltransferase and cytosine. They also suggest that the occurrence of
AB  - muational hot spots at CpG sites may not always be due to spontaneous deamination of
AB  - 5-methylcytosine, but might also be initiated by enzymatic deamination of cytosine and proceed
AB  - through a C to U to T pathway.
ER  -

TY  - JOUR
AU  - Shen, J.
AU  - Rideout, W.M. III
AU  - Jones, P.A.
TI  - The rate of hydrolytic deamination of 5-methylctyosine in double-stranded DNA.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 972
EP  - 976
VL  - 22
AB  - The modified base, 5-methylcytosine, constitutes approximately 1% of human DNA, but sites
AB  - containing 5-methylcytosine account for at least 30% of all germline and somatic point
AB  - mutations. A genetic assay with a sensitivity of 1 in 10/7, based on reversion to neomycin
AB  - resistance of a mutant pSV2-neo plasmid, was utilized to determine and compare the deamination
AB  - rates of 5-methylcytosine and cytosine in double-stranded DNA for the first time. The rate
AB  - constants for spontaneous hydrolytic deamination of 5-methylcytosine and cytosine in
AB  - double-stranded DNA at 37 C were 5.8x10/-13 s/-1 and 2.6 x 10/-13 s/-1, respectively. These
AB  - rates are more than sufficient to explain the observed frequency of mutation at sites
AB  - containing 5-methylcytosine and emphasize the importance of hydrolytic deamination as a major
AB  - source of human mutations.
ER  -

TY  - JOUR
AU  - Shen, J.-C.
AU  - Zingg, J.-M.
AU  - Yang, A.S.
AU  - Schmutte, C.
AU  - Jones, P.A.
TI  - A mutant HpaII methyltransferase functions as a mutator enzyme.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 4275
EP  - 4282
VL  - 23
AB  - DNA (cytosine-5)-methyltransferases can cause deamination of cytosine when the cofactor
AB  - S-adenosylmethionine (AdoMet) is limiting and thus function as sequence-specific C-U mutator
AB  - enzymes.  Here we explored whether mutations causing inactivation of the cofactor binding
AB  - activity of the HpaII methyltransferase, thus mimicking conditions of limiting AdoMet
AB  - concentration, could convert a DNA methyltransferase to a C-U mutator enzyme.  We created two
AB  - mutator enzymes from the HpaII methyltransferase (F38S and G40D) which both showed enhanced
AB  - cytosine deamination activities in vitro and in vivo.  Interestingly, the G:U mispairs
AB  - generated by these enzymes were not repaired completely in bacteria equipped with uracil-DNA
AB  - glycosylase-initiated repair machinery, giving rise to a potent mutator phenotype.  This is
AB  - the first report showing the creation of mutator enzymes from a DNA methyltransferase and the
AB  - demonstration of their mutagenicity in living cells.
ER  -

TY  - JOUR
AU  - Shen, K. et al.
TI  - Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.
JO  - Infect. Immun.
PY  - 2006
SP  - 5272
EP  - 5283
VL  - 74
AB  - The distributed genome hypothesis (DGH) states that each strain within a
AB  - bacterial species receives a unique distribution of genes from a
AB  - population-based supragenome that is many times larger than the genome of
AB  - any given strain. The observations that natural infecting populations are
AB  - often polyclonal and that most chronic bacterial pathogens have highly
AB  - developed mechanisms for horizontal gene transfer suggested the DGH and
AB  - provided the means and the mechanisms to explain how chronic infections
AB  - persist in the face of a mammalian host's adaptive defense mechanisms.
AB  - Having previously established the validity of the DGH for obligate
AB  - pathogens, we wished to evaluate its applicability to an opportunistic
AB  - bacterial pathogen. This was accomplished by construction and analysis of
AB  - a highly redundant pooled genomic library containing approximately 216,000
AB  - functional clones that was constructed from 12 low-passage clinical
AB  - isolates of Pseudomonas aeruginosa, 6 otorrheic isolates and 6 from other
AB  - body sites. Sequence analysis of 3,214 randomly picked clones (mean insert
AB  - size, approximately 1.4 kb) from this library demonstrated that 348
AB  - (10.8%) of the clones were unique with respect to all genomic sequences of
AB  - the P. aeruginosa prototype strain, PAO1. Hypothetical translations of the
AB  - open reading frames within these unique sequences demonstrated protein
AB  - homologies to a number of bacterial virulence factors and other proteins
AB  - not previously identified in P. aeruginosa. PCR and reverse
AB  - transcription-PCR-based assays were performed to analyze the distribution
AB  - and expression patterns of a 70-open reading frame subset of these
AB  - sequences among 11 of the clinical strains. These sequences were unevenly
AB  - distributed among the clinical isolates, with nearly half (34/70) of the
AB  - novel sequences being present in only one or two of the individual
AB  - strains. Expression profiling revealed that a vast majority of these
AB  - sequences are expressed, strongly suggesting they encode functional
AB  - proteins.
ER  -

TY  - JOUR
AU  - Shen, L.
AU  - Gao, G.
AU  - Zhang, Y.
AU  - Zhang, H.
AU  - Ye, Z.
AU  - Huang, S.
AU  - Huang, J.
AU  - Kang, J.
TI  - A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 6054
EP  - 6064
VL  - 38
AB  - Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with
AB  - distinguished biological functions. In mice,
AB  - disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation,
AB  - especially in repetitive sequences, which comprise the large majority of
AB  - methylated DNA in the genome. By measuring DNA methylation activity of
AB  - Dnmt3a and Dnmt3b homologues from five species, we found that mammalian
AB  - Dnmt3b possessed significantly higher methylation activity on chromatin
AB  - DNA than Dnmt3a and non-mammalian Dnmt3b. Sequence comparison and
AB  - mutagenesis experiments identified a single amino acid substitution
AB  - (I662N) in mammalian Dnmt3b as being crucial for its high chromatin DNA
AB  - methylation activity. Further mechanistic studies demonstrated this
AB  - substitution markedly enhanced the binding of Dnmt3b to nucleosomes and
AB  - hence increased the chromatin DNA methylation activity. Moreover, this
AB  - substitution was crucial for Dnmt3b to efficiently methylate repetitive
AB  - sequences, which increased dramatically in mammalian genomes. Consistent
AB  - with our observation that Dnmt3b evolved more rapidly than Dnmt3a during
AB  - the emergence of mammals, these results demonstrated that the I662N
AB  - substitution in mammalian Dnmt3b conferred enhanced chromatin DNA
AB  - methylation activity and contributed to functional adaptation in the
AB  - epigenetic system.
ER  -

TY  - JOUR
AU  - Shen, P.
AU  - Jiang, Y.
AU  - Zhou, Z.
AU  - Zhang, J.
AU  - Yu, Y.
AU  - Li, L.
TI  - Complete nucleotide sequence of pKP96, a 67 850 bp multiresistance plasmid encoding qnrA1, aac(6')-Ib-cr and blaCTX-M-24 from Klebsiella pneumoniae.
JO  - J. Antimicrob. Chemother.
PY  - 2008
SP  - 1252
EP  - 1256
VL  - 62
AB  - OBJECTIVES: The multiresistance plasmid pKP96 from Klebsiella pneumoniae
AB  - was sequenced completely and analysed concerning its genetic environment
AB  - and distributing of antimicrobial resistance genes. METHODS: The complete
AB  - sequence of the plasmid was determined using a whole-genome shotgun
AB  - approach. MICs of 13 antimicrobial agents were determined using Etests. A
AB  - conjugation experiment was performed in liquid medium. RESULTS: pKP96 is a
AB  - circularly closed 67 850 bp multiresistance plasmid with an IncN
AB  - incompatibility group. Seventy putative genes were identified according to
AB  - the annotation of the finished sequence. The backbone region of the
AB  - plasmid, comprising the conjugal transfer and plasmid replication regions,
AB  - showed 91% identity to the IncN plasmid R46. Several mobile elements were
AB  - found to be inserted into pKP96 together with antimicrobial resistance
AB  - genes, including qnrA1, aac(6')-Ib-cr and bla(CTX-M-24). CONCLUSIONS:
AB  - Plasmid pKP96 is a chimera that has acquired its multiple antimicrobial
AB  - resistance determinants horizontally from different sources. It may have
AB  - evolved from an ancestor plasmid similar to R46 through the stepwise
AB  - events of integration or recombination.
ER  -

TY  - JOUR
AU  - Shen, S.
AU  - Li, Q.
AU  - Yan, P.
AU  - Zhou, B.
AU  - Ye, S.
AU  - Lu, Y.
AU  - Wang, D.
TI  - Restriction endonucleases from three strains of Haemophilus influenzae.
JO  - Sci. Sin.
PY  - 1980
SP  - 1435
EP  - 1442
VL  - 23
AB  - The restriction endonucleases, Hin P1I, Hin S1I and Hin S2I are isolated from
AB  - three strains of Haemophilus influenzae respectively.  By polymin P treatment,
AB  - ammonium sulphage precipitation and column chromatography on phosphocellulose
AB  - and on heparin-Sepharose, Hin P1I is partially purified.  No contaminating
AB  - deoxyribonuclease activities have been detected in this purified enzyme
AB  - preparation.  The face that the digestion patterns of Hin P1I and HhaI on phage
AB  - lambda, plasmids ColE1 and pBR 322 DNAs are identical indicates that they are
AB  - isoschizomers but their splitting sites are different.  The banding patterns of
AB  - Hin S1I and Hin S2I are also the same as that of HhaI.
ER  -

TY  - JOUR
AU  - Shen, W.Y.
AU  - Lo, W.S.
AU  - Lai, Y.C.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a Bacterium Isolated from a Horsefly (Tabanus abactor).
JO  - Genome Announcements
PY  - 2016
SP  - e01201
EP  - e01216
VL  - 4
AB  - Spiroplasma helicoides TABS-2T (DSM 22551) was isolated from the gut of a horsefly (Tabanus
AB  - abactor) collected near Ardmore, Oklahoma, USA, in 1987. Here,
AB  - we report the complete genome sequence of this bacterium to facilitate the
AB  - investigation of its biology and the comparative genomics among Spiroplasma
AB  - species.
ER  -

TY  - JOUR
AU  - Shen, X.
AU  - Chen, M.
AU  - Hu, H.
AU  - Wang, W.
AU  - Peng, H.
AU  - Xu, P.
AU  - Zhang, X.
TI  - Genome Sequence of Pseudomonas chlororaphis GP72, a Root-Colonizing Biocontrol Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1269
EP  - 1270
VL  - 194
AB  - Pseudomonas chlororaphis GP72 is a root-colonizing biocontrol strain isolated from a green
AB  - pepper rhizosphere. It can produce several secondary metabolites to
AB  - suppress phytopathogens. Here we present a 6.6-Mb assembly of its genome, which
AB  - is the first genome sequence of the P. chlororaphis group and may provide
AB  - insights into its antifungal activities.
ER  -

TY  - JOUR
AU  - Shen, X.
AU  - Wang, Q.
AU  - Xia, L.
AU  - Zhu, X.
AU  - Zhang, Z.
AU  - Liang, Y.
AU  - Cai, H.
AU  - Zhang, E.
AU  - Wei, J.
AU  - Chen, C.
AU  - Song, Z.
AU  - Zhang, H.
AU  - Yu, D.
AU  - Hai, R.
TI  - Complete Genome Sequences of Yersinia pestis from Natural Foci in China.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3551
EP  - 3552
VL  - 192
AB  - Yersinia pestis, the causative agent of plague, is a deadly bacterium that affects humans.
AB  - Strain D106004 was isolated from a new plague focus in
AB  - Yulong County, China, in 2006. To gain insights into the epidemic origin,
AB  - we have sequenced the genomes of D106004 and strains Z176003 and D182038,
AB  - isolated from neighboring regions.
ER  -

TY  - JOUR
AU  - Shen, Z.
AU  - Sheh, A.
AU  - Young, S.K.
AU  - Abouelliel, A.
AU  - Ward, D.V.
AU  - Earl, A.M.
AU  - Fox, J.G.
TI  - Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques.
JO  - Genome Announcements
PY  - 2014
SP  - e00857
EP  - e00814
VL  - 2
AB  - Draft genome sequences of seven enterohepatic Helicobacter species, H. bilis, H.  canadensis,
AB  - H. canis, H. cinaedi, H. winghamensis, H. pullorum, and H. macacae,
AB  - are presented. These isolates were obtained from clinical patients and a nonhuman
AB  - primate. Due to potential zoonotic risks, we characterized antibiotic resistance
AB  - markers and Helicobacter virulence factors.
ER  -

TY  - JOUR
AU  - Shendure, J.
AU  - Porreca, G.J.
AU  - Reppas, N.B.
AU  - Lin, X.
AU  - McCutcheon, J.P.
AU  - Rosenbaum, A.M.
AU  - Wang, M.D.
AU  - Zhang, K.
AU  - Mitra, R.D.
AU  - Church, G.M.
TI  - Accurate multiplex polony sequencing of an evolved bacterial genome.
JO  - Science
PY  - 2005
SP  - 1728
EP  - 1732
VL  - 309
AB  - We describe a DNA sequencing technology in which a commonly available, inexpensive
AB  - epifluorescence microscope is converted to rapid
AB  - nonelectrophoretic DNA sequencing automation. We apply this technology to
AB  - resequence an evolved strain of Escherichia coli at less than one error
AB  - per million consensus bases. A cell-free, mate-paired library provided
AB  - single DNA molecules that were amplified in parallel to 1-micrometer beads
AB  - by emulsion polymerase chain reaction. Millions of beads were immobilized
AB  - in a polyacrylamide gel and subjected to automated cycles of sequencing by
AB  - ligation and four-color imaging. Cost per base was roughly one-ninth as
AB  - much as that of conventional sequencing. Our protocols were implemented
AB  - with off-the-shelf instrumentation and reagents.
ER  -

TY  - JOUR
AU  - Sheng, B.
AU  - Ni, J.
AU  - Gao, C.
AU  - Ma, C.
AU  - Xu, P.
TI  - Draft Genome Sequence of the Gluconobacter oxydans Strain DSM 2003, an Important  Biocatalyst for Industrial Use.
JO  - Genome Announcements
PY  - 2014
SP  - e00417
EP  - e00414
VL  - 2
AB  - Gluconobacter oxydans strain DSM 2003 can efficiently produce some industrially important
AB  - building blocks, such as (R)-lactic acid and (R)-2-hydroxybutyric acid.
AB  - Here, we present a 2.94-Mb assembly of its genome sequence, which might provide
AB  - further insights into the molecular mechanism of its biocatalysis in order to
AB  - further improve its biotechnological applications.
ER  -

TY  - JOUR
AU  - Sheng, H.
AU  - Duan, M.
AU  - Hunter, S.S.
AU  - Minnich, S.A.
AU  - Settles, M.L.
AU  - New, D.D.
AU  - Chase, J.R.
AU  - Fagnan, M.W.
AU  - Hovde, C.J.
TI  - High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177:H- (fliCH25) Isolates Harboring Virulent stx2 and Multiple   Plasmids.
JO  - Genome Announcements
PY  - 2018
SP  - e01592
EP  - e01517
VL  - 6
AB  - Shiga toxin-producing Escherichia coli (STEC) bacteria are zoonotic pathogens. We report here
AB  - the high-quality complete genome sequences of three STEC O177:H-
AB  - (fliCH25) strains, SMN152SH1, SMN013SH2, and SMN197SH3. The assembled genomes
AB  - consisted of one optical map-verified circular chromosome for each strain, plus
AB  - two plasmids for SMN013SH2 and three plasmids for SMN152SH1 and SMN197SH3,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Sheng, L.
AU  - Zhang, Y.
AU  - Minton, N.P.
TI  - Complete Genome Sequence of Geobacillus thermoglucosidasius NCIMB 11955, the Progenitor of a Bioethanol Production Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01065
EP  - e01016
VL  - 4
AB  - The industrially important thermophile Geobacillus thermoglucosidasius has the potential to
AB  - produce chemicals and fuels from biomass-derived sugar feedstocks.
AB  - Here, we present the genome sequence of strain NCIMB 11955, the progenitor of an
AB  - ethanologenic industrial strain, revealing 11 single-nucleotide polymorphisms and
AB  - 2 indels compared to strain DSM 2542 and two novel plasmids.
ER  -

TY  - JOUR
AU  - Shenoy, S.
AU  - Daigle, K.
AU  - Ehrlich, K.C.
AU  - Gehrke, C.W.
AU  - Ehrlich, M.
TI  - Hydrolysis by restriction endonucleases at their DNA recognition sequences substituted with mismatched base pairs.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 4407
EP  - 4420
VL  - 14
AB  - Restriction endonucleases were tested for their ability to catalyze the
AB  - cleavage of mismatch-containing recognition sites in DNA.  These mismatched
AB  - base pairs were T.G, U.G, or A.C in covalently closed, circular heteroduplexes
AB  - prepared by in vitro extension of chemically synthesized oligonucleotide
AB  - primers annealed to a bacteriophage M13-derived viral DNA.  None of the
AB  - restriction enzymes was able to completely cleave the mismatch-containing
AB  - recognition sites under standard conditions.  However, three of them, SmaI,
AB  - SalI, and SstI, catalyzed partial digestion leading to an accumulation of DNA
AB  - singly nicked at the mismatched recognition site.  The ability of SmaI and SstI
AB  - to partially cleave at a mismatch was shown to depend on the nature and
AB  - position of the mismatch within the corresponding recognition site.  In
AB  - contrast, little or no digestion was obtained with AccI, HincII, HindIII, and
AB  - KpnI at mismatch-containing sites.  Therefore, in some cases a transition-type
AB  - substitution in only one strand of a recognition site inhibits restriction
AB  - endonuclease-catalyzed digestion at that site although in others partial
AB  - digestion occurs.
ER  -

TY  - JOUR
AU  - Shepard, S.M.
AU  - Danzeisen, J.L.
AU  - Isaacson, R.E.
AU  - Seemann, T.
AU  - Achtman, M.
AU  - Johnson, T.J.
TI  - Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli.
JO  - J. Bacteriol.
PY  - 2012
SP  - 395
EP  - 405
VL  - 194
AB  - Porcine enterotoxigenic Escherichia coli (ETEC) continues to result in major morbidity and
AB  - mortality in the swine industry via postweaning diarrhea. The key
AB  - virulence factors of ETEC strains, their serotypes, and their fimbrial components
AB  - have been well studied. However, most studies to date have focused on
AB  - plasmid-encoded traits related to colonization and toxin production, and the
AB  - chromosomal backgrounds of these strains have been largely understudied. Here, we
AB  - generated the genomic sequences of K88-positive and F18-positive porcine ETEC
AB  - strains and examined the phylogenetic distribution of clinical porcine ETEC
AB  - strains and their plasmid-associated genetic content. The genomes of porcine ETEC
AB  - strains UMNK88 and UMNF18 were both found to contain remarkable plasmid
AB  - complements containing known virulence factors, potential novel virulence
AB  - factors, and antimicrobial resistance-associated elements. The chromosomes of
AB  - these strains also possessed several unique genomic islands containing
AB  - hypothetical genes with similarity to classical virulence factors, although
AB  - phage-associated genomic islands dominated the accessory genomes of these
AB  - strains. Phylogenetic analysis of 78 clinical isolates associated with neonatal
AB  - and porcine diarrhea revealed that a limited subset of porcine ETEC lineages
AB  - exist that generally contain common toxin and fimbrial profiles, with many of the
AB  - isolates belonging to the ST10, ST23, and ST169 multilocus sequencing types.
AB  - These lineages were generally distinct from existing human ETEC database
AB  - isolates. Overall, most porcine ETEC strains appear to have emerged from a
AB  - limited subset of E. coli lineages that either have an increased propensity to
AB  - carry plasmid-encoded virulence factors or have the appropriate ETEC core genome
AB  - required for virulence.
ER  -

TY  - JOUR
AU  - Sheppard, A.E.
AU  - Poehlein, A.
AU  - Rosenstiel, P.
AU  - Liesegang, H.
AU  - Schulenburg, H.
TI  - Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry-.
JO  - Genome Announcements
PY  - 2013
SP  - e00158
EP  - e00112
VL  - 1
AB  - Bacillus thuringiensis is an insect pathogen that has been used widely as a biopesticide.
AB  - Here, we report the genome sequence of strain 407 Cry-, which is
AB  - used to study the genetic determinants of pathogenicity. The genome consists of a
AB  - 5.5-Mb chromosome and nine plasmids, including a novel 502-kb megaplasmid.
ER  -

TY  - JOUR
AU  - Sheppard, A.E.
AU  - Stoesser, N.
AU  - Sebra, R.
AU  - Kasarskis, A.
AU  - Deikus, G.
AU  - Anson, L.
AU  - Walker, A.S.
AU  - Peto, T.E.
AU  - Crook, D.W.
AU  - Mathers, A.J.
TI  - Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.
JO  - Genome Announcements
PY  - 2016
SP  - e01649
EP  - e01615
VL  - 4
AB  - Carbapenem resistance in Klebsiella pneumoniae, frequently conferred by the blaKPC gene, is a
AB  - major public health threat. We sequenced a blaKPC-containing
AB  - strain of K. pneumoniae belonging to the emergent lineage ST941, in order to
AB  - better understand the evolution of blaKPC within this species.
ER  -

TY  - JOUR
AU  - Sherburne, C.K.
AU  - Lawley, T.D.
AU  - Gilmour, M.W.
AU  - Blattner, F.R.
AU  - Burland, V.
AU  - Grotbeck, E.
AU  - Rose, D.J.
AU  - Taylor, D.E.
TI  - The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 2177
EP  - 2186
VL  - 28
AB  - Salmonella typhi, the causative agent of typhoid fever, annually infects 16 million people and
AB  - kills 600,000 world wide. Plasmid-encoded multiple drug resistance in S. typhi is always
AB  - encoded by plasmids of incompatibility group H (IncH). The complete DNA sequence of the large
AB  - temperature-sensitive conjugative plasmid R27, the prototype for the IncHI1 family of
AB  - plasmids, has been compiled and analyzed. This 180 kb plasmid contains 210 open reading frames
AB  - (ORFs), of which 14 have been previously identified and 56 exhibit similarity to other plasmid
AB  - and prokaryotic ORFs. A number of insertion elements were found, including the full Tn 10
AB  - transposon, which carries tetracycline resistance genes. Two transfer regions, Tra1 and Tra2,
AB  - are present, which are separated by a minimum of 64 kb. Homologs of the DNA-binding proteins
AB  - TlpA and H-NS that act as temperature-regulated repressors in other systems have been located
AB  - in R27. Sequence analysis of transfer and replication regions supports a mosaic-like structure
AB  - for R27. The genes responsible for conjugation and plasmid maintenance have been identified
AB  - and mechanisms responsible for thermosensitive transfer are discussed.
ER  -

TY  - JOUR
AU  - Sheth, A.
AU  - Ravikumar, M.
AU  - Hosur, R.V.
AU  - Govil, G.
TI  - Two dimensional NMR studies on the solution structure of d-CTCGAGCTCGAG.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1987
SP  - 26
EP  - 34
VL  - 144
AB  - Two dimensional (2D) FT-NMR investigations have been carried out on the
AB  - self-complementary dodecanucleotide d-CTCGAGCTCGAG, which has cleavage sites
AB  - for the restriction enzyme XhoI (between C and T).  The central TCG portion is
AB  - also known to show a preference for DNAase activity.  Complete resonance
AB  - assignments have been obtained for the non-exchangeable sugar and base protons
AB  - of the oligonucleotide.  Information regarding sugar geometries, glycosidic
AB  - torsion angles and other structural parameters has been obtained from the
AB  - relative intensities of the cross peaks in the COSY and NOESY spectra.  The
AB  - results indicate that deoxyribose rings of C1 and C7 adopt a conformation
AB  - different from the remaining sugars in the double helical oligonucleotide.  The
AB  - Central TCG portion also exhibits variations in the backbone structure.  The
AB  - base stacking in the double helix shows interesting sequence dependent effects
AB  - suggesting that the sequence effects are not localised to nearest neighbours
AB  - but extended over longer stretches.
ER  -

TY  - JOUR
AU  - Shetty, A.R. et al.
TI  - Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 55
EP  - 55
VL  - 10
AB  - Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial
AB  - biodegradation is an important means of remediation of PAH-contaminated soil. Delftia
AB  - acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole
AB  - carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined
AB  - to gain insights into  a mechanisms underlying biodegradation of PAH. Three genomic libraries
AB  - were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads),  a 454
AB  - Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size
AB  - of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454
AB  - Titanium standard data and the 454 paired end data were assembled together and the consensus
AB  - sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data
AB  - was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping
AB  - shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer
AB  - walks. A total of 182 additional reactions were needed to close gaps and to raise the quality
AB  - of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging
AB  - 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome
AB  - of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C)
AB  - containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene
AB  - products were assigned to a putative function. Genes encoding phenanthrene degradation were
AB  - localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end
AB  - a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of
AB  - mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence
AB  - included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate
AB  - pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome
AB  - sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH
AB  - biodegradation that may shape the process in the environment.
ER  -

TY  - JOUR
AU  - Shetty, D.
AU  - Grigoryan, A.A.
AU  - Alshalchi, S.
AU  - Withana, G.N.
AU  - Roy, J.
AU  - Lawrence, J.R.
AU  - Vidovic, S.
AU  - Korber, D.R.
TI  - Draft Genome Sequences of Biofilm-Forming and Non-Biofilm-Forming Nontyphoidal Salmonella enterica Serovars.
JO  - Genome Announcements
PY  - 2017
SP  - e01061
EP  - e01017
VL  - 5
AB  - The genetic basis for biofilm formation among nontyphoidal salmonellae (NTS) remains poorly
AB  - understood. This draft genome submission provides initial insights
AB  - on the genetic differences between biofilm-forming and non-biofilm-forming
AB  - clinical and environmental NTS serovars.
ER  -

TY  - JOUR
AU  - Shetty, S.A.
AU  - Marathe, N.P.
AU  - Munot, H.
AU  - Antony, C.P.
AU  - Dhotre, D.P.
AU  - Murrell, J.C.
AU  - Shouche, Y.S.
TI  - Draft Genome Sequence of Methylophaga lonarensis MPLT, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph.
JO  - Genome Announcements
PY  - 2013
SP  - e00202
EP  - e00213
VL  - 1
AB  - Methylophaga lonarensis strain MPL(T) is a haloalkaliphilic methylotroph isolated from Lonar
AB  - Lake, a saline and alkaline lake in Maharashtra, India. Strain MPL(T)
AB  - utilizes methanol as its sole carbon and energy source. Here, we present the
AB  - draft genome sequence of M. lonarensis MPL(T) (VKM B-2684(T) = MCC 1002(T)).
ER  -

TY  - JOUR
AU  - Shetty, S.A.
AU  - Ritari, J.
AU  - Paulin, L.
AU  - Smidt, H.
AU  - De Vos, W.M.
TI  - Complete Genome Sequence of Eubacterium hallii Strain L2-7.
JO  - Genome Announcements
PY  - 2017
SP  - e01167
EP  - e01117
VL  - 5
AB  - The complete genome sequence of Eubacterium hallii strain L2-7 is reported here.  This
AB  - intestinal strain produces butyrate from glucose as well as lactate when
AB  - acetate is provided in the growth medium. In addition, strain L2-7 has been shown
AB  - to improve insulin sensitivity in db/db mice, indicating its application
AB  - potential.
ER  -

TY  - JOUR
AU  - Shetty, V.
AU  - Lamichhane, B.
AU  - Chua, E.G.
AU  - Ballal, M.
AU  - Tay, C.Y.
TI  - Draft Genome Sequences of 42 Helicobacter pylori Isolates from Rural Regions of South India.
JO  - Genome Announcements
PY  - 2018
SP  - e01486
EP  - e01417
VL  - 6
AB  - Helicobacter pylori is a successful human gastric pathogen that is associated with the
AB  - development of gastric cancer. The draft genome sequences of 42 H.
AB  - pylori clinical strains isolated from South Indian rural populations will provide
AB  - further insights into the evolution and genetic makeup of Indian H. pylori
AB  - strains.
ER  -

TY  - JOUR
AU  - Shevchuk, T.
AU  - Kretzner, L.
AU  - Munson, K.
AU  - Axume, J.
AU  - Clark, J.
AU  - Dyachenko, O.V.
AU  - Caudill, M.
AU  - Buryanov, Y.
AU  - Smith, S.S.
TI  - Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 6124
EP  - 6136
VL  - 33
AB  - Several reports suggest that C(m)CWGG methylation tends not to co-exist with (m)CG methylation
AB  - in human cells. We have asked whether or not
AB  - methylation at CCWGG sites can influence CG methylation. DNA from cells
AB  - expressing an M.EcoRII-GFP fusion was actively methylated at CCWGG sites.
AB  - CG methylation as measured by R.HpaII/R.MspI ratios was unchanged in cells
AB  - expressing the transgene. Cloned representatives of C(m)CWGG methylated
AB  - DNA often contained, or were adjacent to an ALU repeat, suggesting that
AB  - M.EcoRII-GFP actively methylated gene-rich R-band DNA. The transgenic
AB  - methyltransferase applied C(m)CWGG methylation to a representative human
AB  - promoter that was heavily methylated at CG dinucleotides (the SERPINB5
AB  - promoter) and to a representative promoter that was essentially
AB  - unmethylated at CG dinucleotides (the APC promoter). In each case, the CG
AB  - methylation pattern remained in its original state, unchanged by the
AB  - presence of neighboring C(m)CWGG sites. Q-PCR measurements showed that RNA
AB  - expression from the APC gene was not significantly altered by the presence
AB  - of C(m)CWGG in its promoter. Kinetic studies suggested that an adjacent
AB  - C(m)CWGG methylation site influences neither the maintenance nor the de
AB  - novo methylation activities of purified human Dnmt1. We conclude that
AB  - C(m)CWGG methylation does not exert a significant effect on CG methylation
AB  - in human kidney cells.
ER  -

TY  - JOUR
AU  - Shevchuk, T.V.
AU  - Buryanov, Y.I.
TI  - DNA methyltransferase-based assay for the cytosine methylation level in the DNA sequence CCWGG.
JO  - Bioorg. Khim.
PY  - 1999
SP  - 630
EP  - 633
VL  - 25
AB  - An assay for the cytosine methylation level in the eukaryotic DNA CCWGG sequence is proposed.
AB  - The method is based on the ability of DNA methylase BstNI to methylate DNA containing in a
AB  - CCWGG site a nonmodified or 5-methylated cytosine to yield N4-methyl- or
AB  - N4,5-dimethylcytosine, respectively.
ER  -

TY  - JOUR
AU  - Shevchuk, T.V.
AU  - Zakharchenko, N.S.
AU  - Dyachenko, O.V.
AU  - Buryanov, Y.I.
TI  - The effect of the gene encoding EcoRII DNA methyltransferase on the phenotype of transgenic tumor cell lines of Nicotiana tabacum and the  methylation level of CpNpG sequences in their genome.
JO  - Russ. J. Plant Physiol.
PY  - 2001
SP  - 478
EP  - 482
VL  - 48
AB  - Several tumor cell lines were obtained by transforming Nicotiana tabacum plants with the
AB  - recombinant Ti plasmid comprising the gene
AB  - encoding EcoRII DNA methyltransferase (M.EcoRII) and subjected to
AB  - analysis. The transformed lines differed in their morphology, growth
AB  - dependence on hormones, and nopaline-synthesizing capacity. Southern
AB  - blot-hybridization showed that the M.EcoRII gene was present in the
AB  - cells of all transformed lines. However, genome analysis using
AB  - polymerase chain reaction with the oligonucleotide primers recognizing
AB  - 5'-ends of the M.EcoRII gene did not exhibit the full-length copies of
AB  - the gene. Lower methylation of CpNpG sequences characteristic of all
AB  - transformed cells could result from the disturbance of one of several
AB  - plant DNA methyltransferase genes following its homologous
AB  - recombination with the M.EcoRII gene.
ER  -

TY  - JOUR
AU  - Shevtsov, A.
AU  - Tarlykov, P.
AU  - Zholdybayeva, E.
AU  - Momynkulov, D.
AU  - Sarsenova, A.
AU  - Moldagulova, N.
AU  - Momynaliev, K.
TI  - Draft Genome Sequence of Rhodococcus erythropolis DN1, a Crude Oil Biodegrader.
JO  - Genome Announcements
PY  - 2013
SP  - e00846
EP  - e00813
VL  - 1
AB  - We report the 6,548-Mb genome sequence of Rhodococcus erythropolis strain DN1, isolated from
AB  - the oil-contaminated soil in the Karagandy region of Kazakhstan.
AB  - The draft genome sequence of strain DN1 might provide new insights into the
AB  - genetic mechanisms of crude oil biodegradation.
ER  -

TY  - JOUR
AU  - Shevtsov, A.
AU  - Tarlykov, P.
AU  - Zholdybayeva, E.
AU  - Shevtsova, E.
AU  - Momynkulov, D.
AU  - Sytnik, I.
AU  - Karibaev, T.
AU  - Chsherbakov, A.
AU  - Momynaliev, K.
TI  - Draft Genome Sequence of the Live Vaccine Strain Brucella abortus 82.
JO  - Genome Announcements
PY  - 2013
SP  - e01101
EP  - e01113
VL  - 1
AB  - Vaccination is a crucial part of the brucellosis eradication programs worldwide.  A live
AB  - vaccine strain of Brucella abortus 82 has been successfully used for the
AB  - vaccination of cattle against brucellosis in the former Soviet republics for the
AB  - last 39 years. Here, we report the genome sequence of Brucella abortus 82.
ER  -

TY  - JOUR
AU  - Shi, C.Y.
AU  - Jia, K.T.
AU  - Yang, B.
AU  - Huang, J.
TI  - Complete genome sequence of a Megalocytivirus (family Iridoviridae) associated with turbot mortality in China.
JO  - Virol. J.
PY  - 2010
SP  - 159
EP  - 159
VL  - 7
AB  - ABSTRACT: BACKGROUND: Turbot reddish body iridovirus (TRBIV) causes
AB  - serious systemic diseases with high mortality in the cultured turbot,
AB  - Scophthalmus maximus. We here sequenced and analyzed the complete genome
AB  - of TRBIV, which was identified in Shandong province, China. RESULTS: The
AB  - genome of TRBIV is a linear double-stranded DNA of 110,104 base pairs,
AB  - comprising 55% G + C. Total 115 open reading frames were identified,
AB  - encoding polypeptides ranging from 40 to 1168 amino acids. Amino acid
AB  - sequences analysis revealed that 39 of the 115 potential gene products of
AB  - TRBIV show significant homology to other iridovirus proteins. Phylogenetic
AB  - analysis of conserved genes indicated that TRBIV is closely related to
AB  - infectious spleen and kidney necrosis virus (ISKNV), rock bream iridovirus
AB  - (RBIV), orange-spotted grouper iridovirus (OSGIV), and large yellow
AB  - croaker iridovirus (LYCIV). The results indicated that TRBIV belongs to
AB  - the genus Megalocytivirus (family Iridoviridae). CONCLUSIONS: The
AB  - determination of the genome of TRBIV will provide useful information for
AB  - comparative study of Megalocytivirus and developing strategies to control
AB  - outbreaks of TRBIV-induced disease.
ER  -

TY  - JOUR
AU  - Shi, L.
AU  - Suetake, I.
AU  - Kawakami, T.
AU  - Aimoto, S.
AU  - Tajima, S.
TI  - Xenopus Eggs Express an Identical DNA Methyltransferase, Dnmt1, to Somatic Cells.
JO  - J. Biochem. (Tokyo)
PY  - 2001
SP  - 359
EP  - 366
VL  - 130
AB  - In mouse, an oocyte-specific short isoform of DNA methyltransferase-1 (Dnmt1) lacking amino
AB  - terminal 118 amino acid residues exists and plays a crucial role in maintaining the
AB  - methylation state of imprinted genes during early embryogenesis [Howell et al. (2001) Cell
AB  - 104, 829-838]. To address the question of whether or not Xenopus oocyte expresses such a short
AB  - isoform, we raised monoclonal antibodies against the amino-terminal portion of Xenopus Dnmt1.
AB  - Two of the isolated monoclonal antibodies, 3C6 and 4A8, were determined to recognize (1-32)
AB  - and (115-126) of Xenopus Dnmt1, respectively. The amounts of Dnmt1 in Xenopus eggs were
AB  - determined to be similar, 10.0 2.5, 8.0 0.8, and 8.2 0.2 ng per egg with monoclonal antibodies
AB  - 3C6 and 4A8, and polyclonal antibodies, respectively. This indicated that Dnmt1 in Xenopus
AB  - mature eggs had an identical amino-terminal sequence to the amino acid sequence deduced from
AB  - the cDNA. Together with the fact that Dnmt1 in A6 cells immuno-reacted with all the monoclonal
AB  - antibodies isolated and with the polyclonal antibodies, we concluded that Dnmt1 expressed in
AB  - Xenopus mature eggs possesses an identical amino-terminal sequence to that in somatic cells.
AB  - Immuno-purified Xenopus Dnmt1 in mature eggs showed similar specific activity to that in
AB  - proliferating A6 cells and that of mouse recombinant Dnmt1.
ER  -

TY  - JOUR
AU  - Shi, W.
AU  - Lu, W.
AU  - Liu, Q.
AU  - Zhi, Y.
AU  - Zhou, P.
TI  - The identification of the nitrate assimilation related genes in the novel Bacillus megaterium NCT-2 accounts for its ability to use nitrate as its only source of nitrogen.
JO  - Funct. Integr. Genomics
PY  - 2014
SP  - 219
EP  - 227
VL  - 14
AB  - Bacillus megaterium NCT-2 is a novel bacterium that can utilize nitrate as its
AB  - only nitrogen source for growth.The nitrate assimilation related genes that are
AB  - involved in this process would be expected to be crucial. However, little is
AB  - known about the genomic background of this bacterium,let alone the sequences of
AB  - the nitrate assimilation related genes. In order to further investigate the
AB  - nitrate assimilation function of the NCT-2, genome sequencing was performed.After
AB  - obtaining the fine map of the NCT-2 genome, which was submitted to the NCBI
AB  - GenBank (AHTF00000000), the sequences of the nitrate assimilation related genes
AB  - (the nitrate reductase electron transfer subunit nasB and the nitrate reductase
AB  - catalytic subunit nasC, the nitrite reductase [NAD(P)H]large subunit nasD and the
AB  - nitrite reductase [NAD(P)H] small subunit nasE, and the glutamine synthetase
AB  - glnA) were identified.Multiple alignments were performed to find out the sequence
AB  - identities of the nitrate assimilation related genes to that of their similar
AB  - species. Through KEGG signaling mapping search, the nitrate assimilation related
AB  - genes were revealed to be located in the nitrogen metabolism signaling pathway.
AB  - The putative 3D protein structures of these genes were modeled by SWISS MODEL,
AB  - and shown to be highly similar to the nitrate assimilation related genes in the
AB  - PDB database. Finally, the sequence validity of the nitrate assimilation related
AB  - genes was verified by PCR with specifically designed primers.
ER  -

TY  - JOUR
AU  - Shi, X.
AU  - Yu, M.
AU  - Yan, S.
AU  - Dong, S.
AU  - Zhang, X.H.
TI  - Genome Sequence of the Thermostable-Agarase-Producing Marine Bacterium Catenovulum agarivorans YM01T, Which Reveals the Presence of a Series of  Agarase-Encoding Genes.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5484
EP  - 5484
VL  - 194
AB  - Marine bacterium Catenovulum agarivorans YM01(T) can produce highly thermostable  agarases.
AB  - The draft genome of YM01(T) is about 5.36 Mb and harbors approximately
AB  - 4,913 genes, including 15 agarase (2 alpha-agarase and 13 beta-agarase)-encoding
AB  - genes, which will provide references to functional characterization of various
AB  - agarases from marine bacteria.
ER  -

TY  - JOUR
AU  - Shi, X.
AU  - Zhu, Y.
AU  - Li, Y.
AU  - Jiang, M.
AU  - Lin, Y.
AU  - Qiu, Y.
AU  - Chen, Q.
AU  - Yuan, Y.
AU  - Ni, P.
AU  - Hu, Q.
AU  - Huang, S.
TI  - Genome Sequence of Proteus mirabilis Clinical Isolate C05028.
JO  - Genome Announcements
PY  - 2014
SP  - e00167
EP  - e00114
VL  - 2
AB  - Genomic DNA of Proteus mirabilis C05028 was sequenced by an Illumina HiSeq platform and was
AB  - assembled to 39 scaffolds with a total length of 3.8 Mb. Next,
AB  - open reading frames (ORFs) were identified and were annotated by the KEGG, COG,
AB  - and NR databases. Finally, we found special virulence factors only existing in P.
AB  - mirabilis C05028.
ER  -

TY  - JOUR
AU  - Shi, Y.
AU  - Chen, Y.
AU  - Li, Z.
AU  - Yang, L.
AU  - Chen, W.
AU  - Mu, Z.
TI  - Complete Genome Sequence of Streptococcus thermophilus MN-BM-A02, a Rare Strain with a High Acid-Producing Rate and Low Post-Acidification Ability.
JO  - Genome Announcements
PY  - 2015
SP  - e00979
EP  - e00915
VL  - 3
AB  - Streptococcus thermophilus MN-BM-A02 was originally isolated from a traditional fermented
AB  - dairy product in China. The characteristics of this bacterium are its high acid-producing rate
AB  - and low post-acidification. This study presents the genome sequence of MN-BM-A02. Its complete
AB  - genome comprises 2,025 genes and 1,850,434 nucleotides with an average G+C content of 39%.
ER  -

TY  - JOUR
AU  - Shi, Y.
AU  - Tian, Z.
AU  - Leclercq, S.O.
AU  - Zhang, H.
AU  - Yang, M.
AU  - Zhang, Y.
TI  - Genetic characterization and potential molecular dissemination mechanism of tet (31) gene in Aeromonas caviae from an oxytetracycline wastewater treatment system.
JO  - J. Environ. Sci. (China)
PY  - 2019
SP  - 259
EP  - 266
VL  - 76
AB  - Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly
AB  - found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated
AB  - from farming animals and related environment. However, its distribution in other bacteria
AB  - and potential molecular dissemination mechanism in environment are still unknown. The
AB  - purpose of this study was to investigate the potential mechanism underlying dissemination
AB  - of tet(31) by analysing the tet(31)-carrying fragments in A. caviae strains isolated from an
AB  - aerobic biofilm reactor treating oxytetracycline bearing wastewater. Twenty-three A. caviae
AB  - strains were screened for the tet(31) gene by polymerase chain reaction (PCR). Three strains
AB  - (two harbouring tet(31), one not) were subjected to whole genome sequencing using
AB  - the PacBio RSII platform. Seventeen A. caviae strains carried the tet(31) gene and exhibited
AB  - high resistance levels to oxytetracycline with minimum inhibitory concentrations (MICs)
AB  - ranging from 256 to 512 mg/L. tet(31) was comprised of the transposon Tn6432 on the
AB  - chromosome of A. caviae, and Tn6432 was also found in 15 additional tet(31)-positive
AB  - A. caviae isolates by PCR. More important, Tn6432 was located on an integrative conjugative
AB  - element (ICE)-like element, which could mediate the dissemination of the tet(31)-carrying
AB  - transposon Tn6432 between bacteria. Comparative analysis demonstrated that Tn6432
AB  - homologs with the structure ISCR2-kphzF-tetR(31)-tet(31)-kglmM-sul2 were also carried by
AB  - A. salmonicida, G. anatis, and O. alkaliphila, suggesting that this transposon can be
AB  - transferred
AB  - between species and even genera. This work provides the first report on the identification of
AB  - the tet(31) gene in A. caviae, and will be helpful in exploring the dissemination mechanisms
AB  - of tet(31) in water environment.
ER  -

TY  - JOUR
AU  - Shi, Y.H.
AU  - Ren, L.
AU  - Jia, Y.
AU  - Yan, Y.C.
TI  - Genome Sequence of Organophosphorus Pesticide-Degrading Bacterium Pseudomonas stutzeri Strain YC-YH1.
JO  - Genome Announcements
PY  - 2015
SP  - e00192
EP  - e00115
VL  - 3
AB  - Pseudomonas stutzeri strain YC-YH1, isolated from pesticide-polluted soil, efficiently
AB  - degrades organophosphorus pesticides (OPPs) such as chlorpyrifos,
AB  - parathion-methyl, triazophos, and parathion. Here, we report the genome sequence
AB  - (4.83 Mb) of P. stutzeri YC-YH1 to facilitate further investigation of the
AB  - OPP-degrading mechanism.
ER  -

TY  - JOUR
AU  - Shi, Z.
AU  - Kaldhone, P.R.
AU  - Khajanchi, B.K.
AU  - Foley, S.L.
AU  - Ricke, S.C.
TI  - Draft Genome Sequences of Salmonella enterica Serovar Enteritidis and Kentucky Isolates from Retail Poultry Sources.
JO  - Genome Announcements
PY  - 2018
SP  - e00193
EP  - e00118
VL  - 6
AB  - The draft genome sequences of four Salmonella enterica serovar Enteritidis and Kentucky
AB  - isolates were evaluated for biofilm formation and antibiotic resistance.
AB  - The Salmonella serovar Kentucky strains CFS84 and CFS85 and Salmonella serovar
AB  - Enteritidis strains CFS86 and CFS87 were isolated from retail poultry sources in
AB  - Arkansas.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Ando, T.
TI  - The restriction endonucleases in Bacillus amyloliquefaciens N strain.  Substrate specificities.
JO  - Biochim. Biophys. Acta
PY  - 1976
SP  - 184
EP  - 196
VL  - 442
AB  - Two species of restriction endonuclease were isolated by gel filtration and
AB  - DEAE-cellulose chromatography from a cell-free extract of Bacillus
AB  - amyloliquefaciens (B. subtilis) N strain; a lower molecular weight endonuclease
AB  - (endonuclease R.BamNI) and a higher molecular-weight one (endonuclease
AB  - R.BamNx).  Both of them required only Mg2+ for their activities.  Endonuclease
AB  - R.BamNx introduced a larger number of site-specific scissions in Escheria coli
AB  - phage lambda DNA than endonuclease R.BamNI did.  Endonuclease R.BamNx cleaved
AB  - Bacillus phage Phi105C DNA at the specific sites which are classified into two
AB  - groups: one type of sites is modified by B. amyloliquefaciens H strain in vivo
AB  - while the other is not affected.  It was also active on DNAs of E. coli phage
AB  - T7, lambda dvl, Simian virus 40 (SV40) and colicinogenic factor ColEI and was
AB  - inactive on DNAs of Bacillus phages Phi29 and M2.  Endonuclease R.BamNi cleaved
AB  - DNA in the same nucleotide sequences as endonuclease R.BamHI isolated from H
AB  - strain by Wilson and Young.  This endonuclease was active on DNAs of phage
AB  - lambda, lambda dvl and SV40, and was inactive of phages Phi105C, Phi29, M2 and
AB  - T7, and ColEI DNA.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Ando, T.
TI  - In vitro Modification and Restriction of Phage Phi105C DNA with Bacillus subtilis N Cell-free Extract.
JO  - Mol. Gen. Genet.
PY  - 1975
SP  - 269
EP  - 279
VL  - 138
AB  - The enzymes involved in host-controlled modification and restriction by
AB  - Bacillus subtilis strain N were detected in cell-free extracts.  In the
AB  - presence of Mg2+, the N-specific endonuclease cleaved unmodified DNA but did
AB  - not attack Phi105C.N DNA carrying N-specific modification.  The restriction
AB  - endonuclease required neither SAM nor ATP for its activity.  The N-specific
AB  - modification enzyme was active only in the presence of SAM, indicating that
AB  - modification in this system is a methylation of DNA.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Ando, T.
TI  - Host controlled modification and restriction in Bacillus subtilis.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 275
EP  - 280
VL  - 131
AB  - The host controlled modification and restriction was found in Bacillus subtilis
AB  - Marburg 168, Bacillus subtilis (B. amyloliquefaciens) N and H, by use of a
AB  - clear plaque mutant of temperate phage Phi105 (Phi105C).  This phenomenon of
AB  - "modification and restriction" was similar to that found in Escherichia coli,
AB  - Haemophilus influenzae and other micro-organisms.  Phi105 carrying Marburg 168
AB  - specific modification (Phi105C.168) plated on B. subtilis N and H with an
AB  - efficiency of 10-5 and 10-2, respectively.  Phi105C carrying the modification
AB  - endowed by B. subtilis N (Phi105C.N) had an efficiency of plating on B.
AB  - subtilis 168 of 4 x 10-2 and was not restricted by B. subtilis H.  Phi105C
AB  - carrying H specific modification (Phi105C.H) plated on B. subtilis 168 and N
AB  - with an efficiency of 10-1-10-2 and 10-5, respectively.  Modification type of
AB  - Phi105C was determined by the last host strain and was not genetic behavior of
AB  - the phage.  Efficiencies of plating of Bacillus phages Phi29 and SPP1 were not
AB  - affected by the modification and restriction described in the ent paper.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Hayase, E.
AU  - Ando, T.
TI  - Simultaneous preparation of a DNA ligase and restriction endonucleases from Bacillus amyloliquefaciens N.
JO  - Agric. Biol. Chem.
PY  - 1978
SP  - 1613
EP  - 1615
VL  - 42
AB  - None
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Ikawa, S.
AU  - Ando, T.
TI  - Genetic study of restriction endonucleases in Bacillus subtilis.
JO  - Microbiology-1982
PY  - 1982
SP  - 71
EP  - 74
VL  - 0
AB  - During this decade, research has revealed that various microorganisms have a
AB  - type of intracellular endodeoxyribonuclease that recognizes specific nucleotide
AB  - sequences in double-stranded DNA and introduces double-stranded scissions at or
AB  - near those sequences.  These endonucleases are called site-specific
AB  - endonucleases or type II restriction endonucleases, although only a few of them
AB  - have been proven to be involved in restriction and modification of genetically
AB  - foreign entities invading into a cell.  Therefore, this type of endonuclease
AB  - might have other biological roles in living cells, such as recombination.  In
AB  - Bacillus subtilis, restriction and modification of phages were not known until
AB  - 1974, when Trautner et al. and we found, independently, that strains of B.
AB  - subtilis, including the 168 strain, exhibited restriction and modification of
AB  - phages SPP1 or Phi105C.  We then found that 13 of 40 B. subtilis strains
AB  - (including B. amyloliquefaciens) and 11 strains of other Bacillus species have
AB  - site-specific endonucleases.  As an initial step in elucidating the biological
AB  - roles of site-specific endonucleases, we analyzed the genes for such
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Ikawa, S.
AU  - Kim, C.
AU  - Ando, T.
TI  - Site-specific Deoxyribonucleases in Bacillus subtilis and other Bacillus strains.
JO  - J. Bacteriol.
PY  - 1976
SP  - 473
EP  - 476
VL  - 128
AB  - We systematically studied site-specific deoxyribonucleases in Bacillus strains
AB  - and detected deoxyribonuclease activities in 20 of 62 strains tested.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Ikawa, S.
AU  - Komatsu, Y.
AU  - Ando, T.
AU  - Saito, H.
TI  - Introduction of host-controlled modification and restriction systems of Bacillus subtilis IAM1247 into Bacillus subtilis 168.
JO  - J. Bacteriol.
PY  - 1979
SP  - 308
EP  - 310
VL  - 139
AB  - Bacillus subtilis IAM1247 had two modification and restriction systems
AB  - (Bsu12471 and Bsu1247II), the former producing an isoschizomer of PstI
AB  - endonuclease.  A transformant clone was isolated which had Bsu 168, BsuR, and
AB  - Bsu12471 systems coexisting within a genome.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Morishima, N.
TI  - Genetic recombination and site-specific endonucleases in mitochondria.
JO  - Tanpakushitsu Kakusan Koso
PY  - 1994
SP  - 589
EP  - 600
VL  - 39
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Morishima, N.
AU  - Nakagawa, K.
TI  - A mitochondrial multi-site specific endonuclease, endo SceI of Saccharomyces cerevisiae.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 154
EP  - 154
VL  - 17C
AB  - There are two classes of sequence specific endonucleases active on double-stranded DNA in
AB  - eukaryotic cells. Endonucleases in one class exhibit very strict site-specificity which allows
AB  - to cut DNA at any one (or a few) sites among the whole genome. These endonucleases have been
AB  - shown to initiate site-specific genetic recombination in vivo including "intron homing".
AB  - Endonucleases in the other class introduce a number of double-stranded breaks in various
AB  - double-stranded DNA like bacterial restriction endonucleases. Until now, three endonucleases
AB  - were biochemically or genetically identified to belong to the latter class; i.e. Endo.SceI and
AB  - Endo.SceII of Saccharomyces cerevisiae, and Endo.SuvI from Saccharomyces uvarum (S.
AB  - carlsbergensis). The active form of Endo.SceII is a heterodimer of 75kDa- and 50kDa- subunits
AB  - and localized in mitochondria. Endo.SceI and Endo.SuvI contain the 50kDa subunit, and each of
AB  - them is a product of the allele of a mitochondrial gene (ENS2). The difference in sequence
AB  - specificity between Endo.SceI and Endo.SuvI is caused by the substitution of two amino acids.
AB  - The cutting sites of Endo.SceI have complex features and the cutting creates staggered ends
AB  - with 4 bases protruding at the 3' ends. These are common featues of all sequence-specific
AB  - endonucleases from yeast. Another common feature is the presence of two clusters of partially
AB  - conserved 12 amino acid sequences. We looked at events around a genetic marker (Oli') which
AB  - was located at ca 200 bps from a cutting site for Endo.SceI in a mitochondrial gene, oli2. The
AB  - site was shown to be partially cleaved in vivo in mitotic cells having active Endo.SceI. We
AB  - found mating-dependent introduction of a double-stranded break at the cutting site in the oli2
AB  - gene in a haploid lacking Endo.ScII upon the mating with a partner having active Endo.SceI. At
AB  - the same time, we observed polarized gene conversion at oli2 locus. The disparity in
AB  - conversion depends on the presence of active Endo.SceI in a parent and the difference in the
AB  - sensitivity of the cutting sites to Endo.SceI between parental strains. Endo.SceI cuts
AB  - mitochondrial DNA at more than 30 sites in vitro and we detected in vivo cutting at the
AB  - cutting sites for Enco.SceI other than that in oli2 in haploid or diploid cells having active
AB  - Endo.SceI. These results suggest that the recombination induced by Endo.SceI is probably
AB  - homologous rather than site-specific recombination. The subunit structure and the mechanism to
AB  - protect genomic DNA from complete cleavage by the endonuclease are different between Endo.SceI
AB  - and endonucleases of the other class. The 75kDa-subunit of Endo.SceI is HSP70, which is
AB  - involved in the import of protein into mitochondria. This suggests a regulatory role for the
AB  - larger subunit of Endo.SceI in vivo. Although Endo.SceI is dispensable, we found another
AB  - site-specific endonuclease from S. cerevisiae lacking a gene for Endo.SceI (Ohta K., Nicolas,
AB  - A., Keszenman-Pereyra, D. and T.S.). Thus, mitochondria have multiple species of site-specific
AB  - endonucleases and the endonucleases or the recombination induced by them plays a basic role in
AB  - this organelle.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Nakagawa, K.-I.
AU  - Morishima, N.
TI  - Multi-site-specific endonucleases and the initiation of homologous genetic recombination in yeast.
JO  - Adv. Biophys.
PY  - 1995
SP  - 77
EP  - 91
VL  - 31
AB  - The notion that homologous recombination is a regulated biological process is not a familiar
AB  - one.  In yeasts, homologous recombination and most site-specific ones are initiated by
AB  - site-specific double-stranded breaks that are introduced within cis-acting elements for the
AB  - recombination.  On the other hand, yeasts have a group of site-specific endonucleases
AB  - (multi-site-specific endonucleases) that have a number of cleavage sites on each DNA.  One of
AB  - them, Endo.SceI of S. cerevisiae, was shown to introduce double-stranded breaks at a number of
AB  - well-defined sites on the mitochondrial DNA in vivo.  An Endo.SceI-induced double-stranded
AB  - break was demonstrated to induce homologous recombination in mitochondria.  Like the case of
AB  - homologous recombination of nuclear chromosomes, the double-stranded break induces gene
AB  - conversion of both genetic markers flanking and in the proximity of the cleavage site, and the
AB  - cleaved DNA acts as a recipient of genetic information from the uncleaved partner DNA.  The 70
AB  - kDa-heat-shock protein (HSP70)-subunit of Endo.SceI and a general role of the HSP70 in the
AB  - regulation of protein-folding suggest the regulation of nucleolytic activity of Endo.SceI and
AB  - a general role of the HSP70 in the regulation of protein-folding suggest the regulation of
AB  - nucleolytic activity of Endo.SceI.
ER  -

TY  - JOUR
AU  - Shibata, T.
AU  - Watabe, H.
AU  - Kaneko, T.
AU  - Iino, T.
AU  - Ando, T.
TI  - On the nucleotide sequence recognized by a eukaryotic site-specific endonuclease, Endo.SceI from yeast.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 10499
EP  - 10506
VL  - 259
AB  - Endo.SceI which is isolated from cells of Saccharomyces cerevisiae is a
AB  - eukaryotic site-specific endonuclease active on double-stranded DNA.  At each
AB  - cleavage site, Endo.SceI cuts only a defined phosphodiester bond in each strand
AB  - of the double helix.  We compared nucleotide sequences around five cleavage
AB  - sites for Endo.SceI using a computer.  We could not find any common specific
AB  - sequence consisting of five base pairs or more among them.  However, we found a
AB  - 26-base pair consensus sequence which included 15 conserved nucleotides,
AB  - allowing any of the five sequences to include a few nucleotides deviated from
AB  - the consensus sequence.  The consensus sequence is
AB  - 5'-CAn*PYnnAnnCYYGTTnnnPnYnnYA-3', where P, Y, n, and * denote purine,
AB  - pyrimidine, any nucleotide, and the center of the cleavage site, respectively.
AB  - The numbers of sites at which the consensus sequence appears in pBR322 DNA,
AB  - PhiX174 replicative form DNA, fd replicative form DNA, or SV40 DNA are close to
AB  - those of the cleavage sites for Endo.SceI.  We found that a 33-base pair
AB  - fragment was efficiently cut at the defined phosphodiester bonds by Endo.SceI.
AB  - This 33-base pair fragment included 25 base pairs out of the 26-base pair
AB  - consensus sequence.  The fragments in which a part of the consensus sequence
AB  - was missing were not cut by Endo.SceI.  These observations suggest that the
AB  - consensus sequence described above is the major characteristic around the
AB  - cleavage sites recognized by Endo.SceI and that the mode of recognition of
AB  - cleavage sites by Endo.SceI is different from that by restriction
AB  - endonucleases.  We found homology between the consensus sequence for Endo.SceI
AB  - and the sequences around the cleavage sites for two other site-specific
AB  - endonucleases of S. cerevisiae: Endo.SceII and YZ-Endo which is involved in
AB  - mating type switching.
ER  -

TY  - JOUR
AU  - Shibata, T.F.
AU  - Maeda, T.
AU  - Nikoh, N.
AU  - Yamaguchi, K.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Nishiyama, T.
AU  - Hasebe, M.
AU  - Fukatsu, T.
AU  - Kikuchi, Y.
AU  - Shigenobu, S.
TI  - Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of  the Bean Bug Riptortus pedestris.
JO  - Genome Announcements
PY  - 2013
SP  - e00441
EP  - e00413
VL  - 1
AB  - We isolated Burkholderia symbiont strain RPE64 from the bean bug Riptortus pedestris. Analysis
AB  - of the complete 6.96-Mb genome, which consists of three
AB  - chromosomes and two plasmids, will facilitate further understanding of
AB  - insect-microbe symbiosis and the development of pest-control technologies.
ER  -

TY  - JOUR
AU  - Shieh, F.K.
AU  - Reich, N.O.
TI  - AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 1157
EP  - 1168
VL  - 373
AB  - The role of Glu119 in S-adenosyl-l-methionine-dependent DNA methyltransferase M.HhaI-catalyzed
AB  - DNA methylation was studied. Glu119
AB  - belongs to the highly conserved Glu/Asn/Val motif found in all DNA
AB  - C5-cytosine methyltransferases, and its importance for M.HhaI function
AB  - remains untested. We show that formation of the covalent intermediate
AB  - between Cys81 and the target cytosine requires Glu119, since conversion to
AB  - Ala, Asp or Gln lowers the rate of methyl transfer 10(2)-10(6) fold.
AB  - Further, unlike the wild-type M.HhaI, these mutants are not trapped by the
AB  - substrate in which the target cytosine is replaced with the
AB  - mechanism-based inhibitor 5-fluorocytosine. The DNA binding affinity for
AB  - the Glu119Asp mutant is decreased 10(3)-fold. Thus, the ability of the
AB  - enzyme to stabilize the extrahelical cytosine is coupled directly to tight
AB  - DNA binding. The structures of the ternary protein/DNA/AdoHcy complexes
AB  - for both the Glu119Ala and Glu119Gln mutants (2.70 A and 2.75 A,
AB  - respectively) show that the flipped base is positioned nearly identically
AB  - with that observed in the wild-type M.HhaI complex. A single water
AB  - molecule in the Glu119Ala structure between Ala119 and the extrahelical
AB  - cytosine N3 is lacking in the Glu119Gln and wild-type M.HhaI structures,
AB  - and most likely accounts for this mutant's partial activity. Glu119 has
AB  - essential roles in activating the target cytosine for nucleophilic attack
AB  - and contributes to tight DNA binding.
ER  -

TY  - JOUR
AU  - Shieh, F.K.
AU  - Youngblood, B.
AU  - Reich, N.O.
TI  - The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 516
EP  - 527
VL  - 362
AB  - Arg165 forms part of a previously identified base flipping motif in the bacterial DNA cytosine
AB  - methyltransferase, M.HhaI. Replacement of Arg165
AB  - with Ala has no detectable effect on either DNA or AdoMet affinity, yet
AB  - causes the base flipping and restacking transitions to be decreased
AB  - approximately 16 and 190-fold respectively, thus confirming the importance
AB  - of this motif. However, these kinetic changes cannot account for the
AB  - mutant's observed 10(5)-fold decreased catalytic rate. The mutant
AB  - enzyme/cognate DNA cocrystal structure (2.79 A resolution) shows the
AB  - target cytosine to be positioned approximately 30 degrees into the major
AB  - groove, which is consistent with a major groove pathway for nucleotide
AB  - flipping. The pyrimidine-sugar chi angle is rotated to approximately +171
AB  - degrees , from a range of -95 degrees to -120 degrees in B DNA, and -77
AB  - degrees in the WT M.HhaI complex. Thus, Arg165 is important for
AB  - maintaining the cytosine positioned for nucleophilic attack by Cys81. The
AB  - cytosine sugar pucker is in the C2'-endo-C3'-exo (South conformation), in
AB  - contrast to the previously reported C3'-endo (North conformation)
AB  - described for the original 2.70 A resolution cocrystal structure of the WT
AB  - M.HhaI/DNA complex. We determined a high resolution structure of the WT
AB  - M.HhaI/DNA complex (1.96 A) to better determine the sugar pucker. This new
AB  - structure is similar to the original, lower resolution WT M.HhaI complex,
AB  - but shows that the sugar pucker is O4'-endo (East conformation),
AB  - intermediate between the South and North conformers. In summary, Arg165
AB  - plays significant roles in base flipping, cytosine positioning, and
AB  - catalysis. Furthermore, the previously proposed M.HhaI-mediated changes in
AB  - sugar pucker may not be an important contributor to the base flipping
AB  - mechanism. These results provide insights into the base flipping and
AB  - catalytic mechanisms for bacterial and eukaryotic DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Shields, S.L.
AU  - Burbank, D.E.
AU  - Grabherr, R.
AU  - Van Etten, J.L.
TI  - Cloning and sequencing the cytosine methyltransferase gene M. CviJI from Chlorella virus IL-3A.
JO  - Virology
PY  - 1990
SP  - 16
EP  - 24
VL  - 176
AB  - The Chlorella virus IL-3A gene encoding the DNA methyltransferase M.CviJI,
AB  - which methylates the internal cytosine in (G/A)GC(T/C/G) sequences, was cloned
AB  - and expressed in Escherichia coli.  The region containing the M.CviJI gene was
AB  - sequenced and a single open reading frame of 1101 bp was identified that could
AB  - code for a polypeptide of 367 amino acids with a predicted molecular weight of
AB  - 41,864.  M.CviJI contained regions of amino acids which were similar to
AB  - bacterial cytosine methyltransferases.  Eighteen other Chlorella viruses, of 36
AB  - tested, contained DNA sequences which hybridized to the M.CviJI gene; DNA from
AB  - some, but not all, of these 18 viruses also contained 5-methylcytosine in
AB  - (G/A)GC(T/C/G) sequences.
ER  -

TY  - JOUR
AU  - Shields, S.L.
AU  - Burbank, D.E.
AU  - Van Etten, J.L.
TI  - Molecular cloning and characterization of the gene encoding the cytosine methyltransferase.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 214
EP  - 214
VL  - 13D
AB  - The gene encoding the DNA methyltransferase, M.CviJI from Chlorella virus IL-3A
AB  - was cloned in pUC19 and expressed in E. coli RR1.  Recombinant plasmid
AB  - pIL-3A.22.8 containing a 3.6 kbp KpnI/Sau3A restriction fragment encoding
AB  - M.CviJI methylates the internal cytosine in PuGCPy sequences or a subset of
AB  - PuGCPy sequences in vivo.  Methylation of these sequences by M.CviJI prevents
AB  - digestion of pIL-3A.22.8 by restriction endonucleases sensitive to cytosine
AB  - methylation in PuGCPy recognition sequences.  Transposon Tn5 mutagenesis
AB  - localized the M.CviJI functional domain on pIL-3A.22.8.  Restriction fragments
AB  - from the HpaI restriction site, 185 bp from the termini of the terminal repeat
AB  - of Tn5, to the SalI and KpnI restriction site of pIL-3A.22.8 polylinker were
AB  - isolated from individual Tn5 mutants.  These restriction fragments containing
AB  - the functional domain and flanking sequences were subcloned in single stranded
AB  - sequencing vectors M13mp18 and M13mp19 for nucleotide sequencing.  The amino
AB  - acid sequence deduced from M.CviJI nucleotide sequence was compared to the
AB  - amino acid sequence of 5-methylcytosine methyltransferases from prokaryotes to
AB  - determine potentially shared protein domains.  The M.CviJI gene was not
AB  - essential for IL-3A replication since a M.CviJI deletion mutant also replicated
AB  - in Chlorella.
ER  -

TY  - JOUR
AU  - Shields-Menard, S.A.
AU  - Brown, S.D.
AU  - Klingeman, D.M.
AU  - Indest, K.
AU  - Hancock, D.
AU  - Wewalwela, J.J.
AU  - French, W.T.
AU  - Donaldson, J.R.
TI  - Draft Genome Sequence of Rhodococcus rhodochrous Strain ATCC 21198.
JO  - Genome Announcements
PY  - 2014
SP  - e00054
EP  - e00014
VL  - 2
AB  - Rhodococcus rhodochrous is a Gram-positive red-pigmented bacterium commonly found in the soil.
AB  - The draft genome sequence for R. rhodochrous strain ATCC 21198 is presented here to provide
AB  - genetic data for a better understanding of its lipid-accumulating capabilities.
ER  -

TY  - JOUR
AU  - Shier, V.K.
TI  - Characterization and inhibition of an essential adenine DNA methyltransferase from Caulobacter crescentus.
JO  - Diss. Abstr.
PY  - 2002
SP  - 3185
EP  - 3186
VL  - 62
AB  - Genetic evidence has established that DNA methylation provides an obligatory signal for the
AB  - proper progression through the Caulobacter crescentus cell cycle.  The enzyme responsible for
AB  - catalyzing this reaction is a cell-cycle regulated adenine DNA methyltransferase (CcrM).  CcrM
AB  - activity is tightly restricted to predivisional cells by a delicate coordination between
AB  - transcription and proteolytic elimination by a Lon-mediated pathway.  Further underscoring the
AB  - importance of this enzyme is the observation that CcrM is essential for C. crescentus
AB  - viability and that it is only the second known DNA methyltransferase that lacks a cognate
AB  - restriction endonuclease.  To further our understanding of the regulatory role played by CcrM,
AB  - we sought to investigate the biophysical and biochemical properties of this enzyme.
AB  - Equilibrium ultracentrifugation, velocity ultracentrifugation, and chemical crosslinking
AB  - reveal that CcrM is dimeric at physiological concentrations.  However, surface plasmon
AB  - resonance experiments evince that CcrM binds as a monomer to DNA containing the CcrM canonical
AB  - methylation sequence, GANTC.  Collectively, these findings suggest that CcrM dimerization
AB  - serves to stabilize CcrM from premature in vivo proteolysis.  The recently sequenced C.
AB  - crescentus genome unveiled the presence of 4,496 CcrM methylation sites.  Following
AB  - semiconservative DNA replication, CcrM must methylate a total of 8,992 sites on the two
AB  - resulting copies of the genome within the strict temporal constraints of the predivisional
AB  - cells.  Using defined, synthetic substrates that contain multiple methylation sites, CcrM
AB  - processively methylates DNA over a minimum distance of 82 base pairs.  Moreover, CcrM is
AB  - capable of methylating GANTC clusters with no apparent effect on methylation efficiency.
AB  - Despite slow kinetic rate constants, these experiments demonstrate that CcrM is kinetically
AB  - competent to support full genomic methylation within the enforced activity interval.
AB  - Homologues of CcrM are found throughout the alpha-subdivision of proteobacteria.  Many of the
AB  - members of this group are pathogens.  The observation that CcrM activity is essential for
AB  - cellular viability in all of these microorganisms, coupled with the absence of adenine methyl
AB  - modification in eukaryotic species, has implicated CcrM as a target for antimicrobial drug
AB  - design.  Efforts to identify and characterize potential inhibitors are discussed with an
AB  - emphasis on a panel of diphenyl borinic esters.
ER  -

TY  - JOUR
AU  - Shier, V.K.
AU  - Hancey, C.J.
AU  - Benkovic, S.J.
TI  - Identification of the active oligomeric state of an essential adenine DNA methyltransferase from Caulobacter crescentus.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 14744
EP  - 14751
VL  - 276
AB  - Caulobacter crescentus contains one of the two known prokaryotic DNA methyltransferases that
AB  - lacks a cognate endonuclease. This endogenous cell cycle regulated adenine DNA
AB  - methyltransferase (CcrM) is essential for C. crescentus cellular viability. DNA methylation
AB  - catalyzed by CcrM provides an obligatory signal for the proper progression through the cell
AB  - cycle. To further our understanding of the regulatory role played by CcrM, we sought to
AB  - investigate its biophysical properties. In this paper we employed equilibrium
AB  - ultracentrifugation, velocity ultracentrifugation, and chemical cross-linking to show that
AB  - CcrM is dimeric at physiological concentrations. However, surface plasmon resonance
AB  - experiments in the presence of S-adenosyl-homocysteine evince that CcrM binds as a monomer to
AB  - a defined hemi-methylated DNA substrate containing the canonical methylation sequence, GANTC.
AB  - Initial velocity experiments demonstrate that dimerization of CcrM does not affect DNA
AB  - methylation. Collectively, these findings suggest that CcrM is active as a monomer and
AB  - provides a possible in vivo role for dimerization as a means to stabilize CcrM from premature
AB  - catabolism.
ER  -

TY  - JOUR
AU  - Shigdel, U.K.
TI  - Developing DNA probes to trap DNA cytosine-5 methyltransferases involved in promoter hypermethylation in cancer.
JO  - Ph.D. Thesis, Univ. of Chicago
PY  - 2009
SP  - 1
EP  - 90
AB  - A major limitation to making significant advances in diagnosing and treating cancer is that we
AB  - do not have a thorough understanding of the mechanisms leading to abnormal DNA methylation in
AB  - cancer cells. Although there is a plethora of information on genes that are hypermethylated in
AB  - cancer cells, we rarely know which DNA cytosine-5 methyltransferase (DNMTs) and what complex
AB  - is involved in methylating particular promoters in cancer cells. I developed two types of DNA
AB  - probes, a diazirine and a disulfide based, which can be incorporated at specific positions of
AB  - oligonucleotides that have potential to trap DNMTs and their cofactors at a particular
AB  - promoter. A diazirine photophore was introduced into either the major or minor groove of DNA
AB  - via a convertible nucleoside methodology. The resulting DNA probes efficiently cross-linked
AB  - with two different proteins studied as examples, the E. coli DNA adenine methyltransferase
AB  - (EcoDam) and the human 06-alkylguanine-DNA alkyltransferase (hAGT). Efficient cross-linking of
AB  - diazirine can be utilized to trap proteins from cell extracts. Taking advantage of DNMTs'
AB  - invariant active site Cys and their base flipping property, a new disulfide-based DNA probe,
AB  - l'-methylenedisulfide deoxyribose, which can efficiently cross-link Haemophilus haemolyticus
AB  - methylase (M. Hhal) and Spiroplasma sp. Methylase (M. SssI) was also developed. Compared to
AB  - commercially available 5-FdC, the new probe cross-links DNMTs quickly. Using a disulfide
AB  - tether on the N4 position of cytosine, catalytic domain of DNMT3A (DNMT3 AC) has been
AB  - crosslinked to DNA in high efficiency. Such a high cross-linking yield of DNMT3AC holds great
AB  - promise in identifying DNMTs and their cofactors that act on particular promoters, as well as
AB  - in structurally characterizing the DNMT3 AC-DNA complex.
ER  -

TY  - JOUR
AU  - Shigdel, U.K.
AU  - He, C.
TI  - A New 1'-Methylenedisulfide Deoxyribose that Forms an Efficient Cross-Link to DNA Cytosine-5 Methyltransferase (DNMT).
JO  - J. Am. Chem. Soc.
PY  - 2008
SP  - 17634
EP  - 17635
VL  - 130
AB  - Although only four bases, adenine, guanine, cytosine, and thymine,
AB  - encode all genetic information in DNA, there is a heritable "fifth" base,
AB  - 5-methylcytosine, which can induce epigenetic changes that alter
AB  - chromatin structures. Methylation at the 5-position of cytosine in a
AB  - CpG dinucleotide is catalyzed by a conserved group of proteins called
AB  - DNA cytosine-5 methyltransferases (DNMTs) by using S-adenosylmethionine
AB  - (SAM) as the cofactor (Figure 1A). This modification has
AB  - a profound effect on gene expression. Many cancer cells are characterized
AB  - by abnormal DNA methylation. Repetitive DNA sequences and
AB  - some genes are hypomethylated and transcriptionally active, whereas
AB  - many genes are hypermethylated and transcriptionally inactive.1
AB  - Inhibition of human DNMTs has been shown to be an effective strategy
AB  - to treat various cancers.
ER  -

TY  - JOUR
AU  - Shigemoto, N.
AU  - Kuwahara, R.
AU  - Kayama, S.
AU  - Shimizu, W.
AU  - Onodera, M.
AU  - Yokozaki, M.
AU  - Hisatsune, J.
AU  - Kato, F.
AU  - Ohge, H.
AU  - Sugai, M.
TI  - Emergence in Japan of an imipenem-susceptible, meropenem-resistant Klebsiella pneumoniae carrying blaIMP-6.
JO  - Diagn. Microbiol. Infect. Dis.
PY  - 2012
SP  - 109
EP  - 112
VL  - 72
AB  - We identified 5 Klebsiella pneumoniae isolates showing high resistance to
AB  - beta-lactams except imipenem and designated them ISMRK (imipenem-susceptible but
AB  - meropenem-resistant Klebsiella). They carried the bla(IMP-6) and bla(CTX-M-2) on
AB  - a self-transmissible plasmid. ISMRK may be falsely categorized as susceptible to
AB  - carbapenems if imipenem is used to screen carbapenem resistance.
ER  -

TY  - JOUR
AU  - Shigenobu, S.
AU  - Watanabe, H.
AU  - Hattori, M.
AU  - Sakaki, Y.
AU  - Ishikawa, H.
TI  - Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.
JO  - Nature
PY  - 2000
SP  - 81
EP  - 86
VL  - 407
AB  - Almost all aphid species (Homoptera, Insecta) have 60-80 huge cells called bacteriocytes,
AB  - within which are round-shaped bacteria that are designated Buchnera. These bacteria are
AB  - maternally transmitted to eggs and embryos through host generations, and the mutualism between
AB  - the host and the bacteria is so obligate that neither can reproduce independently. Buchnera is
AB  - a close relative of Escherichia coli, but it contains more than 100 genomic copies per cell,
AB  - and its genome size is only a seventh of that of E. coli. Here we report the complete genome
AB  - sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and
AB  - two small plasmids. There are genes for the biosyntheses of amino acids essential for the
AB  - hosts in the genome, but those for non-essential amino acids are missing, indicating
AB  - complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks
AB  - genes for the biosynthesis of cell-surface components, including lipopolysaccharides and
AB  - phospholipids, regulator genes and genes involved in defense of the cell. These results
AB  - indicate that Buchnera is completely symbiotic and viable only in its limited niche, the
AB  - bacteriocyte.
ER  -

TY  - JOUR
AU  - Shih, P.M. et al.
TI  - Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2013
SP  - 1053
EP  - 1058
VL  - 110
AB  - The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a
AB  - great breadth of morphologies and ecologies; they play key roles in global carbon
AB  - and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace
AB  - their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest
AB  - as platforms for "green" biotechnology and biofuels. To explore the molecular
AB  - basis of their different phenotypes and biochemical capabilities, we sequenced
AB  - the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial
AB  - strains. Comparison of cyanobacterial genomes reveals the molecular basis for
AB  - many aspects of cyanobacterial ecophysiological diversity, as well as the
AB  - convergence of complex morphologies without the acquisition of novel proteins.
AB  - This phylum-wide study highlights the benefits of diversity-driven genome
AB  - sequencing, identifying more than 21,000 cyanobacterial proteins with no
AB  - detectable similarity to known proteins, and foregrounds the diversity of
AB  - light-harvesting proteins and gene clusters for secondary metabolite
AB  - biosynthesis. Additionally, our results provide insight into the distribution of
AB  - genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this
AB  - study doubles both the amount and the phylogenetic diversity of cyanobacterial
AB  - genome sequence data. Given the exponentially growing number of sequenced
AB  - genomes, this diversity-driven study demonstrates the perspective gained by
AB  - comparing disparate yet related genomes in a phylum-wide context and the insights
AB  - that are gained from it.
ER  -

TY  - JOUR
AU  - Shikara, M.
TI  - Identification of a restriction endonuclease (SacC1) from Saccharomyces cerevisiae.
JO  - J. Yeast Fungal Res.
PY  - 2010
SP  - 127
EP  - 135
VL  - 1
AB  - palindromic sequence 5'CTCGAC3' cleaving both DNA strands upstream and downstream of its
AB  - recognition sequence and makes a staggered cut at the distance of five bases from the
AB  - recognition sequence on the upper strand and at the seventh base on the complementary strand.
AB  - It shares similar
AB  - characteristics with Sac I from Streptomyces achromogenes as well as Sst1 from Streptomyces
AB  - Stanford and Psp124B1 from Pseudomonas species. It has been purified by ammonium sulphate
AB  - precipitation, dialysis, and gel filtration using phosphocellulose, DEAE-cellulose and
AB  - Sephadex G-100
AB  - with an optimal pH range (7.5-8.5), active at 37oC and dependent on Mg+2 or Mn2+ which
AB  - increases its activity by 4- and 2-folds, respectively, while other cations decrease its
AB  - activity to some extents.  Cleavage on both sides of the recognition sequence is
AB  - characteristic of Type IIB systems but all IIB
AB  - enzymes studied so far have been found to recognize discontinuous sites and a distinctive
AB  - subunit/domain organization that is not present in the SacC1 enzyme. There are similarities
AB  - between SacC1 and other homing endonucleases belonging to the LAGLIDADG family such as a
AB  - requirement for Mg2+ (or Mn2+) for cleavage to take place, optimal activity at alkaline pH and
AB  - stimulation of the reaction by moderate concentrations of the monovalent cation.
ER  -

TY  - JOUR
AU  - Shikara, M.
TI  - A specific inhibitory protein to a restriction enzyme from Saccharomyces cerevisiae.
JO  - J. Yeast Fungal Res.
PY  - 2010
SP  - 174
EP  - 182
VL  - 1
AB  - A specific protein inhibitor for the restriction enzyme (SacC1) has been purified from
AB  - Saccharomyces
AB  - cerevisiae approximately 21,000 fold and its inhibitory properties have been characterized.
AB  - The
AB  - isoelectric points (pI) of SacCI and its inhibitor are 9.0 and 5.22, respectively. The
AB  - molecular weight of
AB  - SacC1, the inhibitor and SacC1-inhibitor complex were estimated by gel filtration on a
AB  - Sephadex G-100
AB  - column to be 64,000, 32,000 and 85,000, respectively. The inhibitor protein inhibits SacC1
AB  - catalytic
AB  - activities efficiently, but has no effect on other restriction enzymes tested. Inhibition does
AB  - not occur
AB  - unless SacC1 enzyme is exposed to the inhibitor protein prior to the reaction of the enzyme
AB  - with DNA.
AB  - The inhibitory activity is independent of temperature. The inhibition increased linearly with
AB  - the addition
AB  - of inhibitor to various amounts of SacC1, up to 85% inhibition. The slope of inhibition was
AB  - constant
AB  - irrespective of the initial amount of SacC1 and Ki value of 3.45 x 10-12 was obtained. The
AB  - inhibitor
AB  - interacts strongly with SacC1 and this interaction could increase the stability of the
AB  - complex, possibly
AB  - manifesting itself as SacC1 decreases in the dissociation rate due to the electrostatic
AB  - attraction between
AB  - the two groups or the stability may increase by potentially stronger electrostatic
AB  - interaction. The
AB  - conformational specificity between SacC1 and its inhibitor seems to be essential for their
AB  - interaction.
AB  - The extremely strong affinity of the inhibitor to SacC1 is remarkable and stronger than the
AB  - affinity of
AB  - several restriction enzymes.
ER  -

TY  - JOUR
AU  - Shilov, I.
AU  - Tashlitsky, V.
AU  - Khodoun, M.
AU  - Vasilev, S.
AU  - Alekseev, Y.
AU  - Kuzubov, A.
AU  - Kubareva, E.
AU  - Karyagina, A.
TI  - DNA-methyltransferase SsoII interaction with own promoter region binding site.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 2659
EP  - 2664
VL  - 26
AB  - The investigation of SsoII DNA-methyltransferase interaction with the intergenic region of
AB  - SsoII restriction-modification system was carried out.  Seven guanine residues protected by
AB  - M.SsoII from methylation with dimethylsulfate and thus probably involved in enzyme-DNA
AB  - recognition were identified.  Six of them are located symmetrically within the 15 bp inverted
AB  - repeat inside the SsoII promoter region.  The crosslinking of SsoII methyltransferase with DNA
AB  - duplexes containing 5-bromo-2'-deoxyuridine instead of thymidine was performed.  The
AB  - crosslinked products were obtained in all cases, thus proving that tested thymines were in
AB  - proximity with enzyme.  The ability to produce the crosslinked products in one case was
AB  - 2-5-fold higher than in other ones.  This allowed us to imply that the thymine residue in this
AB  - position of the inverted repeat could be in contact with M.SsoII.  Based on the experimental
AB  - data, two symmetrical 4 bp clusters (GGAC), which could be involved in the interaction with
AB  - M.SsoII in the DNA-protein complex, were identified.  The model of M.SsoII interaction with
AB  - its own promoter was proposed.
ER  -

TY  - JOUR
AU  - Shimizu, M.
AU  - Goda, H.
AU  - Yamasaki, K.
AU  - Oshima, S.
AU  - Ohnishi, K.
AU  - Osaki, Y.
AU  - Kataoka, S.
AU  - Imajoh, M.
TI  - Draft Genome Sequence of Flavobacterium psychrophilum Strain KTEN-1510 with Genotype A/G-C, Isolated from an Ayu (Plecoglossus altivelis altivelis) in the  Kagami River, Kochi, Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e01762
EP  - e01715
VL  - 4
AB  - In this paper, we describe the draft genome sequence of Flavobacterium psychrophilum strain
AB  - KTEN-1510, with genotype A/G-C. This strain was isolated in
AB  - October 2015 from the gills of an ayu (Plecoglossus altivelis altivelis) in the
AB  - upper Kagami River in central Kochi Prefecture on Shikoku Island, Japan.
ER  -

TY  - JOUR
AU  - Shimizu, T.
AU  - Ohtani, K.
AU  - Hirakawa, H.
AU  - Ohshima, K.
AU  - Yamashita, A.
AU  - Shiba, T.
AU  - Ogasawara, N.
AU  - Hattori, M.
AU  - Kuhara, S.
AU  - Hayashi, H.
TI  - Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 996
EP  - 1001
VL  - 99
AB  - Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes
AB  - life-threatening gas gangrene and mild
AB  - enterotoxaemia in humans, although it colonizes as normal intestinal flora of humans and
AB  - animals. The organism is known to produce a
AB  - variety of toxins and enzymes that are responsible for the severe myonecrotic lesions. Here we
AB  - report the complete 3,031,430-bp sequence
AB  - of C. perfringens strain 13 that comprises 2,660 protein coding regions and 10 rRNA genes,
AB  - showing pronounced low overall G + C
AB  - content (28.6%). The genome contains typical anaerobic fermentation enzymes leading to gas
AB  - production but no enzymes for the
AB  - tricarboxylic acid cycle or respiratory chain. Various saccharolytic enzymes were found, but
AB  - many enzymes for amino acid biosynthesis were
AB  - lacking in the genome. Twenty genes were newly identified as putative virulence factors of C.
AB  - perfringens, and we found a total of five
AB  - hyaluronidase genes that will also contribute to virulence. The genome analysis also proved an
AB  - efficient method for finding four members of
AB  - the two-component VirR/VirS regulon that coordinately regulates the pathogenicity of C.
AB  - perfringens. Clearly, C. perfringens obtains
AB  - various essential materials from the host by producing several degradative enzymes and toxins,
AB  - resulting in massive destruction of the host
AB  - tissues.
ER  -

TY  - JOUR
AU  - Shimizu-Kadota, M.
AU  - Kato, H.
AU  - Shiwa, Y.
AU  - Oshima, K.
AU  - Machii, M.
AU  - Araya-Kojima, T.
AU  - Zendo, T.
AU  - Hattori, M.
AU  - Sonomoto, K.
AU  - Yoshikawa, H.
TI  - Genomic Features of Lactococcus lactis IO-1, a Lactic Acid Bacterium That Utilizes Xylose and Produces High Levels of L-Lactic Acid.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2013
SP  - 1804
EP  - 1808
VL  - 77
AB  - Lactococcus lactis IO-1 (JCM7638) produces L-lactic acid predominantly when grown at high
AB  - xylose concentrations, and its utilization is highly desired in the green plastics industry.
AB  - Therefore it is worthwhile studying its genomic traits. In this study, we focused on (i) genes
AB  - of possible horizontal transfer derivation (prophages, the nisin-sucrose transposon, and
AB  - several restriction-modification systems), and (ii) genes for the synthetic pathways of amino
AB  - acids and vitamins in the IO-1 genome. In v ew of the results of this analysis, we consider
AB  - their meanings in strain IO-1.
ER  -

TY  - JOUR
AU  - Shimizu-Kadota, M.
AU  - Shibahara-Sone, H.
TI  - M.HhaI-methylated DNA is resistant to cleavage by R.BbeI.
JO  - Agric. Biol. Chem.
PY  - 1989
SP  - 2841
EP  - 2842
VL  - 53
AB  - Shows that BbeI can cleave GGCG5mCC, GGCGC5mC, but not GG5mCGCC.
ER  -

TY  - JOUR
AU  - Shimoda, N.
AU  - Yamakoshi, K.
AU  - Miyake, A.
AU  - Takeda, H.
TI  - Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene.
JO  - Dev. Dyn.
PY  - 2005
SP  - 1509
EP  - 1516
VL  - 233
AB  - The zebrafish no tail gene (ntl) is indispensable for tail and notochord development. We have
AB  - shown previously that ntl is de novo methylated
AB  - during early embryogenesis. To find the gene that de novo methylates ntl
AB  - and understand the meaning of this methylation, we cloned seven genes that
AB  - encode the conserved catalytic domain of methyltransferases. We found that
AB  - injection of antisense morpholino oligonucleotides against one of them,
AB  - termed dnmt7, into eggs significantly reduced the level of ntl
AB  - methylation, although no apparent phenotype was induced by the injection.
AB  - Inhibition of Dnmt7 activity did not change the level of genome-wide
AB  - methylation nor did it affect de novo methylation of injected plasmid DNA,
AB  - indicating that Dnmt7 specifically methylates ntl in the genome.
ER  -

TY  - JOUR
AU  - Shimoda, Y.
AU  - Hirakawa, H.
AU  - Sato, S.
AU  - Saeki, K.
AU  - Hayashi, M.
TI  - Whole-Genome Sequence of the Nitrogen-Fixing Symbiotic Rhizobium Mesorhizobium loti Strain TONO.
JO  - Genome Announcements
PY  - 2016
SP  - e01016
EP  - e01016
VL  - 4
AB  - Mesorhizobium loti is the nitrogen-fixing microsymbiont for legumes of the genus  Lotus Here,
AB  - we report the whole-genome sequence of a Mesorhizobium loti strain,
AB  - TONO, which is used as a symbiont for the model legume Lotus japonicus The
AB  - whole-genome sequence of the strain TONO will be a solid platform for comparative
AB  - genomics analyses and for the identification of genes responsible for the
AB  - symbiotic properties of Mesorhizobium species.
ER  -

TY  - JOUR
AU  - Shimodaira, J.
AU  - Kamimura, N.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Masai, E.
TI  - Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway.
JO  - Genome Announcements
PY  - 2015
SP  - e00643
EP  - e00615
VL  - 3
AB  - Comamonas sp. strain E6 can degrade o-phthalate, terephthalate, and isophthalate  via the
AB  - protocatechuate 4,5-cleavage pathway. Here, we report the draft genome
AB  - sequence of E6 in order to provide insights into its mechanisms in o-phthalate
AB  - catabolism and its potential use for biotechnological applications.
ER  -

TY  - JOUR
AU  - Shimodaira, J.
AU  - Yonezuka, K.
AU  - Tabata, M.
AU  - Nagase, S.
AU  - Kasai, D.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Fukuda, M.
TI  - Draft Genome Sequence of Comamonas thiooxydans Strain PHE2-6 (NBRC 110656), a Chlorinated-Ethene-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00487
EP  - e00416
VL  - 4
AB  - Comamonas thiooxydans strain PHE2-6 (NBRC 110656), which was isolated from a
AB  - trichloroethene-contaminated site in Japan, utilizes phenol as a sole source of
AB  - carbon and cometabolizes cis- and trans-dichloroethenes. We report here the draft
AB  - genome sequence of this strain, containing 5,309,680 bp, with 60.6% G+C content.
ER  -

TY  - JOUR
AU  - Shimotsu, H.
AU  - Takahashi, H.
AU  - Saito, H.
TI  - Site-specific endonucleases in Streptomyces strains.
JO  - Agric. Biol. Chem.
PY  - 1980
SP  - 1665
EP  - 1666
VL  - 44
AB  - A large number of class II restriction endonucleases have now been isolated
AB  - from various microorganisms.  Since their discovery they have become invaluable
AB  - tools in researches of physical mapping DNA sequencing and gene cloning.  Only
AB  - four Streptomyces strains have been reported to produce restriction-like
AB  - endonucleases; Streptomyces achromogenes (SacI, SacII, and SacIII), S. albus G
AB  - (SalI and SalII), and S. lavendulae (SlaI).  The first two strains produce
AB  - exactly identical enzymes.  In this communication, we report the results of
AB  - survey of restriction-like endonucleases among Streptomyces strains.
ER  -

TY  - JOUR
AU  - Shimotsu, H.
AU  - Takahashi, H.
AU  - Saito, H.
TI  - A new site-specific endonuclease StuI from Streptomyces tubercidicus.
JO  - Gene
PY  - 1980
SP  - 219
EP  - 225
VL  - 11
AB  - A new sequence-specific endonuclease, StuI, produced by Streptomyces
AB  - tubercidicus KCC S-0054, was identified and partially purified.  StuI
AB  - recognizes the hexanucleotide "palindromic" sequence:
AB  - 5'-AGG^CCT-3'
AB  - 3'-TCC^GGA-5'  and cleaves it at the middle, producing blunt ends.
ER  -

TY  - JOUR
AU  - Shimura, Y.
AU  - Hirose, Y.
AU  - Misawa, N.
AU  - Wakazuki, S.
AU  - Fujisawa, T.
AU  - Nakamura, Y.
AU  - Kanesaki, Y.
AU  - Yamaguchi, H.
AU  - Kawachi, M.
TI  - Complete Genome Sequence of a Coastal Cyanobacterium, Synechococcus sp. Strain NIES-970.
JO  - Genome Announcements
PY  - 2017
SP  - e00139
EP  - e00117
VL  - 5
AB  - Members of the cyanobacterial genus Synechococcus are abundant in marine environments. To
AB  - better understand the genomic diversity of marine Synechococcus
AB  - spp., we determined the complete genome sequence of a coastal cyanobacterium,
AB  - Synechococcus sp. NIES-970. The genome had a size of 3.1 Mb, consisting of one
AB  - chromosome and four plasmids.
ER  -

TY  - JOUR
AU  - Shin, H.
AU  - Lee, J.H.
AU  - Ahn, C.S.
AU  - Ryu, S.
AU  - Cho, B.C.
TI  - Complete genome sequence of marine bacterium Pseudoalteromonas phenolica bacteriophage TW1.
JO  - Arch. Virol.
PY  - 2014
SP  - 159
EP  - 162
VL  - 159
AB  - For molecular study of marine bacteria Pseudoalteromonas phenolica using
AB  - bacteriophage, a novel bacteriophage, TW1, belonging to the family Siphoviridae,
AB  - was isolated, and its genome was completely sequenced and analyzed. The phage TW1
AB  - genome consists of 39,940-bp-length double-stranded DNA with a GC content of
AB  - 40.19 %, and it was predicted to have 62 open reading frames (ORFs), which were
AB  - classified into functional groups, including phage structure, packaging, DNA
AB  - metabolism, regulation, and additional function. The phage life style prediction
AB  - using PHACTS showed that it may be a temperate phage. However, genes related to
AB  - lysogeny and host lysis were not detected in the phage TW1 genome, indicating
AB  - that annotation information about P. phenolica phages in the genome databases may
AB  - not be sufficient for the functional prediction of their encoded proteins. This
AB  - is the first report of a P. phenolica-infecting phage, and this phage genome
AB  - study will provide useful information for further molecular research on P.
AB  - phenolica and its phage, as well as their interactions.
ER  -

TY  - JOUR
AU  - Shin, H.
AU  - Lee, J.H.
AU  - Choi, Y.
AU  - Ryu, S.
TI  - Complete Genome Sequence of the Opportunistic Food-Borne Pathogen Cronobacter sakazakii ES15.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4438
EP  - 4439
VL  - 194
AB  - Cronobacter sakazakii is an emerging pathogen associated with several outbreaks of food-borne
AB  - illness in premature infants. To characterize its physiology and
AB  - pathogenicity at the molecular level, C. sakazakii ES15 was isolated and its
AB  - genome was completely sequenced and analyzed. Here, the results are announced and
AB  - major findings from its annotation data are reported.
ER  -

TY  - JOUR
AU  - Shin, H.
AU  - Lee, J.H.
AU  - Kim, Y.
AU  - Ryu, S.
TI  - Complete Genome Sequence of Cronobacter sakazakii Bacteriophage CR3.
JO  - J. Virol.
PY  - 2012
SP  - 6367
EP  - 6368
VL  - 86
AB  - Due to the high risk of Cronobacter sakazakii infection in infants fed powdered
AB  - milk formula and the emergence of antibiotic-resistant strains, an alternative
AB  - biocontrol agent using bacteriophage is needed to control this pathogen. To
AB  - further the development of such an agent, the C. sakazakii-targeting
AB  - bacteriophage CR3 was isolated and its genome was completely sequenced. Here, we
AB  - announce the genomic analysis results of the largest C. sakazakii phage known to
AB  - date and report the major findings from the genome annotation.
ER  -

TY  - JOUR
AU  - Shin, H.
AU  - Lee, J.H.
AU  - Lim, J.A.
AU  - Kim, H.
AU  - Ryu, S.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S.
JO  - J. Virol.
PY  - 2012
SP  - 1284
EP  - 1285
VL  - 86
AB  - To understand the interaction between the host of pathogenic Salmonella enterica
AB  - serovar Typhimurium and its bacteriophage, we isolated the bacteriophage SPN1S.
AB  - It is a lysogenic phage in the Podoviridae family and uses the O-antigen of
AB  - lipopolysaccharides (LPS) as a host receptor. Comparative genomic analysis of
AB  - phage SPN1S and the S. enterica serovar Anatum-specific phage epsilon15 revealed
AB  - different host specificities, probably due to the low homology of host
AB  - specificity-related genes. Here we report the complete circular genome sequence
AB  - of S. Typhimurium-specific bacteriophage SPN1S and show the results of our
AB  - analysis.
ER  -

TY  - JOUR
AU  - Shin, J.
AU  - Soo-Ko, K.
TI  - Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones.
JO  - J. Antimicrob. Chemother.
PY  - 2013
SP  - 969
EP  - 972
VL  - 69
AB  - OBJECTIVES: To determine and compare the complete nucleotide sequences of plasmids carrying
AB  - blaCTX-M-15 from three different Klebsiella pneumoniae clones.
AB  - METHODS: IncFII-type plasmids pKP02022, pKP09085 and pKP007 were extracted from three K.
AB  - pneumoniae strains. These strains belong to sequence types (STs) ST15,
AB  - ST48 and ST23, respectively, and were isolated in Korea. Plasmids were sequenced using the 454
AB  - Genome Sequencer FLX system. RESULTS: The three plasmids, pKP02022
AB  - (203577 bp), pKP09085 (213019 bp) and pKP007 (246 176 bp), all exhibited a very similar
AB  - structure, with a pKPN3-like backbone and a resistance region including blaOXA-1,
AB  - aac(6')-Ib-cr and cat genes as well as blaCTX-M-15. They were also very similar to pUUH239.2,
AB  - previously isolated in Sweden. Iron (III) uptake-related genes were found in pKP007 from the
AB  - ST23 strain, which has been reported to be associated with liver abscesses. The resistance
AB  - region contained several insertion sequences, such as IS26, which may play an important role
AB  - in structural rearrangements of plasmids. CONCLUSIONS: The very similar structure of the three
AB  - plasmids, extracted from different clones, suggests that the spread of CTX-M-producing K.
AB  - pneumoniae isolates might result from the horizontal transfer of plasmids and subsequent
AB  - integration and recombination.
ER  -

TY  - JOUR
AU  - Shin, J.E.
AU  - Lin, C.
AU  - Lim, H.N.
TI  - Horizontal transfer of DNA methylation patterns into bacterial chromosomes.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 460
EP  - 471
VL  - 44
AB  - Horizontal gene transfer (HGT) is the non-inherited acquisition of novel DNA sequences. HGT is
AB  - common and important in bacteria because it enables the rapid generation of new phenotypes
AB  - such as antibiotic resistance. Here we show that in vivo and in vitro DNA methylation patterns
AB  - can be horizontally transferred into bacterial chromosomes to program cell phenotypes. The
AB  - experiments were performed using a synthetic system in Escherichia coli where different DNA
AB  - methylation patterns within the cis-regulatory sequence of the agn43 gene turn on or off a
AB  - fluorescent reporter (CFP). With this system we demonstrated that DNA methylation patterns not
AB  - only accompany the horizontal transfer of genes into the bacterial cytoplasm but can be
AB  - transferred into chromosomes by: (i) bacteriophage P1 transduction; and (ii) transformation of
AB  - extracellular synthetic DNA. We also modified the experimental system by replacing CFP with
AB  - the SgrS small RNA, which regulates glucose and methyl alpha-D-glucoside uptake, and showed
AB  - that horizontally acquired DNA methylation patterns can increase or decrease cell fitness.
AB  - That is, horizontally acquired DNA methylation patterns can result in the selection for and
AB  - against cells that have HGT. Findings from these proof-of-concept experiments have
AB  - applications in synthetic biology and potentially broad implications for bacterial adaptation
AB  - and evolution.
ER  -

TY  - JOUR
AU  - Shin, N.R.
AU  - Whon, T.W.
AU  - Roh, S.W.
AU  - Kim, M.S.
AU  - Jung, M.J.
AU  - Lee, J.
AU  - Bae, J.W.
TI  - Genome Sequence of Corynebacterium nuruki S6-4T, Isolated from Alcohol Fermentation Starter.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4257
EP  - 4257
VL  - 193
AB  - Corynebacterium nuruki S6-4(T), isolated from Korean alcohol fermentation starter, is a
AB  - strictly aerobic, nonmotile, Gram-positive, and rod-shaped
AB  - bacterium belonging to the genus Corynebacterium and the actinomycete
AB  - group. We report here the draft genome sequence of C. nuruki strain
AB  - S6-4(T) (3,106,595 bp, with a G+C content of 69.5%).
ER  -

TY  - JOUR
AU  - Shin, S.C.
AU  - Ahn, D.H.
AU  - Lee, J.K.
AU  - Kim, S.J.
AU  - Hong, S.G.
AU  - Kim, E.H.
AU  - Park, H.
TI  - Genome Sequence of Sphingomonas sp. Strain PAMC 26605, Isolated from Arctic Lichen (Ochrolechia sp.).
JO  - J. Bacteriol.
PY  - 2012
SP  - 1607
EP  - 1607
VL  - 194
AB  - The endosymbiotic bacterium Sphingomonas sp. strain PAMC 26605 was isolated from  Arctic
AB  - lichens (Ochrolechia sp.) on the Svalbard Islands. Here we report the
AB  - draft genome sequence of this strain, which could provide further insights into
AB  - the symbiotic mechanism of lichens in extreme environments.
ER  -

TY  - JOUR
AU  - Shin, S.C.
AU  - Kim, S.J.
AU  - Ahn, D.H.
AU  - Lee, J.K.
AU  - Lee, H.
AU  - Lee, J.
AU  - Hong, S.G.
AU  - Lee, Y.M.
AU  - Park, H.
TI  - Genome Sequence of a Salinibacterium sp. Isolated from Antarctic Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2404
EP  - 2404
VL  - 194
AB  - The draft genome of Salinibacterium sp. PAMC 21357, isolated from permafrost soil of
AB  - Antarctica, was determined. Here we present a 3.1-Mb draft genome sequence of
AB  - Salinibacterium sp. that could provide further insight into the genetic
AB  - determination of its cold-adaptive properties.
ER  -

TY  - JOUR
AU  - Shin, S.C.
AU  - Kim, S.J.
AU  - Ahn-do, H.
AU  - Lee, J.K.
AU  - Park, H.
TI  - Draft Genome Sequence of Sphingomonas echinoides ATCC 14820.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1843
EP  - 1843
VL  - 194
AB  - Sphingomonas is a Gram-negative, yellow-pigmented, chemoheterotrophic, strictly aerobic
AB  - bacterium. The bacterium is known to be metabolically versatile and can
AB  - utilize a wide range of natural compounds as well as some types of environmental
AB  - contaminants, such as creosote, polychlorinated biphenyls, etc. Here, we report
AB  - the draft genome sequence of Sphingomonas echinoides ATCC 14820, which will
AB  - provide additional information to enhance our understanding of metabolic
AB  - versatility of Sphingomonas.
ER  -

TY  - JOUR
AU  - Shin, S.C.
AU  - Kim, S.J.
AU  - Hong, S.G.
AU  - Ahn-do, H.
AU  - Lee, Y.M.
AU  - Lee, H.
AU  - Lee, J.
AU  - Park, H.
TI  - Genome Sequence of Pseudomonas sp. Strain PAMC 25886, Isolated from Alpine Glacial Cryoconite.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1844
EP  - 1844
VL  - 194
AB  - Pseudomonas spp. have shown characteristics of efficiently metabolizing environmental
AB  - pollutants and also producing exopolysaccharides known as biofilms.
AB  - Here we present the draft genome sequence of Pseudomonas sp. strain PAMC 25886,
AB  - which was isolated from glacier cryoconite in the Alps mountain permafrost region
AB  - and which may provide further insight into biodegradative and/or
AB  - biofilm-producing mechanisms in a cold environment.
ER  -

TY  - JOUR
AU  - Shin, S.H.
AU  - Kim, S.
AU  - Kim, J.Y.
AU  - Lee, S.
AU  - Um, Y.
AU  - Oh, M.K.
AU  - Kim, Y.R.
AU  - Lee, J.
AU  - Yang, K.S.
TI  - Complete Genome Sequence of the 2,3-Butanediol-Producing Klebsiella pneumoniae Strain KCTC 2242.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2736
EP  - 2737
VL  - 194
AB  - Here we report the full genome sequence of Klebsiella pneumoniae KCTC 2242,consisting of a
AB  - 5.26-Mb chromosome (57.6% GC%; 5,035 genes [4,923 encoding
AB  - known proteins, 112 RNA genes]) and a 202-kb plasmid (50.2% GC%; 229 genes [229
AB  - encoding known proteins]).
ER  -

TY  - JOUR
AU  - Shin, S.H.
AU  - Kim, S.
AU  - Kim, J.Y.
AU  - Lee, S.
AU  - Um, Y.
AU  - Oh, M.K.
AU  - Kim, Y.R.
AU  - Lee, J.
AU  - Yang, K.S.
TI  - Complete Genome Sequence of Klebsiella oxytoca KCTC 1686, Used in Production of 2,3-Butanediol.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2371
EP  - 2372
VL  - 194
AB  - Here we report the full genome sequence of Klebsiella oxytoca KCTC 1686, which is used in
AB  - production of 2,3-butanediol. The KCTC 1686 strain contains 5,974,109 bp
AB  - with G+C content of 56.05 mol% and contains 5,488 protein-coding genes and 110
AB  - structural RNAs.
ER  -

TY  - JOUR
AU  - Shin, S.H.
AU  - Kim, S.
AU  - Kim, J.Y.
AU  - Lee, S.
AU  - Um, Y.
AU  - Oh, M.K.
AU  - Kim, Y.R.
AU  - Lee, J.
AU  - Yang, K.S.
TI  - Complete Genome Sequence of Enterobacter aerogenes KCTC 2190.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2373
EP  - 2374
VL  - 194
AB  - This is the first complete genome sequence of the Enterobacter aerogenes species. Here we
AB  - present the genome sequence of E. aerogenes KCTC 2190, which contains
AB  - 5,280,350 bp with a G + C content of 54.8 mol%, 4,912 protein-coding genes, and
AB  - 109 structural RNAs.
ER  -

TY  - JOUR
AU  - Shin, S.H.
AU  - Kim, S.
AU  - Kim, J.Y.
AU  - Song, H.Y.
AU  - Cho, S.J.
AU  - Kim, D.R.
AU  - Lee, K.I.
AU  - Lim, H.K.
AU  - Park, N.J.
AU  - Hwang, I.T.
AU  - Yang, K.S.
TI  - Genome Sequence of Paenibacillus terrae HPL-003, a Xylanase-Producing Bacterium Isolated from Soil Found in Forest Residue.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1266
EP  - 1266
VL  - 194
AB  - This article reports on the full genome sequence of Paenibacillus terrae HPL-003, which is a
AB  - Gram-positive, endospore-forming, xylanase-producing bacterium
AB  - isolated from soil found in forest residue on Gara Mountain. The strain HPL-003
AB  - contains 6,083,395 bp with a G+C content of 46.77 mol%, 2,633 protein-coding
AB  - genes, and 117 structural RNAs.
ER  -

TY  - JOUR
AU  - Shin, S.H.
AU  - Um, Y.
AU  - Beak, J.H.
AU  - Kim, S.
AU  - Lee, S.
AU  - Oh, M.K.
AU  - Kim, Y.R.
AU  - Lee, J.
AU  - Yang, K.S.
TI  - Complete Genome Sequence of Raoultella ornithinolytica Strain B6, a 2,3-Butanediol-Producing Bacterium Isolated from Oil-Contaminated Soil.
JO  - Genome Announcements
PY  - 2013
SP  - e00395
EP  - e00313
VL  - 1
AB  - Here we report the full genome sequence of Raoultella ornithinolytica strain B6,  a
AB  - Gram-negative aerobic bacillus belonging to the family Enterobacteriaceae. This
AB  - 2,3-butanediol-producing bacterium was isolated from oil-contaminated soil on
AB  - Backwoon Mountain in South Korea. Strain B6 contains 5,398,151 bp with 4,909
AB  - protein-coding genes, 104 structural RNAs, and 55.88% G+C content.
ER  -

TY  - JOUR
AU  - Shin, S.K.
AU  - Goo, H.
AU  - Cho, Y.J.
AU  - Kwon, S.
AU  - Yong, D.
AU  - Yi, H.
TI  - Non-contiguous finished genome sequence and description of the gliding bacterium  Flavobacterium seoulense sp. nov.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 34
EP  - 34
VL  - 9
AB  - Flavobacterium seoulense strain EM1321(T) is the type strain of Flavobacterium seoulense sp.
AB  - nov., a proposed novel species within the genus Flavobacterium.
AB  - This strain is a Gram-reaction-negative, aerobic, rod-shaped bacterium isolated
AB  - from stream water in Bukhansan National Park, Seoul. This organism is motile by
AB  - gliding. Here, we describe the features of Flavobacterium seoulense EM1321(T),
AB  - together with its genome sequence and annotation. The genome comprised 3,792,640
AB  - bp, with 3,230 protein-coding genes and 52 RNA genes.
ER  -

TY  - JOUR
AU  - Shin, Y.W.
AU  - Choi, M.M.
AU  - Chun, J.H.
AU  - Yu, J.Y.
AU  - Kim, D.W.
AU  - Rhie, G.E.
TI  - Draft Genome Sequence of the First South Korean Clinical Isolate of Burkholderia  pseudomallei, H0901.
JO  - Genome Announcements
PY  - 2018
SP  - e00336
EP  - e00318
VL  - 6
AB  - We report here the draft genome sequence of Burkholderia pseudomallei H0901. This strain was
AB  - isolated in 2003 from the first melioidosis patient in South Korea.
ER  -

TY  - JOUR
AU  - Shinjo, R.
AU  - Uesaka, K.
AU  - Ihara, K.
AU  - Loshakova, K.
AU  - Mizuno, Y.
AU  - Yano, K.
AU  - Tanaka, A.
TI  - Complete Genome Sequence of Kosakonia sacchari Strain BO-1, an Endophytic Diazotroph Isolated from a Sweet Potato.
JO  - Genome Announcements
PY  - 2016
SP  - e00868
EP  - e00816
VL  - 4
AB  - The complete genome sequence of the endophytic diazotroph Kosakonia sacchari, isolated from a
AB  - sweet potato, was analyzed. The 4,902,106-bp genome with 53.7%
AB  - G+C content comprises 4,638 open reading frames, including nif genes, 84 tRNAs,
AB  - and seven complete rRNAs in a circular chromosome.
ER  -

TY  - JOUR
AU  - Shinomiya, T.
AU  - Kobayashi, M.
AU  - Sato, S.
TI  - A second site specific endonuclease from Thermus thermophilus 111, Tth111II.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 3275
EP  - 3285
VL  - 8
AB  - A second site specific endonuclease with novel specificity has been purified
AB  - from Thermus thermophilus strain 111 and named Tth111II.  the enzyme is active
AB  - at temperature up to 80C and requires Mg2+ for endonuclease activity.  Tth111II
AB  - cleaves PhiX174 RFDNA into 11 fragments and lambda DNA into more than 25
AB  - fragments.  From the 5' -terminal sequences of Tth111II fragments of PhiX174
AB  - RFDNA determined by the two dimensional homochromatography and the survey on
AB  - nucleotide sequence PhiX174 RFDNA, it was concluded that Tth111II recognizes
AB  - the DNA sequence 5'CAAPuCA(N)11 ^ 3' 3'GTTPyGT(N)9 ^ 5' and cleaves the sites
AB  - as indicated by the arrows.
ER  -

TY  - JOUR
AU  - Shinomiya, T.
AU  - Kobayashi, M.
AU  - Sato, S.
TI  - A second site specific endonuclease from Thermus thermophilus 111, Tth111II.
JO  - Nucleic Acids Symp. Ser.
PY  - 1980
SP  - S181
EP  - S184
VL  - SS8
AB  - A second site specific endonuclease with a novel specificity has been isolated
AB  - from Thermus thermophilus strain 111 and named Tth111II.  The enzyme is active
AB  - at temperature up to 80C and requires Mg2+ or Mn2+ for activity.  Tth111II
AB  - cleaves PhiX174 RF into 11 fragments.  From the analysis of 5' terminal
AB  - sequences of the PhiX 174 RF DNA fragments produced by Tth111II action, it was
AB  - concluded that Tth111II recognized the DNA sequence 5'CAAPuCA(N)11^3'
AB  - 3'GTTPyGT(N)9^5' and cleaved the sites as indicated by arrows.
ER  -

TY  - JOUR
AU  - Shinomiya, T.
AU  - Kobayashi, M.
AU  - Sato, S.
AU  - Uchida, T.
TI  - A new aspect of a restriction endonuclease Tth111I.  It has a degenerated specificity (Tth111I*).
JO  - J. Biochem. (Tokyo)
PY  - 1982
SP  - 1823
EP  - 1832
VL  - 92
AB  - We previously reported that Thermus thermophilus 111 contained two restriction
AB  - enzymes, Tth111I and Tth111II.  The former does not cleave PhiX174 RFDNA and
AB  - the latter does.  We have now found another endonuclease activity able to
AB  - cleave PhiX174 RFDNA in the cell extract of T. thermophilus 111.
ER  -

TY  - JOUR
AU  - Shinomiya, T.
AU  - Sato, S.
TI  - A site specific endonuclease from Thermus thermophilus 111, Tth111I.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 43
EP  - 56
VL  - 8
AB  - A site specific endonuclease with novel specificity has been isolated from
AB  - Thermus thermophilus strain 111 and named Tth111I.  Tth111I cleaves lambda DNA
AB  - into three fragments of 23.5, 25.7 and 50.8% of the total length, and ColE1 DNA
AB  - into two fragments of nearly equal length.  The sequences around Tth111I
AB  - cleavage sites of ColE1 and lambda DNA were determined by the Maxam and Gilbert
AB  - method and the two dimensional mapping method.  The results suggest that
AB  - Tth111I recognizes the DNA sequence 5'-TGACN^NNGTC-3' 3'-ACTGNN^NCAG-5' site as
AB  - indicated by the arrows.  Assuming that the first T.A pair in the sequence can
AB  - be replaced for any base pair, the Tth111I recognition sequence has the
AB  - symmetry with the two-fold axis as most type II restriction endonucleases do.
ER  -

TY  - JOUR
AU  - Shintani, M.
AU  - Hosoyama, A.
AU  - Ohji, S.
AU  - Tsuchikane, K.
AU  - Takarada, H.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Nojiri, H.
TI  - Complete Genome Sequence of the Carbazole Degrader Pseudomonas resinovorans Strain CA10 (NBRC 106553).
JO  - Genome Announcements
PY  - 2013
SP  - e00488
EP  - e00413
VL  - 1
AB  - Pseudomonas resinovorans strain CA10 can grow on carbazole as its sole carbon and nitrogen
AB  - source. Here, we report the complete nucleotide sequence of the CA10
AB  - genome (a 6,285,863-bp chromosome and a 198,965-bp plasmid). CA10 carries a
AB  - larger number of genes that are potentially responsible for aromatic hydrocarbon
AB  - metabolism than do other previously sequenced Pseudomonas spp.
ER  -

TY  - JOUR
AU  - Shintani, M.
AU  - Ohtsubo, Y.
AU  - Fukuda, K.
AU  - Hosoyama, A.
AU  - Ohji, S.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Nagata, Y.
AU  - Tsuda, M.
AU  - Hatta, T.
AU  - Kimbara, K.
TI  - Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader Geobacillus sp. Strain JF8 (NBRC 109937).
JO  - Genome Announcements
PY  - 2014
SP  - e01213
EP  - e01213
VL  - 2
AB  - Geobacillus sp. strain JF8 (NBRC 109937) utilizes biphenyl and naphthalene as sole carbon
AB  - sources and degrades polychlorinated biphenyl (PCB) at 60 degrees C.
AB  - Here, we report the complete nucleotide sequence of the JF8 genome (a
AB  - 3,446,630-bp chromosome and a 39,678-bp plasmid). JF8 has the smallest genome
AB  - among the known PCB degraders.
ER  -

TY  - JOUR
AU  - Shirai, M.
AU  - Hirakawa, H.
AU  - Kimoto, M.
AU  - Tabuchi, M.
AU  - Kishi, F.
AU  - Ouchi, K.
AU  - Shiba, T.
AU  - Ishii, K.
AU  - Hattori, M.
AU  - Kuhara, S.
AU  - Nakazawa, T.
TI  - Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 2311
EP  - 2314
VL  - 28
AB  - Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis.
AB  - There are many reports of an association between C. pneumoniae infection and atherosclerosis.
AB  - We determined the whole genome sequence of C. pneumoniae strain J138 isolated in Japan in 1994
AB  - and compared it with the sequence of strain CWL029 isolated in the USA before 1987.  The J138
AB  - circular chromosome consists of 1,226,565 nt (40.7% G&C) with 1072 likely protein-coding genes
AB  - that is 3665 nt shorter than the CWL029 genome.  Plasmids, phage- or transposon-like sequences
AB  - were not identified.  The overall genomic organization, gene order and predicted proteomes of
AB  - the two strains are very similar, suggesting a high level of structural and functional
AB  - conservation between the two unrelated isolates.  The most conspicuous differences in the J138
AB  - genome relative to the CWL029 genome are the absence of five DNA segments, ranging in size
AB  - from 89 to 1649 nt, and the presence of three DNA segments, ranging from 27 to 84 nt.  The
AB  - complex organization of these 'different zones' may be attributable to a unique system of
AB  - recombination.
ER  -

TY  - JOUR
AU  - Shiraishi, H.
AU  - Tabuse, Y.
TI  - The AplI Restriction-Modification System in an Edible Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39, Recognizes the Nucleotide Sequence 5'-CTGCAG-3'.
JO  - Biosci. Biotechnol. Biochem.
PY  - 2013
SP  - 782
EP  - 788
VL  - 77
AB  - The degradation of foreign DNAs by restriction enzymes in an edible cyanobacterium,
AB  - Arthrospira platensis, is a potential barrier for gene-transfer experiments in this
AB  - economically valuable organism. We overproduced in Escherichia coli the proteins involved in a
AB  - putative restriction-modification system of A. platensis NIES-39. The protein produced from
AB  - the putative type II restriction enzyme gene NIES39_K04640 exhibited an endonuclease activity
AB  - that cleaved DNA within the sequence 5'-CTGCAG-3' between the A at the fifth position and
AB  - the G at the sixth position. We designated this enzyme AplI. The protein from the adjacent
AB  - gene NIES39_K04650, which encodes a putative DNA (cytosine-5-)-methyltransferase, rendered DNA
AB  - molecules resistant to AplI by modifying the C at the fourth position (but not the C at the
AB  - first position) in the recognition sequence. This modification enzyme, M.AplI, should be
AB  - useful for converting DNA molecules into AplI-resistant forms for use in gene-transfer
AB  - experiments. A summary of restriction enzymes in various Arthrospira strains is also presented
AB  - in this paper.
ER  -

TY  - JOUR
AU  - Shirane, K.
AU  - Toh, H.
AU  - Kobayashi, H.
AU  - Miura, F.
AU  - Chiba, H.
AU  - Ito, T.
AU  - Kono, T.
AU  - Sasaki, H.
TI  - Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases.
JO  - PLoS Genet.
PY  - 2013
SP  - e1003439
EP  - e1003439
VL  - 9
AB  - DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian
AB  - development, retrotransposon silencing, and
AB  - cellular reprogramming. Although methylation mainly occurs on the
AB  - cytosine in a CG site, non-CG methylation is prevalent in pluripotent
AB  - stem cells, brain, and oocytes. We previously identified non-CG
AB  - methylation in several CG-rich regions in mouse germinal vesicle
AB  - oocytes (GVOs), but the overall distribution of non-CG methylation and
AB  - the enzymes responsible for this modification are unknown. Using
AB  - amplification-free whole-genome bisulfite sequencing, which can be used
AB  - with minute amounts of DNA, we constructed the base-resolution
AB  - methylome maps of GVOs, non-growing oocytes (NGOs), and mutant GVOs
AB  - lacking the DNA methyltransferase Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3L. We
AB  - found that nearly two-thirds of all methylcytosines occur in a non-CG
AB  - context in GVOs. The distribution of non-CG methylation closely
AB  - resembled that of CG methylation throughout the genome and showed clear
AB  - enrichment in gene bodies. Compared to NGOs, GVOs were over four times
AB  - more methylated at non-CG sites, indicating that non-CG methylation
AB  - accumulates during oocyte growth. Lack of Dnmt3a or Dnmt3L resulted in
AB  - a global reduction in both CG and non-CG methylation, showing that
AB  - non-CG methylation depends on the Dnmt3a-Dnmt3L complex. Dnmt3b was
AB  - dispensable. Of note, lack of Dnmt1 resulted in a slight decrease in CG
AB  - methylation, suggesting that this maintenance enzyme plays a role in
AB  - non-dividing oocytes. Dnmt1 may act on CG sites that remain
AB  - hemimethylated in the de novo methylation process. Our results provide
AB  - a basis for understanding the mechanisms and significance of non-CG
AB  - methylation in mammalian oocytes.
ER  -

TY  - JOUR
AU  - Shiratori-Takano, H.
AU  - Takano, H.
AU  - Ueda, K.
TI  - Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2  Atmosphere.
JO  - Genome Announcements
PY  - 2016
SP  - e00667
EP  - e00616
VL  - 4
AB  - We report here the genome sequence of Filimonas lacunae, a bacterium of the family
AB  - Chitinophagaceae characterized by high-CO2-dependent growth. The 7.81-Mb
AB  - circular genome harbors many genes involved in carbohydrate degradation and
AB  - related genetic regulation, suggesting the role of the bacterium as a
AB  - carbohydrate degrader in diverse environments.
ER  -

TY  - JOUR
AU  - Shiroma, A.
AU  - Terabayashi, Y.
AU  - Nakano, K.
AU  - Shimoji, M.
AU  - Tamotsu, H.
AU  - Ashimine, N.
AU  - Ohki, S.
AU  - Shinzato, M.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Hirano, T.
TI  - First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach  1884 (DSM 20231T), Determined by PacBio Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2015
SP  - e00800
EP  - e00815
VL  - 3
AB  - The first complete genome sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884
AB  - strain DSM 20231(T), the type strain of the bacterium causing
AB  - staphylococcal disease, were determined using PacBio RS II. The sequences
AB  - represent the chromosome (2,755,072 bp long; G+C content, 32.86%) and a plasmid
AB  - (27,490 bp long; G+C content, 30.69%).
ER  -

TY  - JOUR
AU  - Shirshikov, F.V.
AU  - Korzhenkov, A.A.
AU  - Miroshnikov, K.K.
AU  - Kabanova, A.P.
AU  - Barannik, A.P.
AU  - Ignatov, A.N.
AU  - Miroshnikov, K.A.
TI  - Draft Genome Sequences of New Genomospecies 'Candidatus Pectobacterium maceratum' Strains, Which Cause Soft Rot in Plants.
JO  - Genome Announcements
PY  - 2018
SP  - e00260
EP  - e00218
VL  - 6
AB  - Investigation of collections of phytopathogenic bacteria has revealed some strains distinct
AB  - from known Pectobacterium spp. We report here the draft genome
AB  - sequences of five such strains, isolated during the period of 1947 to 2012. Based
AB  - on comparative genomics, we propose a new candidate genomospecies of the genus
AB  - Pectobacterium, 'Candidatus Pectobacterium maceratum.'
ER  -

TY  - JOUR
AU  - Shiryaev, S.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Three site-specific endonucleases from Thermophilic strain Bacillus species LA are isoschizomers of HhaI, AsuII, and HindIII.
JO  - Biokhimiia
PY  - 1997
SP  - 280
EP  - 290
VL  - 62
AB  - Screening of thermophilic bacterial strains revealed a strain containing three site-specific
AB  - endonucleases: BspLAI, BspLAII, and BspLAIII.  These endonucleases were purified to functional
AB  - purity by sequential chromatography.  Recognition sites, DNA cleavage sites, and some
AB  - properties of the endonucleases were determined.  BspLAI recognizes the sequence 5'-GCG/C-3'
AB  - on the DNA molecule and is an isoschizomer of endonuclease HhaI.  BspLAII recognizes the
AB  - sequence 5'-TT/CGAA-3' and is an isoschizomer of AsuII.  BspLAIII recognizes site
AB  - 5'-A/AGCTT-3' and is an isoschizomer of endonuclease HindIII.  All the three enzymes exhibit
AB  - maximal activity at 55oC.  The optimal buffer is MRB, pH 7.4.  They retain activity on storage
AB  - for 3 weeks at room temperature and thus are highly stable.
ER  -

TY  - JOUR
AU  - Shiryaev, S.A.
AU  - Zheleznyakova, E.N.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Two new site-specific endonucleases from Staphylococcus species strain D5.
JO  - Biokhimiia
PY  - 2000
SP  - 553
EP  - 561
VL  - 65
AB  - Staphylococcus species strain D5 containing two site-specific endonucleases, SspD5I and
AB  - SspD5II, was found during screening of a bacterial strain collection from soil. These
AB  - endonucleases
AB  - were purified to functional homogeneity by sequential chromatography. Site-specific
AB  - endonuclease SspD5I recognizes the sequence 5'-GGTGA(8N/8N)^3' on DNA. Unlike HphI, it
AB  - cleaves DNA at a distance of 8 nucleotides from the recognition sequence on both chains
AB  - producing blunt-end DNA fragments, while endonuclease HphI cleaves DNA forming mononucleotide
AB  - 3'-OH protruding ends. Thus, endonuclease SspD5I is a new type II site-specific endonuclease
AB  - and a neoschizomer of endonuclease HphI. The advantage of this new endonuclease is that the
AB  - blunt-end DNA products of this enzyme can be inserted without additional treatment into vector
AB  - DNAs cleaved with endonucleases yielding DNA blunt-ends. Endonuclease SspD5II recognizes the
AB  - site
AB  - 5'-ATGCA^T-3' and thus is an isoschizomer of endonuclease NsiI. The molecular
AB  - mass of SspD5I is about 35 kD and that of SspD5II is 40 kD. The enzymes exhibit maximal
AB  - activity at 37 C. The optimal buffer for the reaction is HRB (10 mM Tris-HCl, pH 7.5,
AB  - 10 mM MgCl2, 100 mM NaCl, and 1 mM dithiothreitol).
ER  -

TY  - JOUR
AU  - Shishido, K.
AU  - Berg, P.
TI  - Restriction endonuclease from Haemophilus gallinarum (HgaI) cleaves polyoma DNA at four locations.
JO  - J. Virol.
PY  - 1976
SP  - 793
EP  - 798
VL  - 18
AB  - A restriction endonuclease obtained from Haemophilus gallinarum (HgaI) cleaves
AB  - polyoma DNA at four specific sites.  Using the EcoRI, HindIII, and HpaII
AB  - endonuclease restriction sites as reference, the four HgaI cleavage sites were
AB  - mapped at 0.02, 0.14, 0.27, and 0.48 fractional lengths, clockwise, from the
AB  - single EcoRI cleavage site.
ER  -

TY  - JOUR
AU  - Shishido, T.K.
AU  - Jokela, J.
AU  - Fewer, D.P.
AU  - Wahlsten, M.
AU  - Fiore, M.F.
AU  - Sivonen, K.
TI  - Simultaneous Production of Anabaenopeptins and Namalides by the Cyanobacterium Nostoc sp. CENA543.
JO  - ACS Chem. Biol.
PY  - 2017
SP  - 2746
EP  - 2755
VL  - 12
AB  - Anabaenopeptins are a diverse group of cyclic peptides, which contain an unusual
AB  - ureido linkage. Namalides are shorter structural homologues of anabaenopeptins,
AB  - which also contain an ureido linkage. The biosynthetic origins of namalides are
AB  - unknown despite a strong resemblance to anabaenopeptins. Here, we show the
AB  - cyanobacterium Nostoc sp. CENA543 strain producing new (nostamide B-E (2, 4, 5,
AB  - and 6)) and known variants of anabaenopeptins (schizopeptin 791 (1) and
AB  - anabaenopeptin 807 (3)). Surprisingly, Nostoc sp. CENA543 also produced namalide
AB  - B (8) and the new namalides D (7), E (9), and F (10) in similar amounts to
AB  - anabaenopeptins. Analysis of the complete Nostoc sp. CENA543 genome sequence
AB  - indicates that both anabaenopeptins and namalides are produced by the same
AB  - biosynthetic pathway through module skipping during biosynthesis. This unique
AB  - process involves the skipping of two modules present in different nonribosomal
AB  - peptide synthetases during the namalide biosynthesis. This skipping is an
AB  - efficient mechanism since both anabaenopeptins and namalides are synthesized in
AB  - similar amounts by Nostoc sp. CENA543. Consequently, gene skipping may be used to
AB  - increase and possibly broaden the chemical diversity of related peptides produced
AB  - by a single biosynthetic gene cluster. Genome mining demonstrated that the
AB  - anabaenopeptin gene clusters are widespread in cyanobacteria and can also be
AB  - found in tectomicrobia bacteria.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Bandi, S.
AU  - Singh, A.
AU  - Kumar, P.A.
TI  - Draft Genome Sequence of Arthrobacter gangotriensis Strain Lz1yT, Isolated from a Penguin Rookery Soil Sample Collected in Antarctica, near the Indian Station  Dakshin Gangotri.
JO  - Genome Announcements
PY  - 2013
SP  - e00347
EP  - e00313
VL  - 1
AB  - We report here the 4.3-Mb genome of Arthrobacter gangotriensis strain Lz1y(T), isolated from a
AB  - penguin rookery soil sample collected in Antarctica, near the
AB  - Indian station Dakshin Gangotri.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Begum, Z.
AU  - Ruth, M.
AU  - Singh, A.
AU  - Kumar, P.A.
TI  - Draft Genome Sequence of Bhargavaea cecembensis Strain DSE10T, Isolated from a Deep-Sea Sediment Sample Collected at a Depth of 5,904 m from the  Chagos-Laccadive Ridge System in the Indian Ocean.
JO  - Genome Announcements
PY  - 2013
SP  - e00346
EP  - e00313
VL  - 1
AB  - Here, we report the 3.2-Mbp draft genome sequence of Bhargavaea cecembensis strain DSE10(T),
AB  - isolated from a sediment sample collected from the
AB  - Chagos-Laccadive ridge system in the Indian Ocean at a depth of 5,904 m.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Begum, Z.
AU  - Srinivas, T.N.
AU  - Singh, A.
AU  - Kumar, P.A.
TI  - Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16T, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00240
EP  - e00213
VL  - 1
AB  - Here we report the 4.75-Mb genome of Cesiribacter andamanensis strain AMV16(T), isolated from
AB  - a soil sample from a mud volcano in the Andaman Islands, India.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Prasad, S.
AU  - Manasa, B.P.
AU  - Begum, Z.
AU  - Singh, A.
AU  - Kumar, P.A.
TI  - Draft Genome Sequence of Arcticibacter svalbardensis Strain MN12-7T, a Member of  the Family Sphingobacteriaceae Isolated from an Arctic Soil Sample.
JO  - Genome Announcements
PY  - 2013
SP  - e00484
EP  - e00413
VL  - 1
AB  - The 4.69-Mb genome sequence of Arcticibacter svalbardensis strain MN12-7(T), isolated from an
AB  - Arctic soil sample, is reported.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Singh, A.
AU  - Kumar, P.A.
TI  - Draft Genome Sequence of Cyclobacterium qasimii Strain M12-11BT, Isolated from Arctic Marine Sediment.
JO  - Genome Announcements
PY  - 2013
SP  - e00642
EP  - e00613
VL  - 1
AB  - A 6.29-Mb genome sequence of Cyclobacterium qasimii strain M12-11B(T), isolated from an Arctic
AB  - marine sediment sample, is reported.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Singh, A.
AU  - Pinnaka, A.K.
TI  - Draft Genome Sequence of Cecembia lonarensis Strain LW9T, Isolated from Lonar Lake, a Haloalkaline Lake in India.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6631
EP  - 6631
VL  - 194
AB  - The draft genome sequence (4.84 Mb) of Cecembia lonarensis strain LW9(T), isolated from a
AB  - water sample (4.5-m depth) from Lonar Lake, a meteorite-created
AB  - haloalkaline lake in India, is reported. The enzymes produced by these
AB  - microorganisms need to be stable under alkaline conditions prevailing in its
AB  - habitat. Such enzymes would be of immense importance for enzymatic processes
AB  - operating at high pH.
ER  -

TY  - JOUR
AU  - Shivaji, S.
AU  - Ara, S.
AU  - Singh, S.K.
AU  - Bandi, S.
AU  - Singh, A.
AU  - Pinnaka, A.K.
TI  - Draft Genome Sequence of Bacillus isronensis Strain B3W22, Isolated from the Upper Atmosphere.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6624
EP  - 6625
VL  - 194
AB  - We report the 4.0-Mb genome sequence of Bacillus isronensis strain B3W22 isolated from air
AB  - collected at an altitude ranging from 27 to 30 km above the city of
AB  - Hyderabad, in India. This genome sequence will contribute to the objective of
AB  - determining the microbial diversity of the upper atmosphere.
ER  -

TY  - JOUR
AU  - Shivapriya, R.
AU  - Prasad, R.
AU  - Narayanan, I.L.
AU  - Krishnaswamy, S.
AU  - Dharmalingam, K.
TI  - Expression of the mcrA gene of Escherichia coli is regulated post-transcriptionally, possibly by sequestration of the Shine-Dalgarno region.
JO  - Gene
PY  - 1995
SP  - 201
EP  - 207
VL  - 157
AB  - The polypeptides encoded by the mcrA gene were analysed using a T7 expression system.  Cloned
AB  - fragments of 1.6 and 1.0 kb displayed an McrA+/RglA+ phenotype and directed synthesis of a
AB  - 31-kDa polypeptide.  A derivative of these clones altered at an internal HindIII site
AB  - displayed an McrA+/RglA- phenotype and directed production of a 23-kDa polypeptide.  A
AB  - construct carrying the 1.0-kb mcrA insert yielded a single 1.3-kb transcript.  The mcrA
AB  - transcript was found to start from C, G, T and G, namely the fourth, fifth, sixth and seventh
AB  - nucleotides (nt), respectively, downstream from the last nt of the putative -10 region.  Two
AB  - mcrA transcriptional/translational fusions were made in the pT7-7 expression vector and the
AB  - protein encoded by these constructs were analysed.  Regulation of mcrA expression was studied
AB  - by quantitative Northern anlaysis of RNA from various mcrA clones.  Together with a computer
AB  - analysis of the translation initiation region in these mRNAs, the results suggest that the
AB  - expression of mcrA may be regulated at the translational level.
ER  -

TY  - JOUR
AU  - Shiwa, Y.
AU  - Atarashi, H.
AU  - Tanaka, N.
AU  - Okada, S.
AU  - Yoshikawa, H.
AU  - Endo, A.
AU  - Miyaji, T.
AU  - Nakagawa, J.
TI  - Genome Sequences of Three Strains of Lactobacillus paracasei of Different Origins and with Different Cholate Sensitivities.
JO  - Genome Announcements
PY  - 2015
SP  - e00178
EP  - e00115
VL  - 3
AB  - We report here the draft genome sequences of three strains of Lactobacillus paracasei (NRIC
AB  - 0644, NRIC 1781, and NRIC 1917) isolated from different sources.
AB  - The three genomes range from 2.95 to 3.15 Mb with a G+C content of 46% and
AB  - contain approximately 2,700 protein coding sequences.
ER  -

TY  - JOUR
AU  - Shkoporov, A.N.
AU  - Efimov, B.A.
AU  - Khokhlova, E.V.
AU  - Chaplin, A.V.
AU  - Kafarskaya, L.I.
AU  - Durkin, A.S.
AU  - McCorrison, J.
AU  - Torralba, M.
AU  - Gillis, M.
AU  - Sutton, G.
AU  - Weibel, D.B.
AU  - Nelson, K.E.
AU  - Smeianov, V.V.
TI  - Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from  Two Children after a 5-Year Time Period.
JO  - Genome Announcements
PY  - 2013
SP  - e00234
EP  - e00213
VL  - 1
AB  - We report the genome sequences of four isolates of a human gut symbiont, Bifidobacterium
AB  - longum. Strains 44B and 35B were isolated from two 1-year-old
AB  - infants, while 1-6B and 2-2B were isolated from the same children 5 years later.
AB  - The sequences permit investigations of factors enabling long-term colonization of
AB  - bifidobacteria.
ER  -

TY  - JOUR
AU  - Shlyapnikov, S.V.
AU  - Lunin, V.V.
AU  - Blagova, E.V.
AU  - Abaturov, L.V.
AU  - Perbandt, M.
AU  - Betzel, C.
AU  - Mikhailov, A.M.
TI  - A comparative structure-function analysis and molecular mechanism of action of endonucleases from Serratia marcescens and Physarum  polycephalum.
JO  - Bioorg. Khim.
PY  - 2002
SP  - 23
EP  - 31
VL  - 28
AB  - Structural and functional characteristics were compared for wild-type nuclease from Serratia
AB  - marcescens, which belongs to the family of DNA/RNA nonspecific endonucleases, its mutational
AB  - forms, and the nuclease I-PpoI from Physarum polycephalum, which is a representative of the
AB  - Cys-His box-containing subgroup of the superfamily of extremely specific intron-encoded homing
AB  - DNases. Despite the lack of sequence homology and the overall different topology of the
AB  - Serratia marcescens and I-PpoI nucleases, their active sites have a remarkable structural
AB  - similarity. Both of them have a unique magnesium atom in the active site, which is a part of
AB  - the coordinately bonded water-magnesium complex involved in their catalytic acts. In the
AB  - enzyme-substrate complexes, the Mg2+ ion is chelated by an Asp residue, coordinates two oxygen
AB  - atoms of DNA, and stabilizes the transition state of the phosphate anion and 3'-OH group of
AB  - the leaving nucleotide. A new mechanism of the phosphodiester bond cleavage, which is common
AB  - for the Serratia marcescens and I-PpoI nucleases and differs from the known functioning
AB  - mechanism of the restriction and homing endonucleases, was proposed. It presumes a His residue
AB  - as a general base for the activation of a non-cluster water molecule at the nucleophilic in
AB  - line displacement of the 3'-leaving group. A strained metalloenzyme-substrate complex is
AB  - formed during hydrolysis and relaxes to the initial state after the reaction.
ER  -

TY  - JOUR
AU  - Shock, L.S.
AU  - Thakkar, P.V.
AU  - Peterson, E.J.
AU  - Moran, R.G.
AU  - Taylor, S.M.
TI  - DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 3630
EP  - 3635
VL  - 108
AB  - Mitochondrial DNA (mtDNA) has been reported to contain 5-methylcytosine (5mC) at CpG
AB  - dinucleotides, as in the nuclear genome, but neither the
AB  - mechanism generating mtDNA methylation nor its functional significance
AB  - is known. We now report the presence of 5-hydroxymethylcytosine (5hmC)
AB  - as well as 5mC in mammalian mtDNA, suggesting that previous studies
AB  - underestimated the level of cytosine modification in this genome. DNA
AB  - methyltransferase 1 (DNMT1) translocates to the mitochondria, driven by
AB  - a mitochondrial targeting sequence located immediately upstream of the
AB  - commonly accepted translational start site. This targeting sequence is
AB  - conserved across mammals, and the encoded peptide directs a
AB  - heterologous protein to the mitochondria. DNMT1 is the only member of
AB  - the three known catalytically active DNA methyltransferases targeted to
AB  - the mitochondrion. Mitochondrial DNMT1 (mtDNMT1) binds to mtDNA,
AB  - proving the presence of mtDNMT1 in the mitochondrial matrix. mtDNMT1
AB  - expression is up-regulated by NRF1 and PGC1 alpha, transcription
AB  - factors that activate expression of nuclear-encoded mitochondrial genes
AB  - in response to hypoxia, and by loss of p53, a tumor suppressor known to
AB  - regulate mitochondrial metabolism. Altered mtDNMT1 expression
AB  - asymmetrically affects expression of transcripts from the heavy and
AB  - light strands of mtDNA. Hence, mtDNMT1 appears to be responsible for
AB  - mtDNA cytosine methylation, from which 5hmC is presumed to be derived,
AB  - and its expression is controlled by factors that regulate mitochondrial
AB  - function.
ER  -

TY  - JOUR
AU  - Shoemaker, W.R.
AU  - Muscarella, M.E.
AU  - Lennon, J.T.
TI  - Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711.
JO  - Genome Announcements
PY  - 2015
SP  - e00689
EP  - e00615
VL  - 3
AB  - We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural
AB  - soil. The genome provides insight into the ecological strategies of
AB  - this bacterium in free-living and host-associated environments.
ER  -

TY  - JOUR
AU  - Shome, R.
AU  - Krithiga, N.
AU  - Muttannagouda, R.B.
AU  - Veeregowda, B.M.
AU  - Swati, S.
AU  - Shome, B.R.
AU  - Vishnu, U.
AU  - Sankarasubramanian, J.
AU  - Sridhar, J.
AU  - Gunasekaran, P.
AU  - Rahman, H.
AU  - Rajendhran, J.
TI  - Draft Genome Sequence of Brucella melitensis Strain ADMAS-G1, Isolated from Placental Fluids of an Aborted Goat.
JO  - Genome Announcements
PY  - 2013
SP  - e00809
EP  - e00813
VL  - 1
AB  - Here, we report the draft genome sequence and annotation of the Brucella melitensis strain
AB  - designated ADMAS-G1, isolated from placental fluids of an
AB  - aborted goat. The length of the genome is 3,284,982 bp, with a 57.3% GC content.
AB  - A total of 3,325 protein-coding genes and 63 RNA genes were predicted.
ER  -

TY  - JOUR
AU  - Shome, R.
AU  - Krithiga, N.
AU  - Padmashree, B.S.
AU  - Sankarasubramanian, J.
AU  - Vishnu, U.S.
AU  - Sridhar, J.
AU  - Gunasekaran, P.
AU  - Rajendhran, J.
AU  - Rahman, H.
TI  - Draft Genome Sequence of Brucella abortus S99: Designated Antigenic Smooth Reference Strain Used in Diagnostic Tests in India.
JO  - Genome Announcements
PY  - 2014
SP  - e00824
EP  - e00814
VL  - 2
AB  - Brucella abortus strain S99 is widely used for the preparation of colored, plain, recombinant
AB  - and smooth lipopolysaccharide antigens for the preparation of
AB  - Brucella diagnostic kits. The genome of this strain was sequenced and the length
AB  - of the genome was 3,253,175 bp, with 57.2% G+C content. A total of 3,365 protein
AB  - coding genes and 53 RNA genes were predicted.
ER  -

TY  - JOUR
AU  - Shore, A.
AU  - Rossney, A.S.
AU  - Keane, C.T.
AU  - Enright, M.C.
AU  - Coleman, D.C.
TI  - Seven Novel Variants of the Staphylococcal Chromosomal Cassette mec in Methicillin-Resistant Staphylococcus aureus Isolates from Ireland.
JO  - Antimicrob. Agents Chemother.
PY  - 2005
SP  - 2070
EP  - 2083
VL  - 49
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in
AB  - Irish hospitals between 1971 and 2002 were characterized using multilocus
AB  - sequence typing (MLST) (n = 130) and SCCmec typing (n = 172). Where
AB  - atypical SCCmec typing results were obtained, PCR amplification of entire
AB  - SCCmec elements, analysis of amplimer mobility, and nucleotide sequencing
AB  - were undertaken. MLST revealed that 129/130 isolates had the same
AB  - genotypes as internationally spread MRSA clones, including ST239, ST247,
AB  - ST250, ST5, ST22, ST36, and ST8. A novel genotype, ST496, was identified
AB  - in one isolate. Half of the isolates (86/172) had SCCmec type I, IA, II,
AB  - III, or IV. The remaining 86 isolates harbored novel SCCmec variants in
AB  - three distinct genetic backgrounds: (i) 74/86 had genotype ST8 and either
AB  - one of five novel SCCmec II (IIA, IIB, IIC, IID, and IIE) or one of two
AB  - novel SCCmec IV (IVE and IVF) variants; (ii) 3/86 had genotype ST239 and a
AB  - novel SCCmec III variant; (iii) 9/86 had a novel SCCmec I variant
AB  - associated with ST250. SCCmec IVE and IVF were similar to SCCmec IVc and
AB  - IVb, respectively, but differed in the region downstream of mecA. The five
AB  - SCCmec II variants were similar to SCCmec IVb in the region upstream of
AB  - the ccr complex but otherwise were similar to SCCmec II, except for the
AB  - following regions: SCCmec IIA and IID had a novel mec complex, A.4 (Delta
AB  - mecI-IS1182-Delta mecI-mecR1-mecA-IS431mec); SCCmec IIC and IIE had a
AB  - novel mec complex, A.3 (IS1182-Delta mecI-mecR1-mecA-IS431mec); SCCmec IID
AB  - and IIE lacked pUB110; SCCmec IIC and IIE lacked a region of DNA between
AB  - Tn554 and the mec complex; and SCCmec IIB lacked Tn554. This study has
AB  - demonstrated a hitherto-undescribed degree of diversity within SCCmec.
ER  -

TY  - JOUR
AU  - Shore, A.C.
AU  - Rossney, A.S.
AU  - O'Connell, B.
AU  - Herra, C.M.
AU  - Sullivan, D.J.
AU  - Humphreys, H.
AU  - Coleman, D.C.
TI  - Detection of staphylococcal cassette chromosome mec-associated DNA segments in multiresistant methicillin-susceptible Staphylococcus aureus  (MSSA) and identification of Staphylococcus epidermidis ccrAB4 in both  methicillin-resistant S. aureus and MSSA.
JO  - Antimicrob. Agents Chemother.
PY  - 2008
SP  - 4407
EP  - 4419
VL  - 52
AB  - Methicillin-susceptible Staphylococcus aureus (MSSA) can arise from methicillin-resistant S.
AB  - aureus (MRSA) following partial or complete
AB  - excision of staphylococcal cassette chromosome mec (SCCmec). This study
AB  - investigated whether multiresistant MSSA isolates from Irish hospitals,
AB  - where MRSA has been endemic for decades, harbor SCCmec DNA. Twenty-five
AB  - multiresistant MSSA isolates recovered between 2002 and 2006 were tested
AB  - for SCCmec DNA by PCR and were genotyped by multilocus sequence typing and
AB  - spa typing. All isolates lacked mecA. Three isolates (12%) harbored SCCmec
AB  - DNA; two of these (genotype ST8/t190) harbored a 26-kb SCCmec IID
AB  - (II.3.1.2) remnant that lacked part of mecI and all of mecR1, mecA, and
AB  - IS431; the third isolate (ST8/t3209) harbored the SCCmec region from dcs
AB  - to orfX. All three isolates were detected as MRSA using the BD GeneOhm and
AB  - Cepheid's Xpert MRSA real-time PCR assays. Six isolates (ST8/t190, n = 4;
AB  - ST5/t088, n = 2), including both isolates with the SCCmec IID remnant,
AB  - harbored ccrAB4 with 100% identity to ccrAB4 from the Staphylococcus
AB  - epidermidis composite island SCC-CI. This ccrAB4 gene was also identified
AB  - in 23 MRSA isolates representative of ST8/t190-MRSA with variant SCCmec II
AB  - subtypes IIA to IIE, which predominated previously in Irish hospitals.
AB  - ccrAB4 was located 5,549 bp upstream of the left SCCmec junction in both
AB  - the MRSA and MSSA isolates with SCCmec elements and remnants and 5,549 bp
AB  - upstream of orfX in the four MSSA isolates with ccrAB4 only on an SCC-CI
AB  - homologous region. This is the first description of a large SCCmec remnant
AB  - with ccr and partial mec genes in MSSA and of the S. epidermidis SCC-CI
AB  - and ccrAB4 genes in S. aureus.
ER  -

TY  - JOUR
AU  - Shorning, B.Y.
AU  - Vanyushin, B.F.
TI  - Putative DNA-(amino)methyltransferases in eucaryotes.
JO  - Biokhimiia
PY  - 2001
SP  - 753
EP  - 762
VL  - 66
AB  - By computer analysis of the known data bases, we have established that the open reading frames
AB  - (ORF) coding for proteins that possess high degree of homology with procaryotic
AB  - DNA-(amino)methyltransferases are present in the genomes of Leishmania major, Saccharomyces
AB  - cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Drosophila melanogaster,
AB  - Caenorhabditis elegans, and Homo sapiens. Conservative motifs typical for bacterial
AB  - DNA-(amino)methyltransferases are detected in the amino acid sequences of these putative
AB  - proteins. The ORF of all putative eucaryotic DNA-(amino)methyltransferases found are encoded
AB  - in nuclear DNA. In mitochondrial genomes including a few fully sequenced higher plant mtDNA,
AB  - nucleotide sequences significantly homologous to genes of procaryotic
AB  - DNA-(amino)methyltransferases are not found. Thus, ORF homologous to bacterial adenine
AB  - DNA-methyltransferases are present in nuclei of protozoa, yeasts, insects, nematodes,
AB  - vertebrates, higher plants, and other eucaryotes. A special search for corresponding proteins
AB  - and, in particular, adenine DNA-methyltransferases in these organisms and a study of their
AB  - functions are quite promising.
ER  -

TY  - JOUR
AU  - Shouche, Y.S.
AU  - Ramesh, N.
AU  - Brahmachari, S.K.
TI  - Probing of unusual DNA structures in topologically constrained form V DNA: use of restriction enzymes as structural probes.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 267
EP  - 275
VL  - 18
AB  - The ability of DNA sequences to adopt unusual structures under superhelical
AB  - torsional stress has been studied.  Sequences that are forced to adopt an
AB  - unusual conformation in topologically constrained pBR322 form V DNA (Lk=0) were
AB  - mapped using restriction enzymes as probes.  Restriction enzymes such as BamHI,
AB  - PstI, AvaI and HindIII could not cleave their recognition sequences.  The
AB  - removal of topological constraint relieved this inhibition.  The influence of
AB  - neighbouring sequences on the ability of a given sequence to adopt an unusual
AB  - DNA structure, presumbly a left handed Z conformation, was studied through
AB  - single hit analysis.  Using multiple cut restriction enzymes such as NarI and
AB  - FspI, it could be shown that under identical topological strain, the extent of
AB  - structural alteration is greatly influenced by the neighbouring sequences.  In
AB  - light of the variety of sequences and locations that could be mapped to adopt
AB  - non-B conformation in pBR322 form V DNA, restriction enzymes appear as
AB  - potential structural probes for natural DNA sequences.
ER  -

TY  - JOUR
AU  - Showmaker, K.C.
AU  - Arick, M.A.I.I.
AU  - Hsu, C.Y.
AU  - Martin, B.E.
AU  - Wang, X.
AU  - Jia, J.
AU  - Wubben, M.J.
AU  - Nichols, R.L.
AU  - Allen, T.W.
AU  - Peterson, D.G.
AU  - Lu, S.E.
TI  - The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 42
EP  - 42
VL  - 12
AB  - Xanthomonas citri pv. malvacearum is a major pathogen of cotton, Gossypium hirsutum L.. In
AB  - this study we report the complete genome of the X. citri pv.
AB  - malvacearum strain MSCT1 assembled from long read DNA sequencing technology. The
AB  - MSCT1 genome is the first X. citri pv. malvacearum genome with complete coding
AB  - regions for X. citri pv. malvacearum transcriptional activator-like effectors. In
AB  - addition functional and structural annotations are presented in this study that
AB  - will provide a foundation for future pathogenesis studies with MSCT1.
ER  -

TY  - JOUR
AU  - Shrestha, P.M.
AU  - Kube, M.
AU  - Reinhardt, R.
AU  - Liesack, W.
TI  - Transcriptional activity of paddy soil bacterial communities.
JO  - Environ. Microbiol.
PY  - 2008
SP  - 960
EP  - 970
VL  - 11
AB  - Summary Bulk mRNA was used to explore the transcriptional activity of bacterial communities in
AB  - oxic versus anoxic paddy soil. Two microbial cDNA
AB  - libraries were constructed from composite samples using semi-randomly
AB  - primed RT-PCR. cDNAs averaged 500-600 bp in length and were treated as
AB  - expressed sequence tags (ESTs). Clustering analysis of 805 random cDNAs
AB  - resulted in 179 and 155 different ESTs for the oxic and anoxic zones
AB  - respectively. Using an E-value threshold of e(-10), a total of 218
AB  - different ESTs could be assigned by blastx, while 116 ESTs were predicted
AB  - novel. Both the proportion and significance of the EST assignments
AB  - increased with cDNA length. Taxonomic assignment was more powerful in
AB  - discriminating between the aerobic and anaerobic bacterial communities
AB  - than functional inference, as most ESTs in both oxygen zones were putative
AB  - indicators of similar housekeeping functions, in particular ABC-type
AB  - transporters. A few ESTs were putative indicators for community function
AB  - in a biogeochemical context, such as beta-oxidation of long-chain fatty
AB  - acids specifically in the oxic zone. Expressed sequence tags assigned to
AB  - Alpha- and Betaproteobacteria were predominantly found in the oxic zone,
AB  - while those affiliated with Deltaproteobacteria were more frequently
AB  - detected in the anoxic zone. At the genus level, multiple assignments to
AB  - Bradyrhizobium and Geobacter were unique to the oxic and anoxic zones
AB  - respectively. The phylum-level affiliations of 93 16S rRNA sequences
AB  - corresponded well with two taxonomically distinct EST patterns. Expressed
AB  - sequence tags affiliated with Acidobacteria and Chloroflexi were
AB  - frequently detected in both oxygen zones. In summary, the soil
AB  - metatranscriptome is accessible for global analysis and such studies have
AB  - great potential in elucidating the taxonomic and functional status of soil
AB  - bacterial communities, but study significance depends on the number and
AB  - length of cDNAs being randomly analysed.
ER  -

TY  - JOUR
AU  - Shrestha, R.
AU  - Park, D.H.
AU  - Cho, J.M.
AU  - Cho, S.
AU  - Wilson, C.
AU  - Hwang, I.
AU  - Hur, J.H.
AU  - Lim, C.K.
TI  - Genetic organization of the hrp genes cluster in Erwinia pyrifoliae and characterization of HR active domains in HrpNEp protein by mutational analysis.
JO  - Mol. Cells
PY  - 2008
SP  - 30
EP  - 42
VL  - 25
AB  - The disease-specific (dsp) region and the hypersensitive response and
AB  - pathogenicity (hrp) genes, including the hrpW, hrpNEp, and hrpC operons
AB  - have previously been sequenced in Erwinia pyrifoliae WT3 [Shrestha et al.
AB  - (2005a)]. In this study, the remaining hrp genes, including the hrpC,
AB  - hrpA, hrpS, hrpXY, hrpL and hrpJ operons, were determined. The hrp genes
AB  - cluster (ca. 38 kb) was comprised of eight transcriptional units and
AB  - contained nine hrc (hrp conserved) genes. The genetic organization of the
AB  - hrp/hrc genes and their orientation for the transcriptions were also
AB  - similar to and collinear with those of E. amylovora, showing > or = 80%
AB  - homologies. However, ORFU1 and ORFU2 of unknown functions, present between
AB  - the hrpA and hrpS operons of E. amylovora, were absent in E. pyrifoliae.
AB  - To determine the HR active domains, several proteins were prepared from
AB  - truncated fragments of the N-terminal and the C-terminal regions of
AB  - HrpN(Ep) protein of E. pyrifoliae. The proteins prepared from the
AB  - N-terminal region elicited HR, but not from those of the C-terminal region
AB  - indicating that HR active domains are located in only N-terminal region of
AB  - the HrpN(Ep) protein. Two synthetic oligopeptides produced HR on tobacco
AB  - confirming presence of two HR active domains in the HrpN(Ep). The HR
AB  - positive N-terminal fragment (HN delta C187) was further narrowed down by
AB  - deleting C-terminal amino acids and internal amino acids to investigate
AB  - whether amino acid insertion region have role in faster and stronger HR
AB  - activity in HrpN(Ep) than HrpN(Ea). The HrpN(Ep) mutant proteins HN delta
AB  - C187 (D1AIR), HN delta C187 (D2AIR) and HN delta C187 (DM41) retained
AB  - similar HR activation to that of wild-type HrpN(Ep). However, the HrpN(Ep)
AB  - mutant protein HN delta C187 (D3AIR) lacking third amino acid insertion
AB  - region (102 to 113 aa) reduced HR when compared to that of wild-type
AB  - HrpN(Ep). Reduction in HR elicitation could not be observed when single
AB  - amino acids at different positions were substituted at third amino acids
AB  - insertion region. But, substitution of amino acids at L103R, L106K and
AB  - L110R showed reduction in HR activity on tobacco suggesting their
AB  - importance in activation of HR faster in the HrpN(Ep) although it requires
AB  - further detailed analysis.
ER  -

TY  - JOUR
AU  - Shrestha, S.D.
AU  - Guttman, D.S.
AU  - Perron, G.G.
TI  - Draft Genome Sequences of 10 Environmental Pseudomonas aeruginosa Strains Isolated from Soils, Sediments, and Waters.
JO  - Genome Announcements
PY  - 2017
SP  - e00804
EP  - e00817
VL  - 5
AB  - Pseudomonas aeruginosa is an important opportunistic pathogen that has the ability to grow in
AB  - a range of environmental niches. Here, we report the draft
AB  - genome sequences of 10 environmental strains of the bacterium isolated from
AB  - soils, sediments, and waters in various locations in North America and South
AB  - Africa.
ER  -

TY  - JOUR
AU  - Shridhar, P.B.
AU  - Patel, I.R.
AU  - Gangiredla, J.
AU  - Mammel, M.K.
AU  - Noll, L.
AU  - Shi, X.
AU  - Bai, J.
AU  - Elkins, C.A.
AU  - Strockbine, N.
AU  - Nagaraja, T.G.
TI  - Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin.
JO  - Genome Announcements
PY  - 2017
SP  - e00630
EP  - e00617
VL  - 5
AB  - Cattle harbor and shed in their feces several Escherichia coli O104 serotypes. All O104
AB  - strains examined were intimin negative and belonged to the B1
AB  - phylogroup, and some were Shiga toxigenic. We report here the genome sequences of
AB  - bovine O104:H7 (n = 5), O104:H23 (n = 2), O104:H8 (n = 1), and O104:H12 (n = 1)
AB  - isolates and human clinical isolates of O104:H7 (n = 5).
ER  -

TY  - JOUR
AU  - Shtratnikova, V.Y.
AU  - Bragin, E.Y.
AU  - Dovbnya, D.V.
AU  - Pekov, Y.A.
AU  - Schelkunov, M.I.
AU  - Strizhov, N.
AU  - Ivashina, T.V.
AU  - Ashapkin, V.V.
AU  - Donova, M.V.
TI  - Complete Genome Sequence of Sterol-Transforming Mycobacterium neoaurum Strain VKM Ac-1815D.
JO  - Genome Announcements
PY  - 2014
SP  - e01177
EP  - e01113
VL  - 2
AB  - Mycobacterium neoaurum strain VKM Ac-1815D produces 4-androstene-3,17-dione as a  major
AB  - compound from phytosterols. Here, we report the complete genome sequence of
AB  - the strain. The genome consists of a single circular 5,438,190-bp chromosome,
AB  - with a G+C content of 66.88%, containing 5,318 putative open reading frames
AB  - (ORFs), 46 tRNAs, and 6 rRNAs. Arrays of cholesterol metabolism genes are
AB  - randomly clustered throughout the chromosome.
ER  -

TY  - JOUR
AU  - Shtratnikova, V.Y.
AU  - Schelkunov, M.I.
AU  - Dovbnya, D.V.
AU  - Pekov, Y.A.
AU  - Bragin, E.Y.
AU  - Ashapkin, V.V.
AU  - Donova, M.V.
TI  - Complete Genome Sequence of Mycobacterium sp. Strain VKM Ac-1817D, Capable of Producing 9alpha-Hydroxy-androst-4-ene-3,17-dione from Phytosterol.
JO  - Genome Announcements
PY  - 2015
SP  - e01447
EP  - e01414
VL  - 3
AB  - Mycobacterium sp. strain VKM Ac-1817D is capable of converting phytosterol into 9alpha-hydroxy
AB  - androst-4-ene-3,17-dione (9-OH-AD), which is a valuable
AB  - intermediate for the steroid pharmaceutical industry. Here, a complete genome
AB  - sequence of the strain is reported. The genome consists of a single circular
AB  - 6,324,222-bp chromosome with a G+C content of 66.2% and encodes approximately
AB  - 6,000 CDSs, 54 tRNAs, and 6 rRNAs.
ER  -

TY  - JOUR
AU  - Shtratnikova, V.Y.
AU  - Schelkunov, M.I.
AU  - Pekov, Y.A.
AU  - Fokina, V.V.
AU  - Logacheva, M.D.
AU  - Sokolov, S.L.
AU  - Bragin, E.Y.
AU  - Ashapkin, V.V.
AU  - Donova, M.V.
TI  - Complete Genome Sequence of Steroid-Transforming Nocardioides simplex VKM Ac-2033D.
JO  - Genome Announcements
PY  - 2015
SP  - e01406
EP  - e01414
VL  - 3
AB  - Nocardioides simplex VKM Ac-2033D is an effective microbial catalyst for 3-ketosteroid
AB  - 1(2)-dehydrogenation, and it is capable of effective reduction of
AB  - carbonyl groups at C-17 and C-20, hydrolysis of acetylated steroids, and
AB  - utilization of natural sterols. Here, the complete genome sequence is reported.
AB  - An array of genes related to steroid metabolic pathways have been identified.
ER  -

TY  - JOUR
AU  - Shu, H.W.
AU  - Liu, T.T.
AU  - Chan, H.I.
AU  - Liu, Y.M.
AU  - Wu, K.M.
AU  - Shu, H.Y.
AU  - Tsai, S.F.
AU  - Hsiao, K.J.
AU  - Hu, W.S.
AU  - Ng, W.V.
TI  - Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4302
EP  - 4303
VL  - 193
AB  - Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory
AB  - tracts of healthy individuals and AIDS
AB  - patients. The complete genome of the repetitive-sequence-rich M.
AB  - fermentans strain M64 is reported here. Comparative genomics analysis
AB  - revealed dramatic differences in genome size between this strain and the
AB  - recently completely sequenced JER strain.
ER  -

TY  - JOUR
AU  - Shub, D.A.
AU  - Goodrich-Blair, H.
TI  - Protein introns: A new home for endonucleases.
JO  - Cell
PY  - 1992
SP  - 183
EP  - 186
VL  - 71
AB  - An underlying principle of the classical era of molecular biology--that RNA is an exact copy
AB  - of information in one of the DNA strands--was shattered forever with the discovery of RNA
AB  - splicing. Although at first introns could be considered an aberration of eukaryotes and their
AB  - viruses, self-splicing RNAs were soon discovered in mitochondrial, chloroplastic, nuclear,
AB  - bacteriophage, and bacterial genes. Additional modes of gene organization and expression
AB  - continue to emerge with no end in sight. Over the past several years we have witnessed the
AB  - discovery of programmed ribosomal frameshifting and hopping, trans-splicing, RNA editing, and
AB  - cotranslational suppression of nonsense codons. The latest of these surprises is protein
AB  - splicing: the excision of an internal segment of a polypeptide and religation of the flanking
AB  - regions to create a functional protein. The evidence for protein splicing rests on data from
AB  - three genes: VMA1/TFP1, which encodes a subunit of yeast vacuolar ATPase, the gene encoding
AB  - DNA polymerase of the archaen thermophile Thermococcus litoralis (with two "introns"), and the
AB  - recA gene of Mycobacterium tuberculosis. Although the number of examples is small, there is
AB  - one from each of the three major phylogenetic divisions, so the phenomenon may be very widely
AB  - distributed. Phylogenetic distance notwithstanding, these phenomena are remarkably similar:
AB  - findings in each system have foreshadowed similar results in the others. Therefore, although
AB  - specific citations are given, a summary of data from all three systems will be presented.
ER  -

TY  - JOUR
AU  - Shub, D.A.
AU  - Goodrich-Blair, H.
TI  - Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns.
JO  - Trends Biochem. Sci.
PY  - 1994
SP  - 402
EP  - 404
VL  - 19
AB  - Both group I and group II intron RNAs are capable of self splicing, with cleavage-ligation
AB  - proceeding by concerted transesterification reactions. Although they tend to be localized to
AB  - the same cellular compartments (mitochondria and chloroplasts), these two categories of
AB  - self-splicing RNAs bear no features that would indicate a common evolutionary origin. Recent
AB  - attempts to ascribe similarities to the intermolecular structures formed in nuclear
AB  - spliceosomes and the intramolecular structures in group I and group II introns underscore the
AB  - current interest in determining the evolutionary origins and interactions of these
AB  - self-splicing intron classes.
ER  -

TY  - JOUR
AU  - Shub, D.A.
AU  - Gott, J.M.
AU  - Xu, M.Q.
AU  - Lang, B.F.
AU  - Michel, F.
AU  - Tomashewski, J.
AU  - Pedersen-Lane, J.
AU  - Belfort, M.
TI  - Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1988
SP  - 1151
EP  - 1155
VL  - 85
AB  - Three group I introns of bacteriophage T4 have been compared with respect to their sequence
AB  - and structural properties. The introns include the td intervening sequence, as well as the two
AB  - newly described introns in the nrdB and sunY genes of T4. The T4 introns are very closely
AB  - related, containing phylogenetically conserved sequence elements that allow them to be folded
AB  - into a core structure that is characteristic of eukaryotic group IA introns. Similarities
AB  - extend outward to the exon sequences surrounding the three introns. All three introns contain
AB  - open reading frames (ORFs). Although the intron ORFs are not homologous and occur at different
AB  - positions, all three ORFs are looped-out of the structure models, with only the 3' ends of
AB  - each of the ORFs extending into the secondary structure. This arrangement invites interesting
AB  - speculations on the regulation of splicing by translation. The high degree of similarity
AB  - between the T4 introns and the eukaryotic group I introns must reflect a common ancestry,
AB  - resulting either from vertical acquisition of a primordial RNA element or from horizontal
AB  - transfer.
ER  -

TY  - JOUR
AU  - Shub, D.A.
AU  - Xu, M.-Q.
AU  - Gott, J.M.
AU  - Zeeh, A.
AU  - Wilson, L.D.
TI  - A family of autocatalytic group I introns in bacteriophage T4.
JO  - Cold Spring Harb. Symp. Quant. Biol.
PY  - 1987
SP  - 193
EP  - 200
VL  - 52
AB  - The first intron to be discovered in a prokaryotic mRNA was found in the td gene of
AB  - bacteriophage T4.  The presence of an intron in this gene, which encodes thymidylate synthase,
AB  - was detected by sequence comparisons at the DNA and protein levels.  Thus, a stop codon was
AB  - encountered in the DNA sequence before the end of the protein-coding sequence.  Subsequent
AB  - experimentation revealed that the intron in the td gene was excised autocatalytically from
AB  - precursor RNA.  The splicing mechanism resembled that used by group I introns of eukaryotes: a
AB  - series of transesterification reactions triggered by nucleophilic attack by guanosine (or GTP)
AB  - at the 5' splice site.  The primary intron excision product was linear, containing a noncoded
AB  - G at the 5' end.  Although the discovery of an intron in phage T4 was entirely unexpected, it
AB  - encouraged us (in collaboration with M. Belfort) to look for additional group I introns in the
AB  - T4 genome.  Further examples would permit sequence and structural comparisons that might lend
AB  - insight into their evolutionary origin.  Additionally, we hoped that their locations within
AB  - the T4 genome would infer a possible regulatory function in prokaryotic gene expression.  We
AB  - took advantage of the fact that, since G is added to the 5' end of the intron, autocatalytic
AB  - group I introns could be specifically labeled in vitro for use as probes for DNA blotting
AB  - experiments.  If group I introns were in more than just the td gene, multiple RNA species
AB  - would be labeled when total RNA is extracted from T4-infected cells and incubated with
AB  - [a-32P]GTP in vitro.  When used as a probe for a Southern blot of T4 DNA, this RNA should
AB  - hybridize to several DNA bands.
ER  -

TY  - JOUR
AU  - Shukla, H.
AU  - Kobayashi, Y.
AU  - Arenstorf, H.
AU  - Yasukochi, Y.
AU  - Weissman, S.M.
TI  - Purification of BsuE methyltransferase and its application in genome mapping.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 4233
EP  - 4239
VL  - 19
AB  - We have used a combination of BsuE methyltransferase (M.BsuEII) and NotI
AB  - restriction enzyme to cut genomic DNA at a subset of NotI sites.  The
AB  - usefulness of this system is shown in a re-examination of the restriction map
AB  - of the human MHC.  Combinations of methylases and restriction enzymes can be
AB  - used to generate cuts at different frequencies in genomic DNA, such that they
AB  - generate ends complementary to NotI ends, and can be used in conjunction with
AB  - NotI linking clones in chromosome jumping experiments.  These enzyme
AB  - combinations have the potential to produce cutting sites in genomic DNA spaced
AB  - at intervals favorable for extensive mapping, fragment enrichment, and cloning
AB  - efforts.
ER  -

TY  - JOUR
AU  - Shulman, M.J.
TI  - Model for wandering restriction enzymes.
JO  - Nature
PY  - 1974
SP  - 76
EP  - 78
VL  - 252
AB  - None
ER  -

TY  - JOUR
AU  - Shumkova, E.S.
AU  - Olsson, B.E.
AU  - Kudryavtseva, A.V.
AU  - Plotnikova, E.G.
TI  - Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated  Biphenyl Degrader.
JO  - Genome Announcements
PY  - 2015
SP  - e00990
EP  - e00915
VL  - 3
AB  - We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a
AB  - soil polluted with halogenated aromatic compounds in the city of  Perm, Russia. The strain
AB  - degrades polychlorinated biphenyls and a broad range of  aromatic compounds. It possesses
AB  - genes that mediate the degradation of biphenyls/polychlorinated biphenyls, naphthalene, and
AB  - monoaromatic compounds.
ER  -

TY  - JOUR
AU  - Shur, K.V.
AU  - Klimina, K.M.
AU  - Zakharevich, N.V.
AU  - Maslov, D.A.
AU  - Bekker, O.B.
AU  - Zaychikova, M.V.
AU  - Kamaev, E.Y.
AU  - Kravchenko, M.A.
AU  - Skornyakov, S.N.
AU  - Zhang, Y.
AU  - Danilenko, V.N.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis Strain E186hv of Beijing B0/W Lineage with Reduced Virulence.
JO  - Genome Announcements
PY  - 2015
SP  - e00403
EP  - e00415
VL  - 3
AB  - We report a draft genome sequence of Mycobacterium tuberculosis strain E186hv, belonging to
AB  - the Beijing B0/W lineage and isolated from a patient from Kurgan,
AB  - Russia. This clinical isolate showed a reduced virulence phenotype unusual for
AB  - this lineage and resistance to isoniazid, rifampin, ethambutol, pyrazinamide, and
AB  - ofloxacin. We analyzed single nucleotide polymorphisms (SNPs) associated with
AB  - virulence.
ER  -

TY  - JOUR
AU  - Shyaka, A.
AU  - Kusumoto, A.
AU  - Asakura, H.
AU  - Kawamoto, K.
TI  - Whole-Genome Sequences of Eight Campylobacter jejuni Isolates from Wild Birds.
JO  - Genome Announcements
PY  - 2015
SP  - e00315
EP  - e00315
VL  - 3
AB  - We present here the draft genome sequences of 8 Campylobacter jejuni strains isolated from
AB  - wild birds. The strains were initially isolated from swabs taken
AB  - from resident wild birds in the Tokachi area of Japan. The genome sizes range
AB  - from 1.65 to 1.77 Mbp.
ER  -

TY  - JOUR
AU  - Sibley, M.H.
AU  - Raleigh, E.A.
TI  - Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 522
EP  - 534
VL  - 32
AB  - A surprising result of comparative bacterial genomics has been the large amount of DNA found
AB  - to be present in one strain but not in another of the same species. We examine in detail one
AB  - location where gene content varies extensively, the restriction cluster in Escherichia coli.
AB  - This region is designated the Immigration Control Region (ICR) for the density and variability
AB  - of restriction functions found there. To better define the boundaries of this variable locus,
AB  - we determined the sequence of the region from a restrictionless strain, E.coli C. Here we
AB  - compare the 13.7 kb E.coli C sequence spanning the site of the ICR with corresponding
AB  - sequences from five E.coli strains and Salmonella typhimurium LT2. To discuss this variation,
AB  - we adopt the term 'framework' to refer to genes that are stable components of genomes within
AB  - related lineages, while 'migratory' genes are transient inhabitants of the genome.
AB  - Strikingly, seven different migratory DNA segments, encoding different sets of genes and gene
AB  - fragments, alternatively occupy a single well-defined location in the seven strains examined.
AB  - The flanking framework genes, yjiS and yjiA, display approximately normal patterns of
AB  - conservation. The patterns observed are consistent with the action of a site-specific
AB  - recombinase. Since no nearby gene codes for a likely recombinase of known families, such a
AB  - recombinase must be of a new family or unlinked.
ER  -

TY  - JOUR
AU  - Sibponkrung, S.
AU  - Kondo, T.
AU  - Tanaka, K.
AU  - Tittabutr, P.
AU  - Boonkerd, N.
AU  - Teaumroong, N.
AU  - Yoshida, K.I.
TI  - Genome Sequence of Bacillus velezensis S141, a New Strain of Plant Growth-Promoting Rhizobacterium Isolated from Soybean Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e01312
EP  - e01317
VL  - 5
AB  - Bacillus velezensis strain S141 is a plant growth-promoting rhizobacterium
AB  - isolated from soybean (Glycine max) rhizosphere that enhances soybean growth,
AB  - nodulation, and N2 fixation efficiency by coinoculation with Bradyrhizobium
AB  - diazoefficiens USDA110. The S141 genome was identified to comprise a
AB  - 3,974,582-bp-long circular DNA sequence encoding at least 3,817 proteins.
ER  -

TY  - JOUR
AU  - Sidamonidze, K.
AU  - Hang, J.
AU  - Yang, Y.
AU  - Dzavashvili, G.
AU  - Zhgenti, E.
AU  - Trapaidze, N.
AU  - Imnadze, P.
AU  - Nikolich, M.P.
TI  - Genome Sequences of Human and Livestock Isolates of Brucella melitensis and Brucella abortus from the Country of Georgia.
JO  - Genome Announcements
PY  - 2017
SP  - e01518
EP  - e01516
VL  - 5
AB  - Brucellosis, which is among the most widespread global zoonotic diseases, is endemic in the
AB  - nation of Georgia and causes substantial human morbidity and
AB  - economic loss. Here, we report whole-genome sequences of three Brucella
AB  - melitensis and seven Brucella abortus isolates from cattle, sheep, and humans
AB  - that represent genetic groups discovered in Georgia.
ER  -

TY  - JOUR
AU  - Siddaramappa, S. et al.
TI  - Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to 'Dehalococcoides' strains.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 251
EP  - 264
VL  - 6
AB  - Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which
AB  - belongs to a deeply branching lineage within the phylum
AB  - Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming,
AB  - Gram-negative staining bacterium was first isolated from chlorinated solvent
AB  - contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana,
AB  - USA. D. lykanthroporepellens was of interest for genome sequencing for two
AB  - reasons: (a) an unusual ability to couple growth with reductive dechlorination of
AB  - environmentally important polychlorinated aliphatic alkanes and (b) a
AB  - phylogenetic position that is distant from previously sequenced bacteria. The
AB  - 1,686,510 bp circular chromosome of strain BL-DC-9(T) contains 1,720 predicted
AB  - protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus,
AB  - and a single, orphan, small subunit rRNA (16S) locus.
ER  -

TY  - JOUR
AU  - Siddavattam, D.
AU  - Karegoudar, T.B.
AU  - Mudde, S.K.
AU  - Kumar, N.
AU  - Baddam, R.
AU  - Avasthi, T.S.
AU  - Ahmed, N.
TI  - Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading N,N-Dimethylformamide.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5598
EP  - 5599
VL  - 193
AB  - The bacterial genus Paracoccus is comprised of metabolically versatile organisms having
AB  - diverse degradative capabilities and potential industrial
AB  - and environmental applications for bioremediation in particular. We report
AB  - a de novo-assembled sequence and annotation of the genome of a novel
AB  - isolate of Paracoccus denitrificans originally sourced from coal mine
AB  - tailings in India. The isolate was capable of utilizing
AB  - N,N-dimethylformamide (DMF) as a source of carbon and nitrogen and
AB  - therefore holds potential for bioremediation and mineralization of
AB  - industrial pollutants. The genome sequence and biological circuitry
AB  - revealed thereupon will be invaluable in understanding the metabolic
AB  - capabilities, functioning, and evolution of this important bacterial
AB  - organism.
ER  -

TY  - JOUR
AU  - Siddharth, J.
AU  - Membrez, M.
AU  - Chakrabarti, A.
AU  - Betrisey, B.
AU  - Chou, C.J.
AU  - Parkinson, S.J.
TI  - Complete Genome Sequence of Escherichia coli Strain M8, Isolated from ob/ob Mice.
JO  - Genome Announcements
PY  - 2017
SP  - e00449
EP  - e00417
VL  - 5
AB  - Escherichia coli is one of the common inhabitants of the mammalian gastrointestinal track. We
AB  - isolated a strain from an ob/ob mouse and performed
AB  - whole-genome sequencing, which yielded a chromosome of ~5.1 Mb and three plasmids
AB  - of ~160 kb, ~6 kb, and ~4 kb.
ER  -

TY  - JOUR
AU  - Siddique, A.
AU  - Jurkowska, R.Z.
AU  - Jurkowski, T.P.
AU  - Jeltsch, A.
TI  - Auto-methylation of the mouse DNA-(cytosine C5)-methyltransferase Dnmt3a at its active site cysteine residue.
JO  - FEBS J.
PY  - 2011
SP  - 2055
EP  - 2063
VL  - 278
AB  - The Dnmt3a DNA methyltransferase is responsible for establishing DNA methylation patterns
AB  - during mammalian development. We show here that
AB  - the mouse Dnmt3a DNA methyltransferase is able to transfer the methyl
AB  - group from S-adenosyl-L-methionine (AdoMet) to a cysteine residue in
AB  - its catalytic center. This reaction is irreversible and relatively
AB  - slow. The yield of auto-methylation is increased by addition of Dnmt3L,
AB  - which functions as a stimulator of Dnmt3a and enhances its AdoMet
AB  - binding. Auto-methylation was observed in binary Dnmt3a AdoMet
AB  - complexes. In the presence of CpG containing dsDNA, which is the
AB  - natural substrate for Dnmt3a, the transfer of the methyl group from
AB  - AdoMet to the flipped target base was preferred and auto-methylation
AB  - was not detected. Therefore, this reaction might constitute a
AB  - regulatory mechanism which could inactivate unused DNA
AB  - methyltransferases in the cell, or it could simply be an aberrant side
AB  - reaction caused by the high methyl group transfer potential of AdoMet.
ER  -

TY  - JOUR
AU  - Siddiqui, F.M.
AU  - Ibrahim, M.
AU  - Noureen, N.
AU  - Noreen, Z.
AU  - Titball, R.W.
AU  - Champion, O.L.
AU  - Wren, B.W.
AU  - Studholme, D.
AU  - Bokhari, H.
TI  - Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255.
JO  - Genome Announcements
PY  - 2015
SP  - e01223
EP  - e01215
VL  - 3
AB  - The enteropathogen Campylobacter jejuni is a global health disaster, being one of the leading
AB  - causes of bacterial gastroenteritis. Here, we present the draft genome sequence of C. jejuni
AB  - strain cj255, isolated from a chicken source in Islamabad, Pakistan. The draft genome sequence
AB  - will aid in epidemiological studies and quarantine of this broad-host-range pathogen.
ER  -

TY  - JOUR
AU  - Siddiqui, H.
AU  - Yoder-Himes, D.R.
AU  - Mizgalska, D.
AU  - Nguyen, K.A.
AU  - Potempa, J.
AU  - Olsen, I.
TI  - Genome Sequence of Porphyromonas gingivalis Strain HG66 (DSM 28984).
JO  - Genome Announcements
PY  - 2014
SP  - e00947
EP  - e00914
VL  - 2
AB  - Porphyromonas gingivalis is considered a major etiologic agent in adult periodontitis.
AB  - Gingipains are among its most important virulence factors, but
AB  - their release is unique in strain HG66. We present the genome sequence of HG66
AB  - with a single contig of 2,441,680 bp and a G+C content of 48.1%.
ER  -

TY  - JOUR
AU  - Siddiqui, M.A.
AU  - Rashid, N.
AU  - Ayyampalayam, S.
AU  - Whitman, W.B.
TI  - Draft Genome Sequence of Geobacillus thermopakistaniensis Strain MAS1.
JO  - Genome Announcements
PY  - 2014
SP  - e00559
EP  - e00514
VL  - 2
AB  - Geobacillus thermopakistaniensis strain MAS1 was isolated from a hot spring located in the
AB  - Northern Areas of Pakistan. The draft genome sequence was 3.5 Mb
AB  - and identified a number of genes of potential industrial importance, including
AB  - genes encoding glycoside hydrolases, pullulanase, amylopullulanase, glycosidase,
AB  - and alcohol dehydrogenases.
ER  -

TY  - JOUR
AU  - Sidjabat, H.E.
AU  - Cottrell, K.
AU  - Cervin, A.
TI  - Draft Genome Sequences of Burkholderia pseudomallei and Staphylococcus aureus, Isolated from a Patient with Chronic Rhinosinusitis.
JO  - Genome Announcements
PY  - 2015
SP  - e01075
EP  - e01015
VL  - 3
AB  - Here, we report the draft genome sequences of Burkholderia pseudomallei and Staphylococcus
AB  - aureus causing chronic rhinosinusitis. Whole-genome sequencing determined the B. pseudomallei
AB  - as sequence type (ST) 1381 and the S. aureus as ST8. B. pseudomallei possessed the blaOXA-59
AB  - gene. This study illustrates the potential emergence of B. pseudomallei in cases of chronic
AB  - rhinosinusitis.
ER  -

TY  - JOUR
AU  - Sidjabat, H.E.
AU  - Grahn, H.E.
AU  - Cervin, A.
TI  - Draft Genome Sequence of the Oral Commensal Streptococcus oralis 89a with Interference Activity against Respiratory Pathogens.
JO  - Genome Announcements
PY  - 2016
SP  - e01546
EP  - e01515
VL  - 4
AB  - We report the draft genome sequence of the oral commensal Streptococcus oralis 89a isolated
AB  - from the throat of a healthy child during a streptococcal
AB  - tonsillitis outbreak in Umea, Sweden. S. oralis 89a was known to have
AB  - interference activity against respiratory pathogens in which the colicin V was
AB  - the potential bacteriocin-encoding gene.
ER  -

TY  - JOUR
AU  - Sidjabat, H.E.
AU  - Robson, J.
AU  - Paterson, D.L.
TI  - Draft Genome Sequences of Two IMP-4-Producing Escherichia coli Sequence Type 131  Isolates in Australia.
JO  - Genome Announcements
PY  - 2015
SP  - e00983
EP  - e00915
VL  - 3
AB  - We report the draft genome sequences of two unrelated cases of Escherichia coli sequence type
AB  - 131 (ST131) possessing the carbapenemase gene blaIMP-4. The E. coli ST131 SN5 isolate also
AB  - possessed blaSHV-12 and plasmid-mediated quinolone-resistance genes. Wider dissemination of
AB  - blaIMP-4 may occur due to the  blaIMP-4-carrying L/M or HI2 plasmids among E. coli ST131
AB  - isolates.
ER  -

TY  - JOUR
AU  - Sidorova, N.
AU  - Muradymov, S.
AU  - Rau, D.C.
TI  - Specific versus Nonspecific DNA Binding of the Restriction Endonuclease EcoRV Measured by Self-Cleavage Assay.
JO  - J. Biomol. Struct. Dyn.
PY  - 2009
SP  - 896
EP  - 897
VL  - 26
ER  -

TY  - JOUR
AU  - Sidorova, N.
AU  - Rau, D.C.
TI  - The role of water in the EcoRI-DNA binding.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 319
EP  - 337
VL  - 14
AB  - In many respects, Type II restriction endonucleases are prototypical DNA-binding proteins.  In
AB  - order to avoid catastrophic consequences for the cell, however, these enzymes must be far more
AB  - stringent in recognition of their target sequences and subsequent DNA cleavage than other
AB  - specific sequence recognition proteins that regulate gene activity.  In contrast to E. coli
AB  - Lac and lambda Cro repressors, for example, that show gradually decreasing binding energies as
AB  - the recognition sequence is changed, many restriction nucleases are exquisitely specific.
AB  - EcoRI will bind to its recognition sequence, GAATTC, with an association equilibrium constant
AB  - Ka,sp ~10^11 M-1 and to a completely nonspecific sequence with Ka,nonsp ~10^7 M-1.  A change
AB  - of even a single base pair is sufficient to decrease the binding constant at least by 10^3,
AB  - bringing it within a factor ~10 or less of nonspecific binding.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Muradymov, S.
AU  - Rau, D.C.
TI  - Differences in hydration coupled to specific and nonspecific competitive binding and to specific DNA binding of the restriction endonuclease BamHI.
JO  - J. Biol. Chem.
PY  - 2006
SP  - 35656
EP  - 35666
VL  - 281
AB  - Using the osmotic stress technique together with a self-cleavage assay we measure directly
AB  - differences in sequestered water between specific
AB  - and nonspecific DNA-BamHI complexes as well as the numbers of water
AB  - molecules released coupled to specific complex formation. The
AB  - difference between specific and nonspecific binding free energy of the
AB  - BamHI scales linearly with solute osmolal concentration for seven
AB  - neutral solutes used to set water activity. The observed osmotic
AB  - dependence indicates that the nonspecific DNA-BamHI complex sequesters
AB  - some 120-150 more water molecules than the specific complex. The weak
AB  - sensitivity of the difference in number of waters to the solute
AB  - identity suggests that these waters are sterically inaccessible to
AB  - solutes. This result is in close agreement with differences in the
AB  - structures determined by x-ray crystallography. We demonstrate
AB  - additionally that when the same solutes that were used in competition
AB  - experiments are used to probe changes accompanying the binding of free
AB  - BamHI to its specific DNA sequence, the measured number of water
AB  - molecules released in the binding process is strikingly
AB  - solute-dependent ( with up to 10-fold difference between solutes). This
AB  - result is expected for reactions resulting in a large change in a
AB  - surface exposed.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Muradymov, S.
AU  - Rau, D.C.
TI  - A novel self-cleavage assay for measuring DNA binding of restriction endonucleases.
JO  - FEBS J.
PY  - 2005
SP  - 565
EP  - 565
VL  - 272
AB  - DNA-protein interactions can be analyzed by methods based on physical separation of complexes
AB  - from free DNA fragments (gel mobility shift and filter binding assays) or by techniques
AB  - probing DNA-protein equilibrium directly in a solution (e.g. fluorescence and calorimetry).
AB  - These later techniques require larger amounts of materials and do not provide enough
AB  - sensitivity for measuring equilibrium association constants in the range 10^9-10^12 M-1. Both
AB  - gel mobility shift and filter binding assays that can measure these large binding constants,
AB  - however, have been criticized for the danger of disrupting equilibrium by physically
AB  - separating DNA-protein complexes from free species. We have developed a novel self-cleavage or
AB  - self-footprinting assay that uses the nuclease activity of restriction endonucleases to
AB  - measure sensitively their specific binding to DNA. At sufficiently high concentrations of
AB  - neutral osmolytes cleavage reaction can be triggered at only those DNA fragments with bound
AB  - enzyme. Under these conditions the fraction of specific DNA fragment cleaved reliably reflects
AB  - the fraction of DNA initially bound to the enzyme. The self-cleavage assay allows measurement
AB  - of binding equilibrium and kinetics directly in solution avoiding the intrinsic problems of
AB  - gel mobility shift and filter binding assays while providing the same sensitivity level. We
AB  - compare here the self-cleavage and gel mobility shift assays applied to the dissociation
AB  - kinetics and binding equilibrium of two restriction endonucleases, EcoRI and BamHI. The
AB  - technique can be used, in principle, for any protein possessing DNA cleavage activity if its
AB  - interactions with DNA are sensitive to osmotic stress.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Muradymov, S.
AU  - Rau, D.C.
TI  - Solution parameters modulating DNA binding specificity of the restriction endonuclease EcoRV.
JO  - FEBS J.
PY  - 2011
SP  - 2713
EP  - 2727
VL  - 278
AB  - The DNA binding stringency of restriction endonucleases is crucial for their proper function.
AB  - The X-ray structures of the specific and
AB  - non-cognate complexes of the restriction nuclease EcoRV are
AB  - considerably different suggesting significant differences in the
AB  - hydration and binding free energies. Nonetheless, the majority of
AB  - studies performed at pH 7.5, optimal for enzymatic activity, have found
AB  - a < 10-fold difference between EcoRV binding constants to the specific
AB  - and nonspecific sequences in the absence of divalent ions. We used a
AB  - recently developed self-cleavage assay to measure EcoRV-DNA competitive
AB  - binding and to evaluate the influence of water activity, pH and salt
AB  - concentration on the binding stringency of the enzyme in the absence of
AB  - divalent ions. We find the enzyme can readily distinguish specific and
AB  - nonspecific sequences. The relative specific-nonspecific binding
AB  - constant increases strongly with increasing neutral solute
AB  - concentration and with decreasing pH. The difference in number of
AB  - associated waters between specific and nonspecific DNA-EcoRV complexes
AB  - is consistent with the differences in the crystal structures. Despite
AB  - the large pH dependence of the sequence specificity, the osmotic
AB  - pressure dependence indicates little change in structure with pH. The
AB  - large osmotic pressure dependence means that measurement of protein-DNA
AB  - specificity in dilute solution cannot be directly applied to binding in
AB  - the crowded environment of the cell. In addition to divalent ions,
AB  - water activity and pH are key parameters that strongly modulate binding
AB  - specificity of EcoRV.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Muradymov, S.R.
AU  - Royal, R.M.
AU  - Rau, D.C.
TI  - Unusual DNA-Binding Kinetics of the Restriction Endonuclease EcoRV.
JO  - Biophys. J.
PY  - 2011
SP  - 72
EP  - 72
VL  - 100
AB  - We have applied a self-cleavage assay, developed previously by us, to measure
AB  - EcoRV-DNA binding in solution. Self-cleavage assay monitors only enzymatically
AB  - competent complexes of the endonuclease. This technique does not have
AB  - the limitations of more commonly used gel mobility shift assay while providing
AB  - the same level of sensitivity.Wefound that the EcoRV has quite unusual kinetics
AB  - of specific complex formation in the absence of divalent ions that was not reported
AB  - previously. A significant fraction of the total enzyme, ~ 45%, forms enzymatically
AB  - competent complexes unusually slowly, especially at pH 7.6. This
AB  - novel result can be explained by a very slow transition between two conformations
AB  - of the free enzyme in solution. The equilibrium distribution of the slowly
AB  - and quickly associating protein structures and their exchange kinetics may depend
AB  - on many parameters including pH, salt, osmolytes, and divalent cations.
AB  - The observation of at least two kinetics components in association indicates
AB  - that EcoRV is an allosteric protein with at least two conformations. Allosterism
AB  - is now recognized as important concept for DNA-protein complexes, offering an
AB  - additional level of control over binding and activity. We are continuing our investigation
AB  - into the EcoRV structures responsible for the different kinetic classes
AB  - of association.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Rau, D.C.
TI  - Self-footprint of the restriction endonuclease EcoRI.
JO  - Biophys. J.
PY  - 2000
SP  - 299A
EP  - 299A
VL  - 78
AB  - The dissociation rate of the EcoRI-DNA specific complex is strongly linked to water activity.
AB  - In the presence of osmolytes (betaine, sucrose, methyl glucoside, t-butanol, etc.) stability
AB  - of the specific EcoRI-DNA complex increases dramatically.  Osmotic stress technique offers a
AB  - practical way of manipulating dissociation rates controllably and to measure complex
AB  - properties on an experimentally convenient time scale.  It has been shown recently that
AB  - osmotic stress also slows down cleavage reaction of the EcoRI at its specific sequence.  We
AB  - believe this effect is at least partly due to the slowing of the EcoRI dissociation from the
AB  - product of the cleavage reaction.  Using osmotic stress technique we have developed a method
AB  - for using the nuclease activity of EcoRI to measure sensitively its specific binding.  We show
AB  - using gel shift assay that only those sites on DNA initially occupied by protein immediately
AB  - prior to adding Mg2+ are apparently cleaved.  The level of specific DNA fragment cleavage
AB  - remains constant for as long as 40 min.  This self-footprint assay allows measurement of EcoRI
AB  - binding equilibrium and kinetics avoiding intrinsic gel-shift and filter-binding assay
AB  - problems.  There is the possibility of using such a technique for any protein possessing DNA
AB  - cleavage activity given that its interactions with DNA are sensitive to osmotic stress.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Rau, D.C.
TI  - Linkage of EcoRI dissociation from its specific DNA recognition site to water activity, salt concentration, and pH: separating their roles in specific and non-specific binding.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 801
EP  - 816
VL  - 310
AB  - We have measured the dependencies of both the dissociation rate of specifically bound EcoRI
AB  - endonuclease and the ratio of non-specific and specific association constants on water
AB  - activity, salt concentration, and pH in order to distinguish the contributions of these
AB  - solution components to specific and non-specific binding. For proteins such as EcoRI that
AB  - locate their specific recognition site efficiently by diffusing along non-specific DNA, the
AB  - specific site dissociation rate can be separated into two steps: an equilibrium between
AB  - non-specific and specific binding of the enzyme to DNA, and the dissociation of
AB  - non-specifically bound protein. We demonstrated previously that the osmotic dependence of the
AB  - dissociation rate is dominated by the equilibrium between specific and non-specific binding
AB  - that is independent of the osmolyte nature. The remaining osmotic sensitivity linked to the
AB  - dissociation of non-specifically bound protein depends significantly on the particular
AB  - osmolyte used, indicating a change in solute-accessible surface area. In contrast, the
AB  - dissociation of non-specifically bound enzyme accounts for almost all the pH and
AB  - salt-dependencies. We observed virtually no pH-dependence of the equilibrium between specific
AB  - and non-specific binding measured by the competition assay. The observed weak salt-sensitivity
AB  - of the ratio of specific and non-specific association constants is consistent with an osmotic,
AB  - rather than electrostatic, action. The seeming lack of a dependence on viscosity suggests the
AB  - rate-limiting step in dissociation of non-specifically bound protein is a discrete
AB  - conformational change rather than a general diffusion of the protein away from the DNA.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Rau, D.C.
TI  - Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 12272
EP  - 12277
VL  - 93
AB  - The free energy difference between complexes of the restriction nuclease EcoRI with
AB  - nonspecific DNA and with the enzyme's recognition sequence is linearly dependent on the water
AB  - chemical potential of the solution, set using several very different solutes, ranging from
AB  - glycine and glycerol to triethylene glycol and sucrose.  This osmotic dependence indicates
AB  - that the nonspecific complex sequesters some 110 waters more than the specific complex with
AB  - the recognition sequence.  The insensitivity of the difference in number of waters released to
AB  - the solute identity further indicates that this water is sequestered in a space that is
AB  - sterically inaccessible to solutes, most likely at the protein-DNA interface of the
AB  - nonspecific complex.  Calculations based on the structure of the specific complex suggest that
AB  - the apposing DNA and protein surfaces in the nonspecific complex retain approximately a full
AB  - hydration layer of water.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Rau, D.C.
TI  - Removing water from an EcoRI-noncognate DNA complex with osmotic stress.
JO  - J. Biomol. Struct. Dyn.
PY  - 1999
SP  - 19
EP  - 31
VL  - 17
AB  - We recently showed that a nonspecific complex of the restriction nuclease EcoRI with poly
AB  - (dI-dC) sequesters significantly more water at the protein-DNA interface than the complex with
AB  - the specific recognition sequence. The nonspecific complex seems to retain almost a full
AB  - hydration layer at the interface. We now find that at low osmotic pressures a complex of the
AB  - restriction nuclease EcoRI with a DNA sequence that differs by only one base pair from the
AB  - recognition site (a 'star' sequence) sequesters about 70 waters more than the specific one,
AB  - a value virtually indistinguishable from nonspecific DNA. Unlike complexes with oligo (dI-dC)
AB  - or with a sequence that differs by two base pairs from the recognition sequence, however, much
AB  - of the water in the 'star' sequence complex is removed at high osmotic pressures. The energy
AB  - of removing this water can be calculated simply from the osmotic pressure work done on the
AB  - complex. The ability to measure not only the changes in water sequestered by DNA-protein
AB  - complexes for different sequences, but also the work necessary to remove this water is a
AB  - potentially powerful new tool for coupling inferred structural changes and thermodynamics.
ER  -

TY  - JOUR
AU  - Sidorova, N.Y.
AU  - Rau, D.C.
TI  - The dissociation rate of the EcoRI-DNA-specific complex is linked to water activity.
JO  - Biopolymers
PY  - 2000
SP  - 363
EP  - 368
VL  - 53
AB  - In many respects, the dissociation rate constant of a DNA-protein or protein-protein complex
AB  - is as important a physical parameter as the equilibrium constant.  The regulation of most
AB  - cellular activities and developmental control are dynamic rather than static processes.  With
AB  - many techniques, the successful physiochemical characterization of a complex depends
AB  - ciritically on the lifetime of the complex during isolation or measurement.  With present
AB  - technologies, the very powerful, single molecule methods used for mapping the kinetic barriers
AB  - of complex dissociation reactions require lifetimes on the order of minutes.  We report here
AB  - that the dissociation rate of the specific complex between the restriction nuclease EcoRI and
AB  - its recognition DNA sequence is strongly dependent on water activity (in addition to its known
AB  - dependence on salt activity).  This observation means that the dissociation rate of complexes
AB  - in the crowded conditions found within cells cannot be straightforwardly predicted from dilute
AB  - solution measurements, even though salt, temperature, and pH conditions are fixed to those
AB  - found in vivo.  In addition, these results suggest a practical method to extend the lifetime
AB  - of "weak" complexes sufficiently to perform biophysical and biochemical characterizations.
ER  -

TY  - JOUR
AU  - Siebers, B.
AU  - Zaparty, M.
AU  - Raddatz, G.
AU  - Tjaden, B.
AU  - Albers, S.V.
AU  - Bell, S.D.
AU  - Blombach, F.
AU  - Kletzin, A.
AU  - Kyrpides, N.
AU  - Lanz, C.
AU  - Plagens, A.
AU  - Rampp, M.
AU  - Rosinus, A.
AU  - von Jan, M.
AU  - Makarova, K.S.
AU  - Klenk, H.P.
AU  - Schuster, S.C.
AU  - Hensel, R.
TI  - The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota.
JO  - PLoS ONE
PY  - 2011
SP  - E24222
EP  - E24222
VL  - 6
AB  - Here, we report on the complete genome sequence of the hyperthermophilic
AB  - Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078(T)) a type strain
AB  - of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase
AB  - genome harbors no extrachromosomal elements and 2,051 open reading frames
AB  - are identified, covering 90.6% of the complete sequence, which represents
AB  - a high coding density. Derived from the gene content, T. tenax is a
AB  - representative member of the Crenarchaeota. The organism is strictly
AB  - anaerobic and sulfur-dependent with optimal growth at 86 degrees C and pH
AB  - 5.6. One particular feature is the great metabolic versatility, which is
AB  - not accompanied by a distinct increase of genome size or information
AB  - density as compared to other Crenarchaeota. T. tenax is able to grow
AB  - chemolithoautotrophically (CO/H) as well as chemoorganoheterotrophically
AB  - in presence of various organic substrates. All pathways for synthesizing
AB  - the 20 proteinogenic amino acids are present. In addition, two presumably
AB  - complete gene sets for NADH:quinone oxidoreductase (complex I) were
AB  - identified in the genome and there is evidence that either NADH or reduced
AB  - ferredoxin might serve as electron donor. Beside the typical archaeal
AB  - AA-ATP synthase, a membrane-bound pyrophosphatase is found, which might
AB  - contribute to energy conservation. Surprisingly, all genes required for
AB  - dissimilatory sulfate reduction are present, which is confirmed by growth
AB  - experiments. Mentionable is furthermore, the presence of two proteins
AB  - (ParA family ATPase, actin-like protein) that might be involved in cell
AB  - division in Thermoproteales, where the ESCRT system is absent, and of
AB  - genes involved in genetic competence (DprA, ComF) that is so far unique
AB  - within Archaea.
ER  -

TY  - JOUR
AU  - Siedlecki, P.
AU  - Boy, R.G.
AU  - Comagic, S.
AU  - Schirrmacher, R.
AU  - Wiessler, M.
AU  - Zielenkiewicz, P.
AU  - Suhai, S.
AU  - Lyko, F.
TI  - Establishment and functional validation of a structural homology model for human DNA methyltransferase 1.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2003
SP  - 558
EP  - 563
VL  - 306
AB  - Changes in DNA methylation patterns play an important role in tumorigenesis. The DNA
AB  - methyltransferase 1 (DNMT1) protein represents a
AB  - major DNA methyltransferase activity in human cells and is therefore a
AB  - prominent target for experimental cancer therapies. However, there are
AB  - only few available inhibitors and their high toxicity and low specificity
AB  - have so far precluded their broad use in chemotherapy. Based on the strong
AB  - conservation of catalytic DNA methyltransferase domains we have used a
AB  - homology modeling approach to determine the three-dimensional structure of
AB  - the DNMT1 catalytic domain. Our results suggest an overall structural
AB  - conservation with other DNA methyltransferases but also indicate local
AB  - conformational differences. To prove the validity of our model we used it
AB  - as a template to design a novel derivative of the known DNA
AB  - methyltransferase inhibitor 5-azacytidine. The resulting compound
AB  - (N4-fluoroacetyl-5-azacytidine) functioned as an efficient inhibitor of
AB  - DNA methylation in human tumor cell lines and also provides novel
AB  - opportunities for pharmacological applications.
ER  -

TY  - JOUR
AU  - Siedlecki, P.
AU  - Boy, R.G.
AU  - Musch, T.
AU  - Brueckner, B.
AU  - Suhai, S.
AU  - Lyko, F.
AU  - Zielenkiewicz, P.
TI  - Discovery of two novel, small-molecule inhibitors of DNA methylation.
JO  - J. Med. Chem.
PY  - 2006
SP  - 678
EP  - 683
VL  - 49
AB  - DNA methyltransferases are promising targets for cancer therapy. In many cancer cells
AB  - promoters of tumor suppressor genes are hypermethylated,
AB  - which results in gene inactivation. It has been shown that DNA
AB  - methyltransferase inhibitors can suppress tumor growth and have
AB  - significant therapeutic value. However, the established inhibitors are
AB  - limited in their application due to their substantial cytotoxicity. To
AB  - discover novel compounds for the inhibition of human DNA
AB  - methyltransferases, we have screened a set of small molecules available
AB  - from the NCI database. Using a 3-dimensional model of the human DNA
AB  - methyltransferase 1 and a modified docking and scoring procedure, we have
AB  - identified a small list of molecules with high affinities for the active
AB  - site of the enzyme. The two highest scoring structures were found to
AB  - inhibit DNA methyltransferase activity in vitro and in vivo. The newly
AB  - discovered inhibitors validate our screening procedure and also provide a
AB  - useful basis for further rational drug development.
ER  -

TY  - JOUR
AU  - Siegl, T.
AU  - Petzke, L.
AU  - Welle, E.
AU  - Luzhetskyy, A.
TI  - I-SceI endonuclease: a new tool for DNA repair studies and genetic manipulations in streptomycetes.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2010
SP  - 1525
EP  - 1532
VL  - 87
AB  - Actinomycetes are Gram-positive bacteria with a complex life cycle. They
AB  - produce many pharmaceutically relevant secondary metabolites, including
AB  - antibiotics and anticancer drugs. However, there is a limited number of
AB  - biotechnological applications available as opposed to genetic model
AB  - organisms like Bacillus subtilis or Escherichia coli. We report here a
AB  - system for the functional expression of a synthetic gene encoding the
AB  - I-SceI homing endonuclease in several streptomycetes. Using the synthetic
AB  - sce(a) gene, we were able to create controlled genomic DNA double-strand
AB  - breaks. A mutagenesis system, based on the homing endonuclease I-SceI, has
AB  - been developed to construct targeted, non-polar, unmarked gene mutations
AB  - in Streptomyces sp. Tu6071. In addition, we have shown that homologous
AB  - recombination is a major pathway in streptomycetes to repair an
AB  - I-SceI-generated DNA double-strand break. This novel I-SceI-based tool
AB  - will be useful in fundamental studies on the repair mechanism of DNA
AB  - double-strand breaks and for a variety of biotechnological applications.
ER  -

TY  - JOUR
AU  - Sievert, S.M.
AU  - Scott, K.M.
AU  - Klotz, M.G.
AU  - Chain, P.S.
AU  - Hauser, L.J.
AU  - Hemp, J.
AU  - Hugler, M.
AU  - Land, M.
AU  - Lapidus, A.
AU  - Larimer, F.W.
AU  - Lucas, S.
AU  - Malfatti, S.A.
AU  - Meyer, F.
AU  - Paulsen, I.T.
AU  - Ren, Q.
AU  - Simon, J.
AU  - USF, G.C.
TI  - Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 1145
EP  - 1156
VL  - 74
AB  - Sulfur-oxidizing epsilonproteobacteria are common in a variety of
AB  - sulfidogenic environments. These autotrophic and mixotrophic
AB  - sulfur-oxidizing bacteria are believed to contribute substantially to the
AB  - oxidative portion of the global sulfur cycle. In order to better
AB  - understand the ecology and roles of sulfur-oxidizing
AB  - epsilonproteobacteria, in particular those of the widespread genus
AB  - Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas
AB  - denitrificans DSM1251 was sequenced. This genome has many features,
AB  - including a larger size (2.2 Mbp), that suggest a greater degree of
AB  - metabolic versatility or responsiveness to the environment than seen for
AB  - most of the other sequenced epsilonproteobacteria. A branched electron
AB  - transport chain is apparent, with genes encoding complexes for the
AB  - oxidation of hydrogen, reduced sulfur compounds, and formate and the
AB  - reduction of nitrate and oxygen. Genes are present for a complete,
AB  - autotrophic reductive citric acid cycle. Many genes are present that could
AB  - facilitate growth in the spatially and temporally heterogeneous sediment
AB  - habitat from where Sulfurimonas denitrificans was originally isolated.
AB  - Many resistance-nodulation-development family transporter genes (10 total)
AB  - are present; of these, several are predicted to encode heavy metal efflux
AB  - transporters. An elaborate arsenal of sensory and regulatory
AB  - protein-encoding genes is in place, as are genes necessary to prevent and
AB  - respond to oxidative stress.
ER  -

TY  - JOUR
AU  - Sievert, U.
TI  - Determination of the specific recognition sequence of the restriction enzyme Rlu-1I from Rhizobium lupini.
JO  - Ph.D. Thesis, Erlangen University, W. Germany
PY  - 1982
SP  - 1
EP  - 109
AB  - This is the enzyme RluI.
ER  -

TY  - JOUR
AU  - Siezen, R.J.
AU  - Bayjanov, J.
AU  - Renckens, B.
AU  - Wels, M.
AU  - van Hijum, S.A.
AU  - Molenaar, D.
AU  - van Hylckama, V.J.E.
TI  - Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2649
EP  - 2650
VL  - 192
AB  - Lactococcus lactis is a lactic acid bacterium used in the production of many fermented dairy
AB  - products. We report the complete genome sequence of
AB  - L. lactis subsp. lactis KF147, a nondairy strain isolated from mung bean
AB  - sprouts. The circular chromosome of 2,598,144 bp, the largest among the
AB  - sequenced lactococcal strains, encodes many properties related to
AB  - adaptation to the plant environment.
ER  -

TY  - JOUR
AU  - Siezen, R.J.
AU  - Francke, C.
AU  - Renckens, B.
AU  - Boekhorst, J.
AU  - Wels, M.
AU  - Kleerebezem, M.
AU  - van Hijum, S.A.F.T.
TI  - Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.
JO  - J. Bacteriol.
PY  - 2011
SP  - 195
EP  - 196
VL  - 194
AB  - There is growing interest in the beneficial effects of Lactobacillus plantarum on human
AB  - health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using
AB  - Solexa technology. We identified 116 nucleotide corrections and improved function prediction
AB  - for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated
AB  - proteins.
ER  -

TY  - JOUR
AU  - Siezen, R.J.
AU  - Renckens, B.
AU  - van Swam, I.
AU  - Peters, S.
AU  - van Kranenburg, R.
AU  - Kleerebezem, M.
AU  - de Vos, W.M.
TI  - Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment.
JO  - Appl. Environ. Microbiol.
PY  - 2005
SP  - 8371
EP  - 8382
VL  - 71
AB  - Lactococcus lactis strains are known to carry plasmids encoding industrially important traits.
AB  - L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its
AB  - complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372
AB  - bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous
AB  - repB-containing replicons were found, all belonging to the family of lactococcal theta-type
AB  - replicons. Twenty-three complete insertion sequence elements segment the plasmids into
AB  - numerous modules, many of which can be identified as functional units or containing
AB  - functionally related genes. Plasmid-encoded functions previously known to reside on L. lactis
AB  - SK11 plasmids were now mapped in detail, e.g., lactose utilization (lacR-lacABCDFEGX), the
AB  - proteolytic system (prtM-prtP, pepO, pepF), and the oligopeptide permease system (oppDFBCA).
AB  - Newly identified plasmid-encoded functions could facilitate the uptake of various cations,
AB  - while the pabA and pabB genes could be essential for folate biosynthesis. A competitive
AB  - advantage could be obtained by using the putative flavin adenine dinucleotide-dependent
AB  - d-lactate dehydrogenase and oxalate:formate antiporter for enhanced ATP synthesis, while the
AB  - activity of the predicted alpha-acetolactate decarboxylase may contribute to the formation of
AB  - an additional electron sink. Various stress response proteins are plasmid encoded, which could
AB  - enhance strain robustness. A substantial number of these "adaptation" genes have not been
AB  - described before on L. lactis plasmids. Moreover, several genes were identified for the first
AB  - time in L. lactis, possibly reflecting horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Siezen, R.J.
AU  - Starrenburg, M.J.C.
AU  - Boekhorst, J.
AU  - Renckens, B.
AU  - Molenaar, D.
AU  - van Hylckama-Vlieg, J.E.T.
TI  - Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 424
EP  - 436
VL  - 74
AB  - Lactococcus lactis is a primary constituent of many starter cultures used for the
AB  - manufacturing of fermented dairy products, but the species
AB  - also occurs in various nondairy niches such as (fermented) plant
AB  - material. Three genome sequences of L. lactis dairy strains (IL-1403,
AB  - SK11, and MG1363) are publicly available. An extensive molecular and
AB  - phenotypic diversity analysis was now performed on two L. lactis plant
AB  - isolates. Diagnostic sequencing of their genomes resulted in over 2.5
AB  - Mb of sequence for each strain. A high synteny was found with the
AB  - genome of L. lactis IL-1403, which was used as a template for contig
AB  - mapping and locating deletions and insertions in the plant L. lactis
AB  - genomes. Numerous genes were identified that do not have homologs in
AB  - the published genome sequences of dairy L. lactis strains. Adaptation
AB  - to growth on substrates derived from plant cell walls is evident from
AB  - the presence of gene sets for the degradation of complex plant polymers
AB  - such as xylan, arabinan, glucans, and fructans but also for the uptake
AB  - and conversion of typical plant cell wall degradation products such as
AB  - alpha-galactosides, P-glucosides, arabinose, xylose, galacturonate,
AB  - glucuronate, and gluconate. Further niche-specific differences are
AB  - found in genes for defense (nisin biosynthesis), stress response
AB  - (nonribosomal peptide synthesis and various transporters), and
AB  - exopolysaccharide biosynthesis, as well as the expected differences in
AB  - various mobile elements such as prophages, plasmids,
AB  - restrictionmodification systems, and insertion sequence elements. Many
AB  - of these genes were identified for the first time in Lactococcus
AB  - lactis. In most cases good correspondence was found with the phenotypic
AB  - characteristics of these two strains.
ER  -

TY  - JOUR
AU  - Sikora, A.E.
AU  - Smith, J.R.
AU  - Campbell, S.A.
AU  - Firman, K.
TI  - AFM protein-protein interactions within the EcoR124I molecular motor.
JO  - Soft Matter
PY  - 2012
SP  - 6358
EP  - 6363
VL  - 8
AB  - Dynamic Force Spectroscopy (DFS), an Atomic Force Microscopy (AFM) technique, has been used to
AB  - investigate the interaction between the
AB  - HsdR subunit and the core methylase (MTase) of the Type I
AB  - Restriction-Modification (R-M) enzyme EcoR124I. Such systems are of
AB  - interest in bionanotechnology owing to their ability to translocate
AB  - DNA, thus acting as molecular motors. Forces between a glutathione
AB  - S-transferase (GST)-HsdR(PrrI) motor subunit attached to an AFM tip
AB  - using a polyethylene gycol linker and the core MTase on poly-L-lysine
AB  - pre-treated mica were measured at different loading rates. In the
AB  - absence of an applied force, the position of energy barrier x(diss),
AB  - bond dissociation rate k(diss)(0) and lifetime of the bond tau(0) were
AB  - calculated to be 1.35 +/- 0.17 nm, 0.16 s(-1) and 6.3 s, respectively.
AB  - The k(diss)(0) value was a little lower than that obtained from
AB  - magnetic tweezers (0.4 s(-1)), suggesting that the thermodynamic
AB  - equilibrium may be affected by the presence of DNA. This work
AB  - demonstrates that kinetic data concerning protein-protein interactions
AB  - between subunits within Type I R-M enzymes are accessible via AFM. Such
AB  - information is important for structure elucidation and the development
AB  - of nanodevices.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 149
EP  - 157
VL  - 2
AB  - Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus
AB  - Sulfurospirillum. S. deleyianum is a model organism for studying sulfur
AB  - reduction and dissimilatory nitrate reduction as an energy source for growth.
AB  - Also, it is a prominent model organism for studying the structural and functional
AB  - characteristics of cytochrome c nitrite reductase. Here, we describe the features
AB  - of this organism, together with the complete genome sequence and annotation. This
AB  - is the first completed genome sequence of the genus Sulfurospirillum. The
AB  - 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Segniliparus rotundus type strain (CDC 1076).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 203
EP  - 211
VL  - 2
AB  - Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus,  which is
AB  - currently the only genus in the corynebacterial family Segniliparaceae.
AB  - This family is of large interest because of a novel late-emerging genus-specific
AB  - mycolate pattern. The type strain has been isolated from human sputum and is
AB  - probably an opportunistic pathogen. Here we describe the features of this
AB  - organism, together with the complete genome sequence and annotation. This is the
AB  - first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp
AB  - long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Meiothermus silvanus type strain (VI-R2).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 37
EP  - 46
VL  - 3
AB  - Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus
AB  - whose members share relatively low degrees of 16S rRNA gene
AB  - sequence similarity. Meiothermus constitutes an evolutionary lineage separate
AB  - from members of the genus Thermus, from which they can generally be distinguished
AB  - by their slightly lower temperature optima. M. silvanus is of special interest as
AB  - it causes colored biofilms in the paper making industry and may thus be of
AB  - economic importance as a biofouler. This is the second completed genome sequence
AB  - of a member of the genus Meiothermus and only the third genome sequence to be
AB  - published from a member of the family Thermaceae. The 3,721,669 bp long genome
AB  - with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 57
EP  - 65
VL  - 3
AB  - Acetohalobium arabaticum Zhilina and Zavarzin 1990 is of special interest because of its
AB  - physiology and its participation in the anaerobic C(1)-trophic chain in
AB  - hypersaline environments. This is the first completed genome sequence of the
AB  - family Halobacteroidaceae and only the second genome sequence in the order
AB  - Halanaerobiales. The 2,469,596 bp long genome with its 2,353 protein-coding and
AB  - 90 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Sulfurimonas autotrophica type strain (OK10).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 194
EP  - 202
VL  - 3
AB  - Sulfurimonas autotrophica Inagaki et al. 2003 is the type species of the genus Sulfurimonas.
AB  - This genus is of interest because of its significant contribution
AB  - to the global sulfur cycle as it oxidizes sulfur compounds to sulfate and by its
AB  - apparent habitation of deep-sea hydrothermal and marine sulfidic environments as
AB  - potential ecological niche. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is the second
AB  - complete genome sequence of the genus Sulfurimonas and the 15(th) genome in the
AB  - family Helicobacteraceae. The 2,153,198 bp long genome with its 2,165
AB  - protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 304
EP  - 314
VL  - 3
AB  - Ilyobacter polytropus Stieb and Schink 1984 is the type species of the genus Ilyobacter, which
AB  - belongs to the fusobacterial family Fusobacteriaceae. The
AB  - species is of interest because its members are able to ferment quite a number of
AB  - sugars and organic acids. I. polytropus has a broad versatility in using various
AB  - fermentation pathways. Also, its members do not degrade poly-beta-hydroxybutyrate
AB  - but only the monomeric 3-hydroxybutyrate. This is the first completed genome
AB  - sequence of a member of the genus Ilyobacter and the second sequence from the
AB  - family Fusobacteriaceae. The 3,132,314 bp long genome with its 2,934
AB  - protein-coding and 108 RNA genes consists of two chromosomes (2 and 1 Mbp long)
AB  - and one plasmid, and is a part of the Genomic Encyclopedia of Bacteria and
AB  - Archaea project.
ER  -

TY  - JOUR
AU  - Sikorski, J. et al.
TI  - Complete genome sequence of Mahella australiensis type strain (50-1 BON).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 331
EP  - 341
VL  - 4
AB  - Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella,
AB  - which belongs to the family Thermoanaerobacteraceae. The species
AB  - is of interest because it differs from other known anaerobic spore-forming
AB  - bacteria in its G+C content, and in certain phenotypic traits, such as carbon
AB  - source utilization and relationship to temperature. Moreover, it has been
AB  - discussed that this species might be an indigenous member of petroleum and oil
AB  - reservoirs. This is the first completed genome sequence of a member of the genus
AB  - Mahella and the ninth completed type strain genome sequence from the family
AB  - Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974
AB  - protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Grazulis, S.
AU  - Huber, R.
TI  - Structure and function of the tetrameric restriction enzymes.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 237
EP  - 259
VL  - 14
AB  - Type II restriction endonucleases recognize specific DNA sequences, typically 4-8 bp in
AB  - length, and cleave phosphodiester bonds in the presence of Mg2+, within or close to their
AB  - recognition sites.  Around 3500 species, from variety of bacteria with nearly 240 differing
AB  - specificities, have now been characterized.  Most of the sequences recognized by Type II
AB  - restriction endonucleases are palindromic, i.e. possess a twofold rotational axis of symmetry.
AB  - On the basis of this observation, Kelly and Smith proposed the first model for the interaction
AB  - of these restriction enzymes with DNA.  According to their model, recognition of the
AB  - palindromic DNA sequence is achieved by two identical protein subunits related by a twofold
AB  - axis of symmetry.  Each subunit faces the same nucleotide sequence on the opposite DNA strand
AB  - and contains one active site.  Symmetrical nicking of opposite DNA strands by both monomers
AB  - within a homodimer generates the double-strand break.  Hence, the symmetry of the recognition
AB  - sequence implies the oligomeric state of the restriction enzyme.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Pleckaityte, M.
TI  - Catalytic and binding properties of restriction endonuclease Cfr9I.
JO  - Eur. J. Biochem.
PY  - 1993
SP  - 411
EP  - 419
VL  - 217
AB  - The Cfr9I restriction endonuclease recognizes and cleaves the duplex DNA sequence C^CCGG. The
AB  - binding of restriction endonuclease Cfr9I to DNA was examined in the absence of Mg2+ using
AB  - gel-mobility-shift and nitrocellulose-filter-binding assays. It was shown that restriction
AB  - endonuclease Cfr9I bound DNA fragments either containing or lacking the canonical recognition
AB  - sequence with equal affinity. These results suggest that the specificity of restriction
AB  - endonuclease Cfr9I is expressed during the catalytic step. The cleavage of supercoiled pUC18
AB  - DNA by restriction endonuclease Cfr9I showed that at low concentrations of MgCl2, only with
AB  - open-circular DNA, nicks appeared in one strand at the recognition sequence, while the
AB  - cleavage of the second strand was very slow. At these conditions the supercoiled DNA was
AB  - converted to open-circular and linear forms simultaneously rather than consecutively. It was
AB  - shown that open-circular DNA was a poor substrate for restriction endonuclease Cfr9I. These
AB  - results suggested that both Mg2+ and intact recognition sequence are required to drive the
AB  - enzyme into the correct conformation to ensure DNA cleavage.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Pleckaityte, M.
TI  - Role of the reactive cysteine residue in restriction endonuclese Cfr9I.
JO  - Biochim. Biophys. Acta
PY  - 1992
SP  - 199
EP  - 205
VL  - 1160
AB  - Chemical modification studies were performed to elucidate the role of Cys-residues in the
AB  - catalysis/binding of restriction endonuclease Cfr9I. Incubation of restriction endonuclease
AB  - Cfr9I with N-ethylmaleimide (NEM), iodoacetate, 5-5'-dithiobis (2-nitrobenzoic acids) at pH
AB  - 7.5 led to a complete loss of the catalytic activity. However, no enzyme inactivation was
AB  - detectable after modification of the enzyme with iodoacetamide and methyl
AB  - methanethiosulfonate. Complete protection of the enzyme against inactivation by NEM was
AB  - observed in the presence of substrate implying that Cys-residues may be lcoated at or in the
AB  - vicinity of the active site of enzyme. Direct substrate-binding studies of native and modified
AB  - restriction endonuclease Cfr9I using a gel-mobility shift assay indicated that the
AB  - modification of the enzyme by NEM was hindered by substrate binding. A single Cys-residue was
AB  - modified during the titration of the enzyme with DTNB with concomitant loss of the catalytic
AB  - activity. The pH-dependence of inactivation of Cfr9I by NEM revealed the modification of the
AB  - residue with a pKa value of 8.9 +/- 0.2. The dependence of the reaction rate of substrate
AB  - hydrolysis by Cfr9I versus pH revealed two essential residues with pKa values of 6.3 +/- 0.15
AB  - and 8.7 +/- 0.15, respectively. The evidence presented suggests that the restriction
AB  - endonuclease Cfr9I contains a reactive sulfhydryl residue which is non-essential for
AB  - catalysis, but is located at or near the substrate binding site.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Skirgaila, R.
AU  - Sasnauskas, G.
AU  - Urbanke, C.
AU  - Cherny, D.
AU  - Grazulis, S.
AU  - Huber, R.
TI  - The Cfr10I restriction enzyme is functional as a tetramer.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1105
EP  - 1118
VL  - 291
AB  - It is thought that most of the type II restriction endonucleases interact with DNA as
AB  - homodimers. Cfr10I is a typical type II restriction enzyme that recognises the 5'-Pu^CCGGPy
AB  - sequence and cleaves it as indicated by the arrow.  Gel-filtration and analytical
AB  - ultracentrifugation data presented here indicate that Cfr10I is a homotetramer in isolation.
AB  - Only the SfiI restriction enzyme that recognises the long interrupted recognition sequence
AB  - 5'-GGCCNNNNNGGCC has been previously reported to operate as a tetramer however, its structure
AB  - is unknown. Analysis of Cfr10I crystals revealed that a single molecule in the asymmetric unit
AB  - is repeated by D2 symmetry to form a tetramer. To determine whether the packing of the Cfr10I
AB  - in the crystal reflects the quaternary structure of the protein in solution, the tryptophan
AB  - W220 residue located at the putative dimer-dimer interface was mutated to alanine, and the
AB  - structural and functional consequences of the substitution were analysed. Equilibrium
AB  - sedimentation experiments revealed that, in contrast to the wild-type Cfr10I, the W220A mutant
AB  - exists in solution predominantly as a dimer. In addition, the tetramer seems to be a
AB  - catalytically important form of Cfr10I, since the DNA cleavage activity of the W220A mutant is
AB  - < 0.1% of that of the wild-type enzyme. Further, analysis of plasmid DNA cleavage suggests
AB  - that the Cfr10I tetramer is able to interact with two copies of the recognition sequence,
AB  - located on the same DNA molecule. Indeed, electron microscopy studies demonstrated that two
AB  - distant recognition sites are brought together through the DNA looping induced by the
AB  - simultaneous binding of the Cfr10I tetramer to both sites. These data are consistent with the
AB  - tetramer being a functionally important form of Cfr10I.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Tamulaitis, G.
AU  - Zaremba, M.
AU  - Szczepanowski, R.
AU  - Bochtler, M.
TI  - How do restriction enzymes acquire specificities for different target sites?
JO  - FEBS J.
PY  - 2008
SP  - 10
EP  - 10
VL  - 275
AB  - Restriction enzymes recognize 4-8 bp DNA sequences and cut at their target site with exquisite
AB  - specificity.  Many orthodox restriction endonucleases interacting with symmetric recognition
AB  - sites achieve sequence specificity making direct nucleobase-amino acid contacts with their
AB  - target sites.  Ecl18kI and EcoRII-C/PspGI restriction enzymes recognize interrupted
AB  - pentanucleotide sites CCNGG and CCWGG, respectively.  Structural studies demonstrate that
AB  - Ecl18kI/EcoRII-C/PspGI and the NgoMIV restriction enzyme specific for the non-interrupted
AB  - GCCGGC site share striking structural similarities and interact identically with the
AB  - symmetrical CC:GG half-sites.  It turned out that Ecl18kI specific for the CCNGG and
AB  - EcoRII-C/PspGI specific for the CCWGG site flip central nucleotides from DNA double helix to
AB  - interact with the conserved CC:GG parts of their target sequences and achieve cleavage.
AB  - However, Ecl18kI and EcoRII-C/PspGI accept different base pairs at the center, raising a
AB  - question whether the base pair strength/stability or a direct readout of the flipped out bases
AB  - determine the differences in specificity.  Using a combination of the X-ray structural
AB  - analysis and biochemical methods we show that EcoRII-C/PspGI achieve the specificity for the
AB  - CCWGG sequence by a double check mechanism by probing both the stability of the central base
AB  - pair and identity of the flipped out base in the pocket.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Timinskas, A.
AU  - Klimasauskas, S.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage.
JO  - Gene
PY  - 1995
SP  - 311
EP  - 314
VL  - 157
AB  - The type-II restriction endonucleases (ENases) EcoRI (recognition sequence G/AATTC), RsrI
AB  - (G/AATTC), XcyI (C/CCGGG), Cfr9I (C/CCGGG) and MunI (C/AATTG), all cleave hexanucleotide
AB  - palindromic sequences, leaving tetranucleotide 5'-overhangs.  Two regions of similarity that
AB  - appear in the same order and relative position were identified among the amino-acid sequences
AB  - of ENases.  These regions map to the structural elements of EcoRI involved in the building of
AB  - the catalytic site and in interactions with the central nucleotides of the recognized
AB  - sequence.  We propose that these ENases might all share a similar structural organization of
AB  - the active site and structural motifs involved in interactions with specific DNA recognition
AB  - sequences.
ER  -

TY  - JOUR
AU  - Siksnys, V.
AU  - Zareckaja, N.
AU  - Vaisvila, R.
AU  - Timinskas, A.
AU  - Stakenas, P.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI.
JO  - Gene
PY  - 1994
SP  - 1
EP  - 8
VL  - 142
AB  - The genes coding for the MunI restriction-modification (R-M) system, which recognize the
AB  - sequence 5'-CAATTG, have been cloned and expressed in Escherichia coli, and their nucleotide
AB  - sequences have been determined. The restriction endonuclease (ENase: R.MunI) is encoded by an
AB  - open reading frame (ORF) of 606 bp, and a 699-bp ORF codes for the methyltransferase (MTase).
AB  - The two genes are transcribed divergently from a 355-bp region. The gene encoding the ENase is
AB  - preceded by a short co-linear ORF of 222 bp. The deduced amino acid (aa) sequence of this
AB  - short ORF (SORF) closely resembles the sequences of a family of regulatory proteins that are
AB  - associated with other type-II R-M systems. Comparative analysis of the deduced aa sequence of
AB  - R.MunI revealed several regions of similarity to the EcoRI and RsrI ENases that recognize the
AB  - GAATTC sequence. The similar mode of interaction of MunI, EcoRI and RsrI with the
AB  - tetranucleotide AATT, common to the recognition sequences of these ENases, was suggested.
ER  -

TY  - JOUR
AU  - Silanskas, A.
AU  - Foss, M.
AU  - Wende, W.
AU  - Urbanke, C.
AU  - Lagunavicius, A.
AU  - Pingoud, A.
AU  - Siksnys, V.
TI  - Photocaged Variants of the MunI and PvuII Restriction Enzymes.
JO  - Biochemistry
PY  - 2011
SP  - 2800
EP  - 2807
VL  - 50
AB  - Regulation of proteins by light is a new and promising strategy for the external control of
AB  - biological processes. In this study, we demonstrate
AB  - the ability to regulate the catalytic activity of the MunI and PvuII
AB  - restriction endonucleases with light. We used two different approaches
AB  - to attach a photoremovable caging compound, 2-nitrobenzyl bromide
AB  - (NBB), to functionally important regions of the two enzymes. First, we
AB  - covalently attached a caging molecule at the dimer interface of Muni to
AB  - generate an inactive monomer. Second, we attached NBB at the DNA
AB  - binding site of the single-chain variant of PvuII (scPvuII) to prevent
AB  - binding and cleavage of the DNA substrate. Upon removal of the caging
AB  - group by UV irradiation, nearly 50% of the catalytic activity of Muni
AB  - and 80% of the catalytic activity of PvuII could be restored.
ER  -

TY  - JOUR
AU  - Silanskas, A.
AU  - Zaremba, M.
AU  - Sasnauskas, G.
AU  - Siksnys, V.
TI  - Catalytic Activity Control of Restriction Endonuclease-Triplex Forming Oligonucleotide Conjugates.
JO  - Bioconjugate Chem.
PY  - 2012
SP  - 203
EP  - 211
VL  - 23
ER  -

TY  - JOUR
AU  - Silber, K.R.
AU  - Polisson, C.
AU  - Rees, P.A.
AU  - Benner, J.S.
TI  - Cloning, purification and characterization of the M.NdeI methyltransferase from Neisseria denitrificans.
JO  - Gene
PY  - 1988
SP  - 43
EP  - 44
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Silberstein, Z.
AU  - Shalit, M.
AU  - Cohen, A.
TI  - Heteroduplex strand-specificity in restriction-stimulated recombination by the RecE pathway of Escherichia coli.
JO  - Genetics
PY  - 1993
SP  - 439
EP  - 448
VL  - 133
AB  - The RecE recombination pathway is active in Escherichia coli recB recC sbcA mutants. To
AB  - isolate and characterize products and intermediates of RecE-mediated, break-induced,
AB  - intramolecular recombination, we infected recB recC sbcA mutants, expressing EcoRI
AB  - endonuclease, with chimeric gamma phages that allow EcoRI-mediated release of cloned linear
AB  - recombination substrates. Substrates with direct terminal repeats recombined to yield a
AB  - circular product with one copy of the repeated sequence. Some recombinations were
AB  - heteroallelic for the recombining markers. Markers distant to the break were recovered in the
AB  - circular product at a higher frequency than markers close to the break. To examine the
AB  - heteroduplex structures that may have yielded the heteroallelic recombinants, non-replicative
AB  - substrates were employed. Some of the nonreplicative recombination products contained
AB  - heteroduplexes, with a strong bias for paired strands ending 3' at the break. This strand
AB  - bias in heteroduplex formation is consistent with recombination models that postulate
AB  - homologous pairing of protruding 3' single-stranded ends.
ER  -

TY  - JOUR
AU  - Silo-Suh, L.A.
AU  - Suh, S.J.
AU  - Ohman, D.E.
AU  - Wozniak, D.J.
AU  - Pridgeon, J.W.
TI  - Complete Genome Sequence of Pseudomonas aeruginosa Mucoid Strain FRD1, Isolated from a Cystic Fibrosis Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e00153
EP  - e00115
VL  - 3
AB  - We announce here the complete genome sequence of the Pseudomonas aeruginosa mucoid strain
AB  - FRD1, isolated from the sputum of a cystic fibrosis patient. The
AB  - complete genome of P. aeruginosa FRD1 is 6,712,339 bp. This genome will allow
AB  - comparative genomics to be used to identify genes associated with virulence,
AB  - especially those involved in chronic pulmonary infections.
ER  -

TY  - JOUR
AU  - Silva, A. et al.
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis I-19, strain isolated from Israel Bovine mastitis.
JO  - J. Bacteriol.
PY  - 2010
SP  - 323
EP  - 324
VL  - 193
AB  - This work portrays a report on complete and annotated genome sequence of Corynebacterium
AB  - pseudotuberculosis I-19 isolated from an Israel dairy cow
AB  - with sever clinical mastitis. To present the whole-genome sequence, de
AB  - novo assembly approach using 33 million short (25 bp) mate paired SOLiD
AB  - reads only was applied. More so, the automatic, functional and manual
AB  - annotation was attained with the use of several algorithms in a multi-step
AB  - process.
ER  -

TY  - JOUR
AU  - Silva, A. et al.
TI  - Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6663
EP  - 6664
VL  - 194
AB  - Corynebacterium pseudotuberculosis is of major veterinary importance because it
AB  - affects many animal species, causing economically significant livestock diseases
AB  - and losses. Therefore, the genomic sequencing of various lines of this organism,
AB  - isolated from different hosts, will aid in the development of diagnostic methods
AB  - and new prevention and treatment strategies and improve our knowledge of the
AB  - biology of this microorganism. In this study, we present the genome of C.
AB  - pseudotuberculosis Cp31, isolated from a buffalo in Egypt.
ER  -

TY  - JOUR
AU  - Silva, A.S.
AU  - Barauna, R.A.
AU  - de Sa, P.C.
AU  - das Gracas, D.A.
AU  - Carneiro, A.R.
AU  - Thouvenin, M.
AU  - Azevedo, V.
AU  - Badell, E.
AU  - Guiso, N.
AU  - da Silva, A.L.
AU  - Ramos, R.T.
TI  - Draft Genome Sequence of Corynebacterium ulcerans FRC58, Isolated from the Bronchitic Aspiration of a Patient in France.
JO  - Genome Announcements
PY  - 2014
SP  - e01132
EP  - e01113
VL  - 2
AB  - Corynebacterium ulcerans is a bacterial species with high importance because it causes
AB  - infections in animals and, rarely, in humans. Its virulence mechanisms
AB  - remain unclear. The current study describes the draft genome of C. ulcerans
AB  - FRC58, which was isolated from the bronchitic aspiration of a patient in France.
ER  -

TY  - JOUR
AU  - Silva, B.S.
AU  - Nobrega, M.S.
AU  - Leomil, L.
AU  - Tschoeke, D.A.
AU  - Garcia, G.D.
AU  - Dias, G.
AU  - Thompson, C.C.
AU  - Thompson, F.L.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain PAB 2.2 Isolated from Abrolhos Bank (Brazil).
JO  - Genome Announcements
PY  - 2017
SP  - e00016
EP  - e00017
VL  - 5
AB  - We present here the draft genome sequence of Pseudoalteromonas sp. strain PAB 2.2, isolated
AB  - from water of Parcel de Abrolhos coral reef (17 degrees 57'32.7';
AB  - 38 degrees 30'20.3'), on Abrolhos Bank, at a depth of 12 m. The assembly
AB  - consists of 4,434,635 bp and contains 40 contigs, with a G+C content of 41.60%.
ER  -

TY  - JOUR
AU  - Silva, C.
AU  - Calva, E.
AU  - Calva, J.J.
AU  - Wiesner, M.
AU  - Fernandez-Mora, M.
AU  - Puente, J.L.
AU  - Vinuesa, P.
TI  - Complete Genome Sequence of a Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Harboring a Multidrug  Resistance IncA/C Plasmid and a blaCMY-2-Carrying IncF Plasmid.
JO  - Genome Announcements
PY  - 2015
SP  - e01323
EP  - e01315
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico
AB  - City, Mexico, from a patient with a systemic infection, and its
AB  - complete genome sequence was determined using PacBio single-molecule real-time
AB  - technology. Strain 33676 harbors an IncF plasmid carrying the extended-spectrum
AB  - cephalosporin gene blaCMY-2 and a multidrug resistance IncA/C plasmid.
ER  -

TY  - JOUR
AU  - Silva, C.
AU  - Calva, E.
AU  - Puente, J.L.
AU  - Zaidi, M.B.
AU  - Vinuesa, P.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO2 (Sequence Type 302) Isolated from an Asymptomatic Child in Mexico.
JO  - Genome Announcements
PY  - 2016
SP  - e00253
EP  - e00216
VL  - 4
AB  - The complete genome sequence ofSalmonella entericaserovar Typhimurium strain SO2, isolated
AB  - from an asymptomatic child in Mexico, was determined using PacBio
AB  - single-molecule real-time technology. Strain SO2 has six complete chromosomal
AB  - prophages, namely, ST104, Gifsy-2, ST64B, Gifsy-1, ELPhiS, and FSL SP-004, and
AB  - carries aSalmonellavirulence plasmid.
ER  -

TY  - JOUR
AU  - Silva, C.
AU  - Calva, E.
AU  - Puente, J.L.
AU  - Zaidi, M.B.
AU  - Vinuesa, P.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain YU15 (Sequence Type 19) Harboring the Salmonella Genomic Island 1 and Virulence  Plasmid pSTV.
JO  - Genome Announcements
PY  - 2016
SP  - e00252
EP  - e00216
VL  - 4
AB  - The complete genome ofSalmonella entericasubsp.entericaserovar Typhimurium sequence type 19
AB  - (ST19) strain YU15, isolated in Yucatan, Mexico, from a human
AB  - baby stool culture, was determined using PacBio technology. The chromosome
AB  - contains five intact prophages and theSalmonellagenomic island 1 (SGI1). This
AB  - strain carries theSalmonellavirulence plasmid pSTV.
ER  -

TY  - JOUR
AU  - Silva, C.A.
AU  - Blondel, C.J.
AU  - Quezada, C.P.
AU  - Porwollik, S.
AU  - Andrews-Polymenis, H.L.
AU  - Toro, C.S.
AU  - Zaldivar, M.
AU  - Contreras, I.
AU  - McClelland, M.
AU  - Santiviago, C.A.
TI  - Infection of Mice by Salmonella enterica Serovar Enteritidis Involves Additional Genes That Are Absent in the Genome of Serovar Typhimurium.
JO  - Infect. Immun.
PY  - 2012
SP  - 839
EP  - 849
VL  - 80
AB  - Salmonella enterica serovar Enteritidis causes a systemic, typhoid-like infection in newly
AB  - hatched poultry and mice. In the present study, a
AB  - library of 54,000 transposon mutants of S. Enteritidis phage type 4
AB  - (PT4) strain P125109 was screened for mutants deficient in the in vivo
AB  - colonization of the BALB/c mouse model using a microarray-based
AB  - negative-selection screening. Mutants in genes known to contribute to
AB  - systemic infection (e.g., Salmonella pathogenicity island 2 [SPI-2],
AB  - aro, rfa, rfb, phoP, and phoQ) and enteric infection (e.g., SPI-1 and
AB  - SPI-5) in this and other Salmonella serovars displayed colonization
AB  - defects in our assay. In addition, a strong attenuation was observed
AB  - for mutants in genes and genomic islands that are not present in S.
AB  - Typhimurium or in most other Salmonella serovars. These genes include a
AB  - type I restriction/modification system (SEN4290 to SEN4292), the peg
AB  - fimbrial operon (SEN2144A to SEN2145B), a putative pathogenicity island
AB  - (SEN1970 to SEN1999), and a type VI secretion system remnant SEN1001,
AB  - encoding a hypothetical protein containing a lysin motif (LysM) domain
AB  - associated with peptidoglycan binding. Proliferation defects for
AB  - mutants in these individual genes and in exemplar genes for each of
AB  - these clusters were confirmed in competitive infections with wild-type
AB  - S. Enteritidis. A Delta SEN1001 mutant was defective for survival
AB  - within RAW264.7 murine macrophages in vitro. Complementation assays
AB  - directly linked the SEN1001 gene to phenotypes observed in vivo and in
AB  - vitro. The genes identified here may perform novel virulence functions
AB  - not characterized in previous Salmonella models.
ER  -

TY  - JOUR
AU  - Silva, D.M.
AU  - da Silva, M.P.
AU  - Vidigal, P.M.
AU  - Barcelos, R.M.
AU  - Klein, R.C.
AU  - Aguilar, A.P.
AU  - Fabres-Klein, M.H.
AU  - Oliveira, G.
AU  - Ribon, A.O.
TI  - Draft Genome Sequences of Staphylococcus aureus Strains Isolated from Subclinical Bovine Mastitis in Brazil.
JO  - Genome Announcements
PY  - 2016
SP  - e01594
EP  - e01515
VL  - 4
AB  - Here, we present the draft genome sequences of four Staphylococcus aureus strains isolated
AB  - from mastitic milk collected from animals with subclinical
AB  - manifestations. Three of them were typed as sequence type 126 (ST126), a genotype
AB  - with no genome sequence available. ST126 is found in several herds of southern
AB  - Brazil and is described as a bovine pathogen strongly associated with milk around
AB  - the world.
ER  -

TY  - JOUR
AU  - Silva, G.H.
AU  - Belfort, M.
TI  - Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3156
EP  - 3168
VL  - 32
AB  - The general structural fold of the LAGLIDADG endonuclease family consists of two similar
AB  - alpha/beta domains (alpha beta beta alpha beta beta alpha) that assemble either as homodimers
AB  - or monomers with the domains related by pseudo-two-fold symmetry. At the center of this
AB  - symmetry is the closely packed LAGLIDADG two-helix bundle that forms the main inter- or
AB  - intra-molecular contact region between the domains of single- or double-motif proteins,
AB  - respectively. In this work, we further examine the role of the LAGLIDADG residues involved in
AB  - the helix?helix interaction. The interchangeability of the LAGLIDADG helix interaction was
AB  - explored by grafting interfacial residues from the homodimeric I-CreI into the corresponding
AB  - positions in the monomeric I-DmoI. The resulting LAGLIDADG exchange mutant is partially
AB  - active, preferring to nick dsDNA rather than making the customary double-strand break. A
AB  - series of partial revertants within the mutated LAGLIDADG region are shown to restore cleavage
AB  - activity to varying degrees resulting in one I-DmoI mutant that is more active than wild-type
AB  - I-DmoI. The phenotype of some of these mutants was reconciled on the basis of similarity to
AB  - the GxxxG helix interaction found in transmembrane proteins. Additionally, a split variant of
AB  - I-DmoI was created, demonstrating that the LAGLIDADG helices of I-DmoI are capable of forming
AB  - and maintaining the protein?protein interface in trans to create an active heterodimer.
ER  -

TY  - JOUR
AU  - Silva, G.H.
AU  - Belfort, M.
AU  - Wende, W.
AU  - Pingoud, A.
TI  - From monomeric to homodimeric endonucleases and back: Engineering novel specificity of LAGLIDADG enzymes.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 744
EP  - 754
VL  - 361
AB  - Monomeric homing endonucleases of the LAGLIDADG family recognize DNA in a bipartite manner,
AB  - reflecting the underlying structural assembly of two protein domains (A and B) related by
AB  - pseudo 2-fold symmetry. This architecture allows for changes in DNA specificity via the
AB  - distinct combination of these half-site domains. The key to engineering such hybrid proteins
AB  - lies in the LAGLIDADG two-helix bundle that forms both the domain interface and the
AB  - endonuclease active site. In this study, we utilize domain A of the monomeric I-DmoI to
AB  - demonstrate the feasibility of generating functional homodimeric endonucleases that recognize
AB  - palindromic DNA sequences derived from the original, non-palindromic target. Wild-type I-DmoI
AB  - domain A is capable of forming a homodimer (H-DmoA) that binds tightly to, but does not cleave
AB  - efficiently, its anticipated DNA target. Partial restoration of DNA cleavage ability was
AB  - obtained by re-engineering the LAGLIDADG dimerization interface (H-DmoC). Upon fusing two
AB  - copies of H-DmoC via a short peptide linker, a novel, site-specific DNA endonuclease was
AB  - created (H-DmoC2). Like I-DmoI, H-DmoC2 is thermostable and cleaves the new target DNA to
AB  - generate the predicted 4 nt 3'-OH overhangs but, unlike I-DmoI, H-DmoC2 retains stringent
AB  - cleavage specificity when substituting Mn(2+) for Mg(2+) as co-factor. This novel endonuclease
AB  - allows speculation regarding specificity of monomeric LAGLIDADG proteins, while it supports
AB  - the evolutionary genesis of these proteins by a gene duplication event.
ER  -

TY  - JOUR
AU  - Silva, G.H.
AU  - Dalgaard, J.Z.
AU  - Belfort, M.
AU  - Van Roey, P.
TI  - Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1123
EP  - 1136
VL  - 286
AB  - I-DmoI is a 22 kDa endonuclease encoded by an intron in the 23 S rRNA gene of the
AB  - hyperthermophilic archaeon Desulfurococcus mobilis.  The structure of I-DmoI has been
AB  - determined to 2.2 A resolution using multi-wave-length anomalous diffraction techniques.
AB  - I-DmoI, a protein of the LAGLIDADG motif family, represents the first structure of a
AB  - freestanding endonuclease with two LALIDADG motifs, and the first of a thermostable homing
AB  - endonuclease.  I-DmoI consists of two similar alpha/beta domains (alpha beta beta alpha beta
AB  - beta alpha) related by pseudo 2-fold symmetry.  The LAGLIDADG motifs are located at the
AB  - carboxy-terminal end of the first alpha-helix of each domain.  These helices form a two-helix
AB  - bundle at the interface between the domains and are perpendicular to a saddle-shaped DNA
AB  - binding surface, formed by two four-stranded antiparallel beta-sheets. Despite substantially
AB  - different sequences, the overall fold of I-DmoI is similar to that of two other LAGLIDADG
AB  - proteins for which the structures are known, I-CreI and the endonuclease domain of PI-SceI.
AB  - The three structures differ most in the loops connecting the beta-strands, relating to the
AB  - respective DNA target site sizes and geometries.  In addition, the absence of conserved
AB  - residues surrounding the active site, other than those within the LAGLIDADG motif, is of
AB  - mechanistic importance.  Finally, the carboxy-terminal domain of I-DmoI is smaller and has a
AB  - more irregular fold than the amino-terminal domain, which is more similar to I-CreI, a
AB  - symmetric homodimeric endonuclease.  This is reversed compared to PI-SceI, where the
AB  - amino-terminal domain is more similar to carboxy-terminal domain of I-DmoI and to I-CreI, with
AB  - interesting evolutionary implications.
ER  -

TY  - JOUR
AU  - Silva, I.N.
AU  - Duarte, S.
AU  - Moreira, L.M.
AU  - Monteiro, G.A.
TI  - Draft Genome Sequence of the Plasmid-Free Lactococcus lactis subsp. lactis Strain LMG 19460.
JO  - Genome Announcements
PY  - 2017
SP  - e00210
EP  - e00217
VL  - 5
AB  - We report here the draft genome sequence of the plasmid-free Lactococcus lactis subsp. lactis
AB  - strain LMG 19460. This strain has potential application for a
AB  - cost-effective production of food-grade plasmid DNA to use in DNA vaccines,
AB  - produce recombinant proteins, and be used as a mucosal delivery vehicle of
AB  - therapeutic molecules.
ER  -

TY  - JOUR
AU  - Silva, I.N.
AU  - Santos, P.M.
AU  - Moreira, L.M.
TI  - Draft Genome Sequences of Two Burkholderia multivorans Sequential Isolates from a Chronic Lung Infection of a Cystic Fibrosis Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e01531
EP  - e01514
VL  - 3
AB  - Burkholderia multivorans belongs to the Burkholderia cepacia complex, which comprises
AB  - opportunistic pathogens infecting cystic fibrosis (CF) patients. Here,
AB  - we report the genome sequences and annotations of two sequential B. multivorans
AB  - clinical isolates (D2095 and D2214) displaying different traits. The differences
AB  - in the genomic contents of these isolates may provide clues regarding the
AB  - evolution of B. multivorans within the airways of a CF patient.
ER  -

TY  - JOUR
AU  - Silva, S.G.
AU  - Lago-Leston, A.
AU  - Costa, R.
AU  - Keller-Costa, T.
TI  - Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata.
JO  - Genome Announcements
PY  - 2018
SP  - e00142
EP  - e00118
VL  - 6
AB  - Here, we report the draft genome sequence of Sphingorhabdus sp. strain EL138, an
AB  - alphaproteobacterium that shows potential to degrade polycyclic aromatic
AB  - compounds and to cope with various heavy metals and antibiotics. Moreover, the
AB  - strain, isolated from the gorgonian coral Eunicella labiata, possesses several
AB  - genes involved in the biosynthesis of polyphosphates, polyketides, and
AB  - terpenoids.
ER  -

TY  - JOUR
AU  - Silva-Junior, W.J.
AU  - Farias, A.R.G.
AU  - Lima, N.B.
AU  - Benko-Iseppon, A.M.
AU  - Aburjaile, F.
AU  - Balbino, V.Q.
AU  - Falcao, R.M.
AU  - Leitao, P.J.S.S.
AU  - Sousa-Paula, L.C.
AU  - Mariano, R.L.R.
AU  - Souza, E.B.
AU  - Gama, M.A.S.
TI  - Complete Genome Sequence of Xanthomonas citri pv. anacardii Strain IBSBF2579 from Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e01574
EP  - e01517
VL  - 6
AB  - The bacterium Xanthomonas citri pv. anacardii is the agent of angular leaf spot of the cashew
AB  - tree (Anacardium occidentale L.). The complete genome sequencing of the strain IBSBF2579 was
AB  - done on an Illumina HiSeq 2500 platform. The de novo assembly of the X. citri pv. anacardii
AB  - strain IBSBF2579 genome yielded 133 contigs, with a size of 5,329,247 bp and a G+C content of
AB  - 64.03%. The prediction was performed by GeneMarkS and the automatic annotation by Rapid
AB  - Annotations using Subsystems Technology (RAST), with 4,406 identified genes.
ER  -

TY  - JOUR
AU  - Silveira, M.
AU  - Albano, R.
AU  - Asensi, M.
AU  - Assef, A.P.
TI  - The draft genome sequence of multidrug-resistant Pseudomonas aeruginosa strain CCBH4851, a nosocomial isolate belonging to clone SP (ST277) that is prevalent in Brazil.
JO  - Memorias do Instituto Oswaldo Cruz
PY  - 2014
SP  - 1086
EP  - 1087
VL  - 109
AB  - The high occurrence of nosocomial multidrug-resistant (MDR) microorganisms is
AB  - considered a global health problem. Here, we report the draft genome sequence of
AB  - a MDR Pseudomonas aeruginosa strain isolated in Brazil that belongs to the
AB  - endemic clone ST277. The genome encodes important resistance determinant genes
AB  - and consists of 6.7 Mb with a G+C content of 66.86% and 6,347 predicted coding
AB  - regions including 60 RNAs.
ER  -

TY  - JOUR
AU  - Simala-Grant, J.L.
AU  - Lam, E.
AU  - Keelan, M.
AU  - Taylor, D.E.
TI  - Characterization of the DNA adenine 5 '-GATC-3 ' methylase HpyIIIM from Helicobacter pylori.
JO  - Curr. Microbiol.
PY  - 2004
SP  - 47
EP  - 54
VL  - 49
AB  - The effect of inactivation of the 5'-GATC-3' methylase HpyIIIM in Helicobacter pylori (H.
AB  - pylori) on mismatch repair, adherence, and in
AB  - vitro fitness was examined. Chromosomal DNA from 90 H. pylori strains
AB  - was isolated, and restriction enzyme digestion indicated all strains
AB  - examined possess HpyIIIM. Wild-type H. pylori and a strain with an
AB  - inactive HpyIIIM were found to have rifampicin mutation frequencies of
AB  - 2.93 x 10(-7) and 1.05 x 10(-7) (P > 0.05), respectively, indicating
AB  - that HpyIIIM does not appear to be important in mismatch repair.
AB  - Adherence of H. pylori in an in vitro model cell system was also
AB  - unaffected by inactivation of HpyIIIM. Inactivation of HpyIIIM did not
AB  - result in a decrease in fitness, as determined by liquid in vitro
AB  - competition experiments.
ER  -

TY  - JOUR
AU  - Simbochova, G.
AU  - Timko, J.
AU  - Zelinkova, E.
AU  - Zelinka, J.
TI  - Properties and recognition sequence of site-specific endonuclease from Streptomyces aureofaciens.
JO  - Biologia (Bratisl)
PY  - 1986
SP  - 357
EP  - 365
VL  - 41
AB  - A type II restriction endonuclease Sau3239I was purified from Streptomyces
AB  - aureofaciens 3239.  The recognition sequence for the enzyme was determined 5' -
AB  - C ^ T C G A G - 3' 3' - G A G C T ^ C - 5' 	and cleaved at the position
AB  - indicated by the arrows, producing a tetranucleotide 5'-terminal extension.
AB  - Therefore Sau 3239I endonuclease is an isoschizomer of XhoI endonuclease.	The
AB  - contribution of the type II restriction enzymes to recombinant DNA technology
AB  - has stimulated extensive search for these enzymes which have been isolated from
AB  - a great variety of bacteria, including the actinomycetes {Streptomyces
AB  - aureofaciens IKA 18/4} is SauI {Timko et al., 1981}.  Another specific
AB  - restriction endonuclease was found in the chlortetracycline {CTC} producing
AB  - prototrophic strain of Streptomyces aureofaciens CCM 3239 {Gasperik et al.,
AB  - 1983}.  We report here this endonuclease designated as Sau 3239I which was
AB  - isolated from this strain.  The isolation procedure and determination of the
AB  - recognition sequence are described.
ER  -

TY  - JOUR
AU  - Simbochova, G.
AU  - Timko, J.
AU  - Zelinkova, E.
AU  - Zelinka, J.
TI  - Some physical and chemical properties of site-specific endonuclease Sau3239I from Streptomyces aureofaciens.
JO  - Biologia (Bratisl)
PY  - 1987
SP  - 1129
EP  - 1136
VL  - 42
AB  - Sau3239I was isolated and purified from Streptomyces aureofaciens CCM 3239. The
AB  - substrate specificity and the cleavage site of this enzyme is 5' - C^TCGAG - 3'
AB  - and thus it is an isoschizomer of XhoI (Simbochova et al., 1986).  Some of its
AB  - physical properties and substrate specificity are described.
ER  -

TY  - JOUR
AU  - Simcox, T.G.
AU  - Fabian, L.
AU  - Kretz, K.
AU  - Hedden, V.
AU  - Simcox, M.E.C.
TI  - SanDI, a new type-II restriction endonuclease that recognizes 5'-GG/GWCCC-3'.
JO  - Gene
PY  - 1995
SP  - 129
EP  - 130
VL  - 155
AB  - A new restriction endonuclease (ENase), SanDI, has been isolated from an unidentified species
AB  - of Streptomyces. SanDI recognizes the 7-bp interrupted palindrome 5'-GG/GWCCC-3' (W=A or T)
AB  - and cleaves double-stranded DNA after the second G in the sequence, producing 3-nt long 5'
AB  - protruding ends. SanDI is a rare-cutting ENase and should therefore be useful for megabase
AB  - mapping and vector constructions.
ER  -

TY  - JOUR
AU  - Simcox, T.G.
AU  - Marsh, S.J.
AU  - Gross, E.A.
AU  - Lernhardt, W.
AU  - Davis, S.
AU  - Simcox, M.E.C.
TI  - SrfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence,.
JO  - Gene
PY  - 1991
SP  - 121
EP  - 123
VL  - 109
AB  - A new restriction endonuclease, SrfI, has been isolated from an unidentified
AB  - species of Streptomyces.  SrfI recognizes the 8-bp palindrome, 5'-GCCCGGGC and
AB  - cleaves double-stranded DNA after the third C in the sequence, producing blunt
AB  - ends.  SrfI is a rare-cutting enzyme and should therefore be useful for
AB  - megabase mapping.
ER  -

TY  - JOUR
AU  - Simmon, V.F.
AU  - Lederberg, S.
TI  - Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1972
SP  - 161
EP  - 169
VL  - 112
AB  - Wild-type bacteria which restrict the deoxyribonucleic acid (DNA) of infecting
AB  - phage when the phage do not carry the proper host modification rapidly degrade
AB  - that restricted DNA to acid-soluble products.  The purified restriction enzyme
AB  - acts as an endonuclease in vitro to cleave restrictable DNA and does not
AB  - further degrade the DNA fragment products.  We have examined mutants of
AB  - Escherichia coli K-12 which lack various nucleases in order to determine which
AB  - nucleases are involved in the rapid acid solubilization in vivo of unmodified
AB  - lambda DNA following restriction.  Bacteria which are wild type, recA-, or
AB  - polA1- degrade about 50% of the unmodified phage DNA within 10 min of
AB  - infection, with little subsequent degradation.  Mutants which are recB- or
AB  - recC- degrade unmodified DNA very slowly, solubilizing about 15% of the DNA by
AB  - 10 min after infection.  Two classes of phenotypic revertants of recB-/C-
AB  - mutants were also tested.  Bacteria which are sbcA- restrict poorly and do not
AB  - degrade much of the restricted DNA.  Bacteria which are sbcB- restrict
AB  - normally.  This mutation does not appear to affect degradation of restricted
AB  - phage DNA in recB-/C- mutants, but such degradation is decreased in recB+/C+
AB  - bacteria.  The presence of a functional lambda exonuclease gene is not required
AB  - for degradation after restriction.
ER  -

TY  - JOUR
AU  - Simmons, W.L.
AU  - Daubenspeck, J.M.
AU  - Osborne, J.D.
AU  - Balish, M.F.
AU  - Waites, K.B.
AU  - Dybvig, K.
TI  - Type 1 and type 2 strains of Mycoplasma pneumoniae form different biofilms.
JO  - Microbiology
PY  - 2013
SP  - 737
EP  - 747
VL  - 159
AB  - Several mycoplasma species have been shown to form biofilms that confer resistance to
AB  - antimicrobials and which may affect the host immune system, thus making treatment and
AB  - eradication of the pathogens difficult. The present study shows that the biofilms formed by
AB  - two strains of the human pathogen Mycoplasma pneumoniae differ quantitatively and
AB  - qualitatively. Compared with strain UAB PO1, strain M129 grows well but forms biofilms that
AB  - are less robust, with towers that are less smooth at the margins. A polysaccharide containing
AB  - N-acetylglucosamine is secreted by M129 into the culture medium but found in tight association
AB  - with the cells of UAB PO1. The polysaccharide may have a role in biofilm formation,
AB  - contributing to differences in virulence, chronicity and treatment outcome between strains of
AB  - M. pneumoniae. The UAB PO1 genome was found to be that of a type 2 strain of M. pneumoniae,
AB  - whereas M129 is type 1. Examination of other M.
AB  - pneumoniae isolates suggests that the robustness of the biofilm correlates with the strain
AB  - type.
ER  -

TY  - JOUR
AU  - Simoliunas, E.
AU  - Kaliniene, L.
AU  - Truncaite, L.
AU  - Klausa, V.
AU  - Zajanckauskaite, A.
AU  - Meskys, R.
TI  - Genome of Klebsiella sp.-Infecting Bacteriophage vB_KleM_RaK2.
JO  - J. Virol.
PY  - 2012
SP  - 5406
EP  - 5406
VL  - 86
AB  - Despite the fact that multidrug-resistant Klebsiella sp. strains emerge rapidly
AB  - (Xu J, et al., Adv. Mater. Res. 268-270:1954-1956, 2011) and bacteriophages have
AB  - been reported to be useful in controlling these bacteria (Kumari S, Harjai K,
AB  - Chhibber S, J. Med. Microbiol. 60:205-210, 2011), the complete genome sequences
AB  - of only five Klebsiella phages (four siphoviruses and one myovirus) can be found
AB  - in databases. In this paper, we report on the complete genome sequence of
AB  - Klebsiella sp.-infecting bacteriophage vB_KleM_RaK2. With a genome size of
AB  - 345,809 bp, this is the second largest myovirus and the largest Klebsiella phage
AB  - sequenced to date. This phage differs substantially from other myoviruses since
AB  - 411 out of 534 vB_KleM_RaK2 open reading frames have no known functions and lack
AB  - any reliable database matches. Comparative analysis of the genome sequence of
AB  - vB_KleM_RaK2 suggests that this phage forms a distinct phylogenetic branch within
AB  - the family Myoviridae of tailed bacteriophages.
ER  -

TY  - JOUR
AU  - Simon, D.
AU  - Grunert, F.
AU  - Acken, U.V.
AU  - Doring, H.P.
AU  - Kroger, H.
TI  - DNA-methylase from regenerating rat liver: purification and characterisation.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 2153
EP  - 2167
VL  - 5
AB  - DNA methylase has been purified 660-fold from nuclei from regenerating rat liver. The enzyme
AB  - is able to methylate single stranded (ss) and double stranded (ds) DNA, the only reaction
AB  - product being 5-methylcytosine. Previously unmethylated double stranded DNA from prokaryotes
AB  - (M. luteus) as well as from eukaryotes (Ascaris suis) can serve as substrates. The synthetic
AB  - copolymers (dG-dC)n. (dC-dG)n and (dG,dC)n are also methylated. While SV40 DNA is almost not
AB  - methylated, PM2 DNA is a good substrate even in the supercoiled form. The enzyme methylates 1
AB  - in 17 bases in heterologous M. luteus DNA, but only 1 in 590 in homologous rat liver DNA. The
AB  - high methylation level of M. luteus DNA, an analysis of the methylated pyrimidine isostichs
AB  - and a preliminary dinucleotide analysis suggest that all the CpGs in a DNA can be methylated.
ER  -

TY  - JOUR
AU  - Simoncsits, A.
AU  - Tjornhammar, M.L.
AU  - Rasko, T.
AU  - Kiss, A.
AU  - Pongor, S.
TI  - Covalent joining of the subunits of a homodimeric type II restriction endonuclease: single-chain PvuII endonuclease.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 89
EP  - 97
VL  - 309
AB  - The PvuII restriction endonuclease has been converted from its natural homodimeric form into a
AB  - single polypeptide chain by tandemly linking
AB  - the two subunits through a short peptide Linker. The arrangement of the
AB  - single-chain PvuII (sc PvuII) is (2-157)-GlySerGlyGly-(2-157), where
AB  - (2-157) represents the amino acid residues of the enzyme subunit and
AB  - Gly-SerGlyGly is the peptide linker. By introducing the corresponding
AB  - tandem gene into Escherichia coli, PvuII endonuclease activity could
AB  - be detected in functional in vivo assays. The sc enzyme was expressed
AB  - at high level as a soluble protein. The purified enzyme was shown to
AB  - have the molecular mass expected for the designed sc protein. Based on
AB  - the DNA cleavage patterns obtained with different substrates, the
AB  - cleavage specificity of the sc PvuII is indistinguishable from that of
AB  - the wild-type (wt) enzyme. The sc enzyme binds specifically to the
AB  - cognate DNA site under non-catalytic conditions, in the presence of
AB  - Ca2+, with the expected 1:1 stoichiometry. Under standard catalytic
AB  - conditions, the sc enzyme cleaves simultaneously the two DNA strands in
AB  - a concerted manner. Steady-state kinetic parameters of DNA cleavage by
AB  - the sc and wt PvuII showed that the sc enzyme is a potent, but somewhat
AB  - less efficient catalyst; the k(cat)/K-M values are 1.11 x 10^9 and
AB  - 3.50 x 10^9 min^-1 M^-1 for the sc and wt enzyme, respectively. The
AB  - activity decrease is due to the lower turnover number and to the lower
AB  - substrate affinity. The sc arrangement provides a facile route to
AB  - obtain asymmetrically modified heterodimeric enzymes.
ER  -

TY  - JOUR
AU  - Simons, M.
AU  - Diffin, F.M.
AU  - Szczelkun, M.D.
TI  - ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 12082
EP  - 12091
VL  - 42
AB  - We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the
AB  - bacterial Type I restriction-modification enzyme EcoKI during restriction alleviation (RA). RA
AB  - is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind
AB  - unmodified recognition sites on the host genome. These conditions arise upon acquisition of a
AB  - new system by a naive host, upon generation of new sites by genome rearrangement/mutation or
AB  - during homologous recombination between hemimethylated DNA. Using recombinant DNA and proteins
AB  - in vitro, we demonstrate that ClpXP targets EcoKI HsdR during dsDNA translocation on circular
AB  - DNA but not on linear DNA. Protein roadblocks did not activate HsdR proteolysis. We suggest
AB  - that DNA translocation lifetime, which is elevated on circular DNA relative to linear DNA, is
AB  - important to RA. To identify the ClpX degradation tag (degron) in HsdR, we used bioinformatics
AB  - and biochemical assays to design N- and C-terminal mutations that were analysed in vitro and
AB  - in vivo. None of the mutants produced a phenotype consistent with loss of the degron,
AB  - suggesting an as-yet-unidentified recognition pathway. We note that an EcoKI nuclease mutant
AB  - still produces cell death in a clpx- strain, consistent with DNA damage induced by unregulated
AB  - motor activity.
ER  -

TY  - JOUR
AU  - Simons, M.
AU  - Szczelkun, M.D.
TI  - Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 7656
EP  - 7666
VL  - 39
AB  - The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM
AB  - that form a methyltransferase (MTase) and HsdR
AB  - that associates with the MTase and catalyses Adenosine-5'-triphosphate
AB  - (ATP)-dependent DNA translocation and cleavage. Here, we examine whether
AB  - the MTase and HsdR components can 'turnover' in vitro, i.e. whether they
AB  - can catalyse translocation and cleavage events on one DNA molecule,
AB  - dissociate and then re-bind a second DNA molecule. Translocation
AB  - termination by both EcoKI and EcoR124I leads to HsdR dissociation from
AB  - linear DNA but not from circular DNA. Following DNA cleavage, the HsdR
AB  - subunits appear unable to dissociate even though the DNA is linear,
AB  - suggesting a tight interaction with the cleaved product. The MTases of
AB  - EcoKI and EcoAI can dissociate from DNA following either translocation or
AB  - cleavage and can initiate reactions on new DNA molecules as long as free
AB  - HsdR molecules are available. In contrast, the MTase of EcoR124I does not
AB  - turnover and additional cleavage of circular DNA is not observed by
AB  - inclusion of RecBCD, a helicase-nuclease that degrades the linear DNA
AB  - product resulting from Type I cleavage. Roles for Type I restriction
AB  - endonuclease subunit dynamics in restriction alleviation in the cell are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Simpson, A.J. et al.
TI  - The genome sequence fo the plant pathogen Xylella fastidiosa.
JO  - Nature
PY  - 2000
SP  - 151
EP  - 157
VL  - 406
AB  - Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of
AB  - economically important plant diseases.  Here we report the complete genome sequence of X.
AB  - fastidiosa clone 9a5c, which causes citrus variegated chlorosis-a serious disease of orange
AB  - trees.  The genome comprises a 52.7% GC-rich 2,679,305-base-pair circular chromosome and two
AB  - plasmids of 51,158 bp and 1,285 bp.  We can assign putative functions to 47% of the 2,904
AB  - predicted coding regions.  Efficient metabolic functions are predicted, with sugars as the
AB  - principal energy and carbon source, supporting existence in the nutrient-poor xylem sap.  The
AB  - mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion
AB  - sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated
AB  - by a range of proteins.  Orthologues of some of these proteins have only been identified in
AB  - animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis
AB  - for bacterial pathogenicity is both conserved and independent of host.  At least 83 genes are
AB  - bacteriophage-derived and include virulence-associated genes from other bacteria, providing
AB  - direct evidence of phage-mediated horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Simpson, J.T.
AU  - Workman, R.E.
AU  - Zuzarte, P.C.
AU  - David, M.
AU  - Dursi, L.J.
AU  - Timp, W.
TI  - Detecting DNA cytosine methylation using nanopore sequencing.
JO  - Nat. Methods
PY  - 2017
SP  - 407
EP  - 410
VL  - 14
AB  - In nanopore sequencing devices, electrolytic current signals are sensitive to base
AB  - modifications, such as 5-methylcytosine (5-mC). Here we quantified the
AB  - strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By
AB  - using synthetically methylated DNA, we were able to train a hidden Markov model
AB  - to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence
AB  - the methylome of human DNA, without requiring special steps for library
AB  - preparation.
ER  -

TY  - JOUR
AU  - Sims, D. et al.
TI  - Complete genome sequence of Kytococcus sedentarius type strain (541).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 12
EP  - 20
VL  - 1
AB  - Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of
AB  - the species, and is of phylogenetic interest because of its
AB  - location in the Dermacoccaceae, a poorly studied family within the
AB  - actinobacterial suborder Micrococcineae. Kytococcus sedentarius is known for the
AB  - production of oligoketide antibiotics as well as for its role as an opportunistic
AB  - pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted
AB  - keratolysis. It is strictly aerobic and can only grow when several amino acids
AB  - are provided in the medium. The strain described in this report is a free-living,
AB  - nonmotile, Gram-positive bacterium, originally isolated from a marine
AB  - environment. Here we describe the features of this organism, together with the
AB  - complete genome sequence, and annotation. This is the first complete genome
AB  - sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long
AB  - single replicon genome with its 2639 protein-coding and 64 RNA genes is part of
AB  - the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Simuth, J.
AU  - Trnovsky, J.
AU  - Jelokova, J.
TI  - Inhibition of bacterial DNA-dependent RNA polymerases and restriction endonuclease by UV-absorbing components from Propolis.
JO  - Pharmazie
PY  - 1986
SP  - 131
EP  - 132
VL  - 41
AB  - Several UV-absorbing substances inhibiting the DNA-dependent RNA polymerases of
AB  - Escherichia coli and Streptomyces aureofaciens, as well as the restriction
AB  - endonuclease EcoRI have been isolated from the water-soluble extract of
AB  - Propolis by two-dimensional paper chromatography.  The inhibition of bacterial
AB  - RNA-polymerases by the components of Propolis was probably due to the loss of
AB  - their ability to bind to DNA.  The general characteristic of the UV-absorbing
AB  - component of Propolis with the most pronounced inhibitory effect upon
AB  - transcription in vitro is described.
ER  -

TY  - JOUR
AU  - Sineva, E.V.
AU  - Zakharova, G.G.
AU  - Tarutina, Z.E.
AU  - Kravetz, A.N.
AU  - Solonin, A.S.
TI  - Class II restriction-modification systems in Enterobacter cloacae.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1993
SP  - 10
EP  - 13
VL  - 0
AB  - Various clinical strains of Enterobacter cloacae have been examined for the presence of
AB  - site-specific endonuclease activities. Type II restriction endonucleases have been isolated
AB  - from 6 strains. Recognition sequences for all of these enzymes have been determined and the
AB  - cleavage sites were identified for two of them. The enzymes proved to be isoschizomers of
AB  - EcoRII and PstI. Restriction endonucleases Ecl2zI and Ecl37kI recognize the nucleotide
AB  - sequences CTGCA/G and are true isoschizomers of PstI. The genes for Ecl54kI and Ecl57kI
AB  - restriction modification systems (isoschizomers of EcoRII) were found to be located on the
AB  - IncN group of plasmids, whereas the genes for Ecl2zI and Ecl699kI seem to be located on the
AB  - chromosomes of the host cells.
ER  -

TY  - JOUR
AU  - Sing, W.D.
AU  - Klaenhammer, T.R.
TI  - Plasmid-induced abortive infection in Lactococci: a review.
JO  - J. Dairy Sci.
PY  - 1990
SP  - 2239
EP  - 2251
VL  - 73
AB  - The longevity of mesophilic lactococci in dairy fermentations depends to a large extent on
AB  - whether or not the strains carry effective phage-resistance mechanisms.  Among the different
AB  - systems that exist in lactococci, abortive infection is highly significant because it is the
AB  - cell's strongest defense against the phages that most often disrupt cheese making.
AB  - Phage-resistant strains that carry plasmids encoding abortive defenses have already been
AB  - constructed using genetic strategies.  These strains have been used successfully in commercial
AB  - cheese making since 1986.  Still, our knowledge of the molecular mechanisms underlying
AB  - abortive infection and the means through which it retards phage development is limited.  This
AB  - review addresses abortive infection in lactococci relative to similar phenomena in other
AB  - bacteria.  Further understanding of the abortive infection process should accelerate genetic
AB  - efforts to strengthen this phage defense as well as facilitate efforts to combine it with
AB  - other mechanisms in the construction of specialized strains that are insensitive to attack by
AB  - phage.
ER  -

TY  - JOUR
AU  - Sing, W.D.
AU  - Klaenhammer, T.R.
TI  - Characteristics of phage abortion conferred in lactococci by the conjugal plasmid pTR2030.
JO  - J. Gen. Microbiol.
PY  - 1990
SP  - 1807
EP  - 1815
VL  - 136
AB  - The effect of pTR2030 on phage DNA injection, transfection, release of progeny phage, and cell
AB  - death was evaluated for a number of lactococcal phages. Infection by prolate phage c2 and
AB  - small isometric phage p2 of derivatives of Lactococcus lactis LM2301 with or without pTR2030,
AB  - and infection by small isometric phage phi31 of derivatives of L. lactis NCK202 with or
AB  - without pTR2030 was studied. Phage DNA injection was not affected by pTR2030 when examined
AB  - using blender-resistant-complex assays with 32P-labelled DNA or by observaton of phage
AB  - labelled with the fluorescent dye 4',6-diamidino-2-phenylindole(DAPI). Successful
AB  - transfection of hosts bearing pTR2030 indicated that the plasmid did not retard passage of
AB  - naked phage DNA across the membrane. Infective-centre assays were used to determine whether
AB  - progeny were released from phage-infected pTR2030 hosts that do not support plaque formation
AB  - by small isometric phages. In all cases, pTR2030 reduced the number of infected hosts which
AB  - generated viable phage. When progeny were released, the phage burst size was reduced. The data
AB  - confirmed that pTR2030 interferes with development of prolate and small isometric phages in a
AB  - similar manner via a classical abortive infection mechanism.
ER  -

TY  - JOUR
AU  - Sing, W.D.
AU  - Klaenhammer, T.R.
TI  - Characterization of a recombinant plasmid, pTRK12, encoding restriction/modification and proteolytic activities in lactic streptococci.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1988
SP  - 147
EP  - 147
VL  - 88
AB  - Restriction and modification (R+/M+) activities are widely distributed in
AB  - lactic streptococci and often associated with plasmid DNA.  A
AB  - lactose-fermenting (Lac+) transconjugant (designated Streptococcus lactis
AB  - NCK40) was isolated from matings between S. cremoris TDM1 and a plasmid-free
AB  - recipient.  NCK40 contained a plasmid approximating 100 kb (pTRK11) that
AB  - correlated with Lac+ and conjugal transfer ability (Tra+) and a 13 kb plasmid
AB  - (pTRK10) which was linked to proteolytic activity (Prt+).  S. lactis NCK40
AB  - exhibited phage restriction and modification; the efficiency of plaquing (EOP)
AB  - for phage c2 was 10-3.  Two types of Lac- derivatives of NCK40, both cured of
AB  - pTRK11, were isolated.  One exhibited R-/M- Prt+ and contained pTRK10.  The
AB  - second type was R+/M+ Prt+ and contained a new 30 kb plasmid (pTRK12).  pTRK10
AB  - and pTRK11 were not detected in the R+/M+ Prt+ variant.  Restriction analyses
AB  - demonstrated that pTRK12 (R+/M+ Prt+) contained all detectable regions of
AB  - pTRK10 (Prt+).  Hybridization experiments using a 32P-pTRK11 probe identified
AB  - regions of pTRK12 that originated from the 100 kb plasmid, pTRK11.  These data
AB  - demonstrated that formation of a new 30 kb plasmid encoding R+/M+ and Prt+ was
AB  - the result of recombination events between pTRK10 and pTRK11 occurring upon
AB  - destabilization of Lac+.
ER  -

TY  - JOUR
AU  - Sing, W.D.
AU  - Klaenhammer, T.R.
TI  - Characterization of restriction-modification plasmids from Lactococcus lactis ssp. cremoris and their effects when combined with pTR2030.
JO  - J. Dairy Sci.
PY  - 1991
SP  - 1133
EP  - 1144
VL  - 74
AB  - Three different restriction-modification plasmids (pTRK12, pTRK30, pTRK317)
AB  - were isolated from an industrial starter strain, Lactococcus lactis ssp.
AB  - cremoris TDM1.  A lactose-fermenting transconjugant, Lactococcus lactis ssp.
AB  - lactis NCK40, was isolated from matings between L. lactis ssp. cremoris TDM1
AB  - and a plasmid-free recipient.  The NCK40 transmissible plasmid (pTRK11)
AB  - encoding for restriction modification and a 13.5-kb plasmid (pTRK10) encoding
AB  - proteolytic activity.  Following isolation of lactose-negative derivatives from
AB  - NCK40, a 30.5-kb plasmid, pTRK12, was identified that encoded proteolytic and
AB  - restriction-modification of the identical specificity as pTRK11.  Restriction
AB  - analyses and hybridization experiments indicated that pTRK12 contained
AB  - sequences from pTRK11 and all of pTRK10.  Cotransformation of total plasmid DNA
AB  - from L. lactis ssp. cremoris TDM1 with vector pVS2 identified two other
AB  - restriction-modification plasmids, pTRK30 (28.0 kb) and pTRK317 (15.5 kb).
AB  - Efficiencies of plaquing from phage c2 on restriction-modification
AB  - transconjugants and transformants was 10/2 to 10/4.  The specificity of
AB  - restriction-modification activities conferred by each of the three plasmids was
AB  - different.  When the abortive infection plasmid pTR2030 was combined with
AB  - pTRK30, both phage inhibition phenotypes were expressed.  However, when pTR2030
AB  - was combined with pTRK12, the abortive infection phenotype was not fully
AB  - expressed.  Significant cell death occurred when abortive infection cells
AB  - containing only pTR2030 were infected with phage.  Combining the
AB  - restriction-modification system of pTRK30 with pTR2030 significantly improved
AB  - cell survival following phage infection.  Operation of restriction-modification
AB  - systems in conjunction with the abortive defense mechanism maximized cell
AB  - survival.  The data suggest that cell death is minimized when the lytic cycle
AB  - is halted by restriction before abortive infection responses induce phage
AB  - abortion and kill the cell.
ER  -

TY  - JOUR
AU  - Sing, W.D.
AU  - Klaenhammer, T.R.
TI  - Conjugal transfer of bacteriophage resistance determinants on pTR2030 into Streptococcus cremoris strains.
JO  - Appl. Environ. Microbiol.
PY  - 1986
SP  - 1264
EP  - 1271
VL  - 51
AB  - Agar surface conjugal matings were used to introduce heat-sensitive phage
AB  - resistance (hsp+) determinants carried on the conjugal plasmid pTR2030 into
AB  - Streptococcus cremoris KH, HP, 924, and TDM1.  Lactose-fermenting (Lac+)
AB  - transconjugants were selected from matings of Lac- variants of S. cremoris KH,
AB  - HP, 924, and TDM1 with Streptococcus lactis ME2 or a high-frequency donor, S.
AB  - lactis T-EK1 (pTR1040, Lac+; pTR2030, Hsp+).  For all of the S. cremoris
AB  - strains examined, select Lac+ transconjugants were completely resistant to
AB  - plaquing by their homologous lytic phages.  In all cases the plaquing
AB  - efficiencies were less than 10-9.  Acquisition of a 30-megadalton plasmid
AB  - (pTR2030) in the S. cremoris phage-resistant transconjugants was demonstrated
AB  - by direct plasmid analysis, by hybridization with 32P-labeled probes, or by
AB  - conugal transfer of pTR2030 out of the phage-resistant transconjugants into a
AB  - plasmid-cured recipient, S. lactis LM2302.  Acid production, coagulation
AB  - ability, and proteolytic activity of phage-resistant transconjugants in milk
AB  - were comparable to those of their phage-sensitive parents.  Further, S.
AB  - cremoris phage-resistant transconjugants were not attacked by phage in starter
AB  - culture activity tests, which included a 40C incubation period.  The results
AB  - demonstrated that phage resistance determinants on pTR2030 could be conjugally
AB  - transferred to a variety of S. cremoris strains and confer resistance to phage
AB  - under conditions encountered during cheese manufacture.  Phage-resistant
AB  - transconjugants of S. cremoris M43 and HP were also constructed without the use
AB  - of antibiotic markers to select conjugal recipients from mating mixtures.
ER  -

TY  - JOUR
AU  - Sing, W.D.
AU  - Klaenhammer, T.R.
TI  - A strategy for rotation of different bacteriophage defenses in a lactococcal single-strain started culture system.
JO  - Appl. Environ. Microbiol.
PY  - 1993
SP  - 365
EP  - 372
VL  - 59
AB  - A new strategy for starter culture rotations was developed for a series of phage-resistant
AB  - clones genetically derived from a single strain of Lactococcus lactis subsp. lactis.
AB  - Phage-resistant derivatives carrying different defense systems were constructed via
AB  - conjugatiion with various plasmids encoding abortive infection (Abi/Hsp) and/or restriction
AB  - and modification (R/M) systems of different specificity. The plasmids included pTR2030 (Hsp+
AB  - R+/M+),pTN20 (Abi+ R+/M+), pTRK11 (R+/M+), and pTRK68 (R+/M+). Selected phage-resistant
AB  - transconjugants or transformants were evaluated in different rotation sequences through cycles
AB  - of the Heap-Lawrence starter culture activity test in milk contaminated with phage and when
AB  - from the previous cycle. When used in consecutive sequences, derivative strains carrying the
AB  - R/M systems encoded by pTN20, pTRK11, and pTRK68 retarded phage development when the initial
AB  - levels of phage contamination were below 102 PFU/ml but not when levels were increased to 103
AB  - PFU/ml. Use of a derivative bearing pTR2030 (Hsp+ R+/M+) at the beginning of the rotation
AB  - prevented phage development, even when the inital levels of phage contamination were high (106
AB  - PFU/ml). Alternating the type and specificity of R/M and Abi defenses through the rotation
AB  - prevented phage proliferation and in some cases eliminated contaminting phages. A model
AB  - rotation sequence for the phage defense rotation strategy was developed and performed
AB  - sucessfully over nine cycles of the Heap-Lawrence starter culture activity test in the
AB  - presence of high-titer commercial phage composites. This phage defense rotation strategy is
AB  - designed to protect a highly specilized Lactococcus strain from phage attack during continuous
AB  - and extended use in the dairy industry.
ER  -

TY  - JOUR
AU  - Singh, A.
AU  - Jangir, P.K.
AU  - Kumari, C.
AU  - Sharma, R.
TI  - Genome Sequence of Nitratireductor aquibiodomus Strain RA22.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6307
EP  - 6307
VL  - 194
AB  - The genus Nitratireductor represents nitrate-reducing bacteria from the family
AB  - Phyllobacteriaceae. Here we report the draft genome sequence of Nitratireductor
AB  - aquibiodomus strain RA22, which contains 4,592,790 bp, with a G+C content of
AB  - 61.30%, and has 4,241 protein coding genes.
ER  -

TY  - JOUR
AU  - Singh, A.
AU  - Kumar, J.P.
AU  - Sharma, R.
AU  - Singh, A.
AU  - Kumar, P.A.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of Indibacter alkaliphilus Strain LW1T, Isolated from Lonar Lake, a Haloalkaline Lake in the Buldana District of Maharashtra, India.
JO  - Genome Announcements
PY  - 2013
SP  - e00513
EP  - e00513
VL  - 1
AB  - We report the 5.0-Mb genome sequence of Indibacter alkaliphilus strain LW1(T), isolated from a
AB  - haloalkaline crater lake in the Buldana district, Maharashtra,
AB  - India.
ER  -

TY  - JOUR
AU  - Singh, A.
AU  - Sreenivas, A.
AU  - Sathyanarayana, R.G.
AU  - Pinnaka, A.K.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of Lutibaculum baratangense Strain AMV1T, Isolated from a Mud Volcano in Andamans, India.
JO  - Genome Announcements
PY  - 2014
SP  - e00735
EP  - e00714
VL  - 2
AB  - The 4.3-Mb genome of Lutibaculum baratangense strain AMV1(T), isolated from a soil sample
AB  - collected from a mud volcano in Andamans, India, is reported. The
AB  - draft genome of strain Lutibaculum baratangense AMV1(T) consists of 4,300,776 bp
AB  - with a G+C content of 66.93 mol% and 4,198 predicted coding regions, including 56
AB  - RNAs.
ER  -

TY  - JOUR
AU  - Singh, A.
AU  - Zubko, E.
AU  - Meyer, P.
TI  - Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana.
JO  - Plant J.
PY  - 2008
SP  - 814
EP  - 823
VL  - 56
AB  - Maintenance of cytosine methylation in plants is controlled by three DNA methyltransferases.
AB  - MET1 maintains CG methylation, and DRM1/2 and
AB  - CMT3 act redundantly to enforce non-CG methylation. RPS, a repetitive
AB  - hypermethylated DNA fragment from Petunia hybrida, attracts DNA
AB  - methylation when transferred into Petunia or other species. In
AB  - Arabidopsis thaliana, which does not contain any RPS homologues, RPS
AB  - transgenes are efficiently methylated in all sequence contexts. To test
AB  - which DNA methylation pathways regulate RPS methylation, we examined
AB  - maintenance of RPS methylation in various mutant backgrounds.
AB  - Surprisingly, CG methylation was lost in a drm1/2/cmt3 mutant, and
AB  - non-CG methylation was almost completely eliminated in a met1 mutant.
AB  - An unusual cooperative activity of all three DNA methyltransferases is
AB  - therefore required for maintenance of both CG and non-CG methylation in
AB  - RPS. Other unusual features of RPS methylation are the independence of
AB  - its non-CG methylation from the RNA-directed DNA methylation (RdDM)
AB  - pathway and the exceptional maintenance of methylation at a CC(m)TGG
AB  - site in some epigenetic mutants. This is indicative of activity of a
AB  - methylation system in plants that may have evolved from the DCM
AB  - methylation system that controls CC(m)WGG methylation in bacteria. Our
AB  - data suggest that strict separation of CG and non-CG methylation
AB  - pathways does not apply to all target regions, and that caution is
AB  - required in generalizing methylation data obtained for individual
AB  - genomic regions.
ER  -

TY  - JOUR
AU  - Singh, A.K.
AU  - Chaudhary, P.
AU  - Macwan, A.S.
AU  - Diwedi, U.N.
AU  - Kumar, A.
TI  - Selective loss of lin genes from hexachlorocyclohexane-degrading Pseudomonas aeruginosa ITRC-5 under different growth conditions.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2007
SP  - 895
EP  - 901
VL  - 76
AB  - The chlorinated insecticide a-hexachlorocyclohexane
AB  - (a-HCH) is sequentially metabolized by the
AB  - products of linA, linB, linC, linD, linE, and linF genes to
AB  - a-ketoadipate, which is subsequently mineralized. Two or
AB  - more copies of these genes are present in the bacterium
AB  - Pseudomonas aeruginosa ITRC-5 that was isolated earlier
AB  - by selective enrichment on technical-HCH. At least one
AB  - copy of linA, linB, linC, linD, and possibly linE is lost from
AB  - ITRC-5 upon its growth on a-HCH. All the lin genes,
AB  - however, are lost when the bacterium was grown in Luria-
AB  - Bertani (LB) medium. The loss of lin genes is accompanied
AB  - with the loss/rearrangement of insertion sequence IS6100
AB  - genes. Concomitant to the loss of lin genes, the degradation
AB  - of HCH-isomers by "a-HCH grown cells" is slower, when
AB  - compared with "technical-HCH grown cells", and is
AB  - completely lost by "LB-grown cells". The selective loss
AB  - of lin genes during different growth conditions has not been
AB  - reported before and is expected to help in understanding the
AB  - dynamism of degradative genes.
ER  -

TY  - JOUR
AU  - Singh, A.K.
AU  - Chettri, B.
AU  - Ghosh, A.
AU  - Chikara, S.K.
AU  - Tripathi, T.
TI  - Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Acinetobacter pittii Strain ABC Isolated from Noonmati Refinery, Assam, India.
JO  - Genome Announcements
PY  - 2017
SP  - e01264
EP  - e01217
VL  - 5
AB  - We report here the 3.84-Mb draft genome sequence of hydrocarbon-degrading Acinetobacter pittii
AB  - strain ABC isolated from oil-contaminated soil in Guwahati,
AB  - India. The genome sequence contains 3,602 coding sequences and a G+C content of
AB  - 38.83%. This is the first report of the genome sequence of an Acinetobacter
AB  - pittii from an oil-contaminated environment.
ER  -

TY  - JOUR
AU  - Singh, A.K.
AU  - Chettri, B.
AU  - Ghosh, A.
AU  - Chikara, S.K.
AU  - Tripathi, T.
TI  - Draft Genome Sequence of Novosphingobium panipatense Strain P5:ABC, Isolated from Hydrocarbon-Contaminated Soil from Noonmati Refinery, Assam, India.
JO  - Genome Announcements
PY  - 2017
SP  - e01265
EP  - e01217
VL  - 5
AB  - Novosphingobium panipatense P5:ABC is a hydrocarbon-degrading bacterium isolated  from
AB  - petroleum-contaminated soil. Here, we present the 5.74-Mb draft genome
AB  - sequence with 5,206 genes and an average G+C content of 64.7%. The genomic
AB  - information will improve our understanding of the diversity of N. panipatense and
AB  - the mechanisms of microbe-based hydrocarbon degradation.
ER  -

TY  - JOUR
AU  - Singh, A.K.
AU  - Karaulia, P.
AU  - Chopra, S.
AU  - Dasgupta, A.
TI  - Draft Genome Sequence of Mycobacterium fortuitum Isolated from Murine Brain.
JO  - Genome Announcements
PY  - 2016
SP  - e00191
EP  - e00116
VL  - 4
AB  - Mycobacterium fortuitumsubsp.fortuitumATCC 6841 is a type and standard laboratory testing
AB  - quality control strain. We report here the completed draft genome
AB  - sequence for a strain isolated from the brains ofM. fortuitum-infected mice.
ER  -

TY  - JOUR
AU  - Singh, A.K.
AU  - Sangwan, N.
AU  - Sharma, A.
AU  - Gupta, V.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Draft Genome Sequence of Sphingobium quisquiliarum Strain P25T, a Novel Hexachlorocyclohexane (HCH)-Degrading Bacterium Isolated from an HCH Dumpsite.
JO  - Genome Announcements
PY  - 2013
SP  - e00717
EP  - e00713
VL  - 1
AB  - Here, we report the draft genome sequence (4.2 Mb) of Sphingobium quisquiliarum strain P25(T),
AB  - a natural lin (genes involved in degradation of hexachlorocyclohexane [HCH] isomers) variant
AB  - genotype, isolated from a heavily contaminated (450 mg HCH/g of soil) HCH dumpsite.
ER  -

TY  - JOUR
AU  - Singh, D.
AU  - Chandrababunaidu, M.M.
AU  - Panda, A.
AU  - Sen, D.
AU  - Bhattacharyya, S.
AU  - Adhikary, S.P.
AU  - Tripathy, S.
TI  - Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India.
JO  - Genome Announcements
PY  - 2015
SP  - e00064
EP  - e00015
VL  - 3
AB  - The draft genome assembly of Hassallia byssoidea strain VB512170 with a genome size of ~13 Mb
AB  - and 10,183 protein-coding genes in 62 scaffolds is reported here
AB  - for the first time. This is a terrestrial hydrophobic cyanobacterium isolated
AB  - from monuments in India. We report several copies of luciferase and antibiotic
AB  - genes in this organism.
ER  -

TY  - JOUR
AU  - Singh, D.K.
AU  - Kumar, A.
AU  - Tiwari, A.K.
AU  - Sankarasubramanian, J.
AU  - Vishnu, U.S.
AU  - Sridhar, J.
AU  - Gunasekaran, P.
AU  - Rajendhran, J.
TI  - Draft Genome Sequence of Brucella abortus Virulent Strain 544.
JO  - Genome Announcements
PY  - 2015
SP  - e00419
EP  - e00415
VL  - 3
AB  - Here, we present the draft genome sequence and annotation of Brucella abortus virulent strain
AB  - 544. The genome of this strain is 3,289,405 bp long, with 57.2%
AB  - G+C content. A total of 3,259 protein-coding genes and 60 RNA genes were
AB  - predicted.
ER  -

TY  - JOUR
AU  - Singh, I.
AU  - Beuck, C.
AU  - Bhattacharya, A.
AU  - Hecker, W.
AU  - Parmar, V.S.
AU  - Weinhold, E.
AU  - Seitz, O.
TI  - Abasic site stabilization by aromatic DNA base surrogates: High-affinity binding to a base-flipping DNA-methyltransferase.
JO  - Pure Appl. Chem.
PY  - 2004
SP  - 1563
EP  - 1570
VL  - 76
AB  - DNA-methyltransferases catalyze the sequence-specific transfer of the methyl group of
AB  - S-adenosylmethionine to target bases in genomic DNA.
AB  - For gaining access to their target embedded within a double-helical
AB  - structure, DNA-methyltransferases (DNA-MTases) rotate the target base
AB  - out of the DNA helix. This base-flipping leads to the formation of an
AB  - apparent abasic site. MTases such as cytosine-specific M.HhaI and
AB  - M.HaeIII and also the repair enzyme uracil DNA glycosylase (UDG)
AB  - insert amino acid side chains into the opened space and/or rearrange
AB  - base-pairing. The adenine-specific DNA MTase M.TaqI binds without
AB  - amino acid insertion. This binding mode allows for a substitution of
AB  - the orphaned thymine with larger DNA base surrogates without steric
AB  - interference by inserted amino acid side chains. DNA containing
AB  - pyrenyl, naphthyl, acenaphthyl, and biphenyl residues was tested in
AB  - M.TaqI binding studies. The synthesis of DNA building blocks required
AB  - the formation of a C-glycosidic bond, which was established by using
AB  - protected 1-chloro-2-deoxyribose as glycosyl donor and organocuprates
AB  - as glycosyl acceptors. It is shown that all of the base surrogates
AB  - enhanced the binding affinity to M.TaqI. Incorporation of pyrene
AB  - increased the binding affinity by a factor of 400. Interestingly, there
AB  - is a correlation between the observed order of dissociation constants
AB  - and the ability of a base surrogate to stabilize abasic sites in model
AB  - duplexes.
ER  -

TY  - JOUR
AU  - Singh, J.
AU  - Klar, A.J.S.
TI  - Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast.
JO  - Genes Dev.
PY  - 1992
SP  - 186
EP  - 196
VL  - 6
AB  - Unlike higher eukaryotes, where an inverse correlation has been generally
AB  - observed between gene expression and methylation of CpG sites, the budding
AB  - yeast Saccharomyces cerevisiae lacks DNA methylation.  Gene regulatory
AB  - mechanisms can function independently of DNA methylation in yeast, and yeast
AB  - strains expressing foreign DNA methylases that modify adenine and CpG residues
AB  - have been found to be viable.  We have used such strains to determine whether
AB  - the transcriptional status of genes can influence the level of their DNA
AB  - methylation in vivo.  Several genes were tested, for example, GAL1, -7, and
AB  - -10, PHO5, HMRa and HML alpha, and STE2 and STE3.  Surprisingly, we found that
AB  - all the genes displayed several fold more methylation in the expressed state as
AB  - compared to the repressed state.  This procedure serves as a novel in vivo
AB  - probe for the chromatin structure of yeast and potentially for higher
AB  - eukaryotes.
ER  -

TY  - JOUR
AU  - Singh, M.
AU  - Sasaki, T.
AU  - Matsuo, M.
AU  - Morimoto, Y.
AU  - Aiba, Y.
AU  - Hiramatsu, K.
TI  - Complete Genome Sequence of the Drug-Naive Classical Staphylococcus aureus Strain FDA209P.
JO  - Genome Announcements
PY  - 2015
SP  - e01343
EP  - e01315
VL  - 3
AB  - We report the complete genome sequence of the methicillin-sensitive Staphylococcus aureus
AB  - (MSSA) strain FDA209P (ATCC 6538P and NCTC 7447).
ER  -

TY  - JOUR
AU  - Singh, M.P.
AU  - Lown, J.W.
TI  - Inhibitory effects of a GC-sequence- and minor groove-binding Hoechst 33258 analogue on DNA cleavage by selected restriction endonucleases.
JO  - J. Biomol. Struct. Dyn.
PY  - 1995
SP  - A220
EP  - A220
VL  - 12
AB  - In continuance of our research efforts in the area of employing the important features of
AB  - ligand-DNA molecular recognition in expanding the design and development of minor groove
AB  - binding class of compounds, we recently reported a bis(pyridoimidazole) analogue of Hoechst
AB  - 33258 and demonstrated its preference for selective binding to a GC-rich sequence.  Such
AB  - compounds offer an approach to the experimental manipulation of sequence-specific protein-DNA
AB  - interactions.  A convenient way to test this hypothesis is to look for the effects on the
AB  - DNA-cleavage activity of restriction enzymes with recognition sites that are comparable in
AB  - size and nature to the ligand binding sites.  We have observed distinct inhibitory effects of
AB  - the bis(pyridoimidazole) compound on the cleavage of EcoRI-linearized pBR322 DNA in individual
AB  - agarose gel electrophoresis assays by three selected endonucleases, MscI (at 5'-TGGCCA),
AB  - NruI (at 5'TCGCGA), and FspI (at 5'-TGCGCA).  The extent to which this minor groove binding
AB  - ligand provides protection of the GC-rich sites towards restriction cleavage can be ranked, in
AB  - qualitative terms, as TGGCCA >> TCGCGA > TGCGCA.  It is important to recognize that the
AB  - restriction enzymes are widely believed to interact through the major groove of their cognate
AB  - DNA sequences and the observed effects presumably arise from changes in the helix conformation
AB  - brought about by the minor groove binding ligand.
ER  -

TY  - JOUR
AU  - Singh, N.
AU  - Duenas-Gonzalez, A.
AU  - Lyko, F.
AU  - Medina-Franco, J.L.
TI  - Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1.
JO  - ChemMedChem
PY  - 2009
SP  - 792
EP  - 799
VL  - 4
AB  - DNA methyltransferases (DNMTs) are a family of enzymes that methylate DNA at the C5 position
AB  - of cytosine residues and their inhibition is a
AB  - promising strategy for the treatment of various developmental and
AB  - proliferative diseases, particularly cancers. In the present study, a
AB  - binding model for hydralazine, with a validated homology model of human
AB  - DNMT, was developed by the use of automated molecular docking and
AB  - molecular dynamics simulations. The docking protocol was validated by
AB  - predicting the binding mode of 2'-deoxycytidine, 5-azacytidine, and
AB  - 5-aza-2'-deoxycytidine. The inhibitory activity of hydralazine toward
AB  - DNMT may be rationalized at the molecular level by similar interactions
AB  - within the binding pocket (e.g., by a similar pharmacophore) as
AB  - established by substrate-like deoxycytidine analogues. These
AB  - interactions involve a complex network of hydrogen bonds with arginine
AB  - and glutamic acid residues that also play a major role in the mechanism
AB  - of DNA methylation. Despite the different scaffolds of other
AB  - non-nucleoside DNMT inhibitors such as procaine and procainamide, the
AB  - current modeling work reveals that these drugs exhibit similar
AB  - interactions within the DNMT1 binding site. These findings are valuable
AB  - in guiding the rational design and virtual screening of novel DNMT
AB  - inhibitors.
ER  -

TY  - JOUR
AU  - Singh, N.K.
AU  - Carlson, C.
AU  - Sani, R.K.
AU  - Venkateswaran, K.
TI  - Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep-Subsurface Environment.
JO  - Genome Announcements
PY  - 2017
SP  - e00405
EP  - e00417
VL  - 5
AB  - The whole-genome sequences of seven thermophiles that could grow at >55 degrees C, but not at
AB  - 37 degrees C, were generated. These thermophilic bacteria will play
AB  - a useful role as model microorganisms, and analyzing their genomes will help to
AB  - understand the observed production of novel bioactive compounds, including
AB  - thermozymes and macromolecules.
ER  -

TY  - JOUR
AU  - Singh, N.K.
AU  - Kumar, S.
AU  - Raghava, G.P.
AU  - Mayilraj, S.
TI  - Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16.
JO  - Genome Announcements
PY  - 2013
SP  - e0013713
EP  - e0013713
VL  - 1
AB  - We report the 4.0-Mb draft genome sequence of Acinetobacter baumannii strain MSP4-16, isolated
AB  - from a mangrove soil sample from Parangipettai (11 degrees
AB  - 30'N, 79 degrees 47'E), Tamil Nadu, India. The draft genome sequence of strain
AB  - MSP4-16 consists of 3,944,542 bp, with a G+C content of 39%, 5,387 protein coding
AB  - genes, and 69 RNAs.
ER  -

TY  - JOUR
AU  - Singh, N.N.
AU  - Lambowitz, A.M.
TI  - Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 361
EP  - 386
VL  - 309
AB  - Group II intron mobility occurs by a target DNA-primed reverse transcription mechanism in
AB  - which the intron RNA reverse splices directly into one strand of a double-stranded DNA target
AB  - site, while the intron-encoded protein cleaves the opposite strand and uses it as a primer to
AB  - reverse transcribe the inserted intron RNA. The group II intron endonuclease, which mediates
AB  - this process, is an RNP particle that contains the intron-encoded protein and the excised
AB  - intron RNA and uses both cooperatively to recognize DNA target sequences. Here, we analyzed
AB  - the interaction of the Lactococcus lactis Ll.LtrB group II intron endonuclease with its DNA
AB  - target site by DNA footprinting and modification-interference approaches. In agreement with
AB  - previous mutagenesis experiments showing a relatively large target site, DNase I protection
AB  - extends from position -25 to +19 from the intron-insertion site on the top strand and from -28
AB  - to +16 on the bottom strand. Our results suggest that the protein first recognizes a small
AB  - number of specific bases in the distal 5'-exon region of the DNA target site via major-groove
AB  - interactions. These base interactions together with additional phosphodiester-backbone
AB  - interactions along one face of the helix promote DNA unwinding, enabling the intron RNA to
AB  - base-pair to DNA top-strand positions -12 to +3 for reverse splicing. Notably, DNA unwinding
AB  - extends to at least position +6, somewhat beyond the region that base-pairs with the intron
AB  - RNA, but is not dependent on interaction of the conserved endonuclease domain with the 3'
AB  - exon. Bottom-strand cleavage occurs after reverse splicing and requires recognition of a small
AB  - number of additional bases in the 3' exon, the most critical being T+5 in the now
AB  - single-stranded downstream region of the target site. Our results provide the first detailed
AB  - view of the interaction of a group II intron endonuclease with its DNA target site. Copyright
AB  - 2001 Academic Press.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Aronoff, D.M.
AU  - Davies, H.D.
AU  - Manning, S.D.
TI  - Draft Genome Sequence of an Invasive Streptococcus agalactiae Isolate Lacking Pigmentation.
JO  - Genome Announcements
PY  - 2016
SP  - e00015
EP  - e00016
VL  - 4
AB  - This report provides the whole-genome sequence of Streptococcus agalactiae isolate GB00037
AB  - isolated from a newborn in Calgary, Canada. This serotype V
AB  - isolate is unique because it lacks pigment production previously shown to be
AB  - critical for S. agalactiae virulence.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Kapse, N.
AU  - Roy, U.
AU  - Singh, S.M.
AU  - Dhakephalkar, P.K.
TI  - Draft Genome Sequence of Permafrost Bacterium Nesterenkonia sp. Strain PF2B19, Revealing a Cold Adaptation Strategy and Diverse Biotechnological Potential.
JO  - Genome Announcements
PY  - 2017
SP  - e00133
EP  - e00117
VL  - 5
AB  - Nesterenkonia sp. strain PF2B19, a psychrophilic bacterium, was isolated from 44,800-year-old
AB  - permafrost. The draft genome sequence of this strain revealed the
AB  - presence of genes involved in the production of cold active enzymes, carotenoid
AB  - biosynthesis, fatty acid biosynthesis, and resistance to heavy metals. These
AB  - results show the immense potential of the strain.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Kumari, R.
AU  - Mukherjee, U.
AU  - Saxena, A.
AU  - Sood, U.
AU  - Lal, R.
TI  - Draft Genome Sequence of Rifamycin Derivatives Producing Amycolatopsis mediterranei Strain DSM 46096/S955.
JO  - Genome Announcements
PY  - 2014
SP  - e00837
EP  - e00814
VL  - 2
AB  - Amycolatopsis mediterranei DSM 46096 produces antibiotics of the rifamycin family,
AB  - 27-demethoxy-27-hydroxyrifamycin B,
AB  - 25-desacetyl-27-demethoxy-27-hydroxyrifamycin, and
AB  - 27-demethoxy-27-hydroxyrifamycin SV, which are effective against Gram-negative
AB  - bacteria. Here, we present the draft genome of A. mediterranei 46096 (approx.
AB  - 10.2 Mbp) having 104 contigs with a GC content of 71.3% and 9,382 coding
AB  - sequences.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Mosci, R.
AU  - Rudrik, J.T.
AU  - Manning, S.D.
TI  - Draft Genome Sequence of a Diarrheagenic Morganella morganii Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e01165
EP  - e01115
VL  - 3
AB  - This is a report of the whole-genome draft sequence of a diarrheagenic Morganella morganii
AB  - isolate from a patient in Michigan, USA. This genome represents an important addition to the
AB  - limited number of pathogenic M. morganii genomes available.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Springman, A.C.
AU  - Davies, H.D.
AU  - Manning, S.D.
TI  - Whole-Genome Shotgun Sequencing of a Colonizing Multilocus Sequence Type 17 Streptococcus agalactiae Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6005
EP  - 6005
VL  - 194
AB  - This report highlights the whole-genome shotgun draft sequence for a Streptococcus agalactiae
AB  - strain representing multilocus sequence type (ST) 17,
AB  - isolated from a colonized woman at 8 weeks postpartum. This sequence represents
AB  - an important addition to the published genomes and will promote comparative
AB  - genomic studies of S. agalactiae recovered from diverse sources.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Tripathi, P.
AU  - Muniyappa, K.
TI  - Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are  crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not.
JO  - Protein Sci.
PY  - 2010
SP  - 111
EP  - 123
VL  - 19
AB  - Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing
AB  - endonuclease (PI-MleI). Most inteins (intein
AB  - endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their
AB  - active center. A common feature of LAGLIDADG-type homing endonucleases
AB  - is that they recognize and cleave the same or very similar DNA
AB  - sequences. However, PI-MleI is distinctive from other members of the
AB  - family of LAGLIDADG-type HEases for its modular structure with
AB  - functionally separable domains for DNA-binding and cleavage, each with
AB  - distinct sequence preferences. Sequence alignment analyses of PI-MleI
AB  - revealed three putative LAGLIDADG motifs; however, there is conflicting
AB  - bioinformatics data in regard to their identity and specific location
AB  - within the intein polypeptide. To resolve this conflict and to
AB  - determine the active-site residues essential for DNA target site
AB  - recognition and double-stranded DNA cleavage, we performed
AB  - site-directed mutagenesis of presumptive catalytic residues in the
AB  - LAGLIDADG motifs. Analysis of target DNA recognition and kinetic
AB  - parameters of the wild-type PI-MleI and its variants disclosed that the
AB  - two amino acid residues, Asp(122) (in Block C) and Asp(193) (in
AB  - functional Block E), are crucial to the double-stranded DNA
AB  - endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not.
AB  - However, despite the reduced catalytic activity, the PI-MleI variants,
AB  - like the wild-type PI-MleI, generated a footprint of the same length
AB  - around the insertion site. The D122T variant showed significantly
AB  - reduced catalytic activity, and D122A and D193A mutations although
AB  - failed to affect their DNA-binding affinities, but abolished the
AB  - double-stranded DNA cleavage activity. On the other hand, D122C variant
AB  - showed approximately twofold higher double-stranded DNA cleavage
AB  - activity, compared with the wild-type PI-MleI. These results provide
AB  - compelling evidence that Asp(122) and Asp(193) in DOD motif I and II,
AB  - respectively, are bona fide active-site residues essential for DNA
AB  - cleavage activity. The implications of these results are discussed in
AB  - this report.
ER  -

TY  - JOUR
AU  - Singh, P.
AU  - Tripathi, P.
AU  - Silva, G.H.
AU  - Pingoud, A.
AU  - Muniyappa, K.
TI  - Characterization of Mycobacterium leprae RecA Intein, a LAGLIDADG Homing Endonuclease, Reveals a Unique Mode of DNA Binding, Helical Distortion, and Cleavage Compared with a Canonical LAGLIDADG Homing Endonuclease.
JO  - J. Biol. Chem.
PY  - 2009
SP  - 25912
EP  - 25928
VL  - 284
AB  - Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of
AB  - essential genes, has retained intervening
AB  - sequences in four of its genes implicating a vital role for them in the
AB  - survival of the leprosy bacillus. A single in-frame intervening
AB  - sequence has been found embedded within its recA gene. Comparison of
AB  - the M. leprae recA intervening sequence with the known intervening
AB  - sequences indicated that it has the consensus amino acid sequence
AB  - necessary for being a LAGLIDADG-type homing endonuclease. In light of
AB  - massive gene decay and function loss in the leprosy bacillus, we sought
AB  - to investigate whether its recA intervening sequence encodes a
AB  - catalytically active homing endonuclease. Here we show that the
AB  - purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and
AB  - displays endonuclease activity in the presence of alternative divalent
AB  - cations, Mg2+ or Mn2+. A combination of approaches, including four
AB  - complementary footprinting assays such as DNase I,
AB  - copper-phenanthroline, methylation protection, and KMnO4, enhancement
AB  - of 2-aminopurine fluorescence, and mapping of the cleavage site
AB  - revealed that PI-MleI binds to cognate DNA flanking its insertion site,
AB  - induces helical distortion at the cleavage site, and generates two
AB  - staggered double strand breaks. Taken together, these results implicate
AB  - that PI-MleI possesses a modular structure with separate domains for
AB  - DNA target recognition and cleavage, each with distinct sequence
AB  - preferences. From a biological standpoint, it is tempting to speculate
AB  - that our findings have implications for understanding the evolution of
AB  - the LAGLIDADG family of homing endonucleases.
ER  -

TY  - JOUR
AU  - Singh, R.
AU  - Gradnigo, J.
AU  - White, D.
AU  - Lipzen, A.
AU  - Martin, J.
AU  - Schackwitz, W.
AU  - Moriyama, E.
AU  - Blum, P.
TI  - Complete Genome Sequence of an Evolved Thermotoga maritima Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00557
EP  - e00515
VL  - 3
AB  - Thermotoga maritima is a hyperthermophilic bacterium with a small genome (1.86 Mbp). Genome
AB  - resequencing of Tma200, a derivative produced by experimental
AB  - microbial evolution, revealed the occurrence of deletions and substitution
AB  - mutations. Their identification contributes to a better understanding of genome
AB  - instability in this organism.
ER  -

TY  - JOUR
AU  - Singh, R.N.
AU  - Gaba, S.
AU  - Yadav, A.N.
AU  - Gaur, P.
AU  - Gulati, S.
AU  - Kaushik, R.
AU  - Saxena, A.K.
TI  - First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 54
EP  - 54
VL  - 11
AB  - Arthrobacter agilis strain L77, is a plant growth promoting and cold active hydrolytic enzymes
AB  - producing psychrotrophic bacterium, isolated from Pangong
AB  - Lake, a subglacial lake in north western Himalayas, India. Genome analysis
AB  - revealed metabolic versatility with genes involved in metabolism and cold shock
AB  - adaptation, utilization and biosynthesis of diverse structural and storage
AB  - polysaccharides such as plant based carbon polymers. The genome of Arthrobacter
AB  - agilis strain L77 consists of 3,608,439 bp (3.60 Mb) of a circular chromosome.
AB  - The genome comprises of 3316 protein coding genes and 74 RNA genes, 725
AB  - hypothetical proteins, 25 pseudo-genes and 1404 unique genes.
ER  -

TY  - JOUR
AU  - Singh, R.N.
AU  - Saldanha, R.J.
AU  - D'Souza, L.M.
AU  - Lambowitz, A.M.
TI  - Binding of a group II intron-encoded reverse transcriptase/maturase to its high affinity intron RNA binding site involves sequence-specific recognition and autoregulates translation.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 287
EP  - 303
VL  - 318
AB  - Mobile group II introns encode reverse transcriptases that bind specifically to the intron
AB  - RNAs to promote both intron mobility and RNA splicing (maturase activity). Previous studies
AB  - with the Lactococcus lactis Ll.LtrB intron suggested a model in which the intron-encoded
AB  - protein (LtrA) binds first to a primary high-affinity binding site in intron subdomain DIVa,
AB  - an idiosyncratic structure at the beginning of the LtrA coding sequence, and then makes
AB  - additional contacts with conserved regions of the intron to fold the RNA into the
AB  - catalytically active structure. Here, we analyzed the DIVa binding site by iterative in vitro
AB  - selection and in vitro mutagenesis. Our results show that LtrA binds to a small region at the
AB  - distal end of DIVa that contains the ribosome-binding site and initiation codon of the LtrA
AB  - open reading frame. The critical elements are in a small stem-loop structure emanating from a
AB  - purine-rich internal loop, with both sequence and structure playing a role in LtrA
AB  - recognition. The ribosome-binding site falls squarely within the LtrA-binding region and is
AB  - sequestered directly by the binding of LtrA or by stabilization of the small stem-loop or
AB  - both. Finally, by using LacZ fusions in Escherichia coli, we show that the binding of LtrA to
AB  - DIVa down-regulates translation. This mode of regulation limits accumulation of the
AB  - potentially deleterious intron-encoded protein and may facilitate splicing by halting ribosome
AB  - entry into the intron. The recognition of the DIVa loop-stem-loop structure accounts, in part,
AB  - for the intron specificity of group II intron maturases and has parallels in
AB  - template-recognition mechanisms used by other reverse transcriptases.
ER  -

TY  - JOUR
AU  - Singh, S.K.
AU  - Major, S.R.
AU  - Cai, H.
AU  - Chen, F.
AU  - Hill, R.T.
AU  - Li, Y.
TI  - Draft Genome Sequences of Cloacibacterium normanense IMET F, a Microalgal Growth-Promoting Bacterium, and Aeromonas jandaei IMET J, a Microalgal  Growth-Inhibiting Bacterium.
JO  - Genome Announcements
PY  - 2018
SP  - e00503
EP  - e00518
VL  - 6
AB  - We report here the whole-genome sequencing results of two bacterial isolates, Aeromonas
AB  - jandaei IMET J and Cloacibacterium normanense IMET F, that inhibit
AB  - (possibly due to denitrifying gene clusters) and promote (possibly due to an
AB  - ammonification system), respectively, the growth of the microalgal strains
AB  - Scenedesmus HTB1 and Chlorella vulgaris 1807.
ER  -

TY  - JOUR
AU  - Singh, S.V.
AU  - Kumar, N.
AU  - Singh, S.N.
AU  - Bhattacharya, T.
AU  - Sohal, J.S.
AU  - Singh, P.K.
AU  - Singh, A.V.
AU  - Singh, B.
AU  - Chaubey, K.K.
AU  - Gupta, S.
AU  - Sharma, N.
AU  - Kumar, S.
AU  - Raghava, G.P.
TI  - Genome Sequence of the 'Indian Bison Type' Biotype of Mycobacterium avium subsp.  paratuberculosis Strain S5.
JO  - Genome Announcements
PY  - 2013
SP  - e00005
EP  - e00013
VL  - 1
AB  - We report the 4.79-Mb genome sequence of the 'Indian Bison Type' biotype of subsp. strain
AB  - S5, isolated from a terminally sick Jamunapari goat at the CIRG
AB  - (Central Institute for Research on Goats) farm in India. This draft genome will
AB  - help in studying novelties of this biotype, which is widely distributed in
AB  - animals and human beings in India.
ER  -

TY  - JOUR
AU  - Singh, T.R.
AU  - Pardasani, K.R.
TI  - In silico Analysis of Evolutionary Patterns in Restriction Endonucleases.
JO  - In Silico Biology
PY  - 2009
SP  - 45
EP  - 53
VL  - 9
AB  - Restriction endonucleases represent one of the best studied examples of DNA binding proteins.
AB  - Type II restriction endonucleases recognize short
AB  - sequences of foreign DNA and cleave the target on both strands with
AB  - remarkable sequence specificity. Type II restriction endonucleases are
AB  - part of restriction modification systems. Restriction modification
AB  - systems occur ubiquitously among bacteria and archaea. Restriction
AB  - endonucleases are indispensable tools in molecular biology and
AB  - biotechnology. They are important model system for specific
AB  - protein-nucleic acid interactions and also serve as good example for
AB  - investigating structural, functional and evolutionary relationships
AB  - among various biomolecules. The interaction between restriction
AB  - endonucleases and their recognition sequences plays a crucial role in
AB  - biochemical activities like catalytic site/metal binding, DNA repair
AB  - and recombination etc. We study various patterns in restriction
AB  - endonucleases type II and analyzed their structural, functional and
AB  - evolutionary role. Our studies support X-ray crystallographic studies,
AB  - arguing for divergence and molecular evolution. Conservation patterns
AB  - of the nuclease superfamily have also been analyzed by estimating
AB  - site-specific evolutionary rates for the analyzed structures related to
AB  - respective chains in this study.
ER  -

TY  - JOUR
AU  - Singh-Moodley, A.
AU  - Perovic, O.
AU  - Mtshali, S.
AU  - Ismail, A.
AU  - Allam, M.
TI  - Draft Genome Sequence of a Multidrug-Resistant Serratia marcescens Strain, Isolated from a Patient with Peritoneal Cancer in South Africa.
JO  - Genome Announcements
PY  - 2017
SP  - e00580
EP  - e00517
VL  - 5
AB  - We report here the draft genome sequence of Serratia marcescens ML2637, isolated  from a South
AB  - African pediatric patient in the intensive care unit with peritoneal
AB  - cancer. The genome comprised 5,718,350 bp, with a 59.1% G+C content. There were
AB  - 5,594 predicted genes, including 5,301 protein-coding genes, 199 pseudogenes, and
AB  - 94 RNA genes.
ER  -

TY  - JOUR
AU  - Singha, H.
AU  - Malik, P.
AU  - Saini, S.
AU  - Khurana, S.K.
AU  - Elschner, M.C.
AU  - Mertens, K.
AU  - Barth, S.A.
AU  - Tripathi, B.N.
AU  - Singh, R.K.
TI  - Draft Genome Sequences of Two Clinical Isolates of Burkholderia mallei Obtained from Nasal Swabs of Glanderous Equines in India.
JO  - Genome Announcements
PY  - 2017
SP  - e00063
EP  - e00017
VL  - 5
AB  - Burkholderia mallei is a Gram-negative coccobacillus which causes glanders-a fatal disease of
AB  - equines that may occasionally be transmitted to humans. Several
AB  - cases of outbreaks have been reported from India since 2006. This paper presents
AB  - draft genome sequences of two B. mallei strains isolated from equines affected by
AB  - glanders in India.
ER  -

TY  - JOUR
AU  - Singha, L.P.
AU  - Kotoky, R.
AU  - Pandey, P.
TI  - Draft Genome Sequence of Pseudomonas fragi Strain DBC, Which Has the Ability To Degrade High-Molecular-Weight Polyaromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2017
SP  - e01347
EP  - e01317
VL  - 5
AB  - Pseudomonas fragi strain DBC was isolated from crude oil-contaminated soil. The genome of P.
AB  - fragi DBC is comprised of 5,072,304 bp with 54.09% GC content. Genes
AB  - for degradation of polyaromatic hydrocarbons were found in the genome, in
AB  - addition to genetic elements for related physiological functions such as
AB  - chemotaxis, detoxification, and quorum sensing.
ER  -

TY  - JOUR
AU  - Singleton, D.R.
AU  - Dickey, A.N.
AU  - Scholl, E.H.
AU  - Wright, F.A.
AU  - Aitken, M.D.
TI  - Complete Genome Sequence of a Novel Bacterium within the Family Rhodocyclaceae That Degrades Polycyclic Aromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2015
SP  - e00251
EP  - e00215
VL  - 3
AB  - A polycyclic aromatic hydrocarbon-degrading bacterium designated strain Ca6, a member of the
AB  - family Rhodocyclaceae and a representative of the uncharacterized
AB  - pyrene group 1 (PG1), was isolated and its genome sequenced. The presence of
AB  - several genes suspected to be associated with PG1 was confirmed, and additional
AB  - genes for aromatic compound metabolism were detected.
ER  -

TY  - JOUR
AU  - Singleton, D.R.
AU  - Dickey, A.N.
AU  - Scholl, E.H.
AU  - Wright, F.A.
AU  - Aitken, M.D.
TI  - Complete Genome Sequence of a Bacterium Representing a Deep Uncultivated Lineage  within the Gammaproteobacteria Associated with the Degradation of Polycyclic  Aromatic Hydrocarbons.
JO  - Genome Announcements
PY  - 2016
SP  - e01086
EP  - e01016
VL  - 4
AB  - The bacterial strain TR3.2, representing a novel deeply branching lineage within  the
AB  - Gammaproteobacteria, was isolated and its genome sequenced. This isolate is
AB  - the first cultivated representative of the previously described 'Pyrene Group 2'
AB  - (PG2) and represents a variety of environmental sequences primarily associated
AB  - with petrochemical contamination and aromatic hydrocarbon degradation.
ER  -

TY  - JOUR
AU  - Sinha, D.
AU  - Bakhshi, M.R.
AU  - Vora, R.K.
AU  - Kirby, E.P.
AU  - Budzynski, A.Z.
TI  - Engineering DNA and protein chimeras utilizing coding sequences of restriction sites.
JO  - Anal. Biochem.
PY  - 1996
SP  - 205
EP  - 208
VL  - 238
AB  - Various engineering strategies have been employed so far to generate chimeric proteins for the
AB  - purpose of structure-function studies.  None of these methods, except splicing by overlap
AB  - extension (SOE)3, however, can be considered as providing a general methodology for generating
AB  - chimeras.  SOE is a powerful technique considering its simplicity and versatility.  One
AB  - limitation of the SOE procedure, however, is the difficulty in amplification when the chimera
AB  - is large.  In the present report, we describe a procedure for generating chimeras by altering
AB  - the codon sequences of one amino acid pair of the seven around the junction using the PCR
AB  - technique.  The altered nucleotide sequence of the amino acid pair creates a restriction site
AB  - that is utilized for formation of the desired chimera.  This procedure, like the SOE method,
AB  - eliminates the need for single-stranded template and viral vector intermediates, and thus does
AB  - not require a cloning and screening step.  However, in engineering relatively long chimeras,
AB  - the described procedure is more advantageous because this method amplifies smaller fragments.
AB  - The present technique is simple and 100% efficient.
ER  -

TY  - JOUR
AU  - Sinha, D.
AU  - Shamayeva, K.
AU  - Ramasubramani, V.
AU  - Reha, D.
AU  - Bialevich, V.
AU  - Khabiri, M.
AU  - Guzanova, A.
AU  - Milbar, N.
AU  - Weiserova, M.
AU  - Csefalvay, E.
AU  - Carey, J.
AU  - Ettrich, R.
TI  - Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.
JO  - J. Mol. Model.
PY  - 2014
SP  - 2334
EP  - 2334
VL  - 20
AB  - Restriction-modification systems protect bacteria from foreign DNA. Type I
AB  - restriction-modification enzymes are multifunctional heteromeric complexes with DNA-cleavage
AB  - and ATP-dependent DNA translocation activities located on endonuclease/motor subunit HsdR. The
AB  - recent structure of the first intact motor subunit of the type I restriction enzyme from
AB  - plasmid EcoR124I suggested a mechanism by which stalled translocation triggers DNA cleavage
AB  - via a lysine residue on the endonuclease domain that contacts ATP bound between the two
AB  - helicase domains. In the present work, molecular dynamics simulations are used to explore this
AB  - proposal. Molecular dynamics simulations suggest that the Lys-ATP contact alternates with a
AB  - contact with a nearby loop housing the conserved QxxxY motif that had been implicated in DNA
AB  - cleavage. This model is tested here using in vivo and in vitro experiments. The results
AB  - indicate how local interactions are transduced to domain motions within the endonuclease/motor
AB  - subunit.
ER  -

TY  - JOUR
AU  - Sinha, R.K.
AU  - Krishnan, K.P.
AU  - Kurian, P.J.
TI  - Draft Genome Sequence of Idiomarina sp. Strain 5.13, a Highly Stress-Resistant Bacterium Isolated from the Southwest Indian Ridge.
JO  - Genome Announcements
PY  - 2017
SP  - e01747
EP  - e01716
VL  - 5
AB  - Idiomarina sp. strain 5.13, able to produce biopolymer and exopolysaccharide, was isolated
AB  - from a sediment sample collected from the Southwest Indian Ridge, Indian
AB  - Ocean. Analysis of its draft genome sequence provides insights into its
AB  - remarkable stress tolerance and offers the genetic basis for harnessing the
AB  - biotechnological potential of this strain.
ER  -

TY  - JOUR
AU  - Siozios, S.
AU  - Cestaro, A.
AU  - Kaur, R.
AU  - Pertot, I.
AU  - Rota-Stabelli, O.
AU  - Anfora, G.
TI  - Draft Genome Sequence of the Wolbachia Endosymbiont of Drosophila suzukii.
JO  - Genome Announcements
PY  - 2013
SP  - e00032
EP  - e00013
VL  - 1
AB  - is one of the most successful and abundant symbiotic bacteria in nature, infecting more than
AB  - 40% of the terrestrial arthropod species. Here we report the
AB  - draft genome sequence of a novel strain named 'Suzi' that was retrieved from the
AB  - genome sequencing of its host, the invasive pest .
ER  -

TY  - JOUR
AU  - Siqueira, F.M.
AU  - Cibulski, S.P.
AU  - Teixeira, T.F.
AU  - Mayer, F.Q.
AU  - Roehe, P.M.
TI  - Draft Genome Sequence of Acholeplasma laidlawii, a Common Contaminant of Cell Cultures.
JO  - Genome Announcements
PY  - 2017
SP  - e01578
EP  - e01516
VL  - 5
AB  - Mollicutes are important cell culture contaminants which may eventually affect the results of
AB  - biological assays or affect their interpretation. Acholeplasma
AB  - laidlawii is one of the most frequent contaminants of cell cultures. Here, we
AB  - report the complete genome sequence of A. laidlawii strain MDBK/IPV, recovered
AB  - from Madin-Darby bovine kidney (MDBK) cells.
ER  -

TY  - JOUR
AU  - Siqueira, F.M.
AU  - Thompson, C.E.
AU  - Virginio, V.G.
AU  - Gonchoroski, T.
AU  - Reolon, L.
AU  - Almeida, L.G.
AU  - da Fonseca, M.M.
AU  - de Souza, R.
AU  - Prosdocimi, F.
AU  - Schrank, I.S.
AU  - Ferreira, H.B.
AU  - de Vasconcelos, A.T.
AU  - Zaha, A.
TI  - New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis.
JO  - BMC Genomics
PY  - 2013
SP  - 175
EP  - 175
VL  - 14
AB  - BACKGROUND: Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma
AB  - hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium,
AB  - is genetically closely related to M. hyopneumoniae, the causative agent of
AB  - enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing
AB  - polyserositis and arthritis. In this work, we present the genome sequences of M.
AB  - flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with
AB  - the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome.
AB  - These analyses were performed to identify possible characteristics that may help
AB  - to explain the different behaviors of these species in swine respiratory tracts.
AB  - RESULTS: The overall genome organization of three species was analyzed, revealing
AB  - that the ORF clusters (OCs) differ considerably and that inversions and
AB  - rearrangements are common. Although M. flocculare and M. hyopneumoniae display a
AB  - high degree of similarity with respect to the gene content, only some genomic
AB  - regions display considerable synteny. Genes encoding proteins that may be
AB  - involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display
AB  - differences in genomic structure and organization. Some genes encoding adhesins
AB  - of the P97 family are absent in M. flocculare and some contain sequence
AB  - differences or lack of domains that are considered to be important for adhesion
AB  - to host cells. The phylogenetic relationship of the three species was confirmed
AB  - by a phylogenomic approach. The set of genes involved in metabolism, especially
AB  - in the uptake of precursors for nucleic acids synthesis and nucleotide
AB  - metabolism, display some differences in copy number and the presence/absence in
AB  - the three species. CONCLUSIONS: The comparative analyses of three mycoplasma
AB  - species that inhabit the swine respiratory tract facilitated the identification
AB  - of some characteristics that may be related to their different behaviors. M.
AB  - hyopneumoniae and M. flocculare display many differences that may help to explain
AB  - why one species is pathogenic and the other is considered to be commensal.
AB  - However, it was not possible to identify specific virulence determinant factors
AB  - that could explain the differences in the pathogenicity of the analyzed species.
AB  - The M. hyorhinis genome contains differences in some components involved in
AB  - metabolism and evasion of the host's immune system that may contribute to its
AB  - growth aggressiveness. Several horizontal gene transfer events were identified.
AB  - The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis
AB  - in the hyopneumoniae clade.
ER  -

TY  - JOUR
AU  - Sirota-Madi, A.
AU  - Olender, T.
AU  - Helman, Y.
AU  - Brainis, I.
AU  - Finkelshtein, A.
AU  - Roth, D.
AU  - Hagai, E.
AU  - Leshkowitz, D.
AU  - Brodsky, L.
AU  - Galatenko, V.
AU  - Nikolaev, V.
AU  - Gutnick, D.L.
AU  - Lancet, D.
AU  - Ben-Jacob, E.
TI  - Genome Sequence of the Pattern-Forming Social Bacterium Paenibacillus dendritiformis C454 Chiral Morphotype.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2127
EP  - 2128
VL  - 194
AB  - Paenibacillus dendritiformis is a Gram-positive, soil-dwelling, spore-forming social
AB  - microorganism. An intriguing collective faculty of this strain is
AB  - manifested by its ability to switch between different morphotypes, such as the
AB  - branching (T) and the chiral (C) morphotypes. Here we report the 6.3-Mb draft
AB  - genome sequence of the P. dendritiformis C454 chiral morphotype.
ER  -

TY  - JOUR
AU  - Sirota-Madi, A.
AU  - Olender, T.
AU  - Helman, Y.
AU  - Ingham, C.
AU  - Brainis, I.
AU  - Roth, D.
AU  - Hagi, E.
AU  - Brodsky, L.
AU  - Leshkowitz, D.
AU  - Galatenko, V.
AU  - Nikolaev, V.
AU  - Mugasimangalam, R.C.
AU  - Bransburg-Zabary, S.
AU  - Gutnick, D.L.
AU  - Lancet, D.
AU  - Ben-Jacob, E.
TI  - Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.
JO  - BMC Genomics
PY  - 2010
SP  - 710
EP  - 710
VL  - 11
AB  - BACKGROUND: The pattern-forming bacterium Paenibacillus vortex is notable for its
AB  - advanced social behavior, which is reflected in development of colonies with
AB  - highly intricate architectures. Prior to this study, only two other Paenibacillus
AB  - species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced.
AB  - However, no genomic data is available on the Paenibacillus species with
AB  - pattern-forming and complex social motility. Here we report the de novo genome
AB  - sequence of this Gram-positive, soil-dwelling, sporulating bacterium. RESULTS:
AB  - The complete P. vortex genome was sequenced by a hybrid approach using 454 Life
AB  - Sciences and Illumina, achieving a total of 289x coverage, with 99.8% sequence
AB  - identity between the two methods. The sequencing results were validated using a
AB  - custom designed Agilent microarray expression chip which represented the coding
AB  - and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open
AB  - reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis
AB  - with 500 complete bacterial genomes revealed exceptionally high number of
AB  - two-component system (TCS) genes, transcription factors (TFs), transport and
AB  - defense related genes. Additionally, we have identified genes involved in the
AB  - production of antimicrobial compounds and extracellular degrading enzymes.
AB  - CONCLUSIONS: These findings suggest that P. vortex has advanced faculties to
AB  - perceive and react to a wide range of signaling molecules and environmental
AB  - conditions, which could be associated with its ability to reconfigure and
AB  - replicate complex colony architectures. Additionally, P. vortex is likely to
AB  - serve as a rich source of genes important for agricultural, medical and
AB  - industrial applications and it has the potential to advance the study of social
AB  - microbiology within Gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Sisakova, E.
AU  - Seidel, R.
AU  - Szczelkun, M.
AU  - Weiserova, M.
TI  - Study of DNA translocation by EcoR124I type I RM enzyme.
JO  - FEBS J.
PY  - 2007
SP  - 305
EP  - 305
VL  - 274
AB  - EcoR124I, Type I restriction-modification enzyme, is multifunctional, hetero-oligomeric enzyme
AB  - complex, able of ATP hydrolysis coupled to DNA translocation, the 1-D motion along the DNA
AB  - lattice. These activities are conferred by superfamily 2 (SF2) helicase motifs in the HsdR
AB  - subunit, however, the helicase motifs are not involved in DNA unwinding.
AB  - For studying DNA translocation activity of this enzyme, we prevented in vitro experiments to
AB  - be hampered by cleavage of DNA substrates by making substitutions of the conserved amino acid
AB  - residues in endonuclease motif D-X13-14-E-X-K of the HsdR subunit, responsible for restriction
AB  - activity of the enzyme(the substitutions made: D151A, E165A, E165D, E165H and K167A). Mutant
AB  - HsdR subunits were purified and endonucleases reconstituted from the wt methylase and
AB  - individual mutant HsdR subunits were analysed in vitro. DNA translocation activity and ATPase
AB  - activity of these mutants were analysed using a combination of bulk stopped-flow experiments
AB  - and single-molecule magnetic tweezers technique. The cleavage mutants of the EcoR124I enzyme
AB  - showed initiation and translocation rates similar to wild-type. However, ATPase activity of
AB  - the mutants was lower than of the wt enzyme. These results open new questions about HsdR
AB  - structure and its conformation in the subunit assembly. Only the K167A mutant had DNA
AB  - translocation and ATPase activity comparable to the wild type, which could be used as a useful
AB  - model for further investigation of the mechanism of DNA translocation of SF2 helicases.
ER  -

TY  - JOUR
AU  - Sisakova, E.
AU  - Stanley, L.K.
AU  - Weiserova, M.
AU  - Szczelkun, M.D.
TI  - A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 3939
EP  - 3949
VL  - 36
AB  - The Type I restriction-modification enzyme EcoR124I is an ATP-dependent endonuclease that uses
AB  - dsDNA translocation to locate and cleave distant
AB  - non-specific DNA sites. Bioinformatic analysis of the HsdR subunits of
AB  - EcoR124I and related Type I enzymes showed that in addition to the
AB  - principal PD-(E/D)xK Motifs, I, II and III, a QxxxY motif is also present
AB  - that is characteristic of RecB-family nucleases. The QxxxY motif resides
AB  - immediately C-terminal to Motif III within a region of predicted
AB  - alpha-helix. Using mutagenesis, we examined the role of the Q and Y
AB  - residues in DNA binding, translocation and cleavage. Roles for the QxxxY
AB  - motif in coordinating the catalytic residues or in stabilizing the
AB  - nuclease domain on the DNA are discussed.
ER  -

TY  - JOUR
AU  - Sisakova, E.
AU  - van Aelst, K.
AU  - Diffin, F.M.
AU  - Szczelkun, M.D.
TI  - The Type ISP Restriction-Modification enzymes LlaBIII and LlaGI use a translocation-collision mechanism to cleave non-specific DNA distant from their  recognition sites.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 1071
EP  - 1080
VL  - 41
AB  - The Type ISP Restriction-Modification (RM) enzyme LlaBIII is encoded on plasmid pJW566 and can
AB  - protect Lactococcus lactis strains against bacteriophage
AB  - infections in milk fermentations. It is a single polypeptide RM enzyme comprising
AB  - Mrr endonuclease, DNA helicase, adenine methyltransferase and target-recognition
AB  - domains. LlaBIII shares >95% amino acid sequence homology across its first three
AB  - protein domains with the Type ISP enzyme LlaGI. Here, we determine the
AB  - recognition sequence of LlaBIII (5'-TnAGCC-3', where the adenine complementary to
AB  - the underlined base is methylated), and characterize its enzyme activities.
AB  - LlaBIII shares key enzymatic features with LlaGI; namely, adenosine
AB  - triphosphate-dependent DNA translocation ( approximately 309 bp/s at 25 degrees
AB  - C) and a requirement for DNA cleavage of two recognition sites in an inverted
AB  - head-to-head repeat. However, LlaBIII requires K(+) ions to prevent non-specific
AB  - DNA cleavage, conditions which affect the translocation and cleavage properties
AB  - of LlaGI. By identifying the locations of the non-specific dsDNA breaks
AB  - introduced by LlaGI or LlaBIII under different buffer conditions, we validate
AB  - that the Type ISP RM enzymes use a common translocation-collision mechanism to
AB  - trigger endonuclease activity. In their favoured in vitro buffer, both LlaGI and
AB  - LlaBIII produce a normal distribution of random cleavage loci centred midway
AB  - between the sites. In contrast, LlaGI in K(+) ions produces a far more
AB  - distributive cleavage profile.
ER  -

TY  - JOUR
AU  - Sisakova, E.
AU  - Weiserova, M.
TI  - Mutagenic analysis of the HsdR motor subunit of type IC restriction modification enzyme EcoR124I.
JO  - FEBS J.
PY  - 2005
SP  - 336
EP  - 336
VL  - 272
AB  - Enzyme EcoR124I belongs to the IC family of restriction modification enzymes, intelligent
AB  - molecular motors. It is able to detect the methylation status of its DNA target sequence and
AB  - respond with alternative activities, methylation or translocation of DNA. While bound to its
AB  - target site, it translocates DNA towards itself simultaneously in both directions (500bp/sec).
AB  - It uses the free energy associated with ATP hydrolysis to translocate DNA so that DNA cleavage
AB  - occurs remote from the asymmetric recognition site. The enzyme EcoR124I is a multifunctional,
AB  - multi-subunit enzyme, composed of three different subunits, which are encoded by the genes
AB  - hsdR, hsdM and hsdS. Products of all three genes are required for DNA cleavage, producing the
AB  - endonuclease. HsdR subunit is a multifunctional motor protein, which has been shown to possess
AB  - ATPase, helicase and restriction activity. To provide a fully functional molecular motor,
AB  - which can never cleave DNA, the amino acid motif X, the active site of the endonuclease domain
AB  - of the HsdR subunit, was subjected to site-directed mutagenesis. The complementation analysis
AB  - proved that the substitutions D151A, E165A, E165D, E165H, K167A in the HsdR subunit fully
AB  - removed the restriction activity in vivo of the EcoR124I enzyme. The mutant subunits were
AB  - separately overproduced, purified and mixed with purified methylase to reconstitute the
AB  - EcoR124I endonuclease in vitro. As a substrate for DNA cleavage in vitro we used the plasmid
AB  - pCFD30 containing a single site for EcoR124I. The test of restriction activity showed that
AB  - reconstituted endonucleases were not able to cleave covalently closed plasmid DNA to linear
AB  - DNA in contrast to the wild-type enzyme.
ER  -

TY  - JOUR
AU  - Sisakova, E.
AU  - Weiserova, M.
AU  - Dekker, C.
AU  - Seidel, R.
AU  - Szczelkun, M.D.
TI  - The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 1273
EP  - 1286
VL  - 384
AB  - The type I restriction-modification enzyme EcoR124I comprises three subunits with the
AB  - stoichiometry HsdR(2)/HsdM(2)/HsdS(1). The HsdR subunits
AB  - are archetypical examples of the fusion between nuclease and helicase
AB  - domains into a single polypeptide, a linkage that is found in a great many
AB  - other DNA processing enzymes. To explore the interrelationship between
AB  - these physically linked domains, we examined the DNA translocation
AB  - properties of EcoR124I complexes in which the HsdR subunits had been
AB  - mutated in the RecB-like nuclease motif II or III. We found that nuclease
AB  - mutations can have multiple effects on DNA translocation despite being
AB  - distinct from the helicase domain. In addition to reductions in DNA
AB  - cleavage activity, we also observed decreased translocation and ATPase
AB  - rates, different enzyme populations with different characteristic
AB  - translocation rates, a tendency to stall during initiation and altered
AB  - HsdR turnover dynamics. The significance of these observations to our
AB  - understanding of domain interactions in molecular machines is discussed.
ER  -

TY  - JOUR
AU  - Sistla, S.
AU  - Krishnamurthy, V.
AU  - Rao, D.N.
TI  - Single-stranded DNA binding and methylation by EcoP1I DNA methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2004
SP  - 159
EP  - 165
VL  - 314
AB  - EcoP1I methyltransferase (M.EcoP1I) belongs to the type III restriction-modification system
AB  - encoded by prophage PI that infects
AB  - Escherichia coli. Binding of M.EcoP1I to double-stranded DNA and
AB  - single-stranded DNA has been characterized. Binding to both single- and
AB  - double-stranded DNA could be competed out by unlabeled single-stranded
AB  - DNA. Metal ions did not influence DNA binding. Interestingly, M.EcoP1I
AB  - was able to methylate single-stranded DNA. Kinetic parameters were
AB  - determined for single and double-stranded DNA methylation. This feature
AB  - of the enzyme probably functions in protecting the phage genome from
AB  - restriction by type III restriction enzymes and thus could be
AB  - considered as an anti-restriction system. This study describing in
AB  - vitro methylation of single-stranded DNA by the type III
AB  - methyltransferase EcoP1I allows understanding of the mechanism of
AB  - action of these enzymes and also their role in the biology of
AB  - single-stranded phages.
ER  -

TY  - JOUR
AU  - Sistla, S.
AU  - Rao, D.N.
TI  - S-adenosyl-L-methionine-dependent restriction enzyme.
JO  - Crit. Rev. Biochem. Mol. Biol.
PY  - 2004
SP  - 1
EP  - 19
VL  - 39
AB  - Restriction-modification (R-M) enzymes are classified into type I, II, III, and IV, based on
AB  - their recognition sequence, subunit composition,
AB  - cleavage position, and cofactor requirements. While the role of
AB  - S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the
AB  - methylation reaction is undisputed, its requirement in DNA cleavage
AB  - reaction has been subject to intense study. AdoMet is a prerequisite
AB  - for the DNA cleavage by most type I enzymes known so far, with the
AB  - exception of R.EcoR124I. A number of new type 11 restriction enzymes
AB  - belonging to the type IIB and IIG family were found to show AdoMet
AB  - dependence for their cleavage reaction. The type III enzymes have been
AB  - found to require AdoMet for their restriction function. AdoMet
AB  - functions as an allosteric effector of the DNA cleavage reaction and
AB  - has been shown to bring about conformational changes in the protein
AB  - upon binding.
ER  -

TY  - JOUR
AU  - Sit, C.S.
AU  - Van Arnam, E.B.
AU  - Ramadhar, T.R.
TI  - Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2015
SP  - 13150
EP  - 13154
VL  - 112
AB  - Objectives: The mec and bla systems, among other genetic factors, are critical in regulating
AB  - the expression of methicillin resistance in Staphylococcus aureus. We examined by WGS a
AB  - naturally occurring oxacillin-susceptible mecA-positive S. aureus isolate to identify the
AB  - mechanism conferring oxacillin susceptibility.
AB  - Methods: The mecA-positive oxacillin-susceptible S. aureus isolate GR2 (penicillin and
AB  - oxacillin MICs 0.094 and
AB  - 1 mg/L, respectively), belonging to clonal complex 80,was characterized. DNA fragment
AB  - libraries were sequenced on Roche 454 and Illumina MiSeq sequencers and de novo assembly of
AB  - the genome was generated using SeqMan NGen software. Plasmid curing was conducted by SDS
AB  - treatment. Expression of mecA was quantified without/with b-lactam pressure.
AB  - Results: The genome of GR2 consisted of a 2792802 bp chromosome and plasmids pGR2A (28895 bp)
AB  - and pGR2B (2473 bp). GR2 carried SCCmec type IV, with a truncated/non-functional mecR1 gene
AB  - and no mecI. A single copy of the bla system, with an organization unique for S. aureus, was
AB  - found, harboured by plasmid pGR2A. Particularly, the blaZ gene was orientated like its
AB  - regulatory genes, blaI and blaR1, and a gene encoding transposase IS66 was integrated between
AB  - blaZ and the regulatory genes deleting the 5-end of blaR1; blaI,
AB  - encoding blaZ/mecA repressor, was intact. After plasmid loss, GR2 became penicillin and
AB  - oxacillin resistant (MICs 0.5 and 6 mg/L, respectively).
AB  - Conclusions: We can conclude that after exposure to b-lactams, the non-functional BlaR1 does
AB  - not cleave the mecA repressor BlaI, derepression does not occur and mecA is not efficiently
AB  - expressed. Removal of the bla system
AB  - after curing of pGR2A allows constitutive expression of mecA, resulting in oxacillin and
AB  - penicillin resistance.
ER  -

TY  - JOUR
AU  - Sitaraman, R.
TI  - Helicobacter pylori DNA methyltransferases and the epigenetic field effect in cancerization.
JO  - Front. Microbiol.
PY  - 2014
SP  - 115
EP  - 115
VL  - 5
AB  - Helicobacter pylori, a Gram-negative, microaerophilic bacterium, has co-existed with human
AB  - beings as a prominent member of their gastric microbiota for approximately 105 years.  It
AB  - infects approximately half the world's population, and most infected individuals are
AB  - asymptomatic, but histologically exhibit superficial gastritis.  Only a minority of infected
AB  - individuals develop gastric or duodenal ulcers that necessitate treatment.  Prolonged
AB  - inflammation caused by chronic (often lifelong) infection predisposes a small fraction of
AB  - infected individuals to develop gastric adenocarcinoma or lymphoma of the mucosa-associated
AB  - lymphoid tissue (MALT lymphoma).  Unfortunately, the prognosis for cases of gastric cancer is
AB  - very poor, with 5-year survival rates being lower than 15%.
ER  -

TY  - JOUR
AU  - Sitaraman, R.
AU  - Dybvig, K.
TI  - Restriction-modification systems and chromosomal rearrangements in mycoplasmas.
JO  - Mol. Biol. Pathog. Mycoplasmas
PY  - 2002
SP  - 371
EP  - 390
VL  - 0
AB  - The restriction-modification (R-M) systems are so named because of their ability to degrade
AB  - foreign DNA (restrict viral infection) and to methylate (modify) unmethylated and
AB  - hemimethylated DNA.  They were discovered as genetic elements that determined the
AB  - susceptibility of E. coli and S. typhimurium to phage infection in a strain-dependent manner,
AB  - with bacteriophage plaquing efficiency being reduced upon infection of a heterologous host
AB  - strain.  At the time of writing, 3154 R-M enzymes, many with overlapping DNA recognition
AB  - specificities, have been catalogued in the restriction enzyme database (REBASE).  R-M systems
AB  - are ubiquitous and arose early in prokaryotic evolution.
ER  -

TY  - JOUR
AU  - Sitaraman, R.
AU  - Dybvig, K.
TI  - The hsd loci of Mycoplasma pulmonis: organization, rearrangements and expression of genes.
JO  - Mol. Microbiol.
PY  - 1997
SP  - 109
EP  - 120
VL  - 26
AB  - Two paralogous, site-specific invertible loci, designated hsd1 and hsd2, have been identified
AB  - in the Mycoplasma pulmonis genome.  They encode putative type I restriction and modification
AB  - systems with maximum sequence homology to the type IC family, which includes EcoR124II and
AB  - EcoDXXI.  Each locus encodes an endonuclease subunit, a methylase subunit and two DNA
AB  - specificity subunits.  The gene organization at each locus is such that hsdR and hsdM are
AB  - flanked by two hsdS genes.  Within each locus, one of the hsdS genes, hsdR and hsdM, is
AB  - encoded in tandem by the same DNA strand, while the second hsdS gene is encoded by the
AB  - complementary strand but without overlap with the other three hsd genes.  The hsdR and hsdM
AB  - sequences of one locus are almost identical to their counterparts in the other.  The four hsdS
AB  - genes (two per locus) are highly homologous at their 5' ends and also share sequence
AB  - similarities in the 3' ends of their corresponding coding regions.  Owing to the disposition
AB  - of and sequence similarities among the hsdS genes, they form inverted repeats at each locus.
AB  - Analysis by polymerase chain reaction has shown that both loci behave as site-specific DNA
AB  - invertible elements with multiple inversion sites, termed 'vipareetus', occurring within the
AB  - hsdS genes.  The inversions lead to a reassortment of hsdS sequences, generating an array of
AB  - recombinant genes that probably encode S subunits possessing alternative DNA-binding
AB  - specificities.  Sequence information obtained from the analysis of hsd2 transcripts by 5'
AB  - RACE indicates that inversion induces the transcription of alternative hsdS genes by the
AB  - relocation of coding sequences downstream of a promoter and ribosome-binding sites situated at
AB  - one end of each locus.
ER  -

TY  - JOUR
AU  - Sitaraman, R.
AU  - Dybvig, K.
TI  - Functional analysis of a unique site-specific recombinase from Mycoplasma pulmonis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 388
EP  - 388
VL  - 101
AB  - Mycoplasma pulmonis has been shown to undergo high-frequency phase variation at different loci
AB  - within its genome - the two paralogous hsd
AB  - (host specificity determinant) loci that encode type I restriction and
AB  - modification (R-M) systems, and the vsa (variable surface antigen)
AB  - locus that encodes surface lipoproteins. Analyses of the hsd and vsa
AB  - gene loci have shown that they are organized as site-specific
AB  - invertible elements. Recently, the genome of M. pulmonis strain UAB
AB  - CTIP has been completely sequenced. Based on sequence homology, an open
AB  - reading frame near the vsa locus was predicted to encode a
AB  - site-specific recombinase. This is the only known site-specific
AB  - recombinase identified in Mollicutes that is not part of a viral and/or
AB  - transposable element. To test the functionality and sequence
AB  - specificity of the predicted recombinase, two assay systems have been
AB  - designed in an E. coli background using information about the regions
AB  - of the hsd and vsa genes that are actually involved in site-specific
AB  - recombination. Two copies of the relevant hsd (or vsa) regions were
AB  - cloned in opposite orientation into plasmid vectors. E. coli harboring
AB  - these "reporter" plasmids were then transformed with a compatible
AB  - plasmid containing the putative recombinase gene. The clones so
AB  - obtained were screened by PCR for inversion at the hsd- or vsa-derived
AB  - inverted repeats. The resulting amplicons corresponding to DNA
AB  - inversions were also sequenced, further verifying the occurrence of the
AB  - predicted inversions. This work proves that the putative recombinase is
AB  - functional and catalyzes site-specific inversions of the hsd- and
AB  - vsa-derived sequences that are known to undergo inversions in M.
AB  - pulmonis. The use of a single enzyme to catalyze DNA inversions at
AB  - different genetic loci is consistent with the observed genetic economy
AB  - of mycoplasmas. In view of the sequence differences between the sites
AB  - of inversion at the vsa and hsd loci, experiments to determine the
AB  - minimal sequence requirements for site-specific recombination are in
AB  - progress.
ER  -

TY  - JOUR
AU  - Sitaraman, R.
AU  - Leppla, S.H.
TI  - Methylation-dependent DNA restriction in Bacillus anthracis.
JO  - Gene
PY  - 2012
SP  - 44
EP  - 50
VL  - 494
AB  - Bacillus anthracis, the causative agent of anthrax, is poorly transformed with DNA that is
AB  - methylated on adenine or cytosine. Here we characterize
AB  - three genetic loci encoding type IV methylation-dependent restriction
AB  - enzymes that target DNA containing C5-methylcytosine (m5C). Strains in
AB  - which these genes were inactivated, either singly or collectively, showed
AB  - increased transformation by methylated DNA. Additionally, a triple mutant
AB  - with an ~30-kb genomic deletion could be transformed by DNA obtained from
AB  - Dam(+)Dcm(+)E. coli, although at a low frequency of ~10(-3)
AB  - transformants/10(6)cfu. This strain of B. anthracis can potentially serve
AB  - as a preferred host for shuttle vectors that express recombinant proteins,
AB  - including proteins to be used in vaccines. The gene(s) responsible for the
AB  - restriction of m6A-containing DNA in B. anthracis remain unidentified, and
AB  - we suggest that poor transformation by such DNA could in part be a
AB  - consequence of the inefficient replication of hemimethylated DNA in B.
AB  - anthracis.
ER  -

TY  - JOUR
AU  - Sitbon, E.
AU  - Pietrokovski, S.
TI  - New types of conserved sequence domains in DNA-binding regions of homing endonucleases.
JO  - Trends Biochem. Sci.
PY  - 2003
SP  - 473
EP  - 477
VL  - 28
AB  - We have identified four new types of short conserved sequence domains in homing endonucleases
AB  - and related proteins. These domains are modular,
AB  - appearing in various combinations. One domain includes a motif known by
AB  - structure as a novel sequence-specific DNA-binding helix. Sequence
AB  - similarity shows two other domains to be new types of helix-turn-helix
AB  - DNA-binding domains. We term the new domains nuclease-associated modular
AB  - DNA-binding domains (NUMODs).
ER  -

TY  - JOUR
AU  - Sivaraman, G.K.
AU  - Vanik, D.
AU  - Visnuvinayagam, S.
AU  - Prasad, M.M.
AU  - Murugadas, V.
AU  - Nadella, R.K.
AU  - Ravishankar, C.N.
TI  - Draft Genome Sequence of a Methicillin-Resistant Sequence Type 39 Staphylococcal  Isolate Obtained from Seafood.
JO  - Genome Announcements
PY  - 2017
SP  - e01193
EP  - e01117
VL  - 5
AB  - The draft genome sequence of a methicillin-resistant Staphylococcus aureus (MRSA) sequence
AB  - type 39 (ST 39) isolate obtained from the dried ribbonfish of Gujarat,
AB  - India, is reported here. Staphylococcus-specific genes were present in this MRSA
AB  - isolate. The whole-genome sequence of this strain contains 2,693 protein-coding
AB  - genes and 70 RNAs within the 2.82-Mb genome.
ER  -

TY  - JOUR
AU  - Sivaraman, G.K.
AU  - Vanik, D.
AU  - Visnuvinayagam, S.
AU  - Prasad, M.M.
AU  - Ravishankar, C.N.
TI  - Draft Genome Sequence of a Methicillin-Resistant Staphylococcus aureus Isolate (Sequence Type 1) from Seafood.
JO  - Genome Announcements
PY  - 2017
SP  - e00776
EP  - e00717
VL  - 5
AB  - The draft genome sequence of a methicillin-resistant Staphylococcus aureus (MRSA) isolate
AB  - (sequence type 1 [ST 1]) from the salted dried ribbonfish from Gujarat,
AB  - India, is reported here. Staphylococcus genus-specific genes were present in this
AB  - MRSA isolate. The whole-genome sequence of this strain contains 2,797
AB  - protein-coding genes and 80 RNAs within the 2.85-Mb genome.
ER  -

TY  - JOUR
AU  - Siwek, W.
AU  - Czapinska, H.
AU  - Bochtler, M.
AU  - Bujnicki, J.M.
AU  - Skowronek, K.
TI  - Crystal structure and mechanism of action of the N6-methyladenine-dependent type  IIM restriction endonuclease R.DpnI.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 7563
EP  - 7572
VL  - 40
AB  - DNA methylation-dependent restriction enzymes have many applications in genetic engineering
AB  - and in the analysis of the epigenetic state of eukaryotic genomes.
AB  - Nevertheless, high-resolution structures have not yet been reported, and
AB  - therefore mechanisms of DNA methylation-dependent cleavage are not understood.
AB  - Here, we present a biochemical analysis and high-resolution DNA co-crystal
AB  - structure of the N(6)-methyladenine (m6A)-dependent restriction enzyme R.DpnI.
AB  - Our data show that R.DpnI consists of an N-terminal catalytic PD-(D/E)XK domain
AB  - and a C-terminal winged helix (wH) domain. Surprisingly, both domains bind DNA in
AB  - a sequence- and methylation-sensitive manner. The crystal contains R.DpnI with
AB  - fully methylated target DNA bound to the wH domain, but distant from the
AB  - catalytic domain. Independent readout of DNA sequence and methylation by the two
AB  - domains might contribute to R.DpnI specificity or could help the monomeric enzyme
AB  - to cut the second strand after introducing a nick.
ER  -

TY  - JOUR
AU  - Sizova, I.A.
AU  - Glibin, E.N.
AU  - Ginzburg, O.F.
AU  - Tereshin, I.M.
TI  - Inhibition of the restriction of DNA by endonucleases in the presence of Actinomycin D, Distamycin A, and their analogs.
JO  - Bioorg. Khim.
PY  - 1982
SP  - 470
EP  - 477
VL  - 8
AB  - The cleavage of phage lambda cI857s7 by the restriction endonucleases EcoRI and
AB  - SmaI in the presence of actinomycin D, distamycin A, and the distamycin analog
AB  - distamine, and also of polyfunctional ligands -- distaccins -- has been
AB  - studied.  Distamine suppresses the cleavage of phage lambda DNA by endonuclease
AB  - EcoRI in the same way as distamycin A.  Actinomycin D selectively blocks the
AB  - action of endonucleases SmaI and EcoRI; in the latter case the cleavage of only
AB  - one recognition site is suppressed.  In the inhibition of the action of
AB  - endonuclease EcoRI simultaneously by two ligands, actinomycin D and distamycin
AB  - A or actinomycin D and distamine, "additivity" of their action on the
AB  - recognition site present at the point of contact of the EcoRI fragments E and F
AB  - was detected.  When DNA was cleaved by endonuclease SmaI in the presence of
AB  - these ligands no "additivity" was revealed.  In this case, a rise in the degree
AB  - of cleavage of the DNA at the points of contact of the SmaI fragments A and B,
AB  - and D and C, as compared with the action of actinomycin D alone, was observed.
AB  - Distaccins are nonspecific inhibitors of the cleavage of DNA under the
AB  - influence of the enzymes EcoRI and SmaI; distaccin-O protects the sections of
AB  - the recognition of endonuclease SmaI and does not block the action of
AB  - endonuclease EcoRI.
ER  -

TY  - JOUR
AU  - Sizova, M.V.
AU  - Chilaka, A.
AU  - Earl, A.M.
AU  - Doerfert, S.N.
AU  - Muller, P.A.
AU  - Torralba, M.
AU  - McCorrison, J.M.
AU  - Durkin, A.S.
AU  - Nelson, K.E.
AU  - Epstein, S.S.
TI  - High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of  the family Peptostreptococcaceae.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 37
EP  - 37
VL  - 10
AB  - Here we report a summary classification and the features of five anaerobic oral bacteria from
AB  - the family Peptostreptococcaceae. Bacterial strains were isolated
AB  - from human subgingival plaque. Strains ACC19a, CM2, CM5, and OBRC8 represent the
AB  - first known cultivable members of 'yet uncultured' human oral taxon 081; strain
AB  - AS15 belongs to 'cultivable' human oral taxon 377. Based on 16S rRNA gene
AB  - sequence comparisons, strains ACC19a, CM2, CM5, and OBRC8 are distantly related
AB  - to Eubacterium yurii subs. yurii and Filifactor alocis, with 93.2 - 94.4 % and
AB  - 85.5 % of sequence identity, respectively. The genomes of strains ACC19a, CM2,
AB  - CM5, OBRC8 and AS15 are 2,541,543; 2,312,592; 2,594,242; 2,553,276; and 2,654,638
AB  - bp long. The genomes are comprised of 2277, 1973, 2325, 2277, and 2308
AB  - protein-coding genes and 54, 57, 54, 36, and 28 RNA genes, respectively. Based on
AB  - the distinct characteristics presented here, we suggest that strains ACC19a, CM2,
AB  - CM5, and OBRC8 represent a novel genus and species within the family
AB  - Peptostreptococcaceae, for which we propose the name Peptoanaerobacter stomatis
AB  - gen. nov., sp. nov. The type strain is strain ACC19a(T) (=HM-483(T); =DSM
AB  - 28705(T); =ATCC BAA-2665(T)).
ER  -

TY  - JOUR
AU  - Sjodin, A.
AU  - Ohrman, C.
AU  - Backman, S.
AU  - Larkeryd, A.
AU  - Granberg, M.
AU  - Lundmark, E.
AU  - Karlsson, E.
AU  - Nilsson, E.
AU  - Vallesi, A.
AU  - Tellgren-Roth, C.
AU  - Stenberg, P.
AU  - Thelaus, J.
TI  - Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi.
JO  - Genome Announcements
PY  - 2014
SP  - e01227
EP  - e01214
VL  - 2
AB  - A strain of Francisella endociliophora was isolated from a laboratory culture of  the marine
AB  - ciliate Euplotes raikovi. Here, we report the complete genome sequence
AB  - of the bacterial strain FSC1006 (Francisella Strain Collection, Swedish Defence
AB  - Research Agency, Umea, Sweden).
ER  -

TY  - JOUR
AU  - Sjolund-Karlsson, M.
AU  - Reimer, A.
AU  - Folster, J.P.
AU  - Walker, M.
AU  - Dahourou, G.
AU  - Batra, D.G.
AU  - Martin, I.
AU  - Joyce, K.
AU  - Parsons, M.B.
AU  - Boncy, J.
AU  - Whichard, J.M.
AU  - Gilmour, M.W.
TI  - Drug-Resistance Mechanisms in Vibrio cholerae O1 Outbreak Strain, Haiti, 2010.
JO  - Emerg. Infect. Dis.
PY  - 2011
SP  - 2151
EP  - 2154
VL  - 17
AB  - To increase understanding of drug-resistant Vibrio cholerae, we studied selected
AB  - molecular mechanisms of antimicrobial drug resistance in the 2010 Haiti V.
AB  - cholerae outbreak strain. Most resistance resulted from acquired genes located on
AB  - an integrating conjugative element showing high homology to an integrating
AB  - conjugative element identified in a V. cholerae isolate from India.
ER  -

TY  - JOUR
AU  - Sjostrom, J.E.
AU  - Lofdahl, S.
AU  - Philipson, L.
TI  - Biological characteristics of a Type I restriction-modification system in Staphylococcus aureus.
JO  - J. Bacteriol.
PY  - 1978
SP  - 1144
EP  - 1149
VL  - 133
AB  - Two restriction-modification systems, S1 and S2, are present in Staphylococcus aureus RN450
AB  - (S. Iordanescu and M. Surdeanu, J. Gen. Microbiol., 96:277-281,1976).  System S2 affects phage
AB  - multiplication after both infection and transfection.  Unmodified plasmid and chromosomal DNAs
AB  - are also not expressed following transduction and transformation into a restrictive host.
AB  - Restricted phages are, however, capable of conferring phage-mediated competence, although the
AB  - state of competence does not affect the restriction-modification system. The restricting
AB  - activity of system S2 is inactivated by heat treatment of the cells.  An enzymatic activity
AB  - that restricts unmodified phage DNA in the presence of ATP, Mg2+, and S-adenosylmethionine was
AB  - recovered from cell-free extracts of a strain RN450 derivative.
ER  -

TY  - JOUR
AU  - Skarin, H.
AU  - Hafstrom, T.
AU  - Westerberg, J.
AU  - Segerman, B.
TI  - Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.
JO  - BMC Genomics
PY  - 2011
SP  - 185
EP  - 185
VL  - 12
AB  - ABSTRACT: BACKGROUND: Clostridium botulinum strains can be divided into
AB  - four physiological groups that are sufficiently diverged to be considered
AB  - as separate species. We here presentHere we present the first complete
AB  - genome of a C. botulinum strain from physiological group III, causing
AB  - animal botulism. We also compare the sequence to three new draft genomes
AB  - from the same physiological group. RESULTS: The 2.77 Mb chromosome was
AB  - highly conserved between the isolates and also closely related to that of
AB  - C. novyi. However, the sequence was very different from the human C.
AB  - botulinum group genomes. Replication-directed translocations were rare and
AB  - conservation of synteny was high. The largest difference between C.
AB  - botulinum group III isolates occurred within their surprisingly large
AB  - plasmidomes and in the pattern of mobile elements insertions. Five
AB  - plasmids, constituting 13.5% of the total genetic material, were present
AB  - in the completed genome. Interestingly, the set of plasmids differed
AB  - compared to other isolates. The largest plasmid, the botulinum- neurotoxin
AB  - carrying prophage, was conserved to at a level similar to that of the
AB  - chromosome while the medium-sized plasmids seemed to be undergoing faster
AB  - genetic drift. These plasmids also contained more mobile elements than
AB  - other replicons. Several toxins and resistance genes were identified, many
AB  - of which were located on the plasmids. CONCLUSIONS: The completion of the
AB  - genome of C. botulinum group III has revealed it to be a genome withof
AB  - dual identity. It belongs to the pathogenic species C. botulinum, but as a
AB  - genotypic species it should also include C. novyi and C. haemolyticum. The
AB  - genotypic species share a conserved chromosomal core that can be
AB  - transformed into various pathogenic variants by modulation of the highly
AB  - plastic plasmidome.
ER  -

TY  - JOUR
AU  - Skavronskaya, A.G.
AU  - Aleshkin, G.I.
AU  - Demkin, V.V.
TI  - Specificity of modification-restriction of bacteriophages P1 and lambda in strains of Escherichia coli K-12 controlled by the R124 plasmid.
JO  - Genetika
PY  - 1979
SP  - 1719
EP  - 1723
VL  - 15
AB  - The specificities of restriction of bacteriophages P1 and lambda controlled by
AB  - R plasmids in Escherichia coli have been investigated.  The isogenic strains
AB  - harbouring the plasmids pAS26 coding for restriction endonuclease R.EcoRI, R245
AB  - coding for restriction endonuclease R.EcoRII and R124 have been investigated in
AB  - the present work.  Modification-restriction controlled by R124 has been found
AB  - to differ in specificity from those controlled by R245 and pAS26.  Frequencies
AB  - of restriction of bacteriophages P1vir and lambdavir specified by R124 plasmid
AB  - differ from the frequencies in the strains harbouring pAS26 and R245 plasmids
AB  - as well.  The difference is due to the specificity of restriction-modification
AB  - controlled by R124.  The data obtained are consistent with the determination of
AB  - R124 specified restriction-modification activity as a novel one designated
AB  - R.EcoRIII.
ER  -

TY  - JOUR
AU  - Skennerton, C.T.
AU  - Angly, F.E.
AU  - Breitbart, M.
AU  - Bragg, L.
AU  - He, S.
AU  - McMahon, K.D.
AU  - Hugenholtz, P.
AU  - Tyson, G.W.
TI  - Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System.
JO  - PLoS ONE
PY  - 2011
SP  - e20095
EP  - e20095
VL  - 6
AB  - The relationship between phage and their microbial hosts is difficult to elucidate in complex
AB  - natural ecosystems. Engineered systems performing
AB  - enhanced biological phosphorus removal (EBPR), offer stable, lower
AB  - complexity communities for studying phage-host interactions. Here,
AB  - metagenomic data from an EBPR reactor dominated by Candidatus
AB  - Accumulibacter phosphatis (CAP), led to the recovery of three complete and
AB  - six partial phage genomes. Heat-stable nucleoid structuring (H-NS)
AB  - protein, a global transcriptional repressor in bacteria, was identified in
AB  - one of the complete phage genomes (EPV1), and was most similar to a
AB  - homolog in CAP. We infer that EPV1 is a CAP-specific phage and has the
AB  - potential to repress up to 6% of host genes based on the presence of
AB  - putative H-NS binding sites in the CAP genome. These genes include CRISPR
AB  - associated proteins and a Type III restriction-modification system, which
AB  - are key host defense mechanisms against phage infection. Further, EPV1 was
AB  - the only member of the phage community found in an EBPR microbial
AB  - metagenome collected seven months prior. We propose that EPV1 laterally
AB  - acquired H-NS from CAP providing it with a means to reduce bacterial
AB  - defenses, a selective advantage over other phage in the EBPR system. Phage
AB  - encoded H-NS could constitute a previously unrecognized weapon in the
AB  - phage-host arms race.
ER  -

TY  - JOUR
AU  - Skirgaila, R.
AU  - Grazulis, S.
AU  - Bozic, D.
AU  - Huber, R.
AU  - Siksnys, V.
TI  - Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 473
EP  - 481
VL  - 279
AB  - According to the crystal structure of Cfr10I restriction endonuclease the acidic residues
AB  - D134, E71 and E204 are clustered together and presumably chelate metal ion(s) at the active
AB  - site.  Indeed, investigation of the DNA cleavage properties of substitutional mutants of
AB  - Cfr10I D134A, E71Q, E71A and E204Q reveals that D134, E71 and E204 residues are essential for
AB  - cleavage activity, supporting their active site function.  Structural comparison indicates
AB  - that the D134 residue of Cfr10I spatially overlaps with aspartate residues D91 and D74, from
AB  - the invariant active site motifs 90PD(X19)EAK and 73 PD(X15)DIK of EcoRI and EcoRV,
AB  - respectively.  However, structural studies in conjunction with mutational analyses suggest
AB  - that the sequence motif 133PD(X55)K(X13)E corresponds to the active site of Cfr10I, but
AB  - differs from the canonical active site motifs of EcoRI and EcoRV.  According to the crystal
AB  - structure of Cfr10I the serine S188 residue from the 188SVK sequence motif is a spatial
AB  - equivalent of the acidic residue from the (E/D)XK-part of the active site motif, which is
AB  - conserved between EcoRI and EcoRV.  Site-directed mutagenesis experiments of Cfr10I, however,
AB  - revealed that S188 was not so important for catalysis while the E204 residue located 2.8A away
AB  - indeed was essential for cleavage, suggesting that the glutamate E204 rather than the S188
AB  - residue contributes to the metal binding site in Cfr10I.  In addition, model-building studies
AB  - suggest that mutual interchange of the E204 and S188 residues should lead only to minor
AB  - positional differences of the carboxylate residues of glutamate side-chains.  The double
AB  - mutant S188E/E204S was therefore prepared by site-directed mutagenesis where the active site
AB  - motif 133 PD(X55)K(X13)E of Cfr10I was changed to a canonical motif 133PD(X53)EVK, which is
AB  - similar to that of EcoRI and EcoRV.  Interestingly, the double mutant S188E/E204S of Cfr10I
AB  - with redesigned active site structure, exhibited 10% of Wt cleavage activity in a lambda DNA
AB  - cleavage assay.  Thus, structure guided redesign of the catalytic/metal binding site of
AB  - Cfr10I, provides novel experimental evidence to suggest that spatial rather than sequence
AB  - conservation plays the dominant role in the formation of restriction enzyme active sites.
ER  -

TY  - JOUR
AU  - Skirgaila, R.
AU  - Siksnys, V.
TI  - Ca2+-ions stimulate DNA binding specificity of Cfr10I restriction enzyme.
JO  - Biol. Chem.
PY  - 1998
SP  - 595
EP  - 598
VL  - 379
AB  - The Cfr10I restriction enzyme recognizes the degenerate hexanucleotide sequence
AB  - 5'-Pu/CCGGPy-3' and cleaves it as indicated.  DNA binding studies of Cfr10I endonuclease
AB  - were performed using gel mobility shift assay.  Analysis of Cfr10I binding to DAN revealed
AB  - that in the absence of metal ions Cfr10I binds to DNA containing or lacking the recognition
AB  - sequence with similar low affinity.  Addition of Ca2+ to the binding specificity of Cfr10I.
ER  -

TY  - JOUR
AU  - Sklar, R.
AU  - Altman, D.
AU  - Sager, R.
TI  - An endonuclease from Chlamydomonas reinhardtii that cleaves the sequence TATA.
JO  - J. Biol. Chem.
PY  - 1986
SP  - 6806
EP  - 6810
VL  - 261
AB  - An endodeoxyribonuclease, designated CreI, was purified 16,000-fold from
AB  - zygotes of the eukaryote Chlamydomonas reinhardtii.  CreI preferentially
AB  - attacks the sequence TATA producing double stsrand breaks with
AB  - 3'-phosphomonoester and 5'-hydroxyl termini.  The endonuclease has an Mr =
AB  - 27,000 and requires Ca2+ at pH 7.5 for optimal activity.
ER  -

TY  - JOUR
AU  - Skoglund, A.
AU  - Bjorkholm, B.
AU  - Nilsson, C.
AU  - Andersson, A.F.
AU  - Jernberg, C.
AU  - Schirwitz, K.
AU  - Enroth, C.
AU  - Krabbe, M.
AU  - Engstrand, L.
TI  - Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pylori.
JO  - J. Bacteriol.
PY  - 2007
SP  - 8914
EP  - 8921
VL  - 189
AB  - A large number of genes encoding restriction-modification (R-M) systems are found in the
AB  - genome of the human pathogen Helicobacter pylori. R-M
AB  - genes comprise approximately 10% of the strain-specific genes, but the
AB  - relevance of having such an abundance of these genes is not clear. The
AB  - type II methyltransferase (MTase) M.HpyAIV, which recognizes GANTC sites,
AB  - was present in 60% of the H. pylori strains analyzed, whereof 69% were
AB  - resistant to restriction enzyme digestion, which indicated the presence of
AB  - an active MTase. H. pylori strains with an inactive M.HpyAIV phenotype
AB  - contained deletions in regions of homopolymers within the gene, which
AB  - resulted in premature translational stops, suggesting that M.HpyAIV may be
AB  - subjected to phase variation by a slipped-strand mechanism. An M.HpyAIV
AB  - gene mutant was constructed by insertional mutagenesis, and this mutant
AB  - showed the same viability and ability to induce interleukin-8 in
AB  - epithelial cells as the wild type in vitro but had, as expected, lost the
AB  - ability to protect its self-DNA from digestion by a cognate restriction
AB  - enzyme. The M.HpyAIV from H. pylori strain 26695 was overexpressed in
AB  - Escherichia coli, and the protein was purified and was able to bind to DNA
AB  - and protect GANTC sites from digestion in vitro. A bioinformatic analysis
AB  - of the number of GANTC sites located in predicted regulatory regions of H.
AB  - pylori strains 26695 and J99 resulted in a number of candidate genes.
AB  - katA, a selected candidate gene, was further analyzed by quantitative
AB  - real-time reverse transcription-PCR and shown to be significantly
AB  - down-regulated in the M.HpyAIV gene mutant compared to the wild-type
AB  - strain. This demonstrates the influence of M.HpyAIV methylation in gene
AB  - expression.
ER  -

TY  - JOUR
AU  - Skoglund, A.
AU  - Bjorkholm, B.
AU  - Nilsson, C.
AU  - Krabbe, M.
AU  - Engstrand, L.
TI  - Are hsdS-subunits in restriction-modification systems involved in Helicobacter pylori virulence?
JO  - Helicobacter
PY  - 2003
SP  - 492
EP  - 492
VL  - 8
AB  - Few regulatory genes are present in the H. pylori genome, but there is an abundance of genes
AB  - homologous to restriction-modification systems, that may play a role in gene regulation.  Each
AB  - strain has its own unique set of R-M genes.  In a recent study, the presence of hsdS genes
AB  - (specificity subunits of type I R-M systems) in clinical isolates was associated with
AB  - induction of a more robust host response in gnotobiotic transgenic mice.  We aim to study hsdS
AB  - genes and their involvement in virulence.  By PCR-amplification, two hsdS genes were detected
AB  - in 100% of the isolates, however, the amplified products had variable sizes.  We have
AB  - sequenced one hsdS locus in nine clinical isolates.  The sequenced locus reveal large
AB  - variations between the strains, but there were also conserved regions.  One of the conserved
AB  - domain is known as the target recognition domain.  We have constructed insertion mutants in
AB  - type I hsdS and hsdM (modification subunit of type I systems) genes: jhp0726, HP0790, HP0462
AB  - and HP0463.  Preliminary results indicate that one of the mutant strains (HP0462::km) has
AB  - reduced growth compared with the wild-type strain.  Strains deficient in hsdS and hsdM genes
AB  - do not show altered ability to induce IL-8 production in AGS-cells.  The effects of
AB  - inactivation of the hsdS genes on global gene expression are now being investigated using a
AB  - whole-genome microarray.  To investigate the involvement of hsdS genes in virulence, the
AB  - host-response of mutant compared with wild-type strains will be studied in germfree mice.
ER  -

TY  - JOUR
AU  - Skoglund, A.
AU  - Bjorkholm, B.
AU  - Nilsson, C.
AU  - Krabbe, M.
AU  - Engstrand, L.
TI  - Are hsdS-subunits in restriction-modification systems involved in Helicobacter pylori virulence?
JO  - Int. J. Med. Microbiol.
PY  - 2003
SP  - 125
EP  - 125
VL  - 293
AB  - Few regulatory genes are present in the H. pylori genome, but there is an abundance of genes
AB  - homologous to restriction-modification systems, that may play a role in gene regulation.  Each
AB  - strain has its own unique set of R-M genes.  In a recent study, the presence of hsdS genes
AB  - (specifically subunits of type I R-M systems) in clinical isolates was associated with
AB  - induction of a more robust host response in gnotobiotic transgenic mice.  We aim to study hsdS
AB  - genes and their involvement in virulence.  By PCR-amplification, two hsdS genes were detected
AB  - in 100% of the isolates, however the amplified products had variable sizes.  We have sequenced
AB  - one hsdS locus in 9 clinical isolates.  The sequenced locus reveals large variations between
AB  - the strains, but there were also conserved regions.  One of the conserved domains is known as
AB  - the target recognition domain.  We have constructed insertion mutants in type I hsdS and hsdM
AB  - (modification subunit of type I systems) genes: jhp0726, HP0790, HP0462 and HP0463.
AB  - Preliminary results indicate that one of the mutant strains (HP0462::km) has reduced growth
AB  - compared to the wild-type strain.  Strains deficient in hsdS and hsdM genes do not show
AB  - altered ability to induce IL-8 production in AGS-cells.  The effects of inactivation of the
AB  - hsdS genes on global gene expression are now being investigated using a whole-genome
AB  - microarray.  To investigate the involvement of hsdS genes in virulence, the host-response of
AB  - mutant compared to wild-type strains will be studied in germfree mice.
ER  -

TY  - JOUR
AU  - Skoglund, A.
AU  - Engstrand, L.
AU  - Krabbe, M.E.
TI  - DNA methyltransferases in Helicobacter pylori.
JO  - Int. J. Med. Microbiol.
PY  - 2001
SP  - 94
EP  - 95
VL  - 291S
AB  - DNA methyltransferases are enzymes that modify specific sequences in DNA.  In bacteria, this
AB  - modification is important as protection of "self" DNA in restriction-modification systems and
AB  - in cellular processes such as DNA repair, control of cell division and regulation of virulence
AB  - genes.  We are interested in the role of multiple methyltransferases in H. pylori.  To
AB  - determine the distribution of methyltransferase genes in DNA prepared from clinical isolates
AB  - of H. pylori, oligonucleotide pairs directed towards conserved regions of 18 MT genes were
AB  - used in PCR.  The PCR reaction for four genes, HPO260, HPO263, HPO478 and HPO910, were present
AB  - in all the DNA isolates tested, whereas other MT genes were only present in a subset of the
AB  - strains.  We are now proceeding to inactivate these and four additional MT genes in H. pylori
AB  - strain 26695 by insertion of a Kanamycin cassette (aphA) from Campylobacter coli into the MT
AB  - reading frame to determine the phenotypical effect of loss of the MT activity.  The first of
AB  - our inactivation constructs, HP0483 (not conserved in clinical isolates) was interrupted
AB  - without any obvious effect on the growth of the mutant as compared with wild-type bacteria.
AB  - This indicates that the restriction enzyme encoded downstream of the MT gene was not expressed
AB  - under the conditions used, since that likely would have resulted in degradation of the
AB  - chromosomal DNA in the mutant.  We will continue to analyze this and other MT mutants for
AB  - their phenotype.  We are also interested in gene regulation and we will investigate whether
AB  - these MT genes are regulated by environmental stimuli.
ER  -

TY  - JOUR
AU  - Skoglund, C.M.
AU  - Smith, H.O.
AU  - Chandrasegaran, S.
TI  - Construction of an efficient overproducer clone of HinfI restriction endonuclease using the polymerase chain reaction.
JO  - Gene
PY  - 1990
SP  - 1
EP  - 5
VL  - 88
AB  - We describe the use of the polymerase chain reaction (PCR) technique to alter
AB  - transcriptional and translational signals surrounding a gene so as to achieve
AB  - overexpression in Escherichia coli.  By changing the ribosome-binding site
AB  - sequence preceding the hinfIR gene to match the consensus E. coli signal and by
AB  - adding a transcription terminator sequence immediately following the gene, the
AB  - yield of HinfI was increased about tenfold over that obtained from the natural
AB  - Haemophilus influenzae signals.  The addition of the positive retroregulator
AB  - stem-loop sequence derived from the crystal protein-encoding gene of Bacillus
AB  - thuringiensis downstream from the hinfIR gene further increased yields by
AB  - twofold to a level of 13% of the total cellular protein.
ER  -

TY  - JOUR
AU  - Skogman, G.S.
AU  - Bjork, G.R.
TI  - Effects of the phage P1 restriction system on Coliphage PhiW: Degradation and complex formation of phage PhiW DNA.
JO  - J. Gen. Virol.
PY  - 1976
SP  - 9
EP  - 20
VL  - 31
AB  - Growth of phages PhiW and T7 was restricted in Escherichia coli lysogenic for phage P1.  Only
AB  - a fraction of the infected cells gave burst of phages.  Cells permitting phage growth gave
AB  - normal burst size.  Host strains carrying P1 mutants with defective endonuclease gave no
AB  - restriction of phages T7 and Phi3, the latter a host-range mutant of PhiW.  Degradation but
AB  - not modification of parental phage DNA could be demonstrated.  Although no DNA, RNA or protein
AB  - was synthesized in PhiW infected P1 lysogenic cells, the parental phage DNA was found in
AB  - increasingly larger complexes during the course of infection.  At early times after infection,
AB  - parental phage DNA was found to sediment about twice as fast as mature phage DNA.  At later
AB  - times during the infection the parental phage DNA was recovered as a very rapidly sedimenting
AB  - material.  Such material was also found in alkaline sucrose gradient centrifugation after
AB  - treatment of the cell extract with sodium dodecyl sulphate, pronase digestion and phenol
AB  - extractions.
ER  -

TY  - JOUR
AU  - Skov, K.A.
AU  - Adomat, H.
AU  - Konway, D.C.
AU  - Farrell, N.P.
TI  - Assessment of DNA binding of platinum-radio-sensitizer complexes by inhibition of restriction enzymes.
JO  - Chem. Biol. Interact.
PY  - 1987
SP  - 117
EP  - 129
VL  - 62
AB  - A simple and rapid method has been used to compare the binding of platinum
AB  - complexes to DNA, in a relatively qualitative manner.  A compound bound at or
AB  - near the restriction site inhibits enzymatic cleavage of DNA; inhibition of
AB  - BamHI and EcoRI activity by complexes was assessed in this study using
AB  - linearized pSV2-gpt plasmid.  Our particular interest was in DNA binding by
AB  - complexes of platinum (Pt) with known organic radiosensitizers (RS), to
AB  - determine whether the Pt was able to target the RS to the DNA. Although the
AB  - Pt-RS complexes investiaged themselves have moderate radiosensitizing ability
AB  - (like the inorganic complexes, cis- or trans-diamminedichloroplatinum(II), c-
AB  - or t-DDP) none of the Pt-RS inhibit to the same extent as c- or t-DDP.
AB  - However, there appears to be some correlation between enhanced
AB  - radiosensitization by Pt-RS over Pt(RS), with the degree of Pt binding (as
AB  - assessed by our assay).  Our results using isolated DNA suggest that not all
AB  - complexes bind well (e.g. Pt with two RS ligands), but that in certain cases
AB  - (e.g. Pt with only one RS), it is possible to target the drug to the DNA.  An
AB  - ammine or amine ligand may be required in order to target a radiosensitizer to
AB  - DNA using platinum.
ER  -

TY  - JOUR
AU  - Skowron, P.
AU  - Kaczorowski, T.
AU  - Tucholski, J.
AU  - Podhajska, A.J.
TI  - Atypical DNA-binding properties of class-IIS restriction endonucleases:evidence for recognition of the cognate sequence by a FokI monomer.
JO  - Gene
PY  - 1993
SP  - 1
EP  - 10
VL  - 125
AB  - The DNA-binding properties of the FokI restriction endonuclease were studied using the
AB  - gel-mobility-shift assay. Specific recognition of the cognate sequence and cleavage of DNA are
AB  - distinguishable functions and can be separated. FokI binds to its recognition site
AB  - predominantly as a monomer. At high concentrations, FokI exhibits a cooperative recognition
AB  - sequence-dependent aggregation. In 20 mM KCl/10 mM Tris-HCl buffer, the binding constant of
AB  - FokI to its cognate site is 6.0-7.9 x 10/8 per mol and is lower than the values for most
AB  - gene-regulatory proteins. FokI binding is 600-1500 times weaker to non-cognate double-stranded
AB  - DNA than to the GGATG site, and 30,000 times weaker to single-stranded DNA or tRNA. The method
AB  - of Bading [Nucleic Acids Res. 16 (1988) 5241-5248], used for determining the stoichometry of
AB  - protein bound to DNA by gel-mobility-shift assay, is extended.
ER  -

TY  - JOUR
AU  - Skowron, P.M.
AU  - Anton, B.P.
AU  - Czajkowska, E.
AU  - Zebrowska, J.
AU  - Sulecka, E.
AU  - Krefft, D.
AU  - Jezewska-Frackowiak, J.
AU  - Zolnierkiewicz, O.
AU  - Witkowska, M.
AU  - Morgan, R.D.
AU  - Wilson, G.G.
AU  - Fomenkov, A.
AU  - Roberts, R.J.
AU  - Zylicz-Stachula, A.
TI  - The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 9005
EP  - 9018
VL  - 45
AB  - Two restriction modification systems have been previously discovered in Thermus aquaticus
AB  - YT-1.  TaqI is a 263-amino acid (aa) Type IIP restriction enzyme that recognizes and cleaves
AB  - within the symmetric sequence 5-TCGA-3. TaqII, in contrast, is a 1105-aa Type IIC
AB  - restriction-and-modification enzyme, one of a family of Thermus homologs. TaqII was originally
AB  - reported to recognize two different asymmetric sequences: 5-GACCGA-3 and 5-CACCCA-3. We
AB  - previously cloned the taqIIRM gene, purified the recombinant protein from Escherichia coli,
AB  - and showed that TaqII recognizes the 5-GACCGA-3 sequence only. Here, we report the discovery,
AB  - isolation, and characterization of TaqIII, the third RM system from T. aquaticus YT-1. TaqIII
AB  - is a 1101-aa Type IIC/IIL enzyme and recognizes the 5-CACCCA-3 sequence previously attributed
AB  - to TaqII. The cleavage site is 11/9 nucleotides downstream of the A residue. The enzyme
AB  - exhibits striking biochemical similarity to TaqII. The 93% identity between their aa sequences
AB  - suggests that they have a common evolutionary origin. The genes are located on two separate
AB  - plasmids, and are probably paralogs or pseudoparalogs. Putative positions and aa that specify
AB  - DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family
AB  - enzymes were predicted.
ER  -

TY  - JOUR
AU  - Skowron, P.M.
AU  - Majewski, J.
AU  - Zylicz-Stachula, A.
AU  - Rutkowska, S.M.
AU  - Jaworowska, I.
AU  - Harasimowicz-Slowinska, R.I.
TI  - A new Thermus sp. class-IIS enzyme sub-family: isolation of a "twin" endonuclease TspDTI with a novel specificity 5'-ATGAA(N11/9)-3', related to TspGWI, TaqII and Tth111II.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - e74
EP  - e74
VL  - 31
AB  - The TspDTI restriction endonuclease, which shows a novel recognition specificity
AB  - 5'-ATGAA(N(11/9))-3', was isolated from Thermus sp. DT. TspDTI
AB  - appears to be a 'twin' of restriction endonuclease TspGWI from Thermus sp.
AB  - GW, as we have previously reported. TspGWI was isolated from the same
AB  - location as TspDTI, it recognizes a related sequence 5'-ACGGA(N(11/9))-3'
AB  - and has conserved cleavage positions. Both enzymes resemble two other
AB  - class-IIS endonucleases from Thermus sp.: TaqII and Tth111II. N-terminal
AB  - amino acid sequences of TspGWI tryptic peptides exhibit 88.9-100%
AB  - similarity to the TaqII sequence. All four enzymes were purified to
AB  - homogeneity; their polypeptide sizes (114.5-122 kDa) make them the largest
AB  - class-IIS restriction endonucleases known to date. The existence of a
AB  - Thermus sp. sub-family of class-IIS restriction endonucleases of a common
AB  - origin is herein proposed.
ER  -

TY  - JOUR
AU  - Skowron, P.M.
AU  - Swaminathan, N.
AU  - McMaster, K.
AU  - George, D.
AU  - Van Etten, J.L.
AU  - Mead, D.A.
TI  - Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella.
JO  - Gene
PY  - 1995
SP  - 37
EP  - 41
VL  - 157
AB  - The gene (cviJIR) encoding the two/three-base R.CviJI eukaryotic restriction endonuclease
AB  - (ENase) from IL-3A virus-infected Chlorella was cloned into Escherichia coli.  A high
AB  - frequency of DNA cleavage by R.CviJI required overexpression of the gene encoding the M.CviJI
AB  - methyltransferase prior to cloning the gene for the ENase.  Both genes were sequenced and
AB  - their organization was determined to be in head-to-tail order.  The open reading frame coding
AB  - for R.CviJI can potentially translate a 41.4-kDa protein; however, in the E. coli host, a
AB  - truncated version of the enzyme is produced (32.5 kDa).  The recombinant ENase does not
AB  - exhibit ATP-induced 'star' activity (R.CviJI cleaves at RGCY, while R.CviJI* also cleaves at
AB  - RGCR and YGCY, but not at YGCR), as is characteristic for native R.CviJI.  The very high
AB  - frequency of DNA cleavage by R.CviJI* was exploited in the development of a quasi-random
AB  - shotgun library method.  R.CviJI*-generated oligodeoxyribonucleotides were applied to improve
AB  - certain molecular biology applications, i.e., DNA labeling, detection, high-resolution
AB  - restriction mapping, amplification and epitope mapping.
ER  -

TY  - JOUR
AU  - Skowron, P.M.
AU  - Vitkute, J.
AU  - Ramanauskaite, D.
AU  - Mitkaite, G.
AU  - Jezewska-Frackowiak, J.
AU  - Zebrowska, J.
AU  - Zylicz-Stachula, A.
AU  - Lubys, A.
TI  - Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus.
JO  - BMC Mol. Biol.
PY  - 2013
SP  - 17
EP  - 17
VL  - 14
AB  - BACKGROUND: In continuing our research into the new family of bifunctional restriction
AB  - endonucleases (REases), we describe the cloning of the tsoIRM gene.
AB  - Currently, the family includes six thermostable enzymes: TaqII, Tth111II,
AB  - TthHB27I, TspGWI, TspDTI, TsoI, isolated from various Thermus sp. and two
AB  - thermolabile enzymes: RpaI and CchII, isolated from mesophilic bacteria
AB  - Rhodopseudomonas palustris and Chlorobium chlorochromatii, respectively. The
AB  - enzymes have several properties in common. They are large proteins (molecular
AB  - size app. 120 kDa), coded by fused genes, with the REase and methyltransferase
AB  - (MTase) in a single polypeptide, where both activities are affected by
AB  - S-adenosylmethionine (SAM). They recognize similar asymmetric cognate sites and
AB  - cleave at a distance of 11/9 nt from the recognition site. Thus far, we have
AB  - cloned and characterised TaqII, Tth111II, TthHB27I, TspGWI and TspDTI. RESULTS:
AB  - TsoI REase, which originate from thermophilic Thermus scotoductus RFL4 (T.
AB  - scotoductus), was cloned in Escherichia coli (E. coli) using two rounds of
AB  - biochemical selection of the T. scotoductus genomic library for the TsoI
AB  - methylation phenotype. DNA sequencing of restriction-resistant clones revealed
AB  - the common open reading frame (ORF) of 3348 bp, coding for a large polypeptide of
AB  - 1116 aminoacid (aa) residues, which exhibited a high level of similarity to
AB  - Tth111II (50% identity, 60% similarity). The ORF was PCR-amplified, subcloned
AB  - into a pET21 derivative under the control of a T7 promoter and was subjected to
AB  - the third round of biochemical selection in order to isolate error-free clones.
AB  - Induction experiments resulted in synthesis of an app. 125 kDa protein,
AB  - exhibiting TsoI-specific DNA cleavage. Also, the wild-type (wt) protein was
AB  - purified and reaction optima were determined. CONCLUSIONS: Previously we
AB  - identified and cloned the Thermus family RM genes using a specially developed
AB  - method based on partial proteolysis of thermostable REases. In the case of TsoI
AB  - the classic biochemical selection method was successful, probably because of the
AB  - substantially lower optimal reaction temperature of TsoI (app. 10-15 degrees C).
AB  - That allowed for sufficient MTase activity in vivo in recombinant E. coli.
AB  - Interestingly, TsoI originates from bacteria with a high optimum growth
AB  - temperature of 67 degrees C, which indicates that not all bacterial enzymes match
AB  - an organism's thermophilic nature, and yet remain functional cell components.
AB  - Besides basic research advances, the cloning and characterisation of the new
AB  - prototype REase from the Thermus sp. family enzymes is also of practical
AB  - importance in gene manipulation technology, as it extends the range of available
AB  - DNA cleavage specificities.
ER  -

TY  - JOUR
AU  - Skowronek, K.
AU  - Boniecki, M.J.
AU  - Kluge, B.
AU  - Bujnicki, J.M.
TI  - Rational engineering of sequence specificity in R.MwoI restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 8579
EP  - 8592
VL  - 40
AB  - R.MwoI is a Type II restriction endonucleases enzyme (REase), which specifically  recognizes a
AB  - palindromic interrupted DNA sequence 5'-GCNNNNNNNGC-3' (where N
AB  - indicates any nucleotide), and hydrolyzes the phosphodiester bond in the DNA
AB  - between the 7th and 8th base in both strands. R.MwoI exhibits remote sequence
AB  - similarity to R.BglI, a REase with known structure, which recognizes an
AB  - interrupted palindromic target 5'-GCCNNNNNGGC-3'. A homology model of R.MwoI in
AB  - complex with DNA was constructed and used to predict functionally important amino
AB  - acid residues that were subsequently targeted by mutagenesis. The model, together
AB  - with the supporting experimental data, revealed regions important for recognition
AB  - of the common bases in DNA sequences recognized by R.BglI and R.MwoI. Based on
AB  - the bioinformatics analysis, we designed substitutions of the S310 residue in
AB  - R.MwoI to arginine or glutamic acid, which led to enzyme variants with altered
AB  - sequence selectivity compared with the wild-type enzyme. The S310R variant of
AB  - R.MwoI preferred the 5'-GCCNNNNNGGC-3' sequence as a target, similarly to R.BglI,
AB  - whereas the S310E variant preferentially cleaved a subset of the MwoI sites,
AB  - depending on the identity of the 3rd and 9th nucleotide residues. Our results
AB  - represent a case study of a REase sequence specificity alteration by a single
AB  - amino acid substitution, based on a theoretical model in the absence of a crystal
AB  - structure.
ER  -

TY  - JOUR
AU  - Skowronek, K.J.
AU  - Kosinski, J.
AU  - Bujnicki, J.M.
TI  - Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.
JO  - Proteins
PY  - 2006
SP  - 1059
EP  - 1068
VL  - 63
AB  - Type II restriction enzymes are commercially important deoxyribonucleases and very attractive
AB  - targets for protein engineering
AB  - of new specificities. At the same time they are a very challenging test
AB  - bed for protein structure prediction methods. Typically, enzymes that
AB  - recognize different sequences show little or no amino acid sequence
AB  - similarity to each other and to other proteins. Based on
AB  - crystallographic analyses that revealed the same PD-(D/E)XK fold for
AB  - more than a dozen case studies, they were nevertheless considered to be
AB  - related until the combination of bioinformatics and mutational analyses
AB  - has demonstrated that some of these proteins belong to other, unrelated
AB  - folds PLD, HNH, and GIY-YIG. As a part of a large-scale project aiming
AB  - at identification of a three-dimensional fold for all type II REases
AB  - with known sequences (currently similar to 1000 proteins), we carried
AB  - out preliminary structure prediction and selected candidates for
AB  - experimental validation. Here, we present the analysis of Hpal REase,
AB  - an ORFan with no detectable homologs, for which we detected a
AB  - structural template by protein fold recognition, constructed a model
AB  - using the FRankenstein monster approach and identified a number of
AB  - residues important for the DNA binding and catalysis. These predictions
AB  - were confirmed by site-directed mutagenesis and in vitro analysis of
AB  - the mutant proteins. The experimentally validated model of Hpal will
AB  - serve as a low-resolution structural platform for evolutionary
AB  - considerations in the subgroup of blunt-cutting REases with different
AB  - specificities. The research protocol developed in the course of this
AB  - work represents a streamlined version of the previously used techniques
AB  - and can be used in a high-throughput fashion to build and validate
AB  - models for other enzymes, especially ORFans that exhibit no sequence
AB  - similarity to any other protein in the database.
ER  -

TY  - JOUR
AU  - Skrypina, N.A.
AU  - Kramarov, V.M.
AU  - Lyannaya, A.M.
AU  - Smolyaninov, V.V.
AU  - Goncharova, G.I.
TI  - Restriction endonucleases from Bifidobacteria.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1988
SP  - 15
EP  - 16
VL  - 0
AB  - The site specific restriction endonucleases were found in four strains among
AB  - the twelve strains of anaerobic bacteria of the genus Bifidobacterium.  Two of
AB  - the restriction endonucleases studied, BadI from B. adolescentis LVA1 and BbfI
AB  - from B. bifidum LVA3, are isoschizomers of XhoI and recognize the nucleotide
AB  - sequence CTCGAG.  The restriction endonucleases Bbf7411I from B. bifidum 7411
AB  - and Bla7920I from B. lactentis 7920 recognize and hydrolyze the nucleotide
AB  - sequence TCCGGA having a specificity analogous to that of the restriction
AB  - endonuclease CauB3I.  Like CauB3I, these restriction endonucleases are unable
AB  - to hydrolyze DNA if the adenine residues in the recognition site are
AB  - methylated.
ER  -

TY  - JOUR
AU  - Skrzypek, E.
AU  - Piekarowicz, A.
TI  - The EcoDXXI restriction and modification system: cloning the genes and homology to Type I restriction and modification systems.
JO  - Plasmid
PY  - 1989
SP  - 195
EP  - 204
VL  - 21
AB  - The Escherichia coli plasmid pDXX1 codes for a type I restriction and
AB  - modification system, EcoDXXI.  A 15.5-kb BamHI fragment from pDXX1 has been
AB  - cloned and contains the hsdR, hsdM, and hsdS genes that encode the EcoDXX1
AB  - system.  The EcoDXX1 hsd genes can complement the gene products of the EcoR124
AB  - and EcoR124/3 hsd systems, but not those of EcoK and EcoB.  Hybridization
AB  - experiments using EcoDXX1 hsd genes as a probe demonstrate homology between
AB  - EcoDXX1 and EcoK or EcoB systems.
ER  -

TY  - JOUR
AU  - Skvortsov, T.
AU  - Hoering, P.
AU  - Arkhipova, K.
AU  - Whitehead, R.C.
AU  - Boyd, D.R.
AU  - Allen, C.C.R.
TI  - Draft Genome Sequences of Pseudomonas putida UV4 and UV4/95, Toluene Dioxygenase-Expressing Producers of cis-1,2-Dihydrodiols.
JO  - Genome Announcements
PY  - 2018
SP  - e01419
EP  - e01417
VL  - 6
AB  - Here, we present draft genome sequences of Pseudomonas putida strains UV4 and UV4/95, which
AB  - demonstrate an ability to conduct a wide range of industrially
AB  - important biotransformations of arenes, alkenes, and phenols.
ER  -

TY  - JOUR
AU  - Slaby, B.M.
AU  - Hentschel, U.
TI  - Draft Genome Sequences of 'Candidatus Synechococcus spongiarum,' Cyanobacterial Symbionts of the Mediterranean Sponge Aplysina aerophoba.
JO  - Genome Announcements
PY  - 2017
SP  - e00268
EP  - e00217
VL  - 5
AB  - We report here four draft genome sequences belonging to clade F of the cyanobacterium
AB  - 'Candidatus Synechococcus spongiarum' of the marine sponge
AB  - Aplysina aerophoba, which were collected from two nearby locations in the
AB  - northern Adriatic Sea. The sequences provide the basis for within-clade
AB  - comparisons between members of this widespread group of cyanobacterial sponge
AB  - symbionts.
ER  -

TY  - JOUR
AU  - Slack, A.
AU  - Cervoni, N.
AU  - Pinard, M.
AU  - Szyf, M.
TI  - Feedback regulation of DNA methyltransferase gene expression by methylation.
JO  - Eur. J. Biochem.
PY  - 1999
SP  - 191
EP  - 199
VL  - 264
AB  - This paper tests the hypothesis that expression of the DNA methyltransferase, dnmt1, gene is
AB  - regulated by a methylation-sensitive DNA element. Methylation of DNA is an attractive system
AB  - for feedback regulation of DNA methyltransferase as the final product of the reaction,
AB  - methylated DNA, can regulate gene expression in cis. We show that an AP-1-dependent regulatory
AB  - element of dnmt1 is heavily methylated in most somatic tissues and in the mouse embryonal cell
AB  - line, P19, and completely unmethylated in a mouse adrenal carcinoma cell line, Y1. dnmt1 is
AB  - highly over expressed in Y1 relative to P19 cell lines. Global inhibition of DNA methylation
AB  - in P19 cells by 5-azadeoxycytidine results in demethylation of the AP-1 regulatory region and
AB  - induction of dnmt1 expression in P19cells, but not Y1 cells.  We propose that this regulatory
AB  - region of dnmt1 acts as a sensor of the DNA methylation capacity of the cell. These results
AB  - provide an explanation for the documented coexistence of global hypomethylation and high
AB  - levels of DNA methyltransferase activity in many cancer cells and for the carcinogenic effect
AB  - of hypomethylating diets.
ER  -

TY  - JOUR
AU  - Sladek, T.L.
AU  - Maniloff, J.
TI  - Endonuclease from Acholeplasma laidlawii strain JA1 associated with in vivo restriction of DNA containing 5-methylcytosine.
JO  - Isr. J. Med. Sci.
PY  - 1987
SP  - 423
EP  - 426
VL  - 23
AB  - Transfection of Acholeplasma laidlawii strain JA1 with viral DNAs that have
AB  - been sequence-specifically methylated in vitro has led us to previously
AB  - postulate that JA1 cells contain an enzyme which cleaves only DNA containing
AB  - 5-methylcytosine, regardless of the nucleotide sequence containing that base.
AB  - In this paper we show that an endonuclease activity is present in extracts from
AB  - JA1 cells but not in extracts from a restriction deficient variant of JA1.  The
AB  - partially purified enzyme cleaves to only DNA containing 5-methylcytosine, but
AB  - also DNA containing no methylated bases.  We discuss why this endonuclease
AB  - activity may not have the same in vitro specificity as would be expected from
AB  - in vivo experiments.
ER  -

TY  - JOUR
AU  - Sladek, T.L.
AU  - Nowak, J.A.
AU  - Maniloff, J.
TI  - Mycoplasma restriction: identification of a new type of restriction specificity for DNA containing 5-methylcytosine.
JO  - J. Bacteriol.
PY  - 1986
SP  - 219
EP  - 225
VL  - 165
AB  - Mycoplasma bacteriophage L51 single-stranded DNA and L2 double-stranded DNA are
AB  - host cell modified and restricted when they transfect Acholeplasma laidlawii
AB  - JA1 and K2 cells.  The L51 genome has a single restriction endonuclease MboI
AB  - site (recognition sequence GATC), which contains 5-methylcytosine when the DNA
AB  - is isolated from L51 phage grown in K2 cells but is unmethylated when the DNA
AB  - is from phage grown in JA1 cells.  This GATC sequence is nonessential, since an
AB  - L51 mutant in which the MboI site was deleted was still viable.  DNA from this
AB  - deletion mutant phage was not restricted during transfection of either strain
AB  - K2 or containing the sequence GAT 5-methylcytosine.  We conclude that K2 cells
AB  - have a restriction system specific for DNA containing the sequence GATC and
AB  - protect their DNA by methylating cytosine in this sequence.  In contrast, JA1
AB  - cells (which contain no methylated DNA bases) have a newly discovered type of
AB  - restriction-modification system.  From results of studies of the restriction of
AB  - specifically methylated DNAs, we conclude that JA1 cells restrict DNA
AB  - containing 5-methylcytosine, regardless of the nucleotide sequence containing
AB  - 5-methylcytosine.  This is the first report of a DNA restriction activity
AB  - specific for a single (methylated) base.  Modification in this system is the
AB  - absence of cytosine methylating activity.  A restriction-deficient variant of
AB  - strain JA1, which retains the JA1 modification phenotype, was isolated,
AB  - indicating that JA1 cells have a gene product with restriction specificity for
AB  - DNA containing 5-methylcytosine.
ER  -

TY  - JOUR
AU  - Slaska-Kiss, K.
AU  - Timar, E.
AU  - Kiss, A.
TI  - Complementation between inactive fragments of SssI DNA methyltransferase.
JO  - BMC Mol. Biol.
PY  - 2012
SP  - 17
EP  - 17
VL  - 13
AB  - Background: Silencing mammalian genes by targeted DNA (cytosine-5) methylation of selected CG
AB  - sites in the genome would be a powerful technique to analyze epigenomic information and to
AB  - study the roles of DNA methylation in physiological and pathological states. A promising
AB  - approach of targeted DNA methylation is based on the ability of split fragments of a monomeric
AB  - DNA methyltransferase (C5-MTase) to associate and form active enzyme. A few C5-MTases of
AB  - different specificities have been shown to possess the ability of fragment complementation,
AB  - but a demonstration of this phenomenon for a C5-MTase, which has CG specificity and thus can
AB  - be targeted to methylate any CG site, has been lacking. The purpose of this study was to test
AB  - whether the CG-specific prokaryotic C5-MTase M.SssI shows the phenomenon of fragment
AB  - complementation.
AB  - Results: We show that truncated inactive N-terminal fragments of M.SssI can assemble with
AB  - truncated inactive C-terminal fragments to form active enzyme in vivo when produced in the
AB  - same E. coli cell. Overlapping and non-overlapping fragments as well as fragments containing
AB  - short appended foreign sequences had complementation capacity. In optimal combinations
AB  - C-terminal fragments started between conserved motif VIII and the predicted target recognizing
AB  - domain of M.SssI. DNA methyltransferase activity in crude extracts of cells with the best
AB  - complementing fragment pairs was ~ 4 per cent of the activity of cells producing the full
AB  - length enzyme.  Fusions of two N-terminal and two C-terminal fragments to 21.6 kDa zinc finger
AB  - domains only slightly reduced complementation ability of the fragments.
AB  - Conclusions: The CG-specific DNA methyltransferase M.SssI shows the phenomenon of fragment
AB  - complementation in vivo in E. coli. Fusion of the split fragments to six unit zinc finger
AB  - domains does not substantially interfere with the formation of active enzyme. These
AB  - observations and the large number of complementing fragment combinations representing a wide
AB  - range of MTase activity offer the possibility to develop M.SssI into a programmable DNA
AB  - ethyltransferase of high specificity.
ER  -

TY  - JOUR
AU  - Slater, S.C. et al.
TI  - Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multi-Chromosome Genomes in Bacteria.
JO  - J. Bacteriol.
PY  - 2009
SP  - 2501
EP  - 2511
VL  - 8
AB  - The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and
AB  - agriculture. Within this family, many Rhizobium and
AB  - Sinorhizobium strains are nitrogen-fixing plant mutualists, while many
AB  - strains designated as Agrobacterium are plant pathogens. These contrasting
AB  - lifestyles are primarily dependent on the transmissible plasmids each
AB  - strain harbors. Members of Rhizobiaceae also have diverse genome
AB  - architectures that include single chromosomes, multiple chromosomes, and
AB  - plasmids of various sizes. Agrobacterium strains have been divided into
AB  - three Biovars, based on physiological and biochemical properties. The
AB  - genome of a Biovar I strain, A. tumefaciens C58, has been previously
AB  - sequenced. In this study the genomes of the Biovar II strain A.
AB  - radiobacter K84, a commercially available biological control strain that
AB  - inhibits certain pathogenic agrobacteria, and the Biovar III strain A.
AB  - vitis S4, a narrow host range strain that infects grapes and invokes a
AB  - hypersensitive response on non-host plants, were fully sequenced and
AB  - annotated. Comparison with other sequenced members of the
AB  - alpha-proteobacteria provides new data on evolution of multi-partite
AB  - bacterial genomes. Primary chromosomes show extensive conservation of both
AB  - gene content and order. In contrast, secondary chromosomes share smaller
AB  - percentages of genes, and conserved gene order is restricted to short
AB  - blocks. We propose that secondary chromosomes originated from an ancestral
AB  - plasmid to which genes have been transferred from a progenitor primary
AB  - chromosome. Similar patterns are observed in select beta- and
AB  - gamma-proteobacteria species. Together these results define the evolution
AB  - of chromosome architecture and gene content among the Rhizobiaceae and
AB  - support a generalized mechanism for second chromosome formation among
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Slatko, B.E.
AU  - Benner, J.S.
AU  - Jager-Quinton, T.
AU  - Moran, L.S.
AU  - Simcox, T.G.
AU  - VanCott, E.M.
AU  - Wilson, G.G.
TI  - Cloning, sequencing and expression of the TaqI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 9781
EP  - 9796
VL  - 15
AB  - The TaqI modification and restriction genes (recognition sequence TCGA) have
AB  - been cloned in E. coli and their DNA sequences have been determined.  Both
AB  - proteins were characterized and the N-terminal sequence of the endonuclease was
AB  - determined.  The genes have the same transcriptional orientation with the
AB  - methylase gene 5' to the endonuclease gene.  The methylase gene is 1089 bp in
AB  - length (363 amino acids, 40,575 daltons); the endonuclease gene is 702 bp in
AB  - length (234 amino acis, 27,523 daltons); they are separated by 132 bp.  Both
AB  - methylase and endonuclease activity can be detected in cell extracts.  The
AB  - clones fully modify the vector and chromosomal DNA but they fail to restrict
AB  - infecting phage.  Clones carrying only the restriction gene are viable even in
AB  - the absence of modification.  The restriction gene contains 7 TaqI sites; the
AB  - modification gene contains none.  This asymmetric distribution of sites could
AB  - be important in the regulation of the expression of the endonuclease gene.
ER  -

TY  - JOUR
AU  - Slatko, B.E.
AU  - Croft, R.
AU  - Moran, L.S.
AU  - Wilson, G.G.
TI  - Cloning and analysis of the HaeIII and HaeII methyltransferase genes.
JO  - Gene
PY  - 1988
SP  - 45
EP  - 50
VL  - 74
AB  - The HaeIII methyltransferase (MTase) gene from Haemophilus aegyptius
AB  - (recognition sequence: 5'-GGCC-3') was cloned into Escherichia coli in the
AB  - plasmid vector pBR322.  The gene was isolated on a single EcoRI fragment and on
AB  - a single HindIII fragment.  Clones carrying additional adjacent fragments were
AB  - found to code also for the HaeII restriction endonuclease and HaeII
AB  - modification MTase (recognition sequence:  5'-PuGCGCPy-3').  The sequence of
AB  - the HaeIII modification gene was determined.  The inferred amino acid sequence
AB  - of the protein was found to share extensive similarity with other sequenced
AB  - m5C-MTases.  The central non-conserved region of the M.HaeIII MTase, thought to
AB  - form the nucleotide sequence-specificity domain, is almost identical to that of
AB  - the M.BsuRI, M.BspRI and M.NgoPII MTases, which also recognize the sequence
AB  - 5'-GGCC-3'.
ER  -

TY  - JOUR
AU  - Slavin, J.W.J.
AU  - Ivanisevic, A.
TI  - Dual restriction enzyme digest of cationic-gold-coated DNA scaffolds.
JO  - Int. J. Nanomedicine
PY  - 2007
SP  - 821
EP  - 825
VL  - 2
AB  - DNA strands coated with AuNPs were cleaved by restriction enzymes while in solution or on a
AB  - surface. Enzymatic activity was verified by gel
AB  - electrophoresis prior to surface analysis. Cleavage results suggest
AB  - that enzymes can recognize the AuNP-coated strands while on the
AB  - surfaces, though specificity in digestion has not yet been verified.
AB  - Development allows for advances in site specific localization of
AB  - components using biological media.
ER  -

TY  - JOUR
AU  - Slesarev, A.I.
AU  - Mezhevaya, K.V.
AU  - Makarova, K.S.
AU  - Polushin, N.N.
AU  - Shcherbinina, O.V.
AU  - Shakhova, V.V.
AU  - Belova, G.I.
AU  - Aravind, L.
AU  - Natale, D.A.
AU  - Rogozin, I.B.
AU  - Tatusov, R.L.
AU  - Wolf, Y.I.
AU  - Stetter, K.O.
AU  - Malykh, A.G.
AU  - Koonin, E.V.
AU  - Kozyavkin, S.A.
TI  - The complete genome of the hyperthermophile Methanopyrus kandleri AV19 and monophyly of Archaeal methanogens.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 4644
EP  - 4649
VL  - 99
AB  - We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus
AB  - kandleri by using a whole direct genome sequencing approach. This approach is based on
AB  - unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and
AB  - cycle sequencing directed by 2'-modified oligonucleotides (Fimers).
AB  - Sequencing redundancy (3.3x) was sufficient to assemble the genome with less than one error
AB  - per 40 kb. Using a combination of sequence database searches and coding potential prediction,
AB  - 1,692 protein-coding genes and 39 genes for
AB  - structural RNAs were identified. M. kandleri proteins show an unusually high content of
AB  - negatively charged amino acids, which might be an adaptation to the high intracellular
AB  - salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a
AB  - very deep branch, close to the root of the archaeal tree. However, genome comparisons indicate
AB  - that, in both trees constructed using concatenated alignments of ribosomal proteins and trees
AB  - based on gene content, M.
AB  - kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of
AB  - genes implicated in
AB  - methanogenesis and, in part, its operon organization with Methanococcus jannaschii and
AB  - Methanothermobacter
AB  - thermoautotrophicum. These findings indicate that archaeal methanogens are monophyletic. A
AB  - distinctive feature of M.
AB  - kandleri is the paucity of proteins involved in signaling and regulation of gene expression.
AB  - Also, M. kandleri appears to
AB  - have fewer genes acquired via lateral transfer than other archaea. These features might
AB  - reflect the extreme habitat of this
AB  - organism. Full author list: Slesarev,A.I., Mezhevaya,K.V., Makarova,K.S., Polushin,N.N.,
AB  - Shcherbinina,O.V., Shakhova,V.V., Belova,G.I., Aravind,L., Natale,D.A., Rogozin,I.B.,
AB  - Tatusov,R.L., Wolf,Y.I., Stetter,K.O., Malykh,A.G., Koonin,E.V., Kozyavkin,S.A.
ER  -

TY  - JOUR
AU  - Sletvold, H.
AU  - Johnsen, P.J.
AU  - Hamre, I.
AU  - Simonsen, G.S.
AU  - Sundsfjord, A.
AU  - Nielsen, K.M.
TI  - Complete sequence of Enterococcus faecium pVEF3 and the detection of an omega-epsilon-zeta toxin-antitoxin module and an ABC transporter.
JO  - Plasmid
PY  - 2008
SP  - 75
EP  - 85
VL  - 60
AB  - Glycopeptide resistant Enterococcus faecium (GREF) persists on Norwegian
AB  - poultry farms despite the ban on the growth promoter avoparcin. The
AB  - biological basis for long-term persistence of avoparcin resistance is not
AB  - fully understood. This study presents the complete DNA sequence of the E.
AB  - faecium R-plasmid pVEF3 and functional studies of some plasmid-encoded
AB  - traits (a toxin-antitoxin (TA) system and an ABC transporter) that may be
AB  - of importance for plasmid persistence. The pVEF3 (63.1 kbp), isolated from
AB  - an E. faecium strain of poultry origin sampled in Norway in 1999, has 71
AB  - coding sequences including the vanA avoparcin/vancomycin resistance
AB  - encoding gene cluster. pVEF3 encodes the TA system omega-epsilon-zeta, and
AB  - plasmid stability tests and transcription analysis show that
AB  - omega-epsilon-zeta is functional in Enterococcus faecalis OGIX, although
AB  - with decreasing effect over time. The predicted ABC transporter was not
AB  - found to confer reduced susceptibility to any of the 28 substances tested.
AB  - The TA system identified in the pVEF-type plasmids may contribute to vanA
AB  - plasmid persistence on Norwegian poultry farms. However, size and
AB  - compositional heterogeneity among E. faecium vanA plasmids suggest that
AB  - additional plasmid maintenance systems in combination with host specific
AB  - factors and frequent horizontal gene transfer and rearrangement causes the
AB  - observed plasmid composition and distribution patterns.
ER  -

TY  - JOUR
AU  - Sloan, D.B.
AU  - Moran, N.A.
TI  - Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids.
JO  - Mol. Biol. Evol.
PY  - 2012
SP  - 3781
EP  - 3792
VL  - 29
AB  - Genome reduction in obligately intracellular bacteria is one of the most
AB  - well-established patterns in the field of molecular evolution. In the extreme,
AB  - many sap-feeding insects harbor nutritional symbionts with genomes that are so
AB  - reduced that it is not clear how they perform basic cellular functions. For
AB  - example, the primary symbiont of psyllids (Carsonella) maintains one of the
AB  - smallest and most AT-rich bacterial genomes ever identified and has surprisingly
AB  - lost many genes that are thought to be essential for its role in provisioning its
AB  - host with amino acids. However, our understanding of this extreme case of genome
AB  - reduction is limited, as genomic data for Carsonella are available from only a
AB  - single host species, and little is known about the functional role of "secondary"
AB  - bacterial symbionts in psyllids. To address these limitations, we analyzed
AB  - complete Carsonella genomes from pairs of congeneric hosts in three divergent
AB  - genera within the Psyllidae (Ctenarytaina, Heteropsylla, and Pachypsylla) as well
AB  - as complete secondary symbiont genomes from two of these host species
AB  - (Ctenarytaina eucalypti and Heteropsylla cubana). Although the Carsonella genomes
AB  - are generally conserved in size, structure, and GC content and exhibit
AB  - genome-wide signatures of purifying selection, we found that gene loss has
AB  - remained active since the divergence of the host species and had a particularly
AB  - large impact on the amino acid biosynthesis pathways that define the symbiotic
AB  - role of Carsonella. In some cases, the presence of additional bacterial symbionts
AB  - may compensate for gene loss in Carsonella, as functional gene content indicates
AB  - a high degree of metabolic complementarity between co-occurring symbionts. The
AB  - genomes of the secondary symbionts also show signatures of long-term evolution as
AB  - vertically transmitted, intracellular bacteria, including more extensive genome
AB  - reduction than typically observed in facultative symbionts. Therefore, a history
AB  - of co-evolution with secondary bacterial symbionts can partially explain the
AB  - ongoing genome reduction in Carsonella. However, the absence of these secondary
AB  - symbionts in other host lineages indicates that the relationships are dynamic and
AB  - that other mechanisms, such as changes in host diet or functional coordination
AB  - with the host genome, must also be at play.
ER  -

TY  - JOUR
AU  - Slocum, H.
AU  - Boyer, H.W.
TI  - Host specificity of Salmonella typhimurium deoxyribonucleic acid restriction and modification.
JO  - J. Bacteriol.
PY  - 1973
SP  - 724
EP  - 726
VL  - 113
AB  - The restriction and modification genes of Salmonella typhimurium which lie near
AB  - the thr locus were transferred to a restrictionless mutant of Escherichia coli.
AB  - These genes were found to be allelic to the E. coli K, B, and A restriction
AB  - and modification genes.  E. coli recombinants with the restriction and
AB  - modfication host specificity of S. typhimurium restricted phage lambda that had
AB  - been modified by each of the seven known host specificities of E. coli at an
AB  - efficiency of plating levels of abobut 10-2.  Phage lambda modified with the S.
AB  - typhimurium host specificity was restricted by six of the seven E. coli host
AB  - specificiteis but not by the RII (fi- R-factor controlled) host specificity.
AB  - It is proposed that the restriction and modification enzymes of this S.
AB  - typhimurium host specificity have two substrates, one of which is a substrate
AB  - for the RII host specificity enzymes.
ER  -

TY  - JOUR
AU  - Slocum, H.C.
TI  - In vitro restriction of DNA.  Demonstration that the DNA of mutant phage are resistant to attack by restriction endonuclease.
JO  - Tex. Rep. Biol. Med.
PY  - 1971
SP  - 405
EP  - 405
VL  - 29
AB  - Various bacterial systems (Escherichia coli, Hemophilus, and others)
AB  - demonstrate a mechanism for rejecting non-homologous DNA, i.e., DNA which
AB  - originates in a cell of a different strain.  This host-controlled restriction,
AB  - more specifically degradation, is brought about by a 2-step enzymatic mechanism
AB  - involving an endonuclease which introduces a limited number of double-strand
AB  - scissions at 2 specific sites (a site being a sequence of nucleotide base
AB  - pairs) on a DNA molecule.  The endonuclease does not recognize or introduce
AB  - double-strand scissions at these sites if there has been a prior methylation of
AB  - 1 or 2 bases in the site (known as host-controlled modification of DNA).  The
AB  - modification methylase and restriction endonuclease recognize the same
AB  - substrate by virtue of the 2 enzymes having a common subunit which recognizes
AB  - the sequence of base pairs.  Small circular phage DNA have 2 sites recognized
AB  - by the endonuclease and methylase per molecule.  The biologic effect of the
AB  - restriction endonuclease is to abort the lytic cycle of the phage.  That is,
AB  - only 1 in 10,000 phage infected are successful.  Phage mutants can be obtained
AB  - that have successful lytic cycles of 1 in 100.  I recombined 2 independent
AB  - mutants to obtain a phage totally resistant to the endonuclease, i.e., a
AB  - probability of 1.0 that the lytic cycle takes place.  In vitro, the single
AB  - mutants are degraded to intact linear molecules, whereas the recombinant is
AB  - completely resistant to degradation, meaning no single strand breaks are made
AB  - at either mutant site.  The results can be interpreted on the basis of the
AB  - substrate being a sequence of base pairs with 2-fold dimensional symmetry.
ER  -

TY  - JOUR
AU  - Slow, S.
AU  - Anderson, T.
AU  - Biggs, P.
AU  - Kennedy, M.
AU  - Murdoch, D.
AU  - Cree, S.
TI  - Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with  Legionnaires' Disease.
JO  - Genome Announcements
PY  - 2018
SP  - e01588
EP  - e01517
VL  - 6
AB  - Legionella sainthelensi is an aquatic environmental bacterium that in humans can  cause
AB  - Legionnaires' disease (LD), an often severe form of pneumonia. Here, we
AB  - report the first complete genome of a L. sainthelensi clinical isolate obtained
AB  - in 2001 from a patient with LD in Canterbury, New Zealand.
ER  -

TY  - JOUR
AU  - Slow, S.
AU  - Anderson, T.
AU  - Miller, J.
AU  - Singh, S.
AU  - Murdoch, D.
AU  - Biggs, P.J.
TI  - Complete Genome Sequence of a Legionella longbeachae Serogroup 1 Strain Isolated  from a Patient with Legionnaires' Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e00564
EP  - e00517
VL  - 5
AB  - Legionella longbeachae serogroup 1, predominantly found in soil and composted plant material,
AB  - causes the majority of cases of Legionnaires' disease (LD) in New
AB  - Zealand. Here, we report the complete genome sequence of an L. longbeachae
AB  - serogroup 1 (sg1) isolate derived from a patient hospitalized with LD in
AB  - Christchurch, New Zealand.
ER  -

TY  - JOUR
AU  - Smajs, D.
AU  - Zobanikova, M.
AU  - Strouhal, M.
AU  - Cejkova, D.
AU  - Dugan-Rocha, S.
AU  - Pospisilova, P.
AU  - Norris, S.J.
AU  - Albert, T.
AU  - Qin, X.
AU  - Hallsworth-Pepin, K.
AU  - Buhay, C.
AU  - Muzny, D.M.
AU  - Chen, L.
AU  - Gibbs, R.A.
AU  - Weinstock, G.M.
TI  - Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay.
JO  - PLoS ONE
PY  - 2011
SP  - e20415
EP  - e20415
VL  - 6
AB  - Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not
AB  - infectious to humans, although its
AB  - genome structure is very closely related to other pathogenic Treponema species including
AB  - Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the
AB  - genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a
AB  - combination of several high-throughput sequencing strategies. Whereas the overall size
AB  - (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those
AB  - of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number
AB  - of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were
AB  - also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded
AB  - proteins of known or predicted function in the Nichols genome. These proteins included
AB  - virulence factors, gene regulators and components of DNA repair and recombination. The
AB  - majority (52 or 61.9%) of the Cuniculi A
AB  - pseudogenes and divergent genes were of unknown function. Our results indicate that T.
AB  - paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized
AB  - host-associated niche (rabbits) during loss of infectivity to humans. The genes that are
AB  - inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important
AB  - in the infectivity and pathogenesis of T. pallidum subspecies.
ER  -

TY  - JOUR
AU  - Smalley, M.D.
AU  - Marinov, G.K.
AU  - Bertani, L.E.
AU  - DeSalvo, G.
TI  - Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1.
JO  - Genome Announcements
PY  - 2015
SP  - e00233
EP  - e00215
VL  - 3
AB  - Here, we report the genome sequence of Magnetospirillum magnetotacticum strain MS-1, which
AB  - consists of of 36 contigs and 4,136 protein-coding genes.
ER  -

TY  - JOUR
AU  - Smet, A.
AU  - Van Nieuwerburgh, F.
AU  - Ledesma, J.
AU  - Flahou, B.
AU  - Deforce, D.
AU  - Ducatelle, R.
AU  - Haesebrouck, F.
TI  - Genome Sequence of Helicobacter heilmannii Sensu Stricto ASB1 Isolated from the Gastric Mucosa of a Kitten with Severe Gastritis.
JO  - Genome Announcements
PY  - 2013
SP  - e00033
EP  - e00012
VL  - 1
AB  - Here we report the genome sequence of Helicobacter heilmannii sensu stricto ASB1  isolated
AB  - from the gastric mucosa of a kitten with severe gastritis. Helicobacter heilmannii sensu
AB  - stricto has also been associated with gastric disease in humans. Availability of this genome
AB  - sequence will contribute to the identification of genes involved in the pathogen's virulence
AB  - and carcinogenic properties.
ER  -

TY  - JOUR
AU  - Smet, A.
AU  - Van Nieuwerburgh, F.
AU  - Vandekerckhove, T.T.
AU  - Martel, A.
AU  - Deforce, D.
AU  - Butaye, P.
AU  - Haesebrouck, F.
TI  - Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences.
JO  - PLoS ONE
PY  - 2010
SP  - E11202
EP  - E11202
VL  - 5
AB  - BACKGROUND: CTX-M-producing Escherichia coli strains are regarded as major
AB  - global pathogens. METHODOLOGY/PRINCIPAL FINDINGS: The nucleotide sequence
AB  - of three plasmids (pEC_B24: 73801-bp; pEC_L8: 118525-bp and pEC_L46:
AB  - 144871-bp) from Escherichia coli isolates obtained from patients with
AB  - urinary tract infections and one plasmid (pEC_Bactec: 92970-bp) from an
AB  - Escherichia coli strain isolated from the joint of a horse with arthritis
AB  - were determined. Plasmid pEC_Bactec belongs to the IncI1 group and carries
AB  - two resistance genes: bla(TEM-1) and bla(CTX-M-15). It shares more than
AB  - 90% homology with a previously published bla(CTX-M)-plasmid from E. coli
AB  - of human origin. Plasmid pEC_B24 belongs to the IncFII group whereas
AB  - plasmids pEC_L8 and pEC_L46 represent a fusion of two replicons of type
AB  - FII and FIA. On the pEC_B24 backbone, two resistance genes, bla(TEM-1) and
AB  - bla(CTX-M-15), were found. Six resistance genes, bla(TEM-1),
AB  - bla(CTX-M-15), bla(OXA-1), aac6'-lb-cr, tetA and catB4, were detected on
AB  - the pEC_L8 backbone. The same antimicrobial drug resistance genes, with
AB  - the exception of tetA, were also identified on the pEC_L46 backbone.
AB  - Genome analysis of all 4 plasmids studied provides evidence of a seemingly
AB  - frequent transposition event of the bla(CTX-M-15)-ISEcp1 element. This
AB  - element seems to have a preferred insertion site at the tnpA gene of a
AB  - bla(TEM)-carrying Tn3-like transposon, the latter itself being inserted by
AB  - a transposition event. The IS26-composite transposon, which contains the
AB  - bla(OXA-1), aac6'-lb-cr and catB4 genes, was inserted into plasmids pEC_L8
AB  - and pEC_L46 by homologous recombination rather than a transposition event.
AB  - Results obtained for pEC_L46 indicated that IS26 also plays an important
AB  - role in structural rearrangements of the plasmid backbone and seems to
AB  - facilitate the mobilisation of fragments from other plasmids. CONCLUSIONS:
AB  - Collectively, these data suggests that IS26 together with ISEcp1 could
AB  - play a critical role in the evolution of diverse multiresistant plasmids
AB  - found in clinical Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Smirnova, N.I.
AU  - Cherkasov, A.V.
AU  - Krasnov, Y.M.
AU  - Agafonov, D.A.
AU  - Kutyrev, V.V.
TI  - Draft Whole-Genome Sequence of a New Variant of Vibrio cholerae O1 El Tor Strain  Isolated from a Cholera Patient in Russia.
JO  - Genome Announcements
PY  - 2014
SP  - e00432
EP  - e00414
VL  - 2
AB  - Draft whole-genome sequencing of the Vibrio cholerae capital O, Cyrillic1 El Tor  clinical
AB  - strain L3226, isolated in Moscow in 2010, was carried out. Various
AB  - mutations in the virulence-associated mobile elements were determined in its
AB  - genome that differentiated this strain from the reference V. cholerae capital O,
AB  - Cyrillic1 El Tor strain N16961.
ER  -

TY  - JOUR
AU  - Smirnova, N.I.
AU  - Krasnov, Y.M.
AU  - Agafonova, E.Y.
AU  - Shchelkanova, E.Y.
AU  - Alkhova, Z.V.
AU  - Kutyrev, V.V.
TI  - Whole-Genome Sequencing of Vibrio cholerae O1 El Tor Strains Isolated in Ukraine  (2011) and Russia (2014).
JO  - Genome Announcements
PY  - 2017
SP  - e01640
EP  - e01616
VL  - 5
AB  - Here, we present the draft whole-genome sequence of Vibrio cholerae O1 El Tor strains 76 and
AB  - M3265/80, isolated in Mariupol, Ukraine, and Moscow, Russia. The
AB  - presence of various mutations detected in virulence-associated mobile elements
AB  - indicates high genetic similarity of the strains reported here with new highly
AB  - virulent variants of the cholera agent V. cholerae.
ER  -

TY  - JOUR
AU  - Smith, A.E.
AU  - Ford, K.G.
TI  - Specific targeting of cytosine methylation to DNA sequences in vivo.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 740
EP  - 754
VL  - 35
AB  - Development of methods that will allow exogenous imposition of inheritable gene-specific
AB  - methylation patterns has potential application in both
AB  - therapeutics and in basic research. An ongoing approach is the use of
AB  - targeted DNA methyltransferases, which consist of a fusion between
AB  - gene-targeted zinc-finger proteins and prokaryotic DNA cytosine
AB  - methyltransferases. These enzymes however have so far demonstrated
AB  - significant and unacceptable levels of non-targeted methylation. We now
AB  - report the development of second-generation targeted methyltransferase
AB  - enzymes comprising enhanced zinc-finger arrays coupled to
AB  - methyltransferase mutants that are functionally dominated by their
AB  - zinc-finger component. Both in vitro plasmid methylation studies and a
AB  - novel bacterial assay reveal a high degree of target-specific methylation
AB  - by these enzymes. Furthermore, we demonstrate for the first time transient
AB  - expression of targeted cytosine methyltransferase in mammalian cells
AB  - resulting in the specific methylation of a chromosomal locus. Importantly,
AB  - the resultant methylation pattern is inherited through successive cell
AB  - divisions.
ER  -

TY  - JOUR
AU  - Smith, A.M.
AU  - Bosco, K.J.
AU  - Nicol, M.P.
AU  - Kleynhans, J.
AU  - McCulloch, M.
AU  - Duze, S.T.
AU  - Ismail, A.
AU  - Allam, M.
AU  - Tau, N.P.
AU  - Keddy, K.H.
TI  - Genome Sequence for Shiga Toxin-Producing Escherichia coli O26:H11, Associated with a Cluster of Hemolytic-Uremic Syndrome Cases in South Africa, 2017.
JO  - Genome Announcements
PY  - 2017
SP  - e00989
EP  - e00917
VL  - 5
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are primarily foodborne pathogens that
AB  - may cause diarrheal outbreaks and are associated with severe
AB  - complications, specifically hemolytic-uremic syndrome (HUS). We report here
AB  - genome sequence data for STEC O26:H11, which is associated with a cluster of
AB  - cases of HUS, a rarely described syndrome in South Africa.
ER  -

TY  - JOUR
AU  - Smith, A.M.
AU  - Naicker, P.
AU  - Bamford, C.
AU  - Shuping, L.
AU  - McCarthy, K.M.
AU  - Sooka, A.
AU  - Smouse, S.L.
AU  - Tau, N.
AU  - Keddy, K.H.
TI  - Genome Sequences for a Cluster of Human Isolates of Listeria monocytogenes Identified in South Africa in 2015.
JO  - Genome Announcements
PY  - 2016
SP  - e00200
EP  - e00216
VL  - 4
AB  - Listeria monocytogenesis a Gram-positive bacterium with a ubiquitous presence in  the
AB  - environment. There is growing concern about the increasing prevalence ofL.
AB  - monocytogenesassociated with food-borne outbreaks. Here we report genome
AB  - sequences for a cluster of human isolates ofL. monocytogenesidentified in South
AB  - Africa in 2015.
ER  -

TY  - JOUR
AU  - Smith, B.A.
AU  - Dougherty, K.M.
AU  - Baltrus, D.A.
TI  - Complete Genome Sequence of the Highly Transformable Pseudomonas stutzeri Strain  28a24.
JO  - Genome Announcements
PY  - 2014
SP  - e00543
EP  - e00514
VL  - 2
AB  - Here, we report the complete genome sequence for an isolate of Pseudomonas stutzeri that is
AB  - highly competent for natural transformation. This sequence
AB  - enables insights into the genetic basis of natural transformation rate variations
AB  - and provides an additional data point for genomic comparisons across a ubiquitous
AB  - and highly diverse bacterial species.
ER  -

TY  - JOUR
AU  - Smith, B.R.
AU  - Unckless, R.L.
TI  - Draft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory-Derived Pathogen of Drosophila melanogaster.
JO  - Genome Announcements
PY  - 2018
SP  - e01571
EP  - e01517
VL  - 6
AB  - Drosophila melanogaster is a model for the study of innate immunity, yet we have  limited
AB  - knowledge of its natural pathogens. In this study, we sequenced the
AB  - genome of Lysinibacillus fusiformis strain Juneja, isolated from laboratory fly
AB  - stocks. As a Gram-positive bacterium with unique peptidoglycans, this strain may
AB  - provide a new model for pathogen recognition.
ER  -

TY  - JOUR
AU  - Smith, C.J.
AU  - Parker, A.
AU  - Rogers, M.B.
TI  - Plasmid transformation of Bacteroides spp. by electroporation.
JO  - Plasmid
PY  - 1990
SP  - 100
EP  - 109
VL  - 24
AB  - Transformation of Bacterioides spp. with a variety of plasmid DNAs was accomplished using
AB  - electroporation. The standard transformation assay system used to deduce the optimal
AB  - electroporation parameters employed a 50-to 100-fold concentrated cell suspension of
AB  - mid-logarithmic phase Bacterioides fragilis strain 638 and the 5.4-kb clindamycin resistance
AB  - (Ccr) vector pBI191. A variety of electroporation buffers were used successfully in
AB  - transformation experiments but of these 1 mM MgCl2 in 10% glycerol was superior. The
AB  - incorporation of MgCl2 was essential for optimum viability prior to electroporation and for
AB  - optimum transformation. Transformants were routinely obtained using 5-ms pulses over a range
AB  - of field strengths from 5 to 12.5 kV/cm, with a maximum of >1000000/ug DNA at 12.5 kV/cm. The
AB  - number of transformants increased linearly with respect to DNA concentration over the range
AB  - 0.01-2 ug tested. Recovery of transformants required an expression period of up to 2.5 h
AB  - following exposure to the electric field. This period, however, was dependent on the
AB  - antibiotic resistance marker used for selection of transformants, with a significantly shorter
AB  - incubation required when chloramphenicol rather than clindamycin was used in the selective
AB  - medium. The effect of the DNA source of transformation was tested using the shuttle vector
AB  - pFD288. Plasmid DNA isolated from Bacteriodes uniformis, Bacteroides ovatus, or Bacteroides
AB  - thetaiotaomicron transformed B. fragilis 638 at frequencies 7.5 to 12.5 fold less than those
AB  - observed for controls with homologous DNA. Further reductions were seen with Escherichia coli
AB  - purified pFD288, which transformed at 1000-fold lower frequencies. Finally, using homologous
AB  - pFD288 or pBI191 isolated from strain 638, several strains of B. fragilis, B. uniformis, and
AB  - B. ovatus were transformed successfully without modification of the standard assay system. Two
AB  - strains each of B. thetaiotaomicron and Baceriodes ruminicola were not transformed using the
AB  - methods described here.
ER  -

TY  - JOUR
AU  - Smith, D.D.
AU  - Kirzinger, M.W.
AU  - Stavrinides, J.
TI  - Draft Genome Sequence of the Antibiotic-Producing Epiphytic Isolate Pantoea ananatis BRT175.
JO  - Genome Announcements
PY  - 2013
SP  - e00902
EP  - e00913
VL  - 1
AB  - Pantoea is a member of the Enterobacteriaceae, whose members have been shown to produce novel
AB  - antibiotics. Here, we report the 4.8-Mb genome sequence of Pantoea
AB  - ananatis strain BRT175, an epiphytic isolate from strawberries that produces an
AB  - antibiotic that is effective against the fire blight pathogen, Erwinia amylovora.
ER  -

TY  - JOUR
AU  - Smith, D.D.
AU  - Kirzinger, M.W.
AU  - Stavrinides, J.
TI  - Draft Genome Sequence of the Antibiotic-Producing Cystic Fibrosis Isolate Pantoea agglomerans Tx10.
JO  - Genome Announcements
PY  - 2013
SP  - e00904
EP  - e00913
VL  - 1
AB  - Pantoea agglomerans is an enteric bacterium that is capable of causing both plant and human
AB  - disease. Here, we report the genome sequence of a cystic fibrosis
AB  - isolate, P. agglomerans Tx10, which produces an antibiotic that is effective
AB  - against Staphylococcus aureus.
ER  -

TY  - JOUR
AU  - Smith, D.E.
AU  - Gemmen, G.J.
AU  - Millin, R.
TI  - DNA looping and cleavage by restriction enzymes studied by manipulation of single DNA molecules with optical tweezers.
JO  - Proc. SPIE-Int. Soc. Opt. Eng.
PY  - 2006
SP  - 1
EP  - 13
VL  - 6326
AB  - Looping and cleavage of single DNA molecules by the two-site restriction endonuclease Sau3AI
AB  - were measured with optical tweezers.  A DNA template containing many recognition sites was
AB  - used, permitting loop sizes from ~10 to 10,000 basepairs.  At high enzyme concentration
AB  - cleavage events were detected within 5 seconds and nearly all molecules were cleaved within 5
AB  - minutes.  Activity decreased ~10-fold as the DNA tension was increased from 0.03 to 0.7 pN.
AB  - Substituting Ca2+ for Mg2+ blocked cleavage, permitting measurement of stable loops.  At low
AB  - tension, the initial rates of cleavage and looping were similar (~0.025 s-1 at 0.1 pN),
AB  - suggesting that looping is rate limiting.  Short loops formed more rapidly than long loops.
AB  - The optimum size decreased from ~250 to 45 bp and the average number of loops (in 1 minute)
AB  - from 4.2 to 0.75 as tension was increased from 0.03 to 0.7 pN.  No looping was detected at 5
AB  - pN.  These findings are in qualitative agreement with recent theoretical predictions
AB  - considering only DNA mechanics, but we observed weaker suppression with tension and smaller
AB  - loop sizes.  Our results suggest that the span and elasticity of the protein complex and
AB  - protein-induced DNA bending and wrapping play an important role.
ER  -

TY  - JOUR
AU  - Smith, D.I.
AU  - Blattner, F.R.
AU  - Davies, J.
TI  - The isolation and partial characterization of a new restriction endonuclease from Providencia stuartii.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 343
EP  - 353
VL  - 3
AB  - We describe the isolation of a new class 2 restriction endonuclease from
AB  - Providencia stuartii 164.  Using the procedure of osmotic shock treatment, we
AB  - have partially purified this enzyme (PstI) and have begun preliminary work to
AB  - characterize its specificity and requirements.  PstI requires Mg++ as the only
AB  - cofactor and produces more than 18 cleavages in wild type lambda.  We have
AB  - determined the location of 7 of these cleavages by the use of deletion and
AB  - insertion mutants of lambda.
ER  -

TY  - JOUR
AU  - Smith, D.I.
AU  - Golembieski, W.
AU  - Gilbert, J.D.
AU  - Kizyma, L.
AU  - Miller, O.J.
TI  - Overabundance of rare-cutting restriction endonuclease sites in the human genome.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 1173
EP  - 1184
VL  - 15
AB  - A human chromosome 3-specific cosmid library was constructed from a somatic
AB  - cell hybrid containing human chromosome 3 as its only human component.  This
AB  - library was screened to identify 230 human recombinants which contained an
AB  - average insert size of 37 kilobases.  DNA prepared from 54 of these cosmids,
AB  - representing 2000 kilobases of human DNA, was then tested for restriction
AB  - endonuclease sites for EcoRI, HindIII, KpnI, XhoI, and DraI, as well as those
AB  - of the rare-cutting restriction endonucleases NotI, SfiI, NruI, MluI, SacII,
AB  - and BssHII.  Sites for the latter enzymes were much more abundant than would be
AB  - expected from theoretical calculations, reflecting non-random clustering of
AB  - these sites.  This has important implications for the use of these enzymes in
AB  - the construction of physical maps of chromosomes.  Some individual cosmids
AB  - contained large numbers of rare sites, offering an alternative means of
AB  - physically mapping chromosomes based upon identifying clusters of rare
AB  - restriction sites.  These clusters appear to be spaced an average of 1000 kb
AB  - apart.
ER  -

TY  - JOUR
AU  - Smith, D.R.
TI  - Restriction endonuclease digestion of DNA..
JO  - Methods Mol. Biol.
PY  - 1996
SP  - 11
EP  - 15
VL  - 58
AB  - The ability to cleave DNA at specific sites is one of the cornerstones of today's methods of
AB  - DNA manipulation.  Restriction endonucleases are bacterial enzymes that cleave duplex DNA at
AB  - specific target sequences with the production of defined fragments.  These enzymes can be
AB  - purchased from the many manufacturers of biotechnology products.  The nomenclature of enzymes
AB  - is based on a simple system, proposed by Smith and Nathans.  The name of the enzyme (such as
AB  - BamHI, EcoRI, and so on) tells us about the origin of the enzyme, but does not give us any
AB  - information about the specificity of cleavage.  This has to be determined for each individual
AB  - enzyme.  The recognition site for most of the commonly used enzymes is a short palindromic
AB  - sequence, usually either 4, 5, or 6 bp in length, such as AGCT (for AluI), GAATTC (for EcoRI),
AB  - and so on.  Each enzyme cuts the palindrome at a particular site, and two different enzymes
AB  - may have the same recognition sequence, but cleave the DNA at different points within that
AB  - sequence.  The cleavage sites fall into three different categories, either flush (or blunt) in
AB  - which the recognition site is cut in the middle, or with either 5'- or 3'-overhangs, in
AB  - which case unpaired bases will be produced on both ends of the fragment.  For a comprehensive
AB  - review of restriction endonucleases, see Fuchs and Blakesley.
ER  -

TY  - JOUR
AU  - Smith, D.R. et al.
TI  - Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics.
JO  - J. Bacteriol.
PY  - 1997
SP  - 7135
EP  - 7155
VL  - 179
AB  - The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium
AB  - thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach.
AB  - A total of 1,855 open reading frames have been identified that appear to encode polypeptides,
AB  - 844 (46%) of which have been assigned putative functions based on their similarities to
AB  - database sequences with assigned functions.  A total of 514 (28%) of the ORF-encoded
AB  - polypeptides are related to sequences with unknown functions, and 496 (27%) have little or no
AB  - homology to sequences in public databases.  Comparisons with Eucarya-, Bacteria-, and
AB  - Archaea-specific databases reveal that 1,013 of the putative gene products (54%) are most
AB  - similar to polypeptide sequences described previously for other organisms in the domain
AB  - Archaea.  Comparisons with the Methanococcus jannaschii genome data underlie the extensive
AB  - divergence that has occurred between these two methanogens; only 352 (19%) of M.
AB  - thermoautotrophicum ORFs encode sequences that are >50% identical to M. jannaschii
AB  - polypeptides, and there is little conservation in the relative locations of orthologous genes.
AB  - When the M. thermoautotrophicum ORFs are compared to sequences from only the eucaryal and
AB  - bacterial domains, 786 (42%) are more similar to bacterial sequences and 241 (13%) are more
AB  - similar to eucaryal sequences.  The bacterial domain-like gene products include the majority
AB  - of those predicted to be involved in cofactor and small molecule biosyntheses, intermediary
AB  - metabolism, transport, nitrogen fixation, regulatory functions, and interactions with the
AB  - environment.  Most proteins predicted to be involved in DNA metabolism, transcription, and
AB  - translation are more similar to eucaryal sequences.  Gene structure and organization have
AB  - features that are typical of the Bacteria, including genes that encode polypeptides closely
AB  - related to eucaryal proteins.  There are 24 polypeptides that could form two-component sensor
AB  - kinase-response regulator systems and homologs of the bacterial Hsp70-response proteins DnaK
AB  - and DnaJ, which are notably absent in M. jannaschii.  DNA replication initiation and
AB  - chromosome packaging in M. thermoautotrophicum are predictd to have eucaryal features, based
AB  - on the presence of two Cdc6 homologs and three histones; however, the presence of an ftsZ gene
AB  - indicates a bacterial type of cell division initiation.  The DNA polymerases include an
AB  - X-family repair type and an unusual archaeal B type formed by two separate polypeptides.  The
AB  - DNA-dependent RNA polymerase subunits A', A", B', B" and H are encoded in a typical archaeal
AB  - RNAP operon, although a second A' subunit-encoding gene is present at a remote location.
AB  - There are two rRNA operons, and 39 tRNA genes are dispersed around the genome, although most
AB  - of these occur in clusters.  Three of the tRNA genes have introns, including the tRNAPro (GGG)
AB  - gene, which contains a second intron at an unprecedented location.  There is no
AB  - selenocysteinyl-tRNA gene nor evidence for classically organized IS elements, prophages, or
AB  - plasmids.  The genome contains one intein and two extended repeats (3.6 and 8.6 kb) that are
AB  - members of a family with 18 representatives in the M. jannaschii genome.
ER  -

TY  - JOUR
AU  - Smith, D.W.
AU  - Crowder, S.W.
AU  - Reich, N.O.
TI  - In vivo specificity of EcoRI DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6091
EP  - 6096
VL  - 20
AB  - The EcoRI adenine DNA methyltransferase forms part of a bacterial restriction/modification
AB  - system; the methyltransferase modifies the second adenine within the canonical site GAATTC,
AB  - thereby preventing the EcoRI endonuclease from cleaving this site. We show that five
AB  - noncanonical EcoRI sites (TAATTC, CAATTC, GTATTC, GGATTC and GAGTTC) are not methylated in
AB  - vivo under conditons when the canonical site is methylated. Only when the methyltransferase is
AB  - overxpressed is partial in vivo methylation of the five sites detected. Our results suggest
AB  - that the methyltransferase does not protect host DNA against potential endonuclease-mediated
AB  - cleavage at noncanonical sites. Our related in vitro analysis of the methyltransferase reveals
AB  - a low level of sequence-discrimination. We propose that the high in vivo specificity may be
AB  - due to the active removal of methylated sequences by DNA repair enzymes (J. Bacteriology
AB  - (1987), 169 3243-3250).
ER  -

TY  - JOUR
AU  - Smith, H.
AU  - Abuyen, K.
AU  - Tremblay, J.
AU  - Savalia, P.
AU  - Perez-Rodriguez, I.
AU  - Emerson, D.
AU  - Tully, B.
AU  - Amend, J.
TI  - Genome Sequence of Geothermobacter sp. Strain HR-1, an Iron Reducer from the Lo'ihi Seamount, Hawai'i.
JO  - Genome Announcements
PY  - 2018
SP  - e00339
EP  - e00318
VL  - 6
AB  - Geothermobacter sp. strain HR-1 was isolated from the Lo'ihi Seamount vent system in the
AB  - Pacific Ocean at a depth of 1,000 m. Reported here is its 3.84-Mb genome
AB  - sequence.
ER  -

TY  - JOUR
AU  - Smith, H.
AU  - Akiyama, T.
AU  - Foreman, C.
AU  - Franklin, M.
AU  - Woyke, T.
AU  - Teshima, H.
AU  - Davenport, K.
AU  - Daligault, H.
AU  - Erkkila, T.
AU  - Goodwin, L.
AU  - Gu, W.
AU  - Xu, Y.
AU  - Chain, P.
TI  - Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00960
EP  - e00913
VL  - 1
AB  - Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a
AB  - psychrotolerant non-violacein-producing bacterium that was isolated from the
AB  - Cotton Glacier supraglacial stream. The genome sequence of this organism will
AB  - provide insight as to the mechanisms necessary for bacteria to survive in
AB  - UV-stressed icy environments.
ER  -

TY  - JOUR
AU  - Smith, H.J.
AU  - Foreman, C.M.
AU  - Akiyama, T.
AU  - Franklin, M.J.
AU  - Devitt, N.P.
AU  - Ramaraj, T.
TI  - Genome Sequence of Janthinobacterium sp. CG23_2, a Violacein-Producing Isolate from an Antarctic Supraglacial Stream.
JO  - Genome Announcements
PY  - 2016
SP  - e01468
EP  - e01415
VL  - 4
AB  - Here, we present the draft genome sequence for the violacein-producing Janthinobacterium sp.
AB  - CG23_2 isolated from an Antarctic supraglacial stream. The
AB  - genome is ~7.85 Mb, with a G+C content of 63.5%. The genome includes 7,247
AB  - candidate protein coding genes, which may provide insight into UV tolerance
AB  - mechanisms.
ER  -

TY  - JOUR
AU  - Smith, H.J.
AU  - Foreman, C.M.
AU  - Ramaraj, T.
TI  - Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences  Single-Molecule Real-Time Sequencing Technology.
JO  - Genome Announcements
PY  - 2014
SP  - e01242
EP  - e01214
VL  - 2
AB  - Polaromonas species are found in a diversity of environments and are particularly common in
AB  - icy ecosystems. Polaromonas sp. strain CG9_12 is an aerobic,
AB  - Gram-negative, catalase-positive, white-pigmented bacterium of the Proteobacteria
AB  - phylum. Here, we present the draft genome sequence of Polaromonas sp. strain
AB  - CG9_12, isolated from an Antarctic supraglacial stream.
ER  -

TY  - JOUR
AU  - Smith, H.O.
TI  - Restriction endonucleases as enzymatic tools for DNA analysis and genetic manipulation.
JO  - PAABS Revista
PY  - 1976
SP  - 313
EP  - 319
VL  - 5
AB  - Living cells contain a variety of nucleases capable of cleaving the
AB  - phosphodiester bonds of nucleic acid chains.  These are generally of two kinds:
AB  - exonucleases that act at chain termini to release nucleotides or
AB  - oligonucleotides, and endonucleases that cleave at internal bonds.  Many
AB  - endonucleases act randomly, cleaving each phosphodiester bond with about equal
AB  - probability regardless of the local base sequence.  Several years ago a new
AB  - class of DNA nucleases that cleave both strands of double-stranded DNA at sites
AB  - of specific base sequence, four to six bases in length, was discovered in
AB  - bacteria.  These endonucleases are called restriction enzymes because they are
AB  - components of bacterial restriction-modification (R-M) systems that determine a
AB  - host-specific DNA immunity mechanism.  Each R-M system consists of a
AB  - restriction endonuclease and a modification methylase of similar site
AB  - specificity.  The modification enzyme methylates sites in the host chromosome
AB  - to protect against cleavage by their restriction endonuclease.  However,
AB  - improperly methylated foreign DNA entering the cell, for example, by virus
AB  - infection, will be cleaved and subsequently degraded to nucleotides by cellular
AB  - exonucleases.  Since their discovery, restriction endonucleases have been
AB  - widely exploited as new tools for DNA analysis because of their ability to
AB  - cleave DNA molecules at only a few sites to produce specific DNA fragments.
AB  - Restriction fragments from a given DNA molecule may be ordered into a physical
AB  - map that can serve as a framework for location of genetic functions and for
AB  - nucleotide sequence analysis.  The possibilities of using restriction
AB  - endonucleases for genetic manipulation have aroused great interest.  Novel
AB  - kinds of recombinant DNA molecules can be constructed by rearranging DNA
AB  - fragments within a chromosome or by joining fragments from one species to those
AB  - of another to form hybrid chromosomes.  Fragments bearing specific genes may be
AB  - joined to self-replicating viral or plasmid chromosomes and isolated by
AB  - molecular cloning in suitable host bacteria.  The recombinant plasmid or virus
AB  - DNAs often exist as multiple copies intracellularly, thus providing large
AB  - quantities of the inserted DNA fragments for sequence analysis and studies of
AB  - gene organization and function.  In many cases, products of inserted genes,
AB  - such as specific enzymes, are obtained in high yield.  In a brief 3 to 4 years,
AB  - a whole new recombinant DNA technology has arisen that has many important
AB  - potential commercial as well as research applications. This review will briefly
AB  - cover properties of restriction endonucleases and their major applications.
AB  - Comprehensive reviews have been written by Arber and Nathans and Smith.
ER  -

TY  - JOUR
AU  - Smith, H.O.
TI  - Nucleotide sequence specificity of restriction endonucleases.
JO  - Science
PY  - 1979
SP  - 455
EP  - 462
VL  - 205
AB  - In the past 7 to 8 years we have witnessed the development of a new DNA
AB  - technology that has fundamentally altered our approach to modern genetics.  The
AB  - basic ingredients of this new technology are the cleavage site-specific
AB  - restriction enzymes: a special class of bacterial endonucleases that can
AB  - recognize specific nucleotide sequenceas in duplex DNA and produce
AB  - double-stranded cleavages.  A collection of these enzymes, each with its own
AB  - particular sequence specificity, can be used to cleave DNA molecules into
AB  - unique sets of fragments for DNA sequencing, chromosome analysis, gene
AB  - isolation, and construction of recombinant DNA.  The latter, together with the
AB  - concept of molecular cloning, has given birth to the new field of genetic
AB  - engineering, and from this many new and exciting medical and research
AB  - applications are expected.  My own role in these developments occurred
AB  - primarily in the period of 1968 to 1970 when my colleagues and I made the
AB  - chance discovery of the first of the cleavage site-specific restriction
AB  - enzymes.  I now briefly present this work in historical context because it
AB  - leads naturally into the main part of my lecture, describing our present
AB  - knowledge of restriction and modification enzymes.  Although many applications
AB  - have been reviewed, I should like to describe in some detail the use of these
AB  - enzymes as model systems for studying sequence-specific interactions of protein
AB  - and DNA, which is one of the major research interests in my laboratory.
ER  -

TY  - JOUR
AU  - Smith, H.O.
TI  - Restriction endonuclease from Hemophilus influenzae Rd.
JO  - Methods Mol. Biol.
PY  - 1974
SP  - 71
EP  - 85
VL  - 7
AB  - A growing number of molecular biologists are turning to restriction enzymes as
AB  - tools for analysis of DNA molecules and chromosomal DNA.  Restriction enzymes
AB  - are site-specific endonucleases that can be isolated from various strains of
AB  - bacteria.  They are capable of recognizing particular base sequences within
AB  - native DNA molecules and producing double-strand cleavage.  Thus viral genomes
AB  - or other DNA molecules may be cleaved in a highly specific and reproducible
AB  - manner into a number of double-stranded fragments.  These are useful for
AB  - localization of genetic functions, DNA base sequencing, and a number of other
AB  - purposes.  This article describes the purification of restriction enzyme from
AB  - H. influenzae Rd.  The procedure is similar to that reported by Smith and
AB  - Wilcox but incorporates modifications which facilitate assay and large scale
AB  - purification.
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Annau, T.M.
AU  - Chandrasegaran, S.
TI  - Finding sequence motifs in groups of functionally related proteins.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1990
SP  - 826
EP  - 830
VL  - 87
AB  - We have developed a method for rapidly finding patterns of conserved amino acid
AB  - residues (motifs) in groups of functionally related proteins.  All 3-amino acid
AB  - patterns in a group of proteins of the type aa1 d1 aa2 d2 aa3, where d1 and d2
AB  - are distances that can be varied in a range up to 24 residues, are accumulated
AB  - into an array.  Segments of the proteins are aligned on each other by a scoring
AB  - method that obtains an average relatedness value for all the amino acids in
AB  - each column of the aligned sequence block based on the Dayhoff relatedness odds
AB  - matrix.  The automated method successfully finds and displays nearly all of the
AB  - sequence motifs that have been previously reported to occur in 33 reverse
AB  - transcriptases, 18 DNA integrases, and 30 DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Birnstiel, M.L.
TI  - A simple method for DNA restriction site mapping.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 2387
EP  - 2399
VL  - 9
AB  - When a DNA molecule, enzymatically labelled with 32P at one end, is partially
AB  - digested with a restriction enzyme labelled DNA fragments are obtained which
AB  - form an overlapping series of molecules, all with a common labelled terminus.
AB  - A restriction map can then be constructed from an analysis of the size
AB  - distribution of these molecules.  This technique has been used for the
AB  - restriction site mapping of cloned histone DNA (h22) where as many as 35
AB  - cleavage sites may be accurately determined in a single experiment.
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Kelly, S.V.
TI  - Methylases of the type II restriction-modification systems.
JO  - DNA Methylation. Biochemistry and Biological Significance.
PY  - 1984
SP  - 39
EP  - 71
VL  - 0
AB  - Most bacteria contain a small fraction (0.5-2%) of methylated cytosine or
AB  - adenine bases in their chromosomes.  Some of this methylation apparently plays
AB  - a role in directing mismatch repair systems to the correct strands in newly
AB  - replicated DNA.  However, in many bacterial strains, a substantial fraction can
AB  - be identified with host-specific restriction-modification (RM) systems.  These
AB  - ubiquitous systems play an important biological role in protecting bacteria
AB  - against viral infections.  Each system has two functional components: 1) a
AB  - restriction endonuclease capable of recognizing sequence-specific sites in DNA
AB  - and producing double-stranded cleavage; and 2) a modification enzyme
AB  - recognizing the same DNA sites as the restriction enzyme and protecting them by
AB  - modification.  So far, all modifications found are either 5-methylcytosine or
AB  - 6-methyladenine.  The modification enzymes are methyltransferases, and AdoMet
AB  - appears to be the exclusively methyl group donor.  (For reviews, see Arber,
AB  - 1974; Modrich, 1979; Smith, 1979; Modrich and Roberts, 1982).
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Kelly, T.J.
AU  - Roy, P.H.
TI  - Enzymatic methods for sequence analysis applied to DNA restriction and methylation sites.
JO  - Methods Enzymol.
PY  - 1974
SP  - 282
EP  - 294
VL  - 29
AB  - Restriction enzymes are site-specific endonucleases produced by various
AB  - bacteria, bacterial plasmids, and viruses.  In those cases where they produce
AB  - double-stranded cleavage of DNA within their recognition sites, sequence
AB  - analysis of the site is equivalent to determination of the 5'- and 3'-terminal
AB  - bases of the restricted DNA.  We have developed special enzymatic methods for
AB  - limited analysis of this type.  In addition, every host that produces a
AB  - restriction endonuclease also produces a companion DNA modification enzyme,
AB  - usually a methylase, with identical or similar site recognition.  This enzyme
AB  - serves to modify and protect the restriction sites of the host chromosome.  In
AB  - the second section of this chapter we describe a procedure for partial analysis
AB  - of methylation sites.
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Marley, G.M.
TI  - Purification and properties of HindII and HindIII endonucleases from Haemophilus influenzae Rd.
JO  - Methods Enzymol.
PY  - 1980
SP  - 104
EP  - 108
VL  - 65
AB  - Haemophilus influenzae Rd is the source for two restriction endonucleases,
AB  - HindII and HindIII, that may be separated and purified using conventional ion
AB  - exchange chromatography media.  The basic steps in the procedure are removal of
AB  - nucleic acids from the cell extract, separation of the two activities by
AB  - DEAE-cellulose chromatography, and chromatography of each activity on
AB  - phosphocellulose as a combined purification and concentration step.
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Nathans, D.
TI  - A suggested nomenclature for bacterial host modification and restriction systems and their enzymes.
JO  - J. Mol. Biol.
PY  - 1973
SP  - 419
EP  - 423
VL  - 81
AB  - In the proposed nomenclature restriction-modification systems are named
AB  - according to host organism and strain.  Different R-M+ systems in a single host
AB  - are designated by Roman numerals.  Restriction nucleases and modification
AB  - methylases are given the general names endonuclase R and methylase M, followed
AB  - by their R-M system name.
ER  -

TY  - JOUR
AU  - Smith, H.O.
AU  - Wilcox, K.W.
TI  - A restriction enzyme from Hemophilus influenzae. I. Purification and general properties.
JO  - J. Mol. Biol.
PY  - 1970
SP  - 379
EP  - 391
VL  - 51
AB  - Extracts of Hemophilus influenzae strain Rd contain an endonuclease activity
AB  - which produces a rapid decrease in the specific viscosity of a variety of
AB  - foreign native DNA's; the specific viscosity of H. influenzae DNA is not
AB  - altered under the same conditions.  This "restriction" endonuclease activity
AB  - has been purified approximately 200-fold.  The purified enzyme contains no
AB  - detectable exo- or endonucleolytic activity against H. influenzae DNA.
AB  - However, with native phage T7 DNA as substrate, it produces about 40
AB  - double-strand 5'-phosphoryl, 3'-hydroxyl cleavages.  The limit product has an
AB  - average length of about 1000 nucleotide pairs and contains no single-strand
AB  - breaks.  The enzyme is inactive on denatured DNA and it requires no special
AB  - co-factors other than magnesium ions.
ER  -

TY  - JOUR
AU  - Smith, H.R.
AU  - Humphreys, G.O.
AU  - Willshaw, G.A.
AU  - Anderson, E.S.
TI  - Characterisation of plasmids coding for the restriction endonuclease EcoRI.
JO  - Mol. Gen. Genet.
PY  - 1976
SP  - 319
EP  - 325
VL  - 143
AB  - The properties of two plasmids coding for the CcoRI restriction and modification enzymes are
AB  - described. Both plasmids are non
AB  - auto-transferring (NTP) but can be mobilised by transfer factors. Strains
AB  - carrying NTP13 produce colicin E1 and the EcoRI enzymes. This plasmid has
AB  - a molecular weight of 6 X 10(6) daltons and is present as approximately 12
AB  - copies per chromosome. The second plasmid, NTP14, was detected after
AB  - mobilisation of the EcoRI plasmid with the R factor RI-19. NTP14 codes for
AB  - ampicillin resistance, synthesis of the EcoRI enzymes and colicin E1. The
AB  - molecular weight of NTP14 is 10.7 X 10(6) daltons and there are about 14
AB  - copies per chromosome. DNA-DNA reassociation experiments were performed to
AB  - determine the interrelationships of NTP13, NTP14, ColE1 and the R factor
AB  - R1-19. NTP13 and NTP14 continue to replicate when cellular protein
AB  - synthesis is inhibited by the addition of chloramphenicol.
ER  -

TY  - JOUR
AU  - Smith, H.S.
TI  - The restriction of T2 bacteriophage by Escherichia coli, strain W.
JO  - Diss. Abstr.
PY  - 1968
SP  - 9292B
EP  - 9292B
VL  - 29
AB  - This thesis presents studies on the restriction of T2 bacteriophage infection
AB  - by Escherichia coli strain W, a bacterial strain lysogenic for a prophage which
AB  - is related to bacteriophage P2.
ER  -

TY  - JOUR
AU  - Smith, J.
AU  - Berg, J.M.
AU  - Chandrasegaran, S.
TI  - A detailed study of the substrate specificity of a chimeric restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 674
EP  - 681
VL  - 27
AB  - Recently, the crystal structure of the designed zinc finger protein, deltaQNK, bound to a
AB  - preferred DNA sequence was reported.  We have converted deltaQNK into a novel site-specific
AB  - endonuclease by linking it to the FokI cleavage domain (FN).  The substrate specificity and
AB  - DNA cleavage properties of the resulting chimeric restriction enzyme (deltaQNK-FN) were
AB  - investigated, and the binding affinities of deltaQNK and deltaQNK-FN for various DNA
AB  - substrates were determined.  Substrates that are bound by deltaQNK with high affinity are the
AB  - same as those that are cleaved efficiently by deltaQNK-FN.  The binding of deltaQNK-FN to each
AB  - substrate was ~2-fold weaker than that for deltaQNK.  Thus, the fusion of the FokI cleavage
AB  - domain to the zinc finger motif does not change the DNA sequence specificity of the zinc
AB  - finger protein and does not change its binding affinity significantly.
ER  -

TY  - JOUR
AU  - Smith, J.
AU  - Bibikova, M.
AU  - Whitby, F.G.
AU  - Reddy, A.R.
AU  - Chandrasegaran, S.
AU  - Carroll, D.
TI  - Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3361
EP  - 3369
VL  - 28
AB  - This study concerns chimeric restriction enzymes that are hybrids between a zinc finger
AB  - DNA-binding domain and the non-specific DNA-cleavage domain from the natural restriction
AB  - enzyme FokI. Because of the flexibility of DNA recognition by zinc fingers, these enzymes are
AB  - potential tools for cleaving DNA at arbitrarily selected sequences. Efficient double-strand
AB  - cleavage by the chimeric nucleases requires two binding sites in close proximity. When cuts
AB  - were mapped on the DNA strands, it was found that they occur in pairs separated by
AB  - approximately 4 bp with a 5' overhang, as for native FokI. Furthermore, amino acid changes
AB  - in the dimer interface of the cleavage domain abolished activity. These results reflect a
AB  - requirement for dimerization of the cleavage domain. The dependence of cleavage efficiency on
AB  - the distance between two inverted binding sites was determined and both upper and lower limits
AB  - were defined. Two different zinc finger combinations binding to non-identical sites also
AB  - supported specific cleavage. Molecular modeling was employed to gain insight into the precise
AB  - location of the cut sites. These results define requirements for effective targets of chimeric
AB  - nucleases and will guide the design of novel specificities for directed DNA cleavage in vitro
AB  - and in vivo.
ER  -

TY  - JOUR
AU  - Smith, J.
AU  - Grizot, S.
AU  - Arnould, S.
AU  - Duclert, A.
AU  - Epinat, J.C.
AU  - Prieto, P.C.
AU  - Redondo, P.
AU  - Blanco, F.J.
AU  - Bravo, J.
AU  - Montoya, G.
AU  - Paques, F.
AU  - Duchateau, P.
TI  - A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - e149
EP  - e149
VL  - 34
AB  - Meganucleases, or homing endonucleases (HEs) are sequence-specific endonucleases with large
AB  - (>14 bp) cleavage sites that can be used to
AB  - induce efficient homologous gene targeting in cultured cells and plants.
AB  - These findings have opened novel perspectives for genome engineering in a
AB  - wide range of fields, including gene therapy. However, the number of
AB  - identified HEs does not match the diversity of genomic sequences, and the
AB  - probability of finding a homing site in a chosen gene is extremely low.
AB  - Therefore, the design of artificial endonucleases with chosen
AB  - specificities is under intense investigation. In this report, we describe
AB  - the first artificial HEs whose specificity has been entirely redesigned to
AB  - cleave a naturally occurring sequence. First, hundreds of novel
AB  - endonucleases with locally altered substrate specificity were derived from
AB  - I-CreI, a Chlamydomonas reinhardti protein belonging to the LAGLIDADG
AB  - family of HEs. Second, distinct DNA-binding subdomains were identified
AB  - within the protein. Third, we used these findings to assemble four sets of
AB  - mutations into heterodimeric endonucleases cleaving a model target or a
AB  - sequence from the human RAG1 gene. These results demonstrate that the
AB  - plasticity of LAGLIDADG endonucleases allows extensive engineering, and
AB  - provide a general method to create novel endonucleases with tailored
AB  - specificities.
ER  -

TY  - JOUR
AU  - Smith, J.D.
AU  - Arber, W.
AU  - Kuhnlein, U.
TI  - Host specificity of DNA by Escherichia coli. XIV.  The role of nucleotide methylation in in vivo B-specific modification.
JO  - J. Mol. Biol.
PY  - 1972
SP  - 1
EP  - 8
VL  - 63
AB  - N-6-methyladenine is the only methylated base detected in bacteriophage fd DNA.
AB  - Its frequency is (1) host dependent: fd grown on a strain providing B-specific
AB  - modification to DNA carries twice as many methyl moieties in its DNA as phage
AB  - grown on a non-modifying host; and (2) dependent on the number of sites with
AB  - affinity for B-specific restriction: the DNA of a B-restriction insensitive
AB  - double mutant of fd is only half as much methylated after growth on B as its
AB  - wild type parent.  These results permit one to correlate methylation of
AB  - specifically located adenines with B-specific modification.  Quantitative
AB  - measurements suggest that one N-6-methyladenine is carried per B-host
AB  - specificity site on the modified, single stranded fd DNA.  Wild-type fd has two
AB  - such sites.  The biological function assigned to methylation brought about by
AB  - B-specific modification is the protection of the DNA from its destruction by
AB  - restriction endonuclese R.B.
ER  -

TY  - JOUR
AU  - Smith, J.L.
AU  - Goldberg, J.M.
AU  - Grossman, A.D.
TI  - Complete Genome Sequences of Bacillus subtilis subsp. subtilis Laboratory Strains JH642 (AG174) and AG1839.
JO  - Genome Announcements
PY  - 2014
SP  - e00663
EP  - e00614
VL  - 2
AB  - The Gram-positive bacterium Bacillus subtilis is widely used for studies of cellular and
AB  - molecular processes. We announce the complete genomic sequences of
AB  - strain AG174, our stock of the commonly used strain JH642, and strain AG1839, a
AB  - derivative that contains a mutation in the replication initiation gene dnaB and a
AB  - linked Tn917.
ER  -

TY  - JOUR
AU  - Smith, L.A.
AU  - Chirikjian, J.G.
TI  - Purification and characterization of the sequence-specific endonuclease BamHI.
JO  - J. Biol. Chem.
PY  - 1979
SP  - 1003
EP  - 1006
VL  - 254
AB  - The specific endonuclease BamHI from Bacillus amyloliquefaciens (RUB 500) has
AB  - been purified to apparent homogeneity.  Two active forms of the enzyme
AB  - corresponding to the dimeric and tetrameric forms have been isolated.  On
AB  - sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the enzyme
AB  - dissociated into Mr = 22,000 _+ 500 subunits.  BamHI has a broad pH optimum on
AB  - the alkaline side and requires Mg2+ which can be partially replaced by Mn2+.
AB  - The enzyme catalysis appears to be governed by a two-step mechanism.
ER  -

TY  - JOUR
AU  - Smith, M.A.
AU  - Mernagh, D.R.
AU  - Kneale, G.G.
TI  - Expression and characterization of the N-terminal fragment of the hsdS subunit of M.EcoR124I.
JO  - Biol. Chem.
PY  - 1998
SP  - 505
EP  - 509
VL  - 379
AB  - The type IC modification methyltransferase M.EcoR124I is a trimeric enzyme of 162 kDa
AB  - consisting of two copies of the modification subunit, HsdM, and a single DNA specificity
AB  - subunit, HsdS.  Studies to date have been largely restricted to the HsdM subunit or the intact
AB  - methyltransferase, since the HsdS subunit is insoluble when expressed independently of HsdM.
AB  - Using PCR, we have cloned and expressed 13 fragments of the gene for the hsdS subunit,
AB  - including the sequences encoding each of the variable and conserved domains and various
AB  - combinations of these.  Only two of these fragments were found to be soluble, an 8.6 kDa
AB  - fragment (S11) comprising the central conserved domain and a 25 kDa N-terminal fragment (S3)
AB  - containing the N-terminal variable domain and the central conserved domain.  Analysis of the
AB  - larger of these fragments by gel retardation shows that the protein binds DNA in the presence
AB  - of HsdM at a subunit stoichiometry of 1:1.  Gel filtration and CD spectroscopy indicate that
AB  - the protein is monomeric and predominantly alpha-helical.
ER  -

TY  - JOUR
AU  - Smith, M.A.
AU  - Read, C.M.
AU  - Kneale, G.G.
TI  - Domain structure and subunit interactions in the type I DNA methyltransferase M.EcoR124I.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 41
EP  - 50
VL  - 314
AB  - The type IC DNA methyltransferase M.EcoR124I is a trimeric enzyme of 162 kDa consisting of two
AB  - modification subunits, HsdM, and a single specificity subunit, HsdS. Studies have been largely
AB  - restricted to the HsdM subunit or to the intact methyltransferase since the HsdS subunit is
AB  - insoluble when over-expressed independently of HsdM. Two soluble fragments of the HsdS subunit
AB  - have been cloned, expressed and purified; a 25 kDa N-terminal fragment (S3) comprising the
AB  - N-terminal target recognition domain together with the central conserved domain, and an 8.6
AB  - kDa fragment (S11) comprising the central conserved domain alone.  Analytical
AB  - ultracentrifugation shows that the S3 subunit exists principally as a dimer of 50 kDa. Gel
AB  - retardation and competition assays show that both S3 and S11 are able to bind to HsdM, each
AB  - with a subunit stoichiometry of 1:1. The tetrameric complex (S3/HsdM)(2) is required for
AB  - effective DNA binding. Cooperative binding is observed and at low enzyme concentration, the
AB  - multisubunit complex dissociates, leading to a loss of DNA binding activity. The (S3/HsdM)(2)
AB  - complex is able to bind to both the EcoR124I DNA recognition sequence GAAN(6)RTCG and a
AB  - symmetrical DNA sequence GAAN(7)TTC, but has a 30-fold higher affinity binding for the latter
AB  - DNA sequence. Exonuclease III footprinting of the (S3/HsdM)(2) -DNA complex indicates that 29
AB  - nucleotides are protected on each strand, corresponding to a region 8 bp on both the 3' and
AB  - 5' sides of the recognition sequence bound by the (S3/HsdM)(2) complex.
ER  -

TY  - JOUR
AU  - Smith, M.D.
AU  - Longo, M.
AU  - Gerard, G.F.
AU  - Chatterjee, D.K.
TI  - Cloning and characterization of genes for the PvuI restriction and modification system.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5743
EP  - 5747
VL  - 20
AB  - The genes encoding the endonuclease and the methylase of the PvuI restriction and modification
AB  - system were cloned in E.coli and characterized. The genes were adjacent in tandem orientation
AB  - spanning a distance of 2200 bases. The PvuI endonuclease was a single polypeptide with a
AB  - calculated molecular weight of 27,950 daltons. The endonuclease was easily detectable when the
AB  - gene was expressed from its endogenous promotor and present on a low copy plasmid, but
AB  - expression was considerably enhanced when the endonuclease gene was placed under the control
AB  - of a strong promotor on a high copy plasmid. The methylase did not completely protect plasmid
AB  - DNA from R.PvuI digeston unitl the methylase gene was placed under lac promotor control in a
AB  - multicopy plasmid. In the absence of the M.PvuI methylase, expression of the R.PvuI
AB  - endonuclease from the lac promotor on a multicopy plasmid was not lethal to wild type E.coli,
AB  - but was lethal in a temperature-sensitive ligase mutant at the non-permissive temperature.
AB  - Moreover, induction of the R.PvuI endonuclease under lambda pL promotor control resulted in
AB  - complete digestion of the E. coli chromosome by R.PvuI.
ER  -

TY  - JOUR
AU  - Smith, M.J.
AU  - Jeddeloh, J.A.
TI  - DNA methylation in lysogens of pathogenic Burkholderia spp. requires prophage induction and is restricted to excised phage DNA.
JO  - J. Bacteriol.
PY  - 2005
SP  - 1196
EP  - 1200
VL  - 187
AB  - Burkholderia mallei-specific phage  E125 encodes DNA methyltransferases in both the lysogenic
AB  - and replication modules within its genome. Characterization of DNA methylation in recombinant
AB  - systems, specifically in  E125 lysogenic strains of B. mallei and Burkholderia thailandensis,
AB  - revealed that, upon induction, cytosine methylation was targeted specifically to the phage
AB  - episome but not the phage provirus or the host chromosome.
ER  -

TY  - JOUR
AU  - Smith, P.
AU  - Lindsey, R.L.
AU  - Rowe, L.A.
AU  - Batra, D.
AU  - Stripling, D.
AU  - Garcia-Toledo, L.
AU  - Drapeau, D.
AU  - Knipe, K.
AU  - Strockbine, N.
TI  - High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing.
JO  - Genome Announcements
PY  - 2018
SP  - e01311
EP  - e01317
VL  - 6
AB  - Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here
AB  - the high-quality whole-genome sequences of 21 ETEC strains
AB  - isolated from patients in the United States, international diarrheal surveillance
AB  - studies, and cruise ship outbreaks.
ER  -

TY  - JOUR
AU  - Smith, R.M.
AU  - Diffin, F.M.
AU  - Savery, N.J.
AU  - Josephsen, J.
AU  - Szczelkun, M.D.
TI  - DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 7206
EP  - 7218
VL  - 37
AB  - LlaGI is a single polypeptide restriction-modification enzyme encoded on the
AB  - naturally-occurring plasmid pEW104 isolated from Lactococcus lactis
AB  - ssp. cremoris W10. Bioinformatics analysis suggests that the enzyme
AB  - contains domains characteristic of an mrr endonuclease, a superfamily 2
AB  - DNA helicase and a gamma-family adenine methyltransferase. LlaGI was
AB  - expressed and purified from a recombinant clone and its properties
AB  - characterised. An asymmetric recognition sequence was identified,
AB  - 5'-CTnGAyG-3' (where n is A, G, C or T and y is C or T). Methylation of
AB  - the recognition site occurred on only one strand (the non-degenerate dA
AB  - residue of 5'-CrTCnAG-3' being methylated at the N6 position). Double
AB  - strand DNA breaks at distant, random sites were only observed when two
AB  - head-to-head oriented, unmethylated copies of the site were present;
AB  - single sites or pairs in tail-to-tail or head-to-tail repeat only
AB  - supported a DNA nicking activity. dsDNA nuclease activity was dependent
AB  - upon the presence of ATP or dATP. Our results are consistent with a
AB  - directional long-range communication mechanism that is necessitated by the
AB  - partial site methylation. In the accompanying manuscript [Smith et al.
AB  - (2009) The single polypeptide restriction-modification enzyme LlaGI is a
AB  - self-contained molecular motor that translocates DNA loops], we
AB  - demonstrate that this communication is via 1-dimensional DNA loop
AB  - translocation. On the basis of this data and that in the third
AB  - accompanying manuscript [Smith et al. (2009) An Mrr-family nuclease motif
AB  - in the single polypeptide restriction-modification enzyme LlaGI], we
AB  - propose that LlaGI is the prototype of a new sub-classification of
AB  - Restriction-Modification enzymes, named Type I SP (for Single
AB  - Polypeptide).
ER  -

TY  - JOUR
AU  - Smith, R.M.
AU  - Jacklin, A.J.
AU  - Marshall, J.J.
AU  - Sobott, F.
AU  - Halford, S.E.
TI  - Organization of the BcgI restriction-modification protein for the transfer of one methyl group to DNA.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 405
EP  - 417
VL  - 41
AB  - The Type IIB restriction-modification protein BcgI contains A and B subunits in a 2:1 ratio: A
AB  - has the active sites for both endonuclease and methyltransferase
AB  - functions while B recognizes the DNA. Like almost all Type IIB systems, BcgI
AB  - needs two unmethylated sites for nuclease activity; it cuts both sites upstream
AB  - and downstream of the recognition sequence, hydrolyzing eight phosphodiester
AB  - bonds in a single synaptic complex. This complex may incorporate four A(2)B
AB  - protomers to give the eight catalytic centres (one per A subunit) needed to cut
AB  - all eight bonds. The BcgI recognition sequence contains one adenine in each
AB  - strand that can be N(6)-methylated. Although most DNA methyltransferases operate
AB  - at both unmethylated and hemi-methylated sites, BcgI methyltransferase is only
AB  - effective at hemi-methylated sites, where the nuclease component is inactive.
AB  - Unlike the nuclease, the methyltransferase acts at solitary sites, functioning
AB  - catalytically rather than stoichiometrically. Though it transfers one methyl
AB  - group at a time, presumably through a single A subunit, BcgI methyltransferase
AB  - can be activated by adding extra A subunits, either individually or as part of
AB  - A(2)B protomers, which indicates that it requires an assembly containing at least
AB  - two A(2)B units.
ER  -

TY  - JOUR
AU  - Smith, R.M.
AU  - Josephsen, J.
AU  - Szczelkun, M.D.
TI  - The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 7219
EP  - 7230
VL  - 37
AB  - To cleave DNA, the single polypeptide restriction-modification enzyme LlaGI must communicate
AB  - between a pair of indirectly repeated recognition
AB  - sites. We demonstrate that this communication occurs by a 1-dimensional
AB  - route, namely unidirectional dsDNA loop translocation rightward of the
AB  - specific recognition sequence 5'-CTnGAyG-3' as written (where n is either
AB  - A, G, C or T and y is either C or T). Motion across thousands of base
AB  - pairs is catalysed by the helicase domain and requires the hydrolysis of
AB  - 1.5-2 ATP per base pair. DNA loop extrusion is accompanied by changes in
AB  - DNA twist consistent with the motor following the helical pitch of the
AB  - polynucleotide track. LlaGI is therefore an example of a polypeptide that
AB  - is a completely self-contained, multi-functional molecular machine.
ER  -

TY  - JOUR
AU  - Smith, R.M.
AU  - Josephsen, J.
AU  - Szczelkun, M.D.
TI  - An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 7231
EP  - 7238
VL  - 37
AB  - Bioinformatic analysis of the putative nuclease domain of the single polypeptide
AB  - restriction-modification enzyme LlaGI reveals amino acid
AB  - motifs characteristic of the Escherichia coli methylated DNA-specific Mrr
AB  - endonuclease. Using mutagenesis, we examined the role of the conserved
AB  - residues in both DNA translocation and cleavage. Mutations in those
AB  - residues predicted to play a role in DNA hydrolysis produced enzymes that
AB  - could translocate on DNA but were either unable to cleave the
AB  - polynucleotide track or had reduced nuclease activity. Cleavage by LlaGI
AB  - is not targeted to methylated DNA, suggesting that the conserved motifs in
AB  - the Mrr domain are a conventional sub-family of the PD-(D/E)XK superfamily
AB  - of DNA nucleases.
ER  -

TY  - JOUR
AU  - Smith, R.M.
AU  - Marshall, J.J.
AU  - Jacklin, A.J.
AU  - Retter, S.E.
AU  - Halford, S.E.
AU  - Sobott, F.
TI  - Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 391
EP  - 404
VL  - 41
AB  - Type IIB restriction-modification systems, such as BcgI, feature a single protein with both
AB  - endonuclease and methyltransferase activities. Type IIB nucleases
AB  - require two recognition sites and cut both strands on both sides of their
AB  - unmodified sites. BcgI cuts all eight target phosphodiester bonds before
AB  - dissociation. The BcgI protein contains A and B polypeptides in a 2:1 ratio: A
AB  - has one catalytic centre for each activity; B recognizes the DNA. We show here
AB  - that BcgI is organized as A(2)B protomers, with B at its centre, but that these
AB  - protomers self-associate to assemblies containing several A(2)B units. Moreover,
AB  - like the well known FokI nuclease, BcgI bound to its site has to recruit
AB  - additional protomers before it can cut DNA. DNA-bound BcgI can alternatively be
AB  - activated by excess A subunits, much like the activation of FokI by its catalytic
AB  - domain. Eight A subunits, each with one centre for nuclease activity, are
AB  - presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction
AB  - may thus involve two A(2)B units, each bound to a recognition site, with two more
AB  - A(2)B units bridging the complexes by protein-protein interactions between the
AB  - nuclease domains.
ER  -

TY  - JOUR
AU  - Smith, R.M.
AU  - Pernstich, C.
AU  - Halford, S.E.
TI  - TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 5809
EP  - 5822
VL  - 42
AB  - Type II restriction-modification systems cleave and methylate DNA at specific sequences.
AB  - However, the Type IIB systems look more like Type I than conventional Type II schemes as they
AB  - employ the same protein for both restriction and modification and for DNA recognition. Several
AB  - Type IIB proteins, including the archetype BcgI, are assemblies of two polypeptides: one with
AB  - endonuclease and methyltransferase roles, another for DNA recognition. Conversely, some IIB
AB  - proteins express all three functions from separate segments of a single polypeptide. This
AB  - study analysed one such single-chain protein, TstI. Comparison with BcgI showed that the one-
AB  - and the two-polypeptide systems differ markedly. Unlike the heterologous assembly of BcgI,
AB  - TstI forms a homotetramer. The tetramer bridges two recognition sites before eventually
AB  - cutting the DNA in both strands on both sides of the sites, but at each site the first
AB  - double-strand break is made long before the second. In contrast, BcgI cuts all eight target
AB  - bonds at two sites in a single step. TstI also differs from BcgI in either methylating or
AB  - cleaving unmodified sites at similar rates. The site may thus be modified before TstI can make
AB  - the second double-strand break. TstI MTase acts best at hemi-methylated sites.
ER  -

TY  - JOUR
AU  - Smith, S.A.
AU  - Krasucki, S.P.
AU  - McDowell, J.V.
AU  - Balke, V.L.
TI  - Complete Genome Sequence of Sphingobacterium sp. Strain ML3W, Isolated from Wings of Myotis lucifugus Infected with White Nose Syndrome.
JO  - Genome Announcements
PY  - 2015
SP  - e01477
EP  - e01414
VL  - 3
AB  - Sphingobacterium sp. strain ML3W was isolated from the wing of a bat infected with white nose
AB  - syndrome. We report the complete 5.33-Mb genome sequence of
AB  - Sphingobacterium sp. strain ML3W, obtained using Pacific Biosciences technology.
AB  - Being the second complete Sphingobacterium sequence, this will increase knowledge
AB  - of the genus.
ER  -

TY  - JOUR
AU  - Smith, S.S.
TI  - Gilbert's conjecture: The search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 1
EP  - 7
VL  - 302
AB  - In 1985 Walter Gilbert challenged members of the DNA methylation community assembled at a
AB  - National Institutes of Health meeting organized by Giulio Cantoni and Ahron Razin with the
AB  - following words: "The most exciting aspect about the methyl groups on DNA is the thought that
AB  - they might provide a locally inherited change in a DNA structure. However, for that to be
AB  - interesting, those changes have to be different in different cells. Furthermore, the
AB  - alterations in methylation have to be freely imposable and have to be maintained. It is not
AB  - yet clear that all these properties are true. So I don't think one will find that methylation
AB  - ever is one of the primary, top-level controls on gene expression." In essence, Gilbert's
AB  - conjecture, that DNA methylation is not one of the top-level controls on gene expression,
AB  - assumes that evidence in favor of both of its testable propositions will not be obtained.
AB  - Evidence for the first proposition, that alterations in methylation status associated with
AB  - gene-expression states have to be maintained, was already available in 1985 and has been
AB  - strengthened by a number of very recent experiments. However, the extensive effort to obtain
AB  - evidence for the second proposition, that alterations in methylation status be freely
AB  - imposable, has not been successful in its original intent. The effort has, on the other hand,
AB  - resulted in the emergence of new functions for 5-methylcytosine and the cytosine
AB  - methyltransferases in eukaryotic DNA repair, recombination and chromosome stability.
ER  -

TY  - JOUR
AU  - Smith, S.S.
TI  - Inhibition of human DNA (cytosine-5) methyltransferase by the 451nt RNA component of human telomerase.
JO  - Mol. Biol. Cell
PY  - 2000
SP  - 438a
EP  - 439a
VL  - 11
AB  - A link between telomerase expression and chromosome stability has been recognized for some
AB  - time, and links between chromosome instability and cytosine methylation have recently been
AB  - firmly established.  Most research indicates that the local hypermethylation and global
AB  - hypomethylation associated with tumorigenesis are markers of chromosome instability, which in
AB  - turn is a hallmark of tumor progression.  The enzymes that apply methylation patterns to DNA
AB  - [DNA (cytosine-5) methyltransferases], are known to show a strong preference for DNA sequences
AB  - capable of adopting multiple secondary structures.  Sequences of this type are present at
AB  - sites that are often prone to clastic mutation (e.g. triplet repeat sequences that expand and
AB  - become methylated in fragile X-linked mental retardation).  These findings, coupled with
AB  - reports that methyltransferase mutations induce clastic mutation, suggest that
AB  - methyltransferases may play a role in the recognition and repair of clastogenic damage in
AB  - organisms that must incorporate sequences prone to secondary structure formation into their
AB  - genomes.  The preference for sequences that adopt secondary structure exhibited by these
AB  - enzymes, extends to RNA.  RNA:DNA hybrids can bind to methyltransferase but are not methylated
AB  - on either strand.  The 451 nt human temomerase RNA (hTR) adopts secondary structures that bind
AB  - to the human placental enzyme and inhibit its action with an inhibition constant in the nM
AB  - range.  Given the widely observed elevation of h TR levels in human cancers, and the
AB  - mechanistic similarities between dyskerin, (a putative pseudouracil synthase involved in hTR
AB  - processing), and the DNA methyltransferase, these data raise the possibility that DNA
AB  - methyltransferase may form a complex with hTR-RNA during tumorigenesis, protecting hTRRNA from
AB  - degradation and promoting chromosome instability by blocking the normal action of DNA
AB  - methyltransferase.
ER  -

TY  - JOUR
AU  - Smith, S.S.
TI  - Stalling of DNA methyltransferase in chromosome stability and chromosome remodelling (Review).
JO  - Int. J. Mol. Med.
PY  - 1998
SP  - 147
EP  - 156
VL  - 1
AB  - As a consequence of their mechanism of action, DNA (cytosine-5) methyltransferases from both
AB  - prokaryotes and eukaryotes necessarily recognize mispaired bases in unusual DNA structures as
AB  - catalytic transition-state analogs.  A review of the available data suggests that the enzymes
AB  - are designed to stall at these sites because they are unable to release substrates or products
AB  - that are fixed in a conformation resembling the transition state.  The enzymes can operate by
AB  - a two-step process in which they first methylate extrahelical cytosines satisfying their
AB  - recognition requirements and subsequently stall at the site of methylation.  On RNA and
AB  - DNA-RNA hybrids they may operate by a similar one-step process in which they stall at
AB  - transition-state analogs without methylating cytosine moieties.  These natural capacities
AB  - suggest that the enzymes may physically participate in stable nucleoprotein assemblies formed
AB  - as components of normal chromatin structure or as intermediates in the repair of unusual
AB  - structures.  The methyltransferases, themselves, may physically participate in chromosome
AB  - remodelling as part of a mechanism of inactivation or imprinting by stabilizing RNA-DNA
AB  - hybrids or RNA-RNA secondary structure involving cis-acting untranslated RNAs like the product
AB  - of the Xist gene.  Methyltransferase may physically participate in the repair of certain
AB  - unusual structures by serving as a nucleation point.  The affinity for secondary structure in
AB  - nucleic acids may account for the spreading of DNA methylation patterns.  Titration of host
AB  - methyltransferase by RNA-DNA hybrids and RNA secondary structure formed during retroviral
AB  - replication in certain tumorigenic retroviruses, like MMTV, may account for global
AB  - hypomethylation observed in retrovirally transformed cells.  In a similar fashion, titration
AB  - of methyltransferase by secondary structures associated with chromosome instability may
AB  - account for global hypomethylation observed in association with local hypermethylation in
AB  - tumorigenesis.
ER  -

TY  - JOUR
AU  - Smith, S.S.
TI  - Conformation space and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases.
JO  - Int. J. Mol. Med.
PY  - 2000
SP  - S11
EP  - S11
VL  - 6
AB  - The existence of a link correlating CpG methylation with gene silencing as seen in mammalian
AB  - gene imprinting, X-chromosome inactivation, and the repression of viral genomes and L1
AB  - elements now seems quite plausible.  The evidence suggests that methylation in certain regions
AB  - of a gene can provide one of the signals necessary for the regional assembly of
AB  - heterochromatin.  On the other hand, work with histone deacetylase inhibitors suggests that
AB  - methylation is not one of the primary controls on transcription because reactivation does not
AB  - require demethylation.  DNA (cytosine-5)methyltransferases, the enzymes that apply methylation
AB  - patterns are known to show a strong preference for DNA sequences from regions with high
AB  - conformation space (i.e. sequences capable of adopting multiple secondary structures).  Such
AB  - sequences are present at sites that are often prone to clastic mutation (e.g. triplet repeat
AB  - sequences that expand in fragile X-linked mental retardation).  Moreover, lesions in
AB  - methyltransferase genes have been shown to promote clastic mutation.  These findings suggest
AB  - that methyltransferases play an additional role in the recognition and repair of clastogenic
AB  - damage in organisms that must incorporate sequences with high conformation spaces into their
AB  - genomes.  Such organisms may use stalled methyltransferase proteins as a cue in the repair of
AB  - inactive chromatin domains containing high conformation-space sequences.  The preference for
AB  - high conformation-space sequences exhibited by these enzymes extends to RNA.  RNA:DNA hybrids
AB  - can bind to methyltransferase but are not methylated on either strand.  Short RNA sequences
AB  - from the Xist gene and the 451nt human telomerase RNA (hTR) adopt secondary structures that
AB  - bind to the human placental enzyme and inhibit its action.  Given the widely observed
AB  - elevation of hTR levels in human cancers, and the mechanistic similarities between dyskerin, a
AB  - putative pseudouracil synthase, and the DNA methyltransferase, the data raise the possibility
AB  - that a DNA methyltransferase-hTR complex may form during tumorigenesis, protecting hTR from
AB  - degradation and promoting chromosome instability by blocking the normal action of DNA
AB  - methyltransferase.  These findings suggest that the elevation of hTR levels in prostate cancer
AB  - cells that we have observed in expressed prostatic secretion may be partially responsible for
AB  - the disruptions in methylation patterning and chromosomal instability that have been noted in
AB  - these tumor specimens.
ER  -

TY  - JOUR
AU  - Smith, S.S.
TI  - Biological implications of the mechanism of action of human DNA (cytosine-5)methyltransferase.
JO  - Prog. Nucleic Acid Res. Mol. Biol.
PY  - 1994
SP  - 65
EP  - 111
VL  - 49
AB  - I. Mechanism of action of the human DNA (cytosine-5)methyltransferase
AB  - A.  Sequence of catalytic events
AB  - B.  sp2-sp3 energetics and stereochemistry at C-6 and C-5 of cytosine
AB  - C.  Conformational change in the enzyme--DNA complex
AB  - D.  Potential for proton-mediated hydrolytic deamination
AB  - II.  Selectivity of human DNA methyltransferases
AB  - A.  De Novo methylation
AB  - B.  Methyl-directed methylation
AB  - C.  Structurally induced methylation
AB  - D.  The three-nucleotide recognition motif
AB  - E.  Enzyme--DNA interaction at the asymmetric DNA-binding site
AB  - III.  Biological implications of the mechanism
AB  - A.  Specificity of human DNA methylation
AB  - B.  Pattern formation as the key to the function of vertebrate DNA methylation
AB  - C.  Key elements of pattern formation are demonstrated by the phenomenon of concerted
AB  - modification
AB  - D.  Enzymology of pattern formation mechanisms
AB  - E.  Enzymology of disturbances in patterning produced by DNA damage
AB  - F.  Deamination at C-G dinucleotides
AB  - IV.  Conclusions
AB  - References
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Baker, D.J.
TI  - Stalling of human methyltransferase at single-strand conformers from the Huntington's locus.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1997
SP  - 73
EP  - 78
VL  - 234
AB  - We describe evidence for a sequence of events in which the human DNA (cytosine-5)
AB  - methyltransferase first methylates spontaneous single-stranded conformers and then stalls at
AB  - the methylated site to produce a complex with the conformationally unusual DNA.  This property
AB  - of the enzyme is a result of its ability to respond to a general loss of symmetry at its CG
AB  - recognition site.  The data suggest that DNA methyltransferase, itself, may physically
AB  - participate in biological processes that distinguish between DNA that is in the normal
AB  - Watson-Crick paired conformation and DNA that is conformationally unusual (e.g. a hairpin loop
AB  - or misassembled replication intermediate).  The in vitro methylation of spontaneous SSCs from
AB  - the Huntington's locus illustrates the phenomenon.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Crocitto, L.
TI  - DNA methylation in eukaryotic chromosome stability revisited: DNA methyltransferase in the management of DNA conformation space.
JO  - Mol. Carcinog.
PY  - 1999
SP  - 1
EP  - 9
VL  - 26
AB  - A previous working hypothesis on the role of DNA methylation in eukaryotic stability presented
AB  - enzymological data suggesting the DNA methylation has evolved as a biological response to the
AB  - formation of unusual DNA structures.  That evidence suggested that human DNA methyltransferase
AB  - is uniquely suited to participate in a repair system that functions to suppress unusual DNA
AB  - structures.  The evolution of this repair system was suggested to be a prerequisite for the
AB  - incorporation of dynamic sequences into the genome, because such sequences are particularly
AB  - prone to the formation of unusual DNA structures that promote clastic mutagenesis.  In the
AB  - intervening period, considerable evidence has accumulated in support of this proposal.  Here,
AB  - we extend the previous working hypothesis in light of the current experimental data to give a
AB  - more detailed picture of the role of DNA methylation in eukaryotic chromosome stability.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Hardy, T.A.
AU  - Baker, D.J.
TI  - Human DNA (cytosine-5)methyltransferase selectively methylates duplex DNA containing mispairs.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 6899
EP  - 6916
VL  - 15
AB  - The presence of the C-C mispair in a defined duplex oligodeoxynucleotide enhanced its capacity
AB  - to serve as a substrate for highly purified human DNA methyltransferase. Analysis of tritiated
AB  - reaction products showed that the C-C mispair acted as a "methylation acceptor" in that it was
AB  - itself rapidly methylated. The m5C-G base pair also enhanced the capacity of the
AB  - oligodeoxynucleotide to serve as a substrate for the enzyme. However, this complementary base
AB  - pair was found to act as a "methylation director". That is, the presence of the m5C in one
AB  - strand induced the enzyme to rapidly methylate at the cytosine residue on the opposite strand
AB  - in an adjacent C-G base pair.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Kan, J.L.C.
AU  - Baker, D.J.
AU  - Kaplan, B.E.
AU  - Dembek, P.
TI  - Recognition of unusual DNA structures by human DNA (cytosine-5) methyltransferase.
JO  - J. Mol. Biol.
PY  - 1991
SP  - 39
EP  - 51
VL  - 217
AB  - The symmetry of the responses of the human DNA (cytosine-5) methyltransferase
AB  - to alternative placements of 5-methylcytosine in model oligodeoxynucleotide
AB  - duplexes containing unusual structures has been examined.  The results of these
AB  - experiments more clearly define the DNA recognition specificity of the enzyme.
AB  - A simple three-nucleotide recognition motif within the CG dinucleotide pair can
AB  - be identified in each enzymatically methylated duplex.  The data can be
AB  - summarized by numbering the four nucleotides in the dinucleotide pair thus: 1
AB  - 4 / 2   3  With reference to this numbering scheme, position 1 can be occupied
AB  - by cytosine or 5-methylcytosine; position 2 can be occupied by guanosine or
AB  - inosine; position 3, the site of enzymatic methylation, can be occupied only by
AB  - cytosine; and position 4 can be occupied by guanosine, inosine,
AB  - O6-methylguanosine, cytosine, adenosine, an abasic site, or the 3' hydroxyl
AB  - group at the end of a gapped molecule.  Replacing the guanosine normally found
AB  - at position 4 with any of the moieties introduces unusual (non-Watson-Crick)
AB  - pairing at position 3 and generally enhances methylation of the cytosine at
AB  - that site.  The exceptional facility of the enzyme in actively methylating
AB  - unusual DNA structures suggests that the evolution of the DNA
AB  - methyltransferase, and perhaps DNA methylation itself may be linked to the
AB  - biological occurrence of unusual DNA structures.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Kaplan, B.E.
AU  - Sowers, L.C.
AU  - Newman, E.M.
TI  - Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 4744
EP  - 4748
VL  - 89
AB  - The properties of the methyl-directed DNA (cytosine-5)-methyltransferase (EC2.1.1.37) suggest
AB  - that it is the enzyme that maintains patterns of methylation in the human genome. Proposals
AB  - for the enzyme's mechanism of action suggest that 5-methyldeoxycytidine is produced from
AB  - deoxycytidine via a dihydrocytosine intermediate. We have used an oligodeoxynucleotide
AB  - containing 5-fluorodeoxycytidine as a suicide substrate to capture the enzyme and the
AB  - dihydrocytosine intermediate. Gel retardation experiments demonstrate the formation of the
AB  - expected covalent complex between duplex DNA containing 5-fluorodeoxycytidine and the human
AB  - enzyme. Formation of the complex was dependent upon the presence of the methyl donor
AB  - S-adenosylmethionine, suggesting that it comprises an enzyme-linked 5-substituted
AB  - dihydrocytosine moiety in DNA. Dihydrocytosine derivatives are extremely labile toward
AB  - hydrolytic deamination in aqueous solution. Because C-to-T transition mutations are especially
AB  - prevalent at CG sites in human DNA, we have used high-performance liquid chromatography to
AB  - search for thymidine that might be generated by hydrolysis during the methyl transfer
AB  - reaction. Despite the potential for deamination inherent in the formation of the intermediate,
AB  - the methyltransferase did not produce detectable amounts of thymidine. The data suggest that
AB  - the ability of the human methyltransferase to preserve genetic information when copying a
AB  - methylation pattern (i.e., its fidelity) is comparable to the ability of a mammalian DNA
AB  - polymerase to preserve genetic information when copying a DNA sequence. Thus the high
AB  - frequency of C-to-T transitions at CG sites in human DNA does not appear to be due to the
AB  - normal enzymatic maintenance of methylation patterns.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Kho, M.R.
AU  - Baker, D.J.
TI  - DNA methyltransferases in the recognition and repair of hairpin loops lacking precise Watson-Crick homology.
JO  - Anticancer Res.
PY  - 1995
SP  - 1671
EP  - 1671
VL  - 15
AB  - Sequences from codon-12 of the c-Ha-ras gene, the trinucleotide repeat region of the FMR-1
AB  - gene and the trinucleotide repeat region of the HuntingtonM-Us disease gene spontaneously form
AB  - hairpin loops under physiological conditions even though these loops lack precise Watson-Crick
AB  - homology.  The formation of loops of this type during replication may provide a new driving
AB  - force for genetic damage during carcinogenesis and the expression of genetic diseases.  The
AB  - exceptional capacity of the human methyltransferase to recognize these loops is a consequence
AB  - of its mechanism of action which requires that it unstack the cytosine ring from the DNA helix
AB  - as it activates the ring for methylation by nucleophilic attack at C6.  The rate of
AB  - methylation is enhanced by the capacity of mispairs (e.g. C.C., C.C+ or A+.C mispairs) in the
AB  - stems of such loops to serve as transition state analogs for the catalysis.  These findings
AB  - suggest that the mechanisms by which methyl groups and chromosomal abnormalities accumulate in
AB  - the c-Ha-ras region of chromosome 11 during carcinogenesis and at the FMR-1 locus during
AB  - repeat expansion involve structurally-induced de novo methylation at sites undergoing local
AB  - conformational change.  Models for the participation of methyltransferases in the recognition
AB  - and repair of looped structures suggest that they might serve to mark looped structures for
AB  - repair.  Cycles of loop formation and repair are expected to produce spreading of de novo
AB  - methylation in the vicinity of affected genes.  Asymmetrically methylated duplexes produced by
AB  - repair of the looped structures would be rapidly converted to symmetrically methylated
AB  - duplexes through the methyl-directed activity of the human methyltransferase.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Laayoun, A.
AU  - Baker, D.J.
AU  - Kho, M.R.
TI  - Recognition of telomere-like structures from the human C-Ha-Ras gene and the trinucleotide repeat of the FMR-1 gene of fragile X by human DNA methyltransferase.
JO  - FASEB J.
PY  - 1995
SP  - A1324
EP  - A1324
VL  - 9
AB  - Telomere-like hairprins from the c-Ha-ras gene and from the FMR-1 gene are exceptional
AB  - substrates for human DNA(cytosine-5)methyltransferases. This is a consequence of the mechanism
AB  - of action of these enzymes which requires that a group at the active site carry out
AB  - nucleophilic attack of an unstacked-cytosine ring in DNA. Thus the rate of methylation is
AB  - enhanced by the capacity of mispairs like C.C or C.C+ found on telomere-like loops formed in
AB  - C-rich DNA strands to serve as transition state analogs for the catalysis. These findings
AB  - suggest that the mechanisms by which methyl groups and chromosomal abnormalities accumulate at
AB  - the FMR-1 locus during repeat expansion in fragile X syndrome and in the c-Ha-ras region of
AB  - chromosome 11 during carcinogenesis may involve structurally-induced de novo methylation at
AB  - sites undergoing local conformational change. Possible roles for cytosine methylation in loop
AB  - repair and trinucleotide repeat expansion will be discussed.
ER  -

TY  - JOUR
AU  - Smith, S.S.
AU  - Lingeman, R.G.
AU  - Kaplan, B.E.
TI  - Recognition of foldback DNA by the human DNA (Cytosine-5-)-methyltransferase.
JO  - Biochemistry
PY  - 1992
SP  - 850
EP  - 854
VL  - 31
AB  - In order to specifiy the recognition requirements of the human DNA
AB  - (cytosine-5-)-methyltransferase, two isomeric 48mers were synthesized so as to
AB  - link a long block of DNA with a shorter complementary block of DNA through a
AB  - tether consisting of five thymidine residues.  These isomeric foldback
AB  - molecules, differing only in the location of the 5-methyldeoxycytosine, were
AB  - shown to be unimolecular, to contain a region of duplex DNA, and to contain a
AB  - region of single-stranded DNA.  When used as substrates for the DNA
AB  - methyltransferase, only one of the isomers was methylated.  A comparison of the
AB  - structures of the two isomers allows us to begin to define the potential sites
AB  - of interaction between the enzyme and the three nucleotides forming a
AB  - structural motif consisting of 5-methyldeoxycytosine, its base-paired
AB  - deoxyguanosine, and a deoxycytosine 5' to the paired deoxyguanosine.
ER  -

TY  - JOUR
AU  - Smith, T.
TI  - Restriction enzyme searches using the word processing software:  LOCOSCRIPT.
JO  - Biochemical Education
PY  - 1988
SP  - 224
EP  - 226
VL  - 16
AB  - One of the most important routine applications of computers in biochemistry and
AB  - molecular biology is the determination of restriction enzyme sites.  In our
AB  - laboratory, we routinely carry out restriction enzyme searches on the
AB  - University's Vax System, using the Staden Molecular Biology software.
AB  - Dedicated molecular biology software, however, can be expensive, and is
AB  - frequently difficult to obtain for the computer system which happens to be
AB  - available, while for those involved in introducing a genetic
AB  - engineering/biotechnology component into the life science courses offered by
AB  - colleges of further education and schools, the purchase of software may prove a
AB  - major hurdle.  Even when the systems and software are available, competition
AB  - from colleagues for terminals can mean constant frustration and delay to the
AB  - biochemist wanting to do a simple restriction enzyme search which is well
AB  - within the capacity of the cheapest PCW.  We now describe a rapid and reliable
AB  - method of performing restriction enzyme searches and other molecular biology
AB  - functions using the word processing software LOCOSCRIPT included with the
AB  - Amstrad PCWQ 8256.  At a total cost for the complete system - computer,
AB  - monitor, dot matrix printer and LOCOSCRIPT - of 299 Pounds plus VAT, this
AB  - brings restriction enzyme searches and similar functions within the range of
AB  - all educational institutes and research labs, and even of the individual
AB  - scientist or teacher, many of whom already possess and use the system as a word
AB  - processor.
ER  -

TY  - JOUR
AU  - Smith, T.J.
TI  - Aurintricarboxylic acid inhibition of restriction endonuclease is not recognition site-specific.
JO  - FASEB J.
PY  - 1988
SP  - A589
EP  - A589
VL  - 2
AB  - Aurintricarboxylic acid (ATA) has been previously shown to inhibit nucleases,
AB  - including restriction endonucleases.  The discovery of restriction
AB  - endonucleases which do not require guanine or cytosine bases within the
AB  - recognition sequence provides an opportunity to determine whether or not the
AB  - presence of these bases is required for inhibition by ATA.  In addition to the
AB  - endonuclease DraI, which does not contain guanine-cytosine (GC) base pairs
AB  - within the recognition sequence, two other restriction enzymes were included as
AB  - controls.  These endonucleases were HaeIII, which has a recognition site
AB  - without adenine-thymine (AT) base pairs, and HindIII, which contains both AT
AB  - and GC base pairs within the recognition sequence.  ATA was included in
AB  - restriction digests with the above endonucleases.  Following termination of the
AB  - reactions, DNA fragments were separated by agarose gel electrophoresis.  The
AB  - results indicate that inhibition by ATA does not require a specific base pair
AB  - within the recognition sequence.
ER  -

TY  - JOUR
AU  - Smith, T.J.
AU  - Hill, K.K.
AU  - Foley, B.T.
AU  - Detter, J.C.
AU  - Munk, A.C.
AU  - Bruce, D.C.
AU  - Doggett, N.A.
AU  - Smith, L.A.
AU  - Marks, J.D.
AU  - Xie, G.
AU  - Brettin, T.S.
TI  - Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4 and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within  Plasmids.
JO  - PLoS ONE
PY  - 2007
SP  - e1271
EP  - e1271
VL  - 2
AB  - BACKGROUND: Clostridium botulinum and related clostridial species express extremely potent
AB  - neurotoxins known as botulinum neurotoxins (BoNTs) that
AB  - cause long-lasting, potentially fatal intoxications in humans and other
AB  - mammals. The amino acid variation within the BoNT is used to categorize
AB  - the species into seven immunologically distinct BoNT serotypes (A-G) which
AB  - are further divided into subtypes. The BoNTs are located within two
AB  - generally conserved gene arrangements known as botulinum progenitor
AB  - complexes which encode toxin-associated proteins involved in toxin
AB  - stability and expression. METHODOLOGY/PRINCIPAL FINDINGS: Because serotype
AB  - A and B strains are responsible for the vast majority of human botulism
AB  - cases worldwide, the location, arrangement and sequences of genes from
AB  - eight different toxin complexes representing four different BoNT/A
AB  - subtypes (BoNT/A1-Ba4) and one BoNT/B1 strain were examined. The bivalent
AB  - Ba4 strain contained both the BoNT/A4 and BoNT/bvB toxin clusters. The
AB  - arrangements of the BoNT/A3 and BoNT/A4 subtypes differed from the BoNT/A1
AB  - strains and were similar to those of BoNT/A2. However, unlike the BoNT/A2
AB  - subtype, the toxin complex genes of BoNT/A3 and BoNT/A4 were found within
AB  - large plasmids and not within the chromosome. In the Ba4 strain, both BoNT
AB  - toxin clusters (A4 and bivalent B) were located within the same 270 kb
AB  - plasmid, separated by 97 kb. Complete genomic sequencing of the BoNT/B1
AB  - strain also revealed that its toxin complex genes were located within a
AB  - 149 kb plasmid and the BoNT/A3 complex is within a 267 kb plasmid.
AB  - CONCLUSIONS/SIGNIFICANCE: Despite their size differences and the BoNT
AB  - genes they contain, the three plasmids containing these toxin cluster
AB  - genes share significant sequence identity. The presence of partial
AB  - insertion sequence (IS) elements, evidence of recombination/gene
AB  - duplication events, and the discovery of the BoNT/A3, BoNT/Ba4 and BoNT/B1
AB  - toxin complex genes within plasmids illustrate the different mechanisms by
AB  - which these genes move among diverse genetic backgrounds of C. botulinum.
ER  -

TY  - JOUR
AU  - Smith, T.J.
AU  - Hill, K.K.
AU  - Xie, G.
AU  - Foley, B.T.
AU  - Williamson, C.H.
AU  - Foster, J.T.
AU  - Johnson, S.L.
AU  - Chertkov, O.
AU  - Teshima, H.
AU  - Gibbons, H.S.
AU  - Johnsky, L.A.
AU  - Karavis, M.A.
AU  - Smith, L.A.
TI  - Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes.
JO  - Infect. Genet. Evol.
PY  - 2014
SP  - 102
EP  - 113
VL  - 30
AB  - The whole genomes for six botulinum neurotoxin-producing clostridial strains were sequenced to
AB  - provide references for under-represented toxin types, bivalent strains or unusual toxin
AB  - complexes associated with a bont gene. The strains include three Clostridium botulinum Group I
AB  - strains (CDC 297, CDC 1436, and Prevot 594), a Group II C. botulinum strain (Eklund 202F), a
AB  - Group IV Clostridium argentinense strain (CDC 2741), and a Group V Clostridium baratii strain
AB  - (Sullivan). Comparisons of the Group I genomic sequences revealed close relationships and
AB  - conservation of toxin gene locations with previously published Group I C. botulinum genomes.
AB  - The bont/F6 gene of strain Eklund 202F was determined to be a chimeric toxin gene composed of
AB  - bont/F1 and bont/F2. The serotype G strain CDC 2741 remained unfinished in 20 contigs with the
AB  - bont/G located within a 1.15Mb contig, indicating a possible chromosomal location for this
AB  - toxin gene. Within the genome of C. baratii Sullivan strain, direct repeats of IS1182
AB  - insertion sequence (IS) elements were identified flanking the bont/F7 toxin complex that may
AB  - be the mechanism of bont insertion into C. baratii.
AB  - Highlights of the six strains are described and release of their genomic sequences will allow
AB  - further study of unusual neurotoxin-producing clostridial strains.
ER  -

TY  - JOUR
AU  - Smits, T.H.
AU  - Guerrero-Prieto, V.M.
AU  - Hernandez-Escarcega, G.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Rezzonico, F.
AU  - Duffy, B.
AU  - Stockwell, V.O.
TI  - Whole-Genome Sequencing of Erwinia amylovora Strains from Mexico Detects Single Nucleotide Polymorphisms in rpsL Conferring Streptomycin Resistance and in the  avrRpt2 Effector Altering Host Interactions.
JO  - Genome Announcements
PY  - 2014
SP  - e01229
EP  - e01213
VL  - 2
AB  - We report draft genome sequences of three Mexican Erwinia amylovora strains. A novel plasmid,
AB  - pEA78, was identified. Comparative genomics revealed an rpsL
AB  - chromosomal mutation conferring high-level streptomycin resistance in two
AB  - strains. In the effector gene avrRpt2, a single nucleotide polymorphism was
AB  - detected that overcomes fire blight disease resistance in Malus x robusta 5.
ER  -

TY  - JOUR
AU  - Smits, T.H.
AU  - Pothier, J.F.
AU  - Ruinelli, M.
AU  - Blom, J.
AU  - Frasson, D.
AU  - Koechli, C.
AU  - Fabbri, C.
AU  - Brandl, H.
AU  - Duffy, B.
AU  - Sievers, M.
TI  - Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii.
JO  - Genome Announcements
PY  - 2015
SP  - e00616
EP  - e00615
VL  - 3
AB  - We sequenced the complete genome of the isolate Pseudomonas sp. CCOS 191. This strain is able
AB  - to dissolve phosphate minerals and form cyanide. The genome
AB  - sequence is used to establish the phylogenetic relationship of this species.
ER  -

TY  - JOUR
AU  - Smits, T.H.
AU  - Rezzonico, F.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Abelli, A.
AU  - Kron, M.R.
AU  - Vanneste, J.L.
AU  - Duffy, B.
TI  - Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.
JO  - Genome Announcements
PY  - 2015
SP  - e01448
EP  - e01415
VL  - 3
AB  - We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c,
AB  - composed of a draft chromosome and two plasmids: the 559-kb
AB  - large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island
AB  - containing pantocin A biosynthesis genes was identified.
ER  -

TY  - JOUR
AU  - Smits, T.H.
AU  - Rezzonico, F.
AU  - Kamber, T.
AU  - Goesmann, A.
AU  - Ishimaru, C.A.
AU  - Stockwell, V.O.
AU  - Frey, J.E.
AU  - Duffy, B.
TI  - Genome Sequence of the Biocontrol Agent Pantoea vagans Strain C9-1.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6486
EP  - 6487
VL  - 192
AB  - Pantoea vagans is a Gram-negative enterobacterial plant epiphyte of a broad range of plants.
AB  - Here we report the 4.89-Mb genome sequence of P.
AB  - vagans strain C9-1 (formerly Pantoea agglomerans), which is commercially
AB  - registered for biological control of fire blight, a disease of pear and
AB  - apple trees caused by Erwinia amylovora.
ER  -

TY  - JOUR
AU  - Smoot, J.C.
AU  - Barbian, K.D.
AU  - Van Gompel, J.J.
AU  - Smoot, L.M.
AU  - Chaussee, M.S.
AU  - Sylva, G.L.
AU  - Sturdevant, D.E.
AU  - Ricklefs, S.M.
AU  - Porcella, S.F.
AU  - Parkins, L.D.
AU  - Beres, S.B.
AU  - Campbell, D.S.
AU  - Smith, T.M.
AU  - Zhang, Q.
AU  - Kapur, V.
AU  - Daly, J.A.
AU  - Veasy, L.G.
TI  - Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 4668
EP  - 4673
VL  - 99
AB  - Acute rheumatic fever (ARF), a sequelae of group A Streptococcus (GAS) infection, is the most
AB  - common cause of preventable childhood heart disease worldwide. The molecular basis of ARF and
AB  - the subsequent rheumatic heart disease are poorly understood. Serotype M18 GAS strains have
AB  - been associated for decades with ARF outbreaks in the U.S. As a first step toward gaining new
AB  - insight into ARF pathogenesis, we sequenced the genome of strain MGAS8232, a serotype M18
AB  - organism isolated from a patient with ARF. The genome is a circular chromosome of 1,895,017
AB  - bp, and it shares 1.7 Mb of closely related genetic material with strain SF370 (a sequenced
AB  - serotype M1 strain). Strain MGAS8232 has 178 ORFs absent in SF370. Phages, phage-like
AB  - elements, and insertion sequences are the major sources of variation between the genomes. The
AB  - genomes of strain MGAS8232 and SF370 encode many of the same proven or putative virulence
AB  - factors. Importantly, strain MGAS8232 has genes encoding many additional secreted proteins
AB  - involved in human-GAS interactions, including streptococcal pyrogenic exotoxin A (scarlet
AB  - fever toxin) and two uncharacterized pyrogenic exotoxin homologues, all phage-associated. DNA
AB  - microarray analysis of 36 serotype M18 strains from diverse localities showed that most
AB  - regions of variation were phages or phage-like elements. Two epidemics of ARF occurring 12
AB  - years apart in Salt Lake City, UT, were caused by serotype M18 strains that were genetically
AB  - identical, or nearly so. Our analysis provides a critical foundation for accelerated research
AB  - into ARF pathogenesis and a molecular framework to study the plasticity of GAS genomes.
ER  -

TY  - JOUR
AU  - Sneider, T.W.
TI  - The 5'-cytosine in CCGG is methylated in two eukaryotic DNAs and MspI is sensitive to methylation at this site.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 3829
EP  - 3840
VL  - 8
AB  - Novikoff rat hepatoma and bovine liver DNAs were digested with MspI or HpaII. Restriction
AB  - fragments were end-labeled using [a-32P]-dCTP and the Klenow fragment of E. coli DNA
AB  - polymerase I and then digested to 2'-deoxyribonucleoside-3'-monophosphates using micrococcal
AB  - nuclease and spleen phosphodiesterase. Mononucleotides were separated by two-dimensional thin
AB  - layer chromatography, localized by radioautography, and the [32P]-label quantitated by
AB  - scintillation spectrometry. This method, based on known specificities of MspI and HpaII, shows
AB  - that CCGG, CMGG, and MCGG (M refers to 5-methylcytosine) occur at frequencies of 89.6%, 1.4%,
AB  - and 9.0%, respectively, in the rat DNA and at 41.6%, 48.3%, and 10.0%, respectively, in the
AB  - ovine DNA. [32P] recovery in 3'-5-MedCMP from end-labeled MspI digests was negligible
AB  - compared to recovery from HpaII digests. Hence, MspI is sensitive to methylation at the 5'
AB  - cytosine in the sequence CCGG.
ER  -

TY  - JOUR
AU  - Snitkin, E.S.
AU  - Zelazny, A.M.
AU  - Thomas, P.J.
AU  - Stock, F.
AU  - Henderson, D.K.
AU  - Palmore, T.N.
AU  - Segre, J.A.
TI  - Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.
JO  - Sci. Transl. Med.
PY  - 2012
SP  - 148RA116
EP  - 148RA116
VL  - 4
AB  - The Gram-negative bacteria Klebsiella pneumoniae is a major cause of nosocomial
AB  - infections, primarily among immunocompromised patients. The emergence of strains
AB  - resistant to carbapenems has left few treatment options, making infection
AB  - containment critical. In 2011, the U.S. National Institutes of Health Clinical
AB  - Center experienced an outbreak of carbapenem-resistant K. pneumoniae that
AB  - affected 18 patients, 11 of whom died. Whole-genome sequencing was performed on
AB  - K. pneumoniae isolates to gain insight into why the outbreak progressed despite
AB  - early implementation of infection control procedures. Integrated genomic and
AB  - epidemiological analysis traced the outbreak to three independent transmissions
AB  - from a single patient who was discharged 3 weeks before the next case became
AB  - clinically apparent. Additional genomic comparisons provided evidence for
AB  - unexpected transmission routes, with subsequent mining of epidemiological data
AB  - pointing to possible explanations for these transmissions. Our analysis
AB  - demonstrates that integration of genomic and epidemiological data can yield
AB  - actionable insights and facilitate the control of nosocomial transmission.
ER  -

TY  - JOUR
AU  - Snopkova, K.
AU  - Sedlar, K.
AU  - Bosak, J.
AU  - Chaloupkova, E.
AU  - Provaznik, I.
AU  - Smajs, D.
TI  - Complete Genome Sequence of Pragia fontium 24613, an Environmental Bacterium from the Family Enterobacteriaceae.
JO  - Genome Announcements
PY  - 2015
SP  - e00740
EP  - e00715
VL  - 3
AB  - The complete genome sequence of Pragia fontium 24613 was determined using PacBio  RSII, Roche
AB  - 454, and SOLiD sequencing. A total of 3,579 genes were predicted,
AB  - including 3,338 protein-coding sequences and 146 pseudogenes. This is the first
AB  - whole-genome sequence of a strain belonging to the environmental genera of the
AB  - family Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Snounou, G.
AU  - Malcolm, A.D.B.
TI  - Supercoiling and the mechanism of restriction endonucleases.
JO  - Eur. J. Biochem.
PY  - 1984
SP  - 275
EP  - 280
VL  - 138
AB  - 1. We have used topoisomerase I in the presence of netropsin and ethidium
AB  - bromide to generate DNA molecules of varying superhelical density.  2.
AB  - Digestion by endonuclease EcoRI is sensitive to supercoiling, being maximal for
AB  - the relaxed form.  Endonucleases AvaI and BamHI, by contrast, are relatively
AB  - unaffected.  3. The results are interpreted in terms of the base composition of
AB  - the DNA in the vicinity of these sites. dA + dT-rich regions are more
AB  - susceptible to deformation than are dG + dC-rich ones.  4. Analysis of the
AB  - rates of disappearance of linear molecules confirms a two-step mechanism for
AB  - EcoRI cleavage but suggests that BamHI and AvaI cleave both strands
AB  - simultaneously.
ER  -

TY  - JOUR
AU  - Snow, A.M.
AU  - Sheardy, R.D.
TI  - Locating cobalt-binding sites on DNA using restriction endonucleases.
JO  - Methods Enzymol.
PY  - 2001
SP  - 519
EP  - 528
VL  - 340
AB  - The interactions of simple metal complexes with DNA have been widely studied.  The interaction
AB  - specificities of these molecules range from simple outside binding, such as observed with
AB  - [Co(NH3)6]3+, to covalent binding as observed with Pt(NH3)2Cl2, to reactions involving DNA
AB  - oxidative cleavage through Fenton or related chemistries.  One important feature of such
AB  - interactions, especially those leading to covalent binding, is the sequence specificity of the
AB  - reaction.  It has been well established that platination of DNA by Pt(NH3)2Cl2 is highly
AB  - sequence specific with a preferential reaction at -GG- sites, although reactions involving
AB  - -GA- and -GC- sites have also been noted.  Reaction at an isolated -GG- or -GA- site results
AB  - in an intrastrand cross-link composed of a pur(N7)-Pt-pur(N7) linkage, whereas the reaction at
AB  - a -GC- site results in an interstrand cross-link with the same type of linkage.  The sequence
AB  - specificity of these and related reactions is due to the accessibility to N7 of purines,
AB  - located in the major groove of the DNA, and to the nucleophilicity of N7, particularly that of
AB  - guanine bases.
ER  -

TY  - JOUR
AU  - Soares, S.C. et al.
TI  - Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production.
JO  - J. Biotechnol.
PY  - 2013
SP  - 135
EP  - 141
VL  - 167
AB  - Corynebacterium pseudotuberculosis is the causative agent of several veterinary
AB  - diseases in a broad range of economically important hosts, which can vary from
AB  - caseous lymphadenitis in sheep and goats (biovar ovis) to ulcerative lymphangitis
AB  - in cattle and horses (biovar equi). Existing vaccines against C.
AB  - pseudotuberculosis are mainly intended for small ruminants and, even in these
AB  - hosts, they still present remarkable limitations. In this study, we present the
AB  - complete genome sequence of C. pseudotuberculosis biovar equi strain 258,
AB  - isolated from a horse with ulcerative lymphangitis. The genome has a total size
AB  - of 2,314,404 bp and contains 2088 predicted protein-coding regions. Using in
AB  - silico analysis, eleven pathogenicity islands were detected in the genome
AB  - sequence of C. pseudotuberculosis 258. The application of a reverse vaccinology
AB  - strategy identified 49 putative antigenic proteins, which can be used as
AB  - candidate vaccine targets in future works.
ER  -

TY  - JOUR
AU  - Soares-Castro, P.
AU  - Marques, D.
AU  - Demyanchuk, S.
AU  - Faustino, A.
AU  - Santos, P.M.
TI  - Draft Genome Sequences of Two Pseudomonas aeruginosa Clinical Isolates with Different Antibiotic Susceptibilities.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5573
EP  - 5573
VL  - 193
AB  - Pseudomonas aeruginosa is a primary cause of opportunistic infections. We have sequenced and
AB  - annotated the genomes of two P. aeruginosa clinical
AB  - isolates evidencing different antibiotic susceptibilities. Registered
AB  - differences in the composition of their accessory genomes may provide
AB  - clues on P. aeruginosa strategies to thrive in different environments like
AB  - infection loci.
ER  -

TY  - JOUR
AU  - Soares-Castro, P.
AU  - Santos, P.M.
TI  - Towards the Description of the Genome Catalogue of Pseudomonas sp. Strain M1.
JO  - Genome Announcements
PY  - 2013
SP  - e00146
EP  - e00112
VL  - 1
AB  - Pseudomonas sp. strain M1 is a soil isolate with remarkable biotechnological potential. The
AB  - genome of Pseudomonas sp. M1 was sequenced using both 454 and
AB  - Illumina technologies. A customized genome assembly pipeline was used to
AB  - reconstruct its genome sequence to a single scaffold.
ER  -

TY  - JOUR
AU  - Sobell, H.M.
TI  - Symmetry in protein-nucleic acid interaction and its genetic implications.
JO  - Adv. Genet.
PY  - 1973
SP  - 411
EP  - 490
VL  - 17
AB  - Symmetry principles are known to play a fundamental role in biological
AB  - organization, governing the assembly of macromolecular subunits into viruses,
AB  - membranes, oligomeric globular and fibrous proteins, and cellular organelles
AB  - (Crick and Watson, 1956; Caspar and Klug, 1962; Monod et al., 1965; for an
AB  - excellent review, see Engstrom and Strandberg, 1968).  Thus, for example, small
AB  - spherical viruses utilize icosahedral symmetry in their construction, identical
AB  - protein subunits being used to form large protein shells in which each subunit
AB  - has, as nearly as possible, the same local environment (Caspar and Klug, 1962;
AB  - Finch and Klug, 1966; Klug and Finch, 1968; Finch et al., 1970; for a review,
AB  - see Klug et al., 1966).
ER  -

TY  - JOUR
AU  - Sobotta, T.
AU  - Pingoud, A.
AU  - Jeltsch, A.
TI  - Mapping of the functional regions of the EcoRV methyltransferase by random mutagenesis and screening for inactive mutants.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S155
EP  - S155
VL  - 376
AB  - To examine the structure and the mechanism of the EcoRV DNA methyltransferase several mutants
AB  - were produced by random mutagenesis and selection for inactive mutants.  Until now, 11
AB  - catalytically inactive single mutants were found: P8L; V20A; F115S; S121P; F139L; F172S;
AB  - C192R; D193G; E212G; W231R and F249V.  Two of the mutant proteins (F139L and F249V) were not
AB  - expressed in the cell, although the promotor sequence was intact, suggesting that these
AB  - proteins are misfolded and rapidly degraded.  For further characterization the other mutant
AB  - enzymes were purified by affinity-chromatography.  It turned out, that all proteins except
AB  - wild type and the W231R mutant were insoluble suggestive of structural alterations caused by
AB  - the mutations.  Whereas the purified wild type enzyme has a specific activity of 1.3 x 10^6
AB  - U/mg, W231R is catalytically inactive in vitro.  Currently, the DNA- and
AB  - S-adenosylmethionine-binding properties of the mutants are investigated.
ER  -

TY  - JOUR
AU  - Sobral, B.W.S.
AU  - McClelland, M.
TI  - Methyltransferases as tools to alter the specificity of restriction endonucleases.
JO  - Methods Mol. Biol.
PY  - 1992
SP  - 159
EP  - 172
VL  - 12
AB  - Pulsed-field gel electrophoresis (PFGE) has allowed the resolution of very large DNA fragments
AB  - from any organism. To apply PFGE to practical problems such as genetic mapping and map-based
AB  - gene cloning, it is necessary to specifically generate large DNA fragments that can then be
AB  - separated by PFGE. Ideally, restriction enzymes would exist that could generate DNA fragments
AB  - of desired sizes. Other factors being equal, and supposing that DNA sequences were random,
AB  - then enzymes with larger target sequences should produce larger DNA fragments. In practice, no
AB  - restriction enzymes are known to have larger than 8-bp-long target sites and, of course, DNA
AB  - sequences are not random. These realities severely limit the observed sizes of DNA fragments
AB  - produced by restriction enzymes acting on genomic DNA particularly in the case of eukaryotic
AB  - genomes, which are large and complex. This chapter describes enzymatic strategies to generate
AB  - large DNA fragments and statistical tools that can aid researchers in choosing the restriction
AB  - enzymes that are most likely to generate large fragments in the genome in question, if a
AB  - sequence data base can be investigated.
ER  -

TY  - JOUR
AU  - Soby, S.D.
TI  - Draft Genome Sequence of Chromobacterium aquaticum CC-SEYA-1, a Nonpigmented Member of the Genus Chromobacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01661
EP  - e01616
VL  - 5
AB  - Chromobacterium aquaticum CC-SEYA-1T, isolated from a spring in Taiwan, shares many
AB  - characteristics with other members of the genus but also contains auxin
AB  - biosynthesis genes and does not produce the pigment violacein. Chromobacterium
AB  - sp. 49, isolated from Brazil, is identified here as C. aquaticum, indicating that
AB  - this is a cosmopolitan species.
ER  -

TY  - JOUR
AU  - Soby, S.D.
TI  - Draft Genome Sequence of Chromobacterium pseudoviolaceum LMG 3953T, an Enigmatic  Member of the Genus Chromobacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01632
EP  - e01616
VL  - 5
AB  - Chromobacterium pseudoviolaceum LMG 3953T was separated from Chromobacterium violaceum in
AB  - 2009, but little is known of its origin or environmental role. Here,
AB  - the genome of LMG 3953T was sequenced to understand the evolution of the genus
AB  - Chromobacterium It is not clear from this sequence that C. pseudoviolaceum is
AB  - taxonomically distinct from C. violaceum.
ER  -

TY  - JOUR
AU  - Soggiu, A.
AU  - Piras, C.
AU  - Gaiarsa, S.
AU  - Bendixen, E.
AU  - Panitz, F.
AU  - Bendixen, C.
AU  - Sassera, D.
AU  - Brasca, M.
AU  - Bonizzi, L.
AU  - Roncada, P.
TI  - Draft Genome Sequence of Clostridium tyrobutyricum Strain DIVETGP, Isolated from  Cow's Milk for Grana Padano Production.
JO  - Genome Announcements
PY  - 2015
SP  - e00213
EP  - e00215
VL  - 3
AB  - We announce the draft genome sequence of Clostridium tyrobutyricum strain DIVETGP. This strain
AB  - was isolated from cow's milk used for Grana Padano cheese
AB  - production. The genome was obtained using Illumina HiSeq technology and comprises
AB  - 45 contigs for 3,018,999 bp, with a G+C content of 30.8%.
ER  -

TY  - JOUR
AU  - Sogutcu, E.
AU  - Emrence, Z.
AU  - Arikan, M.
AU  - Cakiris, A.
AU  - Abaci, N.
AU  - Oner, E.T.
AU  - Ustek, D.
AU  - Arga, K.Y.
TI  - Draft Genome Sequence of Halomonas smyrnensis AAD6T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5690
EP  - 5691
VL  - 194
AB  - Halomonas smyrnensis AAD6(T) is a Gram-negative, aerobic, exopolysaccharide-producing, and
AB  - moderately halophilic bacterium that produces
AB  - levan, a fructose homopolymer with many potential uses in various industries. We
AB  - report the draft genome sequence of H. smyrnensis AAD6(T), which will accelerate
AB  - research on the rational design and optimization of microbial levan production.
ER  -

TY  - JOUR
AU  - Soh, J.Y.K.
AU  - Russell, C.W.
AU  - Fenlon, S.N.
AU  - Chen, S.L.
TI  - Complete Genome Sequence of Photobacterium leiognathi Strain JS01.
JO  - Genome Announcements
PY  - 2018
SP  - e01396
EP  - e01317
VL  - 6
AB  - Photobacterium leiognathi is a bioluminescent symbiont of fish of the Leiognathidae family.
AB  - Here, we present the full-genome sequence of P. leiognathi
AB  - strain JS01, a strain isolated from a nonluminescent Loligo sp. squid of
AB  - Singaporean origin. No finished genome sequence of this species is currently
AB  - publicly available.
ER  -

TY  - JOUR
AU  - Sohail, A.
AU  - Ives, C.L.
AU  - Brooks, J.E.
TI  - Purification and characterization of C.BamHI, a regulator of the BamHI restriction-modification system.
JO  - Gene
PY  - 1995
SP  - 227
EP  - 228
VL  - 157
AB  - The bamHIC gene, controlling the BamHI restriction-modification (R-M) system can functionally
AB  - be replaced by providing pvuIIC or smaIC in trans.  C.BamHI, the protein product encoded by
AB  - bamHIC, has been purified and shown to bind a 345-bp DNA fragment within the BamHI R-M system.
ER  -

TY  - JOUR
AU  - Sohail, A.
AU  - Lieb, M.
AU  - Dar, M.
AU  - Bhagwat, A.S.
TI  - A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene.
JO  - J. Bacteriol.
PY  - 1990
SP  - 4214
EP  - 4221
VL  - 172
AB  - Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these
AB  - mismatches can lead to C-to-T transition mutations. The very short patch (VSP) repair process
AB  - in Escherichia coli counteracts the mutagenic process by repairing the mismatches in favor of
AB  - the G-containing strand. Previously we have shown that a plasmid containing an 11-kilobase
AB  - fragment from the E. coli chromosome can complement a chromosomal mutation defective in both
AB  - cytosine methylation and VSP repair. We have now mapped the regions essential for the two
AB  - phenotypes. In the process, we have constructed plasmids that complement the chromosomal
AB  - mutation for methylation, but not for repair, and vice versa. The genes responsible for these
AB  - phenotypes have been identified by DNA sequence analysis. The gene essential for cytosine
AB  - methylation, dcm, is predicted to code for a 473-amino-acid protein and is not required for
AB  - VSP repair. It is similar to other DNA cytosine methylases and shares extensive sequence
AB  - similarity with its isoschizomer, EcoRII methylase. The segment of DNA essential for VSP
AB  - repair contains a gene that should code for a 156-amino-acid protein. This gene, named vsr, is
AB  - not essential for DNA methylation. Remarkably, the 5' end of this gene appears to overlap the
AB  - 3' end of dcm. The two genes appear to be transcribed from a common promoter but are in
AB  - different translational registers. This gene arrangement may assure that Vsr is produced along
AB  - with Dcm and may minimize the mutagenic effects of cytosine methylation.
ER  -

TY  - JOUR
AU  - Sohail, A.
AU  - Mushtaq, R.
AU  - Khan, E.
AU  - Maqbool, T.
AU  - Riazuddin, S.
TI  - Discovery of two new Type II restriction enzymes.
JO  - Pak. J. Zool.
PY  - 1987
SP  - 371
EP  - 391
VL  - 19
AB  - Eight bacterial strains isolated from local environments have been screened for
AB  - the presence of new restriction enzymes judging from the analysis of 1.4%
AB  - agarose gel patterns of different DNA substrates.  Partially purified protein
AB  - extracts of two of these strains, namely Pseudomonas ovalis and Enterobacter
AB  - agglomerans exhibit the presence of Type II restriction endonucleases.  The new
AB  - enzymes have been highly purified by a combination of gel filtration, ion
AB  - exchange and affinity chromatography and are designated as PovI and EagI,
AB  - respectively.  The identity of the new enzymes have been further confirmed by
AB  - DNA double digest analysis with a variety of substrate DNAs which yielded no
AB  - extra fragment.  This enzyme has been renamed EagMI to avoid confusion with the
AB  - previous EagI.
ER  -

TY  - JOUR
AU  - Sohn, K.H.
AU  - Jones, J.D.
AU  - Studholme, D.J.
TI  - Draft Genome Sequence of Pseudomonas syringae Pathovar Syringae Strain FF5, Causal Agent of Stem Tip Dieback Disease on Ornamental Pear.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3733
EP  - 3734
VL  - 194
AB  - Pseudomonas syringae FF5 causes stem tip dieback disease on ornamental pear (Pyrus
AB  - calleryana). Its genome encodes a complete type III secretion system
AB  - (T3SS) and HopAC1, HopM1, AvrE1, HopI1, HopAA1, HopJ1, HopAH2, HopAH1, HopAG1,
AB  - and HopAZ1. Lacking detectable homologues of other T3SS effectors, it may encode
AB  - novel, undiscovered effectors.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
TI  - Search, isolation and study of restrictases.
JO  - Vestn. Akad. Med. Nauk SSSR
PY  - 1995
SP  - 47
EP  - 51
VL  - 2
AB  - New Class II restrictases were searched in over 800 microorganisms by using a highly sensitive
AB  - toluene micro technique developed in the laboratory. This enabled site-specific endonuclease
AB  - activity to be revealed in 72 strains. Thirty-two new restriction endonucleases were
AB  - identified, which were highly purified and contained no impurities of nonspecific nucleases,
AB  - phosphatases. Many of them (LpII, PaeI, PaeBI, ApiI, CsiAI, BavAI, BavAIII, BbvAI, etc.) are
AB  - of interest for use in molecular genetic studies. Corynebacterium species cells were used to
AB  - isolate a new super coarse hissing restrictase CsiBI that recognizes the 8-nucleotide site
AB  - GCGGCCGC (the isoschizomer NotI) and a fine tool for obtaining enlarged fragments of pro- and
AB  - eukaryotic genome.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
TI  - Current approaches to the search of new restriction endonucleases.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1989
SP  - 3
EP  - 7
VL  - 0
AB  - The main methodological approaches to the search for new restriction
AB  - endonucleases are reviewed.  These methods include obtaining acellular extracts
AB  - by ultrasonic disintegration of microbial cells, osmotic shock effects, the
AB  - effects of organic solvents, mechanical disruption of bacterial cells, biphasic
AB  - division after Albertson and others.  The resolving power of any method
AB  - discussed depends mainly on the level of restriction endonuclease activity, the
AB  - presence of nonspecific endonucleases in the biomass, the presence of
AB  - exonucleases and the taxonomy of the microorganisms used.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
TI  - Restriction endonucleases: Isolation methods and schemes.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1990
SP  - 1
EP  - 6
VL  - 0
AB  - The great successes achieved in the last 10-15 years in the field of recombinant DNA
AB  - technology have been largely due to the practical use of site-specific endonucleases (class II
AB  - restriction endonucleases; EC 3.1.23.X).  We must agree with the opinion of F. Yang, who
AB  - believes that one of the major discoveries that determined the course of development of
AB  - genetic engineering was the discovery of restriction enzymes by S. Luria and M. Human.  The
AB  - enormous interest in restriction endonucleases as research tools is due, on one hand, to their
AB  - unique properites - their ability to form sticky ends on DNA fragments, the variety of
AB  - recognizable nucleotide sequences, and the positions of the points of cleavage of the
AB  - recognition sites.  On the other hand, restriction enodnucleases, which possess extremely high
AB  - specificity with respect to the DNA nucleotide sequences that they recognize and hydrolyze,
AB  - represent a splendid model for the study of the important general biological problems of
AB  - nucleic-protein recognition.  Considering the great interest in restriction endonucleases
AB  - among biochemists, molecular biologists, and specialists in allied fields, it is advisable to
AB  - examine the basic methodological approaches and the most widespread schemes of isolation of
AB  - these enzymes, to assess the difficulties and problems standing in the way of the production
AB  - of purified restriction endonuclease preparations.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Anikeitcheva, N.V.
AU  - Fitsner, A.B.
AU  - Samko, O.T.
AU  - Khoroshutina, E.B.
AU  - Kalugin, A.A.
TI  - Search of strains producing new restriction endonucleases.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1988
SP  - 86
EP  - 89
VL  - 9
AB  - The search for restriction endonucleases in 154 strains belonging to 104
AB  - species of 32 genera of microorganisms has been carried out by the method of
AB  - rapid toluene assay.  In 10 strains the activity of endonucleases specifically
AB  - fragmenting the DNA of phage lambda in the presence of Mg2+ ions has been
AB  - detected.  Restriction enzymes PaeI and PaeII found in two Pseudomonas
AB  - aeruginosa strains have been identified as the true isoschizomers of
AB  - restriction endonucleases SphI and SmaI respectively.  The results of the
AB  - screening of restriction enzyme-producing strains indicate that the production
AB  - of restriction enzymes is widespread among microorganisms of the genus
AB  - Bacillus.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Eldarov, M.A.
AU  - Anikeitcheva, N.V.
AU  - Karpychev, I.V.
AU  - Samko, O.T.
AU  - Fitzner, A.B.
AU  - Kalugin, A.A.
AU  - Choroshoutina, E.B.
AU  - Skryabin, K.G.
TI  - Site-specific endonuclease BbvBI from Bacillus brevis.
JO  - Bioorg. Khim.
PY  - 1992
SP  - 47
EP  - 51
VL  - 18
AB  - A new restriction endonuclease BbvBI free from contaminating non-specific nucleases and
AB  - phosphatases was isolated from the Bacillus brevis cells. The enzyme was purified by
AB  - fractionating the sonicated cell-free extract in a two-phase PEG/dextran system and subsequent
AB  - chromatographies on DEAE-sepharose, blue sepharose and heparin sepharose. The endonuclease
AB  - BbvBI displayed the maximal activity at 45 degrees C, pH between 8.0 and 8.5, MgCl2
AB  - concentration in the range of 5-10 mM and at the low ionic strength. It is shown that the
AB  - enzyme cleaves the sequence G^GYPC'C, with the preferential cleavage of GGTACC and GGACC site
AB  - as compared with GGTGCC and GGCGCC. Thus, the restriction endonuclease BbvBI is a true
AB  - isoschizomer of nuclease BanI.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Eldarov, M.A.
AU  - Anikeitcheva, N.V.
AU  - Karpychev, I.V.
AU  - Samko, O.T.
AU  - Fitzner, A.B.
AU  - Kalugin, A.A.
AU  - Choroshoutina, E.B.
AU  - Skryabin, K.G.
TI  - BcoAI, a new site-specific endonuclease from Bacillus coagulans.
JO  - Bioorg. Khim.
PY  - 1991
SP  - 1188
EP  - 1192
VL  - 17
AB  - A new site-specific endonuclease was detected in toluene lysates of Bacillus
AB  - coagulans AUCM B-732 and designated as BcoAI.  The enzyme was purified by
AB  - fractionation of the cell-free extract in the two-phase PEG/dextran system
AB  - followed by chromatography on DEAE-sepharose and phosphocellulose and shown to
AB  - be free of nonspecific nucleases and phosphatases.  BcoAI has three cleavage
AB  - sites on lambda DNA, but does not cleave SV40, pBR322 and pUC19 DNA.  BcoAI
AB  - recognizes the sequence 5'CAC^GTG3' on double-stranded DNA and cleaves it as
AB  - indicated by the arrow to yield blunt-ended DNA fragments.  Thus, BcoAI is a
AB  - true isoschizomer of PmaCI from Pseudomonas maltophila C.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Eldarov, M.A.
AU  - Rina, M.
AU  - Korolev, S.V.
AU  - Markaki, M.
AU  - Kalugin, A.A.
AU  - Omelyanuk, N.M.
AU  - Skryabin, K.G.
AU  - Bouriotis, V.
TI  - Isolation and characterization of CspBI, a novel NotI isoschizomer from Corynebacterium species B recognizing 5'-GC/GGCCGC-3'.
JO  - Biochem. Mol. Biol. Int.
PY  - 1998
SP  - 433
EP  - 441
VL  - 44
AB  - Sixty-seven bacterial strains were surveyed for the presence of type II restriction
AB  - endonucleases, especially concerning super-rare-cutting enzymes.  Fourteen strains were found
AB  - to contain specific enzymes.  One of them CspBI from Corynebacterium species B was purified
AB  - and characterized as an isoschizomer of NotI, which recognizes the palindromic octanucleotide
AB  - sequence 5'-GC/GGCCGC-3' and cleaves at the position shown by the arrow.  A comparison
AB  - between the cleavage patterns on different DNA's, obtained with partially purified
AB  - endonucleases from other detected producers including some strains of Corynebacterium,
AB  - Cellulomonas, and Rhizobium has shown that these enzymes do not belong to super-rare-cutting
AB  - restriction enodnucleases.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitsner, A.B.
AU  - Anikeitcheva, N.V.
AU  - Choroshoutina, Y.B.
AU  - Samko, O.T.
AU  - Kolosha, V.O.
AU  - Fodor, I.
AU  - Votrin, I.I.
TI  - A site-specific endonuclease from Pseudomonas aeruginosa.
JO  - Mol. Biol. Rep.
PY  - 1985
SP  - 159
EP  - 161
VL  - 10
AB  - PaeI, a new restriction endonuclease from Pseudomonas aeruginosa clinical
AB  - strain was isolated and chracterized.  It recognizes and cleaves the sequence
AB  - 5'-GCATG^C-3' generating DNA fragments with 3'-tetranucleotide sticky ends.
AB  - DNAs of pBR322, SV40 and bacteriophage lambda have one, two and six PaeI
AB  - recognition sites, respectively.Seventy-two strains of Pseudomonas,
AB  - Clostridium, Escherichia coli, Shigella, Proteus and Saccharomyces were
AB  - screened for the presence of site-specific endonucleases.  Here we describe the
AB  - PaeI restriction enzyme found in Pseudomonas aeruginosa; other data will be
AB  - published elsewhere.Earlier Hinkle and Miller isolated from P. aeruginosa a
AB  - PaeR7 restriction endonuclease recognizing and cleaving a sequence
AB  - 5'-C^TCGAG-3'.  Sequence analysis of DNAs cleaved by PaeI shows that the enzyme
AB  - is the isoschizomer of SphI.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitsner, A.B.
AU  - Anikeitcheva, N.V.
AU  - Khoroshutina, E.B.
AU  - Samko, O.T.
TI  - Effect of thio-specific reagent on Pseudomonas aeruginosa PaeI and PaeII restriction endonuclease activity.
JO  - Biull. Eksp. Biol. Med.
PY  - 1986
SP  - 695
EP  - 697
VL  - 102
AB  - Because of their unique properties class II restriction endonucleases are
AB  - widely used in research in molecular biology and genetic engineering.  By now
AB  - more than 400 restriction endonucleases have been described, their
AB  - physicochemical and catalytic properties and the structure of many of these
AB  - enzymes have been reasonably well studied and techniques have been developed
AB  - for seeking them in microorganisms and isolating them.  However, there is
AB  - hardly any information in the literature on sulfhydryl groups of restriction
AB  - endonucleases and their role in interaction with the DNA substrate.  The only
AB  - exception is an investigation of the sensitivity of 11 restriction
AB  - endonucleases to the action of alkylating and mercury compounds.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitsner, A.B.
AU  - Anikeitcheva, N.V.
AU  - Samko, O.T.
AU  - Khoroshutina, E.B.
AU  - Kolosha, V.O.
AU  - Fodor, I.I.
TI  - Pseudomonas aeruginosa restrictases:  Physico-chemical properties, substrate specificity, prospects of application.
JO  - Biotekhnologiya
PY  - 1987
SP  - 578
EP  - 585
VL  - 3
AB  - The optimal conditions of the reaction catalyzed by restrictases PaeI and PaeII
AB  - (the optimum of pH, temperature, effects of divalent cations) were studied.
AB  - The activity of restrictase PaeII is dependent on the K+ ions.  The molecular
AB  - mass of restrictases PaeI and PaeII is approximately 150 and 130 kD,
AB  - respectively.  On the base of data on the substrate specificity and the
AB  - structure of the recognition site, it was determined, that restrictases PaeI
AB  - and PaeII are isoschizomers of restrictases SphI and SmaI, correspondingly.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitsner, A.B.
AU  - Anikeycheva, N.V.
AU  - Kovalenko, N.A.
TI  - Role of bivalent cations in endonucleolysis of DNA catalyzed by restrictases.
JO  - Vopr. Med. Khim.
PY  - 1989
SP  - 66
EP  - 69
VL  - 6
AB  - Electrophoretic analysis of products obtained after hydrolysis of phage lambda
AB  - DNA by means of restrictase PaeI was carried out after preincubation of DNA or
AB  - the enzyme with Mg2+ as well as after preincubation of DNA simultaneously with
AB  - the enzyme and the subsequent addition of the required components into the
AB  - experimental samples.  The analysis showed that Mg2+ ions were apparently not
AB  - required for the enzyme-substrate complex formation and caused destabilization
AB  - of the complex.  Restrictase PaeI was active when Mg2+ was substituted by Mn2+,
AB  - Ca2+, Zn2+, Co2+ but not by Cd2+, Cu2+ or Ni2+.  Experiments with
AB  - o-phenanthroline showed that Zn2+ cations are important for the catalytic
AB  - activity of restrictase PaeI.  Possible functions of Zn2+ in protein-nucleic
AB  - acids recognition are discussed.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitsner, A.B.
AU  - Khoroshutina, E.B.
AU  - Kheislere, M.Y.
TI  - Determination of restriction endonuclease activity in Toluene lysates of bacterial cells.
JO  - Biull. Eksp. Biol. Med.
PY  - 1984
SP  - 163
EP  - 165
VL  - 97
AB  - By now more than 350 restriction endonucleases have been described in the
AB  - literature and they are widely used in molecular biology and in bioengineering
AB  - research.  Selection of strains producing restriction endonucleases with a view
AB  - to finding new and unique restriction enzymes is continuously in progress.  For
AB  - this reason there is an urgent need for quick and reliable ways of determining
AB  - restriction endonuclease activity in bacterial cells.  The method generally
AB  - used to estimate restriction endonuclease activity in bacterial cells involves
AB  - disintegration of the cells with ultrasound followed by high-speed
AB  - centrifugation in order to obtain a cell-free extract.  An essential
AB  - shortcoming of this method is that the extracts contain activity of nonspecific
AB  - endo- and exonucleases, in the presence of whose action it is not always
AB  - possible to reveal specific activity of restriction endonucleases.  For
AB  - instance, according to data in the literature, activity of only three of the 16
AB  - restriction endonucleases studied can be found in unpurified extracts.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitsner, A.B.
AU  - Samko, O.T.
AU  - Khoroshutina, E.B.
AU  - Kalugin, A.A.
TI  - Effect of monovalent cations on activity of site-specific endonuclease PaeII.
JO  - Vopr. Med. Khim.
PY  - 1990
SP  - 65
EP  - 67
VL  - 36
AB  - The activity of restrictase PaeII, contrary to known Type II restriction
AB  - enzymes (except of true isoschizomer SmaI), depended absolutely on monovalent
AB  - cations.  This pattern is atypical for Type II restrictases.  At the same time,
AB  - restrictase PaeII was able to hydrolyze DNA as a substrate in the absence of
AB  - exogenous Mg2+, if the incubation mixture contained cations K+, Rb+, Cs+ and
AB  - NH4+ but not Na+ or Li+.  Mg2+ was found to activate the enzyme in the presence
AB  - of monovalent cations.  Based on the protective effect of K+ against
AB  - inactivation of restrictase PaeII by means of thiol-affecting reagents and high
AB  - temperature as well as on stabilization of the enzyme by KCl during storage,
AB  - monovalent cations appear to participate in formation of protein molecular
AB  - structure, which is optimal for catalytic effect and resistant to inactivation.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Fitzner, A.B.
AU  - Eldarov, M.A.
AU  - Anikeicheva, N.B.
AU  - Kalugin, A.A.
AU  - Samko, O.T.
AU  - Khoroshoutina, E.B.
AU  - Fodor, I.
TI  - BavAI, a restriction endonuclease from Bacillus alvei.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2897
EP  - 2897
VL  - 20
AB  - A restriction endonuclease BavAI, free of contaminating nuclease activity was isolated from
AB  - Bacillus alvei strain 675 using column chromatography on DEAE cellulose and Blue Sepharose
AB  - CL-6B. Optimal conditions for BavAI digestion were determined at 30C in a buffer containing 10
AB  - mM MgCl2, 30 mM KCl at pH 7.5-8.3. The yield of the enzyme from 10 grams of wet cells was
AB  - 22,000 units. The enzyme cleaves lambda phage DNA at 15 sites, Ad-2 DNA at 24 sites and
AB  - plasmid pBR322 DNA at a unique site. The single cleavage site of BavAI on pBR322 DNA was
AB  - mapped by standard double digestion analysis to approximately position 2000. From these data
AB  - we deduced that the restriction enzyme cuts at PvuII sites. This was confirmed by comparing
AB  - patterns of lambda DNA digests obtained with BavAI, PvuII and BavAI + PvuII simultaneously.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Kheislere, M.Y.
AU  - Alexandrova, S.S.
AU  - Zildere, A.M.
AU  - Ansberga, S.E.
TI  - A systematic method to isolate restriction endonucleases.
JO  - Izv. Akad. Nauk Latv. SSR
PY  - 1984
SP  - 54
EP  - 62
VL  - 12
AB  - None
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Kolosha, V.O.
AU  - Fitsner, A.B.
AU  - Anikeitcheva, N.V.
AU  - Khoroshutina, E.B.
AU  - Samko, O.T.
AU  - Fodor, I.
AU  - Votrin, I.I.
TI  - New specific endonucleases PaeI and PaeII from Pseudomonas aeruginosa.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1986
SP  - 24
EP  - 26
VL  - 0
AB  - Specific endonuclease activities have been found in two Pseudomonas aeruginosa
AB  - strains.  Isolation and purification of enzymes and determining their specific
AB  - activities have permitted one to find out that PaeI is an isoshizomer of SphI
AB  - and digests the sequence 5'-GCATG^C-3'.  Another isolated enzyme PaeII is an
AB  - isoschizomer of SmaI and cleaves DNA in a fragment 5'-CCC^GGG-3'.  The use of
AB  - PaeI and PaeII enzymes in genetical engineering and their advantages are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Korolev, S.V.
AU  - Rina, M.
AU  - Eldarov, M.A.
AU  - Gervaziev, Y.V.
AU  - Skryabin, K.G.
AU  - Bouriotis, V.
TI  - New site-specific endonucleases from Brevibacterium species.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1998
SP  - 35
EP  - 38
VL  - 9
AB  - New site-specific endonucleases BecAI and BecAII have been detected in Brevibacterium species
AB  - A.  Endonuclease BecAII free from contaminating nonspecific endonucleases, exonucleases, and
AB  - phosphatases was isolated by column chromatography on phosphocellulose, heparin sepharose, and
AB  - DNA cellulose.  It recognizes and cleaves the 5'-GG/CC-3' sequence and is a true
AB  - isoschizomer of HaeIII restriction enzyme.  The other restriction endonuclease, BecAI, cleaves
AB  - Ad2 DNA at least by 2 sites but not the DNA of phage lambda, T7, SV40, PhiX174, and plasmids
AB  - pBR322 and pUC19.  The substrate specificity of BecAI indicates its appurtenance to the super
AB  - rare restriction endonucleases.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Maneliene, Z.P.
AU  - Butkus, V.V.
AU  - Fitzner, A.B.
AU  - Khoroshutina, E.B.
AU  - Kalugin, A.A.
AU  - Janulaitis, A.
TI  - Site-specific endonucleases LplI and AagI.
JO  - Bioorg. Khim.
PY  - 1990
SP  - 1040
EP  - 1044
VL  - 16
AB  - New site-specific endonucleases LplI and AagI have been isolated from the
AB  - Lactobacillus plantarum and Achromobacter agile cells, respectively.  The
AB  - enzymes' purification stages included treatment of cell-free extracts with
AB  - polyethylenimine, fractionation in a two-phase system by Albertsson's method,
AB  - chromatography on blue Sepharose and DEAE-cellulose.  The results of cleavage
AB  - of a 5'-32P-labelled oligodeoxynucleotide duplex by restriction endonucleases
AB  - LplI and AagI indicate that these enzymes recognize and cut the sequence
AB  - AT^CGAT, being therefore true isoschizomers of the ClaI restriction
AB  - endonuclease from Caryophanon latum.  The L. plantarum strain has 400 fold more
AB  - endonuclease production as compared with the ClaI producer and is preferred for
AB  - preparative isolation of LplI.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Samko, O.T.
AU  - Anikeitcheva, N.V.
AU  - Kalugin, A.A.
AU  - Khoroshutina, E.B.
AU  - Plutalov, O.V.
AU  - Birikh, K.R.
AU  - Berlin, Y.A.
TI  - New site-specific endonucleases from Bacillus strains.
JO  - Bioorg. Khim.
PY  - 1994
SP  - 1334
EP  - 1341
VL  - 20
AB  - In a search for new restriction endonucleases type II, among forty bacterial strains of the
AB  - Bacillus genus two strains producing site-specific endonucleases have been found.
AB  - Endonucleases BbvAIII and BspFI, isolated from B. brevis BLM B-677 and B. species F, are shown
AB  - to be true isoschizomers of BspMII (Kpn2I) and Sau3AI, respectively.
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Votrin, I.I.
TI  - Restriction endonucleases as an instrument in comparative biochemical studies.
JO  - Zh. Evol. Biokhim. Fiziol.
PY  - 1979
SP  - 8
EP  - 21
VL  - 15
ER  -

TY  - JOUR
AU  - Sokolov, N.N.
AU  - Votrin, I.I.
AU  - Fitsner, A.B.
AU  - Anikeitcheva, N.V.
TI  - Isolation and certain properties of restriction endonuclease from Bacillus amyloliquefaciens.
JO  - Biokhimiia
PY  - 1978
SP  - 865
EP  - 871
VL  - 43
AB  - A partially purified preparation of the restriction endonuclease BamHI was
AB  - isolated from cells of Bacillus amyloliquefaciens.  The proposed method of
AB  - purification of restriction enzyme BamHI is a modification of the method
AB  - described by Wilson and Young.  Decomposition of the cells with ultrasound,
AB  - treatment with streptomycin sulfate, fractionation with ammonium sulfate,
AB  - chromatography on DEAE-cellulose and hydroxyapatite, and rechromatography on
AB  - DEAE-cellulose were used for the isolation and purification of the enzyme.  The
AB  - restriction enzyme BamHI splits the linear double-stranded DNA molecule of
AB  - phage lambda into six fragments.  The enzyme is stable to storage in ice in
AB  - sodium or potassium phosphate buffer with beta-mercaptoethanol (10 mM) for
AB  - 1.5-2 months.
ER  -

TY  - JOUR
AU  - Sokolowska, M.
AU  - Czapinska, H.
AU  - Bochtler, M.
TI  - Crystal structure of the {beta}{beta}{alpha}-Me type II restriction endonuclease Hpy99I with target DNA.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 3799
EP  - 3810
VL  - 37
AB  - The betabetaalpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target
AB  - sequence and cleaves it with unusual stagger (five
AB  - nucleotide 5'-recessed ends). Here we present the crystal structure of the
AB  - specific complex of the dimeric enzyme with DNA. The Hpy99I protomer
AB  - consists of an antiparallel beta-barrel and two beta4alpha2 repeats. Each
AB  - repeat coordinates a structural zinc ion with four cysteine thiolates in
AB  - two CXXC motifs. The betabetaalpha-Me region of the second beta4alpha2
AB  - repeat holds the catalytic metal ion (or its sodium surrogate) via Asp148
AB  - and Asn165 and activates a water molecule with the general base His149. In
AB  - the specific complex, Hpy99I forms a ring-like structure around the DNA
AB  - that contacts DNA bases on the major and minor groove sides via the first
AB  - and second beta4alpha2 repeats, respectively. Hpy99I interacts with the
AB  - central base pair of the recognition sequence only on the minor groove
AB  - side, where A:T resembles T:A and G:C is similar to C:G. The Hpy99I-DNA
AB  - co-crystal structure provides the first detailed illustration of the
AB  - betabetaalpha-Me site in REases and complements structural information on
AB  - the use of this active site motif in other groups of endonucleases such as
AB  - homing endonucleases (e.g. I-PpoI) and Holliday junction resolvases (e.g.
AB  - T4 endonuclease VII).
ER  -

TY  - JOUR
AU  - Sokolowska, M.
AU  - Czapinska, H.
AU  - Bochtler, M.
TI  - Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 1554
EP  - 1564
VL  - 39
AB  - The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It
AB  - is found in the eukaryotic flap endonuclease and
AB  - Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision
AB  - repair proteins UvrC and Cho, and in proteins of 'selfish' genetic
AB  - elements. Here we present the structures of the ternary pre- and
AB  - post-cleavage complexes of the type II GIY-YIG restriction endonuclease
AB  - Hpy188I with DNA and a surrogate or catalytic metal ion, respectively. Our
AB  - structures suggest that GIY-YIG nucleases catalyze DNA hydrolysis by a
AB  - single substitution reaction. They are consistent with a previous proposal
AB  - that a tyrosine residue (which we expect to occur in its phenolate form)
AB  - acts as a general base for the attacking water molecule. In contrast to
AB  - the earlier proposal, our data identify the general base with the GIY and
AB  - not the YIG tyrosine. A conserved glutamate residue (Glu149 provided in
AB  - trans in Hpy188I) anchors a single metal cation in the active site. This
AB  - metal ion contacts the phosphate proS oxygen atom and the leaving group
AB  - 3'-oxygen atom, presumably to facilitate its departure. Taken together,
AB  - our data reveal striking analogy in the absence of homology between
AB  - GIY-YIG and betabetaalpha-Me nucleases.
ER  -

TY  - JOUR
AU  - Sokolowska, M.
AU  - Kaus-Drobek, M.
AU  - Czapinska, H.
AU  - Tamulaitis, G.
AU  - Szczepanowski, R.H.
AU  - Urbanke, C.
AU  - Siksnys, V.
AU  - Bochtler, M.
TI  - Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 722
EP  - 734
VL  - 369
AB  - Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for
AB  - C or G, / designates a cleavage position) to generate
AB  - staggered products with single nucleotide 5'-overhangs. Here, we show that
AB  - BcnI functions as a monomer that interacts with its target DNA in 1:1
AB  - molar ratio and report crystal structures of BcnI in the absence and in
AB  - the presence of DNA. In the complex with DNA, BcnI makes specific contacts
AB  - with all five bases of the target sequence and not just with a half-site,
AB  - as the protomer of a typical dimeric restriction endonuclease. Our data
AB  - are inconsistent with BcnI dimerization and suggest that the enzyme
AB  - introduces double-strand breaks by sequentially nicking individual DNA
AB  - strands, although this remains to be confirmed by kinetic experiments.
AB  - BcnI is remotely similar to the DNA repair protein MutH and shares
AB  - approximately 20% sequence identity with the restriction endonuclease
AB  - MvaI, which is specific for the related sequence CC/WGG (W stands for A or
AB  - T). As expected, BcnI is structurally similar to MvaI and recognizes
AB  - conserved bases in the target sequence similarly but not identically. BcnI
AB  - has a unique machinery for the recognition of the central base-pair.
ER  -

TY  - JOUR
AU  - Sokolowska, M.
AU  - Kaus-Drobeka, M.
AU  - Czapinska, H.
AU  - Tamulaitis, G.
AU  - Siksnys, V.
AU  - Bochtler, M.
TI  - Restriction endonucleases that resemble a component of the bacterial DNA repair machinery.
JO  - Cell. Mol. Life Sci.
PY  - 2007
SP  - 2351
EP  - 2357
VL  - 64
AB  - It has long been known that most Type II restriction endonucleases share a conserved core fold
AB  - and similar active-sites. The same core folding motif is also present in the MutH protein, a
AB  - component of the bacterial DNA mismatch repair machinery. In contrast to most Type II
AB  - restriction endonucleases, which assemble into functional dimers and catalyze double-strand
AB  - breaks, MutH is a monomer and nicks hemimethylated DNA. Recent biochemical and
AB  - crystallographic studies demonstrate that the restriction enzymes BcnI and MvaI share many
AB  - additional features with MutH-like proteins, but not with most other restriction
AB  - endonucleases. The structurally similar monomers all recognize approximately symmetric target
AB  - sequences asymmetrically. Differential sensitivities to slight substrate asymmetries, which
AB  - could be altered by protein engineering, determine whether the enzymes catalyze only
AB  - single-strand nicks or double-strand breaks.
ER  -

TY  - JOUR
AU  - Solaiman, D.K.Y.
AU  - Somkuti, G.A.
TI  - Isolation and characterization of a type II restriction endonuclease from Streptococcus thermophilus.
JO  - FEMS Microbiol. Lett.
PY  - 1990
SP  - 261
EP  - 266
VL  - 67
AB  - A type II restriction endonuclease Sth134I was isolated from Streptococcus
AB  - thermophilus strain 134.  The enzyme is an isoschizomer of HpaII. The
AB  - restriction endonuclease is most active at Mg(II) >5 mM; in the pH range of
AB  - 7.5-8; temperature of 50-55C; and (KCl) or (NaCl) below 100 mM.  Double
AB  - digestion and ligation experiments experiments showed that Sth134I apparently
AB  - recognized and cleaves DNA at the sequence CCGG to produce two-base,
AB  - 5'-protruding ends.
ER  -

TY  - JOUR
AU  - Solaiman, D.K.Y.
AU  - Somkuti, G.A.
TI  - A type II restriction endonuclease of Streptococcus thermophilus ST117.
JO  - FEMS Microbiol. Lett.
PY  - 1991
SP  - 75
EP  - 80
VL  - 80
AB  - Streptococcus thermophilus strain 117 produces a type II restriction
AB  - endonuclease designated as Sth117I.  This enzyme was isolated from cell
AB  - extracts by membrane filtration and ammonium sulfate fractionation.  Anion
AB  - exchange chromatography on DE52 yielded an enzyme preparation free of
AB  - nonspecific nucleases.  The optimal reaction conditions for Sth117I are: (1)
AB  - [MgCl2] > 5 mM; (2) pH range of 6.5-7; (3) incubation temperature between 37
AB  - and 50C; and (4) [NaCl] or [KCl] < 50 mM.  The results of single- and
AB  - double-digestion experiments indicated that the Sth117I was an isoschizomer of
AB  - BstNI and EcoRII with the recognition sequence of 5'-CCWGG-3'.  The cleavage
AB  - site of Sth117I was identified as 5'-CC^WGG-3' by 5'-end analysis.  This was
AB  - supported by the results of ligation experiments with Sth117I-restricted DNAs
AB  - and the BstNI- or EcoRII-generated fragments.
ER  -

TY  - JOUR
AU  - Solem, A.
AU  - Chatterjee, P.
AU  - Caprara, M.G.
TI  - A novel mechanism for protein-assisted group I intron splicing.
JO  - RNA
PY  - 2002
SP  - 412
EP  - 425
VL  - 8
AB  - Previously it was shown that the Aspergillus nidulans (A.n.) mitochondrial COB intron
AB  - maturase, I-AniI, facilitates splicing of the
AB  - COB intron in vitro. In this study, we apply kinetic analysis of
AB  - binding and splicing along with RNA deletion analysis to gain insight
AB  - into the mechanism of I-AniI facilitated splicing. Our results are
AB  - consistent with I-AniI and A.n. COB pre-RNA forming a specific but
AB  - labile encounter complex that is resolved into the native,
AB  - splicing-competent complex. Significantly, kinetic analysis of splicing
AB  - shows that the resolution step is rate limiting for splicing. RNA
AB  - deletion studies show that I-Anil requires most of the A.n. COB intron
AB  - for binding suggesting that the integrity of the I-AniI-binding site
AB  - depends on overall RNA tertiary structure. These results, taken
AB  - together with the observation that A.n. COB intron lacks significant
AB  - stable tertiary structure in the absence of protein, support a model in
AB  - which I-AniI preassociates with an unfolded COB intron via a "labile"
AB  - interaction that facilitates correct folding of the intron catalytic
AB  - core, perhaps by resolving misfolded RNAs or narrowing the number of
AB  - conformations sampled by the intron during its search for native
AB  - structure. The active intron conformation is then "locked in" by
AB  - specific binding of I-AniI to its intron interaction site.
ER  -

TY  - JOUR
AU  - Soler-Bistue, A.J.
AU  - Birshan, D.
AU  - Tomaras, A.P.
AU  - Dandekar, M.
AU  - Tran, T.
AU  - Newmark, J.
AU  - Bui, D.
AU  - Gupta, N.
AU  - Hernandez, K.
AU  - Sarno, R.
AU  - Zorreguieta, A.
AU  - Actis, L.A.
AU  - Tolmasky, M.E.
TI  - Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements.
JO  - PLoS ONE
PY  - 2008
SP  - E1800
EP  - E1800
VL  - 3
AB  - BACKGROUND: Dissemination of antimicrobial resistance genes has become an important public
AB  - health and biodefense threat. Plasmids are important contributors to the rapid acquisition of
AB  - antibiotic resistance by pathogenic bacteria. PRINCIPAL FINDINGS: The nucleotide sequence of
AB  - the Klebsiella pneumoniae multiresistance plasmid pMET1 comprises 41,723 bp and includes
AB  - Tn1331.2, a transposon that carries the bla(TEM-1) gene and a perfect duplication of a 3-kbp
AB  - region including the aac(6')-Ib, aadA1, and bla(OXA-9) genes. The replication region of pMET1
AB  - has been identified. Replication is independent of DNA polymerase I, and the replication
AB  - region is highly related to that of the cryptic Yersinia pestis 91001 plasmid pCRY. The
AB  - potential partition region has the general organization known as the parFG locus. The
AB  - self-transmissible pMET1 plasmid includes a type IV secretion system consisting of proteins
AB  - that make up the mating pair formation complex (Mpf) and the DNA transfer (Dtr) system. The
AB  - Mpf is highly related to those in the plasmid pCRY, the mobilizable high-pathogenicity island
AB  - from E. coli ECOR31 (HPI(ECOR31)), which has been proposed to be an integrative conjugative
AB  - element (ICE) progenitor of high-pathogenicity islands in other Enterobacteriaceae including
AB  - Yersinia species, and ICE(Kp1), an ICE found in a K. pneumoniae strain causing primary liver
AB  - abscess. The Dtr MobB and MobC proteins are highly related to those of pCRY, but the
AB  - endonuclease is related to that of plasmid pK245 and has no significant homology with the
AB  - protein of similar function in pCRY. The region upstream of mobB includes the putative oriT
AB  - and shares 90% identity with the same region in the HPI(ECOR31). CONCLUSIONS: The comparative
AB  - analyses of pMET1 with pCRY, HPI(ECOR31), and ICE(Kp1 )show a very active rate of genetic
AB  - exchanges between Enterobacteriaceae including Yersinia species, which represents a high
AB  - public health and biodefense threat due to transfer of multiple resistance genes to pathogenic
AB  - Yersinia strains.
ER  -

TY  - JOUR
AU  - Sollner, S.
AU  - Berkner, S.
AU  - Lipps, G.
TI  - Characterisation of the novel restriction endonuclease SuiI from Sulfolobus islandicus.
JO  - Extremophiles
PY  - 2006
SP  - 629
EP  - 634
VL  - 10
AB  - A restriction endonuclease activity from Sulfolobus islandicus REN2H1 was purified by
AB  - phosphocellulose and cation exchange chromatography.
AB  - The enzyme cuts DNA at the recognition site GCwGC as could be shown by
AB  - restriction analysis of plasmids and short synthetic duplex DNA. The
AB  - cleavage occurs after the first guanosine base and is inhibited by
AB  - 5-methylcytosine methylation. The restriction activity is
AB  - salt-sensitive and has an optimal activity around 70 degrees C.
ER  -

TY  - JOUR
AU  - Solodukhina, L.I.
AU  - Korotayev, A.I.
AU  - Solonin, A.S.
AU  - Kuzmin, N.P.
TI  - Cloning of genes for restriction-modification system Sfl2aI from Shigella flexneri 2a.
JO  - Genetika
PY  - 1990
SP  - 1126
EP  - 1128
VL  - 26
AB  - The Sfl2aI system of restriction-modification (RM) was revealed in the cells of
AB  - Shigella flexneri encoded by pKMR114 plasmid belonging to the IncN
AB  - incompatibility group.  The genes for the Sf12aI RM system were cloned.  The
AB  - system was ascribed to the enzymes of the EcoRII specificity, as shown by in
AB  - vivo and in vitro experiments.  Restriction analysis of these genes' region and
AB  - antigenic properties of the Sfl2aI endonuclease pointed to significant
AB  - differences between this and the EcoRII RM system.
ER  -

TY  - JOUR
AU  - Solodukhina, L.I.
AU  - Manuvakhova, M.S.
AU  - Korotayev, A.I.
TI  - Type II restriction-modification systems from Shigella strains.
JO  - Genetika
PY  - 1989
SP  - 1571
EP  - 1577
VL  - 25
AB  - Two restriction-modification systems specified by two plasmids have been
AB  - discovered in clinical species of Shigella.  The plasmids are designated
AB  - pKMR114 and pKMR115.  Both are of 60800 bp and belong to the IncN
AB  - incompatibility group.  The EcoRI, EcoRV, HindIII restriction patterns of both
AB  - plasmid DNAs are identical.  As shown by the efficiency of plating of
AB  - bacteriophage lambdavir on the strains harbouring plasmids encoding EcoRI,
AB  - EcoRII, EcoRIII, EcoRIV, EcoRV systems and plasmids studied, the new plasmids
AB  - control synthesis of enzymes with the specificity of EcoRII.  The main
AB  - distinctive feature of pKMR114 is the ability to decrease the efficiency of
AB  - plating of bacteriophage T4 having glycosylated DNA.
ER  -

TY  - JOUR
AU  - Solovyeva, N.Y.
AU  - Rautenstein, Y.I.
TI  - On the phenomenon of restriction and modification of temperate phages for the lysogenic Streptomyces hygroscopicus culture.
JO  - Mikrobiologiia
PY  - 1978
SP  - 956
EP  - 959
VL  - 47
AB  - Temperate phages were isolated from the lysogenic culture of Streptomyces hygroscopicus 0485
AB  - in the indicator cultures of S. hygroscopicus 0477 and S. levoris 1331.  The phages were found
AB  - to be identical in the morphology of particles and serological properties.  The phenomenon of
AB  - cross limitation, by the culture of S. hygroscopicus 0477, of the phage growing on the culture
AB  - of S. levoris 1331, and vice versa, was established.  At the same time, the phages were shown
AB  - to be modified by the host cell.
ER  -

TY  - JOUR
AU  - Solovyeva, N.Y.
AU  - Rautenstein, Y.I.
TI  - On the restriction and modification of actinophages by the cultures of Streptomyces hygroscopicus and Streptomyces levoris.
JO  - Mikrobiologiia
PY  - 1980
SP  - 512
EP  - 515
VL  - 49
AB  - The capability for restriction and modification was studied in the cultures of Streptomyces
AB  - hygroscopicus 0477 and Streptomyces levoris 1331, 2340, 2144 toward the active against them
AB  - temperate phages and three polyphages.  All these cultures were found to be capable of the
AB  - restriction and modification of the temperate phage.  Certain differences in restriction and
AB  - modification were established between S. levoris 1331 and the two other cultures of this
AB  - species.  The culture 1331 could modify the temperate phage only with respect to itself rather
AB  - than the two other cultures.  The phage growing on culture 1331 was restricted not only by
AB  - culture 0477, but also by the strains of S. levoris 2340 and 2144.  At the same time, the
AB  - phage growing on the strains 2340 and 2144 gave the identical effectiveness of inoculation on
AB  - any of these cultures, as well as on the culture 1331, and was restricted to the same degree
AB  - by the culture 0477.  One of the examined polyphages 14/3 was not restricted by any of the
AB  - tested cultures. Two other polyphages SH4 and p4 were restricted only by the culture 2144.
AB  - However, the modification by this culture was not observed.  Among the studied cultures of S.
AB  - levoris, the culture 2144 was most capable of the restriction.
ER  -

TY  - JOUR
AU  - Solow, B.T.
AU  - Somkuti, G.A.
TI  - Molecular properties of Streptococcus thermophilus plasmid pER35 encoding a restriction modification system.
JO  - Curr. Microbiol.
PY  - 2001
SP  - 122
EP  - 128
VL  - 42
AB  - Bacteriophage attack on lactic fermentation bacteria (LFB) is costly to the dairy industry
AB  - because it results in product loss. One mechanism
AB  - used by LFB to protect themselves from bacteriophage attack is
AB  - restriction of foreign DNA. Three plasmids, pER16, pER35, and pER36,
AB  - from three different strains of the thermotolerant dairy fermentation
AB  - bacterium Streptococcus thermophilus were sequenced. One of these
AB  - plasmids, pER35, isolated from S. thermophilus ST135, encoded a type IC
AB  - restriction-modification (R-M) system very similar to those encoded on
AB  - plasmids pIL2614 in Lactococcus lactis subsp. lactis and pND861 in
AB  - Lactococcus lactis biovar diacetylactis. The high degree of identity
AB  - between the R-M systems encoded on pER35, pIL2614, and pND861 indicated
AB  - the potential for horizontal transfer of these genes between different
AB  - species of lactic fermentation bacteria. Similar to the functional R-M
AB  - system encoded on pIL2614 that protects the mesophilic L. lactis subsp.
AB  - lactis against phage attack, the R-M system on pER35 most likely
AB  - functions in the same role in S. thermophilus ST135. The plasmid pER16
AB  - was found to encode the specificity subunit of the R-M system, but not
AB  - the R or M subunits. In addition, all three plasmids encoded proteins
AB  - that are present on other S. thermophilus plasmids, including a protein
AB  - for rolling-circle replication (RepA) and a low-molecular-weight stress
AB  - protein (Hsp). The presence of a complete R-M system encoded on a
AB  - plasmid in S. thermophilus, a species that often lacks plasmids, is
AB  - novel and may be beneficial for protecting S. thermophilus from
AB  - bacteriophage attack under dairy fermentation conditions.
ER  -

TY  - JOUR
AU  - Soltys, K.
AU  - Vavrova, S.
AU  - Budis, J.
AU  - Palkova, L.
AU  - Minarik, G.
AU  - Grones, J.
TI  - Draft Genome Sequence of Escherichia coli KL53.
JO  - Genome Announcements
PY  - 2018
SP  - e00220
EP  - e00218
VL  - 6
AB  - Here, we report the draft genome sequence of a clinical isolate of the
AB  - uropathogenic strain Escherichia coli KL53. A total of 5,083,632 bp was de novo
AB  - assembled into 170 contigs containing 89 RNAs and 5,034 protein-coding genes.
AB  - Remarkable is the presence of the tellurite resistance (ter) operon on a plasmid.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Bhagwat, A.S.
AU  - Friedman, S.
TI  - Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 313
EP  - 332
VL  - 15
AB  - The gene coding for the EcoRII modification enzyme has been cloned and the
AB  - nucleotide sequence of 1933 base pairs containing the gene has been determined.
AB  - The gene codes for a protein of 477 amino acids.  Two transcriptional start
AB  - sites have been mapped by S1 mapping.  One deletion that removes 34 N-terminal
AB  - amino acids was found to have partial enzyme activity.  Comparison of the
AB  - EcoRII methylase sequence with other cytosine methylases revealed several
AB  - domains of partial homology among all cytosine methylases.  Cloning the gene in
AB  - multicopy pUC vectors increased the expression by 6-18 fold.  A 40 fold
AB  - overproduction of the EcoRII methylase was obtained by cloning the gene in the
AB  - expression vector carrying the lambda PL promoter.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Characterization of the intergenic region which regulates the MspI restriction-modification system.
JO  - J. Bacteriol.
PY  - 1997
SP  - 964
EP  - 967
VL  - 179
AB  - The 110-bp intergenic region between mspIM and mspIR, the genes encoding the MspI modification
AB  - (M.MspI) and restriction (R.MspI) enzymes, respectively, was fused, in both orientations, with
AB  - lacZ.  Expression of a single-copy mspIM-lacZ fusion is more than 400-fold stronger than
AB  - expression of an mspIR-lacZ fusion.  M.MspI in trans represses expression of the mspIM-lacZ
AB  - fusion by binding to the DNA but does not affect expression of the mspIRlacZ fusion.
AB  - Transcription start sites of the genes were identified, and a set of nonoverlapping promoters
AB  - was assigned.  DNase I footprinting showed that M.MspI binds to a site within the intergenic
AB  - region that includes only the mspIM regulatory elements.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Inhibition of transcription in vitro by binding of DNA(cytosine-5)-methylases to DNA templates containing cytosine analogs.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 25986
EP  - 25991
VL  - 269
AB  - DNA(cytosine-5)-methylases form tight complexes at their methylation sites when the target
AB  - cytosine residue is substituted by analogs such as 5-azacytosine or 5-fluorocytosine. To test
AB  - whether such complexes can block RNA transcription in vitro, template DNA-containing
AB  - methylation sites were prepared, in which cytosine residues in either the (+)- or (-)-strand
AB  - were substituted by the analogs. Such templates, irrespective of the strand in which
AB  - substitution was made, could effectively block the elongation of RNA at specific sites when
AB  - complexed with EcoRII methylase. The protein-DNA complex probably prevents the unwinding of
AB  - the template strands or might directly present itself as a steric block to the advancing RNA
AB  - polymerase. RNA synthesis was also inhibited at specific sites due to complex formation
AB  - between azacytosine-containing DNA and two other methylases, HhaI and HpaII. The 3' ends of
AB  - the interrupted transcripts were mapped and were found to lie within 13-14, 13, and 23
AB  - nucleotides of the binding sites on the (-)-strand for HhaI, HpaII, and EcoRII methylases,
AB  - respectively. Exonuclease III footprinting revealed that the boundaries of the complexed
AB  - methylases, HhaI, HpaII, and EcoRII, on the (-)-strand were within 2-3, 1-2, and 9-10
AB  - nucleotides, respectively, of the last nucleotide copied by the RNA polymerase.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Autogenous regulation of the EcoRII methylase gene at the transcriptional level: effect of 5-azacytidine.
JO  - EMBO J.
PY  - 1993
SP  - 4297
EP  - 4303
VL  - 12
AB  - mRNA of the EcoRII methylase (M.EcoRII), a type II modification enzyme, was induced when
AB  - Escherichia coli carrying a cloned M.EcoRII gene was exposed to the bacteriocidal drug
AB  - 5-azacytidine. Induction occurred only when transcription was initiated from its own promoter.
AB  - When the 5' promoter sequences were deleted or replaced with the lac promoter sequences, no
AB  - induction occurred. The induction was independent of the template DNA level, but the presence
AB  - of an intact M.EcoRII protein was a requirement. The drug is incorporated into DNA which then
AB  - inhibits M.EcoRII by binding tightly to the enzyme. A deletion within the M.EcoRII coding
AB  - region caused a marked increase in the basal level of mRNA transcribed from the M.EcoRII
AB  - promoter, but no induction occurred upon 5-azacytidine treatment. The level could be reduced
AB  - to normal by M.EcoRII in trans. In vitro, the enzyme bound to the sequence upstream of the
AB  - transcription start sites and inhibited the initiation of transcription. These experiments
AB  - indicate that expression of the M.EcoRII gene was autogenously regulated at the
AB  - transcriptional level. Similar regulation is also noted in another DNA (cytosine-5) methylase,
AB  - M.MspI.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Regulation of EcoRII methyltransferase: effect of mutations on gene expression and in vitro binding to the promoter region.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 5347
EP  - 5353
VL  - 22
AB  - EcoRII methyltransferase (M.EcoRII) which methylates the second C in the sequence CCWGG
AB  - (W=A/T) is autogenously regulated by binding to the 5' regulatory region of its gene. DNase I
AB  - footprinting experiments demonstrated that purified M.EcoRII protected a 47-49 bp region of
AB  - DNA immediately upstream of the ecoRIIM coding region. We have studied this interaction with
AB  - mutants of the enzyme, in vitro by DNA binding and in vivo by investigating the repression in
AB  - trans of expression of beta-galactosidase from an ecoRIIM-lacZ operon fusion. Two
AB  - catalytically active mutants failed to repress expression of the fusion whereas catalytically
AB  - inactive mutants had repressor activity. However, with one of the catalytically inactive
AB  - mutants, C186S, in which the catalytic Cys was replaced with Ser, and which bound unmethylated
AB  - CCWGG sequences, repression could only be demonstrated when those sequences in cellular DNA
AB  - were methylated by supplying a cloned dcm gene in trans. In vitro binding of the DNA fragment
AB  - containing the ecoRIIIM regulatory region was detected only with the mutants that showed
AB  - repressor activity, including C186S. Results indicate that down-regulation of the gene in vivo
AB  - and binding to the promoter in vitro are not dependent on the catalytic properties of
AB  - M.EcoRII. Mobility shift experiments with C186S also revealed that it could bind either the
AB  - promoter or unmethylated CCWGG sites, but not both. We conclude that the concentration of
AB  - unmethylated CCWGG sites controls expression from the ecoRIIM promoter.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Photolabeling of the EcoRII DNA methylase with S-adenosyl-L-methionine.
JO  - FASEB J.
PY  - 1988
SP  - A567
EP  - A567
VL  - 2
AB  - Ultraviolet irradiation of EcoRII methylase enzyme in the presence of its
AB  - substrate, S-adenosyl-L-methionine (SAM), results in the formation of a stable
AB  - enzyme-substrate adduct.  Although the extent of photolabeling is low (1-2%),
AB  - it is specific for the enzyme.  Heat inactivated enzyme or proteins for which
AB  - SAM is not a substrate undergo negligible adduct formation upon uv irradiation.
AB  - Formation of the enzyme-substrate adduct can be demonstrated by
AB  - SDS-polyacrylamide gel electrophoresis after irradiation of the enzyme in the
AB  - presence of either [3H]-methyl or [35S] labeled SAM.  At a concentration of 30
AB  - micrograms the SAM analogues S-adenosyl-L-homocysteine (Ki=0.83 micrograms) and
AB  - sinefungin (Ki=4.3 micrograms) are effective inhibitors of photolabeling
AB  - whereas S-adenosyl-D-homocysteine (Ki=46 micrograms) is a poor inhibitor.
AB  - These experiments indicate that SAM becomes covalently bound at the catalytic
AB  - SAM binding site.  Studies in which the SAM-photolabeled methylase has been
AB  - chemically cleaved at selective sites indicate that binding occurs at a
AB  - localized region of the protein.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Identification of a highly conserved domain in the EcoRII DNA methylase that can be photolabeled with S-adenosylmethionine.
JO  - FASEB J.
PY  - 1990
SP  - A1839
EP  - A1839
VL  - 4
AB  - DNA methyltransferases can be specifically labeled with either [3H]-methyl or
AB  - [35S] S-adenosylmethionine (AdoMet) upon uv irradiation (Som and Friedman, J.
AB  - Biol. Chem., 1990, in press).  The labeling is believed to occur at the AdoMet
AB  - binding site.  With the purpose of localizing the AdoMet binding site of one
AB  - such enzyme, the EcoRII methylase (EcoRIIM), we cleaved [3H]-AdoMet labeled
AB  - EcoRIIM by chemical and enzyme-catalyzed reactions and isolated the
AB  - radiolabeled peptides by SDS-PAGE and by HPLC.  Amino-terminal sequencing of
AB  - all such fragments localized a common region where 75-80% of labeling occurred.
AB  - This region includes a highly conserved core sequence present in all the
AB  - cytosine methylases.  One such fragment was further digested with chymotrypsin
AB  - and the amino acid analysis of the resulting radioactive peptide was consistent
AB  - with the sequence AGFP(C)QPFSL.  However, the cysteine residue could not be
AB  - identified as carboxymethylcysteine.  This PC bond was found to be completely
AB  - protected from a cleavage reaction that specifically cleaves the peptide bond
AB  - N-terminal to a cysteine residue.  These results suggest that the cysteine
AB  - residue is modified by the labeling reaction and is probably located at or
AB  - close to the AdoMet binding site.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Identification of a highly conserved domain in the EcoRII methyltransferase which can be photolabeled with S-adenosyl-L-[methyl-3H] methionine.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 2937
EP  - 2945
VL  - 266
AB  - DNA methyltransferases can be photolabeled with S-adenosyl-L-methionine
AB  - (AdoMet).  Specific incorporation of radioactivity has been demonstrated after
AB  - photolabeling with either [methyl-3H]AdoMet or [35S]AdoMet (Som, S., and
AB  - Friedman, S. (1990) J. Biol. Chem. 265, 4278-4283).  The labeling is believed
AB  - to occur at the AdoMet binding site.  With the purpose of localizing the site
AB  - responsible for [methyl-3H]AdoMet photolabeling, we cleaved the labeled EcoRII
AB  - methyltransferase by chemical and enzymatic reactions and isolated the
AB  - radiolabeled peptides by sodium dodecylsulfate-polyacrylamide gel
AB  - electrophoresis and high pressure liquid chromatography.  The labeled peptides
AB  - were identified by amino-terminal sequencing.  A common region was localized
AB  - which accounted for 65-70% of the total label.  This region includes a highly
AB  - conserved core sequence present in all DNA (cytosine 5)-methyltransferases.
AB  - One such fragment was digested further with chymotrypsin, and amino acid
AB  - analysis of the resulting 3H-labeled peptide was consistent with the sequence
AB  - Ala-Gly-Phe-Pro-(Cys)-Gln-Pro-Phe-Ser-Leu.  However, the cysteine residue was
AB  - not recovered as carboxymethylcysteine.  The Pro-Cys bond was found to be
AB  - protected from cleavage at cysteine residues after cyanylation.  These results
AB  - suggest that the cysteine residue is modified by the labeling reaction.  The
AB  - chymotryptic fragment was hydrolyzed enzymatically to single amino acids, and
AB  - the labeled amino acid was identified as S-methylcytsteine by thin layer
AB  - chromatography.  These results indicate that the cysteine residue is located at
AB  - or close to the AdoMet binding site of EcoRII methyltransferase.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Friedman, S.
TI  - Direct photolabeling of the EcoRII methyltransferase with S-Adenosyl-L-methionine.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 4278
EP  - 4283
VL  - 265
AB  - Ultraviolet irradiation of EcoRII methyltransferase in the presence of its substrate,
AB  - S-adenosyl-L-methionine (AdoMet), results in the formation of a stable enzyme-substrate
AB  - adduct. This adduct can be demonstrated by sodium dodecyl sulfate-polyacrylamide gel
AB  - electrophoresis after irradiation of the enzyme in the presence of either [methyl-3H]AdoMet or
AB  - [35S]AdoMet. The extent of photolabeling is low. Under optimal conditions 4.5 pmol of
AB  - [3H]AdoMet is incorporated into 100 pmol of enzyme. Use of the 8-azido derivative of AdoMet as
AB  - the photolabeling substrate increases the incorporation by approximately 2-fold. However, this
AB  - adduct, unlike the one formed with AdoMet, is not stable when treated with thiol reagents or
AB  - precipitated with trichloracetic acid. A catalytically active conformation of the enzyme is
AB  - needed for AdoMet photolabeling. Heat-inactivated enzyme or proteins for which AdoMet is not a
AB  - substrate or cofactor do not undergo adduct formation. Two other methyltransferases, MspI and
AB  - dam methylases are also shown to form adducts with AdoMet upon UV irradiation. The binding
AB  - constant of the EcoRII methyltransferase for AdoMet determined with the photolabeling reaction
AB  - is 11 microM, which is similar to the binding constant of 9 microM previously reported
AB  - (Freidman, S. (1986) Nucleic Acids Res. 14, 4543-4556). The AdoMet analogs
AB  - S-adenosyl-L-homocysteine (Ki=0.83 microM) and sinefungin (Ki=4.3 microM) are effective
AB  - inhibitors of photolabeling, whereas S-adenosyl-D-homocysteine (Ki=46 microM) is a poor
AB  - inhibitor. These experiments indicate that AdoMet becomes covalently bound at the
AB  - AdoMet-binding site on the enzyme molecule. The EcoRII methyltransferase-AdoMet adduct is very
AB  - stable and could be used to identify the AdoMet-binding site on DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Som, S.
AU  - Yang, L.F.
AU  - Friedman, S.
TI  - Insertion and deletion mutants in the presumed target recognition domain of the EcoRII DNA methylase.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - A436
EP  - A436
VL  - 91
AB  - In order to understand the function of various core domains of
AB  - DNA(cytosine-5)-methyltransferases (Mtases) and to locate the target
AB  - recognition domain (TRD), we prepared insertion and deletion mutants of the
AB  - EcoRII methylase.  Insertion of 4 amino acids between residues 107-108, 117-118
AB  - and 186-187 resulted in total loss of catalytic activity.  These insertion are
AB  - either within or near the motifs conserved in all Mtases.  Ten other mutants
AB  - with insertions placed in variable regions of the methylase retained activity.
AB  - In an attempt to prepare mutants with random internal deletions within the
AB  - variable region (residues 295-407) believed to contain the TRD, we randomly
AB  - fused N- and C-terminal segments deleted for part or all of the variable
AB  - region.  Two catalytically active mutants have a deletion of 5 to 7 amino
AB  - acids.  Forty-five active isolates were found to have duplications ranging from
AB  - a few to more than 100 amino acids.  The duplications occurred within the
AB  - entire 400 bp region.  These results indicate that unlike the N-terminal
AB  - variable region which can be deleted with retention of enzyme activity, this
AB  - internal region, although variable in length in different Mtases, cannot accept
AB  - large deletions with retention of activity.
ER  -

TY  - JOUR
AU  - Sommer, R.
AU  - Schaller, H.
TI  - Nucleotide sequence of the recognition site of the B-specific restriction modification system in E. coli.
JO  - Mol. Gen. Genet.
PY  - 1979
SP  - 331
EP  - 335
VL  - 168
AB  - Two sB mutations in the genome of bacteriophage fd were located by sequence analysis in the fd
AB  - sequence at positions 971 and 6341.  Base changes at or close to these positions in phage M13
AB  - and in phage f1 am 124 also correlate with a loss of sensitivity to B restriction.  From the
AB  - sequence homology between the sequences at the two sB sites the recognition signal for the E.
AB  - coli B restriction/modification enzyme is predicted to be:  5' TGA---8N---TGCT 3' 3'
AB  - ACT---8N---ACGA 5'.
ER  -

TY  - JOUR
AU  - Song, C.X.
AU  - Yu, M.
AU  - Dai, Q.
AU  - He, C.
TI  - Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(alpha)I.
JO  - Bioorg. Med. Chem. Lett.
PY  - 2011
SP  - 5075
EP  - 5077
VL  - 21
AB  - 5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA base in mammalian cells that is
AB  - believed to be another important epigenetic
AB  - modification. Here we report the use of a methylation-insensitive
AB  - restriction enzyme Taq(alpha)I coupled with selective chemical labeling
AB  - of 5-hmC in a combined glycosylation restriction analysis (CGRA) to
AB  - detect 5-hmC in TCGA sequences. This method, differentiates fully
AB  - versus hemi-hydroxymethylated cytosine in the CpG dinucleotide, adds a
AB  - new tool to facilitate biological studies of 5-hmC.
ER  -

TY  - JOUR
AU  - Song, G.T.
AU  - Chen, C.E.
AU  - Ren, J.S.
AU  - Qu, X.G.
TI  - A Simple, Universal Colorimetric Assay for Endonuclease/Methyltransferase Activity and Inhibition Based on an  Enzyme-Responsive Nanoparticle System.
JO  - ACS NANO
PY  - 2009
SP  - 1183
EP  - 1189
VL  - 3
AB  - An enzyme responsive nanoparticle system that uses a DNA-gold nanoparticle (AuNP) assembly as
AB  - the substrate has been developed for
AB  - the simple, sensitive, and universal monitoring of restriction
AB  - endonucleases in real time. This new assay takes advantage of the
AB  - palindromic recognition sequence of the restriction nucleases and the
AB  - unique optical properties of AuNPs and is simpler than the procedure
AB  - previously described by by Xu et al. (Angew. Chem. Int. Ed. Engl. 2007,
AB  - 46, 3468-3470). Because it involves only one type of ssDNA modified
AB  - AuNPs, this assay can be directed toward most of the endonucleases by
AB  - simply changing the recognition sequence found within the linker DNA.
AB  - In addition, the endonuclease activity could be quantitatively analyzed
AB  - by the value of the reciprocal of hydrolysis half time (t(1/2)(-1).
AB  - Furthermore, our new design could also be applied to the assay of
AB  - methyltransferase activity since the methylation of DNA inhibits its
AB  - cleavage by the corresponding restriction endonuclease, and thus, this
AB  - new methodology can be easily adapted to high-throughput screening of
AB  - methyltransferase inhibitors.
ER  -

TY  - JOUR
AU  - Song, J.
AU  - Rechkoblit, O.
AU  - Bestor, T.H.
AU  - Patel, D.J.
TI  - Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
JO  - Science
PY  - 2011
SP  - 1036
EP  - 1040
VL  - 331
AB  - Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1
AB  - (DNMT1). We have solved structures of mouse and human
AB  - DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and
AB  - methyltransferase domains bound to DNA-containing unmethylated CpG sites.
AB  - The CXXC specifically binds to unmethylated CpG dinucleotide and positions
AB  - the CXXC-BAH1 linker between the DNA and the active site of DNMT1,
AB  - preventing de novo methylation. In addition, a loop projecting from BAH2
AB  - interacts with the target recognition domain (TRD) of the
AB  - methyltransferase, stabilizing the TRD in a retracted position and
AB  - preventing it from inserting into the DNA major groove. Our studies
AB  - identify an autoinhibitory mechanism, in which unmethylated CpG
AB  - dinucleotides are occluded from the active site to ensure that only
AB  - hemimethylated CpG dinucleotides undergo methylation.
ER  -

TY  - JOUR
AU  - Song, J.
AU  - Teplova, M.
AU  - Ishibe-Murakami, S.
AU  - Patel, D.J.
TI  - Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.
JO  - Science
PY  - 2012
SP  - 709
EP  - 712
VL  - 335
AB  - DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate  gene
AB  - expression, genome imprinting, and X-chromosome inactivation. We report on
AB  - the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex
AB  - containing a central hemimethylated CpG site. The methyl group of methylcytosine
AB  - is positioned within a shallow hydrophobic concave surface, whereas the cytosine
AB  - on the target strand is looped out and covalently anchored within the catalytic
AB  - pocket. The DNA is distorted at the hemimethylated CpG step, with side chains
AB  - from catalytic and recognition loops inserting through both grooves to fill an
AB  - intercalation-type cavity associated with a dual base flip-out on partner
AB  - strands. Structural and biochemical data establish how a combination of active
AB  - and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated
AB  - maintenance DNA methylation.
ER  -

TY  - JOUR
AU  - Song, J.Y.
AU  - Hong, J.
AU  - Kwak, M.J.
AU  - Kwon, S.K.
AU  - Kim, J.F.
TI  - Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).
JO  - Genome Announcements
PY  - 2016
SP  - e00903
EP  - e00916
VL  - 4
AB  - Porphyrobacter dokdonensis strain DSW-74, isolated from seawater off of Dokdo, Republic of
AB  - Korea, is a member of the family Erythrobacteraceae In this study,
AB  - the genome sequence of DSW-74 was determined using the Illumina HiSeq 2000
AB  - platform and assembled into 11 contigs. Its genome is approximately 3.0 Mb with a
AB  - G+C content of 64.8%, in which 2,875 protein-coding sequences and 47 RNA genes
AB  - were predicted.
ER  -

TY  - JOUR
AU  - Song, J.Y.
AU  - Jeong, H.
AU  - Yu, D.S.
AU  - Fischbach, M.A.
AU  - Park, H.S.
AU  - Kim, J.J.
AU  - Seo, J.S.
AU  - Jensen, S.E.
AU  - Oh, T.K.
AU  - Lee, K.J.
AU  - Kim, J.F.
TI  - Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6317
EP  - 6318
VL  - 192
AB  - Streptomyces clavuligerus is an important industrial strain that produces a number of
AB  - antibiotics, including clavulanic acid and cephamycin C. A
AB  - high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain
AB  - was produced by employing a hybrid approach that involved Sanger
AB  - sequencing, Roche/454 pyrosequencing, optical mapping, and partial
AB  - finishing. Its genome, comprising four linear replicons, one chromosome,
AB  - and four plasmids, carries numerous sets of genes involved in the
AB  - biosynthesis of secondary metabolites, including a variety of antibiotics.
ER  -

TY  - JOUR
AU  - Song, J.Y.
AU  - Kim, H.A.
AU  - Kim, J.S.
AU  - Kim, S.Y.
AU  - Jeong, H.
AU  - Kang, S.G.
AU  - Kim, B.K.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Yu, D.S.
AU  - Kim, B.S.
AU  - Kim, S.H.
AU  - Kwon, S.Y.
AU  - Kim, J.F.
TI  - Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain  JS.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3760
EP  - 3761
VL  - 194
AB  - Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium
AB  - Bacillus sp. strain JS enhance the growth of tobacco and lettuce.
AB  - Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb
AB  - genome reveals a number of genes whose products are possibly involved in
AB  - promotion of plant growth or antibiosis.
ER  -

TY  - JOUR
AU  - Song, J.Y.
AU  - Kwak, M.J.
AU  - Lee, K.Y.
AU  - Kong, H.G.
AU  - Kim, B.K.
AU  - Kwon, S.K.
AU  - Lee, S.W.
AU  - Kim, J.F.
TI  - Draft Genome Sequence of the Antifungal-Producing Plant-Benefiting Bacterium Burkholderia pyrrocinia CH-67.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6649
EP  - 6650
VL  - 194
AB  - Burkholderia pyrrocinia CH-67 was isolated from forest soil as a biocontrol agent to be
AB  - utilized in agriculture. Here, we report the 8.05-Mb draft genome sequence
AB  - of this bacterium. Its genome contains genes involved in biosynthesis of
AB  - secondary metabolites and plant growth promotion, which may contribute to
AB  - probiotic effects on plants.
ER  -

TY  - JOUR
AU  - Song, J.Y.
AU  - Yoo, R.H.
AU  - Jang, S.Y.
AU  - Seong, W.K.
AU  - Kim, S.Y.
AU  - Jeong, H.
AU  - Kang, S.G.
AU  - Kim, B.K.
AU  - Kwon, S.K.
AU  - Lee, C.H.
AU  - Yu, D.S.
AU  - Park, M.S.
AU  - Cho, S.H.
AU  - Kim, J.F.
TI  - Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3749
EP  - 3750
VL  - 194
AB  - Enterohemorrhagic Escherichia coli causes severe food-borne disease in the guts of humans and
AB  - animals. Here, we report the high-quality draft genome sequence of
AB  - E. coli NCCP15658 isolated from a patient in the Republic of Korea. Its genome
AB  - size was determined to be 5.46 Mb, and its genomic features, including genes
AB  - encoding virulence factors, were analyzed.
ER  -

TY  - JOUR
AU  - Song, L.
AU  - Ren, L.
AU  - Li, X.
AU  - Yu, D.
AU  - Yu, Y.
AU  - Wang, X.
AU  - Liu, G.
TI  - Complete Genome Sequence of Marinobacter sp. BSs20148.
JO  - Genome Announcements
PY  - 2013
SP  - e00236
EP  - e00213
VL  - 1
AB  - Marinobacter sp. BSs20148 was isolated from marine sediment collected from the Arctic Ocean at
AB  - a water depth of 3,800 m. Here we report the complete genome
AB  - sequence of Marinobacter sp. BSs20148. This genomic information will facilitate
AB  - the study of the physiological metabolism, ecological roles, and evolution of the
AB  - Marinobacter species.
ER  -

TY  - JOUR
AU  - Song, L.
AU  - Yu, Y.
AU  - Feng, L.
AU  - He, J.
AU  - Wang, T.
AU  - Zhu, H.
AU  - Duan, Q.
TI  - Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976.
JO  - Genome Announcements
PY  - 2015
SP  - e01162
EP  - e01115
VL  - 3
AB  - Burkholderia pseudomallei is the etiological agent of the potentially fatal disease
AB  - melioidosis. Here, we report the draft genome sequence of a virulent water isolate obtained
AB  - from the Hainan Province of China in 1976, B. pseudomallei strain 350105.
ER  -

TY  - JOUR
AU  - Song, L.
AU  - Yu, Y.
AU  - Feng, L.
AU  - Wang, T.
AU  - He, J.
AU  - Zhu, H.
AU  - Duan, Q.
TI  - Draft Genome Sequence of Francisella tularensis Strain 410108 from Tibet, China.
JO  - Genome Announcements
PY  - 2015
SP  - e01489
EP  - e01415
VL  - 3
AB  - Francisella tularensis is the etiological agent of the potentially fatal disease  tularemia.
AB  - Here, we report the draft genome sequence of a virulent human isolate
AB  - from Tibet, China in 1962, F. tularensis strain 410108, an intermediate-genotype
AB  - strain of F. tularensis subsp. holarctica between biovar japonica and
AB  - non-japonica strains in the world.
ER  -

TY  - JOUR
AU  - Song, P.
AU  - Xu, X.
AU  - Jiang, L.
AU  - Zhang, R.
AU  - Wang, J.
AU  - Xu, Q.
AU  - Li, S.
TI  - Genome Sequence of Bacillus subtilis SPZ1, an Evolved Strain for Higher Uptake Rate of Tributyrin.
JO  - Genome Announcements
PY  - 2013
SP  - e00511
EP  - e00513
VL  - 1
AB  - The lipase-producing strain Bacillus subtilis SPZ1 is isolated from the medium by tributyrin
AB  - as the sole carbon source. Here, we present a 4.13-Mb assembly of its
AB  - genome sequence, which may provide various kinds of useful information related to
AB  - Bacillus spp., such as mechanisms and control of the substrate uptake and protein
AB  - secretion pathways.
ER  -

TY  - JOUR
AU  - Song, S.
AU  - Yuan, X.
AU  - Liu, S.
AU  - Zhang, N.
AU  - Wang, Y.
AU  - Ke, Y.
AU  - Xu, J.
AU  - Huang, L.
AU  - Chen, Z.
AU  - Li, Y.
TI  - Genome Sequence of Stenotrophomonas maltophilia S028, an Isolate Harboring the AmpR-L2 Resistance Module.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6696
EP  - 6696
VL  - 194
AB  - Multidrug-resistant Stenotrophomonas maltophilia has emerged as an important cause of
AB  - nosocomial infections, which is attributable mainly to the production of
AB  - diverse beta-lactamases by S. maltophilia. The L2 beta-lactamase mediated by the
AB  - AmpR-L2 module is the most represented lactamase. Here, we announce the genome
AB  - sequence of S028, an isolate harboring the AmpR-L2 module.
ER  -

TY  - JOUR
AU  - Song, T.
AU  - Kang, B.S.
AU  - Kim, Y.M.
TI  - XspI, a new Type II restriction endonuclease from a Xanthomonas species.
JO  - Mol. Cells
PY  - 1998
SP  - 370
EP  - 373
VL  - 8
AB  - A new Type II restriction endonuclease, XspI, was purified 11-fold in seven steps to
AB  - homogeneity from Xanthomonas sp. strain YK1 grown aerobically in Luria broth.  The final
AB  - specific activity of the purified enzyme was 3890 micrograms of lambda DNA digested per h per
AB  - mg of protein.  The molecular weight of the native enzyme was determined to be 54,000.  Sodium
AB  - dodecyl sulfate-gel electrophoresis revealed two identical subunits of molecular weight
AB  - 29,000.  The purified enzyme was most active at 37 C in the presence of 100 mM KCl and 5 mM
AB  - MgCl2 under pH range from 7.5 to 8.0.  The enzyme was stable at least for 1 h at 37 C, but was
AB  - inactivated after 20 min at 65 C.  XspI recognized the tetranucleotide sequence, 5'-CTAG-3',
AB  - and cleaved it between C and T, like its isoschizomers MaeI and BfaI.  The ability of the
AB  - source organism to grow aerobically, together with the heat inactivation of the enzyme,
AB  - confers practical advantages upon XspI over its known isoschizomers.
ER  -

TY  - JOUR
AU  - Song, X.H.
AU  - Chen, H.X.
AU  - Zhou, W.S.
AU  - Wang, J.B.
AU  - Liu, M.F.
AU  - Wang, M.S.
AU  - Cheng, A.C.
AU  - Jia, R.Y.
AU  - Chen, S.
AU  - Sun, K.F.
AU  - Yang, Q.
AU  - Wu, Y.
AU  - Chen, X.Y.
AU  - Zhu, D.K.
TI  - Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio  Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2016
SP  - e00769
EP  - e00716
VL  - 4
AB  - Mycobacterium avium is an important pathogenic bacterium in birds and has never,  to our
AB  - knowledge, reported to be isolated from domestic ducks. We present here
AB  - the complete genome sequence of a virulent strain of Mycobacterium avium,
AB  - isolated from domestic Pekin ducks for the first time, which was determined by
AB  - PacBio single-molecule real-time technology.
ER  -

TY  - JOUR
AU  - Song, X.H.
AU  - Zhou, W.S.
AU  - Wang, J.B.
AU  - Liu, M.F.
AU  - Wang, M.S.
AU  - Cheng, A.C.
AU  - Jia, R.Y.
AU  - Chen, S.
AU  - Sun, K.F.
AU  - Yang, Q.
AU  - Wu, Y.
AU  - Chen, X.Y.
AU  - Zhu, D.K.
TI  - Genome Sequence of Riemerella anatipestifer Strain RCAD0122, a Multidrug-Resistant Isolate from Ducks.
JO  - Genome Announcements
PY  - 2016
SP  - e00332
EP  - e00316
VL  - 4
AB  - Riemerella anatipestifer is an important pathogenic bacterium in waterfowl and other avian
AB  - species. We present here the genome sequence of R. anatipestifer
AB  - RCAD0122, a multidrug-resistant strain isolated from infected ducks. The isolate
AB  - contains at least nine types of antibiotic resistance-associated genes.
ER  -

TY  - JOUR
AU  - Song, Y.
AU  - Cho, B.K.
TI  - Draft Genome Sequence of Chemolithoautotrophic Acetogenic Butanol-Producing Eubacterium limosum ATCC 8486.
JO  - Genome Announcements
PY  - 2015
SP  - e01564
EP  - e01514
VL  - 3
AB  - Eubacterium limosum ATCC 8486 is an anaerobic chemolithoautotrophic acetogenic bacterium that
AB  - converts and transforms syngas and isoflavonoids to butanol and
AB  - phytoestrogens, respectively. Here, we report the draft genome sequence of the E.
AB  - limosum ATCC 8486 (4.37 Mb) strain and its annotation information, including
AB  - syngas fermentation and denitrification metabolic pathways.
ER  -

TY  - JOUR
AU  - Song, Y.
AU  - Hwang, S.
AU  - Cho, B.K.
TI  - Draft Genome Sequence of Clostridium aceticum DSM 1496, a Potential Butanol Producer through Syngas Fermentation.
JO  - Genome Announcements
PY  - 2015
SP  - e00258
EP  - e00215
VL  - 3
AB  - Clostridium aceticum DSM 1496 is a Gram-negative anaerobic chemolithoautotrophic  acetogenic
AB  - bacterium that is capable of producing commodity chemicals from syngas
AB  - fermentation. In this study, we report the draft genome sequence of the C.
AB  - aceticum DSM 1496 strain (4.16 Mb) to elucidate the syngas fermentation metabolic
AB  - pathway.
ER  -

TY  - JOUR
AU  - Song, Y.
AU  - Jeong, Y.
AU  - Shin, H.S.
AU  - Cho, B.K.
TI  - Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and  4-Methylphenol.
JO  - Genome Announcements
PY  - 2014
SP  - e00459
EP  - e00414
VL  - 2
AB  - Clostridium scatologenes ATCC 25775 is a strictly anaerobic and chemolithoautotrophic
AB  - acetogenic bacterium that converts syngas into multi-carbon
AB  - compounds such as acetate, indole, 3-methylindole, and 4-methylphenol. Here we
AB  - report the draft genome sequence of C. scatologenes ATCC 25775 (7.3 Mbp) to
AB  - elucidate its metabolic pathway for syngas fermentation.
ER  -

TY  - JOUR
AU  - Song, Y.-H.
AU  - Rueter, T.
AU  - Geiger, R.
TI  - DNA cleavage by AatI and StuI is sensitive to Escherichia coli dcm methylation.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 2718
EP  - 2718
VL  - 16
AB  - While attempting to subclone the StuI - EcoNI fragment of pRIF 309+ we found that the AGGCCT
AB  - site was not cleaved by StuI or its isoschizomer AatI. Upon examination of the DNA sequence it
AB  - became evident that this site overlapped an E. coli dcm methylation site CC(T/)AGG, ie.
AB  - AGGCCTGG, which when methylated could be resistant to cleavage. To test this proposition we
AB  - prepared pRIF 309+ in the dcm- E. coli strain GM 2929 kindly supplied by Dr. B. Bachmann. As
AB  - can be seen in Fig. 1 pRIF 309+ prepared from a dcm- host is cleaved by StuI. An identical
AB  - result was obtained with AatI.
ER  -

TY  - JOUR
AU  - Soni, D.K.
AU  - Singh, K.M.
AU  - Ghosh, A.
AU  - Chikara, S.K.
AU  - Joshi, C.G.
AU  - Dubey, S.K.
TI  - Whole-Genome Sequence of Listeria monocytogenes Strains from Clinical and Environmental Samples from Varanasi, India.
JO  - Genome Announcements
PY  - 2015
SP  - e01496
EP  - e01414
VL  - 3
AB  - We present here the whole-genome sequences of Listeria monocytogenes from Ganges  River water,
AB  - agricultural soil, and human clinical samples from Varanasi, India,
AB  - which will be used for a comparative analysis.
ER  -

TY  - JOUR
AU  - Soni, I.
AU  - Chakrapani, H.
AU  - Chopra, S.
TI  - Draft Genome Sequence of Methicillin-Sensitive Staphylococcus aureus ATCC 29213.
JO  - Genome Announcements
PY  - 2015
SP  - e01095
EP  - e01015
VL  - 3
AB  - Staphylococcus aureus subsp. aureus ATCC 29213 is one of the most commonly used strains in
AB  - drug discovery research and for quality control. We report the completed draft genome sequence
AB  - for the strain.
ER  -

TY  - JOUR
AU  - Sonnenschein, E.C.
AU  - Nielsen, K.F.
AU  - D'Alvise, P.
AU  - Porsby, C.H.
AU  - Melchiorsen, J.
AU  - Heilmann, J.
AU  - Kalatzis, P.G.
AU  - Lopez-Perez, M.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Middelboe, M.
AU  - Gram, L.
TI  - Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis.
JO  - ISME J.
PY  - 2017
SP  - 569
EP  - 583
VL  - 11
AB  - Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have
AB  - primarily been isolated from marine aquaculture and have probiotic
AB  - potential due to inhibition of fish pathogens. We hypothesized that TDA producers
AB  - with additional novel features are present in the oceanic environment. We
AB  - isolated 42 TDA-producing R. mobilis strains during a global marine research
AB  - cruise. While highly similar on the 16S ribosomal RNA gene level (99-100%
AB  - identity), the strains separated into four sub-clusters in a multilocus sequence
AB  - analysis. They were further differentiated to the strain level by average
AB  - nucleotide identity using pairwise genome comparison. The four sub-clusters could
AB  - not be associated with a specific environmental niche, however, correlated with
AB  - the pattern of sub-typing using co-isolated phages, the number of prophages in
AB  - the genomes and the distribution in ocean provinces. Major genomic differences
AB  - within the sub-clusters include prophages and toxin-antitoxin systems. In
AB  - general, the genome of R. mobilis revealed adaptation to a particle-associated
AB  - life style and querying TARA ocean data confirmed that R. mobilis is more
AB  - abundant in the particle-associated fraction than in the free-living fraction
AB  - occurring in 40% and 6% of the samples, respectively. Our data and the TARA data,
AB  - although lacking sufficient data from the polar regions, demonstrate that R.
AB  - mobilis is a globally distributed marine bacterial species found primarily in the
AB  - upper open oceans. It has preserved key phenotypic behaviors such as the
AB  - production of TDA, but contains diverse sub-clusters, which could provide new
AB  - capabilities for utilization in aquaculture.
ER  -

TY  - JOUR
AU  - Sonnenschein, E.C.
AU  - Phippen, C.B.W.
AU  - Nielsen, K.F.
AU  - Mateiu, R.V.
AU  - Melchiorsen, J.
AU  - Gram, L.
AU  - Overmann, J.
AU  - Freese, H.M.
TI  - Phaeobacter piscinae sp. nov., a novel species of the roseobacter group and potential aquaculture probiont.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2017
SP  - 4559
EP  - 4564
VL  - 67
AB  - Four heterotrophic, antimicrobial, motile, marine bacterial strains, 27-4T, 8-1, M6-4.2 and
AB  - S26, were isolated from aquaculture units in Spain, Denmark and Greece. All four strains
AB  - produced the antibiotic compound tropodithietic acid, which is a key molecule in their
AB  - antagonism against fish pathogenic bacteria. Cells of the strains were Gram-reaction-negative,
AB  - rod-shaped and formed star-shaped aggregates in liquid culture and brown-coloured colonies on
AB  - marine agar. The predominant cellular fatty acids were C18 : 1!7c, C16 : 0, C11 methyl C18 :
AB  - 1!7c and C16 : 0 2-OH, and the polar lipids comprised phosphatidylglycerol,
AB  - diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminolipid, a
AB  - phospholipid
AB  - and an unidentified lipid. The strains grew optimally at 3133 C. Growth was observed at a salt
AB  - concentration between 0.5 and 56%NaCl with an optimum at 23 %. The pH range for growth of the
AB  - strains was from pH 6 to 88.5 with an optimum at pH 7. Based on 16S rRNA gene sequence
AB  - analysis, the strains are affiliated with the genus Phaeobacter. The genome sequences of the
AB  - strains have a DNA G+C content of 60.1% and share an average nucleotide identity (ANI) of more
AB  - than 95%.  The four strains are distinct from the type strains of the closely related species
AB  - Phaeobacter gallaeciensis and Phaeobacter
AB  - inhibens based on an ANI of 90.591.7 and 89.690.4 %, respectively, and an in silico DNADNA
AB  - hybridization relatedness of 43.946.9 and 39.841.9 %, respectively. On the basis of
AB  - phylogenetic analyses as well as phenotypic and chemotaxonomic properties, the isolates are
AB  - considered to represent a novel species, for which the name Phaeobacter piscinae sp. nov. is
AB  - proposed. The type strain is 27-4T (=DSM 103509T=LMG 29708T).
ER  -

TY  - JOUR
AU  - Soobramoney, L.A.
AU  - Featherston, J.
AU  - Gray, V.M.
TI  - Draft Whole-Genome Sequence of Xenorhabdus sp. Strain GDc328, Isolated from the Indigenous South African Nematode Host Steinernema khoisanae.
JO  - Genome Announcements
PY  - 2015
SP  - e01239
EP  - e01215
VL  - 3
AB  - Here, we describe the draft genome sequence of Xenorhabdus sp. GDc328, an endosymbiont of the
AB  - native South African entomopathogenic nematode host, Steinernema khoisanae. The total genome
AB  - size of the bacteria is 4.09 Mb. The genome comprises a total of 3,608 genes with a molecular
AB  - G+C content of 44.64%.
ER  -

TY  - JOUR
AU  - Soper, B.W.
TI  - Host restriction-modification as related to gene transfer in the nitrogen-fixing cyanobacterium, Cyanothece sp.
JO  - Ph.D. Thesis, State University of New York, Binghamton, USA
PY  - 1995
SP  - 1
EP  - 132
AB  - Cyanothece sp. strain BH68K (ATCC 51142) is a marine unicellular
AB  - cyanobacterium capable of oxygenic photosynthesis and aerobic nitrogen fixation in a
AB  - single cell without undergoing morphological differentiation.  In order to develop a gene
AB  - transfer system for this organism, shuttle vectors are required that are capable of
AB  - replication
AB  - in E. coli and Cyanothece sp.  Therefore, the plasmids of several clonal isolates have been
AB  - characterized.  Each Cyanothece isolate contains three or four plasmids ranging in size from
AB  - 4.8 kb to 40 kb.  A small 4.8 kb plasmid (pSE480), from the clonal isolate Cyanothece sp.
AB  - strain BH68F, has been subcloned and restriction mapped.  Ten restriction sites have been
AB  - mapped, five of which are unique and are suitable for further subcloning.  Shuttle vectors
AB  - derived from pSE480 were used in an attempt to transfer genes by natural competency and
AB  - electroporation.  Lack of transformation prompted the analysis of Cyanothece sp. strain
AB  - BH68K for restriction barriers.  Cell wash supernatants revealed a cell wall-associated
AB  - nuclease that exhibited non-site-specific degradation of covalently- closed circular and
AB  - linear double-stranded DNA molecules, including Cyanothece sp. strain BH68K
AB  - chromosomal DNA.  The nuclease also degraded Cyanothece sp. total RNA and phage
AB  - M13mp18 ssDNA.  Cyanothece sp. strain BH68K cell extracts contain three type II
AB  - restriction endonucleases, designated Csp68KI, Csp68KII, and Csp68KIII.  Csp68KI is
AB  - an isoschizomer of AvaII and recognizes the nucleotide sequence 5'-G/GWCC-3' (W=A or
AB  - T).  Cleavage occurred between the guanosine nucleotides producing 3-bp 5' overhang
AB  - ends. Csp68KII is an isoschizomer of AsuII and restricts DNA at the recognition sequence
AB  - 5'-TT/CGAA-3'.  Cleavage occurred between thymine and cytosine producing 2-bp 5'
AB  - overhang ends.  The third restriction endonuclease, Csp68KIII, is an isoschizomer of
AB  - AvaIII and restricts DNA at the recognition sequence 5'- ATGCA/T-3'.  Cleavage occurred
AB  - between the 3' adenosine and thymine nucleotides producing 4- bp 3' overhang ends.  The
AB  - methylase genes M.Csp68KI, M.Csp68KIV and M.Csp68KV have been cloned from
AB  - plasmid libraries of Cyanothece sp. strain BH68K.  The last two methylases inhibit
AB  - restriction by the four-base, site-specific enzymes MspI and HaeIII, respectively. Cloned
AB  - methylase genes from host restriction-modification systems can be used to construct helper
AB  - plasmids that methylate shuttle vectors prior to gene transfer.
ER  -

TY  - JOUR
AU  - Soper, B.W.
TI  - Host restriction-modification as related to gene transfer in the nitrogen-fixing cyanobacterium, cyanothece sp.
JO  - Diss. Abstr.
PY  - 1996
SP  - 3585B
EP  - 3585B
VL  - 56
AB  - Cyanothece sp. strain BH68K (ATCC 51142) is a marine unicellular cyanobacterium capable of
AB  - oxygenic photosynthesis and aerobic nitrogen fixation in a single cell without undergoing
AB  - morphological differentiation.  In order to develop a gene transfer system for this organism,
AB  - shuttle vectors are required that are capable of replication in E. coli and Cyanothece sp.
AB  - Therefore, the plasmids of several clonal isolates have been characterized.  Each Cyanothece
AB  - isolate contains three or four plasmids ranging in size from 4.8 kb to 40 kb.  A small 4.8 kb
AB  - plasmid (pSE480), from the clonal isolate Cyanothece sp. strain BH68F, has been subcloned and
AB  - restriction mapped.  Ten restriction sites have been mapped, five of which are unique and are
AB  - suitable for further subcloning.  Shuttle vectors derived from pSE480 were used in attempt to
AB  - transfer genes by natural competency and electroporation.  Lack of transformation prompted the
AB  - analysis of Cyanothece sp. strain BH68K for restriction barriers.  Cell wash supernatants
AB  - revealed a cell wall-associated nuclease that exhibited non-site-specific degradation of
AB  - covalently-closed circular and linear double-stranded DNA molecules, including Cyanothece sp.
AB  - strain BH68K cell extracts contain three type II restriction endonucleases, designated
AB  - Csp68KI, Csp68KII, and Csp68KIII.  Csp68KI is an isoschizomer of AvaII and recognizes the
AB  - nucleotide sequence 5'-G/GWCC-3' (W=A or T).  Cleavage occurred between the guanosine
AB  - nucleotides producing 3-bp 5' overhang ends.  Csp68KII is an isoschizomer of AsuII and
AB  - restricts DNA at the recognition sequence 5'-TT/CGAA-3'.  Cleavage occurred between thymine
AB  - and cytosine producing 2-bp 5' overhang ends.  The third restriction endonuclease, Csp68KIII,
AB  - is an isoschizomer of AvaIII and restricts DNA at the recognition sequence 5'-ATGCA/T-3'.
AB  - Cleavage occurred between the 3' adenosine and thymine nucleotides producing 4-bp 3'
AB  - overhang ends.  The methylase genes M.Csp68KI, M.Csp68KIV and M.Csp68KV have been cloned from
AB  - plasmid libraries of Cyanothece sp. strain BH68K.  The last two methylases inhibit restriction
AB  - by the four-base, site-specific enzymes MspI and HaeIII, respectively.  Cloned methylase genes
AB  - from host restriction-modification systems can be used to construct helper plasmids that
AB  - methylate shuttle vectors prior to gene transfer.
ER  -

TY  - JOUR
AU  - Soper, B.W.
AU  - Hollister, W.R.
AU  - Reddy, K.J.
TI  - Restriction-modification systems in the marine, aerobic, nitrogen-fixing unicellular cyanobacterium Cyanothece sp. ATCC 51142.
JO  - J. Mar. Biotechnol.
PY  - 1998
SP  - 183
EP  - 185
VL  - 6
AB  - Cyanothece sp. ATCC 51142 possesses six host restriction-modification systems (HRMS), and
AB  - these HRMS were designated as Csp68KI to Csp68KVI.  So far, four restriction enzymes have been
AB  - characterized biochemically, and the other two were deduced based on the cloning of
AB  - corresponding DNA methyltransferase genes M. Csp68KIV and M.Csp68KV from the Cyanothece
AB  - genome.  Csp68KI, Csp68KII, Csp68KIII, Csp68KIV, Csp68KV, and Csp68KVI are isoschizomers of
AB  - AvaII, AsuII, AvaIII, MspI, HaeIII, and FnuDII, respectively.  The cleavage specificities for
AB  - Csp68KI, Csp68KII, Csp68KIII, and Csp68KVI were characterized.  The Cyanothece restriction
AB  - enzymes showed different temperature and salt requirements for their optimal activity.  For
AB  - example, the restriction enzyme Csp68KII functions optimally at 50 C and Csp68KIII requires
AB  - higher salt for its activity.
ER  -

TY  - JOUR
AU  - Soper, B.W.
AU  - Hollister, W.R.
AU  - Reddy, K.J.
TI  - Characterization of additional host restriction-modification systems in the unicellular cyanobacterium Cyanothece sp.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1996
SP  - 24
EP  - 30
VL  - 223
AB  - In order to develop a gene transfer system for the unicellular diazotrophic cyanobacterium
AB  - Cyanothece sp. strain BH68K, this organism has been further investigated for the presence of
AB  - additional host restriction-modification enzymes other than Csp68KI, previously reported for
AB  - Cyanothece sp.  Analysis of cell extracts by phosphocellulose and Mono Q fast protein liquid
AB  - chromatography (FPLC) has led to the identification of three new restriction endonucleases.
AB  - These enzymes have been designated Csp68KII, Csp68KIII, and Csp68KVI.  Csp68KII is an
AB  - isoschizomer of AsuII and restricts DNA at the recognition sequence 5'-TT/CGAA-3'.  Cleavage
AB  - occurred between thymine and cytosine producing 2 bp 5' overhang ends.  The third restriction
AB  - enodnuclease, Csp68KII, is an isoschizomer of AvaIII and restricts DNA at the recognition
AB  - sequence 5'-ATGCA/T-3'.  Cleavage occurred between the 3' adenosine and thymine nucleotides
AB  - producing 4 bp 3' overhang ends.  The fourth enzyme identified, Csp68KVI, recognizes CGCG and
AB  - cleaves this sequence between the internal guanine and cytosine nucleotides producing blunt
AB  - ends.
ER  -

TY  - JOUR
AU  - Soper, B.W.
AU  - Reddy, K.J.
TI  - Identification of a nuclease and host restriction-modification in the unicellular, aerobic nitrogen-fixing cyanobacterium Cyanothece sp.
JO  - J. Bacteriol.
PY  - 1994
SP  - 5565
EP  - 5570
VL  - 176
AB  - In the process of developing a gene transfer system for the marine, unicellular,
AB  - nitrogen-fixing cyanobacterium Cyanothece sp. strain BH68K, two major restriction barriers
AB  - have been identified. A cell wall-associated nuclease exhibited non-site-specific degradation
AB  - of covalently closed circular and linear double-stranded DNA molecules, including Cyanothece
AB  - sp. strain BH68K chromosomal DNA. The nuclease is easily released from intact cells by using
AB  - water or buffer containing Triton X-100. Nuclease activity was undetectable in cell extracts
AB  - prepared from water-washed cells. Comparison of the restriction endonuclease susceptibility of
AB  - Cyanothece sp. strain BH68K DNA to that of Anabaena sp. strain PCC 7120 revealed that these
AB  - organisms have a nearly identical pattern of restriction and therefore may contain similar
AB  - systems for DNA methylation. Restriction by DpnI, MboI, and Sau3AI indicated the presence of
AB  - adenine methylation. Cyanothece sp. strain BH68KI was easily detected in cell extracts without
AB  - extensive purification. Csp68KI is an isoschizomer of AvaII and recognizes the nucleotide
AB  - sequence 5'-GG(A/T)CC-3'. Cleavage occurs between the guanosine nucleotides producing 3-bp
AB  - 5' overhang ends.
ER  -

TY  - JOUR
AU  - Soriano, N.
AU  - Vincent, P.
AU  - Auger, G.
AU  - Cariou, M.E.
AU  - Moullec, S.
AU  - Lagente, V.
AU  - Ygout, J.F.
AU  - Kayal, S.
AU  - Faili, A.
TI  - Full-Length Genome Sequence of Type M/emm83 Group A Streptococcus pyogenes Strain STAB1101, Isolated from Clustered Cases in Brittany.
JO  - Genome Announcements
PY  - 2015
SP  - e01459
EP  - e01414
VL  - 3
AB  - Here, we announce the complete annotated genome sequence of a Streptococcus pyogenes M/emm83
AB  - strain, STAB1101, isolated from clustered cases in homeless
AB  - persons in Brittany (France). The genome is composed of 1,709,790 bp, with a G+C
AB  - content of 38.4% and 1,550 identified coding sequences (CDS), and it harbors a
AB  - Tn916-like transposon.
ER  -

TY  - JOUR
AU  - Soriano, N.
AU  - Vincent, P.
AU  - Moullec, S.
AU  - Meygret, A.
AU  - Lagente, V.
AU  - Kayal, S.
AU  - Faili, A.
TI  - Closed Genome Sequence of Noninvasive Streptococcus pyogenes M/emm3 Strain STAB902.
JO  - Genome Announcements
PY  - 2014
SP  - e00792
EP  - e00714
VL  - 2
AB  - We report a closed genome sequence of group A Streptococcus genotype emm3 (GAS M/emm3) strain
AB  - STAB902, isolated from a superficial pyodermatitis. The genome is
AB  - composed of 1,892,124 bp, 6 integrated prophages, and has 1,858 identified coding
AB  - sequences (CDSs). It has been fitted with the two available invasive GAS M/emm3
AB  - strains.
ER  -

TY  - JOUR
AU  - Soriano, N.
AU  - Vincent, P.
AU  - Piau, C.
AU  - Moullec, S.
AU  - Gautier, P.
AU  - Lagente, V.
AU  - Faili, A.
AU  - Kayal, S.
TI  - Complete Genome Sequence of Streptococcus pyogenes M/emm44 Strain STAB901, Isolated in a Clonal Outbreak in French Brittany.
JO  - Genome Announcements
PY  - 2014
SP  - e01174
EP  - e01114
VL  - 2
AB  - We report the complete genome sequence of an invasive isolate of Streptococcus pyogenes
AB  - M/emm44, belonging to a clonal outbreak that occurred in French
AB  - Brittany. The genome is composed of 1,795,608 bp, with a GC content of 38.5%, has
AB  - 1,358 identified coding sequences (CDSs), and harbors a novel Tn916-like
AB  - transposon (Tn6253).
ER  -

TY  - JOUR
AU  - Sorokin, D.Y.
AU  - Kublanov, I.V.
AU  - Gavrilov, S.N.
AU  - Rojo, D.
AU  - Roman, P.
AU  - Golyshin, P.N.
AU  - Slepak, V.Z.
AU  - Smedile, F.
AU  - Ferrer, M.
AU  - Messina, E.
AU  - La Cono, V.
AU  - Yakimov, M.M.
TI  - Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon.
JO  - ISME J.
PY  - 2016
SP  - 240
EP  - 252
VL  - 10
AB  - Archaea domain is comprised of many versatile taxa that often colonize extreme habitats. Here,
AB  - we report the discovery of strictly anaerobic extremely halophilic euryarchaeon, capable of
AB  - obtaining energy by dissimilatory reduction of elemental sulfur using acetate as the only
AB  - electron donor and forming sulfide and CO2 as the only products. This type of respiration has
AB  - never been observed in hypersaline anoxic habitats and is the first example of such metabolic
AB  - capability in the entire Archaea domain. We isolated and cultivated these unusual organisms,
AB  - selecting one representative strain, HSR2, for detailed characterization. Our studies
AB  - including physiological tests, genome sequencing, gene expression, metabolomics and
AB  - [14C]-bicarbonate assimilation assays revealed that HSR2 oxidized acetate completely via the
AB  - tricarboxylic acid cycle. Anabolic assimilation of acetate occurred via activated glyoxylate
AB  - bypass and anaplerotic carboxylation. HSR2 possessed sulfurtransferase and an array of
AB  - membrane-bound polysulfide reductase genes, all of which were expressed during the growth. Our
AB  - findings suggest the biogeochemical contribution of haloarchaea in hypersaline anoxic
AB  - environments must be reconsidered.
ER  -

TY  - JOUR
AU  - Sorokin, D.Y.
AU  - Lucker, S.
AU  - Vejmelkova, D.
AU  - Kostrikina, N.A.
AU  - Kleerebezem, R.
AU  - Rijpstra, W.I.
AU  - Damste, J.S.
AU  - Le Paslier, D.
AU  - Muyzer, G.
AU  - Wagner, M.
AU  - van Loosdrecht, M.C.
AU  - Daims, H.
TI  - Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi.
JO  - ISME J.
PY  - 2012
SP  - 2245
EP  - 2256
VL  - 6
AB  - Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a
AB  - major process of the biogeochemical nitrogen cycle, but the recognized diversity
AB  - of this guild is surprisingly low and only two bacterial phyla contain known NOB.
AB  - Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that
AB  - belongs to the widespread phylum Chloroflexi not previously known to contain any
AB  - nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated
AB  - from a nitrifying reactor. Its tolerance to a broad temperature range (25-63
AB  - degrees C) and low affinity for nitrite (K(s)=1 mM), a complex layered cell
AB  - envelope that stains Gram positive, and uncommon membrane lipids composed of
AB  - 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N.
AB  - hollandicus grows on nitrite and CO(2), and is able to use formate as a source of
AB  - energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the
AB  - presence of all genes required for CO(2) fixation by the Calvin cycle and a
AB  - nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial
AB  - nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of
AB  - the nxr loci unexpectedly indicated functionally important lateral gene transfer
AB  - events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting
AB  - that horizontal transfer of the NXR module was a major driver for the spread of
AB  - the capability to gain energy from nitrite oxidation during bacterial evolution.
AB  - The surprising discovery of N. hollandicus significantly extends the known
AB  - diversity of nitrifying organisms and likely will have implications for future
AB  - research on nitrification in natural and engineered ecosystems.
ER  -

TY  - JOUR
AU  - Sorokin, D.Y.
AU  - Messina, E.
AU  - Smedile, F.
AU  - Roman, P.
AU  - Damste, J.S.S.
AU  - Ciordia, S.
AU  - Mena, M.C.
AU  - Ferrer, M.
AU  - Golyshin, P.N.
AU  - Kublanov, I.V.
AU  - Samarov, N.I.
AU  - Toshchakov, S.V.
AU  - La Cono, V.
AU  - Yakimov, M.M.
TI  - Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats.
JO  - ISME J.
PY  - 2017
SP  - 1245
EP  - 1260
VL  - 11
AB  - Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose
AB  - metabolic and ecological roles remain to be elucidated. Until recently, it was
AB  - believed that energy generation via dissimilatory reduction of sulfur compounds
AB  - is not functional at salt saturation conditions. Recent discovery of the strictly
AB  - anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption
AB  - and the traditional view on haloarchaea as aerobic heterotrophs. Here we report
AB  - on isolation and characterization of a novel group of strictly anaerobic
AB  - lithoheterotrophic haloarchaea, which we propose to classify as a new genus
AB  - Halodesulfurarchaeum. Members of this previously unknown physiological group are
AB  - capable of utilising formate or hydrogen as electron donors and elemental sulfur,
AB  - thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide
AB  - proteomic analysis we have detected the full set of enzymes required for
AB  - anaerobic respiration and analysed their substrate-specific expression. Such
AB  - advanced metabolic plasticity and type of respiration, never seen before in
AB  - haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline
AB  - inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The
AB  - discovery of this novel functional group of sulfur-respiring haloarchaea
AB  - strengthens the evidence of their possible role in biogeochemical sulfur cycling
AB  - linked to the terminal anaerobic carbon mineralisation in so far overlooked
AB  - hypersaline anoxic habitats.
ER  -

TY  - JOUR
AU  - Sorokin, V.
AU  - Severinov, K.
AU  - Gelfand, M.S.
TI  - Large-Scale Identification and Analysis of C-Proteins<BOOK> Computational Biology of Transcription Factor Binding.
JO  - Methods Mol. Biol.
PY  - 2010
SP  - 269
EP  - 282
VL  - 674
AB  - The restriction-modification system is a toxin antitoxin mechanism of bacterial cells to
AB  - resist phage attacks. High efficiency comes at a
AB  - price of high maintenance costs: (1) a host cell dies whenever it loses
AB  - restriction-modification genes and (2) whenever a plasmid with
AB  - restriction-modification genes enters a naive cell, modification enzyme
AB  - (methylase) has to be expressed prior to the synthesis of the
AB  - restriction enzyme (restrictase) or the cell dies. These phenomena
AB  - imply a sophisticated regulatory mechanism. During the evolution
AB  - several such mechanisms were developed, of which one relies on a
AB  - special C(control)protein, a short autoregulatory protein containing an
AB  - HTH-domain. Given the extreme diversity among restriction-modification
AB  - systems, one could expect that C-proteins had evolved into several
AB  - groups that might differ in autoregulatory binding sites architecture.
AB  - However, only a few C-proteins (and the corresponding binding sites)
AB  - were known before this study. Bioinformatics studies applied to
AB  - C-proteins and their binding sites were limited to groups of well-known
AB  - C-proteins and lacked systematic analysis. In this work, the authors
AB  - use bioinformatics techniques to discover 201 C-protein genes with
AB  - predicted autoregulatory binding sites. The systematic analysis of the
AB  - predicted sites allowed for the discovery of 10 structural classes of
AB  - binding sites.
ER  -

TY  - JOUR
AU  - Sorokin, V.
AU  - Severinov, K.
AU  - Gelfand, M.S.
TI  - Systematic prediction of control proteins and their DNA binding sites.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 441
EP  - 451
VL  - 37
AB  - We present here the results of a systematic bioinformatics analysis of control (C) proteins, a
AB  - class of DNA-binding regulators that control
AB  - time-delayed transcription of their own genes as well as restriction
AB  - endonuclease genes in many type II restriction-modification systems.
AB  - More than 290 C protein homologs were identified and DNA-binding sites
AB  - for 70 of new and previously known C proteins were predicted by a
AB  - combination of phylogenetic footprinting and motif searches in DNA
AB  - upstream of C protein genes. Additional analysis revealed that a large
AB  - proportion of C protein genes are translated from leaderless RNA, which
AB  - may contribute to time-delayed nature of genetic switches operated by
AB  - these proteins. Analysis of genetic contexts of newly identified C
AB  - protein genes revealed that they are not exclusively associated with
AB  - restriction-modification genes; numerous instances of associations with
AB  - genes originating from mobile genetic elements were observed. These
AB  - instances might be vestiges of ancient horizontal transfers and
AB  - indicate that during evolution ancestral restriction-modification
AB  - system genes were the sites of mobile elements insertions.
ER  -

TY  - JOUR
AU  - Sorokulova, I.B.
AU  - Kramarov, V.M.
AU  - Reznik, S.R.
AU  - Smirnov, V.V.
TI  - Restriction endonucleases from the genus Bacillus.
JO  - Mikrobiol. Zh.
PY  - 1990
SP  - 8
EP  - 11
VL  - 52
AB  - Production regularities of site-specific endonucleases by aerobic spore-forming bacteria,
AB  - isolated from different ecological sources, have been studied. It is shown that more than 1/3
AB  - of all the cultures studied produce site-specific endonucleases. A dependence of the frequency
AB  - of occurrence of bacterial producers on the ecological niche of their separation has been
AB  - noticed. The data on production of species-specific restrictases have been obtained which can
AB  - serve as additional characteristics for the differentiation of close species of Bacilli.
ER  -

TY  - JOUR
AU  - Sorsa, L.J.
AU  - Dufke, S.
AU  - Schubert, S.
TI  - Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization.
JO  - FEMS Microbiol. Lett.
PY  - 2004
SP  - 203
EP  - 208
VL  - 230
AB  - To identify novel virulence-associated genes in uropathogenic Escherichia coli (UPEC) strains,
AB  - a suppression subtractive hybridization strategy was applied to genomic DNA of four clinical
AB  - UPEC isolates from patients suffering from cystitis or pyelonephritis. The genomic DNA of four
AB  - isolates (tester strains) was subtracted from the DNA of two different driver strains, the
AB  - well characterized UPEC strain CFT073 and the non-pathogenic E. coli K-12 strain MG1655. We
AB  - determined the sequence of 172 tester strain-specific DNA fragments, 86 of which revealed only
AB  - low or no homology to nucleotide sequences of public databases. We further determined the
AB  - virulence association of the 86 novel DNA fragments using each DNA fragment as a probe in
AB  - Southern hybridizations of a reference strain collection consisting of 60 extraintestinal
AB  - pathogenic E. coli isolates, and 40 non-virulent E. coli strains from stool samples. From
AB  - this, 19 novel DNA fragments were demonstrated to be significantly associated with virulent
AB  - strains and thus may represent new virulence traits. Our results support the idea of a
AB  - considerable genetic variability among UPEC strains and suggest that novel genomic
AB  - determinants might contribute to virulence of UPEC.
ER  -

TY  - JOUR
AU  - Sosio, M.
AU  - Gallo, G.
AU  - Pozzi, R.
AU  - Serina, S.
AU  - Monciardini, P.
AU  - Bera, A.
AU  - Stegmann, E.
AU  - Weber, T.
TI  - Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107.
JO  - Genome Announcements
PY  - 2014
SP  - e01198
EP  - e01113
VL  - 2
AB  - We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate
AB  - that produces NAI-107, a new lantibiotic with the potential to treat
AB  - life-threatening infections caused by multidrug-resistant Gram-positive
AB  - pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of
AB  - 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.
ER  -

TY  - JOUR
AU  - Soslau, G.
AU  - Parker, J.
AU  - Nelson, J.W.
TI  - Methylation and restriction endonuclease cleavage of linear Z-DNA in the presence of hexamminecobalt (III) ions.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 7237
EP  - 7252
VL  - 14
AB  - These studies employed the synthetic linear DNA, poly dGdC, in the B and cobalt
AB  - hexammine chloride (Co)-induced Z form to determine the effect of conformation
AB  - on protein-DNA interactions.  The rate of the reaction of the restriction
AB  - endonucleases, HhaI and CfoI, are reduced with Z DNA as compared to B DNA.  The
AB  - ability of both restriction endonucleases to react with an aggregate form of Z
AB  - DNA (Z* DNA) is found to depend upon how the Z* DNA is formed.  When Z* DNA is
AB  - induced by low concentrations of Co (50 microM), the endonucleases remain
AB  - active.  In the presence of 100 microM Co, which causes increased aggregation,
AB  - the endonucleases are inactive.  The HhaI DNA methyltransferase reacts at equal
AB  - rates with the B, Z and low cobalt Z* form.  these results are significantly
AB  - different than those observed with Z form dGdC tracts inserted into circular
AB  - DNA molecules.
ER  -

TY  - JOUR
AU  - Soslau, G.
AU  - Pirollo, K.
TI  - Selective inhibition of restriction endonuclease cleavage by DNA intercalators.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1983
SP  - 484
EP  - 491
VL  - 115
AB  - The preferred dye binding sites and the microenvironment of known nucleotide sequences within
AB  - mitochondrial and plasmid pBR322 DNA was probed in a gross fashion with restriction
AB  - endonucleases.  The intercalating dyes, ethidium bromide and propidium iodide, do not inhibit
AB  - a given restriction endonuclease equally at all of the restriction sites within a DNA
AB  - molecule.  The selective inhibition may be explained, in part, by the potential B to Z
AB  - conformation transition of DNA flanking the restriction site and by preferred dye binding
AB  - sites.  Propidium iodide was found to be a more potent inhibitor than ethidium bromide and the
AB  - inhibition is independent of the type of cut made by the enzyme.
ER  -

TY  - JOUR
AU  - Sosnovtsev, S.V.
AU  - Dedkov, V.S.
AU  - Rechkunova, N.I.
AU  - Zernov, I.P.
AU  - Degtyarev, S.K.
TI  - Determination of substrate specificity of restriction endonuclease Mlu113I.
JO  - Sib. Biol. J.
PY  - 1991
SP  - 66
EP  - 67
VL  - 0
AB  - The recognition sequence and cleavage point of restriction endonuclease Mlu113I have been
AB  - determined as 5'GG/CGCC.
ER  -

TY  - JOUR
AU  - Sotnikova, E.A.
AU  - Shitikov, E.A.
AU  - Malakhova, M.V.
AU  - Kostryukova, E.S.
AU  - Ilina, E.N.
AU  - Atrasheuskaya, A.V.
AU  - Ignatyev, G.M.
AU  - Vinokurova, N.V.
AU  - Gorbachyov, V.Y.
TI  - Complete Genome Sequence of Mycobacterium bovis Strain BCG-1 (Russia).
JO  - Genome Announcements
PY  - 2016
SP  - e00182
EP  - e00116
VL  - 4
AB  - Mycobacterium bovisBCG (Bacille Calmette-Guerin) is a vaccine strain used for protection
AB  - against tuberculosis. Here, we announce the complete genome sequence
AB  - ofM. bovisstrain BCG-1 (Russia). Extensive use of this strain necessitates the
AB  - study of its genome stability by comparative analysis.
ER  -

TY  - JOUR
AU  - Soule, M.
AU  - Kuhn, E.
AU  - Loge, F.
AU  - Gay, J.
AU  - Call, D.R.
TI  - Using DNA microarrays to identify library-independent markers for bacterial source tracking.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 1843
EP  - 1851
VL  - 72
AB  - Bacterial source tracking is used to apportion fecal pollution among
AB  - putative sources. Within this context, library-independent markers are
AB  - genetic or phenotypic traits that can be used to identify the host origin
AB  - without a need for library-dependent classification functions. The
AB  - objective of this project was to use mixed-genome Enterococcus microarrays
AB  - to identify library-independent markers. Separate shotgun libraries were
AB  - prepared for five host groups (cow, dog, elk/deer, human, and waterfowl),
AB  - using genomic DNAs (gDNAs) from ca. 50 Enterococcus isolates for each
AB  - library. Microarrays were constructed (864 probes per library), and 385
AB  - comparative genomic hybridizations were used to identify putative markers.
AB  - PCR assays were used to screen 95 markers against gDNAs from isolates from
AB  - known sources collected throughout the United States. This validation
AB  - process narrowed the selection to 15 markers, with 7 having no recognized
AB  - homologues and the remaining markers being related to genes involved in
AB  - metabolic pathways and DNA replication. In most cases, each marker was
AB  - exclusive to one of four Enterococcus species (Enterococcus casseliflavus,
AB  - E. faecalis, E. hirae, or E. mundtii). Eight markers were highly specific
AB  - to either cattle, humans, or elk/deer, while the remaining seven markers
AB  - were positive for various combinations of hosts other than humans. Based
AB  - on microarray hybridization data, the prevalence of host-specific markers
AB  - ranged from 2% to 45% of isolates collected from their respective hosts. A
AB  - 20-fold difference in prevalence could present challenges for the
AB  - interpretation of library-independent markers.
ER  -

TY  - JOUR
AU  - Soundararajan, M.
AU  - Chang, Z.
AU  - Morgan, R.D.
AU  - Heslop, P.
AU  - Connolly, B.A.
TI  - DNA Binding and Recognition by the IIs Restriction Endonuclease MboII.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 887
EP  - 895
VL  - 277
AB  - The type IIs restriction endonuclease MboII recognizes nonsymmetrical GAAGA sites, cutting 8
AB  - (top strand) and 7 (bottom strand) bases to the right. Gel retardation showed that MboII bound
AB  - specifically to GAAGA sequences, producing two distinct complexes each containing one MboII
AB  - and one DNA molecule. Interference analysis indicated that the initial species formed, named
AB  - complex 1, comprised an interaction between the enzyme and the GAAGA target. Complex 2
AB  - involved interaction of the protein with both the GAAGA and the cutting sites. Only in the
AB  - presence of divalent metal ions such as Ca(2+) is the conversion of complex 1 to 2 rapid.
AB  - Additionally, a very retarded complex was seen with Ca(2+), possibly a (MboII)(2)-(DNA)(2)
AB  - complex. Plasmids containing a single GAAGA site were hydrolyzed slowly by MboII. Plasmids
AB  - containing two sites were cut far more rapidly, suggesting that the enzyme requires two
AB  - recognition sites in the same DNA molecule for efficient hydrolysis. MboII appears to have a
AB  - mechanism similar to the best characterized type IIs enzyme, FokI. Both enzymes initially bind
AB  - DNA as monomers, followed by dimerization to give an (enzyme)(2)-(DNA)(2) complex.
AB  - Dimerization is efficient only when the two target sites are located in the same DNA molecule
AB  - and requires divalent metal ions.
ER  -

TY  - JOUR
AU  - Sousa, T.J.
AU  - Mariano, D.
AU  - Parise, D.
AU  - Parise, M.
AU  - Viana, M.V.
AU  - Guimaraes, L.C.
AU  - Benevides, L.J.
AU  - Rocha, F.
AU  - Bagano, P.
AU  - Ramos, R.
AU  - Silva, A.
AU  - Figueiredo, H.
AU  - Almeida, S.
AU  - Azevedo, V.
TI  - Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 12C.
JO  - Genome Announcements
PY  - 2015
SP  - e00759
EP  - e00715
VL  - 3
AB  - We present here the complete genome sequence of Corynebacterium pseudotuberculosis strain 12C,
AB  - isolated from a sheep abscess in the Brazil. The
AB  - sequencing was performed with the Ion Torrent Personal Genome Machine (PGM)
AB  - system, a fragment library, and a coverage of ~48-fold. The genome presented is a
AB  - circular chromosome with 2,337,451 bp in length, 2,119 coding sequences, 12
AB  - rRNAs, 49 tRNAs, and a G+C content of 52.83%.
ER  -

TY  - JOUR
AU  - Sowajassatakul, A.
AU  - Coker, O.O.
AU  - Prammananan, T.
AU  - Chaiprasert, A.
AU  - Phunpruch, S.
TI  - Draft Genome Sequence of Amikacin- and Kanamycin-Resistant Mycobacterium tuberculosis MT433 without rrs and eis Mutations.
JO  - Genome Announcements
PY  - 2015
SP  - e01363
EP  - e01315
VL  - 3
AB  - We announce the draft genome sequence of amikacin- and kanamycin-resistant Mycobacterium
AB  - tuberculosis MT433, which has been previously described as the
AB  - strain carrying an unknown resistance mechanism.
ER  -

TY  - JOUR
AU  - Sowers, K.R.
TI  - Restriction-modification systems of methanogenic Archaea.
JO  - Archaea: Methanogens: A laboratory manual.
PY  - 1995
SP  - 505
EP  - 506
VL  - 0
AB  - Several type II restriction endonucleases have been isolated from methanogenic Archaea.  MaeI
AB  - is the predominant restriction endonuclease isolated from Methanococcus aeolicus; MaeII and
AB  - MaeIII appear in lower concentrations.  MaeI and MaeII recognize unique palindromic
AB  - tetranucleotide sequences, and MaeIII recognizes a unique palindromic pentanucleotide
AB  - sequence.  All three endonucleases produce 5' protruding ends.  MvnI from Methanococcus
AB  - vanielii recognizes a tetranucleotide sequence and is an isoschizomer of the
AB  - blunt-end-generating endonucleases ThaI and FnuDII.  All four methanogen endonucleases are
AB  - available commercially.  Four endonuclease-methyltransferase systems have been identified.
AB  - MwoI endonuclease (R.MwoI) and methyltransferase (M.MwoI) isolated from Methanobacterium
AB  - wolfei are thermophilic (optimum activity 65oC) and recognize a unique sequence.  R.MwoI
AB  - yields three nucleotide 3'-terminal extensions; M.MwoI is hypothesized to methylate C
AB  - residues.  Both genes have been cloned and expressed at low levels in Escherichia coli.
AB  - Plasmid-encoded R.MthI from Methanobacterium thermoautotrophicum is an isoschizomer of
AB  - blunt-end-generating NgoPII.  Deduced amino acid sequence of R.MthTI is highly similar to that
AB  - of R.NgoII, and M.MthTI has high sequence similarity to M.NgoPII and M.HaeIII.
AB  - Plasmid-encoded MthFI and MthZI from M. thermoautotrophicum are isoschizomers of each other
AB  - and of MaeI.  The restriction endonuclease and methyltransferase recognize a palindromic
AB  - tetranucleotide.  The deduced amino acid sequence of M.MthZI shows significant similarity to
AB  - that of m4C-MTases.  The occurrence of three restriction-modification systems that recognize
AB  - CTAG within the methanogenic Archaea and reports that the CTAG sequence in DNA from species of
AB  - halophilic Archaea is refractory to digestion by CTAG-specific XbaI, SpeI, and NheI suggest
AB  - that CTAG-specific restriction-modification systems are more characteristic in the Archaea
AB  - than in the Bacteria.  Continued characterization of restriction-modification systems in the
AB  - methanogenic Archaea will be important for determining the compatibility of strains and DNA in
AB  - the development of effective transgenic systems among archaeal species.
ER  -

TY  - JOUR
AU  - Sozhamannan, S.
AU  - Dharmalingam, K.
TI  - Molecular cloning and identification of protein products of rglB locus of Escherichia coli.
JO  - Gene
PY  - 1988
SP  - 51
EP  - 52
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Spada, F.
AU  - Rothbauer, U.
AU  - Zolghadr, K.
AU  - Schermelleh, L.
AU  - Leonhardt, H.
TI  - Regulation of DNA methyltransferase 1.
JO  - Adv. Enzyme Regul.
PY  - 2006
SP  - 224
EP  - 234
VL  - 46
AB  - Although essentially all cells of a mammalian organism contain the same genetic information
AB  - they may differ dramatically in form and function.  This cellular differentiation is
AB  - established during development by cascades of transcription factors driving the expression of
AB  - cell-type specific sets of genes.  These cell type specific gene expression patterns are
AB  - established, maintained and changed in conjunction with epigenetic mechanisms including DNA
AB  - methylation, histone modification and chromatin structure.  The most tangible epigenetic mark
AB  - is DNA methylation, a postreplicative modification, which in vertebrates is mainly catalyzed
AB  - by DNA methyltransferases (Dnmts: EC 2.1.1.37) 1, 3a and 3b at palindromic CpG sites.  The DNA
AB  - methylation pattern changes along with cellular differentiation and is generally inversely
AB  - correlated with transcriptional activity.  Over the past decade, several functional links
AB  - between DNA methylation, histone modification, chromatin structure and transcriptional
AB  - regulation have been discovered.  In mammalian cells Dnmt1 is the major and ubiquitously
AB  - expressed Dnmt.  By direct and indirect interactions Dnmt1 plays a central role in the
AB  - epigenetic networks controlling gene expression in development and disease.  We will outline
AB  - results and open questions concerning the regulation of Dnmt1 and dicuss novel approaches to
AB  - study Dnmts in living cells.
ER  -

TY  - JOUR
AU  - Spang, A. et al.
TI  - The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: Insights into metabolic versatility and environmental adaptations.
JO  - Environ. Microbiol.
PY  - 2012
SP  - 3122
EP  - 3145
VL  - 14
AB  - The cohort of the ammonia-oxidizing archaea
AB  - (AOA) of the phylum Thaumarchaeota is a diverse,
AB  - widespread and functionally important group of
AB  - microorganisms in many ecosystems. However, our
AB  - understanding of their biology is still very rudimentary
AB  - in part because all available genome sequences
AB  - of this phylum are from members of the Nitrosopumilus
AB  - cluster. Here we report on the complete
AB  - genome sequence of Candidatus Nitrososphaera
AB  - gargensis obtained from an enrichment culture, representing
AB  - a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial
AB  - environments. With its 2.83 Mb the genome is much
AB  - larger than that of other AOA. The presence of
AB  - a high number of (active) IS elements/transposases,
AB  - genomic islands, gene duplications and a complete
AB  - CRISPR/Cas defence system testifies to its dynamic
AB  - evolution consistent with low degree of synteny
AB  - with other thaumarchaeal genomes. As expected,
AB  - the repertoire of conserved enzymes proposed to be
AB  - required for archaeal ammonia oxidation is encoded
AB  - by N. gargensis, but it can also use urea and possibly
AB  - cyanate as alternative ammonia sources. Furthermore,
AB  - its carbon metabolism is more flexible at the
AB  - central pyruvate switch point, encompasses the
AB  - ability to take up small organic compounds and
AB  - might even include an oxidative pentose phosphate
AB  - pathway. Furthermore, we show that thaumarchaeota
AB  - produce cofactor F420 as well as polyhydroxyalkanoates.
AB  - Lateral gene transfer from bacteria and
AB  - euryarchaeota has contributed to the metabolic
AB  - versatility of N. gargensis. This organisms is well
AB  - adapted to its niche in a heavy metal-containing
AB  - thermal spring by encoding a multitude of heavy
AB  - metal resistance genes, chaperones and mannosylglycerate
AB  - as compatible solute and has the genetic
AB  - ability to respond to environmental changes by signal
AB  - transduction via a large number of two-component
AB  - systems, by chemotaxis and flagella-mediated
AB  - motility and possibly even by gas vacuole formation.
AB  - These findings extend our understanding of thaumarchaeal
AB  - evolution and physiology and offer many testable
AB  - hypotheses for future experimental research on
AB  - these nitrifiers.
ER  -

TY  - JOUR
AU  - Spang, A.
AU  - Saw, J.H.
AU  - Jorgensen, S.L.
AU  - Zaremba-Niedzwiedzka, K.
AU  - Martijn, J.
AU  - Lind, A.E.
AU  - van Eijk, R.
AU  - Schleper, C.
AU  - Guy, L.
AU  - Ettema, T.J.
TI  - Complex archaea that bridge the gap between prokaryotes and eukaryotes.
JO  - Nature
PY  - 2015
SP  - 173
EP  - 179
VL  - 521
AB  - The origin of the eukaryotic cell remains one of the most contentious puzzles in  modern
AB  - biology. Recent studies have provided support for the emergence of the
AB  - eukaryotic host cell from within the archaeal domain of life, but the identity
AB  - and nature of the putative archaeal ancestor remain a subject of debate. Here we
AB  - describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum,
AB  - which forms a monophyletic group with eukaryotes in phylogenomic analyses, and
AB  - whose genomes encode an expanded repertoire of eukaryotic signature proteins that
AB  - are suggestive of sophisticated membrane remodelling capabilities. Our results
AB  - provide strong support for hypotheses in which the eukaryotic host evolved from a
AB  - bona fide archaeon, and demonstrate that many components that underpin
AB  - eukaryote-specific features were already present in that ancestor. This provided
AB  - the host with a rich genomic 'starter-kit' to support the increase in the
AB  - cellular and genomic complexity that is characteristic of eukaryotes.
ER  -

TY  - JOUR
AU  - Sparling, R.
AU  - Bhatti, A.R.
TI  - Restriction endonuclease activities of Neisseria meningitidis.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1983
SP  - 214
EP  - 214
VL  - 83
AB  - Restriction endonuclease activities present in different strains of Neisseria
AB  - meningitidis were studied.  Enzymes from cell free sonicates were partially
AB  - purified by Blue-2 cross linked agarose (Sigma) column chromatography.
AB  - Restriction enzyme activity was eluted by 0.5 M NaCl in Tris-HCl buffer pH 7.6.
AB  - Excess NaCl was dialyzed out against Tris-HCl buffer pH 7.6.  Restriction
AB  - enzyme activity from different strains was assayed by 0.8% agarose slab gel
AB  - electrophoresis.  Enzyme preparations from three different strains (DRES-W34,
AB  - M1011 and DRES-30) gave three distinct restriction endonuclease (NmeI, NmeIII
AB  - and NmeIV) activities.  Using a linear gradient of NaCl (from 0.0 to 0.5 M),
AB  - two restriction endonuclease activities NmeI and NmeII present in DRES-W34 were
AB  - separated into two distinct peaks.  These two enzyme activities were eluted at
AB  - 0.15 M NaCl and 0.25 NaCl respectively.  NmeI and NmeII gave 18 and 28 cleavage
AB  - fragments when incubated with lambda DNA.  NmeII did not cleave SV-40 and
AB  - PhiX174 DNA.  Restriction endonuclease NmeI was further characterized.  It was
AB  - inhibited by 0.4 M NaCl but did require MgCl2 for its enzyme activity.  MgCl2
AB  - at concentration above 0.02 M inhibited its enzyme activity completely.  NmeI
AB  - activity was abolished completely after 30 min of incubation at 65C.  NmeI, II
AB  - and III were quite stable when stored at -70C but NmeIV lost its activity.
ER  -

TY  - JOUR
AU  - Sparling, R.
AU  - Bhatti, A.R.
TI  - NmeI, a restriction endonuclease from Neisseria meningitidis.
JO  - Microbios
PY  - 1984
SP  - 73
EP  - 79
VL  - 41
AB  - A restriction endonuclease, NmeI, present in Neisseria meningitidis was
AB  - partially purified by passing through a blue 2-cross linked agarose column, no
AB  - contaminating nucleases remained detectable.  This enzyme cleaved phage lambda,
AB  - adenovirus type 2 and PhiX174 DNA but did not cleave SV40 DNA.  It had an
AB  - absolute requirement for Mg2+ for its activity and was inhibited by high
AB  - concentrations of NaCl or MgCl2.  NmeI activity was completely abolished after
AB  - 1 h of incubation at 65C.  S-adenosyl-L-methionine and ATP had no effect on its
AB  - activity suggesting that NmeI is a type II restriction endonuclease enzyme.  It
AB  - is the first report of a restriction enzyme present in N. meningitidis.
ER  -

TY  - JOUR
AU  - Spataro, N.
AU  - Farfan, M.
AU  - Albarral, V.
AU  - Sanglas, A.
AU  - Loren, J.G.
AU  - Fuste, M.C.
AU  - Bosch, E.
TI  - Draft Genome Sequence of Aeromonas molluscorum Strain 848TT, Isolated from Bivalve Molluscs.
JO  - Genome Announcements
PY  - 2013
SP  - e00382
EP  - e00313
VL  - 1
AB  - We report here the draft genome sequence of Aeromonas molluscorum 848T, the type  strain of
AB  - this Aeromonas species, which was isolated from wedge shells (Donax
AB  - trunculus) obtained from a retail market in Barcelona, Spain, in 1997.
ER  -

TY  - JOUR
AU  - Spear, M.A.
TI  - Efficient DNA subcloning through selective restriction endonuclease digestion.
JO  - Biotechniques
PY  - 2000
SP  - 660
EP  - 662
VL  - 28
AB  - Described here is a selective restriction endonuclease digestion method that eliminates the
AB  - electrophoresis step that is usually used during the subcloning of new DNA sequences into
AB  - typical E. coli-based plasmids. The method increases yield while decreasing laboratory
AB  - resource and time utilization. By using donor and acceptor sequences that contain unique
AB  - restriction sites found only outside of the intended recombination sequences, the initial
AB  - digestion products can be directly combined without electrophoresis if the ligation step is
AB  - followed by a selective digestion using the unique restriction enzymes before transformation.
AB  - This system is based on the several order of magnitude decrease in transformation efficiency
AB  - of linearized compared to circular plasmids. As an example, this method was used to obtain
AB  - recombinants between a 3.6 kb acceptor plasmid and 3.0 kb insert following one ligation
AB  - reaction after the failure of nine standard reactions using similar amounts of input DNA. It
AB  - is particularly applicable to situations in which low subcloning efficiencies are expected.
AB  - The technique can be extended to a large percentage of planned recombinations by using
AB  - nonidentical compatible cohesive or blunt-ended fragments, or site-directed mutagenesis.
ER  -

TY  - JOUR
AU  - Spence, R.J.
AU  - Pavasovic, A.
AU  - Smith, J.J.
AU  - Prentis, P.J.
TI  - Draft Genome Sequence of Enterococcus faecalis Strain PF3, Isolated from Adelie Penguin Feces from Antarctica.
JO  - Genome Announcements
PY  - 2014
SP  - e01209
EP  - e01213
VL  - 2
AB  - Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common
AB  - commensal organism in humans and other animals. In this study, we
AB  - report a draft genome sequence for the E. faecalis strain PF3, isolated from
AB  - Adelie penguin feces collected from Warriner Island, Antarctica.
ER  -

TY  - JOUR
AU  - Spencer, D.H.
AU  - Kas, A.
AU  - Smith, E.E.
AU  - Raymond, C.K.
AU  - Sims, E.H.
AU  - Hastings, M.
AU  - Burns, J.L.
AU  - Kaul, R.
AU  - Olsen, M.V.
TI  - Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa.
JO  - J. Bacteriol.
PY  - 2003
SP  - 1316
EP  - 1325
VL  - 185
AB  - Whole-genome shotgun sequencing was used to study the sequence variation
AB  - of three Pseudomonas aeruginosa isolates, two from clonal infections of
AB  - cystic fibrosis patients and one from an aquatic environment, relative to
AB  - the genomic sequence of reference strain PAO1. The majority of the PAO1
AB  - genome is represented in these strains; however, at least three prominent
AB  - islands of PAO1-specific sequence are apparent. Conversely, approximately
AB  - 10% of the sequencing reads derived from each isolate fail to align with
AB  - the PAO1 backbone. While average sequence variation among all strains is
AB  - roughly 0.5%, regions of pronounced differences were evident in
AB  - whole-genome scans of nucleotide diversity. We analyzed two such divergent
AB  - loci, the pyoverdine and O-antigen biosynthesis regions, by complete
AB  - resequencing. A thorough analysis of isolates collected over time from one
AB  - of the cystic fibrosis patients revealed independent mutations resulting
AB  - in the loss of O-antigen synthesis alternating with a mucoid phenotype.
AB  - Overall, we conclude that most of the PAO1 genome represents a core P.
AB  - aeruginosa backbone sequence while the strains addressed in this study
AB  - possess additional genetic material that accounts for at least 10% of
AB  - their genomes. Approximately half of these additional sequences are novel.
ER  -

TY  - JOUR
AU  - Speth, D.R.
AU  - Russ, L.
AU  - Kartal, B.
AU  - Op den Camp, H.J.
AU  - Dutilh, B.E.
AU  - Jetten, M.S.
TI  - Draft Genome Sequence of Anammox Bacterium 'Candidatus Scalindua brodae,' Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor   Enrichments.
JO  - Genome Announcements
PY  - 2015
SP  - e01415
EP  - e01414
VL  - 3
AB  - We present the draft genome of anammox bacterium 'Candidatus Scalindua brodae,' which at 282
AB  - contigs is a major improvement over the highly fragmented genome
AB  - assembly of related species 'Ca. Scalindua profunda' (1,580 contigs) which was
AB  - previously published.
ER  -

TY  - JOUR
AU  - Spiegel, P.C.
AU  - Chevalier, B.
AU  - Sussman, D.
AU  - Turmel, M.
AU  - Lemieux, C.
AU  - Stoddard, B.L.
TI  - The Structure of I-CeuI Homing Endonuclease: Evolving Asymmetric DNA Recognition from a Symmetric Protein Scaffold.
JO  - Structure
PY  - 2006
SP  - 869
EP  - 880
VL  - 14
AB  - Homing endonucleases are highly specific catalysts of DNA strand breaks, leading to the
AB  - transfer of mobile intervening sequences containing the
AB  - endonuclease ORF. We have determined the structure and DNA recognition
AB  - behavior of I-CeuI, a homodimeric LAGLIDADG endonuclease from
AB  - Chlamydomonas eugametos. This symmetric endonuclease displays unique
AB  - structural elaborations on its core enzyme fold, and it preferentially
AB  - cleaves a highly asymmetric target site. This latter property represents
AB  - an early step, prior to gene fusion, in the generation of asymmetric DNA
AB  - binding platforms from homodimeric ancestors. The divergence of the
AB  - sequence, structure, and target recognition behavior of homing
AB  - endonucleases, as illustrated by this study, leads to the invasion of
AB  - novel genomic sites by mobile introns during evolution.
ER  -

TY  - JOUR
AU  - Spiess, E.
AU  - Tomassetti, A.
AU  - Hernaiz-Driever, P.
AU  - Pfeifer, G.P.
TI  - Structure of mouse DNA (cytosine-5-)-methyltransferase.
JO  - Eur. J. Biochem.
PY  - 1988
SP  - 29
EP  - 34
VL  - 177
AB  - DNA (cytosine-5-)-methyltransferase was purified as a single polypeptide (190
AB  - kDa by SDS-PAGE) from mouse P815 mastocytoma cells.  This enzyme transfers
AB  - methyl groups to unmethylated as well as to hemimethylated DNA sites with a
AB  - strong preference for the hemimethylated substrate.  A structural analysis of
AB  - the isolated enzyme by electron microscopical techniques was undertaken.  On
AB  - the basis of the results obtained, we propose a model for the enzyme structure.
AB  - This model describes the enzyme as a hemielliptical globular structure with
AB  - dimensions of 5.4-6.7 nm for the height h and 10.3-10.8 nm for the diameter d,
AB  - respectively; this globular structure bears a small appendix at the flat side.
AB  - A molecular mass of 235-250 kDa is calculated from the measured dimensions.
AB  - Limited trypsin digestion of the enzyme led to a 160-kDa fragment which
AB  - preserved the gross morphology of the original material.  The possible
AB  - structure function relationships are discussed.
ER  -

TY  - JOUR
AU  - Spilker, T.
AU  - Darrah, R.
AU  - LiPuma, J.J.
TI  - Complete Genome Sequences of Bordetella flabilis, Bordetella bronchialis, and 'Bordetella pseudohinzii'.
JO  - Genome Announcements
PY  - 2016
SP  - e01132
EP  - e01116
VL  - 4
AB  - We report here the complete genome sequences of Bordetella flabilis and Bordetella bronchialis
AB  - recovered from cultures of individuals with cystic
AB  - fibrosis (CF), and 'Bordetella pseudohinzii' recovered from a CF mouse model.
ER  -

TY  - JOUR
AU  - Spilker, T.
AU  - LiPuma, J.J.
TI  - Draft Genome Sequences of 63 Pseudomonas aeruginosa Isolates Recovered from Cystic Fibrosis Sputum.
JO  - Genome Announcements
PY  - 2016
SP  - e00231
EP  - e00216
VL  - 4
AB  - Here, we report the draft genome sequences of 63 ITALIC! Pseudomonas aeruginosaisolates,
AB  - recovered in culture of sputum from 15 individuals with
AB  - cystic fibrosis (CF) receiving care in a single CF care center over a 13-year
AB  - period. These sequences add value to studies of within-host evolution of
AB  - bacterial pathogens during chronic infection.
ER  -

TY  - JOUR
AU  - Spinard, E.
AU  - Kessner, L.
AU  - Gomez-Chiarri, M.
AU  - Rowley, D.C.
AU  - Nelson, D.R.
TI  - Draft Genome Sequence of the Marine Pathogen Vibrio coralliilyticus RE22.
JO  - Genome Announcements
PY  - 2015
SP  - e01432
EP  - e01415
VL  - 3
AB  - Vibrio coralliilyticus RE22 is a causative agent of vibriosis in larval bivalves. We report
AB  - here the draft genome sequence of V. coralliilyticus RE22 and describe
AB  - additional virulence factors that may provide insight into its mechanism of
AB  - pathogenicity.
ER  -

TY  - JOUR
AU  - Spinard, E.J.
AU  - Dubert, J.
AU  - Nelson, D.R.
AU  - Gomez-Chiarri, M.
AU  - Barja, J.L.
TI  - Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii subsp. europaeus.
JO  - Genome Announcements
PY  - 2016
SP  - e00625
EP  - e00616
VL  - 4
AB  - Vibrio tubiashii subsp. europaeus is a bivalve pathogen isolated during episodes  of mortality
AB  - affecting larval cultures in different shellfish hatcheries. Here,
AB  - we announce the draft genome sequence of the type strain PP-638 and describe
AB  - potential virulence factors, which may provide insight into the mechanism of
AB  - pathogenicity.
ER  -

TY  - JOUR
AU  - Spitzer, E.D.
TI  - Restriction enzymes.  To the Editor.
JO  - Arch. Pathol. Lab. Med.
PY  - 1990
SP  - 1190
EP  - 1190
VL  - 114
AB  - In his article on restriction enzymes in the Archives, Dr. Ross omits the important effects of
AB  - methylation on the activity of restriction enzymes.  The ability of a restriction endonuclease
AB  - to cleave and inactivate invading bacteriophage DNA without destroying the bacterial
AB  - chromosome depends on the presence within the cell of a corresponding modification methylase
AB  - that recognizes the same DNA sequence and methylates either an adenine or a cytosine, thus
AB  - rendering the sequence resistant to cleavage.  It is the methylation of restriction sites
AB  - present on the chromosome, not the absence of such sites (as suggested in the article), that
AB  - enables restriction-modification systems to distinguish "self" from "non- self" DNA;
AB  - bacteriophage DNA that has been modified by the EcoRI methylase is also resistant to the
AB  - action of the EcoRI endonuclease.
ER  -

TY  - JOUR
AU  - Spoerel, N.
AU  - Herrlich, P.
TI  - Colivirus-T3-coded S-adenosylmethionine hydrolase.
JO  - Eur. J. Biochem.
PY  - 1979
SP  - 227
EP  - 233
VL  - 95
AB  - Bacteriophage T3 induces an enzyme activity which hydrolyzes
AB  - S-adenosylmethionine.  This S-adenosylmethionine hydrolase is interesting, not
AB  - only because of its unique activity, but also because the protein has to
AB  - overcome host restriction.  S-adenosylmethionine hydrolase was purified to
AB  - homogeneity using affinity chromatography on S-adenosylhomocysteine-Sepharose.
AB  - The enzyme occurs in two forms, A and B.  Form A consists of the viral peptide
AB  - chain only; its native and subunit molecular weight is 17,000.  Form B
AB  - contains, in addition, a host subunit with a molecular weight of 49,000.  The
AB  - host subunit does not modifiy S-adenosylmethionine cleavage in vitro and no
AB  - apparent relationship to the host-restriction system could be detected.
ER  -

TY  - JOUR
AU  - Spoerel, N.
AU  - Herrlich, P.
AU  - Bickle, T.A.
TI  - A novel bacteriophage defence mechanism: the anti-restriction protein.
JO  - Nature
PY  - 1979
SP  - 30
EP  - 34
VL  - 278
AB  - Bacteriophage T3 and T7 protect their DNA from restriction by producing, as the
AB  - earliest detectable phage functions, anti-restriction proteins.  Although the
AB  - two phage proteins differ in their chromatographic and antigenic properties,
AB  - they act by the same mechanism: the anti-restriction proteins inhibit E. coli
AB  - K12 restriction endonuclease by direct interaction.
ER  -

TY  - JOUR
AU  - Sprague, L.D.
AU  - Neubauer, H.
TI  - Genome Sequence of Yersinia similis Y228T, a Member of the Yersinia pseudotuberculosis Complex.
JO  - Genome Announcements
PY  - 2014
SP  - e00216
EP  - e00214
VL  - 2
AB  - We report here on the genome sequence of Yersinia similis 228(T) isolated in Germany. The
AB  - genome has a size of 4.9 Mb and a G+C content of 47% and is
AB  - predicted to contain 4,135 coding sequences. Annotation of the 60,687-bp
AB  - extrachromosomal element predicted 67 coding sequences and a G+C content of
AB  - 47.8%.
ER  -

TY  - JOUR
AU  - Sprague, L.D.
AU  - Neubauer, H.
TI  - De Novo Genome Sequence of Yersinia aleksiciae Y159T.
JO  - Genome Announcements
PY  - 2015
SP  - e01066
EP  - e01015
VL  - 3
AB  - We report here on the genome sequence of Yersinia aleksiciae Y159(T), isolated in Finland in
AB  - 1981. The genome has a size of 4 Mb, a G+C content of 49%, and is predicted to contain 3,423
AB  - coding sequences.
ER  -

TY  - JOUR
AU  - Sprague, L.D.
AU  - Tadayon, K.
TI  - Genome Sequence of Pasteurella multocida Razi 0002 of Avian Origin.
JO  - Genome Announcements
PY  - 2017
SP  - e00161
EP  - e00117
VL  - 5
AB  - We report here on the genome sequence of Pasteurella multocida Razi 0002 of avian origin,
AB  - isolated in Iran. The genome has a size of 2,289,036 bp, a G+C content of
AB  - 40.3%, and is predicted to contain 2,079 coding sequences.
ER  -

TY  - JOUR
AU  - Sprague, L.D.
AU  - Tadayon, K.
TI  - Genome Sequence of Pasteurella multocida Strain Razi_Pm0001.
JO  - Genome Announcements
PY  - 2017
SP  - e01532
EP  - e01516
VL  - 5
AB  - We report here the genome sequence of Pasteurella multocida Razi_Pm0001 from bovine origin,
AB  - isolated in Iran in 1936. The genome has a size of 2,360,663 bp, a
AB  - G+C content of 40.4%, and is predicted to contain 2,052 coding sequences.
ER  -

TY  - JOUR
AU  - Spring, S. et al.
TI  - Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 304
EP  - 319
VL  - 7
AB  - Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus
AB  - Desulfotomaculum which contains 30 species and is contained in the family
AB  - Peptococcaceae. This species is of interest because it represents one of the few
AB  - sulfate-reducing bacteria that have been isolated from the rumen. Here we
AB  - describe the features of D. ruminis together with the complete genome sequence
AB  - and annotation. The 3,969,014 bp long chromosome with a total of 3,901
AB  - protein-coding and 85 RNA genes is the second completed genome sequence of a type
AB  - strain of the genus Desulfotomaculum to be published, and was sequenced as part
AB  - of the DOE Joint Genome Institute Community Sequencing Program 2009.
ER  -

TY  - JOUR
AU  - Spring, S. et al.
TI  - Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 242
EP  - 253
VL  - 1
AB  - Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing
AB  - bacteria known to grow with acetate as sole energy and carbon
AB  - source. It is able to oxidize substrates completely to carbon dioxide with
AB  - sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All
AB  - available data about this species are based on strain 5575(T), isolated from
AB  - piggery waste in Germany. Here we describe the features of this organism,
AB  - together with the complete genome sequence and annotation. This is the first
AB  - completed genome sequence of a Desulfotomaculum species with validly published
AB  - name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding
AB  - and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea
AB  - project.
ER  -

TY  - JOUR
AU  - Spring, S. et al.
TI  - Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 38
EP  - 48
VL  - 2
AB  - Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus
AB  - Desulfohalobium, which comprises, at the time of writing, two
AB  - species and represents the family Desulfohalobiaceae within the
AB  - Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing
AB  - bacterium, which can utilize H(2) and a limited range of organic substrates,
AB  - which are incompletely oxidized to acetate and CO(2), for growth. The type strain
AB  - HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal.
AB  - Here we describe the features of this organism, together with the complete genome
AB  - sequence and annotation. This is the first completed genome sequence of a member
AB  - of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a
AB  - 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of
AB  - the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Spring, S. et al.
TI  - Complete genome sequence of Thermosphaera aggregans type strain (M11TL).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 245
EP  - 259
VL  - 2
AB  - Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera,
AB  - which comprises at the time of writing only one species. This
AB  - species represents archaea with a hyperthermophilic, heterotrophic, strictly
AB  - anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from
AB  - a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone
AB  - National Park, Wyoming). Here we describe the features of this organism, together
AB  - with the complete genome sequence and annotation. The 1,316,595 bp long single
AB  - replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Spring, S.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Schumann, P.
AU  - Rohde, M.
AU  - Tindall, B.J.
AU  - Klenk, H.P.
TI  - Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.
JO  - ISME J.
PY  - 2016
SP  - 2801
EP  - 2816
VL  - 10
AB  - The recently isolated strain L21-Fru-ABT represents moderately halophilic,
AB  - obligately anaerobic and saccharolytic bacteria that thrive in the suboxic
AB  - transition zones of hypersaline microbial mats. Phylogenetic analyses based on
AB  - 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT
AB  - represents a novel species and genus affiliated with a distinct phylum-level
AB  - lineage originally designated Verrucomicrobia subdivision 5. A survey of
AB  - environmental 16S rRNA gene sequences revealed that members of this newly
AB  - recognized phylum are wide-spread and ecologically important in various anoxic
AB  - environments ranging from hypersaline sediments to wastewater and the intestine
AB  - of animals. Characteristic phenotypic traits of the novel strain included the
AB  - formation of extracellular polymeric substances, a Gram-negative cell wall
AB  - containing peptidoglycan and the absence of odd-numbered cellular fatty acids.
AB  - Unusual metabolic features deduced from analysis of the genome sequence were the
AB  - production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking
AB  - pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of
AB  - the analyses of phenotypic, genomic and environmental data, it is proposed that
AB  - strain L21-Fru-ABT and related bacteria are specifically adapted to the
AB  - utilization of sulfated glycopolymers produced in microbial mats or biofilms.
ER  -

TY  - JOUR
AU  - Spring, S.
AU  - Fiebig, A.
AU  - Riedel, T.
AU  - Goker, M.
AU  - Klenk, H.P.
TI  - Genome Sequence of Gammaproteobacterial Pseudohaliea rubra Type Strain DSM 19751, Isolated from Coastal Seawater of the Mediterranean Sea.
JO  - Genome Announcements
PY  - 2014
SP  - e01208
EP  - e01214
VL  - 2
AB  - Pseudohaliea rubra strain DSM 19751T is an aerobic marine gammaproteobacterium that was
AB  - isolated from surface coastal seawater of the Mediterranean Sea. Here,
AB  - we present its genome sequence and annotation. Genome analysis revealed the
AB  - presence of genes involved in the synthesis of bacteriochlorophyll-a and the
AB  - reserve compound glycogen.
ER  -

TY  - JOUR
AU  - Spuesens, E.B.
AU  - van de Kreeke, N.
AU  - Estevao, S.
AU  - Hoogenboezem, T.
AU  - Sluijter, M.
AU  - Hartwig, N.G.
AU  - van Rossum, A.M.
AU  - Vink, C.
TI  - Variation in a surface-exposed region of the Mycoplasma pneumoniae P40 protein as a consequence of homologous DNA recombination between RepMP5  elements.
JO  - Microbiology
PY  - 2011
SP  - 473
EP  - 483
VL  - 157
AB  - Mycoplasma pneumoniae is a human pathogen that causes a range of respiratory tract infections.
AB  - The first step in infection is adherence of
AB  - the bacteria to the respiratory epithelium. This step is mediated by a
AB  - specialized organelle, which contains several proteins (cytadhesins) that
AB  - have an important function in adherence. Two of these cytadhesins, P40 and
AB  - P90, represent the proteolytic products from a single
ER  -

TY  - JOUR
AU  - Spyridaki, A.
AU  - Matzen, C.
AU  - Lanio, T.
AU  - Jeltsch, A.
AU  - Simoncsits, A.
AU  - Athanasiadis, A.
AU  - Scheuring-Vanamee, E.
AU  - Kokkinidis, M.
AU  - Pingoud, A.
TI  - Structural and Biochemical Characterization of a New Mg2+ Binding Site Near Tyr94 in the Restriction Endonuclease PvuII.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 395
EP  - 406
VL  - 331
AB  - We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+).
AB  - According to the structural data, divalent metal ion
AB  - binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+)
AB  - complex has two distinct metal ion binding sites, one in each monomer. One
AB  - site is formed by the catalytic residues Asp58 and Glu68, and has
AB  - extensive similarities to a catalytically important site found in all
AB  - structurally examined restriction endonucleases. The other binding site is
AB  - located in the other monomer, in the immediate vicinity of the hydroxyl
AB  - group of Tyr94; it has no analogy to metal ion binding sites found so far
AB  - in restriction endonucleases. To assign the number of metal ions involved
AB  - and to better understand the role of Mg(2+) binding to Tyr94 for the
AB  - function of PvuII, we have exchanged Tyr94 by Phe and characterized the
AB  - metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F
AB  - variant. Wild-type PvuII cleaves both strands of the DNA in a concerted
AB  - reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA
AB  - cleavage, occurs with a Hill coefficient of 4, meaning that at least two
AB  - metal ions are bound to each subunit in a cooperative fashion upon
AB  - formation of the active complex. Quenched-flow experiments show that DNA
AB  - cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with
AB  - enzyme or DNA than if preformed enzyme-DNA complexes are mixed with
AB  - Mg(2+). These results show that Mg(2+) cannot easily enter the active
AB  - center of the preformed enzyme-DNA complex, but that for fast cleavage the
AB  - metal ions must already be bound to the apoenzyme and carried with the
AB  - enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to
AB  - wild-type PvuII, does not cleave DNA in a concerted manner and metal ion
AB  - binding occurs with a Hill coefficient of 1. These results indicate that
AB  - removal of the Mg(2+) binding site at Tyr94 completely disrupts the
AB  - cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F
AB  - cleaves DNA about ten times more slowly than wild-type PvuII, regardless
AB  - of the order of mixing. From these results we conclude that wild-type
AB  - PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+)
AB  - required for catalysis are already bound at the enzyme, one of them at
AB  - Tyr94. We suggest that this Mg(2+) is shifted to the active center during
AB  - binding of a specific DNA substrate. These results, for the first time,
AB  - shed light on the pathway by which metal ions as essential cofactors enter
AB  - the catalytic center of restriction endonucleases.
ER  -

TY  - JOUR
AU  - Sreenivas, A.
AU  - Sathyanarayana, R.G.
AU  - Shivaji, S.
TI  - Draft Genome Sequence of a Psychrophilic Bacterium, Sphingomonas antarcticum, Isolated from the Soils of Schirmacher Oasis, Antarctica.
JO  - Genome Announcements
PY  - 2014
SP  - e00696
EP  - e00614
VL  - 2
AB  - We report the 4.5-Mbp genome sequences of Sphingobacterium antarcticum 4BY, a psychrophilic
AB  - bacterium isolated from the soils of Schirmacher Oasis, Antarctica.
AB  - The draft genome of S. antarcticum strain 4BY consists of 4,566,318 bp with 40.4%
AB  - G+C content, 4,234 protein coding genes, and 52 RNAs.
ER  -

TY  - JOUR
AU  - Srikhanta, Y.N.
AU  - Dowideit, S.J.
AU  - Edwards, J.L.
AU  - Falsetta, M.L.
AU  - Wu, H.J.
AU  - Harrison, O.B.
AU  - Fox, K.L.
AU  - Seib, K.L.
AU  - Maguire, T.L.
AU  - Wang, A.H.J.
AU  - Maiden, M.C.
AU  - Grimmond, S.M.
AU  - Apicella, M.A.
AU  - Jennings, M.P.
TI  - Phasevarions Mediate Random Switching of Gene Expression in Pathogenic Neisseria.
JO  - PLoS Pathog.
PY  - 2009
SP  - e1000400
EP  - e1000400
VL  - 5
AB  - Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are
AB  - subject to phase-variable expression
AB  - (high-frequency reversible ON/OFF switching of gene expression). In
AB  - Haemophilus influenzae, the random switching of the modA gene controls
AB  - expression of a phase-variable regulon of genes (a phasevarion), via
AB  - differential methylation of the genome in the modA ON and OFF states.
AB  - Phase-variable mod genes are also present in Neisseria meningitidis and
AB  - Neisseria gonorrhoeae, suggesting that phasevarions may occur in these
AB  - important human pathogens. Phylogenetic studies on phase-variable mod
AB  - genes associated with type III restriction modification (R-M) systems
AB  - revealed that these organisms have two distinct mod genes-modA and
AB  - modB. There are also distinct alleles of modA (abundant: modA11, 12,
AB  - 13; minor: modA4, 15, 18) and modB (modB1, 2). These alleles differ
AB  - only in their DNA recognition domain. ModA11 was only found in N.
AB  - meningitidis and modA13 only in N. gonorrhoeae. The recognition site
AB  - for the modA13 methyltransferase in N. gonorrhoeae strain FA1090 was
AB  - identified as 5'-AGAAA-3'. Mutant strains lacking the modA11, 12 or 13
AB  - genes were made in N. meningitidis and N. gonorrhoeae and their
AB  - phenotype analyzed in comparison to a corresponding mod ON wild-type
AB  - strain. Microarray analysis revealed that in all three modA alleles
AB  - multiple genes were either upregulated or downregulated, some of which
AB  - were virulence-associated. For example, in N. meningitidis MC58
AB  - (modA11), differentially expressed genes included those encoding the
AB  - candidate vaccine antigens lactoferrin binding proteins A and B.
AB  - Functional studies using N. gonorrhoeae FA1090 and the clinical isolate
AB  - O1G1370 confirmed that modA13 ON and OFF strains have distinct
AB  - phenotypes in antimicrobial resistance, in a primary human cervical
AB  - epithelial cell model of infection, and in biofilm formation. This
AB  - study, in conjunction with our previous work in H. influenzae,
AB  - indicates that phasevarions may be a common strategy used by
AB  - host-adapted bacterial pathogens to randomly switch between
AB  - differentiated cell types.
ER  -

TY  - JOUR
AU  - Srikhanta, Y.N.
AU  - Fox, K.L.
AU  - Jennings, M.P.
TI  - The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes.
JO  - Nat. Rev. Microbiol.
PY  - 2010
SP  - 196
EP  - 206
VL  - 8
AB  - In several host-adapted pathogens, phase variation has been found to occur in genes that
AB  - encode methyltransferases associated with type III restriction-modification systems. It was
AB  - recently shown that in the human pathogens Haemophilus influenzae, Neisseria gonorrhoeae and
AB  - Neisseria meningitidis phase variation of a type III DNA methyltransferase, encoded by members
AB  - of the mod gene family, regulates the expression of multiple genes. This novel genetic system
AB  - has been termed the 'phasevarion' (phase-variable regulon). The wide distribution of
AB  - phase-variable mod family genes indicates that this may be a common strategy used by
AB  - host-adapted bacterial pathogens to randomly switch between distinct cell types.
ER  -

TY  - JOUR
AU  - Srikhanta, Y.N.
AU  - Fung, K.Y.
AU  - Pollock, G.L.
AU  - Bennett-Wood, V.
AU  - Howden, B.P.
AU  - Hartland, E.L.
TI  - Phasevarion-Regulated Virulence in the Emerging Pediatric Pathogen Kingella kingae.
JO  - Infect. Immun.
PY  - 2017
SP  - e00319
EP  - e00317
VL  - 85
AB  - Kingella kingae is a common etiological agent of pediatric osteoarticular infections. While
AB  - current research has expanded our understanding of K. kingae
AB  - pathogenesis, there is a paucity of knowledge about host-pathogen interactions
AB  - and virulence gene regulation. Many host-adapted bacterial pathogens contain
AB  - phase variable DNA methyltransferases (mod genes), which can control expression
AB  - of a regulon of genes (phasevarion) through differential methylation of the
AB  - genome. Here, we identify a phase variable type III mod gene in K. kingae,
AB  - suggesting that phasevarions operate in this pathogen. Phylogenetic studies
AB  - revealed that there are two active modK alleles in K. kingae Proteomic analysis
AB  - of secreted and surface-associated proteins, quantitative PCR, and a heat shock
AB  - assay comparing the wild-type modK1 ON (i.e., in frame for expression) strain to
AB  - a modK1 OFF (i.e., out of frame) strain revealed three virulence-associated genes
AB  - under ModK1 control. These include the K. kingae toxin rtxA and the heat shock
AB  - genes groEL and dnaK Cytokine expression analysis showed that the interleukin-8
AB  - (IL-8), IL-1beta, and tumor necrosis factor responses of THP-1 macrophages were
AB  - lower in the modK1 ON strain than in the modK1::kan mutant. This suggests that
AB  - the ModK1 phasevarion influences the host inflammatory response and provides the
AB  - first evidence of this phase variable epigenetic mechanism of gene regulation in
AB  - K. kingae.
ER  -

TY  - JOUR
AU  - Srikhanta, Y.N.
AU  - Gorrell, R.J.
AU  - Power, P.M.
AU  - Tsyganov, K.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Hartland, E.L.
AU  - Jennings, M.P.
AU  - Kwok, T.
TI  - Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.
JO  - Sci. Rep.
PY  - 2017
SP  - 16140
EP  - 16140
VL  - 7
AB  - The Helicobacter pylori phase variable gene modH, typified by gene HP1522 in strain 26695,
AB  - encodes a N(6)-adenosine type III DNA methyltransferase. Our
AB  - previous studies identified multiple strain-specific modH variants (modH1 -
AB  - modH19) and showed that phase variation of modH5 in H. pylori P12 influenced
AB  - expression of motility-associated genes and outer membrane protein gene hopG.
AB  - However, the ModH5 DNA recognition motif and the mechanism by which ModH5
AB  - controls gene expression were unknown. Here, using comparative single molecule
AB  - real-time sequencing, we identify the DNA site methylated by ModH5 as
AB  - 5'-G(m6)ACC-3'. This motif is vastly underrepresented in H. pylori genomes, but
AB  - overrepresented in a number of virulence genes, including motility-associated
AB  - genes, and outer membrane protein genes. Motility and the number of flagella of
AB  - H. pylori P12 wild-type were significantly higher than that of isogenic modH5 OFF
AB  - or DeltamodH5 mutants, indicating that phase variable switching of modH5
AB  - expression plays a role in regulating H. pylori motility phenotypes. Using the
AB  - flagellin A (flaA) gene as a model, we show that ModH5 modulates flaA promoter
AB  - activity in a GACC methylation-dependent manner. These findings provide novel
AB  - insights into the role of ModH5 in gene regulation and how it mediates epigenetic
AB  - regulation of H. pylori motility.
ER  -

TY  - JOUR
AU  - Srikhanta, Y.N.
AU  - Gorrell, R.J.
AU  - Steen, J.A.
AU  - Gawthorne, J.A.
AU  - Kwok, T.
AU  - Grimmond, S.M.
AU  - Robins-Browne, R.M.
AU  - Jennings, M.P.
TI  - Phasevarion Mediated Epigenetic Gene Regulation in Helicobacter pylori.
JO  - PLoS ONE
PY  - 2011
SP  - e27569
EP  - e27569
VL  - 6
AB  - Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are
AB  - subject to phase-variable expression
AB  - (high-frequency reversible ON/OFF switching of gene expression). In
AB  - Haemophilus influenzae and pathogenic Neisseria, the random switching
AB  - of the modA gene, associated with a phase-variable type III restriction
AB  - modification (R-M) system, controls expression of a phase-variable
AB  - regulon of genes (a 'phasevarion'), via differential methylation of
AB  - the genome in the modA ON and OFF states. Phase-variable type III R-M
AB  - systems are also found in Helicobacter pylori, suggesting that
AB  - phasevarions may also exist in this key human pathogen. Phylogenetic
AB  - studies on the phase-variable type III modH gene revealed that there
AB  - are 17 distinct alleles in H. pylori, which differ only in their DNA
AB  - recognition domain. One of the most commonly found alleles was modH5
AB  - (16% of isolates). Microarray analysis comparing the wild-type P12modH5
AB  - ON strain to a P12 Delta modH5 mutant revealed that six genes were
AB  - either up-or down-regulated, and some were virulence-associated. These
AB  - included flaA, which encodes a flagella protein important in motility
AB  - and hopG, an outer membrane protein essential for colonization and
AB  - associated with gastric cancer. This study provides the first evidence
AB  - of this epigenetic mechanism of gene expression in H. pylori.
AB  - Characterisation of H. pylori modH phasevarions to define stable
AB  - immunological targets will be essential for vaccine development and may
AB  - also contribute to understanding H. pylori pathogenesis.
ER  -

TY  - JOUR
AU  - Srikhanta, Y.N.
AU  - Maguire, T.L.
AU  - Stacey, K.J.
AU  - Grimmond, S.M.
AU  - Jennings, M.P.
TI  - The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 5547
EP  - 5551
VL  - 102
AB  - Several host-adapted bacterial pathogens contain methyltransferases associated with type III
AB  - restriction-modification (R-M) systems that are
AB  - subject to reversible, high-frequency on/off switching of expression
AB  - (phase variation). To investigate the role of phase-variable expression of
AB  - R-M systems, we made a mutant strain lacking the methyltransferase (mod)
AB  - associated with a type III R-M system of Haemophilus influenzae and
AB  - analyzed its phenotype. By microarray analysis, we identified a number of
AB  - genes that were either up- or down-regulated in the mod mutant strain.
AB  - This system reports the coordinated random switching of a set of genes in
AB  - a bacterial pathogen and may represent a widely used mechanism.
ER  -

TY  - JOUR
AU  - Srilunchang, M.
AU  - Homchampa, P.
AU  - Proungvitaya, T.
AU  - Wongratanacheewin, S.
TI  - Construction of a marker-free DNA adenine methylase (Dam) mutant of Burkholderia pseudomallei.
JO  - Tissue Antigens
PY  - 2005
SP  - 550
EP  - 550
VL  - 66
AB  - Burkholderia pseudomallei is the causative agent of melioidosis, a severe disease of humans
AB  - and animals.  Presently no vaccine exists to protect against meliodosis.  It has recently been
AB  - shown that DNA adenine methylase mutants of Salmonella enterica serovar Typhimurium are
AB  - markedly attenuated but highly effective as live vaccines against Salmonella infection of mice
AB  - and chickens.  To determine if this observation could be extended to B. pseudomallei, a
AB  - marker-free Dam mutant of B. pseudomallei was constructed and characterized.  The deletion has
AB  - been fully defined at the molecular level with no foreign DNA or drug resistance gene remain
AB  - in the B. pseudomallei mutant strain.  The dam mutant of B. pseudomallei was constructed by
AB  - using in vitro directed mutagenesis.  The first step, the B. pseudomallei dam gene was
AB  - PCR-amplified and the PCR product was digested with SmaI/SalI and ligated into pUC18.  The
AB  - ligated products were introduced into E.coli DH5a by electroporation and one clone with the
AB  - predicted insert size was selected and designated pPHE157.  The cloned gene was sequenced and
AB  - found 100% identity with that of the published sequence.  The next step, the 175 bp StyI/EagI
AB  - fragment located within the dam gene in pPHE157 was deleted to yield pPHE158.  The SmaI/SalI
AB  - fragment containing the Delta-dam was cloned into pEG19Tc replacement vector containing the
AB  - counterselectable sacB marker and transferred from E. coli PHE122-1 to B. pseudomallei
AB  - wild-type strain by conjugation method.  One desired dam mutants of B. pseudomallei designated
AB  - PHB 136 was positively identified on the basis of sucrose tolerance on sucrose containing
AB  - media.  The phenotype of this dam mutant strain was confirmed by its sensitivity to the
AB  - 2-aminopurine and by restriction analysis using MboI endonuclease, which recognize and cleaves
AB  - DNA at non-methylated GATC sequences.  The genotype of the dam mutant was further confirmed by
AB  - PCR and Southern blot analysis.  Studies aimed to determine the attenuation level and vaccine
AB  - efficacy in a mouse model of this dam mutant are underway.
ER  -

TY  - JOUR
AU  - Srinivasan, V.
AU  - Metcalf, B.J.
AU  - Knipe, K.M.
AU  - Ouattara, M.
AU  - McGee, L.
AU  - Shewmaker, P.L.
AU  - Glennen, A.
AU  - Nichols, M.
AU  - Harris, C.
AU  - Brimmage, M.
AU  - Ostrowsky, B.
AU  - Park, C.J.
AU  - Schrag, S.J.
AU  - Frace, M.A.
AU  - Sammons, S.A.
AU  - Beall, B.
TI  - vanG element insertions within a conserved chromosomal site conferring vancomycin resistance to Streptococcus agalactiae and Streptococcus anginosus.
JO  - MBio
PY  - 2014
SP  - E01386
EP  - E01314
VL  - 5
AB  - Three vancomycin-resistant streptococcal strains carrying vanG elements (two
AB  - invasive Streptococcus agalactiae isolates [GBS-NY and GBS-NM, both serotype II
AB  - and multilocus sequence type 22] and one Streptococcus anginosus [Sa]) were
AB  - examined. The 45,585-bp elements found within Sa and GBS-NY were nearly identical
AB  - (together designated vanG-1) and shared near-identity over an ~15-kb overlap with
AB  - a previously described vanG element from Enterococcus faecalis. Unexpectedly,
AB  - vanG-1 shared much less homology with the 49,321-bp vanG-2 element from GBS-NM,
AB  - with widely different levels (50% to 99%) of sequence identity shared among 44
AB  - related open reading frames. Immediately adjacent to both vanG-1 and vanG-2 were
AB  - 44,670-bp and 44,680-bp integrative conjugative element (ICE)-like sequences,
AB  - designated ICE-r, that were nearly identical in the two group B streptococcal
AB  - (GBS) strains. The dual vanG and ICE-r elements from both GBS strains were
AB  - inserted at the same position, between bases 1328 and 1329, within the identical
AB  - RNA methyltransferase (rumA) genes. A GenBank search revealed that although most
AB  - GBS strains contained insertions within this specific site, only sequence type 22
AB  - (ST22) GBS strains contained highly related ICE-r derivatives. The vanG-1 element
AB  - in Sa was also inserted within this position corresponding to its rumA homolog
AB  - adjacent to an ICE-r derivative. vanG-1 insertions were previously reported
AB  - within the same relative position in the E. faecalis rumA homolog. An ICE-r
AB  - sequence perfectly conserved with respect to its counterpart in GBS-NY was
AB  - apparent within the same site of the rumA homolog of a Streptococcus dysgalactiae
AB  - subsp. equisimilis strain. Additionally, homologous vanG-like elements within the
AB  - conserved rumA target site were evident in Roseburia intestinalis. Importance:
AB  - These three streptococcal strains represent the first known vancomycin-resistant
AB  - strains of their species. The collective observations made from these strains
AB  - reveal a specific hot spot for insertional elements that is conserved between
AB  - streptococci and different Gram-positive species. The two GBS strains potentially
AB  - represent a GBS lineage that is predisposed to insertion of vanG elements.
ER  -

TY  - JOUR
AU  - Srivastav, R.
AU  - Singh, A.
AU  - Jangir, P.K.
AU  - Kumari, C.
AU  - Muduli, S.
AU  - Sharma, R.
TI  - Genome Sequence of Staphylococcus massiliensis Strain S46, Isolated from the Surface of Healthy Human Skin.
JO  - Genome Announcements
PY  - 2013
SP  - e00553
EP  - e00513
VL  - 1
AB  - Staphylococcus massiliensis strain S46 was isolated from the surface of healthy human skin.
AB  - Here, we report the draft genome sequence of S. massiliensis S46
AB  - (2,447,110 bp, with a G+C content of 36.3%).
ER  -

TY  - JOUR
AU  - Srivastava, R.
AU  - Gopinathan, K.P.
AU  - Ramakrishnan, T.
TI  - Deoxyribonucleic acid methylation in mycobacteria.
JO  - J. Bacteriol.
PY  - 1981
SP  - 716
EP  - 719
VL  - 148
AB  - Deoxyribonucleic acid modification in six strains of mycobacteria was investigated. The
AB  - presence of 5-methylcytosine in the virulent strain
AB  - Mycobacterium tuberculosis H37Rv and its absence in the avirulent strain M.
AB  - tuberculosis H37Ra and other saprophytic, fast-growing mycobacteria appear to be
AB  - the salient features. However, deoxyribonucleic acid from M. smegmatis SN2
AB  - lysogenized with the temperature phage I3 showed the presence of
AB  - 5-methylcytosine. All of the strains had N6-methyladenine.
ER  -

TY  - JOUR
AU  - Srivastava, S.
AU  - Moraes, C.T.
TI  - Expression of a mitochondrially targeted restriction endonuclease in skeletal muscle causes a mitochondrial myopathy.
JO  - Mitochondrion
PY  - 2003
SP  - 158
EP  - 159
VL  - 3
ER  -

TY  - JOUR
AU  - Srivastava, S.
AU  - Moraes, C.T.
TI  - Manipulating mitochondrial DNA heteroplasmy by a mitochondrially targeted restriction endonuclease.
JO  - Hum. Mol. Genet.
PY  - 2001
SP  - 3093
EP  - 3099
VL  - 10
AB  - Mutations in the mitochondrial DNA (mtDNA) can cause a variety of human diseases. In most
AB  - cases, such mutations are heteroplasmic (i.e. mutated
AB  - and wild-type mtDNA coexist) and a small percentage of wild-type
AB  - sequences can have a strong protective effect against a metabolic
AB  - defect. Because a genetic approach to correct mtDNA mutations is not
AB  - currently available, the ability to modulate heteroplasmy would have a
AB  - major impact in the phenotype of many patients with mitochondrial
AB  - disorders. We show here that a restriction endonuclease targeted to
AB  - mitochondria has this ability. A mitochondrially targeted PstI degraded
AB  - mtDNA harboring PstI sites, in some cases leading to a complete loss of
AB  - mitochondrial genomes. Recombination between DNA ends released by PstI
AB  - was not observed. When expressed in a heteroplasmic rodent cell line,
AB  - containing one mtDNA haplotype with two sites for PstI and another
AB  - haplotype having none, the mitochondrial PstI caused a significant
AB  - shift in heteroplasmy, with an accumulation of the mtDNA haplotype
AB  - lacking PstI sites. These experiments provide proof of the principle
AB  - that restriction endonucleases are feasible tools for genetic therapy
AB  - of a sub-group of mitochondrial disorders. Although this approach is
AB  - limited by the presence of mutation-specific restriction sites,
AB  - patients with neuropathy, ataxia and retinitis pigmentosa (NARP) could
AB  - benefit from it, as the T8399G mutation creates a unique restriction
AB  - site that is not present in wild-type human mitochondrial DNA.
ER  -

TY  - JOUR
AU  - Staab, A.
AU  - Plaut, R.D.
AU  - Pratt, C.
AU  - Lovett, S.P.
AU  - Wiley, M.R.
AU  - Biggs, T.D.
AU  - Bernhards, R.C.
AU  - Beck, L.C.
AU  - Palacios, G.F.
AU  - Stibitz, S.
AU  - Jones, K.L.
AU  - Goodwin, B.G.
AU  - Smith, M.A.
AU  - Sozhamannan, S.
TI  - Whole-Genome Sequences of Variants of Bacillus anthracis Sterne and Their Toxin Gene Deletion Mutants.
JO  - Genome Announcements
PY  - 2017
SP  - e01231
EP  - e01217
VL  - 5
AB  - Here, we report the draft genome sequences of three laboratory variants of Bacillus anthracis
AB  - Sterne and their double (Deltalef Deltacya) and triple
AB  - (Deltapag Deltalef Deltacya) toxin gene deletion derivatives.
ER  -

TY  - JOUR
AU  - Stabler, R.A.
AU  - Negus, D.
AU  - Pain, A.
AU  - Taylor, P.W.
TI  - Draft Genome Sequences of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8, Soil Bacteria That Cooperate To Degrade the  Poly-gamma-d-Glutamic Acid Anthrax Capsule.
JO  - Genome Announcements
PY  - 2013
SP  - e00057
EP  - e00012
VL  - 1
AB  - A mixed culture of Pseudomonas fluorescens BS2 and Pusillimonas noertemannii BS8  degraded
AB  - poly-gamma-d-glutamic acid; when the 2 strains were cultured separately, no hydrolytic
AB  - activity was apparent. Here we report the draft genome sequences of both soil isolates.
ER  -

TY  - JOUR
AU  - Stacey, K.A.
TI  - Intracellular modification of nucleic acids.
JO  - Br. Med. Bull.
PY  - 1965
SP  - 211
EP  - 216
VL  - 21
AB  - None
ER  -

TY  - JOUR
AU  - Stackebrandt, E. et al.
TI  - Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 15
EP  - 25
VL  - 8
AB  - Coriobacterium glomerans Haas and Konig 1988, is the only species of the genus Coriobacterium,
AB  - family Coriobacteriaceae, order Coriobacteriales, phylum
AB  - Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs,
AB  - i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the
AB  - genome of strain PW2(T) is its endosymbiotic life style which is rare among
AB  - members of Actinobacteria. Here we describe the features of this symbiont,
AB  - together with the complete genome sequence and its annotation. This is the first
AB  - complete genome sequence of a member of the genus Coriobacterium and the sixth
AB  - member of the order Coriobacteriales for which complete genome sequences are now
AB  - available. The 2,115,681 bp long single replicon genome with its 1,804
AB  - protein-coding and 54 RNA genes is part of the G enomic E ncyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Stackebrandt, E. et al.
TI  - Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 228
EP  - 238
VL  - 8
AB  - Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was
AB  - established as a result of the reclassification of Leptospira parva
AB  - Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella
AB  - constitutes the family Leptospiraceae, within the order Spirochaetales. Here we
AB  - describe the features of this free-living aerobic spirochete together with the
AB  - complete genome sequence and annotation. This is the first complete genome
AB  - sequence of a member of the genus Turneriella and the 13(th) member of the family
AB  - Leptospiraceae for which a complete or draft genome sequence is now available.
AB  - The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is
AB  - part of the G enomic E ncyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Stackebrandt, E. et al.
TI  - High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 37
EP  - 46
VL  - 8
AB  - At present, Joostella marina Quan et al. 2008 is the sole species with a validly  published
AB  - name in the genus Joostella, family Flavobacteriacae, phylum
AB  - Bacteriodetes. It is a yellow-pigmented, aerobic, marine organism about which
AB  - little has been reported other than the chemotaxonomic features required for
AB  - initial taxonomic description. The genome of J. marina strain En5(T) complements
AB  - a list of 16 Flavobacteriaceae strains for which complete genomes and draft
AB  - genomes are currently available. Here we describe the features of this bacterium,
AB  - together with the complete genome sequence, and annotation. This is the first
AB  - member of the genus Joostella for which a complete genome sequence becomes
AB  - available. The 4,508,243 bp long single replicon genome with its 3,944
AB  - protein-coding and 60 RNA genes is part of the G enomic E ncyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Stadtler, P.
AU  - von Strandmann, R.P.
AU  - Walter, T.
AU  - Frey, B.
AU  - Auer, H.
AU  - Hengstenberg, W.
AU  - Schmitz, G.
TI  - Purification and characterisation of the restriction endonuclease ItaI from Ilyobacter tartaricus recognizing 5'-GC^NGC-3'.
JO  - Gene
PY  - 1993
SP  - 347
EP  - 348
VL  - 137
AB  - ItaI, an isoschizomer of the subclass IIW [Kessler and Manta, Gene 92 (1990) 1-248]
AB  - restriction endonuclease (ENase), Fnu4HI [Leung et al., Nucleic Acids Res. 6 (1979) 17-25],
AB  - has been isolated from Ilyobacter tartaricus. The ENase has the five-base palindromic
AB  - recognition sequence, 5'GC^NGC-3'. It cleaves behind the second nucleotide and produces a
AB  - one--nt 5' overhang.
ER  -

TY  - JOUR
AU  - Stafford, G.P.
AU  - Chaudhuri, R.R.
AU  - Haraszthy, V.
AU  - Friedrich, V.
AU  - Schaffer, C.
AU  - Ruscitto, A.
AU  - Honma, K.
AU  - Sharma, A.
TI  - Draft Genome Sequences of Three Clinical Isolates of Tannerella forsythia Isolated from Subgingival Plaque from Periodontitis Patients in the United  States.
JO  - Genome Announcements
PY  - 2016
SP  - e01286
EP  - e01216
VL  - 4
AB  - We report the genome sequences of three clinical isolates of Tannerella forsythia from the
AB  - subgingival plaque of periodontitis patients attending clinics at the
AB  - School of Dental Medicine, University at Buffalo. The availability of these
AB  - genome sequences will aid the understanding of the pathogenesis of periodontitis.
ER  -

TY  - JOUR
AU  - Stahl, B.
AU  - Barrangou, R.
TI  - Complete Genome Sequences of Probiotic Strains Bifidobacterium animalis subsp. lactis B420 and Bi-07.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4131
EP  - 4132
VL  - 194
AB  - We present the complete genomes of Bifidobacterium animalis subsp. lactis B420 and Bi-07.
AB  - Comparative genomic analysis with the type strain DSMZ10140 revealed
AB  - 40 to 55 single nucleotide polymorphisms (SNPs) and an indel in a clustered
AB  - regularly interspaced short palindromic repeat (CRISPR) locus. These genetic
AB  - differences provide a molecular basis for strain typing within the two main
AB  - phylogenetic groups of this monomorphic species.
ER  -

TY  - JOUR
AU  - Stahl, B.
AU  - Barrangou, R.
TI  - Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14.
JO  - Genome Announcements
PY  - 2013
SP  - e00376
EP  - e00313
VL  - 1
AB  - We present the 1,991,830-bp complete genome sequence of Lactobacillus acidophilus strain La-14
AB  - (SD-5212). Comparative genomic analysis revealed 99.98% similarity
AB  - overall to the L. acidophilus NCFM genome. Globally, 111 single nucleotide
AB  - polymorphisms (SNPs) (95 SNPs, 16 indels) were observed throughout the genome.
AB  - Also, a 416-bp deletion in the LA14_1146 sugar ABC transporter was identified.
ER  -

TY  - JOUR
AU  - Stahl, F.
AU  - Wende, W.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 6175
EP  - 6180
VL  - 93
AB  - Type II restriction endonucleases are dimers of two identical subunits that together form one
AB  - binding site for the double-stranded DNA substrate.  Cleavage within the palindromic
AB  - recognition site occurs in the two strands of the duplex in a concerted manner, due to the
AB  - action of two catalytic centers, one per subunit.  To investigate how the two identical
AB  - subunits of the restriction endonuclease EcoRV cooperate in binding and cleaving their
AB  - substrate, heterodimeric versions of EcoRV with different amino acid substitutions in the two
AB  - subunits were constructed.  For this purpose, the ecorV gene was fused to the coding region
AB  - for the glutathione-binding domain of the glutathione S-transferase and a His6-tag,
AB  - respectively.  Upon cotransformation of Escherichia coli cells with both gene fusions stable
AB  - homo- and heterodimers of the EcoRV variants are produced, which can be separated and purified
AB  - to homogeneity by affinity chromatography over Ni-nitrilotriacetic acid and glutathione
AB  - columns.  A steady-state kinetic analysis shows that the activity of a heterodimeric variant
AB  - with one inactive catalytic center is decreased by 2-fold, demonstrating that the two
AB  - catalytic centers operate independently from each other.  In contrast, heterodimeric variants
AB  - with a defect in one DNA-binding site have a 30- to 50-fold lower activity, indicating that
AB  - the two subunits of EcoRV cooperate in the recognition of the palindromic DNA sequence.  By
AB  - combining a subunit with an inactive catalytic center with a subunit with a defect in the
AB  - DNA-binding site, EcoRV heterodimers were produced that only nick DNA specifically within the
AB  - EcoRV recognition sequence.
ER  -

TY  - JOUR
AU  - Stahl, F.
AU  - Wende, W.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis.
JO  - Biol. Chem.
PY  - 1998
SP  - 467
EP  - 473
VL  - 379
AB  - Three different mechanisms have been proposed to describe DNA cleavage by the type II
AB  - restriction endonuclease EcoRV, which differ in the number and function of metal ions directly
AB  - involved in catalysis and the different roles assigned to amino acid residues in the active
AB  - sites and a phosphate group of the substrate.  There are only four acidic amino acid residues
AB  - close to the scissile bond: the essential Asp74 and Asp90, the non-essential Glu45, and Asp36.
AB  - We show here that Asp36 can be exchanged for alanine, with only minor effects on the cleavage
AB  - rate of the nearby phosphodiester bond, excluding that Asp36 could be directly involved in
AB  - catalysis.  Hence, the two versions of the two-metal-ion mechanism are not compatible with the
AB  - experimental data, because too few ligands for two metal ions are present near the active site
AB  - of EcoRV.  Our result, thus, supports the one-metal-ion mechanism for EcoRV.  We suggest that
AB  - Asp36 has an allosteric effect by which specific contacts between one strand of the DNA and
AB  - one subunit of the enzyme trigger the activation of one catalytic center.  Given the similar
AB  - structures of the active sites of EcoRV, EcoRI, BamHI, PvuII and FokI, as well as the
AB  - occurrence of a characteristic catalytic motif in several other restriction enzymes, we
AB  - conclude that these enzymes most likely share a similar mechanism of DNA cleavage, whose
AB  - characteristic feature is the involvement of only one Mg2+ ion in catalysis.
ER  -

TY  - JOUR
AU  - Stahl, F.
AU  - Wende, W.
AU  - Wenz, C.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Intra- vs intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr37 and Lys38 involved in indirect readout are only important for the catalytic activity of their own subunit.
JO  - Biochemistry
PY  - 1998
SP  - 5682
EP  - 5688
VL  - 37
AB  - EcoRV is a dimer of two identical subunits which together form one binding site for the
AB  - double-stranded DNA substrate.  Concerted cleavage of both strands of the duplex requires
AB  - intersubunit communication to synchronize the two catalytic centers of EcoRV.  Here we address
AB  - the question of how contacts to the DNA backbone trigger conformational changes which lead to
AB  - the activation of both catalytic centers.  The structure of the specific EcoRV-DNA complex
AB  - shows that a region including amino acids Thr37 and Lys38 is involved in interactions with the
AB  - DNA backbone and is a candidate for intersubunit communication.  Homodimeric EcoRV T37A and
AB  - K38A variants have a 1000-fold reduced catalytic activity.  To examine whether Thr37 and Lys38
AB  - of one subunit affect the catalytic center in the same subunit and/or in the other subunit, we
AB  - have produced heterodimeric variants containing a Thr37-Ala or Lys38-Ala substitution in one
AB  - subunit combined with a wild type subunit or with a subunit which contains an amino acid
AB  - substitution (Asp90-Ala) in the active site (D90A/T37A and D90A/K38A).  Cleavage experiments
AB  - with supercoiled pAT153 show that wt/T37A and wt/K38A preferentially nick the DNA.  A
AB  - steady-state kinetic analysis of the cleavage of an oligodeoxynucleotide substrate shows that
AB  - the activity of wt/T37A and wt/K38A is half of that of wild type EcoRV, whereas D90A/T37A and
AB  - D90A/K38A are almost inactive.  These results demonstrate that Thr37 and Lys38 affect
AB  - primarily the catalytic center in their own subunit and that both subunits of EcoRV can be
AB  - activated independently of each other.  We suggest that Thr37 and Lys38 control the catalytic
AB  - activity of the active site in their own subunit by positioning a-helix B.
ER  -

TY  - JOUR
AU  - Stakenas, P.S.
AU  - Zaretskaya, N.M.
AU  - Maneliene, Z.P.
AU  - Mauricas, M.M.
AU  - Butkus, V.V.
AU  - Yanulaitis, A.A.
TI  - MunI mycoplasmic restriction-modification system and its possible role in pathogenesis.
JO  - Mol. Biol. (Mosk)
PY  - 1992
SP  - 546
EP  - 557
VL  - 26
AB  - A restriction-modification system named R-M MunI, isolated from Friend's murine
AB  - erythroleukemia cells, was purified and characterized. This site-specific endonuclease
AB  - recognizes and cleaves the 5'-C'AATTG nucleotide sequence and is an isoschizomer of the MfeI
AB  - restrictase from Mycoplasma fermentans. Site-specific methylation modifies the second adenine
AB  - residue in the same sequence (5'-CAm6ATTG). It was shown that this enzyme system is from a
AB  - Mycoplasma that contaminates the cell line. The Mycoplasma's DNA hybridizes with
AB  - species-specific probes for M. fermentans and Mycoplasma arginini. The possible role of
AB  - mycoplasmic restriction-modification enzymes in the pathogenesis of aquired immune deficiency
AB  - syndrome is discussed.
ER  -

TY  - JOUR
AU  - Stamler, R.A.
AU  - Vereecke, D.
AU  - Zhang, Y.
AU  - Schilkey, F.
AU  - Devitt, N.
AU  - Randall, J.J.
TI  - Complete Genome and Plasmid Sequences for Rhodococcus fascians D188 and Draft Sequences for Rhodococcus Isolates PBTS 1 and PBTS 2.
JO  - Genome Announcements
PY  - 2016
SP  - e00495
EP  - e00416
VL  - 4
AB  - Rhodococcus fascians, a phytopathogen that alters plant development, inflicts significant
AB  - losses in plant production around the world. We report here the
AB  - complete genome sequence of R. fascians D188, a well-characterized model isolate,
AB  - and Rhodococcus species PBTS (pistachio bushy top syndrome) 1 and 2, which were
AB  - shown to be responsible for a disease outbreak in pistachios.
ER  -

TY  - JOUR
AU  - Stamm, L.V.
AU  - Greene, S.R.
AU  - Barnes, N.Y.
AU  - Bergen, H.L.
AU  - Hardham, J.M.
TI  - Identification and characterization of a Treponema pallidum subsp. pallidum gene encoding a DNA adenine methyltransferase.
JO  - FEMS Microbiol. Lett.
PY  - 1997
SP  - 115
EP  - 119
VL  - 155
AB  - The nucleotide sequence of a DNA adenine methyltransferase gene from Treponema pallidum has
AB  - been determined.  Southern blot analysis of T. pallidum chromosomal DNA indicated that this
AB  - gene is present as a single copy.  The dam gene encodes a 303 amino acid protein whose deduced
AB  - sequence has significant homology with DNA (N6-adenine) methyltransferases.  T. pallidum Dam
AB  - can be assigned to group alpha DNA amino methyltransferases based on the order of nine
AB  - conserved motifs that are present in the protein.  Digests of T. pallidum chromosomal DNA
AB  - performed with isoschizomer restriction endonucleases (Sau3AI, DpnI, and MboI) confirmed the
AB  - presence of methylated adenine residues in GATC sequences (Dam+ phenotype).
ER  -

TY  - JOUR
AU  - Stampeggioni, E.
AU  - Palitti, F.
AU  - Carotti, D.
TI  - A convenient assay for DNA methyltransferase.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 226
EP  - 226
VL  - 13D
AB  - Assaying DNA methylase by measuring transfer of tritium from the 5 position of
AB  - DNA cytosine to water rather than labelled methyl transfer from S-adenosyl
AB  - methionine to DNA cuts post-incubation procedures from hours to minutes.  The
AB  - methodology and validating data obtained in our laboratory will be presented.
ER  -

TY  - JOUR
AU  - Stamps, B.W.
AU  - Corsetti, F.A.
AU  - Spear, J.R.
AU  - Stevenson, B.S.
TI  - Draft genome of a novel chlorobi member assembled by tetranucleotide binning of a hot spring metagenome.
JO  - Genome Announcements
PY  - 2014
SP  - e00897
EP  - e00814
VL  - 2
AB  - The genome of a member of the phylum Chlorobi was assembled from a shotgun metagenomic
AB  - sequence of a hot spring in Mammoth Lakes, CA. This organism appears
AB  - to be a novel, aerobic, photosynthetic Chlorobi member, expanding the knowledge
AB  - of this underrepresented phylum.
ER  -

TY  - JOUR
AU  - Stamps, B.W.
AU  - Losey, N.A.
AU  - Lawson, P.A.
AU  - Stevenson, B.S.
TI  - Genome Sequence of Thermoanaerobaculum aquaticum MP-01T, the First Cultivated Member of Acidobacteria Subdivision 23, Isolated from a Hot Spring.
JO  - Genome Announcements
PY  - 2014
SP  - e00570
EP  - e00514
VL  - 2
AB  - Thermoanaerobaculum aquaticum MP-01(T) is currently the only cultivated and described member
AB  - of Acidobacteria subdivision 23. Here, we report the genome
AB  - sequence for this novel microorganism that was isolated from a hot spring.
ER  -

TY  - JOUR
AU  - Stamps, B.W.
AU  - Zingarelli, S.
AU  - Hung, C.S.
AU  - Drake, C.A.
AU  - Varaljay, V.A.
AU  - Stevenson, B.S.
AU  - Crookes-Goodson, W.J.
TI  - Finished Genome Sequence of a Polyurethane-Degrading Pseudomonas Isolate.
JO  - Genome Announcements
PY  - 2018
SP  - e00084
EP  - e00018
VL  - 6
AB  - Pseudomonas sp. strain WP001 is a laboratory isolate capable of polyurethane polymer
AB  - degradation and harbors a predicted lipase precursor gene. The genome of
AB  - strain WP001 is 6.15 Mb in size and is composed of seven scaffolds with a G+C
AB  - content of 60.54%. Strain WP001 is closely related to Pseudomonas fluorescens
AB  - based on ribosomal DNA comparisons.
ER  -

TY  - JOUR
AU  - Stanchev, B.S.
AU  - Grokhovskii, S.L.
AU  - Khorlin, A.A.
AU  - Gottikh, B.P.
AU  - Zhuze, A.L.
AU  - Skamrov, A.V.
AU  - Bibilashvili, R.S.
TI  - Netropsin, distamycin A, bis-netropsins as selective inhibitors of the effect of restrictases and DNaseI.
JO  - Mol. Biol. (Mosk)
PY  - 1986
SP  - 1614
EP  - 1624
VL  - 20
AB  - The influence was investigated of netropsin, a number of bis-netropsins, and
AB  - distamycin A on hydrolysis of DNA fragments by restrictases.  In parallel to
AB  - inhibition of hydrolysis, binding sites were determined for ligands on the same
AB  - DNA fragments according to shielding from partial hydrolysis by DNaseI
AB  - (footprinting).  Combined analysis of ligand binding sites with their capacity
AB  - for inhibition of hydrolysis led to the following conclusions.  1) Inhibition
AB  - of the effect of restrictases by these ligands is associated with formation of
AB  - a complex of ligand with the recognition site on DNA.  Experimental results
AB  - obtained permit definition of the zone required for overlapping of the site of
AB  - restrictase recognition and the binding site of ligand at +/- nucleotides from
AB  - the axis of symmetry of the site of restrictase recognition.  The overlapping
AB  - of the site occupied by one molecule of ligand with the restrictase recognition
AB  - site is not an adequate condition for complete inhibition of hydrolysis.  2)
AB  - Based on known specificity of netropsin for a nucleotide sequence, the
AB  - restrictase recognition sites can be predicted at which inhibition of
AB  - hydrolysis of DNA by restrictases will be observed.  3)  Netropsin and
AB  - bis-netropsins display differing specificities and can be used for selective
AB  - inhibition of restrictases at different recognition sites.
ER  -

TY  - JOUR
AU  - Stancheva, I.
AU  - Hensey, C.
AU  - Meehan, R.R.
TI  - Loss of the maintenance methyltransferase, xDnmt1, induces apoptosis in Xenopus embryos.
JO  - EMBO J.
PY  - 2001
SP  - 1963
EP  - 1973
VL  - 20
AB  - DNA methylation is necessary for normal embryogenesis in animals. Here we show that loss of
AB  - the maintenance methyltransferase, xDnmt1p, triggers an apoptotic response during Xenopus
AB  - development, which accounts for the loss of specific cell populations in hypomethylated
AB  - embryos. Hypomethylation-induced apoptosis is accompanied by a stabilization in xp53 protein
AB  - levels after the mid-blastula transition. Ectopic expression of HPV-E6, which promotes xp53
AB  - degradation, prevents cell death, implying that the apoptotic signal is mediated by xp53. In
AB  - addition, inhibition of caspase activation by overexpression of Bcl-2 results in the
AB  - development of cellular masses that resemble embryonic blastomas. Embryonic tissue explant
AB  - experiments suggest that hypomethylation alters the developmental potential of early embryo
AB  - cells and that apoptosis is triggered by differentiation. Our results imply that loss of DNA
AB  - methylation in differentiated somatic cells provides a signal via p53 that activates cell
AB  - death pathways.
ER  -

TY  - JOUR
AU  - Stancheva, I.
AU  - Koller, T.
AU  - Sogo, J.M.
TI  - Asymmetry of Dam remethylation on the leading and lagging arms of plasmid replicative intermediates.
JO  - EMBO J.
PY  - 1999
SP  - 6542
EP  - 6551
VL  - 18
AB  - In Escherichia coli, adenine methylation at the sequence GATC allows coupling of cellular
AB  - processes to chromosome replication and the cell cycle. The transient presence of
AB  - hemimethylated DNA after replication facilitates post-replicative mismatch repair, induces
AB  - transcription of some genes and allows transposition of mobile elements. We were interested in
AB  - estimating the half-life of hemimethylated DNA behind the replication fork in plasmid
AB  - molecules and in determining whether Dam methyltransferase restores N6 adenine methylation
AB  - simultaneously on both replicative arms. We show that remethylation takes place asynchronously
AB  - on the leading and lagging daughter strands shortly after replication. On the leading arm the
AB  - fully methylated adenine is restored ~2000 bp (corresponding to 2 s) behind the replication
AB  - fork, while remethylation takes twice as long (at 3500-4000 bp or ~3.5-4 s) on the lagging
AB  - replicative arm. This observation suggests that Dam remethylation of the lagging arm requires
AB  - ligated Okazaki fragments.
ER  -

TY  - JOUR
AU  - Stancheva, I.
AU  - Meehan, R.R.
TI  - Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos.
JO  - Genes Dev.
PY  - 2000
SP  - 313
EP  - 327
VL  - 14
AB  - In Xenopus laevis zygotic transcription begins at the midblastula
AB  - transition (MBT). Prior to this the genome is organized into chromatin
AB  - that facilitates rapid cycles of DNA replication but not transcription.
AB  - Here we demonstrate that DNA methylation contributes to the overall
AB  - transcriptional silencing before MBT. Transient depletion of the maternal
AB  - DNA methyltransferase (xDnmt1) by anti sense RNA during cleavage stages is
AB  - associated with a decrease in the genomic 5-methyl-cytosine content and
AB  - leads to the activation of zygotic transcription approximately two cell
AB  - cycles earlier than normal. Hypomethylation allows the early expression of
AB  - mesodermal marker genes such as Xbra, Cerberus, and Otx2, which are
AB  - subsequently down-regulated during gastrulation of the xDnmt1-depleted
AB  - embryos. The temporal switch in gene expression may account for the
AB  - appearance of body plan defects that we observe. Loss of xDnmt1 can be
AB  - rescued by the coinjection of mouse or human Dnmt1 protein. These results
AB  - demonstrate that DNA methylation has a role in the regulation of
AB  - immediately early genes in Xenopus at MBT.
ER  -

TY  - JOUR
AU  - Stanford, N.P.
AU  - Halford, S.E.
AU  - Baldwin, G.S.
TI  - DNA cleavage by the EcoRV restriction endonuclease: pH dependence and proton transfers in catalysis.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 105
EP  - 116
VL  - 288
AB  - To characterize the pH dependence of phosphodiester hydrolysis by the EcoRV endonuclease in
AB  - the presence of Mn2+, single turnover reactions on a 12 bp DNA substrate were examined by
AB  - stopped-flow and quench-flow methods between pH 6.0 and 8.5.  At each pH value, the apparent
AB  - rate constants for phosphodiester hydrolysis increased hyperbolically with the concentration
AB  - of MnCl2, thus allowing values to be determined for the intrinsic rate constant at saturation
AB  - with Mn2+ and the equilibrium dissociation constant for Mn2+.  The equilibrium constants
AB  - showed no systematic variation across the pH range tested, while the rate constants increased
AB  - steeply with increasing pH up to an asymptote above pH 7.5.  At low pH conditions, the
AB  - gradient of a plot of log (rate constant) against pH approached a value of 2.  DNA cleavage by
AB  - EcoRV thus requires the de-protonation of two acidic groups.  To determine whether aspartate
AB  - 36 is one of the groups, mutants of EcoRV were made with other amino acid residues at position
AB  - 36.  Glutamate caused a partial loss of activity, while all other replacements gave near-zero
AB  - activities.  In contrast to wild-type EcoRV, the mutant with glutamate required the
AB  - de-protonation of only one acidic group for DNA cleavage.  A mechanism for EcoRV is proposed
AB  - in which the water molecule that hydrolyses the phosphodiester bond is de-protonated by two
AB  - Bronsted bases, probably the ionized forms of aspartate 36 and glutamate 45.
ER  -

TY  - JOUR
AU  - Stanford, N.P.
AU  - Szczelkun, M.D.
AU  - Marko, J.F.
AU  - Halford, S.E.
TI  - One- and three-dimensional pathways for proteins to reach specific DNA sites.
JO  - EMBO J.
PY  - 2000
SP  - 6546
EP  - 6557
VL  - 19
AB  - Proteins that interact with specific DNA sites bind to DNA at random and then translocate to
AB  - the target site. This may occur by one-dimensional diffusion along the DNA, or through
AB  - three-dimensional space via multiple dissociation/re-associations. To distinguish these
AB  - routes, reactions of the EcoRV endonuclease were studied on substrates with two EcoRV sites
AB  - separated by varied distances. The fraction of encounters between the DNA and the protein that
AB  - resulted in the processive cleavage of both sites decreased as the length of intervening DNA
AB  - was increased, but not in the manner demanded for one-dimensional diffusion. The variation in
AB  - processivity with inter-site spacing shows instead that protein moves from one site to another
AB  - through three-dimensional space, by successive dissociation/re-associations, though each
AB  - re-association to a new site is followed by a search of the DNA immediately adjacent to that
AB  - site.  Although DNA-binding proteins are usually thought to find their target sites by
AB  - one-dimensional pathways, three-dimensional routes may be more common than previously
AB  - anticipated.
ER  -

TY  - JOUR
AU  - Stankevicius, K.
AU  - Lubys, A.
AU  - Timinskas, A.
AU  - Janulaitis, A.
TI  - Bpu10I restriction endonuclease is composed of two nonidentical subunits.
JO  - Biologija
PY  - 1996
SP  - 51
EP  - 53
VL  - 0
AB  - The genes of the Bpu10I restriction-modification (RM) system have been cloned and sequenced.
AB  - Nucleotide sequence analysis revealed four major open reading frames oriented tandemly.
AB  - Comparison of amino acid sequences, subcloning and deletion mapping experiments have been
AB  - applied to investigate all ORFs mentioned. ORFI and ORFII correspond to two
AB  - m5C-methyltransferases.  Four conserved aa blocks including the EXK motif, which is known to
AB  - be involved in the active center formation of restriction endonucleases, were detected by
AB  - comparing aa sequences of ORFIII with ORFIV.  It was demonstrated that the dsDNA could be
AB  - hydrolysed specifically only in the presence of both ORFIII and ORFIV intact, indicating that
AB  - Bpu10I Enase is composed from two heterosubunits.
ER  -

TY  - JOUR
AU  - Stankevicius, K.
AU  - Lubys, A.
AU  - Timinskas, A.
AU  - Vaitkevicius, D.
AU  - Janulaitis, A.
TI  - Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 1084
EP  - 1091
VL  - 26
AB  - The Bpu10I R-M system from Bacillus pumilus 10, which recognizes the asymmetric 5'-CCTNAGC
AB  - sequence, has been cloned, sequenced and expressed in Escherichia coli.  The system comprises
AB  - four adjacent, similarly oriented genes encoding two m5C MTases and two subunits of Bpu10I
AB  - ENase (34.5 and 34 kDa).  Both Bpu10IR genes either in cis or trans are needed for the
AB  - manifestation of R.Bpu10I activity.  Subunits of R.Bpu10I, purified to apparent homogeneity,
AB  - are both required for cleavage activity. This heterosubunit structure distinguishes the Bpu10I
AB  - restriction endonuclease from all other type II restriction enzymes described previously.  The
AB  - subunits reveal 25% amino acid identity.  Significant similarity was also identified between a
AB  - 43 amino acid region of R.DdeI and one of the regions of higher identity shared between the
AB  - Bpu10I subunits, a region that could possibly include the catalytic/Mg2+ binding center.  The
AB  - similarity between Bpu10I and DdeI Mtases is not limited to the conserved motifs typical for
AB  - m5C MTases.  It extends into the variable region that lies between CMs VIII and IX.
AB  - Duplication of a progenitor gene, encoding an enzyme recognizing a symmetric nucleotide
AB  - sequence, followed by concerted divergent evolution, may provide a possible scenario leading
AB  - to the emergence of the Bpu10I ENase, which recognizes an overall asymmetric sequence and
AB  - cleaves within it symmetrically.
ER  -

TY  - JOUR
AU  - Stankevicius, K.
AU  - Povilionis, P.
AU  - Lubys, A.
AU  - Menkevicius, S.
AU  - Janulaitis, A.
TI  - Cloning and characterization of the unusual restriction-modification system comprising two restriction endonucleases and one methyltransferase.
JO  - Gene
PY  - 1995
SP  - 49
EP  - 53
VL  - 157
AB  - An Escherichia coli RFL47 DNA fragment containing the Eco47IR and Eco47II
AB  - restriction-modification (R-M) system has been cloned and sequenced.  A clone carrying this
AB  - system has been selected by its ability to restrict phage lambda in vivo.  The sequence of
AB  - 5360 bp was determined, and its analysis revealed three major open reading frames (ORF)
AB  - corresponding to two restriction endonucleases (ENases) and one DNA methyltransferase (MTase):
AB  - R.Eco47II (239 amino acids (aa)), R.Eco47I (230 aa) and M.Eco47II (417 aa).  The M.Eco47II
AB  - aa  sequence possesses all conserved domains typical for m5C MTases and its variable region
AB  - has a  high homology with M.Sau96I and M.SinI.  The ORF harboring a predicted helix-turn-helix
AB  - motif  upstream from the eco47IR gene has been found.  No sequence resembling the eco47IM
AB  - gene has been detected in the complete fragment sequenced, although disrupted ORF, possibly
AB  - corresponding to the transposase-encoding gene, has been found in the intergenic area between
AB  - eco47IIM and eco47IR.  No homology was found between the ENases; however, both revealed
AB  - homology with their isoschizomers, R.SinI and R.Sau96I.
ER  -

TY  - JOUR
AU  - Stankevicius, K.
AU  - Timinskas, A.
TI  - Expression autoregulation of the Eco47II methyltransferase gene.
JO  - Biologija
PY  - 1996
SP  - 54
EP  - 56
VL  - 0
AB  - Amino acid sequence analysis revealed a strong helix-turn-helix motif in the N-terminus of the
AB  - M.Eco47II, with a standard deviation of 7.1.  The autoregulatory mechanism of the expression
AB  - of the eco47IIM gene has been proved by using the lacZ fusion technique.  We have demonstrated
AB  - that the HTH motif of M.Eco47II is necessary for the repression of the M.Eco47II promoter but
AB  - not for the methylation of the DNA target.  Mutation in the catalytic center of M.Eco47II
AB  - strongly reduces the methylation function, but has no effect on repression.
ER  -

TY  - JOUR
AU  - Stanley, E.
AU  - Walsh, L.
AU  - van der Zwet, A.
AU  - Fitzgerald, G.F.
AU  - van Sinderen, D.
TI  - Identification of four loci isolated from two Streptococcus thermophilus phage genomes responsible for mediating bacteriophage resistance.
JO  - FEMS Microbiol. Lett.
PY  - 2000
SP  - 271
EP  - 277
VL  - 182
AB  - Sequence data derived from the Streptococcus thermophilus phages phiO1205 and phi7201
AB  - indicated that each of these phages contains a distinct DNA
AB  - region dedicated to replication. Southern blotting experiments showed that
AB  - phages infecting S. thermophilus may be divided into at least two groups,
AB  - each containing the presumptive replication functions of either
ER  -

TY  - JOUR
AU  - Stanley, L.K.
AU  - Seidel, R.
AU  - van der Scheer, C.
AU  - Dekker, N.H.
AU  - Szczelkun, M.D.
AU  - Dekker, C.
TI  - When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124l.
JO  - EMBO J.
PY  - 2006
SP  - 2230
EP  - 2239
VL  - 25
AB  - Using a combination of single molecule and bulk solution measurements, we have examined the
AB  - DNA translocation activity of a helicase, the Type
AB  - I restriction modification enzyme EcoR124I. We find that EcoR124I can
AB  - translocate past covalent interstrand crosslinks, inconsistent with an
AB  - obligatory unwinding mechanism. Instead, translocation of the intact
AB  - dsDNA occurs principally via contacts to the sugar-phosphate backbone
AB  - and bases of the 30 - 50 strand; contacts to the 50 - 30 strand are not
AB  - essential for motion but do play a key role in stabilising the motor on
AB  - the DNA. A model for dsDNA translocation is presented that could be
AB  - applicable to a wide range of other enzyme complexes that are also
AB  - labelled as helicases but which do not have actual unwinding activity.
ER  -

TY  - JOUR
AU  - Stanley, L.K.
AU  - Szczelkun, M.D.
TI  - Direct and random routing of a molecular motor protein at a DNA junction.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 4387
EP  - 4394
VL  - 34
AB  - With the aim of investigating how motor proteins negotiate DNA nanostructures, we produced
AB  - test circuits based on recombination
AB  - intermediates in which 1D translocation across a Holliday junction (HJ)
AB  - could be assessed by subsequent triplex displacement signals on each
AB  - DNA arm. Using the EcoR124I restriction-modification enzyme, a 3'-5'
AB  - double-strand DNA (dsDNA) translocase, we could show that the motor
AB  - will tend to follow its translocated strand across a junction.
AB  - Nonetheless, as the frequency of junction bypass events increases, the
AB  - motor will occasionally jump tracks.
ER  -

TY  - JOUR
AU  - Starikov, A.Y.
AU  - Usserbaeva, A.A.
AU  - Sinetova, M.A.
AU  - Sarsekeyeva, F.K.
AU  - Zayadan, B.K.
AU  - Ustinova, V.V.
AU  - Kupriyanova, E.V.
AU  - Los, D.A.
AU  - Mironov, K.S.
TI  - Draft Genome Sequence of Cyanobacterium sp. Strain IPPAS B-1200 with a Unique Fatty Acid Composition.
JO  - Genome Announcements
PY  - 2016
SP  - e01306
EP  - e01316
VL  - 4
AB  - Here, we report the draft genome of Cyanobacterium sp. IPPAS strain B-1200, isolated from Lake
AB  - Balkhash, Kazakhstan, and characterized by the unique fatty
AB  - acid composition of its membrane lipids, which are enriched with myristic and
AB  - myristoleic acids. The approximate genome size is 3.4 Mb, and the predicted
AB  - number of coding sequences is 3,119.
ER  -

TY  - JOUR
AU  - Starkenburg, S.R.
AU  - Larimer, F.W.
AU  - Stein, L.Y.
AU  - Klotz, M.G.
AU  - Chain, P.S.G.
AU  - Sayavedra-Soto, L.A.
AU  - Poret-Peterson, A.T.
AU  - Gentry, M.E.
AU  - Arp, D.J.
AU  - Ward, B.
AU  - Bottomley, P.J.
TI  - Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobactei.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 2852
EP  - 2863
VL  - 74
AB  - The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative
AB  - chemolithoautotroph that conserves energy
AB  - from the oxidation of nitrite to nitrate. Sequencing and analysis of
AB  - the Nitrobacter hamburgensis X14 genome revealed four replicons
AB  - comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and
AB  - 121 kbp). Over 20% of the genome is composed of pseudogenes and
AB  - paralogs. Whole-genome comparisons were conducted between N.
AB  - hamburgensis and the finished and draft genome sequences of Nitrobacter
AB  - winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of
AB  - the plasmid-borne genes were unique to N. hamburgensis and encode a
AB  - variety of functions (central metabolism, energy conservation,
AB  - conjugation, and heavy metal resistance), yet similar to 21 kb of a
AB  - similar to 28-kb "autotrophic" island on the largest plasmid was
AB  - conserved in the chromosomes of Nitrobacter winogradskyi Nb-255 and
AB  - Nitrobacter sp. strain Nb-311A. The N. hamburgensis chromosome also
AB  - harbors many unique genes, including those for heme-copper oxidases,
AB  - cytochrome b(561), and putative pathways for the catabolism of
AB  - aromatic, organic, and one-carbon compounds, which help verify and
AB  - extend its mixotrophic potential. A Nitrobacter "subcore" genome was
AB  - also constructed by removing homologs found in strains of the closest
AB  - evolutionary relatives, Bradyrhizobium japonicum and Rhodapseudomonas
AB  - palustris. Among the Nitrobacter subcore inventory (116 genes), copies
AB  - of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes
AB  - associated with a dissimilatory nitrite reductase (NirK), PII-like
AB  - regulators, and polysaccharide formation were identified. Many of the
AB  - subcore genes have diverged significantly from, or have origins
AB  - outside, the alphaproteobacterial lineage and may indicate some of the
AB  - unique genetic requirements for nitrite oxidation in Nitrobacter.
ER  -

TY  - JOUR
AU  - Starkenburg, S.R.
AU  - Reitenga, K.G.
AU  - Freitas, T.
AU  - Johnson, S.
AU  - Chain, P.S.
AU  - Garcia-Pichel, F.
AU  - Kuske, C.R.
TI  - Genome of the Cyanobacterium Microcoleus vaginatus FGP-2, a Photosynthetic Ecosystem Engineer of Arid Land Soil Biocrusts Worldwide.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4569
EP  - 4570
VL  - 193
AB  - The filamentous cyanobacterium, Microcoleus vaginatus, is found in arid land soils worldwide.
AB  - The genome of M. vaginatus strain FGP-2 allows exploration of genes involved in
AB  - photosynthesis, desiccation tolerance, alkane production, and other features contributing to
AB  - this organism's ability function as a major component of biological soil crusts in arid
AB  - lands.
ER  -

TY  - JOUR
AU  - Starns, D.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Iino, T.
AU  - Yuki, M.
AU  - Inoue, J.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Darby, A.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Cytophaga fermentans JCM 21142T, a Facultative Anaerobe  Isolated from Marine Mud.
JO  - Genome Announcements
PY  - 2014
SP  - e00206
EP  - e00214
VL  - 2
AB  - Cytophaga fermentans strain JCM 21142(T) is a marine-dwelling facultative anaerobe. The draft
AB  - genome sequence of this strain revealed its diverse
AB  - chemoorganotrophic potential, which makes it capable of metabolizing various
AB  - polysaccharide substrates. The genome data will facilitate further studies on its
AB  - taxonomic reclassification, its metabolism, and the mechanisms pertaining to
AB  - bacterial gliding.
ER  -

TY  - JOUR
AU  - Starodumova, I.P.
AU  - Tarlachkov, S.V.
AU  - Prisyazhnaya, N.V.
AU  - Dorofeeva, L.V.
AU  - Ariskina, E.V.
AU  - Chizhov, V.N.
AU  - Subbotin, S.A.
AU  - Evtushenko, L.I.
AU  - Vasilenko, O.V.
TI  - Draft Genome Sequence of Rathayibacter sp. Strain VKM Ac-2630 Isolated from Leaf  Gall Induced by the Knapweed Nematode Mesoanguina picridis on Acroptilon repens.
JO  - Genome Announcements
PY  - 2017
SP  - e00650
EP  - e00617
VL  - 5
AB  - A draft genome sequence of Rathayibacter sp. strain VKM Ac-2630 was derived using Ion Torrent
AB  - sequencing technology. The genome size of this strain is 3.88 Mb,
AB  - with an average G+C content of 72.0%. Genomic evidence of an aerobic mode of
AB  - respiration and a heterotrophic lifestyle of this bacterium was obtained.
ER  -

TY  - JOUR
AU  - Staudova, B.
AU  - Strouhal, M.
AU  - Zobanikova, M.
AU  - Cejkova, D.
AU  - Fulton, L.L.
AU  - Chen, L.
AU  - Giacani, L.
AU  - Centurion-Lara, A.
AU  - Bruisten, S.M.
AU  - Sodergren, E.
AU  - Weinstock, G.M.
AU  - Smajs, D.
TI  - Whole Genome Sequence of the Treponema pallidum subsp. endemicum Strain Bosnia A: The Genome Is Related to Yaws Treponemes but Contains Few Loci Similar to Syphilis Treponemes.
JO  - PLoS Neglected Trop. Dis.
PY  - 2014
SP  - E3261
EP  - E3261
VL  - 8
AB  - BACKGROUND: T. pallidum subsp. endemicum (TEN) is the causative agent of bejel
AB  - (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are
AB  - overlapping and the epidemiological context is important for correct diagnosis of
AB  - both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum
AB  - (TPA), TEN infections are usually spread by direct contact or contaminated
AB  - utensils rather than by sexual contact. Bejel is most often seen in western
AB  - Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in
AB  - Bosnia, southern Europe. METHODOLOGY/PRINCIPAL FINDINGS: The complete genome of
AB  - the Bosnia A strain was amplified and sequenced using the pooled segment genome
AB  - sequencing (PSGS) method and a combination of three next-generation sequencing
AB  - techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total
AB  - combined average genome coverage of 513x was achieved. The size of the Bosnia A
AB  - genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously
AB  - published genomes of uncultivable pathogenic treponemes. Conserved gene synteny
AB  - was found in the Bosnia A genome compared to other sequenced syphilis and yaws
AB  - treponemes. The TEN Bosnia A genome was distinct but very similar to the genome
AB  - of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN
AB  - Bosnia A genome was found to contain several sequences, which so far, have been
AB  - uniquely identified only in syphilis treponemes. CONCLUSIONS/SIGNIFICANCE: The
AB  - genome of TEN Bosnia A contains several sequences thought to be unique to TPA
AB  - strains; these sequences very likely represent remnants of recombination events
AB  - during the evolution of TEN treponemes. This finding emphasizes a possible role
AB  - of repeated horizontal gene transfer between treponemal subspecies in shaping the
AB  - Bosnia A genome.
ER  -

TY  - JOUR
AU  - Stecker, C.
AU  - Johann, A.
AU  - Herzberg, C.
AU  - Averhoff, B.
AU  - Gottschalk, G.
TI  - Complete nucleotide sequence and genetic organization of the 210-Kilobase linear plasmid of Rhodococcus erythropolis BD2.
JO  - J. Bacteriol.
PY  - 2003
SP  - 5269
EP  - 5274
VL  - 185
AB  - The complete nucleotide sequence of the linear plasmid pBD2 from Rhodococcus erythropolis BD2
AB  - comprises 210,205 bp. Sequence analyses of
AB  - pBD2 revealed 212 putative open reading frames (ORFs), 97 of which had an
AB  - annotatable function. These ORFs could be assigned to six functional
AB  - groups: plasmid replication and maintenance, transport and
AB  - metalloresistance, catabolism, transposition, regulation, and protein
AB  - modification. Many of the transposon-related sequences were found to flank
AB  - the isopropylbenzene pathway genes. This finding together with the
AB  - significant sequence similarities of the ipb genes to genes of the linear
AB  - plasmid-encoded biphenyl pathway in other rhodococci suggests that the ipb
AB  - genes were acquired via transposition events and subsequently distributed
AB  - among the rhodococci via horizontal transfer.
ER  -

TY  - JOUR
AU  - Steczkiewicz, K.
AU  - Muszewska, A.
AU  - Knizewski, L.
AU  - Rychlewski, L.
AU  - Ginalski, K.
TI  - Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 7016
EP  - 7045
VL  - 40
AB  - Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse
AB  - superfamily with representatives involved in replication, restriction, DNA repair and
AB  - tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi
AB  - anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and
AB  - classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such
AB  - efforts are complicated, because the superfamily exhibits extreme sequence and structural
AB  - divergence. Using advanced homology detection methods supported with superfamily-wide domain
AB  - architecture and horizontal gene transfer analyses, we provide a comprehensive
AB  - reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases
AB  - span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven
AB  - of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI,
AB  - HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of
AB  - PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small
AB  - numbers of organisms. We observed multiple horizontal gene transfers even between human
AB  - pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly
AB  - elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles
AB  - in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further
AB  - experimental studies aimed at identification of exact biological functions, specific
AB  - substrates and molecular mechanisms of reactions performed by these highly diverse proteins.
ER  -

TY  - JOUR
AU  - Steele, C.L.
AU  - Donaldson, J.R.
AU  - Paul, D.
AU  - Banes, M.M.
AU  - Arick, T.
AU  - Bridges, S.M.
AU  - Lawrence, M.L.
TI  - Genome sequence of lineage III Listeria monocytogenes strain HCC23.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3679
EP  - 3680
VL  - 193
AB  - More than 98% of reported human listeriosis cases are caused by Listeria monocytogenes
AB  - serotypes within lineages I and II. Serotypes within lineage
AB  - III (4a and 4c) are commonly isolated from environmental and food
AB  - specimens. We report the first complete genome sequence of a lineage III
AB  - isolate, HCC23, which will be used for comparative analysis.
ER  -

TY  - JOUR
AU  - Steenson, L.R.
AU  - Klaenhammer, T.R.
TI  - Streptococcus cremoris M12R transconjugants carrying the conjugal plasmid pTR2030 are insensitive to attack by lytic bacteriophages.
JO  - Appl. Environ. Microbiol.
PY  - 1985
SP  - 851
EP  - 858
VL  - 50
AB  - Conjugal transfer of lactose-fermenting ability (Lac+), nisin resistance (Nisr), and phage
AB  - resistance (Hsp+) was demonstrated in mating between Streptococcus lactis ME2 (donor) and
AB  - Streptococcus cremoris M43a (recipient), a derivative of M12R. Transconjugants were detected
AB  - by transfer of Lac+ and were found to exhibit Nisr and harbor a 40-megadalton plasmid
AB  - (pTR1040). Fifty-six percent of Lac+ transconjugants were resistant to the S. cremoris M12R
AB  - lytic phage. Efficiency of plaquing for phage m12r.M12 on a phage-resistant transconjugant,
AB  - T2r-M43a, was <4.3 x 10 -10. Five additional phages which were virulent for S. cremoris M12R
AB  - and isolated from industrial sources failed to plaque on S. cremoris T2r-M43a. Mating
AB  - experiments with T2r-M43a revealed that phage resistance was accompanied by high-frequency
AB  - conjugation ability (Tra+) and the appearance of both pTR1040 and pTR2030 encoding Lac+ Nisr
AB  - and Tra+ Hsp+, respectively, in transconjugants of S. lactis mLM2302. Phage-sensitive Lac+
AB  - transconjugants of S. cremoris M43a. Unlike the S. lactis LM2302 transconjugant carrying
AB  - pTR2030, resistance of T2r-M43a to phage was not affective at high temperatures (35 to 40 deg.
AB  - C) or destabilized in repeated transfers through a starter culture activity test. These
AB  - results demonstrated that phage resistance conferred by pTR2030 in the S. cremoris
AB  - transconjugant was effective against industrially significant phages under fermentation
AB  - conditions normally encountered during cheese manufacture.
ER  -

TY  - JOUR
AU  - Steenson, L.R.
AU  - Klaenhammer, T.R.
TI  - Plasmid heterogeneity in Streptococcus cremoris M12R:  effects on proteolytic activity and host-dependent phage replication.
JO  - J. Dairy Sci.
PY  - 1986
SP  - 2227
EP  - 2236
VL  - 69
AB  - Examination of single colony isolates from a culture of Streptococcus cremoris
AB  - M12R revealed a high degree of variability in plasmid deoxyribonucleic acid
AB  - composition.  Fifty percent of the M12R population displayed proteolytic
AB  - activity and harbored a 13-Mdalton plasmid (pLR2013).  This plasmid was not
AB  - present in proteinase-deficient variants isolated from the culture, which
AB  - provided correlative evidence for linkage of proteinase activity to pLR2013.
AB  - Four percent of the M12R population demonstrated resistance to phage m12r.M12.
AB  - This resistance was identified by restriction and modification activities
AB  - against m12r.M12 phage, which was dependent on the presence of a 20-Md plasmid,
AB  - pLR1020.  Loss of restriction and modification activities was observed upon
AB  - curing of pLR1020.  In conjugal mating studies with Streptococcus lactis ME2,
AB  - transfer frequency of lactose-fermenting ability to a restriction and
AB  - modification-deficient variant of M12R was 100-fold higher than to a variant
AB  - exhibiting restriction and modification activities.  The data provided evidence
AB  - for restriction and modification activities in select S. cremoris M12R variants
AB  - that are linked to pLR1020 and restrict both the plaquing ability of phage and
AB  - efficiency of plasmid transfer by conjugation.
ER  -

TY  - JOUR
AU  - Stefan, C.
AU  - Xia, Y.
AU  - Van Etten, J.L.
TI  - Molecular cloning and characterization of the gene encoding the adenine methyltransferase M.CviRI from Chlorella virus XZ-6E.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 307
EP  - 311
VL  - 19
AB  - The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E
AB  - was cloned and expressed in Escherichia coli.  M.CviRI methylates adenine in
AB  - TGCA sequences.  DNA containing the M.CviRI gene was sequenced and a single
AB  - open reading frame of 1137 bp was identified which could code for a polypeptide
AB  - of 379 amino acids with a predicted molecular weight of 42,814.  Comparison of
AB  - the M.CviRI predicted amino acid sequence with another Chlorella virus and 14
AB  - bacterial adenine methyltransferases revealed extensive similarity to the other
AB  - Chlorella virus enzyme.
ER  -

TY  - JOUR
AU  - Stefanishina, T.V.
AU  - Bogdarina, I.G.
AU  - Buryanov, Y.I.
TI  - Search for the modification-restriction systems.
JO  - Biopol. Kletka
PY  - 1987
SP  - 128
EP  - 131
VL  - 3
AB  - The DNA modification-restriction systems have been studied for their presence
AB  - in 19 Agrobacteria strains, including the virulent ones with Ti-plasmids of
AB  - various classes, the avirulent octopine and nopaline strain derivatives
AB  - obtained by curing the Agrobacteria virulent strains from Ti-plasmids as well
AB  - as natural isolates of avirulent Agrobacteria.  It is shown that the presence
AB  - of the DNA modification-restriction system with EcoRII specificity is a
AB  - characteristic feature of the Agrobacteria octopine strains and of their cured
AB  - avirulent derivatives.  The Agrobacteria nopaline strains, their cured
AB  - avirulent derivatives, and most of the Agrobacteria natural avirulent strains
AB  - contain the DNA modification-restriction systems different from EcoRII.  The
AB  - chromosomal nature of these characters is shown.
ER  -

TY  - JOUR
AU  - Stefanovic, E.
AU  - Casey, A.
AU  - Cotter, P.
AU  - Cavanagh, D.
AU  - Fitzgerald, G.
AU  - McAuliffe, O.
TI  - Draft Genome Sequence of Lactobacillus casei DPC6800, an Isolate with the Potential to Diversify Flavor in Cheese.
JO  - Genome Announcements
PY  - 2016
SP  - e00063
EP  - e00016
VL  - 4
AB  - Lactobacillus casei is a nonstarter lactic acid bacterium commonly present in various types of
AB  - cheeses. It is believed that strains of this species have a
AB  - significant impact on the development of cheese flavor. The draft genome sequence
AB  - of L. casei DPC6800, isolated from a semi-hard Dutch cheese, is reported.
ER  -

TY  - JOUR
AU  - Stefanovic, E.
AU  - Fitzgerald, G.
AU  - McAuliffe, O.
TI  - Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese.
JO  - Genome Announcements
PY  - 2017
SP  - e00655
EP  - e00617
VL  - 5
AB  - Lactobacillus paracasei strains are common members of the nonstarter microbiota present in
AB  - various types of cheeses. The draft genome sequences of three strains
AB  - isolated from mature cheddar cheeses are reported here.
ER  -

TY  - JOUR
AU  - Steffani-Vallejo, J.L.
AU  - Brunck, M.E.
AU  - Acosta-Cruz, E.Y.
AU  - Montiel, R.
AU  - Barona-Gomez, F.
TI  - Genomic insights into Mycobacterium simiae human colonization.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 1
EP  - 1
VL  - 13
AB  - Mycobacterium simiae (Karassova V, Weissfeiler J, Kraszanay E, Acta Microbiol Acad Sci Hung
AB  - 12:275-82, 1965) is a slow-growing nontuberculous Mycobacterium
AB  - species found in environmental niches, and recently evidenced as an opportunistic
AB  - Human pathogen. We report here the genome of a clinical isolate of M. simiae
AB  - (MsiGto) obtained from a patient in Guanajuato, Mexico. With a size of 6,684,413
AB  - bp, the genomic sequence of strain MsiGto is the largest of the three M. simiae
AB  - genomes reported to date. Gene prediction revealed 6409 CDSs in total, including
AB  - 6354 protein-coding genes and 52 RNA genes. Comparative genomic analysis
AB  - identified shared features between strain MsiGto and the other two reported M.
AB  - simiae genomes, as well as unique genes. Our data reveals that M. simiae MsiGto
AB  - harbors virulence-related genes, such as arcD, ESAT-6, and those belonging to the
AB  - antigen 85 complex and mce clusters, which may explain its successful transition
AB  - to the human host. We expect the genome information of strain MsiGto will provide
AB  - a better understanding of infective mechanisms and virulence of this emergent
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Steffani-Vallejo, J.L.
AU  - Zuniga, C.
AU  - Cruz-Morales, P.
AU  - Lozano, L.
AU  - Morales, M.
AU  - Licona-Cassani, C.
AU  - Revah, S.
AU  - Utrilla, J.
TI  - Draft Genome Sequence of Sphingobacterium sp. CZ-UAM, Isolated from a Methanotrophic Consortium.
JO  - Genome Announcements
PY  - 2017
SP  - e00792
EP  - e00717
VL  - 5
AB  - Sphingobacterium sp. CZ-UAM was isolated from a methanotrophic consortium in mineral medium
AB  - using methane as the only carbon source. A draft genome of 5.84 Mb
AB  - with a 40.77% G+C content is reported here. This genome sequence will allow the
AB  - investigation of potential methanotrophy in this isolated strain.
ER  -

TY  - JOUR
AU  - Stegger, M.
AU  - Driebe, E.M.
AU  - Roe, C.
AU  - Lemmer, D.
AU  - Bowers, J.R.
AU  - Engelthaler, D.M.
AU  - Keim, P.
AU  - Andersen, P.S.
TI  - Genome Sequence of Staphylococcus aureus Strain CA-347, a USA600 Methicillin-Resistant Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e00517
EP  - e00513
VL  - 1
AB  - The Staphylococcus aureus clonal lineage CC45 is a predominant colonizer of healthy
AB  - individuals in northern Europe and constitutes a highly basal cluster of
AB  - the S. aureus population. Here, we report the complete genome sequence of S.
AB  - aureus strain CA-347 (NRS648), a representative of the methicillin-resistant
AB  - USA600 clone predominantly found in the United States.
ER  -

TY  - JOUR
AU  - Stegger, M.
AU  - Lindsay, J.A.
AU  - Moodley, A.
AU  - Skov, R.
AU  - Broens, E.M.
AU  - Guardabassi, L.
TI  - Rapid PCR Detection of Staphylococcus aureus Clonal Complex 398 by Targeting the Restriction-Modification System Carrying sau1-hsdS1.
JO  - J. Clin. Microbiol.
PY  - 2011
SP  - 732
EP  - 734
VL  - 49
AB  - A PCR targeting sau1-hsdS1 was developed for rapid detection of Staphylococcus aureus clonal
AB  - complex 398 (CC398). High sensitivity
AB  - (100%) and specificity (100%) were shown by evaluating the test on a
AB  - large strain collection (n = 1,307). We recommend this test for
AB  - accurate, rapid, and inexpensive diagnosis of methicillin-resistant S.
AB  - aureus (MRSA) CC398 in hospitals and on farms.
ER  -

TY  - JOUR
AU  - Stegger, M.
AU  - Price, L.B.
AU  - Larsen, A.R.
AU  - Gillece, J.D.
AU  - Waters, A.E.
AU  - Skov, R.
AU  - Andersen, P.S.
TI  - Genome Sequence of Staphylococcus aureus Strain 11819-97, an ST80-IV European Community-Acquired Methicillin-Resistant Isolate.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1625
EP  - 1626
VL  - 194
AB  - The European methicillin-resistant Staphylococcus aureus (MRSA) clone ST80-IV has historically
AB  - dominated community-associated infections in major parts of Europe
AB  - and is a lineage strongly linked to skin and soft tissue infections. Here, we
AB  - report the genome sequence of an ST80-IV representative, 11819-97, isolated from
AB  - a skin infection in Denmark in 1997.
ER  -

TY  - JOUR
AU  - Steigerwald, S.D.
AU  - Pfeifer, G.P.
AU  - Riggs, A.D.
TI  - Ligation-mediated PCR improves the sensitivity of methylation analysis by restriction enzymes and detection of specific DNA strand breaks.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 1435
EP  - 1439
VL  - 18
AB  - DNA methylation at specific sites is most frequently studied by use of
AB  - methylation-sensitive restriction endonucleases and Southern blotting.  We
AB  - report here that the sensitivity of this method can be increased
AB  - several-hundred-fold by applying a ligation-mediated polymerase chain reaction
AB  - (LM-PCR) procedure followign enzyme treatment.  DNA is cleaved simultaneously
AB  - with two restriction enzymes, one sensitive and one insensitive to methylation.
AB  - After cleavage, a gene-specific oligonucleotide primer is used for primer
AB  - extension, followed by linker ligation and then conventional PCR.  Using this
AB  - technique, we demonstrate that DNA from 100 cells (about 0.6 ng) can be
AB  - prepared and qualitatively analyzed for methylation at sites in an X-linked CpG
AB  - island, and 50 ng of DNA can be analyzed quantitatively.  A site 23 bp
AB  - downstream of the major transcription start site of human phosphoglycerate
AB  - kinase-1 (PGK-1) is 52 +/- 7 percent methylated in DNA from female blood and
AB  - greater than 98 percent unmethylated in DNA from male blood or HeLa cells.
AB  - This method detects quantitatively specific breaks in either double stranded or
AB  - single stranded DNA.  Thus new assays for enzymes and DNA structure can be
AB  - devised.
ER  -

TY  - JOUR
AU  - Stein, D.C.
AU  - Chien, R.
AU  - Seifert, S.H.
TI  - Construction of a Neisseria gonorrhoeae MS11 derivative deficient in NgoMI restriction and modification.
JO  - J. Bacteriol.
PY  - 1992
SP  - 4899
EP  - 4906
VL  - 174
AB  - We have cloned from Neisseria gonorrhoeae MS11 the gene encoding a methylase that modifies the
AB  - sequence GCCGGC. The corresponding restriction enzyme was also encoded by this clone. Sequence
AB  - analysis demonstrated that the methylase shares sequence similarities with other cytosine
AB  - methylases, but the sequence organization of M.NgoMI is different from that seen for other
AB  - cytosine methylases. A deletion was introduced into the chromosome of N. gonorrhoeae MS11 to
AB  - produce strain MUG701, a strain that is inactivated in both the methylase and the restriction
AB  - genes. Although this strain no longer methylated its DNA at the NgoMI recognition sequence,
AB  - cells were viable and had no other significant phenotypic changes. Transformation data
AB  - indicated that MS11 does not produce enough restriction activity to block plasmid
AB  - transformation in the gonococcus, even though restriction activity could be demonstrated in E.
AB  - coli containing the cloned gene.
AB  - [ The enzyme called NgoMI in this abstract has been renamed NgoMIV, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Stein, D.C.
AU  - Gregoire, S.
AU  - Piekarowicz, A.
TI  - Restriction of plasmid DNA during transformation but not conjugation in Neisseria gonorrhoeae.
JO  - Infect. Immun.
PY  - 1988
SP  - 112
EP  - 116
VL  - 56
AB  - Neisseria gonorrhoeae strains WR302 and PGH3-2 were characterized with respect to their
AB  - restriction-modification phenotype.  WR302 DNA was cleaved by HaeIII, indicating the lack of
AB  - methylation at the GGCC sequence.  PGH3-2 produced NgoSI (an isoschizomer of NgoII).  WR302
AB  - produced a restriction enzyme with a recognition sequence different from that of NgoI, NgoII,
AB  - or NgoIII.  Plasmid pFT180 isolated from WR302 was unable to transform PGH3-2, whereas plasmid
AB  - pFT180 isolated from PGH3-2 was able to transform PGH3-2 at a very high frequency.  When
AB  - plasmid pFT180 isolated from WR302 isolated from WR302 was methylated in vitro with methylase
AB  - M.HaeIII, this plasmid was able to transform PGH3-2.  NgoSI was able to restrict WR302 DNA in
AB  - vitro, whereas it was incapable of restricting PGH3-2 DNA in vitro.  When the
AB  - self-transmissible R factor pFT6 was mobilized from WR302 to PGH3-2 by conjugation, a
AB  - 1-order-of-magnitude difference in transfer frequencies was observed, as compared with an
AB  - isogenic cross.  The data indicate that host-mediated restriction can prevent the gonococcus
AB  - from acquiring DNA via transformation but not via conjugation.
AB  - [ The enzyme called NgoSI in this abstract has been renamed NgoSII, Jan/1998. ]
ER  -

TY  - JOUR
AU  - Stein, D.C.
AU  - Gunn, J.S.
AU  - Piekarowicz, A.
TI  - Sequence similarities between the genes encoding the S.NgoI and HaeII restriction/modification systems.
JO  - Biol. Chem.
PY  - 1998
SP  - 575
EP  - 578
VL  - 379
AB  - The DNA sequence encoding the S.NgoI restriction/modification system was identified from a
AB  - gene bank made from Neisseria gonorrhoaea strain WR302 by identifying recombinant plasmids
AB  - that induced the reporter system in a methylase detection strain AP1-200-9 and were resistant
AB  - to digestion with NgoI.  The DNA sequence was determined from one of these (pUCP30).  M.NgoI
AB  - is a protein of 315aa with a predicted MW of 35,296 Da and R.NgoI is a protein of 350aa with a
AB  - predicted MW of 40,650 Da.  The termination codon of M.NgoI overlapped the start codon of
AB  - R.NgoI.  The same strategy was used to clone the R/M system encoding HaeII from Haemophilus
AB  - aegyptius strain ATCC 11116.  The DNA sequence from one clone representing this class (pAP704)
AB  - was determined.  HaeII methylase is a protein of 318aa with a predicted MW of 35,669 Da and
AB  - R.HaeII contains 352aa with a predicted MW of 40,800 Da.  Aa alignments between the two
AB  - methylases indicated that they were 74.3% identical and 79% similar. DNA sequence alignments
AB  - revealed 68% identity.  An aa alignment between the two restriction enzymes indicated that
AB  - they were 60% identical and 68% similar.  DNA sequence alignments revealed 61% identity.  The
AB  - DNA sequences flanking these two systems were identified and used to determine the genomic
AB  - organization of the two systems.  The S.NgoI genes were found between two genes, one with high
AB  - homology to GTP binding proteins of unknown function and one with homology to genes involved
AB  - in tRNA synthetase synthesis.  The HaeII R/M genes were located between two genes, mucF and
AB  - mucE.  The DNA sequence of the HaeII R/M system was compared to the genomic DNA sequence of H.
AB  - influenzae Rd. Although the DNA sequences flanking the HaeII system were >99% identical to
AB  - contiguous DNA fragments found in the genome of H. influenzae Rd, no homology was seen with
AB  - the DNA sequences encoding the HaeII R/M system, indicating that it is not found in this
AB  - strain.  Given the vast difference in the GC content of S.NgoI and HaeII, their apparent
AB  - insertion into polycistronic operons, and their difference in codon usage when compared to the
AB  - species from which they were isolated, the data suggest that these R/M systems originated in
AB  - an organism other than Neisseria or Haemophilus.
ER  -

TY  - JOUR
AU  - Stein, D.C.
AU  - Gunn, J.S.
AU  - Radlinska, M.
AU  - Piekarowicz, A.
TI  - Restriction and modification systems of Neisseria gonorrhoeae.
JO  - Gene
PY  - 1995
SP  - 19
EP  - 22
VL  - 157
AB  - An individual strain of Neisseria gonorrhoeae may produce up to 16 different DNA
AB  - methyltransferases (MTases).  We have used a novel cloning system that is able to detect MTase
AB  - clones in the absence of direct selection to identify 14 different MTase clones.  Initial
AB  - characterization of these clones indicates that at least seven of these MTases are linked to
AB  - restriction endonuclease (ENase) systems.  Six of these systems have been characterized by DNA
AB  - sequence analysis, and the open reading frames encoding each of these systems have been
AB  - identified.  The recognition sequences for the cloned systems have the following
AB  - specificities: S.NgoI, RGCGCY; S.NgoII, GGCC; S.NgoIV, GCCGCC; S.NgoV, GGNNCC; S.NgoVII,
AB  - GCSGC; S.NgoVIIIA, GGTGA; and S.NgoVIIIC, TCACC.  Of those systems that have been cloned,
AB  - NgoI-NgoVII are typical type II R-M systems, with each encoding a DNA MTase that methylates
AB  - cytosine in position 5.  NgoVIII is a type IIS system, containing an ENase and two different
AB  - MTases.  One of these is a cytosine MTase (NgoVIIIC) and the other is an adenine MTase
AB  - (NgoVIIIA).  Although most of our clones encodes both the ENase and the MTase, none of the six
AB  - R-M systems are genetically linked on the chromosome.
ER  -

TY  - JOUR
AU  - Stein, L.Y. et al.
TI  - Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242).
JO  - J. Bacteriol.
PY  - 2011
SP  - 2668
EP  - 2669
VL  - 193
AB  - Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing
AB  - Alphaproteobacterium isolated from an aquifer in southern California. Unlike most
AB  - methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding
AB  - particulate methane monooxygenase but no evidence of the genes encoding soluble methane
AB  - monooxygenase. This is the first reported genome sequence of a member of the Methylocystis
AB  - species of the Methylocystaceae family in the order Rhizobiales.
ER  -

TY  - JOUR
AU  - Stein, L.Y. et al.
TI  - Genome Sequence of the Obligate Methanotroph Methylosinus trichosporium Strain OB3b.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6497
EP  - 6498
VL  - 192
AB  - Methylosinus trichosporium OB3b (for 'oddball' strain 3b) is an obligate aerobic
AB  - methane-oxidizing alphaproteobacterium that was originally
AB  - isolated in 1970 by Roger Whittenbury and colleagues. This strain has
AB  - since been used extensively to elucidate the structure and function of
AB  - several key enzymes of methane oxidation, including both particulate and
AB  - soluble methane monooxygenase (sMMO) and the extracellular copper chelator
AB  - methanobactin. In particular, the catalytic properties of soluble methane
AB  - monooxygenase from M. trichosporium OB3b have been well characterized in
AB  - context with biodegradation of recalcitrant hydrocarbons, such as
AB  - trichloroethylene. The sequence of the M. trichosporium OB3b genome is the
AB  - first reported from a member of the Methylocystaceae family in the order
AB  - Rhizobiales.
ER  -

TY  - JOUR
AU  - Steinweg, C.
AU  - Kuenne, C.T.
AU  - Billion, A.
AU  - Mraheil, M.A.
AU  - Domann, E.
AU  - Ghai, R.
AU  - Barbuddhe, S.B.
AU  - Karst, U.
AU  - Goesmann, A.
AU  - Puhler, A.
AU  - Weisshaar, B.
AU  - Wehland, J.
AU  - Lampidis, R.
AU  - Kreft, J.
AU  - Goebel, W.
AU  - Chakraborty, T.
AU  - Hain, T.
TI  - The complete genome sequence of L. seeligeri, a non-pathogenic member of the genus Listeria.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1473
EP  - 1474
VL  - 192
AB  - We report the complete and annotated genome sequence of the non-pathogenic L. seeligeri
AB  - SLCC3954 serovar 1/2b type strain harboring the smallest completely sequenced genome of the
AB  - genus Listeria.
ER  -

TY  - JOUR
AU  - Steitz, T.A.
TI  - Structural studies of protein-nucleic acid interaction:  the source of sequence-specific binding.
JO  - Q. Rev. Biophys.
PY  - 1990
SP  - 205
EP  - 280
VL  - 23
AB  - 1. Introduction and overview
AB  - 2. Principles of sequence-specific nucleic-acid recognition
AB  - 2.1 The problem that is set: what is being recognized?
AB  - 2.2 Role of the major groove in DNA recognition
AB  - 2.3 Role of nucleic acid bendability
AB  - 2.4 Role of water molecules in sequence recognition
AB  - 2.5 Role of the minor groove in DNA and RNA recognition
AB  - 3. DNA-binding structure motifs
AB  - 3.1 Helix-turn-helix
AB  - 3.2 Zinc fingers
AB  - 3.3 Helices of the dinucleotide fold
AB  - 3.4 other motifs
AB  - 4. Similarities and differences in RNA and DNA recognition
AB  - 5. Sequence-specific DNA-binding proteins
AB  - 5.1 Repressors and activators
AB  - 5.1.1 Lac operon regulation
AB  - (a) E. coli catabolite gene activator protein (CAP)
AB  - (b) E. coli lac repressor protein
AB  - 5.1.2 Structural studies of the bacterial phage repressors
AB  - (a) 434 Repressor fragment complexed with DNA
AB  - (b) Lambda cro
AB  - (c) Lambda cI repressor fragment
AB  - 5.1.3 E. coli Trp repressor
AB  - 5.1.4 E. coli Met repressor
AB  - 5.1.5 Zinc-containing DNA-binding domains (zinc fingers) TFIIIA
AB  - 5.2 Restriction endonuclease - E. coli EcoRI
AB  - 5.3 Site-specific recombination-Gamma Delta Resolvase
AB  - 6. Sequence-independent DNA-binding proteins
AB  - 6.1 Klenow fragment of E. coli DNA Polymerase I
AB  - 6.2 Bovine pancreatic DNase I
AB  - 6.3 E. coli Hu protein
AB  - 7. Sequence-specific RNA-binding proteins
AB  - 7.1 E. coli glutaminyl-tRNA synthetase complexed with tRNA
AB  - 8. Conclusions and prospects
AB  - 9. Acknowledgements
AB  - 10. References
ER  -

TY  - JOUR
AU  - Stelling, S.C.
AU  - Techtmann, S.M.
AU  - Utturkar, S.M.
AU  - Alshibli, N.K.
AU  - Brown, S.D.
AU  - Hazen, T.C.
TI  - Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters.
JO  - Genome Announcements
PY  - 2014
SP  - e01231
EP  - e01214
VL  - 2
AB  - Thalassotalea sp. strain ND16A belongs to the family Colwelliaceae and was isolated from
AB  - eastern Mediterranean Sea water at a depth of 1,055 m. Members of
AB  - Colwelliaceae are ubiquitous marine heterotrophs. Here, we report the draft
AB  - genome sequence of Thalassotalea sp. strain ND16A, a member of the newly
AB  - described genus Thalassotalea.
ER  -

TY  - JOUR
AU  - Stenger, D.C.
AU  - Lee, M.W.
AU  - Rogers, E.E.
AU  - Chen, J.
TI  - Plasmids of Xylella fastidiosa mulberry-infecting strains share extensive sequence identity and gene complement with pVEIS01 from the earthworm symbiont Verminephrobacter eiseniae.
JO  - Physiol. Mol. Plant Pathol.
PY  - 2010
SP  - 238
EP  - 245
VL  - 74
AB  - A ~25 kbp plasmid was present in each of four Californian strains of Xylella fastidiosa from
AB  - mulberry affected with leaf scorch disease.  Fragments of each plasmid were cloned into
AB  - Escherichia coli, sequenced, and assembled into circular contigs of 25,105 bp (pXF-RIV11 and
AB  - pXF-RIV16) or 24,372 bp (pXF-RIV19 and pXF-RIV25).  The four plasmids shared >99.8% sequence
AB  - identity, excluding a 732 bp insertion common to pXF-RIV11 and pXF-RIV16.  BLAST searches
AB  - identified seven regions (totaling 19,252 bp) sharing greater than or equal to 75% nucleotide
AB  - sequence identity with pVEI201, a 31 kbp plasmid from the earthworm symbiont Verminephrobacter
AB  - eiseniae.  Using pXF-RIV11 as a query in BLASTX searches, putative functions of
AB  - plasmid-encoded open reading frames were identified.  Fourteen ORFs were associated with DNA
AB  - transfer (Type IV secretion), four with plasmid stability (plasmid toxin/anti-toxin
AB  - addiction), one with protein export (Type II secretion), one with plasmid DNA replication
AB  - initiation (trfA), and the remaining ORFs associated with other or unknown functions.  The
AB  - putative origin of DNA replication (oriV) was located adjacent to the trfA ORF and was similar
AB  - in structure to that of plasmids belonging to the incP-1 incompatibility group.  E. coli
AB  - plasmids bearing fragments of pXF-RIV11 and the nptII gene as a selectable marker were tested
AB  - for replication in X. fastidiosa strain Temecula1.  Only fragments bearing oriV and trfA were
AB  - competent for replication in X. fastidiosa.  Collectively, these results indicate that
AB  - mulberry strains of X. fastidiosa harbor plasmids encoding genes associated with DNA transfer
AB  - and plasmid stability not previously identified on the chromosome of sequenced X. fastidiosa
AB  - strains and that ancestors of distantly related bacterial species occupying different niches
AB  - appear to have exchanged genetic material.
ER  -

TY  - JOUR
AU  - Stepanov, V.G.
AU  - Roberts, D.J.
AU  - Fox, G.E.
TI  - Draft Genome Sequence of Marinobacter vinifirmus Type Strain FB1.
JO  - Genome Announcements
PY  - 2017
SP  - e01058
EP  - e01017
VL  - 5
AB  - The gammaproteobacterium Marinobacter vinifirmus is associated with moderately saline
AB  - environments and is often found in marine ecosystems. Here, we report the
AB  - draft genome sequence of M. vinifirmus type strain FB1 (3.8 Mbp, 3,588 predicted
AB  - genes). The presented sequence will improve our understanding of the taxonomy and
AB  - evolution of the genus Marinobacter.
ER  -

TY  - JOUR
AU  - Stepanov, V.G.
AU  - Vaishampayan, P.
AU  - Venkateswaran, K.
AU  - Fox, G.E.
TI  - Draft Genome Sequence of Deinococcus phoenicis, a Novel Strain Isolated during the Phoenix Lander Spacecraft Assembly.
JO  - Genome Announcements
PY  - 2014
SP  - e00301
EP  - e00314
VL  - 2
AB  - Deinococcus phoenicis strain 1P10ME(T) is a radiation- and desiccation-resistant  bacterium
AB  - isolated from a cleanroom facility where the Phoenix Lander spacecraft was assembled. In order
AB  - to facilitate investigations of the nature of the extreme resistance of D. phoenicis to
AB  - bactericidal factors, a draft genome sequence of D. phoenicis was determined.
ER  -

TY  - JOUR
AU  - Stepanov, V.G.
AU  - Xiao, Y.
AU  - Lopez, A.J.
AU  - Roberts, D.J.
AU  - Fox, G.E.
TI  - Draft Genome Sequence of Marinobacter sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of  Marine Bacteria.
JO  - Genome Announcements
PY  - 2016
SP  - e01617
EP  - e01615
VL  - 4
AB  - The perchlorate-reducing strain Marinobacter sp. strain P4B1 was isolated from a  long-term
AB  - perchlorate-degrading enrichment culture seeded with marine sediment.
AB  - The draft genome of Marinobacter sp. P4B1 is comprised of the bacterial
AB  - chromosome (3.60 Mbp, G+C 58.51%, 3,269 predicted genes) and its associated
AB  - plasmid pMARS01 (0.14 Mbp, G+C 52.95%, 165 predicted genes).
ER  -

TY  - JOUR
AU  - Stephan, R.
AU  - Grim, C.J.
AU  - Gopinath, G.R.
AU  - Mammel, M.K.
AU  - Sathyamoorthy, V.
AU  - Trach, L.H.
AU  - Chase, H.R.
AU  - Fanning, S.
AU  - Tall, B.D.
TI  - Genome Sequence of Enterobacter turicensis Strain 610/05 (LMG 23731), Isolated from Fruit Powder.
JO  - Genome Announcements
PY  - 2013
SP  - e00996
EP  - e00913
VL  - 1
AB  - We report the draft genome sequence of Enterobacter turicensis strain 610/05 (LMG 23731),
AB  - isolated from fruit powder. The draft genome has a size of 4,182,790 bp
AB  - and a G+C% content of 58.0.
ER  -

TY  - JOUR
AU  - Stephan, R.
AU  - Lehner, A.
AU  - Tischler, P.
AU  - Rattei, T.
TI  - Complete Genome Sequence of Cronobacter turicensis LMG 23827, a foodborne pathogen causing deaths in neonates.
JO  - J. Bacteriol.
PY  - 2010
SP  - 309
EP  - 310
VL  - 193
AB  - Here we report the complete and annotated genome sequence of Cronobacter turicensis, an
AB  - opportunistic foodborne pathogen, which is known as rare but important causes of
AB  - live-threatening neonatal infections. Among all proteins of C. turicensis, 223 have been
AB  - annotated as virulence and disease-related proteins.
ER  -

TY  - JOUR
AU  - Stephanou, A.S.
AU  - Roberts, G.A.
AU  - Cooper, L.P.
AU  - Clarke, D.J.
AU  - Thomson, A.R.
AU  - MacKay, C.L.
AU  - Nutley, M.
AU  - Cooper, A.
AU  - Dryden, D.T.
TI  - Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification.
JO  - J. Mol. Biol.
PY  - 2009
SP  - 565
EP  - 576
VL  - 391
AB  - The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a
AB  - molecular mimic of double-stranded DNA and a highly
AB  - effective competitive inhibitor of the bacterial type I
AB  - restriction/modification system. The surface of Ocr is replete with acidic
AB  - residues that mimic the phosphate backbone of DNA. In addition, Ocr also
AB  - mimics the overall dimensions of a bent 24-bp DNA molecule. In this study,
AB  - we attempted to delineate these two mechanisms of DNA mimicry by
AB  - chemically modifying the negative charges on the Ocr surface. Our analysis
AB  - reveals that removal of about 46% of the carboxylate groups per Ocr
AB  - monomer results in an approximately 50-fold reduction in binding affinity
AB  - for a methyltransferase from a model type I restriction/modification
AB  - system. The reduced affinity between Ocr with this degree of modification
AB  - and the methyltransferase is comparable with the affinity of DNA for the
AB  - methyltransferase. Additional modification to remove approximately 86% of
AB  - the carboxylate groups further reduces its binding affinity, although the
AB  - modified Ocr still binds to the methyltransferase via a mechanism
AB  - attributable to the shape mimicry of a bent DNA molecule. Our results show
AB  - that the electrostatic mimicry of Ocr increases the binding affinity for
AB  - its target enzyme by up to approximately 800-fold.
ER  -

TY  - JOUR
AU  - Stephanou, A.S.
AU  - Roberts, G.A.
AU  - Tock, M.R.
AU  - Pritchard, E.H.
AU  - Turkington, R.
AU  - Nutley, M.
AU  - Cooper, A.
AU  - Dryden, D.T.F.
TI  - A mutational analysis of DNA mimicry by ocr, the gene 0.3 antirestriction protein of bacteriophage T7.
JO  - Biochem. Biophys. Res. Commun.
PY  - 2009
SP  - 129
EP  - 132
VL  - 378
AB  - The ocr protein of bacteriophage T7 is a structural and electrostatic mimic of approximately
AB  - 24 base pairs of double-stranded B-form DNA. As
AB  - such, it inhibits all Type I restriction and modification (R/M) enzymes
AB  - by blocking their DNA binding grooves and inactivates them. This allows
AB  - the infection of the bacterial cell by T7 to proceed unhindered by the
AB  - action of the R/M defence system. We have mutated aspartate and
AB  - glutamate residues on the surface of ocr to investigate their
AB  - contribution to the tight binding between the EcoKI Type I R/M enzyme
AB  - and ocr. Contrary to expectations, all of the single and double site
AB  - mutations of ocr constructed were active as anti-R/M proteins in vivo
AB  - and in vitro indicating that the mimicry of DNA by ocr is very
AB  - resistant to change.
ER  -

TY  - JOUR
AU  - Stephens, C.
AU  - Cho, P.J.
AU  - Afonso-de-Araujo, V.
AU  - Gomes, I.M.
AU  - de Azevedo-Sias, S.M.
AU  - Araujo, C.C.A.
AU  - Riley, L.W.
AU  - Aguiar-Alves, F.
TI  - Draft Genome Sequence of a Community-Associated Methicillin-Resistant Panton-Valentine Leukocidin-Positive Staphylococcus aureus Sequence Type 30  Isolate from a Pediatric Patient with a Lung Infection in Brazil.
JO  - Genome Announcements
PY  - 2015
SP  - e00907
EP  - e00915
VL  - 3
AB  - The sequence of methicillin-resistant Staphylococcus aureus strain B6 (sequence type 30
AB  - [ST30], spa type t433, staphylococcal chromosomal cassette mec element
AB  - [SCCmec] type IVc, Panton-Valentine leukocidin [PVL] positive), isolated from a
AB  - pediatric patient with a lung infection in Niteroi, Rio de Janeiro, Brazil, is
AB  - described here. The draft genome sequence includes a 2.8-Mb chromosome,
AB  - accompanied by a 20-kb plasmid containing blaZ and two small cryptic plasmids.
ER  -

TY  - JOUR
AU  - Stephens, C.
AU  - Reisenauer, A.
AU  - Wright, R.
AU  - Shapiro, L.
TI  - A cell cycle-regulated bacterial DNA methyltransferase is essential for viability.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 1210
EP  - 1214
VL  - 93
AB  - The CcrM adenine DNA methyltransferase, which specifically modifies GANTC sequences, is
AB  - necessary for viability in Caulobacter crescentus.  To our knowledge, this is the first
AB  - example of an essential prokaryotic DNA methyltransferase that is not part of a DNA
AB  - restriction/modification system.  Homologs of CcrM are widespread in the a subdivision of the
AB  - Proteobacteria, suggesting that methylation at GANTC sites may have important functions in
AB  - other members of this diverse group as well.  Temporal control of DNA methylation state has an
AB  - important role in Caulobacter development, and we show that this organism utilizes an unusual
AB  - mechanism for control of remethylation of newly replicated DNA.  CcrM is synthesized de novo
AB  - late in the cell cycle, coincident with full methylation of the chromosome, and is then
AB  - subjected to proteolysis prior to cell division.
ER  -

TY  - JOUR
AU  - Stephens, C.
AU  - Shapiro, L.
TI  - A common regulatory system controls transcription of flagellar genes and an essential DNA methyltransferase in Caulobacter.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 203
EP  - 203
VL  - 94
AB  - Our lab has recently isolated an essential Caulobacter gene (ccrM) encoding a DNA
AB  - methyltransferase which modifies DNA in a cell-cycle dependent manner.  ccrM transcription,
AB  - and CcrM methylation activity, occur only in the predivisional cell as chromosomal replication
AB  - is nearing completion.  Proper temporal control of CcrM activity is crucial, as constitutive
AB  - expression of ccrM results in defects in cell morphology and timing of chromosomal
AB  - replication.  We are thus interested in understanding the control of ccrM transcription.  The
AB  - functional ccrM promoter region was defined by deletion analysis, and the start site of
AB  - transcription was determined.  Immediately upstream of the start site is a sequence with
AB  - striking similarity to the consensus promoter for Caulobacter Class II flagellar genes, which
AB  - are also activated in the predivisional cell.  The RNA polymerase species recognizing these
AB  - promoters is not yet known.  Mutations in bases conserved between the ccrM and Class II
AB  - promoters greatly reduce ccrM transcription.  In addition, ccrM and Class II promoters are
AB  - rapidly repressed when DNA synthesis is inhibited.  It is proposed, therefore, that ccrM is
AB  - transcribed by the same factors used for Class II flagellar genes.  Deletion analysis
AB  - indicated that 20 bp downstream of the transcription start site was also required for ccrM
AB  - promoter activity.  This region contains a 10 bp inverted repeat containing two CcrM
AB  - methylation sites.  Roles for this sequence, and perhaps its methylation state, in promoter
AB  - activation are being examined.
ER  -

TY  - JOUR
AU  - Stephens, C.
AU  - Shapiro, L.
TI  - An essential DNA methyltransferase in Caulobacter crescentus.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1995
SP  - 330
EP  - 330
VL  - 95
AB  - In the dimorphic bacterium Caulobacter crescentus, methylation of GAnTC sites in newly
AB  - replicated DNA only occurs late in the cell cycle, shortly before cell division.  The
AB  - Caulobacter ccM gene, which encodes the DNA methyltransferase (M.CcrII) responsible for
AB  - methylation of GAnTC sites, is transcribed only in the predivisional cell.  We have found that
AB  - ccrM expression depends on a promoter homologous to that used by Caulobacter Class II
AB  - flagellar genes, demonstrating that the system controlling the flagellar genetic hierarchy
AB  - also regulates other genes in the predivisional cell.  Antibodies generated to M.CcrII were
AB  - used to show that this protein is highly unstable, and M.CcrII levels during the cell cycle
AB  - are tightly linked to transcription of ccrM.  Temporal regulation of methylation by M.CcrII is
AB  - necessary for normal development, as strains which express ccrM throughout the cell cycle,
AB  - and which therefore have continuously fully methylated DNA, exhibit abnormalities in control
AB  - of DNA replication and cell division.  We have used gene replacement experiments to
AB  - demonstrate that the ccrM gene is essential for growth and viability.  ccrM is to our
AB  - knowledge the first essential prokaryotic DNA methyltransferase.  To further examine the
AB  - function of M.CcrII in Caulobacter growth and development, we have constructed strains in
AB  - which ccrM expression can be controlled exogeneously.  We are examining the pysiological
AB  - consequences of blocking methylation completely, and of inducing methylation at inappropriate
AB  - times in the cell cycle.
ER  -

TY  - JOUR
AU  - Stephens, C.M.
AU  - Skerker, J.M.
AU  - Sekhon, M.S.
AU  - Arkin, A.P.
AU  - Riley, L.W.
TI  - Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections.
JO  - Genome Announcements
PY  - 2015
SP  - e01241
EP  - e01215
VL  - 3
AB  - Finished genome sequences are presented for four Escherichia coli strains isolated from
AB  - bloodstream infections at San Francisco General Hospital. These
AB  - strains provide reference sequences for four major fimH-identified sublineages
AB  - within the multilocus sequence type (MLST) ST95 group, and provide insights into
AB  - pathogenicity and differential antimicrobial susceptibility within this group.
ER  -

TY  - JOUR
AU  - Stephens, C.M.
AU  - Zweiger, G.
AU  - Shapiro, L.
TI  - Coordinate cell cycle control of a Caulobacter DNA methyltransferase and the flagellar genetic hierarchy.
JO  - J. Bacteriol.
PY  - 1995
SP  - 1662
EP  - 1669
VL  - 177
AB  - The expression of the Caulobacter ccrM gene and the activity of its product, the M.CcrII DNA
AB  - methyltransferase, are limited to a discrete portion of the cell cycle. Temporal control of
AB  - DNA methylation has been shown to be critical for normal development in the dimorphic
AB  - Caulobacter life cycle. To understand the mechanism by which ccrM expression is regulated
AB  - during the cell cycle, we have identified and characterized the ccrM promoter region. We have
AB  - found that it belongs to an unusual promoter family used by several Caulobacter class II
AB  - flagellar genes. The expression of these class II genes initiates assembly of the flagellum
AB  - just prior to activation of the ccrM promoter in the predivisional cell. Mutational analysis
AB  - of two M.CcrII methylation sites located 3' to the ccrM promoter suggests that methylation
AB  - might influence the temporally controlled inactivation of ccrM transcription. An additional
AB  - parallel between the ccrM and class II flagellar promoters is that their transcription
AB  - responds to a cell cycle DNA replication checkpoint. We propose that a common regulatory
AB  - system coordinates the expression of functionally diverse genes during the Caulobacter cell
AB  - cycle.
ER  -

TY  - JOUR
AU  - Stephens, M.A.
TI  - Partial purification and cleavage specificity of a site-specific endonuclease, SciNI, isolated from Spiroplasma citri.
JO  - J. Bacteriol.
PY  - 1982
SP  - 508
EP  - 514
VL  - 149
AB  - A site-specific endonuclease, SciNI, has been partially purified from the plant
AB  - pathogen Spiroplasma citri.  The enzyme recognizes the sequence 5'-G-C-G-C-3'
AB  - and cleaves between the first G and C.  3'-C-G-C-G-5' SciNI is an isoschizomer
AB  - of HhaI, but generates DNA fragments with 5' rather than 3' single-stranded
AB  - protrusions.
ER  -

TY  - JOUR
AU  - Stephens, R.S.
AU  - Kalman, S.
AU  - Lammel, C.J.
AU  - Fan, J.
AU  - Marathe, R.
AU  - Aravind, L.
AU  - Mitchell, W.P.
AU  - Olinger, L.
AU  - Tatusov, R.L.
AU  - Zhao, Q.
AU  - Koonin, E.V.
AU  - Davis, R.W.
TI  - Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis.
JO  - Science
PY  - 1998
SP  - 754
EP  - 759
VL  - 282
AB  - Analysis of the 1,042,519-base pair Chlamydia trachomatis genome revealed unexpected features
AB  - related to the complex biology of chlamydiae. Although chlamydiae lack many biosynthetic
AB  - capabilities, they retain functions for performing key steps and interconversions of
AB  - metabolites obtained from their mammalian host cells. Numerous potential virulence-associated
AB  - proteins also were characterized. Several eukaryotic chromatin-associated domain proteins were
AB  - identified, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and
AB  - decondensation. The phylogenetic mosaic of chlamydial genes, including a large number of genes
AB  - with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to
AB  - obligate intracellular parasitism.  [ Comment in: Science 1998 Oct 23;282(5389):638-9 ]
ER  -

TY  - JOUR
AU  - Stephenson, F.H.
AU  - Ballard, B.T.
AU  - Boyer, H.W.
AU  - Rosenberg, J.M.
AU  - Greene, P.J.
TI  - Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.
JO  - Gene
PY  - 1989
SP  - 1
EP  - 13
VL  - 85
AB  - The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in
AB  - Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase.  A clone
AB  - containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic
AB  - DNA library by hybridization with synthetic oligodeoxyribonucleotide probes
AB  - based on the N-terminal amino acid (aa) sequence of RsrI.  Extracts of E. coli
AB  - containing a subclone of the 11-kb fragment display RsrI activity.  Nucleotide
AB  - sequence analysis reveals an 831-bp open reading frame encoding a polypeptide
AB  - of 277 aa.  A 50% identity exists within a 266-aa overlap between the deduced
AB  - aa sequences of RsrI and EcoRI.  Regions of 75-100% aa sequence identity
AB  - correspond to key structural and functional regions of EcoRI.  The type-II
AB  - ENases have many common properties, and a common origin might have been
AB  - expected.  Nevertheless, this is the first demonstration of aa sequence
AB  - similarity between ENases produced by different organisms.
ER  -

TY  - JOUR
AU  - Stephenson, F.H.
AU  - Greene, P.J.
TI  - Nucleotide sequence of the gene encoding the RsrI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 10503
EP  - 10503
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Stephenson, J.
AU  - Kumaresan, D.
AU  - Hillebrand-Voiculescu, A.M.
AU  - Brooks, E.
AU  - Whiteley, A.S.
AU  - Murrell, J.C.
TI  - Draft Genome Sequence of the Methane-Oxidizing Bacterium 'Candidatus Methylomonas sp. LWB' Isolated from Movile Cave.
JO  - Genome Announcements
PY  - 2017
SP  - e01491
EP  - e01416
VL  - 5
AB  - We describe the draft genome sequence of 'Candidatus Methylomonas sp. LWB' isolated from
AB  - Movile Cave microbial mat samples. The genome contains both the
AB  - soluble and particular methane monooxygenase; however, one of the putative
AB  - particulate methane monooxygenase gene clusters is ordered pmoABC rather than in
AB  - the canonical gene arrangement of pmoCAB.
ER  -

TY  - JOUR
AU  - Steponaviciene, D.
AU  - Maneliene, Z.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - BseSI, a restriction endonuclease from Bacillus stearothermophilus Jo 10-553, which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)/C-3'.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 2644
EP  - 2645
VL  - 27
AB  - A new restriction endonuclease BseSI has been isolated from Bacillus stearothermophilus
AB  - Jo10-553. BseSI recognizes a degenerate hexanucleotide sequence 5'-G(G/T)GC(A/C)^C-3' and
AB  - cleaves DNA to produce 3'-protruding tetranucleotide ends.
ER  -

TY  - JOUR
AU  - Stern, A.
AU  - Sorek, R.
TI  - The phage-host arms race: Shaping the evolution of microbes.
JO  - Bioessays
PY  - 2011
SP  - 43
EP  - 51
VL  - 33
AB  - Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by
AB  - phages that infect them. Faced with the rapid evolution and turnover of phage particles,
AB  - bacteria have evolved various mechanisms to evade phage infection and killing, leading to an
AB  - evolutionary arms race. The extensive co-evolution of both phage and host has resulted in
AB  - considerable diversity on the part of both bacterial and phage defensive and offensive
AB  - strategies. Here, we discuss the unique and common features of phage resistance mechanisms and
AB  - their role in global biodiversity. The commonalities between defense mechanisms suggest
AB  - avenues for the discovery of novel forms of these mechanisms based on their evolutionary
AB  - traits.
ER  -

TY  - JOUR
AU  - Sternberg, N.
TI  - Evidence that adenine methylation influences DNA-protein interactions in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1985
SP  - 490
EP  - 493
VL  - 164
AB  - In this review, most of the information presented will be derived from studies
AB  - with Escherichia coli K-12 (E. coli) and its related bacteriophages, simply
AB  - because more is known about methylation in these organisms than in any other.
AB  - The two methylated bases that have been detected in E. coli are 6-methyladenine
AB  - (6-meAde) and 5-methylcytosine.  Since little is known about the biological
AB  - function of 6-methylcytosine, I will deal exclusively here with the studies on
AB  - 6-meAde.
ER  -

TY  - JOUR
AU  - Sternberg, N.
AU  - Coulby, J.
TI  - Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1990
SP  - 8070
EP  - 8074
VL  - 87
AB  - The packaging of bacteriophage P1 DNA is initiated when the phage packaging
AB  - site (pac) is recognized and cleaved and continues until the phage head is
AB  - full.  We have previously shown that pac is a 162-base-pair segment of P1 DNA
AB  - that contains seven DNA adenine methyltransferase methylation sites (5'-GATC).
AB  - We show here that cleavage of pac is methylation sensitive.  Both in vivo and
AB  - in vitro experiments indicate that methylated pac is cleavable, whereas
AB  - unmethylated pac is not.  Moreover, DNA isolated from P1 phage and containing
AB  - an uncut pac site was a poor substrate for in vitro cleavage until it was
AB  - methylated by the Escherichia coli DNA adenine methyltransferase.  Comparison
AB  - of that uncut pac DNA with other viral DNA fragments by digestion with
AB  - methylation-sensitive restriction enzymes indicated that the uncut pac DNA was
AB  - preferentially undermethylated.  In contrast, virion DNA containing a cut pac
AB  - site was not undermethylated.  We believe these results indicate that pac
AB  - cleavage is regulated by adenine methylation during the phage lytic cycle.
ER  -

TY  - JOUR
AU  - Sternglanz, H.
AU  - Bugg, C.E.
TI  - Conformation of N6-methyladenine, a base involved in DNA modification:restriction processes.
JO  - Science
PY  - 1973
SP  - 833
EP  - 834
VL  - 182
AB  - Crystal structures of N6,N9-dimethyladenine and N6-methyladenine hydrochloride
AB  - were determined from three-dimensional x-ray diffraction data.  The bases
AB  - assume a conformation in which the N(6)-methyl group blocks one of the
AB  - hydrogen-bonding sites normally used by adenine to form Watson-Crick pairs with
AB  - thymine in double-helical DNA.  When in this conformation, N6-methyladenine
AB  - residues might alter the secondary structure of DNA, thereby preventing the
AB  - scission of modified DNA's by restriction enzymes.
ER  -

TY  - JOUR
AU  - Steuer, S.
AU  - Pingoud, V.
AU  - Pingoud, A.
AU  - Wende, W.
TI  - Chimeras of the homing endonuclease PI-Scel and the homologous Candida tropicalis Intein: A study to explore the possibility of exchanging  DNA-binding modules to obtain highly specific endonucleases with  altered specificity.
JO  - Chembiochem
PY  - 2004
SP  - 206
EP  - 213
VL  - 5
AB  - Homing endonucleases are extremely specific endodeoxyribonucleases. In vivo, these enzymes
AB  - confer mobility on their genes by inducing a very
AB  - specific double-strand cut in cognate alleles that lack the cooling
AB  - sequence for the homing endonuclease; the cellular repair of the
AB  - double-strand break with the endonuclease-containing allele as a
AB  - template leads to integration of the endonuclease gene, completing the
AB  - homing process. As a result of their extreme sequence specificity
AB  - homing endonucleases are promising tools for genome engineering, For
AB  - this, purpose, it is desirable to design enzymes with defined new
AB  - specificities. To analyse which DNA-binding elements are potential
AB  - candidates for use in the design of enzymes with modified or even new
AB  - specificity, we produced several chimeric proteins derived from the
AB  - Saccharomyces cerevisiae VMA1 intein (PI-SceI) and the related Candida
AB  - tropicalis VMA1 intein. Although the mature Candida intein is devoid of
AB  - endonucleolytic activity the exchange of two DNA-binding modules of
AB  - PI-Scel with the homologous elements from the Candida intein results in
AB  - an active endonuclease. The low sequence homology in these modules
AB  - indicates that different protein - DNA contacts are responsible for the
AB  - recognition of related DNA sequences. This flexibility in DNA
AB  - recognition should, in principle, allow endonucleases to be produced
AB  - with new specificities useful for genome engineering.
ER  -

TY  - JOUR
AU  - Stevens, D.C.
AU  - Young, J.
AU  - Carmichael, R.
AU  - Tan, J.
AU  - Taylor, R.E.
TI  - Draft Genome Sequence of Gephyronic Acid Producer Cystobacter violaceus Strain Cb vi76.
JO  - Genome Announcements
PY  - 2014
SP  - e01299
EP  - e01214
VL  - 2
AB  - A draft genome sequence of Cystobacter violaceus strain Cb vi76, which produces the eukaryotic
AB  - protein synthesis inhibitor gephyronic acid, has been obtained.
AB  - The genome contains numerous predicted secondary metabolite clusters, including
AB  - the gephyronic acid biosynthetic pathway. This genome will contribute to the
AB  - investigation of secondary metabolism in other Cystobacter strains.
ER  -

TY  - JOUR
AU  - Stevens, M.
AU  - Cheng, J.B.
AU  - Li, D.
AU  - Xie, M.
AU  - Hong, C.
AU  - Maire, C.L.
AU  - Ligon, K.L.
AU  - Hirst, M.
AU  - Marra, M.A.
AU  - Costello, J.F.
AU  - Wang, T.
TI  - Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
JO  - Genome Res.
PY  - 2013
SP  - 1541
EP  - 1553
VL  - 23
AB  - Recent advancements in sequencing-based DNA methylation profiling methods provide an
AB  - unprecedented opportunity to map complete DNA
AB  - methylomes. These include whole-genome bisulfite sequencing (WGBS,
AB  - MethyiC-seq, or BS-seq), reduced-representation bisulfite sequencing
AB  - (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and
AB  - MRE-seq. These methods yield largely comparable results but differ
AB  - significantly in extent of genomic CpG coverage, resolution,
AB  - quantitative accuracy, and cost, at least while using current
AB  - algorithms to interrogate the data. None of these existing methods
AB  - provides single-CpG resolution, comprehensive genome-wide coverage, and
AB  - cost feasibility for a typical laboratory. We introduce methylCRF, a
AB  - novel conditional random fields based algorithm that integrates
AB  - methylated DNA immunoprecipitation (MeDIP-seq) and
AB  - methylation-sensitive restriction enzyme (MRE-seq) sequencing data to
AB  - predict DNA methylation levels at single-CpG resolution. Our method is
AB  - a combined computational and experimental strategy to produce DNA
AB  - methylomes of all 28 million CpGs in the human genome for a fraction
AB  - (<10%) of the cost of whole-genome bisulfite sequencing methods.
AB  - methylCRF was benchmarked for accuracy against Infinium arrays, RRBS,
AB  - WGBS sequencing, and locus-specific bisulfite sequencing performed on
AB  - the same human embryonic stem cell line. methylCRF transformation of
AB  - MeDIP-seq/MRE-seq was equivalent to a biological replicate of WGBS in
AB  - quantification, coverage, and resolution. We used conventional
AB  - bisulfite conversion, PCR, cloning, and sequencing to validate loci
AB  - where our predictions do not agree with whole-genome bisulfite data,
AB  - and in 11 out of 12 cases, methylCRF predictions of methylation level
AB  - agree better with validated results than does whole-genome bisulfite
AB  - sequencing. Therefore, methylCRF transformation of MeDIP-seq/MRE-seq
AB  - data provides an accurate, inexpensive, and widely accessible strategy
AB  - to create full DNA methylomes.
ER  -

TY  - JOUR
AU  - Stevens, M.J.
AU  - Inglin, R.C.
AU  - Meile, L.
TI  - Complete and Assembled Genome Sequence of Vagococcus teuberi DSM 21459T, a Novel  Species Isolated from Fermented Cow Milk in Mali.
JO  - Genome Announcements
PY  - 2017
SP  - e01514
EP  - e01516
VL  - 5
AB  - The genome of Vagococcus teuberi DSM 21459T, a strain isolated from Malian fermented milk, was
AB  - sequenced using single-molecule real-time sequencing. The
AB  - genome of V. teuberi DSM 21459T is the first sequenced genome of this novel
AB  - species and the second genome among the genus Vagococcus.
ER  -

TY  - JOUR
AU  - Stevens, M.J.
AU  - Stephan, R.
AU  - Johler, S.
TI  - Complete and Assembled Genome Sequence of Staphylococcus aureus RKI4, a Food-Poisoning Strain Exhibiting a Novel S. aureus Pathogenicity Island Carrying seb.
JO  - Genome Announcements
PY  - 2015
SP  - e00769
EP  - e00715
VL  - 3
AB  - The genome of Staphylococcus aureus RKI4, a strain isolated from feces of a patient in a case
AB  - of staphylococcal food poisoning, was sequenced using combined
AB  - Illumina and single-molecule real-time sequencing. Hierarchical assembly of the
AB  - genome resulted in a 2,725,654-bp chromosome and a 17,905-bp mobile genetic
AB  - element.
ER  -

TY  - JOUR
AU  - Stevens, M.J.
AU  - Stephan, R.
AU  - Johler, S.
TI  - Draft Genome Sequence of Staphylococcus aureus 1608, a Strain That Caused Toxic Mastitis in Twin Cows.
JO  - Genome Announcements
PY  - 2017
SP  - e01438
EP  - e01416
VL  - 5
AB  - Staphylococcus aureus 1608 is a strain that caused a lethal mastitis in cows. Here, the draft
AB  - genome sequence of the strain is presented.
ER  -

TY  - JOUR
AU  - Stevens, M.J.A.
AU  - Stephan, R.
AU  - Johler, S.
TI  - Draft Genome Sequence of Staphylococcus aureus S681, a Tetracycline-Sensitive Livestock-Associated Methicillin-Resistant Clonal Complex 398 Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e00805
EP  - e00817
VL  - 5
AB  - We present the draft genome sequence of an atypical tetracycline-susceptible
AB  - livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) strain.
AB  - It contains 2,817,340 bp and 2,858 coding sequences, including 6 rRNA operons, 56
AB  - tRNAs, and 4 noncoding RNA (ncRNA) genes. The strain harbors a tet(M) gene, but
AB  - 15 point mutations in amino acids are present that likely impair the
AB  - functionality of TetM.
ER  -

TY  - JOUR
AU  - Stevens, M.J.A.
AU  - Zurfluh, K.
AU  - Althaus, D.
AU  - Corti, S.
AU  - Lehner, A.
AU  - Stephan, R.
TI  - Complete and Assembled Genome Sequence of Salmonella enterica subsp. enterica Serotype Senftenberg N17-509, a Strain Lacking Salmonella Pathogen Island 1.
JO  - Genome Announcements
PY  - 2018
SP  - e00156
EP  - e00118
VL  - 6
AB  - The genome of Salmonella enterica subsp. enterica serotype Senftenberg N17-509, a strain
AB  - isolated from desiccated coconut, was sequenced using single-molecule
AB  - real-time sequencing. It consists of a 5.1-Mbp chromosome and a 29-kb linear
AB  - plasmid.
ER  -

TY  - JOUR
AU  - Stevens, M.J.A.
AU  - Zurfluh, K.
AU  - Stephan, R.
TI  - Complete and Assembled Genome Sequences of Pantoea calida DSM 22759(T) and Pantoea gaviniae DSM 22758(T).
JO  - Genome Announcements
PY  - 2018
SP  - e00157
EP  - e00118
VL  - 6
AB  - The genomes of Pantoea calida DSM 22759(T) and Pantoea gaviniae DSM 22758(T) were sequenced
AB  - using single-molecule real-time sequencing. They consist of a 4.3-Mbp
AB  - chromosome containing 4,092 genes, of which 3,977 encode proteins, and a 4.5-Mbp
AB  - chromosome containing 4,236 genes, of which 4,120 encode proteins, respectively.
ER  -

TY  - JOUR
AU  - Stevens, V.
AU  - Thijs, S.
AU  - McAmmond, B.
AU  - Langill, T.
AU  - Van Hamme, J.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel-Degrading and Plant Growth-Promoting Phyllospheric Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e00027
EP  - e00017
VL  - 5
AB  - We report here the 4.19-Mb draft genome sequence of Bacillus licheniformis VSD4,  a
AB  - Gram-positive bacterium of the Bacillaceae family, isolated from leaves of
AB  - Hedera helix growing at a high-traffic city center in Belgium. Knowledge about
AB  - its genome will help to evaluate its potential as an inoculant in
AB  - phylloremediation applications.
ER  -

TY  - JOUR
AU  - Stevens, V.
AU  - Thijs, S.
AU  - McAmmond, B.
AU  - Langill, T.
AU  - Van Hamme, J.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves.
JO  - Genome Announcements
PY  - 2017
SP  - e01680
EP  - e01616
VL  - 5
AB  - We report here the 6.55-Mb draft genome sequence of Rhodococcus erythropolis VSD3, a
AB  - Gram-positive bacterium of the Nocardiaceae family, isolated from leaves
AB  - of Hedera helix growing at a high-traffic city center in Belgium. The exploration
AB  - of its genome will contribute to the assessment of its application as an
AB  - inoculant in phylloremediation approaches.
ER  -

TY  - JOUR
AU  - Steward, G.F.
AU  - Preston, C.M.
TI  - Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.
JO  - Virol. J.
PY  - 2011
SP  - 287
EP  - 287
VL  - 8
AB  - ABSTRACT: BACKGROUND: Viruses have a profound influence on both the
AB  - ecology and evolution of marine plankton, but the genetic diversity of
AB  - viral assemblages, particularly those in deeper ocean waters, remains
AB  - poorly described. Here we report on the construction and analysis of a
AB  - viral metagenome prepared from below the euphotic zone in a temperate,
AB  - eutrophic bay of coastal California. METHODS: We purified viruses from
AB  - approximately one cubic meter of seawater collected from 200m depth in
AB  - Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and
AB  - cloned with no prior amplification into a plasmid vector and propagated in
AB  - E. coli to produce the MBv200m library. Random clones were sequenced by
AB  - the Sanger method. Sequences were assembled then compared to sequences in
AB  - GenBank and to other viral metagenomic libraries using BLAST analyses.
AB  - RESULTS: Only 26% of the 881 sequences remaining after assembly had
AB  - significant (E </= 0.001) BLAST hits to sequences in the GenBank nr
AB  - database, with most being matches to bacteria (15%) and viruses (8%). When
AB  - BLAST analysis included environmental sequences, 74% of sequences in the
AB  - MBv200m library had a significant match. Most of these hits (70%) were to
AB  - microbial metagenome sequences and only 0.7% were to sequences from viral
AB  - metagenomes. Of the 121 sequences with a significant hit to a known virus,
AB  - 94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae) and 6%
AB  - matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences)
AB  - or the Mimivirus (2 sequences). The largest percentages of hits to viral
AB  - genes of known function were to those involved in DNA modification (25%)
AB  - or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m
AB  - library appeared to be most similar to viral metagenomes from two other
AB  - bays and least similar to a viral metagenome from the Arctic Ocean.
AB  - CONCLUSIONS: Direct cloning of DNA from diverse marine viruses was
AB  - feasible and resulted in a distribution of virus types and functional
AB  - genes at depth that differed in detail, but were broadly similar to those
AB  - found in surface marine waters. Targeted viral analyses are useful for
AB  - identifying those components of the greater marine metagenome that
AB  - circulate in the subcellular size fraction.
ER  -

TY  - JOUR
AU  - Steward, N.
AU  - Kusano, T.
AU  - Sano, H.
TI  - Expression of ZmMET1, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3250
EP  - 3259
VL  - 28
AB  - A cDNA fragment encoding part of a DNA methyltransferase was isolated from maize. The putative
AB  - amino acid sequence identically matched that deduced from a genomic sequence in the database
AB  - (accession no. AF063403), and the corresponding gene was designated as ZmMET1. Bacterially
AB  - expressed ZmMET1 actively methylated DNA in vitro. Transcripts of ZmMET1 could be shown to
AB  - exclusively accumulate in actively proliferating cells of the meristems of mesocotyls and root
AB  - apices, suggesting ZmMET1 expression to be associated with DNA replication. This was confirmed
AB  - by simultaneous decrease of transcripts of ZmMET1 and histone H3, a marker for DNA
AB  - replication, in seedlings exposed to wounding, desiccation and salinity, all of which suppress
AB  - cell division. Cold stress also depressed both transcripts in root tissues. In contrast,
AB  - however, accumulation of ZmMET1 transcripts in shoot mesocotyls was not affected by cold
AB  - stress, whereas those for H3 sharply decreased. Such a differential accumulation of ZmMET1
AB  - transcripts was consistent with ZmMET1 protein levels as revealed by western blotting.
AB  - Expression of ZmMET1 is thus coexistent, but not completely dependent on DNA replication.
AB  - Southern hybridization analysis with a methylation-sensitive restriction enzyme revealed that
AB  - cold treatment induced demethylation of DNA in the Ac/Ds transposon region, but not in other
AB  - genes, and that such demethylation primarily occurred in roots. These results suggested that
AB  - the methylation level was decreased selectively by cold treatment, and that ZmMET1 may, at
AB  - least partly, prevent such demethylation.
ER  -

TY  - JOUR
AU  - Stewart, F.
AU  - Dila, D.
AU  - Raleigh, E.
TI  - The mechanism of action of the McrBC restriction enzyme of E. coli K-12.
JO  - J. Cell Biochem. Suppl.
PY  - 1995
SP  - 118
EP  - 118
VL  - 19A
AB  - As more restriction systems are characterised, their properties are being found to be more
AB  - diverse and the traditional three classes of restriction enzymes (Types I, II and III) are
AB  - becoming inadequate for classification. McrBC is one enzyme which fails to fit neatly into any
AB  - of the three classes. Like enzymes of classes I and III it is a multi-subunit enzyme
AB  - (consisting of 2 proteins, McrB and McrC) which requires two "half-sites" on the DNA for
AB  - cleavage. However, unlike the enzymes so far described in these classes, McrBC recognises only
AB  - methylated DNA, requiring at least one methylated C in each half-site, which is of the form
AB  - 5'-RmC-3'. Unusually, the half-sites can be symmetric or asymmetric as the DNA will be
AB  - cleaved irrespective of which strand(s) the methylated Cs are on. Qualitatively, then, McrBC
AB  - can recognise the half-sites in an orientation-independent manner. However, using synthetic
AB  - oligos with the methylated bases in various configurations, we have shown that the efficiency
AB  - of cleavage varies with the configuration of the methylated Cs.
AB  - Spacing requirements for the half-sites were further investigated using a series of plasmids
AB  - which contain only two McrBC half-sites, flanking a polylinker into which were inserted DNA
AB  - fragments of various sizes, we have also found that cleavage efficiency depends on the spacing
AB  - between the half-sites. Maximal cleavage occurs with a spacing of approximately 40-80bp, but
AB  - cleavage can occur, less efficiently, with spacing of up to and including 1.2kb but not 3kb.
AB  - The DNA is cleaved neither at a single position close to the recognition site like Type III
AB  - enzymes, nor at a site very distant from the recognition site as with Type I enzymes, but
AB  - rather at multiple positions close to only one half-site in each molecule, with no apparent
AB  - preference for one half-site over the other.
AB  - As McrBC shows no sequence similarity to other restriction enzymes (this is the case for
AB  - many restriction enzymes) a clue as to its evolution may be obtained by elucidation of its
AB  - mechanism of action. It is again similar to enzymes of Types I and III in requiring a
AB  - nucleotide for cleavage but differs in its requirement for GTP rather than ATP. By gel
AB  - retardation assays using synthetic oligos containing two appropriately-methylated and
AB  - appropriately-spaced McrBC half-sites, we have shown that GTP is required for the initial
AB  - binding of McrBC to DNA but it remains to be determined whether GTP is further required to
AB  - allow communication between half-sites by McrBC as is true for ATP in the case of Type I and
AB  - Type III enzymes.
ER  -

TY  - JOUR
AU  - Stewart, F.J.
AU  - Panne, D.
AU  - Bickle, T.A.
AU  - Raleigh, E.A.
TI  - Methyl-specific DNA binding by McrBC, a modification-dependent restriction enzyme.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 611
EP  - 622
VL  - 298
AB  - McrBC, a GTP-requiring, modification-dependent endonuclease of Escherichia coli K-12,
AB  - specifically recognizes DNA sites of the form 5' R(m)C 3'. DNA cleavage normally requires
AB  - translocation-mediated coordination between two such recognition elements at distinct sites.
AB  - We have investigated assembly of the cleavage-competent complex with gel-shift and DNase I
AB  - footprint analysis. In the gel-shift system, McrB(L) binding resulted in a fast-migrating
AB  - specific shifted band, in a manner requiring both GTP and Mg(2+). The binding was specific for
AB  - methylated DNA and responded to local sequence changes in the same way that cleavage does.
AB  - Single-stranded DNA competed for McrB(L)-binding in a modification and sequence-specific
AB  - fashion. A supershifted species was formed in the presence of McrC and GTPgammaS. DNase I
AB  - footprint analysis showed modest cooperativity in binding to two sites, and a two-site
AB  - substrate displayed protection in non-specific spacer DNA in addition to the recognition
AB  - elements. The addition of McrC did not affect the footprint obtained. We propose that McrC
AB  - effects a conformational change in the complex rather than a reorganization of the DNA:protein
AB  - interface.
ER  -

TY  - JOUR
AU  - Stewart, F.J.
AU  - Raleigh, E.A.
TI  - Dependence of McrBC cleavage on distance between recognition elements.
JO  - Biol. Chem.
PY  - 1998
SP  - 611
EP  - 616
VL  - 379
AB  - DNA cleavage by the modification-dependent restriction enzyme McrBC requires the presence of
AB  - two suitably modified recognition elements appropriately spaced in the substrate.  To
AB  - characterize the spacing requirement in more detail, we have constructed a plasmid with a
AB  - single McrBC cleavage site, in which the distance between recognition elements could be
AB  - systematically varied while preserving the local sequence surrounding the recognition
AB  - elements.  Optimal separation between elements was 55-103 base pairs, with detectable cleavage
AB  - observed at spacing of 32 bp to 2 kb; no cleavage was seen with spacing of 22 bp or less or
AB  - with 3 kb between elements.  Changing the spacing by 4 basepairs within the optimal range has
AB  - little effect on the efficiency of cleavage, suggesting that the recognition elements need not
AB  - lie on the same face of the DNA helix.
ER  -

TY  - JOUR
AU  - Stewart, L.
AU  - Ford, A.
AU  - Sangal, V.
AU  - Jeukens, J.
AU  - Boyle, B.
AU  - Kukavica-Ibrulj, I.
AU  - Caim, S.
AU  - Crossman, L.
AU  - Hoskisson, P.A.
AU  - Levesque, R.
AU  - Tucker, N.P.
TI  - Draft genomes of 12 host-adapted and environmental isolates of Pseudomonas aeruginosa and their positions in the core genome phylogeny.
JO  - Pathog Dis.
PY  - 2014
SP  - 20
EP  - 25
VL  - 71
AB  - Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen particularly associated with
AB  - the inherited disease cystic fibrosis (CF). Pseudomonas aeruginosa is well known to have a
AB  - large and adaptable genome that enables it to colonise a wide range of ecological niches.
AB  - Here, we have used a comparative genomics approach to identify changes that occur during
AB  - infection of the CF lung.
AB  - We used the mucoid phenotype as an obvious marker of host adaptation and compared these
AB  - genomes to analyse SNPs, indels and islands within near-isogenic pairs. To commence the
AB  - correction of the natural bias towards clinical isolates in genomics studies and to widen our
AB  - understanding of the genomic diversity of P. aeruginosa, we included four environmental
AB  - isolates in our analysis. Our data suggest that genome plasticity plays an important role in
AB  - chronic infection and that the strains sequenced in this study are representative of the two
AB  - major phylogenetic groups as determined by core genome SNP analysis.
ER  -

TY  - JOUR
AU  - Stewart, R.M.
AU  - Wiehlmann, L.
AU  - Ashelford, K.E.
AU  - Preston, S.J.
AU  - Frimmersdorf, E.
AU  - Campbell, B.J.
AU  - Neal, T.J.
AU  - Hall, N.
AU  - Tuft, S.
AU  - Kaye, S.B.
AU  - Winstanley, C.
TI  - Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections.
JO  - J. Clin. Microbiol.
PY  - 2011
SP  - 993
EP  - 1003
VL  - 49
AB  - Pseudomonas aeruginosa is a common opportunistic bacterial pathogen that causes a
AB  - variety of infections in humans. Populations of P. aeruginosa are dominated by
AB  - common clones that can be isolated from diverse clinical and environmental
AB  - sources. To determine whether specific clones are associated with corneal
AB  - infection, we used a portable genotyping microarray system to analyze a set of 63
AB  - P. aeruginosa isolates from patients with corneal ulcers (keratitis). We then
AB  - used population analysis to compare the keratitis isolates to a wider collection
AB  - of P. aeruginosa from various nonocular sources. We identified various markers in
AB  - a subpopulation of P. aeruginosa associated with keratitis that were in strong
AB  - disequilibrium with the wider P. aeruginosa population, including oriC, exoU,
AB  - katN, unmodified flagellin, and the carriage of common genomic islands. The
AB  - genome sequencing of a keratitis isolate (39016; representing the dominant
AB  - serotype O11), which was associated with a prolonged clinical healing time,
AB  - revealed several genomic islands and prophages within the accessory genome. The
AB  - PCR amplification screening of all 63 keratitis isolates, however, provided
AB  - little evidence for the shared carriage of specific prophages or genomic islands
AB  - between serotypes. P. aeruginosa twitching motility, due to type IV pili, is
AB  - implicated in corneal virulence. We demonstrated that 46% of the O11 keratitis
AB  - isolates, including 39016, carry a distinctive pilA, encoding the pilin of type
AB  - IV pili. Thus, the keratitis isolates were associated with specific
AB  - characteristics, indicating that a subpopulation of P. aeruginosa is adapted to
AB  - cause corneal infection.
ER  -

TY  - JOUR
AU  - Stice, S.P.
AU  - Stumpf, S.D.
AU  - Gitaitis, R.D.
AU  - Kvitko, B.H.
AU  - Dutta, B.
TI  - Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as  Well as Accessory Genes Correlated with Onion Pathogenicity.
JO  - Front. Microbiol.
PY  - 2018
SP  - 184
EP  - 184
VL  - 9
AB  - Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen
AB  - with a broad host range. Although P. ananatis strains can be
AB  - aggressive on onion causing foliar necrosis and onion center rot, previous
AB  - genomic analysis has shown that P. ananatis lacks the primary virulence secretion
AB  - systems associated with other plant pathogens. We assessed a collection of fifty
AB  - P. ananatis strains collected from Georgia over three decades to determine
AB  - genetic factors that correlated with onion pathogenic potential. Previous genetic
AB  - analysis studies have compared strains isolated from different hosts with varying
AB  - diseases potential and isolation sources. Strains varied greatly in their
AB  - pathogenic potential and aggressiveness on different cultivated Allium species
AB  - like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA)
AB  - and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not
AB  - observe any correlation between onion pathogenic potential and genetic diversity
AB  - among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of
AB  - 10 strains aided in the identification of a novel series of genetic regions,
AB  - likely plasmid borne, and correlating with onion pathogenicity observed on single
AB  - contigs of the genetic assemblies. We named these loci Onion Virulence Regions
AB  - (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as
AB  - pectate lyase and rhamnogalacturonase genes. Previous studies have not identified
AB  - distinct genetic loci or plasmids correlating with onion foliar pathogenicity or
AB  - pathogenicity on a single host pathosystem. The lack of focus on a single host
AB  - system for this phytopathgenic disease necessitates the pan-genomic analysis
AB  - performed in this study.
ER  -

TY  - JOUR
AU  - Stiens, M.
AU  - Becker, A.
AU  - Bekel, T.
AU  - Godde, V.
AU  - Goesmann, A.
AU  - Niehaus, K.
AU  - Schneiker-Bekel, S.
AU  - Selbitschka, W.
AU  - Weidner, S.
AU  - Schluter, A.
AU  - Puhler, A.
TI  - Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11.
JO  - J. Biotechnol.
PY  - 2008
SP  - 31
EP  - 37
VL  - 136
AB  - Genomic variation between the Sinorhizobium meliloti model strain Rm1021 and the field isolate
AB  - SM11 was assessed by using the genome-wide
AB  - S. meliloti Rm1021 Sm6k-oligonucleotide microarray in a comparative
AB  - genomic hybridisation experiment. Several gene clusters present in the
AB  - Rm1021 genome are missing in the SM11 genome. In detail, three missing
AB  - gene clusters were identified for the chromosome, five for megaplasmid
AB  - pSymA and two for megaplasmid pSymB. To confirm these hybridisation
AB  - results, the draft genome sequence of the S. meliloti field isolate
AB  - SM11 was established by 454-pyrosequencing. Three sequencing runs on
AB  - the ultrafast Genome Sequencer 20 System yielded 112.5 million bases.
AB  - These could be assembled into 905 larger contigs resulting in a nearly
AB  - 15-fold coverage of the 7.1 Mb SM11 genome. The missing gene regions
AB  - identified by comparative genomic hybridisation could be confirmed by
AB  - the results of the 454-sequencing project. An in-depth analysis of
AB  - these gene regions resulted in the following findings: (i) a complete
AB  - type I restriction/modification system encoded by a composite
AB  - transposon is absent in the chromosome of strain SM11. (ii) Most of the
AB  - Rm1021 denitrification genes and the complete siderophore biosynthesis
AB  - operon were found to be missing on SM11 megaplasmid pSymA. (iii) S.
AB  - meliloti SM11 megaplasmid pSymB lacks a complete cell surface
AB  - carbohydrate synthesis gene cluster. (iv) Several genes that are absent
AB  - in the SM11 genome could be assigned to insertion sequences and
AB  - transposons.
ER  -

TY  - JOUR
AU  - Stiens, M.
AU  - Schneiker, S.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - Sequence analysis of the 181-kb accessory plasmid pSmeSM11b, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment.
JO  - FEMS Microbiol. Lett.
PY  - 2007
SP  - 297
EP  - 309
VL  - 271
AB  - The 181 251 bp accessory plasmid pSmeSM11b of Sinorhizobium meliloti
AB  - strain SM11, belonging to a dominant indigenous S. meliloti subpopulation
AB  - identified during a long-term field release experiment, was sequenced.
AB  - This plasmid has 166 coding sequences (CDSs), 42% of which encode proteins
AB  - with homology to proteins of known function. Plasmid pSmeSM11b is a member
AB  - of the repABC replicon family and contains a large gene region coding for
AB  - a conjugation system similar to that of other self-transmissible plasmids
AB  - in Rhizobium and Agrobacterium. Another pSmeSM11b gene region, possibly
AB  - involved in sugar metabolism and polysaccharide catabolism, resembled a
AB  - region of S. meliloti 1021 megaplasmid pSymB and in the genome of
AB  - Sinorhizobium medicae WSM419. Another module of plasmid pSmeSM11b encodes
AB  - proteins similar to those of the nitrogen-fixing actinomycete Frankia
AB  - CcI3, and which are likely to be involved in the synthesis of a secondary
AB  - metabolite. Several ORFs of pSmeSM11b were predicted to play a role in
AB  - nonribosomal peptide synthesis. Plasmid pSmeSM11b has many mobile genetic
AB  - elements, which contribute to the mosaic composition of the plasmid.
ER  -

TY  - JOUR
AU  - Stier, I.
AU  - Kiss, A.
TI  - Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase.
JO  - PLoS ONE
PY  - 2013
SP  - e79003
EP  - e79003
VL  - 8
AB  - The prokaryotic DNA(cytosine-5)methyltransferase M. SssI shares the specificity of eukaryotic
AB  - DNA methyltransferases (CG) and is an important model and experimental tool in the study of
AB  - eukaryotic DNA methylation. Previously, M. SssI was shown to be able to catalyze deamination
AB  - of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing
AB  - from the reaction. To test whether this side-activity of the enzyme can be used to distinguish
AB  - between unmethylated and C5-methylate cytosines in CG dinucleotides, we re-investigated, using
AB  - a sensitive genetic reversion assay, the cytosine deaminase activity of M. SssI. Confirming
AB  - previous results we showed that M. SssI can deaminate cytosine to uracil in a slow reaction in
AB  - the absence of SAM and that the rate of this reaction can be increased by the SAM analogue
AB  - 5'-amino-5'-deoxyadenosine. We could not detect M. SssI-catalyzed deamination of
AB  - C5-methylcytosine (C-m5). We found conditions where the rate of M. SssI mediated C-to-U deamin
AB  - ation was at least 100-fold higher than the rate of C-m5-to-T conversion. Although this
AB  - difference in reactivities suggests that the enzyme could be used to identify C5-methylated
AB  - cytosines in the epigenetically important CG dinucleotides, the rate of M. SssI mediated
AB  - cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction.
AB  - Amino acid replacements in the presumed SAM binding pocket of M. SssI (F17S and G19D) resulted
AB  - in greatly reduced methyltransferase activity. The G1 9D variant showed cytosine deaminase
AB  - activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase
AB  - activity was also detectable in an E. coli ung(+) host proficient in uracil excision repair.
ER  -

TY  - JOUR
AU  - Stier, I.
AU  - Kiss, A.
TI  - The Type II restriction endonuclease MvaI has dual specificity.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 8231
EP  - 8238
VL  - 38
AB  - The MvaI restriction endonuclease cuts 5'-CC downward arrowAGG-3'/5'-CC upward arrowTGG-3'
AB  - sites as indicated by the arrows. N4-methylation of the
AB  - inner cytosines (C(m4)CAGG/C(m4)CTGG) protects the site against MvaI
AB  - cleavage. Here, we show that MvaI nicks the G-strand of the related
AB  - sequence (CCGGG/CCCGG, BcnI site) if the inner cytosines are
AB  - C5-methylated: C(m5)C downward arrowGGG/CC(m5)CGG. At M.SssI-methylated
AB  - SmaI sites, where two oppositely oriented methylated BcnI sites partially
AB  - overlap, double-nicking leads to double-strand cleavage (CC(m5)C downward
AB  - arrowGGG/CC(m5)C upward arrowGGG) generating fragments with blunt ends.
AB  - The double-strand cleavage rate and the stringency of substrate site
AB  - recognition is lower at the methylation-dependent site than at the
AB  - canonical target site. MvaI is the first restriction endonuclease shown to
AB  - possess, besides the 'normal' activity on its unmethylated recognition
AB  - site, also a methylation-directed activity on a different sequence.
ER  -

TY  - JOUR
AU  - Stine, C.B.
AU  - Li, C.
AU  - Crosby, T.C.
AU  - Hasbrouck, N.R.
AU  - Lam, C.
AU  - Tadesse, D.A.
TI  - Draft Whole-Genome Sequences of 18 Flavobacterium spp.
JO  - Genome Announcements
PY  - 2017
SP  - e00865
EP  - e00817
VL  - 5
AB  - We report here the draft whole-genome sequences for 18 Flavobacterium species type strains
AB  - that have historically been associated with fish gill disease.
ER  -

TY  - JOUR
AU  - Stine, C.B.
AU  - Li, C.
AU  - Crosby, T.C.
AU  - Hasbrouck, N.R.
AU  - Lam, C.
AU  - Tadesse, D.A.
TI  - Draft Whole-Genome Sequences of Chryseobacterium piscicola and Chryseobacterium shigense.
JO  - Genome Announcements
PY  - 2018
SP  - e00413
EP  - e00418
VL  - 6
AB  - We report the draft whole-genome sequences for Chryseobacterium piscicola and Chryseobacterium
AB  - shigense type strains, bacteria that have been associated with
AB  - fish gill disease.
ER  -

TY  - JOUR
AU  - Stinear, T.P. et al.
TI  - Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.
JO  - Genome Res.
PY  - 2008
SP  - 729
EP  - 741
VL  - 18
AB  - Mycobacterium marinum, a ubiquitous pathogen of fish and amphibia, is a near relative of
AB  - Mycobacterium tuberculosis, the etiologic agent of
AB  - tuberculosis in humans. The genome of the M strain of M. marinum comprises
AB  - a 6,636,827-bp circular chromosome with 5424 CDS, 10 prophages, and a
AB  - 23-kb mercury-resistance plasmid. Prominent features are the very large
AB  - number of genes (57) encoding polyketide synthases (PKSs) and nonribosomal
AB  - peptide synthases (NRPSs) and the most extensive repertoire yet reported
AB  - of the mycobacteria-restricted PE and PPE proteins, and related-ESX
AB  - secretion systems. Some of the NRPS genes comprise a novel family and seem
AB  - to have been acquired horizontally. M. marinum is used widely as a model
AB  - organism to study M. tuberculosis pathogenesis, and genome comparisons
AB  - confirmed the close genetic relationship between these two species, as
AB  - they share 3000 orthologs with an average amino acid identity of 85%.
AB  - Comparisons with the more distantly related Mycobacterium avium subspecies
AB  - paratuberculosis and Mycobacterium smegmatis reveal how an ancestral
AB  - generalist mycobacterium evolved into M. tuberculosis and M. marinum. M.
AB  - tuberculosis has undergone genome downsizing and extensive lateral gene
AB  - transfer to become a specialized pathogen of humans and other primates
AB  - without retaining an environmental niche. M. marinum has maintained a
AB  - large genome so as to retain the capacity for environmental survival while
AB  - becoming a broad host range pathogen that produces disease strikingly
AB  - similar to M. tuberculosis. The work described herein provides a
AB  - foundation for using M. marinum to better understand the determinants of
AB  - pathogenesis of tuberculosis.
ER  -

TY  - JOUR
AU  - Stipetic, L.H.
AU  - Hamilton, G.
AU  - Dalby, M.J.
AU  - Davies, R.L.
AU  - Meek, R.M.
AU  - Ramage, G.
AU  - Smith, D.G.
AU  - Burgess, K.E.
TI  - Draft Genome Sequence of Isolate Staphylococcus aureus LHSKBClinical, Isolated from an Infected Hip.
JO  - Genome Announcements
PY  - 2015
SP  - e00336
EP  - e00315
VL  - 3
AB  - We report here the genome sequence of a clinical isolate of Staphylococcus aureus from an
AB  - orthopedic infection. Phenotypically diverse Staphylococcus aureus
AB  - strains are associated with orthopedic infections and subsequent implant failure,
AB  - and some are highly resistant to antibiotics. This genome sequence will support
AB  - further analyses of strains causing orthopedic infections.
ER  -

TY  - JOUR
AU  - Stobberingh, E.E.
AU  - Meijers, J.A.
AU  - Van Kats-Renaud, J.H.
TI  - The sensitivity of phage DNA and plasmid DNA for a restriction enzyme from Staphylococcus aureus.
JO  - Antonie Van Leeuwenhoek
PY  - 1979
SP  - 19
EP  - 23
VL  - 45
AB  - In Staphylococcus aureus transduction of different tetracycline and chloramphenicol plasmids
AB  - with a group I III modification was possible to group I and III strains.  Group II strains,
AB  - containing a restriction endonuclease, had a restriction both for the phage and the plasmids:
AB  - two restriction-deficient group II strains were good acceptors for these plasmids.
ER  -

TY  - JOUR
AU  - Stobberingh, E.E.
AU  - Schiphof, R.
AU  - Sussenbach, J.S.
TI  - Occurrence of a Class II Restriction Endonuclease in Staphylococcus aureus.
JO  - J. Bacteriol.
PY  - 1977
SP  - 645
EP  - 649
VL  - 131
AB  - The occurrence of class II restriction endonucleases (enzymes that both
AB  - recognize and cleave a specific nucleotide sequence in deoxyribonucleic acid
AB  - (DNA) in Staphyloccus aureus has been investigated by analysis of crude
AB  - extracts obtained from different propagating strains of the International Phage
AB  - Typing System.  Of the four main groups of strains in the International System,
AB  - only extracts of group II strains were found to contain class II restriction
AB  - endonucleases.  The identical cleavage patterns obtained by incubation of
AB  - different DNAs with cell extracts of group II strains suggest that these
AB  - enzymes all recognize and cleave the same nucleotide sequence.  This
AB  - recognition site has been determined to be 5'-G-A-T-C-3' 3'-C-T-A-G-5' for the
AB  - prototype of these enzymes, Sau3AI (J. Sussenbach et al., Nucl. Acids Res. 3:
AB  - 3192-3202, 1976).  Evidence is presented that the classification of group II
AB  - strains is based on restriction modification and is correlated with the
AB  - presence of a class II restriction endonuclease that recognizes and cleaves the
AB  - above sequence.
ER  -

TY  - JOUR
AU  - Stobberingh, E.E.
AU  - Winkler, K.C.
TI  - Restriction-deficient mutants of Staphylococcus aureus.
JO  - J. Gen. Microbiol.
PY  - 1977
SP  - 359
EP  - 367
VL  - 99
AB  - A series of restriction-deficient mutants was isolated from non-lysogenic strains of
AB  - Staphylococcus aureus belonging to phage groups I and II.  Some mutants were sensitive to all
AB  - phages tested.  With one possible exception, all the mutants were unaffected in their
AB  - modification systems.  The breakdown of DNA of phages, restricted in the parental strains, was
AB  - reduced in both the mutants that were tested.  The restriction in propagating strain 3A could
AB  - be transduced to its restriction-deficient mutant.  The transduction efficiency increased
AB  - after ultraviolet irradiation of the transducing phage suggesting that the gene for
AB  - restriction is present on the bacterial chromosome.
ER  -

TY  - JOUR
AU  - Stoddard, B.
AU  - Belfort, M.
TI  - Social networking between mobile introns and their host genes.
JO  - Mol. Microbiol.
PY  - 2010
SP  - 1
EP  - 4
VL  - 78
AB  - P>Homing endonucleases have long been known as the orchestrators of intron mobility. However,
AB  - the extent of their influence on the intron
AB  - and its genetic and cellular environment is still being elucidated. The
AB  - accompanying paper emphasizes the importance of temporal control of
AB  - endonuclease expression on splicing, expression of the host gene and
AB  - cellular metabolism, while it raises questions to guide future inquiry.
ER  -

TY  - JOUR
AU  - Stoddard, B.L.
TI  - Homing endonuclease structure and function.
JO  - Q. Rev. Biophys.
PY  - 2005
SP  - 49
EP  - 95
VL  - 38
AB  - Homing endonucleases are encoded by open reading frames that are embedded within group I,
AB  - group II and archaeal introns, as well as inteins (intervening sequences that are spliced and
AB  - excised post-translationally). These enzymes initiate transfer of those elements (and
AB  - themselves) by generating strand breaks in cognate alleles that lack the intervening sequence,
AB  - as well as in additional ectopic sites that broaden the range of intron and intein mobility.
AB  - Homing endonucleases can be divided into several unique families that are remarkable in
AB  - several respects: they display extremely high DNA-binding specificities which arise from long
AB  - DNA target sites (14-40 bp), they are tolerant of a variety of sequence variations in these
AB  - sites, and they display disparate DNA cleavage mechanisms. A significant number of homing
AB  - endonucleases also act as maturases (highly specific cofactors for the RNA splicing reactions
AB  - of their cognate introns). Of the known homing group I endonuclease families, two (HNH and
AB  - His-Cys box enzymes) appear to be diverged from a common ancestral nuclease. While crystal
AB  - structures of several representatives of the LAGLIDADG endonuclease family have been
AB  - determined, only structures of single members of the HNH (I-HmuI), His-Cys box (I-PpoI) and
AB  - GIY-YIG (I-TevI) families have been elucidated. These studies provide an important source of
AB  - information for structure-function relationships in those families, and are the centerpiece of
AB  - this review. Finally, homing endonucleases are significant targets for redesign and selection
AB  - experiments, in hopes of generating novel DNA binding and cutting reagents for a variety of
AB  - genomic applications.
ER  -

TY  - JOUR
AU  - Stoddard, B.L.
TI  - Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
JO  - Structure
PY  - 2011
SP  - 7
EP  - 15
VL  - 19
AB  - Homing endonucleases are microbial DNA-cleaving enzymes that mobilize their own reading frames
AB  - by generating double strand breaks at specific genomic invasion sites. These proteins display
AB  - an economy of size, and yet recognize long DNA sequences (typically 20 to 30 base pairs). They
AB  - exhibit a wide range of fidelity at individual nucleotide positions in a manner that is
AB  - strongly influenced by host constraints on the coding sequence of the targeted gene. The
AB  - activity of these proteins leads to site-specific recombination events that can result in the
AB  - insertion, deletion, mutation, or correction of DNA sequences. Over the past fifteen years,
AB  - the crystal structures of representatives from several homing endonuclease families have been
AB  - solved, and methods have been described to create variants of these enzymes that cleave novel
AB  - DNA targets. Engineered homing endonucleases proteins are now being used to generate targeted
AB  - genomic modifications for a variety of biotech and medical applications.
ER  -

TY  - JOUR
AU  - Stoddard, B.L.
AU  - Jurica, M.
AU  - Heath, P.
AU  - Flick, K.
TI  - The structure, function, and convergent evolution of intron-encoded homing endonucleases.
JO  - Biochem. Soc. Trans.
PY  - 1999
SP  - A39
EP  - A39
VL  - 27
AB  - The homing endonucleases are a diverse family of proteins encoded by open reading frames in
AB  - genetically mobile, self-splicing introns.  Similar endonucleases have also been identified as
AB  - optional, independently folded domains in self-splicing protein introns, termed 'inteins'.
AB  - These comparatively small enzymes share the ability to recognize and cleave long DNA sites of
AB  - 20 to 40 bp, and promote the lateral transfer of their host intron or intein to these sites by
AB  - a targeted transposition.  These proteins also display flexibility of site-recognition, and
AB  - are capable of tolerating changes at any position in the target DNA site.  Our laboratory has
AB  - determined the structure of representative members of two families of homing endonucleases,
AB  - both unbound and complexed to their DNA targets: I-CreI (a LAGLIDADG endonuclease) and I-PpoI
AB  - (a his-cys box endonuclease).  The structures both demonstrate an impressive ability of these
AB  - proteins to adopt an economical, elongated fold and to form a DNA complex with sub-saturating
AB  - atomic contacts across the full length of the homing site.  The co-crystal structures indicate
AB  - that the enzymes probably follow two very different structural mechanisms for phosphodiester
AB  - hydrolysis.
ER  -

TY  - JOUR
AU  - Stoddard, B.L.
AU  - Scharenberg, A.M.
AU  - Monnat, R.J. Jr.
TI  - Advances in engineering homing endonucleases for gene targeting: ten years after structures.
JO  - Prog. Gene Ther.
PY  - 2008
SP  - 135
EP  - 167
VL  - 3
AB  - Homing endonucleases are highly site-specific endonucleases that induce homologous
AB  - recombination or gene conversion in vivo by cleaving long (typically >18bp) DNA target sites.
AB  - Homing endonucleases are under development as tools for targeted genetic engineering
AB  - applications, ranging from therapeutic gene correction to metabolic and population
AB  - engineering.  The first structures of homing endonucleases were reported 10 years ago.  Since
AB  - that time, representative structures from each of the known families of homing endonucleases
AB  - have been determined, and the corresponding details of their mechanisms of DNA recognition and
AB  - cleavage have been elucidated.  Using this information, the LAGLIDADG homing endonuclease
AB  - family has been identified as the most tractable for further modification by structure-based
AB  - selection and/or engineering approaches.  Most recently, successful redesign of the I-CreI
AB  - endonuclease has led to the development of reagents that recognize and act on genes associated
AB  - with monogenic diseases, including the human RAG1 and XPC genes.  These studies demonstrate
AB  - the feasibility of using engineered homing endonucleases to promote efficient and target
AB  - site-specific modification of chromosomal loci.  Current studies are rapidly improving the
AB  - throughput and efficiency of homing endonuclease design and selection, and aim to optimize the
AB  - specificity and activity of the resulting endonucleases for targeted genomic applications in
AB  - medicine and biotechnology.
ER  -

TY  - JOUR
AU  - Stojanov, M.
AU  - Blanc, D.S.
TI  - Characterization of the staphylococcal cassette chromosome mec insertion site in 108 isolates lacking the mecA gene and identified as methicillin-resistant Staphylococcus aureus by the Xpert MRSA assay.
JO  - Eur. J. Clin. Microbiol. Infect. Dis.
PY  - 2014
SP  - 1967
EP  - 1971
VL  - 33
AB  - During a 3-year period, 848 patients were detected as carriers of
AB  - methicillin-resistant Staphylococcus aureus (MRSA) by the Xpert MRSA assay
AB  - (Cepheid). Among them, 108 patients (12.7 %) were colonized with strains showing
AB  - methicillin-susceptible phenotypes and absence of the mecA gene, despite being
AB  - positive with the rapid polymerase chain reaction (PCR) assay. DNA sequences of
AB  - the staphylococcal cassette chromosome mec (SCCmec) insertion site of these
AB  - "false-positive" strains was determined by direct sequencing of the genomic DNA.
AB  - More than half (53.7 %) of the strains had DNA sequences unrelated to either SCC
AB  - or SCCmec and one-third had DNA sequences related to non-mec SCC. Only 10.2 % of
AB  - the strains carried sequences related to SCCmec, suggesting that a sequence
AB  - containing the mecA gene was lost from an SCCmec. These findings differ from the
AB  - general idea that all methicillin-susceptible S. aureus having positive Xpert
AB  - MRSA assay results are essentially MRSA that lost the mecA gene.
ER  -

TY  - JOUR
AU  - Stokes, H.W.
AU  - Nesbo, C.L.
AU  - Holley, M.
AU  - Bahl, M.I.
AU  - Gillings, M.R.
AU  - Boucher, Y.
TI  - Class 1 Integrons Potentially Predating the Association with Tn402-Like Transposition Genes Are Present in a Sediment Microbial Community.
JO  - J. Bacteriol.
PY  - 2006
SP  - 5722
EP  - 5730
VL  - 188
AB  - Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a
AB  - consequence of possessing a site-specific recombination system. This system facilitates the
AB  - spread of genes when they are part of mobile cassettes. Most integrons are contained within
AB  - chromosomes and are confined to specific bacterial lineages. However, this is not the case for
AB  - class 1 integrons, which were the first to be identified and are one of the single biggest
AB  - contributors to multidrug-resistant nosocomial infections, carrying resistance to many
AB  - antibiotics in diverse pathogens on a global scale. The rapid spread of class 1 integrons in
AB  - the last 60 years is partly a result of their association with a specific suite of
AB  - transposition functions, which has facilitated their recruitment by plasmids and other
AB  - transposons. The widespread use of antibiotics has acted as a positive selection pressure for
AB  - bacteria, especially pathogens, which harbor class 1 integrons and their associated antibiotic
AB  - resistance genes. Here, we have isolated bacteria from soil and sediment in the absence of
AB  - antibiotic selection. Class 1 integrons were recovered from four different bacterial species
AB  - not known to be human pathogens or commensals. All four integrons lacked the transposition
AB  - genes previously considered to be a characteristic of this class. At least two of these
AB  - integrons were located on a chromosome, and none of them possessed antibiotic resistance
AB  - genes. We conclude that novel class 1 integrons are present in a sediment environment in
AB  - various bacteria of the beta-proteobacterial class. These data suggest that the dispersal of
AB  - this class may have begun before the "antibiotic era."
ER  -

TY  - JOUR
AU  - Stokke, R.
AU  - Hocking, W.P.
AU  - Steinsbu, B.O.
AU  - Steen, I.H.
TI  - Complete Genome Sequence of the Thermophilic and Facultatively Chemolithoautotrophic Sulfate Reducer Archaeoglobus sulfaticallidus Strain  PM70-1T.
JO  - Genome Announcements
PY  - 2013
SP  - e00406
EP  - e00413
VL  - 1
AB  - Dissimilatory sulfate-reducing archaea of the genus Archaeoglobus display divergent
AB  - preferences in the use of energy sources and electron acceptors. Here
AB  - we present the complete genome sequence of the thermophilic Archaeoglobus
AB  - sulfaticallidus strain PM70-1(T), which distinctly couples chemolithoautotrophic
AB  - growth on H2/CO2 to sulfate reduction in addition to heterotrophic growth.
ER  -

TY  - JOUR
AU  - Stolt, P.
AU  - Grampp, B.
AU  - Zillig, W.
TI  - Genes for DNA cytosine methyltransferases and structural proteins, expressed during lytic growth by the phage Phi-H of the archaebacterium Halobacterium salinarium.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1994
SP  - 747
EP  - 757
VL  - 375
AB  - Lytic genes and transcription from the Halobacterium salinarium phage phi-H were studied.
AB  - Genes for three structural proteins were located to the left arm of the linear phage genome.
AB  - The right arm was shown to encode three DNA cytosine methyltransferases, the first such
AB  - sequences reported from an archaebacterium. One cytosine methyltransferase is of the
AB  - N(4)-methyltransferase type. The other two open reading frames (ORFs) seem to be parts of the
AB  - same gene, which has been split by a recombination event. This gene product is of the
AB  - C5-methyltransferase type. The methyltransferase genes are the first phi-H genes detected
AB  - showing high homology to eubacterial proteins. Five of the six described gene products have a
AB  - higher proportion of acidic over basic amino acid residues, a common characteristic of
AB  - halobacterial proteins. Lytic phi-H transcription was shown to produce three RNA species, two
AB  - shorter species encoding the methyltransferase genes and one large species transcribed from
AB  - both the right and the left phage arm and subsequently being processed upstream of the region
AB  - encoding the structural proteins.
ER  -

TY  - JOUR
AU  - Stolyar, S.
AU  - Liu, Z.
AU  - Thiel, V.
AU  - Tomsho, L.P.
AU  - Pinel, N.
AU  - Nelson, W.C.
AU  - Lindemann, S.R.
AU  - Romine, M.F.
AU  - Haruta, S.
AU  - Schuster, S.C.
AU  - Bryant, D.A.
AU  - Fredrickson, J.K.
TI  - Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.
JO  - Genome Announcements
PY  - 2014
SP  - e01060
EP  - e01013
VL  - 2
AB  - The genome of the unicellular cyanobacterium Thermosynechococcus sp. strain NK55a, isolated
AB  - from the Nakabusa hot spring, Nagano Prefecture, Japan, comprises
AB  - a single, circular, 2.5-Mb chromosome. The genome is predicted to contain 2,358
AB  - protein-encoding genes, including genes for all typical cyanobacterial
AB  - photosynthetic and metabolic functions. No genes encoding hydrogenases or
AB  - nitrogenase were identified.
ER  -

TY  - JOUR
AU  - Stone, J.K.
AU  - Johnson, S.L.
AU  - Bruce, D.C.
AU  - Detter, J.C.
AU  - Mayo, M.
AU  - Currie, B.J.
AU  - Gelhaus, H.C.
AU  - Keim, P.
AU  - Tuanyok, A.
TI  - Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305.
JO  - Genome Announcements
PY  - 2013
SP  - e00656
EP  - e00613
VL  - 1
AB  - We describe the complete genome sequence of Burkholderia pseudomallei MSHR305, a  clinical
AB  - isolate taken from a fatal encephalomyelitis case, a rare form of
AB  - melioidosis. This sequence will be used for comparisons to identify the genes
AB  - that are involved in neurological cases.
ER  -

TY  - JOUR
AU  - Storari, M.
AU  - Wuthrich, D.
AU  - Bruggmann, R.
AU  - Berthoud, H.
AU  - Arias-Roth, E.
TI  - Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.
JO  - Genome Announcements
PY  - 2015
SP  - e00078
EP  - e00015
VL  - 3
AB  - Clostridium tyrobutyricum is the main microorganism responsible for late blowing  defect in
AB  - cheeses. Here, we present the draft genome sequences of two C.
AB  - tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two
AB  - draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative
AB  - coding sequences, respectively.
ER  -

TY  - JOUR
AU  - Storm, A.J.
AU  - Jensen, P.A.
TI  - Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites.
JO  - Biotechnol. J.
PY  - 2018
VL  - 13
AB  - DNA libraries containing random 'barcodes' complicate synthetic biology workflows that
AB  - utilize restriction enzymes since restriction sites can appear inside some
AB  - barcodes. By removing bases at particular sites in the barcodes, it is possible
AB  - to create semi-random pools of barcodes that do not contain any restriction
AB  - sites. The challenge is to remove as few bases as possible to maximize the number
AB  - of sequences in the pool while ensuring all sequences are free of restriction
AB  - sites. The authors present CutFree, a computational approach to create pools of
AB  - random DNA barcodes that lack a pre-defined set of restriction sites. The
AB  - resulting pools can be inexpensively produced en masse with standard DNA
AB  - synthesis techniques. CutFree is experimentally validated by blocking digestion
AB  - of pools of barcodes designed to frequently contain restriction sites. Using
AB  - CutFree, a pool of 1.3 billion barcodes that are free from recognition sites for
AB  - 182 commercially available restriction enzymes is designed. CutFree is available
AB  - as a software package and an online tool (http://jensenlab.net/tools).
ER  -

TY  - JOUR
AU  - Stover, C.K. et al.
TI  - Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen.
JO  - Nature
PY  - 2000
SP  - 959
EP  - 964
VL  - 406
AB  - Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three
AB  - causes of opportunistic human infections. A major factor in its prominence as a pathogen is
AB  - its intrinsic resistance to antibiotics and disinfectants. Here we report the complete
AB  - sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest
AB  - bacterial genome sequenced, and the sequence provides insights into the basis of the
AB  - versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome
AB  - size and environmental adaptability, P. aeruginosa contains the highest proportion of
AB  - regulatory genes observed for a bacterial genome and a large number of genes involved in the
AB  - catabolism, transport and efflux of organic compounds as well as four potential chemotaxis
AB  - systems. We propose that the size and complexity of the P. aeruginosa genome reflect an
AB  - evolutionary adaptation permitting it to thrive in diverse environments and resist the effects
AB  - of a variety of antimicrobial substances.
ER  -

TY  - JOUR
AU  - Stover, T.
AU  - Kohler, E.
AU  - Fagin, U.
AU  - Wende, W.
AU  - Wolfes, H.
AU  - Pingoud, A.
TI  - Determination of the DNA bend angle induced by the restriction endonuclease EcoRV in the presence of Mg2++.
JO  - J. Biol. Chem.
PY  - 1993
SP  - 8645
EP  - 8650
VL  - 268
AB  - We have used the method of Zinkel and Crothers (1990, Biopolymers 29: 29-38) to determine the
AB  - degree of bending induced by the binding of the restriction endonuclease EcoRV to its
AB  - recognition sequence (-GATATC-). A set of four calibration DNA fragments was constructed that
AB  - contained zero, two, four, or six phased A-tracts in their centers and an EcoRV site at the
AB  - 5'-end to account for the electrophoretic influence of the bound protein. The mobilities of
AB  - these calibration molecules complexed with EcoRV were compared to that of a test DNA
AB  - containing a central EcoRV site also complexed with EcoRV. The EcoRV-induced bend angle was
AB  - found to be 44 +/- 4. These experiments were performed with a catalytically inactive EcoRV
AB  - mutant that still binds DNA specifically in the presence of Mg2+. In the absence of Mg2+,
AB  - which is necessary for specific binding, there is no difference in the mobilities of the
AB  - fragments with a peripheral or a central EcoRV site complexed with EcoRV, indicating that
AB  - nonspecific binding on average does not lead to measurable DNA bending.
ER  -

TY  - JOUR
AU  - Strabala, T.J.
AU  - Macdonald, L.
AU  - Liu, V.
AU  - Smit, A.-M.
TI  - Draft genome sequence of Novosphingobium nitrogenifigens Y88T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 201
EP  - 201
VL  - 194
AB  - Novosphingobium nitrogenifigens was originally isolated from pulp and paper mill wastewater, a
AB  - low-nitrogen, high-carbon environment.  N. nitrogenifigens is the first known nitrogen-fixing,
AB  - polyhydroxyalkanoate-accumulating sphingomonad, and we report the annotated draft genome
AB  - sequence of the type strain Y88T here.
ER  -

TY  - JOUR
AU  - Strachan, C.R.
AU  - Singh, R.
AU  - VanInsberghe, D.
AU  - Ievdokymenko, K.
AU  - Budwill, K.
AU  - Mohn, W.W.
AU  - Eltis, L.D.
AU  - Hallam, S.J.
TI  - Metagenomic scaffolds enable combinatorial lignin transformation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - 10143
EP  - 10148
VL  - 111
AB  - Engineering the microbial transformation of lignocellulosic biomass is essential
AB  - to developing modern biorefining processes that alleviate reliance on
AB  - petroleum-derived energy and chemicals. Many current bioprocess streams depend on
AB  - the genetic tractability of Escherichia coli with a primary emphasis on
AB  - engineering cellulose/hemicellulose catabolism, small molecule production, and
AB  - resistance to product inhibition. Conversely, bioprocess streams for lignin
AB  - transformation remain embryonic, with relatively few environmental strains or
AB  - enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin
AB  - transformation products compatible with functional screening in E. coli. We use
AB  - this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial
AB  - communities conferring an array of lignin transformation phenotypes that
AB  - synergize in combination. Transposon mutagenesis and comparative sequence
AB  - analysis of active clones identified genes encoding six functional classes
AB  - mediating lignin transformation phenotypes that appear to be rearrayed in nature
AB  - via horizontal gene transfer. Lignin transformation activity was then
AB  - demonstrated for one of the predicted gene products encoding a multicopper
AB  - oxidase to validate the screen. These results illuminate cellular and
AB  - community-wide networks acting on aromatic polymers and expand the toolkit for
AB  - engineering recombinant lignin transformation based on ecological design
AB  - principles.
ER  -

TY  - JOUR
AU  - Strapagiel, D.
AU  - Borowka, P.
AU  - Marciniak, B.
AU  - Bakula, Z.
AU  - van Ingen, J.
AU  - Safianowska, A.
AU  - Brzostek, A.
AU  - Dziadek, J.
AU  - Jagielski, T.
TI  - Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458,  1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental  Sources.
JO  - Genome Announcements
PY  - 2016
SP  - e00456
EP  - e00416
VL  - 4
AB  - Mycobacterium kansasii belongs to the nontuberculous mycobacteria (NTM) and causes
AB  - opportunistic infections with both pulmonary and extrapulmonary
AB  - manifestations. Here, we report the draft genome sequences of six environmental
AB  - M. kansasii strains, designated 1010001495 (type I), 1010001469 (type II),
AB  - 1010001468 (type III), 1010001458 (type IV), 1010001454 (type V), and 1010001493
AB  - (type V), originally isolated in five different European countries.
ER  -

TY  - JOUR
AU  - Strathdee, G.
AU  - Brown, R.
TI  - Epigenetic cancer therapies: DNA methyltransferase inhibitors.
JO  - Expert Opin. Invest. Drugs
PY  - 2002
SP  - 747
EP  - 754
VL  - 11
AB  - Human cancers frequently show altered patterns of DNA methylation, particularly at CpG
AB  - islands.  These CpG islands are sequences of DNA rich in CpG dinucleotides and are often found
AB  - close to gene promoters.  Methylation within islands has been shown to be associated with
AB  - transcriptional repression of the linked gene.  Genes involved in all facets of tumour
AB  - development and progression can become methylated and epigenetically silenced.  Re-expression
AB  - of such silenced genes can lead to suppression of tumour growth or sensitisation to anticancer
AB  - therapies.  Agents that can reverse DNA methylation include nucleoside and non-nucleoside
AB  - inhibitors of DNA methyltransferase.  Such agents are now undergoing preclinical evaluation
AB  - and clinical trials in cancer patients.
ER  -

TY  - JOUR
AU  - Strauch, E.
AU  - Goelz, G.
AU  - Knabner, D.
AU  - Konietzny, A.
AU  - Lanka, E.
AU  - Appel, B.
TI  - A cryptic plasmid of Yersinia enterocolitica encodes a conjugative transfer system related to the regions of CloDF13 Mob and IncX Pil.
JO  - Microbiology
PY  - 2003
SP  - 2829
EP  - 2845
VL  - 149
AB  - Yersinia enterocolitica 29930 (biotype 1A; O : 7,8), the producing strain of the
AB  - phage-tail-like bacteriocin enterocoliticin, possesses a
AB  - plasmid-encoded conjugative type IV transfer system. The genes of the
AB  - conjugative system were found by screening of a cosmid library constructed
AB  - from total DNA of strain 29930. The cosmid Cos100 consists of the vector
AB  - SuperCos1 and an insert DNA of 40 303 bp derived from a cryptic plasmid of
AB  - strain 29930. The conjugative transfer system consists of genes encoding a
AB  - DNA transfer and replication system (Dtr) with close relationship to the
AB  - mob region of the mobilizable plasmid CloDF13 and a gene cluster encoding
AB  - a mating pair formation system (Mpf) closely related to the Mpf system of
AB  - the IncX plasmid R6K. However, a gene encoding a homologue of TaxB, the
AB  - coupling protein of the IncX system, is missing. The whole transfer region
AB  - has a size of approximately 17 kb. The recombinant plasmid Cos100 was
AB  - shown to be transferable between Escherichia coli and Yersinia with
AB  - transfer frequencies up to 0.1 transconjugants per donor. Mutations
AB  - generated by inserting a tetracycline cassette into putative tri genes
AB  - yielded a transfer-deficient phenotype. Conjugative transfer of the
AB  - cryptic plasmid could not be demonstrated in the original host Y.
AB  - enterocolitica 29930. However, a kanamycin-resistance-conferring
AB  - derivative of the plasmid was successfully introduced into E. coli K-12 by
AB  - transformation and was shown to be self-transmissible. Furthermore,
AB  - Southern blot hybridization and PCR experiments were carried out to
AB  - elucidate the distribution of the conjugative transfer system in YERSINIA:
AB  - In total, six Y. enterocolitica biotype 1A strains harbouring closely
AB  - related systems on endogenous plasmids were identified.
ER  -

TY  - JOUR
AU  - Strauch, E.
AU  - Hammerl, J.A.
AU  - Konietzny, A.
AU  - Schneiker-Bekel, S.
AU  - Arnold, W.
AU  - Goesmann, A.
AU  - Puhler, A.
AU  - Beutin, L.
TI  - Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7.
JO  - Infect. Immun.
PY  - 2008
SP  - 5466
EP  - 5477
VL  - 76
AB  - The production of Shiga toxin (Stx) (verocytotoxin) is a major virulence
AB  - factor of Escherichia coli O157:H7 strains (Shiga toxin-producing E. coli
AB  - [STEC] O157). Two types of Shiga toxins, designated Stx1 and Stx2, are
AB  - produced in STEC O157. Variants of the Stx2 type (Stx2, Stx2c) are
AB  - associated with high virulences of these strains for humans. A
AB  - bacteriophage designated 2851 from a human STEC O157 encoding the Stx2c
AB  - variant was described previously. Nucleotide sequence analysis of the
AB  - phage 2851 genome revealed 75 predicted coding sequences and indicated a
AB  - mosaic structure typical for lambdoid phages. Analyses of free phages and
AB  - K-12 phage 2851 lysogens revealed that upon excision from the bacterial
AB  - chromosome, the loss of a phage-encoded IS629 element leads to fusion of
AB  - phage antA and antB genes, with the generation of a recombined antAB gene
AB  - encoding a strong antirepressor. In wild-type E. coli O157 as well as in
AB  - K-12 strains, phage 2851 was found to be integrated in the sbcB locus.
AB  - Additionally, phage 2851 carries an open reading frame which encodes an
AB  - OspB-like type III effector similar to that found in Shigella spp.
AB  - Investigation of 39 stx(2c) E. coli O157 strains revealed that all except
AB  - 1 were positive for most phage 2851-specific genes and possessed a
AB  - prophage with the same border sequences integrated into the sbcB locus.
AB  - Phage 2851-specific sequences were absent from most stx(2c)-negative E.
AB  - coli O157 strains, and we suggest that phage 2851-like phages contributed
AB  - significantly to the dissemination of the Stx2c variant toxin within this
AB  - group of E. coli.
ER  -

TY  - JOUR
AU  - Strauch, M.A.
TI  - Delineation of AbrB-binding sites on the Bacillus subtilis spoOH, kinB, ftsAZ, and pbpE promoters and use of a derived homology to identify a previously unsuspected binding site in the bsuB1 methylase promoter.
JO  - J. Bacteriol.
PY  - 1995
SP  - 6999
EP  - 7002
VL  - 177
AB  - DNase I footprinting experiments showed that AbrB binds to the regulatory regions of the
AB  - spoOH, kinB, ftsAZ, and pbpE genes.  A conserved motif was found in these and other
AB  - AbrB-binding sites.  A search for Bacillus subtilis DNA sequences containing this motif led to
AB  - the prediction that AbrB would bind to the promoter controlling the bsuB1 methylase gene.
AB  - DNase I footprinting experiments confirmed this prediction.
ER  -

TY  - JOUR
AU  - Strausberg, R.L. et al.
TI  - Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 16899
EP  - 16903
VL  - 99
AB  - The National Institutes of Health Mammalian Gene Collection (MGC) Program is a
AB  - multiinstitutional effort to identify and sequence a cDNA clone
AB  - containing a complete ORF for each human and mouse gene. ESTs were
AB  - generated from libraries enriched for full-length cDNAs and analyzed to
AB  - identify candidate full-ORF clones, which then were sequenced to high
AB  - accuracy. The MGC has currently sequenced and verified the full ORF for a
AB  - nonredundant set of >9,000 human and >6,000 mouse genes. Candidate
AB  - full-ORF clones for an additional 7,800 human and 3,500 mouse genes also
AB  - have been identified. All MGC sequences and clones are available without
AB  - restriction through public databases and clone distribution networks (see
AB  - http:mgc.nci.nih.gov).
ER  -

TY  - JOUR
AU  - Streeck, R.E.
TI  - Single-strand and double-strand cleavage at half-modified and fully modified recognition sites for the restriction nucleases Sau3A and TaqI.
JO  - Gene
PY  - 1980
SP  - 267
EP  - 275
VL  - 12
AB  - The influence of cytosine methylation on the cleavage of DNA by the restriction
AB  - nucleases Sau3A and TaqI has been investigated.  Bovine satellite DNA fragments
AB  - containing a GATCGA sequence, i.e. a Sau3A site overlapping with a TaqI site
AB  - have been used in this study.  The methylation of these fragments has been
AB  - determined by sequence analysis.  It has been found that a TaqI site (TCGA)
AB  - methylated at cytosine in both DNA strands is still sensitive to double-strand
AB  - cleavage.  A Sau3A site (GATC), however, is rendered resistant to double-strand
AB  - cleavage by methylation of a single cytosine.  Fragments containing the
AB  - "half-modified" Sau3A site are nicked in the unmethylated DNA strand.  It has
AB  - been shown by sequence analysis of nicked DNA that the single-strand break
AB  - occurs at the same position which is cleaved in unmodified DNA.
ER  -

TY  - JOUR
AU  - Streeter, S.D.
AU  - McGeehan, J.E.
AU  - Kneale, G.G.
TI  - Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp RFL231.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2009
SP  - 898
EP  - 901
VL  - F65
AB  - Restriction-modification controller proteins play an essential role in regulating the temporal
AB  - expression of restriction-modification genes.
AB  - The controller protein C.Csp231I represents a new class of controller
AB  - proteins. The gene was sublconed to allow overexpression in Escherichia
AB  - coli. The protein was purified to homogeneity and crystallized using
AB  - the hanging-drop vapour-diffusion method. The crystals diffracted to
AB  - 2.0 angstrom resolution and belonged to space group P2(1). An
AB  - electrophoretic mobility-shift assay provided evidence of strong
AB  - binding of C.Csp231I to a sequence located upstream of the csp231IC
AB  - start codon.
ER  -

TY  - JOUR
AU  - Streeter, S.D.
AU  - Papapanagiotou, I.
AU  - McGeehan, J.E.
AU  - Kneale, G.G.
TI  - DNA footprinting and biophysical characterization of the controller protein C.AhdI suggests the basis of a genetic switch.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 6445
EP  - 6453
VL  - 32
AB  - We have cloned and expressed the ahdIC gene of the AhdI restriction-modification system and
AB  - have purified the resulting controller (C) protein to homogeneity. The protein sequence shows
AB  - a HTH motif typical of that found in many transcriptional regulators. C.AhdI is found to form
AB  - a homodimer of 16.7 kDa; sedimentation equilibrium experiments show that the dimer dissociates
AB  - into monomers at low concentration, with a dissociation constant of 2.5 microM. DNase I and
AB  - Exo III footprinting were used to determine the C.AhdI DNA-binding site, which is found
AB  - approximately 30 bp upstream of the ahdIC operon. The intact homodimer binds cooperatively to
AB  - a 35 bp fragment of DNA containing the C-protein binding site with a dissociation constant of
AB  - 5-6 nM, as judged both by gel retardation analysis and by surface plasmon resonance, although
AB  - in practice the affinity for DNA is dominated by protein dimerization as DNA binding by the
AB  - monomer is negligible. The location of the C-operator upstream of both ahdIC and ahdIR
AB  - suggests that C.AhdI may act as a positive regulator of the expression of both genes, and
AB  - could act as a molecular switch that is critically dependent on the K(d) for the monomer-dimer
AB  - equilibrium. Moreover, the structure and location of the C.AhdI binding site with respect to
AB  - the putative -35 box preceding the C-gene suggests a possible mechanism for autoregulation of
AB  - C.AhdI expression.
ER  -

TY  - JOUR
AU  - Streiff, M.B.
AU  - Iida, S.
AU  - Bickle, T.A.
TI  - Expression and proteolytic processing of the darA antirestriction gene product of bacteriophage P1.
JO  - Virology
PY  - 1987
SP  - 167
EP  - 171
VL  - 157
AB  - The darA gene coding for one of the two bacteriophage P1 antirestriction functions is
AB  - expressed late after infection or induction.  The protein is made as a high-molecular-weight
AB  - soluble precursor.  This is proteolytically cleaved to the mature form, which is a structural
AB  - component of the phage head.  Defective mutants of the phage have been found in which the
AB  - synthesis of gpdarA is normal but processing does not take place.  These mutations all map to
AB  - the same region of the P1 genome and we propose that they lie in the structural gene for the
AB  - processing protease.
ER  -

TY  - JOUR
AU  - Striebel, H.-M.
AU  - Kessler, C.
TI  - Novel specific endonuclease activity recognizing a 10-bp sequence.
JO  - Gene
PY  - 1996
SP  - 47
EP  - 48
VL  - 172
AB  - We report here the generation of a novel restriction endonuclease (Enase) activity
AB  - with the 10-bp recognition sequence,
AB  - 5'-GmATnnnGmA/-TCnnnA-TC-3'
AB  - 3'-C-TAnnnC-T/mAGnnnTmAG-5'.
AB  - This specificity could be achieved by first methylating a substrate DNA with M.MamI in vivo,
AB  - followed by in vitro R.DpnI restriction.
ER  -

TY  - JOUR
AU  - Striebel, H.-M.
AU  - Schmitz, G.G.
AU  - Kaluza, K.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - MamI, a novel class-II restriction endonuclease from Microbacterium ammoniaphilum recognizing 5'-GATNN^NNATC-3'.
JO  - Gene
PY  - 1990
SP  - 95
EP  - 100
VL  - 91
AB  - A new site-specific class-II restriction endonuclease, MamI, has been discovered in the
AB  - nonsporulating Gram-positive Microbacterium ammoniaphilum. MamI recognition sequence and
AB  - cleavage positions were deduced using experimental and computer-assisted mapping and
AB  - sequencing approaches. MamI cleavage specificity corresponds to: 5'-GATNN^NNATC-3'
AB  - 3'-CTANN^NNTAG-5'. The novel 43-kD enzyme recognizes a palindromic hexanucleotide
AB  - interrupted by four ambiguous nucleotides. MamI cleavage positions are both located in the
AB  - center of the recognition sequence resulting in blunt-ended fragments after cleavage in the
AB  - presence of Mg2+ ions. MamI is inhibited by N6-methyladenine residues. In case of overlapping
AB  - sequences of MamI and Escherichia coli-coded DNA modification methyltransferase M.EcodamI
AB  - (5'-GmATC-3'), cleavage of DNA isolated from E. coli wild-type cells will be inhibited. By
AB  - applying incubation conditions forcing star activity, relaxation of MamI sequence specificity
AB  - is observed (MamI*).
ER  -

TY  - JOUR
AU  - Striebel, H.-M.
AU  - Seeber, S.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - Cloning and characterization of the MamI restriction-modification system from Microbacterium ammoniaphilum in Escherichia coli.
JO  - Gene
PY  - 1996
SP  - 41
EP  - 46
VL  - 172
AB  - The genes encoding a class-IIN restriction-modification (R-M) system (MamI,
AB  - sequence specificity 5'-GATnn/nnATC-3' / 3'-CTAnn/nnTAG-5' from Microbacterium
AB  - ammoniaphilum have been cloned in Escherichia coli.  The vector used for cloning was plasmid
AB  - pUC18 modified by the inclusion of three MamI recognition sites.  Recombinant clones
AB  - containing
AB  - the mamIM gene in its genomic context became fully methylated in vivo and remained completely
AB  - resistant against digestion with the R.MamI restriction enodnuclease (Enase).  Determination
AB  - of the
AB  - nucleotide (nt) sequence revealed three open reading frames with lengths of 1089 bp (ORF1),
AB  - 276
AB  - bp (ORFc) and 927 bp (ORF2).  On the basis of expression and deletion experiments, the 1089-bp
AB  - ORF1 was assigned to mamIM encoding the M.MamI DNA methyltransferase (Mtase).  By amino
AB  - acid sequencing of the N terminus of R.MamI and comparison of the deduced nt sequence with
AB  - ORF2, the 927-bp ORF2 was idenified as the mamIR gene encoding R.MamI.  The 276-bp Orfc,
AB  - located between mamIR and mamIM, is part of the DNA sequence downstream from mamIM
AB  - shown to be necessary for controlled mamIM expression.
ER  -

TY  - JOUR
AU  - Strikhanov, S.N.
AU  - Aleshkin, G.I.
AU  - Skavronskaya, A.G.
TI  - Plasmid recombination stimulated by restriction endonuclease EcoRI in vivo: specificity of recombinant plasmid formation in RecA cells of Escherichia coli.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1985
SP  - 13
EP  - 19
VL  - 5
AB  - The restriction endonuclease EcoRI dependent recombination of compatible plasmids has been
AB  - studied in RecA cells of Escherichia coli.  Plasmid RP4 and the isogenic ColE1 type plasmids
AB  - pSA14 or pSA25, differing in restriction-modification RM EcoRI genes, have been used to study
AB  - this type of recombination.  EcoRI dependent recombination of plasmids is demonstrated in RecA
AB  - cells and, thus, is independent of general system of homologous recombination.  The classes of
AB  - recombinant plasmids isolated from RecA cells differ from the classes isolated from wild type
AB  - cells.  Levels of tetracyclin resistance conferred by plasmid RP4 are shown to be dependent on
AB  - the alleles of recA+ gene, being extremely low in RecA cells.  This property is demonstrated
AB  - to be useful for obtaining the multicopy recombinant plasmids resulting from EcoRI dependent
AB  - recombination in RecA cells of Escherichia coli.
ER  -

TY  - JOUR
AU  - Stringer, S.C.
AU  - Carter, A.T.
AU  - Webb, M.D.
AU  - Wachnicka, E.
AU  - Crossman, L.C.
AU  - Sebaihia, M.
AU  - Peck, M.W.
TI  - Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.
JO  - BMC Genomics
PY  - 2013
SP  - 333
EP  - 333
VL  - 14
AB  - BACKGROUND: Clostridium botulinum is a group of four physiologically and
AB  - phylogenetically distinct bacteria that produce botulinum neurotoxin. While
AB  - studies have characterised variability between strains of Group I (proteolytic)
AB  - C. botulinum, the genetic and physiological variability and relationships between
AB  - strains within Group II (non-proteolytic) C. botulinum are not well understood.
AB  - In this study the genome of Group II strain C. botulinum Eklund 17B (NRP) was
AB  - sequenced and used to construct a whole genome DNA microarray. This was used in a
AB  - comparative genomic indexing study to compare the relatedness of 43 strains of
AB  - Group II C. botulinum (14 type B, 24 type E and 5 type F). These results were
AB  - compared with characteristics determined from physiological tests. RESULTS: Whole
AB  - genome indexing showed that strains of Group II C. botulinum isolated from a wide
AB  - variety of environments over more than 75 years clustered together indicating the
AB  - genetic background of Group II C. botulinum is stable. Further analysis showed
AB  - that strains forming type B or type F toxin are closely related with only toxin
AB  - cluster genes targets being unique to either type. Strains producing type E toxin
AB  - formed a separate subset. Carbohydrate fermentation tests supported the
AB  - observation that type B and F strains form a separate subset to type E strains.
AB  - All the type F strains and most of type B strains produced acid from amylopectin,
AB  - amylose and glycogen whereas type E strains did not. However, these two subsets
AB  - did not differ strongly in minimum growth temperature or maximum NaCl
AB  - concentration for growth. No relationship was found between tellurite resistance
AB  - and toxin type despite all the tested type B and type F strains carrying tehB,
AB  - while the sequence was absent or diverged in all type E strains. CONCLUSIONS:
AB  - Although Group II C. botulinum form a tight genetic group, genomic and
AB  - physiological analysis indicates there are two distinct subsets within this
AB  - group. All type B strains and type F strains are in one subset and all type E
AB  - strains in the other.
ER  -

TY  - JOUR
AU  - Strittmatter, A.W. et al.
TI  - Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.
JO  - Environ. Microbiol.
PY  - 2009
SP  - 1038
EP  - 1055
VL  - 11
AB  - Summary Sulfate-reducing bacteria (SRB) belonging to the metabolically
AB  - versatile Desulfobacteriaceae are abundant in marine sediments and
AB  - contribute to the global carbon cycle by complete oxidation of organic
AB  - compounds. Desulfobacterium autotrophicum HRM2 is the first member of this
AB  - ecophysiologically important group with a now available genome sequence.
AB  - With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about
AB  - 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A
AB  - high number of genome plasticity elements (> 100 transposon-related
AB  - genes), several regions of GC discontinuity and a high number of
AB  - repetitive elements (132 paralogous genes Mbp(-1)) point to a different
AB  - genome evolution when comparing with Desulfovibrio spp. The metabolic
AB  - versatility of Db. autotrophicum HRM2 is reflected in the presence of
AB  - genes for the degradation of a variety of organic compounds including
AB  - long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables
AB  - the organism to completely oxidize acetyl-CoA to CO(2) but also to grow
AB  - chemolithoautotrophically. The presence of more than 250 proteins of the
AB  - sensory/regulatory protein families should enable Db. autotrophicum HRM2
AB  - to efficiently adapt to changing environmental conditions. Genes encoding
AB  - periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have
AB  - been detected as well as genes for the transmembrane TpII-c(3), Hme and
AB  - Rnf complexes. Genes for subunits A, B, C and D as well as for the
AB  - proposed novel subunits L and F of the heterodisulfide reductases are
AB  - present. This enzyme is involved in energy conservation in methanoarchaea
AB  - and it is speculated that it exhibits a similar function in the process of
AB  - dissimilatory sulfate reduction in Db. autotrophicum HRM2.
ER  -

TY  - JOUR
AU  - Strnad, H.
AU  - Lapidus, A.
AU  - Paces, J.
AU  - Ulbrich, P.
AU  - Vlcek, C.
AU  - Paces, V.
AU  - Haselkorn, R.
TI  - Complete Genome Sequence of the Photosynthetic Purple Nonsulfur Bacterium Rhodobacter capsulatus SB 1003.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3545
EP  - 3546
VL  - 192
AB  - Rhodobacter capsulatus SB 1003 belongs to the group of purple nonsulfur bacteria. Its genome
AB  - consists of a 3.7-Mb chromosome and a 133-kb plasmid.
AB  - The genome encodes genes for photosynthesis, nitrogen fixation,
AB  - utilization of xenobiotic organic substrates, and synthesis of
AB  - polyhydroxyalkanoates. These features made it a favorite research tool for
AB  - studying these processes. Here we report its complete genome sequence.
ER  -

TY  - JOUR
AU  - Strnad, H.
AU  - Patek, M.
AU  - Fousek, J.
AU  - Szokol, J.
AU  - Ulbrich, P.
AU  - Nesvera, J.
AU  - Paces, V.
AU  - Vlcek, C.
TI  - Genome Sequence of Rhodococcus erythropolis Strain CCM2595, a Phenol Derivative-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00208
EP  - e00214
VL  - 2
AB  - We announce the completion of the genome sequence of a phenol derivative-degrading bacterium,
AB  - Rhodococcus erythropolis strain CCM2595. This
AB  - bacterium is interesting in the context of bioremediation for its capability to
AB  - degrade phenol, catechol, resorcinol, hydroxybenzoate, hydroquinone,
AB  - p-chlorophenol, p-nitrophenol, pyrimidines, and sterols.
ER  -

TY  - JOUR
AU  - Strnad, H.
AU  - Ridl, J.
AU  - Paces, J.
AU  - Kolar, M.
AU  - Vlcek, C.
AU  - Paces, V.
TI  - Complete Genome Sequence of the Haloaromatic Acids-degrading Bacterium Achromobacter xylosoxidans A8.
JO  - J. Bacteriol.
PY  - 2010
SP  - 791
EP  - 792
VL  - 193
AB  - Achromobacter xylosoxidans strain A8 was isolated from soil contaminated with polychlorinated
AB  - biphenyls. It can use 2-chlorobenzoate and
AB  - 2,5-dichlorobenzoate as sole sources of carbon and energy. This property
AB  - makes it a good starting microorganism for further development towards a
AB  - bioremediation tool. The genome of A. xylosoxidans consists of a 7-Mb
AB  - chromosome and two large plasmids (98 kb, 248 kb). Besides genes for
AB  - utilization of xenobiotic organic substrates it encodes genes associated
AB  - with pathogenesis, toxin production and resistance. Here we report its
AB  - complete genome sequence.
ER  -

TY  - JOUR
AU  - Strobel, S.A.
AU  - Doucette-Stamm, L.A.
AU  - Riba, L.
AU  - Housman, D.E.
AU  - Dervan, P.B.
TI  - Site-specific cleavage of human chromosome 4 mediated by triple-helix formation.
JO  - Science
PY  - 1991
SP  - 1639
EP  - 1642
VL  - 254
AB  - Direct physical isolation of specific DNA segments from the human genome is a
AB  - necessary goal in human genetics.  For testing whether triple-helix mediated
AB  - enzymatic cleavage can liberate a specific segment of a human chromosome, the
AB  - tip of human chromosome 4, which contains the entire candidate region for the
AB  - Huntington's disease gene, was chosen as a target.  A 16-base pyrimidine
AB  - oligodeoxyribonucleotide was able to locate a 16-base pair purine target site
AB  - within more than 10 gigabase pairs of genomic DNA and mediate the exact
AB  - enzymatic cleavage at that site in more than 80 percent yield.  The recognition
AB  - motif is sufficiently generalizable that most cosmids should contain a sequence
AB  - targetable by triple-helix formation.  This method may facilitate the
AB  - orchestrated dissection of human chromosomes from normal and affected
AB  - individuals into megabase sized fragments and facilitate the isolation of
AB  - candidate gene loci.
ER  -

TY  - JOUR
AU  - Strobel, T.
AU  - Al-Dilaimi, A.
AU  - Blom, J.
AU  - Gessner, A.
AU  - Kalinowski, J.
AU  - Luzhetska, M.
AU  - Puhler, A.
AU  - Szczepanowski, R.
AU  - Bechthold, A.
AU  - Ruckert, C.
TI  - Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae.
JO  - BMC Genomics
PY  - 2012
SP  - 465
EP  - 465
VL  - 13
AB  - ABSTRACT: BACKGROUND: The genus Saccharothrix is a representative of the family
AB  - Pseudonocardiaceae, known to include producer strains of a wide variety of potent
AB  - antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of
AB  - the promising new class of heptadecaglycoside antibiotics, active against both
AB  - bacteria and yeast. RESULTS: To better assess its capabilities, the complete
AB  - genome sequence of S. espanaensis was established. With a size of 9,360,653 bp,
AB  - coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large
AB  - genomes. Besides a predicted core genome of 810 genes shared in the family, S.
AB  - espanaensis has a large number of accessory genes: 2,967 singletons when compared
AB  - to the family, of which 1,292 have no clear orthologs in the RefSeq database. The
AB  - genome analysis revealed the presence of 26 biosynthetic gene clusters
AB  - potentially encoding secondary metabolites. Among them, the cluster coding for
AB  - the saccharomicins could be identified. CONCLUSION: S. espanaensis is the first
AB  - completely sequenced species of the genus Saccharothrix. The genome discloses the
AB  - cluster responsible for the biosynthesis of the saccharomicins, the largest
AB  - oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25
AB  - additional putative secondary metabolite gene clusters further suggesting the
AB  - strain's potential for natural product synthesis.
ER  -

TY  - JOUR
AU  - Strobl, J.S.
AU  - Thompson, E.B.
TI  - Methylation of either cytosine in the recognition sequence CGCG inhibits ThaI cleavage of DNA.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 8073
EP  - 8083
VL  - 12
AB  - ThaI (CGCG) sites which overlap HhaI (GCGC) sites in PhiX174 and pBR322 DNA
AB  - were methylated in vitro with HhaI methylase and S-adenosylmethionine to yield
AB  - CGmCG, mCGmCG (5-methylcytosine, mC).  Methylation of either cytosine in the
AB  - ThaI recognition sequence rendered the DNA resistant to ThaI cleavage.  Rat
AB  - pituitary cell genomic DNA was digested with ThaI or 2 other known
AB  - methylation-sensitive enzymes, AvaI or XhoI.  After electrophoresis and
AB  - ethidium bromide staining of the DNA, all 3 enzymes showed the infrequent DNA
AB  - cleavage characteristic of methylation-sensitive enzymes.  Comparison of
AB  - pituitary growth hormone (GH) genes bearing strain-specific degrees of
AB  - methylation showed the less methylated gene to be more frequently cut by either
AB  - AvaI or ThaI.  ThaI resistant sites in GH genes were cleaved by ThaI after
AB  - exposing cells to 5-azacytidine, an inhibitor of DNA methylation.  We conclude
AB  - that ThaI is a useful restriction enzyme for the analysis of mC at CGCG
AB  - sequences in eukaryotic DNA.
ER  -

TY  - JOUR
AU  - Strous, M. et al.
TI  - Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
JO  - Nature
PY  - 2006
SP  - 790
EP  - 794
VL  - 440
AB  - Anaerobic ammonium oxidation (anammox) has become a main focus in
AB  - oceanography and wastewater treatment.  It is also the nitrogen cycle's
AB  - major remaining biochemical enigma.  Among its features, the occurrence of
AB  - hydrazine as a free intermediate of catabolism, the biosynthesis of
AB  - ladderane lipids and the role of cytoplasm differentiation are unique in
AB  - biology.  Here we use environmental genomics - the reconstruction of
AB  - genomic data directly from the environment - to assemble the genome of the
AB  - uncultured anammox bacterium Kuenenia stuttgartiensis from a complex
AB  - bioreactor community.  The genome data illuminate the evolutionary history
AB  - of the Planctomycetes and allow us to expose the genetic blueprint of the
AB  - organism's special properties.  Most significantly, we identified candidate
AB  - genes responsible for ladderane biosynthesis and biological hydrazine
AB  - metabolism, and discovered unexpected metabolic versatility.
ER  -

TY  - JOUR
AU  - Strzelecka, T.
AU  - Dorner, L.
AU  - Schildkraut, I.
AU  - Aggarawal, A.
TI  - Structural studies of the BamHI restriction enzyme.
JO  - Biophys. J.
PY  - 1990
SP  - 68
EP  - 68
VL  - 57
AB  - Type II restriction enzymes are ideal for studying protein-DNA interactions
AB  - because of their high sequence specificity and striking variety.  Large,
AB  - well-ordered BamHI crystals, diffracting to 2.3 angstrom, were obtained from
AB  - PEG solutions.  These crystals occur in two forms:  monoclinic (space group C2,
AB  - unit cell constants: a=76.24 angstrom, b=46.0 angstrom, c=69.4 angstrom and
AB  - beta=110.5 degrees) and orthorhombic (space group C222/1, unit cell constants:
AB  - a=46.7 angstrom, b=76.6 angstrom and c=143.6 angstrom).  In both crystal forms
AB  - there is one protein monomer per asymmetric unit.  Currently, we are searching
AB  - for heavy atom derivatives of the enzyme.  We are also attempting
AB  - cocrystallization of the enzyme with a 12-bp DNA fragment containing the BamHI
AB  - recognition site (5'-GGATCC-3').  We have recently obtained large, plate-like
AB  - crystals, which we are exploring for the presence of DNA by X-ray and
AB  - biochemical methods.
ER  -

TY  - JOUR
AU  - Strzelecka, T.
AU  - Newman, M.
AU  - Dorner, L.F.
AU  - Knott, R.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Crystallization and preliminary X-ray analysis of restriction endonuclease BamHI-DNA complex.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 430
EP  - 432
VL  - 239
AB  - Restriction endonuclease BamHI from Bacillus amyloliquefaciens has been co-crystallized with a
AB  - 12 bp DNA fragment that encompasses its recognition site. The co-crystals diffract to at least
AB  - 1.95 A resolution and belong to space group P212121. The unit cell parameters are a=108.8 A,
AB  - b=81.9 A, c=68.8 A, consistent with one complex in the crystallographic asymmetric unit. The
AB  - direction of the DNA appears to be along the b axis. In order to achieve end to end stacking
AB  - of DNA, the complex must lie on the screw axis along b. A self-rotation function has
AB  - determined the directions of the non-crystallographic 2-fold axes.
ER  -

TY  - JOUR
AU  - Stucken, K.
AU  - John, U.
AU  - Cembella, A.
AU  - Murillo, A.A.
AU  - Soto-Liebe, K.
AU  - Fuentes-Valdes, J.J.
AU  - Friedel, M.
AU  - Plominsky, A.M.
AU  - Vasquez, M.
AU  - Glockner, G.
TI  - The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications.
JO  - PLoS ONE
PY  - 2010
SP  - E9235
EP  - E9235
VL  - 5
AB  - Cyanobacterial morphology is diverse, ranging from unicellular spheres or
AB  - rods to multicellular structures such as colonies and filaments.
AB  - Multicellular species represent an evolutionary strategy to differentiate
AB  - and compartmentalize certain metabolic functions for reproduction and
AB  - nitrogen (N(2)) fixation into specialized cell types (e.g. akinetes,
AB  - heterocysts and diazocytes). Only a few filamentous, differentiated
AB  - cyanobacterial species, with genome sizes over 5 Mb, have been sequenced.
AB  - We sequenced the genomes of two strains of closely related filamentous
AB  - cyanobacterial species to yield further insights into the molecular basis
AB  - of the traits of N(2) fixation, filament formation and cell
AB  - differentiation. Cylindrospermopsis raciborskii CS-505 is a
AB  - cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis
AB  - brookii D9 from Brazil synthesizes neurotoxins associated with paralytic
AB  - shellfish poisoning (PSP). Despite their different morphology, toxin
AB  - composition and disjunct geographical distribution, these strains form a
AB  - monophyletic group. With genome sizes of approximately 3.9 (CS-505) and
AB  - 3.2 (D9) Mb, these are the smallest genomes described for free-living
AB  - filamentous cyanobacteria. We observed remarkable gene order conservation
AB  - (synteny) between these genomes despite the difference in repetitive
AB  - element content, which accounts for most of the genome size difference
AB  - between them. We show here that the strains share a specific set of 2539
AB  - genes with >90% average nucleotide identity. The fact that the CS-505 and
AB  - D9 genomes are small and streamlined compared to those of other
AB  - filamentous cyanobacterial species and the lack of the ability for
AB  - heterocyst formation in strain D9 allowed us to define a core set of genes
AB  - responsible for each trait in filamentous species. We presume that in
AB  - strain D9 the ability to form proper heterocysts was secondarily lost
AB  - together with N(2) fixation capacity. Further comparisons to all available
AB  - cyanobacterial genomes covering almost the entire evolutionary branch
AB  - revealed a common minimal gene set for each of these cyanobacterial
AB  - traits.
ER  -

TY  - JOUR
AU  - Stucken, K.
AU  - Koch, R.
AU  - Dagan, T.
TI  - Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering.
JO  - Biol. Res.
PY  - 2013
SP  - 373
EP  - 382
VL  - 46
AB  - Cyanobacteria display a large diversity of cellular forms ranging from unicellular to complex
AB  - multicellular filaments or aggregates. Species in the group present a wide range of metabolic
AB  - characteristics including the fixation of atmospheric nitrogen, resistance to extreme
AB  - environments, production of hydrogen, secondary metabolites and exopolysaccharides. These
AB  - characteristics led to the growing interest in cyanobacteria across the fields of ecology,
AB  - evolution, cell biology and biotechnology. The nu ber of available cyanobacterial genome
AB  - sequences has increased considerably in recent years, with more than 140 fully sequenced
AB  - genomes to date. Genetic engineering of cyanobacteria is widely applied to the model
AB  - unicellular strains Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942. However
AB  - the establishment of transformation protocols in many other cyanobacterial strains is
AB  - challenging. One obstacle to the development of these novel model organisms is that many
AB  - species have doubling times of 48 h or more, much longer than the bacterial models E. coli or
AB  - B. subtilis. Furthermore, cyanobacterial defense mechanisms against foreign DNA pose a
AB  - physical and biochemical barrier to DNA insertion in most strains. Here we review the various
AB  - barriers to DNA uptake in the context of lateral gene transfer among microbes and the various
AB  - mechanisms for DNA acquisition within the prokaryotic domain. Understanding the cyanobacterial
AB  - defense mechanisms is expected to assist in the development and establishment of novel
AB  - transformation protocols that are specifically suitable for this group.
ER  -

TY  - JOUR
AU  - Stuckle, E.E.
AU  - Emmrich, C.
AU  - Grob, U.
AU  - Nielsen, P.J.
TI  - Statistical analysis of nucleotide sequences.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6641
EP  - 6647
VL  - 18
AB  - In order to scan nucleic acid databases for potentially relevant but as yet
AB  - unknown signals, we have developed an improved statistical model for pattern
AB  - analysis of nucleic acid sequences by modifying previous methods based on
AB  - Markov chains.  We demonstrate the importance of selecting the appropriate
AB  - parameters in order for the method to function at all.  The model allows the
AB  - simultaneous analysis of several short sequences with unequal base frequencies
AB  - and Markov order k+0 as is usually the case in databases.  As a test of these
AB  - modifications, we show that in E. coli sequences there is a bias against
AB  - palindromic hexamers which correspond to known restriction enzyme recognition
AB  - sites.
ER  -

TY  - JOUR
AU  - Studholme, D.J.
AU  - Wasukira, A.
AU  - Paszkiewicz, K.
AU  - Aritua, V.
AU  - Thwaites, R.
AU  - Smith, J.
AU  - Grant, M.
TI  - Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.
JO  - Genes (Basel)
PY  - 2011
SP  - 1050
EP  - 1065
VL  - 2
AB  - We present draft genome sequences for three strains of Xanthomonas species, each of which was
AB  - associated with banana plants (Musa species) but is not closely related to the previously
AB  - sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had
AB  - been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the
AB  - species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas
AB  - sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X.
AB  - sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly
AB  - sequenced strains share many genomic features with the previously sequenced Xanthomonas
AB  - albilineans, for example possessing an unsual metE allele and lacking the Hrp type III
AB  - secretion system. However, they are distinct from Xanthomonas albilineans in many respects,
AB  - for example showing little evidence of genome reduction. They also lack the SPI-1 type III
AB  - secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains
AB  - possess a gum gene cluster. The data reported here provide the first genome-wide survey of
AB  - non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of
AB  - this group. We hope that the availability of complete sequence data for this group of
AB  - organisms is the first step towards understanding their interactions with plants and
AB  - identifying potential virulence factors.
ER  -

TY  - JOUR
AU  - Studier, F.W.
TI  - Gene 0.3 of Bacteriophage T7 Acts to Overcome the DNA Restriction System of the Host.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 283
EP  - 295
VL  - 94
AB  - Wild-type bacteriophage T7 is not subject to restriction by the Escherichia
AB  - coli B and K restriction systems, but T7 mutants that are susceptible to such
AB  - restriction have been isolated.  These mutants are all defective in gene 0.3,
AB  - the first T7 gene to be expressed after infection.  The gene 0.3 protein
AB  - apparently acts to prevent modification as well as restriction, suggesting that
AB  - it may interact with a component of the host restriction-modification system
AB  - that is required for both processes.  Mutants in which gene 0.3 is completely
AB  - deleted are only partially modified by growth on hosts with an active
AB  - restriction-modification system, presumably because the conditions of T7
AB  - infection overload the modifying capacity of the cells.  This is in contrast to
AB  - phages such as lambda that are completely modified during growth.  Since gene
AB  - 0.3 is not essential for growth in non-restricting hosts, it has been possible
AB  - to isolate deletions which extend to the left of gene 0.3 into the region where
AB  - E. coli RNA polymerase initiates the synthesis of T7 early RNA.  Two of the
AB  - three strong initiators from which E. coli RNA polymerase transcribes the early
AB  - region can be deleted.  In the course of searching for T7 mutants that are
AB  - unable to overcome restriction, it was discovered that mutants defective in
AB  - gene 2 are able to plate on E. coli C with essentially normal efficiency, and
AB  - most gene 7 mutants are able to plate on both C and K strains.  It has not been
AB  - determined why genes 2 and 7 seem to be needed for growth in some E. coli
AB  - strains but not in others.
ER  -

TY  - JOUR
AU  - Studier, F.W.
AU  - Bandyopadhyay, P.K.
TI  - Model for how type I restriction enzymes select cleavage sites in DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1988
SP  - 4677
EP  - 4681
VL  - 85
AB  - Under appropriate conditions, digestion of phage T7 DNA by the type I
AB  - restriction enzyme EcoK produces an orderly progression of discrete DNA
AB  - fragments.  All details of the fragmentation pattern can be explained on the
AB  - basis of the known properties of type I enzymes, together with two further
AB  - assumptions:  (i) in the ATP-stimulated translocation reaction, the enzyme
AB  - bound at the recognition sequence translocates DNA toward itself from both
AB  - direction simultaneously; and (ii) when translocation causes neighboring
AB  - enzymes to meet, they cut the DNA between them.  The kinetics of digestion at
AB  - 37C indicates that the rate of translocation of DNA from each side of a bound
AB  - enzyme is about 200 base pairs per second, and the cuts are completed within
AB  - 15-25 sec of the time neighboring enzymes meet.  The resulting DNA fragments
AB  - each contain a single recognition site with an enzyme (or subunit) remaining
AB  - bound to it.  At high enzyme concentrations, such fragments can be further
AB  - degraded, apparently by cooperation between the specifically bound and excess
AB  - enzymes.  This model is consistent with a substantial body of previous work on
AB  - the nuclease activity of EcoB and EcoK, and it explains in a simple way how
AB  - cleavage sites are selected.
ER  -

TY  - JOUR
AU  - Studier, F.W.
AU  - Movva, N.R.
TI  - SAMase gene of bacteriophage T3 is responsible for overcoming host restriction.
JO  - J. Virol.
PY  - 1976
SP  - 136
EP  - 145
VL  - 19
AB  - Deletion and point mutants of T3 have been isolated and used to show that the
AB  - early region of T3 DNA is organized in the same way as that of T7 DNA.
AB  - Homologous early RNAs and proteins of the two phages have been identified by
AB  - electrophoresis on polyacrylamide gels in the presence of sodium dodecyl
AB  - sulfate.  Both phages have five early mRNA's, numbered 0.3, 0.7, 1,1.1, and 1.3
AB  - from left to right, although no T3 protein that corresponds to the 1.1 protein
AB  - of T7 has yet been identified.  In general, corresponding early RNAs and
AB  - proteins of the two phages migrate differently on gels, indicating that they
AB  - differ in molecular weight and/or conformation.  In both T7 and T3, gene 0.3 is
AB  - responsible for overcoming the DNA restriction system of the host, gene 0.7
AB  - specifies a protein kinase, gene 1 specifies a phage-specific RNA polymerase,
AB  - and gene 1.3 specifies a polynucleotide ligase.  The 0.3 protein of T3 is
AB  - responsible for the S-adenosylmethionine cleaving activity (SAMase) induced
AB  - after T3 (but not T7) infection.  However, cleaving of S-adenosylmethionine
AB  - does not appear to be the primary mechanism by which T3 overcomes host
AB  - restriction, since at least one mutant of T3 has lost the SAMase activity
AB  - without losing the ability to overcome host restriction.
ER  -

TY  - JOUR
AU  - Sturino, J.M.
AU  - Rajendran, M.
AU  - Altermann, E.
TI  - Draft Genome Sequence of Lactobacillus animalis 381-IL-28.
JO  - Genome Announcements
PY  - 2014
SP  - e00478
EP  - e00414
VL  - 2
AB  - Lactobacillus animalis 381-IL-28 is an integral component of a multistrain commercial culture
AB  - with food biopreservative and pathogen biocontrol
AB  - functionality. A draft sequence of the L. animalis 381-IL-28 genome is described
AB  - in this paper.
ER  -

TY  - JOUR
AU  - Sturino, J.M.
AU  - Rajendran, M.
AU  - Altermann, E.
TI  - Draft Genome Sequence of the Pediocin-Encoding Biopreservative and Biocontrol Strain Pediococcus acidilactici D3.
JO  - Genome Announcements
PY  - 2013
SP  - e00208
EP  - e00213
VL  - 1
AB  - We describe a draft genome sequence for Pediococcus acidilactici strain D3, a component of
AB  - multistrain commercial cultures with biopreservative and biocontrol
AB  - properties in food-based applications. Strain D3 encodes at least one
AB  - antimicrobial peptide, pediocin AMPd3. The AMPd3-encoding operon exhibits high
AB  - sequence similarity to the archetype pediocin, PA-1, encoded by P. acidilactici
AB  - PAC 1.0.
ER  -

TY  - JOUR
AU  - Sturm, G.
AU  - Buchta, K.
AU  - Kurz, T.
AU  - Rensing, S.A.
AU  - Gescher, J.
TI  - Draft Genome Sequence of Leucobacter chromiiresistens, an Extremely Chromium-Tolerant Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 540
EP  - 541
VL  - 194
AB  - Here we present the draft genome of Leucobacter chromiiresistens. This is the first genome
AB  - sequence of an organism belonging to the genus
AB  - Leucobacter. L. chromiiresistens was sequenced due to its capability to
AB  - tolerate up to 300 mM Cr(VI) in the medium, which is so far a unique
AB  - feature for microorganisms.
ER  -

TY  - JOUR
AU  - Sturm, R.A.
AU  - Yaciuk, P.
TI  - DNA cleavage by restriction endonucleases PflMI is inhibited in recognition sites modified by dcm methylation.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 3615
EP  - 3615
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Sturrock, S.S.
AU  - Dryden, D.T.
AU  - Atanasiu, C.
AU  - Dornan, J.
AU  - Bruce, S.
AU  - Cronshaw, A.
AU  - Taylor, P.
AU  - Walkinshaw, M.D.
TI  - Crystallization and preliminary X-ray analysis of ocr, the product of gene 0.3 of bacteriophage T7.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2001
SP  - 1652
EP  - 1654
VL  - 57
AB  - Ocr, the product of gene 0.3 of bacteriophage T7, prevents the action of restriction
AB  - endonucleases of the host bacteria. The amino-acid sequence of
AB  - ocr has less than 20% similarity to any protein of known three-dimensional
AB  - structure. Ocr has been crystallized in a number of different crystal
AB  - forms and X-ray data for the seleno-L-methionine-substituted form has been
AB  - collected to a resolution of 1.8 A. The presence of caesium was found to
AB  - be required for good crystal growth. Anomalous X-ray data was used to
AB  - identify possible positions for Se and Cs atoms in the unit cell.
ER  -

TY  - JOUR
AU  - Sturrock, S.S.
AU  - Dryden, D.T.F.
TI  - A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3408
EP  - 3414
VL  - 25
AB  - The S subunits of type I DNA restriction/modification enzymes are responsible for recognizing
AB  - the DNA target sequence for the enzyme.  They contain two domains of approximately 150 amino
AB  - acids, each of which is responsible for recognizing one half of the bipartite asymmetric
AB  - target.  In the absence of any known tertiary structure for type I enzymes or recognizable DNA
AB  - recognition motifs in the highly variable amino acid sequences of the S subunits, it has
AB  - previously not been possible to predict which amino acids are responsible for sequence
AB  - recognition.  Using a combination of sequence alignment and secondary structure prediction
AB  - methods to analyze the sequences of S subunits, we predict that all of the 51 known target
AB  - recognition domains have the same tertiary structure.  Furthermore, this structure is similar
AB  - to the structure of the TRD of the C5-cytosine methyltransferase, HhaI, which recognizes its
AB  - DNA target via interactions with two short polypeptide loops and a beta strand.  Our results
AB  - predict the location of these sequence recognition structures within the TRDs of all type I S
AB  - subunits.
ER  -

TY  - JOUR
AU  - Stuy, J.H.
TI  - Restriction Enzymes Do Not Play a Significant Role in Haemophilus Homospecific or Heterospecific Transformation.
JO  - J. Bacteriol.
PY  - 1976
SP  - 212
EP  - 220
VL  - 128
AB  - Competent Haemophilus influenzae Rd recipients, either as phage HP1 restricting
AB  - (r+) or nonrestricting (r-) nonlysogens or defective lysogens, were exposed to
AB  - deoxyribonucleic acids from various wild-type phage HP1 lysogenic H. influenzae
AB  - serotype strains (non-encapsulated derivatives of serotypes alpha, beta, c, d,
AB  - and e), to DNA from lysogenic Haemophilus parahaemolyticus, and to DNA from
AB  - modified and nonmodified phage HP1.  Transformation of antibiotic resistance
AB  - markers and of prophage markers in homospecific crosses was observed to be
AB  - unaffected by the recipient restriction phenotype, whereas the transfection
AB  - response was much reduced in r+ recipients.  Heterospecific transformation of
AB  - prophage markers was reduced by only 80 to 90%, whereas antibiotic resistance
AB  - marker transformation was 1,000 to 10,000 times lower.  Heterospecific
AB  - transfection was at least 100 times lower than homospecific transfection in
AB  - both r+ and r- recipients.  The general conclusion is that neither class I nor
AB  - class II restriction enzymes affect significantly the transformation efficiency
AB  - in homospecific and heterospecific crosses.  The efficiency of heterospecific
AB  - transformation may depend mainly on the deoxyribonucleic acid homology in the
AB  - genetic marker region.
ER  -

TY  - JOUR
AU  - Stynen, A.P. et al.
TI  - Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5871
EP  - 5872
VL  - 193
AB  - Campylobacter fetus subsp. venerealis is the etiologic agent of bovine genital
AB  - campylobacteriosis, a sexually transmitted disease of cattle that
AB  - is of worldwide importance. The complete sequencing and annotation of the
AB  - genome of the type strain C. fetus subsp. venerealis NCTC 10354(T) are
AB  - reported.
ER  -

TY  - JOUR
AU  - Styriak, I.
AU  - Pristas, P.
AU  - Javorsky, P.
TI  - Lack of surface receptors not restriction-modification system determines F4 phage resistance in Streptococcus bovis II/1.
JO  - Folia Microbiol. (Praha)
PY  - 1998
SP  - 35
EP  - 38
VL  - 43
AB  - The resistance of Streptococcus bovis strain II/1, the producer of SbvI restriction
AB  - endonuclease, to F4 phage infection was demonstrated by the double-agar-layer method.  Despite
AB  - the presence of restriction endonuclease SbvI which can cleave F4 phage DNA to numerous
AB  - fragments in vitro, the evidence that adsorption inhibition is the most important defense
AB  - mechanism in phage resistance of S. bovis II/1 strain was obtained by adhesion experiments in
AB  - vivo.  Electron microscopy of phage-host mixtures showed many phage particles on the bacterial
AB  - surface of phage-sensitive S. bovis 47/3 control strain in comparison with no phage particles
AB  - seen on S. bovis II/1 (phage-resistant) strain surface.
ER  -

TY  - JOUR
AU  - Su, C.C.
AU  - Deng, W.L.
AU  - Jan, F.J.
AU  - Chang, C.J.
AU  - Huang, H.
AU  - Chen, J.
TI  - Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan.
JO  - Genome Announcements
PY  - 2014
SP  - e00166
EP  - e00114
VL  - 2
AB  - The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from
AB  - the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported
AB  - here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of
AB  - 53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50
AB  - RNA genes.
ER  -

TY  - JOUR
AU  - Su, F.
AU  - Hua, D.
AU  - Zhang, Z.
AU  - Wang, X.
AU  - Tang, H.
AU  - Tao, F.
AU  - Tai, C.
AU  - Wu, Q.
AU  - Wu, G.
AU  - Xu, P.
TI  - Genome Sequence of Bacillus pumilus S-1, an Efficient Isoeugenol-Utilizing Producer for Natural Vanillin.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6400
EP  - 6401
VL  - 193
AB  - Bacillus pumilus S-1 is an efficient isoeugenol-utilizing producer of natural vanillin. The
AB  - genome of B. pumilus S-1 contains the epoxide
AB  - hydrolase and six candidate monooxygenases that make it possible to
AB  - explore the mechanism involved in conversion of isoenguenol to vanillin in
AB  - the B. pumilus strain.
ER  -

TY  - JOUR
AU  - Su, F.
AU  - Tao, F.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of the Thermophile Bacillus coagulans Hammer, the Type Strain of  the Species.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6294
EP  - 6295
VL  - 194
AB  - Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type
AB  - strain of the species within the genus Bacillus. Genomic analyses
AB  - based on the sequence may provide insights into the phylogeny of the species and
AB  - help to elucidate characteristics of the poorly studied strains of Bacillus
AB  - coagulans.
ER  -

TY  - JOUR
AU  - Su, F.
AU  - Xu, K.
AU  - Zhao, B.
AU  - Tai, C.
AU  - Tao, F.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of the Thermophilic Strain Bacillus coagulans XZL4, an Efficient Pentose-Utilizing Producer of Chemicals.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6398
EP  - 6399
VL  - 193
AB  - Bacillus coagulans XZL4 is an efficient pentose-utilizing producer of important platform
AB  - compounds, such as l-lactic acid, 2,3-butanediol, and
AB  - acetoin. Here we present a 2.8-Mb assembly of its genome. Simple and
AB  - efficient carbohydrate metabolism systems, especially the
AB  - transketolase/transaldolase pathway, make it possible to convert pentose
AB  - sugars to products at high levels.
ER  -

TY  - JOUR
AU  - Su, F.
AU  - Yu, B.
AU  - Sun, J.
AU  - Ou, H.Y.
AU  - Zhao, B.
AU  - Wang, L.
AU  - Qin, J.
AU  - Tang, H.
AU  - Tao, F.
AU  - Jarek, M.
AU  - Scharfe, M.
AU  - Ma, C.
AU  - Ma, Y.
AU  - Xu, P.
TI  - Genome Sequence of the Thermophilic Strain Bacillus coagulans 2-6, an Efficient Producer of High-Optical-Purity L-Lactic Acid.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4563
EP  - 4564
VL  - 193
AB  - Bacillus coagulans 2-6 is an efficient producer of lactic acid. The genome of B. coagulans 2-6
AB  - owns the smallest genome size among the members of genus Bacillus known to date. The
AB  - frameshift mutation at the start of D-lactate dehydrogenase might be responsible for the
AB  - production of high optical purity L-lactic-acid.
ER  -

TY  - JOUR
AU  - Su, H.
AU  - Zhang, T.
AU  - Bao, M.
AU  - Jiang, Y.
AU  - Wang, Y.
AU  - Tan, T.
TI  - Genome Sequence of a Promising Hydrogen-Producing Facultative Anaerobic Bacterium, Brevundimonas naejangsanensis Strain B1.
JO  - Genome Announcements
PY  - 2014
SP  - e00542
EP  - e00514
VL  - 2
AB  - Brevundimonas naejangsanensis strain B1 is a newly isolated, facultative anaerobic bacterium
AB  - capable of producing hydrogen with high efficiency. Here, we
AB  - present a 2.94-Mb assembly of the genome sequence of strain B1, which may provide
AB  - further insights into the molecular mechanism of hydrogen production from
AB  - bioresource.
ER  -

TY  - JOUR
AU  - Su, J.
AU  - Ye, J.
AU  - Zhu, Y.
TI  - Draft Genome Sequence of a Novel Bacterial Strain, LSJC7, Belonging to the Family Enterobacteriaceae with Dual Resistance to Arsenic and Tetracycline.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7005
EP  - 7006
VL  - 194
AB  - Strain LSJC7, with dual resistance to arsenic and tetracycline, was isolated from an antimony
AB  - tailing in China. Its 16S rRNA gene sequence has the highest
AB  - similarity to that of Enterobacter cloacae subsp. dissolvens LMG 2683(T)
AB  - (97.02%). Here we present the approximately 4.6-Mbp draft genome sequence of
AB  - strain LSJC7.
ER  -

TY  - JOUR
AU  - Su, L.
AU  - Wang, T.
AU  - Zhou, L.
AU  - Wu, C.
AU  - Guo, Y.
AU  - Chang, D.
AU  - Liu, Y.
AU  - Jiang, X.
AU  - Yin, S.
AU  - Liu, C.
TI  - Genome Sequence of Bacillus cereus Strain LCT-BC235, Carried by the Shenzhou VIII Spacecraft.
JO  - Genome Announcements
PY  - 2014
SP  - e00665
EP  - e00613
VL  - 2
AB  - In order to explore the effect of space environments on Bacillus cereus, we determined the
AB  - draft genome sequence of a B. cereus strain, LCT-BC235, which was
AB  - isolated after space flight.
ER  -

TY  - JOUR
AU  - Su, L.
AU  - Zhou, T.
AU  - Zhou, L.
AU  - Fang, X.
AU  - Li, T.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Chang, D.
AU  - Wang, Y.
AU  - Li, D.
AU  - Liu, C.
TI  - Draft Genome Sequence of Bacillus cereus Strain LCT-BC244.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3549
EP  - 3549
VL  - 194
AB  - Bacillus cereus is a prevalent, soil-dwelling, Gram-positive bacterium. Some strains are
AB  - harmful to humans and cause food-borne illness, while other strains
AB  - can be beneficial as probiotics for animals. To gain insight into the bacterial
AB  - genetic determinants, we report the genome sequence of a strain, LCT-BC244, which
AB  - was isolated from CGMCC 1.230.
ER  -

TY  - JOUR
AU  - Su, P.
AU  - Im, H.
AU  - Hsieh, H.
AU  - Kanga, S.
AU  - Dunn, N.W.
TI  - LlaFI, a type III restriction and modification system in Lactococcus lactis.
JO  - Appl. Environ. Microbiol.
PY  - 1999
SP  - 686
EP  - 693
VL  - 65
AB  - We describe a type III restriction and modification system, LlaFI, in Lactococcus lactis.
AB  - LlaFI is encoded by a 12-kb native plasmid, pND801, harbored in L. lactis LL42-1.  Sequencing
AB  - revealed two adjacent open reading frames.  One ORF encodes a 680-amino-acid polypeptide, and
AB  - this ORF is followed by a second ORF which encodes an 873-amino-acid polypeptide.  The two
AB  - ORFs appear to be organized in an operon.  A homology search revealed that the two ORFs
AB  - exhibited significant similarity to type III restriction and modification subunits.  The
AB  - complete amino acid sequence of the Mod subunit of LlaFI was aligned with the amino acid
AB  - sequences of four previously described type III methyltransferases.  Both the N-terminal
AB  - regions and the C-terminal regions of the Mod proteins are conserved, while the central
AB  - regions are more variable.  An S-adenosyl methionine binding motif (present in all adenine
AB  - methyltransferases) was found in the N-terminal region of the Mod protein.  The seven
AB  - conserved helicase motifs found in the previously described type III R/M systems were found at
AB  - the same relative positions in the LlaFI Res sequence, LlaFI has cofactor requirements for
AB  - activity that are characteristic of the previously described type III enzymes.  ATP and Mg2+
AB  - are required for endonucleolytic activity; however, the activity is not strictly dependent on
AB  - the presence of Ado-Met but is stimulated by it.  To our knowledge, this is the first type III
AB  - R/M system that has been characterized not just in lactic acid bacteria but also in
AB  - gram-positive bacteria.
ER  -

TY  - JOUR
AU  - Su, P.
AU  - Ng, A.
AU  - Kennelly, V.
AU  - Costello, M.
AU  - Harvey, M.
AU  - Dunn, N.
TI  - Additive effects of two different plasmid-linked restriction and modification systems in Lactococcus.
JO  - Biotechnol. Lett.
PY  - 1998
SP  - 515
EP  - 518
VL  - 20
AB  - Two plasmids, pND801 and pND802, encoding different restriction and modification systems were
AB  - isolated from Lactococcus lactis ssp. lactis LL42-1 and Lactococcus lactis ssp. cremoris
AB  - LC14-1, respectively.  PND802 contained one SphI restriction enzyme site and the whole plasmid
AB  - was cloned into the SphI site of the streptococcal/E. coli shuttle vector pSA3 generating the
AB  - plasmid pND803.  PND803 was stably maintained in L. lactis MG1363 harboring pND801.  The
AB  - combination of the two R/M systems within L. lactis MG1363 resulted in an additive resistance
AB  - towards both isometric phage and prolate phage.
ER  -

TY  - JOUR
AU  - Su, T.-J.
AU  - Connolly, B.A.
AU  - Darlington, C.
AU  - Mallin, R.
AU  - Dryden, D.T.F.
TI  - Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 2223
EP  - 2230
VL  - 32
AB  - The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and
AB  - methylates adenine at the underlined positions. DNA methylation has been shown by
AB  - crystallography to occur via a base flipping mechanism and is believed to be a general
AB  - mechanism for all methyltransferases. If no structure is available, the fluorescence of
AB  - 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence
AB  - when its environment is perturbed. We find that 2-aminopurine gives enhanced fluorescence
AB  - emission not only when it is placed at the M.EcoKI methylation sites but also at a location
AB  - adjacent to the target adenine. Thus it appears that 2-aminopurine fluorescence intensity is
AB  - not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon
AB  - addition of the cofactor S-adenosyl-methionine to the M.EcoKI:DNA complex, the 2-aminopurine
AB  - fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450
AB  - nm. This change requires a fully active enzyme, the correct cofactor and the 2-aminopurine
AB  - located at the methylation site. However, the new fluorescent species is not a covalently
AB  - modified form of 2-aminopurine and we suggest that it represents a hitherto undetected
AB  - physicochemical form of 2-aminopurine.
ER  -

TY  - JOUR
AU  - Su, T.-J.
AU  - Tock, M.R.
AU  - Egelhaaf, S.U.
AU  - Poon, W.C.K.
AU  - Dryden, D.T.F.
TI  - DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 3235
EP  - 3244
VL  - 33
AB  - The maintenance methyltransferase M.EcoKI recognizes the bipartite DNA sequence
AB  - 5'-AACNNNNNNGTGC-3', where N is any nucleotide. M.EcoKI preferentially methylates a sequence
AB  - already containing a methylated adenine at or complementary to the underlined bases in the
AB  - sequence. We find that the introduction of a single-stranded gap in the middle of the
AB  - non-specific spacer, of up to 4 nt in length, does not reduce the binding affinity of M.EcoKI
AB  - despite the removal of non-sequence-specific contacts between the protein and the DNA
AB  - phosphate backbone. Surprisingly, binding affinity is enhanced in a manner predicted by simple
AB  - polymer models of DNA flexibility. However, the activity of the enzyme declines to zero once
AB  - the single-stranded region reaches 4 nt in length. This indicates that the recognition of
AB  - methylation of the DNA is communicated between the two methylation targets not only through
AB  - the protein structure but also through the DNA structure. Furthermore, methylation recognition
AB  - requires base flipping in which the bases targeted for methylation are swung out of the DNA
AB  - helix into the enzyme. By using 2-aminopurine fluorescence as the base flipping probe we find
AB  - that, although flipping occurs for the intact duplex, no flipping is observed upon
AB  - introduction of a gap. Our data and polymer model indicate that M.EcoKI bends the non-specific
AB  - spacer and that the energy stored in a double-stranded bend is utilized to force or flip out
AB  - the bases. This energy is not stored in gapped duplexes. In this way, M.EcoKI can determine
AB  - the methylation status of two adenine bases separated by a considerable distance in
AB  - double-stranded DNA and select the required enzymatic response.
ER  -

TY  - JOUR
AU  - Su, X.
AU  - Cao, G.
AU  - Kuang, D.
AU  - Zhang, J.
AU  - Chen, Y.
AU  - Allard, M.
AU  - Brown, E.
AU  - Shi, X.
AU  - Meng, J.
AU  - Xu, X.
TI  - Draft Genome Sequences of Three Listeria monocytogenes Isolates from Foods in China.
JO  - Genome Announcements
PY  - 2017
SP  - e00220
EP  - e00217
VL  - 5
AB  - Listeria monocytogenes is a foodborne pathogen of global concern because of the high mortality
AB  - rate among patients. The draft genome sequences of three L.
AB  - monocytogenes strains isolated from foods are reported here. The availability of
AB  - these genomes should provide useful information on the genomic diversity of L.
AB  - monocytogenes isolated from foods in China.
ER  -

TY  - JOUR
AU  - Su, Y.C.
AU  - Horhold, F.
AU  - Singh, B.
AU  - Riesbeck, K.
TI  - Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an  Invasive Isolate That Caused Necrotizing Myositis.
JO  - Genome Announcements
PY  - 2013
SP  - e00470
EP  - e00413
VL  - 1
AB  - Haemophilus influenzae serotype f (Hif) is an etiologic agent of bacterial invasive disease.
AB  - Here, we report the first annotated genome sequence of the Hif
AB  - strain KR494, which was isolated from a patient suffering from sepsis and
AB  - necrotizing myositis. The genome sequence will increase the understanding of Hif
AB  - pathogenesis.
ER  -

TY  - JOUR
AU  - Suarez, N.E.
AU  - Saavedra, L.
AU  - Slozilova, I.
AU  - Bonacina, J.
AU  - Demnerova, K.
AU  - Sesma, F.
TI  - Draft Genome Sequence of Enterococcus faecium Strain CRL 1879, Isolated from a Northwestern Argentinian Artisanal Cheese.
JO  - Genome Announcements
PY  - 2013
SP  - e00514
EP  - e00513
VL  - 1
AB  - We report the draft genome sequence of the bacteriocin producer Enterococcus faecium strain
AB  - CRL 1879, isolated from a northwestern Argentinian artisanal
AB  - cheese. The draft genome sequence is composed of 73 contigs for 2,886,747 bp,
AB  - with 3,140 protein-coding genes. Six biosynthetic clusters for bacteriocin class
AB  - II production were found. Typical virulence determinants, which have relevance in
AB  - food safety, were not present.
ER  -

TY  - JOUR
AU  - Suarez, V.
AU  - Zago, M.
AU  - Giraffa, G.
AU  - Reinheimer, J.
AU  - Quiberoni, A.
TI  - Evidence for the presence of restriction/modification systems in Lactobacillus delbrueckii.
JO  - J. Dairy Res.
PY  - 2009
SP  - 433
EP  - 440
VL  - 76
AB  - The bacteriophages Cb1/204 and Cb1/342 were obtained by induction from the commercial strain
AB  - Lactobacillus delbrueckii subsp. lactis Cb1, and
AB  - propagated on Lactobacillus delbrueckii subsp. lactis 204 (Lb.l 204)
AB  - and Lactobacillus delbrueckii subsp. bulgaricus 342 (Lb.b 342),
AB  - respectively. By cross sensitivity, it was possible to detect a delay
AB  - in the lysis of Lb.l 204 with Cb1/342 phage, while the adsorption rate
AB  - was high (99-5%). Modified and unmodified phages were isolated using
AB  - phage Cb1/342 and strain Lb.l 204. The EOP (Efficiency of Plaquing)
AB  - values for the four phages (Cb1/204, Cb1/342, Cb1/342 modified and
AB  - Cb1/342 unmodified) suggested that an R/M system modified the original
AB  - temperate phage, and the Bg/II-DNA restriction patterns of these phages
AB  - might point out the presence of a Type II R/M system. Also, the
AB  - existence of a Type I R/M system was demonstrated by PCR and nucleotide
AB  - sequence, being the percentages of alignment homology with Type I R/M
AB  - systems reported previously higher than 95%. In this study it was
AB  - possible to demonstrate that the native phage resistant mechanisms and
AB  - the occurrence of prophages in commercial host strains, contribute
AB  - strongly to diversify the phage population in a factory environment.
ER  -

TY  - JOUR
AU  - Suarez, V.B.
AU  - Maciel, N.
AU  - Guglielmotti, D.
AU  - Zago, M.
AU  - Giraffa, G.
AU  - Reinheimer, J.
TI  - Phage-resistance linked to cell heterogeneity in the commercial strain Lactobacillus delbrueckii subsp lactis Ab1.
JO  - Int. J. Food Microbiol.
PY  - 2008
SP  - 401
EP  - 405
VL  - 128
AB  - The aim of this work was to study the relationship between the cell morphological
AB  - heterogeneity and the phage-resistance in the commercial
AB  - strain Lactobacillus delbrueckii subsp. lactis Ab1. Two morphological
AB  - variants (named C and T) were isolated from this strain.
AB  - Phage-resistant derivatives were isolated from them and the percentage
AB  - of occurrence of confirmed phage-resistant cells was 0.001% of the
AB  - total cellular population. Within these phage-resistant cell
AB  - derivatives there were T (3 out of 4 total isolates) and C (1 out of 4
AB  - total isolates) variants. The study of some technological properties
AB  - (e.g. proteolytic and acidifying activities) demonstrated that most of
AB  - phage-resistant derivatives were not as good as the parental strain.
AB  - However. for one derivative (a T variant), the technological properties
AB  - Were better than those of the parental strain. On the other hand, it
AB  - was possible to determinate that the system of phage-resistance in the
AB  - T variants was interference in adsorption step, with adsorption rates <
AB  - 15%. For the C variant derivative it was possible to demonstrate the
AB  - presence of a restriction/modification system and, moreover, to
AB  - determinate that this system could be Type 1R/M.
ER  -

TY  - JOUR
AU  - Suarez-Suarez, L.Y.
AU  - Brunet-Galmes, I.
AU  - Pina-Villalonga, J.M.
AU  - Christie-Oleza, J.A.
AU  - Pena, A.
AU  - Bennasar, A.
AU  - Armengaud, J.
AU  - Nogales, B.
AU  - Bosch, R.
TI  - Draft Genome Sequence of Citreicella aestuarii Strain 357, a Member of the Roseobacter Clade Isolated without Xenobiotic Pressure from a Petroleum-Polluted    Beach.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5464
EP  - 5465
VL  - 194
AB  - Citreicella aestuarii 357 is a member of the Roseobacter clade that was isolated  without
AB  - xenobiotic pressure from an oil-polluted sand sample from the Galician
AB  - coast (Spain). Its genome sequence suggests an organoheterotrophic metabolism,
AB  - including a wide catabolic potential for aromatic hydrocarbons.
ER  -

TY  - JOUR
AU  - Subach, F.
AU  - Kirsanova, O.
AU  - Liquier, J.
AU  - Gromova, E.S.
TI  - Resolution of the EcoRII restriction endonuclease-DNA complex structure in solution using fluorescence spectroscopy.
JO  - Biophys. Chem.
PY  - 2008
SP  - 107
EP  - 114
VL  - 138
AB  - The X-ray structure for the type HE EcoRII restriction endonuclease has been resolved (X.E.
AB  - Zhou, Y. Wang, M. Reuter, M. Mucke, D.H. Kruger,
AB  - EJ. Meehan and L. Chen. Crystal structure of type HE restriction
AB  - enclonuclease EcoRII reveals an autoinhibition mechanism by a novel
AB  - effector-binding fold. J. Mol. Biol. 335 (2004) 307319.1, but the
AB  - structure of the R.EcoRII-DNA complex is still unknown. The aim of this
AB  - article was to examine the structure of the pre-reactive R.EcoRII-DNA
AB  - complex in solution by fluorescence spectroscopy. The structure for the
AB  - R.EcoRII-DNA complex was resolved by determining the fluorescence
AB  - resonance energy transfer (FRET) between two fluorescent dyes,
AB  - covalently attached near the EcoRII recognition sites, that were
AB  - located at opposite ends of a lengthy two-site DNA molecule. Analysis
AB  - of the FRET data from the two-site DNA revealed a likely model for the
AB  - arrangement of the two EcoRII recognition sites relative to each other
AB  - in the R.EcoRII-DNA complex in the presence of Ca2+ ions. According to
AB  - this model, the R.EcoRII binds the two-site DNA and forms a DNA loop in
AB  - which the EcoRII recognition sites are 20 +/- 10 A distant to each
AB  - other and situated at an angle of 70 +/- 10 degrees.
ER  -

TY  - JOUR
AU  - Subach, F.V.
AU  - Liquier, J.
AU  - Gromova, E.S.
TI  - Investigation of restriction endonuclease EcoRII complex with DNA in solution by FTIR spectroscopy.
JO  - Russ. J. Gen. Chem.
PY  - 2008
SP  - 1103
EP  - 1109
VL  - 78
AB  - The X-ray structure of type IIE EcoRII restriction endonuclease has been solved but the
AB  - structure of the R.EcoRII-DNA complex is still unknown. We report here on the structure of the
AB  - pre-reactive R.EcoRII-DNA-Ca2+ complex in solution examined by FTIR spectroscopy. The
AB  - secondary structure of R.EcoRII as well as the structure of the target DNA in the
AB  - R.EcoRII-DNA-Ca2+ complex was characterized. It was shown that the R.EcoRII-DNA-Ca2+ complex
AB  - formation is accompanied by changes in the spectrum of both DNA bases and DNA sugar-phosphate
AB  - backbone that suggest contacts of the enzyme with different groups of atoms in DNA. The change
AB  - of the R.EcoRII secondary structure in the R.EcoRII-DNA-Ca2+ complex is also observed.
ER  -

TY  - JOUR
AU  - Subach, F.V.
AU  - Muller, S.
AU  - Tashlitsky, V.N.
AU  - Petrauskene, O.V.
AU  - Gromova, E.S.
TI  - The preparation of DNA duplexes containing internucleotide phosphorothioate groups in various positions of the recognition site for the EcoRII restriction endonuclease.
JO  - Bioorg. Khim.
PY  - 2003
SP  - 623
EP  - 631
VL  - 29
AB  - Twenty-four 12-mer DNA duplexes, each containing a chiral phosphorothioate group successively
AB  - replacing one of the internucleotide phosphate groups
AB  - either in the EcoRII recognition site (5'CCA/TGG) or near to it, were
AB  - obtained for studying the interaction of the restriction endonuclease
AB  - EcoRII with internucleotide DNA phosphates. Twelve of the 12-mer
AB  - oligonucleotides were synthesized as Rp and Sp diastereomeric mixtures.
AB  - Six of them were separated by reversed-phase HPLC using various buffers.
AB  - Homogeneous diastereomers of the other oligonucleotides were obtained by
AB  - enzymatic ligation of the Rp and Sp diastereomers of 5- to 7-mer
AB  - oligonucleotides preliminarily separated by HPLC with the corresponding
AB  - short oligonucleotides on a complementary DNA template. The English
AB  - version of the paper: Russian Journal of Bioorganic Chemistry, 2003, vol.
AB  - 29, no. 6; see also http://www.maik.ru.
ER  -

TY  - JOUR
AU  - Subach, O.M.
AU  - Baskunov, V.B.
AU  - Darii, M.V.
AU  - Maltseva, D.V.
AU  - Alexandrov, D.A.
AU  - Kirsanova, O.V.
AU  - Kolbanovskiy, A.
AU  - Kolbanovskiy, M.
AU  - Johnson, F.
AU  - Bonala, R.
AU  - Geacintov, N.E.
AU  - Gromova, E.S.
TI  - Impact of benzo[a] pyrene-2 '-deoxyguanosine lesions on methylation of DNA by SssI and HhaI DNA methyltransferases.
JO  - Biochemistry
PY  - 2006
SP  - 6142
EP  - 6159
VL  - 45
AB  - DNA damage caused by the binding of the tumorigen 7R, 8S-diol 9S, 10R-epoxide (B[a]PDE), a
AB  - metabolite of bezo[a] pyrene, to guanine in
AB  - CpG dinucleotide sequences could affect DNA methylation and, thus,
AB  - represent a potential epigenetic mechanism of chemical carcinogenesis.
AB  - In this work, we investigated the impact of stereoisomeric (+)- and
AB  - (-)- trans-anti-B[a]P-N-2-dG adducts (B+ and B-) on DNA methylation by
AB  - prokaryotic DNA methyltransferases M. SssI and M. HhaI. These two
AB  - methyltransferases recognize (C) under bar pG and G (C) under bar GC
AB  - sequences, respectively, and transfer a methyl group to the C5 atom of
AB  - cytosine (C). A series of 18-mer unmethylated or hemimethylated
AB  - oligodeoxynucleotide duplexes containing trans-anti-B[a]P-N-2-dG
AB  - adducts was generated. The B+ or B- residues were introduced either 5 '
AB  - or 3 ' adjacent or opposite to the target 2 '-deoxycytidines. The B[a]
AB  - PDE lesions practically produced no effect on M. SssI binding to DNA
AB  - but reduced M. HhaI binding by 1-2 orders of magnitude. In most cases,
AB  - the benzo[ a] pyrenyl residues decreased the methylation efficiency of
AB  - hemimethylated and unmethylated DNA by M. SssI and M. HhaI. An absence
AB  - of the methylation of hemimethylated duplexes was observed when either
AB  - the (+)- or the (-)-trans-anti-B[a]P-N-2-dG adduct was positioned 5 '
AB  - to the target dC. The effects observed may be related to the minor
AB  - groove conformation of the bulky benzo[a]pyrenyl residue and to a
AB  - perturbation of the normal contacts of the methyltransferase catalytic
AB  - loop with the B[a]PDE-modified DNA. Our results indicate that a
AB  - trans-anti-B[a] P-N-2-dG lesion flanking a target dC in the CpG
AB  - dinucleotide sequence on its 5 '- side has a greater adverse impact on
AB  - methylation than the same lesion when it is 3 ' adjacent or opposite to
AB  - the target dC.
ER  -

TY  - JOUR
AU  - Subach, O.M.
AU  - Khoroshaev, A.V.
AU  - Gerasimov, D.N.
AU  - Baskunov, V.B.
AU  - Shchyolkina, A.K.
AU  - Gromova, E.S.
TI  - 2-Pyrimidinone as a probe for studying the EcoRII DNA methyltransferase-substrate interaction.
JO  - Eur. J. Biochem.
PY  - 2004
SP  - 2391
EP  - 2399
VL  - 271
AB  - EcoRII DNA methyltransferase (M.EcoRII) recognizes the 5'...CC*T/AGG...3' DNA sequence and
AB  - catalyzes the transfer of the
AB  - methyl group from S-adenosyl-L-methionine to the C5 position of the
AB  - inner cytosine residue (C*). Here, we study the mechanism of inhibition
AB  - of M.EcoRII by DNA containing 2-pyrimidinone, a cytosine analogue
AB  - lacking an NH2 group at the C4 position of the pyrimidine ring. Also,
AB  - DNA containing 2-pyrimidinone was used for probing contacts of M.EcoRII
AB  - with functional groups of pyrimidine bases of the recognition sequence.
AB  - 2-Pyrimidinone was incorporated into the 5'...CCT/AGG...3' sequence
AB  - replacing the target and nontarget cytosine and central thymine
AB  - residues. Study of the DNA stability using thermal denaturation of
AB  - 2-pyrimidinone containing duplexes pointed to the influence of the
AB  - bases adjacent to 2-pyrimidinone and to a greater destabilizing
AB  - influence of 2-pyrimidinone substitution for thymine than that for
AB  - cytosine. Binding of M.EcoRII to 2-pyrimidinone containing DNA and
AB  - methylation of these DNA demonstrate that the amino group of the outer
AB  - cytosine in the EcoRII recognition sequence is not involved in the
AB  - DNA-M.EcoRII interaction. It is probable that there are contacts
AB  - between the functional groups of the central thymine exposed in the
AB  - major groove and M.EcoRII. 2-Pyrimidinone replacing the target cytosine
AB  - in the EcoRII recognition sequence forms covalent adducts with
AB  - M.EcoRII. In the absence of the cofactor S-adenosyl-L-methionine,
AB  - proton transfer to the C5 position of 2-pyrimidinone occurs and in the
AB  - presence of S-adenosyl-L-methionine, methyl transfer to the C5 position
AB  - of 2-pyrimidinone occurs.
ER  -

TY  - JOUR
AU  - Subach, O.M.
AU  - Maltseva, D.V.
AU  - Shastry, A.
AU  - Kolbanovskiy, A.
AU  - Klimasauskas, S.
AU  - Geacintov, N.E.
AU  - Gromova, E.S.
TI  - The stereochemistry of benzo(a)pyrene-2'-deoxyguanosine adducts affects DNA methylation by SssI and HhaI DNA methyltransferases.
JO  - FEBS J.
PY  - 2007
SP  - 2121
EP  - 2134
VL  - 274
AB  - The biologically most significant genotoxic metabolite of the environmental pollutant
AB  - benzo[a]pyrene (B[a]P), (+)-7R,8S-diol 9S,10R-epoxide, reacts chemically with guanine in DNA,
AB  - resulting in the predominent formation of (+)-trans-B[a]P-N2-dG and, to a lesser extent,
AB  - (+)-cis-B[a]P-N2-dG adducts.  Here, we compare the effects of the adduct stereochemistry and
AB  - conformation on the methylation of cytosine catalyzed by two purified prokaryotic DNA
AB  - methyltransferases, SssI and HhaI, with the lesions positioned within or adjacent to their CG
AB  - and GCGC recognition sites, respectively.  The fluorescence properties of the pyrenyl residues
AB  - of the (+)-cis-B[a]aP-N2-dG and (+)-trans-B[a]P-N2-dG adducts in complexes with MTases are
AB  - enhanced, but to different extents, indicating that aromatic B[a]P residues are positioned in
AB  - different microenvironments in the DNA-protein complexes.  We have previously shown that the
AB  - (+)-trans-isomeric adduct inhibits both the binding and methylating efficiencies (kcat) of
AB  - both MTases.  Here we show that the stereoisomeric (+)-cis-B[a]P-N2-dG lesion has only a
AB  - minimal effect on the binding of these MTases and on kcat.  The minor-groove (+)-trans adduct
AB  - interferes with the formation of the normal DNA minor-groove contacts with the catalytic loop
AB  - of the MTases.  However, the intercalated base-displaced (+)-cis adduct does not interfere
AB  - with the minor-groove DNA-catalytic loop contacts, allowing near-normal binding of the MTases
AB  - and undiminished kcat values.
ER  -

TY  - JOUR
AU  - Subhadra, B.
AU  - Krier, J.
AU  - Hofstee, K.
AU  - Monsul, N.
AU  - Berkes, E.
TI  - Draft Whole-Genome Sequence of Lactobacillus fermentum LfQi6, Derived from the Human Microbiome.
JO  - Genome Announcements
PY  - 2015
SP  - e00423
EP  - e00415
VL  - 3
AB  - We report a 2.21-Mbp draft whole-genome sequence of Lactobacillus fermentum Qi6 (LfQi6). This
AB  - strain demonstrates activity against pathogenic biofilms, enhances
AB  - the skin barrier, and upregulates innate immune defenses. The genome sequence
AB  - information of this strain will help to identify molecules that hold promise for
AB  - the discovery of novel therapeutics for dermatological disorders.
ER  -

TY  - JOUR
AU  - Subramaniam, R.
AU  - Wang, Y.
AU  - Mathews, C.K.
AU  - Santi, D.V.
TI  - On the inhibition of deoxycytidylate hydroxymethylase by 5-fluoro-2'-deoxycytidine 5'-monophosphate .
JO  - Arch. Biochem. Biophys.
PY  - 1989
SP  - 11
EP  - 15
VL  - 275
AB  - Studies were performed to determine whether 5-fluoro-2'-deoxycytidine 5'-monophosphate
AB  - (FdCMP) is an inhibitor of deoxycytidylate hydroxymethylase and whether it could form an
AB  - isolable covalent complex with the enzyme and the cofactor, 5,10-methylenetetrahydrofolate.
AB  - The results showed that although FdCMP is a competitive inhibitor of dCMP hydroxymethylase, it
AB  - does not cause time-dependent inhibition of the enzyme in the presence of cofactor. Further,
AB  - although uv difference spectral evidence was found for a FdCMP-cofactor-enzyme complex, the
AB  - complex was not sufficiently stable to isolate on nitrocellulose filters. We conclude that
AB  - FdCMP is not a mechanism-based inhibitor of dCMP hydroxymethylase.
ER  -

TY  - JOUR
AU  - Suchan, D.M.
AU  - Steve, J.J.
AU  - Pierce, A.J.
AU  - Olshefsky, S.C.
AU  - Kirzinger, M.W.B.
AU  - Perry, B.J.
AU  - Cameron, A.D.S.
AU  - Yost, C.K.
TI  - Draft Whole-Genome Sequence of Deinococcus sp. UR1, a Putative Novel Species Isolated from an External Stainless Steel Surface in the Canadian Prairies.
JO  - Genome Announcements
PY  - 2018
SP  - e01407
EP  - e01417
VL  - 6
AB  - Deinococcus sp. strain UR1, a resilient bacterium isolated from the surface of a  stainless
AB  - steel sign located on the University of Regina campus in Saskatchewan,
AB  - Canada, was sequenced to 56-fold coverage to produce 73 contigs with a consensus
AB  - length of 4,472,838 bp and a G+C content of 69.37%.
ER  -

TY  - JOUR
AU  - Suchkov, S.V.
AU  - Lopatina, N.G.
AU  - Arutyunyan, E.E.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Study of the conditions of activation and stabilization of Shigella sonnei 47 DNA methylases in the process of fractionation, purification, and during storage.
JO  - Biokhimiia
PY  - 1986
SP  - 1369
EP  - 1376
VL  - 51
AB  - A comparative investigation was made of the factors of activation and
AB  - conditions of stabilization of partially purified and individual fractions of
AB  - DNA methylases of the strain Shigella sonnei 47.  The influence of the
AB  - temperature system, glycerin, albumin, protease inhibitors, divalent ions, as
AB  - well as the conditions of storage at the value of the isoelectric point of the
AB  - protein on the activity of the enzymes of methylation was studied.  It was
AB  - shown that the effects of activating factors and levels of stabilization differ
AB  - appreciably, depending on the degree of purification and the composition of the
AB  - enzyme preparations  It was established that glycerin is ineffective as a
AB  - stabilizing agent.  It was shown that of all the divalent cations studied the
AB  - only activator universal for the methylases of Shigella sonnei 47 is Ca2+ ions.
AB  - A pronounced stabilizing effect of albumin on the activity of these DNA
AB  - methylases was demonstrated.  With the exception of one enzymatic fraction, the
AB  - protease inhibitors have virtually no effect on the level of methylating
AB  - activity of the preparations.  The phenomenon of spontaneous fluctuations of
AB  - the methylating activity of Shigella sonnei 47 enzyme preparations during
AB  - storage is described.
ER  -

TY  - JOUR
AU  - Suchkov, S.V.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Isoelectrofocusing of DNA-methylases from Shigella sonnei 47.
JO  - Vopr. Med. Khim.
PY  - 1983
SP  - 117
EP  - 122
VL  - 29
AB  - Fractionation of bacterial methylases was studied by means of the isoelectrofocusing
AB  - technique.  The method exhibited high accuracy, efficiency and reproducibility in studies of
AB  - methylases from Shigella sonnei 47.  High column capacity and distinct focusing effect
AB  - increased the experimental advantages of work with various amounts of protein as compared with
AB  - ion exchange chromatography.  By means of the isoelectrofocusing technique three methylases
AB  - were detected in the strain S. sonnei 47, which were dissimilar in their isoelectric points at
AB  - pH 6.5, 8.4 and 9.8.  These findings indicate the heterogeneous pattern of enzyme methylation
AB  - in the strain studied.  Complete removing of endogenous DNA was the main precondition for
AB  - correct fractionation of methylases by means of the isoelectrofocusing technique.  A procedure
AB  - is described for purification of S. sonnei 47 methylases from traces of endogenous DNA by
AB  - affinity chromatography on heparin-Sepharose.
ER  -

TY  - JOUR
AU  - Suchkov, S.V.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Fractionation and purification of DNA-methylases of Shigella sonnei 47 cells.
JO  - Biokhimiia
PY  - 1985
SP  - 1797
EP  - 1804
VL  - 50
AB  - Possible applications of various column chromatography techniques and isoelectrofocusing for
AB  - the study of DNA-methylases of Shigella sonnei 47 cells were analyzed.  A simple, rapid and
AB  - convenient procedure based on the use of cation-exchange chromatography was developed for
AB  - obtaining a highly active total preparation of methylases.  Affinity chromatography on
AB  - heparin-Sepharose was shown to be a promising approach for separating methylases according to
AB  - their specificity towards nitrogenous bases.  Isoelectrofocusing was used to identify in
AB  - Shigella sonnei 47 cells six individual methylating enzymes differing in their pI values.
AB  - Under the stipulation that Shigella sonnei 47 DNA-methylases show a tendency to aggregate in
AB  - the course of fractionation, column chromatography is of little or no use in isolating and
AB  - purifying individual methylating enzymes of the given strain.  The advantages of the
AB  - isoelectrofocusing technique and its utility in the study of different molecular forms of
AB  - site-specific enzymes are discussed.
ER  -

TY  - JOUR
AU  - Suck, D.
TI  - Flip out and modify.
JO  - Curr. Biol.
PY  - 1994
SP  - 252
EP  - 255
VL  - 4
AB  - The crystal structure of a complex between a methyltransferase and DNA shows that, remarkably,
AB  - the target cytosine base is swung out of the double helix and located next to the enzyme's
AB  - S-adenosyl-L-homocysteine cofactor.
ER  -

TY  - JOUR
AU  - Sudina, A.
AU  - Volkov, E.
AU  - Oretskaya, T.
AU  - Naryshkin, N.
AU  - Ivanovskaya, M.
AU  - Kubareva, E.
TI  - Detection of glycosylase, endonuclease and methyltransferase enzyme activities using immobilized oligonucleotides.
JO  - Life
PY  - 2004
SP  - 139
EP  - 143
VL  - 56
AB  - A novel rapid assay for detection of DNA glycosylase, restriction endonuclease, and DNA
AB  - methyltransferase enzyme activities is presented.
AB  - The assay is based on enzyme-dependent label release (in the case of
AB  - glycosylase and endonuclease), or non-release (in the case of
AB  - methyltransferase) into solution from end-labeled DNA immobilized on a
AB  - solid support (CPG or Tenta Gel S-NH2). The assay has been validated
AB  - for monitoring activity of repair enzyme uracil-DNA glycosylase,
AB  - restriction endonucleases SsoII, MvaI and EcoRII and (cytosine-5)-DNA
AB  - methyltransferase SsoII. Two types of labels have been tested and found
AB  - compatible with the assay: radioactive (32P) and fluorescent
AB  - (rhodamine B and fluorescein). The enzyme activity is estimated as a
AB  - ratio of the label released into solution to the total amount of the
AB  - label. Use of fluorescent labeling facilitates detection while use of
AB  - solid phase-immobilized substrates facilitates product separation,
AB  - improved assay sensitivity, and increases throughput of assay. Proposed
AB  - technique provides an estimate of enzyme activity but not its specific
AB  - activity. Thus, the assay will most valuable in the applications where
AB  - rapid estimation of enzyme activity is necessary.
ER  -

TY  - JOUR
AU  - Sudina, A.E.
AU  - Zatsepin, T.S.
AU  - Pingoud, V.
AU  - Pingoud, A.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - Affinity modification of the restriction endonuclease SsoII by 2'-aldehyde-containing double stranded DNAs.
JO  - Biochemistry
PY  - 2005
SP  - 1137
EP  - 1144
VL  - 70
AB  - Properties of 2'-aldehyde-containing double stranded DNAs (dsDNAs) have been studied for the
AB  - first time as substrate analogs of the restriction endonuclease SsoII. These reactive
AB  - oligonucleotides were successfully cross-linked to the restriction endonuclease SsoII by
AB  - reductive amination, and conditions for DNA-protein conjugate trypsinolysis followed by the
AB  - oligonucleotide-peptide conjugate purification were optimized. Use of MALDI-TOF mass
AB  - spectrometry revealed that covalent linkage forms between the sugar moiety of the central
AB  - pyrimidine nucleoside of the SsoII recognition site and Lys173 of the enzyme. The latter is
AB  - probably involved in initial steps of enzyme-substrate recognition during dsDNA readout.
ER  -

TY  - JOUR
AU  - Suen, G. et al.
TI  - Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5574
EP  - 5575
VL  - 193
AB  - Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum
AB  - Firmicutes. Here, we describe the complete genome of
AB  - this microbe. This genome will be useful for rumen microbiology and
AB  - cellulosome biology and in biofuel production, as one of its major
AB  - fermentation products is ethanol.
ER  -

TY  - JOUR
AU  - Suenaga, H.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Kimura, N.
AU  - Hirose, J.
AU  - Watanabe, T.
AU  - Fujihara, H.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Cupriavidus basilensis KF708 (NBRC 110671) Isolated from Biphenyl-Contaminated  Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00143
EP  - e00115
VL  - 3
AB  - We report the draft genome sequence of Cupriavidus basilensis KF708 (NBRC 110671), which
AB  - utilizes biphenyl as a sole carbon source and degrades
AB  - polychlorinated biphenyls (PCBs). The KF708 strain possesses genes for biphenyl
AB  - catabolism and other genes involved in various aromatic compounds.
ER  -

TY  - JOUR
AU  - Suenaga, H.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Kimura, N.
AU  - Hirose, J.
AU  - Watanabe, T.
AU  - Fujihara, H.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF703 (NBRC 110666) Isolated from Biphenyl-Contaminated Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00142
EP  - e00115
VL  - 3
AB  - Pseudomonas putida KF703 (NBRC 110666) utilizes biphenyl as a sole source of carbon and
AB  - degrades polychlorinated biphenyls (PCBs). Here, we report the draft
AB  - genome sequence of the KF703 strain, which provides insight into the molecular
AB  - mechanisms of adaptation to an environment polluted by aromatic compounds.
ER  -

TY  - JOUR
AU  - Suenaga, H.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Kimura, N.
AU  - Hirose, J.
AU  - Watanabe, T.
AU  - Fujihara, H.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Furukawa, K.
TI  - Complete Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF715 (NBRC 110667) Isolated from Biphenyl-Contaminated Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e01624
EP  - e01616
VL  - 5
AB  - Pseudomonas putida KF715 (NBRC 110667) utilizes biphenyl as a sole source of carbon and
AB  - degrades polychlorinated biphenyls (PCBs). Here, we report a complete
AB  - genome sequence of the KF715 strain, which comprises a circular chromosome and
AB  - four plasmids. Biphenyl catabolic genes were located on the largest plasmid,
AB  - pKF715A.
ER  -

TY  - JOUR
AU  - Suenaga, T.
AU  - Aoyagi, T.
AU  - Hosomi, M.
AU  - Hori, T.
AU  - Terada, A.
TI  - Draft Genome Sequence of Azospira sp. Strain I13, a Nitrous Oxide-Reducing Bacterium Harboring Clade II Type nosZ.
JO  - Genome Announcements
PY  - 2018
SP  - e00414
EP  - e00418
VL  - 6
AB  - We report here a draft genome sequence of Azospira sp. strain I13 in the class
AB  - Betaproteobacteria, a facultative anaerobic bacterium responsible for nitrous
AB  - oxide (N2O) reduction. Deciphering this genome would pave the way for the use of
AB  - Azospira sp. strain I13 to facilitate N2O consumption in a nitrogen-removing
AB  - bioreactor emitting N2O.
ER  -

TY  - JOUR
AU  - Suerbaum, S. et al.
TI  - The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 7901
EP  - 7906
VL  - 100
AB  - Helicobacter hepaticus causes chronic hepatitis and liver cancer in mice. It is the prototype
AB  - enterohepatic Helicobacter species and a close
AB  - relative of Helicobacter pylori, also a recognized carcinogen. Here we
AB  - report the complete genome sequence of H. hepaticus ATCC51449. H.
AB  - hepaticus has a circular chromosome of 1,799,146 base pairs, predicted to
AB  - encode 1,875 proteins. A total of 938, 953, and 821 proteins have
AB  - orthologs in H. pylori, Campylobacter jejuni, and both pathogens,
AB  - respectively. H. hepaticus lacks orthologs of most known H. pylori
AB  - virulence factors, including adhesins, the VacA cytotoxin, and almost all
AB  - cag pathogenicity island proteins, but has orthologs of the C. jejuni
AB  - adhesin PEB1 and the cytolethal distending toxin (CDT). The genome
AB  - contains a 71-kb genomic island (HHGI1) and several genomic islets whose
AB  - G+C content differs from the rest of the genome. HHGI1 encodes three basic
AB  - components of a type IV secretion system and other virulence protein
AB  - homologs, suggesting a role of HHGI1 in pathogenicity. The genomic
AB  - variability of H. hepaticus was assessed by comparing the genomes of 12 H.
AB  - hepaticus strains with the sequenced genome by microarray hybridization.
AB  - Although five strains, including all those known to have caused liver
AB  - disease, were indistinguishable from ATCC51449, other strains lacked
AB  - between 85 and 229 genes, including large parts of HHGI1, demonstrating
AB  - extensive variation of genome content within the species.
ER  -

TY  - JOUR
AU  - Suetake, I.
AU  - Hayata, D.
AU  - Tajima, S.
TI  - The amino-terminus of mouse DNA methyltransferase 1 forms an independent domain and binds to DNA with the sequence involving PCNA binding motif.
JO  - J. Biochem. (Tokyo)
PY  - 2006
SP  - 763
EP  - 776
VL  - 140
AB  - DNA methylation patterns in genome are maintained during replication by a DNA
AB  - methyltransferase Dnmt1. Mouse Dnmt1 is a 180 kDa protein
AB  - comprising the N-terminal regulatory domain, which covers 2/3 of the
AB  - molecule, and the rest C-terminal catalytic domain. In the present
AB  - study, we demonstrated that the limited digestion of full-length Dnmt1
AB  - with different proteases produced a common N-terminal fragment, which
AB  - migrated along with Dnmt1 (1-248) in SDS-polyacrylamide gel
AB  - electrophoresis. Digestion of the N-terminal domains larger than Dnmt1
AB  - (1-248) with chymotrypsin again produced the fragment identical to the
AB  - size of Dnmt1 (1-248). These results indicate that the N-terminal
AB  - domain of 1-248 forms an independent domain. This N-terminal domain
AB  - showed DNA binding activity, and the responsible sequence was narrowed
AB  - to the 79 amino acid residues involving the proliferating cell nuclear
AB  - antigen (PCNA) binding motif. The DNA binding activity did not
AB  - distinguish between DNA methylated and non-methylated states, but
AB  - preferred to bind to the minor groove of AT-rich sequence. The DNA
AB  - binding activity of the N-terminal domain competed with the PCNA
AB  - binding. We propose that DNA binding activity of the N-terminal domain
AB  - contributes to the localization of Dnmt1 to AT-rich sequence such as
AB  - Line 1, satellite, and the promoter of tissue-specific silent genes.
ER  -

TY  - JOUR
AU  - Suetake, I.
AU  - Mishima, Y.
AU  - Kimura, H.
AU  - Lee, Y.-H.
AU  - Goto, Y.
AU  - Takeshima, H.
AU  - Ikegami, T.
AU  - Tajima, S.
TI  - Characterization of DNA-binding activity in the N-terminal domain of the DNA methyltransferase Dnmt3a.
JO  - Biochem. J.
PY  - 2011
SP  - 141
EP  - 148
VL  - 437
ER  -

TY  - JOUR
AU  - Suetake, I.
AU  - Miyazaki, J.
AU  - Murakami, C.
AU  - Takeshima, H.
AU  - Tajima, S.
TI  - Distinct enzymatic properties of recombinant mouse DNA methyltransferases Dnmt3a and Dnmt3b.
JO  - J. Biochem. (Tokyo)
PY  - 2003
SP  - 737
EP  - 744
VL  - 133
AB  - Recombinant mouse Dnmt3a and Dnmt3b were expressed in sf9 cells and purified to near
AB  - homogeneity. The purified Dnmt3a and Dnmt3b gave specific
AB  - activities of 1.8 +/- 0.3 and 1.3 +/- 0.1 mol/h/mol enzyme towards
AB  - poly(dGdC)-poly(dGdC), respectively, which were the highest among those
AB  - reported. Dnmt3a or Dnmt3b showed similar K(m) values towards
AB  - poly(dIdC)-poly(dIdC) and poly(dGdC)-poly(dGdC). The K(m) values for
AB  - S-adenosyl-L-methionine were not affected by the methyl-group acceptors,
AB  - poly(dI-dC)-poly(dIdC) and poly(dG-dC)-poly(dGdC). The results indicate
AB  - that the enzymes are de novo-type DNA methyltransferases. Dnmt3a and
AB  - Dnmt3b activities were inhibited by Mn(2+) and Ni(2+) and showed broad pH
AB  - optima around neutral pH. Both enzymes were susceptible to sodium ions,
AB  - which inhibited their activity at around physiological ionic strength.
AB  - However, Dnmt3a was fully active at physiological potassium concentration,
AB  - but Dnmt3b was not. Using designed oligonucleotides for the analysis of
AB  - cytosine methylation, we demonstrated that, in addition to CpG, Dnmt3a
AB  - methylated CpA but not CpT and CpC, and that Dnmt3b methylated CpA and CpT
AB  - but scarcely CpC. The relative activity of Dnmt3b towards nonCpG sequences
AB  - was higher than that of Dnmt3a. These differences in enzymatic properties
AB  - of Dnmt3a and Dnmt3b may contribute to the distinct functions of these
AB  - enzymes in vivo.
ER  -

TY  - JOUR
AU  - Suetake, I.
AU  - Shi, L.H.
AU  - Watanabe, D.
AU  - Nakamura, M.
AU  - Tajima, S.
TI  - Proliferation stage-dependent expression of DNA methyltransferase (Dnmt1) in mouse small intestine.
JO  - Cell Struct. Funct.
PY  - 2001
SP  - 79
EP  - 86
VL  - 26
AB  - In cultured cells, the maintenance-type DNA methyltransferase (Dnmt1) is highly expressed
AB  - during the proliferation stage. In the present
AB  - study, we detected significant expression of Dnmt1 protein in the
AB  - nuclear fraction of mouse small intestine. From its mobility in SDS
AB  - polyacrylamide gel electrophoresis and the specific antibodies against
AB  - the somatic cell-type Dnmt1, Dnmt1 was determined as a somatic cell
AB  - type. Immunofluorescence study revealed that the Dnmt1 was highly
AB  - expressed in the proliferating stem cells in crypts, and was localized
AB  - in the nuclei. The present results indicate that the expression of
AB  - Dnmt1 in vivo is also under the control of cell proliferation as in
AB  - cultured cells.
ER  -

TY  - JOUR
AU  - Suetake, I.
AU  - Shinozaki, F.
AU  - Miyagawa, J.
AU  - Takeshima, H.
AU  - Tajima, S.
TI  - DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction.
JO  - J. Biol. Chem.
PY  - 2004
SP  - 27816
EP  - 27823
VL  - 279
AB  - In mammals, the resetting of DNA methylation patterns in early embryos and germ cells is
AB  - crucial for development. Two DNA methyltransferases, Dnmt3a and Dnmt3b, are responsible for
AB  - the creation of DNA methylation patterns. Dnmt3L, a member of the Dnmt3 family, has been
AB  - reported to be necessary for maternal methylation imprinting, possibly by interacting with
AB  - Dnmt3a and/or Dnmt3b (Hata et al., Development 129, 1983-1993, 2002). In the present study,
AB  - the effect of DNMT3L, a human homologue of Dnmt3L, on the DNA methylation activity of mouse
AB  - Dnmt3a and Dnmt3b was examined in vitro. DNMT3L enhanced the DNA methylation activity of
AB  - Dnmt3a and Dnmt3b about 1.5-3 fold in a dose-dependent manner, but not that of Dnmt1. Although
AB  - the extents of stimulation were different, a stimulatory effect on the DNA methylation
AB  - activity was observed for all the substrate DNA sequences examined, such as those of the
AB  - maternally methylated SNRPN and Lit-1 imprinting genes, the paternally methylated H19
AB  - imprinting gene, the CpG island of the myoD gene, the 5S ribosomal RNA gene, an artificial 28
AB  - bp DNA, poly(dGdC)-poly(dGdC), and poly(dIdC)-poly(dIdC). DNMT3L could not bind to DNA but
AB  - could to Dnmt3a and Dnmt3b, indicating that the stimulatory effect of DNMT3L on the DNA
AB  - methylation activity may not be due to the guiding of Dnmt3a and Dnmt3b to the targeting DNA
AB  - sequence, but may comprise a direct effect on their catalytic activity. The carboxyl-terminal
AB  - half of DNMT3L was found to be responsible for the enhancement of the enzyme activity.
ER  -

TY  - JOUR
AU  - Sugawara, M.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Morikawa, M.
TI  - Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed.
JO  - Genome Announcements
PY  - 2015
SP  - e00026
EP  - e00015
VL  - 3
AB  - Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was
AB  - isolated from the surface of duckweed. We report here the draft genome  sequence of strain
AB  - P23. The genome data will serve as a valuable reference for understanding the molecular
AB  - mechanism of plant growth promotion in aquatic plants.
ER  -

TY  - JOUR
AU  - Sugawara, M.
AU  - Tsukui, T.
AU  - Kaneko, T.
AU  - Ohtsubo, Y.
AU  - Sato, S.
AU  - Nagata, Y.
AU  - Tsuda, M.
AU  - Mitsui, H.
AU  - Minamisawa, K.
TI  - Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen-Fixing Soybean Symbiont.
JO  - Genome Announcements
PY  - 2017
SP  - e01743
EP  - e01716
VL  - 5
AB  - We report the complete genome sequence of Bradyrhizobium diazoefficiens USDA 122, a
AB  - nitrogen-fixing soybean symbiont. The genome consists of a 9.1 Mb circular
AB  - chromosome, and 8,551 coding sequences (CDSs) were predicted on the genome. The
AB  - sequence will provide insight into the evolution of rhizobial genome, and the
AB  - symbiotic compatibility with host plants.
ER  -

TY  - JOUR
AU  - Sugawara, Y.
AU  - Akeda, Y.
AU  - Sakamoto, N.
AU  - Takeuchi, D.
AU  - Motooka, D.
AU  - Nakamura, S.
AU  - Hagiya, H.
AU  - Yamamoto, N.
AU  - Nishi, I.
AU  - Yoshida, H.
AU  - Okada, K.
AU  - Zin, K.N.
AU  - Aye, M.M.
AU  - Tomono, K.
AU  - Hamada, S.
TI  - Genetic characterization of blaNDM plasmids in carbapenem-resistant Escherichia coli isolated in Myanmar.
JO  - PLoS ONE
PY  - 2017
SP  - e184720
EP  - e184720
VL  - 12
AB  - The bacterial enzyme New Delhi metallo- and #946;-lactamase hydrolyzes almost all  and
AB  - #946;-lactam antibiotics,
AB  - including carbapenems, which are drugs of last resort for severe bacterial infections.
AB  - The spread of carbapenem-resistant Enterobacteriaceae that carry the New Delhi metallo-
AB  - and #946;-lactamase gene, blaNDM, poses a serious threat to public health. In this study, we
AB  - genetically
AB  - characterized eight carbapenem-resistant Escherichia coli isolates from a tertiary care
AB  - hospital in Yangon, Myanmar. The eight isolates belonged to five multilocus-sequence
AB  - types and harbored multiple antimicrobial-resistance genes, resulting in resistance against
AB  - nearly all of the antimicrobial agents tested, except colistin and fosfomycin. Nine plasmids
AB  - harboring blaNDM genes were identified from these isolates. Multiple blaNDM genes were
AB  - found in the distinct Inc-replicon types of the following plasmids: an IncA/C2 plasmid
AB  - harboring
AB  - blaNDM-1 (n = 1), IncX3 plasmids harboring blaNDM-4 (n = 2) or blaNDM-7 (n = 1), IncFII
AB  - plasmids harboring blaNDM-4 (n = 1) or blaNDM-5 (n = 3), and a multireplicon F plasmid
AB  - harboring
AB  - blaNDM-5 (n = 1). Comparative analysis highlighted the diversity of the blaNDM-harboring
AB  - plasmids and their distinct characteristics, which depended on plasmid replicon types. The
AB  - results indicate circulation of phylogenetically distinct strains of carbapenem-resistant
AB  - E. coli with various plasmids harboring blaNDM genes in the hospital.
ER  -

TY  - JOUR
AU  - Sugden, B.
AU  - DeTroy, B.
AU  - Roberts, R.J.
AU  - Sambrook, J.
TI  - Agarose slab-gel electrophoresis equipment.
JO  - Anal. Biochem.
PY  - 1975
SP  - 36
EP  - 46
VL  - 68
AB  - Simple slab-gel molds which utilize the electrophoresis apparatus described by
AB  - F.W. Studier (J. Mol. Biol. 79, 237 (1973)) have been designed for pouring and
AB  - running agarose slab-gels.  Analytical gels in which many samples are run
AB  - simultaneously facilitate the assay of many enzymes which lead to physical
AB  - changes in DNA, whereas the preparative gels allow the separation of large
AB  - quantities (1-20 mg) of DNA fragments.
ER  -

TY  - JOUR
AU  - Sugimoto, Y.
AU  - Maruyama, F.
AU  - Suzuki, S.
TI  - Draft Genome Sequence of a Shewanella halifaxensis Strain Isolated from the Intestine of Marine Red Seabream (Pagrus major), Which Includes an Integrative  Conjugative Element with Macrolide Resistance Genes.
JO  - Genome Announcements
PY  - 2018
SP  - e00297
EP  - e00218
VL  - 6
AB  - Shewanella halifaxensis strain 6JANF4-E-4 was isolated from the intestine of a red seabream
AB  - (Pagrus major). Here, we report the draft genome sequence of this
AB  - bacterium, which includes an integrative conjugative element of the SXT/R391
AB  - family, where the macrolide resistance determinants mef(C) and mph(G) exist.
ER  -

TY  - JOUR
AU  - Sugisaki, H.
TI  - Recognition sequence of a restriction endonuclease from Haemophilus gallinarum.
JO  - Gene
PY  - 1978
SP  - 17
EP  - 28
VL  - 3
AB  - From a comparison of the sequences in and around the cleavage sites of
AB  - restriction endonuclease HgaI isolated from Haemophilus gallinarum, the
AB  - recognition sequence and cleavage site of this enzyme was deduced as below:
AB  - (5')-----N^pN-N-N-N-N-N-N-N-N-N-G-C-G-T-C-N-----(3')
AB  - (3')-----N-N-N-N-N-Np^N-N-N-N-N-C-G-C-A-G-N-----(5') This enzyme recognizes a
AB  - specific but asymmetric penta-nucleotide sequence, GCGTC, and introduces
AB  - staggered cleavages at appointed positions away from the recognition sequence,
AB  - generating protruding 5'-ends of five nucleotides.  The sequences surrounding
AB  - the cleavage sites bear no obvious relation to one another.
ER  -

TY  - JOUR
AU  - Sugisaki, H.
TI  - Nucleotide sequence of the gene of HgaI restriction endonuclease.
JO  - Bull. Inst. Chem. Res. Kyoto Univ.
PY  - 1993
SP  - 338
EP  - 342
VL  - 71
ER  -

TY  - JOUR
AU  - Sugisaki, H.
AU  - Kanazawa, S.
TI  - New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI).
JO  - Gene
PY  - 1981
SP  - 73
EP  - 78
VL  - 16
AB  - Two new restriction endonucleases have been isolated from Flavobacterium
AB  - okeanokoites IFO12536 and Micrococcus luteus IFO12992 and named FokI and MluI,
AB  - respectively.  Based on analysis of the sequences around the restriction sites,
AB  - the recognition sequences and cleavage sites of these endonucleases were
AB  - deduced as below: FokI:	(5')--N-G-G-A-T-G-N-N-N-N-N-N-N-N-N^pN-N-N-N--N--(3')
AB  - 	(3')--N-C-C-T-A-C-N-N-N-N-N-N-N-N-N--N-N-N-Np^N--(5') and
AB  - MluI:	(5')--N-A^pC-G-C-G--T-N--(3') 	(3')--N-T  G-C-G-Cp^A-N--(5') 	MluI
AB  - introduces double-strand cleavages at unique sequences that are completely
AB  - two-fold rotationally symmetric like most type II restriction endonucleases.
AB  - FokI belongs to a class of restriction endonucleases that recognize specific
AB  - but asymmetric nucleotide sequences and introduce staggered cleavages at
AB  - appointed positions away from the recognition sequences.
ER  -

TY  - JOUR
AU  - Sugisaki, H.
AU  - Kita, K.
AU  - Takanami, M.
TI  - The FokI restriction-modification system.  II. Presence of two domains in FokI methylase responsible for modification of different DNA strands.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 5757
EP  - 5761
VL  - 264
AB  - Based on the previous findings that the FokI methylase (MFokI) consists of 647
AB  - amino acid residues and contains two copies of the segment specific for adenine
AB  - methylase, Asp-Pro-Pro-Tyr, at amino acid positions 218-221 and 548-551, the
AB  - role of these copies in the methylation reaction was investigated by
AB  - introduction of a mutation into each segment.  The MFokI gene was inserted into
AB  - M13 vectors, and the Asp residues in the two segments were converted to Gly and
AB  - Ala by oligonucleotide-directed mutagenesis.  The wild-type and mutant genes
AB  - were recloned into an expression vector, from which gene products were
AB  - purified.  A short DNA fragment carrying the FokI recognition site was treated
AB  - with each of these enzymes, and after separation of the two strands by duplex
AB  - formation with M13 viral DNAs carrying the respective strands, the presence or
AB  - absence of modification was judged from susceptibility to FokI endonuclease.
AB  - The results of analysis showed that different strands were modified in an
AB  - asymmetric way by the introduction of mutations into one of the two segments,
AB  - and that the segments at the N-terminal and C-terminal moieties participated in
AB  - modification of the strands carrying 5'-GGATG-3' and 3'-CCTAC-5', respectively.
AB  - We concluded that MFokI contained two functional domains each of which was
AB  - responsible for modification of different strands in the target DNA.
ER  -

TY  - JOUR
AU  - Sugisaki, H.
AU  - Maekawa, Y.
AU  - Kanazawa, S.
AU  - Takanami, M.
TI  - New restriction endonucleases from Acetobacter aceti and Bacillus aneurinolyticus.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 5747
EP  - 5752
VL  - 10
AB  - *
AB  - Two restriction endonucleases with new sequence specificities have been
AB  - isolated from Acetobacter aceti IFO 3281 and Bacillus aneurinolyticus IAM 1077
AB  - and named AatII and BanII, respectively.  Based on analysis of the sequences
AB  - around the restriction sites, the recognition sequences and cleavage sites of
AB  - these endonucleases were deduced as below:
AB  - 
AB  -  AatII:  (5') ---N-G- A-C-G-T^pC-N---  (3')
AB  -          (3') ---N-Cp^T-G-C-A- G-N---  (5')
AB  - 
AB  -  BanII:  (5') --N-G -Pu-G-C-Py^pC-N--  (3')
AB  -          (3') --N-Cp^Py-C-G-Pu- G-N--  (5')
AB  - 
ER  -

TY  - JOUR
AU  - Sugisaki, H.
AU  - Maekawa, Y.
AU  - Kanazawa, S.
AU  - Takanami, M.
TI  - Screening of type II restriction endonucleases.  I.  Isolation and characterization of enzymes from fifteen bacterial strains.
JO  - Bull. Inst. Chem. Res. Kyoto Univ.
PY  - 1982
SP  - 328
EP  - 335
VL  - 60
AB  - One hundred and forty-seven bacterial strains were surveyed for the presence of
AB  - type II restriction endonucleases, and eighteen species of enzymes were
AB  - successfully isolated from fifteen strains in which enzyme activities were
AB  - identified.  Based on analysis of the restriction patterns generated from viral
AB  - and plasmid DNAs and of the sequences around the cleavage-sites, four of
AB  - enzymes named AatII, BanII, FokII and MluI were found to have new
AB  - specificities.  The remaining fourteen enzymes, named AatI, AtuIAMI, BanIII,
AB  - BprI, EcoICRI, GglI, GinI, MauI, PaiI, PanI, PflI, PpuI, and SpaI, were
AB  - isoschizomers of known enzymes.
ER  -

TY  - JOUR
AU  - Sugisaki, H.
AU  - Takanami, M.
TI  - DNA Sequence restricted by restriction endonuclease AP from Haemophilus aphirophilus.
JO  - Nature New Biol.
PY  - 1973
SP  - 138
EP  - 140
VL  - 246
AB  - Many bacterial strains contain strain-specific restriction endonucleases which
AB  - degrade foreign DNA at a limited number of sites.  The site-specific action of
AB  - these enzymes is thought to be a consequence of their ability to recognise
AB  - specific nucleotide sequences.  Such sequences restricted by endonuclease R
AB  - (endoR) from Haemophilus influenzae Rd and RI endonuclease (endo RI) from
AB  - Escherichia coli carrying R factor have been determined.  In our laboratory,
AB  - several species of similar enzymes have been isolated from different
AB  - Haemophilus strains.  Different enzymes seem to have different cleavage site
AB  - specificities, since each enzyme produces different sizes of fragments from
AB  - bacteriophage DNA.  We analysed the terminal nucleotide sequences of fragments
AB  - produced from fd RF-I (doubly closed replicative form) DNA and T3 DNA by
AB  - cleavage with one of the Haemophilus enzymes, endonuclease AP (endo AP)
AB  - isolated from H. aphirophilus, and found that this enzyme cleaved DNA at a
AB  - sequence of four nucleotide pairs with a two-fold rotational symmetry.
ER  -

TY  - JOUR
AU  - Sugisaki, H.
AU  - Yamamoto, K.
AU  - Takanami, M.
TI  - The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 13952
EP  - 13957
VL  - 266
AB  - A DNA fragment of about 3.4 kilobase pairs that expressed the HgaI modification activity was
AB  - cloned from the chromosomal DNA of Haemophilus gallinarum, and its nucleotide sequence was
AB  - determined. Two open reading frames (ORF) which could code for structurally similar proteins
AB  - were identified in the upstream and middle regions and a truncated ORF in the downstream
AB  - region in the same orientation. When the respective ORF's were separately cloned, the clones
AB  - carrying the upstream and middle ORF's both expressed the modification activity, indicating
AB  - that the two genes are involved in modification of the HgaI restriction modification system.
AB  - In order to determine the sites of modification precisely, the respective genes were recloned
AB  - into an expression vector, from which gene products were purified. A short DNA fragment
AB  - carrying the HgaI recognition site was treated with each of these enzymes, and after
AB  - separation of the two strands by duplex formation with M13 viral DNAs carrying the respective
AB  - strands, the presence or absence of modification was judged from susceptibility to HgaI
AB  - endonuclease. The results of analysis showed that different strands were modified in an
AB  - asymmetric way by each gene product. Analysis of the species and positions of modified bases
AB  - by the Maxam-Gilbert method further demonstrated that the gene products from the upstream and
AB  - middle ORF's participated in methylation of the inter cytosine residues of the strands
AB  - carrying 3'-CTGCG-5' and 5'-GACGC-3', respectively. We concluded that the HgaI
AB  - modification system consisted of two cytosine methylase genes responsible for modification of
AB  - different strands in the target DNA.
ER  -

TY  - JOUR
AU  - Sugiura, H.
AU  - Monno, S.
AU  - Yamashita, H.
AU  - Kato, Y.
AU  - Imajoh, M.
TI  - Draft Genome Sequences of Two Edwardsiella piscicida Strains, JF1307 and JF1411,  Isolated from Diseased Olive Flounder (Paralichthys olivaceus) Cultured in Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e00600
EP  - e00618
VL  - 6
AB  - Edwardsiella piscicida strains JF1307 and JF1411 were isolated from cultured olive flounder
AB  - that were diagnosed as being infected with edwardsiellosis. The
AB  - draft genome sequences of the two isolates comprise 3,882,000 bp and 3,827,424 bp
AB  - with G+C contents of 59.5% and 59.6%, respectively.
ER  -

TY  - JOUR
AU  - Suhaili, Z.
AU  - Lean, S.S.
AU  - Yahya, A.
AU  - Mohd, D.M.N.
AU  - Ali, A.M.
AU  - Yeo, C.C.
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus KT/Y21, a Sequence Type 772 (ST772) Strain Isolated from a Pediatric Blood Sample in Terengganu, Malaysia.
JO  - Genome Announcements
PY  - 2014
SP  - e00271
EP  - e00214
VL  - 2
AB  - Here, we report the draft genome sequence of a methicillin-resistant Staphylococcus aureus
AB  - (MRSA) strain, KT/Y21, isolated from a blood sample of a pediatric patient. This strain
AB  - belongs to sequence type 772 (ST772), harbors the staphylococcal cassette chromosome mec
AB  - element (SCCmec) type V, and is positive for the Panton-Valentine leukocidin (PVL) pathogenic
AB  - determinant.
ER  -

TY  - JOUR
AU  - Sui, Z.
AU  - Zhou, W.
AU  - Yao, K.
AU  - Liu, L.
AU  - Zhang, G.
AU  - Yang, Y.
AU  - Feng, J.
TI  - Complete Genome Sequence of Streptococcus pneumoniae Strain A026, a Clinical Multidrug-Resistant Isolate Carrying Tn2010.
JO  - Genome Announcements
PY  - 2013
SP  - e01034
EP  - e01013
VL  - 1
AB  - Streptococcus pneumoniae is a primary cause of bacterial infection in humans. Here, we present
AB  - the complete genome sequence of S. pneumoniae strain A026, which
AB  - is a multidrug-resistant strain isolated from cerebrospinal fluid.
ER  -

TY  - JOUR
AU  - Sukackaite, R.
AU  - Grazulis, S.
AU  - Bochtler, M.
AU  - Siksnys, V.
TI  - The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 1084
EP  - 1093
VL  - 378
AB  - Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA
AB  - strands at fixed positions downstream of the recognition
AB  - site. The restriction endonuclease BpuJI recognizes the asymmetric
AB  - sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of
AB  - the target sequence. BpuJI consists of two physically separate domains,
AB  - with catalytic and dimerization functions in the C-terminal domain and DNA
AB  - recognition functions in the N-terminal domain. Here we report the crystal
AB  - structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A
AB  - resolution. This region folds into two winged-helix subdomains, D1 and D2,
AB  - interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share
AB  - structural similarity with the similar subdomains of the FokI DNA-binding
AB  - domain; however, their orientations in protein-DNA complexes are
AB  - different. Recognition of the 5'-CCCGT target sequence is achieved by
AB  - BpuJI through the major groove contacts of amino acid residues located on
AB  - both the helix-turn-helix motifs and the N-terminal arm. The role of these
AB  - interactions in DNA recognition is also corroborated by mutational
AB  - analysis.
ER  -

TY  - JOUR
AU  - Sukackaite, R.
AU  - Grazulis, S.
AU  - Tamulaitis, G.
AU  - Siksnys, V.
TI  - The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 7552
EP  - 7562
VL  - 40
AB  - DNA cytosine methylation is a widespread epigenetic mark.  Biological effects of DNA
AB  - methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in
AB  - different sequence contexts.  Until now two different structural mechanisms have been
AB  - established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination
AB  - of the 5mC modification is achieved in prokaryotes.  Here we report the crystal structure of
AB  - the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from
AB  - Escherichia coli.  The McrB-N protein shows a novel DNA-binding fold adapted for
AB  - 5-mC-recognition.  In the McrB-N structure in complex with methylated DNA, the 5mC base is
AB  - flipped out from the DNA duplex and positioned within a binding pocket.  Base flipping
AB  - elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation
AB  - [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial
AB  - viruses.  J. Bacteriol., 64, 557-569]: flipped out 5-hydroxymethylcytosine is accommodated in
AB  - the binding pocket but there is no room for the glycosylated base.  The mechanism for 5mC
AB  - recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains,
AB  - despite the differences in their protein folds.
ER  -

TY  - JOUR
AU  - Sukackaite, R.
AU  - Lagunavicius, A.
AU  - Stankevicius, K.
AU  - Urbanke, C.
AU  - Venclovas, C.
AU  - Siksnys, V.
TI  - Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2377
EP  - 2389
VL  - 35
AB  - Type IIS restriction endonucleases (REases) recognize asymmetric DNA sequences and cleave both
AB  - DNA strands at fixed positions downstream of the
AB  - recognition site. REase BpuJI recognizes the asymmetric sequence 5'-CCCGT,
AB  - however it cuts at multiple sites in the vicinity of the target sequence.
AB  - We show that BpuJI is a dimer, which has two DNA binding surfaces and
AB  - displays optimal catalytic activity when bound to two recognition sites.
AB  - BpuJI is cleaved by chymotrypsin into an N-terminal domain (NTD), which
AB  - lacks catalytic activity but binds specifically to the recognition
AB  - sequence as a monomer, and a C-terminal domain (CTD), which forms a dimer
AB  - with non-specific nuclease activity. Fold recognition approach reveals
AB  - that the CTD of BpuJI is structurally related to archaeal Holliday
AB  - junction resolvases (AHJR). We demonstrate that the isolated catalytic CTD
AB  - of BpuJI possesses end-directed nuclease activity and preferentially cuts
AB  - 3 nt from the 3'-terminus of blunt-ended DNA. The nuclease activity of the
AB  - CTD is repressed in the apo-enzyme and becomes activated upon specific DNA
AB  - binding by the NTDs. This leads to a complicated pattern of specific DNA
AB  - cleavage in the vicinity of the target site. Bioinformatics analysis
AB  - identifies the AHJR-like domain in the putative Type III enzymes and
AB  - functionally uncharacterized proteins.
ER  -

TY  - JOUR
AU  - Sulcius, S.
AU  - Alzbutas, G.
AU  - Kvederaviciute, K.
AU  - Koreiviene, J.
AU  - Zakrys, L.
AU  - Lubys, A.
AU  - Paskauskas, R.
TI  - Draft Genome Sequence of the Cyanobacterium Aphanizomenon flos-aquae Strain 2012/KM1/D3, Isolated from the Curonian Lagoon (Baltic Sea).
JO  - Genome Announcements
PY  - 2015
SP  - e01392
EP  - e01314
VL  - 3
AB  - We report here the de novo genome assembly of a cyanobacterium, Aphanizomenon flos-aquae
AB  - strain 2012/KM1/D3, a harmful bloom-forming species in temperate
AB  - aquatic ecosystems. The genome is 5.7 Mb with a G+C content of 38.2%, and it is
AB  - enriched mostly with genes involved in amino acid and carbohydrate metabolism.
ER  -

TY  - JOUR
AU  - Suleimanova, A.D.
AU  - Toymentseva, A.A.
AU  - Boulygina, E.A.
AU  - Kazakov, S.V.
AU  - Mardanova, A.M.
AU  - Balaban, N.P.
AU  - Sharipova, M.R.
TI  - High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 95
EP  - 95
VL  - 10
AB  - Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of
AB  - presence of a high phytate-degrading activity. Strains with such
AB  - activities attract special interest because of its potential use as feed
AB  - additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide
AB  - sequence similarity to different Pantoea species (P. vagans, P. ananatis, P.
AB  - agglomerans, P. anthophila and Pantoea sp.) and exhibits unique biochemical
AB  - properties that do not allow strain identification up to species. Moreover, the
AB  - strain 3.5.1 shows a low ANI and MALDI-TOF Mass Spectrometry scores. Thus, it is
AB  - likely that the strain 3.5.1 represents a new Pantoea species. Here, we present
AB  - the genome sequence of Pantoea sp. strain 3.5.1. The 4,964,649 bp draft genome
AB  - consists of 23 contigs with 4,556 protein-coding and 143 RNA genes. Genome
AB  - sequencing and annotation revealed two phytase genes and putative regulatory
AB  - genes controlling its activity.
ER  -

TY  - JOUR
AU  - Sullivan, J.T.
AU  - Trzebiatowski, J.R.
AU  - Cruickshank, R.W.
AU  - Gouzy, J.
AU  - Brown, S.D.
AU  - Elliot, R.M.
AU  - Fleetwood, D.J.
AU  - McCallum, N.G.
AU  - Rossbach, U.
AU  - Stuart, G.S.
AU  - Weaver, J.E.
AU  - Webby, R.J.
AU  - de Bruijn, F.J.
AU  - Ronson, C.W.
TI  - Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A.
JO  - J. Bacteriol.
PY  - 2002
SP  - 3086
EP  - 3095
VL  - 184
AB  - The Mesorhizobium loti strain R7A symbiosis island is a 502-kb
AB  - chromosomally integrated element which transfers to nonsymbiotic
AB  - mesorhizobia in the environment, converting them to Lotus symbionts. It
AB  - integrates into a phenylalanine tRNA gene in a process mediated by a
AB  - P4-type integrase encoded at the left end of the element. We have
AB  - determined the nucleotide sequence of the island and compared its deduced
AB  - genetic complement with that reported for the 611-kb putative symbiosis
AB  - island of M. loti strain MAFF303099. The two islands share 248 kb of DNA,
AB  - with multiple deletions and insertions of up to 168 kb interrupting highly
AB  - conserved colinear DNA regions in the two strains. The shared DNA regions
AB  - contain all the genes likely to be required for Nod factor synthesis,
AB  - nitrogen fixation, and island transfer. Transfer genes include a trb
AB  - operon and a cluster of potential tra genes which are also present on the
AB  - strain MAFF303099 plasmid pMLb. The island lacks plasmid replication
AB  - genes, suggesting that it is a site-specific conjugative transposon. The
AB  - R7A island encodes a type IV secretion system with strong similarity to
AB  - the vir pilus from Agrobacterium tumefaciens that is deleted from
AB  - MAFF303099, which in turn encodes a type III secretion system not found on
AB  - the R7A island. The 414 genes on the R7A island also include putative
AB  - regulatory genes, transport genes, and an array of metabolic genes. Most
AB  - of the unique hypothetical genes on the R7A island are strain-specific and
AB  - clustered, suggesting that they may represent other acquired genetic
AB  - elements rather than symbiotically relevant DNA.
ER  -

TY  - JOUR
AU  - Sullivan, K.M.
AU  - Macdonald, H.J.
AU  - Saunders, J.R.
TI  - Characterization of DNA restriction and modification activities in Neisseria species.
JO  - FEMS Microbiol. Lett.
PY  - 1987
SP  - 389
EP  - 393
VL  - 44
AB  - Type II restriction endonuclease activities detected in various Neisseria
AB  - species were characterized for sequence specificity and precise site of
AB  - cleavage.  NsiCI isolated from N. sicca C351 cleaves the sequence 5'-GAT^ATC-3'
AB  - (EcoRV isoschizomer); NmeCI from N. meningitidis C114 and NphI from N.
AB  - pharyngis C245 cleave 5'-N^GATCN-3' (MboI isoschizomers); NgoPII and NgoPIII
AB  - from N. gonorrhoeae P9-2 cleave at 5'-GG^CC-3' (HaeIII isoschizomer) and
AB  - 5'-CC^GCGG-3' (SacII isoschizomer), respectively.  Chromosomal DNA isolated
AB  - from these strains and two other N. meningitidis strains (which lacked
AB  - detectable endonuclease activities), was found to be refractive to cleavage by
AB  - various restriction enzymes, implying the presence of methylase activities
AB  - additional to those required for protection against the cellular endonucleases.
AB  - [Note .. the printed abstract was wrong and is corrected here]
ER  -

TY  - JOUR
AU  - Sullivan, K.M.
AU  - Saunders, J.R.
TI  - Determination of the endonuclease and methylase content of Neisseria gonorrhoeae strain P9 and the cloning therefrom of two functional methylase genes.
JO  - Gonococci and Meningococci
PY  - 1988
SP  - 329
EP  - 334
VL  - 0
AB  - Neisseria gonorrhoeae strain P9 possesses five DNA cytosine methyltransferases designated
AB  - M.NgoPI (M.HaeII isoschizomer), M.NgoPII (M.HaeIII), M.NgoPIII (M.SacII), M.NgoPIV (M.NaeI)
AB  - and M.NgoPV.  Two corresponding endonuclease activities, NgoPII (GGCC) and NgoPIII (CCGCGG)
AB  - were also detected.  Recombinant plasmids harbouring functional M.NgoPI (PuGCGCPy) and
AB  - M.NgoPII methyltransferases were isolated by restriction of an amplified gene library with the
AB  - appropriate endonuclease.  After transformation of E. coli RR1, plasmid DNA from individual
AB  - transformants was analysed for protection against HaeII or HaeIII respectively to obtain
AB  - clones carrying the methylase genes.  It was noted that certain E. coli strains, notably DH1
AB  - could not be transformed by plasmids containing the functional M.NgoPI or M.NgoPII genes.
ER  -

TY  - JOUR
AU  - Sullivan, K.M.
AU  - Saunders, J.R.
TI  - Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9:  homologies with other enzymes recognizing the sequence 5'-GGCC-3'.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4369
EP  - 4387
VL  - 16
AB  - Recombinant plasmids harbouring the functional M.NgoPII methyltransferase (specificity
AB  - 5'-GGCC-3') were isolated from amplified gene libraries of gonococcal chromosomal DNA cloned
AB  - in pBR322 and in Escherichia coli RR1.  The M.NgoPII gene was localized by sub-cloning and the
AB  - nucleotide sequence of a cloned 1.6 kb segment of Neisseria gonorrhoeae DNA harbouring the
AB  - methylase gene was determined.  This data, coupled with sub-cloning experiments and in vitro
AB  - transcription-translation studies, indicates a theoretical size of 38.5 kd for the methylase
AB  - protein.  The predicted amino acid sequence of the methylase contains significant regions of
AB  - homology with the projected sequences of other cytosine-modifying methylases, upon which the
AB  - activity of these enzymes is likely to depend.
ER  -

TY  - JOUR
AU  - Sullivan, K.M.
AU  - Saunders, J.R.
TI  - Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae.
JO  - Mol. Gen. Genet.
PY  - 1989
SP  - 380
EP  - 387
VL  - 216
AB  - The NgoPII restriction endonuclease, which recognizes the sequences 5'-GG^CC-3', differs
AB  - from its isoschizomer HaeIII in being sensitive to methylation at the external cytosine
AB  - residue.  The entire nucleotide sequence of a cloned 3.3 kb segment of Neisseria gonorrhoeae
AB  - strain P9 chromosomal DNA which harbours the NgoPII restriction-modification system has been
AB  - determined. This data, coupled with sub-cloning experiments, indicates that the restriction
AB  - endonuclease (R.NgoPII) and modification (M.NgoPII) genes are transcribed from separate
AB  - promoters but are arranged in tandem, with the R.NgoPII gene being located on the 5' side of
AB  - the M.NgoPII gene.  Unlike all previously reported restriction systems the 3' end of the
AB  - endonuclease open reading frame overlaps the 5' end of the methylase open reading frame by 8
AB  - codons.  This overlap may have implications for the regulation of the NgoPII
AB  - restriction-modification system.
ER  -

TY  - JOUR
AU  - Sullivan, M.B. et al.
TI  - Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.
JO  - Environ. Microbiol.
PY  - 2010
SP  - 3035
EP  - 3056
VL  - 12
AB  - T4-like myoviruses are ubiquitous, and their genes are among the most
AB  - abundant documented in ocean systems. Here we compare 26 T4-like genomes,
AB  - including 10 from non-cyanobacterial myoviruses, and 16 from marine
AB  - cyanobacterial myoviruses (cyanophages) isolated on diverse
AB  - Prochlorococcus or Synechococcus hosts. A core genome of 38 virion
AB  - construction and DNA replication genes was observed in all 26 genomes,
AB  - with 32 and 25 additional genes shared among the non-cyanophage and
AB  - cyanophage subsets, respectively. These hierarchical cores are highly
AB  - syntenic across the genomes, and sampled to saturation. The 25 cyanophage
AB  - core genes include six previously described genes with putative functions
AB  - (psbA, mazG, phoH, hsp20, hli03, cobS), a hypothetical protein with a
AB  - potential phytanoyl-CoA dioxygenase domain, two virion structural genes,
AB  - and 16 hypothetical genes. Beyond previously described cyanophage-encoded
AB  - photosynthesis and phosphate stress genes, we observed core genes that may
AB  - play a role in nitrogen metabolism during infection through modulation of
AB  - 2-oxoglutarate. Patterns among non-core genes that may drive niche
AB  - diversification revealed that phosphorus-related gene content reflects
AB  - source waters rather than host strain used for isolation, and that carbon
AB  - metabolism genes appear associated with putative mobile elements. As well,
AB  - phages isolated on Synechococcus had higher genome-wide %G+C and often
AB  - contained different gene subsets (e.g. petE, zwf, gnd, prnA, cpeT) than
AB  - those isolated on Prochlorococcus. However, no clear diagnostic genes
AB  - emerged to distinguish these phage groups, suggesting blurred boundaries
AB  - possibly due to cross-infection. Finally, genome-wide comparisons of both
AB  - diverse and closely related, co-isolated genomes provide a locus-to-locus
AB  - variability metric that will prove valuable for interpreting metagenomic
AB  - data sets.
ER  -

TY  - JOUR
AU  - Sullivan, M.B.
AU  - Coleman, M.L.
AU  - Weigele, P.
AU  - Rohwer, F.
AU  - Chisholm, S.W.
TI  - Three prochlorococcus cyanophage genomes: signature features and ecological interpretations.
JO  - PLoS Biology
PY  - 2005
SP  - E144
EP  - E144
VL  - 3
AB  - The oceanic cyanobacteria Prochlorococcus are globally important,
AB  - ecologically diverse primary producers. It is thought that their viruses
AB  - (phages) mediate population sizes and affect the evolutionary trajectories
AB  - of their hosts. Here we present an analysis of genomes from three
AB  - Prochlorococcus phages: a podovirus and two myoviruses. The morphology,
AB  - overall genome features, and gene content of these phages suggest that
AB  - they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4)
AB  - phages. Using the existing phage taxonomic framework as a guideline, we
AB  - examined genome sequences to establish "core" genes for each phage group.
AB  - We found the podovirus contained 15 of 26 core T7-like genes and the two
AB  - myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to
AB  - these core genes, each genome contains a significant number of
AB  - "cyanobacterial" genes, i.e., genes with significant best BLAST hits to
AB  - genes found in cyanobacteria. Some of these, we speculate, represent
AB  - "signature" cyanophage genes. For example, all three phage genomes contain
AB  - photosynthetic genes (psbA, hliP) that are thought to help maintain host
AB  - photosynthetic activity during infection, as well as an aldolase family
AB  - gene (talC) that could facilitate alternative routes of carbon metabolism
AB  - during infection. The podovirus genome also contains an integrase gene
AB  - (int) and other features that suggest it is capable of integrating into
AB  - its host. If indeed it is, this would be unprecedented among cultured
AB  - T7-like phages or marine cyanophages and would have significant
AB  - evolutionary and ecological implications for phage and host. Further, both
AB  - myoviruses contain phosphate-inducible genes (phoH and pstS) that are
AB  - likely to be important for phage and host responses to phosphate stress, a
AB  - commonly limiting nutrient in marine systems. Thus, these marine
AB  - cyanophages appear to be variations of two well-known phages-T7 and T4-but
AB  - contain genes that, if functional, reflect adaptations for infection of
AB  - photosynthetic hosts in low-nutrient oceanic environments.
ER  -

TY  - JOUR
AU  - Sullivan, M.J.
AU  - Forde, B.M.
AU  - Prince, D.W.
AU  - Ipe, D.S.
AU  - Ben Zakour, N.L.
AU  - Davies, M.R.
AU  - Dougan, G.
AU  - Beatson, S.A.
AU  - Ulett, G.C.
TI  - Complete Genome Sequence of Serotype III Streptococcus agalactiae Sequence Type 17 Strain 874391.
JO  - Genome Announcements
PY  - 2017
SP  - e01107
EP  - e01117
VL  - 5
AB  - Here we report the complete genome sequence of Streptococcus agalactiae strain 874391. This
AB  - serotype III isolate is a member of the hypervirulent sequence type
AB  - 17 (ST-17) lineage that causes a disproportionate number of cases of invasive
AB  - disease in humans and mammals. A brief historical context of the strain is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Sullivan, N.L.
AU  - Septer, A.N.
AU  - Fields, A.T.
AU  - Wenren, L.M.
AU  - Gibbs, K.A.
TI  - The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain.
JO  - Genome Announcements
PY  - 2013
SP  - e00024
EP  - e00013
VL  - 1
AB  - We announce the complete genome sequence for Proteus mirabilis strain BB2000, a model system
AB  - for self recognition. This opportunistic pathogen contains a single,
AB  - circular chromosome (3,846,754 bp). Comparisons between this genome and that of
AB  - strain HI4320 reveal genetic variations corresponding to previously unknown
AB  - physiological and self-recognition differences.
ER  -

TY  - JOUR
AU  - Sumaoka, J.
AU  - Komiyama, M.
TI  - Super restriction enzymes for future biotechnology.
JO  - Kino Zairyo
PY  - 1995
SP  - 19
EP  - 25
VL  - 15
ER  -

TY  - JOUR
AU  - Sumby, P.
AU  - Porcella, S.F.
AU  - Madrigal, A.G.
AU  - Barbian, K.D.
AU  - Virtaneva, K.
AU  - Ricklefs, S.M.
AU  - Sturdevant, D.E.
AU  - Graham, M.R.
AU  - Vuopio-Varkila, J.
AU  - Hoe, N.P.
AU  - Musser, J.M.
TI  - Evolutionary origin and emergence of a highly successful clone of serotype M1 group A Streptococcus involved multiple horizontal gene transfer   events.
JO  - J. Infect. Dis.
PY  - 2005
SP  - 771
EP  - 782
VL  - 192
AB  - To better understand the molecular events involved in the origin of new pathogenic bacteria,
AB  - we studied the evolution of a highly virulent clone
AB  - of serotype M1 group A Streptococcus (GAS). Genomic, DNA-DNA microarray,
AB  - and single-nucleotide polymorphism analyses indicated that this clone
AB  - evolved through a series of horizontal gene transfer events that involved
AB  - (1) the acquisition of prophages encoding streptococcal pyrogenic exotoxin
AB  - A and extracellular DNases and (2) the reciprocal recombination of a 36-kb
AB  - chromosomal region encoding the extracellular toxins NAD(+)-glycohydrolase
AB  - (NADase) and streptolysin O (SLO). These gene transfer events were
AB  - associated with significantly increased production of SLO and NADase.
AB  - Virtual identity in the 36-kb region present in contemporary serotype M1
AB  - and M12 isolates suggests that a serotype M12 strain served as the donor
AB  - of this region. Multiple horizontal gene transfer events were a crucial
AB  - factor in the evolutionary origin and emergence of a very abundant
AB  - contemporary clone of serotype M1 GAS.
ER  -

TY  - JOUR
AU  - Sumby, P.
AU  - Smith, M.C.
TI  - Phase variation in the phage growth limitation system of Streptomyces coelicolor  A3(2).
JO  - J. Bacteriol.
PY  - 2003
SP  - 4558
EP  - 4563
VL  - 185
AB  - The phase-variable phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2) is an
AB  - unusual bacteriophage resistance mechanism that confers
AB  - protection against the temperate phage phiC31 and homoimmune relatives. Pgl is
AB  - subject to phase variation, and data presented here show that this is at least
AB  - partially due to expansion and contraction of a polyguanine tract present within
AB  - the putative adenine-specific DNA methyltransferase gene, pglX. Furthermore, the
AB  - pglX paralogue SC6G9.02, here renamed pglS, was shown to be able to interfere
AB  - with the Pgl phenotype, suggesting that PglS could provide an alternative
AB  - activity to that conferred by PglX.
ER  -

TY  - JOUR
AU  - Sumby, P.
AU  - Smith, M.C.
TI  - Genetics of the phage growth limitation (Pgl) system of Streptomyces coelicolor A3(2).
JO  - Mol. Microbiol.
PY  - 2002
SP  - 489
EP  - 500
VL  - 44
AB  - The phage growth limitation (Pgl) system, encoded by Streptomyces coelicolor A3(2), confers
AB  - protection against the temperate bacteriophage
AB  - phiC31 and its homoimmune relatives. The Pgl phenotype is characterized by
AB  - the ability of Pgl+ hosts to support a phage burst on initial infection
AB  - but subsequent cycles are severely attenuated. Previously, two adjacent
AB  - genes pglY and pglZ were shown to be required for Pgl. It had been shown
AB  - by Southern blotting that Streptomyces lividans, a close relative of S.
AB  - coelicolor and naturally Pgl-, does not contain homologues of pglYZ and
AB  - that introduction of pglYZ into S. lividans is not sufficient to confer a
AB  - Pgl+ phenotype. Moreover, the mechanism of the Pgl+<--> Pgl- phase
AB  - variation associated with this phenotype is also not understood. Here we
AB  - describe two novel genes, pglW and pglX, that were shown to be part of
AB  - this system by complementation of Pgl- mutants and by insertional
AB  - mutagenesis. pglW encodes a 169 kDa protein that includes putative motifs
AB  - for both serine/threonine protein kinase activity and DNA binding. pglX
AB  - encodes a 136 kDa protein with putative adenine-specific DNA
AB  - methyltransferase activity. pglW and pglX have overlapping stop-start
AB  - codons suggesting transcriptional and translational coupling. S1 mapping
AB  - of transcripts initiating up-stream of pglW indicated that, like pglYZ,
AB  - pglWX is expressed in uninfected cultures. A homologue of pglX with 76%
AB  - amino acid identity was identified in S. coelicolor, and insertional
AB  - mutagenesis indicated that this gene was not required for the Pgl+
AB  - phenotype. Southern blots indicated that S. lividans does not contain
AB  - homologues of pglW or pglX. A plasmid encoding pglWXYZ was able to confer
AB  - the Pgl+ phenotype to S. lividans implying that these four genes
AB  - constitute the whole system.
ER  -

TY  - JOUR
AU  - Sumegi, J.
AU  - Breedveld, D.
AU  - Hosenlopp, P.
AU  - Chambon, P.
TI  - A rapid procedure for purification of EcoRI endonuclease.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1977
SP  - 78
EP  - 85
VL  - 1
AB  - A convenient and rapid procedure has been developed to purify restriction
AB  - endonuclease EcoRI.  The method involves sonication of cells at low ionic
AB  - strength, precipitation of the endonuclease with Polymin P (a
AB  - polyethyleneimine), elution of the enzyme from the Polymin P precipitate,
AB  - ammonium sulfate precipitation and chromatography on phosphocellulose.  The
AB  - purified restriction endonuclease is free of exonuclease and other
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Summer, E.J.
AU  - Gonzalez, C.F.
AU  - Bomer, M.
AU  - Carlile, T.
AU  - Embry, A.
AU  - Kucherka, A.M.
AU  - Lee, J.
AU  - Mebane, L.
AU  - Morrison, W.C.
AU  - Mark, L.
AU  - King, M.D.
AU  - LiPuma, J.J.
AU  - Vidaver, A.K.
AU  - Young, R.
TI  - Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex.
JO  - J. Bacteriol.
PY  - 2006
SP  - 255
EP  - 268
VL  - 188
AB  - We have determined the genomic sequences of four virulent myophages, Bcep1, Bcep43, BcepB1A,
AB  - and Bcep781, whose hosts are soil isolates of the
AB  - Burkholderia cepacia complex. Despite temporal and spatial separations
AB  - between initial isolations, three of the phages (Bcep1, Bcep43, and
AB  - Bcep781, designated the Bcep781 group) exhibit 87% to 99% sequence
AB  - identity to one another and most coding region differences are due to
AB  - synonymous nucleotide substitutions, a hallmark of neutral genetic drift.
AB  - Phage BcepB1A has a very different genome organization but is clearly a
AB  - mosaic with respect to many of the genes of the Bcep781 group, as is a
AB  - defective prophage element in Photorhabdus luminescens. Functions were
AB  - assigned to 27 out of 71 predicted genes of Bcep1 despite extreme sequence
AB  - divergence. Using a lambda repressor fusion technique, 10 Bcep781-encoded
AB  - proteins were identified for their ability to support homotypic
AB  - interactions. While head and tail morphogenesis genes have retained
AB  - canonical gene order despite extreme sequence divergence, genes involved
AB  - in DNA metabolism and host lysis are not organized as in other phages.
AB  - This unusual genome arrangement may contribute to the ability of the
AB  - Bcep781-like phages to maintain a unified genomic type. However, the
AB  - Bcep781 group phages can also engage in lateral gene transfer events with
AB  - otherwise unrelated phages, a process that contributes to the
AB  - broader-scale genomic mosaicism prevalent among the tailed phages.
ER  -

TY  - JOUR
AU  - Summers, M.F.
AU  - Powell, C.
AU  - Egan, W.
AU  - Byrd, R.A.
AU  - Wilson, W.D.
AU  - Zon, G.
TI  - Alkyl phosphotriester modified oligodeoxyribonucleotides.  VI. NMR and UV spectroscopic studies of ethyl phosphotriester (Et) modified Rp-Rp and Sp-Sp duplexes, {d[GGAA(Et)TTCC]}2.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 7421
EP  - 7436
VL  - 14
AB  - 1H NMR chemical shift assignments for the title compounds were made for all but
AB  - a few H5' and H5" signals using two-dimensional nuclear Overhauser effect
AB  - (2D-NOE) data, which was also used for the first time to assign absolute
AB  - configuration at phosphorus.  The chemical shifts were, in general, similar to
AB  - those reported [Broido, M.S., et al. (1985) Eur. J. Biochem. 150, 117-128] for
AB  - the B-like conformation of the unmodified, parent duplex, {d(GGAATTCC)]2.
AB  - Differences in chemical shifts for corresponding protons were mostly localized
AB  - to the AA(Et)TT region, and showed some stereochemical dependence.  Unambiguous
AB  - assignment of the phosphotriester 31P signals was achieved in a novel way using
AB  - selective insensitive nucleus enhancement by polarization transfer (selective
AB  - INEPT) NMR.  The Rp-Rp duplex melted ca. 11C lower than either the Sp-Sp or
AB  - parent duplexes, as evidenced by Tm and variable temperature 1H/31P NMR
AB  - measurements.  The 2D-NOE data for the Rp-Rp duplex suggested possible steric
AB  - interactions between the ethyl group and the H3' of the flanking A residue.  At
AB  - low ionic strength, the Sp-Sp and parent duplexes had similar stability but at
AB  - high ionic strength the Sp-Sp duplex was less stable.
ER  -

TY  - JOUR
AU  - Sumrall, E.
AU  - Klumpp, J.
AU  - Shen, Y.
AU  - Loessner, M.J.
TI  - Genome Sequences of Five Nonvirulent Listeria monocytogenes Serovar 4 Strains.
JO  - Genome Announcements
PY  - 2016
SP  - e00179
EP  - e00116
VL  - 4
AB  - We present the complete genome sequences of five nonpathogenicListeria monocytogenesserovar 4
AB  - strains: WSLC 1018 (4e), 1019 (4c), 1020 (4a), 1033 (4d),
AB  - and 1047 (4d). These sequences may help to uncover genes involved in the
AB  - synthesis of the serovar antigens-phenotypic determinants of virulence deemed
AB  - clinically relevant.
ER  -

TY  - JOUR
AU  - Sun, D.
AU  - Cheng, S.
AU  - Wang, A.
AU  - Huang, F.
AU  - Liu, W.
AU  - Xia, X.
TI  - Complete Genome Sequence of Geobacter anodireducens SD-1T, a Salt-Tolerant Exoelectrogenic Microbe in Bioelectrochemical Systems.
JO  - Genome Announcements
PY  - 2016
SP  - e00415
EP  - e00416
VL  - 4
AB  - Strain SD-1 is the type strain of the species Geobacter anodireducens, which was  originally
AB  - isolated from a microbial fuel cell reactor in the United States. The
AB  - characteristic of this bacterium is its high electrochemical activity. Here, we
AB  - report the fully assembled genome and plasmid sequence of G. anodireducens
AB  - SD-1(T).
ER  -

TY  - JOUR
AU  - Sun, D.
AU  - Zhuo, T.
AU  - Hu, X.
AU  - Fan, X.
AU  - Zou, H.
TI  - Identification of a Pseudomonas putida as biocontrol agent for tomato bacterial wilt disease.
JO  - Biol. Control
PY  - 2017
SP  - 45
EP  - 50
VL  - 114
AB  - A bacterial isolate, A1, was collected from the rhizosphere soil of cultivated peanuts. Based
AB  - on its 16 S rRNA sequence, this isolate was identified as a Pseudomonas putida strain. On
AB  - minimal medium supplemented with
AB  - diverse nutrient substrates, the P. putida A1 strain could use fructose and fructosan,
AB  - trehalose, and inositol as sole carbon resources. The ability of these four carbon resources,
AB  - as well as leaf and root exudates, to stimulate cell migration in a chemotaxis assay was
AB  - investigated. P. putida A1 was labelled with GFP to study colonization on the root surface;
AB  - this strain was found to aggregate around wound sites. In addition to forming biofilms in
AB  - vitro, A1 showed antimicrobial activity against several plant pathogenic bacteria, including
AB  - Ralstonia solanacearum, Xanthomonas oryzae pv. oryzae, X. o. pv. oryzicola, and X. citri
AB  - subsp. citri. In evaluations of biocontrol potential of tomato bacterial wilt, this isolate
AB  - delayed the appearance of wilt symptoms for 4 days and reduced wilt disease severity. Overall,
AB  - our results indicate that P. putida A1 could be an effective biocontrol agent for plant
AB  - soil-borne diseases.
ER  -

TY  - JOUR
AU  - Sun, D.K.
AU  - Yoo, O.J.
TI  - Purification and characterization of a restriction endonuclease ZanI from Zymomonas anaerobia.
JO  - Korean Biochem. J.
PY  - 1988
SP  - 419
EP  - 422
VL  - 21
AB  - We described the purification and characterization of a sequence restriction endonuclease,
AB  - ZanI, found from Zymomonas anaerobia (NCI B8227). The purified enzyme is essentially
AB  - homogeneous and the subunit molecular weight is 30,000+/- 1,000 as judged by 10%
AB  - polyacrylamide gel electrophoresis containing 0.1% SDS. The recognition sequence and the
AB  - cleavage site (indicated by the arrow) were determined to be 5'-CC^(AT) GG-3', the same
AB  - sequence as recognized by BstNI and EcoRII. ZanI endonuclease is able to cleave dcm-methylated
AB  - DNA and is maximally active at 37C.
ER  -

TY  - JOUR
AU  - Sun, F.
AU  - Zhou, D.
AU  - Sun, Q.
AU  - Luo, W.
AU  - Tong, Y.
AU  - Zhang, D.
AU  - Wang, Q.
AU  - Feng, W.
AU  - Chen, W.
AU  - Fan, Y.
AU  - Xia, P.
TI  - Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata.
JO  - Sci. Rep.
PY  - 2016
SP  - 33982
EP  - 33982
VL  - 6
AB  - We previously reported the complete sequence of the resistance plasmid
AB  - pP10164-NDM, harboring blaNDM (conferring carbapenem resistance) and bleMBL
AB  - (conferring bleomycin resistance), which is recovered from a clinical Leclercia
AB  - adecarboxylata isolate P10164 from China. This follow-up work disclosed that
AB  - there were still two multidrug-resistant (MDR) plasmids pP10164-2 and pP10164-3
AB  - coexisting in this strain. pP10164-2 and pP10164-3 were completely sequenced and
AB  - shown to carry a wealth of resistance genes, which encoded the resistance to at
AB  - least 10 classes of antibiotics (beta-lactams. macrolides, quinolones,
AB  - aminoglycosides, tetracyclines, amphenicols, quaternary ammonium compounds,
AB  - sulphonamides, trimethoprim, and rifampicin) and 7 kinds of heavy mental
AB  - (mercury, silver, copper, nickel, chromate, arsenic, and tellurium). All of these
AB  - antibiotic resistance genes are associated with mobile elements such as
AB  - transposons, integrons, and insertion sequence-based transposable units,
AB  - constituting a total of three novel MDR regions, two in pP10164-2 and the other
AB  - one in pP10164-3. Coexistence of three resistance plasmids pP10164-NDM, pP10164-2
AB  - and pP10164-3 makes L. adecarboxylata P10164 tend to become extensively
AB  - drug-resistant.
ER  -

TY  - JOUR
AU  - Sun, F.
AU  - Zhou, D.
AU  - Wang, Q.
AU  - Feng, J.
AU  - Feng, W.
AU  - Luo, W.
AU  - Liu, Y.
AU  - Qiu, X.
AU  - Yin, Z.
AU  - Xia, P.
TI  - Genetic characterization of a novel blaDIM-2-carrying megaplasmid p12969-DIM from clinical Pseudomonas putida.
JO  - J. Antimicrob. Chemother.
PY  - 2016
SP  - 909
EP  - 912
VL  - 71
AB  - OBJECTIVES: To characterize a blaDIM-2-carrying 409 kb megaplasmid p12969-DIM of
AB  - Pseudomonas putida 12969 from a patient with pneumonia in China. METHODS: The
AB  - complete nucleotide sequence of p12969-DIM was determined with a paired-end
AB  - library and a mate-pair library using next-generation sequencing technology.
AB  - RESULTS: blaDIM-2, a close blaDIM-1 variant, was identified in p12969-DIM. DIM-2
AB  - differs from DIM-1 by two amino acid substitutions Ser119Leu and Ser209Pro. The
AB  - p12969-DIM backbone is highly similar to pOZ176, but the IncP-2-type
AB  - stability/replication/conjugal transfer system in the pOZ176 backbone is absent
AB  - from p12969-DIM. The p12969-DIM accessory regions, a 45.7 kb MDR and a novel
AB  - insertion sequence, ISPpu23, are almost entirely distinct from pOZ176. The MDR
AB  - region contains a novel Tn21-subgroup transposon Tn6286 inserted with two class 1
AB  - integrons, In1225 and In1226; a Tn5503-family transposon-like element inserted
AB  - with a strAB locus; and a novel Tn21-subgroup transposon-like element inserted
AB  - with a class 1 integron, In1224. The three integrons carry blaDIM-2 as well as a
AB  - number of additional genes conferring resistance to quinolones, aminoglycosides,
AB  - chloramphenicol, florfenicol, trimethoprim, streptomycin, quaternary ammonium
AB  - compounds and sulphonamides. p12969-DIM has two distinct replication/stability
AB  - systems, repA/parAB-parB2 of an unknown incompatibility group in the backbone and
AB  - repABC/mazFE of the IncQ2 group in the MDR region. CONCLUSIONS: The MDR region of
AB  - p12969-DIM harbours many resistance genes as well as a second
AB  - replication/stability system. This article is the first report of a fully
AB  - sequenced blaDIM-carrying plasmid.
ER  -

TY  - JOUR
AU  - Sun, G.
AU  - Wang, L.
AU  - Bao, C.
AU  - Li, T.
AU  - Ma, L.
AU  - Chen, L.
TI  - Complete Genome Sequence of Elizabethkingia meningoseptica, Isolated from a T-Cell Non-Hodgkin's Lymphoma Patient.
JO  - Genome Announcements
PY  - 2015
SP  - e00673
EP  - e00615
VL  - 3
AB  - An Elizabethkingia meningoseptica infection was detected at the end stage of a patient with
AB  - T-cell non-Hodgkin's lymphoma. The complete genome of this isolated
AB  - strain, FMS-007, was generated in one contig with a total size of 3,938,967 bp. A
AB  - preliminary screening indicated that the genome contains drug resistance genes to
AB  - aminoglycosides and beta-lactams. A clustered regularly interspaced short
AB  - palindromic repeats (CRISPR)/CRISPR-associated proteins (CRISPR/Cas) system with
AB  - 16 direct repeats and 15 spacers was identified.
ER  -

TY  - JOUR
AU  - Sun, H. et al.
TI  - Complete genome sequence of Desulfarculus baarsii type strain (2st14).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 276
EP  - 284
VL  - 3
AB  - Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the
AB  - genus Desulfarculus, which represents the family Desulfarculaceae
AB  - and the order Desulfarculales. This species is a mesophilic sulfate-reducing
AB  - bacterium with the capability to oxidize acetate and fatty acids of up to 18
AB  - carbon atoms completely to CO(2). The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is
AB  - used by this species for the complete oxidation of carbon sources and autotrophic
AB  - growth on formate. The type strain 2st14(T) was isolated from a ditch sediment
AB  - collected near the University of Konstanz, Germany. This is the first completed
AB  - genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long
AB  - single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part
AB  - of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Sun, H. et al.
TI  - Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 325
EP  - 336
VL  - 3
AB  - Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus
AB  - Nocardiopsis, which in turn is the type genus of the family
AB  - Nocardiopsaceae. This species is of interest because of its ecological
AB  - versatility. Members of N. dassonvillei have been isolated from a large variety
AB  - of natural habitats such as soil and marine sediments, from different plant and
AB  - animal materials as well as from human patients. Moreover, representatives of the
AB  - genus Nocardiopsis participate actively in biopolymer degradation. This is the
AB  - first complete genome sequence in the family Nocardiopsaceae. Here we describe
AB  - the features of this organism, together with the complete genome sequence and
AB  - annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a
AB  - 0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of
AB  - the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Sun, J.
AU  - He, Z.
AU  - Nechushtai, R.
AU  - Chitnis, P.R.
TI  - Molecular cloning of the PsaA and PsaB genes for the core proteins of photosystem I from the thermophilic cyanobacterium Mastigocladus Iaminosus (Accession No. AF038558).
JO  - Plant Physiol.
PY  - 1998
SP  - 1192
EP  - 1192
VL  - 116
ER  -

TY  - JOUR
AU  - Sun, J.
AU  - Weinstein, H.
TI  - The restriction enzyme BamHI is poised for sliding along DNA in a model of the nonspecific complex.
JO  - Biophys. J.
PY  - 2002
SP  - 463a
EP  - 463a
VL  - 82
AB  - The mechanism by which DNA-binding proteins find their specific binding sites is unclear.  To
AB  - understand how the protein reaches its cognate site within a long piece of DNA, the crystal
AB  - structures of the nonspecific and the specific BamHI-DNA complexes were used as templates to
AB  - study the electrostatic interactions and possible sliding pathways.  A model is proposed for
AB  - the initial nonspecific binding of BamHI to a long stretch of B-form DNA, in which BamHI and
AB  - DNA adopt an orientation different from that in the crystal structures.  This arrangement of a
AB  - nonspecific complex is supported by the salt-dependence of the interaction, which is in good
AB  - agreement with experimental results if calculated in this model, but not in the crystal
AB  - structure.  The electrostatic interaction calculated for different orientations of BamHI
AB  - relative to DNA appears to be sufficient to steer the protein to this favorable configuration
AB  - parallel to the DNA axis.  The results are independent of DNA sequence, so that BamHI could
AB  - bind equally to any site along DNA thus enabling it to slide.  The calculations suggest that
AB  - the DNA helical structure could affect the pathway of sliding: the preference for sliding
AB  - along the DNA helix pitch stems from the ~2.5kcal/mol energy barrier that opposes sliding
AB  - along one face of DNA.
ER  -

TY  - JOUR
AU  - Sun, J.Q.
AU  - Xu, L.
AU  - Wang, L.J.
AU  - Wu, X.L.
TI  - Draft genome sequence of a rhodococcus strain isolated from tannery wastewater treatment sludge.
JO  - Genome Announcements
PY  - 2015
SP  - e01463
EP  - e01414
VL  - 3
AB  - Rhodococcus sp. Chr-9 can degrade pyridine in the presence of chromate. Its draft genome
AB  - sequence revealed that strain Chr-9 harbors sets of genes for resistance
AB  - to heavy metals such as lead, mercury, arsenate, and cobalt, as well as three
AB  - different gene clusters for metabolizing aromatic compounds, such as phenol,
AB  - benzoate, and 4-nitrophenol.
ER  -

TY  - JOUR
AU  - Sun, K.
AU  - Jiao, X.D.
AU  - Zhang, M.
AU  - Sun, L.
TI  - DNA adenine methylase is involved in the pathogenesis of Edwardsiella tarda.
JO  - Vet. Microbiol.
PY  - 2010
SP  - 149
EP  - 154
VL  - 141
AB  - Edwardsiella tarda is a serious aquaculture pathogen that can infect many Cultured fish
AB  - species. The aim of this study was to investigate
AB  - the potential importance of DNA adenine methylase (Dam) in E. tarda
AB  - pathogenesis. The E. tardo dam gene (dam(Et)) was cloned from a
AB  - pathogenic strain, TXD1, isolated from diseased fish. Dam(Et) shares
AB  - high (70.2%) sequence identity with the Dam proteins of Yersinia
AB  - enterocolitica and several other bacterial species. Recombinant Dam(Et)
AB  - is able to complement a dam-deficient Escherichia coli strain and
AB  - methylate the genomic DNA. Attenuation of dam(Et) expression by
AB  - antisense RNA interference had no apparent effect on the growth of
AB  - TXD1, but caused significant attenuation of overall bacterial virulence
AB  - and altered several stress responses including spontaneous mutation,
AB  - recovering from UV radiation and H2O2 exposure, binding to host mucus,
AB  - and dissemination in host blood and liver. In addition, attenuation of
AB  - dam(Et) expression increased luxS expression and AI-2 activities in E.
AB  - tarda. These results indicate that Dam(Et) is a virulence determinant
AB  - and plays a role in the pathogenesis of TXD1, and that temporal
AB  - expression of dam(Et), is essential for optimal bacterial infection.
ER  -

TY  - JOUR
AU  - Sun, L.
TI  - Kinetic studies on cleavage of adenovirus type 5 DNA by restriction endonuclease EcoRI.
JO  - Xibei Daxue Xuebao
PY  - 1989
SP  - 71
EP  - 76
VL  - 19
AB  - The two EcoRI restriction sites on Adenovirus Type 5 DNA have been affirmed and relative
AB  - lengths of EcoRI digest products of Ad5 DNA are 77%, 7%, 16% for the fragment A, C, B
AB  - respectively. The kinetic of cleavage of Ad5 DNA by EcoRI was studied using quantitative
AB  - evaluation of the ethidium bromide fluorescence of DNA fragments separated on agarose gel. The
AB  - overall rate constants of cleavage at different EcoRI site have been determined. The rate
AB  - constants for two cleavage sites depend on the enzyme concentration and reaction temperature.
AB  - Thermodynamic studies have shed light on the importance of the nucleotide sequences around the
AB  - restriction sites, which modulate the activation barriers for the cleavage process itself.
ER  -

TY  - JOUR
AU  - Sun, L.
AU  - Lu, Z.
AU  - Li, J.
AU  - Sun, F.
AU  - Huang, R.
TI  - Comparative genomics and transcriptome analysis of Lactobacillus rhamnosus ATCC 11443 and the mutant strain SCT-10-10-60 with enhanced L-lactic acid production capacity.
JO  - Mol. Genet. Genomics
PY  - 2018
SP  - 265
EP  - 276
VL  - 293
AB  - Mechanisms for high L-lactic acid production remain unclear in many bacteria.
AB  - Lactobacillus rhamnosus SCT-10-10-60 was previously obtained from L. rhamnosus
AB  - ATCC 11443 via mutagenesis and showed improved L-lactic acid production. In this
AB  - study, the genomes of strains SCT-10-10-60 and ATCC 11443 were sequenced. Both
AB  - genomes are a circular chromosome, 2.99 Mb in length with a GC content of
AB  - approximately 46.8%. Eight split genes were identified in strain SCT-10-10-60,
AB  - including two LytR family transcriptional regulators, two Rex redox-sensing
AB  - transcriptional repressors, and four ABC transporters. In total, 60 significantly
AB  - up-regulated genes (log2fold-change >/= 2) and 39 significantly down-regulated
AB  - genes (log2fold-change </= - 2) were identified by a transcriptome comparison
AB  - between strains SCT-10-10-60 and ATCC 11443. KEGG pathway enrichment analysis
AB  - revealed that "pyruvate metabolism" was significantly different (P < 0.05)
AB  - between the two strains. The split genes and the differentially expressed genes
AB  - involved in the "pyruvate metabolism" pathway are probably responsible for the
AB  - increased L-lactic acid production by SCT-10-10-60. The genome and transcriptome
AB  - sequencing information and comparison of SCT-10-10-60 with ATCC 11443 provide
AB  - insights into the anabolism of L-lactic acid and a reference for improving
AB  - L-lactic acid production using genetic engineering.
ER  -

TY  - JOUR
AU  - Sun, L.
AU  - Schnurer, A.
TI  - Draft Genome Sequence of the Cellulolytic Strain Clostridium sp. Bc-iso-3 Isolated from an Industrial-Scale Anaerobic Digester.
JO  - Genome Announcements
PY  - 2016
SP  - e01188
EP  - e01116
VL  - 4
AB  - Clostridium sp. Bc-iso-3 is a cellulolytic strain isolated from a Swedish industrial-scale
AB  - biogas digester. Here, we present the draft genome sequence of
AB  - this strain, which consists of four contigs with a total length of 4,327,139 bp
AB  - and an average coverage of 312.97x.
ER  -

TY  - JOUR
AU  - Sun, L.
AU  - Wang, Y.
AU  - Yu, C.
AU  - Zhao, Y.
AU  - Gan, Y.
TI  - Genome Sequence of Clostridium tunisiense TJ, Isolated from Drain Sediment from a Pesticide Factory.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6950
EP  - 6951
VL  - 194
AB  - Clostridium tunisiense is a Gram-positive, obligate anaerobe that was first isolated in an
AB  - anaerobic evironment under eutrophication. Here we report the
AB  - first genome sequence of the Clostridium tunisiense TJ isolated from drain
AB  - sediment of a pesticide factory in Tianjin, China. The genome is of great
AB  - importance for both basic and application research.
ER  -

TY  - JOUR
AU  - Sun, L.
AU  - Yin, J.
TI  - Initial studies on chemical modification of several amino acid residues of the restriction endonuclease XhoI.
JO  - Xibei Daxue Xuebao
PY  - 1990
SP  - 65
EP  - 71
VL  - 20
AB  - The restriction endonuclease XhoI can be inactivated by some specific protein
AB  - inhibitors.  XhoI is sensitive not only to sulfhydryl reagents but also to
AB  - reagents that modify lysine and arginine residues.  Inactivation of the enzyme
AB  - obeyed pseudo-first-order kinetics and resulted in complete elimination of
AB  - catalysis.  Lambda DNA as substrate is strongly protected against inactivation
AB  - by the reagents.  These data suggest that XhoI has essential lysine and/or
AB  - arginine residues and SH groups which are crucial to the enzymatic activity.
ER  -

TY  - JOUR
AU  - Sun, L.-K.
AU  - Hong, R.
TI  - The influence of DNA conformation and base composition flanking recognition sites on the cleavage rate of restriction.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1989
SP  - 456
EP  - 460
VL  - 21
AB  - The relations between the nucleotide sequences adjacent to the recognition sites and the
AB  - cleavage rate of DNA with restriction endonucleases were investigated.  Our data indicate that
AB  - the recognition sites flanked by the A-T rich sequences are cleaved faster than those flanked
AB  - by G-C rich sequences regardless of the DNA conformation.
ER  -

TY  - JOUR
AU  - Sun, L.-K.
AU  - Ruan, H.
TI  - Kinetics and thermodynamics of specific and non-specific interactions between BglI restriction endonuclease and pBR322-DNA.
JO  - Chinese Biochem. J.
PY  - 1990
SP  - 334
EP  - 338
VL  - 6
AB  - Cleavage of pBR322-DNA by BglI was studied at different temperatures and various incubation
AB  - times. Kinetic constants and thermodynamic parameters of the reaction were evaluated.  The
AB  - similarity between linear and circular DNA in specific and non-specific interaction with
AB  - the restriction endonuclease has been demonstrated by their kinetic constants and
AB  - thermodynamic parameters. The specific binding is about 2 orders of magnitude stronger than
AB  - non-specific binding. Ks is more dependent on temperature then KN. Complex formation is
AB  - weakened with increasing temperature. The values of enthalpy and entropy show that both
AB  - specific and non-specific binding need no activation energy and the "disorder" of the molecule
AB  - is decreased with binding. The key element that limits the cleavage rate is Kc.  From
AB  - the experimental results, it is evident that the recognition site adjacent to the A-T
AB  - rich sequences has a low activation energy for cleavage and can be cleaved fast. This is
AB  - probably due to the fact that the sequences adjacent to the recognition site may regulate the
AB  - activation threshold of the cleavage.
ER  -

TY  - JOUR
AU  - Sun, L.-K.
AU  - Wang, X.
AU  - Hong, R.
TI  - Calculation of cleavage rates of restriction endonuclease on circular DNA.
JO  - Acta Biophys. Sinica
PY  - 1988
SP  - 64
EP  - 66
VL  - 4
AB  - In this paper, we have deduced a set of equations to calculate the cleavage rates of
AB  - restriction endonucleases on circular DNA by mathematical and physiochemical methods. They are
AB  - important to study the kinetics and modification of restriction endonucleases.
ER  -

TY  - JOUR
AU  - Sun, P.
AU  - Cui, J.
AU  - Jia, X.
AU  - Wang, W.
TI  - Complete Genome Sequence of Bacillus velezensis L-1, Which Has Antagonistic Activity against Pear Diseases.
JO  - Genome Announcements
PY  - 2017
SP  - e01271
EP  - e01217
VL  - 5
AB  - Bacillus velezensis L-1 is an effective biocontrol agent against pear diseases. Here, we
AB  - report the complete genome sequence of B. velezensis L-1 in which
AB  - clusters related to the biosynthesis of secondary metabolites were predicted.
AB  - This genome provides insights into the possible biocontrol mechanisms and
AB  - furthers application of this specific bacterium.
ER  -

TY  - JOUR
AU  - Sun, P.
AU  - Luo, H.
AU  - Zhang, X.
AU  - Xu, J.
AU  - Guo, Y.
AU  - He, S.
TI  - Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1.
JO  - Genome Announcements
PY  - 2018
SP  - e01367
EP  - e01317
VL  - 6
AB  - A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific  Biosciences
AB  - (PacBio) single-molecule real-time (SMRT) sequencing technology. The
AB  - strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia,
AB  - China. The single circular chromosome of 1,033,629 bp shows differences between
AB  - complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative
AB  - conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins
AB  - (VSPs), pathogenicity islands (PAIs), etc.
ER  -

TY  - JOUR
AU  - Sun, Q.
AU  - Lan, R.
AU  - Wang, Y.
AU  - Wang, J.
AU  - Wang, Y.
AU  - Li, P.
AU  - Du, P.
AU  - Xu, J.
TI  - Isolation and genomic characterization of SfI, a serotype-converting bacteriophage of Shigella flexneri.
JO  - BMC Microbiol.
PY  - 2013
SP  - 39
EP  - 39
VL  - 13
AB  - ABSTRACT: BACKGROUND: All Shigella flexneri serotypes except serotype 6 share a
AB  - common O-antigen tetrasaccharide backbone and nearly all variation between
AB  - serotypes are due to glucosyl and/or O-acetyl modifications of the common O units
AB  - mediated by glycosyltransferases encoded by serotype-converting bacteriophages.
AB  - Several S. flexneri serotype-converting phages including SfV, SfX, Sf6 and SfII
AB  - have been isolated and characterized. However, S. flexneri serotype-converting
AB  - phage SfI which encodes a type I modification of serotype 1 (1a, 1b, 1c and 1d)
AB  - had not yet been characterized. RESULTS: The SfI phage was induced and purified
AB  - from a S. flexneri serotype 1a clinical strain 019. Electron microscopy showed
AB  - that the SfI phage has a hexagonal head and a long contractile tail,
AB  - characteristic of the members of Myoviridae family. SfI can convert serotype Y to
AB  - serotype 1a and serotype X to serotype 1d, but cannot convert 10 other S.
AB  - flexneri serotypes (1a, 1b, 2a, 2b, 3a, 3b, 4a, 4b, 5a, Xv) tested, suggesting
AB  - that SfI has a narrow host range. Similar to other S. flexneri
AB  - serotype-converting phages, SfI integrates into the tRNA-thrW gene adjacent to
AB  - proA of the host chromosome when lysogenized. The complete sequence of the SfI
AB  - genome was 38,389 bp, encoding 66 open reading frames and two tRNA genes. Phage
AB  - SfI shares significant homology with S. flexneri phage SfV, Escherichia coli
AB  - prophage e14 and lambda, and is classified into the lambdoid phage family. SfI
AB  - was found to use a cos mechanism for DNA packaging similar to that of phage SfV.
AB  - CONCLUSIONS: SfI contains features of lambdoid phages and is closely related to
AB  - S. flexneri phage SfV, E. coli prophage e14 and lambda. The characterization of
AB  - SfI enhances our understanding of serotype conversion of S. flexneri.
ER  -

TY  - JOUR
AU  - Sun, S.
AU  - Yang, X.
AU  - Yuan, Y.
AU  - Dai, X.
AU  - Yan, Y.
AU  - Cao, H.
AU  - Luo, T.
AU  - Guo, R.
AU  - Wang, X.
AU  - Song, Y.
AU  - Yang, R.
AU  - Zhang, Y.
AU  - Cui, Y.
TI  - Draft Genome Sequence of Yersinia pestis Strain 2501, an Isolate from the Great Gerbil Plague Focus in Xinjiang, China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5447
EP  - 5448
VL  - 194
AB  - We deciphered the genome of Yersinia pestis strain 2501, isolated from the Junggar Basin, a
AB  - newly discovered great gerbil plague focus in Xinjiang, China.
AB  - The total length of assembly was 4,597,322 bp, and 4,265 coding sequences were
AB  - predicted within the genome. It is the first Y. pestis genome from this plague
AB  - focus.
ER  -

TY  - JOUR
AU  - Sun, X.
AU  - Meng, J.
AU  - Liu, S.
AU  - Zhang, H.
AU  - Wang, L.
TI  - Draft Genome Sequence of Streptomyces sp. F-3.
JO  - Genome Announcements
PY  - 2016
SP  - e00780
EP  - e00716
VL  - 4
AB  - Streptomyces sp. F-3 is a kind of thermophilic Streptomyces strain that can produce
AB  - cellulolytic enzymes and diverse secondary metabolites. Here, we report
AB  - the complete genome of this organism, whose genome length is 5,303,958 bp,
AB  - containing 6,041 protein-coding genes, 69 tRNA operons, and three rRNA operons.
ER  -

TY  - JOUR
AU  - Sun, X.
AU  - Yang, Y.
AU  - Zhang, N.
AU  - Shen, Y.
AU  - Ni, J.
TI  - Draft Genome Sequence of Dysgonomonas macrotermitis Strain JCM 19375T, Isolated from the Gut of a Termite.
JO  - Genome Announcements
PY  - 2015
SP  - e00963
EP  - e00915
VL  - 3
AB  - Here, we report the draft genome sequence of Dysgonomonas macrotermitis strain JCM 19375(T),
AB  - which was isolated from the hindgut of a fungus-growing termite, Macrotermes barneyi. The
AB  - genome information reveals the role of this strain in lignocellulose degradation and
AB  - adaptation to the gut environment.
ER  -

TY  - JOUR
AU  - Sun, Y.
AU  - Li, X.
AU  - Wang, G.
AU  - Wang, Y.
AU  - Jiang, Y.
AU  - Liu, Y.
AU  - Yu, Z.
AU  - Qin, L.
TI  - Genome Sequence of Enterococcus pernyi, a Pathogenic Bacterium for the Chinese Oak Silkworm, Antheraea pernyi.
JO  - Genome Announcements
PY  - 2016
SP  - e01764
EP  - e01715
VL  - 4
AB  - We report the draft genome assembly of Enterococcus pernyi The genome sequence is 3.09 Mb in
AB  - length with a G+C content of 38.35%. It covers 3,153 genes with an
AB  - average length of 854 bp, and contains 65 tRNAs, 13 small RNAs, and 18 rRNAs.
AB  - Moreover, it contains 9 genomic islands with an average length of 14,058 bp and 3
AB  - prophages with an average length of 37,430 bp.
ER  -

TY  - JOUR
AU  - Sun, Y.
AU  - Song, Y.
AU  - Song, H.
AU  - Liu, J.
AU  - Wang, P.
AU  - Qiu, S.
AU  - Chen, S.
AU  - Zhu, L.
AU  - Ji, X.
AU  - Wang, Z.
AU  - Liu, N.
AU  - Xia, L.
AU  - Chen, W.
AU  - Feng, S.
TI  - Complete Genome Sequence of an Acinetobacter Strain Harboring the NDM-1 Gene.
JO  - Genome Announcements
PY  - 2013
SP  - e00023
EP  - e00012
VL  - 1
AB  - The NDM-1 gene is a significant public health concern. Acinetobacter is one of the most
AB  - prevalent opportunistic pathogens causing recent nosocomial infections
AB  - with NDM-1, and drug-resistant strains pose serious threats to public health
AB  - worldwide. Herein, we present the genomic sequence of Acinetobacter calcoaceticus
AB  - subsp. anitratus XM1570, a multidrug-resistant isolate that carries the blaNDM-1
AB  - gene.
ER  -

TY  - JOUR
AU  - Sun, Y.
AU  - Wang, K.
AU  - Caceres-Moreno, C.
AU  - Jia, W.
AU  - Chen, A.
AU  - Zhang, H.
AU  - Liu, R.
AU  - Macho, A.P.
TI  - Genome sequencing and analysis of Ralstonia solanacearum phylotype I strains FJAT-91, FJAT-452 and FJAT-462 isolated from tomato, eggplant, and chili pepper in China.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 29
EP  - 29
VL  - 12
AB  - Ralstonia solanacearum is an extremely destructive pathogen able to cause disease in a wide
AB  - range of host plants. Here we report the draft genome sequences of the
AB  - strains FJAT-91, FJAT-452 and FJAT-462, isolated from tomato, eggplant, and chili
AB  - pepper, respectively, in China. In addition to the genome annotation, we
AB  - performed a search for type-III secreted effectors in these strains, providing a
AB  - detailed annotation of their presence and distinctive features compared to the
AB  - effector repertoire of the reference phylotype I strain (GMI1000). In this
AB  - analysis, we found that each strain has a unique effector repertoire, encoding
AB  - both strain-specific effector variants and variations shared among all three
AB  - strains. Our study, based on strains isolated from different hosts within the
AB  - same geographical location, provides insight into effector repertoires sufficient
AB  - to cause disease in different hosts, and may contribute to the identification of
AB  - host specificity determinants for R. solanacearum.
ER  -

TY  - JOUR
AU  - Sun, Z. et al.
TI  - Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.
JO  - Nat. Commun.
PY  - 2015
SP  - 8322
EP  - 8322
VL  - 6
AB  - Lactobacilli are a diverse group of species that occupy diverse nutrient-rich
AB  - niches associated with humans, animals, plants and food. They are used widely in
AB  - biotechnology and food preservation, and are being explored as therapeutics.
AB  - Exploiting lactobacilli has been complicated by metabolic diversity, unclear
AB  - species identity and uncertain relationships between them and other commercially
AB  - important lactic acid bacteria. The capacity for biotransformations catalysed by
AB  - lactobacilli is an untapped biotechnology resource. Here we report the genome
AB  - sequences of 213 Lactobacillus strains and associated genera, and their encoded
AB  - genetic catalogue for modifying carbohydrates and proteins. In addition, we
AB  - describe broad and diverse presence of novel CRISPR-Cas immune systems in
AB  - lactobacilli that may be exploited for genome editing. We rationalize the
AB  - phylogenomic distribution of host interaction factors and bacteriocins that
AB  - affect their natural and industrial environments, and mechanisms to withstand
AB  - stress during technological processes. We present a robust phylogenomic framework
AB  - of existing species and for classifying new species.
ER  -

TY  - JOUR
AU  - Sun, Z.
AU  - Chen, X.
AU  - Wang, J.
AU  - Gao, P.
AU  - Zhou, Z.
AU  - Ren, Y.
AU  - Sun, T.
AU  - Wang, L.
AU  - Meng, H.
AU  - Chen, W.
AU  - Zhang, H.
TI  - Complete genome sequence of probiotic Bifidobacterium animalis subsp. lactis strain V9.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4080
EP  - 4081
VL  - 192
AB  - Bifidobacterium animalis subsp. lactis strain V9 is a Chinese commercial bifidobacteria with
AB  - several probiotic functions. It was isolated from a healthy Mongolian child in China. We
AB  - present here the complete genome sequence of V9 and compared it to 3 other published genomes
AB  - of B. animalis subsp. lactis strains. The result indicates the lack of polymorphism among
AB  - strains of this subspecies of different continent origins.
ER  -

TY  - JOUR
AU  - Sun, Z.
AU  - Chen, X.
AU  - Wang, J.
AU  - Zhao, W.
AU  - Shao, Y.
AU  - Guo, Z.
AU  - Zhang, X.
AU  - Zhou, Z.
AU  - Sun, T.
AU  - Wang, L.
AU  - Meng, H.
AU  - Zhang, H.
AU  - Chen, W.
TI  - Complete genome sequence of Lactobacillus delbrueckii subsp. bulgaricus strain ND02.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3426
EP  - 3427
VL  - 193
AB  - Lactobacillus delbrueckii subsp. bulgaricus strain ND02 is a Chinese commercial dairy starter
AB  - used for the manufacture of yoghurt. It was
AB  - isolated from the naturally fermented yak milk in Qinghai, China. Here, we
AB  - report the main genome features of ND02 and several differences with two
AB  - other published genomes of Lactobacillus delbrueckii subsp. bulgaricus
AB  - strains.
ER  -

TY  - JOUR
AU  - Sun, Z.
AU  - Chen, X.
AU  - Wang, J.
AU  - Zhao, W.
AU  - Shao, Y.
AU  - Wu, L.
AU  - Zhou, Z.
AU  - Sun, T.
AU  - Wang, L.
AU  - Meng, H.
AU  - Zhang, H.
AU  - Chen, W.
TI  - Complete genome sequence of Streptococcus thermophilus strain ND03.
JO  - J. Bacteriol.
PY  - 2010
SP  - 793
EP  - 794
VL  - 193
AB  - Streptococcus thermophilus strain ND03 is a Chinese commercial dairy starter used for the
AB  - manufacture of yoghurt. It was isolated from the naturally fermented yak milk in Qinghai,
AB  - China. We present here the complete genome sequence of ND03 and compared it to 3 other
AB  - published genomes of Streptococcus thermophilus strains.
ER  -

TY  - JOUR
AU  - Sun, Z.
AU  - Hsiang, T.
AU  - Zhou, Y.
AU  - Zhou, J.
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens XK-4-1, a Plant Growth-Promoting Endophyte with Antifungal Activity.
JO  - Genome Announcements
PY  - 2015
SP  - e01306
EP  - e01315
VL  - 3
AB  - Here, we report the draft genome sequence of a bacterial plant-growth-promoting endophyte,
AB  - Bacillus amyloliquefaciens XK-4-1, which consists of one circular
AB  - chromosome of 3,941,805 bp with 3,702 coding sequences (CDSs). The data presented
AB  - highlight multiple sets of functional genes associated with its plant-beneficial
AB  - characteristics.
ER  -

TY  - JOUR
AU  - Sun, Z.Y.
AU  - Terragni, J.
AU  - Borgaro, J.G.
AU  - Liu, Y.W.
AU  - Yu, L.
AU  - Guan, S.X.
AU  - Wang, H.
AU  - Sun, D.P.
AU  - Cheng, X.D.
AU  - Zhu, Z.Y.
AU  - Pradhan, S.
AU  - Zheng, Y.
TI  - High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells.
JO  - Cell Rep.
PY  - 2013
SP  - 567
EP  - 576
VL  - 3
AB  - We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI
AB  - coupled with sequencing (Aba-seq) to map
AB  - high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The
AB  - specificity of AbaSI enables sensitive detection of
AB  - 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic
AB  - analysis suggests 5hmCs in genic regions closely follow the 5mC
AB  - distribution. 5hmC is generally depleted in CpG islands and only
AB  - enriched in a small set of repetitive elements. A regularly spaced and
AB  - oscillating 5hmC pattern was observed at the binding sites of CTCF.
AB  - 5hmC is enriched at the poised enhancers with the monomethylated
AB  - histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers
AB  - with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG
AB  - hydroxymethylation appears to be prevalent in the mitochondrial genome.
AB  - We propose that some amounts of transiently stable 5hmCs may indicate a
AB  - poised epigenetic state or demethylation intermediate, whereas others
AB  - may suggest a locally accessible chromosomal environment for the TET
AB  - enzymatic apparatus.
ER  -

TY  - JOUR
AU  - Sung, J.S.
AU  - Chun, J.
AU  - Choi, S.
AU  - Park, W.
TI  - Genome Sequence of the Halotolerant Staphylococcus sp. Strain OJ82, Isolated from Korean Traditional Salt-Fermented Seafood.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6353
EP  - 6354
VL  - 194
AB  - Staphylococcus sp. strain OJ82 was isolated from a Korean traditional fermented squid seafood,
AB  - ojingeo-jeotgal. Staphylococcus sp. OJ82 could grow and show
AB  - extracellular protease and beta-galactosidase activities in the presence of
AB  - extremely high saline (20%). Here, we report the genome sequence of
AB  - Staphylococcus sp. OJ82.
ER  -

TY  - JOUR
AU  - Sung, K.
AU  - Khan, S.
AU  - Marasa, B.
AU  - Min, S.
AU  - Kweon, O.
AU  - Mohamed, N.
AU  - Cerniglia, C.
TI  - Draft Genome Sequence of a vanA-Type Vancomycin-Resistant Reference Strain, Enterococcus faecium ATCC 51559.
JO  - Genome Announcements
PY  - 2015
SP  - e01053
EP  - e01015
VL  - 3
AB  - Vancomycin-resistant Enterococcus faecium has emerged as a multidrug-resistant pathogen in
AB  - hospital settings. Here, we present the draft genome sequence of a high-level
AB  - vancomycin-resistant strain, E. faecium ATCC 51559, which is employed  as a standard
AB  - laboratory vanA genotype-positive control strain for clinical and laboratory studies.
ER  -

TY  - JOUR
AU  - Sung, K.
AU  - Khan, S.
AU  - Marasa, B.
AU  - Min, S.
AU  - Kweon, O.
AU  - Nawaz, M.
AU  - Cerniglia, C.
TI  - Genomic Sequence of a Clinical Vancomycin-Resistant Reference Strain, Enterococcus faecalis ATCC 51299.
JO  - Genome Announcements
PY  - 2015
SP  - e01495
EP  - e01415
VL  - 3
AB  - In this paper, we present a draft genome sequence of a quality control reference  strain,
AB  - Enterococcus faecalis ATCC 51299 (multilocus sequencing type [MLST] ST6),
AB  - which is sensitive to teicoplanin but resistant to vancomycin. It is used in an
AB  - agar screening test for streptomycin, gentamicin, and vancomycin resistance and
AB  - the resistance marker vanB.
ER  -

TY  - JOUR
AU  - Suraiya, S.
AU  - Semail, N.
AU  - Ismail, M.F.
AU  - Abdullah, J.M.
TI  - Complete Genome Sequence of Mycobacterium tuberculosis Clinical Isolate Spoligotype SIT745/EAI1-MYS.
JO  - Genome Announcements
PY  - 2016
SP  - e00323
EP  - e00316
VL  - 4
AB  - Mycobacterium tuberculosis is known to cause pulmonary and extrapulmonary tuberculosis. This
AB  - organism showed special phylogeographical specificity. Here,
AB  - we report the complete genome sequence of M. tuberculosis clinical isolate
AB  - spoligotype SIT745/EAI1-MYS, which was isolated from a Malaysian tuberculosis
AB  - patient.
ER  -

TY  - JOUR
AU  - Surani, M.A.
TI  - Imprinting and the initiation of gene silencing in the germ line.
JO  - Cell
PY  - 1998
SP  - 309
EP  - 312
VL  - 93
AB  - Inheritance of genes in active or repressed states requires appropriate chromosomal
AB  - modifications and DNA methylation.  Imprinting of a determined state into the chromatin
AB  - structure therefore constitutes a memory of all developmental decisions taken within
AB  - individual cells.  Genomic or gametic imprinting is however a unique manifestation of such
AB  - epigenetic inheritance in which expression of certain genes is governed by their parental
AB  - origin, from generation to generation.  Some of these genes show expression after paternal
AB  - inheritance while others are expressed only when inherited from the maternal germ line.  The
AB  - most striking feature of imprinted genes therefore is that the active and inactive parental
AB  - alleles coexist within individual cells.  Over 20 imprinted genes have so far been identified.
AB  - Parental genomes are functionally nonequivalent during development because of the differential
AB  - expression of imprinted genes. A review.
ER  -

TY  - JOUR
AU  - Surby, M.A.
TI  - Facilitated diffusion of the EcoRI DNA methyltransferase under both catalytic and noncatalytic conditions and the potential of Z DNA disrupt protein translocation on DNA.
JO  - Diss. Abstr.
PY  - 1997
SP  - 5631B
EP  - 5632B
VL  - 57
AB  - Previous experiments in our lab have suggested that the EcoRI DNA methyltransferase might
AB  - utilize one-dimensional facilitated diffusion to locate its specific binding site on a DNA
AB  - substrate.  In the current study, initial experiments to characterize this phenomenon with
AB  - regard to the methyltransferase focus on the contribution of nonspecific DNA to enzyme
AB  - efficiency (kcat/Km).  This parameter increases 4-fold as DNA length increases from 14 to 429
AB  - basepairs and increases 2-fold as the distance from the site to the nearest end is increased
AB  - from 29 to 378 basepairs.  No changes in kcat/Km result from further increases in either case.
AB  - A facilitated diffusion mechanism is proposed in which the methyltransferase scans an average
AB  - of <400 base pairs prior to dissociation from a DNA molecule.  The methyltransferase was found
AB  - to methylate two sites on a single DNA molecule in a distributive rather than a processive
AB  - manner, suggesting that the enzyme dissociates from the DNA prior to release of the reaction
AB  - product S-adenosylhomocysteine.  A direct competition experiment with the EcoRI endonuclease
AB  - shows the methyltransferase to be slightly more efficient at specific site location and
AB  - catalysis.  A rationale for the role of facilitated diffusion in this type II
AB  - restriction-modification system is proposed.  In addition, the contribution of nonspecific DNA
AB  - to binding parameters (d, koff, and kon) was determined for the methyltransferase under
AB  - noncatalytic conditions.  An increase in DNA size from 14 to 775 base pairs causes a 20-fold
AB  - decrease in Kd, while koff remains constant over the same range.  The calculated kon increases
AB  - with longer substrates, consistent with a facilitated diffusion mechanism.  However, the
AB  - combined results deviate from the model developed to describe facilitated diffusion.  Our
AB  - results were successfully simulated using numerical integration of a kinetic scheme invoking
AB  - protein dissociation via the ends of DNA.  Consistent with this scheme, the methyltransferase
AB  - dissociates more slowly from a circularized DNA molecule than from the identical linearized
AB  - form.  The final set of experiments is an attempt to determine the effect of Z DNA on the
AB  - ability of proteins to translocate on DNA.  Z DNA formation in a linear substrate is confirmed
AB  - with Z DNA-specific antibody binding and preliminary results with the EcoRI endonuclease
AB  - suggest that Z DNA decreases the rate of DNA cleavage by 2- to 3-fold.  However, subsequent
AB  - experiments with more highly purified endonuclease do not support this conclusion.  Z DNA
AB  - cannot be detected in the linear substrates with chemical modification techniques, so the
AB  - assay was modified to use the methyltransferase and a supercoiled DNA substrate.  Although
AB  - there is an observable effect on kcat and Km in the supercoiled substrate, control experiments
AB  - make an assignment of this effect to the presence of Z DNA unclear.
ER  -

TY  - JOUR
AU  - Surby, M.A.
AU  - Reich, N.O.
TI  - The role of nonspecific DNA in the site location kinetics of the EcoRI DNA methyltransferase.
JO  - FASEB J.
PY  - 1992
SP  - A356
EP  - A356
VL  - 6
AB  - The EcoRI DNA methyltransferase is an extremely efficient enzyme, with a
AB  - kcat/Km of 4.1 X 10/8 s-1M-1 for plasmid DNA.  Its kcat/Km decreases to 0.51 X
AB  - 10/8 s-1M-1 when a 14 basepair synthetic oligonucleotide is used as a
AB  - substrate.  A possible explanation for these observations is that the methylase
AB  - utilizes facilitated diffusion along nonspecific DNA as a mechanism for site
AB  - location.  This was first tested using a processivity assay developed for the
AB  - EcoRI endonuclease (J. Biol. Chem., Oct. 25, 1985, 260 (24) pp 13130-13137).
AB  - In contrast to our results with the endonuclease, no processive methylation was
AB  - observed with this assay.  The role of facilitated diffusion in initial site
AB  - location was then investigated by kinetic analysis of restriction fragments
AB  - ranging in size from 4363 to 108 basepairs, all of which contained a single
AB  - EcoRI site.  There were no differences observed in the rate of methyl group
AB  - incorporation for the various substrates.  This leads us to conclude that the
AB  - specificity enhancement observed for the plasmid DNA is due either to
AB  - nonspecific sequences <108 basepairs away from the canonical site of the DNA
AB  - substrate or to some other phenomenon (e.g. flanking sequence differences).
ER  -

TY  - JOUR
AU  - Surby, M.A.
AU  - Reich, N.O.
TI  - The role of nonspecific DNA in the site-location kinetics of the EcoRI DNA methyltransferase.
JO  - Biochemistry
PY  - 1992
SP  - 2208
EP  - 2208
VL  - 31
AB  - The EcoRI DNA methyltransferase is an extremely efficient enzyme, with a
AB  - kcat/Km of 4.1 x 10/8 S-1M-1 for plasmid DNA.  Its kcat/Km decreases to 0.51 x
AB  - 10.8 S-1 M-1 when a 14-base-pair synthetic oligonucleotide is used as a
AB  - substrate.  Canonical site flanking sequence differences between the plasmid
AB  - and the 14-bp oligonucleotide were shown to have no effect on kcat/Km.  A
AB  - possible explanation for these observations is that the methylase utilizes
AB  - facilitated diffusion along nonspecific DNA as a mechanism for site location.
AB  - This was first tested using a processivity assay developed for the EcoRI
AB  - endonuclease [(1985) J. Biol. Chem. 260 (24), 13130-13137].  In contrast to our
AB  - results with the endonuclease, no processive methylation was observed with this
AB  - assay.  The role of facilitated diffusion in initial site location was then
AB  - investigated by kinetic analysis of restriction fragments ranging in size from
AB  - 4363 to 108 bp, all of which contained a single EcoRI site.  There were no
AB  - differences observed in the rate of methyl group incorporation for various
AB  - substrates.  This leads us to conclude that the specificity enhancement
AB  - observed for the plasmid DNA is due to nonspecific sequences <108 bp away from
AB  - the canonical site of the DNA substrate.
ER  -

TY  - JOUR
AU  - Surby, M.A.
AU  - Reich, N.O.
TI  - Facilitated diffusion of the EcoRI DNA methyltransferase is described by a novel mechanism.
JO  - Biochemistry
PY  - 1996
SP  - 2209
EP  - 2217
VL  - 35
AB  - The contribution of nonspecific DNA to binding parameters (Kd, koff, and kon) was determined
AB  - for the EcoRI DNA methyltransferase under noncatalytic conditions.  An increase in DNA size
AB  - from 14 to 775 base pairs causes a 20-fold decrease in Kd, while koff remains constant over
AB  - the same range.  The calculated kon increases with longer substrates, consistent with a
AB  - facilitated diffusion mechanism.  However, the combined results deviate from the model
AB  - developed to describe facilitated diffusion.  Our results were successfully simulated using
AB  - numerical integration of a kinetic scheme invoking protein dissociation via the ends of DNA.
AB  - Consistent with this scheme, the methyltransferase dissociates more slowly from a circularized
AB  - DNA molecule than from the identical linearized form.  The simulation strategy correctly
AB  - models our data with the methyltransferase and should be generally useful for routine modeling
AB  - of facilitated diffusion involving protein-DNA systems.
ER  -

TY  - JOUR
AU  - Surby, M.A.
AU  - Reich, N.O.
TI  - Contribution of facilitated diffusion and processive catalysis to enzyme efficiency: Implications for the EcoRI restriction-modification system.
JO  - Biochemistry
PY  - 1996
SP  - 2201
EP  - 2208
VL  - 35
AB  - The contribution of nonspecific DNA to enzyme efficiency (kcat/Km) is described for a
AB  - sequence-specific DNA-modifying enzyme.  Our investigation focuses on the EcoRI DNA
AB  - methyltransferase which transfers a methyl group from the cofactor S-adenosylmethionine to the
AB  - second adenine in the double-stranded DNA sequence GAATTC.  kcat/Km increases 4-fold as DNA
AB  - length increases from 14 to 429 base pairs and increases 2-fold as the distance from the site
AB  - to the nearest end is increased from 29 to 378 base pairs.  No changes in kcat/Km result from
AB  - further increases in either case.  A facilitated diffusion mechanism is proposed in which the
AB  - methyltransferase scans an average of <400 base pairs prior to dissociation from a DNA
AB  - molecule.  The methyltransferase was found to methylate two sites on a single DNA molecule in
AB  - a distributive rather than a processive manner, suggesting that the enzyme dissociates from
AB  - the DNA prior to release of the reaction product S-adenosylhomocysteine.  A direct competition
AB  - experiment with the EcoRI endonuclease shows the methyltransferase to be slightly more
AB  - efficient at specific site location and catalysis.  A rationale for the role of facilitated
AB  - diffusion in this type II restriction-modification system is proposed.
ER  -

TY  - JOUR
AU  - Surby, M.A.
AU  - Reich, N.O.
TI  - The role of nonspecific DNA in the site-location kinetics of the EcoRI DNA methyltransferase.
JO  - ACS Abstracts
PY  - 1992
SP  - 110
EP  - BIOL
VL  - 203
AB  - The EcoRI DNA methyltransferase is an extremely efficient enzyme, with a kcat/Km of 4.1 x 10/8
AB  - S-1M-1 for plasmid DNA. Its kcat/Km decreases to 0.51 x 10/8 S-1M-1 when a 14 basepair
AB  - synthetic oligonucleotide is used as a substrate. Cannonical site flanking sequence
AB  - differences between the plasmid and the 14 basepair oligonucleotide were shown to have no
AB  - effect on kcat/Km. A possible explanation for these observations is that the methylase
AB  - utilizes facilitated diffusion along nonspecific DNA as a mechanism for site location. This
AB  - was first tested using a processivity assay developed for the EcoRI endonuclease (J. Biol.
AB  - Chem., Oct. 25,1985, 260 (24), pp 13130-13137). In contrast to our results with the
AB  - endonuclease, no processive methylation was observed with this assay. The role of facilitated
AB  - diffusion in initial site location was then investigated by kinetic analysis of restriction
AB  - fragments ranging in size from 4363 to 108 basepairs, all of which contained a single EcoRI
AB  - site. There were no differences observed in the rate of methyl group incorporation for the
AB  - various substrates. This leads us to conclude that the specificity enhancement observed for
AB  - the plasmid DNA is due to nonspecific sequences <108 basepairs aways from the canonical site
AB  - of the DNA substrate.
ER  -

TY  - JOUR
AU  - Suri, B.
AU  - Bickle, T.A.
TI  - EcoA:  The first member of a new family of Type I restriction modification systems - Gene organization and enzymatic activities.
JO  - J. Mol. Biol.
PY  - 1985
SP  - 77
EP  - 85
VL  - 186
AB  - The characterization of the EcoA restriction-modification enzymes from
AB  - Escherichia coli 15T- is described.  The reactions catalysed by these enzymes
AB  - are very similar to those catalysed by the classical type I restriction and
AB  - modification enzymes, a family of genetically related proteins.  The detailed
AB  - mechanisms, particularly for DNA modification, differ.  The genetic and
AB  - transcriptional organizations are also very similar to those of the classical
AB  - systems, despite the fact that EcoA is not allelic to the others.  We
AB  - demonstrate that the expression of the EcoA genes is controlled following
AB  - conjugative transfer to other strains in such a way that no lethality is
AB  - observed, probably because the reciptient chromosome is completely modified
AB  - before restriction activity is expressed.
ER  -

TY  - JOUR
AU  - Suri, B.
AU  - Nagaraja, V.
AU  - Bickle, T.A.
TI  - Bacterial DNA modification.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 1984
SP  - 1
EP  - 9
VL  - 108
AB  - As first proposed by Arber (1965), DNA restriction/modification systems (R/M
AB  - systems) are mediated by endonucleases and DNA methylases that recognize the
AB  - same DNA sequences.  The endonuclease recognizes its specific sequence as a
AB  - signal to cleave the DNA unless the sequence has been previously methylated by
AB  - the modification enzyme.  Chromosomal DNA from cells harboring the R/M system
AB  - is normally methylated, and is thus not a substrate for the restriction enzyme.
AB  - Foreign DNA lacking the specific methylation pattern and introduced into the
AB  - cell by phase infection, conjugation, or transformation is the only known
AB  - natural substrate for restriction.  R/M systems can therefore be considered
AB  - primitive prokaryotic analogues of the eukaryotic immune system.  A vast body
AB  - of literature on the genetics and biochemistry of R/M systems has accumulated
AB  - since they were first investigated 20 years ago (Arber and Dussoix 1962), and
AB  - it is now clear that R/M systems can be conveniently classified into three
AB  - types (Boyer 1971; Kauc and Piekarowicz 1978; Nathans and Smith 1975).  The
AB  - most complicated of these are the type-I systems, which are mediated by
AB  - complex, multifunctional enzymes and which were the first proteins shown to
AB  - recognize specific DNA sequences.  The restriction enzymes EcoK and EcoB from
AB  - the Escherichia coli strains K12 and B are the two prototypes, and are still
AB  - the only ones to have been studied in detail.
ER  -

TY  - JOUR
AU  - Suri, B.
AU  - Shepherd, J.C.W.
AU  - Bickle, T.A.
TI  - The EcoA restriction and modification system of Escherichia coli 15T-: enzyme structure and DNA recognition sequence.
JO  - EMBO J.
PY  - 1984
SP  - 575
EP  - 579
VL  - 3
AB  - The EcoA restriction enzyme from Escherichia coli 15T- has been isolated.  It
AB  - proves to be an unusual enzyme, clearly related functionally to the classical
AB  - type I restriction enzymes.  The basic enzyme is a two subunit modification
AB  - methylase.  Another protein species can be purified which by itself has not
AB  - enzymatic activities but which converts the modification methylase to an ATP
AB  - and S-adenosylmethionine-dependent restriction endonuclease.  The DNA
AB  - recognition sequence of EcoA has an overall structure that is very similar to
AB  - previously determined type I sequences.  It is:
AB  - 5'-GAGNNNNNNNGTCA-3'3'-CTCNNNNNNNCAGT-5'where N can be any nucleotide.
AB  - Modification methylates the adenosyl residue in the specific trinucleotide and
AB  - the adenosyl residue in the lower strand of the specific tetranucleotide.
ER  -

TY  - JOUR
AU  - Suryaletha, K.
AU  - Narendrakumar, L.
AU  - John, J.
AU  - Reghunathan, D.
AU  - Prasannakumar, M.
AU  - Thomas, S.
TI  - Genomic Insights into Biofilm-Forming Enterococcus faecalis SK460 Isolated from a Chronic Diabetic Ulcer Patient.
JO  - Genome Announcements
PY  - 2018
SP  - e01463
EP  - e01417
VL  - 6
AB  - Enterococcus faecalis is recognized as one of the leading pathogens causing nosocomial
AB  - infections. Here we report a draft genome sequence of Enterococcus
AB  - faecalis SK460, isolated from a chronic diabetic foot ulcer patient. This strain
AB  - exhibits various biofilm-associated genes, virulence genes, and
AB  - antibiotic-resistance genes related to aminoglycoside, macrolide, and
AB  - tetracycline resistance.
ER  -

TY  - JOUR
AU  - Suryavanshi, M.V.
AU  - Paul, D.
AU  - Doijad, S.P.
AU  - Bhute, S.S.
AU  - Hingamire, T.B.
AU  - Gune, R.P.
AU  - Shouche, Y.S.
TI  - Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 15
EP  - 15
VL  - 12
AB  - Probiotic Lactobacillus species offer various health benefits, thus have been employed in
AB  - treatment and prevention of various diseases. Due to the differences
AB  - in the isolation source and the site of action, most of the lactobacilli tested
AB  - in-vitro for probiotics properties fail to extend similar effects in-vivo.
AB  - Consequently, the search of autochthonous, efficacious and probably population
AB  - specific probiotics is a high priority in the probiotics research. In this
AB  - regards, whole genome sequencing of as many Lactobacillus as possible will help
AB  - to deepen our understanding of biology and their health effects. Here, we provide
AB  - the genomic insights of two coherent oxalic acid tolerant Lactobacillus species
AB  - (E2C2 and E2C5) isolated from two different healthy human gut flora. These two
AB  - isolates were found to have higher tolerance towards oxalic acid (300 mM sodium
AB  - oxalate). The draft genome of strain E2C2 consists of 3,603,563 bp with 3289
AB  - protein-coding genes, 94 RNA genes, and 43.99% GC content, while E2C5 contained
AB  - 3,615,168 bp, 3293 coding genes (93.4% of the total genes), 95 RNA genes and
AB  - 43.97% GC content. Based on 16S rRNA gene sequence analysis followed by in silico
AB  - DNA-DNA hybridization studies, both the strains were identified as Lactobacillus
AB  - plantarum belonging to family Lactobacillaceae within the phylum Firmicutes. Both
AB  - the strains were genomically identical, sharing 99.99% CDS that showed 112 SNPs.
AB  - Both the strains also exhibited deconjugation activity for the bile salts while
AB  - genome analysis revealed that the L. plantarum strains E2C2 and E2C5 also have
AB  - the ability to produce vitamins, biotin, alpha- and beta- glucosidase suggesting
AB  - potential probiotic activities of the isolates. The description presented here is
AB  - based on the draft genomes of strains E2C2 and E2C5 which are submitted to
AB  - GenBank under the accession numbers LSST00000000.1 and LTCD00000000.1,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Susanti, D. et al.
TI  - Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka,  Russia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5703
EP  - 5704
VL  - 194
AB  - Desulfurococcus fermentans is the first known cellulolytic archaeon. This hyperthermophilic
AB  - and strictly anaerobic crenarchaeon produces hydrogen from
AB  - fermentation of various carbohydrates and peptides without inhibition by
AB  - accumulating hydrogen. The complete genome sequence reported here suggested that
AB  - D. fermentans employs membrane-bound hydrogenases and novel glycohydrolases for
AB  - hydrogen production from cellulose.
ER  -

TY  - JOUR
AU  - Susanti, D.
AU  - Johnson, E.F.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Reddy, T.B.
AU  - Mukherjee, S.
AU  - Pillay, M.
AU  - Perevalova, A.A.
AU  - Ivanova, N.N.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Mukhopadhyay, B.
TI  - Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a  Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka  Peninsula and Kunashir Island, Russia.
JO  - Genome Announcements
PY  - 2017
SP  - e00078
EP  - e00017
VL  - 5
AB  - Desulfurococcus amylolyticus Z-533T, a hyperthermophilic crenarcheon, ferments peptide and
AB  - starch, generating acetate, isobutyrate, isovalerate, CO2, and
AB  - hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose and is inhibited
AB  - by hydrogen. The reported draft genome sequence of D. amylolyticus Z-533T will
AB  - help to understand the molecular basis for these differences.
ER  -

TY  - JOUR
AU  - Susanti, D.
AU  - Johnson, E.F.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Reddy, T.B.
AU  - Pilay, M.
AU  - Ivanova, N.N.
AU  - Markowitz, V.M.
AU  - Woyke, T.
AU  - Kyrpides, N.C.
AU  - Mukhopadhyay, B.
TI  - Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161,  a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs  of Hveravellir, Iceland.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 3
EP  - 3
VL  - 11
AB  - This report presents the permanent draft genome sequence of Desulfurococcus mobilis type
AB  - strain DSM 2161, an obligate anaerobic hyperthermophilic
AB  - crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland.
AB  - D. mobilis utilizes peptides as carbon and energy sources and reduces elemental
AB  - sulfur to H2S. A metabolic construction derived from the draft genome identified
AB  - putative pathways for peptide degradation and sulfur respiration in this
AB  - archaeon. Existence of several hydrogenase genes in the genome supported previous
AB  - findings that H2 is produced during the growth of D. mobilis in the absence of
AB  - sulfur. Interestingly, genes encoding glucose transport and utilization systems
AB  - also exist in the D. mobilis genome though this archaeon does not utilize
AB  - carbohydrate for growth. The draft genome of D. mobilis provides an additional
AB  - mean for comparative genomic analysis of desulfurococci. In addition, our
AB  - analysis on the Average Nucleotide Identity between D. mobilis and
AB  - Desulfurococcus mucosus suggested that these two desulfurococci are two different
AB  - strains of the same species.
ER  -

TY  - JOUR
AU  - Sussenbach, J.S.
AU  - Monfoort, C.H.
AU  - Schiphof, R.
AU  - Stobberingh, E.E.
TI  - A restriction endonuclease from Staphylococcus aureus.
JO  - Nucleic Acids Res.
PY  - 1976
SP  - 3193
EP  - 3202
VL  - 3
AB  - A specific endonuclease, Sau3AI, has been partially purified from
AB  - Staphylococcus aureus strain 3A by DEAE-cellulose chromatography.  The enzyme
AB  - cleaves adenovirus type 5 DNA many times, SV40 DNA eight times but does not
AB  - cleave double-stranded PhiX174 DNA.  It recognizes the sequence 5' ^-G-A-T-C-
AB  - 3' 3'  -C-T-A-G-^ 5'  and cleaves as indicated by the arrows.  Evidence is
AB  - presented that this enzyme plays a role in the biological
AB  - restriction-modification system of Staphylococcus aureus strain 3A.
ER  -

TY  - JOUR
AU  - Sussenbach, J.S.
AU  - Steenbergh, P.H.
AU  - Rost, J.A.
AU  - van Leeuwen, W.J.
AU  - van Embden, J.D.A.
TI  - A second site-specific restriction endonuclease from Staphylococcus aureus.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 1153
EP  - 1163
VL  - 5
AB  - A site-specific restriction endonuclease has been isolated from Staphylococcus
AB  - aureus PS 96.  This enzyme, Sau96I, recognizes the DNA sequence
AB  - 5'--G-^G-N-C-C--3' 3'--C-C-N-G-^G--5' and cleaves as indicated by the arrows.
AB  - The enzyme cleaves adenovirus type 5 and lambda DNA many times, SV40 DNA 10
AB  - times and PhiX174 RF DNA 2 times.  Evidence is presented that the enzyme is
AB  - involved in biological restriction-modification.
ER  -

TY  - JOUR
AU  - Sussman, D.
AU  - Chadsey, M.
AU  - Fauce, S.
AU  - Engel, A.
AU  - Bruett, A.
AU  - Monnat, R.
AU  - Stoddard, B.L.
AU  - Seligman, L.M.
TI  - Isolation and characterization of new homing endonuclease specificities at individual target site positions.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 31
EP  - 41
VL  - 342
AB  - Homing endonucleases are highly specific DNA endonucleases, encoded within mobile introns or
AB  - inteins, that induce targeted recombination,
AB  - double-strand repair and gene conversion of their cognate target sites.
AB  - Due to their biological function and high level of target specificity,
AB  - these enzymes are under intense investigation as tools for gene
AB  - targeting. These studies require that naturally occurring enzymes be
AB  - redesigned to recognize novel target sites. Here, we report studies in
AB  - which the homodimeric LAGLIDADG homing endonuclease I-CreI is altered
AB  - at individual side-chains corresponding to contact points to distinct
AB  - base-pairs in its target site. The resulting enzyme constructs drive
AB  - specific elimination of selected DNA targets in vivo and display
AB  - shifted specificities of DNA binding and cleavage in vitro. Crystal
AB  - structures of two of these constructs demonstrate that substitution of
AB  - individual side-chain/DNA contact patterns can occur with almost no
AB  - structural deformation or rearrangement of the surrounding complex,
AB  - facilitating an isolated, modular redesign strategy for homing
AB  - endonuclease activity and specificity.
ER  -

TY  - JOUR
AU  - Sutcliffe, B.
AU  - Midgley, D.J.
AU  - Rosewarne, C.P.
AU  - Greenfield, P.
AU  - Li, D.
TI  - Draft Genome Sequence of Thermotoga maritima A7A Reconstructed from Metagenomic Sequencing Analysis of a Hydrocarbon Reservoir in the Bass Strait, Australia.
JO  - Genome Announcements
PY  - 2013
SP  - e00688
EP  - e00613
VL  - 1
AB  - The draft genome sequence of Thermotoga maritima A7A was obtained from a metagenomic assembly
AB  - obtained from a high-temperature hydrocarbon reservoir in
AB  - the Gippsland Basin, Australia. The organism is predicted to be a motile anaerobe
AB  - with an array of catabolic enzymes for the degradation of numerous carbohydrates.
ER  -

TY  - JOUR
AU  - Sutcliffe, J.G.
AU  - Church, G.M.
TI  - The cleavage site of the restriction endonuclease AvaII.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 2313
EP  - 2319
VL  - 5
AB  - We have determined that the type II restriction enzyme AvaII, isolated from
AB  - Anabaena variabilis, recognizes and cuts the sequence 5' - G^GTCC - 3' 3' -
AB  - CCAG^G - 5' The eight AvaII sites of pBR322 have been mapped, as well as a
AB  - unique site for AvaI.
ER  -

TY  - JOUR
AU  - Sutherland, E.
AU  - Coe, L.
AU  - Raleigh, E.A.
TI  - McrBC:  a multisubunit GTP-dependent restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1992
SP  - 327
EP  - 358
VL  - 225
AB  - McrBC-mediated restriction of modified DNA has been studied extensively by genetic methods,
AB  - but little is known of its molecular action. We have used overproducing plasmid constructs to
AB  - facilitate purification of the McrB L and McrC proteins, and report preliminary
AB  - characterization of the activity of the complex. Both proteins are required for cleavage of
AB  - appropriately modified DNA in vitro, in a reaction absolutely dependent on GTP. ATP inhibits
AB  - the reaction. The sequence and modification requirements for cleavage of the substrate reflect
AB  - those seen in vivo. The position of cleavage was examined at the nucleotide level, revealing
AB  - that cleavage occurs at multiple positions in a small region. Based upon these observations,
AB  - and upon cleavage of model oligonucleotide substrates, it is proposed that the recognition
AB  - site for this enzyme consists of the motif RmC(N40-80) RmC, with cleavage occurring at
AB  - multiple positions on both strands between the modified C residues. In subunit composition,
AB  - cofactor requirement, and relation between cleavage and recognition site, McrBC does not fit
AB  - into any of the classes (types I to IV) of restriction enzyme so far described.
ER  -

TY  - JOUR
AU  - Sutton, J.M.
AU  - Baesman, S.M.
AU  - Fierst, J.L.
AU  - Poret-Peterson, A.T.
AU  - Oremland, R.S.
AU  - Dunlap, D.S.
AU  - Akob, D.M.
TI  - Complete Genome Sequence of the Acetylene-Fermenting Pelobacter sp. Strain SFB93.
JO  - Genome Announcements
PY  - 2017
SP  - e01573
EP  - e01516
VL  - 5
AB  - Acetylene fermentation is a rare metabolism that was previously reported as being unique to
AB  - Pelobacter acetylenicus Here, we report the genome sequence of
AB  - Pelobacter sp. strain SFB93, an acetylene-fermenting bacterium isolated from
AB  - sediments collected in San Francisco Bay, CA.
ER  -

TY  - JOUR
AU  - Sutton, J.M.
AU  - Baesman, S.M.
AU  - Fierst, J.L.
AU  - Poret-Peterson, A.T.
AU  - Oremland, R.S.
AU  - Dunlap, D.S.
AU  - Akob, D.M.
TI  - Complete Genome Sequences of Two Acetylene-Fermenting Pelobacter acetylenicus Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e01572
EP  - e01516
VL  - 5
AB  - Acetylene fermentation is a rare metabolism that was serendipitously discovered during
AB  - C2H2-block assays of N2O reductase. Here, we report the genome sequences
AB  - of two type strains of acetylene-fermenting Pelobacter acetylenicus, the
AB  - freshwater bacterium DSM 3246 and the estuarine bacterium DSM 3247.
ER  -

TY  - JOUR
AU  - Suvorova, M.A.
AU  - Tsapieva, A.N.
AU  - Bak, E.G.
AU  - Chereshnev, V.A.
AU  - Kiseleva, E.P.
AU  - Suvorov, A.N.
AU  - Arumugam, M.
TI  - Complete Genome Sequences of emm111 Type Streptococcus pyogenes Strain GUR, with  Antitumor Activity, and Its Derivative Strain GURSA1 with an Inactivated emm  Gene.
JO  - Genome Announcements
PY  - 2017
SP  - e00939
EP  - e00917
VL  - 5
AB  - We present here the complete genome sequence of Streptococcus pyogenes type emm111 strain GUR,
AB  - a throat isolate from a scarlet fever patient, which has been
AB  - used to treat cancer patients in the former Soviet Union. We also present the
AB  - complete genome sequence of its derivative strain GURSA1 with an inactivated emm
AB  - gene.
ER  -

TY  - JOUR
AU  - Suvorova, M.A.
AU  - Tsapieva, A.N.
AU  - Duplik, N.V.
AU  - Kramskoy, T.A.
AU  - Grabovskaya, K.B.
AU  - Kiseleva, E.P.
AU  - Chereshnev, V.A.
AU  - Suvorov, A.N.
TI  - Construction of a Streptococcus strain mutant in the M protein gene.
JO  - Med. Akad. Z.
PY  - 2016
SP  - 235
EP  - 236
VL  - 16
ER  -

TY  - JOUR
AU  - Suzuki, H.
TI  - Host-mimicking strategies in DNA methylation for improved bacterial transformation.
JO  - Methylation - from DNA, RNa and histones to diseases and treatment
PY  - 2012
SP  - 219
EP  - 236
VL  - 0
AB  - In 1928, Griffith reported that soluble substances from virulent pneumococcal cells
AB  - transformed non-virulent pneumococcus to virulent forms.  This substance has now been
AB  - demonstrated to be DNA.  This is considered to be the first report on genetic transformation
AB  - of bacteria by exogenous DNA.  Subsequently, natural competence of Bacillus subtilis was
AB  - reported in 1958 by Young and Spizizen.  They also demonstrated genetic transformation of
AB  - natural competent B. subtilis cells using exogenous DNA.  It was in 1970 that genetic
AB  - transformation of Escherichia coli using chemically competent cells was reported.  Thus,
AB  - genetic transformation of common bacterial models was established at an early stage in the
AB  - development of bacteriology.  The alternative view is that bacterial models such as B.
AB  - subtilis and E. coli have become the mainstay of this field because of high transformation
AB  - ability.  Genetic transformation techniques remain important for studying numerous bacteria
AB  - and for the advancement of bacteriology, biochemistry, applied microbiology, and microbial
AB  - biotechnology.  Moreover, recent developments in the search for new bacteria and genome
AB  - sequencing have provided numerous effective bacteria that are useful for biological studies
AB  - and industrial applications.  With these developments, there is a greater demand for
AB  - establishing genetic transformation methods for more bacteria.
ER  -

TY  - JOUR
AU  - Suzuki, H.
AU  - Dapper, A.L.
AU  - Jackson, C.E.
AU  - Lee, H.
AU  - Pejaver, V.
AU  - Doak, T.G.
AU  - Lynch, M.
AU  - Preer, J.R. Jr.
TI  - Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.
JO  - Genome Announcements
PY  - 2015
SP  - e01310
EP  - e01315
VL  - 3
AB  - Caedibacter varicaedens is a kappa killer endosymbiont bacterium of the ciliate Paramecium
AB  - biaurelia. Here, we present the draft genome sequence of C.
AB  - varicaedens.
ER  -

TY  - JOUR
AU  - Suzuki, H.
AU  - Lefebure, T.
AU  - Hubisz, M.J.
AU  - Pavinski-Bitar, P.
AU  - Lang, P.
AU  - Siepel, A.
AU  - Stanhope, M.J.
TI  - Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution.
JO  - Genome Biol. Evol.
PY  - 2011
SP  - 168
EP  - 185
VL  - 3
AB  - Comparative genomics of closely related bacterial species with different
AB  - pathogenesis and host preference can provide a means of identifying the specifics
AB  - of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two
AB  - subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism
AB  - and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an
AB  - animal pathogen. Here, we present complete genome sequences for both taxa, with
AB  - analyses involving other species of Streptococcus but focusing on adaptation in
AB  - the SD species group. We found little evidence for enrichment in biochemical
AB  - categories of genes carried by each SD strain, however, differences in the
AB  - virulence gene repertoire were apparent. Some of the differences could be
AB  - ascribed to prophage and integrative conjugative elements. We identified
AB  - approximately 9% of the nonrecombinant core genome to be under positive
AB  - selection, some of which involved known virulence factors in other bacteria.
AB  - Analyses of proteomes by pooling data across genes, by biochemical category,
AB  - clade, or branch, provided evidence for increased rates of evolution in several
AB  - gene categories, as well as external branches of the tree. Promoters were
AB  - primarily evolving under purifying selection but with certain categories of genes
AB  - evolving faster. Many of these fast-evolving categories were the same as those
AB  - associated with rapid evolution in proteins. Overall, these results suggest that
AB  - adaptation to changing environments and new hosts in the SD species group has
AB  - involved the acquisition of key virulence genes along with selection of
AB  - orthologous protein-coding loci and operon promoters.
ER  -

TY  - JOUR
AU  - Suzuki, H.
AU  - Takahashi, S.
AU  - Osada, H.
AU  - Yoshida, K.
TI  - Improvement of transformation efficiency by strategic circumvention of restriction barriers in Streptomyces griseus.
JO  - J. Microbiol. Biotechnol.
PY  - 2011
SP  - 675
EP  - 678
VL  - 21
AB  - DNA methylation in Streptomyces griseus IFO 13350 was analyzed by high-performance liquid
AB  - chromatographic analysis and bisulfite-based analysis to
AB  - reveal two methylation sites, 5'-GC5mCGGC-3' and 5'-GAG5mCTC-3'. The methylation
AB  - was reconstituted in Escherichia coli by simultaneous expression of S. griseus
AB  - SGR4675 and S. achromogenes M.SacI. The E. coli cells produced plasmids that
AB  - mimicked the methylation profile of S. griseus DNA, which was readily introduced
AB  - into S. griseus. The results of this study raise the possibility of a promising
AB  - approach to establish efficient transformation in several streptomycetes.
ER  -

TY  - JOUR
AU  - Suzuki, H.
AU  - Yoshida, K.
TI  - Genetic Transformation of Geobacillus kaustophilus HTA426 by Conjugative Transfer of Host-Mimicking Plasmids.
JO  - J. Microbiol. Biotechnol.
PY  - 2012
SP  - 1279
EP  - 1287
VL  - 22
AB  - We established an efficient transformation method for thermophile Geobacillus kaustophilus
AB  - HTA426 using conjugative transfer from
AB  - Escherichia coli of host-mimicking plasmids that imitate DNA
AB  - methylation of strain HTA426 to circumvent its DNA restriction
AB  - barriers. Two conjugative plasmids, pSTE33T and pUCG18T, capable of
AB  - shuttling between E. coli and Geobacillus spp., were constructed. The
AB  - plasmids were first introduced into E. coli BR408, which expressed one
AB  - inherent DNA methylase gene (dam) and two heterologous methylase genes
AB  - from strain HTA426 (GK1380-GK1381 and GK0343-GK0344). The plasmids were
AB  - then directly transferred from E. coli cells to strain HTA426 by
AB  - conjugative transfer using pUB307 or pRK2013 as a helper plasmid.
AB  - pUCG18T was introduced very efficiently (transfer efficiency,
AB  - 10(-5)-10(-3) recipient(-1)). pSTE33T showed lower efficiency
AB  - (10(-7)-10(-6) recipient(-1)) but had a high copy number and high
AB  - segregational stability. Methylase genes in the donor substantially
AB  - affected the transfer efficiency, demonstrating that the host-mimicking
AB  - strategy contributes to efficient transformation. The transformation
AB  - method, along with the two distinguishing plasmids, increases the
AB  - potential of G kaustophilus HTA426 as a thermophilic host to be used in
AB  - various applications and as a model for biological studies of this
AB  - genus. Our results also demonstrate that conjugative transfer is a
AB  - promising approach for introducing exogenous DNA into thermophiles.
ER  -

TY  - JOUR
AU  - Suzuki, K.
AU  - Aziz, F.A.
AU  - Inuzuka, Y.
AU  - Tashiro, Y.
AU  - Futamata, H.
TI  - Draft Genome Sequence of Pseudomonas sp. LAB-08 Isolated from Trichloroethene-Contaminated Aquifer Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00948
EP  - e00916
VL  - 4
AB  - Pseudomonas sp. LAB-08 was isolated from a phenol-fed bioreactor constructed with contaminated
AB  - aquifer soil as the inoculum. Strain LAB-08 utilized phenol as a
AB  - sole carbon and energy source. Here, we report the genome sequence and annotation
AB  - of Pseudomonas sp. LAB-08.
ER  -

TY  - JOUR
AU  - Suzuki, K.
AU  - Nagao, K.
AU  - Tokunaga, J.
AU  - Hirosawa, M.
AU  - Tsubone, H.
AU  - Uyeda, M.
TI  - DMI-1, A new DNA methyltransferase inhibitor produced by Streptomyces sp. strain No. 560.
JO  - J. Enzym. Inhib.
PY  - 1995
SP  - 243
EP  - 252
VL  - 9
AB  - A new inhibitor of DNA methyltransferase named DMI-1 has been discovered in
AB  - the culture filtrate of Streptomyces sp. strain No. 560.  DMI-1 was purified by extraction
AB  - with
AB  - ethyl acetate followed by Diaion HP-20SS and silica gel column chromatography.  The structure
AB  - of
AB  - DMI-1 was determined to be 8-methylpentadecanoic acid (C16H32O2).  DMI-1 is a novel inhibitor
AB  - of methyltransferase isolated from microorganisms and is structurally different from
AB  - sinefungin
AB  - and A9145C which are structural analogs of S-adenosylmethionine (methyl donor).  DMI-1 was a
AB  - strong inhibitor of N6-methyladenine-DNA methyltransferase (M.EcoRI, EC2.1.1.72) in a
AB  - noncompetitive manner and its inhibition depended on the pH and temperature in the assay
AB  - media.
ER  -

TY  - JOUR
AU  - Suzuki, K.
AU  - Nagao, K.
AU  - Tokunaga, J.
AU  - Katayama, N.
AU  - Uyeda, M.
TI  - Inhibition of DNA methyltransferase by microbial inhibitors and fatty acids.
JO  - J. Enzym. Inhib.
PY  - 1996
SP  - 271
EP  - 280
VL  - 10
AB  - Streptomyces sp. strain No. 560 produces four kinds of DNA methyltransferase inhibitors in the
AB  - culture filtrate.  One of them, DMI-4 was distinguished from DMI-1, -2 and -3 previously
AB  - reported with respect to certain properties.  DMI-4 is considered to be a triglyceride
AB  - consisting of the fatty acids anteisopentadecanoic acid (C15:0), isopalmitic acid (C16:0) and
AB  - isostearic acid (C18:0) from the results of gas chromatography analysis.  Since DMI-4 contains
AB  - three molecules of fatty acid, and the previously reported DMI-1, 8-methylpentadecanoic acid,
AB  - is analogous to a fatty acid, the inhibitory activity of various fatty acids and their methyl
AB  - esters has been examined against EcoRI DNA methyltransferase (M.EcoRI).  Oleic acid (C18:1)
AB  - was found to be a potent inhibitor of M.EcoRI.  The inhibitory activity of oleic acid was
AB  - shown to be pH- and temperature-dependent and inhibited M.EcoRI in a noncompetitive manner
AB  - with respect to DNA or S-adenosylmethionine (SAM).  The number of carbon atoms and double
AB  - bonds in the fatty acid molecule affected the inhibitory activity, but their methyl esters
AB  - were not inhibitors.  Our results suggest that the length of the carbon chain, the number of
AB  - double bonds and the presence of a carboxyl group and branched methyl group in the fatty acid
AB  - molecule may play an important role in the inhibition of DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Suzuki, M.
AU  - Matsui, M.
AU  - Suzuki, S.
AU  - Rimbara, E.
AU  - Asai, S.
AU  - Miyachi, H.
AU  - Takata, T.
AU  - Hiraki, Y.
AU  - Kawano, F.
AU  - Shibayama, K.
TI  - Genome Sequences of Multidrug-Resistant Acinetobacter baumannii Strains from Nosocomial Outbreaks in Japan.
JO  - Genome Announcements
PY  - 2013
SP  - e00476
EP  - e00413
VL  - 1
AB  - Acinetobacter baumannii has emerged worldwide as an important nosocomial pathogen in medical
AB  - institutions. Here, we present the draft genome sequences of A.
AB  - baumannii strains MRY09-0642, MRY10-0558, and MRY12-0277 that were isolated from
AB  - nosocomial outbreaks in Japan between 2008 and 2012 and that are resistant to
AB  - antimicrobial agents, including carbapenems, fluoroquinolones, and
AB  - aminoglycosides.
ER  -

TY  - JOUR
AU  - Suzuki, M.
AU  - Nishio, H.
AU  - Asagoe, K.
AU  - Kida, K.
AU  - Suzuki, S.
AU  - Matsui, M.
AU  - Shibayama, K.
TI  - Genome Sequence of a Carbapenem-Resistant Strain of Ralstonia mannitolilytica.
JO  - Genome Announcements
PY  - 2015
SP  - e00405
EP  - e00415
VL  - 3
AB  - Ralstonia mannitolilytica, a Gram-negative aerobic bacterium, is an opportunistic human
AB  - pathogen that is becoming more common in cases of nosocomial infections. We
AB  - report for the first time the whole-genome sequence analysis of R.
AB  - mannitolilytica strain MRY14-0246, which carries the intrinsic
AB  - OXA-443/OXA-22-like and OXA-444/OXA-60-like beta-lactamase genes and is resistant
AB  - to meropenem.
ER  -

TY  - JOUR
AU  - Suzuki, M.
AU  - Suzuki, S.
AU  - Matsui, M.
AU  - Hiraki, Y.
AU  - Kawano, F.
AU  - Shibayama, K.
TI  - Genome Sequence of a Strain of the Human Pathogenic Bacterium Pseudomonas alcaligenes That Caused Bloodstream Infection.
JO  - Genome Announcements
PY  - 2013
SP  - e00919
EP  - e00913
VL  - 1
AB  - Pseudomonas alcaligenes, a Gram-negative aerobic bacterium, is a rare opportunistic human
AB  - pathogen. Here, we report the whole-genome sequence of P.
AB  - alcaligenes strain MRY13-0052, which was isolated from a bloodstream infection in
AB  - a medical institution in Japan and is resistant to antimicrobial agents,
AB  - including broad-spectrum cephalosporins and monobactams.
ER  -

TY  - JOUR
AU  - Suzuki, N.
AU  - Okayama, S.
AU  - Nonaka, H.
AU  - Tsuge, Y.
AU  - Inui, M.
AU  - Yukawa, H.
TI  - Large-scale engineering of the Corynebacterium glutamicum genome.
JO  - Appl. Environ. Microbiol.
PY  - 2005
SP  - 3369
EP  - 3372
VL  - 71
AB  - The engineering of Corynebacterium glutamicum is important for enhanced production of
AB  - biochemicals. To construct an improved C. glutamicum genome,
AB  - we developed a precise genome excision method based on the Cre/loxP
AB  - recombination system and successfully deleted 11 distinct genomic regions
AB  - identified by comparative analysis of C. glutamicum genomes. Despite the
AB  - loss of several predicted open reading frames, the mutant cells exhibited
AB  - normal growth under standard laboratory conditions. With a total of 250 kb
AB  - (7.5% of the genome), the 11 genomic regions were loaded with cryptic
AB  - prophages, transposons, and genes of unknown function which were
AB  - dispensable for cell growth, indicating recent horizontal acquisitions to
AB  - the genome. This provides an interesting background for functional genomic
AB  - studies and can be used in the improvement of cell traits.
ER  -

TY  - JOUR
AU  - Suzuki, S.
AU  - Aono, T.
AU  - Lee, K.B.
AU  - Suzuki, T.
AU  - Liu, C.T.
AU  - Miwa, H.
AU  - Wakao, S.
AU  - Iki, T.
AU  - Oyaizu, H.
TI  - Rhizobial factors required for stem nodule maturation and maintenance in Sesbania rostrata-Azorhizobium caulinodans ORS571 symbiosis.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 6650
EP  - 6659
VL  - 73
AB  - The molecular and physiological mechanisms behind the maturation and maintenance of
AB  - N(2)-fixing nodules during development of symbiosis between
AB  - rhizobia and legumes still remain unclear, although the early events of
AB  - symbiosis are relatively well understood. Azorhizobium caulinodans ORS571
AB  - is a microsymbiont of the tropical legume Sesbania rostrata, forming
AB  - N(2)-fixing nodules not only on the roots but also on the stems. In this
AB  - study, 10,080 transposon-inserted mutants of A. caulinodans ORS571 were
AB  - individually inoculated onto the stems of S. rostrata, and those mutants
AB  - that induced ineffective stem nodules, as displayed by halted development
AB  - at various stages, were selected. From repeated observations on stem
AB  - nodulation, 108 Tn5 mutants were selected and categorized into seven
AB  - nodulation types based on size and N(2) fixation activity. Tn5 insertions
AB  - of some mutants were found in the well-known nodulation, nitrogen
AB  - fixation, and symbiosis-related genes, such as nod, nif, and fix,
AB  - respectively, lipopolysaccharide synthesis-related genes, C(4)
AB  - metabolism-related genes, and so on. However, other genes have not been
AB  - reported to have roles in legume-rhizobium symbiosis. The list of newly
AB  - identified symbiosis-related genes will present clues to aid in
AB  - understanding the maturation and maintenance mechanisms of nodules.
ER  -

TY  - JOUR
AU  - Suzuki, S.
AU  - Kuenen, J.G.
AU  - Schipper, K.
AU  - van der Velde, S.
AU  - Ishii, S.
AU  - Wu, A.
AU  - Sorokin, D.Y.
AU  - Tenney, A.
AU  - Meng, X.Y.
AU  - Morrill, P.L.
AU  - Kamagata, Y.
AU  - Muyzer, G.
AU  - Nealson, K.H.
TI  - Physiological and genomic features of highly-alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site.
JO  - Nat. Commun.
PY  - 2014
SP  - 3900
EP  - 3900
VL  - 5
AB  - Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging
AB  - environments for life in continental sites due to the combination of extremely high pH, low
AB  - salinity and lack of obvious electron acceptors and carbon sources.  Nevertheless, certain
AB  - Betaproteobacteria have been frequently observed in such environments.  Here we describe
AB  - physiological and genomic features of three related Betaprobacterial strains isolated from
AB  - highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California.  All three strains
AB  - are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic
AB  - growth with hydrogen, calcium carbonate and oxygen.  The three strains exhibit differences,
AB  - however, regarding the utilization of organic carbon and electron acceptors.  Their global
AB  - distribution and physiological, genomic and transcriptomic characteristics indicate that the
AB  - strains are adapted to the alkaline and calcium-rich environments represented by the
AB  - terrestrial serpentinizing ecosystems.  We propose placing these strains in a new genus
AB  - 'Serpentinomonas'.
ER  -

TY  - JOUR
AU  - Suzuki, T.
AU  - Kikuchi, M.
AU  - Konno, N.
AU  - Habu, N.
TI  - Draft Genome Sequence of Brevundimonas sp. Strain SH203, Producing Cellouronate (beta-1,4-Linked Polyglucuronate) Lyase.
JO  - Genome Announcements
PY  - 2017
SP  - e00262
EP  - e00217
VL  - 5
AB  - In this study, we report the draft genome sequence of Brevundimonas sp. strain SH203, which
AB  - was previously isolated from natural soil and has the ability to
AB  - degrade beta-1,4-polygluculonate (cellouronate). This genomic information may
AB  - provide new insight into the mechanisms by which cellouronate is degraded.
ER  -

TY  - JOUR
AU  - Suzuki, T.
AU  - Sato, Y.
AU  - Yamada, Y.
AU  - Akagawa-Matsushita, M.
AU  - Yamasato, K.
TI  - A restriction endonuclease (DpaI) from Deleya pacifica IAM 14115, a marine bacterium, an isoschizomer of ScaI.
JO  - Agric. Biol. Chem.
PY  - 1991
SP  - 2647
EP  - 2649
VL  - 55
AB  - The marine bacteria have been considered to be important, but unused, uncommon
AB  - and unknown resources in the fields of applied and industrial microbiology.  In
AB  - previous papers, we reported a new restriction endonuclease, designated AgeI,
AB  - from Agrobacterium gelatinovorum Ahrens 1968 IAM 12617, a marine bacterium.
AB  - During the course of our screenings, we have found another marine bacterium to
AB  - produce a restriction endonuclease (DpaI, isoschizomer of ScaI) in a large
AB  - amount within the cells and the enzyme to have unique physiochemical
AB  - properties.
ER  -

TY  - JOUR
AU  - Suzuki, T.
AU  - Sugimoto, E.
AU  - Tahara, Y.
AU  - Yamada, Y.
TI  - Cloning and nucleotide sequence of ApaLI restriction-modification system from Acetobacter pasteurianus IFO 13753.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1996
SP  - 1401
EP  - 1405
VL  - 60
AB  - The ApaLI restriction-modification system from Acetobacter pasteurianus IFO 13753 recognizes
AB  - the nucleotide sequence GTGCAC.  The gene coding for the ApaLI methylase (M.ApaLI) was cloned
AB  - into Escherichia coli DH5aMCR, and the nucleotide sequence of the gene was analyzed.  The
AB  - M.ApaLI gene coded for a protein of 429 amino acid residues (molecular mass, 46,554 daltons).
AB  - The ApaLI restriction endonuclease (R.ApaLI) gene was analyzed by inverse polymerase chain
AB  - reaction.  The R.ApaLI gene coded for a protein of 375 amino acid residues (molecular mass,
AB  - 42,143 daltons).  The two genes had the same orientation separated by two base pairs.  The
AB  - deduced amino acid sequence of M.ApaLI shows significant similarities to the family of
AB  - cytosine-5 methylases.  However, the deduced amino acid sequence of R.ApaLI did not have as
AB  - much relatedness in the nucleotide sequence, when compared with those of the other restriction
AB  - endonucleases already reported.
ER  -

TY  - JOUR
AU  - Suzuki, T.
AU  - Sugimoto, E.
AU  - Tahara, Y.
AU  - Yamada, Y.
TI  - Cloning and nucleotide sequence of the AgeI methylase gene from Agrobacterium gelatinovorum IAM 12617, a marine bacterium.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1996
SP  - 444
EP  - 447
VL  - 60
AB  - The AgeI restriction-modification system from a marine bacterium, Agrobacterium
AB  - gelatinovorum IAM 12617, recognizes the nucleotide sequence ACCGGT.  The gene coding for
AB  - the AgeI methylase (M.AgeI) was cloned into Escherichia coli DH5 alphaMCR, and the
AB  - nucleotides of the gene were sequenced.  The M.AgeI gene coded for a protein of 429 amino acid
AB  - residues (molecular mass, 47,358 daltons).  The deduced amino acid sequence of M.AgeI was
AB  - compared with those of other methylases and showed that there are high degrees of similarity
AB  - in
AB  - some cytosine-5-methylases.
ER  -

TY  - JOUR
AU  - Suzuki, T.
AU  - Yasui, K.
TI  - Plasmid Artificial Modification: A Novel Method for Efficient DNA Transfer into Bacteria.
JO  - Methods Mol. Biol.
PY  - 2011
SP  - 309
EP  - 326
VL  - 765
AB  - Bacterial transformation is an essential component of many molecular biological techniques,
AB  - but bacterial restriction-modification (R-M)
AB  - systems can preclude the efficient introduction of shuttle vector
AB  - plasmids into target bacterial cells. Whole-genome DNA sequences have
AB  - recently been published for a variety of bacteria. Using homology and
AB  - motif analyses, putative R-M genes can be identified from genome
AB  - sequences. Introducing DNA methyltransferase genes into Escherichia
AB  - coli cells causes subsequently transformed plasmids to be modified by
AB  - these enzymes.We propose a new method, designated Plasmid Artificial
AB  - Modification (PAM). A PAM plasmid encoding the modification enzymes
AB  - expressed by the target bacterial host is transformed into E. coli (PAM
AB  - host). Propagation of a shuttle vector from the PAM host to the target
AB  - bacterium ensures that the plasmid will be modified such that it is
AB  - protected from restriction endonuclease digestion in the target
AB  - bacterium. The result will be a higher transformation efficiency.Here,
AB  - we describe the use of PAM and electroporation to transform
AB  - Bifidobacterium adolescentis ATCC15703. By introducing two genes
AB  - encoding modification enzymes, we improved transformation efficiency
AB  - 10(5)-fold.
ER  -

TY  - JOUR
AU  - Suzuki, Y.
AU  - Gilmore, J.L.
AU  - Yoshimura, S.H.
AU  - Henderson, R.M.
AU  - Lyubchenko, Y.L.
AU  - Takeyasu, K.
TI  - Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region.
JO  - Biophys. J.
PY  - 2011
SP  - 2992
EP  - 2998
VL  - 101
AB  - Many DNA regulatory factors require communication between distantly separated DNA sites for
AB  - their activity.  The type IIF restriction enzyme SfiI is often used as a model system of site
AB  - communication.  Here, we used fast-scanning atomic force microscopy to monitor the DNA
AB  - cleavage process with SfiI and the changes in the single SfiI-DNA complex in the presence of
AB  - either Mg2+ or Ca2+ at a scan rate of 1-2 fps.  The increased time resolution allowed us to
AB  - visualize the concerted cleavage of the protein at two cognate sites.  The four termini
AB  - generated by the cleavage were released in a multistep manner.  The high temporal resolution
AB  - enabled us to visualize the translocation of a DNA strand on a looped complex and
AB  - intersegmental transfer of the SfiI protein in which swapping of the site is performed without
AB  - protein dissociation.  On the basis of our results, we propose that the SfiI tetramer can
AB  - remain bound to one of the sites even after cleavage, allowing the other site on the DNA
AB  - molecule to fill the empty DNA-binding cleft by combining a one-dimensional diffusion-mediated
AB  - sliding and a segment transfer mechanism.
ER  -

TY  - JOUR
AU  - Svab, D.
AU  - Horvath, B.
AU  - Szucs, A.
AU  - Maroti, G.
AU  - Toth, I.
TI  - Draft Genome Sequence of an Escherichia coli O157:H43 Strain Isolated from Cattle.
JO  - Genome Announcements
PY  - 2013
SP  - e00263
EP  - e00213
VL  - 1
AB  - Here we report the draft genome sequence of an Escherichia coli O157:H43 strain,  designated
AB  - T22, with an atypical virulence gene profile and isolated from healthy
AB  - cattle. T22 produces cytolethal distending toxin V (CDT-V) and belongs to
AB  - phylogenetic group B1 and sequence type 155 (ST155).
ER  -

TY  - JOUR
AU  - Svadbina, I.V.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Location of the bases modified by M.BcoKIA and M.BcoKIB methylases in the sequence 5'-CTCTTC-3'/5'-GAAGAG-3'.
JO  - Biochemistry
PY  - 2005
SP  - 1363
EP  - 1366
VL  - 70
AB  - The strain Bacillus coagulans K contains two DNA-methyltransferases, M.BcoKIA and M.BcoKIB,
AB  - which recognize the sequence 5'-CTCTTC-3'/5'-GAAGAG-3' and possess N4-methylcytosine and
AB  - N6-methyladenine specificities, respectively.  A special construct containing the recognition
AB  - site of BcoKI and sits of four IIS restriction endonucleases (IIS restriction endonuclease
AB  - cassette) was designed to locate the nucleotides modified by the methylases.  The modified
AB  - bases were determined as: 5'm4CTCTTC-3'/5'-GAAGAm6G-3'.
ER  -

TY  - JOUR
AU  - Svadbina, I.V.
AU  - Zelinskaya, N.V.
AU  - Kovalevskaya, N.P.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Isolation and characterization of site-specific DNA- methyltransferases from Bacillus coagulans K.
JO  - Biokhimiia
PY  - 2004
SP  - 372
EP  - 379
VL  - 69
AB  - Two site-specific DNA methyltransferases, M.BcoKIA and M.BcoKIB, were isolated from the
AB  - thermophilic strain Bacillus coagulans K. Each of the methylases protects the recognition site
AB  - 5'-CTCTTC-3'/5'-GAAGAG-3' from cleavage with the cognate restriction endonuclease BcoKI.
AB  - It is shown that M.BcoKIB is an N6-adenine specific methylase and M.BcoKIA is an N4-cytosine
AB  - specific methylase. According to bisulfite mapping, M.BcoKIA methylates the first cytosine in
AB  - the sequence 5'-CTCTTC-3'.
ER  -

TY  - JOUR
AU  - Svadbina, I.V.
AU  - Zheleznyakova, E.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Bacillus species LU4 is an effective producer of thermostable site-specific endonuclease BspLU4I, an isoschizomer of AvaI.
JO  - Biokhimiia
PY  - 2003
SP  - 429
EP  - 435
VL  - 68
AB  - The site-specific endonuclease BspLU4I was discovered in the thermophilic Bacillus species LU4
AB  - strain and purified to functionally pure state by
AB  - chromatography on blue agarose, hydroxyapatite HTP, and heparin-Sepharose
AB  - columns. Analysis of cleavage patterns of different DNAs with known
AB  - nucleotide sequences demonstrated that the enzyme recognizes the CPyCGPuG
AB  - site on the DNA. Cleavage points in the sequence were determined with the
AB  - elongated primer method. It was shown that the endonuclease is an
AB  - isoschizomer of AvaI. The final yield of the enzyme is 2.25.10(6) units
AB  - per g wet biomass.
ER  -

TY  - JOUR
AU  - Svedruzic, A.M.
AU  - Reich, N.O.
TI  - DNA cytosine C-5 methyltransferase Dnmt1: Catalysis-dependent release of allosteric inhibition.
JO  - Biochemistry
PY  - 2005
SP  - 9472
EP  - 9485
VL  - 44
AB  - We followed the cytosine C-5 exchange reaction with Dnmt1 to characterize its preference for
AB  - different DNA substrates, its
AB  - allosteric regulation, and to provide a basis for comparison with the
AB  - bacterial enzymes. We determined that the methyl transfer is
AB  - rate-limiting, and steps up to and including the cysteine-cytosine
AB  - covalent intermediate are in rapid equilibrium. Changes in these rapid
AB  - equilibrium steps account for many of the previously described features
AB  - of Dnmt1 catalysis and specificity including faster reactions with
AB  - premethylated DNA versus unmethylated DNA, faster reactions with DNA in
AB  - which guanine is replaced with inosine [poly(dC-dG) vs poly(dI-dC)],
AB  - and 10-100-fold slower catalytic rates with Dnmt1 relative to the
AB  - bacterial enzyme M.HhaI. Dnmt1 interactions with the guanine within the
AB  - CpG recognition site can prevent the premature release of the target
AB  - base and solvent access to the active site that could lead to mutagenic
AB  - deamination. Our results suggest that the beta-elimination step
AB  - following methyl transfer is not mediated by free solvent. Dnmt1 shows
AB  - a kinetic lag in product formation and allosteric inhibition with
AB  - unmethylated DNA that is not observed with premethylated DNA. Thus, we
AB  - suggest the enzyme undergoes a slow relief from allosteric inhibition
AB  - upon initiation of catalysis on unmethylated DNA. Notably, this relief
AB  - from allosteric inhibition is not caused by self-activation through the
AB  - initial methylation reaction, as the same effect is observed during the
AB  - cytosine C5 exchange reaction in the absence of AdoMet. We describe
AB  - limitations in the Michaelis-Menten kinetic analysis of Dnmt1 and
AB  - suggest alternative approaches.
ER  -

TY  - JOUR
AU  - Svedruzic, Z.M.
TI  - Mammalian cytosine DNA methyltransferase Dnmt1: Enzymatic mechanism, novel mechanism-based inhibitors, and RNA-directed DNA methylation.
JO  - Curr. Med. Chem.
PY  - 2008
SP  - 92
EP  - 106
VL  - 15
AB  - This is a review of the enzymatic mechanism of DNA methyltransferase Dnmt1 and analysis of its
AB  - implications on regulation of DNA methylation
AB  - in mammalian cells and design of novel mechanism-based inhibitors. The
AB  - methylation reaction by Dnmt1 has different phases that depend on DNA
AB  - substrate and allosteric regulation. Consequently, depending on the
AB  - phase, the differences in catalytic rates between unmethylated and
AB  - pre-methylated DNA can vary between 30-40 fold, 3-6 fold or only 1
AB  - fold. The allosteric site and the active site can bind different
AB  - molecules. Allosteric activity depends on DNA sequence, methylation
AB  - pattern and DNA structure (single stranded vs. double stranded). Dnmt1
AB  - binds poly(ADP-ribose) and some RNA molecules. The results on kinetic
AB  - preferences, allosteric activity and binding preference of Dnmt1 are
AB  - combined together in one comprehensive model mechanism that can address
AB  - regulation of DNA methylation in cells; namely, inhibition of DNA
AB  - methylation by poly(ADP-ribose), RNA-directed DNA methylation by
AB  - methylated and unmethylated non-coding RNA molecules, and transient
AB  - interactions between Dnmt1 and genomic DNA. Analysis of reaction
AB  - intermediates showed that equilibrium between base-flipping and
AB  - base-restacking events can be the key mechanism in control of enzymatic
AB  - activity. The two events have equal but opposite effect on accumulation
AB  - of early reaction intermediates and methylation rates. The accumulation
AB  - of early reaction intermediates can be exploited to improve the current
AB  - inhibitors of Dnmt1 and achieve inhibition without toxic modifications
AB  - in genomic DNA.
AB  - [1,2-dihydropyrimidin-2-one]-5-methylene-(methylsulfonium)-adenosyl is
AB  - described as the lead compound.
ER  -

TY  - JOUR
AU  - Svedruzic, Z.M.
AU  - Reich, N.O.
TI  - Enzymatic properties of mouse cytosine DNA methyltransferase DNMT1.
JO  - ACS Abstracts
PY  - 2002
SP  - C75
EP  - C75
VL  - 223
AB  - DNA methylation is a gene control and chromatin organization mechanism that has been
AB  - associated with oncogene activation, mutagenic cytosine deamination, cell cycle changes,
AB  - retrovirus silencing, cell differentiation, and aging. This work evaluates the main catalytic
AB  - features of Dnmt1, the principal methyltransferase in eukaryotic cells.  Pre-steady state and
AB  - steady state kinetics were used together with solvent kinetic isotope effect and pH studies to
AB  - analyze catalytic preference for pre-methylated DNA, enzyme processivity on its DNA substrate,
AB  - allosteric regulation and likelihood of mutagenic deamination. The preference for
AB  - pre-methylated DNA is due to a faster target base attack, faster methyl transfer and faster
AB  - acid base catalysis that is likely to come from a specific conformational change in the active
AB  - site. Unlike its bacterial counterparts, Dnmt1 can recognize DNA as pre-methylated even when
AB  - 5mC is one out of fifteen cytosines, however the enzyme is not self activated early in the
AB  - methylation reaction on unmethylated DNA. A novel analysis of processivity rate constants
AB  - showed that the processivity of Dnmt1 depends on the substrate and can be regulated through
AB  - the allosteric site. The extent of allosteric regulation depends on catalytic activity, DNA
AB  - sequence and the methylation status. DNA binding at the allosteric site inhibits catalytic
AB  - action of Dnmt1 and initiates DNA release from its active site. Interaction between Dnmt1 and
AB  - proliferating cell nuclear antigen (PCNA) facilitates the on rate for the substrate DNA, and
AB  - has no effect on enzyme processivity. Analogues of S-Adenosylmethionine and solvent kinetic
AB  - isotope effect studies showed that enzyme mediated mutagenesis and cytosine deamination are
AB  - due to enzymes inability to protect its reactive intermediates. Mutagenesis is likely in
AB  - catalytic action by mammalian and bacterial cytosine methyltransferases, however mammalian
AB  - enzyme is 200 times less likely to be mutagenic in the absence of the cofactor. Presented
AB  - studies give enzymatic insights to biology of DNA methylation and show novel methods to study
AB  - C5 pyrimidine methyltransferases.
ER  -

TY  - JOUR
AU  - Svedruzic, Z.M.
AU  - Reich, N.O.
TI  - Mechanism of allosteric regulation of Dnmt1's processivity.
JO  - Biochemistry
PY  - 2005
SP  - 14977
EP  - 14988
VL  - 44
AB  - We have analyzed the relationship between the allosteric regulation and processive catalysis
AB  - of DNA methyltransferase 1 (Dnmt1). Processivity is
AB  - described quantitatively in terms of turnover rate, DNA dissociation rate,
AB  - and processivity probability. Our results provide further evidence that
AB  - the active site and the allosteric sites on Dnmt1 can bind DNA
AB  - independently. Dnmt1's processive catalysis on unmethylated DNA is
AB  - partially inhibited when the allosteric site binds unmethylated DNA and
AB  - fully inhibited when the allosteric site binds a single-stranded
AB  - oligonucleotide inhibitor. The partial inhibition by unmethylated DNA is
AB  - caused by a decrease in the turnover rate and an increase in the substrate
AB  - DNA dissociation rate. Processive catalysis with premethylated DNA is not
AB  - affected if the allosteric site is exposed to premethylated DNA but is
AB  - fully inhibited if the allosteric site binds unmethylated DNA or
AB  - poly(dA-dT). In sum, the occupancy of the allosteric site modulates the
AB  - enzyme's commitment to catalysis, which reflects the nature of the
AB  - substrate and the DNA bound at the allosteric site. Our in vitro results
AB  - are consistent with the possibility that the processive action of Dnmt1
AB  - may be regulated in vivo by specific regulatory nucleic acids such as DNA,
AB  - RNA, or poly(ADP-ribose).
ER  -

TY  - JOUR
AU  - Svenning, M.M. et al.
TI  - Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6418
EP  - 6419
VL  - 193
AB  - Methylobacter tundripaludum SV96(T) (ATCC BAA-1195) is a psychrotolerant aerobic
AB  - methane-oxidizing gammaproteobacterium (Methylococcales,
AB  - Methylococcaceae) living in High Arctic wetland soil. The strain was
AB  - isolated from soil harvested in July 1996 close to the settlement
AB  - Ny-Alesund, Svalbard, Norway (78 degrees 56'N, 11 degrees 53'E), and
AB  - described as a novel species in 2006. The genome includes pmo and pxm
AB  - operons encoding copper membrane monooxygenases (Cu-MMOs), genes required
AB  - for nitrogen fixation, and the nirS gene implicated in dissimilatory
AB  - nitrite reduction to NO but no identifiable inventory for further
AB  - processing of nitrogen oxides. These genome data provide the basis to
AB  - investigate M. tundripaludum SV96, identified as a major player in the
AB  - biogeochemistry of Arctic environments.
ER  -

TY  - JOUR
AU  - Svensson, D.
AU  - Ohrman, C.
AU  - Backman, S.
AU  - Karlsson, E.
AU  - Nilsson, E.
AU  - Bystrom, M.
AU  - Larkeryd, A.
AU  - Myrtennas, K.
AU  - Stenberg, P.
AU  - Qu, P.H.
AU  - Trygg, J.
AU  - Scholz, H.C.
AU  - Forsman, M.
AU  - Sjodin, A.
TI  - Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.
JO  - Genome Announcements
PY  - 2015
SP  - e00024
EP  - e00015
VL  - 3
AB  - We present the complete genome sequence of Francisella guangzhouensis strain 08HL01032(T),
AB  - which consists of one chromosome (1,658,482 bp) and one plasmid
AB  - (3,045 bp) with G+C contents of 32.0% and 28.7%, respectively.
ER  -

TY  - JOUR
AU  - Swaminathan, C.P.
AU  - Sankpal, U.T.
AU  - Rao, D.N.
AU  - Surolia, A.
TI  - Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 4042
EP  - 4049
VL  - 277
AB  - Energetically competent binary recognition of the cofactor S-adenosyl-L-methionine (AdoMet)
AB  - and the product S-adenosyl-L-homocysteine (AdoHcy) by the DNA (cytosine C-5) methyltransferase
AB  - (M.HhaI) is demonstrated herein. Titration calorimetry reveals a dual mode, involving a
AB  - primary dominant exothermic reaction followed by a weaker endothermic one, for the recognition
AB  - of AdoMet and AdoHcy by M.HhaI. Conservation of the bimodal recognition in W41I and W41Y
AB  - mutants of M.HhaI excludes the cation-Pi interaction between the methylsulfonium group of
AB  - AdoMet and the Pi face of the Trp(41) indole ring from a role in its origin. Small magnitude
AB  - of temperature-independent heat capacity changes upon AdoMet or AdoHcy binding by M.HhaI
AB  - preclude appreciable conformational alterations in the reacting species. Coupled
AB  - osmotic-calorimetric analyses of AdoMet and AdoHcy binding by M.HhaI indicate that a net
AB  - uptake of nearly eight and 10 water molecules, respectively, assists their primary
AB  - recognition. A change in water activity at constant temperature and pH is sufficient to
AB  - engender and conserve enthalpy-entropy compensation, consistent with a true osmotic effect.
AB  - The results implicate solvent reorganization in providing the major contribution to the origin
AB  - of this isoequilibrium phenomenon in AdoMet and AdoHcy recognition by M.HhaI. The observations
AB  - provide unequivocal evidence for the binding of AdoMet as well as AdoHcy to M.HhaI in solution
AB  - state. Isotope partitioning analysis and preincubation studies favor a random mechanism for
AB  - M.HhaI-catalyzed reaction. Taken together, the results clearly resolve the issue of cofactor
AB  - recognition by free M.HhaI, specifically in the absence of DNA, leading to the formation of an
AB  - energetically and catalytically competent binary complex.
ER  -

TY  - JOUR
AU  - Swaminathan, N.
AU  - George, D.
AU  - McMaster, K.
AU  - Szablewski, J.
AU  - Van Etten, J.L.
AU  - Mead, D.A.
TI  - Restriction generated oligonucleotides utilizing the two base recognition endonuclease CviJI.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 1470
EP  - 1475
VL  - 22
AB  - The conversion of an anonymous DNA sample into numerous oligonucleotides is enzymatically
AB  - feasible using an unusual restriction endonuclease, CviJI. Depending on reaction conditions,
AB  - CviJI is capable of digesting DNA at a two or three base recognition sequence. CviJI normally
AB  - cleaves RGCY sites between the G and C to leave blunt ends. Under 'relaxed' conditions CviJI
AB  - cleaves RGCY, and RGCR/YGCY, but not YGCR sites. In theory, CviJI* restriction of pUC19 (2686
AB  - bp) should produce 157 fragments, 75% of which are smaller than 20 bp. Instead, 96% of the
AB  - CviJI* fragments were 18-56 bp long and none of the fragments generates sequence specific
AB  - oligonucleotides homologous for the cognate template. The enzymatic conversion of anonymous
AB  - DNA into sequence specific oligomers has implications for several conventional and novel
AB  - molecular biology procedures.
ER  -

TY  - JOUR
AU  - Swaminathan, N.
AU  - Mead, D.A.
AU  - McMaster, K.
AU  - George, D.
AU  - Van Etten, J.L.
AU  - Skowron, P.M.
TI  - Molecular cloning of the three base restriction endonuclease R.CviJI from eukaryotic Chlorella virus IL-3A.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2463
EP  - 2469
VL  - 24
AB  - R.CviJI is unique among site-specific restriction endonucleases in that its activity can be
AB  - modulated to recognize either a two or three base sequence.  Normally R.CviJI cleaves RGCY
AB  - sites between the G and C to leave blunt ends.  In the presence of ATP, R.CviJI cleaves RGCN
AB  - and YGCY sites, but not YGCR sites.  The gene encoding R.CviJI was cloned from the eukaryotic
AB  - Chlorella virus IL-3A and expressed in Escherichia coli.  The primary E. coli cviJIR gene
AB  - product is a 278 amino acid protein initiated from a GTG codon, rather than the expected 358
AB  - amino acid protein, displays the normal restriction activity but not the R.CviJI* activity of
AB  - the native enzyme.  Nine restriction and modification proteins which recognize a central GC or
AB  - CG sequence share short regions of identity with R.CviJI amino acids 144-235, suggesting that
AB  - this region is the recognition and/or catalytic domain.
ER  -

TY  - JOUR
AU  - Swanson, E.
AU  - Oshone, R.
AU  - Nouioui, I.
AU  - Abebe-Akele, F.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Thomas, W.K.
AU  - Sen, A.
AU  - Ghodhbane-Gtari, F.
AU  - Gtari, M.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing  Actinobacterium Isolated from Root Nodules of Colletia cruciata.
JO  - Genome Announcements
PY  - 2017
SP  - e00530
EP  - e00517
VL  - 5
AB  - Frankia sp. strain Cc1.17 is a member of the Frankia lineage 3, the organisms of  which are
AB  - able to reinfect plants of the Eleagnaceae, Rhamnaceae, and Myricaceae
AB  - families and the genera Gynmnostoma and Alnus Here, we report the 8.4-Mbp draft
AB  - genome sequence, with a G+C content of 72.14% and 6,721 candidate protein-coding
AB  - genes.
ER  -

TY  - JOUR
AU  - Swanson, E.
AU  - Oshone, R.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain AvcI1, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus viridis subsp. crispa  Grown in Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e01511
EP  - e01515
VL  - 3
AB  - Frankia strain AvcI1, isolated from root nodules of Alnus viridis subsp. crispa,  is a member
AB  - of Frankia lineage Ia, which is able to reinfect plants of the
AB  - Betulaceae and Myricaceae families. Here, we report a 7.7-Mbp draft genome
AB  - sequence with a G+C content of 72.41% and 6,470 candidate protein-encoding genes.
ER  -

TY  - JOUR
AU  - Swanson, E.
AU  - Oshone, R.
AU  - Simpson, S.
AU  - Morris, K.
AU  - Abebe-Akele, F.
AU  - Thomas, W.K.
AU  - Tisa, L.S.
TI  - Permanent Draft Genome Sequence of Frankia sp. Strain ACN1ag, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Alnus glutinosa.
JO  - Genome Announcements
PY  - 2015
SP  - e01483
EP  - e01415
VL  - 3
AB  - Frankia strain ACN1(ag) is a member of Frankia lineage Ia, which are able to re-infect plants
AB  - of the Betulaceae and Myricaceae families. Here, we report a
AB  - 7.5-Mbp draft genome sequence with a G+C content of 72.35% and 5,687 candidate
AB  - protein-encoding genes.
ER  -

TY  - JOUR
AU  - Swarbreck, D.
AU  - Wilks, C.
AU  - Lamesch, P.
AU  - Berardini, T.Z.
AU  - Garcia-Hernandez, M.
AU  - Foerster, H.
AU  - Li, D.
AU  - Meyer, T.
AU  - Muller, R.
AU  - Ploetz, L.
AU  - Radenbaugh, A.
AU  - Singh, S.
AU  - Swing, V.
AU  - Tissier, C.
AU  - Zhang, P.
AU  - Huala, E.
TI  - The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - D1009
EP  - D1014
VL  - 36
AB  - The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism
AB  - database for the fully sequenced and intensively studied
AB  - model plant Arabidopsis thaliana. Data in TAIR is derived in large part
AB  - from manual curation of the Arabidopsis research literature and direct
AB  - submissions from the research community. New developments at TAIR include
AB  - the addition of the GBrowse genome viewer to the TAIR site, a redesigned
AB  - home page, navigation structure and portal pages to make the site more
AB  - intuitive and easier to use, the launch of several TAIR web services and a
AB  - new genome annotation release (TAIR7) in April 2007. A combination of
AB  - manual and computational methods were used to generate this release, which
AB  - contains 27,029 protein-coding genes, 3889 pseudogenes or transposable
AB  - elements and 1123 ncRNAs (32,041 genes in all, 37,019 gene models). A
AB  - total of 681 new genes and 1002 new splice variants were added. Overall,
AB  - 10,098 loci (one-third of all loci from the previous TAIR6 release) were
AB  - updated for the TAIR7 release.
ER  -

TY  - JOUR
AU  - Swarnkar, M.K.
AU  - Salwan, R.
AU  - Kasana, R.C.
AU  - Singh, A.K.
TI  - Draft Genome Sequence of Psychrotrophic Acinetobacter sp. Strain MN12 (MTCC 10786), Which Produces a Low-Temperature-Active and Alkaline-Stable Peptidase.
JO  - Genome Announcements
PY  - 2014
SP  - e01167
EP  - e01114
VL  - 2
AB  - We report here the draft genome sequence of Acinetobacter sp. strain MN12 (MTCC 10786), which
AB  - is a psychrotrophic bacterium that produces an extracellular
AB  - low-temperature-active and alkaline-stable peptidase. The draft genome assembly
AB  - of Acinetobacter sp. MN12 has a size of 4.31 Mbp, with a G+C content of 40.75%.
ER  -

TY  - JOUR
AU  - Sweetnam, K.R.
AU  - Reich, N.O.
TI  - Construction of a mechanism-based inhibitor for EcoRI DNA methyltransferase.
JO  - Biochemistry
PY  - 1992
SP  - 2206
EP  - 2206
VL  - 31
AB  - Our results using N-ethylmaleimide modification suggest that cysteine 223 is
AB  - critical for the EcoRI DNA methyltransferase catalyzed methylation of the
AB  - second adenine in the GAATTC recognition sequence.  A plausible catalytic
AB  - mechanism involving this cysteine is shown below: A key feature is the
AB  - formation of a methylase-DNA covalent intermediate.  We are testing this
AB  - mechanism by incorporating a 6-chloropurine riboside into the DNA substrate.
AB  - This substituted analogue is proposed to act as a mechanism-based or active
AB  - site directed inactivator due to the excellent leaving group potential of the
AB  - 6-chloro moiety.  We are submitting this analogue to inactivation analysis and
AB  - isolating the peptide sequence attached to the DNA to determine the reactive
AB  - residue in the catalytic site of EcoRI DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Sweetnam, K.R.
AU  - Reich, N.O.
TI  - Construction of a mechanism-based inhibitor for EcoRI DNA methyltransferase.
JO  - ACS Abstracts
PY  - 1992
SP  - 102
EP  - BIOL
VL  - 203
AB  - Our results using N-ethyl maleimide modification suggest that cysteine 223 is critical for the
AB  - EcoRI DNA methyltransferase catalyzed methylation of the second adenine in the GAATTC
AB  - recognition sequence. A plausible catalytic mechanism involving this cysteine is shown below:
AB  - a key feature is the formation of a methylase-DNA covalent intermediate. We are testing this
AB  - mechanism by incorporating a 6-chloropurine riboside into the DNA substrate. This substituted
AB  - analog is proposed to act as a mechanism based or active site directed inactivator due to the
AB  - excellent leaving group potential of the 6-chloro moiety. We are submitting this analog to
AB  - inactivation analysis and isolating the peptide sequence attached to the DNA to determine the
AB  - reactive residue in the catalytic site of EcoRI DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Swingley, W.D. et al.
TI  - Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 2005
EP  - 2010
VL  - 105
AB  - Acaryochloris marina is a unique cyanobacterium that is able to produce chlorophyll d as its
AB  - primary photosynthetic pigment and thus efficiently
AB  - use far-red light for photosynthesis. Acaryochloris species have been
AB  - isolated from marine environments in association with other oxygenic
AB  - phototrophs, which may have driven the niche-filling introduction of
AB  - chlorophyll d. To investigate these unique adaptations, we have sequenced
AB  - the complete genome of A. marina. The DNA content of A. marina is composed
AB  - of 8.3 million base pairs, which is among the largest bacterial genomes
AB  - sequenced thus far. This large array of genomic data is distributed into
AB  - nine single-copy plasmids that code for >25% of the putative ORFs. Heavy
AB  - duplication of genes related to DNA repair and recombination (primarily
AB  - recA) and transposable elements could account for genetic mobility and
AB  - genome expansion. We discuss points of interest for the biosynthesis of
AB  - the unusual pigments chlorophyll d and alpha-carotene and genes
AB  - responsible for previously studied phycobilin aggregates. Our analysis
AB  - also reveals that A. marina carries a unique complement of genes for these
AB  - phycobiliproteins in relation to those coding for antenna proteins related
AB  - to those in Prochlorococcus species. The global replacement of major
AB  - photosynthetic pigments appears to have incurred only minimal
AB  - specializations in reaction center proteins to accommodate these alternate
AB  - pigments. These features clearly show that the genus Acaryochloris is a
AB  - fitting candidate for understanding genome expansion, gene acquisition,
AB  - ecological adaptation, and photosystem modification in the cyanobacteria.
ER  -

TY  - JOUR
AU  - Swingley, W.D.
AU  - Sadekar, S.
AU  - Mastrian, S.D.
AU  - Matthies, H.J.
AU  - Hao, J.
AU  - Ramos, H.
AU  - Acharya, C.R.
AU  - Conrad, A.L.
AU  - Taylor, H.L.
AU  - Dejesa, L.C.
AU  - Shah, M.K.
AU  - O'huallachain, M.E.
AU  - Lince, M.T.
AU  - Blankenship, R.E.
AU  - Beatty, J.T.
AU  - Touchman, J.W.
TI  - The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.
JO  - J. Bacteriol.
PY  - 2007
SP  - 683
EP  - 690
VL  - 189
AB  - Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light
AB  - energy to enhance growth only in the presence of oxygen
AB  - but do not produce oxygen. The highly adaptive AAPs compose more than 10%
AB  - of the microbial community in some euphotic upper ocean waters and are
AB  - potentially major contributors to the fixation of the greenhouse gas CO2.
AB  - We present the complete genomic sequence and feature analysis of the AAP
AB  - Roseobacter denitrificans, which reveal clues to its physiology. The
AB  - genome lacks genes that code for known photosynthetic carbon fixation
AB  - pathways, and most notably missing are genes for the Calvin cycle enzymes
AB  - ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase.
AB  - Phylogenetic evidence implies that this absence could be due to a gene
AB  - loss from a RuBisCO-containing alpha-proteobacterial ancestor. We describe
AB  - the potential importance of mixotrophic rather than autotrophic CO2
AB  - fixation pathways in these organisms and suggest that these pathways
AB  - function to fix CO2 for the formation of cellular components but do not
AB  - permit autotrophic growth. While some genes that code for the
AB  - redox-dependent regulation of photosynthetic machinery are present, many
AB  - light sensors and transcriptional regulatory motifs found in purple
AB  - photosynthetic bacteria are absent.
ER  -

TY  - JOUR
AU  - Swinton, D.
AU  - Hattman, S.
AU  - Benzinger, R.
AU  - Buchanan-Wollaston, V.
AU  - Beringer, J.
TI  - Replacement of the deoxycytidine residues in Rhizobium bacteriophage RL38JI DNA.
JO  - FEBS Lett.
PY  - 1985
SP  - 294
EP  - 298
VL  - 184
AB  - Rhizobium phage RL38JI DNA is resistant to cleavage by a variety of restriction
AB  - endonucleases, and is only partially sensitive to digestion by pancreatic DNase
AB  - I or by micrococcal nuclease.  We have found that a mixture of DNase I, P1
AB  - nuclease, and bacterial alkaline phosphatase will quantitatively digest RL38JI
AB  - DNA to deoxyribonucleosides.  HPLC analysis revealed that dCyd is nearly
AB  - totally absent among these digestion products, while dGuo, dAdo, and Thd are
AB  - readily detected.  Three additional peaks are always present; their retention
AB  - properties correspond to no known modified deoxyribonucleosides.  Thus it
AB  - appears that dCyd is replaced in phage RL38JI DNA by as many as 3 different
AB  - modified residues.
ER  -

TY  - JOUR
AU  - Swinton, D.
AU  - Hattman, S.
AU  - Crain, P.F.
AU  - Cheng, C.-S.
AU  - Smith, D.L.
AU  - McCloskey, J.A.
TI  - Purification and characterization of the unusual deoxynucleoside, alpha-N-(9-beta-D-2'-deoxyribofuranosylpurin-t-yl) glycinamide, specified by the phage Mu modification function.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1983
SP  - 7400
EP  - 7404
VL  - 80
AB  - Bacteriophage Mu encodes a protein that modifies ~15% of DNA adenine residues
AB  - to a new and unusual form.  Modified DNA was enzymatically digested to
AB  - deoxynucleosides, and the products were fractionated by HPLC.  A modified
AB  - adenine nucleoside, designated dA'/x, was purified and its molecular structure
AB  - was established by mass spectrometry.  We show that dA'/x is
AB  - alpha-N-(9-beta-D-2'-deoxyribofuranosylpurin-t-yl)-glycinamide.  The dA'/x
AB  - obtained from DNA was indistinguishable from the synthetic product with respect
AB  - to its chromatographic behavior (HPLC and gas chromatography) and mass
AB  - spectrum.  Acid hydrolysis degrades dA'/x to produce N6-carboxymethyladenine;
AB  - this compound corresponds to the base Ax observed in earlier studies.
ER  -

TY  - JOUR
AU  - Swithers, K.S. et al.
TI  - Genome Sequence of Thermotoga sp. Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near  Ribeira Quente, the Azores.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5869
EP  - 5870
VL  - 193
AB  - Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome
AB  - sequence allows for an examination of the extent and
AB  - consequences of gene flow within Thermotoga species and strains.
AB  - Thermotoga sp. RQ2 differs from T. maritima in its genes involved in
AB  - myo-inositol metabolism. Its genome also encodes an apparent fructose
AB  - phosphotransferase system (PTS) sugar transporter. This operon is also
AB  - found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales.
AB  - These are the first reported PTS transporters in the Thermotogales.
ER  -

TY  - JOUR
AU  - Swithers, K.S.
AU  - Dipippo, J.L.
AU  - Bruce, D.C.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, S.
AU  - Goodwin, L.A.
AU  - Han, J.
AU  - Woyke, T.
AU  - Pitluck, S.
AU  - Pennacchio, L.
AU  - Nolan, M.
AU  - Mikhailova, N.
AU  - Land, M.L.
AU  - Nesbo, C.L.
AU  - Gogarten, J.P.
AU  - Noll, K.M.
TI  - Genome Sequence of Kosmotoga olearia Strain TBF 19.5.1, a Thermophilic Bacterium with a Wide Growth Temperature Range, Isolated from the Troll B  Oil Platform in the North Sea.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5566
EP  - 5567
VL  - 193
AB  - Kosmotoga olearia strain TBF 19.5.1 is a member of the Thermotogales that grows best at 65
AB  - degrees C and very well even at 37 degrees C. Information
AB  - about this organism is important for understanding the evolution of
AB  - mesophiles from thermophiles. Its genome sequence reveals extensive gene
AB  - gains and a large content of mobile genetic elements. It also contains
AB  - putative hydrogenase genes that have no homologs in the other member of
AB  - the Thermotogales.
ER  -

TY  - JOUR
AU  - Syazni, Y.M.
AU  - Kasuu, M.
AU  - Nakasaki, K.
AU  - Ariga, O.
TI  - Draft Genome Sequence of the Nonmarine Agarolytic Bacterium Cellvibrio sp. OA-2007.
JO  - Genome Announcements
PY  - 2015
SP  - e00468
EP  - e00415
VL  - 3
AB  - Cellvibrio sp. OA-2007 is a Gram-negative, aerobic, and agarolytic bacterium isolated from
AB  - activated sludge. We present the draft genome sequence of strain
AB  - OA-2007, composed of 97 contigs, totaling 4,595,379 bp in size, and containing
AB  - 4,094 open reading frames, with a G+C content of 47.71%.
ER  -

TY  - JOUR
AU  - Syddall, R.
AU  - Stachow, C.
TI  - A site-specific endonuclease from Caulobacter crescentus CB-13: restriction endonuclease CcrI.
JO  - Biochim. Biophys. Acta
PY  - 1985
SP  - 236
EP  - 243
VL  - 825
AB  - A site-specific restriction endonuclease (CcrI) has been identified from
AB  - Caulobacter crescentus CB-13.  This enzyme has been purified to homogeneity and
AB  - the cleavage patterns with various DNAs and sequence data show that CcrI
AB  - recognizes the same sequence as the XhoI restriction endonuclease
AB  - (5'-C^T-C-G-A-G-3').  CcrI has an absolute requirement for magnesium ions with
AB  - an optimum concentration of 4 mM.  The enzyme is optimally active at pH 8.0 and
AB  - is stable up to 70C.  CcrI has a molecular weight of 65300 and exists as a
AB  - monomer in its native state.  Most of the physical characteristics observed for
AB  - CcrI were similar to those observed for XhoI.  Kinetic studies on CcrI and XhoI
AB  - suggest that the enzymes with lambda DNA in the same manner, however with
AB  - PhiX-174 RF DNA, CcrI has a greater affinity for the supercoiled molecule than
AB  - XhoI.
ER  -

TY  - JOUR
AU  - Sydenham, T.V.
AU  - Hasman, H.
AU  - Justesen, U.S.
TI  - Draft Genome Sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., Strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), Isolated  from Blood Cultures from Two Different Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e00005
EP  - e00015
VL  - 3
AB  - We announce here the draft genome sequences of Sanguibacteroides justesenii, gen. nov., sp.
AB  - nov., strains OUH 308042(T) (= DSM 28342(T) = ATCC BAA-2681(T)) and OUH
AB  - 334697 (= DSM 28341 = ATCC BAA-2682), isolated from blood cultures from two
AB  - different patients and composed of 51 and 39 contigs for totals of 3,385,516 and
AB  - 3,410,672 bp, respectively.
ER  -

TY  - JOUR
AU  - Sykilinda, N.N.
AU  - Bondar, A.A.
AU  - Gorshkova, A.S.
AU  - Kurochkina, L.P.
AU  - Kulikov, E.E.
AU  - Shneider, M.M.
AU  - Kadykov, V.A.
AU  - Solovjeva, N.V.
AU  - Kabilov, M.R.
AU  - Mesyanzhinov, V.V.
AU  - Vlassov, V.V.
AU  - Drukker, V.V.
AU  - Miroshnikov, K.A.
TI  - Complete Genome Sequence of the Novel Giant Pseudomonas Phage PaBG.
JO  - Genome Announcements
PY  - 2014
SP  - e00929
EP  - e00913
VL  - 2
AB  - The novel giant Pseudomonas aeruginosa bacteriophage PaBG was isolated from a water sample of
AB  - the ultrafreshwater Lake Baikal. We report the complete genome
AB  - sequence of this Myoviridae bacteriophage, comprising 258,139 bp of
AB  - double-stranded DNA containing 308 predicted open reading frames.
ER  -

TY  - JOUR
AU  - Szabo, Z.
AU  - Gyula, P.
AU  - Robotka, H.
AU  - Bato, E.
AU  - Galik, B.
AU  - Pach, P.
AU  - Pekker, P.
AU  - Papp, I.
AU  - Bihari, Z.
TI  - Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 39
EP  - 39
VL  - 10
AB  - Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and  proved to
AB  - have excellent capabilities in degrading some common fuel oxygenates
AB  - like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along
AB  - with other organic compounds. Here, we report the draft genome sequence of M. sp.
AB  - strain T29 together with the description of the genome properties and its
AB  - annotation. The draft genome consists of 608 contigs with a total size of
AB  - 4,449,424 bp and an average coverage of 150x. The genome exhibits an average G +
AB  - C content of 68.7 %, and contains 4754 protein coding and 52 RNA genes, including
AB  - 48 tRNA genes. 71 % of the protein coding genes could be assigned to COG
AB  - (Clusters of Orthologous Groups) categories. A formerly unknown circular plasmid
AB  - designated as pT29A was isolated and sequenced separately and found to be 86,856
AB  - bp long.
ER  -

TY  - JOUR
AU  - Szatmari, G.
AU  - Hua, N.M.
AU  - Vzdornov, D.
AU  - Daigle, F.
AU  - Smoragiewicz, W.
AU  - Mamet-Bratley, M.D.
AU  - Karska-Wysocki, B.
TI  - In vitro expression of the restriction endonucleases LlaMI and ScrFI isolated from Lactococcus lactis M19 and UC503.
JO  - J. Biotechnol.
PY  - 2006
SP  - 144
EP  - 153
VL  - 121
AB  - A new restriction endonuclease LlaMI has been characterized in Lactococcus lactis subsp.
AB  - cremoris M19. LlaMI recognizes the sequence 5'-CCNGG-3' and cuts after the second cytosine.
AB  - This restriction endonuclease is related to commercially available ScrFI but not identical to
AB  - it. Comparative analysis of the predicted amino acid sequences of LlaMI and ScrFI indicates
AB  - five non-conservative amino acid changes between these two restriction enzymes. These two
AB  - enzymes were expressed in vitro as histidine-tagged fusion proteins. LlaMI was shown to be
AB  - more sensitive to high salt concentration than ScrFI. Southern blotting and hybridization
AB  - analysis indicate that the gene for LlaMI R/M system is chromosomally encoded.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
TI  - How do proteins move along DNA?  Lessons from type-I and type-III restriction endonucleases.
JO  - Essays Biochem.
PY  - 2000
SP  - 131
EP  - 143
VL  - 35
AB  - A fundamental requirement of nearly every genetic event, including DNA replication,
AB  - transcription, cleavage and repair, is the protein-mediated communication between distance DNA
AB  - sites.  Four general mechanisms for this 'action at a distance' were described by Adzuma and
AB  - Mizuuchi and are illustrated in Figure 1.  The first three models, DNA sliding, DNA hopping
AB  - and DNA looping, are driven passively by random thermal fluctuations of the protein or DNA,
AB  - with significant consequences for the efficiency of the reactions.  In DNA sliding, a protein
AB  - bound to non-specific DNA diffuses either leftwards or rightwards without dissociating,
AB  - altering the DNA-binding register by 1 bp.  By confining diffusion to one dimension, the
AB  - probability of finding a second site or protein is increased.  However, the number of physical
AB  - steps needed to move between two DNA loci by linear diffusion has a square power dependence on
AB  - the distance between those sites; for instance, travelling 1000 bp takes 1 x 10^6 steps, which
AB  - in turn requires a linear diffusion rate at least 1 x 10^6 times faster than the DNA
AB  - dissociation rate.  Generally, DNA-binding proteins associate transiently with non-specific
AB  - sequences and DNA sliding would only be feasible over quite short distances, less than 100 bp.
AB  - In DNA hopping, a protein physically releases DNA, diffuses in three dimensions and randomly
AB  - rebinds the same DNA molecule at an alternative site.  The DNA acts as a binding 'reservoir'
AB  - - given enough time, one protein could sample every available binding locus.
AB  - Three-dimensional diffusion on a random coil has a square-root power dependence on the
AB  - distance between target sites, but because sampling is non-linear, sites may be overlooked and
AB  - the protein could even diffuse away from the DNA altogether.  In DNA looping, a protein
AB  - remains bound to a specific DNA sequence whilst segmental diffusion of the polynucleotide
AB  - brings distant DNA sites (and any bound proteins) into close proximity.  In general, the
AB  - tethering of two proteins on to the same DNA molecule increases the probability of
AB  - protein-protein interactions.  However, the probability of juxtaposition decreases as the
AB  - distance between the sites increases, an effect that is particularly marked on linear DNA.
AB  - DNA-looping events are less likely over distances greater than ~1000 bp without the
AB  - cooperation of accessory factors, such as DNA-bending proteins.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
TI  - Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases.
JO  - Biochemistry
PY  - 2002
SP  - 2067
EP  - 2074
VL  - 41
AB  - Digestion of linear DNA by type I restriction endonucleases is generally activated following
AB  - the head-on collision of two
AB  - translocating enzymes. However, the resulting distributions of cleavage
AB  - loci along the DNA vary with different enzymes; in some cases, cleavage
AB  - is located in a discrete region midway between a pair of recognition
AB  - sites while in other cases cleavage is broadly distributed and occurs
AB  - at nearly every intervening locus. Statistical models for DNA
AB  - translocation, collision, and cleavage are described that can account
AB  - for these observations and that are generally applicable to other
AB  - DNA-based motor proteins. If translocation is processive (stepping
AB  - forward is significantly more likely than DNA dissociation), then the
AB  - linear distribution of an ensemble of proteins can be described simply
AB  - using a Poisson relationship. The pattern of cleavage sites resulting
AB  - from collision between two processive type I enzymes over a distance d
AB  - can then be described by a binomial distribution with a standard
AB  - deviation 0.5.d(1/2). Alternatively, if translocation is nonprocessive
AB  - (stepping forward or dissociating become equally likely events), the
AB  - linear distribution is described by a continuum of populated states and
AB  - is thus extended. Comparisons of model data to the kinetics of DNA
AB  - translocation and cleavage discount the nonprocessive model. Instead,
AB  - the observed differences between enzymes are due to asynchronous events
AB  - that occur upon collision. Therefore, type I restriction enzymes can be
AB  - described as having processive DNA translocation but, in some cases,
AB  - nonprocessive DNA cleavage.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
TI  - Roles for Helicases as ATP-Dependent Molecular Switches.
JO  - Adv. Exp. Med. Biol.
PY  - 2013
SP  - 225
EP  - 244
VL  - 767
AB  - On the basis of the familial name, a 'helicase' might be expected to have an enzymatic
AB  - activity that unwinds duplex polynucleotides to form single strands. A more encompassing
AB  - taxonomy that captures alternative enzymatic roles has defined helicases as a sub-class of
AB  - molecular motors that move directionally and processively along nucleic acids, the so-called
AB  - 'translocases'. However, even this definition may be limiting in capturing the full scope of
AB  - helicase mechanism and activity. Discussed here is another, alternative view of helicases-as
AB  - machines which couple NTP-binding and hydrolysis to changes in protein conformation to resolve
AB  - stable nucleoprotein assembly states. This 'molecular switch' role differs from the
AB  - classical view of helicases as molecular motors in that only a single catalytic NTPase cycle
AB  - may be involved. This is illustrated using results obtained with the DEAD-box family of RNA
AB  - helicases and with a model bacterial system, the ATP-dependent Type III
AB  - restriction-modification enzymes. Further examples are discussed and illustrate the
AB  - wide-ranging examples of molecular switches in genome metabolism.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
TI  - Translocation, switching and gating: potential roles for ATP in long-range communication on DNA by Type III restriction endonucleases.
JO  - Biochem. Soc. Trans.
PY  - 2011
SP  - 589
EP  - 594
VL  - 39
AB  - To cleave DNA, the Type III RM (restriction-modification) enzymes must communicate the
AB  - relative orientation of two recognition sequences, which may be separated by many thousands of
AB  - base pairs. This long-range interaction requires ATP hydrolysis by a helicase domain, and both
AB  - active (DNA translocation) and passive (DNA sliding) modes of motion along DNA have been
AB  - proposed. Potential roles for ATP binding and hydrolysis by the helicase domains are
AB  - discussed, with a focus on bipartite ATPases that act as molecular switches.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Connolly, B.A.
TI  - Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acid and cofactor analogues.
JO  - Biochemistry
PY  - 1995
SP  - 10724
EP  - 10733
VL  - 34
AB  - The DNA-binding properties of the EcoRV restriction endonuclease and modification
AB  - methyltransferase with their recognition sequence (GATATC) were analyzed using the
AB  - electrophoretic band-shift assay.  It has previously been observed that the endonuclease does
AB  - not bind specifically to GATATC sequences in the absence of the essential cofactor Mg2+.  To
AB  - investigate any possible roles for Mg2+ in promoting specific DNA binding, a set of
AB  - hydrolysis-resistant oligonucleotide substrates were synthesized that contained either
AB  - phosphate (phosphorothioate, 3'-S-phosphorothiolate), sugar (4'-thiothymidine), or base
AB  - (7-deaza-2'-deoxyadenosine) modifications.  However, it was found that none of these were
AB  - specifically bound by the endonuclease in either the absence or the presence of Mg2+.  In
AB  - contrast, the methylase bound to GATATC sequences much more strongly than to nonspecific
AB  - sites, and it was possible to observe the formation of enzyme-DNA complexes by gel
AB  - retardation.  Binding to GATATC sequences was increased by the addition of sinefungin, a
AB  - nonreactive analogue of the essential cofactor S-adenosyl-L-methionine (AdoMet).  Presumably
AB  - this also occurs with AdoMet although methylation and turnover prevented its direct
AB  - observation.  In the presence of sinefungin the strongest binding was observed with
AB  - hemimethylated EcoRV sequences (Kd=11-13 nM), and unmethylated DNA was bound less well
AB  - (Kd=46nM).  Specific, albeit weaker binding was also seen with the dimethylated product
AB  - (Kd=143 nM).  A difference in electrophoretic mobility was observed between enzyme-substrate
AB  - and enzyme-product complexes suggestive of structural differences between them.  The Kapp
AB  - value found for sinefungin, with the hemimethylated EcoRV sequence, was 10.9 mM.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Dillingham, M.S.
AU  - Janscak, P.
AU  - Firman, K.
AU  - Halford, S.E.
TI  - Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates.
JO  - EMBO J.
PY  - 1996
SP  - 6335
EP  - 6347
VL  - 15
AB  - Type I restriction endonucleases such as EcoR124I cleave DNA at undefined loci, distant from
AB  - their recognition sequences, by a mechanism that involves the enzyme tracking along the DNA
AB  - between recognition and cleavage sites.  This mechanism was examined on plasmids that carried
AB  - recognition sites for EcoR124I and recombination sites for resolvase, the latter to create DNA
AB  - catenanes.  Supercoiled substrates with either one or two restriction sites were linearized by
AB  - EcoR124I at similar rates, although the two-site molecule underwent further cleavage more
AB  - readily than the one-site DNA.  The catenane from the plasmid with one EcoR124I site, carrying
AB  - the site on the smaller of the two rings, was cleaved by EcoR124I exclusively in the small
AB  - ring, and this underwent multiple cleavage akin to the two-site plasmid.  Linear substrates
AB  - derived from the plasmids were cleaved by EcoR124I at very slow rates.  The communication
AB  - between recognition and cleavage sites therefore cannot stem from random looping.  Instead, it
AB  - must follow the DNA contour between the sites.  On a circular DNA, the translocation of
AB  - non-specific DNA past the specifically bound protein should increase negative supercoiling in
AB  - one domain and decrease it in the other.  The ensuing topological barrier may be the trigger
AB  - for DNA cleavage.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Friedhoff, P.
AU  - Seidel, R.
TI  - Maintaining a sense of direction during long-range communication on DNA.
JO  - Biochem. Soc. Trans.
PY  - 2010
SP  - 404
EP  - 409
VL  - 38
AB  - Many biological processes rely on the interaction of proteins with multiple DNA sites
AB  - separated by thousands of base pairs. These
AB  - long-range communication events can be driven by both the thermal
AB  - motions of proteins and DNA, and directional protein motions that are
AB  - rectified by ATP hydrolysis. The present review describes conflicting
AB  - experiments that have sought to explain how the ATP-dependent Type Ill
AB  - restriction-modification enzymes can cut DNA with two sites in an
AB  - inverted repeat, but not DNA with two sites in direct repeat. We
AB  - suggest that an ATPase activity may not automatically indicate a DNA
AB  - translocase, but can alternatively indicate a molecular switch that
AB  - triggers communication by thermally driven DNA sliding. The generality
AB  - of this mechanism to other ATP-dependent communication processes such
AB  - as mismatch repair is also discussed.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Halford, S.E.
TI  - Restriction Endonuclease.
JO  - Encyclopaedia of Genetics
PY  - 2001
SP  - 1693
EP  - 1696
VL  - 0
AB  - The term 'restriction enzyme' was first coined more than 30 years ago, following the classic
AB  - observation that phage grown on one bacterial species would grow poorly on another strain of
AB  - the same species; the phage were 'restricted' in their host range.  The restriction activity
AB  - was dependent on an endonuclease which cleaves double-stranded DNA upon binding a specific
AB  - sequence of nucleotides (the recognition site).  However, transfer of a methyl group from the
AB  - donor S-adenosylmethionine to a particular base on one or both strands of the recognition site
AB  - prevents cleavage.  This modification is catalyzed by a methyltransferase activity.  The host
AB  - DNA can therefore be protected from self-digestion, even during semiconservative replication
AB  - when one strand is temporally unmodified.  Conversely, any invasive DNA is unlikely to carry
AB  - the correct pattern of methylated bases, and will be a target for cleavage.  The presence in
AB  - parallel of endonuclease and methyltransferase activities produces a bacterial equivalent of
AB  - an immune system, capable of distinguishing self from foreign DNA.  Probably as a consequence
AB  - of this custodial role, restriction endonucleases are widespread in nature, appearing in every
AB  - bacterial generus examined.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Halford, S.E.
TI  - Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease.
JO  - EMBO J.
PY  - 1996
SP  - 1460
EP  - 1469
VL  - 15
AB  - The SfiI endonuclease differs from other type II restriction enzymes by cleaving DNA
AB  - concertedly at two copies of its recognition site, its optimal activity being with two sites
AB  - on the same DNA molecule.  The nature of this communication event between distant DNA sites
AB  - was analysed on plasmids with recognition sites for SfiI interspersed with recombination sites
AB  - for resolvase.  These were converted by resolvase to catenanes carrying one SfiI site on each
AB  - ring.  The catenanes were cleaved by SfiI almost as readily as a single ring with two sites,
AB  - in contrast to the slow reactions on DNA rings with one SfiI site.  Interactions between SfiI
AB  - sites on the same DNA therefore cannot follow the DNA contour and, instead, must stem from
AB  - their physical proximity.  In buffer lacking Mg2+, where SfiI is inactive while resolvase is
AB  - active, the addition of SfiI to a plasmid with target sites for both proteins blocked
AB  - recombination by resolvase, due to the restriction enzyme bridging its sites and thus
AB  - isolating the sites for resolvase into separate loops.  The extent of DNA looping by SfiI
AB  - matched its extent of DNA cleavage in the presence of Mg2+.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Janscak, P.
AU  - Firman, K.
AU  - Halford, S.E.
TI  - Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 112
EP  - 123
VL  - 271
AB  - The type IC restriction endonuclease EcoR124I binds specifically to its recognition sequence
AB  - but subsequently translocates non-specific DNA past the complex in an ATP-dependent mechanism.
AB  - The enzyme thus has the potential to cleave DNA at loci distant from the recognition site.  We
AB  - have scrutinized the link between translocation and cleavage on linear and circular DNA
AB  - substrates.  On linear DNA carrying two recognition sites, the majority of cleavages at loci
AB  - distant from the recognition site occurred between the two sites, regardless of the inter-site
AB  - distance or relative orientations.  On circular DNA carrying one site, distant cleavages
AB  - occurred throughout the DNA but an equivalent linear molecule underwent considerably fewer
AB  - cleavages at distant loci.  These results agree with published models for DNA tracking.
AB  - However, on every molecule investigated, discrete cleavage sites were also observed within
AB  - +/-250bp of the recognition sites.  The localized cleavages were not confined to particular
AB  - DNA sequences and were independent of DNA topology.  We propose a model to account for both
AB  - distant and localized cleavage events.  The conformation of the DNA loop extruded during
AB  - tracking may result in two DNA segments being held in proximity to the restriction moiety on
AB  - the protein, one close to the EcoR124I site and another distant from the site: cleavage may
AB  - occur in either segment.  Alternatively, the cutting of DNA close to recogniton sites may be
AB  - the result of multiple nicks being generated in the expanding loop before any extensive
AB  - translocation.
ER  -

TY  - JOUR
AU  - Szczelkun, M.D.
AU  - Jones, H.
AU  - Connolly, B.A.
TI  - Probing the protein-DNA interface of the EcoRV modification methyltransferase bound to its recognition sequence, GATATC.
JO  - Biochemistry
PY  - 1995
SP  - 10734
EP  - 10743
VL  - 34
AB  - The DNA contacts produced between the EcoRV modification methyltransferase and its recognition
AB  - sequence, GATATC, have been determined.  The enzyme's general location in a
AB  - methylase/DNA/sinefungin ternary complex was evaluated by protection from exonuclease III
AB  - digestion.  Important phosphate contacts were resolved using N-ethyl-N-nitrosourea ethylation
AB  - interference footprinting.  Methylation protection and interference using dimethyl sulfate
AB  - were employed to assess significant contacts to purinic bases.  The protein-DNA interface was
AB  - further probed using oligodeoxynucleotides containing base analogues within the GATATC
AB  - sequence.  Most of the experiments were carried out using hemimethylated sequences, i.e.,
AB  - having 6-methyladenosine at the methylation site in one of the strands.  The momomeric
AB  - methylase was found to bind to the DNA in two different orientations for the methylation of
AB  - each strand.  The enzyme approaches the DNA, predominantly from one "side", and makes most of
AB  - its contacts in the major groove.  In either of the two binding events contacts are made to
AB  - the four phosphates NpNpNpGpA and the three bases GAT (where GAT represents the 5' half of
AB  - the GATATC site) on both DNA strands.  The phosphates and bases in the 3' ATC half are much
AB  - less important.  Although the contacts made to the equivalent locations on each strand are
AB  - similar, they display a slight but consistent change dependent on which strand contains the
AB  - 6-methyldeoxyadenosine.  This strand variation shows completely reciprocal behavior, switching
AB  - around exactly, depending entirely on the methylated deoxyadenosine location.  It is this
AB  - that provides evidence for the two binding modes.  The results obtained are discussed in terms
AB  - of possible models for the protein-DNA interface.
ER  -

TY  - JOUR
AU  - Szczepanek, T.
AU  - Gora, M.
AU  - Monteilhet, C.
AU  - Wysocka, M.
AU  - Lazowska, J.
AU  - Golik, P.
TI  - In vivo analysis of the relationships between the splicing and homing activities of a group I intron-encoded I-ScaI/bi2-maturase of  Saccharomyces capensis produced in the yeast cytoplasm.
JO  - FEMS Yeast Res.
PY  - 2006
SP  - 823
EP  - 835
VL  - 6
AB  - The I-ScaI/bi2-maturase of Saccharomyces capensis acts as a specific homing endonuclease
AB  - promoting intron homing, and as a maturase
AB  - promoting intron splicing. Using the universal code equivalent of the
AB  - mitochondrial gene encoding the I-ScaI/bi2-maturase, a number of
AB  - truncated forms of the synthetic gene were constructed, shortened on
AB  - either side, as were several mutated alleles of the protein. The
AB  - shortest translation product that fully retains both activities in vivo
AB  - corresponds to 228 codons of the C-terminal region of the bi2
AB  - intron-encoded protein, whereas proteins resulting from more extensive
AB  - deletions either at the N-terminus or at the C-terminus (up to 73 and
AB  - four residues, respectively) were able to complement wholly the lack of
AB  - endogenous maturase, but all lost the endonuclease activity. Similarly,
AB  - all introduced mutations completely abolished the I-ScaI activity while
AB  - some mutant proteins retained substantial splicing function.
AB  - Immunodetection experiments demonstrated that different cytoplasmically
AB  - translated forms of the I-ScaI/bi2-maturase protein were imported into
AB  - mitochondria and correctly processed. They appeared to be tightly
AB  - associated with mitochondrial membranes. Homology modelling of the
AB  - I-ScaI/bi2-maturase protein allowed us to relate both enzymatic
AB  - activities to elements of enzyme structure.
ER  -

TY  - JOUR
AU  - Szczepanek, T.
AU  - Jamoussi, K.
AU  - Lazowska, J.
TI  - Critical base substitutions that affect the splicing and/or homing activities of the group I intron bi2 of yeast mitochondria.
JO  - Mol. Gen. Genet.
PY  - 2000
SP  - 137
EP  - 144
VL  - 264
AB  - The second intron (bi2) of the cyt b gene from related Saccharomyces species has an
AB  - extraordinarily conserved sequence and can have
AB  - different functions in wild-type cells. The protein encoded by the S.
AB  - cerevisiae intron functions as a maturase to promote intron splicing,
AB  - while the homologous S. capensis intron encodes a bifunctional protein
AB  - that acts both as a maturase and as a homing endonuclease (I-ScaI)
AB  - promoting intron mobility. The protein encoded by intron bi2 belongs to
AB  - a large gene family characterized by the presence of two conserved
AB  - LAGLIDADG motifs (P1 and P2). In this study, we analysed a set of
AB  - splicing-deficient mutants of the S. cerevisiae intron bi2 that carry
AB  - non-directed mutations affecting the maturase activity, and a set of
AB  - directed missense mutations introduced into the bifunctional protein
AB  - encoded by the S. capensis intron. Analysis of these mutations has
AB  - allowed identification of the residues in the conserved P1 and P2
AB  - motifs which are crucial for splicing and homing activities. Moreover,
AB  - several mutations which are located in the C-terminal part of the
AB  - protein have been found to affect both functions.
ER  -

TY  - JOUR
AU  - Szczepanek, T.
AU  - Lazowska, J.
TI  - Replacement of two non-adjacent amino acids in the S. cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity.
JO  - EMBO J.
PY  - 1996
SP  - 3758
EP  - 3767
VL  - 15
AB  - Two homologous group I introns, the second intron of the cyt b gene, from related
AB  - Saccharomyces species differ in their mobility.  The S. capensis intron is mobile and encodes
AB  - the I-ScaI endonuclease promoting intron homing, whilst the homologous S. cerevisiae intron is
AB  - not mobile, but functions as an RNA maturase promoting splicing. These two intron-encoded
AB  - proteins differ by only four amino acid substitutions.  Taking advantage of the remarkable
AB  - similarity of the two intron open reading frames and using biolistic transformation of
AB  - mitochondria, we show that the replacement of only two non- adjacent residues in the S.
AB  - cerevisiae maturase carboxy-terminal sequence is sufficient to induce a homing-endonuclease
AB  - activity without losing the splicing function.  Also, we demonstrate that these two activities
AB  - reside in the S. capensis bi2-encoded protein which functions in both splicing and intron
AB  - mobility in the wild-type cells.  These results provide new insight into our understanding of
AB  - the activity and the evolution of group I intron- encoded proteins.
ER  -

TY  - JOUR
AU  - Szczepanek, T.
AU  - Macadre, C.
AU  - Meunier, B.
AU  - Lazowska, J.
TI  - Two homologous introns from related Saccharomyces species differ in their mobility.
JO  - Gene
PY  - 1994
SP  - 1
EP  - 7
VL  - 139
AB  - We have studied gene conversion initiated by the ai3 intron of the Saccharomyces cerevisiae
AB  - mitochondrial COX1 gene and its homologous intron (S.cap.ai1) from Saccharomyces capensis.
AB  - The approach used involved the measurement of intron transmission amongst the progeny of
AB  - crosses between constructed recipient and donor strains.  We found that the S. cerevisiae ai3
AB  - intron is extremely active as a donor in gene conversion, whereas its homologous S. capensis
AB  - intron is not.  We have established the sequence of S.cap.ai1 and compared its open reading
AB  - frame with that of I-SceIII encoded by the homologous S. cerevisiae intron.  The two
AB  - protein-coding intron sequences are almost identical, except that the S. capensis ORF contains
AB  - an in-frame stop codon.  This finding provides a strong indication that the 3' part of the S.
AB  - cerevisiae intron ORF encoding I-SceIII (which should not be translated in the S. capensis
AB  - intron) must be critical for function of mtDNA endonucleases to mediate intron mobility.
ER  -

TY  - JOUR
AU  - Szczepanowski, R.
AU  - Eikmeyer, F.
AU  - Harfmann, J.
AU  - Blom, J.
AU  - Rogers, L.M.
AU  - Brown, C.J.
AU  - Top, E.M.
AU  - Schluter, A.
TI  - Sequencing and comparative analysis of IncP-1alpha antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions.
JO  - J. Biotechnol.
PY  - 2011
SP  - 95
EP  - 103
VL  - 155
AB  - In spite of the importance of IncP-1 plasmids in horizontal gene transfer
AB  - among bacteria, in particular antibiotic resistance spread, so far only
AB  - three plasmids from the subgroup IncP-1alpha have been completely
AB  - sequenced. In this study we doubled this number. The three IncP-1alpha
AB  - plasmids pB5, pB11 and pSP21 were isolated from bacteria of two different
AB  - sewage treatment plants and sequenced by a combination of next-generation
AB  - and capillary sequencing technologies. A comparative analysis including
AB  - the previously analysed IncP-1alpha plasmids RK2, pTB11 and pBS228
AB  - revealed a highly conserved plasmid backbone (at least 99.9% DNA sequence
AB  - identity) comprising 54 core genes loaded with different accessory
AB  - elements. The accessory elements of the plasmid pB5 constitute a class 1
AB  - integron interrupting the parC gene and an IS6100 copy inserted into the
AB  - integron. In addition, the tetracycline resistance genes tetAR and the
AB  - ISTB11-like element are located between the klc operon and the trfA-ssb
AB  - operon. Plasmid pB11 is loaded with a Tn5053-like mercury resistance
AB  - transposon between the parCBA and parDE operons and contains tetAR that
AB  - are identical to those identified in plasmid pB5 and the insertion
AB  - sequence ISSP21. Plasmid pSP21 harbours an ISPa7 element in a Tn402
AB  - transposon including a class 1 integron between the partitioning genes
AB  - parCBA and parDE. The IS-element ISSP21 (99.89% DNA sequence identity to
AB  - ISSP21 from pB11), inserted downstream of the tetR gene and a copy of
AB  - ISTB11 (identical to ISTB11 on pTB11) inserted between the genes pncA and
AB  - pinR. On all three plasmids the accessory genes are almost always located
AB  - between the backbone modules confirming the importance of the backbone
AB  - functions for plasmid maintenance. The striking backbone conservation
AB  - among the six completely sequenced IncP-1alpha plasmids is in contrast to
AB  - the much higher diversity within the IncP-1beta subgroup.
ER  -

TY  - JOUR
AU  - Szczepanowski, R.H.
AU  - Carpenter, M.A.
AU  - Czapinska, H.
AU  - Zaremba, M.
AU  - Tamulaitis, G.
AU  - Siksnys, V.
AU  - Bhagwat, A.S.
AU  - Bochtler, M.
TI  - Central base pair flipping and discrimination by PspGI.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 6109
EP  - 6117
VL  - 36
AB  - PspGI is a representative of a group of restriction endonucleases that recognize a pentameric
AB  - sequence related to CCNGG. Unlike the previously
AB  - investigated Ecl18kI, which does not have any specificity for the central
AB  - base pair, PspGI prefers A/T over G/C in its target site. Here, we present
AB  - a structure of PspGI with target DNA at 1.7 A resolution. In this
AB  - structure, the bases at the center of the recognition sequence are
AB  - extruded from the DNA and flipped into pockets of PspGI. The flipped
AB  - thymine is in the usual anti conformation, but the flipped adenine takes
AB  - the normally unfavorable syn conformation. The results of this and the
AB  - accompanying manuscript attribute the preference for A/T pairs over G/C
AB  - pairs in the flipping position to the intrinsically lower penalty for
AB  - flipping A/T pairs and to selection of the PspGI pockets against guanine
AB  - and cytosine. Our data show that flipping can contribute to the
AB  - discrimination between normal bases. This adds a new role to base flipping
AB  - in addition to its well-known function in base modification and DNA damage
AB  - repair.
ER  -

TY  - JOUR
AU  - Szczepek, M.
AU  - Brondani, V.
AU  - Buchel, J.
AU  - Serrano, L.
AU  - Segal, D.J.
AU  - Cathomen, T.
TI  - Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.
JO  - Nat. Biotechnol.
PY  - 2007
SP  - 786
EP  - 793
VL  - 25
AB  - Artificial endonucleases consisting of a FokI cleavage domain tethered to engineered
AB  - zinc-finger DNA-binding proteins have proven useful for
AB  - stimulating homologous recombination in a variety of cell types. Because
AB  - the catalytic domain of zinc-finger nucleases (ZFNs) must dimerize to
AB  - become active, two subunits are typically assembled as heterodimers at the
AB  - cleavage site. The use of ZFNs is often associated with significant
AB  - cytotoxicity, presumably due to cleavage at off-target sites. Here we
AB  - describe a structure-based approach to reducing off-target cleavage. Using
AB  - in silico protein modeling and energy calculations, we increased the
AB  - specificity of target site cleavage by preventing homodimerization and
AB  - lowering the dimerization energy. Cell-based recombination assays
AB  - confirmed that the modified ZFNs were as active as the original ZFNs but
AB  - elicit significantly less genotoxicity. The improved safety profile may
AB  - facilitate therapeutic application of the ZFN technology.
ER  -

TY  - JOUR
AU  - Szczepek, M.
AU  - Mackeldanz, P.
AU  - Moncke-Buchner, E.
AU  - Alves, J.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition.
JO  - Mol. Microbiol.
PY  - 2009
SP  - 1011
EP  - 1021
VL  - 72
AB  - Bacterial restriction endonuclease EcoRII requires two recognition sites to cleave DNA.
AB  - Proteolysis of EcoRII revealed the existence of
AB  - two stable domains, EcoRII-N and EcoRII-C. Reduction of the enzyme to
AB  - its C-terminal domain, EcoRII-C, unleashed the enzyme activity; this
AB  - truncated form no longer needed two recognition sites and cleaved DNA
AB  - much more efficiently than EcoRII wild-type. The crystal structure of
AB  - EcoRII showed that probably the N-terminal domain sterically occludes
AB  - the catalytic site, thus apparently controlling the cleavage activity.
AB  - Based on these data, EcoRII was the first restriction endonuclease for
AB  - which an autoinhibition mechanism as regulatory strategy was proposed.
AB  - In this study, we probed this assumption and searched for the
AB  - inhibitory element that mediates autoinhibition. Here we show that
AB  - repression of EcoRII-C is achieved by addition of the inhibitory domain
AB  - EcoRII-N or by single soluble peptides thereof in trans. Moreover, we
AB  - perturbed contacts between the N- and the C-terminal domain of EcoRII
AB  - by site-directed mutagenesis and proved that beta-strand B1 and
AB  - alpha-helix H2 are essential for autoinhibition; deletion of either
AB  - secondary structural element completely relieved EcoRII autoinhibition.
AB  - This potent regulation principle that keeps EcoRII enzyme activity
AB  - controlled might protect bacteria against suicidal restriction of rare
AB  - unmodified recognition sites in the cellular genome.
ER  -

TY  - JOUR
AU  - Szczepinska, T.
AU  - Kutner, J.
AU  - Kopczynski, M.
AU  - Pawlowski, K.
AU  - Dziembowski, A.
AU  - Kudlicki, A.
AU  - Ginalski, K.
AU  - Rowicka, M.
TI  - Probabilistic approach to predicting substrate specificity of methyltransferases.
JO  - PLOS Comp. Biol.
PY  - 2014
SP  - e1003514
EP  - e1003514
VL  - 10
AB  - We present a general probabilistic framework for predicting the substrate specificity of
AB  - enzymes. We designed this approach to be easily applicable to
AB  - different organisms and enzymes. Therefore, our predictive models do not rely on
AB  - species-specific properties and use mostly sequence-derived data. Maximum
AB  - Likelihood optimization is used to fine-tune model parameters and the Akaike
AB  - Information Criterion is employed to overcome the issue of correlated variables.
AB  - As a proof-of-principle, we apply our approach to predicting general substrate
AB  - specificity of yeast methyltransferases (MTases). As input, we use several
AB  - physico-chemical and biological properties of MTases: structural fold,
AB  - isoelectric point, expression pattern and cellular localization. Our method
AB  - accurately predicts whether a yeast MTase methylates a protein, RNA or another
AB  - molecule. Among our experimentally tested predictions, 89% were confirmed,
AB  - including the surprising prediction that YOR021C is the first known MTase with a
AB  - SPOUT fold that methylates a substrate other than RNA (protein). Our approach not
AB  - only allows for highly accurate prediction of functional specificity of MTases,
AB  - but also provides insight into general rules governing MTase substrate
AB  - specificity.
ER  -

TY  - JOUR
AU  - Szeberenyi, J.
TI  - Two restriction endonucleases.
JO  - Biochem. Mol. Biol. Educ.
PY  - 2006
SP  - 228
EP  - 229
VL  - 34
AB  - Terms to be familiar with before you start to solve the test: restriction endonucleases;
AB  - palindromic sequences; blunt ends; cohesive
AB  - ("sticky") ends; in vitro DNA synthesis; radioactive nucleotide
AB  - precursors; template-primer complexes; DNA ligation.|
ER  -

TY  - JOUR
AU  - Szegedi, S.S.
AU  - Gumport, R.I.
TI  - DNA binding properties in vivo and target recognition domain sequence alignment analyses of wild-type and mutant RsrI [N6-adenine] DNA methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3972
EP  - 3981
VL  - 28
AB  - A genetic selection method, the P22 challenge-phage assay, was used to characterize DNA
AB  - binding in vivo by the prokaryotic beta class [N6-adenine] DNA methyltransferase M.RsrI.
AB  - M.RsrI mutants with altered binding affinities in vivo were isolated. Unlike the wild-type
AB  - enzyme, a catalytically compromised mutant, M.RsrI (L72P), demonstrated site-specific DNA
AB  - binding in vivo. The L72P mutation is located near the highly conserved catalytic motif IV,
AB  - DPPY (residues 65-68). A double mutant, M.RsrI (L72P/D173A), showed less binding in vivo than
AB  - did M.RsrI (L72P). Thus, introduction of the D173A mutation deleteriously affected DNA
AB  - binding. D173 is located in the putative target recognition domain (TRD) of the enzyme.
AB  - Sequence alignment analyses of several beta class MTases revealed a TRD sequence element that
AB  - contains the D173 residue. Phylogenetic analysis suggested that divergence in the amino acid
AB  - sequences of these methyltransferases correlated with differences in their DNA target
AB  - recognition sequences. Furthermore, MTases of other classes (alpha and gamma) having the same
AB  - DNA recognition sequence as the beta class MTases share related regions of amino acid
AB  - sequences in their TRDs.
ER  -

TY  - JOUR
AU  - Szegedi, S.S.
AU  - Ma, Z.
AU  - Gumport, R.I.
TI  - A novel scheme for the purification of wildtype and mutant RsrI DNA methyltransferases (MTases).
JO  - FASEB J.
PY  - 1998
SP  - A1437
EP  - A1437
VL  - 12
AB  - RsrI DNA MTase (M.RsrI) is an S-adenosylmethionine-dependent enzyme that recognizes the duplex
AB  - DNA sequence 5-GAATTC-3 and methylates the central adenine at the N6 position.  M.RsrI is
AB  - isocatalytic but not homologous with M.EcoRI.  These two proteins show only 15.6% amino acid
AB  - identity.  Our laboratory has purified M.RsrI and is generating M.RsrI mutants as part of an
AB  - effort to understand how the two dissimilar proteins perform the same catalytic function.  A
AB  - simpler method for purifying the wild-type M.RsrI has been developed, reducing the
AB  - purification steps from six to two.  The isolation of wild-type M.RsrI to >90% purity from
AB  - 8.0g of E. coli cells paste yields approximately 7.5 mg of protein.  This amount represents a
AB  - >4-fold increase in the yield of protein as compared to our previous purification method.  A
AB  - mutant, M.RsrI (L72P), is currently being purified in a similar manner.  This mutant was
AB  - generated by random PCR mutagenesis and isolated using the in vivo DNA binding assay, the
AB  - bacteriophage P22 challenge-phage assay.  Wild-type M.RsrI is toxic and shows no DNA binding
AB  - in the assay.  M.RsrI (L72P), on the other hand, is non-toxic and gives reproducible binding.
AB  - Catalytic assays of >70% pure M.RsrI (L72P) have shown that it retains weak catalytic
AB  - activity.  This mutation lies close to the highly conserved catalytic motif "DPPY", and may
AB  - affect catalysis and/or AdoMet binding.  We will generate more M.RsrI for attempts at
AB  - crystallization, and will purify M.RsrI (L72P) and other mutants recently generated by
AB  - site-directed PCR mutagenesis.
ER  -

TY  - JOUR
AU  - Szegedi, S.S.
AU  - Reich, N.O.
AU  - Gumport, R.I.
TI  - Characterization of the DNA binding and kinetic properties of wild-type Rsr[N6-adenine] methyltransferase (M.RsrI).
JO  - FASEB J.
PY  - 1999
SP  - A1367
EP  - A1367
VL  - 13
AB  - M.RsrI recognizes the DNA sequence GAATTC and catalyzes the transfer of a methyl group from
AB  - S-adenosylmethionine to the exocyclic amino group of the central adenine to form GamATTC and
AB  - S-adenosylhomocysteine.  Our research focuses on the characterization for the DNA binding,
AB  - catalytic and structural properties of M.RsrI.  First the wild-type protein was purified to
AB  - >95% homogeneity using a simplified procedure involving two chromatographic steps.  Gel-shift
AB  - assays of the protein were then performed on 1 or 5 nM canonical unmethylated, hemimethylated,
AB  - and dimethylated, or control (CTTAAG) 25-mer DNA duplexes in the presence of sinefungin, a
AB  - potent inhibitory analogue of AdoMet.  The following KD values obtained: hemimethylated, 3-7
AB  - nM; unmethylated, 30nM; and dimethylated and control, > 2500 nM.  Some pre-steady state
AB  - kinetic parameters of M.RsrI have been determined.  Upon the addition of enzyme pre-incubated
AB  - with radiolabeled AdoMet, M.RsrI shows a "burst" of methylated product formation equivalent to
AB  - the enzyme concentration in the presence of excess hemimethylated 14-mer DNA and radiolabeled
AB  - AdoMet.  This is followed by a slower step that represents the catalytic turnover (kcat).  The
AB  - dissociation constants for AdoMet (8.4 microM), AdoHcy (3.5 microM), and sinefungin (4.6
AB  - microM) have been determined for M.RsrI using an intrinsic tryptophan fluorescence quenching
AB  - assay.
ER  -

TY  - JOUR
AU  - Szegedi, S.S.
AU  - Reich, N.O.
AU  - Gumport, R.I.
TI  - Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 3962
EP  - 3971
VL  - 28
AB  - RsrI [N6-adenine] DNA methyltransferase (M.RsrI), which recognizes GAATTC and is a member of a
AB  - restriction-modification system in Rhodobacter sphaeroides, was purified to >95% homogeneity
AB  - using a simplified procedure involving two ion exchange chromatographic steps. Electrophoretic
AB  - gel retardation assays with purified M.RsrI were performed on unmethylated, hemimethylated,
AB  - dimethylated or non-specific target DNA duplexes (25 bp) in the presence of sinefungin, a
AB  - potent inhibitory analog of AdoMet. M.RsrI binding was affected by the methylation status of
AB  - the DNA substrate and was enhanced by the presence of the cofactor analog. M.RsrI bound DNA
AB  - substrates in the presence of sinefungin with decreasing affinities: hemimethylated >
AB  - unmethylated > dimethylated >> non-specific DNA. Gel retardation studies with DNA substrates
AB  - containing an abasic site substituted for the target adenine DNA provided evidence consistent
AB  - with M.RsrI extruding the target base from the duplex. Consistent with such base flipping, an
AB  - approximately 1.7-fold fluorescence intensity increase was observed upon stoichiometric
AB  - addition of M.RsrI to hemimethylated DNA containing the fluorescent analog 2-aminopurine in
AB  - place of the target adenine. Pre-steady-state kinetic and isotope-partitioning experiments
AB  - revealed that the enzyme displays burst kinetics, confirmed the catalytic competence of the
AB  - M.RsrI-AdoMet complex and eliminated the possibility of an ordered mechanism where DNA is
AB  - required to bind first. The equilibrium dissociation constants for AdoMet, AdoHcy and
AB  - sinefungin were determined using an intrinsic tryptophan fluorescence-quenching assay.
ER  -

TY  - JOUR
AU  - Szekeres, M.
TI  - Phage-induced development of a site-specific endonuclease in Anacystis nidulans, a cyanobacterium.
JO  - Virology
PY  - 1981
SP  - 1
EP  - 10
VL  - 111
AB  - Anacystis nidulans infected by cyanophage AS-1 produces a site-specific endonuclease cleaving
AB  - double-stranded DNA, as judged from the gel electrophoretic analysis of the reaction products
AB  - and the determination of the terminal nucleotide at the 5'-end of the fragments.  The enzyme
AB  - was purified to near electrophoretic homogeneity.  It has a molecular weight of 40,000 +/-
AB  - 4,000.  Only Mg2+ ions are required for enzyme activity.  Limit digestion was not obtained
AB  - even after extensive digestion of substrate DNA with large amounts of the purified enzyme.
AB  - This suggests that the endonuclease splits the substrate at more than one nucleotide sequence
AB  - with a different efficiency for each sequence.  The following observations suggest that the
AB  - endonuclease takes part in the breakdown of host DNA in the infected cell: purified host DNA
AB  - is degraded by, while cyanophage AS-1 DNA is protected against, the enzyme, and the appearance
AB  - of the endonuclease during the lytic cycle coincides with the onset of intensive degradation
AB  - of host DNA.
ER  -

TY  - JOUR
AU  - Szekeres, M.
AU  - Matveyev, A.V.
TI  - Cleavage and sequence recognition of 2,6-diaminopurine-containing DNA by site-specific endonucleases.
JO  - FEBS Lett.
PY  - 1987
SP  - 89
EP  - 94
VL  - 222
AB  - The susceptibility of 2,6-diaminopurine (DAP)-containing bacteriophage DNA to
AB  - several restriction and other endonucleases was examined.  With the only
AB  - exception of TaqI, these enzymes did not accept the modified base as a
AB  - substitute for adenine.  The phage DNA was extensively fragmented by the
AB  - restriction endonucleases which recognized only G and C-containing sites.
AB  - 5'-terminal analysis of the MspI and SmaI fragments revealed that d(DAP-T)
AB  - basepairs can be mistaken by some enzymes for d(G-C) pairs.
ER  -

TY  - JOUR
AU  - Szekeres, M.
AU  - Szmidt, A.E.
AU  - Torok, I.
TI  - Evidence for a restriction/modification-like system in Anacystis nidulans infected by cyanophage AS-1.
JO  - Eur. J. Biochem.
PY  - 1983
SP  - 137
EP  - 141
VL  - 131
AB  - Anacystis nidulans infected by AS-1 cyanophage contains an endonuclease (AS-1
AB  - endonuclease) which splits host DNA but not AS-1 phage DNA [Szekeres, M. (1981)
AB  - Virology, 111, 1-10].  AS-1 phage DNA proved to be resistant not only to AS-1
AB  - endonuclease but also to a number of restriction endonucleases the recognition
AB  - sites of which contain a central dG-dC dinucleotide.  Since an unmodified
AB  - 5'dG-dC dinucleotide was shown to be present at the sites at which DNA is
AB  - cleaved by AS-1 endonuclease, the results suggest that the sites attacked
AB  - preferentially by the AS-1 endonuclease are specifically protected on the AS-1
AB  - DNA molecule.  The modification of AS-1 DNA was shown to occur specifically in
AB  - infected Anacystis because AS-1 DNA fragments which are normally resistant to
AB  - AS-1 endonuclease became susceptible to this enzyme if inserted into pBR322
AB  - plasmid and cloned in Escherichia coli.  AS-1 DNA was shown to contain about 5%
AB  - of a modified nucleotide which was not 5-methyldeoxycytidylic acid.  Results
AB  - presented and our earlier data suggest that in Anacystis infected by AS-1
AB  - phage, a restriction/modification-like system operates which is able to
AB  - elimminate 'unwanted' (host) DNA selectively.
ER  -

TY  - JOUR
AU  - Szeto, M.D.
AU  - Boissel, S.J.S.
AU  - Baker, D.
AU  - Thyme, S.B.
TI  - Mining Endonuclease Cleavage Determinants in Genomic Sequence Data.
JO  - J. Biol. Chem.
PY  - 2011
SP  - 32617
EP  - 32627
VL  - 286
AB  - Homing endonucleases have great potential as tools for targeted gene therapy and gene
AB  - correction, but identifying variants of these enzymes
AB  - capable of cleaving specific DNA targets of interest is necessary
AB  - before the widespread use of such technologies is possible. We
AB  - identified homologues of the LAGLIDADG homing endonuclease I-AniI and
AB  - their putative target insertion sites by BLAST searches followed by
AB  - examination of the sequences of the flanking genomic regions. Amino
AB  - acid substitutions in these homologues that were located close to the
AB  - target site DNA, and thus potentially conferring differences in target
AB  - specificity, were grafted onto the I-AniI scaffold. Many of these
AB  - grafts exhibited novel and unexpected specificities. These findings
AB  - show that the information present in genomic data can be exploited for
AB  - endonuclease specificity redesign.
ER  -

TY  - JOUR
AU  - Szilak, L.
AU  - Der, A.
AU  - Deak, F.
AU  - Venetianer, P.
TI  - Kinetic characterization of the EcaI methyltransferase.
JO  - Eur. J. Biochem.
PY  - 1993
SP  - 727
EP  - 733
VL  - 218
AB  - A kinetic analysis of the EcaI adenine-N6-specific methyltransferase (MTase) is presented. The
AB  - enzyme catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the
AB  - adenine of the GGTNACC sequence with a random rapid-equilibrium mechanism. Experiments with a
AB  - synthetic, 14-bp DNA substrate suggest that recognition of the specific site of DNA occurs
AB  - after the binding of AdoMet. Proton concentration does not affect the dissociation constant of
AB  - AdoMet while Vm and the dissociation constant of DNA show a maximum around pH 8. Increasing
AB  - the amount of S-adenosyl-L-homocysteine decreases the inhibitory effect of methylated DNA
AB  - which proves the active role of AdoMet in site recognition. Experiments with hemimethylated
AB  - DNA show that the methylase binds the double-stranded DNA asymmetrically.
ER  -

TY  - JOUR
AU  - Szilak, L.
AU  - Finta, C.
AU  - Patthy, A.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Self-methylation of BspRI DNA-methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1994
SP  - 2876
EP  - 2881
VL  - 22
AB  - The DNA (cytosine-5)-methyltransferase (m5C-MTase) M.BspRI is able to accept the methyl group
AB  - from the methyl donor S-adenosyl-L-methionine (AdoMet) in the absence of DNA. Transfer of the
AB  - methyl group to the enzyme is a slow reaction relative to DNA methylation. Self-methylation is
AB  - dependent on the native conformation of the enzyme and is inhibited by
AB  - S-adenosyl-L-homocysteine, DNA and sulfhydryl reagents. Amino acid sequencing of proteolytic
AB  - peptides obtained from M.BspRI, which had been methylated with [methyl-3H]AdoMet, and thin
AB  - layer chromatography of the modified amino acid identified two cysteines, Cys156 and Cys181
AB  - that bind the methyl group in the form of S-methylcysteine. One of the acceptor residues,
AB  - Cys156 is the highly conserved cysteine which plays the role of the catalytic nucleophile of
AB  - m5C-MTases.
ER  -

TY  - JOUR
AU  - Szilak, L.
AU  - Finta, C.
AU  - Patthy, A.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Self-methylation of the M.BspRI methyltransferase.
JO  - Gene
PY  - 1995
SP  - 105
EP  - 105
VL  - 157
AB  - In the absence of DNA substrate, the DNA methyltransferase (MTase) M.BspRI can methylate
AB  - itself using the methyl donor S-adenosyl-L-methionine (AdoMet).  The methyl group is
AB  - transferred to two Cys residues of the MTase.
ER  -

TY  - JOUR
AU  - Szilak, L.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Cloning and nucleotide sequence of the genes coding for the Sau96I restriction and modification enzymes.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 4659
EP  - 4664
VL  - 18
AB  - The genes coding for the GGNCC specific Sau96I restriction and modification
AB  - enzymes were cloned and expressed in E. coli.  The DNA sequence predicts a 430
AB  - amino acid protein (Mr: 49,252) for the methyltransferase and a 261 amino acid
AB  - protein (Mr: 30,486) for the endonuclease.  No protein sequence similarity was
AB  - detected between the Sau96I methyltransferase and endonuclease.  The
AB  - methyltransferase contains the sequence elements characteristic for m5C
AB  - methyltransferases.  In addition to this, M.Sau96I shows similarity, also in
AB  - the variable region with one m5C-methyltransferase (M.SinI) which has closely
AB  - related recognition specificity (GGA/TCC).  M.Sau96I methylates the internal
AB  - cytosine within the GGNCC recognition sequence.  The Sau96I endonuclease
AB  - appears to act as a monomer.
ER  -

TY  - JOUR
AU  - Szilak, L.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - Purification and biochemical characterization of the EcaI DNA methyltransferase.
JO  - Eur. J. Biochem.
PY  - 1992
SP  - 391
EP  - 397
VL  - 209
AB  - The EcaI GGTNACC-specific DNA-adenine modification methyltransferase has been purufied to
AB  - apparent homogeneity. The active form of the DNA methyltransferase is a single polypeptide.
AB  - The enzyme has a pH optimum at pH 8.0 and a temperature optimum at 25oC. EcaI DNA
AB  - methyltransferase transfers one methyl group to the adenine of the recognition site in a
AB  - single binding event. The Km was 170 nM for DNA and 1.8 microM for the methyl donor
AB  - S-adenosylmethionine. Methylated DNA is a competitive inhibitor with respect to DNA (Ki-3.5
AB  - nM). The other product of the DNA-methylation reaction, S-adenosylhomocysteine was found to be
AB  - a competitive inhibitor with respect to S-adenosylmethionine (Ki= 2.7 uM). The
AB  - S-adenosylmethionine analog sinefungin was shown to be a very strong inhibitor (Ki = 3.5 nM)
AB  - of the DNA methyltransferase reaction.
ER  -

TY  - JOUR
AU  - Sznyter, L.A.
AU  - Brooks, J.E.
TI  - The characterization and cloning of the NotI restriction-modification system.
JO  - Heredity
PY  - 1988
SP  - 308
EP  - 308
VL  - 61
AB  - NotI, a Type II restriction-modification system from the actinomycete Nocardia
AB  - otitidis-caviarum, recognizes the sequence GCGGCCGC.  We are currently purifying and
AB  - characterizing the proteins of this system.  The endonuclease, which cleaves at GC^GGCCGC, has
AB  - been sized by gel filtration and estimated to be approximately 85,000 daltons.  The NotI
AB  - methylase protein has been partially purified and we are in the process of determining its
AB  - size as well as the site and type (N-4 or C-5) of modification it provides.  The N. otitidis
AB  - genomic DNA has been purified and analyzed by HPLC analysis for base composition and for the
AB  - presence of modified bases.  Two approaches are being used to clone the NotI system.  First
AB  - genomic libraries constructed in E. coli are being selected for methylase expression.  Second,
AB  - genomic libraries will also be made and selected in Streptomyces lividans.  In addition to
AB  - selection for methylase expression, we also will be selecting the libraries with phage.  This
AB  - approach has been successfully used in cloning the SalI restriction-modification system.
ER  -

TY  - JOUR
AU  - Sznyter, L.A.
AU  - Brooks, J.E.
TI  - The characterization and cloning of the EagI restriction-modification system.
JO  - Gene
PY  - 1988
SP  - 53
EP  - 53
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Sznyter, L.A.
AU  - Marcus, A.M.
AU  - Brooks, J.E.
TI  - The cloning and characterization of the EagI restriction-modification system.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 180
EP  - 180
VL  - 89
AB  - EagI is a Type II restriction-modification system from the gram-negative
AB  - enteric bacterium Enterobacter agglomerans.  It recognizes the sequence CGGCCG
AB  - with the endonuclease cleaving at C^GGCCG.  The genomic DNA from this organism
AB  - has been purified and analyzed by HPLC analysis for base composition and for
AB  - the presence of modified bases.  The EagI system has been cloned on a 2.9 kb
AB  - PstI fragment in pLSN3 (a pBR322 derivative containing three NotI sites) by
AB  - selection with the NotI endonuclease.  The 2.9kb PstI fragment was then cloned
AB  - into pUC19 in both orientations.  On this higher copy plasmid, an increase of
AB  - endonuclease activity was found in the crude extracts.  The level of increase
AB  - is dependent on orientation.  These clones are currently being characterized.
AB  - We have explored the Mcr phenotype of the most active EagI containing clone and
AB  - find that it is highly restricted by mcrB.  The boundaries of the genes have
AB  - been assigned by deletion subcloning and Tn5 mutagenesis.  The protein products
AB  - of the EagI system are also being characterized.  The endonuclease has been
AB  - purified and sized by gel filtration.  EagI is estimated to be approximately
AB  - 78,000 daltons.  The EagI methylase protein has been purified and the size as
AB  - well as site and type (N-4 or C-5) of modification it provides is being
AB  - determined.
ER  -

TY  - JOUR
AU  - Sznyter, L.A.
AU  - Slatko, B.
AU  - Moran, L.
AU  - O'Donnell, K.H.
AU  - Brooks, J.E.
TI  - Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 8249
EP  - 8266
VL  - 15
AB  - The DdeI restriction-modification system was previously cloned and has been
AB  - maintained in E. coli on two separate and compatible plasmids.  The nucleotide
AB  - sequence of the endonuclease and methylase genes has now been determined; it
AB  - predicts proteins of 240 amino acids, Mr=27,808, and 415 amino acids,
AB  - Mr=47,081, respectively.  Inspection of the DNA sequence shows that the 3' end
AB  - of the methylase gene had been deleted during cloning.  The clone containing
AB  - the complete methylase gene was made and compared to that containing the
AB  - truncated gene; only clones containing the truncated form support the
AB  - endonuclease gene in E. coli.  Bal-31 deletion studies show that methylase
AB  - expression in the Dde clones is also dependent upon orientation of the gene
AB  - with respect to pBR322.  The truncated and complete forms of the methylase
AB  - protein were purified and compared; the truncated form appears to be more
AB  - stable and active in vitro.  Finally, comparison of the deduced amino acid
AB  - sequence of M.DdeI with that of other known cytosine methylases shows
AB  - significant regions of homology.
ER  -

TY  - JOUR
AU  - Sznyter, L.A.
AU  - Vaccaro, C.M.
AU  - Jager-Quinton, T.
AU  - Wilson, G.
AU  - Brooks, J.E.
TI  - Cloning and characterization of the SphI restriction-modification system from S. phaeochromogenes.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 361
EP  - 361
VL  - 0
AB  - SphI, a Type II restriction-modification system from the actinomycete Streptomyces
AB  - phaeochromogenes, recognizes the sequence GCATGC.  The endonuclease cleaves at GCATG/C leaving
AB  - a 3' four base overhang.  A 5.4kb insert carrying the methylase gene has been cloned into the
AB  - PstI site of pBR322 and expressed in E. coli at a low level as evidenced by incomplete
AB  - modification of chromosomal DNA and lack of modification of phage DNA in vivo.  The clone has
AB  - no endonuclease activity.  The plasmid has been extensively mapped; Tn-5 insertion mutagenesis
AB  - is being used to locate the methylase gene.  The fragment is also being positioned by Southern
AB  - hybridization onto the S. phaeochromogenes chromosome.  Attempts will be made to clone and
AB  - express the complete system in Streptomyces.
ER  -

TY  - JOUR
AU  - Szomolanyi, I.
AU  - Kiss, A.
AU  - Venetianer, P.
TI  - Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli.
JO  - Gene
PY  - 1980
SP  - 219
EP  - 225
VL  - 10
AB  - The gene coding for the sequence-specific modification methylase methM - BspI
AB  - of Bacillus sphaericus R has been cloned in Escherichia coli by means of
AB  - plasmid pBR322.  The selection was based on the expression of the cloned gene
AB  - which rendered the recombinant plasmid resistant to BspI restriction
AB  - endonuclease cleavage.  The gene is carried by a 9 kb BamHI fragment and by a
AB  - smaller 2.5 kb EcoRI fragment derived from the BamHI fragment.  The
AB  - Bsp-specific methylase level was found to be higher in the recombinant clones
AB  - than in the parental strain.  The methylase gene is probably located on the
AB  - Bacillus sphaericus chromosome, and not on a plasmid known to be carried by
AB  - this strain.  The recombinant clones do not exhibit any BspI restriction
AB  - endonuclease activity.
ER  -

TY  - JOUR
AU  - Szwagierczak, A.
AU  - Brachmann, A.
AU  - Schmidt, C.S.
AU  - Bultmann, S.
AU  - Leonhardt, H.
AU  - Spada, F.
TI  - Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5-hydroxymethylcytosine.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 5149
EP  - 5156
VL  - 39
AB  - In mammalian genomes a sixth base, 5-hydroxymethylcytosine ((hm)C), is generated by enzymatic
AB  - oxidation of 5-methylcytosine ((m)C). This
AB  - discovery has raised fundamental questions about the functional relevance
AB  - of (hm)C in mammalian genomes. Due to their very similar chemical
AB  - structure, discrimination of the rare (hm)C against the far more abundant
AB  - (m)C is technically challenging and to date no methods for direct
AB  - sequencing of (hm)C have been reported. Here, we report on a purified
AB  - recombinant endonuclease, PvuRts1I, which selectively cleaves
AB  - (hm)C-containing sequences. We determined the consensus cleavage site of
AB  - PvuRts1I as (hm)CN(11-12)/N(9-10)G and show first data on its potential to
AB  - interrogate (hm)C patterns in mammalian genomes.
ER  -

TY  - JOUR
AU  - Szybalski, W.
TI  - Modifying specificities of restriction enzymes.
JO  - Biotechnology: Bridging Research and Applications
PY  - 1991
SP  - 371
EP  - 376
VL  - 0
AB  - For the last five years, our laboratory has been studying various aspects of
AB  - controlled cleavage of DNA, both for (1) the 50 bp-10 kb range of
AB  - single-stranded (ss) and double-stranded (ds) DNA fragments, plasmids or
AB  - phages, and (2) for very large genomes of bacteria, yeast and higher
AB  - eukaryotes.  We are using commerical restriction enzymes (ENases) either (i) of
AB  - the class-IIS variety (ENase-IIS) (Szybalski, 1985), where the recognition site
AB  - on the DNA for the ENase is separated by several base pairs from the cleavage
AB  - site, together with an adapter oligodeoxynucleotide (oligo), or (ii) various
AB  - combinations of a particular ENase, its cognate methyltransferase (MTase) and
AB  - DNA-binding protein whose binding site contains the corresponding ENase/MTase
AB  - recognition site.  The ENase-IIS enzymes were used either for precise cutting
AB  - (Podhajska and Szybalski, 1985) or for precise trimming of DNA (Hasan et al,
AB  - 1986), whereas the MTase/ENase/DNA-binding protein combination was used for
AB  - very rare cuts in large genomes (Koob et al., 1968; Grimes et al., 1990; Koob
AB  - and Szybalski, 1990).
ER  -

TY  - JOUR
AU  - Szybalski, W.
TI  - Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligodeoxynucleotide and enzyme moieties.
JO  - Gene
PY  - 1985
SP  - 169
EP  - 173
VL  - 40
AB  - Class IIS restriction endonucleases cleave double-stranded (ds) DNA at precise
AB  - distances from their recognition sequences.  A method is proposed which
AB  - utilizes this separation between the recognition site and the cut site to allow
AB  - a class IIS enzyme, e.g., FokI, to cleave practically any predetermined
AB  - sequence by combining the enzyme with a properly designed oligodeoxynucleotide
AB  - adapter.  Such an adapter is constructed from the constant recognition site
AB  - domain (a hairpin containing the ds sequence, e.g., G/C G/C A/T T/A G/C for
AB  - FokI) and a variable, single-stranded (ss) domain complementary to the ss
AB  - sequence to be cleaved (at 9 and 13 nucleotides on the paired strands from the
AB  - recognition sequence in the exampled of FokI).  The ss sequence designated to
AB  - be cleaved could be provided by ss phage DNA (e.g., M13), gapped ds plasmids,
AB  - or supercoiled ds plasmids that were alkali denatured and rapidly neutralized.
AB  - Combination of all three components, namely the class IIS enzyme, the ssDNA
AB  - target sequence, and the complementing adapter, would result in target DNA
AB  - cleavage at the specific predetermined site.  The target ss DNA could be
AB  - converted to the precisely cleaved ds DNA by DNA polymerase, utilizing the
AB  - adapter oligodeoxynucleotide as primer.  This novel procedure represents the
AB  - first example of changing enzyme specificity by synthetic design.  A
AB  - practically unlimited assortment of new restriction specificities could be
AB  - produced.  The method should have many specific and general applications when
AB  - its numerous ramification are exploited.
ER  -

TY  - JOUR
AU  - Szybalski, W.
AU  - Blumenthal, R.M.
AU  - Brooks, J.E.
AU  - Hattman, S.
AU  - Raleigh, E.A.
TI  - Nomenclature for bacterial genes coding for class-II restriction endonucleases and modification methyltransferases.
JO  - Gene
PY  - 1988
SP  - 279
EP  - 280
VL  - 74
AB  - A proposed nomenclature for restriction enzyme and methylase genes.
ER  -

TY  - JOUR
AU  - Szybalski, W.
AU  - Kim, S.C.
AU  - Hasan, N.
AU  - Podhajska, A.J.
TI  - Class-IIS restriction enzymes - a review.
JO  - Gene
PY  - 1991
SP  - 13
EP  - 26
VL  - 100
AB  - Class-IIS restriction enzymes (ENases-IIS) interact with two discrete sites on
AB  - double-stranded DNA: the recognition site, which is 4-7 bp long, and the
AB  - cleavage site, usually 1-20 bp away from the recognition site.  The recognition
AB  - sequences of ENases-IIS are totally (or partially) asymmetric and all of the
AB  - characterized ENases-IIS are monomeric.  A total of 35 ENases-IIS are described
AB  - (80, if all isoschizomers are taken into consideration) together with ten
AB  - related ENases (class IIT), and 15 cognate methyltransferases (MTases-IIS).
AB  - The physical, chemical, and molecular properties of the ENases-IIS and
AB  - MTases-IIS are reviewed and many unique applications of this class of enzymes
AB  - are described, including: precise trimming of DNA; retrieval of cloned
AB  - fragments; gene assembly; use as a universal restriction enzyme; cleavage of
AB  - single-stranded DNA; detection of point mutations; tandem amplification;
AB  - printing-amplification reaction; and localization of methylated bases.
ER  -

TY  - JOUR
AU  - Szybalski, W.
AU  - Skalka, A.
TI  - Nobel prizes and restriction enzymes.
JO  - Gene
PY  - 1978
SP  - 181
EP  - 182
VL  - 4
AB  - We have two reasons to rejoice in the wise choices made by the Nobel Committee in 1978.  The
AB  - discovery of the restriction enzymes and their application in genetic mapping, a main topic of
AB  - our journal, were selected for this award, and one of our Editors, Dr. Hamilton O. Smith, was
AB  - honored as one of the three recipients.
ER  -

TY  - JOUR
AU  - Szyf, M.
TI  - Targeting DNA methyltransferase in cancer.
JO  - Cancer Metastasis Rev.
PY  - 1998
SP  - 219
EP  - 231
VL  - 17
AB  - DNA methyltransferase is an enzyme responsible for generating and maintaining DNA methylation
AB  - patterns.  DNA methylation patterns control different genome functions, thus they are an
AB  - important component of the epigenetic information.  It has been recently postulated that DNA
AB  - methyltransferase plays an important role in oncogenesis and that it is a candidate target for
AB  - anticancer therapy.  This commentary discusses the possible mechanisms through which DNA
AB  - methyltransferase participates in oncogenesis and the rationale for targeting it in cancer.
ER  -

TY  - JOUR
AU  - Szyf, M.
TI  - DNA methylation properties: consequences for pharmacology.
JO  - Trends Pharmacol. Sci.
PY  - 1994
SP  - 233
EP  - 238
VL  - 15
AB  - DNA methylation plays an important role in controlling the profile of gene expression of
AB  - mammalian cells. The hypothesis presented in this article is that DNA methylation patterns are
AB  - determined by an interplay between the level of DNA methyltransferase and demethylase
AB  - activities and site-specific signals. The expression of the DNA methyltransferase gene is
AB  - regulated with the proliferative state of the cell and it is upregulated by cellular oncogenic
AB  - pathways, resulting in hypermethylation and repression of tumour-suppressing loci. DNA
AB  - methyltransferase inhibitors would inhibit the excessive activity of DNA methyltransferase in
AB  - cancer cells and induce the original cellular programme of tumour suppression. They can also
AB  - be used to turn on alternative programmes of gene expression. Specific DNA methyltransferase
AB  - antagonists might provide us with therapeutic agents directed at a nodal point of regulation
AB  - of genetic information.
ER  -

TY  - JOUR
AU  - Szyf, M.
TI  - The role of DNA methyltransferase 1 in growth control.
JO  - Front. Biosci.
PY  - 2001
SP  - D599
EP  - D609
VL  - 6
AB  - Vertebrate DNA contains in addition to the four bases comprising the genetic information a
AB  - modified base, 5-methylcytosine that plays an important role in the epigenome. The methylated
AB  - bases form a pattern of methylation that is cell specific and is faithfully inherited during
AB  - cell division. The enzyme DNA methyltransferase 1 DNMT1 is responsible for copying the DNA
AB  - methylation pattern but other de novo methyltransferase as well as demethylases might also be
AB  - involved. Multiple mechanisms are in place to ensure the coordinate inheritance of the DNA
AB  - methylation pattern with DNA replication. There is a bilateral relationship between the cell
AB  - cycle and DNMT1. The expression of DNMT1 is tightly regulated with the cell cycle while the
AB  - expression of DNMT1 can affect the cell cycle. DNMT1 protein might regulate cell cycle events
AB  - by mechanisms that are independent of its DNA methylation activity through its multiple
AB  - protein-protein interactions. The unique position of DNMT1 in the cell cycle is consistent
AB  - with the hypothesis that it plays an important role in cancer.
ER  -

TY  - JOUR
AU  - Szyf, M.
TI  - DNA methylation and cancer therapy.
JO  - Drug Resistance Updates
PY  - 2003
SP  - 341
EP  - 353
VL  - 6
AB  - Vertebrate DNA is modified by methyl moieties at the 5'-position of cytosine rings residing
AB  - in the di-nucleotide sequence CpG. Approximately
AB  - 80% of CpG dinucleotide sequences are methylated. The pattern of
AB  - distribution of methylated CGs is cell-type specific and correlates with
AB  - gene expression programming and chromatin structure. Three kinds of
AB  - seemingly contradictory aberrations in DNA methylation are observed in
AB  - cancer, global hypomethylation, and regional hypermethylation and
AB  - deregulated level of expression of DNA methyltransferases. It was
AB  - previously proposed that the DNA methylation machinery is a candidate
AB  - target for anticancer therapy. Inhibition of hypermethylation was the
AB  - first therapeutic target. However, recent data suggests that inhibition of
AB  - DNA methylation might have untoward effects such as induction of genes
AB  - involved in metastasis. This review discusses the relative role of the
AB  - three levels of alteration in the DNA methylation in cancer, proposes a
AB  - unified hypothesis on the relative roles of increased DNA
AB  - methyltransferase as well as the coexistence of hypo -and hyper-
AB  - methylation in cancer and its possible implications on anticancer therapy.
ER  -

TY  - JOUR
AU  - Szyf, M.
TI  - The DNA methylation machinery as a therapeutic target.
JO  - Curr. Drug Targets
PY  - 2000
SP  - 101
EP  - 118
VL  - 1
AB  - Pharmacology and therapeutics have traditionally focused on altering the activity of specific
AB  - proteins that play an important physiological role either to counteract disease processes or
AB  - to achieve changes in physiology that are of benefit to the patient.  The explosion in our
AB  - understanding of gene expression programs opens up new horizons for pharmacological
AB  - intervention.  Key processes reversibly controlling genetic programs are attractive drug
AB  - targets.  DNA methylation is a fundamental feature of genomes and the control of their
AB  - function and is therefore a candidate for pharmacological manipulation that might have
AB  - important therapeutic advantage.  This review argues that DNA methylation plays an important
AB  - role in the control of genomic processes, suggests how the DNA methylation machinery is
AB  - involved in cancer, identifies the enzymatic processes that are a target for drug
AB  - intervention, proposes potential therapeutic utilities for agents that manipulate the DNA
AB  - methylation machinery and discusses novel drugs that target the DNA methylation machinery.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Avraham-Haetzni, K.
AU  - Reifman, A.
AU  - Shlomai, J.
AU  - Kaplan, F.
AU  - Oppenheim, A.
AU  - Razin, A.
TI  - DNA methylation pattern is determined by the intracellular level of the methylase.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 3278
EP  - 3282
VL  - 81
AB  - Extrachromosomal plasmid DNA is transiently undermethylated in Escherichia coli during
AB  - amplification in the presence of chloramphenicol. In addition, undermethylation of phage
AB  - lambda DNA was observed after thermal induction of a lambda cI857 lysogen while the integrated
AB  - lambda phage DNA was found to be fully methylated. these methylation pattern changes occur
AB  - under conditions (extensive replication) in which the intracellular methylase level becomes
AB  - limiting. In an E. coli strain that harbors a plasmid that carries the dam methylase gene and
AB  - therefore overproduces dam methylase, there is no undermethylation of dam sites in either of
AB  - the extrachromosomal DNAs. The sites that are methylated by the mec methylase in both plasmid
AB  - and lambda phage DNAs were undermethylated in the dam overproducer as well. These results
AB  - indicate that the intracellular level of the E. coli methylase determines the DNA methylation
AB  - pattern.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Bigey, P.
TI  - Oligonucleotides as inhibitors of DNA methyltransferase: novel antitumor drugs.
JO  - Curr. Res. Mol. Ther.
PY  - 1998
SP  - 93
EP  - 101
VL  - 1
AB  - DNA MeTase is now emerging as an important new therapeutic target.  The recent understanding
AB  - of its critical role in development of cancer leads us to propose that modulation of this
AB  - enzyme will be of therapeutic value.  The hairpin oligonucleotide inhibitors discussed in this
AB  - review are, to our knowledge, the first representatives of novel DNA MeTase inhibitors that
AB  - are bona fide substrate analogs.  They also constitute a new example of the use of DNA as
AB  - antagonists of natural ligands of nuclear proteins.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Gruenbaum, Y.
AU  - Urieli-Shoval, S.
AU  - Razin, A.
TI  - Studies on the biological role of DNA methylation:  V. The pattern of E. coli DNA methylation.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 7247
EP  - 7259
VL  - 10
AB  - The distribution of the methylatable sites GATC and CCA/TGG was studied by analyzing the
AB  - molecular average size of restriction fragments of E. coli DNA. Both sites were found to be
AB  - randomly distributed, reflecting a random pattern of methylation. The methylation pattern of
AB  - specific sequences such as the origin of replication and rRNA genes has been studied in wild
AB  - type E. coli and a methylation deficient (dam- dcm-) mutant. These sequences were found to be
AB  - methylated in wild type cells and unmethylated in the mutant indicating that there is no
AB  - effect of the state of methylation of these sequences on their expression. Analysis of the
AB  - state of methylation of GATC sites in newly replicating DNA using the restriction enzyme DpnI
AB  - (cleaves only when both strands are methylated) revealed no detectable hemimethylated DNA
AB  - suggesting that methylation occurs at the replication fork. Taking together the results
AB  - presented here and previously published data, we arrive at the conclusion that the most likely
AB  - function of E. coli DNA methylations is probably in preventing nuclease activity.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Knox, D.J.
AU  - Milutinovic, S.
AU  - Slack, A.D.
AU  - Araujo, F.D.
TI  - How does DNA methyltransferase cause oncogenic transformation?
JO  - Ann. NY Acad. Sci.
PY  - 2000
SP  - 156
EP  - 174
VL  - 910
AB  - Global hypomethylation of genes and repetitive sequences, as well as hypermethylation of
AB  - certain genes known to be involved in tumor suppression, are observed concurrently in cancer
AB  - cells. Aberrant expression of DNA methyltransferase 1 (dnmt1) is a downstream effector of
AB  - multiple tumorigenic pathways, and several data suggest that dnmt1 plays a causal role in
AB  - these pathways. These data raise two critical questions: Why does ectopic expression of dnmt1
AB  - transform cells? and How can global hypomethylation exist in a cell that bears high levels of
AB  - DNMT1 activity? It is proposed that DNMT1 induces cellular transformation by a mechanism that
AB  - does not involve DNA methylation and that the low level of methylation in cancer cells is a
AB  - result of induction of a DNA demethylase in these cells. Both DNMT1 and the demethylase play a
AB  - causal role in cellular transformation and are candidate anticancer targets.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Meisels, E.
AU  - Razin, A.
TI  - Biological role of DNA methylation:  sequence-specific single-strand breaks associated with hypomethylation of GATC sites in Escherichia coli DNA.
JO  - J. Bacteriol.
PY  - 1986
SP  - 1487
EP  - 1490
VL  - 168
AB  - The effect of methylation of GATC sites in Escherichia coli DNA on the formation of
AB  - single-strand breaks was studied with dam+, dam mutant, and Dam-overproducer strains.
AB  - Single-strand breaks have been observed in dam mutant cells predominantly at TpT and, to a
AB  - lesser extent, at CpC. In dam mutant cells harboring pTP166 (a plasmid containing the dam
AB  - gene), no such nicks were observed.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Ramchandani, S.
AU  - MacLeod, R.
AU  - Croteau, S.
AU  - von Hofe, E.
TI  - Antisense oligonucleotides directed against DNA methyltransferase inhibit tumorigenesis.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1996
SP  - 353
EP  - 353
VL  - 37
AB  - We have previously shown that DNA methyltransferase is a downstream
AB  - effector
AB  - of the Ras oncogenic signaling pathway.  To test the hypothesis that inhibition of DNA
AB  - MeTase
AB  - could reverse tumorigenesis and to test the possibility  that DNA MeTase could serve as an
AB  - anticancer target, we have treated a number of human and mouse cancer cell lines with
AB  - antisense
AB  - phosphorothioate modified oligonucleotides directed at the translation initiation region of
AB  - either
AB  - human or mouse DNA MeTase mRNA as well as control oligonucleotides.  The cell lines
AB  - tested
AB  - were Y1, a mouse adrenocortical cell carcinoma, NCI-H596, a human lung
AB  - adenosquamous
AB  - carcinoma, NCI-H496, a lung small cell carcinoma nd SF126 a human glioma.  The
AB  - antisense
AB  - oligonucleotides inhibited DNA MeTase mRNA, DNA MeTase activity as well as DNA
AB  - methylation in a dose dependent manner (0.1-20 uM).  Focus formation in soft agar was
AB  - dramatically inhibited by DNA MeTase antisense oligonucleotides.  Tumor formation in
AB  - nude mice
AB  - (the NCI-H446 line) was inhibited when the cells expressed an exogenously introduced
AB  - antisense
AB  - DNA MeTase RNA whereas control cells formed tumors.  Injection of DNA MeTase
AB  - antisense
AB  - oligonucleotides (ip) (0.55-30 mg/kg every 48 hours) delayed tumor formation by NCI-
AB  - H446 cells
AB  - in nude mice and by Y1 cells in syngeneic LAF-1 mice.  These studies support the
AB  - hypothesis that
AB  - inhibition of DNA MeTase could reverse tumorigenesis and that DNA MeTase is a target
AB  - for
AB  - anticancer therapy.
ER  -

TY  - JOUR
AU  - Szyf, M.
AU  - Theberge, J.
TI  - Mammalian cells contain a general (CpG) DNA demethylating activity.
JO  - Mol. Biol. Cell
PY  - 1993
SP  - 74a
EP  - 74a
VL  - 4
AB  - A hallmark of vertebrate DNA is the fact that a significant fraction of the cytosines in the
AB  - dinucleotide sequence CpG is methylated generating a pattern of methylation that is site and
AB  - tissue specific. The pattern of methylation is formed during development by de novo
AB  - methylation and demethylation processes. The biochemical mechanisms that are responsible for
AB  - demethylation are unclear. To address the question whether mammalian cells contain a general
AB  - activity that can remove methyl groups from CpG sequences, we transfected an in vitro
AB  - methylated SK plasmid (wih SS1 methylase) into a mouse embryonal teratocarcinoma cell line and
AB  - analyzed the state of methylation of the transfected demethylation between one and two days
AB  - after transfection as judged by a HpaII/MspI analysis of the transfected DNA. All HpaII sites
AB  - were demethylated suggesting that the demethylase activity exhibits limited specificity under
AB  - these conditions. However, demethylation of areas that contain a low density of CpG sequences
AB  - is inefficient relative to that of CpG dense regions. The demethylase activity is limiting in
AB  - embryonal cells as determined by a dose response curve. Demethylase activity is not restricted
AB  - to embryonal cells and demethylation of plasmid DNA was observed in 10T1/2 and C2 cell lines.
AB  - Previous publications have suggested that demethylation involves a base excision repair
AB  - process rather than an active removal of methyl groups. To address this question we developed
AB  - an in vitro assay for demethylation. Using this assay we show that demethylation of methylated
AB  - SK plasmid DNA by a P19 nuclear extract does not require the presence of dNTPs or dCTP. This
AB  - implies that demethylation involves an active removal of methyl groups from DNA. Our results
AB  - demonstrate that parallel to the general DNA methylase activity, mammalian cells contain a
AB  - general DNA demethylase activity. We suggest that the specificity of demethylation during the
AB  - developmental process is determined by factors that limit the accessibility of DNA to the DNA
AB  - demethylase machinery.
ER  -

TY  - JOUR
AU  - Tabata, M.
AU  - Nakajima, K.
AU  - Nyarko, E.
TI  - Metalloporphyrin mediated DNA cleavage by a low concentration of HaeIII restriction enzyme.
JO  - J. Inorg. Biochem.
PY  - 2000
SP  - 383
EP  - 389
VL  - 78
AB  - The plasmid DNA scission by the restriction enzyme HaeIII was investigated in the presence of
AB  - tetrakis(1-methylpyridinium-4-yl)porphyrin (H2TMPyP) and its manganese(III), iron(III),
AB  - nickel(II), cobalt(III) and zinc(II) derivatives. The effect of metalloporphyrins on plasmid
AB  - DNA cleavage was ascertained by gel electrophoresis. UV-Vis absorption spectroscopy and
AB  - circular dichroism (CD) spectroscopy. In the absence of the metalloporphyrins, plasmid DNA
AB  - scission did not occur in the presence of a low concentration of HaeIII (0.2 units microL(-1))
AB  - at 37 degrees C after 1 h incubation. However, DNA cleavage occurred in the presence of the
AB  - metalloporphyrins and HaeIII (0.2 units microL(-1)) at 37 degrees C after 1 h incubation. Gel
AB  - electrophoresis results indicate the catalytic effect of metalloporphyrins (Mn(III)-,
AB  - Fe(III)-, Co(III)- and Zn(II)TMPyP) by binding to both DNA and the enzyme through
AB  - electrostatic interaction, which was confirmed by the change in UV-Vis and CD spectra. A
AB  - mechanism for the enhanced DNA cleavage is proposed.
ER  -

TY  - JOUR
AU  - Tabata, M.
AU  - Ohhata, S.
AU  - Kawasumi, T.
AU  - Nikawadori, Y.
AU  - Kishida, K.
AU  - Sato, T.
AU  - Ohtsubo, Y.
AU  - Tsuda, M.
AU  - Nagata, Y.
TI  - Complete Genome Sequence of a gamma-Hexachlorocyclohexane Degrader, Sphingobium sp. Strain TKS, Isolated from a gamma-Hexachlorocyclohexane-Degrading Microbial  Community.
JO  - Genome Announcements
PY  - 2016
SP  - e00247
EP  - e00216
VL  - 4
AB  - Here, we report the complete genome sequence of a gamma-hexachlorocyclohexane (gamma-HCH)
AB  - degrader,Sphingobiumsp. strain TKS, which was isolated from a
AB  - gamma-HCH-degrading microbial community. The genome of TKS consists of two
AB  - chromosomes and nine plasmids. Thelingenes for conversion of gamma-HCH to
AB  - beta-ketoadipate are dispersed on chromosome 1 and three out of the nine
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Tabata, M.
AU  - Ohhata, S.
AU  - Nikawadori, Y.
AU  - Sato, T.
AU  - Kishida, K.
AU  - Ohtsubo, Y.
AU  - Tsuda, M.
AU  - Nagata, Y.
TI  - Complete Genome Sequence of a gamma-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205.
JO  - Genome Announcements
PY  - 2016
SP  - e00246
EP  - e00216
VL  - 4
AB  - Here, we report the complete genome sequence of a gamma-hexachlorocyclohexane
AB  - (gamma-HCH)-degrading bacterium,Sphingobiumsp. strain MI1205. The genome of
AB  - MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb.
AB  - All thelingenes for gamma-HCH metabolism are dispersed on the four plasmids.
ER  -

TY  - JOUR
AU  - Tabata, M.
AU  - Ohtsubo, Y.
AU  - Ohhata, S.
AU  - Tsuda, M.
AU  - Nagata, Y.
TI  - Complete Genome Sequence of the gamma-Hexachlorocyclohexane-Degrading Bacterium Sphingomonas sp. Strain MM-1.
JO  - Genome Announcements
PY  - 2013
SP  - e00247
EP  - e00213
VL  - 1
AB  - gamma-Hexachlorocyclohexane (gamma-HCH) is a man-made chlorinated insecticide that has caused
AB  - serious environmental problems. Here, we report the complete
AB  - genome sequence of the gamma-HCH-degrading bacterium Sphingomonas sp. strain
AB  - MM-1, which consists of one chromosome and five plasmids. All the specific lin
AB  - genes that are almost identical to those of Sphingobium japonicum UT26 for the
AB  - conversion of gamma-HCH to beta-ketoadipate are dispersed on four out of the five
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Tack, D.S.
AU  - Cole, A.C.
AU  - Shroff, R.
AU  - Morrow, B.R.
AU  - Ellington, A.D.
TI  - Evolving Bacterial Fitness with an Expanded Genetic Code.
JO  - Sci. Rep.
PY  - 2018
SP  - 3288
EP  - 3288
VL  - 8
AB  - Since the fixation of the genetic code, evolution has largely been confined to 20
AB  - proteinogenic amino acids. The development of orthogonal translation systems that
AB  - allow for the codon-specific incorporation of noncanonical amino acids may
AB  - provide a means to expand the code, but these translation systems cannot be
AB  - simply superimposed on cells that have spent billions of years optimizing their
AB  - genomes with the canonical code. We have therefore carried out directed evolution
AB  - experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine
AB  - across from amber codons, creating a 21 amino acid genetic code in which the
AB  - amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. The 21
AB  - amino acid code is enforced through the inclusion of an addicted, essential gene,
AB  - a beta-lactamase dependent upon 3-nitro-L-tyrosine incorporation. After 2000
AB  - generations of directed evolution, the fitness deficit of the original strain was
AB  - largely repaired through mutations that limited the toxicity of the noncanonical.
AB  - While the evolved lineages had not resolved the ambiguous coding of the amber
AB  - codon, the improvements in fitness allowed new amber codons to populate protein
AB  - coding sequences.
ER  -

TY  - JOUR
AU  - Tada, I.
AU  - Saitoh, S.
AU  - Aoyama, H.
AU  - Shinzato, N.
AU  - Yamamoto, N.
AU  - Arita, M.
AU  - Ikematsu, S.
TI  - Genome Sequence of Lactobacillus paracasei Strain LC-Ikematsu, Isolated from a Pineapple in Okinawa, Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01583
EP  - e01516
VL  - 5
AB  - The draft genome sequence of Lactobacillus paracasei strain LC-Ikematsu, isolated from a
AB  - pineapple in Okinawa, was determined. The total length of the 87 contigs
AB  - was 3.08 Mb with a G+C content of 46.2% and 2,946 coding sequences. The genome
AB  - analysis revealed its biosynthetic ability of 11 amino acids.
ER  -

TY  - JOUR
AU  - Tada, T.
AU  - Kitao, T.
AU  - Miyoshi-Akiyama, T.
AU  - Kirikae, T.
TI  - Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa NCGM1179.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6397
EP  - 6397
VL  - 193
AB  - We report the annotated genome sequence of multidrug-resistant Pseudomonas aeruginosa strain
AB  - NCGM1179, which is highly resistant to carbapenems,
AB  - aminoglycosides, and fluoroquinolones and is emerging at medical
AB  - facilities in Japan.
ER  -

TY  - JOUR
AU  - Tadesse, D.A.
AU  - Hoffmann, M.
AU  - Sarria, S.
AU  - Lam, C.
AU  - Brown, E.
AU  - Allard, M.
AU  - McDermott, P.F.
TI  - Complete Genome Sequences of 14 Salmonella enterica Serovar Enteritidis Strains Recovered from Human Clinical Cases between 1949 and 1995 in the United States.
JO  - Genome Announcements
PY  - 2018
SP  - e01406
EP  - e01417
VL  - 6
AB  - Salmonella enterica serovar Enteritidis is one of the most commonly isolated foodborne
AB  - pathogens and is transmitted primarily to humans through consumption of
AB  - contaminated poultry and poultry products. We are reporting completely closed
AB  - genome and plasmid sequences of historical S Enteritidis isolates recovered from
AB  - humans between 1949 and 1995 in the United States.
ER  -

TY  - JOUR
AU  - Tae, H.
AU  - Shallom, S.
AU  - Settlage, R.
AU  - Hawkins, G.N.
AU  - Adams, L.G.
AU  - Garner, H.R.
TI  - Complete Genome Sequence of Brucella suis VBI22, Isolated from Bovine Milk.
JO  - J. Bacteriol.
PY  - 2012
SP  - 910
EP  - 910
VL  - 194
AB  - Brucella suis is the causative agent of swine brucellosis and is known to be able to infect
AB  - several different hosts, including cattle, dogs, and
AB  - horses, without causing disease symptoms. Here we report the complete
AB  - genome sequence of Brucella suis VBI22, which was isolated from raw milk
AB  - from an infected cow.
ER  -

TY  - JOUR
AU  - Tae, H.
AU  - Shallom, S.
AU  - Settlage, R.
AU  - Preston, D.
AU  - Adams, L.G.
AU  - Garner, H.R.
TI  - Revised Genome Sequence of Brucella suis 1330.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6410
EP  - 6410
VL  - 193
AB  - Brucella suis is a causative agent of porcine brucellosis. We report the resequencing of the
AB  - original sample upon which the published sequence of
AB  - Brucella suis 1330 is based and describe the differences between the
AB  - published assembly and our assembly at 12 loci.
ER  -

TY  - JOUR
AU  - Tagami, H.
AU  - Tayama, K.
AU  - Tohyama, T.
AU  - Fukaya, M.
AU  - Okumura, H.
AU  - Kawamura, Y.
AU  - Horinouchi, S.
AU  - Beppu, T.
TI  - Purification and properties of a site-specific restriction endonuclease AaaI from Acetobacter aceti subsp. aceti No. 1023.
JO  - FEMS Microbiol. Lett.
PY  - 1988
SP  - 161
EP  - 166
VL  - 56
AB  - A type II restriction endonuclease, named AaaI, was purified from Acetobacter
AB  - aceti subsp. aceti No. 1023.  The optimum pH and temperature were determined to
AB  - be 8.5 and 37C, respectively.  The enzyme activity was stimulated by the
AB  - addition of either NaCl or KCl and their optimum concentrations were 100 mM for
AB  - both cations.  AaaI recognized the hexanucleotide sequence
AB  - 5'-C^GGCCG-3'/GCCGG^C and cleaved it at the positions indicated by the arrows.
AB  - AaaI is an isoschizomer of XmaIII from Xanthomonas malvacearum and Eco52I from
AB  - Escherichia coli.
ER  -

TY  - JOUR
AU  - Taghavi, S.
AU  - Izquierdo, J.A.
AU  - van der Lelie, D.
TI  - Complete Genome Sequence of Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge.
JO  - Genome Announcements
PY  - 2013
SP  - e00605
EP  - e00613
VL  - 1
AB  - We report the genome sequence of Clostridium sp. strain DL-VIII, a novel Gram-positive,
AB  - endospore-forming, solventogenic bacterium isolated from activated
AB  - anaerobic sludge of a wastewater treatment plant. Aside from a complete sol
AB  - operon, the 6,477,357-bp genome of DL-VIII reveals genes for several unique
AB  - enzymes with applications in lignocellulose degradation, including two phenolic
AB  - acid decarboxylases.
ER  -

TY  - JOUR
AU  - Tagini, F.
AU  - Pillonel, T.
AU  - Asner, S.
AU  - Prod'hom, G.
AU  - Greub, G.
TI  - Draft Genome Sequence of a Cardiobacterium hominis Strain Isolated from Blood Cultures of a Patient with Infective Endocarditis.
JO  - Genome Announcements
PY  - 2016
SP  - e00999
EP  - e00916
VL  - 4
AB  - Cardiobacterium hominis is a well-known commensal bacterium of the oral cavity and an agent of
AB  - infective endocarditis in humans. Here, we provide a draft genome
AB  - sequence of a pathogenic strain isolated from blood cultures of a patient with
AB  - infectious endocarditis.
ER  -

TY  - JOUR
AU  - Tahrioui, A.
AU  - Quesada, E.
AU  - Llamas, I.
TI  - Draft Genome Sequence of the Moderately Halophilic Gammaproteobacterium Halomonas anticariensis FP35T.
JO  - Genome Announcements
PY  - 2013
SP  - e00497
EP  - e00413
VL  - 1
AB  - Halomonas anticariensis strain FP35(T) is a moderately halophilic bacterium isolated from a
AB  - soil sample taken from Fuente de Piedra, a saline wetland in the
AB  - province of Malaga (Spain), which produces an exopolysaccharide and
AB  - quorum-sensing signaling molecules of the type N-acylhomoserine lactone. We
AB  - report here the draft genome sequence of this gammaproteobacterium.
ER  -

TY  - JOUR
AU  - Taiaroa, G.
AU  - Harbison-Price, N.
AU  - Ferguson, S.A.
AU  - Carter, G.P.
AU  - Williamson, D.A.
AU  - Macknight, R.C.
AU  - Cook, G.M.
AU  - Heikal, A.
TI  - Complete Genome Sequence of a New Zealand Isolate of the Bovine Pathogen Streptococcus uberis.
JO  - Genome Announcements
PY  - 2018
SP  - e00119
EP  - e00118
VL  - 6
AB  - Streptococcus uberis forms part of the native microbiota of cattle and is able to
AB  - opportunistically infect the mammary gland; as such, it is a leading cause of
AB  - bovine mastitis globally. Here, we report the complete genome sequence of S.
AB  - uberis NZ01, isolated in New Zealand from a cow with a clinical case of bovine
AB  - mastitis.
ER  -

TY  - JOUR
AU  - Taira, E.
AU  - Iiyama, K.
AU  - Mon, H.
AU  - Mori, K.
AU  - Akasaka, T.
AU  - Tashiro, K.
AU  - Yasunaga-Aoki, C.
AU  - Lee, J.M.
AU  - Kusakabe, T.
TI  - Draft Genome Sequence of Entomopathogenic Serratia liquefaciens Strain FK01.
JO  - Genome Announcements
PY  - 2014
SP  - e00609
EP  - e00614
VL  - 2
AB  - In the present study, we determined the draft genome sequence of the entomopathogenic
AB  - bacterium Serratia liquefaciens FK01, which is highly virulent
AB  - to the silkworm. The draft genome is ~5.28 Mb in size, and the G+C content is
AB  - 55.8%.
ER  -

TY  - JOUR
AU  - Tajima, N.
AU  - Kanesaki, Y.
AU  - Sato, S.
AU  - Yoshikawa, H.
AU  - Maruyama, F.
AU  - Kurokawa, K.
AU  - Ohta, H.
AU  - Nishizawa, T.
AU  - Asayama, M.
AU  - Sato, N.
TI  - Complete Genome Sequence of the Nonheterocystous Cyanobacterium Pseudanabaena sp. ABRG5-3.
JO  - Genome Announcements
PY  - 2018
SP  - e01608
EP  - e01617
VL  - 6
AB  - We report here the complete sequences of the main genome (4.8 Mb) and seven plasmids of the
AB  - semifilamentous, nonheterocystous cyanobacterium Pseudanabaena
AB  - sp. ABRG5-3, a strain isolated from a pond in Japan. These data are expected to
AB  - enhance our understanding of the Pseudanabaena subclade near the root of
AB  - cyanobacterial diversity.
ER  -

TY  - JOUR
AU  - Tajima, S.
TI  - DNA methyltransferase and DNA methylation.
JO  - Gendai Iryo
PY  - 2003
SP  - 936
EP  - 948
VL  - 35
ER  -

TY  - JOUR
AU  - Tajima, S.
AU  - Tsuda, H.
AU  - Wakabayashi, N.
AU  - Asano, A.
AU  - Mizuno, S.
AU  - Nishimori, K.
TI  - Isolation and expression of a chicken DNA methyltransferase cDNA.
JO  - J. Biochem. (Tokyo)
PY  - 1995
SP  - 1050
EP  - 1057
VL  - 117
AB  - A 0.5 kb fragment of chicken DNA methyltransferase cDNA was PCR-amplified using a set of
AB  - degenerate primers.  A clone harboring a 5 kb insert was isolated from a cDNA library by
AB  - screening with the PCR-amplified cDNA fragment as a probe.  The elucidated nucleotide sequence
AB  - gave a 4,614 nucleotide open reading frame, and the predicted protein was highly homologous to
AB  - the mouse and human DNA methyltransferases, especially in  the amino acid sequence of the
AB  - catalytic domain in the carboxyl-terminal region.  The cysteine-rich region and Lys-Gly repeat
AB  - first found in the mouse sequence were also conserved in chicken.  However, about 250 amino
AB  - acid residues in the amino-terminal portion of chicken DNA methyltransferase diverged from the
AB  - amino-terminus of the mouse or human sequence.  Northern blot analysis showed that the message
AB  - of chicken DNA methyltransferase was expressed at high levels in the testis, in the lung and
AB  - in Marek's virus-transformed chicken T-lymphoma cells.  Expression of the chicken DNA
AB  - methyltransferase is COS1 cells demonstrated that the enzyme is a so-called maintenance type
AB  - methylase.  When poly(dG-dC)-poly(dG-dC) was used as the methyl acceptor, to provide a measure
AB  - of de novo methylase activity, the Km value for S-adenosyl-L-methionine was about 5 microM,
AB  - which was 10 times higher than that when poly(dI-dC)-poly(dI-dC) was used.  The affinity of
AB  - DNA methyltransferase for S-adenosyl L-methionine in catalyzing de novo-type methylation
AB  - activity  was lower than that in catalyzing maintenance-type activity, though it was still
AB  - high enough for the enzyme to work as a de novo-type methylase under physiological conditions.
ER  -

TY  - JOUR
AU  - Tak, N. et al.
TI  - Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 304
EP  - 314
VL  - 9
AB  - Ensifer sp. TW10 is a novel N2-fixing bacterium isolated from a root nodule of the perennial
AB  - legume Tephrosia wallichii Graham (known locally as Biyani) found
AB  - in the Great Indian (or Thar) desert, a large arid region in the northwestern
AB  - part of the Indian subcontinent. Strain TW10 is a Gram-negative, rod shaped,
AB  - aerobic, motile, non-spore forming, species of root nodule bacteria (RNB) that
AB  - promiscuously nodulates legumes in Thar Desert alkaline soil. It is fast growing,
AB  - acid-producing, and tolerates up to 2% NaCl and capable of growth at 40(o)C. In
AB  - this report we describe for the first time the primary features of this Thar
AB  - Desert soil saprophyte together with genome sequence information and annotation.
AB  - The 6,802,256 bp genome has a GC content of 62% and is arranged into 57 scaffolds
AB  - containing 6,470 protein-coding genes, 73 RNA genes and a single rRNA operon.
AB  - This genome is one of 100 RNB genomes sequenced as part of the DOE Joint Genome
AB  - Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
AB  - (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Takagi, M.
AU  - Nakano, A.
AU  - Toh, H.
AU  - Oshima, K.
AU  - Arakawa, K.
AU  - Nakajima, F.
AU  - Tashiro, K.
AU  - Kikusui, T.
AU  - Yanagida, F.
AU  - Morita, H.
TI  - Draft Genome Sequence of Streptococcus orisasini SH06, Isolated from a Healthy Thoroughbred Gastrointestinal Tract.
JO  - Genome Announcements
PY  - 2016
SP  - e01566
EP  - e01515
VL  - 4
AB  - Streptococcus orisasini SH06 was isolated from a healthy thoroughbred gastrointestinal tract.
AB  - Here, we report the draft genome sequence of this
AB  - organism. This paper is the first published report of the genomic sequence of S.
AB  - orisasini.
ER  -

TY  - JOUR
AU  - Takagi, M.
AU  - Nishioka, M.
AU  - Kakihara, H.
AU  - Kitabayashi, M.
AU  - Inoue, H.
AU  - Kawakami, B.
AU  - Oka, M.
AU  - Imanaka, T.
TI  - Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR.
JO  - Appl. Environ. Microbiol.
PY  - 1997
SP  - 4504
EP  - 4510
VL  - 63
AB  - The DNA polymerase gene from the archaeon Pyrococcus sp. strain KOD1 (DOD DNA polymerase)
AB  - contains a long open reading frame of 5,013 bases that encodes 1,671 amino acid residues.
AB  - Similarity analysis revealed that the DNA polymerase contained a putative 3'-5' exonuclease
AB  - activity and two in-frame intervening sequences of 1,080 bp (360 amino acids; KOD pol
AB  - intein-1) and 1,611 bp (537 amino acids; KOD pol intein-2), which are located in the middle of
AB  - regions conserved among eukaryotic and archaeal a-like DNA polymerases.  The mature form of
AB  - the DNA polymerase gene was expressed in Escherichia coli, and the recombinant enzyme was
AB  - purified and characterized.  3'-5' exonuclease activity was confirmed, and although KOD DNA
AB  - polymerase's optimum temperature (75 C) and mutation frequency (3.5 x 10^-3) were similar to
AB  - those of a DNA polymerase from Pyrococcus furiosus (Pfu DNA polymerase), the KOD DNA
AB  - polymerase exhibited an extension rate (100 to 130 nucleotides/s) 5 times higher than those of
AB  - Pfu DNA polymerase.  These characteristics enabled the KOD DNA polymerase to perform a more
AB  - accurate PCR in a shorter reaction time.
ER  -

TY  - JOUR
AU  - Takahashi, H.
AU  - Kojima, H.
AU  - Saito, H.
TI  - A new site-specific endonuclease, ScaI, from Streptomyces caespitosus.
JO  - Biochem. J.
PY  - 1985
SP  - 229
EP  - 232
VL  - 231
AB  - A new site-specific endonuclease has been isolated from Streptomyces
AB  - caespitosus and named ScaI.  Based on analysis of sequences around the
AB  - restriction sites in pBR322 and pBR325, the recognition sequence of ScaI
AB  - endonuclease was deduced to be a new hexanucleotide 5'-AGTACT-3'.  The cleavage
AB  - site was determined by comparing the ScaI-cleaved roduct of a primer-extended
AB  - M13mp18-SCA DNA, which contains an AGTACT sequence, with dideoxy chain
AB  - terminator ladders of the same DNA.  ScaI was found to cleave the recognition
AB  - sequence between the internal T and A, leaving flush ends to the cleaved
AB  - fragments.
ER  -

TY  - JOUR
AU  - Takahashi, H.
AU  - Saito, H.
AU  - Ikeda, Y.
TI  - Viable T4 bacteriophage containing cytosine-substituted DNA (T4dC phage).  I.  Behavior towards the restriction-modification systems of Escherichia coli and derivation of a new T4 phage strain (T4dC) having the complete T4 genome.
JO  - J. Gen. Appl. Microbiol.
PY  - 1978
SP  - 297
EP  - 306
VL  - 24
AB  - A multiple mutant of bacteriophage T4, which had been proved to contain
AB  - cytosine-substituted DNA, was grown in a suppressor-containing or
AB  - non-containing (supo) strain of Escherichia coli B or K12, and the progeny
AB  - phage obtained was grown on test strains carrying various restriction systems.
AB  - As a result, the growth of this phage was found to be subject to the rK, rB,
AB  - and rP1 restriction systems.  Two T4 strains, named UNF-r1 and UNF-r+1,
AB  - sensitive to the rK, rB, and rP1 restriction systems, were newly derived by the
AB  - genetic cross and mutagenesis.  The former had the unf-39 mutation instead of
AB  - the alc-8 mutation, the latter had the rII+ region and the unf-39 mutation,
AB  - besides the amE51 (gene 56; dCTPase), denA (endonuclease II), and denB
AB  - (endonuclease IV) mutations.  It was demonstrated that UNF-r+1 DNA possessed a
AB  - SalI recognition site in the rII-denB region which was deleted in UNF-r1 DNA.
ER  -

TY  - JOUR
AU  - Takahashi, H.
AU  - Shao, M.
AU  - Furuya, N.
AU  - Komano, T.
TI  - The genome sequence of the incompatibility group Igamma plasmid R621a: Evolution of IncI plasmids.
JO  - Plasmid
PY  - 2011
SP  - 112
EP  - 121
VL  - 66
AB  - We present the complete genome sequence of the tetracycline resistance plasmid R621a isolated
AB  - from Salmonella typhimurium, which belongs to the incompatibility group Igamma. In the
AB  - 93,185bp circular double-stranded R621a genome, 96 complete ORFs are predicted. In addition,
AB  - one and six different kinds of proteins are produced by translational reinitiation and
AB  - shufflon multiple inversions, respectively. The genome consists of four regions: replication,
AB  - leading, transfer, and miscellaneous regions. The R621a genome is similar to those of IncI1
AB  - plasmids such as R64 and ColIb-P9 and particularly to those of pEK204 and pEC_Bactec. Three
AB  - major differences including inc, parAB, and excA regions were noted between R621a and
AB  - prototype IncI1 plasmids. Seven nucleotide replacements and one nucleotide deletion in the
AB  - putative Inc RNA sequence are found between R621a and IncI1 plasmids irrespective of close
AB  - similarity in the other parts of the rep system. The sequences of R621a parAB and excA genes
AB  - are significantly different from those of R64 and ColIb-P9, while those of R621a parAB and
AB  - excA genes exhibit close similarity to those of pEK204 and pEC_Bactec, respectively. The R621a
AB  - genome is suggested to be formed by acquiring parAB and excA genes from pEK204 and pEC_Bactec
AB  - genomes, respectively, and then novel inc function by the mutations. The insertions in the
AB  - R621a, pEK204, and pEC_Bactec genomes are flanked by direct repeats, suggesting that
AB  - insertions accompanied by long target duplications have also played an important role in the
AB  - evolution of IncI plasmids.
ER  -

TY  - JOUR
AU  - Takahashi, H.
AU  - Shimizu, M.
AU  - Saito, H.
AU  - Ikeda, Y.
AU  - Sugisaki, H.
TI  - A new site-specific endonuclease from Streptomyces lavendulae (SlaI) .
JO  - Gene
PY  - 1979
SP  - 9
EP  - 18
VL  - 5
AB  - A new restriction-like endonuclease, SlaI, was found and partially purified
AB  - from Streptomyces lavendulae ATCC8664.  This endonuclease cleaved bacteriophage
AB  - lambda DNA at only one site, and cytosine-substituted bacteriophage T4 DNA at
AB  - 16 sites.  The recognition sequence was determined by using SlaI fragments of
AB  - cytosine-substituted bacteriophage T4 DNA.  The hexanucleotide recognized by
AB  - SlaI endonuclease was 5'-C^T-C-G-A-G-3' 3'-G-A-G-C-A^C-5' with the sites of
AB  - cleavage as indicated by the arrows.  Therefore, SlaI endonuclease was an
AB  - isoschizomer of XhoI endonuclease.
ER  -

TY  - JOUR
AU  - Takahashi, I.
AU  - Hayano, D.
AU  - Asayama, M.
AU  - Masahiro, F.
AU  - Watahiki, M.
AU  - Shirai, M.
TI  - Restriction barrier composed of an extracellular nuclease and restriction endonuclease in the unicellular cyanobacterium Microcystis sp.
JO  - FEMS Microbiol. Lett.
PY  - 1996
SP  - 107
EP  - 111
VL  - 145
AB  - The unicellular cyanobacterium Microcystis aeruginosa K-81 has two types of restriction
AB  - barrier, an extracellular nuclease and sequence-specific endonucleases.  The nuclease was
AB  - detected in the culture supernatant and it was easily released from the cells by washing with
AB  - water or buffer containing Triton X-100.  This nuclease was identified as a polypeptide of
AB  - about 28 kDa that digested covalently closed circular and linear double-stranded DNAs,
AB  - including chromosomal DNA from M. aeruginosa K-81.  Among another 13 Microcystis strains
AB  - examined, 3 produced an extracellular nuclease.  Furthermore, M. aeruginosa K-81 contained two
AB  - sequence-specific endonucleases, MaeK81I and MaeK81II, which were isoschizomers of SplI and
AB  - Sau96I, respectively.
ER  -

TY  - JOUR
AU  - Takahashi, M.
AU  - Kobayashi, M.
AU  - Uchida, T.
TI  - Molecular multiplicity of nuclease TT1 from Thermus thermophilus HB8.
JO  - J. Biochem. (Tokyo)
PY  - 1981
SP  - 1521
EP  - 1527
VL  - 90
AB  - Purified nuclease TT1 from Thermus thermophilus HB8 has multimolecular weight
AB  - forms, each of which is composed of three different subunits, a (10.8 x 104), b
AB  - (7.8 x 104), and c (4.1 x 104).  The molecular weight of this enzyme were
AB  - estimated by gel filtration, polyacrylamide gel electrophoresis and equilibrium
AB  - sedimentation.  It was found that most of the enzyme has a molecular weight of
AB  - about 22 x 104 being a monomer having the subunit composition of abc.  The
AB  - remaining part of the enzyme has larger molecular weights and is considered to
AB  - be size-isomers of abc.  The alpha-helical content, 5.5-6.5%, and the
AB  - b-structure, about 28% were estimated from the CD spectrum at 4C.
ER  -

TY  - JOUR
AU  - Takahashi, N.
AU  - Naito, Y.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex.
JO  - J. Bacteriol.
PY  - 2002
SP  - 6100
EP  - 6108
VL  - 184
AB  - In prokaryotic genomes, some DNA methyltransferases form a restriction-modification gene
AB  - complex, but some others are present by themselves. Dcm gene product, one of these orphan
AB  - methyltransferases found in Escherichia coli and related bacteria, methylates DNA to generate
AB  - 5'-CmCWGG just as some of its eukaryotic homologues do. Vsr mismatch repair function of an
AB  - adjacent gene prevents C-to-T mutagenesis enhanced by this methylation but promotes other
AB  - types of mutation and likely has affected genome evolution. The reason for the existence of
AB  - the dcm-vsr gene pair has been unclear. Earlier we found that several restriction-modification
AB  - gene complexes behave selfishly in that their loss from a cell leads to cell killing through
AB  - restriction attack on the genome. There is also increasing evidence for their potential
AB  - mobility. EcoRII restriction-modification gene complex recognizes the same sequence as Dcm,
AB  - and its methyltransferase is phylogenetically related to Dcm. In the present work, we found
AB  - that stabilization of maintenance of a plasmid by linkage of EcoRII gene complex, likely
AB  - through postsegregational cell killing, is diminished by dcm function. Disturbance of EcoRII
AB  - restriction-modification gene complex led to extensive chromosome degradation and severe loss
AB  - of cell viability. This cell killing was partially suppressed by chromosomal dcm and
AB  - completely abolished by dcm expressed from a plasmid. Dcm, therefore, can play the role of a
AB  - 'molecular vaccine' by defending the genome against parasitism by a restriction-modification
AB  - gene complex.
ER  -

TY  - JOUR
AU  - Takahashi, N.
AU  - Ohashi, S.
AU  - Sadykov, M.R.
AU  - Mizutani-Ui, Y.
AU  - Kobayashi, I.
TI  - IS-Linked Movement of a Restriction-Modification System.
JO  - PLoS ONE
PY  - 2011
SP  - e16554
EP  - e16554
VL  - 6
AB  - Potential mobility of restriction-modification systems has been suggested by
AB  - evolutionary/bioinformatic analysis of prokaryotic
AB  - genomes. Here we demonstrate in vivo movement of a
AB  - restriction-modification system within a genome under a laboratory
AB  - condition. After blocking replication of a temperature-sensitive
AB  - plasmid carrying a PaeR7I restriction-modification system in
AB  - Escherichia coli cells, the plasmid was found integrated into the
AB  - chromosome of the surviving cells. Sequence analysis revealed that, in
AB  - the majority of products, the restriction-modification system was
AB  - linked to chromosomal insertion sequences (ISs). Three types of
AB  - products were: (I) apparent co-integration of the plasmid and the
AB  - chromosome at a chromosomal IS1 or IS5 copy (24/28 analyzed); (II) de
AB  - novo insertion of IS1 with the entire plasmid except for a 1-3 bp
AB  - terminal deletion (2/28); and (III) reciprocal crossing-over between
AB  - the plasmid and the chromosome involving 1-3 bp of sequence identity
AB  - (2/28). An R-negative mutation apparently decreased the efficiency of
AB  - successful integration by two orders of magnitude. Reconstruction
AB  - experiments demonstrated that the restriction-dependence was mainly due
AB  - to selection against cells without proper integration: their growth was
AB  - inhibited by the restriction enzyme action. These results demonstrate
AB  - collaboration of a mobile element and a restriction-modification system
AB  - for successful joint migration. This collaboration may have promoted
AB  - the spread and, therefore, the long-term persistence of these complexes
AB  - and restriction-modification systems in a wide range of prokaryotes.
ER  -

TY  - JOUR
AU  - Takahashi, S.
AU  - Matsuno, H.
AU  - Furusawa, H.
AU  - Okahata, Y.
TI  - Direct monitoring of EcoRII restriction enzyme reactions on a 27MHz quartz-crystal microbalance.
JO  - Nucleic Acids Res. Suppl.
PY  - 2002
SP  - 71
EP  - 72
VL  - 2
AB  - EcoRII is a type IIE restriction endonuclease characterized by a highly cooperative reaction
AB  - mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of
AB  - its recognition site.  Gaining insights about reaction property of EcoRII binding to its
AB  - recognition site and effect of divalent metal ion on DNA cleavage process, a DNA-immobilized
AB  - quartz crystal microbalance, which enables real-time monitoring both the binding of enzyme and
AB  - the cleavage reaction on DNA strands as mass changes, was utilized.
ER  -

TY  - JOUR
AU  - Takahashi, S.
AU  - Matsuno, H.
AU  - Furusawa, H.
AU  - Okahata, Y.
TI  - Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII.
JO  - J. Biol. Chem.
PY  - 2008
SP  - 15023
EP  - 15030
VL  - 283
AB  - EcoRII is a homodimer with two domains consisting of a DNA-binding N terminus and a catalytic
AB  - C terminus and recognizes two specific
AB  - sequences on DNA. It shows a relatively complicated cleavage reaction
AB  - in bulk solution. After binding to either recognition site, EcoRII
AB  - cleaves the other recognition site of the same DNA (cis-binding) strand
AB  - and/or the recognition site of the other DNA (trans-binding) strand.
AB  - Although it is difficult to separate these two reactions in bulk
AB  - solution, we could simply obtain the binding and cleavage kinetics of
AB  - only the cis-binding by following the frequency (mass) changes of a
AB  - DNA-immobilized quartz-crystal microbalance (QCM) responding to the
AB  - addition of EcoRII in aqueous solution. We obtained the maximum binding
AB  - amounts (Delta m(max)) the dissociation constants (K-d), the binding
AB  - and dissociation rate constants (k(on) and k(off)), and the catalytic
AB  - cleavage reaction rate constants (k(cat)) for wildtype EcoRII, the
AB  - N-terminal-truncated form (EcoRII N-domain), and the mutant derivatives
AB  - in its C-terminal domain (K263A and R330A). It was determined from the
AB  - kinetic analyses that the N-domain, which covers the catalytic C-domain
AB  - in the absence of DNA, preferentially binds to the one DNA recognition
AB  - site while transforming EcoRII into an active form allosterically, and
AB  - then the secondary C-domain binds to and cleaves the other recognition
AB  - site of the DNA strand.
ER  -

TY  - JOUR
AU  - Takai, D.
TI  - Detection of DNA methylation using methylation sensitive restriction enzyme.
JO  - Jikken Igaku Bessatsu
PY  - 2008
SP  - 62
EP  - 68
VL  - JB12
ER  -

TY  - JOUR
AU  - Takai, K.
AU  - Horikoshi, K.
TI  - Molecular phylogenetic analysis of archaeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermal water pool.
JO  - Appl. Environ. Microbiol.
PY  - 1999
SP  - 5586
EP  - 5589
VL  - 65
AB  - Molecular phylogenetic analysis of a naturally occurring microbial community in a
AB  - deep-subsurface geothermal environment indicated that the phylogenetic diversity of the
AB  - microbial population in the environment was extremely limited and that only hyperthermophilic
AB  - archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA
AB  - sequences contained intron-like sequences, some of which had open reading frames with repeated
AB  - homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of
AB  - these homing endonucleases suggested the possible phylogenetic relationship among archaeal
AB  - rRNA-encoded homing endonucleases.
ER  -

TY  - JOUR
AU  - Takami, H.
AU  - Nakasone, K.
AU  - Takaki, Y.
AU  - Maeno, G.
AU  - Sasaki, R.
AU  - Masui, N.
AU  - Fuji, F.
AU  - Hirama, C.
AU  - Nakamura, Y.
AU  - Ogasawara, N.
AU  - Kuhara, S.
AU  - Horikoshi, K.
TI  - Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis.
JO  - Nucleic Acids Res.
PY  - 2000
SP  - 4317
EP  - 4331
VL  - 28
AB  - The 4,202,353 bp genome of the alkaliphilic bacterium Bacillus halodurans C-125 contains 4066
AB  - predicted protein coding sequences (CDSs), 2141 (52.7%) of which have functional assignments,
AB  - 1182 (29%) of which are conserved CDSs with unknown function and 743 (18. 3%) of which have no
AB  - match to any protein database.  Among the total CDSs, 8.8% match sequences of proteins found
AB  - only in Bacillus subtilis and 66.7% are widely conserved in comparison with the proteins of
AB  - various organisms, including B. subtilis. The B. halodurans genome contains 112 transposase
AB  - genes, indicating that transposases have played an important evolutionary role in horizontal
AB  - gene transfer and also in internal genetic rearrangement in the genome. Strain C-125 lacks
AB  - some of the necessary genes for competence, such as comS, srfA and rapC, supporting the fact
AB  - that competence has not been demonstrated experimentally in C-125. There is no paralog of
AB  - tupA, encoding teichuronopeptide, which contributes to alkaliphily, in the C-125 genome and an
AB  - ortholog of tupA cannot be found in the B. subtilis genome. Out of 11 sigma factors which
AB  - belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting
AB  - that they may have a role in the special mechanism of adaptation to an alkaline environment.
ER  -

TY  - JOUR
AU  - Takami, H.
AU  - Takaki, Y.
AU  - Chee, G.-J.
AU  - Nishi, S.
AU  - Shimamura, S.
AU  - Suzuki, H.
AU  - Matsui, S.
AU  - Uchiyama, I.
TI  - Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 6292
EP  - 6303
VL  - 32
AB  - We present herein the first complete genome sequence of a thermophilic Bacillus-related
AB  - species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9
AB  - kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes.
AB  - Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common
AB  - orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839
AB  - genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able
AB  - to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC
AB  - transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by
AB  - stabilizing the nucleic acids. Contrasting results were obtained from the principal component
AB  - analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the
AB  - thermophilic signature of the G. kaustophilus genome. Only in the PCA of the amino acid
AB  - composition were the Bacillus-related species located near, but were distinguishable from, the
AB  - borderline distinguishing thermophiles from mesophiles on the second principal axis. Further
AB  - analysis revealed some asymmetric amino acid substitutions between the thermophiles and the
AB  - mesophiles, which are possibly associated with the thermoadaptation of the organism.
ER  -

TY  - JOUR
AU  - Takami, H.
AU  - Takaki, Y.
AU  - Uchiyama, I.
TI  - Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3927
EP  - 3935
VL  - 30
AB  - Oceanobacillus iheyensis HTE831 is an alkaliphilic and extremely halotolerant Bacillus-related
AB  - species isolated from deep-sea sediment. We present here the complete genome sequence of
AB  - HTE831 along with analyses of genes required for adaptation to highly alkaline and saline
AB  - environments. The genome consists of 3.6 Mb, encoding many proteins potentially associated
AB  - with roles in regulation of intracellular osmotic pressure and pH homeostasis. The candidate
AB  - genes involved in alkaliphily were determined based on comparative analysis with three
AB  - Bacillus species and two other Gram-positive species. Comparison with the genomes of other
AB  - major Gram-positive bacterial species suggests that the backbone of the genus Bacillus is
AB  - composed of approximately 350 genes. This second genome sequence of an alkaliphilic
AB  - Bacillus-related species will be useful in understanding life in highly alkaline environments
AB  - and microbial diversity within the ubiquitous bacilli.
ER  -

TY  - JOUR
AU  - Takamiya, M.
AU  - Ozen, A.
AU  - Rasmussen, M.
AU  - Alter, T.
AU  - Gilbert, T.
AU  - Ussery, D.W.
AU  - Knochel, S.
TI  - Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5546
EP  - 5547
VL  - 193
AB  - Campylobacter jejuni is a food-borne pathogen with a high prevalence in poultry meat, which in
AB  - fresh unfrozen condition is the major source of
AB  - campylobacteriosis. C. jejuni strains DFVF1099 and 305 are considered
AB  - tolerant to several environmental stresses (T. Birk et al., J. Food Prot.
AB  - 73:258-265, 2010; S. L. On et al., Int. J. Med. Microbiol. 296:353-363,
AB  - 2006). Here, we report the genome sequences of C. jejuni 305 and DFVF1099,
AB  - a turkey and a chicken isolate, respectively.
ER  -

TY  - JOUR
AU  - Takamiya, M.
AU  - Ozen, A.
AU  - Rasmussen, M.
AU  - Alter, T.
AU  - Gilbert, T.
AU  - Ussery, D.W.
AU  - Knochel, S.
TI  - Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 113
EP  - 122
VL  - 4
AB  - Campylobacter is one of the leading causes of food-borne gastroenteritis
AB  - and has a high prevalence in poultry. Campylobacter jejuni subsp. jejuni
AB  - 327 is a subspecies of the genus Campylobacter of the family
AB  - Campylobacteraceae in the phylum Proteobacteria. The microaerophilic,
AB  - spiral shaped, catalase positive bacterium obtains energy from the
AB  - metabolism of amino acids and Krebs cycle intermediates. Strain 327 was
AB  - isolated from a turkey slaughter production line and is considered
AB  - environmentally sensitive to food processing (cold, heat, drying) and
AB  - storage conditions. The 327 whole genome shotgun sequence of 1,618,613 bp
AB  - long consists of 1,740 protein-coding genes, 46 tRNA genes and 3 rRNA
AB  - operons. A protein based BLAST analysis places the turkey isolate 327
AB  - close to the human clinical strain 81116 (NCTC 11828).
ER  -

TY  - JOUR
AU  - Takanami, M.
TI  - Specific cleavage of coliphage fd DNA by five different restriction endonucleases from Haemophilus genus.
JO  - FEBS Lett.
PY  - 1973
SP  - 318
EP  - 322
VL  - 34
AB  - None
ER  -

TY  - JOUR
AU  - Takanami, M.
TI  - Restriction endonucleases AP, GA, and H-1 from three Haemophilus strains.
JO  - Methods Mol. Biol.
PY  - 1974
SP  - 113
EP  - 133
VL  - 7
AB  - None
ER  -

TY  - JOUR
AU  - Takanami, M.
AU  - Kojo, H.
TI  - Cleavage site specificity of an endonuclease prepared from Haemophilus influenzae strain H-1.
JO  - FEBS Lett.
PY  - 1973
SP  - 267
EP  - 270
VL  - 29
AB  - None
ER  -

TY  - JOUR
AU  - Takanami, M.
AU  - Okamoto, T.
AU  - Sugimoto, K.
AU  - Sugisaki, H.
TI  - Studies on Bacteriophage fd DNA I.  A Cleavage Map of the fd Genome.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 21
EP  - 31
VL  - 95
AB  - In order to construct a physical map of the bacteriophage fd genome, the doubly
AB  - closed replicative form (RFI) DNA of phage fd was cleaved into unique fragments
AB  - by four different restriction endonucleases (Hap, Hga, HinH and Hind) prepared
AB  - from Haemophilus strains H. aphirophilus, H. gallinarum, H. influenzae H-I and
AB  - H. influenzae Rd, respectively.  As Hind cleaved RFI DNA at a single site, this
AB  - site was used as a reference point for mapping.  HinH cleaved RFI DNA at three
AB  - sites, Hga at six sites and Hap at 13 sites, respectively.  The 5'-termini of
AB  - the fragments produced by either HinH or Hga were labelled with 32P in the
AB  - polynucleotide kinase reaction.  The labelled fragments were separated and
AB  - further cleaved by other enzymes.  The re-digestion products of partially
AB  - digested fragments were also analysed.  On the basis of these data and
AB  - estimates of the size of each fragment, a cleavage map of the phage fd genome
AB  - was constructed.
ER  -

TY  - JOUR
AU  - Takano, T.
AU  - Nakamura, Y.
AU  - Matsuyama, T.
AU  - Sakai, T.
AU  - Shigenobu, Y.
AU  - Sugaya, T.
AU  - Yasuike, M.
AU  - Fujiwara, A.
AU  - Kondo, H.
AU  - Hirono, I.
AU  - Fukuda, Y.
AU  - Nakayasu, C.
TI  - Complete Genome Sequence of Ichthyobacterium seriolicida JBKA-6T, Isolated from Yellowtail (Seriola quinqueradiata) Affected by Bacterial Hemolytic Jaundice.
JO  - Genome Announcements
PY  - 2017
SP  - e01574
EP  - e01516
VL  - 5
AB  - Ichthyobacterium seriolicida is a fish bacterial pathogen that causes hemolytic jaundice in
AB  - farmed yellowtail in Japan. To understand more about the
AB  - characteristics of this bacterium, we determined its complete genome sequence.
AB  - Two hemolysin genes which may be important for its pathogenicity were identified
AB  - in the I. seriolicida genome.
ER  -

TY  - JOUR
AU  - Takano, T.
AU  - Ochi, A.
AU  - Yamamoto, N.
TI  - Restriction enzyme from Lactobacillus fermentum.
JO  - FEMS Microbiol. Rev.
PY  - 1990
SP  - 64
EP  - 64
VL  - 7
AB  - Restriction-modification is important in phage resistance. However, little is known about
AB  - restriction enzymes of lactic acid bacteria. We have found that Lactobacillus fermentum CP-34
AB  - has apparent site-specific endonuclease activity, purified and studied the characteristics of
AB  - the enzyme.
ER  -

TY  - JOUR
AU  - Takano, T.
AU  - Watanabe, T.
AU  - Fukasawa, T.
TI  - Mechanism of host-controlled restriction of bacteriophage lambda by R factors in Escherichia coli K12.
JO  - Virology
PY  - 1968
SP  - 290
EP  - 302
VL  - 34
AB  - In the host-controlled modification of phage lambda by fi- R factors, N-3 and
AB  - R-15, the infectivity of the unmodified lambda DNA was specifically destroyed
AB  - by the sonicated extracts from the restrictive, endonuclease I-less (endo
AB  - I-less) mutant of Escherichia coli K12 carrying N-3 or R-15, to a greater
AB  - extent than by the sonicates from the nonrestrictive, endo I-less bacteria.  In
AB  - the control experiments, the lambda DNA modified by N-3 was inactivated to much
AB  - lesser extents both by the sonicates from the restrictive, endo I-less bacteria
AB  - and by those from the nonrestrictive, endo I-less bacteria.  In all these
AB  - systems of reactions, the phage DNA was hardly degraded into acid-soluble
AB  - forms.  The host specifically inactivated, unmodified lambda DNA, however, was
AB  - split fragmentally as was shown by the patterns of zone sedimentation, but the
AB  - modified lambda DNA was not.  The activity which destroys the infectivity of
AB  - the unmodified lambda DNA resided totally in the spheroplasts of the
AB  - restrictive bacteria.
ER  -

TY  - JOUR
AU  - Takano, T.
AU  - Watanabe, T.
AU  - Fukasawa, T.
TI  - Specific inactivation of infectious lambda DNA by sonicates of restrictive bacteria with R factors.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1966
SP  - 192
EP  - 204
VL  - 25
AB  - In the studies on the host-controlled modification (Arber, 1965a) of
AB  - bacteriophage lambda, certain aspects of two fundamental functions of host
AB  - bacteria have been elucidated:  Modification is a function by which viral DNA
AB  - is subjected to some chemical alterations (Arber, 1965b).  Restriction is
AB  - another function which recognizes the modification pattern or the host
AB  - specificity and serves to restrict the phage mutliplication depending on the
AB  - host specificity (Arber and Dussoix, 1962).  Analogous experiments are now
AB  - under way in the system of P1-controlled restriction in our laboratories.
ER  -

TY  - JOUR
AU  - Takarada, H.
AU  - Sekine, M.
AU  - Kosugi, H.
AU  - Matsuo, Y.
AU  - Fujisawa, T.
AU  - Omata, S.
AU  - Kishi, E.
AU  - Shimizu, A.
AU  - Tsukatani, N.
AU  - Tanikawa, S.
AU  - Fujita, N.
AU  - Harayama, S.
TI  - Complete genome sequence of the soil actinomycete Kocuria rhizophila.
JO  - J. Bacteriol.
PY  - 2008
SP  - 4139
EP  - 4146
VL  - 190
AB  - The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent
AB  - bacterial group for which only a limited
AB  - amount of genomic information is currently available. K. rhizophila is
AB  - also important in industrial applications; e.g., it is commonly used as a
AB  - standard quality control strain for antimicrobial susceptibility testing.
AB  - Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC
AB  - 103217) revealed a single circular chromosome (2,697,540 bp; G+C content
AB  - of 71.16%) containing 2,357 predicted protein-coding genes. Most of the
AB  - predicted proteins (87.7%) were orthologous to actinobacterial proteins,
AB  - and the genome showed fairly good conservation of synteny with
AB  - taxonomically related actinobacterial genomes. On the other hand, the
AB  - genome seems to encode much smaller numbers of proteins necessary for
AB  - secondary metabolism (one each of nonribosomal peptide synthetase and type
AB  - III polyketide synthase), transcriptional regulation, and lateral gene
AB  - transfer, reflecting the small genome size. The presence of probable
AB  - metabolic pathways for the transformation of phenolic compounds generated
AB  - from the decomposition of plant materials, and the presence of a large
AB  - number of genes associated with membrane transport, particularly amino
AB  - acid transporters and drug efflux pumps, may contribute to the organism's
AB  - utilization of root exudates, as well as the tolerance to various organic
AB  - compounds.
ER  -

TY  - JOUR
AU  - Takasaki, Y.
TI  - Two forms of restriction enzyme HindIII.
JO  - J. Biochem. (Tokyo)
PY  - 1994
SP  - 1281
EP  - 1286
VL  - 116
AB  - Restriction endonuclease HindIII was purified from Haemophilus influenzae Rd. Two active
AB  - fractions, P1 and P2, were obtained in phosphocellulose chromatography. HindIII could be
AB  - purified completely from the first fraction, P1, by subsequent DEAE-cellulose chromatography.
AB  - The second fraction, P2, showed HindIII activity higher than that of P1, though it was still
AB  - contaminated with some minor proteins. The HindIII in the P2 fraction showed differences in
AB  - stability, binding to substrate DNA, electrophoretic mobility, etc., from the HindIII in the
AB  - P1 fraction. It is likely that there are two forms of HindIII in the bacterial cell. The
AB  - endonuclease HindIII in the P2 fraction was finally purified by DNA-cellulose chromatography,
AB  - though considerable loss of enzymatic activity resulted. Upon infection of the cells with
AB  - phage T4, the P2 fraction in phosphocellulose chromatography almost disappeared. The presence
AB  - of two forms of HindIII may be related to bacterial defense against viral infection.
ER  -

TY  - JOUR
AU  - Takasaki, Y.
TI  - Alternation of two forms of restriction endonuclease HindIII.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1996
SP  - 396
EP  - 400
VL  - 60
AB  - Two forms of the restriction enzyme HindIII were alternated with each other under
AB  - some physiological or biochemical conditions.  Addition of a low amount of phage T7 to the
AB  - culture of HindIII-producing Haemophilus influenzae Rd, resulted in appearance of some amounts
AB  - of the P2 fraction of HindIII, which was eluted with a high concentration of KCl from a
AB  - phosphocellulose column.  Higher amounts of T7 caused a decrease of the P2 fraction; finally
AB  - the
AB  - alternative P1 fraction of HindIII, which was eluted with a lower concentration of KCl,
AB  - remained
AB  - exclusively.  Addition of disaccharides such as maltose and trehalose to the bacterial
AB  - extract,
AB  - yielded more P2, although the disaccharides inhibited this enzyme.  Urea showed an interesting
AB  - distribution of these two forms of HindIII.  Phosphocellulose chromatography in the presence
AB  - of
AB  - 2M urea generated a broad peak of HindIII activity.  Addition of 4M urea, on the contrary,
AB  - showed
AB  - only one active peak of this enzyme.  The HindIII could be purified by the following DEAE-
AB  - cellulose chromatography.  The results indicate the presence of only one kind of HindIII
AB  - molecule,
AB  - which was alternated between free and bound forms, and a certain kind of factor that would
AB  - equilibrate these two forms.
ER  -

TY  - JOUR
AU  - Takasu, Y.
AU  - Sajwan, S.
AU  - Daimon, T.
AU  - Osanai-Futahashi, M.
AU  - Uchino, K.
AU  - Sezutsu, H.
AU  - Tamura, T.
AU  - Zurovec, M.
TI  - Efficient TALEN construction for Bombyx mori gene targeting.
JO  - PLoS ONE
PY  - 2013
SP  - E73458
EP  - E73458
VL  - 8
AB  - Engineered nucleases are artificial enzymes able to introduce double stranded
AB  - breaks at desired genomic locations. The double stranded breaks start the
AB  - error-prone repair process of non-homologous end-joining (NHEJ), which eventually
AB  - leads to the induction of mutations at target sites. We showed earlier that ZFNs
AB  - and TALENs are able to induce NHEJ mutations in the B. mori genome. In order to
AB  - optimize our mutagenesis protocol, we modified one of the reported truncated
AB  - TALEN scaffolds and optimized it for use in the B. mori embryo. We also
AB  - established a novel B. mori somatic cell assay suitable for the preselection of
AB  - highly efficient TALENs directly in the B. mori model system. We compared the
AB  - efficiency of several TALEN pairs based on three different frameworks using the
AB  - BmBLOS2 gene. The new active TALENs show one order of magnitude higher efficiency
AB  - than those we used previously. We confirmed the utility of our improved protocol
AB  - by mutagenesis of the autosomal gene, red egg (Bm-re) and showed that it allows
AB  - obtaining homozygous mutants in G1. Our procedure minimizes the chance of failure
AB  - in B. mori gene targeting experiments.
ER  -

TY  - JOUR
AU  - Takata, T.
AU  - Aras, R.
AU  - Tavakoli, D.
AU  - Ando, T.
AU  - Olivares, A.Z.
AU  - Blaser, M.J.
TI  - Phenotypic and genotypic variation in methylases involved in type II restriction-modification systems in Helicobacter pylori.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 2444
EP  - 2452
VL  - 30
AB  - To determine relationships between Helicobacter pylori geographical origin and type II
AB  - methylase activity, we examined 122 strains from various locations around the world for
AB  - methylase expression. Most geographic regions possessed at least one strain resistant to
AB  - digestion by each of 14 restriction endonucleases studied. Across all of the strains studied,
AB  - the average number of active methylases was 8.2 +/- 1.9 with no significant variation between
AB  - the major geographic regions. Although seven pairs of isolates showed the same susceptibility
AB  - patterns, their cagA/vacA status differed, and the remaining 108 strains each possessed unique
AB  - patterns of susceptibility. From a single clonal group, 15 of 18 strains showed identical
AB  - patterns of resistance, but diverged with respect to M.MboII activity. All of the methylases
AB  - studied were present in all major human population groupings, suggesting that their horizontal
AB  - acquisition pre-dated the separation of these populations. For the hpyV and hpyAIV
AB  - restriction-modification systems, an in-depth analysis of genotype, indicating extensive
AB  - diversity of cassette size and chromosomal locations regardless of the susceptibility
AB  - phenotype, points toward substantial strain-specific selection involving these loci.
ER  -

TY  - JOUR
AU  - Takata, T.
AU  - Wassenaar, T.M.
AU  - Xu, Q.
AU  - Blaser, M.J.
TI  - The gene product of Campylobacter jejuni gene Cj0208 is a DNA methyltransferase with specificity for GAATTC.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 164
EP  - 164
VL  - 102
AB  - To understand the mechanisms of DNA methylation in Campylobacter jejuni, we examined the
AB  - genetic and phenotypic properties of a putative
AB  - adenine methyltransferase gene, Cj0208. This gene encodes a 364-amino
AB  - acid protein and was present in all 11 C. jejuni strains tested. A
AB  - BLAST search using the Cj208 amino acid sequence revealed that the
AB  - putative protein was most closely related to CATG-recognizing adenine
AB  - DNA methyltransferases, including M. HpyI of Helicobacter pylori.
AB  - However, phylogenetic analysis (using PAUP 4.0b2) revealed that Cj0208
AB  - was closely related to M. Sse9I, which recognizes AATT, and that it's
AB  - next closest relative is M. EcoRI, which recognizes GAATTC. DNA
AB  - isolated from C. jejuni strains was shown to be resistant to digestion
AB  - by EcoRI and susceptible to restriction enzymes recognizing AATT
AB  - (TSP509I), and CATG (NlaIII). After cloning Cj0208 from C. jejuni
AB  - strain 11168, overexpression in an Escherichia coli strain lacking
AB  - endogenous methyltransferases rendered DNA from these cells resistant
AB  - to EcoRI digestion. This suggests that Cj0208 is a methyltransferase
AB  - with specificity for GAATTC. A dot blot assay using antibodies that
AB  - react specifically with DNA containing m6A or m4C modifications
AB  - identified Cj0208 as an m6A methyltransferase. An isogenic Cj0208
AB  - mutant was susceptible to EcoRI, confirming the role of this methylase
AB  - in protecting GAATTC sites. We conclude that Cj0208 encodes a DNA
AB  - methyltransferase with m6A activity and specificity for GAATTC. The
AB  - resistance of C. jejuni strains to EcoRI digestion suggests that this
AB  - gene is well-conserved.
ER  -

TY  - JOUR
AU  - Takatani, N.
AU  - Nakanishi, M.
AU  - Meirelles, P.
AU  - Mino, S.
AU  - Suda, W.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Ohkuma, M.
AU  - Hosokawa, M.
AU  - Miyashita, K.
AU  - Thompson, F.L.
AU  - Niwa, A.
AU  - Sawabe, T.
AU  - Sawabe, T.
TI  - Draft Genome Sequence of Marine Flavobacterium Jejuia pallidilutea Strain 11shimoA1 and Pigmentation Mutants.
JO  - Genome Announcements
PY  - 2014
SP  - e01236
EP  - e01214
VL  - 2
AB  - Here, we present the draft genome sequence of a novel carotenoid 2'-isopentenylsaproxanthin
AB  - producer, Jejuia pallidilutea strain 11shimoA1,
AB  - isolated from the surface of seaweed in Japan, and the ethyl
AB  - methanesulfonate-induced pigmentation mutants. This genomic information will help
AB  - to not only elucidate the 2'-isopentenylsaproxanthin biosynthetic pathway but
AB  - also understand the evolution of flavobacteria.
ER  -

TY  - JOUR
AU  - Takatani, N.
AU  - Nakanishi, M.
AU  - Meirelles, P.
AU  - Mino, S.
AU  - Suda, W.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Ohkuma, M.
AU  - Hosokawa, M.
AU  - Miyashita, K.
AU  - Thompson, F.L.
AU  - Niwa, A.
AU  - Sawabe, T.
AU  - Sawabe, T.
TI  - Draft Genome Sequences of Marine Flavobacterium Algibacter lectus Strains SS8 and NR4.
JO  - Genome Announcements
PY  - 2014
SP  - e01168
EP  - e01114
VL  - 2
AB  - Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium,
AB  - Algibacter lectus strains SS8 and NR4, isolated from coastal
AB  - sediment and rock surfaces in Hakodate, Japan, respectively. This genomic
AB  - information represents the first Algibacter genome sequences, which will help us
AB  - to elucidate the biology and evolution of Flavobacteriaceae bacteria.
ER  -

TY  - JOUR
AU  - Takehara, I.
AU  - Kato, D.I.
AU  - Takeo, M.
AU  - Negoro, S.
TI  - Draft Genome Sequence of the Nylon Oligomer-Degrading Bacterium Arthrobacter sp.  Strain KI72.
JO  - Genome Announcements
PY  - 2017
SP  - e00217
EP  - e00217
VL  - 5
AB  - We report here the 4.6-Mb genome sequence of a nylon oligomer-degrading bacterium,
AB  - Arthrobacter sp. strain KI72. The draft genome sequence of strain KI72
AB  - consists of 4,568,574 bp, with a G+C content of 63.47%, 4,372 coding sequences
AB  - (CDSs), 54 tRNAs, and six rRNAs.
ER  -

TY  - JOUR
AU  - Takeno, A.
AU  - Okamoto, A.
AU  - Tori, K.
AU  - Oshima, K.
AU  - Hirakawa, H.
AU  - Toh, H.
AU  - Agata, N.
AU  - Yamada, K.
AU  - Ogasawara, N.
AU  - Hayashi, T.
AU  - Shimizu, T.
AU  - Kuhara, S.
AU  - Hattori, M.
AU  - Ohta, M.
TI  - Complete Genome Sequence of Bacillus cereus NC7401, Which Produces High Levels of the Emetic Toxin Cereulide.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4767
EP  - 4768
VL  - 194
AB  - We report the complete and annotated genome sequence of Bacillus cereus NC7401, a
AB  - representative of the strain group that causes emetic-type food poisoning. The
AB  - emetic toxin, cereulide, is produced by a nonribosomal protein synthesis (NRPS)
AB  - system that is encoded by a gene cluster on a large resident plasmid, pNCcld.
ER  -

TY  - JOUR
AU  - Takeshima, H.
AU  - Suetake, I.
AU  - Tajima, S.
TI  - Mouse Dnmt3a Preferentially Methylates Linker DNA and Is Inhibited by Histone H1.
JO  - J. Mol. Biol.
PY  - 2008
SP  - 810
EP  - 821
VL  - 383
AB  - In mammals, DNA methylation is crucial for embryonic development and germ cell
AB  - differentiation. The DNA methylation patterns are created by de novo-type DNA
AB  - methyltransferases (Dnmts) 3a and 3b. Dnmt3a is crucial for global methylation, including that
AB  - of imprinted genes in germ cells. In eukaryotic nuclei, genomic DNA is packaged into
AB  - multinucleosomes with linker histone H1, which binds to core nucleosomes, simultaneously
AB  - making contacts in the linker DNA that separates adjacent nucleosomes. In the present study,
AB  - we prepared oligonucleosomes from HeLa nuclei with or without linker histone H1 and used them
AB  - as a substrate for Dnmt3a. Removal of histone H1 enhanced the DNA methylation activity.
AB  - Furthermore, Dnmt3a preferentially methylated the linker between the two nucleosome core
AB  - regions of reconstituted dinucleosomes, and the binding of histone H1 inhibited the DNA
AB  - methylation activity of Dnmt3a towards the linker DNA. Since an identical amount of histone H1
AB  - did not inhibit the activity towards naked DNA, the inhibitory effect of histone H1 was not on
AB  - the Dnmt3a catalytic activity but on its preferential location in the linker DNA of the
AB  - dinucleosomes. The central globular domain and C-terminal tail of the histone H1 molecule were
AB  - indispensable for inhibition of the DNA methylation activity of Dnmt3a. We propose that the
AB  - binding and release of histone H1 from the linker portion of chromatin may regulate the local
AB  - DNA methylation of the genome by Dnmt3a, which is expressed ubiquitously in somatic cells in
AB  - vivo.
ER  -

TY  - JOUR
AU  - Takeshita, K.
AU  - Shibata, T.F.
AU  - Nikoh, N.
AU  - Nishiyama, T.
AU  - Hasebe, M.
AU  - Fukatsu, T.
AU  - Shigenobu, S.
AU  - Kikuchi, Y.
TI  - Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont  of the Bean Bug Riptortus pedestris.
JO  - Genome Announcements
PY  - 2014
SP  - e00556
EP  - e00514
VL  - 2
AB  - Burkholderia sp. strain RPE67 is a bacterial symbiont isolated from a field-collected bean
AB  - bug, Riptortus pedestris. To understand the genetic basis of
AB  - the insect-microbe symbiosis, we performed whole-genome sequencing of the
AB  - Burkholderia strain, revealing an 8.69-Mb genome consisting of three chromosomes
AB  - and three plasmids.
ER  -

TY  - JOUR
AU  - Takeshita, K.
AU  - Suetake, I.
AU  - Yamashita, E.
AU  - Suga, M.
AU  - Narita, H.
AU  - Nakagawa, A.
AU  - Tajima, S.
TI  - Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 9055
EP  - 9059
VL  - 108
AB  - Methylation of cytosine in DNA plays a crucial role in development through inheritable gene
AB  - silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation
AB  - patterns to the next generation via its preferential methylation of hemimethylated CpG sites
AB  - in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here
AB  - we report the crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its
AB  - complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein.
AB  - Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to
AB  - replication foci is inserted into the DNA-binding pocket, indicating that this domain must be
AB  - removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic
AB  - cysteine residue undergoes a conformation transition to a catalytically competent position.
AB  - For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition
AB  - domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent
AB  - report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the
AB  - catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance
AB  - methylation is a multistep process accompanied by structural changes.
ER  -

TY  - JOUR
AU  - Takeuchi, F.
AU  - Watanabe, S.
AU  - Baba, T.
AU  - Yuzawa, H.
AU  - Ito, T.
AU  - Morimoto, Y.
AU  - Kuroda, M.
AU  - Cui, L.
AU  - Takahashi, M.
AU  - Ankai, A.
AU  - Baba, S.
AU  - Fukui, S.
AU  - Lee, J.C.
AU  - Hiramatsu, K.
TI  - Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of Human-colonizing   Staphylococcal species.
JO  - J. Bacteriol.
PY  - 2005
SP  - 7292
EP  - 7308
VL  - 187
AB  - Staphylococcus haemolyticus is an opportunistic bacterial pathogen that colonizes human skin
AB  - and is remarkable for its highly antibiotic-resistant
AB  - phenotype. We determined the complete genome sequence of S.haemolyticus to
AB  - better understand its pathogenicity and evolutionary relatedness to the
AB  - other staphylococcal species. A large proportion of the open reading
AB  - frames in the genomes of S.haemolyticus, Staphylococcus aureus, and
AB  - Staphylococcus epidermidis were conserved in their sequence and order on
AB  - the chromosome. We identified a region of the bacterial chromosome just
AB  - downstream of the origin of replication that showed little homology among
AB  - the species but was conserved among strains within a species. This novel
AB  - region, designated the "oriC environ," likely contributes to the evolution
AB  - and differentiation of the staphylococcal species, since it was enriched
AB  - for species-specific nonessential genes that contribute to the biological
AB  - features of each staphylococcal species. A comparative analysis of the
AB  - genomes of S.haemolyticus, S.aureus, and S.epidermidis elucidated
AB  - differences in their biological and genetic characteristics and pathogenic
AB  - potentials. We identified as many as 82 insertion sequences in the
AB  - S.haemolyticus chromosome that probably mediated frequent genomic
AB  - rearrangements, resulting in phenotypic diversification of the strain.
AB  - Such rearrangements could have brought genomic plasticity to this species
AB  - and contributed to its acquisition of antibiotic resistance.
ER  -

TY  - JOUR
AU  - Takeuchi, H.
AU  - Donahue, J.P.
AU  - Krishna, U.
AU  - Miller, G.G.
AU  - Peek, R.M. Jr.
AU  - Israel, D.A.
TI  - Quantitative detection of expression of the Helicobacter pylori methyltransferase-encoding gene hpyIM in vivo and in vitro.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2002
SP  - 242
EP  - 242
VL  - 102
AB  - Helicobacter pylori are highly diverse bacteria that persist in the human stomach and induce
AB  - chronic gastritis for the virtual lifetime of
AB  - their hosts, a process that increases risk for peptic ulceration,
AB  - gastric adenocarcinoma, and gastric lymphoma. Despite a high degree of
AB  - genetic diversity, particularly among restriction-modification systems,
AB  - hpyIM which encodes a DNA adenine methyltransferase is highly conserved
AB  - among all H. pylori strains. Because of this high level of
AB  - conservation, we sought to determine whether levels of hpyIM expression
AB  - within colonized human mucosa correlated with disease status or mucosal
AB  - injury and whether there was a relationship between levels of
AB  - expression in vivo and in vitro. PCR-light and slot blot hybridizations
AB  - were used to quantitate hypIM transcripts in gastric tissue or in
AB  - broth-grown cells and quantities were normalized to levels of H. pylori
AB  - 16s rRNA. Among 41 clinical biopsies, levels of hpyIM transcripts
AB  - varied dramatically and were not related to disease outcome or severity
AB  - of inflammation. Four strains isolated from biopsies were selected for
AB  - more detailed in vitro studies, and for each strain, levels of hpyIM
AB  - were higher during log-phase growth compared with stationary phase. For
AB  - three of the four strains, levels of hypIM transcripts were lower in
AB  - vitro than in vivo. Since bacterial contact with host cells regulates
AB  - gene expression in other organisms, we next sought to determine if
AB  - adherence of H. pylori to gastric epithelial cells resulted in hpyIM
AB  - expression patterns that more closely reflected levels observed in
AB  - vivo. hpyIM transcript levels after two hours of adherence were not
AB  - related to levels identified within inflamed tissue, suggesting that
AB  - events independent from isolated bacterial:epithelial cell contact may
AB  - regulate hpyIM expression in vivo.
ER  -

TY  - JOUR
AU  - Takeuchi, H.
AU  - Israel, D.A.
AU  - Miller, G.G.
AU  - Donahue, J.P.
AU  - Krishna, U.
AU  - Gaus, K.
AU  - Peek, R.M.
TI  - Characterization of expression of a functionally conserved Helicobacter pylori methyltransferase-encoding gene within inflamed mucosa and  during in vitro growth.
JO  - J. Infect. Dis.
PY  - 2002
SP  - 1186
EP  - 1189
VL  - 186
AB  - Methylation of bacterial DNA can regulate microbial growth and virulence. Expression of hpyIM,
AB  - a conserved methyltransferase of the
AB  - gastric pathogen Helicobacter pylori, was quantitated in gastric biopsy
AB  - specimens from 41 H. pylori-infected patients and during growth in
AB  - vitro, by quantitative reverse transcriptase-polymerase chain reaction
AB  - and/or RNA slot-blot analysis, to determine whether levels of
AB  - transcription were associated with pathologic outcome, as based on both
AB  - severity of gastritis and inflammatory cytokine levels, or were
AB  - regulated by bacterial growth phase. The effects that hpyIM
AB  - inactivation has on bacterial morphology were determined by electron
AB  - microscopy. Expression of hpyIM varied dramatically within colonized
AB  - gastric tissue, and levels were not related to either colonization
AB  - density, severity of inflammation, mucosal IL-8 concentrations, or
AB  - clinical disease. In vitro, hpyIM expression was higher during
AB  - log-phase growth and was required for normal bacterial morphology,
AB  - suggesting that hpyIM expression may be growth-phase regulated within
AB  - the gastric niche.
ER  -

TY  - JOUR
AU  - Takeuchi, K.
AU  - Noda, N.
AU  - Someya, N.
TI  - Complete Genome Sequence of the Biocontrol Strain Pseudomonas protegens Cab57 Discovered in Japan Reveals Strain-Specific Diversity of This Species.
JO  - PLoS ONE
PY  - 2014
SP  - E93683
EP  - E93683
VL  - 9
AB  - The biocontrol strain Pseudomonas sp. Cab57 was isolated from the rhizosphere of
AB  - shepherd's purse growing in a field in Hokkaido by screening the antibiotic
AB  - producers. The whole genome sequence of this strain was obtained by paired-end
AB  - and whole-genome shotgun sequencing, and the gaps between the contigs were closed
AB  - using gap-spanning PCR products. The P. sp. Cab57 genome is organized into a
AB  - single circular chromosome with 6,827,892 bp, 63.3% G+C content, and 6,186
AB  - predicted protein-coding sequences. Based on 16S rRNA gene analysis and whole
AB  - genome analysis, strain Cab57 was identified as P. protegens. As reported in P.
AB  - protegens CHA0 and Pf-5, four gene clusters (phl, prn, plt, and hcn) encoding the
AB  - typical antibiotic metabolites and the reported genes associated with Gac/Rsm
AB  - signal transduction pathway of these strains are fully conserved in the Cab57
AB  - genome. Actually strain Cab57 exhibited typical Gac/Rsm activities and antibiotic
AB  - production, and these activities were enhanced by knocking out the retS gene (for
AB  - a sensor kinase acting as an antagonist of GacS). Two large segments (79 and 115
AB  - kb) lacking in the Cab57 genome, as compared with the Pf-5 genome, accounted for
AB  - the majority of the difference (247 kb) between these genomes. One of these
AB  - segments was the complete rhizoxin analog biosynthesis gene cluster (ca. 79 kb)
AB  - and another one was the 115-kb mobile genomic island. A whole genome comparison
AB  - of those relative strains revealed that each strain has unique gene clusters
AB  - involved in metabolism such as nitrite/nitrate assimilation, which was identified
AB  - in the Cab57 genome. These findings suggest that P. protegens is a ubiquitous
AB  - bacterium that controls its biocontrol traits while building up strain-specific
AB  - genomic repertoires for the biosynthesis of secondary metabolites and niche
AB  - adaptation.
ER  -

TY  - JOUR
AU  - Takeuchi, R.
AU  - Certo, M.
AU  - Caprara, M.G.
AU  - Scharenberg, A.M.
AU  - Stoddard, B.L.
TI  - Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 877
EP  - 890
VL  - 37
AB  - The LAGLIDADG homing endonuclease (LHE) I-AniI has adopted an extremely efficient secondary
AB  - RNA splicing activity that is beneficial to its host,
AB  - balanced against inefficient DNA cleavage. A selection experiment
AB  - identified point mutations in the enzyme that act synergistically to
AB  - improve endonuclease activity. The amino-acid substitutions increase
AB  - target affinity, alter the thermal cleavage profile and significantly
AB  - increase targeted recombination in transfected cells. The RNA splicing
AB  - activity is not affected by these mutations. The improvement in DNA
AB  - cleavage activity is largely focused on one of the enzyme's two active
AB  - sites, corresponding to a rearrangement of a lysine residue hypothesized
AB  - to act as a general base. Most of the constructs isolated in the screen
AB  - contain one or more mutations that revert an amino-acid identity to a
AB  - residue found in one or more close homologues of I-AniI. This implies that
AB  - mutations that have previously reduced the endonuclease activity of I-AniI
AB  - are identified and reversed, sometimes in combination with additional
AB  - 'artificial' mutations, to optimize its in vivo activity.
ER  -

TY  - JOUR
AU  - Takeuchi, R.
AU  - Choi, M.
AU  - Stoddard, B.L.
TI  - Engineering of Customized Meganucleases via In Vitro Compartmentalization and In Cellulo Optimization.
JO  - Methods Mol. Biol.
PY  - 2015
SP  - 105
EP  - 132
VL  - 1239
AB  - LAGLIDADG homing endonucleases (also referred to as 'meganucleases') are compact DNA
AB  - cleaving enzymes that specifically recognize long target sequences (approximately 20 base
AB  - pairs), and thus serve as useful tools for therapeutic genome engineering. While stand-alone
AB  - meganucleases are sufficiently active to introduce targeted genome modification, they can be
AB  - fused to additional sequence-specific DNA binding domains in order to improve their
AB  - performance in target cells. In this chapter, we describe an approach to retarget
AB  - meganucleases to DNA targets of interest (such as sequences found in genes and cis regulatory
AB  - regions), which is feasible in an academic laboratory environment. A combination of two
AB  - selection systems, in vitro compartmentalization and two-plasmid cleavage assay in bacteria,
AB  - allow for efficient engineering of meganucleases that specifically cleave a wide variety of
AB  - DNA sequences.
ER  -

TY  - JOUR
AU  - Takeuchi, R.
AU  - Lambert, A.R.
AU  - Mak, A.N.
AU  - Jacoby, K.
AU  - Dickson, R.J.
AU  - Gloor, G.B.
AU  - Scharenberg, A.M.
AU  - Edgell, D.R.
AU  - Stoddard, B.L.
TI  - Tapping natural reservoirs of homing endonucleases for targeted gene modification.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 13077
EP  - 13082
VL  - 108
AB  - Homing endonucleases mobilize their own genes by generating double-strand breaks at individual
AB  - target sites within potential host DNA. Because of their high specificity, these proteins are
AB  - used for 'genome editing' in higher eukaryotes. However, alteration of homing endonuclease
AB  - specificity is quite challenging. Here we describe the identification and phylogenetic
AB  - analysis of over 200 naturally occurring LAGLIDADG homing endonucleases (LHEs). Biochemical
AB  - and structural characterization of endonucleases from one clade within the phylogenetic tree
AB  - demonstrates strong conservation of protein structure contrasted against highly diverged DNA
AB  - target sites and indicates that a significant fraction of these proteins are sufficiently
AB  - stable and active to serve as engineering scaffolds. This information was exploited to create
AB  - a targeting enzyme to disrupt the endogenous monoamine oxidase B gene in human cells. The
AB  - ubiquitous presence and diversity of LHEs described in this study may facilitate the creation
AB  - of many tailored nucleases for genome editing.
ER  -

TY  - JOUR
AU  - Takiguchi, M.
AU  - Achanzar, W.E.
AU  - Qu, W.
AU  - Li, G.
AU  - Waalkes, M.P.
TI  - Effects of cadmium on DNA-(cytosine-5) methyltransferase activity and DNA methylation status during cadmium-induced cellular transformation.
JO  - Exp. Cell Res.
PY  - 2003
SP  - 355
EP  - 365
VL  - 286
AB  - Cadmium is a human carcinogen that likely acts via epigenetic mechanisms. Since DNA
AB  - methylation alterations represent an important epigenetic event
AB  - linked to cancer, the effect of cadmium on DNA methyltransferase (MeTase)
AB  - activity was examined using in vitro (TRL1215 rat liver cells) and ex vivo
AB  - (M.SssI DNA MeTase) systems. Cadmium effectively inhibited DNA MeTases in
AB  - a manner that was noncompetitive with respect to substrate (DNA),
AB  - indicating an interaction with the DNA binding domain rather than the
AB  - active site. Based on these results, the effects of prolonged cadmium
AB  - exposure on DNA MeTase and genomic DNA methylation in TRL1215 cells were
AB  - studied. After 1 week of exposure to 0-2.5 microM cadmium, DNA MeTase
AB  - activity was reduced (up to 40%) in a concentration-dependent fashion,
AB  - while genomic DNA methylation showed slight but significant reductions at
AB  - the two highest concentrations. After 10 weeks of exposure, the cells
AB  - exhibited indications of transformation, including hyperproliferation,
AB  - increased invasiveness, and decreased serum dependence. Unexpectedly,
AB  - these cadmium-transformed cells exhibited significant increases in DNA
AB  - methylation and DNA MeTase activity. These results indicate that, while
AB  - cadmium is an effective inhibitor of DNA MeTase and initially induces DNA
AB  - hypomethylation, prolonged exposure results in DNA hypermethylation and
AB  - enhanced DNA MeTase activity.
ER  -

TY  - JOUR
AU  - Taktakishvili, M.O.
AU  - Tabdzhun, A.
TI  - Oligodeoxynucleotides, containing 6-O-alkylated guanine segments recognized by HaeIII restriction endonuclease.
JO  - Bioorg. Khim.
PY  - 1991
SP  - 806
EP  - 808
VL  - 17
AB  - A series of self-complementary decadeoxynucleotides containing a native or modified HaeIII
AB  - site GGCC (with one or both guanine residues 6-0-cetylated) have been synthesized by the
AB  - phosphotriester approach.  The nonmodified decanucleotide is normally digested with snake
AB  - venom phosphodiesterase as well as with HaeIII and BspI restriction endonucleases, whereas the
AB  - bulky 6-O-alkyl substitutent strongly inhibits the VPDE hydrolysis and completely prevents
AB  - digestion with the endonucleases.
ER  -

TY  - JOUR
AU  - Talukdar, M.
AU  - Das, D.
AU  - Borah, C.
AU  - Deka-Boruah, H.P.
AU  - Bora, T.C.
AU  - Singh, A.K.
TI  - Draft Genome Sequence of Micromonospora sp. Strain HK10, Isolated from Kaziranga  National Park, India.
JO  - Genome Announcements
PY  - 2016
SP  - e00559
EP  - e00515
VL  - 4
AB  - We report the 6.92-Mbp genome sequence of Micromonospora sp. HK10, isolated from  soil samples
AB  - collected from Kaziranga National Park, Assam, India. The full
AB  - genome of strain Micromonospora sp. strain HK10 consists of 6,911,179 bp with
AB  - 73.39% GC content, 6,196 protein-coding genes, and 86 RNAs.
ER  -

TY  - JOUR
AU  - Tamariz, J.
AU  - Llanos, C.
AU  - Seas, C.
AU  - Montenegro, P.
AU  - Lagos, J.
AU  - Fernandes, M.R.
AU  - Cerdeira, L.
AU  - Lincopan, N.
TI  - Draft Genome Sequence of the First New Delhi Metallo-beta-Lactamase (NDM-1)-Producing Escherichia coli Strain Isolated in Peru.
JO  - Genome Announcements
PY  - 2018
SP  - e00199
EP  - e00118
VL  - 6
AB  - We present here the draft genome sequence of the first New Delhi metallo-beta-lactamase
AB  - (NDM-1)-producing Escherichia coli strain, belonging to
AB  - sequence type 155 (ST155), isolated in Peru. Assembly of this draft genome
AB  - resulted in 5,061,184 bp, revealing a clinically significant resistome for
AB  - beta-lactams, aminoglycosides, tetracyclines, phenicols, sulfonamides,
AB  - trimethoprim, and fluoroquinolones.
ER  -

TY  - JOUR
AU  - Tamaru, H.
AU  - Selker, E.U.
TI  - A histone H3 methyltransferase controls DNA methylation in Neurospora crassa.
JO  - Nature
PY  - 2001
SP  - 277
EP  - 283
VL  - 414
AB  - DNA methylation is involved in epigenetic processes such as X-chromosome inactivation,
AB  - imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a
AB  - DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora
AB  - crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation,
AB  - as well as for normal growth and full fertility. We mapped dim-5 and identified it by
AB  - transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a
AB  - gene related to histone methyltransferases that are involved in heterochromatin formation in
AB  - other organisms.  Transformation of a wild-type strain with a segment of dim-5 reactivated a
AB  - silenced hph gene, apparently by 'quelling' of dim-5. We demonstrate that recombinant DIM-5
AB  - protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with
AB  - either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA
AB  - methylation depends on histone methylation.
ER  -

TY  - JOUR
AU  - Tamaru, Y.
AU  - Miyake, H.
AU  - Kuroda, K.
AU  - Nakanishi, A.
AU  - Kawade, Y.
AU  - Yamamoto, K.
AU  - Uemura, M.
AU  - Fujita, Y.
AU  - Doi, R.H.
AU  - Ueda, M.
TI  - Genome Sequence of the Cellulosome-Producing Mesophilic Organism Clostridium cellulovorans 743B.
JO  - J. Bacteriol.
PY  - 2010
SP  - 901
EP  - 902
VL  - 192
AB  - Clostridium cellulovorans 743B was isolated from a wood chip pile and is an anaerobic and
AB  - mesophilic spore-forming bacterium. This organism
AB  - degrades native substrates in soft biomass such as corn fiber and rice
AB  - straw efficiently by producing an extracellular enzyme complex called the
AB  - cellulosome. Here we report the genome sequence of C. cellulovorans 743B.
ER  -

TY  - JOUR
AU  - Tamas, I.
AU  - Dedysh, S.N.
AU  - Liesack, W.
AU  - Stott, M.B.
AU  - Alam, M.
AU  - Murrell, J.C.
AU  - Dunfield, P.F.
TI  - Complete Genome Sequence of Beijerinckia indica subsp. indica.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4532
EP  - 4533
VL  - 192
AB  - Beijerinckia indica subsp. indica is an aerobic, acidophilic, exopolysaccharide-producing,
AB  - N2-fixing soil bacterium. It is a generalist
AB  - chemoorganotroph that is phylogenetically closely related to facultative
AB  - and obligate methanotrophs of the genera Methylocella and Methylocapsa.
AB  - Here we report the full genome sequence of this bacterium.
ER  -

TY  - JOUR
AU  - Tamas, I.
AU  - Klasson, L.
AU  - Canback, B.
AU  - Naslund, A.K.
AU  - Eriksson, A.-S.
AU  - Wernegreen, J.J.
AU  - Sandstrom, J.P.
AU  - Moran, N.A.
AU  - Andersson, S.G.E.
TI  - 50 million years of genomic stasis in endosymbiotic bacteria.
JO  - Science
PY  - 2002
SP  - 2376
EP  - 2379
VL  - 296
AB  - Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts
AB  - of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or
AB  - gene acquisitions have occurred in the past 50 to 70 million years, despite substantial
AB  - sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes
AB  - of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than
AB  - 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely
AB  - attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola
AB  - is no longer a source of ecological innovation for its hosts.
ER  -

TY  - JOUR
AU  - Tambalo, D.D.
AU  - Perry, B.J.
AU  - Fitzgerald, S.F.
AU  - Cameron, A.D.
AU  - Yost, C.K.
TI  - Draft Genome Sequence and Annotation of Phyllosphere-Persisting Salmonella enterica subsp. enterica Serovar Livingstone Strain CKY-S4, Isolated from an  Urban Lake in Regina, Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e00884
EP  - e00815
VL  - 3
AB  - Here, we report the first draft genome sequence of Salmonella enterica subsp. enterica serovar
AB  - Livingstone. This S. Livingstone strain CKY-S4 displayed biofilm
AB  - formation and cellulose production and could persist on lettuce. This genome may
AB  - help the study of mechanisms by which enteric pathogens colonize food crops.
ER  -

TY  - JOUR
AU  - Tambong, J.T.
AU  - Xu, R.
AU  - Adam, Z.
AU  - Cott, M.
AU  - Rose, K.
AU  - Reid, L.M.
AU  - Daayf, F.
AU  - Briere, S.
AU  - Bilodeau, G.J.
TI  - Draft Genome Sequence of Clavibacter michiganensis subsp. nebraskensis Strain DOAB 397, Isolated from an Infected Field Corn Plant in Manitoba, Canada.
JO  - Genome Announcements
PY  - 2015
SP  - e00768
EP  - e00715
VL  - 3
AB  - In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated  from
AB  - symptomatic corn leaves in Manitoba, Canada. We report the draft genome
AB  - sequence of C. michiganensis subsp. nebraskensis DOAB 397, consisting of 3.059 Mb
AB  - with 73.0% G+C content, 2,922 predicted protein-coding sequences, 45 tRNAs, 3
AB  - rRNAs, and 37 pseudogenes.
ER  -

TY  - JOUR
AU  - Tamhankar, A.J.
AU  - Nerkar, S.S.
AU  - Khadake, P.P.
AU  - Akolkar, D.B.
AU  - Apurwa, S.R.
AU  - Deshpande, U.
AU  - Khedkar, S.U.
AU  - Stalsby-Lundborg, C.
TI  - Draft Genome Sequence of Enterotoxigenic Escherichia coli Strain E24377A, Obtained from a Tribal Drinking Water Source in India.
JO  - Genome Announcements
PY  - 2015
SP  - e00225
EP  - e00215
VL  - 3
AB  - Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease in  humans and
AB  - animals. Its dissemination can occur through water sources
AB  - contaminated by it. Here, we report for the first time the draft genome sequence
AB  - of ETEC strain E24377A, obtained from a tribal drinking water source in India.
ER  -

TY  - JOUR
AU  - Tamulaitiene, G.
AU  - Grazulis, S.
AU  - Janulaitis, A.
AU  - Janowski, R.
AU  - Bujacz, G.
AU  - Jaskolski, M.
TI  - Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I.
JO  - Biochim. Biophys. Acta
PY  - 2004
SP  - 251
EP  - 254
VL  - 1698
AB  - Restriction endonuclease Eco57I from Escherichia coli recognizes asymmetric DNA sequence
AB  - 5'-CTGAAG and has both restriction (DNA cleavage a short distance away from the recognition
AB  - site) and modification (methylation) activities residing in a single polypeptide chain. Single
AB  - crystals of wild-type Eco57I ternary complexes with double-stranded DNA and sinefungin, a
AB  - stimulator of endonuclease activity, were obtained by the vapor diffusion technique and
AB  - characterized crystallographically for different variants of the DNA component. The best data
AB  - for the complex with 25-mer DNA were collected to 4.2-A resolution at 100 K using synchrotron
AB  - radiation. The crystals are orthorhombic, space group P2(1)2(1)2, with a=164.3, b=293.0,
AB  - c=71.1 A, and contain two to four copies of the protein in the asymmetric unit.
ER  -

TY  - JOUR
AU  - Tamulaitiene, G.
AU  - Jakubauskas, A.
AU  - Urbanke, C.
AU  - Huber, R.
AU  - Grazulis, S.
AU  - Siksnys, V.
TI  - The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
JO  - Structure
PY  - 2006
SP  - 1389
EP  - 1400
VL  - 14
AB  - Rare-cutting restriction enzymes are important tools in genome analysis.  We report here the
AB  - crystal structure of SdaI restriction endonuclease, which is specific for the 8 bp sequence
AB  - CCTGCA/GG ("/" designates the cleavage site).  Unlike orthodox Type IIP enzymes, which are
AB  - single domain proteins, the SdaI monomer is composed of two structural domains.  The N domain
AB  - contains a classical winged helix-turn-helix (wHTH) DNA binding motif, while the C domain
AB  - shows a typical restriction endonuclease fold.  The active site of SdaI is located within the
AB  - C domain and represents a variant of the canonical PD-(D/E)XK motif.  SdaI determinants of
AB  - sequence specificity are clustered on the recognition helix of the wHTH motif at the N domain.
AB  - The modular architecture of SdaI, wherein one domain mediates DNA binding while the other
AB  - domain is predicted to catalyze hydrolysis, distinguishes SdaI from previously characterized
AB  - restriction enzymes interacting with symmetric recognition sequences.
ER  -

TY  - JOUR
AU  - Tamulaitiene, G.
AU  - Jovaisaite, V.
AU  - Tamulaitis, G.
AU  - Songailiene, I.
AU  - Manakova, E.
AU  - Zaremba, M.
AU  - Grazulis, S.
AU  - Xu, S.Y.
AU  - Siksnys, V.
TI  - Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 3547
EP  - 3558
VL  - 45
AB  - Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within
AB  - or close to their DNA target sites, they form different
AB  - oligomeric assemblies ranging from monomers, dimers, tetramers to higher order
AB  - oligomers to generate a double strand break in DNA. Type IIP restriction
AB  - endonuclease AgeI recognizes a palindromic sequence 5-A/CCGGT-3 and cuts it ('/'
AB  - denotes the cleavage site) producing staggered DNA ends. Here, we present crystal
AB  - structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar
AB  - to the restriction enzymes that share in their target sites a conserved CCGG
AB  - tetranucleotide and a cleavage pattern. Structure analysis and biochemical data
AB  - indicate, that AgeI is a monomer in the apo-form both in the crystal and in
AB  - solution, however, it binds and cleaves the palindromic target site as a dimer.
AB  - DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.
ER  -

TY  - JOUR
AU  - Tamulaitiene, G.
AU  - Siksnys, V.
TI  - NotI Is Not Boring.
JO  - Structure
PY  - 2008
SP  - 497
EP  - 498
VL  - 16
AB  - Crystal structures of the restriction endonuclease NotI in free and DNA bound forms, presented
AB  - in this issue of Structure (Lambert et al., 2008), provide a unique insight into the
AB  - structural details of 8 base pair  sequence recognition by the restriction enzyme.
ER  -

TY  - JOUR
AU  - Tamulaitiene, G.
AU  - Silanskas, A.
AU  - Grazulis, S.
AU  - Zaremba, M.
AU  - Siksnys, V.
TI  - Crystal structure of the R-protein of the multisubunit ATP-dependent restriction  endonuclease NgoAVII.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 14022
EP  - 14030
VL  - 42
AB  - The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and
AB  - N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III
AB  - ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we
AB  - present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain
AB  - bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD
AB  - domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII
AB  - REases, and in plant transcription factors. Structural comparison of the B3-like domains of
AB  - R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding
AB  - surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII,
AB  - EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the
AB  - majority of the contacts to the target site is much longer. The overall structures of
AB  - R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity,
AB  - R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to
AB  - cleave DNA at the target site. The structures we present will help formulate future
AB  - experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA
AB  - cleavage by R.NgoAVII and related endonucleases.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Lagunavicius, A.
TI  - DNA bending induced by MunI restriction endonuclease.
JO  - Biologija
PY  - 2000
SP  - 11
EP  - 15
VL  - 0
AB  - Bending of DNA induced by the specific binding of the restriction endonuclease MunI has been
AB  - investigated by the empirical method of Thompson and Landy and the method of calibrated
AB  - standards.  The R.MunI induced bending angles were found to be 42o +/- 4o at pH 6.5 and 56o
AB  - +/1 4o at pH 8.3 in the presence of Ca2+ ions.  Similar values of DNA bending angles were
AB  - obtained in the complexes of active site mutants D83A and E98A with specific DNA under the
AB  - same conditions.  Results of bending experiments support the assumption that elimination of
AB  - electrostatic repulsion between charged carboxylates and phosphate oxygens by protonation of
AB  - the active site carboxylate residue(s), their replacement to alanine or neutralization by Ca2+
AB  - binding yields similar DNA-protein complexes.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Mucke, M.
AU  - Siksnys, V.
TI  - Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes.
JO  - FEBS Lett.
PY  - 2006
SP  - 1665
EP  - 1671
VL  - 580
AB  - The archetypal Type BE restriction endonuclease EcoRII is a dimer that has a modular
AB  - structure. DNA binding studies indicate that the isolated
AB  - C-terminal domain dimer has an interface that binds a single cognate
AB  - DNA molecule whereas the N-terminal domain is a monomer that also binds
AB  - a single copy of cognate DNA. Hence, the full-length EcoRII contains
AB  - three putative DNA binding interfaces: one at the C-terminal domain
AB  - dimer and two at each of the N-terminal domains. Mutational analysis
AB  - indicates that the C-terminal domain shares conserved active site
AB  - architecture and DNA binding elements with the tetrameric restriction
AB  - enzyme NgoMIV. Data provided here suggest possible evolutionary
AB  - relationships between different subfamilies of restriction enzymes.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Rutkauskas, M.
AU  - Zaremba, M.
AU  - Grazulis, S.
AU  - Tamulaitiene, G.
AU  - Siksnys, V.
TI  - Functional significance of protein assemblies predicted by the crystal structure  of the restriction endonuclease BsaWI.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 8100
EP  - 8110
VL  - 43
AB  - Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W
AB  - stands for A or T, '/' denotes the cleavage site). It belongs to
AB  - a large family of restriction enzymes that contain a conserved CCGG
AB  - tetranucleotide in their target sites. These enzymes are arranged as dimers or
AB  - tetramers, and require binding of one, two or three DNA targets for their optimal
AB  - catalytic activity. Here, we present a crystal structure and biochemical
AB  - characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an
AB  - 'open' configuration dimer and binds a single DNA copy through a minor groove
AB  - contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via
AB  - the C-terminal domain contacts implying possible higher order aggregates. We show
AB  - that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium,
AB  - but in the presence of specific DNA forms a tetramer bound to two target sites.
AB  - Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a
AB  - tetramer and requires two target sites for optimal activity. We propose BsaWI
AB  - mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona
AB  - fide tetrameric NgoMIV/SfiI enzymes.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Sasnauskas, G.
AU  - Mucke, M.
AU  - Siksnys, V.
TI  - Simultaneous Binding of Three Recognition Sites is Necessary for a Concerted Plasmid DNA Cleavage by EcoRII Restriction Endonuclease.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 406
EP  - 419
VL  - 358
AB  - According to the current paradigm type IIE restriction endonucleases are homodimeric proteins
AB  - that simultaneously bind to two recognition sites but
AB  - cleave DNA at only one site per turnover: the other site acts as an
AB  - allosteric locus, activating the enzyme to cleave DNA at the first.
AB  - Structural and biochemical analysis of the archetypal type IIE restriction
AB  - enzyme EcoRII suggests that it has three possible DNA binding interfaces
AB  - enabling simultaneous binding of three recognition sites. To test if
AB  - putative synapsis of three binding sites has any functional significance,
AB  - we have studied EcoRII cleavage of plasmids containing a single, two and
AB  - three recognition sites under both single turnover and steady state
AB  - conditions. EcoRII displays distinct reaction patterns on different
AB  - substrates: (i) it shows virtually no activity on a single site plasmid;
AB  - (ii) it yields open-circular DNA form nicked at one strand as an
AB  - obligatory intermediate acting on a two-site plasmid; (iii) it cleaves
AB  - concertedly both DNA strands at a single site during a single turnover on
AB  - a three site plasmid to yield linear DNA. Cognate oligonucleotide added in
AB  - trans increases the reaction velocity and changes the reaction pattern for
AB  - the EcoRII cleavage of one and two-site plasmids but has little effect on
AB  - the three-site plasmid. Taken together the data indicate that EcoRII
AB  - requires simultaneous binding of three rather than two recognition sites
AB  - in cis to achieve concerted DNA cleavage at a single site. We show that
AB  - the orthodox type IIP enzyme PspGI which is an isoschisomer of EcoRII,
AB  - cleaves different plasmid substrates with equal rates. Data provided here
AB  - indicate that type IIE restriction enzymes EcoRII and NaeI follow
AB  - different mechanisms. We propose that other type IIE restriction enzymes
AB  - may employ the mechanism suggested here for EcoRII.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Solonin, A.S.
AU  - Siksnys, V.
TI  - Alternative arrangements of catalytic residues at the active sites of restriction enzymes.
JO  - FEBS Lett.
PY  - 2002
SP  - 17
EP  - 22
VL  - 518
AB  - A catalytic sequence motif PDX10-30(E/D)XK is found in many restriction enzymes. On the basis
AB  - of sequence similarities and mapping of the conserved residues to the crystal structure of
AB  - NgoMIV we suggest that residues D160, K182, R186, R188 and E195 contribute to the
AB  - catalytic/DNA binding site of the Ecl18kI restriction endonuclease. Mutational analysis
AB  - confirms the functional significance of the conserved residues of Ecl18kI. Therefore, we
AB  - conclude that the active site motif 159VDX21KX12E of Ecl18kI differs from the canonical
AB  - PDX10-30(E/D)XK motif characteristic for most of the restriction enzymes. Moreover, we propose
AB  - that two subfamilies of endonucleases Ecl18kI/PspGI/EcoRII and Cfr10I/Bse634I/NgoMIV,
AB  - specific, respectively, for CCNGG/CCWGG and RCCGGY/GCCGGC sites, share conserved active site
AB  - architecture and DNA binding elements.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Zaremba, M.
AU  - Szczepanowski, R.H.
AU  - Bochtler, M.
AU  - Siksnys, V.
TI  - How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 6101
EP  - 6108
VL  - 36
AB  - Restriction endonucleases Ecl18kI and PspGI/catalytic domain of EcoRII recognize CCNGG and
AB  - CCWGG sequences (W stands for A or T), respectively.
AB  - The enzymes are structurally similar, interact identically with the
AB  - palindromic CC:GG parts of their recognition sequences and flip the
AB  - nucleotides at their centers. Specificity for the central nucleotides
AB  - could be influenced by the strength/stability of the base pair to be
AB  - disrupted and/or by direct interactions of the enzymes with the flipped
AB  - bases. Here, we address the importance of these contributions. We
AB  - demonstrate that wt Ecl18kI cleaves oligoduplexes containing canonical,
AB  - mismatched and abasic sites in the central position of its target sequence
AB  - CCNGG with equal efficiencies. In contrast, substitutions in the binding
AB  - pocket for the extrahelical base alter the Ecl18kI preference for the
AB  - target site: the W61Y mutant prefers only certain mismatched substrates,
AB  - and the W61A variant cuts exclusively at abasic sites, suggesting that
AB  - pocket interactions play a major role in base discrimination. PspGI and
AB  - catalytic domain of EcoRII probe the stability of the central base pair
AB  - and the identity of the flipped bases in the pockets. This 'double check'
AB  - mechanism explains their extraordinary specificity for an A/T pair in the
AB  - flipping position.
ER  -

TY  - JOUR
AU  - Tamulaitis, G.
AU  - Zaremba, M.
AU  - Szczepanowski, R.H.
AU  - Bochtler, M.
AU  - Siksnys, V.
TI  - Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 4792
EP  - 4799
VL  - 35
AB  - Many DNA modification and repair enzymes require access to DNA bases and therefore flip
AB  - nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within
AB  - or in the vicinity of the target recognition site and do not require base extrusion for the
AB  - sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a
AB  - co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out
AB  - that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides,
AB  - flipping them out from the helix. Sequence and structure conservation predict nucleotide
AB  - flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data
AB  - in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain
AB  - of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the
AB  - centers of their recognition sequences. The fluorescence increase is largest for PspGI,
AB  - intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the
AB  - hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and
AB  - mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the
AB  - Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI,
AB  - EcoRII-C and PspGI flip nucleotides in solution.
ER  -

TY  - JOUR
AU  - Tamura, T.
AU  - Araki, Y.
AU  - Yamaoka, S.
AU  - Inagaki, K.
AU  - Tanaka, H.
TI  - Determination of methylation specificity of sequence-specific DNA methyltransferases using matrix assisted laser desorption/ionization time-of-flight mass spectrometry.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4162
EP  - 4164
VL  - 25
AB  - We describe here a sensitive and straightforward method for characterizing the methylation
AB  - specificity of type II DNA methyltransferases (Mtases) using matrix-assisted laser
AB  - desorption/ionization time-of-flight mass spectrometry.  DNA substrate, prepared by ligation
AB  - of a commercially available oligonucleotide, was modified by the subject MTase and was
AB  - derivatized to a mixture of single-stranded oligonucleotides through endonuclease treatment,
AB  - heat-denaturation and limited digestion by 3'-terminus-specific phosphodiesterase I.
AB  - MALDI-TOF mass spectrometry was used to determine the mass differences between the digestion
AB  - products, and the methylated nucleotide was explicitly identified by the mass increase in 14
AB  - Da due to the base modification.  The method was applicable to the three representative MTases
AB  - M.EcoRI, M.BamHI and M.HaeIII.
ER  -

TY  - JOUR
AU  - Tamura, T.
AU  - Kataoka, A.
AU  - Shu, L.Y.
AU  - Ashida, A.
AU  - Tanaka, H.
AU  - Inagaki, K.
TI  - An in vitro Screening Method for DNA Cytosine-C5-Methylase Inhibitor.
JO  - Nat. Prod. Lett.
PY  - 2002
SP  - 25
EP  - 27
VL  - 16
AB  - A specific inhibitor of DNA cytosine C-5-methylases would be useful for studying genomic
AB  - imprinting, X-chromosome inactivation, carcinogenesis,
AB  - and regulation of tissue-specific gene expression, for these
AB  - physiological phenomena appears to be regulated through DNA methylation
AB  - in promoter sequences. This paper reports a novel convenient in vitro
AB  - assay method for screening DNA cytosine C-5-methylase inhibitor. Our
AB  - method uses a commercially available HaeIII methylase (cytosine C-5
AB  - methylase), its corresponding HaeIII endonuclease, and lambda DNA as
AB  - their substrate.
ER  -

TY  - JOUR
AU  - Tan, A.
AU  - Atack, J.M.
AU  - Jennings, M.P.
AU  - Seib, K.L.
TI  - The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development.
JO  - Front. Immunol.
PY  - 2016
SP  - 586
EP  - 586
VL  - 7
AB  - Infectious diseases are a leading cause of morbidity and mortality worldwide, and vaccines are
AB  - one of the most successful and cost-effective tools for disease prevention. One of the key
AB  - considerations for rational vaccine development is the selection of appropriate antigens.
AB  - Antigens must induce a protective immune response, and this response should be directed to
AB  - stably expressed antigens so the target microbe can always be recognized by the immune system.
AB  - Antigens with variable expression, due to environmental signals or phase variation (i.e., high
AB  - frequency, random switching of expression), are not ideal vaccine candidates because variable
AB  - expression could lead to immune evasion. Phase variation is often mediated by the presence of
AB  - highly mutagenic simple tandem DNA repeats, and genes containing such sequences can be easily
AB  - identified, and their use as vaccine antigens reconsidered. Recent research has identified
AB  - phase variably expressed DNA methyltransferases that act as global epigenetic regulators.
AB  - These phase-variable regulons, known as phasevarions, are associated with altered virulence
AB  - phenotypes and/or expression of vaccine candidates. As such, genes encoding candidate vaccine
AB  - antigens that have no obvious mechanism of phase variation may be subject to indirect,
AB  - epigenetic control as part of a phasevarion. Bioinformatic and experimental studies are
AB  - required to elucidate the distribution and mechanism of action of these DNA
AB  - methyltransferases, and most importantly, whether they mediate epigenetic regulation of
AB  - potential and current vaccine candidates. This process is essential to define the stably
AB  - expressed antigen target profile of bacterial pathogens and thereby facilitate efficient,
AB  - rational selection of vaccine antigens.
ER  -

TY  - JOUR
AU  - Tan, A.
AU  - Blakeway, L.V.
AU  - Bakaletz, L.O.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Korlach, J.
AU  - Jennings, M.P.
AU  - Peak, I.R.
AU  - Seib, K.L.
TI  - Complete Genome Sequence of Moraxella catarrhalis Strain CCRI-195ME, Isolated from the Middle Ear.
JO  - Genome Announcements
PY  - 2017
SP  - e00384
EP  - e00317
VL  - 5
AB  - Moraxella catarrhalis is an important bacterial pathogen that causes otitis media and
AB  - exacerbations of chronic obstructive pulmonary disease. Here, we report the
AB  - complete genome sequence of M. catarrhalis strain CCRI-195ME, which contains the
AB  - phase-variable epigenetic regulator ModM3.
ER  -

TY  - JOUR
AU  - Tan, A.
AU  - Hill, D.M.
AU  - Harrison, O.B.
AU  - Srikhanta, Y.N.
AU  - Jennings, M.P.
AU  - Maiden, M.C.
AU  - Seib, K.L.
TI  - Distribution of the type III DNA methyltransferases modA, modB and modD among Neisseria meningitidis genotypes: implications for gene regulation and virulence.
JO  - Sci. Rep.
PY  - 2016
SP  - 21015
EP  - 21015
VL  - 6
AB  - Neisseria meningitidis is a human-specific bacterium that varies in invasive potential. All
AB  - meningococci are carried in the nasopharynx, and most genotypes
AB  - are very infrequently associated with invasive meningococcal disease; however,
AB  - those belonging to the 'hyperinvasive lineages' are more frequently associated
AB  - with sepsis or meningitis. Genome content is highly conserved between carriage
AB  - and disease isolates, and differential gene expression has been proposed as a
AB  - major determinant of the hyperinvasive phenotype. Three phase variable DNA
AB  - methyltransferases (ModA, ModB and ModD), which mediate epigenetic regulation of
AB  - distinct phase variable regulons (phasevarions), have been identified in N.
AB  - meningitidis. Each mod gene has distinct alleles, defined by their Mod DNA
AB  - recognition domain, and these target and methylate different DNA sequences,
AB  - thereby regulating distinct gene sets. Here 211 meningococcal carriage and >1,400
AB  - disease isolates were surveyed for the distribution of meningococcal mod alleles.
AB  - While modA11-12 and modB1-2 were found in most isolates, rarer alleles (e.g.,
AB  - modA15, modB4, modD1-6) were specific to particular genotypes as defined by
AB  - clonal complex. This suggests that phase variable Mod proteins may be associated
AB  - with distinct phenotypes and hence invasive potential of N. meningitidis strains.
ER  -

TY  - JOUR
AU  - Tan, B.
AU  - Charchuk, R.
AU  - Li, C.
AU  - Nesbo, C.
AU  - Abu, L.N.
AU  - Foght, J.
TI  - Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures.
JO  - Genome Announcements
PY  - 2014
SP  - e00909
EP  - e00914
VL  - 2
AB  - The draft genome of an uncultivated bacterium affiliated with the Peptococcaceae  was
AB  - reconstructed by co-assembling Illumina MiSeq sequences from three single
AB  - cells sorted by microfluidics from two methanogenic alkane-degrading cultures.
AB  - Peptococcaceae SCADC (short-chain alkane-degrading culture) may be genetically
AB  - capable of anaerobic alkane activation by fumarate addition in the absence of
AB  - sulfate.
ER  -

TY  - JOUR
AU  - Tan, B.
AU  - de Araujo, E.S.R.
AU  - Rozycki, T.
AU  - Nesbo, C.
AU  - Foght, J.
TI  - Draft Genome Sequences of Three Smithella spp. Obtained from a Methanogenic Alkane-Degrading Culture and Oil Field Produced Water.
JO  - Genome Announcements
PY  - 2014
SP  - e01085
EP  - e01014
VL  - 2
AB  - Two draft genomes affiliated with Smithella spp. were obtained from a methanogenic
AB  - alkane-degrading enrichment culture by single-cell sorting and
AB  - metagenome contig binning, and a third was obtained by single-cell sorting of oil
AB  - field produced water. Two genomes contained putative assABC genes encoding
AB  - alkylsuccinate synthase, indicating genetic potential for fumarate activation of
AB  - alkanes.
ER  -

TY  - JOUR
AU  - Tan, B.
AU  - Foght, J.
TI  - Draft genome sequences of campylobacterales (epsilonproteobacteria) obtained from methanogenic oil sands tailings pond metagenomes.
JO  - Genome Announcements
PY  - 2014
SP  - e01034
EP  - e01014
VL  - 2
AB  - Draft genome sequences of two Campylobacterales (Sulfurospirillum sp. strain SCADC and
AB  - Sulfuricurvum sp. strain MLSB [Mildred Lake Settling Basin]) were
AB  - obtained by taxonomic binning of metagenomes originating from an oil sands
AB  - tailings pond. Both genomes contain soxABXYZ genes involved in sulfur oxidation,
AB  - highlighting their potential roles in sulfur cycling in oil sands tailings ponds.
ER  -

TY  - JOUR
AU  - Tan, B.F.
AU  - Te, S.H.
AU  - Boo, C.Y.
AU  - Gin, K.Y.
AU  - Thompson, J.R.
TI  - Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 58
EP  - 58
VL  - 11
AB  - A non-axenic unialgal culture containing a Subsection V (Stigonematales) cyanobacterium,
AB  - Hapalosiphon strain MRB 220, was obtained from a benthic
AB  - freshwater algal mat through multiple transfers following growth in sterile
AB  - media. Physiological characterization demonstrated the culture was capable of
AB  - nitrogen-fixation and production of the off flavor compound 2-methylisoborneol
AB  - (2-MIB). Total DNA isolated from this culture was sequenced using Illumina HiSeq
AB  - and de novo assembled into contigs. The genome of MRB 220 was separated from
AB  - co-occurring heterotrophic bacteria using sequence homology and compositional
AB  - approaches, and its purity was confirmed based on best BLAST hit classification
AB  - and principle component analysis of the tetranucleotide frequencies of fragmented
AB  - contigs. The genome of ~7.4 Mbp contains 6,345 protein coding genes with 4,320 of
AB  - these having functional prediction including predicted pathways for biosynthesis
AB  - of the secondary metabolite welwitindolinone. Analyses of 16S rRNA gene and whole
AB  - genome sequence average nucleotide identity indicated close relatedness of MRB
AB  - 220 to the genera Hapalosiphon and Fischerella within the order Stigonematales.
AB  - Microscopic examination showed that MRB 220 formed heterocystous branched
AB  - filaments, thereby supporting identification of strain MRB 220 as a morphospecies
AB  - of Hapalosiphon. Availability of the draft genome of Hapalosiphon strain MRB 220
AB  - enables future work to elucidate the pathway and dynamics for biosynthesis of
AB  - 2-MIB and other secondary metabolites and understand the ecology and physiology
AB  - of Stigonematales cyanobacteria in tropical freshwaters.
ER  -

TY  - JOUR
AU  - Tan, B.F.
AU  - Te, S.H.
AU  - Gin, K.Y.
AU  - Thompson, J.R.
TI  - Draft Genome Sequence of a Tropical Freshwater Cyanobacterium, Limnothrix sp. Strain P13C2.
JO  - Genome Announcements
PY  - 2016
SP  - e01117
EP  - e01116
VL  - 4
AB  - A nonaxenic unialgal culture of Limnothrix sp. strain P13C2 was obtained through  multiple
AB  - subculturing of an inoculum obtained from a tropical freshwater lake.
AB  - Here, we report the genome of P13C2 of 4.6 Mbp, extracted from the metagenome of
AB  - this coculture.
ER  -

TY  - JOUR
AU  - Tan, C.
AU  - Xu, Z.
AU  - Zheng, H.
AU  - Liu, W.
AU  - Tang, X.
AU  - Shou, J.
AU  - Wu, B.
AU  - Wang, S.
AU  - Zhao, G.P.
AU  - Chen, H.
TI  - Genome Sequence of Porcine Extraintestinal Pathogenic Escherichia coli strain.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5038
EP  - 5038
VL  - 193
AB  - Extraintestinal Pathogenic Escherichia coli is an important pathogen which can infect human
AB  - and animals and causing many diseases outside the
AB  - intestinal. Here, we report the first draft genome sequence of a porcine
AB  - ExPEC strain, PCN033, isolated from the pig with meningitis.
ER  -

TY  - JOUR
AU  - Tan, E.
AU  - Chen, Y.
AU  - Kuan, J.
AU  - Lin, C.
AU  - Jagoda, S.S.
AU  - Lin, F.
AU  - Tzou, W.
AU  - Kinoshita, S.
AU  - Watabe, S.
AU  - Asakawa, S.
AU  - Liu, S.
TI  - Draft Genome Sequence of Thermoanaerobacterium saccharolyticum Strain NTOU1, a Thermophilic Bacterium Isolated from Marine Shallow Hydrothermal Vents.
JO  - Genome Announcements
PY  - 2014
SP  - e01019
EP  - e01014
VL  - 2
AB  - Thermoanaerobacterium saccharolyticum strain NTOU1 has the ability to utilize several kinds of
AB  - sugars in lignocellulosic biomass to produce ethanol more
AB  - efficiently than other bacteria. Here, we report the draft genome sequence and
AB  - annotation of this strain, which may provide insights into the possible genes and
AB  - metabolic pathways related to ethanol production.
ER  -

TY  - JOUR
AU  - Tan, H.L.
AU  - Wang, Y.
AU  - Cheng, X.Q.
AU  - Huang, Y.M.
AU  - Liu, W.
AU  - Zhang, L.J.
TI  - Genome Sequence of a Pandrug-Resistant Pseudomonas aeruginosa Strain, YN-1.
JO  - Genome Announcements
PY  - 2014
SP  - e01280
EP  - e01214
VL  - 2
AB  - A highly rampant multidrug-resistant strain of Pseudomonas aeruginosa appeared in a hospital
AB  - in Yunnan Province, China. Here, we report the genome sequence of the
AB  - pandrug-resistant (PDR) P. aeruginosa strain recovered from a patient in 2013.
ER  -

TY  - JOUR
AU  - Tan, H.L.
AU  - Wang, Y.
AU  - Cheng, X.Q.
AU  - Huang, Y.M.
AU  - Liu, W.
AU  - Zhang, L.J.
TI  - Genome Sequence of an Extensively Drug-Resistant Strain of Klebsiella pneumoniae, Strain YN-1, with Carbapenem Resistance.
JO  - Genome Announcements
PY  - 2015
SP  - e01279
EP  - e01214
VL  - 3
AB  - The emergence and spread of multidrug-resistant (MDR) Klebsiella pneumoniae has been regarded
AB  - as one of the major challenges among health care-associated
AB  - infections worldwide. Here, we report the draft genome sequence of an extensively
AB  - drug-resistant (XDR) K. pneumoniae strain isolated in 2013 from Yunnan Province,
AB  - China.
ER  -

TY  - JOUR
AU  - Tan, J.L.
AU  - Ng, H.F.
AU  - Wee, W.Y.
AU  - Ang, M.Y.
AU  - Wong, G.J.
AU  - Ngeow, Y.F.
AU  - Choo, S.W.
TI  - First Whole-Genome Sequence of Mycobacterium iranicum, a Newly Reported Mycobacterial Species.
JO  - Genome Announcements
PY  - 2013
SP  - e00732
EP  - e00713
VL  - 1
AB  - Mycobacterium iranicum is a new species of nontuberculous mycobacterium reported  in 2013.
AB  - Here, we describe the first whole-genome sequence of this species, that
AB  - of M. iranicum strain UM_TJL, isolated from a patient in Malaysia.
ER  -

TY  - JOUR
AU  - Tan, J.Y.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Gene clusters of Hafnia alvei strain FB1 important in survival and pathogenesis: a draft genome perspective.
JO  - Gut Pathog.
PY  - 2014
SP  - 29
EP  - 29
VL  - 6
AB  - BACKGROUND: Hafnia alvei is an opportunistic pathogen involved in various types of nosocomical
AB  - infections. The species has been found to inhabit food and mammalian guts. However, its status
AB  - as an enteropathogen, and whether the food-inhabiting strains could be a source of
AB  - gastrointestinal infection remains obscure. In this report we present a draft genome of H.
AB  - alvei strain FB1 isolated from fish paste meatball, a food popular among Malaysian and Chinese
AB  - populations.
AB  - The data was generated on the Illumina MiSeq platform. RESULTS: A comparative study was
AB  - carried out on FB1 against two other previously sequenced H. alvei genomes. Several gene
AB  - clusters putatively involved in survival and pathogenesis of H. alvei FB1 in food and gut
AB  - environment were characterised in this study.
AB  - These include the widespread colonisation island (WCI), the tad locus that is known to play an
AB  - essential role in biofilm formation, a eut operon that might contribute to advantage in
AB  - nutrient acquisition in gut environment, and genes responsible for siderophore production This
AB  - features enable the bacteria to successful colonise in the host gut environment. CONCLUSION:
AB  - With the whole genome data of H. alvei FB1 presented in this study, we hope to provide an
AB  - insight into future studies on this candidate of enteropathogen by looking into the possible
AB  - mechanisms employed to survive stresses and gain advantage in competitions, which eventually
AB  - leads to successful colonisation and pathogenesis.
AB  - This is to serve as the basis for more effective clinical diagnosis and treatment.
ER  -

TY  - JOUR
AU  - Tan, K.H.
AU  - Sheng, K.Y.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Draft Genome Sequence of a Quorum-Sensing Bacterium, Dickeya sp. Strain 2B12, Isolated from a Freshwater Lake.
JO  - Genome Announcements
PY  - 2015
SP  - e01542
EP  - e01514
VL  - 3
AB  - Dickeya sp. strain 2B12 was isolated from a freshwater lake in Malaysia. Here, we report the
AB  - draft genome sequence of Dickeya sp. 2B12 sequenced by the Illumina
AB  - MiSeq platform. With the genome sequence available, this genome sequence will be
AB  - useful for the study of quorum-sensing activity in this isolate.
ER  -

TY  - JOUR
AU  - Tan, N.-W.
AU  - Li, F.F.L.
TI  - Interaction of oligonucleotides containing 6-O-methylguanine with human DNA (cytosine-5-)-methyltransferase.
JO  - Biochemistry
PY  - 1990
SP  - 9234
EP  - 9240
VL  - 29
AB  - Thirty-base-pair synthetic oligonucleotide duplexes containing a single meG.C
AB  - (meG=6-O-methylguanine) or A.C base pair at the 16th position (i.e.,
AB  - 5'-CCCGTTTAAATATACXTATACCCGGGTACC-3', where X=A or meG) were used to study de
AB  - novo methylation by the purified human DNA (cytosine-5)-methyltransferase
AB  - isolated from CEM cells.  Both duplexes containing meG.C and A.C base pairs
AB  - show enhanced methyl group acceptor properties.  Subsequent introduction of
AB  - hemimethylated sites at the 15th position of the top strand (the C residue next
AB  - to the abnormal base pair) and the 7th, 15th (which represents the C residue in
AB  - the 6meG.C and A.C base pairs), and 27th positions of the bottom strand were
AB  - used to study the maintenance methylation of the hemimethylated duplexes by the
AB  - methylase.  This revealed striking differences in the rate, amount, and sites
AB  - of methylation, which are dependent on the position of the hemimethylated site
AB  - in the duplex.  The possible mechanism of action of the methylase is discussed.
AB  - The data show that 6-O-methylguanine residues in DNA can have other genetic
AB  - effects apart from their miscoding behavior and that meG.C and A.C base pairs
AB  - exert different effects in terms of methylation.
ER  -

TY  - JOUR
AU  - Tan, S.
AU  - Meng, Y.
AU  - Su, A.
AU  - Zhang, C.
AU  - Ren, Y.
TI  - Draft Genome Sequence of Bacillus subtilis subsp. natto Strain CGMCC 2108, a High Producer of Poly-gamma-Glutamic Acid.
JO  - Genome Announcements
PY  - 2016
SP  - e00426
EP  - e00416
VL  - 4
AB  - Here, we report the 4.1-Mb draft genome sequence of Bacillus subtilis subsp. natto strain
AB  - CGMCC 2108, a high producer of poly-gamma-glutamic acid (gamma-PGA).
AB  - This sequence will provide further help for the biosynthesis of gamma-PGA and
AB  - will greatly facilitate research efforts in metabolic engineering of B. subtilis
AB  - subsp. natto strain CGMCC 2108.
ER  -

TY  - JOUR
AU  - Tan, W.
AU  - Wang, G.
AU  - Pan, Z.
AU  - Yin, Y.
AU  - Jiao, X.
TI  - Complete Genome Sequence of Listeria monocytogenes NTSN, a Serovar 4b and Animal  Source Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01403
EP  - e01414
VL  - 3
AB  - Listeria monocytogenes is an important foodborne pathogen that causes infections  in humans
AB  - and animals and has a high mortality rate. The complete genome sequence
AB  - of L. monocytogenes strain NTSN, a highly virulent and serovar 4b strain isolated
AB  - from the brains of sheep in Jiangsu Province, China, is presented here.
ER  -

TY  - JOUR
AU  - Tan, W.G.H.
AU  - Barkman, T.J.
AU  - Gregory, C.V.
AU  - Essani, K.
TI  - Comparative genomic analyses of frog virus 3, type species of the genus Ranavirus (family Iridoviridae).
JO  - Virology
PY  - 2004
SP  - 70
EP  - 84
VL  - 323
AB  - Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To
AB  - better understand the molecular mechanisms involved in the replication of FV3, including
AB  - transcription of its highly methylated DNA genome, we have determined the complete nucleotide
AB  - sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal
AB  - redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential
AB  - open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant
AB  - homology to known proteins of other iridoviruses, whereas twelve of these unique FV3 proteins
AB  - do not share homology to any known protein. A microsatellite containing a stretch of 34
AB  - tandemly repeated CA dinucleotide in a noncoding region was detected. To date, no such
AB  - sequence has been reported in any animal virus.
ER  -

TY  - JOUR
AU  - Tan, W.S.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Understanding the Quorum-Sensing Bacterium Pantoea stewartii Strain M009 with Whole-Genome Sequencing Analysis.
JO  - Genome Announcements
PY  - 2015
SP  - e01509
EP  - e01514
VL  - 3
AB  - Pantoea stewartii is known to be the causative agent of Stewart's wilt, which usually affects
AB  - sweet corn (Zea mays) with the corn flea beetle as the
AB  - transmission vector. In this work, we present the whole-genome sequence of
AB  - Pantoea stewartii strain M009, isolated from a Malaysian tropical rainforest
AB  - waterfall.
ER  -

TY  - JOUR
AU  - Tan, W.S.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Insights into the Quorum-Sensing Activity in Aeromonas hydrophila Strain M013 as  Revealed by Whole-Genome Sequencing.
JO  - Genome Announcements
PY  - 2015
SP  - e01372
EP  - e01314
VL  - 3
AB  - Aeromonas hydrophila species can be found in warm climates and can survive in different
AB  - environments. They possess the ability to communicate within their
AB  - populations, which is known as quorum sensing. In this work, we present the draft
AB  - genome sequence of A. hydrophila M013, a bacterium isolated from a Malaysian
AB  - tropical rainforest waterfall.
ER  -

TY  - JOUR
AU  - Tan, W.S.
AU  - Yin, W.F.
AU  - Chang, C.Y.
AU  - Chan, K.G.
TI  - Whole-Genome Sequencing Analysis of Quorum-Sensing Aeromonas hydrophila Strain M023 from Freshwater.
JO  - Genome Announcements
PY  - 2015
SP  - e01548
EP  - e01514
VL  - 3
AB  - Aeromonas hydrophila is a well-known waterborne pathogen that recently was found to infect
AB  - humans. Here, we report the draft genome of a freshwater isolate from a Malaysian waterfall,
AB  - A. hydrophila strain M023, which portrays N-acylhomoserine lactone-dependent quorum sensing.
ER  -

TY  - JOUR
AU  - Tanabe, Y.
AU  - Yamaguchi, H.
AU  - Watanabe, M.M.
TI  - Draft Genome Sequence of 'Candidatus Phycosocius bacilliformis,' an Alphaproteobacterial Ectosymbiont of the Hydrocarbon-Producing Green Alga  Botryococcus braunii.
JO  - Genome Announcements
PY  - 2018
SP  - e00396
EP  - e00318
VL  - 6
AB  - 'Candidatus Phycosocius bacilliformis' is an alphaproteobacterial ectosymbiont of the
AB  - hydrocarbon-producing green alga Botryococcus braunii We sequenced the whole
AB  - genome of 'Ca. P. bacilliformis' BOTRYCO-2, isolated from a two-membered culture
AB  - with B. braunii The genome contains approximately 3.3 Mb, with an average G+C
AB  - content of 56.91% and 3,125 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Tanaka, R.
AU  - Mizutani, Y.
AU  - Shibata, T.
AU  - Miyake, H.
AU  - Iehata, S.
AU  - Mori, T.
AU  - Kuroda, K.
AU  - Ueda, M.
TI  - Genome Sequence of Formosa haliotis Strain MA1, a Brown Alga-Degrading Bacterium  Isolated from the Gut of Abalone Haliotis gigantea.
JO  - Genome Announcements
PY  - 2016
SP  - e01312
EP  - e01316
VL  - 4
AB  - Formosa haliotis is a brown alga-degrading bacterium isolated from the gut of abalone Haliotis
AB  - gigantea Here, we report the draft genome sequence of this
AB  - bacterium and pointed out possible important features related to alginate
AB  - degradation.
ER  -

TY  - JOUR
AU  - Tanaka, T.
TI  - Restriction of plasmid-mediated transformation in Bacillus subtilis 168.
JO  - Mol. Gen. Genet.
PY  - 1979
SP  - 235
EP  - 237
VL  - 175
AB  - When plasmids carrying leucine genes of Bacillus subtilis 168 were isolated
AB  - from a restriction and modification deficient (r-m-) strain and used for
AB  - transformation of a restricting strain B. subtilis 168 leu recE4, the number of
AB  - transformants was greatly reduced.  Transformation of a rec+ strain
AB  - (transformation by integration of the donor DNA into the chromosome) with the
AB  - plasmids was not affected irrespective of whether the recipient carried the r+
AB  - or r- phenotype.  These results show that the plasmid-mediated transformation
AB  - is subject to the host controlled restriction and suggest that r-m- strains
AB  - should be used for construction of recombinant DNA molecules in B. subtilis
AB  - 168.
ER  -

TY  - JOUR
AU  - Tandeau de Marsac, N.
AU  - Houmard, J.
TI  - Advances in cyanobacterial molecular genetics.
JO  - Cyanobacteria
PY  - 1987
SP  - 251
EP  - 302
VL  - 0
AB  - Until recently, the development of cyanobacteial genetics was limited by our
AB  - inability to transfer genetic material, both within a given species and between
AB  - different cyanobacterial species.  About 300 cyanobacterial strains have been
AB  - isolated as axenic cultures but less than 10, all unicellular species, have
AB  - been shown to be transformable by DNA.  Moreover, while specific
AB  - cyanobacteriophages have been described, gene transduction has not yet been
AB  - demonstrated.  Molecular genetics offers new possibilities for studying various
AB  - properties of cyanobacteria, such as oxygenic photosynthesis, aerobic and
AB  - anaerobic nitrogen fixation, light-regulated gene expression and cell
AB  - differentiation, properties for which biochemical and physiological data are
AB  - already available.  An increasing number of laboratories are now studying this
AB  - widespread and very large group of microorganisms using such genetic
AB  - approaches.  Recent reports that conjugation can occur in Anabaena/Nostoc
AB  - strains pave the way for the transfer of genetic material among filamentous
AB  - cyanobacteria and strengthen the work already initiated in order to understand,
AB  - at the molecular level, the important processes mentioned above.  We will
AB  - review current knowledge on cyanobacterial plasmids and restriction enzymes,
AB  - such data being of special interest for both molecular genetics and the
AB  - development of DNA transfer systems, and we will describe which cyanobacterial
AB  - genes have been cloned and characterized.  Finally, we will present some of the
AB  - features which have emerged from both sequence data and gene expression
AB  - experiments in homologous and/or heterologous hosts, as well as the
AB  - methodological approaches used.
ER  -

TY  - JOUR
AU  - Tandon, K.
AU  - Chiang, P.W.
AU  - Chen, W.M.
AU  - Tang, S.L.
TI  - Draft Genome Sequence of Endozoicomonas acroporae Strain Acr-14(T), Isolated from Acropora Coral.
JO  - Genome Announcements
PY  - 2018
SP  - e01576
EP  - e01517
VL  - 6
AB  - A lacuna exists in our understanding of the genetic makeup of Endozoicomonas bacteria, due to
AB  - scarcity of genome sequences. We report here the first draft
AB  - genome sequence of Endozoicomonas acroporae Acr-14, a type strain isolated from
AB  - the coral Acropora This sequence will foster an understanding of the genetic
AB  - makeup and role of hosts in shaping gene repertoires.
ER  -

TY  - JOUR
AU  - Taneike, I.
AU  - Otsuka, T.
AU  - Dohmae, S.
AU  - Saito, K.
AU  - Ozaki, K.
AU  - Takano, M.
AU  - Higuchi, W.
AU  - Takano, T.
AU  - Yamamoto, T.
TI  - Molecular nature of methicillin-resistant Staphylococcus aureus derived from explosive nosocomial outbreaks of the 1980s in Japan.
JO  - FEBS Lett.
PY  - 2006
SP  - 2323
EP  - 2334
VL  - 580
AB  - Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA)
AB  - with Panton-Valentine leukocidin (PVL) genes is increasing worldwide.
AB  - Nosocomial outbreak-derived (hospital-acquired) MRSA (HA-MRSA) in Japan in
AB  - the 1980s was also largely PVL(+). PVL(+) HA-MRSA and CA-MRSA shared the
AB  - same multi-locus sequence type (ST30) and methicillin resistance cassette
AB  - (SCCmecIV), but were divergent in oxacillin resistance, spa typing, PFGE
AB  - analysis or clfA gene analysis. PVL(+) HA-MRSA, which probably originated
AB  - in PVL(+)S. aureus ST30, was highly adhesive (carrying cna and bbp genes),
AB  - highly-toxic (carrying luk(PV) and sea genes) and highly drug-resistant.
AB  - PVL(+) HA-MRSA was once replaced by other PVL(-) HA-MRSA (e.g., ST5), and
AB  - is re-emerging as CA-MRSA.
ER  -

TY  - JOUR
AU  - Tang, B.
AU  - Wang, Q.
AU  - Yang, M.
AU  - Xie, F.
AU  - Zhu, Y.
AU  - Zhuo, Y.
AU  - Wang, S.
AU  - Gao, H.
AU  - Ding, X.
AU  - Zhang, L.
AU  - Zhao, G.
AU  - Zheng, H.
TI  - ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.
JO  - BMC Genomics
PY  - 2013
SP  - 289
EP  - 289
VL  - 14
AB  - BACKGROUND: With the emergence of next-generation sequencing, the availability of
AB  - prokaryotic genome sequences is expanding rapidly. A total of 5,276 genomes have
AB  - been released since 2008, yet only 1,692 genomes were complete. The final phase
AB  - of microbial genome sequencing, particularly gap closing, is frequently the
AB  - rate-limiting step either because of complex genomic structures that cause
AB  - sequence bias even with high genomic coverage, or the presence of repeat
AB  - sequences that may cause gaps in assembly. RESULTS: We have developed a Cytoscape
AB  - plugin to facilitate gap closing for high-throughput sequencing data from
AB  - microbial genomes. This plugin is capable of interactively displaying the
AB  - relationships among genomic contigs derived from various sequencing formats. The
AB  - sequence contigs of plasmids and special repeats (IS elements, ribosomal RNAs,
AB  - terminal repeats, etc.) can be displayed as well. CONCLUSIONS: Displaying
AB  - relationships between contigs using graphs in Cytoscape rather than tables
AB  - provides a more straightforward visual representation. This will facilitate a
AB  - faster and more precise determination of the linkages among contigs and greatly
AB  - improve the efficiency of gap closing.
ER  -

TY  - JOUR
AU  - Tang, B.
AU  - Yu, Y.
AU  - Cen, X.
AU  - Zhu, Y.
AU  - Dai, R.
AU  - Wang, X.
AU  - Zhao, G.
AU  - Ding, X.
TI  - Draft Genome Sequence of the Streptothricin-Producing Strain Streptomyces sp. fd2-tb.
JO  - Genome Announcements
PY  - 2015
SP  - e01277
EP  - e01215
VL  - 3
AB  - Streptomyces sp. fd2-tb can produce streptothricin class antibiotics with broad antimicrobial
AB  - spectra. To better understand the mechanism of streptothricin
AB  - biosynthesis and to assess the capacity of this strain in secondary metabolism,
AB  - we report the draft genome sequence of Streptomyces sp. strain fd2-tb.
ER  -

TY  - JOUR
AU  - Tang, B.
AU  - Zhao, W.
AU  - Zheng, H.
AU  - Zhuo, Y.
AU  - Zhang, L.
AU  - Zhao, G.P.
TI  - Complete Genome Sequence of Amycolatopsis mediterranei S699 Based on De Novo Assembly via a Combinatorial Sequencing Strategy.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5699
EP  - 5700
VL  - 194
AB  - The genome of Amycolatopsis mediterranei S699 was resequenced and assembled de novo. By
AB  - comparing the sequences of S699 previously released and that of A.
AB  - mediterranei U32, about 10 kb of major indels was found to differ between the two
AB  - S699 genomes, and the differences are likely attributable to their different
AB  - assembly strategies.
ER  -

TY  - JOUR
AU  - Tang, B.L.
AU  - Rong, J.C.
AU  - Dang, Y.R.
AU  - Xie, B.B.
AU  - Chen, X.L.
AU  - Zhang, X.Y.
TI  - Complete Genomic Sequence of Pseudoalteromonas sp. Strain SAO4-4, a Protease-Producing Bacterium Isolated from Seawater of the Atlantic Ocean.
JO  - Genome Announcements
PY  - 2018
SP  - e00284
EP  - e00218
VL  - 6
AB  - The complete genome of Pseudoalteromonas sp. strain SAO4-4, a protease-producing  bacterium
AB  - from seawater, is composed of two circular chromosomes and one plasmid.
AB  - This genome sequence will provide a better understanding of the ecological roles
AB  - of protease-producing bacteria in the degradation of organic matter in marine
AB  - aquatic environments.
ER  -

TY  - JOUR
AU  - Tang, D.
AU  - Ando, S.
AU  - Takasaki, Y.
AU  - Tadano, J.
TI  - Mutational analyses of restriction endonuclease-HindIII mutant E86K with higher activity and altered specificity.
JO  - Protein Eng.
PY  - 2000
SP  - 283
EP  - 289
VL  - 13
AB  - We have performed mutational analyses of restriction endonuclease HindIII in order to identify
AB  - the amino acid residues responsible for enzyme activity. Four of the seven HindIII mutants,
AB  - which had His-tag sequences at the N-termini, were expressed in Escherichia coli, and purified
AB  - to homogeneity. The His-tag sequence did not affect enzyme activity, whereas it hindered
AB  - binding of the DNA probe in gel retardation assays. A mutant E86K in which Lys was substituted
AB  - for Glu at residue 86 exhibited high endonuclease activity. Gel retardation assays showed high
AB  - affinity of this mutant to the DNA probe. Surprisingly, in the presence of a transition metal,
AB  - Mo(2+) or Mn(2+), the E86K mutant cleaved substrate DNA at a site other than HindIII.
AB  - Substitution of Glu for Val at residue 106 (V106E), and Asn for Lys at residue 125 (K125N)
AB  - resulted in a decrease in both endonucleolytic and DNA binding activities of the enzyme.
AB  - Furthermore, substitution of Leu for Asp at residue 108 (D108L) abolished both HindIII
AB  - endonuclease and DNA binding activities. CD spectra of the wild type and the two mutants, E86K
AB  - and D108L, were similar to each other, suggesting that there was little change in conformation
AB  - as a result of the mutations. These results account for the notion that Asp108 could be
AB  - directly involved in HindIII catalytic function, and that the substitution at residue 86 may
AB  - bring about new interactions between DNA and cations.
ER  -

TY  - JOUR
AU  - Tang, G.
AU  - Cui, R.
AU  - Tian, Y.
AU  - Lin, X.
TI  - Draft Genome Sequence of Pacificimonas aurantium Type Strain JLT2012, Isolated from the Seawater of the Pacific Ocean.
JO  - Genome Announcements
PY  - 2017
SP  - e00755
EP  - e00717
VL  - 5
AB  - Type strain JLT2012 was isolated from the southeastern Pacific. Here, we report the draft
AB  - genome sequence and the initial findings from a preliminary analysis of
AB  - strain JLT2012, which represents a novel species and should be classified in the
AB  - existing genus Pacificimonas.
ER  -

TY  - JOUR
AU  - Tang, H.
AU  - Yu, H.
AU  - Li, Q.
AU  - Wang, X.
AU  - Gai, Z.
AU  - Yin, G.
AU  - Su, F.
AU  - Tao, F.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Pseudomonas putida Strain B6-2, a Superdegrader of Polycyclic Aromatic Hydrocarbons and Dioxin-Like Compounds.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6789
EP  - 6790
VL  - 193
AB  - Pseudomonas putida strain B6-2 can efficiently degrade environmental pollutants/toxicants,
AB  - such as polycyclic aromatic hydrocarbons and
AB  - dioxin-like compounds, and has unique tolerance to organic solvents. Here,
AB  - we present a 6.24-Mb draft genome sequence of B6-2, which could provide
AB  - further insights into the biodegradative mechanisms of a diverse range of
AB  - chemical compounds.
ER  -

TY  - JOUR
AU  - Tang, H.
AU  - Yu, H.
AU  - Tai, C.
AU  - Huang, K.
AU  - Liu, Y.
AU  - Wang, L.
AU  - Yao, Y.
AU  - Wu, G.
AU  - Xu, P.
TI  - Genome Sequence of a Novel Nicotine-Degrading Strain, Pseudomonas geniculata N1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3553
EP  - 3554
VL  - 194
AB  - A newly isolated bacterium, Pseudomonas geniculata N1, can efficiently degrade nicotine. Here
AB  - we present a 4.51-Mb assembly of its genome, which is the first
AB  - sequence of the P. geniculata group. The sequence contains the genes related to
AB  - nicotine catabolism and may provide insights into its molecular mechanism for
AB  - N-heterocyclic degradation.
ER  -

TY  - JOUR
AU  - Tang, J.
AU  - Liu, X.
AU  - Peng, J.
AU  - Tang, Y.
AU  - Zhang, Y.
TI  - Genome sequence and genome mining of a marine-derived antifungal bacterium Streptomyces sp. M10.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2015
SP  - 2763
EP  - 2772
VL  - 99
AB  - A marine-derived actinobacteria Streptomyces sp. M10 was identified as a prolific
AB  - antifungal compounds producer and shared a 99.02 % 16S ribosomal RNA (rRNA)
AB  - sequence similarity with that of Streptomyces marokkonensis Ap1(T), which can
AB  - produce polyene macrolides. To further evaluate its biosynthetic potential, the
AB  - 7,207,169 bp Streptomyces sp. M10 linear chromosome was sequenced and mined for
AB  - identifiable secondary metabolite-associated gene clusters. A total of 20
AB  - secondary metabolite-associated gene clusters were deduced, including three
AB  - polyketide synthases (PKSs), four non-ribosomal peptide synthetases (NRPSs), four
AB  - hybrid NRPS-PKSs, three NRPS-independent siderophores, and two lantibiotic and
AB  - four terpene biosynthetic gene clusters. One of the type I PKS gene cluster,
AB  - pks1, shared a 85 % nucleotide similarity with candicidin/FR008 gene cluster,
AB  - indicating the capacity of this organism to produce polyene macrolides. This
AB  - assumption was verified by a scale-up culturing of Streptomyces sp. M10 on A1
AB  - agar plates, which lead to the isolation of two polyene families PF1 and PF2,
AB  - with characteristic UV adsorption at 269, 278, and 290 nm (PF1) and 363, 386, and
AB  - 408 nm (PF2), respectively. Compound 9-04 was further purified from PF1, and its
AB  - chemical structure was partially elucidated to be a typical polyene macrolide by
AB  - NMR and UV spectrum. This study affirmatively identified Streptomyces sp. M10 as
AB  - a source of polyene metabolites and highlighted genome mining of interested
AB  - organism as a powerful tool for natural product discovery.
ER  -

TY  - JOUR
AU  - Tang, J.
AU  - Zhang, Y.
AU  - Meng, H.
AU  - Xue, Z.
AU  - Ma, J.
TI  - Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor.
JO  - Genome Announcements
PY  - 2013
SP  - e01059
EP  - e01013
VL  - 1
AB  - We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the
AB  - rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a
AB  - G+C content of 47.24%, and it may provide useful information about plant-microbe
AB  - interactions and the genetic basis for the tolerance of the strain to various
AB  - environmental stresses.
ER  -

TY  - JOUR
AU  - Tang, K.
AU  - Allman, S.L.
AU  - Chen, C.H.
AU  - Chang, L.Y.
AU  - Schell, M.
TI  - Matrix-assisted laser desorption/ionization of restriction enzyme-digested DNA.
JO  - Rapid Commun. Mass. Spectrom.
PY  - 1994
SP  - 183
EP  - 186
VL  - 8
AB  - Matrix-assisted laser desorption/ionization, by a time-of-flight mass spectrometer, has been
AB  - successfully used for detection of restriction enzyme-digested DNA. However, the
AB  - oligonucleotide segments detected correspond to the molecular weights of single strands.
ER  -

TY  - JOUR
AU  - Tang, K.
AU  - Liu, K.
AU  - Jiao, N.
TI  - Draft Genome Sequence of Oceaniovalibus guishaninsula JLT2003T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6683
EP  - 6683
VL  - 194
AB  - Oceaniovalibus guishaninsula, as a representative of a new genus within the family
AB  - Rhodobacteraceae, was isolated from surface seawater that was sulfidic.
AB  - Here, we present the draft genome sequence of the type strain, JLT2003(T).
ER  -

TY  - JOUR
AU  - Tang, K.
AU  - Liu, K.
AU  - Li, S.
AU  - Jiao, N.
TI  - Draft Genome Sequence of Strain JLT2015T, Belonging to the Family Sphingomonadaceae of the Alphaproteobacteria.
JO  - Genome Announcements
PY  - 2013
SP  - e00226
EP  - e00213
VL  - 1
AB  - Strain JLT2015(T) was isolated from the southeastern Pacific, as a representative of a new
AB  - genus of the family Sphingomonadaceae of the Alphaproteobacteria. Here,
AB  - we present the draft genome sequence of strain JLT2015(T), which provides insight
AB  - into the oligotrophic strategy of this organism.
ER  -

TY  - JOUR
AU  - Tang, L.Y.
AU  - Reddy, M.N.
AU  - Rasheva, V.
AU  - Lee, T.L.
AU  - Lin, M.J.
AU  - Hung, M.S.
AU  - Shen, C.K.
TI  - The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 33613
EP  - 33616
VL  - 278
AB  - DNMT2 is a subgroup of the eukaryotic cytosine-5 DNA methyltransferase gene family. Unlike the
AB  - other family members, proteins encoded by DNMT2
AB  - genes were not known before to possess DNA methyltransferase activities.
AB  - Most recently, we have shown that the genome of Drosophila S2 cells stably
AB  - expressing an exogenous Drosophila dDNMT2 cDNA became anomalously
AB  - methylated at the 5'-positions of cytosines (Reddy, M. N., Tang, L. Y.,
AB  - Lee, T. L., and Shen, C.-K. J. (2003) Oncogene, in press). We present
AB  - evidence here that the genomes of transgenic flies overexpressing the
AB  - dDnmt2 protein also became hypermethylated at specific regions.
AB  - Furthermore, transient transfection studies in combination with sodium
AB  - bisulfite sequencing demonstrated that dDnmt2 as well as its mouse
AB  - ortholog, mDnmt2, are capable of methylating a cotransfected plasmid DNA.
AB  - These data provide solid evidence that the fly and mouse DNMT2 gene
AB  - products are genuine cytosine-5 DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Tang, S.
AU  - Edwards, E.A.
TI  - Complete Genome Sequence of Bacteroidales Strain CF from a Chloroform-Dechlorinating Enrichment Culture.
JO  - Genome Announcements
PY  - 2013
SP  - e01066
EP  - e01013
VL  - 1
AB  - Bacteroidales strain CF is the most abundant nondechlorinating organism in a
AB  - Dehalobacter-containing enrichment culture that consistently reductively
AB  - dechlorinates >50 mg/liter chloroform or 1,1,1-trichloroethane (methyl
AB  - chloroform). We assembled and closed the complete genome sequence of this
AB  - organism from the metagenomic sequencing data for enrichment cultures. This
AB  - organism is predicted to ferment l-lactate and ethanol.
ER  -

TY  - JOUR
AU  - Tang, S.L.
AU  - Nuttall, S.
AU  - Ngui, K.
AU  - Fisher, C.
AU  - Lopez, P.
AU  - Dyall-Smith, M.
TI  - HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome.
JO  - Mol. Microbiol.
PY  - 2002
SP  - 283
EP  - 296
VL  - 44
AB  - HF2 is a haloarchaeal virus infecting two Halorubrum species (Family Halobacteriaceae). It is
AB  - lytic, has a head-and-tail morphology and belongs
AB  - to the Myoviridae (contractile tails). The linear double-stranded DNA
AB  - genome was sequenced and found to be 77 670 bp in length, with a mol% G+C
AB  - of 55.8. A total of 121 likely open reading frames (ORFs) were identified,
AB  - of which 37 overlapped at start and stop codons. The predicted proteins
AB  - were usually acidic (average pI of 4.8), and less than about 12% of them
AB  - had homologues in the sequence databases. Four complete tRNA-like
AB  - sequences (tRNA-Arg, -Asx, -Pro and -Tyr) and an incomplete tRNA-Thr were
AB  - detected. A transcription map showed that most of the genome was
AB  - transcribed and that the synthesis of transcripts occurred in a highly
AB  - organized and reproducible pattern over a 5 h infection cycle. Transcripts
AB  - often spanned multiple ORFs, suggesting that viral genes were organized
AB  - into operons. The predicted ORF and observed transcript directions matched
AB  - well and showed that transcription is mainly directed inwards from the
AB  - genome termini, meeting at about 45-48 kb, and this was also a turning
AB  - point in a cumulative GC-skew plot. The low point in cumulative GC-skew,
AB  - near the left end, was a region rich in short repeats and lacking ORFs,
AB  - which is likely to be an origin of replication. The HF2 genome is a mosaic
AB  - of components from widely different sources, demonstrating clearly that
AB  - viruses of haloarchaea, like their bacteriophage counterparts, are vectors
AB  - for the exchange and transmission of genetic material between wide
AB  - taxonomic distances, even across domains.
ER  -

TY  - JOUR
AU  - Tang, W.J.
AU  - Zhou, Y.
AU  - Ye, B.C.
TI  - Draft Genome Sequence of a Phthalate Ester-Degrading Bacterium, Rhizobium sp. LMB-1, Isolated from Cultured Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00392
EP  - e00315
VL  - 3
AB  - Rhizobium sp. LMB-1, newly isolated from greenhouse soil, can effectively degrade phthalate.
AB  - Here, we present a 5.2-Mb assembly of this Rhizobium sp. genome for
AB  - the first time. It may provide abundant molecular information for the
AB  - transformation of phthalates.
ER  -

TY  - JOUR
AU  - Tani, A.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Kimbara, K.
TI  - Complete Genome Sequence of Methylobacterium aquaticum Strain 22A, Isolated from  Racomitrium japonicum Moss.
JO  - Genome Announcements
PY  - 2015
SP  - e00266
EP  - e00215
VL  - 3
AB  - Methylobacterium species colonize plant surfaces and utilize methanol emitted from plants.
AB  - Methylobacterium aquaticum strain 22A was isolated from a hydroponic
AB  - culture of a moss, Racomitrium japonicum, and is a potent plant growth promoter.
AB  - The complete genome sequencing of the strain confirmed the presence of genes
AB  - related to plant growth promotion and methylotrophy.
ER  -

TY  - JOUR
AU  - Tanimoto, Y.
AU  - Tamai, S.
AU  - Matsuzaki, T.
AU  - Takeuchi, N.
AU  - Noju, T.
AU  - Yanagida, S.
AU  - Kage-Nakadai, E.
AU  - Yamaguchi, Y.
AU  - Kodama, T.
AU  - Nakamura, S.
AU  - Motooka, D.
AU  - Iida, T.
AU  - Nishikawa, Y.
TI  - Diffusely adherent Escherichia coli strains isolated from healthy carriers suppress cytokine secretions of epithelial cells stimulated by inflammatory substances.
JO  - Infect. Immun.
PY  - 2018
SP  - 0
EP  - 0
VL  - 87
AB  - Diarrheagenicity of diffusely adherent Escherichia coli (DAEC) remains controversial.
AB  - Previously, we found that motile DAEC strains isolated from diarrheal patients induced high
AB  - levels of interleukin 8 (IL-8) secretion via Toll-like receptor 5 (TLR5). However, DAEC
AB  - strains from healthy carriers hardly induced IL-8 secretion, irrespective of their possessing
AB  - flagella.  In this study, we demonstrated that SK1144, a DAEC strain from a healthy carrier,
AB  - suppressed IL-8 and IL-6 secretion from human epithelial cell lines. Suppression of IL-8 in
AB  - human embryonic kidney (HEK293) cells that were transformed to express TLR5 was observed not
AB  - only upon inflammatory stimulation by flagellin but also in response to tumor necrosis
AB  - factor-alpha (TNF- and #945;) and phorbol myristate acetate(PMA), despite the fact that the
AB  - TNF- and #945;- and PMA-induced inflammatory pathways reportedly are not TLR5-mediated. SK1144
AB  - neither decreased IL-8 transcript accumulation nor increased intracellular retention of IL-8.
AB  - No suppression was observed when the bacteria were cultured in Transwell cups above the
AB  - epithelial cells; however, a non-adherent bacterial mutant (lacking the afimbrial adhesin
AB  - gene) still inhibited IL-8 secretion. Direct contact between the bacteria and epithelial cells
AB  - was necessary, but diffuse adhesion was dispensable for the inhibitory effects.  Infection in
AB  - the presence of chloramphenicol did not suppress cytokine release by the epithelial cells,
AB  - suggesting that suppression depended on effectors synthesized de novo.  Inflammatory
AB  - suppression was attenuated with infection by a bacterial mutant deleted for hcp (encoding
AB  - a component of a type-VI secretion system). In conclusion, DAEC strains from healthy carriers
AB  - impede epithelial cell cytokine secretion, possibly by interfering with translation via the
AB  - type-VI secretion system.
ER  -

TY  - JOUR
AU  - Tanizawa, Y.
AU  - Fujisawa, T.
AU  - Mochizuki, T.
AU  - Kaminuma, E.
AU  - Nakamura, Y.
AU  - Tohno, M.
TI  - Draft Genome Sequence of Lactobacillus oryzae Strain SG293T.
JO  - Genome Announcements
PY  - 2014
SP  - e00861
EP  - e00814
VL  - 2
AB  - We report the 1.86-Mb draft genome and annotation of Lactobacillus oryzae SG293(T) isolated
AB  - from fermented rice grains. This genome information may provide
AB  - further insights into the mechanisms underlying the fermentation of rice grains.
ER  -

TY  - JOUR
AU  - Tanizawa, Y.
AU  - Fujisawa, T.
AU  - Mochizuki, T.
AU  - Kaminuma, E.
AU  - Suzuki, Y.
AU  - Nakamura, Y.
AU  - Tohno, M.
TI  - Draft Genome Sequence of Weissella oryzae SG25T, Isolated from Fermented Rice Grains.
JO  - Genome Announcements
PY  - 2014
SP  - e00667
EP  - e00614
VL  - 2
AB  - Weissella oryzae was originally isolated from fermented rice grains. Here we report the draft
AB  - genome sequence of the type strain of W. oryzae. This first
AB  - report on the genomic sequence of this species may help identify the mechanisms
AB  - underlying bacterial adaptation to the ecological niche of fermented rice grains.
ER  -

TY  - JOUR
AU  - Tank, M.
AU  - Liu, Z.
AU  - Frigaard, N.U.
AU  - Tomsho, L.P.
AU  - Schuster, S.C.
AU  - Bryant, D.A.
TI  - Complete Genome Sequence of the Photoautotrophic and Bacteriochlorophyll e-Synthesizing Green Sulfur Bacterium Chlorobaculum limnaeum DSM 1677T.
JO  - Genome Announcements
PY  - 2017
SP  - e00529
EP  - e00517
VL  - 5
AB  - Chlorobaculum limnaeum DSM 1677T is a mesophilic, brown-colored, chlorophototrophic green
AB  - sulfur bacterium that produces bacteriochlorophyll e and
AB  - the carotenoid isorenieratene as major pigments. This bacterium serves as a model
AB  - organism in molecular research on photosynthesis, sulfur metabolism, and
AB  - bacteriochlorophyll biosynthesis. We report here the complete genome sequence.
ER  -

TY  - JOUR
AU  - Tanyashin, V.I.
AU  - Li, L.I.
AU  - Muijnieks, I.O.
AU  - Baev, A.A.
TI  - New endonuclease Hind GLU in Haemophilus influenzae Rd123.
JO  - Dokl. Akad. Nauk.
PY  - 1976
SP  - 226
EP  - 228
VL  - 231
AB  - None
ER  -

TY  - JOUR
AU  - Tanyashin, V.I.
AU  - Zimin, A.A.
AU  - Shlyapnikov, M.G.
AU  - Boronin, A.M.
TI  - Transduction of plasmid antibiotic resistance determinants with pseudoT-even bacteriophages.
JO  - Genetika
PY  - 2003
SP  - 914
EP  - 926
VL  - 39
AB  - Transduction of antibiotic resistance determinants of the plasmid pBR322 with pseudoT-even
AB  - bacteriophages RB42, RB43, and RB49 was
AB  - studied. It is established that antibiotic resistance determinants of
AB  - plasmid pBR322 from Escherichia coli recA(+) and recA(-) donor strains
AB  - do not differ significantly in respect to the efficiency of
AB  - transduction. Amber mutants RB43-21, RB43-33, and a double amber mutant
AB  - RB43am21am33 were obtained. These mutants facilitated transduction
AB  - experiments in some cases. Transduction of antibiotic resistance
AB  - markers of the vector plasmid pBR325 and recombinant plasmid pVT123,
AB  - containing a DNA fragment with hoc-segE-uvsW genes of phage T4, was
AB  - studied. The frequency of appearance of transductants resistant to
AB  - pseudoT-even bacteriophages used in transduction was determined, and
AB  - the sensitivity of resistant transductants to 32 RB bacteriophages and
AB  - also to phages lambda, T2, T4, T5, T6, T7, and BF23 was estimated. The
AB  - efficiency of plating pseudoT-even bacteriophages RB42 and RB43 on
AB  - strain E. coli 802 himA hip carrying mutations in genes that encode
AB  - subunits of the Integration Host Factor (IHF) was shown to be higher
AB  - than on isogenic strain E. coli 802. The growth of pseudoT-even
AB  - bacteriophages limited in vivo by modification - restriction systems of
AB  - chromosomal (EcoKI, EcoBI), phage ( EcoP1I), and plasmid (EcoRI,
AB  - EcoR124I, and EcoR124II) localization was analyzed. It was shown that
AB  - these phages were only slightly restricted by the type I modification -
AB  - restriction systems EcoBI, EcoR124I, and EcoR124II. Phage RB42 was
AB  - restricted by systems EcoKI, EcoP1I, and EcoRI; phage RB43, by
AB  - systems EcoKI and EcoRI; and phage RB49, by the Eco RI modification -
AB  - restriction system.
ER  -

TY  - JOUR
AU  - Tao, F.
AU  - Shen, Y.
AU  - Fan, Z.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of Pseudomonas putida S12, a Potential Platform Strain for Industrial Production of Valuable Chemicals.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5985
EP  - 5986
VL  - 194
AB  - Pseudomonas putida strain S12, a well-studied solvent-tolerant bacterium, is considered a
AB  - platform strain for the production of many chemicals. Here, we
AB  - present a 6.28-Mb assembly of its genome sequence. We have annotated 32 coding
AB  - sequences (CDSs) encoding efflux systems of organic compounds and 195 CDSs
AB  - responsible for the metabolism of aromatic compounds.
ER  -

TY  - JOUR
AU  - Tao, F.
AU  - Tai, C.
AU  - Liu, Z.
AU  - Wang, A.
AU  - Wang, Y.
AU  - Li, L.
AU  - Gao, C.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Klebsiella pneumoniae LZ, a Potential Platform Strain for 1,3-Propanediol Production.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4457
EP  - 4458
VL  - 194
AB  - Klebsiella pneumoniae LZ is a bacterium isolated from soil which can produce 1,3-propanediol
AB  - from glycerol. Here we present a 5,431,750-bp assembly of its
AB  - genome sequence. We annotated 9 coding sequences (CDSs) responsible for glycerol
AB  - fermentation to 1,3-propanediol, 19 CDSs encoding glycerol utilization, and 134
AB  - CDSs related to its virulence and defense.
ER  -

TY  - JOUR
AU  - Tao, F.
AU  - Tang, H.
AU  - Gai, Z.
AU  - Su, F.
AU  - Wang, X.
AU  - He, X.
AU  - Xu, P.
TI  - Genome Sequence of Pseudomonas putida Idaho, a Unique Organic-Solvent-Tolerant Bacterium.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7011
EP  - 7012
VL  - 193
AB  - Pseudomonas putida Idaho is an organic-solvent-tolerant strain which can degrade and adapt to
AB  - high concentrations of organic solvents. Here, we
AB  - announce its first draft genome sequence (6,363,067 bp). We annotated 192
AB  - coding sequences (CDSs) responsible for aromatic compound metabolism, 40
AB  - CDSs encoding phospholipid synthesis, and 212 CDSs related to stress
AB  - response.
ER  -

TY  - JOUR
AU  - Tao, F.
AU  - Wang, X.
AU  - Ma, C.
AU  - Yang, C.
AU  - Tang, H.
AU  - Gai, Z.
AU  - Xu, P.
TI  - Genome Sequence of Xanthomonas campestris JX, an Industrially Productive Strain for Xanthan Gum.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4755
EP  - 4756
VL  - 194
AB  - Xanthomonas campestris JX, a soil bacterium, is an industrially productive strain for xanthan
AB  - gum. Here we present a 5.0-Mb assembly of its genome sequence. We
AB  - have annotated 12 coding sequences (CDSs) responsible for xanthan gum
AB  - biosynthesis, 346 CDSs encoding carbohydrate metabolism, and 69 CDSs related to
AB  - virulence, defense, and plant disease.
ER  -

TY  - JOUR
AU  - Tao, F.
AU  - Zhao, P.
AU  - Li, Q.
AU  - Su, F.
AU  - Yu, B.
AU  - Ma, C.
AU  - Tang, H.
AU  - Tai, C.
AU  - Wu, G.
AU  - Xu, P.
TI  - Genome Sequence of Rhodococcus erythropolis XP, a Biodesulfurizing Bacterium with Industrial Potential.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6422
EP  - 6423
VL  - 193
AB  - Rhodococcus erythropolis strains have shown excellent characteristics in petroleum oil
AB  - biodesulfurization. Here we present the first announcement
AB  - of the draft genome sequence of an efficient biodesulfurizing bacterium
AB  - named R. erythropolis XP (7,229,582 bp). The biodesulfurizing genes dszABC
AB  - are located on a plasmid, while the flavin reductase gene dszD is located
AB  - on the chromosome.
ER  -

TY  - JOUR
AU  - Tao, T.
TI  - Characterization of the cloned PvuII type II restriction-modification system in Escherichia coli.
JO  - Diss. Abstr.
PY  - 1992
SP  - 115B
EP  - 115B
VL  - 53
AB  - The PvuII type II restriction-modification system (RMS2) cloned from Proteus vulgaris has been
AB  - sequenced in full and characterized in Escherichia coli. The sequence of pvuIIM showed that
AB  - this N4-methylcytosine (N4mC) generating DNA methyltransferase (MTase) is similar to
AB  - N6-methyladenine (N6mA) DNA MTases. Newly available data on other N4mC MTases support this
AB  - observation. Together with the known DNA structural data, this strongly suggests that these
AB  - two groups of DNA amino MTases are functionally and possibly evolutionarily related. It was
AB  - also found that M.PvuII contains an internal homology so far unique among type II DNA MTases.
AB  - Each homologous part includes its own DPPY and F/GXGXG motifs, which are sequences common to
AB  - all DNA amino MTases. Hypotheses for this homology were proposed. R.PvuII was shown to be a
AB  - homodimer. A segment of R.PvuII was found to be similar to R.BamHI at the amino acid sequence
AB  - level. The importance of this similarity is not known, but such similarities are very rare
AB  - among the sequenced endonuclease genes. A third open reading frame (ORF), 84 codons in length
AB  - with potential transcription and translation elements, was found to be associated with this
AB  - RMS2. Sequence comparison has revealed strong homology between this ORF and that of bacterial
AB  - and bacterial phage repressors. Genetic assays on this ORF showed that mutations introduced
AB  - into this ORF resulted in the reduction of R.PvuII production up to a 10/5-fold in vivo. This
AB  - effect could be complemented by providing the third ORF in trans. The third ORF was named
AB  - pvuIIC (for controller). Further experiments showed that a product of the expected size was
AB  - indeed made by pvuIIC both in vivo and in vitro. The pvuIIC product, C.PvuII, was shown to
AB  - bind to DNA, either alone or with other proteins. The binding site responsible for pvuIIR
AB  - regulation was narrowed down to a 70 bp fragment upstream of pvuIIR by deletion analysis. The
AB  - binding specificity has not yet been defined in vitro. A regulatory mechanism incorporating
AB  - these findings was hypothesized and further experiments to test the hypotheses discussed.
ER  -

TY  - JOUR
AU  - Tao, T.
AU  - Blumenthal, R.M.
TI  - Sequence and subunit structure of restriction endonuclease PvuII.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - 175
EP  - 175
VL  - 91
AB  - We have determined the DNA base sequence of the pvuIIR gene and the subunit
AB  - structure of its protein product.  The pvuIIR gene codes for a type II
AB  - restriction endonuclease, PvuII, which cleaves the sequence 5'-CAGCTG-3'
AB  - between the central two bases.  The pvuIIR open reading frame predicts a 157
AB  - amino acid, 18.4 kDa polypeptide.  The predicted size and amino acid sequence
AB  - are consistent with previous analyses of in vitro translation products and of
AB  - the N-terminal sequence of the purified protein.  The elution profile of active
AB  - PvuII endonuclease from a calibrated gel filtration column suggests a molecular
AB  - mass of about 40.5 kDa, with a Stokes radius of about 1.8nm, implying that the
AB  - enzyme is a homodimer.  The pvuIIR gene shows no obvious relationship to that
AB  - of pvuIIM, which codes for the PvuII methylase, but a region of similarity has
AB  - been found among the amino acid sequences of pvuIIR and those of four other
AB  - restriction endonucleases.  Combining the pvuIIR and pvuIIM sequence data, to
AB  - yield the full sequence of the divergently-transcribed restriction-modification
AB  - system, revealed an additional open reading frame between these two genes.  In
AB  - a separate study, this third open reading frame has been shown to regulate the
AB  - expression of pvuIIR.
ER  -

TY  - JOUR
AU  - Tao, T.
AU  - Blumenthal, R.M.
TI  - Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene.
JO  - J. Bacteriol.
PY  - 1992
SP  - 3395
EP  - 3398
VL  - 174
AB  - An open reading frame partially overlaps pvuIIR, and genetic evidence implies that this open
AB  - reading frame, named pvuIIC, specifies a positive regulator of pvuIIR (T. Tao, J.C. Bourne,
AB  - and R.M. Blumenthal, J. Bacteriol. 173:1367-1375, 1991). Inducible constructs of pvuIIC
AB  - produced a protein of the expected size. The site of C.PvuII action appears to lie within
AB  - pvuIIC itself; thus, pvuIIC may be a self-contained regulatory cassette.
ER  -

TY  - JOUR
AU  - Tao, T.
AU  - Bourne, J.C.
AU  - Blumenthal, R.M.
TI  - A family of regulatory genes associated with Type II restriction-modification systems.
JO  - J. Bacteriol.
PY  - 1991
SP  - 1367
EP  - 1375
VL  - 173
AB  - Restriction-modification systems must be regulated to avoid autorestriction and
AB  - death of the host cell.  An open reading frame (ORF) in the PvuII
AB  - restriction-modification system appears to code for a regulatory protein from a
AB  - previously unrecognized family.  First, interruptions of this ORF result in a
AB  - nonrestricting phenotype.  Second, this ORF can restore restriction competence
AB  - to such interrupted mutants in trans.  Third, the predicted amino acid sequence
AB  - of this ORF resembles those of known DNA-binding proteins and includes a
AB  - probable helix-turn-helix motif.  A survey of unattributed ORFs in 15 other
AB  - type II restriction-modification systems revealed three that closely resemble
AB  - the PvuII ORF.  All four members of this putative regulatory gene family have a
AB  - common position relative to the endonuclease genes, suggesting a common
AB  - regulatory mechanism.
ER  -

TY  - JOUR
AU  - Tao, T.
AU  - Walter, J.
AU  - Brennan, K.J.
AU  - Cotterman, M.M.
AU  - Blumenthal, R.M.
TI  - Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 4161
EP  - 4175
VL  - 17
AB  - The base sequence of the pvuIIM gene has been determined.  This gene codes for
AB  - a DNA-(cytosine N4)-methyltransferase, M.Pvu II.  The base sequence contains a
AB  - single large open reading frame that predicts a 38.3kDa polypeptide, consistent
AB  - with experimental data.  The pvuIIM gene contains some sequences common to DNA
AB  - methyltransferases in general, but includes none of the sequences specifically
AB  - conserved among DNA-(cytosine 5)-methyltransferases.  The pvuIIM sequence also
AB  - reveals an internal homology at the amino acid level, each half of which spans
AB  - over 100 amino acids and is itself homologous to the sequences of some
AB  - DNA-(adenine N6)-methyltransferases.  A derivative of the pvuIIM plasmid was
AB  - constructed to allow high-level production of M.Pvu II.  Specifically, the
AB  - composite Ptac promoter was inserted 5' to pvuIIM, intervening DNA was deleted,
AB  - and the resulting construct was used to transform an mcrB lacIq strain of
AB  - Escherichia coli.  When this transformant was induced with
AB  - isopropyl-B-D-galactopyranoside (IPTG), growth rapidly ceased and M.Pvu II
AB  - accumulated to the point of comprising over 10% of the total soluble protein.
ER  -

TY  - JOUR
AU  - Tao, X.
AU  - Jiang, M.
AU  - Zhang, F.
AU  - Xu, F.
AU  - Wei, H.
TI  - Draft Genome Sequence of Lactobacillus plantarum WLPL04, Isolated from Human Breast Milk.
JO  - Genome Announcements
PY  - 2015
SP  - e01443
EP  - e01415
VL  - 3
AB  - Lactobacillus plantarum WLPL04, a novel strain, was isolated from a breast milk sample from a
AB  - healthy woman and demonstrated several probiotic functions. Here,
AB  - we present the draft genome sequence of this strain, which contains 3,192,587 bp,
AB  - a G+C content of 44.52%, 3,158 protein-coding genes, and 53 tRNA genes.
ER  -

TY  - JOUR
AU  - Tapia, P.
AU  - Flores, F.M.
AU  - Covarrubias, P.C.
AU  - Acuna, L.G.
AU  - Holmes, D.S.
AU  - Quatrini, R.
TI  - Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756.
JO  - J. Virol.
PY  - 2012
SP  - 12452
EP  - 12453
VL  - 86
AB  - Development of reproducible genetic tools in the industrially important
AB  - acidithiobacilli is urgently required. Inducible temperate phages which may be
AB  - modified in vitro, propagated in suitable hosts, and used to transduce relevant
AB  - genetic information to other strains and/or species are potentially valuable
AB  - tools in this field of research. In order to address these current limitations,
AB  - the genome sequence of an inducible temperate Myoviridae-like bacteriophage from
AB  - the Acidithiobacillus caldus type strain was annotated and analyzed
AB  - bioinformatically. Here, we announce the genome sequence of AcaML1 and report
AB  - major findings from its annotation.
ER  -

TY  - JOUR
AU  - Taranto, M.P.
AU  - Villena, J.
AU  - Salva, S.
AU  - Alvarez, S.
AU  - Savoy-de-Giori, G.
AU  - Font-de-Valdez, G.
AU  - Hebert, E.M.
TI  - Draft Genome Sequence of Lactobacillus rhamnosus CRL1505, an Immunobiotic Strain  Used in Social Food Programs in Argentina.
JO  - Genome Announcements
PY  - 2013
SP  - e00627
EP  - e00613
VL  - 1
AB  - We report the draft genome sequence of the probiotic Lactobacillus rhamnosus strain CRL1505.
AB  - This new probiotic strain has been included into official Nutritional Programs in Argentina.
AB  - The draft genome sequence is composed of 3,417,633 bp with 3,327 coding sequences.
ER  -

TY  - JOUR
AU  - Tarasova, G.V.
AU  - Nayakshina, T.N.
AU  - Degtyarev, S.K.
TI  - Substrate specificity of new methyl-directed DNA endonuclease GlaI.
JO  - BMC Mol. Biol.
PY  - 2008
SP  - 7
EP  - 7
VL  - 9
AB  - Recently, we have discovered site-specific endonucleases, which recognize and cleave only DNA
AB  - sequences with 5-methylcytosine. Two specificities of such endonucleases have been described.
AB  - Enzymes BisI, BlsI, and GluI are isoschizomers and hydrolyze the DNA sequence
AB  - 5'-GCNGC-3'/3'-CGNCG-5', which is methylated in different ways. The enzyme GlaI cleaves
AB  - the DNA sequence 5'-GCGC-3'/3'-CGCG-5' if there are two, three or four 5-methylcytosines.
AB  - The goal of the present work is to study in detail the composition of recognition sequence and
AB  - effect of the methylated cytosines on the efficiency of DNA cleavage by the methyl-directed
AB  - DNA endonuclease GlaI. In a recent work we have studied the dependence of GlaI activity on the
AB  - quantity and location of 5-methylcytosines in the enzyme recognition sequence
AB  - 5'-GCGC-3'/3'-CGCG-5'. A significant DNA cleavage has been observed for oligonucleotide
AB  - duplexes, which include either three or four 5-methylcytosines. In this work we have studied
AB  - dependence of the GlaI activity on quantity and location of methylated cytosines, as well as
AB  - on composition of the recognition sequence.The list of good substrates for GlaI includes a
AB  - fully methylated site 5'-CGCG-3'/3'-GCGC-5', sites with three cytosines of a general
AB  - structure 5'-PuMGM-3'/3'-PyGMG-5', and one recognition sequence with two methylated
AB  - cytosines 5'-AMGT-3'/3'-TGMA-5', where M is 5-methylcytosine. GlaI intermediate substrates
AB  - include sites with three methylated cytosines of a general structure
AB  - 5'-GMPuM-3'/3'-MGPyG-5', as well as a site with two methylcytosines
AB  - 5'-GMGT-3'/3'-CGMA-5'. The site 5'-GMGC-3'/3'-CGMG-5' may be considered a low activity
AB  - substrate.
ER  -

TY  - JOUR
AU  - Tarasova, M.V.
AU  - Kuznetsov, V.V.
AU  - Netesova, N.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.C.
TI  - Cloning and analysis of biochemical and catalytic properties of DNA methyltransferase M1.BspACI.
JO  - Vestn. Mosk. Univ.
PY  - 2011
SP  - 38
EP  - 40
VL  - 0
AB  - Genes coding for the DNA methyltransferases of restriction-modification system BspACI from
AB  - Bacillus psychrodurans AC have been cloned in E. coli cells. The analysis of amino acid
AB  - sequences of the proteins showed that both these genes belong to C5 DNA methyltransferases.
AB  - Gene bspACIMI has been subcloned in pJW2 vector. High-purity recombinant enzyme has been
AB  - obtained with chromatography on different carriers. It has been shown that M1.BspACI modifies
AB  - the first cytosine residue in the sequence 5'-CCGC-3'. Kinetic parameters have been
AB  - determined. The catalytic constant appears to be 0,095 +/- 0,002 min(-1), K-m, (Delta HK phi
AB  - ara lambda) - 0,053 +/- 0,007 (MKM), K-m (SAM) - 5,1 +/- 0,3 (MKM).
ER  -

TY  - JOUR
AU  - Tarasova, M.V.
AU  - Kuznetsov, V.V.
AU  - Netesova, N.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Recombinant DNA-Methyltransferase M1.BspACI from Bacillus psychrodurans AC: Purification and Properties.
JO  - Biochemistry
PY  - 2010
SP  - 1484
EP  - 1490
VL  - 75
AB  - A restriction-modification system from Bacillus psychrodurans AC ( recognition sequence
AB  - 5'-CCGC-3') comprises two DNA methyltransferases:
AB  - M1.BspACI and M2.BspACI. The bspACIM1 gene was cloned in the pJW2
AB  - vector and expressed in Escherichia coli cells. High-purity M1.BspACI
AB  - preparation has been obtained by chromatography on different carriers.
AB  - M1.BspACI has a temperature optimum of 30 C and demonstrates maximum
AB  - activity at pH 8.0. M1.BspACI modifies the first cytosine in the
AB  - recognition sequence 5'-CCGC-3'. The kinetic parameters of M1.BspACI
AB  - DNA methylation are as follows: K-m for phage lambda DNA is 0.053 mu M
AB  - and K-m for S-adenosyl-L-methionine is 5.1 mu M. The catalytic constant
AB  - (k(cat)) is 0.095 min(-1).
ER  -

TY  - JOUR
AU  - Tarazona, D.
AU  - Borda, V.
AU  - Galarza, M.
AU  - Agapito, J.C.
AU  - Guio, H.
TI  - Functional Analysis Using Whole-Genome Sequencing of a Drug-Sensitive Mycobacterium tuberculosis Strain from Peru.
JO  - Genome Announcements
PY  - 2014
SP  - e00087
EP  - e00014
VL  - 2
AB  - We report the whole-genome sequence of a Latin American-Mediterranean (LAM) lineage
AB  - drug-sensitive Mycobacterium tuberculosis strain from Peru, INS-SEN. The
AB  - functional analysis revealed more mutations in secondary metabolite biosynthesis,
AB  - transport, and catabolism (clusters of orthologous groups [COG] category Q) than
AB  - for other LAM-sensitive strains. This study contributes to the understanding of
AB  - the genomic diversity of drug-sensitive M. tuberculosis.
ER  -

TY  - JOUR
AU  - Tarazona, D.
AU  - Padilla, C.
AU  - Caceres, O.
AU  - Montenegro, J.D.
AU  - Bailon, H.
AU  - Ventura, G.
AU  - Mendoza, G.
AU  - Anaya, E.
AU  - Guio, H.
TI  - Whole Genome Sequencing and Comparative Analysis of Bartonella bacilliformis Strain INS, the Causative Agent of Carrion's Disease.
JO  - Genome Announcements
PY  - 2013
SP  - e00053
EP  - e00012
VL  - 1
AB  - Bartonella bacilliformis is the etiological agent of human bartonellosis, which is highly
AB  - endemic to Peru. Here, we report the first genome that was sequenced
AB  - and analyzed from an isolate of B. bacilliformis strain INS, which originally was
AB  - isolated from the blood of an infected patient with an acute phase of Carrion's
AB  - disease from Jaen-Cajamarca, Peru.
ER  -

TY  - JOUR
AU  - Tardy-Planechaud, S.
AU  - Fujimoto, J.
AU  - Lin, S.S.
AU  - Sowers, L.C.
TI  - Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 553
EP  - 558
VL  - 25
AB  - Emerging data suggest an important role for cytosine methylation in tumorigenesis.
AB  - Simultaneously, recent studies indicate a significant contribution of endogenous oxidative DNA
AB  - damage to the development of human disease.  Oxidation of the 5-methyl group of
AB  - 5-methylcytosine (5mC) residues in DNA results in the formation of 5-(hydroxymethyl)cytosine
AB  - (hmC).  The biological consequences of hmC residues in vertebrate DNA are as yet unknown;
AB  - however, conversion of the hydrophobic methyl group to the hydrophilic hydroxymethyl group may
AB  - substantially alter the interaction of sequence-specific binding proteins with DNA.  Central
AB  - to both biophysical and biochemical studies on the potential consequences of specific DNA
AB  - damage products such as hmC are efficient methods for the synthesis of oligodeoxynucleotides
AB  - containing such modified bases at selected positions.  In this paper, we describe a method for
AB  - the placement of hmC residues in oligodeoxynucleotides using established phosphoramidite
AB  - chemistry.  In addition, we have examined the influence of specific hmC residues on enzymatic
AB  - cleavage of oligodeoxynucleotides by the methylation-sensitive restriction endonucleases MspI
AB  - and HpaII.
ER  -

TY  - JOUR
AU  - Tareb, R.
AU  - Bernardeau, M.
AU  - Vernoux, J.P.
TI  - Genome Sequence of Lactobacillus rhamnosus Strain CNCM I-3698.
JO  - Genome Announcements
PY  - 2015
SP  - e00582
EP  - e00515
VL  - 3
AB  - Lactobacillus rhamnosus CNCM I-3698 is a commercially available probiotic that is used in
AB  - animal feed as an additive. Here, we announce the draft genome sequence
AB  - for this strain, consisting of 71 contigs corresponding to 2,966,480 bp and a G+C
AB  - content of 46.69%.
ER  -

TY  - JOUR
AU  - Tareb, R.
AU  - Bernardeau, M.
AU  - Vernoux, J.P.
TI  - Genome Sequence of Rough and Smooth Variants of Pleomorphic Strain Lactobacillus  farciminis CNCM-I-3699.
JO  - Genome Announcements
PY  - 2015
SP  - e01059
EP  - e01015
VL  - 3
AB  - The probiotic Lactobacillus farciminis CNCM-I-3699 is a pleomorphic strain exhibiting smooth
AB  - and rough variants. We report their complete genomes consisting of a chromosome of 2, 4 Mb and
AB  - a plasmid of 6,417 bp. The smooth variant differs  by the presence of an additional plasmid of
AB  - 35,418 bp.
ER  -

TY  - JOUR
AU  - Tarkka, M.T.
AU  - Feldhahn, L.
AU  - Buscot, F.
AU  - Wubet, T.
TI  - Genome Sequence of the Mycorrhiza Helper Bacterium Streptomyces sp. Strain AcH 505.
JO  - Genome Announcements
PY  - 2015
SP  - e01386
EP  - e01314
VL  - 3
AB  - A draft genome sequence of Streptomyces sp. strain AcH 505 is presented here. The genome
AB  - encodes 22 secondary metabolite gene clusters and a large arsenal of
AB  - secreted proteins, and their comparative and functional analyses will help to
AB  - advance our knowledge of symbiotic interactions and fungal and plant biomass
AB  - degradation.
ER  -

TY  - JOUR
AU  - Tarkka, M.T.
AU  - Feldhahn, L.
AU  - Kruger, D.
AU  - Arnold, N.
AU  - Buscot, F.
AU  - Wubet, T.
TI  - Draft Genome Sequence of Streptomyces sp. Strain 150FB, a Mushroom Mycoparasite Antagonist.
JO  - Genome Announcements
PY  - 2015
SP  - e01441
EP  - e01414
VL  - 3
AB  - Streptomyces sp. strain 150FB, isolated from the cap surface of a bolete mushroom, inhibits
AB  - the growth of the mycoparasitic Sepedonium species. Functional
AB  - annotation of the strain 150FB draft genome identified 22 putative secondary
AB  - metabolite biosynthetic gene clusters and genes encoding secreted proteins, which
AB  - may contribute to the inhibition of the mycoparasite.
ER  -

TY  - JOUR
AU  - Tarlachkov, S.V.
AU  - Dyachenko, O.V.
AU  - Cherevatenko, A.M.
AU  - Rudenko, N.V.
AU  - Shevchuk, T.V.
TI  - Cloning, purification and characterization of translationally fused protein DNA methyltransferase MoHhaI-EGFP.
JO  - Process. Biochem.
PY  - 2014
SP  - 2170
EP  - 2173
VL  - 49
AB  - Design of the transcriptionally-fused protein MoHhaI-EGFP, composed of bacterial
AB  - DNA-methyltransferase MoHhaI and enhanced green fluorescent protein (GFP) is described. The
AB  - mentioned MoHhaI-EGFP was expressed in Escherichia coli ER1821 and purified by affinity
AB  - chromatography on Ni-NTA agarose. According to expectations MoHhaI-EGFP fused protein retained
AB  - significant features of corresponding original proteins: the ability to transfer methyl group
AB  - to the C5 carbon atom of internal cytosine in CGCG site and absorption-emission spectral
AB  - characteristics. The created transcriptionally-fused protein MoHhaI-EGFP could be used in
AB  - various experiments in molecular biology.
ER  -

TY  - JOUR
AU  - Taron, C.H.
AU  - Van Cott, E.M.
AU  - Wilson, G.G.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Hornstra, L.J.
AU  - Benner, J.S.
AU  - Kucera, R.B.
AU  - Guthrie, E.P.
TI  - Cloning and expression of the NaeI restriction endonuclease-encoding gene and sequence analysis of the NaeI restriction-modification system.
JO  - Gene
PY  - 1995
SP  - 19
EP  - 25
VL  - 155
AB  - NaeI, a type-II restriction-modification (R-M) system from the bacterium Nocardia
AB  - aerocolonigenes, recognizes the sequence 5'-GCCGGC. The NaeI DNA methyltransferase
AB  - (MTase)-encoding gene, naeIM, had been cloned previously in Escherichia coli. However, none of
AB  - these clones expressed detectable levels of the restriction endonuclease (ENase). The absence
AB  - of the intact ENase-encoding gene (naeIR) within the isolated MTase clones was confirmed by
AB  - recloning the MTase clones into Streptomyces lividans. The complete NaeI system was finally
AB  - cloned using E. coli AP1-200 and less stringent MTase-selection conditions. The naeIR gene was
AB  - expressed first by cloning into S. lividans, and later by cloning under control of a regulated
AB  - promoter in an E. coli strain preprotected by the heterologous MspI MTase (M.MspI). The DNA
AB  - sequence of the NaeI R-M system has been determined, analyzed and compared to previously
AB  - sequenced R-M systems.
ER  -

TY  - JOUR
AU  - Taron, C.H.
AU  - Van Cott, E.M.
AU  - Wilson, G.G.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Hornstra, L.J.
AU  - Benner, J.S.
AU  - Kucera, R.B.
AU  - Guthrie, E.P.
TI  - Cloning, sequencing and overexpressing the NaeI restriction endonuclease gene from Nocardia aerocolonigenes.
JO  - J. Cell Biochem. Suppl.
PY  - 1993
SP  - 175
EP  - 175
VL  - 17C
AB  - NaeI is a type II restriction-modification system from Nocardia aerocolonigenes. The
AB  - endonuclease recognizes the palindromic hexanucleotide sequence 5'GCC^GGC 3' and cleaves to
AB  - produce a blunt end. The NaeI methylase gene (naeIM) was cloned previously by Van Cott and
AB  - Wilson (Gene 74: 55-59, 1988). This clone exhibited methylase activity but no levels of
AB  - endonuclease activity were detected, suggesting the endonuclease gene (naeIR) was either not
AB  - present intact on the clone, or was present but not expressed. Subcloning the methylase clone
AB  - into Streptomyces lividans, an organism more closely related to Nocardia, confirmed the
AB  - absence of naeIR. To clone naeIR, a SacI genomic DNA library was made using the original
AB  - methylase clone in pBR322 as a cloning vector. This library was selected for naeIM by
AB  - digestion with NaeI, transformed into E. coli AP1-200 and positive clones appeared as blue
AB  - clonies on LB agar plates containing X-gal. Nucleotide sequencing of naeIM and naeIR yielded
AB  - two large open reading frames (ORFs). The naeIR ORF was identified by correlation of its
AB  - translated peptide sequence to the amino terminal peptide sequence of the NaeI endonuclease.
AB  - The endonuclease gene was amplified by PCR and cloned behind the strong promoter Ptac. This
AB  - clone was transformed into E. coli K802 containing the MspI methylase gene. The MspI
AB  - recognition sequence is 5'CCGG 3' (the internal tetramer of the NaeI recognition site) with
AB  - MspI modification fully protecting against NaeI digestion. This construct yielded
AB  - approximately 750 fold overexpression of NaeI.
ER  -

TY  - JOUR
AU  - Tasara, T.
AU  - Ebner, R.
AU  - Klumpp, J.
AU  - Stephan, R.
TI  - Complete Genome Sequence of Listeria monocytogenes N2306, a Strain Associated with the 2013-2014 Listeriosis Outbreak in Switzerland.
JO  - Genome Announcements
PY  - 2015
SP  - e00553
EP  - e00515
VL  - 3
AB  - We present the complete genome sequence of Listeria monocytogenes N2306, a serotype 4b
AB  - clinical strain isolated during the 2013-2014 nationwide listeriosis
AB  - outbreak in Switzerland.
ER  -

TY  - JOUR
AU  - Tasara, T.
AU  - Fierz, L.
AU  - Klumpp, J.
AU  - Schmidt, H.
AU  - Stephan, R.
TI  - Draft Genome Sequences of Five Shiga Toxin-Producing Escherichia coli Isolates Harboring the New and Recently Described Subtilase Cytotoxin Allelic Variant  subAB2-3.
JO  - Genome Announcements
PY  - 2017
SP  - e01582
EP  - e01516
VL  - 5
AB  - We present here the draft genome sequences of five Shiga toxin-producing Escherichia coli
AB  - (STEC) strains which tested positive in a primary subAB
AB  - screening. Assembly and annotation of the draft genomes revealed that all strains
AB  - harbored the recently described allelic variant subAB2-3 Based on the sequence
AB  - data, primers were designed to identify and differentiate this variant.
ER  -

TY  - JOUR
AU  - Tasara, T.
AU  - Klumpp, J.
AU  - Bille, J.
AU  - Stephan, R.
TI  - Genome Sequences of Listeria monocytogenes Strains Responsible for Cheese- and Cooked Ham Product-Associated Swiss Listeriosis Outbreaks in 2005 and 2011.
JO  - Genome Announcements
PY  - 2016
SP  - e00106
EP  - e00116
VL  - 4
AB  - The complete genome sequences of three Listeria monocytogenes serotype 1/2a strains, Lm 3136,
AB  - Lm 3163, and Lm N1546, which were responsible for listeriosis
AB  - outbreaks in 2005 and 2011 in Switzerland, are presented here.
ER  -

TY  - JOUR
AU  - Tasara, T.
AU  - Morach, M.
AU  - Klumpp, J.
AU  - Stephan, R.
TI  - Complete Genome Sequence of Anoxybacillus flavithermus Strain 52-1A Isolated from a Heat-Processed Powdered Milk Concentrate.
JO  - Genome Announcements
PY  - 2017
SP  - e00800
EP  - e00817
VL  - 5
AB  - The thermophilic spore-forming bacterium Anoxybacillus flavithermus is responsible for
AB  - powdered milk product spoilage, and its presence in dairy
AB  - processing environments is a concern. Here, the complete genome sequence of the
AB  - A. flavithermus strain 52-1A isolated from a heat-processed powdered milk product
AB  - concentrate in Switzerland is presented.
ER  -

TY  - JOUR
AU  - Tasara, T.
AU  - Weinmaier, T.
AU  - Klumpp, J.
AU  - Rattei, T.
AU  - Stephan, R.
TI  - Complete Genome Sequence of Listeria monocytogenes Lm60, a Strain with an Enhanced Cold Adaptation Capacity.
JO  - Genome Announcements
PY  - 2014
SP  - e01248
EP  - e01214
VL  - 2
AB  - The complete genome sequence of Listeria monocytogenes Lm60, a fast cold-adapting serotype
AB  - 1/2a human isolate, is presented.
ER  -

TY  - JOUR
AU  - Tashkandy, N. et al.
TI  - High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM  17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 42
EP  - 42
VL  - 11
AB  - Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum
AB  - Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from
AB  - greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of
AB  - the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp
AB  - long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82
AB  - RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a
AB  - small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo
AB  - and serine peptidases were found most frequently. Among CAZymes, eight glycoside
AB  - hydrolase families, nine glycosyl transferase families, two carbohydrate binding
AB  - module families and four carbohydrate esterase families were identified.
AB  - Suprisingly, polysaccharides utilization loci (PULs) were not found in strain
AB  - GH29-5(T). Based on the coherent physiological and genomic characteristics we
AB  - suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides
AB  - and lipids.
ER  -

TY  - JOUR
AU  - Tasse, L.
AU  - Bercovici, J.
AU  - Pizzut-Serin, S.
AU  - Robe, P.
AU  - Tap, J.
AU  - Klopp, C.
AU  - Cantarel, B.L.
AU  - Coutinho, P.M.
AU  - Henrissat, B.
AU  - Leclerc, M.
AU  - Dore, J.
AU  - Monsan, P.
AU  - Remaud-Simeon, M.
AU  - Potocki-Veronese, G.
TI  - Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.
JO  - Genome Res.
PY  - 2010
SP  - 1605
EP  - 1612
VL  - 20
AB  - The human gut microbiome is a complex ecosystem composed mainly of
AB  - uncultured bacteria. It plays an essential role in the catabolism of
AB  - dietary fibers, the part of plant material in our diet that is not
AB  - metabolized in the upper digestive tract, because the human genome does
AB  - not encode adequate carbohydrate active enzymes (CAZymes). We describe a
AB  - multi-step functionally based approach to guide the in-depth
AB  - pyrosequencing of specific regions of the human gut metagenome encoding
AB  - the CAZymes involved in dietary fiber breakdown. High-throughput
AB  - functional screens were first applied to a library covering 5.4 x 10(9) bp
AB  - of metagenomic DNA, allowing the isolation of 310 clones showing
AB  - beta-glucanase, hemicellulase, galactanase, amylase, or pectinase
AB  - activities. Based on the results of refined secondary screens, sequencing
AB  - efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA,
AB  - corresponding to 26 clones that were particularly efficient for the
AB  - degradation of raw plant polysaccharides. Seventy-three CAZymes from 35
AB  - different families were discovered. This corresponds to a fivefold
AB  - target-gene enrichment compared to random sequencing of the human gut
AB  - metagenome. Thirty-three of these CAZy encoding genes are highly
AB  - homologous to prevalent genes found in the gut microbiome of at least 20
AB  - individuals for whose metagenomic data are available. Moreover, 18
AB  - multigenic clusters encoding complementary enzyme activities for plant
AB  - cell wall degradation were also identified. Gene taxonomic assignment is
AB  - consistent with horizontal gene transfer events in dominant gut species
AB  - and provides new insights into the human gut functional trophic chain.
ER  -

TY  - JOUR
AU  - Tasseron-de Jong, J.G.
AU  - Aker, J.
AU  - Giphart-Gassler, M.
TI  - The ability of the restriction endonuclease EcoRI to digest hemi-methylated versus fully cytosine-methylated DNA of the herpes tk promoter region.
JO  - Gene
PY  - 1988
SP  - 147
EP  - 149
VL  - 74
AB  - None
ER  -

TY  - JOUR
AU  - Tateishi, Y.
AU  - Kitada, S.
AU  - Miki, K.
AU  - Maekura, R.
AU  - Ogura, Y.
AU  - Ozeki, Y.
AU  - Nishiuchi, Y.
AU  - Niki, M.
AU  - Hayashi, T.
AU  - Hirata, K.
AU  - Kobayashi, K.
AU  - Matsumoto, S.
TI  - Whole-Genome Sequence of the Hypervirulent Clinical Strain Mycobacterium intracellulare M.i.198.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6336
EP  - 6336
VL  - 194
AB  - We report herein the draft genome sequence of Mycobacterium intracellulare clinical strain
AB  - M.i.198, which consistently exhibits hypervirulence in human
AB  - patients, human macrophages in vitro, and immunocompetent mice.
ER  -

TY  - JOUR
AU  - Tateishi, Y.
AU  - Tamaru, A.
AU  - Ogura, Y.
AU  - Niki, M.
AU  - Wada, T.
AU  - Yamamoto, T.
AU  - Hirata, K.
AU  - Hayashi, T.
AU  - Matsumoto, S.
TI  - Whole-Genome Sequence of the Potentially Hypertransmissible Multidrug-Resistant Mycobacterium tuberculosis Beijing Strain OM-V02_005.
JO  - Genome Announcements
PY  - 2013
SP  - e00608
EP  - e00613
VL  - 1
AB  - We report the draft genome sequence of Mycobacterium tuberculosis Beijing strain  OM-V02_005,
AB  - which exhibits possible hypertransmissible characteristics among the
AB  - population of patients with multidrug-resistant tuberculosis in Osaka Prefecture,
AB  - the largest urban area in western Japan.
ER  -

TY  - JOUR
AU  - Tatti, K.M.
AU  - Loparev, V.N.
AU  - Ranganathanganakammal, S.
AU  - Changayil, S.
AU  - Frace, M.
AU  - Weil, M.R.
AU  - Sammons, S.
AU  - Maccannell, D.
AU  - Mayer, L.W.
AU  - Tondella, M.L.
TI  - Draft Genome Sequences of Bordetella holmesii Strains from Blood (F627) and Nasopharynx (H558).
JO  - Genome Announcements
PY  - 2013
SP  - e0005613
EP  - e0005613
VL  - 1
AB  - Bordetella holmesii, a human pathogen, can confound the diagnosis of respiratory  illness
AB  - caused by Bordetella pertussis. We present the draft genome sequences of
AB  - two B. holmesii isolates, one from blood, F627, and one from the nasopharynx,
AB  - H558. Interestingly, important virulence genes that are present in B. pertussis
AB  - are not found in B. holmesii.
ER  -

TY  - JOUR
AU  - Tatum, F.M.
AU  - Briggs, R.E.
TI  - Isolation, identification, and cloning of a non-palindromic type II DNA restriction endonuclease, PhaI, from Pasteurella haemolytica.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1993
SP  - 199
EP  - 199
VL  - 93
AB  - Pasteurella haemolytica is an important cause of bovine pneumonic pasteurellosis. PhaI, an
AB  - isoschizomer of SfaNI, was isolated from P. haemolytica, strain #NADC-60, a plasmidless
AB  - isolate of serotype 1. PhaI recognizes the 5 base non-palindromic sequence 5'-GATGC-3'.
AB  - Analysis of the restriction products on sequencing gels showed that cleavage occurs 5 bases to
AB  - the right of the noted recognition site and 9 bases to the right on the opposite strand. A
AB  - clone encoding the PhaI restriction endonuclease and PhaI methyltransferase was isolated from
AB  - a P. haemolytica cosmid library and functional expression of both genes was obtained in
AB  - Escherichia coli. Preliminary results indicate that PhaI restriction activity is a barrier to
AB  - the introduction or establishment of exogenous DNA into this bacterium.
ER  -

TY  - JOUR
AU  - Tauch, A.
AU  - Kaiser, O.
AU  - Hain, T.
AU  - Goesmann, A.
AU  - Weisshaar, B.
AU  - Albersmeier, A.
AU  - Bekel, T.
AU  - Bischoff, N.
AU  - Brune, I.
AU  - Chakraborty, T.
AU  - Kalinowski, J.
AU  - Meyer, F.
AU  - Rupp, O.
AU  - Schneiker, S.
AU  - Viehoever, P.
AU  - Puhler, A.
TI  - Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
JO  - J. Bacteriol.
PY  - 2005
SP  - 4671
EP  - 4682
VL  - 187
AB  - Corynebacterium jeikeium is a "lipophilic" and multidrug-resistant bacterial species of the
AB  - human skin flora that has been recognized with increasing frequency as a serious nosocomial
AB  - pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which
AB  - was initially recovered from the axilla of a bone marrow transplant patient. The genome of C.
AB  - jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp
AB  - bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104
AB  - predicted coding sequences, 52% of which were considered to be orthologous with genes in the
AB  - Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae
AB  - genomes. These genes apparently represent the chromosomal backbone that is conserved between
AB  - the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial
AB  - genomes, many are located close to transposable elements or revealed an atypical G+C content,
AB  - indicating that horizontal gene transfer played an important role in the acquisition of genes
AB  - involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host
AB  - interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the
AB  - "lipophilic" phenotype of C. jeikeium most likely originates from the absence of fatty acid
AB  - synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene
AB  - repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence
AB  - of growth on the presence of exogenous fatty acids. The predicted virulence factors of C.
AB  - jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by
AB  - damaging the host tissue.
ER  -

TY  - JOUR
AU  - Tauch, A.
AU  - Kirchner, O.
AU  - Loffler, B.
AU  - Gotker, S.
AU  - Puhler, A.
AU  - Kalinowski, J.
TI  - Efficient electrotransformation of Corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1.
JO  - Curr. Microbiol.
PY  - 2002
SP  - 362
EP  - 367
VL  - 45
AB  - Efficient transformation of the human pathogen Corynebacterium
AB  - diphtheriae was achieved with novel cloning vectors consisting of a mini-replicon from the
AB  - cryptic C. glutamicum plasmid pGA1 as well as of the aph(3')-IIa or tetA(Z) antibiotic
AB  - resistance genes. Plasmid-containing transformants of C. diphtheriae were recovered at
AB  - frequencies ranging from 1.3 x 10^5 to 4.8 x 10^6 colony forming units (cfu)/microgram of
AB  - plasmid DNA. Vector DNA was directly transferred from Escherichia coli into C. diphtheriae
AB  - with frequencies up to 5.6 x 10^5 cfu/microgram of plasmid DNA. On the basis of the pGA1
AB  - mini-replicon, an expression vector system was established for C. diphtheriae by means of the
AB  - P-tac promoter and the green fluorescent reporter protein. In addition, other commonly used
AB  - vector systems from C. glutamicum, including the pBL1 and pHM1519 replicons, and the sacB
AB  - conditionally lethal selection market from Bacillus subtilis, were shown to be functional in
AB  - C. diphtheriae. Thus, the ability to apply the standard methods of C. glutamicum recombinant
AB  - DNA technology will greatly facilitate the functional analysis of the recently completed C.
AB  - diphtheriae genome sequence.
ER  -

TY  - JOUR
AU  - Tauch, A.
AU  - Kirchner, O.
AU  - Wehmeier, L.
AU  - Kalinowski, J.
AU  - Puhler, A.
TI  - Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli.
JO  - FEMS Microbiol. Lett.
PY  - 1994
SP  - 343
EP  - 347
VL  - 123
AB  - Efficient electroporation of Escherichia coli with plasmid DNA isolated from Corynebacterium
AB  - glutamicum depends on the use of Mcr-deficient E. coli strains. The transformation frequency
AB  - increased nearly 800-fold when the Mcr-deficient E. coli DH5a MCR was used instead of E. coli
AB  - DH5a. We used E. coli strains with different mutations in the methyl-specific restriction
AB  - systems to show that McrBC-deficiency is sufficient to generate this effect. The results imply
AB  - that C. glutamicum DNA contains methylcytosine in specific sequences recognized by the E. coli
AB  - McrBC system.
ER  -

TY  - JOUR
AU  - Tauch, A.
AU  - Krieft, S.
AU  - Kalinowski, J.
AU  - Puhler, A.
TI  - The 51,409-bp R-plasmid pTP10 from the multiresistant clinical isolate Corynebacterium striatum M82B is composed of DNA segments initially identified in soil bacteria and in plant, animal, and human pathogens.
JO  - Mol. Gen. Genet.
PY  - 2000
SP  - 1
EP  - 11
VL  - 263
AB  - The 51,409-bp DNA sequence of the multiresistance plasmid pTP10 from the
AB  - gram-positive opportunistic human pathogen Corynebacterium striatum M82B
AB  - has been determined. Fully automated genome interpretation led to the
AB  - identification of 47 ORFs. Analysis of the genetic organization of pTP10
AB  - suggests that the plasmid is composed of eight DNA segments, the
AB  - boundaries of which are represented by transposons and insertion
AB  - sequences. The DNA segments of pTP10 are highly similar to (1) a
AB  - plasmid-encoded erythromycin resistance region from the human pathogen
AB  - Corynebacterium diphtheriae; (2) a chromosomal DNA region from
AB  - Mycobacterium tuberculosis; (3) a plasmid-encoded chloramphenicol
AB  - resistance region from the soil bacterium Corynebacterium glutamicum; (4)
AB  - transposable elements from phytopathogenic gram-negative Pseudomonas,
AB  - Xanthomonas and Erwinia species; and (5) a plasmid-encoded aminoglycoside
AB  - resistance region from the gram-negative fish pathogen Pasteurella
AB  - piscicida. The complete DNA sequence of pTP10 provides genetic information
AB  - regarding the mechanisms of resistance to 16 antimicrobial agents that
AB  - belong to six structural classes. In addition, the mosaic structure of
AB  - pTP10 represents the evolutionary consolidation into a single plasmid
AB  - molecule of antimicrobial resistances from microorganisms found in
AB  - different habitats by means of mobile elements, resulting in the
AB  - generation of a multiresistant bacterium that can infect humans.
ER  -

TY  - JOUR
AU  - Tauch, A.
AU  - Trost, E.
AU  - Tilker, A.
AU  - Ludewig, U.
AU  - Schneiker, S.
AU  - Goesmann, A.
AU  - Arnold, W.
AU  - Bekel, T.
AU  - Brinkrolf, K.
AU  - Brune, I.
AU  - Gotker, S.
AU  - Kalinowski, J.
AU  - Kamp, P.B.
AU  - Lobo, F.P.
AU  - Viehoever, P.
AU  - Weisshaar, B.
AU  - Soriano, F.
AU  - Droge, M.
AU  - Puhler, A.
TI  - The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
JO  - J. Biotechnol.
PY  - 2008
SP  - 11
EP  - 21
VL  - 136
AB  - Corynebacterium urealyticum is a lipid-requiring, urealytic bacterium of the human skin flora
AB  - that has been recognized as causative agent of
AB  - urinary tract infections. We report the analysis of the complete genome
AB  - sequence of C. urealyticum DSM7109, which was initially recovered from a
AB  - patient with alkaline-encrusted cystitis. The genome sequence was
AB  - determined by a combination of pyrosequencing and Sanger technology. The
AB  - chromosome of C. urealyticum DSM7109 has a size of 2,369,219bp and
AB  - contains 2024 predicted coding sequences, of which 78% were considered as
AB  - orthologous with genes in the Corynebacterium jeikeium K411 genome.
AB  - Metabolic analysis of the lipid-requiring phenotype revealed the absence
AB  - of a fatty acid synthase gene and the presence of a beta-oxidation pathway
AB  - along with a large repertoire of auxillary genes for the degradation of
AB  - exogenous fatty acids. A urease locus with the gene order ureABCEFGD may
AB  - play a pivotal role in virulence of C. urealyticum by the alkalinization
AB  - of human urine and the formation of struvite stones. Multidrug resistance
AB  - of C. urealyticum DSM7109 is mediated by transposable elements, conferring
AB  - resistances to macrolides, lincosamides, ketolides, aminoglycosides,
AB  - chloramphenicol, and tetracycline. The complete genome sequence of C.
AB  - urealyticum revealed a detailed picture of the lifestyle of this
AB  - opportunistic human pathogen.
ER  -

TY  - JOUR
AU  - Tautz, N.
AU  - Kaluza, K.
AU  - Frey, B.
AU  - Jarsch, M.
AU  - Schmitz, G.G.
AU  - Kessler, C.
TI  - SgrAI, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5'-CR/CCGGYG-3' .
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3087
EP  - 3087
VL  - 18
ER  -

TY  - JOUR
AU  - Taveirne, M.E.
AU  - Dunham, D.T.
AU  - Miller, W.G.
AU  - Parker, C.T.
AU  - Huynh, S.
AU  - DiRita, V.J.
TI  - Complete Genome Sequence and Annotation of a Campylobacter jejuni Strain, MTVDSCj20, Isolated from a Naturally Colonized Farm-Raised Chicken.
JO  - Genome Announcements
PY  - 2014
SP  - e00852
EP  - e00814
VL  - 2
AB  - Campylobacter jejuni is a major cause of human food-borne illness, with contaminated poultry
AB  - products serving as a main source of human infection. C.
AB  - jejuni strain MTVDSCj20 was isolated from the cecal contents of a farm-raised
AB  - chicken that was naturally colonized with Campylobacter. We present here the
AB  - complete annotated genome sequence of MTVDSCj20.
ER  -

TY  - JOUR
AU  - Taveirne, M.E.
AU  - Dunham, D.T.
AU  - Perault, A.
AU  - Beauchamp, J.M.
AU  - Huynh, S.
AU  - Parker, C.T.
AU  - DiRita, V.J.
TI  - Complete Annotated Genome Sequences of Three Campylobacter jejuni Strains Isolated from Naturally Colonized Farm-Raised Chickens.
JO  - Genome Announcements
PY  - 2017
SP  - e01407
EP  - e01416
VL  - 5
AB  - Campylobacter jejuni is a leading cause of bacterially derived foodborne illness. Human
AB  - illness is commonly associated with the handling and consumption of
AB  - contaminated poultry products. Three C. jejuni strains were isolated from cecal
AB  - contents of three different naturally colonized farm-raised chickens. The
AB  - complete genomes of these three isolates are presented here.
ER  -

TY  - JOUR
AU  - Tawfik, D.S.
AU  - Griffiths, A.D.
TI  - Man-made cell-like compartments for molecular evolution.
JO  - Nat. Biotechnol.
PY  - 1998
SP  - 652
EP  - 656
VL  - 16
AB  - Cellular compartmentalization is vital for the evolution of all living organisms.  Cells keep
AB  - together the genes, the RNAs and proteins that they encode, and the products of their
AB  - activities, thus linking genotype to phenotype.  We have reproduced this linkage in the test
AB  - tube by transcribing and translating single genes in the aqueous compartments of water-in-oil
AB  - emulsions.  These compartments, with volumes close to those of bacteria, can be recruited to
AB  - select genes encoding catalysts.  A protein or RNA with a desired catalytic activity converts
AB  - a substrate attached to the gene that encodes it to product.  In other compartments,
AB  - substrates attached to genes that do not encode catalysts remain unmodified.  Subsequently,
AB  - genes encoding catalysts are selectively enriched by virtue of their linkage to the product.
AB  - We demonstrate the linkage of genotype to phenotype in man-made compartments using a model
AB  - system.  A selection for target-specific DNA methylation was based on the resistance of the
AB  - product (methylated DNA) to restriction digestion.  Genes encoding HaeIII methyltransferase
AB  - were selected from a 10^7-fold excess of genes encoding another enzyme.
ER  -

TY  - JOUR
AU  - Tay, A.P.
AU  - Kaakoush, N.O.
AU  - Deshpande, N.P.
AU  - Chen, Z.
AU  - Mitchell, H.
AU  - Wilkins, M.R.
TI  - Genome Sequence of Campylobacter showae UNSWCD, Isolated from a Patient with Crohn's Disease.
JO  - Genome Announcements
PY  - 2013
SP  - e00193
EP  - e00112
VL  - 1
AB  - Campylobacter showae UNSWCD was isolated from a patient with Crohn's disease. Here we present
AB  - a 2.1 Mb draft assembly of its genome.
ER  -

TY  - JOUR
AU  - Tay, M.
AU  - Roizman, D.
AU  - Cohen, Y.
AU  - Tolker-Nielsen, T.
AU  - Givskov, M.
AU  - Yang, L.
TI  - Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82.
JO  - Genome Announcements
PY  - 2014
SP  - e01161
EP  - e01113
VL  - 2
AB  - Pseudomonas putida OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever
AB  - since, it has been used as a model organism to study the microbial
AB  - assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft
AB  - genome sequence of P. putida OUS82 and analyze its featured pathways for
AB  - biodegradation.
ER  -

TY  - JOUR
AU  - Tay, N.K.
AU  - Blaschek, H.P.
TI  - Purification and characterization of a restriction endonuclease (CpfI) from Clostridium perfringens 10543A.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 224
EP  - 224
VL  - 94
AB  - Nucleases may play an important role in plasmid recovery and uptake in Clostridium
AB  - perfringens. A type II restriction endonuclease designated CpfI was isolated from C.
AB  - perfringens 10543A. CpfI was purified to homogeneity using a combination of heparin-based
AB  - affinity chromatography, DEAE-anion exchange chromatography, and gel permeation
AB  - chromatography. The molecular weight of the purified enzyme was determined by gel filtration
AB  - and sodium dodecyl sulfate polyacrylamide gel electrophoresis to be 40 and 44 kdal,
AB  - respectively. The isoelectric point of the endonuclease is approximately 3.7, and the activity
AB  - of the enzyme is inhibited above 45oC. Digestion of methylated and non-methylated pBR322 and
AB  - phage DNA substrates suggested CpfI is an isoschizomer of MboI (Sau3A) with a unique
AB  - sensitivity to methylation. Enzymes with this particular specificity may prove to be widely
AB  - distributed in the genus Clostridium.
ER  -

TY  - JOUR
AU  - Taylor, C.
AU  - Ford, K.
AU  - Connolly, B.A.
AU  - Hornby, D.P.
TI  - Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor.
JO  - Biochem. J.
PY  - 1993
SP  - 493
EP  - 504
VL  - 291
AB  - The cloning and overexpression of the MspI DNA methyltransferase as a functional fusion with
AB  - glutathione S-transferase is described. The fusion enzyme reatains full biological activity
AB  - and has been used to investigate the interaction of substrates and inhibitors with MspI DNA
AB  - methyltransferase. The fusion enzyme has been purifed to homogeneity in a single step on
AB  - GSH-agarose and is free from contaminating exonuclease activity. The enzyme can be
AB  - photolabelled with S-adenosyl-L-methionine and the level of incorporation of label is enhanced
AB  - by the presence of a non-specific DNA duplex. In the presence of a cognate
AB  - oligo-deoxynucleotide, no photolabelling was observed since methyl transfer occurs instead.
AB  - The inclusion of a mechanism-based inhibitor of C-5 deoxycytidine DNA methylation (an
AB  - oligodeoxynucleotide containing the base 2-pyrimidinone-1-beta-d-2'-deoxyribofuranoside in
AB  - the position of the deoxycytidine to which methyl addition occurs), which is thought to form a
AB  - covalent interaction with the reactive cysteine of such enzymes, led to an enhancement of
AB  - S-adenosyl-L-methionine photolabelling which suggests that, in contrast with results obtained
AB  - with EcoRII DNA methyltransferase [Som and Friedman (1991) J. Biol. Chem. 266, 2937-2945],
AB  - methylcysteine is not the photolabelled product. The implications of the results obtained with
AB  - this mechanism-based inhibitor are discussed with respect to other C-5-specific DNA
AB  - methyltransferases. Gel-retardation assays in the presence of cognate oligodeoxynucleotides
AB  - that contain the reactive pyrimidinone base in place of the deoxycytidine target base are
AB  - described. These demonstrate that most probably a stable covalent bond is formed between the
AB  - methyltransferase and this oligodeoxynucleotide. However, the alternative of extremely tight
AB  - non-covalent binding cannot be rigorously excluded. Furthermore, the results from these
AB  - experiments indicate that the reaction mechanism proceeds in a manner similar to that of HhaI
AB  - DNA methyltransferase with sequence-specific DNA binding being followed by addition of
AB  - S-adenosyl-L-methionine and concomitant isomerization of the ternary complex leading to methyl
AB  - transfer. S-Adenosyl-L-homocysteine appears to inhibit the reaction pathway was as a result of
AB  - either competition with the methyl donor and potentiation of a high affinity interaction
AB  - between the enzyme and DNA in an abortive ternary complex or through an allosteric
AB  - interaction.
ER  -

TY  - JOUR
AU  - Taylor, D.E.
AU  - Eaton, M.
AU  - Chang, N.
AU  - Salama, S.M.
TI  - Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level.
JO  - J. Bacteriol.
PY  - 1992
SP  - 6800
EP  - 6806
VL  - 174
AB  - Genomic DNA from 30 strains of Helicobacter pylori was subjected to pulsed-field gel
AB  - electrophoresis after digestion with NotI and NruI.  The genome sizes of the strains ranged
AB  - from 1.6 to 1.73 Mb, with an average size of 1.67 Mb. By using NotI and NruI, a circular map
AB  - of H. pylori UA802 (1.7 Mb) which contained three copies of 16S and 23S rRNA genes was
AB  - constructed.  An unusual feature of the H. pylori genome was the separate location of at least
AB  - two copies of 16S and 23S rRNA genes.  Almost all strains had diferent PFGE patterns after
AB  - NotI and NruI digestion, suggesting that the H. pylori genome possesses a considerable degree
AB  - of genetic variability.  However, three strains from different sites (the fundus, antrum, and
AB  - body of the stomach) within the same patient gave identical PFGE patterns.  The genomic
AB  - pattern of individual isolates remained constant during multiple subcultures in vitro.  The
AB  - reason for the genetic diversity observed among H. pylori strains remains to be explained.
ER  -

TY  - JOUR
AU  - Taylor, G.K.
AU  - Heiter, D.F.
AU  - Pietrokovski, S.
AU  - Stoddard, B.L.
TI  - Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 9705
EP  - 9719
VL  - 39
AB  - Novel family of putative homing endonuclease genes was recently discovered during analyses of
AB  - metagenomic and genomic sequence data. One such protein is encoded within a group I intron
AB  - that resides in the recA gene of the Bacillus thuringiensis 03058-36 bacteriophage. Named
AB  - I-Bth0305I, the endonuclease cleaves a DNA target in the uninterrupted recA gene at a position
AB  - immediately adjacent to the intron insertion site. The enzyme displays a multidomain,
AB  - homodimeric architecture and footprints a DNA region of  approximately 60 bp. Its highest
AB  - specificity corresponds to a 14-bp pseudopalindromic sequence that is directly centered across
AB  - the DNA cleavage site. Unlike many homing endonucleases, the specificity profile of the enzyme
AB  - is evenly distributed across much of its target site, such that few single base pair
AB  - substitutions cause a significant decrease in cleavage activity. A crystal structure of its
AB  - C-terminal domain confirms a nuclease fold that is homologous to very short patch repair (Vsr)
AB  - endonucleases. The domain architecture and DNA recognition profile displayed by I-Bth0305I,
AB  - which is the prototype of a homing lineage that we term the 'EDxHD' family, are distinct
AB  - from previously characterized homing endonucleases.
ER  -

TY  - JOUR
AU  - Taylor, G.K.
AU  - Petrucci, L.H.
AU  - Lambert, A.R.
AU  - Baxter, S.K.
AU  - Jarjour, J.
AU  - Stoddard, B.L.
TI  - LAHEDES: the LAGLIDADG homing endonuclease database and engineering server.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - W110
EP  - W116
VL  - 40
AB  - LAGLIDADG homing endonucleases (LHEs) are DNA cleaving enzymes, also termed 'meganucleases'
AB  - that are employed as gene-targeting reagents. This use of LHEs requires that their DNA
AB  - specificity be altered to match sequences in genomic targets. The choice of the most
AB  - appropriate LHE to target a particular gene is facilitated by the growing number of such
AB  - enzymes with well-characterized activities and structures. 'LAHEDES' (The LAGLIDADG Homing
AB  - Endonuclease Database and Engineering Server) provides both an online archive of LHEs with
AB  - validated DNA cleavage specificities and DNA-binding interactions, as well as a tool for the
AB  - identification of DNA sequences that might be targeted by various LHEs. Searches can be
AB  - performed using four separate scoring algorithms and user-defined choices of LHE scaffolds.
AB  - The webserver subsequently provides information regarding clusters of amino acids that should
AB  - be interrogated during engineering and selection experiments. The webserver is fully open
AB  - access and can be found at http://homingendonuclease.net.
ER  -

TY  - JOUR
AU  - Taylor, G.K.
AU  - Stoddard, B.L.
TI  - Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 5189
EP  - 5200
VL  - 40
AB  - Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by
AB  - invasive DNA elements (usually mobile introns or inteins) within the genomes of phage,
AB  - bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that
AB  - collectively span four distinct nuclease catalytic motifs, have been characterized to date.
AB  - Members of each family display structural homology and functional relationships to a wide
AB  - variety of proteins from various organisms. The biological functions of those proteins are
AB  - highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases,
AB  - DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These
AB  - relationships suggest that modern day HEs share common ancestors with proteins involved in
AB  - genome fidelity, maintenance and gene expression. This review summarizes the results of
AB  - structural studies of HEs and corresponding proteins from host organisms that have illustrated
AB  - the manner in which these factors are related.
ER  -

TY  - JOUR
AU  - Taylor, I.
AU  - Patel, J.
AU  - Firman, K.
AU  - Kneale, G.
TI  - Purification and biochemical characterisation of the EcoR124 type I modification methylase.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 179
EP  - 186
VL  - 20
AB  - Large scale purification of the type I modification methylase EcoR124 has been
AB  - achieved from an overexpressing strain by a two step procedure using
AB  - ion-exchange and heparin chromatography.  Pure methylase is obtained at a yield
AB  - of 30mg per gm of cell paste.  Measurements of the molecular weight and subunit
AB  - stoichiometry show that the enzyme is a trimeric complex of 162 kDa consisting
AB  - of two subunits of HsdM (58 kDa) and one subunit of HsdS (46 kDa).  The
AB  - purified enzyme can methylate a DNA fragment bearing its cognate recognition
AB  - sequence.  Binding of the methylase to synthetic DNA fragments containing
AB  - either the EcoR124 recognition sequence GAAN6RT-CG, or the recognition sequence
AB  - GAAN7RTCG of the related enzyme EcoR124/3, was followed by fluorescence
AB  - competition assays and by gel retardation analysis.  The results show that the
AB  - methylase binds to its correct sequence with an affinity of the order 10/8 M-1
AB  - forming a 1:1 complex with the DNA.  The affinity for the incorrect sequence,
AB  - differing by an additional base pair in the non-specific spacer, is almost two
AB  - orders of magnitude lower.
ER  -

TY  - JOUR
AU  - Taylor, I.
AU  - Watts, D.
AU  - Kneale, G.
TI  - Substrate recognition and selectivity in the type IC DNA modification methylase M.EcoR124I.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4929
EP  - 4935
VL  - 21
AB  - The type I DNA modification methylase M.EcoR124I binds sequence specifically to DNA and
AB  - protects a 25bp fragment containing its cognate recognition sequence from digestion by
AB  - exonuclease III. Using modified synthetic oligonucleotide duplexes we have investigated the
AB  - catalytic properties of the methylase, and have established that a specific adenine on each
AB  - strand of DNA is the site of methylation. We show that the rate of methylation of each adenine
AB  - is increased at least 100 fold by prior methylation at the other site. However this is
AB  - accompanied by a significant decrease in the affinity of the methylase for these substrates
AB  - according to competitive gel retardation assays. In contrast, methylation of an adenine in the
AB  - recognitiom site which is not a target for the enzyme results in only a small decrease in both
AB  - DNA binding affinity and rate of methylation by the enzyme.
ER  -

TY  - JOUR
AU  - Taylor, I.A.
TI  - Biochemical characterisation of the EcoR124 type I DNA modification methylase.
JO  - Diss. Abstr.
PY  - 1993
SP  - 3942
EP  - 3942
VL  - 53
AB  - The hsdS and hsdM genes constituting the EcoR124I type I DNA modification methylase have been
AB  - expressed independently in Escherichia coli (E. coli) using the high level expression vectors
AB  - pUM120 and pJS491. Analysis of cell extracts demonstrated that the HsdM potein is found in the
AB  - E. coli soluble fraction whilst the HsdS protein is found only in the E. coli insoluble pellet
AB  - fraction. Protocols have been developed for the purification of both the HsdM and HsdS
AB  - proteins and a preliminary biochemical analysis undertaken involving an investigation of the
AB  - denaturation of both proteins by fluorescence spectroscopy. A more extensive analysis of the
AB  - HsdM protein has allowed estimations of its solution molecular mass and secondary structure to
AB  - be made. The hsdS and hsdM genes have also been co-expressed using the high level expression
AB  - vector pJS4M. The analysis of cell extracts in this case revealed that both polypeptides are
AB  - present in the E. coli soluble fraction. A protocol has been developed in which both
AB  - polypeptides co-purify as a complex which is capable of methylating the EcoR124I recognition
AB  - sequence. The enzyme complex has been shown to exist predominantly in solution as a trimer
AB  - consisting of two copies of the HsdM polypeptide and a single copy of the HsdS polypeptide.
AB  - Further experiments with the purified enzyme show that it can bind its recognition sequence
AB  - with a dissociation constant of around 5x10-9 and that it can also bind the recognition
AB  - sequence of the related type I DNA methylase EcoR124/3I with a lower affinity. A protein
AB  - nucleic acid complex consisting of methylase and a 30 base pair synthetic oligonucleotide
AB  - duplex has been investigated using 1H NMR spectroscopy and footprinting experiments. The
AB  - results suggest that contacts are made between bases within the recognition sequence and the
AB  - protein and also that the normal geometry of the nucleic acid may be distorted.
ER  -

TY  - JOUR
AU  - Taylor, I.A.
AU  - Davis, K.G.
AU  - Watts, D.
AU  - Kneale, G.G.
TI  - DNA binding induces a major structural transition in a type I methyltransferase.
JO  - EMBO J.
PY  - 1994
SP  - 5772
EP  - 5778
VL  - 13
AB  - The type IC DNA methyltransferase M.EcoR124I is a complex multisubunit enzyme that recognizes
AB  - the nonpalindromic DNA sequence GAAN6RTCG. Small angle X-ray scattering has been used to
AB  - investigate the solution structure of the methyltransferase and of complexes of the enzyme
AB  - with unmethylated and hemimethylated 30 bp DNA duplexes containing the specific recognition
AB  - sequence. A major change in the quaternary structure of the enzyme is observed following DNA
AB  - binding, based on a decrease in the radius of gyration from 56 to 40 A and a reduction in the
AB  - maximum dimension of the enzyme from 180 to 112 A. The structural transition observed is
AB  - independent of the methylation state of the DNA. CD shows that there is no change in the
AB  - secondary structure of the protein subunits when DNA is bound. In contrast, there is a large
AB  - increase in the CD signal arising from the DNA, suggesting considerable structural distortion
AB  - which may allow access to the bases targeted for methylation. We propose that DNA binding
AB  - induces a large rotation of the two HsdM subunits towards the DNA, mediated by hinge bending
AB  - domains in the specificity subunit HsdS.
ER  -

TY  - JOUR
AU  - Taylor, I.A.
AU  - Kneale, G.G.
TI  - A competition assay for DNA binding using the fluorescent probe ANS.
JO  - Methods Mol. Biol.
PY  - 2009
SP  - 577
EP  - 587
VL  - 543
AB  - Fluorescence spectroscopy is a technique frequently employed to stud), protein-nucleic acid
AB  - interactions. Often, the intrinsic fluorescence
AB  - emission spectrum of tryptophan residues in a nucleic-acid-binding
AB  - protein is strongly perturbed upon interaction with a target DNA or
AB  - RNA. These spectral changes can then be exploited in order to construct
AB  - binding isotherms and the extract equilibrium association constant
AB  - together with the stoichiometry of an interaction. However, when a
AB  - protein contains many tryptophan residues that are not located in the
AB  - proximity of the nucleic-acid-binding site, changes in the fluorescence
AB  - emission spectrum may not be apparent or the magnitude too small to be
AB  - useful. Here, we make use of an extrinsic fluorescence probe, the
AB  - environmentally sensitive fluorophore 1-anilinonaphthalene-8-sulphonic
AB  - acid (1,8-ANS). Displacement by DNA of 1,8-ANS Molecules from the
AB  - nucleic-acid-binding site of the Type I modification methylase EcoR124I
AB  - results in red shifting and an intensity decrease of the 1,8-ANS
AB  - fluorescence emission spectrum. These spectral changes have been used
AB  - to investigate the interaction of EcoR124I with DNA target recognition
AB  - sequences.
ER  -

TY  - JOUR
AU  - Taylor, I.A.
AU  - Webb, M.
AU  - Kneale, G.G.
TI  - Surface labelling of the type I methyltransferase M.EcoR124I reveals lysine residues critical for DNA binding.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 62
EP  - 73
VL  - 258
AB  - The type IC methyltransferase M.EcoR124I consists of a specificity subunit
AB  - (HsdS) and two methylation subunits (HsdM).  Using chemical modification, we have investigated
AB  - the accessibility of lysine residues in the free enzyme and in the complex with its DNA
AB  - recognition
AB  - sequence.  A total of 41 of the 109 lysine residues in the enzyme are susceptible to
AB  - modification, of
AB  - which 19 are located in the HsdS subunit and 11 in each of the two HsdM subunits.  DNA binding
AB  - results in extensive protection of lysine residues in the HsdS subunit, while those in the
AB  - HsdM
AB  - subunit are only protected weakly.  The DNA binding activity of the methylase is abolished
AB  - when a
AB  - small fraction of the accessible lysine residues are modified.  Peptide mapping and N-terminal
AB  - sequencing has been used to locate the rapidly modified lysine residues in HsdS that are
AB  - critical for
AB  - DNA binding.  Highly modified residues (K297, K261 and K327) are found in the C-terminal
AB  - variable domain that is responsible for DNA recognition, but others (K196, K203 and K210) are
AB  - found in the conserved regions that had not previously been implicated in DNA binding.
ER  -

TY  - JOUR
AU  - Taylor, J.
AU  - Moore, H.
AU  - Beaujean, N.
AU  - Gardner, J.
AU  - Wilmut, I.
AU  - Meehan, R.
AU  - Young, L.
TI  - Cloning and Expression of Sheep DNA Methyltransferase 1 and Its Development-Specific Isoform.
JO  - Mol. Reprod. Dev.
PY  - 2009
SP  - 501
EP  - 513
VL  - 76
AB  - Unlike the mouse embryo, where loss of DNA methylation in the embryonic nucleus leaves
AB  - cleavage stage embryos globally hypomethylated, sheep
AB  - preimplantation embryos retain high levels of methylation until the
AB  - blastocyst stage. We have cloned and sequenced sheep Dnmt1 and found it
AB  - to be highly conserved with both the human and mouse homologues.
AB  - Furthermore, we observed that the transcript normally expressed in
AB  - adult somatic tissues is highly abundant in sheep oocytes. Throughout
AB  - sheep preimplantation development the protein is retained in the
AB  - cytoplasm whereas Dnmt1 transcript production declines after the
AB  - embryonic genome activation at the 8-16 cell stage. Attempts to clone
AB  - oocyte-specific 5' regions of Dnmt1, known to be present in the mouse
AB  - and human gene, were unsuccessful. However, a novel ovine Dnmt1 exon,
AB  - theoretically encoding 13 amino acids, was found to be expressed in
AB  - sheep oocytes, preimplantation embryos and early fetal lineages, but
AB  - not in the adult tissue. RNAi-mediated knockdown of this novel
AB  - transcript resulted in embryonic developmental arrest at the late
AB  - morula stage, suggesting an essential role for this isoform in sheep
AB  - blastocyst formation.
ER  -

TY  - JOUR
AU  - Taylor, J.D.
AU  - Ackroyd, A.J.
AU  - Halford, S.E.
TI  - The gel shift assay for the analysis of DNA-protein interactions.
JO  - The Nucleic Acid Protocols Handbook
PY  - 2000
SP  - 745
EP  - 756
VL  - 0
AB  - The gel shift assay is one of the most powerful methods for the analysis of DNA-protein
AB  - interactions.  The assay itself is simple.  DNA and protein are mixed together, the solution
AB  - subjected to electrophoresis through polyacrylamide, and the gel is then analyzed for DNA,
AB  - usually by autoradiography of radiolabeled DNA.  Binding of the protein to the DNA can result
AB  - in a complex that has a different electrophoretic mobility from the free DNA.  In general, the
AB  - mobility of the complex is retarded relative to the unbound DNA and thus the assay is often
AB  - called gel retardation.  However, with circular DNA substrates (typically, minicircles of
AB  - 200-400 bp), the DNA-protein complex can migrate faster than the free DNA.  The separation of
AB  - the complex from the free DNA, and therefore the detection of the complex, is dependent on a
AB  - variety of factors.  These must be determined experimentally for each system.  However, the
AB  - ease with which the assay can be performed means that the optimal conditions can be discovered
AB  - quickly.  Factors that influence the electrophoretic mobility of DNA-protein complexes include
AB  - the molecular weight of the protein and the DNA, the ionic strength and the pH of the
AB  - electrophoresis buffer, the concentration of the gel matrix, and the temperature. Particularly
AB  - useful accounts of how modifications to the assay can affect the mobility of DNA-protein
AB  - complexes have been published.
ER  -

TY  - JOUR
AU  - Taylor, J.D.
AU  - Ackroyd, A.J.
AU  - Halford, S.E.
TI  - The gel shift assay for the analysis of DNA-protein interactions.
JO  - Methods Mol. Biol.
PY  - 1994
SP  - 263
EP  - 279
VL  - 30
AB  - The gel shift assay is one of the most powerful methods for the analysis of DNA-protein
AB  - interactions.  The assay itself is simple.  DNA and protein are mixed together, the solution
AB  - subjected to electrophoresis through polyacrylamide, and the gel is then analyzed for DNA,
AB  - usually by autoradiography of radiolabeled DNA.  Binding of the protein to the DNA can result
AB  - in a complex that has a different electrophoretic mobility from the free DNA.  In general, the
AB  - mobility of the complex is retarded relative to the unbound DNA and thus the assay is often
AB  - called gel retardation.  However, with circular DNA substrates (typically, minicircles of
AB  - 200-400 bp), the DNA-protein complex can migrate faster than the free DNA.  The separation of
AB  - the complex from the free DNA, and therefore the detection of the complex, is dependent on a
AB  - variety of factors.  These must be determined experimentally for each system.  However, the
AB  - ease with which the assay can be performed means that the optimal conditions can be discovered
AB  - quickly.  Factors that influence the electrophoretic mobility of DNA-protein complexes include
AB  - the molecular weight of the protein and the DNA, the ionic strength and the pH of the
AB  - electrophoresis buffer, the concentration of the gel matrix, and the temperature.
AB  - Particularly useful accounts of how modifications to the assay can affect the mobility of
AB  - DNA-protein complexes have been published.
ER  -

TY  - JOUR
AU  - Taylor, J.D.
AU  - Badcoe, I.G.
AU  - Clarke, A.R.
AU  - Halford, S.E.
TI  - EcoRV restriction endonuclease binds all DNA sequences with equal affinity.
JO  - Biochemistry
PY  - 1991
SP  - 8743
EP  - 8753
VL  - 30
AB  - In the presence of MgCl2, the EcoRV restriction endonuclease cleaves its
AB  - recognition sequence on DNA at least a million times more readily than any
AB  - other sequence.  In this study, the binding of the EcoRV restriction enzyme to
AB  - DNA was examined in the absence of Mg2+.  With each DNA fragment tested,
AB  - several DNA-protein complexes were detected by electrophoresis through
AB  - polyacrylamide.  No differences were observed between isogenic DNA molecules
AB  - that either contained or lacked the EcoRV recognition site.  The number of
AB  - complexes with each fragment varied with the length of the DNA.  Three
AB  - complexes were formed with a DNA molecule of 55 base pairs, corresponding to
AB  - the DNA bound to 1,2,3 molecules of the protein, while >15 complexes were
AB  - formed with a DNA of 381 base pairs.  A new method was developed to analyze the
AB  - binding of a protein to multiple sites on DNA.  The method showed that the
AB  - EcoRV enzyme binds to all DNA sequences, including the EcoRV recognition site,
AB  - with the same equilibrium constant, though two molecules of the protein bind
AB  - preferentially to adjacent sites on the DNA in a cooperative fashion.  All of
AB  - the complexes with a substrate that contained the EcoRV site dissociated upon
AB  - addition of competitor DNA, but when the competitor was mixed with MgCl2, a
AB  - fraction of the substrate was cleaved at the EcoRV site.  The fraction cleaved
AB  - was due mainly to the translocation of the enzyme from nonspecific sites on the
AB  - DNA to the specific site.
ER  -

TY  - JOUR
AU  - Taylor, J.D.
AU  - Goodall, A.J.
AU  - Vermote, C.L.
AU  - Halford, S.E.
TI  - Fidelity of DNA recognition by the EcoRV restriction/modification system in vivo.
JO  - Biochemistry
PY  - 1990
SP  - 10727
EP  - 10733
VL  - 29
AB  - The EcoRV restriction/modification system consists of two enzymes that recognize the DNA
AB  - sequence GATATC. The EcoRV restriction endonuclease cleaves DNA at this site, but the DNA of
AB  - Escherichia coli carrying the EcoRV system is protected from this reaction by the EcoRV
AB  - methyltransferase. However, in vitro, the EcoRV nuclease also cleaves DNA at most sites that
AB  - differ from the recognition sequence by one base pair. Though the reaction of the nuclease at
AB  - these sites is much slower than that at the cognate site, it still appears to be fast enough
AB  - to cleave the chromosome of the cell into many fragments. The possibility that the EcoRV
AB  - methyltransferase also protects the noncognate sites on the chromosome was examined. The
AB  - modification enzyme methylated alternate sites in vivo, but these were not the same as the
AB  - alternate sites for the nuclease. The excess methylation was found at GATC sequences, which
AB  - are also the targets for the dam methyltransferase of E. coli, a protein that is homologous to
AB  - the EcoRV methyltransferase. Methylation at these sites gave virtually no protection against
AB  - the EcoRV nuclease: even when the EcoRV methyltransferase had been overproduced, the cellular
AB  - DNA remained sensitive to the EcoRV nuclease at its noncognate sites. The viability of E. coli
AB  - carrying the EcoRV restriction/modification R/M system was found instead to depend on the
AB  - activity of DNA ligase. Ligase appears to proofread the EcoRV R/M system in vivo: DNA, cut
AB  - initially in one strand at a noncognate site for the nuclease, is presumably repaired by
AB  - ligase before the scission of the second strand.
ER  -

TY  - JOUR
AU  - Taylor, J.D.
AU  - Halford, S.E.
TI  - Discrimination between DNA sequences by the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1989
SP  - 6198
EP  - 6207
VL  - 28
AB  - The EcoRV restriction endonuclease cleaves not only its recognition sequence on
AB  - DNA, GATATC, but also, at vastly reduced rates, a number of alternative DNA
AB  - sequences.  The plasmid pAT153 contains 12 alternative sites, each of which
AB  - differs from the recognition sequence by one base pair.  The EcoRV nuclease
AB  - showed a marked preference for one particular site from among these
AB  - alternatives.  This noncognate site was located at the sequence GTTATC, and the
AB  - mechanism of action of EcoRV at this site was analyzed.  The mechanism differed
AB  - from that at the cognate site in three respects.  First, the affinity of the
AB  - enzyme for the noncognate site was lower than that for the cognate site, but,
AB  - by itself, this cannot account for the specificity of EcoRV as measured from
AB  - the values of Kcat/Km.  Second, the enzyme had a lower affinity for Mg2+ when
AB  - it was bound to the noncognate site than when it was bound to its cognate site:
AB  - this appears to be a key factor in limiting the rates of DNA cleavage at
AB  - alternative sites.  Third, the reaction pathway at the noncognate site differed
AB  - from that at the cognate site.  At the former, the EcoRV enzyme cleaved first
AB  - one strand of the DNA and then the other while at the latter, both strands were
AB  - cut in one concerted reaction.  The difference in reaction pathway allows DNA
AB  - ligase to proofread the activity of EcoRV by selective repair of single-strand
AB  - breaks at noncognate sites, as opposed to double-strand breaks at the cognate
AB  - site.  The addition of DNA ligase to reactions with EcoRV made no difference to
AB  - product formation at the cognate site, but products from reactions at
AB  - noncognate sites were no longer detected.
ER  -

TY  - JOUR
AU  - Taylor, J.D.
AU  - Halford, S.E.
TI  - The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex.
JO  - Biochemistry
PY  - 1992
SP  - 90
EP  - 97
VL  - 31
AB  - The EcoRV restriction endonuclease cleaves DNA not only at its recognition
AB  - sequence but also at most other sequences that differ from the recognition site
AB  - by one base pair.  Compared to the reaction at the recognition site, the
AB  - reactions at noncognate sites are slow but 1 out of the 12 noncognate sites on
AB  - the plasmid pAT153 is cleaved more than 50 times faster than any other.  The
AB  - increase in the reaction rate at the preferred noncognate site, relative to
AB  - other sites, was caused by the DNA sequences in the 4 base pairs from either
AB  - side of the site.  For enhanced activity by EcoRV, particular bases were needed
AB  - immediately adjacent to the site, inside the DNA-protein complex.  At these
AB  - loci, the protein interacts with the phosphate groups in the DNA and the
AB  - flanking sequence may control the activity of the enzyme by determining the
AB  - conformation of the DNA, thus aligning the phosphate contacts.  But the
AB  - preferential cleavage also depended on sequences further away from the site, at
AB  - loci outside the complex.  At external positions, beyond the reach of the
AB  - protein, the EcoRV enzyme required flanking sequences that give rise to
AB  - flexibility in DNA conformation.  These may facilitate the distortion of the
AB  - DNA required for catalysis by EcoRV.
ER  -

TY  - JOUR
AU  - Taylor, J.E.
AU  - Callow, P.
AU  - Swiderska, A.
AU  - Kneale, G.G.
TI  - Structural and functional analysis of the engineered type I DNA methyltransferase EcoR124I(NT).
JO  - J. Mol. Biol.
PY  - 2010
SP  - 391
EP  - 399
VL  - 398
AB  - The Type I R-M system EcoR124I is encoded by three genes. HsdM is responsible for modification
AB  - (DNA methylation), HsdS for DNA sequence
AB  - specificity and HsdR for restriction endonuclease activity. The trimeric
AB  - methyltransferase (M(2)S) recognises the asymmetric sequence
AB  - (GAAN(6)RTCG). An engineered R-M system, denoted EcoR124I(NT), has two
AB  - copies of the N-terminal domain of the HsdS subunit of EcoR124I, instead
AB  - of a single S subunit with two domains, and recognises the symmetrical
AB  - sequence GAAN(7)TTC. We investigate the methyltransferase activity of
AB  - EcoR124I(NT), characterise the enzyme and its subunits by analytical
AB  - ultracentrifugation and obtain low-resolution structural models from
AB  - small-angle neutron scattering experiments using contrast variation and
AB  - selective deuteration of subunits.
ER  -

TY  - JOUR
AU  - Taylor, J.E.
AU  - Swiderska, A.
AU  - Artero, J.-B.
AU  - Callow, P.
AU  - Kneale, G.
TI  - Structural and Functional Analysis of the Symmetrical Type I Restriction Endonuclease R.EcoR124I(NT).
JO  - PLoS ONE
PY  - 2012
SP  - e35263
EP  - e35263
VL  - 7
AB  - Type I restriction-modification (RM) systems are comprised of two multi-subunit enzymes, the
AB  - methyltransferase (similar to 160 kDa),
AB  - responsible for methylation of DNA, and the restriction endonuclease
AB  - (similar to 400 kDa), responsible for DNA cleavage. Both enzymes share
AB  - a number of subunits. An engineered RM system, EcoR124I(NT), based on
AB  - the N-terminal domain of the specificity subunit of EcoR124I was
AB  - constructed that recognises the symmetrical sequence GAAN(7)TTC and is
AB  - active as a methyltransferase. Here, we investigate the restriction
AB  - endonuclease activity of R.EcoR124I(NT) in vitro and the subunit
AB  - assembly of the multi-subunit enzyme. Finally, using small-angle
AB  - neutron scattering and selective deuteration, we present a
AB  - low-resolution structural model of the endonuclease and locate the
AB  - motor subunits within the multi-subunit enzyme. We show that the
AB  - covalent linkage between the two target recognition domains of the
AB  - specificity subunit is not required for subunit assembly or enzyme
AB  - activity, and discuss the implications for the evolution of Type I
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Taylor, J.E.
AU  - Swiderska, A.
AU  - Kneale, G.G.
TI  - A rapid purification procedure for the HsdM protein of EcoR124I and biophysical characterization of the purified protein.
JO  - Protein Expr. Purif.
PY  - 2013
SP  - 136
EP  - 140
VL  - 87
AB  - Type I restriction-modification (R-M) systems are comprised of two multi-subunit enzymes with
AB  - complementary functions: the
AB  - methyltransferase (similar to 160 kDa), responsible for methylation of
AB  - DNA, and the restriction endonuclease (similar to 400 kDa), responsible
AB  - for DNA cleavage. Both enzymes share a number of subunits, including
AB  - HsdM. Characterisation of either enzyme first requires the expression
AB  - and purification of its constituent subunits, before reconstitution of
AB  - the multisubunit complex. Previously, purification of the HsdM protein
AB  - had proved problematic, due to the length of time required for the
AB  - purification and its susceptibility to degradation. A new protocol was
AB  - therefore developed to decrease the length of time required to purify
AB  - the HsdM protein and thus prevent degradation. Finally, we show that
AB  - the HsdM subunit exhibits a concentration dependent monomer-dimer
AB  - equilibrium.
ER  -

TY  - JOUR
AU  - Taylor, J.R.
AU  - Fang, M.M.
AU  - Nie, S.
TI  - Probing specific sequences on single DNA molecules with bioconjugated fluorescent nanoparticles.
JO  - Anal. Chem.
PY  - 2000
SP  - 1979
EP  - 1986
VL  - 72
AB  - Nanometer-sized fluorescent particles (latex nanobeads) have been covalently linked to DNA
AB  - binding proteins to probe specific sequences on stretched single DNA molecules.  In comparison
AB  - with single organic fluorophores, these nanoparticle probes are brighter, are more stable
AB  - against photobleaching, and do not suffer from intermittent on/off light emission (blinking).
AB  - Specifically, we demonstrate that the site-specific restriction enzyme EcoRI can be conjugated
AB  - to 20 nm fluorescent nanoparticles and that the resulting nanoconjugates display DNA binding
AB  - and cleavage activities of the native enzyme.  In the absence of cofactor magnesium ions, the
AB  - EcoRI conjugates bind to specific sequences on double-stranded DNA but do not initiate
AB  - enzymatic cutting.  For single DNA molecules that are stretched and immobilized on a solid
AB  - surface, nanoparticles bound at specific sites can be directly visualized by multicolor
AB  - fluorescence microscopy.  Direct observation os site-specific probes on single DNA molecules
AB  - opens new possibilities in optical gene mapping and in fundamental study of DNA-protein
AB  - interactions.
ER  -

TY  - JOUR
AU  - Taylor, J.W.
AU  - Schmidt, W.
AU  - Cosstick, R.
AU  - Okruszek, A.
AU  - Eckstein, F.
TI  - The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 8749
EP  - 8763
VL  - 13
AB  - The RF IV form of M13 DNA was synthesized enzymatically in vitro, using the
AB  - viral (+)strand as template, to contain phosphorothioate-modified
AB  - internucleotidic linkages of the Rp configuration on the 5' side of every base
AB  - of a particular type in the newly-synthesized (-)strand.  Twenty nine
AB  - restriction enzymes were then tested for their reactions with the appropriate
AB  - modified DNA types having a phosphorothioate linkage placed exactly at the
AB  - cleavage site(s) of these enzymes in the (-)strand.  Eleven of the seventeen
AB  - restriction enzymes tested that had recognition sequences of five bases or more
AB  - could be used to convert the phosphorothioate DNA entirely into the nicked
AB  - form, either by simply allowing the reaction to go to completion with excess
AB  - enzyme (AvaI, AvaII, BanII, HindII, NciI, PstI or PvuI) or by stopping the
AB  - reaction at the appropriate time before the nicked DNA is linearized (BamHI,
AB  - BglI, EcoRI or HindIII).  Only modification of the exact cleavage site in the
AB  - (-)strand could block linearization by the first class of enzymes.  The results
AB  - presented imply that the restriction enzyme-directed nicking of
AB  - phosphorothioate M13 DNA occurs exclusively in the (+)strand.
ER  -

TY  - JOUR
AU  - Taylor, V.L.
AU  - Titball, R.W.
AU  - Oyston, P.C.F.
TI  - Oral immunization with a dam mutant of Yersinia pseudotuberculosis protects against plague.
JO  - Microbiology
PY  - 2005
SP  - 1919
EP  - 1926
VL  - 151
AB  - Inactivation of the gene encoding DNA adenine methylase (dam) has been shown to attenuate some
AB  - pathogens such as Salmonella enterica serovar
AB  - Typhimurium and is a lethal mutation in others such as Yersinia
AB  - pseudotuberculosis strain YPIII. In this study the dam methylase gene
AB  - in Yersinia pseudotuberculosis strain IP32953 was inactivated. Unlike
AB  - the wild-type, DNA isolated from the mutant could be digested with
AB  - Mbol, which is consistent with an altered pattern of DNA methylation.
AB  - The mutant was sensitive to bile salts but not to 2-aminopurine. The
AB  - effect of dam inactivation on gene expression was examined using a DNA
AB  - microarray. In BALB/c mice inoculated orally or intravenously with the
AB  - dam mutant, the median lethal dose (MLD) was at least 10(6)-fold higher
AB  - than the MLD of the wild-type. BALB/c mice inoculated with the mutant
AB  - were protected against a subcutaneous challenge with 100 MLDs of
AB  - Yersinia pestis strain GB and an intravenous challenge with 300 MLDs of
AB  - Y. pseudotuberculosis IP32953.
ER  -

TY  - JOUR
AU  - Tchagang, C.F.
AU  - Xu, R.
AU  - Mehrtash, S.
AU  - Rahimi, S.
AU  - Sidibe, A.
AU  - Li, X.
AU  - Bromfield, E.S.
AU  - Tambong, J.T.
TI  - Draft Genome Sequences of Two Novel Pseudomonas Strains Exhibiting Differential Hypersensitivity Reactions on Tobacco and Corn Seedlings.
JO  - Genome Announcements
PY  - 2016
SP  - e01057
EP  - e01016
VL  - 4
AB  - Two novel Pseudomonas strains (S1E40 and S3E12) isolated from corn roots are antagonistic to
AB  - Rhizoctonia solani and exhibit differential hypersensitivity
AB  - reactions on tobacco and corn seedlings. We report here the draft genome
AB  - sequences of strains S1E40 and S3E12, consisting of 6.98 and 7.06 Mb with 6,150
AB  - and 6,129 predicted protein-coding sequences, respectively.
ER  -

TY  - JOUR
AU  - te Poele, E.M.
AU  - Samborskyy, M.
AU  - Oliynyk, M.
AU  - Leadlay, P.F.
AU  - Bolhuis, H.
AU  - Dijkhuizen, L.
TI  - Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded.
JO  - Plasmid
PY  - 2008
SP  - 202
EP  - 216
VL  - 59
AB  - Actinomycete integrative and conjugative elements (AICEs) are present in
AB  - diverse genera of the actinomycetes, the most important bacterial
AB  - producers of bioactive secondary metabolites. Comparison of pMEA100 of
AB  - Amycolatopsis mediterranei, pMEA300 of Amycolatopsis methanolica and
AB  - pSE211 of Saccharopolyspora erythraea, and other AICEs, revealed a highly
AB  - conserved structural organisation, consisting of four functional modules
AB  - (replication, excision/integration, regulation, and conjugative transfer).
AB  - Features conserved in all elements, or specific for a single element, are
AB  - discussed and analysed. This study also revealed two novel putative AICEs
AB  - (named pSE222 and pSE102) in the Sac. erythraea genome, related to the
AB  - previously described pSE211 and pSE101 elements. Interestingly, pSE102
AB  - encodes a putative aminoglycoside phosphotransferase which may confer
AB  - antibiotic resistance to the host. Furthermore, two of the six pSAM2-like
AB  - insertions in the Streptomyces coelicolor genome described by Bentley et
AB  - al. [Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., et al., 2002.
AB  - Complete genome sequence of the model actinomycete Streptomyces coelicolor
AB  - A3(2). Nature 417, 141-147] could be functional AICEs. Homologues of
AB  - various AICE proteins were found in other actinomycetes, in Frankia
AB  - species and in the obligate marine genus Salinispora and may be part of
AB  - novel AICEs as well. The data presented provide a better understanding of
AB  - the origin and evolution of these elements, and their functional
AB  - properties. Several AICEs are able to mobilise chromosomal markers,
AB  - suggesting that they play an important role in horizontal gene transfer
AB  - and spread of antibiotic resistance, but also in evolution of genome
AB  - plasticity.
ER  -

TY  - JOUR
AU  - Te, S.H.
AU  - Tan, B.F.
AU  - Boo, C.Y.
AU  - Thompson, J.R.
AU  - Gin, K.Y.
TI  - Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 35
EP  - 35
VL  - 12
AB  - Planktothricoides is a free-living filamentous cyanobacterium belonging to the order
AB  - Oscillatoriales and the family Phormidiaceae, capable of forming bloom in
AB  - fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by
AB  - Planktothricoides sp. SR001 was obtained from a freshwater reservoir in
AB  - Singapore. The draft genome presented here is the first tropical freshwater
AB  - Planktothricoides sp. ever sequenced. The genome of 7.0Mbp contains 5,776 genes
AB  - predicted using the JGI IMG pipeline. The whole genome sequence allows
AB  - identification of genes encoding for nitrogen-fixation, accessory photosynthetic
AB  - pigments and biosynthesis of an off-flavor compound, 2-methylisoborneol, which
AB  - has been experimentally verified here based on metabolite detection. In addition,
AB  - strain SR001 genome contains an operon putatively involved in the production of a
AB  - linear tripeptide cyanobactin related to viridisamide A and aeruginosamide, with
AB  - the later known to possess anti-microbial or cytotoxic effect.
ER  -

TY  - JOUR
AU  - Te, S.H.
AU  - Tan, B.F.
AU  - Thompson, J.R.
AU  - Gin, K.Y.
TI  - Draft Genome Sequences of Two Benthic Cyanobacteria, Oscillatoriales USR 001 and  Nostoc sp. MBR 210, Isolated from Tropical Freshwater Lakes.
JO  - Genome Announcements
PY  - 2016
SP  - e01115
EP  - e01116
VL  - 4
AB  - Genomes of two filamentous benthic cyanobacteria were obtained from cocultures obtained from
AB  - two freshwater lakes. The cultures were obtained by first growing
AB  - cyanobacterial trichome on solid medium, followed by subculturing in freshwater
AB  - media. Subsequent shotgun sequencing, de novo assembly, and genomic binning
AB  - yielded almost complete genomes of Oscillatoriales USR 001 and Nostoc sp. MBR
AB  - 210.
ER  -

TY  - JOUR
AU  - Teachman, A.M.
AU  - Gumulak-Smith, J.J.
AU  - Tu, A.T.
AU  - Simecka, J.W.
AU  - Lindsey, J.R.
AU  - Dybvig, K.
TI  - Variations in the surface proteins and in the restriction and modification systems of Mycoplasma pulmonis in the respiratory tract of  infected rats.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2001
SP  - 386
EP  - 386
VL  - 101
AB  - Restriction and modification (R-M) systems are thought to afford bacteria protection from
AB  - invading foreign DNA. We hypothesize that the
AB  - phase-variable R-M systems found within the hsd loci, as well as the
AB  - variable surface antigens, of Mycoplasma pulmonis may additionally have
AB  - a critical role in survival within the rat respiratory tract.
AB  - Populations of M. pulmonis strain X1048 were isolated from
AB  - experimentally infected Fischer F344 rats and assayed by a combination
AB  - of Western blot, PCR and phage plaquing experiments to determine the
AB  - predominant variable surface antigen (Vsa) and Hsd proteins. Isolates
AB  - from the nose were found to produce VsaA and possessed no R-M activity,
AB  - while 38% of isolates from the throat at 14 days postinfection produced
AB  - a protein other than VsaA with 31% having active R-M systems. To assess
AB  - the stability of various isolates from the rat throat, selected
AB  - isolates were passaged 30 times in vitro and were found to revert to a
AB  - phenotype of VsaA with inactive R-M systems. Therefore, the data
AB  - suggest that different selection pressures within tissues influence the
AB  - cell population in regards to surface antigen variation and R-M
AB  - production, and subsequently may affect survival of the mycoplasma
AB  - within an animal.
ER  -

TY  - JOUR
AU  - Teatero, S.
AU  - McGeer, A.
AU  - Tyrrell, G.J.
AU  - Hoang, L.
AU  - Smadi, H.
AU  - Domingo, M.C.
AU  - Levett, P.N.
AU  - Finkelstein, M.
AU  - Dewar, K.
AU  - Plevneshi, A.
AU  - Athey, T.B.
AU  - Gubbay, J.B.
AU  - Mulvey, M.R.
AU  - Martin, I.
AU  - Demczuk, W.
AU  - Fittipaldi, N.
TI  - Canada-Wide Epidemic of emm74 Group A Streptococcus Invasive Disease.
JO  - Open Forum Infect. Dis.
PY  - 2018
SP  - ofy085
EP  - ofy085
VL  - 5
AB  - Background: The number of invasive group A Streptococcus (iGAS) infections due to
AB  - hitherto extremely rare type emm74 strains has increased in several Canadian
AB  - provinces since late 2015. We hypothesized that the cases recorded in the
AB  - different provinces are linked and caused by strains of an emm74 clone that
AB  - recently emerged and expanded explosively. Methods: We analyzed both active and
AB  - passive surveillance data for iGAS infections and used whole-genome sequencing to
AB  - investigate the phylogenetic relationships of the emm74 strains responsible for
AB  - these invasive infections country-wide. Results: Genome analysis showed that
AB  - highly clonal emm74 strains, genetically different from emm74 organisms
AB  - previously circulating in Canada, were responsible for a country-wide epidemic of
AB  - >160 invasive disease cases. The emerging clone belonged to multilocus sequence
AB  - typing ST120. The analysis also revealed dissemination patterns of emm74
AB  - subclonal lineages across Canadian provinces. Clinical data analysis indicated
AB  - that the emm74 epidemic disproportionally affected middle-aged or older male
AB  - individuals. Homelessness, alcohol abuse, and intravenous drug usage were
AB  - significantly associated with invasive emm74 infections. Conclusions: In a period
AB  - of 20 months, an emm74 GAS clone emerged and rapidly spread across several
AB  - Canadian provinces located more than 4500 km apart, causing invasive infections
AB  - primarily among disadvantaged persons.
ER  -

TY  - JOUR
AU  - Tediashivili, M.I.
AU  - Goryan, T.V.
AU  - Koberidse, T.D.
AU  - Chanishvili, T.G.
AU  - Nikolskaya, I.I.
TI  - New systems of host specificity of DNA Pae610 and Pae603.
JO  - Biull. Eksp. Biol. Med.
PY  - 1991
SP  - 91
EP  - 94
VL  - 112
AB  - In order to find new systems of host specificity, wide screening among different strains of P.
AB  - aeruginosa was carried out.  By means of cross-titration of phages BT and FP-series two new
AB  - systems of modification-restriction were identified: Pae610 and Pae603.  They differ from the
AB  - known system of host specificity PaeR7.
ER  -

TY  - JOUR
AU  - Tediashvili, M.I.
AU  - Goryan, T.V.
AU  - Koberidze, T.D.
AU  - Chanishvili, T.G.
AU  - Nikolskaya, I.I.
TI  - New host DNA specificity systems Pae 610 and Pae 603.
JO  - Bull. Exp. Biol. Med.
PY  - 1991
SP  - 91
EP  - 94
VL  - 112
AB  - To find new systems of host specificity (SHS), wide screening among different
AB  - strains of Pseudomonas aeruginosa was carried out.  By means of cross-titration
AB  - of phages BT and FP-series two new systems of restriction-modification were
AB  - identified:  Pae610 and Pae603.  They differ from the known system of host
AB  - specificity PaeR7.
ER  -

TY  - JOUR
AU  - Tediashvili, M.I.
AU  - Uporova, T.M.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Identification of host specific system in Shigella.
JO  - Biull. Eksp. Biol. Med.
PY  - 1980
SP  - 324
EP  - 325
VL  - 90
AB  - The presence of a DNA host specific system in Shigella sonnei 47843 bacteria has been
AB  - demonstrated.  Phage DDIII grown on the cells of Shigella stutzeri 2, in Shigella sonnei 47843
AB  - cells is restricted by a factor of 10^5.  Phage T3 of EcoB phenotype as well as DDIII phage is
AB  - restricted in these cells.  This circumstance means that the restriction-modification system
AB  - of Shigella sonnei 47843 differs in specificity from the well known system E. coli.  The
AB  - results obtained are the second case of host specific system identification in Shigella.  The
AB  - biological properties of the strain (form of the colonies, colicinogenic activity, antibiotic
AB  - resistance, ability to ferment sugars, etc.) have been studied.
ER  -

TY  - JOUR
AU  - Tedim, A.P.
AU  - Lanza, V.F.
AU  - Manrique, M.
AU  - Pareja, E.
AU  - Ruiz-Garbajosa, P.
AU  - Canton, R.
AU  - Baquero, F.
AU  - Coque, T.M.
AU  - Tobes, R.
TI  - Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117,  a Globally Disseminated Multidrug-Resistant Clone.
JO  - Genome Announcements
PY  - 2017
SP  - e01553
EP  - e01516
VL  - 5
AB  - The emergence of nosocomial infections by multidrug-resistant sequence type 117 (ST117)
AB  - Enterococcus faecium has been reported in several European countries.
AB  - ST117 has been detected in Spanish hospitals as one of the main causes of
AB  - bloodstream infections. We analyzed genome variations of ST117 strains isolated
AB  - in Madrid and describe the first ST117 closed genome sequences.
ER  -

TY  - JOUR
AU  - Teel, L.D.
AU  - Melton-Celsa, A.R.
AU  - Schmitt, C.K.
AU  - O'Brien, A.D.
TI  - One of Two Copies of the Gene for the Activatable Shiga Toxin Type 2d in Escherichia coli O91:H21 Strain B2F1 Is Associated with an Inducible Bacteriophage.
JO  - Infect. Immun.
PY  - 2002
SP  - 4282
EP  - 4291
VL  - 70
AB  - Shiga toxin (Stx) types 1 and 2 are encoded within intact or defective temperate
AB  - bacteriophages in Stx-producing Escherichia coli (STEC), and expression of these toxins is
AB  - linked to bacteriophage induction. Among Stx2 variants, only stx(2e) from one human STEC
AB  - isolate has been reported to be carried within a toxin-converting phage. In this study, we
AB  - examined the O91:H21 STEC isolate B2F1, which carries two functional alleles for the potent
AB  - activatable Stx2 variant toxin, Stx2d, for the presence of Stx2d-converting bacteriophages. We
AB  - first constructed mutants of B2F1 that produced one or the other Stx2d toxin and found that
AB  - the mutant that produced only Stx2d1 made less toxin than the Stx2d2-producing mutant.
AB  - Consistent with that result, the Stx2d1-producing mutant was attenuated in a
AB  - streptomycin-treated mouse model of STEC infection. When the mutants were treated with
AB  - mitomycin C to promote bacteriophage induction, Vero cell cytotoxicity was elevated only in
AB  - extracts of the Stx2d1-producing mutant. Additionally, when mice were treated with
AB  - ciprofloxacin, an antibiotic that induces the O157:H7 Stx2-converting phage, the animals were
AB  - more susceptible to the Stx2d1-producing mutant. Moreover, an stx(2d1)-containing lysogen was
AB  - isolated from plaques on strain DH5alpha that had been exposed to lysates of the mutant that
AB  - produced Stx2d1 only, and supernatants from that lysogen transformed with a plasmid encoding
AB  - RecA were cytotoxic when the lysogen was induced with mitomycin C. Finally,
AB  - electron-microscopic examination of extracts from the Stx2d1-producing mutant showed hexagonal
AB  - particles that resemble the prototypic Stx2-converting phage 933W. Together these observations
AB  - provide strong evidence that expression of Stx2d1 is bacteriophage associated. We conclude
AB  - that despite the sequence similarity of the stx(2d1)- and stx(2d2)-flanking regions in B2F1,
AB  - Stx2d1 expression is repressed within the context of its toxin-converting phage while Stx2d2
AB  - expression is independent of phage induction.
ER  -

TY  - JOUR
AU  - Teerawanichpan, P.
AU  - Chandrasekharan, M.B.
AU  - Jiang, Y.M.
AU  - Narangajavana, J.
AU  - Hall, T.C.
TI  - Characterization of two rice DNA methyltransferase genes and RNAi-mediated reactivation of a silenced transgene in rice callus.
JO  - Planta
PY  - 2004
SP  - 337
EP  - 349
VL  - 218
AB  - Two genomic clones (OsMET1-1, AF462029 and OsMET1-2, TPA BK001405), each encoding a
AB  - cytosine-5 DNA methyltransferase (MTase), were isolated
AB  - from rice (Oryza sativa L.) BAC libraries. OsMET1-1 has an open reading
AB  - frame of 4,566 nucleotides with 12 exons and 11 introns while OsMET1-2
AB  - has an open reading frame of 4,491 nucleotides with 11 exons and 10
AB  - introns. Although OsMET1-1 and OsMET1-2 have high sequence similarity
AB  - overall, they share only 24% identity in exon 1, and intron 3 of
AB  - OsMET1-1 is absent from OsMET1-2. As for other eukaryotic DNA MTases of
AB  - the Dnmt1/MET l class, the derived amino acid sequences of OsMET1-1 and
AB  - OsMET1-2 suggest that they are comprised of two-thirds regulatory
AB  - domain and one-third catalytic domain. Most functional domains
AB  - identified for other MTases were present in the rice MET1 sequences.
AB  - Amino acid sequence comparison indicated high similarity (56-75%
AB  - identity) of rice MET1 proteins to other plant MET1 sequences but
AB  - limited similarity (approx. 24% identity) to animal Dnmt1 proteins.
AB  - Genomic blot and database analysis indicated the presence of a single
AB  - copy of OsMET1-1 (on chromosome 3) and single copy of OsMET1-2 (on
AB  - chromosome 7). Ribonuclease protection assays revealed expression of
AB  - both OsMET1-1 and OsMET1-2 in highly dividing cells, but the
AB  - steady-state level of OsMET1-2 was 7- to 12-fold higher than that for
AB  - OsMET1-1 in callus, root and inflorescence. The functional involvement
AB  - of the rice DNA MTases in gene silencing was investigated using an RNAi
AB  - strategy. Inverted repeat constructs of either the N- or C-terminal
AB  - regions of OsMET1-1 were supertransformed into calli derived from a
AB  - rice line bearing a silenced 35S-uidA-nos transgene. Restoration of
AB  - uidA expression in the bombarded calli was consistent with the
AB  - inactivation of maintenance methylation and with previous evidence for
AB  - the involvement of methylation in silencing of this line.
ER  -

TY  - JOUR
AU  - Teerawanichpan, P.
AU  - Jiang, Y.
AU  - Dong, J.
AU  - Hall, T.C.
AU  - Narangajavana, J.
TI  - DNA methyltransferase and developmental processes in rice.
JO  - Plant Biol.
PY  - 2001
SP  - 155
EP  - 156
VL  - 0
AB  - Expression of antisense constructs of Arabidopsis methyltransferase (METI) results in
AB  - decreased methylation and multiple morphological abnormalities. To explore the involvement of
AB  - DNA methylation in monocot plant development and gene silencing, the endogenous Dnmt1 of rice
AB  - (GenBank AF155874) was debilitated by either antisense RNA or dsRNA. N- and C- terminal
AB  - regions (N-Dnmt1 and C-Dnmt1) of rice Dnmt1 in pRM1 were separately cloned into a binary
AB  - vector (pPT2) in order to investigate the importance of each domain in developmental
AB  - processes. Each gene construct had a maize ubiquitin promoter, a nos terminator and included
AB  - either gfp or uidA as a reporter. Agrobacterium-mediated transformation was used to introduce
AB  - either antisense (as-N-Dnmt1 and as-C-Dnmt1) or inverted repeat (ir-N-Dnmt1 or ir-C-Dnmt1)
AB  - constructs of Dnmt1 into rice in order to silence expression of endogenous Dnmt1. Compared
AB  - with wt plants, transgenic plants PT41-1, PT41-2 and PT41-3 (carrying as-N-Dnmt1) showed
AB  - decreased fertility (80-100%), smaller leaves and reduced height (33%). Plants PT41-1 and -2
AB  - had 7-10 tillers while PT41-3 had multiple (20) tillers. Various defects in flower morphology
AB  - were noted, including stunted flowers with curled lemma and palea; stamen with short
AB  - filaments, and anthers with little pollen. Plants containing the dsRNA (ir) constructs are in
AB  - regeneration. Detailed molecular analyses of the methylation-deficient transformants are
AB  - underway and the relationship between the severity of phenotypic defects and DNA methylation
AB  - levels will be determined. The ability of the constructs to release silencing in other rice
AB  - lines is being evaluated using both in vitro and in vivo approaches.
ER  -

TY  - JOUR
AU  - Teerawanichpan, P.
AU  - Krittanai, P.
AU  - Chauvatcharin, N.
AU  - Narangajavana, J.
TI  - Purification and characterization of rice DNA methyltransferase.
JO  - Plant Physiol. Biochem.
PY  - 2009
SP  - 671
EP  - 680
VL  - 47
AB  - Epigenetic modification is essential for normal development and plays important roles in gene
AB  - regulation in higher plants. Multiple factors
AB  - interact to regulate the establishment and maintenance of DNA
AB  - methylation in plant genome. We had previously cloned and characterized
AB  - DNA methyltransferase (DNA MTase) gene homologues (OsMET1) from rice.
AB  - In this present study, determination of DNA MTase activity in different
AB  - cellular compartments showed that DNA MTase was enriched in nuclei and
AB  - the activity was remarkably increased during imbibing dry seeds. We had
AB  - optimized the purification technique for DNA MTase enzyme from shoots
AB  - of 10-day-old rice seedlings using the three successive chromatographic
AB  - columns. The Econo-Pac Q the Hitrap-Heparin and the Superdex-200
AB  - columns yielded a protein fraction of a specific activity of 29, 298
AB  - and 800 purification folds, compared to the original nuclear extract,
AB  - respectively. The purified protein preferred hemi-methylated DNA
AB  - substrate, suggesting the maintenance activity of methylation. The
AB  - native rice DNA MTase was approximately 160-170 kDa and exhibited a
AB  - broad pH optimum in the range of 7.6 and 8.0. The enzyme kinetics and
AB  - inhibitory effects by methyl donor analogs, base analogs, cations, and
AB  - cationic amines on rice DNA MTase were examined. Global cytosine
AB  - methylation status of rice genome during development and in various
AB  - tissue culture systems were monitored and the results suggested that
AB  - the cytosine methylation level is not directly correlated with the DNA
AB  - MTase activity. The purification and characterization of rice DNA MTase
AB  - enzyme are expected to enhance our understanding of this enzyme
AB  - function and their possible contributions in Gramineae plant
AB  - development.
ER  -

TY  - JOUR
AU  - Tegtmeier, D.
AU  - Belitz, A.
AU  - Radek, R.
AU  - Heimerl, T.
AU  - Brune, A.
TI  - Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus (Verrucomicrobia: Opitutaceae).
JO  - Syst. Appl. Microbiol.
PY  - 2018
SP  - 101
EP  - 112
VL  - 41
AB  - We isolated a novel member of the phylum Verrucomicrobia from the hindgut of the
AB  - cockroach Shelfordella lateralis. Strain Ho45 is a yellow-pigmented, motile
AB  - coccus that represents a new genus-level lineage with less than 93% sequence
AB  - similarity to the 16S rRNA genes of other species in the family Opitutaceae.
AB  - Ultrastructural analysis revealed a Gram-negative cell envelope with an outer
AB  - membrane and a periplasmic space. In its ability to ferment sugars to propionate
AB  - and acetate as major products, strain Ho45 resembles its closest relative,
AB  - Opitutus terrae. However, the strains differed in their relationship to oxygen.
AB  - Although strain Ho45 grew and consumed oxygen at sub-atmospheric concentrations
AB  - (1-4%), both growth rate and cell yield decreased strongly with increasing oxygen
AB  - concentration in the headspace. By contrast, O. terrae, previously described as
AB  - an obligate anaerobe, proved to be facultatively aerobic, with highest growth
AB  - rates and cell yields at 2% and 16% oxygen, respectively. Also the closely
AB  - related Didymococcus (Diplosphaera) colitermitum, previously described as an
AB  - obligately aerobic microaerophile, showed a fermentative metabolism under anoxic
AB  - conditions, forming the same products from glucose as strain Ho45 and O. terrae.
AB  - Based on phenotypic and phylogenetic evidence, we propose strain Ho45 as the type
AB  - strain of a novel genus, Ereboglobus luteus gen. nov. sp. nov., and provide an
AB  - emended description of the family Opitutaceae and the genera Opitutus and
AB  - Didymococcus.
ER  -

TY  - JOUR
AU  - Teh, A.H.
AU  - Lee, S.M.
AU  - Dykes, G.A.
TI  - Draft Genome Sequences of Three Multiantibiotic-Resistant Campylobacter jejuni Strains (2865, 2868, and 2871) Isolated from Poultry at Retail Outlets in  Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e00331
EP  - e00316
VL  - 4
AB  - Campylobacter jejuni is a frequent cause of human bacterial gastrointestinal foodborne disease
AB  - worldwide. Antibiotic resistance in this species is of public
AB  - health concern. The draft genome sequences of three multiantibiotic-resistant C.
AB  - jejuni strains (2865, 2868, and 2871) isolated from poultry at retail outlets in
AB  - Malaysia are presented here.
ER  -

TY  - JOUR
AU  - Teh, B.S.
AU  - Lau, N.S.
AU  - Ng, F.L.
AU  - Abdul, R.A.Y.
AU  - Wan, X.
AU  - Saito, J.A.
AU  - Hou, S.
AU  - Teh, A.H.
AU  - Najimudin, N.
AU  - Alam, M.
TI  - Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 76
EP  - 76
VL  - 10
AB  - Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus,  a member of
AB  - the family Thermaceae. Members of the genus Thermus have been widely
AB  - used as a biological model for structural biology studies and to understand the
AB  - mechanism of microbial adaptation under thermal environments. Here, we present
AB  - the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot
AB  - spring in Malaysia, which is the fifth member of the genus Thermus with a
AB  - completely sequenced and publicly available genome (Genbank date of release:
AB  - December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within
AB  - the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid
AB  - of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In
AB  - addition, its genome revealed potential pathways for the synthesis of secondary
AB  - metabolites (isoprenoid) and pigments (carotenoid).
ER  -

TY  - JOUR
AU  - Tekedar, H.C.
AU  - Karsi, A.
AU  - Akgul, A.
AU  - Kalindamar, S.
AU  - Waldbieser, G.C.
AU  - Sonstegard, T.
AU  - Schroeder, S.G.
AU  - Lawrence, M.L.
TI  - Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila AL06-06.
JO  - Genome Announcements
PY  - 2015
SP  - e00368
EP  - e00315
VL  - 3
AB  - Aeromonas hydrophila occurs in freshwater environments and infects fish and mammals. Here, we
AB  - report the complete genome sequence of Aeromonas hydrophila
AB  - AL06-06, which was isolated from diseased goldfish and is being used for
AB  - comparative genomic studies with A. hydrophila strains that cause bacterial
AB  - septicemia in channel catfish aquaculture.
ER  -

TY  - JOUR
AU  - Tekedar, H.C.
AU  - Karsi, A.
AU  - Gillaspy, A.F.
AU  - Dyer, D.W.
AU  - Benton, N.R.
AU  - Zaitshik, J.
AU  - Vamenta, S.
AU  - Banes, M.M.
AU  - Gulsoy, N.
AU  - Aboko-Cole, M.
AU  - Waldbieser, G.C.
AU  - Lawrence, M.L.
TI  - Genome Sequence of the Fish Pathogen Flavobacterium columnare ATCC 49512.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2763
EP  - 2764
VL  - 194
AB  - Flavobacterium columnare is a Gram-negative, rod-shaped, motile, and highly prevalent fish
AB  - pathogen causing columnaris disease in freshwater fish worldwide.
AB  - Here, we present the complete genome sequence of F. columnare strain ATCC 49512.
ER  -

TY  - JOUR
AU  - Tekedar, H.C.
AU  - Kumru, S.
AU  - Kalindamar, S.
AU  - Karsi, A.
AU  - Waldbieser, G.C.
AU  - Sonstegard, T.
AU  - Schroeder, S.G.
AU  - Liles, M.R.
AU  - Griffin, M.J.
AU  - Lawrence, M.L.
TI  - Draft Genome Sequences of Three Aeromonas hydrophila Isolates from Catfish and Tilapia.
JO  - Genome Announcements
PY  - 2017
SP  - e01509
EP  - e01516
VL  - 5
AB  - Aeromonas hydrophila is a Gram-negative bacterium that is particularly adapted to freshwater
AB  - environments and can cause severe infections in fish and humans. Here,
AB  - we report the draft genomes of three A. hydrophila catfish and tilapia isolates.
ER  -

TY  - JOUR
AU  - Tekedar, H.C.
AU  - Kumru, S.
AU  - Karsi, A.
AU  - Waldbieser, G.C.
AU  - Sonstegard, T.
AU  - Schroeder, S.G.
AU  - Liles, M.R.
AU  - Griffin, M.J.
AU  - Lawrence, M.L.
TI  - Draft Genome Sequence of Aeromonas hydrophila TN97-08.
JO  - Genome Announcements
PY  - 2016
SP  - e00436
EP  - e00416
VL  - 4
AB  - Aeromonas hydrophila is an opportunistic pathogen residing in freshwater environments that
AB  - causes infection in fish and mammals. Here, we report the draft
AB  - genome sequence of A. hydrophila strain TN97-08 isolated from a diseased bluegill
AB  - (Lepomis macrochirus) in 1997.
ER  -

TY  - JOUR
AU  - Tekedar, H.C.
AU  - Kumru, S.
AU  - Karsi, A.
AU  - Waldbieser, G.C.
AU  - Sonstegard, T.
AU  - Schroeder, S.G.
AU  - Liles, M.R.
AU  - Griffin, M.J.
AU  - Lawrence, M.L.
TI  - Draft Genome Sequences of Four Virulent Aeromonas hydrophila Strains from Catfish Aquaculture.
JO  - Genome Announcements
PY  - 2016
SP  - e00860
EP  - e00816
VL  - 4
AB  - Since 2009, a clonal group of virulent Aeromonas hydrophila strains has been causing severe
AB  - disease in the catfish aquaculture industry in the southeastern
AB  - United States. Here, we report draft genomes of four A. hydrophila isolates from
AB  - catfish aquaculture that represent this clonal group.
ER  -

TY  - JOUR
AU  - Temperton, B.
AU  - Thomas, S.
AU  - Tait, K.
AU  - Parry, H.
AU  - Emery, M.
AU  - Allen, M.
AU  - Quinn, J.
AU  - Macgrath, J.
AU  - Gilbert, J.
TI  - Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 183
EP  - 190
VL  - 4
AB  - Vibrio tubiashii NCIMB 1337 is a major and increasingly prevalent pathogen of bivalve
AB  - mollusks, and shares a close phylogenetic relationship with both V.
AB  - orientalis and V. coralliilyticus. It is a Gram-negative, curved rod-shaped
AB  - bacterium, originally isolated from a moribund juvenile oyster, and is both
AB  - oxidase and catalase positive. It is capable of growth under both aerobic and
AB  - anaerobic conditions. Here we describe the features of this organism, together
AB  - with the draft genome and annotation. The genome is 5,353,266 bp long, consisting
AB  - of two chromosomes, and contains 4,864 protein-coding and 86 RNA genes.
ER  -

TY  - JOUR
AU  - Templeton, M.D.
AU  - Warren, B.A.
AU  - Andersen, M.T.
AU  - Rikkerink, E.H.
AU  - Fineran, P.C.
TI  - Complete DNA Sequence of Pseudomonas syringae pv. actinidiae, the Causal Agent of Kiwifruit Canker Disease.
JO  - Genome Announcements
PY  - 2015
SP  - e01054
EP  - e01015
VL  - 3
AB  - Pseudomonas syringae pv. actinidiae is the causal agent of bacterial canker of kiwifruit, a
AB  - disease that has rapidly spread worldwide. We have fully sequenced and assembled the
AB  - chromosomal and plasmid DNA from P. syringae pv. actinidiae ICMP 18884 using the PacBio RS II
AB  - platform.
ER  -

TY  - JOUR
AU  - Teng, L.
AU  - Deng, L.
AU  - Dong, X.
AU  - Wei, S.
AU  - Li, J.
AU  - Li, N.
AU  - Zhou, Y.
TI  - Genome Sequence of Hypervirulent Aeromonas hydrophila Strain HZAUAH.
JO  - Genome Announcements
PY  - 2017
SP  - e00012
EP  - e00017
VL  - 5
AB  - Aeromonas hydrophila, a zoonotic bacterium found in an expansive range of aquatic ecosystems,
AB  - has been reported to cause severe diseases in fish, amphibians,
AB  - reptiles, and mammals, including humans. Herein, we report the draft genome of
AB  - the hypervirulent A. hydrophila strain HZAUAH isolated from a crucian in China.
ER  -

TY  - JOUR
AU  - Teng, L.
AU  - Dong, X.
AU  - Zhou, Y.
AU  - Li, Z.
AU  - Deng, L.
AU  - Chen, H.
AU  - Wang, X.
AU  - Li, J.
TI  - Draft Genome Sequence of Hypervirulent and Vaccine Candidate Streptococcus suis Strain SC19.
JO  - Genome Announcements
PY  - 2017
SP  - e01484
EP  - e01416
VL  - 5
AB  - Streptococcus suis, a zoonotic bacterium found primarily in pigs, has been recognized recently
AB  - as an emerging pathogen of humans. Herein, we describe the
AB  - genome of Streptococcus suis strain SC19, a hypervirulent and vaccine candidate
AB  - strain isolated from a pig amid the 2005 outbreak in China.
ER  -

TY  - JOUR
AU  - Teng, L.
AU  - Ginn, A.
AU  - Jeon, S.
AU  - Kang, M.
AU  - Jeong, K.C.
TI  - Complete Genome Sequence of an Escherichia coli O157:H7 Strain Isolated from a Super-Shedder Steer.
JO  - Genome Announcements
PY  - 2016
SP  - e00258
EP  - e00216
VL  - 4
AB  - We report here the complete genome sequence ofEscherichia coliO157:H7 strain JEONG-1266
AB  - isolated from a super- shedder steer in northwest Florida. Cattle are
AB  - considered a primary reservoir ofE. coliO157:H7, and those cattle that excrete
AB  - this pathogen in their feces at levels >/=10(4) CFU/g are known as
AB  - super-shedders.
ER  -

TY  - JOUR
AU  - Tengs, T.
AU  - LaFramboise, T.
AU  - Den, R.B.
AU  - Hayes, D.N.
AU  - Zhang, J.
AU  - DebRoy, S.
AU  - Gentleman, R.C.
AU  - O'Neill, K.
AU  - Birren, B.
AU  - Meyerson, M.
TI  - Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - e121
EP  - e121
VL  - 32
AB  - We have developed a method for genomic representation using Type IIB restriction
AB  - endonucleases. Representation by concatenation of restriction
AB  - digests, or RECORD, is an approach to sample the fragments generated by
AB  - cleavage with these enzymes. Here, we show that the RECORD libraries may
AB  - be used for digital karyotyping and for pathogen identification by
AB  - computational subtraction.
ER  -

TY  - JOUR
AU  - Tenover, F.C.
AU  - Clark, V.L.
AU  - Young, F.E.
TI  - Presence of methyl adenine in the DNA of some strains of Neisseria Gonorrhoeae.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1980
SP  - 1796
EP  - 1800
VL  - 95
AB  - Sixteen strains of Neisseria gonorrhoeae were examined for the presence of
AB  - methyl adenine using the site-specific restriction endonucleases MboI and DpnI.
AB  - The DNA of four strains, all of which require arginine, hypoxanthine and
AB  - uracil for growth, contained methyl adenine.  Plasmid DNA from a
AB  - non-methylating strain transformed into methylating strains contained methyl
AB  - adenine when re-isolated.
ER  -

TY  - JOUR
AU  - Teo, J.
AU  - Tan, S.Y.
AU  - Tay, M.
AU  - Ding, Y.
AU  - Kjelleberg, S.
AU  - Givskov, M.
AU  - Lin, R.T.
AU  - Yang, L.
TI  - First case of E anophelis outbreak in an intensive-care unit.
JO  - Lancet
PY  - 2013
SP  - 855
EP  - 856
VL  - 382
AB  - The hospital infection-control team at the National University Hospital of Singapore
AB  - identified three patients in the cardiothoracic intensive-care unit and two patients from the
AB  - surgical ICU that were colonized with Elizabethkingia during a 3 week period in 2012.  The
AB  - Elizabethkingia strains were identified as Elizabethkingia meningoseptica on the basis of
AB  - matrix-assisted laser desorption-ionization time-of-flight mass spectrometry analysis.  The
AB  - five patients, who were ventilated via tracheostomy and had central venous catheters in situ,
AB  - received multiple courses of brad-spectrum antibiotics.  Before isolation of Elizabethkingia,
AB  - three of the patients had underlying solid-organ malignancy, one patient had multiple
AB  - abdominal surgeries, two patients underwent thoracic surgery, and one patient was on
AB  - extracorporeal membrane oxygenation.  After isolation of the Elizabethkingia strain, all
AB  - patients were treated with intravenous piperacillin and taxobactam, cotrimoxazole, or
AB  - levofloxacin, either alone or in combination.  Three of the five patients died during their
AB  - intensive-care admission, with sepsis contributing to the death of two patients.  Isolates of
AB  - Elizabethkingia (designated as NUHP1, NUHP2, and NUHP3) were obtained from the three patients
AB  - who had been warded at the cardiothoracic ICU.  NUHP1 and NUHP3 isolates were recovered from
AB  - the sputum, whereas NUHP2 was isolated froma blood specimen.  Unfortunately, isolates from
AB  - patients who had been warded in the surgical ICU were no longer available for further
AB  - analysis.
ER  -

TY  - JOUR
AU  - Terabayashi, Y.
AU  - Juan, A.
AU  - Tamotsu, H.
AU  - Ashimine, N.
AU  - Nakano, K.
AU  - Shimoji, M.
AU  - Shiroma, A.
AU  - Teruya, K.
AU  - Satou, K.
AU  - Hirano, T.
TI  - First Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain ATCC 13311 (NCTC 74), a Reference Strain of Multidrug  Resistance, as Achieved by Use of PacBio Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2014
SP  - e00986
EP  - e00914
VL  - 2
AB  - We report the first complete genomic sequence of Salmonella enterica subsp. enterica serovar
AB  - Typhimurium strain ATCC 13311, the leading food-borne pathogen
AB  - and a reference strain used in drug resistance studies. De novo assembly with
AB  - PacBio sequencing completed its chromosome and one plasmid. They will accelerate
AB  - the investigation into multidrug resistance in Salmonella Typhimurium.
ER  -

TY  - JOUR
AU  - Teramoto, M.
AU  - Zhai, Z.
AU  - Komatsu, A.
AU  - Shibayama, K.
AU  - Suzuki, M.
TI  - Genome Sequence of the Psychrophilic Bacterium Tenacibaculum ovolyticum Strain da5A-8 Isolated from Deep Seawater.
JO  - Genome Announcements
PY  - 2016
SP  - e00644
EP  - e00616
VL  - 4
AB  - Some bacterial species of the genus Tenacibaculum, including Tenacibaculum ovolyticum, have
AB  - been known as fish pathogens in the sea. So far, the only published genome sequence for this
AB  - genus is for Tenacibaculum dicentrarchi, which could also be a fish pathogen. Strain da5A-8,
AB  - showing 100% identity to the 16S rRNA gene sequence of T. ovolyticum DSM 18103(T), was
AB  - isolated from seawater at a depth of 344 m in Kochi, Japan, and grew optimally at 10 to 20
AB  - degrees C. The genome sequence of strain da5A-8 revealed the possible virulence genes commonly
AB  - observed in the genus Tenacibaculum.
ER  -

TY  - JOUR
AU  - Teran, L.C.
AU  - Coeuret, G.
AU  - Raya, R.
AU  - Champomier-Verges, M.C.
AU  - Chaillou, S.
TI  - Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e00584
EP  - e00517
VL  - 5
AB  - In this study, we present the draft genome sequence for Lactobacillus curvatus FLEC03. This
AB  - strain was isolated from beef carpaccio packaged in a modified
AB  - atmosphere. The draft genome will contribute to understanding the role of L.
AB  - curvatus strains in food products (fermentation, biopreservation, or spoilage)
AB  - through comparative genomics with other strains.
ER  -

TY  - JOUR
AU  - Terfehr, D.
AU  - Dahlmann, T.A.
AU  - Specht, T.
AU  - Zadra, I.
AU  - Kurnsteiner, H.
AU  - Kuck, U.
TI  - Genome Sequence and Annotation of Acremonium chrysogenum, Producer of the beta-Lactam Antibiotic Cephalosporin C.
JO  - Genome Announcements
PY  - 2014
SP  - e00948
EP  - e00914
VL  - 2
AB  - The filamentous fungus Acremonium chrysogenum is the industrial producer of the beta-lactam
AB  - antibiotic cephalosporin C. Here, we present the genome sequence of
AB  - strain ATCC 11550, which contains genes for 8,901 proteins, 127 tRNAs, and 22
AB  - rRNAs. Genome annotation led to the prediction of 42 gene clusters for secondary
AB  - metabolites.
ER  -

TY  - JOUR
AU  - Terpolilli, J.
AU  - Garau, G.
AU  - Hill, Y.
AU  - Tian, R.
AU  - Howieson, J.
AU  - Brau, L.
AU  - Goodwin, L.
AU  - Han, J.
AU  - Liolios, K.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of  the annual legume Medicago sphaerocarpos.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 420
EP  - 430
VL  - 9
AB  - Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can
AB  - exist as a soil saprophyte or as a legume microsymbiont of Medicago.
AB  - WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago
AB  - sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy).
AB  - WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha
AB  - and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369,
AB  - together with genome sequence information and its annotation. The 6,402,557 bp
AB  - standard draft genome is arranged into 307 scaffolds of 307 contigs containing
AB  - 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome
AB  - is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic
AB  - Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Terpolilli, J.
AU  - Hill, Y.
AU  - Tian, R.
AU  - Howieson, J.
AU  - Brau, L.
AU  - Goodwin, L.
AU  - Han, J.
AU  - Liolios, K.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 315
EP  - 324
VL  - 9
AB  - Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming  rod that can
AB  - exist as a soil saprophyte or as a legume microsymbiont of Medicago.
AB  - WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual
AB  - Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022
AB  - is highly effective at fixing nitrogen with M. truncatula and other annual
AB  - species such as M. tornata and M. littoralis and is also highly effective with
AB  - the perennial M. sativa (alfalfa or lucerne). In common with other characterized
AB  - E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha
AB  - and M. sphaerocarpos and does not nodulate M. murex. Here we describe the
AB  - features of E. meliloti WSM1022, together with genome sequence information and
AB  - its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121
AB  - scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only
AB  - encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE
AB  - Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root
AB  - Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Terpolilli, J.
AU  - Rui, T.
AU  - Yates, R.
AU  - Howieson, J.
AU  - Poole, P.
AU  - Munk, C.
AU  - Tapia, R.
AU  - Han, C.
AU  - Markowitz, V.
AU  - Tatiparthi, R.
AU  - Mavrommatis, K.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Goodwin, L.
AU  - Woyke, T.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 527
EP  - 539
VL  - 9
AB  - Rhizobium leguminosarum bv. trifolii is a soil-inhabiting bacterium that has the  capacity to
AB  - be an effective N2-fixing microsymbiont of Trifolium (clover)
AB  - species. R. leguminosarum bv. trifolii strain WSM1689 is an aerobic, motile,
AB  - Gram-negative, non-spore-forming rod that was isolated from a root nodule of
AB  - Trifolium uniflorum collected on the edge of a valley 6 km from Eggares on the
AB  - Greek Island of Naxos. Although WSM1689 is capable of highly effective
AB  - N2-fixation with T. uniflorum, it is either unable to nodulate or unable to fix
AB  - N2 with a wide range of both perennial and annual clovers originating from
AB  - Europe, North America and Africa. WSM1689 therefore possesses a very narrow host
AB  - range for effective N2 fixation and can thus play a valuable role in determining
AB  - the geographic and phenological barriers to symbiotic performance in the genus
AB  - Trifolium. Here we describe the features of R. leguminosarum bv. trifolii strain
AB  - WSM1689, together with the complete genome sequence and its annotation. The
AB  - 6,903,379 bp genome contains 6,709 protein-coding genes and 89 RNA-only encoding
AB  - genes. This multipartite genome contains six distinct replicons; a chromosome of
AB  - size 4,854,518 bp and five plasmids of size 667,306, 518,052, 341,391, 262,704
AB  - and 259,408 bp. This rhizobial genome is one of 20 sequenced as part of a DOE
AB  - Joint Genome Institute 2010 Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Terry, B.J.
AU  - Jack, W.E.
AU  - Modrich, P.
TI  - Facilitated diffusion during catalysis by EcoRI endonuclease:  nonspecific interactions in EcoRI catalysis.
JO  - J. Biol. Chem.
PY  - 1985
SP  - 13130
EP  - 13137
VL  - 260
AB  - The potential for processive EcoRI endonuclease hydrolysis has been examined on
AB  - several DNA substrates containing two EcoRI sites which were embedded in
AB  - identical sequence environments.  With a 388-base pair circular DNA, in which
AB  - the two recognition sites are separated by 51 base pairs (shorter distance) or
AB  - 337 base pairs (longer distance), 77 and 34% of all events involved processive
AB  - hydrolysis at ionic strengths of 0.059 and 0.13, respectively.  However, the
AB  - frequency of processive action on linear substrates, in which the two sites
AB  - were separated by 51 base pairs, was only 42 and 17% at these ionic strengths,
AB  - values half those observed with the circular DNA.  Processive action not
AB  - detectable on circular or linear substrates at an ionic strength of 0.23.
AB  - These findings indicate that DNA search by the endonuclease occurs by
AB  - facilitated diffusion, a mechanism in which the protein locates and leaves it
AB  - recognition sequence by interacting with nonspecific DNA sites.  We suggest
AB  - that processivity on linear substrates is limited to values half that for small
AB  - circles due to partitioning of the enzyme between the two products generated by
AB  - cleavage of a linear molecule.  Given such topological effects, measured
AB  - processivity values imply that the endonuclease can diffuse within a DNA domain
AB  - to locate and recognize an EcoRI site 50 to 300 base pairs distant from an
AB  - initial binding site, with minimum search efficiencies being 80 and 30% at
AB  - ionic strengths of 0.059 and 0.13, respectively.  The high efficiency of
AB  - processive action indicates that a positionally correlated mode of search plays
AB  - a major role in facilitated diffusion in this system under such conditions.
AB  - Also consistent with this view was the identication of a striking position
AB  - effect when two closely spaced EcoRI sites were asymmetrically positioned near
AB  - the end of a linear DNA.  The endonuclease displays a substantial preference
AB  - for the more centrally located recognition sequence.  This preference does not
AB  - reflect differential sensitivity of the two sites to cleavage per se, but can
AB  - be simply explained by preferential entry of the enzyme via the larger
AB  - nonspecific target available to the more centrally positioned recognition
AB  - sequence.  These conclusions differ from those of a previous qualitative
AB  - analysis of endonuclease processivity over short distances.
ER  -

TY  - JOUR
AU  - Terry, B.J.
AU  - Jack, W.E.
AU  - Modrich, P.
TI  - Mechanism of specific site location and DNA cleavage by EcoRI endonuclease.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 103
EP  - 118
VL  - 5
AB  - The EcoRI restriction and modification system has become one of the most
AB  - convenient systems in which to study protein-DNA interactions.  Both EcoRI
AB  - endonuclease and methylase recognize a two-fold symmetrical DNA sequence.  The
AB  - endonuclease cleaves at sites indicated by arrows while the central adenines
AB  - are methylated on the 6-amino group by the methylase (*), with the latter
AB  - modification rendering the EcoRI sequence resistant to cleavage by the
AB  - endonuclease.  Like all sequence specific proteins, EcoRI endonuclease displays
AB  - finite affinity for nonspecific DNA sequences.  In this context, the problem of
AB  - specific recognition can be divided into two questions:  (i) what is the
AB  - mechanistic basis for discrimination of specific and nonspecific sites in
AB  - thermodynamic and molecular terms?  (ii) what role do nonspecific interactions
AB  - play in the kinetic path(s) utilized for specific site location?  In this paper
AB  - we will summarize work on the thermodynamics of specific and nonspecific
AB  - interactions and will discuss evidence indicating that nonspecific interactions
AB  - are involved in the pathways by which EcoRI endonuclease locates an EcoRI
AB  - sequence and leaves a cleaved site.  For discussion of molecular details of
AB  - endonuclease DNA interactions, see chapter by Rosenberg, et al., this volume.
ER  -

TY  - JOUR
AU  - Terry, B.J.
AU  - Jack, W.E.
AU  - Rubin, R.A.
AU  - Modrich, P.
TI  - Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences.
JO  - J. Biol. Chem.
PY  - 1983
SP  - 9820
EP  - 9825
VL  - 258
AB  - Equilibrium binding of EcoRI endonuclease to DNA has been analyzed by
AB  - nitrocellulose filter and preferential DNA cleavage methods.  Association
AB  - constants for pBR322 and a 34-base pair molecule containing the EcoRI site of
AB  - this plasmid in a central position were determined to be 1.9 x 10(11) M-1 and
AB  - 1.0 x 10(11) M-1 at 37C, respectively, with the stoichiometry of binding being
AB  - 0.8-+ 0.1 mol of endonuclease dimer per mol of DNA.  In contrast, the affinity
AB  - of the enzyme for a pBR322 derivative from which the EcoRI site has been
AB  - deleted is 3.2 x 10(9) M-1 as judged by competitive binding experiments.  If it
AB  - is assumed that each base pair can define the beginning of a nonspecific
AB  - binding site, this value corresponds to an affinity for nonspecific sites of
AB  - 7.4 x 10(5) M-1.  Furthermore, the affinity of the endonuclease for the
AB  - EcoRI-methylated sequence is at least three orders of magnitude less than that
AB  - for the unmodified recognition site.  The dependence on temperature and ionic
AB  - strength of the equilibrium constant governing specific interactions has also
AB  - been examined.  The temperature dependence of the reaction indicates that
AB  - entropy increase accounts for 70% of the free energy of specific binding at
AB  - 37C.  Affinity of the endonuclease for the EcoRI site is highly dependent on
AB  - NaCl concentration.  Analysis of this dependence according to the theory of
AB  - Record and colleagues (Record, T.M., Jr., Lohman, T.M., and deHaseth, P. (1976)
AB  - J. Mol. Biol. 107, 145-158) has implicated 8 ion pairs in the stability of
AB  - specific complexes, a value identical with the number of phosphate contacts
AB  - determined by ethylation interference analysis (Lu, A.L., Jack, W.E., and
AB  - Modrich, P. (1981) J. Biol. Chem. 256, 13200-13206).  Extrapolation to 1 M NaCl
AB  - suggests that nonelectrostatic interactions account for 40% of the free energy
AB  - change associated with specific complex formation.
ER  -

TY  - JOUR
AU  - Terschuren, P.-A.
AU  - Noyer-Weidner, M.
AU  - Trautner, T.A.
TI  - Recombinant derivatives of Bacillus subtilis phage Z containing the DNA methyltransferase genes of related methylation-proficient phages.
JO  - J. Gen. Microbiol.
PY  - 1987
SP  - 945
EP  - 952
VL  - 198
AB  - The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages
AB  - SPR, Phi3T, SPbeta and alpha11 can be transferred by transfection and
AB  - recombination to the genome of the related nonmodifying phage Z.  Integration
AB  - of the Mtase genes occurs in phage Z DNA at a unique location which is
AB  - homologous with the flanking regions of the Mtase genes of the related phages.
AB  - In lysogenic cells carrying recombinant phages, expression of the Mtase genes
AB  - if repressed, irrespective of whether the Mtase genes were derived from phage
AB  - donors which were homo- or heteroimmune to phage Z.
ER  -

TY  - JOUR
AU  - Teru, Y.
AU  - Hikima, J.I.
AU  - Kono, T.
AU  - Sakai, M.
AU  - Takano, T.
AU  - Hawke, J.P.
AU  - Takeyama, H.
AU  - Aoki, T.
TI  - Whole-Genome Sequence of Photobacterium damselae subsp. piscicida Strain 91-197,  Isolated from Hybrid Striped Bass (Morone sp.) in the United States.
JO  - Genome Announcements
PY  - 2017
SP  - e00600
EP  - e00617
VL  - 5
AB  - Photobacterium damselae subsp. piscicida is a causative bacterium of fish pasteurellosis,
AB  - which has caused serious economic damage to aquaculture farms
AB  - worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida
AB  - 91-197, isolated in the United States, suggests that this genome consists of two
AB  - chromosomes and two plasmids.
ER  -

TY  - JOUR
AU  - Tesfazgi-Mebrhatu, M.
AU  - Wywial, E.
AU  - Ghosh, A.
AU  - Michiels, C.W.
AU  - Lindner, A.B.
AU  - Taddei, F.
AU  - Bujnicki, J.M.
AU  - Van Melderen, L.
AU  - Aertsen, A.
TI  - Evidence for an evolutionary antagonism between Mrr and Type III modification systems.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 5991
EP  - 6001
VL  - 39
AB  - The Mrr protein of Escherichia coli is a laterally acquired Type IV restriction endonuclease
AB  - with specificity for methylated DNA. While Mrr nuclease activity can be elicited by
AB  - high-pressure stress in E. coli MG1655, its (over)expression per se does not confer any
AB  - obvious toxicity. In this study, however, we discovered that Mrr of E. coli MG1655 causes
AB  - distinct genotoxicity when expressed in Salmonella typhimurium LT2. Genetic screening enabled
AB  - us to contribute this toxicity entirely to the presence of the endogenous Type III restriction
AB  - modification system (StyLTI) of S. typhimurium LT2. The StyLTI system consists of the Mod DNA
AB  - methyltransferase and the Res restriction endonuclease, and we revealed that expression of the
AB  - LT2 mod gene was sufficient to trigger Mrr activity in E. coli MG1655. Moreover, we could
AB  - demonstrate that horizontal acquisition of the MG1655 mrr locus can drive the loss of
AB  - endogenous Mod functionality present in S. typhimurium LT2 and E. coli ED1a, and observed a
AB  - strong anti-correlation between close homologues of MG1655 mrr and LT2 mod in the genome
AB  - database. This apparent evolutionary antagonism is further discussed in the light of a
AB  - possible role for Mrr as defense mechanism against the establishment of epigenetic regulation
AB  - by foreign DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Tettelin, H. et al.
TI  - Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.
JO  - Science
PY  - 2000
SP  - 1809
EP  - 1815
VL  - 287
AB  - The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a
AB  - causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158
AB  - (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA
AB  - transfer were identified; two of these contain genes encoding proteins involved in
AB  - pathogenicity, and the third island contains coding sequences only for hypothetical proteins.
AB  - Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the
AB  - genome, in which sequences for structural proteins of the pilus are clustered and several
AB  - coding regions unique to serogroup B capsular polysaccharide synthesis can be identified.
AB  - Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen
AB  - studied to date, a mechanism that controls their expression and contributes to the evasion of
AB  - the host immune system.
ER  -

TY  - JOUR
AU  - Tettelin, H. et al.
TI  - Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome".
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2005
SP  - 13950
EP  - 13950
VL  - 102
AB  - The development of efficient and inexpensive genome sequencing methods has revolutionized the
AB  - study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of
AB  - a single genome does not reflect how genetic variability drives pathogenesis within a
AB  - bacterial species and also limits genome-wide screens for vaccine candidates or for
AB  - antimicrobial targets. We have generated the genomic sequence of six strains representing the
AB  - five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal
AB  - infection in humans. Analysis of these genomes and those available in databases showed that
AB  - the S. agalactiae species can be described by a pan-genome consisting of a core genome shared
AB  - by all isolates, accounting for approximately 80% of any single genome, plus a dispensable
AB  - genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of
AB  - the data suggests that the gene reservoir available for inclusion in the S. agalactiae
AB  - pan-genome is vast and that unique genes will continue to be identified even after sequencing
AB  - hundreds of genomes.
ER  -

TY  - JOUR
AU  - Tettelin, H. et al.
TI  - Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
JO  - Science
PY  - 2001
SP  - 498
EP  - 506
VL  - 293
AB  - The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a
AB  - Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media,
AB  - contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role.
AB  - Approximately 5% of the genome is composed of insertion sequences that may contribute to
AB  - genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the
AB  - metabolism of polysaccharides and hexosamines provide a substantial source of carbon and
AB  - nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif
AB  - identified within the signal peptide of proteins is potentially involved in targeting these
AB  - proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several
AB  - surface-exposed proteins that may serve as potential vaccine candidates were identified.
AB  - Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae
AB  - that could contribute to differences in virulence and antigenicity.
ER  -

TY  - JOUR
AU  - Tettelin, H.
AU  - Hooven, T.A.
AU  - Zhao, X.
AU  - Su, Q.
AU  - Sadzewicz, L.
AU  - Tallon, L.J.
AU  - Fraser, C.M.
AU  - Ratner, A.J.
TI  - Whole-Genome Sequences of Bacteremia Isolates of Bordetella holmesii.
JO  - Genome Announcements
PY  - 2017
SP  - e01023
EP  - e01017
VL  - 5
AB  - Bordetella holmesii causes respiratory and invasive diseases in humans, but its pathogenesis
AB  - remains poorly understood. We report here the genome sequences of
AB  - seven bacteremia isolates of B. holmesii, including the type strain. Comparative
AB  - analysis of these sequences may aid studies of B. holmesii biology and assist in
AB  - the development of species-specific diagnostic strategies.
ER  -

TY  - JOUR
AU  - Tettelin, H.
AU  - Sampaio, E.P.
AU  - Daugherty, S.C.
AU  - Hine, E.
AU  - Riley, D.R.
AU  - Sadzewicz, L.
AU  - Sengamalay, N.
AU  - Shefchek, K.
AU  - Su, Q.
AU  - Tallon, L.J.
AU  - Conville, P.
AU  - Olivier, K.N.
AU  - Holland, S.M.
AU  - Fraser, C.M.
AU  - Zelazny, A.M.
TI  - Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5450
EP  - 5450
VL  - 194
AB  - Mycobacterium massiliense (Mycobacterium abscessus group) is an emerging pathogen causing
AB  - pulmonary disease and skin and soft tissue infections. We report the
AB  - genome sequence of the type strain CCUG 48898.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
TI  - Draft Genome Sequence of Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer.
JO  - Genome Announcements
PY  - 2015
SP  - e01202
EP  - e01215
VL  - 3
AB  - We report the draft genome sequence of Acinetobacter sp. strain VT-511, which was obtained
AB  - from the stomach of a patient with gastric cancer. The genome of Acinetobacter sp. VT-511 is
AB  - composed of approximately 3,416,321 bp and includes 3,214 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
TI  - Draft Genome Sequence of Kluyvera intestini Strain GT-16 Isolated from the Stomach of a Patient with Gastric Cancer.
JO  - Genome Announcements
PY  - 2016
SP  - e01432
EP  - e01416
VL  - 4
AB  - Here, we report the complete genome sequence of the novel, non-spore-forming Kluyvera
AB  - intestini strain GT-16, isolated from the stomach of a patient with gastric cancer. The genome
AB  - is 5,868,299 bp in length with a G+C content of 53.0%. It possesses 5,350 predicted
AB  - protein-coding genes encoding virulence factors and  antibiotic resistance proteins.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
TI  - Draft Genome Sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov., Isolated from the Dental Decay Plaque of a Patient with Periodontitis.
JO  - Genome Announcements
PY  - 2018
SP  - e01541
EP  - e01517
VL  - 6
AB  - Here, we report the draft genome sequence of Tetzosporium hominis VT-49 gen. nov., sp. nov.,
AB  - isolated from the dental plaque of a patient with severe
AB  - periodontal disease. The draft genome sequence was 2,780,751 bp in length with a
AB  - 43.3% G+C content. We detected 3,001 genes, which are predicted to encode
AB  - proteins that regulate both virulence and antibiotic resistance.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
TI  - Complete Genome Sequence of Bacilli bacterium Strain VT-13-104 Isolated from the  Intestine of a Patient with Duodenal Cancer.
JO  - Genome Announcements
PY  - 2015
SP  - e00705
EP  - e00715
VL  - 3
AB  - We report the complete genome sequence of Bacilli bacterium strain VT-13-104 isolated from the
AB  - intestine of a patient with duodenal cancer. The genome is
AB  - composed of 3,573,421 bp, with a G+C content of 35.7%. It possesses 3,254
AB  - predicted protein-coding genes encoding multidrug resistance transporters,
AB  - resistance to antibiotics, and virulence factors.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
TI  - Draft Genome Sequence of Chryseobacterium mucoviscidosis sp. nov. Strain VT16-26, Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Cystic Fibrosis.
JO  - Genome Announcements
PY  - 2018
SP  - e01473
EP  - e01417
VL  - 6
AB  - We report here the draft genome sequence of Chryseobacterium mucoviscidosis VT16-26, a novel
AB  - bacterium isolated from the lungs of a patient with cystic
AB  - fibrosis. The genome was composed of 4,403,956 bp and had 36.2% G+C content. We
AB  - detected 4,048 genes with predicted protein-coding functions, including those
AB  - associated with antibiotic resistance and virulence.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
TI  - Complete Genome Sequence of a Novel Bacillus sp. VT 712 Strain Isolated from the  Duodenum of a Patient with Intestinal Cancer.
JO  - Genome Announcements
PY  - 2016
SP  - e00786
EP  - e00716
VL  - 4
AB  - We report here the complete genome sequence of the spore-forming Bacillus sp. strain VT 712
AB  - isolated from the duodenum of a patient with intestinal cancer. The
AB  - genome is 3,921,583 bp, with 37.9% G+C content. It contains 3,768 predicted
AB  - protein-coding genes for multidrug resistance transporters, virulence factors,
AB  - and daunorubicin resistance.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Tetz, V.
AU  - Vecherkovskaya, M.
TI  - Complete Genome Sequence of Paenibacillus sp. Strain VT 400, Isolated from the Saliva of a Child with Acute Lymphoblastic Leukemia.
JO  - Genome Announcements
PY  - 2015
SP  - e00894
EP  - e00815
VL  - 3
AB  - We report here the complete genome sequence of spore-forming Paenibacillus sp. strain VT 400,
AB  - isolated from the saliva of a child with acute lymphoblastic
AB  - leukemia. The genome consists of 6,986,122 bp, with a G+C content of 45.8%. It
AB  - possesses 5,777 predicted protein-coding genes encoding multidrug resistance
AB  - transporters, virulence factors, and resistance to chemotherapeutic drugs.
ER  -

TY  - JOUR
AU  - Tetz, G.
AU  - Vecherkovskaya, M.
AU  - Zappile, P.
AU  - Dolgalev, I.
AU  - Tsirigos, A.
AU  - Heguy, A.
AU  - Tetz, V.
TI  - Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer.
JO  - Genome Announcements
PY  - 2017
SP  - e01184
EP  - e01117
VL  - 5
AB  - We report here an update to the draft genome sequence of Kluyvera intestini sp. nov. strain
AB  - GT-16, generated using MinION long-read sequencing technology. The
AB  - complete genome sequence of the human-derived strain GT-16 measured 5,768,848 bp.
AB  - An improved high-quality complete genome sequence provides insights into the
AB  - mobility potential of resistance genes in this species.
ER  -

TY  - JOUR
AU  - Tetz, V.
AU  - Tetz, G.
TI  - Draft Genome Sequence of a Strain of Bacillus intestinalis sp. nov., a New Member of Sporobiota Isolated from the Small Intestine of a Single Patient with Intestinal Cancer.
JO  - Genome Announcements
PY  - 2017
SP  - e00489
EP  - e00417
VL  - 5
AB  - We report here the draft genome sequence of Bacillus intestinalis strain 1731, a  novel
AB  - spore-forming bacterium isolated from the small intestine of a patient with
AB  - intestinal cancer. The genome comprised 4,047,276 bp, with 43.9% G+C content.
AB  - There were 3,913 predicted protein-coding genes, including those associated with
AB  - antibiotic resistance and virulence.
ER  -

TY  - JOUR
AU  - Tetz, V.
AU  - Tetz, G.
TI  - Draft Genome Sequence of Bacillus obstructivus VT-16-70 Isolated from the Bronchoalveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary  Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e01754
EP  - e01716
VL  - 5
AB  - We report here the draft genome sequence of Bacillus obstructivus VT-16-70, a novel
AB  - spore-forming bacterium isolated from the lungs of a patient with chronic
AB  - obstructive pulmonary disease. The genome comprised 5,220,753 bp, with 35.2% G+C
AB  - content. There were 4,972 predicted protein-coding genes, including those
AB  - associated with antibiotic resistance and virulence.
ER  -

TY  - JOUR
AU  - Tetz, V.
AU  - Tetz, G.
TI  - Draft Genome Sequence of the Uropathogenic Herbaspirillumfrisingense Strain ureolyticus VT-16-41.
JO  - Genome Announcements
PY  - 2017
SP  - e00279
EP  - e00217
VL  - 5
AB  - Herbaspirillum frisingense strain ureolyticus VT-16-41 is a clinical cystitis isolate. Here,
AB  - we report the draft genome sequence of the uropathogenic H.
AB  - frisingense strain ureolyticus VT-16-41, which contains various antibiotic
AB  - resistance genes and virulence factors that enable it to colonize and persist in
AB  - the urinary tract.
ER  -

TY  - JOUR
AU  - Tetz, V.
AU  - Tetz, G.
TI  - Draft Genome Sequence of Bacillus respiratorii VT-16-64, Isolated from the Bronchiolar Alveolar Lavage Fluid of a Patient with Chronic Obstructive Pulmonary  Disease.
JO  - Genome Announcements
PY  - 2017
SP  - e00264
EP  - e00217
VL  - 5
AB  - We report here the draft genome sequence of Bacillus respiratorii VT-16-64, a novel
AB  - spore-forming bacterium isolated from the bronchiolar alveolar lavage fluid
AB  - of a patient with chronic obstructive pulmonary disease. The genome was comprised
AB  - 4,831,386 bp with 4,399 predicted protein-coding genes, including those
AB  - associated with antibiotic resistance and virulence.
ER  -

TY  - JOUR
AU  - Tewari, R.
AU  - Das Mitra, S.
AU  - Das, S.
AU  - Jadhao, S.
AU  - Mishra, G.
AU  - Ganaie, F.
AU  - Shome, R.
AU  - Rahman, H.
AU  - Shome, B.R.
TI  - Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India.
JO  - Genome Announcements
PY  - 2018
SP  - e00205
EP  - e00218
VL  - 6
AB  - We report here the draft genome sequence of a multidrug-resistant Escherichia coli strain
AB  - (NIVEDI-P44) isolated from a chicken fecal sample. The estimated
AB  - genome size is 4.76 Mb, with a G+C content of 50.65%. The genome harbors multiple
AB  - antibiotic resistance genes, blaDHA-1, mph(A), strA, strB, dfrA14, sul-2, tet(A),
AB  - and qnrS1.
ER  -

TY  - JOUR
AU  - Thacker, T.C.
AU  - Lippolis, J.D.
AU  - Brunelle, B.W.
AU  - Casey, T.A.
AU  - Reinhardt, T.A.
AU  - Sacco, R.E.
AU  - Holman, D.B.
TI  - Genome Sequences of Escherichia coli Strains That Cause Persistent and Transient  Mastitis.
JO  - Genome Announcements
PY  - 2017
SP  - e00775
EP  - e00717
VL  - 5
AB  - We report here the genome sequences of two strains of Escherichia coli (ECA-B and ECC-M) that
AB  - cause bovine mastitis. These strains are known to be associated with
AB  - persistent and transient mastitis; strain ECA-B causes a transient infection, and
AB  - ECC-M leads to a persistent infection.
ER  -

TY  - JOUR
AU  - Thanos, D.
AU  - Scarpelis, G.
AU  - Papamatheakis, J.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BseAI.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8881
EP  - 8881
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Thapa, S.P.
AU  - Coaker, G.
TI  - Genome Sequences of Two Pseudomonas syringae pv. tomato Race 1 Strains, Isolated  from Tomato Fields in California.
JO  - Genome Announcements
PY  - 2016
SP  - e01671
EP  - e01615
VL  - 4
AB  - Pseudomonas syringae pv. tomato race 1 strains have evolved to overcome genetic resistance in
AB  - tomato. Here, we present the draft genome sequences of two race 1
AB  - P. syringae pv. tomato strains, A9 and 407, isolated from diseased tomato plants
AB  - in California.
ER  -

TY  - JOUR
AU  - Tharek, M.
AU  - Sim, K.S.
AU  - Khairuddin, D.
AU  - Ghazali, A.H.
AU  - Najimudin, N.
TI  - Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2.
JO  - Genome Announcements
PY  - 2017
SP  - e00305
EP  - e00317
VL  - 5
AB  - Escherichia coli strain USML2 was originally isolated from the inner leaf tissues of
AB  - surface-sterilized phytopathogenic-free oil palm (Elaeis guineensis Jacq.). We
AB  - present here the whole-genome sequence of this plant-endophytic strain. The
AB  - genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted
AB  - coding sequences, and a G+C content of 50.8%.
ER  -

TY  - JOUR
AU  - Thatcher, L.F.
AU  - Myers, C.A.
AU  - O'Sullivan, C.A.
AU  - Roper, M.M.
TI  - Draft Genome Sequence of Rhodococcus sp. Strain 66b.
JO  - Genome Announcements
PY  - 2017
SP  - e00229
EP  - e00217
VL  - 5
AB  - We report here the draft genome sequence and annotation of Rhodococcus sp. strain 66b isolated
AB  - from the soil of southwest Western Australia. This strain exhibits a
AB  - range of bioactivities, including plant growth promotion, biosurfactant
AB  - production, and wax degradation. Whole-genome sequencing was conducted to uncover
AB  - the underlying mechanisms.
ER  -

TY  - JOUR
AU  - Thatcher, L.F.
AU  - Myers, C.A.
AU  - O'Sullivan, C.A.
AU  - Roper, M.M.
TI  - Draft Genome Sequences of Streptomyces sp. Strains MH60 and 111WW2.
JO  - Genome Announcements
PY  - 2018
SP  - e00356
EP  - e00318
VL  - 6
AB  - We report here the draft genome sequences, annotations, and predictions of secondary
AB  - metabolite gene clusters of two endophytic Streptomyces species
AB  - isolated from wheat plants growing in the Western Australian wheat belt. These
AB  - strains, Streptomyces sp. strains MH60 and 111WW2, possess antifungal and/or
AB  - plant growth-promoting activities.
ER  -

TY  - JOUR
AU  - The, A.G.I.
TI  - Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
JO  - Nature
PY  - 2000
SP  - 796
EP  - 815
VL  - 408
AB  - The flowering plant Arabidopsis thaliana is an important model system for identifying genes
AB  - and determining their functions.  Here we report the analysis of the genomic sequence of
AB  - Arabidopsis.  The sequenced regions cover 115.4 megabases of the 125-megabase genome and
AB  - extend into centromeric regions.  The evolution of Arabidopsis involved a whole-genome
AB  - duplication, followed by subsequent gene loss and extensive local gene duplications, giving
AB  - rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor
AB  - of the plastid.  The genome contains 25,498 genes encoding proteins from 11,000 families,
AB  - similar to the functional diversity of Drosophila and Caenorhabditis elegans-the other
AB  - sequenced multicellular eukaryotes.  Arabidopsis has many families of new proteins but also
AB  - lacks several common protein families, indicating that the sets of common proteins have
AB  - undergone differential expansion and contraction in the three multicellular eukaryotes.  This
AB  - is the first complete genome sequence of a plant and provides the foundations for more
AB  - comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of
AB  - plant-specific gene functions and establishing rapid systematic ways to identify genes for
AB  - crop improvement.
ER  -

TY  - JOUR
AU  - Thennarasu, S.
AU  - Polireddy, D.
AU  - Antony, A.
AU  - Yada, M.R.
AU  - Algarawi, S.
AU  - Sivakumar, N.
TI  - Draft Genome Sequence of a Highly Flagellated, Fast-Swimming Archaeon, Methanocaldococcus villosus Strain KIN24-T80 (DSM 22612).
JO  - Genome Announcements
PY  - 2013
SP  - e00481
EP  - e00413
VL  - 1
AB  - We report the draft genome sequence of a hyperthermophilic Methanocaldococcus villosus strain,
AB  - KIN24-T80. The gene associated with its heavy flagellum
AB  - formation was annotated in the 1.2-Mb draft genome sequence, and this strain may
AB  - be a good model system to study the extensive functional role of flagella and
AB  - their fast motor activity.
ER  -

TY  - JOUR
AU  - Theriault, G.
AU  - Roy, P.H.
TI  - Cloning of Pseudomonas plasmid pMG7 and its restriction-modification system in Escherichia coli.
JO  - Gene
PY  - 1982
SP  - 355
EP  - 359
VL  - 19
AB  - Plasmid pMG7 of Pseudomonas aeruginosa codes for a type II DNA
AB  - restriction-modification (r-m) system, PaeR7.  This plasmid has not been
AB  - observed to transfer to Escherichia coli either by conjugation or by
AB  - transformation.  We have cloned BglII linears (42 kb) and the BamHI large
AB  - fragment (37 kb) of pMG7 into cosmid pHC79 (6.4 kb) and introduced the
AB  - recombinant molecules into E. coli by in vitro packaging.  Several clones were
AB  - obtained which demonstrated in vivo restriction of phage u80.  One of these
AB  - clones, GT138, was further tested and showed in vivo modification of Phi80.
AB  - Extracts from two clones, GT138 and GT125, yielded a restriction endonuclease
AB  - activity which produced fragments of u80 DNA identical to those produced by
AB  - PaeR7.  Cosmid cloning should be useful for obtaining substantial yields of
AB  - large fragments of plasmids that are difficult to purify in their native
AB  - strains.
ER  -

TY  - JOUR
AU  - Theriault, G.
AU  - Roy, P.H.
AU  - Howard, K.A.
AU  - Benner, J.S.
AU  - Brooks, J.S.
AU  - Waters, A.F.
AU  - Gingeras, T.R.
TI  - Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 8441
EP  - 8461
VL  - 13
AB  - Bal31 deletion experiments on clones of the PaeR7 restriction-modification
AB  - system from Pseudomonas aeruginosa demonstrate that it is arranged as an
AB  - operon, with the methylase gene preceding the endonuclease gene.  The DNA
AB  - sequence of this operon agrees with in vitro transcription-translation assays
AB  - which predict proteins of 532 amino acids, Mr = 59,260 daltons, and 246 amino
AB  - acids, Mr = 27,280 daltons, coincident with the methylase and endonuclease
AB  - genes, respectively.  These predicted values coincide with the measured
AB  - molecular weights of the purified, denatured PaeR7 endonuclease and methylase
AB  - proteins.  The first twenty amino acids from the amino-terminus of the purified
AB  - endonuclease exactly match those predicted from the DNA sequence.  Finally,
AB  - potential regulatory mechanisms for the expression of phage restriction are
AB  - described based on the properties of several PaeR7 subclones.
ER  -

TY  - JOUR
AU  - Thiaville, J.J.
AU  - Kellner, S.M.
AU  - Yuan, Y.
AU  - Hutinet, G.
AU  - Thiaville, P.C.
AU  - Jumpathong, W.
AU  - Mohapatra, S.
AU  - Brochier-Armanet, C.
AU  - Letarov, A.V.
AU  - Hillebrand, R.
AU  - Malik, C.K.
AU  - Rizzo, C.J.
AU  - Dedon, P.C.
AU  - de Crecy-Lagard, V.
TI  - Novel genomic island modifies DNA with 7-deazaguanine derivatives.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2016
SP  - E1452
EP  - E1459
VL  - 113
AB  - The discovery of approximately 20-kb gene clusters containing a family of paralogs of tRNA
AB  - guanosine transglycosylase genes, called tgtA5, alongside
AB  - 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the
AB  - hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was
AB  - established by detecting 2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in
AB  - enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative
AB  - bacteria Salmonella enterica serovar Montevideo. These modifications were absent
AB  - in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of
AB  - S. Montevideo, each lacking the gene cluster. This led us to rename the genes of
AB  - the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene
AB  - clusters were analyzed in approximately 150 phylogenetically diverse bacteria,
AB  - and the modifications were detected in DNA from other organisms containing these
AB  - clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and
AB  - Sphingopyxis alaskensis. Comparative genomic analysis shows that, in
AB  - Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus,
AB  - and the phylogenetic analysis of the TgtA5 family is consistent with widespread
AB  - horizontal gene transfer. Comparison of transformation efficiencies of modified
AB  - or unmodified plasmids into isogenic S. Montevideo strains containing or lacking
AB  - the cluster strongly suggests a restriction-modification role for the cluster in
AB  - Enterobacteriaceae. Another preQ0 derivative,
AB  - 2'-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli
AB  - bacteriophage 9g, as predicted from the presence of homologs of genes involved in
AB  - the synthesis of the archaeosine tRNA modification. These results illustrate a
AB  - deep and unexpected evolutionary connection between DNA and tRNA metabolism.
ER  -

TY  - JOUR
AU  - Thibessard, A.
AU  - Leblond, P.
TI  - Complete Genome Sequence of Streptomyces ambofaciens DSM 40697, a Paradigm for Genome Plasticity Studies.
JO  - Genome Announcements
PY  - 2016
SP  - e00470
EP  - e00416
VL  - 4
AB  - The sequence of Streptomyces ambofaciens DSM 40697 was completely determined. The genome
AB  - consists of an 8.1-Mbp linear chromosome with terminal inverted repeats of
AB  - 210 kb. Genomic islands were identified, one of which corresponds to a new
AB  - putative integrative and conjugative element (ICE) called pSAM3.
ER  -

TY  - JOUR
AU  - Thiel, T.
AU  - Pratte, B.S.
AU  - Zhong, J.
AU  - Goodwin, L.
AU  - Copeland, A.
AU  - Lucas, S.
AU  - Han, C.
AU  - Pitluck, S.
AU  - Land, M.L.
AU  - Kyrpides, N.C.
AU  - Woyke, T.
TI  - Complete genome sequence of Anabaena variabilis ATCC 29413.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 562
EP  - 573
VL  - 9
AB  - Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has
AB  - served as a model organism, with an extensive literature
AB  - extending over 40 years. The strain has three distinct nitrogenases that function
AB  - under different environmental conditions and is capable of photoautotrophic
AB  - growth in the light and true heterotrophic growth in the dark using fructose as
AB  - both carbon and energy source. While this strain was first isolated in 1964 in
AB  - Mississippi and named Anabaena flos-aquae MSU A-37, it clusters phylogenetically
AB  - with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile,
AB  - growing well at approximately 40( degrees ) C. Here we provide some additional
AB  - characteristics of the strain, and an analysis of the complete genome sequence.
ER  -

TY  - JOUR
AU  - Thiel, V.
AU  - Drautz-Moses, D.I.
AU  - Purbojati, R.W.
AU  - Schuster, S.C.
AU  - Lindemann, S.
AU  - Bryant, D.A.
TI  - Genome Sequence of Prosthecochloris sp. Strain HL-130-GSB from the Phylum Chlorobi.
JO  - Genome Announcements
PY  - 2017
SP  - e00538
EP  - e00517
VL  - 5
AB  - The genome of the green sulfur bacterium Prosthecochloris sp. strain HL-130-GSB,  isolated
AB  - from a cyanobacterial mat obtained from Hot Lake, a saline meromictic
AB  - lake in Washington, USA, comprises 2,437,774 bp in a single contig. The genome is
AB  - predicted to encode 2,565 proteins and contain 47 tRNA genes and 2 rRNA operons.
ER  -

TY  - JOUR
AU  - Thiel, V.
AU  - Hamilton, T.L.
AU  - Tomsho, L.P.
AU  - Burhans, R.
AU  - Gay, S.E.
AU  - Ramaley, R.F.
AU  - Schuster, S.C.
AU  - Steinke, L.
AU  - Bryant, D.A.
TI  - Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes).
JO  - Genome Announcements
PY  - 2014
SP  - e00860
EP  - e00814
VL  - 2
AB  - The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila
AB  - strain Yellowstone (Bacteroidetes), isolated from Octopus Spring
AB  - (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in
AB  - 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes
AB  - and 37 tRNA encoding genes and two rRNA operons.
ER  -

TY  - JOUR
AU  - Thiel, V.
AU  - Hamilton, T.L.
AU  - Tomsho, L.P.
AU  - Burhans, R.
AU  - Gay, S.E.
AU  - Schuster, S.C.
AU  - Ward, D.M.
AU  - Bryant, D.A.
TI  - Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic  Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).
JO  - Genome Announcements
PY  - 2014
SP  - e00872
EP  - e00814
VL  - 2
AB  - The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium
AB  - Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom
AB  - Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183
AB  - bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding
AB  - genes, 49 tRNA encoding genes, and 3 rRNA operons.
ER  -

TY  - JOUR
AU  - Thiel, V.
AU  - Tank, M.
AU  - Tomsho, L.P.
AU  - Burhans, R.
AU  - Gay, S.E.
AU  - Hamilton, T.L.
AU  - Schuster, S.C.
AU  - Bryant, D.A.
TI  - Draft Genome Sequence of Anoxybacillusayderensis Strain MT-Cab (Firmicutes).
JO  - Genome Announcements
PY  - 2017
SP  - e00547
EP  - e00517
VL  - 5
AB  - The draft genome of the Gram-positive spore-forming Anoxybacillus ayderensis strain MT-Cab
AB  - (Firmicutes), isolated from an enrichment culture of
AB  - Chloracidobacterium thermophilum, was sequenced and comprises 2,577,015 bp in 92
AB  - contigs. The draft genome is predicted to consist of 2,699 protein-coding genes,
AB  - 73 tRNA-coding genes, and an estimated 8 rRNA operons.
ER  -

TY  - JOUR
AU  - Thiel, V.
AU  - Tomsho, L.P.
AU  - Burhans, R.
AU  - Gay, S.E.
AU  - Schuster, S.C.
AU  - Ward, D.M.
AU  - Bryant, D.A.
TI  - Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A.
JO  - Genome Announcements
PY  - 2015
SP  - e00202
EP  - e00215
VL  - 3
AB  - The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus  ruber strain
AB  - A, isolated from a cyanobacterial enrichment culture obtained from
AB  - Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170
AB  - contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding
AB  - genes, and 2 rRNA operons.
ER  -

TY  - JOUR
AU  - Thielking, V.
TI  - Oligodeoxynucleotides with basepair mismatches as a substrate for EcoRI and EcoRV.
JO  - Ph.D. Thesis, Medizinische Hochscule Hannover, W. Germany
PY  - 1988
SP  - 1
EP  - 84
ER  -

TY  - JOUR
AU  - Thielking, V.
AU  - Alves, J.
AU  - Fliess, A.
AU  - Maass, G.
AU  - Pingoud, A.
TI  - Accuracy of the EcoRI restriction endonuclease:  Binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.
JO  - Biochemistry
PY  - 1990
SP  - 4682
EP  - 4691
VL  - 29
AB  - We have synthesized a series of 18 non palindromic oligodeoxynucleotides that
AB  - carry all possible base changes within the recognition sequence of EcoRI.
AB  - These single strands can be combined with their complementary single strands to
AB  - obtain all possible EcoRI sequences (left), or they can be combined with a
AB  - single strand containing the canonical sequence to obtain double strands with
AB  - all possible mismatches within the recognition sequence (right):
AB  - GCGCAAATTCCGCG               GCGCAAATTCCGCG
AB  - CGCGTTTAAGGCGC               CGCGCTTAAGGCGC
AB  - The rate of phosphodiester bond cleavage of these oligodeoxynucleotides by
AB  - EcoRI was determined in single-turnover experiments under normal buffer
AB  - conditions in order to find out to what extent the canonical recognition site
AB  - can be distorted and yet serve as a substrate for EcoRI.  Our results show that
AB  - oligodeoxynucleotides containing mismatch base pairs are in general more
AB  - readily attacked by EcoRI than oligodeoxynucleotides containing EcoRI sites and
AB  - that the rates of cleavage of the two complementary strands of degenerate
AB  - oligodeoxynucleotides are quite different.  We have also determined the
AB  - affinities of these oligodeoxynucleotides to EcoRI.  They are higher for
AB  - oligodeoxynucleotides carrying a mismatch within the EcoRI recognition site
AB  - than for oligodeoxynucleotides containing an EcoRI site but otherwise do not
AB  - correlate with the rate with which these oligodeoxynucleotides are cleaved by
AB  - EcoRI.  Our results allow details to be given for the probability of EcoRI
AB  - making mistakes in cleaving DNA not only in its recognition sequence but also
AB  - in sequences closely related to it.  Due to the fact that the rates of cleavage
AB  - in the two strands of a degenerate sequence generally are widely different,
AB  - these mistakes are most likely not occurring in vivo since nicked intermediates
AB  - can be repaired by DNA ligase.
ER  -

TY  - JOUR
AU  - Thielking, V.
AU  - Du Bois, S.
AU  - Eritja, R.
AU  - Guschlbauer, W.
TI  - Dam methyltransferase from Escherichia coli: Kinetic studies using modified DNA oligomers: nonmethylated substrates.
JO  - Biol. Chem.
PY  - 1997
SP  - 407
EP  - 415
VL  - 378
AB  - Steady-state kinetics of the N6-adenine Dam methyltransferase have been measured using as
AB  - substrates non-self-complementary tetradecanucleotide duplexes that contain the GATC target
AB  - sequence.  Modifications in the GATC target sequence of one or both of the strands included
AB  - substitution of guanine by hypoxanthine, thymine by uracil or 5-ethyl-uracil and adenine by
AB  - diamino-purine (2-amino-adenine).  Thermodynamic parameters for the 14-mer duplexes were also
AB  - determined.  DNA methylation of duplexes containing single dI for dG substitution of the Dam
AB  - recognition site was little perturbed compared with the canonical substrate.  Replacement of
AB  - dG residues by dI in both strands resulted in a decrease of the specificity constant.
AB  - Substitution in both strands appears to be cumulative.  Substitution of the methyl-accepting
AB  - adenine residues by 2-amino-adenine resulted in surprisingly little perturbation.  Dam
AB  - methyltransferase is rather tolerant to different substitutions.  The results show much less
AB  - spread than those for the analogous hemimethylated substrates studied previously.  The absence
AB  - of the methylation marker appears to be deleterious to the specificity of the transition state
AB  - of the active complex, while the binding of the DNA substrate to the enzyme appears to be
AB  - mostly determined by the thermodynamic stability of the DNA duplex.
ER  -

TY  - JOUR
AU  - Thielking, V.
AU  - Selent, U.
AU  - Kohler, E.
AU  - Landgraf, Z.
AU  - Wolfes, H.
AU  - Alves, J.
AU  - Pingoud, A.
TI  - Mg2+ confers DNA binding specificity to the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1992
SP  - 3727
EP  - 3732
VL  - 31
AB  - The EcoRV mutant D90A which carries an amino acid substitution in its active center does not
AB  - cleave DNA. Therefore, it is possible to perform DNA binding experiments with the EcoRV-D90A
AB  - mutant both in the absence and in the presence of Mg2+. Like wild-type EcoRV [Taylor et al.
AB  - (1991) Biochemistry 30, 8743-8753], it does not show a pronounced specificity for binding to
AB  - its recognition site in the absence of Mg2+ as judged by the appearance of multiple shifted
AB  - bands in an electrophoresis mobility shift assay with a 377-bp DNA fragment carrying a single
AB  - EcoRV recognition sequence. In the presence of Mg2+, however, only one band corresponding to a
AB  - 1:1 complex appears even with a high excess of protein over DNA. This complex most likely is
AB  - the specific one because its formation is suppressed much more effectively by a 13-bp
AB  - oligodeoxynucleotide with an EcoRV site than by a corresponding oligodeoxynucleotide without
AB  - an EcoRV site. The preferential interaction of the EcoRV-D90A mutant with specific DNA in the
AB  - presence of Mg2+ was also demonstrated directly: a 20-bp oligodeoxynucleotide with an EcoRV
AB  - site is bound with Kass=4x10/8 M-1, while a corresponding oligodeoxynucleotide without an
AB  - EcoRV site is bound with Kass<or=1x10/5 M-1. From these data it appears that Mg2+ confers DNA
AB  - binding specificity to this mutant by lowering the affinity to nonspecific sites and raising
AB  - the affinity to specific sites as compared to binding in the absence of Mg2+. It is concluded
AB  - that this is also true for wild-type EcoRV.
ER  -

TY  - JOUR
AU  - Thielking, V.
AU  - Selent, U.
AU  - Kohler, E.
AU  - Wolfes, H.
AU  - Pieper, U.
AU  - Geiger, R.
AU  - Urbanke, C.
AU  - Winkler, F.K.
AU  - Pingoud, A.
TI  - Site-directed mutagenesis studies with EcoRV restriction endonuclease to identify regions involved in recognition and catalysis.
JO  - Biochemistry
PY  - 1991
SP  - 6416
EP  - 6422
VL  - 30
AB  - Guided by the X-ray structure analysis of a crystalline EcoRV-d(GGGATATCCC)
AB  - complex (Winkler, in preparation), we have begun to identify functionally
AB  - important amino acid residues of EcoRV.  We show here that Asn70, Asp74,
AB  - Ser183, Asn185, Thr186, and Asn188 are most likely involved in the binding
AB  - and/or cleavage of the DNA, because their conservative substitution leads to
AB  - mutants of no or strongly reduced activity.  In addition, C-terminal amino acid
AB  - residues of EcoRV seem to be important for its activity, since their deletion
AB  - inactivates the enzyme.  Following the identification of three functionally
AB  - important regions, we have inspected the sequences of other restriction and
AB  - modification enzymes for homologous regions.  It was found that two restriction
AB  - enzymes that recognize similar sequences as EcoRV (DpnII and HincII), as well
AB  - as two modification enzymes (M.DpnII and, in a less apparent form, M.EcoRV),
AB  - have the sequence motif -SerGlyXXXAsnIleXSer- in common, which in EcoRV
AB  - contains the essential Ser183 and Asn188 residues.  Furthermore, the C-terminal
AB  - region, shown to be essential for EcoRV, is highly homologous to a similar
AB  - region in the restriction endonuclease SmaI.  On the basis of these findings we
AB  - propose that these restriction enzymes and to a certain extent also some of
AB  - their corresponding modification enzymes interact with DNA in a similar manner.
ER  -

TY  - JOUR
AU  - Thieme, F. et al.
TI  - Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete   genome sequence.
JO  - J. Bacteriol.
PY  - 2005
SP  - 7254
EP  - 7266
VL  - 187
AB  - The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the
AB  - causative agent of bacterial spot disease in pepper and
AB  - tomato plants, which leads to economically important yield losses. This
AB  - pathosystem has become a well-established model for studying bacterial
AB  - infection strategies. Here, we present the whole-genome sequence of the
AB  - pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10,
AB  - which comprises a 5.17-Mb circular chromosome and four plasmids. The
AB  - genome has a high G+C content (64.75%) and signatures of extensive genome
AB  - plasticity. Whole-genome comparisons revealed a gene order similar to both
AB  - Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris
AB  - and a structure completely different from Xanthomonas oryzae pv. oryzae. A
AB  - total of 548 coding sequences (12.2%) are unique to X. campestris pv.
AB  - vesicatoria. In addition to a type III secretion system, which is
AB  - essential for pathogenicity, the genome of strain 85-10 encodes all other
AB  - types of protein secretion systems described so far in gram-negative
AB  - bacteria. Remarkably, one of the putative type IV secretion systems
AB  - encoded on the largest plasmid is similar to the Icm/Dot systems of the
AB  - human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons
AB  - with other completely sequenced plant pathogens predicted six novel type
AB  - III effector proteins and several other virulence factors, including
AB  - adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
ER  -

TY  - JOUR
AU  - Thierry, A.
AU  - Perrin, A.
AU  - Boyer, J.
AU  - Fairhead, C.
AU  - Dujon, B.
AU  - Frey, B.
AU  - Schmitz, G.
TI  - Cleavage of yeast and bacteriophage T7 genomes at a single site using the rare cutter endonuclease I-SceI.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 189
EP  - 190
VL  - 19
AB  - It is obvious that the availability of rare cutter restriction endonucleases would facilitate
AB  - large scale genome mapping, cloning and sequencing projects.  Restriction endonucleases of
AB  - bacterial origin have recognition sites of 8 bp long, at most, and even when used in
AB  - combination with methylases they can produce cleavage specificities of up to 12 bp only.
AB  - Artificial endonucleases have been made by chemical modifications of either DNA binding
AB  - proteins or synthetic oligodeoxynucleotides.  Although this last strategy can, in principle,
AB  - be generalized to many sequences, cleavage occurs at low efficiency.  Cleavage of yeast and E.
AB  - coli genomic DNAs at a single predetermined site using a frequent cutter bacterial
AB  - endonuclease has recently been achieved by the Achille's heel method, an elegant three step
AB  - procedure combining the action of the lac repressor on artificially inserted sites with that
AB  - of a methylase.  We present here the first evidence for cleavage of total yeast genomic DNA at
AB  - a single predetermined site in a one step procedure using a new endonuclease, I-SceI, encoded
AB  - by a mobile group I intron of yeast mitochondria.  We further show that, although I-SceI is
AB  - extremely specific, cleavable sites can also be found in natural DNA.
ER  -

TY  - JOUR
AU  - Thijs, S.
AU  - Van Hamme, J.
AU  - Gkorezis, P.
AU  - Rineau, F.
AU  - Weyens, N.
AU  - Vangronsveld, J.
TI  - Draft Genome Sequence of Raoultella ornithinolytica TNT, a Trinitrotoluene-Denitrating and Plant Growth-Promoting Strain Isolated from  Explosive-Contaminated Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e00491
EP  - e00414
VL  - 2
AB  - We report the draft genome of Raoultella ornithinolytica TNT, a Gram-negative bacterium of the
AB  - Enterobacteriaceae isolated from military soil in Belgium.
AB  - Strain TNT uses nitrite released from trinitrotoluene (TNT) for growth and is a
AB  - potent plant growth promoter. An analysis of its 5.6-Mb draft genome will bring
AB  - insights into TNT degradation-reinforcing bioremediation applications.
ER  -

TY  - JOUR
AU  - Thion, L.
AU  - Laurine, E.
AU  - Erard, M.
AU  - Burlet-Schiltz, O.
AU  - Monsarrat, B.
AU  - Masson, J.M.
AU  - Saves, I.
TI  - The two-step cleavage activity of PI-TfuI intein endonuclease demonstrated by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 45442
EP  - 45450
VL  - 277
AB  - PI-TfuI, an intein spliced from the DNA polymerase of Thermococcus fumicolans, is a highly
AB  - specific endonuclease, whose cleavage efficiency and specificity depend on both the substrate
AB  - topology and the divalent cation used as cofactor. An open-circular intermediate was observed
AB  - during the cleavage of supercoiled DNA by PI-TfuI, suggesting a two-step cleavage of the DNA.
AB  - We characterised this nicked intermediate and, through the development of a method of analysis
AB  - of the cleavage reaction based on MALDI-tof mass spectrometry, we demonstrated that the
AB  - cleavage of DNA by PI-TfuI indeed results from two cleavage events. One step results in the
AB  - cleavage of the bottom strand, that is independent of the DNA conformation or choice of the
AB  - metal ion cofactor. A second step, which is slower, leads to the cleavage of the top strand
AB  - and governs the specific requirements of PI-TfuI concerning the essential cofactor and the DNA
AB  - topology. These two steps were shown to be independent in optimal conditions of cleavage.
AB  - These data give support to the existence of two distinct and independent active sites in the
AB  - endonuclease domain of the archaeal intein.
ER  -

TY  - JOUR
AU  - Thole, S.
AU  - Kalhoefer, D.
AU  - Voget, S.
AU  - Berger, M.
AU  - Engelhardt, T.
AU  - Liesegang, H.
AU  - Wollherr, A.
AU  - Kjelleberg, S.
AU  - Daniel, R.
AU  - Simon, M.
AU  - Thomas, T.
AU  - Brinkhoff, T.
TI  - Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life.
JO  - ISME J.
PY  - 2012
SP  - 2229
EP  - 2244
VL  - 6
AB  - Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is
AB  - known to be an effective colonizer of biotic and abiotic marine surfaces.
AB  - Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a
AB  - strong antagonist of many bacteria, including fish and mollusc pathogens. In
AB  - addition to TDA, several other secondary metabolites are produced, allowing the
AB  - mutualistic bacterium to also act as an opportunistic pathogen. Here we provide
AB  - the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395
AB  - and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney,
AB  - Australia, respectively. Despite their isolation sites from the two different
AB  - hemispheres, the genome comparison demonstrated a surprisingly high level of
AB  - synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor
AB  - differences in the genomes result from horizontal gene transfer and phage
AB  - infection. Comparison of the P. gallaeciensis genomes with those of other
AB  - roseobacters revealed unique genomic traits, including the production of
AB  - iron-scavenging siderophores. Experiments supported the predicted capacity of
AB  - both strains to grow on various algal osmolytes. Transposon mutagenesis was used
AB  - to expand the current knowledge on the TDA biosynthesis pathway in strain DSM
AB  - 17395. This first comparative genomic analysis of finished genomes of two closely
AB  - related strains belonging to one species of the Roseobacter clade revealed
AB  - features that provide competitive advantages and facilitate surface attachment
AB  - and interaction with eukaryotic hosts.The ISME Journal advance online
AB  - publication, 21 June 2012; doi:10.1038/ismej.2012.62.
ER  -

TY  - JOUR
AU  - Thomas, A.T.
AU  - Brammar, W.J.
AU  - Wilkins, B.M.
TI  - Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI.
JO  - J. Bacteriol.
PY  - 2003
SP  - 2022
EP  - 2025
VL  - 185
AB  - The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction
AB  - activity of EcoKI, leaving significant levels of
AB  - modification activity under conditions in which restriction was almost
AB  - completely prevented. The results are consistent with the hypothesis that
AB  - ArdA functions in bacterial conjugation to allow an unmodified plasmid to
AB  - evade restriction in the recipient bacterium and yet acquire cognate
AB  - modification.
ER  -

TY  - JOUR
AU  - Thomas, C.B.
AU  - Gumport, R.I.
TI  - Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 806
EP  - 815
VL  - 34
AB  - Dimeric restriction endonucleases and monomeric modification methyltransferases were long
AB  - accepted as the structural paradigm for Type
AB  - II restriction systems. Recent studies, however, have revealed an
AB  - increasing number of apparently dimeric DNA methyltransferases. Our
AB  - initial characterization of RsrI methyltransferase (M.RsrI) was consistent
AB  - with the enzyme functioning as a monomer, but, subsequently, the enzyme
AB  - crystallized as a dimer with 1500 A2 of buried surface area. This result
AB  - led us to re-examine the biochemical properties of M.RsrI. Gel-shift
AB  - studies of M.RsrI binding to DNA suggested that binding cooperativity
AB  - targets hemimethylated DNA preferentially over unmethylated DNA.
AB  - Size-exclusion chromatography indicated that the M.RsrI-DNA complex had a
AB  - size and stoichiometry consistent with a dimeric enzyme binding to the
AB  - DNA. Kinetic measurements revealed a quadratic relationship between enzyme
AB  - velocity and concentration. Site-directed mutagenesis at the dimer
AB  - interface affected the kinetics and DNA-binding of the enzyme, providing
AB  - support for a model proposing an active enzyme dimer. We also identified a
AB  - conserved motif in the dimer interfaces of the beta-class
AB  - methyltransferases M.RsrI, M.MboIIA and M2.DpnII. Taken together, these
AB  - data suggest that M.RsrI may be part of a sub-class of MTases that
AB  - function as dimers.
ER  -

TY  - JOUR
AU  - Thomas, C.B.
AU  - Scavetta, R.
AU  - Churchill, M.E.A.
AU  - Gumport, R.I.
TI  - A tale of three tails, a mutant, and a dimer: Structural studies of RsrI methyltransferase.
JO  - FASEB J.
PY  - 2002
SP  - A923
EP  - A924
VL  - 16
AB  - DNA methyltransferases are a ubiquitous class of enzymes first observed as component enzymes
AB  - of restriction-modification systems and implicated in many biological phenomena.  Recent
AB  - reports have shown them to be involved in genetic diseases such as fragile X-syndrome,
AB  - X-chromosome inactivation, gene regulation, cancer, and immunity.  RsrI DNA methyltransferase
AB  - methylates the exocyclic amino group of the central adenine of the double-stranded DNA
AB  - sequence GAATTC.  Using X-ray crystallography, we report co-crystal structures of the enzyme
AB  - with the methyl donor S-adenosylmethionine, the product S-adenosylhomocysteine, and the
AB  - inhibitor sinefungin.  The co-crystal structures reveal two ligand sites of varying affinity
AB  - and possibly by lipid raft-mediated clustering on the plasma membrane.
ER  -

TY  - JOUR
AU  - Thomas, C.B.
AU  - Scavetta, R.D.
AU  - Gumport, R.I.
AU  - Churchill, M.E.A.
TI  - Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 26094
EP  - 26101
VL  - 278
AB  - The structures of RsrI DNA methyltransferase (M.RsrI) bound to the substrate
AB  - S-adenosyl-l-methionine (AdoMet), the product
AB  - S-adenosyl-l-homocysteine (AdoHcy), the inhibitor sinefungin, as well as a
AB  - mutant apo-enzyme have been determined by x-ray crystallography. Two
AB  - distinct binding configurations were observed for the three ligands. The
AB  - substrate AdoMet adopts a bent shape that directs the activated methyl
AB  - group toward the active site near the catalytic DPPY motif. The product
AB  - AdoHcy and the competitive inhibitor sinefungin bind with a straight
AB  - conformation in which the amino acid moiety occupies a position near the
AB  - activated methyl group in the AdoMet complex. Analysis of ligand binding
AB  - in comparison with other DNA methyltransferases reveals a small, common
AB  - subset of available conformations for the ligand. The structures of M.RsrI
AB  - with the non-substrate ligands contained a bound chloride ion in the
AB  - AdoMet carboxylate-binding pocket, explaining its inhibition by chloride
AB  - salts. The L72P mutant of M.RsrI is the first DNA methyltransferase
AB  - structure without bound ligand. With respect to the wild-type protein, it
AB  - had a larger ligand-binding pocket and displayed movement of a loop
AB  - (223-227) that is responsible for binding the ligand, which may account
AB  - for the weaker affinity of the L72P mutant for AdoMet. These studies show
AB  - the subtle changes in the tight specific interactions of substrate,
AB  - product, and an inhibitor with M.RsrI and help explain how each displays
AB  - its unique effect on the activity of the enzyme.
ER  -

TY  - JOUR
AU  - Thomas, D.K.
AU  - Lone, A.G.
AU  - Selinger, L.B.
AU  - Taboada, E.N.
AU  - Uwiera, R.R.
AU  - Abbott, D.W.
AU  - Inglis, G.D.
TI  - Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts.
JO  - PLoS ONE
PY  - 2014
SP  - E88229
EP  - E88229
VL  - 9
AB  - Campylobacteriosis incited by C. jejuni is a significant enteric disease of human
AB  - beings. A person working with two reference strains of C. jejuni National
AB  - Collection of Type Cultures (NCTC) 11168 developed symptoms of severe enteritis
AB  - including bloody diarrhea. The worker was determined to be infected by C. jejuni.
AB  - In excess of 50 isolates were recovered from the worker's stool. All of the
AB  - recovered isolates and the two reference strains were indistinguishable from each
AB  - other based on comparative genomic fingerprint subtyping. Whole genome sequence
AB  - analysis indicated that the worker was infected with a C. jejuni NCTC 11168
AB  - obtained from the American Type Culture Collection; this strain (NCTC 11168-GSv)
AB  - is the genome sequence reference. After passage through the human host, major
AB  - genetic changes including indel mutations within twelve contingency loci
AB  - conferring phase variations were detected in the genome of C. jejuni. Specific
AB  - and robust single nucleotide polymorphism (SNP) changes in the human host were
AB  - also observed in two loci (Cj0144c, Cj1564). In mice inoculated with an isolate
AB  - of C. jejuni NCTC 11168-GSv from the infected person, the isolate underwent
AB  - further genetic variation. At nine loci, mutations specific to inoculated mice
AB  - including five SNP changes were observed. The two predominant SNPs observed in
AB  - the human host reverted in mice. Genetic variations occurring in the genome of C.
AB  - jejuni in mice corresponded to increased densities of C. jejuni cells associated
AB  - with cecal mucosa. In conclusion, C. jejuni NCTC 11168-GSv was found to be highly
AB  - virulent in a human being inciting severe enteritis. Host-specific mutations in
AB  - the person with enteritis occurred/were selected for in the genome of C. jejuni,
AB  - and many were not maintained in mice. Information obtained in the current study
AB  - provides new information on host-specific genetic adaptation by C. jejuni.
ER  -

TY  - JOUR
AU  - Thomas, G.A.
AU  - Kubasek, W.L.
AU  - Peticolas, W.L.
TI  - Environmentally induced conformational changes in B-type DNA:  Comparison of the conformation of the oligonucleotide d(TCGCGAATTCGCG) in solution and in its crystalline complex with the restriction nuclease EcoRI.
JO  - Biochemistry
PY  - 1989
SP  - 2001
EP  - 2009
VL  - 28
AB  - Raman spectroscopic analysis of the secondary structure of the crystalline
AB  - restriction endonuclease EcoRI, the oligonucleotide d(TCGCGAATTCGCG) in
AB  - solution, and the corresponding crystalline EcoRI-oligonucleotide complex
AB  - reveals structural differences between the complexed and uncomplexed protein
AB  - and oligonucleotide components that appear to be linked to complex formation.
AB  - Structural differences that are spectroscopically identified include (1) an
AB  - increase in the population of furanose rings adopting the C3'-endo conformation
AB  - and (2) spectroscopically observed changes in base stacking which are probably
AB  - associated with the crystallographically observed distortion of the phosphate
AB  - backbone about positions C(3)-G(4) and C(9)-G(10) and unwinding between the
AB  - symmetry-related segments GAA-TTC which make up the central recognition core
AB  - (McClarin et al., 1986).  Changes in base stacking due to distortions and
AB  - unwinding along the oligonucleotide result in differences in the base
AB  - vibrational region between spectra of the complex and the oligonucleotide in
AB  - solution.  The spectroscopic analysis indicates that the C2'-endo population is
AB  - similar for the oligonucleotide in solution and in the complex.  The additional
AB  - C3'-endo population in the complex appears to arise from the conversion of
AB  - rings adopting alternative conformations such as C1'-exo and O1'-endo.
AB  - Analysis of the vibrational bands derived from guanine indicates that the
AB  - population of guanine residues associated with furanose rings in a C2'-endo
AB  - conformation is similar for the oligonucleotide in solution and in the
AB  - crystalline complex.  This implies that the increase in C3'-endo population is
AB  - not associated with guanine residues.  Large conformational distortions such as
AB  - those observed in the crystal are not observed for the oligonucleotide in
AB  - solution.  Furthermore, Raman evidence is presented that these distortions are
AB  - not observed in either the crystal or the solution of the oligomer
AB  - d(CGCGAATTCGCG).  These data suggest that static distortions such as those
AB  - observed in the crystal are not employed for initial sequence recognition.
AB  - They appear either as a secondary response to interaction with the protein or
AB  - as transient fluctuations which exist at a very low level in solution.
ER  -

TY  - JOUR
AU  - Thomas, J.C.
AU  - Godfrey, P.A.
AU  - Feldgarden, M.
AU  - Robinson, D.A.
TI  - Draft Genome Sequences of Staphylococcus aureus Sequence Type 34 (ST34) and ST42  Hybrids.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2740
EP  - 2741
VL  - 194
AB  - Staphylococcus aureus is a major cause of antimicrobial-resistant infections of humans.
AB  - Hybrids of S. aureus, which originate from large-scale chromosomal
AB  - recombinations between parents of distinct genetic backgrounds, are of interest
AB  - from clinical and evolutionary perspectives. We present draft genome sequences of
AB  - two S. aureus hybrids of sequence type 34 (ST34) and ST42.
ER  -

TY  - JOUR
AU  - Thomas, J.C.
AU  - Kong, Y.
AU  - Sabharwal, V.
AU  - Pelton, S.I.
AU  - Pettigrew, M.M.
TI  - Streptococcus pneumoniae serotype 6C: An Intra- and Interclonal Complex Comparison.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3409
EP  - 3410
VL  - 193
AB  - We report the annotated draft genome sequences of four serotype 6C Streptococcus pneumoniae
AB  - isolates of differing genetic backgrounds.
AB  - Serotype 6C isolates are increasing in prevalence and becoming
AB  - progressively more resistant to antibiotics. As a result these strains are
AB  - likely to become more important in the near future.
ER  -

TY  - JOUR
AU  - Thomas, J.M.
AU  - Ghebrendrias, N.
AU  - Rawat, M.
TI  - Genome Sequences of Two Spore-Forming Bacteria Isolated from the Shore of Mono Lake, California.
JO  - Genome Announcements
PY  - 2017
SP  - e01742
EP  - e01716
VL  - 5
AB  - Here, we report the draft genome sequences of two Bacillus spore-forming Gram-positive
AB  - bacteria, isolated from soil on the shore of Mono Lake.
ER  -

TY  - JOUR
AU  - Thomas, M.
AU  - Davis, R.W.
TI  - Studies on the cleavage of bacteriophage lambda DNA with EcoRI restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 315
EP  - 328
VL  - 91
AB  - The five EcoRI restriction sites in bacteriophage lambda DNA have been mapped
AB  - at 0.445, 0.543, 0.656, 0.810, and 0.931 fractional lengths from the left end
AB  - of the DNA molecule.  These positions were determined electron-microscopically
AB  - by single-site cleavage of hydrogen-bonded circular lambda DNA molecules and by
AB  - cleavage of various DNA heteroduplexes between lambda DNA and DNA from well
AB  - defined lambdamutants.  The DNA lengths of the EcoRI fragments are in agreement
AB  - with their electrophoretic mobility on agarose gels but are not in agreement
AB  - with their mobilities on polyacrylamide gels.  These positions are different
AB  - from those previously published by Allet et al. (1973).  Partial cleavage of
AB  - pure lambda DNA by addition of small amounts of EcoRI endonuclease does not
AB  - lead to random cleavage between molecules.  Also, the first site cleaved is not
AB  - randomly distributed among the five sites within a molecule.  The site nearest
AB  - the right end is cleaved first about ten times more frequently than either of
AB  - the two center sites.
ER  -

TY  - JOUR
AU  - Thomas, M.C.
AU  - Arling, V.
AU  - Goji, N.
AU  - Janzen, T.W.
AU  - Duceppe, M.-O.
AU  - Mathews, A.
AU  - Carrillo, C.
AU  - Amoako, K.
TI  - First complete genome sequence of Yersinia massiliensis.
JO  - Genome Announcements
PY  - 2018
SP  - e00416
EP  - e00418
VL  - 6
AB  - Chemotherapeutic options are very limited against Mycobacterium abscessus infections.
AB  - Bedaquiline, a new anti-tuberculosis drug, is effective for the treatment of
AB  - multidrug-resistant TB. However, little data is available on bedaquiline in treating M.
AB  - abscessus infections. In this study, we reported the in vitro susceptibility profile of M.
AB  - abscessus clinical isolates to bedaquiline and investigated the potential molecular mechanisms
AB  - of decreased susceptibility. A total of 197 M. abscessus clinical isolates were collected from
AB  - sputum and bronchoalveolar fluid of patients with lung infections. Standard broth
AB  - microdilution test revealed that bedaquiline exhibited high in vitro killing activity against
AB  - M. abscessus isolates, with MIC50 of 0.062 and MIC90 of 0.125 mg/L. Whole genome sequencing
AB  - data showed that no nonsynonymous mutation occurred in atpE, the gene encoding the bedaquiline
AB  - targeted protein. However, of 6 strains with decreased susceptibility of bedaquiline
AB  - (MIC=0.5-1 mg/L), 3 strains had nonsynonymous mutations in mab_4384, the gene encoding the
AB  - repressor of efflux pump MmpS5/MmpL5. qRT-PCR analysis showed that the expression of
AB  - MmpS5/MmpL5 in the group with decreased susceptibility to bedaquiline were significantly
AB  - higher than those with medium MIC (MIC=0.125-0.5 mg/L) or low MIC group (MIC 0.062 mg/L). Two
AB  - isolates with increased MIC didnt show overexpression 48 of MmpS5/MmpL5, which couldnt be
AB  - explained by known molecular mechanisms. This is the first report showing the association of
AB  - MmpS5/MmpL5 with decreased bedaquiline susceptibility in M. abscessus clinical isolates, and
AB  - suggesting the presence of other yet-to-be identified mechanisms for decreased bedaquiline
AB  - susceptibility in M. abscessus.
ER  -

TY  - JOUR
AU  - Thomas, M.P.
AU  - Brady, R.L.
AU  - Halford, S.E.
AU  - Sessions, R.B.
AU  - Baldwin, G.S.
TI  - Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group.
JO  - Nucleic Acids Res.
PY  - 1999
SP  - 3438
EP  - 3445
VL  - 27
AB  - Following random mutagenesis of the Eco RV endonuclease, a high
AB  - proportion of the null mutants carry substitutions at Gln69. Such
AB  - mutants display reduced rates for the DNA cleavage step in the reaction
AB  - pathway, yet the crystal structures of wild-type Eco RV fail to explain
AB  - why Gln69 is crucial for activity. In this study, crystal structures
AB  - were determined for two mutants of Eco RV, with Leu or Glu at residue
AB  - 69, bound to specific DNA. The structures of the mutants are similar to
AB  - the native protein and no function can be ascribed to the side chain of
AB  - the amino acid at this locus. Instead, the structures of the mutant
AB  - proteins suggest that the catalytic defect is due to the positioning of
AB  - the main chain carbonyl group. In the enzyme-substrate complex for Eco
AB  - RV, the main chain carbonyl of Gln69 makes no interactions with
AB  - catalytic functions but, in the enzyme-product complex, it coordinates
AB  - a metal ion bound to the newly liberated 5'-phosphate. This re-
AB  - positioning may be hindered in the mutant proteins. Molecular dynamics
AB  - calculations indicate that the metal on the phosphoryl oxygen interacts
AB  - with the carbonyl group upon forming the pentavalent intermediate
AB  - during phosphodiester hydrolysis. A main chain carbonyl may thus play a
AB  - role in catalysis by Eco RV.
ER  -

TY  - JOUR
AU  - Thomas, P.
AU  - Semmler, T.
AU  - Eichhorn, I.
AU  - Lubke-Becker, A.
AU  - Werckenthin, C.
AU  - Abdel-Glil, M.Y.
AU  - Wieler, L.H.
AU  - Neubauer, H.
AU  - Seyboldt, C.
TI  - First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis.
JO  - Infect. Genet. Evol.
PY  - 2017
SP  - 287
EP  - 298
VL  - 54
AB  - Clostridium (C.) chauvoei is a Gram-positive, spore forming, anaerobic bacterium. It causes
AB  - black leg in ruminants, a typically fatal histotoxic myonecrosis. High
AB  - quality circular genome sequences were generated for the C. chauvoei type strain
AB  - DSM 7528T (ATCC 10092T) and a field strain 12S0467 isolated in Germany. The
AB  - origin of replication (oriC) was comparable to that of Bacillus subtilis in
AB  - structure with two regions containing DnaA boxes. Similar prophages were
AB  - identified in the genomes of both C. chauvoei strains which also harbored
AB  - hemolysin and bacterial spore formation genes. A CRISPR type I-B system with
AB  - limited variations in the repeat number was identified. Sporulation and
AB  - germination process related genes were homologous to that of the Clostridia
AB  - cluster I group but novel variations for regulatory genes were identified
AB  - indicative for strain specific control of regulatory events. Phylogenomics showed
AB  - a higher relatedness to C. septicum than to other so far sequenced genomes of
AB  - species belonging to the genus Clostridium. Comparative genome analysis of three
AB  - C. chauvoei circular genome sequences revealed the presence of few inversions and
AB  - translocations in locally collinear blocks (LCBs). The species genome also shows
AB  - a large number of genes involved in proteolysis, genes for glycosyl hydrolases
AB  - and metal iron transportation genes which are presumably involved in virulence
AB  - and survival in the host. Three conserved flagellar genes (fliC) were identified
AB  - in each of the circular genomes. In conclusion this is the first comparative
AB  - analysis of circular genomes for the species C. chauvoei, enabling insights into
AB  - genome composition and virulence factor variation.
ER  -

TY  - JOUR
AU  - Thomm, M.
AU  - Frey, G.
AU  - Bolton, B.J.
AU  - Laue, F.
AU  - Kessler, C.
AU  - Stetter, K.O.
TI  - MvnI: a restriction enzyme in the archaebacterium Methanococcus vannielii.
JO  - FEMS Microbiol. Lett.
PY  - 1988
SP  - 229
EP  - 234
VL  - 52
AB  - The methanogenic archaebacerium Methanococcus vannielii contains a type II
AB  - restriction endonuclease.  The enzyme was purified by a simple three-step
AB  - procedure resulting in enzyme preparations free of contaminating unspecific
AB  - nucleases.  The restriction enzyme recognizes and cleaves the sequence
AB  - 5'-CG^CG-3' (FnuDII and ThaI isoschizomer) and generates DNA fragments with
AB  - blunt ends.  Due to its purity and activity at moderate temperatures, MvnI
AB  - might be a useful alternative to FnuDII and ThaI active at 60C.
ER  -

TY  - JOUR
AU  - Thompson, A.J.
AU  - Herrin, D.L.
TI  - In vitro self-splicing reactions of the chloroplast group I intron Cr.LSU from Chlamydomonas reinhardtii and in vivo manipulation via gene-replacement.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 6611
EP  - 6618
VL  - 19
AB  - The group I intron from the chloroplast rRNA large subunit of Chlamydomonas reinhardtii
AB  - (Cr.LSU) undergoes autocatalytic splicing in vitro. Cr.LSU displays a range of reactions
AB  - typical of other group I introns. Under optimal conditions, the 5' cleavage step proceeds
AB  - rapidly, but the exon-ligation step is relatively slow, and no pH dependent hydrolysis of the
AB  - 3' splicing site occurs. A requirement for high temperature and high [Mg2+] suggests
AB  - involvement of additional splicing factors in vivo. The positions of three cyclization sites
AB  - of the free intron have been mapped; two of these sites represent reactions analogous to
AB  - 5'-splice site cleavage, whereas the third is an example of G-exchange. Cr.LSU contains an
AB  - open reading frame (ORF) potentially encoding a 163 amino acid polypeptide. ORF function has
AB  - been investigated by using chloroplast gene replacement via particle bombardment. We have
AB  - shown that the ORF can be deleted from Cr.LSU without affecting splicing in vivo and it thus
AB  - does not encode an essential splicing factor.
ER  -

TY  - JOUR
AU  - Thompson, A.J.
AU  - Yuan, X.
AU  - Kudlicki, W.
AU  - Herrin, D.L.
TI  - Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) endcoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii.
JO  - Gene
PY  - 1992
SP  - 247
EP  - 251
VL  - 119
AB  - Several group-I introns have been shown to specifically invade intron-minus alleles of the
AB  - genes that contain them. This type of intron mobility is referred to as "intron homing" and
AB  - depends on restriction endonucleases (ENases) encoded by the mobile introns. The ENase cleaves
AB  - the intron-minus allele near the site of intron insertion, thereby initiating gene conversion.
AB  - The 23S (LSU) rRNA-encoding gene (LSU) of the chloroplast genome of Chlamydomonas reinhardtii
AB  - contains a self-splicing group-I intron (CrLSU) that has a free-standing open reading frame
AB  - (ORF) of 163 codons. Translation of CrLSU intron RNA in cell-free systems produces a
AB  - polypeptide of approximately 18 kDa, the size expected for correct translation of the ORF. The
AB  - in vitro-synthesized 18-kDa protein cleaves plasmid DNA that contains a portion of LSU where
AB  - the intron normally resides, but lacking the intron itself. Cleavage by the intron-encoded
AB  - enzyme (I-CreI) occurs 5 bp and 1 bp 3' to the intron insertion site (in the 3'-exon) in the
AB  - top (/) and bottom (,) strands, respectively, resulting in 4-nt single-stranded overhangs with
AB  - 3'-OH termini. We also show that the recognition sequence of I-CreI spans the cleavage site
AB  - and is 24 bp in length (5'-CAAAACGTC,GTGA/GACAGTTTGGT).
ER  -

TY  - JOUR
AU  - Thompson, C.C.
AU  - Marin, M.A.
AU  - Dias, G.M.
AU  - Dutilh, B.E.
AU  - Edwards, R.A.
AU  - Iida, T.
AU  - Thompson, F.L.
AU  - Vicente, A.C.
TI  - Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5877
EP  - 5878
VL  - 193
AB  - Vibrio cholerae O1 Amazonia is a pathogen that was isolated from cholera-like diarrhea cases
AB  - in at least two countries, Brazil and Ghana.
AB  - Based on multilocus sequence analysis, this lineage belongs to a distinct
AB  - profile compared to strains from El Tor and classical biotypes. The
AB  - genomic analysis revealed that it contains Vibrio pathogenicity island 2
AB  - and a set of genes related to pathogenesis and fitness, such as the type
AB  - VI secretion system, present in choleragenic V. cholerae strains.
ER  -

TY  - JOUR
AU  - Thompson, R.
AU  - Hughes, S.G.
AU  - Broda, P.
TI  - Plasmid identification using specific endonucleases.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 141
EP  - 149
VL  - 133
AB  - Digestion with specific endonucleases followed by agarose gel electrophoresis
AB  - yields characteristic fragment patterns from different plasmid DNAs.  Since
AB  - even the very closely related R factors F100-1 and R6, for example, can be
AB  - distinguished this method provides a powerful test of the identity of two
AB  - plasmid DNAs.
ER  -

TY  - JOUR
AU  - Thompson, S.A.
AU  - Hall, J.E.
AU  - Baltzegar, A.D.
AU  - Yates, B.D.
AU  - Maani, E.V.
AU  - Pajaniappan, M.
AU  - Falkow, S.
AU  - Gaynor, E.C.
AU  - Mishra, A.K.
AU  - Burns, C.M.
TI  - Mutation of a predicted Campylobacter jejuni DNA methylase affects the expression of multiple genes.
JO  - Int. J. Med. Microbiol.
PY  - 2003
SP  - 21
EP  - 22
VL  - 293
AB  - In the course of studies examining temperature regulated genes of Campylobacter jejuni 81-176,
AB  - we identified an ortholog of NCTC11168 CJ1461 as a gene that is more highly expressed at 37oC
AB  - than at 42oC.  CJ1461 encodes a predicted DNA methylase that is not associated with a cognate
AB  - restriction endonuclease, implying that its cellular role is not to protect DNA from
AB  - restriction endonucleases.  Since DNA methylases may have gene regulatory functions separate
AB  - from their housekeeping roles in protecting DNA from restriction enzymes or in DNA repair, we
AB  - inactivated the CJ1461 ortholog in strain 81-176, suggesting a regulatory role for CJ1461.
AB  - Some of these proteins were shown to be temperature regulated by other methods, suggesting
AB  - that a component of the putative CJ1461 regulon was mediated by growth temperature.
AB  - Importantly, one of the proteins that was over expressed in the CJ1461 mutant was CJ0355.
AB  - CJ0355 itself is the predicted response regulator of a two component regulatory system,
AB  - although CJ0355 is an "orphan" response regulator that lacks an associated histidine kinase
AB  - sensor protein.  These studies suggest that temperature regulation of multiple genes in C.
AB  - jejuni 81-176 may be complex and can be mediated in part by DNA methylation and by an orphan
AB  - response regulator.
ER  -

TY  - JOUR
AU  - Thoms, B.
AU  - Wackernagel, W.
TI  - Expression of ultraviolet-induced restriction alleviation in Escherichia coli K-12.
JO  - Biochim. Biophys. Acta
PY  - 1983
SP  - 42
EP  - 47
VL  - 739
AB  - Ultraviolet-induced restriction alleviation is an SOS function which partially relieves the
AB  - K-12-specific DNA restriction in Escherichia coli.  Restriction alleviation is determined by
AB  - observing elevated survival of unmodified phage lambda in cells irradiated with ultraviolet
AB  - prior to infection.  We demonstrate that restriction of lambda is also relieved when log-phase
AB  - cells are irradiated as late as 50 min after adsorption of lambda.  At this time more than 60%
AB  - of the lambda DNA is already released as acid-soluble material from the cells.  Experiments
AB  - involving reextraction of lambda DNA from infected cells and a mild detergent treatment
AB  - removing adsorbed phages from the cellular surface showed that only a small specific fraction
AB  - of all lambda infections is destined to escape restriction due to restriction alleviation.
AB  - This fraction (10-20%) has a retarded mode of DNA injection (60 min or longer) after
AB  - adsorption which allows the expression of the restriction alleviation function before the
AB  - phage DNA is exposed to restriction endonucleases.  This behavior of a fraction of lambda
AB  - phages explains why the SOS function restriction alleviation could initially be discovered.
AB  - We show that the retarded mode of DNA injection is not required for another SOS function
AB  - acting on lambda DNA, the increased repair of ultraviolet-irradiated DNA (Weigle
AB  - reactivation).
ER  -

TY  - JOUR
AU  - Thoms, B.
AU  - Wackernagel, W.
TI  - UV-induced allevation of lambda restriction in Escherichia coli K-12:  Kinetics of induction and specificity of this SOS function.
JO  - Mol. Gen. Genet.
PY  - 1982
SP  - 111
EP  - 117
VL  - 186
AB  - In UV-irradiated cells of Escherichia coli K-12 a partial release of the
AB  - restriction of non-modified phage lambda is observed when the cells are recA+
AB  - lexA+.  We show here that the induction of this restriction allevation (RA)
AB  - also depends on the recBC enzyme and that the expression of RA requires protein
AB  - synthesis.  Maximum expression was reached within 60 to 90 min after
AB  - irradiation.  Experiments are presented which show that upon UV-irradiation a
AB  - signal is created which triggers the development of RA when protein synthesis
AB  - is allowed.  This signal decayed with a half-life of only a few minutes in
AB  - cells treated with chloramphenicol.  The decay kinetics were similar in uvr+
AB  - and uvrA mutants.  RA appeared to be specific for EcoKI insofar as no
AB  - allevation of lambda restriction by EcoRI, EcoRII and EcoPI occurred.  During
AB  - maximum expression of RA no gross reduction of the activities of the recBC
AB  - enzyme (exonuclease V) and the restriction endonuclease EcoKI was observed and
AB  - no new DNA modifying activity appeared in the cells.  Since, in fully expressed
AB  - cells, up to 75% of the infecting lambda DNA was converted to acid-soluble
AB  - material within 20 min after infection we suggest that only a small specific
AB  - fraction of lambda infections may undergo RA.
ER  -

TY  - JOUR
AU  - Thomson, N.R. et al.
TI  - The Complete Genome Sequence and Comparative Genome Analysis of the High Pathogenicity Yersinia enterocolitica Strain 8081.
JO  - PLoS Genet.
PY  - 2006
SP  - E206
EP  - E206
VL  - 2
AB  - The human enteropathogen, Yersinia enterocolitica, is a significant link
AB  - in the range of Yersinia pathologies extending from mild gastroenteritis
AB  - to bubonic plague. Comparison at the genomic level is a key step in our
AB  - understanding of the genetic basis for this pathogenicity spectrum. Here
AB  - we report the genome of Y. enterocolitica strain 8081 (serotype 0:8;
AB  - biotype 1B) and extensive microarray data relating to the genetic
AB  - diversity of the Y. enterocolitica species. Our analysis reveals that the
AB  - genome of Y. enterocolitica strain 8081 is a patchwork of horizontally
AB  - acquired genetic loci, including a plasticity zone of 199 kb containing an
AB  - extraordinarily high density of virulence genes. Microarray analysis has
AB  - provided insights into species-specific Y. enterocolitica gene functions
AB  - and the intraspecies differences between the high, low, and nonpathogenic
AB  - Y. enterocolitica biotypes. Through comparative genome sequence analysis
AB  - we provide new information on the evolution of the Yersinia. We identify
AB  - numerous loci that represent ancestral clusters of genes potentially
AB  - important in enteric survival and pathogenesis, which have been lost or
AB  - are in the process of being lost, in the other sequenced Yersinia
AB  - lineages. Our analysis also highlights large metabolic operons in Y.
AB  - enterocolitica that are absent in the related enteropathogen, Yersinia
AB  - pseudotuberculosis, indicating major differences in niche and nutrients
AB  - used within the mammalian gut. These include clusters directing, the
AB  - production of hydrogenases, tetrathionate respiration, cobalamin
AB  - synthesis, and propanediol utilisation. Along with ancestral gene
AB  - clusters, the genome of Y. enterocolitica has revealed species-specific
AB  - and enteropathogen-specific loci. This has provided important insights
AB  - into the pathology of this bacterium and, more broadly, into the evolution
AB  - of the genus. Moreover, wider investigations looking at the patterns of
AB  - gene loss and gain in the Yersinia have highlighted common themes in the
AB  - genome evolution of other human enteropathogens.
ER  -

TY  - JOUR
AU  - Thomson, N.R. et al.
TI  - Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.
JO  - Genome Res.
PY  - 2008
SP  - 1624
EP  - 1637
VL  - 18
AB  - We have determined the complete genome sequences of a host-promiscuous Salmonella enterica
AB  - serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar
AB  - Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates
AB  - indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis.
AB  - Significantly, the genome of S. Gallinarum has undergone extensive degradation through
AB  - deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those
AB  - identified previously in other host-adapted bacteria reveals the loss of many common
AB  - functional traits and provides insights into possible mechanisms of host and tissue
AB  - adaptation. We propose that experimental analysis in chickens and mice of S.
AB  - Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S.
AB  - Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis
AB  - of host adaptation in S. enterica.
ER  -

TY  - JOUR
AU  - Thorell, K.
AU  - Collin, B.
AU  - Hernroth, B.
AU  - Sjoling, A.
TI  - Complete Genome Sequences of Two Marine Vibrio cholerae Strains Isolated from the South Coast of Sweden.
JO  - Genome Announcements
PY  - 2016
SP  - e01118
EP  - e01116
VL  - 4
AB  - Vibrio cholerae serogroups O1 and O139 are commonly associated with diarrhea, while
AB  - non-O1-O139 strains may cause wound infections. Here, we present the genome
AB  - sequences of two V. cholerae strains isolated from blue mussels (Mytilus edulis)
AB  - collected in coastal waters of southern Sweden.
ER  -

TY  - JOUR
AU  - Thorogood, H.
AU  - Grasby, J.A.
AU  - Connolly, B.A.
TI  - Influence of the phosphate backbone on the restriction and hydrolysis of DNA by the EcoRV restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 8855
EP  - 8862
VL  - 271
AB  - A set of phosphorothioate-containing oligonucleotides based on pGACGATATCGTC, a
AB  - self-complementary dodecamer that contains the EcoRV recognition sequence (GATATC), has been
AB  - prepared.  The phosphorothioate group has been individually introduced at the central nine
AB  - phosphate positions and the two diastereomers produced at each site separated and purified.
AB  - The Km and Vmax values found for each of these modified DNA molecules with the EcoRV
AB  - restriction endonuclease have been determined and compared with those seen for the unmodified
AB  - all-phosphate-containing dodecamer.  This has enabled an evaluation of the roles that both of
AB  - the non-esterified oxygen atoms in the individual phosphates play in DNA binding and
AB  - hydrolysis by the endonuclease.  The results have also been compared with crystal structures
AB  - of the EcoRV endonuclease, complexed with an oligodeoxynucleotide, to allow further definition
AB  - of phosphate group function during substrate binding and turnover.
ER  -

TY  - JOUR
AU  - Thorogood, H.
AU  - Waters, T.R.
AU  - Parker, A.W.
AU  - Wharton, C.
AU  - Connolly, B.A.
TI  - Resonance raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
JO  - Biochemistry
PY  - 1996
SP  - 8723
EP  - 8733
VL  - 35
AB  - The resonance Raman spectra of 4-thiothymidine [4ST] have been recorded (a) in
AB  - the free deoxynucleoside form, (b) when incorporated into the single stranded
AB  - oligodeoxynucleotide d(AG[4ST]-TC), and (c) within the double-stranded self-complementary
AB  - dodecamer d(GACGA[4sT]ATCGTC).  Vibrational mode assignments of almost all the major
AB  - Raman bands observed in each spectra have been made, mainly by comparison with the published
AB  - assignments of related nucleosides and nucleotides.  Differences between the spectra were
AB  - observed, particularly when [4sT] and d(AG[4ST]TC) were compared to
AB  - d(GACGA[4ST]ATCGTC).  This is explained in terms of the variations in structure between
AB  - single- and double-stranded DNA.  Good quality spectra were obtained at
AB  - nucleotide/oligonucleotide concentrations of between 100 and 500 uM and this coupled with an
AB  - apparatus that uses small volumes (100 uL) allowed measurement of the spectrum of
AB  - d(GACGA[4ST]ATCGTC) bound to the EcoRV endonuclease.  This well characterized nuclease,
AB  - for which crystal structures are available, recognizes d(GATAT) sequences.  When this is
AB  - replaced
AB  - with d(GA[4ST]ATC), a poor substrate results, but turnover can be prevented during data
AB  - accumulation by omission of the essential cation Mg2+.  Large shifts in several of the Raman
AB  - bands were observed, and these have been related to the environment of the [4ST] base in the
AB  - protein-bound oligonucleotide as deduced from the crystal structure.  The wavenumber for the
AB  - C=S stretch vibration in free d(GACGA[4ST]ATCGTC) has been used to calculate the strength of
AB  - the Watson-Crick hydrogen bond between the sulphur atom in [4ST] and the 6-NH2 group on its
AB  - partner dA.  On binding to the enzyme, the shift in the wavenumber of the C=S stretch
AB  - indicates
AB  - this Watson-Crick hydrogen bond is weakened, in good agreement with X-ray structures.  The
AB  - advantage of using [4ST] as a resonance Raman probe is that it absorbs at 340 nM, a wavelength
AB  - where other nucleic acid and protein absorbance is minimal.  Thus the spectra obtained are
AB  - very
AB  - simple and consist of signals that arise predominantly from the thiobase alone, and this
AB  - facilitates
AB  - data interpretation.
ER  -

TY  - JOUR
AU  - Thorpe, P.H.
TI  - The DNA specificity of type I restriction and modification enzymes.
JO  - Ph.D. Thesis
PY  - 1995
SP  - 1
EP  - 176
AB  - The type I restriction and modification enzymes were the first R-M systems characterized and
AB  - provide a valuable system for studying protein-protein and protein-DNA interactions.  These
AB  - complex, multi-subunit enzymes are encoded for by three genes hsdR, M and S, although only one
AB  - of these, hsdS, is responsible for determining the specific DNA target sequence that the
AB  - enzyme recognizes.  Differences in the type I enzymes characterized have lead to their
AB  - subdivision into separate families.  The type I enzymes recognize a bipartite DNA target,
AB  - which has two, short, defined elements separated by a non-specific spacer.  For example, the
AB  - DNA target of EcoKI is 5'AACNNNNNNGTGC3'.  A series of observations and experiments have
AB  - lead to a limited understanding of how the HsdS subunit recognizes its DNA target.  Within
AB  - each family of type I enzymes HsdS subunits share regions of very similar amino acid sequence,
AB  - separating two larger regions of variable sequence.  Each variable region forms a domain that
AB  - specifies one half of the bipartite DNA target, and has been termed a Target Recognition
AB  - Domains (or TRD).  No structural information is available for the TRDs although recent crystal
AB  - structures of type II enzymes may give clues relevant to DNA interactions of type I enzymes.
AB  - A deletion analysis of the hsdS gene of EcoKI was initiated to provide information on the
AB  - roles of the conserved and variable regions.  The aim was to correlate phenotype with an
AB  - analysis of protein products, but attempts to overexpress the hsdS gene of EcoKI in a soluble
AB  - form were unsuccessful, and the HsdS subunit could not be purified.  Another approach to
AB  - studying the interaction of TRDs with their DNA targets is to compare the amino acid sequences
AB  - of those TRDs that specify the same DNA target.  Areas of sequence which are similar within
AB  - these TRDs may reflect a similarity of DNA recognition function.  From amongst the limited
AB  - number of TRDs available, there are several sequence alignments of TRDs which specify the same
AB  - DNA target.  A method based upon the Polymerase Chain Reaction was developed to amplify new
AB  - variable regions, which encode TRDs, from wild-type bacteria.  In a DNA hybridization screen
AB  - of members of the ECOR collection of wild-type Escherichia coli, Barcus et al. (1995) found
AB  - that almost half contained hsd genes.  The conserved regions of the hsd genes were used to
AB  - design primers that would amplify 5' variable regions of members of a given type I family.
AB  - Nine IA family and four IB family 5' variable regions were amplified and their DNA sequences
AB  - determined.  The information derived from these sequences illustrates both the evolutionary
AB  - diversity of the hsdS genes, and the flexible nature of the TRDs as independent target
AB  - recognizing domains.  The sequence of the N-terminal TRD from ECOR17 shares 28% identity with
AB  - those of EcoKI and StySPI.  A method dependent on the construction of hybrid hsdS genes, was
AB  - devised to find the DNA targets of these new TRD sequences.  Hybrid type I hsdS genes have
AB  - been shown to be functional for members of the IA and IC families.  Deletion derivatives of
AB  - the IA and IB family hsdS genes lacking the coding sequence for the amino-TRD were used to
AB  - insert coding sequences for alternative TRDs.  The four hybrid genes isolated all encoded
AB  - functional HsdS polypeptides conferring novel specificities.  The DNA targets of two hybrid
AB  - systems were determined, including that from ECOR17.  The sequence recognized was 5' ATR, and
AB  - not that expected (5' AAC) from its similarity to EcoKI.
ER  -

TY  - JOUR
AU  - Thorpe, P.H.
AU  - Ternent, D.
AU  - Murray, N.E.
TI  - The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 1694
EP  - 1700
VL  - 25
AB  - The type I restriction and modification (R-M) enzyme from Salmonella enterica serovar kaduna
AB  - (StySKI) recognizes the DNA sequence 5'-CGAT(N)7GTTA, an unusual target for a type I R-M
AB  - system in that it comprises two tetranucleotide components.  The amino target recognition
AB  - domain (TRD) of StySKI recognizes 5'-CGAT and shows 35% amino acid identity with the carboxy
AB  - TRD of EcoR124I which recognizes the complementary, but degenerate, sequence 5'-RTCG.
AB  - Current models predict that the amino and carboxy TRDs of the specificity subunit are in
AB  - inverted orientations within a structure with 2-fold rotational symmetry.  The complementary
AB  - target sequences recognized by the amino TRD of StySKI and the carboxy TRD of EcoR124I are
AB  - consistent with the predicted inverted positions of the TRDs.  Amino TRDs of similar amino
AB  - acid sequence have been shown to recognize the same nucleotide sequence.  The similarity
AB  - reported here, the first example of one between amino and carboxy TRDs, while consistent with
AB  - a conserved mechanism of target recognition, offers additional flexibility in the evolution of
AB  - sequence specificity by increasing the potential diversity of DNA targets for a given number
AB  - of TRDs.  StySKI identifies the first member of the IB family in Salmonella species.
ER  -

TY  - JOUR
AU  - Thorsted, P.B.
AU  - Macartney, D.P.
AU  - Akhtar, P.
AU  - Haines, A.S.
AU  - Ali, N.
AU  - Davidson, P.
AU  - Stafford, T.
AU  - Pocklington, M.J.
AU  - Pansegrau, W.
AU  - Wilkins, B.M.
AU  - Lanka, E.
AU  - Thomas, C.M.
TI  - Complete sequence of the IncPbeta plasmid R751: implications for evolution and organisation of the IncP backbone.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 969
EP  - 990
VL  - 282
AB  - The broad host range IncP plasmids are of particular interest because of
AB  - their ability to promote gene spread between diverse bacterial species. To
AB  - facilitate study of these plasmids we have compiled the complete sequence
AB  - of the IncPbeta plasmid R751. Comparison with the sequence of the
AB  - IncPalpha plasmids confirms the conservation of the IncP backbone of
AB  - replication, conjugative transfer and stable inheritance functions between
AB  - the two branches of this family. As in the IncPalpha genome the DNA of
AB  - this backbone appears to have been enriched for the GCCG/CGGC motifs
AB  - characteristic of the genome of organisms with a high G+C content, such as
AB  - P. aeruginosa, suggesting that IncPbeta plasmids have been subjected
AB  - during their evolution to similar mutational and selective forces as
AB  - IncPalpha plasmids and may have evolved in pseudomonad hosts. The IncP
AB  - genome is consistently interrupted by insertion of phenotypic markers
AB  - and/or transposable elements between oriV and trfA and between the tra and
AB  - trb operons. The R751 genome reveals a family of repeated sequences in
AB  - these regions which may form the basis of a hot spot for insertion of
AB  - foreign DNA. Sequence analysis of the cryptic transposon Tn4321 revealed
AB  - that it is not a member of the Tn21 family as we had proposed previously
AB  - from an inspection of its ends. Rather it is a composite transposon
AB  - defined by inverted repeats of a 1347 bp IS element belonging to a
AB  - recently discovered family which is distributed throughout the
AB  - prokaryotes. The central unique region of Tn4321 encodes two predicted
AB  - proteins, one of which is a regulatory protein while the other is
AB  - presumably responsible for an as yet unidentified phenotype. The most
AB  - striking feature of the IncPalpha plasmids, the global regulation of
AB  - replication and transfer by the KorA and KorB proteins encoded in the
AB  - central control operon, is conserved between the two plasmids although
AB  - there appear to be significant differences in the specificity of
AB  - repressor-operator interactions. The importance of these global regulatory
AB  - circuits is emphasised by the observation that the operator sequences for
AB  - KorB are highly conserved even in contexts where the surrounding region,
AB  - either a protein coding or intergenic sequence, has diverged considerably.
AB  - There appears to be no equivalent of the parABCDE region which in the
AB  - IncPalpha plasmids provides multimer resolution, lethality to plasmid-free
AB  - segregants and active partitioning functions. However, we found that the
AB  - continuous sector from co-ordinate 0 to 9100 bp, encoding the co-regulated
AB  - klc and kle operons as well as the central control region, could confer a
AB  - high degree of segregational stability on a low copy number test vector.
AB  - Thus R751 appears to exhibit very clearly what was first revealed by study
AB  - of the IncPalpha plasmids, namely a fully functional co-ordinately
AB  - regulated set of replication, transfer and stable inheritance functions.
ER  -

TY  - JOUR
AU  - Thrash, J.C.
AU  - Cho, J.C.
AU  - Bertagnolli, A.D.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
TI  - Genome sequence of the marine Janibacter sp. strain HTCC2649.
JO  - J. Bacteriol.
PY  - 2010
SP  - 584
EP  - 585
VL  - 193
AB  - Janibacter sp. strain HTCC2649 is a novel marine member of the Actinobacteria, family
AB  - Intrasporangiaceae, closely related to Janibacter melonis CM2104(T) and Knoellia sinensis HKI
AB  - 0119(T). The organism was isolated from a sample collected at Hydrostation S south of Bermuda
AB  - using high throughput culturing techniques. Here we present the genome sequence of Janibacter
AB  - sp. strain HTCC2649.
ER  -

TY  - JOUR
AU  - Thrash, J.C.
AU  - Cho, J.C.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
TI  - Genome sequences of strains HTCC2148 and HTCC2080, belonging to the OM60/NOR5 clade of the Gammaproteobacteria.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3842
EP  - 3843
VL  - 192
AB  - Organisms in the OM60/NOR5 clade of the Gammaproteobacteria are ubiquitous in the
AB  - world's oceans and can make up as much as 11% of bacterial cells in certain
AB  - areas. Isolated from coastal Oregon water, Gammaproteobacteria HTCC2148 and
AB  - HTCC2080 are two members of this important clade. Here we present the genome
AB  - sequences of the OM60 Gammaproteobacteria HTCC2148 and HTCC2080.
ER  -

TY  - JOUR
AU  - Thrash, J.C.
AU  - Cho, J.C.
AU  - Ferriera, S.
AU  - Johnson, J.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
TI  - Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine roseobacter genera.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5552
EP  - 5553
VL  - 192
AB  - Pelagibaca bermudensis HTCC2601(T) and Maritimibacter alkaliphilus HTCC2654(T) represent two
AB  - marine genera in the globally significant
AB  - Roseobacter clade of the Alphaproteobacteria. Here, we present the genome
AB  - sequences of these organisms, isolated from the Sargasso Sea using
AB  - dilution-to-extinction culturing, which offer insight into the genetic
AB  - basis for the metabolic and ecological diversity of this important group.
ER  -

TY  - JOUR
AU  - Thrash, J.C.
AU  - Cho, J.C.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
TI  - Genome Sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T.
JO  - J. Bacteriol.
PY  - 2010
SP  - 3549
EP  - 3550
VL  - 192
AB  - Genome sequences from the prolific Roseobacter clade in the Alphaproteobacteria are beginning
AB  - to reveal the genetic basis for the
AB  - diverse lifestyles of these organisms. Here we present the genome
AB  - sequences of Oceanicola granulosus HTCC2516(T) and Oceanicola batsensis
AB  - HTCC2597(T), two marine Roseobacter species isolated from the Sargasso Sea
AB  - using dilution-to-extinction culturing, whose genomes encode for
AB  - significant differences in metabolic potential.
ER  -

TY  - JOUR
AU  - Thrash, J.C.
AU  - Cho, J.C.
AU  - Vergin, K.L.
AU  - Morris, R.M.
AU  - Giovannoni, S.J.
TI  - Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae.
JO  - J. Bacteriol.
PY  - 2010
SP  - 2938
EP  - 2939
VL  - 192
AB  - Information on the genome content of deeply branching phyla with very few cultured members is
AB  - invaluable for expanding understanding of microbial evolution. Lentisphaera araneosa
AB  - HTCC2155(T) was isolated from the Oregon coast using dilution-to-extinction culturing. It is a
AB  - marine heterotroph found in surface and mesopelagic waters in both the Pacific and Atlantic
AB  - oceans and has the unusual property of producing a net-like matrix of secreted
AB  - exopolysaccharide. Here we present the genome sequence of L.
AB  - araneosa HTCC2155(T), importantly, one of only two sequenced members of
AB  - the phylum Lentisphaerae.
ER  -

TY  - JOUR
AU  - Thyme, S.B.
AU  - Baker, D.
AU  - Bradley, P.
TI  - Improved Modeling of Side-Chain-Base Interactions and Plasticity in Protein-DNA Interface Design.
JO  - J. Mol. Biol.
PY  - 2012
SP  - 255
EP  - 274
VL  - 419
AB  - Combinatorial sequence optimization for protein design requires libraries of discrete
AB  - side-chain conformations. The discreteness of
AB  - these libraries is problematic, particularly for long, polar side
AB  - chains, since favorable interactions can be missed. Previously, an
AB  - approach to loop remodeling where protein backbone movement is directed
AB  - by side-chain rotamers predicted to form interactions previously
AB  - observed in native complexes (termed 'motifs') was described. Here, we
AB  - show how such motif libraries can be incorporated into combinatorial
AB  - sequence optimization protocols and improve native complex
AB  - recapitulation. Guided by the motif rotamer searches, we made
AB  - improvements to the underlying energy function, increasing
AB  - recapitulation of native interactions. To further test the methods, we
AB  - carried out a comprehensive experimental scan of amino acid preferences
AB  - in the I-AniI protein-DNA interface and found that many positions
AB  - tolerated multiple amino acids. This sequence plasticity is not
AB  - observed in the computational results because of the fixed-backbone
AB  - approximation of the model. We improved modeling of this diversity by
AB  - introducing DNA flexibility and reducing the convergence of the
AB  - simulated annealing algorithm that drives the design process. In
AB  - addition to serving as a benchmark, this extensive experimental data
AB  - set provides insight into the types of interactions essential to
AB  - maintain the function of this potential gene therapy reagent.
ER  -

TY  - JOUR
AU  - Thyme, S.B.
AU  - Boissel, S.J.S.
AU  - Quadri, S.
AU  - Arshiya, N.
AU  - Tony, B.
AU  - Dean, A.
AU  - Park, R.U.
AU  - Kusak, L.
AU  - Ashworth, J.
AU  - Baker, D.
TI  - Reprogramming homing endonuclease specificity through computational design and directed evolution.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 2564
EP  - 2576
VL  - 42
AB  - Homing endonucleases (HEs) can be used to induce targeted genome modification to reduce the
AB  - fitness of pathogen vectors such as the malaria-transmitting Anopheles gambiae and to correct
AB  - deleterious mutations in genetic diseases. We describe the creation of an extensive set of HE
AB  - variants with novel DNA cleavage specificities using an integrated experimental and
AB  - computational approach. Using computational modeling and an improved selection strategy, which
AB  - optimizes specificity in addition to activity, we engineered an endonuclease to cleave in a
AB  - gene associated with Anopheles sterility and another to cleave near a mutation that causes
AB  - pyruvate kinase deficiency. In the course of this work we observed unanticipated
AB  - context-dependence between bases which will need to be mechanistically understood for
AB  - reprogramming of specificity to succeed more generally.
ER  -

TY  - JOUR
AU  - Thyme, S.B.
AU  - Jarjour, J.
AU  - Takeuchi, R.
AU  - Havranek, J.J.
AU  - Ashworth, J.
AU  - Scharenberg, A.M.
AU  - Stoddard, B.L.
AU  - Baker, D.
TI  - Exploitation of binding energy for catalysis and design.
JO  - Nature
PY  - 2009
SP  - 1300
EP  - 1304
VL  - 461
AB  - Enzymes use substrate-binding energy both to promote ground-state association and to stabilize
AB  - the reaction transition state
AB  - selectively1. The monomeric homing endonuclease I-AniI cleaves with
AB  - high sequence specificity in the centre of a 20-base-pair ( bp) DNA
AB  - target site, with the amino (N)-terminal domain of the enzyme making
AB  - extensive binding interactions with the left (-) side of the target
AB  - site and the similarly structured carboxy (C)-terminal domain
AB  - interacting with the right (+) side(2). Here we show that, despite the
AB  - approximate twofold symmetry of the enzyme-DNA complex, there is almost
AB  - complete segregation of interactions responsible for substrate binding
AB  - to the (-) side of the interface and interactions responsible for
AB  - transition-state stabilization to the (+) side. Although single
AB  - base-pair substitutions throughout the entire DNA target site reduce
AB  - catalytic efficiency, mutations in the (-) DNA half-site almost
AB  - exclusively increase the dissociation constant (K-D) and the Michaelis
AB  - constant under single-turnover conditions (K-M*), and those in the (+)
AB  - half-site primarily decrease the turnover number (k(cat)*). The
AB  - reduction of activity produced by mutations on the (-) side, but not
AB  - mutations on the (+) side, can be suppressed by tethering the substrate
AB  - to the endonuclease displayed on the surface of yeast. This dramatic
AB  - asymmetry in the use of enzyme-substrate binding energy for catalysis
AB  - has direct relevance to the redesign of endonucleases to cleave genomic
AB  - target sites for gene therapy and other applications. Computationally
AB  - redesigned enzymes that achieve new specificities on the (-) side do so
AB  - by modulating K-M*, whereas redesigns with altered specificities on the
AB  - (+) side modulate k(cat)*. Our results illustrate how classical
AB  - enzymology and modern protein design can each inform the other.
ER  -

TY  - JOUR
AU  - Thyme, S.B.
AU  - Song, Y.
AU  - Brunette, T.J.
AU  - Szeto, M.D.
AU  - Kusak, L.
AU  - Bradley, P.
AU  - Baker, D.
TI  - Massively parallel determination and modeling of endonuclease substrate specificity.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 13839
EP  - 13852
VL  - 42
AB  - We describe the identification and characterization of novel homing endonucleases using genome
AB  - database mining to identify putative target sites, followed by high throughput activity
AB  - screening in a bacterial selection system. We characterized the substrate specificity and
AB  - kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The
AB  - endonuclease specificities revealed by these experiments can be partially recapitulated using
AB  - 3D structure-based computational models. Analysis of these models together with genome
AB  - sequence data provide insights into how alternative endonuclease specificities were generated
AB  - during natural evolution.
ER  -

TY  - JOUR
AU  - Tiago, I.
AU  - Maranha, A.
AU  - Mendes, V.
AU  - Alarico, S.
AU  - Moynihan, P.J.
AU  - Clarke, A.J.
AU  - Macedo-Ribeiro, S.
AU  - Pereira, P.J.
AU  - Empadinhas, N.
TI  - Genome Sequence of Mycobacterium hassiacum DSM 44199, a Rare Source of Heat-Stable Mycobacterial Proteins.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7010
EP  - 7011
VL  - 194
AB  - Mycobacterium hassiacum is a rapidly growing mycobacterium isolated from human urine and so
AB  - far the most thermophilic among mycobacterial species. Its
AB  - thermotolerance and phylogenetic relationship to M. tuberculosis render its
AB  - proteins attractive tools for crystallization and structure-guided drug design.
AB  - We report the draft genome sequence of M. hassiacum DSM 44199.
ER  -

TY  - JOUR
AU  - Tian, B.
AU  - Moran, N.A.
TI  - Genome Sequence of Hafnia alvei bta3_1, a Bacterium with Antimicrobial Properties Isolated from Honey Bee Gut.
JO  - Genome Announcements
PY  - 2016
SP  - e00439
EP  - e00416
VL  - 4
AB  - Hafnia alvei bta3_1, a strain with antibacterial properties, was isolated from honey bee gut
AB  - and cultured under aerobic and anaerobic conditions. To explore the
AB  - potential genetic bases of its antibacterial and possible pathogenic properties,
AB  - the complete genome of this organism was sequenced and analyzed.
ER  -

TY  - JOUR
AU  - Tian, C.F.
AU  - Zhou, Y.J.
AU  - Zhang, Y.M.
AU  - Li, Q.Q.
AU  - Zhang, Y.Z.
AU  - Li, D.F.
AU  - Wang, S.
AU  - Wang, J.
AU  - Gilbert, L.B.
AU  - Li, Y.R.
AU  - Chen, W.X.
TI  - Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - 8629
EP  - 8634
VL  - 109
AB  - The rhizobium-legume symbiosis has been widely studied as the model of
AB  - mutualistic evolution and the essential component of sustainable agriculture.
AB  - Extensive genetic and recent genomic studies have led to the hypothesis that many
AB  - distinct strategies, regardless of rhizobial phylogeny, contributed to the varied
AB  - rhizobium-legume symbiosis. We sequenced 26 genomes of Sinorhizobium and
AB  - Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium
AB  - core genome is disproportionally enriched in lipid and secondary metabolism,
AB  - whereas several gene clusters known to be involved in osmoprotection and
AB  - adaptation to alkaline pH are specific to the Sinorhizobium core genome. These
AB  - features are consistent with biogeographic patterns of these bacteria.
AB  - Surprisingly, no genes are specifically shared by these soybean microsymbionts
AB  - compared with other legume microsymbionts. On the other hand, phyletic patterns
AB  - of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these
AB  - soybean microsymbionts and other rhizobia. Similar analyses with 887 known
AB  - functional genes or the whole pan genome of rhizobia revealed that only the
AB  - phyletic distribution of functional genes was consistent with the species tree of
AB  - rhizobia. Further evolutionary genetics revealed that recombination dominated the
AB  - evolution of core genome. Taken together, our results suggested that faithfully
AB  - vertical genes were rare compared with those with history of recombination
AB  - including lateral gene transfer, although rhizobial adaptations to symbiotic
AB  - interactions and other environmental conditions extensively recruited
AB  - lineage-specific shell genes under direct or indirect control through the
AB  - speciation process.
ER  -

TY  - JOUR
AU  - Tian, G.-L.
AU  - Michel, F.
AU  - Macadre, C.
AU  - Slonimski, P.P.
AU  - Lazowska, J.
TI  - Incipient mitochondrial evolution in yeasts.  II.  The complete sequence of the gene coding for cytochrome b in S. douglasii reveals the presence of both new and conserved introns and discloses major differences in the fixation of mutations in evolution.
JO  - J. Mol. Biol.
PY  - 1991
SP  - 747
EP  - 760
VL  - 218
AB  - We have determined the complete sequence of the mitochondrial gene coding for cytochrome b in
AB  - Saccharomyces douglasii.  The gene is 6310 base-pairs long and is interrupted by four introns.
AB  - The first one (1311 base-pairs) belongs to the group ID of secondary structure, contains a
AB  - fragment open reading frame with a characteristic GIY . . . YIG motif, is absent from
AB  - Saccharomyces cerevisiae and is inserted in the same site in which introns 1 and 2 are
AB  - inserted in Neurospora crassa and Podospora anserina, respectively.  The next three S.
AB  - douglasii introns are homologous to the first three introns of S. cerevisiae, are inserted at
AB  - the same positions and display various degrees of similarity ranging from an almost complete
AB  - identity (intron 2 and 4) to a moderate one (intron 3).  We have compared secondary structures
AB  - of intron RNAs, and nucleotide and amino acid sequences of cytochrome b exons and intron open
AB  - reading grames in the two Saccharomyces species.  The rules that govern fixation of mutations
AB  - in exon and intron open reading frames are different:  the relative proportion of mutations
AB  - occurring in synonymous codons is low in some introns and high in exons.  The overall
AB  - frequency of mutations in cytochrome b exons is much smaller than in nuclear genes of yeasts,
AB  - contrary to what has been found in vertebrates, where mitochrondrial mutations are more
AB  - frequent.  The divergence of the cytochrome b gene is modular: various parts of the gene have
AB  - changed with a different mode and tempo of evolution.
ER  -

TY  - JOUR
AU  - Tian, H.
AU  - Jing, C.
TI  - Genome Sequence of the Aerobic Arsenate-Reducing Bacterium Pantoea sp. Strain IMH.
JO  - Genome Announcements
PY  - 2014
SP  - e00267
EP  - e00214
VL  - 2
AB  - We here report the draft assembly for the genome of Pantoea sp. strain IMH, isolated from
AB  - arsenic-contaminated soil in Inner Mongolia, China, with the ability to aerobically reduce
AB  - arsenate to arsenite. The genome sequence will allow for the characterization of the molecular
AB  - mechanisms of arsenate reduction.
ER  -

TY  - JOUR
AU  - Tian, J.
AU  - Xu, L.
AU  - Zhang, S.
AU  - Sun, W.
AU  - Chu, X.
AU  - Wu, N.
TI  - Draft Genome Sequence of the Organophosphorus-Degrading Bacterium Pseudomonas sp. Strain 1-7, Isolated from Organophosphorus-Polluted Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e00993
EP  - e00914
VL  - 2
AB  - Pseudomonas sp. strain 1-7, isolated from organophosphorus-polluted sludge, is able to degrade
AB  - many organophosphorus compounds. Here, we report the draft genome
AB  - sequence of Pseudomonas sp. strain 1-7.
ER  -

TY  - JOUR
AU  - Tian, R.
AU  - Parker, M.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Baeshen, M.
AU  - Baeshen, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 33
EP  - 33
VL  - 10
AB  - Bradyrhizobium sp. Ai1a-2 is is an aerobic, motile, Gram-negative, non-spore-forming rod that
AB  - was isolated from an effective nitrogen fixing root nodule of Andira inermis collected from
AB  - Tres Piedras in Costa Rica. In this report we describe, for the first time, the genome
AB  - sequence information and annotation of this legume microsymbiont. The 9,029,266 bp genome has
AB  - a GC content of 62.56% with 247 contigs arranged into 246 scaffolds. The assembled genome
AB  - contains 8,482 protein-coding genes and 102 RNA-only encoding genes. This rhizobial genome was
AB  - sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
AB  - Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
ER  -

TY  - JOUR
AU  - Tian, R.
AU  - Parker, M.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Baeshen, M.N.
AU  - Baeshen, N.A.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of  Panama.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 27
EP  - 27
VL  - 10
AB  - Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming  rod that was
AB  - isolated from an effective nitrogen-fixing root nodule of Tachigali
AB  - versicolor collected in Barro Colorado Island of Panama. Here we describe the
AB  - features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft
AB  - genome sequence information and annotation. The 8,496,279 bp high-quality draft
AB  - genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding
AB  - genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part
AB  - of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
AB  - Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Tian, R.
AU  - Parker, M.
AU  - Seshadri, R.
AU  - Reddy, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Baeshen, M.N.
AU  - Baeshen, N.A.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 24
EP  - 24
VL  - 10
AB  - Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming  rod that was
AB  - isolated from an effective nitrogen-fixing root nodule of
AB  - Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the
AB  - features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft
AB  - genome sequence information and annotation. The 10,118,060 high-quality draft
AB  - genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding
AB  - genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as
AB  - part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and
AB  - Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Tian, R.C.
AU  - Huang, W.
TI  - Draft Genome Sequences of the Multiresistant Escherichia coli C20 Strain, Isolated from Domestic Chicken Gut Microbiota.
JO  - Genome Announcements
PY  - 2017
SP  - e00751
EP  - e00717
VL  - 5
AB  - Escherichia coli C20, isolated from domestic chicken gut microbiota, demonstrated multidrug
AB  - resistance to the tested antibiotics. Here, we present the draft
AB  - genomic sequences of E. coli C20, along with that of its plasmid. The final
AB  - assembly yielded a chromosome of 4,640,940 bp and plasmid of 277,380 bp, with
AB  - average coverages of 146.95-fold and 35.63-fold, respectively.
ER  -

TY  - JOUR
AU  - Tian, S.
AU  - Ali, M.
AU  - Xie, L.
AU  - Li, L.
TI  - Draft Genome Sequence of Acinetobacter johnsonii MB44, Exhibiting Nematicidal Activity against Caenorhabditis elegans.
JO  - Genome Announcements
PY  - 2016
SP  - e01772
EP  - e01715
VL  - 4
AB  - Acinetobacter johnsonii MB44 was isolated from a frost-plant-tissue sample, which showed
AB  - noteworthy nematicidal activity against the model organism Caenorhabditis
AB  - elegans. Here, we report the 3.4 Mb draft genome of A. johnsonii MB44, which will
AB  - help in understanding the molecular mechanism of its ability to infect nematodes.
ER  -

TY  - JOUR
AU  - Tian, S.-M.
AU  - Gong, Z.-Z.
AU  - Xie, W.-J.
AU  - Zheng, L.
AU  - Ruan, K.-C.
TI  - Effect of high hydrostatic pressure on activity of restriction endonucleases.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1999
SP  - 523
EP  - 526
VL  - 31
AB  - The effect of high hydrostatic pressure on the activities of type II restriction enzymes
AB  - HindIII and XbaI in digesting plasmid pSPORT1 was studied.  The endonuclease activity of
AB  - HindIII and XbaI at 37 C were gradually inhibited by increasing pressure and completely
AB  - inhibited at 200 and 180 MPa, respectively.  No obvious irreversible effect was observed for
AB  - HindIII after suffering high pressure, while a considerable irreversible inactivation was
AB  - observed for XbaI.  The standard molar volume changes for HindIII and XbaI estimated from the
AB  - inhibition of endonuclease activity at different pressures were 213 and 103 ml/mol,
AB  - respectively.  It was also concluded that pressurization did not change the substrate sequence
AB  - specificity of both HindIII and XbaI.
ER  -

TY  - JOUR
AU  - Tiba-Casas, M.R.
AU  - Lemes-Marques, E.G.
AU  - Almeida, E.A.
AU  - Soares, F.B.
AU  - Camargo, C.H.
TI  - Draft Genome Sequence of a Pathogenic Vibrio vulnificus Strain Isolated in Brazil.
JO  - Genome Announcements
PY  - 2018
SP  - e01274
EP  - e01217
VL  - 6
AB  - We describe the draft genome sequence of the clinical Vibrio vulnificus strain 03_7315,
AB  - isolated in 2016 from the blood of a diabetic patient who died of
AB  - septicemia after ingestion of seafood. The draft genome, with 4,755,588 bp
AB  - covering two chromosomes, presented 4,434 genes, 4,213 coding sequences, and 117
AB  - pseudogenes.
ER  -

TY  - JOUR
AU  - Tice, H. et al.
TI  - Complete genome sequence of Nakamurella multipartita type strain (Y-104).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 168
EP  - 175
VL  - 2
AB  - Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the
AB  - monospecific genus Nakamurella in the actinobacterial suborder
AB  - Frankineae. The nonmotile, coccus-shaped strain was isolated from activated
AB  - sludge acclimated with sugar-containing synthetic wastewater, and is capable of
AB  - accumulating large amounts of polysaccharides in its cells. Here we describe the
AB  - features of the organism, together with the complete genome sequence and
AB  - annotation. This is the first complete genome sequence of a member of the family
AB  - Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415
AB  - protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Tidona, C.A.
AU  - Schnitzler, P.
AU  - Kehm, R.
AU  - Darai, G.
TI  - Identification of the gene encoding the DNA (cytosine-5) methyltransferase of lymphocystis disease virus.
JO  - Virus Genes
PY  - 1996
SP  - 219
EP  - 229
VL  - 12
AB  - The gene encoding the DNA (cytosine-5) methyltransferase (m5C-MTase) of lymphocystis disease
AB  - virus (flounder isolate, LCDV-1) has been identified by polymerase chain reaction (PCR) using
AB  - oligonucleotide primers synthesized corresponding to different regions of the m5C-MTase gene
AB  - of frog virus 3 (FV3).  A DNA fragment of 487 bp was amplified using oligonucleotide primers
AB  - L3 and R4 which correspond to the nucleotide positions 87 to 109 and 530 to 550 of the
AB  - m5C-MTase gene of FV3, respectively.  The DNA nucleotide sequence of the PCR product was
AB  - determined by direct cycle sequencing.  The alignment of the deduced amino acid sequence
AB  - derived from the PCR product and the m5C-MTase protein of FV3 revealed a homology of 55.4%
AB  - identity and 29.1% similarity.  The amino acid sequence which was found to be significantly
AB  - homologous to the amino acid sequence deduced from the nucleotide sequence of the PCR product
AB  - was located at the amino acid position 37 to 175 of the m5C-MTase of FV3 indicating the
AB  - specificity of the amplified PCR product.  The DNA nucleotide sequence of the LCDV-1 genome
AB  - corresponding to the 5' and 3' termini of the m5C-MTase gene was determined by primer
AB  - walking.  The locus of the m5C-MTase gene of LCDV-1 was identified within the EcoRI DNA
AB  - fragment G of LCDV-1 (7.9 kbp; 0.947 to 0.034 map units).  The m5C-MTase gene of LCDV-1
AB  - comprises 684 nucleotides coding for a putative protein of 228 amino acid residues.  A high
AB  - degree of amino acid sequence homology (53.3% identity and 25.8% similarity) was detected
AB  - between the m5C-MTases of LCDV01 and FV3.
ER  -

TY  - JOUR
AU  - Tielen, P.
AU  - Wibberg, D.
AU  - Blom, J.
AU  - Rosin, N.
AU  - Meyer, A.K.
AU  - Bunk, B.
AU  - Schobert, M.
AU  - Tupker, R.
AU  - Schatschneider, S.
AU  - Ruckert, C.
AU  - Albersmeier, A.
AU  - Goesmann, A.
AU  - Vorholter, F.J.
AU  - Jahn, D.
AU  - Puhler, A.
TI  - Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection.
JO  - Genome Announcements
PY  - 2014
SP  - e01174
EP  - e01113
VL  - 2
AB  - Pseudomonas aeruginosa is a notable nosocomial pathogen causing severe chronic infections.
AB  - Here we present the draft genome sequence of P. aeruginosa MH27,
AB  - isolated from a patient with a chronic hospital-acquired catheter-associated
AB  - urinary tract infection. The 7.1-Mb genome sequence organized in 24 scaffolds
AB  - contributes to the understanding of biofilm formation and antibiotic resistance.
ER  -

TY  - JOUR
AU  - Tikchonenko, T.I.
AU  - Karamov, E.V.
AU  - Zavizion, B.A.
AU  - Naroditsky, B.S.
TI  - EcoRI* activity:  Enzyme modification or activation of accompanying endonuclease?
JO  - Gene
PY  - 1978
SP  - 195
EP  - 212
VL  - 4
AB  - A study has been made of the factors and mechanism leading to appearance of the
AB  - so-called EcoRI* activity described by Polisky et al. (1975) in the restrictase
AB  - EcoRI preparations.  The preparations of purified restrictase EcoRI,
AB  - precipitated at 0.9 ammonium sulphate saturation, as well as that obtained
AB  - using standard techniques have been found to contain an admixture of an
AB  - endonuclease which at neutral pH and high ionic strength multiply cleaves those
AB  - DNAs which normally have only one recognition site for EcoRI.  Under the
AB  - standard conditions for EcoRI digestion this activity is found only when large
AB  - amounts of freshly isolated enzyme are added to the incubation mixture and it
AB  - is sharply enhanced by replacement of Mg2+ with Mn2+.  The number and size of
AB  - DNa fragments produced under such conditions practically do not differ from
AB  - those found under the so-called EcoRI* conditions, that is for alkaline pH
AB  - values and low ionic strength.  The optimum incubation mixture for the EcoRI*
AB  - activity has been found to be 10 mM Tris-HCl buffer (pH 8.8) + 2 mM Mn2+.
AB  - Similar activity is induced also by addition to EcoRI solution of 40-50%
AB  - glycerol or a number of organic solvents (dimethylacetamide (DMA),
AB  - dimethylformamide (DMF), dimethylsulphoxide (DMSO), sulphalane (SP)) in
AB  - concentrations from 1 to 6%.  The EcoRI* activity induced by 50% glycerol or at
AB  - alkaline pH values and low ionic strength is suppressed or sharply inhibited by
AB  - 2-3 mM parachloromercuribenzoate (PCMB), while EcoRI is not sensitive to this
AB  - agent.  The DNA fragments cleaved by EcoRI* have cohesive termini and can be
AB  - easily ligated.  It is suggested that the EcoRI* activity can be due not only
AB  - (or largely not) to modification of the "recognizing capacity" of the EcoRI
AB  - restrictase but to activation of a latent specific endonuclease which is
AB  - present in the restrictase preparation as an impurity.
ER  -

TY  - JOUR
AU  - Tikhonova, T.N.
AU  - Malyuta, S.S.
AU  - Nesterenko, V.F.
TI  - DNA-methyltransferases from different Bacillus subtilis and Bacillus natto strains.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1986
SP  - 40
EP  - 44
VL  - 11
AB  - DNA-methyltransferase activity has been detected in some Bacillus subtilis and Bacillus natto
AB  - strains.  Two strains of Bacillus subtilis exhibited DNA-cytosine methyltransferase activity,
AB  - and the strains of Bacillus natto exhibited DNA-adenine methyltransferase activity.  A
AB  - possible effect of DNA-methyltransferase specificity on transformation efficiency is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Tilghman, S.M.
TI  - DNA methylation: A phoenix rises.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 8761
EP  - 8762
VL  - 90
AB  - A report in this issue of the Proceedings by Baylin and his colleagues describes a potential
AB  - new way in which DNA methylation affects the physiology of the mammalian cell. The authors
AB  - begin from the observation that transformed cells often display higher overall levels of DNA
AB  - methylation, as well as increased levels of the hemimethylase, DNA methyltransferase. The
AB  - preferred substrate for this enzyme is double-stranded DNA which is hemimethylated on the
AB  - cytosine residue of the dinucleotide CpG. When the investigators introduced extra copies of
AB  - the enzyme into nontumorigenic NIH 3T3 mouse fibroblasts by gene transfer, the cells acquired
AB  - tumorigenic properties, such as loss of contact inhibition, growth in soft agar, and the
AB  - ability to form tumors in nude mice.
ER  -

TY  - JOUR
AU  - Timar, E.
AU  - Groma, G.
AU  - Kiss, A.
AU  - Venetianer, P.
TI  - Changing the recognition specificity of a DNA-methyltransferase by in vitro evolution.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3898
EP  - 3903
VL  - 32
AB  - The gene coding for the SinI DNA-methyltransferase, a modification enzyme able to recognize
AB  - and methylate the internal cytosine of the GGWCC sequence, was subjected to in vitro
AB  - mutagenesis, DNA-shuffling and a strong selection for relaxed GGNCC recognition specificity.
AB  - As a result of this in vitro evolution experiment, a mutant gene with the required phenotype
AB  - was selected. The mutant SinI methyltransferase carried five amino acid substitutions. None of
AB  - these was found in the 'variable region' that were thought to be responsible for sequence
AB  - specificity. Three were located near the N-terminal end, preceding the first conserved
AB  - structural motif of the enzyme; two were found between conserved motifs VI and VII. A clone
AB  - engineered to carry out only the latter two replacements (L214S and Y229H) displays relaxed
AB  - recognition specificity similar to that of the parental mutant, whereas the clone carrying
AB  - only the N-terminal replacements showed a much weaker change in recognition specificity. The
AB  - enzyme with two internal mutations was purified and characterized. Its catalytic activity
AB  - (kcat/Km) was  5-fold lower towards GGWCC and 20-fold higher towards GGSCC than that of the
AB  - wild-type enzyme.
ER  -

TY  - JOUR
AU  - Timar, E.
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - In vivo DNA protection by relaxed-specificity SinI DNA methyltransferase variants.
JO  - J. Bacteriol.
PY  - 2008
SP  - 8003
EP  - 8008
VL  - 190
AB  - The SinI DNA methyltransferase, a component of the SinI restriction-modification system,
AB  - recognizes the sequence GG(A/T)CC and
AB  - methylates the inner cytosine to produce 5-methylcytosine. Previously
AB  - isolated relaxed-specificity mutants of the enzyme also methylate, at a
AB  - lower rate, GG(G/C)CC sites. In this work we tested the capacity of the
AB  - mutant enzymes to function in vivo as the counterpart of a restriction
AB  - endonuclease, which can cleave either site. The viability of Escherichia
AB  - coli cells carrying recombinant plasmids with the mutant methyltransferase
AB  - genes and expressing the GGNCC-specific Sau96I restriction endonuclease
AB  - from a compatible plasmid was investigated. The sau96IR gene on the latter
AB  - plasmid was transcribed from the araBAD promoter, allowing tightly
AB  - controlled expression of the endonuclease. In the presence of low
AB  - concentrations of the inducer arabinose, cells synthesizing the N172S or
AB  - the V173L mutant enzyme displayed increased plating efficiency relative to
AB  - cells producing the wild-type methyltransferase, indicating enhanced
AB  - protection of the cell DNA against the Sau96I endonuclease. Nevertheless,
AB  - this protection was not sufficient to support long-term survival in the
AB  - presence of the inducer, which is consistent with incomplete methylation
AB  - of GG(G/C)CC sites in plasmid DNA purified from the N172S and V173L
AB  - mutants. Elevated DNA ligase activity was shown to further increase
AB  - viability of cells producing the V173L variant and Sau96I endonuclease.
ER  -

TY  - JOUR
AU  - Timinskas, A.
AU  - Butkus, V.
AU  - Janulaitis, A.
TI  - Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases.  Classification of all DNA methyltransferases.
JO  - Gene
PY  - 1995
SP  - 3
EP  - 11
VL  - 157
AB  - Two additional conserved motifs (CM), CMIs and CMIII, have been found in addition to
AB  - well-known CMI and CMII within the primary amino acid sequences of almost all m6A- and
AB  - m4C-methyltransferases (MTases).  The boundaries of all four CM were defined and their
AB  - consensus sequences characteristic both for different classes, as well as for all N-MTases,
AB  - were derived.  Some regular deviations at fixed positions of the consensus sequences CMIs, CMI
AB  - and CMiI, typical for separate classes of N-MTases, were presumed to correlate.  A possible
AB  - structural basis for the supposed interregional correlations is discussed and experiments for
AB  - verification of the assumed interactions between CM are suggested.  A classification scheme
AB  - for all N-MTases is provided.
ER  -

TY  - JOUR
AU  - Timko, J.
AU  - Horwitz, A.H.
AU  - Zelinka, J.
AU  - Wilcox, G.
TI  - Characterization of a site-specific restriction endonuclease from Streptomyces aureofaciens.
JO  - J. Bacteriol.
PY  - 1981
SP  - 873
EP  - 877
VL  - 145
AB  - A new type II sequence-specific restriction endonuclease, SauI, was isolated
AB  - from Streptomyces aureofaciens IKA18/4.  The purified enzyme was free of
AB  - contaminating exonuclease and phosphatase activities.  SauI cleaved lambda DNA
AB  - at two sites, but did not cleave pBR322, simian virus 40, or PhiX174 DNA.  SauI
AB  - recognized the septanucleotide sequence 5'-CC^TNAGG-3' and cleaved at the
AB  - position indicated by the arrow, producing a trinucleotide 5'-terminal
AB  - extension.
ER  -

TY  - JOUR
AU  - Timko, J.
AU  - Matuskova, M.
AU  - Zelinkova, E.
AU  - Zelinka, J.
TI  - Specific endonucleases in Streptomyces aureofaciens.
JO  - Folia Microbiol. (Praha)
PY  - 1978
SP  - 243
EP  - 245
VL  - 23
AB  - Two strains of Streptomyces aureofaciens were found to contain restriction
AB  - endodeoxynucleases; S. aureofaciens TKA 18/4 contains SauI which splits lambda
AB  - DNA into three fragments, S. aureofaciens IKA 22201 contains SauI which splits
AB  - lambda DNA into more than 15 fragments.
ER  -

TY  - JOUR
AU  - Timko, J.
AU  - Sisova, M.
AU  - Ugorcakova, J.
AU  - Zelinka, J.
TI  - Restriction endonuclease SauI from Streptomyces aureofaciens - some physical and chemical properties.
JO  - Biologia (Bratisl)
PY  - 1988
SP  - 681
EP  - 689
VL  - 43
AB  - Some physical and chemical properties of restriction endonuclease SauI, which
AB  - was isolated from Streptomyces aureofaciens IKA 18/4, were studied.  The
AB  - effects of divalent ions, monovalent ions, pH and temperature on enzyme
AB  - activity were determined.  For cleavage of substrate DNA by endonuclease SauI
AB  - the optimal reaction mixture was determined as: 10 mM Tris-HCl, pH 7.5, 10 mM
AB  - MgCl2, 75 mM NaCl at 37C.
ER  -

TY  - JOUR
AU  - Timko, J.
AU  - Turna, J.
AU  - Zelinka, J.
TI  - Site-specific restriction endonuclease SauBMKI from Streptomyces aureofaciens.
JO  - Metabolism and Enzymology of Nucleic Acids
PY  - 1987
SP  - 107
EP  - 118
VL  - 6
AB  - Type II restriction endonucleases have been isolated from many bacteria
AB  - including Streptomycetes and their specificities have been characterized
AB  - (Roberts, 1985).  From Streptomyces aureofaciens restriction endonucleases SauI
AB  - (Timko et al., 1981) and Sau3239I (Gasperik et al., 1983; Simbochova et al.,
AB  - 1986) have been isolated and characterized.  In this paper we describe a new
AB  - restriction endonuclease, SauBMKI from Streptomyces aureofaciens, strain BM-K,
AB  - producing about 2500 micrograms of CTC per ml.
ER  -

TY  - JOUR
AU  - Timko, J.
AU  - Zelinka, J.
AU  - Wilcox, G.
TI  - Properties of the restriction endonuclease Saul.
JO  - Metabolism and Enzymology of Nucleic Acids
PY  - 1982
SP  - 319
EP  - 324
VL  - 4
AB  - None
ER  -

TY  - JOUR
AU  - Timme, R.E.
AU  - Allard, M.W.
AU  - Luo, Y.
AU  - Strain, E.
AU  - Pettengill, J.
AU  - Wang, C.
AU  - Li, C.
AU  - Keys, C.E.
AU  - Zheng, J.
AU  - Stones, R.
AU  - Wilson, M.R.
AU  - Musser, S.M.
AU  - Brown, E.W.
TI  - Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5994
EP  - 5995
VL  - 194
AB  - Salmonella enterica subsp. enterica serovar Enteritidis is a common food-borne pathogen, often
AB  - associated with shell eggs and poultry. Here, we report draft
AB  - genomes of 21 S. Enteritidis strains associated with or related to the U.S.-wide
AB  - 2010 shell egg recall. Eleven of these genomes were from environmental isolates
AB  - associated with the egg outbreak, and 10 were reference isolates from previous
AB  - years, unrelated to the outbreak. The whole-genome sequence data for these 21
AB  - human pathogen strains are being released in conjunction with the newly formed
AB  - 100K Genome Project.
ER  -

TY  - JOUR
AU  - Timme, R.E.
AU  - Pettengill, J.B.
AU  - Allard, M.W.
AU  - Strain, E.
AU  - Barrangou, R.
AU  - Wehnes, C.
AU  - Van Kessel, J.S.
AU  - Karns, J.S.
AU  - Musser, S.M.
AU  - Brown, E.W.
TI  - Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.
JO  - Genome Biol. Evol.
PY  - 2013
SP  - 2109
EP  - 2123
VL  - 5
AB  - The enteric pathogen Salmonella enterica is one of the leading causes of
AB  - foodborne illness in the world. The species is extremely diverse, containing more
AB  - than 2,500 named serovars that are designated for their unique antigen characters
AB  - and pathogenicity profiles-some are known to be virulent pathogens, while others
AB  - are not. Questions regarding the evolution of pathogenicity, significance of
AB  - antigen characters, diversity of clustered regularly interspaced short
AB  - palindromic repeat (CRISPR) loci, among others, will remain elusive until a
AB  - strong evolutionary framework is established. We present the first large-scale S.
AB  - enterica subsp. enterica phylogeny inferred from a new reference-free k-mer
AB  - approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes.
AB  - The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced)
AB  - reveals two major lineages, each with many strongly supported sublineages. One of
AB  - these lineages is the S. Typhi group; well nested within the phylogeny.
AB  - Lineage-through-time analyses suggest there have been two instances of
AB  - accelerated rates of diversification within the subspecies. We also found that
AB  - antigen characters and CRISPR loci reveal different evolutionary patterns than
AB  - that of the phylogeny, suggesting that a horizontal gene transfer or possibly a
AB  - shared environmental acquisition might have influenced the present character
AB  - distribution. Our study also shows the ability to extract reference-free SNPs
AB  - from a large set of genomes and then to use these SNPs for phylogenetic
AB  - reconstruction. This automated, annotation-free approach is an important step
AB  - forward for bacterial disease tracking and in efficiently elucidating the
AB  - evolutionary history of highly clonal organisms.
ER  -

TY  - JOUR
AU  - Timms, A.R.
AU  - Cambray-Young, J.
AU  - Scott, A.E.
AU  - Petty, N.K.
AU  - Connerton, P.L.
AU  - Clarke, L.
AU  - Seeger, K.
AU  - Quail, M.
AU  - Cummings, N.
AU  - Maskell, D.J.
AU  - Thomson, N.R.
AU  - Connerton, I.F.
TI  - Evidence for a lineage of virulent bacteriophages that target Campylobacter.
JO  - BMC Genomics
PY  - 2010
SP  - 214
EP  - 214
VL  - 11
AB  - Background: Our understanding of the dynamics of genome stability versus gene flux within
AB  - bacteriophage lineages is limited. Recently,
AB  - there has been a renewed interest in the use of bacteriophages as
AB  - 'therapeutic' agents; a prerequisite for their use in such therapies is
AB  - a thorough understanding of their genetic complement, genome stability
AB  - and their ecology to avoid the dissemination or mobilisation of phage
AB  - or bacterial virulence and toxin genes. Campylobacter, a food-borne
AB  - pathogen, is one of the organisms for which the use of bacteriophage is
AB  - being considered to reduce human exposure to this organism.
AB  - Results: Sequencing and genome analysis was performed for two
AB  - Campylobacter bacteriophages. The genomes were extremely similar at the
AB  - nucleotide level (>= 96%) with most differences accounted for by novel
AB  - insertion sequences, DNA methylases and an approximately 10 kb
AB  - contiguous region of metabolic genes that were dissimilar at the
AB  - sequence level but similar in gene function between the two phages.
AB  - Both bacteriophages contained a large number of radical
AB  - S-adenosylmethionine (SAM) genes, presumably involved in boosting host
AB  - metabolism during infection, as well as evidence that many genes had
AB  - been acquired from a wide range of bacterial species. Further
AB  - bacteriophages, from the UK Campylobacter typing set, were screened for
AB  - the presence of bacteriophage structural genes, DNA methylases, mobile
AB  - genetic elements and regulatory genes identified from the genome
AB  - sequences. The results indicate that many of these bacteriophages are
AB  - related, with 10 out of 15 showing some relationship to the sequenced
AB  - genomes.
AB  - Conclusions: Two large virulent Campylobacter bacteriophages were
AB  - found to show very high levels of sequence conservation despite
AB  - separation in time and place of isolation. The bacteriophages show
AB  - adaptations to their host and possess genes that may enhance
AB  - Campylobacter metabolism, potentially advantaging both the
AB  - bacteriophage and its host. Genetic conservation has been shown to
AB  - extend to other Campylobacter bacteriophages, forming a highly
AB  - conserved lineage of bacteriophages that predate upon campylobacters
AB  - and indicating that highly adapted bacteriophage genomes can be stable
AB  - over prolonged periods of time.
ER  -

TY  - JOUR
AU  - Tindall, B.J. et al.
TI  - Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).
JO  - Standards in Genomic Sciences
PY  - 2009
SP  - 270
EP  - 277
VL  - 1
AB  - Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus
AB  - Halomicrobium. It is of phylogenetic interest because of its
AB  - isolated location within the large euryarchaeal family Halobacteriaceae. H.
AB  - mukohataei is an extreme halophile that grows essentially aerobically, but can
AB  - also grow anaerobically under a change of morphology and with nitrate as electron
AB  - acceptor. The strain, whose genome is described in this report, is a free-living,
AB  - motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in
AB  - Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S
AB  - rRNA that differ from each other by up to 9%. Here we describe the features of
AB  - this organism, together with the complete genome sequence and annotation. This is
AB  - the first completed genome sequence from the poorly populated genus
AB  - Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with
AB  - its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of
AB  - Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Tindall, B.J. et al.
TI  - Complete genome sequence of Meiothermus ruber type strain (21T).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 26
EP  - 36
VL  - 3
AB  - Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus
AB  - Meiothermus. This thermophilic genus is of special interest, as its members share relatively
AB  - low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary
AB  - lineage from members of the genus Thermus, from which they can generally be distinguished by
AB  - their slightly lower temperature optima. The temperature related split is in accordance with
AB  - the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the
AB  - low-temperature group. This is the first completed genome sequence of the genus Meiothermus
AB  - and only the third genome sequence to be published from a member of the family Thermaceae. The
AB  - 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the
AB  - Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Tippelt, A.
AU  - Albersmeier, A.
AU  - Brinkrolf, K.
AU  - Ruckert, C.
AU  - Fernandez-Natal, I.
AU  - Soriano, F.
AU  - Tauch, A.
TI  - Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia  Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e01211
EP  - e01214
VL  - 2
AB  - Corynebacterium ureicelerivorans is an opportunistic pathogen with a lipophilic lifestyle and
AB  - an exceptionally high urease activity. The genome sequence of the
AB  - type strain revealed that lipophilism is caused by the lack of a fatty acid
AB  - synthase gene. The ureABCEFGD genes are similar to the urease gene region of
AB  - Corynebacterium glucuronolyticum.
ER  -

TY  - JOUR
AU  - Tippelt, A.
AU  - Mollmann, S.
AU  - Albersmeier, A.
AU  - Jaenicke, S.
AU  - Ruckert, C.
AU  - Tauch, A.
TI  - Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849.
JO  - Genome Announcements
PY  - 2014
SP  - e00845
EP  - e00814
VL  - 2
AB  - The complete chromosomal sequence of the type strain Corynebacterium atypicum DSM 44849
AB  - comprises 2,311,380 bp. A functional annotation revealed the presence of
AB  - genes involved in the synthesis and export of mycolic acids and in trehalose
AB  - corynomycolate biosynthesis, supporting the view that the cell envelope of C.
AB  - atypicum contains mycolic acids.
ER  -

TY  - JOUR
AU  - Tirumalai, M.R.
AU  - Rastogi, R.
AU  - Zamani, N.
AU  - O'Bryant-Williams, E.
AU  - Allen, S.
AU  - Diouf, F.
AU  - Kwende, S.
AU  - Weinstock, G.M.
AU  - Venkateswaran, K.J.
AU  - Fox, G.E.
TI  - Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores.
JO  - PLoS ONE
PY  - 2013
SP  - e66012
EP  - e66012
VL  - 8
AB  - The spores of several Bacillus species, including Bacillus pumilus SAFR-032 and
AB  - B. safensis FO-36b, which were isolated from the spacecraft assembly facility at
AB  - NASA's Jet Propulsion Laboratory, are unusually resistant to UV radiation and
AB  - hydrogen peroxide. In order to identify candidate genes that might be associated
AB  - with these resistances, the whole genome of B. pumilus SAFR-032, and the draft
AB  - genome of B. safensis FO-36b were compared in detail with the very closely
AB  - related type strain B. pumilus ATCC7061(T). 170 genes are considered
AB  - characteristic of SAFR-032, because they are absent from both FO-36b and
AB  - ATCC7061(T). Forty of these SAFR-032 characteristic genes are entirely unique
AB  - open reading frames. In addition, four genes are unique to the genomes of the
AB  - resistant SAFR-032 and FO-36b. Fifty three genes involved in spore coat
AB  - formation, regulation and germination, DNA repair, and peroxide resistance, are
AB  - missing from all three genomes. The vast majority of these are cleanly deleted
AB  - from their usual genomic context without any obvious replacement. Several DNA
AB  - repair and peroxide resistance genes earlier reported to be unique to SAFR-032
AB  - are in fact shared with ATCC7061(T) and no longer considered to be promising
AB  - candidates for association with the elevated resistances. Instead, several
AB  - SAFR-032 characteristic genes were identified, which along with one or more of
AB  - the unique SAFR-032 genes may be responsible for the elevated resistances. These
AB  - new candidates include five genes associated with DNA repair, namely, BPUM_0608 a
AB  - helicase, BPUM_0652 an ATP binding protein, BPUM_0653 an endonuclease, BPUM_0656
AB  - a DNA cytosine-5- methyltransferase, and BPUM_3674 a DNA helicase. Three of these
AB  - candidate genes are in immediate proximity of two conserved hypothetical
AB  - proteins, BPUM_0654 and BPUM_0655 that are also absent from both FO-36b and
AB  - ATCC7061(T). This cluster of five genes is considered to be an especially
AB  - promising target for future experimental work.
ER  -

TY  - JOUR
AU  - Tisa, L.S. et al.
TI  - Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina.
JO  - Genome Announcements
PY  - 2015
SP  - e00889
EP  - e00815
VL  - 3
AB  - Frankia sp. strain DC12, isolated from root nodules of Datisca cannabina, is a member of the
AB  - fourth lineage of Frankia, which is unable to reinfect actinorhizal
AB  - plants. Here, we report its 6.88-Mbp high-quality draft genome sequence, with a
AB  - G+C content of 71.92% and 5,858 candidate protein-coding genes.
ER  -

TY  - JOUR
AU  - Tishchenko, E.N.
AU  - Dubrovnaya, O.V.
TI  - Methyltransferases of plants.
JO  - Biopol. Kletka
PY  - 2005
SP  - 463
EP  - 472
VL  - 21
AB  - In the review the current data on the plant cytosine-C5-DNA-methyltransferases
AB  - (methyltransferase) are summarized.  Three different classes of these enzymes - Snmt1/MET1,
AB  - Dnmt3 and CMT are described. The proposed function, dealing with maintenance and de novo
AB  - methylation of cytosine residues in symmetric and asymmetric motifs of DNA, is under
AB  - discussion.
ER  -

TY  - JOUR
AU  - Titeeva, G.R.
AU  - Vinogradov, S.V.
AU  - Berlin, Y.A.
TI  - Specific features of the restriction endonuclease BamHI interaction with oligodeoxynucleotides.
JO  - Bioorg. Khim.
PY  - 1986
SP  - 640
EP  - 646
VL  - 12
AB  - Interaction of the restriction endonuclease BamHI with a series of synthetic
AB  - oligodeoxynucleotides containing the restriction site has been studied.  The
AB  - enzyme is shown to specifically cut the BamHI site in hexanucleotide (I) and in
AB  - non-selfcomplementary deca- and octanucleotides (II)-(IV).  The data obtained
AB  - led to the conclusion that BamHI reacts with duplex structures, while playing
AB  - an important role in their stabilization.  In 14-mer (V) BamHI cuts a
AB  - non-standard half-site GAA to yield the 5'-terminal tri- (rather than hepta-)
AB  - nucleotide.  Hypothetical mechanisms of the process are discussed basing on
AB  - conception of the role of higher DNA structures in the interaction with
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Titeeva, G.R.
AU  - Vinogradov, S.V.
AU  - Berlin, Y.A.
TI  - Complexes of the phage single-stranded DNA with synthetic oligodeoxynucleotides and their interaction with DNA polymerase and restriction endonucleases.
JO  - Bioorg. Khim.
PY  - 1986
SP  - 1484
EP  - 1491
VL  - 12
AB  - Hybridization of synthetic oligodeoxynucleotides with single-stranded phage
AB  - M13mp2 DNA has been studied in terms of temperature, ionic strength,
AB  - oligonucleotide molar excess and chain length, and DNA secondary structure.
AB  - Combination of two decadeoxynucleotides corresponding to a nicked eicosamer
AB  - (composite primer) was found to be efficient in the template-directed DNA
AB  - polymerase-catalyzed chain elongation, where both decamers separately failed.
AB  - Circular SS DNA was specifically linearized by BamHI cleavage of a SS DNA -
AB  - tetradecadeoxynucleotide duplex.
ER  -

TY  - JOUR
AU  - Titheradge, A.J.
AU  - King, J.
AU  - Ryu, J.
AU  - Murray, N.E.
TI  - Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 4195
EP  - 4205
VL  - 29
AB  - Current genetic and molecular evidence places all the known type I restriction and
AB  - modification systems of Escherichia coli and Salmonella enterica into one of four discrete
AB  - families: type IA, IB, IC or ID. StySBLI is the founder member of the ID family. Similarities
AB  - of coding sequences have identified restriction systems in E.coli and Klebsiella pneumoniae as
AB  - probable members of the type ID family. We present complementation tests that confirm the
AB  - allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of
AB  - the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a
AB  - target recognition domain (TRD). Consistent with two TRDs, StySBLI was shown to recognise a
AB  - bipartite target sequence, but one in which the adenine residues that are the substrates for
AB  - methylation are separated by only 6 bp. Implications of family relationships are discussed and
AB  - evidence is presented that extends the family affiliations identified in enteric bacteria to a
AB  - wide range of other genera.
ER  -

TY  - JOUR
AU  - Titheradge, A.J.B.
AU  - Ternent, D.
AU  - Murray, N.E.
TI  - A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA.
JO  - Mol. Microbiol.
PY  - 1996
SP  - 437
EP  - 447
VL  - 22
AB  - Salmonella enterica serovar blegdam has a restriction and modification system encoded by genes
AB  - linked to serB.  We have cloned these genes, putative alleles of the hsd locus of Escherichia
AB  - coli K-12, and confirmed by the sequence similarities of flanking DNA that the hsd genes of S.
AB  - enterica serovar blegdam have the same chromosomal location as those of E. coli K-12 and
AB  - Salmonella enterica serovar typhimurium LT2.  There is, however, no obvious similarity in
AB  - their nucleotide sequences, and while the gene order in S. enterica serovar blegdam is serB
AB  - hsdM, S and R, that in E. coli K-12 and S. enterica serovar typhimurium LT2 is serB hsdR, M
AB  - and S.  The hsd genes of S. enterica serovar blegdam identify a third family of serB-linked
AB  - hsd genes (type ID).  The polypeptide sequence predicted from the three hsd genes show some
AB  - similarities (18-50% identity) with the polypeptides of known and putative type I restriction
AB  - and modification systems; the highest levels of identity are with sequences of Haemophilus
AB  - influenzae Rd.  The HsdM polypeptide has the motifs characteristic of adenine
AB  - methyltransferases.  Comparisons of the HsdR sequence with those for three other families of
AB  - type I systems and three putative HsdR polypeptides identify two highly conserved regions in
AB  - addition to the seven proposed DEAD-box motifs.
ER  -

TY  - JOUR
AU  - Tiwari, P.K.
AU  - Joshi, K.
AU  - Rehman, R.
AU  - Bhardwaj, V.
AU  - Shamsudheen, K.V.
AU  - Sivasubbu, S.
AU  - Scaria, V.
TI  - Draft Genome Sequence of Urease-Producing Sporosarcina pasteurii with Potential Application in Biocement Production.
JO  - Genome Announcements
PY  - 2014
SP  - e01256
EP  - e01213
VL  - 2
AB  - We describe here the draft genome sequence of Sporosarcina pasteurii, a urease-producing
AB  - bacterium with potential applications in biocement production.
ER  -

TY  - JOUR
AU  - Tiwari, R.
AU  - Howieson, J.
AU  - Yates, R.
AU  - Tian, R.
AU  - Held, B.
AU  - Tapia, R.
AU  - Han, C.
AU  - Seshadri, R.
AU  - Reddy, T.B.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 113
EP  - 113
VL  - 10
AB  - Bradyrhizobium sp. WSM1253 is a novel N2-fixing bacterium isolated from a root nodule of the
AB  - herbaceous annual legume Ornithopus compressus that was growing on
AB  - the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an
AB  - Australian program that was selecting inoculant quality bradyrhizobial strains
AB  - for inoculation of Mediterranean species of lupins (Lupinus angustifolius, L.
AB  - princei, L. atlanticus, L. pilosus). In this report we describe, for the first
AB  - time, the genome sequence information and annotation of this legume
AB  - microsymbiont. The 8,719,808 bp genome has a G + C content of 63.09 % with 71
AB  - contigs arranged into two scaffolds. The assembled genome contains 8,432
AB  - protein-coding genes, 66 RNA genes and a single rRNA operon. This
AB  - improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE
AB  - Joint Genome Institute 2010 Community Sequencing Project.
ER  -

TY  - JOUR
AU  - Tiwari, S. et al.
TI  - Whole-Genome Sequence of Corynebacterium auriscanis Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom.
JO  - Genome Announcements
PY  - 2016
SP  - e00683
EP  - e00616
VL  - 4
AB  - In this work, we describe a set of features of Corynebacterium auriscanis CIP 106629 and
AB  - details of the draft genome sequence and annotation. The genome
AB  - comprises a 2.5-Mbp-long single circular genome with 1,797 protein-coding genes,
AB  - 5 rRNA, 50 tRNA, and 403 pseudogenes, with a G+C content of 58.50%.
ER  -

TY  - JOUR
AU  - Tiwari, S.
AU  - da Costa, M.P.
AU  - Almeida, S.
AU  - Hassan, S.S.
AU  - Jamal, S.B.
AU  - Oliveira, A.
AU  - Folador, E.L.
AU  - Rocha, F.
AU  - de Abreu, V.A.
AU  - Dorella, F.
AU  - Hirata, R.
AU  - de Oliveira, D.M.
AU  - da Silva-Teixeira, M.F.
AU  - Silva, A.
AU  - Barh, D.
AU  - Azevedo, V.
TI  - C. pseudotuberculosis Phop confers virulence and may be targeted by natural compounds.
JO  - Integr Biol (Camb)
PY  - 2014
SP  - 1088
EP  - 1099
VL  - 6
AB  - The bacterial two-component system (TCS) regulates genes that are crucial for
AB  - virulence in several pathogens. One of such TCS, the PhoPR system, consisting of
AB  - a transmembrane sensory histidine kinase protein (PhoR) and an intracellular
AB  - response regulator protein (PhoP), has been reported to have a major role in
AB  - mycobacterial pathogenesis. We knocked out the phoP in C. pseudotuberculosis, the
AB  - causal organism of caseous lymphadenitis (CLA), and using a combination of in
AB  - vitro and in vivo mouse system, we showed for the first time, that the PhoP of C.
AB  - pseudotuberculosis plays an important role in the virulence and pathogenicity of
AB  - this bacterium. Furthermore, we modeled the PhoP of C. pseudotuberculosis and our
AB  - docking results showed that several natural compounds including Rhein, an
AB  - anthraquinone from Rheum undulatum, and some drug-like molecules may target PhoP
AB  - to inhibit the TCS of C. pseudotuberculosis, and therefore may facilitate a
AB  - remarkable attenuation of bacterial pathogenicity being the CLA. Experiments are
AB  - currently underway to validate these in silico docking results.
ER  -

TY  - JOUR
AU  - Tkachuk, J.Y.
AU  - Tkachuk, L.V.
AU  - Kvasnyuk, E.I.
AU  - Zaitseva, G.V.
AU  - Kalinichenko, E.M.
AU  - Mikhailopulo, I.O.
AU  - Matsuka, G.K.
TI  - Functioning of EcoRI, BamHI and HindIII restriction enzymes as affected by (2',5') oligoadenylates.
JO  - Dokl. Akad. Nauk UKR SSR Ser. B Geol. Khim. Biol. Nauk
PY  - 1988
SP  - 78
EP  - 81
VL  - 10
AB  - Peculiarities of the functioning of restriction enzymes EcoRI, BamHI and
AB  - HindIII in the presence of core trimers of (2'-5') oligoadenylic acid, viz.,
AB  - (2'-5') A3 and (2'-5')3'dA3, have been studied.  Depending on the enzyme, the
AB  - structure of the (2'-5') trimer, its concentration and method of its use
AB  - (preincubation of the enzyme and the trimer or successive mixing of the
AB  - reaction components), an inhibition of the restriction reaction, or
AB  - site-specific restriction of lambda DNA or non-specific hydrolysis of lambda
AB  - DNA are observed.  In the latter case, the restriction enzymes function as
AB  - nonspecific DNases.
ER  -

TY  - JOUR
AU  - Tkachuk, Z.Y.
AU  - Tkachuk, L.V.
AU  - Kvasyuk, E.I.
AU  - Zaitseva, G.V.
AU  - Kalinichenko, E.N.
AU  - Mikhailopulo, I.A.
AU  - Matsuka, G.K.
TI  - Changes in functional properties of restriction enzymes under the influence of (2'-5') oligoadenylates in vitro.
JO  - Biopol. Kletka
PY  - 1989
SP  - 69
EP  - 73
VL  - 5
AB  - It is found that core trimers of (2'-5') oligoadenylic acid. viz., (A2'p)2A and
AB  - (3'dA2'p)2/3'dA, exert an influence on functional properties of restriction
AB  - enzymes EcoRI, BamHI, and HindIII.  The presence of (2'-5') trimers in the
AB  - reaction mixture containing DNA and the restriction enzyme results in (i) an
AB  - inhibition of the restriction reaction, (ii) site-specific restriction of DNA
AB  - lambda, or (iii) nonspecific hydrolysis of DNA lambda.  In the last case
AB  - restriction enzymes function as nonspecific DNAses.
ER  -

TY  - JOUR
AU  - Tkaczuk, K.L.
AU  - Obarska, A.
AU  - Bujnicki, J.M.
TI  - Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.
JO  - BMC Evol. Biol.
PY  - 2006
SP  - 6
EP  - 6
VL  - 6
AB  - BACKGROUND: Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential
AB  - enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from
AB  - S-adenosylmethionine to the 2'-OH or 3'-OH group of the last nucleotide of miRNA/miRNA*
AB  - duplexes produced by the nuclease Dicer. Previously it was found that HEN1 possesses a
AB  - Rossmann-fold methyltransferase (RFM) domain and a long N-terminal extension including a
AB  - putative double-stranded RNA-binding motif (DSRM). However, little is known about the details
AB  - of the structure and the mechanism of action of this enzyme, and about its phylogenetic
AB  - origin. RESULTS: Extensive database searches were carried out to identify orthologs and close
AB  - paralogs of HEN1. Based on the multiple sequence alignment a phylogenetic tree of the HEN1
AB  - family was constructed. The fold-recognition approach was used to identify related
AB  - methyltransferases with experimentally solved structures and to guide the homology modeling of
AB  - the HEN1 catalytic domain. Additionally, we identified a La-like predicted RNA binding domain
AB  - located C-terminally to the DSRM domain and a domain with a peptide prolyl cis/trans isomerase
AB  - (PPIase) fold, but without the conserved PPIase active site, located N-terminally to the
AB  - catalytic domain. CONCLUSION: The bioinformatics analysis revealed that the catalytic domain
AB  - of HEN1 is not closely related to any known RNA:2'-OH methyltransferases (e.g. to the
AB  - RrmJ/fibrillarin superfamily), but rather to small-molecule methyltransferases. The structural
AB  - model was used as a platform to identify the putative active site and substrate-binding
AB  - residues of HEN and to propose its mechanism of action.
ER  -

TY  - JOUR
AU  - To, T.T.
AU  - Liu, Q.
AU  - Watling, M.
AU  - Bumgarner, R.E.
AU  - Darveau, R.P.
AU  - McLean, J.S.
TI  - Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504.
JO  - Genome Announcements
PY  - 2016
SP  - e00256
EP  - e00216
VL  - 4
AB  - We present the draft genome ofPorphyromonas gingivalisMP4-504, a low-passage clinical isolate
AB  - obtained from a periodontitis patient. The genome is composed of
AB  - 92 contigs for a length of 2,373,453 bp and a G+C of 48.3%. ThetraA-Qconjugative
AB  - transfer locus is genetically distinct from W83 but highly similar to ATCC 33277.
ER  -

TY  - JOUR
AU  - Tobes, R.
AU  - Codoner, F.M.
AU  - Lopez-Camacho, E.
AU  - Salanueva, I.J.
AU  - Manrique, M.
AU  - Brozynska, M.
AU  - Gomez-Gil, R.
AU  - Martinez-Blanch, J.F.
AU  - Alvarez-Tejado, M.
AU  - Pareja, E.
AU  - Mingorance, J.
TI  - Genome Sequence of Klebsiella pneumoniae KpQ3, a DHA-1 beta-Lactamase-Producing Nosocomial Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e00167
EP  - e00112
VL  - 1
AB  - KpQ3 is a multidrug-resistant isolate obtained from a blood culture of a patient  in a burn
AB  - unit in the Hospital Universitario La Paz (Madrid, Spain) in 2008. The
AB  - genome contains multiple antibiotic resistance genes, including a
AB  - plasmid-mediated DHA-1 cephalosporinase gene.
ER  -

TY  - JOUR
AU  - Tobes, R.
AU  - Manrique, M.
AU  - Brozynska, M.
AU  - Stephan, R.
AU  - Pareja, E.
AU  - Johler, S.
TI  - Noncontiguous Finished Genome Sequence of Staphylococcus aureus KLT6, a Staphylococcal Enterotoxin B-Positive Strain Involved in a Food Poisoning  Outbreak in Switzerland.
JO  - Genome Announcements
PY  - 2013
SP  - e00214
EP  - e00213
VL  - 1
AB  - We present the first complete genome sequence of a Staphylococcus aureus strain assigned to
AB  - clonal complex 12. The strain was isolated in a food poisoning
AB  - outbreak due to contaminated potato salad in Switzerland in 2009, and it produces
AB  - staphylococcal enterotoxin B.
ER  -

TY  - JOUR
AU  - Tobias, N.J.
AU  - Doig, K.D.
AU  - Medema, M.H.
AU  - Chen, H.
AU  - Haring, V.
AU  - Moore, R.
AU  - Seemann, T.
AU  - Stinear, T.P.
TI  - Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans ecovar Liflandii.
JO  - J. Bacteriol.
PY  - 2012
SP  - 556
EP  - 564
VL  - 195
AB  - In 2004, a previously undiscovered mycobacterium resembling Mycobacterium ulcerans (the agent
AB  - of Buruli ulcer) was reported in an outbreak of a lethal mycobacteriosis in a laboratory
AB  - colony of the African clawed-frog Xenopus tropicalis. This mycobacterium makes mycolactone and
AB  - is one of several strains of M. ulcerans-like mycolactone-producing mycobacteria recovered
AB  - from ectotherms around the world. Here we describe the complete 6,399,543 bp genome of this
AB  - frog pathogen (previously unofficially named Mycobacterium 'liflandii') and we show that it
AB  - has undergone an intermediate degree of reductive evolution, between M. ulcerans Agy99 and the
AB  - fish pathogen Mycobacterium marinum M. Like M. ulcerans Agy99, it has the pMUM mycolactone
AB  - plasmid, over 200 chromosomal copies of the insertion sequence IS2404 and a high proportion of
AB  - pseudogenes. However, M. 'liflandii' has a larger genome that is closer in length, sequence
AB  - and architecture to M. marinum M than to M. ulcerans Agy99, suggesting that M. ulcerans Agy99
AB  - has undergone accelerated evolution. Scrutiny of genes specifically lost suggests M.
AB  - 'liflandii' is a tryptophan, tyrosine and phenylalanine auxotroph. A once extensive M.
AB  - marinum-like secondary metabolome has also been diminished through reductive evolution. Our
AB  - analysis shows that M. 'liflandii', like M. ulcerans Agy99, has the characteristics of a
AB  - niche-adapted mycobacterium but with several distinctive features in important metabolic
AB  - pathways that suggests it is responding to different environmental pressures, supporting
AB  - earlier proposals that it could be considered an M. ulcerans ecotype, hence the name M.
AB  - ulcerans ecovar Liflandii.
ER  -

TY  - JOUR
AU  - Tobias, N.J.
AU  - Mishra, B.
AU  - Gupta, D.K.
AU  - Ke, L.P.
AU  - Thines, M.
AU  - Bode, H.B.
TI  - Draft Genome Sequence of Ochrobactrum anthropi Strain ML7 Isolated from Soil Samples in Vinhphuc Province, Vietnam.
JO  - Genome Announcements
PY  - 2015
SP  - e00218
EP  - e00215
VL  - 3
AB  - Ochrobactrum species are widespread in the environment and can colonize a wide variety of
AB  - habitats. Here, we describe the sequencing of a new environmental
AB  - isolate of Ochrobactrum anthropi isolated from northern Vietnam.
ER  -

TY  - JOUR
AU  - Tock, M.R.
AU  - Dryden, D.T.F.
TI  - The biology of restriction and anti-restriction.
JO  - Curr. Opin. Microbiol.
PY  - 2005
SP  - 466
EP  - 472
VL  - 8
AB  - The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were
AB  - first discovered five decades ago but have
AB  - yielded only gradually to rigorous analysis. Work presented at the
AB  - 5(th) New England Biolabs Meeting on Restriction-Modification
AB  - (available on REBASE, http://www.rebase.com) and several recently
AB  - published genetic, biochemical and biophysical analyses indicate that
AB  - these fields continue to contribute significantly to basic science.
AB  - Recently, there have been several studies that have shed light on the
AB  - still developing field of restriction-modification and on the newly
AB  - re-emerging field of anti-restriction.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Hayashi, J.
AU  - Oshima, K.
AU  - Nakano, A.
AU  - Takayama, Y.
AU  - Takanashi, K.
AU  - Morita, H.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Bifidobacterium dentium Strain JCM 1195T, Isolated from Human Dental Caries.
JO  - Genome Announcements
PY  - 2015
SP  - e00284
EP  - e00215
VL  - 3
AB  - Bifidobacterium dentium strain JCM 1195(T) was isolated from human dental caries. Here, we
AB  - report the complete genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Matsubara, T.
AU  - Tomida, S.
AU  - Mimura, I.
AU  - Arakawa, K.
AU  - Kikusui, T.
AU  - Morita, H.
TI  - Draft Genome Sequence of Bifidobacterium lemurum DSM 28807T Isolated from the Gastrointestinal Tracts of Ring-Tailed Lemurs (Lemur catta).
JO  - Genome Announcements
PY  - 2017
SP  - e01656
EP  - e01616
VL  - 5
AB  - Bifidobacterium lemurum DSM 28807T was isolated from the gastrointestinal tracts  of
AB  - ring-tailed lemurs (Lemur catta). Here, we report the first draft genome
AB  - sequence of this organism.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Nakano, A.
AU  - Nguyen, C.T.
AU  - Mimura, I.
AU  - Arakawa, K.
AU  - Tashiro, K.
AU  - Kikusui, T.
AU  - Morita, H.
TI  - Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697T Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds.
JO  - Genome Announcements
PY  - 2016
SP  - e01679
EP  - e01615
VL  - 4
AB  - Lactobacillus equigenerosi NRIC 0697(T) was isolated from the gastrointestinal tracts of
AB  - healthy thoroughbreds. This strain produced unique spherical or oval
AB  - cells, which is rare in the genus Lactobacillus. Here, we report the draft genome
AB  - sequence of this strain.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Oshima, K.
AU  - Nakano, A.
AU  - Takahata, M.
AU  - Murakami, M.
AU  - Takaki, T.
AU  - Nishiyama, H.
AU  - Igimi, S.
AU  - Hattori, M.
AU  - Morita, H.
TI  - Genomic adaptation of the Lactobacillus casei group.
JO  - PLoS ONE
PY  - 2013
SP  - e75073
EP  - e75073
VL  - 8
AB  - Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group
AB  - (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we
AB  - report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the
AB  - draft genome sequence of L. paracasei COM0101, all of which were isolated
AB  - from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also
AB  - known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is
AB  - distinct from other strains previously described as L. paracasei. The core genome of 10
AB  - completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes.
AB  - Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC
AB  - 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334.
AB  - Several genomic islands, including carbohydrate utilization gene clusters, were found at the
AB  - same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was
AB  - first identified in GG, was also found in other strains of the L. casei group, but several L.
AB  - paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher
AB  - number of proteins involved in carbohydrate utilization compared with intestinal
AB  - lactobacilli, and extracellular adhesion proteins, several of which are absent in other
AB  - strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L.
AB  - paracasei strains, the complete genome sequences of L. casei will provide valuable insights
AB  - into the evolution of the L. casei group.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Oshima, K.
AU  - Nakano, A.
AU  - Yamashita, N.
AU  - Iioka, E.
AU  - Kurokawa, R.
AU  - Morita, H.
AU  - Hattori, M.
TI  - Complete Genome Sequence of Bifidobacterium scardovii Strain JCM 12489T, Isolated from Human Blood.
JO  - Genome Announcements
PY  - 2015
SP  - e00285
EP  - e00215
VL  - 3
AB  - Bifidobacterium scardovii strain JCM 12489(T) was isolated from human blood and has the
AB  - largest bifidobacterial genome reported to date. Here, we report the
AB  - complete genome sequence of this organism. This paper is the first report
AB  - demonstrating the fully sequenced and completely annotated genome of a B.
AB  - scardovii strain.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Oshima, K.
AU  - Suzuki, T.
AU  - Hattori, M.
AU  - Morita, H.
TI  - Complete Genome Sequence of the Equol-Producing Bacterium Adlercreutzia equolifaciens DSM 19450T.
JO  - Genome Announcements
PY  - 2013
SP  - e00742
EP  - e00713
VL  - 1
AB  - Adlercreutzia equolifaciens DSM 19450(T) was isolated from human feces and is able to
AB  - metabolize daidzeins (soybean isoflavonoids) to equol. Here, we report
AB  - the finished and annotated genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Oshima, K.
AU  - Toyoda, A.
AU  - Ogura, Y.
AU  - Ooka, T.
AU  - Sasamoto, H.
AU  - Park, S.H.
AU  - Iyoda, S.
AU  - Kurokawa, K.
AU  - Morita, H.
AU  - Itoh, K.
AU  - Taylor, T.D.
AU  - Hayashi, T.
AU  - Hattori, M.
TI  - Complete genome sequence of the wild-type commensal Escherichia coli strain SE15 belonging to phylogenetic group B2.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1165
EP  - 1166
VL  - 192
AB  - Escherichia coli SE15 (O150:H5) is a human commensal bacterium recently isolated from feces of
AB  - a healthy adult and classified into E. coli
AB  - phylogenetic group B2 that includes the majority of extraintestinal
AB  - pathogenic E. coli (ExPEC). Here, we report the finished and annotated
AB  - genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Sharma, V.K.
AU  - Oshima, K.
AU  - Kondo, S.
AU  - Hattori, M.
AU  - Ward, F.B.
AU  - Free, A.
AU  - Taylor, T.D.
TI  - Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp. Strain L, Both Isolated from a Microbial Fuel Cell.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6411
EP  - 6412
VL  - 193
AB  - Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the
AB  - anode biofilm of a microbial fuel
AB  - cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel
AB  - cell. Here we report the finished and annotated genome sequences of these
AB  - organisms.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Weiss, B.L.
AU  - Perkin, S.A.
AU  - Yamashita, A.
AU  - Oshima, K.
AU  - Hattori, M.
AU  - Aksoy, S.
TI  - Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.
JO  - Genome Res.
PY  - 2006
SP  - 149
EP  - 156
VL  - 16
AB  - Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.),
AB  - an insect of medical and veterinary significance. Analysis of the complete sequence of
AB  - Sodalis' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a
AB  - reduced coding capacity of 51%. Furthermore, the chromosome contains 972 pseudogenes, an
AB  - inordinately high number compared with that of other bacterial species. A high proportion of
AB  - these pseudogenes are homologs of known proteins that function either in defense or in the
AB  - transport and metabolism of carbohydrates and inorganic ions, suggesting Sodalis'
AB  - degenerative adaptations to the immunity and restricted nutritional status of the host.
AB  - Sodalis possesses three chromosomal symbiosis regions (SSR): SSR-1, SSR-2, and SSR-3, with
AB  - gene inventories similar to the Type-III secretion system (TTSS) ysa from Yersinia
AB  - enterolitica and SPI-1 and SPI-2 from Salmonella, respectively. While core components of the
AB  - needle structure have been conserved, some of the effectors and regulators typically
AB  - associated with these systems in pathogenic microbes are modified or eliminated in Sodalis.
AB  - Analysis of SSR-specific invA transcript abundance in Sodalis during host development
AB  - indicates that the individual symbiosis regions may exhibit different temporal expression
AB  - profiles. In addition, the Sodalis chromosome encodes a complete flagella structure, key
AB  - components of which are expressed in immature host developmental stages. These features may be
AB  - important for the transmission and establishment of symbiont infections in the intra-uterine
AB  - progeny. The data suggest that Sodalis represents an evolutionary intermediate transitioning
AB  - from a free-living to a mutualistic lifestyle.
ER  -

TY  - JOUR
AU  - Toh, H.
AU  - Yamazaki, Y.
AU  - Tashiro, K.
AU  - Kawarai, S.
AU  - Oshima, K.
AU  - Nakano, A.
AU  - Kim, C.N.
AU  - Mimura, I.
AU  - Arakawa, K.
AU  - Iriki, A.
AU  - Kikusui, T.
AU  - Morita, H.
TI  - Draft Genome Sequence of Bifidobacterium aesculapii DSM 26737T, Isolated from Feces of Baby Common Marmoset.
JO  - Genome Announcements
PY  - 2015
SP  - e01463
EP  - e01415
VL  - 3
AB  - Bifidobacterium aesculapii DSM 26737(T) was isolated from feces of baby common marmoset. Here,
AB  - we report the draft genome sequence of this organism. This paper
AB  - is the first published report of the genomic sequence of B. aesculapii.
ER  -

TY  - JOUR
AU  - Tohya, M.
AU  - Sekizaki, T.
AU  - Miyoshi-Akiyama, T.
TI  - Complete genome sequence of Streptococcus ruminantium sp. nov. GUT-187T (=DSM 104980 T =JCM 31869 T), the type strain of S. ruminantium, and comparison with genome sequences of S. suis strains.
JO  - Genome Biol. Evol.
PY  - 2018
SP  - 1180
EP  - 1184
VL  - 10
AB  - Streptococcus ruminantium sp. nov. of type strain GUT-187T, previously classified as
AB  - Streptococcus suis serotype 33, is a
AB  - recently described novel streptococcal species. This study was designed to determine the
AB  - complete genome sequence of
AB  - S. ruminantium GUT-187T using a combination ofOxford Nanopore and the Illumina platform, and
AB  - to compare this sequence
AB  - with the genomes of 27 S. suis representative strains. The genome of GUT-187T was 2,090,539 bp
AB  - in size, with a GC content
AB  - of 40.01%. This genome contained 1,961 predicted protein coding DNA sequences (CDSs); of
AB  - these, 1,685 (85.9%) showed
AB  - similarity with S. suis CDSs. Of the remaining 276 CDSs, 81 (29.3%) showed some degree of
AB  - similarity with CDSs of other
AB  - streptococcal species. The genome of GUT-187T contained no intact prophage. The numbers of
AB  - prophages and CRISPR
AB  - spacers, as well as the presence or absence of genes encoding CRISPR-associated proteins,
AB  - differed in S. ruminantium and
AB  - S. suis. Aphylogenetic analysis indicates thatGUT-187Tmay be outgroup to the S. suis strains
AB  - in our sample, thereby justifying
AB  - its classification as distinct species. Gene mapping indicated 10.2 times of massive genome
AB  - rearrangements in average
AB  - occurred between S. ruminantium and S. suis. There was no significant statistical difference
AB  - in clusters of orthologous group
AB  - distribution between S. ruminantium and S. suis.
ER  -

TY  - JOUR
AU  - Tokajian, S.
AU  - Eisen, J.A.
AU  - Jospin, G.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Streptococcus pyogenes Strains Associated with Throat and Skin Infections in Lebanon.
JO  - Genome Announcements
PY  - 2014
SP  - e00358
EP  - e00314
VL  - 2
AB  - We present the draft genome sequences of nine clinical Streptococcus pyogenes isolates
AB  - recovered from patients suffering from sore throat and skin infections.
AB  - An average of 2,454,334 paired-end reads per sample were generated, which
AB  - assembled into 21 to 198 contigs, with a G+C content of 38.4 to 38.5%.
ER  -

TY  - JOUR
AU  - Tokajian, S.
AU  - Eisen, J.A.
AU  - Jospin, G.
AU  - Farra, A.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Extended-Spectrum beta-Lactamase-Producing Escherchia coli Strains Isolated from Patients in Lebanon.
JO  - Genome Announcements
PY  - 2014
SP  - e00123
EP  - e00114
VL  - 2
AB  - We present the draft genome sequences of nine extended-spectrum beta-lactamase
AB  - (ESBL)-producing Escherichia coli strains isolated from stool samples collected
AB  - from patients admitted for gastrointestinal and urological procedures/surgeries.
AB  - An average of 3,889,300 paired-end reads per sample were generated, which
AB  - assembled in 77 to 157 contigs.
ER  -

TY  - JOUR
AU  - Tokajian, S.
AU  - Eisen, J.A.
AU  - Jospin, G.
AU  - Farra, A.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Extended-Spectrum beta-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon.
JO  - Genome Announcements
PY  - 2014
SP  - e00121
EP  - e00114
VL  - 2
AB  - We present the draft genome sequence of extended-spectrum beta-lactamase (ESBL)-producing
AB  - Klebsiella pneumoniae isolated from a stool sample collected
AB  - from a patient admitted for a gastrointestinal procedure. The draft genome
AB  - sequence consists of 86 contigs, including a combined 5,632,663 bases with 57%
AB  - G+C content.
ER  -

TY  - JOUR
AU  - Tokajian, S.
AU  - Eisen, J.A.
AU  - Jospin, G.
AU  - Hamze, M.
AU  - Rafei, R.
AU  - Salloum, T.
AU  - Ibrahim, J.
AU  - Coil, D.A.
TI  - Draft Genome Sequences of Acinetobacter baumannii Strains Harboring the blaNDM-1  Gene Isolated in Lebanon from Civilians Wounded during the Syrian Civil War.
JO  - Genome Announcements
PY  - 2016
SP  - e01678
EP  - e01615
VL  - 4
AB  - We present here the draft genome sequences of multidrug-resistant blaNDM-1-positive
AB  - Acinetobacter baumannii strains ACMH-6200 and ACMH-6201,
AB  - isolated in north Lebanon from civilians wounded during the Syrian civil war. The
AB  - draft genomes were contained in 217 contigs for ACMH-6200 and 83 contigs for
AB  - ACMH-6201, including a combined 3,997,237 bases for ACMH-6200 and 3,983,110 bases
AB  - for ACMH-6201, with 39% and 38.9% G+C content, respectively.
ER  -

TY  - JOUR
AU  - Tokajian, S.
AU  - Eisen, J.A.
AU  - Jospin, G.
AU  - Matar, G.
AU  - Araj, G.F.
AU  - Coil, D.A.
TI  - Draft Genome Sequence of Klebsiella pneumoniae KGM-IMP216 Harboring blaCTX-M-15,  blaDHA-1, blaTEM-1B, blaNDM-1, blaSHV-28, and blaOXA-1, Isolated from a Patient  in Lebanon.
JO  - Genome Announcements
PY  - 2016
SP  - e01632
EP  - e01615
VL  - 4
AB  - We present the draft genome of highly drug-resistant Klebsiella pneumoniae KGM-IMP216,
AB  - isolated from a urine sample collected from a patient in Lebanon. The
AB  - draft genome sequence consisted of 77 contigs, including a combined 5,731,500
AB  - bases with 57% G+C content.
ER  -

TY  - JOUR
AU  - Tokovenko, B.
AU  - Ruckert, C.
AU  - Kalinowski, J.
AU  - Mohammadipanah, F.
AU  - Wink, J.
AU  - Rosenkranzer, B.
AU  - Myronovskyi, M.
AU  - Luzhetskyy, A.
TI  - Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease.
JO  - Genome Announcements
PY  - 2017
SP  - e00362
EP  - e00317
VL  - 5
AB  - The genome sequence of alkalohalophilic actinobacterium Nocardiopsis sinuspersici UTMC102 is
AB  - provided. N. sinuspersici UTMC102 produces a highly active serine
AB  - alkaline protease, and contains at least 11 gene clusters encoding the
AB  - biosynthesis of secondary metabolites. The N. sinuspersici UTMC102 genome was
AB  - assembled into a single chromosomal scaffold.
ER  -

TY  - JOUR
AU  - Toksoy, E.
AU  - Onsan, Z.I.
AU  - Kirdar, B.
TI  - Expression of a thermostable restriction endonuclease in recombinant Escherichia coli cells and optimization of fermentation conditions.
JO  - World J. Microbiol. Biotechnol.
PY  - 2002
SP  - 23
EP  - 27
VL  - 18
AB  - TaqI restriction endonuclease gene of the thermophilic eubacterium Thermus aquaticus YT-1
AB  - (ATCC 25104) was successfully cloned and expressed in recombinant Escherichia coli cells under
AB  - the control of the lac promoter/operator system.  Higher TaqI endonuclease specific activities
AB  - and biomass yields were obtained from E. coli ER2508(pUCTaq) cells when they were induced at
AB  - the late-exponential phase of their growth.  TaqI endonuclease expression was found to be
AB  - host-strain-dependent such that, among the three different strains examined, E. coli
AB  - XL1(pUCTaq) produced the highest specific TaqI endonuclease activities for longer induction
AB  - periods.  Decreasing the inducer concentration from 1 to 0.1 mM not only improved the specific
AB  - enzyme activity yields but also is more economical, considering the high cost of
AB  - isopropyl-beta-D-thiogalactopyranoside (PTG).  The optimum culture temperature was found to be
AB  - 37 C.  TaqI endonuclease specific activity recovered from E. coli XL1(pUCTaq) cells was 935
AB  - U/mg under optimum conditions.
ER  -

TY  - JOUR
AU  - Toksoy, E.
AU  - Onsan, Z.I.
AU  - Kirdar, B.
TI  - High-level production of TaqI restriction endonuclease by three different expression systems in Escherichia coli cells using the T7 phage promoter.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2002
SP  - 239
EP  - 245
VL  - 59
AB  - Three different expression systems were constructed for the high-level production of TaqI
AB  - restriction endonuclease in recombinant Escherichia coli cells. In system [R], the TaqI
AB  - endonuclease gene was cloned and expressed under the control of the strong T7 RNA polymerase
AB  - promoter. To protect cellular DNA, methylase protection was provided by constitutive
AB  - co-expression of TaqI methylase activity either by cloning the TaqI methylase gene on a second
AB  - plasmid (system [R,M]) or by constructing a recombinant plasmid harboring both the
AB  - endonuclease and methylase genes (system [R+M]). In batch shake flasks containing complex
AB  - media, co-expression of the methylase gene in systems [R,M] and [R+M] resulted in a 2- and
AB  - 3-fold increase in volumetric productivity over system [R], yielding activities of 250x10^6 U
AB  - l^-1 and 350x10^6 U l^-1, which were 28 and 39 times higher than the data in the
AB  - literature, respectively. Under controlled bioreactor conditions in chemically defined medium,
AB  - co-expression of methylase activity greatly improved the yield and specific TaqI endonuclease
AB  - productivity of the recombinant cells, and reduced acetic acid excretion levels. System [R,M]
AB  - is preferable for high expression levels at longer operation periods, while system [R+M] is
AB  - well-suited for high expression levels in short-term bioreactor operation.
ER  -

TY  - JOUR
AU  - Toksoy, E.
AU  - Onsan, Z.I.
AU  - Kirdar, B.
TI  - Effect of the co-expression of methyltransferase activity on extracellular production of TaqI restriction endonuclease in recombinant E. coli cells.
JO  - Process. Biochem.
PY  - 2001
SP  - 527
EP  - 534
VL  - 37
AB  - TaqI methylase gene was cloned and expressed constitutively under the control of the
AB  - tetracycline resistance gene promoter.  The effect of TaqI methylase protection on the growth
AB  - kinetics, plasmid stability and production of MBP - TaqI fusion protein by recombinant E. coli
AB  - cells was investigated both in shake flasks and under controlled bioreactor conditions.  Shake
AB  - flask experiments indicated that the use of nutritionally richer medium formulations may
AB  - improve the growth characteristics, plasmid stability and also the total and extracellular
AB  - TaqI endonuclease recovery yields by the methylase protected cells.  Under controlled
AB  - bioreactor conditions, co-expression of the methylase gene led to higher plasmid stabilities
AB  - and improved the excretion levels considerably.
ER  -

TY  - JOUR
AU  - Tolen, T.N.
AU  - Xie, Y.
AU  - Hernandez, A.C.
AU  - Kuty, E.G.F.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Myophage Mushroom.
JO  - Genome Announcements
PY  - 2015
SP  - e00154
EP  - e00115
VL  - 3
AB  - Salmonella enterica serovar Typhimurium (S. Typhimurium) is a leading cause of foodborne
AB  - illness worldwide. Over the past two decades, strains resistant to
AB  - antibiotics have begun to emerge, highlighting the need for alternative treatment
AB  - strategies such as bacteriophage therapy. Here, we present the complete genome of
AB  - Mushroom, an S. Typhimurium myophage.
ER  -

TY  - JOUR
AU  - Toliusis, P.
AU  - Tamulaitiene, G.
AU  - Grigaitis, R.
AU  - Tuminauskaite, D.
AU  - Silanskas, A.
AU  - Manakova, E.
AU  - Venclovas, C.
AU  - Szczelkun, M.D.
AU  - Siksnys, V.
AU  - Zaremba, M.
TI  - The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.
JO  - Nucleic Acids Res.
PY  - 2018
SP  - 2560
EP  - 2572
VL  - 46
AB  - CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex
AB  - between: two R-subunits that have site specific-recognition and nuclease domains; and two
AB  - H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and
AB  - C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is
AB  - necessary for long-range movement along DNA that activates nuclease activity. Here, we provide
AB  - biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related
AB  - to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the
AB  - prototype of a previously undescribed monomeric helicase-like motor. The DEAD-Z1 motor has
AB  - unusual Walker A and Motif VI sequences those nonetheless have their expected functions.
AB  - Additionally, it contains DEAD-Z1-specific features: an H/H motif and a loop (aa 163-aa 172),
AB  - that both play a role in the coupling of ATP hydrolysis to DNA cleavage. We also solved the
AB  - crystal structure of the C-terminal domain which has a unique fold, and demonstrate that the
AB  - Z1-C domains are the principal DNA binding interface of the H-subunit. Finally, we use small
AB  - angle X-ray scattering to provide a model for how the H-subunit domains are arranged in a
AB  - dimeric complex.
ER  -

TY  - JOUR
AU  - Toliusis, P.
AU  - Zaremba, M.
AU  - Silanskas, A.
AU  - Szczelkun, M.D.
AU  - Siksnys, V.
TI  - CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction  endonucleases.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - 8435
EP  - 8447
VL  - 45
AB  - The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric
AB  - 5'-GCCGC-3' site and cleaves the DNA 7 and 6/7 nucleotides downstream
AB  - on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent
AB  - reaction. CglI is composed of two different proteins: an endonuclease (R.CglI)
AB  - and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a
AB  - heterotetrameric complex with R2H2 stoichiometry. However, the R2H2.CglI complex
AB  - has only one nuclease active site sufficient to cut one DNA strand suggesting
AB  - that two complexes are required to introduce a double strand break. Here, we
AB  - report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and
AB  - two-site circular DNA substrates we show that CglI does not require two sites on
AB  - the same DNA for optimal catalytic activity. However, one-site linear DNA is a
AB  - poor substrate, supporting a mechanism where CglI complexes must communicate
AB  - along the one-dimensional DNA contour before cleavage is activated. Based on
AB  - experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by
AB  - CglI produces translocation on DNA preferentially in a downstream direction from
AB  - the target, although upstream translocation is also possible. Our results are
AB  - consistent with a mechanism of CglI action that is distinct from that of other
AB  - ATP-dependent restriction-modification enzymes.
ER  -

TY  - JOUR
AU  - Tollefsbol, T.O.
AU  - Hutchinson, C.A. III
TI  - Analysis in Escherichia coli of the effects of in vivo CpG methylation catalyzed by the cloned murine maintenance methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1998
SP  - 670
EP  - 678
VL  - 245
AB  - Due in part to the complexity of mammalian systems, some of the proposed biological influences
AB  - of mammalian DNA methylation have not been fully established.  Escherichia coli cells, which
AB  - normally contain negligible CpG methylation, exhibited progressive slowing of replication and
AB  - lengthened generation times when expressing the murine DNA maintenance methyltransferase.
AB  - Genomic analysis indicated significant amounts of CpG methylation in expressing cells which
AB  - was absent from control cells.  Expressing cells exposed to the cytosine demethylating agent,
AB  - 5-azacytidine, rapidly reverted to propagation levels of controls.  Substitution of cysteine
AB  - with alanine in the carboxyl-terminal region proline-cysteine dipeptide of the
AB  - methyltransferase completely inactivated methylating activity and cells expressing the
AB  - inactive enzyme replicated as well as controls.  These findings strongly implicate a role of
AB  - epigenetic de novo CpG methylation in modulating cellular propagation, demonstrate that the
AB  - maintenance methyltransferase can de novo methylate in vivo, and show that the
AB  - methyltransferase requires an active site cysteine for activity.
ER  -

TY  - JOUR
AU  - Tollefsbol, T.O.
AU  - Hutchison, C.A. III
TI  - Control of methylation spreading in synthetic DNA sequences by the murine DNA methyltransferase.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 494
EP  - 504
VL  - 269
AB  - Methylation spreading, which involves a propensity for the mammalian
AB  - DNA-(cytosine-5)-methyltransferase to de novo methylate cytosine-guanine dinucleotides (CpGs)
AB  - near pre-existing 5-methylcytosine bases, has been implicated in the control of numerous
AB  - biological processes.  We have assessed methylation spreading by the murine DNA
AB  - methyltransferase in vitro using synthetic copolymers and oligonucleotides which differ only
AB  - in their methylation state.  Double-stranded oligonucleotides were found to undergo higher
AB  - levels of de novo methylation overall than other identical single-stranded oligonucleotides.
AB  - This difference reflects the greater number of de novo methylatable cytosine bases in
AB  - double-stranded than single-stranded sequences.  All tested oligonucleotides containing
AB  - pre-existing 5-methyl-cytosine(s) were de novo methylated at several fold the rates of
AB  - non-methylated controls.  No mammalian proteins besides the DNA methyltransferase were
AB  - required for this observed enhancement of de novo methylation.  Studies using oligonucleotides
AB  - differing in patterns of pre-methylation showed that methylation spreading can be initiated by
AB  - hemimethylated or duplex methylated CpGs indicating that recognition of 5-methylcytosine by
AB  - the enzyme is sufficient to stimulate methylation spreading. Double and single-stranded
AB  - oligonucleotides with several bases between CpGs underwent considerably more de novo
AB  - methylation per CpG than sequences containing sequential uninterrupted methylatable sites.
AB  - Spacing preferences by the DNA methyltransferase were also observed in hemimethylated
AB  - oligonucleotides, suggesting that this is a general property of the enzyme.  Although
AB  - methylation spreading outside of CpG dinucleotides was relatively rare, single-stranded DNA
AB  - incurred higher levels of de novo methylation at sites other than CpG as compared to
AB  - double-stranded DNA.  This indicates less specificity of methylation spreading in
AB  - single-stranded sequences.  Finally, enhanced de novo methylation in the presence of fully
AB  - methylated CpG sites in double-stranded oligonucleotides was not as high as the rates of
AB  - methylation of hemimethylated CpGs in otherwise identical oligonucleotides.  These studies
AB  - provide further elucidation of the mechanisms and regulation of the methylation spreading
AB  - process and its potential role in the biological processes it influences.
ER  -

TY  - JOUR
AU  - Tollefsbol, T.O.
AU  - Hutchison, C.A. III
TI  - Mammalian DNA (cytosine-5-)-methyltransferase expressed in Escherichia coli, purified and characterized.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 18543
EP  - 18550
VL  - 270
AB  - Besides modulating specific DNA-protein interactions, methylated cytosine, frequently referred
AB  - to as the fifth base of the genome, also influences DNA structure, recombination,
AB  - transposition, repair, transcription, imprinting, and mutagenesis.  DNA
AB  - (cytosine-5-)-methyltransferase catalyzes cytosine methylation in eukaryotes.  We have cloned
AB  - and expressed this enzyme in Escherichia coli, purified it to apparent homogeneity,
AB  - characterized its properties, and we have shown that it hemimethylates DNA.  The cDNA for
AB  - murine maintenance methyltransferase was reconstructed and cloned for direct expression in
AB  - native form.  Immunoblotting revealed a unique protein (Mr=190,000) not present in control
AB  - cells.  The mostly soluble overexpressed protein was purified by DEAE, Sephadex, and DNA
AB  - cellulose chromatography.  Peak methylating activity correlated with methyltransferase
AB  - immunoblots.  The purified enzyme preferentially transferred radioactive methyl moieties to
AB  - hemimethylated DNA in assays and on autoradiograms.  All of the examined properties of the
AB  - purified recombinant DNA methyltransferase are consistent with the enzyme purified from
AB  - mammalian cells.  Further characterization revealed enhanced in vitro methylation of
AB  - premethylated oligodeoxynucleotides.  The cloning of hemimethyltransferase in E. coli should
AB  - allow facilitated structure-function mutational analysis of this enzyme, studies of its
AB  - biological effects in prokayotes, and potential large scale methyltransferase production for
AB  - crystallography, and it may have broad applications in maintaining the native methylated state
AB  - of cloned DNA.
ER  -

TY  - JOUR
AU  - Tolstoshev, C.M.
AU  - Blakesley, R.W.
TI  - RSITE: a computer program to predict the recognition sequence of a restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 1
EP  - 17
VL  - 10
AB  - A computer program (RSITE) was developed which predicts the recognition
AB  - sequence of a restriction endonuclease.  The sizes of fragments experimentally
AB  - determined on cleavage of a DNA of known sequence were input.  Possible
AB  - recognition sequences producing fragments of sizes matching those determined
AB  - empirically were printed out.  The program faithfully predicted the specificity
AB  - of restriction enzymes of known recognition sequence and also determined the
AB  - recognition sequence of a new restriction enzyme from Haemophilus influenzae GU
AB  - (HinGUII).
ER  -

TY  - JOUR
AU  - Tomaschewski, J.
AU  - Ruger, W.
TI  - Nucleotide sequence and primary structures of gene products coded for by the T4 genome between map positions 48.266 kb and 39.166 kb.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3632
EP  - 3633
VL  - 15
AB  - This sequence comprises 19 open reading frames (orfs) including T4 genes 49 and nrdC which
AB  - were identified. The nomenclature of the orfs within this sequence is in agreement with the T4
AB  - genomic map.
ER  -

TY  - JOUR
AU  - Tomassini, J.
AU  - Roychoudhury, R.
AU  - Wu, R.
AU  - Roberts, R.J.
TI  - Recognition sequence of restriction endonuclease KpnI from Klebsiella pneumoniae.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 4055
EP  - 4064
VL  - 5
AB  - We have determined the recognition sequence of the restriction endonuclease
AB  - KpnI, previously isolated from Klebsiella pneumoniae.  The enzyme cleaves the
AB  - twofold rotationally symmetric sequence 5'-G-G-T-A-C-^C-3' 3'-C-^C-A-T-G-G-5'
AB  - at the positions indicated by the arrows, producing 3' protruding cohesive
AB  - ends, four nucleotides in length.  The specific cleavage site was unambiguously
AB  - deduced using both 3' and 5' end analysis of KpnI generated restriction
AB  - fragments of simian-virus 40 (SV40) DNA (1 site), adenovirus-2 (Ad-2) DNA (8
AB  - sites), and a plasmid (pCRI) DNA (2 sites).
ER  -

TY  - JOUR
AU  - Tomb, J.-F. et al.
TI  - The complete genome sequence of the gastric pathogen Helicobacter pylori.
JO  - Nature
PY  - 1997
SP  - 539
EP  - 547
VL  - 388
AB  - Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590
AB  - predicted coding sequences.  Sequence analysis indicates that H. pylori has well-developed
AB  - systems for motility, for scavenging iron, and for DNA restriction and modification.  Many
AB  - putative adhesins, lipoproteins and other outer membrane proteins were identified,
AB  - underscoring the potential complexity of host-pathogen interaction.  Based on the large number
AB  - of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric
AB  - racts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal
AB  - pathogens, probably uses recombination and slipped-strand mispairing within repeats as
AB  - mechanisms for antigenic variation and adaptive evolution.  Consistent with its restricted
AB  - niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and
AB  - biosynthetic capacity.  Its survival in acid conditions depends, in part, on its ability to
AB  - establish a positive inside-membrane potential in low pH.
ER  -

TY  - JOUR
AU  - Tomihama, T.
AU  - Nishi, Y.
AU  - Sakai, M.
AU  - Ikenaga, M.
AU  - Okubo, T.
AU  - Ikeda, S.
TI  - Draft Genome Sequences of Streptomyces scabiei S58, Streptomyces turgidiscabies T45, and Streptomyces acidiscabies a10, the Pathogens of Potato Common Scab,  Isolated in Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e00062
EP  - e00016
VL  - 4
AB  - The draft genome sequences of the three pathogens of potato common scab, Streptomyces scabiei
AB  - S58, Streptomyces turgidiscabies T45, and Streptomyces
AB  - acidiscabies a10, isolated in Japan, are presented here. The genome size of each
AB  - strain is >10 Mb, and the three pathogenic strains share genes located in a
AB  - pathogenicity island previously described in other pathogenic Streptomyces
AB  - species.
ER  -

TY  - JOUR
AU  - Tomilov, V.N.
AU  - Chernukhin, V.A.
AU  - Abdurashitov, M.A.
AU  - Gonchar, D.A.
AU  - Degtyarev, S.K.
TI  - Cleavage of mammalian chromosomal DNA by restriction enzymes in silico.
JO  - FEBS J.
PY  - 2007
SP  - 73
EP  - 73
VL  - 274
AB  - A theoretical method to simulate the digestion patterns of mammalian chromosomal DNA cleavage
AB  - by restriction endonucleases was proposed. New software for long mammalian DNAs analysis using
AB  - routine personal computers was developed. This computational technique includes short DNA
AB  - sequences searching, DNA cleavage simulation, data treatment and verification. Recently
AB  - published primary structures of mammalian genomes (Rattus norvegicus, Mus musculus and Homo
AB  - sapiens) were presented like databases and the analysis of short nucleotide sequences
AB  - distribution in the corresponding genomes was performed. Computational DNA cleavage of genomes
AB  - within the nucleotides sequences 5'-GGCC-3', 5'GATC-3', 5'-CC(A/T)GG-3' and
AB  - 5'-CCGG-3', which are the recognition sites of well known restriction endonucleases, was
AB  - carried out and the diagrams of chromosomal DNA fragments distribution were obtained.
AB  - Experiments on the chromosomal DNA digestion by corresponding restriction endonucleases were
AB  - undertaken. The comparison of computational diagrams and results of chromosomal DNA cleavage
AB  - was done and a high accordance of theoretical and experimental data was shown.
ER  -

TY  - JOUR
AU  - Tomilova, J.E.
AU  - Chernukhin, V.A.
AU  - Degtyarev, S.K.
TI  - Dependence of site-specific endonuclease GlaI activity on quantity and location of methylcytosines in the recognition sequence 5'-GCGC-3'.
JO  - Ovchinnikov Bull. Biotechnol. Phys. Chem. Biol.
PY  - 2006
SP  - 30
EP  - 39
VL  - 2
AB  - The activity dependence of site-specific endonuclease GlaI that recognizes and hydrolyzes only
AB  - methylated DNA sequence 5'-GCGC-3' on the quantity and location of 5-methylcytosines in
AB  - enzyme's recognition sequence has been studied. A significant DNA cleavage has been observed
AB  - for oligonucleotides duplexes containing four and three 5-methylcytosines or two internal
AB  - modified bases. The cleavage efficiency is maximal for DNA duplex with four 5-methylcytosine
AB  - and decreases when a number of methylated bases are lower. GlaI hydrolyzes recognition
AB  - sequences with 5-methylcytosines but not with N4-methylcytosines.
ER  -

TY  - JOUR
AU  - Tomilova, J.E.
AU  - Kuznetsov, V.V.
AU  - Abdurashitov, M.A.
AU  - Netesova, N.A.
AU  - Degtyarev, S.K.
TI  - Recombinant DNA-methyltransferase M1.Bst19I from Bacillus stearothermophilus 19: Purification, properties, and amino acid sequence analysis.
JO  - Mol. Biol. (Mosk)
PY  - 2010
SP  - 606
EP  - 615
VL  - 44
AB  - The M1.Bst19I DNA-methyltransferase gene from restriction-modification system Bst19I
AB  - (recognition sequence 5'-GCATC-3') in Bacillus
AB  - stearothermophilus 19 has been cloned in the expressing vector pJW that
AB  - carries a tandem of thermo inducible promoters P (R) /P (L) from phage
AB  - lambda. Highly purified enzyme has been isolated by chromatography on
AB  - various resins from Escherichia coli cells where it is accumulated in a
AB  - soluble form. The study of M1.Bst19I properties has revealed that the
AB  - enzyme has a temperature optimum at 50A degrees C and demonstrates
AB  - maximal activity at pH 8.0. M1.Bst19I modifies adenine in sequence
AB  - 5'-GCATC-3'. Kinetic parameters of M1.Bst19I DNA methylation reaction
AB  - have been determined as follows: Km for lambda DNA is 0.68 +/- 0.07 mu
AB  - M, Km for S-adenosyl-L-methionine is 2.02 +/- 0.31 mu M. Catalytical
AB  - constant (k (cat)) is 1.8 +/- 0.05 min(-1). Comparative analysis of
AB  - Target Recognition Domain amino acid sequences for M1.Bst19I and other
AB  - alpha-N6-DNA-methyltransferases has allowed us to suggest the presence
AB  - of two types of the enzymes containing ATG or ATC triplets in the
AB  - recognition sequence.
ER  -

TY  - JOUR
AU  - Tomilova, Y.E.
AU  - Abdurashitov, M.A.
AU  - Golikova, L.N.
AU  - Netesova, N.A.
AU  - Degtyarev, S.K.
TI  - Cloning of the genes for DNA methyltransferases of the SfaNI and Bst19I restriction-modification systems and primary structure analysis of  protein products.
JO  - Mol. Biol. (Mosk)
PY  - 2004
SP  - 850
EP  - 856
VL  - 38
AB  - The Streptococcus faecalis ND547 and Bacillus stearothermophilus 19 genes that code for DNA
AB  - methyltransferases (MTases, M.) of
AB  - restriction-modification (RM) systems with the same recognition
AB  - sequence, 5'-GCATC-3' were cloned and sequenced. The Bst19I RM system
AB  - includes two MTases, M1.Bst19I and M2.Bst19I. The SfaNI RM system has
AB  - only one MTase, M.SfaNI, whose N and C domains are homologous to
AB  - M2.Bst19I and M1.Bst19I, respectively. Both M1.Bst19I and M2.Bst19I and
AB  - the two domains of M.SfaNI contain conserved elements, which are
AB  - arranged in the order characteristic of class alpha N6-adenine MTases.
AB  - The enzymes of the SfaNI and Bst19I RM systems proved to be highly
AB  - homologous to their FokI and BstF5I counterparts, which was explained
AB  - by the presence of the common tetranucleotide 5'-GATG-3' in their
AB  - recognition sites. Based on sequence homology, the spatial arrangement
AB  - of highly conserved amino acid residues was determined using the known
AB  - three-dimensional model of M.DpnIIA, which belongs to the same MTase
AB  - class.
ER  -

TY  - JOUR
AU  - Tomilova, Y.E.
AU  - Dedkov, V.S.
AU  - Shinkarenko, N.M.
AU  - Popichenko, D.V.
AU  - Degtyarev, S.K.
TI  - Restriction endonuclease Bst19I from Bacillus stearothermophilus recognizing the 5'-GCATC-3' DNA sequence.
JO  - Biotekhnologiya
PY  - 2002
SP  - 17
EP  - 20
VL  - 6
AB  - A Bacillus stearothermophilus 19 strain, a producer of a new Bst19I restriction endonuclease
AB  - has been isolated. The indicated enzyme was
AB  - isolated and its characteristics including the substrate specificity
AB  - and site of DNA restriction were studied. The Bst19I restriction
AB  - endonuclease was identified as a heteroschizomer of SfaNI restrictase
AB  - who recognizes the 5'-GCATC-3' DNA sequence and cleaves DNA at the
AB  - distance of 4 and 6 nucleotides from the site of recognition in upper
AB  - and lower chains, respectively.
ER  -

TY  - JOUR
AU  - Tomkins, J.P.
AU  - Wood, T.C.
AU  - Stacey, M.G.
AU  - Loh, J.T.
AU  - Judd, A.
AU  - Goicoechea, J.L.
AU  - Stacey, G.
AU  - Sadowsky, M.J.
AU  - Wing, R.A.
TI  - A marker-dense, sequence-ready map of the Bradyrhizobium japonicum genome.
JO  - Genome Res.
PY  - 2001
SP  - 1434
EP  - 1440
VL  - 11
AB  - Bacterial artificial chromosome (BAC) clones are effective mapping and
AB  - sequencing reagents for use with a wide variety of small and large
AB  - genomes. This report describes the development of a physical framework for
AB  - the genome of Bradyrhizobium japonicum, the nitrogen-fixing symbiont of
AB  - soybean. A BAC library for B. japonicum was constructed that provides a
AB  - 77-fold genome coverage based on an estimated genome size of 8.7 Mb. The
AB  - library contains 4608 clones with an average insert size of 146 kb. To
AB  - generate a physical map, the entire library was fingerprinted with
AB  - HindIII, and the fingerprinted clones were assembled into contigs using
AB  - the software (; Sanger Centre, UK). The analysis placed 3410 clones in six
AB  - large contigs. The ends of 1152 BAC inserts were sequenced to generate a
AB  - sequence-tagged connector (STC) framework. To join and orient the contigs,
AB  - high-density BAC colony filters were probed with 41 known gene probes and
AB  - 17 end sequences from contig boundaries. STC sequences were searched
AB  - against the public databases using and algorithms. Query results allowed
AB  - the identification of 113 high probability matches with putative
AB  - functional identities that were placed on the physical map. Combined with
AB  - the hybridization data, a high-resolution physical map with 194 positioned
AB  - markers represented in two large contigs was developed, providing a marker
AB  - every 45 kb. Of these markers, 177 are known or putative B. japonicum
AB  - genes. Additionally, 1338 significant results (E < 10(-4)) were manually
AB  - sorted by function to produce a functionally categorized database of
AB  - relevant B. japonicum STC sequences that can also be traced to specific
AB  - locations in the physical map.
ER  -

TY  - JOUR
AU  - Tompa, R.
AU  - McCallum, C.M.
AU  - Delrow, J.
AU  - Henikoff, J.G.
AU  - van Steensel, B.
AU  - Henikoff, S.
TI  - Genome-Wide Profiling of DNA Methylation Reveals Transposon Targets of CHROMOMETHYLASE3.
JO  - Curr. Biol.
PY  - 2002
SP  - 65
EP  - 68
VL  - 12
AB  - DNA methylation has been implicated in a variety of epigenetic processes, and abnormal
AB  - methylation patterns have been seen in tumors. Analysis of methylation patterns has
AB  - traditionally been conducted either by using Southern analysis after cleavage with
AB  - methyl-sensitive restriction endonucleases or by bisulfite sequencing. However, neither method
AB  - is practical for analyzing more than a few genes. Here, we describe a simple technique for
AB  - genome-wide mapping of DNA methylation patterns. Fragmentation by a methyl-sensitive
AB  - restriction endonuclease is followed by size fractionation and hybridization to microarrays.
AB  - We demonstrate the utility of this method by characterizing methylation patterns in
AB  - Arabidopsis methylation mutants. This analysis reveals that CHROMOMETHYLASE3 (CMT3), which was
AB  - previously shown to maintain CpXpG methylation, preferentially methylates transposons, even
AB  - when they are present as single copies within the genome. Methylation profiling has potential
AB  - applications in disease research and diagnostic screening.
ER  -

TY  - JOUR
AU  - Tompkins, T.A.
AU  - Barreau, G.
AU  - Broadbent, J.R.
TI  - Complete Genome Sequence of Lactobacillus helveticus R0052, a Commercial Probiotic Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6349
EP  - 6349
VL  - 194
AB  - Lactobacillus helveticus R0052 is a commercially available strain that is widely  used in
AB  - probiotic preparations. The genome sequence consisted of 2,129,425 bases.
AB  - Comparative analysis showed that it was unique among L. helveticus strains in
AB  - that it contained genes encoding mucus-binding proteins similar to those found in
AB  - Lactobacillus acidophilus.
ER  -

TY  - JOUR
AU  - Tompkins, T.A.
AU  - Barreau, G.
AU  - de Carvalho, V.G.
TI  - Draft Genome Sequence of Probiotic Strain Lactobacillus rhamnosus R0011.
JO  - J. Bacteriol.
PY  - 2012
SP  - 902
EP  - 902
VL  - 194
AB  - Lactobacillus rhamnosus R0011 is a commercially available probiotic that is widely used in
AB  - human dietary supplements and pharmaceutical products.
AB  - We prepared a draft genome sequence consisting of 10 contigs totaling
AB  - 2,900,620 bases and a G+C content of 46.7% for this strain.
ER  -

TY  - JOUR
AU  - Tong, H.
AU  - Shang, N.
AU  - Liu, L.
AU  - Wang, X.
AU  - Cai, J.
AU  - Dong, X.
TI  - Complete Genome Sequence of an Oral Commensal, Streptococcus oligofermentans Strain AS 1.3089.
JO  - Genome Announcements
PY  - 2013
SP  - e00353
EP  - e00313
VL  - 1
AB  - Streptococcus oligofermentans, an oral commensal, inhibits the growth of the dental caries
AB  - pathogen Streptococcus mutans by producing large amounts of
AB  - hydrogen peroxide. Therefore, it can be a potential probiotic for oral health.
AB  - Here we report the complete genome sequence of S. oligofermentans strain AS
AB  - 1.3089.
ER  -

TY  - JOUR
AU  - Tong, T.
AU  - Chen, S.
AU  - Wang, L.
AU  - Tang, Y.
AU  - Ryu, J.Y.
AU  - Jiang, S.
AU  - Wu, X.
AU  - Chen, C.
AU  - Luo, J.
AU  - Deng, Z.
AU  - Li, Z.
AU  - Lee, S.Y.
AU  - Chen, S.
TI  - Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2018
SP  - E2988
EP  - E2996
VL  - 115
AB  - The chemical diversity of physiological DNA modifications has expanded with the identification
AB  - of phosphorothioate (PT) modification in which the nonbridging
AB  - oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together
AB  - with DndFGH as cognate restriction enzymes, DNA PT modification, which is
AB  - catalyzed by the DndABCDE proteins, functions as a bacterial
AB  - restriction-modification (R-M) system that protects cells against invading
AB  - foreign DNA. However, the occurrence of dnd systems across a large number of
AB  - bacterial genomes and their functions other than R-M are poorly understood. Here,
AB  - a genomic survey revealed the prevalence of bacterial dnd systems: 1,349
AB  - bacterial dnd systems were observed to occur sporadically across diverse
AB  - phylogenetic groups, and nearly half of these occur in the form of a solitary
AB  - dndBCDE gene cluster that lacks the dndFGH restriction counterparts. A
AB  - phylogenetic analysis of 734 complete PT R-M pairs revealed the coevolution of M
AB  - and R components, despite the observation that several PT R-M pairs appeared to
AB  - be assembled from M and R parts acquired from distantly related organisms.
AB  - Concurrent epigenomic analysis, transcriptome analysis, and metabolome
AB  - characterization showed that a solitary PT modification contributed to the
AB  - overall cellular redox state, the loss of which perturbed the cellular redox
AB  - balance and induced Pseudomonas fluorescens to reconfigure its metabolism to fend
AB  - off oxidative stress. An in vitro transcriptional assay revealed altered
AB  - transcriptional efficiency in the presence of PT DNA modification, implicating
AB  - its function in epigenetic regulation. These data suggest the versatility of PT
AB  - in addition to its involvement in R-M protection.
ER  -

TY  - JOUR
AU  - Tong, Y.J.
AU  - Ji, X.J.
AU  - Liu, L.G.
AU  - Shen, M.Q.
AU  - Huang, H.
TI  - Genome Sequence of Paenibacillus polymyxa ATCC 12321, a Promising Strain for Optically Active (R,R)-2,3-Butanediol Production.
JO  - Genome Announcements
PY  - 2013
SP  - e00572
EP  - e00513
VL  - 1
AB  - Paenibacillus polymyxa is a potential strain for (R,R)-2,3-butanediol production. Here, we
AB  - report an annotated draft genome sequence of P. polymyxa strain ATCC
AB  - 12321, which contains 4,429 protein-coding genes and 49 structural RNAs. This
AB  - genome sequence provides a genetic basis for a better understanding of the
AB  - mechanism for the accumulation of highly optically active (R,R)-2,3-butanediol.
ER  -

TY  - JOUR
AU  - Tong, Y.J.
AU  - Ji, X.J.
AU  - Liu, L.G.
AU  - Shen, M.Q.
AU  - Huang, H.
TI  - Genome Sequence of Klebsiella pneumoniae CICC10011, a Promising Strain for High 2,3-Butanediol Production.
JO  - Genome Announcements
PY  - 2015
SP  - e00802
EP  - e00815
VL  - 3
AB  - Klebsiella pneumoniae CICC10011, a promising 2,3-butanediol producer, has received much
AB  - attention because of its high productivity. Here, the first draft
AB  - genome sequence of this efficient strain may provide the genetic basis for
AB  - further insights into the metabolic and regulatory mechanisms underlying the
AB  - production of 2,3-butanediol at a high titer.
ER  -

TY  - JOUR
AU  - Tonomura, M.
AU  - Ehara, A.
AU  - Suzuki, H.
AU  - Amachi, S.
TI  - Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00472
EP  - e00415
VL  - 3
AB  - Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an
AB  - arsenate-respiring bacterium isolated from arsenic-contaminated soil. It
AB  - contained three distinct arsenic resistance gene clusters (ars operons), while no
AB  - respiratory arsenate reductase gene (arr) was identified.
ER  -

TY  - JOUR
AU  - Too, C.C.
AU  - Ong, K.S.
AU  - Ankenbrand, M.J.
AU  - Lee, S.M.
AU  - Yule, C.M.
AU  - Keller, A.
TI  - Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest.
JO  - Genome Announcements
PY  - 2018
SP  - e00561
EP  - e00518
VL  - 6
AB  - We report the draft genome sequence of a bacterial isolate, Paraburkholderia sp.  strain C35,
AB  - which was isolated from a Malaysian tropical peat swamp forest. The
AB  - putative genes for the biogeochemical processes were annotated and are publicly
AB  - available in the online databases.
ER  -

TY  - JOUR
AU  - Too, C.C.
AU  - Ong, K.S.
AU  - Ankenbrand, M.J.
AU  - Lee, S.M.
AU  - Yule, C.M.
AU  - Keller, A.
TI  - Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest.
JO  - Genome Announcements
PY  - 2018
SP  - e00560
EP  - e00518
VL  - 6
AB  - We report here the draft genome of Klebsiella sp. strain C31, a bacterial isolate from the
AB  - North Selangor peat swamp forest in Malaysia. The putative genes for the
AB  - biogeochemical processes of the genome were annotated and investigated.
ER  -

TY  - JOUR
AU  - Too, C.C.
AU  - Ong, K.S.
AU  - Lee, S.M.
AU  - Yule, C.M.
AU  - Keller, A.
TI  - Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest.
JO  - Genome Announcements
PY  - 2018
SP  - e00459
EP  - e00418
VL  - 6
AB  - We report here the draft genome sequences of a bacterial isolate, Dyella sp. strain C11, which
AB  - was isolated from a Malaysian tropical peat swamp forest. The
AB  - putative genes for the biogeochemical processes were annotated, and the genome
AB  - was deposited in an online database.
ER  -

TY  - JOUR
AU  - Too, P.H.
AU  - Zhu, Z.
AU  - Chan, S.H.
AU  - Xu, S.Y.
TI  - Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 1294
EP  - 1303
VL  - 38
AB  - Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and
AB  - cleaves closer to the recognition sequence. Although
AB  - M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI
AB  - restriction endonucleases do not share significant amino acid sequence
AB  - similarity. BtsCI belongs to a group of Type IIS restriction
AB  - endonucleases, BsmI, Mva1269I and BsrI, that carry two different catalytic
AB  - sites in a single polypeptide. By inactivating one of the catalytic sites
AB  - through mutagenesis, we have generated nicking variants of BtsCI that
AB  - specifically nick the bottom-strand or the top-strand of the target site.
AB  - By treating target DNA sequentially with the appropriate combinations of
AB  - FokI and BtsCI nicking variants, we are able to generate long overhangs
AB  - suitable for fluorescent labeling through end-filling or other techniques
AB  - based on annealing of complementary DNA sequences.
ER  -

TY  - JOUR
AU  - Toothman, P.
TI  - Restriction alleviation by bacteriophages lambda and lambda reverse.
JO  - J. Virol.
PY  - 1981
SP  - 621
EP  - 631
VL  - 38
AB  - Deletion analysis indicated that the phage lambda restriction alleviation
AB  - gene(s) ral resides between the cIII and N genes.  The Ral+ phenotype was expressed only
AB  - when lambda-ral+ carried a modification such that it was resistant to restriction by the host
AB  - specificity system.  Under these conditions, Ral function protected superinfecting
AB  - unmodified phages from restriction by EcoK or EcoB but not from restriction by EcoP1.
AB  - Ral-protected phage DNA was not concomitantly K and B modified, but rather received
AB  - only the modification specified by the system of the restricting host.  Possible mechanisms
AB  - for Ral action are discussed.  Of the other lambdoid phages tested, the hybrid phage
AB  - lambda-rev had Ral activity, whereas omega-80vir and one lambda-P22 hybrid did not.
AB  - The restriction alleviation activity of lambda-rev called Lar, may be the same as the activity
AB  - expressed in sbcA- strains of Escherichia coli, but it was functionally separable from
AB  - exonuclease VIII activity (the product of the recE gene), which is also expressed in sbcA-
AB  - strains.
ER  -

TY  - JOUR
AU  - Topal, M.D.
AU  - Conrad, M.
TI  - Changing endonuclease EcoRII Tyr308 to Phe abolishes cleavage but not recognition: possible homology with the Int-family of recombinases.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2599
EP  - 2603
VL  - 21
AB  - Endonuclease EcoRII is one of a group of type II restriction enzymes, including NaeI, NarI,
AB  - BspMI, HpaII, and SacII, that require binding of an enhancer sequence to cleave DNA.
AB  - Comparison of the EcoRII amino-acid sequence with the amino-acid consensus motifs that
AB  - differentiate between recombinase families uncovered similarity between a 29 amino-acid
AB  - sequence in the carboxyl end of EcoRII and the motif defining the integrase family of
AB  - recombinases. This similarity implied that EcoRII tyrosine 308 should be involved in
AB  - catalyzing hydrolysis of the scissile bond. Site-directed mutagenesis was used to mutate
AB  - Tyr308 to Phe. The phenylalanine-substituted enzyme could not cleave T5 DNA under conditions
AB  - in which wild-type enzyme completely cleaved this DNA. The Tyr308 to Phe mutation abolished
AB  - cleavage activity but not specific binding to DNA. No evidence was found for the existence
AB  - during the cleavage reaction of a covalent linkage between Tyr308 and DNA.
ER  -

TY  - JOUR
AU  - Topal, M.D.
AU  - Thresher, R.J.
AU  - Conrad, M.
AU  - Griffith, J.
TI  - NaeI endonuclease binding to pBR322 DNA induces looping.
JO  - Biochemistry
PY  - 1991
SP  - 2006
EP  - 2010
VL  - 30
AB  - Previous work has demonstrated the existence of both resistant and cleavable
AB  - NaeI sites.  Cleavable sites introduced on exogenous DNA can act in trans to
AB  - increase the catalysis of NaeI endonuclease cleavage at resistant sites without
AB  - affecting the apparent binding affinity of the enzyme for the resistant site
AB  - [Conrad, M. & Topal, M.D. (1988) Proc. Natl. Acad. Sci. 86, 9707-9711].  This
AB  - activation suggests allosteric regulation of NaeI cleavage by distant cis- and
AB  - trans-acting sites in DNAs containing both resistant and cleavable sites.
AB  - Plasmid pBR322 contains four NaeI sites, at least one of which is resistant to
AB  - cleavage.  Electron microscopy is used here to demonstrate that NaeI
AB  - endonuclease simultaneously binds to multiple recognition sites in pBR322 DNA
AB  - to form loops with NaeI protein bound at the loop's base.  The maximum number
AB  - of loops formed with a common base suggests four binding sites per enzyme
AB  - molecule.  Looping was inhibited by addition of enzyme-saturating amounts of
AB  - double-strand oligonucleotide without the NaeI site had no effect.  The number
AB  - of loops seen was not above background when double-stranded M13 DNA, which
AB  - contains only a single NaeI recognition site, was used as substrate.
ER  -

TY  - JOUR
AU  - Topel, M.
AU  - Pinder, M.I.M.
AU  - Johansson, O.N.
AU  - Kourtchenko, O.
AU  - Godhe, A.
AU  - Clarke, A.K.
TI  - Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi.
JO  - Genome Announcements
PY  - 2018
SP  - e01558
EP  - e01517
VL  - 6
AB  - We report here the genome sequence of Loktanella vestfoldensis strain SMR4r, isolated from the
AB  - marine diatom Skeletonema marinoi strain RO5AC. Its
AB  - 3,987,360-bp genome consists of a circular chromosome and two circular plasmids,
AB  - one of which appears to be shared with an S. marinoi-associated Roseovarius
AB  - species.
ER  -

TY  - JOUR
AU  - Topel, M.
AU  - Pinder, M.I.M.
AU  - Johansson, O.N.
AU  - Kourtchenko, O.
AU  - Godhe, A.
AU  - Clarke, A.K.
TI  - Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.
JO  - Genome Announcements
PY  - 2017
SP  - e00394
EP  - e00317
VL  - 5
AB  - We present the genome of Roseovarius mucosus strain SMR3, a marine bacterium isolated from the
AB  - diatom Skeletonema marinoi strain RO5AC sampled from top layer
AB  - sediments at 14 m depth. Its 4,381,426 bp genome consists of a circular
AB  - chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).
ER  -

TY  - JOUR
AU  - Topin, A.N.
AU  - Gritsenko, O.M.
AU  - Brevnov, M.G.
AU  - Gromova, E.S.
AU  - Korshunova, G.A.
TI  - Synthesis of a new photo-cross-linking nucleoside analogue containing an Aryl(trifluoromethyl)Diazirine group: Application for EcoRII and MvaI restriction-modification enzymes.
JO  - Nucleosides and Nucleotides
PY  - 1998
SP  - 1163
EP  - 1175
VL  - 17
AB  - A new photo-cross-linking dU analog,
AB  - 5-[4-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenyl]-2'deoxyuridine, was synthesized and
AB  - incorporated into the recognition site of EcoRII and MvaI restriction-modification enzymes.
AB  - The resulting base-modified 14-mer substrate was tested for cross-linking to these enzymes.
AB  - Cross-linking is effected by irradiation of the enzyme-substrate complexes as 366 nm.
ER  -

TY  - JOUR
AU  - Toro, M.
AU  - Cao, G.
AU  - Rump, L.
AU  - Nagaraja, T.G.
AU  - Meng, J.
AU  - Gonzalez-Escalona, N.
TI  - Genome Sequences of 64 Non-O157:H7 Shiga Toxin-Producing Escherichia coli Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01067
EP  - e01015
VL  - 3
AB  - Shiga toxin-producing Escherichia coli (STEC) strains are human pathogens. Although >400
AB  - non-O157 serotypes have been involved in human disease, whole-genome sequencing information is
AB  - missing for many serotypes. We sequenced 64 STEC strains comprising 38 serotypes, isolated
AB  - from clinical sources, animals, and environmental samples, to improve the phylogenetic
AB  - understanding of these important foodborne pathogens.
ER  -

TY  - JOUR
AU  - Toro, M.
AU  - Retamal, P.
AU  - Allard, M.
AU  - Brown, E.W.
AU  - Evans, P.
AU  - Gonzalez-Escalona, N.
TI  - Draft Genome Sequences of 33 Salmonella enterica Clinical and Wildlife Isolates from Chile.
JO  - Genome Announcements
PY  - 2015
SP  - e00054
EP  - e00015
VL  - 3
AB  - Salmonella enterica causes health problem worldwide. The relationships among strains that are
AB  - from the same serotype but different hosts, countries, and
AB  - continents remain elusive. Few genome sequences are available from S. enterica
AB  - isolates from South America. Therefore, we sequenced the genomes of 33 strains
AB  - from diverse sources isolated in Chile and determined that they were of different
AB  - serotypes. These genomes will improve phylogenetic analysis of Salmonella strains
AB  - from Chile and the rest of South America.
ER  -

TY  - JOUR
AU  - Toro, N.
AU  - Martinez-Abarca, F.
AU  - Nisa-Martinez, R.
TI  - Complete Genome Sequence of the RmInt1 Group II Intronless Sinorhizobium meliloti Strain RMO17.
JO  - Genome Announcements
PY  - 2014
SP  - e01001
EP  - e01014
VL  - 2
AB  - We report the complete genome sequence of the RmInt1 group II intronless Sinorhizobium
AB  - meliloti strain RMO17 isolated from Medicago orbicularis nodules
AB  - from Spanish soil. The genome consists of 6.73 Mb distributed between a single
AB  - chromosome and two megaplasmids (the chromid pSymB and pSymA).
ER  -

TY  - JOUR
AU  - Toropov, V.A.
AU  - Vakhitov, T.Y.
AU  - Shalaeva, O.N.
AU  - Roshchina, E.K.
AU  - Sitkin, S.I.
TI  - Complete Genome Sequences of the Probiotic Lactic Acid Bacteria Lactobacillus helveticus D75 and D76.
JO  - Genome Announcements
PY  - 2018
SP  - e01552
EP  - e01517
VL  - 6
AB  - Lactobacillus helveticus D75 and D76 were isolated from the intestinal tract of a healthy
AB  - child. Both strains possess symbiotic, probiotic, and antagonistic
AB  - activities. We have sequenced and annotated the whole genomes of L. helveticus
AB  - D75 and D76 and have conducted a preliminary genome comparative analysis.
ER  -

TY  - JOUR
AU  - Torosian, M.V.
AU  - Shishkova, O.V.
AU  - Rabinkova, E.V.
TI  - Influence of recB and recA mutations on bacteriophage restriction by different restriction modification plasmid systems of E. coli.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1988
SP  - 36
EP  - 41
VL  - 0
AB  - The effect of recB and recA mutations on lambda vir and P1 vir restriction by
AB  - different restriction-modification plasmid systems of E. coli was studied.  It
AB  - was shown that the effect of RI plasmid coded restriction-modification in E.
AB  - coli K12 and E. coli B strains and pJA4620 plasmid coded restriction in E. coli
AB  - K12 is observed only in RecB+ strain.  Phenomenon of restriction-modification
AB  - determined by R124, R245 plasmids does not depend of recB mutation.  Effect of
AB  - recA mutation has not been found in cultures harbouring R1, R245, R124 pJA4620
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Torosyan, M.V.
AU  - Rainkova, E.V.
AU  - Shishkova, L.A.
AU  - Naumova, L.A.
AU  - Fradkin, G.E.
TI  - Phenomenon of restriction alleviation in Escherichia coli strains.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1987
SP  - 37
EP  - 40
VL  - 10
AB  - The alleviation of foreign DNA restriction after treatment of cells by UV and gamma-rays or
AB  - ocr+-gene product of T3, T7 phages has been studied.  Both UV and gamma-radiation were shown
AB  - to induce restriction alleviation of unmodified phage.  The results of restriction alleviation
AB  - caused by T3 and T7 ocr+-gene products have been evaluated by F-lac+ transfer efficiencies in
AB  - heterologic crosses and plating of unmodified phage lambda.  The phenomenon of restriction
AB  - alleviation was established to depend on the strain used and to be expressed mostly in AB157
AB  - and its derivatives.
ER  -

TY  - JOUR
AU  - Torreblanca, J.
AU  - Casadesus, J.
TI  - DNA adenine methylase mutants of Salmonella typhimurium and a novel Dam-regulated locus.
JO  - Genetics
PY  - 1996
SP  - 15
EP  - 26
VL  - 144
AB  - Mutants of Salmonella typhimurium lacking DNA adenine methylase were isolated; they include
AB  - insertion and deletion alleles.  The dam locus maps at 75 min between cysG and aroB, similar
AB  - to the Escherichia coli dam gene.  Dam- mutants of S. typhimurium resemble those of E. coli in
AB  - the following phenotypes: (1) increased spontaneous mutations, (2) moderate SOS induction, (3)
AB  - enhancement of duplication segregation, (4) inviability of dam recA and dam recB mutants, and
AB  - (5) suppression of the inviability of the dam recA and dam recB combinations by mutations that
AB  - eliminate mismatch repair.  However, differences between S. typhimurium and E. coli dam
AB  - mutants are also found: (1) S. typhimurium dam mutants do not show increased UV sensitivity,
AB  - suggesting that methyl-directed mismatch repair does not participate in the repair of
AB  - UV-induced DNA damage in Salmonella.  (2) S. typhimurium dam recJ mutants are viable,
AB  - suggesting that the Salmonella RecJ function does not participate in the repair of DNA strand
AB  - breaks formed in the absence of Dam methylation.  We also describe a genetic screen for
AB  - detecting novel genes regulated by Dam methylation and a locus repressed by Dam methylation in
AB  - the S. typhimurium virulence (or "cryptic") plasmid.
ER  -

TY  - JOUR
AU  - Torreblanca, J.
AU  - Marques, S.
AU  - Casadesus, J.
TI  - Synthesis of FinP RNA by plasmids F and pSLT is regulated by DNA adenine methylation.
JO  - Genetics
PY  - 1999
SP  - 31
EP  - 45
VL  - 151
AB  - DNA adenine methylase mutants of Salmonella typhimurium contain reduced amounts of FinP, an
AB  - antisense RNA encoded by the virulence plasmid pSLT.  Lowered FinP levels are detected in both
AB  - Dam- FinO+ and Dam- FinO- backgrounds, suggesting that Dam methylation regulates FinP
AB  - production rather than FinP half-life.  Reduced amounts of F-encoded FinP RNA are likewise
AB  - found in Dam- mutants of Escherichia coli.  A consequence of FinP RNA scarcity in the absence
AB  - of DNA adenine methylation is that Dam- mutants of both S. typhimurium and E. coli show
AB  - elevated levels of F plasmid transfer.  Inhibition of F fertility by the S. typhimurium
AB  - virulence plasmid is also impaired in a Dam- background.
ER  -

TY  - JOUR
AU  - Torres, A.C.
AU  - Suarez, N.E.
AU  - Font, G.
AU  - Saavedra, L.
AU  - Taranto, M.P.
TI  - Draft Genome Sequence of Lactobacillus reuteri Strain CRL 1098, an Interesting Candidate for Functional Food Development.
JO  - Genome Announcements
PY  - 2016
SP  - e00806
EP  - e00816
VL  - 4
AB  - We report here the draft genome sequence of Lactobacillus reuteri strain CRL 1098. This strain
AB  - represents an interesting candidate for functional food
AB  - development because of its proven probiotic properties. The draft genome sequence
AB  - is composed of 1,969,471 bp assembled into 45 contigs and an average G+C content
AB  - of 38.8%.
ER  -

TY  - JOUR
AU  - Torres, B.
AU  - Jaenecke, S.
AU  - Timmis, K.N.
AU  - Garcia, J.L.
AU  - Diaz, E.
TI  - A gene containment strategy based on a restriction-modification system.
JO  - Environ. Microbiol.
PY  - 2000
SP  - 555
EP  - 563
VL  - 2
AB  - Engineering barriers to the spread of specific genes are of great interest both to increase
AB  - the predictability of recombinant microorganisms used for environmental applications and to
AB  - study the role of gene transfer in the adaptation of microbial communities to changing
AB  - environments. We report here a new gene containment circuit based on a toxin-antidote pair
AB  - that targets the cell DNA, i.e. the type II EcoRI restriction-modification system. The set-up
AB  - involved linkage of the ecoRIR lethal gene encoding the EcoRI endonuclease (toxin) to the
AB  - contained character in a plasmid and chromosomal insertion of the ecoRIM gene encoding the
AB  - cognate EcoRI methylase (antidote) that protects the target DNA from restriction. Transfer of
AB  - the contained character to a recipient cell lacking the antidote caused EcoRI-mediated
AB  - chromosomal breaks, leading to cell death, thereby preventing gene spread. Using
AB  - transformation and conjugation as mechanisms of DNA transfer and different environmentally
AB  - relevant bacteria as recipients, we have shown that the potentially universal EcoRI-based
AB  - containment system decreases gene transfer frequencies by more than four orders of magnitude.
AB  - Analyses of the survivors escaping killing revealed a number of possible inactivation
AB  - mechanisms.
ER  -

TY  - JOUR
AU  - Torres, B.
AU  - Jaenecke, S.
AU  - Timmis, K.N.
AU  - Garcia, J.L.
AU  - Diaz, E.
TI  - A dual lethal system to enhance containment of recombinant micro-organisms.
JO  - Microbiology
PY  - 2003
SP  - 3595
EP  - 3601
VL  - 149
AB  - Active containment systems based on the controlled expression of a lethal gene are designed to
AB  - increase containment of recombinant micro-organisms
AB  - used for environmental applications. A major drawback in containment is
AB  - the existence of mutations that generate surviving cells that cease to
AB  - respond to the toxic effect of the lethal function. In this work the
AB  - authors have developed for the first time a strategy to reduce the problem
AB  - of mutations and increase the efficiency of containment based on the
AB  - combination of two lethal functions acting on different cellular targets
AB  - of major concern in containment, DNA and RNA, and whose expression is
AB  - under control of different regulatory signals. To engineer the dual gene
AB  - containment circuit, two toxin-antitoxin pairs, i.e. the colicin
AB  - E3-immunity E3 and the EcoRI restriction-modification systems, were
AB  - combined. The genes encoding the immunity E3 and the EcoRI
AB  - methyltransferase proteins (antitoxins) were stably inserted into the
AB  - chromosome of the host cell, whereas the broad-host-range lethal genes
AB  - encoding the colicin E3 RNase and the EcoRI restriction endonuclease
AB  - (toxins) were flanking the contained trait in a plasmid. This dual lethal
AB  - cassette decreased gene transfer frequencies, through killing of the
AB  - recipient cells, by eight orders of magnitude, which provides experimental
AB  - evidence that the anticipated containment level due to the combination of
AB  - single containment systems is generally achieved. Survivors that escaped
AB  - killing were analysed and the mutational events involved were
AB  - characterized.
ER  -

TY  - JOUR
AU  - Torres, D.
AU  - Revale, S.
AU  - Obando, M.
AU  - Maroniche, G.
AU  - Paris, G.
AU  - Perticari, A.
AU  - Vazquez, M.
AU  - Wisniewski-Dye, F.
AU  - Martinez-Abarca, F.
AU  - Cassan, F.
TI  - Genome Sequence of Bradyrhizobium japonicum E109, One of the Most Agronomically Used Nitrogen-Fixing Rhizobacteria in Argentina.
JO  - Genome Announcements
PY  - 2015
SP  - e01566
EP  - e01514
VL  - 3
AB  - We present here the complete genome sequence of Bradyrhizobium japonicum strain E109, one of
AB  - the most used rhizobacteria for soybean inoculation in Argentina since the 1970s. The genome
AB  - consists of a 9.22-Mbp single chromosome and contains several genes related to nitrogen
AB  - fixation, phytohormone biosynthesis, and a rhizospheric lifestyle.
ER  -

TY  - JOUR
AU  - Torres, T.G.
AU  - Lozano, L.
AU  - Gonzalez, V.
AU  - Bustos, P.
AU  - Romero, D.
AU  - Brom, S.
TI  - Draft Genome Sequence of the Bean-Nodulating Sinorhizobium fredii Strain GR64.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6978
EP  - 6978
VL  - 194
AB  - Sinorhizobium fredii GR64 is a peculiar strain that is able to effectively nodulate bean but
AB  - not soybean, the common host of S. fredii. Here we present the
AB  - draft genome of S. fredii GR64. This information will contribute to a better
AB  - understanding of the symbiotic rhizobium-plant interaction and of rhizobial
AB  - evolution.
ER  -

TY  - JOUR
AU  - Torres-Tejerizo, G.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Ormeno-Orrillo, E.
AU  - Martinez-Romero, E.
AU  - Niehaus, K.
AU  - Puhler, A.
AU  - Kalinowski, J.
AU  - Lagares, A.
AU  - Schluter, A.
AU  - Pistorio, M.
TI  - Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.
JO  - Genome Announcements
PY  - 2017
SP  - e01513
EP  - e01516
VL  - 5
AB  - Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai
AB  - grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus
AB  - vulgaris The whole-genome sequence of the type strain, R. tibeticum CCBAU85039T, is reported
AB  - in this study.
ER  -

TY  - JOUR
AU  - Toshchakov, S.V.
AU  - Korzhenkov, A.A.
AU  - Samarov, N.I.
AU  - Mazunin, I.O.
AU  - Mozhey, O.I.
AU  - Shmyr, I.S.
AU  - Derbikova, K.S.
AU  - Taranov, E.A.
AU  - Dominova, I.N.
AU  - Bonch-Osmolovskaya, E.A.
AU  - Patrushev, M.V.
AU  - Podosokorskaya, O.A.
AU  - Kublanov, I.V.
TI  - Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 122
EP  - 122
VL  - 10
AB  - A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka
AB  - hot spring sediment. Isolate 1807-2 grew optimally at 85 degrees C,
AB  - pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA
AB  - gene sequence analysis placed the novel isolate in the crenarchaeal genus
AB  - Thermofilum; Thermofilum pendens was its closest valid relative (95.7 % of
AB  - sequence identity). Strain 1807-2 grew organothrophically using polysaccharides
AB  - (starch and glucomannan), yeast extract or peptone as substrates. The addition of
AB  - other crenarchaea culture broth filtrates was obligatory required for growth and
AB  - could not be replaced by the addition of these organisms' cell wall fractions, as
AB  - it was described for T. pendens. The genome of strain 1807-2 was sequenced using
AB  - Illumina and PGM technologies. The average nucleotide identities between genome
AB  - of strain 1807-2 and T. pendens strain HRK 5(T) and 'T. adornatus' strain 1910b
AB  - were 85 and 82 %, respectively. On the basis of 16S rRNA gene sequence phylogeny,
AB  - ANI calculations and phenotypic differences we propose a novel species
AB  - Thermofilum uzonense with the type strain 1807-2(T) (= DSM 28062(T) = JCM
AB  - 19810(T)). Project information and genome sequence was deposited in Genbank under
AB  - IDs PRJNA262459 and CP009961, respectively.
ER  -

TY  - JOUR
AU  - Toth, A.
AU  - Barna, T.
AU  - Nagy, I.
AU  - Horvath, B.
AU  - Nagy, I.
AU  - Tancsics, A.
AU  - Kriszt, B.
AU  - Baka, E.
AU  - Fekete, C.
AU  - Kukolya, J.
TI  - Draft Genome Sequence of the Lignocellulose Decomposer Thermobifida fusca Strain  TM51.
JO  - Genome Announcements
PY  - 2013
SP  - e00482
EP  - e00413
VL  - 1
AB  - Here, we present the complete genome sequence of Thermobifida fusca strain TM51,  which was
AB  - isolated from the hot upper layer of a compost pile in Hungary. T.
AB  - fusca TM51 is a thermotolerant, aerobic actinomycete with outstanding
AB  - lignocellulose-decomposing activity.
ER  -

TY  - JOUR
AU  - Toth, E.
AU  - Huszar, K.
AU  - Bencsura, P.
AU  - Kulcsar, P.I.
AU  - Vodicska, B.
AU  - Nyeste, A.
AU  - Welker, Z.
AU  - Toth, S.
AU  - Welker, E.
TI  - Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.
JO  - PLoS ONE
PY  - 2014
SP  - e90896
EP  - e90896
VL  - 9
AB  - The procedure described here allows the cloning of PCR fragments containing a recognition site
AB  - of the restriction endonuclease (Type IIP) used for cloning in
AB  - the sequence of the insert. A Type IIS endonuclease - a Body Double of the Type
AB  - IIP enzyme - is used to generate the same protruding palindrome. Thus, the insert
AB  - can be cloned to the Type IIP site of the vector without digesting the PCR
AB  - product with the same Type IIP enzyme. We achieve this by incorporating the
AB  - recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of
AB  - its recognition site in the PCR primer in such a way that the cutting positions
AB  - straddle the desired overhang sequence. Digestion of the PCR product by the Body
AB  - Double generates the required overhang. Hitherto the use of Type IIS restriction
AB  - enzymes in cloning reactions has only been used for special applications, the
AB  - approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for
AB  - general cloning purposes. To assist in finding Body Double enzymes, we summarised
AB  - the available Type IIS enzymes which are potentially useful for Body Double
AB  - cloning and created an online program
AB  - (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection
AB  - of suitable Body Double enzymes and the design of the appropriate primers.
ER  -

TY  - JOUR
AU  - Toth, J.
AU  - Bollins, J.
AU  - Szczelkun, M.D.
TI  - Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by  Type III restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 10870
EP  - 10881
VL  - 43
AB  - DNA cleavage by the Type III restriction enzymes requires long-range protein communication
AB  - between recognition sites facilitated by thermally-driven 1D
AB  - diffusion. This 'DNA sliding' is initiated by hydrolysis of multiple ATPs
AB  - catalysed by a helicase-like domain. Two distinct ATPase phases were observed
AB  - using short oligoduplex substrates; the rapid consumption of approximately 10
AB  - ATPs coupled to a protein conformation switch followed by a slower phase, the
AB  - duration of which was dictated by the rate of dissociation from the recognition
AB  - site. Here, we show that the second ATPase phase is both variable and only
AB  - observable when DNA ends are proximal to the recognition site. On DNA with sites
AB  - more distant from the ends, a single ATPase phase coupled to the conformation
AB  - switch was observed and subsequent site dissociation required little or no
AB  - further ATP hydrolysis. The overall DNA dissociation kinetics (encompassing site
AB  - release, DNA sliding and escape via a DNA end) were not influenced by the second
AB  - phase. Although the data simplifies the ATP hydrolysis scheme for Type III
AB  - restriction enzymes, questions remain as to why multiple ATPs are hydrolysed to
AB  - prepare for DNA sliding.
ER  -

TY  - JOUR
AU  - Toth, J.
AU  - van Aelst, K.
AU  - Salmons, H.
AU  - Szczelkun, M.D.
TI  - Dissociation from DNA of Type III Restriction-Modification enzymes during helicase-dependent motion and following endonuclease activity.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 6752
EP  - 6764
VL  - 40
AB  - DNA cleavage by the Type III Restriction-Modification (RM) enzymes requires the binding of a
AB  - pair of RM enzymes at two distant, inversely orientated recognition
AB  - sequences followed by helicase-catalysed ATP hydrolysis and long-range
AB  - communication. Here we addressed the dissociation from DNA of these enzymes at
AB  - two stages: during long-range communication and following DNA cleavage. First, we
AB  - demonstrated that a communicating species can be trapped in a DNA domain without
AB  - a recognition site, with a non-specific DNA association lifetime of approximately
AB  - 200 s. If free DNA ends were present the lifetime became too short to measure,
AB  - confirming that ends accelerate dissociation. Secondly, we observed that Type III
AB  - RM enzymes can dissociate upon DNA cleavage and go on to cleave further DNA
AB  - molecules (they can 'turnover', albeit inefficiently). The relationship between
AB  - the observed cleavage rate and enzyme concentration indicated independent binding
AB  - of each site and a requirement for simultaneous interaction of at least two
AB  - enzymes per DNA to achieve cleavage. In light of various mechanisms for
AB  - helicase-driven motion on DNA, we suggest these results are most consistent with
AB  - a thermally driven random 1D search model (i.e. 'DNA sliding').
ER  -

TY  - JOUR
AU  - Tothova, T.
AU  - Godany, A.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - Production of SacI and SacII isoschizomers by soil streptomycetes.
JO  - Biologia (Bratisl)
PY  - 2007
SP  - 381
EP  - 385
VL  - 62
AB  - Five fresh soil Streptomyces spp. strains were isolated, phylogenetically characterized on the
AB  - basis of 16S rDNA sequences and
AB  - analyzed for the presence of restriction modification systems. Three
AB  - type II site-specific endonucleases were detected and partially
AB  - purified. Two isolated enzymes were isoschizomers of SacI restriction
AB  - endonuclease recognizing 5'-GAGCTC-3' sequence; the third one
AB  - recognised 5'-CCGCGG-3' sequence and it was an isoschizomer of SacII.
AB  - SacII like modification was observed in other two isolates having no
AB  - detectable restriction activity. The lack of correlation between
AB  - restriction and modification phenotypes and phylogenetic classification
AB  - of the isolates indicates efficient gene transfer mechanism in the
AB  - Streptomyces genus.
ER  -

TY  - JOUR
AU  - Totsika, M.
AU  - Beatson, S.A.
AU  - Sarkar, S.
AU  - Phan, M.D.
AU  - Petty, N.K.
AU  - Bachmann, N.
AU  - Szubert, M.
AU  - Sidjabat, H.E.
AU  - Paterson, D.L.
AU  - Upton, M.
AU  - Schembri, M.A.
TI  - Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage: genome analysis and virulence mechanisms.
JO  - PLoS ONE
PY  - 2011
SP  - E26578
EP  - E26578
VL  - 6
AB  - Escherichia coli strains causing urinary tract infection (UTI) are increasingly
AB  - recognized as belonging to specific clones. E. coli clone O25b:H4-ST131 has
AB  - recently emerged globally as a leading multi-drug resistant pathogen causing
AB  - urinary tract and bloodstream infections in hospitals and the community. While
AB  - most molecular studies to date examine the mechanisms conferring multi-drug
AB  - resistance in E. coli ST131, relatively little is known about their virulence
AB  - potential. Here we examined E. coli ST131 clinical isolates from two
AB  - geographically diverse collections, one representing the major pathogenic
AB  - lineages causing UTI across the United Kingdom and a second representing UTI
AB  - isolates from patients presenting at two large hospitals in Australia. We
AB  - determined a draft genome sequence for one representative isolate, E. coli EC958,
AB  - which produced CTX-M-15 extended-spectrum beta-lactamase, CMY-23 type AmpC
AB  - cephalosporinase and was resistant to ciprofloxacin. Comparative genome analysis
AB  - indicated that EC958 encodes virulence genes commonly associated with
AB  - uropathogenic E. coli (UPEC). The genome sequence of EC958 revealed a transposon
AB  - insertion in the fimB gene encoding the activator of type 1 fimbriae, an
AB  - important UPEC bladder colonization factor. We identified the same fimB
AB  - transposon insertion in 59% of the ST131 UK isolates, as well as 71% of ST131
AB  - isolates from Australia, suggesting this mutation is common among E. coli ST131
AB  - strains. Insertional inactivation of fimB resulted in a phenotype resembling a
AB  - slower off-to-on switching for type 1 fimbriae. Type 1 fimbriae expression could
AB  - still be induced in fimB-null isolates; this correlated strongly with adherence
AB  - to and invasion of human bladder cells and bladder colonisation in a mouse UTI
AB  - model. We conclude that E. coli ST131 is a geographically widespread, antibiotic
AB  - resistant clone that has the capacity to produce numerous virulence factors
AB  - associated with UTI.
ER  -

TY  - JOUR
AU  - Touchon, M. et al.
TI  - Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.
JO  - PLoS Genet.
PY  - 2009
SP  - e1000344
EP  - e1000344
VL  - 5
AB  - The Escherichia coli species represents one of the best-studied model organisms,  but also
AB  - encompasses a variety of commensal and pathogenic strains that diversify
AB  - by high rates of genetic change. We uniformly (re-) annotated the genomes of 20
AB  - commensal and pathogenic E. coli strains and one strain of E. fergusonii (the
AB  - closest E. coli related species), including seven that we sequenced to
AB  - completion. Within the approximately 18,000 families of orthologous genes, we
AB  - found approximately 2,000 common to all strains. Although recombination rates are
AB  - much higher than mutation rates, we show, both theoretically and using
AB  - phylogenetic inference, that this does not obscure the phylogenetic signal, which
AB  - places the B2 phylogenetic group and one group D strain at the basal position.
AB  - Based on this phylogeny, we inferred past evolutionary events of gain and loss of
AB  - genes, identifying functional classes under opposite selection pressures. We
AB  - found an important adaptive role for metabolism diversification within group B2
AB  - and Shigella strains, but identified few or no extraintestinal virulence-specific
AB  - genes, which could render difficult the development of a vaccine against
AB  - extraintestinal infections. Genome flux in E. coli is confined to a small number
AB  - of conserved positions in the chromosome, which most often are not associated
AB  - with integrases or tRNA genes. Core genes flanking some of these regions show
AB  - higher rates of recombination, suggesting that a gene, once acquired by a strain,
AB  - spreads within the species by homologous recombination at the flanking genes.
AB  - Finally, the genome's long-scale structure of recombination indicates lower
AB  - recombination rates, but not higher mutation rates, at the terminus of
AB  - replication. The ensuing effect of background selection and biased gene
AB  - conversion may thus explain why this region is A+T-rich and shows high sequence
AB  - divergence but low sequence polymorphism. Overall, despite a very high gene flow,
AB  - genes co-exist in an organised genome.
ER  -

TY  - JOUR
AU  - Touchon, M.
AU  - Barbier, P.
AU  - Bernardet, J.F.
AU  - Loux, V.
AU  - Vacherie, B.
AU  - Barbe, V.
AU  - Rocha, E.
AU  - Duchaud, E.
TI  - Complete genome sequence of the fish pathogen Flavobacterium branchiophilum.
JO  - Appl. Environ. Microbiol.
PY  - 2011
SP  - 7656
EP  - 7662
VL  - 77
AB  - Members of the genus Flavobacterium occur in a variety of ecological niches and represent an
AB  - interesting diversity of lifestyles. Flavobacterium branchiophilum is the main causative agent
AB  - of bacterial gill disease, a severe condition affecting various cultured freshwater fish
AB  - species worldwide, in particular salmonids in Canada and Japan. We report here the complete
AB  - genome sequence of strain FL-15 isolated from a diseased sheatfish (Silurus glanis) in
AB  - Hungary. The analysis of the F. branchiophilum genome revealed putative mechanisms of
AB  - pathogenicity strikingly different from those of the other, closely related fish pathogen
AB  - Flavobacterium psychrophilum, including the first cholera-like toxin in a non-Proteobacteria
AB  - and a wealth of adhesins. The comparison with available genomes of other Flavobacterium
AB  - species revealed a small genome size, large differences in chromosome organization, and fewer
AB  - rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene
AB  - transfer shaped the evolution of F. branchiophilum, as evidenced by its virulence factors,
AB  - genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats)
AB  - systems. Further functional analysis should help in the understanding of host-pathogen
AB  - interactions and in the development of rational diagnostic tools and control strategies in
AB  - fish farms.
ER  -

TY  - JOUR
AU  - Tourlousse, D.M.
AU  - Honda, T.
AU  - Matsuura, N.
AU  - Ohashi, A.
AU  - Tonouchi, A.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of Bacteroidales Strain 6E, Isolated from a Rice Paddy Field in Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e01167
EP  - e01115
VL  - 3
AB  - We generated a high-quality draft genome sequence of Bacteroidales strain 6E, a strict
AB  - anaerobe newly isolated from Japanese rice paddy field soil. The genome consists of 61
AB  - contigs, with a total size of 4,436,542 bp and mean G+C content of 45.4%. Annotation predicted
AB  - 3,620 protein-coding and 54 RNA genes.
ER  -

TY  - JOUR
AU  - Tourlousse, D.M.
AU  - Matsuura, N.
AU  - Sun, L.
AU  - Toyonaga, M.
AU  - Kuroda, K.
AU  - Ohashi, A.
AU  - Cruz, R.
AU  - Yamaguchi, T.
AU  - Sekiguchi, Y.
TI  - Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.
JO  - Genome Announcements
PY  - 2015
SP  - e01168
EP  - e01115
VL  - 3
AB  - We report here the draft genome sequence of Bacteroidales strain TBC1, isolated from a
AB  - methanogenic wastewater treatment system. The draft genome has a size of 4,514,407 bp and a
AB  - G+C content of 46.7%. The predicted genomic content provides the basis for characterizing the
AB  - metabolism and ecological strategies of strain TBC1.
ER  -

TY  - JOUR
AU  - Touzain, F.
AU  - Le Devendec, L.
AU  - de Boisseson, C.
AU  - Baron, S.
AU  - Jouy, E.
AU  - Perrin-Guyomard, A.
AU  - Blanchard, Y.
AU  - Kempf, I.
TI  - Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from  French broilers.
JO  - PLoS ONE
PY  - 2018
SP  - e0188768
EP  - e0188768
VL  - 13
AB  - Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this
AB  - study was to analyze and compare plasmids coding for resistance
AB  - to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli
AB  - (APEC) strains obtained respectively at slaughterhouse or from diseased broilers
AB  - in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the
AB  - resistances of the transformants were determined. The sequences of the
AB  - ESC-resistance plasmids prepared from transformants were obtained by Illumina (33
AB  - plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids
AB  - contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20
AB  - of them carrying the sul2 or tet(A) genes respectively. Despite their diverse
AB  - origins, several plasmids showed very high percentages of identity. None of the
AB  - blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of
AB  - them were detected in the parental strains. Three plasmids had the blaCMY-2 gene,
AB  - but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB
AB  - replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain
AB  - isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3
AB  - plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT,
AB  - etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid.
AB  - In conclusion, our results show the dominance and high similarity of blaCTX-M-1
AB  - IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a
AB  - blaCMY-2 plasmid.
ER  -

TY  - JOUR
AU  - Tovkach, F.I.
TI  - A study of Erwinia carotovora phage resistance with the use of temperate bacteriophage ZF40.
JO  - Mikrobiologiia
PY  - 2002
SP  - 82
EP  - 88
VL  - 71
AB  - The causes of the unique phage resistance of the pectinolytic phytopathogenic strains of
AB  - Erwinia carotovora were studied with the use of temperate bacteriophage ZF40. It was shown
AB  - that, in these bacteria, the bacteriophage-cell interaction can be substantially blocked at
AB  - the adsorption level. An adequate indicator for studying the temperate bacteriophages of
AB  - Erwinias was developed on the basis of mutants resistant to macromolecular bacteriocins.
AB  - Various restriction-modification systems, which influence cell resistance to bacteriophages,
AB  - were revealed for the first time in E. carotovora. The phage resistance was shown to be
AB  - determined by the wide occurrence of homoimmune temperate viruses in pectinolytic Erwinias.
ER  -

TY  - JOUR
AU  - Tovkach, F.I.
AU  - Chervatyuk, N.V.
TI  - Phage system for studying the restriction-modification system of Erwinia carotovora.
JO  - Mikrobiol. Zh.
PY  - 2006
SP  - 27
EP  - 35
VL  - 68
AB  - A model for revealing and type identifying the systems of restriction-modification of
AB  - phytopathogenic bacterium Ewinia carotovora with the help of two virulent polyvalent phages-FE
AB  - 44 and T7 is proposed in the work.  The joint use of the phages permits to identify both the
AB  - limitations of phages development on the part of RM-systems of three major types, and on the
AB  - part of the competing episomes.  The proposed system also allows to reveal other kinds of
AB  - limitations, in particular those connected with the adsorption of the phage particles.
ER  -

TY  - JOUR
AU  - Town, J.
AU  - Audy, P.
AU  - Boyetchko, S.M.
AU  - Dumonceaux, T.J.
TI  - High-Quality Draft Genome Sequence of Bacillus subtilis Strain WAUSV36.
JO  - Genome Announcements
PY  - 2016
SP  - e00586
EP  - e00516
VL  - 4
AB  - Bacillus subtilis strain WAUSV36 inhibits the growth of and decreases disease symptoms caused
AB  - by the potato pathogen Phytophthora infestans We determined the
AB  - sequence of the 4.7-Mbp genome of this strain. WAUSV36 shared very high
AB  - nucleotide sequence identity with previously sequenced strains of B. subtilis.
ER  -

TY  - JOUR
AU  - Town, J.
AU  - Audy, P.
AU  - Boyetchko, S.M.
AU  - Dumonceaux, T.J.
TI  - High-Quality Draft Genome Sequence of Arthrobacter sp. OY3WO11, a Strain That Inhibits the Growth of Phytophthora infestans.
JO  - Genome Announcements
PY  - 2016
SP  - e00585
EP  - e00516
VL  - 4
AB  - Arthrobacter sp. strain OY3WO11 inhibits the growth of the potato pathogen Phytophthora
AB  - infestans in in vivo growth challenge assays. We determined the
AB  - draft genome sequence of this strain, assembling it into 3 scaffolds of 4.2 Mbp
AB  - total length. OY3WO11 may represent a novel species of Arthrobacter.
ER  -

TY  - JOUR
AU  - Town, J.
AU  - Audy, P.
AU  - Boyetchko, S.M.
AU  - Dumonceaux, T.J.
TI  - High-Quality Draft Genome Sequence of Biocontrol Strain Pantoea sp. OXWO6B1.
JO  - Genome Announcements
PY  - 2016
SP  - e00582
EP  - e00516
VL  - 4
AB  - Pantoea sp. strain OXWO6B1 inhibits the growth of the potato pathogen Phytophthora infestans
AB  - We determined the 5.2-Mbp genome sequence of this strain,
AB  - which featured at least 3 confirmed plasmids of up to 250 kbp. The genome
AB  - sequence of OXWO6B1 is different from that of all previously sequenced strains of
AB  - Pantoea.
ER  -

TY  - JOUR
AU  - Town, J.
AU  - Audy, P.
AU  - Boyetchko, S.M.
AU  - Dumonceaux, T.J.
TI  - Genome Sequence of Pseudomonas chlororaphis Strain 189.
JO  - Genome Announcements
PY  - 2016
SP  - e00581
EP  - e00516
VL  - 4
AB  - Pseudomonas chlororaphis strain 189 is a potent inhibitor of the growth of the potato pathogen
AB  - Phytophthora infestans We determined the complete, finished
AB  - sequence of the 6.8-Mbp genome of this strain, consisting of a single contiguous
AB  - molecule. Strain 189 is closely related to previously sequenced strains of P.
AB  - chlororaphis.
ER  -

TY  - JOUR
AU  - Town, J.
AU  - Cui, N.
AU  - Audy, P.
AU  - Boyetchko, S.
AU  - Dumonceaux, T.J.
TI  - Improved High-Quality Draft Genome Sequence of Pseudomonas fluorescens KENGFT3.
JO  - Genome Announcements
PY  - 2016
SP  - e00428
EP  - e00416
VL  - 4
AB  - Pseudomonas sp. strain KENGFT3 inhibits the growth of Phytophthora infestans and  is a
AB  - potentially useful biopesticide for plant diseases, including potato late
AB  - blight. We sequenced the 6.2-Mbp genome of this strain and assembled it into a
AB  - single scaffold with 9 contigs. KENGFT3 is related to previously sequenced
AB  - strains of P. fluorescens.
ER  -

TY  - JOUR
AU  - Town, J.
AU  - Dumonceaux, T.J.
TI  - High-Quality Draft Genome Sequences of Pantoea agglomerans Isolates Exhibiting Antagonistic Interactions with Wheat Seed-Associated Fungi.
JO  - Genome Announcements
PY  - 2016
SP  - e00511
EP  - e00516
VL  - 4
AB  - Pantoea agglomerans isolates 3 and 4 were retrieved from the bacterial community  associated
AB  - with wheat seeds. These isolates differ in their pattern of growth
AB  - antagonism toward Alternaria species. A comparison of the genome sequences of
AB  - these two isolates revealed a high sequence identity with previously sequenced
AB  - strains of P. agglomerans.
ER  -

TY  - JOUR
AU  - Town, J.R.
AU  - Dumonceaux, T.J.
TI  - Laboratory-scale bioaugmentation relieves acetate accumulation and stimulates methane production in stalled anaerobic digesters.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2016
SP  - 1009
EP  - 1017
VL  - 100
AB  - An imbalance between acidogenic and methanogenic organisms during anaerobic digestion can
AB  - result in increased accumulation of volatile fatty acids, decreased reactor pH, and inhibition
AB  - of methane-producing Archaea.  Most commonly the result of organic input overload or poor
AB  - inoculum selection, these microbiological and biochemical changes severely hamper reactor
AB  - performance, and there are a few tools available to facilitate reactor recovery.  A small,
AB  - stable consortium capable of catabolizing acetate and producing methane was propagated I vitro
AB  - and evaluated as a potential bioaugmentation tool for stimulating methanogenesis in acidified
AB  - reactors.  Replicate laboratory-scale batch digesters were seeded with a combination of
AB  - bioethanol stillage waste and a dairy manure inoculum previously observed to result in high
AB  - volatile fatty acid accumulation and reactor failure.  Experimental reactors were then amended
AB  - with the acetoclastic consortium, and control reactors were amended with sterile culture
AB  - media.  Within 7 days, bioaugmented reactors had significantly reduced acetate accumulation
AB  - and the proportion of methane in the biogas increased from 0.2+/-0 to 74.4+/-9.9% while
AB  - control reactors showed no significant reduction in acetate accumulation or increase in
AB  - methane production.  Organisms from the consortium were enumerated using specific quantitative
AB  - PCR assays to evaluate their growth I the experimental reactors.  While the abundance of
AB  - hydrogenotrophic microorganisms remained stale during the recovery period, an acetoclastic
AB  - methanogen phylogenetically similar to Methanosarcina sp. increased more than 100-fold and is
AB  - hypothesized to be the primary contributor to reactor recovery.  Genomic sequencing of this
AB  - organism revealed genes related to the production of methane from acetate, hydrogen, and
AB  - methanol.
ER  -

TY  - JOUR
AU  - Townsley, L.
AU  - Caro, L.
AU  - Kelkar, H.
AU  - Shank, E.A.
TI  - Draft Genome Sequence of Bacillus luciferensis Isolated from Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01140
EP  - e01116
VL  - 4
AB  - Bacillus luciferensis is a Gram-positive, facultatively anaerobic, motile rod. Here, we report
AB  - the first draft genome sequence, to our knowledge, of a B.
AB  - luciferensis strain (CH01), which will provide useful information for Bacillus
AB  - and soil bacteria research.
ER  -

TY  - JOUR
AU  - Townson, S.A.
AU  - Samuelson, J.C.
AU  - Bao, Y.
AU  - Xu, S.Y.
AU  - Aggarwal, A.K.
TI  - BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning.
JO  - Structure
PY  - 2007
SP  - 449
EP  - 459
VL  - 15
AB  - DNA recognition by proteins is essential for specific expression of genes in a living
AB  - organism. En route to a target DNA site, a protein will often
AB  - sample noncognate DNA sites through nonspecific protein-DNA interactions,
AB  - resulting in a variety of conformationally different binding states. We
AB  - present here the crystal structure of endonuclease BstYI bound to a
AB  - noncognate DNA. Surprisingly, the structure reveals the enzyme in a
AB  - "hemispecific" binding state on the pathway between nonspecific and
AB  - specific recognition. A single base pair change in the DNA abolishes
AB  - binding of only one monomer, with the second monomer bound specifically.
AB  - We show that the enzyme binds essentially as a rigid body, and that one
AB  - end of the DNA is accommodated loosely in the binding cleft while the
AB  - other end is held tightly. Another intriguing feature of the structure is
AB  - Ser172, which has a dual role in establishing nonspecific and specific
AB  - contacts. Taken together, the structure provides a snapshot of an enzyme
AB  - in a "paused" intermediate state that may be part of a more general
AB  - mechanism of scanning DNA.
ER  -

TY  - JOUR
AU  - Townson, S.A.
AU  - Samuelson, J.C.
AU  - Vanamee, E.S.
AU  - Edwards, T.A.
AU  - Escalante, C.R.
AU  - Xu, S.-Y.
AU  - Aggarwal, A.K.
TI  - Crystal structure of BstYI at 1.85 .ANG. resolution: A thermophilic restriction endonuclease with overlapping specificities to BamHI and  BglII.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 725
EP  - 733
VL  - 338
AB  - We report here the structure of BstYI, an "intermediate" type II restriction endonuclease with
AB  - overlapping sequence specificities to BamHI and BglII. BstYI, a thermophilic endonuclease,
AB  - recognizes and cleaves the degenerate hexanucleotide sequence 5'-RGATCY-3' (where R=A or G
AB  - and Y=C or T), cleaving DNA after the 5'-R on each strand to produce four-base (5')
AB  - staggered ends. The crystal structure of free BstYI was solved at 1.85A resolution by
AB  - multi-wavelength anomalous dispersion (MAD) phasing. Comparison with BamHI and BglII reveals a
AB  - strong structural consensus between all three enzymes mapping to the alpha/beta core domain
AB  - and residues involved in catalysis. Unexpectedly, BstYI also contains an additional "arm"
AB  - substructure outside of the core protein, which enables the enzyme to adopt a more compact,
AB  - intertwined dimer structure compared with BamHI and BglII. This arm substructure may underlie
AB  - the thermostability of BstYI. We identify putative DNA recognition residues and speculate as
AB  - to how this enzyme achieves a "relaxed" DNA specificity.
ER  -

TY  - JOUR
AU  - Townson, S.A.
AU  - Samuelson, J.C.
AU  - Xu, S.-Y.
AU  - Aggarwal, A.K.
TI  - Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
JO  - Structure
PY  - 2005
SP  - 791
EP  - 801
VL  - 13
AB  - The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3'
AB  - (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and
AB  - thus raises the question of whether BstYI DNA recognition will be more BamHI-like or
AB  - BglII-like.  We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT).
AB  - We find the complex to be more BglII-like with similarities mapping to DNA conformation,
AB  - domain organization, and residues involved in catalysis.  However, BstYI is unique in
AB  - containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and
AB  - BamHI-like elements.  Further, DNA recognition is more minimal than BglII and BamHI, where
AB  - only two residues mediate recognition of the entire core sequence.  Taken together, the
AB  - structure reveals a mechanism of degenerate DNA recognition and offers insights into the
AB  - possibilities and limitations in altering specificities of closely related restriction
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Toymentseva, A.A.
AU  - Suleimanova, A.D.
AU  - Boulygina, E.A.
AU  - Kazakov, S.V.
AU  - Baranova, D.S.
AU  - Akhmetova, A.I.
AU  - Mardanova, A.M.
AU  - Sharipova, M.R.
TI  - Draft Genome Sequence of Bacillus ginsengihumi Strain M2.11 with Phytase Activity.
JO  - Genome Announcements
PY  - 2015
SP  - e00851
EP  - e00815
VL  - 3
AB  - This paper announces the genome sequence of Bacillus ginsengihumi strain M2.11, which has been
AB  - characterized as a strain which produces the enzyme with the
AB  - ability to degrade phytase. The genome of the strain M2.11 is 3.7 Mb and harbors
AB  - 3,082 coding sequences.
ER  -

TY  - JOUR
AU  - Trachtenberg, A.M.
AU  - Carney, J.G.
AU  - Linnane, J.D.
AU  - Rheaume, B.A.
AU  - Pitts, N.L.
AU  - Mykles, D.L.
AU  - MacLea, K.S.
TI  - Draft Genome Sequence of the Salt Water Bacterium Oceanospirillum linum ATCC 11336T.
JO  - Genome Announcements
PY  - 2017
SP  - e00395
EP  - e00317
VL  - 5
AB  - Oceanospirillum linum ATCC 11336T is an aerobic, bipolar-tufted gammaproteobacterium first
AB  - isolated in the Long Island Sound in the 1950s. This
AB  - announcement offers a genome sequence for O. linum ATCC 11336T, which has a
AB  - predicted genome size of 3,782,189 bp (49.13% G+C content) containing 3,540 genes
AB  - and 3,361 coding sequences.
ER  -

TY  - JOUR
AU  - Trachtenberg, A.M.
AU  - Goen, A.E.
AU  - MacLea, K.S.
TI  - Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain.
JO  - Genome Announcements
PY  - 2018
SP  - e00594
EP  - e00518
VL  - 6
AB  - Genomes from three strains of Kocuria rosea were sequenced. K. rosea ATCC 186, the type
AB  - strain, was 3,958,612 bp in length with a total G+C content of 72.70%.
AB  - When assembled, K. rosea ATCC 516 was 3,862,128 bp with a 72.82% G+C content. K.
AB  - rosea ATCC 49321 was 4,018,783 bp in size with a 72.49% G+C content.
ER  -

TY  - JOUR
AU  - Traglia, G.
AU  - Vilacoba, E.
AU  - Almuzara, M.
AU  - Diana, L.
AU  - Iriarte, A.
AU  - Centron, D.
AU  - Ramirez, M.S.
TI  - Draft Genome Sequence of an Extensively Drug-Resistant Acinetobacter baumannii Indigo-Pigmented Strain.
JO  - Genome Announcements
PY  - 2014
SP  - e01146
EP  - e01114
VL  - 2
AB  - Last year in 2013, we reported an outbreak due to indigo-pigmented Acinetobacter  baumannii
AB  - strains in a hospital from Buenos Aires, Argentina. Here, we present
AB  - the draft genome sequence of one of the strains (A. baumannii A33405) involved in
AB  - the outbreak. This isolate was categorized as extensively drug-resistant (XDR)
AB  - and harbors different genetic elements associated with horizontal genetic
AB  - transfer and multiple antibiotic resistances.
ER  -

TY  - JOUR
AU  - Traglia, G.M.
AU  - Almuzara, M.
AU  - Barberis, C.
AU  - Montana, S.
AU  - Schramm, S.T.
AU  - Enriquez, B.
AU  - Mussi, M.A.
AU  - Vay, C.
AU  - Iriarte, A.
AU  - Ramirez, M.S.
TI  - Draft genome sequence of a taxonomically unique acinetobacter clinical strain with proteolytic and hemolytic activities.
JO  - Genome Announcements
PY  - 2015
SP  - e00030
EP  - e00015
VL  - 3
AB  - Acinetobacter sp. strain A47, which has been recovered from several soft tissue samples from a
AB  - patient undergoing reconstructive surgery due to a traumatic
AB  - amputation, was categorized as a taxonomically unique bacterial strain. The
AB  - molecular analysis based on three housekeeping protein-coding genes (16S rRNA,
AB  - rpoB, and gyrB) showed that strain A47 does not belong to any of the hitherto
AB  - known taxa and may represent a previously undescribed Acinetobacter species.
ER  -

TY  - JOUR
AU  - Traglia, G.M.
AU  - Dixon, C.
AU  - Chiem, K.
AU  - Almuzara, M.
AU  - Barberis, C.
AU  - Montana, S.
AU  - Merino, C.
AU  - Mussi, M.A.
AU  - Tolmasky, M.E.
AU  - Iriarte, A.
AU  - Vay, C.
AU  - Ramirez, M.S.
TI  - Draft Genome Sequence of Empedobacter (Formerly Wautersiella) falsenii comb. nov. Wf282, a Strain Isolated from a Cervical Neck Abscess.
JO  - Genome Announcements
PY  - 2015
SP  - e00235
EP  - e00215
VL  - 3
AB  - Empedobacter (formerly Wautersiella) falsenii comb. nov. strain Wf282 was isolated from a
AB  - cervical neck abscess sample from an 18-year-old female patient.
AB  - The isolate was resistant to many antibiotics, including meropenem and colistin.
AB  - The total DNA from the multidrug-resistant E. falsenii comb. nov. Wf282 clinical
AB  - isolate was sequenced.
ER  -

TY  - JOUR
AU  - Tragut, V.
AU  - Xiao, J.
AU  - Bylina, E.J.
AU  - Borthakur, D.
TI  - Characterization of DNA restriction-modification systems in Spirulina platensis strain pacifica.
JO  - J. Appl. Phycol.
PY  - 1995
SP  - 561
EP  - 564
VL  - 7
AB  - Four unique restriction enzymes were identified in the soluble protein fraction of Spirulina
AB  - platensis strain pacifica, a commercially important strain of marine cyanobacterium that is
AB  - used as a supplement in human diets.  These are SpaI, SpaII, SpaII and SpaIV, which are
AB  - isoschizomers of Tth111I, PvuI, PvuII and HindIII, respectively.  The recognition sites of
AB  - each of these four enzymes were identified by restriction digests of different plasmid DNAs of
AB  - known sequence and determining the cleavage sites by sequencing.  SpaI is the most predominant
AB  - restriction enzyme present in S. platensis strain pacifica.  It shows high activity at 37oC
AB  - compared to 65oC for its isoschizomer Tth111I.
ER  -

TY  - JOUR
AU  - Tran, P.H.
TI  - X-ray crystal structure of N-6 adenine deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae.
JO  - Diss. Abstr.
PY  - 2001
SP  - 4801
EP  - B-4802-B
VL  - 61
AB  - X-ray diffraction by using resonant anomalous scattering has become a popular tool for solving
AB  - crystal structures in the last ten years with the expanded availability of tunable synchrotron
AB  - radiation for protein crystallography.  Mercury atoms were used for phasing.  The crystal
AB  - structure of N-6 deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae
AB  - (DpnM) was solved by using the Multiple Anomalous Diffraction technique.  The crystal
AB  - structure reveals the formation of mercaptide between the mercury ion and the thiol group on
AB  - the cysteine amino acid inn a hydrophobic environment.  The crystal structure contains the
AB  - bound ligand, S-adenosyl-L-methionine on the surface of the concave opening.  The direction of
AB  - the beta-strands on the beta sheets are identical to other solved methyltransferases.  The
AB  - highly conserved motifs, DPPY and the FxGxG, are found to be important in ligand binding and
AB  - possibly in methyl group transfer.  The structure has a concave cleft with an opening on the
AB  - order of 30 Angstroms that can accommodate a DNA duplex.  By molecular modeling coupled to
AB  - sequence alignment, two other highly conserved residues Arg21 and Gly19 are found to be
AB  - important in catalysis.
ER  -

TY  - JOUR
AU  - Tran, P.H.
AU  - Korszun, Z.R.
AU  - Cerritelli, S.
AU  - Springhorn, S.S.
AU  - Lacks, S.A.
TI  - Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine.
JO  - Structure
PY  - 1998
SP  - 1563
EP  - 1575
VL  - 6
AB  - Methyltransferases catalyze the transfer of methyl groups from S-adenosylmethionine to a
AB  - variety of small molecular and macromolecular substrates.  These enzymes contain a
AB  - characteristic alpha/beta structural fold.  Four groups of DNA Mtases have been defined and
AB  - representative structures have been determined for three groups.  DpnM is a DNA Mtase that
AB  - acts on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA Mtases, for
AB  - which no structures are known.
ER  -

TY  - JOUR
AU  - Tran, P.N.
AU  - Tan, N.E.
AU  - Lee, Y.P.
AU  - Gan, H.M.
AU  - Polter, S.J.
AU  - Dailey, L.K.
AU  - Hudson, A.O.
AU  - Savka, M.A.
TI  - Whole-Genome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans).
JO  - Genome Announcements
PY  - 2015
SP  - e01319
EP  - e01315
VL  - 3
AB  - Here, we report the whole-genome sequences and annotation of 11 endophytic bacteria from
AB  - poison ivy (Toxicodendron radicans) vine tissue. Five bacteria
AB  - belong to the genus Pseudomonas, and six single members from other genera were
AB  - found present in interior vine tissue of poison ivy.
ER  -

TY  - JOUR
AU  - Tran, T.D.
AU  - Huynh, S.
AU  - Parker, C.T.
AU  - Hnasko, R.
AU  - Gorski, L.
AU  - McGarvey, J.A.
TI  - Complete Genome Sequences of Three Bacillus amyloliquefaciens Strains That Inhibit the Growth of Listeria monocytogenes In Vitro.
JO  - Genome Announcements
PY  - 2018
SP  - e00579
EP  - e00518
VL  - 6
AB  - Here, we report the complete genome sequences of three Bacillus amyloliquefaciens strains
AB  - isolated from alfalfa, almond drupes, and grapes that inhibited the
AB  - growth of Listeria monocytogenes strain 2011L-2857 in vitro We also report
AB  - multiple gene clusters encoding secondary metabolites that may be responsible for
AB  - the growth inhibition of L. monocytogenes.
ER  -

TY  - JOUR
AU  - Tran-Betcke, A.
AU  - Behrens, B.
AU  - Noyer-Weidner, M.
AU  - Trautner, T.A.
TI  - DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences.
JO  - Gene
PY  - 1986
SP  - 89
EP  - 96
VL  - 42
AB  - The Phi3T DNA methyltransferase (Mtase) and most of the SPbeta Mtase genes have
AB  - been sequenced.  With the exception of their promoters, no difference was found
AB  - between the Phi3T and SPbeta Mtase genes which code for an enzyme with a Mr, of
AB  - 50507, consisting of 443 amino acids (aa).  Comparison of the deduced aa
AB  - sequence of the Phi3T/SPbeta type Mtase (target specificity: GGCC and GCNGC)
AB  - with that of the previously established sequence of the SPR Mtase (Buhk et al.,
AB  - 1984) which has the target specificity GGCC and CCGG, reveals strong
AB  - similarities between these two types of enzymes.  There is, however, one
AB  - striking difference: both the Phi3T/SPbeta and the SPR enzymes contain at
AB  - different positions inserts of 33 aa, which have no homology to each other.  We
AB  - suggest that the methylation specificity unique to each of the two types of
AB  - Mtases (GCNGC in Phi3T/SPbeta ; CCGG in SPR) depends on these inserts, while
AB  - the GGCC-specific modification potential common to all Mtases is determined by
AB  - structures conserved in both types of enzymes.  A DNA fragment of non-modifying
AB  - phage Z, which shows homology to both flanks of the SPR Mtase gene, was also
AB  - sequenced.  This segment can be described as a derivative of SPR DNA, in which
AB  - the Mtase gene and sequences at its 5' end have been deleted, with the deletion
AB  - extending between two direct repeats of 25 bp.
ER  -

TY  - JOUR
AU  - Tran-Nguyen, L.T.
AU  - Kube, M.
AU  - Schneider, B.
AU  - Reinhardt, R.
AU  - Gibb, K.S.
TI  - Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains  OY-M and AY-WB.
JO  - J. Bacteriol.
PY  - 2008
SP  - 3979
EP  - 3991
VL  - 190
AB  - The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I;
AB  - rp-A), associated with dieback in papaya, Australian
AB  - grapevine yellows in grapevine, and several other important plant
AB  - diseases, was determined. The circular chromosome is represented by
AB  - 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes.
AB  - Five hundred two of these protein-coding genes were functionally assigned,
AB  - while 337 genes were hypothetical proteins with unknown function.
AB  - Potential mobile units (PMUs) containing clusters of DNA repeats comprised
AB  - 12.1% of the genome. These PMUs encoded genes involved in DNA replication,
AB  - repair, and recombination; nucleotide transport and metabolism;
AB  - translation; and ribosomal structure. Elements with similarities to phage
AB  - integrases found in these mobile units were difficult to classify, as they
AB  - were similar to both insertion sequences and bacteriophages. Comparative
AB  - analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris"
AB  - strains OY-M and AY-WB showed that the gene order was more conserved
AB  - between the closely related "Ca. Phytoplasma asteris" strains than to "Ca.
AB  - Phytoplasma australiense." Differences observed between "Ca. Phytoplasma
AB  - australiense" and "Ca. Phytoplasma asteris" strains included the
AB  - chromosome size (18,693 bp larger than OY-M), a larger number of genes
AB  - with assigned function, and hypothetical proteins with unknown function.
ER  -

TY  - JOUR
AU  - Trasler, J.M.
AU  - Alcivar, A.A.
AU  - Hake, L.E.
AU  - Bestor, T.
AU  - Hecht, N.B.
TI  - DNA methyltransferase is developmentally expressed in replicating and non-replicating male germ cells.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2541
EP  - 2545
VL  - 20
AB  - Genomic methylation patterns are established during maturation of primordial germ cells and
AB  - during gametogenesis. While methylation is linked to DNA replication in somatic cells, active
AB  - de novo methylation and demethylation occur in post-replicative spermatocytes during meiotic
AB  - prophase. We have examined differentiating male germ cells for alternative forms of DNA
AB  - (cytosine-5)-methyltransfease (DNA MTase) and have found a 6.2 kb DNA MTase mRNA that is
AB  - present in appreciable quantitites only in testis; in post-replicative pachytene spermatocytes
AB  - it is the predominant form of DNA MTase mRNA. The 5.2 kb DNA MTase mRNA, characteristic of all
AB  - somatic cells, was detected in isolated type A and B spermatogonia and haploid round
AB  - spermatids. Immunoblot analysis detected a protein in spermatogenic cells with a relative mass
AB  - of 180,000-200,000, which is close to the known size of the somatic form of mammalian DNA
AB  - MTase. The demonstration of the differential developmental expression of DNA MTase in male
AB  - germ cells argues for a role for testicular DNA methylation events, not only during
AB  - replication in premeiotic cells, but also during meiotic prophase and postmeiotic development.
ER  -

TY  - JOUR
AU  - Trasler, J.M.
AU  - Trasler, D.G.
AU  - Beston, T.H.
AU  - Li, E.
AU  - Ghibu, F.
TI  - DNA methyltransferase in normal and Dnmtn/Dnmtn mouse embryos.
JO  - Dev. Dyn.
PY  - 1996
SP  - 239
EP  - 247
VL  - 206
AB  - The mouse genome experiences a large decrease in net 5-methylcytosine
AB  - between fertilization and implantation; de novo methylation brings 5-methylcytosine to
AB  - adult somatic cell levels between implantation and gastrulation.  Very little is known of the
AB  - regulation of demethylation or de novo methylation.  Levels of the one known form of
AB  - DNA methyltransferase are very high in early embryos, but the enzyme is localized to the
AB  - cytoplasm during most of preimplantation development.  We show here that DNA
AB  - methyltransferase is found exclusively in nuclei of the conceptus after implantation, and
AB  - that nuclei of proximal decidual cells are free of detectable DNA methyltransferase.  High
AB  - levels of DNA methyltransferase were seen in all tissues, including the developing nervous
AB  - system, of 9.5- to 12.5-day embryos.  The large maternal stores of DNA methyltransferase
AB  - become limiting prior to embryonic day 9.5, as shown by barely detectable immunostaining
AB  - in 9.5-day embryos homozygous for a loss-of-function mutation (Dnmtn) in the DNA
AB  - methyltransferase gene.  These mutant embryos failed to develop past the 25-somite stage
AB  - and showed evidence of developmental delay and some developmental asynchrony.
AB  - Normal embryonic and extraembryonic tissues contained similar levels of DNA
AB  - methyltransferase, even though severely reduced methylation levels and a loss of
AB  - imprinting have previously been observed in extraembryonic tissues.  These findings
AB  - suggest that methylation patterns are not a simple function of the concentration of DNA
AB  - methyltransferase, and that unidentified factors must be involved in the regulation of de
AB  - novo methylation during early development of the mouse.
ER  -

TY  - JOUR
AU  - Trautmann, D.
AU  - Voss, B.
AU  - Wilde, A.
AU  - Al-Babili, S.
AU  - Hess, W.R.
TI  - Microevolution in cyanobacteria: re-sequencing a motile substrain of Synechocystis sp. PCC 6803.
JO  - DNA Res.
PY  - 2012
SP  - 435
EP  - 448
VL  - 19
AB  - Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying
AB  - photosynthesis, phototaxis, the production of biofuels and many other aspects.
AB  - Here we present a re-sequencing study of the genome and seven plasmids of one of
AB  - the most widely used Synechocystis sp. PCC 6803 substrains, the glucose tolerant
AB  - and motile Moscow or 'PCC-M' strain, revealing considerable evidence for recent
AB  - microevolution. Seven single nucleotide polymorphisms (SNPs) specifically shared
AB  - between 'PCC-M' and the 'PCC-N and PCC-P' substrains indicate that 'PCC-M'
AB  - belongs to the 'PCC' group of motile strains. The identified indels and SNPs in
AB  - 'PCC-M' are likely to affect glucose tolerance, motility, phage resistance,
AB  - certain stress responses as well as functions in the primary metabolism,
AB  - potentially relevant for the synthesis of alkanes. Three SNPs in intergenic
AB  - regions could affect the promoter activities of two protein-coding genes and one
AB  - cis-antisense RNA. Two deletions in 'PCC-M' affect parts of clustered regularly
AB  - interspaced short palindrome repeats-associated spacer-repeat regions on plasmid
AB  - pSYSA, in one case by an unusual recombination between spacer sequences.
ER  -

TY  - JOUR
AU  - Trautner, T.A.
AU  - Balganesh, T.
AU  - Wilke, K.
AU  - Noyer-Weidner, M.
AU  - Rauhut, E.
AU  - Lauster, R.
AU  - Behrens, B.
AU  - Pawlek, B.
TI  - Organization of target-recognizing domains in the multispecific DNA (cytosine-5) methyltransferases of Bacillus subtilis phages SPR and Phi-3T.
JO  - Gene
PY  - 1988
SP  - 267
EP  - 267
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Trautner, T.A.
AU  - Balganesh, T.S.
AU  - Pawlek, B.
TI  - Chimeric multispecific DNA methyltransferases with novel combinations of target recognition.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 6649
EP  - 6658
VL  - 16
AB  - DNA target recognizing domains of different multispecific
AB  - DNA-cytosine-methyltransferases can be rearranged through engineering of the
AB  - corresponding genes to generate enzymes with novel combinations of target
AB  - recognition.
ER  -

TY  - JOUR
AU  - Trautner, T.A.
AU  - Noyer-Weidner, M.
TI  - Restriction/modification and methylation systems in Bacillus subtilis, related species, and their phages.
JO  - Bacillus subtilis and other gram-positive bacteria: Biochemistry, Physiology, and Molecular Genetics
PY  - 1993
SP  - 539
EP  - 552
VL  - 0
AB  - Several restriction/modification (R/M) systems have been identified in Bacillus subtilis and
AB  - related bacteria and will be described here. Accepting the view that R/M systems have evolved
AB  - to defend bacteria effectively against attack by bacterial viruses, we shall discuss the
AB  - question of what mechanisms bacteriophages have developed to overcome barriers provided by
AB  - host R/M systems. To what extent do R/M systems affect other inter- and intra-specific
AB  - transport of DNA? In this connection, we shall discuss the usefulness of restriction systems,
AB  - with their high substrate specificities for double-stranded DNA, in understanding the
AB  - processing of free or packaged DNA during uptake into B. subtilis cells or subcellular
AB  - structures. Recent progress in the characterization of genes encoding restriction
AB  - endonucleases (ENases) and modification methyltransferases (MTases) from a wide range of
AB  - organisms has made such systems per se interesting paradigms for the study of the evolution of
AB  - highly specific DNA-binding proteins. In particular, our interest is focused here on the
AB  - phylogenetic relationship among the various ENases and MTases of Bacillus and other bacterial
AB  - species. Furthermore, the requirement of coexistence of an ENase with an MTase represents an
AB  - interesting case of obligatory coevolution of two genes. The study of multispecific MTases,
AB  - discovered so far only in some temperate B. subtilis and Bacillus amyloliquefaciens phages,
AB  - has made significant contribution to our present understanding of the nature, function, and
AB  - evolution of R/M systems and particularly of their MTases. The interesting biochemical aspects
AB  - of the action of ENases and MTases will not be covered here. Such discussions are included in
AB  - a recent review.
ER  -

TY  - JOUR
AU  - Trautner, T.A.
AU  - Pawlek, B.
AU  - Behrens, B.
AU  - Willert, J.
TI  - Exact size and organization of DNA target-recognizing domains of multispecific DNA-(cytosine-C5)-methyltransferases.
JO  - EMBO J.
PY  - 1996
SP  - 1434
EP  - 1442
VL  - 15
AB  - A large portion of the sequences of type II DNA-(cytosine-C5)-methyltransferases (C5-MTases)
AB  - represent highly conserved blocks of amino acids.  General steps in the methylation reaction
AB  - performed by C5-MTases have been found to be mediated by some of these domains.  C5-MTases
AB  - carry, in addition at the same relative location, a region variable in size and amino acid
AB  - composition, part of which is associated with the capacity of each C5-MTase to recognize its
AB  - characteristic target.  Individual target-recognizing domains (TRDs) for the targets CCGG (M),
AB  - CC(A/T)GG (E), GGCC (H), GCNGC (F) and G(G/A/T)GC(C/A/T)C (B) could be identified in the
AB  - C-terminal part of the variable region of multispecific C5-MTases.  With experiments reported
AB  - here, we have established the organization of the variable regions of the multispecific MTases
AB  - M.SPRI, M.Phi3TI, M.H2I and M.Rho11sI at the resolution of individual amino acids.  These
AB  - regions comprise 204, 175, 268 and 268 amino acids, respectively.  All variable regions are
AB  - bipartite.  They contain at their N-terminal side a very similar sequence of 71 amino acids.
AB  - The integrity of this sequence must be assured to provide enzyme activity.  Bracketed by 6-10
AB  - linker amino acids, they have, depending on the enzyme studied, towards their C-terminal end
AB  - ensembles of individual TRDs of 38 (M), 39 (E), 40 (H), 44 (F) and 54 (B) amino acids.  TRDs
AB  - of different enzymes with equal specificity have the same size.  TRDs do not overlap but are
AB  - either separated by linker amino acids or abut each other.
ER  -

TY  - JOUR
AU  - Trautner, T.A.
AU  - Pawlek, B.
AU  - Bron, S.
AU  - Anagnostopoulos, C.
TI  - Restriction and Modification in B. subtilis.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 181
EP  - 191
VL  - 131
AB  - Restriction and modification observed in Bacillus subtilis strain "R" affects
AB  - infection and transfection with phages SPP1, Phi105 and SPO2, but not with SP8,
AB  - Phi29, SP82, Sp50, H1 or PBS1.  It affects also PBS1 mediated transduction, but
AB  - not transformation with bacterial DNA.  The marker(s) determining
AB  - restriction/modification map between the origin of replication of the B.
AB  - subtilis chromosome and purA16.
ER  -

TY  - JOUR
AU  - Trautner, T.A.
AU  - Pawlek, B.
AU  - Gunthert, U.
AU  - Canosi, U.
AU  - Jentsch, S.
AU  - Freund, M.
TI  - Restriction and modification in Bacillus subtilis: Identification of a gene in the temperate phage SPbeta coding for a BsuR specific modification methyltransferase.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 361
EP  - 367
VL  - 180
AB  - A gene coding for a modifying DNA-methyltransferase which methylates the
AB  - central C in the BsuR recognition sequence 5'GGCC was identified in the genome
AB  - of the temperate Bacillus subtilis phage SPbeta.  This gene is expressed only
AB  - after induction of the prophage by either mitomycin C or UV.  The presence of
AB  - active methyltransferase in induced cells leads to modification of BsuR
AB  - recognition sites in SPbeta DNA as well as in heterologous DNA.
ER  -

TY  - JOUR
AU  - Travis, A.J.
AU  - Kelly, D.
AU  - Flint, H.J.
AU  - Aminov, R.I.
TI  - Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis.
JO  - Genome Announcements
PY  - 2015
SP  - e01286
EP  - e01215
VL  - 3
AB  - We report here the complete genome sequence of the human gut symbiont Roseburia hominis
AB  - A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces.
AB  - The genome is represented by a 3,592,125-bp chromosome with 3,405 coding
AB  - sequences. A number of potential functions contributing to host-microbe
AB  - interaction are identified.
ER  -

TY  - JOUR
AU  - Travis, J.
TI  - DNA flips out!  Enzymes repair and modify DNA in a surprising way.
JO  - Sci. News
PY  - 1995
SP  - 188
EP  - 189
VL  - 148
AB  - According to recent research, enzymes have another way of tackling DNA.  Some apparently pry
AB  - apart a base pair, then rotate one of the freed nucleotides, bringing its base out of the
AB  - confines of the double helix and into the enzyme's active site, a pocket within the
AB  - protein's structure.  The enzyme can then remove this pocketed base from its nucleotide or
AB  - modify the base and sling it back into its proper position.
ER  -

TY  - JOUR
AU  - Travisany, D.
AU  - Di Genova, A.
AU  - Sepulveda, A.
AU  - Bobadilla-Fazzini, R.A.
AU  - Parada, P.
AU  - Maass, A.
TI  - Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in  Northern Chile.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6327
EP  - 6328
VL  - 194
AB  - Sulfobacillus thermosulfidooxidans strain Cutipay is a mixotrophic, acidophilic,  moderately
AB  - thermophilic bacterium isolated from mining environments of the north
AB  - of Chile, making it an interesting subject for studying the bioleaching of
AB  - copper. We introduce the draft genome sequence and annotation of this strain,
AB  - which provide insights into its mechanisms for heavy metal resistance.
ER  -

TY  - JOUR
AU  - Treangen, T.J.
AU  - Maybank, R.A.
AU  - Enke, S.
AU  - Friss, M.B.
AU  - Diviak, L.F.
AU  - Karaolis, D.K.
AU  - Koren, S.
AU  - Ondov, B.
AU  - Phillippy, A.M.
AU  - Bergman, N.H.
AU  - Rosovitz, M.J.
TI  - Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.
JO  - Genome Announcements
PY  - 2014
SP  - e01110
EP  - e01114
VL  - 2
AB  - Staphylococcus aureus subsp. aureus ATCC 25923 is commonly used as a control strain for
AB  - susceptibility testing to antibiotics and as a quality control strain
AB  - for commercial products. We present the completed genome sequence for the strain,
AB  - consisting of the chromosome and a 27.5-kb plasmid.
ER  -

TY  - JOUR
AU  - Trees, E.
AU  - Strockbine, N.
AU  - Changayil, S.
AU  - Ranganathan, S.
AU  - Zhao, K.
AU  - Weil, R.
AU  - MacCannell, D.
AU  - Sabol, A.
AU  - Schmidtke, A.
AU  - Martin, H.
AU  - Stripling, D.
AU  - Ribot, E.M.
AU  - Gerner-Smidt, P.
TI  - Genome Sequences of 228 Shiga Toxin-Producing Escherichia coli Isolates and 12 Isolates Representing Other Diarrheagenic E. coli Pathotypes.
JO  - Genome Announcements
PY  - 2014
SP  - e00718
EP  - e00714
VL  - 2
AB  - Shiga toxin-producing Escherichia coli (STEC) are a common cause for food-borne diarrheal
AB  - illness outbreaks and sporadic cases. Here, we report the availability
AB  - of the draft genome sequences of 228 STEC strains representing 32 serotypes with
AB  - known pulsed-field gel electrophoresis (PFGE) types and epidemiological
AB  - relationships, as well as 12 strains representing other diarrheagenic E. coli
AB  - pathotypes.
ER  -

TY  - JOUR
AU  - Trefault, N.
AU  - De la Iglesia, R.
AU  - Molina, A.M.
AU  - Manzano, M.
AU  - Ledger, T.
AU  - Perez-Pantoja, D.
AU  - Sanchez, M.A.
AU  - Stuardo, M.
AU  - Gonzalez, B.
TI  - Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic   pollutants and evolution of specialized chloroaromatic degradation   pathways.
JO  - Environ. Microbiol.
PY  - 2004
SP  - 655
EP  - 668
VL  - 6
AB  - Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of
AB  - substituted aromatic pollutants. Several key
AB  - degrading capabilities, encoded by tfd genes, are located in the 88 kb,
AB  - self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the
AB  - 87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is
AB  - reported. Most of the coding sequence corresponds to a well-conserved
AB  - IncP-1 beta backbone and the previously reported tfd genes. In addition,
AB  - we found hypothetical proteins putatively involved in the transport of
AB  - aromatic compounds and short-chain fatty acid oxidation. ORFs related to
AB  - mobile elements, including the Tn501-encoded mercury resistance
AB  - determinants, an IS1071-based composite transposon and a cryptic class II
AB  - transposon, are also present in pJP4. These mobile elements are
AB  - inefficient in transposition and are located in two regions of pJP4 that
AB  - are rich in remnants of lateral gene transfer events. pJP4 plasmid was
AB  - able to capture chromosomal genes and form hybrid plasmids with the IncP-1
AB  - alpha plasmid RP4. These observations are integrated into a model for the
AB  - evolution of pJP4, which reveals mechanisms of bacterial adaptation to
AB  - degrade pollutants.
ER  -

TY  - JOUR
AU  - Treml, S.
AU  - Draveling, C.
AU  - Huang, C.
AU  - Heaster, J.
AU  - Walker, D.
AU  - DiFrancesco, R.
AU  - Jolly, J.
TI  - Ambient-temperature-stable restriction endonucleases for use in forensic DNA applications.
JO  - Clin. Chem.
PY  - 1994
SP  - 1092
EP  - 1092
VL  - 40
AB  - We have stabilized restriction endonucleases including HaeIII, HinfI, and PstI, which are
AB  - commonly used in forensic and paternity DNA profiling. Using a patented process (US patents
AB  - 5098893 and 5250429) the enzyme and reaction buffer are stabilized as a glassy matrix of
AB  - carbohydrate polymers. These glassified reaction systems show excellent stability at ambient
AB  - temperatures for prolonged periods of time. The glass transition temperature (Tg) is a
AB  - physical property of the material and can be determined using a Differential Scanning
AB  - Calorimeter. At temperatures equal to or lower than the Tg the material remains a glass.
AB  - Stability studies show the recovery of enzyme activity immediately after processing is 75-100%
AB  - of activity prior to processing, and there is no further loss of activity over extended
AB  - periods of time provided the enzyme is stored at temperatures below the Tg. We have dried the
AB  - enzymes HinfI, HaeIII, and PstI by this process. The Gg's (oC) were 41.0, 45.2, and 47.4
AB  - respectively. After processing, the enzymes were stored at 25, 37, and 55oC for extended
AB  - periods of time. After 34 weeks HinfI retains 100% of initial activity at 25 and 37oC and 70%
AB  - of initial activity at 55oC. After 30 weeks HaeIII retains 100% initial activity at all three
AB  - storage temperatures. PstI after 36 weeks of storage retains 100% initial activity at all
AB  - three storage temperatures. PstI after 36 weeks of storage retains 100% of initial activity at
AB  - 25 and 37oC and 75% of initial activity at 55oC. These pre-mixed single dose reactions also
AB  - offer convenience and reproducibility by reducing pipeting steps and possible cross
AB  - contamination. Since the enzymes are stable at ambient temperatures they offer the added
AB  - convenience of room temperature shipping and storage. The enzymes are readily rehydrated by
AB  - simply adding water and the DNA to be analyzed. The stabilizer used in this process eliminates
AB  - the need for glycerol in the enzyme preparation. The absence of glycerol reduces star activity
AB  - that is sometimes observed when digests are carried out in the presence of high glycerol
AB  - concentrations due to a high ratio of enzyme units to DNA. The stabilized enzymes have been
AB  - used in side by side studies with standard RFLP protocols. A PstI paternity analysis was done
AB  - using Lifecodes procedures with standard PstI and our stabilized PstI. The analysis done with
AB  - standard PstI resulted in an extra band due to partial digestions. The extra band was not
AB  - present in the analysis done with stabilized PstI. The stabilized restriction enzymes offer
AB  - quick, reliable and reproducible results for standard forensic and paternity profiling
AB  - protocols.
ER  -

TY  - JOUR
AU  - Treu, L.
AU  - de Diego-Diaz, B.
AU  - Papadimitriou, K.
AU  - Tsakalidou, E.
AU  - Giacomini, A.
AU  - Corich, V.
TI  - Whole-Genome Sequences of Three Streptococcus macedonicus Strains Isolated from Italian Cheeses in the Veneto Region.
JO  - Genome Announcements
PY  - 2017
SP  - e01358
EP  - e01317
VL  - 5
AB  - We report here the genome sequences of three Streptococcus macedonicus strains isolated from
AB  - different cheeses in the Veneto region of Italy. The presented data
AB  - aim at increasing the scarce genomic information available for this species,
AB  - which is frequently encountered in fermented foods and appears to be a promising
AB  - technological microorganism.
ER  -

TY  - JOUR
AU  - Treu, L.
AU  - Vendramin, V.
AU  - Bovo, B.
AU  - Campanaro, S.
AU  - Corich, V.
AU  - Giacomini, A.
TI  - Genome Sequences of Streptococcus thermophilus Strains MTH17CL396 and M17PTZA496  from Fontina, an Italian PDO Cheese.
JO  - Genome Announcements
PY  - 2014
SP  - e00067
EP  - e00014
VL  - 2
AB  - Here is presented the whole-genome sequences of Streptococcus thermophilus strains MTH17CL396
AB  - and M17PTZA496, isolated from fontina protected designation of
AB  - origin (PDO) cheese in the Valle d'Aosta Region (Italy). S. thermophilus is a
AB  - lactic acid bacterium widely present in dairy products, and these are the first
AB  - publicly available genome sequences of S. thermophilus strains isolated from
AB  - cheese.
ER  -

TY  - JOUR
AU  - Treu, L.
AU  - Vendramin, V.
AU  - Bovo, B.
AU  - Campanaro, S.
AU  - Corich, V.
AU  - Giacomini, A.
TI  - Whole-Genome Sequences of Streptococcus thermophilus Strains TH1435 and TH1436, Isolated from Raw Goat Milk.
JO  - Genome Announcements
PY  - 2014
SP  - e01129
EP  - e01113
VL  - 2
AB  - We report the genome sequences of two Streptococcus thermophilus strains, TH1435  and TH1436,
AB  - isolated from raw goat milk devoted to the production of artisanal
AB  - cheese in the Friuli-Venezia Giulia region in Italy. The genome sequences of
AB  - these two quickly acidifying strains are the first available genome sequences of
AB  - S. thermophilus strains isolated in Italy.
ER  -

TY  - JOUR
AU  - Treu, L.
AU  - Vendramin, V.
AU  - Bovo, B.
AU  - Campanaro, S.
AU  - Corich, V.
AU  - Giacomini, A.
TI  - Genome Sequences of Four Italian Streptococcus thermophilus Strains of Dairy Origin.
JO  - Genome Announcements
PY  - 2014
SP  - e00126
EP  - e00114
VL  - 2
AB  - This report describes the genome sequences of four Streptococcus thermophilus strains, namely,
AB  - TH982, TH985, TH1477, and 1F8CT, isolated from different dairy
AB  - environments from the Campania and the Veneto regions in Italy. These data are
AB  - aimed at increasing the genomic information available on this species, which is
AB  - of paramount importance for the dairy industry.
ER  -

TY  - JOUR
AU  - Treu, L.
AU  - Vendramin, V.
AU  - Bovo, B.
AU  - Giacomini, A.
AU  - Corich, V.
AU  - Campanaro, S.
TI  - Genome Sequence of Lactobacillus fabifermentans Strain T30PCM01, Isolated from Fermenting Grape Marc.
JO  - Genome Announcements
PY  - 2014
SP  - e00060
EP  - e00014
VL  - 2
AB  - Here, we report the draft genome assembly of Lactobacillus fabifermentans strain  T30PCM01
AB  - isolated from grape marc. Its genome is the largest (3.58 Mbp) among
AB  - Lactobacillus species and reveals an enormous potential for carbohydrate
AB  - utilization and transcriptional regulation.
ER  -

TY  - JOUR
AU  - Treuner-Lange, A.
AU  - Bruckskotten, M.
AU  - Rupp, O.
AU  - Goesmann, A.
AU  - Sogaard-Andersen, L.
TI  - Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing.
JO  - Genome Announcements
PY  - 2017
SP  - e01127
EP  - e01117
VL  - 5
AB  - Members of the Myxococcales order initiate a developmental program in response to starvation
AB  - that culminates in formation of spore-filled fruiting bodies. To
AB  - investigate the genetic basis for fruiting body formation, we present the
AB  - complete 8.9-Mb genome sequence of Myxococcus macrosporus strain DSM 14697,
AB  - generated using the PacBio sequencing platform.
ER  -

TY  - JOUR
AU  - Treuner-Lange, A.
AU  - Bruckskotten, M.
AU  - Rupp, O.
AU  - Goesmann, A.
AU  - Sogaard-Andersen, L.
TI  - Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71.
JO  - Genome Announcements
PY  - 2017
SP  - e01227
EP  - e01217
VL  - 5
AB  - In response to starvation, members of the order Myxococcales form morphologically very
AB  - different fruiting bodies. To determine whether fruiting myxobacteria share
AB  - a common genetic program that leads to fruiting body formation, we sequenced and
AB  - assembled the genome of Nannocystis exedens DSM 71 as two contigs with a total GC
AB  - content of 72%.
ER  -

TY  - JOUR
AU  - Treuner-Lange, A.
AU  - Bruckskotten, M.
AU  - Rupp, O.
AU  - Goesmann, A.
AU  - Sogaard-Andersen, L.
TI  - Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713.
JO  - Genome Announcements
PY  - 2017
SP  - e01262
EP  - e01217
VL  - 5
AB  - The formation of spore-filled fruiting bodies in response to starvation represents a hallmark
AB  - of many members of the order Myxococcales Here, we present
AB  - the complete 9.9-Mb genome of the fruiting type strain Melittangium boletus DSM
AB  - 14713, the first member of this genus to have its genome sequenced.
ER  -

TY  - JOUR
AU  - Treuner-Lange, A.
AU  - Bruckskotten, M.
AU  - Rupp, O.
AU  - Goesmann, A.
AU  - Sogaard-Andersen, L.
TI  - Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655.
JO  - Genome Announcements
PY  - 2017
SP  - e01196
EP  - e01117
VL  - 5
AB  - Among myxobacteria, the genus Cystobacter is known not only for fruiting body formation but
AB  - also for formation of secondary metabolites, such as cystobactamids
AB  - and cystothiazols. Here, we present the complete genome sequence of the
AB  - Cystobacter fuscus strain DSM 52655, which comprises 12,349,744 bp and 9,836
AB  - putative protein-coding sequences.
ER  -

TY  - JOUR
AU  - Treven, P.
AU  - Trmcic, A.
AU  - Bogovic, M.B.
AU  - Rogelj, I.
TI  - Improved Draft Genome Sequence of Probiotic Strain Lactobacillus gasseri K7.
JO  - Genome Announcements
PY  - 2014
SP  - e00725
EP  - e00714
VL  - 2
AB  - Lactobacillus gasseri K7 is an isolate from infant feces and has in vitro and in  vivo
AB  - established probiotic properties. Here, we report the improved version of
AB  - the draft genome sequence, which comprises 8 scaffolds (13 contigs), a total
AB  - length of 1.99 Mb, and 1,841 predicted protein-coding sequences.
ER  -

TY  - JOUR
AU  - Trevors, J.T.
TI  - Review: Bacterial population genetics.
JO  - World J. Microbiol. Biotechnol.
PY  - 1998
SP  - 1
EP  - 5
VL  - 14
AB  - Bacterial population genetics is the study of natural bacterial genetic diversity arising from
AB  - evolutionary processes.  The roles of molecular mistakes, restriction-modification, plasmids
AB  - and gene transfer in bacteria are also important components of population genetics.  These
AB  - aspects are of considerable scientific importance from a fundamental perspective, because of
AB  - the short generation times of bacteria, their microscopic cell size, the large population
AB  - sizes bacteria can achieve and their different mechanisms of gene transfer.
ER  -

TY  - JOUR
AU  - Trevors, J.T.
TI  - Molecular evolution in bacteria: genome size, cell size, restriction-modification and recognition.
JO  - Bull. Inst. Pasteur
PY  - 1998
SP  - 25
EP  - 33
VL  - 96
AB  - The ability of bacteria to alter their genome sizes and the order of their genes, yet maintain
AB  - a relatively constant genome, provides a mechanism for diversity and evolution in bacteria.
AB  - Moreover, bacteria may have evolved by increasing their genome sizes and rearranging gene
AB  - orders with the assistance of restriction endonucleases cleaving foreign DNA and providing a
AB  - diverse pool of DNA sequences for genetic recombination.  This review examines some of these
AB  - evolutionary aspects of bacteria including molecular recognition of biomolecules.
ER  -

TY  - JOUR
AU  - Trevors, J.T.
TI  - Molecular evolution in bacteria.
JO  - Antonie Van Leeuwenhoek
PY  - 1995
SP  - 315
EP  - 324
VL  - 67
AB  - Recent advances in microbiology and molecular biology have a unifying influence on our
AB  - understanding of genetic diversity/similarity and evolutionary relationships in
AB  - microorganisms.  This article attempts to unify information from diverse areas such as
AB  - microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay
AB  - interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to
AB  - molecular evolution of bacteria.  The possibility is discussed that the first informational
AB  - molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and
AB  - these first micro-assemblers may have been precursors of ribosomes.
ER  -

TY  - JOUR
AU  - Tribelli, P.M.
AU  - Raiger, I.L.J.
AU  - Catone, M.V.
AU  - Di Martino, C.
AU  - Revale, S.
AU  - Mendez, B.S.
AU  - Lopez, N.I.
TI  - Genome Sequence of the Polyhydroxybutyrate Producer Pseudomonas extremaustralis,  a Highly Stress-Resistant Antarctic Bacterium.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2381
EP  - 2382
VL  - 194
AB  - Pseudomonas extremaustralis 14-3b presents genes involved in the synthesis of different
AB  - polyhydroxyalkanoates, in tolerance and degradation of pollutants, and
AB  - in microaerobic metabolism. Several genomic islands were detected. Genetic
AB  - machinery could contribute to the adaptability to stressful conditions. This is
AB  - the first genome sequence reported from a Pseudomonas isolated from cold
AB  - environments.
ER  -

TY  - JOUR
AU  - Trieu-Cuot, P.
AU  - Derlot, E.
AU  - Courvalin, P.
TI  - Enhanced conjugative transfer of plasmid DNA from Escherichia coli to Staphylococcus aureus and Listeria monocytogenes.
JO  - FEMS Microbiol. Lett.
PY  - 1993
SP  - 19
EP  - 23
VL  - 109
AB  - Transfer of mobilizable shuttle cloning vectors by conjugation from Escherichia coli to
AB  - Staphylococcus aureus occurred at a very low frequency (10-9 transconjugants per donor
AB  - colony-forming unit after the mating period). It was observed that subinhibitory
AB  - concentrations of penicillins (oxacillin or penicillin G) in the mating medium resulted in
AB  - increased transfer frequency by conjugation of the shuttle vector pAT18 from E. coli SM10 to
AB  - S. aureus 80CR5 Str (54-fold) and to Listeria monocytogenes LO17RF (45-fold). These results
AB  - were interpreted as indicating that the cell wall of Gram-positive bacteria constitutes an
AB  - important barrier for conjugative transfer of genetic information delivered from E. coli. It
AB  - was also demonstrated that the presence of a restriction system(s) in S. aureus recipients
AB  - represented a major barrier to introduction of foreign DNA.
ER  -

TY  - JOUR
AU  - Trimble, W.L.
AU  - Phung, L.T.
AU  - Meyer, F.
AU  - Gilbert, J.A.
AU  - Silver, S.
TI  - Draft Genome Sequence of Agrobacterium albertimagni Strain AOL15.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6986
EP  - 6987
VL  - 194
AB  - Agrobacterium albertimagni strain AOL15 is an alphaproteobacterium isolated from
AB  - arsenite-oxidizing biofilms whose draft genome contains 5.1 Mb in 55 contigs with
AB  - 61.2% GC content and includes a 21-gene arsenic gene island. This is the first
AB  - available genome for this species and the second Agrobacterium arsenic gene
AB  - island.
ER  -

TY  - JOUR
AU  - Trimble, W.L.
AU  - Phung, L.T.
AU  - Meyer, F.
AU  - Silver, S.
AU  - Gilbert, J.A.
TI  - Draft Genome Sequence of Achromobacter piechaudii Strain HLE.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6355
EP  - 6355
VL  - 194
AB  - Achromobacter piechaudii strain HLE is a betaproteobacterium (previously known as Alcaligenes
AB  - faecalis) that was an early isolate with arsenite oxidase activity.
AB  - This draft genome of 6.89 Mb is the second available genome for this species in
AB  - the opportunistic pathogen Alcaligenaceae family.
ER  -

TY  - JOUR
AU  - Trinh, S.A.
AU  - Leyn, S.A.
AU  - Rodionov, I.D.
AU  - Godzik, A.
AU  - Satchell, K.J.F.
TI  - Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.
JO  - Genome Announcements
PY  - 2018
SP  - e01387
EP  - e01317
VL  - 6
AB  - Vibrio parahaemolyticus is a Gram-negative pathogen associated with gastrointestinal and wound
AB  - infections after exposure to raw seafood or
AB  - contaminated waters. We report here the whole-genome sequences of two stool
AB  - isolates (CDC-AM50933 and CDC-AM43539) from patients in Colorado presenting with
AB  - gastroenteritis after ingesting raw seafood.
ER  -

TY  - JOUR
AU  - Tripathi, C.
AU  - Mahato, N.K.
AU  - Rani, P.
AU  - Singh, Y.
AU  - Kamra, K.
AU  - Lal, R.
TI  - Draft genome sequence of Lampropedia cohaerens strain CT6(T) isolated from arsenic rich microbial mats of a Himalayan hot water spring.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 64
EP  - 64
VL  - 11
AB  - Lampropedia cohaerens strain CT6(T), a non-motile, aerobic and coccoid strain was isolated
AB  - from arsenic rich microbial mats (temperature ~45 degrees C) of a hot
AB  - water spring located atop the Himalayan ranges at Manikaran, India. The present
AB  - study reports the first genome sequence of type strain CT6(T) of genus
AB  - Lampropedia cohaerens. Sequencing data was generated using the Illumina HiSeq
AB  - 2000 platform and assembled with ABySS v 1.3.5. The 3,158,922 bp genome was
AB  - assembled into 41 contigs with a mean GC content of 63.5 % and 2823 coding
AB  - sequences. Strain CT6(T) was found to harbour genes involved in both the
AB  - Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6(T) also
AB  - contained genes responsible for imparting resistance to arsenic, copper, cobalt,
AB  - zinc, cadmium and magnesium, providing survival advantages at a thermal location.
AB  - Additionally, the presence of genes associated with biofilm formation,
AB  - pyrroloquinoline-quinone production, isoquinoline degradation and mineral
AB  - phosphate solubilisation in the genome demonstrate the diverse genetic potential
AB  - for survival at stressed niches.
ER  -

TY  - JOUR
AU  - Trivedi, V.D.
AU  - Jangir, P.K.
AU  - Sharma, R.
AU  - Phale, P.S.
TI  - Draft Genome Sequence of Carbaryl-Degrading Soil Isolate Pseudomonas sp. Strain C5pp.
JO  - Genome Announcements
PY  - 2016
SP  - e00526
EP  - e00516
VL  - 4
AB  - We report the draft genome sequence of carbaryl-degrading Pseudomonas sp. strain  C5pp. Genes
AB  - encoding salicylate and gentisate metabolism, large amounts of
AB  - oxygenase, nitrogen metabolism, and heavy metal tolerance were identified. The
AB  - sequence will provide further insight into the biochemical and evolutionary
AB  - aspects of carbaryl degradation.
ER  -

TY  - JOUR
AU  - Trotsenko, Y.A.
AU  - Shmareva, M.N.
AU  - Doronina, N.V.
AU  - Tarlachkov, S.V.
AU  - Mustakhimov, I.I.
AU  - Vasilenko, O.V.
TI  - Draft Genome Sequence of Methylophaga muralis Bur 1, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph Isolated from a Soda Lake.
JO  - Genome Announcements
PY  - 2016
SP  - e01227
EP  - e01216
VL  - 4
AB  - The draft genome sequence of Methylophaga muralis strain Bur 1 (VKM B-3046T), a
AB  - non-methane-utilizing methylotroph isolated from a soda lake, is reported here.
AB  - Strain Bur 1 possesses genes for methanol and methylamine (methylamine
AB  - dehydrogenase and N-methylglutamate pathway) oxidation. Genes for the
AB  - biosynthesis of ectoine were also found.
ER  -

TY  - JOUR
AU  - Trotter, M.
AU  - McAuliffe, O.
AU  - Callanan, M.
AU  - Edwards, R.
AU  - Fitzgerald, G.F.
AU  - Coffey, A.
AU  - Ross, R.P.
TI  - Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactic provides insight into its adaptable nature.
JO  - Gene
PY  - 2006
SP  - 189
EP  - 199
VL  - 366
AB  - Analysis of the complete nucleotide sequence of the lactococcal phage 4268, which is lytic for
AB  - the cheese starter Lactococcus lactis DPC4268, is presented. Phage 4268 has a linear genome of
AB  - 36,596 bp, which is modularly organised and encompasses 49 open reading frames. Putative
AB  - functions were assigned to approximately 45% of the predicted products of these open reading
AB  - frames based on sequence similarity with known proteins, N-terminal sequence analysis and
AB  - identification of conserved domains. Significantly, a segment of the genome has homology to
AB  - the recently sequenced lysogenic module in lactococcal phage phi 31 that contains a lytic
AB  - switch but no phage integrase or attachment site. This suggests that it is derived from a
AB  - prophage. A phage 4268-encoded and a host-encoded methylase were found to be highly similar,
AB  - having only two nucleotide mismatches, suggesting that the phage acquired the methylase gene
AB  - to protect it from a host endonuclease. Comparative genomic analysis revealed significant
AB  - homology between phage 4268 and the lactococcal phage BK5-T. The comparative analysis also
AB  - supported the classification of phage 4268 and other BK5-T-related phage as separate from the
AB  - proposed P335 species of lactococcal phage.
ER  -

TY  - JOUR
AU  - Trotter, M.
AU  - Ross, R.P.
AU  - Fitzgerald, G.F.
AU  - Coffey, A.
TI  - Lactococcus lactis DPC5598, a plasmid-free derivative of a commercial starter, provides a valuable alternative host for culture improvement studies.
JO  - J. Appl. Microbiol.
PY  - 2002
SP  - 134
EP  - 143
VL  - 93
AB  - Aims: To generate a plasmid-free derivative of an extensively used industrial starter strain
AB  - Lactococcus lactis DPC4268, which could be used as a backbone strain for starter improvement
AB  - programmes. Methods and Results: DPC4268, containing four large plasmids, was subjected to
AB  - high temperature plasmid curing resulting in derivatives, each with a different plasmid
AB  - complement of one, two or three different plasmids in addition to a plasmid-free derivative.
AB  - Industrially relevant phenotypes were assigned to each plasmid on the basis of detailed
AB  - phenotypic and genetic analyses and these were (a) proteinase activity (Prt, 60 kb) (b)
AB  - lactose fermentation (Lac, 55 kb) (c) bacteriophage adsorption inhibition (Ads, 44 kb) and (d)
AB  - type I restriction/modification (R/M, 40 kb). The plasmid-free variant of DPC4268 was shown to
AB  - be transformable at frequencies comparable to the common laboratory strain L. lactis MG1614.
AB  - Furthermore its genome was demonstrated to be significantly different from the laboratory
AB  - strains L. lactis MG1614 and the recently sequenced L. lactis IL1403 genomes by pulsed-field
AB  - gel electrophoresis. Conclusions: This study produced an easily transformable plasmid-free
AB  - derivative which was genomically different from both MG1614 and IL1403. In addition, important
AB  - plasmid-borne industrial traits, including two phage-resistance mechanisms, were identified in
AB  - DPC4268. Significance and Impact of the Study: L. DPC4268 is a vitally important commercial
AB  - strain used in the manufacture of Cheddar cheese. The generation of a plasmid-free derivative
AB  - may provide an important backbone strain as a basis for future strain improvement purposes.
ER  -

TY  - JOUR
AU  - Trouillet-Assant, S. et al.
TI  - Adaptive processes of Staphylococcus aureus isolates during the progression from acute to chronic bone and joint infections in patients.
JO  - Cell. Microbiol.
PY  - 2016
SP  - 1405
EP  - 1414
VL  - 18
AB  - Staphylococcus aureus bone and joint infection (BJI) is associated with significant rates of
AB  - chronicity and relapse. In this study, we investigated how S. aureus is able to adapt to the
AB  - human environment by comparing isolates from single patients with persisting or relapsing BJIs
AB  - that were recovered during the initial and recurrent BJI episodes. In vitro and in vivo assays
AB  - and whole-genome sequencing analyses revealed that the recurrent isolates induced a reduced
AB  - inflammatory response, formed more biofilm, persisted longer in the intracellular compartments
AB  - of host bone cells, were less cytotoxic and induced less mortality in a mouse infection model
AB  - compared to the initial isolates despite the lack of significant changes at the genomic level.
AB  - These findings suggest that S. aureus BJI chronicization is associated with an in vivo
AB  - bacterial phenotypical adaptation that leads to decreased virulence and host immune escape,
AB  - which is linked to increased intraosteoblastic persistence and biofilm formation. This article
AB  - is protected by copyright. All rights reserved.
ER  -

TY  - JOUR
AU  - Trowbridge, J.J.
AU  - Snow, J.W.
AU  - Kim, J.
AU  - Orkin, S.H.
TI  - DNA Methyltransferase 1 Is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells.
JO  - Cell Stem Cell
PY  - 2009
SP  - 442
EP  - 449
VL  - 5
AB  - DNA methylation is essential for development and in diverse biological processes. The DNA
AB  - methyltransferase Dnmt1 maintains parental cell
AB  - methylation patterns on daughter DNA strands in mitotic cells; however,
AB  - the precise role of Dnmt1 in regulation of quiescent adult stem cells
AB  - is not known. To examine the role of Dnmt1 in adult hematopoietic stem
AB  - cells (HSCs), we conditionally disrupted Dnmt1 in the hematopoietic
AB  - system. Defects were observed in Dnmt1 deficient HSC self-renewal,
AB  - niche retention, and in the ability of Dnmt1-deficient HSCs to give
AB  - rise to multilineage hematopoiesis. Loss of Dnmt1 also had specific
AB  - impact on myeloid progenitor cells, causing enhanced cell cycling and
AB  - inappropriate expression of mature lineage genes. Dnmt1 regulates
AB  - distinct patterns of methylation and expression of discrete gene
AB  - families in long-term HSCs and multipotent and lineage-restricted
AB  - progenitors, suggesting that Dnmt1 differentially controls these
AB  - populations. These findings establish a unique and critical role for
AB  - Dnmt1 in the primitive hematopoietic compartment.
ER  -

TY  - JOUR
AU  - Troxell, B.
AU  - Fink, R.C.
AU  - Dickey, A.N.
AU  - Scholl, E.H.
AU  - Hassan, H.M.
TI  - Complete Genome Sequence of NC983, a Live Attenuated Strain of Salmonella enterica Serovar Typhimurium.
JO  - Genome Announcements
PY  - 2016
SP  - e01074
EP  - e01016
VL  - 4
AB  - Foodborne infections caused by Salmonella enterica serovars are a significant problem
AB  - worldwide. Presented here is the genome sequence of the nontyphoidal S.
AB  - enterica serovar Typhimurium mutant strain NC983, a potential vaccine candidate.
ER  -

TY  - JOUR
AU  - Trubitsyn, D.
AU  - Abreu, F.
AU  - Ward, F.B.
AU  - Taylor, T.
AU  - Hattori, M.
AU  - Kondo, S.
AU  - Trivedi, U.
AU  - Staniland, S.
AU  - Lins, U.
AU  - Bazylinski, D.A.
TI  - Draft Genome Sequence of Magnetovibrio blakemorei Strain MV-1, a Marine Vibrioid  Magnetotactic Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e01330
EP  - e01316
VL  - 4
AB  - We report here the genome sequence of Magnetovibrio blakemorei MV-1, a marine vibrioid
AB  - magnetotactic bacterium with a single polar flagellum. The current
AB  - assembly consists of 91 contigs with a combined size of 3,638,804 bp (54.3% G+C
AB  - content). This genome allows for further investigations of the molecular
AB  - biomineralization mechanisms of magnetosome formation.
ER  -

TY  - JOUR
AU  - Trubitsyn, D.
AU  - Geurink, C.
AU  - Pikuta, E.
AU  - Lefevre, C.T.
AU  - McShan, W.M.
AU  - Gillaspy, A.F.
AU  - Bazylinski, D.A.
TI  - Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1.
JO  - Genome Announcements
PY  - 2014
SP  - e00741
EP  - e00714
VL  - 2
AB  - Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate
AB  - reduction, was isolated from Mono Lake, California. Here we report the
AB  - 3.92-Mb draft genome sequence comprising 34 contigs and some results of its
AB  - automated annotation. These data will improve our knowledge of mechanisms by
AB  - which bacteria withstand extreme environments.
ER  -

TY  - JOUR
AU  - Trujillo, L.E.
AU  - Brito, J.E.
AU  - Reyes, G.
AU  - Garcia, O.
TI  - Purification of SmaI restriction enzyme.
JO  - Biotecnol. Apl.
PY  - 1990
SP  - 326
EP  - 332
VL  - 7
AB  - SmaI restriction endonuclease produced by Serratia marcescens, has been
AB  - purified in our laboratory using PEG-6000 precipitation and ion exchange
AB  - chromatography in Phosphocellulose (P-11 Whatman).  We have obtained by this
AB  - way a final enzymatic preparation with a specific activity of 2972 U/mg of
AB  - total protein and 35% of global recovery of the process, that may be used in
AB  - cloning and other recombinant DNA techniques.
ER  -

TY  - JOUR
AU  - Trujillo, L.E.
AU  - Pupo, E.
AU  - Miranda, F.
AU  - Perez, E.
AU  - Gonzalez, E.
TI  - Correspondence between radioactive and functional methods in the quality control of DNA restriction and modifying enzymes.
JO  - Rev. Latinoam. Microbiol.
PY  - 1996
SP  - 31
EP  - 37
VL  - 38
AB  - We evaluated the use of two radiolabeled lambda DNA/HpaII substrates to detect 5'-3' single
AB  - and double stranded DNA dependent exonuclease and phosphatase activities found as contaminants
AB  - in restriction and modifying enzyme preparations.  Looking for the meaning of the radioactive
AB  - assays results in a real cloning experience, we performed a cloning simulation assay using the
AB  - same conditions established for the radioactive assay (enzyme units and pmols of DNA ends).
AB  - As a result, we found that for degradation percentages of the radioactive DNA substrate per
AB  - enzyme unit below 0.5, the false positives in the cloning simulation assay were less than 5%.
AB  - This conditions could ensure a good performance of the enzyme preparations for cloning
AB  - experiments.  Finally, we described the use of the radiolabeled [gamma 32P] ATP lambda HpaII
AB  - DNA substrate to detect 5'-3' single stranded DNA dependent exonuclease and phosphatase
AB  - contaminating activities in some critical steps of the purification process of the restriction
AB  - enzyme KpnI.
ER  -

TY  - JOUR
AU  - Trujillo, L.E.
AU  - Reyes, G.
AU  - Bayolo, E.
AU  - Vazquez, M.M.
AU  - Garcia, O.
TI  - Purification of NciI restriction endonuclease.
JO  - Biotecnol. Apl.
PY  - 1990
SP  - 320
EP  - 325
VL  - 7
AB  - NciI restriction endonuclease isolated from Neisseria cinerea, has been
AB  - purified in our laboratory using affinity and ion exchange chromatography.  We
AB  - have obtained an enzymatic preparation with a specific activity of 20,000 U/mg
AB  - of proteins and 67.2% of global recovery of the process, that may be used in
AB  - different genetic engineering techniques.
ER  -

TY  - JOUR
AU  - Tsai, R.
AU  - Correa, I.R.
AU  - Xu, M.Y.
AU  - Xu, S.Y.
TI  - Restriction and modification of deoxyarchaeosine (dG+)-containing phage 9 g DNA.
JO  - Sci. Rep.
PY  - 2017
SP  - 8348
EP  - 8348
VL  - 7
AB  - E. coli phage 9 g contains the modified base deoxyarchaeosine (dG+) in its genome. The phage
AB  - encodes its own primase, DNA ligase, DNA polymerase, and
AB  - enzymes necessary to synthesize and incorporate dG+. Here we report phage 9 g DNA
AB  - sensitivity to >200 Type II restriction endonucleases (REases). Among the REases
AB  - tested approximately 29% generated complete or partial digestions, while the
AB  - remaining 71% displayed resistance to restriction. Phage 9 g restriction
AB  - fragments can be degraded by DNA exonucleases or ligated by T3 and T4 DNA
AB  - ligases. In addition, we examined a number of cytosine and adenine
AB  - methyltransferases to generate double base modifications. M.AluI, M.CviPI,
AB  - M.HhaI, and M.EcoGII were able to introduce 5mC or N6mA into 9 g DNA as confirmed
AB  - by partial resistance to restriction and by liquid chromatography-mass
AB  - spectrometry. A number of wild-type E. coli bacteria restricted phage 9 g,
AB  - indicating natural restriction barriers exist in some strains. A BlastP search of
AB  - GenBank sequences revealed five glutamine amidotransferase-QueC homologs in
AB  - Enterobacteria and Pseudomonas phage, and distant homologs in other phage and
AB  - bacterial genomes, suggesting that dG+ is not a rare modification. We also mapped
AB  - phage 9 g DNA packaging (pac) site containing two 21-bp direct repeats and a
AB  - major terminase cleavage site in the phage genome.
ER  -

TY  - JOUR
AU  - Tsai, S.P.
AU  - Hartin, R.J.
AU  - Ryu, J.-I.
TI  - Transformation in restriction-deficient Salmonella typhimurium LT2.
JO  - J. Gen. Microbiol.
PY  - 1989
SP  - 2561
EP  - 2567
VL  - 135
AB  - Stable restriction-deficient, modification-proficient galE (JR501) and F'galE+
AB  - (JR502) strains of Salmonella typhimurium were constructed and the effects of
AB  - restriction on transformation by plasmid pBR322 were tested.  Several factors
AB  - which affect transformation efficiency were systematically examined to
AB  - determine optimum transformation conditions and a simplified method is
AB  - presented.
ER  -

TY  - JOUR
AU  - Tsai, Y.C.
AU  - Conlan, S.
AU  - Deming, C.
AU  - Segre, J.A.
AU  - Kong, H.H.
AU  - Korlach, J.
AU  - Oh, J.
TI  - Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.
JO  - MBio
PY  - 2016
SP  - e01948
EP  - e01915
VL  - 7
AB  - Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition
AB  - and function of complex microbial communities. Computational approaches to assemble genome
AB  - fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes
AB  - from these communities. However, the resultant "genomes" are typically fragmented and
AB  - incomplete due to the limited ability of short-read sequence data to assemble complex or
AB  - low-coverage regions.
AB  - Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality,
AB  - closed genome of a previously uncharacterized Corynebacterium simulans and its companion
AB  - bacteriophage from a skin metagenomic sample.
AB  - Considerable improvement in assembly quality occurs in hybrid approaches incorporating
AB  - short-read data, with even relatively small amounts of long-read data being sufficient to
AB  - improve metagenome reconstruction. Using short-read data to evaluate strain variation of this
AB  - C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C.
AB  - simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate
AB  - the utility of SMRT sequencing and hybrid approaches in metagenome quantitation,
AB  - reconstruction, and annotation. IMPORTANCE: The species comprising a microbial community are
AB  - often difficult to deconvolute due to technical limitations inherent to most short-read
AB  - sequencing technologies. Here, we leverage new advances in sequencing technology,
AB  - single-molecule sequencing, to significantly improve reconstruction of a complex human skin
AB  - microbial community. With this long-read technology, we were able to reconstruct and annotate
AB  - a closed, high-quality genome of a previously uncharacterized skin species. We demonstrate
AB  - that hybrid approaches with short-read technology are sufficiently powerful to reconstruct
AB  - even single-nucleotide polymorphism level variation of species in this a community.
ER  -

TY  - JOUR
AU  - Tsai, Y.M.
AU  - Lo, W.S.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma corruscae EC-1T (DSM 19793), a Bacterium  Isolated from a Lampyrid Beetle (Ellychnia corrusca).
JO  - Genome Announcements
PY  - 2017
SP  - e00964
EP  - e00917
VL  - 5
AB  - Spiroplasma corruscae EC-1T (DSM 19793) was isolated from the gut of a lampryid beetle
AB  - (Ellychnia corrusca) collected in Beltsville, MD, USA, in 1983. Here, we
AB  - report the complete genome sequence of this bacterium to facilitate the
AB  - investigation of its biology and the comparative genomics among Spiroplasma
AB  - species.
ER  -

TY  - JOUR
AU  - Tsai, Y.M.
AU  - Lo, W.S.
AU  - Wu, P.S.
AU  - Cho, S.T.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma monobiae MQ-1(T) (ATCC 33825), a Bacterium Isolated from the Vespid Wasp (Monobia quadridens).
JO  - Genome Announcements
PY  - 2018
SP  - e00347
EP  - e00318
VL  - 6
AB  - Spiroplasma monobiae MQ-1(T) (ATCC 33825) was isolated from the hemolymph of an adult vespid
AB  - wasp (Monobia quadridens) collected in Maryland. Here, we report the
AB  - complete genome sequence of this bacterium to facilitate the investigation of its
AB  - biology and the comparative genomics among Spiroplasma species.
ER  -

TY  - JOUR
AU  - Tsai, Y.M.
AU  - Wu, P.S.
AU  - Lo, W.S.
AU  - Kuo, C.H.
TI  - Complete Genome Sequence of Spiroplasma floricola 23-6(T) (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.).
JO  - Genome Announcements
PY  - 2018
SP  - e00302
EP  - e00318
VL  - 6
AB  - Spiroplasma floricola 23-6(T) (ATCC 29989) was isolated from the flower surface of a tulip
AB  - tree (Liriodendron tulipifera L.). Here, we report the complete genome
AB  - sequence of this bacterium to facilitate the investigation of its biology and the
AB  - comparative genomics among Spiroplasma species.
ER  -

TY  - JOUR
AU  - Tsang, H.L.
AU  - Huang, J.L.
AU  - Lin, Y.H.
AU  - Huang, K.F.
AU  - Lu, P.L.
AU  - Lin, G.H.
AU  - Khine, A.A.
AU  - Hu, A.
AU  - Chen, H.P.
TI  - Borneol dehydrogenase from Pseudomonas sp. TCU-HL1 catalyzes the oxidation of (+)-borneol and its isomers to camphor.
JO  - Appl. Environ. Microbiol.
PY  - 2016
SP  - 6378
EP  - 6385
VL  - 82
AB  - Most plant-produced monoterpenes can be degraded by soil microorganisms. Borneol is a plant
AB  - terpene which is widely used in traditional Chinese medicine. Neither microbial borneol
AB  - dehydrogenase (BDH) nor a microbial borneol degradation pathway has been reported previously.
AB  - One borneol-degrading strain, Pseudomonas sp. TCU-HL1, was isolated by our group. Its genome
AB  - was sequenced and annotated. The genome of TCU-HL1 consists of a 6.2-Mbp circular chromosome
AB  - and one circular plasmid, pTHL1 (12.6 kbp). Our results suggest that borneol is first
AB  - converted into camphor by BDH in TCU-HL1, and further decomposed through a camphor degradation
AB  - pathway. The recombinant BDH was produced in the form of inclusion bodies. The apparent Km
AB  - values of refolded recombinant BDH for (+)-borneol and (-)-borneol are 0.20 +/- 0.01 and 0.16
AB  - +/- 0.01 mM, and the kcat values for (+)-borneol and (-)-borneol are 0.75 +/- 0.01, and 0.53
AB  - +/- 0.01 sec-1, respectively. Two plant BDH genes have been previously reported. The kcat and
AB  - kcat/Km values of lavender's BDH are about 1800-fold and 500-fold lower than those of
AB  - TCU-HL1. IMPORTANCE: The degradation of borneol in a soil microorganism through a camphor
AB  - degradation pathway was first shown in this study. This is also the first microbial borneol
AB  - dehydrogenase reported. The kcat and kcat/Km values of lavender's BDH are about 1800-fold and
AB  - 500-fold lower than those of TCU-HL1. This indigenous isolated borneol and camphor-degrading
AB  - strain TCU-HL1 reminds us of the time one hundred years ago when Taiwan was the major producer
AB  - of natural camphor in the world.
ER  -

TY  - JOUR
AU  - Tsao, D.H.H.
AU  - Maki, A.H.
TI  - Optically detected magnetic resonance study of the interaction of an Arsenic(III) derivative of cacodylic acid with EcoRI methyl transferase.
JO  - Biochemistry
PY  - 1991
SP  - 4565
EP  - 4572
VL  - 30
AB  - The interaction of the enzyme Escherichia coli RI methyl transferase
AB  - (methylase) with an arsenic(III) derivative of cacodylic acid has been
AB  - investigated by optical detection of triplet-state magnetic resonance (ODMR)
AB  - spectroscopy in zero applied magnet field.  The reactive derivative (CH3)2AsSR
AB  - is formed by the reduction of cacodylate by a thiol.  The As(III) derivative
AB  - binds to the enzyme by mercaptide exchange with a cysteine (Cys) residue
AB  - located close to a tryptophan (Trp) site.  The arsenical binding selectively
AB  - induces an external heavy-atom effect, perturbing the nearby Trp residue in the
AB  - enzyme.  Zero-field splittings (ZFS) and total decay rate constants of the
AB  - individual triplet-state sublevels of the Trp residue in the presence and
AB  - absence of perturbation by As(III) have been determined.  The perturbed Trp
AB  - shows a large reduction in the overall decay lifetime compared with unperturbed
AB  - Trp residue, exhibiting a high selectivity for the Tx sublevel.  This
AB  - selectivity suggests that the As atom lies in the xz plane of the principal
AB  - magnetic axis system of Trp, but not directly along the z (out-of-plane) axis.
AB  - The accessibility of this enzyme binding site to the arsenical is decreased
AB  - upon forming a ternary complex of methylase with sinefungin and a DNA oligomer,
AB  - d[GCGAA(BrU)(BrU)CGC], containing two 5-bromouracil (BrU) bases in place of
AB  - thymine within the hexadeoxynucleotide recognition sequence.  This result
AB  - indicates that the arsenical binding site in methylase which produces the Trp
AB  - heavy-atom effect is protected from this ligand by ternary complex formation or
AB  - the enzyme undergoes a conformation change, removing the Cys from the Trp site.
AB  - This protection is also observed in fluorescence quenching experiments.  The
AB  - As(III) reagent, upon binding to methylase, quenches the Trp fluorescence by
AB  - 46%.  When the ternary complex is formed, the quenching of Trp fluorescence is
AB  - only 17%.  A binding constant for the arsenical to the high-affinity enzyme
AB  - site was obtained which is at least 27 times that of binding to a free
AB  - sulfhydryl residue.  The addition of a 1:1 molar ratio of the arsenical to
AB  - methylase did not affect the activity of the enzyme, but incubation with excess
AB  - arsenical quenches the activity, suggesting that the high-affinity Cys residue
AB  - is not involved in the DNA methylation process.  In the ternary complex
AB  - methylase-sinefungin-DNA, no heavy-atom perturbation of the two Trp residues in
AB  - the enzyme by BrU was observed, demonstrating that Trp residues are not
AB  - involved in close-range interactions with the two heavy-atom-derivatized
AB  - nucleic acid bases.  A similar result was observed previously with the
AB  - analogous E. coli RI endonuclease-decanucleotide complex [John, N.-I.,
AB  - Casas-Finet, J.R., Maki, A.H., & Modrich, P. (1988) Biochim. Biophys. Acta 949,
AB  - 189-194].
ER  -

TY  - JOUR
AU  - Tschoeke, D.A.
AU  - Moreira, A.P.
AU  - Chimetto, T.L.A.
AU  - de Mesquita, M.M.
AU  - Gregoracci, G.B.
AU  - Gomez-Gil, B.
AU  - Valle, R.
AU  - Thompson, C.C.
AU  - Thompson, F.L.
TI  - Exploring the Genome of Cheese Starter Lactic Acid Bacterium Lactococcus lactis subsp. lactis CECT 4433.
JO  - Genome Announcements
PY  - 2014
SP  - e01142
EP  - e01114
VL  - 2
AB  - Here, we present the draft genome sequences of Lactococcus lactis subsp. lactis CECT 4433, a
AB  - cheese fermentation starter strain. The genome provides further
AB  - insight into the genomic plasticity, biocomplexity (including gene strain
AB  - specifics), and evolution of these genera.
ER  -

TY  - JOUR
AU  - Tse, H.
AU  - Tsoi, H.W.
AU  - Leung, S.P.
AU  - Lau, S.K.
AU  - Woo, P.C.
AU  - Yuen, K.Y.
TI  - Complete Genome Sequence of Staphylococcus lugdunensis strain HKU09-01.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1471
EP  - 1472
VL  - 192
AB  - Staphylococcus lugdunensis is a member of the coagulase-negative staphylococci and commonly
AB  - found as part of the human skin flora. It is a significant cause of catheter-related
AB  - bacteremia, and also causes serious infections like native valve endocarditis in previously
AB  - healthy individuals. We report the complete genome sequence of this medically important
AB  - bacterium.
ER  -

TY  - JOUR
AU  - Tse, H.
AU  - Tsoi, H.W.
AU  - Leung, S.P.
AU  - Urquhart, I.J.
AU  - Lau, S.K.
AU  - Woo, P.C.
AU  - Yuen, K.Y.
TI  - Complete genome sequence of the veterinary pathogen Staphylococcus pseudintermedius strain HKU10-03 isolated from a case of canine pyoderma.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1783
EP  - 1784
VL  - 193
AB  - Staphylococcus pseudintermedius is a member of the coagulase-positive staphylococci, and is
AB  - the commonest cause of canine pyoderma. We report the first genome sequence of S.
AB  - pseudintermedius, which showed the presence of numerous virulence factors akin to the related
AB  - human pathogen Staphylococcus aureus.
ER  -

TY  - JOUR
AU  - Tseng, S.P.
AU  - Hsueh, P.R.
AU  - Tsai, J.C.
AU  - Teng, L.J.
TI  - Tn6001, a Transposon-Like Element Containing the blaVIM-3-Harboring Integron In450.
JO  - Antimicrob. Agents Chemother.
PY  - 2007
SP  - 4187
EP  - 4190
VL  - 51
AB  - We describe the structure of a transposon-like element named Tn6001, which
AB  - contains a bla(VIM-3)-harboring integron In450, which was derived from a
AB  - multidrug-resistant Pseudomonas aeruginosa clinical isolate in Taiwan. The
AB  - transposon backbone structure is most closely related to those of Tn1404*
AB  - and Tn1403. Tn6001 was inserted into the chromosome of the clinical
AB  - isolate.
ER  -

TY  - JOUR
AU  - Tsirigos, A.
AU  - Rigoutsos, I.
TI  - A new computational method for the detection of horizontal gene transfer events.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 922
EP  - 933
VL  - 33
AB  - In recent years, the increase in the amounts of available genomic data has made it easier to
AB  - appreciate the extent by which organisms increase
AB  - their genetic diversity through horizontally transferred genetic
AB  - material. Such transfers have the potential to give rise to extremely
AB  - dynamic genomes where a significant proportion of their coding DNA has
AB  - been contributed by external sources. Because of the impact of these
AB  - horizontal transfers on the ecological and pathogenic character of the
AB  - recipient organisms, methods are continuously sought that are able to
AB  - computationally determine which of the genes of a given genome are
AB  - products of transfer events. In this paper, we introduce and discuss a
AB  - novel computational method for identifying horizontal transfers that
AB  - relies on a gene's nucleotide composition and obviates the need for
AB  - knowledge of codon boundaries. In addition to being applicable to
AB  - individual genes, the method can be easily extended to the case of
AB  - clusters of horizontally transferred genes. With the help of an
AB  - extensive and carefully designed set of experiments on 123 archaeal and
AB  - bacterial genomes, we demonstrate that the new method exhibits
AB  - significant improvement in sensitivity when compared to previously
AB  - published approaches. In fact, it achieves an average relative
AB  - improvement across genomes of between 11 and 41% compared to the Codon
AB  - Adaptation Index method in distinguishing native from foreign genes.
AB  - Our method's horizontal gene transfer predictions for 123 microbial
AB  - genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.
ER  -

TY  - JOUR
AU  - Tsonos, J.
AU  - Adriaenssens, E.M.
AU  - Klumpp, J.
AU  - Hernalsteens, J.P.
AU  - Lavigne, R.
AU  - De Greve, H.
TI  - Complete Genome Sequence of the Novel Escherichia coli Phage phAPEC8.
JO  - J. Virol.
PY  - 2012
SP  - 13117
EP  - 13118
VL  - 86
AB  - Bacteriophage phAPEC8 is an Escherichia coli-infecting myovirus, isolated on an
AB  - avian pathogenic Escherichia coli (APEC) strain. APEC strains cause
AB  - colibacillosis in poultry, resulting in high mortality levels and important
AB  - economic losses. Genomic analysis of the 147,737-bp double-stranded DNA phAPEC8
AB  - genome revealed that 53% of the 269 encoded proteins are unique to this phage.
AB  - Its closest relatives include the Salmonella phage PVP-SE1 and the coliphage rv5,
AB  - with 19% and 18% similar proteins, respectively. As such, phAPEC8 represents a
AB  - novel, phylogenetically distinct clade within the Myoviridae, with molecular
AB  - properties suitable for phage therapy applications.
ER  -

TY  - JOUR
AU  - Tsubouchi, T.
AU  - Kaneko, Y.
TI  - Draft Genome Sequence of the Arsenic-Resistant Bacterium Brevundimonas denitrificans TAR-002T.
JO  - Genome Announcements
PY  - 2017
SP  - e01326
EP  - e01317
VL  - 5
AB  - We report the 3.2-Mb draft genome sequence of Brevundimonas denitrificans strain  TAR-002T,
AB  - isolated from deep-sea floor sediment. The draft genome sequence of
AB  - strain TAR-002T consists of 3,231,216 bp in 44 contigs, with a G+C content of
AB  - 68.47%, 3,866 potential coding sequences (CDSs), 3 rRNAs, and 45 tRNAs.
ER  -

TY  - JOUR
AU  - Tsubouchi, T.
AU  - Nishi, S.
AU  - Maruyama, T.
AU  - Hatada, Y.
TI  - Draft Genome Sequence of Aneurinibacillus tyrosinisolvens LL-002T, Which Possesses Some Pseudouridine Synthases.
JO  - Genome Announcements
PY  - 2015
SP  - e00529
EP  - e00515
VL  - 3
AB  - We report the 5.7-Mb draft genome sequence of Aneurinibacillus tyrosinisolvens strain
AB  - LL-002(T), isolated from organic- and methane-rich sea sediments. The
AB  - draft genome sequence of strain LL-002(T) consists of 5,693,818 bp in 136
AB  - contigs, with a G+C content of 44.5%, 5,946 potential coding sequences (CDS), 2
AB  - rRNAs, and 39 tRNAs.
ER  -

TY  - JOUR
AU  - Tsubouchi, T.
AU  - Nishi, S.
AU  - Usui, K.
AU  - Shimane, Y.
AU  - Takaki, Y.
AU  - Maruyama, T.
AU  - Hatada, Y.
TI  - Draft Genome Sequence of the Dimorphic Prosthecate Bacterium Brevundimonas abyssalis TAR-001T.
JO  - Genome Announcements
PY  - 2013
SP  - e00826
EP  - e00813
VL  - 1
AB  - We report the 3.0-Mb draft genome sequence of Brevundimonas abyssalis strain TAR-001(T),
AB  - isolated from deep-sea floor sediment. The draft genome sequence of
AB  - strain TAR-001(T) consists of 2,979,700 bp in 128 contigs, with a G+C content of
AB  - 68.2%, 2,946 potential coding sequences (CDS), 3 rRNAs, and 41 tRNAs.
ER  -

TY  - JOUR
AU  - Tsuchida, S.
AU  - Nezuo, M.
AU  - Tsukahara, M.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Ushida, K.
TI  - Draft Genome Sequence of Lactobacillus gorillae Strain KZ01T, Isolated from a Western Lowland Gorilla.
JO  - Genome Announcements
PY  - 2015
SP  - e01196
EP  - e01115
VL  - 3
AB  - Here, we report the draft genome sequence of Lactobacillus gorillae strain KZ01(T) isolated
AB  - from a western lowland gorilla (Gorilla gorilla gorilla). This genome sequence will be helpful
AB  - for the comparative genomics between human and nonhuman primate-associated Lactobacillus.
ER  -

TY  - JOUR
AU  - Tsuge, K.
AU  - Matsui, K.
AU  - Itaya, M.
TI  - One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - e133
EP  - e133
VL  - 31
AB  - A universal method to reconstitute sets of genes was developed. Owing to the intrinsic nature
AB  - of the plasmid establishment mechanism in Bacillus
AB  - subtilis, the assembly of five antibiotic resistance genes with a defined
AB  - order and orientation was achieved. These five fragments and the plasmid
AB  - have three-base protruding sequences at both ends. The protruding
AB  - sequences are designed so that each fragment is ligated once in a row
AB  - according to the pairing. Ligation by T4 DNA ligase in the presence of 150
AB  - mM NaCl and 10% polyethylene glycol at 37 degrees C yielded high molecular
AB  - tandem repeat linear form DNA. This multimeric form of DNA was
AB  - preferentially used for plasmid establishment in B.subtilis. The method,
AB  - referred to as Ordered Gene Assembly in B.subtilis (OGAB), allows for the
AB  - design of multiple fragments with very high efficiency and great fidelity.
ER  -

TY  - JOUR
AU  - Tsui, C.K.M.
AU  - Wong, D.
AU  - Narula, G.
AU  - Gardy, J.L.
AU  - Hsiao, W.W.H.
AU  - Av-Gay, Y.
TI  - Genome Sequences of the Mycobacterium tuberculosis H37Rv-ptkA Deletion Mutant and Its Parental Strain.
JO  - Genome Announcements
PY  - 2017
SP  - e01156
EP  - e01117
VL  - 5
AB  - Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the  most
AB  - devastating infectious agents in the world. Here, we report the draft genome
AB  - sequences of the M. tuberculosis protein tyrosine kinase (ptkA) deletion mutant
AB  - and its parental strain H37Rv, which are used in genetic studies and for drug
AB  - discovery.
ER  -

TY  - JOUR
AU  - Tsui, W.-C.
AU  - Elgar, G.
AU  - Merrill, C.
AU  - Maunders, M.
TI  - RspX I:  a new restriction endonuclease with a recognition sequence of 5'T^CATGA3'.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4178
EP  - 4178
VL  - 16
AB  - A new TypeII restriction endonuclease, RspXI, was purified from a Rhodococcus
AB  - species isolated in our laboratory.  The Rhodococcus species grows well at 30C
AB  - in the following medium:  0.8% glucose, 0.8% yeast extract and 2% malt extract
AB  - at pH 7.2.  The yield of cell is 5 g/l.  RspXI recognizes the sequence
AB  - 5'TCATGA3' and cleaves between T and C giving a four base 5' overhang.  An
AB  - enzyme BspH1 reported recently has the same cutting site.  (1) the enzyme was
AB  - purified by the following chromatographic steps:   1) phosphocellulose 2)
AB  - biorex-70 3) S-200.  It was judged to be essentially free of contaminating
AB  - nuclease activity.  After 10 fold overdigestion on lambda DNA greater than 95%
AB  - of the DNA fragments can be ligated and greater than 95% of the ligated DNA can
AB  - be recut by RspXI.  At 37C, the optimal conditions for RspXI activity are:  10
AB  - mM Tris, pH 7.5, 50 mM NaCl, 50 mM KCl and 10 mM MgCl2.  KCl is essential for
AB  - optimal activity.  The number of fragments generated by digestion with RspXI on
AB  - the following DNAs are:  lambda, 9; pBR322, 4; phiX174, 3; Adeno 2, 4 and
AB  - M13mp18, 1 (Fig. 1).  A computer search with Microgenie(TM) (Beckman Inst.
AB  - Inc.) suggested a recognition sequence of 5'TCATGA3'.  The cleavage site was
AB  - determined as follows:  pBR322 DNA was digested with RspXI.  DNA fragments were
AB  - then end-filled with DNA polymerase (Klenow fragment).  The resulting blunt-end
AB  - fragments were ligated into SmaI site of pUC18.  The recombinant plasmids were
AB  - transformed into E. Coli K803.  Ampicillin resistant and Lac- clones were
AB  - identified and plasmid DNAs were prepared from these clones.  The sequence of
AB  - the DNA fragment cloned into SmaI was determined by dideoxy Chain-termination
AB  - method (2).  The sequence over the cloning site is CATGAGCCC on one gel (not
AB  - shown) and is CATGAGCGT on the other gel.  This confirms that the cutting site
AB  - is between bases T and C.
ER  -

TY  - JOUR
AU  - Tsujimoto, Y.
AU  - Saito, R.
AU  - Sahara, T.
AU  - Kimura, N.
AU  - Tsuruoka, N.
AU  - Shigeri, Y.
AU  - Watanabe, K.
TI  - Draft Genome Sequence of Caenibacillus caldisaponilyticus B157T, a Thermophilic and Phospholipase-Producing Bacterium Isolated from Acidulocompost.
JO  - Genome Announcements
PY  - 2017
SP  - e00089
EP  - e00017
VL  - 5
AB  - Caenibacillus caldisaponilyticus B157T (= NBRC 111400T = DSM 101100T), in the family
AB  - Sporolactobacillaceae, was isolated from acidulocompost as a thermophilic
AB  - and phospholipid-degrading bacterium. Here, we report the 3.36-Mb draft genome
AB  - sequence, with a G+C content of 51.8%, to provide the genetic information coding
AB  - for phospholipases.
ER  -

TY  - JOUR
AU  - Tsukahara, K.
AU  - Kita, A.
AU  - Nakashimada, Y.
AU  - Hoshino, T.
AU  - Murakami, K.
TI  - Genome-guided analysis of transformation efficiency and carbon dioxide assimilation by Moorella thermoacetica Y72.
JO  - Gene
PY  - 2014
SP  - 150
EP  - 155
VL  - 535
AB  - We determined a draft genome sequence for Moorella thermoacetica strain Y72, a
AB  - syngas-assimilating bacterium with high transformation efficiency. This strain was confirmed
AB  - to be M. thermoacetica because its overall genome sequence characteristics were similar to
AB  - those of M. thermoacetica strain ATCC39073. Y72 was confirmed to carry all the genes encoding
AB  - the enzymes in the reductive acetyl-CoA pathway, with very high similarities to those of
AB  - ATCC39073. In addition, it was confirmed to assimilate carbon dioxide using this pathway.
AB  - However, although both Y72 and ATCC39073 carried common genes encoding several enzymes related
AB  - to the reductive tricarboxylic acid (TCA) cycle, their gene sets were different. Our results
AB  - suggested that the reason for higher transformation efficiency in Y72 than that in ATC09073, a
AB  - reference strain of M. thermoacetica, may be that Y72 possesses only 2 sets of genes
AB  - considered to be involved in a restriction-modification system, which was half of those found
AB  - in ATCC39073.
ER  -

TY  - JOUR
AU  - Tsukahara, S.
AU  - Kim, S.-G.
AU  - Takaku, H.
TI  - Inhibition of restriction endonuclease cleavage site via triple helix formation by homopyrimidine phosphorothioate oligonucleotides.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1993
SP  - 990
EP  - 996
VL  - 196
AB  - The ability of pyrimidine rich oligonucleotide phosphorothioate to form stable triple helical
AB  - structures with the sequence containing the recognition site for the class IIS restriction
AB  - enzyme Ksp632I was examined. First, we synthesized double strand oligonucleotides
AB  - corresponding to the SV40 sites and studied their interaction with homopyrimidine
AB  - oligodeoxyribonucleotides including replacement of the other chain either with PS group
AB  - (SO-ODNs) in the second nucleotide position (from 5'-terminus) and end capped with the PS
AB  - group at both 3'- and 5'-ends (S2O-ODNs). The resulting perfect DNA triplexes were detected
AB  - by gel-mobility shift. The phosphorothioate oligonucleotide analogues (SO-ODNs) and (S2O-ODNs)
AB  - were shown to inhibit enzymatic cleavage under conditions that allow for triple helix
AB  - formation. Inhibition is sequence-specific and occurs in the micromolar concentration range.
AB  - Of particular interest is the Sp-phosphorothioate analogue (Sp-SO-ODNs) which inhibited the
AB  - endonuclease more than the other phosphorothioate oligonucleotide analogues (Rp-SO-ODNs or
AB  - S2O-ODNs).
ER  -

TY  - JOUR
AU  - Tsukahara, S.
AU  - Yamakawa, H.
AU  - Takai, K.
AU  - Takaku, H.
TI  - Inhibition of restriction enzyme Ksp632I via triple helix formation by phosphorothioate oligonucleotides.
JO  - Nucleosides and Nucleotides
PY  - 1994
SP  - 1617
EP  - 1626
VL  - 13
AB  - The ability of pyrimidine-rich oligonucleotide phosphorothioate to form stable triple helical
AB  - structures with the sequence containing the recognition site for the class II-S restriction
AB  - enzyme Ksp632I was examined. First, we prepared double strand oligonucleotides corresponding
AB  - to the major groove of SV40 DNA at 17 base pair homopurine-homopyrimidine sequences, and
AB  - studied their interaction with homopyrimidine oligodeoxyribonucleotides including replacement
AB  - of the PS group in the second nucleotide position from the 5'-terminus (SO-ODNs) and of the
AB  - PS group at both the 3'- and 5'ends (S2O-ODNs). The resulting perfect DNA triplexes were
AB  - detected by the gel-mobility shift. The phosphorothioate oligonucleotide analogues (SO-ODNs)
AB  - and (S2O-ODNs) were shown to inhibit enzymatic cleavage under conditions that allow for triple
AB  - helix formation. Inhibition is sequence-specific and occurs in the micromolar concentration
AB  - range. Of particular interest is the Sp-phosphorothioate analogue (Sp-SO-ODNs) which inhibited
AB  - endonuclease more than the other phosphorothioate oligonucleotide analogues (Rp-SO-ODNs or
AB  - S2O-ODNs).
ER  -

TY  - JOUR
AU  - Tsukatani, Y.
AU  - Hirose, Y.
AU  - Harada, J.
AU  - Misawa, N.
AU  - Mori, K.
AU  - Inoue, K.
AU  - Tamiaki, H.
TI  - Complete Genome Sequence of the Bacteriochlorophyll b-Producing Photosynthetic Bacterium Blastochloris viridis.
JO  - Genome Announcements
PY  - 2015
SP  - e01006
EP  - e01015
VL  - 3
AB  - We report the complete genome sequence of the purple photosynthetic bacterium Blastochloris
AB  - viridis belonging to alpha-Proteobacteria. This is the first completed genome sequence of a
AB  - phototroph producing bacteriochlorophyll b. The genome information will be useful for further
AB  - analysis of the photosynthetic energy conversion system and bacteriochlorophyll pigment
AB  - biosynthesis.
ER  -

TY  - JOUR
AU  - Tsumura, A.
AU  - Hayakawa, T.
AU  - Kumaki, Y.
AU  - Takebayashi, S.
AU  - Sakaue, M.
AU  - Matsuoka, C.
AU  - Shimotohno, K.
AU  - Ishikawa, F.
AU  - Li, E.
AU  - Ueda, H.R.
AU  - Nakayama, J.
AU  - Okano, M.
TI  - Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b.
JO  - Genes Cells
PY  - 2006
SP  - 805
EP  - 814
VL  - 11
AB  - DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b cooperatively regulate cytosine methylation in
AB  - CpG dinucleotides in mammalian genomes,
AB  - providing an epigenetic basis for gene silencing and maintenance of
AB  - genome integrity. Proper CpG methylation is required for the normal
AB  - growth of various somatic cell types, indicating its essential role in
AB  - the basic cellular function of mammalian cells. Previous studies using
AB  - Dnmt1(-/-) or Dnmt3a(-/-)Dnmt3b(-/-) ES cells, however, have shown that
AB  - undifferentiated embryonic stem (ES) cells can tolerate hypomethylation
AB  - for their proliferation. In an attempt to investigate the effects of
AB  - the complete loss of CpG DNA methyltransferase function, we established
AB  - mouse ES cells lacking all three of these enzymes by gene targeting.
AB  - Despite the absence of CpG methylation, as demonstrated by genome-wide
AB  - methylation analysis, these triple knockout (TKO) ES cells grew
AB  - robustly and maintained their undifferentiated characteristics. TKO ES
AB  - cells retained pericentromeric heterochromatin domains marked with
AB  - methylation at Lys9 of histone H3 and heterochromatin protein-1, and
AB  - maintained their normal chromosome numbers. Our results indicate that
AB  - ES cells can maintain stem cell properties and chromosomal stability in
AB  - the absence of CpG methylation and CpG DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Tsuru, T.
AU  - Kawai, M.
AU  - Mizutani-Ui, Y.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.
JO  - Mol. Biol. Evol.
PY  - 2006
SP  - 1269
EP  - 1285
VL  - 23
AB  - Analysis of evolution of paralogous genes in a genome is central to our understanding of
AB  - genome evolution. Comparison of closely related
AB  - bacterial genomes, which has provided clues as to how genome sequences
AB  - evolve under natural conditions, would help in such an analysis. With
AB  - species Staphylococcus aureus, whole-genome sequences have been decoded
AB  - for seven strains. We compared their DNA sequences to detect large
AB  - genome polymorphisms and to deduce mechanisms of genome rearrangements
AB  - that have formed each of them. We first compared strains N315 and Mu50,
AB  - which make one of the most closely related strain pairs, at the
AB  - single-nucleotide resolution to catalogue all the middle-sized (more
AB  - than 10 bp) to large genome polymorphisms such as indels and
AB  - substitutions. These polymorphisms include two paralogous gene sets,
AB  - one in a tandem paralogue gene cluster for toxins in a genomic island
AB  - and the other in a ribosomal RNA operon. We also focused on two other
AB  - tandem paralogue gene clusters and type I restriction-modification (RM)
AB  - genes on the genomic islands. Then we reconstructed rearrangement
AB  - events responsible for these polymorphisms, in the paralogous genes and
AB  - the others, with reference to the other five genomes. For the tandem
AB  - paralogue gene clusters, we were able to infer sequences for homologous
AB  - recombination generating the change in the repeat number. These
AB  - sequences were conserved among the repeated paralogous units likely
AB  - because of their functional importance. The sequence specificity (S)
AB  - subunit of type I RM systems showed recombination, likely at the
AB  - homology of a conserved region, between the two variable regions for
AB  - sequence specificity. We also noticed novel alleles in the ribosomal
AB  - RNA operons and suggested a role for illegitimate recombination in
AB  - their formation. These results revealed importance of recombination
AB  - involving long conserved sequence in the evolution of paralogous genes
AB  - in the genome.
ER  -

TY  - JOUR
AU  - Tsurumaru, H.
AU  - Kanesaki, Y.
AU  - Hashimoto, S.
AU  - Okizaki, K.
AU  - Yoshikawa, H.
AU  - Yamakawa, T.
TI  - Draft Genome Sequence of Bradyrhizobium japonicum Is-34, Which Is Incompatible with Rj4 Genotype Soybeans.
JO  - Genome Announcements
PY  - 2014
SP  - e01316
EP  - e01314
VL  - 2
AB  - We report here the draft genome sequence of Bradyrhizobium japonicum Is-34, which is
AB  - incompatible with Rj4 genotype soybeans. A candidate gene involved in this
AB  - incompatibility was found to be present in this genome.
ER  -

TY  - JOUR
AU  - Tsutakawa, S.E.
AU  - Jingami, H.
AU  - Morikawa, K.
TI  - Recognition of a TG mismatch: The crystal structure of very short patch repair endonuclease in complex with a DNA duplex.
JO  - Cell
PY  - 1999
SP  - 615
EP  - 623
VL  - 99
AB  - The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and
AB  - with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli,
AB  - the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of
AB  - methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine.
AB  - Extensive interactions between the DNA and the protein characterize a novel recognition
AB  - mechanism, where three aromatic residues intercalate from the major groove into the DNA to
AB  - strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in
AB  - the active center, the structure of the Vsr/DNA complex provides detailed insights into the
AB  - catalytic mechanism for endonuclease activity.
ER  -

TY  - JOUR
AU  - Tsutakawa, S.E.
AU  - Morikawa, K.
TI  - New recognition mode for a TG mismatch: The atomic structure of a very short patch repair endonuclease-DNA complex.
JO  - Cold Spring Harb. Symp. Quant. Biol.
PY  - 2000
SP  - 233
EP  - 239
VL  - 65
AB  - The crystal structure determination of the T4 endo-V pyrimidine photodimer DNA glycosylase
AB  - provided the first direct view of DNA lesion recognition by a repair enzyme.  Similar damaged
AB  - DNA recognition modes, involving nucleotide flipping, were observed in various base excision
AB  - repair enzymes.  The implications of nucleotide flipping raised the new question of how DNA
AB  - endonucleases other than base excision repair enzymes recognize mismatched base pairs.  The
AB  - Escherichia coli very short patch repair endonuclease is a good target to address this
AB  - question in terms of three-dimensional structures.  The Vsr endonuclease is involved in the
AB  - initial reaction for the repair of mismatched TG base pairs generated through spontaneous
AB  - deamination of methylated cytosine.  This enzyme recognizes a TG mismatch within the duplex
AB  - 5'CT(A/T)GG, where the second T forms the mismatch and all of the other bases are in standard
AB  - Watson-Crick base pairing.  It catalyzes the cleavage at the 5' side of the thymine, leaving
AB  - a 5' phosphate and a 3' hydroxyl at the termini.  The crystal structure of a truncated form
AB  - of this endonuclease was determined at 1.8 angstroms resolution.  The protein was found to
AB  - contain one structural zinc-binding module.  Unexpectedly, its overall topology resembles
AB  - members of the type II restriction endonuclease family, although the catalytic center with
AB  - critical histidines is distinct from those of restriction enzymes.  More recently, the crystal
AB  - structure of Vsr endonuclease in complex with DNA has been determined at 2.3 angstroms
AB  - resolution.  This endonuclease has been found to employ a novel mismatch base-pair recognition
AB  - scheme that does not involve base flipping-out.  Extensive interactions between the DNA and
AB  - the protein characterize the recognition mechanism, where three aromatic residues intercalate
AB  - from the major groove into the DNA to strikingly deform the base-pair stacking.  An
AB  - amino-terminal alpha-helix is accommodated into the expanded minor groove so that the amino
AB  - acid side chains make additional contacts with the DNA duplexes.  With the presence of a
AB  - cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides
AB  - detailed insights into the catalytic mechanism for endonuclease activity.
ER  -

TY  - JOUR
AU  - Tsutakawa, S.E.
AU  - Morikawa, K.
TI  - The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 3775
EP  - 3783
VL  - 29
AB  - Endonucleases in DNA repair must be able to recognize damaged DNA as well as cleave the
AB  - phosphodiester backbone. These functional prerequisites are manifested in very short patch
AB  - repair (Vsr) endonuclease through a common endonuclease topology that has been tailored for
AB  - recognition of TG mismatches. Structural and biochemical comparison with type II restriction
AB  - enzymes illustrates how Vsr resembles these endonucleases in overall topology but also how Vsr
AB  - diverges in terms of the detailed catalytic mechanism. A histidine and two metal-water
AB  - clusters catalyze the phosphodiester cleavage. The mode of DNA damage recognition is also
AB  - unique to Vsr. All other structurally characterized DNA damage-binding enzymes employ a
AB  - nucleotide flipping mechanism for substrate recognition and for catalysis. Vsr, on the other
AB  - hand, recognizes the TG mismatch as a wobble base pair and penetrates the DNA with three
AB  - aromatic residues on one side of the mismatch. Thus, Vsr endonuclease provides important
AB  - counterpoints in our understanding of endonucleolytic mechanisms and of damaged DNA
AB  - recognition.
ER  -

TY  - JOUR
AU  - Tsutakawa, S.E.
AU  - Muto, T.
AU  - Kawate, T.
AU  - Jingami, H.
AU  - Kunishima, N.
AU  - Ariyoshi, M.
AU  - Kohda, D.
AU  - Nakagawa, M.
AU  - Morikawa, K.
TI  - Crystallographic and functional studies of very short patch repair endonuclease.
JO  - Mol. Cell
PY  - 1999
SP  - 621
EP  - 628
VL  - 3
AB  - Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are
AB  - generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the
AB  - mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. We have
AB  - determined the crystal structure of a truncated form of this endonuclease at 1.8 A resolution.
AB  - The protein contains one structural zinc-binding module. Unexpectedly, its overall topology
AB  - resembles members of the type II restriction endonuclease family. Subsequent mutational and
AB  - biochemical analyses showed that certain elements in the catalytic site are also conserved.
AB  - However, the identification of a critical histidine and evidence of an active site
AB  - metal-binding coordination that is novel to endonucleases indicate a distinct catalytic
AB  - mechanism.
ER  -

TY  - JOUR
AU  - Tsvetkova, N.V.
TI  - Development of rational schemes of the purification of restriction endonucleases.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1987
SP  - 77
EP  - 81
VL  - 7
AB  - The work deals with the search for rational schemes of the purification of
AB  - endonucleases, suitable for the isolation of different enzymes.  The scheme
AB  - using the combination of Blue Sepharose and phosphocellulose has proved to be
AB  - most universal.  The expediency of starting the purification of Haemophilus
AB  - enzymes on Biogel A-0.5 m has been established.
ER  -

TY  - JOUR
AU  - Tsvetkova, N.V.
AU  - Mileikovskaya, M.M.
AU  - Gruber, I.M.
AU  - Polyachenko, V.M.
AU  - Butkus, V.V.
AU  - Janulaitis, A.
AU  - Sudzhyuvene, O.F.
AU  - Tarasov, A.P.
TI  - Purification and determination of the substrate specificity of restriction endonuclease BcmI.
JO  - Mol. Gen. Mikrobiol. Virusol.
PY  - 1987
SP  - 19
EP  - 22
VL  - 0
AB  - The vigorous development of recombinant DNA and biotechnology is leading to
AB  - growing requirements for varied restriction enzymes; therefore the search for
AB  - new specific endonucleases remains urgent.  The restriction endonuclease BcmI
AB  - has been isolated from a Bacillus strain.  It was purified by chromatography on
AB  - blue Sepharose, phosphocellulose P-II, and heparin-Sepharose.  The new domestic
AB  - adsorbent, orange Sepharose, can also be used for the purification of the
AB  - restriction endonuclease.  The nucleotide sequence recognized by BcmI was
AB  - determined by a comparison of the nature of the digestion of DNA by known
AB  - enzymes and by the investigated enzyme.  The site of cleavage of the substrate
AB  - was determined by direct methods on pBR322 DNA.  The aggregate of data obtained
AB  - permits us to assert that the restriction endonuclease BcmI is a true
AB  - isoschizomer of the restriction endonuclease ClaI.
ER  -

TY  - JOUR
AU  - Tsymbal, N.V.
AU  - Samoilenko, V.A.
AU  - Tovkach, F.I.
TI  - Site-specific endonuclease activity of filamentous cyanobacterium Plectonema boryanum.
JO  - Dopov. Nats. Akad. Nauk Ukr.
PY  - 2011
SP  - 146
EP  - 149
VL  - 0
AB  - The site-specific endonuclease PboI was isolated from the filamentous cyanobacterium
AB  - Plectonema boryanum.  The purification included successive column chromatographies on
AB  - DEAE-Toyopearl, phosphocellulose, and blue sepharose.  Purified enzyme recognizes and cleaves
AB  - GGATCC-palindrome sequence is analogously to BamHI.  The enzyne belongs to type II restriction
AB  - endonucleases.  The enzyme activity is optimal at a temperature 45oC, pH 7.5, and ionic
AB  - stength 100mM.
ER  -

TY  - JOUR
AU  - Tu, C.-P.D.
AU  - Jay, E.
AU  - Bahl, C.P.
AU  - Wu, R.
TI  - A reliable mapping method for sequence determination of oligodeoxyribonucleotides by mobility shift analysis.
JO  - Anal. Biochem.
PY  - 1976
SP  - 73
EP  - 93
VL  - 74
AB  - The method for sequence analysis of large oligodeoxyribonucleotides based on
AB  - the characteristic mobility shifts of their sequential partial degradation
AB  - products on two-dimensional homochromatography has been perfected using a large
AB  - number of synthetic oligodeoxyribonucleotides of defined sequences as
AB  - standards.  Flat bed electrophoresis with careful temperature control gave
AB  - entirely reproducible mobilities in the first dimension.  Using this
AB  - information, an accurate formula has been derived for calculating the relative
AB  - electrophoretic mobilities of oligodeoxyribonucleotides of any composition.
AB  - This formula is used to calculate the mobility shifts between two consecutive
AB  - oligodeoxyribonucleotides in a series of partial products of an unknown
AB  - oligomer distributed in the two-dimensional homochromatogram which differ by
AB  - one nucleotide in length.  This is compared with the observed mobility shift
AB  - value to identify the added nucleotide.  This provides a direct and rapid
AB  - method for obtaining the unambiguous sequence of an entire
AB  - oligodeoyribonucleotide up to 15 nucleotides in length.
ER  -

TY  - JOUR
AU  - Tu, C.-P.D.
AU  - Roychoudhury, R.
AU  - Wu, R.
TI  - Nucleotide recognition sequence at the cleavage site of Haemophilus aegyptius II (HaeII) restriction endonuclease.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1976
SP  - 355
EP  - 362
VL  - 72
AB  - We have determined the nucleotide sequence recognized by the restriction
AB  - endonuclease HaeII from Haemophilus aegyptius which cleaves the simian virus 40
AB  - (SV40) DNA at a single specific site.  By using terminal radioactive labeling
AB  - of the cleavage site at both the 5' and 3'-ends we have deduced the recognition
AB  - sequence, 3'...A-G-C-G-C^pT...3' 3'..Tp^C-G-C-G--A...5' with elements of a
AB  - two-fold rotational symmetry.  The endonuclease produces staggered ends with
AB  - protruding 3'-terminated single-strands, four nucleotides in length.  In
AB  - plasmid RSF 2124 DNA, which contains multiple HaeII cleavage sites, it was
AB  - observed that the 5th nucleotide from the 3' terminus is either a pdA or a pdG,
AB  - indicating alternating recognition sequences.
ER  -

TY  - JOUR
AU  - Tucholski, J.
AU  - Skowron, P.M.
AU  - Podhajska, A.J.
TI  - MmeI, a class-IIS restriction endonuclease: purification and characterization.
JO  - Gene
PY  - 1995
SP  - 87
EP  - 92
VL  - 157
AB  - Two restriction endonucleases, MmeI and MmeII, from Methylophilus methylotrophus were purified
AB  - to homogeneity.  Both enzymes belong to the class-II restriction endonucleases (ENases) but
AB  - exhibit very different enzymatic and physical properties.  MmeII is a typical member of
AB  - class-II ENases.  It is a polymeric protein composed of 50-kDa subunits.  In contrast to
AB  - MmeII, MmeI is a monomeric protein of 101 kDa, cleaving a DNA molecule 20/18 nucleotides away
AB  - from the asymmetric recognition sequence (5'-TCCRAC-3'); therefore, it is classified as a
AB  - member of subclass-IIS.  MmeI has a pI of 7.85 and is active in the pH range 6.5 to 10 with
AB  - the optimum at 7 to 8.  Increasing salt concentration creates an inhibitory effect on MmeI: 40
AB  - mM KCl decreases activity by 50%, 100 mM completely inhibits DNA cleavage.  Tris.HCl (pH
AB  - 7.5)  at a concentration exceeding 20 mM inhibits MmeI activity.  Mg2+ stimulates MmeI in the
AB  - range  of 0.2 to 35 mM, with the optimum between 0.5 and 10 mM.
ER  -

TY  - JOUR
AU  - Tucholski, J.
AU  - Zmijewski, J.W.
AU  - Podhajska, A.J.
TI  - Two intertwined methylation activities of the MmeI restriction-modification class-IIS system from Methylophilus methylotrophus.
JO  - Gene
PY  - 1998
SP  - 293
EP  - 302
VL  - 223
AB  - The class-IIS restriction endonuclease, R.MmeI, was isolated from Methylophilus
AB  - methylotrophus.  It was originally described as a monomeric enzyme, with the native Mr
AB  - 105,000+/-7,000, which did not cleave DNA efficiently.  However, it was discovered that R.MmeI
AB  - endonucleolytic activity is enhanced by S-adenosyl-L-methionine and sinefungin, an analogue of
AB  - AdoMet.  Surprisingly, the purified R.MmeI endonuclease was found to have a second enzymatic
AB  - activity, namely methylation of the adenine residue to N6-methyladenine in the top strand of
AB  - the MmeI-recognition sequence, 5'-TCCR*AC-3' (*A = meA).  The R.MmeI methylating activity
AB  - requires AdoMet and is increased in the presence of several divalent cations, 20-fold by Mg2+
AB  - or Ca2+, and less by Mn2+, Zn2+ and Co2+; however, methylation is inhibited entirely by
AB  - sinefungin, at concentrations above 9 microM.  The latter observation shows that the enhancing
AB  - effect of AdoMet or sinefungin on the DNA cleavage was not related to the process of DNA
AB  - methylation.  Furthermore, a second component of the MmeI restriction-modification system, an
AB  - M.MmeI methyltransferase, was isolated and purified.  The M.MmeI protein was found to have an
AB  - Mr of 48,000 +/- 2,000 (under denaturing conditions) and to methylate both adenine residues
AB  - (*A) in the MmeI-recognition sequence 5'-TCCR*AC-3'/3'-*AGGYTG-5'.  Methylation of the top
AB  - strand does not inhibit the DNA cleavage by R.MmeI, whereas methylation of both DNA strands
AB  - blocks the cleavage process.
ER  -

TY  - JOUR
AU  - Tucker, K.L.
TI  - A genetic investigation of the establishment of genomic imprinting.
JO  - Ph.D. Thesis, MIT, USA
PY  - 1997
SP  - 1
EP  - 80
AB  - Much evidence indicates that in vertebrates the methylation of DNA at cytosine residues
AB  - correlates with gene inactivity.  A single methyltransferase activity, DNA
AB  - (cytosine-5)-methyltransferase, has been purified from mammalian cells and its gene (Dnmt)
AB  - cloned.  The crucial importance of DNA methylation in development was demonstrated by the
AB  - targeted mutation of Dnmt in murine embryonic stem cells.  Embryos with homozygous disruptions
AB  - of Dnmt die in mid-gestation.  In contrast, homozygous mutant ES cells proliferate normally
AB  - with their DNA highly demethylated, though they die upon differentiation.  The research
AB  - presented in this thesis focused on expressing the Dnmt cDNA in the backgroud of Dnmt mutant
AB  - ES cells.  Initial attempts using a cDNA and a corresponding promoter region were unsuccessful
AB  - in effecting adequate levels of functional Mtase expression.  A complete cDNA sequence was
AB  - obtained through the cloning of two new 5'-proximal exons, which extend the open reading
AB  - frame up to 171 codons upstream of the previously defined start site.  This showed the
AB  - previously-reported promoter sequence to lie in the second intron of the gene, with no
AB  - evidence that it functions in ES cells.  It was found that the extra coding sequence was
AB  - necessary for functional expression of the gene in ES cells.  Expression of the wild type Dnmt
AB  - cDNA in mutant ES cells caused an increase in methylation of bulk DNA to normal levels, but
AB  - did not restore the methylation of imprinted genes, whose expression is monoallelic and
AB  - dependent upon their parental derivation.  The expression of these genes was deregulated
AB  - because of this hypomethylation, as shown previously in Dnmt mutant embryos.  Full restoration
AB  - of monoallelic methylation and expression was imposed on imprinted genes upon germline
AB  - transmission.  These results are consistent with the presence of distanct de novo DNA
AB  - methyltransferase activities during oogenesis and spermatogenesis which specifically recognize
AB  - imprinted genes but which are absent in the post-implantation embryo and in ES cells.  Because
AB  - the "rescued" ES cells display biallelic hypomethylation and expression of imprinted genes,
AB  - their developmental capacities may be impaired, as is seen with cells derived from
AB  - parthenogenetic or androgenetic embryos, which also display biallelic expression of imprinted
AB  - genes.  Alternatively, the rescued ES cells may have normal developmental capacities, as
AB  - predicted by a model which explains genomic imprinting as a nonessential,
AB  - evolutionarily-recent addition to the basic mammalian developmental program.  Rescued cells
AB  - differentiated normally in vitro, formed teratomas with a wide variety of differentiated cell
AB  - types, and contributed substantially to coat color in adult chimeras.  Further analysis of
AB  - tissue-specific distribution of rescued ES cells in chimeras will allow a full assessment of
AB  - the developmental potential of a mouse lacking an imprinted genome.
ER  -

TY  - JOUR
AU  - Tucker, K.L.
AU  - Beard, C.
AU  - Dausman, J.
AU  - Jackson-Grusby, L.
AU  - Laird, P.W.
AU  - Lei, H.
AU  - Li, E.
AU  - Jaenisch, R.
TI  - Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes.
JO  - Genes Dev.
PY  - 1996
SP  - 1008
EP  - 1020
VL  - 10
AB  - Embryonic stem cells homozygous for a disruption of the DNA (cytosine-5)-methyltransferase
AB  - gene (Dnmt) proliferate normally with their DNA highly demethylated but die upon
AB  - differentiation.  Expression of the wild-type Dnmt cDNA in mutant male ES cells caused an
AB  - increase in methylation of bulk DNA and of the Xist and Igf2 genes to normal levels, but did
AB  - not restore the methylation of the imprinted genes H19 and Igf2r.  These cells differentiated
AB  - normally in vitro and contributed substantially to adult chimeras.  While the Xist gene was
AB  - not expressed in the remethylated male ES cells, no restoration of the normal expression
AB  - profile was seen for H19, Igf2r, or Igf2.  This indicates that ES cells can faithfully
AB  - reestablish normal methylation and expression patterns of nonimprinted genes but lack the
AB  - ability to restore those of imprinted genes.  Full restoration of monoallelic methylation and
AB  - expression was imposed on H19, Igf2, and Igf2r upon germ-line transmission.  These results are
AB  - consistent with the presence of distinct de novo DNA methyltransferase activities during
AB  - oogenesis and spermatogenesis, which specifically recognize imprinted genes but are absent in
AB  - the postimplantation embryo and in ES cells.
ER  -

TY  - JOUR
AU  - Tucker, K.L.
AU  - Talbot, D.
AU  - Lee, M.A.
AU  - Leonhardt, H.
AU  - Jaenisch, R.
TI  - Complementation of methylation deficiency in embryonic stem cells by a DNA methyltransferase minigene.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1996
SP  - 12920
EP  - 12925
VL  - 93
AB  - Previous attempts to express functional DNA cytosine methyltransferase (EC 2.1.1.37) in cells
AB  - transfected with the available Dnmt cDNAs have met with little or no success.  We show that
AB  - the published Dnmt sequence encodes an amino terminal-truncated protein that is tolerated only
AB  - at very low levels when stably expressed in embryonic stem cells.  Normal expression levels
AB  - were, however, obtained with constructs containing a continuation of an ORF with a coding
AB  - capacity of up to 171 amino acids upstream of the previously defined start site.  The protein
AB  - encoded by these constructs comigrated in SDS/PAGE with the endogenous enzyme and restored
AB  - methylation activity in transfected cells.  This was shown by functional rescue of Dnmt mutant
AB  - embryonic stem cells that contain highly demethylated genomic DNA and fail to differentiate
AB  - normally.  When transfected with the minigene construct, the genomic DNA became remethylated
AB  - and the cells regained the capacity to form teratomas that displayed a wide variety of
AB  - differentiated cell types.  Our results define an amino-terminal domain of the mammalian Mtase
AB  - that is crucial for stable expression and function in vivo.
ER  -

TY  - JOUR
AU  - Tufariello, J.M.
AU  - Kerantzas, C.A.
AU  - Vilcheze, C.
AU  - Calder, R.B.
AU  - Nordberg, E.K.
AU  - Fischer, J.A.
AU  - Hartman, T.E.
AU  - Yang, E.
AU  - Driscoll, T.
AU  - Cole, L.E.
AU  - Sebra, R.
AU  - Maqbool, S.B.
AU  - Wattam, A.R.
AU  - Jacobs, W.R. Jr.
TI  - The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements.
JO  - MBio
PY  - 2015
SP  - e01313
EP  - e01315
VL  - 6
AB  - Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical
AB  - syndromes, most commonly skin infections in immunocompromised
AB  - individuals. M. haemophilum exhibits a unique requirement for iron
AB  - supplementation to support its growth in culture, but the basis for this property
AB  - and how it may shape pathogenesis is unclear. Using a combination of Illumina,
AB  - PacBio, and Sanger sequencing, the complete genome sequence of M. haemophilum was
AB  - determined. Guided by this sequence, experiments were performed to define the
AB  - basis for the unique growth requirements of M. haemophilum. We found that M.
AB  - haemophilum, unlike many other mycobacteria, is unable to synthesize iron-binding
AB  - siderophores known as mycobactins or to utilize ferri-mycobactins to support
AB  - growth. These differences correlate with the absence of genes associated with
AB  - mycobactin synthesis, secretion, and uptake. In agreement with the ability of
AB  - heme to promote growth, we identified genes encoding heme uptake machinery.
AB  - Consistent with its propensity to infect the skin, we show at the whole-genome
AB  - level the genetic closeness of M. haemophilum with Mycobacterium leprae, an
AB  - organism which cannot be cultivated in vitro, and we identify genes uniquely
AB  - shared by these organisms. Finally, we identify means to express foreign genes in
AB  - M. haemophilum. These data explain the unique culture requirements for this
AB  - important pathogen, provide a foundation upon which the genome sequence can be
AB  - exploited to improve diagnostics and therapeutics, and suggest use of M.
AB  - haemophilum as a tool to elucidate functions of genes shared with M. leprae.
AB  - IMPORTANCE: Mycobacterium haemophilum is an emerging pathogen with an unknown
AB  - natural reservoir that exhibits unique requirements for iron supplementation to
AB  - grow in vitro. Understanding the basis for this iron requirement is important
AB  - because it is fundamental to isolation of the organism from clinical samples and
AB  - environmental sources. Defining the molecular basis for M. haemophilium's growth
AB  - requirements will also shed new light on mycobacterial strategies to acquire iron
AB  - and can be exploited to define how differences in such strategies influence
AB  - pathogenesis. Here, through a combination of sequencing and experimental
AB  - approaches, we explain the basis for the iron requirement. We further demonstrate
AB  - the genetic closeness of M. haemophilum and Mycobacterium leprae, the causative
AB  - agent of leprosy which cannot be cultured in vitro, and we demonstrate methods to
AB  - genetically manipulate M. haemophilum. These findings pave the way for the use of
AB  - M. haemophilum as a model to elucidate functions of genes shared with M. leprae.
ER  -

TY  - JOUR
AU  - Tuffery, P.
AU  - Dessen, P.
AU  - Mugnier, C.
AU  - Hazout, S.
TI  - Restriction map construction using a 'complete sentences compatibility' algorithm.
JO  - Comput. Appl. Biosci.
PY  - 1988
SP  - 103
EP  - 110
VL  - 4
AB  - We have developed a new algorithm 'Complete sentences compatibility' (CSC)
AB  - which uses single and double digestion fragments to rapidly determine
AB  - restriction maps of circular DNA.  From possible combinations of fragments of
AB  - each simple digestion, which we call "sentences of decomposition", we construct
AB  - a restriction map which combines the sentences while taking into account
AB  - compatibility rules.  The algorithm can also deal with experimental errors of
AB  - fragment weight and can suggest solutions that account for non-readable bands
AB  - (fragments of zero length or multiple bands) on the gel.  Because experiments
AB  - using pairs of restrictive enzymes often result in multiple solutions, a
AB  - complementary algorithm tries to reduce the number of proposed solutions by
AB  - establishing consensus maps.  The restriction map construction algorithm was
AB  - tested on real cases, some containing more than fifteen fragments.  Execution
AB  - times range from 1-10 s on an IBM PC compatible microcomputer.
ER  -

TY  - JOUR
AU  - Tukel, C.
AU  - Sanlibaba, P.
AU  - Ozden, B.
AU  - Akcelik, M.
TI  - Identification of adsorption inhibition, restriction/modification and abortive infection type phage resistance systems in Lactococcus lactis strains.
JO  - Acta Biol. Hung.
PY  - 2006
SP  - 377
EP  - 385
VL  - 57
AB  - 98 Lactococcus lactis strains were isolated from traditional fermented milk products in Turkey
AB  - tested against 60 lactococcal lytic phages to
AB  - determine their resistance levels. While 82 L. lactis strains were
AB  - sensitive against lactic phages at different levels, 16 L. lactis
AB  - strains showed resistance to all phages tested. Types of phage
AB  - resistance among 16 L. lactis strains were identified as phage
AB  - adsorption inhibition in eight strains, restriction/modification in six
AB  - strains and abortive infection (heat sensitive phage resistance) in two
AB  - strains, using three broad-spectrum phages Phi p11 98-32, Phi pld 67-42
AB  - and Phi pld 67-44.
ER  -

TY  - JOUR
AU  - Tully, B.
AU  - Savalia, P.
AU  - Abuyen, K.
AU  - Baughan, C.
AU  - Romero, E.
AU  - Ronkowski, C.
AU  - Torres, B.
AU  - Tremblay, J.
AU  - Trujillo, A.
AU  - Tyler, M.
AU  - Perez-Rodriguez, I.
AU  - Amend, J.
TI  - Genome Sequence of Geothermobacter sp. Strain EPR-M, a Deep-Sea Hydrothermal Vent Iron Reducer.
JO  - Genome Announcements
PY  - 2017
SP  - e00424
EP  - e00417
VL  - 5
AB  - Geothermobacter sp. strain EPR-M was isolated from a hydrothermal vent on the East Pacific
AB  - Rise and has been shown to participate in the reduction of Fe(III)
AB  - oxides. Here, we report its 3.73-Mb draft genome sequence.
ER  -

TY  - JOUR
AU  - Tumbula, D.L.
AU  - Makula, R.A.
AU  - Whitman, W.B.
TI  - Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system.
JO  - FEMS Microbiol. Lett.
PY  - 1994
SP  - 309
EP  - 314
VL  - 121
AB  - An optimized polyethylene glycol (PEG) method of transformation was developed for
AB  - Methanococcus maripaludis using the pKAS102 integration vector. The frequency of
AB  - transformation with 0.8 ug of plasmid and 3x10/9 cells was 4.8x10-5 transformants cfu-1, or
AB  - 1.8x10/5 transformants per ug, which was four orders of magnitude greater than with the
AB  - natural transformation method. A PstI restriction activity in M. maripaludis was also
AB  - identified. Methylation of the plasmid with PstI methylase increased the methanococcal
AB  - transformation frequency at least four-fold. Also, chromosomal DNA from M. maripaludis was
AB  - resistant to digestion by the PstI endonuclease.
ER  -

TY  - JOUR
AU  - Tummings, S.
AU  - Panescu, J.
AU  - Daly, R.A.
AU  - Wrighton, K.C.
AU  - Mouser, P.J.
TI  - Draft Genome Sequences of Marinobacter Strains Recovered from Utica Shale-Produced Fluids.
JO  - Genome Announcements
PY  - 2018
SP  - e00155
EP  - e00118
VL  - 6
AB  - The genomes of three Marinobacter strains, isolated from saline fluids produced from a
AB  - Utica-Point Pleasant shale well, have been sequenced. These genomes
AB  - provide novel information on the degradation of petroleum distillates and
AB  - virulence mechanisms under microaerophilic conditions in fractured shale.
ER  -

TY  - JOUR
AU  - Tuohimaa, A.
AU  - Riipinen, K.A.
AU  - Brandt, K.
AU  - Alatossava, T.
TI  - The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages.
JO  - Arch. Virol.
PY  - 2006
SP  - 947
EP  - 965
VL  - 151
AB  - The complete 36,466-bp genome sequence of the virulent phage Lc-Nu of probiotic Lactobacillus
AB  - rhamnosus was determined. The linear dsDNA with
AB  - a GC-content of 44.2% contained 3' single-stranded cohesive ends of 12
AB  - nucleotides. A total of 51 putative open reading frames (orfs) were
AB  - predicted. Lc-Nu showed to be evolutionary closely related to the
AB  - temperate Lactobacillus casei phages phi AT3 and A2. High DNA homology
AB  - with phi AT3 was shared over the late transcribed genes, and the
AB  - highest homology with A2 was within the genetic switch region. The
AB  - truncated cI-like repressor was the only lysogeny related gene left,
AB  - which strongly suggested Lc-Nu to be recently evolved from a temperate
AB  - origin. Three putative methylases and endonucleases were detected from
AB  - the region of early-transcribed genes. The putative origin of
AB  - replication within the putative gene orf34 homologous to replisome
AB  - organizers resembled to that of lambdoid phages. The present study
AB  - suggested Lc-Nu to be a new candidate for the proposed Sfi21-like
AB  - species.
ER  -

TY  - JOUR
AU  - Tupa, P.R.
AU  - Masuda, H.
TI  - Draft Genome Sequence of a Propanotroph, Rhodococcus sp. Strain ENV425, Capable of Degrading Methyl tert-Butyl Ether and N-Nitrosodimethylamine.
JO  - Genome Announcements
PY  - 2018
SP  - e00051
EP  - e00018
VL  - 6
AB  - In this study, the draft genome of Rhodococcus sp. strain ENV425 was determined.  The
AB  - propane-grown strain ENV425 cometabolically degrades environmental
AB  - contaminants such as methyl tert-butyl ether and N-nitrosodimethylamine. The
AB  - sequence revealed the presence of multiple hydrocarbon metabolic genes that could
AB  - play pivotal roles in the biodegradation of pollutants.
ER  -

TY  - JOUR
AU  - Tupikin, A.E.
AU  - Kalmykova, A.I.
AU  - Kabilov, M.R.
TI  - Draft Genome Sequence of the Probiotic Bifidobacterium longum subsp. longum Strain MC-42.
JO  - Genome Announcements
PY  - 2016
SP  - e01411
EP  - e01416
VL  - 4
AB  - Here, we report the draft genome sequence of Bifidobacterium longum subsp. longum strain MC-42
AB  - isolated from the feces of a healthy infant, and which was used in
AB  - the commercially available probiotic product Biovestin.
ER  -

TY  - JOUR
AU  - Turk, P.W.
AU  - Laayoun, A.
AU  - Smith, S.S.
AU  - Weitzman, S.A.
TI  - DNA adduct 8-hydroxyl-2'-deoxyguanosine (8-hydroxyguanine) affects function of human DNA methyltransferase.
JO  - Carcinogenesis
PY  - 1995
SP  - 1253
EP  - 1255
VL  - 16
AB  - 8-Hydroxyl-2'-deoxyguanosine (also referred to as 8-hydroxyguanine [8-OH-dG] or
AB  - 7,8-dihydro-8-oxoguanine), a common DNA adduct resulting from injury to DNA via reactive
AB  - oxygen species, affects the in vitro methylation of nearby cytosine moieties by the human DNA
AB  - methyltransferase. The exact position of 8-OH-deoxyguanosine relative to a CpG dinucleotide
AB  - appears important to this effect. Our data indicate that 8-OH-deoxyguanosine diminishes the
AB  - ability of the methyltransferase to methylate a target cytosine when the 8-OH-deoxyguanosine
AB  - is one or two nucleotides 3' from the cytosine, on the same strand. On the other hand
AB  - 8-OH-deoxyguanosine does not diminish the ability of the enzyme to respond to a methyl
AB  - director (5-methylcytosine) when the 8-OH-deoxyguanosine is on the same strand but one or two
AB  - nucleotides 3' from the methyl director. Differences in methylation rates as great as 13-fold
AB  - have been detected using various 8-OH-deoxyguanosine-containing oligonucleotides as substrates
AB  - in methylation assays. Our findings suggest that oxidative damage of parental strand guanines
AB  - would permit normal copying of methylation patterns through maintenance methylation, while
AB  - oxidative damage of guanines in the nascent strand DNA would inhibit such methylation.
ER  -

TY  - JOUR
AU  - Turk, P.W.
AU  - Weitzman, S.A.
TI  - Free radical DNA adduct 8-OH-deoxyguanosine affects activity of HpaII and MspI restriction endonuclease.
JO  - Free Radic. Res.
PY  - 1995
SP  - 255
EP  - 258
VL  - 23
AB  - 8-OH-deoxyguanosine can diminish the ability of the restriction endonucleases HpaII and MspI
AB  - to cleave DNA.  The exact position of the adduct within the recognition site appears to
AB  - determine the extent of the effect.
ER  -

TY  - JOUR
AU  - Turmel, M.
AU  - Boulanger, J.
AU  - Schnare, M.N.
AU  - Gray, M.W.
AU  - Lemieux, C.
TI  - Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos.
JO  - J. Mol. Biol.
PY  - 1991
SP  - 293
EP  - 311
VL  - 218
AB  - The chloroplast large subunit rRNA gene of Chlamydomonas eugametos and its 5' flanking region
AB  - encoding tRNA-Ile (GAU) and tRNA-Ala (UGC) have been sequenced. The DNA sequence data along
AB  - with the results of a detailed RNA analysis disclosed two unusual features of this green algal
AB  - large subunit rRNA gene: (1) the presence of six group I introns (CeLSU.1-CeLSU.6) whose
AB  - insertion positions have not been described previously, and (2) the presence of three short
AB  - internal transcribed spacers that are post-transcriptionally excised to yield four rRNA
AB  - species of 380, 52, 810 and 1720 nucleotides, positioned in this order (5' to 3') in the
AB  - primary transcript. Together, these RNA species can assume a secondary structure that is
AB  - almost identical to that proposed for the 23S rRNA of Escherichia coli. All three internal
AB  - transcribed spacers map to variable regions of primary sequence and/or potential secondary
AB  - structure, whereas all six introns lie within highly conserved regions. The first three
AB  - introns are inserted within the sequence encoding the 810 nucleotide rRNA species and map
AB  - within domain II of the large subunit rRNA structure; the remaining introns, found in the
AB  - sequence encoding the 1720 nucleotide rRNA species, lie within either domain IV or V, as is
AB  - the case for all other large subunit rDNA introns that have been documented to date. CeLSU.5
AB  - and CeLSU.6 each contain a long open reading frame (ORF) of more than 200 codons. While the
AB  - CeLSU.6 ORF is not related to any known ORFs, the CeLSU.5 ORF belongs to a fmaily of ORFs that
AB  - have been identified in Podospora and Neuospora mitochondrial group I introns. The finding
AB  - that a polymorphic marker showing unidirectional gene conversion during crosses between C.
AB  - eugametos and Chlamydomonas moewusii is located within the CeLSU.5 ORF makes it likely that
AB  - this intron is a mobile element and that its ORF encodes a site-specific endonuclease
AB  - promoting the transfer of the intron DNA sequence.
ER  -

TY  - JOUR
AU  - Turmel, M.
AU  - Cote, V.
AU  - Otis, C.
AU  - Mercier, J.-P.
AU  - Gray, M.W.
AU  - Lonergan, K.M.
AU  - Lemieux, C.
TI  - Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion).
JO  - Mol. Biol. Evol.
PY  - 1995
SP  - 533
EP  - 545
VL  - 12
AB  - We describe here a case of homologous introns containing homologous open reading frames (ORFs)
AB  - that are inserted at the same site in the large subunit (LSU) rRNA gene of different
AB  - organelles in distantly related organisms.  We show that the chloroplast LSU rRNA gene of the
AB  - green alga Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2) encoding a
AB  - site-specific endonuclease (I-CpaI).  This intron is inserted at the identical site
AB  - (corresponding to positions 1931-1932 of the Escherichia coli 23S rRNA sequence) as a group I
AB  - intron (AcLSU.m1) in the mitochondrial LSU rRNA gene of the amoeboid protozoon Acanthamoeba
AB  - castellanii.  The CpLSU.2 intron displays a rmarkable degree of nucleotide similarity in both
AB  - primary sequence and secondary structure to the AcLSU.m1 intron; moreover, the Acanthamoeba
AB  - intron contains an ORF in the same location within its secondary structure as the CpLSU.2 ORF
AB  - and shares with it a strikingly high level of amino acid similarity (65%; 42% identity).  A
AB  - comprehensive survey of intron distribution at site 1931 of the chloroplast LSU rRNA gene
AB  - reveals a rather restricted occurrence within the polyphyletic genus Chlamydomonas, with no
AB  - evidence of this intron among a number of non-Chlamydomonad green algae surveyed, nor in land
AB  - plants.  A parallel survey of homologues of a previously described and similar intron/ORF pair
AB  - (C. reinhardtii chloroplast CrLSU/A. castellanii mitochondrial AcLSU.m3) also shows a
AB  - restricted occurrence of this intron (site 2593) among chloroplasts, although the intron
AB  - distribution is somewhat broader than that observed at site 1931, with site-2593 introns
AB  - appearing in several green algal branches outside of the Chlamydomonas lineage.  The available
AB  - data, while not definitive, are most consistent with a relatively recent horizontal transfer
AB  - of both site-1931 and site-2593 introns (and their contained ORFs) between the chloroplast of
AB  - a Chlamydomonas-type organism and the mitochondrial of an Acanthamoeba-like organism, probably
AB  - in the direction chlorplast to mitochondrion.  The data also suggest that both introns could
AB  - have been acquired in a single event.
ER  -

TY  - JOUR
AU  - Turmel, M.
AU  - Gutell, R.R.
AU  - Mercier, J.-P.
AU  - Otis, C.
AU  - Lemieux, C.
TI  - Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa.
JO  - J. Mol. Biol.
PY  - 1993
SP  - 446
EP  - 467
VL  - 232
AB  - Previous reports on the chloroplast large subunit rRNA genes of the two distantly related
AB  - green algae Chlamydomonas eugametos and Chlamydomonas reinhardtii indicate differences in the
AB  - distribution of group I introns and suggest a different arrangement of internal transcribed
AB  - spacers. To provide insights into the origin of these two types of intervening sequences, we
AB  - have undertaken the sequencing of the chlorplast rrnL genes of 15 additional Chlamydomonas
AB  - taxa and have characterized the mature large subunit rRNA species they encode in addition to
AB  - those specified by the C. reinhardtii rrnL. These analyses disclosed the presence of three
AB  - internal transcribed spaces sharing the same positions in all of the 17 taxa as well as the
AB  - presence of a total of 39 group I introns representing 12 insertion sites. Of these insertion
AB  - sites, only one has been identified in non-Chlamydomonas taxa. The distribution of
AB  - Chlamydomonas introns is highly variable and, in many respects, is not consistent with the
AB  - phylogeny deduced from chloroplast rRNA sequence comparisons. This phylogeny features two main
AB  - lineages of Chlamydomonas taxa forming sister groups. Because earlier branching organisms in
AB  - the green algal/land plant lineage display no chloroplast rRNA introns, it appears that all of
AB  - the intron insertion positions in Chlamydomonas are of recent origins, with some of the
AB  - positions having arisen subsequent to the divergence of the two main Chlamydomonas lineages.
AB  - Remarkably, the rRNA regions corresponding to most of the group I intron insertion positions
AB  - in rRNA genes have been assigned functional roles suggesting that they lie in exposed regions
AB  - of the ribosome. On the basis of this striking correlation between exposed rRNA regions and
AB  - intron insertion sites, we speculate that the reversal of the self-splicing reaction has
AB  - played a major role in the creation of the multiple intron insertion positions found in rRNA
AB  - genes as well as in the proliferation of group I introns elsewhere in the Chlamydomonas
AB  - chloroplast genome.
ER  -

TY  - JOUR
AU  - Turmel, M.
AU  - Mercier, J.-P.
AU  - Cote, V.
AU  - Otis, C.
AU  - Lemieux, C.
TI  - The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 2519
EP  - 2525
VL  - 23
AB  - Two group I introns (CpSSU.1 and CpSSU.2) that each potentially encode a protein with two
AB  - copies of the LAGLI-DADG motif were identified in the Chlamydomonas pallidostigmatica
AB  - chloroplast small subunit rRNA gene. They both belong to subgroup IA3 and represent novel
AB  - insertion positions in this gene (sites 508 and 793 in the Escherichia coli 16S rRNA). The
AB  - proteins encoded by the two introns were synthesized in vitro and tested for their ability to
AB  - cleave the homing site of their respective introns. Only the CpSSU.1-encoded protein (I-CpaII)
AB  - was found to display specific DNA endonuclease activity. At 0.1 mM MgCl2, I-CpaII nicks only
AB  - the bottom (transcribed) DNA strand, but at concentrations ranging from 0.5 to 5.0 mM, it
AB  - cleaves both DNA strands (leaving a 4 nucleotide single-stranded extension with 3'-OH
AB  - overhangs) while preferentially nicking the bottom strand. The rate of cleavage of the top
AB  - strand increases with increasing concentration of MgCl2. The preliminary data derived from
AB  - these endonuclease assays suggest that the mode of DNA cleavage by I-CpaII is directed by the
AB  - availability of Mg2+ and the affinity of different binding sites for this cation.
ER  -

TY  - JOUR
AU  - Turmel, M.
AU  - Otis, C.
AU  - Cote, V.
AU  - Lemieux, C.
TI  - Evolutionarily conserved and functionally important residues in the I-CeuI homing endonuclease.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2610
EP  - 2619
VL  - 25
AB  - Two approaches were used to discern critical amino acid residues for the function of the
AB  - I-CeuI homing endonuclease: sequence comparison of subfamilies of homologous proteins and
AB  - genetic selection.  The first approach revealed residues potentially involved in catalysis and
AB  - DNA recognition.  Because I-CeuI is lethal in Escherichia coli, enzyme variants not perturbing
AB  - cell viability were readily selected from an expression library.  A collection of 49 variants
AB  - with single amino acid substitutions at 37 positions was assembled.  Most of these positions
AB  - are clustered within or around the LAGLI-DADG dodecapeptide and the TQH sequence, two motifs
AB  - found in all protein subfamilies examined.  The Km and kcat values of the wild-type and nine
AB  - variant enzymes synthesized in vitro were determined.  Three variants, including one showing a
AB  - substituion of the glutamine residue in the TQH motif, revealed no detectable endonuclease
AB  - activity; five others showed reduced activity compared to the wild-type enzyme; whereas the
AB  - remaining variant cleaved the top strand about three times more efficiently than the
AB  - wild-type.  Our results not only confirm recent reports indicating that amino acids in the
AB  - LAGLI-DADG dodecapeptide are functionally critical, but they also suggest that some residues
AB  - outside this motif directly participate in catalysis.
ER  -

TY  - JOUR
AU  - Turna, J.
AU  - Mikulasova, D.
AU  - Timko, J.
AU  - Zelinka, J.
TI  - Purification of restriction endonuclease SauBMKI.
JO  - Biologia (Bratisl)
PY  - 1990
SP  - 281
EP  - 288
VL  - 45
AB  - The type II restriction endonuclease designated SauBMKI was isolated from Streptomyces
AB  - aureofaciens, strain BMK.  The enzyme was purified by chromatography using DEAE-cellulose,
AB  - ssDNA cellulose and phosphocellulose to the grade when no unspecific endo- and exonucleases
AB  - were detectable.  The optimal reaction conditions were established: glycine 20 mmol/l (pH
AB  - 8.7), NaCl 20 mmol/l, MgCl2 20 mmol/l, 2-ME 7 mmol/l and BSA 100 micrograms/ml.
ER  -

TY  - JOUR
AU  - Turner, D.P.
AU  - Connolly, B.A.
TI  - Interaction of the E-coli DNA G : T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 765
EP  - 778
VL  - 304
AB  - The Escherichia coli vsr endonuclease recognises G:T base-pair mismatches in double-stranded
AB  - DNA and initiates a repair pathway by
AB  - hydrolysing the phosphate group 5' to the incorrectly paired T. The
AB  - enzyme shows a preference for G:T mismatches within a particular
AB  - sequence context, derived from the recognition site of the E. coli dcm
AB  - DNA-methyltransferase (CC[A/T]GG). Thus, the preferred substrate for
AB  - the vsr protein is (CT[A/T]GG), where the underlined T is opposed by a
AB  - dG base. This paper provides quantitative data for the interaction of
AB  - the vsr protein with a number of oligonucleotides containing G:T
AB  - mismatches. Evaluation of specificity constant (k(st)/K-D; k(st) = rate
AB  - constant for single turnover, K-D = equilibrium dissociation constant)
AB  - confirms vsr's preference for a G:T mismatch within a hemi-methylated
AB  - dcm sequence, i.e. the best substrate is a duplex (both strands written
AB  - in the 5'-3' orientation) composed of CT[A/T]CG and C-5Me[T/A]GG.
AB  - Conversion of the mispaired T (underlined) to dU or the d(5Me)C to dC
AB  - gave poorer substrates. No interaction was observed with
AB  - oligonucleotides that lacked a G:T mismatch or did not possess a dcm
AB  - sequence. An analysis of the fraction of active protein, by
AB  - "reverse-titration" (i.e. adding increasing amounts of DNA to a fixed
AB  - amount of protein followed by gel-mobility shift analysis) showed that
AB  - less than 1% of the vsr endonuclease was able to bind to the substrate.
AB  - This was confirmed using "competitive titrations" (where competitor
AB  - oligonucleotides are used to displace a P-32-labelled nucleic acid from
AB  - the vsr protein) and burst kinetic analysis. This result is discussed
AB  - in the light of previous in vitro and in vivo data which indicate that
AB  - the MutL protein may be needed for full vsr activity.
ER  -

TY  - JOUR
AU  - Turner, P.C.
AU  - Yomano, L.P.
AU  - Jarboe, L.R.
AU  - York, S.W.
AU  - Baggett, C.L.
AU  - Moritz, B.E.
AU  - Zentz, E.B.
AU  - Shanmugam, K.T.
AU  - Ingram, L.O.
TI  - Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes.
JO  - J. Ind. Microbiol. Biotechnol.
PY  - 2012
SP  - 629
EP  - 639
VL  - 39
AB  - Escherichia coli KO11 (ATCC 55124) was engineered in 1990 to produce ethanol by
AB  - chromosomal insertion of the Zymomonas mobilis pdc and adhB genes into E. coli W
AB  - (ATCC 9637). KO11FL, our current laboratory version of KO11, and its parent E.
AB  - coli W were sequenced, and contigs assembled into genomic sequences using optical
AB  - NcoI restriction maps as templates. E. coli W contained plasmids pRK1 (102.5 kb)
AB  - and pRK2 (5.4 kb), but KO11FL only contained pRK2. KO11FL optical maps made with
AB  - AflII and with BamHI showed a tandem repeat region, consisting of at least 20
AB  - copies of a 10-kb unit. The repeat region was located at the insertion site for
AB  - the pdc, adhB, and chloramphenicol-resistance genes. Sequence coverage of these
AB  - genes was about 25-fold higher than average, consistent with amplification of the
AB  - foreign genes that were inserted as circularized DNA. Selection for higher levels
AB  - of chloramphenicol resistance originally produced strains with higher pdc and
AB  - adhB expression, and hence improved fermentation performance, by increasing the
AB  - gene copy number. Sequence data for an earlier version of KO11, ATCC 55124,
AB  - indicated that multiple copies of pdc adhB were present. Comparison of the W and
AB  - KO11FL genomes showed large inversions and deletions in KO11FL, mostly enabled by
AB  - IS10, which is absent from W but present at 30 sites in KO11FL. The early KO11
AB  - strain ATCC 55124 had no rearrangements, contained only one IS10, and lacked most
AB  - accumulated single nucleotide polymorphisms (SNPs) present in KO11FL. Despite
AB  - rearrangements and SNPs in KO11FL, fermentation performance was equal to that of
AB  - ATCC 55124.
ER  -

TY  - JOUR
AU  - Turroni, F. et al.
TI  - Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 19514
EP  - 19519
VL  - 107
AB  - The human intestine is densely populated by a microbial consortium whose
AB  - metabolic activities are influenced by, among others, bifidobacteria.
AB  - However, the genetic basis of adaptation of bifidobacteria to the human
AB  - gut is poorly understood. Analysis of the 2,214,650-bp genome of
AB  - Bifidobacterium bifidum PRL2010, a strain isolated from infant stool,
AB  - revealed a nutrient-acquisition strategy that targets host-derived
AB  - glycans, such as those present in mucin. Proteome and transcriptome
AB  - profiling revealed a set of chromosomal loci responsible for mucin
AB  - metabolism that appear to be under common transcriptional control and with
AB  - predicted functions that allow degradation of various O-linked glycans in
AB  - mucin. Conservation of the latter gene clusters in various B. bifidum
AB  - strains supports the notion that host-derived glycan catabolism is an
AB  - important colonization factor for B. bifidum with concomitant impact on
AB  - intestinal microbiota ecology.
ER  -

TY  - JOUR
AU  - Tushar, L.
AU  - Sasi, J.T.S.
AU  - Sasikala, C.
AU  - Ramana, C.V.
TI  - Draft Genome Sequence of Antimicrobial-Producing Clostridium sp. JC272, Isolated  from Marine Sediment.
JO  - Genome Announcements
PY  - 2015
SP  - e00650
EP  - e00615
VL  - 3
AB  - We announce the draft genome sequence of Clostridium sp. JC272, isolated from a sediment
AB  - sample collected from marine habitats of Gujarat, India. Clostridium sp.
AB  - JC272 is an obligate anaerobe and has the ability to produce antimicrobial
AB  - compounds. The genome sequence indicates the strain's capability of producing
AB  - small peptides (microcins), which are potential novel antibiotics.
ER  -

TY  - JOUR
AU  - Tushar, L.
AU  - Sravanthi, T.
AU  - Sasikala, C.
AU  - Ramana, C.V.
TI  - Draft Genome Sequence of Spirochaeta sp. Strain JC202, an Endosymbiont of the Termite (Isoptera) Gut.
JO  - Genome Announcements
PY  - 2015
SP  - e01481
EP  - e01414
VL  - 3
AB  - We announce here the draft genome sequence of Spirochaeta sp. strain JC202 isolated from gut
AB  - of a termite (Isoptera). The genome suggests that Spirochaeta
AB  - sp. JC202 has the capability for natural conjugation with the help of fimbriae
AB  - and pili. Experimental evidence and the genome sequence suggest that strain JC202
AB  - is capable of producing colicin V and a bacteriocin group of peptides in a
AB  - specific interaction.
ER  -

TY  - JOUR
AU  - Tuzikov, F.V.
AU  - Tuzikova, N.A.
AU  - Naumochkin, A.N.
AU  - Zinovev, V.V.
AU  - Malygin, E.G.
TI  - Study of the equilibrium interation of T4 phage Dam-DNA-(N-adenine)-methyltransferase with substrates and ligands by fluorescence quenching method.
JO  - Mol. Biol. (Mosk)
PY  - 1997
SP  - 86
EP  - 90
VL  - 31
ER  -

TY  - JOUR
AU  - Tuzikov, F.V.
AU  - Tuzikova, N.A.
AU  - Naumochkin, A.N.
AU  - Zinovev, V.V.
AU  - Malygin, E.G.
TI  - Fluorescence quenching study of equilibrium binding of phage T4 dam DNA-[N6-adenine]-methyltransferase with substrates and ligands.
JO  - Mol. Biol. (Mosk)
PY  - 1997
SP  - 73
EP  - 76
VL  - 31
AB  - Selective fluorescence quenching by iodide ions was used to evaluate the surface accessibility
AB  - of tryptophan residues in T4 Dam DNA methyltransferase (T4 MTase).  Two of the three MTase
AB  - tryptophans proved fully accessible for iodide ions, suggesting that they are located near the
AB  - surface of the molecule.  Quenching of intrinsic fluorescence of T4 MTase tryptophans was used
AB  - to determine the parameters of enzyme binding with substrates (20-bp oligonucleotide duplex
AB  - with a GATC site, and S-adenosyl-L-methionine (SAM)) and substrate analogs (duplex without a
AB  - GATC site and S-adenosyl-L-homocysteine (SAH)).  Enzyme binding with small ligands (SAM and
AB  - SAH) conforms with the modified Sterm-Volmer equation applicable to 1:1 complexes.  The
AB  - dissociation constants for SAM and SAH were 0.24 and 2.3 microM, respectively.  In both cases,
AB  - about one third of the total Mtase fluorescence could be quenched by these ligands.
AB  - Saturating binding of oligonucleotide duplexes resulted in 12% (oligonucleotide with GATC) or
AB  - 19% (without GATC) quenching.  In both cases, experimental quenching curves did not fit the
AB  - modified Sterm-Volmer equation, suggesting that the mechanism of oligonucleotide binding is
AB  - more complex than that for small ligands.
ER  -

TY  - JOUR
AU  - Tuzikov, F.V.
AU  - Zinovev, V.V.
AU  - Vavilin, V.I.
AU  - Malygin, E.G.
AU  - Buryanov, Y.I.
AU  - Baev, A.A.
TI  - Interaction between Ecodam methylase and double-stranded oligodeoxyribonucleotides.
JO  - Dokl. Akad. Nauk.
PY  - 1989
SP  - 231
EP  - 234
VL  - 304
AB  - None
ER  -

TY  - JOUR
AU  - Tweedie, S.
AU  - Ng, H.-H.
AU  - Barlow, A.L.
AU  - Turner, B.M.
AU  - Hendrich, B.
AU  - Bird, A.
TI  - Vestiges of a DNA methylation system in Drosophila melanogaster?
JO  - Nat. Genet.
PY  - 1999
SP  - 389
EP  - 390
VL  - 23
AB  - The insect Drosophila melanogaster belongs to an atypical group of animals with no detectable
AB  - genomic 5-methylcytosine.  We found, unexpectedly, that the Drosophila genome potentially
AB  - encodes two proteins that resemble a cytosine DNA methyltransferase and a mammalian
AB  - methyl-CpG-binding -domain protein, respectively.  The hypothetical DNA methyltransferase,
AB  - dDNMT, is closely related to the pmt1/DNMT2 family identified in fission yeast and mouse.
ER  -

TY  - JOUR
AU  - Twomey, D.P.
AU  - Davis, R.
AU  - Daly, C.
AU  - Fitzgerald, G.F.
TI  - Sequence of the gene encoding a second ScrFI m5C methyltransferase of Lactococcus lactis.
JO  - Gene
PY  - 1993
SP  - 205
EP  - 209
VL  - 136
AB  - The nucleotide (nt) sequence of a second methyltransferase (MTase) encoding gene associated
AB  - with the ScrFI restriction/modification (R/M) system (5'CCNGG3') of Lactococcus lactis ssp.
AB  - cremoris UC503 has been determined. The coding region was 1080 nt in length and capable of
AB  - specifying a 41,847-Da protein of 360 amino acids (aa). The deduced aa sequence displayed
AB  - motifs characteristic of all prokaryotic 5-methylcytosine (m5C) MTases. Significant similarity
AB  - was observed with other m5C MTases, apart from the variable region which has been deemed
AB  - responsible for target sequence specificity. A larger than normal spacing between motif II and
AB  - motif III, comparable in length and bearing homology to a similar region in the SssI MTase,
AB  - was observed. A second open reading frame (ORF) of unknown function, which has the capacity to
AB  - encode a protein of 155 aa, was observed three nt upstream from the m5C MTase ORF.
ER  -

TY  - JOUR
AU  - Twomey, D.P.
AU  - Davis, R.
AU  - Daly, C.
AU  - Fitzgerald, G.F.
TI  - Molecular characterisation of the ScrFI restriction-modification system.
JO  - Irish J. Agr. Food Res.
PY  - 1993
SP  - 217
EP  - 217
VL  - 32
AB  - The elucidation of the genetic determinants of bacteriophage resistance assists rational
AB  - approaches to designing and improving cheese-starter cultures. Lactococcus lactis subsp.
AB  - cremoris UC503 exhibits restriction-modification (R/M) activity, through the restriction
AB  - endonuclease, ScrFI, and the products of two methylase genes. Both of these methylases
AB  - independently confer resistance to ScrFI digestion in E. coli ED8739. These genes, designated
AB  - mscrFIA and mscrFIB, have been cloned from the chromosome of strain UC503 and their nucleotide
AB  - sequences determined. Both of the predicted amino acid sequences display 10 motifs with an
AB  - alignment and architecture characteristic of all procaryotic 5-methylcytosine methylases. The
AB  - so-called variable regions, located between motif VIII and motif IX, are responsible for the
AB  - target sequence specificity of these enzymes. However, the respective variable regions of
AB  - M.ScrFIA and M.ScrFIB display no significant similarity to each other, suggesting that the
AB  - enzymes have different recognition specificities. The variable region of M.ScrFIA displayed
AB  - substantial similarity to equivalent regions in M.EcoRII and dcm, both of which recognise 5'
AB  - CC(A/T)GG 3', a subset of the ScrFI endonuclease recognition site. In M.ScrFIA, a larger than
AB  - normal spacing between motifs II and III, comparable in length and bearing marginal homology
AB  - to a similar region in the SssI methylase, was observed. Recent evidence suggests that the
AB  - ScrFI restriction endonuclease gene resides in the 1 kb intervening region between mscrFIA and
AB  - mscrFIB. Furthermore, it is proposed that a gene (orfX) located three nucleotides upstream of
AB  - mscrFIB encodes a repair endonuclease which compensates for the inherent ability of
AB  - 5-methylcytosine to deaminate spontaneously to thymine.
ER  -

TY  - JOUR
AU  - Twomey, D.P.
AU  - De Urraza, P.J.
AU  - McKay, L.L.
AU  - O'Sullivan, D.J.
TI  - Characterization of AbiR, a novel multicomponent abortive infection mechanism encoded by plasmid pKR223 of Lactococcus lactis subsp. lactis KR2.
JO  - Appl. Environ. Microbiol.
PY  - 2000
SP  - 2647
EP  - 2651
VL  - 66
AB  - The native lactococcal plasmid pKR223 encodes two distinct phage resistance mechanisms, a
AB  - restriction and modification (R/M) system designated LlaKR2I and an abortive infection
AB  - mechanism (Abi) which affects prolate-headed-phage proliferation. The nucleotide sequence of a
AB  - 16,174-bp segment of pKR223 encompassing both the R/M and Abi determinants has been
AB  - determined, and sequence analysis has validated the novelty of the Abi system, which has now
AB  - been designated AbiR. Analysis of deletion and insertion clones demonstrated that AbiR was
AB  - encoded by two genetic loci, separated by the LlaKR2I R/M genes. Mechanistic studies on the
AB  - AbiR phenotype indicated that it was heat sensitive and that it impeded phage DNA replication.
AB  - These data indicated that AbiR is a novel multicomponent, heat-sensitive, "early"-functioning
AB  - Abi system and is the first lactococcal Abi system described which is encoded by two separated
AB  - genetic loci.
ER  -

TY  - JOUR
AU  - Twomey, D.P.
AU  - Gabillet, N.
AU  - Daly, C.
AU  - Fitzgerald, G.F.
TI  - Molecular characterization of the restriction endonuclease gene (scrFIR) associated with the ScrFI restriction/modification system from Lactococcus lactis subsp. cremoris UC503.
JO  - Microbiology
PY  - 1997
SP  - 2277
EP  - 2286
VL  - 143
AB  - The nucleotide sequence of the chromosomally encoded type II ScrFI restriction/modification
AB  - system from Lactococcus lactis subsp. cremoris UC503 was completed.  The ScrFI restriction
AB  - endonuclease has previously been shown to specifically recognize 5' CCNGG 3' sites, cleaving
AB  - after the second cytosine and the degenerate central base.  The Enase gene was located
AB  - between, and co-directionally transcribed with, two formerly characterized 5-methylcytosine
AB  - methyltransferase genes, which encode proteins that independently confer protection against
AB  - ScrFI digestion.  scrFIR codes for a protein of 272 amino acids with a predicted molecular
AB  - mass of 31470 Da, which agrees favorably with a previously estimated molecular mass of 34 kDa
AB  - for this enzyme.  The deduced sequence of this protein did not show any significant homology
AB  - with known protein sequences, including the isoschizomeric SsoII Enase from Shigella sonnei.
AB  - The Enase gene was cloned and expressed in Escherichia coli and lactococcus; however, no in
AB  - vivo restriction of phage was observed, suggesting that expression of the Enase gene may be
AB  - repressed, or that the appropriate expression signals may be absent in the cloned constructs.
AB  - The ability of ScrFi to cleave non-canonically modified 5'CCNGG3' sequences suggested that
AB  - some ScrFI sites may require complex modifications to fully impair digestion by this enzyme.
ER  -

TY  - JOUR
AU  - Twomey, D.P.
AU  - McKay, L.L.
AU  - O'Sullivan, D.J.
TI  - Molecular characterization of the Lactococcus lactis LlaKR2I restriction-modification system and effect of an IS982 element positioned between the restriction and modification genes.
JO  - J. Bacteriol.
PY  - 1998
SP  - 5844
EP  - 5854
VL  - 180
AB  - The nucleotide sequence of the plasmid-encoded LlaKR2I restriction-modification system of
AB  - Lactococcus lactis subsp. lactis biovar diacetylactis KR2 was determined.  This R-M system
AB  - comprises divergently transcribed endonuclease (llaKR2IR) and methyltransferase llaKR2IM)
AB  - genes; located in the intergenic region is a copy of the insertion element IS982, whose
AB  - putative transposase gene is codirectionally transcribed with llaKR2IM.  The deduced sequence
AB  - of the LlaKR2I endonuclease shared homology with the type II endonuclease Sau3AI and with the
AB  - MutH mismatch repair protein, both of which recognize and cleave the sequence 5'GATC3'.  In
AB  - addition, M.LlaKR2I displayed homology with the 5-methycytosine methyltransferase family of
AB  - proteins, exhibiting greatest identity with M.Sau3AI.  Both of these proteins shared notable
AB  - homology throughout their putative target recognition domains.  Furthermore, subclones of the
AB  - native parental lactococcal plasmid pKR223, which encode M.LlaKR2I, all remained undigested
AB  - after treatment with Sau3AI despite the presence of multiple 5'GATC3' sites.  The
AB  - combination of these data suggested that the specificity of the LlaKR2I R-M system was likely
AB  - to be 5'GATC3', with the cytosine residue being modified to 5-methylcytosine.  The IS982
AB  - element located within the LlaKR2I R-M system contained at its extremities two 16-bp perfect
AB  - inverted repeats flanked by two 7-bp direct repeats.  A perfect extended promoter consensus,
AB  - which represented the likely original promoter of the llaKR21I gene, was shown to overlap the
AB  - direct repeat sequence on the other side of IS982.  Specific deletion of IS982 and one of
AB  - these direct repeats via a PCR strategy indicated that the LlaKR2I R-M determinants do not
AB  - rely on elements within IS982 for expression and that the efficiency of bacteriophage
AB  - restriction was not impaired.
ER  -

TY  - JOUR
AU  - Twomey, D.P.
AU  - McKay, L.L.
AU  - O'Sullivan, D.J.
TI  - Molecular characterization of the LlaKR2I restriction and modification system from Lactococcus lactis ssp. lactis KR2.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1997
SP  - 426
EP  - 426
VL  - 97
AB  - Lactococcus lactis ssp. lactis KR2 contains at least two plasmid-encoded restriction and
AB  - modification (R/M) systems and the genetic determinants of one of these systems, designated
AB  - LlaKR2I, have been localized on the 36 kb plasmid, pKR223, and sequenced.  The LlaKR2I R/M
AB  - genes were found to be divergently transcribed with respect to each other, with a complete
AB  - copy of the IS-like element, IS982, located in the intergenic region.  The deduced protein
AB  - sequence of the modification component displayed greatest identity with M.Sau3AI throughout
AB  - the entire length of the protein.  Both methylases contained motifs characteristic of
AB  - 5-methylcytosine methylases and shared extensive homology throughout their predicted target
AB  - recognition domains, regions responsible for the sequence specificity of these proteins.  In
AB  - pKR223, and various derivatives, M.LlaKR2I prevented Sau3AI from digesting at 5' GATC 3'
AB  - sites.  Furthermore, since the deduced protein sequence of the LlaKR2I endonuclease shared
AB  - significant homology with Sau3AI, the specificity of the LlaKR2I R/M system is believed to be
AB  - 5' GATC 3', with the cytosine residue the target base for methylation.  The small
AB  - isometric-headed phage, osk11, was only modestly restricted on lactococcal cells harboring the
AB  - LlaKR2I R/M system and despite the presence of 5' GATC 3' sites in the genome of the
AB  - prolate-headed phage oc2, no detectable restriction occurred.  The poor in vivo restriction
AB  - may have resulted from either decreased expression of the endonuclease and/or enhanced
AB  - expression of the methylase and may be due, in part, to the presence of IS982 located between
AB  - the endonuclease and methylase genes, whose putative transposase gene is co-directionally
AB  - transcribed with the methylase gene.
ER  -

TY  - JOUR
AU  - Tyndall, C.
AU  - Lehnherr, H.
AU  - Sandmeier, U.
AU  - Kulik, E.
AU  - Bickle, T.A.
TI  - The type IC hsd loci of the enterobacteria are flanked by DNA with high homology to the phage P1 genome: implications for the evolution and spread of DNA restriction systems.
JO  - Mol. Microbiol.
PY  - 1997
SP  - 729
EP  - 736
VL  - 23
AB  - EcoR124I, EcoDXXI and EcoprrI are the known members of the type IC family of DNA restriction
AB  - and modification systems.  The first three are carried on large conjugative plasmids, while
AB  - EcoprrI is chromosomally encoded.  The enzymes are coded by three genes, hsdR, hsdM and hsdS.
AB  - Analysis of the DNA sequences upstream and downstream of the type IC hsd loci shows that all
AB  - are highly homologous to each other and also to sequences present in the bacteriophage P1
AB  - genome.  The upstream sequences include functional phd and doc genes, which encode an
AB  - addiction system that stabilizes the P1 prophage state, and extend to and beyond pac, the site
AB  - at which phage DNA packaging begins.  Downstream of the hsd loci, P1 DNA sequences begin at
AB  - exactly the same place for all of the systems.  For EcoDXXI and EcoprrI the P1 homology
AB  - extends for thousands of base pairs while for EcoR124I an IS1 insertion and an associated
AB  - deletion have removed most of the P1-homologous sequences.  The significance of these results
AB  - for the evolution of DNA restriction and modification systems is discussed.
ER  -

TY  - JOUR
AU  - Tyndall, C.
AU  - Meister, J.
AU  - Bickle, T.A.
TI  - The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 266
EP  - 274
VL  - 237
AB  - The prr locus was originally described as coding a ribonuclease that is activated after phage
AB  - T4 infection to cut within the anticodon of a specific tRNA, inactivating protein synthesis
AB  - and thus blocking phage development. Wild-type T4 phage has two genes coding the enzymes
AB  - polynucleotide kinase and RNA ligase, whose only function seems to be to repair the damage
AB  - done by the anticodon nuclease. As the only apparent function of the prr ribonuclease is to
AB  - combat phage infection, it can be considered as an RNA-based restriction enzyme. In
AB  - non-infected cells, the prr enzyme is kept inactive in a complex with three other proteins
AB  - which were predicted on the basis of DNA homologies to be the subunits of a type IC DNA
AB  - restriction and modifiction system. Unlike other type IC systems so far characterized, prr is
AB  - chromosomally rather than plasmid coded. However, sequences upstream from prr also have
AB  - homology with sequences from the plasmid R124 and the prophage P1. We have now investigated
AB  - the prr system and shown that it is indeed a bona fide type IC system which we call EcoprrI,
AB  - and which is active both in vivo and in vitro. The system is fully functional even in the
AB  - absence of the anticodon nuclease and seems to be a typical type I enzyme. EcoprrI recognizes
AB  - the sequence CCA(N7)RTGC. One peculiarity is that, with low efficiency, EcoprrI will recognize
AB  - and methylate variants of its recognition sequence such as CCT(N7)ATGC, which is methylated in
AB  - one strand of the DNA only.
ER  -

TY  - JOUR
AU  - Tyson, G.W.
AU  - Chapman, J.
AU  - Hugenholtz, P.
AU  - Allen, E.E.
AU  - Ram, R.J.
AU  - Richardson, P.M.
AU  - Solovyev, V.V.
AU  - Rubin, E.M.
AU  - Rokhsar, D.S.
AU  - Banfield, J.F.
TI  - Community structure and metabolism through reconstruction of microbial genomes from the environment.
JO  - Nature
PY  - 2004
SP  - 37
EP  - 43
VL  - 428
AB  - Microbial communities are vital in the functioning of all ecosystems; however, most
AB  - microorganisms are uncultivated, and their roles in natural
AB  - systems are unclear. Here, using random shotgun sequencing of DNA from a
AB  - natural acidophilic biofilm, we report reconstruction of near-complete
AB  - genomes of Leptospirillum group II and Ferroplasma type II, and partial
AB  - recovery of three other genomes. This was possible because the biofilm was
AB  - dominated by a small number of species populations and the frequency of
AB  - genomic rearrangements and gene insertions or deletions was relatively
AB  - low. Because each sequence read came from a different individual, we could
AB  - determine that single-nucleotide polymorphisms are the predominant form of
AB  - heterogeneity at the strain level. The Leptospirillum group II genome had
AB  - remarkably few nucleotide polymorphisms, despite the existence of
AB  - low-abundance variants. The Ferroplasma type II genome seems to be a
AB  - composite from three ancestral strains that have undergone homologous
AB  - recombination to form a large population of mosaic genomes. Analysis of
AB  - the gene complement for each organism revealed the pathways for carbon and
AB  - nitrogen fixation and energy generation, and provided insights into
AB  - survival strategies in an extreme environment.
ER  -

TY  - JOUR
AU  - Tytgat, H.L.
AU  - Douillard, F.P.
AU  - Laine, P.K.
AU  - Paulin, L.
AU  - Willems, R.J.
AU  - de Vos, W.M.
TI  - Complete Genome Sequence of Enterococcus faecium Commensal Isolate E1002.
JO  - Genome Announcements
PY  - 2016
SP  - e00113
EP  - e00116
VL  - 4
AB  - The emergence of vancomycin-resistant enterococci (VRE) has been associated with  an increase
AB  - in multidrug-resistant nosocomial infections. Here, we report the
AB  - 2.614-Mb genome sequence of the Enterococcus faecium commensal isolate E1002,
AB  - which will be instrumental in further understanding the determinants of the
AB  - commensal and pathogenic lifestyle of E. faecium.
ER  -

TY  - JOUR
AU  - Uchida, K.
AU  - Pyle, A.M.
AU  - Morii, T.
AU  - Barton, J.K.
TI  - High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 10259
EP  - 10279
VL  - 17
AB  - The complex bis(phenanthrenequinone diimine)(bipyridyl)rhodium(III),
AB  - Rh(phi)2(bpy)3+, cleaves DNA efficiently in a sequence-neutral fashion upon
AB  - photoactivation so as to provide a novel, high resolution, chemical
AB  - photofootprinting reagent.  Photofootprinting of two crystallographically
AB  - characterized DNA-binding agents, distamycin, a small natural product which
AB  - binds to DNA in the minor groove, and the endonuclease EcoRI, which binds in
AB  - the major groove, gave respectively a 5-7 base pair footprint for the drug at
AB  - its A6 binding site and a 10-12 base pair footprint for the enzyme centered at
AB  - its recognition site (5'-GAATTC-3').  Both footprints agree closely with the
AB  - crystallographic results.  The photocleavage reaction can be performed using
AB  - either a high intensity lamp or, conveniently, a simple transilluminator box,
AB  - and the photoreaction is not inhibited by moderate concentrations of reagents
AB  - which are sometimes required for examining interactions of molecules with DNA.
AB  - When compared with other popular footprinting agents, the rhodium complex shows
AB  - a number of distinct advantages:  sequence-neutrality, high resolution, ability
AB  - to footrpint major as well as minor groove-binding ligands, applicability in
AB  - the presence of additives such as Mg2+ or glycerol, ease of handling, and a
AB  - sharply footprinted pattern.  Light activated footprinting reactions
AB  - furthermore offer the possibility of examining DNA-binding interactions with
AB  - time resolution and within the cell.
ER  -

TY  - JOUR
AU  - Uchimura, Y.
AU  - Wyss, M.
AU  - Brugiroux, S.
AU  - Limenitakis, J.P.
AU  - Stecher, B.
AU  - McCoy, K.D.
AU  - Macpherson, A.J.
TI  - Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2.
JO  - Genome Announcements
PY  - 2016
SP  - e00951
EP  - e00916
VL  - 4
AB  - We report here the complete genome sequences of 12 bacterial species of stable defined
AB  - moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize
AB  - germ-free mice with defined microbes. Whole-genome sequencing of these species
AB  - was performed using the PacBio sequencing platform yielding circularized genome
AB  - sequences of all 12 species.
ER  -

TY  - JOUR
AU  - Uchino, Y.
AU  - Miura, T.
AU  - Hosoyama, A.
AU  - Ohji, S.
AU  - Yamazoe, A.
AU  - Ito, M.
AU  - Takahata, Y.
AU  - Suzuki, K.
AU  - Fujita, N.
TI  - Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 102
EP  - 102
VL  - 10
AB  - A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with
AB  - chlorinated ethenes in Japan. This strain is capable of
AB  - dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to
AB  - ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has
AB  - presented a challenge. In this study, we developed a differential reads picking
AB  - method for mixed genomic DNA obtained from a co-culture, and applied it to the
AB  - sequencing of strain UCH007. The genome of strain UCH007 consists of a
AB  - 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative
AB  - reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria
AB  - subgroup found to possess the pceA, tceA and vcrA genes.
ER  -

TY  - JOUR
AU  - Uebe, R.
AU  - Schuler, D.
AU  - Jogler, C.
AU  - Wiegand, S.
TI  - Reevaluation of the Complete Genome Sequence of Magnetospirillum gryphiswaldense  MSR-1 with Single-Molecule Real-Time Sequencing Data.
JO  - Genome Announcements
PY  - 2018
SP  - e00309
EP  - e00318
VL  - 6
AB  - Magnetospirillum gryphiswaldense is a key organism for understanding magnetosome  formation
AB  - and magnetotaxis. As earlier studies suggested a high genomic
AB  - plasticity, we (re)sequenced the type strain MSR-1 and the laboratory strain
AB  - R3/S1. Both sequences differ by only 11 point mutations, but organization of the
AB  - magnetosome island deviates from that of previous genome sequences.
ER  -

TY  - JOUR
AU  - Ueda, K.
AU  - Yamashita, A.
AU  - Ishikawa, J.
AU  - Shimada, M.
AU  - Watsuji, T.-o.
AU  - Morimura, K.
AU  - Ikeda, H.
AU  - Hattori, M.
AU  - Beppu, T.
TI  - Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalisms.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 4937
EP  - 4944
VL  - 32
AB  - Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends
AB  - on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium
AB  - belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57
AB  - Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences,
AB  - out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the
AB  - genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive
AB  - bacteria. This provides evidence for the presence of an undefined category in the
AB  - Gram-positive bacterial group. The presence of both spo and related genes and microscopic
AB  - observation indicate that S.thermophilum is the first high G + C organism that forms
AB  - endospores. The S.thermophilum genome is also characterized by the widespread insertion of
AB  - class C group II introns, which are oriented in the same direction as chromosomal replication.
AB  - The genome has many membrane transporters, a number of which are involved in the uptake of
AB  - peptides and amino acids. The genes involved in primary metabolism are largely identified,
AB  - except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also
AB  - has a variety of respiratory systems including Nap nitrate reductase, which has been found
AB  - only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is
AB  - adaptable to and thus lives in various environments, such that its growth requirement could be
AB  - a substance or a physiological condition that is generally available in the natural
AB  - environment rather than a highly specific substance that is present only in a limited niche.
AB  - The genomic information from S.thermophilum offers new insights into microbial diversity and
AB  - evolutionary sciences, and provides a framework for characterizing the molecular basis
AB  - underlying microbial commensalism.
ER  -

TY  - JOUR
AU  - Ueno, H.
AU  - Kato, I.
AU  - Ishino, Y.
TI  - Cloning and expression of the BalI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2268
EP  - 2270
VL  - 24
AB  - BalI, a type II restriction-modification (R-M) system from the bacterium,
AB  - Brevibacterium albidum, recognizes the DNA sequence 5'-TGGCCA-3'.  We cloned the genes
AB  - encoding the BalI restriction endonuclease and methyltransferase and expressed them in
AB  - Escherichia coli.  The two genes were aligned tail-to-tail and their termination codons
AB  - overlapped.
AB  - BalI restriction endonuclease and methyltransferase comprise 260 and 280 amino acids,
AB  - respectively, and have molecular weights of 29,043 and 31,999 Da.  The amino acid sequence of
AB  - BalI methyltransferase is similar to that of other m6A Mtases, although it has been
AB  - categorized as
AB  - an m5C methyltransferase.  A high expression system for the BalI restriction endonuclease was
AB  - constructed in E.coli for the production of large quantities of enzyme.
ER  -

TY  - JOUR
AU  - Ueno, H.
AU  - Kita, A.
AU  - Miyahara, M.
AU  - Ishiwata, N.
AU  - Mise, K.
AU  - Kato, I.
AU  - Ishino, Y.
TI  - Production of new restriction endonuclease VpaK11BI recognizing sequence 5'-GGWCC-3' in a Haemolysin-less mutant of Vibrio parahaemolyticus.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1997
SP  - 2129
EP  - 2130
VL  - 61
AB  - High restriction endonuclease activity was found in a haemolysinless mutant of the Vibrio
AB  - parahaemolyticus 1743-1 strain.  The endonuclease, named VpaK11BI, recognized the palindromic
AB  - pentanucleotide sequence of 5'-GGWCC-3' and cleaved double-stranded DNA after the first G,
AB  - which is exactly the same as the specificity of AvaII.  The haemolysin-less mutant of V.
AB  - parahaemolyticus is now available for producing the valuable restriction endonuclease on a
AB  - commercial scale.
ER  -

TY  - JOUR
AU  - Ueno, T.
AU  - Ito, H.
AU  - Kimizuka, F.
AU  - Kotani, H.
AU  - Nakajima, K.
TI  - Gene structure and expression of the MboI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2309
EP  - 2313
VL  - 21
AB  - The genes from Moraxella bovis encoding the MboI restriction-modification system were cloned
AB  - and expressed in Escherichia coli. Three open reading frames were found in the sequence
AB  - containing the genes. These genes, which we named mboA, mboB, and mboC, had the same
AB  - orientation in the genome. Genes mboA and mboC encoded MboI methyltransferases (named M.MboA
AB  - and M.MboC) with 294 and 273 amino acid residues, respectively. The mboB gene coded for MboI
AB  - restriction endonuclease (R.MboI) with 280 amino acid residues. Recombinant E. coli-MBOI,
AB  - which contained the whole MboI system, overproduced R.MboI. R.MboI activity from E.coli-MBOI
AB  - was 480-fold that of M.bovis. The amino acid sequences deduced from these genes were compared
AB  - with those of other restriction-modification systems. The protein sequences of the MboI system
AB  - had 38-49% homology with those of the DpnII system.
ER  -

TY  - JOUR
AU  - Ueno, T.
AU  - Ito, H.
AU  - Kotani, H.
AU  - Kimizuka, F.
AU  - Nakajima, K.
TI  - Cloning and expression of the NspV restriction modification genes of Nostoc sp. strain PCC7524.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 3899
EP  - 3899
VL  - 21
AB  - The NspV restriction-modification system of the filamentous cyanobacterium Nostoc sp. strain
AB  - PCC7524 consists of NspV restriction endonuclease (R.NspV) and NspV modification enzyme
AB  - (M.NspV). R.NspV recognizes and cleaves double-stranded DNA at the sequence 5'-TTCGAA-3',
AB  - and M.NspV recognizes and protects this sequence by methylation against R.NspV. We cloned the
AB  - genes in Escherichia coli and analyzed their structure.
ER  -

TY  - JOUR
AU  - Ueno, T.
AU  - Ito, I.
AU  - Kotani, H.
AU  - Nakajima, K.
TI  - Nsp7524V restriction-modification genes.
JO  - Biotech. Advances
PY  - 1996
SP  - 465
EP  - 465
VL  - 14
AB  - To provide Nsp7524V restriction-modification genes and a method for producing Nsp7524V
AB  - restriction enzyme and Nsp7524V modification enzyme by using a novel microorganism having,
AB  - introduced thereinto, plasmids containing said genes, Nsp7524V restriction-modification genes.
AB  - A method for producing Nsp7524V restriction enzyme and/or Nsp7524V modification enzyme which
AB  - comprises incubating a microorganism carrying a plasmid having, integrated thereinto, Nsp7524V
AB  - restriction-modification genes, and recovering the Nsp7524V restriction enzyme and/or Nsp7524V
AB  - modification enzyme thus produced from the culture.  It becomes possible to efficiently
AB  - produce Nsp7524V restriction enzyme and/or Nsp7524V modification enzyme which are useful in
AB  - the field of genetic engineering.
ER  -

TY  - JOUR
AU  - Uetake, H.
AU  - Toyama, S.
AU  - Hagiwara, S.
TI  - On the mechanism of host-induced modification:  Multiplicity activation and thermolabile factor responsible for phage growth restriction.
JO  - Virology
PY  - 1964
SP  - 202
EP  - 213
VL  - 22
AB  - Salmonella phage sigma15 grown undergoes host-induced modification (HIM).
AB  - Phage sigma15[A] (phage sigma15 grown on Salmonella anatum, called strain A)
AB  - plates with low EOP on Salmonella butantan (=I-1) and vice versa.  The
AB  - restricting properties of the host cells on phage growth can be overcome by
AB  - multiple infection (multiplicity activation) with restricted normal phage or
AB  - with its temperature-sensitive mutant, but not with ultraviolet
AB  - (UV)-inactivated phage.  The phage-growth restricting factor is inactivated by
AB  - a short exposure of cells to slight heat, and its synthesis is inhibited by
AB  - chloramphenicol, but not by mitomycin C.  Experiments with P32-labeled phages
AB  - shown that the DNA of the restricted phage is degraded rapidly after injection
AB  - of the nonpermissive host, and that the degradation of injected DNA is
AB  - prevented by heating the host cells prior to infection or by UV irradiation of
AB  - the restricted phage.
ER  -

TY  - JOUR
AU  - Ugalde, J.A.
AU  - Narasingarao, P.
AU  - Kuo, S.
AU  - Podell, S.
AU  - Allen, E.E.
TI  - Draft Genome Sequence of 'Candidatus Halobonum tyrrellensis' Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.
JO  - Genome Announcements
PY  - 2013
SP  - e01001
EP  - e01013
VL  - 1
AB  - We report the draft 3.675-Mbp genome sequence of 'Candidatus Halobonum tyrrellensis' strain
AB  - G22, a novel halophilic archaeon isolated from the surface
AB  - hypersaline waters of Lake Tyrrell, Australia. The availability of the first
AB  - genome from the 'Candidatus Halobonum' genus provides a new genomic resource for
AB  - the comparative genomic analysis of halophilic Archaea.
ER  -

TY  - JOUR
AU  - Uhlemann, A.C.
AU  - Porcella, S.F.
AU  - Trivedi, S.
AU  - Sullivan, S.B.
AU  - Hafer, C.
AU  - Kennedy, A.D.
AU  - Barbian, K.D.
AU  - McCarthy, A.J.
AU  - Street, C.
AU  - Hirschberg, D.L.
AU  - Lipkin, W.I.
AU  - Lindsay, J.A.
AU  - DeLeo, F.R.
AU  - Lowy, F.D.
TI  - Identification of a highly transmissible animal-independent Staphylococcus aureus ST398 clone with distinct genomic and cell adhesion properties.
JO  - MBio
PY  - 2012
SP  - e00027
EP  - e00012
VL  - 3
AB  - A methicillin-resistant Staphylococcus aureus (MRSA) clone known as ST398 has
AB  - emerged as a major cause of acute infections in individuals who have close
AB  - contact with livestock. More recently, the emergence of an animal-independent
AB  - ST398 methicillin-sensitive S. aureus (MSSA) clone has been documented in several
AB  - countries. However, the limited surveillance of MSSA has precluded an accurate
AB  - assessment of the global spread of ST398 and its clinical relevance. Here we
AB  - provide evidence that ST398 is a frequent source of MSSA infections in northern
AB  - Manhattan and is readily transmitted between individuals in households. This
AB  - contrasts with the limited transmissibility of livestock-associated ST398
AB  - (LA-ST398) MRSA strains between humans. Our whole-genome sequence analysis
AB  - revealed that the chromosome of the human-associated ST398 MSSA clone is smaller
AB  - than that of the LA-ST398 MRSA reference strain S0385, due mainly to fewer mobile
AB  - genetic elements (MGEs). In contrast, human ST398 MSSA isolates harbored the
AB  - prophage varphi3 and the human-specific immune evasion cluster (IEC) genes chp
AB  - and scn. While most of the core genome was conserved between the human ST398 MSSA
AB  - clone and S0385, these strains differed substantially in their repertoire and
AB  - composition of intact adhesion genes. These genetic changes were associated with
AB  - significantly enhanced adhesion of human ST398 MSSA isolates to human skin
AB  - keratinocytes and keratin. We propose that the human ST398 MSSA clone can spread
AB  - independent of animal contact using an optimized repertoire of MGEs and adhesion
AB  - molecules adapted to transmission among humans. IMPORTANCE: Staphylococcus aureus
AB  - strains have generally been considered to be species specific. However,
AB  - cross-species transfers of S. aureus clones, such as ST398 methicillin-resistant
AB  - S. aureus (MRSA), from swine to humans have been reported. Recently, we observed
AB  - the emergence of ST398 methicillin-susceptible S. aureus (MSSA) as a colonizing
AB  - strain of humans in northern Manhattan. Here we report that ST398 is a frequent
AB  - cause of MSSA infections in this urban setting. The ST398 MSSA clone was readily
AB  - transmitted within households, independent of animal contact. We discovered that
AB  - human ST398 MSSA genomes were smaller than that of the LA-ST398 strain S0385 due
AB  - to fewer mobile genetic elements. Human and LA-ST398 strains also differed in
AB  - their composition of adhesion genes and their ability to bind to human skin
AB  - keratinocytes, providing a potential mechanism of S. aureus host adaptation. Our
AB  - findings illustrate the importance of implementing molecular surveillance of MSSA
AB  - given the evidence for the rapid and clinically undetected spread of ST398 MSSA.
ER  -

TY  - JOUR
AU  - Uhlich, G.A.
AU  - Paoli, G.C.
AU  - Chen, C.Y.
AU  - Cottrell, B.J.
AU  - Zhang, X.
AU  - Yan, X.
TI  - Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain EDL932 (ATCC 43894).
JO  - Genome Announcements
PY  - 2016
SP  - e00647
EP  - e00616
VL  - 4
AB  - The genome sequence of Escherichia coli serotype O157:H7 EDL933, a ground beef isolate from a
AB  - 1983 hemorrhagic colitis outbreak, is a standard reference for
AB  - comparative genomic studies of Shiga toxin-producing E. coli strains. Here, we
AB  - report the genome sequence of a patient stool isolate from that outbreak, strain
AB  - EDL932.
ER  -

TY  - JOUR
AU  - Uhlich, G.A.
AU  - Paoli, G.C.
AU  - Zhang, X.
AU  - Dudley, E.G.
AU  - Figler, H.M.
AU  - Cottrell, B.J.
AU  - Andreozzi, E.
TI  - Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain PA20.
JO  - Genome Announcements
PY  - 2017
SP  - e01460
EP  - e01416
VL  - 5
AB  - Escherichia coli serotype O157:H7 strain PA20 is a Pennsylvania Department of Health clinical
AB  - isolate. It has been used to study biofilm formation in O157:H7
AB  - clinical isolates, where the high incidence of prophage insertions in the mlrA
AB  - transcription factor disrupts traditional csgD biofilm regulation. Here, we
AB  - report the complete PA20 genome sequence.
ER  -

TY  - JOUR
AU  - Uhlich, G.A.
AU  - Reichenberger, E.R.
AU  - Cottrell, B.J.
AU  - Fratamico, P.
AU  - Andreozzi, E.
TI  - Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain B6914-ARS.
JO  - Genome Announcements
PY  - 2017
SP  - e01191
EP  - e01117
VL  - 5
AB  - Escherichia coli serotype O157:H7 strain B6914-MS1 is an isolate from the Centers for Disease
AB  - Control and Prevention that is missing both Shiga toxin genes and has
AB  - been used extensively in applied research studies. Here we report the genome
AB  - sequence of strain B6914-ARS, a B6914-MS1 clone that has unique biofilm
AB  - properties.
ER  -

TY  - JOUR
AU  - Uhlig, R.
AU  - Poehlein, A.
AU  - Fischer, R.J.
AU  - Daniel, R.
AU  - Bahl, H.
TI  - Genome Sequence of the Autotrophic Acetogen Clostridium magnum DSM 2767.
JO  - Genome Announcements
PY  - 2016
SP  - e00464
EP  - e00416
VL  - 4
AB  - Here we report the draft genome sequence (6.6 Mbp) of the type strain Clostridium magnum, an
AB  - acetogen with two operons coding for two separate Rnf complexes. C.
AB  - magnum grows on a broad range of organic substrates and converts CO2 and H2 to
AB  - acetate using the Wood-Ljungdahl pathway.
ER  -

TY  - JOUR
AU  - Ukanis, M.
AU  - Sapranauskas, R.
AU  - Lubys, A.
TI  - Screening for catalytically active Type II restriction endonucleases using segregation-induced methylation deficiency.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - e149
EP  - e149
VL  - 40
AB  - Type II restriction endonucleases (REases) are one of the basic tools of recombinant DNA
AB  - technology. They also serve as models for elucidation of
AB  - mechanisms for both site-specific DNA recognition and cleavage by proteins.
AB  - However, isolation of catalytically active mutants from their libraries is
AB  - challenging due to the toxicity of REases in the absence of protecting
AB  - methylation, and techniques explored so far had limited success. Here, we present
AB  - an improved SOS induction-based approach for in vivo screening of active REases,
AB  - which we used to isolate a set of active variants of the catalytic mutant,
AB  - Cfr10I(E204Q). Detailed characterization of plasmids from 64 colonies screened
AB  - from the library of approximately 200 000 transformants revealed 29 variants of
AB  - cfr10IR gene at the level of nucleotide sequence and 15 variants at the level of
AB  - amino acid sequence, all of which were able to induce SOS response. Specific
AB  - activity measurements of affinity-purified mutants revealed >200-fold variance
AB  - among them, ranging from 100% (wild-type isolates) to 0.5% (S188C mutant),
AB  - suggesting that the technique is equally suited for screening of mutants
AB  - possessing high or low activity and confirming that it may be applied for
AB  - identification of residues playing a role in catalysis.
ER  -

TY  - JOUR
AU  - Ulge, U.Y.
AU  - Baker, D.A.
AU  - Monnat, R.J. Jr.
TI  - Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 4330
EP  - 4339
VL  - 39
AB  - Homing endonucleases (HEs) cleave long ( approximately 20 bp) DNA target sites with high site
AB  - specificity to catalyze the lateral transfer of
AB  - parasitic DNA elements. In order to determine whether comprehensive
AB  - computational design could be used as a general strategy to engineer new
AB  - HE target site specificities, we used RosettaDesign (RD) to generate 3200
AB  - different variants of the mCreI LAGLIDADG HE towards 16 different base
AB  - pair positions in the 22 bp mCreI target site. Experimental verification
AB  - of a range of these designs demonstrated that over 2/3 (24 of 35 designs,
AB  - 69%) had the intended new site specificity, and that 14 of the 15
AB  - attempted specificity shifts (93%) were achieved. These results
AB  - demonstrate the feasibility of using structure-based computational design
AB  - to engineer HE variants with novel target site specificities to facilitate
AB  - genome engineering.
ER  -

TY  - JOUR
AU  - Ullrich, S.R.
AU  - Poehlein, A.
AU  - Voget, S.
AU  - Hoppert, M.
AU  - Daniel, R.
AU  - Leimbach, A.
AU  - Tischler, J.S.
AU  - Schlomann, M.
AU  - Muhling, M.
TI  - Permanent draft genome sequence of Acidiphilium sp. JA12-A1.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 56
EP  - 56
VL  - 10
AB  - The tenacious association between strains of the heterotrophic alphaproteobacterial genus
AB  - Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this
AB  - context the genome of the heterotroph Acidiphilium sp. JA12-A1, an isolate from an iron
AB  - oxidizing mixed culture derived from a pilot plant for bioremediation of acid mine drainage,
AB  - was determined with  the aim to reveal metabolic properties that are fundamental for the
AB  - syntrophic interaction between Acidiphilium sp. JA12-A1 and the co-occurring
AB  - chemolithoautotrophic iron oxidizer. The genome sequence consists of 4.18 Mbp on  297 contigs
AB  - and harbors 4015 protein-coding genes and 50 RNA genes. Additionally, the molecular and
AB  - functional organization of the Acidiphilium sp. JA12-A1 draft genome was compared to those of
AB  - the close relatives Acidiphilium cryptum JF-5, Acidiphilium multivorum AIU301 and Acidiphilium
AB  - sp. PM DSM 24941. The comparative genome analysis underlines the close relationship between
AB  - these strains and the highly similar metabolic potential supports the idea that other
AB  - Acidiphilium strains play a similar role in various acid mine drainage communities.
AB  - Nevertheless, in contrast to other closely related strains Acidiphilium sp. JA12-A1 may be
AB  - able to take up phosphonates as an additional source of phosphor.
ER  -

TY  - JOUR
AU  - Ulyanova, V.
AU  - Shah, M.R.
AU  - Dudkina, E.
AU  - Vershinina, V.
AU  - Ilinskaya, O.
TI  - Draft Whole Genome Sequence of Bacillus pumilus Strain 3-19, a Chemical Mutant Overproducing Extracellular Ribonuclease.
JO  - Genome Announcements
PY  - 2014
SP  - e00724
EP  - e00714
VL  - 2
AB  - Here, we present a draft genome sequence of Bacillus pumilus strain 3-19. It was  derived from
AB  - soil-isolated B. pumilus 7P using chemical mutagenesis and is
AB  - characterized by elevated production of extracellular ribonuclease which is known
AB  - to possess different biological activities with potential of applications in
AB  - experimental research, medicine, and biotechnology.
ER  -

TY  - JOUR
AU  - Um, J.
AU  - Park, C.
AU  - Lee, K.
TI  - Alteration of specificity of restriction endonuclease EcoRI in organic solvent.
JO  - Korean Biochem. J.
PY  - 1994
SP  - 401
EP  - 407
VL  - 27
AB  - In molecular biology, type-II restriction endonucleases, which specifically cleave DNA at a
AB  - limited number of sites, have been exploited as a means of characterizing DNA fragments, DNA
AB  - mapping and of modifying DNA for genetic engineering. Recently, many type-II restriction
AB  - endonucleases have been found to decrease their substrate specificity under modified
AB  - conditions such as extreme pH, low ionic strength, high enzyme concentration, substitution of
AB  - metallic cofactors, or addition of organic solvents. This study used restriction endonuclease
AB  - EcoRI which is used most frequently in genetic engineering. We investigated their specificity
AB  - change in buffer conditions including various organic solvents. The specificity of cleavage of
AB  - EcoRI is altered in the presence of hydrophobic reagents, such as ethanol, ethyleneglycol and
AB  - DMSO. The enzyme recognition site was not changed randomly but by preferential order by
AB  - increasing the concentration of organic solvent. When EcoRI reacted with substrate pGEM3
AB  - vector which has one canonical recognition site (GAATTC), EcoRI cleaved the noncanonical
AB  - TAATTC and GAGTTC subsequently in more than 10% DMSO solution. These changes of specificities
AB  - depended on the hydrophobicity of organic solvent (LogP: partition coefficient). As a result,
AB  - the recognition sequence site was changed in the presence of organic solvents whose LogP are
AB  - -2.0 to 0. The specificities were not easily changed in enzyme inactivating organic solvent
AB  - such as acetone, 2-methyl-2-propanol, 2-methyl-1-propanol. These results show that restriction
AB  - enzyme could be used to cleave at unusual site by changing the reaction conditions.
ER  -

TY  - JOUR
AU  - Umezawa, K.
AU  - Watanabe, T.
AU  - Miura, A.
AU  - Kojima, H.
AU  - Fukui, M.
TI  - The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T).
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 71
EP  - 71
VL  - 11
AB  - Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria
AB  - belonging to the family Acidiferrobacteraceae in the
AB  - order Acidiferrobacterales. The type strains of these species, strain skN76(T)
AB  - and strain HA5(T), were isolated from lakes in Japan. Here we describe the
AB  - complete genome sequences of Sulfurifustis variabilis skN76(T) and Sulfuricaulis
AB  - limicola HA5(T). The genome of Sulfurifustis variabilis skN76(T) consists of one
AB  - circular chromosome with size of 4.0 Mbp including 3864 protein-coding sequences.
AB  - The genome of Sulfuricaulis limicola HA5(T) is 2.9 Mbp chromosome with 2763
AB  - protein-coding sequences. In both genomes, 46 transfer RNA-coding genes and one
AB  - ribosomal RNA operon were identified. In the genomes, redundancies of the genes
AB  - involved in sulfur oxidation and inorganic carbon fixation pathways were
AB  - observed. This is the first report to show the complete genome sequences of
AB  - bacteria belonging to the order Acidiferrobacterales in the class
AB  - Gammaproteobacteria.
ER  -

TY  - JOUR
AU  - Undabarrena, A.
AU  - Beltrametti, F.
AU  - Claverias, F.P.
AU  - Gonzalez, M.
AU  - Moore, E.R.
AU  - Seeger, M.
AU  - Camara, B.
TI  - Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile.
JO  - Front. Microbiol.
PY  - 2016
SP  - 1135
EP  - 1135
VL  - 7
AB  - Bioprospecting natural products in marine bacteria from fjord environments are
AB  - attractive due to their unique geographical features. Although, Actinobacteria
AB  - are well known for producing a myriad of bioactive compounds, investigations
AB  - regarding fjord-derived marine Actinobacteria are scarce. In this study, the
AB  - diversity and biotechnological potential of Actinobacteria isolated from marine
AB  - sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by
AB  - culture-based approaches. The 16S rRNA gene sequences revealed that members
AB  - phylogenetically related to the Micrococcaceae, Dermabacteraceae,
AB  - Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae,
AB  - Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A
AB  - high diversity of cultivable Actinobacteria (10 genera) was retrieved by using
AB  - only five different isolation media. Four isolates belonging to Arthrobacter,
AB  - Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity
AB  - <98.7% suggesting that they are novel species. Physiological features such as
AB  - salt tolerance, artificial sea water requirement, growth temperature,
AB  - pigmentation and antimicrobial activity were evaluated. Arthrobacter,
AB  - Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed
AB  - strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia
AB  - coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria
AB  - monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and
AB  - Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are
AB  - a suitable source of bioactive compounds. In addition, all strains bear at least
AB  - one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II
AB  - (73%). Our results indicate that the Comau fjord is a promising source of novel
AB  - Actinobacteria with biotechnological potential for producing biologically active
AB  - compounds.
ER  -

TY  - JOUR
AU  - Undabarrena, A.
AU  - Ugalde, J.A.
AU  - Castro-Nallar, E.
AU  - Seeger, M.
AU  - Camara, B.
TI  - Genome Sequence of Streptomyces sp. H-KF8, a Marine Actinobacterium Isolated from a Northern Chilean Patagonian Fjord.
JO  - Genome Announcements
PY  - 2017
SP  - e01645
EP  - e01616
VL  - 5
AB  - Streptomyces sp. H-KF8 is a fjord-derived marine actinobacterium capable of producing
AB  - antimicrobial activity. Streptomyces sp. H-KF8 was isolated from
AB  - sediments of the Comau fjord, located in the northern Chilean Patagonia. Here, we
AB  - report the 7.7-Mb genome assembly, which represents the first genome of a Chilean
AB  - marine actinobacterium.
ER  -

TY  - JOUR
AU  - Underhill, P.A.
AU  - Johnson, P.H.
TI  - Site-specific mutagenesis of the EcoRI restriction endonuclease: substitution of cysteine-217 with glycine affects in vivo but not in vitro enzyme function.
JO  - Fed. Proc.
PY  - 1986
SP  - 1875
EP  - 1875
VL  - 45
AB  - Using oligonucleotide-directed mutagenesis, we have introduced a T - G
AB  - transversion mutation in the cloned EcoRI restriction endonuclease gene,
AB  - thereby substituting a glycine for the single cysteine-217.  Mutant clones were
AB  - identified by differential colony hybridization using the mutagenesis
AB  - oligonucleotide.  The structure of the mutant was confirmed by DNA sequence
AB  - analysis.  Cells producing the mutant endonuclease showed a four-log increase
AB  - in sensitivity to infection by bacteriophage lambda.  The mutant enzyme was
AB  - partially purified and characterized.  It did not show any changes in
AB  - recognition site-specificity or in kinetic behavior compared with that of the
AB  - wild-type enzyme either in standard assay buffer or under altered solvent
AB  - conditions that promoted its ability to cleave subcanonical sequences.  The
AB  - mutant and wild-type enzymes behaved identically during analytical gel
AB  - chromatography.  Reaction of the wild-type endonuclease with the sulfhydryl
AB  - inhibitor parahydroxymercuribenzoate resulted in a complete loss of enzyme
AB  - activity compared with less than tenfold inhibition for the mutant enzyme.We
AB  - conclude that cysteine-217 may play an important role in the in vivo function
AB  - of the EcoRI endonuclease but not in its in vitro enzymatic activity.
ER  -

TY  - JOUR
AU  - Unverferth, C.A.
AU  - Santisteban, I.C.
AU  - Setterdahl, A.T.
TI  - Draft Genome Sequence of the Novel Black-Pigmented Planococcus sp. Strain CAU13.
JO  - Genome Announcements
PY  - 2014
SP  - e01160
EP  - e01114
VL  - 2
AB  - Presented here is the whole-genome sequence of a previously uncharacterized species of the
AB  - genus Planococcus. A 16S sequence analysis shows that this
AB  - bacterium exhibits 98% sequence identity to the closest relative of Planococcus
AB  - kocurii. Whereas most species of Planococcus produce yellow to orange pigments,
AB  - the species described here produces black pigmentation.
ER  -

TY  - JOUR
AU  - Unzaga, T.V.
AU  - Diaz-Ricci, J.C.
AU  - Rhee, J.I.
AU  - Hernandez, M.R.
AU  - Schugerl, K.
TI  - Modeling of the controlled expression of a harmful protein by a three-plasmid harboring system.
JO  - Biotechnol. Bioeng.
PY  - 2002
SP  - 544
EP  - 551
VL  - 80
AB  - A genetically structured mathematical model was developed and used to evaluate the influence
AB  - of molecular parameters involved in the expression
AB  - of a harmful recombinant protein (SPA::EcoRI). The system consists of the
AB  - controlled expression of the endonuclease EcoRI cloned in the plasmid
AB  - pMTC48. The control is exerted by the lambda Cl repressor expressed from
AB  - the plasmid pRK248clts. The deleterious effect of the activity of the
AB  - enzyme EcoRl on the host DNA is prevented by the action of the EcoRl
AB  - methylase that is expressed constitutively from a third plasmid, pEcoR4.
AB  - The model includes molecular mechanisms involved in the regulation of the
AB  - expression of these genes and is used to determine cultural conditions
AB  - that maximize the production of the recombinant protein.
ER  -

TY  - JOUR
AU  - Uozumi, T.
AU  - Hoshino, T.
AU  - Miwa, K.
AU  - Horinouchi, S.
AU  - Beppu, T.
AU  - Arima, K.
TI  - Restriction and modification in Bacillus species.
JO  - Mol. Gen. Genet.
PY  - 1977
SP  - 65
EP  - 69
VL  - 152
AB  - Host specific restriction was detected in 13 Bacillus strains, when 63 strains of Bacillus
AB  - subtilis and 15 other Bacillus strains were tested with phage phi 105C. These 13 strains were
AB  - classified into 8 groups (M,H,C,N,E,F,G,P) by the type of restriction. M-type strains (B.
AB  - subtilis Marburg 168, its derivatives, and two other strains) showed relatively weak
AB  - restriction, restricting phi 105C from other groups of Bacillus by ratios of 10(-1) to 10(-3).
AB  - Strains of groups H,C,N,E,F,G, and P restricted phi 105C from other groups by ratios of 10(-2)
AB  - to 10(-8). It was confirmed with some of the strains that type-specific modification was
AB  - endowed only by the last host. Furthermore, we isolated one restriction deficient mutant of B.
AB  - subtilis Marburg 168-YS11, which had also lost its modification phenotype.
ER  -

TY  - JOUR
AU  - Upadrasta, A.
AU  - Pitta, S.
AU  - Madempudi, R.S.
TI  - Draft Genome Sequence of Bacillus clausii UBBC07, a Spore-Forming Probiotic Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e00235
EP  - e00216
VL  - 4
AB  - ITALIC! Bacillus clausiiUBBC07 is a safe endospore-forming strain, characterized  for defined
AB  - therapeutic effects. The finished draft whole-genome sequence is
AB  - presented here to scan its genetic constitution for its expanded use as a
AB  - probiotic in various health sectors.
ER  -

TY  - JOUR
AU  - Upadrasta, A.
AU  - Pitta, S.
AU  - Madempudi, R.S.
TI  - Draft Genome Sequence of the Spore-Forming Probiotic Strain Bacillus coagulans Unique IS-2.
JO  - Genome Announcements
PY  - 2016
SP  - e00225
EP  - e00216
VL  - 4
AB  - ITALIC! Bacillus coagulansUnique IS-2 is a potential spore-forming probiotic that is
AB  - commercially available on the market. The draft genome sequence presented here
AB  - provides deep insight into the beneficial features of this strain for its safe
AB  - use as a probiotic for various human and animal health applications.
ER  -

TY  - JOUR
AU  - Uporova, T.M.
AU  - Kartasheva, I.M.
AU  - Skripkin, E.A.
AU  - Lopareva, E.N.
AU  - Nikolskaya, I.I.
AU  - Debov, S.S.
TI  - Restricting endonucleases from Shigella sonnei 47.
JO  - Vopr. Med. Khim.
PY  - 1985
SP  - 131
EP  - 136
VL  - 31
AB  - Two restrictases SsoI and SsoII, belonging to the enzymes of restriction of the class II, were
AB  - isolated from a strain of dysenteric bacteria.  The structure of the site sensitive to SsoI
AB  - and SsoII was studied after fragmentation of testor DNA as well as by means of direct
AB  - determination of nucleotide sequency.  SsoI was shown to be an isoschizomer of the EcoRI
AB  - restrictase from E. coli. Restrictase SsoII proved to a new enzyme, which hydrolyzed the
AB  - sequence 5'...CCNGG..3' and was distinct from the known restrictases as shown by studies of
AB  - the type of DNA hydrolyzed.  A three-step procedure is developed for isolation of SsoII
AB  - restrictase involving the consecutive chromatography on blue sepharose, phosphocellulose P11
AB  - and phenyl-sepharose.  Restrictases SsoI and EcoRI were isolated by means of
AB  - isoelectrofocusing using ampholines.
ER  -

TY  - JOUR
AU  - Uporova, T.M.
AU  - Nikolskaya, I.I.
AU  - Rubtsova, E.N.
AU  - Debov, S.S.
TI  - Purification and identification of Eco CK restrictional endonuclease.
JO  - Vestn. Akad. Med. Nauk SSSR
PY  - 1981
SP  - 21
EP  - 26
VL  - 2
AB  - A fundamentally new scheme for purifying the restrictional endonuclease from E.
AB  - coli CK cells has been developed, involving 3 consecutive stages:  gel
AB  - filtration (on biogel A-0.5 m), chromatography on single-stranded
AB  - DNA-cellulose, and fractionation on heparin-sepharose.  The proposed variant of
AB  - REco CK purification results in an enzyme preparation completely free from
AB  - nonspecific endonucleases and exonucleases which can be used in genetic
AB  - engineering and physical mapping work.  The fragmentation pattern of phage
AB  - lambda DNA has been defined more precisely:  as a result of complete
AB  - hydrolysis, 4 fragments with molecular masses of 13.25, 12.0, 5.15, and 0.7
AB  - megadaltons are formed.  It is shown that in as far as the fragmentation
AB  - pattern of the test phage lambda DNA is concerned, the REco CK enzyme has no
AB  - analogues among the enzymes described so far in the literature.
ER  -

TY  - JOUR
AU  - Urakawa, H.
AU  - Garcia, J.C.
AU  - Nielsen, J.L.
AU  - Le, V.Q.
AU  - Kozlowski, J.A.
AU  - Stein, L.Y.
AU  - Lim, C.K.
AU  - Pommerening-Roser, A.
AU  - Martens-Habbena, W.
AU  - Stahl, D.A.
AU  - Klotz, M.G.
TI  - Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2015
SP  - 242
EP  - 250
VL  - 65
AB  - A Gram-negative, spiral-shaped, chemolithotrophic, ammonia-oxidizing bacterium,
AB  - designated APG3(T), was isolated into pure culture from sandy lake sediment
AB  - collected from Green Lake, Seattle, WA, USA. Phylogenetic analyses based on the
AB  - 16S rRNA gene sequence showed that strain APG3(T) belongs to cluster 0 of the
AB  - genus Nitrosospira, which is presently not represented by described species, with
AB  - Nitrosospira multiformis (cluster 3) as the closest species with a validly
AB  - published name (identity of 98.6 % to the type strain). Strain APG3(T) grew at 4
AB  - degrees C but could not grow at 35 degrees C, indicating that this bacterium is
AB  - psychrotolerant. Remarkably, the strain was able to grow over a wide range of pH
AB  - (pH 5-9), which was greater than the pH range of any studied ammonia-oxidizing
AB  - bacteria in pure culture. The DNA G+C content of the APG3(T) genome is 53.5 %,
AB  - which is similar to that of Nitrosospira multiformis ATCC 25196(T) (53.9 %) but
AB  - higher than that of Nitrosomonas europaea ATCC 19718 (50.7 %) and Nitrosomonas
AB  - eutropha C71 (48.5 %). The average nucleotide identity (ANI) calculated for the
AB  - genomes of strain APG3(T) and Nitrosospira multiformis ATCC 25196(T) was 75.45 %,
AB  - significantly lower than the value of 95 % ANI that corresponds to the 70 %
AB  - species-level cut-off based on DNA-DNA hybridization. Overall polyphasic taxonomy
AB  - study indicated that strain APG3(T) represents a novel species in the genus
AB  - Nitrosospira, for which the name Nitrosospira lacus sp. nov. is proposed (type
AB  - strain APG3(T) = NCIMB 14869(T) = LMG 27536(T) = ATCC BAA-2542(T)).
ER  -

TY  - JOUR
AU  - Urbanczyk, H.
AU  - Ogura, Y.
AU  - Hayashi, T.
TI  - Contrasting inter- and intraspecies recombination patterns in the 'Harveyi clade' Vibrio collected over large spatial and temporal scales.
JO  - Genome Biol. Evol.
PY  - 2014
SP  - 71
EP  - 80
VL  - 7
AB  - Recombination plays an important role in the divergence of bacteria, but the frequency of
AB  - interspecies and intraspecies recombination events remains poorly understood. We investigated
AB  - recombination events that occurred within core genomes of 35 Vibrio strains (family
AB  - Vibrionaceae, Gammaproteobacteria), from six closely related species in the so-called "Harveyi
AB  - clade." The strains were selected from a collection of strains isolated in the last 90 years,
AB  - from various environments worldwide. We found a close relationship between the number of
AB  - interspecies recombination events within core genomes of the 35 strains and the overall
AB  - genomic identity, as inferred from calculations of the average nucleotide identity. The
AB  - relationship between the overall nucleotide identity and the number of detected interspecies
AB  - recombination events was comparable when analyzing strains isolated over 80 years apart, from
AB  - different hemispheres, or from different ecologies, as well as in strains isolated from the
AB  - same geographic location within a short time frame. We further applied the same method of
AB  - detecting recombination events to analyze 11 strains of Vibrio campbellii, and identified
AB  - disproportionally high number of intraspecies recombination events within the core genomes of
AB  - some, but not all, strains. The high number of recombination events was detected between V.
AB  - campbellii strains that have significant temporal (over 18 years) and geographical (over
AB  - 10,000 km) differences in their origins of isolation. Results of this study reveal a
AB  - remarkable stability of Harveyi clade species, and give clues about the origins and
AB  - persistence of species in the clade.
ER  -

TY  - JOUR
AU  - Urbanczyk, H.
AU  - Ogura, Y.
AU  - Hendry, T.A.
AU  - Gould, A.L.
AU  - Kiwaki, N.
AU  - Atkinson, J.T.
AU  - Hayashi, T.
AU  - Dunlap, P.V.
TI  - Genome Sequence of Photobacterium mandapamensis svers. 1.1., Bioluminescent Symbiont of the Cardinalfish Siphamia versicolor.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3144
EP  - 3145
VL  - 193
AB  - Photobacterium mandapamensis is one of three luminous Photobacterium species able to form
AB  - species-specific bioluminescent symbioses with marine
AB  - fishes. Here, we present the draft genome sequence of P. mandapamensis
AB  - svers.1.1, bioluminescent symbiont of the cardinalfish, Siphamia
AB  - versicolor, the first genome of a symbiotic, luminous Photobacterium
AB  - species to be sequenced. Analysis of the sequence provides insight into
AB  - differences between P. mandapamensis and other luminous and symbiotic
AB  - bacteria in genes involved in quorum sensing regulation of light
AB  - production and establishment of symbiosis.
ER  -

TY  - JOUR
AU  - Urbieta, M.S.
AU  - Rascovan, N.
AU  - Castro, C.
AU  - Revale, S.
AU  - Giaveno, M.A.
AU  - Vazquez, M.
AU  - Donati, E.R.
TI  - Draft Genome Sequence of the Novel Thermoacidophilic Archaeon Acidianus copahuensis Strain ALE1, Isolated from the Copahue Volcanic Area in Neuquen,  Argentina.
JO  - Genome Announcements
PY  - 2014
SP  - e00259
EP  - e00214
VL  - 2
AB  - Acidianus copahuensis is a recently characterized thermoacidophilic archaeon isolated from the
AB  - Copahue volcanic area in Argentina. Here, we present its draft
AB  - genome sequence, in which we found genes involved in key metabolic pathways for
AB  - developing under Copahue's extreme environmental conditions, such as sulfur and
AB  - iron oxidation, carbon fixation, and metal tolerance.
ER  -

TY  - JOUR
AU  - Urieli-Shoval, S.
AU  - Gruenbaum, Y.
AU  - Razin, A.
TI  - Sequence and substrate specificity of isolated DNA methylases from Escherichia coli C.
JO  - J. Bacteriol.
PY  - 1983
SP  - 274
EP  - 280
VL  - 153
AB  - Two DNA methylase activities of Escherichia coli C, the mec (designates DNA-cytosine-methylase
AB  - gene, which is also designated dcm) and dam gene products, were physically separated by
AB  - DEAE-cellulose column chromatography. The sequence and substrate specificity of the two
AB  - enzymes were studied in vitro. The experiments revealed that both enzymes show their expected
AB  - sequence specificity under in vitro conditions, methylating symmetrically on both DNA strands.
AB  - The mec enzyme methylates exclusively the internal cytosine residue of CC(A/T)GG sequences,
AB  - and the dam enzyme methylates adenine residues at GATC sites. Substrate specificity
AB  - experiments revealed that both enzyes methylate in vitro unmethylated duplex DNA as
AB  - efficiently as hemimethylated DNA. The results of these experiments suggest that the
AB  - methylation at a specific site takes place by two independent events. A methyl group in a site
AB  - on one strand of the DNA does not facilitate the methylation of the same site on the opposite
AB  - strand. With the dam methylase it was found that enzyme is incapable of methylating GATC sites
AB  - located at the ends of DNA molecules.
ER  -

TY  - JOUR
AU  - Urig, S.
AU  - Gowher, H.
AU  - Hermann, A.
AU  - Beck, C.
AU  - Fatemi, M.
AU  - Humeny, A.
AU  - Jeltsch, A.
TI  - The Escherichia coli Dam DNA methyltransferase modifies DNA in a highly processive reaction.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 1085
EP  - 1096
VL  - 319
AB  - The Escherichia coli dam adenine-N6 methyltransferase modifies DNA at G A TC sequences. It is
AB  - involved in post-replicative mismatch repair, control of DNA replication and gene regulation.
AB  - We show that E. coli dam acts as a functional monomer and methylates only one strand of the
AB  - DNA in each binding event. The preferred way of ternary complex assembly is that the enzyme
AB  - first binds to DNA and then to S-adenosylmethionine. The enzyme methylates an oligonucleotide
AB  - containing two dam sites and an 879 bp PCR product with four sites in a fully processive
AB  - reaction. On -DNA comprising 48,502 bp and 116 dam sites, E. coli dam scans 3000 dam sites per
AB  - binding event in a random walk, that on average leads to a processive methylation of 55 sites.
AB  - Processive methylation of DNA considerably accelerates DNA methylation. The highly processive
AB  - mechanism of E. coli dam could explain why small amounts of E. coli dam are able to maintain
AB  - the methylation state of dam sites during DNA replication. Furthermore, our data support the
AB  - general rule that solitary DNA methyltransferase modify DNA processively whereas
AB  - methyltransferases belonging to a restriction-modification system show a distributive
AB  - mechanism, because processive methylation of DNA would interfere with the biological function
AB  - of restriction-modification systems.
ER  -

TY  - JOUR
AU  - Uritani, M.
AU  - Takai, M.
AU  - Yoshinaga, K.
TI  - Protective effect of disaccharides on restriction endonucleases during drying under vacuum.
JO  - J. Biochem. (Tokyo)
PY  - 1995
SP  - 774
EP  - 779
VL  - 117
AB  - Desiccation by vacuum-drying inactivates the restriction endonuclease HindIII completely.
AB  - However, when dried in the presence of a disaccharide such as trehalose, maltose, or sucrose,
AB  - the endonuclease retains its phage DNA-cleaving activity and produces the same digestive
AB  - fragments as does the intact enzyme. Thus, the disaccharides are effective in protecting the
AB  - restriction enzyme in terms of both recognition and accurate cleavage of the substrate. Among
AB  - the disaccharides, trehalose protects the enzyme most effectively; and it also stabilizes the
AB  - enzyme during dilution in aqueous solution. The restriction enzyme dried with trehalose
AB  - maintains its activity without detectable loss for at least 4 days at 37oC, but it shows
AB  - reduced activity after 30-day storage at either 4oC or room temperature. Trehalose also
AB  - protects other restriction endonucleases, EcoRI and BamHI, from inactivation during
AB  - vacuum-drying, whereas drying them alone leads to severe loss of their activity. The
AB  - restriction endonucleases dried with trehalose retain their activities for at least 20 days at
AB  - 4oC and for 7 days at room temperature.
ER  -

TY  - JOUR
AU  - Uron, P.
AU  - Giachini, A.J.
AU  - Glick, B.R.
AU  - Rossi, M.J.
AU  - Nascimento, F.X.
TI  - Near-Complete Genome Sequence of Pseudomonas palleroniana MAB3, a Beneficial 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacterium Able To Promote  the Growth of Mushrooms and Plants.
JO  - Genome Announcements
PY  - 2018
SP  - e00242
EP  - e00218
VL  - 6
AB  - The near-complete genome sequence of Pseudomonas palleroniana MAB3, a
AB  - 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from an
AB  - environmental soil Amanita mushroom, is presented here. The genome of P.
AB  - palleroniana MAB3 contains a single circular chromosome of 6.29 Mb and an average
AB  - GC content of 60.5%.
ER  -

TY  - JOUR
AU  - Uroz, S.
AU  - Oger, P.
TI  - Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering  Ability.
JO  - Genome Announcements
PY  - 2015
SP  - e00798
EP  - e00715
VL  - 3
AB  - We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated
AB  - from the Oak-Scleroderma citrinum ectomycorrhizosphere in the
AB  - experimental forest site of Breuil-Chenue (France).
ER  -

TY  - JOUR
AU  - Uroz, S.
AU  - Tech, J.J.
AU  - Sawaya, N.A.
AU  - Frey-Klett, P.
AU  - Leveau, J.H.J.
TI  - Structure and function of bacterial communities in ageing soils: insights from the Mendocino ecological staircase.
JO  - Soil Biol. Biochem.
PY  - 2014
SP  - 265
EP  - 274
VL  - 69
ER  -

TY  - JOUR
AU  - Urshev, Z.
AU  - Hajo, K.
AU  - Lenoci, L.
AU  - Bron, P.A.
AU  - Dijkstra, A.
AU  - Alkema, W.
AU  - Wels, M.
AU  - Siezen, R.J.
AU  - Minkova, S.
AU  - van Hijum, S.A.
TI  - Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.
JO  - Genome Announcements
PY  - 2016
SP  - e01090
EP  - e01016
VL  - 4
AB  - Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 originates from homemade Bulgarian yogurt
AB  - and was selected for its ability to form a strong association
AB  - with Streptococcus thermophilus The genome sequence will facilitate elucidating
AB  - the genetic background behind the contribution of LBB.B5 to the taste and aroma
AB  - of yogurt and its exceptional protocooperation with S. thermophilus.
ER  -

TY  - JOUR
AU  - Urushibara, N.
AU  - Kawaguchiya, M.
AU  - Kobayashi, N.
TI  - Two novel arginine catabolic mobile elements and staphylococcal chromosome cassette mec composite islands in community-acquired methicillin-resistant Staphylococcus aureus genotypes ST5-MRSA-V and ST5-MRSA-II.
JO  - J. Antimicrob. Chemother.
PY  - 2012
SP  - 1828
EP  - 1834
VL  - 67
AB  - Objectives: The arginine catabolic mobile element (ACME) is a novel staphylococcal genetic
AB  - island. ACME is located downstream of the staphylococcal cassette chromosome mec (SCCmec),
AB  - forming the ACME-SCCmec composite island. Recently, ACME II (located upstream of SCCmec IV)
AB  - was described from a methicillin-resistant Staphylococcus aureus (MRSA) strain M1 in Denmark
AB  - (ST8-MRSA-IVa) and 15 MRSA isolates in Ireland (ST22- MRSA-IVh). We report the novel genetic
AB  - characteristics of the ACME-SCCmec composite islands found in Japanese community-acquired MRSA
AB  - (CA-MRSA) isolates.  Methods: ACME-SCCmec composite islands from two ACME-arcA-positive
AB  - CA-MRSA isolates with the genotypes ST5-MRSA-V (SR141) and ST5-MRSA-II (SR388) were
AB  - characterized using long-range PCR and nucleotide sequencing. Results: Both isolates harboured
AB  - a 12 kb DNA region primarily identified in ACME II in Staphylococcus epidermidis ATCC 12228
AB  - upstream of each SCCmec. The arcA and its flanking regions in SR141 and SR388 showed high
AB  - sequence identity (99.8% at the highest) to those in MRSA M1 and M08/0126 (the representative
AB  - of 15 Irish ST22-MRSA-IVh isolates), suggesting that the ACMEs of these four isolates
AB  - originated from the same ancestral gene. The ACME II-like element in SR141 included an
AB  - insertion sequence IS1182 at a position close to SCCmec, resulting in a new variant. SR388
AB  - contained approximately 11.5 kb of the J1 region of type I SCCmec (J1 SCCmecI) between orfX
AB  - and ACME (orfX-J1 SCCmecI-ACME II), unlike the homologous region in M08/0126 (orfX-ACME II-J1
AB  - SCCmecI).  Conclusions: This is the first report of the ACME II-like element inserted upstream
AB  - of SCCmec in CA-MRSA with the genotypes ST5-MRSA-V and ST5-MRSA-II.
ER  -

TY  - JOUR
AU  - Useh, N.M.
AU  - Ngbede, E.O.
AU  - Akange, N.
AU  - Thomas, M.
AU  - Foley, A.
AU  - Keena, M.C.
AU  - Nelson, E.
AU  - Christopher-Hennings, J.
AU  - Tomita, M.
AU  - Suzuki, H.
AU  - Scaria, J.
TI  - Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.
JO  - Genome Announcements
PY  - 2016
SP  - e00315
EP  - e00316
VL  - 4
AB  - Here, we report the availability of draft genomes of several Salmonella serotypes, isolated
AB  - from poultry sources from Nigeria. These genomes will help to
AB  - further understand the biological diversity of S. enterica and will serve as
AB  - references in microbial trace-back studies to improve food safety.
ER  -

TY  - JOUR
AU  - Ushakova, T.A.
AU  - Puchkova, L.I.
AU  - Gutorov, V.V.
AU  - Kuvshinov, V.N.
AU  - Repin, V.E.
TI  - Restriction endonuclease Sst12I from a strain of Streptomyces - Recognizing the nucleotide sequence 5 '-CTGCAG-3 '.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 2002
SP  - 25
EP  - 28
VL  - 38
AB  - A new restriction endonuclease Sst12I belonging to type II and recognizing the sequence
AB  - 5'-CTGCAG-3' was isolated from the bacterial
AB  - strain Streptomyces sp. St-12. The enzyme hydrolyzes DNA between
AB  - adenine and guanine residues thus, it is a true isoschizomer of
AB  - restrictase PstI. In contrast to PstI, the restriction endonuclease
AB  - Sst12I hydrolyses DNA both at 37 and 55 C and remains active
AB  - after long-term storage.
ER  -

TY  - JOUR
AU  - Ushakova, T.A.
AU  - Puchkova, L.I.
AU  - Gutorov, V.V.
AU  - Totmenina, O.D.
AU  - Repin, V.E.
TI  - Restriction endonuclease Asi256I recognizes and cuts the nucleotide sequence 5'-GATC-3'.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 2008
SP  - 28
EP  - 31
VL  - 44
AB  - A strain producing a restriction endonuclease was isolated from soil samples and identified as
AB  - the Arthrobacter sp. strain Ck256. The enzyme
AB  - produced by this strain was termed Asi256I. The isolation procedure for
AB  - this enzyme was described, and the optimal conditions for its function
AB  - were determined. It was shown that the restriction endonuclease Asi256I
AB  - is a true isoschizomer of MboI, it has a temperature optimum of 6
AB  - degrees C, and can be used in molecular-biological and
AB  - genetic-engineering studies performed at low temperatures.
ER  -

TY  - JOUR
AU  - Ushakova, T.A.
AU  - Puchkova, L.I.
AU  - Radionenko, Y.V.
AU  - Gutorov, V.V.
AU  - Kuvshinov, V.N.
AU  - Repin, V.E.
TI  - Restriction endonuclease SpmI recognizing the 5'-AT/CGAT-3' nucleotide sequence.
JO  - Biotekhnologiya
PY  - 2004
SP  - 38
EP  - 42
VL  - 0
AB  - A strain producer of a restriction endonuclease (restrictase), that was identified as a
AB  - species of Sphingobacterium mizutae has been isolated from snow water, and its restrictase was
AB  - named SpmI.  The method of the enzymne isolation was described, and optimal conditions of its
AB  - action were determined.  It was shown that SpmI restrictase is a true isoschizomer of ClaI
AB  - restrictase.  The temperature optimum of SpmI restrictase is 6oC, and it can be used in
AB  - molecular biology and genetic engineering researches that need carrying out at low
AB  - temperatures.
ER  -

TY  - JOUR
AU  - Ushakova, T.A.
AU  - Puchkova, L.I.
AU  - Radionenko, Y.V.
AU  - Kuvshinov, V.N.
AU  - Repin, V.E.
TI  - Restriction endonuclease Bst221 from Bacillus stearothermophilus 22 strain recognizing the 5'-CCNNNNN^NNGG-3' nucleotide sequence.
JO  - Biotekhnologiya
PY  - 2003
SP  - 11
EP  - 15
VL  - 0
AB  - A strain producing the restriction endonuclease (restrictase) which was identified as a
AB  - species of Bacillus stearothermophilus 22 has been isolated by the authors, and its
AB  - restrictase was called Bst221.  The method of the enzyme isolation was described, and optimal
AB  - conditions of its action were determined.  It was shown that Bst221 restrictase is a true
AB  - isoschizomer of BsiYI restrictase.  Bst221 restrictase is active in a broad temperature range
AB  - and shows promise for molecular biology research.
ER  -

TY  - JOUR
AU  - Ushay, H.M.
AU  - Tullius, T.D.
AU  - Lippard, S.J.
TI  - Inhibition of the BamHI cleavage and unwinding of pBR322 deoxyribonucleic acid by the antitumor drug cis-dichlorodiammineplatinum(II).
JO  - Biochemistry
PY  - 1981
SP  - 3744
EP  - 3748
VL  - 20
AB  - The antitumor drug cis-dichlorodiammineplatinum(II) (cis-DDP) binds to pBR322 DNA and inhibits
AB  - the cleavage of this circular DNA into a linear form by the restriction endonuclease BamHI.
AB  - The binding of platinum to DNA was monitored by agarose gel electrophoresis, and the amount of
AB  - platinum bound per nucleotide (rb) was measured by carbon rod atomic absorption spectroscopy.
AB  - Electrophoretic mobility changes reflect a shortening and unwinding of the DNA duplex upon
AB  - platinum binding as observed previously for the reaction of cis- and trans-DDP with pSM2 DNA
AB  - [Cohen, G.L., Bauer, W.R., Barton, J.K., & Lippard, S.J. (1979) Science (Washington, DC) 203,
AB  - 1014-1016].  The inhibition of BamHI nuclease activity occurs at very low binding levels and
AB  - is complete at rb = 0.045.  This value corresponds to the binding of one platinum atom within
AB  - +/- 3 base pairs of the recognition sequence of the enzyme shown below.  Treatment of the DNA
AB  - with 0.2 M sodium cyanide after BamHI cutting removes the platinum but does not alter the
AB  - point at which cis-DDP inhibits the formation of the linear form III DNA.  This result is in
AB  - contrast with a previous report claiming that BamHI could cut across a cis-DDP-induced GpG
AB  - cross-link in DNA which could be subsequently revealed by cyanide reversal of platinum
AB  - binding.  When the platinum is removed by cyanide treatment, the drug-induced mobility changes
AB  - are reversed and there is a pronounced sharpening of the bands in the gel. Quantitative study
AB  - of the cyanide reversal shows the presence of a small amount of unremovable platinum tightly
AB  - bound to the DNA at high ratios (~0.1) of bound platinum per nucleotide -G^GATCC- -CCTAG^G-.
ER  -

TY  - JOUR
AU  - Ushida, K.
AU  - Tsuchida, S.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Sawada, A.
AU  - Hanya, G.
TI  - Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese  Macaques in Yakushima Island.
JO  - Genome Announcements
PY  - 2016
SP  - e01694
EP  - e01615
VL  - 4
AB  - We report the draft genome sequences of Sarcina ventriculi strains 14 and 17, both isolated
AB  - from feces of wild Yakushima macaques (Macaca fuscata yakui). These
AB  - genomic sequences will be helpful for the phylogenetic consideration of the
AB  - family Clostridiaceae and understanding of the contribution of intestinal
AB  - microbiota to the survival of Yakushima macaques.
ER  -

TY  - JOUR
AU  - Ushijima, B.
AU  - Videau, P.
AU  - Aeby, G.S.
AU  - Callahan, S.M.
TI  - Draft Genome Sequence of Vibrio coralliilyticus Strain OCN008, Isolated from Kane'ohe Bay, Hawai'i.
JO  - Genome Announcements
PY  - 2013
SP  - e00786
EP  - e00713
VL  - 1
AB  - Vibrio coralliilyticus is a Gram-negative bacterium found in seawater and is associated with
AB  - diseased marine organisms. Strains of V. coralliilyticus have
AB  - been shown to infect coral from multiple genera. We report the draft genome
AB  - sequence of V. coralliilyticus strain OCN008, the third V. coralliilyticus genome
AB  - to be sequenced.
ER  -

TY  - JOUR
AU  - Ushijima, B.
AU  - Videau, P.
AU  - Poscablo, D.
AU  - Vine, V.
AU  - Salcedo, M.
AU  - Aeby, G.
AU  - Callahan, S.M.
TI  - Complete Genome Sequence of Vibrio coralliilyticus Strain OCN014, Isolated from a Diseased Coral at Palmyra Atoll.
JO  - Genome Announcements
PY  - 2014
SP  - e01318
EP  - e01314
VL  - 2
AB  - Vibrio coralliilyticus is a marine gammaproteobacterium that has been implicated  as an
AB  - etiological agent of disease for multiple coral genera on reefs worldwide.
AB  - We report the complete genome of V. coralliilyticus strain OCN014, isolated from
AB  - a diseased Acropora cytherea colony off the western reef terrace of Palmyra
AB  - Atoll.
ER  -

TY  - JOUR
AU  - Ushijima, K.
AU  - Ishibashi, T.
AU  - Tsukahara, S.
AU  - Takai, K.
AU  - Takaku, H.
TI  - Inhibition of restriction endonuclease cleavage by triplex formation with oligo-2'-O-methyl-ribonucleotides containing 8-oxo-2'-O-methyladenosine in place of cytidine.
JO  - Heterocycles
PY  - 2000
SP  - 389
EP  - 398
VL  - 52
AB  - The ability of homopyrimidine oligoribonucleotides and oligo-2'-O-methyl-ribonucleotides
AB  - containing 8-oxo-adenosine and 8-oxo-2'-O-methyl-adenosine to form stable, triple-helical
AB  - structures with sequences containing the recognition site for the class II-S restriction
AB  - enzyme, Ksp632I, was studied as a function of pH.  The AOH- and AmOH-substituted
AB  - oligoribonucleotides and oligo-2'-O-methyl-ribonucleotides were shown to bind within the
AB  - physiological pH range in a pH-independent fashion, without a compromise in specificity.  The
AB  - substitutions of three cytidine residues with AOH showed higher endonuclease inhibition than
AB  - the substitution of either one or two cytidine residues with AOH.  In particular, the
AB  - oligo-2'-O-methyl-ribonucleotide with only one cytidine substituted with AmOH showed higher
AB  - endonuclease inhibition.  Increased resistance to nucleases is observed with the introduction
AB  - of 2-O-methylnucleosides.  This stabilization should help us to design much more efficient
AB  - third strand homopyrimidine oligomer and antisense nucleic acid, which can be used as tools in
AB  - cellular biology and anti-viral therapy.
ER  -

TY  - JOUR
AU  - Ushijima, K.
AU  - Ishibashi, T.
AU  - Yamakawa, H.
AU  - Tsukahara, S.
AU  - Takai, K.
AU  - Maruyama, T.
AU  - Takaku, H.
TI  - Inhibition of restriction endonuclease cleavage by triple helix formation with RNA and 2'-O-methyl RNA oligonucleotides containing 8-oxo-adenosine in place of cytidine.
JO  - Biochemistry
PY  - 1999
SP  - 6570
EP  - 6575
VL  - 38
AB  - The ability of homopyrimidine oligoribonucleotides (RNA) and
AB  - oligo-2'-O-methyl-ribonucleotides (2'-O-methyl RNA) containing 8-oxo-adenosine (AOH) and
AB  - 8-oxo-2'-O-methyl (AmOH) adenosine to form stable, triple-helical structures with sequences
AB  - containing the recognition site for the class II-S restriction enzyme, Ksp632-I, was studied
AB  - as a function of pH. The AOH- and AmOH-substituted RNA and 2'-O-methyl RNA oligonucleotides
AB  - were shown to bind within the physiological pH range in a pH-independent fashion, without a
AB  - compromise in specificity. The substitutions of three cytidine residues with AOH showed higher
AB  - endonuclease inhibition than the substitution of either one or two cytidine residues with AOH.
AB  - In particular, the 2'-O-methyl RNA oligonucleotide with only one cytidine substituted with
AB  - AmOH showed higher endonuclease inhibition than the homopyrimidine RNA and 2'-O-methyl RNA
AB  - oligonucleotides and the RNA oligonucleotides containing either one or two AOH moieties.
AB  - Furthermore, the AmOH-substituted 2'-O-methyl RNA oligonucleotides were stable (53%) after an
AB  - incubation in 10% fetal bovine serum for 8 h, whereas the RNA oligonucleotides were completely
AB  - degraded. Increased resistance to nucleases is observed with the introduction of
AB  - 2'-O-methylnucleosides. This stabilization should help us to design much more efficient third
AB  - strand homopyrimidine oligomer and antisense nucleic acid-based antiviral therapies, which
AB  - could be used as tools in cellular biology.
ER  -

TY  - JOUR
AU  - Ustinova, V.
AU  - Smirnova, T.
AU  - Blagodatskikh, K.
AU  - Varlamov, D.
AU  - Sochivko, D.
AU  - Larionova, E.
AU  - Andreevskaya, S.
AU  - Andrievskaya, I.
AU  - Chernousova, L.
TI  - First Draft Genome Sequence of a Mycobacterium gordonae Clinical Isolate.
JO  - Genome Announcements
PY  - 2016
SP  - e00638
EP  - e00616
VL  - 4
AB  - Here, we report the first draft genome sequence of the clinically relevant species
AB  - Mycobacterium gordonae The clinical isolate Mycobacterium gordonae 14-8773 was obtained from
AB  - the sputum of a patient with mycobacteriosis.
ER  -

TY  - JOUR
AU  - Ustinova, V.
AU  - Smirnova, T.
AU  - Varlamov, D.
AU  - Monakhova, Y.
AU  - Larionova, E.
AU  - Andreevskaya, S.
AU  - Andrievskaya, I.
AU  - Chernousova, L.
AU  - Ergeshov, A.
TI  - Draft Genome Sequence of a Mycobacterium heckeshornense Clinical Isolate.
JO  - Genome Announcements
PY  - 2018
SP  - e00178
EP  - e00118
VL  - 6
AB  - We report here the draft genome sequence of Mycobacterium heckeshornense, isolated from the
AB  - sputum of a patient admitted to a tuberculosis hospital with
AB  - suspected pulmonary tuberculosis.
ER  -

TY  - JOUR
AU  - Utter, B.
AU  - Deutsch, D.R.
AU  - Schuch, R.
AU  - Winer, B.Y.
AU  - Verratti, K.
AU  - Bishop-Lilly, K.
AU  - Sozhamannan, S.
AU  - Fischetti, V.A.
TI  - Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus.
JO  - PLoS ONE
PY  - 2014
SP  - E100502
EP  - E100502
VL  - 9
AB  - In Staphylococcus aureus, the disease impact of chromosomally integrated
AB  - prophages on virulence is well described. However, the existence of
AB  - extra-chromosomal prophages, both plasmidial and episomal, remains obscure.
AB  - Despite the recent explosion in bacterial and bacteriophage genomic sequencing,
AB  - studies have failed to specifically focus on extra-chromosomal elements. We
AB  - selectively enriched and sequenced extra-chromosomal DNA from S. aureus isolates
AB  - using Roche-454 technology and uncovered evidence for the widespread distribution
AB  - of multiple extra-chromosomal prophages (ExPPhis) throughout both
AB  - antibiotic-sensitive and -resistant strains. We completely sequenced one such
AB  - element comprised of a 43.8 kbp, circular ExPPhi (designated capital EF,
AB  - CyrillicBU01) from a vancomycin-intermediate S. aureus (VISA) strain. Assembly
AB  - and annotation of capital EF, CyrillicBU01 revealed a number of putative
AB  - virulence determinants encoded within a bacteriophage immune evasion cluster
AB  - (IEC). Our identification of several potential ExPPhis and mobile genetic
AB  - elements (MGEs) also revealed numerous putative virulence factors and antibiotic
AB  - resistance genes. We describe here a previously unidentified level of genetic
AB  - diversity of stealth extra-chromosomal elements in S. aureus, including phages
AB  - with a larger presence outside the chromosome that likely play a prominent role
AB  - in pathogenesis and strain diversity driven by horizontal gene transfer (HGT).
ER  -

TY  - JOUR
AU  - Utturkar, S.M. et al.
TI  - Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
JO  - Genome Announcements
PY  - 2016
SP  - e01043
EP  - e01016
VL  - 4
AB  - We and others have shown the utility of long sequence reads to improve genome assembly
AB  - quality. In this study, we generated PacBio DNA sequence data to improve
AB  - the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium
AB  - thermocellum LQRI, and Pelosinus fermentans R7.
ER  -

TY  - JOUR
AU  - Utturkar, S.M.
AU  - Bollmann, A.
AU  - Brzoska, R.M.
AU  - Klingeman, D.M.
AU  - Epstein, S.E.
AU  - Palumbo, A.V.
AU  - Brown, S.D.
TI  - Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals.
JO  - Genome Announcements
PY  - 2013
SP  - e00322
EP  - e00313
VL  - 1
AB  - Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from
AB  - subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy
AB  - due to its tolerance to high concentrations of heavy metals, such as uranium,
AB  - nickel, cobalt, and cadmium, and we present its draft genome sequence here.
ER  -

TY  - JOUR
AU  - Utturkar, S.M.
AU  - Bollmann, A.
AU  - Brzoska, R.M.
AU  - Klingeman, D.M.
AU  - Epstein, S.E.
AU  - Palumbo, A.V.
AU  - Brown, S.D.
TI  - Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential  for Bioremediation.
JO  - Genome Announcements
PY  - 2013
SP  - e00321
EP  - e00313
VL  - 1
AB  - Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from
AB  - subsurface sediments in Oak Ridge, TN. A member of this genus has
AB  - been described as a potential bioremediation agent. Strain OR214 is tolerant to
AB  - various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present
AB  - its draft genome sequence here.
ER  -

TY  - JOUR
AU  - Utturkar, S.M.
AU  - Huber, H.
AU  - Leptihn, S.
AU  - Loh, B.
AU  - Brown, S.D.
AU  - Stetter, K.O.
AU  - Podar, M.
TI  - Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105 degrees C.
JO  - Genome Announcements
PY  - 2016
SP  - e00016
EP  - e00016
VL  - 4
AB  - We report here the draft genome sequence of Pyrodictium occultum PL19(T), a marine
AB  - hyperthermophilic archaeon. The genome provides insights into molecular
AB  - and cellular adaptation mechanisms to life in extreme environments and the
AB  - evolution of early organisms on Earth.
ER  -

TY  - JOUR
AU  - Uyar, A.
AU  - Kurkcuoglu, O.
AU  - Nilsson, L.
AU  - Doruker, P.
TI  - The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases.
JO  - Phys. Biol.
PY  - 2011
SP  - 056001
EP  - 056001
VL  - 8
AB  - The vibrational dynamics of various type II restriction endonucleases, in complex with
AB  - cognate/non-cognate DNA and in the apo form, are
AB  - investigated with the elastic network model in order to reveal common
AB  - functional mechanisms in this enzyme family. Scissor-like and tong-like
AB  - motions observed in the slowest modes of all enzymes and their
AB  - complexes point to common DNA recognition and cleavage mechanisms.
AB  - Normal mode analysis further points out that the scissor-like motion
AB  - has an important role in differentiating between cognate and
AB  - non-cognate sequences at the recognition site, thus implying its
AB  - catalytic relevance. Flexible regions observed around the DNA-binding
AB  - site of the enzyme usually concentrate on the highly conserved
AB  - beta-strands, especially after DNA binding. These beta-strands may have
AB  - a structurally stabilizing role in functional dynamics for target site
AB  - recognition and cleavage. In addition, hot spot residues based on
AB  - high-frequency modes reveal possible communication pathways between the
AB  - two distant cleavage sites in the enzyme family. Some of these hot
AB  - spots also exist on the shortest path between the catalytic sites and
AB  - are highly conserved.
ER  -

TY  - JOUR
AU  - Uyen, N.T.
AU  - Nishi, K.
AU  - Park, S.Y.
AU  - Choi, J.W.
AU  - Lee, H.J.
AU  - Kim, J.S.
TI  - Crystallization and preliminary X-ray diffraction analysis of the HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2008
SP  - 926
EP  - 928
VL  - 64
AB  - Type I restriction enzymes are multimeric proteins that consist of three subunits. The HsdS
AB  - and HsdM subunits form a complex protein that
AB  - shows methyltransferase activity, while the HsdR subunit functions as
AB  - an endonuclease as well as as a translocase. Of these three subunits,
AB  - no structural information on the HsdR subunit is yet available. The
AB  - putative HsdR gene from Vibrio vulnificus YJ016 (HsdR Vv) was cloned
AB  - and expressed and the expressed protein HsdR Vv was purified. HsdR Vv
AB  - was crystallized from 8%(w/v) polyethylene glycol 3350, 0.15 M ammonium
AB  - chloride, 0.1 M HEPES pH 7.5 and 2 mM beta-mercaptoethanol. Diffraction
AB  - data were collected to 2.60 angstrom resolution using synchrotron
AB  - radiation. The crystal belongs to the orthorhombic space group
AB  - P2(1)2(1)2(1), with unit-cell parameters a = 71.01, b = 89.04, c =
AB  - 113.66 angstrom. With one HsdR Vv molecule in the asymmetric unit, the
AB  - Matthews coefficient was 2.14 angstrom(3) Da(-1) and the solvent
AB  - content was 42%.
ER  -

TY  - JOUR
AU  - Uyen, N.T.
AU  - Park, S.Y.
AU  - Choi, J.W.
AU  - Lee, H.J.
AU  - Nishi, K.
AU  - Kim, J.S.
TI  - The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and  translocation activity.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 6960
EP  - 6969
VL  - 37
AB  - Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its
AB  - methylation status, type I enzymes composed of three subunits are interesting because of their
AB  - unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR).
AB  - The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus
AB  - YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease
AB  - domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding
AB  - site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is
AB  - located close to the probable DNA-binding site for translocation, which is far from the NTD
AB  - nucleolytic core. Comparison of relative domain arrangements with other functionally related
AB  - ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism
AB  - of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that
AB  - a linker helix connecting two RDs and an extended region within the nuclease domain may play a
AB  - central role in switching the DNA translocation into the restriction activity.
ER  -

TY  - JOUR
AU  - Uzelac, G.
AU  - Bertani, I.
AU  - Kojic, M.
AU  - Paszkiewicz, K.H.
AU  - Studholme, D.J.
AU  - Passos-da-Silva, D.
AU  - Venturi, V.
TI  - Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.
JO  - Genome Announcements
PY  - 2014
SP  - e00654
EP  - e00614
VL  - 2
AB  - Pseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain
AB  - isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic
AB  - in two nonmammalian infection models. Here we report the draft genome sequence of P.
AB  - aeruginosa PUPa3.
ER  -

TY  - JOUR
AU  - Vacheron, J.
AU  - Dubost, A.
AU  - Chapulliot, D.
AU  - Prigent-Combaret, C.
AU  - Muller, D.
TI  - Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere.
JO  - Genome Announcements
PY  - 2017
SP  - e00122
EP  - e00117
VL  - 5
AB  - We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated
AB  - from the rhizosphere of maize during a greenhouse experiment. JV274
AB  - harbors genes involved in flexirubin production (darA and darB genes), bacterial
AB  - competition (type VI secretion system), and gliding (bacterial motility; type IX
AB  - secretion system).
ER  -

TY  - JOUR
AU  - Vader, A.
AU  - Nielsen, H.
AU  - Johansen, S.
TI  - In vivo expression of the nucleolar group I intron-encoded I-DirI homing endonuclease involves the removal of a spliceosomal intron.
JO  - EMBO J.
PY  - 1999
SP  - 1003
EP  - 1013
VL  - 18
AB  - The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual
AB  - twin-ribozyme organization.  One of the ribozymes (DiGIR2) catalyses intron excision and exon
AB  - ligation.  The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open
AB  - reading frame is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1
AB  - and IPS2) located at its 3' end.  Examination of the in vivo expression of DiSSU1 shows that
AB  - after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed
AB  - cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of
AB  - the ORF 3' end.  A spliceosomal intron, the first to be reported within a group I intron and
AB  - the rDNA, is removed before the I-DirI mRNA associates with the polysomes.  Taken together,
AB  - our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity
AB  - and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein
AB  - to be produced from the RNA polymerase I-transcribed rDNA.
ER  -

TY  - JOUR
AU  - Vaid, R.K.
AU  - Jindal, N.
AU  - Anand, T.
AU  - Bera, B.C.
AU  - Riyesh, T.
AU  - Virmani, N.
AU  - Barua, S.
AU  - Gupta, R.
AU  - Mahajan, N.K.
AU  - Joshi, C.G.
AU  - Singh, R.K.
TI  - First Draft Genome Sequence of Salmonella enterica Serovar Gallinarum Strain VTCCBAA614, Isolated from Chicken in India.
JO  - Genome Announcements
PY  - 2015
SP  - e01221
EP  - e01215
VL  - 3
AB  - Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum causes fowl typhoid
AB  - (FT), which results in huge economic losses to poultry farmers in India. We report the draft
AB  - genome sequence of Salmonella biovar Gallinarum strain VTCCBAA614, isolated from a chicken in
AB  - an FT affected broiler flock.
ER  -

TY  - JOUR
AU  - Vaid, R.K.
AU  - Shanmugasundaram, K.
AU  - Boora, A.
AU  - Bera, B.C.
AU  - Shukla, B.N.
AU  - Anand, T.
AU  - Singha, H.
AU  - Riyesh, T.
AU  - Virmani, N.
AU  - Barua, S.
AU  - Ahir, V.B.
AU  - Koringa, P.G.
AU  - Sajnani, M.R.
AU  - Bhat, V.D.
AU  - Rana, N.
AU  - Singh, K.P.
AU  - Malik, P.
AU  - Singh, R.K.
AU  - Joshi, C.G.
TI  - Draft Genome Sequence of Pasteurella multocida subsp. multocida B:2 Strain VTCCBAA264 Isolated from Bubalus bubalis in North India.
JO  - Genome Announcements
PY  - 2014
SP  - e00755
EP  - e00714
VL  - 2
AB  - The Pasteurella multocida subsp. multocida B:2 serotype causes hemorrhagic septicemia in
AB  - bubalines with high morbidity and mortality in the Indian
AB  - subcontinent. We report the draft genome sequence of Pasteurella multocida strain
AB  - VTCCBAA264 isolated from the small-intestine of a buffalo calf that died of high
AB  - fever.
ER  -

TY  - JOUR
AU  - Vairapandi, M.
AU  - Duker, N.J.
TI  - Enzymic removal of 5-methylcytosine from DNA by a hyman DNA-glycosylase.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 5323
EP  - 5327
VL  - 21
AB  - DNA 5-methylcytosine is a major factor in the silencing of mammalian genes; it is involved in
AB  - gene expression, differentiation, embryogenesis and neoplastic transformation. A decrease in
AB  - DNA 5-methylcytosine content is associated with activation of specific genes. There is much
AB  - evidence indicating this to be an enzymic process, with replacement of 5-methylcytosine by
AB  - cytosine. We demonstrate here enzymic release of 5-methylcytosines from DNA by a human
AB  - 5-methylcytosine-DNA glycosylase activity, which affords a possible mechanism for such
AB  - replacement. This activity generates promutagenic apyrimidinic sites, which can be related to
AB  - the high frequency of mutations found at DNA 5-methylcytosine loci. The recovery of most
AB  - released pyrimidines as thymines indicates subsequent deamination of free 5-methylcytosines by
AB  - a 5-methylcytosine deaminase activity. This prevents possible recycling of 5-methylcytosine
AB  - into replicative DNA synthesis via a possible 5-methyl-dCTP intermediate synthesized through
AB  - the pyrimidine salvage pathway. Taken together, these findings indicate mechanisms for removal
AB  - of 5-methylcytosines from DNA, hypermutability of DNA 5-methylcytosine sites, and exclusion of
AB  - 5-methylcytosines from DNA during replication.
ER  -

TY  - JOUR
AU  - Vaishampayan, P.A.
AU  - Kuehl, J.V.
AU  - Froula, J.L.
AU  - Morgan, J.L.
AU  - Ochman, H.
AU  - Francino, M.P.
TI  - Comparative metagenomics and population dynamics of the gut microbiota in mother and infant.
JO  - Genome Biol. Evol.
PY  - 2010
SP  - 53
EP  - 66
VL  - 2
AB  - Colonization of the gastrointestinal tract (GIT) of human infants with a suitable microbial
AB  - community is essential for numerous aspects of health, but the progression of events by which
AB  - this microbiota becomes established is poorly understood. Here, we investigate two previously
AB  - unexplored areas of microbiota development in infants: the deployment of functional
AB  - capabilities at the community level and the population genetics of its most abundant genera.
AB  - To assess the progression of the infant microbiota toward an adult-like state and to evaluate
AB  - the contribution of maternal GIT bacteria to the infant gut, we compare the infant's
AB  - microbiota with that of the mother at 1 and 11 months after delivery. These comparisons reveal
AB  - that the infant's microbiota rapidly acquires and maintains the range of gene functions
AB  - present in the mother, without replicating the phylogenetic composition of her microbiota.
AB  - Microdiversity analyses for Bacteroides and Bifidobacterium, two of the main microbiota
AB  - constituents, reveal that by 11 months, the phylotypes detected in the infant are distinct
AB  - from those in the mother, although the maternal Bacteroides phylotypes were transiently
AB  - present at 1 month of age. The configuration of genetic variants within these genera reveals
AB  - populations far from equilibrium and likely to be undergoing rapid growth, consistent with
AB  - recent population turnovers. Such compositional turnovers and the associated loss of maternal
AB  - phylotypes should limit the potential for long-term coadaptation between specific bacterial
AB  - and host genotypes.
ER  -

TY  - JOUR
AU  - Vaisvila, R.
AU  - Rasmussen, L.J.
AU  - Lobner-Olesen, A.
AU  - von Freiesleben, U.
AU  - Marinus, M.G.
TI  - The LipB protein is a negative regulator of dam gene expression in Escherichia coli.
JO  - Biochim. Biophys. Acta
PY  - 2000
SP  - 43
EP  - 53
VL  - 1494
AB  - Transcription initiation of the major promoter (P2) of the Escherichia coli dam gene increases
AB  - with growth rate.  The presence of three partially palindromic motifs, (TTCAGT(N(20))TGAG),
AB  - designated G (growth)-boxes, within the -52 to +31 region of the promoter, may be related to
AB  - growth rate control. Deletion of two of these repeats, downstream of the transcription
AB  - initiation point, result in constitutive high activity of the promoter. The unlinked
AB  - cde-4::miniTn10 insertion also results in several fold higher activity of the dam P2 promoter,
AB  - suggesting that this mutation resulted in the loss of a putative dam P2 repressor. The cde-4
AB  - mutation was mapped to the lipB (lipoic acid) gene, which we show encodes a 24 kDa protein
AB  - initiating at a TTG codon. LipB is a highly conserved protein in animal and plant species,
AB  - other bacteria, Archaea, and yeast. Plasmids expressing the native or hexahistidine-tagged
AB  - LipB complement the phenotype of the cde-4 mutant strain. The level of LipB in vivo was higher
AB  - in exponentially growing cells than those in the stationary phase. Three G-box motifs were
AB  - also found in the lipB region. Models for the regulation of expression of the two genes are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Vaisvila, R.
AU  - Sliesaraviciute, Z.
AU  - Kulakauskas, S.
AU  - Janulaitis, A.
TI  - Cloning of the ppu21IM gene using a in vivo selection method.
JO  - Gene
PY  - 1995
SP  - 55
EP  - 57
VL  - 157
AB  - A genetic system enabling the in vivo selection of genes encoding the DNA-modifying enzymes
AB  - was developed.  A gene library is transformed into a strain harboring the
AB  - restriction-modification (R-M) system which a recognition sequence is a subset of the target
AB  - sequence of the DNA methyltransferase (MTase) to be cloned.  If the residing MTase is
AB  - temperature sensitive, the inability of transformants to grow at 42oC provides a simple and
AB  - convenient procedure for the isolation of new MTase-encoding genes.  The feasibility of this
AB  - procedure has been demonstrated by the isolation of the ppu21IM gene from a Pseudomonas putida
AB  - RFL21 gene library.
ER  -

TY  - JOUR
AU  - Vaisvila, R.
AU  - Vilkaitis, G.
AU  - Janulaitis, A.
TI  - Identification of a gene encoding a DNA invertase-like enzyme adjacent to the PaeR7I restriction-modification system.
JO  - Gene
PY  - 1995
SP  - 81
EP  - 84
VL  - 157
AB  - A gene encoding a DNA invertase-like enzyme was identified adjacent to the PaeR7I
AB  - restriction-modification system (R-M), and was named paeR7IN (N for iNvertase).  Sequence
AB  - analysis revealed that this gene has the same polarity as the PaeR7IRM operon, and would
AB  - encode a polypeptide of 21,506 Da.  An amino-acid sequence similarity of 45-49% was found
AB  - between the deduced protein product and various DNA invertases.
ER  -

TY  - JOUR
AU  - Vaitkevicius, D.
AU  - Naureckiene, S.
AU  - Janulaitis, A.
TI  - Advanced method for obtaining highly purified restriction enzyme preparations.
JO  - Biotekhnologiya
PY  - 1991
SP  - 35
EP  - 41
VL  - 1
AB  - Using Eco130I restrictase isolated from cells of Escherichia coli RFL 130, a
AB  - possibility was investigated for selecting a scheme for restriction enzyme
AB  - purification under static conditions by analyzing the binding of protein to
AB  - various absorbents and evaluating the functional purity of the samples of
AB  - enzyme preparations.  The nature of restrictase and adsorbent interaction under
AB  - static conditions made it possible to define the restrictase's sorption
AB  - behavior in column chromatography and to select chromatography conditions.
AB  - Evaluation of concomitant nonspecific nucleases allowed to specify the
AB  - adsorbents that could be most effective from the point of view of functional
AB  - purification.  A highly effective scheme for Eco130I restrictase purification
AB  - has been developed.  Fractionation of cell-free extracts of E. coli RFL 130 on
AB  - heparin-sepharose, DEAE-cellulose and phosphocellulose yielded an enzyme
AB  - preparation of high functional purity.
ER  -

TY  - JOUR
AU  - Valat, C.
AU  - Goldstone, R.J.
AU  - Hirchaud, E.
AU  - Haenni, M.
AU  - Smith, D.G.
AU  - Madec, J.Y.
TI  - Draft Genome Sequences of Enterohemorrhagic Escherichia coli Encoding Extended-Spectrum Beta-Lactamases.
JO  - Genome Announcements
PY  - 2016
SP  - e01633
EP  - e01615
VL  - 4
AB  - Extended-spectrum beta-lactamases (ESBLs) have rarely been observed among Shiga toxigenic
AB  - Escherichia coli (STEC), and, to our best knowledge, only three
AB  - ESBL-positive isolates of the enterohemorrhagic E. coli (EHEC) subpathotype have
AB  - been reported. Here, we present the first draft genome sequences of two
AB  - ESBL-positive EHEC isolates belonging to serotypes O111:H8 and O151:H16.
ER  -

TY  - JOUR
AU  - Valderrama, K.
AU  - Soto-Davila, M.
AU  - Santander, J.
TI  - Draft Genome Sequence of the Type Strain Aeromonas salmonicida subsp. salmonicida ATCC 33658.
JO  - Genome Announcements
PY  - 2017
SP  - e01064
EP  - e01017
VL  - 5
AB  - Here, we report the draft genome sequence of the type strain Aeromonas salmonicida subsp.
AB  - salmonicida ATCC 33658 isolated from Salmo salar The size of
AB  - the genome is 4,728,143 bp with a G+C content of 58.5%. The A. salmonicida subsp.
AB  - salmonicida ATCC 33658 genome lacks essential virulence genes that were likely
AB  - lost during genomic rearrangements.
ER  -

TY  - JOUR
AU  - Valdes, J.
AU  - Ossandon, F.
AU  - Quatrini, R.
AU  - Dopson, M.
AU  - Holmes, D.S.
TI  - Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the  Evolution of the Acidithiobacillus Genus.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7003
EP  - 7004
VL  - 193
AB  - Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic
AB  - gammaproteobacterium that derives energy from the
AB  - oxidation of sulfur and inorganic sulfur compounds. Here we present the
AB  - draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the
AB  - identification of genes for survival and colonization of extremely acidic
AB  - environments.
ER  -

TY  - JOUR
AU  - Valdes, J.
AU  - Quatrini, R.
AU  - Hallberg, K.
AU  - Dopson, M.
AU  - Valenzuela, P.D.
AU  - Holmes, D.S.
TI  - Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus.
JO  - J. Bacteriol.
PY  - 2009
SP  - 5877
EP  - 5878
VL  - 191
AB  - Acidithiobacillus caldus is an extremely acidophilic, moderately thermophilic,
AB  - chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation
AB  - of sulfur and reduced inorganic sulfur compounds. Here we present the draft
AB  - genome sequence of Acidithiobacillus caldus ATCC 51756 (the type strain of the
AB  - species), which has permitted the prediction of genes for survival in extremely
AB  - acidic environments, including genes for sulfur oxidation and nutrient
AB  - assimilation.
ER  -

TY  - JOUR
AU  - Valdes, N.
AU  - Rivera-Araya, J.
AU  - Bijman, J.
AU  - Escudero, L.
AU  - Demergasso, C.
AU  - Fernandez, S.
AU  - Ferrer, A.
AU  - Chavez, R.
AU  - Levican, G.
TI  - Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat.
JO  - Genome Announcements
PY  - 2014
SP  - e01144
EP  - e01114
VL  - 2
AB  - We report Nitrincola sp. strain A-D6, which was characterized as an arsenic-resistant
AB  - bacterium isolated from the Ascotan Salt Flat in northern
AB  - Chile. The size of the genome is 3,795,776 bp, with a G+C content of 49.96%.
AB  - Genes for the arsenic-resistant Ars system and arsenic oxidation have been
AB  - encoded.
ER  -

TY  - JOUR
AU  - Valdes, N.
AU  - Soto, P.
AU  - Cottet, L.
AU  - Alarcon, P.
AU  - Gonzalez, A.
AU  - Castillo, A.
AU  - Corsini, G.
AU  - Tello, M.
TI  - Draft genome sequence of strain MTR reveals its mechanism of capnophilic behavior.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 110
EP  - 110
VL  - 10
AB  - Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment
AB  - with antimicrobial and antitumor properties. Janthinobacterium lividum
AB  - colonizes the skin of some amphibians and confers protection against fungal
AB  - pathogens. The mechanisms underlying this association are not well understood. In
AB  - order to identify the advantages for the bacterium to colonize amphibian skin we
AB  - sequenced Janthinobacterium lividum strain MTR, a strain isolated from Cajon del
AB  - Maipo, Chile. The strain has capnophilic behavior, with growth favored by high
AB  - concentrations (5 %) of carbon dioxide. Its genome is 6,535,606 bp in size, with
AB  - 5,362 coding sequences and a G + C content of 62.37 %. The presence of genes
AB  - encoding for products that participate in the carbon fixation pathways (dark CAM
AB  - pathways), and the entire set of genes encoding for the enzymes of the glyoxylate
AB  - cycle may explain the capnophilic behavior and allow us to propose that the CO2
AB  - secreted by the skin of amphibians is the signal molecule that guides
AB  - colonization by Janthinobacterium lividum.
ER  -

TY  - JOUR
AU  - Valdezate, S.
AU  - Monzon, S.
AU  - Garrido, N.
AU  - Zaballos, A.
AU  - Medina-Pascual, M.J.
AU  - Azcona-Gutierrez, J.M.
AU  - Vilar, B.
AU  - Cuesta, I.
TI  - First Insight into the Genome Sequences of Two Linezolid-Resistant Nocardia farcinica Strains Isolated from Patients with Cystic Fibrosis.
JO  - Genome Announcements
PY  - 2017
SP  - e01212
EP  - e01217
VL  - 5
AB  - The draft genome sequences of two Nocardia farcinica strains isolated from two patients with
AB  - cystic fibrosis (CF), resistant to trimethoprim/sulfamethoxazole
AB  - and linezolid, are reported here. The estimated genome sizes were 5.8 Mb with a
AB  - 70.63% G+C content. Transposases from Tn916 were detected, but not 23S rRNA
AB  - mutation (G2576T) related to linezolid resistance.
ER  -

TY  - JOUR
AU  - Vale, A.
AU  - Vitor, J.
TI  - Helicobacter pylori genomic DNA methylation status: strain typing.
JO  - Int. J. Med. Microbiol.
PY  - 2003
SP  - 109
EP  - 109
VL  - 293
AB  - The complete genome sequence of two different strains of H. pylori, revealed extreme genetic
AB  - diversity.  It also showed that both strains have an unusually high number of restriction and
AB  - modification systems (RM).  Based on the knowledge that in RM systems the restriction
AB  - endonuclease (ENase) impose high pressure on the expression of the companion methyltransferase
AB  - (MTase) it was hypothesised that genomic DNA methylation status could be used to develop a new
AB  - typing method of H. pylori.  To test this hypothesis 51 strains of H. pylori were studied, 28
AB  - of which were epidemiologically related.  Genomic DNA was isolated and digested with 33
AB  - different ENases.  After reisolation of DNA from seven strains we replicated 3.5% of the ENase
AB  - digests (59/1683) with 100% concordance.  The results were grouped as a data matrix, where "0"
AB  - means presence of unmethylated DNA and "1" presence of methylated DNA.  Dendrograms were
AB  - constructed with UPGMA method and Jaccard coefficient. After statistical cluster analysis
AB  - (NTSYSpc) and correspondence factorial analysis (PSS 11.0) ENases were gradually eliminated
AB  - until a final group of 16 ENases were selected as a tool to type H. pylori: Acil, BssHII,
AB  - BstUI, DdeI, DraI, FauI, HaeIII, Hpy181I, Hpy99I, HpyCH4III, HpyCH4IV, HpyCH4V, MspI, Sau96I,
AB  - ScrFI and TaqI.  The method has high discriminatory power (Simpson index of diversity=0,99,
AB  - strain group frequency nj/N=0.039), has adequate cophenetic correlation coefficient, r=0.782
AB  - and high typability.  That is adequate for typing H. pylori. A high number of MTases were
AB  - expressed in all strains (between 14 and 22) and 9 of which were common (M.ApaI, M.BseRI,
AB  - M.DpnI, M.EagI, M.HhaI, M.HinT1I, M.NaeI, M.NgoMIV and M.NIaIII).
ER  -

TY  - JOUR
AU  - Vale, F.F.
AU  - Encarnacao, P.
AU  - Vitor, J.M.B.
TI  - A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case.
JO  - Bioinformatics
PY  - 2008
SP  - 383
EP  - 388
VL  - 24
AB  - Motivation: The genomic methylation analysis is useful to type bacteria that have a high
AB  - number of expressed type II methyltransferases.
AB  - Methyltransferases are usually committed to Restriction and
AB  - Modification (R-M) systems, in which the restriction endonuclease
AB  - imposes high pressure on the expression of the cognate
AB  - methyltransferase that hinder R-M system loss. Conventional cluster
AB  - methods do not reflect this tendency. An algorithm was developed for
AB  - dendrogram construction reflecting the propensity for conservation of
AB  - R-M Type II systems.
AB  - Results: The new algorithm was applied to 52 Helicobacter pylori
AB  - strains from different geographical regions and compared with
AB  - conventional clustering methods. The algorithm works by first grouping
AB  - strains that share a common minimum set of R-M systems and gradually
AB  - adds strains according to the number of the R-M systems acquired.
AB  - Dendrograms revealed a cluster of African strains, which suggest that
AB  - R-M systems are present in H.pylori genome since its human host
AB  - migrates from Africa.
ER  -

TY  - JOUR
AU  - Vale, F.F.
AU  - Megraud, F.
AU  - Vitor, J.M.
TI  - Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration.
JO  - BMC Microbiol.
PY  - 2009
SP  - 193
EP  - 193
VL  - 9
AB  - ABSTRACT: BACKGROUND: Helicobacter pylori colonizes the human stomach and is associated with
AB  - gastritis, peptic ulcer, and gastric cancer. This
AB  - ubiquitous association between H. pylori and humans is thought to be
AB  - present since the origin of modern humans. The H. pylori genome encodes
AB  - for an exceptional number of restriction and modifications (R-M) systems.
AB  - To evaluate if R-M systems are an adequate tool to determine the
AB  - geographic distribution of H. pylori strains, we typed 221 strains from
AB  - Africa, America, Asia, and Europe, and evaluated the expression of 29
AB  - methyltransferases. RESULTS: Independence tests and logistic regression
AB  - models revealed that 10 R-M systems correlate with geographical
AB  - localization. The distribution pattern of these methyltransferases may
AB  - have been originated by co-divergence of regional H. pylori after its
AB  - human host migrated out of Africa. The expression of specific
AB  - methyltransferases in the H. pylori population may also reflect the
AB  - genetic and cultural background of its human host. Methyltransferases
AB  - common to all strains, M.HhaI and M.NaeI, are likely conserved in H.
AB  - pylori, and may have been present in the bacteria genome since the human
AB  - diaspora out of Africa. CONCLUSIONS: This study indicates that
AB  - methyltransferases are useful geomarkers, which allow discrimination of
AB  - bacterial populations, and that can be added to our tools to investigate
AB  - human migrations.
ER  -

TY  - JOUR
AU  - Vale, F.F.
AU  - Vitor, J.M.
TI  - Genomic Methylation: a Tool for Typing Helicobacter pylori Isolates.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 4243
EP  - 4249
VL  - 73
AB  - The genome sequences of three Helicobacter pylori strains revealed an abundant number of
AB  - putative restriction and modification (R-M) systems
AB  - within a small genome (1.60 to 1.67 Mb). Each R-M system includes an
AB  - endonuclease that cleaves a specific DNA sequence and a DNA
AB  - methyltransferase that methylates either adenosine or cytosine within the
AB  - same DNA sequence. These are believed to be a defense mechanism,
AB  - protecting bacteria from foreign DNA. They have been classified as selfish
AB  - genetic elements; in some instances it has been shown that they are not
AB  - easily lost from their host cell. Possibly because of this phenomenon, the
AB  - H. pylori genome is very rich in R-M systems, with considerable variation
AB  - in potential recognition sequences. For this reason the protective aspect
AB  - of the methyltransferase gene has been proposed as a tool for typing H.
AB  - pylori isolates. We studied the expression of H. pylori methyltransferases
AB  - by digesting the genomic DNAs of 50 strains with 31 restriction
AB  - endonucleases. We conclude that methyltransferase diversity is
AB  - sufficiently high to enable the use of the genomic methylation status as a
AB  - typing tool. The stability of methyltransferase expression was assessed by
AB  - comparing the methylation status of genomic DNAs from strains that were
AB  - isolated either from the same patient at different times or from different
AB  - stomach locations (antrum and corpus). We found a group of five
AB  - methyltransferases common to all tested strains. These five may be
AB  - characteristic of the genetic pool analyzed, and their biological role may
AB  - be important in the host/bacterium interaction.
ER  -

TY  - JOUR
AU  - Vale, F.F.
AU  - Vitor, J.M.B.
TI  - Genomic methylation status for discrimination among Helicobacter species: A bioinformatics approach.
JO  - J. Proteomics Bioinformatics
PY  - 2008
SP  - 258
EP  - 266
VL  - 1
AB  - The genus Helicobacter comprises several species of both gastric and enterohepatic intestinal
AB  - bacteria. H. pylori, the type species of the genus, is associated with gastritis, peptic ulcer
AB  - and gastric cancer in humans. H. pylori genome has a high number of restriction and
AB  - modification (R-M) systems and their diversity is useful for strain typing. To analyse if such
AB  - a high number of expressed methyltransferases is a characteristic of the genus Helicobacter,
AB  - the genomic methylation of five non-pylori Helicobacter spp. (H. canadensis, H. canis, H.
AB  - felis, H.mustelae and H. pullorum) was determined. The results revealed that the number of R-M
AB  - systems among nonpylori Helicobacter spp. is smaller than those observed among a group of 221
AB  - H. pylori strains (p<0,001), but is greater than those observed for the mean of all bacteria
AB  - sequenced genomes (p=0,005). 16S ribosomal RNA analysis of H. pylori sequenced strains and
AB  - five non-pylori Helicobacter spp. clearly isolate H. pylori species.  Surprisingly, the
AB  - analysis of the genomic methylation status by MCRM algorithm performs similarly. This suggests
AB  - that R-M systems do not appear to be spread in a miscellaneous manner, once even that these
AB  - genes may be subjected to acquisition and loss; their expression still allows discriminating
AB  - among Helicobacter spp.
ER  -

TY  - JOUR
AU  - Valenzuela, C.
AU  - Ugalde, J.A.
AU  - Mora, G.C.
AU  - Alvarez, S.
AU  - Contreras, I.
AU  - Santiviago, C.A.
TI  - Draft Genome Sequence of Salmonella enterica Serovar Typhi Strain STH2370.
JO  - Genome Announcements
PY  - 2014
SP  - e00104
EP  - e00114
VL  - 2
AB  - We report the draft genome sequence of Salmonella enterica serovar Typhi strain STH2370,
AB  - isolated from a typhoid fever patient in Santiago, Chile. This clinical
AB  - isolate has been used as the reference wild-type strain in numerous studies
AB  - conducted in our laboratories during the last 15 years.
ER  -

TY  - JOUR
AU  - Valera, M.J.
AU  - Poehlein, A.
AU  - Torija, M.J.
AU  - Haack, F.S.
AU  - Daniel, R.
AU  - Streit, W.R.
AU  - Mateo, E.
AU  - Mas, A.
TI  - Draft Genome Sequence of Komagataeibacter europaeus CECT 8546, a Cellulose-Producing Strain of Vinegar Elaborated by the Traditional Method.
JO  - Genome Announcements
PY  - 2015
SP  - e01231
EP  - e01215
VL  - 3
AB  - The present article reports the draft genome sequence of the strain Komagataeibacter europaeus
AB  - CECT 8546, an acetic acid bacterium characterized by its ability to overproduce cellulose.
AB  - This species is highly resistant to acetic  acid and commonly found during vinegar
AB  - elaboration.
ER  -

TY  - JOUR
AU  - Valeriani, F.
AU  - Biagini, T.
AU  - Giampaoli, S.
AU  - Crognale, S.
AU  - Santoni, D.
AU  - Romano, S.V.
TI  - Draft Genome Sequence of Tepidimonas taiwanensis Strain VT154-175.
JO  - Genome Announcements
PY  - 2016
SP  - e00942
EP  - e00916
VL  - 4
AB  - The slightly thermophilic bacterium Tepidimonas taiwanensis strain VT154-175 has  been
AB  - isolated from a hot spring in the area of Viterbo, Italy. The whole draft
AB  - genome of 2.9 Mb obtained by paired-end next-generation sequencing and divided
AB  - into 60 scaffolds is presented.
ER  -

TY  - JOUR
AU  - Valinluck, B.
TI  - Characterization of restriction-modification systems in Klebsiella pneumoniae.
JO  - Diss. Abstr.
PY  - 1992
SP  - 2701B
EP  - 2701B
VL  - 53
AB  - Two restriction-modification (R-M) systems, KpnAI and KpnBI, found in Klebsiella pneumoniae
AB  - strains M5a1 and GM236, respectively, have been studied and confirmed to be different from
AB  - other R-M systems reported in K. pneumoniae. Mutant studies suggest that the KpnAI and KpnBI
AB  - systems may belong to either a type I or type III system, since approximately equal numbers of
AB  - r-m+ and r-m- mutants were obtained. However, a DNA hybridization study using representative
AB  - type I and type III probes from E. coli and S. typhimurium failed to show homologies to either
AB  - KpnAI or KpnBI. The restriction endonuclease KpnBI was found to be temperature-sensitive with
AB  - maximum restriction activity at 30oC and no restriction activity at 42oC. Further, the
AB  - activity of endonuclease KpnBI was found to be reduced to almost zero level by growing the
AB  - bacteria in the presence of 10% glycerol. Although the mechanism is not known, this is the
AB  - first time such a phenomenon has been observed in any of the reported R-M systems. These
AB  - studies also compared the efficiency of transformation in K. pneumoniae of three plasmid
AB  - transformation methods; CaCl2 heat-shock; freezing and thawing in the presence of CaCl2; and
AB  - electroporation. Electroporation was shown to be the most efficient method. Transformation
AB  - efficiency in both the r+KpnAI and r+KpnBI strains was 20- to 100-fold less than the
AB  - transformation efficiency of the r- strains, depending on plasmid size. Four different
AB  - approaches have been used to clone the hsd genes of the KpnBI system. Two clones were
AB  - obtained; these were named pKpnB1 and pKpnB2. The pKpnB1 and pKpnB2 clones were found to
AB  - complement the restriction activity of an r- KpnBIm+KpnBI K. pneumoniae mutant and were also
AB  - found to complement both the restriction and modification activities of an r-KpnBIm-KpnBI K.
AB  - pneumoniae mutant. A quick subcloning method which involves making subclones from a plasmid
AB  - clone in a single step was also developed. A preliminary analysis, based on complementation
AB  - studies, of the gene structure suggested that the KpnBI system may consist of three structural
AB  - genes, a characteristic of the type I R-M system.
ER  -

TY  - JOUR
AU  - Valinluck, B.
AU  - Lee, N.S.
AU  - Ryu, J.
TI  - A new restriction-modification system, KpnBI, recognized in Klebsiella pneumoniae.
JO  - Gene
PY  - 1995
SP  - 59
EP  - 62
VL  - 167
AB  - A unique DNA restriction-modification (R-M) system has been identified in the GM236 strain of
AB  - Klebsiella pneumoniae using the newly isolated phage, SBS.  The system was designated KpnBI.
AB  - The gene (hsdRKpnBI) complementing the restriction activity of the KpnBI system was cloned in
AB  - pBR322.  The nucleotide sequence of the cloned DNA revealed one open reading frame (ORF) of
AB  - 3035 bp.  Analysis of the deduced amino-acid sequence shows seven helicase motifs which are
AB  - common to the restriction (R) subunit of both type-I and type-III R-M systems.  Computer
AB  - analysis (Dendrogram) of the R polypeptide of KpnBI suggests a closer relationship to
AB  - EcoR124/3I, a member of type-IC family, than to other representative type-I and type-III
AB  - systems.
ER  -

TY  - JOUR
AU  - Valinluck, B.
AU  - Reyno, M.
AU  - Ryu, J.
TI  - Two new restriction-modification systems, KpnA and KpnB, in Klebsiella pneumoniae.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1989
SP  - 180
EP  - 180
VL  - 89
AB  - Strains of K. pneumoniae, M5a1 and GM236, each possess a unique restriction-modification (R-M)
AB  - system. These two systems differ from KpnI, a type II system reported previously in K.
AB  - pneumoniae, since the KpnI endonuclease degrades chromosomal DNA from both M5a1 and GM236. No
AB  - plasmids or type II restriction endonuclease activity have so far been identified from these
AB  - two strains. Mutant analysis suggests that these two Klebsiella R-M systems may be classified
AB  - as type I since almost equal numbers of r- m+ and r- m- mutants were obtained from a single
AB  - mutagenic treatment. DNA hybridization revealed a weak but significant homology between an
AB  - hsdSB probe derived from S. typhimurium and GM236 chromosome. No homology was observed between
AB  - an hsdA probe derived from E. coli 15T and chromosomal DNA from either of the two Klebsiella
AB  - strains. A 7.2 kb EcoRI fragment of GM236 identified by its hybridization to the S.
AB  - typhimurium hsdSB probe was cloned in pBluescript (Stratagene). Only one PvuII fragment (1.7
AB  - kb) derived from it showed hybridization to hsdM region of hsdSB and hsdK (from E. coli K12)
AB  - clones. From the above observations, we concluded that M5a1 and GM236 have new R-M systems
AB  - which we designated provisionally KpnA and KpnB, respectively.
ER  -

TY  - JOUR
AU  - Valinluck, V.
AU  - Sowers, L.C.
TI  - Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1.
JO  - Cancer Res.
PY  - 2007
SP  - 946
EP  - 950
VL  - 67
AB  - Alterations in cytosine methylation patterns are usually observed in human tumors. The
AB  - consequences of altered cytosine methylation patterns
AB  - include both inappropriate activation of transforming genes and
AB  - silencing of tumor suppressor genes. Despite the biological effect of
AB  - methylation changes, little is known about how such changes are caused.
AB  - The heritability of cytosine methylation patterns from parent to
AB  - progeny cells is attributed to the fidelity of the
AB  - methylation-sensitive human maintenance methyltransferase DNMT1, which
AB  - methylates with high specificity the unmethylated strand of a
AB  - hemimethylated CpG sequence following DNA replication. We have been
AB  - studying DNA damage that might alter the specificity of DNMTl, either
AB  - inhibiting the methylation of hemimethylated sites or triggering the
AB  - inappropriate methylation of previously unmethylated sites. Here, we
AB  - show that known forms of endogenous DNA damage can cause either
AB  - hypermethylation or hypomethylation. Inflammation-induced 5-halogenated
AB  - cytosine damage products, including 5-chlorocytosine, mimic
AB  - 5-methylcytosine and induce inappropriate DNMTl methylation within a
AB  - CpG sequence. In contrast, oxidation damage of the methyl group of
AB  - 5-methylcytosine, with the formation of 5-hydroxymethylcytosine,
AB  - prevents DNMTI methylation of the target cytosine. We propose that
AB  - reduced DNMTI selectivity resulting from DNA damage could cause
AB  - heritable changes in cytosine methylation patterns, resulting in human
AB  - tumor formation. These data may provide a mechanistic link for the
AB  - associations documented between inflammation and cancer.
ER  -

TY  - JOUR
AU  - Valinluck, V.
AU  - Wu, W.
AU  - Liu, P.F.
AU  - Neidigh, J.W.
AU  - Sowers, L.C.
TI  - Impact of cytosine 5-halogens on the interaction of DNA with restriction endonucleases and methyltransferase.
JO  - Chem. Res. Toxicol.
PY  - 2006
SP  - 556
EP  - 562
VL  - 19
AB  - Growing evidence from both prokaryotes and eukaryotes indicates that pyrimidine 5-methyl
AB  - groups can have profound biological consequences
AB  - that are mediated by the affinity of DNA-protein interactions. The
AB  - presence of the 5-methyl group could potentially create a steric block
AB  - preventing the binding of some proteins whereas the affinity of many
AB  - other proteins is substantially increased by pyrimidine methylation. In
AB  - this paper, we have constructed a series of oligonucleotides containing
AB  - cytosine and a series of 5-substituted cytosine analogues including all
AB  - halogens. This set of oligonucleotides has been used to probe the
AB  - relationship between the size of the substituent and its capacity to
AB  - modulate cleavage by the methylation-sensitive restriction
AB  - endonucleases MspI and HpaII. Additionally, we have examined the impact
AB  - of the halogen substitution on the corresponding bacterial
AB  - methyltransferase (M.HpaII). We observed that MspI cleavage is only
AB  - subtly affected by substituted cytosine analogues at the inner position
AB  - of the CCGG recognition site. In contrast, HpaII cleaves
AB  - cytosine-containing oligonucleotides completely whereas
AB  - 5-fluorocytosine-containing oligonucleotides are cleaved at a reduced
AB  - rate. The presence of the larger halogens Cl, Br, or I as well as a
AB  - methyl group completely prevents cleavage by HpaII. These data suggest
AB  - that the steric wall is encountered by HpaII slightly beyond the
AB  - fluorine substituent, at about 2.65 angstrom from the pyrimidine
AB  - C5-position. It is known that 5-fluorocytosine in an oligonucleotide
AB  - can form a covalent irreversible suicide complex with either
AB  - prokaryotic or eukaryotic methyltransferases. Kinetic data reported
AB  - here suggest that the 5-fluorocytosine-containing oligonucleotide can
AB  - also inhibit M.HpaII by formation of a reversible, noncovalent complex.
AB  - Our results indicate that although a 5-Cl substituent has electronic
AB  - properties similar to 5-F, 5-chlorocytosine duplexes neither form a
AB  - complex with M.HpaII nor inhibit enzymatic methylation. Emerging data
AB  - suggest that halogenation of cytosine can occur in DNA in vivo from
AB  - inflammation-mediated reactive molecules. The results reported here
AB  - suggest that the inadvertent halogenation of cytosine residues in DNA
AB  - could alter the affinity of sequence-specific DNA-binding proteins.
ER  -

TY  - JOUR
AU  - Vallenet, D. et al.
TI  - Comparative analysis of Acinetobacters: three genomes for three lifestyles.
JO  - PLoS ONE
PY  - 2008
SP  - e1805
EP  - e1805
VL  - 3
AB  - Acinetobacter baumannii is the source of numerous nosocomial infections in humans and
AB  - therefore deserves close attention as multidrug or even pandrug
AB  - resistant strains are increasingly being identified worldwide. Here we
AB  - report the comparison of two newly sequenced genomes of A. baumannii. The
AB  - human isolate A. baumannii AYE is multidrug resistant whereas strain SDF,
AB  - which was isolated from body lice, is antibiotic susceptible. As reference
AB  - for comparison in this analysis, the genome of the soil-living bacterium
AB  - A. baylyi strain ADP1 was used. The most interesting dissimilarities we
AB  - observed were that i) whereas strain AYE and A. baylyi genomes harbored
AB  - very few Insertion Sequence elements which could promote expression of
AB  - downstream genes, strain SDF sequence contains several hundred of them
AB  - that have played a crucial role in its genome reduction (gene disruptions
AB  - and simple DNA loss); ii) strain SDF has low catabolic capacities compared
AB  - to strain AYE. Interestingly, the latter has even higher catabolic
AB  - capacities than A. baylyi which has already been reported as a very
AB  - nutritionally versatile organism. This metabolic performance could explain
AB  - the persistence of A. baumannii nosocomial strains in environments where
AB  - nutrients are scarce; iii) several processes known to play a key role
AB  - during host infection (biofilm formation, iron uptake, quorum sensing,
AB  - virulence factors) were either different or absent, the best example of
AB  - which is iron uptake. Indeed, strain AYE and A. baylyi use
AB  - siderophore-based systems to scavenge iron from the environment whereas
AB  - strain SDF uses an alternate system similar to the Haem Acquisition System
AB  - (HAS). Taken together, all these observations suggest that the genome
AB  - contents of the 3 Acinetobacters compared are partly shaped by life in
AB  - distinct ecological niches: human (and more largely hospital environment),
AB  - louse, soil.
ER  -

TY  - JOUR
AU  - Vallone, P.M.
AU  - Benight, A.S.
TI  - Thermodynamic, spectroscopic, and equilibrium binding studies of DNA sequence context effects in four 40 base pair deoxyoligonucleotides.
JO  - Biochemistry
PY  - 2000
SP  - 7835
EP  - 7846
VL  - 39
AB  - Effects of different end sequences on melting, circular dichroism spectra (CD), and enzyme
AB  - binding properties were investigated for four 40 base pair, non-self-complementary duplex DNA
AB  - oligomers. The center sequences of these oligoduplexes have either of two 22 base pair modules
AB  - flanked on both sides by sequences differing in AT content. Temperature-induced melting
AB  - transitions monitored by differential scanning calorimetry (DSC) and ultraviolet absorbance
AB  - were measured for the six duplexes in buffered 115 mM Na(+) solutions. Values of the melting
AB  - transition enthalpy, DeltaH(cal), and entropy, DeltaS(cal), were obtained directly from DSC
AB  - experiments. Melting transition parameters, DeltaH(vH) and DeltaS(vH), were also estimated
AB  - from a van't Hoff analysis of optical melting curves collected as a function of DNA
AB  - concentration, assuming that the melting transition is two-state. Melting free energies (20
AB  - degrees C) evaluated from DSC melting experiments on the four duplex DNAs ranged from -52.2 to
AB  - -77.5 kcal/mol. Free energies based on the van't Hoff analysis were -37.9 to -58.8 kcal/mol.
AB  - Although the values are different, trends in the melting free energies of the four duplex DNAs
AB  - as a function of sequence were identical in both DSC and optical analyses. Subject to several
AB  - assumptions, values for the initiation free energy were estimated for each duplex, defined as
AB  - DeltaG(int) = DeltaG(cal) - DeltaG(pred), where DeltaG(cal) is the experimental free energy at
AB  - 20 degrees C determined from the experimentally measured values of the transition enthalpy,
AB  - DeltaH(cal), and entropy, DeltaS(cal). The predicted free energy of the sequence,
AB  - DeltaG(pred)(20 degrees C), is obtained using published nearest-neighbor sequence stability
AB  - values. For three of the four duplexes, values of DeltaG(int) are essentially nil. In
AB  - contrast, the duplex with 81.8% GC has a considerably higher estimate of DeltaG(int) = 7.1
AB  - kcal/mol. The CD spectra for the six duplexes collected over the wavelength range from 200 to
AB  - 320 nm are also sequence-dependent. Factor analysis of the CD spectra by singular value
AB  - decomposition revealed that the experimental CD spectra could be reconstructed from linear
AB  - combinations of two minor and one major subspectra. Changes in the coefficients of the major
AB  - subspectrum for different sequences reflect incremental sequence-dependent variations of the
AB  - CD spectra. Equilibrium binding by BamHI restriction endonuclease to the 40 base pair DNAs
AB  - whose central eight base pairs contain the recognition sequence for BamHI restriction enzyme
AB  - bounded by A.T base pairs, 5'-A-GGATCC-A-3' was investigated. Binding assays were performed
AB  - by titering BamHI against a constant concentration of each of the duplex DNA substrates, in
AB  - the absence of Mg(2+), followed by analysis by gel retardation. Under the conditions employed,
AB  - the enzyme binds but does not cleave the DNAs. Results of the assays revealed two binding
AB  - modes with retarded gel mobilities. Binding isotherms for the fraction of bound DNA species
AB  - versus enzyme concentration for each binding mode were constructed and analyzed with a simple
AB  - two-step equilibrium binding model. This analysis provided semiquantitative estimates on the
AB  - equilibrium binding constants for BamHI to the four DNAs. Values obtained for the binding
AB  - constants varied only 7-fold and ranged from 6 x 10^-8 to 42 x 10^-8 M, with binding
AB  - free energies from -8.6 to -9.7 (+/- 0.2) kcal/mol depending on the sequence that flanks the
AB  - enzyme binding site. Unlike what was found earlier in binding studies of the 22 base pair
AB  - duplexes that constitute the core modules of the present 40-mers [Riccelli, P. V., Vallone, P.
AB  - M., Kashin, I., Faldasz, B. D., Lane, M. J., and Benight, A. S. (1999) Biochemistry 38,
AB  - 11197-11208], no obvious relationship between binding and stability was found for these longer
AB  - DNAs. Apparently, effects of flanking sequence stability on restriction enzyme binding may
AB  - only be measurable in very short duplex deoxyoligonucleotides.
ER  -

TY  - JOUR
AU  - Valot, B.
AU  - Rohmer, L.
AU  - Jacobs, M.A.
AU  - Miller, S.I.
AU  - Bertrand, X.
AU  - Hocquet, D.
TI  - Comparative Genomic Analysis of Two Multidrug-Resistant Clinical Isolates of ST395 Epidemic Strain of Pseudomonas aeruginosa Obtained 12 Years Apart.
JO  - Genome Announcements
PY  - 2014
SP  - e00515
EP  - e00514
VL  - 2
AB  - Pseudomonas aeruginosa can cause large and prolonged outbreaks in hospitals. We have sequenced
AB  - and annotated the genomes of two multidrug-resistant P. aeruginosa
AB  - isolates from the same strain obtained 12 years apart from different patients.
AB  - Genomic analysis provided insight on the genes acquired and lost by P. aeruginosa
AB  - during its spread.
ER  -

TY  - JOUR
AU  - Valseth, K.
AU  - Nesbo, C.L.
AU  - Easterday, W.R.
AU  - Turner, W.C.
AU  - Olsen, J.S.
AU  - Stenseth, N.C.
AU  - Haverkamp, T.H.
TI  - Draft Genome Sequences of Two Bacillus anthracis Strains from Etosha National Park, Namibia.
JO  - Genome Announcements
PY  - 2016
SP  - e00861
EP  - e00816
VL  - 4
AB  - Bacillus anthracis strains K1 and K2 were isolated from two plains zebra anthrax  carcasses in
AB  - Etosha National Park, Namibia. These are draft genomes obtained by
AB  - Illumina MiSeq sequencing of isolates collected from culture of blood-soaked soil
AB  - from each carcass.
ER  -

TY  - JOUR
AU  - Valton, J.
AU  - Daboussi, F.
AU  - Leduc, S.
AU  - Molina, R.
AU  - Redondo, P.
AU  - Macmaster, R.
AU  - Montoya, G.
AU  - Duchateau, P.
TI  - 5 '-Cytosine-Phosphoguanine (CpG) Methylation Impacts the Activity of Natural and Engineered Meganucleases.
JO  - J. Biol. Chem.
PY  - 2012
SP  - 30139
EP  - 30150
VL  - 287
AB  - In this study, we asked whether CpG methylation could influence the DNA binding affinity and
AB  - activity of meganucleases used for genome
AB  - engineering applications. A combination of biochemical and structural
AB  - approaches enabled us to demonstrate that CpG methylation decreases
AB  - I-CreI DNA binding affinity and inhibits its endonuclease activity in
AB  - vitro. This inhibition depends on the position of the methylated
AB  - cytosine within the DNA target and was almost total when it is located
AB  - inside the central tetrabase. Crystal structures of I-CreI bound to
AB  - methylated cognate target DNA suggested a molecular basis for such
AB  - inhibition, although the precise mechanism still has to be specified.
AB  - Finally, we demonstrated that the efficacy of engineered meganucleases
AB  - can be diminished by CpG methylation of the targeted endogenous site,
AB  - and we proposed a rational design of the meganuclease DNA binding
AB  - domain to alleviate such an effect. We conclude that although activity
AB  - and sequence specificity of engineered meganucleases are crucial
AB  - parameters, target DNA epigenetic modifications need to be considered
AB  - for successful gene editions.
ER  -

TY  - JOUR
AU  - van Aalten, D.M.F.
AU  - Erlanson, D.A.
AU  - Verdine, G.L.
AU  - Joshua-Tor, L.
TI  - A structural snapshot of base-pair opening in DNA.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 11809
EP  - 11814
VL  - 96
AB  - The response of double-helical DNA to torsional stress may be a driving force for many
AB  - processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide
AB  - d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine
AB  - bases depicts how the duplex can accommodate such torsional stress. We have captured in the
AB  - same crystal two rather different conformational states. One duplex contains a strained
AB  - crosslink that is stabilized by calcium ion binding in the major groove, directly opposite the
AB  - crosslink. For the other duplex, the strain in the crosslink is relieved through partial
AB  - rupture of a base pair and partial extrusion of a cytosine accompanied by helix bending. The
AB  - sequence used is the target sequence for the HaeIII methylase, and this partially flipped
AB  - cytosine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics
AB  - simulations of these structures show an increased mobility for the partially flipped-out
AB  - cytosine.
ER  -

TY  - JOUR
AU  - van Aelst, K.
AU  - Saikrishnan, K.
AU  - Szczelkun, M.D.
TI  - Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 10430
EP  - 10443
VL  - 43
AB  - The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising
AB  - an Mrr-family nuclease, a superfamily 2 helicase-like ATPase,
AB  - a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon
AB  - recognising an unmodified DNA target site, the helicase-like domain hydrolyzes
AB  - ATP to cause site release (remodeling activity) and to then drive downstream
AB  - translocation consuming 1-2 ATP per base pair (motor activity). On an invading
AB  - foreign DNA, double-strand breaks are introduced at random wherever two
AB  - translocating enzymes form a so-called collision complex following long-range
AB  - communication between a pair of target sites in inverted (head-to-head) repeat.
AB  - Paradoxically, structural models for collision suggest that the nuclease domains
AB  - are too far apart (>30 bp) to dimerise and produce a double-strand DNA break
AB  - using just two strand-cleavage events. Here, we examined the organisation of
AB  - different collision complexes and how these lead to nuclease activation. We
AB  - mapped DNA cleavage when a translocating enzyme collides with a static enzyme
AB  - bound to its site. By following communication between sites in both head-to-head
AB  - and head-to-tail orientations, we could show that motor activity leads to
AB  - activation of the nuclease domains via distant interactions of the helicase or
AB  - MTase-TRD. Direct nuclease dimerization is not required. To help explain the
AB  - observed cleavage patterns, we also used exonuclease footprinting to demonstrate
AB  - that individual Type ISP domains can swing off the DNA. This study lends further
AB  - support to a model where DNA breaks are generated by multiple random nicks due to
AB  - mobility of a collision complex with an overall DNA-binding footprint of
AB  - approximately 30 bp.
ER  -

TY  - JOUR
AU  - van Aelst, K.
AU  - Sisakova, E.
AU  - Szczelkun, M.D.
TI  - DNA cleavage by Type ISP Restriction-Modification enzymes is initially targeted to the 3'-5' strand.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 1081
EP  - 1090
VL  - 41
AB  - The mechanism by which a double-stranded DNA break is produced following collision of two
AB  - translocating Type I Restriction-Modification enzymes is not
AB  - fully understood. Here, we demonstrate that the related Type ISP
AB  - Restriction-Modification enzymes LlaGI and LlaBIII can cooperate to cleave DNA
AB  - following convergent translocation and collision. When one of these enzymes is a
AB  - mutant protein that lacks endonuclease activity, DNA cleavage of the 3'-5' strand
AB  - relative to the wild-type enzyme still occurs, with the same kinetics and at the
AB  - same collision loci as for a reaction between two wild-type enzymes. The DNA
AB  - nicking activity of the wild-type enzyme is still activated by a protein variant
AB  - entirely lacking the Mrr nuclease domain and by a helicase mutant that cannot
AB  - translocate. However, the helicase mutant cannot cleave the DNA despite the
AB  - presence of an intact nuclease domain. Cleavage by the wild-type enzyme is not
AB  - activated by unrelated protein roadblocks. We suggest that the nuclease activity
AB  - of the Type ISP enzymes is activated following collision with another Type ISP
AB  - enzyme and requires adenosine triphosphate binding/hydrolysis but, surprisingly,
AB  - does not require interaction between the nuclease domains. Following the initial
AB  - rapid endonuclease activity, additional DNA cleavage events then occur more
AB  - slowly, leading to further processing of the initial double-stranded DNA break.
ER  -

TY  - JOUR
AU  - van Aelst, K.
AU  - Toth, J.
AU  - Ramanathan, S.P.
AU  - Schwarz, F.W.
AU  - Seidel, R.
AU  - Szczelkun, M.D.
TI  - Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 9123
EP  - 9128
VL  - 107
AB  - Cleavage of viral DNA by the bacterial Type III Restriction-Modification enzymes requires the
AB  - ATP-dependent long-range communication between a
AB  - distant pair of DNA recognition sequences. The classical view is that Type
AB  - III endonuclease activity is only activated by a pair of asymmetric sites
AB  - in a specific head-to-head inverted repeat. Based on this assumption and
AB  - due to the presence of helicase domains in Type III enzymes, various
AB  - motor-driven DNA translocation models for communication have been
AB  - suggested. Using both single-molecule and ensemble assays we demonstrate
AB  - that Type III enzymes can also cleave DNA with sites in tail-to-tail
AB  - repeat with high efficiency. The ability to distinguish both inverted
AB  - repeat substrates from direct repeat substrates in a manner independent of
AB  - DNA topology or accessory proteins can only be reconciled with an
AB  - alternative sliding mode of communication.
ER  -

TY  - JOUR
AU  - van Belkum, A.
AU  - Jacobs, B.
AU  - van Beek, E.
AU  - Louwen, R.
AU  - van Rijs, W.
AU  - Debruyne, L.
AU  - Gilbert, M.
AU  - Li, J.
AU  - Jansz, A.
AU  - Megraud, F.
AU  - Endtz, H.
TI  - Can Campylobacter coli induce Guillain-Barre syndrome?
JO  - Eur. J. Clin. Microbiol. Infect. Dis.
PY  - 2009
SP  - 557
EP  - 560
VL  - 28
AB  - Campylobacter jejuni enteritis is the most frequently identified infection preceding the
AB  - Guillain-Barre syndrome (GBS) and neural damage is thought to be induced through molecular
AB  - mimicry between C. jejuni lipo-oligosaccharide (LOS) and human gangliosides [1]. It has been
AB  - questioned whether or not other Campylobacter species, including C. curvus, C. upsaliensis and
AB  - C. coli, could be similarly involved [2-4]. This is relevant because it would imply that
AB  - bacterial factors considered important in the aetiology of GBS crossed species barriers. Two
AB  - prior reports have appeared where C. coli was putatively associated with a case of GBS.
ER  -

TY  - JOUR
AU  - van Belkum, M.J.
AU  - Lohans, C.T.
AU  - Vederas, J.C.
TI  - Draft Genome Sequences of Paenibacillus polymyxa NRRL B-30509 and Paenibacillus terrae NRRL B-30644, Strains from a Poultry Environment That Produce Tridecaptin   A and Paenicidins.
JO  - Genome Announcements
PY  - 2015
SP  - e00372
EP  - e00315
VL  - 3
AB  - Paenibacillus polymyxa NRRL B-30509 and Paenibacillus terrae NRRL B-30644 produce tridecaptin
AB  - A that is inhibitory to Campylobacter jejuni, as well as lantibiotics
AB  - in the paenicidin family. Here, we report the draft genome sequences of P.
AB  - polymyxa NRRL B-30509 and P. terrae NRRL B-30644 that contain gene clusters for
AB  - various nonribosomal lipopeptides.
ER  -

TY  - JOUR
AU  - van Bemmel, D.M.
AU  - Brank, A.S.
AU  - Eritja, R.
AU  - Marquez, V.E.
AU  - Christman, J.K.
TI  - DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site.
JO  - Biochem. Pharmacol.
PY  - 2009
SP  - 633
EP  - 641
VL  - 78
AB  - Aberrant cytosine methylation in promoter regions leads to gene silencing associated with
AB  - cancer progression. A number of DNA
AB  - methyltransferase inhibitors are known to reactivate silenced genes:
AB  - including 5-azacytidine and 2-(1H)-pyrimidinone riboside (zebularine).
AB  - Zebularine is a more stable, less cytotoxic inhibitor compared to
AB  - 5-azacytidine. To determine the mechanistic basis for this difference,
AB  - we carried out a detailed comparisons of the interaction between
AB  - purified DNA methyltransferases and oligodeoxyribonucleotides (ODNs)
AB  - containing either 5-azacytosine or 2-(1H)-pyrimidinone in place of the
AB  - cytosine targeted for methylation. When incorporated into small ODNs,
AB  - the rate of C5 DNA methyltransferase inhibition by both nucleosides is
AB  - essentially identical. However, the stability and reversibility of the
AB  - enzyme complex in the absence and presence of cofactor differs.
AB  - 5-Azacytosine ODNs form complexes with C5 DNA methyltransferases that
AB  - are irreversible when the 5-azacytosine ring is intact. ODNs containing
AB  - 2-(1H)-pyrimidinone at the enzymatic target site are competitive
AB  - inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases.
AB  - We determined that the ternary complexes between the enzymes,
AB  - 2-(1H)-pyrimidinone inhibitor, and the cofactor S-adenosyl methionine
AB  - are maintained through the formation of a reversible covalent
AB  - interaction. The differing stability and reversibility of the covalent
AB  - bonds may partially account for the observed differences in
AB  - cytotoxicity between zebularine and 5-azacytidine inhibitors.
ER  -

TY  - JOUR
AU  - Van Bemmel, D.M.
AU  - Marquez, V.E.
AU  - Christman, J.K.
TI  - Characterization of the cytidine analog zebularine as an inhibitor of mammalian DNA (cytosine C5)-methyltransferase.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 2003
SP  - 430
EP  - 430
VL  - 44
AB  - Aberrant methylation of the promoter regions of genes has been shown to result in gene
AB  - silencing associated with cancer progression.  Reactivation of silenced genes in cultured
AB  - cells by methylation inhibitors can be induced by 5-azacytidine (5-AzaC) and
AB  - 5-aza-2-deoxycytidine (5-AzadC), which inhibit DNA methyltransferases when incorporated into
AB  - DNA.  Since both 5-AzaC and 5-AzadC are chemically unstable and toxic, these results have
AB  - stimulated the search for alternate inhibitors of the mammalian methyltransferase DNMT1.  We
AB  - analyzed the inhibitory capacity of the cytidine analog zebularine (2-H pyrimidione).
AB  - Zebularine is stable under both acidic and neutral conditions, and is minimally cytotoxic,
AB  - making it a promising therapeutic agent.  We show that, when incorporated in place of the
AB  - cytosine target in double stranded or looped oligodeoxyribonucleotides containing recognition
AB  - sites for the bacterial methyltransferase (M.HhaI) and DNMT1 respectively, zebularine is
AB  - equivalent to
AB  - 5-AzaC as an inhibitor of DNA methylation.  Despite the effective inhibition of DNMT1 in vitro
AB  - by ODNs containing zebularine, no decrease in DNA methylation was observed in LNCaP cells
AB  - treated with zebularine.  GSTP1 transcription was detected by RT-PCR after 5-AzadC treatment
AB  - but not after zebularine treatment.  Analysis of the heavily methylated promoter region of the
AB  - GSTP1 gene by bisulfite sequencing of DNA showed that DNA methylation was inhibited by 5-AzadC
AB  - but not zebularine.  Interestingly, LNCaP cells grown in the presence of zebularine did
AB  - display a marked change in morphology.  These results suggest that zebularine may not be
AB  - efficiently incorporated into DNA in vivo, but may be able to alter cellular phenotype by
AB  - interfering with other processes including RNA methylation.
ER  -

TY  - JOUR
AU  - van Blokland, R.
AU  - Ross, S.
AU  - Corrado, G.
AU  - Scollan, C.
AU  - Meyer, P.
TI  - Developmental abnormalities associated with deoxyadenosine methylation in transgenic tobacco.
JO  - Plant J.
PY  - 1998
SP  - 543
EP  - 551
VL  - 15
AB  - As in other higher eukaryotes, DNA methylation in plants is predominantly found at
AB  - deoxycytosine residues, while deoxyadenosine residues are not methylated at significant
AB  - levels. 6mdA methylation has been successfully introduced into yeast and Drosophila via
AB  - expression of a heterologous methyltransferase, but similar attempts in tobacco had, up until
AB  - now, proved unsuccessful despite the correct expression of a methyltransferase construct. It
AB  - was unclear whether this result reflected the failure of heterologous methyltransferases to
AB  - enter the nucleus, or whether 6mdA methylation, which has been shown to interfere with
AB  - promoter activity, was toxic for plants. Here we show that 6mdA methylation can be
AB  - successfully introduced into transgenic tobacco plants via expression of the bacterial dam
AB  - enzyme. The efficiency of 6mdA methylation was directly proportional to expression levels of
AB  - the dam construct, and methylation of all GATC sites was observed in a highly expressing line.
AB  - Increasing expression levels of the enzyme in different plants correlated with increasingly
AB  - abnormal phenotypes affecting leaf pigmentation, apical dominance, and leaf and floral
AB  - structure. Whilst introduction of dam-specific methylation does not cause any developmental
AB  - abnormalities in yeast or Drosophila, our data suggest that methylation of deoxyadenine
AB  - residues in plants interferes with the expression of genes involved in leaf and floral
AB  - development.
ER  -

TY  - JOUR
AU  - van Boven, C.P.A.
TI  - Restriction and modification of phages in Staphylococcal phage typing.
JO  - Ann. NY Acad. Sci.
PY  - 1974
SP  - 376
EP  - 388
VL  - 236
AB  - Staphylococcus aureus is a remarkably versatile species, which has been very successful in
AB  - establishing itself as a commensal in various niches on the human and animal body.  No two
AB  - staphylococci are really alike, even if they have the same phage pattern or drug sensitivity.
ER  -

TY  - JOUR
AU  - Van Cleve, M.
AU  - Gumport, R.I.
TI  - Effect of flanking sequence length on EcoRI endonuclease reaction.
JO  - Fed. Proc.
PY  - 1987
SP  - 2041
EP  - 2041
VL  - 46
AB  - Michaelis-Menten parameters were determined for the cleavages by EcoRI
AB  - endonuclease of both scission points in a duplex composed of the pentadecamer
AB  - d(pATCGAATTCCGGCCA) and its complement.  The Km for this substrate is 38.6 +/-
AB  - 2 nM, a value between those determined for plasmid DNA and an octameric
AB  - oligodeoxyribonucleotide.  Since the two scission points are flanked by
AB  - different lengths of sequence, comparison of turnover numbers for the two
AB  - cleavages may reflect interactions of the enzyme with nucleotides outside its
AB  - recognition sequence.  Preliminary results indicate that the scissile bond in
AB  - the above indicated oligomer is cleaved twice as fast as the hydrolyzed bond in
AB  - its complement.  The more rapidly cleaved bond is four residues from the 5'
AB  - terminus, whereas the more slowly hydrolyzed bond is seven base pairs from the
AB  - end of the duplex.
ER  -

TY  - JOUR
AU  - Van Cleve, M.
AU  - Gumport, R.I.
TI  - Effect of flanking sequence length on EcoRI endonuclease reaction.
JO  - J. Cell Biol.
PY  - 1988
SP  - 403a
EP  - 403a
VL  - 107
AB  - Michaelis-Menten parameters were determined for the cleavages by EcoRI
AB  - endonuclease at both scission points in a series of oligomeric DNA duplexes.
AB  - Each member of the series contains the EcoRI recognition sequence (GAATTC)
AB  - located with six base pairs flanking the 3' end and from zero to three base
AB  - pairs flanking the 5' end, e.g., ATCGAATTCCGGCCA.  Thus, cleavage at both
AB  - strands produces two different sized and 32P-labeled products, in the above
AB  - case a tetramer and heptamer.  Kinetic parameters were determined for both
AB  - strands independently.  In each duplex tested, the cleavage rates are different
AB  - for the two oligomers, with the rate for each strand varying inversely as the
AB  - length of its 5' flanking sequence from Kcat=11.5 min-1 with three base pairs,
AB  - to 14.0 min-1 with two, to 20.0 min-1 with one.  Km's also vary with length,
AB  - and are different for the two strands at each duplex.
ER  -

TY  - JOUR
AU  - Van Cleve, M.D.
AU  - Gumport, R.I.
TI  - Influence of enzyme-substrate contacts located outside the EcoRI recognition site on cleavage of duplex oligodeoxyribonucleotide substrates by EcoRI endonuclease.
JO  - Biochemistry
PY  - 1992
SP  - 334
EP  - 339
VL  - 31
AB  - A complete understanding of the sequence-specific interaction between the EcoRI
AB  - restriction endonuclease and its DNA substrate requires identification of all
AB  - contacts between the enzyme and substrate, and evaluation of their
AB  - significance.  We have searched for possible contacts adjacent to the
AB  - recognition site, GAATTC, by using a series of substrates with differing
AB  - lengths of flanking sequence.  Each substrate is a duplex of
AB  - non-self-complementary oligodeoxyribonucleotides in which the recognition site
AB  - is flanked by six base pairs on one side and from zero to three base pairs on
AB  - the other.  Steady-state kinetic values were determined for the cleavage of
AB  - each strand of these duplexes.  A series of substrates in which the length of
AB  - flanking sequences was varied on both sides of the hexamer was also examined.
AB  - The enzyme cleaved both strands of each of the substrates.  Decreasing the
AB  - flanking sequence to fewer than three base pairs on one side of the recognition
AB  - site induced an asymmetry in the rates of cleavage of the two strands.  The
AB  - scissile bond nearest the shortening sequence was hydrolyzed with increasing
AB  - rapidity as base pairs were successively removed.  Taken together, the Km and
AB  - kcat values obtained may be interpreted to indicate the relative importance of
AB  - several likely enzyme-substrate contacts located outside the canonical
AB  - hexameric recognition site.
ER  -

TY  - JOUR
AU  - Van Cott, E.M.
AU  - Wilson, G.G.
TI  - Cloning the FnuDI, NaeI, NcoI and XbaI restriction-modification systems.
JO  - Gene
PY  - 1988
SP  - 55
EP  - 59
VL  - 74
AB  - Methyltransferase genes from the FnuDI, NaeI, NcoI, and XbaI
AB  - restriction-modification systems have been isolated in Escherichia coli by
AB  - shot-gun cloning bacterial DNA fragments into plasmid vectors and selecting for
AB  - protectively modified molecules that resist digestion by the corresponding
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - van de Guchte, M. et al.
TI  - The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 9274
EP  - 9279
VL  - 103
AB  - Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of
AB  - lactic acid-producing bacteria, mainly known for its worldwide application in yogurt
AB  - production. The genome sequence of this bacterium has been determined and shows the signs of
AB  - ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic
AB  - pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus
AB  - genome support the hypothesis that the genome is in a phase of rapid evolution. (i)
AB  - Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that
AB  - the L. bulgaricus genome has known a recent phase of important size reduction, in agreement
AB  - with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC
AB  - content at codon position 3 than expected on the basis of the overall GC content suggests that
AB  - the composition of the genome is evolving toward a higher GC content; and (iii) the presence
AB  - of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature
AB  - in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results
AB  - indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein
AB  - and lactose-rich milk environment through the loss of superfluous functions and
AB  - protocooperation with Streptococcus thermophilus.
ER  -

TY  - JOUR
AU  - van den Bogert, B.
AU  - Boekhorst, J.
AU  - Smid, E.J.
AU  - Zoetendal, E.G.
AU  - Kleerebezem, M.
TI  - Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human  Small Intestine.
JO  - Genome Announcements
PY  - 2013
SP  - e01013
EP  - e01013
VL  - 1
AB  - Enterococcus sp. strain HSIEG1 was isolated from the human small intestine. Its draft genome
AB  - predicts a broad carbohydrate fermentation capability, which matches
AB  - well with the observed physiological characteristics of this strain. This
AB  - metabolic flexibility is expected to be of importance for survival and growth in
AB  - the small intestinal habitat.
ER  -

TY  - JOUR
AU  - van den Bogert, B.
AU  - Boekhorst, J.
AU  - Smid, E.J.
AU  - Zoetendal, E.G.
AU  - Kleerebezem, M.
TI  - Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.
JO  - Genome Announcements
PY  - 2013
SP  - e00977
EP  - e00913
VL  - 1
AB  - Veillonella species are frequently encountered commensals in the human small intestine. Here,
AB  - we report the draft genome sequence of the first cultured
AB  - representative from this ecosystem, Veillonella parvula strain HSIVP1. The genome
AB  - is predicted to encode all the necessary enzymes required for the pathway
AB  - involved in the conversion of lactate to propanoate.
ER  -

TY  - JOUR
AU  - van den Broek, B.
AU  - Noom, M.C.
AU  - Wuike, G.J.L.
TI  - DNA-tension dependence of restriction enzyme cleavage reveals details of the reaction pathway.
JO  - Biophys. J.
PY  - 2005
SP  - 184A
EP  - 184A
VL  - 88
AB  - Restriction endonucleases cleave recognition sequences on double-stranded DNA with
AB  - extraordinary specificity.  This capability arises from conformation changes in enzyme and/or
AB  - DNA upon binding to such a recognition site.  Here we present measurements of energy and rate
AB  - changes in the raction pathway as a function of tension on the DNA.  The experiments were
AB  - performed using single DNA molecules held between beads kept in laser tweezers while recording
AB  - the cleavage times after introduction of the restriction enzymes.  The data shows that EcoRV
AB  - cleavage rates drop with increasing tension, while BamHI activity does not decrease.  From the
AB  - force-rate curves of EcoRV, we are able to obtain values for the DNA bending angle (51o),
AB  - induced-fit rate (~100 s-1) and dsDNA hydrolysis (0.28 s-1).  BamHI, however, does not show
AB  - any sign of DNA bending.  For both enzymes a reduced association rate of ~5.106 M-1 s-1 is
AB  - found, presumably due to absence of intradomain dissociation-reassociation (jumping) between
AB  - non-specific sites on stretched DNA.  These measurements thus illustrate the relative
AB  - importance of jumping in the searching process.  Moreover, the tension dependence of the
AB  - induced-fit reaction reveals some of the underlying energetics of binding a specific site.
AB  - Finally, single-molecule detection of DNA cleavage allows for direct measurements of many of
AB  - the reaction steps and is generally applicable to other type II restriction enzymes.
ER  -

TY  - JOUR
AU  - van den Broek, B.
AU  - Noom, M.C.
AU  - Wuite, G.J.L.
TI  - DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 2676
EP  - 2684
VL  - 33
AB  - Type II restriction endonucleases protect bacteria against phage infections by cleaving
AB  - recognition sites on foreign double-stranded DNA (dsDNA) with extraordinary specificity. This
AB  - capability arises primarily from large conformational changes in enzyme and/or DNA upon target
AB  - sequence recognition. In order to elucidate the connection between the mechanics and the
AB  - chemistry of DNA recognition and cleavage, we used a single-molecule approach to measure rate
AB  - changes in the reaction pathway of EcoRV and BamHI as a function of DNA tension. We show that
AB  - the induced-fit rate of EcoRV is strongly reduced by such tension. In contrast, BamHI is found
AB  - to be insensitive, providing evidence that both substrate binding and hydrolysis are not
AB  - influenced by this force. Based on these results, we propose a mechanochemical model of
AB  - induced-fit reactions on DNA, allowing determination of induced-fit rates and DNA bend angles.
AB  - Finally, for both enzymes a strongly decreased association rate is obtained on stretched DNA,
AB  - presumably due to the absence of intradomain dissociation/re-association between non-specific
AB  - sites (jumping). The obtained results should apply to many other DNA-associated proteins.
ER  -

TY  - JOUR
AU  - van den Broek, B.
AU  - Schmidt, C.F.
AU  - Wuite, G.J.L.
TI  - The effect of DNA tension on restriction-enzyme cutting rates studied with optical tweezers.
JO  - Biophys. J.
PY  - 2003
SP  - 141a
EP  - 141a
VL  - 84
AB  - Restriction enzymes recognize base pair sequences on DNA with high specificity.  These sites
AB  - trigger a conformational change in the enzyme and/or DNA, permitting the cleavage of both
AB  - strands.  Here we report single-molecule measurements of the effect of DNA tension on the
AB  - cleavage rate of restriction enzymes BamHI, EcoRV,
ER  -

TY  - JOUR
AU  - van den Broek, B.
AU  - Vanzi, F.
AU  - Normanno, D.
AU  - Pavone, F.S.
AU  - Wuite, G.J.L.
TI  - Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.
JO  - Nucleic Acids Res.
PY  - 2006
SP  - 167
EP  - 174
VL  - 34
AB  - Many restriction enzymes require binding of two copies of a recognition sequence for DNA
AB  - cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE
AB  - restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA
AB  - molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect
AB  - small polystyrene beads to a glass surface. The position of a bead is tracked through video
AB  - microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific
AB  - change in Brownian motion of the bead. With this method we are able to directly follow DNA
AB  - looping kinetics of single protein-DNA complexes to obtain loop stability and loop formation
AB  - times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific
AB  - size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in
AB  - effective DNA compaction for higher enzyme concentrations. Addition of Ca2+ increases the
AB  - NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI.
AB  - Finally, for both enzymes we observe exponentially distributed loop formation times,
AB  - indicating that looping is dominated by (re)binding the second recognition site.
ER  -

TY  - JOUR
AU  - van den Broek, B.
AU  - Wuite, G.J.L.
TI  - Single molecule study of DNA tension on restriction enzyme cleavage activity.
JO  - Biophys. J.
PY  - 2002
SP  - 51a
EP  - 51a
VL  - 82
AB  - Restriction enzymes recognizes dsDNA at highly specific base pair sequences.  These sites
AB  - trigger a large conformational change in the enzyme, permitting the cleavage of DNA.  During
AB  - this conformational change the DNA is often bent, although some enzymes do not deform the DNA
AB  - at all.  While the biochemistry and structure of many restriction enzymes are well studied,
AB  - these studies only superficially address the dynamics of enzyme-DNA interactions.  Here we
AB  - report single molecule measurements of the effect of DNA tension on the cleavage activity of
AB  - restriction enzymes in order to elucidate some of the enzyme dynamics.  DNA is held under
AB  - various tensions between two beads in optical tweezers while the time it takes for the enzymes
AB  - to cut is recorded; this allows us to obtain force vs. rate curves.  We present our first
AB  - results for the restriction enzyme NaeI, which kinks the DNA by 45 degrees before cutting it.
AB  - We expect to see several trends: DNA tension reduces the binding energy of the sugar backbone,
AB  - suggesting an increase in cutting rate.  At the same time, this tension opposes the DNA
AB  - bending by the enzyme.  Moreover, pulling on the DNA slightly deforms the base stacking,
AB  - degrading the recognition efficiency.  These effects should slow down the cutting.
ER  -

TY  - JOUR
AU  - van den Hondel, C.A.M.J.J.
AU  - van Leen, R.W.
AU  - van Arkel, G.A.
AU  - Duyvesteyn, M.
AU  - de Waard, A.
TI  - Sequence-specific nucleases from the cyanobacterium Fremyella diplosiphon, and a peculiar resistance of its chromosomal DNA towards cleavage by other restriction enzymes.
JO  - FEMS Microbiol. Lett.
PY  - 1983
SP  - 7
EP  - 12
VL  - 16
AB  - The filamentous cyanobacterium Fremyella diplosiphon PCC7601 is facultatively
AB  - heterotrophic.  Cells can grow in the dark at the expense of certain organic
AB  - substrates like sugars as an exogenous energy source, the utilization of which
AB  - probably depends on the presence in the cell of the appropriate permeases.  As
AB  - a first step in cloning the F. diplosiphon genetic information for these
AB  - permeases into the transformable strain R-2 of the unicellular, strictly
AB  - photoautotrophic cyanobacterium Anacystis nidulans, chromosomal DNA of F.
AB  - diplosiphon was digested with several bacterial sequence-specific
AB  - endodeoxyribonucleases.  As the DNA appeared to be resistant to an unexpectedly
AB  - large number of them, a restriction enzyme analysis with 31 different
AB  - endonucleases was made to elucidate the underlying modification pattern.  In
AB  - addition, F. diplosiphon cells were anlysed for the presence of restriction
AB  - endonucleases, and two were found:  FdiI and FdiII, which cleave the nucleotide
AB  - sequences 5'-G^G(A/T)CC and 5'-TGC^GCA, respectively.  EndoR.FdiI is an
AB  - isoschizomer of AvaII and endoR.FdiII is an isoschizomer of AosI.
ER  -

TY  - JOUR
AU  - Van den Wyngaert, I.
AU  - Sprengel, J.
AU  - Kass, S.U.
AU  - Luyten, W.H.M.L.
TI  - Cloning and analysis of a novel human putative DNA methyltransferase.
JO  - FEBS Lett.
PY  - 1998
SP  - 283
EP  - 289
VL  - 426
AB  - DNA methylation is intricately involved in a variety of cellular processes, such as
AB  - differentiation, cell cycle progression, X-chromosome inactivation and genomic imprinting.
AB  - However, little is known about how specific DNA methylation patterns are established and
AB  - maintained.  Previously one mammalian DNA methyltransferase has been described, but there has
AB  - been considerable speculation about the presence of a second activity capable of methylation.
AB  - Here we report the identification and characterization of a novel human putative DNA
AB  - methyltransferase.  Using a bioinformatics screen we have identified several expressed
AB  - sequence tags which show high sequence similarity to the Schizosaccharomyces pombe gene pmt1+.
AB  - The cDNA for PuMet was cloned and the predicted amino acid sequence deduced.  The gene is
AB  - ubiquitously expressed, albeit at low levels.  Like several other DNA methyltransferases, the
AB  - bacterially overexpressed protein is not active in methylation assays.
ER  -

TY  - JOUR
AU  - Van der Auwera, G.A.
AU  - Feldgarden, M.
AU  - Kolter, R.
AU  - Mahillon, J.
TI  - Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus Sensu Lato.
JO  - Genome Announcements
PY  - 2013
SP  - e00380
EP  - e00313
VL  - 1
AB  - Bacillus cereus sensu lato is a species complex that includes the anthrax pathogen Bacillus
AB  - anthracis and other bacterial species of medical, industrial,
AB  - and ecological importance. Their phenotypes of interest are typically linked to
AB  - large plasmids that are closely related to the anthrax plasmids pXO1 and pXO2.
AB  - Here, we present the draft genome sequences of 94 isolates of B. cereus sensu
AB  - lato, which were chosen for their plasmid content and environmental origins.
ER  -

TY  - JOUR
AU  - van der Graaf-van, B.L.
AU  - Miller, W.G.
AU  - Yee, E.
AU  - Bono, J.L.
AU  - Rijnsburger, M.
AU  - Campero, C.
AU  - Wagenaar, J.A.
AU  - Duim, B.
TI  - First Closed Genome Sequence of Campylobacter fetus subsp. venerealis bv. intermedius.
JO  - Genome Announcements
PY  - 2014
SP  - e01246
EP  - e01213
VL  - 2
AB  - Campylobacter fetus subsp. venerealis bv. intermedius is a variant of C. fetus subsp.
AB  - venerealis, the causative agent of bovine genital campylobacteriosis, a
AB  - venereal disease associated with abortion and infertility in cattle. We report
AB  - the first closed whole-genome sequence of this biovar.
ER  -

TY  - JOUR
AU  - van der Gun, B.T.F.
AU  - Maluszynska-Hoffman, M.
AU  - Kiss, A.
AU  - Arendzen, A.J.
AU  - Ruiters, M.H.J.
AU  - McLaughlin, P.M.J.
AU  - Weinhold, E.
AU  - Rots, M.G.
TI  - Targeted DNA Methylation by a DNA Methyltransferase Coupled to a Triple Helix Forming Oligonucleotide To Down-Regulate the Epithelial Cell Adhesion Molecule.
JO  - Bioconjugate Chem.
PY  - 2010
SP  - 1239
EP  - 1245
VL  - 21
AB  - The epithelial cell adhesion molecule (EpCAM) is a membrane glycoprotein that has been
AB  - identified as a marker of cancer-initiating
AB  - cells. EpCAM is highly expressed on most carcinomas, and transient
AB  - silencing of EpCAM expression leads to reduced oncogenic potential. To
AB  - silence (he EpCAM gene in a persistent manner via targeted DNA
AB  - methylation, a low activity mutant (C141S) of the CpG-specific DNA
AB  - methyltransferase M.Sssl was coupled to a triple-helix-forming
AB  - oligonucleotide (TFO-C141S) specifically designed for the EpCAM gene.
AB  - Reporter plasmids encoding the green fluorescent protein under control
AB  - of different EpCAM promoter fragments were treated with the TFO-C141S
AB  - conjugate to determine the specificity of targeted DNA methylation in
AB  - the context of a functional EpCAM promoter. Treatment of the plasmids
AB  - with TFO-C141S resulted in efficient and specific methylation of the
AB  - targeted CpG located directly downstream of the triple helix forming
AB  - site (TFS). No background DNA methylation was observed neither in a 700
AB  - bp region of the EpCAM promoter nor in a 400 bp region of the reporter
AB  - gene downstream of the TFS. Methylation of the target CpG did not have
AB  - a detectable effect on promoter activity. This study shows that the
AB  - combination of a specific TFO and a reduced activity methyltransferase
AB  - variant can be used to target DNA methylation to predetermined sites
AB  - with high specificity, allowing determination of crucial CpGs for
AB  - promoter activity.
ER  -

TY  - JOUR
AU  - van der Mee-Marquet, N.
AU  - Hernandez, D.
AU  - Bertrand, X.
AU  - Quentin, R.
AU  - Corvaglia, A.R.
AU  - Francois, P.
TI  - Whole-Genome Sequence of the Ancestral Animal-Borne ST398 Staphylococcus aureus Strain S123.
JO  - Genome Announcements
PY  - 2013
SP  - e00692
EP  - e00613
VL  - 1
AB  - Sequence type 398 (ST398) Staphylococcus aureus was originally reported in livestock. We
AB  - announce the complete genome sequence of an ST398
AB  - methicillin-susceptible S. aureus strain of animal origin, S123. The genome
AB  - sequence reveals a wild-type genome that probably corresponds to an ancestral
AB  - clone.
ER  -

TY  - JOUR
AU  - van der Ploeg, L.H.T.
AU  - Flavell, R.A.
TI  - DNA methylation in the human cdb-globin locus in Erythroid and Nonerythroid tissues.
JO  - Cell
PY  - 1980
SP  - 947
EP  - 958
VL  - 19
AB  - We have analyzed DNA modification in the human cdb-globin gene region at 17
AB  - cleavage sites of restriction endonucleases which are unable to cleave DNA if
AB  - 5-methylcytosine is present at certain positions in their respective cleavage
AB  - sites.  Using this criterion, all sites tested in the globin gene region are
AB  - fully modified in the germ line (sperm) DNA.  In somatic tissues, however,
AB  - methyl groups are absent at specific sites in the globin gene region.  In
AB  - tissues not expressing the genes, these losses range from one of these cleavage
AB  - sites in lymphocyte DNA to essentially all of these sites in the entire region
AB  - in placental DNA.  In the DNA of tissues expressing the globin genes, the
AB  - region surrounding and including the genes expressed shows a low level of
AB  - modification, whereas the neighboring DNA regions have a high level of
AB  - modification.  The data suggest that a low level of DNA methylation may be a
AB  - necessary, but not a sufficient, condition for gene expression in higher
AB  - eucaryotes.
ER  -

TY  - JOUR
AU  - van der Woerd, M.J.
AU  - Pelletier, J.J.
AU  - Xu, S.-Y.
AU  - Friedman, A.M.
TI  - Restriction enzyme BsoBI-DNA complex: A tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
JO  - Structure
PY  - 2001
SP  - 133
EP  - 144
VL  - 9
AB  - Background: Restriction endonucleases form a diverse family of proteins with substantial
AB  - variation in sequence, structure, and interaction with recognition site DNA. BsoBI is a
AB  - thermophilic restriction endonuclease that exhibits both base-specific and degenerate
AB  - recognition within the sequence CPyCGPuG.  Results: The structure of BsoBI complexed to
AB  - cognate DNA has been determined to 1.7 Angstrom resolution, revealing several unprecedented
AB  - features. Each BsoBI monomer is formed by inserting a helical domain into an expanded
AB  - EcoRI-type catalytic domain. DNA is completely encircled by a BsoBI dimer. Recognition
AB  - sequence DNA lies within a 20 Angstrom long tunnel of protein that excludes bulk solvent.
AB  - Interactions with the specific bases are made in both grooves through direct and
AB  - water-mediated hydrogen bonding. Interaction with the degenerate position is mediated by a
AB  - purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the
AB  - purine N6/O6 and pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active
AB  - site residues of the DXn(E/D)ZK restriction enzyme motif, His253 is positioned to act as a
AB  - general base.  Conclusions: A catalytic mechanism employing His253 and two metal ions is
AB  - proposed. If confirmed, this would be the first example of histidine-mediated catalysis in a
AB  - restriction endonuclease. The structure also provides two novel examples of the role of water
AB  - in protein-DNA interaction. Degenerate recognition may be mediated by employing water as a
AB  - hydrogen bond donor or acceptor. The structure of DNA in the tunnel may also be influenced by
AB  - the absence of bulk solvent.
ER  -

TY  - JOUR
AU  - van der Woude, M.
AU  - Hale, W.B.
AU  - Low, D.A.
TI  - Formation of DNA methylation patterns: Nonmethylated GATC sequences in gut and pap operons.
JO  - J. Bacteriol.
PY  - 1998
SP  - 5913
EP  - 5920
VL  - 180
AB  - Most of the adenine residues in GATC sequences in the Escherichia coli chromosome are
AB  - methylated by the enzyme deoxyadenosine methyltransferase.  However, at least 20 GATC
AB  - sequences remain nonmethylated throughout the cell cycle.  Here we examined how the DNA
AB  - methylation patterns of GATC sequences within the regulatory regions of the
AB  - pyelonephritis-associated pilus operon and the glucitol utilization operon were formed.  The
AB  - results obtained with an in vitro methylation protection assay showed that the addition of the
AB  - leucine-responsive regulatory protein to pap DNA was sufficient to protect the two GATC
AB  - sequences in the pap regulatory region, GATC-I and GATC-II, from methylation by Dam.  This
AB  - finding was consistent with previously published data showing that Lrp was essential for
AB  - methylation protection of these DNA sites in vivo.  Methylation protection also occurred at a
AB  - GATC site (GATC-44.5) centered 44.5 bp upstream of the transcription start site of the gutABD
AB  - operon.  Two proteins, GutR and the catabolite gene activator protein, bound to DNA sites
AB  - overlapping the GATC-44.5-containing region of the gutABD operon.  GutR, an operon-specific
AB  - repressor, was essential for methylation protection in vivo, and binding of GutR protected
AB  - GATC-44.5 from methylation in vitro.  In contrast, binding of CAP at a site overlapping
AB  - GATC-44.5 did not protect this site from methylation.  Mutational anlayses indicated that
AB  - gutABD gene regulation was not controlled by methylation of GATC-44.5, in contrast to
AB  - regulation of Pap pilus expression, which is directly controlled by methylation of the pap
AB  - GATC-I and GATC-II sites.
ER  -

TY  - JOUR
AU  - van der Woude, M.W.
TI  - Some types of bacterial phase variation are epigenetic.
JO  - Microbe
PY  - 2008
SP  - 21
EP  - 26
VL  - 3
AB  - Individual bacterial cells can vary phenotypically, even within a clonal population.  Phase
AB  - variation provides a means for regulating specific genes between an expressed, or "on" state,
AB  - and a nonexpressed, or "off" state; these two expression states are heritable and reversible.
AB  - The mechanisms that lead to phase variation are either genetic or epigenetic; if epigenetic,
AB  - they entail no changes in DNA sequence.  More generally, phase variation apparently provides a
AB  - means for generating diversity and thereby increasing the changes of survival amid changing
AB  - environmental conditions.  Understanding phase variation may allow us to manipulate bacterial
AB  - populations to provide health benefits, including better diagnostic tests and vaccines.
ER  -

TY  - JOUR
AU  - van der Woude, M.W.
AU  - Baumler, A.J.
TI  - Phase and antigenic variation in bacteria.
JO  - Clin. Microbiol. Rev.
PY  - 2004
SP  - 581
EP  - 611
VL  - 17
AB  - Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial
AB  - population, in which individual cells either express the phase-variable protein(s) or not, or
AB  - express one of multiple antigenic forms of the protein, respectively. This form of regulation
AB  - has been identified mainly, but by no means exclusively, for a wide variety of surface
AB  - structures in animal pathogens and is implicated as a virulence strategy. This review provides
AB  - an overview of the many bacterial proteins and structures that are under the control of phase
AB  - or antigenic variation. The context is mainly within the role of the proteins and variation
AB  - for pathogenesis, which reflects the main body of literature. The occurrence of phase
AB  - variation in expression of genes not readily recognizable as virulence factors is highlighted
AB  - as well, to illustrate that our current knowledge is incomplete. From recent genome sequence
AB  - analysis, it has become clear that phase variation may be more widespread than is currently
AB  - recognized, and a brief discussion is included to show how genome sequence analysis can
AB  - provide novel information, as well as its limitations. The current state of knowledge of the
AB  - molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the
AB  - way in which these mechanisms form part of the general regulatory network of the cell is
AB  - addressed. Arguments both for and against a role of phase and antigenic variation in immune
AB  - evasion are presented and put into new perspective by distinguishing between a role in
AB  - bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally,
AB  - examples are presented to illustrate that phase-variable gene expression should be taken into
AB  - account in the development of diagnostic assays and in the interpretation of experimental
AB  - results and epidemiological studies.
ER  -

TY  - JOUR
AU  - van der Woude, M.W.
AU  - Braaten, B.A.
AU  - Low, D.A.
TI  - Evidence for global regulatory control of pilus expression in Escherichia coli by Lrp and DNA methylation: model building based on analysis of pap.
JO  - Mol. Microbiol.
PY  - 1992
SP  - 2429
EP  - 2435
VL  - 6
AB  - Pyelonephritis-associated pilus (Pap) expression is regulated by a phase variation control
AB  - mechanism involving PapB, Papl, catabolite activator protein (CAP), leucine-responsive
AB  - regulatory protein (Lrp) and deoxyadenosine methylase (Dam). Lrp and Papl bind to a specific
AB  - non-methylated pap regulatory DNA region containing the sequence 'GATC' and facilitate the
AB  - formation of an active transcriptional complex.  Evidence indicates that binding of Lrp and
AB  - Papl to this region inhibits methylation of the GATC site by Dam.  However, if this GATC site
AB  - is first methylated by Dam, binding of Lrp and Papl is inhibited. These events lead to the
AB  - formation of two different pap methylation states characteristic of active (ON) and inactive
AB  - (OFF) pap transcription states. The fae (K88), daa (F1845) and sfa (S) pilus operons share
AB  - conserved 'GATC-box' domains with pap and may be subject to a similar regulatory control
AB  - mechanism involving Lrp and DNA methylation.
ER  -

TY  - JOUR
AU  - Van Dongen, W.M.A.M.
AU  - Van Vlerken, M.M.A.
AU  - De Graaf, F.K.
TI  - Nucleotide sequence of a DNA fragment encoding a Vibrio cholerae haemagglutinin.
JO  - Genetics (Life Sci. Adv.)
PY  - 1987
SP  - 85
EP  - 91
VL  - 6
ER  -

TY  - JOUR
AU  - Van Emburgh, B.O.
AU  - Robertson, K.D.
TI  - Modulation of Dnmt3b function in vitro by interactions with Dnmt3L, Dnmt3a and Dnmt3b splice variants.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 4984
EP  - 5002
VL  - 39
AB  - DNA methylation, an essential regulator of transcription and chromatin structure, is
AB  - established and maintained by the coordinated action of
AB  - three DNA methyltransferases: DNMT1, DNMT3A and DNMT3B, and the inactive
AB  - accessory factor DNMT3L. Disruptions in DNMT3B function are linked to
AB  - carcinogenesis and genetic disease. DNMT3B is also highly alternatively
AB  - spliced in a tissue- and disease-specific manner. The impact of
AB  - intra-DNMT3 interactions and alternative splicing on the function of DNMT3
AB  - family members remains unclear. In the present work, we focused on DNMT3B.
AB  - Using a panel of in vitro assays, we examined the consequences of DNMT3B
AB  - splicing and mutations on its ability to bind DNA, interact with itself
AB  - and other DNMT3's, and methylate DNA. Our results show that, while the
AB  - C-terminal catalytic domain is critical for most DNMT3B functions, parts
AB  - of the N-terminal region, including the PWWP domain, are also important.
AB  - Alternative splicing and domain deletions also influence DNMT3B's cellular
AB  - localization. Furthermore, our data reveal the existence of extensive
AB  - DNMT3B self-interactions that differentially impact on its activity.
AB  - Finally, we show that catalytically inactive isoforms of DNMT3B are
AB  - capable of modulating the activity of DNMT3A-DNMT3L complexes. Our studies
AB  - therefore suggest that seemingly 'inactive' DNMT3B isoforms may influence
AB  - genomic methylation patterns in vivo.
ER  -

TY  - JOUR
AU  - Van Emburgh, B.O.
AU  - Robertson, K.D.
TI  - DNA methyltransferases and methyl-CPG binding proteins as multifunctional regulators of chromatin structure and development in mammalian cells.
JO  - EPIGENETICS
PY  - 2008
SP  - 23
EP  - 61
VL  - 0
AB  - The epigenetic modification of DNA with 5-methylcytosine is an important regulatory event
AB  - involved in chromatin structure, genomic imprinting, inactivation of the X chromosome,
AB  - transcription, and retrotransposon silencing. This modification is catalysed and maintained by
AB  - the DNA methyltransferases and is interpreted by the methyl-CpG binding proteins. DNA
AB  - methyltransferases are not limited to catalysing DNA methylation, but also take part in the
AB  - regulation of gene expression through interactions with other proteins that repress
AB  - transcription and modify chromatin structure. The use of mouse models, as well as human
AB  - diseases resulting from deficiencies in the rnethylation machinery, have been integral parts
AB  - of understanding the role of these proteins in development and cellular homeostasis. More and
AB  - more studies are reporting additional roles within the cell beyond their DNA methyltransferase
AB  - and methyl-CpG binding properties. There is at this point, though, only limited understanding
AB  - of how these enzymes and proteins are targeted to specific genomic regions. The
AB  - methyltransferases that will be discussed in this review include DNMT1, DNMT2, and the DNMT3
AB  - family of enzymes as well as the methyl-CpG binding proteins MeCP2, MBD1, MBD2, MBD3, and
AB  - MBD4. The function of these enzymes, as well as their interactions with other cellular
AB  - proteins and each other, will be discussed along with the diseases attributed to aberrations
AB  - in the DNA methylation machinery.
ER  -

TY  - JOUR
AU  - Van Etten, J.L.
TI  - DNA methyltransferases and DNA site-specific endonucleases encoded by Chlorella viruses.
JO  - J. Phycol.
PY  - 1991
SP  - 74
EP  - 74
VL  - 27
AB  - Thirty seven large, polyhedral, dsDNA-containing (>300 kb in size),
AB  - plaque-forming viruses which infect a unicellular, eukaryotic, green alga,
AB  - Chlorella strain NC64A have been partially characterized.  Each of the viral
AB  - DNAs contains 5mC; the concentration of 5mC as a percentage of cytosine, ranges
AB  - from 0.1 to 47%.  In addition, 25 of the 37 viral DNAs also contain 6mA; the
AB  - concentration of 6mA, as a percentage of adenine, ranges from 1.45% to 37%.
AB  - The finding that methylation is sequence specific led to the discovery that at
AB  - least some of the viruses code for DNA methyltransferases and DNA site-specific
AB  - (restriction) endonucleases.  Some of the site-specific endonucleases recognize
AB  - and cleave the same base sequences as bacterial enzymes whereas, others have
AB  - unique specificities and cleavage sites.  Two additional site-specific
AB  - endonucleases are unusual because they cleave one strand of DNA at specific
AB  - sequences.  The presence of DNA methylating and site-specific endonucleases in
AB  - the virus infected cells leads to two questions. (i) What is the evolutionary
AB  - origin of these enzymes? (ii) What is the function of these enzymes.
AB  - Experiments designed to address these questions will be presented.
ER  -

TY  - JOUR
AU  - Van Etten, J.L.
AU  - Meints, R.H.
TI  - Giant viruses infecting algae.
JO  - Annu. Rev. Microbiol.
PY  - 1999
SP  - 447
EP  - 494
VL  - 53
AB  - Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large,
AB  - icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain
AB  - unicellular, eukaryotic chlorella-like green algae. DNA sequence analysis of its 330, 742-bp
AB  - genome leads to the prediction that this phycodnavirus has 376 protein-encoding genes and 10
AB  - transfer RNA genes. The predicted gene products of approximately 40% of these genes resemble
AB  - proteins of known function. The chlorella viruses have other features that distinguish them
AB  - from most viruses, in addition to their large genome size. These features include the
AB  - following: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific
AB  - endonucleases; (b) PBCV-1 encodes at least part, if not the entire machinery to glycosylate
AB  - its proteins; (c) PBCV-1 has at least two types of introns--a self-splicing intron in a
AB  - transcription factor-like gene and a splicesomal processed type of intron in its DNA
AB  - polymerase gene. Unlike the chlorella viruses, large double-stranded-DNA-containing viruses
AB  - that infect marine, filamentous brown algae have a circular genome and a lysogenic phase in
AB  - their life cycle.
ER  -

TY  - JOUR
AU  - Van Etten, J.L.
AU  - Schuster, A.M.
AU  - Girton, L.
AU  - Burbank, D.E.
AU  - Swinton, D.
AU  - Hattman, S.
TI  - DNA methylation of viruses infecting a eukaryotic Chlorella-like green alga.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 3471
EP  - 3478
VL  - 13
AB  - The genomic DNAs of the eukaryotic Chlorella-like green alga, strain NC64A, and
AB  - eleven of its viruses all contain significant levels of 5-methyldeoxycytidine.
AB  - In addition, the host DNA as well as six of the viral DNAs also contain
AB  - N6-methyldeoxyadenosine.  At least some of the methylated bases in the host
AB  - reside in different base sequences than the methylated bases in the viruses as
AB  - shown by differential susceptibility to restriction endonuclease enzymes.  This
AB  - suggests that the viruses encode for DNA methyltransferases with sequence
AB  - specificities different from that of the host enzyme.
ER  -

TY  - JOUR
AU  - Van Etten, J.L.
AU  - Xia, Y.
AU  - Burbank, D.E.
TI  - Viruses infecting a eukaryotic green alga are a new source of DNA methyltransferases and DNA site-specific endonucleases.
JO  - J. Cell Biochem. Suppl.
PY  - 1989
SP  - 199
EP  - 199
VL  - 13D
AB  - We have isolated and partially characterized several large, complex, dsDNA
AB  - containing (ca. 330kbp), plaque forming viruses (NC64A viruses) which infect
AB  - the unicellular, eukaryotic, Chlorella-like green alga strain NC64A.  These
AB  - viruses can be distinguished on the basis of plaque size, reaction with
AB  - antibody, and the nature and abundance of methylated bases in their genomic
AB  - DNAs.  The concentration of methylated bases varies from viruses containing no
AB  - 6-methyladenine (6mA) and 0.1% 5-methylcytosine (5mC) to one virus with 37% 6mA
AB  - and 45% 5mC.  Even though the host nuclear DNA contains 21% 5mC and 0.6% 6mA,
AB  - at least some of the methylated bases in the viruses reside in different DNA
AB  - sequences than those in the host.  This result led to the finding that virus
AB  - infection of the host results in the synthesis of DNA methyltransferases and
AB  - DNA site-specific (restriction) endonucleases.  Five different site-specific
AB  - endonucleases have been identified so far.  For example, virus NC-1A infected
AB  - Chlorella NC64A cells contain an endonuclease, named CviBI, which recognizes
AB  - the sequence GANTC and cleaves between G and A; CviBI does not cleave GmANTC
AB  - sequences.  NC-1A infected Chlorella cells contain the cognate
AB  - methyltransferase, M.CviBI, which specifically methylates adenine in GANTC
AB  - sequences and at least two other distinct methyltransferases; M.CviBII and
AB  - M.CviBIII methylate adenine in GATC and TCGA sequences, respectively.  The
AB  - M.CviBIII gene was cloned, sequenced and a single open reading frame of 1131 bp
AB  - identified.  A comparison of the predicted amino acid sequence of M.CviBIII
AB  - with M.TaqI, a bacterial isoschizomer, revealed 39% identity.  A second family
AB  - of viruses that infect another strain of Chlorella (Pbi) have recently been
AB  - isolated.  Like the NC64A viruses, the Pbi viruses contain large dsDNAs genomes
AB  - with various levels of methylated bases.  Infection of Chlorella Pbi with the
AB  - Pbi viruses also results in the synthesis of DNA methyltransferases and DNA
AB  - site-specific endonucleases.  Thus these Chlorella viruses are a new source of
AB  - both adenine and cytosine methyltransferases and DNA site-specific
AB  - endonucleases.
ER  -

TY  - JOUR
AU  - Van Etten, J.L.
AU  - Xia, Y.
AU  - Burbank, D.E.
AU  - Narva, K.E.
TI  - Chlorella viruses code for restriction and modification enzymes.
JO  - Gene
PY  - 1988
SP  - 113
EP  - 115
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Van Heuverswyn, H.
AU  - Fiers, W.
TI  - Recognition sequence for the restriction endonuclease BglI from Bacillus globigii.
JO  - Gene
PY  - 1980
SP  - 195
EP  - 203
VL  - 9
AB  - Restriction endonuclease BglI recognizes the DNA sequence ...CCCNNNN^NGGC...3'
AB  - ...CGGN^NNNNCCG...5' and cleaves each strand at the site indicated, thus
AB  - generating 3' protruding ends.  The recognition sequence was deduced by
AB  - correlating mapping data with nucleotide sequence information and the position
AB  - of cleavage was unambiguously determined by 32P labeling of 5' termini produced
AB  - by BglI digestion.
ER  -

TY  - JOUR
AU  - van Hijum, S.A.
AU  - Szalowska, E.
AU  - van der Maarel, M.J.
AU  - Dijkhuizen, L.
TI  - Biochemical and molecular characterization of a levansucrase from Lactobacillus reuteri.
JO  - Microbiology
PY  - 2004
SP  - 621
EP  - 630
VL  - 150
AB  - Lactobacillus reuteri strain 121 employs a fructosyltransferase (FTF) to synthesize a fructose
AB  - polymer [a fructan of the levan type, with
AB  - beta(2-->6) linkages] from sucrose or raffinose. Purification of this FTF
AB  - (a levansucrase), and identification of peptide amino acid sequences,
AB  - allowed isolation of the first Lactobacillus levansucrase gene (lev),
AB  - encoding a protein (Lev) consisting of 804 amino acids. Lev showed highest
AB  - similarity with an inulosucrase of L. reuteri 121 [Inu; producing an
AB  - inulin polymer with beta(2-->1)-linked fructosyl units] and with FTFs from
AB  - streptococci. Expression of lev in Escherichia coli resulted in an active
AB  - FTF (Lev Delta 773His) that produced the same levan polymer [with only 2-3
AB  - % beta(2-->1-->6) branching points] as L. reuteri 121 cells grown on
AB  - raffinose. The low degree of branching of the L. reuteri levan is very
AB  - different from bacterial levans known up to now, such as that of
AB  - Streptococcus salivarius, having up to 30 % branches. Although Lev is
AB  - unusual in showing a higher hydrolysis than transferase activity,
AB  - significant amounts of levan polymer are produced both in vivo and in
AB  - vitro. Lev is strongly dependent on Ca(2+) ions for activity. Unique
AB  - properties of L. reuteri Lev together with Inu are: (i) the presence of a
AB  - C-terminal cell-wall-anchoring motif causing similar expression problems
AB  - in Escherichia coli, (ii) a relatively high optimum temperature for
AB  - activity for FTF enzymes, and (iii) at 50 degrees C, kinetics that are
AB  - best described by the Hill equation.
ER  -

TY  - JOUR
AU  - Van Horn, C.
AU  - Chang, C.J.
AU  - Chen, J.
TI  - De Novo Whole-Genome Sequence of Xylella fastidiosa subsp. multiplex Strain BB01  Isolated from a Blueberry in Georgia, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e01598
EP  - e01516
VL  - 5
AB  - This study reports a de novo-assembled draft genome sequence of Xylella fastidiosa subsp.
AB  - multiplex strain BB01 causing blueberry bacterial leaf scorch
AB  - in Georgia, USA. The BB01 genome is 2,517,579 bp, with a G+C content of 51.8%,
AB  - 2,943 open reading frames (ORFs), and 48 RNA genes.
ER  -

TY  - JOUR
AU  - Van Houdt, R.
AU  - Van der Lelie, D.
AU  - Izquierdo, J.A.
AU  - Aertsen, A.
AU  - Masschelein, J.
AU  - Lavigne, R.
AU  - Michiels, C.W.
AU  - Taghavi, S.
TI  - Genome Sequence of Serratia plymuthica RVH1, Isolated from a Raw Vegetable-Processing Line.
JO  - Genome Announcements
PY  - 2014
SP  - e00021
EP  - e00014
VL  - 2
AB  - We announce the genome sequence of Serratia plymuthica strain RVH1, a psychroloterant strain
AB  - that was isolated from a raw vegetable-processing line and
AB  - that regulates the production of primary metabolites (acetoin and butanediol),
AB  - antibiotics, and extracellular enzymes through quorum sensing.
ER  -

TY  - JOUR
AU  - van Ingen, J. et al.
TI  - Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.
JO  - Lancet Infect Dis
PY  - 2017
SP  - 1033
EP  - 1041
VL  - 17
AB  - Since 2013, over 100 severe cases of Mycobacterium chimaera infections, often fatal, have been
AB  - notified in four European countries (Switzerland, Germany, the Netherlands, and the UK), the
AB  - USA, and Australia, all among patients who had undergone cardiothoracic surgery.17 Initial
AB  - epidemiological investigations suggested a link to the use of specific heatercooler units
AB  - (HCUs) that are used to control temperature within the extracorporeal circulation during
AB  - cardiac surgery.17 The possibility of a global outbreak caused by HCUs sparked investigations
AB  - by the European Centre for Disease Prevention and Control (ECDC) and the US Centers for
AB  - Disease Control and Prevention (CDC).
ER  -

TY  - JOUR
AU  - van Kranenburg, R.
AU  - de Vos, W.M.
TI  - Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in   Lactococcus lactis.
JO  - J. Bacteriol.
PY  - 1998
SP  - 5285
EP  - 5290
VL  - 180
AB  - We characterized the regions involved in replication and mobilization of the 40-kb plasmid
AB  - pNZ4000, encoding exopolysaccharide (EPS) production in
AB  - Lactococcus lactis NIZO B40. The plasmid contains four highly conserved
AB  - replication regions with homologous rep genes (repB1, repB2, repB3, and
AB  - repB4) that belong to the lactococcal theta replicon family. Subcloning of
AB  - each replicon individually showed that all are functional and compatible
AB  - in L. lactis. Plasmid pNZ4000 and genetically labeled derivatives could be
AB  - transferred to different L. lactis strains by conjugation, and pNZ4000 was
AB  - shown to be a mobilization plasmid. Two regions involved in mobilization
AB  - were identified near two of the replicons; both included an oriT sequence
AB  - rich in inverted repeats. Conjugative mobilization of the nonmobilizable
AB  - plasmid pNZ124 was promoted by either one of these oriT sequences,
AB  - demonstrating their functionality. One oriT sequence was followed by a
AB  - mobA gene, coding for a trans-acting protein, which increased the
AB  - frequency of conjugative transfer 100-fold. The predicted MobA protein and
AB  - the oriT sequences show protein and nucleotide similarity, respectively,
AB  - with the relaxase and with the inverted repeat and nic site of the oriT
AB  - from the Escherichia coli plasmid R64. The presence on pNZ4000 of four
AB  - functional replicons, two oriT sequences, and several insertion
AB  - sequence-like elements strongly suggests that this EPS plasmid is a
AB  - naturally occurring cointegrate.
ER  -

TY  - JOUR
AU  - van Kranenburg, R.
AU  - Kleerebezem, M.
AU  - de Vos, W.M.
TI  - Nucleotide sequence analysis of the lactococcal EPS plasmid pNZ4000.
JO  - Plasmid
PY  - 2000
SP  - 130
EP  - 136
VL  - 43
AB  - The complete 42180-bp nucleotide sequence of the mobilization plasmid
AB  - pNZ4000, coding for exopolysaccharide (EPS) production in Lactococcus
AB  - lactis, was determined. This plasmid contains a region involved in EPS
AB  - biosynthesis, four functional replicons, a region containing mobilization
AB  - genes, and three origin of transfer (oriT) sequences. Sequences identical
AB  - to these oriT sequences were also found on two other lactococcal plasmids
AB  - and a plasmid from Lactobacillus helveticus. Several complete and partial
AB  - IS elements were identified on pNZ4000, including iso-ISS1, iso-IS946, and
AB  - iso-IS982 sequences. Furthermore, pNZ4000 contains a gene cluster that may
AB  - encode a cobalt transport system and a gene that encodes a CorA homologue
AB  - which may function as a magnesium transporter.
ER  -

TY  - JOUR
AU  - Van Laar, T.A.
AU  - Chen, T.
AU  - Childers, B.M.
AU  - Chen, P.
AU  - Abercrombie, J.J.
AU  - Leung, K.P.
TI  - Genome Sequence of a Multidrug-Resistant Strain of Klebsiella pneumoniae, BAMC 07-18, Isolated from a Combat Injury Wound.
JO  - Genome Announcements
PY  - 2014
SP  - e01230
EP  - e01214
VL  - 2
AB  - Klebsiella pneumoniae is an important infectious agent of surgical sites and combat wounds.
AB  - Antibiotic resistance and tolerance are common impediments to the
AB  - healing of chronic infections. Here, we report the genome sequence of a highly
AB  - multidrug-resistant strain of K. pneumoniae, BAMC 07-18, isolated from a combat
AB  - wound of a soldier.
ER  -

TY  - JOUR
AU  - van Luijk, N.
AU  - Stierli, M.P.
AU  - Schwenninger, S.M.
AU  - Herve, C.
AU  - Dasen, G.
AU  - Jore, J.P.M.
AU  - Pouwels, P.H.
AU  - van der Werf, M.J.
AU  - Teuber, M.
AU  - Meile, L.
TI  - Genetics and molecular biology of propionibacteria.
JO  - Lait
PY  - 2002
SP  - 45
EP  - 57
VL  - 82
AB  - Research in the genetics and molecular biology of propionibacteria is currently making much
AB  - progress. In order to develop efficient DNA
AB  - transfer systems for the genus Propionibacterium, dairy and
AB  - environmental propionibacteria were screened for the presence of
AB  - suitable plasmids as a first step. Following nucleotide sequence
AB  - analysis, potential replication functions were identified on several
AB  - Propionibacterium plasmids such as pLME 106/pRGO1, p545 and pLME108.
AB  - Furthermore, ppnA, the gene encoding the propionicin SM1, was detected
AB  - on pLME106. Three of these plasmids which had been fused with
AB  - antibiotic resistance selection markers (ermE, cml, hygB) originating
AB  - from bacteria with high G+C DNA content were recently successfully used
AB  - as Escherichia coli - Propionibacterium shuttle vectors. DNA
AB  - restriction/modification systems observed in propionibacteria have to
AB  - be taken into account since successful DNA transformation at high rates
AB  - (up to 10^8 Propionibacterium transformants/microgram of DNA) succeeds only
AB  - with plasmid DNA originating from propionibacteria with the same
AB  - restriction/modification system(s) as the strain to be transformed, and
AB  - not from E. coli hosts. The basis for an integrating vector has been
AB  - set up after identification of a potential attP site and an adjacent
AB  - integrase gene from a Propionibacterium phage/prophage system. Finally,
AB  - approximately 30 gene sequences with attributed coding functions from
AB  - propionibacteria are available on databases.
ER  -

TY  - JOUR
AU  - van Mastrigt, O.
AU  - Abee, T.
AU  - Smid, E.J.
TI  - Complete Genome Sequences of Lactococcus lactis subsp. lactis bv. diacetylactis FM03 and Leuconostoc mesenteroides FM06 Isolated from Cheese.
JO  - Genome Announcements
PY  - 2017
SP  - e00633
EP  - e00617
VL  - 5
AB  - Here, the genome sequences of Lactococcus lactis subsp. lactis bv. diacetylactis  FM03 and
AB  - Leuconostoc mesenteroides FM06, both isolated from cheese, are
AB  - presented. FM03 and FM06 contain 7 and 3 plasmids, respectively, that carry genes
AB  - encoding functions important for growth and survival in dairy fermentations.
ER  -

TY  - JOUR
AU  - van Noort, J.
AU  - van der Heijden, T.
AU  - Dutta, F.C.
AU  - Firman, K.
AU  - Dekker, C.
TI  - Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 6540
EP  - 6547
VL  - 32
AB  - Recognition of 'foreign' DNA by Type I restriction-modification (R-M) enzymes elicits an
AB  - ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation
AB  - by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with
AB  - a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However, the EcoR124I R-M enzyme can also
AB  - exist as a cleavage deficient, sub-assembly of HsdR1:HsdM2:HsdS1 (R1-complex). ATPS was used
AB  - to trap initial translocation complexes, which were visualized by Atomic Force Microscopy
AB  - (AFM). In the R1-complex, a small bulge, associated with a shortening in the contour-length of
AB  - the DNA of 8 nm, was observed. This bulge was found to be sensitive to single-strand DNA
AB  - nucleases, indicative of non-duplexed DNA. R2-complexes appeared larger in the AFM images and
AB  - the DNA contour length showed a shortening of approximately 11 nm, suggesting that two bulges
AB  - were formed. Disclosure of the structure of the first stage after the
AB  - recognition-translocation switch of Type I restriction enzymes forms an important first step
AB  - in resolving a detailed mechanistic picture of DNA translocation by SF-II DNA translocation
AB  - motors.
ER  -

TY  - JOUR
AU  - van Noort, J.
AU  - van der Heijden, T.
AU  - van der Scheer, C.
AU  - Firman, K.
AU  - Dekker, C.
TI  - Single molecule characterization of DNA translocation by the type I restriction enzyme EcoR124I.
JO  - Biophys. J.
PY  - 2003
SP  - 304a
EP  - 304a
VL  - 84
AB  - In bacteria, viral DNA is degraded by dedicated type I restriction enzymes.  When DNA is not
AB  - methylated, it is recognized as foreign and the enzyme starts DNA translocation consuming ATP,
AB  - to form a loop.  Cleavage will occur when translocation is blocked.  In this study the motor
AB  - properties of EcoR124I are investigated with Atomic Force Microscopy and Magnetic Tweezers.
AB  - Energetic barriers due to DNA bending and torsion, can be expected when EcoR124I moves over
AB  - DNA.  In the initial DNA EcoR124I complex AFM images show DNA tightly wrapped around the
AB  - enzyme.  In circular DNA no supercoiling is observed in front and behind the complex after
AB  - translocation.  Magnetic tweezers data however, show that the translocation does impose a
AB  - twist on the DNA.  Time traces of the length of single DNA molecules being processed by
AB  - EcoR124I show a non-constant translocation velocity, and repeated hick-ups.  A discrepancy is
AB  - observed between the translocation distance and the expected imposed twist.  The observed
AB  - behavior is consistent with frequent slipping events, both in translation and in rotation.
ER  -

TY  - JOUR
AU  - van Ormondt, H.
AU  - Gorter, J.
AU  - Havelaar, K.J.
AU  - de Waard, A.
TI  - Specificity of a deoxyribonucleic acid transmethylase induced by bacteriophage T2.  I. Nucleotide sequences isolated from Micrococcus luteus DNA methylated in vitro.
JO  - Nucleic Acids Res.
PY  - 1975
SP  - 1391
EP  - 1400
VL  - 2
AB  - Deoxyribonucleic acid from Micrococcus luteus was methylated in vitro in the presence of
AB  - S-adenosyl-(14C methyl)methionine with a DNA methyltransferase purified from extracts of E.
AB  - coli infected with bacteriophage T2. The labelled DNA was degraded by enzymatic and specific
AB  - chemical methods and the resulting short oligonucleotides were separated and characterized.
AB  - The analytical data permit the conclusion that the DNA transmethylase reacts specifically with
AB  - N-G-A-T-C-N sequences in which it converts adenine to a 6-methyl-aminopurine residue.
ER  -

TY  - JOUR
AU  - van Ormondt, H.
AU  - Lautenberger, J.A.
AU  - Linn, S.
AU  - de Waard, A.
TI  - Methylated oligonucleotides derived from bacteriophage fd RF-DNA modified in vitro by E. coli B modification methylase.
JO  - FEBS Lett.
PY  - 1973
SP  - 177
EP  - 180
VL  - 33
AB  - E. coli B modification methylase converts four adenine residues (presumably two
AB  - per strand) to N(6)-methylaminopurine in wild-type unmodified fd RF-DNA.  When
AB  - RF-DNA of the one-site mutant fd sB01 sB2 (strain 101) is the substrate, the
AB  - DNA receives two methyl groups while fd sB01 sB02 RF-DNA has lost is
AB  - susceptibility to the methylase by mutation.  This methylation is concomitant
AB  - with an increase in infectivity on E. coli B spheroplasts.  These results
AB  - probably mean that wild-type RF-DNA has two recognizable and specific
AB  - nucleotide sequences ("sites"), fd sB01 sB2 one, and fd sB01 sB02 none, which
AB  - by becoming methylated confer resistance to the E. coli B restriction enzyme.
AB  - The present study was undertaken to elucidate the structure of those sites
AB  - which bear "E. coli B specificity".  To this end, unmodified RF-DNA of
AB  - wild-type fd was methylated in vitro in the presence of purified modification
AB  - methylase from E. coli B and methyl tritiated S-adenosylmethionine.  The
AB  - [3H-methyl]RF-DNA was degraded to small fragments, and the tritiated
AB  - oligonucleotides characterized as to their sequence. Although a definitive
AB  - sequence was not obtained by this approach, an analysis of the sequenced
AB  - oligonucleotides showed the 3'- and 5'-nearest neighbors of the methylated
AB  - adenine residues to be A or C, G or C, respectively.  This finding demonstrates
AB  - that the sequence surrounding the modified base does not contain a twofold
AB  - rotational symmetry.
ER  -

TY  - JOUR
AU  - van Passel, M.W. et al.
TI  - Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human  gastro-intestinal tract.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2373
EP  - 2374
VL  - 193
AB  - Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel
AB  - phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this
AB  - phylum are known, and V. vadensis therefore represents an important organism for evolutionary
AB  - studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human
AB  - gastro-intestinal tract.
ER  -

TY  - JOUR
AU  - van Passel, M.W. et al.
TI  - Genome sequence of the Verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2367
EP  - 2368
VL  - 193
AB  - Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured, yet commonly
AB  - detected in metagenomic libraries from aquatic, terrestrial and intestinal environments. We
AB  - have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this
AB  - phylum, isolated from rice paddy soil and capable of propionate production from plant-derived
AB  - polysaccharides.
ER  -

TY  - JOUR
AU  - Van Pel, A.
AU  - Colson, C.
TI  - DNA restriction and modification systems in Salmonella:  II. Genetic complementation between the K and B systems of Escherichia coli and the Salmonella typhimurium system SB, with the same chromosomal location.
JO  - Mol. Gen. Genet.
PY  - 1974
SP  - 51
EP  - 60
VL  - 135
AB  - E. coli x S. typhimurium partially diploid hybrids were constructed to
AB  - investigate the possibility of genetic complementation between the SA and the
AB  - SB restriction and modification systems of S. typhimurium and the K and B
AB  - systems of E. coli.  An hsdR-K mutation was complemented in a stable hybrid in
AB  - which the hsd+SA-hsd+SB-serB+ portion of the S. typhimurium chromosome was
AB  - integrated at a non-homologous locus.  By isolating hsd- mutants in that
AB  - hybrid, it was shown that complementation occurred between K and SB, but not
AB  - between K and SA.  Similarly, in a set of F-prime merodiploids bearing the SA,
AB  - SB and B systems, complementation was observed between B and SB, but not
AB  - between B and SA.
ER  -

TY  - JOUR
AU  - Van Roey, P.
AU  - Belfort, M.
AU  - Derbyshire, V.
TI  - Homing endonuclease I-TevI: An atypical zinc finger with a novel function.
JO  - Zinc Finger Proteins: from Atomic Contact to Cellular Function; Molecular Biology Intelligence Unit
PY  - 2005
SP  - 35
EP  - 38
VL  - 0
AB  - I-TevI is a site-specific, sequence-tolerant homing endonuclease encoded by the td intron of
AB  - bacteriophage T4.  The enzyme consists of an N-terminal catalytic domain and a C-terminal
AB  - DNA-binding domain that are connected by a long, flexible linker.  The crystal structure of
AB  - the DNA-binding domain of I-TevI, residues 130 to 245, complexed with the 20-bp primary
AB  - binding region of its DNA target, reveals the presence of a zinc finger, comprising residues
AB  - 151 to 167, that makes backbone contacts with the DNA from the minor groove.  Biochemical data
AB  - have shown that the zinc finger does not contribute to the DNA-binding affinity or to the
AB  - specificity of the enzyme, but rather that it has a novel function and acts as a distance
AB  - determinant that controls the relative positions of the catalytic and DNA-binding domains.
ER  -

TY  - JOUR
AU  - Van Roey, P.
AU  - Derbyshire, V.
TI  - GIY-YIG homing endonucleases - beads on a string.
JO  - Nucleic Acids Mol. Biol.
PY  - 2005
SP  - 67
EP  - 83
VL  - 16
AB  - Homing endonucleases are intron- and intein-encoded proteins that initiate the mobility of
AB  - their particular host elements.  They recognize an intron- or intein-less version of their
AB  - host gene and introduce a double-strand break in the DNA.  This break is then repaired by
AB  - copying the intron- or intein-plus allele, using the hosts cellular machinery.  This results
AB  - in a gene-conversion event whereby both alleles become intron- or intein-plus.  Homing
AB  - endonucleases can be classified into four distinct families, based on the presence of
AB  - conserved sequence elements: the LAGLIDADG, GIY-YIG, His-Cys box, and HNH families.  However,
AB  - the His-Cys box and HNH families have been hypothesized to constitute a single bba-Me family,
AB  - and recent structural data support this classification.
ER  -

TY  - JOUR
AU  - Van Roey, P.
AU  - Meehan, L.
AU  - Kowalski, J.C.
AU  - Belfort, M.
AU  - Derbyshire, V.
TI  - Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.
JO  - Nat. Struct. Biol.
PY  - 2002
SP  - 806
EP  - 811
VL  - 9
AB  - I-TevI, a member of the GIY-YIG family of homing endonucleases, consists of an N-terminal
AB  - catalytic domain and a C-terminal DNA-binding domain joined by a flexible linker. The GIY-YIG
AB  - motif is in the N-terminal domain of I-TevI, which corresponds to a phylogenetically
AB  - widespread catalytic cartridge that is often associated with mobile genetic elements. The
AB  - crystal structure of the catalytic domain of I-TevI, the first of any GIY-YIG endonuclease,
AB  - reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked
AB  - by three helices. The most conserved and putative catalytic residues are located on a shallow,
AB  - concave surface and include a metal coordination site. Similarities in the three-dimensional
AB  - arrangement of the catalytically important residues and the cation-binding site with those of
AB  - the His-Cys box endonuclease I-PpoI suggest the possibility of mechanistic relationships among
AB  - these different families of homing endonucleases despite completely different folds.
ER  -

TY  - JOUR
AU  - Van Roey, P.
AU  - Waddling, C.A.
AU  - Fox, K.M.
AU  - Belfort, M.
AU  - Derbyshire, V.
TI  - Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.
JO  - EMBO J.
PY  - 2001
SP  - 3631
EP  - 3637
VL  - 20
AB  - I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the
AB  - DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target
AB  - reveals an unusually extended structure composed of three subdomains: a Zn finger, an
AB  - elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The
AB  - protein wraps around the DNA, mostly following the minor groove, contacting the phosphate
AB  - backbone along the full length of the duplex. Surprisingly, while the minor groove-binding
AB  - helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific
AB  - hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion
AB  - site. The multiple base-specific interactions over a long segment of the substrate are
AB  - consistent with the observed high site specificity in spite of sequence tolerance, while the
AB  - modular composition of the domain is pertinent to the evolution of homing endonucleases.
ER  -

TY  - JOUR
AU  - van Schaik, W.
AU  - Top, J.
AU  - Riley, D.R.
AU  - Boekhorst, J.
AU  - Vrijenhoek, J.E.
AU  - Schapendonk, C.M.
AU  - Hendrickx, A.P.
AU  - Nijman, I.J.
AU  - Bonten, M.J.
AU  - Tettelin, H.
AU  - Willems, R.J.
TI  - Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island.
JO  - BMC Genomics
PY  - 2010
SP  - 239
EP  - 239
VL  - 11
AB  - BACKGROUND: The Gram-positive bacterium Enterococcus faecium is an
AB  - important cause of nosocomial infections in immunocompromized patients.
AB  - RESULTS: We present a pyrosequencing-based comparative genome analysis of
AB  - seven E. faecium strains that were isolated from various sources. In the
AB  - genomes of clinical isolates several antibiotic resistance genes were
AB  - identified, including the vanA transposon that confers resistance to
AB  - vancomycin in two strains. A functional comparison between E. faecium and
AB  - the related opportunistic pathogen E. faecalis based on differences in the
AB  - presence of protein families, revealed divergence in plant carbohydrate
AB  - metabolic pathways and oxidative stress defense mechanisms. The E. faecium
AB  - pan-genome was estimated to be essentially unlimited in size, indicating
AB  - that E. faecium can efficiently acquire and incorporate exogenous DNA in
AB  - its gene pool. One of the most prominent sources of genomic diversity
AB  - consists of bacteriophages that have integrated in the genome. The
AB  - CRISPR-Cas system, which contributes to immunity against bacteriophage
AB  - infection in prokaryotes, is not present in the sequenced strains. Three
AB  - sequenced isolates carry the esp gene, which is involved in urinary tract
AB  - infections and biofilm formation. The esp gene is located on a large
AB  - pathogenicity island (PAI), which is between 64 and 104 kb in size.
AB  - Conjugation experiments showed that the entire esp PAI can be transferred
AB  - horizontally and inserts in a site-specific manner. CONCLUSIONS: Genes
AB  - involved in environmental persistence, colonization and virulence can
AB  - easily be aquired by E. faecium. This will make the development of
AB  - successful treatment strategies targeted against this organism a challenge
AB  - for years to come.
ER  -

TY  - JOUR
AU  - Van Sluys, M.A. et al.
TI  - Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa.
JO  - J. Bacteriol.
PY  - 2003
SP  - 1018
EP  - 1026
VL  - 185
AB  - Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes
AB  - diseases in many plants, including
AB  - grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa
AB  - has an unusually broad host range, has an extensive geographical
AB  - distribution throughout the American continent, and induces diverse
AB  - disease phenotypes. Previous molecular analyses indicated three distinct
AB  - groups of X. fastidiosa isolates that were expected to be genetically
AB  - divergent. Here we report the genome sequence of X. fastidiosa (Temecula
AB  - strain), isolated from a naturally infected grapevine with Pierce's
AB  - disease (PD) in a wine-grape-growing region of California. Comparative
AB  - analyses with a previously sequenced X. fastidiosa strain responsible for
AB  - citrus variegated chlorosis (CVC) revealed that 98% of the PD X.
AB  - fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain
AB  - 9a5c genes. Furthermore, the average amino acid identity of the open
AB  - reading frames in the strains is 95.7%. Genomic differences are limited to
AB  - phage-associated chromosomal rearrangements and deletions that also
AB  - account for the strain-specific genes present in each genome. Genomic
AB  - islands, one in each genome, were identified, and their presence in other
AB  - X. fastidiosa strains was analyzed. We conclude that these two organisms
AB  - have identical metabolic functions and are likely to use a common set of
AB  - genes in plant colonization and pathogenesis, permitting convergence of
AB  - functional genomic strategies.
ER  -

TY  - JOUR
AU  - van Soolingen, D.
AU  - de Haas, P.E.W.
AU  - Blumenthal, R.M.
AU  - Kremer, K.
AU  - Sluijter, M.
AU  - Pijnenburg, J.E.M.
AU  - Schouls, L.M.
AU  - Thole, J.E.R.
AU  - Desens-Kroon, M.W.G.
AU  - van Embden, J.D.A.
AU  - Hermans, P.W.M.
TI  - Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis.
JO  - J. Bacteriol.
PY  - 1996
SP  - 78
EP  - 84
VL  - 178
AB  - Restriction endonuclease PvuII plays a central role in restriction fragment length
AB  - polymorphism analysis of Mycobacterium tuberculosis complex isolates with IS6110 as a genetic
AB  - marker.  We have investigated the basis for an apparent dichotomy in PvuII restriction
AB  - fragment patterns observed among strains of the M. tuberculosis complex.  The chromosomal
AB  - regions of two modified PvuII restriction sites, located upstream of the katG gene and
AB  - downstream of an IS108I insertion sequence, were studied in more detail.  An identical 10-bp
AB  - DNA sequence (CAGCTGGAGC) containing a PvuII site was found in both regions, and site-directed
AB  - mutagenesis analysis revealed that this sequence was a target for modification.
AB  - Strain-specific modification of PvuII sites was identified in DNA from over 80% of the nearly
AB  - 800 isolates examined.  Furthermore, the proportion of modifying and nonmodifying strains
AB  - differs significantly from country to country.
ER  -

TY  - JOUR
AU  - van Steensel, B.
AU  - Henikoff, S.
TI  - Epigenomic profiling using microarrays.
JO  - Biotechniques
PY  - 2003
SP  - 346
EP  - 357
VL  - 35
AB  - Genes occupy only a minor fraction of genomes such as ours; however, histone and nonhistone
AB  - chromosomal proteins and methylated DNA bases are
AB  - distributed over both genic and nongenic regions. These widespread
AB  - "epigenomic" features can be mapped and characterized by alternative
AB  - applications of the same microarray technologies that have been used for
AB  - conventional transcriptional profiling. Here we describe diverse
AB  - microarray-based strategies for profiling patterns of DNA methylation, DNA
AB  - replication, DNA binding, and chromatin-associated proteins and histone
AB  - modifications. The rapid progress that is being made in developing and
AB  - applying epigenomic profiling methods and the increasing availability of
AB  - microarrays mean that epigenomic profiling is likely to become a standard
AB  - research tool for understanding chromatin structure and gene expression
AB  - during development.
ER  -

TY  - JOUR
AU  - van Steensel, B.
AU  - Henikoff, S.
TI  - Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase.
JO  - Nat. Biotechnol.
PY  - 2000
SP  - 424
EP  - 428
VL  - 18
AB  - We have developed a novel technique, named DamID, for the identification of DNA loci that
AB  - interact in vivo with specific nuclear proteins in eukaryotes. By tethering Escherichia coli
AB  - DNA adenine methyltransferase (Dam) to a chromatin protein, Dam can be targeted in vivo to
AB  - native binding sites of this protein, resulting in local DNA methylation. Sites of methylation
AB  - can subsequently be mapped using methylation-specific restriction enzymes or antibodies. We
AB  - demonstrate the successful application of DamID both in Drosophila cell cultures and in whole
AB  - flies. When Dam is tethered to the DNA-binding domain of GAL4, targeted methylation is limited
AB  - to a region of a few kilobases surrounding a GAL4 binding sequence. Using DamID, we identified
AB  - a number of expected and unexpected target loci for Drosophila heterochromatin protein 1.
AB  - DamID has potential for genome-wide mapping of in vivo targets of chromatin proteins in
AB  - various eukaryotes.
ER  -

TY  - JOUR
AU  - van Zyl, L.J.
AU  - Deane, S.M.
AU  - Louw, L.A.
AU  - Rawlings, D.E.
TI  - Presence of a family of plasmids (29 to 65 kilobases) with a 26-kilobase common region in different strains of the sulfur-oxidizing bacterium Acidithiobacillus caldus.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 4300
EP  - 4308
VL  - 74
AB  - Three large cryptic plasmids from different isolates of Acidithiobacillus caldus were rescued
AB  - by using an in vitro
AB  - transposition system that delivers a kanamycin-selectable marker and an
AB  - Escherichia coli plasmid origin of replication. The largest of the
AB  - plasmids, the 65-kb plasmid pTcM1, was isolated from a South African A.
AB  - caldus strain, MNG. This plasmid was sequenced and compared to that of
AB  - pTcF1 (39 kb, from strain "f," South Africa) and pC-SH12 (29 kb, from
AB  - strain C-SH12, Australia). With the exception of a 2.7-kb insertion
AB  - sequence, pC-SH12 appears to represent the DNA common to all three
AB  - plasmids and includes a number of accessory genes plus the plasmid
AB  - "backbone" containing the replication region. The two larger plasmids
AB  - carry, in addition, a number of insertion sequences of the ISL3 family
AB  - and a composite transposon related to the Tn21 subfamily containing a
AB  - highly mosaic region within the borders of the inverted repeats. Genes
AB  - coding for arsenic resistance, plasmid mobilization, plasmid stability,
AB  - and a putative restriction-modification system occur within these
AB  - mosaic regions.
ER  -

TY  - JOUR
AU  - van Zyl, L.J.
AU  - Matobole, R.
AU  - Augustin, N.B.F.
AU  - Klein, T.
AU  - Kirby, B.
AU  - Trindade, M.
TI  - Draft Genome Sequences of Three Bacillus Species from South African Marine Sponges.
JO  - Genome Announcements
PY  - 2016
SP  - e00143
EP  - e00116
VL  - 4
AB  - The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with
AB  - antimicrobial activity. This brief report describes the genome
AB  - sequence of threeBacillusspecies isolates from South African marine sponges,
AB  - which produce compounds with antimicrobial activity. A search for secondary
AB  - metabolite clusters revealed several secondary metabolite pathways in these
AB  - genomes, which may hold promise as novel antibiotics.
ER  -

TY  - JOUR
AU  - Vanamee, E.S.
AU  - Aggarwal, A.K.
TI  - Metal-dependent type II restriction endonucleases.
JO  - Handbook of Metalloproteins
PY  - 2004
SP  - 742
EP  - 756
VL  - 3
AB  - Restriction endonucleases are phosphodiesterases that bind double-stranded DNA with high
AB  - specificity and cleave the DNA to yield 5'-phosphate and 3'-hydroxyl groups as products.
AB  - Restriction endonucleases with their corresponding methyltransferases form the
AB  - restriction-modification systems of bacteria.  R-M systems are ubiquitous in bacteria; only a
AB  - few are known not to contain any R-M gene.  The recently sequenced Helicobacter pylori strain
AB  - 26695, for instance, reveals more than a dozen R-M systems, though less than 30% are
AB  - functional.
ER  -

TY  - JOUR
AU  - Vanamee, E.S.
AU  - Berriman, J.
AU  - Aggarwal, A.K.
TI  - An EM View of the FokI Synaptic Complex by Single Particle Analysis.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 207
EP  - 212
VL  - 370
AB  - FokI is a type IIS restriction endonuclease that recognizes the 5'-GGATG-3' sequence and
AB  - cleaves non-specifically at 9 and 13 base-pairs away on the top and bottom strands,
AB  - respectively, to produce a 5' overhang. FokI is a bipartite endonuclease with separate
AB  - recognition and cleavage domains. Because of its bipartite nature, FokI has received
AB  - considerable interest in generating chimeric nucleases for use in biotechnology, and recently
AB  - as possible therapeutic agents in gene therapy by initiating homologous gene recombination and
AB  - repair. Here we show, using single-particle electron microscopic studies, that the FokI active
AB  - complex prefers a single conformation in which the subunits are arranged in a doughnut shape
AB  - complex with protein-protein and possibly protein-DNA interactions stabilizing the cleavage
AB  - complex. Our electron microscopy (EM) model provides new insights into the activation
AB  - mechanism of FokI and how non-specific cleavage is avoided.
ER  -

TY  - JOUR
AU  - Vanamee, E.S.
AU  - Hsieh, P.C.
AU  - Zhu, Z.Y.
AU  - Yates, D.
AU  - Garman, E.
AU  - Xu, S.Y.
AU  - Aggarwal, A.K.
TI  - Glucocorticoid receptor-like Zn(Cys)(4) motifs in BslI restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 595
EP  - 603
VL  - 334
AB  - BslI restriction endonuclease cleaves the symmetric sequence CCN(7)GG (where N=A, C, G or T).
AB  - The enzyme is composed of two subunits, alpha and
AB  - beta, that form a heterotetramer (alpha(2)beta(2)) in solution. The alpha
AB  - subunit is believed to be responsible for DNA recognition, while the beta
AB  - subunit is thought to mediate cleavage. Here, for the first time, we
AB  - provide experimental evidence that BslI binds Zn(II). Specifically, using
AB  - X-ray absorption spectroscopic analysis we show that the alpha subunit of
AB  - BslI contains two Zn(Cys)(4)-type zinc motifs similar to those in the
AB  - DNA-binding domain of the glucocorticoid receptor. This conclusion is
AB  - supported by genetic analysis of the zinc-binding motifs, whereby amino
AB  - acid substitutions in the zinc finger motifs are demonstrated to abolish
AB  - or impair cleavage activity. An additional putative zinc-binding motif was
AB  - identified in the beta subunit, consistent with the X-ray absorption data.
AB  - These data were corroborated by proton induced X-ray emission measurements
AB  - showing that full BslI contains at least three fully occupied Zn sites per
AB  - alpha/beta heterodimer. On the basis of these data, we propose a role for
AB  - the BslI Zn motifs in protein-DNA as well as protein-protein interactions.
ER  -

TY  - JOUR
AU  - Vanamee, E.S.
AU  - Santagata, S.
AU  - Aggarwal, A.K.
TI  - FokI requires two specific DNA sites for cleavage.
JO  - J. Mol. Biol.
PY  - 2001
SP  - 69
EP  - 78
VL  - 309
AB  - FokI is a bipartite restriction endonuclease that recognizes a non-palindromic DNA sequence,
AB  - and then makes double-stranded cuts
AB  - outside of that sequence to leave a 5' overhang. Earlier kinetic and
AB  - crystallographic studies suggested that FokI might function as a dimer.
AB  - Here, we show, using dynamic light-scattering, gel-filtration and
AB  - analytical ultracentrifugation, that FokI dimerizes only in the
AB  - presence of divalent metal ions. Furthermore, analysis of the DNA-bound
AB  - complex reveals that two copies of the recognition sequence are
AB  - incorporated into the dimeric complex and that formation of this
AB  - complex is essential for full activation of cleavage. These results
AB  - have broad implications for the mechanism by which monomeric type II
AB  - endonucleases achieve high fidelity.
ER  -

TY  - JOUR
AU  - Vanamee, E.S.
AU  - Viadiu, H.
AU  - Chan, S.H.
AU  - Ummat, A.
AU  - Hartline, A.M.
AU  - Xu, S.Y.
AU  - Aggarwal, A.K.
TI  - Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 712
EP  - 719
VL  - 39
AB  - Restriction enzymes share little or no sequence homology with the exception of isoschizomers,
AB  - or enzymes that recognize and cleave the same DNA sequence. We present here the structure of a
AB  - BamHI isoschizomer, OkrAI, bound to the same DNA sequence (TATGGATCCATA) as that
AB  - cocrystallized with BamHI. We show that OkrAI is a more minimal version of BamHI, lacking not
AB  - only the N- and C-terminal helices but also an internal 3(10) helix and containing ?-strands
AB  - that are shorter than those in BamHI. Despite these structural differences, OkrAI recognizes
AB  - the DNA in a remarkably similar manner to BamHI, including asymmetric contacts via C-terminal
AB  - 'arms' that appear to 'compete' for the minor groove. However, the arms are shorter than
AB  - in BamHI. We observe similar DNA-binding affinities between OkrAI and BamHI but OkrAI has
AB  - higher star activity (at 37=B0C) compared to BamHI. Together, the OkrAI and BamHI structures
AB  - offer a rare opportunity to compare two restriction enzymes that work on exactly the same DNA
AB  - substrate.
ER  -

TY  - JOUR
AU  - Vanamee, E.S.
AU  - Viadiu, H.
AU  - Kucera, R.
AU  - Dorner, L.
AU  - Picone, S.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
JO  - EMBO J.
PY  - 2005
SP  - 4198
EP  - 4208
VL  - 24
AB  - Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic
AB  - complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave
AB  - two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex
AB  - with cognate DNA. The structures reveal two different binding states of SfiI: one with both
AB  - DNA-binding sites fully occupied and the other with fully and partially occupied sites. These
AB  - two states provide details on how SfiI recognizes and cleaves its target DNA sites, and gives
AB  - insight into sequential binding events. The SfiI recognition sequence (GGCCNNNN[downward
AB  - arrow]NGGCC) is a subset of the recognition sequence of BglI (GCCNNNN[downward arrow]NGGC),
AB  - and both enzymes cleave their target DNAs to leave 3-base 3' overhangs. We show that even
AB  - though SfiI is a tetramer and BglI is a dimer, and there is little sequence similarity between
AB  - the two enzymes, their modes of DNA recognition are unusually similar.
ER  -

TY  - JOUR
AU  - Vanat, I.
AU  - Pristas, P.
AU  - Kutejova, E.
AU  - Judova, J.
AU  - Godany, A.
AU  - Jovorsky, P.
TI  - SbvI restriction endonuclease from Streptococcus bovis.
JO  - Lett. Appl. Microbiol.
PY  - 1993
SP  - 297
EP  - 299
VL  - 17
AB  - Restriction endonuclease SbvI, an isoschizomer of HaeIII, has been isolated from the rumen
AB  - amylolytic bacterium Streptococcus bovis II/1. SbvI was purified from a cell extract by
AB  - phosphocellulose chromatography and heparin-Sepharose chromatography. The recognition sequence
AB  - of SbvI was identified by digestion of pBR322, pUC9 and lambda DNA and comparing the cleavage
AB  - patterns obtained with computer-derived data. SbvI recognizes the 4-bp palindrome,
AB  - 5'-GGCC-3' and cleaves DNA after the second G in the sequence, producing blunt ends.
ER  -

TY  - JOUR
AU  - Vanat, I.
AU  - Pristas, P.
AU  - Rybosoval, E.
AU  - Godany, A.
AU  - Javorsky, P.
TI  - SruI restriction endonuclease from Selenomonas ruminantium.
JO  - FEMS Microbiol. Lett.
PY  - 1993
SP  - 129
EP  - 132
VL  - 113
AB  - SruI, specific restriction endonuclease, has been characterized from Selenomonas ruminantium
AB  - isolated from the rumen of fallow deer. Results from the study demonstrate that S. ruminantium
AB  - 18D possesses a type II restriction endonuclease, which recognizes the sequence 5'TTTAAA 3'.
AB  - The recognition sequence of SruI was identified using digestions on pBR322, pBR328, pUC18,
AB  - M13mp18RF, pACYC184 and lambda DNA. The cleavage patterns obtained were compared with
AB  - computer-derived data. SruI recognizes the palindromic hexanucleotide sequence and cleaves DNA
AB  - after the third T in the sequence, producing blunt ends. The purification and characterization
AB  - of restriction endonuclease SruI presented here is the first described for Selenomonas
AB  - ruminantium spp. and demonstrates that this microorganism possesses a DNA-cleaving enzyme with
AB  - the same specificity as DraI or AhaIII.
ER  -

TY  - JOUR
AU  - Vancheva, T.
AU  - Bogatzevska, N.
AU  - Moncheva, P.
AU  - Lefeuvre, P.
AU  - Koebnik, R.
TI  - Draft Genome Sequences of Two Xanthomonas vesicatoria Strains from the Balkan Peninsula.
JO  - Genome Announcements
PY  - 2015
SP  - e01558
EP  - e01514
VL  - 3
AB  - Xanthomonas vesicatoria causes bacterial spot disease of pepper and tomato plants. We report
AB  - here the first genome sequences of X. vesicatoria strains that
AB  - have been isolated from pepper plants. These data will be used for comparative
AB  - genomics and will allow the development of new detection and typing tools for
AB  - epidemiological surveillance.
ER  -

TY  - JOUR
AU  - Vancheva, T.
AU  - Lefeuvre, P.
AU  - Bogatzevska, N.
AU  - Moncheva, P.
AU  - Koebnik, R.
TI  - Draft Genome Sequences of Two Xanthomonas euvesicatoria Strains from the Balkan Peninsula.
JO  - Genome Announcements
PY  - 2015
SP  - e01528
EP  - e01514
VL  - 3
AB  - We report the draft genome sequences of two Xanthomonas euvesicatoria strains from the Balkan
AB  - Peninsula, which were isolated from symptomatic pepper plants.
AB  - The availability of these genome sequences will facilitate the development of
AB  - modern genotyping assays for X. euvesicatoria strains and to define targets for
AB  - resistance breeding.
ER  -

TY  - JOUR
AU  - Vandecandelaere, I.
AU  - Van Nieuwerburgh, F.
AU  - Deforce, D.
AU  - Nelis, H.J.
AU  - Coenye, T.
TI  - Draft Genome Sequence of Methicillin-Resistant Staphylococcus epidermidis Strain  ET-024, Isolated from an Endotracheal Tube Biofilm of a Mechanically Ventilated  Patient.
JO  - Genome Announcements
PY  - 2014
SP  - e00527
EP  - e00514
VL  - 2
AB  - Staphylococcus epidermidis strain ET-024 was isolated from a biofilm on an endotracheal tube
AB  - of a mechanically ventilated patient. This strain is resistant
AB  - to methicillin, and the draft genome sequence shares some characteristics with
AB  - other nosocomial S. epidermidis strains (such as S. epidermidis RP62A).
ER  -

TY  - JOUR
AU  - Vandenbogaert, M.
AU  - Makeev, V.
TI  - Analysis of bacterial RM-systems through genome-scale analysis and related taxonomy issues.
JO  - In Silico Biology
PY  - 2003
SP  - 127
EP  - 143
VL  - 3
AB  - Recognition sites for type II restriction and modification enzymes in genomes of several
AB  - bacteria are recognized as semi-palindromic motifs and
AB  - are avoided at a significant degree. The key idea of contrast word
AB  - analysis with respect to RMS recognition sites, is that under-represented
AB  - words are likely to be selected against. Starting from over- or
AB  - underrepresented words corresponding to RMS recognition sites in specific
AB  - clades, the specificity of unknown R-M systems can be highlighted. Among
AB  - the known restriction enzymes, that are described in the REBASE database
AB  - of restriction and modification systems, many of their recognition sites
AB  - are still uncharacterized. Eventually, this motivates studies aimed at
AB  - assessing horizontal transferring events of RMS in micro-organisms through
AB  - the analysis of word usage biases in well-determined genomic regions. A
AB  - probabilistic model is built on a first-order Markovian chain. Statistics
AB  - on the k-neighborhood of a word is carried out to assess the biological
AB  - significance of a genomic motif. Efficient word counting procedures have
AB  - been implemented and statistics are used for the assessment of the
AB  - significance of individual words in large sequences. On the basis of the
AB  - set of most avoided words, and in accordance to the IUPAC coding
AB  - standards, suggestions are made regarding potential recognition sequences.
AB  - In certain cases, a comparison of avoided palindromic words in
AB  - taxonomically related bacteria shows a pattern of relatedness of their R-M
AB  - systems. For strengthening this analysis, the primary protein structure of
AB  - all type II R-M systems known in REBASE have been blasted against the
AB  - nr-GENBANK database. The combination of these analyses has revealed some
AB  - interesting examples of possible horizontal transfer events of R-M
AB  - systems.
ER  -

TY  - JOUR
AU  - Vandersteegen, K.
AU  - Kropinski, A.M.
AU  - Nash, J.H.
AU  - Noben, J.P.
AU  - Hermans, K.
AU  - Lavigne, R.
TI  - Romulus and Remus, Two Phage Isolates Representing a Distinct Clade within the Twortlikevirus Genus, Display Suitable Properties for Phage Therapy Applications.
JO  - J. Virol.
PY  - 2013
SP  - 3237
EP  - 3247
VL  - 87
AB  - The renewed interest in controlling Staphylococcus aureus infections using their
AB  - natural enemies, bacteriophages, has led to the isolation of a limited number of
AB  - virulent phages so far. These phages are all members of the Twortlikevirus,
AB  - displaying little variance. We present two novel closely related (95.9% DNA
AB  - homology) lytic myoviruses, Romulus and Remus, with double-stranded DNA (dsDNA)
AB  - genomes of 131,333 bp and 134,643 bp, respectively. Despite their relatedness to
AB  - Staphylococcus phages K, G1, ISP, and Twort and Listeria phages A511 and P100,
AB  - Romulus and Remus can be proposed as isolates of a new species within the
AB  - Twortlikevirus genus. A distinguishing feature for these phage genomes is the
AB  - unique distribution of group I introns compared to that in other staphylococcal
AB  - myoviruses. In addition, a hedgehog/intein domain was found within their DNA
AB  - polymerase genes, and an insertion sequence-encoded transposase exhibits splicing
AB  - behavior and produces a functional portal protein. From a phage therapy
AB  - application perspective, Romulus and Remus infected approximately 70% of the
AB  - tested S. aureus isolates and displayed promising lytic activity against these
AB  - isolates. Furthermore, both phages showed a rapid initial adsorption and
AB  - demonstrated biofilm-degrading capacity in a proof-of-concept experiment.
ER  -

TY  - JOUR
AU  - Vandzurova, A.
AU  - Hraskova, I.
AU  - Judova, J.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - Antibiotic resistance and restriction endonucleases in fecal enterococci of chamois (Rupicapra rupicapra Linnaeus, 1758).
JO  - Folia Microbiol. (Praha)
PY  - 2012
SP  - 355
EP  - 358
VL  - 57
AB  - Two hundred eighty-four isolates of enterococci from feces of wild living chamois from alpine
AB  - environments were tested for sensitivity to
AB  - three antibiotics. Low frequency of resistance was observed in studied
AB  - enterococcal populations (about 5 % for tetracycline and erythromycin
AB  - and 0 % for ampicillin). In six animals, the population of enterococci
AB  - lacked any detectable resistance. Our data indicated that enterococcal
AB  - population in feces of the majority of studied animals did not
AB  - encounter mobile genetic elements encoding antibiotic resistance
AB  - probably due to spatial separation and/or due to low exposure to the
AB  - antibiotics. Based on resistance profiles observed, three populations
AB  - were analyzed for the presence of restriction endonucleases. The
AB  - restriction enzymes from two isolates-31K and 1K-were further purified
AB  - and characterized. Restriction endonuclease Efa1KI recognizes CCWGG
AB  - sequence and is an isoschizomer of BstNI. Endonuclease Efc31KI, a BsmAI
AB  - isoschizomer, recognizes the sequence GTCTC and it is a first
AB  - restriction endonuclease identified in Enterococcus faecium. Our data
AB  - indicate that restriction-modification (R-M) systems do not represent
AB  - an efficient barrier for antibiotic resistance spreading; enterococcal
AB  - populations colonized by antibiotics resistance genes were also
AB  - colonized by the R-M systems.
ER  -

TY  - JOUR
AU  - Vanek, P.G.
TI  - Cloning and characterization of the BamHI restriction-modification methylase gene from Bacillus amyloliquefaciens.
JO  - Ph.D. Thesis, Georgetown University, USA
PY  - 1991
SP  - 1
EP  - 195
AB  - The gene encoding the restriction-modification methylase (M.BamHI) from Bacillus
AB  - amyloliquefaciens has been successfully cloned into Escherichia coli. The clone encodes a 423
AB  - amino acids methyltransferase with identical sequence specificity as the BamHI endonuclease.
AB  - Plasmid pBamM9.0 containing this methylase gene was isolated from a Bacillus amyloliquefaciens
AB  - genomic library in the pSP64 cloning vector. A subclone, pBamH2.0, contains a 1.86 kb
AB  - HindIII/XmnI fragment of pBamM9.0 ligated into plasmid pSP64. Plasmid and genomic DNA isolated
AB  - from Epicurean Coli SURE cells harboring plasmid pBamM2.0 was resistant to cleavage by BamHI
AB  - endonuclease. During the course of cloning the cellular methylase gene, a provirally encoded
AB  - methylase (M.BamH2) with identical sequence specificity as the cellular methylase was also
AB  - cloned. Restriction mapping and Southern analysis confirmed the identity of two separate
AB  - methylase genes. The sequence predicted from the cellular methylase DNA clone show two
AB  - distinct regions of sequence similarity with N6-methyladenine and N4-methycytosine
AB  - methyltransferases. These two regions were very highly conserved in the cellular and proviral
AB  - methylases at both the protein and DNA level. Amino terminal sequencing of the cellular
AB  - methylase protein produced in E. coli indicated that translation begins at a rare UUG
AB  - initiation site. Southern analysis using the cloned methylase gene as a probe identified
AB  - similar genes in Bacillus amyloliquefaciens strains F and H, but not in any other BamHI
AB  - isoschizomeric bearing strains. The DNA sequence contains a 1269 base pair open reading frame
AB  - (ORF) which encodes a 49.1 kDa protein. A cell free DNA directed transcription translation
AB  - assay using a subclone pBSBamM2.0 as a template produced a single protein with an apparent
AB  - molecular weight of 49,000, which is in agreement with the molecular weight predicted from the
AB  - cloned sequence and of the purified protein. The methylase protein was purified to apparent
AB  - homogeneity by a three step chromatographic procedure utilizing phosphocellulose,
AB  - phenyl-sepharose, and sephadex G-150 column matrices. Fourty-four grams of E. coli harboring
AB  - pBamM2.0 yielded 1.75 mg methylase protein, an approximate 100 fold increase in protein
AB  - production as compared to Bacillus amyloliquefaciens (Nardone et al. 1983).
ER  -

TY  - JOUR
AU  - Vanek, P.G.
AU  - Connaughton, J.F.
AU  - Kaloss, W.D.
AU  - Chirikijian, G.
TI  - Comparison of cellular and viral methyltransferase genes from Bacillus amyloliquefaciens.
JO  - FASEB J.
PY  - 1990
SP  - A2295
EP  - A2295
VL  - 4
AB  - The restriction modification system of B. amyloliquefaciens consists of a
AB  - restriction endonuclease, BamHI, and a cognate methyltransferase, each of which
AB  - recognize the hexanucleotide palindrome GGATCC.  In addition to the 56 kd
AB  - cellular methyltransferase, B. amyloliquefaciens contains a 30 kd prophage
AB  - encoded methylase which exhibits identical sequences specificity.  Recombinant
AB  - clones of both methyltransferases have been characterized in our laboratory.
AB  - The two clones, pBamM2.5 (prophage methylase), and pBamM2.0 (cellular
AB  - methylase) have been shown to produce methyltransferases capable of protecting
AB  - host genomic DNA from BamHI endonuclease.  Further, a lysate from cells
AB  - harboring clone pBamM2.0 has been shown to be capable of protecting lamda DNA
AB  - from BamHI cleavage in an in vitro assay.  For sequence comparison restriction
AB  - fragments from both pBamM2.5 and pBamM2.0 have been subcloned into M13 and
AB  - sequenced by dideoxy sequence analysis.  The clones have also been tested as
AB  - probes for the identification of methyltransferase genes in each of the
AB  - following BamHI isoschizomer containing strains; B. amyloliquefaciens strain F,
AB  - B. amyloliquefaciens strain N, A. liquefaciens NCIB 9417, B.
AB  - stearothermophilus, G. industricus IFO3260, and G. oxydans sub. melonogenes.
AB  - Southern blot analysis using pBamM2.5 as a probe has identified prophage
AB  - methyltransferase genes in each of the isoschizomer bearing bacterial strains
AB  - identified above.  The characterization of the two clones should facilitate
AB  - further studies of the restriction modification system of B. amyloliquefaciens.
ER  -

TY  - JOUR
AU  - Vanek, P.G.
AU  - Connaughton, J.F.
AU  - Kaloss, W.D.
AU  - Chirikjian, J.G.
TI  - The complete sequence of the Bacillus amyloliquefaciens strain H, cellular BamHI methylase gene.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 6145
EP  - 6145
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Vannier, P.
AU  - Marteinsson, V.T.
AU  - Fridjonsson, O.H.
AU  - Oger, P.
AU  - Jebbar, M.
TI  - Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon Thermococcus barophilus MP.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1481
EP  - 1482
VL  - 193
AB  - Thermococcus barophilus is a hyperthermophilic, anaerobic, mixed heterotrophic, and
AB  - carboxydotrophic euryarchaeon isolated from the deep
AB  - sea hydrothermal vent Snakepit site on the mid-Atlantic ridge at a depth
AB  - of 3,550 m. T. barophilus is the first true piezophilic, hyperthermophilic
AB  - archaeon isolated, having an optimal growth at 40 MPa. Here we report the
AB  - complete genome sequence of strain MP, the type strain of T. barophilus.
AB  - The genome data reveal a close proximity with Thermococcus sibiricus,
AB  - another Thermococcus isolated from the deep biosphere and a possible
AB  - connection to life in the depths.
ER  -

TY  - JOUR
AU  - VanWagoner, T.M.
AU  - Morton, D.J.
AU  - Seale, T.W.
AU  - Mussa, H.J.
AU  - Cole, B.K.
AU  - Whitby, P.W.
AU  - Stull, T.L.
TI  - Draft Genome Sequences of Six Nontypeable Haemophilus influenzae Strains That Establish Bacteremia in the Infant Rat Model of Invasive Disease.
JO  - Genome Announcements
PY  - 2015
SP  - e00899
EP  - e00815
VL  - 3
AB  - Haemophilus influenzae is an important cause of invasive disease. The infant rat  is the
AB  - accepted model of invasive H. influenzae disease. Here, we report the genome sequences of six
AB  - nontypeable H. influenzae strains that establish bacteremia in the infant rat.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
TI  - Enzymatic DNA methylation is an epigenetic control for genetic functions of the cell.
JO  - Biochemistry
PY  - 2005
SP  - 598
EP  - 611
VL  - 70
AB  - In eukaryotic cells nuclear DNA is subjected to enzymatic methylation resulting in formation
AB  - of 5-methylcytosine residues mainly in CG and
AB  - CNG sequences. In plants and animals, this DNA methylation is species-,
AB  - tissue-, and organelle-specific. It changes (diminishes) with age and
AB  - is regulated by hormones. On the other hand, genome methylation can
AB  - control hormonal signal. There are replicative and postreplicative DNA
AB  - methylations. They are served by multiple DNA-methyl-transferases with
AB  - different site specificity. Replication is accompanied by appearance of
AB  - hemimethylated sites in DNA; pronounced asymmetry of DNA chain
AB  - methylation disappears at the end of the cell cycled a model of
AB  - regulation of replication by DNA methylation is suggested. DNA
AB  - methylation controls all genetic processes in the cell (replication,
AB  - transcription, DNA repair, recombination, gene transposition) and it is
AB  - a mechanism of cell differentiation, gene discrimination, and
AB  - silencing. Prohibition of DNA methylation stops development
AB  - (embryogenesis), switches on apoptosis, and is usually lethal.
AB  - Distortions in DNA methylations result in cancerous cell
AB  - transformation, and the DNA methylation pattern is one of the safe
AB  - cancer diagnostics at early stages of carcinogenesis. The malignant
AB  - cell has a different DNA methylation pattern and a set of
AB  - DNA-methyltransferase activities expressed as compared with normal
AB  - cells. Inhibition of DNA methylation in plants is accompanied by
AB  - induction of genes of seed storage proteins and flowering. In
AB  - eukaryotes one and the same gene can be methylated both on cytosine and
AB  - adenine residues; thus, there are, at least, two different and probably
AB  - interdependent systems of DNA methylation in the cell. First higher
AB  - eukaryotic adenine DNA-methyltransferase was isolated from plants; this
AB  - enzyme methylates DNA with formation of N-6-methyladenine residues in
AB  - the sequence TGATCA -> TGm(6)ATCA. Plants have AdoMet-dependent
AB  - endonucleases sensitive to DNA methylation status, therefore, like
AB  - microorganisms, plants seem to have a restriction-modification (R-S)
AB  - system. Revelation of an essential role of DNA methylation in the
AB  - regulation of genetic processes has laid a foundation for and
AB  - materialized epigenetics and epigenomics.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
TI  - DNA methylation in plants.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 2006
SP  - 67
EP  - 122
VL  - 301
AB  - DNA in plants is highly methylated, containing 5-methylcytosine (m(5)C) and N-6-methyladenine
AB  - (m(6)A); m(5)C is located mainly in symmetrical CG and CNG sequences but it may occur also in
AB  - other non-symmetrical contexts. m(6)A but not m(5)C was found in plant mitochondrial DNA. DNA
AB  - methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by
AB  - phytohormones and changes on seed germination, flowering and under the influence of various
AB  - pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development,
AB  - with particular involvement in regulation of gene expression and DNA replication. DNA
AB  - replication is accompanied by the appearance of under-methylated, newly formed DNA strands
AB  - including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of
AB  - the cell cycle. A model for regulation of DNA replication by methylation is suggested.
AB  - Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is
AB  - carried out by the families of specific enzymes that belong to at least three classes of DNA
AB  - methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in
AB  - plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase
AB  - (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria
AB  - replication. Like in animals, DNA methylation in plants is closely associated with histone
AB  - modifications and it affects binding of specific proteins to DNA and formation of respective
AB  - transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is
AB  - methylated both at cytosine and adenine residues; thus, at least two different, and probably
AB  - interdependent, systems of DNA modification are present in plants. Plants seem to have a
AB  - restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in
AB  - plants; it involves de novo methylation of almost all cytosine residues in a region of
AB  - siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical
AB  - methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic
AB  - viral RNA can affect methylation of homologous nuclear sequences and it may be one of the
AB  - feedback mechanisms between the cytoplasm and the nucleus to control gene expression.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
TI  - A view of an elemental naturalist at the DNA world (base composition, sequences, methylation).
JO  - Biochemistry
PY  - 2007
SP  - 1289
EP  - 1298
VL  - 72
AB  - The pioneering data on base composition and pyrimidine sequences in DNA of pro- and eukaryotes
AB  - are considered , and their significance for the origin of genosystematics is discussed. The
AB  - modern views on specificity and functional role of enzymatic DNA methylation in eukaryotes are
AB  - described. DNA methylation controls all genetic functions and is a mechanism of cellular
AB  - differentiation and gene silencing. A model of regulation of DNA replication by methylation is
AB  - suggested . Adenine DNA methylation in higher eukaryotes ( higher plants) was first observed,
AB  - and it was established that one and the same gene can be methylated at both cytosine and
AB  - adenine moieties. Thus, there are at least two different and seemingly interdependent DNA
AB  - methylation systems present in eukaryotic cells. The first eukaryotic adenine DNA-methyl-
AB  - transferase is isolated from wheat seedlings and described: the enzyme methylates DNA with
AB  - formation of N-6-methylade- nine in the sequence TGATCA -> TGm(6)ATCA. It is found that higher
AB  - plants have endonucleases that are dependent on S- adenosyl-L-methionine (SAM) and sensitive
AB  - to DNA methylation status. Therefore, as in bacteria, plants seem to have a
AB  - restriction-modification (R-M) system. A system of conjugated up- and down-regulation of
AB  - SAM-dependent endonucleases by SAM modulations is found in plants. Revelation of an essential
AB  - role of DNA methylation in regulation of genetic processes is a fundament of materialization
AB  - of epigenetics and epigenomics.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
AU  - Aleksandrushkina, N.I.
AU  - Agarkova, O.A.
TI  - Cytokinins do not markedly affect the methylation of DNA adenine residues in cell cultures of Escherichia coli B.
JO  - Biokhimiia
PY  - 1989
SP  - 1666
EP  - 1672
VL  - 54
AB  - 6-Benzylaminopurine (1mg/ml) does not influence the growth of E. coli B cell cultures or the
AB  - number of [8-14C] labeled N6-methyladenine residues in the total DNA [(100 m6A/(A + m6A)=
AB  - 1.7].  The growth of bacterial cells in the presence of adenine or cytokinins (6-BAP, kinetin,
AB  - zeatin) (1 mg/ml) was unaccompanied by significant changes in the intracellular content of
AB  - plasmid pBR322.  The mode of restriction by endonuclease CfuI hydrolyzing the Gm6ATC site of
AB  - plasmid pBR322 from E. coli B cells grown in the presence of adenine or one of the
AB  - above-mentioned cytokinins is identical.  These plasmids also have identical restriction
AB  - products with MboI or Sau3AI.  Thus, the cytokinins under study do not markedly affect the
AB  - methylation of adenine residues in total DNA of E. coli B cell cultures and the GATC sequence
AB  - in plasmids pBR322 isolated from these cells.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
AU  - Buryanov, Y.I.
AU  - Belozersky, A.N.
TI  - Distribution of N6-methyladenine in DNA of T2 phage and its host Escherichia coli B.
JO  - Nature New Biol.
PY  - 1971
SP  - 25
EP  - 27
VL  - 230
AB  - N6-methyladenine (6-MeAde) and 5-methylcytosine occur as minor bases in
AB  - bacterial and phage DNA and seem to result from the selective methylation of
AB  - adenine and cytosine residues by specific DNA methylases.  Methylation is the
AB  - final stage in DNA synthesis and is essential for the phenomenon of host
AB  - modification of phages; it is one of the mechanisms controlling DNA replication
AB  - in the cell.  A study of the distribution of minor bases in DNA is important
AB  - not only for the elucidation of the specificity and mechanism of action of DNA
AB  - methylases but also for an understanding of the purpose of this methylation.
AB  - Until recently there has been a lack of adequate methods for an analysis of the
AB  - distribution of purines, including 6-MeAde, in DNA.  We have developed a method
AB  - for the specific chemical degradation of DNA into purine sequences, based on
AB  - the hydrolysis of apyrimidinic DNA by aniline, which facilities a study of the
AB  - content and position of 6-MeAde residues in unmodified purine sequences.  By
AB  - means of this method we have hydrolysed E. coli B and T2 phage DNA to yield
AB  - purine sequences and have determined the frequency of different purine
AB  - isostichs (fragments with equal numbers of nucleotide residues) and the amounts
AB  - of 6-MeAde in each.  We have checked that 6-MeAde, and also the isolated purine
AB  - sequences, do not undergo marked degradation either in the course of DNA
AB  - hydrazinolysis or in the subsequent hydrolysis of the apyrimidinic acid by
AB  - aniline.  DNA was isolated from T2 phage and E. coli B cells collected at the
AB  - end of the logarithmic phage of growth, according to the procedure of Marmur,
AB  - with additional phenol deproteinziation.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
AU  - Danilevich, V.N.
TI  - Location of 5-methylcytosine in Escherichia coli and phage DD7 DNA.
JO  - Biokhimiia
PY  - 1974
SP  - 1293
EP  - 1301
VL  - 39
AB  - After the cultivation of E. coli C Met cells, infected and uninfected by phage
AB  - DD7, with (H3-methyl)-Met, the bacterial and phage DNA were isolated and the
AB  - distribution and location of 5-methylcytosine (MC) were studied in different
AB  - pyrimidine sequences.  Methylcytosine was not found in the monopyrimidine
AB  - fragments of phage DD7 and E. coli C MC DNA and was present mainly in the di-
AB  - and tripyrimidine sequences (about 75% of all the MC).  A small amount of MC
AB  - was found in long pyrimidine units (4-7 long).  The DNAs of different strains
AB  - of E. coli (C and K12) did not differ in frequency of occurrence of MC in
AB  - different isopliths and were very similar to the DNA of phage DD7.  The
AB  - specificity of the methylation of cytosine residues in phage DD7 DNA and its
AB  - host E. coli C was the same.  In phage DD7 and E. coli C-MC DNA MC is located
AB  - in the following sequences: ...Pu-C-MC-Pu...; ...Pu-C-MC-C-Pu...;
AB  - Pu-C-MC-T-Pu...
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
AU  - Dobritsa, A.P.
TI  - On the nature of the cytosine-methylated sequence in DNA of Bacillus brevis var. G.-B.
JO  - Biochim. Biophys. Acta
PY  - 1975
SP  - 61
EP  - 72
VL  - 407
AB  - On growing the cells of Bacillus brevis S methionine-auxotroph mutant in the
AB  - presence of [Me-3 H] methionine, practically all the radioactivity incorporated
AB  - into DNA is found to exist in 5-methylcytosine and N6-methyladenine.  The
AB  - analysis of pyrimidine isopliths isolated from DNA shows that radioactivity
AB  - only exists in mono- and dinucleotides and the content of 5-methylcytosine in
AB  - R-m5 C-R and R-m5 C-T-R oligonucleotides is equal.  The analysis of
AB  - dinucleotides isolated from DNA by means of pancreatic DNAase hydrolysis allows
AB  - the nature of purine residues neighbouring 5-methylcytosine to be identified
AB  - and shows that 5-methylcytosine localizes in G-m5 C-A and G-m5 C-T-R fragments.
AB  - B. brevis S DNA methylase modifying cytosine residues recognizes the GC(A/T)GC
AB  - degenerate nucleotide sequence which is a part of the following complementary
AB  - structure with a two-fold rotational axis of symmetry: (5')
AB  - ...N'-G-C*-T-G-C-N... (3') (3') ...N -C-G-A-C*-G-N'... (5') (Methylated
AB  - cytosine residues are asterisked).  Cytosine-modifying DNA methylase activity
AB  - is isolated from B. brevis cells; it is capable of methylating in vitro
AB  - homologous and heterologous DNA.  Hence DNA in bacterial cells can be
AB  - undermethylated.  This enzyme methylates cytosine residues in native and
AB  - denatured DNA in the same nucleotide sequences.  Specificity of methylation of
AB  - cytosine residues in vitro and in vivo does not depend on the nature of
AB  - substrate DNA.  DNA methylases of different variants of B. brevis (R, S, P+,
AB  - P-) methylate cytosine residues in the same nucleotide sequences.  It means
AB  - that specificity or methylation of DNA cytosine residues in the cells of
AB  - different variants of B. brevis is the same.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
AU  - Dobritsa, A.P.
TI  - Specificity of the methylation of the cytosine residues in the DNA of Bacillus brevis var. G-B.
JO  - Mol. Biol. (Mosk)
PY  - 1975
SP  - 283
EP  - 295
VL  - 9
AB  - After the growth of a methionine-auxotrophic mutant of Bacillus brevis S in the
AB  - prsence of [methyl-3H]-methionine, practically all the label incorporated into
AB  - DNA was detected in 5-methylcytosine and N6-methyladenine.  In an analysis of
AB  - the pyrimidine isopliths isolated from DNA, it was shown that all the
AB  - radioactivity of MC is uniformly contained in the oligonucleotides Pur-MC-Pur
AB  - and Pur-MC-T-Pur.  An analysis of the dinucleotides isolated from the DNA by
AB  - pancreatic DNAase made it possible to establish that MC is localized in the
AB  - fragments G-MC-A and G-MC-T-Pur.  DNA methylase of B. brevis S, which modifies
AB  - cytosine residues, recognizes the degenerate nucleotide sequence GC(T/A)GC,
AB  - which is included in the complementary structure with second-order rotational
AB  - symmetry:   (5') ...N'-G-MC-T-G-C-N...(3') (3') ....N-C-G-A-MC-G-N'...(5') an
AB  - extract possessing cytosine-modifying methylase activity and capable of
AB  - methylating homologous and heterologous DNA's in vitro was isolated from cells
AB  - of B. brevis.  This means that in the cells of the bacterium, DNA may be
AB  - partially undermethylated.  This enzyme methylates cytosine residues in native
AB  - and denatured DNA's in the same nucleotide sequence.  In comparison with the
AB  - native DNA, in the denatured DNA the level of methylation of the adenine
AB  - residues, but not of the cytosine residues, is decreased.  The specificity of
AB  - the methylation of the cytosine residues in vitro and in vivo is the same and
AB  - does not depend on the nature of the substrate DNA's (calf thymus, Pseudomonas
AB  - aeruginosa, etc.).  DNA methylases from different variants of B. brevis
AB  - (R,S,P+,P-) methylate the cytosine residues in the same nucleotide sequences.
AB  - Consequently, the specificity of the methylation of the cytosine residues in
AB  - the cells of different variants of B. brevis is the same.
ER  -

TY  - JOUR
AU  - Vanyushin, B.F.
AU  - Poirier, L.A.
TI  - Drosophila melanogaster genomic DNA sequence homologous to mammalian cytosine DNA-methyltransferase gene.
JO  - Biochem. Mol. Biol. Int.
PY  - 1996
SP  - 353
EP  - 358
VL  - 39
AB  - Using the Southern blotting procedure we have shown that Drosophila genomic
AB  - DNA hybridizes with 4423-bp C-terminal fragment of murine cytosine DNA-methyltransferase
AB  - gene.  Thus, the Drosophila genome has a sequence homologous to the mammalian cytosine DNA-
AB  - methyltransferase gene.  We assume that DNA methylation most likely responsible for strong CpG
AB  - suppression in the Drosophila genome mainly was catalyzed by a cytosine DNA-methyltransferase
AB  - that has since been lost.
ER  -

TY  - JOUR
AU  - Varani, A.M.
AU  - Lemos, M.V.
AU  - Fernandes, C.C.
AU  - Lemos, E.G.
AU  - Alves, E.C.
AU  - Desiderio, J.A.
TI  - Draft Genome Sequence of Bacillus thuringiensis var. thuringiensis Strain T01-328, a Brazilian Isolate That Produces a Soluble Pesticide Protein, Cry1Ia.
JO  - Genome Announcements
PY  - 2013
SP  - e00817
EP  - e00813
VL  - 1
AB  - Bacillus thuringiensis var. thuringiensis strain T01-328, isolated from Cubatao county (Sao
AB  - Paulo State, Brazil), produces a soluble pesticide protein, Cry1Ia,
AB  - during vegetative growth. Here, we report the 7.089-Mbp draft genome sequence,
AB  - composed of a 5.5-Mb chromosome and 14 plasmids, which is the largest B.
AB  - thuringiensis genome sequenced to date.
ER  -

TY  - JOUR
AU  - Vardimon, L.
AU  - Gunthert, U.
AU  - Doerfler, W.
TI  - In vitro methylation of the BsuRI (5'-GGCC-3') sites in the E2a region of adenovirus type 2 DNA does not affect expression in Xenopus laevis oocytes.
JO  - Mol. Cell. Biol.
PY  - 1982
SP  - 1574
EP  - 1580
VL  - 2
AB  - The early region 2a (E2a) of adenovirus type 2 (Ad2) DNA codes for a 72,000-dalton DNA-binding
AB  - protein and is expressed in the Ad2-transformed hamster cell line HE1 but not in cell lines
AB  - HE2 and HE3 (H. Esche, J. Virol. 41:1076-1082, 1982; K. Johansson et al., J. Virol.
AB  - 27:628-639, 1978). An inverse correlation between DNA methylation at the 5'-CCGG-3' sites of
AB  - the E2a region and of gene expression in these cell lines has been observed (L. Vardimon et
AB  - al., Nucleic Acids Res. 8:2461-2473, 1980). When the cloned E2a region of Ad2 DNA is
AB  - methylated in vitro at the 5'-CCGG-3' sites, the gene is not transcribed after being
AB  - injected into the nuclei of Xenopus laevis oocytes, whereas unmethylated DNA is expressed (L.
AB  - Vardimon et al., Eur. J. Cell Biol. 25:13-15, 1981; L. Vardimon et al., Proc. Natl. Acad. Sci.
AB  - U.S.A. 79:1073-1077, 1982). These data demonstrate that DNA methylation is directly involved
AB  - in the shut-off of transcription. In the present communication we investigated in detail the
AB  - control region of the gene for the DNA-binding protein in Ad2-transformed cell lines and
AB  - showed that the first late control region (map coordinate 72 on the viral DNA) of the E2a
AB  - region is present in its entirety in cell lines HE1, HE2, and HE3. The HaeIII sites
AB  - (5'-GGCC-3') in the E2a region in all three cell lines were not methylated. When the DNA
AB  - methyltransferase BsuRI was used, all 5'-GGCC-3' sites in the cloned E2a region of Ad2 DNA
AB  - were methylated in vitro. It was shown that methylation of these sites did not inhibit the
AB  - expression of this viral gene in X. laevis oocytes. Thus, for methylation to affect gene
AB  - expression in the E2a region it has to occur at specific sites (e.g., 5'-CCGG-3') which may
AB  - be different for other genes.
ER  -

TY  - JOUR
AU  - Vardimon, L.
AU  - Rich, A.
TI  - In Z-DNA the sequence G-C-G-C is neither methylated by HhaI methyltransferase nor cleaved by HhaI restriction endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1984
SP  - 3268
EP  - 3272
VL  - 81
AB  - Plasmids carrying 24- or 32-base-pair inserts of alternating (dG-dC) residues
AB  - were used to analyze the level of methylation of the G-C-G-C sites by HhaI DNA
AB  - methyltransferase and their cleavage by HhaI endonuclease in the B-DNA or Z-DNA
AB  - conformation.  In supercoiled plasmids in which the inserts formed Z-DNA, the
AB  - extent of methylation at the insert G-C-G-C sites was dramatically lower than
AB  - the level of methylation at the G-C-G-C sites located outside the insert in the
AB  - same plasmid.  Similarly, cleavage by HhaI endonuclease was sharply lowered
AB  - when the insert was in the Z-DNA form.  In the relaxed plasmid, all its G-C-G-C
AB  - sites were methylated to the same extent and the unmethylated sites were
AB  - readily cleaved.  After treatment with the methylase, the supercoiled plasmid
AB  - was linearized and then digested with Hha restriction endonuclease.  This
AB  - exposed unmethylated G-C-G-C sites from the insert that had been protected
AB  - against cleavage in the Z conformation.  A chemical reaction was used to study
AB  - the distribution of the unmethylated cytosine residues.  No accumulation of
AB  - unmethylated cytosine residues was found anywhere along the entire 32-base-pair
AB  - insert, which is consistent with a cooperative B-Z transition.
ER  -

TY  - JOUR
AU  - Varga, J.J.
AU  - Losada, L.
AU  - Zelazny, A.M.
AU  - Brinkac, L.
AU  - Harkins, D.
AU  - Radune, D.
AU  - Hostetler, J.
AU  - Sampaio, E.P.
AU  - Ronning, C.M.
AU  - Nierman, W.C.
AU  - Greenberg, D.E.
AU  - Holland, S.M.
AU  - Goldberg, J.B.
TI  - Draft Genome Sequence Determination for Cystic Fibrosis and Chronic Granulomatous Disease Burkholderia multivorans Isolates.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6356
EP  - 6357
VL  - 194
AB  - Burkholderia multivorans is a Gram-negative bacterium and a member of the Burkholderia cepacia
AB  - complex, which is frequently associated with respiratory
AB  - infections in people with cystic fibrosis (CF) and chronic granulomatous disease
AB  - (CGD). We are reporting the genome sequences of 4 B. multivorans strains, 2 from
AB  - CF patients and 2 from CGD patients.
ER  -

TY  - JOUR
AU  - Varga, J.J.
AU  - Losada, L.
AU  - Zelazny, A.M.
AU  - Kim, M.
AU  - McCorrison, J.
AU  - Brinkac, L.
AU  - Sampaio, E.P.
AU  - Greenberg, D.E.
AU  - Singh, I.
AU  - Heiner, C.
AU  - Ashby, M.
AU  - Nierman, W.C.
AU  - Holland, S.M.
AU  - Goldberg, J.B.
TI  - Draft Genome Sequences of Burkholderia cenocepacia ET12 Lineage Strains K56-2 and BC7.
JO  - Genome Announcements
PY  - 2013
SP  - e00841
EP  - e00813
VL  - 1
AB  - The Burkholderia cepacia complex (BCC) is a group of closely related bacteria that are
AB  - responsible for respiratory infections in immunocompromised humans, most
AB  - notably those with cystic fibrosis (CF). We report the genome sequences for
AB  - Burkholderia cenocepacia ET12 lineage CF isolates K56-2 and BC7.
ER  -

TY  - JOUR
AU  - Varni, V.
AU  - Koval, A.
AU  - Nagel, A.
AU  - Ruybal, P.
AU  - Caimi, K.
AU  - Amadio, A.F.
TI  - First Genome Sequence of Leptospira interrogans Serovar Pomona, Isolated from a Bovine Abortion.
JO  - Genome Announcements
PY  - 2016
SP  - e00345
EP  - e00316
VL  - 4
AB  - Leptospirosis is a widespread zoonosis and a re-emergent disease of global distribution with
AB  - major relevance in veterinary production. Here, we report the
AB  - whole-genome sequence of Leptospira interrogans serovar Pomona strain AKRFB,
AB  - isolated from a bovine abortion during a leptospirosis outbreak in Argentina.
ER  -

TY  - JOUR
AU  - Varshney, H.
AU  - Iqbal, J.
AU  - Seleemuddin, M.
TI  - Immobilization of the restriction endonuclease EcoRI.  Usefulness of a polyclonal antibody support.
JO  - Enzyme Microb. Technol.
PY  - 1999
SP  - 172
EP  - 176
VL  - 25
AB  - The restriction enzyme EcoRI has been immobilized by using an immunoaffinity-based procedure
AB  - on Sepharose 4B.  The antibody support, prepared by coupling the gamma-globulin fraction of
AB  - serum of immunized rabbits to CNBr-activated Sepharose-4B, was highly effective in binding
AB  - EcoRI from solution although only about half of the bound activity appeared to be expressed by
AB  - the immobilized preparations.  Restriction activity of EcoRI immobilized on the antibody
AB  - support was indistinguishable from that of soluble enzyme on the linear phage-DNA and
AB  - supercoiled plasmids pBR322 and pBHLUC P.  Binding to the antibody support markedly enhanced
AB  - the resistance of EcoRI to heat inactivation, and the preparation, unlike the native enzyme,
AB  - retained significant activity after exposure to a temperature of 65 C.  It was also possible
AB  - to immobilize EcoRI directly from the cell lysates of Escherichia coli pMB4, an EcoRI
AB  - overproducing strain.  The immobilized preparation did not possess nonspecific nuclease
AB  - activity that was prominent in the lysates, suggesting specificity in the binding of EcoRI to
AB  - the antibody support.
ER  -

TY  - JOUR
AU  - Varshney, H.
AU  - Saleemuddin, M.
AU  - Rhee, J.I.
AU  - Schugerl, K.
TI  - Immobilization of SpA::EcoRI on IgG support improves the thermal stability of restriction activity.
JO  - Process. Biochem.
PY  - 2001
SP  - 275
EP  - 278
VL  - 37
AB  - A plasmid-harbouring E. coli JM109 (3P) strain was cultivated for the overproduction of the
AB  - genetically engineered fusion protein SpA::EcoRI. The fusion protein could be affinity bound
AB  - selectively and directly from the 25-50% ammonium sulphate fraction of the lysate of E. coli
AB  - JM109 on to IgG-Sepharose.  The preparation obtained thus exhibited high restriction activity
AB  - on lambda DNA and linearized the plasmids pBR322 and pUC19.  As compared to the native EcoRI
AB  - the activity of the immobilized preparation was more resistant to thermal inactivation.
ER  -

TY  - JOUR
AU  - Varshney, R.K. et al.
TI  - Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.
JO  - Nat. Biotechnol.
PY  - 2013
SP  - 240
EP  - 246
VL  - 31
AB  - Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean,
AB  - accounting for a substantial proportion of human dietary nitrogen intake
AB  - and playing a crucial role in food security in developing countries. We report
AB  - the approximately 738-Mb draft whole genome shotgun sequence of CDC Frontier, a
AB  - kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing
AB  - and analysis of 90 cultivated and wild genotypes from ten countries identifies
AB  - targets of both breeding-associated genetic sweeps and breeding-associated
AB  - balancing selection. Candidate genes for disease resistance and agronomic traits
AB  - are highlighted, including traits that distinguish the two main market classes of
AB  - cultivated chickpea--desi and kabuli. These data comprise a resource for chickpea
AB  - improvement through molecular breeding and provide insights into both genome
AB  - diversity and domestication.
ER  -

TY  - JOUR
AU  - Vasconcellos, R.L.
AU  - Mendes, R.
AU  - Taketani, R.G.
AU  - Zucchi, T.D.
AU  - Melo, I.S.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain CMAA 1215, a Plant Growth-Promoting Bacterium Isolated from a Brazilian Mangrove.
JO  - Genome Announcements
PY  - 2013
SP  - e00995
EP  - e00913
VL  - 1
AB  - The aim of this study was to sequence the genome of the plant growth-promoting Pseudomonas sp.
AB  - strain CMAA 1215, an osmotolerant bacterium isolated from
AB  - mangrove soil.
ER  -

TY  - JOUR
AU  - Vasconcelos, A.T. et al.
TI  - Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae.
JO  - J. Bacteriol.
PY  - 2005
SP  - 5568
EP  - 5577
VL  - 187
AB  - This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic
AB  - (7448) and a nonpathogenic (J) strain of the swine
AB  - pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen
AB  - Mycoplasma synoviae; the genome sizes of the three strains were 920,079
AB  - bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared
AB  - with other sequenced mycoplasma genomes reported in the literature to
AB  - examine several aspects of mycoplasma evolution. Strain-specific regions,
AB  - including integrative and conjugal elements, and genome rearrangements and
AB  - alterations in adhesin sequences were observed in the M. hyopneumoniae
AB  - strains, and all of these were potentially related to pathogenicity.
AB  - Genomic comparisons revealed that reduction in genome size implied loss of
AB  - redundant metabolic pathways, with maintenance of alternative routes in
AB  - different species. Horizontal gene transfer was consistently observed
AB  - between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a
AB  - likely transfer event of hemagglutinin-coding DNA sequences from M.
AB  - gallisepticum to M. synoviae.
ER  -

TY  - JOUR
AU  - Vasilenko, O.V.
AU  - Doronina, N.V.
AU  - Shmareva, M.N.
AU  - Tarlachkov, S.V.
AU  - Trotsenko, Y.A.
TI  - Draft Genome Sequence of Methyloligella halotolerans capital ES, Cyrillic2T, a New Halotolerant Methylotroph, Accumulating Poly-3-Hydroxybutyrate and Ectoine.
JO  - Genome Announcements
PY  - 2016
SP  - e01189
EP  - e01116
VL  - 4
AB  - Methyloligella halotolerans capital ES, Cyrillic2T is a moderate halophilic obligate
AB  - methylotroph, accumulating ultra-high-molecular-weight
AB  - poly-3-hydroxybutyrate (up to 8 to 10 MDa) from methanol. Here we report a draft
AB  - genome and annotation of Methyloligella halotolerans C2T (VKM B-2706T = CCUG
AB  - 61687T = DSM 25045T).
ER  -

TY  - JOUR
AU  - Vasilenko, O.V.
AU  - Starodumova, I.P.
AU  - Tarlachkov, S.V.
AU  - Dorofeeva, L.V.
AU  - Avtukh, A.N.
AU  - Evtushenko, L.I.
TI  - Draft Genome Sequence of 'Rathayibacter tanaceti' Strain VKM Ac-2596 Isolated from Tanacetum vulgare Infested by a Foliar Nematode.
JO  - Genome Announcements
PY  - 2016
SP  - e00512
EP  - e00516
VL  - 4
AB  - The draft genome of 'Rathayibacter tanaceti' VKM Ac-2596 is 3.17 Mb in size with  an average
AB  - G+C content of 70.7% and comprises at least two nonidentical copies of
AB  - ribosomal small subunit (SSU-rRNA) genes. The semiconductor sequencing platform
AB  - Ion Torrent was used.
ER  -

TY  - JOUR
AU  - Vasiljeva, L.Y.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A site-specific endonuclease BspR7I from Thermophilic strain.
JO  - Biokhimiia
PY  - 1996
SP  - 2147
EP  - 2157
VL  - 61
AB  - A site-specific endonuclease BspR7I preparation has been isolated and purified to homogeneity
AB  - from the thermophilic strain Bacillus sp. R7.  DNA cleavage proceeds according to the scheme
AB  - 5'-CC/TNAGC-3' 3'-GGANT/CC-5' and thus the enzyme belongs to the second class of
AB  - restriction endonucleases and is an isoschizomer of Bsu36I.  The isolated protein has a
AB  - molecular mass of 37 kD and is present in solution in the form of a monomer.  BspR7I is active
AB  - over a wide range of temperatures, from 37 to 48oC.  The enzyme is relatively stable.
ER  -

TY  - JOUR
AU  - Vasiljeva, L.Y.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Cloning and expression of a new site-specific methyltransferase M.SscL1I from Staphylococcus sp. L1.
JO  - Biokhimiia
PY  - 2000
SP  - 565
EP  - 570
VL  - 65
AB  - The gene of the new site-specific methyltransferase M.SscL1I belonging to the same
AB  - modification-restriction system as the previously described site-specific endonuclease
AB  - SscL1I has been cloned from the natural strain Staphylococcus sp. L1. A plasmid to express the
AB  - methylase gene under control of the T7 phage-specific promoter has been constructed.
AB  - Conditions were found to express the recombinant methylase M.SscL1I and to purify it to near
AB  - homogeneity. It is shown that the methylase modifies the adenine base in the recognition site
AB  - 5'-GANTC-3'.
ER  -

TY  - JOUR
AU  - Vasiljeva, L.Y.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease SscL1I from strain Staphylococcus species L1.
JO  - Biokhimiia
PY  - 1998
SP  - 212
EP  - 218
VL  - 63
AB  - A site-specific endonuclease SscL1I preparation has been isolated and purified to near
AB  - homogeneity from the strain Staphylococcus sp. L1 without admixtures of other nuclease
AB  - activity.  DNA cleavage proceeds according to the scheme: 5'-G/ANTC-3' 3'-CTNA/G-5, and
AB  - thus the isolated enzyme is an isoschizomer of restriction endonuclease HinfI and belongs to
AB  - the second class of restriction endonucleases.  SscL1I works over a broad range of temperature
AB  - and pH.  The enzyme is characterized by high stability during storage.
ER  -

TY  - JOUR
AU  - Vasilyev, I.
AU  - Siniagina, M.
AU  - Malanin, S.
AU  - Boulygina, E.
AU  - Grygoryeva, T.
AU  - Yarullina, D.
AU  - Ilinskaya, O.
TI  - Draft Genome Sequence of Agreia bicolorata Strain AC-1804, a Producer of Large Amounts of Carotenoid Pigments, Isolated from Narrow Reed Grass Infected by the  Phytoparasitic Nematode.
JO  - Genome Announcements
PY  - 2015
SP  - e01383
EP  - e01315
VL  - 3
AB  - Here, we report the draft genome sequence of Agreia bicolorata strain AC-1804, isolated from
AB  - narrow reed grass galls induced by a plant-parasitic nematode which
AB  - is able to produce large amounts of carotenoid pigments. The draft genome
AB  - sequence of 3,919,485 bp provides a resource for carotenoid pathway research.
ER  -

TY  - JOUR
AU  - Vasquez, C.
TI  - Isolation and partial characterization of BstVI, a thermostable isoschizomer of XhoI.
JO  - Biochem. Int.
PY  - 1985
SP  - 655
EP  - 662
VL  - 10
AB  - A type II restriction endonuclease, which has been named BstVI, was isolated and partially
AB  - purified from a spore-forming, gram-positive thermophilic bacilli.  On the basis of its
AB  - digestion patterns on varous DNA's, it was concluded that this enzyme is an isoschizomer of
AB  - XhoI, isolated originally from Xanthomonas holcicola.  Besides being highly thermostable, the
AB  - enzyme is produced in very large amounts by this bacterial strain.  A single purification step
AB  - renders it free of unspecific nucleases and suitable for performing restriction analysis and
AB  - cloning experiments.
ER  -

TY  - JOUR
AU  - Vasquez, C.
TI  - Structural and biochemical characterization of the modification-restriction system of Bacillus stearothermophilus V.
JO  - Arch. Biol. Med. Exp. (Santiago)
PY  - 1988
SP  - r338
EP  - r338
VL  - 21
AB  - None
ER  -

TY  - JOUR
AU  - Vasquez, C.
AU  - Adasme, A.
AU  - Gonzalez, E.
TI  - Aislamiento Y caracterizacion de endonucleasas termoestables:  BstVI, un isosquizomero de XhoI (isolation and characterization of thermostable endonucleases:  BstVI, an isoschizomer of XhoI).
JO  - Arch. Biol. Med. Exp. (Santiago)
PY  - 1985
SP  - r371
EP  - r371
VL  - 18
AB  - Recientemente hemos purificado una endonucleasa de restriccion tipo II, la cual
AB  - fue aislade de un bacilo termofilico gram positivo.  De acuerdo a pruebas
AB  - microbiologicas estandares, la bacteria resulto ser del tipo Bacillus
AB  - stearothersophilus y la enzima fue denominada BstVI.  Sobre la base de los
AB  - patrones de digestion de los diversos DNAs utilizados como sustrato, hemos
AB  - concluido que BstVI es un isosquizomero de XhoI, aislada originalmente de
AB  - Xanthomonas holcicola.  Ademas de ser muy termoestable (tempertura optima de
AB  - 75C), BstVI es producida en gran cantidad por esta cepa bacteriana.
AB  - Practicamente un solo paso de purificacion hace possible la eliminacion de
AB  - nucleasas inespecificas y port lo tanto, su uso con fines de analisis de
AB  - restriccion y de clonamiento molecular.  Se han determinado algunas de las
AB  - condiciones optimas para la activated enzimatica, ademas de probar la
AB  - estabilidad de la enzima frente a una serie de agentes desnaturantes de
AB  - proteinas.
ER  -

TY  - JOUR
AU  - Vasquez, C.
AU  - Saavedra, C.
AU  - Gonzalez, E.
TI  - Cloning the BstVI restriction-modification system in Escherichia coli.
JO  - Gene
PY  - 1991
SP  - 83
EP  - 85
VL  - 102
AB  - A standard DNA modification methyltransferase (MTase) selection protocol was
AB  - followed to clone the BstVI restriction and modification system from Bacillus
AB  - stearothermophilus in Escherichia coli.  Both genes were contained in a 4.4-kb
AB  - EcoRI fragment from B. stearothermophilus V chromosomal DNA.  The heterologous
AB  - expression of these genes did not depend on their orientation in the vector,
AB  - suggesting that the genes are expressed in E. coli under the control of
AB  - promoters located on the cloned fragment.  Subcloning experiments demonstrated
AB  - that the bstVIR gene was expressed in the absence of its cognate MTase.
ER  -

TY  - JOUR
AU  - Vasquez, C.
AU  - Vicuna, R.
TI  - The genus Thermus: restriction endonucleases and modification methylases.
JO  - Arch. Biol. Med. Exp. (Santiago)
PY  - 1982
SP  - 417
EP  - 421
VL  - 15
AB  - This work reviews the present knowledge of the site-specific endonucleases and
AB  - methylases involved in the restriction-modification systems in bacteria
AB  - belonging to the genus Thermus.  In addition, we describe part of our work
AB  - concerning the purification and properties of these enzymes from Thermus
AB  - thermophilus HB8 and Thermus flavus AT-62.
ER  -

TY  - JOUR
AU  - Vasquez, C.C.
AU  - Saavedra, C.P.
AU  - Pichuantes, S.E.
TI  - Nucleotide sequence of the gene encoding the BstLVI DNA methyltransferase: comparison with other amino-DNA methyltransferases.
JO  - Curr. Microbiol.
PY  - 2000
SP  - 114
EP  - 118
VL  - 40
AB  - The nucleotide sequence of a 2837-base pairs (bp) EcoRI-PvuI fragment of Bacillus
AB  - stearothermophilus LV chromosomal DNA encoding the bstLVIM gene was determined. It revealed a
AB  - large open reading frame (ORF) of 1737 bp specifying a methylase of 579 amino acid (aa)
AB  - residues and Mr 66,831. This was in agreement with the size estimated for the M. BstLVI (
AB  - approximately 67 kDa) purified from Escherichia coli cells harboring a recombinant plasmid
AB  - containing the bstLVIM gene and with results of transcription-translation experiments
AB  - performed in vitro. Upstream the bstLVIM gene and in the opposite transcriptional orientation,
AB  - there is an 81-aa ORF that showed great homology with the regulatory C proteins identified in
AB  - other type II restriction and modification (R-M) systems. This 81-aa ORF precedes a truncated
AB  - ORF of 86 aa which in turn may represent the structural gene for the BstLVI restriction
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Vasu, K.
AU  - Nagamalleswari, E.
AU  - Nagaraja, V.
TI  - Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2012
SP  - E1287
EP  - E1293
VL  - 109
AB  - Most bacterial genomes harbor restriction-modification systems, encoding a REase  and its
AB  - cognate MTase. On attack by a foreign DNA, the REase recognizes it as
AB  - nonself and subjects it to restriction. Should REases be highly specific for
AB  - targeting the invading foreign DNA? It is often considered to be the case.
AB  - However, when bacteria harboring a promiscuous or high-fidelity variant of the
AB  - REase were challenged with bacteriophages, fitness was maximal under conditions
AB  - of catalytic promiscuity. We also delineate possible mechanisms by which the
AB  - REase recognizes the chromosome as self at the noncanonical sites, thereby
AB  - preventing lethal dsDNA breaks. This study provides a fundamental understanding
AB  - of how bacteria exploit an existing defense system to gain fitness advantage
AB  - during a host-parasite coevolutionary 'arms race.'
ER  -

TY  - JOUR
AU  - Vasu, K.
AU  - Nagamalleswari, E.
AU  - Zahran, M.
AU  - Imhof, P.
AU  - Xu, S.Y.
AU  - Zhu, Z.
AU  - Chan, S.H.
AU  - Nagaraja, V.
TI  - Increasing cleavage specificity and activity of restriction endonuclease KpnI.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 9812
EP  - 9824
VL  - 41
AB  - Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for
AB  - DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of
AB  - different atomic radii for DNA cleavage. Although Mg2+ ion higher than 500 muM mediates
AB  - promiscuous activity, Ca2+ suppresses the promiscuity and induces high cleavage fidelity.
AB  - Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu
AB  - results in the elimination of the Ca2+-mediated cleavage but imparting high cleavage fidelity
AB  - with Mg2+. High cleavage fidelity of the mutant D148E is achieved through better
AB  - discrimination of the target site at the binding and cleavage steps. Biochemical experiments
AB  - and molecular dynamics simulations suggest that the mutation inhibits Ca2+-mediated cleavage
AB  - activity by altering the geometry of the Ca2+-bound HNH active site. Although the D148E mutant
AB  - reduces the specific activity of the enzyme, we identified a suppressor mutation that
AB  - increases the turnover rate to restore the specific activity of the high fidelity mutant to
AB  - the wild-type level. Our results show that active site plasticity in coordinating different
AB  - metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination
AB  - is a plausible way to reduce promiscuous activity of metalloenzymes.
ER  -

TY  - JOUR
AU  - Vasu, K.
AU  - Nagaraja, V.
TI  - Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense.
JO  - Microbiol. Mol. Biol. Rev.
PY  - 2013
SP  - 53
EP  - 72
VL  - 77
AB  - Restriction-modification (R-M) systems are ubiquitous and are often considered primitive
AB  - immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are
AB  - an indication of their success as a defense mechanism against invading genomes. However, their
AB  - cellular defense function does not adequately explain the basis for their immaculate
AB  - specificity in sequence recognition and nonuniform distribution, ranging from none to too
AB  - many, in diverse species. The present review deals with new developments which provide
AB  - insights into the roles of these enzymes in other aspects of cellular function. In this
AB  - review, emphasis is placed on novel hypotheses and various findings that have not yet been
AB  - dealt with in a critical review. Emerging studies indicate their role in various cellular
AB  - processes other than host defense, virulence, and even controlling the rate of evolution of
AB  - the organism. We also discuss how R-M systems could have successfully evolved and be involved
AB  - in additional cellular portfolios, thereby increasing the relative fitness of their hosts in
AB  - the population.
ER  -

TY  - JOUR
AU  - Vasu, K.
AU  - Saravanan, M.
AU  - Bujnicki, J.M.
AU  - Nagaraja, V.
TI  - Structural integrity of the Beta Beta Alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.
JO  - Biochim. Biophys. Acta
PY  - 2008
SP  - 269
EP  - 275
VL  - 1784
AB  - Restriction endonuclease (REase) R.KpnI from Klebsiella pneumoniae is a homodimeric enzyme,
AB  - which recognizes palindromic sequence GGTAC|C and
AB  - cleaves generating 4 base 3' end overhangs. R.KpnI belongs to the HNH
AB  - superfamily of nucleases, which are characterized by the presence of the
AB  - beta beta alpha-Me finger motif. Structurally, this motif consists of a
AB  - twisted beta-hairpin followed by an alpha-helix, and serves as a scaffold
AB  - for side chains of residues involved in co-ordination of a divalent metal
AB  - ion that is required for catalysis. Homology modeling studies of R.KpnI
AB  - suggested a crossover structure for the alpha-helix, which could possibly
AB  - form dimeric interface and/or structural scaffold for the active site. We
AB  - have evaluated the role of the residues present in this alpha-helix in
AB  - intersubunit interactions and/or stabilization of the active site. We show
AB  - here that mutations of residues in the alpha-helix lead to a loss of the
AB  - enzyme activity, but not dimerization ability. Intrinsic fluorescence and
AB  - circular dichroism studies revealed that the loss of function phenotype
AB  - was due to the structural perturbation of the beta beta alpha-Me finger
AB  - motif. The results of mutational analysis suggest that the alpha-helix of
AB  - the beta beta alpha-Me finger of R.KpnI plays an important role for the
AB  - stability of the protein-DNA complex.
ER  -

TY  - JOUR
AU  - Vasu, K.
AU  - Saravanan, M.
AU  - Rajendra, B.V.R.N.
AU  - Nagaraja, V.
TI  - Generation of a Manganese Specific Restriction Endonuclease with Nicking Activity.
JO  - Biochemistry
PY  - 2010
SP  - 8425
EP  - 8433
VL  - 49
AB  - A typical feature of type II restriction endonucleases (REases) is their obligate sequence
AB  - specificity and requirement for Mg2+ during
AB  - catalysis. R.KpnI is an exception. Unlike most other type II REases,
AB  - the active site of this enzyme can accommodate Mg2+, Mn2+, Ca2+, or
AB  - Zn2+ and cleave DNA. The enzyme belongs to the HNH superfamily of
AB  - nucleases and is characterized by the presence of a beta beta alpha-Me
AB  - finger motif. Residues D148, H149, and Q175 together form the HNH
AB  - active site and are essential for Mg2+ binding and catalysis. The
AB  - unique ability of the enzyme to cleave DNA in the presence of different
AB  - metal ions is exploited to generate mutants that are specific to one
AB  - particular metal ion. We describe the generation of a Mn2+-dependent
AB  - sequence specific endonuclease, defective in DNA cleavage with Mg2+ and
AB  - other divalent metal ions. In the engineered mutant, only Mn2+ is
AB  - selectively bound at the active site, imparting Mn2+-mediated cleavage.
AB  - The mutant is impaired in concerted double-stranded DNA cleavage,
AB  - leading to accumulation of nicked intermediates. The nicking activity
AB  - of the mutant enzyme is further enhanced by altered reaction
AB  - conditions. The active site fluidity of R Eases allowing flexible
AB  - accommodation of catalytic cofactors thus forms a basis for engineering
AB  - selective metal ion-dependent REase additionally possessing nicking
AB  - activity.
ER  -

TY  - JOUR
AU  - Vasudev, V.
AU  - Obe, G.
TI  - Evidence for a receptor-mediated endocytosis of AluI in chinese hamster ovary cells.
JO  - Mutat. Res.
PY  - 1988
SP  - 109
EP  - 116
VL  - 197
AB  - Pretreatment of Chinese hamster ovary cells with proteases or with NaN3 leads to less
AB  - chromosomal aberrations when the cells are posttreated with AluI compared to the treatment of
AB  - cells with AluI alone.  The same result is obtained when the cells are treated with AluI at
AB  - 0oC instead of 37oC.  The cells recover from the protease treatment when they are kept in
AB  - medium before treatment with AluI.  These results are interpreted to mean that AluI is bound
AB  - by surface receptors and that the AluI-receptor complexes are internalized by an
AB  - energy-dependent endocytotic process.
ER  -

TY  - JOUR
AU  - Vater, A. et al.
TI  - Draft Genome Sequences of Shewanella sp. Strain UCD-FRSP16_17 and Nine Vibrio Strains Isolated from Abalone Feces.
JO  - Genome Announcements
PY  - 2016
SP  - e00977
EP  - e00916
VL  - 4
AB  - We present here the draft genome sequences for nine strains of Vibrio (V. cyclitrophicus, V.
AB  - splendidus, V. tasmaniensis, and three unidentified) and one
AB  - Shewanella strain. Strains were isolated from red (Haliotis rufescens) and white
AB  - (Haliotis sorenseni) abalone, with and without exposure to 'Candidatus
AB  - Xenohaliotis californiensis,' the causative agent of abalone withering syndrome.
ER  -

TY  - JOUR
AU  - Vatlin, A.A.
AU  - Bekker, O.B.
AU  - Lysenkova, L.N.
AU  - Danilenko, V.N.
TI  - Draft Genome Sequence of Streptomyces fradiae olg1-1, a Strain Resistant to Nitrone-Oligomycin.
JO  - Genome Announcements
PY  - 2015
SP  - e01252
EP  - e01215
VL  - 3
AB  - We report a draft genome sequence of Streptomyces fradiae olg1-1, a mutant strain derived from
AB  - the model object S. fradiae ATCC 19609, which is resistant to nitrone-oligomycin and has a
AB  - mutation in the DNA-binding domain of a transcriptional regulator PadR.
ER  -

TY  - JOUR
AU  - Vaughn, J.C.
AU  - Mason, M.T.
AU  - Sper-Whitis, G.L.
AU  - Kuhlman, P.
AU  - Palmer, J.D.
TI  - Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.
JO  - J. Mol. Evol.
PY  - 1995
SP  - 563
EP  - 572
VL  - 41
AB  - We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene
AB  - arose recently by horizontal transfer from a fungal donor species.  A 1,716-bp fragment of the
AB  - mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the
AB  - polymerase chain reaction and sequenced.  Comparison to other coxI genes revealed a 966-bp
AB  - group I intron, which, based on homology with the related yeast coxI intron aI4, potentially
AB  - encodes a 279-amino-acid site-specific DNA endonuclease.  This intron, which is believed to
AB  - function as a ribozyme during its own splicing, is not present in any of 19 coxI genes
AB  - examined from other diverse vascular plant species.  Phylogenetic analysis of intron origin
AB  - was carried out using three different tree-generating algorithms, and on a variety of
AB  - nucleotide and amino acid data sets from the intron and its flanking exon sequences.  These
AB  - analyses show that the Peperomia coxI gene intron and exon sequences are of fundamentally
AB  - different evolutionary origin. The Peperomia intron is more closely related to several fungal
AB  - mitochondrial introns, two of which are located at identical positions in coxI, than to
AB  - identically located coxI introns from the land plant Marchantia and the green alga Prototheca.
AB  - Conversely, the exon sequence of this gene is, as expected, most closely related to other
AB  - angiosperm coxI genes.  These results, together with evidence suggestive of co-conversion of
AB  - exonic markers immediately flanking the intron insertion site, lead us to conclude that the
AB  - Peperomia coxI intron probably arose by horizontal transfer from a fungal donor, using the
AB  - double-strand-break repair pathway.  The donor species may have been one of the symbiotic
AB  - mycorrhizal fungi that live in close obligate association with most plants.
ER  -

TY  - JOUR
AU  - Vaz-Moreira, I.
AU  - Tamames, J.
AU  - Martinez, J.L.
AU  - Manaia, C.M.
TI  - Draft Genome Sequences of Two Ralstonia pickettii Strains with Different Aminoglycoside Resistance Phenotypes.
JO  - Genome Announcements
PY  - 2016
SP  - e01257
EP  - e01216
VL  - 4
AB  - The genomes of two Ralstonia pickettii strains (H2Cu2 and H2Cu5), isolated from hospital
AB  - effluent in a selective medium containing CuSO4, were sequenced. They
AB  - presented MICs of >256 and 6 microg/ml for the aminoglycoside gentamicin,
AB  - respectively. The 5.2-Mb draft genomes have 40 contigs for strain H2Cu2 and 113
AB  - for H2Cu5.
ER  -

TY  - JOUR
AU  - Vazquez, R.
AU  - Brito, J.
AU  - Guerra, M.
TI  - Purification of the restriction endonuclease SacI, free of SacII and SacIII contaminants.
JO  - Biotecnol. Apl.
PY  - 1996
SP  - 21
EP  - 24
VL  - 13
AB  - The restriction endonuclease SacI was isolated from Streptomyces achromogenes and was purified
AB  - to homogeneity, until no contaminant nuclease activities were detected.  On the basis of ion
AB  - exchange chromatography (Q-Sepharose and phosphocellulose P-11), SacI can be obtained with a
AB  - high level of purity and used in molecular cloning.  The practical utility of SacI enzyme is
AB  - given by a high stability, high yield, easy handling of producing cells, and the ability to
AB  - recognize new sequences, such as GAGCTC.  The molecular weight (MW) of this enzyme was
AB  - estimated by High Performance Liquid Chromatography and SDS polyacrylamide gel
AB  - electrophoresis, being of about 50 kDa approximately.  According to the results obtained from
AB  - the accelerated stability study, the enzyme preparation is stable for at least 20 months.
ER  -

TY  - JOUR
AU  - Vazquez, R.
AU  - Martinez, D.
AU  - Reyes, G.
AU  - Marquez, G.
AU  - Ryes, N.
AU  - Diaz, Y.
AU  - Luis, M.
AU  - Gonzalez, B.
AU  - Gonzalez, N.
TI  - Purification of NcoI restriction endonuclease free of exonucleases and contaminant endonucleases.
JO  - Biotecnol. Apl.
PY  - 1996
SP  - 289
EP  - 290
VL  - 13
ER  -

TY  - JOUR
AU  - Vazquez-Gutierrez, P.
AU  - Lacroix, C.
AU  - Chassard, C.
AU  - Klumpp, J.
AU  - Jans, C.
AU  - Stevens, M.J.
TI  - Complete and Assembled Genome Sequence of Bifidobacterium kashiwanohense PV20-2,  Isolated from the Feces of an Anemic Kenyan Infant.
JO  - Genome Announcements
PY  - 2015
SP  - e01467
EP  - e01414
VL  - 3
AB  - The complete genome sequence of Bifidobacterium kashiwanohense strain PV20-2, an  infant feces
AB  - isolate, was determined using single-molecule real-time sequencing
AB  - (SMRT). Hierarchical genome assembly resulted in a completely assembled genome of
AB  - 2,370,978 bp. The B. kashiwanohense PV20-2 genome is the first completely
AB  - sequenced and assembled genome of the species.
ER  -

TY  - JOUR
AU  - Vazquez-Gutierrez, P.
AU  - Lacroix, C.
AU  - Chassard, C.
AU  - Klumpp, J.
AU  - Stevens, M.J.
AU  - Jans, C.
TI  - Bifidobacterium pseudolongum Strain PV8-2, Isolated from a Stool Sample of an Anemic Kenyan Infant.
JO  - Genome Announcements
PY  - 2015
SP  - e01469
EP  - e01414
VL  - 3
AB  - The complete genome sequence of Bifidobacterium pseudolongum PV8-2, isolated from feces of an
AB  - anemic Kenyan infant, was determined using single-molecule real-time
AB  - (SMRT) technology. The genome consists of a 2-Mbp chromosome and a 4-kb plasmid.
ER  -

TY  - JOUR
AU  - Vazquez-Hernandez, M.
AU  - Ceapa, C.D.
AU  - Rodriguez-Luna, S.D.
AU  - Rodriguez-Sanoja, R.
AU  - Sanchez, S.
TI  - Draft Genome Sequence of Streptomyces scabrisporus NF3, an Endophyte Isolated from Amphipterygium adstringens.
JO  - Genome Announcements
PY  - 2017
SP  - e00267
EP  - e00217
VL  - 5
AB  - We report the draft genome sequence of Streptomyces scabrisporus NF3, an endophyte isolated
AB  - from Amphipterygium adstringens in Chiapas, Mexico. This
AB  - strain produces a new modified linaridin peptide. The genome harbors at least 50
AB  - gene clusters for synthases of polyketide and nonribosomal peptides, suggesting a
AB  - prospective production of various secondary metabolites.
ER  -

TY  - JOUR
AU  - Vecherkovskaya, M.F.
AU  - Tetz, G.V.
AU  - Tetz, V.V.
TI  - Complete Genome Sequence of the Streptococcus sp. Strain VT 162, Isolated from the Saliva of Pediatric Oncohematology Patients.
JO  - Genome Announcements
PY  - 2014
SP  - e00647
EP  - e00614
VL  - 2
AB  - Streptococcus sp. strain VT 162 was isolated from the saliva of pediatric oncohematology
AB  - patients. Its full genome is 2,045,418 bp. The availability of
AB  - this genome will provide insights into the composition of microbial flora among
AB  - pediatric oncohematology patients and the host interaction and pathogenicity of
AB  - this species.
ER  -

TY  - JOUR
AU  - Vedantam, G.
AU  - Hecht, D.W.
TI  - Isolation and characterization of BTF-37: Chromosomal DNA captured from Bacteroides fragilis that confers self-transferability and expresses a pilus-like structure in Bacteroides spp. and Escherichia coli.
JO  - J. Bacteriol.
PY  - 2002
SP  - 728
EP  - 738
VL  - 184
AB  - We report the isolation and preliminary characterization of BTF-37, a new 52-kb transfer
AB  - factor isolated from Bacteroides fragilis clinical isolate LV23. BTF-37 was obtained by the
AB  - capture of new DNA in the nonmobilizable Bacteroides-Escherichia coli shuttle vector
AB  - pGAT400DeltaBglII using a functional assay. BTF-37 is self-transferable within and from
AB  - Bacteroides and also self-transfers in E. coli. Partial DNA sequencing, colony hybridization,
AB  - and PCR revealed the presence of Tet element-specific sequences in BTF-37. In addition,
AB  - Tn5520, a small mobilizable transposon that we described previously (G. Vedantam, T. J.
AB  - Novicki, and D. W. Hecht, J. Bacteriol. 181:2564-2571, 1999), was also coisolated within
AB  - BTF-37. Scanning and transmission electron microscopy of Tet element-containing Bacteroides
AB  - spp. and BTF-37-harboring Bacteroides and E. coli strains revealed the presence of pilus-like
AB  - cell surface structures. These structures were visualized in Bacteroides spp. only when BTF-37
AB  - and Tet element strains were induced with subinhibitory concentrations of tetracycline and
AB  - resembled those encoded by E. coli broad-host-range plasmids. We conclude that we have
AB  - captured a new, self-transferable transfer factor from B. fragilis LV23 and that this new
AB  - factor encodes a tetracycline-inducible Bacteroides sp. conjugation apparatus.
ER  -

TY  - JOUR
AU  - Vedler, E.
AU  - Vahter, M.
AU  - Heinaru, A.
TI  - The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation.
JO  - J. Bacteriol.
PY  - 2004
SP  - 7161
EP  - 7174
VL  - 186
AB  - The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium
AB  - Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains
AB  - plasmid pEST4011. This plasmid ensures its host a stable 2,4-D(+)
AB  - phenotype. We determined the complete 76,958-bp nucleotide sequence of
AB  - pEST4011. This plasmid is a deletion and duplication derivative of pD2M4,
AB  - the 95-kb highly unstable laboratory ancestor of pEST4011, and was
AB  - self-generated during different laboratory manipulations performed to
AB  - increase the stability of the 2,4-D(+) phenotype of the original strain,
AB  - strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a
AB  - transposon-like structure with identical copies of the hybrid insertion
AB  - element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011
AB  - and pJP4, the best-studied 2,4-D-degradative plasmid, both contain
AB  - homologous, tfd-like genes for complete 2,4-D degradation, but they have
AB  - little sequence similarity other than that. The backbone genes of pEST4011
AB  - are most similar to the corresponding genes of broad-host-range
AB  - self-transmissible IncP1 plasmids. The backbones of the other three IncP1
AB  - catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid
AB  - pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic
AB  - plasmid pADP-1) are nearly identical to the backbone of R751, the
AB  - archetype plasmid of the IncP1 beta subgroup. We show that despite the
AB  - overall similarity in plasmid organization, the pEST4011 backbone is
AB  - sufficiently different (51 to 86% amino acid sequence identity between
AB  - individual backbone genes) from the backbones of members of the three
AB  - IncP1 subgroups (the alpha, beta, and gamma subgroups) that it belongs to
AB  - a new IncP1subgroup, the delta subgroup. This conclusion was also
AB  - supported by a phylogenetic analysis of the trfA2, korA, and traG gene
AB  - products of different IncP1 plasmids.
ER  -

TY  - JOUR
AU  - Veeraraghavan, B.
AU  - Anandan, S.
AU  - Ragupathi, N.K.
AU  - Vijayakumar, S.
AU  - Sethuvel, D.P.
AU  - Biswas, I.
TI  - Draft Genome Sequence of Colistin-Resistant Acinetobacter baumannii Strain VB22595 Isolated from a Central Line-Associated Bloodstream Infection.
JO  - Genome Announcements
PY  - 2016
SP  - e00835
EP  - e00816
VL  - 4
AB  - Acinetobacter baumannii is an important emerging pathogen that causes health care-associated
AB  - infections. In this study, we determined the genome of a
AB  - multidrug-resistant clinical strain, VB22595, isolated from a hospital in
AB  - Southern India. The draft genome indicates that strain VB22595 encodes a genome
AB  - of ~3.92 Mb in size and does not contain plasmid derived MCR-1 for colistin
AB  - resistance.
ER  -

TY  - JOUR
AU  - Veeraraghavan, B.
AU  - Anandan, S.
AU  - Rajamani, S.S.K.
AU  - Gopi, R.
AU  - Devanga, R.N.K.
AU  - Ramesh, S.
AU  - Verghese, V.P.
AU  - Korulla, S.
AU  - Mathai, S.
AU  - Sangal, L.
AU  - Joshi, S.
TI  - First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India.
JO  - Genome Announcements
PY  - 2016
SP  - e01316
EP  - e01316
VL  - 4
AB  - We report here the draft genome sequences of five Corynebacterium diphtheriae isolates of
AB  - Indian origin. The C. diphtheriae isolates TH1141, TH510, TH1526,
AB  - TH1337, and TH2031 belong to sequence type ST-50, ST-295, ST-377, ST-405, and
AB  - ST-405, with an average genome size of 2.5 Mbp.
ER  -

TY  - JOUR
AU  - Veeraraghavan, B.
AU  - Neeravi, A.R.
AU  - Devanga, R.N.K.
AU  - Inbanathan, F.Y.
AU  - Pragasam, A.K.
AU  - Verghese, V.P.
TI  - Whole-Genome Shotgun Sequencing of the First Observation of Neisseria meningitidis Sequence Type 6928 in India.
JO  - Genome Announcements
PY  - 2016
SP  - e01232
EP  - e01216
VL  - 4
AB  - Neisseria meningitidis is one of the leading global causes of bacterial meningitis. Here, we
AB  - discuss the draft genome sequences of two N. meningitidis
AB  - strains, isolated from bloodstream infections in two pediatric patients at a
AB  - tertiary care hospital in South India. The sequence data indicate that strains
AB  - VB13856 and VB15548 encode genomes of ~2.09 Mb in size with no plasmids.
ER  -

TY  - JOUR
AU  - Veeraraghavan, B.
AU  - Perumalla, S.K.
AU  - Devanga, R.N.K.
AU  - Pragasam, A.K.
AU  - Muthuirulandi, S.D.P.
AU  - Inian, S.
AU  - Inbanathan, F.Y.
TI  - Coexistence of Fosfomycin and Colistin Resistance in Klebsiella pneumoniae: Whole-Genome Shotgun Sequencing.
JO  - Genome Announcements
PY  - 2016
SP  - e01303
EP  - e01316
VL  - 4
AB  - Resistance to colistin is a major threat that limits therapeutic choices for treating
AB  - carbapenem-resistant Klebsiella pneumoniae infections. Herein, we report
AB  - the draft genome sequences of two colistin-resistant K. pneumoniae isolates
AB  - (BA41763 and B6753). The sequence data indicate that BA41763 and B6753 contain
AB  - genomes of ~5.9 and 5.7 Mb in size with several plasmids.
ER  -

TY  - JOUR
AU  - Veiga, H.
AU  - Pinho, M.G.
TI  - Inactivation of the SauI Type I Restriction-Modification System Is Not Sufficient To Generate Staphylococcus aureus Strains Capable of Efficiently Accepting Foreign DNA.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 3034
EP  - 3038
VL  - 75
AB  - Genetic manipulation of Staphylococcus aureus is limited by the availability of only a single
AB  - strain, RN4220, that is capable of easily
AB  - accepting foreign DNA. Inactivation of the hsdR gene of the SauI type I
AB  - restriction-modification system was shown previously to be responsible
AB  - for the high transformation efficiency of RN4220 (D. E. Waldron and J.
AB  - A. Lindsay, J Bacteriol. 188:5578-5585, 2006). However, deletion of
AB  - this gene in three different S. aureus strains was not sufficient to
AB  - make them readily transformable, which would be remarkably useful for
AB  - genetic studies of this pathogenic organism. These results indicate
AB  - that another unknown factor(s) is required for the transformable
AB  - phenotype in S. aureus.
ER  -

TY  - JOUR
AU  - Veith, B.
AU  - Herzberg, C.
AU  - Steckel, S.
AU  - Feesche, J.
AU  - Maurer, K.H.
AU  - Ehrenreich, P.
AU  - Baumer, S.
AU  - Henne, A.
AU  - Liesegang, H.
AU  - Merkl, R.
AU  - Ehrenreich, A.
AU  - Gottschalk, G.
TI  - The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential.
JO  - J. Mol. Microbiol. Biotechnol.
PY  - 2004
SP  - 204
EP  - 211
VL  - 7
AB  - The genome of Bacillus licheniformis DSM13 consists of a single chromosome that has a size of
AB  - 4,222,748 base pairs. The average G+C ratio is 46.2%. 4,286 open
AB  - reading frames, 72 tRNA genes, 7 rRNA operons and 20 transposase genes were
AB  - identified. The genome shows a marked co-linearity with Bacillus subtilis but
AB  - contains defined inserted regions that can be identified at the sequence as well
AB  - as at the functional level. B. licheniformis DSM13 has a well-conserved secretory
AB  - system, no polyketide biosynthesis, but is able to form the lipopeptide
AB  - lichenysin. From the further analysis of the genome sequence, we identified
AB  - conserved regulatory DNA motives, the occurrence of the glyoxylate bypass and the
AB  - presence of anaerobic ribonucleotide reductase explaining that B. licheniformis
AB  - is able to grow on acetate and 2,3-butanediol as well as anaerobically on
AB  - glucose. Many new genes of potential interest for biotechnological applications
AB  - were found in B. licheniformis; candidates include proteases, pectate lyases,
AB  - lipases and various polysaccharide degrading enzymes.
ER  -

TY  - JOUR
AU  - Veitinger, S.
AU  - Schmitz, G.G.
AU  - Kaluza, K.
AU  - Jarsch, M.
AU  - Braun, V.
AU  - Kessler, C.
TI  - SfuI, a novel AsuII isoschizomer from Streptomyces fulvissimus recognizing 5'-TT/CGAA-3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3424
EP  - 3424
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Vejarano, F.
AU  - Suzuki-Minakuchi, C.
AU  - Ohtsubo, Y.
AU  - Tsuda, M.
AU  - Okada, K.
AU  - Nojiri, H.
TI  - Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00935
EP  - e00918
VL  - 7
AB  - We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium
AB  - isolated from Tokyo Bay and capable of degrading carbazole. The genome
AB  - consists of a 3.3-Mb circular chromosome that carries the gene clusters involved
AB  - in carbazole degradation and biosynthesis of the photosynthetic apparatus of
AB  - aerobic anoxygenic phototrophic bacteria.
ER  -

TY  - JOUR
AU  - Velasco-Bucheli, R.
AU  - Del Cerro, C.
AU  - Hormigo, D.
AU  - Acebal, C.
AU  - Arroyo, M.
AU  - Garcia, J.L.
AU  - de la Mata, I.
TI  - Draft Genome Sequence of Actinoplanes utahensis NRRL 12052, a Microorganism Involved in Industrial Production of Pharmaceutical Intermediates.
JO  - Genome Announcements
PY  - 2015
SP  - e01411
EP  - e01414
VL  - 3
AB  - Here, we describe the draft genome sequence of Actinoplanes utahensis NRRL 12052, a
AB  - filamentous bacterium that encodes an aculeacin A acylase and a putative
AB  - N-acyl-homoserine lactone acylase of biotechnological interest. Moreover, several
AB  - nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) clusters and
AB  - antibiotic resistance genes have been identified.
ER  -

TY  - JOUR
AU  - Velichko, N.
AU  - Rayko, M.
AU  - Chernyaeva, E.
AU  - Lapidus, A.
AU  - Pinevich, A.
TI  - Draft genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027), the chlorophyll a/b-containing filamentous cyanobacterium.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 82
EP  - 82
VL  - 11
AB  - Prochlorothrix hollandica is filamentous non-heterocystous cyanobacterium which possesses the
AB  - chlorophyll a/b light-harvesting complexes. Despite the growing
AB  - interest in unusual green-pigmented cyanobacteria (prochlorophytes) to date only
AB  - a few sequenced genome from prochlorophytes genera have been reported. This study
AB  - sequenced the genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027). The
AB  - produced draft genome assembly (5.5 Mb) contains 3737 protein-coding genes and
AB  - 114 RNA genes.
ER  -

TY  - JOUR
AU  - Velkov, V.V.
TI  - How environmental factors regulate mutagenesis and gene transfer in microorganisms.
JO  - J. Biosci.
PY  - 1999
SP  - 529
EP  - 559
VL  - 24
AB  - This review is focused on the physiological and evolutionary strategies of the processes
AB  - occurring during the entry of microbial cells into
AB  - stationary phase and the subsequent period of stasis. The molecular
AB  - mechanisms adapting microorganisms from exponential growth to a static
AB  - state involve activation and complex regulation of the stationary
AB  - factor Sigma-S, which directs RNA polymerase to the specific promoters.
AB  - As a result the static cells acquire general resistance (simultaneous
AB  - tolerances) to different environmental stresses. In parallel with the
AB  - physiological adaptation to stasis, diverse genetical processes are
AB  - aimed towards resuming the growth of the static cells. Different types
AB  - of mutagenesis occur: (i) in cells entering stasis and (ii) in static
AB  - cells (adaptive mutagenesis). Cessation of growth induces the transient
AB  - hypermutator state resulting in the accumulation of random mutations in
AB  - the subpopulation of the static cells. If by chance, one or a few of
AB  - such mutations lead to resumption of division, the growing cell will
AB  - return to a normal mechanism of spontaneous mutagenesis. Another
AB  - mechanism for generating genetical variability in stressed cells
AB  - involves transposons and conjugative plasmids. Stresses can stimulate
AB  - the excision of some transposons, which, in turn, can generate
AB  - chromosomal mutations and activate intracellular mechanisms of
AB  - mutagenesis. Under stress some conjugative plasmids activate genes
AB  - encoding antirestriction proteins that repress restriction-modification
AB  - systems of the recipient cells. Moreover, under stress special cellular
AB  - mechanisms decrease (alleviate) the activity of
AB  - restriction-modification systems which, in turn, enhance the
AB  - probability of gene transfer into the stressed cells. Under stress, the
AB  - efficiency of inter-species genetical barriers also decreases. This,
AB  - stimulates inter-species gene transfer and may lead to a burst of
AB  - incipient speciation in the population of non-growing cells. After
AB  - resumption of growth the genetical barriers leading to isolation will
AB  - be restored. In general, the cessation of growth "switches on", and
AB  - resumption of growth "switches off", a set of special processes that
AB  - are responsible for generating bursts of genetical variability in
AB  - populations of microorganisms.
ER  -

TY  - JOUR
AU  - Vellarikkal, S.K.
AU  - Singh, A.V.
AU  - Singh, P.K.
AU  - Garg, P.
AU  - Katoch, V.M.
AU  - Katoch, K.
AU  - Chauhan, D.S.
AU  - Sivasubbu, S.
AU  - Scaria, V.
TI  - Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium  tuberculosis Belonging to a Novel Spoligotype.
JO  - Genome Announcements
PY  - 2013
SP  - e00965
EP  - e00913
VL  - 1
AB  - We describe the genome sequencing and analysis of a multidrug-resistant (MDR) clinical isolate
AB  - of Mycobacterium tuberculosis, strain OSDD105 from India,
AB  - belonging to a novel spoligotype.
ER  -

TY  - JOUR
AU  - Vellarikkal, S.K.
AU  - Singh, A.V.
AU  - Singh, P.K.
AU  - Garg, P.
AU  - Katoch, V.M.
AU  - Katoch, K.
AU  - Chauhan, D.S.
AU  - Sivasubbu, S.
AU  - Scaria, V.
TI  - Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical  Isolate OSDD515, Belonging to the Uganda I Genotype.
JO  - Genome Announcements
PY  - 2013
SP  - e00750
EP  - e00713
VL  - 1
AB  - We describe the genome sequencing and analysis of a clinical isolate of the
AB  - multidrug-resistant Mycobacterium tuberculosis Uganda I genotype (OSDD515) from
AB  - India.
ER  -

TY  - JOUR
AU  - Velly, H.
AU  - Renault, P.
AU  - Abraham, A.L.
AU  - Loux, V.
AU  - Delacroix-Buchet, A.
AU  - Fonseca, F.
AU  - Bouix, M.
TI  - Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis subsp. lactis TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese.
JO  - Genome Announcements
PY  - 2014
SP  - e01121
EP  - e01114
VL  - 2
AB  - Lactococcus lactis is a lactic acid bacterium used in the production of many fermented foods,
AB  - such as dairy products. Here, we report the genome sequence of
AB  - L. lactis subsp. lactis TOMSC161, isolated from nonscalded curd pressed cheese.
AB  - This genome sequence provides information in relation to dairy environment
AB  - adaptation.
ER  -

TY  - JOUR
AU  - Velusamy, N.
AU  - Prakash, L.
AU  - Sivakumar, N.
AU  - Antony, A.
AU  - Prajna, L.
AU  - Mohankumar, V.
AU  - Devarajan, B.
TI  - Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates.
JO  - Genome Announcements
PY  - 2014
SP  - e00168
EP  - e00114
VL  - 2
AB  - Sequence type 22 (ST22) and ST672 are the two major emerging clones of community-acquired
AB  - methicillin-resistant Staphylococcus aureus in India. ST672
AB  - strains were found to cause severe ocular infections. We report the draft genome
AB  - sequences of two emerging strains of methicillin-resistant S. aureus, AMRF1
AB  - (ST22) and AMRF2 (ST672), isolated from patients with ocular infections.
ER  -

TY  - JOUR
AU  - Venclovas, C.
AU  - Siksnys, V.
TI  - Different enzymes with similar structures involved in Mg2+-mediated polynucleotidyl transfer.
JO  - Nat. Struct. Biol.
PY  - 1995
SP  - 838
EP  - 841
VL  - 2
AB  - Comparison of x-ray structures of restriction endonucleases and polynucleotidyl transferase
AB  - superfamily enzymes reveals a structural resemblance.  Transfer of polynucleotidyl residues
AB  - plays a fundamental role in such critical cellular events as genetic recombination,
AB  - transposition and viral DNA integration.  A number of different enzymes is directly implicated
AB  - in this process.  Recently X-ray structures of RuvC protein, a Holliday junction resolvase
AB  - from Escherichia coli and HIV-1 integrase, involved in viral DNA integration, have been
AB  - solved.  Surprisingly, RuvC, HIV-integrase and ribonuclease H (RNase H) appear to have similar
AB  - three-dimensional structures, despite the lack of protein sequence similarities.  On the
AB  - basis of fold resemblance it was proposed that all these enzymes belong to the new superfamily
AB  - of polynucleotidyl transferases (PNT).
ER  -

TY  - JOUR
AU  - Venclovas, C.
AU  - Timinskas, A.
AU  - Siksnys, V.
TI  - Five-stranded beta-sheet sandwiched with two a-helices: a structural link between restriction endonucleases EcoRI and EcoRV.
JO  - Proteins
PY  - 1994
SP  - 279
EP  - 282
VL  - 20
AB  - Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with
AB  - their cognate DNA revealed a common structural element, which forms the core of both proteins.
AB  - This element consists of a five-stranded beta-sheet and two alpha-helices packed against it
AB  - and could be described as alpha-beta sandwich in which helices and beta-strands lie in two
AB  - stacked layers. While the spatial structure of this alpha-beta sandwich is conserved in both
AB  - enzymes, there are no detectable similarities between amino acid sequences except of a few
AB  - residues involved in active site formation. Probably, other restriction endonucleases which
AB  - have similar organization of the active site might possess similar structural element
AB  - regardless of DNA sequence recognized and recognition elements in the enzyme used.
ER  -

TY  - JOUR
AU  - Venditti, S.
AU  - Wells, R.D.
TI  - A DNA conformational alteration induced by a neighboring oligopurine tract on GAATTA enables nicking by EcoRI.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 16786
EP  - 16790
VL  - 266
AB  - The pseudo EcoRI site GAATTA in the U3 region of the long terminal repeat of
AB  - human immunodeficiency virus, which is flanked by a 26-base pair oligopurine
AB  - tract, is readily nicked by either EcoRI or RsrI.  The strand-specific nick
AB  - occurs predominantly between the G and A residues and is independent of
AB  - negative supercoiling.  Other GAATTA sites surrounded by random
AB  - (non-oligopurine) sequences are not nicked by these restriction endonucleases.
AB  - However, other types and lengths of oligopurine tracts are effective in
AB  - inducing the nicking in neighboring GAATTA sites.  Hence, we propose that the
AB  - flanking oligopurine tracts induce an altered DNA conformation on the GAATTA
AB  - target site which may be similar to the transition state induced by EcoRI when
AB  - binding to its canonical recognition site.  Gel retardation analyses on
AB  - restriction fragments containing the oligopurine-GAATTA-oligopurine sequences
AB  - suggest the presence of helical axis distortions which are consistent with this
AB  - interpretation.
ER  -

TY  - JOUR
AU  - Vendramin, V.
AU  - Treu, L.
AU  - Bovo, B.
AU  - Campanaro, S.
AU  - Corich, V.
AU  - Giacomini, A.
TI  - Whole-Genome Sequence of Streptococcus macedonicus Strain 33MO, Isolated from the Curd of Morlacco Cheese in the Veneto Region (Italy).
JO  - Genome Announcements
PY  - 2014
SP  - e00746
EP  - e00714
VL  - 2
AB  - A genetic characterization of Streptococcus macedonicus is important to better understand the
AB  - characteristics of this lactic acid bacterium, frequently detected
AB  - in fermented food bacteria communities. This report presents the draft genome
AB  - sequence description of strain 33MO, the first publicly available genome sequence
AB  - of an Italian S. macedonicus isolate.
ER  -

TY  - JOUR
AU  - Venegas, A.
AU  - Motles, M.
AU  - Vasquez, C.
AU  - Vicuna, R.
TI  - Conditions affecting DNA cleavage by TthI at a TthI endonuclease-dam methylase overlapping sequence.
JO  - FEBS Lett.
PY  - 1981
SP  - 272
EP  - 274
VL  - 130
AB  - The Escherichia coli dam gene codes for a site-specific DNA methylase which methylates adenine
AB  - in the sequence GATC at the N6 position of the purine ring. The effect of this modification on
AB  - the action of several restriction enzymes whose recognition sites are equal or include the
AB  - methylated sequence depends on the endonuclease itself. For example, the enzymes MboI, BclI
AB  - and DpnII do not cleave a sequence containing GAme^TC, while DpnI requires the presence of
AB  - 6MeAde in GATC sites in order to cleave the DNA. On the other hand, isoschizomers Sau3AI,
AB  - FnuEI and PfaI actively hydrolyze sequences that have undergone adenine methylation; Sau3AI,
AB  - however, is inhibited by the methylation of cytosine of the indicated sequence.
ER  -

TY  - JOUR
AU  - Venegas, A.
AU  - Vicuna, R.
AU  - Alonso, A.
AU  - Valdes, F.
AU  - Yudelevich, A.
TI  - A rapid procedure for purifying a restriction endonuclease from Thermus thermophilus (TthI).
JO  - FEBS Lett.
PY  - 1980
SP  - 156
EP  - 158
VL  - 109
AB  - Restriction enzymes have proved to be a powerful tool for mapping genomes and
AB  - developing molecular cloning and DNA sequencing techniques.  A few restriction
AB  - enzymes have been isolated from thermophilic bacteria, showing a high
AB  - thermostability and resistance to protein denaturing agents.  These properties
AB  - could be useful to study DNA structure at higher temperatures.  Looking for a
AB  - stable enzyme with a new recognition sequence, we have isolated TthI, an enzyme
AB  - from the extreme thermophile Thermus thermophilus HB8. This thermostable enzyme
AB  - turned out to be an isoschizomer of TaqI, which recognizes the sequence
AB  - 5'-TCGA-3'.  Thermus thermophilus is a very convenient source for purifying
AB  - this enzyme since this bacterium does not produce the pigmented 'slime'
AB  - described in Thermus aquaticus, which interferes with the Purification of TawI
AB  - and other enzymes.  Furthermore, TthI was readily released by osmotic shock,
AB  - which allowed us to develop a simplified, rapid two-step procedure to obtain an
AB  - enzyme preparation free of contaminating nucleases.  We report here the
AB  - purifiction method and some of the properties of TthI.
ER  -

TY  - JOUR
AU  - Venetianer, P.
TI  - Purification and properties of the Bsp endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 109
EP  - 112
VL  - 65
AB  - None
ER  -

TY  - JOUR
AU  - Venetianer, P.
AU  - Kiss, A.
TI  - The restriction-modification enzymes of Bacillus sphaericus R.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 209
EP  - 215
VL  - 1
AB  - *
AB  -   I. Biochemical characterization of the BspI restriction endonuclease
AB  -  II. Biochemical characterization of the BspI modification methylase
AB  - III. The genes of the Bsp restriction-modification system
AB  -  IV. Conclusion
AB  - 
ER  -

TY  - JOUR
AU  - Venetianer, P.
AU  - Orosz, A.
TI  - BcefI, a new type IIS restriction endonuclease.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 3053
EP  - 3060
VL  - 16
AB  - A new Type IIS restriction endonuclease was identified, partially purified and characterized
AB  - from a Bacillus cereus subsp. fluorescens strain.  The enzyme recognized the nonpalindromic
AB  - sequence ACGGC and cleaves at a distance from it.  The cleavage appears to occur with a +/-1
AB  - basepair uncertainity.  Thus the cleavage and recognition site is as shown below:
AB  - ACGGC(N) 11-13
AB  - TGCCG(N) 12-14.
ER  -

TY  - JOUR
AU  - Venetianer, P.
AU  - Orosz, A.
TI  - Isolation and characterization of two new restriction endonucleases (BepI and BcefI) .
JO  - Gene
PY  - 1988
SP  - 99
EP  - 99
VL  - 74
AB  - Meeting Abstract
ER  -

TY  - JOUR
AU  - Venetianer, P.
AU  - Orosz, A.
TI  - BepI restriction endonuclease, a new isoschizomer of FnuDII.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 350
EP  - 350
VL  - 16
AB  - A new TypeII restriction endonuclease was isolated and characterized from a bacterial strain
AB  - identified as Brevibacterium epidermidis by Dr. M. Konkoly-Thege (Budapest).  The strain grows
AB  - well in yeast-tryptone broth aerobically with a doubling time of 50 min at 25-30 C.  The
AB  - enzyme was purified by a conventional procedure, employing Bio-Gel A-0.5 m, DEAE-cellulose and
AB  - phosphocellulose chromatography.  The enzyme at this stage of purification was applicable for
AB  - all practical purposes, it was virtually free from contaminating nucleases.  The yield of the
AB  - enzyme was approximately 3-400 units/g wet weight of cell.  The optimal conditions for the
AB  - activity of the enzyme are as follows:  temperature 25-30 C., Mg2+ ions 10 mM, pH 7.4, no
AB  - salts.  The cleavage pattern of the enzyme tested with known DNA molecules (lambda phage,
AB  - pBR322) was identical with the pattern obtained with FnuDII.  This identity was confirmed by
AB  - parallel digestions with the new enzyme and commercial FnuDII, and double digestions with both
AB  - enzymes, that resulted in unaltered digestion patterns. The cleavage site was established by
AB  - running a Maxam-Gilbert sequence gel from a DNA fragment of known sequence, which contained a
AB  - FnuDII site.  The same end-labelled DNA fragment was then digested with the new enzyme, and it
AB  - was electrophoresed alongside the sequence ladder.  This experiment unambiguously proved that
AB  - the cleavage occured in the middle of the palindromic CGCG sequence, generating flush ends.
AB  - Thus the enzyme does not represent a new specificity, it is an isoschizomer of the well known
AB  - FnuDII enzyme. Nevertheless it offers some practical advantages.  The Fusobacterium nucleatum
AB  - strain, from which FnuDII is isolated, is an obligately anaerobic pathogenic microorganism,
AB  - therefore FnuDII is fairly expensive.  The only other commercially available isoschisomer,
AB  - ThaI is purified from an extremely thermophilic and acidophilic organism, the other described
AB  - isoschisomers (3,4) have not been characterized.  It is hoped that the BepI enzyme will be a
AB  - better substitute for these isoschisomers.
ER  -

TY  - JOUR
AU  - Venkatesan, M.M.
AU  - Goldberg, M.B.
AU  - Rose, D.J.
AU  - Grotbeck, E.J.
AU  - Burland, V.
AU  - Blattner, F.R.
TI  - Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri.
JO  - Infect. Immun.
PY  - 2001
SP  - 3271
EP  - 3285
VL  - 69
AB  - The complete sequence analysis of the 210-kb Shigella flexneri 5a
AB  - virulence plasmid was determined. Shigella spp. cause dysentery and
AB  - diarrhea by invasion and spread through the colonic mucosa. Most of the
AB  - known Shigella virulence determinants are encoded on a large plasmid that
AB  - is unique to virulent strains of Shigella and enteroinvasive Escherichia
AB  - coli; these known genes account for approximately 30 to 35% of the
AB  - virulence plasmid. In the complete sequence of the virulence plasmid, 286
AB  - open reading frames (ORFs) were identified. An astonishing 153 (53%) of
AB  - these were related to known and putative insertion sequence (IS) elements;
AB  - no known bacterial plasmid has previously been described with such a high
AB  - proportion of IS elements. Four new IS elements were identified. Fifty
AB  - putative proteins show no significant homology to proteins of known
AB  - function; of these, 18 have a G+C content of less than 40%, typical of
AB  - known virulence genes on the plasmid. These 18 constitute potentially
AB  - unknown virulence genes. Two alleles of shet2 and five alleles of ipaH
AB  - were also identified on the plasmid. Thus, the plasmid sequence suggests a
AB  - remarkable history of IS-mediated acquisition of DNA across bacterial
AB  - species. The complete sequence will permit targeted characterization of
AB  - potential new Shigella virulence determinants.
ER  -

TY  - JOUR
AU  - Venkateswaran, K. et al.
TI  - Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains,  Isolated from the International Space Station.
JO  - Genome Announcements
PY  - 2017
SP  - e00680
EP  - e00617
VL  - 5
AB  - The draft genome sequences of six Bacillus strains, isolated from the International Space
AB  - Station and belonging to the Bacillus anthracis-B. cereus-B.
AB  - thuringiensis group, are presented here. These strains were isolated from the
AB  - Japanese Experiment Module (one strain), U.S. Harmony Node 2 (three strains), and
AB  - Russian Segment Zvezda Module (two strains).
ER  -

TY  - JOUR
AU  - Venkatramanan, R.
AU  - Prakash, O.
AU  - Woyke, T.
AU  - Chain, P.
AU  - Goodwin, L.A.
AU  - Watson, D.
AU  - Brooks, S.
AU  - Kostka, J.E.
AU  - Green, S.J.
TI  - Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment.
JO  - Genome Announcements
PY  - 2013
SP  - e00449
EP  - e00413
VL  - 1
AB  - Genome sequences for three strains of denitrifying bacteria (Alphaproteobacteria-Afipia sp.
AB  - strain 1NLS2 and Hyphomicrobium denitrificans
AB  - strain 1NES1; Firmicutes-Bacillus sp. strain 1NLA3E) isolated from the nitrate-
AB  - and uranium-contaminated subsurface of the Oak Ridge Integrated Field Research
AB  - Challenge (ORIFRC) site, Oak Ridge Reservation, TN, are reported.
ER  -

TY  - JOUR
AU  - Venter, J.C. et al.
TI  - Environmental Genome Shotgun Sequencing of the Sargasso Sea.
JO  - Science
PY  - 2004
SP  - 66
EP  - 74
VL  - 304
AB  - We have applied "whole-genome shotgun sequencing" to microbial populations
AB  - collected en masse on tangential flow and impact filters from seawater
AB  - samples collected from the Sargasso Sea near Bermuda. A total of 1.045
AB  - billion base pairs of nonredundant sequence was generated, annotated, and
AB  - analyzed to elucidate the gene content, diversity, and relative abundance
AB  - of the organisms within these environmental samples. These data are
AB  - estimated to derive from at least 1800 genomic species based on sequence
AB  - relatedness, including 148 previously unknown bacterial phylotypes. We
AB  - have identified over 1.2 million previously unknown genes represented in
AB  - these samples, including more than 782 new rhodopsin-like photoreceptors.
AB  - Variation in species present and stoichiometry suggests substantial
AB  - oceanic microbial diversity.
ER  -

TY  - JOUR
AU  - Ventura, M. et al.
TI  - The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.
JO  - PLoS Genet.
PY  - 2009
SP  - e1000785
EP  - e1000785
VL  - 5
AB  - Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota,
AB  - are considered one of the key groups of beneficial
AB  - intestinal bacteria (probiotic bacteria). However, in addition to
AB  - health-promoting taxa, the genus Bifidobacterium also includes
AB  - Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic
AB  - basis for the ability of B. dentium to survive in the oral cavity and
AB  - contribute to caries development is not understood. The genome of B.
AB  - dentium Bd1, a strain isolated from dental caries, was sequenced to
AB  - completion to uncover a single circular 2,636,368 base pair chromosome
AB  - with 2,143 predicted open reading frames. Annotation of the genome
AB  - sequence revealed multiple ways in which B. dentium has adapted to the
AB  - oral environment through specialized nutrient acquisition, defences
AB  - against antimicrobials, and gene products that increase fitness and
AB  - competitiveness within the oral niche. B. dentium Bd1 was shown to
AB  - metabolize a wide variety of carbohydrates, consistent with genome-based
AB  - predictions, while colonization and persistence factors implicated in
AB  - tissue adhesion, acid tolerance, and the metabolism of human
AB  - saliva-derived compounds were also identified. Global transcriptome
AB  - analysis demonstrated that many of the genes encoding these predicted
AB  - traits are highly expressed under relevant physiological conditions. This
AB  - is the first report to identify, through various genomic approaches,
AB  - specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium
AB  - dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral
AB  - cavity. In silico analysis and comparative genomic hybridization
AB  - experiments clearly reveal a high level of genome conservation among
AB  - various B. dentium strains. The data indicate that the genome of this
AB  - opportunistic cariogen has evolved through a very limited number of
AB  - horizontal gene acquisition events, highlighting the narrow boundaries
AB  - that separate commensals from opportunistic pathogens.
ER  -

TY  - JOUR
AU  - Venturini, C.
AU  - Beatson, S.A.
AU  - Djordjevic, S.P.
AU  - Walker, M.J.
TI  - Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid.
JO  - FASEB J.
PY  - 2010
SP  - 1160
EP  - 1166
VL  - 24
AB  - Enterohemorrhagic Escherichia coli (EHEC) strains are zoonotic pathogens
AB  - responsible for a range of severe human disease. The repertoire of
AB  - virulence determinants promoting EHEC disease is encoded on both the main
AB  - chromosome and virulence plasmid. We examined a multiply
AB  - antibiotic-resistant O26 EHEC strain for carriage of resistance genes on
AB  - the virulence plasmid. The EHEC virulence plasmid containing a complex
AB  - antibiotic-resistance gene locus, designated as pO26-CRL, was purified
AB  - from EHEC O26:H(-) (patient with hemorrhagic colitis) and subjected to
AB  - shotgun-sequencing and bioinformatic analysis. Determination of the
AB  - 111,481-bp sequence of pO26-CRL revealed genes encoding a functional
AB  - enterohemolysin operon (ehxCABD), STEC-specific extracellular serine
AB  - protease (espP), putative EHEC adhesin (toxB), catalase/peroxidase (katP),
AB  - and myristoyl transferase (msbB) involved in lipid A synthesis. A
AB  - 22,609-bp Tn21 derivative is inserted within the conjugal transfer gene
AB  - traC and encodes resistance to trimethoprim, streptomycin, sulfathiozole,
AB  - kanamycin, neomycin, beta-lactams, and mercuric chloride. Plasmid pO26-CRL
AB  - is nonconjugative but is mobilizable. This is the first report of an EHEC
AB  - virulence plasmid containing a complex antibiotic resistance locus, and
AB  - raises the concern that antibiotic use will coselect for virulence
AB  - determinants, leading to increased disease potential in both commensal and
AB  - pathogenic E. coli populations.-Venturini, C., Beatson, S. A., Djordjevic,
AB  - S. P., Walker, M. J. Multiple antibiotic resistance gene recruitment onto
AB  - the enterohemorrhagic Escherichia coli virulence plasmid.
ER  -

TY  - JOUR
AU  - Venturini, C.
AU  - Hassan, K.A.
AU  - Roy-Chowdhury, P.
AU  - Paulsen, I.T.
AU  - Walker, M.J.
AU  - Djordjevic, S.P.
TI  - Sequences of Two Related Multiple Antibiotic Resistance Virulence Plasmids Sharing a Unique IS26-Related Molecular Signature Isolated from Different Escherichia coli Pathotypes from Different Hosts.
JO  - PLoS ONE
PY  - 2013
SP  - E78862
EP  - E78862
VL  - 8
AB  - Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli
AB  - (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant
AB  - to multiple antibiotics. Here we describe two plasmids, pO26-CRL125 (125 kb) from
AB  - a human O26:H- EHEC, and pO111-CRL115 (115kb) from a bovine O111 aEPEC, that
AB  - impart resistance to ampicillin, kanamycin, neomycin, streptomycin,
AB  - sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1
AB  - integrons with an identical IS26-mediated deletion in their 3 -conserved segment.
AB  - Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are
AB  - essentially identical except for a 9.7 kb fragment, present in the backbone of
AB  - pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment
AB  - encodes IncI-associated genes involved in plasmid stability during conjugation, a
AB  - putative transposase gene and three imperfect repeats. Contiguous sequence
AB  - identical to regions within these pO26-CRL125 imperfect repeats was identified in
AB  - pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be
AB  - mobile. Sequences shared between the plasmids include a complete IncZ replicon, a
AB  - unique toxin/antitoxin system, IncI stability and maintenance genes, a novel
AB  - putative serine protease autotransporter, and an IncI1 transfer system including
AB  - a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an
AB  - atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to
AB  - trimethoprim, and 24 bp of the 3 -conserved segment followed by Tn6026, which
AB  - encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and
AB  - sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721,
AB  - encoding resistance to tetracycline, via a region containing the IncP-1alpha
AB  - oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons,
AB  - indicates that homologous recombination events played a key role in the formation
AB  - of this complex antibiotic resistance gene locus. Comparative sequence analysis
AB  - of these closely related plasmids reveals aspects of plasmid evolution in
AB  - pathogenic E. coli from different hosts.
ER  -

TY  - JOUR
AU  - Venyaminov, S.Y.
AU  - Kosykh, V.G.
AU  - Kholodkov, O.A.
AU  - Buryanov, Y.I.
TI  - UV- and CD-spectra of restriction endonuclease EcoRII and DNA-methylase EcoRII.
JO  - Bioorg. Khim.
PY  - 1990
SP  - 47
EP  - 51
VL  - 16
AB  - UV- and CD-spectra of homogeneous enzymes have been measured.  Extinction
AB  - coefficients estimated from the UV-spectra are 0.97 for restriction
AB  - endonuclease EcoRII at 279.5 nm and 1.17 for DNA-methylase EcoRII at 279 nm.
AB  - As it follows from the CD spectra, both enzymes have a well developed tertiary
AB  - structure and a highly ordered secondary structure, which consists of 22%
AB  - alpha-helices, 64% beta-structure and 9% bends for R.EcoRII and of 44%
AB  - alpha-helices, 48% beta-structure and 4% bends for M.EcoRII.  Restriction
AB  - endonuclease denatures at 50C, while DNA -methylase denatures at 45C, with
AB  - partial reversibility upon cooling.
ER  -

TY  - JOUR
AU  - Vera-Cabrera, L.
AU  - Ortiz-Lopez, R.
AU  - Elizondo-Gonzalez, R.
AU  - Campos-Rivera, M.P.
AU  - Gallardo-Rocha, A.
AU  - Molina-Torres, C.A.
AU  - Ocampo-Candiani, J.
TI  - Draft Genome Sequence of Actinomadura madurae LIID-AJ290, Isolated from a Human Mycetoma Case.
JO  - Genome Announcements
PY  - 2014
SP  - e00201
EP  - e00214
VL  - 2
AB  - Here we present the draft genome sequence of a member of the Thermomonosporaceae, Actinomadura
AB  - madurae LIID-AJ290, isolated from a human case of mycetoma. The
AB  - assembly contains 10,308,866 bp. This is to our knowledge the first reported
AB  - genome of a human-pathogenic Actinomadura species.
ER  -

TY  - JOUR
AU  - Vera-Cabrera, L.
AU  - Ortiz-Lopez, R.
AU  - Elizondo-Gonzalez, R.
AU  - Perez-Maya, A.A.
AU  - Ocampo-Candiani, J.
TI  - Complete Genome Sequence of Nocardia brasiliensis HUJEG-1.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2761
EP  - 2762
VL  - 194
AB  - In Mexico, actinomycetoma is mainly caused by Nocardia brasiliensis, which is a soil
AB  - inhabitant actinobacterium. Here, we report for the first time the draft
AB  - genome of a strain isolated from a human case that has largely been found in in
AB  - vitro and experimental models of actinomycetoma, N. brasiliensis HUJEG-1.
ER  -

TY  - JOUR
AU  - Verce, M.
AU  - De Vuyst, L.
AU  - Weckx, S.
TI  - Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101.
JO  - Genome Announcements
PY  - 2018
SP  - e00256
EP  - e00218
VL  - 6
AB  - Lactobacillus fermentum is a species of lactic acid bacteria that is frequently found in
AB  - sourdough, a fermented flour-water mixture used in the production of
AB  - bread and other baked goods. Here, we present the complete genome sequence of L.
AB  - fermentum IMDO 130101, a candidate sourdough starter culture strain isolated from
AB  - a backslopped rye sourdough.
ER  -

TY  - JOUR
AU  - Verdet, C.
AU  - Gautier, V.
AU  - Chachaty, E.
AU  - Ronco, E.
AU  - Hidri, N.
AU  - Decre, D.
AU  - Arlet, G.
TI  - Genetic context of plasmid-carried blaCMY-2-like genes in Enterobacteriaceae.
JO  - Antimicrob. Agents Chemother.
PY  - 2009
SP  - 4002
EP  - 4006
VL  - 53
AB  - Analysis of 15 European clinical Enterobacteriaceae isolates showed that
AB  - differences in the genetic context of blaCMY-2-like genes reflected the
AB  - replicon type, usually IncA/C or IncI1. These blaCMY-2 loci may originate
AB  - from the same ISEcp1-mediated mobilization from the Citrobacter freundii
AB  - chromosome as structures described in earlier studies.
ER  -

TY  - JOUR
AU  - Verdine, G.
TI  - The flip side of DNA methylation.
JO  - Cell
PY  - 1994
SP  - 197
EP  - 200
VL  - 76
AB  - DNA methylation has come of age. For more than 40 years, it has been known that eukaryotes tag
AB  - their DNA by the covalent addition of a methyl group to cytosine residues; however, until very
AB  - recently, the functional significance of this modification has remained on a precariously
AB  - speculative footing. A series of discoveries over the last few years has thrust DNA
AB  - methylation firmly into the mainstream of biology and medicine, thereby invigorating the field
AB  - with a firmly established sense of mission. Fragile X syndrome, the leading cause of inherited
AB  - mental retardation, has been traced to expansion and abnormal methylation of a triplet repeat,
AB  - through which transcription of the FMR-1 gene becomes silenced (Trottier et al., 1993).
AB  - Aberrant promoter methylation of tumor suppressor genes has now emerged as an epigenetic
AB  - inactivation pathway contributing to tumorigenesis; evidence increasingly supports the notion
AB  - that ectopic methylation may play a broad role in gene inactivation and mutation in mammals
AB  - (reviewed by Bestor and Coxon, 1993). Much excitement has revolved around the role of DNA
AB  - methylation in genomic imprinting, a phenomenon in which parental alleles of the same gene are
AB  - expressed at unequal dosages (Barlow, 193). Abnormal expression of imprinted loci is now
AB  - implicated in several human disorders (Ogawa et al., 1993; Rainier et al., 1993; Davies,
AB  - 1992), and more instances seem likely to be discovered. The entire field of DNA methylation,
AB  - with its foundations resting largely on the strength of correlative data, took both a
AB  - collective breath of relief and a bold step forward with the direct demonstration of Li et al.
AB  - (1992) that the DNA MTase gene is essential for development in mice. A molecular mechanism for
AB  - spatiotemporal coupling of DNA replication and methylation has been suggested by the finding
AB  - that DNA MTase interacts directly with the replication apparatus (Leonhardt et al., 1992).
ER  -

TY  - JOUR
AU  - Verdine, G.L.
AU  - Bruner, S.D.
TI  - How do DNA repair proteins locate damaged bases in the genome?
JO  - Chem. Biol.
PY  - 1997
SP  - 329
EP  - 334
VL  - 4
AB  - The genome is susceptible to the attack of reactive species that chemically modify the bases
AB  - of DNA.  If genetic information is to be transmitted faithfully to successive generations, it
AB  - is essential that the genome be repaired.  All organisms express proteins specifically
AB  - dedicated to this task.  But how do these proteins find the aberrant bases amongst the
AB  - enormous number of normal ones?
ER  -

TY  - JOUR
AU  - Vereijken, J.M.
AU  - van Mansfeld, A.D.M.
AU  - Baas, P.D.
AU  - Jansz, H.S.
TI  - Arthrobacter luteus Restriction endonuclease Cleavage Map of PhiX174 RF DNA.
JO  - Virology
PY  - 1975
SP  - 221
EP  - 233
VL  - 68
AB  - Cleavage of PhiX174 RF DNA with the restriction endonuclease from Arthrobacter
AB  - luteus (AluI) produces 23 fragments of approximately 24-1100 base pairs in
AB  - length.  The order of most of these fragments has been established by digestion
AB  - of Haemophilus influenzae Rd (HindII) and Haemophilus aegyptius (HaeIII)
AB  - endonuclease fragments of PhiX RF with AluI and by reciprocal digestions of
AB  - AluI fragments with HindII and HaeIII.  In this way the Arthrobacter luteus map
AB  - could be aligned with the HindII and HaeIII cleavage maps of PhiX174 RF DNA of
AB  - A.S. Lee and R.L. Sinsheimer (1974) Proc. Natl. Acad. Sci. USA 71: 2882-2886).
ER  -

TY  - JOUR
AU  - Veress, A.
AU  - Wilk, T.
AU  - Kiss, J.
AU  - Olasz, F.
AU  - Papp, P.P.
TI  - Draft Genome Sequences of Saccharibacter sp. Strains 3.A.1 and M18 Isolated from  Honey and a Honey Bee (Apis mellifera) Stomach.
JO  - Genome Announcements
PY  - 2017
SP  - e00744
EP  - e00717
VL  - 5
AB  - The annotated draft genome sequences of two recent Saccharibacter sp. strains isolated from
AB  - honey and a honey bee stomach in 2014 are reported here. Currently,
AB  - two Saccharibacter whole-genome sequences are available in databases; thus, the
AB  - sequences of our new isolates will contribute to a better understanding of
AB  - Saccharibacter genomes.
ER  -

TY  - JOUR
AU  - Veress, A.
AU  - Wilk, T.
AU  - Kiss, J.
AU  - Papp, P.P.
AU  - Olasz, F.
TI  - Two Draft Genome Sequences of Sphingobacterium sp. Strains Isolated from Honey.
JO  - Genome Announcements
PY  - 2017
SP  - e01364
EP  - e01317
VL  - 5
AB  - Here, we report two annotated draft genome sequences of Sphingobacterium sp. strains isolated
AB  - from honey. The genomes of strains 1.A.4 and 1.A.5 show a
AB  - limited similarity to each other and to genomes of other Sphingobacterium
AB  - species, indicating that these isolates may represent new species.
ER  -

TY  - JOUR
AU  - Verhoef, J.
AU  - van Boven, C.P.A.
AU  - Holtrigter, B.
TI  - Restriction and modification of phages in Staphylococcus epidermidis.
JO  - Informative molecules in biological systems.
PY  - 1971
SP  - 213
EP  - 220
VL  - 0
AB  - The present results demonstrate the occurrence of host-controlled modification
AB  - of phage DNA in coagulase-negative staphylococci.  Three modification and
AB  - restriction systems, which seem to determine the observed phage typing patterns
AB  - to a large extent, could be detected.  In these staphylococci, restrictive
AB  - cells appear to break down modified DNA.
ER  -

TY  - JOUR
AU  - Verhoef, J.
AU  - van Boven, C.P.A.
AU  - Holtrigter, B.
TI  - Restriction and modification of phages in coagulase-negative staphylococci.
JO  - Antonie Van Leeuwenhoek
PY  - 1971
SP  - 256
EP  - 267
VL  - 37
AB  - Phage typing of coagulase-negative staphylococci showed that certain
AB  - combination of phage reactions (phage patterns a-g) occurred frequently.  Six
AB  - of these could be arranged in three groups (M1, M2, M3) leaving the strains
AB  - with pattern g which are sensitive to all phages.  The differences in
AB  - susceptibility in patterns a to g were not due to resistance (as all strains
AB  - adsorbed all phages) and could not be explained by immunity.  A correlation was
AB  - observed between host range of the phage and the pattern of the propagating
AB  - strain.
ER  -

TY  - JOUR
AU  - Verhoef, J.
AU  - van Boven, C.P.A.
AU  - Holtrigter, B.
TI  - Host-controlled modification and restriction of phages in coagulase-negative Staphylococci.
JO  - J. Gen. Microbiol.
PY  - 1972
SP  - 231
EP  - 239
VL  - 71
AB  - Three host-controlled modification and restriction systems occurring among
AB  - coagulase-negative staphlococci belonging to the Staphylococcus subgroup II are
AB  - described.  The phage patterns, observed by typing the staphylococci with a
AB  - provisional typing set of eighteen phages, are mainly determined by these host
AB  - specificity systems.  A strain, which was not restrictive to the phages did not
AB  - become restrictive after lysogenization with any of the eighteen phages.
AB  - Infection of a restricting host with 3H-labelled phages was followed by a rapid
AB  - breakdown of phage DNA, as demonstrated by the appearance of radioactive label
AB  - in the cold-acid-soluble DNA fraction of extracted adsorption mixtures.
ER  -

TY  - JOUR
AU  - Verma, M.
AU  - Kaur, J.
AU  - Kumar, M.
AU  - Kumari, K.
AU  - Saxena, A.
AU  - Anand, S.
AU  - Nigam, A.
AU  - Ravi, V.
AU  - Raghuvanshi, S.
AU  - Khurana, P.
AU  - Tyagi, A.K.
AU  - Khurana, J.P.
AU  - Lal, R.
TI  - Whole Genome Sequence of the Rifamycin B-Producing Strain Amycolatopsis mediterranei S699.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5562
EP  - 5563
VL  - 193
AB  - Amycolatopsis mediterranei S699 is an actinomycete that produces an important antibiotic,
AB  - rifamycin B. Semisynthetic derivatives of rifamycin
AB  - B are used for the treatment of tuberculosis, leprosy, and AIDS-related
AB  - mycobacterial infections. Here, we report the complete genome sequence
AB  - (10.2 Mb) of A. mediterranei S699, with 9,575 predicted coding sequences.
ER  -

TY  - JOUR
AU  - Vermersch, P.S.
AU  - Bennett, G.N.
TI  - The use of a selectable FokI cassette in DNA replacement mutagenesis of the R388 dihydrofolate reductase gene.
JO  - Gene
PY  - 1987
SP  - 229
EP  - 238
VL  - 54
AB  - FokI, a class-IIS restriction endonuclease, cleaves double-stranded DNA to
AB  - produce a protruding 5' end consisting of four nucleotides, 10-13 residues 3'
AB  - from the nonpalindromic recognition sequence, GGATG.  Cassettes which utilize
AB  - this separation of cleavage and recognition site have been constructed for the
AB  - purpose of linker mutagenesis and DNA replacement experiments.  The cassettes
AB  - are flanked by FokI recognition sequences oriented such that the FokI cleavage
AB  - sites are several nucleotides beyond the cassette/vector fusion sites.  FokI
AB  - excises the cassette and several base pairs of the neighboring vector sequence.
AB  - The ends produced in the vector by FokI cleavage are generally
AB  - noncomplementary and suitable for the insertion of a segment of synthesized
AB  - double-stranded replacement DNA.  A cassette which contains a tyrosine tRNA
AB  - suppressor gene (supF) is selectable by the suppression of amber mutations in
AB  - the recipient host.  A vector containing a pBR322-derived origin of
AB  - replication, the Escherichia coli xanthine-guanine phosphoribosyl tranasferase
AB  - gene as a selectable marker, and no FokI sites has been constructed for use
AB  - with the FokI cassettes.  An experiment which utilized the FokI/supF cassette
AB  - to modify the N-terminal coding region of the R388 dihydrofolate reductase gene
AB  - is described.
ER  -

TY  - JOUR
AU  - Vermote, C.L.M.
AU  - Halford, S.E.
TI  - EcoRV restriction endonuclease:  communication between catalytic metal ions and DNA recognition.
JO  - Biochemistry
PY  - 1992
SP  - 6082
EP  - 6089
VL  - 31
AB  - In the absence of magnesium ions, the EcoRV restriction endonuclease binds all DNA sequences
AB  - with equal affinity but cannot cleave DNA. In the presence of Mg2+, the EcoRV endonuclease
AB  - cleaves a DNA at one particular sequence, GATATC, at least a million times more readily than
AB  - any other sequence. To elucidate the role of the metal ion, the reactions of the EcoRV
AB  - restriction enzyme were studied in the presence of MnCl2 instead of MgCl2. The reaction at the
AB  - EcoRV recognition site was slower with Mn2+. This was caused partly by reduced rates for
AB  - phosphodiester hydrolysis but also by the translocation of the enzyme along the DNA after
AB  - cleaving it in one strand. In contrast, alternative sites that differ from the recognition
AB  - site by one base pair were cleaved faster in the presence of Mn2+ relative to Mg2+. When
AB  - located at an alternative site on the DNA, the EcoRV enzyme bound Mn2+ ions readily but had a
AB  - very low affinity for Mg2+. The EcoRV nuclease is thus restrained from cleaving DNA at
AB  - alternate sites in the presence of Mg2+, but the restraint fails to operate with Mn2+. A
AB  - discrimination factor, which measures the ratio of the activity of the EcoRV nuclease at its
AB  - recognition site over that at an alternative site, had values of 3 x 10/5 in MgCl2 and 6 in
AB  - MnCl2.
ER  -

TY  - JOUR
AU  - Vermote, C.L.M.
AU  - Vipond, I.B.
AU  - Halford, S.E.
TI  - EcoRV restriction endonuclease:  communication between DNA recognition and catalysis.
JO  - Biochemistry
PY  - 1992
SP  - 6089
EP  - 6097
VL  - 31
AB  - A genetic system was constructed for the mutagenesis of the EcoRV restriction endonuclease and
AB  - for the overproduction of mutant proteins. The system was used to make two mutants of EcoRV,
AB  - with Ala in place of either Asn185 or Asn188. In the crystal structure of the EcoRV-DNA
AB  - complex, both Asn185 and Asn188 contact the DNA within the EcoRV recognition sequence. But
AB  - neither mutation affected the ability of the protein to bind to DNA. In the absence of metal
AB  - ion cofactors, the mutants bound DNA with almost the same affinity as that of the wild-type
AB  - enzyme. In the presence of Mg2+, both mutants retained the ability to cleave DNA specifically
AB  - at the EcoRV recognition sequence, but their activities were severely depressed relative to
AB  - that of the wild-type. In contrast, with Mn2+ as the cofactor, the mutant enzymes cleaved the
AB  - EcoRV recognition site with activities that were close to that of the wild-type. When bound to
AB  - DNA at the EcoRV recognition site, the mutant proteins bound Mn2+ ions readily, but they had
AB  - much lower affinities for Mg2+ ions than the wild-type enzyme. This was the reason for their
AB  - low activities with Mg2+ as the cofactor. The arrangement of the DNA recognition functions, at
AB  - one location in the EcoRV restriction enzyme, are therefore responsible for organizing the
AB  - catalytic functions at a separate location in the protein.
ER  -

TY  - JOUR
AU  - Vertes, A.A.
AU  - Inui, M.
AU  - Kobayashi, M.
AU  - Kurusu, Y.
AU  - Yukawa, H.
TI  - Presence of mrr- and mcr-like restriction systems in coryneform bacteria.
JO  - Res. Microbiol.
PY  - 1993
SP  - 181
EP  - 185
VL  - 144
AB  - Efficient transformation of Brevibacterium flavum MJ233C and Corynebacterium glutamicum ATCC
AB  - 31831 (up to 5.0 x 107 transformants/ug DNA) depends on the source of plasmid DNA. The
AB  - transformation efficiencies of B. flavum MJ233C and C. glutamicum ATCC 31831 increased nearly
AB  - 103-fold when plasmid DNA was isolated from the recipient strain itself or from a damdcm
AB  - Escherichia coli mutant, as compared with DNA passed through a modification-proficient E. coli
AB  - strain. These results suggest the presence of a methyl-specific restriction system in certain
AB  - strains of coryneform bacteria. In addition, electroporation conditions were optimized.
ER  -

TY  - JOUR
AU  - Vertino, P.M.
TI  - Eukaryotic DNA methyltransferases.
JO  - S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions.
PY  - 1999
SP  - 341
EP  - 372
VL  - 0
AB  - The post-replicative modification of cytosine is an important part of many
AB  - restriction-modification systems that defend prokaryotic organisms from invading parasitic
AB  - sequences.  DNA cytosine methylation may also play a role in genome defense in eukaryotes, but
AB  - has also evolved into a key determinant of epigenetic regulation (for an excellent
AB  - comprehensive volume on the topic of epigenetics, the reader is referred to ref 136) and is
AB  - involved in such diverse biological functions as gene repression, X-chromosome inactivation,
AB  - genome imprinting, and replication timing.  DNA methylation is essential for the normal
AB  - development of plant and animal species.  Moreover, somatic alterations in genome methylation
AB  - patterns contribute to the genesis of human cancers.  Therefore, just as preservation of the
AB  - primary genetic code is important, proper establishment and maintenance of DNA methylation
AB  - patterns is also critical to the well-being of the organism.  Until very recently, a single
AB  - species of DNA MTase was thought to be responsible for all cytosine methylation in eukaryotes.
AB  - Over the last two years, the identification of several new eukaryotic DNA MTases suggests that
AB  - the establishment of methylation patterns in early development and their maintenance in the
AB  - adult organism requires the activity of several enzymes with distinct cellular or
AB  - developmental roles.  This chapter will start with an overview of genome methylation patterns
AB  - in higher organisms and the current understanding of how these patterns are established and
AB  - maintained, before moving into a discussion of what is known about the structure and function
AB  - of the eukaryotic DNA MTases.  I will also discuss some of the evidence suggesting that DNA
AB  - MTases affect genome function not only through the passive maintenance of methylation patterns
AB  - but also by actively participating in the organization of chromatin and in the genesis of
AB  - human disease.
ER  -

TY  - JOUR
AU  - Vertino, P.M.
AU  - Coll, J.M.
AU  - Applegren, N.
AU  - Malkas, L.H.
TI  - Identification of DNA (cytosine-5)-methyltransferase as a component of a multiprotein DNA replication complex isolated from human cells.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1998
SP  - 92
EP  - 92
VL  - 39
AB  - The aberrant methylation of normally unmethylated CpG island-containing gene promoters is a
AB  - somatic genetic alteration that has been implicated in the inactivation tumor suppressor and
AB  - other genes in human cancers.  The mechanisms underlying aberrant methylation are not well
AB  - understood, but recent studies showing that increased levels of the enzyme that normally
AB  - catalyzes DNA methylation in mammalian cells, DNA (cytosine-5)-methyltransferase (DNA MTase),
AB  - can promote aberrant CpG island methylation suggest that DNA MTase itself could play a role.
AB  - Little is known about the normal regulation of DNA MTase nor the precise molecular
AB  - determinants of its activity in vivo.  In this study, we show that DNA MTase is a component of
AB  - the DNA 'synthesome', a multiprotein complex isolated from whole cells that fully supports
AB  - origin-dependent DNA synthesis in a cell-free system.  DNA synthesome was purified from two
AB  - human cell lines through a series of cell fractionation and chromatography steps.  DNA MTase
AB  - protein and activity co-purified with DNA replication activity and were found only in the
AB  - replication-competent fractions.  DNA MTase in the replication complex displayed substrate
AB  - specificity similar to DNA MTase activity from whole cells.  Specific activity determinations
AB  - suggested that most of the cellular DNA MTase exists in a larger complex with the replication
AB  - machinery.  Other proteins that have been identified in the synthesome include DNA polymerases
AB  - a, b, and e, RP-A, RF-C, DNA primase, PCNA, and topoisomerases I and II.  The definition of
AB  - the molecular interactions between DNA MTase and other proteins in replication complex in
AB  - normal and neoplastic cells will provide further insight into the regulation of cellular DNA
AB  - methylation and the role of DNA/MTase in the establishment of altered DNA methylation patterns
AB  - during carcinogenesis.
ER  -

TY  - JOUR
AU  - Vertino, P.M.
AU  - Yen, R.-W.C.
AU  - Gao, J.
AU  - Baylin, S.B.
TI  - De Novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase.
JO  - Mol. Cell. Biol.
PY  - 1996
SP  - 4555
EP  - 4565
VL  - 16
AB  - Recent studies showing a correlation between the levels of DNA (cytosine-5-)-methyltransferase
AB  - (DNA Mtase) enzyme activity and tumorigenicity have implicated this enzyme in the carcinogenic
AB  - process.  Moreover, hypermethylation of CpG island-containing promoters is associated with the
AB  - inactivation of genes important to tumor initiation and progression.  One proposed role for
AB  - DNA Mtase in tumorigenesis is therefore a direct role in the de novo methylation of these
AB  - otherwise unmethylated CpG islands.  In this study, we sought to determine whether increased
AB  - levels of DNA Mtase could directly affect CpG island methylation.  A full-length cDNA for
AB  - human DNA Mtase driven by the cytomegalovirus promoter was constitutively expressed in human
AB  - fibroblasts.  Individual clones derived from cells transfected with DNA Mtase (HMT) expressed
AB  - 1- to 50-fold the level of DNA Mtase protein and enzyme activity of the parental cell line or
AB  - clones transfected with the control vector alone (neo).  To determine the effects of DNA Mtase
AB  - overexpression on CpG island methylation, we examined 12 endogenous CpG island loci in the HMT
AB  - clones.  HMT clones expressing greater-than or equal-to 9-fold the parental levels of DNA
AB  - Mtase activity was significantly hypermethylated relative to at least 11 Neo clones at five
AB  - CpG island loci.  In the HMT clones, methylation reached nearly 100% at susceptible CpG island
AB  - loci with time in culture.  In contrast, there was little change in the methylation status in
AB  - the Neo clones over the same time frame.  Taken together, the data indicate that
AB  - overexpression of DNA Mtase can drive the de novo methylation of susceptible CpG island loci,
AB  - thus providing support for the idea that DNA Mtase can contribute to tumor progression through
AB  - CpG island methylation-mediated gene inactivation.
ER  -

TY  - JOUR
AU  - Veseli, I.A.
AU  - Mascarenhas, D.S.A.C.
AU  - Juarez, O.
AU  - Stark, B.C.
AU  - Pombert, J.F.
TI  - Complete Genome Sequence of Vitreoscilla sp. Strain C1, Source of the First Bacterial Hemoglobin.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00922
EP  - e00918
VL  - 7
AB  - Vitreoscilla sp. strain C1 is of historical importance as the source of the first prokaryotic
AB  - hemoglobin identified. Vitreoscilla spp. rely on their hemoglobin and
AB  - cytochrome oxidase to grow in microaerobic environments despite their aerobic
AB  - nature. To help characterize this historically relevant strain, we sequenced the
AB  - complete Vitreoscilla sp. strain C1 genome.
ER  -

TY  - JOUR
AU  - Veseli, I.A.
AU  - Tang, C.
AU  - Pombert, J.F.
TI  - Complete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters.
JO  - Genome Announcements
PY  - 2017
SP  - e00572
EP  - e00517
VL  - 5
AB  - Despite their relevance to human health, not all staphylococcal species have been
AB  - characterized. As such, the potential zoonotic threats posed by uninvestigated
AB  - species and their contribution to the staphylococcal pangenome are unclear. Here,
AB  - we report the complete genome sequence of Staphylococcus lutrae ATCC 700373, a
AB  - coagulase-positive species isolated from deceased otters.
ER  -

TY  - JOUR
AU  - Veselkov, A.G.
AU  - Demidov, V.V.
AU  - Nielsen, P.E.
AU  - Frank-Kamenetskii, M.D.
TI  - A new class of genome rare cutters.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2483
EP  - 2487
VL  - 24
AB  - Although significant efforts have been directed at developing efficient techniques
AB  - for rare and super rare genome cutting, only limited success has been achieved.  Here we
AB  - propose
AB  - a new approach to solve this problem.  We demonstrate that peptide nucleic acid 'clamps'
AB  - (bis-
AB  - PNAs) bind strongly and sequence specifically to short homopyrimidine sites on lambda and
AB  - yeast
AB  - genomic DNAs.  Such binding efficiently shields methylation/restriction sites which overlap
AB  - with
AB  - the bis-PNA binding sites from enzymatic methylation.  After removing the bis-PNA, the genomic
AB  - DNAs are quantitatively cleaved by restriction enzymes into a limited number of pieces of
AB  - lengths
AB  - from several hundred kbp to several Mbp.  By combining various bis-PNAs with different
AB  - methylation/restriction enzyme pairs, a huge new class of genome rare cutters can be created.
AB  - These cutters cover the range of recognition specificities where very few, if any, cutters are
AB  - now
AB  - available.
ER  -

TY  - JOUR
AU  - Vesely, Z.
AU  - Muller, A.
AU  - Schmitz, G.G.
AU  - Kaluza, K.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - RleAI: a novel class-IIS restriction endonuclease from Rhizobium leguminosarum recognizing 5'-CCCACA(N)12-3' and 3'-GGGTGT(N)9-5'.
JO  - Gene
PY  - 1990
SP  - 129
EP  - 131
VL  - 95
AB  - The novel class-IIS restriction endonuclease, RleAI, has the
AB  - 5'-CCCACA(N)12-3'
AB  - 3'-GGGTGT(N)9-5' specificity.
ER  -

TY  - JOUR
AU  - Vesely, Z.
AU  - Schmitz, G.G.
AU  - Jarsch, M.
AU  - Kessler, C.
TI  - BbrPI, a novel PmaCI isoschizomer from Bacillus brevis recognizing 5'-CAC/GTG-3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3423
EP  - 3423
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Vettath, V.K. et al.
TI  - Complete Genome Sequence of Bacillus altitudinis Type Strain SGAir0031 Isolated from Tropical Air Collected in Singapore.
JO  - Genome Announcements
PY  - 2017
SP  - e01260
EP  - e01217
VL  - 5
AB  - Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples
AB  - collected in Singapore. Its genome was assembled using short reads and
AB  - single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and
AB  - one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81
AB  - tRNAs, and 24 rRNAs.
ER  -

TY  - JOUR
AU  - Vettath, V.K. et al.
TI  - Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated  from Tropical Air Collected in Singapore.
JO  - Genome Announcements
PY  - 2018
SP  - e00230
EP  - e00218
VL  - 6
AB  - Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The
AB  - strain SGAir0564 was isolated from air samples collected in
AB  - Singapore. The complete genome is 3.1 Mb and was assembled using a combination of
AB  - short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs,
AB  - and 21 rRNA subunits.
ER  -

TY  - JOUR
AU  - Veyrier, F.J.
AU  - Ecobichon, C.
AU  - Boneca, I.G.
TI  - Draft Genome Sequence of Strain X47-2AL, a Feline Helicobacter pylori Isolate.
JO  - Genome Announcements
PY  - 2013
SP  - e01095
EP  - e01013
VL  - 1
AB  - Helicobacter pylori is a human-specific pathogen that exclusively inhabits the human gastric
AB  - mucosa. However, occasionally, humans transmit H. pylori to
AB  - susceptible animal hosts bred in colonies. Here, we report the genome sequence of
AB  - strain X47-2AL, isolated from a domestic cat and used in anti-H. pylori
AB  - immunization studies.
ER  -

TY  - JOUR
AU  - Veyrier, F.J.
AU  - Hong, E.
AU  - Deghmane, A.E.
AU  - Taha, M.K.
TI  - Draft Genome Sequence of a Neisseria meningitidis Serogroup C Isolate of Sequence Type 11 Linked to an Outbreak among Men Who Have Sex with Men.
JO  - Genome Announcements
PY  - 2013
SP  - e00795
EP  - e00713
VL  - 1
AB  - Meningococcal disease occurs as sporadic cases in developed countries, with the occasional
AB  - emergence of new clones of Neisseria meningitidis. Here, we report the
AB  - genome sequence of N. meningitidis strain LNP27256, an isolate of sequence type
AB  - 11 linked to a recent outbreak among men who have sex with men in Europe.
ER  -

TY  - JOUR
AU  - Viadiu, H.
AU  - Aggarwal, A.K.
TI  - Structure of BamHI bound to nonspecific DNA: A model for DNA sliding.
JO  - Mol. Cell
PY  - 2000
SP  - 889
EP  - 895
VL  - 5
AB  - The central problem faced by DNA binding proteins is how to select the correct DNA sequence
AB  - from the sea of nonspecific sequences in a cell.  The problem is particularly acute for
AB  - bacterial restriction enzymes because cleavage at an incorrect DNA site could be lethal.  To
AB  - understand the basis of this selectivity, we report here the crystal structure of endonuclease
AB  - BamHI bound to noncognate DNA.  We show that, despite only a single base pair change in the
AB  - recognition sequence, the enzyme adopts an open configuration that is on the pathway between
AB  - free and specifically bound forms of the enzyme.  Surprisingly, the DNA drops out of the
AB  - binding cleft with a total loss of base-specific and backbone contacts.  Taken together, the
AB  - structure provides a remarkable snapshot of an enzyme poised for linear diffusion (rather than
AB  - cleavage) along the DNA.
ER  -

TY  - JOUR
AU  - Viadiu, H.
AU  - Aggarwal, A.K.
TI  - The role of metals in catalysis by the restriction endonuclease BamHI.
JO  - Nat. Struct. Biol.
PY  - 1998
SP  - 910
EP  - 916
VL  - 5
AB  - Type II restriction enzymes are characterized by their remarkable specificity and simplicity.
AB  - They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the
AB  - hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in
AB  - the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage.
AB  - Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of
AB  - Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results
AB  - support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.
ER  -

TY  - JOUR
AU  - Viadiu, H.
AU  - Kucera, R.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Crystallization of Restriction Endonuclease BamHI with Nonspecific DNA.
JO  - J. Struct. Biol.
PY  - 2000
SP  - 81
EP  - 85
VL  - 130
AB  - Restriction endonucleases show extraordinary specificity in distinguishing specific from
AB  - nonspecific DNA sequences. A single basepair change within the recognition sequence results in
AB  - over a million-fold loss in activity. To understand the basis of this sequence discrimination,
AB  - it is just as important to study the nonspecific complex as the specific complex. We describe
AB  - here the crystallization of restriction endonuclease BamHI with several nonspecific
AB  - oligonucleotides. The 11-mer, 5'-ATGAATCCATA-3', yielded cocrystals with BamHI, in the
AB  - presence of low salt, that diffracted to 1.9 A with synchrotron radiation. The cocrystals
AB  - belong to the space group P2(1)2(1)2(1) with unit cell dimensions of a = 114.8 A, b = 91.1 A,
AB  - c = 66.4 A, alpha = 90 degrees, beta = 90 degrees, gamma = 90 degrees. This success in the
AB  - cocrystallization of BamHI with a nonspecific DNA provides insights for future attempts at
AB  - crystallization of other nonspecific DNA-protein complexes. Copyright 2000 Academic Press.
ER  -

TY  - JOUR
AU  - Viadiu, H.
AU  - Vanamee, E.S.
AU  - Jacobson, E.M.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Crystallization of restriction endonuclease SfiI in complex with DNA.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2003
SP  - 1493
EP  - 1495
VL  - 59
AB  - The SfiI endonuclease from Streptomyces fimbriatus (EC 3.1.21.4) is a tetrameric enzyme that
AB  - binds simultaneously to two recognition sites and
AB  - cleaves both sites concertedly. It serves as a good model system for
AB  - studying both specificity and cooperative DNA binding. Crystals of the
AB  - enzyme were obtained by the hanging-drop vapor-diffusion method in complex
AB  - with a 21-mer oligonucleotide. The crystals are trigonal, with unit-cell
AB  - parameters a = b = 85.7, c = 202.6 A, and diffract to 2.6 A resolution on
AB  - a rotating-anode X-ray generator. Preliminary X-ray analysis reveals the
AB  - space group to be either P3(1)21 or P3(2)21. Interestingly, the crystals
AB  - change to space group P6(1)22, with unit-cell parameters a = b = 85.5, c =
AB  - 419.6 A, when the selenomethionyl (SeMet) derivative of the enzyme is
AB  - co-crystallized with the same DNA. Phase information is currently being
AB  - derived from this SeMet SfiI-DNA complex.
ER  -

TY  - JOUR
AU  - Viadiu-Ilarraza, H.
TI  - Structural study of specificity and catalysis by restriction endonuclease BamHI.
JO  - Diss. Abstr.
PY  - 2000
SP  - 5978
EP  - 5978
VL  - 60
AB  - The restriction endonuclease BamHI is a phosphoryl-transferase that recognizes the DNA
AB  - sequence 5'-GGATCC-3' and cleaves the phosphodiester bond between the first and the second
AB  - bases.  In this work we used X-ray crystallography to analyze the different steps in the
AB  - mechanism of DNA recognition and catalysis by BamHI.  BamHI, a polypeptide of 213 amino acids,
AB  - forms a dimer in solution and starts its catalytic mechanism binding DNA non-specifically.
AB  - Initially, the crystal structure of BamHI bound to a non-specific DNA (5'-GAATCC-3') at 2.0
AB  - A is presented.  The analysis of the non-specific DNA-BamHI structure shows striking
AB  - differences with the previously reported specific complex.  In the non-specific complex, BamHI
AB  - has very few contacts to the DNA which shows exceptionally high B-factors and its position in
AB  - the DNA cavity drops 7A with respect to the specific complex.  Although the protein
AB  - conformation is symmetrical and it closely resembles the one in the absence of DNA, the
AB  - quaternary arrangement results in a DNA cavity with an intermediate width between the ones
AB  - observed for the five protein and the specific complex.  In summary, the non-specific
AB  - DNA-BamHI complex explains the electrostatic character of the non-specific DNA-protein binding
AB  - and suggest that BamHI is trapped in a conformation suitable for sliding along the DNA.  Once
AB  - BamHI has found the specific site, it cleaves both DNA strands in a sequential manner.  In
AB  - this work, the crystal structures of BamHI before and after the reaction are presented, at 2.0
AB  - A and 1.8 A respectively.  These data shows evidence to support a two-metal mechanism for
AB  - BamHI catalysis.  The metals are coordinated by three acidic residues and they stabilize the
AB  - transition state.  The residue Glu113 was identified as a general base.  A water molecule
AB  - attacking the phosphate group, and a water donating a proton to the leaving group were also
AB  - located.  Furthermore, the comparison of BamHI, BamHI Glu113Lys mutant, and other restriction
AB  - endonucleases suggest a catalytic mechanism for those enzymes that contain three acidic
AB  - residues and a lysine in the active site.  Overall the work presented here represents the most
AB  - comprehensive study of different stages in the catalytic cycle of a restriction endonuclease.
ER  -

TY  - JOUR
AU  - Viana, M.V.
AU  - Wattam, A.R.
AU  - Govil, B.D.
AU  - Boisvert, S.
AU  - Brettin, T.S.
AU  - Frace, M.
AU  - Xia, F.
AU  - Azevedo, V.
AU  - Tiller, R.
AU  - Hoffmaster, A.R.
TI  - Genome Sequences of Two Brucella suis Strains Isolated from the Same Patient, 8 Years Apart.
JO  - Genome Announcements
PY  - 2017
SP  - e01687
EP  - e01616
VL  - 5
AB  - Brucella suis is a Gram-negative, facultative intracellular pathogen that has pigs as its
AB  - preferred host, but it can also infect humans. Here, we report the
AB  - draft genome sequences of two B. suis strains that were isolated from the same
AB  - patient, 8 years apart.
ER  -

TY  - JOUR
AU  - Viana, M.V.
AU  - Wattam, A.R.
AU  - Govil, B.D.
AU  - Boisvert, S.
AU  - Brettin, T.S.
AU  - Frace, M.
AU  - Xia, F.
AU  - Azevedo, V.
AU  - Tiller, R.
AU  - Hoffmaster, A.R.
TI  - Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog.
JO  - Genome Announcements
PY  - 2017
SP  - e01688
EP  - e01616
VL  - 5
AB  - Brucella canis is a facultative intracellular pathogen that preferentially infects members of
AB  - the Canidae family. Here, we report the genome sequencing of
AB  - two Brucella canis strains isolated from humans and one isolated from a dog host.
ER  -

TY  - JOUR
AU  - Viberg, L.T.
AU  - Price, E.P.
AU  - Kidd, T.J.
AU  - Bell, S.C.
AU  - Currie, B.J.
AU  - Sarovich, D.S.
TI  - Whole-Genome Sequences of Five Burkholderia pseudomallei Isolates from Australian Cystic Fibrosis Patients.
JO  - Genome Announcements
PY  - 2015
SP  - e00254
EP  - e00215
VL  - 3
AB  - We report here five improved high-quality draft genomes of Burkholderia pseudomallei isolated
AB  - from Australian cystic fibrosis (CF) patients. This
AB  - pathogen is rarely seen in CF patients. These genomes will be used to better
AB  - understand chronic carriage of B. pseudomallei in the CF lung and the within-host
AB  - evolution of longitudinal isolates from these patients.
ER  -

TY  - JOUR
AU  - Victoria, A.J.
AU  - Cao, E.
AU  - Salmaso, N.
AU  - Segata, N.
AU  - Donati, C.
TI  - Draft Genome Sequence of the Cadmium-Resistant Strain JJU2, Belonging to the Family Hapalosiphonaceae of the Cyanobacteria.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00876
EP  - e00818
VL  - 7
AB  - Here, we report the genome of strain JJU2, a cyanobacterium of the family Hapalosiphonaceae
AB  - known to be resistant to high cadmium levels, assembled from a
AB  - nonaxenic, unialgal culture from Marinduque, Philippines. The draft genome is 7.1
AB  - Mb long with a GC content of 40.05% and contains 5,625 protein-coding genes.
ER  -

TY  - JOUR
AU  - Victoria, J.G.
AU  - Kapoor, A.
AU  - Li, L.
AU  - Blinkova, O.
AU  - Slikas, B.
AU  - Wang, C.
AU  - Naeem, A.
AU  - Zaidi, S.
AU  - Delwart, E.
TI  - Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis.
JO  - J. Virol.
PY  - 2009
SP  - 4642
EP  - 4651
VL  - 83
AB  - We analyzed viral nucleic acids in stool samples collected from 35 South
AB  - Asian children with nonpolio acute flaccid paralysis (AFP).
AB  - Sequence-independent reverse transcription and PCR amplification of
AB  - capsid-protected, nuclease-resistant viral nucleic acids were followed by
AB  - DNA sequencing and sequence similarity searches. Limited Sanger sequencing
AB  - (35 to 240 subclones per sample) identified an average of 1.4 distinct
AB  - eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses
AB  - per sample. In addition to bacteriophage and plant viruses, we detected
AB  - known enteric viruses, including rotavirus, adenovirus, picobirnavirus,
AB  - and human enterovirus species A (HEV-A) to HEV-C, as well as numerous
AB  - other members of the Picornaviridae family, including parechovirus, Aichi
AB  - virus, rhinovirus, and human cardiovirus. The viruses with the most
AB  - divergent sequences relative to those of previously reported viruses
AB  - included members of a novel Picornaviridae genus and four new viral
AB  - species (members of the Dicistroviridae, Nodaviridae, and Circoviridae
AB  - families and the Bocavirus genus). Samples from six healthy contacts of
AB  - AFP patients were similarly analyzed and also contained numerous viruses,
AB  - particularly HEV-C, including a potentially novel Enterovirus genotype.
AB  - Determining the prevalences and pathogenicities of the novel genotypes,
AB  - species, genera, and potential new viral families identified in this study
AB  - in different demographic groups will require further studies with
AB  - different demographic and patient groups, now facilitated by knowledge of
AB  - these viral genomes.
ER  -

TY  - JOUR
AU  - Vida, C.
AU  - de Vicente, A.
AU  - Cazorla, F.M.
TI  - Draft Genome Sequence of the Rhizobacterium Pseudomonas chlororaphis PCL1601, Displaying Biocontrol against Soilborne Phytopathogens.
JO  - Genome Announcements
PY  - 2017
SP  - e00130
EP  - e00117
VL  - 5
AB  - In this study, we present the draft genome sequence of the bacterial strain Pseudomonas
AB  - chlororaphis PCL1601. This bacterium was isolated from the
AB  - rhizosphere of healthy avocado trees and displayed antagonistic and biological
AB  - control activities against different soilborne phytopathogenic fungi and
AB  - oomycetes.
ER  -

TY  - JOUR
AU  - Viedma, E.
AU  - Juan, C.
AU  - Otero, J.R.
AU  - Oliver, A.
AU  - Chaves, F.
TI  - Draft Genome Sequence of VIM-2-Producing Multidrug-Resistant Pseudomonas aeruginosa ST175, an Epidemic High-Risk Clone.
JO  - Genome Announcements
PY  - 2013
SP  - e00112
EP  - e00113
VL  - 1
AB  - The VIM-2-producing multidrug-resistant high-risk clone Pseudomonas aeruginosa sequence type
AB  - (ST) 175 was isolated in the setting of a large outbreak in
AB  - Hospital Universitario 12 de Octubre (Spain) from 2007 to 2010. This strain was
AB  - resistant to all beta-lactams, fluoroquinolones, and aminoglycosides, with the
AB  - exception of amikacin, and has become an endemic clone in our institution.
ER  -

TY  - JOUR
AU  - Viedma, E.
AU  - Villa, J.
AU  - Juan, C.
AU  - Oliver, A.
AU  - Chaves, F.
TI  - Draft Genome Sequence of Colistin-Only-Susceptible Pseudomonas aeruginosa Strain  ST235, a Hypervirulent High-Risk Clone in Spain.
JO  - Genome Announcements
PY  - 2014
SP  - e01097
EP  - e01014
VL  - 2
AB  - We report the genome of colistin-only-susceptible Pseudomonas aeruginosa strain ST235
AB  - (PA_ST235). This isolate was obtained in the setting of an outbreak in a
AB  - tertiary hospital in Spain. This clone was apparently associated with a
AB  - significantly higher mortality rate. The ST235 clone also appears to be
AB  - associated with greater virulence.
ER  -

TY  - JOUR
AU  - Vienozinskis, M.T.
AU  - Nesterenko, V.F.
AU  - Kanopkaite, S.I.
AU  - Buryanov, Y.I.
TI  - Effect of 5-azacytidine on E. coli cells with different DNA methylases.
JO  - Biokhimiia
PY  - 1985
SP  - 749
EP  - 754
VL  - 50
AB  - A correlation was found between the bacteriocide effect of 5-aza-C and the amount of cytosine
AB  - DNA-methylases in E. coli cells.  5-Aza-C-DNA on cytosine DNA-methylases was due to the
AB  - formation of stable inactive complexes between the enzyme and the non-methylating cytosine
AB  - analog in the recognition sites.  Cytosine DNA-methylase EcoRII formed a relatively firm bond
AB  - with 5-aza-C-DNA, which could be disrupted by 1 M KCl; this disruption restores the
AB  - DNA-methylase activity and the inhibiting capacity of 5-aza-C-DNA.  Thus, the binding of
AB  - cytosine DNA-methylase to 5-aza-C in DNA is noncovalent; the inhibition of the enzyme by
AB  - 5-aza-C-DNA is reversible.
ER  -

TY  - JOUR
AU  - Vijaykumar, S.
AU  - Balaji, V.
AU  - Biswas, I.
TI  - Complete Genome Sequence of Acinetobacter baumannii Strain B8300, Which Displays  High Twitching Motility.
JO  - Genome Announcements
PY  - 2015
SP  - e00956
EP  - e00915
VL  - 3
AB  - Acinetobacter baumannii has emerged as an important nosocomial pathogen causing health
AB  - care-associated infections. In this study, we determined the genome of a
AB  - twitching-positive clinical strain, B8300, isolated from a hospital in southern
AB  - India. De novo assembly of PacBio long-read sequencing data generated the B8300
AB  - genome that consists of a chromosome of 3.82 Mbp and a plasmid of 25.15 kbp.
ER  -

TY  - JOUR
AU  - Vijaykumar, S.
AU  - Balaji, V.
AU  - Biswas, I.
TI  - Complete Genome Sequence of Acinetobacter baumannii Strain B8342, a Motility-Positive Clinical Isolate.
JO  - Genome Announcements
PY  - 2015
SP  - e00925
EP  - e00915
VL  - 3
AB  - Acinetobacter baumannii is an emerging Gram-negative pathogen responsible for health
AB  - care-associated infections. In this study, we determined the genome of a
AB  - motility-positive clinical strain, B8342, isolated from a hospital in southern
AB  - India. The B8342 genome, which is 3.94 Mbp, was generated by de novo assembly of
AB  - PacBio long-read sequencing data.
ER  -

TY  - JOUR
AU  - Vijesurier, R.M.
TI  - Regulation of the gene expression of the PvuII restriction-modification system.
JO  - Diss. Abstr.
PY  - 1997
SP  - 7379B
EP  - 7380B
VL  - 57
AB  - The pvuIIC gene of the PvuII restriction-modification system of Proteus vulgaris encodes the
AB  - 9.4 kDa C.PvuII protein.  This protein has a helix-turn-helix motif and is a DNA binding
AB  - protein.  The C.PvuII protein binds to the C-box sequence located within the pvuIIM gene;
AB  - C.PvuII binding to its target sequence would interfere with transcription of pvuIIM.
AB  - Therefore, C.PvuII may play the role of a repressor of methyltransferase expression.  Previous
AB  - studies have shown that the overexpression of the methyltransferase is lethal to the cell; as
AB  - such, the C.PvuII protein may be involved in preventing the overexpression of the
AB  - methyltransferase, thereby preventing the deleterious effects of hypermethylation.  This work
AB  - shows that the overexpression of C.PvuII is lethal to cells also containing the intact PvuII
AB  - restriction-modification system, perhaps due to the repression of pvuIIM, paving the way for
AB  - autorestriction.  The C.PvuII protein does not appear to regulate the transcription of either
AB  - the pvuIIC or pvuIIR genes, as seen in primer extension analyses.  In addition, the pvuIIC and
AB  - pvuIIR genes are transcribed as a polycistronic message, since the pvuIIR gene itself does not
AB  - appear to have a strong promoter; the polycistronic message originates from the relatively
AB  - stronger pvuIIC promoter.  The 'C-proteins', of which C.PvuII is a member, are encoded by
AB  - genes of several restriction-modification systems, and appear to enhance endonuclease
AB  - expression, while downregulating that of the methyltransferase.  This work suggests that
AB  - C.PvuII, like its counterparts of other restriction-modification systems, diminishes
AB  - methyltransferase expression.
ER  -

TY  - JOUR
AU  - Vijesurier, R.M.
AU  - Carlock, L.
AU  - Blumenthal, R.M.
AU  - Dunbar, J.C.
TI  - Role and mechanism of action of C.PvuII, a regulatory protein conserved among restriction-modification systems.
JO  - J. Bacteriol.
PY  - 2000
SP  - 477
EP  - 487
VL  - 182
AB  - The PvuII restriction-modification system is a type II system, which means that its
AB  - restriction endonuclease and modification methyltransferase are independently active proteins.
AB  - The PvuII system is carried on a plasmid, and its movement into a new host cell is expected to
AB  - be followed initially by expression of the methyltransferase gene alone so that the new
AB  - host's DNA is protected before endonuclease activity appears.  Previous studies have
AB  - identified a regulatory gene (pvuIIC) between the divergently oriented genes for the
AB  - restriction endonuclease (pvuIIR) and modification methyltransferase (pvuIIM), with pvuIIC in
AB  - the same orientation as and partially overlapping pvuIIR.  This product of pvuIIC, C.PvuII,
AB  - was found to act in trans and to be required for expression of pvuIIR.  In this study we
AB  - demonstrate that premature expression of pvuIIC prevents establishment of the PvuII genes,
AB  - consistent with the model that requiring C.PvuII for pvuIIR expression provides a timing delay
AB  - essential for protection of the new host's DNA.  We find that the opposing pvuIIC and pvuIIM
AB  - transcripts overlap by over 60 nucleotides at their 5' ends, raising the possibility that
AB  - their hybridization might play a regulatory role.  We furthermore characterize the action of
AB  - C.PvuII, demonstrating that it is a sequence-specific DNA-binding protein that binds to the
AB  - pvuIIC promoter and stimulates transcription of both pvuIIC and pvuIIR into a polycistronic
AB  - mRNA.  The apparent location of C.PvuII binding, overlapping the -10 promoter hexamer and the
AB  - pvuIICR transcriptional starting points, is highly unusual for transcriptional activators.
ER  -

TY  - JOUR
AU  - Vikram, S.
AU  - Kumar, S.
AU  - Subramanian, S.
AU  - Raghava, G.P.
TI  - Draft Genome Sequence of the Nitrophenol-Degrading Actinomycete Rhodococcus imtechensis RKJ300.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3543
EP  - 3543
VL  - 194
AB  - We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from
AB  - pesticide-contaminated soil in Punjab, India. The genome sequence
AB  - of the strain RKJ300 will be helpful in exploring the molecular pathways involved
AB  - in the degradation of nitrophenols.
ER  -

TY  - JOUR
AU  - Vikram, S.
AU  - Kumar, S.
AU  - Vaidya, B.
AU  - Pinnaka, A.K.
AU  - Raghava, G.P.
TI  - Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon.
JO  - Genome Announcements
PY  - 2013
SP  - e0005813
EP  - e0005813
VL  - 1
AB  - We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium
AB  - Arthrobacter sp. strain SJCon,
AB  - isolated from a pesticide-contaminated site. The draft genome sequence of strain
AB  - SJCon will be helpful in studying the genetic pathways involved in the
AB  - degradation of several aromatic compounds.
ER  -

TY  - JOUR
AU  - Vilacoba, E.
AU  - Deraspe, M.
AU  - Traglia, G.M.
AU  - Roy, P.H.
AU  - Ramirez, M.S.
AU  - Centron, D.
TI  - Draft Genome Sequence of an International Clonal Lineage 1 Acinetobacter baumannii Strain from Argentina.
JO  - Genome Announcements
PY  - 2014
SP  - e01190
EP  - e01114
VL  - 2
AB  - In the last few years Acinetobacter baumannii has emerged worldwide as an important nosocomial
AB  - pathogen in medical institutions. Here, we present the draft
AB  - genome sequence of the international clonal lineage 1 (ICL1) A. baumannii strain
AB  - A144 that was isolated in a hospital in Buenos Aires City in the year 1997. The
AB  - strain is susceptible to carbapenems and resistant to trimethoprim and
AB  - gentamicin.
ER  -

TY  - JOUR
AU  - Vilain, A.
AU  - Apiou, F.
AU  - Dutrillaux, B.
AU  - Malfoy, B.
TI  - Assignment  of candidate DNA methyltransferase gene (DNMT2) to human chromosome band 10p15.1 by in situ hybridization.
JO  - Cytogenet. Cell Genet.
PY  - 1998
SP  - 120
EP  - 120
VL  - 82
AB  - Methylation of deoxycytidine in mammalian DNA is thought to be involved in many biological
AB  - phenomena.  Only one DNA methyltransferase was known in human.  The gene (DNMT1) was localized
AB  - to 19p13.2.  Recently a putative new DNA methyltransferase (DNMT2) has been cloned and
AB  - characterized.  Using a panel of radiation hybrids, this gene has been mapped to 10p14-p12.
ER  -

TY  - JOUR
AU  - Vilas-Boas, L.A.
AU  - Headley, S.A.
AU  - Goncalves, K.B.
AU  - Scarpassa, J.A.
AU  - Pretto-Giordano, L.G.
TI  - Complete Genome Sequence of Streptococcus iniae UEL-Si1, Isolated in Diseased Nile Tilapia (Oreochromis niloticus) from Northern Parana, Southern Brazil.
JO  - Genome Announcements
PY  - 2017
SP  - e01458
EP  - e01416
VL  - 5
AB  - The Streptococcus iniae UEL-Si1 strain was isolated from diseased Nile tilapia within the
AB  - Paranapanema River Basin, Northern Parana, Brazil. This is an emerging
AB  - infectious disease agent of fish from Brazil, and sequencing of the complete
AB  - genome is fundamental to understanding aspects relative to pathogenesis,
AB  - infection, epidemiology, and immunity.
ER  -

TY  - JOUR
AU  - Vilchez, J.I.
AU  - Tang, Q.
AU  - Kaushal, R.
AU  - Chen, S.
AU  - Liu, R.
AU  - Zhang, H.
TI  - Genome Sequence of Bacillus cereus Strain TG1-6, a Plant-Beneficial Rhizobacterium That Is Highly Salt Tolerant.
JO  - Genome Announcements
PY  - 2018
SP  - e00351
EP  - e00318
VL  - 6
AB  - The complete genome sequence of Bacillus cereus strain TG1-6, which is a highly salt-tolerant
AB  - rhizobacterium that enhances plant tolerance to drought stress, is
AB  - reported here. The sequencing process was performed based on a combination of
AB  - pyrosequencing and single-molecule sequencing. The complete genome is estimated
AB  - to be approximately 5.42 Mb, containing a total of 5,610 predicted protein-coding
AB  - DNA sequences (CDSs).
ER  -

TY  - JOUR
AU  - Vilchez, J.I.
AU  - Tang, Q.
AU  - Kaushal, R.
AU  - Wang, W.
AU  - Lv, S.
AU  - He, D.
AU  - Chu, Z.
AU  - Zhang, H.
AU  - Liu, R.
AU  - Zhang, H.
TI  - Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment.
JO  - Genome Announcements
PY  - 2018
SP  - e00527
EP  - e00518
VL  - 6
AB  - Here, we report the complete genome sequence for Bacillus megaterium strain YC4-R4, a highly
AB  - salt-tolerant rhizobacterium that promotes growth in plants. The
AB  - sequencing process was performed by combining pyrosequencing and single-molecule
AB  - sequencing techniques. The complete genome is estimated to be approximately 5.44
AB  - Mb, containing a total of 5,673 predicted protein-coding DNA sequences (CDSs).
ER  -

TY  - JOUR
AU  - Vilkaitis, G.
AU  - Dong, A.
AU  - Weinhold, E.
AU  - Cheng, X.
AU  - Klimasauskas, S.
TI  - Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 38722
EP  - 38730
VL  - 275
AB  - DNA cytosine-5-methyltransferase HhaI recognizes the GCGC sequence and flips the inner
AB  - cytosine out of the DNA helix and into the catalytic site for methylation. The 5'-phosphate
AB  - of the flipped out cytosine is in contact with the conserved Thr-250 from the target
AB  - recognition domain. We have produced 12 mutants of Thr-250 and examined their methylation
AB  - potential in vivo. Six active mutants were subjected to detailed biochemical and structural
AB  - studies. Mutants with similar or smaller side chains (Ser, Cys, and Gly) are very similar to
AB  - wild-type enzyme in terms of steady-state kinetic parameters k(cat), K(m)(DNA), K(m)(AdoMet).
AB  - In contrast, the mutants with bulkier side chains (Asn, Asp, and His) show increased K(m)
AB  - values for both substrates. Fluorescence titrations and stopped-flow kinetic analysis of
AB  - interactions with duplex oligonucleotides containing 2-aminopurine at the target base position
AB  - indicate that the T250G mutation leads to a more polar but less solvent-accessible position of
AB  - the flipped out target base. The x-ray structure of the ternary M.HhaI(T250G).DNA. AdoHcy
AB  - complex shows that the target cytosine is locked in the catalytic center of enzyme. The space
AB  - created by the mutation is filled by water molecules and the adjacent DNA backbone atoms
AB  - dislocate slightly toward the missing side chain. In aggregate, our results suggest that the
AB  - side chain of Thr-250 is involved in constraining the conformation the DNA backbone and the
AB  - target base during its rotation into the catalytic site of enzyme.
ER  -

TY  - JOUR
AU  - Vilkaitis, G.
AU  - Klimasauskas, S.
TI  - Bisulfite sequencing protocol displays both 5-methylcytosine and N4-methylcytosine.
JO  - Anal. Biochem.
PY  - 1999
SP  - 116
EP  - 119
VL  - 271
AB  - DNA premethylated in vitro or in vivo with a DNA cytosine-N4 methyltransferase, M.MvaI, was
AB  - analyzed using a bisulfite DNA sequencing technique. We find that, under reaction conditions
AB  - reliably displaying 5-methylcytosine on the sequencing ladder, N4-methylcytosine residues are
AB  - displayed with efficiencies from 33 to 100%, depending on a sequence context. This finding
AB  - offers a convenient tool for determining sequence specificity of cytosine-N4
AB  - methyltransferases and demonstrates that the two types of biological cytosine methylation are
AB  - not reliably distinguished by this technique.
ER  -

TY  - JOUR
AU  - Vilkaitis, G.
AU  - Lubys, A.
AU  - Merkiene, E.
AU  - Timinskas, A.
AU  - Janulaitis, A.
AU  - Klimasauskas, S.
TI  - Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 1547
EP  - 1557
VL  - 30
AB  - Sequence analysis of the BcnI restriction-modification system from Bacillus centrosporus
AB  - revealed four open reading frames (bcnIC, bcnIR, bcnIB and bcnIA) that are arranged as two
AB  - converging collinear pairs. One pair encodes a putative small regulatory protein, C.BcnI, and
AB  - the restriction endonuclease R.BcnI. The other two gene products are the DNA cytosine-N4
AB  - methyltransferases M.BcnIA and M.BcnIB, which differ by circular permutation of conserved
AB  - sequence motifs. The BcnI methyltransferases are isospecific on double-stranded DNA
AB  - [methylation specificity CC(C/G)GG], but M.BcnIA can also methylate the target sites in
AB  - single-stranded DNA. Functional analysis shows that bcnIA is dispensable (bcnIB is capable of
AB  - protecting the DNA against the in vivo activity of bcnIR); in contrast, no stable clones were
AB  - obtained if bcnIB alone was deleted from the system. By analogy with the DpnII system, the
AB  - second methylase M.BcnIA may play a role in the transformation proficiency of its
AB  - gram-positive host. The interchangeability of homologous elements in the beta class of
AB  - cytosine-N4 methylases was probed by hybrid formation between M.BcnIB and its closest homolog
AB  - M.Cfr9I (CCCGGG) employing a novel semi-random strategy combined with selection for catalytic
AB  - activity. The fusion points in the active hybrids mapped in a narrow region located between
AB  - sequence motifs X and I. Our data illustrate that recombination of two related sequences by
AB  - circular permutation may serve as an evolutionary mechanism for creating new specificities of
AB  - amino MTases.
ER  -

TY  - JOUR
AU  - Vilkaitis, G.
AU  - Merkiene, E.
AU  - Serva, S.
AU  - Weinhold, E.
AU  - Klimasauskas, S.
TI  - The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase.
JO  - J. Biol. Chem.
PY  - 2001
SP  - 20924
EP  - 20934
VL  - 276
AB  - Kinetic and binding studies involving a model DNA cytosine-5-methyltransferase, M.HhaI, and a
AB  - 37-mer DNA duplex containing a single hemimethylated target site were applied to characterize
AB  - intermediates on the reaction pathway. Stopped-flow fluorescence studies reveal that cofactor
AB  - S-adenosyl-l-methionine (AdoMet) and product S-adenosyl-l-homocysteine (AdoHcy) form similar
AB  - rapidly reversible binary complexes with the enzyme in solution. The M.HhaI.AdoMet complex
AB  - (k(off) = 22 s^-1, KD = 6 microM) is partially converted into products during
AB  - isotope-partitioning experiments, suggesting that it is catalytically competent. Chemical
AB  - formation of the product M.HhaI.(Me)DNA.AdoHcy (k(chem) = 0.26 s^-1) is followed by a slower
AB  - decay step (k(off) = 0.045 s^-1), which is the rate-limiting step in the catalytic cycle
AB  - (k(cat) = 0.04 s^-1). Analysis of reaction products shows that the hemimethylated substrate
AB  - undergoes complete (>95%) conversion into fully methylated product during the initial burst
AB  - phase, indicating that M.HhaI exerts high binding selectivity toward the target strand. The
AB  - T250N, T250D, and T250H mutations, which introduce moderate perturbation in the catalytic
AB  - site, lead to substantially increased KD(DNA(ternary)), k(off)(DNA(ternary)),
AB  - KM(AdoMet(ternary)) values but small changes in KD(DNA(binary)), KD(AdoMet(binary)),
AB  - k(chem), and k(cat). When the target cytosine is replaced with 5-fluorocytosine, the chemistry
AB  - step leading to an irreversible covalent M.HhaI.DNA complex is inhibited 400-fold
AB  - (k(chem)(5FC) = 0.7 x 10^-3 s^-1), and the Thr-250 mutations confer further dramatic
AB  - decrease of the rate of the covalent methylation k(chem). We suggest that activation of the
AB  - pyrimidine ring via covalent addition at C-6 is a major contributor to the rate of the
AB  - chemistry step (k(chem)) in the case of cytosine but not 5-fluorocytosine. In contrast to
AB  - previous reports, our results imply a random substrate binding order mechanism for M.HhaI.
ER  -

TY  - JOUR
AU  - Vilkaitis, G.
AU  - Suetake, I.
AU  - Klimasauskas, S.
AU  - Tajima, S.
TI  - Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase.
JO  - J. Biol. Chem.
PY  - 2005
SP  - 64
EP  - 72
VL  - 280
AB  - DNA methyltransferase Dnmt1 ensures clonal transmission of lineage-specific DNA methylation
AB  - patterns in a mammalian genome during
AB  - replication. Dnmt1 is targeted to replication foci, interacts with
AB  - PCNA, and favors methylating the hemimethylated form of CpG sites. To
AB  - understand the underlying mechanism of its maintenance function, we
AB  - purified recombinant forms of full-length Dnmt1, a truncated form of
AB  - Dnmt1-(291-1620)lacking the binding sites for PCNA and DNA and examined
AB  - their processivity using a series of long unmethylated and
AB  - hemimethylated DNA substrates. Direct analysis of methylation patterns
AB  - using bisulfite-sequencing and hairpin-PCR techniques demonstrated that
AB  - full-length Dnmt1 methylates hemimethylated DNA with high processivity
AB  - and a fidelity of over 95%, but unmethylated DNA with much less
AB  - processivity. The truncated form of Dnmt1 showed identical properties
AB  - to full-length Dnmt1 indicating that the N-terminal 290-amino acid
AB  - residue region of Dnmt1 is not required for preferential activity
AB  - toward hemimethylated sites or for processivity of the enzyme.
AB  - Remarkably, our analyses also revealed that Dnmt1 methylates
AB  - hemimethylated CpG sites on one strand of double-stranded DNA during a
AB  - single processive run. Our findings suggest that these inherent
AB  - enzymatic properties of Dnmt1 play an essential role in the faithful
AB  - and efficient maintenance of methylation patterns in the mammalian
AB  - genome.
ER  -

TY  - JOUR
AU  - Villa, A.A.
AU  - Kropinski, A.M.
AU  - Abbasifar, R.
AU  - Griffiths, M.W.
TI  - Complete Genome Sequence of Vibrio parahaemolyticus Bacteriophage vB_VpaM_MAR.
JO  - J. Virol.
PY  - 2012
SP  - 13138
EP  - 13139
VL  - 86
AB  - Vibrio parahaemolyticus is a major pathogen that is mainly associated with seafood and is a
AB  - global food safety issue. Our objective was to isolate and completely sequence a specific
AB  - phage against this bacterium. Phage vB_VpaM_MAR is able to lyse 76% of the V. parahaemolyticus
AB  - strains tested. MAR belongs to the Myoviridae family and has a genome comprised of
AB  - double-stranded DNA with a size of 41,351 bp, a G+C content of 51.3%, and 62 open reading
AB  - frames (ORFs). Bioinformatic analysis showed that phage MAR is closely related to Vibrio
AB  - phages VHML, VP58.5, and VP882 and Halomonas aquamarina phage PhiHAP-1.
ER  -

TY  - JOUR
AU  - Villa, J.
AU  - Viedma, E.
AU  - Branas, P.
AU  - Mingorance, J.
AU  - Chaves, F.
TI  - Draft Whole-Genome Sequence of OXA-48-Producing Multidrug-Resistant Klebsiella pneumoniae KP_ST11_OXA-48.
JO  - Genome Announcements
PY  - 2014
SP  - e00737
EP  - e00714
VL  - 2
AB  - We present the draft genome sequence of a blood culture isolate of OXA-48-producing Klebsiella
AB  - pneumoniae (sequence type 11 [ST11]) obtained in the
AB  - course of a hospital outbreak in Spain. Sequence analysis showed 121 genes
AB  - related to antibiotic and antiseptic resistance, including blaOXA-48, which was
AB  - located in an IncL/M plasmid.
ER  -

TY  - JOUR
AU  - Villa, J.
AU  - Viedma, E.
AU  - Otero, J.R.
AU  - Chaves, F.
TI  - Draft Whole-Genome Sequence of VIM-1-Producing Multidrug-Resistant Enterobacter cloacae EC_38VIM1.
JO  - Genome Announcements
PY  - 2013
SP  - e00694
EP  - e00613
VL  - 1
AB  - The VIM-1-producing multidrug-resistant strain Enterobacter cloacae was isolated  from blood
AB  - culture. The strain showed multiple resistances to clinically used
AB  - antibiotics, including all beta-lactams, fluoroquinolones, aminoglycosides, and
AB  - sulfonamides. Sequence analysis showed the presence of 14 genes associated with
AB  - resistance to antibiotics, including the metallo-beta-lactamase VIM-1 gene, which
AB  - was located in a class 1 integron.
ER  -

TY  - JOUR
AU  - Villa, L.
AU  - Feudi, C.
AU  - Fortini, D.
AU  - Iacono, M.
AU  - Bonura, C.
AU  - Endimiani, A.
AU  - Mammina, C.
AU  - Carattoli, A.
TI  - Complete Genome Sequence of KPC-3- and CTX-M-15-Producing Klebsiella pneumoniae Sequence Type 307.
JO  - Genome Announcements
PY  - 2016
SP  - e00213
EP  - e00216
VL  - 4
AB  - Klebsiella pneumoniaesequence type (ST) 307,
AB  - carryingblaKPC-3,blaCTX-M-15,blaOXA-1,aac(6')-Ib-cr, andqnrB1 genes, is replacing
AB  - the predominant hyperepidemic ST258 clone in Italy. Whole-genome and complete
AB  - plasmid sequencing of one ST307 strain was performed and new features were
AB  - identified.
ER  -

TY  - JOUR
AU  - Villamizar, G.A.
AU  - Daniel, R.
AU  - Poehlein, A.
TI  - First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic  Sporomusa sphaeroides Strain E (DSM 2875).
JO  - Genome Announcements
PY  - 2017
SP  - e00037
EP  - e00017
VL  - 5
AB  - Here, we report the draft genome sequence of Sporomusa sphaeroides strain E (DSM  2875), a
AB  - strict anaerobic homoacetogenic bacterium. It is able to grow
AB  - autotrophically on different one-carbon compounds. The strain possesses several
AB  - genes of the Wood-Ljungdahl pathway. The genome consists of a single chromosome
AB  - (4.98 Mb).
ER  -

TY  - JOUR
AU  - Villanueva, J.
AU  - Switala, J.
AU  - Ivancich, A.
AU  - Loewen, P.C.
TI  - Genome Sequence of Bacillus pumilus MTCC B6033.
JO  - Genome Announcements
PY  - 2014
SP  - e00327
EP  - e00314
VL  - 2
AB  - Bacillus pumilus is a Gram-positive, rod-shaped, aerobic bacterium isolated from
AB  - the soil. B. pumilus strain B6033 was originally selected as a biocatalyst for
AB  - the stereospecific oxidation of beta-lactams. Here, we present a 3.8-Mb assembly
AB  - of its genome, which is the second fully assembled genome of a B. pumilus strain.
ER  -

TY  - JOUR
AU  - Villarma, A.
AU  - Gulvik, C.A.
AU  - Rowe, L.A.
AU  - Sheth, M.
AU  - Juieng, P.
AU  - Nicholson, A.C.
AU  - Loparev, V.N.
AU  - McQuiston, J.R.
TI  - Twelve Complete Reference Genomes of Clinical Isolates in the Capnocytophaga Genus.
JO  - Genome Announcements
PY  - 2017
SP  - e01186
EP  - e01117
VL  - 5
AB  - We report here 1 near-complete genome sequence and 12 complete genome sequences for clinical
AB  - Capnocytophaga isolates. Total read coverages ranged from 211x to
AB  - 737x, and genome sizes ranged from 2.41 Mb to 3.10 Mb. These genomes will enable
AB  - a more comprehensive taxonomic evaluation of the Capnocytophaga genus.
ER  -

TY  - JOUR
AU  - Villena, J.
AU  - Masumizu, Y.
AU  - Iida, H.
AU  - Ikeda-Ohtsubo, W.
AU  - Albarracin, L.
AU  - Makino, S.
AU  - Ohkawara, S.
AU  - Kimura, K.
AU  - Saavedra, L.
AU  - Hebert, E.M.
AU  - Kitazawa, H.
TI  - Draft Genome Sequence of the Immunobiotic Strain Lactobacillus jensenii TL2937.
JO  - Genome Announcements
PY  - 2017
SP  - e00005
EP  - e00017
VL  - 5
AB  - The genome of the immunomodulatory strain Lactobacillus jensenii TL2937 is described here. The
AB  - draft genome has a total length of 1,678,416 bp, a G+C
AB  - content of 34.3%, and 1,470 predicted protein-coding sequences. The genome
AB  - information will be useful for gaining insight into the immunomodulatory
AB  - properties of the TL2937 strain in the porcine host.
ER  -

TY  - JOUR
AU  - Villena, J.
AU  - Saavedra, L.
AU  - Hebert, E.M.
AU  - Masumizu, Y.
AU  - Sato, N.
AU  - Humayun, K.A.K.
AU  - Albarracin, L.
AU  - Ikeda-Ohtsubo, W.
AU  - Makino, S.
AU  - Kimura, K.
AU  - Ohkawara, S.
AU  - Kitazawa, H.
TI  - Draft Genome Sequence of Lactobacillus plantarum TL2766, a Strain with the Ability To Ferment Wakame.
JO  - Genome Announcements
PY  - 2016
SP  - e01328
EP  - e01316
VL  - 4
AB  - The genome sequence of Lactobacillus plantarum TL2766, a strain with the ability  to ferment
AB  - wakame (Undaria pinnatifida), is described here. The reads were
AB  - assembled into contigs, with a total size of 3,310,195 bp. The genome information
AB  - will be useful for further specific genetic studies of this strain and for its
AB  - biotechnological applications.
ER  -

TY  - JOUR
AU  - Villena, J.
AU  - Saavedra, L.
AU  - Hebert, E.M.
AU  - Suda, Y.
AU  - Masumizu, Y.
AU  - Albarracin, L.
AU  - Clua, P.
AU  - Ikeda-Ohtsubo, W.
AU  - Kitazawa, H.
TI  - Draft Genome Sequence of Lactobacillus plantarum MPL16, a Wakame-Utilizing Immunobiotic Strain Isolated from Swine Feces.
JO  - Genome Announcements
PY  - 2017
SP  - e00006
EP  - e00017
VL  - 5
AB  - The genome of the immunomodulatory Lactobacillus plantarum MPL16, a strain able to ferment
AB  - wakame (Undaria pinnatifida), is described here. The reads were
AB  - assembled into contigs with a total size 3,278,495 bp. The genome information
AB  - will be useful for further specific genetic studies of this strain that evaluate
AB  - its immunomodulatory and biotechnological properties.
ER  -

TY  - JOUR
AU  - Villeneuve, C.
AU  - Martineau, C.
AU  - Mauffrey, F.
AU  - Villemur, R.
TI  - Complete Genome Sequences of Methylophaga sp. Strain JAM1 and Methylophaga sp. Strain JAM7.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4126
EP  - 4127
VL  - 194
AB  - Methylophaga sp. strains JAM1 and JAM7 have been isolated from a denitrification  system.
AB  - Strain JAM1 was the first Methylophaga strain reported to be able to grow
AB  - under denitrifying conditions. Here, we report the complete genome sequences of
AB  - the two strains, which allowed prediction of gene clusters involved in
AB  - denitrification in strain JAM1.
ER  -

TY  - JOUR
AU  - Villion, M.
AU  - Chopin, M.C.
AU  - Deveau, H.
AU  - Ehrlich, S.D.
AU  - Moineau, S.
AU  - Chopin, A.
TI  - P087, a lactococcal phage with a morphogenesis module similar to an Enterococcus faecalis prophage.
JO  - Virology
PY  - 2009
SP  - 49
EP  - 56
VL  - 388
AB  - The virulent lactococcal phage P087 was isolated from a dairy environment
AB  - in 1978. This phage was then recognized as the reference member for one of
AB  - the ten phage groups currently known to infect Lactococcus lactis strains.
AB  - The double-stranded DNA genome of this Siphoviridae phage is composed of
AB  - 60,074 bp and is circularly permuted. Five tRNA and 88 orfs were found
AB  - within an uncommon genome architecture. Eleven structural proteins were
AB  - also identified through SDS-PAGE and LC-MS/MS analyses. Of note, 11
AB  - translated orfs from the structural module of phage P087 have identities
AB  - to gene products found in a prophage located in the genome of Enterococcus
AB  - faecalis V583. The alignment of both genomic sequences suggests that DNA
AB  - exchanges could occur between these two phages which are infecting low G+C
AB  - bacteria found in similar ecological niches.
ER  -

TY  - JOUR
AU  - Vilo, C.
AU  - Benedik, M.J.
AU  - Ilori, M.
AU  - Dong, Q.
TI  - Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Clorobenzoic Acid-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00664
EP  - e00614
VL  - 2
AB  - We report the draft genome sequence of Cupriavidus sp. strain SK-3, which can use
AB  - 4-chlorobiphenyl and 4-clorobenzoic acid as the sole carbon source for growth.
AB  - The draft genome sequence allowed the study of the polychlorinated biphenyl
AB  - degradation mechanism and the recharacterization of the strain SK-3 as a
AB  - Cupriavidus species.
ER  -

TY  - JOUR
AU  - Vilo, C.
AU  - Benedik, M.J.
AU  - Ilori, M.
AU  - Dong, Q.
TI  - Draft Genome Sequence of Cupriavidus sp. Strain SK-4, a di-ortho-Substituted Biphenyl-Utilizing Bacterium Isolated from Polychlorinated Biphenyl-Contaminated   Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e00474
EP  - e00414
VL  - 2
AB  - Cupriavidus sp. strain SK-4 is a bacterium capable of growing aerobically on
AB  - monochlorobiphenyls and dichlorobiphenyls as the sole carbon sources for growth.
AB  - Here, we report its draft genome sequence with the aim of facilitating an
AB  - understanding of polychlorinated biphenyl biodegradation mechanisms.
ER  -

TY  - JOUR
AU  - Vilo, C.
AU  - Galetovic, A.
AU  - Araya, J.E.
AU  - Gomez-Silva, B.
AU  - Dong, Q.
TI  - Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.
JO  - Genome Announcements
PY  - 2015
SP  - e00955
EP  - e00915
VL  - 3
AB  - We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora
AB  - of Nostoc colonies grown at the Andean wetlands in northern Chile.
AB  - We consider this genome sequence to be a molecular tool for exploring microbial
AB  - relationships and adaptation strategies to the prevailing extreme conditions at
AB  - the Atacama Desert.
ER  -

TY  - JOUR
AU  - Vilpo, J.A.
AU  - Vilpo, L.M.
TI  - Restriction, methylation and ligation of 5-hydroxymethyluracil-containing DNA.
JO  - Mutat. Res.
PY  - 1995
SP  - 123
EP  - 131
VL  - 316
AB  - Oxidation of DNA and its components can cause genetic mutations and chromosomal instability.
AB  - These changes have generally been implicated in aging. Oxidation of the methyl group of
AB  - thymidine residues in DNA is known to result in the formation of
AB  - 5-hydroxymethyl-2'-deoxyuridine (5HmdUrd). We have utilized Bacillus subtilis phage SPO1 DNA
AB  - as a model of oxidatively damaged DNA. In this phage, all thymine (Thy) residues are replaced
AB  - by 5-hydroxymethyluracil (5HmUra), but the species is naturally devoid of other
AB  - oxidatively-induced DNA lesions. Particular attention was paid to the behavior of
AB  - 5HmUra-containing DNA as a target for several enzymes employing DNA as substrate; restriction
AB  - endonucleases, dam DNA methylase and T4 DNA ligase. We noticed that susceptibility of SPO1 DNA
AB  - varied when different restriction endonucleases having 5HmUra in the restriction sites were
AB  - tested. Endonucleolytic cleavage brought about by Sau3AI proceeded as effectively with SPO1
AB  - DNA as with conventional DNA (lambda phage). The same was true when the ligation of Sau3AI
AB  - sites was performed with T7 DNA ligase. In contrast, both endonucleolytic cleavage and
AB  - ligation were slower in SPO1 DNA, compared with lambda phage, when TaqI and T4 DNA ligase were
AB  - used for restriction and ligation, respectively. We also noticed that SPO1 phage does not
AB  - naturally contain N6-methyladenine (N6MeAde) opposite 5HmUra, i.e., no hydrolysis of SPO1 DNA
AB  - was observed when assessed with methylation-dependent restriction endonuclease DpnI. Our
AB  - results show that the presence of 5HmUra in the respective site of DNA does not, per se,
AB  - prevent the activity of restriction endonucleases, ligases or DNA methylases. These data
AB  - support the view that oxidation of Thy to 5HmUra in target DNA does not necessarily result in
AB  - substantial deterioration in the functions of DNA processing enzymes.
ER  -

TY  - JOUR
AU  - Vincent, A.T.
AU  - Charette, S.J.
TI  - Completion of genome of Aeromonas salmonicida subsp. salmonicida 01-B526 reveals how sequencing technologies can influence sequence quality and result interpretations.
JO  - New Microbes New Infect.
PY  - 2018
SP  - 24
EP  - 26
VL  - 25
AB  - Aeromonas salmonicida subsp. salmonicida is a pathogen that primarily infects
AB  - salmonids. A strain of this bacterium, 01-B526, has been used in several studies
AB  - as a reference. The genomic sequence of this strain is available, but comes from
AB  - pyrosequencing and is the second most fragmented assembly for this bacterium. We
AB  - generated its closed genome sequence and found a pitfall in result
AB  - interpretations associated with low-quality genomic sequences.
ER  -

TY  - JOUR
AU  - Vincent, A.T.
AU  - Freschi, L.
AU  - Jeukens, J.
AU  - Kukavica-Ibrulj, I.
AU  - Emond-Rheault, J.G.
AU  - Leduc, A.
AU  - Boyle, B.
AU  - Jean-Pierre, F.
AU  - Groleau, M.C.
AU  - Deziel, E.
AU  - Barbeau, J.
AU  - Charette, S.J.
AU  - Levesque, R.C.
TI  - Genomic characterisation of environmental Pseudomonas aeruginosa isolated from dental unit waterlines revealed the insertion sequence ISPa11 as a chaotropic element.
JO  - FEMS Microbiol. Ecol.
PY  - 
SP  - fix106
EP  - fix106
VL  - 93
AB  - The bacterium Pseudomonas aeruginosa is well known to have a remarkable adaptive capacity
AB  - allowing it to colonise many environments. A recent study on environmental isolates from
AB  - dental unit waterlines (DUWLs) hinted at a genetic clustering into two groups. Isolates from
AB  - one of these groups, named cluster III, were shown to have unusual phenotypes for
AB  - environmental isolates, such as an increased biofilm production. To have a better ecological
AB  - view, more specifically on isolates from cluster III, the complete genomes of 39 isolates
AB  - including 16 from DUWLs were sequenced. In addition to an investigation of antibiotic
AB  - resistance and secretion system gene content, a molecular phylogeny allowed confirmation of
AB  - the split of the 16 environmental isolates in two groups and also sheds light on a correlation
AB  - between the phylogenetic positions and the serotypes of the isolates. Isolates from cluster
AB  - III harboured insertion sequences ISPa11 inserted into the O-specific antigen biosynthesis
AB  - clusters and the gene lasR, encoding for a master regulator of the quorum sensing.
AB  - Investigation of key regulators revealed another truncated gene, gacS. Alteration in lasR and
AB  - gacS genes was consistent with phenotypic assays confirming their inactivation. These results
AB  - bring new perspectives regarding the ecological adaptive potential of P. aeruginosa.
ER  -

TY  - JOUR
AU  - Vincent, A.T.
AU  - Rouleau, F.D.
AU  - Moineau, S.
AU  - Charette, S.J.
TI  - Study of mesophilic Aeromonas salmonicida A527 strain sheds light on the species lifestyles and taxonomic dilemma.
JO  - FEMS Microbiol. Lett.
PY  - 2017
SP  - fnx239
EP  - fnx239
VL  - 364
AB  - The Gram-negative bacterium Aeromonas salmonicida contains five subspecies:
AB  - salmonicida, smithia, achromogenes, masoucida and pectinolytica. Pectinolytica is
AB  - a mesophilic subspecies with the ability to thrive at a wide range of
AB  - temperatures, including 37 degrees C, while the four other subspecies are
AB  - psychrophilic, restricted to lower temperatures. The psychrophilic subspecies are
AB  - known to infect a wide range of fishes. However, there is no evidence of
AB  - pathogenicity for the mesophilic subspecies pectinolytica. Study of the
AB  - differences between the mesophilic and psychrophilic subspecies is hampered by
AB  - the lack of completely sequenced and closed genomes from the mesophilic
AB  - subspecies. A previous study reported that insertion sequences, which can induce
AB  - genomic rearrangements at temperatures around 25 degrees C, could be one of the
AB  - determinants explaining the differences in lifestyle (mesophilic or
AB  - psychrophilic) between the subspecies. In this study, the genome of mesophilic
AB  - strain A527 of A. salmonicida was sequenced, closed and analyzed to investigate
AB  - the mesophilic-psychrophilic discrepancy. This reference genome supports the
AB  - hypothesis that insertion sequences are major determinants of the lifestyle
AB  - differences between the A. salmonicida subspecies. Moreover, the phylogenetic
AB  - analysis performed to position strain A527 within the taxonomy raises an issue
AB  - regarding the intraspecies structure of A. salmonicida.
ER  -

TY  - JOUR
AU  - Vincent, A.T.
AU  - Trudel, M.V.
AU  - Paquet, V.E.
AU  - Boyle, B.
AU  - Tanaka, K.H.
AU  - Dallaire-Dufresne, S.
AU  - Daher, R.K.
AU  - Frenette, M.
AU  - Derome, N.
AU  - Charette, S.J.
TI  - Detection of Variants of the pRAS3, pAB5S9, and pSN254 Plasmids in Aeromonas salmonicida subsp. salmonicida: Multidrug Resistance, Interspecies Exchanges, and Plasmid Reshaping.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 7367
EP  - 7374
VL  - 58
AB  - The ubiquitous water-borne Gram-negative bacterium Aeromonas salmonicida subsp.
AB  - salmonicida is the causative agent of furunculosis, a worldwide disease in fish
AB  - farms. Plasmids carrying antibiotic resistance genes have already been described
AB  - for this bacterium. The aim of the present study was to identify and characterize
AB  - additional multidrug resistance plasmids in A. salmonicida subsp. salmonicida. We
AB  - sequenced the plasmids present in two multiple antibiotic-resistant isolates
AB  - using high-throughput technologies. We also investigated 19 other isolates with
AB  - various multidrug resistance profiles by genotyping PCR and assessed their
AB  - resistance to tetracycline. We identified variants of the pAB5S9 and pSN254
AB  - plasmids that carry several antibiotic resistance genes and that have been
AB  - previously reported in bacteria other than A. salmonicida subsp. salmonicida,
AB  - which suggests a high level of interspecies exchange. Genotyping analyses and the
AB  - antibiotic resistance profiles of the 19 other isolates support the idea that
AB  - multiple versions of pAB5S9 and pSN254 exist in A. salmonicida subsp.
AB  - salmonicida. We also identified variants of the pRAS3 plasmid. The present study
AB  - revealed that A. salmonicida subsp. salmonicida harbors a wide variety of
AB  - plasmids, which suggests that this ubiquitous bacterium may contribute to the
AB  - spread of antibiotic resistance genes in the environment.
ER  -

TY  - JOUR
AU  - Vincze, T.
AU  - Posfai, J.
AU  - Roberts, R.J.
TI  - NEBcutter: a program to cleave DNA with restriction enzymes.
JO  - Nucleic Acids Res.
PY  - 2003
SP  - 3688
EP  - 3691
VL  - 31
AB  - NEBcutter, version 1.0, is a program available via a web server
AB  - (http://tools.neb.com/NEBcutter) that will accept an input DNA sequence
AB  - and produce a comprehensive report of the restriction enzymes that will
AB  - cleave the sequence. It produces a variety of outputs including
AB  - restriction enzyme maps, theoretical digests and links into the
AB  - restriction enzyme database, REBASE (http://www.neb.com/rebase).
AB  - Importantly, its table of recognition sites is updated daily from REBASE
AB  - and it marks all sites that are potentially affected by DNA methylation
AB  - (Dam, Dcm, etc.). Many options exist to choose the enzymes used for
AB  - digestion, including all known specificities, subsets of those that are
AB  - commercially available or sets of enzymes that produce compatible termini.
ER  -

TY  - JOUR
AU  - Vinella, D.
AU  - Jaffe, A.
AU  - D'Ari, R.
AU  - Kohiyama, M.
AU  - Hughes, P.
TI  - Chromosome partitioning in Escherichia coli in the absence of Dam-directed methylation.
JO  - J. Bacteriol.
PY  - 1992
SP  - 2388
EP  - 2390
VL  - 174
AB  - Escherichia coli dam mutants, lacking the GATC DNA methylase, do not produce anucleate cells
AB  - at high frequencies, suggesting that hemimethylation of the chromosome origin of replication,
AB  - oriC, is not essential for correct chromosome partitioning.
ER  -

TY  - JOUR
AU  - Vinogradova, M.N.
AU  - Gromova, E.S.
AU  - Gryaznova, O.I.
AU  - Isagulyants, M.D.
AU  - Kuznetsova, S.A.
AU  - Kosych, V.G.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  IX:  Cleavage of substrates with point modifications in the recognition site and flanking sequences.
JO  - Bioorg. Khim.
PY  - 1987
SP  - 1194
EP  - 1204
VL  - 13
AB  - Ability of the EcoRII restriction endonuclease to cleave 14-base-pair DNA
AB  - duplexes with nucleotide substitutions in the recognition site CC(A/T)GG and in
AB  - the adjacent base pair has been studied.  Modifications leading to a local
AB  - change in the substrate conformation (rU residue in and outside the recognition
AB  - site, A.A- or A.C-pairs in the flanking sequences) reduce the rate of
AB  - hydrolysis, the effect being maximal when the modified base pair is outside the
AB  - recognition site.  No digestion occurs when the internal dC-residue of the
AB  - recognition site is 5-methylated in one or both strands.  Replacement of dT
AB  - residue in the EcoRII recognition site by dF5U residue results in a dramatic
AB  - inhibition of hydrolysis.  Km and Kcat for the cleavage of 14-base-pair DNA
AB  - duplex have been determined.  The cleavage rate of the dT-containing strand of
AB  - the recognition site is 1.5 fold higher comparing with the dA-containing
AB  - strand.  The cleavage of both strands of the substrate by EcoRII endonuclease
AB  - is confirmed to proceed in one enzyme-substrate complex.
ER  -

TY  - JOUR
AU  - Vinogradova, M.N.
AU  - Gromova, E.S.
AU  - Kosykh, V.G.
AU  - Buryanov, Y.I.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  XI. Determination of the EcoRII binding site.
JO  - Mol. Biol. (Mosk)
PY  - 1990
SP  - 847
EP  - 850
VL  - 24
AB  - EcoRII restriction endonuclease binding site has been determined on the basis
AB  - of comparison of the binding parameters of the enzyme with synthetic
AB  - DNA-duplexes of concatemer type containing a different number of EcoRII
AB  - recognition sites.  It has been shown that it consists of 21 +/- 1 base pairs.
ER  -

TY  - JOUR
AU  - Vinogradova, M.N.
AU  - Gromova, E.S.
AU  - Purmal, A.A.
AU  - Kosykh, V.G.
AU  - Shabarova, Z.A.
TI  - Interaction of restriction and modification enzymes EcoRII with synthetic fragments of DNA.
JO  - Mol. Biol. (Mosk)
PY  - 1986
SP  - 1329
EP  - 1336
VL  - 20
AB  - It was shown by the method of binding on nitrocellulose filters that the
AB  - restriction endonuclease EcoRII in the absence of Mg2+ ions is specifically
AB  - bonded to synthetic DNA duplexes of the concatamer type of different lengths,
AB  - containing natural recognition sites for the enzyme CAA/TGG, as well as with
AB  - substrates possessing a noncomplementary AA or TT pair in the recognition site
AB  - of cleavage by the enzyme.  The degree of binding of substrates containing a
AB  - central AT, TT, or AA pair in the recognition site decreases in the series AT >
AB  - TT >> AA.  Replacement of the phosphodiester bond in the recognition site by a
AB  - pyrophosphate or phosphoamide bond has little effect on the stability of the
AB  - complexes.  The affinity of the enzyme for nonspecific DNA sequences is two
AB  - orders of magnitude lower than for the specific recognition sites of EcoRII.
AB  - The equilibrium constant of association for a substrate with one recognition
AB  - site is 3.9 x 10(8) M-1.  The introduction of Mg2+ ions into the incubation
AB  - mixture leads to destabilization of the complex of EcoRII endonuclease with the
AB  - DNA duplex containing pyrophosphate bonds.  The rate constants of dissociation
AB  - and the half-lives of the cocomplexes of the endonuclease EcoRII with synthetic
AB  - substrates were determined.
ER  -

TY  - JOUR
AU  - Vinogradova, M.N.
AU  - Gromova, E.S.
AU  - Uporova, T.M.
AU  - Nikolskaya, I.I.
AU  - Shabarova, Z.A.
TI  - Restriction endonuclease SsoII:  interaction with modified substrates.
JO  - Dokl. Akad. Nauk.
PY  - 1987
SP  - 732
EP  - 736
VL  - 295
AB  - None
ER  -

TY  - JOUR
AU  - Vinuesa, P.
AU  - Ochoa-Sanchez, L.E.
TI  - Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico,  Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide  Biosynthesis.
JO  - Genome Announcements
PY  - 2015
SP  - e01433
EP  - e01415
VL  - 3
AB  - Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila
AB  - strain, generated with PacBio RS II single-molecule real-time
AB  - technology, consisting of a single circular chromosome of 4.13 Mb. We annotated
AB  - mobile genetic elements and natural product biosynthesis clusters, including a
AB  - novel class-II lasso peptide with a 7-residue macrolactam ring.
ER  -

TY  - JOUR
AU  - Vinuesa, P.
AU  - Ochoa-Sanchez, L.E.
AU  - Contreras-Moreira, B.
TI  - GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.
JO  - Front. Microbiol.
PY  - 2018
SP  - 771
EP  - 771
VL  - 9
AB  - The massive accumulation of genome-sequences in public databases promoted the proliferation of
AB  - genome-level phylogenetic analyses in many areas of biological research. However, due to
AB  - diverse evolutionary and genetic processes, many loci have undesirable properties for
AB  - phylogenetic reconstruction. These, if undetected, can result in erroneous or biased
AB  - estimates, particularly when estimating species trees from concatenated datasets. To deal with
AB  - these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality
AB  - markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome
AB  - matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters
AB  - are applied to exclude recombinant alignments and those producing anomalous or poorly resolved
AB  - trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in
AB  - parallel on multi-core computers. A ML species tree is estimated from the concatenated set of
AB  - top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT).
AB  - The latter is used by default due to its superior performance revealed in an extensive
AB  - benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.
AB  - We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome
AB  - sequences available in RefSeq and 10 new complete genomes of Mexican environmental S.
AB  - maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM
AB  - analyses was used to revise the molecular systematics of the genus. An unsupervised learning
AB  - approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a
AB  - core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with
AB  - strongly supported clades on the core- and pan-genome trees. In addition, we identified 16
AB  - misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the
AB  - broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a
AB  - detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3
AB  - license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling
AB  - GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.
AB  - docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
ER  -

TY  - JOUR
AU  - Vinuesa, P.
AU  - Puente, J.L.
AU  - Calva, E.
AU  - Zaidi, M.B.
AU  - Silva, C.
TI  - Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO3 (Sequence Type 302) Isolated from a Baby with Meningitis in Mexico.
JO  - Genome Announcements
PY  - 2016
SP  - e00285
EP  - e00216
VL  - 4
AB  - The complete genome of ITALIC! Salmonella entericaserovar Typhimurium strain SO3  (sequence
AB  - type 302), isolated from a fatal meningitis infection in Mexico, was
AB  - determined using PacBio technology. The chromosome hosts six complete prophages
AB  - and is predicted to harbor 51 genomic islands, including 13 pathogenicity islands
AB  - (SPIs). It carries the ITALIC! Salmonellavirulence plasmid (pSTV).
ER  -

TY  - JOUR
AU  - Vipond, B.
AU  - Halford, S.E.
TI  - Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage.
JO  - Mol. Microbiol.
PY  - 1993
SP  - 225
EP  - 231
VL  - 9
AB  - The EcoRV restriction endonuclease cleaves DNA at its recognition sequence at least a million
AB  - times faster than at any other DNA sequence. The only cofactor it requires for activity is
AB  - Mg2+; but in binding to DNA in the absence of Mg2+, the EcoRV enzyme shows no specificity for
AB  - its recognition site. Instead, the reason why EcoRV cuts one DNA sequence faster than any
AB  - other is that the rate of cleavage is controlled by the binding of Mg2+ to EcoRV-DNA
AB  - complexes; the complex at the recognition site has a high affinity for Mg2+, while the
AB  - complexes at other DNA sequences have low affinities for Mg2+. The structures of the EcoRV
AB  - endonuclease, and of its complexes with either specific or non-specific DNA, have been solved
AB  - by X-ray crystallography. In the specific complex, the protein interacts with the bases in the
AB  - recognition sequence and the DNA takes up a highly distorted structure. In the non-specific
AB  - complex with an unrelated DNA sequence, there are virtually no interactions with the bases and
AB  - the DNA retains a B-like structure. Since the free energy changes for the formation of
AB  - specific and non-specific complexes are the same, the energy from the specific interactions
AB  - balances that required for the distortion of the DNA. The distortion inserts the phosphate at
AB  - the scissile bond into the active site of the enzyme, where it forms part of the binding site
AB  - for Mg2+. Without this distortion, the EcoRV-DNA complex would be unable to bind Mg2+ and thus
AB  - unable to cleave DNA. The specificity of the EcoRV restriction enzyme is therefore governed,
AB  - not by DNA binding as such, but by its ability to organize the structure of the DNA to which
AB  - it is bound.
ER  -

TY  - JOUR
AU  - Vipond, I.B.
AU  - Baldwin, G.S.
AU  - Halford, S.E.
TI  - Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases.
JO  - Biochemistry
PY  - 1995
SP  - 697
EP  - 704
VL  - 34
AB  - Restriction enzymes cannot cleave DNA without a metal ion cofactor. The specificities of the
AB  - EcoRV and EcoRI endonucleases for metals were studied by measuring DNA cleavage rates with
AB  - several metal ions and with combinations of metal ions. Both EcoRV and EcoRI had optimal
AB  - activities with Mg2+, were less active with several other ions including Mn2+, and had
AB  - virtually no activity with Ca2+. But the activities of EcoRV and EcoRI with either Mg2+ or
AB  - Mn2+ were perturbed by Ca2+. For EcoRI, both Mg2+- and Mn2+-dependent activities, at both
AB  - cognate and noncognate sites, were all inhibited by Ca2+. The activity of EcoRV at its
AB  - recognition site with Mg2+ was also inhibited by Ca2+. But the Mn2+-dependent reaction at the
AB  - EcoRV recognition site was stimulated by Ca2+. EcoRV activities at noncognate sites with
AB  - either Mg2+ or Mn2+ displayed a biphasic response to Ca2+: stimulation at low concentrations
AB  - of Ca2+ and inhibition at higher concentrations. These observations, together with the known
AB  - structures of the proteins, indicate that EcoRI needs only one metal ion per active site and
AB  - is inactive when Mg2+ is displaced by Ca2+, while EcoRV needs two and that the displacement of
AB  - one by Ca2+ can enhance activity. We propose a mechanism for phosphodiester hydrolysis by
AB  - EcoRV that involves two metal ions.
ER  -

TY  - JOUR
AU  - Vipond, I.B.
AU  - Baldwin, G.S.
AU  - Oram, M.
AU  - Erskine, S.G.
AU  - Wentzell, L.M.
AU  - Szczelkun, M.D.
AU  - Nobbs, T.J.
AU  - Halford, S.E.
TI  - A general assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates.
JO  - Mol. Biotechnol.
PY  - 1995
SP  - 259
EP  - 268
VL  - 4
AB  - A procedure for measuring the activities of enzymes that alter the covalent structure of DNA
AB  - is described.  The assay utilizes covalently closed circles of DNA as the substrate and yields
AB  - quantitative data on the fraction of this DNA converted to both open-circle and linear forms.
ER  -

TY  - JOUR
AU  - Vipond, I.B.
AU  - Halford, S.E.
TI  - Random mutagenesis targeted to the active site of the EcoRV restriction endonuclease.
JO  - Biochemistry
PY  - 1996
SP  - 1701
EP  - 1711
VL  - 35
AB  - Two segments of the gene for the EcoRV restriction endonuclease, each encoding 10 amino acids
AB  - at the active site, were subjected to random mutagenesis with degenerate oligonucleotides.
AB  - Mutations that abolished the activity of the EcoRV endonuclease were selected by viability in
AB  - a strain of Escherichia coli that lacks the EcoRV methyltransferase, under conditions where
AB  - the gene for the wild-type endonuclease is lethal to the cell.  Sixty-five mutants were
AB  - isolated and analyzed by DNA sequencing to identify the mutations.  The collection of null
AB  - mutants contained 49 with single amino acid substitutions, 15 with double substitutions, and
AB  - one with a triple substitution.  The single substitutions were located at many different
AB  - positions within the two 10-amino acid segments, though several hot-spots gave rise to null
AB  - mutants at high frequencies.  Some hot-spots were readily explained by reference to the
AB  - crystal structure of EcoRV since they were at the amino acids immediately adjacent to the
AB  - scissile phosphodiester bond: for example, Asp90 and Lys92.  These residues may be directly
AB  - involved in the catalytic mechanism.  Other hot-spots, such as Gln69, Tyr72, and Ala88, were
AB  - at unexpected positions that appear to have no direct role in DNA binding or catalysis.  At
AB  - some of the unexpected hot-spots, the side chain of the amino acid lies distant from the DNA,
AB  - yet the enzyme was still inactivated by conservative substitutions at these positions.  The
AB  - sensitivity of the EcoRV endonuclease to conservative substitutions may be due to its
AB  - requirement to take up one particular conformation at the DNA--protein interface out of a
AB  - large number of alternative conformations.
ER  -

TY  - JOUR
AU  - Vipond, I.B.
AU  - Halford, S.E.
TI  - Specific DNA recognition by EcoRV restriction endonuclease induced by Calcium ions.
JO  - Biochemistry
PY  - 1995
SP  - 1113
EP  - 1119
VL  - 34
AB  - In the presence of Mg2+, the EcoRV restriction endonuclease cleaves DNA specifically at its
AB  - recognition sequence, but in the absence of divalent metal ions, it binds DNA without any
AB  - specificity: gel-shift experiments had revealed multiple EcoRV-DNA complexes, due to the
AB  - binding of one, two, three, or more molecules of protein per molecule of DNA, with the same
AB  - equilibrium constant for each association. In this study, the binding of EcoRV to DNA was
AB  - measured by gel shift in the presence of Ca2+, an ion that perturbs the Mg2+-dependent
AB  - activity of EcoRV but that fails to support DNA cleavage. With Ca2+, and at a lower
AB  - concentration of EcoRV protein than that required for binding in the absence of divalent metal
AB  - ions, a single complex was observed with DNA containing the EcoRV recognition site. This
AB  - complex was not formed with DNA that had been methylated at the EcoRV site nor with an
AB  - isogenic DNA lacking the EcoRV recognition site. The single complex thus is due to the
AB  - specific binding of EcoRV to its recognition site on the DNA. From gel shifts with a permuted
AB  - set of DNA fragments, the degree of DNA bending by EcoRV at this recognition site was
AB  - estimated to be 53 degrees +/- 4 degrees. This angle is similar to that seen in the crystal
AB  - structure of the cognate DNA-protein complex. Calcium ions thus appear to mimic the role of
AB  - Mg2+ in generating a specific protein-metal-DNA complex, but in contrast to Mg2+, Ca2+ gives a
AB  - stable ternary complex in which the DNA-bound nuclease cannot cleave the DNA.
ER  -

TY  - JOUR
AU  - Vipond, I.B.
AU  - Moon, B.-J.
AU  - Halford, S.E.
TI  - An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.
JO  - Biochemistry
PY  - 1996
SP  - 1712
EP  - 1721
VL  - 35
AB  - The EcoRV restriction endonuclease cleaves DNA at its recognition sequence more readily with
AB  - Mg2+ as the cofactor than with Mn2+ but, at noncognate sequences that differ from the EcoRV
AB  - site by one base pair, Mn2+ gives higher rates than Mg2+.  A mutant of EcoRV, in which an
AB  - isoleucine near the active site was replaced by leucine, showed the opposite behavior.  It had
AB  - low activity with Mg2+, but, in the presence of Mn2+ ions, it cleaved the recognition site
AB  - faster than wild-type EcoRV with either Mn2+ or Mg2+.  The mutant was also more specific for
AB  - the recognition sequence than the native enzyme: the noncognate DNA cleavages by wild-type
AB  - EcoRV and Mn2+ were not detected with the mutant.  Further mutagenesis showed that the protein
AB  - required the same acidic residues at its active site as wild-type EcoRV.  The Ile-Leu mutation
AB  - seems to perturb the configuration of the metal-binding ligands at the active site so that the
AB  - protein has virtually no affinity for Mg2+ yet it can still bind Mn2+ ions, though the latter
AB  - only occurs when the protein is at the recognition site.  This contrasts to wild-type EcoRV,
AB  - where Mn2+ ions bind readily to complexes with either cognate and noncognate DNA and only Mg2+
AB  - shows the discrimination between the complexes.  The structural perturbation is a specific
AB  - consequence of leucine in place of isoleucine, since mutants with valine or alanine were
AB  - similar to wild-type EcoRV.
ER  -

TY  - JOUR
AU  - Vipond, I.B.
AU  - Moon, B.J.
AU  - Halford, S.E.
TI  - An Ile-to-Leu mutant of the EcoRV restriction endonuclease that requires Mn2+ as catalytic cofactor.
JO  - Biochem. Soc. Trans.
PY  - 1994
SP  - 301S
EP  - 301S
VL  - 22
AB  - The EcoRV restriction endonuclease recognizes and cleaves the sequence GAT^ATC with extreme
AB  - precision. The accuracy is such that alternate sites one bp different are cleaved at least a
AB  - million times slower. However, contrary to many DNA binding proteins, the basis of this
AB  - specificity is not due to preferred binding by EcoRV to its recognition sequence. In fact, the
AB  - EcoRV nuclease binds all DNA sequences with equal affinity. Instead, it is due to the affinity
AB  - of the enzyme-DNA complex for the divalent metal ion which serves as the catalytic cofactor.
AB  - Thus, EcoRV bound to GATATC has a high affinity for Mg2+, while the enzyme bound to any other
AB  - sequence has a low affinity for the metal ion.
ER  -

TY  - JOUR
AU  - Viprey, V.
AU  - Rosenthal, A.
AU  - Broughton, W.J.
AU  - Perret, X.
TI  - Genetic snapshots of the Rhizobium species NGR234 genome.
JO  - Genome Biology
PY  - 2000
SP  - RESEARCH0014
EP  - RESEARCH0014
VL  - 1
AB  - BACKGROUND: In nitrate-poor soils, many leguminous plants form
AB  - nitrogen-fixing symbioses with members of the bacterial family
AB  - Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad
AB  - host range, which includes more than I 12 genera of legumes. Unlike the
AB  - genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb
AB  - chromosome, that of NGR234 is partitioned into three replicons: a
AB  - chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and
AB  - pNGR234a, a 536,165 bp plasmid that carries most of the genes required for
AB  - symbioses with legumes. Symbiotic loci represent only a small portion of
AB  - all the genes coded by rhizobial genomes, however. To rapidly characterize
AB  - the two largest replicons of NGR234, the genome of strain ANU265 (a
AB  - derivative strain cured of pNGR234a) was analyzed by shotgun sequencing.
AB  - RESULTS: Homology searches of public databases with 2,275 random sequences
AB  - of strain ANU265 resulted in the identification of 1,130 putative
AB  - protein-coding sequences, of which 922 (41%) could be classified into
AB  - functional groups. In contrast to the 18% of insertion-like sequences
AB  - (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun
AB  - sequences represent known ISs, suggesting that pNGR234a is enriched in
AB  - such elements. Hybridization data also indicate that the density of known
AB  - transposable elements is higher in pNGR234b (the megaplasmid) than on the
AB  - chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were
AB  - found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously
AB  - thought to be present only in Rhizobium meliloti. As non-overlapping
AB  - shotgun sequences together represent approximately 10% of ANU265 genome,
AB  - the chromosome and megaplasmid may carry a total of over 200 RIMEs.
AB  - CONCLUSIONS: 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light
AB  - on the fine structure and evolution of its replicons, as well as on the
AB  - integration of symbiotic functions in the genome of a soil bacterium.
AB  - Although most putative coding sequences could be distributed into
AB  - functional classes similar to those in Bacillus subtilis, functions
AB  - related to transposable elements were more abundant in NGR234. In contrast
AB  - to ISs that accumulated in pNGR234a and pNGR234b, the hundreds of RIME
AB  - elements seem mostly attributes of the chromosome.
ER  -

TY  - JOUR
AU  - Viratyosin, W.
AU  - Kulawonganunchai, S.
AU  - Smittipat, N.
AU  - Juthayothin, T.
AU  - Penpassakarn, P.
AU  - Pasomsub, E.
AU  - Chantratita, W.
AU  - Chaiprasert, A.
AU  - Palittapongarnpim, P.
TI  - Draft Genome Sequence of the Mycobacterium tuberculosis Strain 43-16836, Belonging to the Indo-Oceanic Lineage, Isolated From Tuberculous Meningitis in  Thailand.
JO  - Genome Announcements
PY  - 2013
SP  - e00801
EP  - e00813
VL  - 1
AB  - We present the draft genome sequence of Mycobacterium tuberculosis strain 43-16836, belonging
AB  - to the Indo-Oceanic lineage, isolated from a tuberculous
AB  - meningitis patient in Thailand. The genome is 4,381,942 bp long with 4,316
AB  - protein-coding genes and contains new single nucleotide polymorphisms (SNPs),
AB  - including SNPs of genes that may encode cell wall components and possibly
AB  - influence virulence.
ER  -

TY  - JOUR
AU  - Vishnivetskaya, T.A. et al.
TI  - Draft genome sequences of 10 strains of the genus exiguobacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01058
EP  - e01014
VL  - 2
AB  - High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to
AB  - provide insight into their evolutionary strategies for
AB  - speciation and environmental adaptation. The selected genomes include
AB  - psychrotrophic and thermophilic species from a range of habitats, which will
AB  - allow for a comparison of metabolic pathways and stress response genes.
ER  -

TY  - JOUR
AU  - Visnovsky, S.B.
AU  - Fiers, M.
AU  - Lu, A.
AU  - Panda, P.
AU  - Taylor, R.
AU  - Pitman, A.R.
TI  - Draft Genome Sequences of 18 Strains of Pseudomonas Isolated from Kiwifruit Plants in New Zealand and Overseas.
JO  - Genome Announcements
PY  - 2016
SP  - e00061
EP  - e00016
VL  - 4
AB  - In this paper, we present the draft sequences of 18 genetically diversePseudomonasstrains
AB  - isolated from kiwifruit plants in New Zealand and
AB  - overseas, including a number that are currently not fully characterized. These
AB  - sequences will aid in the diagnosis ofPseudomonason kiwifruit for future pest
AB  - management and border security decision-making.
ER  -

TY  - JOUR
AU  - Visnovsky, S.B.
AU  - Lu, A.
AU  - Panda, P.
AU  - Taylor, R.
AU  - Pitman, A.R.
TI  - Draft Genome Sequences of 14 Strains of Pseudomonas Isolated from Prunus sp. Plants.
JO  - Genome Announcements
PY  - 2018
SP  - e01481
EP  - e01417
VL  - 6
AB  - We present here the draft genome sequences of 14 Pseudomonas strains isolated from Prunus sp.
AB  - plants in New Zealand and overseas. These new genomic data will
AB  - be used to improve the detection of Pseudomonas strains found in imported plant
AB  - material at the New Zealand border, improving the time involved in the process of
AB  - biosecurity decision-making.
ER  -

TY  - JOUR
AU  - Visnovsky, S.B.
AU  - Panda, P.
AU  - Taylor, R.
AU  - Pitman, A.R.
TI  - Draft Genome Sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, Two Strains Isolated from Actinidia chinensis with Symptoms of  Summer Canker in South Korea.
JO  - Genome Announcements
PY  - 2017
SP  - e00104
EP  - e00117
VL  - 5
AB  - Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit
AB  - plants in South Korea. We report here the draft genome sequences of
AB  - two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which
AB  - were originally isolated from Actinidia chinensis with symptoms of summer canker.
AB  - These genome sequences will aid in the identification of genetic traits
AB  - associated with their unusual capacity to cause canker and help understanding of
AB  - the threat these exotic enterobacteria pose to the New Zealand kiwifruit
AB  - industry.
ER  -

TY  - JOUR
AU  - Vissel, B.
AU  - Choo, K.H.
TI  - Altered activity of restriction endonuclease MnlI cleavage of mouse satellite DNA.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4731
EP  - 4731
VL  - 16
AB  - MnlI is reported to recognise the sequence CCTCN7, cleaving after the N7
AB  - position to produce a blunt ended fragment.  However, we have observed that
AB  - following MnlI cleavage of mouse satellite DNA, the monomeric units that were
AB  - subsequently cloned uniformly lacked the N7 base.  Mouse satellite DNA is
AB  - composed of tandemly repeated 234bp monomeric units, most of which contain an
AB  - MnlI site.  As shown in Fig. 1, direct cloning and sequencing of the MnlI
AB  - monomeric units revealed that the N7 base was consistently absent from the end
AB  - of the clone with the MnlI site (Fig. 1C, D and G).  These results suggest that
AB  - cleavage of mouse satellite DNA by MnlI occurs after the N6, in addition to
AB  - after the N7 position.  It is not clear, however, if MnlI removes the N7 base
AB  - from both strands simultaneously, or, cleaves to leave a single-base 5' or 3'
AB  - extension that is subsequently lost during the cloning procedure.  This unusual
AB  - activity of MnlI may be related to the high AT content or methylated nature of
AB  - the mouse satellite DNA.
ER  -

TY  - JOUR
AU  - Visser, M. et al.
TI  - Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of  Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum  nigrificans.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 655
EP  - 675
VL  - 9
AB  - Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the
AB  - polyphyletic spore-forming genus Desulfotomaculum in the family
AB  - Peptococcaceae. They are phylogenetically very closely related and belong to
AB  - 'subgroup a' of the Desulfotomaculum cluster 1. D. nigrificans and D.
AB  - carboxydivorans have a similar growth substrate spectrum; they can grow with
AB  - glucose and fructose as electron donors in the presence of sulfate. Additionally,
AB  - both species are able to ferment fructose, although fermentation of glucose is
AB  - only reported for D. carboxydivorans. D. nigrificans is able to grow with 20%
AB  - carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can
AB  - grow at 100% CO with and without sulfate. Hydrogen is produced during growth with
AB  - CO by D. carboxydivorans. Here we present a summary of the features of D.
AB  - nigrificans and D. carboxydivorans together with the description of the complete
AB  - genome sequencing and annotation of both strains. Moreover, we compared the
AB  - genomes of both strains to reveal their differences. This comparison led us to
AB  - propose a reclassification of D. carboxydivorans as a later heterotypic synonym
AB  - of D. nigrificans.
ER  -

TY  - JOUR
AU  - Visser, M. et al.
TI  - Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T).
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 69
EP  - 87
VL  - 8
AB  - Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic
AB  - spore-forming genus Desulfotomaculum in the family Peptococcaceae.
AB  - This species is of interest because it originates from deep subsurface thermal
AB  - mineral water at a depth of about 3,000 m. D. kuznetsovii is a rather versatile
AB  - bacterium as it can grow with a large variety of organic substrates, including
AB  - short-chain and long-chain fatty acids, which are degraded completely to carbon
AB  - dioxide coupled to the reduction of sulfate. It can grow methylotrophically with
AB  - methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it
AB  - does not require any vitamins. Here, we describe the features of D. kuznetsovii
AB  - together with the genome sequence and annotation. The chromosome has 3,601,386 bp
AB  - organized in one contig. A total of 3,567 candidate protein-encoding genes and 58
AB  - RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in
AB  - heterotrophic growth with acetate and methanol, and in CO2 fixation during
AB  - autotrophic growth are present. Genomic comparison revealed that D. kuznetsovii
AB  - shows a high similarity with Pelotomaculum thermopropionicum. Genes involved in
AB  - propionate metabolism of these two strains show a strong similarity. However,
AB  - main differences are found in genes involved in the electron acceptor metabolism.
ER  -

TY  - JOUR
AU  - Vitkute, J.
AU  - Maneliene, Z.
AU  - Janulaitis, A.
TI  - AbeI, a restriction endonuclease from Azotobacter beijerinckii, which recognizes the asymmetric heptanucleotide sequence 5'-CCTCAGC-3'(-5/-2).
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 4917
EP  - 4918
VL  - 26
AB  - A new restriction endonuclease AbeI has been isolated from Azotobacter beijerinckii.  This
AB  - enzyme recognizes the asymmetric heptanucleotide sequence 5'-CCTCAGC-3' and cleaves within
AB  - it symmetrically at positions -5/-2 in the opposing strands, producing three base protruding
AB  - 5'-ends.
ER  -

TY  - JOUR
AU  - Vitkute, J.
AU  - Maneliene, Z.
AU  - Janulaitis, A.
TI  - Two new thermostable type II restriction endonucleases from Thermus aquaticus: TatI and TauI, which recognize the novel nucleotide sequences 5'-W^GTACW-3' and 5'-GCSG^C-3' respectively.
JO  - FEMS Microbiol. Lett.
PY  - 2001
SP  - 253
EP  - 257
VL  - 204
AB  - One hundred and forty isolates of thermophilic bacteria from the genus Thermus were screened
AB  - for the presence of restriction endonuclease activity. Thermostable isoschizomers of
AB  - restriction endonucleases, such as AceIII, BbvI, BglI, BsePI, FnuDII, HgiAI, MaeII, MboI,
AB  - MseI, PvuII, StuI, TaqI, Tsp4CI, TspEI, XhoI and XmaIII, were isolated. Two restriction
AB  - enzymes, TatI and TauI, recognizing novel degenerate sequences 5'-W^GTACW-3' and
AB  - 5'-GCSG^C-3' respectively were partially purified and the recognition and cleavage sites
AB  - were determined.
ER  -

TY  - JOUR
AU  - Vitkute, J.
AU  - Maneliene, Z.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - BplI, a new BcgI-like restriction endonuclease, which recognizes a symmetric sequence.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 4444
EP  - 4446
VL  - 25
AB  - BcgI and BcgI-like restriction endonucleases cleave double stranded DNA specifically on both
AB  - sides of their asymmetric recognition sequences which are interrupted by several ambiguous
AB  - base pairs.  Their heterosubunit structure, bifunctionality and stimulation by AdoMet make
AB  - them different from other classified restriction enzymes.  Here we report on a new BcgI-like
AB  - enzyme, which in contrast to all other BcgI-like enzymes, recognizes a symmetric interrupted
AB  - sequence, and which, like BcgI, cleaves double stranded DNA upstream and downstream of its
AB  - recognition sequence (8/13)GAGN5CTC(13/8).  Like BcgI, BplI is a bifunctional enzyme revealing
AB  - both DNA cleavage and methyltransferase activities.  There are two polypeptides in the
AB  - homogeneous preparation of BplI with molecular masses of ~74 and 37 kDa.  The sizes of the
AB  - BplI subunits are close to those of BcgI, but the proportion 1:1 in the final preparation is
AB  - different from that of 2:1 in BcgI.  Low activity observed with Mg2+ increases >100-fold in
AB  - the presence of AdoMet.  Even with AdoMet though, specific cleavage is incomplete.
AB  - S-adenosyl-homocysteine (AdoHcy) or sinefungin can replace AdoMet in the cleavage reaction.
AB  - AdoHcy activated BplI yields complete cleavage of DNA.
ER  -

TY  - JOUR
AU  - Vitkute, J.
AU  - Maneliene, Z.
AU  - Petrusyte, M.
AU  - Janulaitis, A.
TI  - BfiI, a restriction endonuclease from Bacillus firmus S8120, which recognizes the novel non-palindromic sequence 5'-ACTGGG(N)5/4-3'.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 3348
EP  - 3349
VL  - 26
AB  - A new type IIS restriction endonuclease BfiI has been partially purified from Bacillus firmus
AB  - S8120.  BfiI recognizes the non-palindromic hexanucleotide sequence 5'-ACTGGG(N)5/4-3' and
AB  - makes a staggered cut at the fifth base pair downstream of the recognition sequence on the
AB  - upper strand, producing a single base 3' protruding end.
ER  -

TY  - JOUR
AU  - Vitkute, J.
AU  - Stankevicius, K.
AU  - Tamulaitiene, G.
AU  - Maneliene, Z.
AU  - Timinskas, A.
AU  - Berg, D.E.
AU  - Janulaitis, A.
TI  - Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695.
JO  - J. Bacteriol.
PY  - 2001
SP  - 443
EP  - 450
VL  - 183
AB  - Methyltransferases (MTases) of prokaryotes affect general cellular processes such as mismatch
AB  - repair, regulation of transcription, replication, and transposition, and in some cases may be
AB  - essential for viability. As components of restriction-modification systems, they contribute to
AB  - bacterial genetic diversity. The genome of Helicobacter pylori strain 26695 contains 25 open
AB  - reading frames encoding putative DNA MTases. To assess which MTase genes are active, strain
AB  - 26695 genomic DNA was tested for cleavage by
AB  - 147 restriction endonucleases; 24 were found that did not cleave this DNA. The specificities
AB  - of 11 expressed MTases and the genes encoding them were identified from this restriction data,
AB  - combined with the known sensitivities of restriction endonucleases to specific DNA
AB  - modification, homology searches, gene cloning and genomic mapping of the methylated bases m4C,
AB  - m5C, and m6A.
ER  -

TY  - JOUR
AU  - Vitkute, J.
AU  - Tamulaitiene, G.
AU  - Chalkauskas, H.
AU  - Janulaitis, A.
TI  - Potential of H. pylori to produce R-M enzymes and their possible biological role.
JO  - Int. J. Med. Microbiol.
PY  - 2001
SP  - 95
EP  - 95
VL  - 291S
AB  - The unprecedented abundance of putative restriction-modification (R-M) genes found in H.
AB  - pylori genomes raises question on their role in life cycle of bacteria.  As a prerequisite to
AB  - such studies we screened 156 independent isolates for restriction endonucleases to assess
AB  - expression and specificity variability of H. pylori enzymes.  386 REs has been characterized
AB  - with 26 different specificities.  Every screened strain contained REs and their set was
AB  - specific for the majority of them.  In addition a set of seven selected strains was
AB  - investigated for DNA methylases, including J99 and 26695 strains.  We found 87 MTases with 22
AB  - different specificities.  Given that cognate MTase accompanies every RE, altogether 32 MTases
AB  - of different specificity has been identified.  Modeling indicates that this variability is
AB  - near the limit of potential specificity variability for R-M enzymes in H. pylori.  The
AB  - conclusion reinforces previous observations in Enterobacteriaceae on the phenomenon of
AB  - taxonomic specificity of R-M systems.  The character of taxonospecificity represents the first
AB  - nonexperimental evidence supporting hypothesis on "selfishness" of R-M genes.  The main role
AB  - of H. pylori R-M systems is likely to modulate involvement of H. pylori and non-H. pylori DNA
AB  - in genetic exchange of the bacteria.  Arguments are provided to support this hypothesis.
AB  - Other possible functions of R-M systems are also discussed.
ER  -

TY  - JOUR
AU  - Vitor, J.M.B.
TI  - Restriction and modification systems in Campylobacter jejuni and Campylobacter coli.
JO  - Ph.D. Thesis, University of Lisbon
PY  - 1999
SP  - 1
EP  - 220
AB  - The restriction endonucleases are one of the most widely used
AB  - tools in molecular biology and acronyms like EcoRI or BamHI are used
AB  - daily in any laboratory all over the world.  Although ubiquitous among
AB  - the prokaryotes there are only a few scientific groups studying these
AB  - systems.  The RE are a part of the restriction and modification systems
AB  - and it is believed that they are a defense mechanism of the host
AB  - bacteria against bacteriophages, although not all scientists agree with
AB  - this theory.  It is also believed that RM systems can act as intra and
AB  - inter-specific barriers to the exchange of genetic information and may
AB  - be involved in genetic recombination since they produce DNA fragments
AB  - that can be integrated in the host genome or in an extrachromosomal
AB  - element.
ER  -

TY  - JOUR
AU  - Vitor, J.M.B.
AU  - Alves, P.
AU  - Marques, M.
AU  - Vital, J.
TI  - Helicobacter pylori type IIG restriction and modification loci.
JO  - Helicobacter
PY  - 2011
SP  - 98
EP  - 98
VL  - 16
AB  - Helicobacter pylori complete sequenced genomes have a large number of putative restriction and
AB  - modification systems between 26 and 34.  The major consequence of RMS is keeping the bacterial
AB  - genomes free from alien DNA, acting as a speciation barrier.  RMS are classified into four
AB  - major types and several subtypes.  The H. pylori genomes annotated in REBASE were analyzed and
AB  - it was found that RMS are not randomly distributed over the genome.  Using H. pylori 26695 as
AB  - model, four type IIG RMS loci were found: 1st - glpC.horF; 2nd - nadC-HINFIM; 3rd - tmk-polA;
AB  - 4th - res-nusA.  Primers were designed for the four loci and tested in 17 different H. pylori
AB  - strains, isolated from asymptomatic patients.  PCR products were obtained in all loci but
AB  - differences were observed among them.  All the PCR products were digested with HindIII to
AB  - evaluate the variability of the amplified genes.  Locus 1 and 4 are empty in a large
AB  - percentage of strains, 64.7 and 52.9 respectively.  Locus 2 has a high percentage of strains
AB  - with unspecific PCR products, 58.8%.  Different HindIII profiles were observed: 2 in locus 1,
AB  - 5 in locus 2 and 4, and 6 in locus 3.  This might correspond to 18 different type IIG RMS in
AB  - 17 strains, thus being one more example of H. pylori genetic diversity although their species
AB  - genomic organization might be conservative.
ER  -

TY  - JOUR
AU  - Vitor, J.M.B.
AU  - Costa, L.
AU  - Pires, I.
AU  - Cabrita, J.
AU  - Correia, R.V.
TI  - Restriction enzymes in Campylobacter strains.
JO  - Microb. Ecol. Health Dis.
PY  - 1991
SP  - S50
EP  - S50
VL  - 4
AB  - Restriction enzymes (RE) are very important tools in Genetic Engineering.  They
AB  - are a part of the Restriction Modification (RM) systems, that are ubiquitous in
AB  - prokaryotes.  We have searched for RE activity in 100 enteropathogenic
AB  - Campylobacter strains (52 C. jejuni and 58 C. coli strains) from human and
AB  - animal origin.  The strains were isolated, subcultured and identified by
AB  - routine methods.  DNAse activity was searched for as described by Lior and the
AB  - RE screening by Whitehead and Brown's method, with modifications concerning the
AB  - time of lysis by lysozyme, the time and temperature of the detergent step and
AB  - the saline concentration of the digestion buffer.  The DNA used was from
AB  - bacteriophage lambda methyl free.
ER  -

TY  - JOUR
AU  - Vitor, J.M.B.
AU  - Morgan, R.D.
TI  - Two novel restriction endonucleases from Campylobacter jejuni.
JO  - Gene
PY  - 1995
SP  - 109
EP  - 110
VL  - 157
AB  - We have discovered two unusual restriction endonucleases (ENases) in two Campylobacter jejuni
AB  - strains that recognize asymmetrical, interrupted sequences and cleave the DNA both before and
AB  - after their recognition sites.  Both enzymes require AdoMet as a cofactor for their ENase
AB  - activity.
ER  -

TY  - JOUR
AU  - Vitor, J.M.B.
AU  - Polisson, C.
AU  - Cabrita, J.
AU  - Silva, R.V.C.
TI  - Restriction enzymes from Campylobacter coli strains.
JO  - Acta Gastroenterol. Belg.
PY  - 1993
SP  - 41
EP  - 41
VL  - 56
AB  - The type II restriction enzymes (RE) are ubiquitous among Prokaryotes. These enzymes belong to
AB  - restriction-modification systems, which include a methyltransferase. One function is thought
AB  - to protect the genomic information from other genetic pools. Also it is believed that when a
AB  - strain exhibits restriction activity there will be a methyltransferase. Eight Campylobacter
AB  - coli strains known to have RE activity from previous screening, isolated from human, pig and
AB  - chicken, were plated on BHI agar and incubated for 20h at 42C, in an anaerobic jar (5% O2, 10%
AB  - CO2). 1g of cells were lysed by sonication and centrifuged 25 min at 40,000g. The assay for RE
AB  - was made in NEB buffer no2, 1h at 37C with lambda and T7 DNAs. If necessary, the extract was
AB  - purified by affinity chromatography, with Heparin-Sepharose CL-6B. We have identified nine RE:
AB  - CcoP95I (GCGC) isoschizomer of HhaI; CcoP215I and CcoP216I (GCNGC) isoschizomers of Fnu4HI;
AB  - CcoP31I, CcoP84I and CcoP219I (GATC) isoschizomers of MboI; CcoP73I and CcoP76I (GTAC)
AB  - isoschizomers of RsaI. Although we have studied a small number of isolates, the results
AB  - suggest that the REs detected in Campylobacter coli recognize mainly GC-rich sequences. This
AB  - finding may explain the prevalence in those strains of AT-rich plasmid DNA as well as the low
AB  - chromosomal GC content (32-34%) of them.
ER  -

TY  - JOUR
AU  - Vitoriano, I.
AU  - Vitor, J.M.B.
AU  - Oleastro, M.
AU  - Roxo-Rosa, M.
AU  - Vale, F.F.
TI  - Proteome variability among Helicobacter pylori isolates clustered according to genomic methylation.
JO  - J. Appl. Microbiol.
PY  - 2013
SP  - 1817
EP  - 1832
VL  - 114
AB  - Aims To understand whether the variability found in the proteome of Helicobacter pylori
AB  - relates to the genomic methylation, virulence and
AB  - associated gastric disease. Methods and Results We applied the
AB  - Minimum-Common-Restriction-Modification (MCRM) algorithm to genomic
AB  - methylation data of 30 Portuguese H.pylori strains, obtained by genome
AB  - sensitivity to Type II restriction enzymes' digestion. All the
AB  - generated dendrograms presented three clusters with no association with
AB  - gastric disease. Comparative analysis of two-dimensional gel
AB  - electrophoresis (2DE) maps obtained for total protein extracts of 10 of
AB  - these strains, representative of the three main clusters, revealed that
AB  - among 70 matched protein spots (in a universe of 300), 16 were
AB  - differently abundant (P<0 center dot 05) among clusters. Of these, 13
AB  - proteins appear to be related to the cagA genotype or gastric disease.
AB  - The abundance of three protein species, DnaK, GlnA and HylB, appeared
AB  - to be dictated by the methylation status of their gene promoter.
AB  - Conclusions Variations in the proteome profile of strains with common
AB  - geographic origin appear to be related to differences in cagA genotype
AB  - or gastric disease, rather than to clusters organized according to
AB  - strain genomic methylation. Significance and Impact of the Study The
AB  - simultaneous study of the genomic methylation and proteome is important
AB  - to correlate epigenetic modifications with gene expression and pathogen
AB  - virulence.
ER  -

TY  - JOUR
AU  - Vizoso, P.
AU  - Pacheco, N.
AU  - Bastias-Molina, M.
AU  - Meneses, C.
AU  - Poblete-Castro, I.
TI  - Draft Genome Sequence of the Phenol-Degrading Bacterium Pseudomonas putida H.
JO  - Genome Announcements
PY  - 2015
SP  - e00936
EP  - e00915
VL  - 3
AB  - In this study, we report the draft genome of Pseudomonas putida H, a well-known bacterium
AB  - capable of degrading various aromatic compounds. Its genome size is
AB  - 6,065 Mbp with a GC content of 61.6%. This work will aid future studies on this
AB  - versatile bacterium.
ER  -

TY  - JOUR
AU  - Vizoso-Pinto, M.G.
AU  - Saavedra, L.
AU  - Hebert, E.M.
AU  - Raya, T.F.
AU  - Albarracin, L.
AU  - Alvarez, S.
AU  - Kitazawa, H.
AU  - Villena, J.
TI  - Draft Genome Sequence of Immunobiotic Lactobacillus rhamnosus Strain IBL027, a Potential Adjuvant for Mucosal Vaccine Development.
JO  - Genome Announcements
PY  - 2017
SP  - e01268
EP  - e01217
VL  - 5
AB  - The genome sequence of the immunomodulatory strain Lactobacillus rhamnosus strain IBL027 is
AB  - described here. The reads were assembled into contigs with a total size
AB  - 2,898,501 bp. The genome information will be useful for further specific genetic
AB  - studies of this strain to evaluate its immunomodulatory and biotechnological
AB  - properties as a vaccine adjuvant.
ER  -

TY  - JOUR
AU  - Vizzotto, C.S.
AU  - Lopes, F.A.C.
AU  - Green, S.J.
AU  - Steindorff, A.S.
AU  - Walter, J.M.
AU  - Thompson, F.L.
AU  - Kruger, R.H.
TI  - Draft Genome Sequence of Muricauda sp. Strain K001 Isolated from a Marine Cyanobacterial Culture.
JO  - Genome Announcements
PY  - 2018
SP  - e00451
EP  - e00418
VL  - 6
AB  - We report the whole-genome sequence of Muricauda sp. strain K001 isolated from a  marine
AB  - cyanobacterial culture. This genome sequence will improve our
AB  - understanding of the influence of heterotrophic bacteria on the physiology of
AB  - cyanobacteria and may contribute to the development of new natural products.
ER  -

TY  - JOUR
AU  - Vlasova, T.I.
AU  - Demidenko, Z.N.
AU  - Kirnos, M.
AU  - Vanyushin, B.F.
TI  - In vitro DNA methylation by wheat nuclear cytosine DNA methyltransferase: effect of phytohormones.
JO  - Gene
PY  - 1995
SP  - 279
EP  - 281
VL  - 157
AB  - Cytosine DNA methyltransferases (MTases) were isolated from nuclei of wheat seedlings and
AB  - germinating embryos.  The MTases isolated from both sources were able to perform de novo and
AB  - maintenance DNA methylations.  The most purified MTase fraction showed the presence of one
AB  - main 67-kDa protein (embryos) and of an 85-kDa protein (in seedlings) in SDS-PAGE.  Some plant
AB  - growth regulators (gibberellic acid A3, 6-benzylaminopurine and fusicoccin) elevate by 30-65%
AB  - the extent of in vitro DNA methylation by nuclear extracts with a maximal effect at 10 microM
AB  - phytohormone concentration.  The same phytohormones do not increase the extent of in vitro
AB  - DNA methylation by purified wheat MTase; rather they inhibit it at concentrations of 10/-4 to
AB  - 10/-5 M.  Thus, DNA methylation in the plant nucleus is controlled by phytohormones.  The
AB  - phytohormone effect may be mediated by other proteins in nuclear extracts.
ER  -

TY  - JOUR
AU  - Vlasova, T.I.
AU  - Kirnos, M.D.
AU  - Vanyushin, B.F.
TI  - Cytosine DNA-methyltransferase from wheat seedlings.
JO  - Biokhimiia
PY  - 1996
SP  - 774
EP  - 780
VL  - 61
AB  - A cytosine DNA methyltransferase has been isolated from wheat seedling nuclei and purified by
AB  - chromatography on DEAE-cellulose, heparin-Sepharose, and Mono-Q FPLC.  The specific activity
AB  - of the enzyme was 236 units/mg protein; its molecular mass by SDS-PAGE was 85-kD.  The enzyme
AB  - catalyzes in vitro DNA methylation for a relatively long period, but it is very unstable in
AB  - solution in the absence of substrates.  The apparent Km value for S-adenosylmethionine is 6
AB  - microM.  The enzyme is active over a wide pH range (5.5-8.5); it is inhibited by NaCl and by
AB  - the reaction product S-adenosylhomocysteine with [I]50 values of 0.2M and 12uM, respectively.
AB  - The enzyme catalyzes both de novo and maintenance DNA methylation and displays a high rate of
AB  - de novo methylation.  The wheat seedling enzyme is similar to known plant cytosine DNA
AB  - methyltransferases.
ER  -

TY  - JOUR
AU  - Vlasova, T.I.
AU  - Vanyushin, B.F.
TI  - DNA methylation by wheat cytosine DNA methyltransferase: modulation by protease inhibitor E-64.
JO  - Biochem. Mol. Biol. Int.
PY  - 1998
SP  - 145
EP  - 153
VL  - 45
AB  - Cytosine DNA methyltransferase isolated from wheat seedlings and purified in the presence of
AB  - metalloprotease and serine protease inhibitors has molecular mass and specific activity equal
AB  - to about 85 kDa and 250 units/mg protein, respectively.  Apparent Km for AdoMet and [I]50 for
AB  - AdoHcy values are about 6 microM and 12 microM, respectively.  The enzyme is active in a wide
AB  - pH range (pH 5.5 - 8.5) and is inhibited by NaCl.  The enzyme rapidly loses its
AB  - methyltransferase activity in the absence of substrates.  Using the cysteine protease
AB  - inhibitor E-64 it has been shown that rapid enzyme inactivation is caused by disappearance of
AB  - essential enzyme SH-groups but is not due to proteolytic enzyme cleavage.
ER  -

TY  - JOUR
AU  - Vlatakis, G.
AU  - Bouriotis, V.
TI  - Affinity partitioning of restriction endonucleases:  Application to the purification of EcoRI and EcoRV.
JO  - J. Chromatogr.
PY  - 1991
SP  - 311
EP  - 321
VL  - 538
AB  - Partitioning of restriction endonucleases between two liquid aqueous phases can
AB  - be strongly influenced by group-specific ligands included in the two-phase
AB  - system.  Three restriction endonucleases, namely EcoRI, EcoRV and BamHI, were
AB  - partitioned within an aqueous dextran-polyethylene glycol (PEG) system.  The
AB  - enzymes could be extracted into the upper PEG phase by using either triazine
AB  - dyes or herring DNA as affinity ligands.  The influence of the endogenous
AB  - bacterial nucleic acids, concentration of polymer-bound dye and concentration
AB  - of sodium chloride on the system were examined.  A partial purification of
AB  - EcoRI (up to 52-fold) and EcoRV (up to 37-fold) was achieved using a
AB  - combination of affinity partitioning and ion-exchange chromatography, providing
AB  - an extremely fast and economical method for the isolation of restriction
AB  - endonucleases free from contaminating nuclease activities.
ER  -

TY  - JOUR
AU  - Vlatakis, G.
AU  - Bouriotis, V.
TI  - Sequence-specific DNA affinity chromatography:  Application to the purification of EcoRI and SphI.
JO  - Anal. Biochem.
PY  - 1991
SP  - 352
EP  - 357
VL  - 195
AB  - Several rapid and effective methods have been described to obtain restriction
AB  - endonucleases suitable for commercial exploitation.  However, lengthy and
AB  - laborious protocols have been necessary to obtain homogeneous enzymes.  We now
AB  - report the use of sequence-specific DNA affinity chromatography to purify
AB  - restriction endonucleases to near homogeneity.  Restriction endonucleases EcoRI
AB  - and SphI from the microorganisms Escherichia coli RY 13 and Streptomyces
AB  - phaeochromogenes, respectively, were purified to near homogeneity employing a
AB  - two-step procedure which involves DNA-cellulose chromatography and
AB  - oligonucleotide-ligand affinity chromatography.
ER  -

TY  - JOUR
AU  - Vlatakis, G.
AU  - Clark, D.
AU  - Bouriotis, V.
TI  - Isolation and identification of restriction endonuclease BshFI.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 8882
EP  - 8882
VL  - 17
AB  - None
ER  -

TY  - JOUR
AU  - Vlatakis, G.
AU  - Skarpelis, G.
AU  - Stratidaki, I.
AU  - Bouriotis, V.
TI  - Dye-ligand chromatography for the resolution and purification of restriction endonucleases.
JO  - Appl. Biochem. Biotechnol.
PY  - 1987
SP  - 201
EP  - 212
VL  - 15
AB  - The resolution of restriction endonucleases from the same microorganism is
AB  - conventionally achieved by length fractionation protocols.  We now report
AB  - effective single-step procedures that exploit dye-ligand chromatography for the
AB  - resolution and purification of restriction enzymes.  After suitable initial
AB  - screening, we demonstrated that resolution of two restriction activities can be
AB  - achieved in one chromatographic step, and further purification can subsequently
AB  - be effected using selected dye-adsorbents.  Accordingly, we resolved in one
AB  - step, HpaI from HpaII, HindII from HindIII, and SacI from SacII.  Furthermore,
AB  - a three-step chromatographic procedure has been developed to purify EcoRV
AB  - suitable for commercial exploitation, as judged by the overdigestion and
AB  - cut-ligate-recut quality control tests.
ER  -

TY  - JOUR
AU  - Vockler, C.J.
AU  - Greenfield, P.
AU  - Tran-Dinh, N.
AU  - Midgley, D.J.
TI  - Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia.
JO  - Genome Announcements
PY  - 2014
SP  - e00279
EP  - e00214
VL  - 2
AB  - Despite its global abundance, Bacillus pumilus is poorly studied. The Fairview strain was
AB  - obtained from a methanogenic anaerobic coal digester. The draft genome sequence was 3.8 Mbp
AB  - long and contained 3,890 protein-coding genes. Like the SAFR-032 strain, it includes B.
AB  - pumilus-specific proteins that likely confer enhanced resistance to environmental stresses.
ER  -

TY  - JOUR
AU  - Voelker, L.L.
AU  - Dybvig, K.
TI  - Gene transfer in Mycoplasma arthritidis: Transformation, conjugal transfer of Tn916, and evidence for a restriction system recognizing AGCT.
JO  - J. Bacteriol.
PY  - 1996
SP  - 6078
EP  - 6081
VL  - 178
AB  - Mycoplasma arthritidis is a rat pathogen causing a severe polyarthritis.  The study of its
AB  - pathogenic mechanisms has been hampered by the lack of genetic systems for use with M.
AB  - arthritidis.  Described here are procedures for genetic transformation of M. arthritidis and
AB  - conjugal transfer of Tn916 from an enterococcal donor to M. arthritidis.  The location of
AB  - Tn916 insertion sites in the mycoplasmal chromosome was random, suggesting that Tn916 may be
AB  - useful as an insertional mutagen in this organism.  Additionally, a restriction and
AB  - modification system was identified which presented a strong barrier to gene transfer.  For
AB  - transformation, the restriction system was circumvented by using DNA that was modified in
AB  - vitro with the appropriate site-specific methylase (AluI).
ER  -

TY  - JOUR
AU  - Voelker, L.L.
AU  - Dybvig, K.
TI  - Sequence analysis of the Mycoplasma arthritidis bacteriophage MAV1 genome identifies the putative virulence factor.
JO  - Gene
PY  - 1999
SP  - 101
EP  - 107
VL  - 233
AB  - The bacteriophage MAV1 is required for the development of arthritis in rats after infection
AB  - with its host Mycoplasma arthritidis.  To identify the phage-encoded virulence factor for this
AB  - arthritis, the complete nucleotide sequence of MAV1 was determined. The linear double-stranded
AB  - genome of MAV1 is 15644bp and contains 15 ORFs. Putative protein products from these ORFs were
AB  - identified by comparison of the deduced amino acid sequences to known proteins and comprise
AB  - DNA replication, restriction-modification, structural, regulatory, and integration/excision
AB  - proteins. Eight putative promoters were identified; four of these would produce polycistronic
AB  - transcripts. Translation of each ORF appears to be initiated independently, with each having
AB  - its own RBS. A single ORF, vir, was identified on the minus strand of the phage genome. The
AB  - putative protein product of vir contains a classic prokaryotic lipoprotein signal sequence and
AB  - is a strong candidate for the MAV1-encoded virulence determinant.
ER  -

TY  - JOUR
AU  - Voet, J.G.
AU  - Voet, D.
TI  - DNA structure and restriction/modification visualized with kinemages.
JO  - FASEB J.
PY  - 1997
SP  - A843
EP  - A843
VL  - 11
AB  - Teaching nucleic acid structure in more than a cursory way can be difficult.  What is it that
AB  - is different about the structures of the A and B conformations of DNA?  How do we identify the
AB  - Major and Minor grooves?  How do proteins interact with DNA in a specific manner?  How do
AB  - proteins cleave and modify DNA?  Students carry out restriction digestion of DNA and make
AB  - restriction maps in introductory biology courses.  But do they actually know what is
AB  - happening?  We have tried to remedy this problem by instituting the use of Kinemage
AB  - visualizations.  These accompany a set of laboratory experiments derived largely from Micklos,
AB  - D.A. and Freyer, G.A., DNA Science, a first course in recombinant DNA Technology, Cold Spring
AB  - Harbor Laboratory Press, 1990, on plasmid isolation, restriction mapping, and the effect of
AB  - methylation on restriction.  The kinemages we have made show the different conformations of
AB  - DNA and the complementary base pairs but, in addition, identify the functional groups of the
AB  - bases that line the major and minor grooves and how the different types of sugar puckers
AB  - associated with the different conformations.  We have also made kinemages showing the specific
AB  - interactions of EcoRI and EcoRV restriction endonucleases with DNA as well as the interactions
AB  - of HhaI methylase with DNA.  In this last kinemage we show the mechanism of methylation as
AB  - well as the dramatic conformational change in the DNA induced by the enzyme and the
AB  - protein-DNA interactions involved.  We will demonstrate these kinemages at the poster session.
ER  -

TY  - JOUR
AU  - Voeykova, T.A.
AU  - Lomovskaya, N.D.
TI  - Restriction and modification of Actinophage omega-C31.
JO  - Genetika
PY  - 1981
SP  - 1132
EP  - 1135
VL  - 17
AB  - Actinophage omega-C31 was shown to be insensitive to a number of restriction and modification
AB  - systems.  Phage sensitivity to RM systems of those strains to which phage cannot adsorb, may
AB  - be tested using protoplast transfection.  For instance, the absence of omega-C13 transfection
AB  - in Streptomyces griseus Kr15 protoplasts, as compared to efficient transfection in protoplasts
AB  - of R- M+ mutant of this strain seems to imply the sensitivity of omega-C31 to the RM system of
AB  - S. griseus Kr15.  Restriction of mutant omega-C31 phage modified by S. albus G RM system has
AB  - been detected in S. coelicolor A3(2).  This effect being dependent on a previous host may
AB  - indicate that the mutant phage was rendered sensitive to an RM system of S. coelicolor A3(2).
ER  -

TY  - JOUR
AU  - Voeykova, T.A.
AU  - Slavinskaya, E.V.
AU  - Orechov, A.V.
AU  - Lomovskaya, N.D.
TI  - Identification of restriction and modification systems in Streptomyces strains.
JO  - Genetika
PY  - 1979
SP  - 1746
EP  - 1754
VL  - 15
AB  - Host range of actinophage phi C31, VP5 and Pg81 in respect to 109 strains of Streptomyces
AB  - genus and hybrid strain Rcg2 from the cross S. coelicolor
AB  - A3(2)XS. griseus Kr was studied. The existence of RM-systems in strains S.
AB  - griseus Kr15, S. griseus Kr20, Rcg2, S. griseofovillus 43 was shown using
AB  - phage Pg81. Mutants of Pg81 were observed which to some extent lost
AB  - snesitivity to RM-system in the strain Rcg2. The presence of RM-system in
AB  - S. lividans 67 was demonstrated by the phage VP5.
ER  -

TY  - JOUR
AU  - Vogel, V.
AU  - Falquet, L.
AU  - Calderon-Copete, S.P.
AU  - Basset, P.
AU  - Blanc, D.S.
TI  - Short term evolution of a highly transmissible methicillin-resistant Staphylococcus aureus clone (ST228) in a tertiary care hospital.
JO  - PLoS ONE
PY  - 2012
SP  - E38969
EP  - E38969
VL  - 7
AB  - Staphylococcus aureus is recognized as one of the major human pathogens and is by
AB  - far one of the most common nosocomial organisms. The genetic basis for the
AB  - emergence of highly epidemic strains remains mysterious. Studying the
AB  - microevolution of the different clones of S. aureus is essential for identifying
AB  - the forces driving pathogen emergence and spread. The aim of the present study
AB  - was to determine the genetic changes characterizing a lineage belonging to the
AB  - South German clone (ST228) that spread over ten years in a tertiary care hospital
AB  - in Switzerland. For this reason, we compared the whole genome of eight isolates
AB  - recovered between 2001 and 2008 at the Lausanne hospital. The genetic comparison
AB  - of these isolates revealed that their genomes are extremely closely related. Yet,
AB  - a few more important genetic changes, such as the replacement of a plasmid, the
AB  - loss of large fragments of DNA, or the insertion of transposases, were observed.
AB  - These transfers of mobile genetic elements shaped the evolution of the ST228
AB  - lineage that spread within the Lausanne hospital. Nevertheless, although the
AB  - strains analyzed differed in their dynamics, we have not been able to link a
AB  - particular genetic element with spreading success. Finally, the present study
AB  - showed that new sequencing technologies improve considerably the quality and
AB  - quantity of information obtained for a single strain; but this information is
AB  - still difficult to interpret and important investments are required for the
AB  - technology to become accessible for routine investigations.
ER  -

TY  - JOUR
AU  - Vogelsang-Wenke, H.
AU  - Oesterhelt, D.
TI  - Isolation of a halobacterial phage with a fully cytosine-methylated genome.
JO  - Mol. Gen. Genet.
PY  - 1988
SP  - 407
EP  - 414
VL  - 211
AB  - A new bacteriophage from Halobacterium halobium has been isolated and partially characterized.
AB  - It is not homologous to the phage PhiH (Schnabel et al. 1982) which infects the same
AB  - bacterium, though it appeared spontaneously in a culture of PhiH adapted to H. halobium
AB  - NRL/JW. The size and morphology of PhiN are comparable to that of other known halophages. The
AB  - genome of PhiN consists of linear double-stranded DNA, 56 kb in size, whose dCMP is totally
AB  - replaced by 5-methyl-dCMP. This is the second case of a fully cytosine-methylated genome, the
AB  - bacteriophage XP12 from Xanthomonas oryzae being so far the only one reported. Like PhiH, the
AB  - PhiN genome seems to have terminal redundancy and circular permutation. PhiN is the first
AB  - halobacterial phage which survives prolonged exposure to low ionic strength environments.
AB  - After 48 h incubation in distilled water a loss in infectivity of less than 50% is observed.
ER  -

TY  - JOUR
AU  - Vogensen, F.K.
AU  - Pedersen, B.M.
AU  - Nielsen, E.W.
AU  - Josephsen, J.
TI  - Genetic and biological evidence for 5 different plasmid-encoded restriction and modification systems in Streptococcus cremoris strains.
JO  - FEMS Microbiol. Rev.
PY  - 1987
SP  - 44
EP  - 44
VL  - 46
AB  - From plasmid curing data it was indicated that restriction- and modification systems
AB  - (R/M-systems) were plasmid-encoded in Streptococcus cremoris KH, V32.2, T29W5 and Tk5-56 (2
AB  - R/M-systems on different plasmids). 4 of the suspected R/M encoding plasmids were purified and
AB  - cotransformed together with pVS2 into Streptococcus lactis MG1614. Transformants containing
AB  - the individual suspected R/M encoding plasmids together with pVS2, showed restriction against
AB  - Phijj50 grown on S. lactis MG1614 containing pVS2, giving genetic evidence that the suspected
AB  - plasmids actually coded for R/M systems. The strength in the new host were in two cases lower
AB  - than that in the original host. Whether this is due to the host or the different phage is not
AB  - known. When Phijj50 were grown on transformants containing the different R/M encoding plasmids
AB  - it was in all cases restricted by the other R/M containing transformants, indicating 4
AB  - biological different R/M-systems were acting. The size of the 4 plasmids were in the range of
AB  - 13-18 Kb. Additionally S. cremoris Tk5-56 contained a second plasmid encoded R/M-system. From
AB  - curing data and from transformation with total plasmid DNA from S. cremoris Tk5-56 into S.
AB  - lactis MG1614 it could be concluded that the second R/M-system is encoded either on
AB  - approximately 18 Kb or approximately 45 Kb plasmids. From biological data it can be concluded
AB  - that this system differs from the above 4 R/M systems mentioned.
ER  -

TY  - JOUR
AU  - Voget, S.
AU  - Billerbeck, S.
AU  - Simon, M.
AU  - Daniel, R.
TI  - Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter.
JO  - Genome Announcements
PY  - 2015
SP  - e01051
EP  - e01015
VL  - 3
AB  - The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878)  belongs to
AB  - the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the
AB  - Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the
AB  - genus Octadecabacter and the type strain of the species.
ER  -

TY  - JOUR
AU  - Voget, S.
AU  - Bruns, H.
AU  - Wagner-Dobler, I.
AU  - Schulz, S.
AU  - Daniel, R.
TI  - Draft Genome Sequence of Roseovarius tolerans EL-164, a Producer of N-Acylated Alanine Methyl Esters and N-Acylhomoserine Lactones.
JO  - Genome Announcements
PY  - 2015
SP  - e01096
EP  - e01015
VL  - 3
AB  - Roseovarius tolerans EL-164 is a member of the Roseobacter clade, a group of marine bacteria
AB  - within the Alphaproteobacteria. It produces different N-acylhomoserine lactone (AHL)
AB  - autoinducers as well as five AHL-related but functionally different compounds, the N-acylated
AB  - alanine methyl esters. The size  of the draft genome is 3,749,755 bp.
ER  -

TY  - JOUR
AU  - Voget, S.
AU  - Diaz, V.S.M.
AU  - von Hoyningen-Huene, A.J.
AU  - Nattramilarasu, P.K.
AU  - Vollheyde, K.
AU  - Xiao, S.
AU  - Daniel, R.
TI  - Genome Sequence of Jannaschia aquimarina GSW-M26, a Member of the Roseobacter Clade.
JO  - Genome Announcements
PY  - 2015
SP  - e00353
EP  - e00315
VL  - 3
AB  - The Gram-negative alphaproteobacterium Jannaschia aquimarina GSW-M26 (DSM 28248)  is a member
AB  - of the Roseobacter clade. The size of the draft genome is 4.1 Mb.
AB  - Genome analysis revealed the presence of genes encoding a complete gene transfer
AB  - agent and aerobic anoxygenic photosynthesis. The latter indicated a
AB  - photoheterotrophic lifestyle.
ER  -

TY  - JOUR
AU  - Voget, S.
AU  - Klippel, B.
AU  - Daniel, R.
AU  - Antranikian, G.
TI  - Complete Genome Sequence of Carnobacterium sp. 17-4.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3403
EP  - 3404
VL  - 193
AB  - Members of the Carnobacteria have been extensively studied as probiotic cultures in
AB  - aquacultures and protective cultures in seafood, diary and
AB  - meat. We report on the finished genome sequence of Carnobacterium sp.
AB  - 17-4, which has been isolated from permanently cold seawater. The genetic
AB  - information reveals a new circular bacteriocin biosynthesis cluster.
ER  -

TY  - JOUR
AU  - Voget, S.
AU  - Wemheuer, B.
AU  - Brinkhoff, T.
AU  - Vollmers, J.
AU  - Dietrich, S.
AU  - Giebel, H.A.
AU  - Beardsley, C.
AU  - Sardemann, C.
AU  - Bakenhus, I.
AU  - Billerbeck, S.
AU  - Daniel, R.
AU  - Simon, M.
TI  - Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses.
JO  - ISME J.
PY  - 2015
SP  - 371
EP  - 384
VL  - 9
AB  - The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene
AB  - sequence similarity of >98%, is the largest cluster of the marine Roseobacter
AB  - clade and most abundant in temperate to (sub)polar oceans, constituting up to 35%
AB  - of total bacterioplankton. The genome analysis of the first described species of
AB  - the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic
AB  - lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of
AB  - homologous genes with any other organism of this clade. The genome is the
AB  - smallest of all closed genomes of the Roseobacter clade, exhibits various
AB  - features of genome streamlining and encompasses genes for aerobic anoxygenic
AB  - photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical
AB  - significance of the RCA cluster we investigated a phytoplankton spring bloom in
AB  - the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean
AB  - 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that
AB  - the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some
AB  - variations during day and night. The genome of P. temperata RCA23 was also
AB  - retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82%
AB  - from stations of the Global Ocean Sampling expedition in the northwestern
AB  - Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of
AB  - P. temperata RCA23. This abundant taxon appears to be a major player in ocean
AB  - biogeochemistry.The ISME Journal advance online publication, 1 August 2014;
AB  - doi:10.1038/ismej.2014.134.
ER  -

TY  - JOUR
AU  - Voigt, J.M.
AU  - Topal, M.D.
TI  - O6 methylguanine in place of guanine causes asymmetric single-strand cleavage of DNA by some restriction enzymes.
JO  - Biochemistry
PY  - 1990
SP  - 1632
EP  - 1637
VL  - 29
AB  - The interactions of restriction enzymes with their cognate DNA recognition sequences present a
AB  - model for protein-DNA interactions. We have investigated the effect of O6-methylguanine on
AB  - restriction enzyme cleavage of DNA; O6-methylguanine is a carcinogenic lesion and a structural
AB  - analogue of the biological restriction inhibitor N6-methyladenine. O6-methylguanine was
AB  - synthesized into oligonucleotides at unique positions. The oligonucleotides were purified and
AB  - analyzed by high-pressure liquid chromatography to assure that, within the limits of our
AB  - detection, O6-methylguanine was the only modified base present. These oligonucleotides were
AB  - annealed with their complement so that cytosine, and in one case thymine, opposed
AB  - O6-methylguanine. DNA cleavage by restriction enzymes that recognize a unique DNA sequence,
AB  - HpaII, HhaI, HinPI, NaeI, NarI, PvuII, and XhoI, was inhibited by a single O6-methylguanine in
AB  - place of guanine (adenine for PvuII) within the appropriate recognition sequences. However,
AB  - only the modified strand was nicked by HpaII, NaeI, and XhoI with O6-methylguanine at certain
AB  - positions, indicating asymmetric strand cleavage. For all the restriction enzymes studied but
AB  - AhaII, BanI, and NarI, lack of double- or single-strand cleavage correlated with inability of
AB  - the O6-methylguanine-containing recognition sequence to measurably bind enzyme. None of the
AB  - restriction enzymes studied were inhibited by O6-methylguanine outside their cognate
AB  - recognition sequences.
ER  -

TY  - JOUR
AU  - Voing, K.
AU  - Harrison, A.
AU  - Soby, S.D.
TI  - Draft Genome Sequence of Chromobacterium vaccinii, a Potential Biocontrol Agent against Mosquito (Aedes aegypti) Larvae.
JO  - Genome Announcements
PY  - 2015
SP  - e00477
EP  - e00415
VL  - 3
AB  - Chromobacterium vaccinii has been isolated only from cranberry bogs in Massachusetts. While it
AB  - is unknown what role these bacteria play in their natural
AB  - environments, they hold potential as biological control agents against the larvae
AB  - of insect pests. Potential virulence genes were identified, including the
AB  - violacein synthesis pathway, siderophores, and chitinases.
ER  -

TY  - JOUR
AU  - Voing, K.
AU  - Harrison, A.
AU  - Soby, S.D.
TI  - Draft Genome Sequence of Chromobacterium subtsugae MWU12-2387 Isolated from a Wild Cranberry Bog in Truro, Massachusetts.
JO  - Genome Announcements
PY  - 2017
SP  - e01633
EP  - e01616
VL  - 5
AB  - Chromobacterium subtsugae MWU12-2387 was isolated from the rhizosphere of cranberry plants.
AB  - While it is unknown what environmental role these bacteria play
AB  - in bog soils, they hold potential as biological control agents against nematodes
AB  - and insect pests. Potential virulence genes were identified, including the
AB  - violacein synthesis pathway, siderophores, and several chitinases.
ER  -

TY  - JOUR
AU  - Voing, K.
AU  - Harrison, A.
AU  - Soby, S.D.
TI  - Draft Genome Sequences of Three Chromobacterium subtsugae Isolates from Wild and  Cultivated Cranberry Bogs in Southeastern Massachusetts.
JO  - Genome Announcements
PY  - 2015
SP  - e00998
EP  - e00915
VL  - 3
AB  - Chromobacterium subtsugae was isolated from cranberry bogs in Massachusetts. While it is
AB  - unknown what environmental role these bacteria play in bog soils, they hold potential as
AB  - biological control agents against the larvae of insect pests. Potential virulence genes were
AB  - identified, including the violacein synthesis pathway, siderophores, and several chitinases.
ER  -

TY  - JOUR
AU  - Volland, S.
AU  - Rachinger, M.
AU  - Strittmatter, A.
AU  - Daniel, R.
AU  - Gottschalk, G.
AU  - Meyer, O.
TI  - Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5043
EP  - 5043
VL  - 193
AB  - We report on genome sequencing of Oligotropha carboxidovorans strain OM4 and resequencing of
AB  - strain OM5. The genomes of both are composed of one
AB  - chromosome and two plasmids. The presence of two plasmids in the OM5
AB  - genome is inconsistent with the previously published sequence in which
AB  - only one plasmid was described (D. Paul, S. Bridges, S. Burgess, Y.
AB  - Dandass, and M. Lawrence. BMC Genomics 11:511, 2010).
ER  -

TY  - JOUR
AU  - Volna, P.
AU  - Jarjour, J.
AU  - Baxter, S.
AU  - Roffler, S.R.
AU  - Monnat, R.J. Jr.
AU  - Stoddard, B.L.
AU  - Scharenberg, A.M.
TI  - Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 2748
EP  - 2758
VL  - 35
AB  - LAGLIDADG homing endonucleases (LHEs) cleave 18-24 bp DNA sequences and are promising enzymes
AB  - for applications requiring sequence-specific DNA cleavage amongst genome-sized DNA
AB  - backgrounds. Here, we report a method for cell surface display of LHEs, which facilitates
AB  - analysis of their DNA binding and cleavage properties by flow cytometry. Cells expressing
AB  - surface LHEs can be stained with fluorescently conjugated double-stranded oligonucleotides
AB  - (dsOligos) containing their respective target sequences. The signal is absolutely sequence
AB  - specific and undetectable with dsOligos carrying single base-pair substitutions. LHE-dsOligo
AB  - interactions facilitate rapid enrichment and viable recovery of rare LHE expressing cells by
AB  - both fluorescence-activated cell sorting (FACS) and magnetic cell sorting (MACS).
AB  - Additionally, dsOligos conjugated with unique fluorophores at opposite termini can be tethered
AB  - to the cell surface and used to detect DNA cleavage. Recapitulation of DNA binding and
AB  - cleavage by surface-displayed LHEs provides a high-throughput approach to library screening
AB  - that should facilitate rapid identification and analysis of enzymes with novel sequence
AB  - specificities.
ER  -

TY  - JOUR
AU  - Volozhantsev, N.V.
AU  - Kislichkina, A.A.
AU  - Lev, A.I.
AU  - Mukhina, T.N.
AU  - Bogun, A.A.
AU  - Ershova, O.N.
AU  - Alexandrova, I.A.
AU  - Fursova, N.K.
TI  - Genome Sequences of Two NDM-1 Metallo-beta-Lactamase-Producing Multidrug-Resistant Strains of Klebsiella pneumoniae with a High Degree of  Similarity, One of Which Contains Prophage.
JO  - Genome Announcements
PY  - 2017
SP  - e01173
EP  - e01117
VL  - 5
AB  - We report genome sequences of two NDM-1 metallo-beta-lactamase-producing multidrug-resistant
AB  - Klebsiella pneumoniae isolates of sequence type 147 (ST147)
AB  - from one hospital. The genomes are highly similar and differ in prophage located
AB  - in the chromosome of K. pneumoniae KPB-1470/16 and in the additional
AB  - plasmid-carrying blaOXA-48 gene in K. pneumoniae KPB-417/16.
ER  -

TY  - JOUR
AU  - von Jan, M. et al.
TI  - Complete genome sequence of Archaeoglobus profundus type strain (AV18).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 327
EP  - 346
VL  - 2
AB  - Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the
AB  - euryarchaeal class Archaeoglobi, which is currently represented by the single
AB  - family Archaeoglobaceae, containing six validly named species and two strains
AB  - ascribed to the genus 'Geoglobus' which is taxonomically challenged as the
AB  - corresponding type species has no validly published name. All members were
AB  - isolated from marine hydrothermal habitats and are obligate anaerobes. Here we
AB  - describe the features of the organism, together with the complete genome sequence
AB  - and annotation. This is the second completed genome sequence of a member of the
AB  - class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52
AB  - RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Vongs, A.
AU  - Kakutani, T.
AU  - Martienssen, R.A.
AU  - Richards, E.J.
TI  - Arabidopis thaliana DNA methylation mutants.
JO  - Science
PY  - 1993
SP  - 1926
EP  - 1928
VL  - 260
AB  - Three DNA hypomethylation mutants of the flowering plant Arabidopsis thaliana were isolated by
AB  - screening mutagenized populations for plants containing centromeric repetitive DNA arrays
AB  - susceptible to digestion by restriction endonuclease that was sensitive to methylated
AB  - cytosines. The mutations are recessive, and at least two are alleles of a single locus,
AB  - designated DDM1 (for decrease in DNA methylation). Amounts of 5-methylcytosine were reduced
AB  - over 70 percent in ddm1 mutants. Despite this reduction in DNA methylation levels, ddm1
AB  - mutants developed normally and exhibited no striking morphological phenotypes. However, the
AB  - ddm1 mutations are associated with a segregation distortion phenotype. The ddm1 mutations were
AB  - used to demonstrate that de novo DNA methylation in vivo is slow.
ER  -

TY  - JOUR
AU  - Vongsawan, A.A.
AU  - Kapatral, V.
AU  - Vaisvil, B.
AU  - Burd, H.
AU  - Serichantalergs, O.
AU  - Venkatesan, M.M.
AU  - Mason, C.J.
TI  - The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis.
JO  - FEMS Microbiol. Lett.
PY  - 2015
SP  - fnv011
EP  - fnv011
VL  - 362
AB  - We sequenced and analyzed Shigella dysenteriae strain Sd1617 serotype 1 that is widely used as
AB  - model strain for vaccine design, trials and research. A combination of next-generation
AB  - sequencing platforms and assembly yielded two contigs representing a chromosome size of 4.34
AB  - Mb and the large virulence plasmid of 177 kb. This genome sequence is compared with other
AB  - Shigella genomes in order to understand gene complexity and pathogenic factors.
ER  -

TY  - JOUR
AU  - Voo, K.
AU  - Carlone, D.
AU  - Jacobsen, B.
AU  - Flodin, A.
AU  - Skalnik, D.
TI  - Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1.
JO  - Blood
PY  - 1999
SP  - 469a
EP  - 469a
VL  - 0
AB  - Cytosine methylation of DNA at CpG motifs provides an important mechanism for controlling gene
AB  - expression.  Hypermethylation or hypomethylation of tumor suppressor genes and oncogenes,
AB  - respectively, has been associated with the progression of cancer.  Ligand screening was
AB  - utilized to isolate a human cDNA that encodes a novel CpG binding protein (hCGBP) that is
AB  - highly expressed in hematopoietic cell lines.  This factor contains three cysteine rich
AB  - domains, two of which exhibit homology to the plant homeodomain finger motif.  A third
AB  - cysteine rich domain conforms to the CXXC motif identified in DNA methyltransferase, human
AB  - thithorax, and methyl-CpG binding domain protein 1.  Interestingly, database searching
AB  - revealed that the hCGBP gene is located within 1 kilobase of the gene encoding methyl-CpG
AB  - binding domain protein 1, a factor that binds to methylated CpG motifs and functions as a
AB  - transcriptional repressor.  A fragment of hCGBP that contains the CXXC domain binds to an
AB  - oligonucleotide probe containing a single CpG site, and this complex is disrupted by distinct
AB  - oligonucleotide competitors that also contain CpG motif(s).  However, hCGBP fails to bind
AB  - oligonucleotides in which the CpG motif is either mutated or methylated.  Native hCGBP is
AB  - detected as an 88 kDa protein by Western analysis and is ubiquitously expressed.  The
AB  - DNA-binding activity of native hCGBP is apparent in electrophoretic mobility shift assays, and
AB  - hCGBP trans-activates promoters that contain CpG motifs, but not promoters in which the CpG is
AB  - ablated.  These data indicate that hCGBP is a transcriptional activator that recognizes
AB  - unmethylated CpG dinucleotides, suggesting a role in modulating the expression of genes
AB  - located within CpG islands.
ER  -

TY  - JOUR
AU  - Vorholt, J.A.
AU  - Vaupel, M.
AU  - Thauer, R.K.
TI  - A selenium-dependent and a selenium-independent formylmethanofuran dehydrogenase and their transcriptional regulation in the hyperthermophilic Methanopyrus kandleri.
JO  - Mol. Microbiol.
PY  - 1997
SP  - 1033
EP  - 1042
VL  - 23
AB  - The genome of Methanopyrus kandleri was found to harbour a gene, fwuB, predicted to encode the
AB  - catalytic subunit of a tungsten formylmethanofuran dehydrogenase with an active site
AB  - selenocysteine, and a second gene, fwcB, encoding a tungsten formylmethanofuran dehydrogenase
AB  - with an active site cysteine. Northern blot and primer-extension analysis revealed that both
AB  - genes were differentially transcribed. During growth of the methanogen on medium supplemented
AB  - with selenium only fwuB was transcribed, whereas transcription of both fwuB and fwcB was
AB  - observed on selenium-deprived medium. Growth of M. kandleri was stimulated by tungstate and
AB  - selenite but not by molybdate. The findings indicate that the hyperthermophilic archaeon
AB  - contains two tungsten isoenzymes of formylmethanofuran dehydrogenase, one of which is a novel
AB  - selenium enzyme. They also indicate that the hyperthermophilic methanogen probably does not
AB  - contain a molybdenum formylmethanofuran dehydrogenase which appears to be present only in
AB  - thermophilic and mesophilic methanogens.
ER  -

TY  - JOUR
AU  - Vorholter, F.J.
AU  - Arnold, M.
AU  - Wibberg, D.
AU  - Blom, J.
AU  - Winkler, A.
AU  - Viehoever, P.
AU  - Albersmeier, A.
AU  - Goesmann, A.
AU  - Zange, S.
AU  - Heesemann, J.
AU  - Puhler, A.
AU  - Hogardt, M.
TI  - Draft Genome Sequence of Pseudomonas aeruginosa Strain WS394, a Multidrug-Resistant and Highly Cytotoxic Wound Isolate from Chronic Ulcus Cruris.
JO  - Genome Announcements
PY  - 2014
SP  - e01325
EP  - e01314
VL  - 2
AB  - Pseudomonas aeruginosa is a frequent human pathogen that increasingly causes chronic
AB  - infections of nonhealing wounds. Here we present the 6.8 Mb draft genome
AB  - of strain WS394, a multidrug-resistant chronic ulcer isolate that exhibited
AB  - outstanding high cell cytotoxicity despite defective secretion of exotoxin U,
AB  - suggesting a habitat-dependent adaptation process.
ER  -

TY  - JOUR
AU  - Vorholter, F.J.
AU  - Schneiker, S.
AU  - Goesmann, A.
AU  - Krause, L.
AU  - Bekel, T.
AU  - Kaiser, O.
AU  - Linke, B.
AU  - Patschkowski, T.
AU  - Ruckert, C.
AU  - Schmid, J.
AU  - Sidhu, V.K.
AU  - Sieber, V.
AU  - Tauch, A.
AU  - Watt, S.A.
AU  - Weisshaar, B.
AU  - Becker, A.
AU  - Niehaus, K.
AU  - Puhler, A.
TI  - The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
JO  - J. Biotechnol.
PY  - 2008
SP  - 33
EP  - 45
VL  - 134
AB  - The complete genome sequence of the Xanthomonas campestris pv. campestris strain B100 was
AB  - established. It consisted of a chromosome of 5,079,003bp,
AB  - with 4471 protein-coding genes and 62 RNA genes. Comparative genomics
AB  - showed that the genes required for the synthesis of xanthan and xanthan
AB  - precursors were highly conserved among three sequenced X. campestris pv.
AB  - campestris genomes, but differed noticeably when compared to the remaining
AB  - four Xanthomonas genomes available. For the xanthan biosynthesis genes
AB  - gumB and gumK earlier translational starts were proposed, while gumI and
AB  - gumL turned out to be unique with no homologues beyond the Xanthomonas
AB  - genomes sequenced. From the genomic data the biosynthesis pathways for the
AB  - production of the exopolysaccharide xanthan could be elucidated. The first
AB  - step of this process is the uptake of sugars serving as carbon and energy
AB  - sources wherefore genes for 15 carbohydrate import systems could be
AB  - identified. Metabolic pathways playing a role for xanthan biosynthesis
AB  - could be deduced from the annotated genome. These reconstructed pathways
AB  - concerned the storage and metabolization of the imported sugars. The
AB  - recognized sugar utilization pathways included the Entner-Doudoroff and
AB  - the pentose phosphate pathway as well as the Embden-Meyerhof pathway
AB  - (glycolysis). The reconstruction indicated that the nucleotide sugar
AB  - precursors for xanthan can be converted from intermediates of the pentose
AB  - phosphate pathway, some of which are also intermediates of glycolysis or
AB  - the Entner-Doudoroff pathway. Xanthan biosynthesis requires in particular
AB  - the nucleotide sugars UDP-glucose, UDP-glucuronate, and GDP-mannose, from
AB  - which xanthan repeat units are built under the control of the gum genes.
AB  - The updated genome annotation data allowed reconsidering and refining the
AB  - mechanistic model for xanthan biosynthesis.
ER  -

TY  - JOUR
AU  - Vorholter, F.J.
AU  - Tielen, P.
AU  - Wibberg, D.
AU  - Narten, M.
AU  - Schobert, M.
AU  - Tupker, R.
AU  - Blom, J.
AU  - Schatschneider, S.
AU  - Winkler, A.
AU  - Albersmeier, A.
AU  - Goesmann, A.
AU  - Puhler, A.
AU  - Jahn, D.
TI  - Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.
JO  - Genome Announcements
PY  - 2015
SP  - e00115
EP  - e00115
VL  - 3
AB  - Pseudomonas aeruginosa is a frequent agent of complicated catheter-associated urinary tract
AB  - infections (CAUTIs). Here, we present the improved 7.1-Mb draft
AB  - genome sequence of P. aeruginosa MH19, which was isolated from a patient with an
AB  - acute hospital-acquired CAUTI. It includes unique genes not represented in other
AB  - P. aeruginosa genomes.
ER  -

TY  - JOUR
AU  - Vorobeva, O.V.
AU  - Karyagina, A.S.
AU  - Volkov, E.M.
AU  - Viryasov, M.B.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - An analysis of methyltransferase SsoII-DNA contacts in the enzyme-substrate complex.
JO  - Bioorg. Khim.
PY  - 2002
SP  - 402
EP  - 410
VL  - 28
AB  - The functional groups of the DNA methylation site that are involved in the DNA interaction
AB  - with methyltransferase SsoII at the recognition stage were identified. The contacts in the
AB  - enzyme-substrate complex were analyzed in the presence of S-adenosyl-L-homocysteine using the
AB  - interference footprinting assay with formic acid, hydrazine, dimethyl sulfate, or
AB  - N-ethyl-N-nitrosourea as a modifying reagent. It was shown that the replacement of the central
AB  - A.T by the G.C pair in the methylation site did not affect the enzyme-DNA interaction, whereas
AB  - the use of a substrate with one chain methylated (monomethylated substrate) instead of the
AB  - unmethylated substrate dramatically changes the DNA contacts. The binding constants of
AB  - unmethylated and monomethylated substrates with methyltransferase Ssoll in the presence of
AB  - S-adenosyl-L-homocysteine were calculated.
ER  -

TY  - JOUR
AU  - Vorobeva, O.V.
AU  - Romanenkov, A.S.
AU  - Metelev, V.G.
AU  - Karyagina, A.S.
AU  - Lavrova, N.V.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - Crosslinking of Cys142 of Methyltransferase SsoII with DNA Duplexes Containing a Single Internucleotide Phosphoryldisulfide Link.
JO  - Mol. Biol. (Mosk)
PY  - 2003
SP  - 906
EP  - 915
VL  - 37
AB  - DNA duplexes containing a single phosphoryldisulfide link in place of the natural
AB  - internucleotide phosphodiester bond were employed in affinity
AB  - modification of Cys142 in cytosine-C5 DNA methyltransferase SsoII
AB  - (M.SsoII). The possibility of duplex-M.SsoII conjugation as a result of
AB  - disulfide exchange was demonstrated. The crosslinking efficiency proved to
AB  - depend on the DNA primary structure, modification position, and the
AB  - presence of S-adenosyl-L-homocysteine, a nonreactive analog of the
AB  - methylation cofactor. The SH group of M.SsoII Cys142 was assumed to be
AB  - close to the DNA sugar-phosphate backbone in the DNA-enzyme complex.
ER  -

TY  - JOUR
AU  - Vorobeva, O.V.
AU  - Vasilev, S.A.
AU  - Karyagina, A.S.
AU  - Oretskaya, T.S.
AU  - Kubareva, E.A.
TI  - Analysis of DNA-protein contacts in a complex between methyltransferase SsoII and a promoter region of the SsoII restriction-modification genes.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 1074
EP  - 1080
VL  - 34
AB  - .
ER  -

TY  - JOUR
AU  - Voros, A.
AU  - Horvath, B.
AU  - Hunyadkurti, J.
AU  - McDowell, A.
AU  - Barnard, E.
AU  - Patrick, S.
AU  - Nagy, I.
TI  - Complete Genome Sequences of Three Propionibacterium acnes Isolates from the Type IA2 Cluster.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1621
EP  - 1622
VL  - 194
AB  - Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide
AB  - range of opportunistic human infections and conditions, most
AB  - notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). We
AB  - now present the whole-genome sequences of three P. acnes strains from the type
AB  - IA(2) cluster which were recovered from ophthalmic infections (A. McDowell et
AB  - al., Microbiology 157:1990-2003, 2011).
ER  -

TY  - JOUR
AU  - Vorwerk, H.
AU  - Huber, C.
AU  - Mohr, J.
AU  - Bunk, B.
AU  - Bhuju, S.
AU  - Wensel, O.
AU  - Sproer, C.
AU  - Fruth, A.
AU  - Flieger, A.
AU  - Schmidt-Hohagen, K.
AU  - Schomburg, D.
AU  - Eisenreich, W.
AU  - Hofreuter, D.
TI  - A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose.
JO  - Mol. Microbiol.
PY  - 2015
SP  - 809830
EP  - 809830
VL  - 98
AB  - Thermophilic Campylobacter species colonize the intestine of agricultural and
AB  - domestic animals commensally, but cause severe gastroenteritis in humans. In
AB  - contrast to other enteropathogenic bacteria, Campylobacter have been considered
AB  - to be non-glycolytic, a metabolic property originally used for their taxonomic
AB  - classification. Contrary to this dogma, we demonstrate that several Campylobacter
AB  - coli strains are able to utilize glucose as a growth substrate. Isotopologue
AB  - profiling experiments with 13 C-labeled glucose suggested that these strains
AB  - catabolize glucose via the pentose phosphate and Entner-Doudoroff (ED) pathways
AB  - and use glucose efficiently for de novo synthesis of amino acids and cell surface
AB  - carbohydrates. Whole genome sequencing of glycolytic C. coli isolates identified
AB  - a genomic island located within a ribosomal RNA gene cluster that encodes for all
AB  - ED pathway enzymes and a glucose permease. We could show in vitro that a
AB  - non-glycolytic C. coli strain could acquire glycolytic activity through natural
AB  - transformation with chromosomal DNA of C. coli and C. jejuni subsp. doylei
AB  - strains possessing the ED pathway encoding plasticity region. These results
AB  - reveal for the first time the ability of a Campylobacter species to catabolize
AB  - glucose and provide new insights into how genetic macrodiversity through intra-
AB  - and interspecies gene transfer expand the metabolic capacity of this food-borne
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Vosberg, H.-P.
AU  - Eckstein, F.
TI  - Effect of deoxynucleoside phosphorothioates incorporated in DNA on cleavage by restriction enzymes.
JO  - J. Biol. Chem.
PY  - 1982
SP  - 6595
EP  - 6599
VL  - 257
AB  - DNA synthesized in vitro using deoxynucleoside phosphorothioates as substrates is quite
AB  - similar to normal DNA in its biochemical properties. In order to investigate the effect of
AB  - phosphorothioate groups in DNA on the cleavage pattern of restriction endonucleases
AB  - phosphorothioate double-stranded, circular, replicative form of fd DNA was synthesized in
AB  - vitro with Escherichia coli DNA polymerase I using native single-stranded DNA as template and
AB  - mixtures of three normal nucleotides and one nucleoside phosphorothioate analogue as
AB  - substrates. The double-stranded products were hybrids with respect to their phosphorothioate
AB  - content. Restriction analysis of normal and phosphorothioate DNA with the restriction
AB  - endonucleases HaeIII, BamHI, HpaII, HindII, Alu I, and TaqI showed that the enzymes were
AB  - inhibited to different degrees depending on which of the nucleotides was replaced by the
AB  - phosphorothioate. Most significant, inhibition was seen throughout with those DNAs which
AB  - contained a phosphorothioate exactly at the cleavage site. Phosphorothioate substitutions at
AB  - other positions, but still within the recognition sequences, were, except for AluI, not or
AB  - weakly inhibitory. Phosphorothioate nucleotides not present in the recognition sequences did
AB  - not affect at all the fragment patterns. The results show that recognition sequences of
AB  - restriction endonucleases can be selectively protected against cleavage by base-specific
AB  - introduction of phosphorothioate groups into DNA.
ER  -

TY  - JOUR
AU  - Voss, B.
AU  - Bolhuis, H.
AU  - Fewer, D.P.
AU  - Kopf, M.
AU  - Moke, F.
AU  - Haas, F.
AU  - El-Shehawy, R.
AU  - Hayes, P.
AU  - Bergman, B.
AU  - Sivonen, K.
AU  - Dittmann, E.
AU  - Scanlan, D.J.
AU  - Hagemann, M.
AU  - Stal, L.J.
AU  - Hess, W.R.
TI  - Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
JO  - PLoS ONE
PY  - 2013
SP  - E60224
EP  - E60224
VL  - 8
AB  - Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates
AB  - the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena
AB  - also is common in brackish water bodies worldwide, suggesting special adaptation
AB  - allowing it to thrive at moderate salinities. A draft genome analysis of N.
AB  - spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in
AB  - length on which genes for 5,294 proteins were annotated. A subsequent
AB  - strand-specific transcriptome analysis identified more than 6,000 putative
AB  - transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led
AB  - us to predict 764 non-coding RNAs, among them 70 copies of a possible
AB  - retrotransposon and several potential RNA regulators, some of which are also
AB  - present in other N2-fixing cyanobacteria. Approximately 4% of the total coding
AB  - capacity is devoted to the production of secondary metabolites, among them the
AB  - potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin.
AB  - The transcriptional complexity associated with genes involved in nitrogen
AB  - fixation and heterocyst differentiation is considerably smaller compared to other
AB  - Nostocales. In contrast, sophisticated systems exist for the uptake and
AB  - assimilation of iron and phosphorus compounds, for the synthesis of compatible
AB  - solutes, and for the formation of gas vesicles, required for the active control
AB  - of buoyancy. Hence, the annotation and interpretation of this sequence provides a
AB  - vast array of clues into the genomic underpinnings of the physiology of this
AB  - cyanobacterium and indicates in particular a competitive edge of N. spumigena in
AB  - nutrient-limited brackish water ecosystems.
ER  -

TY  - JOUR
AU  - Vovis, G.F.
AU  - Horiuchi, K.
AU  - Hartman, N.
AU  - Zinder, N.D.
TI  - Restriction endonuclease B and f1 heteroduplex DNA.
JO  - Nature New Biol.
PY  - 1973
SP  - 13
EP  - 16
VL  - 246
AB  - In many strains of Escherichia coli, strain-specific restriction system
AB  - recognises phage and bacterial DNA synthesis in a different strain and
AB  - initiates its degradation.  The recognition and initial hydrolysis can
AB  - apparently occur at the same or different sites on the DNA molecule (resistance
AB  - transfer factor R1, (refs 1-3) and E. coli B4 restriction, respectively) and
AB  - are mediated by a strain-specific endonuclease.  Protection is afforded by
AB  - modification (glucosylation and methylation) and mutation of the DNA,
AB  - presumably at the recognition site(s).  A DNA duplex, only one of whose strands
AB  - is modified (by methylation) is resistant to restriction endonuclease K.
AB  - Similar conclusions about the sensitivity of hybrid molecules containing one
AB  - modified DNA strand were made from in vivo observations with T2 and lambda
AB  - phage with regard to restriction in E. coli B and P1 lysogens, respectively.
ER  -

TY  - JOUR
AU  - Vovis, G.F.
AU  - Horiuchi, K.
AU  - Zinder, N.D.
TI  - Endonuclease R.EcoRII restriction of bacteriophage f1 DNA in vitro:  Ordering of genes V and VII, location of an RNA promotor for Gene VIII.
JO  - J. Virol.
PY  - 1975
SP  - 674
EP  - 684
VL  - 16
AB  - Replicative form DNA of bacteriophage f1 was found to be sensitive in vitro to
AB  - restriction by endonuclease R.EcoRII if the DNA was isolated from an
AB  - Escherichia coli strain deficient in cytosine methylase activity.  A similar
AB  - observation was previously made with DNA from the closely related bacteriophage
AB  - fd (S. Schlagman, S. Hattman, M.S. May and L. Berger, submitted for
AB  - publication).  The two DNA fragments produced by the endo R.EcoRII digestion of
AB  - f1 DNA were localized on the f1 cleavage map and their genetic content was
AB  - determined.  The polypeptides synthesized in a "coupled"
AB  - transcription-translation system under the direction of each RII fragment were
AB  - examined.  The results of such experiments allow the ordering of genes V and
AB  - VII and indicate the location of a RNA promoter for gene VIII.
ER  -

TY  - JOUR
AU  - Vovis, G.F.
AU  - Horiuchi, K.
AU  - Zinder, N.D.
TI  - Kinetics of methylation of DNA by a restriction endonuclease from Escherichia coli B.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1974
SP  - 3810
EP  - 3813
VL  - 71
AB  - The restriction endonuclease from E. coli B is both an endonuclease and a DNA
AB  - methylase.  Both activities either require or are stimulated by Mg++, adenosine
AB  - triphosphate, and S-adenosyl-L-methionine.  The particular activity which the
AB  - enzyme exhibits depends upon the nature of the SB sites, the genetic sites that
AB  - identify substrate DNA.  Enzymatic treatment of DNA that has an unmodified,
AB  - wild-type SB site results in either rapid restriction of the DNA or very slow
AB  - methylation of the SB site.  On the other hand, a hybrid SB site (modified),
AB  - which protects the DNA molecule from restriction, results in rapid methylation
AB  - of that SB site.
ER  -

TY  - JOUR
AU  - Vovis, G.F.
AU  - Lacks, S.
TI  - Complementary action of restriction enzymes Endo R.DpnI and Endo R.DpnII on bacteriophage f1 DNA.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 525
EP  - 538
VL  - 115
AB  - Bacteriophage f1 duplex DNA was isolated from Escherichia coli strains containing different
AB  - DNA methylases and assayed for its sensitivity to endonucleolytic cleavage by the enzymes endo
AB  - R.DpnI and endo R.DpnII. the former enzyme is specific for methylated DNA, the latter for
AB  - unmethylated DNA (Lacks & Greenberg, 1975). The E. coli dam methylase was found to be
AB  - responsible for making f1 resistant to endo R.DpnII and sensitive to endo R.DpnI. Endo R.DpnI
AB  - cleaved f1 DNA from dam+ cells at four sites. Additional methylation by enzymes other than the
AB  - dam methylase gave no further cleavage. Endo R.DpnII cleaved f1 DNA from dam- cells also at
AB  - four sites to give restriction fragments identical to those obtained with endo R.DpnI
AB  - cleavage. Thus, the two enzymes are complementary in that they recognize and cleave within the
AB  - same DNA sequence, one if the DNA is methylated, the other if it is unmethylated. DNA duplexes
AB  - containing one methylated strand (dam+) and one unmethylated strand (dam-) were prepared in
AB  - vitro. These methylated hybrids were refractory to endonucleolytic cleavage by both endo
AB  - R.DpnI and endo R.DpnII. Neither enzyme, therefore, appears to make even a single strand break
AB  - at a methylated/unmethylated hybrid site.
ER  -

TY  - JOUR
AU  - Vovis, G.F.
AU  - Zinder, N.D.
TI  - Methylation of f1 DNA by a restriction endonuclease from Escherichia coli B.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 557
EP  - 568
VL  - 95
AB  - Bacteriophage f1 duplex DNA containing hybrid SB sites, the genetic sites which
AB  - confer upon DNA sensitivity to Escherichia coli B-specific restriction and
AB  - modification, were prepared in vitro.  The hybrid SB sites (modified and
AB  - mutant) were tested for their ability to be methylated in vitro by endonuclease
AB  - R.EcoB, the enzyme responsible for both B-specific restriction and modification
AB  - in vivo.  DNA containing hybrid (modified) SB sites can be methylated.  One
AB  - methyl group is added to the DNA per hybrid (modified) SB site.  On the other
AB  - hand, DNA containing hybrid (mutant) SB sites is refractory to modification.
AB  - The nature and the function of the SB site as well as the implications of these
AB  - observations for f1 recombination are discussed.
ER  -

TY  - JOUR
AU  - Vranken, C.
AU  - Deen, J.
AU  - Dirix, L.
AU  - Stakenborg, T.
AU  - Dehaen, W.
AU  - Leen, V.
AU  - Hofkens, J.
AU  - Neely, R.K.
TI  - Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - e50
EP  - e50
VL  - 42
AB  - We demonstrate an approach to optical DNA mapping, which enables near single-molecule
AB  - characterization of whole bacteriophage genomes. Our approach
AB  - uses a DNA methyltransferase enzyme to target labelling to specific sites and
AB  - copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA.
AB  - We achieve a labelling efficiency of approximately 70% with an average labelling
AB  - density approaching one site every 500 bp. Such labelling density bridges the gap
AB  - between the output of a typical DNA sequencing experiment and the long-range
AB  - information derived from traditional optical DNA mapping. We lay the foundations
AB  - for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for
AB  - their ability to direct sequence-specific DNA transalkylation; the first step of
AB  - the DNA labelling process and by optimizing reaction conditions for fluorophore
AB  - coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the
AB  - cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
ER  -

TY  - JOUR
AU  - Vuilleumier, S. et al.
TI  - Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.
JO  - PLoS ONE
PY  - 2009
SP  - E5584
EP  - E5584
VL  - 4
AB  - BACKGROUND: Methylotrophy describes the ability of organisms to grow on
AB  - reduced organic compounds without carbon-carbon bonds. The genomes of two
AB  - pink-pigmented facultative methylotrophic bacteria of the
AB  - Alpha-proteobacterial genus Methylobacterium, the reference species
AB  - Methylobacterium extorquens strain AM1 and the dichloromethane-degrading
AB  - strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS: The 6.88 Mb
AB  - genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid
AB  - and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94
AB  - Mb chromosome and two plasmids. The chromosomes are highly syntenic and
AB  - share a large majority of genes, while plasmids are mostly
AB  - strain-specific, with the exception of a 130 kb region of the strain AM1
AB  - megaplasmid which is syntenic to a chromosomal region of strain DM4. Both
AB  - genomes contain large sets of insertion elements, many of them
AB  - strain-specific, suggesting an important potential for genomic plasticity.
AB  - Most of the genomic determinants associated with methylotrophy are nearly
AB  - identical, with two exceptions that illustrate the metabolic and genomic
AB  - versatility of Methylobacterium. A 126 kb dichloromethane utilization
AB  - (dcm) gene cluster is essential for the ability of strain DM4 to use DCM
AB  - as the sole carbon and energy source for growth and is unique to strain
AB  - DM4. The methylamine utilization (mau) gene cluster is only found in
AB  - strain AM1, indicating that strain DM4 employs an alternative system for
AB  - growth with methylamine. The dcm and mau clusters represent two of the
AB  - chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau
AB  - cluster is flanked by mobile elements, but the dcm cluster disrupts a gene
AB  - annotated as chelatase and for which we propose the name "island
AB  - integration determinant" (iid). CONCLUSION/SIGNIFICANCE: These two genome
AB  - sequences provide a platform for intra- and interspecies genomic
AB  - comparisons in the genus Methylobacterium, and for investigations of the
AB  - adaptive mechanisms which allow bacterial lineages to acquire
AB  - methylotrophic lifestyles.
ER  -

TY  - JOUR
AU  - Vuilleumier, S. et al.
TI  - Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z.
JO  - J. Bacteriol.
PY  - 2012
SP  - 551
EP  - 552
VL  - 194
AB  - Methylomicrobium strains are widespread in saline environments. Here, we report the complete
AB  - genome sequence of Methylomicrobium alcaliphilum 20Z,
AB  - a haloalkaliphilic methanotrophic bacterium, which will provide the basis
AB  - for detailed characterization of the core pathways of both single-carbon
AB  - metabolism and responses to osmotic and high-pH stresses. Final assembly
AB  - of the genome sequence revealed that this bacterium contains a 128-kb
AB  - plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of
AB  - known genome sequence for which a plasmid has been reported.
ER  -

TY  - JOUR
AU  - Vuilleumier, S.
AU  - Nadalig, T.
AU  - Ul-Haque, M.F.
AU  - Magdelenat, G.
AU  - Lajus, A.
AU  - Roselli, S.
AU  - Muller, E.E.
AU  - Gruffaz, C.
AU  - Barbe, V.
AU  - Medigue, C.
AU  - Bringel, F.
TI  - Complete Genome Sequence of the Chloromethane-Degrading Hyphomicrobium sp. Strain MC1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5035
EP  - 5036
VL  - 193
AB  - Hyphomicrobium sp. strain MC1 is an aerobic methylotroph originally isolated from industrial
AB  - sewage. This prosthecate bacterium was the first
AB  - strain reported to grow with chloromethane as the sole carbon and energy
AB  - source. Its genome, consisting of a single 4.76-Mb chromosome, is the
AB  - first for a chloromethane-degrading bacterium to be formally reported.
ER  -

TY  - JOUR
AU  - Vyle, J.S.
AU  - Connolly, B.A.
AU  - Kemp, D.
AU  - Cosstick, R.
TI  - Sequence- and strand-specific cleavage in oligodeoxyribonucleotides and DNA containing 3'-thiothymidine.
JO  - Biochemistry
PY  - 1992
SP  - 3012
EP  - 3018
VL  - 31
AB  - Oligonucleotides containing a 3'-thiothymidine residue (T3's) at the cleavage site for the
AB  - EcoRV restriction endonuclease (between the central T and A residues of the sequence GATATC)
AB  - have been prepared on an automated DNA synthesizer using 5'-O-monomethoxytritylthymidine
AB  - 3'-S-(2-cyanoethyl N,N-di-isopropylphosphorothioamidite).  The self-complementary sequence
AB  - GACGAT3'sATCGTC was completely resistant to cleavage by EcoRV, while the heteroduplex
AB  - composed of 5'-TCTGAT3'sATCCTC and 5'-GAGGATATCAGA (duplex 4) was cleaved only in the
AB  - unmodified strand (5'-GAGGATATCAGA).  In contrast, strands containing a
AB  - 3'-S-phosphorothiolate linkage could be chemically cleaved specifically at this site with
AB  - Ag+.  A T3's residue has also been incorporated in the (-) strand of double-stranded closed
AB  - circular (RF IV) M13mp18 DNA at the cleavage site of a unique EcoRV recognition sequence by
AB  - using 5'-pCGAGCTCGAT3'sATCGTAAT as a primer for polymerization on the template (+) strand of
AB  - M13mp18 DNA.  On treatment of this substrate with EcoRV, only one strand was cleaved to
AB  - produce the RFII or nicked DNA.  Taken in conjunction with the cleavage studies on the
AB  - oligonucleotides, this result demonstrates that the 3'-S-phosphorothiolate linkage is
AB  - resistant to scission by EcoRV.  Additionally, the phosphorothiolate-containing strand of the
AB  - M13mp18 DNA could be cleaved specifically at the point of modification using iodine in aqueous
AB  - pyridine.  The combination of enzymatic and chemical techniques provides, for the first time,
AB  - a demonstrated method for the sequence-specific cleavage of either the (+) or (-) strand.
ER  -

TY  - JOUR
AU  - Waalwijk, C.
AU  - Flavell, R.A.
TI  - MspI, an isochizomer of HpaII which cleaves both unmethylated and methylated HpaII sites.
JO  - Nucleic Acids Res.
PY  - 1978
SP  - 3231
EP  - 3236
VL  - 5
AB  - The cleavage of DNA by restriction endonucleases HpaII and HapII is prevented
AB  - by the presence of a 5-methyl group at the internal C residue of its
AB  - recognition sequence CCGG.  MspI, an isoschizomer of HpaII available from New
AB  - England Biolabs, cleaves DNA irrespective of the presence of a methyl group at
AB  - this position.  This enzyme cleaves DNA from Haemophilus parainfluenzae and
AB  - Haemophilus aphrophilus readily while HpaII and HapII cannot degrade these
AB  - DNAs.  Practically all HpaII sites in mammalian sperm DNA are also protected by
AB  - methylation at the internal C position since HpaII and HapII barely cleave this
AB  - DNA (average molecular weight 40 kb).  MspI, however, cleaves the DNA to an
AB  - average size of about 5 kb.
ER  -

TY  - JOUR
AU  - Wachino, J.
AU  - Shibayama, K.
AU  - Kurokawa, H.
AU  - Kimura, K.
AU  - Yamane, K.
AU  - Suzuki, S.
AU  - Shibata, N.
AU  - Ike, Y.
AU  - Arakawa, Y.
TI  - Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse  aminoglycosides.
JO  - Antimicrob. Agents Chemother.
PY  - 2007
SP  - 4401
EP  - 4409
VL  - 51
AB  - We have isolated a multiple-aminoglycoside-resistant Escherichia coli strain, strain ARS3, and
AB  - have been the first to identify a novel plasmid-mediated 16S
AB  - rRNA methyltransferase, NpmA. This new enzyme shared a relatively low level of
AB  - identity (30%) to the chromosomally encoded 16S rRNA methyltransferase (KamA) of
AB  - Streptomyces tenjimariensis, an actinomycete aminoglycoside producer. The
AB  - introduction of a recombinant plasmid carrying npmA could confer on E. coli
AB  - consistent resistance to both 4,6-disubstituted 2-deoxystreptamines, such as
AB  - amikacin and gentamicin, and 4,5-disubstituted 2-deoxystreptamines, including
AB  - neomycin and ribostamycin. The histidine-tagged NpmA elucidated methyltransferase
AB  - activity against 30S ribosomal subunits but not against 50S subunits and the
AB  - naked 16S rRNA molecule in vitro. We further confirmed that NpmA is an adenine
AB  - N-1 methyltransferase specific for the A1408 position at the A site of 16S rRNA.
AB  - Drug footprinting data indicated that binding of aminoglycosides to the target
AB  - site was apparently interrupted by methylation at the A1408 position. These
AB  - observations demonstrate that NpmA is a novel plasmid-mediated 16S rRNA
AB  - methyltransferase that provides a panaminoglycoside-resistant nature through
AB  - interference with the binding of aminoglycosides toward the A site of 16S rRNA
AB  - through N-1 methylation at position A1408.
ER  -

TY  - JOUR
AU  - Wachsman, J.T.
TI  - DNA methylation and the association between genetic and epigenetic changes: relation to carcinogenesis.
JO  - Mutat. Res.
PY  - 1997
SP  - 1
EP  - 8
VL  - 375
AB  - This paper examines the relationship between DNA mutagenic lesions, DNA methylation and the
AB  - involvement of these changes in the process of carcinogenesis.  Many types of DNA damage
AB  - (oxidative lesions, alkylation of bases, abasic sites, photodimers, etc.) interfere with the
AB  - ability of mammalian cell  DNA to be methylated at CpG dinucleotides by DNA-methyltransferases
AB  - (DNA-MTases).  This can result in altered patterns in the distribution of 5-methylcytosine
AB  - (5MeC) residues at CpG sites.  Methylation of DNA is an epigenetic change that by definition
AB  - is heritable, can result in changes in chromatin structure, and is often accompanied by
AB  - modified patterns of gene expression.  The presence of 5MeC in DNA, as well as oxidative
AB  - stress induced by the free radical nitric oxide, can interfere with the repair of alkylation
AB  - damage, thereby increasing the level fo potentially mutagenic lesions. CpG sites in DNA
AB  - represent mutational hotspots, with both the presence of 5MeC in DNA and the catalytic
AB  - activity of DNA-MTases being intrinsically mutagenic.  The process of carcinogenesis has
AB  - frequently been associated with an increased expression of DNA-MTase activity, accompanied by
AB  - either hypermethylation or hypomethylation of target cell (progenitor tumor cell) DNA.  In
AB  - addition, there is evidence that overexpression of DNA-MTase activity could result in
AB  - increased cytosine methylation at non-CpG sites.  A variety of chemicals can alter the extent
AB  - of DNA methylation in mammalian cells.  These include inhibitors of topisomerase II, as well
AB  - as inhibitors of DNA synthesis, microtubule formation, histone deacetylation,
AB  - transmethylation, etc.  Genetic and epigenetic changes in DNA have a profound influence on one
AB  - another and could play a major role in the process of carcinogenesis, by modulating both the
AB  - extent and the pattern of gene expression.
ER  -

TY  - JOUR
AU  - Wada, T.
AU  - Hijikata, M.
AU  - Maeda, S.
AU  - Hang, N.T.L.
AU  - Thuong, P.H.
AU  - Hoang, N.P.
AU  - Hung, N.V.
AU  - Keicho, N.
TI  - Complete Genome Sequence of a Mycobacterium tuberculosis Strain Belonging to the  East African-Indian Family in the Indo-Oceanic Lineage, Isolated in Hanoi,  Vietnam.
JO  - Genome Announcements
PY  - 2017
SP  - e00509
EP  - e00517
VL  - 5
AB  - The East African-Indian (EAI) family of Mycobacterium tuberculosis is an endemic  group mainly
AB  - observed in Southeast Asia. Here, we report the complete genome
AB  - sequence of an M. tuberculosis strain isolated as a member of the EAI family in
AB  - Hanoi, Vietnam, a country with a high incidence of tuberculosis.
ER  -

TY  - JOUR
AU  - Wada, T.
AU  - Hijikata, M.
AU  - Maeda, S.
AU  - Hang, N.T.L.
AU  - Thuong, P.H.
AU  - Hoang, N.P.
AU  - Hung, N.V.
AU  - Keicho, N.
TI  - Complete Genome Sequences of Three Representative Mycobacterium tuberculosis Beijing Family Strains Belonging to Distinct Genotype Clusters in Hanoi, Vietnam, during 2007 to 2009.
JO  - Genome Announcements
PY  - 2017
SP  - e00510
EP  - e00517
VL  - 5
AB  - We present here three complete genome sequences of Mycobacterium tuberculosis Beijing family
AB  - strains isolated in Hanoi, Vietnam. These three strains were
AB  - selected from major genotypic clusters (15-MIRU-VNTR) identified in a previous
AB  - population-based study. We emphasize their importance and potential as reference
AB  - strains in this Asian region.
ER  -

TY  - JOUR
AU  - Wada, Y.
TI  - Physiological functions of plant DNA methyltransferases.
JO  - Plant Biotechnol.
PY  - 2005
SP  - 71
EP  - 80
VL  - 22
AB  - Epigenetic regulation is defined as mechanisms that control gene expression without altering
AB  - base sequences.  Cytosine methylation, chromatin remodeling, and modifications at the
AB  - N-termini of core histones are key factors in this regard.  Epigenetic modifications are found
AB  - throughout the eukaryotes, suggesting that they developed at an early stage in biological
AB  - evolution, although actual molecular mechanisms show considerable variation among species.  In
AB  - particular, plants are unique in establishment and maintenance of epigenetic states, as
AB  - examplified by species-specific enzymes that catalyze DNA methylation.  Since the function and
AB  - diversity of DNA methyltransferases in individual species are not fully understood, I here
AB  - summarize recent findings in plant epigenetics, focusing on DNA methyltransferases classified
AB  - into three major groups.  Their possible biological functions are also discussed with
AB  - reference to histone modification and chromatin remodeling.
ER  -

TY  - JOUR
AU  - Wada, Y.
TI  - Separate analysis of complementary strands of restriction enzyme-digested DNA.  An application of restriction fragment mass mapping by matrix-assisted laser desorption/ionization mass spectrometry.
JO  - J. Mass Spectrom.
PY  - 1998
SP  - 187
EP  - 192
VL  - 33
AB  - Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry   MALDI/TOF-MS)
AB  - of a restriction endonuclease digest determines the molecular mass of PCR-amplified DNA more
AB  - easily than measurement of undigested DNA. With this method, a 664 bp region from the FAS gene
AB  - could be analyzed and a two-nucleotide deletion in the L1CAM gene was detected in a
AB  - restriction fragment of 105 nucleotides. Furthermore, the analysis of smaller fragments
AB  - allowed separate detection of single-stranded oligonucleotides comprising individual digested
AB  - fragments. This mixture analysis of restriction enzyme digests improves the resolution,
AB  - sensitivity and accuracy of MALDI/TOF-MS of DNA and is thus expected to facilitate its
AB  - application to genetic diagnosis.
ER  -

TY  - JOUR
AU  - Wada, Y.
AU  - Ohya, H.
AU  - Yamaguchi, Y.
AU  - Koizumi, N.
AU  - Sano, H.
TI  - Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 42386
EP  - 42393
VL  - 278
AB  - In plant DNA, cytosines in symmetric CpG and CpNpG (N is A, T, or C) are thought to be
AB  - methylated by DNA methyltransferases, MET1 and CMT3,
AB  - respectively. Cytosines in asymmetric CpNpN are also methylated, and
AB  - genetic analysis has suggested the responsible enzyme to be domains
AB  - rearranged methyltransferase (DRM). We cloned a tobacco cDNA, encoding a
AB  - novel protein consisting of 608 amino acids, that resembled DRMs found in
AB  - maize and Arabidopsis and designated this as NtDRM1. The protein could be
AB  - shown to be localized exclusively in the nucleus and exhibit methylation
AB  - activity toward unmethylated synthetic as well as native DNA samples upon
AB  - expression in Sf9 insect cells. It also methylated hemimethylated DNA, but
AB  - the activity was lower than that for unmethylated substrates. Methylation
AB  - mapping of a 962-bp DNA, treated with NtDRM1 in vitro, directly
AB  - demonstrated methylation of approximately 70% of the cytosines in
AB  - methylatable CpNpN and CpNpG sequences but only 10% in CpG. Further
AB  - analyses indicated that the enzyme apparently non-selectively methylates
AB  - any cytosines except in CpG, regardless of the adjacent nucleotide at both
AB  - 5' and 3' ends. Transcripts of NtDRM1 ubiquitously accumulated in all
AB  - tissues and during the cell cycle in tobacco cultured BY2 cells. These
AB  - results indicate that NtDRM1 is a de novo cytosine methyltransferase,
AB  - which actively excludes CpG substrate.
ER  -

TY  - JOUR
AU  - Wafula, E.N.
AU  - Brinks, E.
AU  - Becker, B.
AU  - Huch, M.
AU  - Trierweiler, B.
AU  - Mathara, J.M.
AU  - Oguntoyinbo, F.A.
AU  - Cho, G.S.
AU  - Franz, C.M.A.P.
TI  - Draft Genome Sequence of Lactobacillus fermentum BFE 6620, a Potential Starter Culture for African Vegetable Foods, Isolated from Fermented Cassava.
JO  - Genome Announcements
PY  - 2017
SP  - e00801
EP  - e00817
VL  - 5
AB  - We report the draft genome sequence of Lactobacillus fermentum BFE 6620 from fermented cassava
AB  - used as a potential starter culture for African vegetable
AB  - fermentation. Sequence analysis showed the assembled genome size to be 1,982,893
AB  - bp, encoding a predicted total of 2,003 protein-coding genes, 14 rRNAs, 54 tRNAs,
AB  - and 3 noncoding RNAs (ncRNAs).
ER  -

TY  - JOUR
AU  - Wagenfuhr, K.
AU  - Pieper, S.
AU  - Mackeldanz, P.
AU  - Linscheid, M.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Structural domains in the type III restriction endonuclease EcoP15I: Characterization by limited proteolysis, mass spectrometry and insertional mutagenesis.
JO  - J. Mol. Biol.
PY  - 2007
SP  - 93
EP  - 102
VL  - 366
AB  - The Type III restriction endonuclease EcoP15I forms a hetero-oligomeric enzyme complex that
AB  - consists of two modification (Mod) subunits and two
AB  - restriction (Res) subunits. Structural data on Type III restriction
AB  - enzymes in general are lacking because of their remarkable size of more
AB  - than 400 kDa and the laborious and low-yield protein purification
AB  - procedures. We took advantage of the EcoP15I-overexpressing vector pQEP15
AB  - and affinity chromatography to generate a quantity of EcoP15I high enough
AB  - for comprehensive proteolytic digestion studies and analyses of the
AB  - proteolytic fragments by mass spectrometry. We show here that in the
AB  - presence of specific DNA the entire Mod subunit is protected from trypsin
AB  - digestion, whereas in the absence of DNA stable protein domains of the Mod
AB  - subunit were not detected. In contrast, the Res subunit is comprised of
AB  - two trypsin-resistant domains of approximately 77-79 kDa and 27-29 kDa,
AB  - respectively. The cofactor ATP and the presence of DNA, either specific or
AB  - unspecific, are important stabilizers of the Res subunit. The large
AB  - N-terminal domain of Res contains numerous functional motifs that are
AB  - predicted to be involved in ATP-binding and hydrolysis and/or DNA
AB  - translocation. The C-terminal small domain harbours the catalytic center.
AB  - Based on our data, we conclude that both structural Res domains are
AB  - connected by a flexible linker region that spans 23 amino acid residues.
AB  - To confirm this conclusion, we have investigated several EcoP15I enzyme
AB  - mutants obtained by insertion mutagenesis in and around the predicted
AB  - linker region within the Res subunit. All mutants tolerated the genetic
AB  - manipulation and did not display loss of function or alteration of the DNA
AB  - cleavage position.
ER  -

TY  - JOUR
AU  - Wagner, E.
AU  - Schmitz, G.G.
AU  - Kaluza, K.
AU  - Jarsch, M.
AU  - Gotz, F.
AU  - Kessler, C.
TI  - BmyI, a novel SduI isoschizomer from Bacillus mycoides recognizing 5'-GDGCH/C-3'.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3088
EP  - 3088
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Wah, D.A.
TI  - Structural study of the type IIs restriction endonuclease FokI.
JO  - Ph.D. Thesis, Columbia University
PY  - 1998
SP  - 1
EP  - 108
AB  - This work presents the first three-dimensional structures of a type IIs restriction
AB  - endonuclease.  The type IIs restriction endonucleases are an unusual class of enzymes that
AB  - recognize a specific DNA sequence and cleave DNA non-specifically a short distance away from
AB  - that sequence.  FokI, from Flavobacterium okeanokoites, is a type IIs restriction endonuclease
AB  - that binds the cognate sequence 5'-GGATG-3' and cleaves DNA phosphodiester groups 9 base
AB  - pairs away on this strand and 13 base pairs away on the complementary strand.  Because of its
AB  - unusual bipartite nature, FokI has been used to create artificial enzymes with new DNA-binding
AB  - specificities.  The three-dimensional structures of the complete FokI enzyme in complex with
AB  - DNA and without DNA have been determined by X-ray crystallography at 2.8A and 2.3A resolution,
AB  - respectively.  As anticipated, the enzyme contains amino- and carboxy-terminal domains
AB  - corresponding to the DNA-recognition and cleavage functions.  The recognition domain is made
AB  - of three smaller subdomains that are evolutionarily related to the helix-turn-helix containing
AB  - DNA-binding domain of the catabolite gene activator protein CAP.  However, the CAP core has
AB  - been extensively embellished in the first two subdomains while in the third subdomain it has
AB  - been co-opted for protein-protein interactions.  Surprisingly, the cleavage domain resembles a
AB  - monomer of the type II restriction endonuclease BamHI and contains only a single catalytic
AB  - center.  Unexpectedly, the cleavage domain is sequestered in a "piggyback" fashion by the
AB  - recognition domain until its DNA cleavage activity is required.  The structure of FokI in the
AB  - absence of DNA reveals a dimer.  In corroboration with binding data, a model is proposed in
AB  - which DNA cleavage requires the dimerization of two FokI molecules, each recognizing an
AB  - independent FokI cognate sequence.  Taken together, the structures have implications for the
AB  - evolution of helix-turn-helix domains, suggest a novel mechanism of nuclease activation, and
AB  - provide a framework for the design of chimeric enzymes with altered specificities.
ER  -

TY  - JOUR
AU  - Wah, D.A.
TI  - Structural study of the type IIs restriction endonuclease FokI.
JO  - Diss. Abstr.
PY  - 1998
SP  - 6439B
EP  - 6439B
VL  - 58
AB  - This work represents the first three-dimensional structures of a type IIs restriction
AB  - endonuclease.  The type IIs restriction endonucleases are an unusual class of enzymes that
AB  - recognize a specific DNA sequence and cleave DNA non-specifically a short distance away from
AB  - that sequence.  FokI, from Flavobacterium okeanokoites, is a type IIs restriction endonuclease
AB  - that binds the cognate sequence 5'-GGATG-3' and cleaves DNA phosphodiester groups 9 base
AB  - pairs away on this strand and 13 base pairs away on the complementary strand.  Because of its
AB  - unusual bipartite nature, FokI has been used to create artificial enzymes with new DNA-binding
AB  - specificities.  The three-dimensional structures of the complete FokI enzyme in complex with
AB  - DNA and without DNA have been determined by X-ray crystallography at 2.8 and 2.3 angstroms
AB  - resolution, respectively.  As anticipated, the enzyme contains amino- and carboxy-terminal
AB  - domains corresponding to the DNA-recognition and cleavage functions.  The recognition domain
AB  - is made of three smaller subdomains that are evolutionarily related to the helix-turn-helix
AB  - containing DNA-binding domain of the catabolite gene activator protein CAP.  However, the CAP
AB  - core has been extensively embellished in the first two subdomains while in the third subdomain
AB  - it has been co-opted for protein-protein interactions.  Surprisingly, the cleavage domain
AB  - resembles a monomer of the type II restriction endonuclease BamHI and contains only a single
AB  - catalytic center.  Unexpectedly, the cleavage domain is sequestered in a "piggyback" fashion
AB  - by the recognition domain until its DNA cleavage activity is required.  The structure of FokI
AB  - in the absence of DNA reveals a dimer.  In corroboration with binding data, a model is
AB  - proposed in which DNA cleavage requires the dimerization of two FokI molecules, each
AB  - recognizing an independent FokI cognate sequence.  Taken together, the structures have
AB  - implications for the evolution of helix-turn-helix domains, suggest a novel mechanism of
AB  - nuclease activation, and provide a framework for the design of chimeric enzymes with altered
AB  - specificities.
ER  -

TY  - JOUR
AU  - Wah, D.A.
AU  - Bitinaite, J.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Structure of FokI has implications for DNA cleavage.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1998
SP  - 10564
EP  - 10569
VL  - 95
AB  - FokI is a member of an unusual class of restriction enzymes that recognize a specific DNA
AB  - sequence and cleave nonspecifically a short distance away from that sequence.  FokI consists
AB  - of an N-terminal DNA recognition domain and a C-terminal cleavage domain.  The bipartite
AB  - nature of FokI has led to the development of artificial enzymes with novel specificities.  We
AB  - have solved the structure of FokI to 2.3 A resolution.  The structure reveals a dimer, in
AB  - which the dimerization interface is mediated by the cleavage domain.  Each monomer has an
AB  - overall conformation similar to that found in the FokI-DNA complex, with the cleavage domain
AB  - packing alongside the DNA recognition domain.  In corroboration with the cleavage data
AB  - presented in the accompanying paper in this issue of Proceedings, we propose a model for FokI
AB  - DNA cleavage that requires the dimerization of FokI on DNA to cleave both DNA strands.
ER  -

TY  - JOUR
AU  - Wah, D.A.
AU  - Hirsch, J.A.
AU  - Dorner, L.F.
AU  - Schildkraut, I.
AU  - Aggarwal, A.K.
TI  - Structure of the multimodular endonuclease FokI bound to DNA.
JO  - Nature
PY  - 1997
SP  - 97
EP  - 100
VL  - 388
AB  - FokI is a member of an unusual class of bipartite restriction enzymes that recognize a
AB  - specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence.
AB  - Because of its unusual bipartite nature, FokI has been used to create artificial enzymes with
AB  - new specificities.  We have determined the crystal structure at 2.8A resolution of the
AB  - complete FokI enzyme bound to DNA.  As anticipated, the enzyme contains amino- and
AB  - carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions,
AB  - respectively.  The recognition domain is made of three smaller subdomains (D1, D2 and D3)
AB  - which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the
AB  - catabolite gene activator protein CAP.  The CAP core has been extensively embellished in the
AB  - first two subdomains, whereas in the third subdomain it has been co-opted for protein-protein
AB  - interactions.  Surprisingly, the cleavage domain contains only a single catalytic center,
AB  - raising the question of how monomeric FokI manages to cleave both DNA strands.  Unexpectedly,
AB  - the cleavage domain is sequestered in a 'piggyback' fashion by the recognition domain.  The
AB  - structure suggests a new mechanism for nuclease activation and provides a framework for the
AB  - design of chimeric enzymes with altered specificities.
ER  -

TY  - JOUR
AU  - Wahab, T.
AU  - Ferrari, S.
AU  - Lindberg, M.
AU  - Backman, S.
AU  - Kaden, R.
TI  - Draft Genome Sequences of Brucella suis Biovar 4 Strain NCTC 10385, Brucella ceti Strain NCTC 12891T, Brucella inopinata Strain CAMP 6436T, and Brucella neotomae  Strain ATCC 23459T.
JO  - Genome Announcements
PY  - 2014
SP  - e00783
EP  - e00714
VL  - 2
AB  - With the aim of developing quantitative PCR methods for the detection and differentiation of
AB  - Brucella species, the genomes of Brucella ceti, Brucella
AB  - inopinata, Brucella netotomae, and Brucella suis biovar 4 were sequenced and
AB  - analyzed.
ER  -

TY  - JOUR
AU  - Wahnon, D.C.
AU  - Shier, V.K.
AU  - Benkovic, S.J.
TI  - Mechanism-based inhibition of an essential bacterial adenine DNA methyltransferase: Rationally designed antibiotics.
JO  - J. Am. Chem. Soc.
PY  - 2001
SP  - 976
EP  - 977
VL  - 123
AB  - The emergence of bacteria resistant to available antibiotics has caused great concern in the
AB  - medical community and has created a need for the discovery of novel antibiotic agents.  In the
AB  - past, new antibiotics have been discovered by the random screening of natural products and the
AB  - subsequent identification of the target protein.  In addition to this drug discovery method,
AB  - the recent advances in genome sequencing have made it possible to envision a complementary
AB  - drug discovery method in which a bacterial enzyme target is first identified and new
AB  - antibiotic compounds are discovered from the targeted inhibition of this enzyme.  Successful
AB  - antibiotics would be inhibitors of an essential bacterial enzyme that is unique to bacteria
AB  - and has no mammalian homologue.  Here we report on the progress toward the development of
AB  - small-molecule selective inhibitors of an essential bacterial N-6 adenine DNA
AB  - methyltransferase, using a mechanism-based multisubstrate adduct approach and demonstrate the
AB  - inhibition using CcrM (cell cycle regulated DNA MTase) from the pathogenic Brucella abortus.
ER  -

TY  - JOUR
AU  - Wailan, A.M.
AU  - Paterson, D.L.
AU  - Caffery, M.
AU  - Sowden, D.
AU  - Sidjabat, H.E.
TI  - Draft Genome Sequence of NDM-5-Producing Escherichia coli Sequence Type 648 and Genetic Context of blaNDM-5 in Australia.
JO  - Genome Announcements
PY  - 2015
SP  - e00194
EP  - e00115
VL  - 3
AB  - We report here the draft genome sequence of uropathogenic Escherichia coli sequence type 648
AB  - (ST648) possessing blaNDM-5 from a 55-year-old female in
AB  - Australia with a history of travel to India. The plasmid-mediated blaNDM-5 was in
AB  - a genetic context nearly identical to that of the GenBank entry of an IncX3
AB  - blaNDM-5 plasmid previously reported from India (Klebsiella pneumoniae MGR-K194).
ER  -

TY  - JOUR
AU  - Waite-Rees, P.A.
AU  - Keating, C.J.
AU  - Moran, L.S.
AU  - Slatko, B.E.
AU  - Hornstra, L.J.
AU  - Benner, J.S.
TI  - Characterization and expression of the Escherichia coli Mrr restriction system.
JO  - J. Bacteriol.
PY  - 1991
SP  - 5207
EP  - 5219
VL  - 173
AB  - The mrr gene of Escherichia coli K-12 is involved in the acceptance of foreign DNA which is
AB  - modified.  The introduction of plasmids carrying the HincII, HpaI, and TaqI R and M genes is
AB  - severely restricted in E. coli strains that are Mrr+. A 2-kb EcoRI fragment from the plasmid
AB  - pBg3 (B. Sain and N.E. Murray, Mol. Gen. Genet. 180:35-46, 1980) was cloned.  The resulting
AB  - plasmid restores Mrr function to mrr strains of E. coli.  The boundaries of the mrr gene were
AB  - determined from an analysis of subclones, and plasmids with a functional mrr gene produce a
AB  - polypeptide of 33.5 kDa.  The nucleotide sequence of the entire fragment was determined; in
AB  - addition to mrr, it includes two open reading frames, one of which encodes part of the hsdR.
AB  - By using Southern blot analysis, E. coli RR1 and HB101 were found to lack the region
AB  - containing mrr. The acceptance of various cloned methylases in E. coli containing the cloned
AB  - mrr gene was tested.  Plasmid constructs containing the AccI, CviRI, HincII, HinfI (HhaII),
AB  - HpaI, NlaIII, PstI, and TaqI N6-adenine methylases and SssI and HhaI C5-cytosine methylases
AB  - were found to be restricted.  Plasmid constructs containing 16 other adenine methylases and 12
AB  - cytosine methylases were not restricted.  No simple consensus sequence causing restriction has
AB  - been determined.  The Mrr protein has been overproduced, an antibody has been prepared, and
AB  - the expression of mrr under various conditions has been examined. The use of mrr strains of E.
AB  - coli is suggested for the cloning of N6-adenine and C5-cytosine methyl-containing DNA.
ER  -

TY  - JOUR
AU  - Wajima, T.
AU  - Sabui, S.
AU  - Kano, S.
AU  - Ramamurthy, T.
AU  - Chatterjee, N.S.
AU  - Hamabata, T.
TI  - Entire sequence of the colonization factor coli surface antigen 6-encoding plasmid pCss165 from an enterotoxigenic Escherichia coli clinical isolate.
JO  - Plasmid
PY  - 2013
SP  - 343
EP  - 352
VL  - 70
AB  - Coli surface antigen 6 (CS6) is one of the most prevalent colonization factors among
AB  - enterotoxigenic Escherichia coli (ETEC) isolated in developing countries. Although it is known
AB  - that CS6 is encoded by a plasmid, there are no reports on the sequence analysis of the
AB  - CS6-encoding plasmid or genes exhibiting similar behavior to CS6. Here, we report the
AB  - isolation of the CS6-encoding plasmid, pCss165Kan, from 4266 DcssB::kanamycin (Km) and its
AB  - complete nucleotide sequence. This plasmid consisted of 165,311 bp and 222 predicted coding
AB  - sequences. Remarkably, there were many insertion sequence (IS) elements, which comprised 24.4%
AB  - of the entire sequence. Virulence-associated genes such as heat-stable enterotoxin, homologues
AB  - of ATP-binding cassette transporter in enteroaggregative E. coli (EAEC), and ETEC
AB  - autotransporter A were also present, although the ETEC autotransporter A gene was disrupted by
AB  - the integration of IS629. We found that 2 transcriptional regulators belonging to the AraC
AB  - family were not involved in CS6 expression. Interestingly, pCss165 had conjugative transfer
AB  - genes, as well as 3 toxin-antitoxin
AB  - systems that potentially exclude other plasmid-free host bacteria. These genes might be
AB  - involved in the prevalence of CS6 among ETEC isolates
ER  -

TY  - JOUR
AU  - Wakefield, R.I.D.
AU  - Smith, B.O.
AU  - Nan, X.
AU  - Free, A.
AU  - Soteriou, A.
AU  - Uhrin, D.
AU  - Bird, A.P.
AU  - Barlow, P.N.
TI  - The solution structure of the domain from MeCP2 that binds to methylated DNA.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1055
EP  - 1065
VL  - 291
AB  - MeCP2 is an abundant mammalian protein that binds methylated CpG (mCpG) sequences within
AB  - double-stranded DNA, represses transcription by recruiting histone deacetylases, and is
AB  - essential for embryonic development. It is one of a family of proteins which mediate the
AB  - biological consequences of DNA methylation. These proteins each possess a sequence motif of
AB  - about 70 residues which, in MeCP2, form a domain necessary and sufficient for binding to mCpG.
AB  - The solution structure of the mCpG-binding domain (MBD) from MeCP2 has been solved and the
AB  - DNA-binding surface of the domain mapped using NMR spectroscopy. Residues 95-162 of MeCP2
AB  - adopt a novel fold forming a wedge-shaped structure. An N-terminal four-stranded antiparallel
AB  - beta-sheet forms one face of the wedge, while the other face is formed mainly by a C-terminal
AB  - helical region. The thin end of the wedge is extended by a long loop between beta-strands B
AB  - and C containing many basic residues. The B-C loop together with residues in strands B, C and
AB  - D, and at the N terminus of the alpha-helix, appears to form an interface with methylated DNA.
AB  - Unstructured residues at the NH2 terminus of the domain are also involved in formation of the
AB  - complex. The presence of numerous arginine and lysine side-chains on the DNA-binding surface
AB  - of MBD is consistent with the requirement for the mCpG site to be flanked by non-specific
AB  - sequences of base-pairs. The absence of symmetry in the domain implies that recognition does
AB  - not exploit the symmetry of the binding site. A conserved hydrophobic pocket containing the
AB  - side-chains of Tyr123 and Ile125 on the positively charged beta-sheet face is a candidate for
AB  - the region of contact with the methyl-groups of the modified cytosine residues.
ER  -

TY  - JOUR
AU  - Walczak, A.B.
AU  - Yee, N.
AU  - Young, L.Y.
TI  - Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated  from a pyrite rock outcrop in New Jersey.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 6
EP  - 6
VL  - 13
AB  - This genome report describes the draft genome and physiological characteristics of Bosea sp.
AB  - WAO (=DSM 102914), a novel strain of the genus Bosea in the family
AB  - Bradyrhizobiaceae. Bosea sp. WAO was isolated from pulverized pyritic shale
AB  - containing elevated levels of arsenic. This aerobic, gram negative microorganism
AB  - is capable of facultative chemolithoautotrophic growth under aerobic conditions
AB  - by oxidizing the electron donors arsenite, elemental sulfur, thiosulfate,
AB  - polysulfide, and amorphous sulfur. The draft genome is of a single circular
AB  - chromosome 6,125,776 bp long consisting of 21 scaffolds with a G + C content of
AB  - 66.84%. A total 5727 genes were predicted of which 5665 or 98.92% are
AB  - protein-coding genes and 62 RNA genes. We identified the genes aioA and aioB,
AB  - which encode the large and small subunits of the arsenic oxidase respectively. We
AB  - also identified the genes for the complete sulfur oxidation pathway sox which is
AB  - used to oxidize thiosulfate to sulfate.
ER  -

TY  - JOUR
AU  - Walder, R.
AU  - Walder, J.
AU  - Donelson, J.
TI  - The DNA Sequence and Organization of the PstI Restriction-Modification Genes.
JO  - Fed. Proc.
PY  - 1981
SP  - 1647
EP  - 1647
VL  - 40
AB  - We have determined the sequence of a 4000 base pair DNA fragment from P. stuartii 164 that
AB  - contains the genes for the PstI restriction-modification system.  The cloning and expression
AB  - of these genes in E. coli and their re-introduction into P. stuartii 164 was reported earlier
AB  - (Fed. proc. 39 (6) 1413, (198); Proc. Natl. Acad. Sci., in press).  Within the sequence, two
AB  - large open reading frames were identified; one corresponding to the restriction enzyme, the
AB  - other to the modification methylase as determined by site directed mutagenesis and subcloning
AB  - experiments.  The genes are encoded on opposite DNA strands, unlike the two other
AB  - restriction-modification systems that have been studied, HhaII and EcoRI, in which the two
AB  - genes are colinear on the same strand (Fed. Proc. 39 (6) 946, (1980); Fed. Proc. 39 (6) 1415,
AB  - 91980)).  This rules out the possibility, at least in this system, that the two genes are
AB  - expressed on a polycistronic transcript.  The locations of the putative promoters for the two
AB  - genes corresponds well with the sites of initiation of transcription mapped in vitro.  The
AB  - 4000 base pair fragment is now being used to study the control of expression of these two
AB  - genes.
ER  -

TY  - JOUR
AU  - Walder, R.Y.
TI  - The cloning and sequence organization of the PstI restriction-modification system.
JO  - Ph.D. Thesis
PY  - 1984
SP  - 1
EP  - 228
AB  - The genes for the type II restriction and modification enzymes of the bacterium Providencia
AB  - stuartii 164, were cloned and expressed in the Escherichia coli strain HB101.  The two genes
AB  - are closely linked and are located within a 4.0 kilobase DNA region.  The complete nucleotide
AB  - sequence of the 4.0 kilobase fragment was determined.  Two large open reading frames were
AB  - identified within the sequence and were ascribed to the restriction endonuclease (PstI) and
AB  - the modification (methylase) enzyme by the analysis of a series of deletion and insertion
AB  - mutants.  The two genes are encoded on opposite DNA strands, and hence must be transcribed
AB  - from separate promoters rather than as a polycistronic message.  The sequence of the first ten
AB  - amino acids of the restriction endonuclease was determined by sequential Edman degradation of
AB  - the purified protein, permitting the alignment of the polypeptide with the DNA sequence.  The
AB  - amino terminus of the modification enzyme was established by sequential Edman degradation of
AB  - the protein synthesized in bacterial minicells with different radiolabeled amino acids.  The
AB  - initiation codons of the two genes are separated by 130 base pairs.  The deduced amino acid
AB  - sequences indicate that the restriction endonuclease contains 326 amino acids with a
AB  - calculated molecular weight of 37,370; the modification enzyme is composed of 507 amino acids
AB  - with a calculated molecular weight of 56,830.  There is no significant homology between the
AB  - two proteins at the level of the primary structure.  Antibody raised against the purified
AB  - restriction endonuclease did not immunoprecipitate the modification enzyme.  The transcription
AB  - initiation sites were mapped using mung bean nuclease.  Both of the transcripts begin with
AB  - adenosine.  The initiation sites are separated by only 70 base pairs.  This close proximity
AB  - requires that the promoter sites for the two divergent genes overlap.  Dnase I protection
AB  - experiments show a higher affinity of E. coli RNA polymerase for the methylase promoter than
AB  - for the restriction enzyme promoter.  The expression of the PstI restriction and modification
AB  - genes was also examined in bacteriophage lambda and in yeast.
ER  -

TY  - JOUR
AU  - Walder, R.Y.
AU  - Hartley, J.L.
AU  - Donelson, J.E.
AU  - Walder, J.A.
TI  - Cloning of the PstI restriction-modification system.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 217
EP  - 226
VL  - 1
AB  - I. Introduction II. Selection and characterization of clones carrying the PstI
AB  - restriction-modification system III. Transformation of P. stuartii 164:
AB  - Construction of a stable overproducing strain IV. Gene products of the PstI
AB  - restriction-modification system V. In vitro transcription of the PstI system
AB  - VI. Discussion
ER  -

TY  - JOUR
AU  - Walder, R.Y.
AU  - Hartley, J.L.
AU  - Donelson, J.E.
AU  - Walder, J.A.
TI  - Cloning and expression of the PstI restriction-modification system in Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1981
SP  - 1503
EP  - 1507
VL  - 78
AB  - Here we report the cloning and preliminary characterization of the PstI
AB  - restriction-modification system of Providencia stuartii 164.  Transformants of
AB  - Escherichia coli carrying the PstI gene system inserted into the cloning vector
AB  - pBR322 were selected on the basis of acquired resistance to bacteriophage
AB  - lambda infection.  PstI endonuclease was detected in osmotic shock fluid from
AB  - each of the resistant clones.  Plasmid and chromosomal DNA from these clones
AB  - could not be digested by PstI, indicating that the gene for the corresponding
AB  - modification enzyme had also been cloned and was being expressed.  The smallest
AB  - recombinant plasmid encoding both activities, pPst201, contains an insert of
AB  - approximately 4000 base pairs.  In vitro transcription studies indicate that
AB  - this DNA fragment also contains the endogenous promoter(s) of the system.  When
AB  - pPst201 was introduced into a minicell-producing strain of E. coli, two new
AB  - proteins, 32,000 and 35,000 daltons, were synthesized.  We have assigned these
AB  - to the PstI modification (methylase) and restriction enzymes, respectively.
AB  - The active form of the restriction enzyme is a dimer, as determined by gel
AB  - filtration.  Constructed transformants of P. stuartii 164 that carry the PstI
AB  - system inserted into pBR322 produce approximately 10 times more PstI
AB  - endonuclease activity than does the native strain.
ER  -

TY  - JOUR
AU  - Walder, R.Y.
AU  - Langtimm, C.J.
AU  - Catterjee, R.
AU  - Walder, J.A.
TI  - Cloning of the MspI modification enzyme.
JO  - J. Biol. Chem.
PY  - 1983
SP  - 1235
EP  - 1241
VL  - 258
AB  - The gene for the MspI modification enzyme from Moraxella was cloned in
AB  - Escherichia coli using the plasmid vector pBR322.  Selection of transformants
AB  - carrying the gene was based on the resistance of the modified plasmid encoding
AB  - the enzyme to cleavage by MspI.  Both chromosomal and plasmid DNA were modified
AB  - in the selected clones.  None of the clones obtained produced the cognate
AB  - restriction enzyme which suggests that in this system the genes for the
AB  - restriction enzyme and methylase are not closely linked.  Crude cell extracts
AB  - prepared from the recombinant strains, but not the host (E. coli HB101),
AB  - contain an S-adenosylmethionine-dependent methyltransferase specific for the
AB  - MspI recognition site, CCGG.  Production of the enzyme is 3-4-fold greater in
AB  - the transformants than in the original Moraxella strain.  5-Methylcytosine was
AB  - identified as the product of the reaction chromatographically.  The outer
AB  - cytosine of the recognition sequence, *CCGG, was shown to be the site of
AB  - methylation by DNA-sequencing methods.  This modification blocks cleavage by
AB  - both MspI and its isoschizomer HpaII.  HpaII, but not MspI, is able to cleave
AB  - the unmethylated strand of a hemimethylated substrate.  The relevance of these
AB  - results to the use of MspI and HpaII to analyze patterns of methylation in
AB  - genomic DNA is discussed.
ER  -

TY  - JOUR
AU  - Walder, R.Y.
AU  - Langtimm, C.J.
AU  - Chatterjee, R.
AU  - Walder, J.A.
TI  - Cloning of the MspI modification enzyme:  the site of modification and its effects on cleavage by MspI and HpaII.
JO  - Fed. Proc.
PY  - 1982
SP  - 1199
EP  - 1199
VL  - 41
AB  - The gene for the MspI modification enzyme from Moraxella was cloned in E. coli
AB  - using the plasmid vector pBR322.  Selection of transformants carrying the gene
AB  - was based on the resistance of the modified plasmid encoding the enzyme to
AB  - cleavage by MspI.  Both chromosomal and plasmid DNA were modified in these
AB  - clones.  None of the clones obtained produced the cognate restriction enzyme
AB  - indicating either that the genes for the restriction enzyme and methylase are
AB  - not closely linked or that simply the restriction enzyme is not expressed in E.
AB  - coli.  Crude extracts prepared from these clones, but not the host (E. coli
AB  - HB101), contain a methyl transferase specific for the MspI recognition
AB  - sequence, CCGG, which uses SAM as the methyl donor.  The level of this activity
AB  - is approximately 3 fold greater in the transformants than in the original
AB  - Moraxella strain.  5-methylcytidine was identified as the product of the
AB  - reaction by thin layer chromatography.  DNA sequencing showed that only the
AB  - external cytidine residue within the recognition sequence is methylated.  This
AB  - modification blocks cleavage by both MspI and its isoschizomer HpaII.  A
AB  - hemimethylated substance constructed in vitro was cleaved, although at a much
AB  - reduced rate, on the unmethylated strand by HpaII but not MspI.  The relevance
AB  - of these results to the use of MspI and HpaII to analyze patterns of
AB  - methylation in genomic DNA will be discussed.
ER  -

TY  - JOUR
AU  - Walder, R.Y.
AU  - Walder, J.A.
TI  - The organization and control of expression of the PstI restriction modification system.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 209
EP  - 226
VL  - 5
AB  - In Volume I of this series, we first reported the cloning and expression of the
AB  - PstI restriction-modification system in Escherichia coli.  The PstI restriction
AB  - enzyme and methylasae genes were isolated from a genomic library of Providencia
AB  - stuartii 164 DNA in E. coli HB101 on the basis of acquired resistance of the
AB  - host to infection by bacteriophage lambda.  Subcloning experiments localized
AB  - the two genes to a 4.0 kilobase HindIII fragment, the complete sequence of
AB  - which has been determined.  In this report we review the organization and
AB  - studies of the expression of the PstI genes, and report the cloning of the PstI
AB  - restriction enzyme and methylase genes in yeast.
ER  -

TY  - JOUR
AU  - Walder, R.Y.
AU  - Walder, J.A.
AU  - Donelson, J.E.
TI  - The Organization and Complete Nucleotide Sequence of the PstI Restriction-Modification System.
JO  - J. Biol. Chem.
PY  - 1984
SP  - 8015
EP  - 8026
VL  - 259
AB  - We have determined the nucleotide sequence of a 4.0-kilobase DNA fragment
AB  - containing the genes of the PstI restriction-modification system.  Two large
AB  - open reading frames were identified within the sequence and were ascribed to
AB  - the restriction enzyme and methylase by the analysis of a series of deletion
AB  - mutants.  The two genes are encoded on opposite DNA strands, and hence must be
AB  - transcribed from separate promoters rather than as a polycistronic message.
AB  - The sequence of the first 10 amino acids of the restriction endonuclease was
AB  - determined by sequential Edman degradation of the purified protein, permitting
AB  - the alignment of the polypeoptide with the DNA sequence.  The NH2 terminus of
AB  - the modification enzme was established by sequential Edman degradation of the
AB  - protein synthesized in bacterial minicells with different radiolabeled amino
AB  - acids.  The initiation codons of the two genes are separated by 130 base pairs.
AB  - The deduced amino acid sequences indicate that the restriction endonuclease
AB  - contains 326 amino acids with a calculated Mr = 37,370; the modification enzyme
AB  - is composed of 507 amino acids with a calculated Mr = 56,830.  There is no
AB  - significant homology between the two proteins at the level of the primary
AB  - structure.  Antibody raised against the purified restriction endonuclease did
AB  - not immunoprecipitate the modification enzyme.  The transcription initiation
AB  - sites were mapped using mung bean nuclease.  Both of the transcripts begin with
AB  - adenosine.  The initiation sites are separated by only 70 base pairs.  This
AB  - close proximity suggests that the promoters for the two divergent genes
AB  - overlap.  DNase I protection experiments show that Escherichia coli RNA
AB  - polymerase has a higher affinity for the methylase promoter than for the
AB  - restriction enzyme promoter.
ER  -

TY  - JOUR
AU  - Waldman, B.-A.H.
AU  - Yerushalmi, R.
AU  - Wachtel, C.
AU  - Barbiro-Michaely, E.
AU  - Sompolinsky, D.
AU  - Gerber, D.
TI  - Draft Genome Sequence of the Suttonellaornithocola Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01592
EP  - e01516
VL  - 5
AB  - We report here the draft genome sequence of the Suttonella ornithocola bacterium. To date,
AB  - this bacterium, found in birds, passed only phylogenetic and phenotypic
AB  - analyses. To our knowledge, this is the first publication of the Suttonella
AB  - ornithocola genome sequence. The genetic profile provides a basis for further
AB  - analysis of its infection pathways.
ER  -

TY  - JOUR
AU  - Waldman-Ben-Asher, H.
AU  - Yerushalmi, R.
AU  - Wachtel, C.
AU  - Barbiro-Michaely, E.
AU  - Sompolinsky, D.
AU  - Gerber, D.
TI  - Draft Genome Sequence of a New Bacterium Named Rappaport israeli, gen. nov., sp.  nov., Isolated from a Blood Culture.
JO  - Genome Announcements
PY  - 2017
SP  - e01595
EP  - e01516
VL  - 5
AB  - Here, we report the draft genome sequence of a Gram-negative microbe found in a blood culture
AB  - (B08008) from a patient. The organism was proposed to be from a new unknown genus and species.
AB  - This publication will increase worldwide microbial knowledge and may improve microbial
AB  - identification and antibiotic treatment for patients.
ER  -

TY  - JOUR
AU  - Waldron, D.E.
AU  - Lindsay, J.A.
TI  - Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S.  aureus isolates of different lineages.
JO  - J. Bacteriol.
PY  - 2006
SP  - 5578
EP  - 5585
VL  - 188
AB  - The Sau1 type I restriction-modification system is found on the chromosome of all nine
AB  - sequenced strains of Staphylococcus aureus and includes a single hsdR (restriction) gene and
AB  - two copies of hsdM (modification) and sdS (sequence specificity) genes. The strain S. aureus
AB  - RN4220 is a vital intermediate for laboratory S. aureus manipulation, as it can accept plasmid
AB  - DNA from Escherichia coli. We show that it carries a mutation in the sau1hsdR gene and that
AB  - complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced
AB  - conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may
AB  - explain why only four vancomycin-resistant S. aureus strains have been identified despite
AB  - substantial selective pressure in the clinical setting. Using a multistrain S. aureus
AB  - microarray, we show that the two copies of sequence specificity genes (sau1hsdS1 and
AB  - sau1hsdS2) vary substantially between isolates and that the variation corresponds to the 10
AB  - dominant S. aureus lineages. Thus, RN4220 complemented with sau1hsdR was resistant to
AB  - bacteriophage lysis but only if the phage was grown on S. aureus of a different lineage.
AB  - Similarly, it could be transduced with DNA from its own lineage but not with the phage grown
AB  - on different S. aureus lineages.  Therefore, we propose that Sau1 is the major mechanism for
AB  - blocking transfer of resistance genes and other mobile genetic elements into S. aureus
AB  - isolates from other species, as well as for controlling the spread of resistance genes between
AB  - isolates of different S. aureus lineages.  Blocking Sau1 should also allow genetic
AB  - manipulation of clinical strains of S. aureus.
ER  -

TY  - JOUR
AU  - Waldron, D.E.
AU  - Owen, P.
AU  - Dorman, C.J.
TI  - Competitive interaction of the OxyR DNA-binding protein and the Dam methylase at the antigen 43 gene regulatory region in Escherichia coli.
JO  - Mol. Microbiol.
PY  - 2002
SP  - 509
EP  - 520
VL  - 44
AB  - The antigen 43 surface protein of Escherichia coli is expressed in a phase-variable manner by
AB  - a mechanism involving alternative activation
AB  - and repression of transcription of the agn43 gene. The repressor is the
AB  - OxyR DNA-binding protein, and its binding site was found to be located
AB  - downstream of the agn43 transcription start site in a region of DNA
AB  - that encompasses three 5' -GATC-3' sequences that are subject to
AB  - Dam-mediated DNA methylation. It has been suggested previously that the
AB  - phase-variable expression of antigen 43 results from a competition
AB  - between Dam methylase and the OxyR repressor for these sites. The 5'
AB  - -GATC-3' sequences were inactivated for methylation by site-directed
AB  - mutagenesis, and all possible combinations of inactive and active sites
AB  - were assessed for effects on phase-variable expression of the agn43
AB  - gene. Inactivation of any 5' -GATC-3' site individually had no effect;
AB  - at least two sites had to be inactivated to disrupt the normal pattern
AB  - of expression. Studies of OxyR interaction with agn43 DNA showed that
AB  - methylation of any two 5' -GATC-3' sites was necessary and sufficient
AB  - to block binding of the repressor. It was also found that the adenines
AB  - of the second and third 5' -GATC-3' sites are required for OxyR
AB  - binding, demonstrating that the sites for Dam methylation and for
AB  - repressor binding are intimately associated. This is consistent with a
AB  - competition model in which Dam and OxyR share a preference for specific
AB  - DNA sequences in the regulatory region of the agn43 gene.
ER  -

TY  - JOUR
AU  - Waleron, K.
AU  - Nakonieczna, J.
AU  - Waleron, M.
AU  - Podhajska, A.J.
TI  - 50 years of studies of restriction - modification systems (Systemy restrykcyjno-modyfikacyjne - 50 lat badan).
JO  - Biotechnologia (Poznan)
PY  - 2006
SP  - 65
EP  - 88
VL  - 2
AB  - The basic function of restriction endonucleases and methyltransferases is protection of the
AB  - host genome against foreign DNA. Their
AB  - recombination and transposition related functions are still being
AB  - discussed. Some authors postulate that R-M genes may act as selfish
AB  - genetic elements. Restriction endonucleases are indispensable tools in
AB  - molecular biology. As these enzymes recognize DNA sequence very
AB  - specifically, they serve as a model for protein-DNA interaction.
AB  - Restriction-modification genes have also played the same role as a
AB  - model for evolutionary studies as well as protein structure - function
AB  - relations. So far, there have been more than 3500 bacterial strains
AB  - studied which possessed R-M genes of more than 280 different
AB  - specificities towards recognition sequence and cleavage sites. They
AB  - became a very good commercial product for many biotechnological
AB  - companies. At present, in a genome sequencing era, R-M genes seem to be
AB  - much more common than it was thought before.
ER  -

TY  - JOUR
AU  - Waleron, K.
AU  - Waleron, M.
AU  - Osipiuk, J.
AU  - Podhajska, A.J.
AU  - Lojkowska, E.
TI  - Identification of a DNA restriction-modification system in Pectobacterium carotovorum strains isolated from Poland.
JO  - J. Appl. Microbiol.
PY  - 2006
SP  - 343
EP  - 351
VL  - 100
AB  - Aims: Polish isolates of pectinolytic bacteria from the species Pectobacterium carotovorum
AB  - were screened for the presence of a DNA
AB  - restriction-modification (R-M) system.
AB  - Methods and Results: Eighty-nine strains of P. carotovorum were
AB  - isolated from infected potato plants. Sixty-six strains belonged to P.
AB  - carotovorum ssp. atrosepticum and 23 to P. carotovorum ssp.
AB  - carotovorum. The presence of restriction enzyme Pca17AI, which is an
AB  - isoschizomer of EcoRII endonuclease, was observed in all isolates of P.
AB  - c. atrosepticum but not in P. c. carotovorum. The biochemical
AB  - properties, PCR amplification, and sequences of the Pca17AI restriction
AB  - endonuclease and methyltransferase genes were compared with the
AB  - prototype EcoRII R-M system genes. Only when DNA isolated from cells of
AB  - P. c. atrosepticum was used as a template, amplification of a 680 bp
AB  - homologous to the gene coding EcoRII endonuclease.
AB  - Conclusions: Endonuclease Pca17AI, having a relatively low
AB  - temperature optimum, was identified. PCR amplification revealed that
AB  - the nucleotide sequence of genes for EcoRII and Pca17AI R-M are
AB  - different. Dcm methylation was observed in all strains of
AB  - Pectobacterium and other Erwinia species tested. The sequence of a DNA
AB  - fragment coding Dcm methylase in P. carotovorum was different from that
AB  - of Escherichia coli.
AB  - Significance and Impact of the Study: Pca17AI is the first
AB  - psychrophilic isoschizomer of EcoRII endonuclease. The presence of
AB  - specific Dcm methylation in chromosomal DNA isolated from P.
AB  - carotovorum is described for the first time. A 680 bp PCR product,
AB  - unique for P. c. atrosepticum strains, could serve as a molecular
AB  - marker for detection of these bacteria in environmental samples.
ER  -

TY  - JOUR
AU  - Walker, C.A.
AU  - Mannering, S.A.
AU  - Shields, S.
AU  - Blake, D.P.
AU  - Brownlie, J.
TI  - Complete Genome Sequence of Mycoplasma cynos Strain C142.
JO  - Genome Announcements
PY  - 2013
SP  - e00196
EP  - e00112
VL  - 1
AB  - Here we report the de novo genome sequencing of Mycoplasma cynos strain C142, isolated from a
AB  - dog with canine infectious respiratory disease (CIRD) in the
AB  - United States.
ER  -

TY  - JOUR
AU  - Walker, C.B. et al.
TI  - Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 8818
EP  - 8823
VL  - 107
AB  - Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now
AB  - thought to be significant contributors to carbon and
AB  - nitrogen cycling. The isolation of Candidatus 'Nitrosopumilus maritimus'
AB  - strain SCM1 provided the opportunity for linking its chemolithotrophic
AB  - physiology with a genomic inventory of the globally distributed archaea.
AB  - Here we report the 1,645,259-bp closed genome of strain SCM1, revealing
AB  - highly copper-dependent systems for ammonia oxidation and electron
AB  - transport that are distinctly different from known ammonia-oxidizing
AB  - bacteria. Consistent with in situ isotopic studies of marine archaea, the
AB  - genome sequence indicates N. maritimus grows autotrophically using a
AB  - variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon
AB  - assimilation, while maintaining limited capacity for assimilation of
AB  - organic carbon. This unique instance of archaeal biosynthesis of the
AB  - osmoprotectant ectoine and an unprecedented enrichment of multicopper
AB  - oxidases, thioredoxin-like proteins, and transcriptional regulators points
AB  - to an organism responsive to environmental cues and adapted to handling
AB  - reactive copper and nitrogen species that likely derive from its
AB  - distinctive biochemistry. The conservation of N. maritimus gene content
AB  - and organization within marine metagenomes indicates that the unique
AB  - physiology of these specialized oligophiles may play a significant role in
AB  - the biogeochemical cycles of carbon and nitrogen.
ER  -

TY  - JOUR
AU  - Walker, G.T.
AU  - Little, M.C.
AU  - Nadeau, J.G.
AU  - Shank, D.D.
TI  - Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1992
SP  - 392
EP  - 396
VL  - 89
AB  - An isothermal in vitro DNA amplification method was developed based upon the
AB  - following sequence of reaction events.  Restriction enzyme cleavage and
AB  - subsequent heat denaturation of a DNA sample generates two single-stranded
AB  - target DNA fragments (T1 and T2). Present in excess are two DNA amplification
AB  - primers (P1 and P2).  The 3' end of P1 binds to the 3' end of T1, forming a
AB  - duplex with 5' overhangs.  Likewise, P2 binds to T2.  The 5' overhangs of P1
AB  - and P2 contain a recognition sequence (5'-GTTGAC-3') for the restriction enzyme
AB  - HincII.  An exonuclease-deficient form of the large fragment of Escherichia
AB  - coli DNA polymerase I (exo- Klenow polymerase) [Derbyshire, V., Freemont, P.S.,
AB  - Sanderson, M.R., Beese, L., Friedman, J.M., Joyce, C.M. & Steitz, T.A. (1988)]
AB  - Science 240, 199-201] extends the 3' ends of the duplexes using dGTP, dCTP,
AB  - TTP, and deoxyadenosine 5'-[alpha-thio] triphosphate, which produces
AB  - hemiphosphorothioate recognition sites on P1T1 and P2T2.  HincII nicks the
AB  - unprotected primer strands of the hemiphosphorothioate recognition sites,
AB  - leaving intact the modified complementary strands.  The exo- Klenow polymerase
AB  - extends the 3' end at the nick on P1T1 and displaces the downstream strand that
AB  - is functionally equivalent to T2.  Likewise, extension at the nick on P2T2
AB  - results in displacement of a downstream strand functionally equivalent to T1.
AB  - Nicking and polymerization/displacement steps cycle continuously on P1T1 and
AB  - P2T2 because extension at a nick regenerates a nickable HincII recognition
AB  - site.  Target amplification is exponential because strands displaced from P1T1
AB  - serve as targets for P2 and strands displaced from P2T2 serve as targets for
AB  - P1.  A 10/6-fold amplification of a genomic sequence from Mycobacterium
AB  - tuberculosis or Mycobacterium bovis was achieved in 4 h at 37C.
ER  -

TY  - JOUR
AU  - Walker, J.N.B.
AU  - Dean, P.D.G.
AU  - Saunders, J.R.
TI  - Identification and characterisation of PmaCI an endonuclease of novel specificity from Pseudomonas maltophila.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 1293
EP  - 1301
VL  - 14
AB  - We report the use of MonoQ FPLC (Fast Protein Liquid Chromatography) for the
AB  - rapid purification of a novel Type II restriction endonuclease PmaCI, from
AB  - Pseudomonas maltophila, which recognises the sequence 5'-CAC^GTG-3'.  The
AB  - resulting enzyme is free of other nucleases to a level suitable for its
AB  - characterisation by multiple-substrate digestion and DNA sequencing techniques.
AB  - This method appears to be widely applicable and we have used it for the
AB  - isolation of restriction endonucleases of comparable purity from a range of
AB  - other organisms.  Also described is a rapid method for screening a library of
AB  - small inserted regions in recombinant M13 molecules for the presence and
AB  - subsequent screening of restriction sites of interest.
ER  -

TY  - JOUR
AU  - Walker, R.
AU  - Watkin, E.
AU  - Tian, R.
AU  - Brau, L.
AU  - O'Hara, G.
AU  - Goodwin, L.
AU  - Han, J.
AU  - Lobos, E.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 551
EP  - 561
VL  - 9
AB  - Burkholderia sp. strain WSM2230 is an aerobic, motile, Gram-negative, non-spore-forming
AB  - acid-tolerant rod isolated from acidic soil collected in 2001
AB  - from Karijini National Park, Western Australia, using Kennedia coccinea (Coral
AB  - Vine) as a host. WSM2230 was initially effective in nitrogen-fixation with K.
AB  - coccinea, but subsequently lost symbiotic competence. Here we describe the
AB  - features of Burkholderia sp. strain WSM2230, together with genome sequence
AB  - information and its annotation. The 6,309,801 bp high-quality-draft genome is
AB  - arranged into 33 scaffolds of 33 contigs containing 5,590 protein-coding genes
AB  - and 63 RNA-only encoding genes. The genome sequence of WSM2230 failed to identify
AB  - nodulation genes and provides an explanation for the observed failure of the
AB  - laboratory grown strain to nodulate. The genome of this strain is one of 100
AB  - sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for
AB  - Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Walker, R.
AU  - Watkin, E.
AU  - Tian, R.
AU  - Brau, L.
AU  - O'Hara, G.
AU  - Goodwin, L.
AU  - Han, J.
AU  - Reddy, T.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavromatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1168
EP  - 1180
VL  - 9
AB  - Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming
AB  - acid-tolerant rod that was trapped in 2001 from acidic soil
AB  - collected from Karijini National Park (Australia) using Gastrolobium capitatum as
AB  - a host. WSM2232 was effective in nitrogen fixation with G. capitatum but
AB  - subsequently lost symbiotic competence during long-term storage. Here we describe
AB  - the features of Burkholderia sp. strain WSM2232, together with genome sequence
AB  - information and its annotation. The 7,208,311 bp standard-draft genome is
AB  - arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes
AB  - and 61 RNA-only encoding genes. The loss of symbiotic capability can now be
AB  - attributed to the loss of nodulation and nitrogen fixation genes from the genome.
AB  - This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome
AB  - Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria
AB  - (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Walker, S.A.
AU  - Klaenhammer, T.R.
TI  - The Genetics of Phage Resistance in Lactococcus lactis.
JO  - Genetics of Phage Resistance
PY  - 2003
SP  - 291
EP  - 315
VL  - 3
ER  -

TY  - JOUR
AU  - Walkinshaw, M.D.
AU  - Taylor, P.
AU  - Sturrock, S.S.
AU  - Atanasiu, C.
AU  - Berge, T.
AU  - Henderson, R.M.
AU  - Edwardson, J.M.
AU  - Dryden, D.T.
TI  - Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA.
JO  - Mol. Cell
PY  - 2002
SP  - 187
EP  - 194
VL  - 9
AB  - We have solved, by X-ray crystallography to a resolution of 1.8 A, the structure of a protein
AB  - capable of mimicking approximately 20 base pairs of
AB  - B-form DNA. This ocr protein, encoded by gene 0.3 of bacteriophage T7,
AB  - mimics the size and shape of a bent DNA molecule and the arrangement of
AB  - negative charges along the phosphate backbone of B-form DNA. We also
AB  - demonstrate that ocr is an efficient inhibitor in vivo of all known
AB  - families of the complex type I DNA restriction enzymes. Using atomic force
AB  - microscopy, we have also observed that type I enzymes induce a bend in DNA
AB  - of similar magnitude to the bend in the ocr molecule. This first structure
AB  - of an antirestriction protein demonstrates the construction of structural
AB  - mimetics of long segments of B-form DNA.
ER  -

TY  - JOUR
AU  - Wall, L.G. et al.
TI  - Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis.
JO  - Genome Announcements
PY  - 2013
SP  - e00503
EP  - e00513
VL  - 1
AB  - Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome
AB  - sequence for Frankia sp. strain BCU110501, a nitrogen-fixing
AB  - actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia
AB  - region of Argentina.
ER  -

TY  - JOUR
AU  - Wall, T.
AU  - Bath, K.
AU  - Britton, R.A.
AU  - Jonsson, H.
AU  - Versalovic, J.
AU  - Roos, S.
TI  - The Early Response to Acid Shock in Lactobacillus reuteri Involves the ClpL Chaperone and a Putative Cell Wall-Altering Esterase.
JO  - Appl. Environ. Microbiol.
PY  - 2007
SP  - 3924
EP  - 3935
VL  - 73
AB  - To be able to function as a probiotic, bacteria have to survive the
AB  - passage through the gastrointestinal tract. We have examined survival and
AB  - gene expression of Lactobacillus reuteri ATCC 55730 after a sudden shift
AB  - in environmental acidity to a pH close to the conditions in the human
AB  - stomach. More than 80% of the L. reuteri cells survived at pH 2.7 for 1 h.
AB  - A genomewide expression analysis experiment using microarrays displayed 72
AB  - differentially expressed genes at this pH. The early response to severe
AB  - acid shock in L. reuteri differed from long-term acid adaptation to milder
AB  - acid stress studied in other lactic acid bacteria. The genes induced
AB  - included the following: clpL, genes putatively involved in alterations of
AB  - the cell membrane and the cell wall; genes encoding transcriptional
AB  - regulators; phage genes; and genes of unknown function. Two genes, clpL,
AB  - encoding an ATPase with chaperone activity, and lr1516, encoding a
AB  - putative esterase, were selected for mutation analyses. The mutants were
AB  - significantly more sensitive to acid than the wild type was. Thus, these
AB  - genes could contribute to the survival of L. reuteri in the
AB  - gastrointestinal tract.
ER  -

TY  - JOUR
AU  - Wallace, C.J.A.
TI  - The curious case of protein splicing: mechanistic insights suggested by protein semisynthesis.
JO  - Protein Sci.
PY  - 1993
SP  - 697
EP  - 705
VL  - 2
AB  - The gradual accumulation of examples of protein splicing, in which a
AB  - nested intervening sequence is spliced out of the interior of a polyprotein precursor,
AB  - suggests that this curious phenomenon might prove to have universal phylogenetic
AB  - distribution and biological significance.  The known examples are reviewed, with the aim
AB  - of establishing underlying patterns, and a generalized mechanism of autocatalytic protein
AB  - splicing is proposed.  The testable consequences of such a proposal and the possible
AB  - evolutionary origins of the phenomenon are discussed.
ER  -

TY  - JOUR
AU  - Wallace, J.G.
AU  - Breaker, R.R.
TI  - Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125.
JO  - Lett. Appl. Microbiol.
PY  - 2011
SP  - 430
EP  - 432
VL  - 52
AB  - Aims: Bacillus halodurans C-125 is a Gram-positive bacterium that was the
AB  - first alkaliphilic species to have its genome completely sequenced.
AB  - Despite its many years as a model for alkaliphily and source of
AB  - industrially important enzymes, genetic manipulation of B. halodurans
AB  - C-125 remains difficult, and therefore, we sought to develop a robust
AB  - method to allow routine transformation of this organism.
AB  - Methods and Results:
AB  - A plasmid artificial modification system (PAM system, <link
AB  - rid='b7'>Yasui et al. 2008) for B. halodurans C-125 was created that
AB  - increases transformation efficiency by 10- to 1000-fold. Also,
AB  - recovering transformed protoplasts on succinate nutrient agar (SNA)
AB  - yields faster, more robust colony recovery than on the traditional
AB  - recovery medium. Combining these two techniques often allows recovery
AB  - of transformants in as little as 48 h.
AB  - Conclusions:
AB  - Use of the B. halodurans C-125 PAM system and SNA greatly improves
AB  - the efficiency and speed of protoplast transformation of B. halodurans
AB  - C-125.
AB  - Significance and Impact of the Study:
AB  - These techniques allow routine genetic manipulation of B.
AB  - halodurans C-125, a model alkaliphilic bacterium with important
AB  - industrial properties.
ER  -

TY  - JOUR
AU  - Walsh, C.P.
AU  - Bestor, T.H.
TI  - Cytosine methylation and mammalian development.
JO  - Genes Dev.
PY  - 1999
SP  - 26
EP  - 34
VL  - 13
AB  - Programmed methylation and demethylation of regulatory sequences has been proposed to play a
AB  - central role in vertebrate development.  We report here that the methylation status of the 5'
AB  - regions of a panel of tissue-specific genes could not be correlated with expression in tissues
AB  - of fetal and newborn mice.  Genes reported to be regulated by reversible methylation were not
AB  - expressed ectopically or precociously in Dnmt1-deficient mouse embryos under conditions where
AB  - demethylation caused biallelic expression of imprinted genes and activated transcription of
AB  - endogenous retroviruses of the IAP class.  These and other data suggest that the numerous
AB  - published expression-methylation correlations may have described not a cause but a consequence
AB  - of transcriptional activation.  A model is proposed under which cytosine methylation
AB  - represents a biochemical specialization of large genomes that participates in specialized
AB  - biological functions such as allele-specific gene expression and the heritable transcriptional
AB  - silencing of parasitic sequence elements, whereas cellular differentiation is controlled by
AB  - conserved regulatory networks that do not depend on covalent modification of the genome.
ER  -

TY  - JOUR
AU  - Walsh, C.P.
AU  - Xu, G.L.
TI  - Cytosine methylation and DNA repair.
JO  - Curr. Top. Microbiol. Immunol.
PY  - 2006
SP  - 283
EP  - 315
VL  - 301
AB  - Cytosine methylation is a common form of post-replicative DNA modification seen in both
AB  - bacteria and eukaryotes. Modified cytosines have long been known to act as hotspots for
AB  - mutations due to the high rate of spontaneous deamination of this base to thymine, resulting
AB  - in a G/T mismatch. This will be fixed as a C -> T transition after replication if not repaired
AB  - by the base excision repair (BER) pathway or specific repair enzymes dedicated to this
AB  - purpose. This hypermutability has led to depletion of the target dinucleotide CpG outside of
AB  - special CpG islands in mammals, which are normally unmethylated. We review the importance of C
AB  - -> T transitions at non-island CpGs in human disease: When these occur in the germline, they
AB  - are a common cause of inherited diseases such as epidermolysis bullosa and
AB  - mucopolysaccharidosis, while in the soma they are frequently found in the genes for tumor
AB  - suppressors such as p53 and the retinoblastoma protein, causing cancer. We also examine the
AB  - specific repair enzymes involved, namely the endonuclease Vsr in Escherichia coli and two
AB  - members of the uracil DNA glycosylase (UDG) superfamily in mammals, TDG and MBD4. Repair
AB  - brings its own problems, since it will require remethylation of the replacement cytosine,
AB  - presumably coupling repair to methylation by either the maintenance methylase Dnmt1 or a de
AB  - novo enzyme such as Dnmt3a. Uncoupling of methylation from repair may be one way to remove
AB  - methylation from DNA. We also look at the possible role of specific cytosine deaminases such
AB  - as Aid and Apobec in accelerating deamination of methylcytosine and consequent DNA
AB  - demethylation.
ER  -

TY  - JOUR
AU  - Walsh, D.A.
AU  - Zaikova, E.
AU  - Howes, C.G.
AU  - Song, Y.C.
AU  - Wright, J.J.
AU  - Tringe, S.G.
AU  - Tortell, P.D.
AU  - Hallam, S.J.
TI  - Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones.
JO  - Science
PY  - 2009
SP  - 578
EP  - 582
VL  - 326
AB  - Oxygen minimum zones, also known as oceanic "dead zones," are widespread
AB  - oceanographic features currently expanding because of global warming. Although
AB  - inhospitable to metazoan life, they support a cryptic microbiota whose metabolic
AB  - activities affect nutrient and trace gas cycling within the global ocean. Here,
AB  - we report metagenomic analyses of a ubiquitous and abundant but uncultivated
AB  - oxygen minimum zone microbe (SUP05) related to chemoautotrophic gill symbionts of
AB  - deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire
AB  - of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate
AB  - respiration responsive to a wide range of water-column redox states. Our analysis
AB  - provides a genomic foundation for understanding the ecological and biogeochemical
AB  - role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential
AB  - sensitivity to environmental changes.
ER  -

TY  - JOUR
AU  - Walsh, D.A.
AU  - Zaikova, E.
AU  - Howes, C.L.
AU  - Song, Y.C.
AU  - Wright, J.
AU  - Tringe, S.G.
AU  - Tortell, P.D.
AU  - Hallam, S.J.
TI  - Metagenome of a versatile chemolithoautotroph from expanding oxygen minimum zones.
JO  - Science
PY  - 2009
SP  - 578
EP  - 582
VL  - 326
AB  - Oxygen minimum zones, also known as oceanic "dead zones", are widesprad oceanographic features
AB  - currently expanding because of global warming.  Although inhospitable to metazoan life, they
AB  - support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling
AB  - within the global ocean.  Here, we report metagenomic analyses of a ubiquitous and abundant
AB  - but uncultivated oxygen minimum zone microbe (SUPO5) related to chemoautotrophic gill
AB  - symbionts of deep-sea clams and mussels.  The SUP05 metagenome harbors a versatile repertoire
AB  - of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate respiration
AB  - responsive to a wide range of water-column redox states. Our analysis provides a genomic
AB  - foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in
AB  - oxygen-deficient oceanic waters and its potential sensitivity to environmental changes.
ER  -

TY  - JOUR
AU  - Walsh, P.
AU  - Bekaert, M.
AU  - Carroll, J.
AU  - Manning, T.
AU  - Kelly, B.
AU  - O'Driscoll, A.
AU  - Lu, X.
AU  - Smith, C.
AU  - Dickinson, P.
AU  - Templeton, K.
AU  - Ghazal, P.
AU  - Sleator, R.D.
TI  - Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's  Royal Infirmary.
JO  - Genome Announcements
PY  - 2015
SP  - e00471
EP  - e00415
VL  - 3
AB  - Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis
AB  - clones, cultivated from blood taken from different preterm neonatal
AB  - sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
ER  -

TY  - JOUR
AU  - Walter, F.
AU  - Hartmann, M.
AU  - Roth, M.
TI  - Purification and characterization of a site specific endonuclease from Streptomyces hygroscopicus.
JO  - Abstracts of 12th FEBS Symposium, Dresden.
PY  - 1978
SP  - 648
EP  - 648
VL  - 0
AB  - The isolation procedure of a new site specific endonuclease from Streptomyces
AB  - hygroscopicus J 0477 is described.  Using the Lysozyme treatment, we have
AB  - partially purified this enzyme (ShyI) by chromatography on Bio-Gel A0.5m, DEAE
AB  - Cellulose and Sepharose 4B coupled with 1,5-Diaminopentan ShyI require Mg2+ as
AB  - cofactor.  Salt concentrations higher than 0.2M NaCl inhibit the enzyme.  The
AB  - enzyme cleaves wild type lambda-DNA at two sites.
ER  -

TY  - JOUR
AU  - Walter, J.
AU  - Noyer-Weidner, M.
AU  - Trautner, T.A.
TI  - The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases.
JO  - EMBO J.
PY  - 1990
SP  - 1007
EP  - 1013
VL  - 9
AB  - The Bacillus subtilis FI DNA methyltransferase (M.BsuFI) modifies the outer
AB  - cytosine of the DNA sequence CCGG, causing resistance against R.BsuFI and
AB  - R.MspI restriction.  The M.BsuFI gene was cloned and expressed in B.subtilis
AB  - and Escherichia coli.  As derived from the nucleotide sequence, the M.BsuFI
AB  - protein has 409 amino acids, corresponding to a molecular mass of 46918
AB  - daltons.  Including these data we have compared the nucleotide and amino acid
AB  - sequences of different CCGG recognizing enzymes.  These analyses showed that
AB  - M.BsuFI is highly related to two other CCGG specific methyltransferases, M.MspI
AB  - and M.HpaII, which were isolated from Gram-negative bacteria.  Between M.BsuFI
AB  - and M.MspI the sequence similarity is particularly significant in a region,
AB  - which has been postulated to contain the target recognition domains (TRDs) of
AB  - cytosine-specific DNA methyltransferases.  Apparently M.BsuFI and M.MspI,
AB  - derived from phylogenetic distant organisms, use highly conserved structural
AB  - elements for the recognition of the CCGG target sequence.  In contrast the very
AB  - same region of M.HpaII is quite different from those of M.BsuFI and M.MspI.  We
AB  - attribute this difference to the different targeting of methylation within the
AB  - sequence CCGG, where M.HpaII methylates the inner, M.BsuFI/M.MspI the outer
AB  - cytosine.  Also the CCGG recognizing TRD of the multispecific B. subtilis phage
AB  - SPR Mtase is distinct from that of the host enzyme, possibly indicating
AB  - different requirements for TRDs operative in mono- and multispecific enzymes.
ER  -

TY  - JOUR
AU  - Walter, J.
AU  - Trautner, T.A.
AU  - Noyer-Weidner, M.
TI  - High plasticity of multispecific DNA methyltransferases in the region carrying DNA target recognizing enzyme modules.
JO  - EMBO J.
PY  - 1992
SP  - 4445
EP  - 4450
VL  - 11
AB  - Multispecific cytosine C5 DNA methyltransferases (MTases) methylate more than one specific DNA
AB  - target. This is due to the presence of several target recognizing domains (TRDs) in these
AB  - enzymes. Such TRDs form part of a variable center in the MTase primary sequence, which
AB  - separates conserved enzyme core sequences responsible for general steps in the methylation
AB  - reaction. By deleting, rearranging and exchanging several TRDs of multispecific MTases, we
AB  - demonstrate their modular character; they mediate target recognition independent of a
AB  - particular TRD or core sequence context. We show also that multipsecific MTases can
AB  - accommodate inert material of non-MTase origin within their variable region without losing
AB  - their activity. The remarkable plasticity with respect to the material that can be integrated
AB  - into this region suggests that the enzyme core sequences preceding or following it form
AB  - separable functional domains. In spite of the documented flexibitity multispecific MTass could
AB  - not be endowed with novel specificities by integration of putative TRDs of monospecific
AB  - MTases, pointing to differences between multi-and monospecific MTases in the way their core
AB  - and TRD sequences interact.
ER  -

TY  - JOUR
AU  - Wambui, J.
AU  - Stevens, M.
AU  - Njage, P.M.K.
AU  - Wuthrich, D.
AU  - Egli, A.
AU  - Stephan, R.
AU  - Tasara, T.
TI  - Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya.
JO  - Genome Announcements
PY  - 2018
SP  - e00446
EP  - e00418
VL  - 6
AB  - We present here draft genome sequences of Enterococcus mundtii strains K7-EM, P2-EM, C11-EM,
AB  - and H18-EM, which were isolated from slaughterhouse equipment,
AB  - carcasses, and personnel of small- and medium-sized beef slaughterhouses in
AB  - Kenya.
ER  -

TY  - JOUR
AU  - Wan, K.H.
AU  - Yu, C.
AU  - Park, S.
AU  - Hammonds, A.S.
AU  - Booth, B.W.
AU  - Celniker, S.E.
TI  - Complete Genome Sequence of Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5,  an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.
JO  - Genome Announcements
PY  - 2017
SP  - e01333
EP  - e01317
VL  - 5
AB  - Acetobacter pomorum Oregon-R-modENCODE strain BDGP5 was isolated from Drosophila  melanogaster
AB  - for functional host-microbe interaction studies. The complete genome
AB  - is composed of a single chromosomal circle of 2,848,089 bp, with a G+C content of
AB  - 53% and three plasmids of 131,455 bp, 19,216 bp, and 9,160 bp.
ER  -

TY  - JOUR
AU  - Wan, K.H.
AU  - Yu, C.
AU  - Park, S.
AU  - Hammonds, A.S.
AU  - Booth, B.W.
AU  - Celniker, S.E.
TI  - Complete Genome Sequence of Bacillus kochii Oregon-R-modENCODE Strain BDGP4, Isolated from Drosophila melanogaster Gut.
JO  - Genome Announcements
PY  - 2017
SP  - e01074
EP  - e01017
VL  - 5
AB  - Bacillus kochii Oregon-R-modENCODE strain BDGP4 was isolated from the gut of Drosophila
AB  - melanogaster for functional host microbial interaction studies. The
AB  - complete genome comprised a single chromosomal circle of 4,557,232 bp with a G+C
AB  - content of 37% and a single plasmid of 137,143 bp.
ER  -

TY  - JOUR
AU  - Wan, K.H.
AU  - Yu, C.
AU  - Park, S.
AU  - Hammonds, A.S.
AU  - Booth, B.W.
AU  - Celniker, S.E.
TI  - Complete Genome Sequence of Enterococcus durans Oregon-R-modENCODE Strain BDGP3,  a Lactic Acid Bacterium Found in the Drosophila melanogaster Gut.
JO  - Genome Announcements
PY  - 2017
SP  - e01041
EP  - e01017
VL  - 5
AB  - Enterococcus durans Oregon-R-modENCODE strain BDGP3 was isolated from the Drosophila
AB  - melanogaster gut for functional host-microbe interaction studies. The
AB  - complete genome is composed of a single circular genome of 2,983,334 bp, with a
AB  - G+C content of 38%, and a single plasmid of 5,594 bp.
ER  -

TY  - JOUR
AU  - Wan, K.H.
AU  - Yu, C.
AU  - Park, S.
AU  - Hammonds, A.S.
AU  - Booth, B.W.
AU  - Celniker, S.E.
TI  - Complete Genome Sequence of Lactobacillus plantarum Oregon-R-modENCODE Strain BDGP2 Isolated from Drosophila melanogaster Gut.
JO  - Genome Announcements
PY  - 2017
SP  - e01155
EP  - e01117
VL  - 5
AB  - Lactobacillus plantarum Oregon-R-modENCODE strain BDGP2 was isolated from the gut of
AB  - Drosophila melanogaster for functional host microbial interaction studies. The
AB  - complete genome comprised a single circular genome of 3,407,160 bp, with a G+C
AB  - content of 44%, and four plasmids.
ER  -

TY  - JOUR
AU  - Wan, K.H.
AU  - Yu, C.
AU  - Park, S.
AU  - Hammonds, A.S.
AU  - Booth, B.W.
AU  - Celniker, S.E.
TI  - Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.
JO  - Genome Announcements
PY  - 2017
SP  - e01020
EP  - e01017
VL  - 5
AB  - Acetobacter tropicalis Oregon-R-modENCODE strain BDGP1 was isolated from Drosophila
AB  - melanogaster for functional host-microbe interaction studies. The
AB  - complete genome comprises a single chromosomal circle of 3,988,649 bp with a G+C
AB  - content of 56% and a conjugative plasmid of 151,013 bp.
ER  -

TY  - JOUR
AU  - Wan, T.W.
AU  - Higuchi, W.
AU  - Khokhlova, O.E.
AU  - Hung, W.C.
AU  - Iwao, Y.
AU  - Wakayama, M.
AU  - Inomata, N.
AU  - Takano, T.
AU  - Lin, Y.T.
AU  - Peryanova, O.V.
AU  - Kojima, K.K.
AU  - Salmina, A.B.
AU  - Teng, L.J.
AU  - Yamamoto, T.
TI  - Genomic comparison between Staphylococcus aureus GN strains clinically isolated from a familial infection case: IS1272 transposition through a novel inverted repeat-replacing mechanism.
JO  - PLoS ONE
PY  - 2017
SP  - E0187288
EP  - E0187288
VL  - 12
AB  - A bacterial insertion sequence (IS) is a mobile DNA sequence carrying only the
AB  - transposase gene (tnp) that acts as a mutator to disrupt genes, alter gene
AB  - expressions, and cause genomic rearrangements. "Canonical" ISs have historically
AB  - been characterized by their terminal inverted repeats (IRs), which may form a
AB  - stem-loop structure, and duplications of a short (non-IR) target sequence at both
AB  - ends, called target site duplications (TSDs). The IS distributions and virulence
AB  - potentials of Staphylococcus aureus genomes in familial infection cases are
AB  - unclear. Here, we determined the complete circular genome sequences of familial
AB  - strains from a Panton-Valentine leukocidin (PVL)-positive ST50/agr4 S. aureus
AB  - (GN) infection of a 4-year old boy with skin abscesses. The genomes of the
AB  - patient strain (GN1) and parent strain (GN3) were rich for "canonical" IS1272
AB  - with terminal IRs, both having 13 commonly-existing copies (ce-IS1272). Moreover,
AB  - GN1 had a newly-inserted IS1272 (ni-IS1272) on the PVL-converting prophage, while
AB  - GN3 had two copies of ni-IS1272 within the DNA helicase gene and near rot. The
AB  - GN3 genome also had a small deletion. The targets of ni-IS1272 transposition were
AB  - IR structures, in contrast with previous "canonical" ISs. There were no TSDs.
AB  - Based on a database search, the targets for ce-IS1272 were IRs or "non-IRs".
AB  - IS1272 included a larger structure with tandem duplications of the left (IRL)
AB  - side sequence; tnp included minor cases of a long fusion form and truncated form.
AB  - One ce-IS1272 was associated with the segments responsible for immune evasion and
AB  - drug resistance. Regarding virulence, GN1 expressed cytolytic peptides
AB  - (phenol-soluble modulin alpha and delta-hemolysin) and PVL more strongly than
AB  - some other familial strains. These results suggest that IS1272 transposes through
AB  - an IR-replacing mechanism, with an irreversible process unlike that of
AB  - "canonical" transpositions, resulting in genomic variations, and that, among the
AB  - familial strains, the patient strain has strong virulence potential based on
AB  - community-associated virulence factors.
ER  -

TY  - JOUR
AU  - Wan, T.W.
AU  - Khokhlova, O.E.
AU  - Iwao, Y.
AU  - Higuchi, W.
AU  - Hung, W.C.
AU  - Reva, I.V.
AU  - Singur, O.A.
AU  - Gostev, V.V.
AU  - Sidorenko, S.V.
AU  - Peryanova, O.V.
AU  - Salmina, A.B.
AU  - Reva, G.V.
AU  - Teng, L.J.
AU  - Yamamoto, T.
TI  - Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256's Spread, and Evolution of Russia ST8-IV.
JO  - PLoS ONE
PY  - 2016
SP  - E0164168
EP  - E0164168
VL  - 11
AB  - ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus
AB  - (CA-MRSA) has been a common threat, with large USA300 epidemics in the United
AB  - States. The global geographical structure of ST8/SCCmecIV has not yet been fully
AB  - elucidated. We herein determined the complete circular genome sequence of
AB  - ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome
AB  - was inverted relative to USA300. Two IS256, oppositely oriented, at
AB  - IS256-enriched hot spots were implicated with the one-megabase genomic inversion
AB  - (MbIN) and vSabeta split. The behavior of IS256 was flexible: its insertion site
AB  - (att) sequences on the genome and junction sequences of extrachromosomal circular
AB  - DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was
AB  - detected, even in prevalent ST239 healthcare-associated MRSA in Russia,
AB  - suggesting IS256's strong transmission potential and advantage in evolution.
AB  - Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and
AB  - Far Eastern Russia, examined had MbIN, and geographical expansion accompanied
AB  - divergent spa types and resistance to fluoroquinolones, chloramphenicol, and
AB  - often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening
AB  - infections such as pneumonia and sepsis in both community and hospital settings.
AB  - Regarding virulence, the OC8 genome carried a series of toxin and immune evasion
AB  - genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a
AB  - pan-regulatory gene. These results suggest that unique single
AB  - ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and
AB  - this was followed by large geographical expansion, with MbIN as an
AB  - epidemiological marker, and fluoroquinolone resistance, multiple virulence
AB  - factors, and possibly a multi-IS256 system as selective advantages.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Dasilveira, L.
AU  - Hou, S.
AU  - Saito, J.A.
AU  - Donachie, S.P.
TI  - Draft Genome Sequence of Terasakiispira papahanaumokuakeensis PH27AT, a Spiral Bacterium from the Northwestern Hawaiian Islands.
JO  - Genome Announcements
PY  - 2016
SP  - e01166
EP  - e01116
VL  - 4
AB  - The genus Terasakiispira hosts only Terasakiispira papahanaumokuakeensis PH27AT,  cultivated
AB  - from an anchialine pond on Pearl and Hermes Atoll, Northwestern
AB  - Hawaiian Islands. The strain's genome sequence may provide insights into the
AB  - evolution of free-living Oceanospirillaceae.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Hou, S.
AU  - Burns, S.L.
AU  - Saito, J.A.
AU  - Donachie, S.P.
TI  - Draft Genome Sequence of a Novel Marinobacter sp. Strain from Honolulu Harbor, Hawai'i.
JO  - Genome Announcements
PY  - 2016
SP  - e01354
EP  - e01316
VL  - 4
AB  - Marinobacter sp. strain X15-166BT was cultivated from sediment in Honolulu Harbor, Hawai'i.
AB  - The X15-166BT draft genome of 3,490,661 bp encodes 3,115
AB  - protein-coding open reading frames. We anticipate that the genome will provide
AB  - insights into the strain's lifestyle and the evolution of Marinobacter.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Hou, S.
AU  - Hayashi, K.
AU  - Anderson, J.
AU  - Donachie, S.P.
TI  - Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook  off O'ahu, Hawai'i.
JO  - Genome Announcements
PY  - 2016
SP  - e01390
EP  - e01316
VL  - 4
AB  - Rheinheimera salexigens KH87T is an obligately halophilic gammaproteobacterium. The strain's
AB  - draft genome sequence, generated by the Roche 454 GS FLX+ platform,
AB  - comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding
AB  - sequences and 58 tRNA coding regions. The G+C content is 42 mol%.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Hou, S.
AU  - Phan, N.
AU  - Malone, M.J.S.
AU  - Donachie, S.P.
AU  - Alam, M.
TI  - Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii.
JO  - Genome Announcements
PY  - 2015
SP  - e00321
EP  - e00315
VL  - 3
AB  - Most Pantoea spp. have been isolated from plant sources or clinical samples. However, we
AB  - cultivated Pantoea anthophila 11-2 from hypersaline water from the
AB  - lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2
AB  - provides a molecular basis for studies in evolution and pathogenicity in Pantoea
AB  - spp.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Hou, S.
AU  - Saito, J.A.
AU  - Kaneshiro, K.Y.
AU  - Donachie, S.P.
TI  - Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub.
JO  - Genome Announcements
PY  - 2015
SP  - e01222
EP  - e01215
VL  - 3
AB  - Flavobacterium spp. have been cultivated from diverse aquatic and terrestrial habitats. F.
AB  - akiainvivens IK-1(T) was cultivated from decaying wood of Wikstroemia oahuensis, an endemic
AB  - Hawaiian shrub. The strain's genome sequence may provide insights into niche adaptation and
AB  - evolution of the genus in a mid-ocean archipelago.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Lee, A.J.
AU  - Hou, S.
AU  - Ushijima, B.
AU  - Nguyen, Y.P.
AU  - Thawley, J.A.
AU  - Donachie, S.P.
TI  - Draft Genome Sequence of Piscirickettsia litoralis, Isolated from Seawater.
JO  - Genome Announcements
PY  - 2016
SP  - e01252
EP  - e01216
VL  - 4
AB  - One species of Piscirickettsia, a pathogen of salmonid fish, has been described.  The genome
AB  - sequence of a putative second and free-living species may provide
AB  - insights into the evolution of pathogenicity in the genus.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Miller, J.M.
AU  - Rowley, S.J.
AU  - Hou, S.
AU  - Donachie, S.P.
TI  - Draft Genome Sequence of a Novel Luteimonas sp. Strain from Coral Mucus, Hawai'i.
JO  - Genome Announcements
PY  - 2016
SP  - e01228
EP  - e01216
VL  - 4
AB  - Luteimonas sp. strain JM171 was cultivated from mucus collected around the coral  Porites
AB  - lobata The JM171 draft genome of 2,992,353 bp contains 2,672
AB  - protein-coding open reading frames, 45 tRNA coding regions, and encodes a
AB  - putative globin-coupled diguanylate cyclase, JmGReg.
ER  -

TY  - JOUR
AU  - Wan, X.
AU  - Qian, L.
AU  - Hou, S.
AU  - Drees, K.P.
AU  - Foster, J.T.
AU  - Douglas, J.T.
TI  - Complete Genome Sequences of Beijing and Manila Family Strains of Mycobacterium tuberculosis.
JO  - Genome Announcements
PY  - 2014
SP  - e01135
EP  - e01114
VL  - 2
AB  - The majority of isolates from tuberculosis patients in Hawaii arrive through the  immigration
AB  - of infected individuals from the western Pacific. We report here on
AB  - the annotated complete genomes of two strains of Mycobacterium tuberculosis from
AB  - the two main lineages/families in Hawaii, Beijing and Manila.
ER  -

TY  - JOUR
AU  - Wan, Y.
AU  - Gorrie, C.L.
AU  - Jenney, A.
AU  - Mirceta, M.
AU  - Holt, K.E.
TI  - Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.
JO  - Genome Announcements
PY  - 2015
SP  - e01007
EP  - e01015
VL  - 3
AB  - Serratia marcescens strain AH0650_Sm1 is a clinical multidrug-resistant isolate from
AB  - Australia. Here, we report its annotated draft genome comprising 20 contigs. We identified
AB  - chromosomal antimicrobial resistance genes including a tet(41) variant, an aac(6')-Ic
AB  - variant, ampC, a metallo-beta-lactamase, and several putative multidrug efflux pumps, as well
AB  - as a novel prophage.
ER  -

TY  - JOUR
AU  - Wanchanthuek, P.
AU  - Bellgard, M.I.
AU  - La, T.
AU  - Ryan, K.
AU  - Moolhuijzen, P.
AU  - Chapman, B.
AU  - Black, M.
AU  - Schibeci, D.
AU  - Hunter, A.
AU  - Barrero, R.
AU  - Phillips, N.D.
AU  - Hampson, D.J.
TI  - The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes.
JO  - PLoS ONE
PY  - 2010
SP  - E11455
EP  - E11455
VL  - 5
AB  - BACKGROUND: The anaerobic spirochete Brachyspira pilosicoli colonizes the
AB  - large intestine of various species of birds and mammals, including humans.
AB  - It causes "intestinal spirochetosis", a condition characterized by mild
AB  - colitis, diarrhea and reduced growth. This study aimed to sequence and
AB  - analyse the bacterial genome to investigate the genetic basis of its
AB  - specialized ecology and virulence. METHODOLOGY/PRINCIPAL FINDINGS: The
AB  - genome of B. pilosicoli 95/1000 was sequenced, assembled and compared with
AB  - that of the pathogenic Brachyspira hyodysenteriae and a near-complete
AB  - sequence of Brachyspira murdochii. The B. pilosicoli genome was circular,
AB  - composed of 2,586,443 bp with a 27.9 mol% G+C content, and encoded 2,338
AB  - genes. The three Brachyspira species shared 1,087 genes and showed
AB  - evidence of extensive genome rearrangements. Despite minor differences in
AB  - predicted protein functional groups, the species had many similar features
AB  - including core metabolic pathways. Genes distinguishing B. pilosicoli from
AB  - B. hyodysenteriae included those for a previously undescribed
AB  - bacteriophage that may be useful for genetic manipulation, for a glycine
AB  - reductase complex allowing use of glycine whilst protecting from oxidative
AB  - stress, and for aconitase and related enzymes in the incomplete TCA cycle,
AB  - allowing glutamate synthesis and function of the cycle during oxidative
AB  - stress. B. pilosicoli had substantially fewer methyl-accepting chemotaxis
AB  - genes than B. hyodysenteriae and hence these species are likely to have
AB  - different chemotactic responses that may help to explain their different
AB  - host range and colonization sites. B. pilosicoli lacked the gene for a new
AB  - putative hemolysin identified in B. hyodysenteriae WA1. Both B. pilosicoli
AB  - and B. murdochii lacked the rfbBADC gene cluster found on the B.
AB  - hyodysenteriae plasmid, and hence were predicted to have different
AB  - lipooligosaccharide structures. Overall, B. pilosicoli 95/1000 had a
AB  - variety of genes potentially contributing to virulence.
AB  - CONCLUSIONS/SIGNIFICANCE: The availability of the complete genome sequence
AB  - of B. pilosicoli 95/1000 will facilitate functional genomics studies aimed
AB  - at elucidating host-pathogen interactions and virulence.
ER  -

TY  - JOUR
AU  - Wanees, A.E.
AU  - Zaslow, S.J.
AU  - Potter, S.J.
AU  - Hsieh, B.P.
AU  - Boss, B.L.
AU  - Izquierdo, J.A.
TI  - Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4,  Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata.
JO  - Genome Announcements
PY  - 2018
SP  - e00410
EP  - e00418
VL  - 6
AB  - Sphingobium sp. strain AEW4 is a novel isolate from rhizosphere soil attached to  the root of
AB  - the American beachgrass Ammophila breviligulata The genomic sequence
AB  - consisted of 4,678,518 bp and 4,428 protein-coding sequences. Here we report the
AB  - draft genome sequence of this strain and some initial insights on its plant
AB  - growth-promoting capabilities.
ER  -

TY  - JOUR
AU  - Wang, A.
AU  - Pattemore, J.
AU  - Ash, G.
AU  - Williams, A.
AU  - Hane, J.
TI  - Draft Genome Sequence of Bacillus thuringiensis Strain DAR 81934, Which Exhibits  Molluscicidal Activity.
JO  - Genome Announcements
PY  - 2013
SP  - e0017512
EP  - e0017512
VL  - 1
AB  - Bacillus thuringiensis has been widely used as a biopesticide for a long time. Its
AB  - molluscicidal activity, however, is rarely realized. Here, we report the
AB  - genome sequence of B. thuringiensis strain DAR 81934, a strain with molluscicidal
AB  - activity against the pest snail Cernuella virgata.
ER  -

TY  - JOUR
AU  - Wang, B.
AU  - Jian, J.
AU  - Lu, Y.
AU  - Cai, S.
AU  - Huang, Y.
AU  - Tang, J.
AU  - Wu, Z.
TI  - Complete Genome Sequence of Streptococcus agalactiae ZQ0910, a Pathogen Causing Meningoencephalitis in the GIFT Strain of Nile Tilapia (Oreochromis niloticus).
JO  - J. Bacteriol.
PY  - 2012
SP  - 5132
EP  - 5133
VL  - 194
AB  - Streptococcus agalactiae (group B streptococcus [GBS]) is a pathogen that causes
AB  - meningoencephalitis in Nile tilapia (Oreochromis niloticus). Here, we reported
AB  - the complete genome sequence of S. agalactiae strain ZQ0910, which was isolated
AB  - from the GIFT strain of Nile tilapia in Guangdong, China.
ER  -

TY  - JOUR
AU  - Wang, B.
AU  - Liu, H.
AU  - Ma, H.
AU  - Wang, C.
AU  - Liu, K.
AU  - Li, Y.
AU  - Hou, Q.
AU  - Ge, R.
AU  - Zhang, T.
AU  - Liu, F.
AU  - Ma, J.
AU  - Wang, Y.
AU  - Wang, H.
AU  - Xu, B.
AU  - Yao, G.
AU  - Xu, W.
AU  - Fan, L.
AU  - Ding, Y.
AU  - Du, B.
TI  - Complete Genome Sequence of Biocontroller Bacillus velezensis Strain JTYP2, Isolated from Leaves of Echeveria laui.
JO  - Genome Announcements
PY  - 2017
SP  - e00505
EP  - e00517
VL  - 5
AB  - Bacillus velezensis JTYP2 was isolated from the leaves of Echeveria laui in Qingzhou, China,
AB  - and may control some of the fungal pathogens of the plant. Here,
AB  - we present the complete genome sequence of B. velezensis JTYP2. Several gene
AB  - clusters related to its biosynthesis of antimicrobial compounds were predicted.
ER  -

TY  - JOUR
AU  - Wang, C.
AU  - Chen, Q.
AU  - Wang, R.
AU  - Shi, C.
AU  - Yan, X.
AU  - He, J.
AU  - Hong, Q.
AU  - Li, S.
TI  - A Novel Angular Dioxygenase Gene Cluster, Encoding 3-Phenoxybenzoate 1', 2' -Dioxygenase in Sphingobium wenxiniae JZ-1.
JO  - Appl. Environ. Microbiol.
PY  - 2014
SP  - 3811
EP  - 3818
VL  - 80
AB  - Sphingobium wenxiniae JZ-1 utilizes a wide range of pyrethroids and their
AB  - metabolic product 3-phenoxybenzoate as source of carbon and energy. A mutant
AB  - MJZ-1 defective in the degradation of 3-phenoxybenzoate was obtained by
AB  - successive streaking on LB agar. Comparison of the draft genomes of strain JZ-1
AB  - and MJZ-1 revealed that a 29,371 bp DNA fragment containing a putative angular
AB  - dioxygenase gene cluster pbaA1A2B is missing in strain MJZ-1. PbaA1, PbaA2 and
AB  - PbaB share 65%, 52% and 10% identities with the corresponding alpha, beta
AB  - subunits and the ferredoxin component of dioxin dioxygenase from Sphingomonas
AB  - wittichii RW1, respectively. Complementation of pbaA1A2B in strain MJZ-1 resulted
AB  - in the active 3-phenoxybenzoate 1' , 2' -dioxygenase, but the enzyme activity in
AB  - Escherichia coli cells was achieved only through the co-expression of pbaA1A2B
AB  - and a GR (glutathione reductase)-type reductase gene pbaC, indicating that the
AB  - 3-phenoxybenzoate 1' , 2' -dioxygenase belongs to Type IV Rieske non-heme iron
AB  - aromatic ring-hydroxylating oxygenase system consisting of an hetero-oligomeric
AB  - oxygenase, a [2Fe-2S]-type ferredoxin and a GR-type reductase. pbaC gene is not
AB  - located in the immediate vicinity of pbaA1A2B. 3-Phenoxybenzoate 1' , 2'
AB  - -dioxygenase catalyzes the hydroxylation in the 1' , 2' -positions of the phenol
AB  - moiety of 3-phenoxybenzoate, yielding 3-hydroxybenzoate and catechol. The
AB  - transcription of pbaA1A2B and pbaC were both induced by 3-phenoxybenzoate, but
AB  - the transcription level of pbaC was far low than that of pbaA1A2B, implying the
AB  - possibility that PbaC may be not the only reductase that can physiologically
AB  - transfer electrons to PbaA1A2B in strain JZ-1. Some GR-type reductases from other
AB  - sphingomonad strains could also transfer electrons to PbaA1A2B, suggesting that
AB  - PbaA1A2B has low specificity for reductase.
ER  -

TY  - JOUR
AU  - Wang, C.
AU  - Hu, X.
AU  - Liu, K.
AU  - Hou, Q.
AU  - Yang, Q.
AU  - Ding, Y.
AU  - Du, B.
TI  - Draft Genome Sequence of Bacillus methylotrophicus FKM10, a Plant Growth-Promoting Rhizobacterium Isolated from Apple Rhizosphere.
JO  - Genome Announcements
PY  - 2016
SP  - e01739
EP  - e01715
VL  - 4
AB  - Bacillus methylotrophicus FKM10 is a strain of plant growth-promoting rhizobacterium with
AB  - antimicrobial activity, which was isolated from apple
AB  - rhizosphere. Here, we present the genome sequence of B. methylotrophicus FKM10.
AB  - Two scaffolds were finally assembled, and several functional genes related to its
AB  - antimicrobial activity were discovered.
ER  -

TY  - JOUR
AU  - Wang, C.M.
AU  - Wu, Z.Y.
AU  - Shia, W.Y.
AU  - Jhou, Y.J.
AU  - Tung, K.C.
AU  - Shyu, C.L.
TI  - Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain Pet-3, Isolated from a Lizard (Hydrosaurus pustulatus).
JO  - Genome Announcements
PY  - 2015
SP  - e01420
EP  - e01414
VL  - 3
AB  - The whole-genome sequence for Campylobacter fetus subsp. testudinum, a pathogen isolated from
AB  - humans and turtles, has been reported recently. We present another  completed genome sequence
AB  - of the C. fetus subsp. testudinum strain pet-3, which was isolated from a lizard in Taiwan,
AB  - for further genomic comparison study.
ER  -

TY  - JOUR
AU  - Wang, C.X.
AU  - Zhu, S.L.
AU  - Wang, X.Y.
AU  - Feng, Y.
AU  - Li, B.
AU  - Li, Y.G.
AU  - Johnston, R.N.
AU  - Liu, G.R.
AU  - Zhou, J.
AU  - Liu, S.L.
TI  - Complete genome sequence of Salmonella enterica subspecies arizonae str. RKS2983.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 30
EP  - 30
VL  - 10
AB  - Salmonella arizonae (also called Salmonella subgroup IIIa) is a Gram-negative,
AB  - non-spore-forming, motile, rod-shaped, facultatively anaerobic bacterium. S.
AB  - arizonae strain RKS2983 was isolated from a human in California, USA. S. arizonae
AB  - lies somewhere between Salmonella subgroups I (human pathogens) and V (also
AB  - called S. bongori; usually non-pathogenic to humans) and so is an ideal model
AB  - organism for studies of bacterial evolution from non-human pathogen to human
AB  - pathogens. We hence sequenced the genome of RKS2983 for clues of genomic events
AB  - that might have led to the divergence and speciation of Salmonella into distinct
AB  - lineages with diverse host ranges and pathogenic features. The 4,574,836 bp
AB  - complete genome contains 4,203 protein-coding genes, 82 tRNA genes and 7 rRNA
AB  - operons. This genome contains several characteristics not reported to date in
AB  - Salmonella subgroup I or V and may provide information about the genetic
AB  - divergence of Salmonella pathogens.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Boukhalfa, H.
AU  - Ware, D.S.
AU  - Daligault, H.E.
TI  - Draft Genome Sequence of a Chromium-Reducing Strain, Pseudomonas fluorescens S613, Isolated from a Chromium-Contaminated Aquifer in Los Alamos, New Mexico.
JO  - Genome Announcements
PY  - 2017
SP  - e00241
EP  - e00217
VL  - 5
AB  - In this report, a chromium-reducing bacterium, Pseudomonas fluorescens strain S613, was
AB  - isolated from a Cr(VI)-contaminated aquifer at Los Alamos, NM, and
AB  - sequenced. The size of the draft genome sequence is approximately 6.7 Mb.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Boukhalfa, H.
AU  - Ware, D.S.
AU  - Reimus, P.W.
AU  - Daligault, H.E.
AU  - Gleasner, C.D.
AU  - Johnson, S.L.
AU  - Li, P.E.
TI  - Genome Sequence of a Chromium-Reducing Strain, Bacillus cereus S612.
JO  - Genome Announcements
PY  - 2015
SP  - e01392
EP  - e01315
VL  - 3
AB  - We report here the genome sequence of an effective chromium-reducing bacterium, Bacillus
AB  - cereus strain S612. The size of the draft genome sequence is
AB  - approximately 5.4 Mb, with a G+C content of 35%, and it is predicted to contain
AB  - 5,450 protein-coding genes.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Han, C.S.
AU  - Dichosa, A.E.
AU  - Gleasner, C.D.
AU  - Johnson, S.L.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Li, P.E.
AU  - Pierson, E.A.
AU  - Pierson, L.S.I.I.I.
TI  - Draft Genome Sequence of Enterobacter cloacae Strain S611.
JO  - Genome Announcements
PY  - 2014
SP  - e00710
EP  - e00714
VL  - 2
AB  - We report draft genomes of Enterobacter cloacae strain S611, an endophytic bacterium isolated
AB  - from surface-sterilized germinating wheat seeds. We present
AB  - the assembly and annotation of its genome, which may provide insights into the
AB  - metabolic pathways involved in adaptation.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Han, C.S.
AU  - Dichosa, A.E.
AU  - Gleasner, C.D.
AU  - Johnson, S.L.
AU  - Daligault, H.E.
AU  - Davenport, K.W.
AU  - Li, P.E.
AU  - Pierson, E.A.
AU  - Pierson, L.S.I.I.I.
TI  - Draft Genome Sequence of Pseudomonas putida Strain S610, a Seed-Borne Bacterium of Wheat.
JO  - Genome Announcements
PY  - 2013
SP  - e01048
EP  - e01013
VL  - 1
AB  - We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The
AB  - size of the draft genome sequence is approximately 4.6 Mb, which
AB  - is the smallest among all P. putida strains sequenced to date.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Hildebrand, F.
AU  - Ye, L.
AU  - Wei, Q.
AU  - Ma, L.Z.
TI  - Genome Sequence of Mucoid Pseudomonas aeruginosa Strain FRD1.
JO  - Genome Announcements
PY  - 2015
SP  - e00376
EP  - e00315
VL  - 3
AB  - Pseudomonas aeruginosa is an important opportunistic pathogen. Strain FRD1 is a mucoid isolate
AB  - from the sputum of a cystic fibrosis patient. It has been widely
AB  - studied and has many different phenotypes compared to nonmucoid strains. Here, we
AB  - present the draft genome sequence of P. aeruginosa strain FRD1 to gain insight
AB  - into mucoid isolates.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Miyazono, K.I.
AU  - Tanokura, M.
TI  - Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.
JO  - Sci. Rep.
PY  - 2016
SP  - 35197
EP  - 35197
VL  - 6
AB  - R.PabI is a type II restriction enzyme that recognizes the 5'-GTAC-3' sequence and belongs
AB  - to the HALFPIPE superfamily. Although most restriction enzymes cleave
AB  - phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine
AB  - and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes
AB  - the N-glycosidic bond of the flipped adenine in a similar manner to DNA
AB  - glycosylases. In this study, we determined the structure of R.PabI in complex
AB  - with double-stranded DNA without the R.PabI recognition sequence by X-ray
AB  - crystallography. The 1.9 A resolution structure of the complex showed that R.PabI
AB  - forms a tetrameric structure to sandwich the double-stranded DNA and the
AB  - tetrameric structure is stabilized by four salt bridges. DNA binding and DNA
AB  - glycosylase assays of the R.PabI mutants showed that the residues that form the
AB  - salt bridges (R70 and D71) are essential for R.PabI to find the recognition
AB  - sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize
AB  - the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide
AB  - along it to find the recognition sequence.
ER  -

TY  - JOUR
AU  - Wang, D.
AU  - Zhu, F.
AU  - Zhu, X.
AU  - Zheng, S.
AU  - Wang, R.
AU  - Wang, G.
TI  - Draft genomic sequence of a selenite-reducing bacterium, Paenirhodobacter enshiensis DW2-9(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 38
EP  - 38
VL  - 10
AB  - Paenirhodobacter enshiensis is a non-photosynthetic species that belongs to family
AB  - Rhodobacteraceae. Here we report the draft genome sequence of
AB  - Paenirhodobacter enshiensis DW2-9(T) and comparison results to the available
AB  - related genomes. The strain has a 3.4 Mbp genome sequence with G + C content of
AB  - 66.82 % and 2781 protein-coding genes. It lacks photosynthetic gene clusters and
AB  - putative proteins necessary in Embden-Meyerhof-Parnas (EMP) pathway, but contains
AB  - proteins in Entner-Doudoroff (ED) pathway instead. It shares 699 common genes
AB  - with nine related Rhodobacteraceae genomes, and possesses 315 specific genes.
ER  -

TY  - JOUR
AU  - Wang, F.
AU  - Elmquist, C.E.
AU  - Rizzo, C.J.
AU  - Stone, M.P.
TI  - Base-displaced intercalated structure of the food mutagen 2-amino-3methylimidazo[4,5-f]quinoline (IQ) in the recognition sequence  of the NarI restriction enzyme, a hotspot for-2 bp deletions.
JO  - ACS Abstracts
PY  - 2005
SP  - U1858
EP  - U1859
VL  - 230
AB  - 2-Amino-3-methylimidazo[4,5-f]quinoline (IQ) is a prominent member of heterocyclic mutagens
AB  - and carcinogens found during the cooking of meats. The C-G1-G2-C-G3-C-C recognition sequence
AB  - of the NarI restriction enzyme represents a hot spot for -2 frameshift mutations at G3. We
AB  - prepared and purified the oligodeoxynucleotide duplex containing the [IQ]dG adduct positioned
AB  - in the C-[IQ]G3-C NarI context, which was named NarIIQ3. NMR data revealed a base-displaced
AB  - intercalated conformation. Watson-Crick base pairing was perturbed at the adduct site. The
AB  - largest chemical shift perturbations were observed for the base aromatic protons in the
AB  - complementary strand, opposite to the adduct. Chemical shift perturbations were also observed
AB  - for the 31P resonances corresponding to the linkages between C6 and [IQ]G7, [IQ]G7 and C8, G17
AB  - and C18, and C18 and G19, the phosphodiesters around the adduct. There were twenty-one NOEs
AB  - observed between the IQ moiety and DNA protons. The [IQ]G3 aromatic protons had strong NOEs
AB  - with the sugar protons of the opposite C18, G17 and G19 in the complementary strand, and the
AB  - methyl protons of [IQ]G3 showed NOEs to C8 H6, G19 H8, G17 NH1 and G19 NH1. Deoxyribose
AB  - pseudorotational angles (P) were estimated by examining the 3JHH of sugar protons. J1'-2'
AB  - and J1'-2' were measured from ECOSY spectra, while the intensities of H2'-H3' and
AB  - H3'-H4' crosspeaks were determined from DQF-COSY spectra. Molecular dynamics calculations on
AB  - NarIIQ3, restrained by 1H NOEs and J couplings, yielded ensembles of intercalated structures
AB  - in which the modified guanine was in a syn alignment and displaced. NOE intensities calculated
AB  - using complete relaxation matrix theory were in agreement with experimental NOE intensities.
AB  - Structural differences between NarIIQ3 and NarIAF3 could provide insight into the greater
AB  - biological activity of IQ than that of AF. Funded by grant CA-55678.
ER  -

TY  - JOUR
AU  - Wang, F.
AU  - Gong, L.
AU  - Zhou, L.
AU  - Liang, J.
TI  - Complete Genome Sequence of the Poly-gamma-Glutamate-Synthesizing Bacterium Bacillus subtilis Bs-115.
JO  - Genome Announcements
PY  - 2018
SP  - e00197
EP  - e00118
VL  - 6
AB  - Bacillus subtilis Bs-115 was isolated from the soil of a corn field in Yutai County, Jinan
AB  - City, Shandong Province, People's Republic of China, and is
AB  - characterized by the efficient synthesis of poly-gamma-glutamate (gamma-PGA),
AB  - with corn saccharification liquid as the sole energy and carbon source during the
AB  - process of gamma-PGA formation. Here, we report the complete genome sequence of
AB  - Bacillus subtilis Bs-115 and the genes associated with poly-gamma-glutamate
AB  - synthesis.
ER  -

TY  - JOUR
AU  - Wang, F.
AU  - Wang, J.
AU  - Jian, H.
AU  - Zhang, B.
AU  - Li, S.
AU  - Wang, F.
AU  - Zeng, X.
AU  - Gao, L.
AU  - Bartlett, D.H.
AU  - Yu, J.
AU  - Hu, S.
AU  - Xiao, X.
TI  - Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3.
JO  - PLoS ONE
PY  - 2008
SP  - E1937
EP  - E1937
VL  - 3
AB  - Shewanella species are widespread in various environments. Here, the
AB  - genome sequence of Shewanella piezotolerans WP3, a piezotolerant and
AB  - psychrotolerant iron reducing bacterium from deep-sea sediment was
AB  - determined with related functional analysis to study its environmental
AB  - adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs
AB  - (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or
AB  - gene clusters which help it to cope with extreme living conditions such as
AB  - genes for two sets of flagellum systems, structural RNA modification,
AB  - eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and
AB  - synthesis. And WP3 contains 55 open reading frames encoding putative
AB  - c-type cytochromes which are substantial to its wide environmental
AB  - adaptation ability. The mtr-omc gene cluster involved in the insoluble
AB  - metal reduction in the Shewanella genus was identified and compared. The
AB  - two sets of flagellum systems were found to be differentially regulated
AB  - under low temperature and high pressure; the lateral flagellum system was
AB  - found essential for its motility and living at low temperature.
ER  -

TY  - JOUR
AU  - Wang, G.
AU  - Barrett, N.H.
AU  - McCarthy, P.J.
TI  - Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.
JO  - Genome Announcements
PY  - 2017
SP  - e01508
EP  - e01516
VL  - 5
AB  - The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge
AB  - Leiodermatium sp. Here, we report the draft genome sequence of
AB  - this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%.
AB  - The results will aid deep-sea microbial ecology, evolution, and sponge-microbe
AB  - association studies.
ER  -

TY  - JOUR
AU  - Wang, G.H.
TI  - High-Efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR) for Determination of a Highly Degenerated Prophage WO Genome in a Wolbachia Strain Infecting a Fig Wasp Species.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 7476
EP  - 7481
VL  - 79
ER  -

TY  - JOUR
AU  - Wang, G.L.
AU  - Zhou, L.Y.
AU  - Luo, H.Q.
AU  - Li, N.B.
TI  - Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity.
JO  - Anal. Chim. Acta
PY  - 2013
SP  - 76
EP  - 81
VL  - 768
AB  - The present work demonstrates a novel signal-off electrochemical method for the determination
AB  - of DNA methylation and the assay of
AB  - methyltransferase activity using the electroactive complex
AB  - [Ru(NH3)(6)](3+) (RuHex) as a signal transducer. The assay exploits the
AB  - electrostatic interactions between RuHex and DNA strands. Thiolated
AB  - single strand DNA1 was firstly self-assembled on a gold electrode via
AB  - Au-S bonding, followed by hybridization with single strand DNA2 to form
AB  - double strand DNA containing specific recognition sequence of DNA
AB  - adenine methylation MTase and methylation-responsive restriction
AB  - endonuclease Dpn I. The double strand DNA may adsorb lots of
AB  - electrochemical species (Ru(NH3)(6)](3+)) via the electrostatic
AB  - interaction, thus resulting in a high electrochemical signal. In the
AB  - presence of DNA adenine methylation methyltransferase and
AB  - S-adenosyl-L-methionine, the formed double strand DNA was methylated by
AB  - DNA adenine methylation methyltransferase, then the double strand DNA
AB  - can be cleaved by methylation-responsive restriction endonuclease Dpn
AB  - I, leading to the dissociation of a large amount of signaling probes
AB  - from the electrode. As a result, the adsorption amount of RuHex
AB  - reduced, resulting in a decrease in electrochemical signal. Thus, a
AB  - sensitive electrochemical method for detection of DNA methylation is
AB  - proposed. The proposed method yielded a linear response to
AB  - concentration of Dam MTase ranging from 0.25 to IOU mL(-1) with a
AB  - detection limit of 0.18 U mL(-1) (S/N = 3), which might promise this
AB  - method as a good candidate for monitoring DNA methylation in the
AB  - future.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Chen, Y.
AU  - Ayers, S.
AU  - Melka, D.
AU  - Laasri, A.
AU  - Payne, J.S.
AU  - Zheng, J.
AU  - Son, I.
AU  - Timme, R.
AU  - Kastanis, G.
AU  - Hammack, T.S.
AU  - Strain, E.
AU  - Allard, M.W.
AU  - Evans, P.S.
AU  - Brown, E.W.
TI  - Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Give, Isolated from an Imported Chili Powder Product.
JO  - Genome Announcements
PY  - 2015
SP  - e00726
EP  - e00715
VL  - 3
AB  - We report the genome sequence of Salmonella enterica subsp. enterica serovar Give
AB  - (CFSAN012622), isolated from imported chili powder in 2014. This genome contains
AB  - genes previously reported to be specific only to S. enterica serovar Enteritidis.
AB  - This strain shows a unique pulsed-field gel electrophoresis (PFGE) pattern
AB  - clustering with serovar Enteritidis (JEG X01.0005).
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Guan, S.
AU  - Quimby, A.
AU  - Cohen-Karni, D.
AU  - Pradhan, S.
AU  - Wilson, G.
AU  - Roberts, R.J.
AU  - Zhu, Z.
AU  - Zheng, Y.
TI  - Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 9294
EP  - 9305
VL  - 39
AB  - PvuRts1I is a modification-dependent restriction endonuclease that recognizes
AB  - 5-hydroxymethylcytosine (5hmC) as well as
AB  - 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA. Using
AB  - PvuRts1I as the founding member, we define a family of homologous proteins
AB  - with similar DNA modification-dependent recognition properties. At the
AB  - sequence level, these proteins share a few uniquely conserved features. We
AB  - show that these enzymes introduce a double-stranded cleavage at the
AB  - 3'-side away from the recognized modified cytosine. The distances between
AB  - the cleavage sites and the modified cytosine are fixed within a narrow
AB  - range, with the majority being 11-13 nt away in the top strand and 9-10 nt
AB  - away in the bottom strand. The recognition sites of these enzymes
AB  - generally require two cytosines on opposite strand around the cleavage
AB  - sites, i.e. 5'-CN(11-13) downward arrowN(9-10)G-3'/3'-GN(9-10) downward
AB  - arrowN(11-13)C-5', with at least one cytosine being modified for efficient
AB  - cleavage. As one potential application for these enzymes is to provide
AB  - useful tools for selectively mapping 5hmC sites, we have compared the
AB  - relative selectivity of a few PvuRts1I family members towards different
AB  - forms of modified cytosines. Our results show that the inherently
AB  - different relative selectivity towards modified cytosines can have
AB  - practical implications for their application. By using AbaSDFI, a PvuRts1I
AB  - homolog with the highest relative selectivity towards 5ghmC, to analyze
AB  - rat brain DNA, we show it is feasible to map genomic 5hmC sites close to
AB  - base resolution. Our study offers unique tools for determining more
AB  - accurate hydroxymethylomes in mammalian cells.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Li, H.
AU  - Shao, Z.
AU  - Liao, S.
AU  - Johnstone, L.
AU  - Rensing, C.
AU  - Wang, G.
TI  - Genome Sequence of Deep-Sea Manganese-Oxidizing Bacterium Marinobacter manganoxydans MnI7-9.
JO  - J. Bacteriol.
PY  - 2012
SP  - 899
EP  - 900
VL  - 194
AB  - Here we report the draft genome of Marinobacter manganoxydans MnI7-9, isolated from a deep-sea
AB  - hydrothermal vent in the Indian Ocean and capable
AB  - of oxidizing manganese even when there is a very high concentration of
AB  - Mn(2+). The strain also displayed high resistance and adsorption ability
AB  - toward many metal(loid)s.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Lin, H.
AU  - Tran-Dinh, N.
AU  - Li, D.
AU  - Greenfield, P.
AU  - Midgley, D.J.
TI  - Draft Genome Sequence of Ruminoclostridium sp. Ne3, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.
JO  - Genome Announcements
PY  - 2015
SP  - e00305
EP  - e00315
VL  - 3
AB  - The draft genome sequence of Ruminoclostridium sp. Ne3 was reconstructed from the metagenome
AB  - of a hydrogenogenic microbial consortium growing on xylan. The
AB  - organism is likely the primary hemicellulose degrader within the consortium.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Lin, H.
AU  - Tran-Dinh, N.
AU  - Li, D.
AU  - Greenfield, P.
AU  - Midgley, D.J.
TI  - Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.
JO  - Genome Announcements
PY  - 2015
SP  - e00304
EP  - e00315
VL  - 3
AB  - The draft genome sequence of Clostridium sp. Ne2 was reconstructed from a metagenome of a
AB  - hydrogenogenic microbial consortium. The organism is most closely
AB  - related to Clostridium magnum and is a strict anaerobe that is predicted to
AB  - ferment a range of simple sugars.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Lin, H.
AU  - Tran-Dinh, N.
AU  - Li, D.
AU  - Greenfield, P.
AU  - Midgley, D.J.
TI  - Draft Genome Sequence of Clostridium beijerinckii Ne1, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes  exitiosus.
JO  - Genome Announcements
PY  - 2015
SP  - e00303
EP  - e00315
VL  - 3
AB  - The draft genome of Clostridium beijerinckii strain Ne1 was reconstructed from the metagenomic
AB  - sequence of a mixed-microbial consortium that produced
AB  - commercially significant quantities of hydrogen from xylan as a sole feedstock.
AB  - The organism possesses relatively limited hemicellulolytic capacity and likely
AB  - requires the action of other organisms to completely degrade xylan.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Sivonen, K.
AU  - Rouhiainen, L.
AU  - Fewer, D.P.
AU  - Lyra, C.
AU  - Rantala-Ylinen, A.
AU  - Vestola, J.
AU  - Jokela, J.
AU  - Rantasarkka, K.
AU  - Li, Z.
AU  - Liu, B.
TI  - Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90.
JO  - BMC Genomics
PY  - 2012
SP  - 613
EP  - 613
VL  - 13
AB  - ABSTRACT: BACKGROUND: Cyanobacteria can form massive toxic blooms in fresh and
AB  - brackish bodies of water and are frequently responsible for the poisoning of
AB  - animals and pose a health risk for humans. Anabaena is a genus of filamentous
AB  - diazotrophic cyanobacteria commonly implicated as a toxin producer in blooms in
AB  - aquatic ecosystems throughout the world. The biology of bloom-forming
AB  - cyanobacteria is poorly understood at the genome level. RESULTS: Here, we report
AB  - the complete sequence and comprehensive annotation of the bloom-forming Anabaena
AB  - sp. strain 90 genome. It comprises two circular chromosomes and three plasmids
AB  - with a total size of 5.3 Mb, encoding a total of 4,738 genes. The genome is
AB  - replete with mobile genetic elements. Detailed manual annotation demonstrated
AB  - that almost 5% of the gene repertoire consists of pseudogenes. A further 5% of
AB  - the genome is dedicated to the synthesis of small peptides that are the products
AB  - of both ribosomal and nonribosomal biosynthetic pathways. Inactivation of the
AB  - hassallidin (an antifungal cyclic peptide) biosynthetic gene cluster through a
AB  - deletion event and a natural mutation of the buoyancy-permitting gvpG gas vesicle
AB  - gene were documented. The genome contains a large number of genes encoding
AB  - restriction-modification systems. Two novel excision elements were found in the
AB  - nifH gene that is required for nitrogen fixation. CONCLUSIONS: Genome analysis
AB  - demonstrated that this strain invests heavily in the production of bioactive
AB  - compounds and restriction-modification systems. This well-annotated genome
AB  - provides a platform for future studies on the ecology and biology of these
AB  - important bloom-forming cyanobacteria.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Wang, L.
AU  - Ju, J.
AU  - Yu, B.
AU  - Ma, Y.
TI  - Genome Sequence of Sporolactobacillus laevolacticus DSM442, an Efficient Polymer-Grade D-Lactate Producer from Agricultural Waste Cottonseed as a Nitrogen  Source.
JO  - Genome Announcements
PY  - 2013
SP  - e01100
EP  - e01113
VL  - 1
AB  - Sporolactobacillus laevolacticus DSM442 is an efficient polymer-grade d-lactic acid producer
AB  - from low-cost agricultural waste cottonseed powder as the sole
AB  - nitrogen source. Here we present a 3.59-Mb assembly of its genome sequence, which
AB  - might provide useful information to further improve the strain for higher
AB  - production titers.
ER  -

TY  - JOUR
AU  - Wang, H.
AU  - Zheng, J.
AU  - Ayers, S.
AU  - Melka, D.C.
AU  - Curry, P.E.
AU  - Payne, J.S.
AU  - Laasri, A.
AU  - Wang, C.
AU  - Hammack, T.S.
AU  - Brown, E.W.
TI  - Draft Genome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium and Nottingham Isolated from Food Products.
JO  - Genome Announcements
PY  - 2016
SP  - e00699
EP  - e00616
VL  - 4
AB  - A quantitative real-time PCR (qPCR) designed to detect Salmonella enterica subsp. enterica
AB  - serovar Enteritidis, targeting the sdf gene, generated positive results
AB  - for S. enterica subsp. enterica serovar Typhimurium (CFSAN033950) and S. enterica
AB  - subsp. enterica serovar Nottingham (CFSAN006803) isolated from food samples. Both
AB  - strains show pulsed-field gel electrophoresis (PFGE) patterns distinct from those
AB  - of S Enteritidis. Here, we report the genome sequences of these two strains.
ER  -

TY  - JOUR
AU  - Wang, H.-L.
AU  - Wang, H.-R.
AU  - Zhang, W.-W.
AU  - Sun, L.
TI  - Cloning and analysis of the Vibrio harveyi dam gene.
JO  - Wei Sheng Wu Xue Bao
PY  - 2007
SP  - 855
EP  - 859
VL  - 47
AB  - The DNA adenine methylase (dam) gene was cloned by degenerate PCR from Vibrio harveyi strain
AB  - T4. The gene was 840bp in length and encoded a
AB  - putative protein of 279 amino acids that shared relatively high
AB  - homology with the Dam of other Vibrias, especially with that of V.
AB  - parahaemolyticus (96% in identity). The V. harveyi dam gene was
AB  - subcloned into plasmid pBR322 and the resulting plasmid pBD was
AB  - introduced into the E. coli strain ER2925 in which the dam gene had
AB  - been knocked out. Dpn I, Dpn II, and Sau3A I restriction enzyme
AB  - analysis of the genomic DNA of ER2925 transformed with p13D indicated
AB  - that the cloned V. harveyi dam gene could functionally complement the
AB  - E. coli dam mutant and methylate E. coli chromosome at the GATC sites.
AB  - The 3251 bp upstream region of V. harveyi dam was obtained by genome
AB  - walking and analyzed at the sequence level. It was found that this 3251
AB  - bp region contained two complete open reading frames (ORF) : one was of
AB  - 1101 bp in length and the other was of 1503 bp in length. The predicted
AB  - amino acid sequence of ORF1101 shared 91% identity with the
AB  - 3-dehydroquinate synthase of V. parahaemolyticus. The amino acid
AB  - sequence of ORF1503 shared 80% identity with V. parahaemolylicus DamX.
AB  - A truncated ORF was found at the upstream of ORF1101, encoding 169
AB  - amino acids that shared 94% identity with the shikimate kinase of V.
AB  - parahaemolyticus. These three genes, together with dam, were arranged
AB  - in the order of shikimate kinase-3-dehydroquinate synthase-damX-dam.
AB  - The region immediate upstream of the V. harveyi dam structural gene was
AB  - cloned in three fragments of different length: 78bp, 112 bp and 477bp
AB  - (named P78, P112, and P477, respectively) and tested for promoter
AB  - activity. The results showed that, while all the three fragments had
AB  - detectable promoter activities, the activity of P78 appeared to be
AB  - higher than that of P-112 and P-477.
ER  -

TY  - JOUR
AU  - Wang, H.C.
AU  - Cheng, F.C.
AU  - Wu, M.S.
AU  - Shu, H.Y.
AU  - Sun, H.S.
AU  - Wang, Y.C.
AU  - Su, I.J.
AU  - Wu, C.J.
TI  - Genome Sequences of Three Helicobacter pylori Strains from Patients with Gastric  Mucosa-Associated Lymphoid Tissue Lymphoma.
JO  - Genome Announcements
PY  - 2015
SP  - e00229
EP  - e00215
VL  - 3
AB  - Most of the published complete genome sequences of Helicobacter pylori strains are limited to
AB  - clinical isolates associated with gastritis, peptic ulcers, or
AB  - gastric cancer. The genome sequences of three H. pylori strains isolated from
AB  - patients with gastric mucosa-associated lymphoid tissue (MALT) lymphoma are
AB  - presented here to facilitate studies of H. pylori-associated MALT
AB  - lymphomagenesis.
ER  -

TY  - JOUR
AU  - Wang, H.C.
AU  - Ko, W.C.
AU  - Shu, H.Y.
AU  - Chen, P.L.
AU  - Wang, Y.C.
AU  - Wu, C.J.
TI  - Genome Sequence of Aeromonas taiwanensis LMG 24683T, a Clinical Wound Isolate from Taiwan.
JO  - Genome Announcements
PY  - 2014
SP  - e00579
EP  - e00514
VL  - 2
AB  - Aeromonas taiwanensis was first described in 2010 on the basis of one clinical wound isolate
AB  - (strain LMG 24683(T) = A2-50(T) = CECT 7403(T)) from Taiwan. We
AB  - present here the genome sequence of A. taiwanensis LMG 24683(T), which carries
AB  - several genes encoding virulence determinants and Ambler class C and D
AB  - beta-lactamases.
ER  -

TY  - JOUR
AU  - Wang, H.F.
AU  - Muren, N.B.
AU  - Ordinario, D.
AU  - Gorodetsky, A.A.
AU  - Barton, J.K.
AU  - Nuckolls, C.
TI  - Transducing methyltransferase activity into electrical signals in a carbon nanotube-DNA device.
JO  - Chem. Sci.
PY  - 2012
SP  - 62
EP  - 65
VL  - 3
AB  - This study creates a device where the DNA is electronically integrated to serve as both the
AB  - biological target and electrical transducer in a CNT-DNA-CNT device. We detect DNA binding and
AB  - methylation by the methyltransferase M.SssI at the single molecule level. We demonstrate
AB  - sequence-specific, reversible binding of M.SssI and protein-catalyzed methylation that alters
AB  - the protein-binding affinity of the device. This device, which relies on the exquisite
AB  - electrical sensitivity of DNA, represents a unique route for the specific, single molecule
AB  - detection of enzymatic activity.
ER  -

TY  - JOUR
AU  - Wang, H.X.
AU  - Wang, Y.S.
TI  - 6-Thioguanine Perturbs Cytosine Methylation at the CpG Dinucleotide Site by DNA Methyltransferases in Vitro and Acts as a DNA Demethylating Agent in Vivo.
JO  - Biochemistry
PY  - 2009
SP  - 2290
EP  - 2299
VL  - 48
AB  - Thiopurines are among the most successful chemotherapeutic agents for treating a number of
AB  - human diseases including acute lymphoblastic
AB  - leukemia. The mechanisms through which the thiopurines elicit their
AB  - cytotoxic effects remain unclear. We postulate that the incorporation
AB  - of 6-thioguanine into the CpG site may perturb the
AB  - methyltransferase-mediated cytosine methylation at this site, thereby
AB  - interfering with the epigenetic pathways of gene regulation. To gain
AB  - biochemical evidence for this hypothesis, we assessed, by using a
AB  - restriction enzyme digestion coupled with LC-MS/MS method, the impact
AB  - of 6-thioguanine on cytosine methylation mediated by two DNA
AB  - methyltransferases, human DNMT1 and bacterial HpaII. Our results
AB  - revealed that the incorporation of 6-thioguanine into the CpG site
AB  - could affect the methylation of the cytosine residue by both
AB  - methyltransferases and the effect on cytosine methylation is dependent
AB  - on the position of 6-thioguanine with respect to the cytosine to be
AB  - methylated. The presence of 6-thioguanine at the methylated CpG site
AB  - enhanced the DNMT1-mediated methylation of the opposing cytosine in the
AB  - complementary strand, whereas the presence of 6-thioguanine at the
AB  - unmethylated CpG site abolished almost completely the methylation of
AB  - its 5' adjacent cytosine by both DNMT1 and HpaII. We further
AB  - demonstrated that the treatment of Jurkat T cells, which were derived
AB  - from acute lymphoblastic leukemia, with 6-thioguanine could result in
AB  - an appreciable drop in the level of global cytosine methylation. These
AB  - results showed that 6-thioguanine, after being incorporated into DNA,
AB  - may perturb the epigenetic pathway of gene regulation.
ER  -

TY  - JOUR
AU  - Wang, H.Z.
AU  - Wong, M.M.L.
AU  - O'Toole, D.
AU  - Mak, M.M.H.
AU  - Wu, R.S.S.
AU  - Kong, R.Y.C.
TI  - Identification of a DNA methyltransferase gene carried on a pathogenicity island-like element (VPAI) in Vibrio parahaemolyticus and  its prevalence among clinical and environmental isolates.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 4455
EP  - 4460
VL  - 72
AB  - In this study we identified a putative virulence-associated DNA methyltransferase (MTase) gene
AB  - carried on a novel 22.79-kb
AB  - pathogenicity island-like element (VPAI) in V. parahaemolyticus. The V.
AB  - parahaemolyticus MTase gene was shown by PCR to be prevalent (> 98%) in
AB  - pandemic thermostable direct hemolysin gene-positive isolates, which
AB  - suggests that VPAI may confer unique virulence traits to pandemic
AB  - strains of V. parahaemolyticus.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Geng, K.
AU  - Farhan, Ul.H.M.
AU  - Crombie, A.
AU  - Street, L.E.
AU  - Wookey, P.A.
AU  - Ma, K.
AU  - Murrell, J.C.
AU  - Pratscher, J.
TI  - Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph  Isolated from Permafrost.
JO  - Genome Announcements
PY  - 2018
SP  - e00040
EP  - e00018
VL  - 6
AB  - Permafrost environments play a crucial role in global carbon and methane cycling. We report
AB  - here the draft genome sequence of Methylocella silvestris TVC, a new
AB  - facultative methanotroph strain, isolated from the Siksik Creek catchment in the
AB  - continuous permafrost zone of Inuvik (Northwest Territories, Canada).
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Hevi, S.
AU  - Kurash, J.K.
AU  - Lei, H.
AU  - Gay, F.
AU  - Bajko, J.
AU  - Su, H.
AU  - Sun, W.
AU  - Chang, H.
AU  - Xu, G.
AU  - Gaudet, F.
AU  - Li, E.
AU  - Chen, T.
TI  - The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation.
JO  - Nat. Genet.
PY  - 2009
SP  - 125
EP  - 129
VL  - 41
AB  - Histone methylation and DNA methylation cooperatively regulate chromatin structure and gene
AB  - activity. How these two systems coordinate with each
AB  - other remains unclear. Here we study the biological function of
AB  - lysine-specific demethylase 1 (LSD1, also known as KDM1 and AOF2), which
AB  - has been shown to demethylate histone H3 on lysine 4 (H3K4) and lysine 9
AB  - (H3K9). We show that LSD1 is required for gastrulation during mouse
AB  - embryogenesis. Notably, targeted deletion of the gene encoding LSD1
AB  - (namely, Aof2) in embryonic stem (ES) cells induces progressive loss of
AB  - DNA methylation. This loss correlates with a decrease in DNA
AB  - methyltransferase 1 (Dnmt1) protein, as a result of reduced Dnmt1
AB  - stability. Dnmt1 protein is methylated in vivo, and its methylation is
AB  - enhanced in the absence of LSD1. Furthermore, Dnmt1 can be methylated by
AB  - Set7/9 (also known as KMT7) and demethylated by LSD1 in vitro. Our
AB  - findings suggest that LSD1 demethylates and stabilizes Dnmt1, thus
AB  - providing a previously unknown mechanistic link between the histone and
AB  - DNA methylation systems.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Hu, W.
AU  - Lux, R.
AU  - He, X.
AU  - Li, Y.
AU  - Shi, W.
TI  - Natural Transformation of Myxococcus xanthus.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2122
EP  - 2132
VL  - 193
AB  - Myxococcus xanthus belongs to the delta class of the proteobacteria and is notable for its
AB  - complex life-style with social behaviors and
AB  - relatively large genome. Although previous observations have suggested
AB  - the existence of horizontal gene transfer in M. xanthus, its ability to
AB  - take up exogenous DNA via natural transformation has not been
AB  - experimentally demonstrated. In this study, we achieved natural
AB  - transformation in M. xanthus using the autonomously replicating
AB  - myxobacterial plasmid pZJY41 as donor DNA. M. xanthus exopolysaccharide
AB  - (EPS) was shown to be an extracellular barrier for transformation.
AB  - Cells deficient in EPS production, e. g., mutant strains carrying Delta
AB  - difA or Delta epsA, became naturally transformable. Among the inner
AB  - barriers to transformation were restriction-modification systems in M.
AB  - xanthus, which could be partially overcome by methylating DNA in vitro
AB  - using cell extracts of M. xanthus prior to transformation. In addition,
AB  - the incubation time of DNA with cells and the presence of divalent
AB  - magnesium ion affected transformation frequency of M. xanthus.
AB  - Furthermore, we also observed a potential involvement of the type IV
AB  - pilus system in the DNA uptake machinery of M. xanthus. The natural
AB  - transformation was totally eliminated in the Delta pilQ/epsA and Delta
AB  - tgl/epsA mutants, and null mutation of pilB or pilC in an Delta epsA
AB  - background diminished the transformation rate. Our study, to the best
AB  - of our knowledge, provides the first example of a naturally
AB  - transformable species among deltaproteobacteria.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Hurley, D.
AU  - McGrath, K.
AU  - Bai, L.
AU  - Hachler, H.
AU  - Stephan, R.
AU  - Fanning, S.
TI  - Draft Genome Sequence of Escherichia coli 26R 793, a Plasmid-Free Recipient Strain Commonly Used in Conjugation Assays.
JO  - Genome Announcements
PY  - 2016
SP  - e00707
EP  - e00716
VL  - 4
AB  - Here, we report the draft genome sequence of the lactose-negative, rifampin-resistant,
AB  - Escherichia coli strain 26R 793. This isolate has been widely
AB  - used in conjugation experiments as a general recipient strain.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Jiang, Y.
AU  - Vincent, M.
AU  - Sun, Y.
AU  - Yu, H.
AU  - Wang, J.
AU  - Bao, Q.
AU  - Kong, H.
AU  - Hu, S.
TI  - Complete genome sequence of bacteriophage T5.
JO  - Virology
PY  - 2005
SP  - 45
EP  - 65
VL  - 332
AB  - The 121,752-bp genome sequence of bacteriophage T5 was determined; the
AB  - linear, double-stranded DNA is nicked in one of the strands and has large
AB  - direct terminal repeats of 10,139 bp (8.3%) at both ends. The genome
AB  - structure is consistently arranged according to its lytic life cycle. Of
AB  - the 168 potential open reading frames (ORFs), 61 were annotated; these
AB  - annotated ORFs are mainly enzymes involved in phage DNA replication,
AB  - repair, and nucleotide metabolism. At least five endonucleases that
AB  - believed to help inducing nicks in T5 genomic DNA, and a DNA ligase gene
AB  - was found to be split into two separate ORFs. Analysis of T5 early
AB  - promoters suggests a probable motif AAA{3, 4 T}nTTGCTT{17, 18
AB  - n}TATAATA{12, 13 W}{10 R} for strong promoters that may strengthen the
AB  - step modification of host RNA polymerase, and thus control transcription
AB  - of phage DNA. The distinct protein domain profile and a mosaic genome
AB  - structure suggest an origin from the common genetic pool.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Kim, H.-H.
AU  - Yuan, X.
AU  - Herrin, D.L.
TI  - Purification, biochemical characterization and protein-DNA interactions of the I-CreI endonuclease produced in Escherichia coli.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3767
EP  - 3776
VL  - 25
AB  - I-CreI is a member of the LAGLI-DADG family of homing nucleases; however, unlike most members
AB  - of this family it contains only a single copy of this signature motif.  I-CreI was
AB  - over-expressed in Escherichia coli, and a simple purification protocol developed that gave
AB  - reasonably pure protein in high yield.  Size-exclusion chromatography and chemical
AB  - cross-linking indicated that the protein is a dimer in solution.  DNA cleavage by I-CreI was
AB  - absolutely dependent on Mg2+ (or Mn2+), and was inhibited by monovalent cations.  I-CreI
AB  - displayed a surprisingly high temperature optimum (>50oC), with full activity occurring even
AB  - at 70oC.  Interestingly, SDS was needed for efficient release of the cleavage products from
AB  - the protein, indicating formation of very stable DNA-protein complexes.  In contrast to these
AB  - robust characteristics, purified I-CreI was unstable; however, it could be stabilized by the
AB  - addition of either target or non-target DNA.  Mobility shift assays revealed that I-CreI binds
AB  - to DNA in the absence of Mg2+.  Hydroxyl radical footprinting showed that I-CreI strongly
AB  - protected the backbone of a continuous stretch of at least 12 nt on each strand that were
AB  - shifted, relative to each other, by 2 bp in the 3' direction.  Methylation protection and
AB  - interference analyses were also performed, and together with the hydroxyl radical
AB  - footprinting, indicate that I-CreI binds in both the major and minor grooves of its target
AB  - DNA.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Kuenzel, S.
AU  - Baines, J.F.
TI  - Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species.
JO  - Genome Announcements
PY  - 2014
SP  - e01148
EP  - e01113
VL  - 2
AB  - We report here the draft genome sequences of 11 strains of Staphylococcus epidermidis, a
AB  - common bacterium inhabiting the skin of humans and other animals.
AB  - These isolates, obtained from five mouse species, provide valuable information on
AB  - the native Staphylococcus spp. of this important model organism and form a basis
AB  - for studying host-bacterial interactions in their natural environment.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Li, X.
AU  - Li, J.
AU  - Hurley, D.
AU  - Bai, X.
AU  - Yu, Z.
AU  - Cao, Y.
AU  - Wall, E.
AU  - Fanning, S.
AU  - Bai, L.
TI  - Complete genetic analysis of a Salmonella enterica serovar Indiana isolate accompanying four plasmids carrying mcr-1, ESBL and other resistance genes in China.
JO  - Vet. Microbiol.
PY  - 2017
SP  - 142
EP  - 146
VL  - 210
AB  - One mcr-1-carrying Salmonella enterica serovar Indiana strain D90, was identi and #64257;ed
AB  - from 1320 Salmonella enterica isolates from poultry slaughterhouse in 2012 in China. The
AB  - objective of this study was to verify the transferability of the mcr-1 gene and also
AB  - completely characterize the sequence of the strain at the whole-genome level. Broth matting
AB  - assays were carried out to detect the transferability and whole-genome sequencing (WGS) of S.
AB  - enterica serovar Indiana D90 was performed using the PacBio RS II system. Open reading frames
AB  - were assigned using Rapid Annotation using Subsystem Technology (RAST) and analysed by BLASTn
AB  - and BLASTp. Salmonella Pathogenisity Islands (SPIs) were annotated by SPIFinder platform. The
AB  - complete genome sequence of S. enterica serovar Indiana D90 contained a circular 4,779,514-bp
AB  - chromosome and four plasmids. Genome analysis and sequencing revealed that 24 multi-drug
AB  - resistance (MDR) genes were located on plasmids. The largest plasmid pD90-1, was found to be
AB  - of an IncHI2/HI2A/Q1/N type that encoded a blaCTX-M-65 gene along with 20 additional
AB  - antimicrobial resistance genes. A 60.5-kbp IncI2 plasmid pD90-2 contained a nikA-nikB-mcr-1
AB  - genetic structure, that can be successfully transferred to E. coli and S. enterica serovar
AB  - Typhimurium at low transfer rates. Interestingly, comparative sequence analysis revealed the
AB  - plasmids pD90-1 and pD90-2 showed considerable nucleotide similarity to pHNSHP45-2 and
AB  - pHNSHP45, respectively. Moreover, the genome and the plasmid pD90-2 also showed high
AB  - similarity to one carbapenem resistant S. enterica serovar Indiana strain, C629 and its
AB  - plasmid pC629, respectively. This is the  and #64257;rst report of the complete nucleotide
AB  - sequence of one mcr-1-carrying MDR S. enterica serovar Indiana strain.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Li, Y.
AU  - Guo, J.
AU  - Zhang, X.
AU  - Guo, Y.
AU  - Chang, D.
AU  - Li, T.
AU  - Xu, G.
AU  - Dai, W.
AU  - Liu, C.
TI  - Genome Sequence of Staphylococcus aureus Strain LCT-SA67, a Space Flight Strain with Altered Carbon Source Utilization Properties.
JO  - Genome Announcements
PY  - 2014
SP  - e00095
EP  - e00014
VL  - 2
AB  - An increasing number of studies have confirmed that space flight environments can have a
AB  - significant effect on a variety of microbial properties. To explore the
AB  - effect of these environments on Staphylococcus aureus, we present the draft
AB  - genome sequence of an S. aureus strain, named LCT-SA67, which was isolated after
AB  - space flight.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Liu, Y.
AU  - Wan, D.
AU  - Fang, X.
AU  - Li, T.
AU  - Guo, Y.
AU  - Chang, D.
AU  - Su, L.
AU  - Wang, Y.
AU  - Zhao, J.
AU  - Liu, C.
TI  - Whole-Genome Sequence of Staphylococcus aureus Strain LCT-SA112.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4124
EP  - 4124
VL  - 194
AB  - Staphylococcus aureus is a facultative anaerobic Gram-positive coccal bacterium.  S. aureus is
AB  - the most common species of Staphylococcus to cause staphylococcal
AB  - infections, which are very common in clinical medicine. Here we report the genome
AB  - sequence of S. aureus strain LCT-SA112, which was isolated from S. aureus subsp.
AB  - aureus CGMCC 1.230.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - McIntosh, F.
AU  - Radomski, N.
AU  - Dewar, K.
AU  - Simeone, R.
AU  - Enninga, J.
AU  - Brosch, R.
AU  - Rocha, E.P.
AU  - Veyrier, F.J.
AU  - Behr, M.A.
TI  - Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii.
JO  - Genome Biol. Evol.
PY  - 2015
SP  - 856
EP  - 870
VL  - 7
AB  - By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium
AB  - tuberculosis. Yet, although both organisms cause pulmonary disease,
AB  - M. tuberculosis is a global health menace, whereas M. kansasii is an
AB  - opportunistic pathogen. To illuminate the differences between these organisms, we
AB  - have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478)
AB  - and conducted side-by-side in vitro and in vivo investigations of these two
AB  - organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than
AB  - that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise
AB  - comparisons reveal conserved and discordant genes and genomic regions. A notable
AB  - example of genomic conservation is the virulence locus ESX-1, which is intact and
AB  - functional in the low-virulence M. kansasii, potentially mediating phagosomal
AB  - disruption. Differences between these organisms include a decreased predicted
AB  - metabolic capacity, an increased proportion of toxin-antitoxin genes, and the
AB  - acquisition of M. tuberculosis-specific genes in the pathogen since their common
AB  - ancestor. Consistent with their distinct epidemiologic profiles, following
AB  - infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over
AB  - 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3
AB  - weeks. Together, these data suggest that M. kansasii can serve as an image of the
AB  - environmental ancestor of M. tuberculosis before its emergence as a professional
AB  - pathogen, and can be used as a model organism to study the switch from an
AB  - environmental opportunistic pathogen to a professional host-restricted pathogen.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Niu, Y.D.
AU  - Chen, J.
AU  - McAllister, T.A.
AU  - Stanford, K.
TI  - Complete Genome Sequence of Escherichia coli O145:NM Bacteriophage vB_EcoM_AYO145A, a New Member of O1-Like Phages.
JO  - Genome Announcements
PY  - 2015
SP  - e00539
EP  - e00515
VL  - 3
AB  - Previously, bacteriophage vB_EcoM_AYO145A, which lyses Shiga toxin-producing Escherichia coli
AB  - O145:NM, was classified as an O1-like virus of the Myoviridae
AB  - family. Here, we report the complete genome sequence of this phage and a
AB  - comparative genomic analysis with other known O1-like phages.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Song, L.
AU  - Jiao, Q.
AU  - Yang, S.
AU  - Gao, R.
AU  - Lu, X.
AU  - Zhou, G.
TI  - Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease.
JO  - BMC Genomics
PY  - 2018
SP  - 689
EP  - 689
VL  - 19
AB  - BACKGROUND: JWB phytoplasma is a kind of insect-transmitted and uncultivable
AB  - bacterial plant pathogen causeing a destructive Jujube disease. To date, no
AB  - genome information about JWB phytoplasma has been published, which hindered its
AB  - characterization at genomic level. To understand its pathogenicity and ecology,
AB  - the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with
AB  - other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement.
AB  - RESULTS: The complete genome sequence of JWB phytoplasma (jwb-nky) was
AB  - determined, which consisting of one circular chromosome of 750,803 bp with a GC
AB  - content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31
AB  - tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA
AB  - repeats were identified. Based on PHIbaes analysis, a large number of genes were
AB  - genome-specific and approximately 13% of JWB phytoplasma genes were predicted to
AB  - be associated with virulence. Although transporters for maltose,
AB  - dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine
AB  - were identified, KEGG pathway analysis revealed the reduced metabolic
AB  - capabilities of JWB phytoplasma. Comparative genome analyses between JWB
AB  - phytoplasma and other phytoplasmas shows the occurrence of large-scale gene
AB  - rearrangements. The low synteny with other phytoplasmas indicated that the
AB  - expansion of multiple gene families/duplication probably occurred separately
AB  - after differentiation. CONCLUSIONS: In this study, the complete genome sequence
AB  - of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for
AB  - the first time and a number of species-specific genes were identified in the
AB  - genome. The study enhanced our understandings about genomic basis and the
AB  - pathogenicity mechanism of this pathogen, which will aid in the development of
AB  - improved strategies for efficient management of JWB diseases.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Stephan, R.
AU  - Power, K.
AU  - Yan, Q.
AU  - Hachler, H.
AU  - Fanning, S.
TI  - Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans.
JO  - J. Antimicrob. Chemother.
PY  - 2014
SP  - 2658
EP  - 2668
VL  - 69
AB  - OBJECTIVES: Nine extended-spectrum beta-lactamase (ESBL)-producing Escherichia
AB  - coli isolated from healthy humans and food-producing animals were found to
AB  - transfer their cefotaxime resistance marker at high frequency in laboratory
AB  - conjugation experiments. The objective of this study was to completely
AB  - characterize 16 transmissible plasmids that were detected in these bacterial
AB  - isolates. METHODS: The nucleotide sequences of all 16 plasmids were determined
AB  - from transconjugants using next-generation sequencing technology. Open reading
AB  - frames were assigned using Rapid Annotation using Subsystem Technology and
AB  - analysed by BLASTn and BLASTp. The standard method was used for plasmid
AB  - multilocus sequence typing (pMLST) analysis. Plasmid structures were subsequently
AB  - confirmed by PCR amplification of selected regions. RESULTS: The complete
AB  - circularized nucleotide sequence of 14 plasmids was determined, along with that
AB  - of a further two plasmids that could not be confirmed as closed. These ranged in
AB  - size from 1.8 to 166.6 kb. Incompatibility groups and pMLSTs identified included
AB  - IncI1/ST3, IncI1/ST36, IncN/ST1, IncF and IncB/O, and those of the same Inc types
AB  - presented a similar backbone structure despite being isolated from different
AB  - sources. Eight plasmids contained bla(CTX-M-1) genes that were associated with
AB  - either ISEcp1 or IS26 insertion sequence elements. Six plasmids isolated from
AB  - humans and chickens were identical or closely related to the IncI1 reference
AB  - plasmid, R64. CONCLUSIONS: These data, based on comparative sequence analysis,
AB  - highlight the successful spread of blaESBL-harbouring plasmids of different Inc
AB  - types among isolates of human and food-producing animal origin and provide
AB  - further evidence for potential dissemination routes.
ER  -

TY  - JOUR
AU  - Wang, J.
AU  - Wang, L.
AU  - Cao, G.
AU  - Zhang, M.
AU  - Guo, Y.
TI  - Draft Genome Sequence of Leifsonia xyli subsp. xyli Strain gdw1.
JO  - Genome Announcements
PY  - 2016
SP  - e01128
EP  - e01116
VL  - 4
AB  - Here, we report the draft genome sequence of Leifsonia xyli subsp. xyli strain gdw1, isolated
AB  - from the stem of Badila sugarcane located at the Guangdong Key
AB  - Laboratory for Crops Genetic Improvement (Guanzhou, China), that causes ratoon
AB  - stunting disease of sugarcane. The de novo genome of Leifsonia xyli subsp. xyli
AB  - was assembled with 48 scaffolds and a G+C content of 67.68%, and contained 2.6 Mb
AB  - bp and 2,838 coding sequences.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Che, J.M.
AU  - Chen, Z.
AU  - Chen, M.
AU  - Shi, H.
TI  - Draft Genome Sequence of Brevibacillus choshinensis HPD52T (DSM 8552), a Bacterial Host for Efficient Expression of Heterologous Proteins.
JO  - Genome Announcements
PY  - 2016
SP  - e01688
EP  - e01615
VL  - 4
AB  - Brevibacillus choshinensis HPD52(T) (DSM 8552) is a Gram-positive, spore-forming, and
AB  - protein-producing bacterium. Here, we report the 6.28-Mb draft genome
AB  - sequence of B. choshinensis HPD52(T), which will promote its application and
AB  - provide useful information for genomic taxonomy and phylogenomics of
AB  - Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Chen, D.J.
AU  - Chen, Q.Q.
AU  - Zhu, Y.J.
AU  - Chen, Z.
AU  - Che, J.M.
TI  - Draft Genome Sequence of Bacillus marisflavi TF-11T (JCM 11544), a Carotenoid-Producing Bacterium Isolated from Seawater from a Tidal Flat in the  Yellow Sea.
JO  - Genome Announcements
PY  - 2015
SP  - e01451
EP  - e01415
VL  - 3
AB  - Bacillus marisflavi TF-11(T) (JCM 11544) is a Gram-positive, spore-forming, and
AB  - carotenoid-producing bacterium isolated from seawater from a tidal flat in the
AB  - Yellow Sea. Here, we report the first draft genome sequence of B. marisflavi
AB  - TF-11(T), which comprises 4.31 Mb in 11 scaffolds with a G+C content of 48.57%.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Chen, D.J.
AU  - Ge, C.B.
AU  - Chen, Z.
AU  - Che, J.M.
TI  - Genome Sequence of Brevibacillus reuszeri NRRL NRS-1206T, an l-N-Carbamoylase-Producing Bacillus-Like Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01063
EP  - e01015
VL  - 3
AB  - Brevibacillus reuszeri NRRL NRS-1206(T) is a Gram-positive, spore-forming, and strictly
AB  - aerobic bacterium. Here, we report the draft 6.98-Mb genome sequence of  B. reuszeri NRRL
AB  - NRS-1206(T), which is the first genome information of B. reuszeri and will provide useful
AB  - information for genomic taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Chen, D.J.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
AU  - Ge, C.B.
TI  - Genome Sequence of Bacillus butanolivorans K9T (DSM 18926), an n-Butanol-Consuming Bacterium Isolated from Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e01228
EP  - e01215
VL  - 3
AB  - Bacillus butanolivorans K9(T) (DSM 18926) is a Gram-positive, spore-forming, strictly aerobic,
AB  - and n-butanol-consuming bacterium. Here, we report the 5.68-Mb  genome sequence of B.
AB  - butanolivorans K9(T), which is the first genomic information of this species that will provide
AB  - useful information for the genomic  taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Chen, D.J.
AU  - Zhu, Y.J.
AU  - Chen, Z.
AU  - Che, J.M.
TI  - Genome Sequence of Virgibacillus pantothenticus DSM 26T (ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e01064
EP  - e01015
VL  - 3
AB  - Virgibacillus pantothenticus DSM 26(T) is a Gram-positive, spore-forming, aerobic, mesophilic,
AB  - and halotolerant bacterium. Here, we report its 4.76-Mb draft genome sequence, which is the
AB  - first genome information of V. pantothenticus and will promote biological research and
AB  - biotechnological application for the species.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Chen, Q.
AU  - Pan, Z.
AU  - Zheng, X.F.
AU  - Chen, M.
TI  - Draft Genome Sequence of Bacillus muralis LMG 20238T (DSM 16288), a Spore-Forming Bacterium Isolated from Deteriorated Mural Paintings.
JO  - Genome Announcements
PY  - 2016
SP  - e01691
EP  - e01615
VL  - 4
AB  - Bacillus muralis LMG 20238(T) is a Gram-positive, aerobic, and spore-forming bacterium. Here,
AB  - we report the 5.18-Mb draft genome sequence of B. muralis LMG
AB  - 20238(T), which is the first genome sequence of this species and will promote its
AB  - fundamental research.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Chen, Q.Q.
AU  - Zhu, Y.J.
AU  - Chen, Z.
AU  - Che, J.M.
TI  - Genome Sequence of Brevibacillus formosus F12T for a Genome-Sequencing Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria.
JO  - Genome Announcements
PY  - 2015
SP  - e00753
EP  - e00715
VL  - 3
AB  - Brevibacillus formosus F12(T) is a Gram-positive, spore-forming, and strictly aerobic
AB  - bacterium. Here, we report the draft 6.215-Mb genome sequence of B.
AB  - formosus F12(T), which will provide useful information for genomic taxonomy and
AB  - phylogenomics of Bacillus-like bacteria, as well as for the functional gene
AB  - mining and application of B. formosus.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Ge, C.B.
AU  - Chen, Q.Q.
AU  - Che, J.M.
AU  - Chen, D.J.
TI  - Draft Genome Sequence of Bacillus cecembensis PN5T (DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier.
JO  - Genome Announcements
PY  - 2016
SP  - e01687
EP  - e01615
VL  - 4
AB  - Bacillus cecembensis PN5(T) is a Gram-positive, aerobic, and spore-forming bacterium with very
AB  - high intrinsic heat resistance. Here, we report the 4.72-Mb
AB  - draft genome sequence of B. cecembensis PN5(T), the first genome sequence of this
AB  - species, which will promote its fundamental research.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Ge, C.B.
AU  - Chen, Q.Q.
AU  - Zhu, Y.J.
AU  - Chen, Z.
TI  - Genome Sequence of Anaerobacillus macyae JMM-4T (DSM 16346), the First Genomic Information of the Newly Established Genus Anaerobacillus.
JO  - Genome Announcements
PY  - 2015
SP  - e00922
EP  - e00915
VL  - 3
AB  - Anaerobacillus macyae JMM-4(T) (DSM 16346) is a Gram-positive, spore-forming, strictly
AB  - anaerobic, and arsenate-respiring bacterium. Here, we report the 4.26-Mb
AB  - genome sequence of A. macyae JMM-4(T), which is the first genome information of
AB  - the newly established genus Anaerobacillus.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Ge, C.B.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
TI  - Draft Genome Sequence of Bacillus farraginis R-6540T (DSM 16013), a Spore-Forming Bacterium Isolated at Dairy Farms.
JO  - Genome Announcements
PY  - 2016
SP  - e00562
EP  - e00516
VL  - 4
AB  - Bacillus farraginis R-6540(T) is a Gram-positive, aerobic, and spore-forming bacterium with
AB  - very high intrinsic heat resistance. Here, we report the 5.32-Mb
AB  - draft genome sequence of B. farraginis R-6540(T), which is the first genome
AB  - sequence of this species and will promote its fundamental research.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Ge, C.B.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
TI  - Draft Genome Sequence of Bacillus plakortidis P203T (DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e01690
EP  - e01615
VL  - 4
AB  - Bacillus plakortidis P203(T) is a Gram-positive, spore-forming, and alkali- and salt-tolerant
AB  - marine bacterium. Here, we report the 3.97-Mb draft genome sequence
AB  - of B. plakortidis P203(T), which will promote its fundamental research and
AB  - provide useful information for genomic taxonomy and phylogenomics of
AB  - Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Ge, C.B.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
TI  - Draft Genome Sequence of Bacillus shackletonii LMG 18435T, Isolated from Volcanic Mossy Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01689
EP  - e01615
VL  - 4
AB  - Bacillus shackletonii LMG 18435(T) is a Gram-positive, aerobic, and spore-forming bacterium.
AB  - Here, we report the 5.30-Mb draft genome sequence of B. shackletonii
AB  - LMG 18435(T), which will promote its fundamental research and provide useful
AB  - information for genomic taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Ge, C.B.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
TI  - High-Quality Draft Genome Sequence of Aneurinibacillus migulanus ATCC 9999T (DSM  2895), a Gramicidin S-Producing Bacterium Isolated from Garden Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e01227
EP  - e01215
VL  - 3
AB  - Aneurinibacillus migulanus ATCC 9999(T) (DSM 2895) is a Gram-positive, round-spore-forming,
AB  - and gramicidin S-producing bacterium. Here, we report the 6.35-Mb high-quality draft genome
AB  - sequence of A. migulanus ATCC 9999(T), which will provide useful information for the genomic
AB  - taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Pan, Z.
AU  - Xiao, R.F.
AU  - Chen, M.
AU  - Chen, D.J.
TI  - Draft Genome Sequence of Bacillus humi LMG 22167T (DSM 16318), an Endospore-Forming Bacterium Isolated from Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01692
EP  - e01615
VL  - 4
AB  - Bacillus humi LMG 22167(T) is a Gram-positive, aerobic, and spore-forming bacterium Here, we
AB  - report the 4.80-Mb draft genome sequence of B. humi LMG
AB  - 22167(T), which is the first genome sequence of this species and will promote its
AB  - fundamental research.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
AU  - Ge, C.B.
TI  - Draft Genome Sequence of Bacillus pseudalcaliphilus PN-137T (DSM 8725), an Alkaliphilic Halotolerant Bacterium Isolated from Garden Soils.
JO  - Genome Announcements
PY  - 2015
SP  - e00919
EP  - e00915
VL  - 3
AB  - Bacillus pseudalcaliphilus PN-137(T) (DSM 8725) is a Gram-positive, spore-forming,
AB  - alkaliphilic, and halotolerant bacterium. Here, we report the
AB  - 4.49-Mb genome sequence of B. pseudalcaliphilus PN-137(T), which will accelerate
AB  - the application of this alkaliphile and provide useful information for genomic
AB  - taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
AU  - Ge, C.B.
TI  - Draft Genome Sequence of Sporosarcina globispora W 25T (DSM 4), a Psychrophilic Bacterium Isolated from Soil and River Water.
JO  - Genome Announcements
PY  - 2015
SP  - e01230
EP  - e01215
VL  - 3
AB  - Sporosarcina globispora W 25(T) (DSM 4) is a Gram-positive, round-spore-forming,  and
AB  - psychrophilic bacterium. Here, we report the 5.66-Mb genome sequence of S. globispora W 25(T),
AB  - which will accelerate the application of this psychrophile and provide useful information for
AB  - genomic taxonomy and phylogenomics of Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, J.P.
AU  - Liu, B.
AU  - Liu, G.H.
AU  - Xiao, R.F.
AU  - Zheng, X.F.
AU  - Shi, H.
AU  - Ge, C.B.
TI  - Draft Genome Sequence of Bacillus murimartini LMG 21005T, an Alkalitolerant Bacterium Isolated from a Church Wall Mural in Germany.
JO  - Genome Announcements
PY  - 2015
SP  - e01229
EP  - e01215
VL  - 3
AB  - Bacillus murimartini LMG 21005(T) is a Gram-positive, spore-forming, and alkalitolerant
AB  - bacterium isolated from a church wall mural. Here, we report the 4.17-Mb genome sequence of B.
AB  - murimartini LMG 21005(T), which will accelerate the application of this alkalitolerant
AB  - bacterium and provide useful information for genomic taxonomy and phylogenomics of
AB  - Bacillus-like bacteria.
ER  -

TY  - JOUR
AU  - Wang, K.
AU  - Chen, J.
AU  - Yao, H.
AU  - Lu, C.
TI  - Whole-Genome Sequence of Streptococcus suis Serotype 3 Strain YB51.
JO  - Genome Announcements
PY  - 2013
SP  - e00884
EP  - e00813
VL  - 1
AB  - We report here the second complete genome sequence of Streptococcus suis serotype 3 (strain
AB  - YB51). The genome is 2,043,655 bp in length, which is 14,840 bp longer
AB  - than the first reported genome of the same serotype, and it covers 2,012 coding
AB  - sequences, 56 tRNAs, and 4 rRNA loci.
ER  -

TY  - JOUR
AU  - Wang, K.
AU  - Chen, J.
AU  - Yao, H.
AU  - Lu, C.
TI  - Whole-Genome Sequence of Streptococcus suis Serotype 4 Reference Strain 6407.
JO  - Genome Announcements
PY  - 2014
SP  - e00770
EP  - e00714
VL  - 2
AB  - We report here the second complete genome sequence of Streptococcus suis serotype 4 (strain
AB  - 6407). The genome is 2,292,360 bp in length, covering 2,239 coding
AB  - sequences, 58 tRNAs, and 4 rRNA loci.
ER  -

TY  - JOUR
AU  - Wang, K.
AU  - Fan, W.
AU  - Cai, L.
AU  - Huang, B.
AU  - Lu, C.
TI  - Genetic analysis of the capsular polysaccharide synthesis locus in 15 Streptococcus suis serotypes.
JO  - FEMS Microbiol. Lett.
PY  - 2011
SP  - 117
EP  - 124
VL  - 324
ER  -

TY  - JOUR
AU  - Wang, K.
AU  - Yao, H.
AU  - Lu, C.
AU  - Chen, J.
TI  - Complete Genome Sequence of Streptococcus suis Serotype 16 Strain TL13.
JO  - Genome Announcements
PY  - 2013
SP  - e00394
EP  - e00313
VL  - 1
AB  - We report here the first complete genome sequence of Streptococcus suis serotype  16, which
AB  - has been identified to be zoonotic. The sequenced strain TL13 was
AB  - isolated from a pig in China. The genome is 2,038,146 bp in length, covering
AB  - 1,950 coding sequences, 53 tRNAs, and 4 rRNA loci.
ER  -

TY  - JOUR
AU  - Wang, K.-Y.
AU  - Chen, C.-C.
AU  - Shen, C.-Kun.J.
TI  - Active DNA demethylation of the vertebrate genomes by DNA methyltransferases: deaminase, dehydroxymethylase or demethylase?
JO  - Epigenomics
PY  - 2014
SP  - 353
EP  - 363
VL  - 6
AB  - Vertebrate DNA methyltransferases (DNMTs) have been thought to primarily function to
AB  - covalently add a methyl group to the 5-position of cytosine. However, recent discovery of the
AB  - DNA demethylation and dehydroxymethylation activities of DNMTs in vitro suggest new routes to
AB  - complete the dynamic cycle of DNA methylation-demethylation of the vertebrate genomes. The in
AB  - vitro reaction conditions suggest that vertebrate DNMTs can switch from DNA methylases to DNA
AB  - dehydroxymethylases under oxidative stress and to DNA demethylases in the presence of calcium
AB  - ion under nonreducing conditions. These environmental parameters provide clues regarding the
AB  - choices in vivo of DNMT activities utilized in different physiological systems. In particular,
AB  - the nature of these parameters suggest that the DNA demethylation and dehydroxymethylation
AB  - activities of the vertebrate DNMTs play essential roles in multiple biological processes
AB  - including early embryo development, regulation of neuronal plasticity, tumorigenesis and
AB  - hormone-regulated transcription.
ER  -

TY  - JOUR
AU  - Wang, K.Y.
AU  - Liu, T.
AU  - Wang, J.
AU  - Chen, D.F.
AU  - Wu, X.J.
AU  - Jiang, J.
AU  - Liu, J.X.
TI  - Complete Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain SC09, Isolated from Diseased Ictalurus punctatus in China.
JO  - Genome Announcements
PY  - 2015
SP  - e01327
EP  - e01314
VL  - 3
AB  - Yersinia ruckeri SC09 is a Gram-negative bacterium isolated from a moribund Ictalurus
AB  - punctatus collected in Jianyang, China. Here, we report the complete
AB  - genome sequence of this microorganism to facilitate the investigation of its
AB  - pathogenicity and to reevaluate its taxonomic position.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Chen, S.
AU  - Deng, Z.
TI  - Phosphorothioation:  An unusual post-replicative modification on the DNA backbone.
JO  - DNA Replication-Current Advances
PY  - 2011
SP  - 57
EP  - 74
AB  - DNA molecules are polymers composed of basic repeating subunits of deoxyribonucleotides, which
AB  - consist of the deoxyribose sugar, phosphate groups, and a nitrogenous base.  They appear to
AB  - fulfill all requirements necessary to maintain the genetic function of DNA.  The five elements
AB  - of nitrogen, phosphorus, carbon, hydrogen, and oxygen had been regarded as the canonical
AB  - composition of DNA until the discovery of phosphorothioation, with a sixth element, sulfur,
AB  - identified as an additional naturally occurring constituent on the DNA backbone, as a
AB  - sequence-selective, stereospecific post-replicative modification governed by the dnd gene
AB  - cluster.  Unlike any other DNA or RNA modification system, DNA phosphorothioation is the
AB  - first-described physiological modification of the DNA sugar-phosphorothioation is the
AB  - first-described physiological modification of the DNA sugar-phosphate backbone.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Chen, S.
AU  - Vergin, K.L.
AU  - Giovannoni, S.J.
AU  - Chan, S.W.
AU  - Demott, M.S.
AU  - Taghizadeh, K.
AU  - Cordero, O.X.
AU  - Cutler, M.
AU  - Timberlake, S.
AU  - Alm, E.J.
AU  - Polz, M.F.
AU  - Pinhassi, J.
AU  - Deng, Z.
AU  - Dedon, P.C.
TI  - DNA phosphorothioation is widespread and quantized in bacterial genomes.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 2963
EP  - 2968
VL  - 108
AB  - Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate
AB  - oxygen, was recently discovered as a product of the
AB  - dnd genes found in bacteria and archaea. Given our limited understanding
AB  - of the biological function of PT modifications, including sequence
AB  - context, genomic frequencies, and relationships to the diversity of dnd
AB  - gene clusters, we undertook a quantitative study of PT modifications in
AB  - prokaryotic genomes using a liquid chromatography-coupled tandem
AB  - quadrupole mass spectrometry approach. The results revealed a diversity of
AB  - unique PT sequence contexts and three discrete genomic frequencies in a
AB  - wide range of bacteria. Metagenomic analyses of PT modifications revealed
AB  - unique ecological distributions, and a phylogenetic comparison of dnd
AB  - genes and PT sequence contexts strongly supports the horizontal transfer
AB  - of dnd genes. These results are consistent with the involvement of PT
AB  - modifications in a type of restriction-modification system with wide
AB  - distribution in prokaryotes.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Chen, S.
AU  - Xu, T.
AU  - Taghizadeh, K.
AU  - Wishnok, J.S.
AU  - Zhou, X.
AU  - You, D.
AU  - Deng, Z.
AU  - Dedon, P.C.
TI  - Phosphorothioation of DNA in bacteria by dnd genes.
JO  - Nat. Chem. Biol.
PY  - 2007
SP  - 709
EP  - 710
VL  - 3
AB  - Modifications of the canonical structures of DNA and RNA play critical roles in cell
AB  - physiology, DNA replication, transcription and translation in all organisms.
AB  - We now report that bacterial dnd gene clusters incorporate sulfur into the DNA
AB  - backbone as a sequence-selective, stereospecific phosphorothioate modification.
AB  - To our knowledge, unlike any other DNA or RNA modification systems, DNA
AB  - phosphorothioation by dnd gene clusters is the first physiological modification
AB  - described on the DNA backbone.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Gao, C.
AU  - Tang, N.
AU  - Hu, S.
AU  - Wu, Q.
TI  - Identification of genetic variations associated with epsilon-poly-lysine biosynthesis in Streptomyces albulus ZPM by genome sequencing.
JO  - Sci. Rep.
PY  - 2015
SP  - 9201
EP  - 9201
VL  - 5
AB  - The biosynthesis of the antibiotic epsilon-poly-lysine (epsilon-PL) in Streptomyces albulus is
AB  - performed by polylysine synthase (pls); however, the regulatory mechanism of this process is
AB  - still unknown. Here, we first obtained the complete genome sequence of S. albulus ZPM, which
AB  - consists of 9,784,577 bp and has a GC content of 72.2%. The genome houses 44 gene clusters for
AB  - secondary metabolite biosynthesis, in which 20 gene clusters are involved in the biosynthesis
AB  - of polyketides and nonribosomally synthesized peptides.
AB  - High-throughput sequencing was further performed, and genetic variants were identified from
AB  - pooled libraries consisting of the 30 highest-yield mutants or 30 lowest-yield mutants. More
AB  - than 350 genetic variants associated with epsilon-PL yield have been identified. One hundred
AB  - sixty-two affected proteins, from important metabolic enzymes to novel transcriptional
AB  - regulators, were identified as being related to epsilon-PL synthesis. HrdD, one of the
AB  - affected genes, is a sigma factor that shows the most sensitive response to pH change and
AB  - contains a non-synonymous mutation (A132V) in mutant strains with lower epsilon-PL yields.
AB  - Electrophoretic mobility shift assays showed that the pls gene is likely regulated by
AB  - transcriptional activator HrdD. The data obtained in this study will facilitate future studies
AB  - on epsilon-PL yield improvement and industrial bioprocess optimization.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Hatem, A.
AU  - Catalyurek, U.V.
AU  - Morrison, M.
AU  - Yu, Z.
TI  - Metagenomic insights into the carbohydrate-active enzymes carried by the microorganisms adhering to solid digesta in the rumen of cows.
JO  - PLoS ONE
PY  - 2013
SP  - E78507
EP  - E78507
VL  - 8
AB  - The ruminal microbial community is a unique source of enzymes that underpin the
AB  - conversion of cellulosic biomass. In this study, the microbial consortia adherent
AB  - on solid digesta in the rumen of Jersey cattle were subjected to an
AB  - activity-based metagenomic study to explore the genetic diversity of
AB  - carbohydrolytic enzymes in Jersey cows, with a particular focus on cellulases and
AB  - xylanases. Pyrosequencing and bioinformatic analyses of 120 carbohydrate-active
AB  - fosmids identified genes encoding 575 putative Carbohydrate-Active Enzymes
AB  - (CAZymes) and proteins putatively related to transcriptional regulation,
AB  - transporters, and signal transduction coupled with polysaccharide degradation and
AB  - metabolism. Most of these genes shared little similarity to sequences archived in
AB  - databases. Genes that were predicted to encode glycoside hydrolases (GH) involved
AB  - in xylan and cellulose hydrolysis (e.g., GH3, 5, 9, 10, 39 and 43) were well
AB  - represented. A new subfamily (S-8) of GH5 was identified from contigs assigned to
AB  - Firmicutes. These subfamilies of GH5 proteins also showed significant
AB  - phylum-dependent distribution. A number of polysaccharide utilization loci (PULs)
AB  - were found, and two of them contained genes encoding Sus-like proteins and
AB  - cellulases that have not been reported in previous metagenomic studies of samples
AB  - from the rumens of cows or other herbivores. Comparison with the large
AB  - metagenomic datasets previously reported of other ruminant species (or cattle
AB  - breeds) and wallabies showed that the rumen microbiome of Jersey cows might
AB  - contain differing CAZymes. Future studies are needed to further explore how host
AB  - genetics and diets affect the diversity and distribution of CAZymes and
AB  - utilization of plant cell wall materials.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Qiu, Y.
AU  - Chen, Z.
AU  - Xu, J.
AU  - Wang, Z.
AU  - Ke, Y.
AU  - Li, T.
AU  - Wang, D.
AU  - Huang, L.
AU  - Yu, Y.
AU  - Zhen, Q.
TI  - Draft Genome Sequence of Brucella abortus BCB027, a Strain Isolated from a Domestic Deer.
JO  - Genome Announcements
PY  - 2013
SP  - e00130
EP  - e00112
VL  - 1
AB  - Many Brucella species are isolated from nonpreferred hosts, and these bacteria may show
AB  - genetic differences from isolates from the preferred hosts. Here, we report the draft genome
AB  - sequence of Brucella abortus BCB027, a novel strain isolated from a domestic deer.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Wang, S.
AU  - He, Q.
AU  - Yu, T.
AU  - Li, Q.
AU  - Hong, B.
TI  - Draft Genome Sequence of Streptomyces globisporus C-1027, Which Produces an Antitumor Antibiotic Consisting of a Nine-Membered Enediyne with a Chromoprotein.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4144
EP  - 4144
VL  - 194
AB  - Streptomyces globisporus C-1027 is the producer of antitumor antibiotic C-1027, a
AB  - nine-membered enediyne-containing compound. Here we present a draft genome
AB  - sequence of S. globisporus C-1027 containing the intact biosynthetic gene cluster
AB  - for this antibiotic. The genome also carries numerous sets of genes for the
AB  - biosynthesis of diverse secondary metabolites.
ER  -

TY  - JOUR
AU  - Wang, L.
AU  - Xie, Y.
AU  - Li, Q.
AU  - He, N.
AU  - Yao, E.
AU  - Xu, H.
AU  - Yu, Y.
AU  - Chen, R.
AU  - Hong, B.
TI  - Draft Genome Sequence of Streptomyces sp. Strain SS, Which Produces a Series of Uridyl Peptide Antibiotic Sansanmycins.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6988
EP  - 6989
VL  - 194
AB  - Streptomyces sp. SS produces a series of uridyl peptide antibiotic sansanmycins.  Here, we
AB  - present a draft genome sequence of Streptomyces sp. SS containing the
AB  - biosynthetic gene cluster for the antibiotics. The identification of the
AB  - biosynthetic gene cluster of sansanmycins may provide further insight into
AB  - biosynthetic mechanisms for uridyl peptide antibiotics.
ER  -

TY  - JOUR
AU  - Wang, N.
AU  - Ng, I.S.
AU  - Chen, P.T.
AU  - Li, Y.
AU  - Chen, Y.C.
AU  - Chen, B.Y.
AU  - Lu, Y.
TI  - Draft Genome Sequence of the Bioelectricity-Generating and Dye-Decolorizing Bacterium Proteus hauseri Strain ZMd44.
JO  - Genome Announcements
PY  - 2014
SP  - e00992
EP  - e00913
VL  - 2
AB  - Proteus hauseri ZMd44 (CGMCC 6746), as a crucial biodecolorizing, bioelectricity-generating,
AB  - and copper-resistant bacterium, is distinguished from
AB  - the urinary pathogens Proteus penneri and Proteus mirabilis. To further
AB  - investigate the genetic functions of this strain, the genome sequence and
AB  - annotation of its open reading frames, which consist of 3,875,927 bp (G+C
AB  - content, 38.12%), are presented here.
ER  -

TY  - JOUR
AU  - Wang, P.
AU  - Brank, A.S.
AU  - Banavali, N.K.
AU  - Nicklaus, M.C.
AU  - Marquez, V.E.
AU  - Christman, J.K.
AU  - MacKerell, A.D. Jr.
TI  - Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase.
JO  - J. Am. Chem. Soc.
PY  - 2000
SP  - 12422
EP  - 12434
VL  - 122
AB  - X-ray crystallographic studies of HhaI DNA (cytosine-C5)-methyltransferase covalently linked
AB  - to methylated 5-fluorocytosine in DNA provided the first direct evidence that the cytosine
AB  - residue targeted for methylation was "flipped" out of the helix during the transfer reaction.
AB  - Subsequent studies indicated that removal of the target cytosine base, i.e., introduction of
AB  - an abasic site, enhanced binding of M.HhaI to DNA and that the conformation of the
AB  - sugar-phosphate backbone at the abasic site in the resultant complexes was the same as that of
AB  - the sugar attached to a "flipped" cytosine.  In the present study, pseudorotationally
AB  - constrained sugar analogues, based on bicyclo[3.1.0]hexane templates, were placed in DNA
AB  - duplexes as abasic target sites in the M.HhaI recognition sequence.  Biochemical studies
AB  - demonstrate that binding affinity of M.HhaI for abasic sites increases when the abasic target
AB  - sugar analogue is constrained to the south conformation and decreases when it is constrained
AB  - to the north conformation.  In native gel-shift assays, M.HhaI exhibits a "closed"
AB  - conformation when bound to the abasic south or abasic furanose analogues, whereas an "open"
AB  - conformation predominates with the abasic north analogue.  A structural understanding of these
AB  - results was obtained via molecular dynamics simulations of the DNA duplex alone and in ternary
AB  - complex with M.HhaI and cofactor, along with quantum mechanical calculations on model
AB  - compounds representative of the abasic and modified sugars.  Binding affinities are shown to
AB  - be related to the ability of the abasic sugar analogues to spontaneously flip out of the DNA
AB  - duplex.  Enhanced binding of the abasic south analogue is suggested to be due to its increased
AB  - capacity for sampling the experimentally observed conformation of the DNA target site in the
AB  - M.HhaI ternary complex.  Decreased binding of the north analogue is due to decreased
AB  - flexibility of the phosphodiester backbone associated with a north pseudorotation angle,
AB  - thereby inhibiting spontaneous flipping of the sugar moiety out of the DNA duplex.
AB  - Spontaneous flipping of the sugar moiety out of the DNA duplex is also suggested to facilitate
AB  - formation of a "closed" complex between M.HhaI and DNA whereas partial or no flipping favor
AB  - the "open" conformation.  These results show that introduction of structural constraints into
AB  - DNA that induce enhanced sampling of protein-bound conformations facilitate DNA-protein
AB  - binding.  Implications of the present results with respect to the mechanism of vase flipping
AB  - in the M.HhaI catalytic cycle are discussed.
ER  -

TY  - JOUR
AU  - Wang, P.
AU  - Harvey, S.S.
AU  - Sims, P.F.G.
AU  - Broda, P.
TI  - The construction of Streptomyces cyaneus genomic libraries in Escherichia coli is dependent upon the use of Mcr-deficient strains.
JO  - Gene
PY  - 1992
SP  - 127
EP  - 129
VL  - 119
AB  - Streptomyces cyaneus genomic DNA ligated into either lambda phage or plasmid vectors was very
AB  - inefficiently cloned into standard Escherichia coli host strains. However, the same material
AB  - could be efficiently cloned using Mcr-deficient E. coli strains. These results suggest that
AB  - the S. cyaneus genome contains 5-methylcytosine residues, some of which occur with the
AB  - recognition sequences of the E. coli Mcr restriction system.
ER  -

TY  - JOUR
AU  - Wang, P.
AU  - Li, L.
AU  - Chen, X.
AU  - Jiang, N.
AU  - Liu, G.
AU  - Chen, L.
AU  - Xu, J.
AU  - Song, H.
AU  - Chen, Z.
AU  - Ma, Y.
TI  - Draft Genome Sequence of Alicyclobacillus hesperidum Strain URH17-3-68.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6348
EP  - 6348
VL  - 194
AB  - Alicyclobacillus hesperidum is a thermoacidophilic bacterium. We isolated strain  URH17-3-68
AB  - from hot spring sludge in Tengchong, Yunnan province, China. Its
AB  - extracellular products include heat- and acid-stable enzymes which are important
AB  - for industrial applications. Here we report the draft genome of this strain.
ER  -

TY  - JOUR
AU  - Wang, Q.
AU  - Shao, Z.
AU  - Wang, X.
AU  - Gao, Y.
AU  - Li, M.
AU  - Xu, L.
AU  - Xu, J.
AU  - Wang, L.
TI  - Genetic Study of Capsular Switching between Neisseria meningitidis Sequence Type 7 Serogroup A and C Strains.
JO  - Infect. Immun.
PY  - 2010
SP  - 3883
EP  - 3888
VL  - 78
AB  - Neisseria meningitidis is a leading cause of septicemia and meningitis
AB  - worldwide. N. meningitidis capsular polysaccharides have been classified
AB  - into 13 distinct serogroups which are defined by antibody reactivity and
AB  - structural analysis, and the capsule plays an important role in virulence.
AB  - Serogroups A, B, C, W135, and Y have been reported to be clinically
AB  - important. Several newly identified serogroup C isolates belonging to the
AB  - unique sequence type 7 (ST-7) were identified in China. Since most ST-7
AB  - isolates from China belonged to serogroup A, the newly identified ST-7
AB  - serogroup C strains were proposed to have arisen from those belonging to
AB  - ST-7 serogroup A. In this study, six ST-7 serogroup C and three ST-7
AB  - serogroup A isolates were analyzed by pulsed-field gel electrophoresis to
AB  - confirm their sequence type. In order to clarify the genetic basis of
AB  - capsular switching between ST-7 serogroup A and C strains, the whole
AB  - capsular gene clusters and surrounding genes of the two representative
AB  - ST-7 strains belonging to serogroups A and C, respectively, were sequenced
AB  - and compared. Potential recombination sites were analyzed using the RDP3
AB  - beta software, and recombination-related regions in two other ST-7
AB  - serogroup A and five ST-7 serogroup C strains were also sequenced and
AB  - compared to the representative ST-7 serogroup A and C strain sequences.
ER  -

TY  - JOUR
AU  - Wang, Q.
AU  - Tsukahara, S.
AU  - Yamakawa, H.
AU  - Takai, K.
AU  - Takaku, H.
TI  - pH-independent inhibition of restriction endonuclease cleavage via triple helix formation by oligonucleotides containing 8-oxo-2'-deoxyadenosine.
JO  - FEBS Lett.
PY  - 1994
SP  - 11
EP  - 14
VL  - 355
AB  - The ability of homopyrimidine oliogonucleotides containing 8-oxo-2'-deoxyadenosine to form
AB  - stable, triple helical structures with the sequence containing the recognition site for the
AB  - class II-S restriction enzyme, Ksp632I, was studied as a function of pH. The
AB  - 8-oxo-2'-deoxyadenosine-substituted oligomers were shown to inhibit enzymatic cleavage and to
AB  - bind within the physiological pH range in a pH-independent fashion without compromising
AB  - specificity.
ER  -

TY  - JOUR
AU  - Wang, Q.
AU  - Yang, M.
AU  - Xiao, J.
AU  - Wu, H.
AU  - Wang, X.
AU  - Lv, Y.
AU  - Xu, L.
AU  - Zheng, H.
AU  - Wang, S.
AU  - Zhao, G.
AU  - Liu, Q.
AU  - Zhang, Y.
TI  - Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches.
JO  - PLoS ONE
PY  - 2009
SP  - E7646
EP  - E7646
VL  - 4
AB  - BACKGROUND: Edwardsiella tarda is the etiologic agent of edwardsiellosis,
AB  - a devastating fish disease prevailing in worldwide aquaculture industries.
AB  - Here we describe the complete genome of E. tarda, EIB202, a highly
AB  - virulent and multi-drug resistant isolate in China. METHODOLOGY/PRINCIPAL
AB  - FINDINGS: E. tarda EIB202 possesses a single chromosome of 3,760,463 base
AB  - pairs containing 3,486 predicted protein coding sequences, 8 ribosomal
AB  - rRNA operons, and 95 tRNA genes, and a 43,703 bp conjugative plasmid
AB  - harboring multi-drug resistant determinants and encoding type IV A
AB  - secretion system components. We identified a full spectrum of genetic
AB  - properties related to its genome plasticity such as repeated sequences,
AB  - insertion sequences, phage-like proteins, integrases, recombinases and
AB  - genomic islands. In addition, analysis also indicated that a substantial
AB  - proportion of the E. tarda genome might be devoted to the growth and
AB  - survival under diverse conditions including intracellular niches, with a
AB  - large number of aerobic or anaerobic respiration-associated proteins,
AB  - signal transduction proteins as well as proteins involved in various
AB  - stress adaptations. A pool of genes for secretion systems, pili formation,
AB  - nonfimbrial adhesions, invasions and hemagglutinins, chondroitinases,
AB  - hemolysins, iron scavenging systems as well as the incomplete flagellar
AB  - biogenesis might feature its surface structures and pathogenesis in a fish
AB  - body. CONCLUSION/SIGNIFICANCE: Genomic analysis of the bacterium offered
AB  - insights into the phylogeny, metabolism, drug-resistance, stress
AB  - adaptation, and virulence characteristics of this versatile pathogen,
AB  - which constitutes an important first step in understanding the
AB  - pathogenesis of E. tarda to facilitate construction of a practical
AB  - effective vaccine used for combating fish edwardsiellosis.
ER  -

TY  - JOUR
AU  - Wang, Q.Y.
AU  - Xie, N.Z.
AU  - Huang, Y.Y.
AU  - Song, L.F.
AU  - Du, Q.S.
AU  - Yu, B.
AU  - Chen, D.
AU  - Huang, R.B.
TI  - Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a  Species in the Genus Tumebacillus.
JO  - Genome Announcements
PY  - 2014
SP  - e01189
EP  - e01114
VL  - 2
AB  - We present here the first genome sequence of a species in the genus Tumebacillus. The draft
AB  - genome sequence of Tumebacillus flagellatus GST4 provides a genetic
AB  - basis for future studies addressing the origins, evolution, and ecological role
AB  - of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding
AB  - genes for further studies.
ER  -

TY  - JOUR
AU  - Wang, R.
AU  - Jin, Y.
AU  - Norris, D.
TI  - Identification of a protein that binds to the HO endonuclease recognition sequence at the yeast mating type locus.
JO  - Mol. Cell. Biol.
PY  - 1997
SP  - 770
EP  - 777
VL  - 17
AB  - Mating type switching in Saccharomyces cerevisiae initiates when HO endonuclease makes a
AB  - site-specific double-stranded break at MAT, the yeast mating type locus.  To identify other
AB  - proteins involved in this process, we examined whether extracts prepared from ho- mutants
AB  - contain additional factors that bind near the recognition sequence for HO.  Using an
AB  - electrophoretic mobility shift assay, we isolated a chromatographic fraction that contains an
AB  - activity, named YZbp, which binds to two sequences flanking the recognition sequence at
AB  - MATalpha and to one sequence overlapping it at MATa.  MAT plasmids carrying mutations in the
AB  - YZbp recognition sequence are cleaved by purified Ho at wild-type efficiencies in an in vitro
AB  - assay.  These same plasmids, however, are not cleaved by Ho inside cells, demonstrating that
AB  - YZbp acts as a positive activator of in vivo cleavage.  YZbp is present in all cell types,
AB  - even those not undergoing mating type switching, suggesting that it has additional cellular
AB  - functions.
ER  -

TY  - JOUR
AU  - Wang, R.
AU  - Li, L.
AU  - Luo, F.
AU  - Liang, W.
AU  - Gan, X.
AU  - Chen, M.
TI  - Genome Sequence of Streptococcus agalactiae Strain H002, Serotype III, Isolated in China from a Pregnant Woman.
JO  - Genome Announcements
PY  - 2015
SP  - e01109
EP  - e01115
VL  - 3
AB  - Here, we report the first whole-genome sequence of Streptococcus agalactiae strain H002,
AB  - serotype III, isolated in China from a woman 32 weeks pregnant. This sequence represents an
AB  - important addition to the published genomes and will promote comparative genomic studies of S.
AB  - agalactiae spp. isolated from diverse regions, particularly when compared with Chinese
AB  - strains.
ER  -

TY  - JOUR
AU  - Wang, R.
AU  - Tekedar, H.C.
AU  - Lawrence, M.L.
AU  - Chouljenko, V.N.
AU  - Kim, J.
AU  - Kim, N.
AU  - Kousoulas, K.G.
AU  - Hawke, J.P.
TI  - Draft Genome Sequences of Edwardsiella ictaluri Strains LADL11-100 and LADL11-194 Isolated from Zebrafish Danio rerio.
JO  - Genome Announcements
PY  - 2015
SP  - e01449
EP  - e01415
VL  - 3
AB  - Here, we report the draft genome sequences of Edwardsiella ictaluri strains LADL11-100 and
AB  - LADL11-194, two isolates from natural outbreaks of edwardsiellosis
AB  - in the zebrafish Danio rerio, as well as the sequences of the plasmids carried by
AB  - the zebrafish strain of E. ictaluri.
ER  -

TY  - JOUR
AU  - Wang, R.Y.-H.
AU  - Shedlarski, J.G.
AU  - Farber, M.B.
AU  - Kuebbing, D.
AU  - Ehrlich, M.
TI  - Two sequence-specific endonucleases from Xanthomonas oryzae.  Characterization and unusual properties.
JO  - Biochim. Biophys. Acta
PY  - 1980
SP  - 371
EP  - 385
VL  - 606
AB  - XorI and XorII, two sequence-specific endonucleases, have been partially
AB  - purified from Xanthomas oryzae.  XorI and XorII were shown to be isoschizomers
AB  - of PstI and PvuI, respectively.  X. oryzae is a particularly good source of
AB  - this PvuI isoschizomer because of the high yield of XorII, its simple
AB  - purification scheme, and its relative stability.  Furthermore, XorII was shown
AB  - to cleave at different positions in its recognition sequence than do at least
AB  - two of its known isoschizomers; XorII cleaves between the C and the G at the
AB  - 3'-end of its palindromic recognition sequence, 5'-CGATC^G-3'.  There is a
AB  - single XorII site in each of the plasmid-cloning vehicles pBR313 and pBR322.
AB  - Two unusual aspects of XorII digestion are discussed, namely, the kinetics of
AB  - digestion of pBR313 and pBR322 and the resistance of human DNA to XorII.
ER  -

TY  - JOUR
AU  - Wang, R.Y.-H.
AU  - Shenoy, S.
AU  - Ehrlich, M.
TI  - DNA methylation inhibits the transfecting activity of replicative-form PhiX174 DNA.
JO  - J. Virol.
PY  - 1984
SP  - 674
EP  - 679
VL  - 49
AB  - Replacement of virtually all the cytosine residues with 5-methylcytosine residues in the
AB  - complementary strand of the replicative form (RF) of PhiX174 DNA caused a 300- to 500-fold
AB  - loss in its transfecting activity.  Similar results were obtained with analogously methylated
AB  - M13 RF.  Transfection experiments with PhiX RF hemimethylated in only part of the molecule, as
AB  - assessed by analysis with restriction endonucleases, indicated that gene A of PhiX, which
AB  - needs to be nicked at a specific site by the gene A protein for RF replication, was not the
AB  - main target for this inhibition by DNA methylation.  We propose that the loss of transfecting
AB  - activity was due to hemimethylation of the PhiX RF interfering with the processively catalyzed
AB  - movement of the replication fork.
ER  -

TY  - JOUR
AU  - Wang, R.Y.-H.
AU  - Zhang, X.-Y.
AU  - Ehrlich, M.
TI  - A human DNA-binding protein is methylation-specific and sequence-specific.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 1599
EP  - 1614
VL  - 14
AB  - A nuclear protein isolated from human placenta, methylated DNA-binding protein, binds
AB  - selectively to DNA enriched in 5-methylcytosine.  We now demonstrate that MDBP is a
AB  - sequence-specific, as well as methylation-specific, DNA-binding protein.  From restriction
AB  - fragments of pBR322 DNA methylated with human DNA methyltransferase, one was bound to mDBP
AB  - very much more strongly than any of the others.  For this preferential binding to MDBP, the
AB  - DNA had to be methylated.  By a DNase I protection experiment (DNase I footprinting), a
AB  - 22-base sequence within this methylated restriction fragment was shown to be specifically
AB  - protected by MDP.  The sequence-specificity of MDBP coupled with its dependence on DNA
AB  - methylation suggests that this is one of the proteins which modulates important functions of
AB  - human DNA methylation in vivo.
ER  -

TY  - JOUR
AU  - Wang, R.Y.-H.
AU  - Zhang, X.-Y.
AU  - Khan, R.
AU  - Zhou, Y.
AU  - Huang, L.-H.
AU  - Ehrlich, M.
TI  - Methylated DNA-binding protein from human placenta recognizes specific methylated sites on several prokaryotic DNAs.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 9843
EP  - 9860
VL  - 14
AB  - Methylated DNA-binding protein (MDBP) from human placenta recognizes specific
AB  - DNA sequences containing 5-methylcytosine (m5C) residues.  Comparisons of
AB  - binding of various prokaryotic DNAs to MDBP indicate that m5CpG is present in
AB  - the recognition sites for this protein but is only part of the recognition
AB  - sequence.  Specific binding to MDBP was observed for bacteriophage XP12 DNA,
AB  - which naturally contains ~1/3 of its residues as m5C, and for Micrococcus
AB  - luteus DNA, M13mp8 replicative form (RF) DNA, and pBR322 when these three DNAs
AB  - were methylated at CpG sites by human DNA methyltransferase.  Five DNA regions
AB  - binding to MDBP have been localized by DNase I footprinting or restriction
AB  - mapping in methylated pBR322 and M13mp8 RF DNAs.  A comparison of their
AB  - sequences reveals a common 5'-m5CGRm5CG-3' element or closely related sequence
AB  - in which one of the m5C residues may be replaced by a T.  In addition to this
AB  - motif, one upstreaem and one downstream m5CpG as well as other common residues
AB  - over an ~20-bp long region may be recognized by MDBP.
ER  -

TY  - JOUR
AU  - Wang, S.
AU  - Chng, K.R.
AU  - Wilm, A.
AU  - Zhao, S.
AU  - Yang, K.L.
AU  - Nagarajan, N.
AU  - He, J.
TI  - Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2014
SP  - 12103
EP  - 12108
VL  - 111
AB  - Fastidious anaerobic bacteria play critical roles in environmental bioremediation of
AB  - halogenated compounds. However, their characterization and application have
AB  - been largely impeded by difficulties in growing them in pure culture. Thus far,
AB  - no pure culture has been reported to respire on the notorious polychlorinated
AB  - biphenyls (PCBs), and functional genes responsible for PCB detoxification remain
AB  - unknown due to the extremely slow growth of PCB-respiring bacteria. Here we
AB  - report the successful isolation and characterization of three Dehalococcoides
AB  - mccartyi strains that respire on commercial PCBs. Using high-throughput
AB  - metagenomic analysis, combined with traditional culture techniques,
AB  - tetrachloroethene (PCE) was identified as a feasible alternative to PCBs to
AB  - isolate PCB-respiring Dehalococcoides from PCB-enriched cultures. With PCE as an
AB  - alternative electron acceptor, the PCB-respiring Dehalococcoides were boosted to
AB  - a higher cell density (1.2 x 10(8) to 1.3 x 10(8) cells per mL on PCE vs. 5.9 x
AB  - 10(6) to 10.4 x 10(6) cells per mL on PCBs) with a shorter culturing time (30 d
AB  - on PCE vs. 150 d on PCBs). The transcriptomic profiles illustrated that the
AB  - distinct PCB dechlorination profile of each strain was predominantly mediated by
AB  - a single, novel reductive dehalogenase (RDase) catalyzing chlorine removal from
AB  - both PCBs and PCE. The transcription levels of PCB-RDase genes are 5-60 times
AB  - higher than the genome-wide average. The cultivation of PCB-respiring
AB  - Dehalococcoides in pure culture and the identification of PCB-RDase genes deepen
AB  - our understanding of organohalide respiration of PCBs and shed light on in situ
AB  - PCB bioremediation.
ER  -

TY  - JOUR
AU  - Wang, S.
AU  - Chng, K.R.
AU  - Wu, C.
AU  - Wilm, A.
AU  - Nagarajan, N.
AU  - He, J.
TI  - Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides  mccartyi Strain SG1, Which Carries a Circular Putative Plasmid.
JO  - Genome Announcements
PY  - 2014
SP  - e00901
EP  - e00914
VL  - 2
AB  - Dehalococcoides mccartyi strain SG1, isolated from digester sludge, dechlorinates
AB  - polychlorinated biphenyls (PCBs) to lower congeners. Here we report the draft
AB  - genome sequence of SG1, which carries a 22.65 kbp circular putative plasmid.
ER  -

TY  - JOUR
AU  - Wang, S.
AU  - Dong, L.
AU  - Zhao, B.
AU  - Xu, S.
AU  - Wu, K.
AU  - Wang, H.
TI  - Draft Genome Sequence of Bacillus sp. Strain YSP-3, a Halophilic, Alkaliphilic Bacterium Isolated from a Salt Lake.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00882
EP  - e00818
VL  - 7
AB  - The halophilic, alkaliphilic bacterium Bacillus sp. strain YSP-3 was isolated from a salt
AB  - lake. It grows optimally at 8% (wt/vol) NaCl (pH 9.0). The draft
AB  - genome is composed of 4,006 predicted genes. Genomic analysis showed that various
AB  - genes are potentially involved in the adaptation mechanisms for osmotic stress
AB  - and pH homeostasis.
ER  -

TY  - JOUR
AU  - Wang, S.
AU  - Feng, L.
AU  - Zhang, D.
AU  - Xue, Y.
AU  - Xun, Y.
AU  - Ke, Y.
AU  - Zhu, H.
TI  - Genome Sequence of Lactobacillus plantarum JMCC0013, Isolated from Traditional Chinese Fermented Milk.
JO  - Genome Announcements
PY  - 2018
SP  - e00407
EP  - e00418
VL  - 6
AB  - Fermented food products have been consumed for thousands of years in China, so fermented
AB  - Chinese foods may contain huge lactic acid bacterial resources. Here,
AB  - we report the draft genome sequence of a Lactobacillus plantarum isolate,
AB  - JMCC0013, collected from traditional Chinese fermented milk, which provides a
AB  - precious resource for the genomic analysis of Lactobacillus strains.
ER  -

TY  - JOUR
AU  - Wang, S.
AU  - Hao, B.
AU  - Li, J.
AU  - Gu, H.
AU  - Peng, J.
AU  - Xie, F.
AU  - Zhao, X.
AU  - Frech, C.
AU  - Chen, N.
AU  - Ma, B.
AU  - Li, Y.
TI  - Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics.
JO  - BMC Genomics
PY  - 2014
SP  - 440
EP  - 440
VL  - 15
AB  - BACKGROUND: Evidence based on genomic sequences is urgently needed to confirm the
AB  - phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii.
AB  - To define underlying causes for the rather striking difference in host
AB  - specificity between M. huakuii strain 7653R and MAFF303099, several probable
AB  - determinants also require comparison at the genomic level. An improved
AB  - understanding of mobile genetic elements that can be integrated into the main
AB  - chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge
AB  - of how genome dynamics may contribute to Mesorhizobium evolution in general.
AB  - RESULTS: In this study, we sequenced the complete genome of 7653R and compared it
AB  - with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found
AB  - to share a large set of orthologs and, most importantly, a conserved chromosomal
AB  - backbone and even larger perfectly conserved synteny blocks. We also identified
AB  - candidate molecular differences responsible for the different host specificities
AB  - of these two strains. Finally, we reconstructed an ancestral Mesorhizobium
AB  - genomic island that has evolved into diverse forms in different Mesorhizobium
AB  - species. CONCLUSIONS: Our ortholog and synteny analyses firmly establish
AB  - MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and
AB  - secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host
AB  - specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have
AB  - arisen by excision of the original genomic island from the 7653R chromosome.
ER  -

TY  - JOUR
AU  - Wang, S.
AU  - Zhu, H.
AU  - He, F.
AU  - Luo, Y.
AU  - Kang, Z.
AU  - Lu, C.
AU  - Feng, L.
AU  - Lu, X.
AU  - Xue, Y.
AU  - Wang, H.
TI  - Whole Genome Sequence of the Probiotic Strain Lactobacillus paracasei N1115, Isolated from Traditional Chinese Fermented Milk.
JO  - Genome Announcements
PY  - 2014
SP  - e00059
EP  - e00014
VL  - 2
AB  - Lactobacillus paracasei N1115 is a new strain with probiotic properties isolated  from
AB  - traditional homemade dairy products in Inner Mongolia, China. Here, we
AB  - report the complete genome sequence of L. paracasei N1115, which shows high
AB  - similarity to the well-studied probiotic Lactobacillus rhamnosus GG, and 3
AB  - structures turned out to be inversions, according to the colinearity analysis of
AB  - the BLAST alignment.
ER  -

TY  - JOUR
AU  - Wang, S.Y.
AU  - Wei, J.Q.
AU  - Chen, H.
TI  - Complete Genome Sequence of a Putative New Bacterial Strain, I507, Isolated from  the Indian Ocean.
JO  - Genome Announcements
PY  - 2018
SP  - e00246
EP  - e00218
VL  - 6
AB  - Bacterial strain I507 was isolated from the central Indian Ocean and may be a potential novel
AB  - species, according to the 16S rRNA gene sequence. Here, we
AB  - present its complete genome sequence and expect that it will provide researchers
AB  - with valuable information to further understand its classification and function
AB  - in the future.
ER  -

TY  - JOUR
AU  - Wang, T.
AU  - Sun, B.
AU  - Yang, Y.
AU  - Zhao, T.
TI  - Genome Sequence of Acidovorax citrulli Group 1 Strain pslb65 Causing Bacterial Fruit Blotch of Melons.
JO  - Genome Announcements
PY  - 2015
SP  - e00327
EP  - e00315
VL  - 3
AB  - Acidovorax citrulli is typed into two groups, mainly based on the host. We determined the
AB  - draft genome of A. citrulli group 1 strain pslb65. The strain was
AB  - isolated from melon collected from Xinjiang province, China. The A. citrulli
AB  - pslb65 genome contains 4,903,443 bp and has a G+C content of 68.8 mol%.
ER  -

TY  - JOUR
AU  - Wang, T.
AU  - Yang, Y.
AU  - Zhao, T.
TI  - Genome Sequence of a Pseudomonas syringae pv. tabaci Strain, yuexi-1, Causing Wildfire Disease in Tobacco.
JO  - Genome Announcements
PY  - 2015
SP  - e00180
EP  - e00115
VL  - 3
AB  - We determined the draft genome sequence of the Pseudomonas syringae pv. tabaci strain yuexi-1.
AB  - It was isolated from tobacco sample of yuexi-1, Sichuan province,
AB  - China, by our laboratory. The genome contains 6,232,497 bp and has a G+C content
AB  - of 58.2 mol%.
ER  -

TY  - JOUR
AU  - Wang, T.
AU  - Yang, Y.
AU  - Zhao, T.
TI  - Genome Sequence of a Copper-Resistant Strain of Acidovorax citrulli Causing Bacterial Fruit Blotch of Melons.
JO  - Genome Announcements
PY  - 2015
SP  - e00310
EP  - e00315
VL  - 3
AB  - Bacterial fruit blotch (BFB) of melons is a seed-borne disease caused by Acidovorax citrulli.
AB  - We determined the draft genome of A. citrulli Tw6. The
AB  - strain was isolated from a watermelon collected from Beijing, China. The A.
AB  - citrulli Tw6 genome contains 5,080,614 bp and has a G+C content of 68.7 mol%.
ER  -

TY  - JOUR
AU  - Wang, T.-S.
TI  - PflI, a restriction endonuclease from Pseudomonas fluorescens Migula.
JO  - K'o Hsueh T'ung Pao
PY  - 1981
SP  - 815
EP  - 817
VL  - 26
AB  - Over two hundred kinds of restriction endonucleases from 39 genuses, 94
AB  - species, and 159 strains have been found up to now according to Roberts'
AB  - statistics.  Many of them are isoschizomers.  Nothing about restriction
AB  - endonucleases from Psuedomonas fluorescens Migula has been published.  This is
AB  - a report on restriction endonuclease extracted from Pseudomonas fluorescens
AB  - Migula.
ER  -

TY  - JOUR
AU  - Wang, W.
AU  - Liu, F.
AU  - Peng, Z.
AU  - Li, F.
AU  - Ma, A.
TI  - Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China.
JO  - Genome Announcements
PY  - 2016
SP  - e00662
EP  - e00616
VL  - 4
AB  - The carbapenem-resistant Salmonella enterica subsp. enterica serovar Indiana strain C629 was
AB  - isolated from a chicken carcass collected from a slaughterhouse
AB  - in Qingdao, China. The complete genome sequence of C629 contains a circular
AB  - 4,791,723-bp chromosome and a circular 210,106-bp plasmid. Genes involved in
AB  - carbapenem resistance of this bacterium were identified by whole-genome analysis.
ER  -

TY  - JOUR
AU  - Wang, W.
AU  - Ma, T.
AU  - Ren, Y.
AU  - Li, G.
TI  - Draft Genome Sequence of a Benzothiophene-Desulfurizing Bacterium, Gordona terrae Strain C-6.
JO  - Genome Announcements
PY  - 2013
SP  - e00381
EP  - e00313
VL  - 1
AB  - Gordona terrae strain C-6 was isolated from oil-contaminated soil and is capable  of
AB  - desulfurizing benzothiophene (BT). Here we report the draft genome sequence of
AB  - G. terrae strain C-6, which may help to reveal the genetic basis of the BT
AB  - biodesulfurization pathway.
ER  -

TY  - JOUR
AU  - Wang, W.
AU  - Zheng, S.S.
AU  - Sharshov, K.
AU  - Sun, H.
AU  - Wu, X.Q.
AU  - Yang, F.
AU  - Wang, X.L.
AU  - Li, L.X.
TI  - Draft Genome Sequence of Staphylococcus hominis BHG17 Isolated from Wild Bar-Headed Goose (Anser indicus) Feces.
JO  - Genome Announcements
PY  - 2017
SP  - e01552
EP  - e01516
VL  - 5
AB  - Staphylococcus hominis belongs to a group of coagulase-negative staphylococci and is an
AB  - opportunistic pathogen, usually found on the skin and mucous membranes.
AB  - Studies involving S. hominis isolated from wild birds are scarce. Here, we report
AB  - a 2.365-Mb draft genome sequence of S. hominis BHG17, isolated from the feces of
AB  - a bar-headed goose.
ER  -

TY  - JOUR
AU  - Wang, W.
AU  - Zheng, S.S.
AU  - Sun, H.
AU  - Cao, J.
AU  - Yang, F.
AU  - Wang, X.L.
AU  - Li, L.X.
TI  - Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (Anser indicus) Feces on the Qinghai-Tibet Plateau.
JO  - Genome Announcements
PY  - 2016
SP  - e00317
EP  - e00316
VL  - 4
AB  - Bacillus megaterium is a soil-inhabiting Gram-positive bacterium that is routinely used in
AB  - industrial applications for recombinant protein production and
AB  - bioremediation. Studies involving Bacillus megaterium isolated from waterfowl are
AB  - scarce. Here, we report a 6.26-Mbp draft genome sequence of Bacillus megaterium
AB  - BHG1.1, which was isolated from feces of a bar-headed goose.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Chen, M.
AU  - Xiao, J.
AU  - Hao, L.
AU  - Crowley, D.E.
AU  - Zhang, Z.
AU  - Yu, J.
AU  - Huang, N.
AU  - Huo, M.
AU  - Wu, J.
TI  - Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.
JO  - PLoS ONE
PY  - 2015
SP  - E0132881
EP  - E0132881
VL  - 10
AB  - Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to
AB  - degrade a variety of aromatic hydrocarbon compounds, although the degradation
AB  - pathways and substrate versatilities remain largely unknown. Here we studied the
AB  - bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural
AB  - asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon
AB  - source. Genome sequencing of C. gilardii CR3 was carried out to elucidate
AB  - possible mechanisms for the naphthenic acid biodegradation. The genome of C.
AB  - gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of
AB  - respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3
AB  - encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other
AB  - non-coding genes. Many genes were associated with xenobiotic biodegradation and
AB  - metal resistance functions. Pathway prediction for degradation of
AB  - cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that
AB  - naphthenic acid undergoes initial ring-cleavage, after which the ring fission
AB  - products can be degraded via several plausible degradation pathways including a
AB  - mechanism similar to that used for fatty acid oxidation. The final metabolic
AB  - products of these pathways are unstable or volatile compounds that were not toxic
AB  - to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals,
AB  - which was mainly achieved by self-detoxification through ion efflux,
AB  - metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism.
AB  - Our genomic analysis suggests that CR3 is well adapted to survive the harsh
AB  - environment in natural asphalts containing naphthenic acids and high
AB  - concentrations of heavy metals.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Ding, C.
AU  - Han, X.
AU  - Wang, S.
AU  - Yue, J.
AU  - Hou, W.
AU  - Cao, S.
AU  - Zou, J.
AU  - Yu, S.
TI  - Complete Genome Sequence of Riemerella anatipestifer Serotype 1 Strain CH3.
JO  - Genome Announcements
PY  - 2015
SP  - e01594
EP  - e01514
VL  - 3
AB  - Riemerella anatipestifer is a well-described pathogenic bacterium, which is reported worldwide
AB  - as the cause of epizootic infectious polyserositis of waterfowl and other avian species. Here,
AB  - we present the complete genome sequence  of R. anatipestifer strain CH3, the serotype 1
AB  - prevalent in China.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Ding, C.
AU  - Wang, S.
AU  - Han, X.
AU  - Yu, S.
TI  - Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2.
JO  - Appl. Environ. Microbiol.
PY  - 2015
SP  - 5093
EP  - 5102
VL  - 81
AB  - Riemerella anatipestifer is a well-described pathogen of waterfowl and other avian species
AB  - that can cause septicemic and exudative diseases. In this study, we sequenced the complete
AB  - genome of R. anatipestifer strain Yb2 and analyzed it against the published genomic sequences
AB  - of R. anatipestifer strains DSM15868, RA-GD, RA-CH-1, and RA-CH-2. The Yb2 genome contains one
AB  - circular chromosome of
AB  - 2,184,066 bp with a 35.73% GC content and no plasmid. The genome has 2,021 open reading frames
AB  - that occupy 90.88% of the genome. A comparative genomic analysis revealed that genome
AB  - organization is highly conserved among R. anatipestifer strains, except for four inversions of
AB  - a sequence segment in Yb2. A phylogenetic analysis found that the closest neighbor of Yb2 is
AB  - RA-GD. Furthermore, we constructed a library of 3,175 mutants by random transposon
AB  - mutagenesis, and 100 mutants exhibiting more than 100-fold-attenuated virulence were obtained
AB  - by animal screening experiments. Southern blot analysis and genetic characterization of the
AB  - mutants led to the identification of 49 virulence genes. Of these, 25 encode cytoplasmic
AB  - proteins, 6 encode cytoplasmic membrane proteins, 4 encode outer membrane proteins, and the
AB  - subcellular localization of the remaining 14 gene products is unknown. The functional
AB  - classification of orthologous-group clusters revealed that 16 genes are associated with
AB  - metabolism, 6 are associated with cellular processing and signaling, and 4 are associated with
AB  - information storage and processing. The functions of the other 23 genes are poorly
AB  - characterized or unknown. This genome-wide study identified genes important to the virulence
AB  - of R. anatipestifer.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Gao, Z.
AU  - Xu, X.
AU  - Ruan, L.
TI  - Complete Genome Sequence of Thermococcus sp. Strain 4557, a Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent  Area.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5544
EP  - 5545
VL  - 193
AB  - Thermococcus sp. strain 4557 is a hyperthermophilic anaerobic archaeon isolated from the
AB  - deep-sea hydrothermal vent Guaymas Basin site in the
AB  - Gulf of California at a depth of 2,000 m. Here, we present the complete
AB  - genome sequence of Thermococcus sp. 4557, which consists of a single
AB  - circular chromosome of 2,011,320 bp with a G+C content of 56.08%.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Greenfield, P.
AU  - Li, D.
AU  - Hendry, P.
AU  - Volk, H.
AU  - Sutherland, T.D.
TI  - Complete Genome Sequence of a Nonculturable Methanococcus maripaludis Strain Extracted in a Metagenomic Survey of Petroleum Reservoir Fluids.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5595
EP  - 5595
VL  - 193
AB  - Extraction of genome sequences from metagenomic data is crucial for reconstructing the
AB  - metabolism of microbial communities that cannot be
AB  - mimicked in the laboratory. A complete Methanococcus maripaludis genome
AB  - was generated from metagenomic data derived from a thermophilic subsurface
AB  - oil reservoir. M. maripaludis is a hydrogenotrophic methanogenic species
AB  - that is common in mesophilic saline environments. Comparison of the genome
AB  - from the thermophilic, subsurface environment with the genome of the type
AB  - species will provide insight into the adaptation of a methanogenic genome
AB  - to an oil reservoir environment.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Hao, H.
AU  - Xu, Z.
AU  - Zheng, H.
AU  - Liu, C.
AU  - Wei, L.
AU  - Zhang, R.
AU  - Bi, D.
AU  - Chen, H.
AU  - Tan, C.
TI  - Plasmid-mediated multidrug resistance and virulence in an avian pathogenic Escherichia coli strain isolated in China.
JO  - J. Glob. Antimicrob. Resist.
PY  - 2014
SP  - 57
EP  - 58
VL  - 2
AB  - Avian pathogenic Escherichia coli is the causative agent of avian colisepticaemia and has been
AB  - previously reported as a potential zoonotic risk.  APEC strains often display a multidrug
AB  - restance pattern including resistance to aminoglycosides, B-lactams, chloramphenicol,
AB  - fluoroquinolones, tetracycles and trimethoprim/sulfamethoxazole.  In this study, an APEC
AB  - strain (ACN001) isolated from the liver of a diseased chicken in China in 2010 was
AB  - characterised.  ACN001 was shown to belong to phylogenetic group B2 and was confirmed to be
AB  - highly virulent in chicken and mouse models using previously described methods.  Antimicrobial
AB  - susceptibility testing performed according to Clinical and Laboratory Standards Institute
AB  - standards revealed that the strain was multidrug-resistant, with high minimum inhibitory
AB  - concentrations to amikacin (>16 ug/mL), ampicillin (256 ug/mL), chlooramphenical (256 ug/mL),
AB  - ciprofloxacin (64 ug/mL), florfenicol (256 ug/mL), gentamicin (256 ug/mL), norfloxacin (64
AB  - ug/mL), streptomycin (256 ug/mL) and tetracycline (256 ug/mL).
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Hinshaw, K.C.
AU  - Macdonald, S.J.
AU  - Chandler, J.R.
TI  - Draft Genome Sequence of Chromobacterium violaceum Strain CV017.
JO  - Genome Announcements
PY  - 2016
SP  - e00080
EP  - e00016
VL  - 4
AB  - We announce the draft genome sequence for Chromobacterium violaceum strain CV017, used as a
AB  - model and tool to understand acyl-homoserine lactone-dependent quorum
AB  - sensing. The assembly consists of 4,774,638-bp contained in 211 scaffolds.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Wu, L.
AU  - An, W.
AU  - Chen, Y.
AU  - Zhao, L.
TI  - Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01215
EP  - e01213
VL  - 2
AB  - Brevibacillus panacihumi strain W25 was isolated from hydrocarbon-contaminated saline soil.
AB  - Here, we report the 5.5-Mb draft genome sequence of this strain,
AB  - which may provide insights into the mechanism of microbial hydrocarbon
AB  - degradation in saline environments.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Wu, L.
AU  - An, W.
AU  - Zhao, L.
TI  - Draft Genome Sequence of Gordonia alkanivorans Strain CGMCC6845, a Halotolerant Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e01274
EP  - e01213
VL  - 2
AB  - Gordonia alkanivorans strain CGMCC6845 is a halotolerant hydrocarbon-degrading bacterium
AB  - isolated from petroleum-contaminated saline soil. Here we present the
AB  - 5.0-Mb draft genome sequence of this strain, which will improve our understanding
AB  - of the diversity of G. alkanivorans and the mechanisms of microbial hydrocarbon
AB  - degradation in saline environment.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Wu, L.
AU  - An, W.
AU  - Zhao, L.
TI  - Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00003
EP  - e00014
VL  - 2
AB  - Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading
AB  - bacterium isolated from PAH-contaminated marine sediments. Here,
AB  - we report the 4.8-Mb draft genome sequence of this strain, which will provide
AB  - insights into the diversity of A. kashmirensis and the mechanism of PAH
AB  - degradation in the marine environment.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Wu, L.
AU  - Qi, L.
AU  - Li, C.
AU  - An, W.
AU  - Chen, Y.
TI  - Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2.
JO  - Genome Announcements
PY  - 2014
SP  - e01049
EP  - e01014
VL  - 2
AB  - Pseudomonas bauzanensis W13Z2 is a halotolerant polycyclic aromatic hydrocarbon
AB  - (PAH)-degrading bacterium isolated from petroleum-contaminated drill cuttings in
AB  - the Bohai Sea. Here, we report the 8.6-Mb draft genome sequence of this strain,
AB  - which will provide insights into the diversity of Pseudomonas and the mechanism
AB  - of PAHs degradation in drill cuttings.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Zhang, Z.
TI  - Draft Genome Sequence of Aquamicrobium defluvii Strain W13Z1, a Psychrotolerant Halotolerant Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00984
EP  - e00915
VL  - 3
AB  - Aquamicrobium defluvii W13Z1 was isolated from petroleum-contaminated drill cuttings from the
AB  - Bohai Sea and could degrade petroleum hydrocarbon with 5% NaCl  at 15 degrees C. Here, we
AB  - present the 4.8-Mb draft genome sequence of this strain, which may provide useful information
AB  - about the mechanism of petroleum degradation in drill cuttings.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Zhang, Z.
TI  - Draft Genome Sequence of Ochrobactrum anthropi Strain W13P3, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00867
EP  - e00815
VL  - 3
AB  - Ochrobactrum anthropi W13P3 was isolated from saline soil contaminated by polycyclic aromatic
AB  - hydrocarbons (PAHs) and could degrade PAHs with 5% NaCl. We
AB  - report the 5.3-Mb draft genome sequence of this strain, which is helpful for
AB  - understanding the diversity of Ochrobactrum spp. and the mechanism of PAH
AB  - degradation in saline environments.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Zhang, Z.
TI  - Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e01675
EP  - e01615
VL  - 4
AB  - Pannonibacter phragmitetus CGMCC9175 is a halotolerant polycyclic aromatic hydrocarbon
AB  - (PAH)-degrading bacterium isolated from PAH-contaminated intertidal
AB  - zone sediment. Here, we report the 5.7-Mb draft genome sequence of this strain,
AB  - which will provide insights into the diversity of Pannonibacter and the mechanism
AB  - of PAH degradation in sediments.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Li, Y.
AU  - Jing, H.
AU  - Ren, Y.
AU  - Zhou, Z.
AU  - Wang, S.
AU  - Kan, B.
AU  - Xu, J.
AU  - Wang, L.
TI  - Complete Genome Sequence of a Yersinia enterocolitica 'Old World' (3/O:9) Strain and Comparison with the 'New World' (1B/O:8) Strain.
JO  - J. Clin. Microbiol.
PY  - 2011
SP  - 1251
EP  - 1259
VL  - 49
AB  - Yersinia enterocolitica is a heterogeneous bacterial species with a wide
AB  - range of animal reservoirs through which human intestinal illness can be
AB  - facilitated. In contrast to the epidemiological pattern observed in the
AB  - United States, infections in China present a pattern similar to those in
AB  - European countries and Japan, wherein "Old World" strains (biotypes 2-5)
AB  - are prevalent. To gain insights into the evolution of Y. enterocolitica
AB  - and pathogenic properties toward human hosts, we sequenced the genome of a
AB  - biotype 3 strain 105.5R(r) (O:9) obtained from a Chinese patient.
AB  - Comparative genome sequence analysis with strain 8081 (1B/O:8) revealed
AB  - new insights into Y. enterocolitica. Both strains have more than 14%
AB  - specific genes. In strain 105.5R(r), putative virulence factors were found
AB  - in strain-specific genomic pathogenicity islands that comprised a novel
AB  - type III secretion system and rtx-like genes. Many of the loci
AB  - representing ancestral clusters, which are believed to contribute to
AB  - enteric survival and pathogenesis, are present in strain 105.5R(r) but
AB  - lost in strain 8081. Insertion elements in 105.5R(r) have a distinct
AB  - pattern from those in strain 8081, and were exclusively located in a
AB  - strain-specific region. In summary, our comparative genome analysis
AB  - indicates that these two strains may have attained their pathogenicity by
AB  - completely separate evolutionary events, and the 105.5R(r) strain, a
AB  - representative of the "Old World" biogroup, lies in a branch of Y.
AB  - enterocolitica that is distinct from the "New World" 8081 strain.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Liu, X.
AU  - Hou, T.
AU  - Li, W.
AU  - Li, F.
TI  - Highly sensitive homogeneous electrochemical assay for methyltransferase activity based on methylation-responsive exonuclease III-assisted signal amplification.
JO  - Sens. Actuators B Chem.
PY  - 2015
SP  - 575
EP  - 580
VL  - 208
AB  - DNA methylation catalyzed by methyltransferase (MTase) plays a critical role in many
AB  - biological processes. In this paper, a novel and highly sensitive homogeneous electrochemical
AB  - assay was developed for the detection of DNA MTase based on methylation-responsive exonuclease
AB  - III-assisted signal amplification. Upon the action of MTase/endonuclease on hairpin probe 1
AB  - (HP 1) containing the methylation responsive sequence, single-stranded DNA segments are
AB  - generated to hybridize with methylene blue (MB)-labeled hairpin probe 2 (HP 2). Then the
AB  - digestion of HP 2 from the blunt 3' terminus by exonuclease III is activated, resulting in
AB  - the release of MB-labeled mononucleotides and the complementary DNA segment which could
AB  - hybridize with another HP 2 to initiate the signal amplification process. The MB-labeled
AB  - mononucleotide, due to its less negative charge and smaller size, diffuses easily to the
AB  - negatively charged indium tin oxide (ITO) electrode, generating an amplified electrochemical
AB  - signal. The detection limit of the proposed assay was estimated to be 0.04 U/mL, which was
AB  - better than or comparable to that of the biosensors previously reported. To the best of our
AB  - knowledge, it is the first time to adopt exonuclease III-assisted signal amplification for
AB  - homogeneous electrochemical assay of MTase activity, and this strategy exhibits the advantages
AB  - of high sensitivity as well as simplicity. Since this assay is carried out in a homogeneous
AB  - solution phase instead of on an electrode/solution interface, sophisticated probe
AB  - immobilization processes could be avoided. The as-proposed strategy exhibits promising
AB  - potential for MTase functional studies and related researches.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Luo, C.
AU  - Chen, Z.
TI  - Genome Sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. Strain  916.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5467
EP  - 5468
VL  - 194
AB  - Bacillus sp. strain 916, isolated from the soil, showed strong activity against Rhizoctonia
AB  - solani. Here, we present the high-quality draft genome sequence of
AB  - Bacillus sp. strain 916. Its 3.9-Mb genome reveals a number of genes whose
AB  - products are possibly involved in promotion of plant growth or antibiosis.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Luo, Y.
AU  - Liu, D.
AU  - Wang, J.
AU  - Wei, S.
AU  - Zhao, L.
TI  - Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 18
EP  - 18
VL  - 13
AB  - Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia
AB  - pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province,
AB  - China. M. amorphae CCNWGS0123 is an aerobic, Gram-negative, non-spore-forming rod
AB  - strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete
AB  - genome sequence information and genome annotation. The 7,374,589 bp long genome
AB  - which encodes 7136 protein-coding genes and 63 RNA coding genes, contains one
AB  - chromosome and four plasmids. Moreover, a chromosome with no gaps was assembled.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Tao, F.
AU  - Gai, Z.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of the Welan Gum-Producing Strain Sphingomonas sp. ATCC 31555.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5989
EP  - 5990
VL  - 194
AB  - Sphingomonas sp. strain ATCC 31555 can produce an anionic heteropolysaccharide, welan gum,
AB  - which shows excellent stability and viscosity retention even at high
AB  - temperatures. Here we present a 4.0-Mb assembly of its genome sequence. We have
AB  - annotated 10 coding sequences (CDSs) responsible for the welan gum biosynthesis
AB  - and 55 CDSs related to monosaccharide metabolism.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Wang, Q.
AU  - Zhang, W.
AU  - Wang, Y.
AU  - Li, L.
AU  - Wen, T.
AU  - Zhang, T.
AU  - Zhang, Y.
AU  - Xu, J.
AU  - Hu, J.
AU  - Li, S.
AU  - Liu, L.
AU  - Liu, J.
AU  - Jiang, W.
AU  - Tian, J.
AU  - Li, Y.
AU  - Schuler, D.
AU  - Wang, L.
AU  - Li, J.
TI  - Complete Genome Sequence of Magnetospirillum gryphiswaldense MSR-1.
JO  - Genome Announcements
PY  - 2014
SP  - e00171
EP  - e00114
VL  - 2
AB  - We report the complete genomic sequence of Magnetospirillum gryphiswaldense MSR-1 (DSM 6361),
AB  - a type strain of the genus Magnetospirillum belonging to the
AB  - Alphaproteobacteria. Compared to the reported draft sequence, extensive
AB  - rearrangements and differences were found, indicating high genomic flexibility
AB  - and 'domestication' by accelerated evolution of the strain upon repeated
AB  - passaging.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Wei, L.
AU  - Wang, B.
AU  - Zhang, R.
AU  - Liu, C.
AU  - Bi, D.
AU  - Chen, H.
AU  - Tan, C.
TI  - Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 13
EP  - 13
VL  - 11
AB  - Avian pathogenic Escherichia coli is an important etiological agent of avian colibacillosis,
AB  - which manifests as respiratory, hematogenous, meningitic, and
AB  - enteric infections in poultry. It is also a potential zoonotic threat to human
AB  - health. The diverse genomes of APEC strains largely hinder disease prevention and
AB  - control measures. In the current study, pyrosequencing was used to analyze and
AB  - characterize APEC strain ACN001 (= CCTCC 2015182(T) = DSMZ 29979(T)), which was
AB  - isolated from the liver of a diseased chicken in China in 2010. Strain ACN001
AB  - belongs to extraintestinal pathogenic E. coli phylogenetic group B1, and was
AB  - highly virulent in chicken and mouse models. Whole genome analysis showed that it
AB  - consists of six different plasmids along with a circular chromosome of 4,936,576
AB  - bp, comprising 4,794 protein-coding genes, 108 RNA genes, and 51 pseudogenes,
AB  - with an average G + C content of 50.56 %. As well as 237 coding sequences, we
AB  - identified 39 insertion sequences, 12 predicated genomic islands, 8
AB  - prophage-related sequences, and 2 clustered regularly interspaced short
AB  - palindromic repeats regions on the chromosome, suggesting the possible occurrence
AB  - of horizontal gene transfer in this strain. In addition, most of the virulence
AB  - and antibiotic resistance genes were located on the plasmids, which would assist
AB  - in the distribution of pathogenicity and multidrug resistance elements among E.
AB  - coli populations. Together, the information provided here on APEC isolate ACN001
AB  - will assist in future study of APEC strains, and aid in the development of
AB  - control measures.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Zhang, Z.
AU  - Hao, Q.
AU  - Wu, J.
AU  - Xiao, J.
AU  - Jing, H.
TI  - Complete Genome Sequence of Acinetobacter baumannii ZW85-1.
JO  - Genome Announcements
PY  - 2014
SP  - e01083
EP  - e01013
VL  - 2
AB  - Acinetobacter baumannii is an aerobic, nonmotile Gram-negative bacterium that causes
AB  - nosocomial infections worldwide. Here, we report the complete genome
AB  - sequence of Acinetobacter baumannii strain ZW85-1 and its two plasmids. One of
AB  - the plasmids carries genes for NDM-1, which can hydrolyze a wide range of
AB  - antibiotics.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Zhang, Z.
AU  - Jin, D.
AU  - Zhou, L.
AU  - Wu, L.
AU  - Li, C.
AU  - Zhao, L.
AU  - An, W.
AU  - Chen, Y.
TI  - Draft Genome Sequence of Brachybacterium phenoliresistens Strain W13A50, a Halotolerant Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2014
SP  - e00899
EP  - e00814
VL  - 2
AB  - Brachybacterium phenoliresistens strain W13A50 was isolated from a petroleum-contaminated
AB  - saline site, which could degrade hydrocarbon under high
AB  - salinity conditions. Here, we present 4.2-Mb draft genome sequence of this
AB  - strain, which will provide insights into the diversity of Brachybacterium and the
AB  - mechanism of hydrocarbon degradation in saline environments.
ER  -

TY  - JOUR
AU  - Wang, X.
AU  - Zhu, D.
AU  - Wang, M.
AU  - Cheng, A.
AU  - Jia, R.
AU  - Zhou, Y.
AU  - Chen, Z.
AU  - Luo, Q.
AU  - Liu, F.
AU  - Wang, Y.
AU  - Chen, X.Y.
TI  - Complete Genome Sequence of Riemerella anatipestifer Reference Strain.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3270
EP  - 3271
VL  - 194
AB  - Riemerella anatipestifer is an infectious pathogen causing serositis in ducks. We had the
AB  - genome of the R. anatipestifer reference strain ATCC 11845 sequenced. The
AB  - completed draft genome consists of one circular chromosome with 2,164,087 bp.
AB  - There are 2,101 genes in the draft, and its GC content is 35.01%.
ER  -

TY  - JOUR
AU  - Wang, X.J.
AU  - Yan, Y.J.
AU  - Zhang, B.
AU  - An, J.
AU  - Wang, J.J.
AU  - Tian, J.
AU  - Jiang, L.
AU  - Chen, Y.H.
AU  - Huang, S.X.
AU  - Yin, M.
AU  - Zhang, J.
AU  - Gao, A.L.
AU  - Liu, C.X.
AU  - Zhu, Z.X.
AU  - Xiang, W.S.
TI  - Genome Sequence of the Milbemycins-producing Bacterium Streptomyces bingchenggensis.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4526
EP  - 4527
VL  - 192
AB  - Streptomyces bingchenggensis is a soil dwelling bacterium producing the commercially important
AB  - anthelmintic macrolide milbemycins. Besides
AB  - milbemycins, the insecticidal polyether antibiotic nanchangmycin and some
AB  - other antibiotics have also been isolated from this strain. Here we report
AB  - the complete genome sequence of S. bingchenggensis. The availability of
AB  - the genome sequence of S. bingchenggensis should enable us to understand
AB  - the biosynthesis of these structurally intricate antibiotics better and
AB  - facilitate rational improvement of this strain to increase their titers.
ER  -

TY  - JOUR
AU  - Wang, X.Q.
AU  - Showmaker, K.C.
AU  - Yu, X.Q.
AU  - Bi, T.
AU  - Hsu, C.Y.
AU  - Baird, S.M.
AU  - Peterson, D.G.
AU  - Li, X.D.
AU  - Lu, S.E.
TI  - Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens.
JO  - Genome Announcements
PY  - 2014
SP  - e00991
EP  - e00914
VL  - 2
AB  - Burkholderia pyrrocinia strain Lyc2 was isolated from the tobacco rhizosphere in  China. This
AB  - bacterium exhibits a remarkable capacity to inhibit the growth of
AB  - multiple pathogens and shows strong suppression of cotton seedling damping-off.
AB  - Here, we present the draft genome sequence of Burkholderia pyrrocinia strain
AB  - Lyc2.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Chen, C.
AU  - Ai, L.
AU  - Zhou, F.
AU  - Zhou, Z.
AU  - Wang, L.
AU  - Zhang, H.
AU  - Chen, W.
AU  - Guo, B.
TI  - Complete genome sequence of probiotic Lactobacillus plantarum ST-III.
JO  - J. Bacteriol.
PY  - 2010
SP  - 313
EP  - 314
VL  - 193
AB  - Lactobacillus plantarum strain ST-III, a probiotic strain with several functions, was isolated
AB  - from kimchi. Here we report the complete genome sequence of ST-III and compared it with two
AB  - published L. plantarum genomes.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Chen, W.
AU  - He, L.
AU  - Wang, Q.
AU  - Sheng, X.F.
TI  - Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e00969
EP  - e00916
VL  - 4
AB  - Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release
AB  - Fe, Si, and Al from rock under nutrient-poor conditions.
AB  - Here, we report the draft genome sequence of strain M78, which may facilitate a
AB  - better understanding of the molecular mechanism involved in mineral weathering by
AB  - the bacterium.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Du, Y.
AU  - Yuan, Y.
AU  - Guo, Y.
AU  - Wang, J.
AU  - Li, T.
AU  - Chang, D.
AU  - Liu, Y.
AU  - Jiang, X.
AU  - Dai, W.
AU  - Liu, C.
TI  - Draft Genome Sequence of Serratia marcescens Strain LCT-SM166, a Space Flight Strain with a Specific Carbon Source Utilization Pattern.
JO  - Genome Announcements
PY  - 2014
SP  - e00069
EP  - e00014
VL  - 2
AB  - Serratia marcescens has been detected in space habitats. To explore the influence of the space
AB  - flight environment on this bacterium, we investigated the genome
AB  - sequence of LCT-SM166, which was isolated after space flight and has a specific
AB  - carbon source utilization pattern.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - He, K.
AU  - Jiang, Y.
AU  - Shen, J.
AU  - Yu, B.
TI  - Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits  Robust Nutrient Metabolism in Harsh Environments.
JO  - Genome Announcements
PY  - 2016
SP  - e00997
EP  - e00916
VL  - 4
AB  - Pontibacter akesuensis strain AKS 1T was found in Akesu, Xinjiang Province, China, and
AB  - exhibits the extraordinary ability to metabolize various substrates
AB  - and is resistant to solar radiation. To gain insight into the bacterial genetic
AB  - determinants for this adaptability, we report the complete genome sequence of
AB  - strain AKS 1T.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Jorda, M.
AU  - Jones, P.L.
AU  - Maleszka, R.
AU  - Ling, X.
AU  - Robertson, H.M.
AU  - Mizzen, C.A.
AU  - Peinado, M.A.
AU  - Robinson, G.E.
TI  - Functional CpG methylation system in a social insect.
JO  - Science
PY  - 2006
SP  - 645
EP  - 647
VL  - 314
AB  - DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila
AB  - melanogaster and other invertebrates remains
AB  - controversial. Using the recently sequenced honey bee genome, we present a
AB  - bioinformatic, molecular, and biochemical characterization of a functional
AB  - DNA methylation system in an insect. We report on catalytically active
AB  - orthologs of the vertebrate DNA methyltransferases Dnmt1 and Dnmt3a and b,
AB  - two isoforms that contain a methyl-DNA binding domain, genomic
AB  - 5-methyl-deoxycytosine, and CpG-methylated genes. The honey bee provides
AB  - an opportunity to study the roles of methylation in social contexts.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Ke, Y.
AU  - Gao, G.
AU  - Zhen, Q.
AU  - Yuan, X.
AU  - Wang, Z.
AU  - Xu, J.
AU  - Li, T.
AU  - Wang, D.
AU  - Huang, L.
AU  - Xu, X.
AU  - Chen, Z.
TI  - Complete Genome Sequence of Brucella abortus 134, a Biovar 1 Strain Isolated from Human.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6658
EP  - 6658
VL  - 194
AB  - Brucella abortus is one of the common pathogens causing brucellosis in China. Here, we report
AB  - the genome sequence of B. abortus strain 134, a strain isolated
AB  - from a human patient and belonging to biovar 1, the most highly represented
AB  - biovar among B. abortus strains in China.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Ke, Y.
AU  - Zhen, Q.
AU  - Yuan, X.
AU  - Xu, J.
AU  - Qiu, Y.
AU  - Wang, Z.
AU  - Li, T.
AU  - Wang, D.
AU  - Huang, L.
AU  - Chen, Z.
TI  - Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6697
EP  - 6698
VL  - 194
AB  - Brucella canis is considered a rare cause of human brucellosis because of difficulties in
AB  - presumptive diagnosis and underestimation of the incidence. Here,
AB  - we report the draft genome sequence of a Brucella canis isolate, BCB018, isolated
AB  - from a human patient, providing precious resources for comparative genomics
AB  - analysis of Brucella field strains.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Li, C.
AU  - Gao, C.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of the Nonpathogenic Pseudomonas aeruginosa Strain ATCC 15442.
JO  - Genome Announcements
PY  - 2014
SP  - e00421
EP  - e00414
VL  - 2
AB  - Pseudomonas aeruginosa ATCC 15442 is an environmental strain of the Pseudomonas genus. Here,
AB  - we present a 6.77-Mb assembly of its genome sequence. Besides giving
AB  - insights into characteristics associated with the pathogenicity of P. aeruginosa,
AB  - such as virulence, drug resistance, and biofilm formation, the genome sequence
AB  - may provide some information related to biotechnological utilization of the
AB  - strain.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Liu, H.
AU  - Liu, K.
AU  - Wang, C.
AU  - Ma, H.
AU  - Li, Y.
AU  - Hou, Q.
AU  - Liu, F.
AU  - Zhang, T.
AU  - Wang, H.
AU  - Wang, B.
AU  - Ma, J.
AU  - Ge, R.
AU  - Xu, B.
AU  - Yao, G.
AU  - Xu, W.
AU  - Fan, L.
AU  - Ding, Y.
AU  - Du, B.
TI  - Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e00577
EP  - e00517
VL  - 5
AB  - Bacillus paralicheniformis MDJK30 was isolated from the rhizosphere of a peony. It could
AB  - control the pathogen of peony root rot. Here, we report the complete
AB  - genome sequence of B. paralicheniformis MDJK30. Eleven secondary metabolism gene
AB  - clusters were predicted.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Luo, X.
AU  - Zhang, L.
TI  - Draft Genome Sequence of Glycomyces fuscus TRM 49117, Isolated from a Hypersaline Soil Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e01258
EP  - e01217
VL  - 5
AB  - Glycomyces spp. are rare actinomycetes that are potential antibiotic producers. Here, we
AB  - report the draft genome sequence of Glycomyces fuscus TRM 49117. This is
AB  - the first genome report of a bacterium belonging to the genus Glycomyces The
AB  - genome information of G. fuscus will contribute to studies on the structure and
AB  - function of antibiotics.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Qin, Y.
AU  - Kot, W.
AU  - Zhang, F.
AU  - Zheng, S.
AU  - Wang, G.
AU  - Hansen, L.H.
AU  - Rensing, C.
TI  - Genome Sequence of Selenium-Solubilizing Bacterium Caulobacter vibrioides T5M6.
JO  - Genome Announcements
PY  - 2016
SP  - e01721
EP  - e01715
VL  - 4
AB  - Caulobacter vibrioides T5M6 is a Gram-negative strain that strongly solubilizes selenium (Se)
AB  - mineral into Se(IV) and was isolated from a selenium mining area in
AB  - Enshi, southwest China. This strain produces the phytohormone IAA and promotes
AB  - plant growth. Here we present the genome of this strain containing a large number
AB  - of genes encoding resistances to copper and antibiotics.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Ran, S.
AU  - Yang, G.
TI  - Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.
JO  - Sci. Rep.
PY  - 2014
SP  - 5897
EP  - 5897
VL  - 4
AB  - DNA looping and aggregation induced by restriction endonuclease BspMI are studied by atomic
AB  - force microscopy (AFM) and magnetic tweezers (MT). With Ca2+ substituted for the normal enzyme
AB  - cofactor Mg2+ and enzyme concentration below the critical concentration of 6 units/mL, AFM
AB  - images of DNA-BspMI complex show that the number of binding and looping events increases with
AB  - enzyme concentration. At the critical concentration 6 of units/mL, all the BspMI binding sites
AB  - are saturated. It is worth noting that nonspecific BspMI binding to DNA at saturation
AB  - concentration represents more than 8% of the total BspMI-DNA complexes directly observed in
AB  - AFM images. Furthermore, we used MT to prove that additional loops can form when enzyme
AB  - concentration is higher than its saturation valueand the complex is incubated for a long time
AB  - (>2 hrs). We ascribe this phenomenon to the aggregation of enzymes. The force spectroscopy of
AB  - the BspMI-DNA complex shows that the pulling force required to open the loop of the complex at
AB  - less than saturation concentration has a peak at about 3 pN, which is lower than the force
AB  - required to open additional loops due to enzyme aggregation at higher than saturation
AB  - concentration (>6 pN).
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Rocha, E.P.C.
AU  - Leung, F.C.C.
AU  - Danchin, A.
TI  - Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes.
JO  - J. Mol. Evol.
PY  - 2004
SP  - 692
EP  - 700
VL  - 58
AB  - CpG dinucleotide deficiency has been found in viruses, mitochondria, prokaryotes, and
AB  - eukaryotes. The consensual explanation is that it is
AB  - due to deamination of methylated cytosines, as established for
AB  - vertebrate and plants. However, we still do not know whether C5
AB  - cytosine methylation is also the major cause of CpG deficiency in
AB  - bacteria. By combining annotation and experimental data identifying the
AB  - presence of C5 cytosine methyltransferases with analysis of CpG
AB  - relative abundance in 67 bacterial species, we found that CpG relative
AB  - abundance in most bacterial genomes that have cytosine C5
AB  - methyltransferases tends to be in the normal range (observed/expected
AB  - values between 0.82 and 1.21). In contrast, many bacterial species
AB  - likely to be lacking C5 cytosine methylation showed CpG deficiency.
AB  - Furthermore, when comparing genomes with one another, TpG and CpA
AB  - relative abundances were found to be independent from CpG relative
AB  - abundance. This contrasted with intragenome analyses, where C(3)pG(1)
AB  - relative abundance (the subscripts refer to position of a nucleotide in
AB  - a codon) was found to be generally positively correlated with T(3)pG(1)
AB  - relative abundances when plotted against GC content in protein coding
AB  - sequences (CDSs). This suggests the existence of alternative mechanisms
AB  - contributing to CpG deficiency in bacteria.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Roos, K.P.
AU  - Taylor, D.E.
TI  - Transformation of Helicobacter pylori  by chromosomal metronidazole resistance and by a plasmid with a selectable chloramphenicol resistance marker.
JO  - J. Gen. Microbiol.
PY  - 1993
SP  - 2485
EP  - 2493
VL  - 139
AB  - Most strains of Helicobacter pylori are naturally competent for uptake of chromosomal DNA.
AB  - Transformation frequencies for streptomycin resistance or rifampicin resistance markers ranged
AB  - from 1 x 10^-4 to 1 x 10^-3 per viable cell using a plate transformation procedure.
AB  - Transformation of a metronidazole resistance marker was demonstrated when either a
AB  - laboratory-derived mutant or an MtrR clinical isolate were used as the source of donor DNA.
AB  - MtrR was transformed at a frequency of 3 x 10^-5 per viable cell.  All H. pylori strains
AB  - tested produce large amounts of DNAase, which may reduce DNA available for transformation.
AB  - Four H. pylori plasmids were isolated.  DNA fragments from H. pylori plasmids were deleted or
AB  - rearranged when cloned in pUC19 and propagated in Escherichia coli DH5a.  An H. pylori
AB  - plasmid, pUOA26 which contained a chloramphenicol resistance determinant from Campylobacter
AB  - coli, was constructed in H. pylori.  This plasmid could be successfully introduced by natural
AB  - transformation only into H. pylori recipients which contained a homologous resident plasmid.
AB  - Transformation of pUOA26 into plasmid-free cells of H. pylori was achieved by electroporation.
AB  - Transformation frequencies were 1 x 10^-4 transformants per viable cell when plasmid DNA was
AB  - isolated from the same strain; however, introduction of pUOA26 DNA derived from H. pylori 8091
AB  - into a different H. pylori strain, NCTC 11639, resulted in transformation at much lower
AB  - frequencies (less than or equal to 1 x 10-7 per viable cell). Changes in plasmid restriction
AB  - patterns were also noted when pUOA26 was isolated from H. pylori NCTC 11639, suggesting the
AB  - presence of at least two different DNA restriction and modification systems in H. pylori which
AB  - may interfere with uptake of plasmid DNA.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Tao, F.
AU  - Li, C.
AU  - Li, L.
AU  - Xu, P.
TI  - Genome Sequence of Klebsiella pneumoniae Strain ATCC 25955, an Oxygen-Insensitive Producer of 1,3-Propanediol.
JO  - Genome Announcements
PY  - 2013
SP  - e00587
EP  - e00513
VL  - 1
AB  - Klebsiella pneumoniae strain ATCC 25955 is a 1,3-propanediol-producing bacterium  that is
AB  - insensitive to oxygen. Here, we present a 5.29-Mb assembly of its genome
AB  - sequence. We have annotated 10 coding sequences (CDSs) for 1,3-propanediol
AB  - fermentation and 18 CDSs for glycerol uptake. The CDSs related to virulence and
AB  - by-product formation were also annotated.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Tao, F.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol.
JO  - Genome Announcements
PY  - 2013
SP  - e00542
EP  - e00513
VL  - 1
AB  - Clostridium diolis strain DSM 15410 is considered one of the best natural producers of
AB  - 1,3-propanediol because of its appreciable substrate-tolerant
AB  - ability, yield, and productivity. Here, we present a 5.85-Mb assembly of its
AB  - genome sequence. We have annotated the coding sequences responsible for glycerol
AB  - utilization and 1,3-propanediol fermentation.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Wang, J.
AU  - Ahmed, Z.
AU  - Bai, X.
AU  - Wang, J.
TI  - Complete Genome Sequence of Lactobacillus kefiranofaciens ZW3.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4280
EP  - 4281
VL  - 193
AB  - Lactobacillus kefiranofaciens ZW3 was isolated in Tibet, China, from kefir grain, a
AB  - traditional dairy product that is known to provide many health
AB  - benefits to humans. Here, we present the genome features of L.
AB  - kefiranofaciens ZW3 and the identification of a gene cluster related to
AB  - the synthesis of exopolysaccharide, an important constituent of the
AB  - Tibetan kefir.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Wang, X.
AU  - Greenfield, P.
AU  - Jin, D.
AU  - Bai, Z.
TI  - Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant  Growth-Promoting Bacterium Isolated from Rice Rhizosphere.
JO  - Genome Announcements
PY  - 2014
SP  - e00732
EP  - e00714
VL  - 2
AB  - Bacillus amyloliquefaciens strain EBL11 is a bacterium that can promote plant growth by
AB  - inhibiting the growth of fungi on plant surfaces and providing
AB  - nutrients as a nonchemical biofertilizer. The estimated genome of this strain is
AB  - 4.05 Mb in size and harbors 3,683 coding genes (CDSs).
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Wang, Y.
AU  - Lang, C.
AU  - Wei, D.
AU  - Xu, P.
AU  - Xie, J.
TI  - Genome Sequence of Lactobacillus curieae CCTCC M 2011381T, a Novel Producer of Gamma-aminobutyric Acid.
JO  - Genome Announcements
PY  - 2015
SP  - e00552
EP  - e00515
VL  - 3
AB  - Lactobacillus curieae CCTCC M 2011381(T) is a novel species of the genus Lactobacillus and a
AB  - gamma-aminobutyric acid producer that was isolated from
AB  - stinky tofu brine. Here, we present a 2.19-Mb assembly of its genome, which may
AB  - provide further insights into the molecular mechanisms underlying its beneficial
AB  - properties.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Yuan, Y.
AU  - Zhou, L.
AU  - Su, Q.
AU  - Fang, X.
AU  - Li, T.
AU  - Wang, J.
AU  - Chang, D.
AU  - Su, L.
AU  - Xu, G.
AU  - Guo, Y.
AU  - Yang, R.
AU  - Liu, C.
TI  - Draft Genome Sequence of Serratia marcescens Strain LCT-SM213.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4477
EP  - 4478
VL  - 194
AB  - Serratia marcescens is a species of Gram-negative, rod-shaped bacterium of the family
AB  - Enterobacteriaceae. S. marcescens can cause nosocomial infections,
AB  - particularly catheter-associated bacteremia, urinary tract infections, and wound
AB  - infections. Here, we present the draft genome sequence of Serratia marcescens
AB  - strain LCT-SM213, which was isolated from CGMCC 1.1857.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Zhang, R.
AU  - Zheng, Q.
AU  - Jiao, N.
TI  - Draft Genome Sequences of Two Marine Phototrophic Bacteria, Erythrobacter longus  Strain DSM 6997 and Erythrobacter litoralis Strain DSM 8509.
JO  - Genome Announcements
PY  - 2014
SP  - e00677
EP  - e00614
VL  - 2
AB  - Aerobic anoxygenic phototrophic bacteria (AAPB) are important functional groups and are widely
AB  - distributed in the global upper ocean. Here we report the draft
AB  - genomic sequences of two marine AAPB isolates belonging to the genus
AB  - Erythrobacter, Erythrobacter longus strain DSM 6997 and Erythrobacter litoralis
AB  - strain DSM 8509.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Zhang, T.
AU  - Lin, W.
AU  - Zhang, B.
AU  - Cai, Y.
AU  - Yang, C.
AU  - Li, J.
AU  - Xu, H.
AU  - Pan, Y.
TI  - Complete Genome Sequence of Magnetospirillum sp. Strain XM-1, Isolated from the Xi'an City Moat, China.
JO  - Genome Announcements
PY  - 2016
SP  - e01171
EP  - e01116
VL  - 4
AB  - The magnetotactic bacterium Magnetospirillum sp. strain XM-1 was recently isolated from the
AB  - Xi'an City moat, China. It belongs to the Rhodospirillaceae
AB  - family in the Alphaproteobacteria class. Here, we report the complete genome
AB  - sequence of XM-1. The genome contains a single circular chromosome of 4,825,187
AB  - bp and a plasmid of 167,290 bp.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Zheng, Y.
AU  - Wang, M.
AU  - Gao, Y.
AU  - Xiao, Y.
AU  - Peng, H.
TI  - Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13(T)), a strictly thermophilic and organic  solvent-tolerant bacterium.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 735
EP  - 743
VL  - 9
AB  - Anoxybacillus flavithermus subsp. yunnanensis is the only strictly thermophilic bacterium that
AB  - is able to tolerate a broad range of toxic solvents at its optimal
AB  - temperature of 55-60 degrees C. The type strain E13(T) was isolated from
AB  - water-sediment slurries collected from a hot spring. This study presents the
AB  - draft genome sequence of A. flavithermus subsp. yunnanensis E13(T) and its
AB  - annotation. The 2,838,393bp long genome (67 contigs) contains 3,035
AB  - protein-coding genes and 85 RNA genes, including 10 rRNA genes, and no plasmids.
AB  - The genome information has been used to compare with the genomes from A.
AB  - flavithermus subsp. flavithermus strains.
ER  -

TY  - JOUR
AU  - Wang, Y.
AU  - Zhuang, X.
AU  - Zhong, Y.
AU  - Zhang, C.
AU  - Zhang, Y.
AU  - Zeng, L.
AU  - Zhu, Y.
AU  - He, P.
AU  - Dong, K.
AU  - Pal, U.
AU  - Guo, X.
AU  - Qin, J.
TI  - Distribution of Plasmids in Distinct Leptospira Pathogenic Species.
JO  - PLoS Neglected Trop. Dis.
PY  - 2015
SP  - E0004220
EP  - E0004220
VL  - 9
AB  - Leptospirosis, caused by pathogenic Leptospira, is a worldwide zoonotic
AB  - infection. The genus Leptospira includes at least 21 species clustered into three
AB  - groups-pathogens, non-pathogens, and intermediates-based on 16S rRNA phylogeny.
AB  - Research on Leptospira is difficult due to slow growth and poor transformability
AB  - of the pathogens. Recent identification of extrachromosomal elements besides the
AB  - two chromosomes in L. interrogans has provided new insight into genome complexity
AB  - of the genus Leptospira. The large size, low copy number, and high similarity of
AB  - the sequence of these extrachromosomal elements with the chromosomes present
AB  - challenges in isolating and detecting them without careful genome assembly. In
AB  - this study, two extrachromosomal elements were identified in L. borgpetersenii
AB  - serovar Ballum strain 56604 through whole genome assembly combined with S1
AB  - nuclease digestion following pulsed-field gel electrophoresis (S1-PFGE) analysis.
AB  - Further, extrachromosomal elements in additional 15 Chinese epidemic strains of
AB  - Leptospira, comprising L. borgpetersenii, L. weilii, and L. interrogans, were
AB  - successfully separated and identified, independent of genome sequence data.
AB  - Southern blot hybridization with extrachromosomal element-specific probes,
AB  - designated as lcp1, lcp2 and lcp3-rep, further confirmed their occurrences as
AB  - extrachromosomal elements. In total, 24 plasmids were detected in 13 out of 15
AB  - tested strains, among which 11 can hybridize with the lcp1-rep probe and 11 with
AB  - the lcp2-rep probe, whereas two can hybridize with the lcp3-rep probe. None of
AB  - them are likely to be species-specific. Blastp search of the lcp1, lcp2, and
AB  - lcp3-rep genes with a nonredundant protein database of Leptospira species genomes
AB  - showed that their homologous sequences are widely distributed among clades of
AB  - pathogens but not non-pathogens or intermediates. These results suggest that the
AB  - plasmids are widely distributed in Leptospira species, and further elucidation of
AB  - their biological significance might contribute to our understanding of biology
AB  - and infectivity of pathogenic spirochetes.
ER  -

TY  - JOUR
AU  - Wang, Y.H.
AU  - He, X.X.
AU  - Wang, K.M.
AU  - Su, J.
AU  - Chen, Z.F.
AU  - Yan, G.P.
AU  - Du, Y.D.
TI  - A label-free electrochemical assay for methyltransferase activity detection based on the controllable assembly of single wall carbon nanotubes.
JO  - Biosensors and Bioelectronics
PY  - 2013
SP  - 238
EP  - 243
VL  - 41
AB  - A sensitive label-free 'signal-on' electrochemical approach for detection of
AB  - methyltransferases (MTase) activity is developed based on
AB  - the signal transduction and amplification of single wall carbon
AB  - nanotubes (SWCNTs). In this method, the oligonucleotide I is first
AB  - self-assembled on the electrode via Au-S bonding. After hybridization
AB  - with its complement ssDNA (oligonucleotide II), duplex strand DNA
AB  - (dsDNA) probes containing specific recognition sequence of Dam MTase
AB  - and methylation-sensitive restriction endonuclease Dpn I is then formed
AB  - on the electrode. In the presence of Dam MTase and Dpn I, the dsDNA
AB  - probes are methylated and subsequently cleaved into two dsDNA
AB  - fragments. After heating, the remained dsDNA fragments on the electrode
AB  - melted into ssDNA fragments. Then the SWCNTs can be controllably
AB  - assembled on the ssDNA fragments remained on the electrode, mediating
AB  - efficient electron transfer between the electrode and electroactive
AB  - species. It generates measurable current signal (eT ON), which is
AB  - related to the concentration of the Dam MTase. The resulting change in
AB  - electron transfer efficiency is readily measured by differential pulse
AB  - voltammetry at Dam MTase concentrations as low as 0.04 U/mL. This
AB  - method does not need electroactive molecules labeling on the
AB  - methylation-responsive DNA probes. The linear response of the developed
AB  - facile signal-on electrochemical sensing system for Dam MTase is in the
AB  - range of 0.1-1.0 U/mL. In addition, such a SWCNTs based electrochemical
AB  - assay also has the ability to screen inhibitors for Dam MTase.
ER  -

TY  - JOUR
AU  - Wang, Y.P.
AU  - Jarjour, J.
AU  - Boissel, S.
AU  - Thyme, S.
AU  - Khan, I.
AU  - Pangallo, J.
AU  - Baker, D.
AU  - Stoddard, B.
AU  - Scharenberg, A.M.
AU  - Rawlings, D.J.
TI  - Engineering an XID-Site Specific I-AniI Homing Endonuclease through Combination of Rational Design and Directed Evolution.
JO  - Mol. Ther.
PY  - 2013
SP  - S122
EP  - S123
VL  - 21
AB  - LAGLIDADG homing endonucleases (LHEs) are highly specific compact endonucleases with typical
AB  - 20 base pair recognition sites, and thus are ideal scaffolds for engineering site-specific
AB  - enzymes for genome editing applications.  Here, we describe a progressive approach to LHE
AB  - engineering that combines rational design with directed evolution using yeast surface
AB  - display-based high throughput cleavage selection.  This approach was employed to alter the
AB  - binding and cleavage specificity of the I-Anil LHE to recognize a specific, unique mutation in
AB  - the mouse Bruton tyrosine kinase (Btk) gene - this mutation is known to cause mouse X-linked
AB  - immunodeficiency (XID) - a model of human X-linked agammaglobulimemia (XLA).  The required
AB  - retargeting of I-AniI involved resculpting of the DNA contact interface to accommodate nine
AB  - base differences from the native sequence.  As a first step, multiple site-specific variants
AB  - were engineered through randomization of amino acid residues contacting clusters of base pairs
AB  - altered in the partial targets.  As directly combining these "cluster target" LHE variants
AB  - failed to generate active enzymes cleaving the combined targets, variants with successful
AB  - re-specification of residue clusters proximal to the active site were subjected to a
AB  - progressive redesign strategy in which specificity and activity were extended outward across
AB  - the N-terminal and C-terminal XID half-site interfaces.  Successful "half-site" redesigns were
AB  - then combined to generate an active enzyme recognizing the full XID target site, and this
AB  - enzyme was refined by random mutatgenesis to create an enzyme with wildtype-level activity in
AB  - vitro and in cellulo reporter assays.  Finally, the in cellulo activity of this enzyme was
AB  - further increased by fusing to Transcription Activator-Like Effector (TALE) site-specific DNA
AB  - binding domain to copensate the partially reduced binding affinity of engineered XID enzyme.
AB  - This study not only provides a valuable roadmap for further LHE engineering by effectively
AB  - combining rationale and directed evolution strategies, but also demonstrates a novel means to
AB  - increase the binding affinity, thus the cleavage efficacy of engineered LHEs.
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Chang, X.
AU  - Yang, X.
AU  - Pan, L.
AU  - Dai, J.
TI  - Draft Genome Sequence of Polaromonas glacialis Strain R3-9, a Psychrotolerant Bacterium Isolated from Arctic Glacial Foreland.
JO  - Genome Announcements
PY  - 2014
SP  - e00695
EP  - e00614
VL  - 2
AB  - Here we report the draft genome sequence of the psychrotolerant Polaromonas glacialis strain
AB  - R3-9, isolated from Midtre Lovenbreen glacial foreland near
AB  - Ny-Alesund, Svalbard Archipelago, Norway.
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Eddie, B.J.
AU  - Malanoski, A.P.
AU  - Hervey, W.J. IV
AU  - Lin, B.
AU  - Strycharz-Glaven, S.M.
TI  - Complete Genome Sequence of Marinobacter sp. CP1, Isolated from a Self-Regenerating Biocathode Biofilm.
JO  - Genome Announcements
PY  - 2015
SP  - e01103
EP  - e01115
VL  - 3
AB  - Marinobacter sp. CP1 was isolated from a self-regenerating and self-sustaining biocathode
AB  - biofilm that can fix CO2 and generate electric current. We present the complete genome
AB  - sequence of this strain, which consists of a circular 4.8-Mbp chromosome, to understand the
AB  - mechanism of extracellular electron transfer in a microbial consortium.
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Eddie, B.J.
AU  - Malanoski, A.P.
AU  - Hervey, W.J. IV
AU  - Lin, B.
AU  - Strycharz-Glaven, S.M.
TI  - Complete Genome Sequence of Labrenzia sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm.
JO  - Genome Announcements
PY  - 2016
SP  - e00354
EP  - e00316
VL  - 4
AB  - Here, we present the complete genome sequence of Labrenzia sp. strain CP4, isolated from an
AB  - electricity-consuming marine biocathode biofilm. Labrenzia sp.
AB  - strain CP4 consists of a circular 5.2 Mbp chromosome and an 88 Kbp plasmid.
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Hervey, W.J. IV
AU  - Kim, S.
AU  - Lin, B.
AU  - Vora, G.J.
TI  - Complete Genome Sequence of the Bioluminescent Marine Bacterium Vibrio harveyi ATCC 33843 (392 [MAV]).
JO  - Genome Announcements
PY  - 2015
SP  - e01493
EP  - e01414
VL  - 3
AB  - Vibrio harveyi is a Gram-negative marine gamma-proteobacterium that is known to be a
AB  - formidable pathogen of aquatic animals and is a model organism for the study
AB  - of bacterial bioluminescence and quorum sensing. In this report, we describe the
AB  - complete genome sequence of the most studied strain of this species: V. harveyi
AB  - ATCC 33843 (392 [MAV]).
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Kadouri, D.
AU  - Wu, M.
TI  - Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13.
JO  - BMC Genomics
PY  - 2011
SP  - 453
EP  - 453
VL  - 12
AB  - Background: Although bacterial predators play important roles in the dynamics of natural
AB  - microbial communities,
AB  - little is known about the molecular mechanism of bacterial predation and the evolution of
AB  - diverse predatory
AB  - lifestyles.
AB  - Results: We determined the complete genome sequence of Micavibrio aeruginosavorus ARL-13, an
AB  - obligate
AB  - bacterial predator that feeds by "leeching" externally to its prey. Despite being an obligate
AB  - predator depending on
AB  - prey for replication, M. aeruginosavorus encodes almost all major metabolic pathways. However,
AB  - our genome
AB  - analysis suggests that there are multiple amino acids that it can neither make nor import
AB  - directly from the
AB  - environment, thus providing a simple explanation for its strict dependence on prey.
AB  - Remarkably, despite apparent
AB  - genome reduction, there is a massive expansion of genomic islands of foreign origin. At least
AB  - nine genomic islands
AB  - encode many genes that are likely important for Micavibrio-prey interaction such as
AB  - hemolysin-related proteins.
AB  - RNA-Seq analysis shows substantial transcriptome differences between the attack phase, when M.
AB  - aeruginosavorus
AB  - seeks its prey, and the attachment phase, when it feeds and multiplies. Housekeeping genes as
AB  - well as genes
AB  - involved in protein secretion were all dramatically up-regulated in the attachment phase. In
AB  - contrast, genes
AB  - involved in chemotaxis and flagellum biosynthesis were highly expressed in the attack phase
AB  - but were shut down
AB  - in the attachment phase. Our transcriptomic analysis identified additional genes likely
AB  - important in Micavibrio
AB  - predation, including porins, pilins and many hypothetical genes.
AB  - Conclusions: The findings from our phylogenomic and transcriptomic analyses shed new light on
AB  - the biology and
AB  - evolution of the epibiotic predatory lifestyle of M. aeruginosavorus. The analysis reported
AB  - here and the availability of
AB  - the complete genome sequence should catalyze future studies of this organism.
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Lin, B.
AU  - Hervey, W.J. IV
AU  - Vora, G.J.
TI  - Draft Genome Sequence of the Fast-Growing Marine Bacterium Vibrio natriegens Strain ATCC 14048.
JO  - Genome Announcements
PY  - 2013
SP  - e00589
EP  - e00513
VL  - 1
AB  - Vibrio natriegens bacteria are Gram-negative aquatic microorganisms that are found primarily
AB  - in coastal seawater and sediments and are perhaps best known for
AB  - their high growth rates (generation time of <10 min). In this study, we report
AB  - the first sequenced genome of this species, that of the type strain Vibrio
AB  - natriegens ATCC 14048, a salt marsh mud isolate from Sapelo Island, GA.
ER  -

TY  - JOUR
AU  - Wang, Z.
AU  - Wu, M.
TI  - Complete Genome Sequence of the Endosymbiont of Acanthamoeba Strain UWC8, an Amoeba Endosymbiont Belonging to the 'Candidatus Midichloriaceae' Family in  Rickettsiales.
JO  - Genome Announcements
PY  - 2014
SP  - e00791
EP  - e00714
VL  - 2
AB  - The endosymbiont of Acanthamoeba strain UWC8 is an obligate amoeba endosymbiont belonging to
AB  - the family of 'Candidatus Midichloriaceae' in Rickettsiales. We
AB  - report here the complete genome sequence of this bacterium, which should catalyze
AB  - future studies of amoeba-symbiont interactions.
ER  -

TY  - JOUR
AU  - Wang, Z.-G.
AU  - Wu, J.-X.
TI  - DNA methyltransferases: classification, functions and research progress.
JO  - Yichuan
PY  - 2009
SP  - 903
EP  - 912
VL  - 31
AB  - DNA methylation is a postreplicative modification occurred in most prokaryotic and eukaryotic
AB  - genomes, which has a variety of important biological functions including regulation of gene
AB  - expression, gene imprinting, preservation of chromosomal integrity, and X-chromosome
AB  - inactivation. According to their structure and functions, DNA methyltransferases (Dnmts) are
AB  - divided into two major families in mammalian cells: maintenance methyltransferase (Dnmt1) and
AB  - de novo methyltransferases (Drmt3a, Dnmt3b, and Dnmt3L). In addition, Dnmt2 also displays weak
AB  - DNA methyltransferase catalytic activity, but newly founded function is to methylate cytosine
AB  - 38 in the anti-codon loop of tRNA A,p. These Dnmts are crucial for mammalian growth and
AB  - development. Dnmts deficiency will lead to embryonic development defects, cancer, and other
AB  - diseases. Therefore, Dnmts could be important therapeutical targets. This article Summarizes
AB  - the classification, function, and recent research progress in DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Wang, Z.G.
AU  - Wu, Z.
AU  - Xu, S.L.
AU  - Zha, J.
TI  - Genome Sequence of the Human-Pathogenetic Bacterium Vibrio vulnificus B2.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7019
EP  - 7019
VL  - 194
AB  - Vibrio vulnificus, which can lead to rapidly expanding cellulitis or septicemia,  is present
AB  - in the marine environment. Here, we present the draft genome sequence
AB  - of strain B2, which was isolated from a septicemia patient in 2010.
ER  -

TY  - JOUR
AU  - Wani, A.A.
AU  - Stephens, R.E.
AU  - D'Ambrosio, S.M.
AU  - Hart, R.W.
TI  - A new sequence-specific endonuclease from Micrococcus radiodurans.
JO  - Fed. Proc.
PY  - 1981
SP  - 1848
EP  - 1848
VL  - 40
AB  - A new sequence specific endonuclease MraI has been purified from Micrococcus
AB  - radiodurans (ATCC 13939).  The procedure involves ammonium sulfate
AB  - precipitation of crude cell lysates followed by chromatography on Biogel-A,
AB  - DEAE-Biogel, Cibacron blue F3GA agarose, and phosphocellulose columns.  The
AB  - enzyme cleaves phage lambda DNA at three sites, and adenovirus type 2 DNA at
AB  - more than 12 sites.  It has no sites on SV40, PhiX174, PBR322 and PM2 DNA.  The
AB  - three sites on phage lambda DNA recognized by MraI are different from those
AB  - cleaved by SmaI, since the fragments obtained by the digestion of DNA with
AB  - these two enzymes are different and the double digestion generates new
AB  - fragments.  The sites of double digestion generates new fragments.  The sites
AB  - of cleavage on lambda DNA maps at 42.6, 44.9 and 83.4 percent genome length.
AB  - The enzyme requires Mg++ for its absolute activity but is active in the absence
AB  - of added 2-mercaptoethanol.  The enzyme shows activity at a broad range of
AB  - temperature and pH with optimum at 45C and pH 7.0.  Determination of the
AB  - nucleotide sequence that this enzyme recognizes is under investigation.
ER  -

TY  - JOUR
AU  - Wani, A.A.
AU  - Stephens, R.E.
AU  - D'Ambrosio, S.M.
AU  - Hart, R.W.
TI  - A sequence specific endonuclease from Micrococcus radiodurans.
JO  - Biochim. Biophys. Acta
PY  - 1982
SP  - 178
EP  - 184
VL  - 697
AB  - A new sequence specific endonuclease, MraI has been purified from Micrococcus
AB  - radiodurans.  This enzyme cleaves bacteriophage lambda DNA at three sites,
AB  - adenovirus type 2 DNA at more than 12 sites and has a unique site on PhiX174
AB  - DNA.  It has no sites on SV40, PM2 and pBR322 DNA.  The three sites on phage
AB  - lambda DNA are different from those cleaved by SmaI, XmaI and XorII.  The sites
AB  - of cleavage are located at 0.424, 0.447 and 0.834 fractional lengths on the
AB  - physical map of lambda DNA.  MraI is shown to be an isoschizomer of SacII and
AB  - SstII recognizing the palindromic nucleotide sequence '5-CCGC^GG-3'.  The
AB  - enzyme shows an absolute requirement of Mg2+, but is active in the absence of
AB  - added 2-mercaptoethanol.  The enzyme shows activity at a broad range of
AB  - temperature and pH with an optimum at 45C and pH 7.0 MraI represents the first
AB  - restriction enzyme from a bacterium whose DNA lacks modified methylated bases.
ER  -

TY  - JOUR
AU  - Wank, H.
AU  - SanFilippo, J.
AU  - Singh, R.N.
AU  - Matsuura, M.
AU  - Lambowitz, A.M.
TI  - A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA.
JO  - Mol. Cell
PY  - 1999
SP  - 239
EP  - 250
VL  - 4
AB  - Group II introns encode reverse transcriptases that promote RNA splicing (maturase activity)
AB  - and then with the excised intron form a DNA endonuclease that mediates intron mobility by
AB  - target DNA-primed reverse transcription (TPRT).  Here, we show that the primary binding site
AB  - for the maturase (LtrA) encoded by the Lactococcus lactis Ll.LtrB intron is within a region of
AB  - intron domain IV that includes the start codon of the LtrA ORF. This binding is enhanced by
AB  - other elements, particularly domain I and the EBS/IBS interactions, and helps position LtrA to
AB  - initiate cDNA synthesis in the 3' exon as occurs during TPRT. Our results suggest how the
AB  - maturase functions in RNA splicing and support the hypothesis that the reverse transcriptase
AB  - coding region was derived from an independent genetic element that was inserted into a
AB  - preexisting group II intron.
ER  -

TY  - JOUR
AU  - Wannemuehler, M.J.
AU  - Overstreet, A.M.
AU  - Ward, D.V.
AU  - Phillips, G.J.
TI  - Draft genome sequences of the altered schaedler flora, a defined bacterial community from gnotobiotic mice.
JO  - Genome Announcements
PY  - 2014
SP  - e00287
EP  - e00214
VL  - 2
AB  - The altered Schaedler flora (ASF) is a bacterial community that supports normal growth and
AB  - development of gnotobiotic mice. We report here the draft genome sequences of the 8 bacteria
AB  - that comprise the ASF.
ER  -

TY  - JOUR
AU  - Wanzala, S.I.
AU  - Nakavuma, J.
AU  - Travis, D.A.
AU  - Kia, P.
AU  - Ogwang, S.
AU  - Sreevatsan, S.
TI  - Draft Genome Sequences of Mycobacterium bovis BZ 31150 and Mycobacterium bovis B2 7505, Pathogenic Bacteria Isolated from Archived Captive Animal Bronchial Washes  and Human Sputum Samples in Uganda.
JO  - Genome Announcements
PY  - 2015
SP  - e01102
EP  - e01115
VL  - 3
AB  - Bovine tuberculosis (BTB), a zoonotic infection of cattle caused by Mycobacterium bovis,
AB  - results in losses of $3 billion to the global agricultural industry and represents the fourth
AB  - most important livestock disease worldwide. M. bovis as a source of human infection is likely
AB  - underreported due to the culture medium conditions used to isolate the organism from sputum or
AB  - other sample sources. We report here the draft genome sequences of M. bovis BZ 31150, isolated
AB  - from a bronchial washing from a captive chimpanzee, and M. bovis B2 7505, isolated from  a
AB  - human sputum sample in Uganda.
ER  -

TY  - JOUR
AU  - Ward, A.C.
AU  - Davidson, B.E.
AU  - Hillier, A.J.
AU  - Powell, I.B.
TI  - Conjugally transferable phage resistance activities from Lactococcus lactis DRC1.
JO  - J. Dairy Sci.
PY  - 1992
SP  - 683
EP  - 691
VL  - 75
AB  - Lactococcus lactis ssp. lactis strain HID600 is a phage-resistant transconjugant produced by
AB  - mating HID113 (an antibiotic-resistant variant of plasmid-free strain LM0230) with L. lactis
AB  - ssp. lactis strain DRC1. Analysis of HID600 revealed that it had conjugally acquired phage
AB  - resistance, bacteriocin production, proteolytic activity, and a 131-kb plasmid. The
AB  - interaction of phages c2 and sk1 with HID113 and HID600 was studied. Plaque assays indicated
AB  - that only about 12.5% of c2 infections of HID600 produced infective centers and that c2
AB  - infections of HID600 had a longer latent period and smaller average burst size than did
AB  - infections of HID113. Less than .2% of sk1 infections of HID600 were apparently productive; no
AB  - burst was detected. The resistance to phage infection involved restriction-modification and
AB  - abortive infection effects. Such resistance might be useful in the construction of cheese
AB  - starter strains with reduced susceptibility to phage infection, although phage variants able
AB  - to infect HID600 with increased efficiency were observed.
ER  -

TY  - JOUR
AU  - Ward, B.
TI  - Type IIS restriction enzyme footprint I.  Measurement of a triple helix dissociation constant with Eco57I at 25oC.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 2435
EP  - 2440
VL  - 24
AB  - A method is described to measure triple helix dissociation constants by inhibiting
AB  - the cleavage of a plasmid constructed to contain a target sequence for the triplex forming
AB  - oligonucleotide (TFO) dT20 by the type IIS restriction enzyme Eco57I.  The method relies upon
AB  - the TFO's ability to block the cleavage reaction by occupying the enzyme's cleavage site but
AB  - not its
AB  - specific binding sequence.  Using this protocol, the dissociation constant for dT20 bound to
AB  - its
AB  - target was ~0.16 uM at 25oC.  The accuracy of this experiment was demonstrated by measuring
AB  - the Kd of an affinity cleavage TFO using Eco57I and Quantitative Affinity Cleavage Titration.
AB  - Type IIS restriction endonuclease footprinting should be useful for the qualitative and
AB  - quantitative
AB  - investigation of ligand-DNA interactions.
ER  -

TY  - JOUR
AU  - Ward, C.M.
AU  - Baxter, S.W.
TI  - Draft Genome Assembly of a Wolbachia Endosymbiont of Plutella australiana.
JO  - Genome Announcements
PY  - 2017
SP  - e01134
EP  - e01117
VL  - 5
AB  - Wolbachia spp. are endosymbiotic bacteria that infect around 50% of arthropods and cause a
AB  - broad range of effects, including manipulating host reproduction.
AB  - Here, we present the annotated draft genome assembly of Wolbachia strain wAus,
AB  - which infects Plutella australiana, a cryptic ally of the major Brassica pest
AB  - Plutella xylostella (diamondback moth).
ER  -

TY  - JOUR
AU  - Ward, L.J.H.
AU  - Heap, H.A.
AU  - Kelly, W.J.
TI  - Characterization of closely related lactococcal starter strains which show differing patterns of bacteriophage sensitivity.
JO  - J. Appl. Microbiol.
PY  - 2004
SP  - 144
EP  - 148
VL  - 96
AB  - Aims: To characterize a group of closely related Lactococcus lactis subsp. lactis casein
AB  - starter strains used commercially, which differ in
AB  - their sensitivity to bacteriophages isolated from the same industrial
AB  - environment.
AB  - Methods and Results: Nine strains of L. lactis, six of which had
AB  - been used as starter cultures for lactic casein manufacture, were shown
AB  - to be closely related by pulsed-field gel electrophoresis and total DNA
AB  - profiles. Nineteen phages, which propagated on one or more of these
AB  - starter strains were isolated from industrial casein whey samples. The
AB  - phages were all small isometric-headed and could be divided into five
AB  - groups on the basis of host range on the nine strains. Most of the
AB  - phages did not give a PCR product with primers designed to detect the
AB  - two most common lactococcal small isometric phage species (936 and
AB  - P335). The hosts could be divided into six groups depending on their
AB  - phage sensitivity. Plasmids encoding genes for the cell envelope
AB  - associated PI-type proteinase, lactose metabolism and specificity
AB  - subunits of a type I restriction/modification system were identified.
AB  - Conclusions: This work demonstrates how isolates of the same
AB  - starter strain may come to be regarded as separate cultures because of
AB  - their different origins, and how these closely related strains may
AB  - differ in some of their industrially relevant characteristics.
AB  - Significance and Impact of the Study: This situation may be very
AB  - common among lactococci used as dairy starter cultures, and implies
AB  - that the dairy industry worldwide depends on a small number of
AB  - different strains.
ER  -

TY  - JOUR
AU  - Ward, L.M.
AU  - Hemp, J.
AU  - Pace, L.A.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae.
JO  - Genome Announcements
PY  - 2015
SP  - e01356
EP  - e01315
VL  - 3
AB  - We present the draft genome sequence of Leptolinea tardivitalis YMTK-2, a member  of the
AB  - Chloroflexi phylum. This organism was initially characterized as a
AB  - strictly anaerobic nonmotile fermenter; however, genome analysis demonstrates
AB  - that it encodes for a flagella and might be capable of aerobic respiration.
ER  -

TY  - JOUR
AU  - Ward, L.M.
AU  - Hemp, J.
AU  - Pace, L.A.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Herpetosiphon geysericola GC-42, a Nonphototrophic Member of the Chloroflexi Class Chloroflexia.
JO  - Genome Announcements
PY  - 2015
SP  - e01352
EP  - e01315
VL  - 3
AB  - We report here the draft genome sequence of Herpetosiphon geysericola GC-42, a predatory
AB  - nonphototrophic member of the class Chloroflexia in the phylum
AB  - Chloroflexi. This genome provides insight into the evolution of phototrophy and
AB  - aerobic respiration within the Chloroflexi.
ER  -

TY  - JOUR
AU  - Ward, L.M.
AU  - McGlynn, S.E.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of a Divergent Anaerobic Member of the Chloroflexi Class Ardenticatenia from a Sulfidic Hot Spring.
JO  - Genome Announcements
PY  - 2018
SP  - e00571
EP  - e00518
VL  - 6
AB  - Here, we present a draft genome sequence of Nak82, the second genome sequence available for
AB  - the Chloroflexi class Ardenticatenia and the first from a sulfidic
AB  - terrestrial hot spring. Nak82 is genetically and metabolically distinct from
AB  - Ardenticatena maritima and likely represents a new genus- or family-level lineage
AB  - lacking high-potential respiratory pathways.
ER  -

TY  - JOUR
AU  - Ward, L.M.
AU  - McGlynn, S.E.
AU  - Fischer, W.W.
TI  - Draft Genome Sequences of Two Basal Members of the Anaerolineae Class of Chloroflexi from a Sulfidic Hot Spring.
JO  - Genome Announcements
PY  - 2018
SP  - e00570
EP  - e00518
VL  - 6
AB  - Here, we describe the first genome sequences of the Anaerolineae from a sulfidic  environment,
AB  - expanding the environmental distribution of sequenced Anaerolineae
AB  - These genomes represent basal Anaerolineae lineages, branching soon after the
AB  - divergence of the sister class 'Candidatus Thermofonsia,' expanding our
AB  - understanding of the metabolic evolution of this group.
ER  -

TY  - JOUR
AU  - Ward, L.M.
AU  - McGlynn, S.E.
AU  - Fischer, W.W.
TI  - Draft Genome Sequence of Chloracidobacterium sp. CP2_5A, a Phototrophic Member of the Phylum Acidobacteria Recovered from a Japanese Hot Spring.
JO  - Genome Announcements
PY  - 2017
SP  - e00821
EP  - e00817
VL  - 5
AB  - The phylum Acidobacteria contains a single known phototrophic member, Chloracidobacterium
AB  - thermophilum, which was recovered from a hot spring
AB  - metagenome from Yellowstone National Park. Here, we expand the diversity of the
AB  - genus Chloracidobacterium with a genome recovered from a hot spring in Japan,
AB  - extending the known range of this lineage to a new continent.
ER  -

TY  - JOUR
AU  - Ward, L.M.
AU  - McGlynn, S.E.
AU  - Fischer, W.W.
TI  - Draft Genome Sequences of a Novel Lineage of Armatimonadetes Recovered from Japanese Hot Springs.
JO  - Genome Announcements
PY  - 2017
SP  - e00820
EP  - e00817
VL  - 5
AB  - Here, we report two draft genome sequences from a novel lineage within the Armatimonadetes
AB  - phylum recovered from metagenomes sequenced from Japanese hot
AB  - spring microbial mats. These organisms are aerobic and represent a new lineage
AB  - related to the characterized Chthonomonas and Fimbriimonas groups, and they
AB  - expand the diversity of this enigmatic phylum.
ER  -

TY  - JOUR
AU  - Ward, N. et al.
TI  - Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath).
JO  - PLoS Biology
PY  - 2004
SP  - 1616
EP  - 1628
VL  - 2
AB  - Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon
AB  - and energy source for growth, thus playing major roles in global carbon cycles, and in
AB  - particular, substantially reducing emissions of biologically generated methane to the
AB  - atmosphere. Despite their importance, and in contrast to organisms that play roles in other
AB  - major parts of the carbon cycle such as photosynthesis, no genome-level studies have been
AB  - published on the biology of methanotrophs. We report the first complete genome sequence to our
AB  - knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the
AB  - shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a
AB  - methanotrophic lifestyle, including redundant pathways predicted to be involved in
AB  - methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases.
AB  - We used phylogenomic analysis, gene order information, and comparative analysis with the
AB  - partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown
AB  - function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests
AB  - the ability of M. capsulatus to scavenge copper (including a previously unreported
AB  - nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the
AB  - exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project
AB  - is evidence suggesting the existence of previously unsuspected metabolic flexibility in M.
AB  - capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and
AB  - sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph
AB  - ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our
AB  - understanding of methanotroph biology and its relationship to global carbon cycles. We have
AB  - gained evidence for greater metabolic flexibility than was previously known, and for genetic
AB  - components that may have biotechnological potential.
ER  -

TY  - JOUR
AU  - Ward, N.L. et al.
TI  - Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.
JO  - Appl. Environ. Microbiol.
PY  - 2009
SP  - 2046
EP  - 2056
VL  - 75
AB  - The complete genomes of three strains from the phylum Acidobacteria were compared.
AB  - Phylogenetic analysis placed them as a unique phylum. They share
AB  - genomic traits with members of the Proteobacteria, the Cyanobacteria, and
AB  - the Fungi. The three strains appear to be versatile heterotrophs. Genomic
AB  - and culture traits indicate the use of carbon sources that span simple
AB  - sugars to more complex substrates such as hemicellulose, cellulose, and
AB  - chitin. The genomes encode low-specificity major facilitator superfamily
AB  - transporters and high-affinity ABC transporters for sugars, suggesting
AB  - that they are best suited to low-nutrient conditions. They appear capable
AB  - of nitrate and nitrite reduction but not N(2) fixation or denitrification.
AB  - The genomes contained numerous genes that encode siderophore receptors,
AB  - but no evidence of siderophore production was found, suggesting that they
AB  - may obtain iron via interaction with other microorganisms. The presence of
AB  - cellulose synthesis genes and a large class of novel high-molecular-weight
AB  - excreted proteins suggests potential traits for desiccation resistance,
AB  - biofilm formation, and/or contribution to soil structure. Polyketide
AB  - synthase and macrolide glycosylation genes suggest the production of novel
AB  - antimicrobial compounds. Genes that encode a variety of novel proteins
AB  - were also identified. The abundance of acidobacteria in soils worldwide
AB  - and the breadth of potential carbon use by the sequenced strains suggest
AB  - significant and previously unrecognized contributions to the terrestrial
AB  - carbon cycle. Combining our genomic evidence with available culture
AB  - traits, we postulate that cells of these isolates are long-lived, divide
AB  - slowly, exhibit slow metabolic rates under low-nutrient conditions, and
AB  - are well equipped to tolerate fluctuations in soil hydration.
ER  -

TY  - JOUR
AU  - Waring, R.B.
AU  - Davies, R.W.
AU  - Scazzocchio, C.
AU  - Brown, T.A.
TI  - Internal structure of the mitochondrial intron of Aspergillus nidulans.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1982
SP  - 6332
EP  - 6336
VL  - 79
AB  - The intron of the mitochondrial apocytochrome b gene, cobA, of Aspergillus nidulans has been
AB  - subjected to sequence analysis.  It contains an open reading frame of 957 base pairs
AB  - contiguous with the preceding exon.  Regions of the translated open reading frames of cobA and
AB  - the third intron of the cob gene in yeast show high amino acid homology.  Comparison of the
AB  - cobA intron with this and other yeast introns indicates that cobA codes for a maturase protein
AB  - that splices out the intron encoding it and possibly other mitochondrial introns.  Two very
AB  - similar decamer peptides are found in the protein sequences of the cobA intron, four
AB  - mitochondrial yeast introns, and the yeast mitochondrial sequence reading frame 1 and may be
AB  - diagnostic of one class of maturase-coding introns.  Four short DNA sequences, two of which
AB  - are in the region defined by box9 and box2 mutations in the cob gene of yeast, are conserved
AB  - in cobA and certain yeast introns.  Comparison with three yeast introns strongly suggests that
AB  - the first 200 base pairs of the open reading frame of the cobA intron do not code for any
AB  - amino acids present in the putative maturase protein but are required for splicing or the
AB  - control of splicing, or both.
ER  -

TY  - JOUR
AU  - Warncke, S.
AU  - Gegout, A.
AU  - Carell, T.
TI  - Phosphorothioation of Oligonucleotides Strongly Influences the Inhibition of Bacterial (M.Hhal) and Human (Dnmt1) DNA Methyltransferases.
JO  - Chembiochem
PY  - 2009
SP  - 728
EP  - 734
VL  - 10
AB  - The cytidine analogue 5-fluoro-2'-deoxycytidine (dC(F)) is a mechanism-based inhibitor of DNA
AB  - methyltransferases. We report the
AB  - synthesis of short 18-mer dsDNA oligomers containing a
AB  - triple-hemimethylated CpG motive as a recognition sequence for the
AB  - human methyltransferase Dnmt1. The DNA strands carry within these CpG
AB  - islands dC(F) building blocks that function as mechanism-based
AB  - inhibitors of the analyzed methyltransferases. In addition, we replaced
AB  - the phosphodiester backbones at defined positions by phosphorothioates.
AB  - These hypermodified DNA strands were investigated as inhibitors of the
AB  - DNA methyltransferases M.Hhal and Dnmtl in vitro. We could show that
AB  - both methylases behave substantially differently in respect to the
AB  - amount of DNA backbone modification.
ER  -

TY  - JOUR
AU  - Warnecke, F. et al.
TI  - Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.
JO  - Nature
PY  - 2007
SP  - 560
EP  - 565
VL  - 450
AB  - From the standpoints of both basic research and biotechnology, there is
AB  - considerable interest in reaching a clearer understanding of the diversity
AB  - of biological mechanisms employed during lignocellulose degradation.
AB  - Globally, termites are an extremely successful group of wood-degrading
AB  - organisms and are therefore important both for their roles in carbon
AB  - turnover in the environment and as potential sources of biochemical
AB  - catalysts for efforts aimed at converting wood into biofuels. Only
AB  - recently have data supported any direct role for the symbiotic bacteria in
AB  - the gut of the termite in cellulose and xylan hydrolysis. Here we use a
AB  - metagenomic analysis of the bacterial community resident in the hindgut
AB  - paunch of a wood-feeding 'higher' Nasutitermes species (which do not
AB  - contain cellulose-fermenting protozoa) to show the presence of a large,
AB  - diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of
AB  - these genes were expressed in vivo or had cellulase activity in vitro, and
AB  - further analyses implicate spirochete and fibrobacter species in gut
AB  - lignocellulose degradation. New insights into other important symbiotic
AB  - functions including H2 metabolism, CO2-reductive acetogenesis and N2
AB  - fixation are also provided by this first system-wide gene analysis of a
AB  - microbial community specialized towards plant lignocellulose degradation.
AB  - Our results underscore how complex even a 1-microl environment can be.
ER  -

TY  - JOUR
AU  - Warnecke, P.M.
AU  - Bestor, T.H.
TI  - Cytosine methylation and human cancer.
JO  - Curr. Opin. Oncol.
PY  - 2000
SP  - 68
EP  - 73
VL  - 12
AB  - Abnormalities of genomic methylation patterns have been attributed a role in carcinogenesis
AB  - since the early 1980s, when large-scale demethylation of the genome
AB  - was thought be an early event in multistep colorectal carcinogenesis. In the 1990s, local de
AB  - novo methylation (with or without global demethylation) at tumor suppressor loci
AB  - was held to be involved in silencing of tumor suppressor genes. The mechanisms that might
AB  - mediate methylation and demethylation in carcinogenesis remain obscure, and
AB  - there are questions as to whether the methylation changes are a cause or consequence of
AB  - cellular transformation and clonal expansion. It is also important to derive a set of
AB  - defined criteria by which a tumor suppressor gene can be concluded to have been inactivated by
AB  - DNA methylation in a manner that contributes to carcinogenesis.
ER  -

TY  - JOUR
AU  - Warnecke, P.M.
AU  - Biniszkiewicz, D.
AU  - Jaenisch, R.
AU  - Frommer, M.
AU  - Clark, S.J.
TI  - Sequence-specific methylation of the Mouse H19 gene in embryonic cells deficient in the Dnmt-1 gene.
JO  - Dev. Genet.
PY  - 1998
SP  - 111
EP  - 121
VL  - 22
AB  - We have used Dnmtc/c ES cells that are homozygous for disruption of the DNA methyltransferase
AB  - gene to address how de novo methylation is propagated and whether it is directed to specific
AB  - sites in the early embryo.  We examined the imprinted H19 gene and the specific-sequence
AB  - region implicated as an "imprinting mark" to determine whether de novo methylation was
AB  - occurring at a restricted set of sites.  Since the "imprinting mark" was found to be
AB  - methylated differentially at all stages of development, we reasoned that the sequence may
AB  - still be a target for the de novo methylation activity found in the Dnmtc/c cells, even though
AB  - the loss of maintenance methylase activity renders the H19 promoter active.  We used bisulfite
AB  - genomic sequencing to determine the methylation state of the imprinted region of the H19 gene
AB  - and found a low level of DNA methylation at specific single CpG sites in the upstream region
AB  - of the imprinted H19 sequence in the Dnmtc/c mutant ES cells.  Moreover, these CpG sites
AB  - appeared to be favored targets for further de novo methylation of neighboring CpG sites in
AB  - rescued ES cells, which possess apparently normal maintenance activity.  Our data provide
AB  - further evidence for a separate methylating activity in ES cells and indicate that this
AB  - activity displays sequence specificity.
ER  -

TY  - JOUR
AU  - Warren, R.A.J.
TI  - Modified Bases in Bacteriophage DNAs.
JO  - Annu. Rev. Microbiol.
PY  - 1980
SP  - 137
EP  - 158
VL  - 34
AB  - This review considers bacteriophage DNAs in which all or a major proportion of
AB  - one of the four bases found commonly in DNA is replaced by a modified base.  It
AB  - does not consider the methylated bases that are found in small amounts in DNA
AB  - and that function usually to protect DNA against specific restriction
AB  - endonucleases.  The first modified base in a bacteriophage DNA,
AB  - 5-hydroxymethylcytosine (hmCyt), was discovered 27 years ago.  It played a
AB  - crucial role in the development of the biochemistry of T-even phage-infected
AB  - Escherichia coli.  Since then, modified bases have been found in a variety of
AB  - other bacteriophages.  They are of interest from the point of view of their
AB  - biochemistry and, more recently, their effects on DNA conformation and
AB  - function.  The biosynthesis of some of these bases has been reviewed
AB  - extensively.  This review emphasizes the more recent developments in modified
AB  - base biochemistry and considers also some of their effects on DNA structure and
AB  - function.
ER  -

TY  - JOUR
AU  - Warren, W.
AU  - Merion, M.
TI  - Rapid HPLC purification of a restriction enzyme from Sphaerotilus sp.
JO  - BioChromatography
PY  - 1988
SP  - 225
EP  - 230
VL  - 3
AB  - The rapid purification of the Type II restriction endonuclease SspI from
AB  - contaminating exo- and endonucleases contained in a cell lysate of the
AB  - bacterium Sphaerotilus sp. is described using a combination of anion and cation
AB  - exchange media.  Nucleic acids and a substantial portion of non-restriction
AB  - enzyme proteins were quickly removed from the initial cell lysate via solid
AB  - phase extraction using an anion exchange cartridge.  The SspI was subsequently
AB  - purified free from contaminating nucleases using cation exchange column
AB  - chromatography.  Compared to the initial cell lysate, the overall recovery of
AB  - SspI activity in the final product was greater than 75%.  In addition this
AB  - rapid 2-step procedure resulted in a 330-fold increase in enzyme specific
AB  - activity.
ER  -

TY  - JOUR
AU  - Waschkau, B.
AU  - Waldeck, J.
AU  - Wieland, S.
AU  - Eichstadt, R.
AU  - Meinhardt, F.
TI  - Generation of readily transformable Bacillus licheniformis mutants.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2008
SP  - 181
EP  - 188
VL  - 78
AB  - A set of mutants was generated by targeted deletion of the hsdR loci of two type I restriction
AB  - modification systems ( RMS) identified in
AB  - Bacillus licheniformis DSM13. Single as well as double knock-outs
AB  - resulted in strains being readily transformable with plasmids isolated
AB  - from Bacilli. Introduction of shuttle plasmids isolated from
AB  - Escherichia coli was routinely possible when the double mutant B.
AB  - licheniformis MW3 (Delta hsdR1, Delta hsdR2) was used in transformation
AB  - experiments. Growth and secretion of extracellular enzymes were not
AB  - affected in any of the mutants. Thus, along with an optimized
AB  - transformation protocol, this study makes available an urgently needed
AB  - transformation system for this industrially exploited species.
ER  -

TY  - JOUR
AU  - Wasels, F.
AU  - Barbanti, F.
AU  - Spigaglia, P.
TI  - Draft Genome Sequence of Clostridium difficile Strain IT1118, an Epidemic Isolate Belonging to the Emerging PCR Ribotype 018.
JO  - Genome Announcements
PY  - 2016
SP  - e00717
EP  - e00716
VL  - 4
AB  - Clostridium difficile PCR ribotype 018 has emerged in Italy, South Korea, and Japan, causing
AB  - severe infections and outbreaks. In this study, we sequenced the
AB  - genome of IT1118, an Italian clinical isolate, to clarify the molecular features
AB  - contributing to the success of this epidemic type.
ER  -

TY  - JOUR
AU  - Wasels, F.
AU  - Clement, B.
AU  - Lopes, F.N.
TI  - Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923).
JO  - Genome Announcements
PY  - 2016
SP  - e00048
EP  - e00016
VL  - 4
AB  - Here, we report the draft genome sequence of Clostridium tyrobutyricum CIP I-776  (IFP923), an
AB  - efficient producer of butyric acid. The genome consists of a single
AB  - chromosome of 3.19 Mb and provides useful data concerning the metabolic
AB  - capacities of the strain.
ER  -

TY  - JOUR
AU  - Wassenegger, M.
TI  - RNA-directed DNA methylation.
JO  - Plant Mol. Biol.
PY  - 2000
SP  - 203
EP  - 220
VL  - 43
AB  - RNA-DNA interactions can serve as a signal that triggers de novo DNA methylation in plants. As
AB  - yet, this RNA-directed DNA methylation mechanism merely targets transgenes, but it appears
AB  - likely that methylation of some endogenous sequences is also directed by RNA. RNA-directed
AB  - methylation of cytosine residues specifically occurs along the DNA regions that are
AB  - complementary to the directing RNA pointing to the formation of a putative RNA-DNA duplex.
AB  - Dense methylation patterns and the methylation of cytosine residues at symmetric and
AB  - asymmetric sites are detectable on both DNA strands within these regions. Methylation
AB  - progressively decreases in the sequences adjacent to the putative RNA-DNA duplex. The extreme
AB  - sensitivity of RNA-directed DNA methylation was demonstrated by analyzing a short 30 bp DNA
AB  - region that was complementary to the targeting RNA. Association of RNA-directed DNA
AB  - methylation with homology-dependent gene silencing indicated that the methylation-directing
AB  - RNA molecules may be double-stranded or may contain double-stranded regions. Whereas the
AB  - function of DNA methylation in transcriptional gene silencing is nearly understood, its role
AB  - in post-transcriptional gene silencing is still under discussion. In mammals, X-chromosome
AB  - inactivation and genomic imprinting are associated with DNA methylation but how methylation is
AB  - initiated is unclear. The observation of a correlation between specific antisense RNAs and
AB  - transcriptional and post-transcriptional gene silencing may indicate that RNA-directed DNA
AB  - methylation is involved in epigenetic gene regulation throughout eukaryotes.
ER  -

TY  - JOUR
AU  - Watabe, H.
AU  - Iino, T.
AU  - Kaneko, T.
AU  - Shibata, T.
AU  - Ando, T.
TI  - A new class of site-specific endodeoxyribonucleases.
JO  - J. Biol. Chem.
PY  - 1983
SP  - 4663
EP  - 4665
VL  - 258
AB  - We had found that yeasts had intracellular endodeoxyribonucleases that cut
AB  - phage DNA into a set of double-stranded fragments with discrete chain lengths.
AB  - We purified one of them to apparent homogeneity from Saccharomyces cerevisiae
AB  - and designated it Endo.Sce.I.  Sequence analysis around 5 cleavage site in
AB  - plasmid DNA and phage DNA revealed that Endo.SceI cuts a defined phosphodiester
AB  - bond in each strand of double helix at the cleavage sites and produces free
AB  - cohesive ends consisting of 4 nucleotides protruding at 3'-termini.  However,
AB  - unlike in the case of prokaryotic type II-restriction endonucleases, (i)
AB  - Endo.SceI seems to consist of two nonidentical subunits, (ii) no common
AB  - palindrome or consensus sequence including more than 5 base pairs is detected
AB  - at or near these cleavage sites, and (iii) Endo.SceI can cut the DNA isolated
AB  - from the cells that produced Endo.SceI.  All of the 5 cleavage sites are
AB  - included in inverted repeats, but these inverted repeats are variable in size,
AB  - nucleotide sequence, and distance between repeating units.  An inverted repeat
AB  - itself is not a structure recognized by Endo.SceI.  This study shows that
AB  - Endo.SceI is the first example of eukaryotic site-specific endonuclease and has
AB  - properties, as described above, which distinguish it from prokaryotic
AB  - restriction endoncleases.
ER  -

TY  - JOUR
AU  - Watabe, H.
AU  - Shibata, T.
AU  - Ando, T.
TI  - Site-specific endo-deoxyribonucleases in eukaryotes: endonucleases of yeasts, Saccharomyces and Pichia.
JO  - J. Biochem. (Tokyo)
PY  - 1981
SP  - 1623
EP  - 1632
VL  - 90
AB  - A class of endo-deoxyribonucleases was found in cell-free extracts from yeasts;
AB  - Saccharomyces cerevisiae, S. uvarum and Pichia membranaefaciens.  These
AB  - endonucleases cleaved double-stranded DNA so that the treated DNA exhibited a
AB  - set of discrete bands on an agarose gel-electrophoregram.  The profiles
AB  - obtained with a certain DNA were unique to each endonuclease, suggesting that
AB  - these yeast endonucleases cleave DNA at well-defined sites specific to each
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Watabe, H.-O.
AU  - Shibata, T.
AU  - Iino, T.
AU  - Ando, T.
TI  - Purification of a eukaryotic site-specific endonuclease, Endo.SceI, from Saccharomyces cerevisiae and effectors on its specificity and activity.
JO  - J. Biochem. (Tokyo)
PY  - 1984
SP  - 1677
EP  - 1690
VL  - 95
AB  - A site-specific endonuclease (Endo.SceI) which caused double-strand scission of DNA was highly
AB  - purified from a eukaryote, Saccharomyces cerevisiae IAM4274.  The molecular weight of the
AB  - active form of Endo.SceI was estimated to be 120,000 and 110,000 by sedimentation analysis on
AB  - a glycerol density gradient and gel filtration on Ultrogel AcA34, respectively.  Analysis of
AB  - the fractions from the last column chromatography by polyacrylamide gel electrophoresis in the
AB  - presence of sodium dodecyl sulfate and by an assay of the endonucleolytic activities suggested
AB  - that Endo.SceI consists of two non-identical subunits with molecular weights of 75,000 and
AB  - 50,000.  Unlike restriction endonucleases, Endo.SceI was active on chromosomal DNA of the
AB  - cells which produced Endo.SceI.  Single-stranded DNA was not cleaved by Endo.SceI, but
AB  - inhibited the endonucleolytic activity of the enzyme on double-stranded DNA.  The
AB  - endonucleolytic activity of Endo.SceI required magnesium ions (Mg2+) as a sole cofactor; Mg2+
AB  - could not be replaced by Ca2+ or Zn2+.  When Mg2+ was replaced by manganese ions (Mn2+),
AB  - extensively purified Endo.SceI cleaved double-stranded DNA at many other sites in addition to
AB  - the sites at which DNA was cleaved in the presence of Mg2+.  Experiments indicated that this
AB  - is not the activation of contaminating endonuclease in the preparation of Endo.SceI, but the
AB  - result of relaxation in the site-specificity of cleavage.
ER  -

TY  - JOUR
AU  - Watahiki, S.
AU  - Kimura, N.
TI  - Draft Genome Sequence of a Caffeine-Utilizing Bacterium, Cupriavidus sp. Strain D384.
JO  - Genome Announcements
PY  - 2017
SP  - e00370
EP  - e00317
VL  - 5
AB  - Cupriavidus sp. D384 was isolated from forest soil in Japan and is known to utilize caffeine
AB  - as a sole source of carbon and energy. We report here the
AB  - 6,835,230-bp genome sequence for this strain, which contains 6,116 predicted
AB  - coding sequences, including gene operon for alkaloid degradation.
ER  -

TY  - JOUR
AU  - Watanabe, K.
AU  - Suzuki, H.
AU  - Nakao, R.
AU  - Shimizu, T.
AU  - Watarai, M.
TI  - Draft Genome Sequences of Five Legionella pneumophila Strains Isolated from Environmental Water Samples.
JO  - Genome Announcements
PY  - 2015
SP  - e00474
EP  - e00415
VL  - 3
AB  - Legionella pneumophila is the causative agent of legionellosis. Here, we report the draft
AB  - genome sequences of five L. pneumophila strains, Bnt314, Ofk308,
AB  - Twr292, Ymg289, and Ymt294, isolated from environmental water samples.
AB  - Comparative analyses of these genomes may reveal the survival mechanisms and
AB  - virulence of L. pneumophila in the natural environment.
ER  -

TY  - JOUR
AU  - Watanabe, K.I.
AU  - Ehara, M.
AU  - Inagaki, Y.
AU  - Ohama, T.
TI  - Distinctive origins of group I introns found in the COXI genes of three green algae.
JO  - Gene
PY  - 1998
SP  - 1
EP  - 7
VL  - 213
AB  - Upon surveying the cytochrome c oxidase subunit I (COXI) gene of green algae, we found group I
AB  - introns in three species of algae, Chlorella vulgaris (Cv), Scenedesmus quadricauda (Sq) and
AB  - Protosiphon botryoides (Pb). The comparative analysis of these nucleotide sequences and their
AB  - secondary structures revealed that the introns of Cv, Sq, and Pb belong to groups IB1, ID, and
AB  - IB2, respectively. Each of the three introns contained an open reading frame (ORF) that showed
AB  - a similarity to the sequence of the LAGLIDADG endonuclease family. However, each of the
AB  - intronic ORFs in Sq and Pb had a discontinuity in the middle of the sequences coding for the
AB  - LAGLIDADG endonuclease. Either of the two ORFs could be restored to a sequence homologous to
AB  - the LAGLIDADG endonuclease by the insertion of a nucleotide in the appropriate position. In
AB  - Sq, a putative pseudo-knot structure was detected in the intronic ORF. This suggests the
AB  - occurrence of a ribosomal frameshift in the translation of the ORF, because such pseudo-knot
AB  - structures are common in viral ORFs employing a (-1) ribosomal frameshift. In the phylogenetic
AB  - tree that was inferred from the amino acid sequences of algal and non-algal intronic ORFs, the
AB  - three algal ORFs did not make a cluster, but were scattered throughout the tree. In addition.
AB  - Each of the three algal ORFs showed a close relationship to the ORFs of non-algal introns that
AB  - were inserted at the corresponding site of the COXI gene, suggesting distinctive origins of
AB  - the three algal introns via independent horizontal transfers.
ER  -

TY  - JOUR
AU  - Watanabe, M.
AU  - Kojima, H.
AU  - Fukui, M.
TI  - Draft genome sequence of Desulfoplanes formicivorans Pf12BT, a sulfate-reducing bacterium of the family Desulfomicrobiaceae.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 34
EP  - 34
VL  - 12
AB  - Desulfoplanes formicivorans strain Pf12BT is the type strain of the type species  in the genus
AB  - Desulfoplanes, which is the one of the genera in the family
AB  - Desulfomicrobiaceae within the order Desulfovibrionales. This
AB  - deltaproteobacterium was isolated from a blackish meromictic lake sediment. D.
AB  - formicivorans strain Pf12BT is a Gram-negative, motile and sulfate-reducing
AB  - bacterium. Cells of strain Pf12BT are characterized by possession of vibroid
AB  - morphology and red fluorescent pigment. Here we describe the features, draft
AB  - genome sequence and annotation of this organism, the sole species of the genus
AB  - Desulfoplanes. The genome comprised 3,000,979 bp, 2,657 protein-coding genes and
AB  - 58 RNA genes.
ER  -

TY  - JOUR
AU  - Watanabe, M.
AU  - Tokizawa, R.
AU  - Kojima, H.
AU  - Fukui, M.
TI  - High-quality draft genome sequence of Effusibacillus lacus strain skLN1(T), facultative anaerobic spore-former isolated from freshwater lake sediment.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 76
EP  - 76
VL  - 12
AB  - 10.1601/nm.25721 strain skLN1(T) is the type strain of the type species in the genus
AB  - 10.1601/nm.25720 which is the one of the genera in the family
AB  - 10.1601/nm.5070 within the phylum 10.1601/nm.3874. 10.1601/nm.25721 strain
AB  - skLN1(T) is a Gram-positive, spore-forming thermophilic neutrophile isolated from
AB  - freshwater lake sediment. Here, we present the draft genome sequence of strain
AB  - skLN1(T), which consists of 3,902,380 bp with a G + C content of 50.38%.
ER  -

TY  - JOUR
AU  - Watanabe, M.
AU  - Yuzawa, H.
AU  - Handa, N.
AU  - Kobayashi, I.
TI  - Hyperthermophilic DNA methyltransferase M.Pabl from the archaeon Pyrococcus abyssi.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 5367
EP  - 5375
VL  - 72
AB  - Genome sequence comparisons among multiple species of Pyrococcus, a hyperthermophilic
AB  - archaeon, revealed a linkage between a putative
AB  - restriction-modification gene complex and several large genome
AB  - polymorphisms/rearrangements. From a region apparently inserted into
AB  - the Pyrococcus abyssi genome, a hyperthermoresistant restriction enzyme
AB  - [PabI; 5'-(GTA/C)] with a novel structure was discovered. In the
AB  - present work, the neighboring methyltransferase homologue, M.PabI, was
AB  - characterized. Its N-terminal half showed high similarities to the M
AB  - subunit of type I systems and a modification enzyme of an atypical type
AB  - II system, M.AhdI, while its C-terminal half showed high similarity to
AB  - the S subunit of type I systems. M.PabI expressed within Escherichia
AB  - coli protected PahI sites from RsaI, a PabI isoschizomer. M.PabI,
AB  - purified following overexpression, was shown to generate 5'-GTm6AC,
AB  - which provides protection against PabI digestion. M.PabI was found to
AB  - be highly thermophilic; it showed methylation at 95 degrees C and
AB  - retained at least half the activity after 9 min at 95 degrees C. This
AB  - hyperthermophilicity allowed us to obtain activation energy and other
AB  - thermodynamic parameters for the first time for any DNA
AB  - methyltransferases. We also determined the kinetic parameters of
AB  - k(cat), K-m,K- DNA, and K-m,K- AdoMet. The activity of M.PabI was
AB  - optimal at a slightly acidic pH and at an NaCl concentration of 200 to
AB  - 500 mM and was inhibited by Zn2+ but not by Mg2+, Ca2+, or Mn2+. These
AB  - and previous results suggest that this unique methyltransferase and
AB  - PahI constitute a type II restriction-modification gene complex that
AB  - inserted into the P. abyssi genome relatively recently. As the most
AB  - thermophilic of all the characterized DNA methyltransferases, M.PabI
AB  - may help in the analysis of DNA methylation and its application to DNA
AB  - engineering.
ER  -

TY  - JOUR
AU  - Watanabe, N.
AU  - Takasaki, Y.
AU  - Sato, C.
AU  - Ando, S.
AU  - Tanaka, I.
TI  - Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2009
SP  - 1326
EP  - 1333
VL  - 65
AB  - The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without
AB  - divalent cations were solved at 2.17 and
AB  - 2.00 angstrom resolution, respectively. HindIII forms a dimer. The
AB  - structures showed that HindIII belongs to the EcoRI-like (alpha-class)
AB  - subfamily of type II restriction endonucleases. The cognate DNA-complex
AB  - structures revealed the specific DNA-recognition mechanism of HindIII
AB  - by which it recognizes the palindromic sequence A/AGCTT. In the Mg2+
AB  - ion-soaked structure the DNA was cleaved and two ions were bound at
AB  - each active site, corresponding to the two-metal-ion mechanism.
ER  -

TY  - JOUR
AU  - Watanabe, S.
AU  - Sasahara, T.
AU  - Arai, N.
AU  - Sasaki, K.
AU  - Aiba, Y.
AU  - Sato'o, Y.
AU  - Cui, L.
TI  - Complete Genome Sequence of Streptococcus pyogenes Strain JMUB1235 Isolated from  an Acute Phlegmonous Gastritis Patient.
JO  - Genome Announcements
PY  - 2016
SP  - e01133
EP  - e01116
VL  - 4
AB  - Acute phlegmonous gastritis is an uncommon endogenous bacterial gastritis presenting with a
AB  - high mortality rate. Here, we report the complete genome
AB  - sequence of an emm89 Streptococcus pyogenes strain, JMUB1235, which is the
AB  - causative agent of acute phlegmonous gastritis.
ER  -

TY  - JOUR
AU  - Watanabe, S.
AU  - Shiwa, Y.
AU  - Itaya, M.
AU  - Yoshikawa, H.
TI  - Complete Sequence of the First Chimera Genome Constructed by Cloning the Whole Genome of Synechocystis Strain PCC6803 into the Bacillus subtilis 168 Genome.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7007
EP  - 7007
VL  - 194
AB  - Genome synthesis of existing or designed genomes is made feasible by the first successful
AB  - cloning of a cyanobacterium, Synechocystis PCC6803, in Gram-positive,
AB  - endospore-forming Bacillus subtilis. Whole-genome sequence analysis of the
AB  - isolate and parental B. subtilis strains provides clues for identifying single
AB  - nucleotide polymorphisms (SNPs) in the 2 complete bacterial genomes in one cell.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Kojima, H.
AU  - Fukui, M.
TI  - Draft Genome Sequence of Mizugakiibacter sediminis skMP5T.
JO  - Genome Announcements
PY  - 2015
SP  - e01185
EP  - e01115
VL  - 3
AB  - Strain skMP5(T) is a moderately thermophilic and facultatively anaerobic bacterium, described
AB  - as a representative of Mizugakiibacter sediminis. Here, we report the annotated draft genome
AB  - sequence of strain skMP5(T).
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Kojima, H.
AU  - Fukui, M.
TI  - Draft Genome Sequence of a Sulfur-Oxidizing Autotroph, Sulfuricella sp. Strain T08, Isolated from a Freshwater Lake.
JO  - Genome Announcements
PY  - 2015
SP  - e00498
EP  - e00415
VL  - 3
AB  - Sulfuricella sp. strain T08 is a sulfur-oxidizing autotroph newly isolated from a freshwater
AB  - lake in Japan. Strain T08 is the second isolate of the genus
AB  - Sulfuricella. Here, we report the annotated draft genome sequence of the isolate.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Kojima, H.
AU  - Fukui, M.
TI  - Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation.
JO  - Appl. Environ. Microbiol.
PY  - 2012
SP  - 6545
EP  - 6549
VL  - 78
AB  - Except for several conspicuous cases, very little is known about sulfur oxidizers
AB  - living in natural freshwater environments. Sulfuricella denitrificans skB26 is a
AB  - psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a
AB  - representative of a new genus in the class Betaproteobacteria. In this study, an
AB  - approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the
AB  - draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and
AB  - 3,133 coding sequences were identified. The identified genes include those
AB  - required for sulfur oxidation, denitrification, and carbon fixation. Comparative
AB  - proteomic analysis was conducted to assess cold adaptation mechanisms of this
AB  - organism. From cells grown at 22 degrees C and 5 degrees C, proteins were
AB  - extracted for analysis by nano-liquid chromatography-electrospray
AB  - ionization-tandem mass spectrometry. In the cells cultured at 5 degrees C,
AB  - relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box
AB  - RNA helicases were increased in comparison to those at 22 degrees C. These
AB  - results suggest that maintenance of proper translation is critical for growth
AB  - under low-temperature conditions, similar to the case for other cold-adapted
AB  - prokaryotes.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Maruyama, F.
AU  - Nozawa, T.
AU  - Aoki, A.
AU  - Okano, S.
AU  - Shibata, Y.
AU  - Oshima, K.
AU  - Kurokawa, K.
AU  - Hattori, M.
AU  - Nakagawa, I.
AU  - Abiko, Y.
TI  - Complete Genome Sequence of the Bacterium Porphyromonas gingivalis TDC60, Which Causes Periodontal Disease.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4259
EP  - 4260
VL  - 193
AB  - Porphyromonas gingivalis is a black-pigmented asaccharolytic anaerobe and a major causative
AB  - agent of periodontitis. Here, we report the complete
AB  - genome sequence of P. gingivalis strain TDC60, which was recently isolated
AB  - from a severe periodontal lesion in a Japanese patient.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Nishida, H.
AU  - Ogata, C.
AU  - Arai, T.
AU  - Sato, S.
TI  - Episome-mediated transfer of drug resistance in enterobacteriaceae.  VII.  Two types of naturally occurring R factors.
JO  - J. Bacteriol.
PY  - 1964
SP  - 716
EP  - 726
VL  - 88
AB  - Naturally occurring R factors are classified into two types, fi+ and fi-,
AB  - depending on their fi characters.  The term fi is an abbreviation of fertility
AB  - inhibition and fi+ and fi- mean, respectively, the presence and absence of
AB  - suppression of the functions of the sex factor F of Escherichia coli K-12.  It
AB  - was found that fi- R factors reduce the efficiency of plating of phages lambda
AB  - and T1 in K-12; fi+ R factors did not have this inhibitory action.  One of the
AB  - fi- R factors reduced the efficiency of plating of phage T7 as well.  Phages
AB  - lambda and T1 underwent host-induced modifications in the host carrying some
AB  - fi- R factors.  At least two types of fi- R factors were recognized by the
AB  - types of their restriction and host-induced modification of these phages.
AB  - CaCl2 exhibited antagonistic actions against the restrictions of phages lambda
AB  - and T1 by fi- R factors.  Transduction of the ability to ferment galactose with
AB  - HFT lysates of lambda was reduced by fi- R factors.  Ultraviolet induction of
AB  - lambda was not affected by any R factors.  Furthermore, adsorption of phages
AB  - lambda and T1 was not altered by the presence of any R factors.  From these
AB  - results, we concluded that the suppression of progeny formation of these phages
AB  - by fi- R factors is due to some step(s) after adsorption of the phages to the
AB  - bacteria.  Superinfection immunity and mutual exclusion were found between two
AB  - different fi+ R factors but not between fi+ and fi- R factors.  The two
AB  - different fi+ R factors were frequently genetically recombined, but fi+ and fi-
AB  - R factors were not genetically recombined, as indicated by findings of
AB  - independent transfer of these R factors by conjugation and by transduction from
AB  - the donors having these two R factors.  It was assumed from these findings that
AB  - fi+ and fi- R factors are considerably different episomes having different
AB  - resistance-transfer factors.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Takano, T.
AU  - Arai, T.
AU  - Nishida, H.
AU  - Sato, S.
TI  - Episome-mediated transfer of drug resistance in Enterobacteriaceae.   X.  Restriction and modification of phages by fi- R factors.
JO  - J. Bacteriol.
PY  - 1966
SP  - 477
EP  - 486
VL  - 92
AB  - A fi- R factor, which restricts phages lambda, T1, and T7 without modifying
AB  - them, was found to restrict and not to modify an F- specific phage, W-31, in
AB  - Escherichia coli K-12, but not to restrict phage P-22 in Salmonella typhimurium
AB  - LT-2, whereas other fi- R factors restricted and modified P-22 but not W-31;
AB  - fi+ R factors did not restrict these phages.  Transduction and lysogenization
AB  - with phages lambda and P-22 were reduced by these fi- R factors in K-23 and
AB  - LT-2, respectively, and the transducing phages lambda and P-22 were modified by
AB  - these fi- R factors.  Spontaneous as well as ultraviolet-induced production of
AB  - phage P-22 and zygotic induction of phage lambda were not significantly
AB  - affected by any R factor.  Injection of the nucleic acids of phages T1 and
AB  - lambda was not affected by R factors, but the injected phage nucleic acids were
AB  - rapidly broken down in the bacteria carrying fi- R factors.  The nucleic acids
AB  - of the modified phages were not broken down in these bacteria.  It was assumed
AB  - from these results that the mechanism of restriction of phages by fi- R factors
AB  - is due to the breakdown of the injected phage nucleic acids by a
AB  - deoxyribonuclease(s), presumably located near the cell surface in the cells
AB  - carrying fi- R factors.  The deoxyribonuclease(s), formed in the cells carrying
AB  - the nonmodifying fi- R factor, is considered to be different from that
AB  - synthesized in the cells carrying the modifying fi- R factors.  It was further
AB  - shown that the average burst sizes of the unmodified as well as modified phages
AB  - are slightly reduced by the presence of the fi- R factors.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Fujihara, H.
AU  - Suenaga, H.
AU  - Hirose, J.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Kimura, N.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of Pseudomonas toyotomiensis KF710, a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00223
EP  - e00215
VL  - 3
AB  - Pseudomonas toyotomiensis KF710 utilizes biphenyl and degrades polychlorinated biphenyls
AB  - (PCBs). Here, we report the genome sequence of the KF710 strain,
AB  - consisting of 5,596,721 bp with 5,155 coding sequences. The biphenyl catabolic
AB  - genes were almost identical to those of Pseudomonas pseudoalcaligenes KF707, one
AB  - of the most well-characterized biphenyl-utilizing strains.
ER  -

TY  - JOUR
AU  - Watanabe, T.
AU  - Yamazoe, A.
AU  - Hosoyama, A.
AU  - Fujihara, H.
AU  - Suenaga, H.
AU  - Hirose, J.
AU  - Futagami, T.
AU  - Goto, M.
AU  - Kimura, N.
AU  - Furukawa, K.
TI  - Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing  Bacterium Isolated from Biphenyl-Contaminated Soil.
JO  - Genome Announcements
PY  - 2015
SP  - e00222
EP  - e00215
VL  - 3
AB  - We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises
AB  - 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes
AB  - biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer
AB  - coding sequences involved in the degradation of aromatic compounds than other
AB  - strains belonging to the Betaproteobacteria.
ER  -

TY  - JOUR
AU  - Waterbury, P.G.
AU  - Rehfuss, R.P.
AU  - Carroll, W.T.
AU  - Smardon, A.M.
AU  - Faldasz, B.D.
AU  - Huckaby, C.S.
AU  - Lane, M.J.
TI  - Specific cleavage of the yeast genome at 5'-ATCGATCGAT-3'.
JO  - Nucleic Acids Res.
PY  - 1989
SP  - 9493
EP  - 9493
VL  - 17
AB  - M.ClaI followed by DpnI cleavage.  Conditions are described for complete
AB  - cleavage of yeast DNA.
ER  -

TY  - JOUR
AU  - Waterman, S.R.
AU  - Hackett, J.
AU  - Manning, P.A.
TI  - Isolation of a restriction-less mutant and development of a shuttle vector for the genetic analysis of Campylobacter hyointestinalis.
JO  - Gene
PY  - 1993
SP  - 19
EP  - 24
VL  - 125
AB  - A cosmid shuttle cloning vector, pCHI15, was constructed which could be mobilized from
AB  - Escherichia coli K-12 to a putative restriction-less mutant of Campylobacter hyointestinalis,
AB  - C. fetus subsp. fetus, and C. fetus subsp. venerealis at a frequency of 10-4 transconjugants
AB  - per donor. A previously described C. coli shuttle vector, pILL550, could not be mobilized into
AB  - the C. hyointestinalis restriction-less mutant, implying that the C. coli replicon was not
AB  - functional in a C. hyointestinalis host. The type strains of C. jejuni, C. coli, C. fetus
AB  - subsp. fetus, and C. hyointestinalis were analysed for their ability to be transformed by
AB  - plasmid DNA which had been modified by other Campylobacter species. Each Campylobacter species
AB  - was found to be most efficiently transformed by plasmid DNA that had been previously passaged
AB  - in the same species. pCHI15 could be mobilized from C. coli into C. fetus subsp. fetus and the
AB  - putative restriction-less mutant of C. hyointestinalis at a frequency of 3.0 x 10-4 and 2.5 x
AB  - 10-3 transconjugants per donor, respectively.
ER  -

TY  - JOUR
AU  - Waters, E. et al.
TI  - The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2003
SP  - 12984
EP  - 12988
VL  - 100
AB  - The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with
AB  - the crenarchaeon Ignicoccus. Ribosomal protein and
AB  - rRNA-based phylogenies place its branching point early in the archaeal
AB  - lineage, representing the new archaeal kingdom Nanoarchaeota. The N.
AB  - equitans genome (490,885 base pairs) encodes the machinery for information
AB  - processing and repair, but lacks genes for lipid, cofactor, amino acid, or
AB  - nucleotide biosyntheses. It is the smallest microbial genome sequenced to
AB  - date, and also one of the most compact, with 95% of the DNA predicted to
AB  - encode proteins or stable RNAs. Its limited biosynthetic and catabolic
AB  - capacity indicates that N. equitans' symbiotic relationship to Ignicoccus
AB  - is parasitic, making it the only known archaeal parasite. Unlike the small
AB  - genomes of bacterial parasites that are undergoing reductive evolution, N.
AB  - equitans has few pseudogenes or extensive regions of noncoding DNA. This
AB  - organism represents a basal archaeal lineage and has a highly reduced
AB  - genome.
ER  -

TY  - JOUR
AU  - Waters, T.R.
AU  - Connolly, B.A.
TI  - Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect.
JO  - Anal. Biochem.
PY  - 1992
SP  - 204
EP  - 209
VL  - 204
AB  - A continuous spectrophotometric assay for the EcoRV restriction endonuclease has been
AB  - developed. The synthetic self-complementary oligonucleotide d(GACGATATCGTC) (which is double
AB  - stranded under the assay conditions) is used as the substrate. The EcoRV endonuclease
AB  - recognizes d(GATATC)sequences cutting between the cental T and dA bases. Thus d(GACGATATCGTC)
AB  - is converted to d(GACGAT) and d(pATCGTC) during catalysis. Both of the hexameric products are
AB  - single stranded under the assay conditions. The conversion of the dodecameric substrate to the
AB  - two hexameric products and the concomitant change from double- to single-stranded DNA is
AB  - associated with an increase in absorbance at 254 nm due to the hyperchromic effect. This
AB  - change can be used to monitor column effluents for endonuclease activity and also for Km and
AB  - kcat determination under steady-state kinetic conditions.
ER  -

TY  - JOUR
AU  - Waters, T.R.
AU  - Connolly, B.A.
TI  - Interaction of the restriction endonuclease EcoRV with the deoxyguanosine and deoxycytidine bases in its recognition sequence.
JO  - Biochemistry
PY  - 1994
SP  - 1812
EP  - 1819
VL  - 33
AB  - The interaction of the EcoRV restriction endonuclease with the dG and the dC bases in its
AB  - recognition sequence (GATATC) has been studied using base analogues. These modified dG and dC
AB  - bases each have a single potential protein contact removed. The analogues have been
AB  - incorporated into the self-complementary dodecamer d(pGACGATATCGTC) at the appropriate
AB  - positions (underlined). Many of the analogues caused no change in the Tm of the duplex or else
AB  - lowered the Tm by a small amount such that a duplex was still formed at temperatures suitable
AB  - for enzyme assay. However, the dG analogue 2-aminopurine-1-beta-D-2'-deoxyriboside
AB  - destabilized the duplex to such an extent that the 12'-mer could not be used for enzyme
AB  - assays. To overcome this, a longer self-complementary 18'-mer was used with this modified
AB  - base. The circular dichroism spectra of the modified base containing 12'-mers (and the
AB  - 18'-mer in the case of 2-aminopurine) were very similar to the parent sequences lacking
AB  - modified bases. This demonstrates the formation of B-DNA structures in all cases and similar
AB  - overall conformations. The km and kcat values for the various modified oligomers have been
AB  - determined, and these data have been used to assess the roles that functional groups on the dG
AB  - and dC bases play in the recognition and hydrolysis of GATATC sequences by the endonuclease.
AB  - The results obtained here have been compared to the crystal structures of the EcoRV complexed
AB  - with a GATATC sequence, and this has allowed a critical evaluation of the base analogue
AB  - approach. Both methods indicate that the 6-keto oxygen and 7-ring nitrogen of dG exposed in
AB  - the major groove are vital for DNA recognition and hydrolysis.
ER  -

TY  - JOUR
AU  - Watrob, H.
AU  - Liu, W.
AU  - Chen, Y.
AU  - Bartlett, S.G.
AU  - Jen-Jacobson, L.
AU  - Barkley, M.D.
TI  - Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor.
JO  - Biochemistry
PY  - 2001
SP  - 683
EP  - 692
VL  - 40
AB  - EcoRI endonuclease has two tryptophans at positions 104 and 246 on the protein surface. A
AB  - single tryptophan mutant containing Trp246 and a
AB  - single cysteine labeling site at the N-terminus was used to determine
AB  - the position of the N-terminus in the protein structure. The N-termini
AB  - of EcoRI endonuclease are essential for tight binding and catalysis yet
AB  - are not resolved in any of the crystal structures. Resonance energy
AB  - transfer was used to measure the distance from the Trp246 donor to IAEDANS
AB  - or MIANS acceptors at Cys3. The distance is 36 angstroms in the apoenzyme,
AB  - decreasing to 26 angstroms in the DNA complex. Molecular modeling
AB  - suggests that the N-termini are located at the dimer interface formed
AB  - by the loops comprising residues 221-232. Protein conformational
AB  - changes upon binding of cognate DNA and cofactor Mg2+ were monitored by
AB  - tryptophan fluorescence of the single tryptophan mutant and wild-type
AB  - endonuclease. The fluorescence decay of Trp246 is a triple exponential
AB  - with lifetimes of 7, 3.5, and 0.7 ns. The decay-associated spectra of
AB  - the 7- and 3.5-ns components have emission maxima at approximately 345 and
AB  - approximately 338 nm in the apoenzyme, which shift to approximately 340 and
AB  - approximately 348 nm in the DNA complex. The fluorescence quantum yield of
AB  - the single tryptophan mutant drops 30% in the DNA complex, as compared
AB  - to 10% for the wild-type endonuclease. Fluorescence changes of Trp 104 upon
AB  - binding of DNA were inferred by comparison of the decay-associated
AB  - spectra of wild type and single tryptophan mutant. Fluorescence changes
AB  - are related to changes in proximity and orientation of quenching
AB  - functional groups in the tryptophan microenvironments, as seen in the
AB  - crystal structures.
ER  -

TY  - JOUR
AU  - Watson, M.A.
AU  - Gowers, D.M.
AU  - Halford, S.E.
TI  - Alternative geometries of DNA looping: an analysis using the SfiI endonuclease.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 461
EP  - 475
VL  - 298
AB  - Many processes are governed by proteins that bind to separate sites in DNA and loop out the
AB  - intervening DNA, but the geometries of the loops have seldom been determined. The SfiI
AB  - endonuclease cleaves DNA after interacting with two recognition sites, and is a favourable
AB  - system for the analysis of DNA looping. A gel-shift assay was used here to examine the binding
AB  - of SfiI to a series of linear DNA molecules containing two SfiI sites separated by 109-170
AB  - base-pairs. The complexes in which SfiI trapped a loop by binding to two sites in the same DNA
AB  - were separated from the complexes containing SfiI bound to separate DNA molecules. Step-wise
AB  - changes in the inter-site spacing generated two forms of the looped complex with different
AB  - electrophoretic mobilities. The yields of each looped complex and the complexes from
AB  - intermolecular synapses all varied cyclically with the inter-site spacing, with similar
AB  - periodicities ( approximately 10.5 base-pairs) but with different phases. One looped complex
AB  - predominated whenever the DNA between the sites needed to be underwound in order to produce
AB  - the correct helical orientation of the binding sites. The other looped complex predominated
AB  - whenever the intervening DNA needed to be overwound. We conclude that the former has trapped a
AB  - right-handed loop with a negative node and the latter a left-handed loop with a positive node.
ER  -

TY  - JOUR
AU  - Watson, M.E.
AU  - Jarisch, J.
AU  - Smith, A.L.
TI  - Inactivation of deoxyadenosine methyltransferase (dam) attenuates Haemophilus influenzae virulence.
JO  - Mol. Microbiol.
PY  - 2004
SP  - 651
EP  - 664
VL  - 53
AB  - Mutants in deoxyadenosine methyltransferase (dam) from many Gram-negative pathogens suggest
AB  - multiple roles for Dam methylase:
AB  - directing post-replicative DNA mismatch repair to the correct strand,
AB  - guiding the temporal control of DNA replication and regulating the
AB  - expression of multiple genes (including virulence factors) by
AB  - differential promoter methylation. Dam methylase (HI0209) in strain Rd
AB  - KW20 was inactivated in Haemophilus influenzae strains Rd KW20, Strain
AB  - 12 and INT-1; restriction with Dam methylation-sensitive enzymes DpnI
AB  - and DpnII confirmed the absence of Dam methylation, which was restored
AB  - by complementation with a single copy of dam ectopically expressed in
AB  - cis. Despite the lack of increased mutation frequency, the dam mutants
AB  - had a 2-aminopurine-susceptible phenotype that could be suppressed by
AB  - secondary mutations in mutS, suggesting a role for Dam in H. influenzae
AB  - DNA mismatch repair. Invasion of human brain microvascular endothelial
AB  - cells (HBMECs) and human respiratory epithelial cells (NCI-H292) by the
AB  - dam mutants was significantly attenuated in all strains, suggesting the
AB  - absence of a Dam-regulated event necessary for uptake or invasion of
AB  - host cells. Intracellular replication was inhibited only in the Strain
AB  - 12 dam mutant, whereas in the infant rat model of infection, the INT-1
AB  - dam mutant was less virulent. Dam activity appears to be necessary for
AB  - both in vitro and in vivo virulence in a strain-dependent fashion and
AB  - may function as a regulator of gene expression including virulence
AB  - factors.
ER  -

TY  - JOUR
AU  - Watson, R.
AU  - Zuker, M.
AU  - Martin, S.M.
AU  - Visentin, L.P.
TI  - A new site-specific endonuclease from Neisseria cinerea.
JO  - FEBS Lett.
PY  - 1980
SP  - 47
EP  - 50
VL  - 118
AB  - Sequence-specific deoxyribonucleases have greatly facilitated the analysis and
AB  - in vitro manipulation of DNA.  Most of the known type II restriction enzymes
AB  - recognize palindromic DNA sequences.  Although a large number of these enzymes
AB  - have been characterized, many of the possible palindromic DNA sequences are not
AB  - recognized by any known enzyme.  New restriction enzymes with unique
AB  - recognition sites are desirable, as they increase the flexibility of
AB  - recombinant DNA techniques.  We have screened a number of species of the genus
AB  - Neisseria for restriction endonucleases, and report here the isolation and
AB  - characterization of an enzyme from Neisseria cinerea which cleaves DNA at an
AB  - unreported recognition sequence 5' . . . CC(C/G)GG . .3'.  The identification
AB  - of this sequence was assisted by a computer compilation of the number of each
AB  - tetra-, penta- and hexa-palindromic base sequence in pBR322.  PhiX174 and SV40
AB  - DNAs, which is presented here as an aid to other investigators.
ER  -

TY  - JOUR
AU  - Watson, R.J.
AU  - Schildkraut, I.
AU  - Qiang, B.-Q.
AU  - Martin, S.M.
AU  - Visentin, L.P.
TI  - NdeI: a restriction endonuclease from Neisseria denitrificans which cleaves DNA at 5'-CATATG-3' sequences.
JO  - FEBS Lett.
PY  - 1982
SP  - 114
EP  - 116
VL  - 150
AB  - Type II restriction endonucleases recognize and cleave near specific DNA
AB  - sequences, usually 4-6 base pair palindromes.  They are of fundamental
AB  - importance as tools for the recombinant DNA technology as they provide the
AB  - selective cleavages required for the analysis and restructuring of DNA in
AB  - vitro.  The flexibility of these techniques is proportional to the number of
AB  - DNA sequences which can be cleaved by available enzymes.  Here, we describe the
AB  - isolation and characterization of a restriction enzyme from Neisseria
AB  - denitrificans with a new recognition sequence, 5'-CATATG-3'.
ER  -

TY  - JOUR
AU  - Watt, A.E.
AU  - Browning, G.F.
AU  - Legione, A.R.
AU  - Bushell, R.N.
AU  - Stent, A.
AU  - Cutler, R.S.
AU  - Young, N.D.
AU  - Marenda, M.S.
TI  - A novel Glaesserella sp. isolated from severe respiratory infections in pigs has a mosaic genome with virulence factors putatively acquired by horizontal transfer.
JO  - Appl. Environ. Microbiol.
PY  - 2018
SP  - 0
EP  - 0
VL  - 84
AB  - An unknown member of the family Pasteurellaceae was repeatedly isolated from
AB  - severe pulmonary lesions in 20-24 week old pigs reared on the same farm in
AB  - Victoria, Australia. The aetiological diagnosis of the disease was inconclusive.
AB  - The complete genome sequence analysis of one strain, 15-184, revealed some
AB  - phylogenic proximity to Glaesserella (Haemophilus) parasuis, the cause of
AB  - Glasser's disease. However, sequences of the 16S rRNA and housekeeping genes, as
AB  - well as average nucleotide identity scores, differed from all other known species
AB  - in the family Pasteurellaceae The protein content of 15-184 was composite, with
AB  - 60% of coding sequences matching known G. parasuis products while more than 20%
AB  - had a closer relative in the genera Actinobacillus, Mannheimia, Pasteurella or
AB  - Bibersteinia Several putative virulence genes absent from G. parasuis but present
AB  - in other Pasteurellaceae were also found, including the apxIII RTX toxin gene
AB  - from Actinobacillus pleuropneumoniae, ABC transporters from Actinobacillus minor
AB  - and iron transporters from various species. Three prophages and one Integrative
AB  - Conjugative Element were present in the isolate. Horizontal gene transfers might
AB  - explain the mosaic genomic structure and atypical metabolic and virulence
AB  - characteristics of 15-184. This organism has not been assigned a taxonomic
AB  - position in the family, but this study underlines the need for a large scale
AB  - epidemiological and clinical characterisation of this novel pathogen in swine
AB  - populations, as genomic analysis suggests it could have a severe impact on pig
AB  - health.Importance Several species of Pasteurellaceae cause a range of significant
AB  - diseases in pigs. A novel member of this family was recently isolated from
AB  - Australian pigs suffering from severe respiratory infections. Comparative whole
AB  - genome analyses suggest that this bacterium represents a new species, which
AB  - possesses a number of virulence genes horizontally acquired from a diverse range
AB  - of other Pasteurellaceae While the possible contribution of other co-infecting,
AB  - non cultivable agents to the disease hasn't been ruled out in this study, the
AB  - repertoire of virulence genes found in this organism may nevertheless explain
AB  - some aspects of the associated pathology observed in the farm. The prevalence of
AB  - this novel pathogen within pig populations is currently unknown. This finding is
AB  - of particular importance for the pig industry as this organism can have a serious
AB  - impact on the health of these animals.
ER  -

TY  - JOUR
AU  - Watve, S.S.
AU  - Chande, A.T.
AU  - Rishishwar, L.
AU  - Marino-Ramirez, L.
AU  - Jordan, I.K.
AU  - Hammer, B.K.
TI  - Whole-Genome Sequences of 26 Vibrio cholerae Isolates.
JO  - Genome Announcements
PY  - 2016
SP  - e01396
EP  - e01316
VL  - 4
AB  - The human pathogen Vibrio cholerae employs several adaptive mechanisms for environmental
AB  - persistence, including natural transformation and type VI secretion, creating a reservoir for
AB  - the spread of disease. Here, we report whole-genome sequences of 26 diverse V. cholerae
AB  - isolates, significantly increasing the sequence diversity of publicly available V. cholerae
AB  - genomes.
ER  -

TY  - JOUR
AU  - Waugh, D.S.
AU  - Sauer, R.T.
TI  - A novel class of FokI restriction endonuclease mutants that cleave hemi-methylated substrates.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 12298
EP  - 12303
VL  - 269
AB  - A genetic screen was used to identify amino acid substitutions that enable the FokI
AB  - restriction endonuclease to cleave DNA in cells that express the cognate methyltransferase
AB  - activity. Missense mutations that give rise to this phenotype were isolated at eight different
AB  - positions (G188K, P196S, T343I, S388N, S395F, E407K, E410K, D421N), clustered in two regions
AB  - of the polypeptide sequence of FokI. Two of the mutant endonucleases (P196S and D421N) were
AB  - purified to homogeneity and analyzed in detail. Both mutants cleave FokI target sites
AB  - (5'-GGATG-3') in a manner similar to the wild-type enzyme. Neither mutant cleaved
AB  - noncanonical sequences, but both efficiently cleaved DNA substrates containing hemi-methylated
AB  - FokI sites. This class of mutations has not been observed with other restriction enzymes.
ER  -

TY  - JOUR
AU  - Waugh, D.S.
AU  - Sauer, R.T.
TI  - Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 9596
EP  - 9600
VL  - 90
AB  - Single alanine substitution mutations at Asp-450 or Asp-467 of the type IIS restriction enzyme
AB  - FokI have no effect on the ability of the enzyme to bind strongly and selectively to its
AB  - recognition site but completely eliminate its ability to cleave either strand of substrate
AB  - DNA. Since wild-type FokI shows no kinetic preference or required order of strand cleavage,
AB  - these results indicate that FokI, which evidently functions as a monomer, uses a single
AB  - catalytic center to cleave both strands of DNA. In this respect, FokI may resemble other
AB  - monomeric enzymes that cleave double-stranded DNA.
ER  -

TY  - JOUR
AU  - Wawrik, C.B.
AU  - Callaghan, A.V.
AU  - Stamps, B.W.
AU  - Wawrik, B.
TI  - Genome Sequence of Youngiibacter fragilis, the Type Strain of the Genus Youngiibacter.
JO  - Genome Announcements
PY  - 2014
SP  - e01183
EP  - e01113
VL  - 2
AB  - The genome of Youngiibacter fragilis, the type strain of the newly described genus
AB  - Youngiibacter, was sequenced. The genome consists of 3.996 Mb, with a G+C
AB  - content of 46.6 mol%. Y. fragilis originates from coal-bed methane-produced water
AB  - and may provide insight into the microbiological basis of biogas production in
AB  - coal beds.
ER  -

TY  - JOUR
AU  - Wayne, J.
AU  - Holden, M.
AU  - Xu, S.-Y.
TI  - The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host.
JO  - Gene
PY  - 1997
SP  - 83
EP  - 88
VL  - 202
AB  - Thermus species YS45 harbors two small cryptic plasmids of 5.8 (pTsp45s) and approximately 12
AB  - kb (pTsp45I).  Plasmid pTsp45s has been entirely sequenced, revealing three significant ORFs.
AB  - In addition to a previously reported thermophilic plasmid-encoded replication protein, pTsp45s
AB  - contains two genes for the Tsp45I methyltransferase and restriction endonuclease (Tsp45I).
AB  - These two converging genes (tsp45IM and tsp45IR) overlap by 4 bp at their stop codons within
AB  - an XbaI site.  M.Tsp45I (413 aa, 47.0 kDa, recognizing 5'-GTSAC-3') is highly homologous to
AB  - other m6A-methyltransferases, especially M.EcaI (recognizing 5'-GGTNACC-3').  Tsp45I (332
AB  - aa, 37.4 kDa, cleaving 5'-/GTSAC-3') is not homologous to M.Tsp45I, or to other restriction
AB  - endonucleases.  Recombinant Tsp45I is stably produced in E. coli, and cleaves DNA at 65oC with
AB  - the same specificity as the native enzyme.  Therefore, the thermophilic Tsp45I
AB  - restriction-modification system is plasmid-borne within its native host.
ER  -

TY  - JOUR
AU  - Webb, A.L.
AU  - Kruczkiewicz, P.
AU  - Selinger, L.B.
AU  - Inglis, G.D.
AU  - Taboada, E.N.
TI  - Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri.
JO  - BMC Microbiol.
PY  - 2015
SP  - 94
EP  - 94
VL  - 15
AB  - BACKGROUND: Molecular typing methods are critical for epidemiological
AB  - investigations, facilitating disease outbreak detection and source
AB  - identification. Study of the epidemiology of the emerging human pathogen
AB  - Arcobacter butzleri is currently hampered by the lack of a subtyping method that
AB  - is easily deployable in the context of routine epidemiological surveillance. In
AB  - this study we describe a comparative genomic fingerprinting (CGF) method for
AB  - high-resolution and high-throughput subtyping of A. butzleri. Comparative
AB  - analysis of the genome sequences of eleven A. butzleri strains, including eight
AB  - strains newly sequenced as part of this project, was employed to identify
AB  - accessory genes suitable for generating unique genetic fingerprints for
AB  - high-resolution subtyping based on gene presence or absence within a strain.
AB  - RESULTS: A set of eighty-three accessory genes was used to examine the population
AB  - structure of a dataset comprised of isolates from various sources, including
AB  - human and non-human animals, sewage, and river water (n=156). A streamlined assay
AB  - (CGF40) based on a subset of 40 genes was subsequently developed through marker
AB  - optimization. High levels of profile diversity (121 distinct profiles) were
AB  - observed among the 156 isolates in the dataset, and a high Simpson's Index of
AB  - Diversity (ID) observed (ID > 0.969) indicate that the CGF40 assay possesses high
AB  - discriminatory power. At the same time, our observation that 115 isolates in this
AB  - dataset could be assigned to 29 clades with a profile similarity of 90% or
AB  - greater indicates that the method can be used to identify clades comprised of
AB  - genetically similar isolates. CONCLUSIONS: The CGF40 assay described herein
AB  - combines high resolution and repeatability with high throughput for the rapid
AB  - characterization of A. butzleri strains. This assay will facilitate the study of
AB  - the population structure and epidemiology of A. butzleri.
ER  -

TY  - JOUR
AU  - Webb, H.
AU  - Kaszubska, W.
AU  - Gumport, R.I.
TI  - Overexpression of RsrI DNA methyltransferase in E. coli.
JO  - FASEB J.
PY  - 1990
SP  - A1795
EP  - A1795
VL  - 4
AB  - RsrI DNA methyltransferase (M.RsrI) from Rhodobacter sphaeroides catalyzes
AB  - methylation of the same central adenine residue in the duplex recognition
AB  - sequence d(GAATTC) as does M.EcoRI.  M.RsrI has been purified to homogeneity
AB  - from Rhodobacter sphaeroides, and its gene cloned and sequenced (Kaszubska, W.
AB  - et al., Nucl. Acids Res., (1989) 17, 10403-101701.  M.RsrI has now been
AB  - overexpressed in E. coli and the purification improved.  A fragment of R.
AB  - sphaeroides chromosomal DNA, containing both the rsrIM and rsrIR genes was
AB  - inserted downstream of the T7 promoter in a pTZ18U vector.  M.RsrI was purified
AB  - to homogeneity from E. coli BL21(DE3)plysS cells with a 100-fold increase in
AB  - yield over that from R. sphaeroides.  The purification was simplified by the
AB  - substitution of a DNA-cellulose-sinefungin affinity column for the
AB  - hydroxylapatite and weak cation exchange chromatography steps.  Sinefungin, an
AB  - S-adenosylmethionine analogue, inhibits methyl group transfer by M.RsrI.  We
AB  - are presently further characterizing M.RsrI by determining its kinetic
AB  - constants and the number of methyl groups transferred per binding event.
ER  -

TY  - JOUR
AU  - Webb, J.L.
AU  - King, G.
AU  - Ternent, D.
AU  - Titheradge, A.J.B.
AU  - Murray, N.E.
TI  - Restriction by EcoKI is enhanced by cooperative interactions between target sequences and is dependent on DEAD box motifs.
JO  - EMBO J.
PY  - 1996
SP  - 2003
EP  - 2009
VL  - 15
AB  - One subunit of both type I and type III restriction and modification enzymes
AB  - contains motifs characteristic of DEAD box proteins, which implies that these enzymes may be
AB  - DNA helicases.  This subunit is essential for restriction, but not modification.  The current
AB  - model
AB  - for restriction by both types of enzyme postulates that DNA cutting is stimulated when two
AB  - enzyme
AB  - complexes bound to neighboring target sequences meet as the consequence of ATP-dependent
AB  - DNA translocation.  For type I enzymes, this model is supported by in vitro experiments, but
AB  - the
AB  - predicted cooperative interactions between targets have not been detected by assays that
AB  - monitor
AB  - restriction in vivo.  The experiments reported here clearly establish the required synergistic
AB  - effect
AB  - but, in contrast to earlier experiments, they use Escherichia coli K-12 strains deficient in
AB  - the
AB  - restriction alleviation function associated with the Rac prophage.  In bacteria with elevated
AB  - levels of
AB  - EcoKI the cooperative interactions are obscured, consistent with cooperation between free
AB  - enzyme
AB  - and that bound at target sites.  We have made changes in three of the motifs characteristic of
AB  - DEAD
AB  - box proteins, including motif III, which in RecG is implicated in the migration of Holliday
AB  - junctions.  Conservative changes in each of the three motifs impair restriction.
ER  -

TY  - JOUR
AU  - Webb, M.
AU  - Taylor, I.A.
AU  - Firman, K.
AU  - Kneale, G.G.
TI  - Probing the domain structure of the type IC DNA methyltransferase M.EcoR124I by limited proteolysis.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 181
EP  - 190
VL  - 250
AB  - Limited proteolysis has been used to probe the domain structure of the type I DNA
AB  - methyltransferase M.EcoR124I. Trypsin digestion of the methyltransferase generates two
AB  - fragments derived from the HsdS subunit, a 28 kDa N-terminal domain and a 19 kDa C-terminal
AB  - domain, leaving the HsdM subunit intact. Extensive digestion by chymotrypsin, however, removes
AB  - 59 amino acid residues from the N terminus of the HsdM subunit to leave a 52 kDa C-terminal
AB  - domain. Binding of the cofactor S-adenosyl methionine has no appreciable effect on the rate of
AB  - cleavage, but binding of a 30 bp DNA duplex containing the cognate recognition sequence
AB  - confers almost total protection. Following trypsin cleavage of the methyltransferase, a stable
AB  - proteolytic product is produced which has been purified for biochemical characterization. The
AB  - trypsinized enzyme is shown to be a multimeric complex containing two intact HsdM subunits and
AB  - both fragments of the HsdS subunit, consistent with the circular model proposed for the
AB  - organization of domains in the specificity subunit in type IC methyltransferases. Gel
AB  - retardation studies show that the proteolysed enzyme still retains DNA binding activity, but
AB  - its specificity for the DNA recognition sequence is dramatically reduced.
ER  -

TY  - JOUR
AU  - Weber, R.E.
AU  - Layer, F.
AU  - Fuchs, S.
AU  - Bender, J.K.
AU  - Fiedler, S.
AU  - Werner, G.
AU  - Strommenger, B.
TI  - Complete Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Isolates Representing a Population Subset Highly Prevalent in Human Colonization.
JO  - Genome Announcements
PY  - 2016
SP  - e00716
EP  - e00716
VL  - 4
AB  - Here, we report the high-quality draft genome sequences of two methicillin-susceptible
AB  - Staphylococcus aureus isolates, 08-02119 and 08-02300.
AB  - Belonging to sequence type 582 (ST582) and ST7, both isolates are representatives
AB  - of clonal lineages often associated with asymptomatic colonization of humans.
ER  -

TY  - JOUR
AU  - Wegmann, U.
AU  - Goesmann, A.
AU  - Carding, S.R.
TI  - Complete Genome Sequence of Bacteroides ovatus V975.
JO  - Genome Announcements
PY  - 2016
SP  - e01335
EP  - e01316
VL  - 4
AB  - The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of
AB  - a single circular chromosome of 6,475,296 bp containing five
AB  - rRNA operons, 68 tRNA genes, and 4,959 coding genes.
ER  -

TY  - JOUR
AU  - Wegmann, U.
AU  - Louis, P.
AU  - Goesmann, A.
AU  - Henrissat, B.
AU  - Duncan, S.H.
AU  - Flint, H.J.
TI  - Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans.
JO  - Environ. Microbiol.
PY  - 2014
SP  - 2879
EP  - 2890
VL  - 16
AB  - The recently isolated bacterial strain 80/3 represents one of the most abundant 16S rRNA
AB  - phylotypes detected in the healthy human large intestine and belongs to the Ruminococcaceae
AB  - family of Firmicutes. The completed genome sequence reported here is the first for a member of
AB  - this important family of bacteria from the human colon. The genome comprises two large
AB  - chromosomes of 2.24 and 0.73 Mbp, leading us to propose the name Ruminococcus bicirculans for
AB  - this new species.
AB  - Analysis of the carbohydrate active enzyme complement suggests an ability to utilize certain
AB  - hemicelluloses, especially beta-glucans and xyloglucan, for growth that was confirmed
AB  - experimentally. The enzymatic machinery enabling the degradation of cellulose and xylan by
AB  - related cellulolytic ruminococci is however lacking in this species. While the genome
AB  - indicated the capacity to synthesize purines, pyrimidines and all 20 amino acids, only genes
AB  - for the synthesis of nicotinate, NAD+, NADP+ and coenzyme A were detected among the essential
AB  - vitamins and co-factors, resulting in multiple growth requirements. In vivo, these growth
AB  - factors must be supplied from the diet, host or other gut microorganisms. Other features of
AB  - ecological interest include two type IV pilins, multiple extracytoplasmic function-sigma
AB  - factors, a urease and a bile salt hydrolase.
ER  -

TY  - JOUR
AU  - Wegmann, U.
AU  - Nueno, P.C.
AU  - Mayer, M.J.
AU  - Crost, E.
AU  - Narbad, A.
TI  - Complete Genome Sequence of Desulfovibrio piger FI11049.
JO  - Genome Announcements
PY  - 2017
SP  - e01528
EP  - e01516
VL  - 5
AB  - The complete genome sequence of Desulfovibrio piger FI11049 was determined. The genome
AB  - consists of a single circular chromosome of 2,807,531 bp encoding seven
AB  - rRNA operons, 76 tRNA genes, and 2,535 coding genes.
ER  -

TY  - JOUR
AU  - Wegmann, U.
AU  - O'Connell-Motherway, M.
AU  - Zomer, A.
AU  - Buist, G.
AU  - Shearman, C.
AU  - Canchaya, C.
AU  - Ventura, M.
AU  - Goesmann, A.
AU  - Gasson, M.J.
AU  - Kuipers, O.P.
AU  - van Sinderen, D.
AU  - Kok, J.
TI  - Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.
JO  - J. Bacteriol.
PY  - 2007
SP  - 3256
EP  - 3270
VL  - 189
AB  - Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people
AB  - worldwide. This paper describes the genome sequence of
AB  - Lactococcus lactis subsp. cremoris MG1363, the lactococcal strain most
AB  - intensively studied throughout the world. The 2,529,478-bp genome contains
AB  - 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47
AB  - belong to the COG (clusters of orthologous groups) functional category
AB  - "carbohydrate metabolism and transport," by far the largest category of
AB  - novel proteins in comparison with L. lactis subsp. lactis IL1403. Nearly
AB  - one-fifth of the 71 insertion elements are concentrated in a specific
AB  - 56-kb region. This integration hot-spot region carries genes that are
AB  - typically associated with lactococcal plasmids and a repeat sequence
AB  - specifically found on plasmids and in the "lateral gene transfer hot spot"
AB  - in the genome of Streptococcus thermophilus. Although the parent of L.
AB  - lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis
AB  - MG1363 carries four remnant/satellite phages and two apparently complete
AB  - prophages. The availability of the L. lactis MG1363 genome sequence will
AB  - reinforce its status as the prototype among lactic acid bacteria through
AB  - facilitation of further applied and fundamental research.
ER  -

TY  - JOUR
AU  - Wegmann, U.
AU  - Overweg, K.
AU  - Horn, N.
AU  - Goesmann, A.
AU  - Narbad, A.
AU  - Gasson, M.J.
AU  - Shearman, C.
TI  - The complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry.
JO  - J. Bacteriol.
PY  - 2009
SP  - 7142
EP  - 7143
VL  - 191
AB  - Lactobacillus johnsonii is a member of the acidophilus group of lactobacilli. Because of their
AB  - probiotic properties including attachment
AB  - to epithelial cells, immunomodulation and competitive exclusion of
AB  - pathogens representatives of this group are being intensively studied.
AB  - Here we report the complete annotated genome sequence of Lactobacillus
AB  - johnsonii FI9785, a strain which prevents the colonisation of specific
AB  - pathogen-free chicks by Clostridium perfringens.
ER  -

TY  - JOUR
AU  - Wegner, C.E.
AU  - Richter-Heitmann, T.
AU  - Klindworth, A.
AU  - Klockow, C.
AU  - Richter, M.
AU  - Achstetter, T.
AU  - Glockner, F.O.
AU  - Harder, J.
TI  - Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula.
JO  - Marine Genomics
PY  - 2012
SP  - 51
EP  - 61
VL  - 9
AB  - The whole genome sequence of Rhodopirellula baltica SH1(T), published nearly 10years ago,
AB  - already revealed a high amount of sulfatase genes. So far, little is known about the diversity
AB  - and potential functions mediated by sulfatases in Planctomycetes. We combined in vivo and in
AB  - silico techniques to gain insights into the ecophysiology of planktomycetal sulfatases.
AB  - Comparative genomics of nine recently sequenced Rhodopirellula strains detected 1120 open
AB  - reading frames annotated as sulfatases (Enzyme Commission number (EC) 3.1.6.*). These were
AB  - clustered into 173 groups of orthologous and paralogous genes. To analyze the functional
AB  - aspects, 708 sulfatase protein sequences from these strains were aligned with 67 sulfatase
AB  - reference sequences of reviewed functionality. Our analysis yielded 22 major similarity
AB  - clusters, but only five of these clusters contained Rhodopirellula sequences homologous to
AB  - reference sequences, indicating a surprisingly high diversity. Exemplarily, R. baltica SH1(T)
AB  - was grown on different sulfated polysaccharides, chondroitin sulfate, lambda-carrageenan and
AB  - fucoidan. Subsequent gene expression analyses using whole genome microarrays revealed distinct
AB  - sulfatase expression profiles based on substrates tested. This might be indicative for a high
AB  - structural diversity of sulfated polysaccharides as potential substrates. The pattern of
AB  - sulfatases in individual planctomycete species may reflect ecological niche adaptation.
ER  -

TY  - JOUR
AU  - Wei, D.D.
AU  - Wan, L.G.
AU  - Liu, Y.
TI  - Draft Genome Sequence of an NDM-1- and KPC-2-Coproducing Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Strain Isolated from Burn Wound  Infections.
JO  - Genome Announcements
PY  - 2018
SP  - e00192
EP  - e00118
VL  - 6
AB  - We report here the draft genome sequence of an NDM-1- and KPC-2-coproducing hypervirulent
AB  - carbapenem-resistant Klebsiella pneumoniae strain, isolated from a
AB  - 58-year-old male in the People's Republic of China with a burn injury.
ER  -

TY  - JOUR
AU  - Wei, H.
AU  - Therrien, C.
AU  - Blanchard, A.
AU  - Guan, S.
AU  - Zhu, Z.
TI  - The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - e50
EP  - e50
VL  - 36
AB  - Restriction endonucleases are the basic tools of molecular biology. Many restriction
AB  - endonucleases show relaxed sequence recognition, called star
AB  - activity, as an inherent property under various digestion conditions
AB  - including the optimal ones. To quantify this property we propose the
AB  - concept of the Fidelity Index (FI), which is defined as the ratio of the
AB  - maximum enzyme amount showing no star activity to the minimum amount
AB  - needed for complete digestion at the cognate recognition site for any
AB  - particular restriction endonuclease. Fidelity indices for a large number
AB  - of restriction endonucleases are reported here. The effects of reaction
AB  - vessel, reaction volume, incubation mode, substrate differences, reaction
AB  - time, reaction temperature and additional glycerol, DMSO, ethanol and
AB  - Mn(2+) on the FI are also investigated. The FI provides a practical
AB  - guideline for the use of restriction endonucleases and defines a
AB  - fundamental property by which restriction endonucleases can be
AB  - characterized.
ER  -

TY  - JOUR
AU  - Wei, J.
AU  - Goldberg, M.B.
AU  - Burland, V.
AU  - Venkatesan, M.M.
AU  - Deng, W.
AU  - Fournier, G.
AU  - Mayhew, G.F.
AU  - Plunkett, G. III
AU  - Rose, D.J.
AU  - Darling, A.
AU  - Mau, B.
AU  - Perna, N.T.
AU  - Payne, S.M.
AU  - Runyen-Janecky, L.J.
AU  - Zhou, S.
AU  - Schwartz, D.C.
AU  - Blattner, F.R.
TI  - Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.
JO  - Infect. Immun.
PY  - 2003
SP  - 2775
EP  - 2786
VL  - 71
AB  - We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T
AB  - (4,599,354 bp). Shigella species cause >1 million deaths
AB  - per year from dysentery and diarrhea and have a lifestyle that is markedly
AB  - different from those of closely related bacteria, including Escherichia
AB  - coli. The genome exhibits the backbone and island mosaic structure of E.
AB  - coli pathogens, albeit with much less horizontally transferred DNA and
AB  - lacking 357 genes present in E. coli. The strain is distinctive in its
AB  - large complement of insertion sequences, with several genomic
AB  - rearrangements mediated by insertion sequences, 12 cryptic prophages, 372
AB  - pseudogenes, and 195 S. flexneri-specific genes. The 2457T genome was also
AB  - compared with that of a recently sequenced S. flexneri 2a strain, 301. Our
AB  - data are consistent with Shigella being phylogenetically indistinguishable
AB  - from E. coli. The S. flexneri-specific regions contain many genes that
AB  - could encode proteins with roles in virulence. Analysis of these will
AB  - reveal the genetic basis for aspects of this pathogenic organism's
AB  - distinctive lifestyle that have yet to be explained.
ER  -

TY  - JOUR
AU  - Wei, S.
AU  - Guo, Z.
AU  - Li, T.
AU  - Zhang, T.
AU  - Li, X.
AU  - Zhou, Z.
AU  - Li, Z.
AU  - Liu, M.
AU  - Luo, R.
AU  - Bi, D.
AU  - Chen, H.
AU  - Zhou, R.
AU  - Jin, H.
TI  - Genome Sequence of Mycoplasma iowae Strain 695, an Unusual Pathogen Causing Deaths in Turkeys.
JO  - J. Bacteriol.
PY  - 2012
SP  - 547
EP  - 548
VL  - 194
AB  - Mycoplasma iowae is associated mainly with reduced hatchability in turkeys and is well known
AB  - for the unusual ability of phenotypic variation in the
AB  - Mycoplasma surface components as well as a relative resistance to heat,
AB  - bile salts, and many antimicrobials. A subset of unique genes and a gene
AB  - cluster responsible for these characteristics could be identified from the
AB  - genome. Here, we report the first genome sequence of this species.
ER  -

TY  - JOUR
AU  - Wei, W.
AU  - Gao, C.
AU  - Xiong, Y.
AU  - Zhang, Y.
AU  - Liu, S.
AU  - Pu, Y.
TI  - A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII.
JO  - Talanta
PY  - 2015
SP  - 342
EP  - 347
VL  - 131
AB  - DNA methylation plays an important role in many biological events and is associated with
AB  - various diseases. Most traditional methods for detection of DNA methylation are based on the
AB  - complex and expensive bisulfite method. In this paper, we report a novel fluorescence method
AB  - to detect DNA and DNA methylation based on graphene oxide (GO) and restriction endonuclease
AB  - HpaII. The skillfully designed probe DNA labeled with 5-carboxyfluorescein (FAM) and optimized
AB  - GO concentration keep the probe/target DNA. still adsorbed on the GO. After the cleavage
AB  - action of HpaII the labeled FAM is released from the GO surface and its fluorescence recovers,
AB  - which could be used to detect DNA in the linear range of 50 pM-50 nM with a detection limit of
AB  - 43 pM. DNA methylation induced by transmethylase (Mtase) or other chemical reagents prevents
AB  - HpaII from recognizing and cleaving the specific site; as a result, fluorescence cannot
AB  - recover. The fluorescence recovery efficiency is closely related to the DNA methylation level,
AB  - which can be used to detect DNA methylation by comparing it with the fluorescence in the
AB  - presence of intact target DNA. The method for detection of DNA and DNA methylation is simple,
AB  - reliable and accurate.
ER  -

TY  - JOUR
AU  - Wei, X.
AU  - Ge, X.
AU  - Li, Y.
AU  - Yu, Z.
TI  - Draft Genome Sequence of Methylocaldum sp. SAD2, a Methanotrophic Strain That Can Convert Raw Biogas to Methanol in the Presence of Hydrogen Sulfide.
JO  - Genome Announcements
PY  - 2017
SP  - e00716
EP  - e00717
VL  - 5
AB  - The draft genome sequence of Methylocaldum sp. SAD2, a methanotrophic strain isolated from a
AB  - hydrogen sulfide-rich anaerobic digester, is reported here.
AB  - Strain SAD2 possesses genes for methane oxidation in the presence of H2S.
ER  -

TY  - JOUR
AU  - Wei, X.
AU  - Ge, X.
AU  - Li, Y.
AU  - Yu, Z.
TI  - Draft Genome Sequence of Methylocaldum sp. Strain 14B, an Obligate Hydrogen Sulfide-Tolerant Methanotrophic Strain That Can Convert Biogas to Methanol.
JO  - Genome Announcements
PY  - 2017
SP  - e00153
EP  - e00117
VL  - 5
AB  - The draft genome sequence of Methylocaldum sp. 14B, an obligate methanotrophic strain isolated
AB  - from solid-state anaerobic digestion systems, is reported here.
AB  - Strain 14B possesses genes for methane oxidation and exhibited tolerance to H2S.
ER  -

TY  - JOUR
AU  - Wei, Y.
AU  - Cao, J.
AU  - Fang, J.
AU  - Kato, C.
AU  - Cui, W.
TI  - Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor.
JO  - Genome Announcements
PY  - 2017
SP  - e01621
EP  - e01616
VL  - 5
AB  - Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic
AB  - bacterium isolated from coal-bearing sediment down to ~2.4 km below
AB  - the ocean floor in the northwestern Pacific. The strain is a Gram-positive
AB  - spore-forming bacterium, closely related to Bacillus subtilis within the phylum
AB  - Firmicutes This is the first complete genome sequence of a Bacillus subtilis
AB  - strain from the deep biosphere. The genome sequence will provide a valuable
AB  - resource for comparative studies of microorganisms from the surface and
AB  - subsurface environments.
ER  -

TY  - JOUR
AU  - Wei, Y.
AU  - Cao, J.
AU  - Fang, J.
AU  - Kato, C.
AU  - Cui, W.
TI  - First Complete Genome Sequence of Marinilactibacilluspiezotolerans Strain 15R, a  Marine Lactobacillus Isolated from Coal-Bearing Sediment 2.0 Kilometers below the  Seafloor, Determined by PacBio Single-Molecule Real-Time Technology.
JO  - Genome Announcements
PY  - 2017
SP  - e01625
EP  - e01616
VL  - 5
AB  - Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic
AB  - lactobacillus isolated from deep marine subsurface sediment nearly
AB  - 2 km below the seafloor in the northwestern Pacific. We report here the first
AB  - whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908
AB  - bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences,
AB  - with no identified plasmids.
ER  -

TY  - JOUR
AU  - Wei, Y.
AU  - Yang, Y.
AU  - Zhou, L.
AU  - Liu, Z.
AU  - Wang, X.
AU  - Yang, R.
AU  - Su, Q.
AU  - Zhou, Y.
AU  - Zhao, J.
AU  - Yang, J.
TI  - Genome Sequence of Enterobacter cancerogenus YZ1.
JO  - Genome Announcements
PY  - 2013
SP  - e00023
EP  - e00013
VL  - 1
AB  - is usually known as an opportunistic human pathogen. Recently, it has attracted great
AB  - attention for its capability to produce bioemulsifier, degrade xenobiotics,
AB  - and resist alkalis and antibiotics. Here we report the complete genome of YZ1,
AB  - isolated from a bran-feeding insect's frass.
ER  -

TY  - JOUR
AU  - Wei, Y.
AU  - Zhou, H.
AU  - Zhang, L.
AU  - Zhang, J.
AU  - Wang, Y.
AU  - Wang, S.
AU  - Zhou, Z.
AU  - Yan, X.
TI  - Draft Genome Sequence of Clostridium ultunense Strain BS (DSMZ 10521), Recovered  from a Mixed Culture.
JO  - Genome Announcements
PY  - 2014
SP  - e01269
EP  - e01213
VL  - 2
AB  - Clostridium ultunense BS is the first isolated strain (type strain) of C. ultunense that was
AB  - identified as a mesophilic syntrophic acetate-oxidizing
AB  - bacterium (SAOB). Here, we report the draft genome sequence of this strain, which
AB  - will help us to elucidate the mechanism of syntrophic acetate oxidization.
ER  -

TY  - JOUR
AU  - Wei, Y.X.
AU  - Zhang, Z.Y.
AU  - Liu, C.
AU  - Zhu, Y.Z.
AU  - Zhu, Y.Q.
AU  - Zheng, H.J.
AU  - Zhao, G.P.
AU  - Wang, S.Y.
AU  - Guo, X.K.
TI  - Complete Genome Sequence of Bifidobacterium longum JDM301.
JO  - J. Bacteriol.
PY  - 2010
SP  - 4076
EP  - 4077
VL  - 192
AB  - Bifidobacteria, known as probiotic bacteria, are high G+C Gram-positive bacteria, which
AB  - naturally inhabit the human gastrointestinal tract (GIT) and vagina. Recently, we have a
AB  - Bifidobacterium longum JDM301 completely sequenced, which is a widely used Chinese commercial
AB  - strain with several probiotic properties.
ER  -

TY  - JOUR
AU  - Weidner, S.
AU  - Baumgarth, B.
AU  - Gottfert, M.
AU  - Jaenicke, S.
AU  - Puhler, A.
AU  - Schneiker-Bekel, S.
AU  - Serrania, J.
AU  - Szczepanowski, R.
AU  - Becker, A.
TI  - Genome Sequence of Sinorhizobium meliloti Rm41.
JO  - Genome Announcements
PY  - 2013
SP  - e00013
EP  - e00012
VL  - 1
AB  - Sinorhizobium meliloti Rm41 nodulates alfalfa plants, forming indeterminate type  nodules. It
AB  - is characterized by a strain-specific K-antigen able to replace exopolysaccharides in
AB  - promotion of nodule invasion. We present the Rm41 genome, composed of one chromosome, the
AB  - chromid pSymB, the megaplasmid pSymA, and the nonsymbiotic plasmid pRme41a.
ER  -

TY  - JOUR
AU  - Weidner, S.
AU  - Becker, A.
AU  - Bonilla, I.
AU  - Jaenicke, S.
AU  - Lloret, J.
AU  - Margaret, I.
AU  - Puhler, A.
AU  - Ruiz-Sainz, J.E.
AU  - Schneiker-Bekel, S.
AU  - Szczepanowski, R.
AU  - Vinardell, J.M.
AU  - Zehner, S.
AU  - Gottfert, M.
TI  - Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1617
EP  - 1618
VL  - 194
AB  - Sinorhizobium fredii HH103 is a fast-growing rhizobial strain that is able to nodulate legumes
AB  - that develop determinate nodules, e.g., soybean, and legumes
AB  - that form nodules of the indeterminate type. Here we present the genome of HH103,
AB  - which consists of one chromosome and five plasmids with a total size of 7.22 Mb.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Changayil, S.
AU  - Kulasekarapandian, Y.
AU  - Tondella, M.L.
TI  - Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans.
JO  - Genome Announcements
PY  - 2015
SP  - e00965
EP  - e00915
VL  - 3
AB  - Bordetella hinzii is primarily recovered from poultry but can also colonize mammalian hosts
AB  - and immunocompromised humans. Here, we report the first complete  genome sequences of B.
AB  - hinzii in two isolates recovered from humans. The availability of these sequences will
AB  - hopefully aid in identifying host-specific determinants variably present within this species.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Peng, Y.
AU  - Cassiday, P.K.
AU  - Loparev, V.N.
AU  - Johnson, T.
AU  - Juieng, P.
AU  - Nazarian, E.J.
AU  - Weening, K.
AU  - Tondella, M.L.
AU  - Williams, M.M.
TI  - Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions.
JO  - Genome Announcements
PY  - 2017
SP  - e00973
EP  - e00917
VL  - 5
AB  - Clinical isolates of the respiratory pathogen Bordetella pertussis in the United  States have
AB  - become predominantly deficient for the acellular vaccine immunogen
AB  - pertactin through various independent mutations. Here, we report the complete
AB  - genome sequences for four B. pertussis isolates that harbor novel deletions
AB  - responsible for pertactin deficiency.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Peng, Y.
AU  - Loparev, V.
AU  - Batra, D.
AU  - Bowden, K.E.
AU  - Burroughs, M.
AU  - Cassiday, P.K.
AU  - Davis, J.K.
AU  - Johnson, T.
AU  - Juieng, P.
AU  - Knipe, K.
AU  - Mathis, M.H.
AU  - Pruitt, A.M.
AU  - Rowe, L.
AU  - Sheth, M.
AU  - Tondella, M.L.
AU  - Williams, M.M.
TI  - The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement.
JO  - J. Bacteriol.
PY  - 2017
SP  - e00806
EP  - e00816
VL  - 199
AB  - Despite high pertussis vaccine coverage, reported cases of whooping cough
AB  - (pertussis) have increased over the last decade in the United States and other
AB  - developed countries. Although Bordetella pertussis is well known for its limited
AB  - gene sequence variation, recent advances in long-read sequencing technology have
AB  - begun to reveal genomic structural heterogeneity among otherwise
AB  - indistinguishable isolates, even within geographically or temporally defined
AB  - epidemics. We have compared rearrangements among complete genome assemblies from
AB  - 257 B. pertussis isolates to examine the potential evolution of the chromosomal
AB  - structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete
AB  - changes in gene order were identified that differentiated genomes from vaccine
AB  - reference strains and clinical isolates of various genotypes, frequently along
AB  - phylogenetic boundaries defined by single nucleotide polymorphisms. The observed
AB  - rearrangements were primarily large inversions centered on the replication origin
AB  - or terminus and flanked by IS481, a mobile genetic element with >240 copies per
AB  - genome and previously suspected to mediate rearrangements and deletions by
AB  - homologous recombination. These data illustrate that structural genome evolution
AB  - in B. pertussis is not limited to reduction but also includes rearrangement.
AB  - Therefore, although genomes of clinical isolates are structurally diverse,
AB  - specific changes in gene order are conserved, perhaps due to positive selection,
AB  - providing novel information for investigating disease resurgence and molecular
AB  - epidemiology.IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis,
AB  - has resurged in the United States even though the coverage with
AB  - pertussis-containing vaccines remains high. The rise in reported cases has
AB  - included increased disease rates among all vaccinated age groups, provoking
AB  - questions about the pathogen's evolution. The chromosome of B. pertussis includes
AB  - a large number of repetitive mobile genetic elements that obstruct genome
AB  - analysis. However, these mobile elements facilitate large rearrangements that
AB  - alter the order and orientation of essential protein-encoding genes, which
AB  - otherwise exhibit little nucleotide sequence diversity. By comparing the complete
AB  - genome assemblies from 257 isolates, we show that specific rearrangements have
AB  - been conserved throughout recent evolutionary history, perhaps by eliciting
AB  - changes in gene expression, which may also provide useful information for
AB  - molecular epidemiology.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Peng, Y.
AU  - Loparev, V.
AU  - Batra, D.
AU  - Bowden, K.E.
AU  - Cassiday, P.K.
AU  - Davis, J.K.
AU  - Johnson, T.
AU  - Juieng, P.
AU  - Miner, C.E.
AU  - Rowe, L.
AU  - Sheth, M.
AU  - Tondella, M.L.
AU  - Williams, M.M.
TI  - Complete Genome Sequences of Four Different Bordetella sp. Isolates Causing Human Respiratory Infections.
JO  - Genome Announcements
PY  - 2016
SP  - e01080
EP  - e01016
VL  - 4
AB  - Species of the genus Bordetella associate with various animal hosts, frequently causing
AB  - respiratory disease. Bordetella pertussis is the primary agent of
AB  - whooping cough and other Bordetella species can cause similar cough illness.
AB  - Here, we report four complete genome sequences from isolates of different
AB  - Bordetella species recovered from human respiratory infections.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Peng, Y.
AU  - Loparev, V.
AU  - Batra, D.
AU  - Burroughs, M.
AU  - Johnson, T.
AU  - Juieng, P.
AU  - Rowe, L.
AU  - Tondella, M.L.
AU  - Williams, M.M.
TI  - Complete Genome Sequences of Bordetella pertussis Vaccine Reference Strains 134 and 10536.
JO  - Genome Announcements
PY  - 2016
SP  - e00979
EP  - e00916
VL  - 4
AB  - Vaccine formulations and vaccination programs against whooping cough (pertussis)  vary
AB  - worldwide. Here, we report the complete genome sequences of two divergent
AB  - Bordetella pertussis reference strains used in the production of pertussis
AB  - vaccines.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Peng, Y.
AU  - Loparev, V.
AU  - Johnson, T.
AU  - Juieng, P.
AU  - Gairola, S.
AU  - Kumar, R.
AU  - Shaligram, U.
AU  - Gowrishankar, R.
AU  - Moura, H.
AU  - Rees, J.
AU  - Schieltz, D.M.
AU  - Williamson, Y.
AU  - Woolfitt, A.
AU  - Barr, J.
AU  - Tondella, M.L.
AU  - Williams, M.M.
TI  - Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains  from Serum Institute of India.
JO  - Genome Announcements
PY  - 2016
SP  - e01404
EP  - e01416
VL  - 4
AB  - Serum Institute of India is among the world's largest vaccine producers. Here, we report the
AB  - complete genome sequences for four Bordetella pertussis strains used by Serum Institute of
AB  - India in the production of whole-cell pertussis vaccines.
ER  -

TY  - JOUR
AU  - Weigand, M.R.
AU  - Ryu, H.
AU  - Bozcek, L.
AU  - Konstantinidis, K.T.
AU  - Santo, D.J.W.
TI  - Draft Genome Sequence of Catellicoccus marimammalium, a Novel Species Commonly Found in Gull Feces.
JO  - Genome Announcements
PY  - 2013
SP  - e00019
EP  - e00012
VL  - 1
AB  - Catellicoccus marimammalium is a relatively uncharacterized Gram-positive facultative anaerobe
AB  - with potential utility as an indicator of waterfowl fecal
AB  - contamination. Here, we report an annotated draft genome sequence that suggests
AB  - that this organism may be a symbiotic gut microbe.
ER  -

TY  - JOUR
AU  - Weil, M.D.
AU  - McClelland, M.
TI  - Enzymatic cleavage of a bacterial genome at a 10-base-pair recognition site.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1989
SP  - 51
EP  - 55
VL  - 86
AB  - The circular genome of Staphylococcus aureus was cut into two fragments by a
AB  - simple enzymatic method that cleaves a 10-base-pair site.  The recognition
AB  - sequence, A-T-C-G-mA^T-C-G-mA-T, was created by the combined use of the
AB  - methylase M.ClaI (A-T-C-G-mA-T) and the restriction endonuclease DpnI
AB  - (G-mA^T-C).  This technique is insensitive to CpG methylation and in human DNA
AB  - is predicted to produce fragments that, on average, are greater than five
AB  - million base pairs.  The ability to create such long pieces of DNA should
AB  - facilitate mapping of large, complex chromosomes.
ER  -

TY  - JOUR
AU  - Weilharter, A.
AU  - Mitter, B.
AU  - Shin, M.V.
AU  - Chain, P.S.
AU  - Nowak, J.
AU  - Sessitsch, A.
TI  - Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3383
EP  - 3384
VL  - 193
AB  - Burkholderia phytofirmans PsJN(T) is able to efficiently colonize the rhizosphere, root and
AB  - above-ground plant tissues of a wide variety of
AB  - genetically unrelated plants such as potato, canola, maize and grapevine.
AB  - Strain PsJN shows strong plant growth-promoting effects and was reported
AB  - to enhance plant vigour and resistance to biotic and abiotic stresses.
AB  - Here, we report the genome sequence of this strain, which indicates the
AB  - presence of multiple traits relevant for endophytic colonization and plant
AB  - growth promotion.
ER  -

TY  - JOUR
AU  - Weimer, C.M.
AU  - Deitzler, G.E.
AU  - Robinson, L.S.
AU  - Park, S.
AU  - Hallsworth-Pepin, K.
AU  - Wollam, A.
AU  - Mitreva, M.
AU  - Lewis, W.G.
AU  - Lewis, A.L.
TI  - Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women.
JO  - Genome Announcements
PY  - 2016
SP  - e00882
EP  - e00816
VL  - 4
AB  - The presence of bacteria in urine can pose significant risks during pregnancy. However, there
AB  - are few reference genome strains for many common urinary bacteria.
AB  - We isolated 12 urinary strains of Streptococcus, Staphylococcus, Citrobacter,
AB  - Gardnerella, and Lactobacillus These strains and their genomes are now available
AB  - to the research community.
ER  -

TY  - JOUR
AU  - Weiner, M.
AU  - Costa, G.
TI  - New methodologies for the directional and bidirectional cloning and expression of PCR-generated DNA fragments.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1994
SP  - 249
EP  - 249
VL  - 94
AB  - We have optimized conditions for the efficient cloning of blunt-ended DNA fragments generated
AB  - by the polymerase chain reaction (PCR). In the bidirectional cloning procedure, the PCR
AB  - fragment is incubated with SrfI endonuclease-treated (recognition site: 5'GCCC^GGGC3')
AB  - plasmid DNA, SrfI endonuclease, and T4 DNA ligase. The ligation reaction is allowed to proceed
AB  - for 1 hour and transformed into E. coli. The presence of the endonuclease in the ligation
AB  - reaction reduces nonrecombinant background and increases the amount of linear vector available
AB  - for recombinant insertion. Directional PCR cloning is achieved by creating a
AB  - monophosphorylated vector and a monophosphorylated PCR fragment. Circularization of the cloned
AB  - product during subsequent incubation with SrfI and T4 DNA ligase occurs only when the
AB  - insertion is in the desired orientation. The plasmid vectors have been optimized for
AB  - expression using T7 RNA polymerase for transcriptional control.
ER  -

TY  - JOUR
AU  - Weingarten, R.A.
AU  - Johnson, R.C.
AU  - Conlan, S.
AU  - Ramsburg, A.M.
AU  - Dekker, J.P.
AU  - Lau, A.F.
AU  - Khil, P.
AU  - Odom, R.T.
AU  - Deming, C.
AU  - Park, M.
AU  - Thomas, P.J.
AU  - Henderson, D.K.
AU  - Palmore, T.N.
AU  - Segre, J.A.
AU  - Frank, K.M.
TI  - Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.
JO  - MBio
PY  - 2018
SP  - e02011
EP  - e02017
VL  - 9
AB  - The hospital environment is a potential reservoir of bacteria with plasmids conferring
AB  - carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling
AB  - of high-touch surfaces, sinks, and other locations in the hospital.
AB  - Over a 2-year period, additional sampling was conducted at a broader range of locations,
AB  - including housekeeping closets, wastewater from hospital internal pipes, and external
AB  - manholes. We compared these data with previously collected information from 5 years of patient
AB  - clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates
AB  - provided comprehensive characterization of blaKPC/blaNDM-positive isolates, enabling an
AB  - in-depth genetic comparison. Strikingly, despite a very low prevalence
AB  - of patient infections with blaKPC-positive organisms, all samples from the intensive care unit
AB  - pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs),
AB  - suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and
AB  - we noted species and susceptibility profile differences between environmental and patient
AB  - populations of CPOs. However, there were plasmid backbones
AB  - common to both populations, highlighting a potential environmental reservoir of mobile
AB  - elements that may contribute to the spread of resistance genes. Clear associations between
AB  - patient and environmental isolates were uncommon based on sequence analysis and epidemiology,
AB  - suggesting reasonable infection control compliance at our institution. Nonetheless, a probable
AB  - nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was
AB  - detected by this extensive surveillance. These data and analyses further our understanding of
AB  - CPOs in the hospital environment and are broadly relevant to the design of infection control
AB  - strategies in many infrastructure
AB  - settings.
ER  -

TY  - JOUR
AU  - Weinmaier, T.
AU  - Riesing, M.
AU  - Rattei, T.
AU  - Bille, J.
AU  - Arguedas-Villa, C.
AU  - Stephan, R.
AU  - Tasara, T.
TI  - Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland.
JO  - Genome Announcements
PY  - 2013
SP  - e00152
EP  - e00112
VL  - 1
AB  - The complete genome sequence of Listeria monocytogenes LL195, a serotype 4b clinical strain
AB  - isolated during the 1983-1987 listeriosis epidemic in
AB  - Switzerland, is presented.
ER  -

TY  - JOUR
AU  - Weinstock, G.M.
AU  - Robinson, G.E.
TI  - Insights into social insects from the genome of the honeybee Apis mellifera.
JO  - Nature
PY  - 2006
SP  - 931
EP  - 949
VL  - 443
AB  - Here we report the genome sequence of the honeybee Apis mellifera, a key model for social
AB  - behaviour and essential to global ecology through pollination.  Compared with other sequenced
AB  - insect genomes,the A. mellifera genome has a high A + T and CpG contents, lacks major
AB  - transposon families, evolves more slowly, and is more similar to vertebrates for circadian
AB  - rhythm, RNA interference and DNA methylation genes, among others.  Furthermore, A. mellifera
AB  - has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and
AB  - gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen
AB  - utilization, consistent with its ecology and social organization.  Copmpared to Drosophila,
AB  - genes in early developmental pathways differ in Apis, whereas similarities exist for functions
AB  - that differ markedly, such as sex determination, brain function and behaviour.  Population
AB  - genetics suggests a novel African origin for the species A. mellifera nad insights into
AB  - whether Africanized bees spread throughout the New World via hybridization or displacement.
ER  -

TY  - JOUR
AU  - Weis, A.M.
AU  - Clothier, K.A.
AU  - Huang, B.C.
AU  - Kong, N.
AU  - Weimer, B.C.
TI  - Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock.
JO  - Genome Announcements
PY  - 2016
SP  - e01324
EP  - e01316
VL  - 4
AB  - Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This
AB  - publication announces the public release of 15 Campylobacter
AB  - jejuni genome sequences from isolates linked to abortion in livestock. These
AB  - isolates are part of the 100K Pathogen Genome Project and are from clinical cases
AB  - at the University of California (UC) Davis.
ER  -

TY  - JOUR
AU  - Weis, A.M.
AU  - Clothier, K.A.
AU  - Huang, B.C.
AU  - Kong, N.
AU  - Weimer, B.C.
TI  - Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California.
JO  - Genome Announcements
PY  - 2017
SP  - e00171
EP  - e00117
VL  - 5
AB  - Campylobacter jejuni is an enteric bacterium that can cause abortion in livestock. This is the
AB  - release of a multidrug-resistant Campylobacter jejuni
AB  - genome from an isolate that caused an abortion in a cow in northern California.
AB  - This isolate is part of the 100K Pathogen Genome Project.
ER  -

TY  - JOUR
AU  - Weis, A.M.
AU  - Gilpin, B.
AU  - Huang, B.C.
AU  - Kong, N.
AU  - Chen, P.
AU  - Weimer, B.C.
TI  - Shigella Draft Genome Sequences: Resources for Food Safety and Public Health.
JO  - Genome Announcements
PY  - 2017
SP  - e00176
EP  - e00117
VL  - 5
AB  - Shigella is a major foodborne pathogen that infects humans and nonhuman primates  and is the
AB  - major cause of dysentery and reactive arthritis worldwide. This is the
AB  - initial public release of 16 Shigella genome sequences from four species
AB  - sequenced as part of the 100K Pathogen Genome Project.
ER  -

TY  - JOUR
AU  - Weis, A.M.
AU  - Huang, B.C.
AU  - Storey, D.B.
AU  - Kong, N.
AU  - Chen, P.
AU  - Arabyan, N.
AU  - Gilpin, B.
AU  - Mason, C.
AU  - Townsend, A.K.
AU  - Smith, W.A.
AU  - Byrne, B.A.
AU  - Taff, C.C.
AU  - Weimer, B.C.
TI  - Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project.
JO  - Genome Announcements
PY  - 2017
SP  - e00925
EP  - e00916
VL  - 5
AB  - Campylobacter is a food-associated bacterium and a leading cause of foodborne illness
AB  - worldwide, being associated with poultry in the food supply. This is the
AB  - initial public release of 202 Campylobacter genome sequences as part of the 100K
AB  - Pathogen Genome Project. These isolates represent global genomic diversity in the
AB  - Campylobacter genus.
ER  -

TY  - JOUR
AU  - Weisenberger, D.J.
AU  - Velicescu, M.
AU  - Cheng, J.C.
AU  - Gonzales, F.A.
AU  - Liang, G.N.
AU  - Jones, P.A.
TI  - Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation.
JO  - Mol. Cancer Res.
PY  - 2004
SP  - 62
EP  - 72
VL  - 2
AB  - Several alternatively spliced variants of DNA methyltransferase (DNMT) 3b have been described.
AB  - Here, we identified new murine Dnmt3b mRNA
AB  - isoforms and found that mouse embryonic stem (ES) cells expressed only
AB  - Dnmt3b transcripts that contained exons 10 and 11, whereas the Dnmt3b
AB  - transcripts in somatic cells lacked these exons, suggesting that this
AB  - region is important for embryonic development. DNMT3b2 and 3b3 were the
AB  - major isoforms expressed in human cell lines and the mRNA levels of
AB  - these isoforms closely correlated with their protein levels. Although
AB  - DNMT3b3 may be catalytically inactive, it still may be biologically
AB  - important because D4Z4 and satellites 2 and 3 repeat sequences, all
AB  - known DNMT3b target sequences, were methylated in cells that
AB  - predominantly expressed DNMT3b3. Treatment of cells with the
AB  - mechanism-based inhibitor 5-aza-2'-deoxycytidine (5-Aza-CdR) caused a
AB  - complete depletion of DNMT1, 3a, 3b1, and 3b2 proteins. Human DNMT3b3
AB  - and the murine Dnmt3b3-like isoform, Dnmt3b6, were also depleted
AB  - although less efficiently, suggesting that DNMT3b3 also may be capable
AB  - of DNA binding. Moreover, de novo methylation of D4Z4 in T24 cancer
AB  - cells after 5-Aza-CdR treatment only occurred when DNMT3b3 was
AB  - expressed, reinforcing its role as a contributing factor of DNA
AB  - methylation. The expression of either DNMT3b2 or 3b3, however, was not
AB  - sufficient to explain the abnormal methylation of DNMT3b target
AB  - sequences in human cancers, which may therefore be dependent on factors
AB  - that affect DNMT3b targeting. Methylation analyses of immunodeficiency,
AB  - chromosomal instabilities, and facial abnormalities cells revealed that
AB  - an Alu repeat sequence was highly methylated, suggesting that Alu
AB  - sequences are not DNMT3b targets.
ER  -

TY  - JOUR
AU  - Weisenberger, D.J.
AU  - Velicescu, M.
AU  - Preciado-Lopez, M.A.
AU  - Gonzales, F.A.
AU  - Tsai, Y.C.
AU  - Liang, G.
AU  - Jones, P.A.
TI  - Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells.
JO  - Gene
PY  - 2002
SP  - 91
EP  - 99
VL  - 298
AB  - CpG methylation is mediated by the functions of at least three active DNA methyltransferases
AB  - (DNMTs). While DNMT1 is thought to perform maintenance methylation, the more recently
AB  - discovered DNMT3a and DNMT3b enzymes are thought to facilitate de novo methylation. Murine
AB  - Dnmt3a and 3b are developmentally regulated and a new Dnmt3a isoform, Dnmt3a2, has been
AB  - recently shown to be expressed preferentially in mouse embryonic stem (ES) cells. Here we have
AB  - characterized four alternatively spliced variants of human and mouse DNMT3a. These transcripts
AB  - included a novel exon 1 (1beta) that was spliced into the same exon 2 acceptor splice site
AB  - used by the original exon 1 (1alpha). Cloning and sequencing of the 5' region of the human
AB  - DNMT3a gene revealed that exon 1beta was situated upstream of exon 1alpha and that the entire
AB  - region was contained within a CpG island. We also identified other alternatively spliced
AB  - species containing intron 4 inclusions that were associated with either exon 1alpha or 1beta.
AB  - These were expressed at low levels in mouse and human cells. All transcripts were highly
AB  - conserved between human and mouse. The levels of Dnmt3a mRNA containing exon 1beta were
AB  - 3-25-fold greater in mouse ES cells than in various somatic cells as determined by
AB  - semiquantitative reverse transcription-polymerase chain reaction analysis, while the levels of
AB  - exon 1alpha-containing transcripts were slightly higher in human and mouse somatic cells. The
AB  - preferential expression of the beta transcript in ES cells suggests that this transcript, in
AB  - addition to Dnmt3a2, may also be important for de novo methylation during development.
ER  -

TY  - JOUR
AU  - Weiserova, M.
AU  - Dutta, C.F.
AU  - Firman, K.
TI  - A novel mutant of the type I restriction-modification enzyme EcoR124I is altered at a key stage of the subunit assembly pathway.
JO  - J. Mol. Biol.
PY  - 2000
SP  - 301
EP  - 310
VL  - 304
AB  - The HsdS subunit of a type I restriction-modification (R-M) system plays an essential role in
AB  - the activity of both the modification methylase and the restriction endonuclease. This subunit
AB  - is responsible for DNA binding, but also contains conserved amino acid sequences responsible
AB  - for protein-protein interactions. The most important protein-protein interactions are those
AB  - between the HsdS subunit and the HsdM (methylation) subunit that result in assembly of an
AB  - independent methylase (MTase) of stoichiometry M(2)S(1). Here, we analysed the impact on the
AB  - restriction and modification activities of the change Trp(212)-->Arg in the distal border of
AB  - the central conserved region of the EcoR124I HsdS subunit. We demonstrate that this point
AB  - mutation significantly influences the ability of the mutant HsdS subunit to assemble with the
AB  - HsdM subunit to produce a functional MTase. As a consequence of this, the mutant MTase has
AB  - drastically reduced DNA binding, which is restored only when the HsdR (restriction) subunit
AB  - binds with the MTase. Therefore, HsdR acts as a chaperon allowing not only binding of the
AB  - enzyme to DNA, but also restoring the methylation activity and, at sufficiently high
AB  - concentrations in vitro of HsdR, restoring restriction activity.
ER  -

TY  - JOUR
AU  - Weiserova, M.
AU  - Firman, K.
TI  - Isolation of a non-classical mutant of the DNA recognition subunit of the type I restriction endonuclease R.EcoR124I.
JO  - Biol. Chem.
PY  - 1998
SP  - 585
EP  - 589
VL  - 379
AB  - We have used deletion mutagenesis and PCR-based misincorporation mutagenesis to produce a
AB  - collection of mutations in the central conserved region of the DNA binding subunit of the type
AB  - IC restriction endonuclease EcoR124I.  It has been proposed that this domain is involved in
AB  - protein-protein interactions during the assembly of the endonuclease.  While a large
AB  - percentage of these mutations gave a classical Res- Mod- phenotype, one mutant was isolated
AB  - with a nonclassical Res-Mod+ phenotype.  The loss of restriction activity, but retention of
AB  - the ability to modify indicates that this mutation cannot affect DNA binding and must alter
AB  - the assembly of the endonuclease in such a way as to prevent DNA cleavage but allow
AB  - methylation.  This mutant resulted from a single amino acid change Trp212-Arg.  The location
AB  - of the single amino acid change is at the border of the central conserved region and the
AB  - second target recognition domain and suggests that this region is extremely important for the
AB  - assembly of the methylase with the HsdR subunit into a functional restriction endonuclease.
ER  -

TY  - JOUR
AU  - Weiserova, M.
AU  - Janscak, P.
AU  - Benada, O.
AU  - Hubacek, J.
AU  - Vitaly, E.A.
AU  - Glover, S.W.
AU  - Firman, K.
TI  - Cloning, production and characterization of wild type and mutant forms of the R.EcoK endonucleases.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 373
EP  - 379
VL  - 21
AB  - The hsdR, hsdM and hsdS genes coding for R.EcoK restriction endonucleases, both with and
AB  - without a temperature sensitive mutation (ts-1) in the hsdS gene, were cloned in pBR322
AB  - plasmid and introduced into E. coli C3-6. The presence of the hsdS ts-1 mutation has no effect
AB  - on the R-M phenotype of this contruct in bacteria grown at 42 degrees C. However, DNA
AB  - sequencing indicates that the mutation is still present on the pBR322-hsd ts1 operon. The
AB  - putative temperature-sensitive endonuclease was purified from bacteria carrying this plasmid
AB  - and the ability to cleave and methylate plasmid DNA was investigated. The mutant endonuclease
AB  - was found to show temperature-sensitivity for restriction. Modification was dramatically
AB  - reduced at both the permissive and non-permissive temperatures. The wild type enzyme was found
AB  - to cleave circular DNA in a manner which strongly suggests that only one endonuclease molecule
AB  - is required per cleavage event. Circular and linear DNA appear to be cleaved using different
AB  - mechanisms, and cleavage of linear DNA may require a second endonuclease molecule. The subunit
AB  - composition of the purified endonucleases was investigated and compared to the level of
AB  - subunit production in minicells. There is no evidence that HsdR is prevented from assembling
AB  - with HsdM and HsdS ts-1 to produce the mutant endonuclease. The data also suggests that the
AB  - level of HsdR subunit may be limiting within the cell. We suggest that an excess of HsdM and
AB  - HsdS may produce the methylase in vivo and that assembly of the endonuclease may be dependent
AB  - upon the prior production of this methylase.
ER  -

TY  - JOUR
AU  - Weiserova, M.
AU  - Janscak, P.
AU  - Zinkevich, V.
AU  - Hubacek, J.
TI  - Overproduction of the Hsd subunits leads to the loss of temperature-sensitive restriction and modification phenotype.
JO  - Folia Microbiol. (Praha)
PY  - 1994
SP  - 452
EP  - 458
VL  - 39
AB  - The genes hsdM and hsdS for M.EcoKI modification methyltransferase and the complete set of
AB  - hsdR, hsdM and hsdS genes coding for R.EcoKI restriction endonuclease, both with and without a
AB  - temperature-sensitive (ts) mutation in hsdS gene, were cloned in pBR322 plasmid and introduced
AB  - into E. coli C (a strain without a natural restriction-modification (R-M) system).  The
AB  - strains producing only the methyltransferase, or together with the endonuclease, were thus
AB  - obtained.  The hsdSts-1 mutation, mapped previously in the distal variable region of the hsdS
AB  - gene with C1245-T transition has no effect on the R-M phenotype expressed from cloned genes in
AB  - bacteria grown at 42oC.  In clones transformed with the whole hsd region an alleviation of R-M
AB  - functions was observed immediately after the transformation, but after subculture the
AB  - transformants expressed the wild-type R-M phenotype irrespective of whether the wild-type or
AB  - the mutant hsdS allele was present in the hybrid plasmid.  Simultaneous overproduction of HsdS
AB  - and HsdM subunits impairs the ts effect of the hsdSts-1 mutation on restriction and
AB  - modification.
ER  -

TY  - JOUR
AU  - Weiserova, M.
AU  - Ryu, J.C.
TI  - Characterization of a restriction modification system from the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31).
JO  - BMC Microbiol.
PY  - 2008
SP  - 106
EP  - 106
VL  - 8
AB  - Background: Type I restriction-modification (R-M) systems are the most complex restriction
AB  - enzymes discovered to date. Recent years have
AB  - witnessed a renaissance of interest in R-M enzymes Type I. The massive
AB  - ongoing sequencing programmes leading to discovery of, so far, more
AB  - than 1 000 putative enzymes in a broad range of microorganisms
AB  - including pathogenic bacteria, revealed that these enzymes are widely
AB  - represented in nature. The aim of this study was characterisation of a
AB  - putative R-M system EcoA0ORF42P identified in the commensal Escherichia
AB  - coli A0 34/86 (O83: K24: H31) strain, which is efficiently used at
AB  - Czech paediatric clinics for prophylaxis and treatment of nosocomial
AB  - infections and diarrhoea of preterm and newborn infants.
AB  - Results: We have characterised a restriction-modification system
AB  - EcoA0ORF42P of the commensal Escherichia coli strain A0 34/86 ( O83:
AB  - K24: H31). This system, designated as EcoAO831, is a new functional
AB  - member of the Type IB family, whose specificity differs from those of
AB  - known Type IB enzymes, as was demonstrated by an immunological
AB  - cross-reactivity and a complementation assay. Using the plasmid
AB  - transformation method and the RM search computer program, we identified
AB  - the DNA recognition sequence of the EcoAO83I as GGA(8N)ATGC. In
AB  - consistence with the amino acids alignment data, the 3' TRD component
AB  - of the recognition sequence is identical to the sequence recognized by
AB  - the EcoEI enzyme. The A-T ( modified adenine) distance is identical to
AB  - that in the EcoAI and EcoEI recognition sites, which also indicates
AB  - that this system is a Type IB member. Interestingly, the recognition
AB  - sequence we determined here is identical to the previously reported
AB  - prototype sequence for Eco377I and its isoschizomers.
AB  - Conclusion: Putative restriction-modification system EcoA0ORF42P in
AB  - the commensal Escherichia coli strain A0 34/86 ( O83: K24: H31) was
AB  - found to be a member of the Type IB family and was designated as
AB  - EcoAO83I. Combination of the classical biochemical and bacterial
AB  - genetics approaches with comparative genomics might contribute
AB  - effectively to further classification of many other putative Type-I
AB  - enzymes, especially in clinical samples.
ER  -

TY  - JOUR
AU  - Weiss, A.
AU  - Keshet, I.
AU  - Razin, A.
AU  - Cedar, H.
TI  - DNA demethylation in vitro: Involvement of RNA.
JO  - Cell
PY  - 1996
SP  - 709
EP  - 718
VL  - 86
AB  - An in vitro system for studying DNA demethylation has been established using extracts from
AB  - tissue culture cells.  This reaction, which is unusually resistant to proteinase K, takes
AB  - place through the removal of a 5-methylcytosine nucleotide unit from the DNA substrate and its
AB  - conversion to an RNAse-sensitive form.  It is likely that this represents the in vivo
AB  - mechanism as well, since extracts from L8 myoblasts specifically demethylate an alpha-actin
AB  - gene, while extracts from F9 teratocarcinoma cells specifically demodify the Aprt CpG island.
AB  - After pretreatment with proteinase K, these extracts demethylate both genes equally,
AB  - suggesting that gene specificity may be controlled by protein factors.
ER  -

TY  - JOUR
AU  - Weiss, M.
AU  - Kesberg, A.I.
AU  - Labutti, K.M.
AU  - Pitluck, S.
AU  - Bruce, D.
AU  - Hauser, L.
AU  - Copeland, A.
AU  - Woyke, T.
AU  - Lowry, S.
AU  - Lucas, S.
AU  - Land, M.
AU  - Goodwin, L.
AU  - Kjelleberg, S.
AU  - Cook, A.M.
AU  - Buhmann, M.
AU  - Thomas, T.
AU  - Schleheck, D.
TI  - Permanent draft genome sequence of Comamonas testosteroni KF-1.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 239
EP  - 254
VL  - 8
AB  - Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel  biochemical
AB  - degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC)
AB  - formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear
AB  - alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an
AB  - average G+C content of 61.79% and is predicted to encode 5,492 protein-coding
AB  - genes and 114 RNA genes.
ER  -

TY  - JOUR
AU  - Weiss, V.A.
AU  - Faoro, H.
AU  - Tadra-Sfeir, M.Z.
AU  - Raittz, R.T.
AU  - de Souza, E.M.
AU  - Monteiro, R.A.
AU  - Cardoso, R.L.
AU  - Wassem, R.
AU  - Chubatsu, L.S.
AU  - Huergo, L.F.
AU  - Muller-Santos, M.
AU  - Steffens, M.B.
AU  - Rigo, L.U.
AU  - Pedrosa, F.O.
AU  - Cruz, L.M.
TI  - Draft Genome Sequence of Herbaspirillum lusitanum P6-12, an Endophyte Isolated from Root Nodules of Phaseolus vulgaris.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4136
EP  - 4137
VL  - 194
AB  - Herbaspirillum lusitanum strain P6-12 (DSM 17154) is, so far, the only species of
AB  - Herbaspirillum isolated from plant root nodules. Here we report a draft genome
AB  - sequence of this organism.
ER  -

TY  - JOUR
AU  - Weissgerber, T.
AU  - Zigann, R.
AU  - Bruce, D.
AU  - Chang, Y.-j.
AU  - Detter, J.C.
AU  - Han, C.
AU  - Hauser, L.
AU  - Jeffries, C.D.
AU  - Land, M.
AU  - Munk, A.C.
AU  - Tapia, R.
AU  - Dahl, C.
TI  - Complete genome sequence of Allochromatium vinosum DSM 180.
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 311
EP  - 330
VL  - 5
AB  - Allochromatium vinosum formerly Chromatium vinosum is a mesophilic purple sulfur bacte-rium
AB  - belonging to the family Chromatiaceae in the bacterial class Gammaproteobacteria. The genus
AB  - Allochromatium contains currently five species. All members were isolated from fresh-water,
AB  - brackish water or marine habitats and are predominately obligate phototrophs. Here we describe
AB  - the features of the organism, together with the complete genome sequence and annotation. This
AB  - is the first completed genome sequence of a member of the Chromatiaceae within the purple
AB  - sulfur bacteria thriving in globally occurring habitats. The 3,669,074 bp ge-nome with its
AB  - 3,302 protein-coding and 64 RNA genes was sequenced within the Joint Ge-nome Institute
AB  - Community Sequencing Program.
ER  -

TY  - JOUR
AU  - Weitzman, C.L.
AU  - Tillett, R.L.
AU  - Sandmeier, F.C.
AU  - Tracy, C.R.
AU  - Alvarez-Ponce, D.
TI  - High quality draft genome sequence of Mycoplasma testudineum strain BH29(T), isolated from the respiratory tract of a desert tortoise.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 9
EP  - 9
VL  - 13
AB  - Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease
AB  - in desert tortoises, Gopherus agassizii. We sequenced the genome of
AB  - M. testudineum BH29(T) (ATCC 700618(T) = MCCM 03231(T)), isolated from the upper
AB  - respiratory tract of a Mojave desert tortoise with upper respiratory tract
AB  - disease. The sequenced draft genome, organized in 25 scaffolds, has a length of
AB  - 960,895 bp and a G + C content of 27.54%. A total of 788 protein-coding
AB  - sequences, six pseudogenes and 35 RNA genes were identified. The potential
AB  - presence of cytadhesin-encoding genes is investigated. This genome will enable
AB  - comparative genomic studies to help understand the molecular bases of the
AB  - pathogenicity of this and other Mycoplasma species.
ER  -

TY  - JOUR
AU  - Welch, R.A. et al.
TI  - Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2002
SP  - 17020
EP  - 17024
VL  - 99
AB  - We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A
AB  - three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory
AB  - strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of
AB  - proteins actually are common to all three strains. The pathogen genomes are as different from
AB  - each other as each pathogen is from the benign strain. The difference in disease potential
AB  - between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system
AB  - or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The
AB  - CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins,
AB  - autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking
AB  - differences exist between the large pathogenicity islands of CFT073 and two other well-studied
AB  - uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal
AB  - pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli
AB  - pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas
AB  - many islands interrupting this common backbone have been acquired by different horizontal
AB  - transfer events in each strain.
ER  -

TY  - JOUR
AU  - Welch, S.G.
AU  - Al-Awadhi, S.
AU  - Williams, R.A.D.
TI  - Isoschizomers of the restriction endonuclease TaqI (T/CGA) requiring different metal ion concentrations and having a range of thermal stabilities from Thermus species from different continents.
JO  - Microbiology
PY  - 1998
SP  - 167
EP  - 175
VL  - 144
AB  - One-hundred-and-fifty-two isolates of the genus Thermus, collected from hot springs on four
AB  - continents, were screened for evidence of the presence of the thermophilic Type II restriction
AB  - endonuclease TaqI (T/CGA).  The presence of isoschizomers of TaqI in 27 of the isolates,
AB  - originating from hot springs in New Zealand, Iceland, USA, Japan, mainland Portugal and the
AB  - island of Sao Miguel in the Azores, is reported.  Six of the TaqI-containing isolates from
AB  - diverse geographical locations, identified by means of DNA/DNA homology and 16S rRNA sequence
AB  - alignment as belonging to the Thermus species T. aquaticus, T. filiformis, T. themophilus, T.
AB  - scotoductus and T. brockianus, were selected for comparative studies.  The TaqI isoschizomers
AB  - from each of the six isolates were partially purified.  They differed in their magnesium ion
AB  - requirements, isoelectric points, subunit molecular masses and thermal stability.
ER  -

TY  - JOUR
AU  - Welch, S.G.
AU  - Williams, R.A.D.
TI  - Two thermostable type II restriction endonucleases from Icelandic strains of the genus Thermus: Tsp4C I (ACN/GT), a novel type II restriction endonuclease, and Tsp8E I, an isoschizomer of the mesophilic enzyme BglI (GCCNNNN/NGGC).
JO  - Biochem. J.
PY  - 1995
SP  - 595
EP  - 599
VL  - 309
AB  - Sixteen isolates of thermophilic bacteria from the genus Thermus, isolated from neutral and
AB  - alkaline hot water springs in the southwest region of Iceland, were tested for the presence of
AB  - restriction endonucleases.  Extracts from five of the isolates showed evidence of the
AB  - presence of restriction endonuclease activity by producing discrete nucleotide fragments when
AB  - incubated at 65oC with lambda phage DNA.  Two of the isolates (Tsp4C and Tsp8E) were found to
AB  - have particularly high levels of restriction endonuclease activity, and the respective enzymes
AB  - from these two Thermus isolates were partially purified and characterized and their
AB  - recognition and cleavage sites were determined.  Enzyme Tsp4C I is a novel type II restriction
AB  - endonuclease recognizing the interrupted palindromic tetranucleotide sequence ACNGT, where N
AB  - can be any one of the four bases in DNA.  Tsp4CI, which retains full enzyme activity when
AB  - incubated for 10 min at temperatures up to 76oC, hydrolyses the phosphodiester bond in both
AB  - strands of a double-stranded DNA substrate between the third and fourth bases of the
AB  - recognition sequence (ACN/GT), generating fragments with a single base 3'-OH overhang.
AB  - Enzyme Tsp8EI is a thermostable isoschizomer of the mesophilic type II restriction
AB  - endonuclease BglI (GCCNNNN/NGGC), generating fragments with a three base 3'-OH overhang.
AB  - However, unlike BglI, Tsp8EI exhibits considerable thermal stability, retaining full enzyme
AB  - activity when incubated for 10 min at temperatures up to 78oC.  Both Tsp4CI and Tsp8EI
AB  - represent significant additions to the small but expanding list of the extremely thermostable
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Welch, S.G.
AU  - Williams, R.A.D.
TI  - Taq52I, a novel and thermostable type II restriction endonuclease from the genus Thermus, recognising the pentanucleotide sequence GC(A or T)GC and cleaving DNA between the first and second bases of the recognition sequence: G/C(A or T)GC.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 4573
EP  - 4575
VL  - 23
AB  - 127 isolates of the genus Thermus, from neutral and alkaline hot water springs on four
AB  - continents, have been screened for the presence of restriction endonuclease activity.  An
AB  - isolate (YS52) from Yellowstone National Park, USA, showed a high level of restriction
AB  - endonuclease activity when a cell free extract was incubated with lambda phage DNA at 65oC.  A
AB  - type II restriction endonuclease (Taq52I) has been partially purified from this isolate and
AB  - the recognition and cleavage site determined.  Taq52I has a novel interrupted palindromic
AB  - tetranucleotide recognition sequence GCWGC, where W can be either adenine (A) or thymine (T).
AB  - It hydrolyses the phosphodiester bond in both strands of the substrate between the first and
AB  - second bases of the recognition sequence: 5'G/CWGC3', producing three-base 5'-OH overhangs
AB  - (sticky ends).  The enzyme has a pH optimum of 7.0, requires 8 mM MgCl2 for maximum activity
AB  - and is thermally stable, retaining full enzyme activity following incubation at 79oC for 10
AB  - min.  Taq52I not only represents a new addition to the type II restriction endonucleases, but
AB  - also increases the small list of thermostable restriction endonucleases.
ER  -

TY  - JOUR
AU  - Welch, S.G.
AU  - Williams, R.A.D.
TI  - Two different isoschizomers of the type-II restriction endonuclease TaqI (T/CGA) within the same Thermus isolate: Tsp32I, an enzyme with similar heat stability properties to the prototype enzyme TaqI, & Tsp32II, a hyperthermostable isoschizomer of TaqI.
JO  - Biochem. J.
PY  - 1995
SP  - 505
EP  - 510
VL  - 312
AB  - We have recently screened 112 separate isolates of the genus Thermus, collected from neutral
AB  - and alkaline hot water springs on four continents, for the presence of the Type-II restriction
AB  - endonuclease TaqI (T/CGA).  One particular isolate from the Azores (strain 32) was found to
AB  - contain high levels of a restriction endonuclease with the same recognition and cleavage site
AB  - as TaqI.  Initial studies revealed that the partially purified enzyme from strain 32 was
AB  - considerably more resistant to heat inactivation than the prototype enzyme TaqI, being able to
AB  - withstand temperatures at least 10oC higher than TaqI, before showing evidence of heat
AB  - inactivation.  Subsequently it became clear that the partially purified extract from strain 32
AB  - contains two separate enzymes, both of which are isoschizomers of TaqI.  One of the enzymes,
AB  - Tsp32I, has similar thermal stability characteristics to TaqI, whereas the second TaqI
AB  - isoschizomer, Tsp32II, found in the same Thermus isolate as Tsp32I, is considerably more
AB  - thermostable than TaqI, retaining full enzyme activity up to a temperature of 85oC.  Tsp32I
AB  - and Tsp32II were further distinguished by virtue of their different requirements for magnesium
AB  - ions.
ER  -

TY  - JOUR
AU  - Welch, S.G.
AU  - Williams, R.A.D.
TI  - Tsp49I (ACGT^), a thermostable neoschizomer of the type II restriction endonuclease MaeII (A^CGT), discovered in isolates of the genus thermus from the Azores, Iceland and New Zealand.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 1799
EP  - 1801
VL  - 24
AB  - One hundred and forty eight isolates of the genus Thermus, from neutral and
AB  - alkaline hot water springs on four continents, have been screened for the presence of
AB  - restriction
AB  - enodnuclease activity.  An isolate (SM49) from the island of Sao Miguel, in the Azores, showed
AB  - a
AB  - high level of restriction endonuclease activity when a cell-free extract was incubated with
AB  - lambda
AB  - phage DNA at 65oC.  A type II restriction endonuclease (Tsp49I) has been partially purified
AB  - from
AB  - this isolate and the recognition and cleavage site determined.  Tsp49I recognizes the four
AB  - base
AB  - sequence ACGT, which is the same as the recognition sequence of the mesophilic type II
AB  - restriction endonuclease MaeII.  However, unlike MaeII, which cleaves DNA between the first
AB  - and
AB  - second base of the recognition sequence (A^CGT), Tsp49I hydrolyses the phosphodiester bond in
AB  - both strands of the substrate after the last base of the recognition sequence 5'-ACGT^-3',
AB  - producing four base 3'-OH overhangs (sticky ends).  The enzyme has a pH optimum of 9.0,
AB  - requires 3 mM MgCl2 for maximum activity and retains full enzyme activity following incubation
AB  - for 10 min at temperatures up to 80oC.  Two further examples of the same restriction
AB  - endonuclease
AB  - specificity as Tsp49I were detected in Thermus isolates from Iceland (TspIDSI) and New Zealand
AB  - (TspWAM8AI).  The three MaeII neoschizomers, Tsp49I, TspIDSI and TspWAM8AI, exhibit
AB  - similar pH optima, heat stabilities and MgCl2 requirements, but differ in their requirements
AB  - for
AB  - NaCl and KCl.
ER  -

TY  - JOUR
AU  - Welch, T.J.
AU  - Fricke, W.F.
AU  - McDermott, P.F.
AU  - White, D.G.
AU  - Rosso, M.L.
AU  - Rasko, D.A.
AU  - Mammel, M.K.
AU  - Eppinger, M.
AU  - Rosovitz, M.J.
AU  - Wagner, D.
AU  - Rahalison, L.
AU  - LeClerc, J.E.
AU  - Hinshaw, J.M.
AU  - Lindler, L.E.
AU  - Cebula, T.A.
AU  - Carniel, E.
AU  - Ravel, J.
TI  - Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk.
JO  - PLoS ONE
PY  - 2007
SP  - e309
EP  - e309
VL  - 2
AB  - Antimicrobial resistance in Yersinia pestis is rare, yet constitutes a significant
AB  - international public health and biodefense threat.  In 1995, the first multidrug resistant
AB  - isolate of Y. pestis (strain IP275) was identified, and was shown to contain a
AB  - self-transmissible plasmid (pIP1202) that conferred resistance to many of the antimicrobials
AB  - recommended for plague treatment and prophylaxis.  Comparative analysis of the DNA sequence of
AB  - Y. pestis plasmid pIP1202 revealed a near identical IncA/C plasmid backbone that is shared by
AB  - MDR plasmids isolated from Salmonella enterica serotype Newport SL254 and the fish pathogen
AB  - Yersinia ruckeri YR71.  The high degree of sequence identity and gene synteny between the
AB  - plasmid backbones suggests recent acquisition of these plasmids from a common ancestor.  In
AB  - addition, the Y. pestis pIP1202-like plasmid backbone was detected in numerous MDR
AB  - enterobacterial pathogens iosolated from retail meat samples collected between 2002 and 2005
AB  - in the United States.  Plasmid-positive strains were isolated from beef, chicken, turkey and
AB  - pork, and were found in samples from the following states: California, Colorado, Connecticut,
AB  - Georgia, Maryland, Minnesota, New Mexico, New York and Oregon.  Our studies reveal that this
AB  - common plasmid backbone is broadly disseminated among MDR zoonotic pathogens associated with
AB  - agriculture.  This reservoir of mobile resistance determinants has the potential to
AB  - disseminate to Y. pestis and other human and zoonotic bacterial pathogens and therefore
AB  - represents a significant public health concern.
ER  -

TY  - JOUR
AU  - Weller, R.L.
AU  - Rajski, S.R.
TI  - Design, synthesis, and preliminary biological evaluation of a DNA methyltransferase-directed alkylating agent.
JO  - Chembiochem
PY  - 2006
SP  - 243
EP  - 245
VL  - 7
AB  - DNA-binding and -damaging agents often derive their sequence selectivity from a finite set of
AB  - specific contacts between the molecule of interest and select nucleotides.  Many such agents
AB  - are of great interest due to their medicinally useful properties, although for many of these
AB  - substances, it remains unclear that all relevant mechanisms of action have been fully
AB  - elucidated.  In the context of DNA damage however, it seems that damage at certain sites is
AB  - likely to have a greater impact than at others.  At the heart of DNA sequence selectivity is
AB  - the resounding influence of a limited set of interactions between target nucleotides and the
AB  - small molecule of interest.  We hypothesized that DNA alkylation selectivity can be drived
AB  - from the extensive contacts between a sequence-specific DNA-modifying enzyme and its
AB  - recognition site.  Indeed, precedence for this strategy has been noted for DNA
AB  - methyltransferases.  However, to date, the structures of such MTase-dependent DNa-alkylating
AB  - agents have lacked the functionalities expected to be necessary for optimum activity, by
AB  - analogy to the natural cofactor S-adenosyl-L-methionine.
ER  -

TY  - JOUR
AU  - Weller, R.L.
AU  - Rajski, S.R.
TI  - DNA methyltransferase-moderated click chemistry.
JO  - Org. Lett.
PY  - 2005
SP  - 2141
EP  - 2144
VL  - 7
AB  - Biological methylation plays a vital role in regulatory mechanisms of gene transcription.
AB  - Methylation of both promoter sequences within the
AB  - genome, as well as protein substrates, has a profound impact upon gene
AB  - transcription. Yet, few tools exist by which to identify sites of
AB  - biological methylation in complex biological mixtures. We have
AB  - generated a novel adenosine-derived N-mustard that serves as an
AB  - efficient synthetic cofactor and allows for subsequent "click"
AB  - chemistry involving the modified nucleic acid substrate.
ER  -

TY  - JOUR
AU  - Weller-Stuart, T.
AU  - Chan, W.Y.
AU  - Coutinho, T.A.
AU  - Venter, S.N.
AU  - Smits, T.H.
AU  - Duffy, B.
AU  - Goszczynska, T.
AU  - Cowan, D.A.
AU  - de Maayer, P.
TI  - Draft Genome Sequences of the Onion Center Rot Pathogen Pantoea ananatis PA4 and  Maize Brown Stalk Rot Pathogen P. ananatis BD442.
JO  - Genome Announcements
PY  - 2014
SP  - e00750
EP  - e00714
VL  - 2
AB  - Pantoea ananatis is an emerging phytopathogen that infects a broad spectrum of plant hosts.
AB  - Here, we present the genomes of two South African isolates, P.
AB  - ananatis PA4, which causes center rot of onion, and BD442, isolated from brown
AB  - stalk rot of maize.
ER  -

TY  - JOUR
AU  - Wells, R.D.
AU  - Klein, R.D.
AU  - Singleton, C.K.
TI  - Type II restriction enzymes.
JO  - The Enzymes
PY  - 1981
SP  - 157
EP  - 191
VL  - 14
AB  - The current status of type II restriction endonuclease enzymology is quite
AB  - unusual due to the history of this segment of molecular biology.  More than 210
AB  - restriction endonucleases have been purified, at least partially, and their
AB  - recognition sites identified.  However, the genetic and biochemical
AB  - characterization of these enzymes is meager.  Indeed, they have usually been
AB  - isolated as site-specific DNA endonucleases without genetically determining if
AB  - they are involved in DNA restriction-modification.  Moreover, the vast majority
AB  - of the restriction endonucleases are relatively crude preparations, and little
AB  - or nothing is known about the properties of the enzymes.
ER  -

TY  - JOUR
AU  - Wells, R.D.
AU  - Neuendorf, S.K.
TI  - Cleavage of single-stranded viral DNAs by certain restriction endonucleases.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 101
EP  - 111
VL  - 1
AB  - *
AB  -    I. Introduction
AB  -   II. Characterization of the HaeIII reaction on O/X174, M13 and f1 DNAs
AB  -  III. Features of DNA structure recognized by the endonucleases
AB  -   IV. Characteristics of other restriction endonucleases
AB  -    V. Types of DNA substrates cleaved
AB  -   VI. Some properties of isoschizomers
AB  -  VII. Application of the technique for cleaving other DNAs
AB  - VIII. Reaction of DNA methylases on single-stranded DNA
AB  -   IX. Prospects for the future
AB  - 
ER  -

TY  - JOUR
AU  - Wels, M.
AU  - Backus, L.
AU  - Boekhorst, J.
AU  - Dijkstra, A.
AU  - Beerthuyzen, M.
AU  - Siezen, R.J.
AU  - Bachmann, H.
AU  - van Hijum, S.A.
TI  - Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e01739
EP  - e01716
VL  - 5
AB  - The lactic acid bacterium Lactococcus lactis is widely used for the fermentation  of dairy
AB  - products. Here, we present the draft genome sequences of 11 L. lactis
AB  - subsp. cremoris strains isolated from different environments.
ER  -

TY  - JOUR
AU  - Wels, M.
AU  - Serrano, L.M.
AU  - Eibrink, B.J.
AU  - Backus, L.
AU  - Bongers, R.S.
AU  - Vriesendorp, B.
AU  - Siezen, R.J.
AU  - van Hijum, S.A.
AU  - Meijer, W.C.
TI  - Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.
JO  - Genome Announcements
PY  - 2015
SP  - e01377
EP  - e01315
VL  - 3
AB  - The lactic acid bacterium Streptococcus thermophilus is widely used for the fermentation of
AB  - dairy products. Here, we present the draft genome sequence of S.
AB  - thermophilus C106 isolated from an artisanal cheese produced in the countryside
AB  - of Ireland.
ER  -

TY  - JOUR
AU  - Welsh, A.J.
AU  - Halford, S.E.
AU  - Scott, D.J.
TI  - Analysis of Type II restriction endonucleases that interact with two recognition sites.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 297
EP  - 317
VL  - 14
AB  - Many students of molecular biology know for certain that the Type II restriction endonucleases
AB  - are dimeric proteins that recognize a palindromic DNA sequence, 4-8 bp (base pairs) long, and
AB  - cut this single sequence with exquisite specificity.  This idea is also propagated by many
AB  - text-books and commonly-used laboratory manuals in molecular biology.  Like most
AB  - generalizations, it is in fact wrong.  The Type II restriction enzymes encompass not only
AB  - dimeric proteins but also monomers, tetramers and higher assemblies.  Their recognition
AB  - sequences are not always unique palindromes but can instead be degenerate, discontinuous or
AB  - asymmetric sequences.  The sites at which they cleave the DNA are not necessarily within the
AB  - recognition sequence.  Many cleave the DNA at fixed positions several bp away from their
AB  - recognition sequence.  Most excitingly, many of the Type II enzymes have to interact with two
AB  - copies of their recognition sites before they can cleave DNA.  When these enzymes bind two
AB  - sites in the same DNA molecule, the intervening DNA is sequestered in a loop.  DNA-looping
AB  - interactions play central roles in many genetic processes, such as replication, recombination
AB  - and transcription, but these processes are often difficult to study.  In contrast, the
AB  - reactions of restriction enzymes can be monitored by a variety of simple techniques, so these
AB  - enzymes make good tools for analyzing the nature of long-range interactions between distant
AB  - DNA sites.  Indeed, the restriction enzymes that act at two DNA sites have become one of the
AB  - principal paradigms for studying such interactions.
ER  -

TY  - JOUR
AU  - Welsh, E.A.
AU  - Liberton, M.
AU  - Stockel, J.
AU  - Loh, T.
AU  - Elvitigala, T.
AU  - Wang, C.
AU  - Wollam, A.
AU  - Fulton, R.S.
AU  - Clifton, S.W.
AU  - Jacobs, J.M.
AU  - Aurora, R.
AU  - Ghosh, B.K.
AU  - Sherman, L.A.
AU  - Smith, R.D.
AU  - Wilson, R.K.
AU  - Pakrasi, H.B.
TI  - The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2008
SP  - 15094
EP  - 15099
VL  - 105
AB  - Unicellular cyanobacteria have recently been recognized for their contributions to nitrogen
AB  - fixation in marine environments, a function
AB  - previously thought to be filled mainly by filamentous cyanobacteria such
AB  - as Trichodesmium. To begin a systems level analysis of the physiology of
AB  - the unicellular N(2)-fixing microbes, we have sequenced to completion the
AB  - genome of Cyanothece sp. ATCC 51142, the first such organism. Cyanothece
AB  - 51142 performs oxygenic photosynthesis and nitrogen fixation, separating
AB  - these two incompatible processes temporally within the same cell, while
AB  - concomitantly accumulating metabolic products in inclusion bodies that are
AB  - later mobilized as part of a robust diurnal cycle. The 5,460,377-bp
AB  - Cyanothece 51142 genome has a unique arrangement of one large circular
AB  - chromosome, four small plasmids, and one linear chromosome, the first
AB  - report of a linear element in the genome of a photosynthetic bacterium. On
AB  - the 429,701-bp linear chromosome is a cluster of genes for enzymes
AB  - involved in pyruvate metabolism, suggesting an important role for the
AB  - linear chromosome in fermentative processes. The annotation of the genome
AB  - was significantly aided by simultaneous global proteomic studies of this
AB  - organism. Compared with other nitrogen-fixing cyanobacteria, Cyanothece
AB  - 51142 contains the largest intact contiguous cluster of nitrogen
AB  - fixation-related genes. We discuss the implications of such an
AB  - organization on the regulation of nitrogen fixation. The genome sequence
AB  - provides important information regarding the ability of Cyanothece 51142
AB  - to accomplish metabolic compartmentalization and energy storage, as well
AB  - as how a unicellular bacterium balances multiple, often incompatible,
AB  - processes in a single cell.
ER  -

TY  - JOUR
AU  - Wemheuer, F.
AU  - Hollensteiner, J.
AU  - Poehlein, A.
AU  - Granzow, S.
AU  - Daniel, R.
AU  - Vidal, S.
AU  - Wemheuer, B.
TI  - Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.
JO  - Genome Announcements
PY  - 2017
SP  - e00086
EP  - e00017
VL  - 5
AB  - Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of
AB  - Festuca rubra L. Functional annotation of the draft genome (7.1 Mb)
AB  - revealed 6,272 predicted protein-encoding genes. The genome provides insights
AB  - into the biocontrol and plant growth-promoting potential of P. putida GM4FR.
ER  -

TY  - JOUR
AU  - Wemheuer, F.
AU  - Hollensteiner, J.
AU  - Poehlein, A.
AU  - Liesegang, H.
AU  - Daniel, R.
AU  - Wemheuer, B.
TI  - Draft Genome Sequence of the Endophyte Bacillus mycoides Strain GM6LP Isolated from Lolium perenne.
JO  - Genome Announcements
PY  - 2018
SP  - e00011
EP  - e00018
VL  - 6
AB  - Bacillus mycoides GM6LP is an endophyte isolated from plant tissues of Lolium perenne L. Here,
AB  - we report its draft genome sequence (6.2 Mb), which contains 96
AB  - contigs and 6,129 protein-coding genes. Knowledge about its genome will enable us
AB  - to evaluate the potential use of GM6LP as a plant growth-promoting bacterium.
ER  -

TY  - JOUR
AU  - Wemheuer, F.
AU  - Wemheuer, B.
AU  - Hollensteiner, J.
AU  - Daniel, R.
AU  - Poehlein, A.
TI  - Draft Genome Sequence of the Endophyte Paenibacillus sp. Strain GM2FR Isolated from Festuca rubra.
JO  - Genome Announcements
PY  - 2018
SP  - e00017
EP  - e00018
VL  - 6
AB  - Here, we report the 7.4-Mb draft genome sequence of Paenibacillus sp. strain GM2FR, an
AB  - endophytic bacterium isolated from aerial plant tissues of Festuca
AB  - rubra L. Genome analysis revealed 6,652 coding gene sequences and several gene
AB  - clusters involved in plant growth promotion, such as that for the siderophore
AB  - bacillibactin.
ER  -

TY  - JOUR
AU  - Wemhoff, S.
AU  - Meinhardt, F.
TI  - Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2013
SP  - 7805
EP  - 7819
VL  - 97
AB  - Bacillus pumilus mutants were generated by targeted deletion of a set of genes eventually
AB  - facilitating genetic handling and assuring biological containment. The
AB  - well-defined and stable mutants do not form functional endospores due to the
AB  - deletion of yqfD, an essential sporulation gene; they are affected in DNA repair,
AB  - as DeltauvrBA rendered them UV hypersensitive and, thus, biologically contained;
AB  - they are deficient for the uracil phosphoribosyl-transferase (Deltaupp), allowing
AB  - for 5-fluorouracil-based counterselection facilitating rapid allelic exchanges;
AB  - and they are readily transformable due to the deletion of the restrictase
AB  - encoding locus (DeltahsdR) of a type I restriction modification system.
AB  - Vegetative growth as well as extracellular enzyme production and secretion are in
AB  - no case affected. The combination of such gene deletions allows for development
AB  - of B. pumilus strains suited for industrial use and further improvements.
ER  -

TY  - JOUR
AU  - Wen, T.N.
AU  - Tung, P.H.
AU  - Chen, C.S.
TI  - Purification and some properties of a restriction endonuclease Ccy I from Clostridium cylindrosporum.
JO  - Bot. Bull. Acad. Sinica
PY  - 1989
SP  - 91
EP  - 98
VL  - 30
AB  - The restriction endonuclease CcyI has been purified to homogeneity from an
AB  - anaerobic bacterium, Clostridium cylindrosporum, by the procedures involving
AB  - streptomycin sulfate precipitation, ammonium sulfate fractionation and
AB  - chromatography on phosphocellulose, heparin-Sepharose 4 B and Ultrogel AcA 34.
AB  - This enzyme recognizes the sequence
AB  - 5'-^GATC-3'
AB  - 3' -CTAG-5^' and cleaves the phosphodiester bond at the 5' side of G as
AB  - indicated.  Several isoschizomers of CcyI have been found previously which
AB  - include Sau3AI and MboI.  Optimal NaCl concentration, pH and temperature for
AB  - the enzyme to digest lambda DNA was 100 mM, 7.0-8.0 and 30-35C, respectively.
AB  - CcyI is both acid-labile and heat-labile.
ER  -

TY  - JOUR
AU  - Wende, W.
AU  - Grindl, W.
AU  - Christ, F.
AU  - Pingoud, A.
AU  - Pingoud, V.
TI  - Binding, bending and cleavage of DNA substrates by the homing endonuclease PI-SceI.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 4123
EP  - 4132
VL  - 24
AB  - To characterize the interaction between the homing endonuclease PI-SceI and DNA, we prepared
AB  - different DNA substrates containing the natural recognition sequence or parts thereof.
AB  - Depending on the nature of the substrates, efficient cleavage is observed with a DNA
AB  - containing ~30 bp of the natural recognition sequence using supercoiled plasmids, ~40-50 bp
AB  - using linearized plasmids and >50 bp using synthetic double-stranded oligodeoxynucleotides.
AB  - Cleavage of supercoiled plasmids occurs without accumulation of the nicked intermediate.  In
AB  - the presence of Mn2+ DNA cleavage by PI-SceI is more efficient than with Mg2+ and already
AB  - occurs with substrates containing a shorter part of the recognition sequence.  The
AB  - requirements for strong binding are less stringent: a 35 bp oligodeoxynucleotide which is not
AB  - cleaved is bound as firmly as other longer oligodeoxynucleotides.  PI-SceI binds with high
AB  - affinity to one of its cleavage products, a finding which may explain why PI-SceI hardly shows
AB  - enzymatic turnover in vitro.  Upon binding, two complexes are formed, which differ in the
AB  - degree of bending (45o versus 75o).  According to a phasing analysis bending is directed into
AB  - the major groove.  Strong binding, not, however, cleavage is also observed with the
AB  - genetically engineered enzymatically inactive variant comprising amino acids 1-277.  Models
AB  - for binding and cleavage of DNA by PI-SceI are discussed based on these results.
ER  -

TY  - JOUR
AU  - Wende, W.
AU  - Pingoud, A.
TI  - Cloning, overexpression, purification and characterization of the VDE homing endonuclease.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1994
SP  - S110
EP  - S110
VL  - 375
AB  - Homing endonucleases propagate their encoding sequences (introns) from a donor
AB  - (intron-containing) allele into an intronless recipient allele. Only the intronless allele
AB  - contains the specific target sequence. The homing endonuclease cleaves the DNA on both
AB  - strands, and the repair of the intronless allele results in the insertion of the sequence
AB  - encoding the homing endonuclease. The target sites are generally asymmetric and long, ranging
AB  - from 15 bp to 40 bp. The VDE (VMA1-derived endonuclease) cleaves intronless yeast genomic DNA
AB  - only at a single site. Thus these enzymes are extremely rare cutters and, therefore, important
AB  - tools for chromosomal mapping, sequencing and gene targeting. In order to study the
AB  - DNA/protein interactions of this interesting class of enzymes, we constructed a His6-tagged
AB  - variant of the VDE from Saccharomyces cervisiae and overexpressed it in E. coli. The affinity
AB  - tag allows for a rapid purification to near homogeneity. The protein sequence of our VDE
AB  - differs in 3 positions from the published sequence. Analysis of circular dichroism spectra
AB  - suggests that the protein consists of 43% alpha-helix and 48% beta-sheet. The specific
AB  - activity of the His6-tagged VDE variant is comparable with the native protein. Preliminary
AB  - studies show that the minimal recognition site is larger than the published one. We are
AB  - currently engaged in DNA binding and cleavage studies with the His6-VDE, the results of which
AB  - will be presented.
ER  -

TY  - JOUR
AU  - Wende, W.
AU  - Schottler, S.
AU  - Grindl, W.
AU  - Christ, F.
AU  - Steuer, S.
AU  - Noel, A.J.
AU  - Pingoud, V.
AU  - Pingoud, A.
TI  - A mutational analysis of DNA binding and cleavage by the homing endonuclease PI-SceI.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 1054
EP  - 1064
VL  - 34
AB  - We have carried out an extensive mutational analysis of PI-SceI, the best studied intein-like
AB  - homing endonuclease of the LAGLIDADG family,
AB  - to find out which amino acid residues are involved in substrate binding
AB  - and processing. Our analysis was focused on domain I, in which two
AB  - regions were shown to be in contact with DNA, and on domain II, in
AB  - which the amino acid residues making up catalytic centers I and II were
AB  - identified and their role in catalysis investigated. As a result of our
AB  - comprehensive mutational analysis a model is presented for DNA binding
AB  - and cleavage by PI-SceI.
ER  -

TY  - JOUR
AU  - Wende, W.
AU  - Stahl, F.
AU  - Pingoud, A.
TI  - The production and characterization of artificial heterodimers of the restriction endonuclease EcoRV.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1996
SP  - 625
EP  - 632
VL  - 377
AB  - A novel approach to studying the inter- and intrasubunit communication required for the
AB  - activity of homodimeric proteins is described. It was developed for the restriction
AB  - endonuclease EcoRV, but should also be useful for other homodimeric enzymes.  Two ecorV genes
AB  - encoding different EcoRV mutants are coexpressed in the same Escherichia coli cell leading to
AB  - homo- and heterodimeric variants of the enzyme.  The two ecorV genes carry either a 5'
AB  - extension coding for the glutathione-S-transferase or a His6-tag.  The EcoRV heterodimer
AB  - produced in vivo is separated from the two EcoRV homodimers and purified to homogeneity by
AB  - affinity chromatography.  Purified EcoRV heterodimers are stable and are not subject to
AB  - reassortment of the subunits.  To investigate the interdependence of the two catalytic
AB  - centers, EcoRV heterodimers consisting of one subunit with wild type sequence and one subunit
AB  - with amino acid substitutions in the PD...(D/E)XK motif, characteristic for the active sites
AB  - of many restriction endonucleases, were produced.  While the homodimeric EcoRV active site
AB  - mutants are catalytically inactive, the heterodimeric EcoRV variants with one active and one
AB  - inactive catalytic center display a twofold reduced activity toward oligodeoxynucleotide
AB  - substrates compared to the wild type, and preferentially nick supercoiled plasmid DNA.  From
AB  - these results we conclude that in the wild type enzyme both catalytic centers function
AB  - independently of each other.
ER  -

TY  - JOUR
AU  - Weng, S.F.
AU  - Luo, A.C.
AU  - Lin, C.J.
AU  - Tseng, T.T.
TI  - High-Quality Genome Sequence of Xanthomonas axonopodis pv. glycines Strain 12609  Isolated in Taiwan.
JO  - Genome Announcements
PY  - 2017
SP  - e01695
EP  - e01616
VL  - 5
AB  - The genomic sequence was determined for Xanthomonas axonopodis pv. glycines strain 12609,
AB  - isolated in Taiwan. Based on the genome sequence, we predicted the
AB  - encoded genes, rRNA, tRNA, a plasmid sequence, secretion systems, cyclic GMP- and
AB  - cyclic di-GMP-mediated pathways, and the gene cluster rpfABCHGDE (regulation of
AB  - pathogenicity factor).
ER  -

TY  - JOUR
AU  - Weng, X.B.
AU  - Mi, Z.H.
AU  - Wang, C.X.
AU  - Zhu, J.M.
TI  - Draft Genome Sequence of a Klebsiella pneumoniae Strain (New Sequence Type 2357)  Carrying Tn3926.
JO  - Genome Announcements
PY  - 2016
SP  - e00986
EP  - e00916
VL  - 4
AB  - We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase-producing
AB  - sequence type 2357 (ST2357) strain, NB60, which contains
AB  - drug-resistant genes encoding resistance to beta-lactams, fluoroquinolones,
AB  - aminoglycosides, trimethoprim-sulfamethoxazole, colistin, macrolides, and
AB  - tetracycline. Strain NB60 was isolated from human blood, making it an important
AB  - tool for studying K. pneumoniae pathogenesis.
ER  -

TY  - JOUR
AU  - Weng, X.B.
AU  - Mi, Z.H.
AU  - Wang, C.X.
AU  - Zhu, J.M.
TI  - Draft Genome Sequence of Uropathogenic Escherichia coli Strain NB8.
JO  - Genome Announcements
PY  - 2016
SP  - e00944
EP  - e00916
VL  - 4
AB  - Escherichia coli NB8 is a clinical pyelonephritis isolate. Here, we report the draft genome
AB  - sequence of uropathogenic E. coli NB8, which contains drug
AB  - resistance genes encoding resistance to beta-lactams, aminoglycosides,
AB  - quinolones, macrolides, colistin, sulfonamide-trimethoprim, and tetracycline. NB8
AB  - infects the kidney and bladder, making it an important tool for studying E. coli
AB  - pathogenesis.
ER  -

TY  - JOUR
AU  - Wenner, J.R.
AU  - Bloomfield, V.A.
TI  - A novel kinetic mechanism for the cleavage of plasmid DNA by the restriction enzyme EcoRV accounts for nonspecific binding.
JO  - J. Biophys.
PY  - 1997
SP  - A98
EP  - A98
VL  - 72
AB  - The cleavage of pBR322 by the restriction enzyme EcoRV was assayed by quantifyingDNA bands on
AB  - agarose gels.  The nonlinear reaction kinetics were fit by the mechanism.  Good fits were
AB  - obtained only if nonspecific binding and slow product release were included.  A key parameter
AB  - is the fraction of total binding that results in specific binding.  EcoRV must cycle through
AB  - the nonspecific binding process a number of times before the specific site is located.  This
AB  - kinetic picture will be used to measure how macromolecular crowding with inert agents affects
AB  - the rate at which EcoRV finds its specific cleavage site.
ER  -

TY  - JOUR
AU  - Wenner, J.R.
AU  - Bloomfield, V.A.
TI  - Osmotic pressure effects on EcoRV cleavage and binding.
JO  - J. Biomol. Struct. Dyn.
PY  - 1999
SP  - 461
EP  - 471
VL  - 17
AB  - Investigations of DNA binding proteins frequently measure pH and salt dependence, but
AB  - relatively few studies measure protein binding in high concentrations of small molecules often
AB  - found in vivo. We have measured kinetics of the restriction enzyme EcoRV in concentrated
AB  - solutions of three small cosolvents that produce osmotic pressures from 0.25 to 2.5 mol/kg (6
AB  - to 62 atm or water activity of 0.995 to 0.956). We have correlated DNA cleavage and binding
AB  - parameters with four solution parameters (dielectric constant, viscosity, water concentration,
AB  - and water activity). We found that the responses of maximum velocity (Vmax) and the
AB  - dissociation constant for nonspecific binding (Kd,ns) best correlate with water activity. The
AB  - Michaelis constant (Km) correlates with both water activity and solution viscosity, the latter
AB  - due to the highly dilute reactant concentrations, which make enzyme-substrate combination
AB  - diffusion limited. Dielectric constant does not influence any of the kinetic parameters, which
AB  - is consistent with a view that protein and DNA are preferentially hydrated, and excluded
AB  - solutes cannot affect the local dielectric constant.
ER  -

TY  - JOUR
AU  - Wenner, J.R.
AU  - Bloomfield, V.A.
TI  - Buffer effects on EcoRV kinetics as measured by fluorescent staining and digital imaging of plasmid cleavage.
JO  - Anal. Biochem.
PY  - 1999
SP  - 201
EP  - 212
VL  - 268
AB  - We have developed a protocol to quantify polymer DNA cleavage which replaces the traditional
AB  - radiolabeling and scintillation counting with fluorescent staining and digital imaging. This
AB  - procedure offers high sensitivity, speed, and convenience, while avoiding waste and error
AB  - associated with traditional 32P radiolabeling. This protocol was used to measure cleavage of
AB  - pBR322 plasmid DNA by EcoRV, a type II restriction enzyme. EcoRV was found to exhibit an order
AB  - of magnitude difference in binding in two apparently similar buffers used in previous
AB  - investigations. To determine the origin of this effect, we measured reaction kinetics in
AB  - buffers of different chemical nature and concentration: Tris, bis-Tris propane, Tes, Hepes,
AB  - and cacodylate. We found that buffer concentration and identity had significant effects on
AB  - EcoRV reaction velocity through large changes in specific binding and nonspecific binding
AB  - (reflected in the Michaelis constant Km and the dissociation constant for nonspecific binding
AB  - Kns). There were only small changes in Vmax. The source of the buffer effect is the protonated
AB  - amines common to many pH buffers. These buffer cations likely act as counterions screening DNA
AB  - phosphates, where both the protonated buffer structure and concentration affect enzyme binding
AB  - strength. It appears that by choosing anionic buffers or zwitterionic buffers with a buried
AB  - positive charge, buffer influence on the protein binding to DNA can be largely eliminated.
ER  -

TY  - JOUR
AU  - Wenren, L.M.
AU  - Sullivan, N.L.
AU  - Cardarelli, L.
AU  - Septer, A.N.
AU  - Gibbs, K.A.
TI  - Two Independent Pathways for Self-Recognition in Proteus mirabilis Are Linked by Type VI-Dependent Export.
JO  - MBio
PY  - 2013
SP  - e00374
EP  - e00313
VL  - 4
AB  - ABSTRACT Swarming colonies of the bacterium Proteus mirabilis are capable of
AB  - self-recognition and territorial behavior. Swarms of independent P. mirabilis
AB  - isolates can recognize each other as foreign and establish a visible boundary
AB  - where they meet; in contrast, genetically identical swarms merge. The ids genes,
AB  - which encode self-identity proteins, are necessary but not sufficient for this
AB  - territorial behavior. Here we have identified two new gene clusters: one (idr)
AB  - encodes rhs-related products, and another (tss) encodes a putative type VI
AB  - secretion (T6S) apparatus. The Ids and Idr proteins function independently of
AB  - each other in extracellular transport and in territorial behaviors; however,
AB  - these self-recognition systems are linked via this type VI secretion system. The
AB  - T6S system is required for export of select Ids and Idr proteins. Our results
AB  - provide a mechanistic and physiological basis for the fundamental behaviors of
AB  - self-recognition and territoriality in a bacterial model system. IMPORTANCE Our
AB  - results support a model in which self-recognition in P. mirabilis is achieved by
AB  - the combined action of two independent pathways linked by a shared machinery for
AB  - export of encoded self-recognition elements. These proteins together form a
AB  - mechanistic network for self-recognition that can serve as a foundation for
AB  - examining the prevalent biological phenomena of territorial behaviors and
AB  - self-recognition in a simple, bacterial model system.
ER  -

TY  - JOUR
AU  - Wentz, T.G.
AU  - Muruvanda, T.
AU  - Lomonaco, S.
AU  - Thirunavukkarasu, N.
AU  - Hoffmann, M.
AU  - Allard, M.W.
AU  - Hodge, D.R.
AU  - Pillai, S.P.
AU  - Hammack, T.S.
AU  - Brown, E.W.
AU  - Sharma, S.K.
TI  - Closed Genome Sequence of Chryseobacterium piperi Strain CTM(T)/ATCC BAA-1782, a  Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences.
JO  - Genome Announcements
PY  - 2017
SP  - e01296
EP  - e01217
VL  - 5
AB  - Clostridial neurotoxins, including botulinum and tetanus neurotoxins, are among the deadliest
AB  - known bacterial toxins. Until recently, the horizontal mobility of
AB  - this toxin gene family appeared to be limited to the genus Clostridium We report
AB  - here the closed genome sequence of Chryseobacterium piperi, a Gram-negative
AB  - bacterium containing coding sequences with homology to clostridial neurotoxin
AB  - family proteins.
ER  -

TY  - JOUR
AU  - Wentz, T.G.
AU  - Yao, K.
AU  - Schill, K.M.
AU  - Reddy, N.R.
AU  - Skinner, G.E.
AU  - Morrissey, T.R.
AU  - Wang, Y.
AU  - Muruvanda, T.
AU  - Manickam, G.
AU  - Pillai, C.A.
AU  - Thirunavukkarasu, N.
AU  - Hoffmann, M.
AU  - Hammack, T.S.
AU  - Brown, E.W.
AU  - Allard, M.W.
AU  - Sharma, S.K.
TI  - Closed Genome Sequence of Clostridium botulinum Strain CFSAN064329 (62A).
JO  - Genome Announcements
PY  - 2018
SP  - e00528
EP  - e00518
VL  - 6
AB  - Clostridium botulinum is a strictly anaerobic, Gram-positive, spore-forming bacterium that
AB  - produces botulinum neurotoxin, a potent and deadly proteinaceous
AB  - exotoxin. Clostridium botulinum strain CFSAN064329 (62A) produces an A1
AB  - serotype/subtype botulinum neurotoxin and is frequently utilized in food
AB  - challenge and detection studies. We report here the closed genome sequence of
AB  - Clostridium botulinum strain CFSAN064329 (62A).
ER  -

TY  - JOUR
AU  - Wentzell, L.M.
AU  - Halford, S.E.
TI  - DNA looping by the SfiI restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 433
EP  - 444
VL  - 281
AB  - The SfiI endonuclease has to interact with two copies of its recognition sequence before it
AB  - can cleave DNA.  To demonstrate that the reaction of SfiI on a DNA with two sites involves the
AB  - formation of a DNA loop, and to characterize the looping interactions on supercoiled and
AB  - linear DNA, a series of plasmids was constructed with lengths of DNA between two SfiI sites
AB  - varying from 104 to 211 bp.  Both supercoiled and linear forms of each DNA were tested as
AB  - substrates for SfiI.  The reactions were monitored from the rates of DNA cleavage and from the
AB  - generation of partially cleaved products, the latter indicating loop disruption before
AB  - cleavage of both sites.  On both supercoiled and linear DNA, the stabilities of the complexes
AB  - spanning two SfiI sites varied in sinusoidal fashion with the distance between the sites, in
AB  - the manner characteristic of a process governed by the helical periodicity of DNA.  In all
AB  - cases, the looping interaction was stabilized by DNA supercoiling.  The sinusoidal variation
AB  - from SfiI reactions on supercoiled DNA at 50 C yielded a helical repeat of about 11.5
AB  - base-pairs per turn.
ER  -

TY  - JOUR
AU  - Wentzell, L.M.
AU  - Nobbs, T.J.
AU  - Halford, S.E.
TI  - The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence.
JO  - J. Mol. Biol.
PY  - 1995
SP  - 581
EP  - 595
VL  - 248
AB  - The SfiI endonuclease cleaves DNA by a mechanism that differs from other restriction enzymes.
AB  - While most restriction enzymes are dimeric proteins that interact with a single DNA site, SfiI
AB  - exists in solution as a tetramer and it appears to interact with two copies of its recognition
AB  - sequence before it can cleave DNA. Its primary reaction is then to cut both strands at both
AB  - sites in a concerted process. The two sites can be on either the same or different DNA
AB  - molecules, so SfiI provides a test system for long-range interactions on DNA. On either
AB  - supercoiled or linear DNA with two sites separated by 1 kb, the bridging interaction between
AB  - the sites is an intramolecular event: the majority of the DNA is converted directly to
AB  - products cleaved at both sites, bypassing intermediates cut at one site. Sites on separate DNA
AB  - molecules, or two sites on linear DNA several kb apart, engage in an intermolecular
AB  - interaction prior to cleavage. The interaction between two DNA molecules with one site on each
AB  - is impeded by supercoiling in both partners but is permitted when one partner is linear: it
AB  - may require reptation of one DNA through another. SfiI reactions have marked similarities to
AB  - some of the reactions catalysed by site-specific recombination enzymes.
ER  -

TY  - JOUR
AU  - Wentzell, L.M.
AU  - Oram, M.
AU  - Halford, S.E.
TI  - Purification and characterisation of the SfiI restriction endonuclease.
JO  - Biochem. Soc. Trans.
PY  - 1994
SP  - 302S
EP  - 302S
VL  - 22
AB  - Type II restriction endonucleases recognise specific DNA sequences and cleave at a defined
AB  - point within or close to that sequence. They require Mg2+ as a cofactor. In the presence of
AB  - Mg2+ they cut their recognition sites at least a million times faster than at any other DNA
AB  - sequence. At present over 2400 different type II restriction enzymes have been identified
AB  - representing over 188 different specificities. Most type II enzymes cleave DNA within
AB  - symmetrical sequences, termed palindromes. These are usually continuous sequences of 4 or 6
AB  - base pairs, or fairly rarely 8 base pairs. Some of these enzymes cleave at unique DNA
AB  - sequences as for EcoRV (GATATC), while others recognize degenerate sequences as for HindII
AB  - (GTYRAC). Other enzymes, SfiI being one of them, recognize discontinuous sequences in which
AB  - one or more unspecified bases interrupt the sequence of specified bases. A further group of
AB  - enzymes known as type IIs, recognize asymmetric sequences and cleave at a fixed point from
AB  - that sequence.
ER  -

TY  - JOUR
AU  - Wenz, C.
AU  - Hahn, M.
AU  - Pingoud, A.
TI  - Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site.
JO  - Biochemistry
PY  - 1998
SP  - 2234
EP  - 2242
VL  - 37
AB  - The present work describes mutants of the restriction enzyme EcoRV that discriminate very
AB  - efficiently between oligodeoxynucleotide substrates with an EcoRV recognition sequence in
AB  - different sequence contexts.  All of these EcoRV variants harbor substitutions at position
AB  - 226, where in the cocrystal structure of the specific EcoRV/DNA complex an arginine contacts
AB  - the backbone of the DNA substrate upstream of the recognition sequence, and cleave an
AB  - oligodeoxynucleotide with an EcoRV site in a nonflexible sequence context (the recognition
AB  - site being flanked by runs of A and T) with much higher catalytic efficiency (kcat/Km) than an
AB  - oligodeoxynucleotide with an EcoRV site in a flexible sequence context (the recognition site
AB  - being flanked by runs of AT), in contrast to the wild-type enzyme, that cleaves both
AB  - substrates with the same catalytic efficiency.  Steady-state and single-turnover kinetics
AB  - indicate that the enhanced selectivity of the mutants is due to the catalytic step of the
AB  - reaction.  It is possible to enhance the discriminatory power of these EcoRV variants through
AB  - the choice of appropriate reaction conditions, in particular low salt concentration and low
AB  - reaction temperatures.  It must be emphasized that the enhanced selectivity of these EcoRV
AB  - variants toward EcoRV sites in a flexible and nonflexible sequence context, respectively, is
AB  - not only seen with oligodeoxynucleotides, but also with plasmid substrates.
ER  -

TY  - JOUR
AU  - Wenz, C.
AU  - Jeltsch, A.
AU  - Pingoud, A.
TI  - Probing the indirect readout of the restriction enzyme EcoRV.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 5565
EP  - 5573
VL  - 271
AB  - According to the crystal structure of the specific EcoRV.DNA complex, not only the functional
AB  - groups of the nucleobases but also the phosphate groups of the DNA backbone are contacted by
AB  - the enzyme.  To examine the contribution of backbone contacts to substrate recognition and
AB  - catalysis by EcoRV, we exchanged 12 amino acids residues located close to phosphate groups by
AB  - site-directed mutagenesis.  We purified the resulting EcoRV mutants and characterized them
AB  - with respect to their DNA binding and cleavage activity.  According to our steady state
AB  - kinetic analysis, there are strong interactions between three basic amino acid residues
AB  - (Lys-119, Arg-140, and Arg-226) and the phosphate backbone that support specific binding
AB  - presumably by inducing and maintaining the kinked conformation of the DNA observed in the
AB  - specific EcoRV.DNA complex.  These contacts are important in both the ground state and the
AB  - transition state.  Other, uncharged residues (Thr-93 and Ser-112), which could be involved in
AB  - hydrogen bonds to the phosphate groups, are needed primarily to stabilize the transition
AB  - state.  An especially important amino acid residue is Thr-37, which seems to couple
AB  - recognition to catalysis by indirect readout.
ER  -

TY  - JOUR
AU  - Wenz, C.
AU  - Pingoud, A.
TI  - Probing the indirect readout of the restriction enzyme EcoRV; mutational analysis of contacts to the DNA-backbone.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S168
EP  - S168
VL  - 376
AB  - Specific recognition of DNA does not only include interactions between the protein and the
AB  - bases (direct readout), but also contacts to the phosphate groups of the DNA, which means that
AB  - the protein also recognizes a specific, sequence dependent conformation of the phosphodiester
AB  - backbone (indirect readout).  To examine contribution of phosphate contacts for the
AB  - recognition process we have carried out a mutational analysis: The amino acid residues which
AB  - are, according to the crystal structure of the specific EcoRV/DNA complex, in the vicinity of
AB  - phosphate groups of the DNA and bear functional groups suited for hydrogen bonds or ionic
AB  - interactions, were exchanged to Ala (Arg, Lys, Ser, Thr) or to Phe (Tyr) via PCR-mutagenesis.
AB  - All mutants displayed residual activity with plasmid-DNA and oligodeoxynucleotide substrates
AB  - and could, therefore, be analysed in terms of specific binding (with Ca2+ ions), steady state
AB  - and single turnover kinetics, linear diffusion and selectivity towards modified
AB  - oligodeoxynucleotides and various substrates with different sequences flanking the EcoRV-site
AB  - GAT/ATC- (the arrow denotes the position of phosphodiester bond cleavage).  Several mutants
AB  - displayed an altered selectivity for substrates with different flanking sequences, and/or a
AB  - different ability to bind specifically to DNA and to diffuse along the DNA.  These results
AB  - suggest that EcoRV makes use of phosphate contacts to locate EcoRV sites on macromolecular DNA
AB  - by linear diffusion and to attack different EcoRV sites more or less evenly.  Furthermore, our
AB  - results indicate that it should be possible to engineer mutants with an expanded specificity
AB  - by taking advantage of an altered selectivity towards substrates with different flanking
AB  - sequences.
ER  -

TY  - JOUR
AU  - Wenz, C.
AU  - Pingoud, A.
TI  - Protein engineering of the restriction endonuclease EcoRV.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1994
SP  - S110
EP  - S110
VL  - 375
AB  - Specific recognition of DNA does not only include interactions between the protein and the
AB  - bases (direct readout), but also contacts to the phosphate groups of the DNA: the protein
AB  - recognizes a specific, sequence dependent conformation of the phosphodiester backbone
AB  - (indirect readout). Consequently, it should be possible to alter the specificity of a
AB  - restriction enzyme through manipulation of the phosphate contacts. Our approach to modulate
AB  - the specificity of EcoRV is to delete functional groups of amino acids which are in direct
AB  - contact with the phosphate groups of the DNA. Some of these EcoRV variants display a markedly
AB  - changed specificity, e.g. the mutant Arg140 -> Ala, which shows in comparison to the wild type
AB  - enzyme a strong preference for EcoRV sites with AT-rich flanking sequences. However, this is
AB  - accompanied with a decrease in specific activity. It remains to be seen, whether by other
AB  - and/or additinoal mutations the selectivity can be further increased without losing too much
AB  - of the activity of the wild type enzyme.
ER  -

TY  - JOUR
AU  - Wenz, C.
AU  - Selent, U.
AU  - Wende, W.
AU  - Jeltsch, A.
AU  - Wolfes, H.
AU  - Pingoud, A.
TI  - Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates.
JO  - Biochim. Biophys. Acta
PY  - 1994
SP  - 73
EP  - 80
VL  - 1219
AB  - According to the crystal structure analysis of a specific EcoRV/DNA complex, the thymine
AB  - residues of the recognition sequence -GATATC- are not in direct contact with any amino acid
AB  - residue of the protein. However, several amino acid residues are sufficiently close that it
AB  - seemed worthwhile trying to create variants of EcoRV with altered specificity by site-directed
AB  - mutagenesis. Guided by molecular modelling we have replaced Asn-188 in the catalytic center of
AB  - EcoRV by Gln to produce a mutant with a relative preference (compared to wild type EcoRV) for
AB  - substrates in which one thymine of the recognition sequence is replaced by uracil. We have
AB  - purified and characterized the resulting N188Q mutant. The selectivity value for the
AB  - engineered enzyme (the ratio of the kcat/KM values for -GATAUC- versus -GATATC-) differs from
AB  - that of the wild type enzyme by a factor of more than 200.
ER  -

TY  - JOUR
AU  - Wenzel, C.
AU  - Guschlbauer, W.
TI  - Dam methyltransferase from Escherichia coli:  sequence of a peptide segment involved in S-adenosyl-methionine binding.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 4604
EP  - 4609
VL  - 21
AB  - DNA adenine methyltransferase (Dam methylase) has been crosslinked with its cofactor
AB  - S-adenosyl methionine (AdoMet) by UV irradiation. About 3% of the enzyme was radioactively
AB  - labeled after the crosslinking reaction performed either with (methyl-3H)-AdoMet or with
AB  - (carboxy-14C)-AdoMet. Radiolabelled peptides were purified after trypsinolysis by high
AB  - performance liquid chromatography in two steps. They could not be sequenced due to radiolysis.
AB  - Therefore we performed the same experiment using non-radioactive AdoMet and were able to
AB  - identify the peptide modified by the crosslinking reaction by comparison of the separation
AB  - profiles obtained from two analytical control experiments performed with 3H-AdoMet and Dam
AB  - methylase without crosslink, respectively. This approach was possible due to the high
AB  - reproducibility of the chromatography profiles. In these three experiments only one
AB  - radioactively labelled peptide was present in the tryptic digestions of the crosslinked
AB  - enzyme. Its sequence was found to be XA-GGK, corresponding to amino acids 10 - 14 of Dam
AB  - methylase. The non-identified amino acid in the first sequence cycle should be a tryptophan,
AB  - which is presumably modified by the crosslinking reaction. The importance of this region near
AB  - the N-terminus for the structure and function of the enzyme was also demonstrated by
AB  - proteolysis and site-directed mutagenesis experiments.
ER  -

TY  - JOUR
AU  - Wenzel, C.
AU  - Moulard, M.
AU  - Lobner-Olesen, A.
AU  - Guschlbauer, W.
TI  - Crosslinking of Dam methyltransferase with S-adenosyl-methionine.
JO  - FEBS J.
PY  - 1991
SP  - 147
EP  - 151
VL  - 280
AB  - Highly purified DNA-adenine methyltransferase was irradiated in the presence of different
AB  - concentrations of radiolabelled S-adenosyl-methionine (AdoMet) with a conventional Mineralight
AB  - UV-lamp from several minutes up to 1 h while incubating in ice. Incorporation of radioactivity
AB  - was monitored by electrophoresis of the crosslink between S-adenosyl-methionine and Dam
AB  - methylase on SDS-polyacrylamide gels followed by fluorography. Crosslinking reached a maximum
AB  - in presence of 10 uM S-adenosyl-methionine; it was inhibited in the presence of substances
AB  - which competitively inhibit methylation of DNA by DAM methylase, like sinefungin or
AB  - S-adenosyl-homocysteine, but not in the presence of non-inhibitors like ATP or
AB  - S-isobutyl-adenosine. The crosslink obtained was resistant against a wide range of even
AB  - drastic conditions commonly used in protein and peptide chemistry. Proteins, which do not bind
AB  - S-adenosyl-methionine, as well as heat inactivated Dam methylase were not photolabelled. After
AB  - limited proteolysis the radioactive label appeared only in certain of the peptides obtrained.
AB  - From Western blots carried out with polyclonal antibodies produced against a synthetic peptide
AB  - corresponding in its sequence to amino acids 92-106 of the Dam methylase, the crosslinking of
AB  - AdoMet could be tentatively mapped at a position after amino acid 106.
ER  -

TY  - JOUR
AU  - Wenzlau, J.M.
AU  - Saldanha, R.J.
AU  - Butow, R.A.
AU  - Perlman, P.S.
TI  - A latent intron-encoded maturase is also an endonuclease needed for intron mobility.
JO  - Cell
PY  - 1989
SP  - 421
EP  - 430
VL  - 56
AB  - Some yeast mitochondrial introns encode proteins that promote either splicing (maturases) or
AB  - intron propagation via gene conversion (the fit1 endonuclease). We surveyed introns in the
AB  - cox1 gene for their ability to engage in gene conversion and found that the group I intron,
AB  - aI4alpha, was efficiently transmitted to genes lacking it. An endonucleolytic cleavage is
AB  - detectable in recipient DNA molecules near the site of intron insertion in vivo and in vitro.
AB  - Conversion is dependent on an intact aI4alpha open reading frame. This intron product is a
AB  - latent maturase, but these data show that it is also a potent endonuclease involved in
AB  - recombination. Dual function proteins that cleave DNA and facilitate RNA splicing may have
AB  - played a pivotal role in the propagation and tolerance of introns.
ER  -

TY  - JOUR
AU  - Werbowy, O.
AU  - Boratynski, R.
AU  - Dekowska, A.
AU  - Kaczorowski, T.
TI  - Genetic analysis of maintenance of pEC156, a naturally occurring Escherichia coli plasmid that carries genes of the EcoVIII restriction-modification system.
JO  - Plasmid
PY  - 2015
SP  - 39
EP  - 50
VL  - 77
AB  - In the present study the role of the mechanisms responsible for maintenance of a  natural
AB  - plasmid pEC156, that carries genes of the EcoVIII
AB  - restriction-modification system was investigated. Analysis of this plasmid's
AB  - genetic content revealed the presence of genetic determinants suggesting two such
AB  - mechanisms. The first of them relies on site specific recombination utilizing the
AB  - Xer/cer molecular machinery, while the second involves a restriction-modification
AB  - system as an addiction module. Our analysis indicated that three factors affect
AB  - the maintenance of pEC156: (i) a cis-acting cer site involved in resolution of
AB  - plasmid multimers, (ii) a gene coding for EcoVIII endonuclease, and (iii) plasmid
AB  - copy number control. The lowest stability was observed with pEC156 derivatives
AB  - deprived of the cer site. Decreased stability of pEC156 derivatives was also
AB  - observed in E.coli strains deficient in genes coding for proteins involved in
AB  - plasmid multimer resolution (XerC, XerD, ArgR and PepA). A similar effect, but to
AB  - a much lesser extent was observed for the pEC156 derivative without a functional
AB  - gene coding for EcoVIII endonuclease. Our results indicate that the presence of
AB  - the cer site is more important for pEC156 stable maintenance than the presence of
AB  - a functional gene coding for EcoVIII endonuclease. In our work we also tested
AB  - maintenance of pEC156 possessing a ColE1-type replicon in bacteria belonging to
AB  - Enterobacteriaceae family. We have found that pEC156 was most stably maintained
AB  - in Enterobacter cloacae and Klebsiella oxytoca representing coli-type
AB  - enterobacteria. We have found that in all enterobacteria tested pEC156
AB  - derivatives deficient in the cer site were significantly less stably maintained
AB  - than cer(+) variants.
ER  -

TY  - JOUR
AU  - Werbowy, O.
AU  - Kaczorowski, T.
TI  - Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable  among Enterobacteria.
JO  - PLoS ONE
PY  - 2016
SP  - e0148355
EP  - e0148355
VL  - 11
AB  - Type II restriction-modification systems are ubiquitous in prokaryotes. Some of them are
AB  - present in naturally occurring plasmids, which may facilitate the spread
AB  - of these systems in bacterial populations by horizontal gene transfer. However,
AB  - little is known about the routes of their dissemination. As a model to study
AB  - this, we have chosen an Escherichia coli natural plasmid pEC156 that carries the
AB  - EcoVIII restriction modification system. The presence of this system as well as
AB  - the cis-acting cer site involved in resolution of plasmid multimers determines
AB  - the stable maintenance of pEC156 not only in Escherichia coli but also in other
AB  - enterobacteria. We have shown that due to the presence of oriT-type F and
AB  - oriT-type R64 loci it is possible to mobilize pEC156 by conjugative plasmids (F
AB  - and R64, respectively). The highest mobilization frequency was observed when
AB  - pEC156-derivatives were transferred between Escherichia coli strains,
AB  - Enterobacter cloacae and Citrobacter freundii representing coliform bacteria. We
AB  - found that a pEC156-derivative with a functional EcoVIII restriction-modification
AB  - system was mobilized in enterobacteria at a frequency lower than a plasmid
AB  - lacking this system. In addition, we found that bacteria that possess the EcoVIII
AB  - restriction-modification system can efficiently release plasmid content to the
AB  - environment. We have shown that E. coli cells can be naturally transformed with
AB  - pEC156-derivatives, however, with low efficiency. The transformation protocol
AB  - employed neither involved chemical agents (e.g. CaCl2) nor temperature shift
AB  - which could induce plasmid DNA uptake.
ER  -

TY  - JOUR
AU  - Werner, E.
AU  - Wende, W.
AU  - Pingoud, A.
AU  - Heinemann, U.
TI  - High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3962
EP  - 3971
VL  - 30
AB  - The homing endonuclease PI-SceI from Saccharomyces cerevisiae consists of two domains. The
AB  - protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a
AB  - precursor protein and the religation of the flanking amino acid sequences (exteins) to a
AB  - functional protein. Furthermore, domain I is involved in binding and recognition of the
AB  - specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally
AB  - homologous to other homing endonucleases from the LAGLIDADG family, harbors the
AB  - endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a
AB  - double-strand cut in the 35 bp recognition sequence. At 1.35 angstrom resolution, the crystal
AB  - structure of PI-SceI domain I provides a detailed view of the part of the protein that is
AB  - responsible for tight and specific DNA binding. A geometry-based docking of the 75 degree bent
AB  - recognition sequence to the full-length protein implies a conformational change or hinge
AB  - movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major
AB  - groove near base pairs +16 to +18.
ER  -

TY  - JOUR
AU  - Werner, E.A.R.
TI  - Intracellular events following infection by bacteriophage P1:  development of host controlled modification and restriction.
JO  - Diss. Abstr.
PY  - 1968
SP  - 3420
EP  - 3420
VL  - 29
AB  - Investigations of the kinetics of development of host controlled restriction
AB  - and modification and of lysogenic immunology of P1-infected Shigella
AB  - dysenteriae were carried out.  The relationships between the three events are
AB  - of interest in order to elucidate their correlation to other events in the
AB  - intracellular life cycle of P1.
ER  -

TY  - JOUR
AU  - Werner, E.R.
AU  - Christensen, J.R.
TI  - Infection by bacteriophage P1 and development of host-controlled restriction and modification and of Lysogenic immunity.
JO  - J. Virol.
PY  - 1969
SP  - 363
EP  - 368
VL  - 3
AB  - Shigella dysenteriae cells were infected with phage P1 or P1c1.  The outcome of
AB  - superinfection of these cells with phage T1.Sh or T1.Sh(P1) or P1c1 was studied
AB  - as a function of time after the initial infection.  Cells undergoing either a
AB  - lytic responses or a lysogenic response to the primary infection develop the
AB  - ability to specifically restrict T1.Sh between 30 and 45 min.  Between 15 and
AB  - 30 min, the cells seem to develop the ability to produce T1.Sh(P1) after
AB  - infection by T1.Sh.  However, reasons are given for believing that this
AB  - apparent time difference is consistent with a simultaneous development of the
AB  - two capacities (restriction and modification) within the cell.  This
AB  - development occurs between 30 and 45 min.  Cells infected with P1c1 and
AB  - superinfected 45 or more min later with T1.Sh(P1) can yield both P1cl and T1.
AB  - Cells infected with P1 become resistant to infection by P1cl within 5 to 10
AB  - min.  It is argued that this early immunity is not necessarily different in
AB  - mechanism from true lysogenic immunity.
ER  -

TY  - JOUR
AU  - Werner, J. et al.
TI  - Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.
JO  - Environ. Microbiol.
PY  - 2014
SP  - 2525
EP  - 2537
VL  - 16
AB  - Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats
AB  - worldwide, yet are represented by only two isolates: Halorhabdus utahensis
AB  - AX-2(T) from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea
AB  - SARL4B(T) from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea.
AB  - We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among
AB  - sequenced archaea, H. tiamatea features the highest number of glycoside
AB  - hydrolases, the majority of which were expressed in proteome experiments.
AB  - Annotations and glycosidase activity measurements suggested an adaptation towards
AB  - recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were
AB  - higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen
AB  - conditions. Likewise, proteomics indicated quinone-mediated electron transport at
AB  - 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea
AB  - furthermore encodes proteins characteristic for thermophiles and light-dependent
AB  - enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was
AB  - mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment
AB  - and metagenomics, we could demonstrate presence of similar glycoside
AB  - hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which
AB  - supports that Halorhabdus species can occupy a distinct niche as polysaccharide
AB  - degraders in hypersaline environments.
ER  -

TY  - JOUR
AU  - Wernette, C.
AU  - Saldanha, R.
AU  - Smith, D.
AU  - Ming, D.
AU  - Perlman, P.S.
AU  - Butow, R.A.
TI  - Complex recognition site for the group I intron-encoded endonuclease I-SceII.
JO  - Mol. Cell. Biol.
PY  - 1992
SP  - 716
EP  - 723
VL  - 12
AB  - We have characterized features of the site recognized by a double-stranded DNA endonuclease,
AB  - I-SceII, encoded by intron 4a of the yeast mitochondrial COX1 gene.  We determined the effects
AB  - of 36 point mutations on the cleavage efficiency of natural and synthetic substrates
AB  - containing the Saccharomyces capensis I-SceII site.  Most mutations of the 18-bp I-SceII
AB  - recognition site are tolerated by the enzyme, and those mutant sites are cleaved between 42
AB  - and 100% as well as the wild-type substrate is.  Nine mutants blocked cleavage to less than or
AB  - equal to 33% of the wild-type, whereas only three point mutations, G-4-C, G-12-T, and G-15-C,
AB  - block cleavage completely.  Competition experiments indicate that these three substrates are
AB  - not cleaved, at least in part because of a marked reduction in the affinity of the enzyme for
AB  - those mutant DNAs.  About 90% of the DNAs derived from randomization of the nucleotide
AB  - sequence of the 4-bp staggered I-SceII cleavage site are not cleaved by the enzyme.  I-SceII
AB  - cleaves cloned DNA derived from human chromosome 3 about once every 110 kbp.  The I-SceII
AB  - recognition sites in four randomly chosen human DNA clones have 56 to 78% identity with the
AB  - 18-bp site in yeast mitochondrial DNA; they are cleaved at least 50% as well as the wild-type
AB  - mitochondrial substrate despite the presence of some substitutions that individually
AB  - compromise
ER  -

TY  - JOUR
AU  - Wernette, C.M.
TI  - Structure and activity of the mitochondrial intron-encoded endonuclease, I-SceIV.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1998
SP  - 127
EP  - 133
VL  - 248
AB  - Starting with crude yeast mitochondria, the intron homing endonuclease, I-SceIV, was purified
AB  - to near homogeneity.  This highly purified enzyme differs from some other well-characterized
AB  - yeast mitochondrial intron-encoded endonucleases in terms of its structure and DNA cleavage
AB  - specificity.  The enzyme is a heterodimer with a native molecular mass of 92 kDa.  A small
AB  - catalytic subunit (32 kDa) is probably encoded largely or entirely by intron 5a of the
AB  - cytochrome oxidase subunit I gene.  A larger polypeptide subunit (60 kDa) may be a nuclear
AB  - factor necessary for intron mobility.  I-SceIV exhibits a low DNA sequence specificity as it
AB  - cleaves a variety of DNA substrates.  Analysis of kinetic parameters shows that the purified
AB  - enzyme has a very high affinity for DNA and exhibits low turnover which may have implications
AB  - for subsequent steps in the intron homing process.
ER  -

TY  - JOUR
AU  - Wernette, C.M.
AU  - Saldahna, R.
AU  - Perlman, P.S.
AU  - Butow, R.A.
TI  - Purification of a site-specific endonuclease, I-Sce II, encoded by intron 4 alpha of the mitochondrial coxI gene of Saccharomyces cerevisiae.
JO  - J. Biol. Chem.
PY  - 1990
SP  - 18976
EP  - 18982
VL  - 265
AB  - We have purified to near homogeneity a site-specific, double-stranded DNA
AB  - endonuclease (I-Sce II) encoded by intron 4 alpha (aI4 alpha) of the yeast
AB  - mitochondrial coxI gene.  Our purification starts with a high salt extract of
AB  - mitochondria isolated from a yeast strain that overproduces the enzyme because
AB  - of a block in splicing of aI4 alpha.  The final step of purification is an
AB  - affinity column consisting of covalently bound double-stranded DNA multimers of
AB  - a synthetic sequence, 5'-TTGGTCATCCAGAAGTAT-3', which contains the I-Sce II
AB  - cleavage/recognition site.  Typical yields of enzyme are 3-5% with a specific
AB  - activity of approximately 500,000 units/mg, where 1 unit of activity cleaves 50
AB  - ng of DNA substrate/h at 30C.  I-Sce II has a monomer molecular mass of 31 kDa
AB  - as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
AB  - Active enzyme purifies as a 55-kDa species, which we presume to be a homodimer.
AB  - I-Sce II monomer comigrates with an in vivo synthesized mitochondrial
AB  - translation product made in the strain that overproduces the enzyme.  We
AB  - conclude that I-Sce II is derived by proteolytic processing of a precursor
AB  - polypeptide, p62, encoded by an in-frame fusion of coxI exons 1-4 with the
AB  - downstream aI4 alpha reading frame.  I-Sce II is most active at pH 7.5 and at
AB  - 20-30C.  Endonuclease activity is sensitive to salt and is dependent upon Mg2+
AB  - or Mn2+, but is unaffected by inclusion of ATP or GTP.  I-Sce II is the first
AB  - intron-encoded protein to be purified and characterized from yeast
AB  - mitochondria.
ER  -

TY  - JOUR
AU  - Wernick, D.G.
AU  - Choi, K.Y.
AU  - Tat, C.A.
AU  - Lafontaine, R.J.G.
AU  - Liao, J.C.
TI  - Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297.
JO  - Genome Announcements
PY  - 2013
SP  - e00967
EP  - e00913
VL  - 1
AB  - Bacillus marmarensis strain DSM 21297 is an extreme obligate alkaliphile able to  grow in
AB  - medium up to pH 12.5. A whole-shotgun strategy and de novo assembly led
AB  - to the generation of a 4-Mbp genome of this strain. The genome features
AB  - alkaliphilic adaptations and pathways for n-butanol and poly(3-hydroxybutyrate)
AB  - synthesis.
ER  -

TY  - JOUR
AU  - Wesselink, J.J.
AU  - Lopez-Camacho, E.
AU  - de la Pena, S.
AU  - Ramos-Ruiz, R.
AU  - Ruiz-Carrascoso, G.
AU  - Lusa-Bernal, S.
AU  - Fernandez-Soria, V.M.
AU  - Gomez-Gil, R.
AU  - Gomez-Puertas, P.
AU  - Mingorance, J.
TI  - Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6981
EP  - 6981
VL  - 194
AB  - Klebsiella pneumoniae KpO3210 is a OXA-48 carbapenemase-producing isolate obtained from a
AB  - blood culture in the context of an outbreak in Hospital
AB  - Universitario La Paz (Madrid, Spain) in 2010. It belongs to the major clone
AB  - detected during the outbreak and is resistant to all beta-lactams and to several
AB  - other antibiotics.
ER  -

TY  - JOUR
AU  - Westberg, J.
AU  - Persson, A.
AU  - Holmberg, A.
AU  - Goesmann, A.
AU  - Lundeberg, J.
AU  - Johansson, K.E.
AU  - Pettersson, B.
AU  - Uhlen, M.
TI  - The Genome Sequence of Mycoplasma mycoides subsp. mycoides SC Type Strain PG1T, the Causative Agent of Contagious Bovine Pleuropneumonia (CBPP).
JO  - Genome Res.
PY  - 2004
SP  - 221
EP  - 227
VL  - 14
AB  - Mycoplasma mycoides subsp. mycoidesSC (MmymySC)is the etiological agent of
AB  - contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory
AB  - disease in cattle. The genome of Mmymy SC type strain PG1(T) has been
AB  - sequenced to map all the genes and to facilitate further studies regarding
AB  - the cell function of the organism and CBPP. The genome is characterized by
AB  - a single circular chromosome of 1211703 bp with the lowest G content (24
AB  - mole%)and the highest density of insertion sequences (13% of the genome
AB  - size)of all sequenced bacterial genomes. The genome contains 985 putative
AB  - genes, of which 72 are part of insertion sequences and encode
AB  - transposases. Anomalies in the GC-skew pattern and the presence of large
AB  - repetitive sequences indicate a high genomic plasticity. A variety of
AB  - potential virulence factors was identified, including genes encoding
AB  - putative variable surface proteins and enzymes and transport proteins
AB  - responsible for the production of hydrogen peroxide and the capsule, which
AB  - is believed to have toxic effects on the animal.
ER  -

TY  - JOUR
AU  - Westphal, L.L.
AU  - Sauvey, P.
AU  - Champion, M.M.
AU  - Ehrenreich, I.M.
AU  - Finkel, S.E.
TI  - Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase.
JO  - mSystems
PY  - 2016
SP  - e00130
EP  - e00116
VL  - 1
AB  - DNA methylation in prokaryotes is widespread. The most common modification of the genome is
AB  - the methylation of adenine at the N-6 position. In Escherichia coli
AB  - K-12 and many gammaproteobacteria, this modification is catalyzed by DNA adenine
AB  - methyltransferase (Dam) at the GATC consensus sequence and is known to modulate
AB  - cellular processes including transcriptional regulation of gene expression,
AB  - initiation of chromosomal replication, and DNA mismatch repair. While studies
AB  - thus far have focused on the motifs associated with methylated adenine (meA), the
AB  - frequency of meA across the genome, and temporal dynamics during early periods of
AB  - incubation, here we conduct the first study on the temporal dynamics of adenine
AB  - methylation in E. coli by Dam throughout all five phases of the bacterial life
AB  - cycle in the laboratory. Using single-molecule real-time sequencing, we show that
AB  - virtually all GATC sites are significantly methylated over time; nearly complete
AB  - methylation of the chromosome was confirmed by mass spectroscopy analysis.
AB  - However, we also detect 66 sites whose methylation patterns change significantly
AB  - over time within a population, including three sites associated with sialic acid
AB  - transport and catabolism, suggesting a potential role for Dam regulation of these
AB  - genes; differential expression of this subset of genes was confirmed by
AB  - quantitative real-time PCR. Further, we show significant growth defects of the
AB  - dam mutant during long-term stationary phase (LTSP). Together these data suggest
AB  - that the cell places a high premium on fully methylating the chromosome and that
AB  - alterations in methylation patterns may have significant impact on patterns of
AB  - transcription, maintenance of genetic fidelity, and cell survival. IMPORTANCE
AB  - While it has been shown that methylation remains relatively constant into early
AB  - stationary phase of E. coli, this study goes further through death phase and
AB  - long-term stationary phase, a unique time in the bacterial life cycle due to
AB  - nutrient limitation and strong selection for mutants with increased fitness. The
AB  - absence of methylation at GATC sites can influence the mutation frequency within
AB  - a population due to aberrant mismatch repair. Therefore, it is important to
AB  - investigate the methylation status of GATC sites in an environment where cells
AB  - may not prioritize methylation of the chromosome. This study demonstrates that
AB  - chromosome methylation remains a priority even under conditions of nutrient
AB  - limitation, indicating that continuous methylation at GATC sites could be under
AB  - positive selection.
ER  -

TY  - JOUR
AU  - Weyler, L.
AU  - Engelbrecht, M.
AU  - Forsberg, M.M.
AU  - Brehwens, K.
AU  - Vare, D.
AU  - Vielfort, K.
AU  - Wojcik, A.
AU  - Aro, H.
TI  - Restriction Endonucleases from Invasive Neisseria gonorrhoeae Cause Double-Strand Breaks and Distort Mitosis in Epithelial Cells during Infection.
JO  - PLoS ONE
PY  - 2014
SP  - e114208
EP  - e114208
VL  - 9
AB  - The host epithelium is both a barrier against, and the target for microbial infections.
AB  - Maintaining regulated cell growth ensures an intact protective layer towards microbial-induced
AB  - cellular damage. Neisseria gonorrhoeae infections disrupt host cell cycle regulation machinery
AB  - and the infection causes DNA double strand breaks that delay progression through the G2/M
AB  - phase. We show that intracellular gonococci upregulate and release restriction endonucleases
AB  - that enter the nucleus and damage human chromosomal DNA. Bacterial lysates containing
AB  - restriction endonucleases were able to fragment genomic DNA as detected by PFGE. Lysates were
AB  - also microinjected into the cytoplasm of cells in interphase and after 20 h, DNA double strand
AB  - breaks were identified by 53BP1 staining. In addition, by using live-cell microscopy and
AB  - NHS-ester stained live gonococci we visualized the subcellular location of the bacteria upon
AB  - mitosis. Infected cells show dysregulation of the spindle assembly checkpoint proteins MAD1
AB  - and MAD2, impaired and prolonged M-phase, nuclear swelling, micronuclei formation and
AB  - chromosomal instability. These data highlight basic molecular functions of how gonococcal
AB  - infections affect host cell cycle regulation, cause DNA double strand breaks and predispose
AB  - cellular malignancies.
ER  -

TY  - JOUR
AU  - Whang, Y.
AU  - Chae, K.S.
AU  - Jang, W.H.
AU  - Kim, K.T.
AU  - Yoo, O.J.
TI  - A new restriction endonuclease from Xanthomonas citri.
JO  - Korean J. Microbiol.
PY  - 1986
SP  - 406
EP  - 410
VL  - 24
AB  - The isolation and characterization of a type II restriction endonuclease from
AB  - Xanthomonas citri IFO3835 were described.  This enzyme (XciI endonuclease) is
AB  - an isoschizomer of SalI endonuclease recognizing 5'-GTCGAC-3' and cleaving at
AB  - the site indicated by the arrow.  Unlike SalI endonuclease, XciI endonuclease
AB  - requires a NaCl concentration of 50 mM for its maximum activity.
ER  -

TY  - JOUR
AU  - Whiley, S.J.
AU  - Lanser, J.A.
AU  - Manning, P.A.
AU  - Murray, C.
AU  - Steele, T.W.
TI  - Plasmid profile analysis of a Salmonellosis outbreak and identification of a restriction and modification system.
JO  - Appl. Environ. Microbiol.
PY  - 1988
SP  - 1591
EP  - 1594
VL  - 54
AB  - After an outbreak of salmonellosis in humans caused by Salmonella typhimurium
AB  - bacteriophage type 135, 62 isolates from human, animal, and water sources were
AB  - retained for further analysis.  Most of the isolates (92%) could be placed in
AB  - one of five plasmmid pattern groups, with a majority containing a common
AB  - 60-kilobase plasmid and a smaller 3.8-kilobase-pair plasmid.  This small
AB  - plasmid, pIMVS1, was labeled with [32P]phosphate and used as a probe in
AB  - subsequent colony and Southern hybridization studies.  We concluded that pIMVS1
AB  - from isolates obtained from humans was genetically different from plasmids of a
AB  - similar size found in isolates from chickens.  Studies to characterize pIMVS1
AB  - were undertaken to determine if it codes for known virulence factors.  It did
AB  - not appear to be associated with the formation of attachment pili or major
AB  - outer membrane proteins.  By using transposon mutagenesis techniques, Tn3(Apr)
AB  - was inserted into pIMVS1, and the existence of a restriction and modification
AB  - system was deduced.
ER  -

TY  - JOUR
AU  - Whitaker, R.D.
AU  - Dorner, L.F.
AU  - Schildkraut, I.
TI  - A mutant of BamHI restriction endonuclease which requires N6-methyladenine for cleavage.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 1525
EP  - 1536
VL  - 285
AB  - Amino acid residues Asn116 and Ser118 of the restriction endonuclease BamHI make several
AB  - sequence-specific and water-bridged contacts to the DNA bases.  An in vivo selection was used
AB  - to isolate BamHI variants at position 116, 118 and 122 which maintained sequence specificity
AB  - to GGATCC sites.  Here, the variants N116H, N116H/S118G and S118G were purified and
AB  - characterized.  The variants N116H and N116H/S118G were found to have lost their ability to
AB  - cleave unmethylated GGATCC sequences by more than two orders of magnitude, while maintaining
AB  - nearly wild-type levels of activity on the N6-methyladenine-containing sequence, GGmATCC.  In
AB  - contrast, wild-type BamHI and variant S118G have only a three- to fourfold lower activity on
AB  - unmethylated GGATCC sequences compared with GGmATCC sequences.  The N116 to H116 mutation has
AB  - effectively altered the specificity of BamHI from an endonuclease which recognizes and cleaves
AB  - GGATCC and GGmATC, to an endonuclease which only cleaves GGmATCC.  The N116H change of
AB  - specificity is due to the lowered binding affinity for the unmethylated sequence because of
AB  - the loss of two asparagine-DNA hydrogen bonds and the introduction of a favorable van der
AB  - Waals contact between the imidazole group of histidine and the N6-methyl group of adenine.
ER  -

TY  - JOUR
AU  - White, J.R.
AU  - Escobar-Paramo, P.
AU  - Mongodin, E.F.
AU  - Nelson, K.E.
AU  - DiRuggiero, J.
TI  - Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 6447
EP  - 6451
VL  - 74
AB  - The extent of chromosome rearrangements in Pyrococcus isolates from marine
AB  - hydrothermal vents in Vulcano Island, Italy, was evaluated by
AB  - high-throughput genomic methods. The results illustrate the dynamic nature
AB  - of the genomes of the genus Pyrococcus and raise the possibility of a
AB  - connection between rapidly changing environmental conditions and adaptive
AB  - genomic properties.
ER  -

TY  - JOUR
AU  - White, O. et al.
TI  - Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
JO  - Science
PY  - 1999
SP  - 1571
EP  - 1577
VL  - 286
AB  - The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1
AB  - is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base
AB  - pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284,156 base
AB  - pairs.  Multiple components distributed on the chromosomes and megaplasmid that contribute to
AB  - the ability of D. radiodurans to survive under conditions of starvation, oxidative stress, and
AB  - high amounts of DNA damage were identified.  Deinococcus radiodurans represents an organism in
AB  - which all systems for DNA repair, DNA damage export, desiccation and starvation recovery, and
AB  - genetic redundancy are present in one cell.
ER  -

TY  - JOUR
AU  - White, R.A.I.I.I.
AU  - Grassa, C.J.
AU  - Suttle, C.A.
TI  - Draft Genome Sequence of Exiguobacterium pavilionensis Strain RW-2, with Wide Thermal, Salinity, and pH Tolerance, Isolated from Modern Freshwater  Microbialites.
JO  - Genome Announcements
PY  - 2013
SP  - e00597
EP  - e00513
VL  - 1
AB  - We report the draft genome sequence of Exiguobacterium pavilionensis strain RW-2, isolated
AB  - from a cold thrombolytic microbialite. The isolate grows at temperatures
AB  - from 4 to 50 degrees C, at pH levels from 5 to 11, and in media without added
AB  - NaCl or KCl or with 7% added NaCl.
ER  -

TY  - JOUR
AU  - White, R.A.I.I.I.
AU  - Grassa, C.J.
AU  - Suttle, C.A.
TI  - First draft genome sequence from a member of the genus agrococcus, isolated from  modern microbialites.
JO  - Genome Announcements
PY  - 2013
SP  - e00391
EP  - e00313
VL  - 1
AB  - We report the first draft genome sequence from a member of the genus Agrococcus,  isolated
AB  - from cold thrombolytic microbialites within Pavilion Lake, British
AB  - Columbia, Canada. The draft genome assembly for Agrococcus pavilionensis strain
AB  - RW-1 has a size of 2,878,403 bp with a G+C content of 72.56%.
ER  -

TY  - JOUR
AU  - White, R.A.I.I.I.
AU  - Suttle, C.A.
TI  - The Draft Genome Sequence of Sphingomonas paucimobilis Strain HER1398 (Proteobacteria), Host to the Giant PAU Phage, Indicates That It Is a Member of  the Genus Sphingobacterium (Bacteroidetes).
JO  - Genome Announcements
PY  - 2013
SP  - e00598
EP  - e00513
VL  - 1
AB  - The draft genome sequence of Sphingomonas paucimobilis host index number (HER) 1398, host of
AB  - the giant PAU phage isolated from silk moths (Bombyx mori),
AB  - indicates that this isolate belongs within the genus Sphingobacterium. We suggest
AB  - that Sphingomonas paucimobilis strain HER1398 be reclassified as Sphingobacterium
AB  - paucimobilis strain HER1398.
ER  -

TY  - JOUR
AU  - Whitehead, E.P.
AU  - Taddeo, B.
AU  - Stampeggioni, E.
AU  - Palitti, F.
AU  - Carotti, D.
TI  - Measurement of DNA methylase activity by tritium release from DNA cytosine.
JO  - Cell Biophys.
PY  - 1989
SP  - 145
EP  - 147
VL  - 15
AB  - The advantages of assaying DNA methylase by measuring the transfer to water of
AB  - tritium from the 5-position of DNA cytosine, rather than the transfer to DNA of
AB  - labeled methyl groups are discussed.
ER  -

TY  - JOUR
AU  - Whitehead, P.R.
AU  - Brown, N.L.
TI  - A simple and rapid method for screening bacteria for type II restriction endonucleases:  enzymes in Aphanothece halophytica.
JO  - Arch. Microbiol.
PY  - 1985
SP  - 70
EP  - 74
VL  - 141
AB  - A method is described which allows a large number of bacterial strains to be
AB  - rapidly and easily screened for the presence of site-specific endonucleases.
AB  - The method involves selective permeabilization of the bacterial cell and
AB  - analysis of the exuded material.  Type II restriction endonucleases from
AB  - cyanobacteria and Gram-negative eubacteria have been detected and new enzymes
AB  - have been found.  The method should be widely applicable and easy to modify for
AB  - use in genera other than those tested.  Three-site-specific endonuclease
AB  - activities, detected by this method in Apanothece halophytica PCC 7412, were
AB  - purified and their recognition and cleavage specificies were determined AhaI
AB  - and AhaII recognise and cleave the same DNA sequences as CauII and AcyI
AB  - respectively; the specificity of AhaIII (TTT^AAA) has been reported previously
AB  - (Whitehead and Brown, 1982, FEBS Lett. 143: 296-300).
ER  -

TY  - JOUR
AU  - Whitehead, P.R.
AU  - Brown, N.L.
TI  - EaeI: a restriction endonuclease from Enterobacter aerogenes.
JO  - FEBS Lett.
PY  - 1983
SP  - 97
EP  - 101
VL  - 155
AB  - We describe the isolation and characterization of a type II restriction endonuclease from
AB  - Enterobacter aerogenes.  This recognises and cleaves the family of related sequences:
AB  - 5'-Py^G-G-C-C--Pu-3' to generate DNA fragments with 5'-tetranucleotide extensions.  EaeI
AB  - may be useful in molecular cloning experiments, especially in conjunction with other enzymes
AB  - which generate the same terminal extensions.  Potential problems in the methods used to
AB  - determine the cleavage specificity are discussed.
ER  -

TY  - JOUR
AU  - Whitehead, P.R.
AU  - Brown, N.L.
TI  - Three restriction endonucleases from Anabaena flos-aquae.
JO  - J. Gen. Microbiol.
PY  - 1985
SP  - 951
EP  - 958
VL  - 131
AB  - Three site-specific endonucleases, AflI, AflII and AflIII, have been partially
AB  - purified from the cyanobacterium Anabaena flos-aquae CCAP 1403/13f.  Their
AB  - recognition and cleavage specificities have been determined to be:AflI
AB  - 5'-G-^G-(A/T)-C-C-3'AflII 5'-C-^T-T-A-A-G-3'AflIII 5'-A-^C-Pu-Py-G-T-3'AflII
AB  - and AflIII are new specificities and may be useful in molecular cloning, as
AB  - well as in the anlaysis of DNA.  The distribution of type II restriction
AB  - endonucleases in the cyanobacteria is briefly discussed.
ER  -

TY  - JOUR
AU  - Whitehead, P.R.
AU  - Brown, N.L.
TI  - AhaIII: A restriction endonuclease with a recognition sequence containing only A:T basepairs.
JO  - FEBS Lett.
PY  - 1982
SP  - 296
EP  - 300
VL  - 143
AB  - None
ER  -

TY  - JOUR
AU  - Whitehead, P.R.
AU  - Brown, N.L.
TI  - The characterization of novel restriction endonuclease specificities.
JO  - Biochem. Soc. Trans.
PY  - 1981
SP  - 272P
EP  - 272P
VL  - 9
AB  - A very rapid method has been developed for DNA sequence analysis of the
AB  - recognition and cleavage sites of type II restriction endonucleases.  DNA
AB  - fragments containing the cleavage site for a novel restriction endonuclease are
AB  - cloned in vectors derived from bacteriophage M13, for sequence analysis by the
AB  - chain-termination method.  The phosphodiester bonds in both DNA strands cleaved
AB  - by the restriction enzyme are identified in parallel with the sequence
AB  - determination.  The recognition and cleavage specificity of the enzyme AspAI,
AB  - has been determined to be the symmetrical sequence 5'-G-^G-T-N-A-C-C-3', and
AB  - the recognition and cleavage specificities of other enzymes will be presented.
ER  -

TY  - JOUR
AU  - Whitehead, P.R.
AU  - Jacobs, D.
AU  - Brown, N.L.
TI  - Restriction endonucleases from Herpetosiphon giganteus:  an example of the evolution of DNA recognition specificity.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 7031
EP  - 7045
VL  - 14
AB  - We describe the partial purification and characterisation of five Type II
AB  - restriction endonucleases from two strains of Herpetosiphon giganteus.  One of
AB  - the activities, HgiJII, was the first enzyme found that cleaves DNA at the
AB  - family of related sequences 5'-G-R-G-C-Y/C-3'.  This enzyme may be related to
AB  - the enzyme HgiAI from a different strain of the same species, and which cleaves
AB  - at the sites 5'-G-W-G-C-W/C-3'.  We have shown that DNAs from the strains
AB  - producing HgiAI and HgiJII are resistant to both of these restriction
AB  - endonucleases.   The remaining four enzymes described here share recognition
AB  - and cleavage specificities with other restriction endonucleases.  The evolution
AB  - of Type II restriction-modification systems and their role in vivo are
AB  - discussed.
ER  -

TY  - JOUR
AU  - Whiteson, K.L.
AU  - Hernandez, D.
AU  - Lazarevic, V.
AU  - Gaia, N.
AU  - Farinelli, L.
AU  - Francois, P.
AU  - Pilo, P.
AU  - Frey, J.
AU  - Schrenzel, J.
TI  - A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.
JO  - BMC Genomics
PY  - 2014
SP  - 169
EP  - 169
VL  - 15
AB  - BACKGROUND: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped
AB  - bacterium was discovered in the lungs of a dead parakeet (Melopsittacus
AB  - undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The
AB  - organism is described with a chemotaxonomic profile and the nearly complete
AB  - genome sequence obtained through the assembly of short sequence reads. RESULTS:
AB  - Genome sequence analysis and characterization of respiratory quinones, fatty
AB  - acids, polar lipids, and biochemical phenotype is presented here. Comparison of
AB  - gene sequences revealed that the most similar species is Pelistega europaea, with
AB  - BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene,
AB  - and a similar GC content (~43%) as the organism isolated from the parakeet, DSM
AB  - 24701 (40%). The closest full genome sequences are those of Bordetella spp. and
AB  - Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa
AB  - platform were assembled with the Edena de novo assembler to form 195 contigs
AB  - comprising the ~2 Mb genome. Genome annotation with RAST, construction of
AB  - phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and
AB  - phylogenetic placement using other highly conserved marker genes with ML Tree all
AB  - suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis
AB  - of samples from cages with healthy parakeets suggested that the newly discovered
AB  - bacterial species is not widespread in parakeet living quarters. CONCLUSIONS:
AB  - Classification of this organism in the current taxonomy system requires the
AB  - formation of a new genus and species. We designate the new genus Basilea and the
AB  - new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM
AB  - 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111
AB  - and GI 406042063).
ER  -

TY  - JOUR
AU  - Wiatr, C.L.
AU  - Witmer, H.J.
TI  - Selective protection of 5'..GGCC..3' and 5'...GCNGC...3' sequences by the hypermodified oxopyrimidine in Bacillus subtilis bacteriophage SP10 DNA.
JO  - J. Virol.
PY  - 1984
SP  - 47
EP  - 54
VL  - 52
AB  - The DNA of Bacillus subtilis bacteriophage SP10 is partially resistant to
AB  - cleavage and methylation in vitro by restriction enzyme R.BsuRI and its cognate
AB  - methylase even though >20 copies of the target sequence, 5'...GGCC...3', are
AB  - present on the phage genome.  YThy, a hypermodified oxopyrimidine that replaces
AB  - a fraction of the thymine residues in SP10 DNA, was responsible for this
AB  - protection, since YThy-free DNA was no longer resistant.  Sites that were
AB  - normally resistant could nevertheless be cleaved or methylated in vitro if the
AB  - salt concentration was reduced or dimethyl sulfoxide was added to the reaction
AB  - buffer.  Analysis of the termini produced by cleavage suggested that resistant
AB  - sites occurred in the sequence 5'...GGCC-YThy ...3', whereas sensitive sites,
AB  - of which there were only two per genome, occurred in the sequence
AB  - 5'...GGCCG...3'.  These in vitro results provide an explanation for the in vivo
AB  - resistance of SP10 to restriction-modification by B. subtilis R.  They also
AB  - suggest ways in which the presence of the atypical base XThy in regions that
AB  - flank the target might upset critical DNA-enzyme interactions necessary to
AB  - locate and recognize the specific site of cleavage or methylation.  YThy also
AB  - strongly protected 5'...GCNGC...3' (R.Fnu4HI) sequences on SP10 DNA, but the
AB  - biological relevance of this protection is unclear.
ER  -

TY  - JOUR
AU  - Wibberg, D.
AU  - Blom, J.
AU  - Jaenicke, S.
AU  - Kollin, F.
AU  - Rupp, O.
AU  - Scharf, B.
AU  - Schneiker-Bekel, S.
AU  - Sczcepanowski, R.
AU  - Goesmann, A.
AU  - Setubal, J.C.
AU  - Schmitt, R.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - Complete Genome Sequencing of Agrobacterium sp H13-3, the former Rhizobium lupini H13-3, Reveals a Tripartite Genome Consisting of a Circular and a Linear Chromosome and an Accessory Plasmid but Lacking a Tumor-Inducing Ti-Plasmid.
JO  - J. Biotechnol.
PY  - 2011
SP  - 50
EP  - 62
VL  - 155
AB  - Agrobacterium sp. H13-3, formerly known as Rhizobium lupini H13-3, is a soil bacterium that
AB  - was isolated from the rhizosphere of Lupinus luteus. The isolate has been established as a
AB  - model system for studying novel features of flagellum structure, motility and chemotaxis
AB  - within the family Rhizobiaceae. The complete genome sequence of Agrobacterium sp. H13-3 has
AB  - been established and the genome structure and phylogenetic assignment of the organism was
AB  - analysed. For de novo sequencing of the Agrobacterium sp. H13-3 genome, a combined strategy
AB  - comprising 454-pyrosequencing on the Genome Sequencer FLX platform and PCR-based amplicon
AB  - sequencing for gap closure was applied. The finished genome consists of three replicons and
AB  - comprises 5,573,770 bases. Based on phylogenetic analyses, the isolate could be assigned to
AB  - the genus Agrobacterium biovar I and represents a genomic species G1 strain within this
AB  - biovariety. The highly conserved circular chromosome (2.82Mb) of Agrobacterium sp. H13-3
AB  - mainly encodes housekeeping functions characteristic for an aerobic, heterotrophic bacterium.
AB  - Agrobacterium sp. H13-3 is a motile bacterium driven by the rotation of several complex
AB  - flagella. Its behaviour towards external stimuli is regulated by a large chemotaxis regulon
AB  - and a total of 17 chemoreceptors. Comparable to the genome of Agrobacterium tumefaciens C58,
AB  - Agrobacterium sp. H13-3 possesses a linear chromosome (2.15Mb) that is related to its
AB  - reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid
AB  - pAspH13-3a (0.6Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and
AB  - shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3
AB  - indicating that it is a non-virulent isolate.
ER  -

TY  - JOUR
AU  - Wibberg, D.
AU  - Bremges, A.
AU  - Dammann-Kalinowski, T.
AU  - Maus, I.
AU  - Igeno, M.I.
AU  - Vogelsang, R.
AU  - Konig, C.
AU  - Luque-Almagro, V.M.
AU  - Roldan, M.D.
AU  - Sczyrba, A.
AU  - Moreno-Vivian, C.
AU  - Blasco, R.
AU  - Puhler, A.
AU  - Schluter, A.
TI  - Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time  sequencing.
JO  - J. Biotechnol.
PY  - 2016
SP  - 61
EP  - 68
VL  - 232
AB  - Pseudomonas pseudoalcaligenes CECT5344 tolerates cyanide and is also able to utilize cyanide
AB  - and cyano-derivatives as a nitrogen source under alkaline
AB  - conditions. The strain is considered as candidate for bioremediation of habitats
AB  - contaminated with cyanide-containing liquid wastes. Information on the genome
AB  - sequence of the strain CECT5344 became available previously. The P.
AB  - pseudoalcaligenes CECT5344 genome was now resequenced by applying the single
AB  - molecule, real-time (SMRT((R))) sequencing technique developed by Pacific
AB  - Biosciences. The complete and finished genome sequence of the strain consists of
AB  - a 4,696,984 bp chromosome featuring a GC-content of 62.34%. Comparative analyses
AB  - between the new and previous versions of the P. pseudoalcaligenes CECT5344 genome
AB  - sequence revealed additional regions in the new sequence that were missed in the
AB  - older version. These additional regions mostly represent mobile genetic elements.
AB  - Moreover, five additional genes predicted to play a role in sulfoxide reduction
AB  - are present in the newly established genome sequence. The P. pseudoalcaligenes
AB  - CECT5344 genome sequence is highly related to the genome sequences of different
AB  - Pseudomonas mendocina strains. Approximately, 70% of all genes are shared between
AB  - P. pseudoalcaligenes and P. mendocina. In contrast to P. mendocina, putative
AB  - pathogenicity genes were not identified in the P. pseudoalcaligenes CECT5344
AB  - genome. P. pseudoalcaligenes CECT5344 possesses unique genes for nitrilases and
AB  - mercury resistance proteins that are of importance for survival in habitats
AB  - contaminated with cyano- and mercury compounds. As an additional feature of the
AB  - SMRT sequencing technology, the methylome of P. pseudoalcaligenes was
AB  - established. Six sequence motifs featuring methylated adenine residues (m6A) were
AB  - identified in the genome. The genome encodes several methyltransferases, some of
AB  - which may be considered for methylation of the m6A motifs identified. The
AB  - complete genome sequence of the strain CECT5344 now provides the basis for
AB  - exploitation of genetic features for biotechnological purposes.
ER  -

TY  - JOUR
AU  - Wibberg, D.
AU  - Tielen, P.
AU  - Blom, J.
AU  - Rosin, N.
AU  - Schobert, M.
AU  - Tupker, R.
AU  - Schatschneider, S.
AU  - Spilker, D.
AU  - Albersmeier, A.
AU  - Goesmann, A.
AU  - Vorholter, F.J.
AU  - Puhler, A.
AU  - Jahn, D.
TI  - Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38.
JO  - Genome Announcements
PY  - 2014
SP  - e00161
EP  - e00114
VL  - 2
AB  - Pseudomonas aeruginosa is a major nosocomial bacterial pathogen causing complicated
AB  - catheter-associated urinary tract infections (CAUTIs). Here, we
AB  - present the 6.9-Mb draft genome sequence of P. aeruginosa MH38 isolated from an
AB  - acute nosocomial CAUTI. It exhibits resistance to several antibiotics but
AB  - revealed low-level production of virulence factors.
ER  -

TY  - JOUR
AU  - Wibberg, D.
AU  - Tielen, P.
AU  - Narten, M.
AU  - Schobert, M.
AU  - Blom, J.
AU  - Schatschneider, S.
AU  - Meyer, A.K.
AU  - Neubauer, R.
AU  - Albersmeier, A.
AU  - Albaum, S.
AU  - Jahn, M.
AU  - Goesmann, A.
AU  - Vorholter, F.J.
AU  - Puhler, A.
AU  - Jahn, D.
TI  - Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.
JO  - Genome Announcements
PY  - 2015
SP  - e00788
EP  - e00715
VL  - 3
AB  - Pseudomonas aeruginosa is known to cause complicated urinary tract infections (UTI). The
AB  - improved 7.0-Mb draft genome sequence of P. aeruginosa RN21, isolated
AB  - from a patient with an acute UTI, was determined. It carries three (pro)phage
AB  - genomes, genes for two restriction/modification systems, and a clustered
AB  - regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)
AB  - system.
ER  -

TY  - JOUR
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Straube, E.
AU  - Karrasch, M.
AU  - Keller, P.M.
AU  - Kalinowski, J.
TI  - Draft Genome Sequence of the Vaccination Strain Mycobacterium bovis BCG S4-Jena.
JO  - Genome Announcements
PY  - 2016
SP  - e00296
EP  - e00216
VL  - 4
AB  - Here, we present the draft genome sequence of ITALIC! Mycobacterium bovisBCG S4-Jena, a
AB  - tuberculosis vaccine strain. The genome of S4-Jena is represented by
AB  - 48 scaffolds, consisting of 132 scaffolded contigs and amounting to a size of
AB  - about 4.2 Mb. New genes potentially encoding a phage fragment were identified in
AB  - the genome.
ER  -

TY  - JOUR
AU  - Wiegand, S.
AU  - Rabausch, U.
AU  - Chow, J.
AU  - Daniel, R.
AU  - Streit, W.R.
AU  - Liesegang, H.
TI  - Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00092
EP  - e00013
VL  - 1
AB  - Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular
AB  - thermostable lipases. The completely sequenced and annotated 3.6-Mb
AB  - genome encodes 3,478 proteins. The strain is genetically equipped to utilize a
AB  - broad range of different substrates and might develop natural competence.
ER  -

TY  - JOUR
AU  - Wiens, G.D.
AU  - LaPatra, S.E.
AU  - Welch, T.J.
AU  - Rexroad, C.I.I.I.
AU  - Call, D.R.
AU  - Cain, K.D.
AU  - LaFrentz, B.R.
AU  - Vaisvil, B.
AU  - Schmitt, D.P.
AU  - Kapatral, V.
TI  - Complete Genome Sequence of Flavobacterium psychrophilum Strain CSF259-93, Used To Select Rainbow Trout for Increased Genetic Resistance against Bacterial Cold  Water Disease.
JO  - Genome Announcements
PY  - 2014
SP  - e00889
EP  - e00814
VL  - 2
AB  - The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow
AB  - trout (Oncorhynchus mykiss), consists of a single circular genome of
AB  - 2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has
AB  - been used to select a line of rainbow trout with increased genetic resistance
AB  - against bacterial cold water disease.
ER  -

TY  - JOUR
AU  - Wiens, J.
AU  - Ho, R.
AU  - Fernando, D.
AU  - Kumar, A.
AU  - Loewen, P.C.
AU  - Brassinga, A.K.
AU  - Anderson, W.G.
TI  - Complete Genome Sequence of a Rhodococcus Species Isolated from the Winter Skate  Leucoraja ocellata.
JO  - Genome Announcements
PY  - 2016
SP  - e00918
EP  - e00916
VL  - 4
AB  - We report here a genome sequence for Rhodococcus sp. isolate UM008 isolated from  the
AB  - renal/interrenal tissue of the winter skate Leucoraja ocellata Genome
AB  - sequence analysis suggests that Rhodococcus bacteria may act in a novel
AB  - mutualistic relationship with their elasmobranch host, serving as biocatalysts in
AB  - the steroidogenic pathway of 1alpha-hydroxycorticosterone.
ER  -

TY  - JOUR
AU  - Wiesner, M.
AU  - Calva, E.
AU  - Fernandez-Mora, M.
AU  - Cevallos, M.A.
AU  - Campos, F.
AU  - Zaidi, M.B.
AU  - Silva, C.
TI  - Salmonella Typhimurium ST213 is associated with two types of IncA/C plasmids carrying multiple resistance determinants.
JO  - BMC Microbiol.
PY  - 2011
SP  - 9
EP  - 9
VL  - 11
AB  - BACKGROUND: Salmonella Typhimurium ST213 was first detected in the Mexican
AB  - Typhimurium population in 2001. It is associated with a multi-drug
AB  - resistance phenotype and a plasmid-borne blaCMY-2 gene conferring
AB  - resistance to extended-spectrum cephalosporins. The objective of the
AB  - current study was to examine the association between the ST213 genotype
AB  - and blaCMY-2 plasmids. RESULTS: The blaCMY-2 gene was carried by an IncA/C
AB  - plasmid. ST213 strains lacking the blaCMY-2 gene carried a different
AB  - IncA/C plasmid. PCR analysis of seven DNA regions distributed throughout
AB  - the plasmids showed that these IncA/C plasmids were related, but the
AB  - presence and absence of DNA stretches produced two divergent types I and
AB  - II. A class 1 integron (dfrA12, orfF and aadA2) was detected in most of
AB  - the type I plasmids. Type I contained all the plasmids carrying the
AB  - blaCMY-2 gene and a subset of plasmids lacking blaCMY-2. Type II included
AB  - all of the remaining blaCMY-2-negative plasmids. A sequence comparison of
AB  - the seven DNA regions showed that both types were closely related to
AB  - IncA/C plasmids found in Escherichia, Salmonella, Yersinia,
AB  - Photobacterium, Vibrio and Aeromonas. Analysis of our Typhimurium strains
AB  - showed that the region containing the blaCMY-2 gene is inserted between
AB  - traA and traC as a single copy, like in the E. coli plasmid pAR060302. The
AB  - floR allele was identical to that of Newport pSN254, suggesting a mosaic
AB  - pattern of ancestry with plasmids from other Salmonella serovars and E.
AB  - coli. Only one of the tested strains was able to conjugate the IncA/C
AB  - plasmid at very low frequencies (10-7 to 10-9). The lack of conjugation
AB  - ability of our IncA/C plasmids agrees with the clonal dissemination trend
AB  - suggested by the chromosomal backgrounds and plasmid pattern associations.
AB  - CONCLUSIONS: The ecological success of the newly emerging Typhimurium
AB  - ST213 genotype in Mexico may be related to the carriage of IncA/C
AB  - plasmids. We conclude that types I and II of IncA/C plasmids originated
AB  - from a common ancestor and that the insertion and deletion of DNA
AB  - stretches have shaped their evolutionary histories.
ER  -

TY  - JOUR
AU  - Wigler, M.
AU  - Levy, D.
AU  - Perucho, M.
TI  - The somatic replication of DNA methylation.
JO  - Cell
PY  - 1981
SP  - 33
EP  - 40
VL  - 24
AB  - We have tested the hypothesis that DNA methylation patterns are replicated in the somatic
AB  - cells of vertebrates. Using M.HpaII, the modification enzyme from Haemophilus parainfluenzae
AB  - which methylates the internal cytosine residues in the sequence 5'CCGG/3'GGCC, we methylated
AB  - bacteriophage PhiX174 RF DNA and the cloned chicken thymidine kinase (tk) gene in vitro and
AB  - then introduced these DNAs and unmethylated controls into tk- cultured mouse cells by
AB  - DNA-mediated transformation. Twenty-five cell generations later, the state of methylation of
AB  - transferred DNA was examined by restriction endonuclease analysis and blot hybridization. We
AB  - conclude that methylation at HpaII sites is replicated by these cultured cells but not with
AB  - 100% fidelity. We have also noted that methylation of the cloned chicken tk gene decreases its
AB  - apparent transformation efficiency relative to unmethylated molecules.
ER  -

TY  - JOUR
AU  - Wijetunge, D.S.
AU  - Karunathilake, K.H.
AU  - Chaudhari, A.
AU  - Katani, R.
AU  - Dudley, E.G.
AU  - Kapur, V.
AU  - DebRoy, C.
AU  - Kariyawasam, S.
TI  - Complete nucleotide sequence of pRS218, a large virulence plasmid, that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218.
JO  - BMC Microbiol.
PY  - 2014
SP  - 203
EP  - 203
VL  - 14
AB  - BACKGROUND: Escherichia coli is the most predominant Gram-negative bacterial
AB  - pathogen associated with neonatal meningitis. Previous studies indicated that the
AB  - prototypic neonatal meningitis E. coli (NMEC) strain RS218 (O18:K1:H7) harbors
AB  - one large plasmid. Objectives of the present study were to analyze the complete
AB  - nucleotide sequence of this large plasmid (pRS218) and its contribution to NMEC
AB  - pathogenesis using in vitro and in vivo models of neonatal meningitis. RESULTS:
AB  - The plasmid is 114,231 bp in size, belongs to the incompatibility group FIB/IIA
AB  - (IncFIB/IIA), and contains a genetic load region that encodes several virulence
AB  - and fitness traits such as enterotoxicity, iron acquisition and copper tolerance.
AB  - The nucleotide sequence of pRS218 showed a 41- 46% similarity to other neonatal
AB  - meningitis-causing E. coli (NMEC) plasmids and remarkable nucleotide sequence
AB  - similarity (up to 100%) to large virulence plasmids of E. coli associated with
AB  - acute cystitis. Some genes located on pRS218 were overly represented by NMEC
AB  - strains compared to fecal E. coli isolated from healthy individuals. The
AB  - plasmid-cured strain was significantly attenuated relative to the RS218 wild-type
AB  - strain as determined in vitro by invasion potential to human cerebral
AB  - microvascular endothelial cells and in vivo by mortalities, histopathological
AB  - lesions in the brain tissue, and bacterial recovery from the cerebrospinal fluid
AB  - of infected rat pups. CONCLUSIONS: The pRS218 is an IncFIB/IIA plasmid which
AB  - shares a remarkable nucleotide sequence similarity to large plasmids of E. coli
AB  - associated with cystitis. Both in vitro and in vivo experiments indicated that
AB  - pRS218 plays an important role in NMEC pathogenesis.
ER  -

TY  - JOUR
AU  - Wijetunge, D.S.
AU  - Katani, R.
AU  - Kapur, V.
AU  - Kariyawasam, S.
TI  - Complete Genome Sequence of Escherichia coli Strain RS218 (O18:H7:K1), Associated with Neonatal Meningitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00804
EP  - e00815
VL  - 3
AB  - Escherichia coli RS218 is the prototypic strain of neonatal meningitis-causing E. coli (NMEC)
AB  - and has been used in many studies related to NMEC pathogenesis. In
AB  - the present study, the genome of E. coli RS218 was sequenced together with its
AB  - plasmid, pRS218. Here, we report the fully closed genome sequence of E. coli
AB  - RS218.
ER  -

TY  - JOUR
AU  - Wijsman, E.M.
TI  - Optimizing selection of restriction enzymes in the search for DNA variants.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 9209
EP  - 9226
VL  - 12
AB  - A model is developed for predicting the relative efficiencies of different
AB  - enzymes for detecting DNA variants when such variants are the result of single
AB  - base-pair changes.  71 enzymes are analyzed for this ability in human DNA.
AB  - Their relative ranked efficiencies are influenced by the sizes of the probes
AB  - used, and the size of the smallest detectable fragment produced.
ER  -

TY  - JOUR
AU  - Wilk, T.
AU  - Szabo, M.
AU  - Szmolka, A.
AU  - Kiss, J.
AU  - Barta, E.
AU  - Nagy, T.
AU  - Olasz, F.
AU  - Nagy, B.
TI  - Genome Sequences of Multidrug-Resistant Salmonella enterica subsp. enterica Serovar Infantis Strains from Broiler Chicks in Hungary.
JO  - Genome Announcements
PY  - 2016
SP  - e01400
EP  - e01416
VL  - 4
AB  - Three strains of Salmonella enterica serovar Infantis isolated from healthy broiler chickens
AB  - from 2012 to 2013 have been sequenced. Comparison of these and
AB  - previously published S Infantis genome sequences of broiler origin in 1996 and
AB  - 2004 will provide new insight into the genome evolution and recent spread of S
AB  - Infantis in poultry.
ER  -

TY  - JOUR
AU  - Wilk, T.
AU  - Szabo, M.
AU  - Szmolka, A.
AU  - Kiss, J.
AU  - Olasz, F.
AU  - Nagy, B.
TI  - Genome Sequences of Salmonella enterica subsp. enterica Serovar Infantis Strains  from Hungary Representing Two Peak Incidence Periods in Three Decades.
JO  - Genome Announcements
PY  - 2017
SP  - e01735
EP  - e01716
VL  - 5
AB  - Four strains of Salmonella enterica subsp. enterica serovar Infantis isolated from humans
AB  - (1980 to 1982) and broiler chickens (2016) have been sequenced. They
AB  - represent the early and recent peak incidences of this serovar in Hungary. Genome
AB  - sequences of these isolates provide comparative data on the evolution and rise of
AB  - an endemic S Infantis clone in Hungary.
ER  -

TY  - JOUR
AU  - Wilke, K.
AU  - Rauhut, E.
AU  - Noyer-Weidner, M.
AU  - Lauster, R.
AU  - Pawlek, B.
AU  - Behrens, B.
AU  - Trautner, T.A.
TI  - Sequential order of target-recognizing domains in multispecific DNA-methyltransferases.
JO  - EMBO J.
PY  - 1988
SP  - 2601
EP  - 2609
VL  - 7
AB  - In the multispecific DNA (cytosine-5)-methyltransferases (Mtases) of Bacillus
AB  - subtilis phages SPR and Phi3T the domains responsible for recognition of DNA
AB  - methylation targets CC(A/T)GG, CCGG, GGCC (SPR) and GCNGC, GGCC (Phi3T)
AB  - represent contiguous sequences of approximately 50 amino acids each.  These
AB  - domains are tandemly arranged and do not overlap.  They are part of a variable
AB  - segment within the enzymes which is flanked by conserved amino acids, which are
AB  - very similar amongst bacterial monospecific and the multispecific Mtases
AB  - studied here.  These results follow from a mutational analysis of the SPR and
AB  - Phi3T Mtase genes.  They further support our concept of a modular enzyme
AB  - organization, according to which variability of type II Mtases with respect to
AB  - target recognition is achieved by a combination of the same enzyme core with a
AB  - variety of target-recognizing domains.
ER  -

TY  - JOUR
AU  - Wilkes, T.
AU  - Darby, A.C.
AU  - Choi, J.
AU  - Colborne, J.K.
AU  - Werren, J.H.
AU  - Hurst, G.D.D.
TI  - The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis.
JO  - Insect Mol. Biol.
PY  - 2010
SP  - 59
EP  - 73
VL  - 19
AB  - Four percent of female Nasonia vitripennis carry the son-killer bacterium Arsenophonus
AB  - nasoniae, a microbe with notably different biology from other inherited parasites and
AB  - symbionts. In this paper, we examine a draft genome sequence of the bacterium for open reading
AB  - frames (ORFs), structures and pathways involved in interactions with its insect host. The
AB  - genome data suggest that A. nasoniae carries multiple type III secretion systems, and an array
AB  - of toxin and virulence genes found in Photorhabdus, Yersinia and other gammaproteobacteria. Of
AB  - particular note are ORFs similar to those known to affect host innate immune functioning in
AB  - other bacteria, and four ORFs related to pro-apoptotic exotoxins. The genome sequences for
AB  - both A. nasoniae and its Nasonia host are useful tools for examining functional genomic
AB  - interactions of microbial survival in hostile immune environments, and mechanisms of passage
AB  - through gut epithelia, in a whole organism context.
ER  -

TY  - JOUR
AU  - Wilkins, B.M.
TI  - Plasmid promiscuity: meeting the challenge of DNA immigration control.
JO  - Environ. Microbiol.
PY  - 2002
SP  - 495
EP  - 500
VL  - 4
AB  - Bacterial plasmids are ubiquitous components of the genomes of naturally occurring bacteria
AB  - and are typically transmissible between cells by the process of bacterial conjugation (see
AB  - reviews in Thomas, 2000).  A remarkable feature of conjugation is its promiscuity, allowing
AB  - DNA transfer between phylogenetically remote bacteria and even from bacteria to plant and
AB  - mammalian cells (Waters, 2001).  Conjugative promiscuity is biologically important in
AB  - dispersing the diverse cargoes of medically and environmentally significant genes carried on
AB  - plasmids, as well as contributing to the horizontal transfer of 'fitness islands',
AB  - consisting of clustered chromosomal loci that enable pathogens and symbionts to interact with
AB  - their eukaryotic hosts (Finan, 2002).
ER  -

TY  - JOUR
AU  - Wilkins, B.M.
AU  - Chilley, P.M.
AU  - Thomas, A.T.
AU  - Pocklington, M.J.
TI  - Distribution of restriction enzyme recognition sequences on broad host range plasmid RP4: molecular and evolutionary implications.
JO  - J. Mol. Biol.
PY  - 1996
SP  - 447
EP  - 456
VL  - 258
AB  - IncPalpha plasmids, exemplified by RP4, are remarkable for their broad host range.  They
AB  - contain strikingly few cleavage sites for many commonly used type II restriction enzymes but
AB  - an overabundance of sites for certain enzymes that target G + C-rich sequences. To identify
AB  - factors responsible for these distributions, the recently compiled nucleotide sequence of RP4
AB  - was analyzed to determine the frequency of tetra- and hexanucleotide motifs in the 49 kb
AB  - plasmid backbone.  This is defined as the sectors encoding basic plasmid functions.  The
AB  - overabundant restriction targets in RP4 are concentrated in the backbone and contain
AB  - overlapping copies of CGGC/GCCG, identified as the most abundant tetranucleotide motif in the
AB  - plasmid. Motif frequencies in the RP4 backbone are shown to be similar to those in Pseudomonas
AB  - aeruginosa, a natural host of RP4, with the notable exception that a number of 6-bp
AB  - palindromes are underrepresented in the plasmid.  It is proposed that 6-bp palindromes were
AB  - counterselected as type II restriction enzyme recognition sequences.  Conjugative transfer of
AB  - RP4 and R751 (IncPbeta) is usually sensitive to restriction compared to enterobacterial
AB  - plasmids of the IncFII and IncI1 groups, implying that IncP plasmids experienced particularly
AB  - strong selection for loss of restriction targets.  Pseudomonas spp. of rRNA homology group I
AB  - specify many type II restriction enzymes that target 6-bp palindromes and are candidates for
AB  - the evolutionary hosts of IncPalpha plasmids.
ER  -

TY  - JOUR
AU  - Wilkins, K.E.
AU  - Booher, N.J.
AU  - Wang, L.
AU  - Bogdanove, A.J.
TI  - TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.
JO  - Front. Plant Sci.
PY  - 2015
SP  - 1
EP  - 5
VL  - 6
AB  - Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial
AB  - leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription
AB  - activator-like (TAL) effectors to upregulate host susceptibility genes.  By pathogen whole
AB  - genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL
AB  - effector content and rice transcriptional responses across 10 geographically diverse Xoc
AB  - strains.  TAL effector content is surprisingly conserved overall, yet distinguishes Asian from
AB  - African isolates.  Five TAL effectors are conserved across all strains. In a prior laboratory
AB  - assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the
AB  - strict conservation indicates all five may e important, in different rice genotypes or in the
AB  - field.  Concatenated and aligned, TAL effector content across strains largely reflects
AB  - relationships based on housekeeping genes, suggesting predominantly vertical transmission.
AB  - Rice transcriptional responses did not reflect these relationship, and on average, only 28% of
AB  - genes upregulated and 22% of genes downregulated by a strain and up- and down-regulated
AB  - (respectively) by all strains.  However, when only known TAL effector targets were considered,
AB  - the relationships resembled those of the TAL effectors.  Toward identifying new targets, we
AB  - used the TAL effector-DNA recognition code to predict effector binding elements in promoters
AB  - of genes upregulated by each strain, but found that for every strain, all upregulated genes
AB  - had at least one.  Filtering with a classifier we developed previously decreases the number of
AB  - predicted binding elements across the genome, suggesting that it may reduce false positives
AB  - among upregulated genes.  Applying this filter and eliminating genes for which upregulation
AB  - did not strictly correlate with presence of the corresponding TAL effector, we generated
AB  - testable numbers of candidate targets for four of the five strictly conserved TAL effectors.
ER  -

TY  - JOUR
AU  - Wilkinson, C.R.M.
AU  - Bartlett, R.
AU  - Nurse, P.
AU  - Bird, A.P.
TI  - The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 203
EP  - 210
VL  - 23
AB  - DNA methylation of cytosine residues is a widespread phenomenon and has been implicated in a
AB  - number of biological processes in both prokaryotes and eukaryotes. This methylation occurs at
AB  - the 5-position of cytosine and is catalyzed by a distinct family of conserved enzymes, the
AB  - cytosine-5 methyltransferases (m5C-MTases). We have cloned a fission yeast gene pmt1+ (pombe
AB  - methyltransferase) which encodes a protein that shares significant homology with both
AB  - prokaryotic and eukaryotic m5C-MTases. All 10 conserved domains found in these enzymes are
AB  - present in the pmt1 protein. This is the first m5C-MTase homologue cloned from a fungal
AB  - species. Its presence is surprising, given the inability to detect DNA methylation in yeasts.
AB  - Haploid cells lacking the pmt1+ gene are viable, indicating that pmt1+ is not an essential
AB  - gene. Purified, bacterially produced pmt1 protein does not possess obvious methyltransferase
AB  - activity in vitro. Thus the biological significance of this m5C-MTase homologue in fission
AB  - yeast is currently unclear.
ER  -

TY  - JOUR
AU  - Wilkinson, P. et al.
TI  - Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens.
JO  - BMC Genomics
PY  - 2009
SP  - 302
EP  - 302
VL  - 10
AB  - BACKGROUND: The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has
AB  - been recovered from human infections in both North America and Australia.
AB  - Recently, Pa has been shown to have a nematode vector that can also infect
AB  - insects, like its sister species the insect pathogen P. luminescens (Pl).
AB  - To understand the relationship between pathogenicity to insects and humans
AB  - in Photorhabdus we have sequenced the complete genome of Pa strain
AB  - ATCC43949 from North America. This strain (formerly referred to as
AB  - Xenorhabdus luminescens strain 2) was isolated in 1977 from the blood of
AB  - an 80 year old female patient with endocarditis, in Maryland, USA. Here we
AB  - compare the complete genome of Pa ATCC43949 with that of the previously
AB  - sequenced insect pathogen P. luminescens strain TT01 which was isolated
AB  - from its entomopathogenic nematode vector collected from soil in Trinidad
AB  - and Tobago. RESULTS: We found that the human pathogen Pa had a smaller
AB  - genome (5,064,808 bp) than that of the insect pathogen Pl (5,688,987 bp)
AB  - but that each pathogen carries approximately one megabase of DNA that is
AB  - unique to each strain. The reduced size of the Pa genome is associated
AB  - with a smaller diversity in insecticidal genes such as those encoding the
AB  - Toxin complexes (Tc's), Makes caterpillars floppy (Mcf) toxins and the
AB  - Photorhabdus Virulence Cassettes (PVCs). The Pa genome, however, also
AB  - shows the addition of a plasmid related to pMT1 from Yersinia pestis and
AB  - several novel pathogenicity islands including a novel Type Three Secretion
AB  - System (TTSS) encoding island. Together these data suggest that Pa may
AB  - show virulence against man via the acquisition of the pMT1-like plasmid
AB  - and specific effectors, such as SopB, that promote its persistence inside
AB  - human macrophages. Interestingly the loss of insecticidal genes in Pa is
AB  - not reflected by a loss of pathogenicity towards insects. CONCLUSION: Our
AB  - results suggest that North American isolates of Pa have acquired virulence
AB  - against man via the acquisition of a plasmid and specific virulence
AB  - factors with similarity to those shown to play roles in pathogenicity
AB  - against humans in other bacteria.
ER  -

TY  - JOUR
AU  - Willcock, D.F.
AU  - Dryden, D.T.F.
AU  - Murray, N.E.
TI  - A mutational analysis of the two motifs common to adenine methyltransferases.
JO  - EMBO J.
PY  - 1994
SP  - 3902
EP  - 3908
VL  - 13
AB  - All methyltransferases that use S-adenosyl methionine as the methyl group donor contain a
AB  - sequence similar to (D/E/S)XFXGXG which has been postulated to form part of the cofactor
AB  - binding site. In N6-adenine DNA methyltransferases there is a second motif, (D/N)PP(Y/F),
AB  - which has been proposed to play a role similar to the catalytically essential PC motif
AB  - conserved in all C5-cytosine DNA methyltransferases. We have made a series of amino acid
AB  - changes in these two motifs in the EcoKI N6-adenine DNA methyltransferase. The mutant enzymes
AB  - have been purified to homogeneity and characterized by physical biochemical methods. The first
AB  - G is the most conserved residue in motif I. Changing this G to D completely abolishes
AB  - S-adenosyl methionine binding, but left enzyme structure and DNA target recognition unaltered,
AB  - thus documenting the S-adenosyl methionine binding function of motif I in N6-adenine
AB  - methyltransferases. Substitution of the N with D, or F with either G or C, in motif II
AB  - abolished enzyme activity, but left S-adenosyl methionine and DNA binding unaltered. Changes
AB  - of F to Y or W resulted in partial enzyme activity, implying that an aromatic residue is
AB  - important for methylation. The substitution of W for F greatly enhanced UV-induced
AB  - cross-linking between the enzyme and S-adenosyl methionine, suggesting that the aromatic
AB  - residue is close in space to the methyl-group donor.
ER  -

TY  - JOUR
AU  - Willems, A.
AU  - Tian, R.
AU  - Brau, L.
AU  - Goodwin, L.
AU  - Han, J.
AU  - Liolios, K.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Mavrommatis, K.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Reeve, W.
TI  - Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 484
EP  - 494
VL  - 9
AB  - Burkholderia mimosarum strain LMG 23256(T) is an aerobic, motile, Gram-negative,
AB  - non-spore-forming rod that can exist as a soil saprophyte or as a legume
AB  - microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256(T) was isolated
AB  - from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan.
AB  - LMG 23256(T) is highly effective at fixing nitrogen with M. pigra. Here we
AB  - describe the features of B. mimosarum strain LMG 23256(T), together with genome
AB  - sequence information and its annotation. The 8,410,967 bp high-quality-draft
AB  - genome is arranged into 268 scaffolds of 270 contigs containing 7,800
AB  - protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial
AB  - genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic
AB  - Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Williams, B.J.
AU  - Golomb, M.
AU  - Phillips, T.
AU  - Brownlee, J.
AU  - Olson, M.V.
AU  - Smith, A.L.
TI  - Bacteriophage HP2 of Haemophilus influenzae.
JO  - J. Bacteriol.
PY  - 2002
SP  - 6893
EP  - 6905
VL  - 184
AB  - Temperate bacteriophages effect chromosomal evolution of their bacterial hosts, mediating
AB  - rearrangements and the acquisition of novel genes from other taxa. Although the Haemophilus
AB  - influenzae genome shows evidence of past phage-mediated lateral transfer, the phages presumed
AB  - responsible have not been identified. To date, six different H. influenzae phages are known;
AB  - of these, only the HP1/S2 group, which lyosogenizes exclusively Rd strains (which were
AB  - originally encapsulated serotype d), is well characterized. Phages in this group are
AB  - genetically very similar, with a highly conserved set of genes. Because the majority of H.
AB  - influenzae strains are nonencapsulated (nontypeable), it is important to characterize phages
AB  - infecting this larger, genetically more diverse group of respiratory pathogens. We have
AB  - identified and sequenced HP2, a bacteriophage of nontypeable H. influenzae. Although related
AB  - to the fully sequenced HP1 (and even more so to the partially sequenced S2) and similar in
AB  - genetic organization, HP2 has a few novel genes and differs in host range; HP2 will not infect
AB  - or lysogenize Rd strains. Genomic comparisons between HP1/S2 and HP2 suggest recent
AB  - divergence, with new genes completely replacing old ones at certain loci. Sequence comparisons
AB  - suggest that H. influenzae phages evolve by recombinational exchange of genes with each other,
AB  - with cryptic prophages, and with the host chromosome.
ER  -

TY  - JOUR
AU  - Williams, D.M.
AU  - Benseler, F.
AU  - Eckstein, F.
TI  - Properties of 2'-fluorothymidine-containing oligonucleotides:  Interaction with restriction endonuclease EcoRV.
JO  - Biochemistry
PY  - 1991
SP  - 4001
EP  - 4009
VL  - 30
AB  - 2'-Fluorothymidine (Tf) was synthesized via an improved procedure with
AB  - (diethylamino) sulfur trifluoride.  The compatibility of the analogue with DNA
AB  - synthesis via the phosphoramidite method was demonstrated after complete
AB  - enzymatic digestion of the oligonucleotides d(TfuT) and d(Tf3T), the sole
AB  - products of which were 2'-fluorothymidine and thymidine in the expected ratio.
AB  - The 2'-fluorothymidine was also incorporated into the EcoRV recognition
AB  - sequence, within the complementary oligonucleotide d(CAAACCGATATCGTTGTG) and
AB  - d(CACAACGATATCGGTTTG).  Thermal melting characteristics of these duplexes
AB  - showed a significant decrease in stability only when both of the thymidine
AB  - residues in one of the strands were replaced.  In contrast, when all of one
AB  - strand of a duplex contained 2'-fluorothymidine, as in d(TfuT)-d(A12), a
AB  - substantially higher Tm and cooperativity of melting was observed relative to
AB  - the unmodified structure.  EcoRV cleaved a duplex that contained a
AB  - 2'-fluorothymidine at the scissile linkage in each strand at two-thirds of the
AB  - rate obtained for the unmodified structure.  A duplex containing two
AB  - 2'-fluorothymidine residues in one strand and none in the other was cleaved at
AB  - one-third of the rate in its unsubstituted strand, whereas the cleavage rate
AB  - was reduced to 22% in its modified strand.
ER  -

TY  - JOUR
AU  - Williams, K.
AU  - Savageau, M.A.
AU  - Blumenthal, R.M.
TI  - A bistable hysteretic switch in an activator-repressor regulated restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 2013
SP  - 6045
EP  - 6057
VL  - 41
AB  - Restriction-modification (RM) systems are extremely widespread among bacteria and archaea, and
AB  - are often specified by mobile genetic elements. In type II RM systems, where the restriction
AB  - endonuclease (REase) and protective DNA methyltransferase (MTase) are separate proteins, a
AB  - major regulatory challenge is delaying expression of the REase relative to the MTase after RM
AB  - genes enter a new host cell. Basic understanding of this regulation is available for few RM
AB  - systems, and detailed understanding for none. The PvuII RM system is one of a large subset in
AB  - which the central regulatory role is played by an activator-repressor protein (called C, for
AB  - controller). REase expression depends upon activation by C, whereas expression of the MTase
AB  - does not. Thus delay of REase expression depends on the rate of C-protein accumulation. This
AB  - is a nonlinear process, as C also activates transcription of its own gene. Mathematical
AB  - modeling of the PvuII system led to the unexpected predictions of responsiveness to a factor
AB  - not previously studied in RM system control-gene copy number-and of a hysteretic response. In
AB  - this study, those predictions have been confirmed experimentally. The results may apply to
AB  - many other C-regulated RM systems, and help explain their ability to spread so widely.
ER  -

TY  - JOUR
AU  - Williams, L.E.
AU  - Baltrus, D.A.
AU  - O'Donnell, S.D.
AU  - Skelly, T.J.
AU  - Martin, M.O.
TI  - Complete Genome Sequence of the Predatory Bacterium Ensifer adhaerens Casida A.
JO  - Genome Announcements
PY  - 2017
SP  - e01344
EP  - e01317
VL  - 5
AB  - We report here the complete genome sequence of the facultative predatory bacterium Ensifer
AB  - adhaerens strain Casida A. The genome was assembled into three
AB  - circular contigs, with a main chromosome as well as two large secondary
AB  - replicons, that totaled 7,267,502 bp with 6,641 predicted open reading frames.
ER  -

TY  - JOUR
AU  - Williams, L.E.
AU  - Detter, C.
AU  - Barry, K.
AU  - Lapidus, A.
AU  - Summers, A.O.
TI  - Facile Recovery of Individual High-Molecular-Weight, Low-Copy-Number Natural Plasmids for Genomic Sequencing.
JO  - Appl. Environ. Microbiol.
PY  - 2006
SP  - 4899
EP  - 4906
VL  - 72
AB  - Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate
AB  - horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from
AB  - individual plasmids of this class. We report here that a kit method previously devised for
AB  - purification of bacterial artificial chromosomes (BACs) can be adapted for effective
AB  - preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive
AB  - bacteria. Individual plasmid DNA recovered from less than 10 ml of Escherichia coli,
AB  - Staphylococcus, and Corynebacterium cultures was of sufficient quantity and quality for
AB  - construction of high-coverage libraries, as shown by sequencing five native plasmids ranging
AB  - in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize
AB  - plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on
AB  - mobile genetic element biology derived from these sequences. Adaptation of this BAC method for
AB  - large plasmid isolation removes one major technical hurdle to expanding our knowledge of the
AB  - natural plasmid gene pool.
ER  -

TY  - JOUR
AU  - Williams, M.L.
AU  - Gillaspy, A.F.
AU  - Dyer, D.W.
AU  - Thune, R.L.
AU  - Waldbieser, G.C.
AU  - Schuster, S.C.
AU  - Gipson, J.
AU  - Zaitshik, J.
AU  - Landry, C.
AU  - Banes, M.M.
AU  - Lawrence, M.L.
TI  - Genome Sequence of Edwardsiella ictaluri 93-146, a Strain Associated with a Natural Channel Catfish Outbreak of Enteric Septicemia of Catfish.
JO  - J. Bacteriol.
PY  - 2012
SP  - 740
EP  - 741
VL  - 194
AB  - Edwardsiella ictaluri is the cause of extensive mortalities and economic losses to the channel
AB  - catfish industry of the southeast United States.
AB  - Here we report the complete genome of Edwardsiella ictaluri 93-146.
AB  - Whole-genome sequence analysis of E. ictaluri provides a tool for
AB  - understanding the genomic regions specific to the species and the
AB  - Edwardsiella genus.
ER  -

TY  - JOUR
AU  - Williams, M.M.
AU  - Sen, K.A.
AU  - Weigand, M.R.
AU  - Skoff, T.H.
AU  - Cunningham, V.A.
AU  - Halse, T.A.
AU  - Tondella, M.L.
TI  - Bordetella pertussis strain lacking pertactin and pertussis toxin.
JO  - Emerg. Infect. Dis.
PY  - 2016
SP  - 319
EP  - 322
VL  - 22
AB  - A Bordetella pertussis strain lacking 2 acellular vaccine immunogens, pertussis toxin and
AB  - pertactin, was isolated from an unvaccinated infant in New York State in 2013. Comparison with
AB  - a French strain that was pertussis toxindeficient, pertactin wild-type showed that the strains
AB  - carry the same 28-kb deletion in similar genomes.
ER  -

TY  - JOUR
AU  - Williams, R.J.
TI  - Restriction endonucleases: Classification, properties, and applications.
JO  - Mol. Biotechnol.
PY  - 2003
SP  - 225
EP  - 243
VL  - 23
AB  - Restriction endonucleases have become a fundamental tool of molecular biology with many
AB  - commercial vendors and extensive product lines. While a
AB  - significant amount has been learned about restriction enzyme diversity,
AB  - genomic organization, and mechanism, these continue to be active areas of
AB  - research and assist in classification efforts. More recently, one focus
AB  - has been their exquisite specificity for the proper recognition sequence
AB  - and the lack of homology among enzymes recognizing the same DNA sequence.
AB  - Some questions also remain regarding in vivo function. Site-directed
AB  - mutagenesis and fusion proteins based on known endonucleases show promise
AB  - for custom-designed cleavage. An understanding of the enzymes and their
AB  - properties can improve their productive application by maintaining
AB  - critical digest parameters and enhancing or avoiding alternative
AB  - activities.
ER  -

TY  - JOUR
AU  - Williams, R.J.
TI  - Restriction endonucleases and their uses.
JO  - Methods Mol. Biol.
PY  - 2001
SP  - 409
EP  - 429
VL  - 160
AB  - Restriction endonucleases, which cleave DNA in a site-specific manner, are a fundamental tool
AB  - of molecular biology.  The discovery of endonucleases began in the 1960s and led to commercial
AB  - availability in the early 1970s.  The number of characterized enzymes continues to grow, as
AB  - does the number of vendors and the size of their product lines.  Although many similarities
AB  - exist among endonucleases in terms of their structures, mechanisms, and uses, important
AB  - differences remain.  Now a staple of molecular biology, restriction endonucleases are an area
AB  - of active research as models of site-specific DNA recognition, cleavage mechanism, in vivo
AB  - function, and evolutionary origins.  New enzymes continue to be discovered or developed by
AB  - using protein engineering to modify the specificity of existing enzymes.
ER  -

TY  - JOUR
AU  - Williams, R.J.
TI  - Isolation and characterization of an unknown restriction endonuclease.
JO  - Methods Mol. Biol.
PY  - 2001
SP  - 431
EP  - 442
VL  - 160
AB  - Currently, there are approximately 3000 restriction endonucleases known, recognizing 235
AB  - different sequences.  Although primarily found in bacteria, they also exist in archaea,
AB  - viruses, and eukaryotes.  An estimated 25% of bacteria examined contain at least one
AB  - restriction endonuclease, and therefore the probability of encountering new ones is relatively
AB  - high.  Indeed, many new enzymes have been "discovered" in contaminated bacterial cultures.
AB  - The presence of three restriction activities in a single organism is not unusual.  Neisseria
AB  - strains appear to be particularly rich in restriction endonucleases and their corresponding
AB  - methyltransferases.  As many as seven different endonucleases from a single strain have been
AB  - identified through cloning.  The first enzyme discovered which recognizes a unique sequence,
AB  - although it may not be commercially available or commonly known, is designated the prototype.
AB  - Although few new prototypes have been discovered recently, two potential four-base palindromes
AB  - and seven potential six-base palindromes are not cleaved by any known restriction
AB  - endonucleases.  Most databases are arranged alphabetically by prototype, with isoschizomers
AB  - listed under the prototype heading.  A database of all known endonucleases, maintained by Dr.
AB  - Richard J. Roberts, is available at http://www.neb.com/rebase.  A number of formats are
AB  - available, and references are provided.  Detailed information on restriction endonuclease
AB  - biology, classification, structure, specificity, and catalytic mechanism is provided elsewhere
AB  - in this book.
ER  -

TY  - JOUR
AU  - Williams, S.A.
AU  - Halford, S.E.
TI  - Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 387
EP  - 394
VL  - 318
AB  - The SfiI endonuclease is a tetrameric protein with two DNA-binding clefts. It has to bind two
AB  - copies of its recognition sequence, one at each cleft, before it cleaves DNA. While SfiI binds
AB  - cooperatively to two cognate sites, it binds only one non-cognate DNA molecule at a time and
AB  - the resultant complex is precluded from binding cognate DNA at the vacant cleft. To examine
AB  - the communications between separate binding sites in a protein that synapses two segments of
AB  - DNA, SfiI was tested with oligonucleotide duplexes containing its recognition sequence but
AB  - with either R(p) or S(p) phosphorothioate linkages at the scissile bonds. Though SfiI has low
AB  - activity on the R(p) and none against the S(p) diastereoisomer, it bound these duplexes in the
AB  - same cooperative manner as oxyester duplexes, though with a reduced affinity for the S(p)
AB  - derivative. It also formed complexes with one phosphorothioate-duplex and one oxyester-duplex
AB  - but, when Mg(2+) was added to the hybrid complexes, the phosphorothioate moiety at one
AB  - DNA-binding cleft prevented the enzyme from cleaving the oxyester duplex at the other cleft.
AB  - SfiI is thus restrained from catalytic action until it recognises the correct nucleotide
AB  - sequence at two DNA loci and the correct phosphodiester functions at both loci.
ER  -

TY  - JOUR
AU  - Williams, S.A.
AU  - Halford, S.E.
TI  - SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.
JO  - Nucleic Acids Res.
PY  - 2001
SP  - 1476
EP  - 1483
VL  - 29
AB  - The SfiI endonuclease cleaves DNA at the sequence GGCCNNNNNGGCC, where N is any base and  is
AB  - the point of cleavage.  Proteins that recognise discontinuous sequences in DNA can be affected
AB  - by the unspecified sequence between the specified base pairs of the target site. To examine
AB  - whether this applies to SfiI, a series of DNA duplexes were made with identical sequences
AB  - apart from discrete variations in the 5 bp spacer. The rates at which SfiI cleaved each duplex
AB  - were measured under steady-state conditions: the steady-state rates were determined by the DNA
AB  - cleavage step in the reaction pathway. SfiI cleaved some of these substrates at faster rates
AB  - than other substrates. For example, the change in spacer sequence from AACAA to AAACA caused a
AB  - 70-fold increase in reaction rate. In general, the extrapolated values for kcat and Km were
AB  - both higher on substrates with inflexible spacers than those with flexible structures. The
AB  - dinucleotide at the site of cleavage was largely immaterial. SfiI activity is thus highly
AB  - dependent on conformational variations in the spacer DNA.
ER  -

TY  - JOUR
AU  - Williamson, A.
AU  - De Santi, C.
AU  - Altermark, B.
AU  - Karlsen, C.
AU  - Hjerde, E.
TI  - Complete genome sequence of Halomonas sp. R5-57.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 62
EP  - 62
VL  - 11
AB  - The marine Arctic isolate Halomonas sp. R5-57 was sequenced as part of a bioprospecting
AB  - project which aims to discover novel enzymes and organisms from
AB  - low-temperature environments, with potential uses in biotechnological
AB  - applications. Phenotypically, Halomonas sp. R5-57 exhibits high salt tolerance
AB  - over a wide range of temperatures and has extra-cellular hydrolytic activities
AB  - with several substrates, indicating it secretes enzymes which may function in
AB  - high salinity conditions. Genome sequencing identified the genes involved in the
AB  - biosynthesis of the osmoprotectant ectoine, which has applications in food
AB  - processing and pharmacy, as well as those involved in production of
AB  - polyhydroxyalkanoates, which can serve as precursors to bioplastics. The
AB  - percentage identity of these biosynthetic genes from Halomonas sp. R5-57 and
AB  - current production strains varies between 99 % for some to 69 % for others, thus
AB  - it is plausible that R5-57 may have a different production capacity to currently
AB  - used strains, or that in the case of PHAs, the properties of the final product
AB  - may vary. Here we present the finished genome sequence (LN813019) of Halomonas
AB  - sp. R5-57 which will facilitate exploitation of this bacterium; either as a
AB  - whole-cell production host, or by recombinant expression of its individual
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Williamson, M.R.
AU  - Doherty, J.P.
AU  - Woodcock, D.M.
TI  - Modified-cytosine restriction-system-induced recombinant cloning artefacts in Escherichia coli.
JO  - Gene
PY  - 1993
SP  - 37
EP  - 44
VL  - 124
AB  - We have tested whether, and to what extent, recombinant clones from DNA segments with
AB  - 5-methylation of cytosines recovered in methylation-restriction (mcr+) hosts contain
AB  - mutations. We constructed a model system in which the tetracycline-resistance-encoding gene
AB  - (tet) from pBR322 was cloned into the plasmid pGEM3Zf+. The central regon of tet was removed
AB  - from the construct, methylated in vitro and then religated back into the unmethylated
AB  - remainder of the construct. The central region of tet was either (1) methylated with a
AB  - combination of four bacterial methyltransferases (M.AluI, M.HaeIII, M.HpaII plus M.HhaI) or
AB  - (2) methylated with M.SssI which methylates at all CpG dinucleotides. These two protocols
AB  - generated theoretical levels of DNA methylation in the central fragment of 10.5% and 33%
AB  - respectively. The construct was transformed into a series of isogenic (recA+) bacterial
AB  - strains that were mcrA+ mcrB+C+, mcrA+, mcrB-C+, mcrA-, mcrB+C+, mcrA-mcrB-C+ or mcrA- mcrBC,
AB  - and also into a set of isogenic recA- derivatives of these strains. With the two methylation
AB  - protocols, there was an average 48- and 141-fold reduction, respectively, in the number of
AB  - transformants recovered from the recA+ mcr+ hosts compared with a methylation-tolerant host
AB  - (mcr-). Of the clones recovered in recA+ mcr+ hosts >20% of clones had an inactivation g
AB  - mutation in tet. The majority of such mutant clones contained deletions that frequently
AB  - extended into the unmethylated portion of tet and even into the plasmid sequences beyond the
AB  - end of the polylinker. With the recA- mcr+ hosts, effective restriction was much more
AB  - stringent, rendering the plasmid containing the methylated segment effectively unclonable. By
AB  - implication, any collection of clones derived from methylated genomic DNA using a recA+ mcr+
AB  - host may contain significant frequencies of sequence artefacts.
ER  -

TY  - JOUR
AU  - Willis, A.
AU  - Parks, M.
AU  - Burford, M.A.
TI  - Draft Genome Assembly of Filamentous Brackish Cyanobacterium Limnoraphis robusta  Strain CS-951.
JO  - Genome Announcements
PY  - 2015
SP  - e00846
EP  - e00815
VL  - 3
AB  - Limnoraphis robusta CS-951 is a sheathed, filamentous benthic, nonheterocystous
AB  - cyanobacterium. It was isolated from brackish water and identified morphologically as Lyngbya
AB  - majuscula. We report the draft genome of L. robusta CS-951, with a genome size of 7,314,117
AB  - bp, a 41.6% GC content, and 6,791 putative protein-coding genes assembled into 361contigs.
ER  -

TY  - JOUR
AU  - Willis, D.B.
AU  - Goorha, R.
AU  - Granoff, A.
TI  - DNA methyltransferase induced by frog virus 3.
JO  - J. Virol.
PY  - 1984
SP  - 86
EP  - 91
VL  - 49
AB  - Over 20% of the cytosine bases in frog virus 3 DNA are methylated at the 5-carbon position. To
AB  - determine whether this high degree of methylation is the result of a virus-specific enzyme, we
AB  - examined the kinetics of induction and the substrate specificity of a DNA methyltransferase
AB  - from frog virus 3-infected fathead minnow cells.  A novel DNA methyltransferase activity
AB  - appeared in the cytoplasm of infected cells at 3 h postinfection.  This activity was induced
AB  - in the absence of viral DNA replication and was therefore probably an early viral enzyme.  In
AB  - contrast to the methyltransferase activity extracted from uninfected cell nuclei, the
AB  - cytoplasmic enzyme showed a strong template preference for double-stranded over
AB  - single-stranded and for unmethylated over hemimethylated DNA.  The dinucleotide sequence dCpdG
AB  - was a necessary and sufficient exogenous substrate for methylation in vitro.  A mutant of frog
AB  - virus 3, isolated as resistant to 5-azacytidine and having unmethylated virion DNA, did not
AB  - induce cytoplasmic DNA methyltransferase, leading to the conclusion that this activity is
AB  - coded for by the virus.
ER  -

TY  - JOUR
AU  - Wilson, A.K.
AU  - Watral, V.G.
AU  - Kent, M.L.
AU  - Sharpton, T.J.
AU  - Gaulke, C.A.
TI  - Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria).
JO  - Genome Announcements
PY  - 2017
SP  - e01090
EP  - e01017
VL  - 5
AB  - Here, we report the draft genome sequence of Pseudomonas sp. strain DrBHI1. The total assembly
AB  - length is 5,649,751 bp in 146 contigs. This strain was isolated
AB  - from zebrafish (Danio rerio) feces.
ER  -

TY  - JOUR
AU  - Wilson, B.D.
AU  - Strauss, M.
AU  - Stickells, B.J.
AU  - Hoal-van Helden, E.G.
AU  - van Helden, P.D.
TI  - An assay for O6-alkylguanine-DNA alkyltransferase based on restriction endonuclease inhibition and magnetic bead separation of products.
JO  - Carcinogenesis
PY  - 1994
SP  - 2143
EP  - 2148
VL  - 15
AB  - We describe an improved, rapid and cost effective assay for measuring O6-alkylguanine-DNA
AB  - alkyltransferase (AGT) levels in large numbers of small biological samples. The assay is based
AB  - on the use of a synthetic O6-methylguanine oligonucleotide bound to magnetic beads via a
AB  - biotin-streptavidin linkage and bound to its complement. A 35S label is incorporated into the
AB  - free end of the duplex. The basis of the assay lies in the observation that the restriction
AB  - enzyme PvuII will not cleave the bead-bound duplex oligonucleotide having an O6-methylguanine
AB  - within the restriction sequence. However, on removal of the methyl group by AGT present in
AB  - cell extracts prior to incubation with PvuII, the 35S-labelled oligonucleotide is cleaved by
AB  - the restriction enzyme, releasing a 35S-labelled 8 bp fragment. Due to the stoichiometric
AB  - nature of the AGT reaction, quantitation of AGT is easily achieved by counting an aliquot of
AB  - the supernatant after pelleting the unrestricted bead complexes with a magnet. AGT levels
AB  - measured in certain cell lines and human lymphocytes by the reported assay are comparable to
AB  - other methods. The assay can be performed in basic laboratories and allows for the rapid
AB  - processing of many samples simultaneously, which could prove useful in clinical and
AB  - epidemiological studies.
ER  -

TY  - JOUR
AU  - Wilson, G.A.
AU  - Williams, M.T.
AU  - Baney, H.W.
AU  - Young, F.E.
TI  - Characterization of temperate bacteriophages of Bacillus subtilis by the restriction endonuclease EcoRI: Evidence for three different temperate bacteriophages.
JO  - J. Virol.
PY  - 1974
SP  - 1013
EP  - 1016
VL  - 14
AB  - Temperate bacteriophages of Bacillus subtilis were characterized according to
AB  - host range and digestion of the bacteriophage genome by endonuclease EcoRI.
AB  - The three bacteriophages, Phi3T, SPO2, and Phi105, were all heteroimmune, and
AB  - the DNA digests showed dissimilar patterns by agarose-ethidium bromide gel
AB  - electrophoresis.
ER  -

TY  - JOUR
AU  - Wilson, G.A.
AU  - Young, F.E.
TI  - Restriction and modification in the Bacillus subtilis genospecies.
JO  - Microbiology-1976
PY  - 1976
SP  - 350
EP  - 357
VL  - 0
AB  - Restriction and modification have not been as intensively studied in
AB  - gram-positive bacilli as in enterobacteriaceae.  This is particularly
AB  - surprising since the Bacillus subtilis genospecies appears to be one in which
AB  - restriction and modification can be studied quite readily.  Included among the
AB  - advantages is the high frequency of genetic exchange among closely related
AB  - members of the genospecies.  This high rate of transformation usually occurs
AB  - with a limited number of genetic loci.  In addition, recent emphasis on the
AB  - genetic organization of B. subtilis has resulted in a detailed map of the
AB  - chromosome (Anagnostopoulos and Trowsdale, p. 44).  The presence of the
AB  - plasmids in closely related strains affords the possibility of using these
AB  - elements in restriction and cloning studies.  The variety of methods for
AB  - genetic exchange and the ease of transformation afford one of the best
AB  - opportunities to study restriction and modification of the isolated DNA.
AB  - Restriction and modification enzymes have been demonstrated in this
AB  - genospecies, and a number of these appear to be unique in the sequence of
AB  - nucleotides they recognize, thus increasing the usefulness of these enzymes in
AB  - the field of recombinant molecule technology.  The bacilli also undergo a
AB  - carefully regulated series of morpho-genetic events leading to the production
AB  - of an endospore.  Finally, unlike the enterobacteriaceae, bacilli have been the
AB  - organisms of choice for the production of a large number of fermentation
AB  - products.  Because of the desire to study morphogenesis and to construct
AB  - strains of commercial importance, an examination of the factors contributing
AB  - toward (or hampering) efficient genetic exchange within the genospecies has
AB  - been intensified.
ER  -

TY  - JOUR
AU  - Wilson, G.A.
AU  - Young, F.E.
TI  - Restriction and modification in the Bacillus subtilis genospecies:  Isolation of an endonuclease in Bacillus amyloliquefaciens.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1975
SP  - 103
EP  - 103
VL  - 75
AB  - Previous studies in this laboratory have demonstrated that deoxyribonucleic
AB  - acid (DNA) is capable of effecting DNA-mediated transformation of B. subtilis.
AB  - Inefficiency of heterospecific transformation prompted a search for restriction
AB  - in the genospecies.  Accordingly mutants of SP02 (SP01clh2 and SP02clh5) were
AB  - isolated that infect B. amyloliquefaciens H.  When propagated on B.
AB  - amyloliquefaciens H, these viruses infected B. amyloliquefaciens H, but were
AB  - markedly restricted by B. subtilis 168.  Restriction was overcome by passage of
AB  - virus on B. subtilis 168.  Transfection of B. subtilis occurred with DNA
AB  - isolated from SP02clh2 propagated on B. subtilis but not with DNA isolated from
AB  - SP02clh2 propagated on B. amyloliquefaciens.  In the latter case biologic
AB  - activity could be recovered by superinfection marker rescue or transfection of
AB  - restriction deficient mutants of B. subtilis.  An endonuclease (BamHI) was
AB  - purified from B. amyloliquefaciens H by (NH4)2S04 precipitation and
AB  - chromatography on DEAE cellulose and phosphocellulose.  Analysis of cleavage
AB  - patterns of standard viral DNA preparations (lambda, SV40, adeno and SP02) by
AB  - gel electrophoresis established that BamHI is different from previously
AB  - described nucleases.  Biochemical tests indicate that BamHI recognized unique
AB  - sites in DNA and may be responsible for restriction in B. amyloliquefaciens.
ER  -

TY  - JOUR
AU  - Wilson, G.A.
AU  - Young, F.E.
TI  - Isolation of a sequence-specific endonuclease (BamI) from Bacillus amyloliquefaciens H.
JO  - J. Mol. Biol.
PY  - 1975
SP  - 123
EP  - 125
VL  - 97
AB  - A restriction endonuclease has been isolated from Bacillus amyloliquefaciens H
AB  - (strain RUB500).  The enzyme, BamI, cleaves adenovirus-2 DNA at three sites,
AB  - phage lambda DNA at five sites, lambda plac DNA at four sites, Phi80 pt DNA at
AB  - 14 sites, and Phi3T+ DNA at four sites.  However, it does not cleave DNA from
AB  - bacteriophage SP02, Phi105 or Phi29.
ER  -

TY  - JOUR
AU  - Wilson, G.A.
AU  - Young, F.E.
TI  - Purification and properties of the BamHI endonuclease.
JO  - Methods Enzymol.
PY  - 1980
SP  - 147
EP  - 153
VL  - 65
AB  - Site-specific endonucleases have been isolated from a diverse variety of microorganisms and
AB  - used extensively in analyzing and manipulating complex genomes.  In fact, the utility of these
AB  - enzymes has resulted in an emphasis on their application and inadvertently hampered a thorough
AB  - examination of the properties and biological functions of these endonucleases.  For example,
AB  - the role of site-specific endonucleases in vivo has not been determined, although, restriction
AB  - and modification properties have been confirmed by genetic studies for EcoRI, EcoRII, BamHI,
AB  - BsuI, Bst1503, BglI, and BglII.  Although the methods of isolation and optimal reaction
AB  - conditions have not been systematically examined, most of the enzymes can be readily isolated
AB  - and purified from contaminating endonucleases and exonucleases.  BamHI proved to be a useful
AB  - enzyme because it produced a single-stranded end after cleaving between the guanine bases at
AB  - the site of 5'-GGATCC-3', thus providing a useful substrate for ligation.  In addition, a
AB  - number of cloning vectors existed or were developed that contained a single recognition site
AB  - for BamHI including vectors SV40, pMB9, pBR313, and pBR322.  These advantages contributed to
AB  - the extensive use of this enzyme and to the development of modifications of our original
AB  - purification procedure that were kindly communicated to us by numerous investigators.  This
AB  - report will summarize the methods of isolation of BamHI and related enzymes from the Bacillus
AB  - genospecies as well as indicate what progress has been made in characterizing these enzymes.
ER  -

TY  - JOUR
AU  - Wilson, G.G.
TI  - Type II restriction-modification systems.
JO  - Trends Genet.
PY  - 1988
SP  - 314
EP  - 318
VL  - 4
AB  - Restriction-modification (R-M) systems are enzymatic mechanisms that occur
AB  - primarily in bacteria.  Their principal function is defensive:  they enable
AB  - cells to resist infections by phage and plasmid DNA molecules that would
AB  - otherwise parasitize them, and they limit the spread of these molecules within
AB  - the population.  R-M systems are traditionally classified into three groups,
AB  - types I, II and III, according to their enzymology and cofactor requirements.
AB  - Type II systems are best understood, and are regarded as the simplest; they are
AB  - also the most familiar to molecular biologists since it is from these systems
AB  - that the restriction enzymes used in recombinant DNA research are purified.  A
AB  - summary of the biology of the type II systems is presented here; the type I and
AB  - type II systems have been reviewed elsewhere.
ER  -

TY  - JOUR
AU  - Wilson, G.G.
TI  - Cloned restriction-modification systems - a review.
JO  - Gene
PY  - 1988
SP  - 281
EP  - 289
VL  - 74
AB  - The genes for numerous restriction endonucleases and modification methylases
AB  - have been cloned into Escherichia coli.  A summary is given for the clones
AB  - isolated so far (115 entries) and of the procedures used to obtain them.
ER  -

TY  - JOUR
AU  - Wilson, G.G.
TI  - Organization of restriction-modification systems.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 2539
EP  - 2566
VL  - 19
AB  - The genes for over 100 restriction-modification systems have now been cloned,
AB  - and approximately one-half have been sequenced.  Despite their similar
AB  - function, they are exceedingly heterogeneous.  The heterogeneity is evident at
AB  - three levels: in the gene arrangements; in the enzyme compositions; and in the
AB  - protein sequences.  This paper summarizes the main features of the R-M systems
AB  - that have been cloned.
ER  -

TY  - JOUR
AU  - Wilson, G.G.
TI  - Amino acid sequence arrangements of DNA-methyltranferases.
JO  - Methods Enzymol.
PY  - 1992
SP  - 259
EP  - 279
VL  - 216
ER  -

TY  - JOUR
AU  - Wilson, G.G.
AU  - Murray, N.E.
TI  - Restriction and Modification Systems.
JO  - Annu. Rev. Genet.
PY  - 1991
SP  - 585
EP  - 627
VL  - 25
AB  - *
AB  - CONTENTS
AB  - INTRODUCTION
AB  - BIOLOGY OF RESTRICTION AND MODIFICATION
AB  -    Restriction and modification enzymes
AB  -    Occurrence of R-M systems
AB  -    Restriction and modification of viruses
AB  -    Cloning restriction and modification genes
AB  - CHARACTERISTICS OF R-M SYSTEMS
AB  -    Type I systems
AB  -    Type II systems
AB  -    Type IIs systems
AB  -    Type III systems
AB  -    Other system types
AB  -    Modification-requiring systems
AB  -    Regulation of expression
AB  - CONTRASTS AND COMPARISONS AMONG R-M SYSTEMS
AB  -    Type I systems
AB  -    Type II systems
AB  -    Type II endonucleases
AB  -    Methyltransferases
AB  - DISCUSSION
AB  - 
ER  -

TY  - JOUR
AU  - Wilson, G.G.
AU  - Wang, H.
AU  - Heiter, D.F.
AU  - Lunnen, K.D.
TI  - Restriction enzymes in microbiology, biotechnology and biochemistry.
JO  - Encuentro
PY  - 2012
SP  - 19
EP  - 48
VL  - 93
AB  - Since their discovery in the nineteen-seventies, a collection of simple enzymes termed Type II
AB  - restriction endonucleases, made by microbes to ward off viral infections, have transformed
AB  - molecular biology, spawned the multi-billion dollar Biotechnology industry, and yielded
AB  - fundamental insights into the biochemistry of life, health and disease.  In this article we
AB  - describe how these enzymes were discovered, and we review their properties, organizations and
AB  - genetics.  We summarize current ideas about the mechanism underlying their remarkable ability
AB  - to recognize and bind to specific base pair sequences in DNA, and we discuss why these ideas
AB  - might not be correct.  We conclude by proposing an alternative explanation for
AB  - sequence-recognition that resolves certain inconsistencies and provides, in our view, a more
AB  - satisfactory account of the mechanism.
ER  -

TY  - JOUR
AU  - Wilson, G.W.
AU  - Edgell, D.R.
TI  - Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 7110
EP  - 7123
VL  - 37
AB  - Homing endonucleases are site-specific DNA endonucleases that typically function as mobile
AB  - genetic elements by introducing a double-strand break
AB  - (DSB) in genomes that lack the endonuclease, resulting in a unidirectional
AB  - gene conversion event that mobilizes the homing endonuclease gene and
AB  - flanking DNA. Here, we characterize phage T4-encoded mobE, a predicted
AB  - free-standing HNH family homing endonuclease. We show that mobE is
AB  - promoterless and dependent on upstream transcription for expression, and
AB  - that an internal intrinsic terminator regulates mobE transcript levels.
AB  - Crucially, in vivo mapping experiments revealed a MobE-dependent,
AB  - strand-specific nick in the non-coding strand of the nrdB gene of phage
AB  - T2. An internal deletion of the predicted HNH catalytic motif of MobE
AB  - abolishes nicking, and reduces high-frequency inheritance of mobE.
AB  - Sequence polymorphisms of progeny phage that inherit mobE are consistent
AB  - with DSB repair pathways. Significantly, we found that mobility of the
AB  - neighboring I-TevIII, a defunct homing endonuclease encoded within a group
AB  - I intron interrupting the nrdB gene of phage T4, was dependent on an
AB  - intact mobE gene. Thus, our data indicate that the stagnant nrdB intron
AB  - and I-TevIII are mobilized in trans as a consequence of a MobE-dependent
AB  - gene conversion event, facilitating persistence of genetic elements that
AB  - have no inherent means of promoting their own mobility.
ER  -

TY  - JOUR
AU  - Wilson, J.G.
AU  - French, W.T.
AU  - Lipzen, A.
AU  - Martin, J.
AU  - Schackwitz, W.
AU  - Woyke, T.
AU  - Shapiro, N.
AU  - Bullard, J.W.
AU  - Champlin, F.R.
AU  - Donaldson, J.R.
TI  - Draft Genome Sequence of Enterobacter cloacae Strain JD6301.
JO  - Genome Announcements
PY  - 2014
SP  - e00381
EP  - e00314
VL  - 2
AB  - Enterobacter cloacae strain JD6301 was isolated from a mixed culture with wastewater collected
AB  - from a municipal treatment facility and oleaginous
AB  - microorganisms. A draft genome sequence of this organism indicates that it has a
AB  - genome size of 4,772,910 bp, an average G+C content of 53%, and 4,509
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Wilson, R. et al.
TI  - 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.
JO  - Nature
PY  - 1994
SP  - 32
EP  - 38
VL  - 368
AB  - As part of our effort to sequence the 100-megabase (Mb) genome of the nematode Caenorhabditis
AB  - elegans, we have completed the nucleotide sequence of a contiguous 2,181,032 base pairs in the
AB  - central gene cluster of chromosome III. Analysis of the finished sequence has indicated an
AB  - average density of about one gene per five kilobases; comparison with the public sequence
AB  - databases reveals similarities to previously known genes for about one gene in three. In
AB  - addition, the genomic sequence contains several intriguing features, including putative gene
AB  - duplications and a variety of other repeats with potential evolutionary implications. [
AB  - Comment in: Nature 1994 Mar 3;368(6466):14-5 ]
ER  -

TY  - JOUR
AU  - Wilson, W.W.
AU  - Hoffman, R.M.
TI  - Methylation of intact chromosomes by bacterial methylases in agarose plugs suitable for pulsed-field electrophoresis.
JO  - Anal. Biochem.
PY  - 1990
SP  - 370
EP  - 375
VL  - 191
AB  - Conditions were determined for the methylation of intact yeast chromosomes by
AB  - EcoRI, HhaI, and MspI bacterial methylases using an endonuclease protection
AB  - assay while the chromosomes were embedded in agarose plugs suitable for
AB  - transverse-field electrophoresis.  Parameters were also established for the
AB  - methylation of human chromosomes by EcoRI methylase.  Methylation of embedded
AB  - chromosomes by EcoRI methylase required prewashes with EDTA.  EcoRI, HhaI, and
AB  - MspI methylases showed optimal activity when nonacetylated bovine serum
AB  - albumin, high levels of S-adenosylmethionine, and high levels of methylase were
AB  - used.  The use of bacterial methylases for methylation of embedded chromosomes
AB  - will allow investigators to normalize variations in cellular DNA methylation
AB  - prior to restriction and create new and rare endonuclease recognition sites
AB  - which will facilitate the detection of chromosomal alterations and deletions.
ER  -

TY  - JOUR
AU  - Wilson, W.W.
AU  - Mebane, E.W.
AU  - Hoffman, R.M.
TI  - Creation of ultra-rare restriction sites in intact eucaryotic chromosomes mediated by bacterial methylases: An approach to sequencing and analyzing tumor and normal genomes.
JO  - Anticancer Res.
PY  - 1993
SP  - 17
EP  - 20
VL  - 13
AB  - The limited restriction of eucaryotic chromosomes would facilitate our understanding of the
AB  - aberrant genomes of genetic diseases and cancer. We have described methods for methylating
AB  - eucaryotic chromosomes embedded in agarose plugs (1). We now describe how ClaI methylase can
AB  - be utilized in a methylation-dependent restriction cleavage with DpnI to restrict eucaryotic
AB  - genomes into a limited number of fragments. We have restricted the genomes of Saccharomyces
AB  - cerevisiae at four sites and cleaved the three chromosomes of Schizosaccharomyces pombe into
AB  - eleven fragments. Unlike the recently published methodologies (2,3,4,5) using DNA sequences
AB  - inserted into procaryotic and eucaryotic genomes, the methodologies described here use
AB  - unaltered eucaryotic genomes for highly limited restriction. This methodology has applications
AB  - in speeding, simplifying, and reducing the cost of sequence the human genome.
ER  -

TY  - JOUR
AU  - Winckler, K.
AU  - Bach, B.
AU  - Obe, G.
TI  - Survival of Saccharomyces cerevisiae after treament with the restriction endonuclease AluI.
JO  - Int. J. Radiat. Biol.
PY  - 1988
SP  - 563
EP  - 566
VL  - 54
AB  - Treatment of yeast cells proficient in the repair of radiation damage
AB  - (Saccharomyces cervisiae) with the restriction endonuclease AluI leads to a
AB  - positive dose-effect relationship between inactivation level and enzyme
AB  - concentration.  The data suggest an uptake of the active restriction enzyme
AB  - into the cells and a relationship between induction of DNA double-strand breaks
AB  - and cell killing.
ER  -

TY  - JOUR
AU  - Windbichler, N.
AU  - Schroeder, R.
TI  - Double duty.
JO  - Nat. Struct. Mol. Biol.
PY  - 2004
SP  - 910
EP  - 911
VL  - 11
AB  - A second high-affinity binding site for the I-TevI homing endonuclease has been discovered.
AB  - Surprisingly, the DNA sequence recognized is the
AB  - protein's own operator; at this site, the endonuclease represses its
AB  - own transcription instead of cleaving the DNA and inducing intron
AB  - homing.
ER  -

TY  - JOUR
AU  - Windolph, S.
AU  - Alves, J.
TI  - Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.
JO  - Eur. J. Biochem.
PY  - 1997
SP  - 134
EP  - 139
VL  - 244
AB  - To understand the functional role of the inner arm region of EcoRI for the interaction with
AB  - its DNA substrate, we mutated each of the positively charged amino acid residues Lys130 and
AB  - Arg131 to Ala or Glu.  The resulting cleavage activities are only about tenfold reduced but
AB  - DNA binding in the absence of divalent cations is totally disrupted for three of the mutants
AB  - ([Ala130]EcoRI, [Glu130]EcoRI and [Glu131]EcoRI).  The binding can be rescued by adding 1 mM
AB  - Ca2+.  This binding behavior resembles that of the blunt end cutter EcoRV.  Furthermore, the
AB  - cleavage activity of the [Glu130]EcoRI is stimulated by Ca2+.  Therefore, a second metal
AB  - binding site is involved in [Glu130]EcoRI catalyzed DNA cleavage.  Its location is postulated
AB  - to be in the inner arm region at positions 133 and 135 presenting an Asp-Xaa-Asp motif typical
AB  - for Ca2+ binding.  A new positive charge at the tip of the inner arm due to the basic amino
AB  - acids Lys130 and Arg131 in the wild-type enzyme or due to binding of a divalent cation in the
AB  - mutants is important for DNA recognition by EcoRI.  However, a direct phosphate contact
AB  - providing an indirect readout is not observed.  Implications of the binding and cleavage
AB  - behavior with regard to mechanistic differences between blunt end and sticky end cutters and a
AB  - general catalytic mechanism of restriction enzymes are discussed.
ER  -

TY  - JOUR
AU  - Windolph, S.
AU  - Fritz, A.
AU  - Oelgeschlager, T.
AU  - Wolfes, H.
AU  - Alves, J.
TI  - Sequence context influencing cleavage activity of the K130E mutant of the restriction endonuclease EcoRI identified by a site selection assay.
JO  - Biochemistry
PY  - 1997
SP  - 9478
EP  - 9485
VL  - 36
AB  - We have generated several EcoRI mutants which exhibit a decreased cleavage rate on one of the
AB  - five specific cleavage sites in bacteriophage lambda-DNA.  To study the influence of the
AB  - sequence context on the cleavage rate in more detail, we developed a site selection assay.
AB  - From a complete set of 4096 plasmid substrates, differing in three bases on both sides of a
AB  - recognition sequence, optimal (best cut) and unfavorable (worst cut) sequences were selected
AB  - by repeated limited digestion, separation, and in vivo amplification of cleaved and uncleaved
AB  - plasmids.  In order to compare the sequence preferences of the inner arm mutant K130E and the
AB  - wild type enzyme, the cleavage rates and sequences of individual plasmids from the resulting
AB  - pools were determined.  The inner arm mutant K130E selected pools with clearly defined
AB  - consensus sequences and a high amount of palindromic sequences.  The cleavage rates of the
AB  - selected sequences are specific for the K130E mutant as is shown by their cleavage with other
AB  - mutants.  In contrast, wild type EcoRI does not lead to a selection in this assay.  Pre-steady
AB  - state kinetics show that preferences for a certain sequence context are a result of
AB  - differences in the dissociation rates of the wild type enzyme.  EcoRI is evolved to
AB  - efficiently recognize and cleave each nonmethylated DNA invading the cell.  Therefore, a fast
AB  - dissociation after cleavage is not mandatory.
ER  -

TY  - JOUR
AU  - Winegar, R.A.
AU  - Land, M.C.
AU  - Morgan, W.F.
TI  - Increased chromosomal radiosensitivity of a Chinese hamster ovary cell line that inducibly expresses the EcoRI restriction endonuclease.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1989
SP  - 1079
EP  - 1084
VL  - 160
AB  - We have transfected a Chinese hamster ovary cell line (CHO 6) with a plasmid
AB  - that inducibly expresses the EcoRI restriction endonuclease gene in the
AB  - presence of cadmium sulfate (CdSO4).  Expression of EcoRI results in DNA
AB  - double-strand breaks, which can lead to chromosome aberrations.  The new line,
AB  - designated CHO 10, also has a low level of constitutive expression of EcoRI in
AB  - the absence of CdSO4 without any cytogenetic effect.  This suggested that these
AB  - cells may be efficient at repairing low levels of DNA double-strand breaks.  To
AB  - test this, both cell lines were exposed to ionizing radiation, and aberration
AB  - yields were analyzed with or without induction of EcoRI.  CHO 10 cells showed
AB  - increased radiosensitivity after G1 irradiation, but after G2 exposure, only
AB  - doses > 0.4 Gy caused more damage in CHO 10 cells.  We conclude that CHO 10
AB  - cells can tolerate constitutive expression of EcoRI, but that when the cells
AB  - are subjected to additional stress, in this case ionizing radiation, they
AB  - become very sensitive to DNA double-strand breaks.
ER  -

TY  - JOUR
AU  - Winegar, R.A.
AU  - Phillips, J.W.
AU  - Youngblom, J.H.
AU  - Morgan, W.F.
TI  - Cell electroporation is a highly efficient method for introducing restriction endonucleases into cells.
JO  - Mutat. Res.
PY  - 1989
SP  - 49
EP  - 53
VL  - 225
AB  - Restriction endonucleases that make either blunt- or cohesive-end DNA
AB  - double-strand breaks can induce chromosome aberrations.  We have used cell
AB  - electroporation with great success to permeabilize Chinese hamster ovary cells
AB  - for the introduction of restriction enzymes.  The introduction of restriction
AB  - enzymes by this method resulted in extremely high frequences (>90%) of aberrant
AB  - metaphase cells and also a dramatic decrease in cell survival, as measured by
AB  - subsequent colony formation.  Cell electroporation by itself caused no increase
AB  - in aberrant chromosomes and had only a slight effect on cell survival.
ER  -

TY  - JOUR
AU  - Wines, D.R.
AU  - Talbert, P.B.
AU  - Clark, D.V.
AU  - Henikoff, S.
TI  - Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo.
JO  - Chromosoma
PY  - 1996
SP  - 332
EP  - 340
VL  - 104
AB  - The dam DNA methyltransferase gene from Escherichia coli was introduced into Drosophila in
AB  - order to probe chromatin structure in vivo.  Expression of the gene caused no visible defects
AB  - or developmental delay even at high levels of active methylase.  About half of each target
AB  - site was found to be methylated in vivo, apparently reflecting a general property of chromatin
AB  - packaged in nucleosomes.  Although site-specific differences were detected, most euchromatic
AB  - and heterochromatic sites showed comparable degrees of methylation, at least at high methylase
AB  - levels.  Methylase accessibility of a lacZ reporter gene subject to position-effect
AB  - variegation throughout development was only slightly reduced, consistent with studies of
AB  - chromatin accessibility in vitro.  Silencing of lacZ during development differed from
AB  - silencing of an adjacent white eye pigment reporter gene in the adult, as though chromatin
AB  - structure can undergo dynamic alterations during development.
ER  -

TY  - JOUR
AU  - Winget, D.M.
AU  - Wommack, K.E.
TI  - Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness.
JO  - Appl. Environ. Microbiol.
PY  - 2008
SP  - 2612
EP  - 2618
VL  - 74
AB  - Recent discoveries have uncovered considerable genetic diversity among
AB  - aquatic viruses and raised questions about the variability of this
AB  - diversity within and between environments. Studies of the temporal and
AB  - spatial dynamics of aquatic viral assemblages have been hindered by the
AB  - lack of a common genetic marker among viruses for rapid diversity
AB  - assessments. Randomly amplified polymorphic DNA (RAPD) PCR bypasses this
AB  - obstacle by sampling at the genetic level without requiring viral
AB  - isolation or previous sequence knowledge. In this study, the utility of
AB  - RAPD-PCR for assessing DNA viral richness within Chesapeake Bay water
AB  - samples was evaluated. RAPD-PCR using single 10-mer oligonucleotide
AB  - primers successfully produced amplicons from a variety of viral samples,
AB  - and banding patterns were highly reproducible, indicating that each band
AB  - likely represents a single amplicon originating from viral template DNA.
AB  - In agreement with observations from other community profiling techniques,
AB  - resulting RAPD-PCR banding patterns revealed more temporal than spatial
AB  - variability in Chesapeake Bay virioplankton assemblages. High-quality
AB  - hybridization probes and sequence information were also easily generated
AB  - from single RAPD-PCR products or whole reactions. Thus, the RAPD-PCR
AB  - technique appears to be practical and efficient for routine use in
AB  - high-resolution viral diversity studies by providing assemblage
AB  - comparisons through fingerprinting, probing, or sequence information.
ER  -

TY  - JOUR
AU  - Winkle, S.A.
AU  - Aloyo, M.C.
AU  - Morales, N.
AU  - Zambrano, T.Y.
AU  - Sheardy, R.D.
TI  - Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI.
JO  - Biochemistry
PY  - 1991
SP  - 10601
EP  - 10606
VL  - 30
AB  - We have been investigating the structure, dynamics, and ligand-binding
AB  - properties of the interface that exists between a right-handed conformation and
AB  - a left-handed conformation (i.e., a B-Z junction) in synthetic DNA oligomers.
AB  - Since exo- and endonuclease activity is known to be sensitive to the
AB  - conformation of the template DNA, we have designed and synthesized a DNA
AB  - oligonucleotide of 20 base pairs (designated as BZ-III) with an MboI
AB  - recognition site (GATC) at the location of a potential B-Z junction.  The
AB  - activity of the MboI enzyme toward this molecule and DNA oligomers that contain
AB  - multiple MboI sites located at B-Z junctions was monitored in the absence and
AB  - presence of the Z-conformation-inducing reagent cobalt hexaammine.  In all
AB  - cases, the activity of the enzyme was enhanced in the presence of cobalt
AB  - hexaammine.  The activity of MboI toward BZ-III, in the presence and absence of
AB  - cobalt hexaammine, was also examined when the DNA oligomer is also in the
AB  - presence of the DNA binding drugs actinomycin D, ametantrone, or ethidium
AB  - bromide.  In all cases, the activity of the enzyme was inhibited in the
AB  - presence of drug.  The results suggest that B-Z junctions are structurally
AB  - unique and that this uniqueness may alter nuclease activity at sites in or near
AB  - the junction.
ER  -

TY  - JOUR
AU  - Winkle, S.A.
AU  - Aloyo, M.C.
AU  - Smoller, J.H.
AU  - Herrera, J.E.
AU  - Chaires, J.B.
AU  - Sheardy, R.D.
TI  - Junctions affect the sensitivity of DNAs to reactions with enzymes.
JO  - FASEB J.
PY  - 1992
SP  - A219
EP  - A219
VL  - 6
AB  - We have investigated the reactions of various enzymes with DNAs possessing junctions, for
AB  - example: BZI C*GC*GC*GC*GACTGACTG; BZIII ATC*GC*GC*GC*GATCAGTCAGT; BZIV TCGACGCGCGCGATCAGTCA
AB  - (where C* is 5-methylC and where potential junctions are underlined). DNase I and Exonuclease
AB  - III show inhibited cleavage at the junctions both under low salt B conditions and in the
AB  - presence of Z-inducing cobalt hexamine. Restriction enzymes attacking either the junction or,
AB  - when BZ IV is inserted into a plasmid, sequences flanking the inserted BZ IV sequence show
AB  - enhanced cleavage in the presence of cobalt hexamine or supercoiling. Dam methylase has
AB  - enhanced reactivity for the GATC at the junction of BZ IV in the presence of cobalt hexamine.
AB  - These results suggest that these junctions have a structural distinctiveness recognizable by
AB  - various enzyme types.
ER  -

TY  - JOUR
AU  - Winkle, S.A.
AU  - Thomson, H.
AU  - Aguilar, L.P.
AU  - Sheardy, R.D.
TI  - The effects of alternate DNA structures on restriction enzyme and polymerase binding and activities with DNAS.
JO  - Biophys. J.
PY  - 2002
SP  - 463a
EP  - 463a
VL  - 82
AB  - The variety of structural motifs which DNA molecules may assume, depending upon sequence,
AB  - affects the activities of proteins using DNA as a substrate.  We have examined the effects of
AB  - the (CG)3 segment and cruciform structures found in phiX174 RF DNA (in the linear and
AB  - supercoiled forms) on E. coli DNA polymerase I binding and activity.  Gel mobility shift
AB  - assays of DNA fragments containing these features suggest that DNA polymerase binds to these
AB  - structural features.  Polymerase activity studies, including studies under PCR conditions,
AB  - indicate that the structures alter the activity.  Cleavage studies at or near these structures
AB  - by restriction enzymes, e.g., BssHII, HhaI, also show anomalies.  Binding of restriction
AB  - enzymes and DNA polymerase I to small DNA hairpins was also investigated using gel mobility
AB  - shift assays.  The results of these studies suggest that local structures do affect the
AB  - workings of enzymes and thus these structures may help regulate enzyme activities.
ER  -

TY  - JOUR
AU  - Winkler, F.K.
TI  - Structure and function of restriction endonucleases.
JO  - Curr. Opin. Struct. Biol.
PY  - 1992
SP  - 93
EP  - 99
VL  - 2
AB  - New insight into how restriction endonucleases achieve their remarkable sequence specificity
AB  - has been gained by comparing the structures of EcoRI and EcoRV endonucleases complexed with
AB  - DNA fragments that contain their respective canonical sites. Despite the lack of overall
AB  - structural homology, essential features of the catalytic site, including the locations of two
AB  - acidic and one lysine residue, are structurally conserved. Mutagenesis studies, newly
AB  - initiated for the EcoRV enzyme, have confirmed the essential nature of these particular
AB  - residues but have also yielded interesting effects that were quite unforeseen.
ER  -

TY  - JOUR
AU  - Winkler, F.K.
TI  - DNA totally flipped-out by methylase.
JO  - Structure
PY  - 1994
SP  - 79
EP  - 83
VL  - 2
AB  - In research, surprises are always refreshing and stimulating. The latest such example in the
AB  - field of protein-DNA interactions is provided by Klimasauskas et al. reporting the crystal
AB  - structure determination of the enzyme HhaI methylase from Haemophilus haemolyticus, a DNA
AB  - cytosine-5-methyltransferase (m5C-MTase), covalently bound to a 13-mer DNA duplex (Fig.1). The
AB  - covalent complex represents a chemically trapped reaction intermediate and also contains
AB  - S-adenosyl-L-methionine (AdoMet). The most spectacular and unexpected feature of this
AB  - structure is that the target cytosine base is completely flipped out of the DNA duplex and in
AB  - its place the DNA is infiltrated by a glutamine and a serine side chain from the major and
AB  - minor groove side respectively. Just as we are becoming accustomed to drastic amounts of
AB  - bending, kinking, unwinding and base-pair unstacking, most notably by the TATA box binding
AB  - protein or the endonucleases EcoRI and EcoRV, this enzyme goes even further by forcing its
AB  - substrate DNA to flip out the base it is going to methylate.
ER  -

TY  - JOUR
AU  - Winkler, F.K.
TI  - Restriction endonucleases, the ultimate in sequence specific DNA recognition.
JO  - J. Mol. Recognit.
PY  - 1994
SP  - 9
EP  - 9
VL  - 6
AB  - X-ray crystallographic and NMR spectroscopic studies with a variety of proteins that interact
AB  - in a sequence-specific manner with DNA have revealed a wealth of detailed structural
AB  - information over the past few years. It has become clear that DNA sequence recognition or
AB  - discrimination can be achieved in many different ways and that conformational changes in
AB  - protein and DNA often accompany the binding. Among the systems studied, mostly DNA binding
AB  - proteins involved in transcriptional control, restriction endonucleases demonstrate the
AB  - highest discrimination between cognate and noncognate DNA sequences. The structures of two
AB  - type II restriction endonucleases, EcoRI and EcoRV recognizing the hexamer sequences GAATTC
AB  - and GATATC respectively, have thus far been determined as complexes with cognate DNA
AB  - fragments. The structural and functional data now available for these two enzymes have yielded
AB  - important insights into how they achieve their remarkable specificity. The two enzymes show no
AB  - structural similarity except in their active site region where the arrangement of two acidic
AB  - and one basic residue appears conserved. Both enzymes bind their cognate DNA fragments in
AB  - rather distorted conformations but the distortions are completely different in the two cases.
AB  - Recognition involves the formation of hydrogen bonds to the base pairs in the major groove and
AB  - the extended set of interactions appears highly cooperative. However, the distorted
AB  - conformation of productively bound DNA plays an important role too. It provides extra
AB  - discrimination against noncognate sequences and appears crucial in coupling proper recognition
AB  - to efficient catalysis.
ER  -

TY  - JOUR
AU  - Winkler, F.K.
AU  - Banner, D.W.
AU  - Oefner, C.
AU  - Tsernoglou, D.
AU  - Brown, R.S.
AU  - Heathman, S.P.
AU  - Bryan, R.K.
AU  - Martin, P.D.
AU  - Petratos, K.
AU  - Wilson, K.S.
TI  - The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.
JO  - EMBO J.
PY  - 1993
SP  - 1781
EP  - 1795
VL  - 12
AB  - The crystal structure of EcoRV endonuclease has been determined at 2.5 A resolution and that
AB  - of its complexes with the cognate DNA decamer GGGATATCC (recognition sequence underlined) and
AB  - the non-cognate DNA octamer CGAGCTCG at 3.0 A resolution. Two octamer duplexes of the
AB  - non-cognate DNA, stacked end-to-end, are bound to the dimeric enzyme in B-DNA like
AB  - conformations. The protein-DNA interactions of this complex are prototypic for non-specific
AB  - DNA binding. In contrast, only one cognate decamer duplex is bound and deviates considerably
AB  - from canonical B-form DNA. Most notably, a kink of approximately 50 degrees is observed at the
AB  - central TA step with a concomitant compression of the major groove. Base-specific hydrogen
AB  - bonds between the enzyme and the recognition base pairs occur exclusively in the major groove.
AB  - These interactions appear highly co-operative as they are all made through one short surface
AB  - loop comprising residues 182-186. Numerous contacts with the sugar phosphate backbone
AB  - extending beyond the recognition sequence are observed in both types of complex. However, the
AB  - total surface area buried on complex formation is >1800 A2 larger in the case of cognate DNA
AB  - binding. Two acidic side chains, Asp74 and Asp90, are close to the reactive phosphodiester
AB  - group in the cognate complex and most probably provide oxygen ligands for binding the
AB  - essential cofactor Mg2+. An important role is also indicated for Lys92, which together with
AB  - the two acidic functions appears to be conserved in the otherwise unrelated structure of EcoRI
AB  - endonuclease. The structural results give new insight into the physical basis of the
AB  - remarkable sequence specificity of this enzyme.
ER  -

TY  - JOUR
AU  - Winkler, F.K.
AU  - Brown, R.S.
AU  - Leonard, K.
AU  - Berriman, J.
TI  - Structural studies of EcoRV endonuclease and of its complexes with short DNA fragments.
JO  - Nato Advanced Studies: Crystallography in Molecular Biology
PY  - 1987
SP  - 345
EP  - 352
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Winkler, F.K.
AU  - D'Arcy, A.
AU  - Blocker, H.
AU  - Frank, R.
AU  - van Boom, J.H.
TI  - Crystallization of complexes of EcoRV endonuclease with cognate and non-cognate DNA fragments.
JO  - J. Mol. Biol.
PY  - 1991
SP  - 235
EP  - 238
VL  - 217
AB  - Complexes of the type II restriction endonuclease EcoRV with a variety of
AB  - short, self-complementary deoxyoligonucleotides have been crystallized.  The
AB  - best crytals diffract to about 2.7 angstrom resolution and consist of 1:1
AB  - complexes between endonuclease dimers and duplexes of the cognate decamer
AB  - GGGATATCCC containing the hexameric EcoRV recognition sequence GATATC.
AB  - Crystals with the non-cognate DNA octamer duplexes CGAGCTCG and CGAATTCG
AB  - diffract to 3.0 and 3.5 angstrom resolution, respectively, and contain two DNA
AB  - duplexes per enzyme dimer.
ER  -

TY  - JOUR
AU  - Winkler, F.K.
AU  - Prota, A.E.
TI  - Structure and function of EcoRV endonuclease.
JO  - Nucleic Acids Mol. Biol.
PY  - 2004
SP  - 179
EP  - 214
VL  - 14
AB  - The homodimeric, orthodox Type II restriction endonuclease EcoRV cleaves double-stranded DNA
AB  - with high specificity at hexameric GAT/ATC sites in a blunt-ended fashion.  Like most of the
AB  - restriction enzymes used as tools in recombinant DNA technology it can be considered as a
AB  - simple hydrolytic enzyme of relatively small size with precisely defined substrate specificity
AB  - and the rather common requirement for Mg2+ ions.  Yet, these apparently simple enzymes become
AB  - fascinating objects for structural and functional studies, and their molecular simplicity
AB  - becomes an advantage once we start asking detailed mechanistic questions.  For example, it is
AB  - quite obvious that these enzymes have been engineered by evolution to deal with the problem of
AB  - efficiently locating a specific site on DNA, which is immersed in a huge molar excess of
AB  - other, partly very similar sites.
ER  -

TY  - JOUR
AU  - Winkler, K.-P.
TI  - Isolation and characterization of a sequence specific restriction endonuclease from Rhizobium lupini.
JO  - Ph.D. Thesis, Erlangen University, W. Germany
PY  - 1980
SP  - 1
EP  - 135
AB  - None
ER  -

TY  - JOUR
AU  - Winter, M.
TI  - Investigation of de novo methylation activity in mutants of the EcoKI methyltransferase.
JO  - Ph.D. Thesis, University of Edinburgh, Edinburgh, Scotland
PY  - 1997
SP  - 1
EP  - 216
AB  - A group of mutants of the EcoKI R/M-system displaying de novo methylation activity have been
AB  - isolated.  The mutated genes were transferred into an overexpressing plasmid vector.  Two of
AB  - the over-expressed proteins were purified to near homogeneity from clones transformed with the
AB  - plasmids.  Cofactor binding activities of wild-type and the two mutant enzymes were compared
AB  - by 1,8-anilino-napthalene sulphonic acid fluorescence displacement experiments.  A DNA
AB  - methylation assay based upon the transfer of a tritiated methyl group from the cofactor AdoMet
AB  - to the substrate DNA was established and used to examine the dependency of the reaction on
AB  - cofactor, substrate, and enzyme concentration.  In addition the stability of the trimeric
AB  - enzyme at different protein concentrations was followed by HPLC gel filtration.  Sequence
AB  - alignments, secondary structure predictions, and tertiary structural modelling were used to
AB  - show the similarity of the Type I system EcoKI with methyltransferases from other classes
AB  - (especially Type II methyltransferases), thereby establishing a structural and suggesting an
AB  - evolutionary link between the different methyltransferase classes.  The information obtained
AB  - by these comparisons enabled the subsequent modelling of a more refined model of the EcoKI
AB  - structure.  A model is proposed to explain the different activities observed in wild-type and
AB  - mutant enzymes based on the biochemical and structural data obtained during these
AB  - investigations.
ER  -

TY  - JOUR
AU  - Wion, D.
AU  - Casadesus, J.
TI  - N-6-methyl-adenine: an epigenetic signal for DNA-protein interactions.
JO  - Nat. Rev. Microbiol.
PY  - 2006
SP  - 183
EP  - 192
VL  - 4
AB  - N6-methyl-adenine is found in the genomes of bacteria, archaea, protists and fungi.  Most
AB  - bacterial DNA adenine methyltransferases are part of restriction-modification systems.
AB  - Certain groups of Proteobacteria also harbour solitary DNA adenine methyltransferases that
AB  - provide signals for DNA-protein interactions.  In gamma-proteobacteria, Dam methylation
AB  - regulates chromosome replication, nucleoid segregation, DNA repair, transposition of insertion
AB  - elements and transcription of specific genes.  In Salmonella, Haemophilus, Yersinia and Vibrio
AB  - species and in pathogenic Escherichia coli, Dam methylation is required for virulence.  In
AB  - alpha-proteobacteria, CcrM methylation regulates the cell cycle in Caulobacter, Rhizobium and
AB  - Agrobacterium, and has a role in Brucella abortus infection.
ER  -

TY  - JOUR
AU  - Wirth, R. et al.
TI  - Complete genome sequence of Thermocrinis albus type strain (HI 11/12).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 194
EP  - 202
VL  - 2
AB  - Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in
AB  - the family Aquificaceae. Members of this family have become of
AB  - significant interest because of their involvement in global biogeochemical cycles
AB  - in high-temperature ecosystems. This interest had already spurred several genome
AB  - sequencing projects for members of the family. We here report the first completed
AB  - genome sequence a member of the genus Thermocrinis and the first type strain
AB  - genome from a member of the family Aquificaceae. The 1,500,577 bp long genome
AB  - with its 1,603 protein-coding and 47 RNA genes is part of the Genomic
AB  - Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Wirth, R. et al.
TI  - Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 173
EP  - 182
VL  - 4
AB  - Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus
AB  - Desulfurococcus, which belongs to the crenarchaeal family Desulfurococcaceae. The
AB  - species is of interest because of its position in the tree of life, its ability
AB  - for sulfur respiration, and several biotechnologically relevant thermostable and
AB  - thermoactive extracellular enzymes. This is the third completed genome sequence
AB  - of a member of the genus Desulfurococcus and already the 8(th) sequence from a
AB  - member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371
AB  - protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Wise, K.S.
AU  - Calcutt, M.J.
AU  - Foecking, M.F.
AU  - Madupu, R.
AU  - Deboy, R.T.
AU  - Roske, K.
AU  - Hvinden, M.L.
AU  - Martin, T.R.
AU  - Durkin, A.S.
AU  - Glass, J.I.
AU  - Methe, B.A.
TI  - Complete Genome Sequences of Mycoplasma leachii Strain PG50T and the Pathogenic Mycoplasma mycoides subsp. mycoides Small Colony Biotype Strain Gladysdale.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4448
EP  - 4449
VL  - 194
AB  - Mycoplasma mycoides subsp. mycoides small colony biotype (SC) is the high-consequence animal
AB  - pathogen causing contagious bovine pleuropneumonia. We
AB  - report the complete genome sequences of the pathogenic strain M. mycoides subsp.
AB  - mycoides SC Gladysdale and a close phylogenetic relative, Mycoplasma leachii
AB  - PG50(T), another bovine pathogen of the M. mycoides phylogenetic clade.
ER  -

TY  - JOUR
AU  - Wisniewski-Dye, F. et al.
TI  - Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.
JO  - PLoS Genet.
PY  - 2011
SP  - e1002430
EP  - e1002430
VL  - 7
AB  - Fossil records indicate that life appeared in marine environments ,3.5 billion years ago (Gyr)
AB  - and transitioned to terrestrial
AB  - ecosystems nearly 2.5 Gyr. Sequence analysis suggests that 'hydrobacteria' and
AB  - 'terrabacteria' might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum
AB  - are associated with roots of terrestrial plants; however, virtually all their close relatives
AB  - are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene
AB  - origins.
AB  - While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives,
AB  - this lineage has obtained nearly half of its genome from terrestrial organisms. The majority
AB  - of genes encoding functions critical for association with plants are among horizontally
AB  - transferred genes. Our results show that transition of some aquatic bacteria to terrestrial
AB  - habitats
AB  - occurred much later than the suggested initial divergence of hydro- and terrabacterial clades.
AB  - The birth of the genus Azospirillum approximately coincided with the emergence of vascular
AB  - plants on land.
ER  -

TY  - JOUR
AU  - Wissuwa, J.
AU  - Bauer, S.L.
AU  - Steen, I.H.
AU  - Stokke, R.
TI  - Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 5
EP  - 5
VL  - 12
AB  - Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a  biofilm
AB  - growing on the surface of a black smoker chimney at the Loki's Castle
AB  - vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L.
AB  - profundi LP1T is the first genome to be published within the genus Lutibacter. L.
AB  - profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC
AB  - content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA
AB  - species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains
AB  - genes for all central carbohydrate metabolic pathways. However, genes for the
AB  - oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the
AB  - tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not
AB  - present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon
AB  - sources. In accordance, the genome harbours 130 proteases and 104
AB  - carbohydrate-active enzymes, indicating a specialization in degrading organic
AB  - matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the
AB  - possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization
AB  - cluster was identified. Furthermore, a variety of enzymes may be secreted via
AB  - T9SS and contribute to the hydrolytic variety of the microorganism. Genes for
AB  - gliding motility are present, which may enable the bacteria to move within the
AB  - biofilm. A substantial number of genes encoding for extracellular polysaccharide
AB  - synthesis pathways, curli fibres and attachment to surfaces could mediate
AB  - adhesion in the biofilm and may contribute to the biofilm formation. In addition
AB  - to aerobic respiration, the complete denitrification pathway and genes for
AB  - sulphide oxidation e.g. sulphide:quinone reductase are present in the genome.
AB  - sulphide:quinone reductase and denitrification may serve as detoxification
AB  - systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched
AB  - environment. The information gained from the genome gives a greater insight in
AB  - the functional role of L. profundi LP1T in the biofilm and its adaption strategy
AB  - in an extreme environment.
ER  -

TY  - JOUR
AU  - Wissuwa, J.
AU  - Stokke, R.
AU  - Fedoy, A.E.
AU  - Lian, K.
AU  - Smalas, A.O.
AU  - Steen, I.H.
TI  - Isolation and complete genome sequence of the thermophilic Geobacillus sp. 12AMOR1 from an Arctic deep-sea hydrothermal vent site.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 16
EP  - 16
VL  - 11
AB  - Members of the genus Geobacillus have been isolated from a wide variety of habitats worldwide
AB  - and are the subject for targeted enzyme utilization in various
AB  - industrial applications. Here we report the isolation and complete genome
AB  - sequence of the thermophilic starch-degrading Geobacillus sp. 12AMOR1. The strain
AB  - 12AMOR1 was isolated from deep-sea hot sediment at the Jan Mayen hydrothermal
AB  - Vent Site. Geobacillus sp. 12AMOR1 consists of a 3,410,035 bp circular chromosome
AB  - and a 32,689 bp plasmid with a G + C content of 52 % and 47 %, respectively. The
AB  - genome comprises 3323 protein-coding genes, 88 tRNA species and 10 rRNA operons.
AB  - The isolate grows on a suite of sugars, complex polysaccharides and proteinous
AB  - carbon sources. Accordingly, a versatility of genes encoding carbohydrate-active
AB  - enzymes (CAZy) and peptidases were identified in the genome. Expression,
AB  - purification and characterization of an enzyme of the glycoside hydrolase family
AB  - 13 revealed a starch-degrading capacity and high thermal stability with a melting
AB  - temperature of 76.4 degrees C. Altogether, the data obtained point to a new
AB  - isolate from a marine hydrothermal vent with a large bioprospecting potential.
ER  -

TY  - JOUR
AU  - Withers, B.E.
AU  - Ambroso, L.A.
AU  - Dunbar, J.C.
TI  - Structure and evolution of the XcyI restriction-modification system.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6267
EP  - 6273
VL  - 20
AB  - The XcyI restriction-modificaton system from Xanthomonas cyanopsidis recognizes the sequence,
AB  - CCCGGG. The XcyI endonuclease and methylase genes have been cloned and sequenced and were
AB  - found to be aligned in a head to tail orientation with the methylase preceding and overlapping
AB  - the endonuclease by one base pair. The nucleotide sequence codes for an N4 cytosine
AB  - methyltransferase with a predicted molecular weight of 33,500 and an endonuclease comprised of
AB  - 333 codons and a molecular weight of 36,600. Sequence comparisons revealed significant
AB  - similarity between the XcyI, CfrI and SmaI methylisomers. in contrast, no similarity was
AB  - detected between the primary structures of the XcyI and SmaI endonucleases. The XcyI
AB  - restriction-modification system is highly homologous to the XmaI genes, although the DNA
AB  - sequences flanking the genes rapidly diverge. The sequence of the XcyI endonuclease contains
AB  - two motifs which have recently been identified as essential to the activity of the EcoRV
AB  - endonuclease.
ER  -

TY  - JOUR
AU  - Withers, B.E.
AU  - Dunbar, J.C.
TI  - DNA determinants in sequence-specific recognition by XmaI endonuclease.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 3571
EP  - 3577
VL  - 23
AB  - The XmaI endonuclease recognizes and cleaves the sequence C/CCGGG.  Magnesium is required for
AB  - catalysis, however, the enzyme forms stable, specific complexes with DNA in the absence of
AB  - magnesium.  An association constant of 1.2 x 10/9 M was estimated for the affinity of the
AB  - enzyme for a specific 195 bp fragment.  Competition assays revealed that the site-specific
AB  - association constant represented an approximately 10/4-fold increase in affinity over that for
AB  - non-cognate sites.  Missing nucleoside analyses suggested an interaction of the enzyme with
AB  - each of the cytosines and guanines within the recognition site.  Recognition of each of the
AB  - guanines was also indicated by dimethylsulfate interference footprinting assays.  The
AB  - phosphates 5' to the guanines within the recognition site appeared to be the major sites of
AB  - interaction of XmaI with the sugar-phosphate backbone.  No significant interaction of the
AB  - protein was observed with phosphates flanking the recognition sequence.  Comparison of the
AB  - footprinting patterns of XmaI with those of the neoschizomer SmaI (CCC/GGG) revealed that the
AB  - two enzymes utilize the same DNA determinants in their specific interaction with the CCCGGG
AB  - recognition site.
ER  -

TY  - JOUR
AU  - Withers, B.E.
AU  - Dunbar, J.C.
TI  - The endonuclease isoschizomers, SmaI and XmaI bend DNA in opposite orientations.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 2571
EP  - 2577
VL  - 21
AB  - The SmaI and XmaI endonucleases are imperfect isoschizomers that recognize the sequence
AB  - CCCGGG. SmaI cleaves between the internal CpG to produce blunt end scissions whereas XmaI
AB  - cleaves between the external cytosines to produce a four base, five prime overhang. Each of
AB  - the endonucleases forms stable, specific complexes with DNA in the absence of magnesium.
AB  - Circular permutation analyses of the protein-DNA complexes revealed that each of the
AB  - endonucleases induces bending of the DNA. Phase sensitive detection analyses verified the
AB  - existence of the SmaI and XmaI induced bends. Furthermore bending of the helix axis by the
AB  - endonucleases appeared to be directed in opposite orientations. The orientation of the
AB  - SmaI-induced bend appeared to be towards the major groove and is reminiscent of the direction
AB  - of the bend induced by EcoRV which similarly induces blunt end scissions. Conversely, XmaI
AB  - appeared to bend the DNA towards the minor groove.
ER  -

TY  - JOUR
AU  - Withers, B.E.
AU  - Dunbar, J.C.
TI  - Sequence-specific DNA recognition by the SmaI endonuclease.
JO  - J. Biol. Chem.
PY  - 1995
SP  - 6496
EP  - 6504
VL  - 270
AB  - SmaI endonuclease recognizes and cleaves the sequence CCC/GGG. The enzyme requires magnesium
AB  - for catalysis; however, equilibrium binding assays revealed that the enzyme binds specifically
AB  - to DNA in the absence of magnesium. A specific association constant of 0.9 x 10/8 M-1 was
AB  - determined for SmaI binding to a 22-base duplex oligonucleotide. Furthermore, the KA was a
AB  - function of the length of the DNA substrate and the enzyme exhibited an affinity of 1.2 x 10/9
AB  - M-1 for a 195-base pair fragment and which represented a 10/4-fold increase in affinity over
AB  - binding to nonspecific sequences. A Km of 17.5 nM was estimated from kinetic assays based on
AB  - cleavage of the 22-base oligonucleotide and is not significantly different from the KD
AB  - estimated from the thermodynamic analyses. Footprinting (dimethyl sulfate and missing
AB  - nucleoside) analyses revealed that SmaI interacts with each of the base pairs within the
AB  - recognition sequence. Ethylation interference assays suggested that the protein contacts three
AB  - adjacent phosphages on each strand of the recognition sequence. Significantly, a predicted
AB  - protein contact with the phosphate 3' of the scissile bond may have implications in the
AB  - mechanism of catalysis by SmaI.
ER  -

TY  - JOUR
AU  - Withers, T.R.
AU  - Johnson, S.L.
AU  - Yu, H.D.
TI  - Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579, a Mucoid Derivative of PAO381.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6617
EP  - 6617
VL  - 194
AB  - Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection
AB  - in individuals afflicted with cystic fibrosis. Here, we announce
AB  - the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing
AB  - derivative of strain PAO381.
ER  -

TY  - JOUR
AU  - Witmer, H.
AU  - Franks, M.
TI  - Restriction and modification of Bacteriophage SP10 DNA by Bacillus subtilis Marburg 168: Stabilization of SP10 DNA in restricting hosts preinfected with a heterologous phage, SP18.
JO  - J. Virol.
PY  - 1981
SP  - 148
EP  - 155
VL  - 37
AB  - SP10 phage cannot propagate in Bacillus subtilis Marburg 168 containing the
AB  - wild-type allele of either gene nonA or gene nonB.  The latter gene codes for
AB  - the intrinsic cellular restriction activity.  SP10 DNA was degraded in nonB+
AB  - derivatives of Marburg 168.  The degree of degradation depended upon the
AB  - previous host in which SP10 was propagated.  In the case of SP10 grown in B.
AB  - subtilis W23 (a nonrestricting, nonmodifying bacterium), 90% of the phage DNA
AB  - was hydrolyzed to acid solubles, and the residual acid-precipitable material
AB  - was recovered as 0.5- to 1-megadalton fragments.  In contrast, if SP10 was
AB  - propagated in B. subtilis PS9W7 (a nonA nonB derivative of Marbury 168 that
AB  - retains modifying activity), 40 to 50% of the input DNA was degraded to acid
AB  - solubles, and most of the remainder was recovered as 15- to 20-megadalton
AB  - fragments.  In nonA+ nonB cells, SP10 DNA was conerved as unit-length molecules
AB  - (ca. 80 megadalton).  Prior infection of nonB+ cells with SP18 protected
AB  - superinfecting SP10 DNA, even when rifampin or chloramphenicol was added before
AB  - the primary infection.  The data are discussed in terms of the following
AB  - conclusions.  (i) The nonB gene product of B. subtilis Marburg 168 is required
AB  - for restriction of SP10 DNA.  (ii) Some sites on SP10 DNA are sensitive to both
AB  - the restricting and modifying activities, whereas other sites are nonmodifiable
AB  - even though they are sensitive to the restriction enzyme.  (iii)  In some
AB  - manner, SP18 antagonizes the action of the nonB gene product.
ER  -

TY  - JOUR
AU  - Wittmann, J.
AU  - Riedel, T.
AU  - Bunk, B.
AU  - Sproer, C.
AU  - Gronow, S.
AU  - Overmann, J.
TI  - Complete Genome Sequence of the Novel Temperate Clostridium difficile Phage phiCDIF1296T.
JO  - Genome Announcements
PY  - 2015
SP  - e00839
EP  - e00815
VL  - 3
AB  - Clostridium difficile contains many integrated and extrachromosomal genetic elements. In this
AB  - study, we determined, annotated, and analyzed the complete
AB  - genome of the C. difficile bacteriophage phiCDIF1296T using single-molecule
AB  - real-time sequencing technology. To our knowledge, this represents the largest
AB  - genome (131 kb) of a temperate C. difficile phage recognized so far.
ER  -

TY  - JOUR
AU  - Wittmayer, P.K.
AU  - McKenzie, J.L.
AU  - Raines, R.T.
TI  - Degenerate DNA recognition by I-PpoI endonuclease.
JO  - Gene
PY  - 1998
SP  - 11
EP  - 21
VL  - 206
AB  - The I-PpoI endonuclease is encoded by a group I intron found in the slime mold Physarum
AB  - polycephalum.  To initiate homing of its encoding intron, I-PpoI catalyzes a specific
AB  - double-stranded break within a 15-bp recognition site.  The high substrate specificities of
AB  - I-PpoI and other homing endonucleases make these enzymes valuable tools for genomic mapping
AB  - and sequencing.  Here, we report on the ability of I-PpoI to cleave recognition sites that
AB  - contain a wide variety of mutations generated randomly or deliberately.  We find that much
AB  - degeneracy is tolerated within the recognition site of I-PpoI.  Few single substitutions
AB  - prevent cleavage completely.  In addition, many sites with multiple substitutions are cleaved
AB  - efficiently. In contrast, deletions or insertions within the I-PpoI recognition site are
AB  - detrimental to catalysis, indicating that proper registry between the protein and its
AB  - substrate is critical.  Finally, we find that the sequence of the flanking regions can
AB  - influence catalysis by I-PpoI.  Thus, I-PpoI has both the complex binding specificity of a
AB  - transcription factor and the catalytic ability of a restriction endonuclease.
ER  -

TY  - JOUR
AU  - Witzel, K.
AU  - Gwinn-Giglio, M.
AU  - Nadendla, S.
AU  - Shefchek, K.
AU  - Ruppel, S.
TI  - Genome Sequence of Enterobacter radicincitans DSM16656T, a Plant Growth-Promoting Endophyte.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5469
EP  - 5469
VL  - 194
AB  - Enterobacter radicincitans sp. nov. DSM16656(T) represents a new species of the genus
AB  - Enterobacter which is a biological nitrogen-fixing endophytic bacterium
AB  - with growth-promoting effects on a variety of crop and model plant species. The
AB  - presence of genes for nitrogen fixation, phosphorous mobilization, and
AB  - phytohormone production reflects this microbe's potential plant growth-promoting
AB  - activity.
ER  -

TY  - JOUR
AU  - Wohlrab, F.
AU  - Wells, R.D.
TI  - Enzymatic probes for left-handed Z-DNA.
JO  - Gene Amplif. Anal.
PY  - 1987
SP  - 247
EP  - 256
VL  - 5
AB  - DNA is a polymorphic molecule and can adopt a variety of conformations depending mainly on
AB  - base sequence and environmental conditions.  Recent interest in this polymorphism has been
AB  - prompted to a large part by the discovery of Z-DNA, a structure possessing a left-handed helix
AB  - sense as opposed to the canonical right-handed state (B-DNA).  Several findings imply a
AB  - biological function for Z-DNA or B-to-Z transitions.
ER  -

TY  - JOUR
AU  - Wojciechowski, M.
AU  - Czapinska, H.
AU  - Bochtler, M.
TI  - CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2013
SP  - 105
EP  - 110
VL  - 110
AB  - Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to
AB  - account for CpG underrepresentation. Whether scarcity of CpGs in
AB  - prokaryotic genomes is diagnostic for methylation is not clear. Here, we report
AB  - that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively
AB  - expressed or phase variable CpG-specific DNA methyltransferases. The very CpG
AB  - poor Mycoplasma penetrans and its constitutively active CpG-specific
AB  - methyltransferase M.MpeI were chosen for further characterization. Genome-wide
AB  - sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target
AB  - sites both in vivo and in vitro in a locus-nonselective manner. A crystal
AB  - structure of M.MpeI with DNA at 2.15-A resolution showed that the substrate base
AB  - was flipped and that its place in the DNA stack was taken by a glutamine residue.
AB  - A phenylalanine residue was intercalated into the 'weak' CpG step of the
AB  - nonsubstrate strand, indicating mechanistic similarities in the recognition of
AB  - the short CpG target sequence by prokaryotic and eukaryotic DNA
AB  - methyltransferases.
ER  -

TY  - JOUR
AU  - Wolcke, J.
TI  - The kinetic mechanism of the DNA methyltransferase from Thermus aquaticus and selection of a DNA binding peptide using phage display.
JO  - Ph.D. Thesis, University of Dortmund, Germany
PY  - 1998
SP  - 1
EP  - 164
ER  -

TY  - JOUR
AU  - Wolcke, J.
AU  - Weinhold, E.
TI  - A DNA-binding peptide from a phage display library.
JO  - Nucleosides Nucleotides Nucleic Acids
PY  - 2001
SP  - 1239
EP  - 1241
VL  - 20
AB  - A DNA-binding peptide was selected from a random peptide phage display library. For
AB  - competitive elution using the DNA methyltransferase M.TaqI in the selection step, a
AB  - biotin-labeled duplex oligodeoxyribonucleotide containing the 5'-TCGA-3' recognition
AB  - sequence of M.TaqI was employed. Nine of ten phages selected were found to have the same
AB  - deduced amino acid sequence SVSVGMKPSPRP. The selected phage binds to DNA, as demonstrated in
AB  - an ELISA.
ER  -

TY  - JOUR
AU  - Wolcke, J.
AU  - Weinhold, E.
TI  - Substrate specificity of the DNA-methyltransferase from Thermus aquaticus: influence of the 3'-neighbor base.
JO  - Biol. Chem. Hoppe Seyler
PY  - 1995
SP  - S169
EP  - S169
VL  - 376
AB  - The DNA-methyltransferase from Thermus aquaticus (M.TaqI) catalyzes the methyl group transfer
AB  - from S-adenosyl-L-methionine (SAM) to the N6-position of adenine within the double-stranded
AB  - DNA sequence 5' TCGA 3'.  We have investigated the effect of changing the 3' neighboring
AB  - base of adenine which gets methylated.  We find that steady-state kinetic rates for the
AB  - methylation of adenine by M.TaqI depend on the nature of the 3'-neighboring base.  In
AB  - general, doublestranded deoxyoligo-nucleotides containing the pyrimidine bases thymine or
AB  - cytosine next to adenine give higher rates than those containing the purine bases adenine or
AB  - guanine.  This observed kinetic effect correlates inversely with the lower base stacking
AB  - energies between purine and pyrimidine bases compared to those between two purine bases.  A
AB  - contribution of the energy needed to break the base stacking between the adenine and its
AB  - 3'-neighbor to the rate limiting step is therefore suggested.  Correlation of the influence
AB  - of the neighbor base pair on the rate with the stacking energy between base pair neighbors,
AB  - which might indicate a distortion of both strands, however would predict a different kinetic
AB  - effect.  In light of the large distance (15A) between the cofactor and the DNA-binding site
AB  - observed in the crystal structure of M.TaqI complexed with SAM, the influence of the 3'
AB  - neighbor on the steady state rate gives the first experimental evidence, that a base flipping
AB  - out mechanism described for (cytosine-5)-DNA-Methyltransferases might also operate in adenine
AB  - specific DNA-Methyltransferases.
ER  -

TY  - JOUR
AU  - Wolf, Y.I.
AU  - Rogozin, I.B.
AU  - Kondrashov, A.S.
AU  - Koonin, E.V.
TI  - Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
JO  - Genome Res.
PY  - 2001
SP  - 356
EP  - 372
VL  - 11
AB  - Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only
AB  - several operons, primarily those that code for
AB  - physically interacting proteins, are conserved in all or most of the
AB  - bacterial and archaeal genomes. Nevertheless, even the limited
AB  - conservation of operon organization that is observed can provide
AB  - valuable evolutionary and functional clues through multiple genome
AB  - comparisons. A program for constructing gapped local alignments of
AB  - conserved gene strings in two genomes was developed. The statistical
AB  - significance of the local alignments was assessed using Monte Carlo
AB  - simulations. Sets of local alignments were generated for all pairs of
AB  - completely sequenced bacterial and archaeal genomes, and for each
AB  - genome a template-anchored multiple alignment was constructed. In most
AB  - pairwise genome comparisons, <10% of the genes in each genome belonged
AB  - to conserved gene strings. When closely related pairs of species (i.e.,
AB  - two mycoplasmas) are excluded, the total coverage of genomes by
AB  - conserved gene strings ranged from <5% for the cyanobacterium
AB  - Synechocystis sp. to 24% for the minimal genome of Mycoplasma
AB  - genitalium, and 23% in Thermotoga maritima. The coverage of the
AB  - archaeal genomes was only slightly lower than that of bacterial
AB  - genomes. The majority of the conserved gene strings are known operons,
AB  - with the ribosomal superoperon being the top-scoring string in most
AB  - genome comparisons. However, in some of the bacterial-archaeal pairs,
AB  - the superoperon is rearranged to the extent that other operons,
AB  - primarily those subject to horizontal transfer, show the greatest level
AB  - of conservation, such as the archaeal-type H+-ATPase operon or ABC-type
AB  - transport cassettes. The level of gene order conservation among
AB  - prokaryotic genomes was compared to the cooccurrence of genomes in
AB  - clusters of orthologous genes (COGs) and to the conservation of protein
AB  - sequences themselves. Only limited correlation was observed between
AB  - these evolutionary variables. Gene order conservation shows a much
AB  - lower variance than the cooccurrence of genomes in COGs, which
AB  - indicates that intragenome homogenization via recombination occurs in
AB  - evolution much faster than intergenome homogenization via horizontal
AB  - gene transfer and lineage-specific gene loss. The potential of using
AB  - template-anchored multiple-genome alignments for predicting functions
AB  - of uncharacterized genes was quantitatively assessed. Functions were
AB  - predicted or significantly clarified for approximately 90 COGs (approximately 4% of the total
AB  - of 2414 analyzed COGs). The most significant
AB  - predictions were obtained for the poorly characterized archaeal
AB  - genomes; these include a previously uncharacterized
AB  - restriction-modification system, a nuclease-helicase combination
AB  - implicated in DNA repair, and the probable archaeal counterpart of the
AB  - eukaryotic exosome. Multiple genome alignments are a resource for
AB  - studies on operon rearrangement and disruption, which is central to our
AB  - understanding of the evolution of prokaryotic genomes. Because of the
AB  - rapid evolution of the gene order, the potential of genome alignment
AB  - for prediction of gene functions is limited, but nevertheless, such
AB  - predictions information significantly complements the results obtained
AB  - through protein sequence and structure analysis.
ER  -

TY  - JOUR
AU  - Wolfes, H.
AU  - Alves, J.
AU  - Fliess, A.
AU  - Geiger, R.
AU  - Pingoud, A.
TI  - Site directed mutagenesis experiments suggest that Glu 111, Glu 144 and Arg 145 are essential for endonucleolytic activity of EcoRI.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 9063
EP  - 9080
VL  - 14
AB  - We have constructed a plasmid (pRIF 309+) carrying the EcoRI restriction
AB  - endonuclease gene and the f1 origin of replication.  Upon transformation of
AB  - this plasmid into E. coli and infection with bacteriophage f1 single stranded
AB  - plasmids are produced which can be used for sequencing and site directed
AB  - mutagenesis.  Using this single stranded DNA and synthetic
AB  - oligodeoxynucleotides we have introduced point mutations at defined positions
AB  - of the EcoRI gene.  Since in pRIF309+ the EcoRI gene is under the control of
AB  - the pL- promoter, high level expression of the mutated EcoRI gene could be
AB  - obtained upon induction.  Mutant EcoRI enzymes were purified to homogeneity and
AB  - characterized in structural and functional terms.  Our results demonstrate that
AB  - the Glu 111 -> Gln, Glu 144 -> Gln and Arg 145 -> Lys -mutants adopt a very
AB  - similar conformation as the wild type enzyme, but have by two orders of
AB  - magnitude smaller specific activities than the wild type enzyme, mainly due to
AB  - a reduction of the Vmax-value.
ER  -

TY  - JOUR
AU  - Wolfes, H.
AU  - Fliess, A.
AU  - Pingoud, A.
TI  - A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI.
JO  - Eur. J. Biochem.
PY  - 1985
SP  - 105
EP  - 110
VL  - 150
AB  - We have investigated the structural requirements for DNA cleavage by the
AB  - isoschizomers HaeIII, BspRI and BsuRI which recognize the sequence -d(GGCC)-.
AB  - For this purpose decadeoxynucleotides were synthesized by the solid-phase
AB  - phosphotriester method and purified by high-performance liquid chromatography.
AB  - The kinetics of cleavage of these oligodeoxynucleotides were determined for the
AB  - three isoschizomers with the following results.  1)  The sequence adjacent to
AB  - the recognition site strongly influences the rate of cleavage.  The preference
AB  - is qualitatively the same for all three enzymes:  AGGCCT > TGGCCA > GGGCCC ~
AB  - CGGCCG, and follows the thermal stability of the different decanucleotides.  2)
AB  - Substitutions within the recognition site, namely dI for dG and dU for dC,
AB  - affect the rate of cleavage differently for the three enzymes.  The results can
AB  - be rationalized in terms of an interaction of HaeIII with the major and minor
AB  - groove of the DNA of BspRI mainly with the minor groove and of BsuRI with the
AB  - major groove of DNA.  It is obvious from our data that the mechanism of
AB  - recognition of the same site is different for the three isoschizomers.
ER  -

TY  - JOUR
AU  - Wolfes, H.
AU  - Fliess, A.
AU  - Winkler, F.
AU  - Pingoud, A.
TI  - Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases.
JO  - Eur. J. Biochem.
PY  - 1986
SP  - 267
EP  - 273
VL  - 159
AB  - We have synthesized several self-complementary oligodeoxynucleotides which
AB  - contain bromodeoxyuridine in various positions within and outside of te
AB  - recognition sequence for the EcoRI and EcoRV restriction endonucleases.  These
AB  - oligodeoxynucleotides are cleaved in the presence of Mg2+ by their respective
AB  - enzyme.  Upon irradiation by long-wavelength ultraviolet light and in the
AB  - absence of Mg2+ they are cross-linked in low yield to their enzymes, forming
AB  - 1:1 and 1:2 (oligodeoxynucleotide: enzyme subunit) adducts.  Cross-linking
AB  - occurs with both specific and non-specific complexes.  With EcoRI the site of
AB  - cross-linking was determined to be at or close to Met-137, i.e. in a region of
AB  - the molecule implicated by other studies from our laboratory [Scholtissek et
AB  - al. (1986) J. Biol. Chem. 261,1118-1134] in the binding and cleavage of the
AB  - substrate.
ER  -

TY  - JOUR
AU  - Wolffe, A.P.
AU  - Jones, P.L.
AU  - Wade, P.A.
TI  - DNA demethylation.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 5894
EP  - 5896
VL  - 96
AB  - Cytosine 5' methylation of CpG dinucleotides within and around genes exerts a major influence
AB  - on transcription in many plants and animals. DNA methylation can be causal for transcriptional
AB  - silencing and targets the machinery necessary to assemble specialized chromatin enriched in
AB  - deacetylated histones. Once established in somatic cells, CpG methylation patterns within the
AB  - genome are very stable and provide an attractive mechanism for segregating a large fraction of
AB  - stably repressed chromatin.  In contrast, DNA methylation is remarkably dynamic during early
AB  - mammalian development and in certain tumor cells.  Alterations in the methylation status of
AB  - the entire genome, individual chromosomes, and specific genes are essential for normal
AB  - development and can promote tumorigenesis.  Understanding how these important transitions
AB  - might be regulated requires the biochemical definition of the enzymatic processes that both
AB  - methylate and demethylate the genome.
ER  -

TY  - JOUR
AU  - Wolk, C.P.
AU  - Kraus, J.
TI  - Two approaches to obtaining low, extracellular deoxyribonuclease activity in cultures of heterocyst-forming cyanobacteria.
JO  - Arch. Microbiol.
PY  - 1982
SP  - 302
EP  - 307
VL  - 131
AB  - Six out of 158 axenic strains of heterocyst-forming cyanobacteria consistently
AB  - failed to produce circles of clearing in agar medium containing DNA-methyl
AB  - green.  When tested with [3H]DNA and coliphage lambda DNA, supernatant fluids
AB  - from cultures of two of these strains [University of Texas Culture Collection
AB  - (UTEX) strain 2014 and 19-6C-C] showed no detectable deoxyribonuclease
AB  - activity, and such fluids from another two of the six, and four others, showed
AB  - low but detectable deoxyribonuclease activity.  Covalently closed circular
AB  - (plasmid) DNA was not detectably degraded by supernatant fluids from UTEX 2014
AB  - and 19-6C-C and from four of the other strains.  When lambda DNA was incubated
AB  - with whole cells of certain strains, a series of fragments of discrete size was
AB  - produced, perhaps by cell-bound, periplasmic, restriction endonucleases.
AB  - Inclusion of one-tenth strength saline sodium citrate (SSC) in an eight-fold
AB  - dilution of the medium of Allen and Arnon had little effect on growth of
AB  - Anabaena variabilis American Type Culture Collection (ATCC) strain 29413 yet
AB  - prevented all but slight degradation of plasmid pBR322 or of lambda DNA.
ER  -

TY  - JOUR
AU  - Wong, C.F.
AU  - Niu, H.
AU  - Jiang, J.
AU  - Li, J.
AU  - Chan, C.M.
AU  - Leung, D.Y.
AU  - Leung, F.C.
TI  - Genome Sequence of Pseudomonas mendocina DLHK, Isolated from a Biotrickling Reactor.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6326
EP  - 6326
VL  - 194
AB  - Pseudomonas mendocina DLHK is an aerobic bacterium isolated from a biotrickling reactor which
AB  - can remove nitric oxide, a common air pollutant from combustion
AB  - exhaust gas. Here, we present the draft genome of Pseudomonas mendocina DLHK.
ER  -

TY  - JOUR
AU  - Wong, D.L.
AU  - Pavlovich, J.G.
AU  - Reich, N.O.
TI  - Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoRI DNA methyltransferase complexes.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 645
EP  - 649
VL  - 26
AB  - We describe a novel strategy combining photocrosslinking and HPLC-based electrospray
AB  - ionization mass spectrometry to identify UV crosslinked DNA-protein complexes.  EcoRI DNA
AB  - methyltransferase modifies the second adenine within the recognition sequence GAATTC.
AB  - Substitution of 5-iodouracil for the thymine adjacent to the target base (GAATTC) does not
AB  - detectably alter the DNA-protein complex.  Irradiation of the 5-iodouracil-substituted
AB  - DNA-protein complex at various wavelengths was optimized, with a crosslinking yield >60% at
AB  - 313 nm after 1 min.  No protein degradation was observed under these conditions.  The
AB  - crosslinked DNA-protein complex was further anlayzed by electrospray ionization mass
AB  - spectrometry.  The total mass is consistent with irradiation-dependent covalent bond formation
AB  - between one strand of DNA and the protein.  These preliminary results support the possibility
AB  - of identifying picomole quantities of crosslinked peptides by similar strategies.
ER  -

TY  - JOUR
AU  - Wong, D.L.
AU  - Reich, N.O.
TI  - Identification of tyrosine 204 as the photo-cross-linking site in the DNA - EcoRI DNA methyltransferase complex by electrospray ionization mass spectrometry.
JO  - Biochemistry
PY  - 2000
SP  - 15410
EP  - 15417
VL  - 39
AB  - We describe a highly sensitive strategy combining laser-induced photo-cross-linking and
AB  - HPLC-based electrospray ionization mass
AB  - spectrometry to identify amino acid residues involved in protein-DNA
AB  - recognition. The photoactivatible cross-linking thymine isostere,
AB  - 5-iodouracil, was incorporated at a single site within the sequence
AB  - recognized by EcoRI DNA methyltransferase (GAATTC). UV irradiation of
AB  - the DNA-protein complex at 313 nm results in a >60% cross-linking
AB  - yield. SDS-polyacrylamide gel electrophoresis and mass spectrometry
AB  - were used to analyze the covalent cross-linked complex. The total mass
AB  - is consistent with covalent bond formation between one strand of DNA
AB  - and the protein with 1:1 stoichiometry. Protease digestion of the
AB  - cross-linked complex yields several peptide-DNA adducts that were
AB  - purified by anion-exchange column chromatography. A combination of mass
AB  - spectrometric analysis and amino acid sequencing revealed that tyrosine
AB  - 204 was cross-linked to the DNA. Electrospray mass spectrometric
AB  - analysis of the peptide-nucleoside adduct confirmed this assignment.
AB  - Tyrosine 204 resides in a peptide motif previously thought to be
AB  - involved in AdoMet binding and methyl transfer. Thus, amino acids
AB  - within loop segments but outside of "DNA binding" motifs can be
AB  - critical to DNA recognition. Our method provides an accurate
AB  - characterization of picomole quantities of DNA-protein complexes.
ER  -

TY  - JOUR
AU  - Wong, D.M.
AU  - Wetmur, J.G.
TI  - Some class-IIS restriction endonucleases can cleave across a three-way DNA junction.
JO  - Gene
PY  - 1994
SP  - 63
EP  - 66
VL  - 150
AB  - Three-way DNA junctions were synthesized with class-IIS restriction endonuclease (ENase)
AB  - recognition sites and potential cleavage sites located on separate arms. Cleavage was
AB  - investigated with junctions labeled in each of the three strands. BpmI and BsaI failed to
AB  - cleave either strand of either arm, whereas BsmAI cleaved one strand. FokI and HphI cleaved
AB  - both strands of both arms at the expected nucleotide positions. FokI cleavage was independent
AB  - of the spacing between the recognition site and the junction. This new activity of class-IIS
AB  - may be useful for investigating branched DNA structures.
ER  -

TY  - JOUR
AU  - Wong, K.K.
AU  - McClelland, M.
TI  - PCR with 5-methyl-dCTP replacing dCTP.
JO  - Nucleic Acids Res.
PY  - 1991
SP  - 1081
EP  - 1085
VL  - 19
AB  - When dCTP is replaced by methyl-5-dCTP in the polymerase chain reaction some templates cannot
AB  - be efficiently amplified by Taq polymerase or Vent tm polymerase using standard cycling
AB  - parameters. However, this phenomenon can be overcome by increasing the temperature of the
AB  - denaturation steps to 100 C, or by adding dITP to destabilize the m5dC:dG base pairs. Once the
AB  - block to amplification of m5dC-substituted DNA was overcome, methylated DNA from the
AB  - superpolylinker of the plasmid pSL1180 was used as a substrate to check the methyl-sensitivity
AB  - of a variety of restriction endonucleases. The m5dC-substituted DNAs should also be valuable
AB  - substrates for defining the specificity of methyl-dependent endonucleases.
ER  -

TY  - JOUR
AU  - Wong, R.M.-Y.
AU  - Wong, K.K.
AU  - Benson, N.R.
AU  - McClelland, M.
TI  - Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome.
JO  - FEMS Microbiol. Lett.
PY  - 1999
SP  - 411
EP  - 423
VL  - 173
AB  - As part of the ongoing sequencing of the complete Salmonella typhimurium
AB  - LT2 genome, a partly ordered set of 416 lambda clones has been developed,
AB  - representing over 90% of the genome. The average insert size is 17 kb.
AB  - Sequences were obtained from both ends of each clone in this set. A total
AB  - of over 600 kb of sequence has been deposited in the genome survey
AB  - sequence section of GenBank. This resource of clones is available from the
AB  - Salmonella Genome Stock Center. A preliminary comparison with the
AB  - Escherichia coli K12 genome indicates that there are likely to be many
AB  - hundred insertion deletion events, encompassing more than one gene, that
AB  - distinguish these genomes. Fully 30% of the S. typhimurium sequences have
AB  - no close homologs in the GenBank database.
ER  -

TY  - JOUR
AU  - Wong, S.K.
AU  - Yoshizawa, S.
AU  - Nakajima, Y.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Hamasaki, K.
TI  - Draft Genome Sequence of Lewinella sp. Strain 4G2 Isolated from the Coastal Sea Surface Microlayer.
JO  - Genome Announcements
PY  - 2016
SP  - e00754
EP  - e00716
VL  - 4
AB  - We report here the draft genome of Lewinella sp. strain 4G2, isolated from the sea surface
AB  - microlayer (SML) of a coastal marine inlet. The genome sequence of
AB  - strain 4G2 should contribute to understanding the lifestyles of bacteria living
AB  - in the SML.
ER  -

TY  - JOUR
AU  - Wong, Y.L.
AU  - Choo, S.W.
AU  - Tan, J.L.
AU  - Ong, C.S.
AU  - Ng, K.P.
AU  - Ngeow, Y.F.
TI  - Draft Genome Sequence of Mycobacterium bolletii Strain M24, a Rapidly Growing Mycobacterium of Contentious Taxonomic Status.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4475
EP  - 4475
VL  - 194
AB  - The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar
AB  - lavage fluid of a Malaysian patient, is reported here. The
AB  - circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of
AB  - this organism within the M. abscessus complex and revealed the presence of
AB  - proteins potentially important for pathogenicity in a human host.
ER  -

TY  - JOUR
AU  - Wong, Y.M.
AU  - Juan, J.C.
AU  - Gan, H.M.
AU  - Austin, C.M.
TI  - Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e00077
EP  - e00014
VL  - 2
AB  - Clostridium bifermentans strain WYM is an effective biohydrogen producer isolated from
AB  - landfill leachate sludge. Here, we present the assembly and annotation of
AB  - its genome, which may provide further insights into the metabolic pathways
AB  - involved in efficient biohydrogen production.
ER  -

TY  - JOUR
AU  - Wong, Y.M.
AU  - Juan, J.C.
AU  - Gan, H.M.
AU  - Austin, C.M.
TI  - Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e00064
EP  - e00014
VL  - 2
AB  - Clostridium perfringens strain JJC is an effective biohydrogen and biochemical producer that
AB  - was isolated from landfill leachate sludge. Here, we present the
AB  - assembly and annotation of its genome, which may provide further insights into
AB  - the gene interactions involved in efficient biohydrogen production.
ER  -

TY  - JOUR
AU  - Wong, Y.M.
AU  - Juan, J.C.
AU  - Ting, A.
AU  - Wu, T.Y.
AU  - Gan, H.M.
AU  - Austin, C.M.
TI  - Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e00078
EP  - e00014
VL  - 2
AB  - Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species  isolated
AB  - from landfill leachate sludge. Here we present the assembly and
AB  - annotation of its genome, which may provide further insights into its gene
AB  - interactions for efficient biohydrogen production.
ER  -

TY  - JOUR
AU  - Wons, E.
AU  - Mruk, I.
AU  - Kaczorowski, T.
TI  - Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes.
JO  - J. Appl. Genet.
PY  - 2015
SP  - 539
EP  - 546
VL  - 56
AB  - RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops.
AB  - Their susceptibility to modification by DNA-specific or RNA-specific
AB  - enzymes is, thus, a biologically relevant question, which, in addition, has
AB  - possible biotechnological implications. In this study, we investigated the
AB  - activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI,
AB  - M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one
AB  - 5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the
AB  - beta-group of adenine N6-methyltransferases and recognize the palindromic DNA
AB  - sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these
AB  - isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the
AB  - addition of agents that generally relax specificity, such as dimethyl sulfoxide
AB  - (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by
AB  - M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated.
AB  - The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge,
AB  - the first report that demonstrates such activity by prokaryotic DNA
AB  - methyltransferases. Possible applications of these findings in a laboratory
AB  - practice are also discussed.
ER  -

TY  - JOUR
AU  - Woo, H.L. et al.
TI  - Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm.
JO  - Genome Announcements
PY  - 2016
SP  - e01297
EP  - e01216
VL  - 4
AB  - Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment
AB  - laboratory microcosms enriched on insoluble organosolv lignin under
AB  - oxic conditions. The near-complete genome sequence presented here will facilitate
AB  - analyses into this deep-ocean bacterium's ability to degrade recalcitrant
AB  - organics such as lignin.
ER  -

TY  - JOUR
AU  - Woo, H.L.
AU  - Ballor, N.R.
AU  - Hazen, T.C.
AU  - Fortney, J.L.
AU  - Simmons, B.
AU  - Davenport, K.W.
AU  - Goodwin, L.
AU  - Ivanova, N.
AU  - Kyrpides, N.C.
AU  - Mavromatis, K.
AU  - Woyke, T.
AU  - Jansson, J.
AU  - Kimbrel, J.
AU  - DeAngelis, K.M.
TI  - Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain  BRL6-2.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 19
EP  - 19
VL  - 9
AB  - In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated
AB  - Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the
AB  - sole carbon source. This organism was isolated anaerobically from tropical forest
AB  - soils collected from the Bisley watershed at the Ridge site in the El Yunque
AB  - National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological
AB  - Research Station. At this site, the soils experience strong fluctuations in redox
AB  - potential and are characterized by cycles of iron oxidation and reduction. Genome
AB  - sequencing was targeted because of its ability to grow on lignin anaerobically
AB  - and lignocellulolytic activity via in vitro enzyme assays. The genome of
AB  - Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes
AB  - a relatively small arsenal of genes encoding lignocellulolytic carbohydrate
AB  - active enzymes. The genome revealed four putative peroxidases including
AB  - glutathione and DyP-type peroxidases, and a complete protocatechuate pathway
AB  - encoded in a single gene cluster. Physiological studies revealed Klebsiella sp.
AB  - strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions.
AB  - It grows in increasing concentrations of ionic liquid
AB  - (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.
ER  -

TY  - JOUR
AU  - Woo, H.L.
AU  - DeAngelis, K.M.
AU  - Teshima, H.
AU  - Davenport, K.
AU  - Daligault, H.
AU  - Erkkila, T.
AU  - Goodwin, L.
AU  - Gu, W.
AU  - Lo, C.C.
AU  - Munk, C.
AU  - Scholz, M.
AU  - Xu, Y.
AU  - Chain, P.
AU  - Bruce, D.
AU  - Detter, C.
AU  - Tapia, R.
AU  - Han, C.
AU  - Simmons, B.A.
AU  - Hazen, T.C.
TI  - High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp.,  Variovorax sp., and Vogesella sp.
JO  - Genome Announcements
PY  - 2017
SP  - e00300
EP  - e00317
VL  - 5
AB  - Here, we report the high-quality draft genome sequences of four phylogenetically  diverse
AB  - lignocellulose-degrading bacteria isolated from tropical soil (Gordonia
AB  - sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the
AB  - genetic basis of their ability to degrade lignocellulose. These isolates may
AB  - provide novel enzymes for biofuel production.
ER  -

TY  - JOUR
AU  - Woo, H.L.
AU  - Utturkar, S.
AU  - Klingeman, D.
AU  - Simmons, B.A.
AU  - DeAngelis, K.M.
AU  - Brown, S.D.
AU  - Hazen, T.C.
TI  - Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil.
JO  - Genome Announcements
PY  - 2014
SP  - e00637
EP  - e00614
VL  - 2
AB  - Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant
AB  - aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30
AB  - was isolated from wet tropical forest soil and is capable of utilizing lignin as
AB  - a sole carbon source. Here we report the draft genome sequence of Burkholderia
AB  - sp. strain LIG30.
ER  -

TY  - JOUR
AU  - Woo, P.C.
AU  - Lau, S.K.
AU  - Tse, H.
AU  - Teng, J.L.
AU  - Curreem, S.O.
AU  - Tsang, A.K.
AU  - Fan, R.Y.
AU  - Wong, G.K.
AU  - Huang, Y.
AU  - Loman, N.J.
AU  - Snyder, L.A.
AU  - Cai, J.J.
AU  - Huang, J.D.
AU  - Mak, W.
AU  - Pallen, M.J.
AU  - Lok, S.
AU  - Yuen, K.Y.
TI  - The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.
JO  - PLoS Genet.
PY  - 2009
SP  - E1000416
EP  - E1000416
VL  - 5
AB  - Laribacter hongkongensis is a newly discovered Gram-negative bacillus of
AB  - the Neisseriaceae family associated with freshwater fish-borne
AB  - gastroenteritis and traveler's diarrhea. The complete genome sequence of
AB  - L. hongkongensis HLHK9, recovered from an immunocompetent patient with
AB  - severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content
AB  - of 62.35%. Genome analysis reveals different mechanisms potentially
AB  - important for its adaptation to diverse habitats of human and freshwater
AB  - fish intestines and freshwater environments. The gene contents support its
AB  - phenotypic properties and suggest that amino acids and fatty acids can be
AB  - used as carbon sources. The extensive variety of transporters, including
AB  - multidrug efflux and heavy metal transporters as well as genes involved in
AB  - chemotaxis, may enable L. hongkongensis to survive in different
AB  - environmental niches. Genes encoding urease, bile salts efflux pump,
AB  - adhesin, catalase, superoxide dismutase, and other putative virulence
AB  - factors-such as hemolysins, RTX toxins, patatin-like proteins,
AB  - phospholipase A1, and collagenases-are present. Proteomes of L.
AB  - hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and
AB  - 20 degrees C (freshwater habitat temperature) showed differential gene
AB  - expression, including two homologous copies of argB, argB-20, and argB-37,
AB  - which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20
AB  - and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher
AB  - expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37
AB  - degrees C. NAGK-20 also had a lower optimal temperature for enzymatic
AB  - activities and was inhibited by arginine probably as negative-feedback
AB  - control. Similar duplicated copies of argB are also observed in bacteria
AB  - from hot springs such as Thermus thermophilus, Deinococcus geothermalis,
AB  - Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that
AB  - similar mechanisms for temperature adaptation may be employed by other
AB  - bacteria. Genome and proteome analysis of L. hongkongensis revealed novel
AB  - mechanisms for adaptations to survival at different temperatures and
AB  - habitats.
ER  -

TY  - JOUR
AU  - Woo, Y.H.
AU  - Rajagopalan, P.T.R.
AU  - Benkovic, S.J.
TI  - A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening.
JO  - Anal. Biochem.
PY  - 2005
SP  - 336
EP  - 340
VL  - 340
AB  - We have developed a nonradioactive assay method for DNA methyltransferases based on the
AB  - ability to protect substrate DNA from
AB  - restriction. DNA immobilized to a microplate well was treated
AB  - sequentially with methyltransferase and an appropriate endonuclease.
AB  - The amount of methylated DNA product is reflected by a proportional
AB  - decrease in endonuclease cleavage, which is in turn reflected by
AB  - increased retention of the end-labeled affinity probe. A single
AB  - universal substrate was designed to assay multiple methyltransferases
AB  - including those that do not have a cognate endonuclease. The
AB  - methodology developed is suited to screen a large number of compounds
AB  - for inhibitors of various methyltransferases.
ER  -

TY  - JOUR
AU  - Wood, D.W. et al.
TI  - The genome of the natural genetic engineer Agrobacterium tumefaciens C58.
JO  - Science
PY  - 2001
SP  - 2317
EP  - 2323
VL  - 294
AB  - The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a
AB  - circular chromosome, a linear chromosome, and two plasmids.  Extensive orthology and
AB  - nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont
AB  - Sinorhizobium meliloti suggest a recent evolutionary divergence.  Their similarities include
AB  - metabolic, transport, and regulatory systems that promote survival in the highly competitive
AB  - rhizosphere; differences are apparent in their genome structure and virulence gene complement.
AB  - Availability of the A. tumefaciens sequence will facilitate investigations into the molecular
AB  - basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.
ER  -

TY  - JOUR
AU  - Wood, K.M.
AU  - Daniels, L.E.
AU  - Halford, S.E.
TI  - Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAl.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 240
EP  - 253
VL  - 350
AB  - The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition
AB  - sequence, cleaving both sites concertedly.
AB  - While most restriction enzymes that act concurrently at two sites are
AB  - tetramers, SgrAI is a dimer in solution. Its reaction at two cognate
AB  - sites involves the association of two DNA-bound dimers. SgrAI can also
AB  - bridge cognate and secondary sites, the latter being certain sequences
AB  - that differ from the cognate by one base-pair. The mechanisms for
AB  - cognate-cognate and cognate-secondary communications were examined for
AB  - sites in the following topological relationships: in cis, on plasmids
AB  - with two sites in a single DNA molecule; on catenanes containing two
AB  - interlinked rings of DNA with one site in each ring; and in trans, on
AB  - oligoduplexes carrying either a single site or the DNA termini
AB  - generated by SgrAI. Both cognate-cognate and cognate-secondary
AB  - interactions occur through 3-D space and not by 1-D tracking along the
AB  - DNA. Both sorts of communication arise more readily when the sites are
AB  - tethered to each other, either in cis on the same molecule of DNA or by
AB  - the interlinking of catenane rings, than when released from the tether.
AB  - However, the dimer bound to an oligoduplex carrying either a cognate or
AB  - a secondary site could be activated to cleave that duplex by
AB  - interacting with a second dimer bound to the recognition site, provided
AB  - both duplexes are at least 30 base-pairs long: the second dimer could
AB  - alternatively be bound to the two duplexes that correspond to the
AB  - products of DNA cleavage by SgrAI.
ER  -

TY  - JOUR
AU  - Wood, R.J.
AU  - Maynard-Smith, M.D.
AU  - Robinson, V.L.
AU  - Oyston, P.C.F.
AU  - Titball, R.W.
AU  - Roach, P.L.
TI  - Kinetic analysis of Yersinia pestis DNA adenine methyltransferase activity using a hemimethylated molecular break light oligonucleotide.
JO  - PLoS ONE
PY  - 2007
SP  - e801
EP  - e801
VL  - 2
AB  - Background. DNA adenine methylation plays an important role in several critical bacterial
AB  - processes including mismatch repair, the timing of DNA replication and the transcriptional
AB  - control of gene expression. The dependence of bacterial virulence on DNA adenine
AB  - methyltransferase (Dam) has led to the proposal that selective Dam inhibitors might function
AB  - as broad spectrum antibiotics. Methodology/Principal Findings. Herein we report the expression
AB  - and purification of Yersinia pestis Dam and the development of a continuous fluorescence based
AB  - assay for DNA adenine methyltransferase activity that is suitable for determining the kinetic
AB  - parameters of the enzyme and for high throughput screening against potential Dam inhibitors.
AB  - The assay utilised a hemimethylated break light oligonucleotide substrate containing a GATC
AB  - methylation site. When this substrate was fully methylated by Dam, it became a substrate for
AB  - the restriction enzyme DpnI, resulting in separation of fluorophore (fluorescein) and quencher
AB  - (dabcyl) and therefore an increase in fluorescence. The assays were monitored in real time
AB  - using a fluorescence microplate reader in 96 well format and were used for the kinetic
AB  - characterisation of Yersinia pestis Dam, its substrates and the known Dam inhibitor,
AB  - S-adenosylhomocysteine. The assay has been validated for high throughput screening, giving a
AB  - Z-factor of 0.7160.07 indicating that it is a sensitive assay for the identification of
AB  - inhibitors. Conclusions/Significance. The assay is therefore suitable for high throughput
AB  - screening for inhibitors of DNA adenine methyltransferases and the kinetic characterisation of
AB  - the inhibition.
ER  -

TY  - JOUR
AU  - Wood, R.J.
AU  - McKelvie, J.C.
AU  - Maynard-Smith, M.D.
AU  - Roach, P.L.
TI  - A real-time assay for CpG-specific cytosine-C5 methyltransferase activity.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - e107
EP  - e107
VL  - 38
AB  - A real-time assay for CpG-specific cytosine-C5 methyltransferase activity has been developed.
AB  - The assay applies a break light oligonucleotide in
AB  - which the methylation of an unmethylated 5'-CG-3' site is enzymatically
AB  - coupled to the development of a fluorescent signal. This sensitive assay
AB  - can measure rates of DNA methylation down to 0.34 +/- 0.06 fmol/s. The
AB  - assay is reproducible, with a coefficient of variation over six
AB  - independent measurements of 4.5%. Product concentration was accurately
AB  - measured from fluorescence signals using a linear calibration curve, which
AB  - achieved a goodness of fit (R(2)) above 0.98. The oligonucleotide
AB  - substrate contains three C5-methylated cytosine residues and one
AB  - unmethylated 5'-CG-3' site. Methylation yields an oligonucleotide
AB  - containing the optimal substrate for the restriction enzyme GlaI. Cleavage
AB  - of the fully methylated oligonucleotide leads to separation of fluorophore
AB  - from quencher, giving a proportional increase in fluorescence. This method
AB  - has been used to assay activity of DNMT1, the principle maintenance
AB  - methyltransferase in human cells, and for the kinetic characterization of
AB  - the bacterial cytosine-C5 methyltransferase M.SssI. The assay has been
AB  - shown to be suitable for the real-time monitoring of DNMT1 activity in a
AB  - high-throughput format, with low background signal and the ability to
AB  - obtain linear rates of methylation over long periods, making this a
AB  - promising method of high-throughput screening for inhibitors.
ER  -

TY  - JOUR
AU  - Wood, V. et al.
TI  - The genome sequence of Schizosaccharomyces pombe.
JO  - Nature
PY  - 2002
SP  - 871
EP  - 880
VL  - 415
AB  - We have sequenced and annotated the genome of fission yeast
AB  - (Schizosaccharomyces pombe), which contains the smallest number of
AB  - protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres
AB  - are between 35 and 110 kilobases (kb) and contain related repeats
AB  - including a highly conserved 1.8-kb element. Regions upstream of genes are
AB  - longer than in budding yeast (Saccharomyces cerevisiae), possibly
AB  - reflecting more-extended control regions. Some 43% of the genes contain
AB  - introns, of which there are 4,730. Fifty genes have significant similarity
AB  - with human disease genes; half of these are cancer related. We identify
AB  - highly conserved genes important for eukaryotic cell organization
AB  - including those required for the cytoskeleton, compartmentation,
AB  - cell-cycle control, proteolysis, protein phosphorylation and RNA splicing.
AB  - These genes may have originated with the appearance of eukaryotic life.
AB  - Few similarly conserved genes that are important for multicellular
AB  - organization were identified, suggesting that the transition from
AB  - prokaryotes to eukaryotes required more new genes than did the transition
AB  - from unicellular to multicellular organization.
ER  -

TY  - JOUR
AU  - Wood, W.B.
TI  - Host specificity of DNA produced by Escherichia coli:  bacterial mutations affecting the restriction and modification of DNA.
JO  - J. Mol. Biol.
PY  - 1966
SP  - 118
EP  - 133
VL  - 16
AB  - Bacterial mutants lacking the ability to restrict lambda phage of foreign host
AB  - specificity have been isolated from Escherichia coli strains K12 and B using a
AB  - convenient selection technique.  About half of the mutants still impart host
AB  - specificity to lambda; the remainder are deficient in modification as well as
AB  - restriction.  In both K12 and B, mutations affecting restriction map close to
AB  - the thr locus on the side opposite to leu.  Behavior of the mutant strains in
AB  - conjugation experiments is consistent with the view that bacterial DNA is
AB  - restricted and modified by the same factors which act upon the DNA of phage
AB  - lambda, and that this restriction isi responsible for the abnormally low
AB  - frequency of recombinant formation observed in K12 X B crosses.  The properties
AB  - of the modification-restriction system in E. coli suggest that it serves as a
AB  - defense mechanism against incoming nucleic acid, preventing the expression or
AB  - integration of foreign DNA without hindering genetic exchange among cells of
AB  - the same strain.
ER  -

TY  - JOUR
AU  - Wood, W.B.
TI  - Mutations in E. coli affecting the host-controlled modification bacteriophage lambda.
JO  - Pathol. Microbiol. (Basel)
PY  - 1965
SP  - 73
EP  - 76
VL  - 28
AB  - This report describes the isolation and some properties of K12 and B strains
AB  - which have lost the restriction (r) and modification (m) functions as a result
AB  - of either spontaneous or ethyl-methane sulfonate (EMS)-induced mutations.
AB  - Glover et al. have recently described similar mutations carried by P1 prophage
AB  - which affect the host-controlled modification of lambda.K in lysogenic E. coli
AB  - K12 (P1) strains.
ER  -

TY  - JOUR
AU  - Woodbury, C.P. Jr.
AU  - Downey, R.L.
AU  - von Hippel, P.H.
TI  - EcoRI Methylase: On its substrate specificity and use in radioactive labeling of DNA.
JO  - Fed. Proc.
PY  - 1978
SP  - 1415
EP  - 1415
VL  - 37
AB  - While investigating the mechanisms of the EcoRI endonuclease and methylase, we
AB  - have examined the effect of alterations in reaction conditions on the
AB  - methylation process.  We find that in 100 mM Tris, 2 mM EDTA, 50% glycerol (pH
AB  - 9), the methylase transfers many more methyl groups to both ColE1 plasmid and
AB  - phage lambda DNA than can be accommodated in the known "canonical" substrate
AB  - sites of these DNAs.  We have confirmed that "non-canonical" sites are
AB  - methylated under these conditions by demonstrating the incorporation of
AB  - substantial amounts of label into phage PhiX174 DNA, which contains no
AB  - canonical sequences, as well as into in vivo-methylated E. coli strain RY13
AB  - (rRI+, mRI+) chromosomal DNA.  We have also incorporated label into both duplex
AB  - poly[d(A-T)] and poly(dA).poly(dT).  The rate of methylation of these
AB  - substrates decreases in the order: canonical sites > non-canonical sites
AB  - >duplex poly[d(A-T)] > poly(dA).poly(dT).  The implications of these findings
AB  - for mechanisms in the EcoRI system will be discussed.  In addition to its
AB  - mechanistic interest, this nonspecific methylation procedure provides a
AB  - convenient way to radioactively label DNA in vitro; we have achieved ~105
AB  - cpm/microgram with various DNAs, a level comparable to that obtainable by in
AB  - vivo 32P-labeling.  Examples of the use of this technique will be described.
ER  -

TY  - JOUR
AU  - Woodbury, C.P. Jr.
AU  - Downey, R.L.
AU  - von Hippel, P.H.
TI  - DNA site recognition and overmethylation by the EcoRI methylase.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 11526
EP  - 11533
VL  - 255
AB  - The EcoRI modification methylase exhibits reduction of in vitro substrate
AB  - specificity under conditions of alkaline pH, low ionic strength, and igh
AB  - glycerol content.  Under these conditions the enzyme transfers many more methyl
AB  - groups to both plasmid ColE1 DNA and phage lambda DNA than can be accommodated
AB  - in the known "canonical" recognition sites of these DNAs.  Substantial
AB  - methylation of phage PhiX174 replicative form DNA, which contains no canonical
AB  - sites, has also been demonstrated.  This "noncanonical" methylation occurs at
AB  - sites recognized by the EcoRI restriction endonuclease under parallel
AB  - conditions of low ionic strength and alkaline pH, as evidenced by protection of
AB  - the overmethylated ColE1 or PhiX174 DNAs against attack by the nuclease
AB  - (Woodbury, C.P., Jr., Hagenbuchle, O., and von Hippel, P.H. (1980) J. Biol.
AB  - Chem. 255, 11534-11546).  The methylase also modifies, at a much lower rate,
AB  - the double-stranded form of the alternating copolymer, poly[d(A-T)], but does
AB  - not transfer appreciable numbers of methyl groups to the homoduplex,
AB  - poly(dA).poly(dT).  The substrates methylated, in order of decreasing specific
AB  - rate, are: canonical DNA sites > noncanonical DNA sites > duplex poly[d(A-T)] >
AB  - poly(dA).poly(dT).  In addition, this enzyme (under noncanonical methylating
AB  - conditions) modifies in vivo methylated Escherichia coli RY13 (r+ RI, M+RI)
AB  - chromosomal DNA, but at a much lower rate than the other DNAs tested.  This
AB  - suggests that the noncanonical (as well as the canonical) sites of this DNA
AB  - have been largely modified in vivo.  The high level of methyl group
AB  - incorporation attainable using the noncanonical activity of the EcoRI methylase
AB  - has also been employed as a tool to radioactively label DNA in vitro.
AB  - Double-stranded lambda plac DNA has been labeled easily to 130,000
AB  - cpm/microgram by this technique; this modified DNA has been shown to be fully
AB  - functional as operator in lac operator-repressor filter-binding assays.
ER  -

TY  - JOUR
AU  - Woodbury, C.P. Jr.
AU  - Hagenbuchle, O.
AU  - von Hippel, P.H.
TI  - DNA site recognition and reduced specificity of the EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 11534
EP  - 11546
VL  - 255
AB  - It has been shown previously (Polisky, B., Green, P., Garfin, D.E., McCarthy,
AB  - B.J., Goodman, H.M. and Boyer, H.W. (1975) Proc. Natl. Acad. Sci. USA 72:
AB  - 3310-3314; Hsu, M., and Berg, P. (1978) Biochemistry 17: 131-138) that the
AB  - cleavage sequence specificity of EcoRI endonuclease can be "relaxed" by various
AB  - means.  In this paper this phenomenon is explored in detail, in order to obtain
AB  - further insight into the nature and selectivity of sequence recognition
AB  - patterns between proteins and double-stranded nucleic acids.  Using conditions
AB  - of low ionic strength and alkaline pH, we have mapped the positions of
AB  - potentially cleavable sites in the (completely sequenced) replicative form of
AB  - the bacteriophage PhiX174 genome, and have deduced their sequence.  The time
AB  - course of digestion of PhiX174 DNA suggests that double-stranded sequences
AB  - reading GGATTT, AAATTT, GAATTT, and GAATTA (only "top" strands, written 5' -
AB  - 3', are shown) are cleaved readily under these conditions, while sequences
AB  - reading CAATTN (N = A,T,G) resist attack.  Cleavages at (at least) the more
AB  - labile sites result in cohesive ends that are religatable.  End group analysis
AB  - of cleaved PhiX174 DNA fragments indicates the presence of a 5' - terminal
AB  - adenine residue on most of the fragments; some fragments may carry a
AB  - 5'-terminal guanine residue, consistent with the cleavage site sequences
AB  - suggested above.  Addition of Mn2+ to cleavage reactions carried out at
AB  - moderate salt concentrations and near-neutral pH indices the same pattern of
AB  - cleavage seen at low ionic strength and alkaline pH.  These results are
AB  - combined with those from other studies, and are interpreted in terms of a model
AB  - for the site-specific interation of the EcoRI endonuclease with its substrate,
AB  - considering both the effects of changes in DNA sequence and of environmental
AB  - alterations.  The resulting model is compared with data developed on similar
AB  - grounds for EcoRI methylase (see Woodbury, C.P., Downey, R.L., and von Hippel,
AB  - Ph.H. (1980) J. Biol. Chem. 255: 11526-11533), and attempts are made to define
AB  - both common and differing molecular facets of the DNA recognition specificity
AB  - of these companion (but genetically distinct enzymes.
ER  -

TY  - JOUR
AU  - Woodbury, C.P. Jr.
AU  - von Hippel, P.H.
TI  - Relaxed sequence specificities of EcoRI endonuclease and methylase: Mechanisms, possible practical applications, and uses in defining protein-nucleic acid recognition mechanisms.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 181
EP  - 207
VL  - 1
AB  - *
AB  -    I. Introduction
AB  -   II. Conditions for relaxation of enzymatic specificity
AB  -  III. Sequence specificity of noncanonical EcoRI activities
AB  -   IV. Is relaxed specificity due to an impurity
AB  -    V. The role of binding affinity in relaxed specificity
AB  -   VI. Recognition contacts for the endonuclease
AB  -  VII. Recognition contacts for the methylase
AB  - VIII. General features of the endonuclease recognition sequence
AB  -   IX. Free energy considerations in non-sequence-specific and sequence-specific binding
AB  -    X. Applications of the relaxed-specificity reactions of endonuclease and methylase
AB  -   XI. Appendix
AB  - 
ER  -

TY  - JOUR
AU  - Woodcock, D.M.
AU  - Crowther, P.J.
AU  - Diver, W.P.
AU  - Graham, M.
AU  - Bateman, C.
AU  - Baker, D.J.
AU  - Smith, S.S.
TI  - RglB facilitated cloning of highly methylated eukaryotic DNA:  the human L1 transposon, plant DNA, and DNA methylated in vitro with human DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4465
EP  - 4482
VL  - 16
AB  - In vitro methylation of Bluescribe plasmid DNA (pBS) with human placental DNA
AB  - methyltransferase to 6% 5-methylcytosine (mC) reduced transformation
AB  - efficiencies in rglB+ host strains C600 and DS410 by almost 2 orders of
AB  - magnitude.  By contrast, the rglB- derivative of DS410 showed no reduction in
AB  - transformation efficiency with methylation while the rglB- derivative of C600
AB  - was partially tolerant to methylation.  Further, we show that the 1.8 kilobase
AB  - (kb) and 1.2 kb KpnI fragments derived from the human L1 repeat have
AB  - respectively 18.3% and 2.3% mC in vivo.  Using these hyper- and hypo-methylated
AB  - genomic segments ligated into the pBS plasmid, transformants with the highly
AB  - methylated 1.8 kb L1 insert were recovered at 17 to 40 fold higher frequency
AB  - with the rglB- host strains than with the rglB+ hosts.  In addition,
AB  - recombinant phage (lambda 2001) containing inserts of plant genomic DNA with
AB  - 26.7% mC (from Petunia hybrida) when plated on rglB- hosts gave titres up to
AB  - 222 times higher than on rglB+ strains.
ER  -

TY  - JOUR
AU  - Woodcock, D.M.
AU  - Lisenmeyer, M.E.
AU  - Warren, W.D.
TI  - DNA methylation in mouse A-repeats in DNA methyltransferase-knockout ES cells and in normal cells determined by bisulfite genomic sequencing.
JO  - Gene
PY  - 1998
SP  - 63
EP  - 67
VL  - 206
AB  - Mouse ES cells with a null mutation of the known DNA methyltransferase retain some residual
AB  - DNA methylation and can methylate foreign sequences de novo.  We have used bisulfite genomic
AB  - sequencing to examine the sequence specificity and distributions of methylation of a
AB  - hypermethylated CG island sequence, mouse A-repeats.  There were 13 CG dinucleotides in the
AB  - region examined, 12 of which were methylated to variable extents in all DNAs.  We found that:
AB  - (1) there is considerable residual DNA methylation in ES cells lacking the known DNA
AB  - methyltransferase (29% of normal methylation in the complete knockout ES DNA); (2) this other
AB  - activity methylates at exactly the same CG sites as the major methyltransferase; and (3)
AB  - differences in the distribution of methylated sites between A-repeats in these DNAs are
AB  - consistent with this other activity methylating in a random de novo fashion.  Also, the lack
AB  - of any methylation in non-CG sites argues that, in other studies where non-CG methylation
AB  - sites have been found by bisulfite sequencing, detection of such sites of non-CG methylation
AB  - is not an inherent artifact in this methodology.
ER  -

TY  - JOUR
AU  - Woodford, N.
AU  - Carattoli, A.
AU  - Karisik, E.
AU  - Underwood, A.
AU  - Ellington, M.J.
AU  - Livermore, D.M.
TI  - Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom,  all belonging to the international O25:H4-ST131 clone.
JO  - Antimicrob. Agents Chemother.
PY  - 2009
SP  - 4472
EP  - 4482
VL  - 53
AB  - We determined the complete nucleotide sequences of three plasmids that encode CTX-M
AB  - extended-spectrum beta-lactamases (ESBLs) in pulsed-field gel
AB  - electrophoresis-defined United Kingdom variants (strains A, C, and D) of the
AB  - internationally prevalent Escherichia coli O25:H4-ST131 clone. Plasmid pEK499
AB  - (strain A; 117,536 bp) was a fusion of type FII and FIA replicons and harbored
AB  - the following 10 antibiotic resistance genes conferring resistance to eight
AB  - antibiotic classes: bla(CTX-M-15), bla(OXA-1), bla(TEM-1,) aac6'-Ib-cr, mph(A),
AB  - catB4, tet(A), and the integron-borne dfrA7, aadA5, and sulI genes. pEK516
AB  - (strain D; 64,471 bp) belonged to incompatibility group IncFII and carried seven
AB  - antibiotic resistance genes: bla(CTX-M-15), bla(OXA-1), bla(TEM-1), aac6'-Ib-cr,
AB  - catB4, and tet(A), all as in pEK499. It also carried aac3-IIa, conferring
AB  - gentamicin resistance, and was highly related to pC15-1a, a plasmid encoding the
AB  - CTX-M-15 enzyme in Canada. By contrast, pEK204 (strain C; 93,732 bp) belonged to
AB  - incompatibility group IncI1 and carried only two resistance genes, bla(CTX-M-3)
AB  - and bla(TEM-1). It probably arose by the transposition of Tn3 and
AB  - ISEcp1-bla(CTX-M-3) elements into a pCOLIb-P9-like plasmid. We conclude that (i)
AB  - United Kingdom variants of the successful E. coli ST131 clone have acquired
AB  - different plasmids encoding CTX-M ESBLs on separate occasions, (ii) the
AB  - bla(CTX-M-3) and bla(CTX-M-15) genes on pEK204 and pEK499/pEK516 represent
AB  - separate escape events, and (iii) IncFII plasmids harboring bla(CTX-M-15) have
AB  - played a crucial role in the global spread of CTX-M-15 ESBLs in E. coli.
ER  -

TY  - JOUR
AU  - Woodhead, J.L.
AU  - Bhave, N.
AU  - Malcolm, D.B.
TI  - Cation dependence of restriction endonuclease EcoRI activity.
JO  - Eur. J. Biochem.
PY  - 1981
SP  - 293
EP  - 296
VL  - 115
AB  - Restriction endonuclease EcoRI cleaves the DNA sequence 5'd(-G-^A-A-T-T-C-)
AB  - under optimum digestion conditions.  A variation in pH and ionic strength can
AB  - result in EcoRI* activity when 5'd(-^A-A-T-T-) is cut. A divalent cation,
AB  - usually Mg2+, is required for enzyme activity, though Mn2+ can also be used.
AB  - Eight different cations with ionic radius/charge ratios similar to Mg2+ were
AB  - tested and Co2+ and Zn2+ were also found to act as cofactors for EcoRI.  A
AB  - comprehensive study has been made of the effect of NaCl and pH on the
AB  - EcoRI/EcoRI* transition in the presence of the above four cations.  Generally,
AB  - a decrease in NaCl and/or an increase in pH caused a decrease in enzyme
AB  - specificity.  The changeover depended on the cation.  They may be placed in
AB  - order of their ability to increase EcoRI specificity thus: Co2+ > Zn2+ > Mg2+ >
AB  - Mn2+.  The Km of EcoRI for ColE1 DNA, in the presence of Co2+, was found to be
AB  - 0.4 nM, compared to 3 nM with Mg2+, whereas the turnover was only one
AB  - double-stranded scission/min with Co2+ compared to eight/min with Mg2+.  The
AB  - implications of all these findings on the enzyme's mechanism are discussed.
ER  -

TY  - JOUR
AU  - Woodhead, J.L.
AU  - Malcolm, A.D.B.
TI  - Restriction endonuclease EcoRI binds non-specifically to deoxyribonucleic acid.
JO  - Biochem. Soc. Trans.
PY  - 1980
SP  - 90
EP  - 91
VL  - 8
AB  - EcoRI is a type-II restriction endonuclease.  These enzymes recognize and cleave specific DNA
AB  - sequences.  Despite the widespread use of these enzymes for genetic manipulation and DNA
AB  - mapping, little is known about the mechanism of any of them, or how they achieve their
AB  - specificity.  EcoRI recognizes and cleaves the DNA sequence 5'...G/A-A-T-T-C...3' at the
AB  - point indicated.  This activity occurs at around neutral pH and at salt concentrations above
AB  - 50mM, but at lower salt concentrations and at pH values above 8, the enzyme exhibits EcoRI
AB  - activity when 5'...N/A-A-T-T-N...3' is cut.  Mg2+ is required for both activities.  We have
AB  - shown that EcoRI not only binds to DNA containing EcoRI or EcoRI sites but will also bind to
AB  - DNA containing neither site.
ER  -

TY  - JOUR
AU  - Woodhead, J.L.
AU  - Malcolm, A.D.B.
TI  - Non-specific binding of restriction endonuclease EcoRI to DNA.
JO  - Nucleic Acids Res.
PY  - 1980
SP  - 389
EP  - 402
VL  - 8
AB  - Restriction endonuclease, EcoR1 cleaves the DNA sequence (5' - 3')G -^ A - A -
AB  - T - T - C (3' - 5')C - T - T - A - A -^ G at the points indicated.  Under
AB  - certain conditions, EcoRI activity is observed when (5' - 3')N1 -^ A - A - T -
AB  - T - N2 (3' - 5')N3 - T - T - A - A -^ N4 is cut.  Mg2+ is required for both
AB  - activities.  We find that in addition to binding to the above sites, EcoRI will
AB  - also bind, although less strongly, to DNA containing neither site.  Methyl
AB  - acetimidate, which reacts specifically with lysine residues, inactivates the
AB  - enzyme.  This specific effect can be prevented by SV40 DNA and lambda DNA which
AB  - contain EcoRI and EcoRI sites, by PhiX174 DNA, which has only EcoRI sites and
AB  - also by Polyd(AT) and polyd(GC) containing neither site.  Protection occurs in
AB  - the absence or presence of magnesium.  The significance of this non-specific
AB  - binding, both for the use and mechanism of EcoR1 will be discussed.
ER  -

TY  - JOUR
AU  - Woodhead, J.L.
AU  - Malcolm, A.D.B.
TI  - The essential carboxyl group in restriction endonuclease EcoRI.
JO  - Eur. J. Biochem.
PY  - 1981
SP  - 125
EP  - 128
VL  - 120
AB  - We have carried out studies on type II restriction endonuclease R.EcoRI, wich
AB  - cleaves the DNA sequence 5'd(G^A-A-T-T-C-)3', as indicated.  The active form of
AB  - the enzyme consists of two subunits, each 31063 molecular weight.  A
AB  - water-soluble reagent, 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide
AB  - metho-p-sulphonate, which reacts with carboxyl groups and also with tyrosine
AB  - and cysteine residues, has been found to inactivate this enzyme.  Results are
AB  - presented which show the following. (1) This specific inactivation is not due
AB  - to modification of tyrosine or cysteine residues.  (2) There is one carboxyl
AB  - group per subunit which, when modified with carbodiimide, inactivates the
AB  - enzyme.  (3) PhiX174 DNA (which does not contain EcoRI sites) partially
AB  - protects the enzyme from the carbodiimide; protection is unaffected by the
AB  - additional presence of Mg2+, but significantly greater with Co2+ and
AB  - PhiX174DNA.
ER  -

TY  - JOUR
AU  - Woodhouse, J.N.
AU  - Makower, A.K.
AU  - Grossart, H.P.
AU  - Dittmann, E.
TI  - Draft Genome Sequences of Two Uncultured Armatimonadetes Associated with a Microcystis sp. (Cyanobacteria) Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00717
EP  - e00717
VL  - 5
AB  - Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments,
AB  - have been previously described. Here, two additional
AB  - Armatimonadetes genome sequences were obtained via single-molecule real-time
AB  - (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium
AB  - Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The
AB  - genomes are most closely affiliated with the class Fimbriimonadales, although
AB  - they are smaller than the 5.6-Mbp type strain genome.
ER  -

TY  - JOUR
AU  - Woods, D.E.
AU  - Jeddeloh, J.A.
AU  - Fritz, D.L.
AU  - DeShazer, D.
TI  - Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei.
JO  - J. Bacteriol.
PY  - 2002
SP  - 4003
EP  - 4017
VL  - 184
AB  - Burkholderia thailandensis is a nonpathogenic gram-negative bacillus that is closely related
AB  - to Burkholderia mallei and Burkholderia pseudomallei. We found that B. thailandensis E125
AB  - spontaneously produced a bacteriophage, termed phiE125, which formed turbid plaques in top
AB  - agar containing B. mallei ATCC 23344. We examined the host range of phiE125 and found that it
AB  - formed plaques on B. mallei but not on any other bacterial species tested, including B.
AB  - thailandensis and B. pseudomallei. Examination of the bacteriophage by transmission electron
AB  - microscopy revealed an isometric head and a long noncontractile tail. B. mallei NCTC 120 and
AB  - B. mallei DB110795 were resistant to infection with phiE125 and did not produce
AB  - lipopolysaccharide (LPS) O antigen due to IS407A insertions in wbiE and wbiG, respectively.
AB  - wbiE was provided in trans on a broad-host-range plasmid to B. mallei NCTC 120, and it
AB  - restored LPS O-antigen production and susceptibility to phiE125. The 53,373-bp phiE125 genome
AB  - contained 70 genes, an IS3 family insertion sequence (ISBt3), and an attachment site (attP)
AB  - encompassing the 3' end of a proline tRNA (UGG) gene. While the overall genetic organization
AB  - of the phiE125 genome was similar to lambda-like bacteriophages and prophages, it also
AB  - possessed a novel cluster of putative replication and lysogeny genes. The phiE125 genome
AB  - encoded an adenine and a cytosine methyltransferase, and purified bacteriophage DNA contained
AB  - both N6-methyladenine and N4-methylcytosine. The results presented here demonstrate that
AB  - phiE125 is a new member of the lambda supergroup of Siphoviridae that may be useful as a
AB  - diagnostic tool for B. mallei.
ER  -

TY  - JOUR
AU  - Wooten, J.
AU  - Liu, X.
AU  - Miller, M.J.
TI  - Draft Genome Sequence of Lactobacillus crispatus JCM5810, Which Can Reduce Campylobacter jejuni Colonization in Chicken Intestine.
JO  - Genome Announcements
PY  - 2016
SP  - e00255
EP  - e00216
VL  - 4
AB  - We present the 2.05-Mb draft genome sequence ofLactobacillus crispatusJCM5810, a  chicken
AB  - intestinal isolate with the ability to reduceCampylobacter
AB  - jejunicolonization in chickens. The genome sequence will provide insights on the
AB  - probiotic mechanisms ofL. crispatusJCM5810.
ER  -

TY  - JOUR
AU  - Worden, A.Z. et al.
TI  - Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
JO  - Science
PY  - 2009
SP  - 268
EP  - 272
VL  - 324
AB  - Picoeukaryotes are a taxonomically diverse group of organisms less than 2
AB  - micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus
AB  - Micromonas thrive in ecosystems ranging from tropical to polar and could serve as
AB  - sentinel organisms for biogeochemical fluxes of modern oceans during climate
AB  - change. These broadly distributed primary producers belong to an anciently
AB  - diverged sister clade to land plants. Although Micromonas isolates have high 18S
AB  - ribosomal RNA gene identity, we found that genomes from two isolates shared only
AB  - 90% of their predicted genes. Their independent evolutionary paths were
AB  - emphasized by distinct riboswitch arrangements as well as the discovery of
AB  - intronic repeat elements in one isolate, and in metagenomic data, but not in
AB  - other genomes. Divergence appears to have been facilitated by selection and
AB  - acquisition processes that actively shape the repertoire of genes that are
AB  - mutually exclusive between the two isolates differently than the core genes.
AB  - Analyses of the Micromonas genomes offer valuable insights into ecological
AB  - differentiation and the dynamic nature of early plant evolution.
ER  -

TY  - JOUR
AU  - Workentine, M.L.
AU  - Surette, M.G.
AU  - Bernier, S.P.
TI  - Draft Genome Sequence of Burkholderia dolosa PC543 Isolated from Cystic Fibrosis  Airways.
JO  - Genome Announcements
PY  - 2014
SP  - e00043
EP  - e00014
VL  - 2
AB  - Burkholderia dolosa is a member of the Burkholderia cepacia complex, a group of opportunistic
AB  - bacterial pathogens often associated with fatal chronic infections
AB  - in the lungs of patients suffering from cystic fibrosis (CF). Here, we announce
AB  - the draft genome sequence of B. dolosa PC543 (LMG 19468), a CF airway isolate.
ER  -

TY  - JOUR
AU  - Woudstra, C.
AU  - Brito, R.B.
AU  - Fonseca, J.A.A.
AU  - Silva, R.O.S.
AU  - Lobato, F.C.F.
AU  - Fach, P.
TI  - Draft Genome Sequences of Five Brazilian Clostridium botulinum Group III Type D/C Strains.
JO  - Genome Announcements
PY  - 2017
SP  - e00349
EP  - e00317
VL  - 5
AB  - Animal botulism is mainly associated with Clostridium botulinum group III-producing neurotoxin
AB  - types C, C/D, D, and D/C. In this report, we present the
AB  - draft genome sequences of the first five strains of Clostridium botulinum type
AB  - D/C isolated in Brazil and used for vaccination purposes.
ER  -

TY  - JOUR
AU  - Woudstra, C.
AU  - Fach, P.
AU  - Chomel, B.B.
AU  - Haddad, N.
AU  - Boulouis, H.J.
TI  - Draft Genome Sequences of 12 Feline Bartonella henselae Isolates.
JO  - Genome Announcements
PY  - 2017
SP  - e00075
EP  - e00017
VL  - 5
AB  - Bartonella henselae is the main causative agent of cat scratch disease. In this report, we
AB  - present the draft genome sequences of 12 strains of Bartonella
AB  - henselae originating from the United States, Denmark, and France. These strains
AB  - were isolated from cats and belonged to either 16S rRNA genotype I or 16S rRNA
AB  - genotype II.
ER  -

TY  - JOUR
AU  - Woudstra, C.
AU  - Le Marechal, C.
AU  - Souillard, R.
AU  - Bayon-Auboyer, M.H.
AU  - Mermoud, I.
AU  - Desoutter, D.
AU  - Fach, P.
TI  - Draft Genome Sequences of 17 French Clostridium botulinum Group III Strains.
JO  - Genome Announcements
PY  - 2015
SP  - e01105
EP  - e01115
VL  - 3
AB  - Animal botulism is mainly associated with Clostridium botulinum group III strains producing
AB  - neurotoxin types C, C/D, D, and D/C. In this report, we present the draft genome sequences of
AB  - fourteen strains of Clostridium botulinum producing type C/D and two strains producing type
AB  - D/C isolated in France, and one strain producing type D/C that originated from New Caledonia.
ER  -

TY  - JOUR
AU  - Woyke, T. et al.
TI  - Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 21
EP  - 29
VL  - 5
AB  - Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within
AB  - the family Cryomorphaceae. The species is of interest because
AB  - of its isolated phylogenetic location in the genome-sequenced fraction of the
AB  - tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated
AB  - bacteria represented in freshwater 16S rRNA gene libraries. A similar
AB  - phylogenetic differentiation occurs between freshwater and marine bacteria in the
AB  - family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is
AB  - the inability of this freshwater bacterium to grow in the presence of Na(+) ions.
AB  - All other genera in the family Cryomorphaceae are from marine habitats and have
AB  - an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the
AB  - first member of the family Cryomorphaceae with a completely sequenced and
AB  - publicly available genome. The 4,633,577 bp long genome with its 4,082
AB  - protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria
AB  - and Archaea project.
ER  -

TY  - JOUR
AU  - Wright, D.J.
AU  - Jack, W.E.
AU  - Modrich, P.
TI  - The kinetic mechanism of EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1999
SP  - 31896
EP  - 31902
VL  - 274
AB  - Steady-state parameters governing cleavage of pBR322 DNA by EcoRI endonuclease are highly
AB  - sensitive to ionic environment, with K(m) and k(cat) increasing 1,000-fold and 15-fold,
AB  - respectively, when ionic strength is increased from 0.059 to 0.23 M.  By contrast,
AB  - pre-steady-state analysis has shown that recognition, as well as first and second strand
AB  - cleavage events that occur once the enzyme has arrived at the EcoRI site, are essentially
AB  - insensitive to ionic strength, and has demonstrated that the rate-limiting step for
AB  - endonuclease turnover occurs after double-strand cleavage under all conditions tested.
AB  - Furthermore, processive cleavage of a pBR322 variant bearing two closely spaced EcoRI sites is
AB  - governed by the same turnover number as hydrolysis of parental pBR322, which contains only a
AB  - single EcoRI sequence, ruling out slow release of the enzyme from the cleaved site or a slow
AB  - conformational change subsequent to double-strand cleavage. We attribute the effects of ionic
AB  - strength on steady-state parameters to nonspecific endonuclease.DNA interactions, reflecting
AB  - facilitated diffusion processes, that occur prior to EcoRI sequence recognition and subsequent
AB  - to DNA cleavage.
ER  -

TY  - JOUR
AU  - Wright, D.J.
AU  - King, K.
AU  - Modrich, P.
TI  - The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease.
JO  - J. Biol. Chem.
PY  - 1989
SP  - 11816
EP  - 11821
VL  - 264
AB  - King et al. JBC (1989) 264, 11807-11815 have shown that Glu-111 is required for
AB  - DNA cleavage by EcoRI endonuclease and have suggested that this residue is
AB  - required for activation of the cleavage center upon specific recognition.  We
AB  - have substituted Gln or Asp for Glu-111 by oligonucleotide-directed
AB  - mutagenesis.  First and second strand cleavage rate constants are reduced by a
AB  - factor of more than 10/4 by the Gln-111 substitution.  However, these rate
AB  - constants are enhanced 9-fold when pH is increased from 7.6 to 8.5, which
AB  - enhances strand cleavage at EcoRI sites by wild type endonuclease to a similar
AB  - degree.  The specific affinity of Gln-111 endonuclease for EcoRI sites is 1000
AB  - times greater than that of wild type enzyme reflecting a decrease in the rate
AB  - constant governing specific complex dissociation.  In contrast to Gln-111
AB  - endonuclease, the equilibrium specific affinity of Asp-111 endonuclease for the
AB  - EcoRI sequence is similar to that of wild type enzyme, and first and second
AB  - strand cleavage rate constants are reduced only 100-fold relative to wild type
AB  - enzyme.  These results suggest that a negative charge on residue 111 is
AB  - required for strand cleavage and are consistent with participation of Glu-111
AB  - in activation of the DNA cleavage center, with energy associated with specific
AB  - sequence recognition driving this process.
ER  -

TY  - JOUR
AU  - Wright, M.S.
AU  - Perez, F.
AU  - Brinkac, L.
AU  - Jacobs, M.R.
AU  - Kaye, K.
AU  - Cober, E.
AU  - van Duin, D.
AU  - Marshall, S.H.
AU  - Hujer, A.M.
AU  - Rudin, S.D.
AU  - Hujer, K.M.
AU  - Bonomo, R.A.
AU  - Adams, M.D.
TI  - Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. hospitals.
JO  - Antimicrob. Agents Chemother.
PY  - 2014
SP  - 4961
EP  - 4965
VL  - 58
AB  - Genome sequencing of carbapenem-resistant Klebsiella pneumoniae isolates from
AB  - regional U.S. hospitals was used to characterize strain diversity and the
AB  - bla(KPC) genetic context. A phylogeny based on core single-nucleotide variants
AB  - (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups.
AB  - The primary differences between the groups are in the capsular polysaccharide
AB  - locus (cps) and their plasmid contents. A strict association between clade and
AB  - KPC variant was found. The bla(KPC) gene was found on variants of two plasmid
AB  - backbones. This study indicates that highly similar K. pneumoniae subpopulations
AB  - coexist within the same hospitals over time.
ER  -

TY  - JOUR
AU  - Wright, R.
AU  - Stephens, C.
AU  - Shapiro, L.
TI  - The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus.
JO  - J. Bacteriol.
PY  - 1997
SP  - 5869
EP  - 5877
VL  - 179
AB  - the Caulobacter crescentus DNA methyltransferase CcrM (M.CcrMI) methylates the adenine residue
AB  - in the sequence GANTC.  The CcrM DNA methyltransferase is essential for viability, but it does
AB  - not appear to be part of a DNA restriction-modification system.  CcrM homologs are widespread
AB  - in the alpha subdivision of gram-negative bacteria.  We have amplified and sequenced a 258-bp
AB  - region of the ccrM gene from several of these bacteria, including Rhizobium meliloti, Brucella
AB  - abortus, Agrobacterium tumefaciens, and Rhodobacter capsulatus.  Alignment of the deduced
AB  - amino acid sequences revealed that these proteins constitute a highly conserved DNA
AB  - methyltransferase family.  Isolation of the full-length ccrM genes from the aquatic bacterium
AB  - C. crescentus, the soil bacterium R. meliloti, and the intracellular pathogen B. abortus
AB  - showed that this sequence conservation extends over the entire protein.  In at least two alpha
AB  - subdivision bacteria, R. meliloti and C. crescentus, CcrM-mediated methylation has important
AB  - cellular functions.  In both organisms, CcrM is essential for viability.  Over-expression of
AB  - CcrM in either bacterium results in the defects in cell division and cell morphology and in
AB  - the initiation of DNA replication.  Finally, the C. crescentus and R. meliloti ccrM genes are
AB  - functionally interchangeable, as the complemented strains are viable and the chromosomes are
AB  - methylated.  Thus, in both R. meliloti and C. crescentus, CcrM methylation is an integral
AB  - component of the cell cycle.  We speculate that CcrM-mediated DNA methylation is likely to
AB  - have similar roles among alpha subdivision bacteria.
ER  -

TY  - JOUR
AU  - Wright, R.
AU  - Stephens, C.
AU  - Zweiger, G.
AU  - Shapiro, L.
AU  - Alley, M.R.K.
TI  - Caulobacter Lon protease has a critical role in cell-cyle control of DNA methylation.
JO  - Genes Dev.
PY  - 1996
SP  - 1532
EP  - 1542
VL  - 10
AB  - CcrM an adenine DNA methyltransferase, is essential for viability in Caulobacter crescentus.
AB  - The CcrM protein is present only in the predivisional stage of the cell cycle, resulting in
AB  - cell-cycle-dependent variation of the DNA methylation state of the chromosome.  The
AB  - availability of CcrM is controlled in two ways: (1) the ccrM gene is transcribed only in the
AB  - predivisional cell, and (2) the CcrM protein is rapidly degraded prior to cell division.  We
AB  - demonstrate here that CcrM is an important target of the Lon protease pathway in C.
AB  - crescentus.  In a lon null mutant, ccrM transcription is still temporally regulated, but the
AB  - CcrM protein is present throughout the cell cycle because of a dramatic increase in its
AB  - stability that results in a fully methylated chromosome throughout the cell cycle.  Because
AB  - the Lon protease is present throughout the cell cycle, it is likely that the level of CcrM in
AB  - the cell is controlled by a dynamic balance between temporally varied transcription and
AB  - constitutive degradation.  We have shown previously that restriction of CcrM to the C.
AB  - crescentus predivisional cell is essential for normal morphogenesis and progression through
AB  - the cell cycle.  Comparison of the lon null mutant strain with a strain whose DNA remains
AB  - fully methylated as a result of constitutive expression of ccrM suggests that the effect of
AB  - Lon on DNA methylation contributes to several developmental defects observed in the lon
AB  - mutant.  These defects include a frequent failure to complete cell abnormalities exhibited by
AB  - the lon null mutant, such as the formation of abnormally long stalks, appear to be unrelated
AB  - to altered chromosome methylation state.  The Lon protease thus exhibits pleiotropic effects
AB  - in C. crescentus growth and development.
ER  -

TY  - JOUR
AU  - Wright, R.J.
AU  - Stephens, C.
AU  - Alley, D.
AU  - Zweiger, G.
AU  - Shapiro, L.
TI  - Cell cycle turnover of a DNA methyltransferase in Caulobacter is dependent on the Lon protease.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1996
SP  - 527
EP  - 527
VL  - 96
AB  - CcrM, an adenine DNA methyltransferase, is essential for viability in Caulobacter
AB  - crescentus.  CcrM is present only in the predivisional state of the Caulobacter cell cycle.
AB  - As a
AB  - consequence, the DNA methylation state of the chromosome is cell cycle regulated.  CcrM levels
AB  - are controlled in two ways (a) transcription of the ccrM gene is limited to the predivisional
AB  - cell and
AB  - (b) the CcrM protein is degraded prior to cell division.  This transient presence of CcrM is
AB  - important, as constitutive expression of ccrM causes developmental defects.  In our efforts to
AB  - identify the protease responsible for CcrM turnover, the Caulobacter Lon homolog was isolated.
AB  - In a Lon null mutant, CcrM is present throughout the cell cycle.  Thus, the Lon protease is
AB  - required
AB  - for turnover of CcrM, and is necessary for cell cycle regulation of DNA methylation.  We are
AB  - currently constructing mutant alleles of CcrM to examine the requirements of Lon-dependent
AB  - CcrM
AB  - proteolysis.  We have demonstrated that CcrM homologs are widespread in the alpha-subdivision
AB  - of purple gram negative bacteria and are currently cloning several of these homologs.
ER  -

TY  - JOUR
AU  - Wright, S.
AU  - Wilson, S.
AU  - Miller, W.G.
AU  - Mandrell, R.E.
AU  - Siletzky, R.M.
AU  - Kathariou, S.
TI  - Differences in Methylation at GATC Sites in Genomic DNA of Campylobacter coli from Turkeys and Swine.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 7314
EP  - 7317
VL  - 76
AB  - A significant fraction (46/108, 43%) of swine isolates of Campylobacter coli but none of 81
AB  - isolates of C. coli from turkeys had genomic DNA
AB  - that was resistant to digestion by MboI, suggesting methylation of
AB  - adenines at GATC sites. No consistent association was noted between
AB  - antimicrobial resistance and MboI resistance. Seven swine-associated
AB  - multilocus sequence typing-based sequence types (STs) were detected
AB  - among multiple isolates with MboI-resistant DNA. The data suggest
AB  - host-associated DNA modification system(s) specific for adenine at GATC
AB  - sites in C. coli from swine.
ER  -

TY  - JOUR
AU  - Wright, S.M.
AU  - Carroll, C.
AU  - Walters, A.
AU  - Newell, P.D.
AU  - Chaston, J.M.
TI  - Genome Sequence of Leuconostoc citreum DmW_111, Isolated from Wild Drosophila.
JO  - Genome Announcements
PY  - 2017
SP  - e00507
EP  - e00517
VL  - 5
AB  - Isolates of the lactic acid bacterium Leuconostoc citreum are a major part of fermentation
AB  - processes, especially in Korean kimchi. Here, we present the genome
AB  - of L. citreum DmW_111, isolated from wild Drosophila melanogaster; analysis of
AB  - this genome will expand the diversity of genome sequences for non-Lactobacillus
AB  - spp. isolated from D. melanogaster.
ER  -

TY  - JOUR
AU  - Wrobel, A.
AU  - Ottoni, C.
AU  - Leo, J.C.
AU  - Gulla, S.
AU  - Linke, D.
TI  - The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a 'Y. ruckeri invasin-like molecule', (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen.
JO  - J. Struct. Biol.
PY  - 2018
SP  - 171
EP  - 183
VL  - 201
AB  - Inverse autotransporters comprise the recently identified type Ve secretion system and are
AB  - exemplified by intimin from enterohaemorrhagic Escherichia coli
AB  - and invasin from enteropathogenic Yersiniae. These proteins share a common domain
AB  - architecture and promote bacterial adhesion to host cells. Here, we identified
AB  - and characterized two putative inverse autotransporter genes in the fish pathogen
AB  - Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for
AB  - Y. ruckeri invasin-like molecule). When trying to clone the highly repetitive
AB  - genes for structural and functional studies, we experienced problems in obtaining
AB  - PCR products. PCR failures and the highly repetitive nature of inverse
AB  - autotransporters prompted us to sequence the genome of Y. ruckeri NVH_3758 using
AB  - PacBio sequencing, which produces some of the longest average read lengths
AB  - available in the industry at this moment. According to our sequencing data, YrIlm
AB  - is composed of 2603 amino acids (7812bp) and has a molecular mass of 256.4kDa.
AB  - Based on the new genome information, we performed PCR analysis on four
AB  - non-sequenced Y. ruckeri strains as well as the sequenced. Y. ruckeri type
AB  - strain. We found that the genes are variably present in the strains, and that the
AB  - length of yrIlm, when present, also varies. In addition, the length of the gene
AB  - product for all strains, including the type strain, was much longer than expected
AB  - based on deposited sequences. The internal repeats of the yrInv gene product are
AB  - highly diverged, but represent the same bacterial immunoglobulin-like domains as
AB  - in yrIlm. Using qRT-PCR, we found that yrIlm and yrInv are differentially
AB  - expressed under conditions relevant for pathogenesis. In addition, we compared
AB  - the genomic context of both genes in the newly sequenced Y. ruckeri strain to all
AB  - available PacBio-sequenced Y. ruckeri genomes, and found indications of recent
AB  - events of horizontal gene transfer. Taken together, this study demonstrates and
AB  - highlights the power of Single Molecule Real-Time technology for sequencing
AB  - highly repetitive proteins, and sheds light on the genetic events that gave rise
AB  - to these highly repetitive genes in a commercially important fish pathogen.
ER  -

TY  - JOUR
AU  - Wu, A.K.
AU  - Kropinski, A.M.
AU  - Lumsden, J.S.
AU  - Dixon, B.
AU  - MacInnes, J.I.
TI  - Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 3
EP  - 3
VL  - 10
AB  - Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and
AB  - rainbow trout fry mortality syndrome in salmonid fishes and is
AB  - associated with significant losses in the aquaculture industry. The virulence
AB  - factors and molecular mechanisms of pathogenesis of F. psychrophilum are poorly
AB  - understood. Moreover, at the present time, there are no effective vaccines and
AB  - control using antimicrobial agents is problematic due to growing antimicrobial
AB  - resistance and the fact that sick fish don't eat. In the hopes of identifying
AB  - vaccine and therapeutic targets, we sequenced the genome of the type strain ATCC
AB  - 49418 which was isolated from the kidney of a Coho salmon (Oncorhychus kisutch)
AB  - in Washington State (U.S.A.) in 1989. The genome is 2,715,909 bp with a G+C
AB  - content of 32.75%. It contains 6 rRNA operons, 49 tRNA genes, and is predicted to
AB  - encode 2,329 proteins.
ER  -

TY  - JOUR
AU  - Wu, Bo.
AU  - He, M.
AU  - Feng, H.
AU  - Zhang, Y.
AU  - Hu, Q.
AU  - Zhang, Y.
TI  - Construction and Characterization of Restriction-Modification Deficient Mutants in Zymomonas mobilis ZM4.
JO  - Chin. J. Appl. Environ. Biol.
PY  - 2013
SP  - 189
EP  - 197
VL  - 19
AB  - Low transformation efficiency is an obstacle to genetic or molecular manipulations in
AB  - ethanologen Zymomonas mobilis. In the present study, 5 defective strains were constructed in
AB  - Z. mobilis strain ZM4 by inactivating restriction-modification (R-M) system candidate genes.
AB  - Inactivation of ZMO0028 (mrr) and ZMO1933 significantly improved electroporation efficiency by
AB  - 17 folds and 2 folds when ZM4 was transformed with the methylated plasmid DNA. Disruption of
AB  - ZMO0575 significantly decreased the transfor ation efficiency when transformed with both
AB  - methylated and unmethylated plasmid DNAs. In comparison with other mutants, Zmmrr and Zm1933
AB  - displayed high stability. Furthermore, fermentation results showed that R-M mutants did not
AB  - significantly alter the major bacterial traits such as growth, glucose utilization and ethanol
AB  - yield. In conclusion, R-M systems in Z. mobilis were investigated in this study, and the
AB  - characterization of those R-M genes contributed to creating engineering strains suitable for
AB  - genet ic and molecular manipulations.
ER  -

TY  - JOUR
AU  - Wu, C.-T.
AU  - Li, W.-G.
AU  - Gao, X.-S.
AU  - Zhang, X.-F.
TI  - Bioinformatics analysis of DNA methyltransferase from plants.
JO  - Xinan Daxue Xuebao, Ziran Kexueban
PY  - 2010
SP  - 83
EP  - 89
VL  - 32
AB  - The nucleic acid sequences and amino acid sequences of DNA methyltransferase from oil palm,
AB  - Prunus, Pisum, Daucus and Arabidopsis, which were registerd in GenBank, were predicted and
AB  - analyzed, using bioinformatics tools according to the composition of nucleic acid sequences
AB  - and amino acid sequences, physical and chemical properties, homology alignments, signal
AB  - peptides, transmembrane topological structure, hydrophobicity and hydrophilicity, secondary
AB  - and tertiary structures of protein and molecular phylogenetic evolution.  The results
AB  - indicated that the full-length cDNA of DNMT contains 5'-untranslated region, an open reading
AB  - frame and 3'-untranslated region, that DNMT has no signal peptides and transmembrane peptides
AB  - and is a hydrophilic protein, including two BAH domains and a DNA methylase, and that alpha
AB  - helix and random coil are the main components of its secondary structure and all domains bind
AB  - in turn by means of electrostatic interaction.
ER  -

TY  - JOUR
AU  - Wu, C.H.
AU  - Chen, C.Y.
AU  - Morales, C.
AU  - Kiang, D.
TI  - Draft Genome Sequence of an ortho-Nitrophenyl-beta-d-Galactoside (ONPG)-Negative  Strain of Vibrio cholerae, Isolated from Drakes Bay, California.
JO  - Genome Announcements
PY  - 2016
SP  - e00135
EP  - e00116
VL  - 4
AB  - We present the draft whole-genome sequence of a Vibrio cholerae strain (Vc25-3) isolated from
AB  - Drakes Bay, California. This environmental isolate has an atypical
AB  - morphology and is ortho-nitrophenyl-beta-d-galactoside (ONPG)-negative.
ER  -

TY  - JOUR
AU  - Wu, C.H.
AU  - Zhang, P.
AU  - Morales, C.Q.
AU  - Kiang, D.
TI  - Draft Whole-Genome Sequences of Three Shiga Toxin-Producing Escherichia coli O91:H21 Isolates, Two from Hemolytic Uremic Syndrome Patients and One of Porcine   Origin.
JO  - Genome Announcements
PY  - 2014
SP  - e01000
EP  - e01014
VL  - 2
AB  - This study presents three genomes of O91:H21 isolates, two from hemolytic uremic  syndrome
AB  - patients and one of porcine origin. Genome analyses reveal that one of
AB  - the human isolates contains both Shiga toxin-encoding genes (stx1 and stx2), and
AB  - all three isolates contain putative adhesin (iha and eaeH) and antibiotic
AB  - resistance (ampC) genes.
ER  -

TY  - JOUR
AU  - Wu, C.J.
AU  - Wang, H.C.
AU  - Chen, C.S.
AU  - Shu, H.Y.
AU  - Kao, A.W.
AU  - Chen, P.L.
AU  - Ko, W.C.
TI  - Genome Sequence of a Novel Human Pathogen, Aeromonas aquariorum.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4114
EP  - 4115
VL  - 194
AB  - Aeromonas aquariorum, a recently described species, is associated with a variety  of human
AB  - diseases. We present here the first genome sequence of A. aquariorum
AB  - strain AAk1, which was isolated as the sole pathogen from the blood of a patient
AB  - with septicemia and necrotizing fasciitis.
ER  -

TY  - JOUR
AU  - Wu, D.
AU  - Raymond, J.
AU  - Wu, M.
AU  - Chatterji, S.
AU  - Ren, Q.
AU  - Graham, J.E.
AU  - Bryant, D.A.
AU  - Robb, F.
AU  - Colman, A.
AU  - Tallon, L.J.
AU  - Badger, J.H.
AU  - Madupu, R.
AU  - Ward, N.L.
AU  - Eisen, J.A.
TI  - Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.
JO  - PLoS ONE
PY  - 2009
SP  - E4207
EP  - E4207
VL  - 4
AB  - In order to enrich the phylogenetic diversity represented in the available
AB  - sequenced bacterial genomes and as part of an "Assembling the Tree of
AB  - Life" project, we determined the genome sequence of Thermomicrobium roseum
AB  - DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative
AB  - extreme thermophile isolated from a hot spring that possesses both an
AB  - atypical cell wall composition and an unusual cell membrane that is
AB  - composed entirely of long-chain 1,2-diols. Its genome is composed of two
AB  - circular DNA elements, one of 2,006,217 bp (referred to as the chromosome)
AB  - and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though
AB  - few standard housekeeping genes are found on the megaplasmid, it does
AB  - encode a complete system for chemotaxis including both chemosensory
AB  - components and an entire flagellar apparatus. This is the first known
AB  - example of a complete flagellar system being encoded on a plasmid and
AB  - suggests a straightforward means for lateral transfer of flagellum-based
AB  - motility. Phylogenomic analyses support the recent rRNA-based analyses
AB  - that led to T. roseum being removed from the phylum Thermomicrobia and
AB  - assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching
AB  - member of this phylum, analysis of its genome provides insights into the
AB  - evolution of the Chloroflexi. In addition, even though this species is not
AB  - photosynthetic, analysis of the genome provides some insight into the
AB  - origins of photosynthesis in the Chloroflexi. Metabolic pathway
AB  - reconstructions and experimental studies revealed new aspects of the
AB  - biology of this species. For example, we present evidence that T. roseum
AB  - oxidizes CO aerobically, making it the first thermophile known to do so.
AB  - In addition, we propose that glycosylation of its carotenoids plays a
AB  - crucial role in the adaptation of the cell membrane to this bacterium's
AB  - thermophilic lifestyle. Analyses of published metagenomic sequences from
AB  - two hot springs similar to the one from which this strain was isolated,
AB  - show that close relatives of T. roseum DSM 5159 are present but have some
AB  - key differences from the strain sequenced.
ER  -

TY  - JOUR
AU  - Wu, D.Q.
AU  - Cheng, H.
AU  - Wang, C.
AU  - Zhang, C.
AU  - Wang, Y.
AU  - Shao, J.
AU  - Duan, Q.
TI  - Genome Sequence of Pseudomonas aeruginosa Strain AH16, Isolated from a Patient with Chronic Pneumonia in China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5976
EP  - 5977
VL  - 194
AB  - Pseudomonas aeruginosa AH16 is a virulent strain isolated from a patient with chronic
AB  - pneumonia in China. Here, we present a 6.8-Mb (G+C content, 66.13%)
AB  - assembly of its genome with 6,332 putative coding sequences, which may provide
AB  - insights into the genomic basis of activity of the clinical P. aeruginosa strain
AB  - in China.
ER  -

TY  - JOUR
AU  - Wu, D.Q.
AU  - Ye, J.
AU  - Ou, H.Y.
AU  - Wei, X.
AU  - Huang, X.
AU  - He, Y.W.
AU  - Xu, Y.
TI  - Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18.
JO  - BMC Genomics
PY  - 2011
SP  - 438
EP  - 438
VL  - 12
AB  - ABSTRACT: BACKGROUND: Our previously published reports have described an
AB  - effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA
AB  - sequence and several regulator genes share homologous sequences with those
AB  - of P. aeruginosa, but there are several unusual phenotypic features. This
AB  - study aims to explore its strain specific genomic features and gene
AB  - expression patterns at different temperatures. RESULTS: The complete M18
AB  - genome is composed of a single chromosome of 6,327,754 base pairs
AB  - containing 5684 open reading frames. Seven genomic islands, including two
AB  - novel prophage clusters and five specific non-phage islands were
AB  - identified besides the conserved P. aeruginosa core genome. Each prophage
AB  - contains a putative chitinase coding gene, and the prophage II contains a
AB  - capB gene encoding a putative cold stress protein. The non-phage GIs
AB  - contain genes responsible for pyoluteorin biosynthesis, environmental
AB  - substance degradation and type I and III restriction-modification systems.
AB  - Compared with other P. aeruginosa strains, the fewest number (3) of
AB  - insertion sequences and the most number (3) of clustered regularly
AB  - interspaced short palindromic repeats in M18 genome may contribute to the
AB  - relative genome stability. Although the M18 genome is most closely related
AB  - to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible
AB  - to several antimicrobial agents and easier to be erased in a mouse acute
AB  - lung infection model than the strain LESB58. The whole M18 transcriptomic
AB  - analysis indicated that 10.6% of the expressed genes are
AB  - temperature-dependent, with 22 genes up-regulated at 28 degrees Celsius in
AB  - three GIs and one prophage but none at 37 degrees Celsius. CONCLUSIONS:
AB  - The P. aeruginosa strain M18 has its evolved specific genomic structures
AB  - and temperature dependent expression patterns to meet the requirement of
AB  - its fitness and competitiveness under selective pressures imposed on the
AB  - strain in rhizosphere niche.
ER  -

TY  - JOUR
AU  - Wu, F.
AU  - Deng, X.
AU  - Liang, G.
AU  - Huang, J.
AU  - Cen, Y.
AU  - Chen, J.
TI  - Whole-Genome Sequence of 'Candidatus Profftella armatura' from Diaphorina citri in Guangdong, China.
JO  - Genome Announcements
PY  - 2015
SP  - e01282
EP  - e01215
VL  - 3
AB  - The genome of 'Candidatus Profftella armatura' strain YCPA from Diaphorina citri  in
AB  - Guangdong, China, was sequenced. The strain has a chromosome of 457,565 bp,
AB  - 24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNAs, and a
AB  - plasmid, pYCPA54, of 5,458 bp with 23.9% G+C content and 5 ORFs.
ER  -

TY  - JOUR
AU  - Wu, F.
AU  - Deng, X.
AU  - Liang, G.
AU  - Wallis, C.
AU  - Trumble, J.T.
AU  - Prager, S.
AU  - Chen, J.
TI  - De Novo Genome Sequence of 'Candidatus Liberibacter solanacearum' from a Single Potato Psyllid in California.
JO  - Genome Announcements
PY  - 2015
SP  - e01500
EP  - e01515
VL  - 3
AB  - The draft genome sequence of 'Candidatus Liberibacter solanacearum' strain RSTM from a
AB  - potato psyllid (Bactericera cockerelli) in California is reported here.
AB  - The RSTM strain has a genome size of 1,286,787 bp, a G+C content of 35.1%, 1,211
AB  - predicted open reading frames (ORFs), and 43 RNA genes.
ER  -

TY  - JOUR
AU  - Wu, F.
AU  - Kumagai, L.
AU  - Liang, G.
AU  - Deng, X.
AU  - Zheng, Z.
AU  - Keremane, M.
AU  - Chen, J.
TI  - Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from a Citrus Tree in San Gabriel, California.
JO  - Genome Announcements
PY  - 2015
SP  - e01508
EP  - e01515
VL  - 3
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain SGCA5 from an orange
AB  - citrus tree in San Gabriel, California, is reported here. SGCA5
AB  - has a genome size of 1,201,445 bp, a G+C content of 36.4%, 1,152 predicted open
AB  - reading frames (ORFs), and 42 RNA genes.
ER  -

TY  - JOUR
AU  - Wu, F.
AU  - Zheng, Z.
AU  - Deng, X.
AU  - Cen, Y.
AU  - Liang, G.
AU  - Chen, J.
TI  - Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from Diaphorina citri in Guangdong, China.
JO  - Genome Announcements
PY  - 2015
SP  - e01316
EP  - e01315
VL  - 3
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain YCPsy from an Asian
AB  - citrus psyllid (Diaphorina citri) in Guangdong, China, is reported
AB  - here. The YCPsy strain has a genome size of 1,233,647 bp, 36.5% G+C content,
AB  - 1,171 open reading frames (ORFs), and 53 RNAs.
ER  -

TY  - JOUR
AU  - Wu, H.
AU  - Borriss, R.
AU  - Xue, P.
AU  - Liu, F.
AU  - Qiao, J.
AU  - Schneider, A.
AU  - Lasch, P.
AU  - Gao, X.
TI  - Draft Genome Sequences of Plant-Associated Bacillus Strains Isolated from the Qinghai-Tibetan Plateau.
JO  - Genome Announcements
PY  - 2018
SP  - e00375
EP  - e00318
VL  - 6
AB  - Here, we report the draft genome sequences of 45 plant-associated Bacillus strains isolated
AB  - from the Qinghai-Tibetan plateau. According to their genome
AB  - sequences, 28 isolates were assigned to 10 Bacillus species. Seventeen strains
AB  - could not be assigned and are subjects of further research.
ER  -

TY  - JOUR
AU  - Wu, H.
AU  - Lippmann, J.E.
AU  - Oza, J.P.
AU  - Zeng, M.
AU  - Fives-Taylor, P.
AU  - Reich, N.O.
TI  - Inactivation of DNA adenine methyltransferase alters virulence factors in Actinobacillus actinomycetemcomitans.
JO  - Oral Microbiol. Immunol.
PY  - 2006
SP  - 238
EP  - 244
VL  - 21
AB  - DNA adenine methyltransferase (DAM) plays critical roles in diverse biological pathways in
AB  - gram-negative bacteria, and specifically in
AB  - regulating the expression of virulence genes in several organisms.
AB  - Actinobacillus actinomycetemcomitans plays an important role in the
AB  - pathogenesis of juvenile and adult periodontal disease, yet little is
AB  - known about its mechanisms of gene regulation. DAM is shown here to
AB  - directly or indirectly affect well-known A. actinomycetemcomitans
AB  - virulence factors. A mutant A. actinomycetemcomitans strain lacking the
AB  - dam gene was created by homologous recombination and shows normal
AB  - growth phenotypes when grown exponentially. This mutant strain has four
AB  - sixfold increased levels of extracellular leukotoxin, altered cellular
AB  - levels of leukotoxin, and significant changes in bacterial invasion of
AB  - KB oral epithelial cells. These results provide a basis for further
AB  - characterization of regulatory mechanisms that control A.
AB  - actinomycetemcomitans virulence.
ER  -

TY  - JOUR
AU  - Wu, H.
AU  - Qiao, J.
AU  - Blom, J.
AU  - Rueckert, C.
AU  - Reva, O.
AU  - Gao, X.
AU  - Borriss, R.
TI  - The Rhizobacterium Bacillus amyloliquefaciens subsp. plantarum NAU-B3 Contains a  Large Inversion within the Central Portion of the Genome.
JO  - Genome Announcements
PY  - 2013
SP  - e00941
EP  - e00913
VL  - 1
AB  - The genome of rhizobacterium Bacillus amyloliquefaciens subsp. plantarum strain NAU-B3 is
AB  - 4,196,170 bp in size and harbors 4,001 genes. Nine giant gene clusters
AB  - are dedicated to the nonribosomal synthesis of antimicrobial lipopeptides and
AB  - polyketides. Remarkably, NAU_B3 contains a large inversion within the central
AB  - portion of the genome.
ER  -

TY  - JOUR
AU  - Wu, H.N.
AU  - Nakura, Y.
AU  - Motooka, D.
AU  - Nakamura, S.
AU  - Nishiumi, F.
AU  - Ishino, S.
AU  - Kawai, Y.
AU  - Tanaka, T.
AU  - Takeuchi, M.
AU  - Nakayama, M.
AU  - Fujita, T.
AU  - Yanagihara, I.
TI  - Complete Genome Sequence of Ureaplasma parvum Serovar 3 Strain SV3F4, Isolated in Japan.
JO  - Genome Announcements
PY  - 2014
SP  - e00256
EP  - e00214
VL  - 2
AB  - Here, we present the complete genome sequence of Ureaplasma parvum serovar 3, clinical strain
AB  - SV3F4, isolated from a Japanese patient with a history of an
AB  - infectious abortion.
ER  -

TY  - JOUR
AU  - Wu, H.N.
AU  - Nakura, Y.
AU  - Yoshimura, M.
AU  - Gaddi-Tantengco, O.A.
AU  - Nomiyama, M.
AU  - Takayanagi, T.
AU  - Fujita, T.
AU  - Yasukawa, K.
AU  - Yanagihara, I.
TI  - Type II restriction modification system in Ureaplasma parvum OMC-P162 strain.
JO  - PLoS ONE
PY  - 2018
SP  - e0205328
EP  - e0205328
VL  - 13
AB  - Ureaplasma parvum serovar 3 strain, OMC-P162, was isolated from the human
AB  - placenta of a preterm delivery at 26 weeks' gestation. In this study, we
AB  - sequenced the complete genome of OMC-P162 and compared it with other serovar 3
AB  - strains isolated from patients with different clinical conditions. Ten unique
AB  - genes in OMC-P162, five of which encoded for hypothetical proteins, were
AB  - identified. Of these, genes UPV_229 and UPV_230 formed an operon whose open
AB  - reading frames were predicted to code for a DNA methyltransferase and a
AB  - hypothetical protein, respectively. DNA modification analysis of the OMC-P162
AB  - genome identified N4-methylcytosine (m4C) and N6-methyladenine (m6A), but not
AB  - 5-methylocytosine (m5C). UPV230 recombinant protein displayed endonuclease
AB  - activity and recognized the CATG sequence, resulting in a blunt cut between A and
AB  - T. This restriction enzyme activity was identical to that of the cultivated
AB  - OMC-P162 strain, suggesting that this restriction enzyme was naturally expressed
AB  - in OMC-P162. We designated this enzyme as UpaP162. Treatment of pT7Blue plasmid
AB  - with recombinant protein UPV229 completely blocked UpaP162 restriction enzyme
AB  - activity. These results suggest that the UPV_229 and UPV_230 genes act as a type
AB  - II restriction-modification system in Ureaplasma OMC-P162.
ER  -

TY  - JOUR
AU  - Wu, J.
AU  - Herman, J.G.
AU  - Wilson, G.
AU  - Lee, R.Y.
AU  - Yen, R.-W.C.
AU  - Mabry, M.
AU  - de Bustros, A.
AU  - Nelkin, B.D.
AU  - Baylin, S.B.
TI  - Expression of prokaryotic HhaI DNA methyltransferase is transforming and lethal to NIH 3T3 cells.
JO  - Cancer Res.
PY  - 1996
SP  - 616
EP  - 622
VL  - 56
AB  - In neoplastic cells, levels of DNA methyltransferase activity are often increased, and
AB  - evidence is accruing to suggest an important role for this event in tumorigenesis.  To
AB  - evaluate this possibility further, and to investigate the contribution of increasing de novo,
AB  - as opposed to maintenance, DNA methylation in mammalian cells, we expressed the bacterial HhaI
AB  - methyltransferase in cultured murine fibroblasts.  This enzyme is a pure de novo DNA
AB  - methytransferase that methylates the internal C in the sequence GCGC.  We find that both
AB  - constitutive and induced expression of the wild-type HhaI results, primarily, in lethality to
AB  - the cells.  However, surviving cell clones that express low levels of M.HhaI demonstrate
AB  - increased tumorigenicity as assessed by soft agar cloning efficiency (8.6% for sense
AB  - HhaI-transduced PA 317 cells versus 0.4% for antisense controls; 1.7% for sense
AB  - HhaI-transfected NIH 3T3 cells versus 0% for a mutant HhaI control) and tumorigenicity in nude
AB  - mouse heterotransplants (75% for sense HhaI-transduced PA 317 cells versus 18.5% for antisense
AB  - controls).  DNA isolated from the clonogenic sense HhaI clones, versus clones expressing the
AB  - mutant HhaI gene, has no increase in overall CpG methylation but an average of 27% (range,
AB  - 16.7-38.9) increase in methylcytosine content at GCGC sites.  These findings suggest that
AB  - eukaryotic cells tolerate a narrow window of increased de novo DNA methylating capacity, above
AB  - which cell death occurs and within which cell transformation results.  Our results further
AB  - emphasize the potential role of increased DNA methyltransferase activity in the evolution of
AB  - cancer.
ER  -

TY  - JOUR
AU  - Wu, J.
AU  - Issa, J.P.
AU  - Herman, J.
AU  - Bassett, D.E.
AU  - Nelkin, B.D.
AU  - Baylin, S.B.
TI  - Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1993
SP  - 8891
EP  - 8895
VL  - 90
AB  - Abnormal regional increases in DNA methylation, which have potential for causing gene
AB  - inactivation and chromosomal instability, are consistently found in immortalized and
AB  - tumorigenic cells. Increased DNA methyltransferase activity, which is also a characteristic of
AB  - such cells, is a candidate to mediate these abnormal DNA methylation patterns. We now show
AB  - that in NIH 3T3 mouse fibroblasts constitutive overexpression of an exogenous mouse DNA
AB  - methyltransferase gene results in a marked increase in overall DNA methylation which is
AB  - accompanied by tumorigenic transformation. These transformation changes can also be elicited
AB  - by dexamethasone-inducible expression of an exogenous DNA methyltransferase gene. Our findings
AB  - provide strong evidence that the increase in DNA methyltransferase activity associated with
AB  - tumor progression could be a key step in carcinogenesis and provide a model system that can be
AB  - used to further study this possibility.
ER  -

TY  - JOUR
AU  - Wu, J.C.
AU  - Santi, D.V.
TI  - Kinetic and catalytic mechanism of HhaI methyltransferase.
JO  - J. Biol. Chem.
PY  - 1987
SP  - 4778
EP  - 4786
VL  - 262
AB  - Kinetic and catalytic properties of the DNA (cytosine-5)-methyltransferase HhaI
AB  - are described.  With poly(dG-dC) as substrate, the reaction proceeds by an
AB  - equilibrium (or processive) ordered Bi-Bi mechanism in which DNA binds to the
AB  - enzyme first, followed by S-adenosylmethionine (AdoMet).  After methyl
AB  - transfer, S-adenosylhomocysteine (AdoHcy) dissociates followed by methylated
AB  - DNA.  AdoHcy is a potent competitive inhibitor with respect to AdoMet (K=2.0
AB  - microM) and its generation during reactions results in non-linear kinetics.
AB  - AdoMet and AdoHcy significantly interact with only the substrate enzyme-DNA
AB  - complex; they do not bind to free enzyme and bind poorly to the methylated
AB  - enzyme-DNA complex.  In the absence of AdoMet, HhaI methylase catalyzes
AB  - exchange of the 5-H of substrate cytosines for protons of water at about 7-fold
AB  - the rate of methylation.  The 5-H exchange reaction is inhibited by AdoMet or
AB  - AdoHcy.  In the enzyme-DNA-AdoHcy complex, AdoHcy also suppresses dissociation
AB  - of DNA and reassociation of the enzyme with other substrate sequences.  Our
AB  - studies reveal that the catalytic mechanism of DNA
AB  - (cytosine-5)-methyl-transferases involves attack of the C6 of substrate
AB  - cytosines by an enzyme nucleophile and formation of a transient covalent
AB  - adduct.  Based on precedents of other enzymes which catalyze similar reactions
AB  - and the susceptibilitiy of HhaI to inactivation by N-ethylmaleimide, we propose
AB  - that the sulfhydryl group of a cysteine residue is the nucleophilic catalyst.
AB  - Furthermore, we propose that Cys-81 is the active-site catalyst in HhaI.  This
AB  - residue is found in a Pro-Cys doublet which is conserved in all DNA
AB  - (cytosine-5)-methyltransferases whose sequences have been determined to date
AB  - and is found in related enzymes.  Finally, we discuss the possibility that
AB  - covalent adducts between C6 of pyrimidines and nucleophiles of proteins may be
AB  - important general components of protein-nucleic acid interactions.
ER  -

TY  - JOUR
AU  - Wu, J.C.
AU  - Santi, D.V.
TI  - High level expression and purification of HhaI methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 703
EP  - 717
VL  - 16
AB  - A cloning system for the DNA- (cytosine-5) -methyltransferase MHhaI and high
AB  - level expression of the enzyme are described.  A parent plasmid was constructed
AB  - from fragments of the MHhaI gene and synthetic oligonucleotides.  The construct
AB  - permits introduction of various restriction sites for cloning at precise
AB  - positions near the initiation codon, and beyond the termination codon.  The
AB  - entire MHhaI coding sequence was introduced as a 1042 b.p. NdeI-XbaI fragment
AB  - into the vector pAR3040 which contains the T7 RNA polymerase promoter.  The
AB  - resultant plasmid pTNX3 (MHhaI-pAR3040) was introduced into McrB- E. coli
AB  - strains HB101 and GM2929, and expression of MHhaI was induced by infection with
AB  - the lambda phage CE6 carrying the T7 RNA polymerase gene.  In induced cells,
AB  - catalytically active MHhaI was produced at a level that corresponds to about 8%
AB  - of the total soluble protein; an insoluble form of the protein was also formed,
AB  - but could be readily removed.  The expressed soluble enzyme from HB101/pTNX3
AB  - was purified to apparent homogeneity in about 50% yield by a two-step
AB  - chromatographic procedure involving DEAE-cellulose and Heparin-Sepharose; a one
AB  - liter culture gave about 2.5 mg of pure enzyme.  The molecular weight and
AB  - kinetic properties of the expressed protein are identical to those reported for
AB  - the authentic MHhaI, and its amino terminal sequence agrees with that predicted
AB  - from the DNA sequence.
ER  -

TY  - JOUR
AU  - Wu, J.C.
AU  - Santi, D.V.
TI  - On the mechanism and inhibition of DNA cytosine methyltransferases.
JO  - Biochemistry and Biology of DNA Methylation
PY  - 1985
SP  - 119
EP  - 129
VL  - 0
AB  - Enzyme catalyzed methylation of the 5-position of pyrimidine nucleotides occurs in a number of
AB  - branches of nucleic acid biochemistry. Examples of this reaction include the formation of
AB  - thymidine 5'-monophosphate (TMP) from deoxyuridine 5'-monophosphate (dUMP) by thymidylate
AB  - synthetase (TS), post-transcriptional methylation of RNA molecules, and the methylation of DNA
AB  - cytosine residues by methyltransferases (DCMTases) found in eukaryotic cells and in bacteria.
AB  - While thymidylate synthetase uses 5,10-methylenetetrahydrofolate as the methyl group donor,
AB  - most of the other enzymes require S-adenosylmethionine (AdoMet) for their methyltransferase
AB  - activity.
ER  -

TY  - JOUR
AU  - Wu, J.J.
AU  - de Jager, V.C.
AU  - Deng, W.L.
AU  - Leveau, J.H.
TI  - Finished Genome Sequence of Collimonas arenae Cal35.
JO  - Genome Announcements
PY  - 2015
SP  - e01408
EP  - e01414
VL  - 3
AB  - We announce the finished genome sequence of soil forest isolate Collimonas arenae Cal35, which
AB  - comprises a 5.6-Mbp chromosome and 41-kb plasmid. The Cal35 genome
AB  - is the second one published for the bacterial genus Collimonas and represents the
AB  - first opportunity for high-resolution comparison of genome content and synteny
AB  - among collimonads.
ER  -

TY  - JOUR
AU  - Wu, J.J.
AU  - Issa, J.P.
AU  - Herman, J.
AU  - Nelkin, B.D.
AU  - Baylin, S.B.
TI  - Expression of an exogenous eukaryotic DNA methyltransferase gene induces transformation of NIH 3T3 cells.
JO  - Amer. Soc. Hum. Gen.
PY  - 1992
SP  - A74
EP  - A74
VL  - 4
ER  -

TY  - JOUR
AU  - Wu, K.-Y.
AU  - Liu, G.-R.
AU  - Liu, W.-Q.
AU  - Wang, A.Q.
AU  - Zhan, S.
AU  - Sanderson, K.E.
AU  - Johnston, R.N.
AU  - Liu, S.-L.
TI  - The genome of Salmonella enterica serovar gallinarum: Distinct insertions/deletions and rare rearrangements.
JO  - J. Bacteriol.
PY  - 2005
SP  - 4720
EP  - 4727
VL  - 187
AB  - Salmonella enterica serovar Gallinarum is a fowl-adapted pathogen, causing typhoid fever in
AB  - chickens. It has the same antigenic formula (1,9,12:-:-) as S. enterica serovar Pullorum,
AB  - which is also adapted to fowl but causes pullorum disease (diarrhea). The close relatedness
AB  - but distinct pathogeneses make this pair of fowl pathogens good models for studies of
AB  - bacterial genomic evolution and the way these organisms acquired pathogenicity. To locate and
AB  - characterize the genomic differences between serovar Gallinarum and other salmonellae, we
AB  - constructed a physical map of serovar Gallinarum strain SARB21 by using I-CeuI, XbaI, and
AB  - AvrII with pulsed-field gel electrophoresis techniques. In the 4,740-kb genome, we located two
AB  - insertions and six deletions relative to the genome of S. enterica serovar Typhimurium LT2,
AB  - which we used as a reference Salmonella genome. Four of the genomic regions with reduced
AB  - lengths corresponded to the four prophages in the genome of serovar Typhimurium LT2, and the
AB  - others contained several smaller deletions relative to serovar Typhimurium LT2, including
AB  - regions containing srfJ, std, and stj and gene clusters encoding a type I restriction system
AB  - in serovar Typhimurium LT2. The map also revealed some rare rearrangements, including two
AB  - inversions and several translocations. Further characterization of these insertions,
AB  - deletions, and rearrangements will provide new insights into the molecular basis for the
AB  - specific host-pathogen interactions and mechanisms of genomic evolution to create a new
AB  - pathogen.
ER  -

TY  - JOUR
AU  - Wu, K.M.
AU  - Li, L.H.
AU  - Yan, J.J.
AU  - Tsao, N.
AU  - Liao, T.L.
AU  - Tsai, H.C.
AU  - Fung, C.P.
AU  - Chen, H.J.
AU  - Liu, Y.M.
AU  - Wang, J.T.
AU  - Fang, C.T.
AU  - Chang, S.C.
AU  - Shu, H.Y.
AU  - Liu, T.T.
AU  - Chen, Y.T.
AU  - Shiau, Y.R.
AU  - Lauderdale, T.L.
AU  - Su, I.J.
AU  - Kirby, R.
AU  - Tsai, S.F.
TI  - Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis.
JO  - J. Bacteriol.
PY  - 2009
SP  - 4492
EP  - 4501
VL  - 191
AB  - Nosocomial infections caused by antibiotic-resistant Klebsiella pneumoniae are emerging as a
AB  - major health problem worldwide, while community-acquired
AB  - K. pneumoniae infections present with a range of diverse clinical pictures
AB  - in different geographic areas. In particular, an invasive form of K.
AB  - pneumoniae that causes liver abscesses was first observed in Asia and then
AB  - was found worldwide. We are interested in how differences in gene content
AB  - of the same species result in different diseases. Thus, we sequenced the
AB  - whole genome of K. pneumoniae NTUH-K2044, which was isolated from a
AB  - patient with liver abscess and meningitis, and analyzed differences
AB  - compared to strain MGH 78578, which was isolated from a patient with
AB  - pneumonia. Six major types of differences were found in gene clusters that
AB  - included an integrative and conjugative element, clusters involved in
AB  - citrate fermentation, lipopolysaccharide synthesis, and capsular
AB  - polysaccharide synthesis, phage-related insertions, and a cluster
AB  - containing fimbria-related genes. We also conducted comparative genomic
AB  - hybridization with 15 K. pneumoniae isolates obtained from
AB  - community-acquired or nosocomial infections using tiling probes for the
AB  - NTUH-K2044 genome. Hierarchical clustering revealed three major groups of
AB  - genomic insertion-deletion patterns that correlate with the strains'
AB  - clinical features, antimicrobial susceptibilities, and virulence
AB  - phenotypes with mice. Here we report the whole-genome sequence of K.
AB  - pneumoniae NTUH-K2044 and describe evidence showing significant genomic
AB  - diversity and sequence acquisition among K. pneumoniae pathogenic strains.
AB  - Our findings support the hypothesis that these factors are responsible for
AB  - the changes that have occurred in the disease profile over time.
ER  -

TY  - JOUR
AU  - Wu, M. et al.
TI  - Phylogenomics of the reproductive parasite Wolbachia pipientis wMeI: A streamlined genome overrun by mobile genetic elements.
JO  - PLoS Biology
PY  - 2004
SP  - 327
EP  - 341
VL  - 2
AB  - The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate
AB  - intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are
AB  - found in a variety of invertebrate species, are of great interest due to their diverse
AB  - interactions with different hosts, which range from many forms of reproductive parasitism to
AB  - mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons
AB  - with other intracellular bacteria, has revealed many insights into the biology and evolution
AB  - of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced
AB  - obligate intracellular species in both being highly streamlined and containing very high
AB  - levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple
AB  - evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel,
AB  - most likely owing to the occurrence of repeated population bottlenecks. Genome analysis
AB  - predicts many metabolic differences with the closely related Rickettsia species, including the
AB  - presence of intact glycolysis and purine synthesis, which may compensate for an inability to
AB  - obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent
AB  - inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding
AB  - proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the
AB  - ability of wMel to infect the germline of its host, we find no evidence for either recent
AB  - lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia
AB  - and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a
AB  - common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of
AB  - mitochondria with species in the order Rickettsiales. With the availability of the complete
AB  - genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster
AB  - symbiosis is now an ideal system for studying the biology and evolution of Wolbachia
AB  - infections.
ER  -

TY  - JOUR
AU  - Wu, M.
AU  - McNulty, N.P.
AU  - Rodionov, D.A.
AU  - Khoroshkin, M.S.
AU  - Griffin, N.W.
AU  - Cheng, J.
AU  - Latreille, P.
AU  - Kerstetter, R.A.
AU  - Terrapon, N.
AU  - Henrissat, B.
AU  - Osterman, A.L.
AU  - Gordon, J.I.
TI  - Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.
JO  - Science
PY  - 2015
SP  - AAC5992
EP  - AAC5992
VL  - 350
AB  - Libraries of tens of thousands of transposon mutants generated from each of four
AB  - human gut Bacteroides strains, two representing the same species, were introduced
AB  - simultaneously into gnotobiotic mice together with 11 other wild-type strains to
AB  - generate a 15-member artificial human gut microbiota. Mice received one of two
AB  - distinct diets monotonously, or both in different ordered sequences. Quantifying
AB  - the abundance of mutants in different diet contexts allowed gene-level
AB  - characterization of fitness determinants, niche, stability, and resilience and
AB  - yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the
AB  - community. The approach described is generalizable and should be useful for
AB  - defining mechanisms critical for sustaining and/or approaches for deliberately
AB  - reconfiguring the highly adaptive and durable relationship between the human gut
AB  - microbiota and host in ways that promote wellness.
ER  -

TY  - JOUR
AU  - Wu, P.
AU  - Qiu, C.
AU  - Sohail, A.
AU  - Zhang, X.
AU  - Bhagwat, A.S.
AU  - Cheng, X.
TI  - Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
JO  - J. Biol. Chem.
PY  - 2003
SP  - 5285
EP  - 5291
VL  - 278
AB  - MBD4 is a member of the methyl-CpG-binding protein family. It contains two DNA binding
AB  - domains, an amino-proximal methyl-CpG binding domain (MBD) and
AB  - a C-terminal mismatch-specific glycosylase domain. Limited in vitro
AB  - proteolysis of mouse MBD4 yields two stable fragments: a 139-residue
AB  - fragment including the MBD, and the other 155-residue fragment including
AB  - the glycosylase domain. Here we show that the latter fragment is active as
AB  - a glycosylase on a DNA duplex containing a G:T mismatch within a CpG
AB  - sequence context. The crystal structure confirmed the C-terminal domain is
AB  - a member of the helix-hairpin-helix DNA glycosylase superfamily. The MBD4
AB  - active site is situated in a cleft that likely orients and binds DNA.
AB  - Modeling studies suggest the mismatched target nucleotide will be flipped
AB  - out into the active site where candidate residues for catalysis and
AB  - substrate specificity are present.
ER  -

TY  - JOUR
AU  - Wu, Q.
AU  - Liu, Z.
AU  - Li, Y.
AU  - Guan, G.
AU  - Niu, Q.
AU  - Chen, Z.
AU  - Luo, J.
AU  - Yin, H.
TI  - Genome Sequence of Borrelia garinii Strain SZ, Isolated in China.
JO  - Genome Announcements
PY  - 2014
SP  - e00010
EP  - e00014
VL  - 2
AB  - We announce the genome sequence of Borrelia garinii strain SZ, isolated from Dermacentor ticks
AB  - collected in northeastern China. B. garinii strain SZ carries
AB  - numerous plasmids, both 10 circular and 9 linear plasmids. The 902,487-bp linear
AB  - chromosome (28.2% GC content) contains 820 open reading frames, 33 tRNAs, and 4
AB  - complete rRNAs. The plasmid cp32-10 contains one clustered regularly interspaced
AB  - short palindromic repeat (CRISPR) with four repeats.
ER  -

TY  - JOUR
AU  - Wu, Q.
AU  - Peng, S.
AU  - Yu, Y.
AU  - Li, Y.
AU  - Xu, Y.
TI  - Genome Sequence of Bacillus licheniformis CGMCC3963, a Stress-Resistant Strain Isolated in a Chinese Traditional Solid-State Liquor-Making Process.
JO  - Genome Announcements
PY  - 2013
SP  - e00060
EP  - e00012
VL  - 1
AB  - Bacillus licheniformis CGMCC3963 is an important mao-tai flavor-producing strain. It was
AB  - isolated from the starter (Daqu) of a Chinese mao-tai-flavor liquor
AB  - fermentation process with solid-state fermentation. We report its genome of
AB  - 4,525,096 bp here. Many potential insertion genes that are responsible for the
AB  - unique properties of B. licheniformis CGMCC3963 in mao-tai-flavor liquor
AB  - production were identified.
ER  -

TY  - JOUR
AU  - Wu, Q.
AU  - Tun, H.M.
AU  - Leung, F.C.C.
AU  - Shah, N.P.
TI  - Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275.
JO  - Sci. Rep.
PY  - 2014
SP  - 4974
EP  - 4974
VL  - 4
ER  -

TY  - JOUR
AU  - Wu, Q.
AU  - Zhu, L.
AU  - Jiang, L.
AU  - Xu, X.
AU  - Xu, Q.
AU  - Zhang, Z.
AU  - Huang, H.
TI  - Genome Sequence of Paenibacillus wulumuqiensis sp. nov., a Bioflocculant-Producing Species.
JO  - Genome Announcements
PY  - 2015
SP  - e00795
EP  - e00715
VL  - 3
AB  - Paenibacillus wulumuqiensis sp. nov. is a novel strain that can produce bioflocculants. Here,
AB  - we report 5.37-Mb assembly of its genome sequence and other
AB  - useful information, including the coding sequences (CDSs) responsible for the
AB  - biosynthesis of polysaccharide-based bioflocculants, cold-shock protein, and
AB  - vitamin production.
ER  -

TY  - JOUR
AU  - Wu, R.
AU  - King, C.T.
AU  - Jay, E.
TI  - A new sequence-specific endonuclease from Streptococcus faecalis subsp. zymogenes.
JO  - Gene
PY  - 1978
SP  - 329
EP  - 336
VL  - 4
AB  - A new sequence-specific endonuclease, SfaI, has been partially purified from
AB  - Streptococcus faecalis subsp. zymogenes.  SfaI recognizes the tetranucleotide
AB  - sequence.
ER  -

TY  - JOUR
AU  - Wu, R.S.
AU  - Hurst-Calderone, S.
AU  - Kohn, K.W.
TI  - Measurement of O6-alkylguanine-DNA alkyltransferase activity in human cells and tumor tissues by restriction endonuclease inhibition.
JO  - Cancer Res.
PY  - 1987
SP  - 6229
EP  - 6235
VL  - 47
AB  - A sensitive assay for O6-alkylguanine-DNA alkyltransferase activity in cell or
AB  - tumor extracts has been devised.  The theoretical basis of the new assay lies
AB  - in the observation that certain restriction enzymes will not cleave DNA
AB  - containing methylated bases.  Thus, if a synthetic oligodeoxynucleotide with a
AB  - restriction sequence containing O6-methylguanine wee incubated with the
AB  - restriction enzyme, this synthetic oligodeoxynucleotide should remain intact.
AB  - However, if the guanine-O6 methyl group were first removed by
AB  - O6-alkylguanine-DNA alkyltransferase present in certain cell or tissue extracts
AB  - the synthetic oligodeoxynucleotide would be cleaved by the restriction enzyme.
AB  - The parental oligodeoxynucleotide and its restriction products are separated
AB  - from each other and analyzed on denaturing polyacrylamide gels.  The extent of
AB  - cleavage by the restriction enzyme is a direct assay of the content of
AB  - O6-alkylguanine-DNA alkyltransferase in the cell/tumor extracts.  The assay has
AB  - been tested against cell culture and xenograft tumor systems and has performed
AB  - in a predictive manner, correctly predicting five Mer- and three Mer+
AB  - phenotypes.  Furthermore, the assay is quantitative and the number of molecules
AB  - of the O6-alkylguanine-DNA alkyltransferase per cell estimated using this assay
AB  - agrees with those that have been published.
ER  -

TY  - JOUR
AU  - Wu, S.Y.
AU  - Lee, K.F.
AU  - Kam, K.M.
AU  - Shaw, P.C.
TI  - Restriction enzyme BliHKI from a thermophilic Bacillus licheniformis strain.
JO  - Biosci. Biotechnol. Biochem.
PY  - 1993
SP  - 1193
EP  - 1194
VL  - 57
AB  - Thermophilic Bacillus is a rich source of restriction enzymes. Using a screening method
AB  - described in ref. 1, we have isolated a thermophilic Bacillus licheniformis strain HK which
AB  - grows at 55 degrees C in L broth and contains a type II restriction enzyme, BliHKI.
ER  -

TY  - JOUR
AU  - Wu, T.-H.
AU  - Grelland, E.
AU  - Boye, E.
AU  - Marinus, M.G.
TI  - Identification of a weak promoter for the dam gene of Escherichia coli.
JO  - Biochim. Biophys. Acta
PY  - 1992
SP  - 47
EP  - 52
VL  - 1131
AB  - We have used a combination of techniques to identify a weak promoter located about 70
AB  - nucleotides before the start site of translation of the Escherichia coli dam gene which
AB  - encodes a DNA methyltransferase.  The promoter activity was identified by the use of lacZ
AB  - fusions to fragments containing different lengths of upstream DNA.  In vitro run-off
AB  - transcription and primer extension determinations revealed transcription initiation sites at
AB  - either 69 or 73 nucleotides prior to the ARG of the dam coding sequence.  No ribosome binding
AB  - sequence was present close to the ATG codon suggesting that the transcript may be
AB  - inefficiently translated.
ER  -

TY  - JOUR
AU  - Wu, T.T.
TI  - Locus determining P1 phage restriction in Escherichia coli.
JO  - J. Bacteriol.
PY  - 1969
SP  - 314
EP  - 314
VL  - 98
AB  - The locus determing P1 phage restriction has been mapped at 89.3 min on the
AB  - Escherichia coli map, about 0.2 min away from the hsp marker.
ER  -

TY  - JOUR
AU  - Wu, T.T.
AU  - Matsuda, A.
AU  - Cavalieri, L.F.
TI  - The restriction and modification enzymes of Escherichia coli.
JO  - Fed. Proc.
PY  - 1969
SP  - 465
EP  - 465
VL  - 28
AB  - An E. coli endonuclease (MW ca. 78,000) which acts specifically on unmodified
AB  - lambda-DNA has been purified.  The endonuclease fraction, together with
AB  - S-adenosylmethionine (SAM) and another protein fraction, is required for the
AB  - methylation of DNA.  SAM can be eliminated from the methylation reaction, if it
AB  - is first allowed to react with the endonuclease fraction, forming a
AB  - methyl-donating complex.  The same enzyme fraction from a restrictionless
AB  - mutant has no endonucleaese activity but retains the property of reacting with
AB  - SAM.  The formation of this methyl-donating complex is partially inhibited by a
AB  - protein present only in modificationless mutants of E. coli.  This protein (MW
AB  - da. 52,000) has also been purified.  Recombinants having mostly E. coli B
AB  - chromosomes except for small segments which contain the restriction and
AB  - modification markers from E. coli K12 have been selected.  The DNA of these
AB  - recombinants contains both methylcytosine and methyladenine, whereas E. coli
AB  - and DNA contains only the later.
ER  -

TY  - JOUR
AU  - Wu, W.
AU  - Wood, D.W.
AU  - Belfort, G.
AU  - Derbyshire, V.
AU  - Belfort, M.
TI  - Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 4864
EP  - 4871
VL  - 30
AB  - An intein-mediated approach was developed for expression and affinity purification of a
AB  - protein that is lethal to Escherichia coli. The protein, I-TevI, is an intron-encoded
AB  - endonuclease. The approach involved the insertional inactivation of I-TevI with a controllable
AB  - mini-intein placed in front of a cysteine required for splicing (an I-TevI::intein fusion).
AB  - The purification was facilitated by a chitin-binding domain inserted into the mini-intein.
AB  - Affinity purification of the I-TevI::intein fusion precursor on a chitin column was followed
AB  - by pH-controllable splicing to restore the structure and function of I-TevI. To study the
AB  - impact of the insertion context on I-TevI inactivation, the chimeric intein was inserted
AB  - independently in front of seven cysteines of I-TevI. One of the seven intein integrants
AB  - yielded I-TevI of high activity. This technique is, in principle, generalizable to the
AB  - expression and purification of other cytotoxic proteins and is amenable to scale-up.
ER  -

TY  - JOUR
AU  - Wu, W.
AU  - Zheng, H.
AU  - Zhang, L.
AU  - Wen, Z.
AU  - Zhang, S.
AU  - Pei, H.
AU  - Yu, G.
AU  - Zhu, Y.
AU  - Cui, Z.
AU  - Hu, Z.
AU  - Wang, H.
AU  - Li, Y.
TI  - A genome-wide analysis of multidrug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis Beijing genotype.
JO  - Mol. Genet. Genomics
PY  - 2013
SP  - 425
EP  - 436
VL  - 288
AB  - The Beijing genotype of Mycobacterium tuberculosis (MTB) is one of the most successful MTB
AB  - lineages that has disseminated in the world. In China, the rate of
AB  - multidrug-resistant (MDR) tuberculosis is significantly higher than the global
AB  - average rate, and the Beijing genotype strains take the largest share of MDR
AB  - strains. To study the genetic basis of the epidemiological findings that Beijing
AB  - genotype has often been associated with tuberculosis outbreaks and drug
AB  - resistance, we determined the genome sequences of four clinical isolates: two
AB  - extensively drug resistant (XDR1219, XDR1221) and two multidrug resistant (WX1,
AB  - WX3), using whole-genome sequencing. A large number of individual and shared SNPs
AB  - of the four Beijing strains were identified. Our isolates harbored almost all
AB  - classic drug resistance-associated mutations. The mutations responsible for drug
AB  - resistance in the two XDR strains were consistent with the clinical quantitative
AB  - drug resistance levels. COG analysis revealed that Beijing strains have
AB  - significantly higher abundances of the mutations responsible for cell
AB  - wall/membrane/envelope biogenesis (COG M), secondary metabolites biosynthesis,
AB  - transport and catabolism (COG Q), lipid transport and metabolism (COG I) and
AB  - defense mechanisms (COG V). The shared mutated genes of the four studied Beijing
AB  - strains were significantly overrepresented in three DNA repair pathways. Our
AB  - analyses promote the understanding of the genome polymorphism of the Beijing
AB  - family strains and provide the molecular genetic basis for their wide
AB  - dissemination capacity and drug resistance.
ER  -

TY  - JOUR
AU  - Wu, X.
AU  - Deutschbauer, A.M.
AU  - Kazakov, A.E.
AU  - Wetmore, K.M.
AU  - Cwick, B.A.
AU  - Walker, R.M.
AU  - Novichkov, P.S.
AU  - Arkin, A.P.
AU  - Chakraborty, R.
TI  - Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.
JO  - Genome Announcements
PY  - 2017
SP  - e00582
EP  - e00517
VL  - 5
AB  - We present here the draft genome sequences of two Janthinobacterium lividum strains, GW456P
AB  - and GW458P, isolated from groundwater samples collected from a
AB  - background site at the Oak Ridge Field Research Center. Production of a purple
AB  - pigment by these two strains was observed when grown on diluted (1/10) LB agar
AB  - plates.
ER  -

TY  - JOUR
AU  - Wu, X.
AU  - Zhao, C.
AU  - Guo, Z.
AU  - Hao, Y.
AU  - Li, J.
AU  - Shi, H.
AU  - Sun, Y.
TI  - Genome Sequence of Lactobacillus johnsonii Strain W1, Isolated from Mice.
JO  - Genome Announcements
PY  - 2016
SP  - e00561
EP  - e00516
VL  - 4
AB  - Lactobacillus johnsonii, a member of the gut lactobacilli, plays an important role in normal
AB  - gut functioning. Here, we report the draft genome sequence of L.
AB  - johnsonii strain W1 isolated from ICR mice.
ER  -

TY  - JOUR
AU  - Wu, Y.
AU  - Fu, Y.
AU  - Yuan, Y.
AU  - Gao, M.
TI  - Complete Genome Sequence of Bacillus thuringiensis subsp. jinghongiensis Reference Strain YGd22-03.
JO  - Genome Announcements
PY  - 2017
SP  - e00740
EP  - e00717
VL  - 5
AB  - Bacillus thuringiensis is widely used in producing ecofriendly microbial agents for the
AB  - purpose of controlling insect pests. In this study, we determined the
AB  - complete genome sequence of B. thuringiensis subsp. jinghongiensis reference
AB  - strain YGd22-03, which contains three cry genes and one cerecidin biosynthetic
AB  - gene cluster.
ER  -

TY  - JOUR
AU  - Wu, Y.
AU  - Wang, Y.
AU  - Li, J.
AU  - Hu, J.
AU  - Chen, K.
AU  - Wei, Y.
AU  - Bazhanov, D.P.
AU  - Bazhanova, A.A.
AU  - Yang, H.
TI  - Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode.
JO  - Genome Announcements
PY  - 2015
SP  - e00015
EP  - e00015
VL  - 3
AB  - Stenotrophomonas maltophilia strain B418 was isolated from a barley rhizosphere in China. This
AB  - bacterium exhibits broad-spectrum inhibitory activities against plant pathogens and root-knot
AB  - nematode along with growth-promoting effects. Here, we present the draft genome sequence of S.
AB  - maltophilia B418.
ER  -

TY  - JOUR
AU  - Wu, Y.
AU  - Zheng, J.
AU  - Wang, Y.
AU  - Li, S.
AU  - Jin, H.
AU  - Li, Z.
AU  - Bi, D.
AU  - Sun, M.
AU  - Liu, M.
TI  - Draft Genome Sequence of Listeria monocytogenes LM201, Isolated from Foodstuff.
JO  - Genome Announcements
PY  - 2015
SP  - e01417
EP  - e01414
VL  - 3
AB  - Listeria monocytogenes is a facultative intracellular foodborne pathogen that can cause
AB  - listeriosis in humans and animals. L. monocytogenes LM201 was isolated from
AB  - foodstuff. The draft genome sequence of strain LM201 provides the genetic basis
AB  - for the application of this strain in biotechnological vaccine production.
ER  -

TY  - JOUR
AU  - Wu, Y.F.
AU  - Zhang, B.
AU  - Xing, P.
AU  - Wu, Q.L.
AU  - Liu, S.J.
TI  - Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2015
SP  - 2194
EP  - 2198
VL  - 65
AB  - Bacterial strain THMBR28(T) was isolated from decomposing algal scum that was
AB  - collected during an algal bloom in Taihu lake, China. Cells of strain THMBR28(T)
AB  - were Gram-staining-positive, facultatively anaerobic and rod-shaped. Growth was
AB  - observed at 20-45 degrees C (optimum, 30 degrees C), at pH 5.0-9.5 (optimum, pH
AB  - 6.5-7.5), and in the presence of 0-1.0% (w/v) NaCl (optimum, 0.5%). Strain
AB  - THMBR28(T) contained MK-7 as the major menaquinone and iso-C15 : 0 as the major
AB  - cellular fatty acid. The polar lipid profile contained phosphatidylglycerol,
AB  - phosphatidylmonomethylethanolamine, phosphatidylethanolamine and six unidentified
AB  - polar lipids. The diamino acid found in the cell-wall peptidoglycan was
AB  - meso-diaminopimelic acid. The DNA G+C content was 57.6 mol% (Tm). Phylogenetic
AB  - analysis of 16S rRNA gene sequences showed that strain THMBR28(T) belonged to the
AB  - genus Tumebacillus, most closely related to Tumebacillus ginsengisoli DSM
AB  - 18389(T) (95.0%) and Tumebacillus permanentifrigoris Eur1 9.5(T) (93.4%). Based
AB  - on phylogenetic and phenotypic characterization, it is concluded that strain
AB  - THMBR28(T) represents a novel species of the genus Tumebacillus, for which the
AB  - name Tumebacillus algifaecis sp. nov. is proposed, with THMBR28(T) ( = CGMCC
AB  - 1.10949(T) = NBRC 108765(T)) as the type strain.
ER  -

TY  - JOUR
AU  - Wu, Y.H.
AU  - Cheng, H.
AU  - Huo, Y.Y.
AU  - Xu, L.
AU  - Liu, Q.
AU  - Wang, C.S.
AU  - Xu, X.W.
TI  - Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9(T).
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 88
EP  - 88
VL  - 12
AB  - Croceicoccus marinus E4A9(T)was isolated from deep-sea sediment collected from the East
AB  - Pacific polymetallic nodule area. The strain is able to produce
AB  - esterase, which is widely used in the food, perfume, cosmetic, chemical,
AB  - agricultural and pharmaceutical industries. Here we describe the characteristics
AB  - of strain E4A9, including the genome sequence and annotation, presence of
AB  - esterases, and metabolic pathways of the organism. The genome of strain E4A9(T)
AB  - comprises 4,109,188 bp, with one chromosome (3,001,363 bp) and two large circular
AB  - plasmids (761,621 bp and 346,204 bp, respectively). Complete genome contains 3653
AB  - coding sequences, 48 tRNAs, two operons of 16S-23S-5S rRNA gene and three ncRNAs.
AB  - Strain E4A9(T) encodes 10 genes related to esterase, and three of the esterases
AB  - (E3, E6 and E10) was successfully cloned and expressed in Escherichia coli
AB  - Rosetta in a soluble form, revealing its potential application in
AB  - biotechnological industry. Moreover, the genome provides clues of metabolic
AB  - pathways of strain E4A9(T), reflecting its adaptations to the ambient
AB  - environment. The genome sequence of C. marinus E4A9(T) now provides the
AB  - fundamental information for future studies.
ER  -

TY  - JOUR
AU  - Wu, Y.H.
AU  - Zhou, P.
AU  - Cheng, H.
AU  - Wang, C.S.
AU  - Wu, M.
AU  - Xu, X.W.
TI  - Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment.
JO  - Genome Announcements
PY  - 2015
SP  - e00642
EP  - e00615
VL  - 3
AB  - Microbacterium profundi strain Shh49(T) was isolated from deep-sea sediment from  a
AB  - polymetallic nodule area located in the East Pacific Ocean. Strain Shh49(T)
AB  - contains genes related to the reduction/oxidation of metals. It has potential
AB  - application in the bioremediation of heavy metal-contaminated environments.
ER  -

TY  - JOUR
AU  - Wu, Y.R.
AU  - Li, Y.
AU  - Yang, K.L.
AU  - He, J.
TI  - Draft Genome Sequence of Butanol-Acetone-Producing Clostridium beijerinckii Strain G117.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5470
EP  - 5471
VL  - 194
AB  - A recently discovered wild-type strain, Clostridium beijerinckii G117, is unique  in producing
AB  - butanol and acetone but negligible amounts of ethanol, unlike
AB  - previously identified acetone-butanol-ethanol (ABE)-generating microbes. Here we
AB  - report the draft genome sequence of strain G117 (5,806,675 bp; GC content, 29.7%)
AB  - and the novel findings obtained from its genome annotations.
ER  -

TY  - JOUR
AU  - Wu, Y.R.
AU  - Lin, B.
AU  - Yu, Y.
TI  - Draft Genome Sequence of a Xylanase-Producing Bacterial Strain, Cellvibrio mixtus J3-8.
JO  - Genome Announcements
PY  - 2014
SP  - e01281
EP  - e01214
VL  - 2
AB  - The xylanase-producing bacterial strain Cellvibrio mixtus J3-8 was isolated from  grassland
AB  - giant snails. The draft genome of strain J3-8 comprises 5,171,890 bp in
AB  - 152 contigs with a G+C content of 46.66%. This is the first genome report about
AB  - this bacterial species.
ER  -

TY  - JOUR
AU  - Wu, Y.W.
AU  - Shao, Y.
AU  - Khanipov, K.
AU  - Golovko, G.
AU  - Pimenova, M.
AU  - Fofanov, Y.
AU  - Chu, K.H.
TI  - Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing  Poly(3-Hydroxybutyrate).
JO  - Genome Announcements
PY  - 2017
SP  - e00948
EP  - e00917
VL  - 5
AB  - Zobellella denitrificans ZD1, isolated from sediments of an estuarine mangrove ecosystem in
AB  - Taiwan, exhibits growth-associated production of biopolymer
AB  - poly(3-hydroxybutyrate) (PHB). This work reports the 4.05-Mbp draft genome
AB  - sequence of Z. denitrificans ZD1, consisting of 217 contigs with a G+C content of
AB  - 63.8% and 3,672 protein-coding sequences.
ER  -

TY  - JOUR
AU  - Wu, Z.
AU  - Li, F.
AU  - Liu, D.
AU  - Xue, H.
AU  - Zhao, X.
TI  - Novel Type XII Staphylococcal Cassette Chromosome mec Harboring a New Cassette Chromosome Recombinase, CcrC2.
JO  - Antimicrob. Agents Chemother.
PY  - 2015
SP  - 7597
EP  - 7601
VL  - 59
AB  - Excision and integration of staphylococcal cassette chromosome mec (SCCmec) are
AB  - mediated by cassette chromosome recombinases (Ccr), which play a crucial role in
AB  - the worldwide spread of methicillin resistance in staphylococci. We report a
AB  - novel ccr gene, ccrC2, in the SCCmec of a Staphylococcus aureus isolate, BA01611,
AB  - which showed 62.6% to 69.4% sequence identities to all published ccrC1 sequences.
AB  - A further survey found that the ccrC2 gene was mainly located among
AB  - coagulase-negative staphylococci (CoNS) and could be found in staphylococcal
AB  - isolates from China, the United States, France, and Germany. The ccr gene complex
AB  - harboring the ccrC2 gene was designated a type 9 complex, and the SCCmec of
AB  - BA01611 was considered a novel type and was designated type XII (9C2). This novel
AB  - SCCmec element in BA01611 was flanked by a pseudo-SCC element (PsiSCCBA01611)
AB  - carrying a truncated ccrA1 gene. Both individual SCC elements and a composite SCC
AB  - were excised from the chromosome based on detection of extrachromosomal circular
AB  - intermediates. We advocate inclusion of the ccrC2 gene and type 9 ccr gene
AB  - complex during revision of the SCCmec typing method.
ER  -

TY  - JOUR
AU  - Wu, Z.G.
AU  - Zhang, D.F.
AU  - Liu, Y.L.
AU  - Wang, F.
AU  - Jiang, X.
AU  - Li, C.
AU  - Li, S.P.
AU  - Hong, Q.
AU  - Li, W.J.
TI  - Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system.
JO  - Antonie Van Leeuwenhoek
PY  - 2013
SP  - 123
EP  - 128
VL  - 104
AB  - A bacterial strain, designated J6(T), was isolated from activated sludge,
AB  - collected from a chemical wastewater treatment system in Zhejiang Province of
AB  - China. The cells stained Gram-negative, were aerobic, pale-yellow, and non-motile
AB  - short rods. Phylogenetic analysis of the 16S rRNA gene sequence indicated that
AB  - the closest relative of this organism was Paracoccus aminophilus KACC 12262(T) =
AB  - JCM 7686(T) (97.4 % sequence similarity). Strain J6(T) grew at 10-37 degrees C
AB  - (optimum 30 degrees C), at pH 6.0-8.0 (optimum pH 7.0) and with 0-5 % NaCl
AB  - (optimum 3 %, w/v). The predominant cellular fatty acid found was summed feature
AB  - 8(C18:1 omega7c and/or C18:1 omega6c; 82.8 %). The major respiratory
AB  - quinone-detected was Q-10 and the DNA G+C content was 61.9 mol %. The polar lipid
AB  - profile consisted of phosphatidylethanolamine, phosphatidylglycerol,
AB  - diphosphatidylglycerol, phosphatidylcholine and several unknown polar lipids.
AB  - Strain J6(T) showed low DNA-DNA relatedness values with P. aminophilus KACC
AB  - 12262(T) (28 +/- 3 %). The phylogenetic analysis, DNA-DNA hybridization,
AB  - whole-cell fatty acid composition as well as biochemical characteristics allowed
AB  - clear differentiation of the isolate from the other type strains of already
AB  - described Paracoccus species. It is evident from the genotypic, phenotypic and
AB  - chemotaxonomic analyses that strain J6(T) should be classified as a novel species
AB  - of the genus Paracoccus, for which the name P. zhejiangensis sp. nov. is
AB  - proposed. The type strain is J6(T) (KACC 16703(T) = CCTCC AB 2012031(T)).
ER  -

TY  - JOUR
AU  - Wulff, N.A.
AU  - Zhang, S.
AU  - Setubal, J.
AU  - Almeida, N.F.
AU  - Martins, E.C.
AU  - Harakava, R.
AU  - Kumar, D.
AU  - Rangel, L.T.
AU  - Foissac, X.
AU  - Bove, J.M.
AU  - Gabriel, D.W.
TI  - The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing.
JO  - Mol. Plant Microbe Interact.
PY  - 2014
SP  - 163
EP  - 176
VL  - 27
AB  - Liberibacters form a Rhizobiaceae clade of phloem-limited pathogens of limited host range.
AB  - Two obligately parasitic species have been sequenced: Candidatus Liberibacter asiaticus Las),
AB  - which causes citrus Huanglongbing (HLB) world-wide, and Ca. L. solanacearum (Lso), which
AB  - causes potato "zebra chip" disease. A third species, Liberibacter crescens (Lcr),
AB  - was isolated from mountain papaya, grown in axenic culture and sequenced. In an effort to
AB  - identify common host determinants, the complete genomic DNA sequence of a second HLB species,
AB  - Ca. L. americanus (Lam) strain "Sao Paulo" was determined. The circular genome of 1,195,201 bp
AB  - had an average 31.12% GC content and 983 predicted protein encoding genes, 800 (81.4%) of
AB  - which had a predicted function. There were 658 genes common to all sequenced liberibacters and
AB  - only 8 genes common to Lam and Las but not found in Lso.   Surprisingly, most of the
AB  - lipopolysaccharide biosynthetic genes were missing from the Lam genome, as well OmpA and a key
AB  - regulator of flagellin, all indicating a Lam strategy of avoiding production of major
AB  - pathogen-associated molecular patterns (PAMPs) present in Las and Lso. As with Las, one of two
AB  - Lam prophages replicated as an excision plasmid and carried potential lysogenic conversion
AB  - genes that appeared fragmentary or degenerated in Lso.
ER  -

TY  - JOUR
AU  - Wyczechowska, D.
AU  - Fabianowska-Majewska, K.
TI  - Does 2-chlorodeoxyadenosine contribute to alteration of DNA methyltransferase activity?
JO  - Purine and Pyrimidine Metabolism in Man IX
PY  - 1998
SP  - 595
EP  - 598
AB  - 2-Chlorodeoxyadenosine (2CdA) is a new and effective drug for indolent lymphoid malignancies.
AB  - However, the mechanisms which link 2CdA action and tumor cell death (by apoptosis) are not
AB  - fully clarified.  2CdA is rapidly taken up by the target cells and phosphorylated by cytosolic
AB  - deoxycytidine kinase (dCK).  Its triphosphate is a potent inhibitor of human ribonucleotide
AB  - reductase and a good substrate for human DNA polymerases.  However, phosphorylation of 2CdA is
AB  - clearly not the only event responsible for its cytotoxic effect.  The 2CdA phosphorylation in
AB  - hairy cell leukemia was not higher than in chronic lymphocytic leukemia, despite a better
AB  - response to 2CdA therapy.  Using different cell lines, it was shown that  a wide range of cell
AB  - sensitivity to 2CdA could not be explained by different levels of 2CdA nucleotide.  2CdA was
AB  - also shown to inhibit the growth of myeloid progenitor cell in which the levels of dCK are
AB  - low.  Finally, we have recently shown that in vitro the inhibitory effect of 2CdA results from
AB  - complete suppression of deoxyadenosine phosphorylation by dCK in both human normal lymphocytes
AB  - and in lymphoma cells obtained from patients with a central nervous system involvement.  Also
AB  - an inhibition of adenosine deaminase activity in lysate of both types of cells was observed.
AB  - Moreover, we observed a large decrease in the activity of adenosine deaminase and
AB  - S-adenosylhomocysteine hydrolase, in the erythrocyte lysates of patients, after one week
AB  - treatment with 2CdA6.  We assumed that inhibitory effect of 2CdA on deoxyadenosine metabolism
AB  - could lead to inactivation of SAH-hydrolase with perturbation of methylation reactions.
ER  -

TY  - JOUR
AU  - Wynne, J.W.
AU  - Seemann, T.
AU  - Bulach, D.M.
AU  - Coutts, S.A.
AU  - Talaat, A.M.
AU  - Michalski, W.P.
TI  - Resequencing the Mycobacterium avium subsp. paratuberculosis K10 Genome: Improved Annotation and Revised Genome Sequence.
JO  - J. Bacteriol.
PY  - 2010
SP  - 6319
EP  - 6320
VL  - 192
AB  - We report the resequencing and revised annotation of the Mycobacterium avium subsp.
AB  - paratuberculosis K10 genome. A total of 90 single-nucleotide
AB  - errors and a 51-bp indel in the original K10 genome were corrected, and
AB  - the whole genome annotation was revised. Correction of these sequencing
AB  - errors resulted in 28 frameshift alterations. The amended genome sequence
AB  - is accessible via the supplemental section of study SRR060191 in the NCBI
AB  - Sequence Read Archive and will serve as a valuable reference genome for
AB  - future studies.
ER  -

TY  - JOUR
AU  - Wyres, K.L.
AU  - van Tonder, A.
AU  - Lambertsen, L.M.
AU  - Hakenbeck, R.
AU  - Parkhill, J.
AU  - Bentley, S.D.
AU  - Brueggemann, A.B.
TI  - Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974.
JO  - BMC Genomics
PY  - 2013
SP  - 500
EP  - 500
VL  - 14
AB  - BACKGROUND: Antimicrobial resistance among pneumococci has greatly increased over
AB  - the past two to three decades. Resistance to tetracycline (tet(M)),
AB  - chloramphenicol (cat) and macrolides (erm(B) and/or mef(A/E)) is generally
AB  - conferred by acquisition of specific genes that are associated with mobile
AB  - genetic elements, including those of the Tn916 and Tn5252 families. The first
AB  - tetracycline-, chloramphenicol- and macrolide-resistant pneumococci were detected
AB  - between 1962 and 1970; however, until now the oldest pneumococcus shown to
AB  - harbour Tn916 and/or Tn5252 was isolated in 1974. In this study the genomes of 38
AB  - pneumococci isolated prior to 1974 were probed for the presence of tet(M), cat,
AB  - erm(B), mef(A/E) and int (integrase) to indicate the presence of
AB  - Tn916/Tn5252-like elements. RESULTS: Two Tn916-like, tet(M)-containing, elements
AB  - were identified among pneumococci dated 1967 and 1968. The former element was
AB  - highly similar to that of the PMEN1 multidrug-resistant, globally-distributed
AB  - pneumococcal reference strain, which was isolated in 1984. The latter element was
AB  - associated with a streptococcal phage. A third, novel genetic element, designated
AB  - ICESpPN1, was identified in the genome of an isolate dated 1972. ICESpPN1
AB  - contained a region of similarity to Tn5252, a region of similarity to a
AB  - pneumococcal pathogenicity island and novel lantibiotic
AB  - synthesis/export-associated genes. CONCLUSIONS: These data confirm the existence
AB  - of pneumococcal Tn916 elements in the first decade within which pneumococcal
AB  - tetracycline resistance was described. Furthermore, the discovery of ICESpPN1
AB  - demonstrates the dynamic variability of pneumococcal genetic elements and is
AB  - contrasted with the evidence for Tn916 stability.
ER  -

TY  - JOUR
AU  - Wyszomirski, K.H.
AU  - Curth, U.
AU  - Alves, J.
AU  - Mackeldanz, P.
AU  - Moncke-Buchner, E.
AU  - Schutkowski, M.
AU  - Kruger, D.H.
AU  - Reuter, M.
TI  - Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing  one Res subunit with several DNA-binding regions and ATPase activity.
JO  - Nucleic Acids Res.
PY  - 2012
SP  - 3610
EP  - 3622
VL  - 40
AB  - For efficient DNA cleavage, the Type III restriction endonuclease EcoP15I communicates with
AB  - two inversely oriented recognition sites in an ATP-dependent process. EcoP15I consists of
AB  - methylation (Mod) and restriction (Res) subunits forming a multifunctional enzyme complex able
AB  - to methylate or to cleave DNA. In this study, we determined by different analytical methods
AB  - that EcoP15I contains a single Res subunit in a Mod(2)Res stoichiometry. The Res subunit
AB  - comprises a translocase (Tr) domain carrying functional motifs of superfamily 2 helicases and
AB  - an endonuclease domain with a PD..D/EXK motif. We show that the isolated Tr domain retains
AB  - ATP-hydrolyzing activity and binds single- and double-stranded DNA in a sequence-independent
AB  - manner. To localize the regions of DNA binding, we screened peptide arrays representing the
AB  - entire Res sequence for their ability to interact with DNA. We discovered four DNA-binding
AB  - regions in the Tr domain and two DNA-binding regions in the endonuclease domain. Modelling of
AB  - the Tr domain shows that these multiple DNA-binding regions are located on the surface, free
AB  - to interact with DNA. Interestingly, the positions of the DNA-binding regions are conserved
AB  - among other Type III restriction endonucleases.
ER  -

TY  - JOUR
AU  - Wyszynski, M.W.
TI  - Investigation of the molecular mechanism and mutagenic effect of C5-methyltransferases by mutational analysis.
JO  - Diss. Abstr.
PY  - 1994
SP  - 1426B
EP  - 1427B
VL  - 55
AB  - It has been proposed that a cysteine conserved among all DNA (cytosine-5)-methyltransferases
AB  - initiates catalysis by attacking the C6 of cytosine. I have changed this cysteine to other
AB  - amino acids for the E. coli methylase M.EcoRII; which methylates the second cytosine in the
AB  - sequence 5'-CCWGG-3'. Replacement of the conserved cysteine with glycine, valine, tryptophan
AB  - or serine led to an apparent loss of methyl transferring ability. Unexpectedly, substitution
AB  - of the cysteine with glycine results in the inhibition of cell growth. In DNA binding studies
AB  - I show that mutants with either serine or glycine substitution bind tightly to substrate DNA
AB  - in a manner which resembles the wild-type enzyme. Hence the conserved cysteine is not
AB  - essential for the specific stable binding of the enzyme to its substrate. Further, I show that
AB  - a DNA substrate for M.EcoRII in which the target cytosine is replaced by 5-fluorocytosine is a
AB  - mechanism-based inhibitor of the enzyme. As expected, this modified substrate does not form
AB  - irreversible complexes with the mutants. Sites of cytosine methylation are hot-spots for
AB  - cytosine (C) to thymine (T) mutations in E. coli DNA. To study this phenomenon, I have
AB  - developed a genetic system based on the reversion of a mutation in a kanamycin-resistance gene
AB  - that allows direct selection of C to T mutations at a site of methylation. Using this system I
AB  - show that enzyme-catalyzed deaminations of cytosine do not play a major role in making Dcm
AB  - methylation sites hot-spots for mutations. Further, I have developed a genetic reversion assay
AB  - that quantitates the frequency of C to T mutations at Dcm sites and the reduction of such
AB  - mutations by DNA repair processes. Using this assay, the repair of U:G mismatches in DNA to
AB  - C:G have been studied. The results shown here demonstrate that the E. coli base mismatch
AB  - correction system called VSP repair is capable of correcting U:G mismatches.
ER  -

TY  - JOUR
AU  - Wyszynski, M.W.
AU  - Gabbara, S.
AU  - Bhagwat, A.S.
TI  - Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 319
EP  - 326
VL  - 20
AB  - The proposed mechanism for DNA (cytosine-5)-methyltransferases envisions a key
AB  - role for a cysteine residue.  It is expected to form a covalent link with
AB  - carbon 6 of the target cytosine, activating the normally inactive carbon 5 for
AB  - methyl transfer.  There is a single conserved cysteine among all DNA
AB  - (cytosine-5)-methyltransferases making it the candidate nucleophile.  We have
AB  - changed this cysteine to other amino acids for the EcoRII methylase; which
AB  - methylates the second cytosine in the sequence 5'-CCWGG-3'.  Mutants were
AB  - tested for their methyl transferring ability and for their ability to form
AB  - covalent complexes with DNA.  The latter property was tested indirectly with
AB  - the use of a genetic assay involving sensitivity of cells to 5-azacytidine.
AB  - Replacement of the conserved cysteine with glycine, valine, tryptophan or
AB  - serine led to an apparent loss of methyl transferring ability.  Interestingly,
AB  - cells carrying the mutant with serine did show sensitivity to 5-azacytidine,
AB  - suggesting the ability to link to DNA.  Unexpectedly, substitution of the
AB  - cysteine with glycine results in the inhibition of cell growth and the mutant
AB  - allele can be maintained in the cells only when it is poorly expressed.  These
AB  - results suggest that the conserved cysteine in the EcoRII methylase is
AB  - essential for methylase action and it may play more than one role in it.
ER  -

TY  - JOUR
AU  - Wyszynski, M.W.
AU  - Gabbara, S.
AU  - Kubareva, E.A.
AU  - Romanova, E.A.
AU  - Oretskaya, T.S.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
AU  - Bhagwat, A.S.
TI  - The cysteine conserved among DNA cytosine methylases is required for methyl transfer, but not for specific DNA binding.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 295
EP  - 301
VL  - 21
AB  - All DNA (cytosine-5)-methyltransferases contain a single conserved cysteine. It has been
AB  - proposed that this cysteine initiates catalysis by attacking the C6 of cytosine and thereby
AB  - activating the normally inert C5 position. We show here that substitutions of this cysteine in
AB  - the E. coli methylases M.EcoRII with either serine or trypotophan results in a complete loss
AB  - of ability to transfer methyl groups to DNA. Interestingly, mutants with either serine or
AB  - glycine substitution bind tightly to substrate DNA. These mutants resemble the wild-type
AB  - enzyme in that their binding to substrate is not eliminated by the presence of non-specific
AB  - DNA in the reaction, it is sensitive to methylation status of the substrate and is stimulated
AB  - by an analog of the methyl donor. Hence the conserved cysteine is not essential for the
AB  - specifc stable binding of the enzyme to its substrate. However, substitution of the cysteine
AB  - with the bulkier tryptophan does reduce DNA binding. We also report here a novel procedure for
AB  - the synthesis of DNA containing 5-fluorocytosine. Further, we show that a DNA substrate for
AB  - M.EcoRII in which the target cytosine is replaced by 5-fluorocytosine is a mechanism-based
AB  - inhibitor of the enzyme and that it forms an irreversible complex with the enzyme. As
AB  - expected, this modified substrate does not form irreversible complexes with the mutants.
ER  -

TY  - JOUR
AU  - Wyszynski, W.
AU  - Garbara, S.
AU  - Bhagwat, A.S.
TI  - Cytosine deaminations catalyzed by DNA cytosine methyltransferases are unlikely to be the major cause of mutational hot spots at sites of cytosine methylation in Escherichia coli.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1994
SP  - 1574
EP  - 1578
VL  - 91
AB  - Sites of cytosine methylation are hot spots for C to T mutations in Escherichia coli DNA. We
AB  - have developed a genetic reversion assay that allows direct selection of C to T mutations at a
AB  - site of methylation. Because the mutant gene is on a plasmid, this system can be used to study
AB  - mutational effects of biochemical agents in vitro as well as in vivo. Using this system we
AB  - show that in vitro an E. coli methyltransferase can cause C to U deaminations at a site of
AB  - methylation. Reaction conditions that are known to inhibit a side reaction of the
AB  - methyltransferase also suppress reversion frequency, suggesting that this side reaction is
AB  - required for deamination. Furthermore, a mutation in the enzyme that eliminates its catalytic
AB  - activity but not its ability to bind DNA eliminates the ability of the enzyme to cause C to U
AB  - deaminations. Despite this, in vivo experiments strongly suggest that enzyme-catalyzed
AB  - deaminations of cytosine do not play a major role in making methylation sites in E. coli hot
AB  - spots for mutations. For example, although uracil-DNA glycosylase (Ung) suppresses the
AB  - occurrence of mutations due to C to U deaminations, the frequency of C to T mutations at a
AB  - methylation site remains high in ung+ cells. Furthermore, the reversion frequencies in ung+
AB  - and ung- cells are quite similar.
ER  -

TY  - JOUR
AU  - Xavier, B.B.
AU  - Lammens, C.
AU  - Butaye, P.
AU  - Goossens, H.
AU  - Malhotra-Kumar, S.
TI  - Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms.
JO  - J. Antimicrob. Chemother.
PY  - 2016
SP  - 2342
EP  - 2344
VL  - 71
AB  - The monumental increase in antibiotic resistance among
AB  - important bacterial pathogens, driven by inappropriate and
AB  - appropriate use of ineffective drugs, is currently recognized as
AB  - one of the most pressing threats to human health by the
AB  - WHO. In particular, the last decade has seen a significant rise
AB  - in infections caused by MDR and XDR Gram-negative pathogens
AB  - such as Escherichia coli, Klebsiella pneumoniae, Pseudomonas
AB  - aeruginosa and Acinetobacter baumannii. Antibiotics of the
AB  - polymyxin group such as colistin are sometimes the only drugs
AB  - to which these bacteria show susceptibility and, therefore,
AB  - reports of emergence of a plasmid-mediated mcr-1-encoded
AB  - mechanism of resistance to colistin have been especially alarming.
ER  -

TY  - JOUR
AU  - Xavier, B.B.
AU  - Vervoort, J.
AU  - Stewardson, A.
AU  - Adriaenssens, N.
AU  - Coenen, S.
AU  - Harbarth, S.
AU  - Goossens, H.
AU  - Malhotra-Kumar, S.
TI  - Complete Genome Sequences of Nitrofurantoin-Sensitive and -Resistant Escherichia coli ST540 and ST2747 Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e00239
EP  - e00214
VL  - 2
AB  - Widespread multidrug resistance in Escherichia coli has necessitated the
AB  - reintroduction of older antibiotics, such as nitrofurantoin. However, mechanisms
AB  - by which resistance to nitrofurantoin emerges in E. coli are not well elucidated.
AB  - Toward this aim, we sequenced two nitrofurantoin-sensitive E. coli sequence types
AB  - (ST540 and ST2747) and their four nitrofurantoin-resistant derivatives generated
AB  - in vitro under aerobic and anaerobic growth conditions.
ER  -

TY  - JOUR
AU  - Xi, J.
AU  - Sheng, X.
AU  - He, L.
TI  - Draft Genome Sequence of Rhizobium sp. H41, a Rock-Weathering Bacterium from a Weathered Rock Surface.
JO  - Genome Announcements
PY  - 2014
SP  - e01127
EP  - e01114
VL  - 2
AB  - Rhizobium sp. H41 isolated from weathered tuff can weather tuff and release Fe, Si, and Al
AB  - from the rock under nutrient-poor conditions. Here, we report the
AB  - draft genome sequence of strain H41, which may facilitate a better understanding
AB  - of the molecular mechanism involved in rock weathering by the bacterium.
ER  -

TY  - JOUR
AU  - Xia, E.
AU  - Khong, W.X.
AU  - Marimuthu, K.
AU  - Xu, W.
AU  - Ong, R.T.
AU  - Tan, E.L.
AU  - Krishnan, P.U.
AU  - Ang, B.S.
AU  - Lye, D.C.
AU  - Chow, A.L.
AU  - Teo, Y.Y.
AU  - Ng, O.T.
TI  - Draft Genome Sequence of a Multidrug-Resistant New Delhi Metallo-beta-Lactamase-1 (NDM-1)-Producing Escherichia coli Isolate Obtained in Singapore.
JO  - Genome Announcements
PY  - 2013
SP  - e01020
EP  - e01013
VL  - 1
AB  - We report the draft genome sequence of a New Delhi metallo-beta-lactamase-1 (NDM-1)-positive
AB  - Escherichia coli isolate obtained from a surgical patient. The
AB  - assembled data indicate the presence of 3 multidrug resistance plasmids, 1 of
AB  - which shares 100% identity with an NDM-1 plasmid isolated previously from a
AB  - nearby hospital, suggesting possible local transmission.
ER  -

TY  - JOUR
AU  - Xia, H.
AU  - Wu, S.
TI  - Construction of DNA transfer system of Streptomyces tenebrarius.
JO  - Wei Sheng Wu Xue Bao
PY  - 2002
SP  - 181
EP  - 185
VL  - 42
AB  - To establish a gene transfer system in Streptomyces tenebrarius, several methods including
AB  - PEG-mediated transformation of protoplasts,
AB  - conjugal transfer were investigated. Many attempts were made to
AB  - introduce plasmid pIJ702 into Streptomyces tenebrarius. It was found
AB  - that plasmid pIJ702 isolated from S. lividans TK24 failed to transform
AB  - the protoplasts of Streptomyces tenebrarius. No transformant was
AB  - achieved even if the protoplast was inactivated by heat treatment or
AB  - dsDNA was converted ssDNA before transformation. All the results
AB  - suggested that Streptomyces tenebrarius exists a strong restriction and
AB  - modification system for the transformation of foreign DNA. A
AB  - recombinant E. coli ET12567 (pUZ8002, pHZ132) was obtained by
AB  - transforming E. coli ET12567 (pUZ8002) with oriT-containing E.
AB  - coli-Streptomyces shuttle plasmid pHZ132. In mating experiments, E. coli
AB  - ET12567 (pUZ8002, pHZ132) was the donor, and the recipient was
AB  - Streptomyces tenebrarius 9904 spores after pregerminating by heat shock.
AB  - Matings between donor and recipient were conducted. Plasmid pHZ132 was
AB  - introduced into Streptomyces tenebrarius 9904 by conjugation from E.
AB  - coli ET12567. The transfer system of Streptomyces tenebrarius was
AB  - established by conjugation. S. tenebrarius 9904 protoplasts were
AB  - transformed by plasmid DNA modified by the host itself, and the
AB  - transformation frequency was about 10^3/mug DNA (pHZ132).
ER  -

TY  - JOUR
AU  - Xia, L.
AU  - Cai, J.
AU  - Wang, B.
AU  - Huang, Y.
AU  - Jian, J.
AU  - Lu, Y.
TI  - Draft Genome Sequence of Nocardia seriolae ZJ0503, a Fish Pathogen Isolated from  Trachinotus ovatus in China.
JO  - Genome Announcements
PY  - 2015
SP  - e01223
EP  - e01214
VL  - 3
AB  - Nocardia seriolae is a pathogen that causes nocardiosis in marine and freshwater  fish. Here,
AB  - we report the draft genome sequence of N. seriolae strain ZJ0503,
AB  - which was isolated from Trachinotus ovatus in Guangdong, China.
ER  -

TY  - JOUR
AU  - Xia, X.
AU  - Li, J.
AU  - Liao, S.
AU  - Zhou, G.
AU  - Wang, H.
AU  - Li, L.
AU  - Xu, B.
AU  - Wang, G.
TI  - Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 48
EP  - 48
VL  - 11
AB  - Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative,
AB  - rod-shaped bacterium isolated from soil of a copper and iron mine.
AB  - This strain efficiently reduces chromate (Cr(6+)) to the much less toxic Cr(3+).
AB  - In addition, it reduces sulfate (SO4 (2-)) to S(2-). The S(2-) could react with
AB  - Cd(2+) to generate precipitated CdS. Thus, strain WH16-1 shows a great potential
AB  - to bioremediate Cr and Cd contaimination. Here we describe the features of this
AB  - organism, together with the draft genome and comparative genomic results among
AB  - strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp,
AB  - 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative
AB  - chromate- and sulfate-reducing genes are identified.
ER  -

TY  - JOUR
AU  - Xia, X.
AU  - Li, J.
AU  - Zhou, Z.
AU  - Wang, D.
AU  - Huang, J.
AU  - Wang, G.
TI  - High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7(T).
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 29
EP  - 29
VL  - 13
AB  - Pseudaminobacter manganicus JH-7(T) (= KCTC 52258(T) = CCTCC AB 2016107(T)) is a
AB  - Gram-staining-negative, aerobic and non-motile strain that was isolated from a
AB  - manganese mine. The strain JH-7(T) shows multiple heavy metal resistance and can
AB  - effectively remove Mn(2+) and Cd(2+). In addition, it is able to produce
AB  - exopolysaccharides (EPS), which may contribute to metal remove/adsorption. Thus,
AB  - strain JH-7(T) shows a great potential in bioremediation of heavy
AB  - metal-contaminated environment. In this study, we report the draft genomic
AB  - sequence of P. manganicus JH-7(T) and compare it to related genomes. Strain
AB  - JH-7(T) has a 4,842,937 bp genome size with a G + C content of 61.2%, containing
AB  - 4504 protein-coding genes and 71 RNA genes. A large number of putative genes
AB  - associated with heavy metal resistance and EPS synthesis are found in the genome.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Burbank, D.E.
AU  - Uher, L.
AU  - Rabussay, D.
AU  - Van Etten, J.L.
TI  - Restriction endonuclease activity induced by PBCV-1 virus infection of a chlorella-like green alga.
JO  - Mol. Cell. Biol.
PY  - 1986
SP  - 1430
EP  - 1439
VL  - 6
AB  - An enzyme was isolated from a eucaryotic, Chlorella-like green alga infected with the virus
AB  - PBCV-1 which exhibits type II restriction endonuclease activity. The enzyme recognized the
AB  - sequence GATC and cleaved DNA 5' to the G. Methylation of deoxyadenosine in the GATC sequence
AB  - inhibited enzyme activity. In vitro the enzyme cleaved host Chlorella nuclear DNA but not
AB  - viral DNA because host DNA contains GATC and PBCV-1 DNA contains GmATC sequences.  PBCV-1 DNA
AB  - is probably methylated in vivo by the PBCV-1-induced methyltransferase described elsewhere
AB  - (Y.Xia and J.L. Van Etten, Mol. Cell. Biol. 6: 1440-1445). Restriction endonuclease activity
AB  - was first detected 30 to 60 min after viral infection; the appearance of enzyme activity
AB  - required de novo protein synthesis, and the enzyme is probably virus encoded.  Appearance of
AB  - enzyme activity coincided with the onset of host DNA degradation after PBCV-1 infection.  We
AB  - propose that the PBCV-1-induced restriction endonuclease participates in host DNA degradation
AB  - and is part of a virus-induced restriction and modification system in PBCV-1-infected
AB  - Chlorella cells.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Burbank, D.E.
AU  - Uher, L.
AU  - Rabussay, D.
AU  - Van Etten, J.L.
TI  - IL-3A virus infection of a Chlorella-like green alga induces a DNA restriction endonuclease with novel sequence specificity.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 6075
EP  - 6090
VL  - 15
AB  - A type II restriction endonuclease, named CviJI, was isolated from a eukaryotic Chlorella-like
AB  - green alga infected with the dsDNA containing virus IL-3A. CviJI is the first restriction
AB  - endonuclease to recognize the sequence PuGCPy; CviJI cleaves DNA between the G and C.
AB  - Methylation of the cytosine in PuGCPy sequences prevents cleavage by CviJI. CviJI cleaved DNA
AB  - into smaller but defined fragments in the presence of ATP. This "star activity" was stimulated
AB  - by dithiothreitol and/or S-adenosylmethionine but did not occur under conditions which favor
AB  - "star activity" of other restriction endonuclease.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Burbank, D.E.
AU  - Van Etten, J.L.
TI  - Restriction endonuclease activity induced by NC-1A virus infection of a Chlorella-like green alga.
JO  - Nucleic Acids Res.
PY  - 1986
SP  - 6017
EP  - 6030
VL  - 14
AB  - A type II restriction endonuclease, CviBI, was isolated from a eukaryotic,
AB  - Chlorella-like green alga infected with the dsDNA containing virus NC-1A.  The
AB  - enzyme recognizes the sequence GANTC and cleaves DNA between the G and A.
AB  - Methylation of deoxyadenosine in the GANTC sequence probably inhibits enzyme
AB  - activity.  In vitro CviBI cleaves host nuclear DNA but not viral DNA.  A survey
AB  - of 18 other viruses which infect the same Chlorella sp. revealed that infection
AB  - with 5 of these viruses also induced a restriction endonuclease which cleaves
AB  - DNA into the same size fragments as CviBI.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Morgan, R.
AU  - Schildkraut, I.
AU  - Van Etten, J.L.
TI  - A site-specific single strand endonuclease activity induced by NYs-1 virus infection of a Chlorella-like green alga.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 9477
EP  - 9487
VL  - 16
AB  - A site-specific endonuclease was isolated from a eukaryotic Chlorella-like
AB  - green alga infected with the dsDNA-containing virus NYs-1.  The enzyme
AB  - recognizes the sequence 5'-CC-3' and cleaves 5' to the first C.  It cleaves
AB  - 5'-CmC-3' sequences but not 5'-mCC-3' sequences.  The enzyme creates breaks in
AB  - dsDNA whenever two 5'-CC-3' sequences on opposite strands are close enough for
AB  - the two strands to separate; when the 5'-CC-3' sequences on opposite strands
AB  - are further apart only a portion of the strands separate.  Consequently, NYs-1
AB  - endonuclease does not produce a completely stable DNA digestion pattern.  The
AB  - enzyme probably does not cleave ssDNA and definitely does not cleave ssRNA or
AB  - dsRNA.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Narva, K.E.
AU  - Van Etten, J.L.
TI  - The cleavage site of the RsaI isoschizomer, CviII, is G^TAC.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 10063
EP  - 10063
VL  - 15
AB  - Infection of the green alga, Chlorella NC64A, with the dsDNA virus NY-2A
AB  - results in the synthesis of a restriction endonuclease CviII.  Chlorella cells
AB  - infected with NY-2A (m.o.i. of f10) were collected by centrifugation at 12 hr
AB  - p.i.  Note: this has been renamed CviQI.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Van Etten, J.L.
TI  - DNA methyltransferase induced by PBCV-1 virus infection of a chlorella-like green alga.
JO  - Mol. Cell. Biol.
PY  - 1986
SP  - 1440
EP  - 1445
VL  - 6
AB  - A DNA methyltransferase was isolated from a eucaryotic, Chlorella-like green
AB  - alga infected with the virus PBCV-1.  The enzyme recognized the sequence GATC
AB  - and methylated deoxyadenosine solely in GATC sequences.  Host DNA, which
AB  - contains GATC sequences, but not PBCV-1 DNA, which contains GmATC sequences,
AB  - was a good substrate for the enzyme in vitro.  The DNA methyltransferase
AB  - activity was first detected about 1 h after viral infection; PBCV-1 DNA
AB  - synthesis and host DNA degradation also began at about this time.  The
AB  - appearance of the DNA methyltransferase activity required de novo protein
AB  - synthesis, and the enzyme was probably virus encoded.  Methylation of DNAs with
AB  - the PBCV-1-induced methyltransferase conferred resistance of the DNAs to a
AB  - PBCV-1-induced restriction endonuclease enzyme described previously (Y. Xia,
AB  - D.E. Burbank, L. Uher, D. Rabussay, and J.L. Van Etten, Mol. Cell Biol. 6:
AB  - 1430-1439).  We propose that the PBCV-1-induced methyltransferase protects
AB  - viral DNA from the PBCV-1-induced restriction endonuclease and is part of a
AB  - virus-induced restriction and modification system in PBCV-1-infected Chlorella
AB  - cells.
ER  -

TY  - JOUR
AU  - Xia, Y.
AU  - Van Etten, J.L.
AU  - Dobos, P.
AU  - Ling, Y.Y.
AU  - Krell, P.J.
TI  - Adenine DNA methyltransferase M.CviRI expression accelerates apoptosis in baculovirus-infected insect cells.
JO  - Virology
PY  - 1993
SP  - 817
EP  - 824
VL  - 196
AB  - The adenine DNA methyltransferase M.CviRI (TGCmA) gene from chlorella virus XZ-6E was cloned
AB  - into the Autographa californica nuclear polyhedrosis virus (AcMNPV) genome and expressed in
AB  - Spodoptera frugiperda insect cells under the control of two tandemly arranged viral promoters,
AB  - the early ETL promoter and the late polyhedrin promoter. M.CviRI activity was first detected
AB  - at 10 hr p.i. and reached a maximum at 48 hr p.i. Viral DNA synthesized in insect cells
AB  - infected with M.CviRI expressing virus (AcMTRI) was methylated at all TGCA sites.
AB  - Unexpectedly, AcMTRI-infected cells lysed 48 hr earlier than wild-type AcMNPV-infected cells.
AB  - Moreover, cellular DNA, but not viral DNA, from AcM-TRI-infected cells was degraded to
AB  - fragment sizes characteristic of apoptosis. Thse results suggest that M.CviRI methylation
AB  - influences the onset of viral cytopathic effects and induces an apoptosis-like response.
ER  -

TY  - JOUR
AU  - Xia, Z.-G.
AU  - Zhu, R.-F.
AU  - Cao, X.-W.
AU  - Zou, G.-L.
TI  - Purification and characterization of restriction endonuclease Bsp78I.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1987
SP  - 27
EP  - 34
VL  - 19
AB  - Two kinds of direct single-step method using DNA-Sepharose and heparin-Sepharose affinity
AB  - chromatography to purify restriction endonuclease Bsp78I are reported. Chromatographic
AB  - conditions which may increase the purity and yield of the enzyme were studied. The purified
AB  - enzymes, obtained by the two methods, were found to be free of detectable contamination by
AB  - other DNases (exo and endo) caused by excess enzyme digestion of lambda DNA and by ligation
AB  - and recutting of enzymatic digests of pBR322 DNA. The specific activities and the yields of
AB  - the enzymes obtained by the two methods are both about 17,000 units per mg protein and 4,000
AB  - units per g wet bacteria, respectively. Some properties of the restriction endonuclease Bsp78I
AB  - are determined quantitatively. The optimal range of Mg++ concentration and optimal Tris-HCl
AB  - concentration are 20-30 m mol/L and 50 m mol/L respectively. The optimal pH is 7.5 and the
AB  - optimal temperature 40 C. 78I is very sensitive to PCMB.
ER  -

TY  - JOUR
AU  - Xiang, X.Y.
AU  - Chen, L.M.
AU  - Huang, X.X.
AU  - Luo, Y.M.
AU  - She, Q.X.
AU  - Huang, L.
TI  - Sulfolobus tengchongensis spindle-shaped virus STSV1: Virus-host interactions and genomic features.
JO  - J. Virol.
PY  - 2005
SP  - 8677
EP  - 8686
VL  - 79
AB  - A virus infecting the hyperthermophilic archaeon Sulfolobus tengchongensis has been isolated
AB  - from a field sample from Tengchong,
AB  - China, and characterized. The virus, denoted STSV1 (Sulfolobus
AB  - tengchongensis spindle-shaped virus 1), has the morphology of a spindle
AB  - (230 by 107 nm) with a tail of variable length (68 nm on average) at
AB  - one end and is the largest of the known spindle-shaped viruses. After
AB  - infecting its host, the virus multiplied rapidly to high titers (>
AB  - 10(10) PFU/ml). Replication of the virus retarded host growth but did
AB  - not cause lysis of the host cells. STSV1 did not integrate into the
AB  - host chromosome and existed in a carrier state. The STSV1 DNA was
AB  - modified in an unusual fashion, presumably by virally encoded
AB  - modification systems. STSV1 harbors a double-stranded DNA genome of
AB  - 75,294 bp, which shares no significant sequence similarity to those of
AB  - fuselloviruses. The viral genome contains a total of 74 open reading
AB  - frames (ORFs), among which 14 have a putative function. Five ORFs
AB  - encode viral structural proteins, including a putative coat protein of
AB  - high abundance. The products of the other nine ORFs are probably
AB  - involved in polysaccharide biosynthesis, nucleotide metabolism, and DNA
AB  - modification. The viral genome divides into two nearly equal halves of
AB  - opposite gene orientation. This observation as well as a GC-skew
AB  - analysis point to the presence of a putative viral origin of
AB  - replication in the 1.4-kb intergenic region between ORF1 and ORF74.
AB  - Both morphological and genomic features identify STSV1 as a novel virus
AB  - infecting the genus Sulfolobus.
ER  -

TY  - JOUR
AU  - Xiao, J.
AU  - Luo, Y.
AU  - Xu, J.
TI  - Genome Sequence of Serinicoccus profundi, a Novel Actinomycete Isolated from Deep-Sea Sediment.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6413
EP  - 6413
VL  - 193
AB  - Serinicoccus profundi MCCC 1A05965(T) was isolated from deep-sea sediment collected from the
AB  - Indian Ocean. It was a Gram-positive, moderately
AB  - halophilic, aerobic bacterium. Here, we describe the 3.4-Mbp draft genome
AB  - sequence of S. profundi MCCC 1A05965(T).
ER  -

TY  - JOUR
AU  - Xiao, L.
AU  - Ptacek, T.
AU  - Osborne, J.D.
AU  - Crabb, D.M.
AU  - Simmons, W.L.
AU  - Lefkowitz, E.J.
AU  - Waites, K.B.
AU  - Atkinson, T.P.
AU  - Dybvig, K.
TI  - Comparative genome analysis of Mycoplasma pneumoniae.
JO  - BMC Genomics
PY  - 2015
SP  - 610
EP  - 610
VL  - 16
AB  - BACKGROUND: Mycoplasma pneumoniae is a common pathogen that causes upper and
AB  - lower respiratory tract infections in people of all ages, responsible for up to
AB  - 40 % of community-acquired pneumonias. It also causes a wide array of
AB  - extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the
AB  - organism have been generally restricted to specific genes or regions of the
AB  - genome, because whole genome sequencing has been completed for only 4 strains. To
AB  - better understand the physiology and pathogenicity of this important human
AB  - pathogen, we performed comparative genomic analysis of 15 strains of M.
AB  - pneumoniae that were isolated between the 1940s to 2009 from respiratory
AB  - specimens and cerebrospinal fluid originating from the USA, China and England.
AB  - RESULTS: Illumina MiSeq whole genome sequencing was performed on the 15 strains
AB  - and all genome sequences were completed. Results from the comparative genomic
AB  - analysis indicate that although about 1500 SNP and indel variants exist between
AB  - type1 and type 2 strains, there is an overall high degree of sequence similarity
AB  - among the strains (>99 % identical to each other). Within the two subtypes,
AB  - conservation of most genes, including the CARDS toxin gene and arginine deiminase
AB  - genes, was observed. The major variation occurs in the P1 and ORF6 genes
AB  - associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of
AB  - type I restriction enzyme) with variable tandem repeat copy numbers were found in
AB  - all 15 genomes. CONCLUSIONS: These data indicate that despite conclusions drawn
AB  - from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is
AB  - extraordinarily stable over time and geographic distance across the globe with a
AB  - striking lack of evidence of horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Xie, B.
AU  - Dupras, A.A.
AU  - Duceppe, M.O.
AU  - Fattahi-Ghazi, N.
AU  - Goodridge, L.
AU  - Ogunremi, D.
TI  - Genome Sequences of 13 Isolates of Salmonella enterica Serovar Typhimurium var. Copenhagen Obtained from Wild Pigeons in Canada.
JO  - Genome Announcements
PY  - 2018
SP  - e00392
EP  - e00318
VL  - 6
AB  - Pigeon-adapted strains of Salmonella enterica serovar Typhimurium var. Copenhagen phage types
AB  - 2 and 99 obtained from the provinces of Alberta, British Columbia,
AB  - and Ontario, Canada, were analyzed using whole-genome sequencing. All isolates
AB  - contained the Salmonella virulence plasmid despite the low pathogenicity of this
AB  - lineage in their avian host.
ER  -

TY  - JOUR
AU  - Xie, B.B.
AU  - Shu, Y.L.
AU  - Qin, Q.L.
AU  - Rong, J.C.
AU  - Zhang, X.Y.
AU  - Chen, X.L.
AU  - Shi, M.
AU  - He, H.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Genome sequences of type strains of seven species of the marine bacterium Pseudoalteromonas.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2746
EP  - 2747
VL  - 194
AB  - There are over 30 species in the marine bacterial genus Pseudoalteromonas.
AB  - However, our knowledge about this genus is still limited. We sequenced the
AB  - genomes of type strains of seven species in the genus, facilitating the study of
AB  - the physiology, adaptation, and evolution of this genus.
ER  -

TY  - JOUR
AU  - Xie, B.B.
AU  - Shu, Y.L.
AU  - Qin, Q.L.
AU  - Rong, J.C.
AU  - Zhang, X.Y.
AU  - Chen, X.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Genome Sequence of the Cycloprodigiosin-Producing Bacterial Strain Pseudoalteromonas rubra ATCC 29570T.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1637
EP  - 1638
VL  - 194
AB  - The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome
AB  - of a cycloprodigiosin-producing bacterial strain,
AB  - Pseudoalteromonas rubra ATCC 29570(T). Analysis revealed a probable
AB  - cycloprodigiosin biosynthetic cluster, providing a good model for the study of
AB  - cycloprodigiosin synthesis and regulation.
ER  -

TY  - JOUR
AU  - Xie, F.
TI  - Mechanistic studies of specific DNA cleavage by PvuII restriction endonuclease.
JO  - Ph.D. Thesis, University of Missouri
PY  - 2008
AB  - PvuII restriction endonuclease is a homodimeric protein which recognizes and cleaves the
AB  - palindromic sequence (CAG^CTG) in the presence of Mg(II) ions. Starting with PvuII as a model
AB  - system, pKa calculations with crystallographically defined metal ligated water are applied to
AB  - PD...D/ExK motif metallonucleases in order to investigate the activation of nucleophile in
AB  - metal dependent DNA hydrolysis. These results establish the electrostatic contributions of the
AB  - metal ions and the conserved Lys in lowering water pKa. The calculated pKa values of metal
AB  - ligands have been used to simulate the pH dependence of Mg(II) binding to PvuII. The bell
AB  - shaped pH-rate profile is dissected into three ionizations. One is recognized as from the
AB  - metal ligands, and the other two have pKa's similar to calculated metal ligated water pKa in
AB  - the absence of DNA. The determined pH profiles agree well with previous pH dependence studies
AB  - on metallonucleases, and the correlation with pKa calculations indicates the direct
AB  - involvement of metal activated water in catalysis. iii The different metal occupancies
AB  - observed in crystal structures lead to controversy regarding the number and function of metal
AB  - ions involved in DNA hydrolysis by type II restriction endonucleases. Quench flow experiments
AB  - are used to monitor Mg(II) dependent single and multiple turnover DNA cleavage reactions with
AB  - PvuII. Several models which differ in order of binding and the number of metal ions supporting
AB  - catalysis are examined by global fits using DynaFit. The best fitted model has a preference of
AB  - binding order in the reaction scheme and supports one-metal ion catalysis with 50 fold reduced
AB  - activity compared with two-metal ion catalysis. The same model is also found to account for
AB  - multiple turnover data in fits and simulations. A unique reaction scheme for PvuII is
AB  - established to interpret the determined Mg(II) dependence of kinetic data, which provides an
AB  - insight into Mg(II) participation in substrate binding, catalysis and product dissociation by
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Xie, G.
AU  - Chastain-Gross, R.P.
AU  - Belanger, M.
AU  - Kumar, D.
AU  - Whitlock, J.A.
AU  - Liu, L.
AU  - Farmerie, W.G.
AU  - Daligault, H.E.
AU  - Han, C.S.
AU  - Brettin, T.S.
AU  - Progulske-Fox, A.
TI  - Genome Sequence of Porphyromonas gingivalis Strain AJW4.
JO  - Genome Announcements
PY  - 2015
SP  - e01304
EP  - e01315
VL  - 3
AB  - Porphyromonas gingivalis is associated with oral and systemic diseases. Strain-specific P.
AB  - gingivalis invasion phenotypes have been correlated with
AB  - disease presentation in infected laboratory animals. Here, we present the genome
AB  - sequence of AJW4, a minimally invasive strain, with a single contig of 2,372,492
AB  - bp and a G+C content of 48.27%.
ER  -

TY  - JOUR
AU  - Xie, G.
AU  - Chastain-Gross, R.P.
AU  - Belanger, M.
AU  - Kumar, D.
AU  - Whitlock, J.A.
AU  - Liu, L.
AU  - Farmerie, W.G.
AU  - Zeng, C.L.
AU  - Daligault, H.E.
AU  - Han, C.S.
AU  - Brettin, T.S.
AU  - Progulske-Fox, A.
TI  - Genome Sequence of Porphyromonas gingivalis Strain A7A1-28.
JO  - Genome Announcements
PY  - 2017
SP  - e00021
EP  - e00017
VL  - 5
AB  - Porphyromonas gingivalis is an oral opportunistic pathogen. Sequenced P. gingivalis laboratory
AB  - strains display limited diversity in antigens that modulate
AB  - host responses. Here, we present the genome sequence of A7A1-28, a strain
AB  - possessing atypical fimbrillin and capsule types, with a single contig of
AB  - 2,249,024 bp and a G+C content of 48.58%.
ER  -

TY  - JOUR
AU  - Xie, G.
AU  - Cui, Z.
AU  - Tao, Z.
AU  - Qiu, H.
AU  - Liu, H.
AU  - Ibrahim, M.
AU  - Zhu, B.
AU  - Jin, G.
AU  - Sun, G.
AU  - Almoneafy, A.
AU  - Li, B.
TI  - Genome Sequence of the Rice Pathogen Pseudomonas fuscovaginae CB98818.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5479
EP  - 5480
VL  - 194
AB  - Pseudomonas fuscovaginae is a phytopathogenic bacterium causing bacterial sheath  brown rot of
AB  - cereal crops. Here, we present the draft genome sequence of P.
AB  - fuscovaginae CB98818, originally isolated from a diseased rice plant in China.
AB  - The draft genome will aid in epidemiological studies, comparative genomics, and
AB  - quarantine of this broad-host-range pathogen.
ER  -

TY  - JOUR
AU  - Xie, G.
AU  - Ramirez, M.S.
AU  - Marshall, S.H.
AU  - Hujer, K.M.
AU  - Lo, C.C.
AU  - Johnson, S.
AU  - Li, P.E.
AU  - Davenport, K.
AU  - Endimiani, A.
AU  - Bonomo, R.A.
AU  - Tolmasky, M.E.
AU  - Chain, P.S.
TI  - Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain  VA360).
JO  - Genome Announcements
PY  - 2013
SP  - e00168
EP  - e00113
VL  - 1
AB  - We report the sequences of two Klebsiella pneumoniae clinical isolates, strains JHCK1 and
AB  - VA360, from a newborn with meningitis in Buenos Aires, Argentina, and
AB  - from a tertiary care medical center in Cleveland, OH, respectively. Both isolates
AB  - contain one chromosome and at least five plasmids; isolate VA360 contains the
AB  - Klebsiella pneumoniae carbapenemase (KPC) gene.
ER  -

TY  - JOUR
AU  - Xie, G.L.
AU  - Zhang, G.Q.
AU  - Liu, H.
AU  - Lou, M.M.
AU  - Tian, W.X.
AU  - Li, B.
AU  - Zhou, X.P.
AU  - Zhu, B.
AU  - Jin, G.L.
TI  - Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5013
EP  - 5014
VL  - 193
AB  - Acidovorax avenae subsp. avenae is a phytobacterium which is the causal agent of several
AB  - economic plant diseases. Here, we present the draft
AB  - genome sequence of strain RS-1, which was isolated from rice shoot in rice
AB  - field of China. This strain can cause bacterial stripe of rice.
ER  -

TY  - JOUR
AU  - Xie, J.
AU  - Huang, J.F.
AU  - Shi, X.F.
AU  - Liu, C.Q.
TI  - Analysis of the characteristic sequence of intein and revision of its motifs.
JO  - Chinese Sci. Bull.
PY  - 2001
SP  - 758
EP  - 761
VL  - 46
AB  - Since the first intein (Sce VMA) was found in Saccharomyces cerevisiae ATPase gene in 1990,
AB  - more and more inteins were identified. It is necessary to analyze the new inteins to
AB  - understand the sequence characteristics of inteins. By searching protein and nucleic acid
AB  - database systematically, 101 inteins were found, of which 69 inteins contain homing
AB  - endonuclease moths. We only analyze the 69 inteins since most inteins are the classic inteins
AB  - with homing endonuclease motifs. We found that the distribution of these inteins is particular
AB  - among species and protein. By multiple sequence alignment, some new sequence characteristics
AB  - were found and the motifs described previously were revised.
ER  -

TY  - JOUR
AU  - Xie, J.
AU  - Juliao, P.C.
AU  - Gilsdorf, J.R.
AU  - Ghosh, D.
AU  - Patel, M.
AU  - Marrs, C.F.
TI  - Identification of New Genetic Regions More Prevalent in Nontypeable Haemophilus influenzae Otitis Media Strains than in Throat Strains.
JO  - J. Clin. Microbiol.
PY  - 2006
SP  - 4316
EP  - 4325
VL  - 44
AB  - Nontypeable (NT) Haemophilus influenzae strains cause significant respiratory illness and are
AB  - isolated from up to half of middle ear aspirates from children with acute otitis media.
AB  - Previous studies have identified two genes, lic2B and hmwA, that are associated with NT H.
AB  - influenzae strains isolated from the middle ears of children with otitis media but that are
AB  - not associated with NT H. influenzae strains isolated from the throats of healthy children,
AB  - suggesting that they may play a role in virulence in otitis media. In this study, genomic
AB  - subtraction was used to identify additional genetic regions unique to middle ear strains. The
AB  - genome of NT H. influenzae middle ear strain G622 was subtracted from that of NT H. influenzae
AB  - throat strain 23221, and the resultant gene regions unique to the middle ear strain were
AB  - identified. Subsequently, the relative prevalence of the middle ear-specific gene regions
AB  - among a large panel of otitis media and throat strains was determined by dot blot
AB  - hybridization. By this approach, nine genetic regions were found to be significantly more
AB  - prevalent in otitis media strains. Classification tree analysis of lic2B, hmwA, and the nine
AB  - new potential otitis media virulence genes revealed two H. influenzae pathotypes associated
AB  - with otitis media.
ER  -

TY  - JOUR
AU  - Xie, J.B.
AU  - Du, Z.
AU  - Bai, L.
AU  - Tian, C.
AU  - Zhang, Y.
AU  - Xie, J.Y.
AU  - Wang, T.
AU  - Liu, X.
AU  - Chen, X.
AU  - Cheng, Q.
AU  - Chen, S.
AU  - Li, J.
TI  - Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes.
JO  - PLoS Genet.
PY  - 2014
SP  - E1004231
EP  - E1004231
VL  - 10
AB  - We provide here a comparative genome analysis of 31 strains within the genus
AB  - Paenibacillus including 11 new genomic sequences of N2-fixing strains. The
AB  - heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus
AB  - strains) was reflected in the large size of the shell genome, which makes up
AB  - approximately 65.2% of the genes in pan genome. Large numbers of transposable
AB  - elements might be related to the heterogeneity. We discovered that a minimal and
AB  - compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN,
AB  - nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing
AB  - strains. The nif cluster is under control of a sigma(70)-depedent promoter and
AB  - possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S]
AB  - cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore,
AB  - we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix
AB  - nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that
AB  - Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275
AB  - single-copy core genes suggests that the ancestral Paenibacillus did not fix
AB  - nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif
AB  - cluster via horizontal gene transfer (HGT) from a source related to Frankia.
AB  - During the history of evolution, the nif cluster was lost, producing some
AB  - non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding
AB  - Fe-nitrogenase was acquired, causing further diversification of some strains. In
AB  - addition, some N2-fixing strains have additional nif and nif-like genes which may
AB  - result from gene duplications. The evolution of nitrogen fixation in
AB  - Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf
AB  - genes. This study not only reveals the organization and distribution of nitrogen
AB  - fixation genes in Paenibacillus, but also provides insight into the complex
AB  - evolutionary history of nitrogen fixation.
ER  -

TY  - JOUR
AU  - Xie, S.
AU  - Wang, Z.
AU  - Okano, M.
AU  - Nogami, M.
AU  - Li, Y.
AU  - He, W.-W.
AU  - Okumura, K.
AU  - Li, E.
TI  - Cloning, expression and chromosome locations of the human DNMT3 gene family.
JO  - Gene
PY  - 1999
SP  - 87
EP  - 95
VL  - 236
AB  - DNA methylation plays an important role in animal development and gene regulation. In mammals,
AB  - several genes encoding DNA cytosine methyltransferases have been identified. DNMT1 is
AB  - constitutively expressed and is required for the maintenance of global methylation after DNA
AB  - replication. In contrast, the murine Dnmt3 family genes appear to be developmentally regulated
AB  - and behave like de novo DNA methyltransferases in vitro. In this study, we have cloned human
AB  - DNMT3A and DNMT3B that encode full-length DNMT3A and DNMT3B proteins with 98% and 94% amino
AB  - acid sequence identity to their murine homologues. The DNMT3A and DNMT3B show high homology in
AB  - the carboxy terminal catalytic domain and contain a conserved cysteine-rich region, which
AB  - shares homology with the X-linked ATRX gene of the SNF2/SWI family. We have mapped human
AB  - DNMT3A and DNMT3B to chromosomes 2p23 and 20q11.2 respectively, and determined the DNMT3B
AB  - genomic structure. We further show that DNMT3A expression is ubiquitous and can be readily
AB  - detected in most adult tissues, whereas DNMT3B is expressed at very low levels in most tissues
AB  - except testis, thyroid and bone marrow. Significantly, both DNMT3A and DNMT3B expression is
AB  - elevated in several tumor cell lines to levels comparable to DNMT1. The cloning of the human
AB  - DNMT3 genes will facilitate further biochemical and genetic studies of their functions in
AB  - establishment of DNA methylation patterns, regulation of gene expression and tumorigenesis.
ER  -

TY  - JOUR
AU  - Xie, X.
AU  - Yu, Y.
AU  - Liu, G.
AU  - Yuan, Z.
AU  - Song, J.
TI  - Complexity and entropy analysis of DNA methyltransferase.
JO  - J. Data Min. Genomics Proteomics
PY  - 2010
SP  - 1000105
EP  - 1000105
VL  - 1
AB  - The application of complexity information on DNA sequence and protein in biological processes
AB  - are well established in this study.  Available sequences for DNMT1 gene were thoroughly
AB  - explored in the informaion complexities.  DNMT1 gene is a maintenance methyltransferase
AB  - responsible for copy in DNA methylation patterns to the daughter strands during DNA
AB  - replication in different species.  We found that the entropy of DNMT1 gene in differnt species
AB  - is DNA base composition dependent, and its complexity in mammals is lower in introns than in
AB  - coding regions.  We also demonstrated the impacts of entropy on domains and non-domains(s) of
AB  - the DNMT1 gene.  The results from DNA and protein sequences indicated that DNA evolution has a
AB  - tendency toward complexity.  The most interest is that the methylation's changes of the gene
AB  - over aging in a unique chick model showed aging-driven entropy characteristics, which may give
AB  - an explanation of aging processes.  In summary, the information complexity of DNNT1 gene is
AB  - related to its genomic composition, which thereby associates to evolutionary and aging
AB  - processing, even though the intrinsic mechanism is not to be studied yet.
ER  -

TY  - JOUR
AU  - Xin, B.
AU  - Tao, F.
AU  - Wang, Y.
AU  - Gao, C.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Clostridium butyricum Strain DSM 10702, a Promising Producer of Biofuels and Biochemicals.
JO  - Genome Announcements
PY  - 2013
SP  - e00563
EP  - e00513
VL  - 1
AB  - Clostridium butyricum strains have been considered promising producers of biofuels and
AB  - biochemicals, such as hydrogen, butanol, butyric acid, and
AB  - 1,3-propanediol. Here, we present a 4.59-Mb assembly of the genome sequence of
AB  - DSM 10702 (VPI 3266), a type strain of C. butyricum.
ER  -

TY  - JOUR
AU  - Xin, D.
AU  - El Karkouri, K.
AU  - Robert, C.
AU  - Raoult, D.
AU  - Fournier, P.E.
TI  - Genomic Comparison of Rickettsia honei Strain RBT and Other Rickettsia Species.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4145
EP  - 4145
VL  - 194
AB  - Rickettsia honei strain RB(T) was isolated from a febrile patient on Flinders Island,
AB  - Australia, in 1991 and has been demonstrated to be the agent of Flinders
AB  - Island spotted fever, a disease transmitted to humans by ticks. The comparison of
AB  - this 1.27-Mb genome with other Rickettsia genomes provides additional insight
AB  - into the mechanisms of evolution in Rickettsia species.
ER  -

TY  - JOUR
AU  - Xing, P.
AU  - Hahnke, R.L.
AU  - Unfried, F.
AU  - Markert, S.
AU  - Huang, S.
AU  - Barbeyron, T.
AU  - Harder, J.
AU  - Becher, D.
AU  - Schweder, T.
AU  - Glockner, F.O.
AU  - Amann, R.I.
AU  - Teeling, H.
TI  - Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom.
JO  - ISME J.
PY  - 2015
SP  - 1410
EP  - 1422
VL  - 9
AB  - Members of the flavobacterial genus Polaribacter thrive in response to North Sea
AB  - spring phytoplankton blooms. We analyzed two respective Polaribacter species by
AB  - whole genome sequencing, comparative genomics, substrate tests and proteomics.
AB  - Both can degrade algal polysaccharides but occupy distinct niches. The liquid
AB  - culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an
AB  - overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization
AB  - loci (PULs) and features proteorhodopsin, whereas the agar plate isolate
AB  - Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even
AB  - peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing
AB  - algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other
AB  - sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs,
AB  - supporting earlier assumptions that Polaribacter take part in the decomposition
AB  - of sulfated polysaccharides. Both strains grow on algal laminarin and the
AB  - sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified
AB  - by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced
AB  - CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin
AB  - sulfate recognition. These and other data suggest that strain Hel1_33_49 is a
AB  - planktonic flavobacterium feeding on proteins and a small subset of algal
AB  - polysaccharides, while the more versatile strain Hel1_85 can decompose a broader
AB  - spectrum of polysaccharides and likely associates with algae.
ER  -

TY  - JOUR
AU  - Xing, S.
AU  - Pan, X.
AU  - Sun, Q.
AU  - Pei, G.
AU  - An, X.
AU  - Mi, Z.
AU  - Huang, Y.
AU  - Zhao, B.
AU  - Tong, Y.
TI  - Complete Genome Sequence of a Novel Multidrug-Resistant Klebsiella pneumoniae Phage, vB_Kpn_IME260.
JO  - Genome Announcements
PY  - 2017
SP  - e00055
EP  - e00017
VL  - 5
AB  - Klebsiella pneumoniae is the most common clinically important opportunistic bacterial pathogen
AB  - and its infection is often iatrogenic. Its drug resistance
AB  - poses a grave threat to public health. The genomic data reported here comprise an
AB  - important resource for research on phage therapy in the control of drug-resistant
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Xiong, J.
AU  - Deraspe, M.
AU  - Iqbal, N.
AU  - Krajden, S.
AU  - Chapman, W.
AU  - Dewar, K.
AU  - Roy, P.H.
TI  - Complete Genome of a Panresistant Pseudomonas aeruginosa Strain, Isolated from a  Patient with Respiratory Failure in a Canadian Community Hospital.
JO  - Genome Announcements
PY  - 2017
SP  - e00458
EP  - e00417
VL  - 5
AB  - We report here the complete genome sequence of a panresistant Pseudomonas aeruginosa strain,
AB  - isolated from a patient with respiratory failure in Canada. No
AB  - carbapenemase genes were identified. Carbapenem resistance is attributable to a
AB  - frameshift in the oprD gene; the basis for colistin resistance remains
AB  - undetermined.
ER  -

TY  - JOUR
AU  - Xiong, J.
AU  - Li, D.
AU  - Li, H.
AU  - He, M.
AU  - Miller, S.J.
AU  - Yu, L.
AU  - Rensing, C.
AU  - Wang, G.
TI  - Genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, Comamonas testosteroni S44.
JO  - Res. Microbiol.
PY  - 2011
SP  - 671
EP  - 679
VL  - 162
AB  - A novel and multiple metal(loid)-resistant strain Comamonas testosteroni S44 with
AB  - a high Zn(2+) resistance level (10 mM) was isolated. To understand the molecular
AB  - basis for the high zinc resistance, whole genome sequencing was performed and
AB  - revealed a large number of genes encoding putative metal(loid) resistance
AB  - proteins, mobile genetic elements (MGEs) and horizontal gene transfer (HGT)
AB  - events that may have occurred to adapt to a metal(loid)-contaminated environment.
AB  - In particular, 9 putative Zn(2+) transporters [4 znt operons encoding putative
AB  - Zn(2+)-translocating P-type ATPases and 5 czc operons encoding putative
AB  - RND-driven (resistance, nodulation, cell division protein family)] tripartite
AB  - protein complexes were identified. Real-time RT-PCR analysis revealed that the
AB  - four zntA-like genes were all induced by Zn(2+), while czcA genes were either
AB  - Zn(2+)-induced or downregulated by Zn(2+). Furthermore, a zntR1A1 operon encoding
AB  - a ZntR-type regulator and a P-type ATPase was studied in detail. The zntR1
AB  - deletion strain (S44DeltazntR1) displayed intermediate resistance to Zn(2+) (6
AB  - mM) and accumulated more intracellular Zn(2+). Reporter gene expression assays
AB  - indicated that ZntR1 responded to Zn(2+), Cd(2+) and Pb(2+), with Zn(2+) being
AB  - the best inducer. Gene transcription analysis indicated that ZntR1 was a
AB  - regulator for transcription of zntA1, while other putative ZntR-type regulators
AB  - may also regulate the transcription expression of zntA1.
ER  -

TY  - JOUR
AU  - Xiong, X.H.
AU  - Han, S.
AU  - Wang, J.H.
AU  - Jiang, Z.H.
AU  - Chen, W.
AU  - Jia, N.
AU  - Wei, H.L.
AU  - Cheng, H.
AU  - Yang, Y.X.
AU  - Zhu, B.
AU  - You, S.
AU  - He, J.Y.
AU  - Hou, W.
AU  - Chen, M.X.
AU  - Yu, C.J.
AU  - Jiao, Y.H.
AU  - Zhang, W.C.
TI  - Complete genome sequence of the bacteria Ketogulonicigenium vulgare Y25.
JO  - J. Bacteriol.
PY  - 2010
SP  - 315
EP  - 316
VL  - 193
AB  - Ketogulonicigenium vulgare is characterized by the efficient production of 2KGA from
AB  - L-sorbose. Ketogulonicigenium vulgare Y25 is known as a 2-keto-L-gulonic acid producing strain
AB  - in vitamin C industry. Here we report the finished, annotated genome sequence of
AB  - Ketogulonicigenium vulgare Y25.
ER  -

TY  - JOUR
AU  - Xiong, X.H.
AU  - Zhi, J.J.
AU  - Yang, L.
AU  - Wang, J.H.
AU  - Zhao, Y.
AU  - Wang, X.
AU  - Cui, Y.J.
AU  - Dong, F.
AU  - Li, M.X.
AU  - Yang, Y.X.
AU  - Wei, N.
AU  - An, J.J.
AU  - Du, B.H.
AU  - Liang, L.
AU  - Zhang, J.S.
AU  - Zhou, W.
AU  - Cheng, S.F.
AU  - He, T.
AU  - Wang, L.
AU  - Chen, H.P.
AU  - Liu, D.S.
AU  - Zhang, W.C.
TI  - Complete genome sequence of the bacterium Methylovorus sp. strain MP688, a high-level producer of pyrroloquinolone quinone.
JO  - J. Bacteriol.
PY  - 2011
SP  - 1012
EP  - 1013
VL  - 193
AB  - Methylotrophic bacteria are widespread microbes which can use one carbon compound as their
AB  - only carbon and energy sources. Here we report the finished, annotated
AB  - genome sequence of the methylotrophic bacterium Methylovorus sp. strain MP688,
AB  - which was isolated from soil for high-level production of pyrroloquinolone
AB  - quinone (PQQ) in our lab.
ER  -

TY  - JOUR
AU  - Xiong, Y.
AU  - Elckbush, T.H.
TI  - Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm.
JO  - Cell
PY  - 1988
SP  - 235
EP  - 246
VL  - 55
AB  - A fraction of the 28S ribosomal genes in certain insect species is interrupted by the
AB  - insertion elements R1 and R2. These two elements from the silkworm Bombyx mori (R~1Bm and
AB  - R2Bm) are retrotransposons capable of transposing in a highly sequence-specific manner. We
AB  - report here the functional expression in E. coli of the entire single open reading frame of
AB  - R2Bm and show that it encodes a double-stranded endonuclease (integrase) that can specifically
AB  - cleave the 28S gene at the R2 insertion site. The resulting cleavage is a 4 bp staggered 5'
AB  - overhang. Deletion analysis of the 28S gene revealed that the DNA sequence required for
AB  - specific cleavage is asymmetric with respect to the actual insertion (cleavage) site, with
AB  - fewer than 10 bp required at one side and at least 24 bp at the other side of the site. A
AB  - model is proposed based on these and previous data to account for the sequence-specific
AB  - integration of the R2 retrotransposon.
ER  -

TY  - JOUR
AU  - Xiong, Y.
AU  - Wang, P.
AU  - Lan, R.
AU  - Ye, C.
AU  - Wang, H.
AU  - Ren, J.
AU  - Jing, H.
AU  - Wang, Y.
AU  - Zhou, Z.
AU  - Bai, X.
AU  - Cui, Z.
AU  - Luo, X.
AU  - Zhao, A.
AU  - Wang, Y.
AU  - Zhang, S.
AU  - Sun, H.
AU  - Wang, L.
AU  - Xu, J.
TI  - A Novel Escherichia coli O157:H7 Clone Causing a Major Hemolytic Uremic Syndrome Outbreak in China.
JO  - PLoS ONE
PY  - 2012
SP  - E36144
EP  - E36144
VL  - 7
AB  - An Escherichia coli O157:H7 outbreak in China in 1999 caused 177 deaths due to
AB  - hemolytic uremic syndrome. Sixteen outbreak associated isolates were found to
AB  - belong to a new clone, sequence type 96 (ST96), based on multilocus sequence
AB  - typing of 15 housekeeping genes. Whole genome sequencing of an outbreak isolate,
AB  - Xuzhou21, showed that the isolate is phylogenetically closely related to the
AB  - Japan 1996 outbreak isolate Sakai, both of which share the most recent common
AB  - ancestor with the US outbreak isolate EDL933. The levels of IL-6 and IL-8 of
AB  - peripheral blood mononuclear cells induced by Xuzhou21 and Sakai were
AB  - significantly higher than that induced by EDL933. Xuzhou21 also induced a
AB  - significantly higher level of IL-8 than Sakai while both induced similar levels
AB  - of IL-6. The expression level of Shiga toxin 2 in Xuzhou21 induced by mitomycin C
AB  - was 68.6 times of that under non-inducing conditions, twice of that induced in
AB  - Sakai (32.7 times) and 15 times higher than that induced in EDL933 (4.5 times).
AB  - Our study shows that ST96 is a novel clone and provided significant new insights
AB  - into the evolution of virulence of E. coli O157:H7.
ER  -

TY  - JOUR
AU  - Xiong, Z.
AU  - Jiang, Y.
AU  - Qi, D.
AU  - Lu, H.
AU  - Yang, F.
AU  - Yang, J.
AU  - Chen, L.
AU  - Sun, L.
AU  - Xu, X.
AU  - Xue, Y.
AU  - Zhu, Y.
AU  - Jin, Q.
TI  - Complete genome sequence of the extremophilic Bacillus cereus strain Q1 with industrial applications.
JO  - J. Bacteriol.
PY  - 2009
SP  - 1120
EP  - 1121
VL  - 191
AB  - Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil
AB  - field in northeastern China. This strain is
AB  - able to produce biosurfactants and to survive in extreme environments.
AB  - Here we report the finished and annotated genome sequence of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Xiong, Z.
AU  - Laird, P.W.
TI  - COBRA: a sensitive and quantitative DNA methylation assay.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 2532
EP  - 2534
VL  - 25
AB  - We report here on a quantitative technique called COBRA to determine DNA methylation levels at
AB  - specific gene loci in small amounts of genomic DNA.  Restriction enzyme digestion is used to
AB  - reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated
AB  - DNA as described previously.  We show that methylation levels in the original DNA sample are
AB  - represented by the relative amounts of digested and undigested PCR product in a linearly
AB  - quantitative fashion across a wide spectrum of DNA methylation levels.  In addition, we show
AB  - that this technique can be reliably applied to DNA obtained from microdissected
AB  - paraffin-embedded tissue samples.  COBRA thus combines the powerful features of ease of use,
AB  - quantitative accuracy, and compatibility with paraffin sections.
ER  -

TY  - JOUR
AU  - Xiong, Z.Q.
AU  - Wang, Y.
TI  - Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated  from the Yellow Sea, China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6622
EP  - 6623
VL  - 194
AB  - Here, we report the draft genome sequence of Streptomyces sp. strain AA0539, isolated from
AB  - marine sediment of the Yellow Sea, China. Its small genome (
AB  - approximately 5.8 Mb) contains large, unique genes and gene clusters for diverse
AB  - secondary metabolites, suggesting great potential as a source for the discovery
AB  - of novel natural products.
ER  -

TY  - JOUR
AU  - Xiong, Z.Q.
AU  - Wang, Y.
TI  - Draft Genome Sequence of the Marine Streptomyces sp. Strain AA1529, Isolated from the Yellow Sea.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5474
EP  - 5475
VL  - 194
AB  - Here we report the draft genome sequence of a Streptomyces strain, AA1529, isolated from
AB  - marine sediment from the Yellow Sea. Its genome contains a subset
AB  - of unique genes and gene clusters that encode diverse secondary metabolites,
AB  - suggesting great potential as a source for the discovery of novel gene clusters
AB  - and bioactive compounds.
ER  -

TY  - JOUR
AU  - Xu, A.
AU  - Hertrich, S.
AU  - Needleman, D.S.
AU  - Sheen, S.
AU  - Sommers, C.
TI  - Draft Genome Sequences of Four Uropathogenic Escherichia coli Serotype O4:H5 Isolates (ATCC 700414, 700415, 700416, and 700417).
JO  - Genome Announcements
PY  - 2018
SP  - e00134
EP  - e00118
VL  - 6
AB  - Uropathogenic Escherichia coli serotype O4:H5 isolates (ATCC 700414, 700415, 700416, and
AB  - 700417) were recovered from women with first-time urinary tract
AB  - infections. Here, we report the draft genome sequences for these four E. coli
AB  - isolates, which are currently being used to validate food safety processing
AB  - technologies.
ER  -

TY  - JOUR
AU  - Xu, A.
AU  - Johnson, J.R.
AU  - Sheen, S.
AU  - Needleman, D.S.
AU  - Sommers, C.
TI  - Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia  coli Isolates from Retail Chicken Meat.
JO  - Genome Announcements
PY  - 2018
SP  - e00449
EP  - e00418
VL  - 6
AB  - Potential extraintestinal pathogenic Escherichia coli strains DP254, WH333, WH398, F356,
AB  - FEX675, and FEX725 were isolated from retail chicken meat products.
AB  - Here, we report the draft genome sequences for these six E. coli isolates, which
AB  - are currently being used in food safety research.
ER  -

TY  - JOUR
AU  - Xu, A.
AU  - Johnson, J.R.
AU  - Sheen, S.
AU  - Sommers, C.
TI  - Draft Genome Sequences of Five Neonatal Meningitis-Causing Escherichia coli Isolates (SP-4, SP-5, SP-13, SP-46, and SP-65).
JO  - Genome Announcements
PY  - 2018
SP  - e00091
EP  - e00018
VL  - 6
AB  - Neonatal meningitis-causing Escherichia coli isolates (SP-4, SP-5, SP-13, SP-46,  and SP-65)
AB  - were recovered between 1989 and 1997 from infants in the Netherlands.
AB  - Here, we report the draft genome sequences of these five E. coli isolates, which
AB  - are currently being used to validate food safety processing technologies.
ER  -

TY  - JOUR
AU  - Xu, A.
AU  - Tilman, S.
AU  - Wisser-Parker, K.
AU  - Scullen, O.J.
AU  - Sommers, C.H.
TI  - Draft Genomic Sequences of Nine Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Skin.
JO  - Microbiol. Resour. Announc.
PY  - 2018
SP  - e00859
EP  - e00818
VL  - 7
AB  - Extraintestinal pathogenic Escherichia coli strains were isolated from retail chicken skin.
AB  - Here, we report the draft genomic sequences for these nine E. coli
AB  - isolates, which are currently being used in agricultural and food safety
AB  - research.
ER  -

TY  - JOUR
AU  - Xu, C.
AU  - Song, J.
AU  - Ding, Y.
AU  - Yu, F.
AU  - Sun, L.
AU  - Tang, L.
AU  - Hu, X.
AU  - Zhang, Z.
AU  - He, J.
TI  - Crystallization and preliminary X-ray analysis of Sau3AI/E64A mutant protein.
JO  - Protein Pept. Lett.
PY  - 2007
SP  - 505
EP  - 506
VL  - 14
AB  - Sau3AI is a type II restriction endonuclease that recognizes the palindromic sequence
AB  - 5'-GATC-3' and cleaves 5' to G residue on each
AB  - strand. The E64A mutant full length protein was cloned and expressed in
AB  - Escherichia coli. The purified (His) (6)-tagged protein has monomer and
AB  - dimer fraction and was crystallized by the hanging-drop vapor-diffusion
AB  - technique. The dimer protein crystals can diffract to 3.0A. resolution and
AB  - the monomer protein crystals can diffract to better than 2.8A. resolution.
AB  - One completed dataset has been collected and it shows that the monomer
AB  - orthorhombic Sau3AI/E64A crystal is in space group C2221 with unit cell
AB  - parameters (69.44, 197.60, 191.46, 90, 90, 90) and contains two molecules
AB  - in one asymmetric unit.
ER  -

TY  - JOUR
AU  - Xu, D.
AU  - Cisar, J.O.
AU  - Poly, F.
AU  - Yang, J.
AU  - Albanese, J.
AU  - Dharmasena, M.
AU  - Wai, T.
AU  - Guerry, P.
AU  - Kopecko, D.J.
TI  - Genome Sequence of Salmonella enterica Serovar Typhi Oral Vaccine Strain Ty21a.
JO  - Genome Announcements
PY  - 2013
SP  - e00650
EP  - e00613
VL  - 1
AB  - Attenuated Salmonella enterica serovar Typhi strain Ty21a is an important vaccine for
AB  - controlling typhoid fever and serves as an oral vector for delivering
AB  - heterologous antigens. The key attenuating features of this randomly mutated
AB  - strain remain in question. Genome sequencing has revealed 679 single nucleotide
AB  - polymorphisms (SNPs), and will help define alterations contributing to Ty21a
AB  - safety and immunogenicity.
ER  -

TY  - JOUR
AU  - Xu, F.
AU  - Gonzalez-Escalona, N.
AU  - Drees, K.P.
AU  - Sebra, R.P.
AU  - Cooper, V.S.
AU  - Jones, S.H.
AU  - Whistler, C.A.
TI  - Parallel evolution of two clades of a major Atlantic endemic Vibrio parahaemolyticus pathogen lineage by independent acquisition of related pathogenicity islands.
JO  - Appl. Environ. Microbiol.
PY  - 2017
SP  - e01168
EP  - e01117
VL  - 83
AB  - Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased
AB  - from locations with historically low disease incidence, such as the Northeast
AB  - United States (US). This change coincided with a bacterial population shift
AB  - towards human pathogenic variants occurring in part through the introduction of
AB  - several Pacific native lineages (ST36, ST43 and ST636) to near-shore areas off
AB  - the Atlantic coast of the Northeast US. Concomitantly, ST631 emerged as a major
AB  - endemic pathogen. Phylogenetic trees of clinical and environmental isolates
AB  - indicated that two clades diverged from a common ST631 ancestor, and in each of
AB  - these clades, a human pathogenic variant evolved independently through
AB  - acquisition of distinct Vibrio pathogenicity islands (VPaI). These VPaI differ
AB  - from each other and bear little resemblance to hemolysin-containing VPaI from
AB  - isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored
AB  - no hemolysins, or contained a chromosome I-inserted island we call VPaIbeta that
AB  - encodes a type three secretion system (T3SS2beta) typical of Trh
AB  - hemolysin-producers. The more clinically prevalent and clonal ST631 clade II had
AB  - an island we call VPaIgamma that encodes both tdh and trh and that was inserted
AB  - in chromosome II. VPaIgamma was derived from VPaIbeta but with some additional
AB  - acquired elements in common with VPaI carried by pandemic isolates, exemplifying
AB  - the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon
AB  - assays identified VPaIgamma-type islands containing tdh inserted adjacent to the
AB  - ure cluster in the three introduced Pacific and most other emergent lineages.
AB  - that collectively cause 67% of Northeast US infections as of 2016.IMPORTANCE The
AB  - availability of three different hemolysin genotypes in the ST631 lineage provided
AB  - a unique opportunity to employ genome comparisons to further our understanding of
AB  - the processes underlying pathogen evolution. The fact that two different
AB  - pathogenic clades arose in parallel from the same potentially benign lineage by
AB  - independent VPaI acquisition is surprising considering the historically low
AB  - prevalence of community members harboring VPaI in waters along the Northeast US
AB  - coast that could serve as the source of this material. This illustrates a
AB  - possible predisposition of some lineages to not only acquire foreign DNA but also
AB  - to become human pathogens. Whereas the underlying cause for the expansion of V.
AB  - parahaemolyticus lineages harboring VPaIgamma along the US Atlantic coast and
AB  - spread of this element to multiple lineages that underlies disease emergence is
AB  - not known, this work underscores the need to define the environment factors that
AB  - favor bacteria harboring VPaI in locations of emergent disease.
ER  -

TY  - JOUR
AU  - Xu, F.
AU  - Mao, C.
AU  - Ding, Y.
AU  - Rui, C.
AU  - Wu, L.
AU  - Shi, A.
AU  - Zhang, H.
AU  - Zhang, L.
AU  - Xu, Z.
TI  - Molecular and Enzymatic Profiles of Mammalian DNA Methyltransferases: Structures and Targets for Drugs.
JO  - Curr. Med. Chem.
PY  - 2010
SP  - 4052
EP  - 4071
VL  - 17
AB  - DNA methylation is an epigenetic event involved in a variety array of processes that may be
AB  - the foundation of genetic phenomena and diseases.
AB  - DNA methyltransferase is a key enzyme for cytosine methylation in DNA,
AB  - and can be divided into two functional families (Dnmt1 and Dnmt3) in
AB  - mammals. All mammalian DNA methyltransferases are encoded by their own
AB  - single gene, and consisted of catalytic and regulatory regions (except
AB  - Dnmt2). Via interactions between functional domains in the regulatory
AB  - or catalytic regions and other adaptors or cofactors, DNA
AB  - methyltransferases can be localized at selective areas (specific
AB  - DNA/nucleotide sequence) and linked to specific chromosome status
AB  - (euchromatin/ heterochromatin, various histone modification status).
AB  - With assistance from UHRF1 and Dnmt3L or other factors in Dnmt1 and
AB  - Dnmt3a/Dnmt3b, mammalian DNA methyltransferases can be recruited, and
AB  - then specifically bind to hemimethylated and unmethylated
AB  - double-stranded DNA sequence to maintain and de novo setup patterns for
AB  - DNA methylation. Complicated enzymatic steps catalyzed by DNA
AB  - methyltransferases include methyl group transferred from cofactor
AB  - Ado-Met to C5 position of the flipped-out cytosine in targeted DNA
AB  - duplex. In the light of the fact that different DNA methyltransferases
AB  - are divergent in both structures and functions, and use unique
AB  - reprogrammed or distorted routines in development of diseases, design
AB  - of new drugs targeting specific mammalian DNA methyltransferases or
AB  - their adaptors in the control of key steps in either maintenance or de
AB  - novo DNA methylation processes will contribute to individually treating
AB  - diseases related to DNA methyltransferases.
ER  -

TY  - JOUR
AU  - Xu, F.
AU  - Miao, D.
AU  - Du, Y.
AU  - Chen, X.
AU  - Zhang, P.
AU  - Sun, H.
TI  - Draft Genome Sequence of Avibacterium paragallinarum Strain 221.
JO  - Genome Announcements
PY  - 2013
SP  - e00290
EP  - e00213
VL  - 1
AB  - Avibacterium paragallinarum is the causative agent of infectious coryza. Here we  report the
AB  - draft genome sequence of reference strain 221 of A. paragallinarum serovar A. The genome is
AB  - composed of 135 contigs for 2,685,568 bp with a 41% G+C content.
ER  -

TY  - JOUR
AU  - Xu, G.
AU  - Davis, M.
AU  - Glickman, F.
AU  - Reich, N.
TI  - Purification and initial characterization of the murine cytosine DNA methyltransferase.
JO  - FASEB J.
PY  - 1993
SP  - A1175
EP  - A1175
VL  - 7
AB  - The murine DNA (cytosine-5-)-methyltransferase (MTase EC 2.1.1.37) transfers methyl groups
AB  - from S-adenosylmethionine to the 5-position of cytosine in the nucleotide pair dCpdG of DNA.
AB  - The methylation of cytosine residues on mammalian DNA has been implicated in the regulation of
AB  - gene expression. Our goal is to study the chemical mechanism of cytosine methylation and to
AB  - characterize the basis of the enzyme specificity. DNA MTase was purified to homogeneity from
AB  - nuclear extracts of Friend murine erythroleukemia cells (MEL cells). Chromatographic
AB  - purification of DNA MTase carried out on DEAE-Sepharose Fast Flow medium brought about a
AB  - 6-fold increase in the specific activity of DNA MTase. Further purification of the enzyme was
AB  - achieved by precipitation by 30% saturated ammonium sulfate solution and chromatography on
AB  - Phenyl-Sepharose 6 Fast Flow medium. The purification step brought a 21-fold increase in
AB  - specific activity of the enzyme. After chromatographic separation of DNA MTase on
AB  - phenylsepharose, purification using a Hiload superdex 200 column provided DNA MTase with
AB  - 80-fold higher specific activity. We are currently characterizing the enzyme-substrate
AB  - interaction.
ER  -

TY  - JOUR
AU  - Xu, G.
AU  - Flynn, J.
AU  - Glickman, J.F.
AU  - Reich, N.O.
TI  - Purification and stabilization of mouse DNA methyltransferase.
JO  - Biochem. Biophys. Res. Commun.
PY  - 1995
SP  - 544
EP  - 551
VL  - 207
AB  - Cytosine methylation within DNA has been implicated in genetic imprinting, X-chromosome
AB  - inactivation, regulation of tissue-specific gene expression, aging, and cancer. Unfortunately,
AB  - DNA (cytosine-5)-methyltransferases (EC 2.1.1.37) from various mammalian sources have been
AB  - difficult to isolate and stabilize, precluding investigations of these critical enzymes. We
AB  - describe a novel FPLC purification of the 190,000 Mr DNA methyltransferase from mouse Friend
AB  - erythroleukemia cells. The homogeneous 190 kD Mr form of the enzyme is the only polypeptide
AB  - detected at various stages of cell growth and has not undergone detectable N-terminal
AB  - proteolysis.
ER  -

TY  - JOUR
AU  - Xu, G.
AU  - Hu, J.
AU  - Fang, X.
AU  - Zhang, X.
AU  - Wang, J.
AU  - Guo, Y.
AU  - Li, T.
AU  - Chen, Z.
AU  - Dai, W.
AU  - Liu, C.
TI  - Genome Sequence of Pseudomonas aeruginosa Strain LCT-PA220, Which Was Selected after Space Flight by Using Biolog's Powerful Carbon Source Utilization  Technology.
JO  - Genome Announcements
PY  - 2014
SP  - e00169
EP  - e00114
VL  - 2
AB  - To explore the changes of Pseudomonas aeruginosa in space flight, we present the  draft genome
AB  - sequence of P. aeruginosa strain LCT-PA220, which originated from a
AB  - P. aeruginosa strain, ATCC 27853, that traveled on the Shenzhou-VIII spacecraft.
ER  -

TY  - JOUR
AU  - Xu, G.
AU  - Willert, J.
AU  - Kapfer, W.
AU  - Trautner, T.A.
TI  - BsuCI, a type-I restriction-modification system in Bacillus subtilis.
JO  - Gene
PY  - 1995
SP  - 59
EP  - 59
VL  - 157
AB  - A type-I R-M system was identified in B. subtilis.  The genes comprising the system have
AB  - striking similarity to type-I R-M systems observed in Enterobacteriaceae.
ER  -

TY  - JOUR
AU  - Xu, G.-L.
AU  - Bestor, T.H.
TI  - Cytosine methylation targetted to pre-determined sequences.
JO  - Nat. Genet.
PY  - 1997
SP  - 376
EP  - 378
VL  - 17
AB  - The incidence or severity of a number of human diseases is proportional to the activity of
AB  - individual viral transcription units or mutant endogenous genes.  Targetted methylation of
AB  - regulatory sites is proposed as a new method for selective gene inactivation that stimulates
AB  - an existing biological response.  Mammalian promoters are usually inactive when methylated at
AB  - CpG dinucleotides, and patterns of methylated CpG sites are replicated with the DNA during S
AB  - phase.  Pre-determined sequence specificities have now been conferred upon a DNA
AB  - methyltransferase by fusion to zinc-finger proteins.  The sequence specificity of zinc-finger
AB  - proteins can be modified to direct cytosine methylation to the promoters of target genes.
ER  -

TY  - JOUR
AU  - Xu, G.-L.
AU  - Bestor, T.H.
AU  - Bourchis, D.
AU  - Hsieh, C.-L.
AU  - Tommerup, N.
AU  - Bugge, M.
AU  - Hulten, M.
AU  - Qu, X.
AU  - Russo, J.J.
AU  - Viegas-Pequignot, E.
TI  - Chromosome instability and imunodeficiency syndrome caused by mutations in a DNA methyltransferase gene.
JO  - Nature
PY  - 1999
SP  - 187
EP  - 191
VL  - 402
AB  - The recessive autosomal disorder known as ICF syndrome (for immunodeficiency, centromere
AB  - instability and facial anomalies; Mendelian Inheritance in Man number 242860) is characterized
AB  - by variable reductions in serum immunoglobulin levels which cause most ICF patients to succumb
AB  - to infectious diseases before adulthood.  Mild facial anomalies include hypertelorism, low-set
AB  - ears, epicanthal folds and macroglossia.  The cytogenetic abnormalities in lymphocytes are
AB  - exuberant: juxtacentromeric heterochromatin is greatly elongated and thread-like in metaphase
AB  - chromsomes, which is associated with the formation of complex multiradiate chromosomes.  The
AB  - same juxtacentromeric regions are subject to persistent interphase self-associations and are
AB  - extruded into nuclear blebs or micronuclei.  Abnormalities are largely confined to tracts of
AB  - classical satellites 2 and 3 at juxtacentromeric regions of chromosomes 1, 9 and 16.
AB  - Classical satellite DNA is normally heavily methylated at cytosine residues, but in ICF
AB  - syndrome it is almost completely unmethylated in all tissues.  ICF syndrome is the only
AB  - genetic disorder known to involve constitutive abnormalities of genomic methylation patterns.
AB  - Here we show that five unrelated ICF patients have mutations in both alleles of the gene that
AB  - encodes DNA methyltransferase 3B.  Cytosine methylation is essential for the organization and
AB  - stabilization of a specific type of heterochromatin, and this methylation appears to be
AB  - carried out by an enzyme specialized for the purpose.
ER  -

TY  - JOUR
AU  - Xu, G.L.
AU  - Kapfer, W.
AU  - Walter, J.
AU  - Trautner, T.A.
TI  - BsuBI-an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 6517
EP  - 6523
VL  - 20
AB  - The enzymes of the Bacillus subtilis BsuBI restriction/modification (R/M) system recognize the
AB  - target sequence 5'CTGCAG. The genes of the BsuBI R/M system have been cloned and sequenced
AB  - and their products have been characterized following overexpression and purification. The gene
AB  - of the BsuBI DNA methyltransferase (M.BsuBI) consists of 1503 bp, encoding a protein of 501
AB  - amino acids with a calculated Mr of 57.2 kD. The gene of the restriction endonuclease
AB  - (R.BsuBI), comprising 948 bp, codes for a protein of 316 amino acids with a predicted Mr of
AB  - 36.2 kD. M.BsuBI modifies the adenine (A) residue of the BsuBI target site, thus representing
AB  - the first A-N6_DNA methyltransferase identified in B. subtilis. Like R.PstI, R.BsuBI cleaves
AB  - between the A residue and the 3' terminal G of the target site. Both enzymes of the BsuBI R/M
AB  - system are, therefore, functionally identical with those of the PstI R/M system, encoded by
AB  - the Gram negative species Providencia stuartii. This functional equivalence coincides with a
AB  - pronounced similarity of the BsuBI/PstI DNA methyltransferases (41% amino acid identity) and
AB  - restriction endonucleases (46% amino acid identity). Since the genes are also very similar
AB  - (58% nucleotide identity), the BsuBI and PstI R/M systems apparently have a common
AB  - evolutionary origin. In spite of the sequence conservation the gene organization is strikingly
AB  - different in the two R/M systems. While the genes of the PstI R/M system are separated and
AB  - transcribed divergently, the genes of the BsuBI R/M system are transcribed in the same
AB  - direction with the 3' end of the M gene overlapping the 5' end of the R gene by 17 bp.
ER  -

TY  - JOUR
AU  - Xu, H.
AU  - Han, D.
AU  - Xu, Z.
TI  - Overexpression of a lethal methylase, M.TneDI, in E-coli B1(DE3).
JO  - Biotechnol. Lett.
PY  - 2014
SP  - 1853
EP  - 1859
VL  - 36
AB  - A pET-based vector pDH21 expressing the methylase, M.TneDI (recognizing CGCG) from Thermotoga
AB  - was constructed, and transformed into E. coli B1(DE3). Despite E. coli B1(DE3) being McrBC
AB  - positive, 30 transformants were isolated, which were suspected to be McrBC(-) mutants. The
AB  - overexpression of M.TneDI was verified by SDS-PAGE analysis. Compared to the previously
AB  - constructed pJC340 vector, a pACYC184 derivative expressing M.TneDI from a tet promotor, the
AB  - newly constructed pDH21 vector improved the expression of the methylase about fourfold,
AB  - allowing complete protection of DNA substrates. This study not only demonstrates a practical
AB  - approach to overexpressing potential lethal proteins in E. coli but also delivers a production
AB  - strain of M.TneDI that may be useful in various in vitro methylation applications.
ER  -

TY  - JOUR
AU  - Xu, J. et al.
TI  - Evolution of Symbiotic Bacteria in the Distal Human Intestine.
JO  - PLoS Biology
PY  - 2007
SP  - e156
EP  - e156
VL  - 5
AB  - The adult human intestine contains trillions of bacteria, representing hundreds of species and
AB  - thousands of subspecies. Little is known about the
AB  - selective pressures that have shaped and are shaping this community's
AB  - component species, which are dominated by members of the Bacteroidetes and
AB  - Firmicutes divisions. To examine how the intestinal environment affects
AB  - microbial genome evolution, we have sequenced the genomes of two members
AB  - of the normal distal human gut microbiota, Bacteroides vulgatus and
AB  - Bacteroides distasonis, and by comparison with the few other sequenced gut
AB  - and non-gut Bacteroidetes, analyzed their niche and habitat adaptations.
AB  - The results show that lateral gene transfer, mobile elements, and gene
AB  - amplification have played important roles in affecting the ability of
AB  - gut-dwelling Bacteroidetes to vary their cell surface, sense their
AB  - environment, and harvest nutrient resources present in the distal
AB  - intestine. Our findings show that these processes have been a driving
AB  - force in the adaptation of Bacteroidetes to the distal gut environment,
AB  - and emphasize the importance of considering the evolution of humans from
AB  - an additional perspective, namely the evolution of our microbiomes.
ER  -

TY  - JOUR
AU  - Xu, J.
AU  - Bjursell, M.K.
AU  - Himrod, J.
AU  - Deng, S.
AU  - Carmichael, L.K.
AU  - Chiang, H.C.
AU  - Hooper, L.V.
AU  - Gordon, J.I.
TI  - A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.
JO  - Science
PY  - 2003
SP  - 2074
EP  - 2076
VL  - 299
AB  - The human gut is colonized with a vast community of indigenous microorganisms that help shape
AB  - our biology. Here, we present the complete
AB  - genome sequence of the Gram-negative anaerobe Bacteroides
AB  - thetaiotaomicron, a dominant member of our normal distal intestinal
AB  - microbiota. Its 4779-member proteome includes an elaborate apparatus for
AB  - acquiring and hydrolyzing otherwise indigestible dietary polysaccharides
AB  - and an associated environment-sensing system consisting of a large
AB  - repertoire of extracytoplasmic function sigma factors and one- and
AB  - two-component signal transduction systems. These and other expanded
AB  - paralogous groups shed light on the molecular mechanisms underlying
AB  - symbiotic host-bacterial relationships in our intestine.
ER  -

TY  - JOUR
AU  - Xu, J.
AU  - Xu, M.
AU  - Liu, K.
AU  - Peng, Q.
AU  - Tao, M.
TI  - Complete Genome Sequence of Streptomyces sp. Sge12, Which Produces Antibacterial  and Fungicidal Activities.
JO  - Genome Announcements
PY  - 2017
SP  - e00415
EP  - e00417
VL  - 5
AB  - Streptomyces sp. Sge12 was isolated from forest soil and exhibited remarkable antimicrobial
AB  - activities against selected fungi and Gram-positive bacteria. Here,
AB  - we report the complete genome sequence of this strain, which contains 37 putative
AB  - secondary metabolite gene clusters.
ER  -

TY  - JOUR
AU  - Xu, J.
AU  - Zheng, H.J.
AU  - Liu, L.
AU  - Pan, Z.C.
AU  - Prior, P.
AU  - Tang, B.
AU  - Xu, J.S.
AU  - Zhang, H.
AU  - Tian, Q.
AU  - Zhang, L.Q.
AU  - Feng, J.
TI  - Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain Po82.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4261
EP  - 4262
VL  - 193
AB  - Ralstonia solanacearum strain Po82, a phylotype IIB/sequevar 4 strain, was found to be
AB  - pathogenic to both solanaceous plants and banana. Here, we
AB  - report the complete genome sequence of Po82 and its comparison with seven
AB  - published R. solanacearum genomes.
ER  -

TY  - JOUR
AU  - Xu, K.
AU  - Su, F.
AU  - Tao, F.
AU  - Li, C.
AU  - Ni, J.
AU  - Xu, P.
TI  - Genome Sequences of Two Morphologically Distinct and Thermophilic Bacillus coagulans Strains, H-1 and XZL9.
JO  - Genome Announcements
PY  - 2013
SP  - e00254
EP  - e00213
VL  - 1
AB  - Two thermophilic Bacillus coagulans strains, H-1 and XZL9, both of which were isolated from
AB  - soils, have different morphological properties. Strain XZL9 but not
AB  - H-1 is an efficient pentose-utilizing producer of important platform compounds,
AB  - such as l-lactic acid and 2,3-butanediol. Here we announce the 2.86- and 3.43-Mb
AB  - sequences of their genomes.
ER  -

TY  - JOUR
AU  - Xu, L.
AU  - Shi, W.
AU  - Zeng, X.C.
AU  - Yang, Y.
AU  - Zhou, L.
AU  - Mu, Y.
AU  - Liu, Y.
TI  - Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 11
EP  - 11
VL  - 12
AB  - Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium, isolated
AB  - from the arsenic-contaminated aquifer sediment in the Datong
AB  - basin, China. This strain displays high resistance to arsenic, and can
AB  - dynamically transform arsenic under aerobic condition. Here, we described the
AB  - high quality draft genome sequence, annotations and the features of Arthrobacter
AB  - sp. B6. The G + C content of the genome is 64.67%. This strain has a genome size
AB  - of 4,663,437 bp; the genome is arranged in 8 scaffolds that contain 25 contigs.
AB  - From the sequences, 3956 protein-coding genes, 264 pseudo genes and 89
AB  - tRNA/rRNA-encoding genes were identified. The genome analysis of this strain
AB  - helps to better understand the mechanism by which the microbe efficiently
AB  - tolerates arsenic in the arsenic-contaminated environment.
ER  -

TY  - JOUR
AU  - Xu, L.
AU  - Yin, M.
AU  - Zhu, T.
AU  - Liu, Y.
AU  - Ying, Y.
AU  - Lu, J.
AU  - Lin, C.
AU  - Ying, J.
AU  - Xu, T.
AU  - Ni, L.
AU  - Bao, Q.
AU  - Lu, S.
TI  - Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989.
JO  - Int. J. Genomics
PY  - 2018
SP  - 1242819
EP  - 1242819
VL  - 2018
AB  - Pantoea vagans, a gram-negative bacterium from the genus Pantoea and family
AB  - Enterobacteriaceae, is present in various natural environments and considered to
AB  - be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic
AB  - and sequenced its whole genome. Besides a chromosome DNA molecule, it also
AB  - harboured three large plasmids. A comparative genomics analysis was performed for
AB  - the smallest plasmid, pPV989-94. It can be divided into four regions, including
AB  - three conservative regions related to replication (R1), transfer conjugation
AB  - (R2), and transfer leading (R3), and one variable region (R4). Further analysis
AB  - showed that pPV989-94 is most similar to plasmids LA637P2 and pEA68 of Erwinia
AB  - amylovora strains isolated from fruit trees. These three plasmids share three
AB  - conservative regions (R1, R2, and R3). Interestingly, a fragment (R4') in R4,
AB  - mediated by phage integrase and phage integrase family site-specific recombinase
AB  - and encoding 9 genes related to glycometabolism, resistance, and DNA repair, was
AB  - unique in pPV989-94. Homologues of R4' were found in other plasmids or
AB  - chromosomes, suggesting that horizontal gene transfer (HGT) occurred among
AB  - different bacteria of various species or genera. The acquired functional genes
AB  - may play important roles in the adaptation of bacteria to different hosts or
AB  - environmental conditions.
ER  -

TY  - JOUR
AU  - Xu, M.
AU  - Fang, Y.
AU  - Liu, J.
AU  - Chen, X.
AU  - Sun, G.
AU  - Guo, J.
AU  - Hua, Z.
AU  - Tu, Q.
AU  - Wu, L.
AU  - Zhou, J.
AU  - Liu, X.
TI  - Draft Genome Sequence of Shewanella decolorationis S12, a Dye-Degrading Bacterium Isolated from a Wastewater Treatment Plant.
JO  - Genome Announcements
PY  - 2013
SP  - e00993
EP  - e00913
VL  - 1
AB  - Shewanella decolorationis is a valuable microorganism for degrading diverse synthetic textile
AB  - dyes. Here, we present an annotated draft genome sequence of S.
AB  - decolorationis S12, which contains 4,219 protein-coding genes and 86 structural
AB  - RNAs. This information regarding the genetic basis of this bacterium can greatly
AB  - advance our understanding of the physiology of this species.
ER  -

TY  - JOUR
AU  - Xu, M.
AU  - Kladde, M.P.
AU  - Van Etten, J.L.
AU  - Simpson, R.T.
TI  - Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC.
JO  - Nucleic Acids Res.
PY  - 1998
SP  - 3961
EP  - 3966
VL  - 26
AB  - A novel gene encoding a cytosine-5-DNA methyltransferase recognizing the dinucleotide GpC was
AB  - cloned from Chlorella virus NYs-1 and expressed in both Escherichia coli and Saccharomyces
AB  - cerevisiae.  The gene was sequenced and a predicted polypeptide of 362 amino acids with a
AB  - molecular weight of 41.903 kDa was identified.  The protein contains several amino acid motifs
AB  - with high similarity to those of other known 5-methylcytosine-forming methyltransferases.  In
AB  - addition, this enzyme, named M.CviPI, shares 66% identity and 76% similarity with M.CviJI, the
AB  - other only cytosine-5-DNA methyltransferase cloned from a Chlorella virus.  The short,
AB  - frequently occurring recognition sequence of the new methyltransferase will be very useful for
AB  - in vivo chromatin structure studies in both yeast and higher organisms.
ER  -

TY  - JOUR
AU  - Xu, M.-Q.
AU  - Comb, D.G.
AU  - Paulus, H.
AU  - Noren, C.J.
AU  - Shao, Y.
AU  - Perler, F.B.
TI  - Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation.
JO  - EMBO J.
PY  - 1994
SP  - 5517
EP  - 5522
VL  - 13
AB  - Protein splicing involves the excision of an internal domain from a
AB  - precursor protein and the ligation of the external domains so as to generate two new
AB  - proteins.  Study of this process has recently been facilitated by the isolation of a precursor
AB  - and a branched intermediate from a thermophilic protein splicing element expressed in a
AB  - foreign protein context.  Two aspects of protein splicing are examined in this paper.  We
AB  - demonstrate a succinimide at the C-terminus of the spliced internal protein, implicating
AB  - cyclization of asparagine in resolution of the branched intermediate, and we identify an
AB  - alkali-labile bond in the branched intermediate.  A revised protein splicing model based on
AB  - these experimental results is presented.
ER  -

TY  - JOUR
AU  - Xu, M.-Q.
AU  - Perler, F.B.
TI  - The mechanism of protein splicing and its modulation by mutation.
JO  - EMBO J.
PY  - 1996
SP  - 5146
EP  - 5153
VL  - 15
AB  - Protein splicing results in the expression of two mature proteins from a single gene.  After
AB  - synthesis of a precursor protein, an internal segment (the intein) is excised and the external
AB  - domains are joined together.  A self-catalyzed mechanism for this cleavage-ligation reaction
AB  - is presented, based on mutagenesis data and analysis of splicing intermediates.  Mutations
AB  - were used to block various steps in the protein splicing pathway, allowing each isolated step
AB  - to be studied independently.  A linear ester intermediate was identified and functional roles
AB  - for the four conserved splice junction residues were determined.  Understanding the mechanism
AB  - of protein splicing provides a basis for protein engineering studies.  For example, inteins
AB  - can be constructed which fail to splice, but instead cleave the peptide bond at a chosen
AB  - splice junction.
ER  -

TY  - JOUR
AU  - Xu, M.-Q.
AU  - Shub, D.A.
TI  - The catalytic core of the sunY intron of bacteriophage T4.
JO  - Gene
PY  - 1989
SP  - 77
EP  - 82
VL  - 82
AB  - The self-splicing sunY intron of bacteriophage T4 shares a common
AB  - secondary structure with
AB  - other group I introns.  A long open reading frame within the intron is entirely 3' of the
AB  - structural elements
AB  - conserved in all group I introns.  This catalytic core is the smallest yet described for a
AB  - self-
AB  - splicing intron.
AB  - An internal deletion of 728 nucleotides, leaving 196 nt at the 5' end and 109 nt at the 3'
AB  - end, allows normal
AB  - self-splicing.  Transcripts terminating 196 nt 3' of the 5' splice site retain catalytic
AB  - activity.
ER  -

TY  - JOUR
AU  - Xu, M.-Q.
AU  - Southworth, M.W.
AU  - Mersha, F.B.
AU  - Hornstra, L.J.
AU  - Perler, F.B.
TI  - In vitro protein splicing of purified precursor and the identification of a branched intermediate.
JO  - Cell
PY  - 1993
SP  - 1371
EP  - 1377
VL  - 75
AB  - Protein splicing is a posttranslational processing event in which an internal polypeptide is
AB  - excised from a protein precursor and the terminal polypeptides are then ligated together,
AB  - resulting in the production of two proteins. This report presents direct evidence for protein
AB  - splicing by demonstrating in vitro splicing of purified precursor that accumulated when the
AB  - protein splicing element from Pyrococcus DNA polymerase was cloned into a foreign gene. In
AB  - vitro splicing was temperature and pH dependent. A slowly migrating species exhibited kinetic
AB  - properties of a splicing intermediate and was shown to be a branched molecular by N-terminal
AB  - sequencing. The precursor and slowly migrating species were interconvertible in response to pH
AB  - shifts.
ER  -

TY  - JOUR
AU  - Xu, P.
AU  - Alves, J.M.
AU  - Kitten, T.
AU  - Brown, A.
AU  - Chen, Z.
AU  - Ozaki, L.S.
AU  - Manque, P.
AU  - Ge, X.
AU  - Serrano, M.G.
AU  - Puiu, D.
AU  - Hendricks, S.
AU  - Wang, Y.
AU  - Chaplin, M.D.
AU  - Akan, D.
AU  - Paik, S.
AU  - Peterson, D.L.
AU  - Macrina, F.L.
AU  - Buck, G.A.
TI  - Genome of the opportunistic pathogen Streptococcus sanguinis.
JO  - J. Bacteriol.
PY  - 2007
SP  - 3166
EP  - 3175
VL  - 189
AB  - The genome of S. sanguinis is a circular DNA molecule of 2,388,435 base pairs, 177-590 kb
AB  - larger than the other 21 sequenced streptococcal genomes. The GC content of the S. sanguinis
AB  - genome is 43.4%, considerably higher than that of other streptococci. The genome encodes 2,274
AB  - predicted proteins, 61 tRNAs and 4 ribosomal RNA operons. A 70-kb region containing pathways
AB  - for vitamin B12 biosynthesis and degradation of ethanolamine and propanediol was apparently
AB  - acquired by horizontal gene transfer. The gene complement suggests new hypotheses for the
AB  - pathogenesis and virulence of S. sanguinis, and provides comparative contrasts with other
AB  - pathogenic and non-pathogenic streptococci. In particular, S. sanguinis possesses a remarkable
AB  - abundance of putative surface proteins, which may permit it to serve as a primary colonizer of
AB  - the oral cavity and agent of streptococcal endocarditis and infection in neutropenic patients.
ER  -

TY  - JOUR
AU  - Xu, P.
AU  - Widmer, G.
AU  - Wang, Y.
AU  - Ozaki, L.S.
AU  - Alves, J.M.
AU  - Serrano, M.G.
AU  - Puiu, D.
AU  - Manque, P.
AU  - Akiyoshi, D.
AU  - Mackey, A.J.
AU  - Pearson, W.R.
AU  - Dear, P.H.
AU  - Bankier, A.T.
AU  - Peterson, D.L.
AU  - Abrahamsen, M.S.
AU  - Kapur, V.
AU  - Tzipori, S.
AU  - Buck, G.A.
TI  - The genome of Cryptosporidium hominis.
JO  - Nature
PY  - 2004
SP  - 1107
EP  - 1112
VL  - 431
AB  - Cryptosporidium species cause acute gastroenteritis and diarrhoea worldwide. They are members
AB  - of the Apicomplexa--protozoan pathogens that invade host cells by using a specialized apical
AB  - complex and are usually transmitted by an invertebrate vector or intermediate host. In
AB  - contrast to other Apicomplexans, Cryptosporidium is transmitted by ingestion of oocysts and
AB  - completes its life cycle in a single host. No therapy is available, and control focuses on
AB  - eliminating oocysts in water supplies. Two species, C. hominis and C. parvum, which differ in
AB  - host range, genotype and pathogenicity, are most relevant to humans. C. hominis is restricted
AB  - to humans, whereas C. parvum also infects other mammals. Here we describe the eight-chromosome
AB  - approximately 9.2-million-base genome of C. hominis. The complement of C. hominis
AB  - protein-coding genes shows a striking concordance with the requirements imposed by the
AB  - environmental niches the parasite inhabits. Energy metabolism is largely from glycolysis. Both
AB  - aerobic and anaerobic metabolisms are available, the former requiring an alternative electron
AB  - transport system in a simplified mitochondrion. Biosynthesis capabilities are limited,
AB  - explaining an extensive array of transporters. Evidence of an apicoplast is absent, but genes
AB  - associated with apical complex organelles are present. C. hominis and C. parvum exhibit very
AB  - similar gene complements, and phenotypic differences between these parasites must be due to
AB  - subtle sequence divergence.
ER  -

TY  - JOUR
AU  - Xu, P.
AU  - Yu, H.
AU  - Chakrabarty, A.M.
AU  - Xun, L.
TI  - Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100.
JO  - Genome Announcements
PY  - 2013
SP  - e00600
EP  - e00613
VL  - 1
AB  - Burkholderia phenoliruptrix strain AC1100 (ATCC 53867) degrades a variety of recalcitrant
AB  - xenobiotics, including 2,4,5-trichlorophenoxyacetate. The molecular
AB  - mechanism of 2,4,5-trichlorophenoxyacetate degradation has been extensively
AB  - studied. Here we present a 7.8-Mb assembly of the genome sequence of this
AB  - 2,4,5-trichlorophenoxyacetate-degrading strain, which may provide useful
AB  - information related to the degradation of chlorinated aromatic compounds.
ER  -

TY  - JOUR
AU  - Xu, Q.
TI  - Molecular analysis of restriction-modification systems in Helicobacter pylori.
JO  - Ph.D. Thesis, Vanderbilt University, Nashville, Tennessee
PY  - 1999
SP  - 1
EP  - 156
AB  - The phenomenon of restriction and modification in prokaryotes was first recognized more than
AB  - 40 years ago when investigators worked on phage infections.  Certain bacterial strains of
AB  - bacteria were found to inhibit the propagation of phages grown previously on a different
AB  - bacterial strain.  The effect was later traced to a DNA sequence-specific endonuclease.  The
AB  - DNA of phages previously grown on the different strain was degraded by this certain strain's
AB  - endonuclease, because the phage DNA lacked specific methylation in the sequence recognized by
AB  - the endonuclease.  However, the few phages that did succeed in infecting the bacteria, were
AB  - modified so that they grew normally on the new host in a second cycle of infection.  By the
AB  - beginning of the 1970's, first several restriction endonucleases including HindII, HindIII,
AB  - and EcoRI, were purified.  Sequence-specific endonucleases were later found to be useful for
AB  - analyzing and rearranging DNA.  Subsequent applications not only led to a major breakthrough
AB  - in the field of molecular biology, but also led to the extensive search for new ones.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Blaser, M.J.
TI  - Promoters of the CATG-specific methyltransferase gene hpyIM differ between iceA1 and iceA2 Helicobacter pylori strains.
JO  - J. Bacteriol.
PY  - 2001
SP  - 3875
EP  - 3884
VL  - 183
AB  - Helicobacter pylori strains can be divided into two groups, based on the presence of two
AB  - unrelated genes, iceA1 and iceA2, that occupy the same genomic locus. hpyIM, located
AB  - immediately downstream of either gene, encodes a functional CATG-specific methyltransferase.
AB  - Despite the strong conservation of the hpyIM open reading frame (ORF) among all H. pylori
AB  - strains, the sequences upstream of the ORF in iceA1 and iceA2 strains are substantially
AB  - different. To explore the roles of these upstream sequences in hpyIM regulation, promoter
AB  - analysis of hpyIM was performed. Both deletion mutation and primer extension analyses
AB  - demonstrate that the hpyIM promoters differ between H. pylori strains 60190 (iceA1) and J188
AB  - (iceA2). In strain 60190, hpyIM has two promoters, P(a) or P(I), which may function
AB  - independently, whereas only one hpyIM promoter, P(c), was found in strain J188. The XylE assay
AB  - showed that the hpyIM transcription level was much higher in strain 60190 than in strain J188,
AB  - indicating that regulation of hpyIM transcription differs between the H. pylori iceA1 strain
AB  - (60190) and iceA2 strains (J188). Since the iceA1 and iceA2 sequences are highly conserved
AB  - within iceA1 or iceA2 strains, we conclude that promoters of the CATG-specific methylase gene
AB  - hpyIM differ between iceA1 and iceA2 strains, which leads to differences in regulation of
AB  - hpyIM transcription.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Morgan, R.D.
AU  - Roberts, R.J.
AU  - Blaser, M.J.
TI  - Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2000
SP  - 9671
EP  - 9676
VL  - 97
AB  - A total of 22 type II restriction endonucleases with 18 distinct specificities have been
AB  - identified in six Helicobacter pylori strains. Among these 18 specificities are three
AB  - completely new endonucleases, Hpy178III, Hpy99I, and Hpy188I, that specifically cleave DNA at
AB  - TCNNGA, CGWCG, and TCNGA sites, respectively. The set of endonucleases identified in each
AB  - strain varies, but all have four- or five-base recognition sequences. Among 16 H. pylori
AB  - strains, examination of the DNA modification status at the recognition sites of 15 restriction
AB  - endonucleases reveals that each strain has a substantially different complement of type II
AB  - modification systems. We conclude that the type II restriction-modification systems in H.
AB  - pylori are highly diverse between strains, a unique characteristic of H. pylori. The diverse
AB  - methylation status of H. pylori chromosomal DNA may serve as a new typing system to
AB  - discriminate H. pylori isolates for epidemiological and clinical purposes. This study also
AB  - demonstrates that H. pylori is a rich source of type II restriction endonucleases.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Morgan, R.D.
AU  - Roberts, R.J.
AU  - Xu, S.Y.
AU  - van Doorn, L.J.
AU  - Donahue, J.P.
AU  - Miller, G.G.
AU  - Blaser, M.J.
TI  - Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - 3839
EP  - 3847
VL  - 30
AB  - iceA1 in Helicobacter pylori is a homolog of nlaIIIR, which encodes the CATG-specific
AB  - restriction endonuclease NlaIII in Neisseria lactamica. Analysis of iceA1 sequences from 49
AB  - H.pylori strains shows that a full-length NlaIII-like ORF is present in 10 strains, including
AB  - CH4, but in other strains, including strain 60190, the ORFs are truncated due to a variety of
AB  - mutations. Our goal was to determine whether iceA1 can encode a NlaIII-like endonuclease.
AB  - Overexpression in Escherichia coli of iceA1 from CH4, but not from 60190, yielded NlaIII-like
AB  - activity, indicating that the full-length iceA1 is a functional endonuclease gene. Repair of
AB  - the iceA1 frameshift mutation in strain 60190 and its expression in E.coli yielded functional
AB  - NlaIII-like activity. We conclude that iceA1 in CH4 is a functional restriction endonuclease
AB  - gene, while iceA1 in 60190 is not, due to a frameshift mutation, but that its repair restores
AB  - its restriction endonuclease activity.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Morgan, R.D.
AU  - Xu, S.Y.
AU  - van Doorn, L.J.
AU  - Donahue, J.P.
AU  - Miller, G.G.
AU  - Blaser, M.J.
TI  - H. pylori iceA1 is capable of encoding an NlaIII-like restriction endonuclease.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 2000
SP  - 291
EP  - 291
VL  - 100
AB  - H. pylori iceA1 has strong homology to nlaIIIR, which encodes NlaIII, a restriction
AB  - endonuclease in N. lactamica.  Our goal was to determine whether iceA1 encodes an NlaIII-like
AB  - RE.  Analysis of iceA1 sequences from 19 H. pylori strains was performed.  A full-length
AB  - NlaIII-like ORF is present in 4 strains including CH4, but iceA1 from 15 others, including
AB  - strain 60190, have various mutations.  Overexpression of iceA1 from CH4, but not from 60190,
AB  - in pAII17 vector in E. coli yielded NlaIII-like RE activity, indicating that it is a
AB  - functional gene.  To investigate the effect of mutations on iceA1 function, the frameshift
AB  - mutation of 60190 iceA1 was repaired.  The repaired 60190 iceA1 in pAII17 enabled expression
AB  - of a functional NlaIII-like RE in E. coli.  These results are consistent with biochemical
AB  - analysis of H. pylori, in which NlaIIII-like RE activity was detected in CH4, but not in 60190
AB  - cells.  We conclude that iceA1 in CH4 is a functional RE gene, and in 60190 is degenerate, but
AB  - that repair of its frameshift mutation restores its activity.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - O'Loughlin, T.J.
AU  - Kucera, R.B.
AU  - Schildkraut, I.
AU  - Guo, H.-C.
TI  - Structural study of restriction enzyme MspI/DNA complex by x-ray crystallography.
JO  - Biophys. J.
PY  - 2001
SP  - 296a
EP  - 296a
VL  - 80
AB  - The MspI restriction endonuclease is a type II restriction enzyme.  It recognizes the
AB  - palindromic sequence of four base pairs 5'-CCGG-3' and cleaves it between two cytosines,
AB  - leaving 5' two-base overhangs.  Owing to the nature of its cleavage pattern that is different
AB  - from all other restriction enzymes with known structure, it is likely that MspI could
AB  - represent a novel structural class of restriction endonucleases.  Solving the crystal
AB  - structure of MspI/DNA complex will allow us to examine the hypothesis that the cleavage
AB  - pattern is a result of intermediate organization of core architectures.  In addition, the
AB  - structure would provide us more information about the DNA recognition, specificity and
AB  - catalytic mechanisms of these enzymes.  Native crystals of the dimeric MspI restriction enzyme
AB  - bound to a duplex DNA molecule containing the specific recognition have been obtained in a P21
AB  - monoclinic unit cell with dimensions of a = 50.2A, b = 131.6A, c= 59.3A, beta = 109.7o.  The
AB  - crystals contain one dimeric complex in the asymmetric unit.  A complete native data set has
AB  - been collected to a resolution of 2.05A at beamline X12c at National Synchrotron Light Source
AB  - at Brookhaven National Laboratory.  Moreover, a complete MAD data set of Hg derivative and a
AB  - data set of Sm derivative have also been collected at X12c to the resolution of 3.2A and 2.6A,
AB  - respectively.  Phasing from these derivative data sets are currently underway.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Peek, R.
AU  - Miller, G.
AU  - Blaser, M.
TI  - Identification of an adenine methylase gene in Helicobacter pylori.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1997
SP  - 38
EP  - 38
VL  - 97
AB  - DNA methylation has been demonstrated to be involved in several important cellular processes
AB  - such as host-specific defense mechanisms, DNA mismatch repair, regulation of initiation of
AB  - chromosomal replication, regulation of gene transcription, and DNA transposition.  To
AB  - understand mechanisms of DNA methylation in H. pylori, a human pathogen associated with peptic
AB  - ulcer disease and adenocarcinoma, we cloned a putative adenine methylase gene, hpyIM. This
AB  - gene contains a 990bp ORF encoding a 330 aa protein, M.HpyI.  Sequence analysis revealed that
AB  - M.HpyI was closely related to a CATG-recognizing adenine methylase, M.NlaIII in N. lactamica
AB  - (76% similarity).  Both Pcr and Southern blotting show that hpyIM is present in all 14 H.
AB  - pylori strains tested.  To investigate possible modification effects of M.HpyI, an isogenic
AB  - hpyIM mutant of H. pylori strain 88-23 was made by inserting a kanamycin resistance gene into
AB  - hpyIM.  SphI and NlaIII recognize DNA at sites containing CATG, and were used to test CATG
AB  - modification status.  DNA from wild type strains was resistant to digestion, whereas the hpyIM
AB  - mutant was susceptible, indicating lack of modification.  To further confirm that M.HpyI
AB  - modifies DNA at CATG sites, hpyIM was cloned into the expression vector pGEX-5X-1 to creat
AB  - pQX101.  DNA from BL21 was cleaved by NlaIII, as was the strain transformed with pGEX-5X-1.
AB  - However, DNA from BL21 with pQX101 encoding the GST-M.HpyI fusion protein was resistant,
AB  - confirming the role of hpyIM in modifying CATG sites.  We conclude that hpyIM encodes a
AB  - CATG-recognizing adenine methylase and is well-conserved among diverse H.pylori strains.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Peek, R.M. Jr.
AU  - Miller, G.G.
AU  - Blaser, M.J.
TI  - The Helicobacter pylori genome is modified at CATG by the product of hpyIM.
JO  - J. Bacteriol.
PY  - 1997
SP  - 6807
EP  - 6815
VL  - 179
AB  - To understand mechanisms of DNA methylation in Helicobacter pylori, a human pathogen
AB  - associated with peptic ulcer disease and gastric adenocarcinoma, we cloned a putative DNA
AB  - methyltransferase gene, hpyIM.  This gene contains a 990-bp open reading frame encoding a
AB  - 329-amino-acid protein, M.HpyI.  Sequence analysis revealed that M.HpyI was closely related to
AB  - CATG-recognizing adenine DNA methyltransferases, including M.NlaIII in N. lactamica.  hpyIM
AB  - was present in all H. pylori strains tested.  DNA from wild-type H. pylori strains was
AB  - resistant to digestion by SphI and NlaIII, which recognize DNA at sites containing CATG,
AB  - whereas their isogenic hpyIM mutants were susceptible, indicating lack of modification.
AB  - Overexpression of hpyIM in Escherichia coli rendered DNA from these cells resistant to NlaIII
AB  - digestion, confirming the role of hpyIM in modifying CATG sites.  We conclude that hpyIM
AB  - encodes a DNA methyltransferase, M.HpyI, that is well conserved among diverse H. pylori
AB  - strains and that modifies H. pylori genomes at CATG sites.
ER  -

TY  - JOUR
AU  - Xu, Q.
AU  - Stickel, S.
AU  - Roberts, R.J.
AU  - Blaser, M.J.
AU  - Morgan, R.D.
TI  - Purification of the Novel Endonuclease, Hpy188I, and Cloning of Its Restriction-Modification Genes Reveal Evidence of Its Horizontal Transfer to the Helicobacter pylori Genome.
JO  - J. Biol. Chem.
PY  - 2000
SP  - 17086
EP  - 17093
VL  - 275
AB  - We have isolated a novel restriction endonuclease, Hpy188I, from Helicobacter pylori strain
AB  - J188. Hpy188I recognizes the unique sequence, TCNGA, and cleaves the DNA between nucleotides N
AB  - and G in its recognition sequence to generate a one-base 3' overhang. Cloning and sequence
AB  - analysis of the Hpy188I modification gene in strain J188 reveal that hpy188IM has a 1299-base
AB  - pair (bp) open reading frame (ORF) encoding a 432-amino acid product. The predicted protein
AB  - sequence of M.Hpy188I contains conserved motifs typical of aminomethyltransferases, and
AB  - Western blotting indicates that it is an N-6 adenine methyltransferase. Downstream of hpy188IM
AB  - is a 513-bp ORF encoding a 170-amino acid product, that has a 41-bp overlap with hpy188IM. The
AB  - predicted protein sequence from this ORF matches the amino acid sequence obtained from
AB  - purified Hpy188I, indicating that it encodes the endonuclease. The Hpy188I R-M genes are not
AB  - present in either strain of H. pylori that has been completely sequenced but are found in two
AB  - of 11 H. pylori strains tested. The significantly lower G + C content of the Hpy188I R-M genes
AB  - implies that they have been introduced relatively recently during the evolution of the H.
AB  - pylori genome.
ER  -

TY  - JOUR
AU  - Xu, Q.S.
TI  - Crystal structures of restriction endonuclease MspI-DNA complex and glycosylasparaginase.
JO  - Ph.D. Thesis, Boston University
PY  - 2003
SP  - 1
EP  - 161
AB  - This dissertation is composed of two parts: (I) Chapter I, II, III and IV discuss the crystal
AB  - structures of restriction endonuclease MspI-DNA complex. (II) Chapter V depicts the
AB  - crystallographic studies of glycosylasparaginase.   Part I: MspI is a Type II restriction
AB  - endonuclease that recognizes and cleaves the palindromic tetranucleotide sequence C^CGG (the
AB  - arrowhead indicates the cleavage site) to produce two-base 5' overhanging ends. Since the
AB  - nature of this cleavage pattern is different from all other restriction enzymes with known
AB  - structures, MspI is anticipated to represent a new structural class of restriction
AB  - endonucleases.  This study reports two crystal structures of MspI bound to its cognate DNA.
AB  - One has been determined at 1.95 angstroms resolution in P21 space group, and the other at 2.7
AB  - angstroms resolution in P212121 space group. The two structures are essentially identical and
AB  - reveal several novel features. In the crystals, one MspI molecule is bound to a half-site of
AB  - its DNA recognition sequence. This is the first time that this binding mode has been observed
AB  - for Type IIP restriction endonucleases, suggesting a possibility that MspI may function as a
AB  - monomer although the dimer mechanism can't be ruled out at this point. DNA recognition is
AB  - accomplished mainly through a small three-stranded (-sheet region that is structurally
AB  - conserved in BglI, EcoRV as well as PvuII. While the architecture of the MspI active site is
AB  - similar to other restriction enzymes, an asparagine, instead of a conserved acidic residue, is
AB  - found in the catalytic sequence motif of Type II restriction enzymes. Meanwhile, although no
AB  - metal is found near the scissile phosphate, a cation can be seen at a position homologous to
AB  - the 74/45 metal site of EcoRV. Taken together, it appears that MspI is indeed a very unique
AB  - restriction enzyme.  Part II: Glycosylasparaginase (GA) is a member of a novel family of
AB  - N-terminal nucleophile hydrolases and is activated from a single chain precursor by
AB  - intramolecular autoproteolysis. The crystallographic studies of bacterial glycosylasparaginase
AB  - in mature form and its precursor reveal the catalytic mechanism of its hydrolase activity and
AB  - a novel mechanism of intramolecular autoproteolysis via an N-O or N-S acyl shift.
ER  -

TY  - JOUR
AU  - Xu, Q.S.
AU  - Kucera, R.B.
AU  - Roberts, R.J.
AU  - Guo, H.-C.
TI  - An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.
JO  - Structure
PY  - 2004
SP  - 1741
EP  - 1747
VL  - 12
AB  - Most well-known restriction endonucleases recognize palindromic DNA sequences and are
AB  - classified as Type IIP. Due to the recognition and cleavage symmetry, Type IIP enzymes are
AB  - usually found to act as homodimers in forming 2-fold symmetric enzyme-DNA complexes. Here we
AB  - report an asymmetric complex of the Type IIP restriction enzyme MspI in complex with its
AB  - cognate recognition sequence. Unlike any other Type IIP enzyme reported to date, an MspI
AB  - monomer and not a dimer binds to a palindromic DNA sequence. The enzyme makes specific
AB  - contacts with all 4 base pairs in the recognition sequence, by six direct and five
AB  - water-mediated hydrogen bonds and numerous van der Waal contacts. This MspI-DNA structure
AB  - represents the first example of asymmetric recognition of a palindromic DNA sequence by two
AB  - different structural motifs in one polypeptide. A few possible pathways are discussed for MspI
AB  - to cut both strands of DNA, either as a monomer or dimer.
ER  -

TY  - JOUR
AU  - Xu, Q.S.
AU  - Roberts, R.J.
AU  - Guo, H.C.
TI  - Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
JO  - Protein Sci.
PY  - 2005
SP  - 2590
EP  - 2600
VL  - 14
AB  - The crystal structure of the Type IIP restriction endonuclease MspI bound to DNA containing
AB  - its cognate recognition sequence has been
AB  - determined in both monoclinic and orthorhombic space. groups.
AB  - Significantly, these two independent crystal forms present an identical
AB  - structure of a novel monomer-DNA complex, suggesting a functional role
AB  - for this novel enzyme-DNA complex. In both crystals, MspI interacts
AB  - with the CCGG DNA recognition sequence as a monomer, using an
AB  - asymmetric mode of recognition by two different structural motifs in a
AB  - single polypeptide. In the crystallographic asymmetric unit, the two
AB  - DNA molecules in the two MspI-DNA complexes appear to stack with each
AB  - other forming an end-to-end pseudo-continuous 19-mer duplex. They are
AB  - primarily B-form and no major bends or kinks are observed. For DNA
AB  - recognition, most of the specific contacts between the enzyme and the
AB  - DNA are preserved in the orthorhombic structure compared with the
AB  - monoclinic structure. A cation is observed near the catalytic center in
AB  - the monoclinic structure at a position homologous to the 74/45 metal
AB  - site of EcoRV, and the orthorhombic structure also shows signs of this
AB  - same cation. However, the coordination ligands of the metal are
AB  - somewhat different from those of the 74/45 metal site of EcoRV.
AB  - Combined with structural information from other solved structures of
AB  - Type II restriction enzymes, the possible relationship between the
AB  - structures of the enzymes and their cleavage behaviors is discussed.
ER  -

TY  - JOUR
AU  - Xu, S.
AU  - Schildkraut, I.
TI  - Protecting recognition sequences on DNA by a cleavage-deficient restriction endonuclease.
JO  - Biotechniques
PY  - 1993
SP  - 310
EP  - 315
VL  - 15
AB  - This report describes the use of a biochemical tool that has been developed to aid in the
AB  - manipulation of DNA. A DNA binding-proficient and cleavage-deficient BamHI mutant protein,
AB  - E113K, was used in vitro to protect its recognition sequence (5'-GGATCC-3') against the
AB  - catalytic action of site-specific endonuclease, exonuclease and methylase. In vitro conditions
AB  - are reported here in which the E113K protein protects BamHI sites (5'-GGATCC-3') from
AB  - cleavage by BamHI endonuclease or Sau3AI endonuclease (5'-GATC-3'); protects a neighboring
AB  - restriction site 5'-CCCGGG-3' from SmaI endonuclease digestion; blocks methylation of
AB  - 5'-GGATCC-3' by Dam methylase (5'-GATC-3'); and blocks Bal31 exonuclease progression at a
AB  - BamHI site. The Bal31 procedure could be used to generate unidirectional deletions of a DNA
AB  - fragment. The use of mutant endonucleases that are binding-proficient and cleavage-deficient
AB  - to shield DNA from nuclease digestion or methylase modification expands the repertoire of
AB  - methods to manipulate DNA in vitro.
ER  -

TY  - JOUR
AU  - Xu, S.-Y.
AU  - Fomenkov, A.
TI  - Construction of pSC101 derivatives with Camr and Tetr for selection or LacZ' for blue/white screening.
JO  - Biotechniques
PY  - 1994
SP  - 57
EP  - 57
VL  - 17
AB  - Methylase genes and a mutant bamhIR gene have been cloned in the vectors described.
ER  -

TY  - JOUR
AU  - Xu, S.-Y.
AU  - Schildkraut, I.
TI  - Isolation of BamHI variants with reduced cleavage activities.
JO  - J. Biol. Chem.
PY  - 1991
SP  - 4425
EP  - 4429
VL  - 266
AB  - Derivation of the bamhIR sequence (Brooks, J.E., Nathan, P.D., Landry, D.,
AB  - Sznyter, L.A., Waite-Rees, P., Ives, C.C., Mazzola, L.M., Slatko, B.E., and
AB  - Benner, J.S. (1991) Nucleic Acids Res., in press), the gene coding for BamHI
AB  - endonuclease, has facilitated construction of an Escherichia coli strain that
AB  - overproduces BamHI endonuclease (W.E. Jack, L. Greenough, L.F. Dorner, S.Y. Xu,
AB  - T. Strezelecka, A.K. Aggarwal, and I. Schildkraut, submitted for publication).
AB  - As expected, low-level constitutive expression of the bamhIR gene in E. coli
AB  - from the Ptac promoter construct is lethal to the host unless the bamHIM gene,
AB  - which encodes the BamHI methylase, is also expressed within the cell.  We
AB  - identified four classes of BamHI endonuclease variants deficient in catalysis
AB  - by selecting for survival of a host deficient for bamHIM gene, transformed with
AB  - mutagenized copies of the bamhIR gene, and then screening the surviving cell
AB  - extracts for DNA cleavage and binding activities.  Class I variants (G56S,
AB  - G91S/T153I, G130R, E135K, T153I, T157I, G194D) displayed 0.1-1% of the
AB  - wild-type cleavage activity; class II variant (D94N) lacked cleavage activity
AB  - but retained wild-type DNA binding specificity; class III variants (E77K,
AB  - E113K) lacked cleavage activity but bound DNA more tightly; class IV variants
AB  - (G56D, G90D, G91S, R122H, R155H) lacked both binding and cleavage activities.
AB  - Variants with residual cleavage activities induced the E. coli SOS response and
AB  - thus are presumed to cleave chromosomal DNA in vivo.  We conclude that Glu77,
AB  - Asp94, and Glu113 residues are essential for BamHI catalytic function.
ER  -

TY  - JOUR
AU  - Xu, S.-Y.
AU  - Schildkraut, I.
TI  - Cofactor requirements of BamHI mutant endonuclease E77K and its suppressor mutants.
JO  - J. Bacteriol.
PY  - 1991
SP  - 5030
EP  - 5035
VL  - 173
AB  - A mutant BamHI endonuclease, E77K, belongs to a class of catalytic mutants that
AB  - bind DNA efficiently but cleave DNA at a rate more than 10/3-fold lower than
AB  - that of the wild-type enzyme (S.Y. Xu and I. Schildkraut, J. Biol. Chem.
AB  - 266:4425-4429, 1991).  The preferred cofactor for the wild-type BamHI is Mg2+.
AB  - BamHI is 10-fold less active with Mn2+ as the cofactor.  In contrast, the E77K
AB  - variant displays an increased activity when Mn2+ is substituted for Mg2+ in the
AB  - reaction buffer.  Mutations that partially suppress the E77K mutation were
AB  - isolated by using an Escherichia coli indicator strain containing the
AB  - dinD::lacZ fusion.  These pseudorevertant endonucleases induce E. coli SOS
AB  - response (as evidenced by blue colony formation) and thus presumably nick or
AB  - cleave chromosomal DNA in vivo.  Consistent with the in vivo result, the
AB  - pseudorevertant endonucleases in the crude cell extract display site-specific
AB  - partial DNA cleavage activity.  DNA sequencing revealed two unique suppressing
AB  - mutations that were located within two amino acid residues of the original
AB  - mutation.  Both pseudorevertant proteins were purified and shown to increase
AB  - specific activity at least 50-fold.  Like the wild-type enzyme, both
AB  - pseudorevertant endonucleases prefer Mg2+ as the cofactor.  Thus, the
AB  - second-site mutation not only restores partial cleavage activity but also
AB  - suppresses the metal preference as well.  These results suggest that the Glu-77
AB  - residue may play a role in metal ion binding or in enzyme activation
AB  - (allosteric transition) following sequence-specific recognition.
ER  -

TY  - JOUR
AU  - Xu, S.-Y.
AU  - Xiao, J.-P.
AU  - Ettwiller, L.
AU  - Holden, M.
AU  - Aliotta, J.
AU  - Poh, C.L.
AU  - Dalton, M.
AU  - Robinson, D.P.
AU  - Petronzio, T.R.
AU  - Moran, L.
AU  - Ganatra, M.
AU  - Ware, J.
AU  - Slatko, B.
AU  - Benner, J.
TI  - Cloning and expression of the ApaLI, NspI, NspHI, SacI, ScaI, and SapI restriction-modification systems in Escherichia coli.
JO  - Mol. Gen. Genet.
PY  - 1998
SP  - 226
EP  - 231
VL  - 260
AB  - The genes encoding the ApaLI (5'-G^TGCAC-3'), NspI (5'-GCATG^Y-3'), NspHI
AB  - (5'-RCATG^Y-3'), SacI (5'-GAGCT^C-3'), SapI (5'-GCTCTTCN1^-3', 5'-^N4GAAGAGC-3') and
AB  - ScaI (5'-AGT^ACT-3') restriction-modification systems have been cloned in E. coli.  Amino
AB  - acid sequence comparison of M.ApaLI, M.NspI, M.NspHI, and M.SacI with known methylases
AB  - indicated that they contain the ten conserved motifs characteristic of C5 cytosine methylases.
AB  - NspI and NspHI restriction-modification systems are highly homologous in amino acid sequence.
AB  - The C-termini of the NspI and NlaIII (5'-CATG-3') restriction endonucleases share
AB  - significant similarity.  5mC modification of the internal C in a SacI site renders it
AB  - resistant to SacI digestion.  External 5mC modification of a SacI site has no effect on SacI
AB  - digestion.  N4mC modification of the second base in the sequence 5'-GCTCTTC-3' blocks SapI
AB  - digestion.  N4mC modification of the other cytosines in the SapI site does not affect SapI
AB  - digestion.  N4mC modification of ScaI site blocks ScaI digestion.  A DNA invertase homolog was
AB  - found adjacent to the ApaLI restriction-modification system.  A DNA transposase subunit
AB  - homolog was found upstream of the SapI restriction endonuclease gene.
ER  -

TY  - JOUR
AU  - Xu, S.-Y.
AU  - Xiao, J.-P.
AU  - Posfai, J.
AU  - Maunus, R.
AU  - Benner, J.
TI  - Cloning of the BssHII restriction-modification system in Escherichia coli: BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 3991
EP  - 3994
VL  - 25
AB  - BssHII restriction endonuclease cleaves 5'-GCGCGC-3' on double-stranded DNA between the
AB  - first and second bases to generate a four base 5' overhang.  BssHII restriction endonuclease
AB  - was purified from the native Bacillus stearothermophilus H3 cells and its N-terminal amino
AB  - acid sequence was determined.  Degenerate PCR primers were used to amplify the first 20 codons
AB  - of the BssHII restriction endonuclease gene.  The BssHII restriction endonuclease gene
AB  - (bssHIIR) and the cognate ssHII methyltransferase gene (bssHIIM) were cloned in Escherichia
AB  - coli by amplification of Bacillus stearothermophilus genomic DNA using PCR and inverse PCR.
AB  - BssHII methyltransferase (M.BssHII) contains all 10 conserved cytosine-5 methyltransferase
AB  - motifs, but motifs IX and X precede motifs I-VIII.  Thus, the conserved motifs of M.BssHII are
AB  - circularly permuted relative to the motif organizations of other cytosine-5
AB  - methyltransferases.  M.BssHII and the noncognate multi-specific PhiBssHII methyltransferase,
AB  - M.PhiBssHII share 34% identity in amino acid sequences from motifs I-VIII, and 40% identity in
AB  - motifs IX-X.  A conserved arginine is located upstream of a TV dipeptide in the N-terminus of
AB  - M.BssHII that may be responsible for the recognition of the guanine 5' of the target
AB  - cytosine.  The BssHII restriction enodnuclease gene was expressed in E.coli via a T7
AB  - expression vector.
ER  -

TY  - JOUR
AU  - Xu, S.Y.
AU  - Boitano, M.
AU  - Clark, T.A.
AU  - Vincze, T.
AU  - Fomenkov, A.
AU  - Kumar, S.
AU  - Too, P.H.
AU  - Gonchar, D.
AU  - Degtyarev, S.K.
AU  - Roberts, R.J.
TI  - Complete Genome Sequence Analysis of Bacillus subtilis T30.
JO  - Genome Announcements
PY  - 2015
SP  - e00395
EP  - e00315
VL  - 3
AB  - The complete genome sequence of Bacillus subtilis T30 was determined by SMRT sequencing. The
AB  - entire genome contains 4,138 predicted genes. The genome carries
AB  - one intact prophage sequence (37.4 kb) similar to Bacillus phage SPBc2 and one
AB  - incomplete prophage genome of 39.9 kb similar to Bacillus phage phi105.
ER  -

TY  - JOUR
AU  - Xu, S.Y.
AU  - Corvaglia, A.R.
AU  - Chan, S.H.
AU  - Zheng, Y.
AU  - Linder, P.
TI  - A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300.
JO  - Nucleic Acids Res.
PY  - 2011
SP  - 5597
EP  - 5610
VL  - 39
AB  - A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and
AB  - expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography.
AB  - The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and
AB  - 5-hydroxymethylcytosine. Cleavage of 5mC-modified plasmids indicated that the sites S5mCNGS (S
AB  - = C or G) are preferentially digested. The endonuclease activity requires the presence of
AB  - adenosine triphosphate (ATP) or dATP whereas the non-hydrolyzable gamma-S-ATP does not support
AB  - activity. SauUSI activity was inhibited by ethylenediaminetetraacetic acid. It is most active
AB  - in Mg(++) buffers. No companion methylase gene was found near the SauUSI restriction gene. The
AB  - absence of a cognate methylase and cleavage of modified DNA indicate that SauUSI belongs to
AB  - type IV restriction endonucleases, a group that includes EcoK McrBC and Mrr. SauUSI belongs to
AB  - a family of highly similar homologs found in other sequenced S. aureus, S. epidermidis and S.
AB  - carnosus genomes. More distant SauUSI orthologs can be found in over 150 sequenced
AB  - bacterial/archaea genomes. Finally, we demonstrated the biological function of the type IV
AB  - REase in restricting 5mC-modified plasmid DNA by transformation into clinical S. aureus strain
AB  - SA564, and in restricting phage lambda infection when the endonuclease is expressed in E.
AB  - coli.
ER  -

TY  - JOUR
AU  - Xu, S.Y.
AU  - Klein, P.
AU  - Degtyarev, S.K.
AU  - Roberts, R.J.
TI  - Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes.
JO  - Sci. Rep.
PY  - 2016
SP  - 28579
EP  - 28579
VL  - 6
AB  - The methylation-dependent restriction endonuclease (REase) BisI (G(m5)C downward  arrow NGC)
AB  - is found in Bacillus subtilis T30. We expressed and purified the BisI
AB  - endonuclease and 34 BisI homologs identified in bacterial genomes. 23 of these
AB  - BisI homologs are active based on digestion of (m5)C-modified substrates. Two
AB  - major specificities were found among these BisI family enzymes: Group I enzymes
AB  - cut GCNGC containing two to four (m5)C in the two strands, or hemi-methylated
AB  - sites containing two (m5)C in one strand; Group II enzymes only cut GCNGC sites
AB  - containing three to four (m5)C, while one enzyme requires all four cytosines to
AB  - be modified for cleavage. Another homolog, Esp638I cleaves GCS downward arrow SGC
AB  - (relaxed specificity RCN downward arrow NGY, containing at least four (m5)C). Two
AB  - BisI homologs show degenerate specificity cleaving unmodified DNA. Many homologs
AB  - are small proteins ranging from 150 to 190 amino acid (aa) residues, but some
AB  - homologs associated with mobile genetic elements are larger and contain an extra
AB  - C-terminal domain. More than 156 BisI homologs are found in >60 bacterial genera,
AB  - indicating that these enzymes are widespread in bacteria. They may play an
AB  - important biological function in restricting pre-modified phage DNA.
ER  -

TY  - JOUR
AU  - Xu, S.Y.
AU  - Nugent, R.L.
AU  - Kasamkattil, J.
AU  - Fomenkov, A.
AU  - Gupta, Y.
AU  - Aggarwal, A.
AU  - Wang, X.
AU  - Li, Z.
AU  - Zheng, Y.
AU  - Morgan, R.
TI  - Characterization of Type II and III restriction-modification systems from Bacillus cereus strains ATCC10987 and ATCC14579.
JO  - J. Bacteriol.
PY  - 2012
SP  - 49
EP  - 60
VL  - 194
AB  - The genomes of two Bacillus cereus strains (ATCC10987 and ATCC14579) have been sequenced. Here
AB  - we report the specificities of Type II/III restriction (R) and modification (M) enzymes. Found
AB  - in the ATCC10987 strain, BceSI is a restriction endonuclease (REase) with the recognition and
AB  - cut site CGAAG 24-25/27-28. BceSII is an isoschizomer of AvaII (G/GWCC). BceSIII cleaves at
AB  - ACGGC 12/14. The BceSIII C-terminus resembles the catalytic domains of AlwI, MlyI, and
AB  - Nt.BstNBI. BceSIV is composed of two subunits and cleaves on both sides of GCWGC. BceSIV
AB  - activity is strongly stimulated by the addition of cofactor ATP or GTP. The large subunit (R1)
AB  - of BceSIV contains conserved motifs of NTPases and DNA helicases. The R1 subunit has no
AB  - endonuclease activity by itself; it strongly stimulates REase activity when in complex with
AB  - the R2 subunit. BceSIV was demonstrated to hydrolyze GTP and ATP in vitro. BceSIV is similar
AB  - to CglI (GCSGC), and homologs of R1 are found in 11 sequenced bacterial genomes where they are
AB  - paired with specificity subunits. In addition, homologs of BceSIV R1-R2 fusion are found in
AB  - many sequenced microbial genomes. An orphan methylase M.BceSV was found to modify GCNGC, GGCC,
AB  - CCGG, GGNNCC, and GCGC sites. A ParB-methylase fusion protein appears to nick DNA
AB  - non-specifically. The ATCC14579 genome encodes an active enzyme Bce14579I (GCWGC). BceSIV and
AB  - Bce14579I belong to the phospholipase D (PLD) family of endonucleases that are widely
AB  - distributed among Bacteria and Archaea. A survey of Type II and III R-M genes is presented
AB  - from sequenced B. cereus, B. anthracis, and B. thuringiensis strains.
ER  -

TY  - JOUR
AU  - Xu, S.Y.
AU  - Zhu, Z.
AU  - Zhang, P.
AU  - Chan, S.H.
AU  - Samuelson, J.C.
AU  - Xiao, J.
AU  - Ingalls, D.
AU  - Wilson, G.G.
TI  - Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - 4608
EP  - 4618
VL  - 35
AB  - BsrDI and BtsI restriction endonucleases recognize and cleave double-strand DNA at the
AB  - sequences GCAATG (2/0) and GCAGTG (2/0),
AB  - respectively. We have purified and partially characterized these two
AB  - enzymes, and analyzed the genes that encode them. BsrDI and BtsI are
AB  - unusual in two respects: each cleaves DNA as a heterodimer of one large
AB  - subunit (B subunit) and one small subunit (A subunit); and, in the absence
AB  - of their small subunits, the large subunits behave as sequence-specific
AB  - DNA nicking enzymes and only nick the bottom strand of the sequences at
AB  - these respective positions: GCAATG (-/0) and GCAGTG (-/0). We refer to the
AB  - single subunit, the bottom-strand nicking forms as 'hemidimers'. Amino
AB  - acid sequence comparisons reveal that BsrDI and BtsI belong to a family of
AB  - restriction enzymes that possess two catalytic sites: a canonical
AB  - PD-X(n)-EXK and a second non-canonical PD-X(n)-E-X(12)-QR. Interestingly,
AB  - the other family members, which include BsrI (ACTGG 1/-1) and
AB  - BsmI/Mva1269I (GAATGC 1/-1) are single polypeptide chains, i.e. monomers,
AB  - rather than heterodimers. In BsrDI and BtsI, the two catalytic sites are
AB  - found in two separate subunits. Site-directed mutagenesis confirmed that
AB  - the canonical catalytic site located at the N-terminus of the large
AB  - subunit is responsible for the bottom-strand cleavage, whereas the
AB  - non-canonical catalytic site located in the small subunit is responsible
AB  - for hydrolysis of the top strand. Top-strand specific nicking variants,
AB  - Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the
AB  - catalytic-deficient B subunit with wild-type A subunit.
ER  -

TY  - JOUR
AU  - Xu, T.
AU  - Liang, J.
AU  - Chen, S.
AU  - Wang, L.
AU  - He, X.
AU  - You, D.
AU  - Wang, Z.
AU  - Li, A.
AU  - Xu, Z.
AU  - Zhou, X.
AU  - Deng, Z.
TI  - DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.
JO  - BMC Microbiol.
PY  - 2009
SP  - 41
EP  - 41
VL  - 9
AB  - BACKGROUND: A novel DNA phosphorothioate modification (DNA sulfur modification),  in which one
AB  - of the non-bridging oxygen atoms in the phosphodiester bond linking
AB  - DNA nucleotides is exchanged by sulphur, was found to be genetically determined
AB  - by dnd or dnd-counterpart loci in a wide spectrum of bacteria from diverse
AB  - habitats. A detailed mutational analysis of the individual genes within the dnd
AB  - locus in Streptomyces lividans responsible for DNA phosphorothioation was
AB  - performed and is described here. It should be of great help for the mechanistic
AB  - study of this intriguing system. RESULTS: A 6,665-bp DNA region carrying just
AB  - five ORFs (dndA-E) was defined as the sole determinant for modification of the
AB  - DNA backbone in S. lividans to form phosphorothioate. This provides a
AB  - diagnostically reliable and easily assayable Dnd (DNA degradation) phenotype.
AB  - While dndA is clearly transcribed independently, dndB-E constitute an operon, as
AB  - revealed by RT-PCR analysis. An efficient mutation-integration-complementation
AB  - system was developed to allow for detailed functional analysis of these dnd
AB  - genes. The Dnd- phenotype caused by specific in-frame deletion of the dndA, C, D,
AB  - and E genes or the enhanced Dnd phenotype resulting from in-frame deletion of
AB  - dndB could be restored by expression vectors carrying the corresponding dnd
AB  - genes. Interestingly, overdosage of DndC or DndD, but not other Dnd proteins, in
AB  - vivo was found to be detrimental to cell viability. CONCLUSION: DNA
AB  - phosphorothioation is a multi-enzymatic and highly coordinated process controlled
AB  - by five dnd genes. Overexpression of some proteins in vivo prevented growth of
AB  - host strain, suggesting that expression of the gene cluster is strictly regulated
AB  - in the native host.
ER  -

TY  - JOUR
AU  - Xu, T.
AU  - Yao, F.
AU  - Zhou, X.
AU  - Deng, Z.
AU  - You, D.
TI  - A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 7133
EP  - 7141
VL  - 38
AB  - A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered,
AB  - but its in vivo function(s) have remained obscure.
AB  - Here, we report that the enteropathogenic Salmonella enterica serovar
AB  - Cerro 87, which possesses S-modified DNA, restricts DNA isolated from
AB  - Escherichia coli, while protecting its own DNA by site-specific
AB  - phosphorothioation. A cloned 15-kb gene cluster from S. enterica conferred
AB  - both host-specific restriction and DNA S-modification on E. coli.
AB  - Mutational analysis of the gene cluster proved unambiguously that the
AB  - S-modification prevented host-specific restriction specified by the same
AB  - gene cluster. Restriction activity required three genes in addition to at
AB  - least four contiguous genes necessary for DNA S-modification. This
AB  - functional overlap ensures that restriction of heterologous DNA occurs
AB  - only when the host DNA is protected by phosphorothioation. Meanwhile, this
AB  - novel type of host-specific restriction and modification system was
AB  - identified in many diverse bacteria. As in the case of
AB  - methylation-specific restriction systems, targeted inactivation of this
AB  - gene cluster should facilitate genetic manipulation of these bacteria, as
AB  - we demonstrate in Salmonella.
ER  -

TY  - JOUR
AU  - Xu, W.L.
AU  - Muller, S.J.
TI  - Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping.
JO  - Lab on a Chip
PY  - 2011
SP  - 435
EP  - 442
VL  - 11
AB  - We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence
AB  - detection and obtaining kinetic information
AB  - for restriction endonucleases on dsDNA. In this method, a microfluidic
AB  - stagnation point flow is designed to trap, hold, and linearize
AB  - double-stranded (ds) genomic DNA to which a restriction endonuclease
AB  - has been pre-bound sequence-specifically. By introducing the cofactor
AB  - magnesium, we determine the binding location of the enzyme by the
AB  - cleavage process of dsDNA as in optical restriction mapping, however
AB  - here the DNA need not be immobilized on a surface. We note that no
AB  - special labeling of the enzyme is required, which makes it simpler than
AB  - our previous scheme using stagnation point flows for sequence
AB  - detection. Our accuracy in determining the location of the recognition
AB  - site is comparable to or better than other single molecule techniques
AB  - due to the fidelity with which we can control the linearization of the
AB  - DNA molecules. In addition, since the cleavage process can be followed
AB  - in real time, information about the cleavage kinetics, and subtle
AB  - differences in binding and cleavage frequencies among the recognition
AB  - sites, may also be obtained. Data for the five recognition sites for
AB  - the type II restriction endonuclease EcoRI on lambda-DNA are presented
AB  - as a model system. While the roles of the varying fluid velocity and
AB  - tension along the chain backbone on the measured kinetics remain to be
AB  - determined, we believe this new method holds promise for a broad range
AB  - of studies of DNA-protein interactions, including the kinetics of other
AB  - DNA cleavage processes, the dissociation of a restriction enzyme from
AB  - the cleaved substrate, and other macromolecular cleavage processes.
ER  -

TY  - JOUR
AU  - Xu, X.
AU  - Chen, L.
AU  - Chen, C.
AU  - Tang, Y.J.
AU  - Bai, F.W.
AU  - Su, C.
AU  - Zhao, X.Q.
TI  - Genome mining of the marine actinomycete Streptomyces sp. DUT11 and discovery of tunicamycins as anti-complement agents.
JO  - Front. Microbiol.
PY  - 2018
SP  - 1318
EP  - 1318
VL  - 9
AB  - Marine actinobacteria are potential producers of various secondary metabolites with diverse
AB  - bioactivities. Among various bioactive compounds, anti-complement agents have received great
AB  - interest for drug discovery to treat numerous diseases caused by inappropriate activation of
AB  - the human complement system. However, marine streptomycetes producing anti-complement agents
AB  - are still poorly explored. In this study, a marine-derived strain Streptomyces sp. DUT11
AB  - showing superior anti-complement activity was focused, and its genome sequence was analyzed.
AB  - Gene clusters showing high similarities to that of tunicamycin and nonactin were identified,
AB  - and their corresponding metabolites were also detected. Subsequently, tunicamycin I, V and VII
AB  - were isolated from Streptomyces sp. DUT11. Anti-complement assay showed that tunicamycin I, V,
AB  - VII inhibited complement activation through the classic pathway, whereas no anti-complement
AB  - activity of nonactin was detected. This is the first time that tunicamycins are reported to
AB  - have such activity. In addition, genome analysis indicates that Streptomyces sp. DUT11 has the
AB  - potential to produce novel lassopeptides and lantibiotics. These results suggest that marine
AB  - Streptomyces are rich sources of anti-complement agents for drug discovery.
ER  -

TY  - JOUR
AU  - Xu, X.
AU  - Jiang, L.
AU  - Zhang, Z.
AU  - Shi, Y.
AU  - Huang, H.
TI  - Genome Sequence of a Gamma- and UV-Ray-Resistant Strain, Deinococcus wulumuqiensis R12.
JO  - Genome Announcements
PY  - 2013
SP  - e00206
EP  - e00213
VL  - 1
AB  - Deinococcus wulumuqiensis R12, isolated from radiation-polluted soil, is a red-pigmented
AB  - strain of the extremely radioresistant genus Deinococcus. It
AB  - contains a major carotenoid, namely, deinoxanthin. Here, we present a 3.39-Mb
AB  - assembly of its genome sequence, which might provide various kinds of useful
AB  - information related to Deinococcus, such as about the key enzymes of its
AB  - radioresistance mechanism and carotenoid biosynthetic pathways.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Kersten, R.D.
AU  - Nam, S.J.
AU  - Lu, L.
AU  - Al-Suwailem, A.M.
AU  - Zheng, H.
AU  - Fenical, W.
AU  - Dorrestein, P.C.
AU  - Moore, B.S.
AU  - Qian, P.Y.
TI  - Bacterial Biosynthesis and Maturation of the Didemnin Anti-cancer Agents.
JO  - J. Am. Chem. Soc.
PY  - 2012
SP  - 8625
EP  - 8632
VL  - 134
AB  - The anti-neoplastic agent didemnin B from the Caribbean tunicate Trididemnum
AB  - solidum was the first marine drug to be clinically tested in humans. Because of
AB  - its limited supply and its complex cyclic depsipeptide structure, considerable
AB  - challenges were encountered during didemnin B's development that continue to
AB  - limit aplidine (dehydrodidemnin B), which is currently being evaluated in
AB  - numerous clinical trials. Herein we show that the didemnins are bacterial
AB  - products produced by the marine alpha-proteobacteria Tistrella mobilis and
AB  - Tistrella bauzanensis via a unique post-assembly line maturation process.
AB  - Complete genome sequence analysis of the 6,513,401 bp T. mobilis strain
AB  - KA081020-065 with its five circular replicons revealed the putative didemnin
AB  - biosynthetic gene cluster (did) on the 1,126,962 bp megaplasmid pTM3. The did
AB  - locus encodes a 13-module hybrid non-ribosomal peptide synthetase-polyketide
AB  - synthase enzyme complex organized in a collinear arrangement for the synthesis of
AB  - the fatty acylglutamine ester derivatives didemnins X and Y rather than didemnin
AB  - B as first anticipated. Imaging mass spectrometry of T. mobilis bacterial
AB  - colonies captured the time-dependent extracellular conversion of the didemnin X
AB  - and Y precursors to didemnin B, in support of an unusual post-synthetase
AB  - activation mechanism. Significantly, the discovery of the didemnin biosynthetic
AB  - gene cluster may provide a long-term solution to the supply problem that
AB  - presently hinders this group of marine natural products and pave the way for the
AB  - genetic engineering of new didemnin congeners.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Liu, J.
AU  - Zheng, Q.
AU  - Liu, Y.
AU  - Jiao, N.
TI  - Genome Sequence of Salegentibacter salarius KCTC 12974, Isolated from a Marine Solar Saltern of the Yellow Sea in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e01308
EP  - e01316
VL  - 4
AB  - Salegentibacter salarius KCTC 12974 is isolated from a marine solar saltern of the Yellow Sea
AB  - in South Korea. Here, we report the draft genome sequence of
AB  - Salegentibacter salarius KCTC 12974. Various glycoside hydrolase genes in even
AB  - numbers in the genome reflect the ecological adaption of KCTC 12974 to its
AB  - habitat.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Liu, Y.
AU  - Yao, S.
AU  - Li, J.
AU  - Cheng, C.
TI  - Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands.
JO  - Genome Announcements
PY  - 2014
SP  - e00854
EP  - e00814
VL  - 2
AB  - Noni is a plant reported to have nutritional and therapeutic properties. Paenibacillus
AB  - polymyxa CICC 10580 is a strain that was isolated from the fruit of
AB  - noni and showed comprehensive antagonistic activity against many pathogens. Its
AB  - genome was sequenced and assembled (6.10 Mb). The coding sequences (CDSs)
AB  - correlated with antagonistic activity were annotated.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Lunnen, K.D.
AU  - Kong, H.
TI  - Engineering a nicking endonuclease N.AlwI by domain swapping.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2001
SP  - 12990
EP  - 12995
VL  - 98
AB  - Changing enzymatic function through genetic engineering still presents a challenge to
AB  - molecular biologists.  Here we present an example in which changing the oligomerization state
AB  - of an enzyme changes its function.  Type IIs restriction endonucleases such as AlwI usually
AB  - fold into two separate domains: A DNA-binding domain and a catalytic/dimerization domain.  We
AB  - have swapped the putative dimerization domain of AlwI with a nonfunctional dimerization domain
AB  - from a nicking enzyme, N.BstNBI.  The resulting chimeric enzyme, N.AlwI, no longer forms a
AB  - dimer.  Interestingly, the monomeric N.AlwI still recognizes the same sequence as AlwI but
AB  - only cleaves the DNA strand containing the sequence 5'-GGATC-3' (top strand).  In contrast,
AB  - the wild-type AlwI exists as a dimmer in solution and cleaves two DNA strands; the top strand
AB  - is cleaved by an enzyme binding to that sequence, and its complementary bottom strand is
AB  - cleaved by the second enzyme dimerized with the first enzyme.  N.AlwI is unable to form a
AB  - dimer and therefore nicks DNA as a monomer.  In addition, the engineered nicking enzyme is at
AB  - least as active as the wild-type AlwI and is thus a useful enzyme.  To our knowledge, this is
AB  - the first report of creating a nicking enzyme by domain swapping.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Nagy, A.
AU  - Yan, X.
AU  - Haley, B.J.
AU  - Kim, S.W.
AU  - Liu, N.T.
AU  - Nou, X.
TI  - Genome Sequences of Ralstonia insidiosa Type Strain ATCC 49129 and Strain FC1138, a Strong Biofilm Producer Isolated from a Fresh-Cut Produce-Processing Plant.
JO  - Genome Announcements
PY  - 2016
SP  - e00847
EP  - e00816
VL  - 4
AB  - Ralstonia insidiosa is an opportunistic pathogen and a strong biofilm producer. Here, we
AB  - present the complete genome sequences of R. insidiosa FC1138 and ATCC
AB  - 49129. Both strains have two circular chromosomes of approximately 3.9 and 1.9 Mb
AB  - and a 50-kb plasmid. ATCC 49129 also possesses a megaplasmid of approximately 318
AB  - kb.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Ren, C.
AU  - Chen, R.
AU  - Zeng, R.
TI  - Draft Genome Sequence of Oil-Degrading Bacterium Gallaecimonas pentaromativorans  Strain YA_1 from the Southwest Indian Ocean.
JO  - Genome Announcements
PY  - 2016
SP  - e00764
EP  - e00716
VL  - 4
AB  - Gallaecimonas pentaromativorans has been previously reported to be capable of degrading crude
AB  - oil and diesel oil. G. pentaromativorans strain YA_1 was isolated
AB  - from the southwest Indian Ocean and can degrade crude oil. This study reports the
AB  - draft genome sequence of G. pentaromativorans, which can provide insights into
AB  - the mechanisms of microbial oil biodegradation.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Tan, G.
AU  - Ke, M.
AU  - Li, J.
AU  - Tang, Y.
AU  - Meng, S.
AU  - Niu, J.
AU  - Wang, Y.
AU  - Liu, R.
AU  - Wu, H.
AU  - Bai, L.
AU  - Zhang, L.
AU  - Zhang, B.
TI  - Enhanced lincomycin production by co-overexpression of metK1 and metK2 in Streptomyces lincolnensis.
JO  - J. Ind. Microbiol. Biotechnol.
PY  - 2018
SP  - 345
EP  - 355
VL  - 45
AB  - Streptomyces lincolnensis is generally utilized for the production of lincomycin
AB  - A (Lin-A), a clinically useful antibiotic to treat Gram-positive bacterial
AB  - infections. Three methylation steps, catalyzed by three different
AB  - S-adenosylmethionine (SAM)-dependent methyltransferases, are required in the
AB  - biosynthesis of Lin-A, and thus highlight the significance of methyl group supply
AB  - in lincomycin production. In this study, we demonstrate that externally
AB  - supplemented SAM cannot be taken in by cells and therefore does not enhance Lin-A
AB  - production. Furthermore, bioinformatics and in vitro enzymatic assays revealed
AB  - there exist two SAM synthetase homologs, MetK1 (SLCG_1651) and MetK2 (SLCG_3830)
AB  - in S. lincolnensis that could convert L-methionine into SAM in the presence of
AB  - ATP. Even though we attempted to inactivate metK1 and metK2, only metK2 was
AB  - deleted in S. lincolnensis LCGL, named as DeltametK2. Following a reduction of
AB  - the intracellular SAM concentration, DeltametK2 mutant exhibited a significant
AB  - decrease of Lin-A in comparison to its parental strain. Individual overexpression
AB  - of metK1 or metK2 in S. lincolnensis LCGL either elevated the amount of
AB  - intracellular SAM, concomitant with 15% and 22% increase in Lin-A production,
AB  - respectively. qRT-PCR assays showed that overexpression of either metK1 or metK2
AB  - increased the transcription of lincomycin biosynthetic genes lmbA and lmbR, and
AB  - regulatory gene lmbU, indicating SAM may also function as a transcriptional
AB  - activator. When metK1 and metK2 were co-expressed, Lin-A production was increased
AB  - by 27% in LCGL, while by 17% in a high-yield strain LA219X.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Wang, A.
AU  - Tao, F.
AU  - Su, F.
AU  - Tang, H.
AU  - Ma, C.
AU  - Xu, P.
TI  - Genome Sequence of Enterobacter cloacae subsp. dissolvens SDM, an Efficient Biomass-Utilizing Producer of Platform Chemical 2,3-Butanediol.
JO  - J. Bacteriol.
PY  - 2012
SP  - 897
EP  - 898
VL  - 194
AB  - Enterobacter cloacae subsp. dissolvens SDM has an extraordinary characteristic of biomass
AB  - utilization for 2,3-butanediol production. Here
AB  - we present a 4.9-Mb assembly of its genome. The key genes for regulation
AB  - and metabolism of 2,3-butanediol production were annotated, which could
AB  - provide further insights into the molecular mechanism of high-yield
AB  - production of 2,3-butanediol.
ER  -

TY  - JOUR
AU  - Xu, Y.
AU  - Yu, M.
AU  - Shen, A.
TI  - Complete Genome Sequence of the Polychlorinated Biphenyl Degrader Rhodococcus sp. WB1.
JO  - Genome Announcements
PY  - 2016
SP  - e00996
EP  - e00916
VL  - 4
AB  - Rhodococcus sp. WB1 is a polychlorinated biphenyl degrader which was isolated from
AB  - contaminated soil in Zhejiang, China. Here, we present the complete genome
AB  - sequence. The analysis of this genome indicated that a biphenyl-degrading gene
AB  - cluster and several xenobiotic metabolism pathways are harbored.
ER  -

TY  - JOUR
AU  - Xu, Z. et al.
TI  - Genome Biology of Actinobacillus pleuropneumoniae JL03, an Isolate of Serotype 3 Prevalent in China.
JO  - PLoS ONE
PY  - 2008
SP  - e1450
EP  - e1450
VL  - 3
AB  - Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia,
AB  - a cause of considerable world wide economic
AB  - losses in the swine industry. We sequenced the complete genome of A.
AB  - pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its
AB  - genome is a single chromosome of 2,242,062 base pairs containing 2,097
AB  - predicted protein-coding sequences, six ribosomal rRNA operons, and 63
AB  - tRNA genes. Preliminary analysis of the genomic sequence and the functions
AB  - of the encoded proteins not only confirmed the present physiological and
AB  - pathological knowledge but also offered new insights into the metabolic
AB  - and virulence characteristics of this important pathogen. We identified a
AB  - full spectrum of genes related to its characteristic chemoheterotrophic
AB  - catabolism of fermentation and respiration with an incomplete TCA system
AB  - for anabolism. In addition to confirming the lack of ApxI toxin,
AB  - identification of a nonsense mutation in apxIVA and a 5'-proximal
AB  - truncation of the flp operon deleting both its promoter and the
AB  - flp1flp2tadV genes have provided convincing scenarios for the low
AB  - virulence property of JL03. Comparative genomic analysis using the
AB  - available sequences of other serotypes, probable strain
AB  - (serotype)-specific genomic islands related to capsular polysaccharides
AB  - and lipopolysaccharide O-antigen biosyntheses were identified in JL03,
AB  - which provides a foundation for future research into the mechanisms of
AB  - serotypic diversity of A. pleuropneumoniae.
ER  -

TY  - JOUR
AU  - Xu, Z.
AU  - Chen, X.
AU  - Li, L.
AU  - Li, T.
AU  - Wang, S.
AU  - Chen, H.
AU  - Zhou, R.
TI  - Comparative genomic characterization of Actinobacillus pleuropneumoniae.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5625
EP  - 5636
VL  - 192
AB  - The Gram-negative bacterium Actinobacillus pleuropneumoniae is the
AB  - etiologic agent of porcine contagious pleuropneumoniae, a lethal
AB  - respiratory infectious disease causing great economic losses in the swine
AB  - industry worldwide. In order to better interpret the genetic background of
AB  - serotypic diversity, nine genomes of A. pleuropneumoniae reference strains
AB  - of serovars 1, 2, 4, 6, 9, 10, 11, 12, and 13 were sequenced by using
AB  - rapid high-throughput approach. Based on 12 genomes of corresponding
AB  - serovar reference strains including three publicly available complete
AB  - genomes (serovars 3, 5b, and 7) of this bacterium, we performed a
AB  - comprehensive analysis of comparative genomics and first reported a global
AB  - genomic characterization for this pathogen. Clustering of 26,012 predicted
AB  - protein-coding genes showed that the pan genome of A. pleuropneumoniae
AB  - consists of 3,303 gene clusters, which contain 1,709 core genome genes,
AB  - 822 distributed genes, and 772 strain-specific genes. The genome
AB  - components involved in the biogenesis of capsular polysaccharide and
AB  - lipopolysaccharide O antigen relative to serovar diversity were compared,
AB  - and their genetic diversity was depicted. Our findings shed more light on
AB  - genomic features associated with serovar diversity of A. pleuropneumoniae
AB  - and provide broader insight into both pathogenesis research and
AB  - clinical/epidemiological application against the severe disease caused by
AB  - this swine pathogen.
ER  -

TY  - JOUR
AU  - Xu, Z.
AU  - Puranik, R.
AU  - Hu, J.
AU  - Xu, H.
AU  - Han, D.
TI  - Complete genome sequence of Thermotoga sp. strain RQ7.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 62
EP  - 62
VL  - 12
AB  - Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales.
AB  - It is a Gram negative, hyperthermophilic, and strictly anaerobic
AB  - bacterium. It grows on diverse simple and complex carbohydrates and can use
AB  - protons as the final electron acceptor. Its complete genome is composed of a
AB  - chromosome of 1,851,618 bp and a plasmid of 846 bp. The chromosome contains 1906
AB  - putative genes, including 1853 protein coding genes and 53 RNA genes. The genetic
AB  - features pertaining to various lateral gene transfer mechanisms are analyzed. The
AB  - genome carries a complete set of putative competence genes, 8 loci of CRISPRs,
AB  - and a deletion of a well-conserved Type II R-M system.
ER  -

TY  - JOUR
AU  - Xu, Z.
AU  - Xia, J.
AU  - Feng, X.
AU  - Li, S.
AU  - Xu, H.
AU  - Bo, F.
AU  - Sun, Z.
TI  - Genome Sequence of Streptomyces albulus PD-1, a Productive Strain for Epsilon-Poly-L-Lysine and Poly-L-Diaminopropionic Acid.
JO  - Genome Announcements
PY  - 2014
SP  - e00297
EP  - e00214
VL  - 2
AB  - Streptomyces albulus PD-1, a productive strain for epsilon-poly-l-lysine and
AB  - poly-l-diaminopropionic acid, was isolated from soils. We present the genome sequence of S.
AB  - albulus PD-1, which may provide abundant information regarding the production of
AB  - epsilon-poly-l-lysine and poly-l-diaminopropionic acid.
ER  -

TY  - JOUR
AU  - Xu, Z.
AU  - Yin, H.
AU  - Tian, Z.
AU  - Zhou, Y.
AU  - Ai, S.
TI  - Electrochemical immunoassays for the detection the activity of DNA methyltransferase by using the rolling circle amplification technique.
JO  - Microchimica Acta
PY  - 2014
SP  - 471
EP  - 477
VL  - 181
AB  - We report on an electrochemical method for the determination of the activity of the enzyme
AB  - methyltransferase (MTase). The methyl-binding domain-1 protein was applied to recognize
AB  - symmetrically methylated cytosine in CpG (-C-phosphate-G-) islands of ds-DNA which then
AB  - specifically bind to anti-His tag antibody. Hyperbranched rolling circle amplification (RCA)
AB  - was used to improve sensitivity. When the dsDNA was treated with M.Sss I methyltransferase,
AB  - the sequence 5'-CCGG-3' was methylated and recognize by the methyl binding protein. In turn,
AB  - the anti-His tag, biotinylated IgG, streptavidin and biotinylated oligonucleotide were
AB  - captured successively on the surface of an electrode. Subsequently, the RCA reaction was
AB  - initiated and streptavidin-labeled alkaline phosphatase immobilized on the surface of the
AB  - electrode. ALP was able to catalyze the hydrolysis of 1-naphthyl phosphate to form 1-naphthol
AB  - at pH 9.8. The oxidation peak current of 1-naphthol was used to monitor the methylation
AB  - process. The response  obtained by differential pulse voltammetry was linearly related to the
AB  - concentration of M.Sss I MTase in the range from 0.1 to 40 unit mL(-1), and the detection
AB  - limit was 0.03 unit mL(-1) (at an SNR of 3). The inhibitory action of paclitaxel on the
AB  - activity of M.Sss I MTase also was investigated.
ER  -

TY  - JOUR
AU  - Xu, Z.
AU  - Zhang, X.Y.
AU  - Su, H.N.
AU  - Yu, Z.C.
AU  - Liu, C.
AU  - Li, H.
AU  - Chen, X.L.
AU  - Song, X.Y.
AU  - Xie, B.B.
AU  - Qin, Q.L.
AU  - Zhou, B.C.
AU  - Shi, M.
AU  - Huang, Y.
AU  - Zhang, Y.Z.
TI  - Oceanisphaera profunda sp. nov., a marine bacterium isolated from deep-sea sediment, and emended description of the genus Oceanisphaera.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 1252
EP  - 1256
VL  - 64
AB  - A Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated,
AB  - rod-shaped bacterial strain, designated SM1222(T), was isolated from the deep-sea
AB  - sediment of the South China Sea. The strain grew at 4-35 degrees C and with 0.5-8
AB  - % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences revealed
AB  - that strain SM1222(T) was affiliated with the genus Oceanisphaera in the class
AB  - Gammaproteobacteria. It shared the highest sequence similarity with the type
AB  - strain of Oceanisphaera ostreae (96.8 %) and 95.4-96.6 % sequence similarities
AB  - with type strains of other species of the genus Oceanisphaera with validly
AB  - published names. Strain SM1222(T) contained summed feature 3 (C16 : 1omega7c
AB  - and/or iso-C15 : 0 2-OH), C18 : 1omega7c, C16 : 0, C12 : 0 and summed feature 2
AB  - (C14 : 0 3-OH and/or iso-C16 : 1 I) as the major fatty acids and ubiquinone Q-8
AB  - as the predominant respiratory quinone. The major polar lipids were
AB  - phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The
AB  - genomic DNA G+C content of strain SM1222(T) was 51.5 mol%. On the basis of the
AB  - evidence presented in this study, strain SM1222(T) represents a novel species of
AB  - the genus Oceanisphaera, for which the name Oceanisphaera profunda sp. nov. is
AB  - proposed. The type strain of Oceanisphaera profunda is SM1222(T) ( = CCTCC AB
AB  - 2013241(T) = KCTC 32510(T)). An emended description of the genus Oceanisphaera
AB  - Romanenko et al. 2003 emend. Choi et al. 2011 is also proposed.
ER  -

TY  - JOUR
AU  - Xu, Z.H.
AU  - Han, D.M.
AU  - Cao, J.J.
AU  - Saini, U.
TI  - Cloning and characterization of the TneDI restriction-modification system of Thermotoga neapolitana.
JO  - Extremophiles
PY  - 2011
SP  - 665
EP  - 672
VL  - 15
AB  - A putative Type II restriction-modification system of Thermotoga neapolitana, TneDI, was
AB  - cloned into Escherichia coli XL1-Blue MRF' and
AB  - characterized. Gene CTN 0339 specifies the endonuclease R.TneDI, while
AB  - CTN 0340 encodes the cognate DNA methyltransferase M.TneDI. Both
AB  - enzymes were purified simply by heating the cell lysates of E. coli
AB  - followed by centrifugation. The enzymes were active over a broad range
AB  - of temperatures, from 42A degrees C to at least 77A degrees C, with the
AB  - highest activities observed at 77A degrees C. R.TneDI cleaved at the
AB  - center of the recognition sequence (CGa dagger'CG) and generated
AB  - blunt-end cuts. Overexpression of R.TneDI in BL21(DE3) was confirmed by
AB  - both SDS-PAGE and Western blotting.
ER  -

TY  - JOUR
AU  - Xue, C.
AU  - Cao, L.
AU  - Zhang, R.
AU  - He, J.
AU  - Li, S.
AU  - Hong, Q.
TI  - Draft Genome Sequence of Sphingobium sp. Strain BHC-A, Revealing Genes for the Degradation of Hexachlorocyclohexane.
JO  - Genome Announcements
PY  - 2014
SP  - e00254
EP  - e00214
VL  - 2
AB  - Here, we report the draft genome sequence of Sphingobium sp. strain BHC-A, a lin  gene-based
AB  - hexachlorocyclohexane (HCH)-degrading strain, isolated from soil that suffered long-term HCH
AB  - contamination in an insecticide factory.
ER  -

TY  - JOUR
AU  - Xue, J.
AU  - He, Z.
TI  - Enzymology of BamHI DNA methylase.
JO  - Shengwu Huaxue Zazhi
PY  - 1991
SP  - 13
EP  - 20
VL  - 7
AB  - The enzymology of BamHI DNA methylase has been studied.  The optimum pH is 7.8.
AB  - It is unstable in heat treatment and dependent on K+ or Na+.  The Km is 7.69 x
AB  - 10-6 mol/L for SAM and the Ki is 7.33 x 10-4 mol/L in the presence of 1 mmol/L
AB  - SAH by Lineweaver-Burke plot.  The two lines intersected at the ordinate on L-B
AB  - plot.  This result shows that SAH is the competitive inhibitor for BamHI DNA
AB  - methylase.  The study of substrate specificity for different DNA shows that the
AB  - single-stranded M.L. DNA is the best substrate for this enzyme.  The enzyme
AB  - activity was assayed in the presence of different metabolites such as cytosine,
AB  - 5-azacytosine, adenosine, 6-azacytosine, 5-azacytidine and 5-methylcytosine.
AB  - The enzyme activity could be inhibited by divalent cations such as Mn2+, Mg2+,
AB  - Zn2+, but was stimulated strongly by F-, WO3-/4, MoO2-/4.  Results from the
AB  - chemical modification by iodoacetamide and protection by DTT or
AB  - 2-mercaptoethanol of this enzyme showed that the SH group is essential in
AB  - active site of this enzyme.  It has been proved by HPLC that this enzyme
AB  - transferred the methyl group from SAM to cytosine of DNA.  The methylation
AB  - level of Micrococcus luteus (M.L.) DNA is 2.39% when it was incubated with
AB  - BamHI DNA methylase for 30'.  It has been proved by electrophoresis on 1%
AB  - agarose that the BamHI DNA methylase modified DNA cannot be cleaved by BamHI
AB  - restriction endonuclease.
ER  -

TY  - JOUR
AU  - Xydas, S.
AU  - Lange, C.S.
AU  - Phil, D.
AU  - Neimark, H.C.
TI  - Effect of methylation on the electrophoretic mobility of chromosomal DNA in pulse-field agarose gels.
JO  - Appl. Theor. Electrophor.
PY  - 1996
SP  - 43
EP  - 47
VL  - 6
AB  - Factors other than molecular weight are known to affect DNA electrophoretic mobility.  DNA
AB  - methylation has been found to affect the curvature of DNA, causing anomalous mobility in
AB  - polyacrylamide gels; the effect of methylation on the mobility of large DNA molecules in
AB  - agarose gels was unknown.  Chromosomal DNA from Mycoplasma capricolum, a wall-less prokaryote
AB  - which has a low intrinsic methylation rate, was methylated in agarose blocks by SssI
AB  - methylase, a de novo methylase with a CpG recognition sequence.  (A surprising finding was
AB  - that SssI methylase altered the structure of InCert, but not SeaKem Gold, agarose.)
AB  - Restriction enzyme analysis was used to estimate the extent of CpG methylation.  DNA
AB  - methylation was found to have no effect on the electrophoretic mobility of full-length
AB  - chromosomal DNA (1,120 kbp) in agarose gels.  Therefore, methylation is not a source of error
AB  - in PFGE-based size estimation for chromosomal DNA molecules less than 1.12 Mbp in agarose
AB  - gels.
ER  -

TY  - JOUR
AU  - Yaakop, A.S.
AU  - Chan, C.S.
AU  - Kahar, U.M.
AU  - Ee, R.
AU  - Chan, K.G.
AU  - Goh, K.M.
TI  - Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e00457
EP  - e00415
VL  - 3
AB  - Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor,
AB  - Malaysia. Here, we present the draft genome and suggest potential
AB  - applications of this bacterium.
ER  -

TY  - JOUR
AU  - Yaakop, A.S.
AU  - Chan, K.G.
AU  - Gan, H.M.
AU  - Goh, K.M.
TI  - Draft Genome Sequence of Yellow Pigmented Jeotgalibacillus alimentarius JY-13T, the First Halophile Strain of the Genus Jeotgalibacillus.
JO  - Genome Announcements
PY  - 2015
SP  - e01224
EP  - e01215
VL  - 3
AB  - Jeotgalibacillus alimentarius JY-13(T) (=KCCM 80002(T) = JCM 10872(T)) is a moderate
AB  - halophile. In 2001, this was the first strain of the newly proposed Jeotgalibacillus genus.
AB  - The draft genome of J. alimentarius was found to consist  of 32 contigs (N50, 315,125 bp) with
AB  - a total size of 3,364,745 bp. This genome information will be helpful for studies on
AB  - pigmentation as well as applications for this bacterium.
ER  -

TY  - JOUR
AU  - Yacoub, E.
AU  - Sirand-Pugnet, P.
AU  - Barre, A.
AU  - Blanchard, A.
AU  - Hubert, C.
AU  - Maurier, F.
AU  - Bouilhol, E.
AU  - Ben Abdelmoumen, M.B.
TI  - Genome Sequences of Two Tunisian Field Strains of Avian Mycoplasma, M. meleagridis and M. gallinarum.
JO  - Genome Announcements
PY  - 2016
SP  - e00558
EP  - e00516
VL  - 4
AB  - Mycoplasma meleagridis and Mycoplasma gallinarum are bacteria that affect birds,  but little
AB  - is known about the genetic basis of their interaction with chickens
AB  - and other poultry. Here, we sequenced the genomes of M. meleagridis strain
AB  - MM_26B8_IPT and M. gallinarum strain Mgn_IPT, both isolated from chickens showing
AB  - respiratory symptoms, poor growth, reduction in hatchability, and loss of
AB  - production.
ER  -

TY  - JOUR
AU  - Yacoub, E.
AU  - Sirand-Pugnet, P.
AU  - Blanchard, A.
AU  - Ben Abdelmoumen, M.B.
TI  - Genome Sequence of Mycoplasma meleagridis Type Strain 17529.
JO  - Genome Announcements
PY  - 2015
SP  - e00484
EP  - e00415
VL  - 3
AB  - Mycoplasma meleagridis is a prominent turkey bacterial pathogen associated with airsacculitis
AB  - and reproductive disorders. Notwithstanding the economic losses
AB  - caused by M. meleagridis, its genome has still not been sequenced. For a better
AB  - understanding of its genetic background and pathogenicity mechanisms, we
AB  - sequenced the genome of M. meleagridis type strain ATCC 25294.
ER  -

TY  - JOUR
AU  - Yagubi, A.I.
AU  - Castle, A.J.
AU  - Kropinski, A.M.
AU  - Banks, T.W.
AU  - Svircev, A.M.
TI  - Complete Genome Sequence of Erwinia amylovora Bacteriophage vB_EamM_Ea35-70.
JO  - Genome Announcements
PY  - 2014
SP  - e00413
EP  - e00414
VL  - 2
AB  - The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is
AB  - 271,084 bp, encodes 318 putative proteins, and contains one tRNA.
AB  - Comparative analysis with other Myoviridae genomes suggests that Ea35-70 is
AB  - related to the Phikzlikevirus genus within the family Myoviridae, since 26% of
AB  - Ea35-70 proteins share homology to proteins in Pseudomonas phage phiKZ.
ER  -

TY  - JOUR
AU  - Yahara, K.
AU  - Furuta, Y.
AU  - Oshima, K.
AU  - Yoshida, M.
AU  - Azuma, T.
AU  - Hattori, M.
AU  - Uchiyama, I.
AU  - Kobayashi, I.
TI  - Chromosome painting in silico in a bacterial species reveals fine population structure.
JO  - Mol. Biol. Evol.
PY  - 2013
SP  - 1454
EP  - 1464
VL  - 30
AB  - Identifying population structure forms an important basis for genetic and evolutionary
AB  - studies. Most current methods to identify population structure have limitations in analyzing
AB  - haplotypes and recombination across the genome. Recently, a method of chromosome painting in
AB  - silico has been developed to overcome these shortcomings and has been applied to multiple
AB  - human genome sequences. This method detects the
AB  - genome-wide transfer of DNA sequence chunks through homologous recombination.
AB  - Here, we apply it to the frequently recombining bacterial species Helicobacter pylori, which
AB  - has infected Homo sapiens since their birth in Africa and shows wide phylogeographic
AB  - divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa,
AB  - Japan, that we recently sequenced. The newer method revealed a finer population structure than
AB  - revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic
AB  - network analysis of the core genome. Novel subgroups were found in Europe, Amerind and East
AB  - Asia groups.  Examination of genetic flux showed some singleton strains to be hybrids of
AB  - subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of
AB  - Asia. We expect this approach to further our understanding of intraspecific bacterial
AB  - evolution by revealing population structure at a finer scale.
ER  -

TY  - JOUR
AU  - Yahara, K.
AU  - Horie, R.
AU  - Kobayashi, I.
AU  - Sasaki, A.
TI  - Evolution of DNA double-strand break repair by gene conversion: Coevolution between a phage and a restriction-modification system.
JO  - Genetics
PY  - 2007
SP  - 513
EP  - 526
VL  - 176
AB  - The necessity to repair genome damage has been considered to be an immediate factor
AB  - responsible for the origin of sex. Indeed, attack by a
AB  - cellular restriction enzyme of invading DNA from several bacteriophages
AB  - initiates recombinational repair by gene conversion if there is
AB  - homologous DNA. In this work, we modeled the interaction between a
AB  - bacteriophage and a bacterium carrying a restriction enzyme as
AB  - antagonistic coevolution. We assume a locus on the bacteriophage genome
AB  - has either a restriction-sensitive or a restriction-resistant allele,
AB  - and another locus determines whether it is recombination/repair
AB  - proficient or defective. A restriction break can be repaired by a
AB  - co-infecting phage genome if one of them is recombination/repair
AB  - proficient. We define the fitness of phage (resistant/sensitive and
AB  - repair-positive/-negative) genotypes and bacterial
AB  - (restriction-positive/-negative) genotypes by assuming random encounter
AB  - of the genotypes, with given probabilities of single and double
AB  - infections, and the costs of resistance, repair, and restriction. Our
AB  - results show the evolution of the repair allele depends on b(1)/b(0),
AB  - the ratio of the burst size b, under damage to host cell physiology
AB  - induced by an unrepaired double-strand break to the default burst size
AB  - b(0). It was not until this effect was taken into account that the
AB  - evolutionary advantage of DNA repair became apparent.
ER  -

TY  - JOUR
AU  - Yahara, K.
AU  - Kobayashi, I.
TI  - Evolution of selfish homing endonuclease genes in the absence of horizontal transfer.
JO  - Saibo Kogaku
PY  - 2010
SP  - 190
EP  - 195
VL  - 29
ER  -

TY  - JOUR
AU  - Yaharaa, K.
AU  - Fukuyo, M.
AU  - Sasaki, A.
AU  - Kobayashi, I.
TI  - Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2009
SP  - 18861
EP  - 18866
VL  - 106
AB  - Homing endonuclease genes are ``selfish' mobile genetic elements whose endonuclease promotes
AB  - the spread of its own gene by creating a break at
AB  - a specific target site and using the host machinery to repair the break
AB  - by copying and inserting the gene at this site. Horizontal transfer
AB  - across the boundary of a species or population within which mating
AB  - takes place has been thought to be necessary for their evolutionary
AB  - persistence. This is based on the assumption that they will become
AB  - fixed in a host population, where opportunities of homing will
AB  - disappear, and become susceptible to degeneration. To test this
AB  - hypothesis, we modeled behavior of a homing endonuclease gene that
AB  - moves during meiosis through double-strand break repair. We
AB  - mathematically explored conditions for persistence of the homing
AB  - endonuclease gene and elucidated their parameter dependence as phase
AB  - diagrams. We found that, if the cost of the pseudogene is lower than
AB  - that of the homing endonuclease gene, the 2 forms can persist in a
AB  - population through autonomous periodic oscillation. If the cost of the
AB  - pseudogene is higher, 2 types of dynamics appear that enable
AB  - evolutionary persistence: bistability dependent on initial frequency or
AB  - fixation irrespective of initial frequency. The prediction of long
AB  - persistence in the absence of horizontal transfer was confirmed by
AB  - stochastic simulations in finite populations. The average time to
AB  - extinction of the endonuclease gene was found to be thousands of
AB  - meiotic generations or more based on realistic parameter values. These
AB  - results provide a solid theoretical basis for an understanding of these
AB  - and other extremely selfish elements. POPULATION BIOLOGY
ER  -

TY  - JOUR
AU  - Yaish, M.W.
TI  - Draft Genome Sequence of the Endophytic Bacillus aryabhattai Strain SQU-R12, Identified from Phoenix dactylifera L. Roots.
JO  - Genome Announcements
PY  - 2017
SP  - e00718
EP  - e00717
VL  - 5
AB  - Bacillus aryabhattai strain SQU-R12 was isolated from date palm seedlings, where  it showed a
AB  - growth-promoting capacity by being able to synthesize indole-3-acetic
AB  - acid phytohormone and reduce ethylene biosynthesis by producing
AB  - 1-aminocyclopropane-1-carboxylic acid deaminase. The draft genome sequence of
AB  - this strain is reported here.
ER  -

TY  - JOUR
AU  - Yaish, M.W.
TI  - Draft Genome Sequence of Endophytic Bacterium Enterobacter asburiae PDA134, Isolated from Date Palm (Phoenix dactylifera L.) Roots.
JO  - Genome Announcements
PY  - 2016
SP  - e00848
EP  - e00816
VL  - 4
AB  - In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This
AB  - bacterial strain was isolated from the root tissue of a date
AB  - palm, where it has the ability to produce 1-aminocyclopropane-1-carboxylic acid
AB  - (ACC) deaminase and indole-3-acetic acid (IAA) under salinity stress.
ER  -

TY  - JOUR
AU  - Yamada, T.
AU  - Chuchird, N.
AU  - Kawasaki, T.
AU  - Nishida, K.
AU  - Hiramatsu, S.
TI  - Chlorella viruses as a source of novel enzymes.
JO  - J. Biosci. Bioeng.
PY  - 1999
SP  - 353
EP  - 361
VL  - 88
AB  - A special advantage has been conferred upon Chlorella cells as tools in biotechnology when
AB  - viruses (Phycodnaviridae) infecting Chlorella cells
AB  - were discovered and isolated. The viruses are large icosahedral
AB  - particles (150-200 nm in diameter), containing a giant, 330-380 kbp
AB  - long, linear dsDNA genome. Recently, the nucleotide sequence of the
AB  - 330,740-bp genome of PBCV-1, the prototype virus of Phycodnaviridae,
AB  - was determined, and up to 702 open reading frames (ORFs) were
AB  - identified along the genome. The possible genes present include those
AB  - encoding a variety of enzymes involved in the modification of DNA, RNA,
AB  - protein and polysaccharides as well as those involved in the metabolism
AB  - of sugars, amino acids, lipids, nucleotides and nucleosides. Many of
AB  - these genes are actually expressed during viral infection, with
AB  - functional enzymes detected in the host cytoplasm or incorporated into
AB  - the virion. The successful utilization of these viral enzymes as
AB  - various DNA restriction and modification enzymes (Cvi enzymes) that are
AB  - now commercially available is well documented. Also noteworthy are
AB  - virion-associated chitinase and chitosanase activities that have
AB  - potentially important applications in the recycling of natural
AB  - resources. The virions of Chlorella viruses contain more than 50
AB  - different structural proteins, ranging in size from 10 to 200 kDa. Some
AB  - of these proteins may be replaced with useful foreign proteins using
AB  - recombinant DNA technology. The proteins of interest can be recovered
AB  - easily from the viral particles, and collected by centrifugation after
AB  - complete lysis of the host Chlorella cells.
ER  -

TY  - JOUR
AU  - Yamada, Y.
AU  - Mizuno, H.
AU  - Sato, H.
AU  - Akagawa, M.
AU  - Yamasato, K.
TI  - A new restriction endonuclease from Agrobacterium gelatinovorum, a marine agrobacterium (AgeI).
JO  - Agric. Biol. Chem.
PY  - 1989
SP  - 1747
EP  - 1749
VL  - 53
AB  - Type II restriction endonucleases, which are indispensable for gene analyses
AB  - and gene manipulation, have been recovered from prokaryotic cells such as those
AB  - of bacteria and cyanobacteria.  We have been studying acetic acid bacteria from
AB  - taxonomical, physiological and biochemical points of view.  The new restriction
AB  - endonuclease ApaLI was reported in Acetobacter pasteurianus IFO 13753.  During
AB  - the course of our screening of marine bacteria, we found a new restriction
AB  - endonuclease, designated as AgeI, in Agrobacterium gelatinovorum IAM 12617.
AB  - This paper describes its purification and properties and determination of its
AB  - recognition sequence and cleavage site.
ER  -

TY  - JOUR
AU  - Yamada, Y.
AU  - Murakami, M.
TI  - A new restriction endonuclease from Acetobacter pasteurianus (ApaI).
JO  - Agric. Biol. Chem.
PY  - 1985
SP  - 3627
EP  - 3629
VL  - 49
AB  - Type II restriction endonucleases indispensable for gene manipulation and gene
AB  - analyses have been recovered from procaryotic cells such as those of bacteria
AB  - and cyanobacteria.  We have been studying acetic acid bacteria from the
AB  - viewpoints of taxonomy, physiology, biochemistry and genetics.  During the
AB  - course of our studies, we found a new type II restriction endonuclease,
AB  - designated as ApaLI, in a strain of Acetobacter pasteurianus (Hansen 1879)
AB  - Beijerinck 1916.  This communication describes its purification and properties
AB  - and determination of its recognition sequence and cleavage sites in DNA
AB  - molecules.
ER  -

TY  - JOUR
AU  - Yamada, Y.
AU  - Sasaki, J.
TI  - Distribution of Restriction Enzymes in Strains of Acetobacter (Gluconoacetobacter) Liquefaciens.
JO  - J. Gen. Appl. Microbiol.
PY  - 1984
SP  - 309
EP  - 312
VL  - 30
AB  - Acetobacter (Gluconoacetobacter) liquefaciens was first described by ASAI as a
AB  - species of the genus Gluconobacter. Three strains, G-1, AC-8, and U-4, were
AB  - reported.  Concerning the taxonomic position, these strains were designated as
AB  - pigment-producing strains of A. aceti because of their peritrichous
AB  - flagellation and ability to oxidize acetate to carbon dioxide and water.  In
AB  - contrast, Asai et al. stated their uniqueness in phenotypic features and
AB  - designated them as 'intermediate.'  Subsequently, Yamada et al. found that
AB  - these three strains and two other strains isolated by Komagata are
AB  - distinguishable from A. aceti strains by their coenzyme Q or ubiquinone system;
AB  - the five intermediate strains have Q-10[Q-9] whereas the A. aceti strains have
AB  - Q-9[Q-8].  In Bergey's Manual 8th Edition, however, these 'anomalous' strains
AB  - are classified as A. aceti subsp. liquefaciens.  The Approved Lists 1980
AB  - included A. aceti subsp. liquefaciens (Asai 1935) De Ley and Frateur 1974.
AB  - This subspecies was elevated to A. liquefaciens separate from A. aceti on the
AB  - basis of the ubiquinone system, numerical analyses of phenotypic features and
AB  - protein gel electrophoretic patterns of enzymes.  Recently, Yamada and Kondo
AB  - have set up a new subgenus, Gluconoacetobacter and classified these strains as
AB  - Acetobacter (Gluconoacetobacter) liquefaciens (Asai 1935) Gossele et al. 1983.
AB  - In previous papers, the authors have purified two restriction enzymes of A.
AB  - liquefaciens IAM 1834 and AJ 2881 to a homogeneous state and determined their
AB  - recognition sequences and cleavage sites on DNA molecules.  The enzymes have
AB  - been found to be isoschizomers of BamHI and PstI, respectively.  This paper
AB  - describes distribution of restriction enzymes in the five strains mentioned
AB  - above.
ER  -

TY  - JOUR
AU  - Yamada, Y.
AU  - Sato, H.
TI  - The manganese ion strongly activates restriction endonuclease AatII from Acetobacter aceti IFO 3281.
JO  - Agric. Biol. Chem.
PY  - 1989
SP  - 1745
EP  - 1746
VL  - 53
AB  - Type II restriction endonucleases are indispensable for gene analyses and gene
AB  - manipulation, and their occurrence is widespread in the prokaryotic kingdom.
AB  - We have been studying restriction endonucleases of acetic acid bacteria.
AB  - During the course of our studies, restriction endonuclease ApaLI was found in
AB  - Acetobacter pasteurianus IFO 13753.  Restriction endonuclease AatII was
AB  - reported by Sugisaki et al. as a new enzyme from Acetobacter aceti IFO 3281.
AB  - However, the characteristics of the enzyme have remained unclarified as yet
AB  - except for its recognition sequence and cleavage site.  This paper reports that
AB  - the enzyme purified to a homogeneous state is strongly activated on the
AB  - addition of not Mg2+ but Mn2+.
ER  -

TY  - JOUR
AU  - Yamada, Y.
AU  - Yoshioka, H.
AU  - Sasaki, J.
AU  - Tahara, Y.
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from "Acetobacter liquefaciens".
JO  - J. Gen. Appl. Microbiol.
PY  - 1983
SP  - 157
EP  - 166
VL  - 29
AB  - A type II restriction endonuclease was purified from "Acetobacter liquefaciens"
AB  - IAM 1834 by consecutive column chromatography on heparin-Sepharose CL-6B,
AB  - DEAE-Sepharose CL-6B and Sephacryl S-400 superfine.  The purified enzyme was
AB  - homogeneous on polyacrylamide gel disc electrophoresis.  The enzyme preparation
AB  - was essentially free from other nuclease activity, as judged by constancy of a
AB  - lambda DNA-digest electrophoretic pattern after prolonged incubation for 24 hr.
AB  - The enzyme was optimally active at 37o at pH 7.5, and did not require NaCl,
AB  - which rather inhibited its activity.  The recognition sequence for the enzyme
AB  - was determined to be 5'-G-G-A-T-C-C-3', and the enzyme was found to cut between
AB  - G and G in the sequence, being an isoschizomer of the endonuclease from
AB  - "Bacillus amyloliquefaciens" H (Bam HI).
ER  -

TY  - JOUR
AU  - Yamaguchi, H.
AU  - Shimura, Y.
AU  - Suzuki, S.
AU  - Yamagishi, T.
AU  - Tatarazako, N.
AU  - Kawachi, M.
TI  - Complete Genome Sequence of Cyanobium sp. NIES-981, a Marine Strain Potentially Useful for Ecotoxicological Bioassays.
JO  - Genome Announcements
PY  - 2016
SP  - e00736
EP  - e00716
VL  - 4
AB  - Cyanobium sp. NIES-981 is a marine cyanobacterium isolated from tidal flat sands  in Okinawa,
AB  - Japan. Here, we report the complete 3.0-Mbp genome sequence of
AB  - NIES-981, which is composed of a single chromosome, and its annotation. This
AB  - sequence information may provide a basis for developing an ecotoxicological
AB  - bioassay using this strain.
ER  -

TY  - JOUR
AU  - Yamaguchi, H.
AU  - Suzuki, S.
AU  - Kawachi, M.
TI  - Improved Draft Genome Sequence of Microcystis aeruginosa NIES-298, a Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e01551
EP  - e01517
VL  - 6
AB  - Microcystis aeruginosa is a globally well-known bloom-forming cyanobacterium. An  improved
AB  - draft whole-genome sequence of M. aeruginosa NIES-298, which is a
AB  - microcystin-producing strain isolated from Lake Kasumigaura, Japan, is published
AB  - here. The genome comprises approximately 5.0 Mbp, with an average G+C content of
AB  - 42.6% and 4,537 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Yamaguchi, H.
AU  - Suzuki, S.
AU  - Kawachi, M.
TI  - Draft Genome Sequence of Microcystis aeruginosa NIES-87, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan.
JO  - Genome Announcements
PY  - 2018
SP  - e01596
EP  - e01517
VL  - 6
AB  - Microcystis aeruginosa is a problematic cyanobacterium in freshwater lakes distributed
AB  - worldwide. Here, we report the draft genome sequence of M. aeruginosa
AB  - NIES-87, isolated from Lake Kasumigaura, Japan. The genome is approximately 4.9
AB  - Mb in size, with an average G+C content of 42.9% and 4,355 predicted
AB  - protein-coding genes.
ER  -

TY  - JOUR
AU  - Yamaguchi, H.
AU  - Suzuki, S.
AU  - Sano, T.
AU  - Tanabe, Y.
AU  - Nakajima, N.
AU  - Kawachi, M.
TI  - Draft Genome Sequence of Microcystis aeruginosa NIES-98, a Non-Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan.
JO  - Genome Announcements
PY  - 2016
SP  - e01187
EP  - e01116
VL  - 4
AB  - Microcystis aeruginosa is a well-known bloom-forming cyanobacterium. We newly sequenced the
AB  - whole genome of M. aeruginosa NIES-98, which is a
AB  - non-microcystin-producing strain isolated from Lake Kasumigaura, Japan. The
AB  - genome contains approximately 5.0 Mbp, with an average G+C content of 42.41% and
AB  - 5,140 predicted protein-coding genes.
ER  -

TY  - JOUR
AU  - Yamaguchi, H.
AU  - Suzuki, S.
AU  - Tanabe, Y.
AU  - Osana, Y.
AU  - Shimura, Y.
AU  - Ishida, K.
AU  - Kawachi, M.
TI  - Complete Genome Sequence of Microcystis aeruginosa NIES-2549, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e00551
EP  - e00515
VL  - 3
AB  - Microcystis aeruginosa NIES-2549 is a freshwater bloom-forming cyanobacterium isolated from
AB  - Lake Kasumigaura, Japan. We report the complete 4.29-Mbp genome
AB  - sequence of NIES-2549 and its annotation and discuss the genetic diversity of M.
AB  - aeruginosa strains. This is the third genome sequence of M. aeruginosa isolated
AB  - from Lake Kasumigaura.
ER  -

TY  - JOUR
AU  - Yamaguchi, T.
AU  - Asano, Y.
TI  - Draft Genome Sequence of an Aldoxime Degrader, Rhodococcus sp. Strain YH3-3.
JO  - Genome Announcements
PY  - 2016
SP  - e00406
EP  - e00416
VL  - 4
AB  - Rhodococcus sp. strain YH3-3 has been isolated as an (E)-pyridine-3-aldoxime degrader. Here,
AB  - we report the draft genome sequence of this strain, with a size
AB  - of 7,316,908 bp, average G+C content of 62.15%, and 7,281 predicted
AB  - protein-coding sequences.
ER  -

TY  - JOUR
AU  - Yamaguchi, T.
AU  - Asano, Y.
TI  - Complete Genome Sequence of an Aldoxime Degrader, Bacillus sp. OxB-1.
JO  - Genome Announcements
PY  - 2015
SP  - e00025
EP  - e00015
VL  - 3
AB  - Bacillus sp. OxB-1 has been characterized as a strain that produces a new enzyme, aldoxime
AB  - dehydratase, which catalyzes the dehydration of aldoxime to form nitrile. Here, its complete
AB  - genome sequence (3,594,618 bp, with a GC content of 47.85%), comprising a circular chromosome,
AB  - is announced.
ER  -

TY  - JOUR
AU  - Yamaguchi, T.
AU  - Nishifuji, K.
AU  - Sasaki, M.
AU  - Fudaba, Y.
AU  - Aepfelbacher, M.
AU  - Takata, T.
AU  - Ohara, M.
AU  - Komatsuzawa, H.
AU  - Amagai, M.
AU  - Sugai, M.
TI  - Identification of the Staphylococcus aureus etd pathogenicity island which encodes a novel exfoliative toxin, ETD, and EDIN-B.
JO  - Infect. Immun.
PY  - 2002
SP  - 5835
EP  - 5845
VL  - 70
AB  - We identified a novel pathogenicity island in Staphylococcus aureus which contains open
AB  - reading frames (ORFs) similar to the exfoliative
AB  - toxin (ET) gene, glutamyl endopeptidase gene, and edin-B gene in tandem
AB  - and the phage resistance gene, flanked by hsdM, hsdS (restriction and
AB  - modification system), and IS256. The protein encoded by the ET-like
AB  - gene showed 40, 59, and 68% amino acid sequence identities with
AB  - exfoliative toxin A (ETA), exfoliative toxin B (ETB), and
AB  - Staphylococcus hyicus ETB (ShETB), respectively. When injected into
AB  - neonatal mice, the recombinant protein derived from the ET-like gene
AB  - induced exfoliation of the skin with loss of cell-to-cell adhesion in
AB  - the upper part of the epidermis as observed in histological
AB  - examinations, just as was found in neonatal mice injected with ETA or
AB  - ETB. Western blot analysis indicated that the recombinant protein is
AB  - serologically distinct from ETA and ETB. Therefore, the product encoded
AB  - by this new ORF is a new ET member produced by S. aureus and is termed
AB  - ETD. ETD did not induce blisters in 1-day-old chickens. In the skins of
AB  - mice injected with ETD, cell surface staining of desmoglein 1 (Dsg1), a
AB  - cadherin type cell-to-cell adhesion molecule in desmosomes, was
AB  - abolished without affecting that of desmoglein 3 (Dsg3). Furthermore,
AB  - in vitro incubation of the recombinant extracellular domains of Dsg1
AB  - and Dsg3 with the recombinant protein demonstrated that both mouse and
AB  - human Dsg1, but not Dsg3, were directly cleaved in a dose-dependent
AB  - manner. These results demonstrate that ETD and ETA induce blister
AB  - formation by identical pathophysiological mechanisms. Clinical strains
AB  - positive for edin-B were suggested to be clonally associated, and all
AB  - edin-B-positive strains tested were positive for etd. Among 18
AB  - etd-positive strains, 12 produced ETD extracellularly. Interestingly,
AB  - these strains are mainly isolated from other sources of infections and
AB  - not from patients with bullous impetigo or staphylococcal scalded-skin
AB  - syndrome. This strongly suggests that ETD might play a pathogenic role
AB  - in a broader spectrum of bacterial infections than previously
AB  - considered.
ER  -

TY  - JOUR
AU  - Yamaichi, Y.
AU  - Chao, M.C.
AU  - Sasabe, J.
AU  - Clark, L.
AU  - Davis, B.M.
AU  - Yamamoto, N.
AU  - Mori, H.
AU  - Kurokawa, K.
AU  - Waldor, M.K.
TI  - High-resolution genetic analysis of the requirements for horizontal transmission  of the ESBL plasmid from Escherichia coli O104:H4.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 348
EP  - 360
VL  - 43
AB  - Horizontal dissemination of the genes encoding extended spectrum beta-lactamases  (ESBLs) via
AB  - conjugative plasmids is facilitating the increasingly widespread
AB  - resistance of pathogens to beta-lactam antibiotics. However, there is relatively
AB  - little known about the regulatory factors and mechanisms that govern the spread
AB  - of these plasmids. Here, we carried out a high-throughput, transposon insertion
AB  - site sequencing analysis (TnSeq) to identify genes that enable the maintenance
AB  - and transmission of pESBL, an R64 (IncI1)-related resistance plasmid that was
AB  - isolated from Escherichia coli O104:H4 linked to a recent large outbreak of
AB  - gastroenteritis. With a few exceptions, the majority of the genes identified as
AB  - required for maintenance and transmission of pESBL matched those of their
AB  - previously defined R64 counterparts. However, our analyses of the high-density
AB  - transposon insertion library in pESBL also revealed two very short and linked
AB  - regions that constitute a previously unrecognized regulatory system controlling
AB  - spread of IncI1 plasmids. In addition, we investigated the function of the
AB  - pESBL-encoded M.EcoGIX methyltransferase, which is also encoded by many other
AB  - IncI1 and IncF plasmids. This enzyme proved to protect pESBL from restriction in
AB  - new hosts, suggesting it aids in expanding the plasmid's host range.
AB  - Collectively, our work illustrates the power of the TnSeq approach to enable
AB  - rapid and comprehensive analyses of plasmid genes and sequences that facilitate
AB  - the dissemination of determinants of antibiotic resistance.
ER  -

TY  - JOUR
AU  - Yamamoto, K.
AU  - Asano, Y.
TI  - Genome Sequence of Microbacterium sp. Strain TPU 3598, a Lumichrome Producer.
JO  - Genome Announcements
PY  - 2017
SP  - e00204
EP  - e00217
VL  - 5
AB  - We report here the genome sequence of Microbacterium sp. strain TPU 3598, previously described
AB  - as a producer of lumichrome. The sequenced genome size is
AB  - 3,787,270 bp, the average G+C content is 68.39%, and 3,674 protein-coding
AB  - sequences are predicted.
ER  -

TY  - JOUR
AU  - Yamamoto, K.
AU  - Tamaki, H.
AU  - Cadillo-Quiroz, H.
AU  - Imachi, H.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Zinder, S.H.
AU  - Kamagata, Y.
AU  - Liu, W.T.
TI  - Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge.
JO  - Genome Announcements
PY  - 2014
SP  - e00876
EP  - e00814
VL  - 2
AB  - Here, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1(T), a
AB  - methanogenic archaeon isolated from an anaerobic digested sludge.
AB  - This is the first genome report of the genus Methanolinea isolate belonging to
AB  - the family Methanoregulaceae, a recently proposed novel family within the order
AB  - Methanomicrobiales.
ER  -

TY  - JOUR
AU  - Yamamoto, K.
AU  - Tamaki, H.
AU  - Cadillo-Quiroz, H.
AU  - Imachi, H.
AU  - Kyrpides, N.
AU  - Woyke, T.
AU  - Goodwin, L.
AU  - Zinder, S.H.
AU  - Kamagata, Y.
AU  - Liu, W.T.
TI  - Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge   Blanket Reactor.
JO  - Genome Announcements
PY  - 2014
SP  - e00870
EP  - e00814
VL  - 2
AB  - Methanoregula formicica SMSP(T) is a mesophilic H2/formate-utilizing methanogenic archaeon and
AB  - a representative of the family Methanoregulaceae, a recently
AB  - proposed novel family within the order Methanomicrobiales. Here, we report a
AB  - 2.8-Mb complete genome sequence of this methanogenic archaeon.
ER  -

TY  - JOUR
AU  - Yamamoto, N.
AU  - Inoue, D.
AU  - Kuroda, M.
AU  - Ike, M.
TI  - Draft Genome Sequence of Pseudonocardia sp. Strain N23, a 1,4-Dioxane-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2017
SP  - e01240
EP  - e01217
VL  - 5
AB  - Pseudonocardia sp. strain N23 is a 1,4-dioxane-degrading bacterium that is capable of
AB  - utilizing 1,4-dioxane as the sole carbon and energy source. Here, we
AB  - report the draft genome sequence of strain N23, with a size of 6.5 Mbp, to
AB  - identify the genes associated with 1,4-dioxane degradation.
ER  -

TY  - JOUR
AU  - Yamamoto, S.
AU  - Lee, K.I.
AU  - Morita, M.
AU  - Arakawa, E.
AU  - Izumiya, H.
AU  - Ohnishi, M.
TI  - Single Circular Chromosome Identified from the Genome Sequence of the Vibrio cholerae O1 bv. El Tor Ogawa Strain V060002.
JO  - Genome Announcements
PY  - 2018
SP  - e00564
EP  - e00518
VL  - 6
AB  - We report here the complete genome sequence of the Vibrio cholerae O1 bv. El Tor  Ogawa strain
AB  - V060002, isolated in 1997. The data demonstrate that this clinical
AB  - strain has a single chromosome resulting from recombination of two prototypical
AB  - chromosomes.
ER  -

TY  - JOUR
AU  - Yamamoto, Y. et al.
TI  - Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features.
JO  - DNA Res.
PY  - 1997
SP  - 91
EP  - 113
VL  - 4
AB  - The contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the
AB  - genetic map of the Escherichia coli K-12 (W3110) was constructed by the determination of DNA
AB  - sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short
AB  - gaps in the 57.9-68.8 min region whose sequences had been registered in the DNA databases. We
AB  - analyzed its sequence features and found that this region contained at least 894 potential
AB  - open reading frames (ORFs), of which 346 (38.7%) were previously reported, 158 (17.7%) were
AB  - homologous to other known genes, 232 (26.0%) were identical or similar to hypothetical genes
AB  - registered in databases, and the remaining 158 (17.7%) showed no significant similarity to any
AB  - other genes. A homology search of the ORFs also identified several new gene clusters. Those
AB  - include two clusters of fimbrial genes, a gene cluster of three genes encoding homologues of
AB  - the human long chain fatty acid degradation enzyme complex in the mitochondrial membrane, a
AB  - cluster of at least nine genes involved in the utilization of ethanolamine, a cluster of the
AB  - secondary set of 11 hyc genes participating in the formate hydrogenlyase reaction and a
AB  - cluster of five genes coding for the homologues of degradation enzymes for aromatic
AB  - hydrocarbons in Pseudomonas putida. We also noted a variety of novel genes, including two
AB  - ORFs, which were homologous to the putative genes encoding xanthine dehydrogenase in the fly
AB  - and a protein responsible for axonal guidance and outgrowth of the rat, mouse and nematode. An
AB  - isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min.
ER  -

TY  - JOUR
AU  - Yamamura, H.
AU  - Ohnishi, Y.
AU  - Ishikawa, J.
AU  - Ichikawa, N.
AU  - Ikeda, H.
AU  - Sekine, M.
AU  - Harada, T.
AU  - Horinouchi, S.
AU  - Otoguro, M.
AU  - Tamura, T.
AU  - Suzuki, K.
AU  - Hoshino, Y.
AU  - Arisawa, A.
AU  - Nakagawa, Y.
AU  - Fujita, N.
AU  - Hayakawa, M.
TI  - Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431(T) (= NBRC 102363(T)).
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 294
EP  - 303
VL  - 7
AB  - Actinoplanes missouriensis Couch 1963 is a well-characterized member of the genus
AB  - Actinoplanes, which is of morphological interest because its members typically
AB  - produce sporangia containing motile spores. The sporangiospores are motile by
AB  - means of flagella and exhibit chemotactic properties. It is of further interest
AB  - that members of Actinoplanes are prolific sources of novel antibiotics, enzymes,
AB  - and other bioactive compounds. Here, we describe the features of A. missouriensis
AB  - 431(T), together with the complete genome sequence and annotation. The 8,773,466
AB  - bp genome contains 8,125 protein-coding and 79 RNA genes.
ER  -

TY  - JOUR
AU  - Yamaoka, S.
AU  - Tamura, T.
AU  - Takenobu, H.
AU  - Kojo, T.
AU  - Tanaka, H.
AU  - Inagaki, K.
TI  - Cloning and nucleotide sequence of the genes encoding restriction-modification system from acidophilic bacterium Acidocella facilis 22M.
JO  - Sci. Reports. Fac. Agric. Okayama Univ.
PY  - 2003
SP  - 9
EP  - 15
VL  - 92
AB  - The gene encoding the Afa22MI restriction-modification system recognizing the sequence
AB  - 5'-CGATCG-3' was cloned from Acidocella facilis 22M and sequenced.  The cloned DNA fragment
AB  - contained three genes encoding the Afa22MI methylase (M.Afa22MI), the putative restriction
AB  - endonuclease Afa22MI (R.Afa22MI) and a very short patch repair endonuclease (Afa22MI vsr).  M.
AB  - Afa22MI gene has the conserved motifs of C5-cytosine methyltransferase.  Afa22MI vsr gene was
AB  - localized upstream of M.Afa22MI gene in opposite orientation, and an open reading frame of
AB  - R.Afa22MI gene was localized downstream of M.Afa22Mi gene in the same orientation.  M.Afa22MI
AB  - has about 63% sequence similarity to the entire amino acid sequence of M.XorII, and about 53%
AB  - sequence similarity to the amino acid sequence for the variable region of M.XorII.  Afa22MI
AB  - vsr has about 66% sequence similarity to the amino acid sequence of XorII vsr which was
AB  - associated with M.XorII.
ER  -

TY  - JOUR
AU  - Yamauchi, T.
AU  - Moritoh, S.
AU  - Johzuka-Hisatomi, Y.
AU  - Ono, A.
AU  - Terada, R.
AU  - Nakamura, I.
AU  - Iida, S.
TI  - Alternative splicing of the rice OsMET1 genes encoding maintenance DNA methyltransferase.
JO  - J. Plant Physiol.
PY  - 2008
SP  - 1774
EP  - 1782
VL  - 165
AB  - While the Arabidopsis genome carries one copy of the methyltransferase 1 (MET1) gene for DNA
AB  - methyltransferase, which is mainly responsible
AB  - for maintaining CpG methylation, the rice genome bears two copies of
AB  - the MET1 genes, OsMET1a and OsMET1b. The transcripts of OsMET1b
AB  - accumulate more abundantly than those of OsMET1a in all of the tissues
AB  - examined, and both genes actively transcribed at the callus, imbibed
AB  - embryo, root, meristem, young panicle, anther, pistil, and endosperm,
AB  - all of which contain actively dividing cells. The OsMET1a transcripts
AB  - contain two 5'-untranslated exons and alternatively spliced 3'-terminal
AB  - exons. The alternatively spliced transcripts consist of 14, 15, or 16
AB  - exons, and all of them encode a putative protein of 1527 amino acids.
AB  - While the 3'-terminal exon of OsMET1b is unique, alternative splicing
AB  - occurs in the T-terminal regions, which comprise either exons
AB  - containing 5'-untranslated regions or an exon bearing the initiation
AB  - codon. Depending upon alternative usage of 5' exons by alternative
AB  - splicing, the OsMET1b transcripts comprise 11, 12, 13, or 14 exons, and
AB  - the former two and the tatter two longer transcripts encode putative
AB  - proteins of 1486 and 1529 amino acids, respectively. Moreover, the 5'
AB  - splicing patterns of OsMET1b can vary in different tissues. These
AB  - findings are discussed with respect to the possible regulation of the
AB  - OsMET1 genes.
ER  -

TY  - JOUR
AU  - Yamazaki, T.
AU  - Matsuo, J.
AU  - Kikuchi, M.
AU  - Miyamoto, K.
AU  - Oka, K.
AU  - Takahashi, M.
AU  - Takahashi, S.
AU  - Okubo, T.
AU  - Yamaguchi, H.
TI  - Draft Genome Sequence of Chlamydia trachomatis Strain 54, Isolated from the Urogenital Tract of a Male in Japan.
JO  - Genome Announcements
PY  - 2015
SP  - e01242
EP  - e01215
VL  - 3
AB  - We report the draft genome sequence of Chlamydia trachomatis strain 54, isolated  from the
AB  - urogenital tract of a male in Japan, with unique polymorphic membrane proteins. Detailed
AB  - genomic analysis will aid our understanding of the selective pressures that lead to sexual
AB  - differentiation in chlamydial adaptive evolution.
ER  -

TY  - JOUR
AU  - Yan, B.-X.
AU  - Li, N.
AU  - Wu, C.-X.
TI  - The true recognizing sequence of the restriction enzyme whose recognizing sequence is nonpalindromic.
JO  - Yichuan
PY  - 2002
SP  - 420
EP  - 422
VL  - 24
AB  - The recognizing sequence of restriction enzyme includes palindrome and nonpalindromic, and DNA
AB  - is double helix complementary strands. So the
AB  - recognizing sequences of palindrome enzyme in two strands of DNA were
AB  - identical, and can be considered of one sequence. But for
AB  - nonpalindromic restriction enzyme, the recognizing sequences of two
AB  - strands of DNA were not identical. Therefore the true recognizing
AB  - sequences are not only one. In this experiment, an enzyme cleavage
AB  - reaction was carried out which confirmed that the true recognizing
AB  - sites/sequences of non-palindromic enzyme are two instead of one.
ER  -

TY  - JOUR
AU  - Yan, J.
AU  - Deforet, M.
AU  - Boyle, K.E.
AU  - Rahman, R.
AU  - Liang, R.
AU  - Okegbe, C.
AU  - Dietrich, L.E.P.
AU  - Qiu, W.
AU  - Xavier, J.B.
TI  - Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.
JO  - PLoS Comput. Biol.
PY  - 2017
SP  - e1005677
EP  - e1005677
VL  - 13
AB  - Bacteria of many species rely on a simple molecule, the intracellular secondary
AB  - messenger c-di-GMP (Bis-(3'-5')-cyclic dimeric guanosine monophosphate), to make
AB  - a vital choice: whether to stay in one place and form a biofilm, or to leave it
AB  - in search of better conditions. The c-di-GMP network has a bow-tie shaped
AB  - architecture that integrates many signals from the outside world-the input
AB  - stimuli-into intracellular c-di-GMP levels that then regulate genes for biofilm
AB  - formation or for swarming motility-the output phenotypes. How does the
AB  - 'uninformed' process of evolution produce a network with the right input/output
AB  - association and enable bacteria to make the right choice? Inspired by new data
AB  - from 28 clinical isolates of Pseudomonas aeruginosa and strains evolved in
AB  - laboratory experiments we propose a mathematical model where the c-di-GMP network
AB  - is analogous to a machine learning classifier. The analogy immediately suggests a
AB  - mechanism for learning through evolution: adaptation though incremental changes
AB  - in c-di-GMP network proteins acquires knowledge from past experiences and enables
AB  - bacteria to use it to direct future behaviors. Our model clarifies the elusive
AB  - function of the ubiquitous c-di-GMP network, a key regulator of bacterial social
AB  - traits associated with virulence. More broadly, the link between evolution and
AB  - machine learning can help explain how natural selection across fluctuating
AB  - environments produces networks that enable living organisms to make sophisticated
AB  - decisions.
ER  -

TY  - JOUR
AU  - Yan, J.
AU  - Skoko, D.
AU  - Marko, J.F.
TI  - Near-field-magnetic-tweezer manipulation of single DNA molecules.
JO  - Phys. Rev. E Stat. Nonlin. Soft Matter Phys.
PY  - 2004
SP  - 011905
EP  - 011905
VL  - 70
AB  - We have developed an instrument for micromanipulation of single
AB  - DNA molecules end labeled with 3-microm-diameter paramagnetic particles. A
AB  - small, permanent magnet that can be moved as close as 10 microm to the
AB  - particle being manipulated can generate forces in excess of 200 pN,
AB  - significantly larger than obtained in other recent "magnetic-tweezer"
AB  - studies. Our instrument generates these forces in the focal plane of a
AB  - microscope objective, allowing straightforward real-time observation of
AB  - molecule extension with a position resolution of approximately 30 nm. We
AB  - show how our magnetic manipulation system can be combined with
AB  - manipulation and force measurement using glass micropipettes to allow
AB  - rapid switching between measurements in fixed-force and fixed-extension
AB  - ensembles. We demonstrate the use of our system to study formation of DNA
AB  - loops by an enzyme which strongly binds two copies of a specific
AB  - 6-base-pair sequence.
ER  -

TY  - JOUR
AU  - Yan, L.
AU  - Yan, M.
AU  - Xu, L.
AU  - Wei, L.
AU  - Zhang, L.
TI  - Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide.
JO  - Genome Announcements
PY  - 2016
SP  - e01609
EP  - e01615
VL  - 4
AB  - Pseudomonas aeruginosa is a Gram-negative bacterium, which uses a variety of organic chemicals
AB  - as carbon sources. Here, we report the genome sequence of the
AB  - Cu1510 isolate from wastewater containing a high concentration of N,N-dimethyl
AB  - formamide.
ER  -

TY  - JOUR
AU  - Yan, P.-F.
AU  - Ye, S.-Y.
AU  - Wang, P.-Z.
AU  - Li, Q.-L.
AU  - Lu, Y.-Y.
AU  - Zhou, B.
TI  - The restriction endonucleases from Bacillus.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1982
SP  - 151
EP  - 158
VL  - 14
AB  - The activities of restriction endonucleases were found in 10 out of 66 strains
AB  - of Bacillus isolated and examined in our country.  These enzymes were partially
AB  - purified and their recognition sequences were characterized.  Bsp211I, Bsp226I
AB  - and Bce71I are the isoschizomers of HaeIII.  Bsp211I and HaeIII have the same
AB  - cleavage sites as indicated by the arrow in the sequence 5'-GG^CC-3'.  The
AB  - purification procedure of Bsp211I is very simple and its yield is rather high.
AB  - The recognition sequences of Bsp105I, Bsp67I, Bsp64I, Bsp74I and Bsp76I are the
AB  - same as that of MboI, which recognizes the sequence 5'-^GATC-3', the arrow
AB  - indicating the cleavage sites for Bsp 105I and Bsp67I.  While Bsp105I does not
AB  - digest modified DNA, Bsp67I digests DNA whether the adenine residue is
AB  - methylated or not.  Bsp63I and Bsp78I are isoschizomers of PstI, whose
AB  - recognition sequence is 5'-CTGCA^G-3'.  The cutting sites of Bsp 63I and PstI
AB  - are identical.
ER  -

TY  - JOUR
AU  - Yan, W.
AU  - Zhang, R.
AU  - Wei, S.
AU  - Zeng, Q.
AU  - Xiao, X.
AU  - Wang, Q.
AU  - Yan, H.
AU  - Jiao, N.
TI  - Draft Genome Sequence of Prochlorococcus marinus Strain XMU1401, Isolated from the Western Tropical North Pacific Ocean.
JO  - Genome Announcements
PY  - 2018
SP  - e01431
EP  - e01417
VL  - 6
AB  - Prochlorococcus marinus is the most abundant photosynthetic organism in the tropical and
AB  - subtropical oceans. Here, we report the draft genome sequence of
AB  - Prochlorococcus marinus XMU1401, which was isolated from the Western Tropical
AB  - North Pacific Ocean.
ER  -

TY  - JOUR
AU  - Yan, X.
AU  - Ge, H.
AU  - Huang, T.
AU  - Hindra, Y.D.
AU  - Teng, Q.
AU  - Crnovcic, I.
AU  - Li, X.
AU  - Rudolf, J.D.
AU  - Lohman, J.R.
AU  - Gansemans, Y.
AU  - Zhu, X.
AU  - Huang, Y.
AU  - Zhao, L.X.
AU  - Jiang, Y.
AU  - Van Nieuwerburgh, F.
AU  - Rader, C.
AU  - Duan, Y.
AU  - Shen, B.
TI  - Strain Prioritization and Genome Mining for Enediyne Natural Products.
JO  - MBio
PY  - 2016
SP  - e02104
EP  - e02116
VL  - 7
AB  - The enediyne family of natural products has had a profound impact on modern
AB  - chemistry, biology, and medicine, and yet only 11 enediynes have been
AB  - structurally characterized to date. Here we report a genome survey of 3,400
AB  - actinomycetes, identifying 81 strains that harbor genes encoding the enediyne
AB  - polyketide synthase cassettes that could be grouped into 28 distinct clades based
AB  - on phylogenetic analysis. Genome sequencing of 31 representative strains
AB  - confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster.
AB  - A genome neighborhood network allows prediction of new structural features and
AB  - biosynthetic insights that could be exploited for enediyne discovery. We
AB  - confirmed one clade as new C-1027 producers, with a significantly higher C-1027
AB  - titer than the original producer, and discovered a new family of enediyne natural
AB  - products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a
AB  - broad spectrum of cancer cell lines. Our results demonstrate the feasibility of
AB  - rapid discovery of new enediynes from a large strain collection. IMPORTANCE:
AB  - Recent advances in microbial genomics clearly revealed that the biosynthetic
AB  - potential of soil actinomycetes to produce enediynes is underappreciated. A great
AB  - challenge is to develop innovative methods to discover new enediynes and produce
AB  - them in sufficient quantities for chemical, biological, and clinical
AB  - investigations. This work demonstrated the feasibility of rapid discovery of new
AB  - enediynes from a large strain collection. The new C-1027 producers, with a
AB  - significantly higher C-1027 titer than the original producer, will impact the
AB  - practical supply of this important drug lead. The TNMs, with their extremely
AB  - potent cytotoxicity against various cancer cells and their rapid and complete
AB  - cancer cell killing characteristics, in comparison with the payloads used in
AB  - FDA-approved antibody-drug conjugates (ADCs), are poised to be exploited as
AB  - payload candidates for the next generation of anticancer ADCs. Follow-up studies
AB  - on the other identified hits promise the discovery of new enediynes, radically
AB  - expanding the chemical space for the enediyne family.
ER  -

TY  - JOUR
AU  - Yan, X.J.
AU  - Xu, J.
AU  - Gu, Z.H.
AU  - Pan, C.M.
AU  - Lu, G.
AU  - Shen, Y.
AU  - Shi, J.Y.
AU  - Zhu, Y.M.
AU  - Tang, L.
AU  - Zhang, X.W.
AU  - Liang, W.X.
AU  - Mi, J.Q.
AU  - Song, H.D.
AU  - Li, K.Q.
AU  - Chen, Z.
AU  - Chen, S.J.
TI  - Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia.
JO  - Nat. Genet.
PY  - 2011
SP  - 309
EP  - 315
VL  - 43
AB  - Abnormal epigenetic regulation has been implicated in oncogenesis. We report here the
AB  - identification of somatic mutations by exome sequencing
AB  - in acute monocytic leukemia, the M5 subtype of acute myeloid leukemia
AB  - (AML-M5). We discovered mutations in DNMT3A (encoding DNA
AB  - methyltransferase 3A) in 23 of 112 (20.5%) cases. The DNMT3A mutants
AB  - showed reduced enzymatic activity or aberrant affinity to histone H3 in
AB  - vitro. Notably, there were alterations of DNA methylation patterns
AB  - and/or gene expression profiles (such as HOXB genes) in samples with
AB  - DNMT3A mutations as compared with those without such changes. Leukemias
AB  - with DNMT3A mutations constituted a group of poor prognosis with
AB  - elderly disease onset and of promonocytic as well as monocytic
AB  - predominance among AML-M5 individuals. Screening other leukemia
AB  - subtypes showed Arg882 alterations in 13.6% of acute myelomonocytic
AB  - leukemia (AML-M4) cases. Our work suggests a contribution of aberrant
AB  - DNA methyltransferase activity to the pathogenesis of acute monocytic
AB  - leukemia and provides a useful new biomarker for relevant cases.
ER  -

TY  - JOUR
AU  - Yan, Y.
AU  - Zhao, C.W.
AU  - Zhang, Y.Z.
AU  - Zhang, Z.H.
AU  - Pan, G.L.
AU  - Liu, W.W.
AU  - Ma, Q.Y.
AU  - Hou, R.
AU  - Tan, X.M.
TI  - Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6928
EP  - 6929
VL  - 194
AB  - Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed
AB  - the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1
AB  - from the feces of a giant panda in China. Genes encoding a beta-lactamase and
AB  - efflux pumps, as well as other factors, have been found in the genome.
ER  -

TY  - JOUR
AU  - Yan, Y.W.
AU  - Zhang, P.P.
AU  - Zhu, T.
AU  - Quan, Z.X.
TI  - Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture.
JO  - Genome Announcements
PY  - 2018
SP  - e00465
EP  - e00418
VL  - 6
AB  - Here, we report the draft whole-genome sequence of a bacterial strain, Acinetobacter sp.
AB  - strain BS1, isolated from black soil during ethane oxidation
AB  - culture. Medium- or long-chain alkane oxidation-related genes were identified;
AB  - however, the short-chain alkane monooxygenase was not detected.
ER  -

TY  - JOUR
AU  - Yanagisawa, Y.
AU  - Ito, E.
AU  - Yuasa, Y.
AU  - Maruyama, K.
TI  - The human DNA methyltransferases DNMT3A and DNMT3B have two types of promoters with different CpG contents.
JO  - Biochim. Biophys. Acta
PY  - 2002
SP  - 457
EP  - 457
VL  - 1577
AB  - DNA modification that is established by de novo methylation is involved in the epigenetic
AB  - control of genome functions. The DNMT3A and DNMT3B genes encode putative de novo
AB  - methyltransferases. In this paper, we investigated the transcriptional regulatory regions of
AB  - the human DNMT3A and DNMT3B genes. We found that the DNMT3A and DNMT3B genes have multiple
AB  - transcriptional start points (TSPs) that are separated on the chromosome and the expressions
AB  - of these genes are controlled by multiple promoters. The DNMT3A gene has at least four TSPs
AB  - and the expression is controlled by three different promoters. All three promoters lack
AB  - typical TATA sequences adjacent to the TSPs. Two of them bear CpG-rich promoters and the other
AB  - a CpG-poor promoter. The DNMT3B gene has at least two TSPs which exist in different exons and
AB  - the expression is controlled by different promoters. Both promoter regions of the DNMT3B gene
AB  - lack typical TATA sequences, where one promoter contains a CpG-rich area near the TSP, the
AB  - other promoter is CpG-poor. Together with the data that the human DNMT1 gene has both CpG-rich
AB  - and CpG-poor promoters, it is suggested that transcriptional regulation by two types of
AB  - promoters, CpG-rich and CpG-poor, might be common characteristics in the DNMT gene family.
ER  -

TY  - JOUR
AU  - Yang, A.S.
AU  - Jones, P.A.
AU  - Shibata, A.
TI  - The mutational burden of 5-methylcytosine.
JO  - Epigenetic Mechanisms of Gene Regulation
PY  - 1996
SP  - 77
EP  - 94
VL  - 0
AB  - The importance of the epigenetic modification of cytosine to 5-methylcytosine is discussed in
AB  - other chapters of this volume.  In this chapter, we address the heavy mutational burden
AB  - induced by the methylation of C at CpG dinucleotides, which is the price that must be paid for
AB  - having a m5C epigenetic system.  The mutability of m5C to thymine has presumably led to a
AB  - depletion of the CpG dinucleotide in the mammalian genome over the course of evolution.
AB  - Furthermore, m5C residues, which comprise only about 1% of the human genome, account for about
AB  - 30% of the base substitution mutations found in genetic disease and 25% of the mutations found
AB  - in tumor suppressor genes.  The mutability of m5C was first demonstrated in Escherichia coli.
AB  - Cytosine bases that were methylated in the E. coli lacI gene were found to be hot spots for
AB  - spontaneous base substitution mutations, and the hot spots disappeared when the same sites
AB  - were unmethylated.  It was speculated that the reason for this increase was that whereas C
AB  - deaminates to uracil, m5C deaminates to T, which is a normal DNA base and therefore inherently
AB  - more difficult to repair.  This mechanism of DNA mutation is unique in that it is not induced
AB  - by exogenous chemicals and it occurs in nonreplicating DNA.  The deamination of m5C is a
AB  - first-order chemical process, which is consistent with the fact that deamination occurs on
AB  - both the transcribed and nontranscribed strand of DNA with equal probability.
ER  -

TY  - JOUR
AU  - Yang, A.S.
AU  - Shen, J.-C.
AU  - Zingg, J.-M.
AU  - Mi, S.
AU  - Jones, P.A.
TI  - DNA (cytosine-5) methyltransferase blocks DNA repair.
JO  - Proc. Amer. Assoc. Cancer Res.
PY  - 1995
SP  - 538
EP  - 538
VL  - 36
AB  - the CpG dinucleotide is markedly underrepresented in the human genome, yet is the site of
AB  - about one third of all point mutations found in the germline and in cancer. The hydrolytic
AB  - deamination of 5-methylcytosine (5mC) to thymine (T) is believed to be responsible for the
AB  - increased mutability of the CpG dinucleotide. We have previously shown an alternate possible
AB  - mechanism in which HpaII DNA-(cytosine-5) methyltransferase (M.HpaII), a bacterial enzyme
AB  - which carries out methylation by a similar mechanism of action to human methyltransferase, can
AB  - enzymatically deaminate cytosine (C) to uracil (U) in DNA. Both the hydrolytic deamination of
AB  - 5mC to T and enzymatic deamination of C to U create premutagenic DNA mismatches (G:U and G:T)
AB  - with the guanine (G) originally paired to the original C. Surprisingly, we found that
AB  - methyltransferase has a higher affinity for these mismatches than for the normal target G:C.
AB  - Methyltransferase was also shown to transfer a methyl group to the 5-position of U creating T,
AB  - presenting a new possible mechanism for C to T transition mutations. This binding by
AB  - methyltransferase prevented the repair of G:U mismatches by uracil DNA glycosylase in vitro.
AB  - Mutant forms of M.HhaI which bind to the target sequence but lack catalytic activity when
AB  - expressed in E. coli bestowed a mutator phenotype presumably due to the blockage of DNA
AB  - repair.
ER  -

TY  - JOUR
AU  - Yang, A.S.
AU  - Shen, J.-C.
AU  - Zingg, J.-M.
AU  - Mi, S.
AU  - Jones, P.A.
TI  - HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair.
JO  - Nucleic Acids Res.
PY  - 1995
SP  - 1380
EP  - 1387
VL  - 23
AB  - The hydrolytic deamination of 5-methylcytosine (5-mC) to thymine (T) is believed to be
AB  - responsible for the high mutability of the CpG dinucleotide in DNA. We have shown a possible
AB  - alternate mechanism for mutagenesis at CpG in which HpaII DNA-(cytosine-5) methyltransferase
AB  - (M.HpaII) can enzymatically deaminate cytosine (C) to uracil (U) in DNA. Both the hydrolytic
AB  - deamination of 5-mC and enzymatic deamination of C create premutagenic DNA mismatches (G:U and
AB  - G:T) with the guanine (G) originally paired to the normal C. Surprisingly, we found that
AB  - DNA-(cytosine-5) methyltransferases have higher affinities for these DNA mismatches than for
AB  - their normal G:C targets and are capable of transferring a methyl group to the 5-position of
AB  - U, creating T at low efficiencies. This binding by methyltransferase to mismatches at the
AB  - recognition site prevented repair of G:U mismatches by uracil DNA glycosylase in vitro.
ER  -

TY  - JOUR
AU  - Yang, C.
AU  - Zhang, W.
AU  - Ren, M.
AU  - Song, L.
AU  - Li, T.
AU  - Zhao, J.
TI  - Whole-Genome Sequence of Microcystis aeruginosa TAIHU98, a Nontoxic Bloom-Forming Strain Isolated from Taihu Lake, China.
JO  - Genome Announcements
PY  - 2013
SP  - e00333
EP  - e00313
VL  - 1
AB  - Microcystis aeruginosa is a dominant bloom-forming cyanobacterium in many freshwater lakes.
AB  - This report describes the first whole-genome sequence of the
AB  - nontoxic strain of M. aeruginosa TAIHU98, which was isolated from Taihu Lake in
AB  - eastern China.
ER  -

TY  - JOUR
AU  - Yang, C.C.
AU  - Baxter, B.K.
AU  - Topal, M.D.
TI  - DNA cleavage by NaeI: protein purification, rate-limiting step, and accuracy.
JO  - Biochemistry
PY  - 1994
SP  - 14918
EP  - 14925
VL  - 33
AB  - NaeI endonuclease must bind two DNA sites for cleavage to occur. NaeI was purified to apparent
AB  - homogeneity and used to determine the rate-limiting step for DNA cleavage and to measure
AB  - NaeI's specificity for its cognate recognition site. Steady-state cleavage by NaeI in the
AB  - presence of effector DNA (activated) gave values of 0.045s-1 and 10 nM for kcat and KM for M13
AB  - DNA substrate, respectively, but values of 0.4s-1 and 170 nM, respectively, for an M13 DNA
AB  - fragment substrate. Single-turnover cleavage of M13 DNA cleavage by NaeI showed an initial
AB  - burst of substrate cleavage that was proportional to NaeI concentration, implying that product
AB  - release is rate-limiting for turnover of NaeI. The NaeI effector and substrate binding sites
AB  - were found to prefer cognate over noncognate sequences by 1000-fold and at least 40-500-fold,
AB  - respectively. kcat for noncognate recognition sequence was at least 10/6-fold lower than that
AB  - for cognate. The specificity for activated NaeI, as measured by kcat/KM, for noncognate
AB  - recognition sequence was 10/8-fold lower than that for cognate, and over 10/11-fold lower when
AB  - the decreased affinity for noncognate sequence at the effector binding site was taken into
AB  - account. This specificity is approximately 10/4-fold larger than for any other restriction
AB  - enzyme measured.
ER  -

TY  - JOUR
AU  - Yang, C.C.
AU  - Topal, M.D.
TI  - Nonidentical DNA-binding sites of endonuclease NaeI recognize different families of sequences flanking the recognition site.
JO  - Biochemistry
PY  - 1992
SP  - 9657
EP  - 9664
VL  - 31
AB  - NaeI endonuclease uses a two-site binding mechanism to cleave substrate DNA: reaction-rate
AB  - studies imply that occupancy of the second DNA site causes an allosteric change in the protein
AB  - that enables DNA cleavage at the first site [Conrad, M., & Topal, M.D. (1989) Proc. Natl.
AB  - Acad. Sci. U.S.A. 86, 9707-9711]. Measurements of relative binding affinities for 14-base-pair
AB  - DNA fragments containing the NaeI recognition sequence GCCGGC and various flanking sequencs
AB  - showed that the two DNA-binding sites are not identical. G-C-rich flanking sequences were
AB  - preferred by the activator binding site, whereas A-T-rich flanking sequences were preferred by
AB  - the substrate binding site: GGGTGCCGGCAGGG was preferred 8-fold more by the activator site but
AB  - 14-fold less by the substrate site than TTTCGCCGGCGTTT. Substitution of pyrimidine or
AB  - 7-deazapurine for purine immediately 3'to GCCGGC reduced DNA affinity for only the activator
AB  - site by up to 26-fold, implying that the activator DNA-binding site requires N-7 base contacts
AB  - immediately flanking GCCGGC. The implications of nonidentical DNA-binding sites, one of which
AB  - binds a specific DNA site to allosterically activate the other, are discussed.
ER  -

TY  - JOUR
AU  - Yang, C.H.
AU  - Wu, C.C.
AU  - Cheng, W.S.
AU  - Chung, M.C.
AU  - Tsai, Y.C.
AU  - Chang, C.H.
TI  - A17, the First Sequenced Strain of Lactococcus lactis subsp. cremoris with Potential Immunomodulatory Functions.
JO  - Genome Announcements
PY  - 2015
SP  - e01563
EP  - e01514
VL  - 3
AB  - Lactococcus lactis subsp. cremoris A17, isolated from Taiwan fermented cabbage, is the first
AB  - sequenced strain of L. lactis subsp. cremoris with immunomodulatory
AB  - activity and antiallergic functions. The resulting A17 draft genome contains
AB  - 2,679,936 bp and indicates that A17 is a potential exopolysaccharide-producing
AB  - strain without any known virulence gene.
ER  -

TY  - JOUR
AU  - Yang, F. et al.
TI  - Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 6445
EP  - 6458
VL  - 33
AB  - The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public
AB  - health. The genus status and species
AB  - classification appear no longer valid, as compelling evidence indicates
AB  - that Shigella, as well as enteroinvasive Escherichia coli, are derived
AB  - from multiple origins of E.coli and form a single pathovar. Nevertheless,
AB  - Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella
AB  - boydii is restricted to the Indian subcontinent, while Shigella flexneri
AB  - and Shigella sonnei are prevalent in developing and developed countries
AB  - respectively. To begin to explain these distinctive epidemiological and
AB  - pathological features at the genome level, we have carried out comparative
AB  - genomics on four representative strains. Each of the Shigella genomes
AB  - includes a virulence plasmid that encodes conserved primary virulence
AB  - determinants. The Shigella chromosomes share most of their genes with that
AB  - of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300
AB  - approximately 700 copies of insertion sequence (IS) elements, and numerous
AB  - deletions, insertions, translocations and inversions. There is extensive
AB  - diversity of putative virulence genes, mostly acquired via
AB  - bacteriophage-mediated lateral gene transfer. Hence, via convergent
AB  - evolution involving gain and loss of functions, through
AB  - bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements
AB  - and formation of pseudogenes, the Shigella spp. became highly specific
AB  - human pathogens with variable epidemiological and pathological features.
ER  -

TY  - JOUR
AU  - Yang, F.
AU  - Li, H.
AU  - Zhang, S.
AU  - Wang, X.
TI  - Draft Genome Sequence of Streptococcus agalactiae Serotype Ia Strain M19, a Multidrug-Resistant Isolate from a Cow with Bovine Mastitis.
JO  - Genome Announcements
PY  - 2016
SP  - e01093
EP  - e01016
VL  - 4
AB  - Streptococcus agalactiae is a major contagious pathogen causing bovine mastitis worldwide. We
AB  - report here the draft sequence of S. agalactiae Ia strain M19, a
AB  - multidrug-resistant isolate from a bovine mastitis case in Ningxia Hui autonomous
AB  - region, China.
ER  -

TY  - JOUR
AU  - Yang, F.
AU  - Tang, C.
AU  - Wang, Y.
AU  - Zhang, H.
AU  - Yue, H.
TI  - Genome Sequence of Mycoplasma ovipneumoniae Strain SC01.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5018
EP  - 5018
VL  - 193
AB  - Mycoplasma ovipneumoniae is associated with chronic non-progressive pneumonia in both sheep
AB  - and goats. Studies concerning its molecular
AB  - pathogenesis, genetic analysis and vaccine development have been hindered
AB  - due to limited genomic information. Here, we announce the first complete
AB  - genome sequence of this organism.
ER  -

TY  - JOUR
AU  - Yang, G.
AU  - Chen, J.
AU  - Zhou, S.
TI  - Novibacillus thermophilus gen. nov., sp. nov., a Gram-staining-negative and moderately thermophilic member of the family Thermoactinomycetaceae.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2015
SP  - 2591
EP  - 2597
VL  - 65
AB  - Two Gram-staining-negative, facultatively anaerobic bacterial strains, SG-1T and
AB  - SG-2, were isolated from a saline soil sample and a compost sample, respectively.
AB  - The cells were non-motile rods that occurred singly or in chains, and endospores
AB  - were not observed under tested growth conditions. Optimum growth occurred at 50
AB  - degrees C, pH 7.5-8.0 and with 5-7 % (w/v) NaCl. The DNA G+C content was
AB  - 49.5-50.5 mol%. The strains contained MK-7 as the predominant menaquinone and
AB  - iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The polar lipids
AB  - consisted mainly of diphosphatidylglycerol and phosphatidylglycerol. The
AB  - cell-wall peptidoglycan type was A1gamma (meso-DAP direct). Phylogenetic analyses
AB  - revealed that the new isolates belonged to the family Thermoactinomycetaceae,
AB  - exhibiting low 16S rRNA gene sequence similarity (90.8-91.3 %) to the nearest
AB  - type strain, Mechercharimyces asporophorigenens YM11-542T, and formed a
AB  - well-supported lineage that was clearly distinguished from all currently
AB  - described genera in this family. Based on our polyphasic taxonomic
AB  - characterization, we propose that strains SG-1T and SG-2 represent a novel genus
AB  - and species within the family Thermoactinomycetaceae, for which we propose the
AB  - name Novibacillus thermophilus gen. nov., sp. nov. The type strain of
AB  - Novibacillus thermophilus is SG-1T ( = KCTC 33118T = CGMCC 1.12771T).
ER  -

TY  - JOUR
AU  - Yang, G.
AU  - Chen, S.
AU  - Zhou, S.
AU  - Liu, Y.
TI  - Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 118
EP  - 118
VL  - 10
AB  - Strain GSS01(T) (=KCTC 4545=MCCC 1 K00269) is the type strain of the species Geobacter soli.
AB  - G. soli strain GSS01(T) is of interest due to its ability to
AB  - reduce insoluble Fe(III) oxides with a wide range of electron donors. Here we
AB  - describe some key features of this strain, together with the whole genome
AB  - sequence and annotation. The genome of size 3,657,100 bp contains 3229
AB  - protein-coding and 54 RNA genes, including 2 16S rRNA genes. The genome of strain
AB  - GSS01(T)contains 76 predicted cytochrome genes, 24 pilus assembly protein genes
AB  - and several other genes, which were proposed to be related to the reduction of
AB  - insoluble Fe(III) oxides. The genes associated with the electron donors and
AB  - acceptors of strain GSS01(T) were predicted in the genome. Information gained
AB  - from its sequence will be relevant to the future elucidation of extracellular
AB  - electron transfer mechanism during the reduction of Fe(III) oxides.
ER  -

TY  - JOUR
AU  - Yang, G.
AU  - Guo, J.
AU  - Zhuang, L.
AU  - Yuan, Y.
AU  - Zhou, S.
TI  - Desulfotomaculum ferrireducens sp. nov., a moderately thermophilic sulfate-reducing and dissimilatory Fe(III)-reducing bacterium isolated from compost.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2016
SP  - 3022
EP  - 3028
VL  - 66
AB  - A novel dissimilatory Fe(III)-reducing bacterium, designated strain GSS09T, was
AB  - isolated from a compost sample by using a solid medium containing acetate and
AB  - ferrihydrite as electron donor and electron acceptor, respectively. Cells of
AB  - strain GSS09T were anaerobic, Gram-stain-positive, motile, endospore-forming and
AB  - rod-shaped. Growth occurred at 30-55 degrees C (optimum 50 degrees C), at pH
AB  - 6.5-9.0 (optimum pH 7.5) and in the presence of 0-3 % (w/v) NaCl (optimum 1 %).
AB  - Both sulfur compounds such as sulfate, sulfite and thiosulfate and Fe(III) oxides
AB  - such as ferrihydrite could be utilized as electron acceptors. Phylogenetic
AB  - analysis based on 16S rRNA gene sequences revealed that strain GSS09T was related
AB  - closely to Desulfotomaculum hydrothermale Lam5T (94.5 % sequence similarity). The
AB  - major fatty acids were C16 : 0 and C16 : 1omega7c/C16 : 1omega6c. The G+C content
AB  - of the genomic DNA was 49.1 mol%. On the basis of phylogenetic analysis,
AB  - phenotypic characterization and physiological tests, strain GSS09T is considered
AB  - to represent a novel species of the genus Desulfotomaculum, for which the name
AB  - Desulfotomaculum ferrireducens sp. nov. is proposed. The type strain is GSS09T
AB  - (=KCTC 15523T=MCCC 1K01254T).
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - Carlson, B.
AU  - Geornaras, I.
AU  - Woerner, D.
AU  - Sofos, J.
AU  - Belk, K.
TI  - Draft Genome Sequence of Shiga Toxin-Negative Escherichia coli O157:H7 Strain C1-057, Isolated from Feedlot Cattle.
JO  - Genome Announcements
PY  - 2016
SP  - e00049
EP  - e00016
VL  - 4
AB  - Escherichia coli O157:H7 is one of the major foodborne pathogens in the United States. We
AB  - isolated a variant Shiga toxin-negative E. coli O157:H7 strain from
AB  - feedlot cattle. We report here the draft genome sequence of this isolate,
AB  - consisting of a chromosome of ~4.8 Mb and two plasmids of ~96 kb and ~14 kb.
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - Fitz-Gibbon, S.
AU  - Marcotte, E.M.
AU  - Tai, J.H.
AU  - Hyman, E.C.
AU  - Miller, J.H.
TI  - Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum.
JO  - J. Bacteriol.
PY  - 2000
SP  - 1272
EP  - 1279
VL  - 182
AB  - U/G and T/G mismatches commonly occur due to spontaneous deamination of cytosine and
AB  - 5-methylcytosine in double-stranded DNA. This mutagenic
AB  - effect is particularly strong for extreme thermophiles, since the
AB  - spontaneous deamination reaction is much enhanced at high temperature.
AB  - Previously, a U/G and T/G mismatch-specific glycosylase (Mth-MIG) was
AB  - found on a cryptic plasmid of the archaeon Methanobacterium
AB  - thermoautotrophicum, a thermophile with an optimal growth temperature of
AB  - 65 degrees C. We report characterization of a putative DNA glycosylase
AB  - from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal
AB  - growth temperature is 100 degrees C. The open reading frame was first
AB  - identified through a genome sequencing project in our laboratory. The
AB  - predicted product of 230 amino acids shares significant sequence homology
AB  - to [4Fe-4S]-containing Nth/MutY DNA glycosylases. The histidine-tagged
AB  - recombinant protein was expressed in Escherichia coli and purified. It is
AB  - thermostable and displays DNA glycosylase activities specific to U/G and
AB  - T/G mismatches with an uncoupled AP lyase activity. It also processes
AB  - U/7,8-dihydro-oxoguanine and T/7,8-dihydro-oxoguanine mismatches. We
AB  - designate it Pa-MIG. Using sequence comparisons among complete bacterial
AB  - and archaeal genomes, we have uncovered a putative MIG protein from
AB  - another hyperthermophilic archaeon, Aeropyrum pernix. The unique conserved
AB  - amino acid motifs of MIG proteins are proposed to distinguish MIG proteins
AB  - from the closely related Nth/MutY DNA glycosylases.
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - He, T.
AU  - Wu, W.
AU  - Zhu, W.
AU  - Lu, B.
AU  - Sun, W.
TI  - Whole-Genome Shotgun Assembly and Analysis of the Genome of Streptomyces mobaraensis DSM 40847, a Strain for Industrial Production of Microbial  Transglutaminase.
JO  - Genome Announcements
PY  - 2013
SP  - e0014313
EP  - e0014313
VL  - 1
AB  - Here, we report the draft annotated genome sequence of Streptomyces mobaraensis strain DSM
AB  - 40847, which is used in industry to produce microbial
AB  - transglutaminase. The genome sequence will allow for the characterization of the
AB  - molecular mechanisms underlying the beneficial properties of this organism.
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - Liao, Y.
AU  - Wang, B.
AU  - Lin, Y.
AU  - Pan, L.
TI  - Genome Sequence of Escherichia coli XH140A, Which Produces L-Threonine.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6090
EP  - 6091
VL  - 193
AB  - Here we report the draft annotated genome sequence of Escherichia coli XH140A, which is used
AB  - to produce l-threonine in industry. The genome
AB  - sequence will allow the characterization of the molecular mechanisms
AB  - underlying its beneficial properties.
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - Liao, Y.
AU  - Wang, B.
AU  - Lin, Y.
AU  - Pan, L.
TI  - Draft Genome Sequence of Escherichia coli XH001, a Producer of L-Threonine in Industry.
JO  - J. Bacteriol.
PY  - 2011
SP  - 6406
EP  - 6407
VL  - 193
AB  - l-Threonine has been widely used as a supplement in the food, pharmaceutical, and cosmetic
AB  - industries. Here, we present a high-quality
AB  - draft annotated genome sequence of Escherichia coli XH001, a producer of
AB  - l-threonine in industry. Its genome and plasmid sequence will provide
AB  - clues about the molecular mechanisms underlying its beneficial properties.
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - Liao, Y.
AU  - Wang, B.
AU  - Lin, Y.
AU  - Pan, L.
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens XH7, Which Exhibits Production of Purine Nucleosides.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5593
EP  - 5594
VL  - 193
AB  - Here, we report the complete annotated genome sequence of Bacillus amyloliquefaciens XH7,
AB  - which is used to produce purine nucleosides in
AB  - industry. The genome sequence will allow for the characterization of the
AB  - molecular mechanisms underlying its beneficial properties.
ER  -

TY  - JOUR
AU  - Yang, H.
AU  - Zhang, Z.
AU  - Yan, R.
AU  - Wang, Y.
AU  - Zhu, D.
TI  - Draft Genome Sequence of Streptomyces sp. Strain PRh5, a Novel Endophytic Actinomycete Isolated from Dongxiang Wild Rice Root.
JO  - Genome Announcements
PY  - 2014
SP  - e00012
EP  - e00014
VL  - 2
AB  - Here, we report the draft genome sequence of Streptomyces sp. strain PRh5 (China  Center for
AB  - Type Culture Collection [CCTCC] number 2013487), which is used to produce nigericin and
AB  - nocardamine. The genome sequence will allow for the characterization of the molecular
AB  - mechanisms underlying its beneficial properties.
ER  -

TY  - JOUR
AU  - Yang, J.
AU  - Deng, C.
AU  - Hemati, N.
AU  - Hanash, S.M.
AU  - Richardson, B.C.
TI  - Effect of mitogenic stimulation and DNA methylation on human T cell DNA methyltransferase expression and activity.
JO  - J. Immunol.
PY  - 1997
SP  - 1303
EP  - 1309
VL  - 159
AB  - DNA methylation, a mechanism modifying gene expression, is mediated in part by the enzyme DNA
AB  - methyltransferase.  Reduced levels of T cell DNA methyltransferase have been observed in
AB  - lupus-like diseases, and increased levels have been reported in malignancies.  Little is known
AB  - concerning the regulation of human DNA methyltransferase.  In this report we demonstrate that
AB  - mitogenic T cell stimulation causes an increase in DNA methyltransferase mRNA and enzyme
AB  - activity.  We also show that pharmacologic inhibition of T cell DNA methylation causes an
AB  - increase in the rate of DNA methyltransferase mRNA transcription and a corresponding increase
AB  - in mRNA levels and enzyme activity.  This suggests that DNA methyltransferase is itself
AB  - regulated in part by DNA methylation status, possibly representing a feedback mechanism.  DNA
AB  - methylation inhibition also resulted in an increase in Ha-ras and c-jun mRNA levels,
AB  - overexpression of which increases DNA methyltransferase in murine systems.  These results thus
AB  - identify two mechanisms regulating levels of human T cell DNA methyltransferase and raise the
AB  - possibility that abnormalities in either could contribute to disorders associated with altered
AB  - DNA methylation.
ER  -

TY  - JOUR
AU  - Yang, J.
AU  - Dong, C.X.
AU  - Huang, X.
AU  - Zhao, J.D.
TI  - Sulfonation of polyvinylidene difluoride resin and its application in extraction of restriction enzymes from DNA digestion solutions.
JO  - Anal. Biochem.
PY  - 2003
SP  - 99
EP  - 103
VL  - 322
AB  - Sulfonation of polyvinylidene difluoride (PVDF) resin was achieved by incubation of the resin
AB  - with sulfuric acid at a moderately high
AB  - temperature. The sulfonated PVDF (SPVDF) resin was studied for its ability
AB  - to extract restriction enzymes from DNA digestion solutions. The SPVDF
AB  - resin was effective in adsorbing restriction enzymes such as EcoRI and
AB  - BamHI and the extraction procedure was easy and simple to perform. The
AB  - adsorption depended upon the amount of the resin added. We found that 1 mg
AB  - of the SPVDF resin could completely remove all restriction enzyme activity
AB  - routinely used in DNA digestion within 2 min after its addition. Treatment
AB  - of a digestion solution with the SPVDF resin did not change the reaction
AB  - solution and the same digestion buffer could be used for another digestion
AB  - of the same DNA with other enzymes. We also found that, in comparison with
AB  - normal PVDF, the SPVDF resin adsorbed less DNA, resulting in less loss of
AB  - DNA in the extraction step. The potential application of the SPVDF resin
AB  - in other procedures of molecular cloning and enzyme purification is
AB  - discussed.
ER  -

TY  - JOUR
AU  - Yang, J.
AU  - Malik, H.S.
AU  - Eickbush, T.H.
TI  - Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1999
SP  - 7847
EP  - 7852
VL  - 96
AB  - The non-long terminal repeat retrotransposon, R2, encodes a sequence-specific endonuclease
AB  - responsible for its insertion at a unique site in the 28S rRNA genes of arthropods.  Although
AB  - most non-LTR retrotransposons encode an apurinic-like endonuclease upstream of a common
AB  - reverse transcriptase domain, R2 and many other site-specific non-LTR elements do not (CRE1
AB  - and 2, SLACS, CZAR, Dong, R4).  Sequence comparison of these site-specific elements has
AB  - revealed that the region downstream of their reverse transcriptase domain is conserved and
AB  - shares sequence features with various prokaryotic restriction endonucleases.  In particular,
AB  - these non-LTR elements have a Lys/Arg-Pro-Asp-X12-14aa-Asp/Glu motif known to lie near the
AB  - scissile phosphodiester bonds in the protein-DNA complexes of restriction enzymes.
AB  - Site-directed mutagenesis of the R2 protein was used to provide evidence that this motif is
AB  - also part of the active site of the endonuclease encoded by this element.  Mutations of this
AB  - motif eliminate both DNA-cleavage activities of the R2 protein: first-strand cleavage in which
AB  - the exposed 3' end is used to prime reverse transcription of the RNA template and
AB  - second-strand cleavage, which occurs after reverse transcription.  The general organization of
AB  - the R2 protein appears similar to the type IIS restriction enzyme, FokI, in which specific DNA
AB  - binding is controlled by a separate domain located amino terminal to the cleavage domain.
AB  - Previous phylogenetic analysis of their reverse transcriptase domains has indicated that the
AB  - non-LTR elements identified here as containing restriction-like endonucleases are the oldest
AB  - lineages of non-LTR elements, suggesting a scenario for the evolution of non-LTR elements.
ER  -

TY  - JOUR
AU  - Yang, J.
AU  - Mohr, G.
AU  - Perlman, P.S.
AU  - Lambowitz, A.M.
TI  - Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity of aI1 and reverse splicing into DNA transposition sites in vitro.
JO  - J. Mol. Biol.
PY  - 1998
SP  - 505
EP  - 523
VL  - 282
AB  - The retrohoming of the yeast mtDNA intron aI1 occurs by a target DNA-primed reverse
AB  - transcription (TPRT) mechanism in which the intron RNA reverse splices directly into the
AB  - recipient DNA and is then copied by the intron-encoded reverse transcriptase. Here, we carried
AB  - out biochemical characterization of the intron-encoded reverse transcriptase and site-specific
AB  - DNA endonuclease activities required for this process. We show that the aI1 reverse
AB  - transcriptase has high TPRT activity in the presence of appropriate DNA target sites, but
AB  - differs from the closely related reverse transcriptase encoded by the yeast aI2 intron in
AB  - being unable to use artificial substrates efficiently. Characterization of TPRT products shows
AB  - that the fully reverse spliced intron RNA is an efficient template for cDNA synthesis, while
AB  - reverse transcription of partially reverse spliced intron RNA is impeded by the branch point.
AB  - Novel features of the aI1 reaction include a prominent open-circular product in which cDNAs
AB  - are incorporated at a nick at the antisense-strand cleavage site. The aI1 endonuclease
AB  - activity, which catalyzes the DNA cleavage and reverse splicing reactions, is associated with
AB  - ribonucleoprotein particles containing the intron-encoded protein and the excised intron RNA.
AB  - As shown for the aI2 endonuclease, both the RNA and protein components are used for DNA target
AB  - site recognition, but the aI1 protein has less stringent nucleotide sequence requirements for
AB  - the reverse splicing reaction. Finally, perhaps reflecting this relaxed target specificity, in
AB  - vitro experiments show that aI1 can reverse splice directly into ectopic mtDNA transposition
AB  - sites, consistent with the previously suggested possibility that this mechanism is used for
AB  - ectopic transposition of group II introns in vivo.
ER  -

TY  - JOUR
AU  - Yang, J.
AU  - Zimmerly, S.
AU  - Perlman, P.S.
AU  - Lambowitz, A.M.
TI  - Efficient integration of an intron RNA into double-stranded DNA by reverse splicing.
JO  - Nature
PY  - 1996
SP  - 332
EP  - 335
VL  - 381
AB  - Some group II introns are mobile elements as well as catalytic RNAs.  Introns aI1 and aI2
AB  - found in the gene COX1 in yeast mitochondria encode reverse transcriptases which promote
AB  - site-specific insertion of the intron into intronless alleles ('homing').  For aI2 this
AB  - predominantly occurs by reverse transcription of unspliced precursor RNA at a break in
AB  - double-strand DNA made by an endonuclease encoded by the intron.  The aI2 endonuclease
AB  - involves both the excised intron RNA, which cleaves the DNA's sense strand by partial reverse
AB  - splicing; and the intron-encoded reverse transcriptase which cleaves the antisense strand.
AB  - Here we show that aI1 encodes an analogous endonuclease specific for a different target site
AB  - compatible with the different exon-binding sequences of the intron RNA.  Over half of aI1
AB  - undergoes complete reverse splicing in vitro, thus integrating linear intron RNA directly into
AB  - the DNA.  This unprecedented reaction has implications for both intron mobility and evolution,
AB  - and potential genetic engineering applications.
ER  -

TY  - JOUR
AU  - Yang, J.A.
AU  - Kwon, K.K.
AU  - Oh, H.M.
TI  - Complete Genome Sequence of Flavobacteriales Bacterium Strain UJ101 Isolated from a Xanthid Crab.
JO  - Genome Announcements
PY  - 2017
SP  - e01551
EP  - e01516
VL  - 5
AB  - Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab species  collected
AB  - from the East Sea of Korea. Here, we report the complete genome
AB  - sequence of strain UJ101 for the study of major metabolic pathways related to
AB  - microbial species from marine invertebrate species.
ER  -

TY  - JOUR
AU  - Yang, J.L.
AU  - Guo, X.P.
AU  - Chen, Y.R.
AU  - Gao, W.
AU  - Ding, D.W.
TI  - Draft Genome Sequence of Shewanella sp. ECSMB14102, a Mussel Recruitment-Promoting Bacterium Isolated from the East China Sea.
JO  - Genome Announcements
PY  - 2015
SP  - e00670
EP  - e00615
VL  - 3
AB  - Shewanella sp. ECSMB14102, which promotes recruitment of the mussel Mytilus coruscus, was
AB  - isolated from natural biofilms formed on glass slides submerged in
AB  - the East China Sea. Here, we present the draft genome sequence, which comprises
AB  - 4.41 Mb with a G+C content of 52.2%. The genomic information in this strain will
AB  - contribute to deepening our understanding of bacteria-animal interaction.
ER  -

TY  - JOUR
AU  - Yang, J.L.
AU  - Guo, X.P.
AU  - Ding, D.W.
TI  - Draft Genome Sequence of Shewanella sp. ECSMB14101, Isolated from the East China  Sea.
JO  - Genome Announcements
PY  - 2015
SP  - e01388
EP  - e01314
VL  - 3
AB  - Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea. The
AB  - draft genome sequence comprises 4,272,451 bp with a G+C content of
AB  - 49.82%. Information on this draft genome will contribute to the understanding of
AB  - bacterium-animal interactions.
ER  -

TY  - JOUR
AU  - Yang, J.M.
AU  - Deurraza, P.J.
AU  - Matvienko, N.
AU  - O'sullivan, D.J.
TI  - Involvement of the LlaKR2I Methylase in Expression of the AbiR Bacteriophage Defense System in Lactococcus lactis subsp. lactis biovar   diacetylactis KR2.
JO  - J. Bacteriol.
PY  - 2006
SP  - 1920
EP  - 1928
VL  - 188
AB  - The native lactococcal plasmid, pKR223, from Lactococcus lactis subsp. lactis biovar
AB  - diacetylactis KR2 encodes two distinct
AB  - bacteriophage-resistant mechanisms, the LlaKR2I restriction and
AB  - modification (R/M) system and the abortive infection (Abi) mechanism,
AB  - AbiR, that impedes bacteriophage DNA replication. This study completed the
AB  - characterization of AbiR, revealing that it is the first Abi system to be
AB  - encoded by three genes, abiRa, abiRb, and abiRc, arranged in an operon and
AB  - that it requires the methylase gene from the LlaKR2I R/M system. An
AB  - analysis of deletion and insertion clones demonstrated that the AbiR
AB  - operon was toxic in L. lactis without the presence of the LlaKR2I
AB  - methylase, which is required to protect L. lactis from AbiR toxicity. The
AB  - novelty of the AbiR system resides in its original gene organization and
AB  - the unusual protective role of the LlaKR2I methylase. Interestingly, the
AB  - AbiR genetic determinants are flanked by two IS982 elements generating a
AB  - likely transposable AbiR composite. This observation not only
AB  - substantiated the novel function of the LlaKR2I methylase in the AbiR
AB  - system but also illustrated the evolution of the LlaKR2I methylase toward
AB  - a new and separate cellular function. This unique structure of both the
AB  - LlaKR2I R/M system and the AbiR system may have contributed to the
AB  - evolution of the LlaKR2I methylase toward a novel role comparable to that
AB  - of the cell cycle-regulated methylases that include Dam and CcrM
AB  - methylases. This new role for the LlaKR2I methylase offers a unique
AB  - snapshot into the evolution of the cell cycle-regulated methylases from an
AB  - existing R/M system.
ER  -

TY  - JOUR
AU  - Yang, L.
AU  - Chen, Y.
AU  - Li, Z.
AU  - Shi, Y.
AU  - Li, Z.
AU  - Zhao, X.
TI  - Complete Genome Sequence of Lactobacillus acidophilus MN-BM-F01.
JO  - Genome Announcements
PY  - 2016
SP  - e01699
EP  - e01615
VL  - 4
AB  - Lactobacillus acidophilus MN-BM-F01 was originally isolated from a traditional fermented dairy
AB  - product in China. The characteristics of this bacterium are its
AB  - low post-acidification ability and high acid-producing rate. Here, we report the
AB  - main genome features of L. acidophilus MN-BM-F01.
ER  -

TY  - JOUR
AU  - Yang, L.F.
AU  - Som, S.
AU  - Friedman, S.
TI  - Effect of N-terminal deletions on the activity of EcoRII DNA methylase.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - A436
EP  - A436
VL  - 91
AB  - DNA(cytosine-5)-methyltransferases (Mtases) contain highly conserved core
AB  - sequences and variable regions.  One of the variable regions is at the
AB  - N-terminus where about 100 amino acids present in the enzymes M.EcoRII or
AB  - M.MspI are almost totally absent in other Mtases.  In order to determine the
AB  - function of the N-terminal residues in M.EcoRII we prepared a series of
AB  - N-terminal deletion mutants in pUC19.  Analysis of the mutants showed that
AB  - almost the entire region N-terminal to the first conserved motif can be deleted
AB  - with retention of enzyme activity.  In some mutants translation starts with an
AB  - internal ATG codon of the gene.  Other active constructs are either fused in
AB  - frame with lac z or utilize an ATG codon in the cloning site of the vector.
AB  - Deletion of 96 residues resulted in marked decrease in activity.  Longer
AB  - deletions were inactive.  One such mutant protein deleted of 85 residues was
AB  - purified and characterized.  In vitro methylation studies showed that this
AB  - truncated mutant retained specificity.  However, the Km for AdoMet was 15 fold
AB  - higher than the Km found with the wild type enzyme.  The results indicate that
AB  - the N-terminal region of the protein is not vital for retention of catalytic
AB  - activity but increases the affinity of the enzyme for AdoMet.
ER  -

TY  - JOUR
AU  - Yang, M.
AU  - Lv, Y.
AU  - Xiao, J.
AU  - Wu, H.
AU  - Zheng, H.
AU  - Liu, Q.
AU  - Zhang, Y.
AU  - Wang, Q.
TI  - Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms.
JO  - PLoS ONE
PY  - 2012
SP  - E36987
EP  - E36987
VL  - 7
AB  - Edwardsiella bacteria are leading fish pathogens causing huge losses to
AB  - aquaculture industries worldwide. E. tarda is a broad-host range pathogen that
AB  - infects more than 20 species of fish and other animals including humans while E.
AB  - ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish
AB  - (ESC). Thus, these two species consist of a useful comparative system for
AB  - studying the intricacies of pathogen evolution. Here we present for the first
AB  - time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri
AB  - isolates. Genome-based phylogenetic analysis revealed that E. tarda could be
AB  - separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII)
AB  - based on the sequence similarity. E. tarda strains of EdwGI were clustered
AB  - together with the E. ictaluri lineage and showed low sequence conservation to E.
AB  - tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct
AB  - Edwardsiella strains also supports the new taxonomic relationship of the
AB  - lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as
AB  - well as iron scavenging related genes that fulfilled the criteria of a key
AB  - evolutionary factor likely facilitating the virulence evolution and adaptation to
AB  - a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may
AB  - underlie the adaptive evolution of E. ictaluri in the host specification
AB  - processes. Virulence and competition assays of the null mutants of the
AB  - representative genes experimentally confirmed their contributive roles in the
AB  - evolution/niche adaptive processes. We also reconstructed the hypothetical
AB  - evolutionary pathway to highlight the virulence evolution and niche adaptation
AB  - mechanisms of Edwardsiella. This study may facilitate the development of
AB  - diagnostics, vaccines, and therapeutics for this under-studied pathogen.
ER  -

TY  - JOUR
AU  - Yang, M.-K.
AU  - Ser, S.-C.
AU  - Lee, C.-H.
TI  - Involvement of E. coli dcm methylase in Tn3 transposition.
JO  - Proc. Natl. Sci. Counc. Repub. China B
PY  - 1989
SP  - 276
EP  - 283
VL  - 13
AB  - The effects of DNA methyltransferases on Tn3 transposition were investigated. The E. coli dam
AB  - (deoxyadenosine methylase) gene was found to have no effect on Tn3 transposition. In contrast,
AB  - Tn3 was found to transpose more frequently in dcm+ (deoxycytosine methylase) cells than in
AB  - dcm- mutants. When the EcoRII methylase gene was introduced into dcm- cells (E. coli strain
AB  - GM208), the frequency of Tn3 transposition in GM208 was dramatically increased. The EcoRII
AB  - methylase recognizes and methylates the same sequence as does the dcm methylase. These results
AB  - suggest tht deoxycytosine methylase modified DNA may be a preferred target for Tn3
AB  - transposition. Experiments were also performed to determine whether the Tn3 transposase was
AB  - involved in DNA modification. Plasmid DNA isolated from dcm- E. Coli containing the Tn3
AB  - transposase gene was susceptible to ApyI digestion but resistant to EcoRII digestion,
AB  - suggesting that Tn3 transposase modified the dcm recognition sequence. In addition,
AB  - restriction enzymes TaqI, AvaII, BglI and HpaII did not digest this DNA completely, suggesting
AB  - that the recognition sequences of TaqI, AvaII, BglI and HpaII were modified by Tn3 transposase
AB  - to a certain degree. The type(s), the extent and mechanism(s) of this modification remain to
AB  - be investigated.
ER  -

TY  - JOUR
AU  - Yang, Q. et al.
TI  - Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms.
JO  - Nat. Commun.
PY  - 2017
SP  - 2054
EP  - 2054
VL  - 8
AB  - MCR-1 is a lipid A modifying enzyme that confers resistance to the antibiotic
AB  - colistin. Here, we analyse the impact of MCR-1 expression on E. coli morphology,
AB  - fitness, competitiveness, immune stimulation and virulence. Increased expression
AB  - of mcr-1 results in decreased growth rate, cell viability, competitive ability
AB  - and significant degradation in cell membrane and cytoplasmic structures, compared
AB  - to expression of catalytically inactive MCR-1 (E246A) or MCR-1 soluble component.
AB  - Lipopolysaccharide (LPS) extracted from mcr-1 strains induces lower production of
AB  - IL-6 and TNF, when compared to control LPS. Compared to their parent strains,
AB  - high-level colistin resistance mutants (HLCRMs) show reduced fitness (relative
AB  - fitness is 0.41-0.78) and highly attenuated virulence in a Galleria mellonella
AB  - infection model. Furthermore, HLCRMs are more susceptible to most antibiotics
AB  - than their respective parent strains. Our results show that the bacterium is
AB  - challenged to find a delicate equilibrium between expression of MCR-1-mediated
AB  - colistin resistance and minimalizing toxicity and thus ensuring cell survival.
ER  -

TY  - JOUR
AU  - Yang, Q.H.
AU  - Zhou, C.
AU  - Lin, Q.
AU  - Lu, Z.
AU  - He, L.B.
AU  - Guo, S.L.
TI  - Draft Genome Sequence of Aeromonas sobria Strain 08005, Isolated from Sick Rana catesbeiana.
JO  - Genome Announcements
PY  - 2017
SP  - e01352
EP  - e01316
VL  - 5
AB  - Aeromonas sobria is a Gram-negative, rod-shaped, and ubiquitous bacterium. We present here the
AB  - draft genome sequence of A. sobria strain 08005, isolated from
AB  - an infected bullfrog. It is composed of 66 contigs totaling 4,678,951 bp,
AB  - contains 4,252 coding DNA sequences (CDSs), four rRNAs, and 88 tRNA sequences,
AB  - and shows the presence of various putative virulence-related genes.
ER  -

TY  - JOUR
AU  - Yang, R.
AU  - Liu, G.
AU  - Chen, T.
AU  - Zhang, W.
AU  - Zhang, G.
AU  - Chang, S.
TI  - The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 23
EP  - 23
VL  - 13
AB  - Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin,
AB  - can use crude oil as its sole source of carbon and energy at 20
AB  - degrees C. The genome of P. maritimus strain Y42 has been sequenced to provide
AB  - information on its properties. Genomic analysis shows that the genome of strain
AB  - Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC
AB  - content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although
AB  - the strain Y42 did not show a remarkably higher ability in degrading crude oil
AB  - than other oil-degrading bacteria, the existence of strain Y42 played a
AB  - significant role to reducing the overall environmental impact as an indigenous
AB  - oil-degrading bacterium. In addition, genome annotation revealed that strain Y42
AB  - has many genes responsible for hydrocarbon degradation. Structural features of
AB  - the genomes might provide a competitive edge for P. maritimus strain Y42 to
AB  - survive in oil-polluted environments and be worthy of further study in oil
AB  - degradation for the recovery of crude oil-polluted environments.
ER  -

TY  - JOUR
AU  - Yang, S.
AU  - Pappas, K.M.
AU  - Hauser, L.J.
AU  - Land, M.L.
AU  - Chen, G.L.
AU  - Hurst, G.B.
AU  - Pan, C.
AU  - Kouvelis, V.N.
AU  - Typas, M.A.
AU  - Pelletier, D.A.
AU  - Klingeman, D.M.
AU  - Chang, Y.J.
AU  - Samatova, N.F.
AU  - Brown, S.D.
TI  - Improved genome annotation for Zymomonas mobilis.
JO  - Nat. Biotechnol.
PY  - 2009
SP  - 893
EP  - 894
VL  - 27
AB  - The first genome sequence of the enthanologenic bacterium Zymomonas mobilis ZM4 was reported
AB  - in your journal five years ago.  Because of its productivity, high level of ethanol tolerance
AB  - and ability to be genetically manipulated, Z. mobilis is a promising industrial bacterium for
AB  - fermenting lignocellulosic biomass into enthanol, which is being advanced as an alternative to
AB  - petroleum-derived transportation fuels.  Strains of the bacterium have been developed to
AB  - ferment both hexoses and pantoses into ethanol, and the genome sequence will provide further
AB  - opportunities for strain developments as well as providing more fundamental insights.  We have
AB  - observed many differences between the primary annotation and one performed by the J. Craig
AB  - Venter Institute (JCVI) and have detected differential gene expression in genes predicted by
AB  - JCVI (http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?org=ntzm01) that were absent from the
AB  - primary annotation in our previous work.  We present here an improved version of the ZM4
AB  - genome annotation based on the original primary gene sequence, new epxerimental data generated
AB  - by 454 pyrosequencing and mass spectrometry-based proteomics, a novel gene prediction
AB  - algorithm called Prodigal (prokaryotic dynamic programming genefinding algorithm) that is
AB  - incorporated into an annotation pipeline, and manual curation.
ER  -

TY  - JOUR
AU  - Yang, S.
AU  - Vera, J.M.
AU  - Grass, J.
AU  - Savvakis, G.
AU  - Moskvin, O.V.
AU  - Yang, Y.
AU  - McIlwain, S.J.
AU  - Lyu, Y.
AU  - Zinonos, I.
AU  - Hebert, A.S.
AU  - Coon, J.J.
AU  - Bates, D.M.
AU  - Sato, T.K.
AU  - Brown, S.D.
AU  - Himmel, M.E.
AU  - Zhang, M.
AU  - Landick, R.
AU  - Pappas, K.M.
AU  - Zhang, Y.
TI  - Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032.
JO  - Biotechnol. Biofuels.
PY  - 2018
SP  - 125
EP  - 125
VL  - 11
AB  - Background: Zymomonas mobilis is a natural ethanologen being developed and deployed as an
AB  - industrial biofuel
AB  - producer. To date, eight Z. mobilis strains have been completely sequenced and found to
AB  - contain 28 native plasmids.
AB  - However, systematic verification of predicted Z. mobilis plasmid genes and their contribution
AB  - to cell fitness has not
AB  - been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis
AB  - model strain ZM4 have
AB  - been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing
AB  - studies for this model
AB  - biofuel-producing strain.
AB  - Results: In this study, we determined the complete chromosome and plasmid sequences of ZM4 and
AB  - its engineered
AB  - xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4
AB  - chromosome sequences,
AB  - the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well
AB  - as a 2400-bp
AB  - insertion. Four plasmids were identified in all three strains, with 150 plasmid genes
AB  - predicted in strain ZM4 and 2032,
AB  - and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for
AB  - expanded substrate
AB  - utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems
AB  - biology data analyses, and
AB  - most genes were found to have apparent orthologs in other organisms or identifiable conserved
AB  - domains. To verify
AB  - plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene
AB  - expression under various
AB  - growth conditions, including anaerobic and aerobic conditions, or growth in different
AB  - concentrations of biomass
AB  - hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate
AB  - concentrations than to oxygen
AB  - availability. Additionally, our results indicated that although all plasmids were present in
AB  - low copy number (about 12 per cell), the copy number of some plasmids varied under specific
AB  - growth conditions or due to heterologous gene
AB  - insertion.
AB  - Conclusions: The complete genome of ZM4 and two xylose-utilizing derivatives is reported in
AB  - this study, with an
AB  - emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation,
AB  - expression levels at
AB  - growth conditions of interest, and contribution to host fitness are reported for the first
AB  - time.
ER  -

TY  - JOUR
AU  - Yang, S.J.
AU  - Kang, I.
AU  - Cho, J.C.
TI  - Genome Sequence of Strain IMCC14465, Isolated from the East Sea, Belonging to the PS1 Clade of Alphaproteobacteria.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6952
EP  - 6953
VL  - 194
AB  - Strain IMCC14465 was isolated from surface seawater of the East Sea using
AB  - dilution-to-extinction culturing. Phylogenetic analysis indicated that the strain
AB  - belongs to the PS1 clade, which is closely related to the OCS116 clade in the
AB  - Alphaproteobacteria. Here, we report the genome sequence of IMCC14465, the first
AB  - isolate of the PS1 clade.
ER  -

TY  - JOUR
AU  - Yang, W.
AU  - Lee, J.Y.
AU  - Nowotny, M.
TI  - Making and breaking nucleic acids: Two-Mg2+-ion catalysis and substrate specificity.
JO  - Mol. Cell
PY  - 2006
SP  - 5
EP  - 13
VL  - 22
AB  - DNA and a large proportion of RNA are antiparallel duplexes composed of an unvarying
AB  - phosphosugar backbone surrounding uniformly stacked and
AB  - highly similar base pairs. How do the myriad of enzymes (including
AB  - ribozymes) that perform catalysis on nucleic acids achieve exquisite
AB  - structure or sequence specificity? In all DNA and RNA polymerases and
AB  - many nucleases and transposases, two Mg2+ ions are jointly coordinated
AB  - by the nucleic acid substrate and catalytic residues of the enzyme.
AB  - Based on the exquisite sensitivity Of Mg2+ ions to the ligand geometry
AB  - and electrostatic environment, we propose that two-metal-ion catalysis
AB  - greatly enhances substrate recognition and catalytic specificity.
ER  -

TY  - JOUR
AU  - Yang, W.
AU  - Li, N.
AU  - Li, M.
AU  - Zhang, D.
AU  - An, G.
TI  - Complete Genome Sequence of Fish Pathogen Aeromonas hydrophila JBN2301.
JO  - Genome Announcements
PY  - 2016
SP  - e01615
EP  - e01615
VL  - 4
AB  - Aeromonas hydrophila is one of the most important fish pathogens in China. Here,  we report
AB  - complete genome sequence of a virulent strain, A. hydrophila JBN2301,
AB  - which was isolated from diseased crucian carp.
ER  -

TY  - JOUR
AU  - Yang, X. et al.
TI  - A public genome-scale lentiviral expression library of human ORFs.
JO  - Nat. Methods
PY  - 2011
SP  - 659
EP  - 661
VL  - 8
AB  - Functional characterization of the human genome requires tools for systematically
AB  - modulating gene expression in both loss-of-function and gain-of-function
AB  - experiments. We describe the production of a sequence-confirmed, clonal
AB  - collection of over 16,100 human open-reading frames (ORFs) encoded in a versatile
AB  - Gateway vector system. Using this ORFeome resource, we created a genome-scale
AB  - expression collection in a lentiviral vector, thereby enabling both targeted
AB  - experiments and high-throughput screens in diverse cell types.
ER  -

TY  - JOUR
AU  - Yang, X.
AU  - Cao, X.
AU  - Wang, N.
AU  - Wang, J.
AU  - Bie, P.
AU  - Lyu, Y.
AU  - Wu, Q.
TI  - Complete Genome Sequences of Four Brucella Strains Isolated from China.
JO  - Genome Announcements
PY  - 2017
SP  - e01034
EP  - e01017
VL  - 5
AB  - Brucella spp. are facultative intracellular pathogens that cause a contagious zoonotic
AB  - disease. Twelve different species are currently identified. This study
AB  - presents the complete genome sequences of four Brucella strains. These complete
AB  - genomes were annotated and the contents compared to those of other strains
AB  - isolated from China.
ER  -

TY  - JOUR
AU  - Yang, X.
AU  - Chen, C.
AU  - Wang, D.
AU  - Yang, S.
AU  - Wu, R.
TI  - Cloning and overexpression of the restriction gene of EcoRI.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1990
SP  - 599
EP  - 606
VL  - 22
AB  - Cloning and expression of the EcoRI genes are reported here.  A plasmid
AB  - containing the EcoRI (r/m) genes was extracted from the EcoRI producing strain
AB  - E. coli RI, and a 4.9 kb BamHI-HindIII fragment encoding the EcoRI genes was
AB  - cloned into pBR322, producing a hybrid plasmid pER101.  pER302, containing the
AB  - methylase gene of EcoRI, was obtained by inserting the 1.7 kb fragment from
AB  - pER101 into pACYC184.  pER304, in which the sequence coding for the C-terminal
AB  - of EcoRI was downstream from the lambda PL promoter, was constructed from pAS1
AB  - and pER101.  After cloning the 1.5 kb SalI-BglII fragment of pER101 into
AB  - pER304, an EcoRI overproducing plasmid pER306 was created using the strong
AB  - promoter PL as well as the endogenous promoter Pe to overexpress the EcoRI(r)
AB  - gene.  To delete the Pe promoter to control expression of EcoRI only by the PL
AB  - promoter, a 0.65 kb BamHI-HindIII fragment from pER401 was used to replace the
AB  - small BamHI-HindIII fragment downstream from PL promoter, resulting in another
AB  - overproducing plasmid pER307.  When transforming GI139 and GI139/pER302 the
AB  - relative survival efficiency of pER306 and pER307 was both 10/5, but when using
AB  - TG1/pRK248CIts and GI139/pER302 as hosts the efficiency was 10/5 and 1
AB  - respectively.  Therefore, in certain hosts, pER307 can express EcoRI in the
AB  - absence of its cognate methylase.  After heat induction, pER307
AB  - [TG1/pRK248CIts] produces EcoRI at a level of 10/5 units per gram of wet cell,
AB  - which is about 1-2 orders of magnitude lower than that of pER306/[GI139/pER302]
AB  - or pER307/[GI139/pER302].
ER  -

TY  - JOUR
AU  - Yang, X.
AU  - Huang, E.
AU  - Yesil, M.
AU  - Xiaoli, L.
AU  - Dudley, E.G.
AU  - Yousef, A.E.
TI  - Draft Genome Sequence of Brevibacillus laterosporus OSY-I1, a Strain That Produces Brevibacillin, Which Combats Drug-Resistant Gram-Positive Bacteria.
JO  - Genome Announcements
PY  - 2017
SP  - e01093
EP  - e01017
VL  - 5
AB  - Brevibacillus laterosporus OSY-I1 is a Gram-positive spore-forming bacterium isolated from
AB  - soil. The bacterium produces brevibacillin, an antimicrobial
AB  - lipopeptide effective against several drug-resistant Gram-positive bacteria.
AB  - Here, we present the draft genome sequence of the strain OSY-I1 and the gene
AB  - cluster responsible for the biosynthesis of brevibacillin.
ER  -

TY  - JOUR
AU  - Yang, X.
AU  - Wang, Y.
AU  - Huo, G.
TI  - Complete Genome Sequence of Lactococcus lactis subsp. lactis KLDS4.0325.
JO  - Genome Announcements
PY  - 2013
SP  - e00962
EP  - e00913
VL  - 1
AB  - We report the complete genome sequence of Lactococcus lactis subsp. lactis KLDS4.0325, a
AB  - probiotic bacterium isolated from homemade koumiss in Xinjiang,
AB  - China. We have determined the complete genome sequence of strain KLDS4.0325,
AB  - which consists of a chromosome and three plasmids and reveals genes that are
AB  - likely to be involved in dairy fermentation and that have probiotic qualities.
ER  -

TY  - JOUR
AU  - Yang, X.
AU  - Xu, M.
AU  - Yang, S.T.
TI  - Restriction modification system analysis and development of in vivo methylation for the transformation of Clostridium cellulovorans.
JO  - Appl. Microbiol. Biotechnol.
PY  - 2016
SP  - 2289
EP  - 2299
VL  - 100
AB  - Clostridium cellulovorans, a cellulolytic bacterium producing butyric and acetic  acids as
AB  - main fermentation products, is a promising host for biofuel production
AB  - from cellulose. However, the transformation method of C. cellulovorans was not
AB  - available, hindering its genetic engineering. To overcome this problem, its
AB  - restriction modification (RM) systems were analyzed and a novel in vivo
AB  - methylation was established for its successful transformation in the present
AB  - study. Specifically, two RM systems, Cce743I and Cce743II, were determined. R.
AB  - Cce743I has the same specificity as LlaJI, recognizing 5'-GACGC-3' and
AB  - 5'-GCGTC-3', while M. Cce743I methylates the external cytosine in the strand
AB  - (5'-GACG(m)C-3'). R. Cce743II, has the same specificity as LlaI, recognizing
AB  - 5'-CCAGG-3' and 5'-CCTGG-3', while M. Cce743II methylates the external cytosine
AB  - of both strands. An in vivo methylation system, expressing M. Cce743I and M.
AB  - Cce743II from C. cellulovorans in Escherichia coli, was then established to
AB  - protect plasmids used in electrotransformation. Transformants expressing an
AB  - aldehyde/alcohol dehydrogenase (adhE2), which converted butyryl-CoA to n-butanol
AB  - and acetyl-CoA to ethanol, were obtained. For the first time, an effective
AB  - transformation method was developed for metabolic engineering of C. cellulovorans
AB  - for biofuel production directly from cellulose.
ER  -

TY  - JOUR
AU  - Yang, X.
AU  - Xue, R.
AU  - Shen, C.
AU  - Li, S.
AU  - Gao, C.
AU  - Wang, Q.
AU  - Zhao, X.
TI  - Genome sequence of Rhodococcus sp. R04, a polychlorinated biphenyl biodegrader.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5032
EP  - 5033
VL  - 193
AB  - The genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites
AB  - and application of a microbial biocatalyst. Rhodococcous
AB  - sp. strain R04, isolated from oil contaminated soil, could biodegrade
AB  - polychlorinated biphenyls. Here we report the draft genome sequence of
AB  - Rhodococcous sp. strain R04, which could be used to predict genes for
AB  - xenobiotic biodegradation and provide important insights into the
AB  - applications of this strain.
ER  -

TY  - JOUR
AU  - Yang, X.J.
AU  - Wang, S.
AU  - Cao, J.M.
AU  - Hou, J.H.
TI  - Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China.
JO  - Genome Announcements
PY  - 2016
SP  - e00930
EP  - e00916
VL  - 4
AB  - Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting,
AB  - facultative anaerobic, rod-shaped bacterium. Here we present
AB  - draft genome assemblies of Klebsiella pneumoniae AS, which was isolated in China.
AB  - The genomic information will provide a better understanding of the physiology,
AB  - adaptation, and evolution of K. pneumoniae.
ER  -

TY  - JOUR
AU  - Yang, Y.
AU  - Li, Q.
TI  - Restriction enzyme SnaBI is sensitive to methylation of cytosine within its recognition sequence.
JO  - Nucleic Acids Res.
PY  - 1990
SP  - 3083
EP  - 3083
VL  - 18
AB  - None
ER  -

TY  - JOUR
AU  - Yang, Y.
AU  - Yu, X.
AU  - Zhang, R.
TI  - Draft Genome Sequence of Ochrobactrum pseudogrignonense Strain CDB2, a Highly Efficient Arsenate-Resistant Soil Bacterium from Arsenic-Contaminated Cattle Dip   Sites.
JO  - Genome Announcements
PY  - 2013
SP  - e00173
EP  - e00113
VL  - 1
AB  - We report the 4.97-Mb draft genome sequence of a highly efficient arsenate-resistant
AB  - bacterium, Ochrobactrum sp. strain CDB2. It contains a novel
AB  - arsenic resistance (ars) operon (arsR-arsC1-ACR3-arsC2-arsH-mfs) and two
AB  - non-operon-associated ars genes, arsC3 and arsB. The genome information will aid
AB  - in the understanding of the arsenic resistance mechanism of this and other
AB  - bacterial species.
ER  -

TY  - JOUR
AU  - Yang, Y.
AU  - Zhang, R.
TI  - Draft Genome Sequence of Bacillus sp. Strain CDB3, an Arsenic-Resistant Soil Bacterium Isolated from Cattle Dip Sites.
JO  - Genome Announcements
PY  - 2017
SP  - e00429
EP  - e00417
VL  - 5
AB  - Bacillus sp. strain CDB3, isolated from cattle dip sites in Australia, is highly  resistant to
AB  - arsenic. It contains 22 arsenic resistance (ars) genes, of which 17
AB  - are organized in 3 ars clusters. Here, we report the draft genome sequence of
AB  - CDB3, which will assist us in understanding the overall ars mechanism.
ER  -

TY  - JOUR
AU  - Yang, Y.T.
AU  - Chen, I.T.
AU  - Lee, C.T.
AU  - Chen, C.Y.
AU  - Lin, S.S.
AU  - Hor, L.I.
AU  - Tseng, T.C.
AU  - Huang, Y.T.
AU  - Sritunyalucksana, K.
AU  - Thitamadee, S.
AU  - Wang, H.C.
AU  - Lo, C.F.
TI  - Draft Genome Sequences of Four Strains of Vibrio parahaemolyticus, Three of Which Cause Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease in Shrimp   in China and Thailand.
JO  - Genome Announcements
PY  - 2014
SP  - e00816
EP  - e00814
VL  - 2
AB  - We sequenced four Vibrio parahaemolyticus strains, three of which caused serious  acute
AB  - hepatopancreatic necrosis disease. Sequence analysis of the virulent
AB  - strains revealed not only genes related to cholera toxin and the type IV
AB  - pilus/type IV secretion system but also a unique, previously unreported, large
AB  - extrachromosomal plasmid that encodes a homolog to the insecticidal Photorhabdus
AB  - insect-related binary toxin PirAB.
ER  -

TY  - JOUR
AU  - Yang, Z.
AU  - Horton, J.R.
AU  - Maunus, R.
AU  - Wilson, G.G.
AU  - Roberts, R.J.
AU  - Cheng, X.
TI  - Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
JO  - Nucleic Acids Res.
PY  - 2005
SP  - 1892
EP  - 1901
VL  - 33
AB  - HinP1I, a type II restriction endonuclease, recognizes and cleaves a palindromic
AB  - tetranucleotide sequence (G/CGC) in double-stranded DNA,
AB  - producing 2 nt 5' overhanging ends. Here, we report the structure of
AB  - HinP1I crystallized as one protein monomer in the crystallographic
AB  - asymmetric unit. HinP1I displays an elongated shape, with a conserved
AB  - catalytic core domain containing an active-site motif of SDX18QXK and a
AB  - putative DNA-binding domain. Without significant sequence homology, HinP1I
AB  - displays striking structural similarity to MspI, an endonuclease that
AB  - cleaves a similar palindromic DNA sequence (C/CGG) and binds to that
AB  - sequence crystallographically as a monomer. Almost all the structural
AB  - elements of MspI can be matched in HinP1I, including both the DNA
AB  - recognition and catalytic elements. Examining the protein-protein
AB  - interactions in the crystal lattice, HinP1I could be dimerized through two
AB  - helices located on the opposite side of the protein to the active site,
AB  - generating a molecule with two active sites and two DNA-binding surfaces
AB  - opposite one another on the outer surfaces of the dimer. A possible
AB  - functional link between this unusual dimerization mode and the tetrameric
AB  - restriction enzymes is discussed.
ER  -

TY  - JOUR
AU  - Yang, Z.
AU  - Horton, J.R.
AU  - Zhou, L.
AU  - Zhang, X.J.
AU  - Dong, A.P.
AU  - Zhang, X.
AU  - Schlagman, S.L.
AU  - Kossykh, V.
AU  - Hattman, S.
AU  - Cheng, X.D.
TI  - Structure of the bacteriophage T4 DNA adenine methyltransferase.
JO  - Nat. Struct. Biol.
PY  - 2003
SP  - 849
EP  - 855
VL  - 10
AB  - DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene
AB  - expression as well as bacterial virulence. We
AB  - report here the crystal structures of the bacteriophage T4Dam DNA adenine
AB  - methyltransferase (MTase) in a binary complex with the methyl-donor
AB  - product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a
AB  - synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a
AB  - seven-stranded catalytic domain that harbors the binding site for AdoHcy
AB  - and a DNA binding domain consisting of a five-helix bundle and a
AB  - beta-hairpin that is conserved in the family of GATC-related MTase
AB  - orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a
AB  - nonspecific mode that contained two Dam monomers per synthetic duplex,
AB  - even though the DNA contains a single GATC site. The ternary structure
AB  - provides a rare snapshot of an enzyme poised for linear diffusion along
AB  - the DNA.
ER  -

TY  - JOUR
AU  - Yangtse, W.
AU  - Zhou, Y.
AU  - Lei, Y.
AU  - Qiu, Y.
AU  - Wei, X.
AU  - Ji, Z.
AU  - Qi, G.
AU  - Yong, Y.
AU  - Chen, L.
AU  - Chen, S.
TI  - Genome Sequence of Bacillus licheniformis WX-02.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3561
EP  - 3562
VL  - 194
AB  - Bacillus licheniformis is an important bacterium that has been used extensively for
AB  - large-scale industrial production of exoenzymes and peptide antibiotics. B.
AB  - licheniformis WX-02 produces poly-gamma-glutamate increasingly when fermented
AB  - under stress conditions. Here its genome sequence (4,270,104 bp, with G+C content
AB  - of 46.06%), which comprises a circular chromosome, is announced.
ER  -

TY  - JOUR
AU  - Yankovsky, N.K.
AU  - Fonstein, M.Y.
AU  - Lashina, S.Y.
AU  - Bukanov, N.O.
AU  - Yakubovich, N.V.
AU  - Ermakova, L.M.
AU  - Rebentish, B.A.
AU  - Janulaitis, A.
AU  - Debabov, V.G.
TI  - Phasmids as effective and simple tools for construction and analysis of gene libraries.
JO  - Gene
PY  - 1989
SP  - 203
EP  - 210
VL  - 81
AB  - Phasmid lambda-pMYF131, a hybrid of phage lambda vectors and plasmid pUC19, was
AB  - constructed.  The phasmid and its derivatives were shown to be efficient
AB  - vectors for construction and analysis of gene libraries in Escherichia coli
AB  - cells.  The lambda-pMYF131 DNA molecule contains all the genes and regions
AB  - essential for phage lytic development.  The plasmid cannot be packaged either
AB  - in the monomeric or the oligomeric form due to its specific length.  Elongation
AB  - of the DNA molecule by ligation with fragments of foreign DNA can make it
AB  - packageable and this is easily detected by plaque formation. Hence, the
AB  - procedures used to construct genomic libraries can be simplified by selection
AB  - of only recombinant DNA molecules just at the time and on the basis of their
AB  - packaging in vitro.  The output of recombinant clones per vector molecule was
AB  - several times higher for vector lambda-pMYF131, compared to phage vector
AB  - lambdaL47.1AB, and attained 3x10/6 clones per microgram DNA.  Vector and
AB  - recombinant phasmids can be obtained in large quantities in plasmid form.
AB  - Lambda-pMYF131 contains nine unique restriction sites which allow the cloning
AB  - of DNA fragments with blunt ends and of fragments with various types of
AB  - cohesive ends, obtained by digestion with 14 prototype restriction enzymes.
AB  - The maximal size of the cloned DNA fragments is approximately 20 kb for
AB  - lambda-pMYF131.  Phasmid vectors were used to construct libraries of bovine,
AB  - pig and quail genomes, and genomic libraries of 17 species of bacteria.
AB  - Application of suitable methods allowed the identification 13 individual genes
AB  - within these libraries.  Reports the cleavage sites for EcoICRI and Ecl136II.
ER  -

TY  - JOUR
AU  - Yano, H.
AU  - Iwamoto, T.
AU  - Nishiuchi, Y.
AU  - Nakajima, C.
AU  - Starkova, D.A.
AU  - Mokrousov, I.
AU  - Narvskaya, O.
AU  - Yoshida, S.
AU  - Arikawa, K.
AU  - Nakanishi, N.
AU  - Osaki, K.
AU  - Nakagawa, I.
AU  - Ato, M.
AU  - Suzuki, Y.
AU  - Maruyama, F.
TI  - Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis.
JO  - Genome Biol. Evol.
PY  - 2017
SP  - 2403
EP  - 2417
VL  - 9
AB  - Mycobacterium avium subsp. hominissuis (MAH) is one of the most common
AB  - nontuberculous mycobacterial species responsible for chronic lung disease in
AB  - humans. Despite increasing worldwide incidence, little is known about the genetic
AB  - mechanisms behind the population evolution of MAH. To elucidate the local
AB  - adaptation mechanisms of MAH, we assessed genetic population structure, the
AB  - mutual homologous recombination, and gene content for 36 global MAH isolates,
AB  - including 12 Japanese isolates sequenced in the present study. We identified five
AB  - major MAH lineages and found that extensive mutual homologous recombination
AB  - occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant
AB  - in the Japanese isolates. We identified alleles unique to these two East Asian
AB  - lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in
AB  - one mammalian cell entry operon, which presumably originated from as yet
AB  - undiscovered mycobacterial lineages. Several genes and alleles unique to East
AB  - Asian strains were located in the fragments introduced via recombination between
AB  - East Asian lineages, suggesting implication of recombination in local adaptation.
AB  - These patterns of MAH genomes are consistent with the signature of distribution
AB  - conjugative transfer, a mode of sexual reproduction reported for other
AB  - mycobacterial species.
ER  -

TY  - JOUR
AU  - Yanofsky, S.
AU  - Boyer, H.
AU  - Grable, J.
AU  - McClarin, J.
AU  - Rosenberg, J.
AU  - Greene, P.
TI  - Mutational analysis of the EcoRI endonuclease.
JO  - J. Cell Biochem. Suppl.
PY  - 1987
SP  - 211
EP  - 211
VL  - 11C
AB  - Using in vitro mutagenesis with hydroxylamine a large number of null mutants of
AB  - the EcoRI endonuclease have been generated.  Fifty per cent of the 121 mutants
AB  - examined by western blot tested positive against anti-RI.  The entire
AB  - endonuclease gene from twenty-seven western positive mutants was sequenced by
AB  - using dideoxy sequencing directly from double stranded plasmid DNA.  Twenty of
AB  - these were single base change substitutions, with 10 of the mutants falling
AB  - within the region from ala 139 to glu 144.  Examination of the mutants with
AB  - respect to the structure of the EcoRI endonuclease-DNA co-crystal reveals that
AB  - all of the null mutants map at either the protein-DNA interface or at the
AB  - subunit-subunit interface.  Molecular weight determination of purified protein
AB  - on a BioSil TS250 HPLC column demonstrates that wild type EcoRI endonuclease
AB  - runs as a dimer of 60Kd.  Three mutants with alterations at the protein-DNA
AB  - interface (AT139, GS140 and RQ203) run as dimers while 3 mutants mapping at the
AB  - subunit-subunit interface (EK144, EK152 and GR210) run as monomers.
ER  -

TY  - JOUR
AU  - Yanofsky, S.
AU  - Boyer, H.
AU  - Greene, P.
TI  - Positive control of EcoRI endonuclease expression by the EcoRI methylase.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1985
SP  - 106
EP  - 106
VL  - 85
AB  - The presence of a wild type EcoRI endonuclease in cells lacking the cognate
AB  - methylase is lethal.  We have isolated a mutant endonuclease in which serine
AB  - replaces arginine at residue 187.  The Ser 187 enzyme retains RI specificity
AB  - but has reduced in vivo activity (as measured by ability to restrict growth of
AB  - lambda phage).  Cells carrying the Ser 187 endonuclease can survive when the
AB  - methylase is deleted.  Deletion of the methylase results in drastically reduced
AB  - endonuclease production but levels can be restored to near normal by the
AB  - presence of the methylase provided in trans on pSC101, a compatible low-copy
AB  - number plasmid.  We have constructed a number of strains in which the methylase
AB  - gene is truncated at different sites.  Analysis of these strains has allowed us
AB  - to define a domain within the methylase gene which activates endonuclease
AB  - production.  In some of the methylase-deficient strains we are able to increase
AB  - endonuclease production by induction of a linked lac promoter.  This induction
AB  - is lethal into the cell, and it is clear that survival depends upon both low
AB  - production of the Ser 187 endonuclease as well as its reduced in vivo activity.
AB  - This positive control of endonuclease production by methylase provides a
AB  - mechanism for establishment and maintenance of this system in a cell without
AB  - damaging cellular DNA.
ER  -

TY  - JOUR
AU  - Yanofsky, S.D.
AU  - Love, R.
AU  - McClarin, J.A.
AU  - Rosenberg, J.M.
AU  - Boyer, H.W.
AU  - Greene, P.J.
TI  - Clustering of null mutations in the EcoRI endonuclease.
JO  - Proteins
PY  - 1987
SP  - 273
EP  - 282
VL  - 2
AB  - EcoRI endonuclease mutants were isolated in a methylase-deficient background
AB  - following in vitro hydroxylamine mutagenesis of plasmid pKG2 (Kuhn et al.: Gene
AB  - 44:253-263, 1986).  Mutants which survived high-level endonuclease expression
AB  - (IPTG induction) were termed null mutants.  Sixty-two of 121 null mutants
AB  - tested by Western blot contained normal levels of endonuclease cross-reacting
AB  - protein.  The complete endonuclease gene was sequenced for 27 null mutants.
AB  - This group was found to consist of 20 single base-change missense mutantations,
AB  - 6 double mutations, and 1 triple mutation.  Ten of the 20 single mutations were
AB  - clustered between residues 139 and 144.  When examined with respect to the
AB  - structure of the EcoRI-DNA complex (McClarin et al.:  Science 234:1526-1541,
AB  - 1986), these alterations were found to fall predominantly into two classes:
AB  - substitutions at the protein-DNA interface or substitutions at the
AB  - protein-protein (dimer) interface.  Protein from several of the mutants was
AB  - purified and sized by using HPLC.  Wild-type EcoRI endonuclease and protein
AB  - from three of the DNA interface mutations (Ala139->Thr, Gly140->Ser,
AB  - Arg203->Gln) appeared to be dimeric, while protein from subunit interface
AB  - mutations (glu->Lys, Glu152->Lys, Gly210->Arg) migrated as monomers.
ER  -

TY  - JOUR
AU  - Yao, K.
AU  - Muruvanda, T.
AU  - Allard, M.W.
AU  - Hoffmann, M.
TI  - Complete Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Saintpaul Isolates Associated with a 2013 Multistate Outbreak in the United  States.
JO  - Genome Announcements
PY  - 2017
SP  - e00456
EP  - e00417
VL  - 5
AB  - In 2013, a multistate outbreak of Salmonella enterica subsp. enterica serovar Saintpaul from
AB  - cucumber caused 84 cases of salmonellosis in the United States. In
AB  - this announcement, we report the complete genome sequences of three clinical
AB  - Salmonella Saintpaul isolates associated with the 2013 outbreak.
ER  -

TY  - JOUR
AU  - Yao, K.
AU  - Muruvanda, T.
AU  - Roberts, R.J.
AU  - Payne, J.
AU  - Allard, M.W.
AU  - Hoffmann, M.
TI  - Complete Genome and Methylome Sequences of Two Salmonella enterica spp.
JO  - Genome Announcements
PY  - 2016
SP  - e01599
EP  - e01515
VL  - 4
AB  - Salmonella enterica is responsible for major foodborne outbreaks worldwide. It can cause
AB  - gastroenteritis characterized by diarrhea, vomiting, and fever.
AB  - Salmonella infections raise public health concerns along with consequential
AB  - economic impacts. In this report, we announce the first complete genome sequences
AB  - of Salmonella enterica subsp. enterica serovar Choleraeuis (S. Choleraeuis) ATCC
AB  - 10708 and Salmonella enterica subsp. enterica serovar Pullorum (S. Pullorum) ATCC
AB  - 9120, isolated from patients with diarrhea.
ER  -

TY  - JOUR
AU  - Yao, K.
AU  - Muruvanda, T.
AU  - Roberts, R.J.
AU  - Payne, J.
AU  - Allard, M.W.
AU  - Hoffmann, M.
TI  - Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar  Sloterdijk (ATCC 15791).
JO  - Genome Announcements
PY  - 2016
SP  - e00133
EP  - e00116
VL  - 4
AB  - Salmonella enterica spp. are pathogenic bacteria commonly associated with food-borne outbreaks
AB  - in human and animals. Salmonella enterica spp. are
AB  - characterized into more than 2,500 different serotypes, which makes
AB  - epidemiological surveillance and outbreak control more difficult. In this report,
AB  - we announce the first complete genome and methylome sequences from two Salmonella
AB  - type strains associated with food-borne outbreaks, Salmonella enterica subsp.
AB  - enterica serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica
AB  - serovar Sloterdijk (ATCC 15791).
ER  -

TY  - JOUR
AU  - Yao, K.
AU  - Roberts, R.J.
AU  - Allard, M.W.
AU  - Hoffmann, M.
TI  - Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection.
JO  - Genome Announcements
PY  - 2017
SP  - e00031
EP  - e00017
VL  - 5
AB  - In this announcement, we report the complete genome and methylome sequences of three
AB  - Salmonella enterica strains from the SARA and SARB collection: S. enterica
AB  - subsp. enterica serovar Typhimurium (SARA13), S. enterica subsp. enterica serovar
AB  - Saintpaul (SARA26), and S. enterica subsp. enterica serovar Stanleyville
AB  - (SARB61).
ER  -

TY  - JOUR
AU  - Yao, L.
AU  - Yu, L.L.
AU  - Zhang, J.J.
AU  - Xie, X.T.
AU  - Tao, Q.
AU  - Yan, X.
AU  - Hong, Q.
AU  - Qiu, J.G.
AU  - He, J.
AU  - Ding, D.R.
TI  - A Tetrahydrofolate-Dependent Methyltransferase Catalyzing the Demethylation of Dicamba in Sphingomonas sp. Strain Ndbn-20.
JO  - Appl. Environ. Microbiol.
PY  - 2016
SP  - 5621
EP  - 5630
VL  - 82
AB  - UNLABELLED: Sphingomonas sp. strain Ndbn-20 degrades and utilizes the herbicide
AB  - dicamba as its sole carbon and energy source. In the present study, a
AB  - tetrahydrofolate (THF)-dependent dicamba methyltransferase gene, dmt, was cloned
AB  - from the strain, and three other genes, metF, dhc, and purU, which are involved
AB  - in THF metabolism, were found to be located downstream of dmt A transcriptional
AB  - study revealed that the four genes constituted one transcriptional unit that was
AB  - constitutively transcribed. Lysates of cells grown with glucose or dicamba
AB  - exhibited almost the same activities, which further suggested that the dmt gene
AB  - is constitutively expressed in the strain. Dmt shared 46% and 45% identities with
AB  - the methyltransferases DesA and LigM from Sphingomonas paucimobilis SYK-6,
AB  - respectively. The purified Dmt catalyzed the transfer of methyl from dicamba to
AB  - THF to form the herbicidally inactive metabolite 3,6-dichlorosalicylic acid
AB  - (DCSA) and 5-methyl-THF. The activity of Dmt was inhibited by 5-methyl-THF but
AB  - not by DCSA. The introduction of a codon-optimized dmt gene into Arabidopsis
AB  - thaliana enhanced resistance against dicamba. In conclusion, this study
AB  - identified a THF-dependent dicamba methyltransferase, Dmt, with potential
AB  - applications for the genetic engineering of dicamba-resistant crops. IMPORTANCE:
AB  - Dicamba is a very important herbicide that is widely used to control more than
AB  - 200 types of broadleaf weeds and is a suitable target herbicide for the
AB  - engineering of herbicide-resistant transgenic crops. A study of the mechanism of
AB  - dicamba metabolism by soil microorganisms will benefit studies of its
AB  - dissipation, transformation, and migration in the environment. This study
AB  - identified a THF-dependent methyltransferase, Dmt, capable of catalyzing dicamba
AB  - demethylation in Sphingomonas sp. Ndbn-20, and a preliminary study of its
AB  - enzymatic characteristics was performed. Introduction of a codon-optimized dmt
AB  - gene into Arabidopsis thaliana enhanced resistance against dicamba, suggesting
AB  - that the dmt gene has potential applications for the genetic engineering of
AB  - herbicide-resistant crops.
ER  -

TY  - JOUR
AU  - Yao, N.
AU  - Ren, Y.
AU  - Wang, W.
TI  - Genome Sequence of a Thermophilic Bacillus, Geobacillus thermodenitrificans DSM465.
JO  - Genome Announcements
PY  - 2013
SP  - e01046
EP  - e01013
VL  - 1
AB  - Geobacillus thermodenitrificans NG80-2 encodes a LadA-mediated alkane degradation pathway,
AB  - while G. thermodenitrificans DSM465 cannot utilize alkanes. Here, we
AB  - report the draft genome sequence of G. thermodenitrificans DSM465, which may help
AB  - reveal the genomic differences between these two strains in regards to the
AB  - biodegradation of alkanes.
ER  -

TY  - JOUR
AU  - Yao, S.
AU  - Xu, Y.
AU  - Xin, C.
AU  - Xu, L.
AU  - Liu, Y.
AU  - Li, H.
AU  - Li, J.
AU  - Zhao, J.
AU  - Cheng, C.
TI  - Genome Sequence of Thermoactinomyces daqus H-18, a Novel Thermophilic Species Isolated from High-Temperature Daqu.
JO  - Genome Announcements
PY  - 2015
SP  - e01394
EP  - e01314
VL  - 3
AB  - Thermoactinomyces daqus H-18 is a new species of Thermoactinomyces isolated from
AB  - high-temperature Daqu used in the fermentation of Bandongjing sesame-flavor
AB  - liquor. Its genome was sequenced and assembled (3.44 Mb). The coding sequences
AB  - (CDSs) that correlated to high-temperature tolerance were annotated. The
AB  - metabolic pathways for the compounds responsible for flavor were also found.
ER  -

TY  - JOUR
AU  - Yao, X.
AU  - Sun, Q.
AU  - Liu, W.
AU  - Yin, X.
AU  - Pei, G.
AU  - Wang, Y.
AU  - An, X.
AU  - Mi, Z.
AU  - Luo, Y.
AU  - Tong, Y.
AU  - Chen, S.
TI  - Complete Genome Sequence of Serratia rubidaea Isolated in China.
JO  - Genome Announcements
PY  - 2016
SP  - e00283
EP  - e00216
VL  - 4
AB  - We report here the first complete genome of Serratia rubidaea, isolated from a patient in
AB  - China.
ER  -

TY  - JOUR
AU  - Yao, Y.
AU  - Falgenhauer, L.
AU  - Kempf, V.A.
AU  - Hogardt, M.
AU  - Gottig, S.
AU  - Imirzalioglu, C.
AU  - Chakraborty, T.
TI  - Draft Genome Sequences of Pandrug-Resistant Serratia marcescens Clinical Isolates Harboring blaNDM-1.
JO  - Genome Announcements
PY  - 2017
SP  - e01481
EP  - e01416
VL  - 5
AB  - The draft genome sequences of two clonal, pandrug-resistant Serratia marcescens clinical
AB  - isolates were determined. The resistance phenotype was plasmid driven,
AB  - as 14 of 17 resistance genes were present on large IncFIB(K), IncHI2, and IncA/C2
AB  - plasmids indicating a large pool of transmissible antibiotic resistance genes.
ER  -

TY  - JOUR
AU  - Yao, Y.
AU  - Imirzalioglu, C.
AU  - Hain, T.
AU  - Kaase, M.
AU  - Gatermann, S.
AU  - Exner, M.
AU  - Mielke, M.
AU  - Hauri, A.
AU  - Dragneva, Y.
AU  - Bill, R.
AU  - Wendt, C.
AU  - Wirtz, A.
AU  - Domann, E.
AU  - Chakraborty, T.
TI  - Complete Nucleotide Sequence of a Citrobacter freundii Plasmid Carrying KPC-2 in  a Unique Genetic Environment.
JO  - Genome Announcements
PY  - 2014
SP  - e01157
EP  - e01114
VL  - 2
AB  - The complete and annotated nucleotide sequence of a 54,036-bp plasmid harboring a blaKPC-2
AB  - gene that is clonally present in Citrobacter isolates from different
AB  - species is presented. The plasmid belongs to incompatibility group N (IncN) and
AB  - harbors the class A carbapenemase KPC-2 in a unique genetic environment.
ER  -

TY  - JOUR
AU  - Yao, Y.
AU  - Tang, H.
AU  - Ren, H.
AU  - Yu, H.
AU  - Wang, L.
AU  - Xu, P.
TI  - Genome sequence of a nicotine-degrading strain of arthrobacter.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5714
EP  - 5715
VL  - 194
AB  - We announce a 4.63-Mb genome assembly of an isolated bacterium that is the first  sequenced
AB  - nicotine-degrading Arthrobacter strain. Nicotine catabolism genes of
AB  - the nicotine-degrading plasmid pAO1 were predicted, but plasmid function genes
AB  - were not found. These results will help to better illustrate the molecular
AB  - mechanism of nicotine degradation by Arthrobacter.
ER  -

TY  - JOUR
AU  - Yao, Z.
AU  - Feng, Y.
AU  - Lin, J.
AU  - Zong, Z.
TI  - Draft Genome Sequence of a Colistin-Resistant Klebsiella pneumoniae Clinical Strain Carrying the blaNDM-1 Carbapenemase Gene.
JO  - Genome Announcements
PY  - 2017
SP  - e01654
EP  - e01616
VL  - 5
AB  - Klebsiella pneumoniae strain WCHKP1845, recovered from the sputum of a patient with pneumonia,
AB  - was resistant to colistin and carried the carbapenemase gene
AB  - blaNDM-1 Here, we report its 5.4-Mb draft genome sequence, comprising 140 contigs
AB  - with an average 57.33% G+C content. The genome contains 5,118 coding sequences
AB  - and 88 tRNA genes.
ER  -

TY  - JOUR
AU  - Yao, Z.
AU  - Feng, Y.
AU  - Wei, L.
AU  - Zong, Z.
TI  - Draft Genome Sequence of a Sequence Type 11 Klebsiella pneumoniae Clinical Strain Carrying a blaKPC-2 Carbapenemase Gene and an rmtB 16S rRNA Methylase Gene.
JO  - Genome Announcements
PY  - 2017
SP  - e01549
EP  - e01516
VL  - 5
AB  - Klebsiella pneumoniae strain WCHKP649, recovered from a human wound, carried the
AB  - carbapenemase gene blaKPC-2 and 16S rRNA methylase gene rmtB Here, we report its
AB  - 5.6-Mb draft genome sequence, comprising 171 contigs with an average 57.34% G+C
AB  - content. The genome contained 5,284 coding sequences and 84 tRNA genes.
ER  -

TY  - JOUR
AU  - Yap, H.Y.
AU  - Ghazali, K.
AU  - Wan, M.N.W.F.
AU  - Mat, I.M.N.
AU  - Zakaria, Z.
AU  - Omar, A.R.
TI  - Draft Genome Sequence of Pasteurella multocida subsp. multocida Strain PMTB, Isolated from a Buffalo.
JO  - Genome Announcements
PY  - 2013
SP  - e00872
EP  - e00813
VL  - 1
AB  - Pasteurella multocida serotypes B:2 and E:2 are the main causative agents of ruminant
AB  - hemorrhagic septicemia in Asia and Africa, respectively. Pasteurella
AB  - multocida strain PMTB was isolated from a buffalo with hemorrhagic septicemia and
AB  - has been determined to be serotype B:2. Here we report the draft genome sequence
AB  - of strain PMTB.
ER  -

TY  - JOUR
AU  - Yap, K.P.
AU  - Gan, H.M.
AU  - Teh, C.S.
AU  - Baddam, R.
AU  - Chai, L.C.
AU  - Kumar, N.
AU  - Tiruvayipati, S.A.
AU  - Ahmed, N.
AU  - Thong, K.L.
TI  - Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5970
EP  - 5971
VL  - 194
AB  - Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly
AB  - in developing countries. In this article, we describe the whole
AB  - genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever
AB  - carrier in Kelantan, Malaysia. These data will further enhance the understanding
AB  - of its host persistence and adaptive mechanism.
ER  -

TY  - JOUR
AU  - Yap, K.P.
AU  - Teh, C.S.
AU  - Baddam, R.
AU  - Chai, L.C.
AU  - Kumar, N.
AU  - Avasthi, T.S.
AU  - Ahmed, N.
AU  - Thong, K.L.
TI  - Insights from the Genome Sequence of a Salmonella enterica Serovar Typhi Strain Associated with a Sporadic Case of Typhoid Fever in Malaysia.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5124
EP  - 5125
VL  - 194
AB  - Salmonella enterica serovar Typhi is the causative agent of typhoid fever, which  causes
AB  - nearly 21.7 million illnesses and 217,000 deaths globally. Herein, we
AB  - describe the whole-genome sequence of the Salmonella Typhi strain ST0208,
AB  - isolated from a sporadic case of typhoid fever in Kuala Lumpur, Malaysia. The
AB  - whole-genome sequence and comparative genomics allow an in-depth understanding of
AB  - the genetic diversity, and its link to pathogenicity and evolutionary dynamics,
AB  - of this highly clonal pathogen that is endemic to Malaysia.
ER  -

TY  - JOUR
AU  - Yarmolinsky, M.B.
TI  - Programmed cell death in bacterial populations.
JO  - Science
PY  - 1995
SP  - 836
EP  - 837
VL  - 267
AB  - Multicellular organisms benefit not only from the death of competitors, but often, quite
AB  - dramatically, from the programmed death of specific subpopulations of their own cells. Popular
AB  - opinion to the contrary, programmed cell death is also alive and well in the microbial world.
AB  - A striking report by Naito et al. in this issue of Science is a case in point.
ER  -

TY  - JOUR
AU  - Yasar-Yildiz, S.
AU  - Kambourova, M.
AU  - Arga, K.Y.
AU  - Toksoy, O.E.
TI  - Draft Genome Sequence of Exopolysaccharide-Producing Thermophilic Bacterium Brevibacillus thermoruber Strain 423.
JO  - Genome Announcements
PY  - 2013
SP  - e00774
EP  - e00713
VL  - 1
AB  - Brevibacillus thermoruber strain 423 is a Gram-positive, spore-forming, aerobic,  and
AB  - thermophilic bacterium that produces mannogalactoglucan exopolysaccharide (EPS). We report the
AB  - draft genome sequence of B. thermoruber 423, which will accelerate research on the cellular
AB  - organization of thermophilic bacteria, as well as the rational design and optimization of EPS
AB  - production.
ER  -

TY  - JOUR
AU  - Yasawong, M. et al.
TI  - Complete genome sequence of Arcanobacterium haemolyticum type strain (11018).
JO  - Standards in Genomic Sciences
PY  - 2010
SP  - 126
EP  - 135
VL  - 3
AB  - Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the  type species
AB  - of the genus Arcanobacterium, which belongs to the family
AB  - Actinomycetaceae. The strain is of interest because it is an obligate parasite of
AB  - the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin
AB  - lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The
AB  - strain described in this study was isolated from infections amongst American
AB  - soldiers of certain islands of the North and West Pacific. This is the first
AB  - completed sequence of a member of the genus Arcanobacterium and the ninth type
AB  - strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with
AB  - its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia
AB  - of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Yassin, A.F.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Reddy, T.B.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
TI  - High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 50
EP  - 50
VL  - 10
AB  - Corynebacterium ulceribovis strain IMMIB L-1395(T) (= DSM 45146(T)) is an aerobic to
AB  - facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that
AB  - was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell
AB  - wall of C. ulceribovis contains corynemycolic acids.  The cellular fatty acids are those
AB  - described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we
AB  - describe the features of C. ulceribovis strain IMMIB L-1395(T), together with genome sequence
AB  - information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding
AB  - genes and 54 RNA-encoding genes and is part of the Genomic Encyclopedia of Type Strains, Phase
AB  - I: the one thousand microbial genomes (KMG) project.
ER  -

TY  - JOUR
AU  - Yasui, K.
AU  - Kano, Y.
AU  - Tanaka, K.
AU  - Watanabe, K.
AU  - Shimizu-Kadota, M.
AU  - Yoshikawa, H.
AU  - Suzuki, T.
TI  - Improvement of bacterial transformation efficiency using plasmid artificial modification.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - e3
EP  - e3
VL  - 37
AB  - We have developed a method to improve the transformation efficiency in genome-sequenced
AB  - bacteria, using 'Plasmid Artificial Modification' (PAM),
AB  - using the host's own restriction system. In this method, a shuttle vector
AB  - was pre-methylated in Escherichia coli cells, which carry all the putative
AB  - genes encoding the DNA modification enzymes of the target microorganism,
AB  - before electroporation was performed. In the case of Bifidobacterium
AB  - adolescentis ATCC15703 and pKKT427 (3.9 kb E. coli-Bifidobacterium shuttle
AB  - vector), introducing two Type II DNA methyltransferase genes lead to an
AB  - enhancement in the transformation efficiency by five orders of magnitude.
AB  - This concept was also applicable to a Type I restriction system. In the
AB  - case of Lactococcus lactis IO-1, by using PAM with a putative Type I
AB  - methyltransferase system, hsdMS1, the transformation efficiency was
AB  - improved by a factor of seven over that without PAM.
ER  -

TY  - JOUR
AU  - Yasuike, M.
AU  - Nakamura, Y.
AU  - Kai, W.
AU  - Fujiwara, A.
AU  - Fukui, Y.
AU  - Satomi, M.
AU  - Sano, M.
TI  - Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine  Bacterium.
JO  - Genome Announcements
PY  - 2013
SP  - e00367
EP  - e00313
VL  - 1
AB  - Agarivorans albus is a Gram-negative, strictly aerobic, and agar-hydrolyzing marine bacterium.
AB  - We present the draft genome sequence of the A. albus strain MKT
AB  - 106(T), which is composed of 67 contigs (>500 bp) totaling 4,734,285 bp and
AB  - containing 4,397 coding DNA sequences (CDSs), four rRNAs, and 64 tRNA sequences.
ER  -

TY  - JOUR
AU  - Yasuike, M.
AU  - Nishiki, I.
AU  - Iwasaki, Y.
AU  - Nakamura, Y.
AU  - Fujiwara, A.
AU  - Shimahara, Y.
AU  - Kamaishi, T.
AU  - Yoshida, T.
AU  - Nagai, S.
AU  - Kobayashi, T.
AU  - Katoh, M.
TI  - Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species.
JO  - PLoS ONE
PY  - 2017
SP  - E0173198
EP  - E0173198
VL  - 12
AB  - Nocardiosis caused by Nocardia seriolae is one of the major threats in the
AB  - aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S.
AB  - dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete
AB  - nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured
AB  - yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C
AB  - content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1
AB  - predicted genes, we found orthologs of virulence factors of pathogenic
AB  - mycobacteria and human clinical Nocardia isolates involved in host cell invasion,
AB  - modulation of phagocyte function and survival inside the macrophages. The
AB  - virulence factor candidates provide an essential basis for understanding their
AB  - pathogenic mechanisms at the molecular level by the fish nocardiosis research
AB  - community in future studies. We also found many potential antibiotic resistance
AB  - genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four
AB  - existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N.
AB  - cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes
AB  - were present in all five Nocardia genomes (core genes) and 1,982 genes were
AB  - unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a
AB  - greater number of mobile elements and genes of unknown function that comprise the
AB  - differences in structure and gene content from the other Nocardia genomes. In
AB  - addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC
AB  - transport system. Because of limited resources in ocean environments, these N.
AB  - seriolae UTF1 specific ABC transporters might facilitate adaptation strategies
AB  - essential for marine environment survival. Thus, the availability of the complete
AB  - N. seriolae UTF1 genome sequence will provide a valuable resource for comparative
AB  - genomic studies of N. seriolae isolates, as well as provide new insights into the
AB  - ecological and functional diversity of the genus Nocardia.
ER  -

TY  - JOUR
AU  - Yates, R.
AU  - Howieson, J.
AU  - De Meyer, S.E.
AU  - Tian, R.
AU  - Seshadri, R.
AU  - Pati, A.
AU  - Woyke, T.
AU  - Markowitz, V.
AU  - Ivanova, N.
AU  - Kyrpides, N.
AU  - Loi, A.
AU  - Nutt, B.
AU  - Garau, G.
AU  - Sulas, L.
AU  - Reeve, W.
TI  - High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592;  a Hedysarum coronarium microsymbiont from Sassari, Italy.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 44
EP  - 44
VL  - 10
AB  - Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was
AB  - isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived
AB  - perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was
AB  - isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering
AB  - Sassari, Sardinia in 1995. WSM1592  is highly effective at fixing nitrogen with H. coronarium,
AB  - and is currently the commercial Sulla inoculant strain in Australia. Here we describe the
AB  - features of  R. sullae strain WSM1592, together with genome sequence information and its
AB  - annotation. The 7,530,820 bp high-quality permanent draft genome is arranged into 118
AB  - scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes.
AB  - This rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic
AB  - Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
ER  -

TY  - JOUR
AU  - Yau, E.K.
AU  - Coward, J.K.
TI  - The synthesis of complex 6'-alkynyl-6'-dethia analogs of s-adenosylhomocysteine as potential inhibitors of methyltransferases.
JO  - ACS Abstracts
PY  - 1989
SP  - 100
EP  - 100
VL  - 198
AB  - A new series of multisubstrate adduct inhibitors was designed for
AB  - S-adenosylmethionine-dependent methyltransferases.  Three synthetic routes to
AB  - this class of compounds were investigated and
AB  - 5'-(6-amino-6-carboxy-1-phenyl-1-hexynyl-3-)-5'-deoxyadenosine was synthesized
AB  - as a prototype.  The key step in the successful synthesis was the arylation of
AB  - N6-benzoyl-2',3'-isopropylidene-5'(5-tert-butyldiphenylsilyloxy-1-pentynyl-3)-5
AB  - '-deoxyadenosine, a terminal acetylene, with an aryl iodide in the presence of
AB  - Pd(II) and CuI catalysts.  This method should be generally useful for the
AB  - synthesis of specific inhibitors of S-adenosylmethionine-dependent
AB  - methyltransferases.  5'-(4-Amino-4-carboxybutyl-1-)-5'-deoxyadenosine, a
AB  - 6'-carbon analog of S-adenosylhomocysteine, was also synthesized in the process
AB  - of investigating methods for constructing an amino acid moiety on the side
AB  - chain of this class of compounds.
ER  -

TY  - JOUR
AU  - Yau, S.
AU  - Lauro, F.M.
AU  - DeMaere, M.Z.
AU  - Brown, M.V.
AU  - Thomas, T.
AU  - Raftery, M.J.
AU  - Andrews-Pfannkoch, C.
AU  - Lewis, M.
AU  - Hoffman, J.M.
AU  - Gibson, J.A.
AU  - Cavicchioli, R.
TI  - Virophage control of antarctic algal host-virus dynamics.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2011
SP  - 6163
EP  - 6168
VL  - 108
AB  - Viruses are abundant ubiquitous members of microbial communities and in
AB  - the marine environment affect population structure and nutrient cycling by
AB  - infecting and lysing primary producers. Antarctic lakes are microbially
AB  - dominated ecosystems supporting truncated food webs in which viruses exert
AB  - a major influence on the microbial loop. Here we report the discovery of a
AB  - virophage (relative of the recently described Sputnik virophage) that
AB  - preys on phycodnaviruses that infect prasinophytes (phototrophic algae).
AB  - By performing metaproteogenomic analysis on samples from Organic Lake, a
AB  - hypersaline meromictic lake in Antarctica, complete virophage and
AB  - near-complete phycodnavirus genomes were obtained. By introducing the
AB  - virophage as an additional predator of a predator-prey dynamic model we
AB  - determined that the virophage stimulates secondary production through the
AB  - microbial loop by reducing overall mortality of the host and increasing
AB  - the frequency of blooms during polar summer light periods. Virophages
AB  - remained abundant in the lake 2 y later and were represented by
AB  - populations with a high level of major capsid protein sequence variation
AB  - (25-100% identity). Virophage signatures were also found in neighboring
AB  - Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh),
AB  - an estuary, and an ocean upwelling site. These findings indicate that
AB  - virophages regulate host-virus interactions, influence overall carbon flux
AB  - in Organic Lake, and play previously unrecognized roles in diverse aquatic
AB  - ecosystems.
ER  -

TY  - JOUR
AU  - Yaung, S.J.
AU  - Esvelt, K.M.
AU  - Church, G.M.
TI  - Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68.
JO  - Genome Announcements
PY  - 2015
SP  - e01122
EP  - e01114
VL  - 3
AB  - T4-like bacteriophages have been explored for phage therapy and are model organisms for phage
AB  - genomics and evolution. Here, we describe the sequencing of
AB  - 11 T4-like phages. We found a high nucleotide similarity among the T4, RB55, and
AB  - RB59; RB32 and RB33; and RB3, RB5, RB6, RB7, RB9, and RB10 phages.
ER  -

TY  - JOUR
AU  - Yazdanparast, S.
AU  - Toma, E.
AU  - Karska-Wysocki, B.
TI  - Characterization of methicillin-resistant Staphylococcus aureus isolated at Hotel-Dieu Hospital, Montreal.
JO  - Ottawa Life Sciences Internl Conf. and Exhibit.
PY  - 2001
SP  - Abstract #P301
EP  - Abstract #P301
VL  - 0
AB  - The first objective of this study was to characterize fifty methicillin resistant
AB  - Staphylococcus aureus (MRSZA) strains, isolated in 1999/2000 from Hotel-Dieu Hospital
AB  - patients, by using antibiogram and DNA analysis.  The second objective was to determine
AB  - whether our recently discovered restriction enzyme LlaGI shows a digestive activity towards
AB  - MRSA DNA.  The evaluation of antibiotic resistance (by MIC) to methicillin, oxacillin,
AB  - erythromycin and cephazolin, showed multi resistance for these drugs for all fifty MRSA
AB  - strains.  In contrast, all MRSA strains were sensitive to vancomycin.  We purified the DNA
AB  - (plasmidic
ER  -

TY  - JOUR
AU  - Yazdanparast, S.
AU  - Toma, E.
AU  - Karska-Wysocki, B.
TI  - Restriction enzyme activity for subgenomic discrimination of  Methicillin-resistant Staphylococcus aureus.
JO  - Abstracts of IBC's 7th Annual World Congress
PY  - 2002
SP  - abstract #100
EP  - abstract #100
VL  - 0
AB  - The dissemination of methicillin-resistant Staphylococcus aureus has important consequences in
AB  - health-care as it is the source of many outbreaks in hospital centers.  Presently, the primary
AB  - focus of most hospital infection control programs is to reduce the prevalence of MRSA
AB  - infection by rapidly detecting the source of these organisms and by interrupting their
AB  - transmission to patients.  We previously reported the development of a strain discrimination
AB  - procedure using fifty MRSA clinical isolates from a hospital center.  After evaluation of the
AB  - multidrug-resistance of MRSA strains, we determined their electrophoretic plasmid DNA profile.
AB  - We can differentiate fifty strains into eleven groups.  In addition, we have investigated the
AB  - Restriction Fragment Length Polymorphism of plasmidic and genomic DNA after digestion with
AB  - EcoRI, HindIII and the recently discovered LlaGI restriction enzyme.  In this study we
AB  - characterized the plasmid DNA fragments of MRSA strains digested by LlaGI.  This procedure was
AB  - followed by analysis of genomic DNA amplicons profiles generated by arbitrarily primed PCR.
AB  - We were able to subtype our representative MRSA isolates into 3 types which were clearly
AB  - different from each other.  The discriminatory power of genomic DNA AP-PCR fingerprinting can
AB  - be increased, after digestion of amplicons with restriction enzyme and analysis the generated
AB  - electrophoretic fragments profiles.  In order to discriminate more precisely the MRSA strains,
AB  - we digested AP-PCR amplicons by AluI.  After analysis of the electrophoretic digest patterns
AB  - of these amplicons, we were able to identify the individual strains.  To our knowledge, this
AB  - is the first report of MRSA strain identification with RFLP or AP-PCR-RFLP procedures, using
AB  - these two enzymes, LlaGI and AluI, respectively.  We conclude that the combination of
AB  - procedures, such as analysis of electrophoretic plasmid profiles, analysis of genomic DNA
AB  - using AP-PCR and AP-PCR-RFLP were most efficacious for identification of individual MRSA
AB  - strains.  Our development of a new typing schema demonstrates the novel restriction enzyme
AB  - activity application for subgenomic discrimination of MRSA strains.
ER  -

TY  - JOUR
AU  - Ybazeta, G.
AU  - Douglas, L.
AU  - Graham, J.
AU  - Fraleigh, N.L.
AU  - Murad, Y.
AU  - Perez, J.
AU  - Diaz-Mitoma, F.
AU  - Tilbe, K.
AU  - Nokhbeh, R.
TI  - Complete Genome Sequence of Enterococcus thailandicus Strain a523 Isolated from Urban Raw Sewage.
JO  - Genome Announcements
PY  - 2017
SP  - e01298
EP  - e01217
VL  - 5
AB  - We report here the first complete circularly closed genome sequence of Enterococcus
AB  - thailandicus strain a523 isolated from raw urban sewage. This genome
AB  - contains 2,646,250 bp with a G+C content of 36.8%, 2,499 genes, 2,370
AB  - protein-coding sequences, 6 rRNA operons, 65 tRNAs, and 6 clustered regularly
AB  - interspaced short palindromic repeat arrays.
ER  -

TY  - JOUR
AU  - Ye, C.
AU  - Zheng, H.
AU  - Zhang, J.
AU  - Jing, H.
AU  - Wang, L.
AU  - Xiong, Y.
AU  - Wang, W.
AU  - Zhou, Z.
AU  - Sun, Q.
AU  - Luo, X.
AU  - Du, H.
AU  - Gottschalk, M.
AU  - Xu, J.
TI  - Clinical, experimental, and genomic differences between intermediately pathogenic, highly pathogenic, and epidemic Streptococcus suis.
JO  - J. Infect. Dis.
PY  - 2009
SP  - 97
EP  - 107
VL  - 199
AB  - BACKGROUND: Streptococcus suis emerged to cause an unusual outbreak of
AB  - streptococcal toxic-shock-like syndrome (STSLS) in 2005. The mechanisms
AB  - involved are unknown. METHODS: Clinical, laboratory, and epidemiologic
AB  - data on patients infected with culture-confirmed S. suis were analyzed.
AB  - The strain involved in the outbreak, "epidemic" strain ST7, was compared
AB  - with both a classical highly pathogenic strain, ST1, and an intermediately
AB  - pathogenic strain, ST25, to determine both its capacity to induce
AB  - cytokines in experimentally infected mice and its genomic difference.
AB  - RESULTS: Of 38 patients infected with culture-confirmed S. suis, 14
AB  - presented with STSLS. During the early phase of the disease, serum levels
AB  - of interleukin (IL)-1beta, IL-6, IL-8, IL-12p70, interferon-gamma, and
AB  - tumor necrosis factor-alpha were more elevated in patients with STSLS than
AB  - in those with meningitis only. Serum levels of proinflammatory cytokines
AB  - were significantly higher in mice infected with ST7 than in those infected
AB  - with either ST1 or ST25. Genomic comparisons with ST25 showed that ST1 had
AB  - acquired 132 genomic islands, including 5 pathogenicity islands, and that
AB  - ST7, the epidemic strain, had acquired an additional 5 genomic islands.
AB  - CONCLUSION: Intermediately pathogenic strain ST25 has evolved to become
AB  - highly pathogenic strain ST1, which, in turn, has more recently evolved to
AB  - become epidemic strain ST7. ST7 has the ability to stimulate the
AB  - production of massive amounts of proinflammatory cytokines, leading to
AB  - STSLS.
ER  -

TY  - JOUR
AU  - Ye, J.
AU  - Ren, C.
AU  - Shan, X.
AU  - Zeng, R.
TI  - Draft Genome Sequence of Aldehyde-Degrading Strain Halomonas axialensis ACH-L-8.
JO  - Genome Announcements
PY  - 2016
SP  - e00287
EP  - e00216
VL  - 4
AB  - Halomonas axialensisACH-L-8, a deep-sea strain isolated from the South China Sea, has the
AB  - ability to degrade aldehydes. Here, we present an annotated draft genome
AB  - sequence of this species, which could provide fundamental molecular information
AB  - on the aldehydes-degrading mechanism.
ER  -

TY  - JOUR
AU  - Ye, L.
AU  - Hildebrand, F.
AU  - Dingemans, J.
AU  - Ballet, S.
AU  - Laus, G.
AU  - Matthijs, S.
AU  - Berendsen, R.
AU  - Cornelis, P.
TI  - Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens.
JO  - PLoS ONE
PY  - 2014
SP  - E110038
EP  - E110038
VL  - 9
AB  - Pseudomonas putida is a member of the fluorescent pseudomonads known to produce
AB  - the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated
AB  - from a stream in Brussels, was found to produce compound(s) with antimicrobial
AB  - activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas
AB  - aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual
AB  - characteristic for P. putida. The active compound production only occurred in
AB  - media with low iron content and without organic nitrogen sources. Transposon
AB  - mutants which lost their antimicrobial activity had the majority of insertions in
AB  - genes involved in the biosynthesis of pyoverdine, although purified pyoverdine
AB  - was not responsible for the antagonism. Separation of compounds present in
AB  - culture supernatants revealed the presence of two fractions containing highly
AB  - hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome
AB  - confirmed the presence of putisolvin biosynthesis genes and the corresponding
AB  - lipopeptides were found to contribute to the antimicrobial activity. One cluster
AB  - of ten genes was detected, comprising a NAD-dependent epimerase, an
AB  - acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain
AB  - dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P.
AB  - putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors,
AB  - conferring a high capacity to utilize pyoverdines from other pseudomonads. One
AB  - unique feature of W15Oct28 is also the presence of different secretion systems
AB  - including a full set of genes for type IV secretion, and several genes for type
AB  - VI secretion and their VgrG effectors.
ER  -

TY  - JOUR
AU  - Ye, M.
AU  - Tu, J.
AU  - Jiang, J.
AU  - Bi, Y.
AU  - You, W.
AU  - Zhang, Y.
AU  - Ren, J.
AU  - Zhu, T.
AU  - Cao, Z.
AU  - Yu, Z.
AU  - Shao, C.
AU  - Shen, Z.
AU  - Ding, B.
AU  - Yuan, J.
AU  - Zhao, X.
AU  - Guo, Q.
AU  - Xu, X.
AU  - Huang, J.
AU  - Wang, M.
TI  - Clinical and Genomic Analysis of Liver Abscess-Causing Klebsiella pneumoniae Identifies New Liver Abscess-Associated Virulence Genes.
JO  - Front Cell Infect Microbiol
PY  - 2016
SP  - 165
EP  - 165
VL  - 6
AB  - Hypervirulent variants of Klebsiella pneumoniae (hvKp) that cause invasive
AB  - community-acquired pyogenic liver abscess (PLA) have emerged globally. Little is
AB  - known about the virulence determinants associated with hvKp, except for the
AB  - virulence genes rmpA/A2 and siderophores (iroBCD/iucABCD) carried by the
AB  - pK2044-like large virulence plasmid. Here, we collected most recent clinical
AB  - isolates of hvKp from PLA samples in China, and performed clinical, molecular,
AB  - and genomic sequencing analyses. We found that 90.9% (40/44) of the pathogens
AB  - causing PLA were K. pneumoniae. Among the 40 LA-Kp, K1 (62.5%), and K2 (17.5%)
AB  - were the dominant serotypes, and ST23 (47.5%) was the major sequence type.
AB  - S1-PFGE analyses demonstrated that although 77.5% (31/40) of the LA-Kp isolates
AB  - harbored a single large virulence plasmid varied in size, 5 (12.5%) isolates had
AB  - no plasmid and 4 (10%) had two or three plasmids. Whole genome sequencing and
AB  - comparative analysis of 3 LA-Kp and 3 non-LA-Kp identified 133 genes present only
AB  - in LA-Kp. Further, large scale screening of the 133 genes in 45 LA-Kp and 103
AB  - non-LA-Kp genome sequences from public databases identified 30 genes that were
AB  - highly associated with LA-Kp, including iroBCD, iucABCD and rmpA/A2 and 21 new
AB  - genes. Then, these 21 new genes were analyzed in 40 LA-Kp and 86 non-LA-Kp
AB  - clinical isolates collected in this study by PCR, showing that new genes were
AB  - present 80-100% among LA-Kp isolates while 2-11% in K. pneumoniae isolates from
AB  - sputum and urine. Several of the 21 genes have been proposed as virulence factors
AB  - in other bacteria, such as the gene encoding SAM-dependent methyltransferase and
AB  - pagO which protects bacteria from phagocytosis. Taken together, these genes are
AB  - likely new virulence factors contributing to the hypervirulence phenotype of
AB  - hvKp, and may deepen our understanding of virulence mechanism of hvKp.
ER  -

TY  - JOUR
AU  - Ye, P.
AU  - Luan, Y.
AU  - Chen, K.
AU  - Liu, Y.
AU  - Xiao, C.
AU  - Xie, Z.
TI  - MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine  generated by single-molecular real-time sequencing.
JO  - Nucleic Acids Res.
PY  - 2017
SP  - D85
EP  - D89
VL  - 45
AB  - DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine
AB  - (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the
AB  - most common types. Previous efforts have been largely focused on 5mC, providing
AB  - invaluable insights into epigenetic regulation through DNA methylation. Recently
AB  - developed single-molecule real-time (SMRT) sequencing technology provides a
AB  - unique opportunity to detect the less studied DNA 6mA and 4mC modifications at
AB  - single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing
AB  - data generated, there is an emerging demand to systematically explore DNA 6mA and
AB  - 4mC modifications from these data sets. MethSMRT is the first resource hosting
AB  - DNA 6mA and 4mC methylomes. All the data sets were processed using the same
AB  - analysis pipeline with the same quality control. The current version of the
AB  - database provides a platform to store, browse, search and download epigenome-wide
AB  - methylation profiles of 156 species, including seven eukaryotes such as
AB  - Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes.
AB  - It also offers a genome browser to visualize the methylation sites and related
AB  - information such as single nucleotide polymorphisms (SNP) and genomic annotation.
AB  - Furthermore, the database provides a quick summary of statistics of methylome of
AB  - 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is
AB  - publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use
AB  - restriction.
ER  -

TY  - JOUR
AU  - Ye, W.
AU  - Ye, S.
AU  - Liu, J.
AU  - Chang, S.
AU  - Chen, M.
AU  - Zhu, B.
AU  - Guo, L.
AU  - An, Q.
TI  - Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os34, Isolated from Rice Roots.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6993
EP  - 6994
VL  - 194
AB  - Most Herbaspirillum seropedicae strains are beneficial endophytes to plants. In contrast, H.
AB  - seropedicae strain Os34, isolated from rice roots, is pathogenic.
AB  - The draft genome sequence of strain Os34 presented here allows in-depth
AB  - comparative genome analyses to understand the specific mechanisms of beneficial
AB  - and pathogenic Herbaspirillum-plant interactions.
ER  -

TY  - JOUR
AU  - Ye, Y.
AU  - Stivers, J.T.
TI  - Fluorescence-based high-throughput assay for human DNA (cytosine-5)-methyltransferase 1.
JO  - Anal. Biochem.
PY  - 2010
SP  - 168
EP  - 172
VL  - 401
AB  - We have developed the first economical and rapid nonradioactive assay method that is suitable
AB  - for high-throughput screening of the important
AB  - pharmacological target human DNA (cytosine-5)-methyltransferase 1
AB  - (DNMT1). The method combines three key innovations: the use of a
AB  - truncated form of the enzyme that is highly active on a 26-bp
AB  - hemimethylated DNA duplex substrate, the introduction of the
AB  - methylation site into the recognition sequence of a restriction
AB  - endonuclease, and the use of a fluorogenic read-out method. The extent
AB  - of DNMT1 methylation is reflected in the protection of the DNA
AB  - substrate from endonuclease cleavage that would otherwise result in a
AB  - large fluorescence increase. The assay has been validated in a
AB  - high-throughput format, and trivial changes in the substrate sequence
AB  - and endonuclease allow adaptation of the method to any bacterial or
AB  - human DNA methyltransferase.
ER  -

TY  - JOUR
AU  - Yebra, M.J.
AU  - Bhagwat, A.S.
TI  - A cytosine methyltransferase converts 5-methylcytosine in DNA to thymine.
JO  - Biochemistry
PY  - 1995
SP  - 14752
EP  - 14757
VL  - 34
AB  - Sites of cytosine methylation are known to be hot spots for C.G to T.A mutations in a number
AB  - of systems, including human cells.  Traditionally, spontaneous hydrolytic deamination of
AB  - 5-methylcytosine to thymine has been invoked as the cause of this phenomenon.  We show here
AB  - that a bacterial cytosine methyltransferase can convert 5-methylcytosine in DNA to thymine and
AB  - that this reaction creates a mutational hot spot at a site of DNA methylation.  The reaction
AB  - is fairly insensitive to the methyl donor in the reaction, S-adenosylmethionine.  In many
AB  - cancers, the most frequent class of mutations is C to T changes within CG dinucleotides of the
AB  - tumor suppressor gene p53.  Because of the similarities of the reaction mechanisms of
AB  - mammalian and bacterial enzymes and the physiology of the cancer cells, this reaction is
AB  - expected to contribute to mutations at CG dinucleotides in precancerous cells.
ER  -

TY  - JOUR
AU  - Yebra, M.J.
AU  - Bhagwat, A.S.
TI  - A novel repetitive sequence lies near the gene encoding a cytosine methyltransferase in the cyanobacterium Dactylococcopsis salina.
JO  - Gene
PY  - 1995
SP  - 71
EP  - 74
VL  - 164
AB  - An unusual cluster of tandemly repeated DNA sequences (TRS) was found downstream from the gene
AB  - encoding DsaV methyltransferase, the DNA modification enzyme in the DsaV
AB  - restriction-modification system found in a strain of Dactylococcopsis salina (Ds).  The repeat
AB  - unit is about 32-bp long and is present 13 times in the cluster.  Each repeat unit can be
AB  - divided into two distinct parts based on the level of sequence conservation and evolution.
AB  - Hybridization of Ds DNA with a probe specific for this cluster revealed that there were at
AB  - least two additional sites within the genome with similar TRS.  The TRS units are localized in
AB  - one region of the Ds genome.  They do not share significant sequence similarity with other TRS
AB  - found in prokaryotes.
ER  -

TY  - JOUR
AU  - Yebra, M.J.
AU  - Bhagwat, A.S.
TI  - A rapid and sensitive method to measure DNA endonuclease activity.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 5797
EP  - 5798
VL  - 21
AB  - The high affinity of biotin for streptavidin has been used to isolate DNA-binding proteins
AB  - from cells. This is achieved by mixing DNA oligomers and containing biotin with cell extracts
AB  - and then passing the mixture over immobilized streptavidin. We describe below an adaptation of
AB  - this method to quantitate the activities of endonucleases. It should be useful for detecting
AB  - endonuclease activity during enzyme purification, for studying inhibitors and activators of
AB  - nucleases and for determining kinetic properties of endonucleases.
ER  -

TY  - JOUR
AU  - Yebra, M.J.
AU  - Novella, I.S.
AU  - Barbes, C.
AU  - Aparicio, J.F.
AU  - Martin, C.G.
AU  - Hardisson, C.
AU  - Sanchez, J.
TI  - Characterization of Rrh4273I, a restriction-modification system of Rhodococcus rhodochrous ATCC 4273 (Nocardia corallina) which recognizes the same sequence as the Streptomyces albus G SalI restriction-modification system.
JO  - J. Gen. Microbiol.
PY  - 1991
SP  - 1279
EP  - 1284
VL  - 137
AB  - Rhodococcus rhodochrous ATCC 4273 (Nocardia corallina) has a
AB  - restriction-modification system with the same recognition sequence, methylation
AB  - site and cleavage site as the SalI restriction-modification system.  Both the
AB  - restriction endonuclease and the DNA-methyltransferase (DNA-MTase) have been
AB  - partially purified and characterized.  The nuclease has requirements for
AB  - activity similar to SalI, and a native Mr of about 46,000.  The DNA-MTase is a
AB  - protein with an Mr of about 67,000.  No DNA homology was detected between the
AB  - cloned SalI restriction-modification genes of Streptomyces albus and R.
AB  - rhodochrous chromosomal DNA.
ER  -

TY  - JOUR
AU  - Yebra, M.J.
AU  - Sanchez, J.
AU  - Martin, C.G.
AU  - Hardisson, C.
AU  - Barbes, C.
TI  - The effect of sinefungin and synthetic analogues on RNA and DNA methyltransferase from Streptomyces.
JO  - J. Antibiot. (Tokyo)
PY  - 1991
SP  - 1141
EP  - 1147
VL  - 44
AB  - Sinefungin is an antibiotic structurally related to S-adenosylmethionine.  It
AB  - has been described as an inhibitor of RNA transmethylation reactions in viruses
AB  - and eukaryotic organisms, but not in bacteria.  We show here that sinefungin
AB  - strongly inhibits RNA methyltransferase activity, but not the biosynthesis of
AB  - these enzymes in Streptomyces.  All the methylated bases found in Streptomyces
AB  - RNA (1-methyladenine, N6-methyladenine, N6,N6-dimethyladenine and
AB  - 7-methylguanine) are inhibited by this antibiotic.  Experiments with sinefungin
AB  - analogues show that specific changes in the ornithine radical of the molecule
AB  - still preserve its inhibitory capability.  The substitution of the adenine
AB  - radical by uridine causes the loss of inhibitory effect.  These results and our
AB  - former studies on Streptomyces DNA methylation, suggest that nucleic acid
AB  - modification is the main target of sinefungin in Streptomyces.
ER  -

TY  - JOUR
AU  - Yee, L.
AU  - Hosoyama, A.
AU  - Ohji, S.
AU  - Tsuchikane, K.
AU  - Shimodaira, J.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Suzuki-Minakuchi, C.
AU  - Nojiri, H.
TI  - Complete Genome Sequence of a Dimethyl Sulfide-Utilizing Bacterium, Acinetobacter guillouiae Strain 20B (NBRC 110550).
JO  - Genome Announcements
PY  - 2014
SP  - e01048
EP  - e01014
VL  - 2
AB  - Acinetobacter guillouiae strain 20B can utilize dimethyl sulfide (DMS) as the sole sulfur
AB  - source and degrade chloroethylenes. We report here the complete
AB  - 4,648,418-bp genome sequence for this strain, which contains 4,367 predicted
AB  - coding sequences (CDSs), including a well-characterized DMS degradative operon.
ER  -

TY  - JOUR
AU  - Yee, M.
AU  - Klinzing, D.
AU  - Wei, J.R.
AU  - Gengenbacher, M.
AU  - Rubin, E.J.
AU  - Chien, J.Y.
AU  - Hsueh, P.R.
AU  - Dick, T.
TI  - Draft Genome Sequence of Mycobacterium avium 11.<jour_book>Genome Announc.
JO  - 
PY  - 2017
SP  - e00766
EP  - e00717
VL  - 5
AB  - Mycobacterium avium accounts for most lung disease caused by nontuberculous mycobacteria
AB  - (NTM). The lack of effective chemotherapy calls for the discovery of
AB  - new drugs. Here, we report the draft genome sequence of M. avium 11, a clinical
AB  - isolate used as a screening strain for NTM-focused drug discovery.
ER  -

TY  - JOUR
AU  - Yee, M.
AU  - Klinzing, D.
AU  - Wei, J.R.
AU  - Gengenbacher, M.
AU  - Rubin, E.J.
AU  - Dick, T.
TI  - Draft Genome Sequence of Mycobacterium abscessus Bamboo.
JO  - Genome Announcements
PY  - 2017
SP  - e00388
EP  - e00317
VL  - 5
AB  - Mycobacterium abscessus, an intrinsically multidrug-resistant pathogen, causes chronic
AB  - incurable lung disease. New drugs for this emerging pathogen represent an
AB  - urgent unmet medical need. Here, we report a draft genome sequence of M.
AB  - abscessus Bamboo, a clinical isolate used as a screening strain for drug
AB  - discovery.
ER  -

TY  - JOUR
AU  - Yen, Ly.H.T.
AU  - Park, S.-Y.
AU  - Kim, J.-S.
TI  - Cloning, crystallization and preliminary X-ray diffraction analysis of an intact DNA methyltransferase of a type I restriction-modification enzyme from Vibrio vulnificus.
JO  - Acta Crystallogr. F Struct. Biol. Cryst. Commun.
PY  - 2014
SP  - 489
EP  - 492
VL  - 70
AB  - Independently of the restriction (HsdR) subunit, the specificity (HsdS) and methylation (HsdM)
AB  - subunits interact with each other, and function as a methyltransferase in type I
AB  - restriction-modification systems. A single gene that combines the HsdS and HsdM subunits in
AB  - Vibrio vulnificus YJ016 was expressed and purified. A crystal suitable for X-ray diffraction
AB  - was obtained from 25%(w/v) polyethylene glycol monomethylether 5000, 0.1 M HEPES pH 8.0, 0.2 M
AB  - ammonium sulfate at 291 K by hanging-drop vapour diffusion. Diffraction data were collected to
AB  - a resolution of 2.31 angstrom using synchrotron radiation. The crystal belonged to the
AB  - primitive monoclinic space group P2(1), with unit-cell parameters a = 93.25, b = 133.04, c =
AB  - 121.49 angstrom, beta = 109.7 degrees. With four molecules in the asymmetric unit, the crystal
AB  - volume per unit protein weight was 2.61 angstrom(3) Da(-1), corresponding to a solvent content
AB  - of 53%.
ER  -

TY  - JOUR
AU  - Yen, R.-W.C.
AU  - Vertino, P.M.
AU  - Nelkin, B.D.
AU  - Yu, J.J.
AU  - El-Deiry, W.
AU  - Cumaraswamy, A.
AU  - Lennon, G.G.
AU  - Trask, B.J.
AU  - Celano, P.
AU  - Baylin, S.B.
TI  - Isolation and characterization of the cDNA encoding human DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 2287
EP  - 2291
VL  - 20
AB  - We have cloned a series of overlapping cDNA clones encoding a 5194 bp transcript for human DNA
AB  - methyltransferase (DNA MTase). This sequence potentially codes for a protein of 1495 amino
AB  - acids with a predicted molecular weight of 169 kDa. The human DNA MTase cDNA has eighty
AB  - percent homology at the nucleotide level, and the predicted protein has seventy-four percent
AB  - identity at the amino acid level, to the DNA MTase cDNA cloned from mouse cells. Like the
AB  - murine DNA MTase, the amino terminal two-thirds of the human protein contains a cysteine-rich
AB  - region suggestive of a metal-binding domain. The carboxy terminal one-third of the protein
AB  - shows considerable similarity to prokaryotic (cytosine-5)-methyltransferases. The arrangement
AB  - of multiple motifs conserved in the prokaryotic genes is preserved in the human DNA MTase,
AB  - including the relative position of a proline-cysteine dipeptide thought to be an essential
AB  - catalytic site in all (cytosine-5)-methyltransferases. A single 5.2 kb transcript was detected
AB  - in all human tissues tested, with the highest levels of expression observed in RNA from
AB  - placenta, brain, heart and lung. DNA MTase cDNA clones were used to screen a chromosome 19
AB  - genomic cosmid library. The DNA MTase-positive cosmids which are estimated to span a genomic
AB  - distance of 93 kb have been localized to 19p13.2-p13.3 by fluorescence in situ hybridization.
AB  - Isolation of the cDNA for human DNA MTase will further study the regulation of DNA MTase
AB  - expression, and of the role of this enzyme in establishing DNA methylation patterns in both
AB  - normal and neoplastic cells.
ER  -

TY  - JOUR
AU  - Yeo, C.C.
AU  - Tham, J.M.
AU  - Kwong, S.M.
AU  - Poh, C.L.
TI  - Characterization of the Pac25I restriction-modification genes isolated from the endogenous pRA2 plasmid of Pseudomonas alcaligenes NCIB 9867.
JO  - Plasmid
PY  - 1998
SP  - 203
EP  - 213
VL  - 40
AB  - Genes for the class II Pseudomonas alcaligenes NCIB 9867 restriction-modification (R-M)
AB  - system, Pac25I, have been cloned from its 33-kb endogenous plasmid, pRA2. The Pac25I
AB  - endonuclease and methylase genes were found to be aligned in a head-to-tail orientation with
AB  - the methylase gene preceding and overlapping the endonuclease gene by 1 bp. The deduced amino
AB  - acid sequence of the Pac25I methylase revealed significant similarity with the XcyI, XmaI,
AB  - Cfr9I, and SmaI methylases. High sequence similarity was displayed between the Pac25I
AB  - endonuclease and the XcyI, XmaI, and Cfr9I endonucleases which cleave between the external
AB  - cytosines of the recognition sequence (i.e., 5'-C^CCGGG-3') and are thus perfect
AB  - isoschizomers. However, no sequence similarity was detected between the Pac25I endonuclease
AB  - and the SmaI endonuclease which cleaves between the internal CpG of the recognition sequence
AB  - (i.e., 5'-CCC^GGG-3'). Both the Pac25I methylase and endonuclease were expressed in
AB  - Escherichia coli. An open reading frame encoding a protein which shows significant similarity
AB  - to invertases and resolvases was located immediately upstream of the Pac25I R-M operon. In
AB  - addition, a transposon designated Tn5563 was located 1531 bp downstream of the R-M genes. The
AB  - location on a self-transmissible plasmid as well as the close association with genes involved
AB  - in DNA mobility suggests horizontal transfer as a possible mode of distribution of this family
AB  - of R-M genes in various bacteria.
ER  -

TY  - JOUR
AU  - Yeo, I.C.
AU  - Lee, N.K.
AU  - Hahm, Y.T.
TI  - Genome Sequencing of Bacillus subtilis SC-8, Antagonistic to the Bacillus cereus Group, Isolated from Traditional Korean Fermented-Soybean Food.
JO  - J. Bacteriol.
PY  - 2012
SP  - 536
EP  - 537
VL  - 194
AB  - Bacillus subtilis SC-8 is a Gram-positive bacterium displaying narrow antagonistic activity
AB  - for the Bacillus cereus group. B. subtilis SC-8 was
AB  - isolated from Korean traditional fermented-soybean food. Here we report
AB  - the draft genome sequence of B. subtilis SC-8, including biosynthetic
AB  - genes for antibiotics that may have beneficial effects for control of
AB  - food-borne pathogens.
ER  -

TY  - JOUR
AU  - Yeoman, C.J.
AU  - Yildirim, S.
AU  - Thomas, S.M.
AU  - Durkin, A.S.
AU  - Torralba, M.
AU  - Sutton, G.
AU  - Buhay, C.J.
AU  - Ding, Y.
AU  - Dugan-Rocha, S.P.
AU  - Muzny, D.M.
AU  - Qin, X.
AU  - Gibbs, R.A.
AU  - Leigh, S.R.
AU  - Stumpf, R.
AU  - White, B.A.
AU  - Highlander, S.K.
AU  - Nelson, K.E.
AU  - Wilson, B.A.
TI  - Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.
JO  - PLoS ONE
PY  - 2010
SP  - E12411
EP  - E12411
VL  - 5
AB  - BACKGROUND: Gardnerella vaginalis is described as a common vaginal
AB  - bacterial species whose presence correlates strongly with bacterial
AB  - vaginosis (BV). Here we report the genome sequencing and comparative
AB  - analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and
AB  - 594 (ATCC 14018) were isolated from the vaginal tracts of women with
AB  - symptomatic BV, while Strain 409-05 was isolated from a healthy,
AB  - asymptomatic individual with a Nugent score of 9. PRINCIPAL FINDINGS:
AB  - Substantial genomic rearrangement and heterogeneity were observed that
AB  - appeared to have resulted from both mobile elements and substantial
AB  - lateral gene transfer. These genomic differences translated to differences
AB  - in metabolic potential. All strains are equipped with significant
AB  - virulence potential, including genes encoding the previously described
AB  - vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm
AB  - formation, and antimicrobial resistance systems, We also observed systems
AB  - promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains
AB  - possess a large number of genes that may enhance their ability to compete
AB  - with and exclude other vaginal colonists. These include up to six
AB  - toxin-antitoxin systems and up to nine additional antitoxins lacking
AB  - cognate toxins, several of which are clustered within each genome. All
AB  - strains encode bacteriocidal toxins, including two lysozyme-like toxins
AB  - produced uniquely by strain 409-05. Interestingly, the BV isolates encode
AB  - numerous proteins not found in strain 409-05 that likely increase their
AB  - pathogenic potential. These include enzymes enabling mucin degradation, a
AB  - trait previously described to strongly correlate with BV, although
AB  - commonly attributed to non-G. vaginalis species. CONCLUSIONS:
AB  - Collectively, our results indicate that all three strains are able to
AB  - thrive in vaginal environments, and therein the BV isolates are capable of
AB  - occupying a niche that is unique from 409-05. Each strain has significant
AB  - virulence potential, although genomic and metabolic differences, such as
AB  - the ability to degrade mucin, indicate that the detection of G. vaginalis
AB  - in the vaginal tract provides only partial information on the
AB  - physiological potential of the organism.
ER  -

TY  - JOUR
AU  - Yeon, S.M.
AU  - Kim, Y.C.
TI  - Complete sequence and organization of the Sphingobium chungbukense DJ77 pSY2 plasmid.
JO  - J. Microbiol.
PY  - 2011
SP  - 684
EP  - 688
VL  - 49
AB  - Sphingobium chungbukense DJ77 is capable of metabolizing priority
AB  - chemicals of human health concern such as polycyclic aromatic hydrocarbons
AB  - (PAHs), extracellular polysaccharide (EPS), and antibiotics. Here, we
AB  - report the complete DNA and genetic organization of the plasmid pSY2 from
AB  - strain DJ77. A DNA sequence analysis revealed that pSY2 comprises 18,779
AB  - bp encoding 22 open reading frames (ORFs) with 59.5% G+C content. The ORFs
AB  - on pSY2 were classified into DNA replication, conjugative function,
AB  - transposition, plasmid stability/partition, and other functional groups
AB  - (transport, fatty acid biosynthesis, stress, and growth rate regulation).
AB  - Three ORFs on pSY2 were hypothetical proteins.
ER  -

TY  - JOUR
AU  - Yergeau, E.
AU  - Lawrence, J.R.
AU  - Waiser, M.J.
AU  - Korber, D.R.
AU  - Greer, C.W.
TI  - Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 5432
EP  - 5439
VL  - 76
AB  - Pharmaceutical products are released at low concentrations into aquatic
AB  - environments following domestic wastewater treatment. Such low
AB  - concentrations have been shown to induce transcriptional responses in
AB  - microorganisms, which could have consequences on aquatic ecosystem
AB  - dynamics. In order to test if these transcriptional responses could also
AB  - be observed in complex river microbial communities, biofilm reactors were
AB  - inoculated with water from two rivers of differing trophic statuses and
AB  - subsequently treated with environmentally relevant doses (ng/liter to
AB  - microg/liter range) of four pharmaceuticals (erythromycin [ER],
AB  - gemfibrozil [GM], sulfamethazine [SN], and sulfamethoxazole [SL]). To
AB  - monitor functional gene expression, we constructed a 9,600-feature
AB  - anonymous DNA microarray platform onto which cDNA from the biofilms was
AB  - hybridized. Pharmaceutical treatments induced both positive and negative
AB  - transcriptional responses from biofilm microorganisms. For instance, ER
AB  - induced the transcription of several stress, transcription, and
AB  - replication genes, while GM, a lipid regulator, induced transcriptional
AB  - responses from several genes involved in lipid metabolism. SN caused
AB  - shifts in genes involved in energy production and conversion, and SL
AB  - induced responses from a range of cell membrane and outer envelope genes,
AB  - which in turn could affect biofilm formation. The results presented here
AB  - demonstrate for the first time that low concentrations of small molecules
AB  - can induce transcriptional changes in a complex microbial community. The
AB  - relevance of these results also demonstrates the usefulness of anonymous
AB  - DNA microarrays for large-scale metatranscriptomic studies of communities
AB  - from differing aquatic ecosystems.
ER  -

TY  - JOUR
AU  - Yerrapragada, S. et al.
TI  - Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601.
JO  - Genome Announcements
PY  - 2015
SP  - e00355
EP  - e00315
VL  - 3
AB  - Tolypothrix sp. PCC 7601 is a freshwater filamentous cyanobacterium with complex  responses to
AB  - environmental conditions. Here, we present its 9.96-Mbp draft genome
AB  - sequence, containing 10,065 putative protein-coding sequences, including 305
AB  - predicted two-component system proteins and 27 putative phytochrome-class
AB  - photoreceptors, the most such proteins in any sequenced genome.
ER  -

TY  - JOUR
AU  - Yesufu, H.M.I.
AU  - Hanley, A.
AU  - Rinaldi, A.
AU  - Adams, R.L.P.
TI  - DNA methylase from Pisum sativum.
JO  - Biochem. J.
PY  - 1991
SP  - 469
EP  - 475
VL  - 273
AB  - DNA methylase activity was detected in nuclei from pea shoots.  The enzyme can only be
AB  - extracted by low-salt treatment if the nuclei are pretreated with micrococcal nuclease.  Only
AB  - a single enzyme was detected, and it was purified to a specific activity of 1620 units/mg of
AB  - protien.  It has an Mr of 160,000 on gel filtration and SDS/PAGE.  Pea DNA methylase
AB  - methylates cytosine in all four dinucleotides, and this is interpreted to show that it acts on
AB  - CNG trinucleotides.  Although it shows a strong preference for hemi-methylated double-stranded
AB  - DNA, it is also capable of methylation de novo.  Homologous DNA is the best natural substrate.
AB  - In vitro the enzyme interacts with DNA to form a salt-resistant complex with DNA that is
AB  - stable for at least 4h.
ER  -

TY  - JOUR
AU  - Yew, S.M.
AU  - Chan, C.L.
AU  - Soo-Hoo, T.S.
AU  - Na, S.L.
AU  - Ong, S.S.
AU  - Hassan, H.
AU  - Ngeow, Y.F.
AU  - Hoh, C.C.
AU  - Lee, K.W.
AU  - Yee, W.Y.
AU  - Ng, K.P.
TI  - Draft Genome Sequence of Dematiaceous Coelomycete Pyrenochaeta sp. Strain UM 256, Isolated from Skin Scraping.
JO  - Genome Announcements
PY  - 2013
SP  - e00158
EP  - e00113
VL  - 1
AB  - Pyrenochaeta, classified under the order Pleosporales, is known to cause diseases in plants
AB  - and humans. Here, we report a draft genome sequence of a Pyrenochaeta
AB  - sp. isolated from a skin scraping, with an estimated genome size of 39.4 Mb.
AB  - Genes associated with the synthesis of proteases, toxins, plant cell wall
AB  - degradation, and multidrug resistance were found.
ER  -

TY  - JOUR
AU  - Yi, C.Q.
AU  - Fong, C.C.
AU  - Chen, W.W.
AU  - Qi, S.J.
AU  - Tzang, C.H.
AU  - Lee, S.T.
AU  - Yang, M.S.
TI  - Interactions between carbon nanotubes and DNA polymerase and restriction endonucleases.
JO  - Nanotechnol.
PY  - 2007
SP  - 025102
EP  - 025102
VL  - 18
AB  - Effects of multi-walled carbon nanotubes (MWCNT) and single-walled carbon nanotubes (SWCNT)
AB  - functionalized with and without carboxylic
AB  - groups on polymerase chain reaction (PCR) and restriction digestion
AB  - reaction were investigated. The results showed that CNT can reduce and
AB  - even inhibit PCR and restriction digestion reaction, possibly due to
AB  - the decrease of respective enzyme activity. The inhibition effect on
AB  - double restriction digestion reaction and PCR was increased in the
AB  - order of CNT-COOH > pristine CNT and SWCNT > MWCNT. This study
AB  - demonstrated that CNT may significantly affect the efficiency of
AB  - biochemical reactions through different action mechanisms, which is
AB  - critical for understanding how nanomaterials impact biological systems.
ER  -

TY  - JOUR
AU  - Yi, H.
AU  - Cho, Y.J.
AU  - Hur, H.G.
AU  - Chun, J.
TI  - Genome sequence of Escherichia coli AA86, isolated from cow feces.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3681
EP  - 3681
VL  - 193
AB  - Escherichia coli AA86 (= KACC 15541) is an enteric bacterium that was isolated from a sample
AB  - of healthy cow feces. Its genome sequence revealed
AB  - that it is most closely related to the human fecal strain E. coli SE15 and
AB  - could be classified under E. coli phylogenetic group B2. Here, we report
AB  - the genome sequence of E. coli AA86 consisting of 3 contigs and 2
AB  - plasmids.
ER  -

TY  - JOUR
AU  - Yi, H.
AU  - Cho, Y.J.
AU  - Yong, D.
AU  - Chun, J.
TI  - Genome Sequence of Escherichia coli J53, a Reference Strain for Genetic Studies.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3742
EP  - 3743
VL  - 194
AB  - Escherichia coli J53 (F(-) met pro Azi(r)) is a derivative of E. coli K-12 which  is resistant
AB  - to sodium azide. This strain has been widely used as a general
AB  - recipient strain for various conjugation experiments. Here, we report the genome
AB  - sequence of E. coli J53 (=KACC 16628).
ER  -

TY  - JOUR
AU  - Yi, J.L.
AU  - Wang, J.
AU  - Li, Q.
AU  - Liu, Z.X.
AU  - Zhang, L.
AU  - Liu, A.X.
AU  - Yu, J.F.
TI  - Draft Genome Sequence of the Bacterium Lysobacter capsici X2-3, with a Broad Spectrum of Antimicrobial Activity against Multiple Plant-Pathogenic Microbes.
JO  - Genome Announcements
PY  - 2015
SP  - e00589
EP  - e00515
VL  - 3
AB  - Lysobacter capsici strain X2-3 was isolated from the wheat rhizosphere in China and exhibits a
AB  - remarkable capacity to inhibit the growth of multiple pathogens.
AB  - Here, we report the draft genome sequence of L. capsici strain X2-3 in China.
ER  -

TY  - JOUR
AU  - Yi, L.
AU  - Guo, X.
AU  - Liu, L.
AU  - Shao, C.
AU  - Lu, X.
TI  - First Report on the Complete Genome Sequence of Lactobacillus crustorum MN047, a  Potent Probiotic Strain Isolated from Koumiss in China.
JO  - Genome Announcements
PY  - 2017
SP  - e00048
EP  - e00017
VL  - 5
AB  - The complete genome sequence of Lactobacillus crustorum deciphered by PacBio RS II and
AB  - Illumina HiSeq 4000 sequencing was first reported with one chromosome and
AB  - two plasmids. Sequence analysis of L. crustorum MN047 showed probiotic
AB  - characteristics.
ER  -

TY  - JOUR
AU  - Yi, L.
AU  - Tang, C.
AU  - Peng, Q.
AU  - Peng, Q.
AU  - Chai, L.
TI  - Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1.
JO  - Genome Announcements
PY  - 2015
SP  - e00935
EP  - e00915
VL  - 3
AB  - Pseudomonas parafulva YAB-1, isolated from perfluorinated compound-contaminated soil, has the
AB  - ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome
AB  - sequence and annotation of the PFOA-degrading bacterium P. parafulva YAB-1. The data provide
AB  - the basis to investigate the molecular mechanism of PFOA metabolism.
ER  -

TY  - JOUR
AU  - Yi, Y.
AU  - de Jong, A.
AU  - Spoelder, J.
AU  - Elzenga, J.T.
AU  - van Elsas, J.D.
AU  - Kuipers, O.P.
TI  - Draft Genome Sequence of Bacillus mycoides M2E15, a Strain Isolated from the Endosphere of Potato.
JO  - Genome Announcements
PY  - 2016
SP  - e00031
EP  - e00016
VL  - 4
AB  - We present the draft genome sequence of Bacillus mycoides M2E15, a bacterium isolated from
AB  - potato endosphere. Analysis of the 6.08-Mbp draft genome sequence
AB  - identified 6,386 protein-encoding sequences, including potential plant growth
AB  - promoting genes. Specifically, genes for proteins involved in phosphate
AB  - utilization, iron acquisition, and bacteriocin production were identified.
ER  -

TY  - JOUR
AU  - Yilder, C.
AU  - Onsan, Z.I.
AU  - Kirdar, B.
TI  - Optimization of starting time and period of induction and inducer concentration in the production of the restriction enzyme EcoRI from recombinant Escherichia coli 294.
JO  - Turk. J. Chem.
PY  - 1998
SP  - 221
EP  - 226
VL  - 22
AB  - Induction parameters including inducer concentration, period of induction and the cell
AB  - concentration at which inducer is to be added to the fermentation broth were optimized in
AB  - order to increase the yield of the EcoRI restriction endonuclease isolated from recombinant E.
AB  - coli.  Bacterial cells harboring the plasmid pPG430 containing EcoRI endonuclease and the
AB  - methylase genes under the control of lac promoter were used in the experiments where induction
AB  - was accomplished by using lactose isopropyl-B-D-thiogalactoside.  An IPTG concentration of
AB  - 0.1mM, the late exponential phase of growth (at an optical density of 1.2 at 595 nm) and an
AB  - induction period of 6 hours were determined to be the optimum conditions for induction.
ER  -

TY  - JOUR
AU  - Yildirim, S.
AU  - Elhanafi, D.
AU  - Lin, W.
AU  - Hitchins, A.D.
AU  - Siletzky, R.M.
AU  - Kathariou, S.
TI  - Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes among Listeria monocytogenes Epidemic Clone I and Selected Strains of Serotype 1/2a.
JO  - Appl. Environ. Microbiol.
PY  - 2010
SP  - 5577
EP  - 5584
VL  - 76
AB  - Listeria monocytogenes is a food-borne pathogen with a clonal population structure and
AB  - apparently limited gene flow between strains
AB  - of different lineages. Strains of epidemic clone I (ECI) have been
AB  - responsible for numerous outbreaks and invariably have DNA that is
AB  - resistant to digestion by Sau3AI, suggesting methylation of cytosine at
AB  - GATC sites. A putative restriction-modification (RM) gene cassette has
AB  - been identified in the genome of the ECI strain F2365 and all other
AB  - tested ECI strains but is absent from other strains of the same
AB  - serotype (4b). Homologous RM cassettes have not been reported among L.
AB  - monocytogenes isolates of other serotypes. Furthermore, conclusive
AB  - evidence for the involvement of this RM cassette in the Sau3AI
AB  - resistance phenotype of ECI strains has been lacking. In this study, we
AB  - describe a highly conserved RM cassette in certain strains of serotypes
AB  - 1/2a and 4a that have Sau3AI-resistant DNA. In these strains the RM
AB  - cassette was in the same genomic location as in the ECI reference
AB  - strain F2365. The cassette included a gene encoding a putative
AB  - recombinase, suggesting insertion via site-specific recombination.
AB  - Deletion of the RM cassette in the ECI strain F2365 and the serotype
AB  - 1/2a strain A7 rendered the DNA of both strains susceptible to Sau3AI
AB  - digestion, providing conclusive evidence that the cassette includes a
AB  - gene required for methylation of cytosine at GATC sites in both
AB  - strains. The findings suggest that, in addition to its presence in ECI
AB  - strains, this RM cassette and the accompanying genomic DNA methylation
AB  - is also encountered among selected strains of other lineages.
ER  -

TY  - JOUR
AU  - Yildirim, S.
AU  - Lin, W.
AU  - Hitchins, A.D.
AU  - Jaykus, L.A.
AU  - Altermann, E.
AU  - Klaenhammer, T.R.
AU  - Kathariou, S.
TI  - Epidemic clone I-specific genetic markers in strains of Listeria monocytogenes serotype 4b from foods.
JO  - Appl. Environ. Microbiol.
PY  - 2004
SP  - 4158
EP  - 4164
VL  - 70
AB  - Listeria monocytogenes contamination of ready-to-eat foods has been implicated in numerous
AB  - outbreaks of food-borne listeriosis. However,
AB  - the health hazards posed by L. monocytogenes detected in foods may
AB  - vary, and speculations exist that strains actually implicated in
AB  - illness may constitute only a fraction of those that contaminate foods.
AB  - In this study, examination of 34 serogroup 4 (putative or confirmed
AB  - serotype 4b) isolates of L. monocytogenes obtained from various foods
AB  - and food-processing environments, without known implication in illness,
AB  - revealed that many of these strains had methylation of cytosines at
AB  - GATC sites in the genome, rendering their DNA resistant to digestion by
AB  - the restriction endonuclease Sau3AI. These strains also harbored a gene
AB  - cassette with putative restriction-modification system genes as well as
AB  - other, genomically unlinked genetic markers characteristic of the major
AB  - epidemic-associated lineage of L. monocytogenes (epidemic clone 1),
AB  - implicated in numerous outbreaks in Europe and North America. This may
AB  - reflect a relatively high fitness of strains with these genetic markers
AB  - in foods and food-related environments relative to other serotype 4b
AB  - strains and may partially account for the repeated involvement of such
AB  - strains in human food-borne listeriosis.
ER  -

TY  - JOUR
AU  - Yim, A.K.
AU  - Kwok, J.S.
AU  - Yu, A.C.
AU  - Leung, A.K.
AU  - Lau, H.H.
AU  - Chan, T.F.
AU  - Ip, M.
AU  - Tsui, S.K.
TI  - Draft Genome Sequence of Extensively Drug-Resistant Acinetobacter baumannii Strain CUAB1 from a Patient in Hong Kong, China.
JO  - Genome Announcements
PY  - 2015
SP  - e00442
EP  - e00415
VL  - 3
AB  - We report the draft genome sequence of an extensively drug-resistant strain of Acinetobacter
AB  - baumannii, CUAB1, isolated from a patient in a local Hong Kong
AB  - hospital. MIC testing was performed, and genes previously associated with drug
AB  - resistance were located.
ER  -

TY  - JOUR
AU  - Yin, C.
AU  - Chen, D.S.
AU  - Zhuge, J.
AU  - McKenna, D.
AU  - Sagurton, J.
AU  - Wang, G.
AU  - Huang, W.
AU  - Dimitrova, N.
AU  - Fallon, J.T.
TI  - Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA.
JO  - Genome Announcements
PY  - 2018
SP  - e01537
EP  - e01517
VL  - 6
AB  - Complete genome sequences of four toxigenic Clostridium difficile isolates from patients in
AB  - the lower Hudson Valley, New York, USA, were achieved. These isolates
AB  - represent four common sequence types (ST1, ST2, ST8, and ST42) belonging to two
AB  - distinct phylogenetic clades. All isolates have a 4.0- to 4.2-Mb circular
AB  - chromosome, and one carries a phage.
ER  -

TY  - JOUR
AU  - Yin, H.
AU  - Zhang, X.
AU  - Liang, Y.
AU  - Xiao, Y.
AU  - Niu, J.
AU  - Liu, X.
TI  - Draft Genome Sequence of the Extremophile Acidithiobacillus thiooxidans A01, Isolated from the Wastewater of a Coal Dump.
JO  - Genome Announcements
PY  - 2014
SP  - e00222
EP  - e00214
VL  - 2
AB  - The draft genome of Acidithiobacillus thiooxidans A01 contains 3,820,158 bp, with a G+C
AB  - content of 53.08% and 3,660 predicted coding sequences (CDSs). The bacterium contains a series
AB  - of specific genes involved in the oxidation of elemental sulfur and reduced inorganic sulfur
AB  - compounds (RISCs).
ER  -

TY  - JOUR
AU  - Yin, H.S.
AU  - Zhou, Y.L.
AU  - Xu, Z.N.
AU  - Chen, L.J.
AU  - Zhang, D.
AU  - Ai, S.Y.
TI  - An electrochemical assay for DNA methylation, methyltransferase activity and inhibitor screening based on methyl binding domain protein.
JO  - Biosensors and Bioelectronics
PY  - 2013
SP  - 492
EP  - 497
VL  - 41
AB  - DNA methylation is one of important epigenetics events, and responsible to transcription,
AB  - genomic imprinting and cellular differentiation.
AB  - Aberrant DNA methylation is always contacted with various diseases.
AB  - Methyl binding domain (MBD) proteins can specifically bind to the
AB  - methylated CpG dinucleotides. Conventional assay for DNA methylation
AB  - normally need bisulfide treatment, methylated nucleotide labeling or
AB  - PCR amplification. Here, we fabricated a novel electrochemical
AB  - biosensor for detection of DNA methylation, assay of DNA
AB  - methyltransferase (MTase) activity and screening of MTase inhibitor
AB  - based on MBD protein and coomassie brilliant blue G250 (CBB-G250),
AB  - where the electrochemical signal of CBB-G250 was used to monitor the
AB  - methylation event. After the hybrids of DNA S1 and DNA S2 were treated
AB  - with M. SssI MTase in the presence of S-adenosylmethionine, the MBD
AB  - proteins were specifically conjugated to the methylation site of CpG
AB  - dinucleotides, and then, the MBD proteins were stained with CBB-G250.
AB  - The electrochemical signal of CBB-G250 increased linearly with
AB  - increasing M. SssI MTase concentration in the range from 0.1 to 40
AB  - unit/mL. Furthermore, the inhibition investigation demonstrates that
AB  - fisetin and chlorogenic acid can inhibit the M. SssI MTase activity
AB  - with the IC50 value of 153.12 and 137.07 mu M, respectively. Therefore,
AB  - we think that this study may provide a sensitive platform for screening
AB  - of DNA MTase inhibitors.
ER  -

TY  - JOUR
AU  - Yin, J.
AU  - Chen, J.
AU  - Liu, G.
AU  - Yu, Y.
AU  - Song, L.
AU  - Wang, X.
AU  - Qu, X.
TI  - Complete Genome Sequence of Glaciecola psychrophila Strain 170T.
JO  - Genome Announcements
PY  - 2013
SP  - e00199
EP  - e00113
VL  - 1
AB  - Here, we report the complete genome sequence of Glaciecola psychrophila strain 170(T), a novel
AB  - species of the genus Glaciecola, isolated from sea ice at
AB  - high-latitude Arctic locations. The genome consists of a single chromosome
AB  - (5,413,691 bp) and 5,363 genes. The genomics information will facilitate the
AB  - study of the physiology, cold adaptation, and evolution of this genus.
ER  -

TY  - JOUR
AU  - Yin, M.
TI  - Molecular characteristics and comparative genomics analysis of a clinical Enterococcus casseliflavus with a resistance plasmid.
JO  - Infection and Drug Resistance
PY  - 2018
SP  - 2159
EP  - 2167
VL  - 11
AB  - Purpose: The aim of this work was to investigate the molecular characterization of a clinical
AB  - Enterococcus casseliflavus strain with a resistance plasmid. Materials and methods: En.
AB  - casseliflavus EC369 was isolated from a patient in a hospital in southern China. The minimum
AB  - inhibitory concentration was found by means of the agar dilution method to determine the
AB  - antimicrobial susceptibilities of the strains. Whole-genome
AB  - sequencing and mechanism of antibiotic resistance and the horizontal gene transfer of the
AB  - resistance gene-related mobile genetic elements.
AB  - Results: En. casseliflavus EC369 showed resistance to erythromycin, kanamycin, and
AB  - streptomycin, but was susceptible to vancomycin, ampicillin, and streptothricin and other
AB  - antimicrobials. There were six resistance genes (aph3 and #8242;, ant6, bla, sat4, and two
AB  - ermBs) carried by a transposon
AB  - identified on the plasmid pEC369 and a complete resistance gene cluster of vancomycin and a
AB  - tet (M) gene encoded on the chromosome. This is the first complete plasmid sequence reported
AB  - in clinically isolated En. casseliflavus. The plasmid with the greatest sequence identity with
AB  - pEC369 was the plasmid of Enterococcus sp. FDAARGOS_375, followed by the plasmids of
AB  - Enterococcus faecium strains F12085 and pRE25, whereas the sequence with the greatest
AB  - identity to the resistance genes carrying a transposon of pEC369 was on the chromosome of
AB  - Staphylococcus aureus strain GD1677. Conclusion: The resistance profiles of En. casseliflavus
AB  - EC369 might contribute to the resistance
AB  - genes encoded on the plasmid. The fact that the most similar sequence to the transposon
AB  - carrying resistance genes of pEC369 was encoded in the chromosome of a S. aureus strain
AB  - provides insights into the mechanism of dissemination of multidrug resistance between bacteria
AB  - of different species or genera through horizontal gene transfer.
ER  -

TY  - JOUR
AU  - Yin, M.
AU  - Jiang, M.
AU  - Ren, Z.
AU  - Dong, Y.
AU  - Lu, T.
TI  - The complete genome sequence of Streptomyces autolyticus CGMCC 0516, the producer of geldanamycin, autolytimycin, reblastatin and elaiophylin.
JO  - J. Biotechnol.
PY  - 2017
SP  - 27
EP  - 31
VL  - 252
AB  - Streptomyces autolyticus CGMCC 0516 produces the anti-tumor benzoquinone
AB  - ansamycins geldanamycin, autolytimycin, and reblastatin and the 16-membered
AB  - macrodiolide elaiophylin. Here, we report the complete genome sequence of S.
AB  - autolyticus CGMCC 0516, which consists of a 10,029,028bp linear chromosome and
AB  - seven circular plasmids. Fifty-seven putative biosynthetic gene clusters for
AB  - secondary metabolites were found. The geldanamycin, autolytimycin, and
AB  - reblastatin biosynthetic gene clusters were located on the left arm (2.06-2.15Mb)
AB  - of the chromosome, and the elaiophylin gene cluster was located on the right arm
AB  - (9.45-9.53Mb). Twenty-one putative gene clusters with high or moderate similarity
AB  - to important antibiotic biosynthetic gene clusters were found, including the
AB  - antitumor agents echoside, bafilomycin, hygrocin, and toxoflavin; the
AB  - antibacterial/antifungal agents nigericin, skyllamycin, kanamycin, naphthomycin,
AB  - eco-02301, and bottromycin A2; the immunosuppressants meridamycin and
AB  - brasilicardin A; the anti-inflammatory agent cyclooctatin; and the acute iron
AB  - poisoning medication desferrioxamine B. The genome sequence reported here will
AB  - enable us to study the biosynthetic mechanism of these important antibiotics and
AB  - will facilitate the discovery of novel secondary metabolites with potential
AB  - applications to human health.
ER  -

TY  - JOUR
AU  - Yin, M.
AU  - Ma, Z.
AU  - Cai, Z.
AU  - Lin, G.
AU  - Zhou, J.
TI  - Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila strain KOR1, Isolated from a Mangrove Plant (Kandelia  obovata).
JO  - Genome Announcements
PY  - 2015
SP  - e01461
EP  - e01415
VL  - 3
AB  - Aeromonas hydrophila strain KOR1, isolated from mangrove rhizosphere soil, has the ability to
AB  - produce the quorum-sensing signal molecule. Here, we report the
AB  - 4.78-Mb genome sequence of strain KOR1, and found its quorum-sensing encoding
AB  - gene LuxR. The data will be crucial to understanding the quorum-sensing-dependent
AB  - phenotypes of this bacterium.
ER  -

TY  - JOUR
AU  - Yin, X.
AU  - Luan, X.
AU  - Xu, A.
AU  - Li, Q.
AU  - Cui, Z.
AU  - Valentine, D.L.
TI  - Genome Sequence of a Marine Alkane Degrader, Alcanivorax sp. Strain 97CO-6.
JO  - Genome Announcements
PY  - 2018
SP  - e00087
EP  - e00018
VL  - 6
AB  - Alcanivorax sp. strain 97CO-6 was isolated from a crude oil-consuming bacterial consortium,
AB  - enriched from Yellow Sea sediments from China. Here, we present the
AB  - draft genome of strain 97CO-6, which contains 3,253,423 bp, with a G+C content of
AB  - 54.53%, as well as 2,931 protein-coding genes and 42 tRNAs.
ER  -

TY  - JOUR
AU  - Yin, Y.
AU  - Withers, T.R.
AU  - Govan, J.R.
AU  - Johnson, S.L.
AU  - Yu, H.D.
TI  - Draft Genome Sequence of a Stable Mucoid Strain of Pseudomonas aeruginosa PAO581  with a mucA25 Mutation.
JO  - Genome Announcements
PY  - 2013
SP  - e00834
EP  - e00813
VL  - 1
AB  - A mutation in the mucA gene, which encodes a negative regulator of alginate production in
AB  - Pseudomonas aeruginosa, is the main mechanism underlying the
AB  - conversion to mucoidy in clinical isolates from patients with cystic fibrosis
AB  - (CF). Here, we announce the draft genome sequence of the stable
AB  - alginate-overproducing mucoid strain P. aeruginosa PAO581 with a mucA25 mutation,
AB  - a derivative from the nonmucoid strains P. aeruginosa PAO381 and PAO1.
ER  -

TY  - JOUR
AU  - Yin, Y.
AU  - Withers, T.R.
AU  - Johnson, S.L.
AU  - Yu, H.D.
TI  - Draft Genome Sequence of a Mucoid Isolate of Pseudomonas aeruginosa Strain C7447m from a Patient with Cystic Fibrosis.
JO  - Genome Announcements
PY  - 2013
SP  - e00837
EP  - e00813
VL  - 1
AB  - Alginate overproduction by Pseudomonas aeruginosa, or mucoidy, plays an important role in the
AB  - pathogenesis of chronic lung infections in cystic fibrosis (CF)
AB  - patients. Here we report the draft genome sequence of a clinical isolate of
AB  - mucoid P. aeruginosa strain C7447m from a CF patient with chronic lung infection.
ER  -

TY  - JOUR
AU  - Yin, Y.
AU  - Withers, T.R.
AU  - Niles, R.M.
AU  - Johnson, S.L.
AU  - Yu, H.D.
TI  - Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13.
JO  - Genome Announcements
PY  - 2013
SP  - e01031
EP  - e01013
VL  - 1
AB  - The small envelope protein MucE and the sensor kinase KinB are a positive and negative
AB  - alginate regulator, respectively. Here, we announce the draft genome
AB  - sequences of the alginate-overproducing variants Pseudomonas aeruginosa PAO1-VE2
AB  - (PAO1 with constitutive expression of mucE) and PAO1-VE13 (PAO1 with kinB
AB  - inactivated). Both mutants were generated from a transposon mutagenesis screen.
ER  -

TY  - JOUR
AU  - Yin, Y.
AU  - Yue, G.
AU  - Gao, Q.
AU  - Wang, Z.
AU  - Peng, F.
AU  - Fang, C.
AU  - Yang, X.
AU  - Pan, L.
TI  - Genome Sequence of Pedobacter arcticus sp. nov., a Sea Ice Bacterium Isolated from Tundra Soil.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6688
EP  - 6688
VL  - 194
AB  - Pedobacter arcticus sp. nov. was originally isolated from tundra soil collected from
AB  - Ny-Alesund, in the Arctic region of Norway. It is a Gram-negative bacterium
AB  - which shows bleb-shaped appendages on the cell surface. Here, we report the draft
AB  - annotated genome sequence of Pedobacter arcticus sp. nov., which belongs to the
AB  - genus Pedobacter.
ER  -

TY  - JOUR
AU  - Yoder, J.A.
AU  - Bestor, T.H.
TI  - A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast.
JO  - Hum. Mol. Genet.
PY  - 1998
SP  - 279
EP  - 284
VL  - 7
AB  - Trace levels of 5-methylcytosine persist in the DNA of mouse embryonic stem cells that are
AB  - homozygous for null mutations in Dnmt1, the gene for the one previously recognized metazoan
AB  - DNA methyltransferase.  This residual 5-methylcytosine may be the product of a candidate
AB  - second DNA methyltransferase, Dnmt2, that has now been identified in human and mouse.  Dnmt2
AB  - contains all the sequence motifs diagnostic of DNA (cytosine-5)-methyltransferases but appears
AB  - to lack the large N-terminal regulatory domain common to other eukaryotic methyltransferases.
AB  - Dnmt2 is more similar to a putative DNA methyltransferase of the fission yeast
AB  - Schizosaccharomyces pombe than to Dnmt1.  Dnmt2 produces multiple mRNA species that are
AB  - present at low levels in all tissues of human and mouse and is not restricted to those cell
AB  - types known to be active in de novo methylation.  The human DNMT2 gene was mapped to
AB  - chromosome 10p12-10p14 in a panel of radiation hybrids.  Dnmt2 is a candidate for the activity
AB  - that methylates newly integrated retroviral DNA and maintains trace levels of 5-methylcytosine
AB  - in the DNA of embryonic stem cells homozygous for null mutations in Dnmt1.
ER  -

TY  - JOUR
AU  - Yoder, J.A.
AU  - Bestor, T.H.
TI  - Genetic analysis of genomic methylation patterns in plants and mammals.
JO  - Biol. Chem.
PY  - 1996
SP  - 605
EP  - 610
VL  - 377
AB  - While it is now accepted that methylation of cytosine residues plays a role in various
AB  - epigenetic phenomena in mammals and flowering plants, the involvement of methylation patterns
AB  - in the regulation of normal development has remained a controversial and essentially untested
AB  - issue in the 20 years since such a role was first proposed.  Antisense suppression of a DNA
AB  - methyltransferase in Arabidopsis and characterization of methylation-defective mutants of
AB  - Arabidopsis have shown that perturbations of methylation patterns disrupt the development of
AB  - plants, and targeted mutation of the murine gene that encodes the one known form of DNA
AB  - methyltransferase has shown that methylation is required for cellular differentiation, genomic
AB  - imprinting, and X chromosome inactivation in mammals.  Ectopic expression of homeotic genes
AB  - and homeotic transformations of floral organs in methylation-defective plants suggest that (in
AB  - plants and perhaps mammals) heritable methylation patterns reinforce and may have supplanted
AB  - heritable gene control mediated by chromosomal proteins of the Polycomb and trithorax groups.
AB  - It is also possible that the developmental abnormalities are the result of ectopic gene
AB  - expression caused by activation of transcription from nearby parasitic sequence elements that
AB  - are normally repressed by methylation.  Application of modern methods of genetic analysis
AB  - promises to give definite answers to long-standing questions as to the roles and significance
AB  - of genomic methylation patterns in normal development and genome defense.
ER  -

TY  - JOUR
AU  - Yoder, J.A.
AU  - Soman, N.S.
AU  - Verdine, G.L.
AU  - Bestor, T.H.
TI  - DNA (cytosine-5)-methyltransferases in mouse cells and tissues.  Studies with a mechanism-based probe.
JO  - J. Mol. Biol.
PY  - 1997
SP  - 385
EP  - 395
VL  - 270
AB  - The mechanisms that establish and maintain methylation patterns in the mammalian genome are
AB  - very poorly understood, even though perturbations of methylation patterns lead to a loss of
AB  - genomic imprinting, ectopic X chromosome inactivation, and death of mammalian embryos.  A
AB  - family of sequence-specific DNA methyltransferases has been proposed to be responsible for the
AB  - wave of de novo methylation that occurs in the early embryo, although no such enzyme has been
AB  - identified.  A universal mechanism-based probe for DNA (cytosine-5)-methyltransferases was
AB  - used to screen tissues and cell types known to be active in de novo methylation for new
AB  - species of DNA methyltransferase.  All identifiable de novo methyltransferase activity was
AB  - found to reside in Dnmt1.  As this enzyme is the predominant de novo methyltransferase at all
AB  - developmental stages inspected, it does not fit the definition of maintenance
AB  - methyltransferase or hemimethylase.  Recent genetic data indicate that de novo methylation of
AB  - retroviral DNA in embryonic stem cells is likely to involve one or more additional DNA
AB  - methyltransferases.  Such enzymes were not detected and are either present in very small
AB  - amounts or are very different from Dnmt1.  A new method was developed and used to determine
AB  - the sequence specificity of intact Dnmt1 in whole-cell lysates.  Specificity was found to be
AB  - confined to the sequence 5'-CpG-3'; there was little dependence on sequence context or
AB  - density of CpG dinucleotides.  These data suggest that any sequence-specific de novo
AB  - methylation mediated by Dnmt1 is either under the control of regulatory factors that interact
AB  - with Dnmt1, or is cued by alternative secondary structures in DNA.
ER  -

TY  - JOUR
AU  - Yoder, J.A.
AU  - Walsh, C.P.
AU  - Bestor, T.H.
TI  - Cytosine methylation and the ecology of intragenomic parasites.
JO  - Trends Genet.
PY  - 1997
SP  - 335
EP  - 340
VL  - 13
AB  - Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized
AB  - intragenomic parasites that represent at least 35% of the genome.  Transposon promoters are
AB  - inactive when methylated and, over time, C-T transition mutations at methylated sites destroy
AB  - many transposons.  Apart from that subset of genes subject to X inactivation and genomic
AB  - imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a
AB  - pattern that prevents transcription.  It has become increasingly difficult to hold that
AB  - reversible promoter methylation is commonly involved in developmental gene control; instead,
AB  - suppression of parasitic sequence elements appears to be the primary function of cytosine
AB  - methylation, with crucial secondary roles in allele-specific gene expression as seen in X
AB  - inactivation and genomic imprinting.
ER  -

TY  - JOUR
AU  - Yoder, J.A.
AU  - Yen, R.-W.C.
AU  - Vertino, P.M.
AU  - Bestor, T.H.
AU  - Baylin, S.B.
TI  - New 5' regions of the murine and human genes for DNA (cytosine-5)-methyltransferase.
JO  - J. Biol. Chem.
PY  - 1996
SP  - 31092
EP  - 31097
VL  - 271
AB  - DNA (cytosine-5)-methyltransferases (EC 2.1.1.37)  maintain patterns of methylated cytosine
AB  - residues in the mammalian genome; faithful maintenance of methylation patterns is required for
AB  - normal development of mice, and aberrant methylation patterns are associated with certain
AB  - human tumors and developmental abnormalities.  The organization of coding sequences at the
AB  - 5'-end of the murine and human DNA methyltransferase genes was investigated, and the DNA
AB  - methyltransferase open reading frame was found to be longer than previously suspected.
AB  - Expression of the complete open reading frame by in vitro transcription-translation and by
AB  - transfection of expression constructs into COS7 cells resulted in the production of an active
AB  - DNA methyltransferase of the same apparent mass as the endogenous protein, while translation
AB  - from the second inframe ATG codon produced a slightly smaller but fully active protein.
AB  - Characterization of mRNA 5' sequences and the intron-exon structure of the 5' region of the
AB  - murine and human genes indicated that a previously described promoter element actually lies in
AB  - an intron that is more than 5 kilobases downstream of the transcription start sites.
ER  -

TY  - JOUR
AU  - Yohda, M. et al.
TI  - Isolation and genomic characterization of a Dehalococcoides strain suggests genomic rearrangement during culture.
JO  - Sci. Rep.
PY  - 2017
SP  - 2230
EP  - 2230
VL  - 7
AB  - We have developed and characterized a bacterial consortium that reductively
AB  - dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S
AB  - rRNA and reductive dehalogenase genes showed that the consortium is highly
AB  - enriched with Dehalococcoides spp. that have two vinyl chloride reductive
AB  - dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase
AB  - gene, tceA. The metagenome analysis of the consortium by the next generation
AB  - sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp. that is highly
AB  - homologous to D. mccartyi 195 and equipped with vcrA and tceA exists in the
AB  - consortium. We isolated this Dehalococcoides sp. and designated it as D. mccartyi
AB  - UCH-ATV1. As the growth of D. mccartyi UCH-ATV1 is too slow under isolated
AB  - conditions, we constructed a consortium by mixing D. mccartyi UCH-ATV1 with
AB  - several other bacteria and performed metagenomic sequencing using the single
AB  - molecule DNA sequencer PacBio RS II. We successfully determined the complete
AB  - genome sequence of D. mccartyi UCH-ATV1. The strain is equipped with vcrA and
AB  - tceA, but lacks bvcA. Comparison with tag sequences of SOLiD 3 Plus from the
AB  - original consortium shows a few differences between the sequences. This suggests
AB  - that a genome rearrangement of Dehalococcoides sp. occurred during culture.
ER  -

TY  - JOUR
AU  - Yokochi, T.
AU  - Robertson, K.D.
TI  - Preferential methylation of unmethylated DNA by mammalian de novo DNA methyltransferase Dnmt3a.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 11735
EP  - 11745
VL  - 277
AB  - DNA methylation is an epigenetic modification of DNA. There are currently three catalytically
AB  - active mammalian DNA methyltransferases,
AB  - DNMT1, -3a, and -3b. DNMT1 has been shown to have a preference for
AB  - hemimethylated DNA and has therefore been termed the maintenance
AB  - methyltransferase. Although previous studies on DNMT3a and -3b revealed
AB  - that they act as functional enzymes during development, there is little
AB  - biochemical evidence about how new methylation patterns are established
AB  - and maintained. To study this mechanism we have cloned and expressed
AB  - Dnmt3a using a baculovirus expression system. The substrate specificity
AB  - of Dnmt3a and molecular mechanism of its methylation reaction were then
AB  - analyzed using a novel and highly reproducible assay. We report here
AB  - that Dnmt3a is a true de novo methyltransferase that prefers
AB  - unmethylated DNA substrates more than 3-fold to hemimethylated DNA.
AB  - Furthermore, Dnmt3a binds DNA nonspecifically, regardless of the
AB  - presence of CpG dinucleotides in the DNA substrate. Kinetic analysis
AB  - supports an Ordered Bi Bi mechanism for Dnmt3a, where DNA binds first,
AB  - followed by S-adenoSyl-L-methionine.
ER  -

TY  - JOUR
AU  - Yokochi, T.
AU  - Robertson, K.D.
TI  - Dimethyl sulfoxide stimulates the catalytic activity of de novo DNA methyltransferase 3a (Dnmt3a) in vitro.
JO  - Bioorg. Chem.
PY  - 2004
SP  - 234
EP  - 243
VL  - 32
AB  - Mammalian DNA methyltransferase Dnmt3a is required for de novo methylation of CpG
AB  - dinucleotides in genomic DNA. While DNA
AB  - methyltransferase inhibitors have been extensively utilized both in
AB  - vitro and in vivo, no stimulator of catalytic activity has been
AB  - identified thus far. Here we show that the methyltransfer activity of
AB  - Dnmt3a is stimulated by the addition of dimethyl sulfoxide (DMSO) to
AB  - the reaction solution in vitro. Enzymatic analysis of initial reaction
AB  - velocity suggests that the DMSO stimulation effect depends on the
AB  - interaction between DMSO and the reaction substrates (DNA and AdoMet),
AB  - but not the enzyme itself.
ER  -

TY  - JOUR
AU  - Yokochi, T.
AU  - Robertson, K.D.
TI  - DMB (DNMT-magnetic beads) assay: Measuring DNA methyltransferase activity in vitro.
JO  - Methods Mol. Biol.
PY  - 2004
SP  - 285
EP  - 296
VL  - 287
AB  - DNA methylation is an epigenetic modification of DNA that leads to heritable alterations in
AB  - transcriptional regulation and conformational changes in chromatin structure of higher
AB  - eukaryotes.  Mammalian DNA methyltransferases, which are the enzymes responsible for DNA
AB  - methylation, have attracted the attention of both basic and clinical researchers because they
AB  - appear to participate in embryogenesis and carcinogenesis via chromatin modification.  DNA
AB  - methyltransferase catalyzes the traansfer of a methyl group into DNA strands.  Since
AB  - traditional assays for DNA methyltransferase activity in vitro have insufficient
AB  - reproducibility, there is a need in the art for more sensitive and quantitative methods for
AB  - measuring enzymatic activity.  We report a novel assay system, in which the actiity of a DNA
AB  - methyltransferase is measured as the incorporation of tritium into biotinylated DNA
AB  - oligonucleotides.  The DNA is immobilized onto magnetic beads with streptavidin covalently
AB  - attached to the bead surface.  The radioactive DNA can easily be separated from the unreacted
AB  - radioactive substrate using a magnet.  The radioactivity is counted by the liquid
AB  - scintillation system.  This DMB assay is simple and easy, has very low background, and, most
AB  - importantly, is highly reproducible for the precise enzymatic analysis of any DNA
AB  - methyltransferase in vitro.
ER  -

TY  - JOUR
AU  - Yokoyama, K.
AU  - Makino, K.
AU  - Kubota, Y.
AU  - Watanabe, M.
AU  - Kimura, S.
AU  - Yutsudo, C.H.
AU  - Kurokawa, K.
AU  - Ishii, K.
AU  - Hattori, M.
AU  - Tatsuno, I.
AU  - Abe, H.
AU  - Yoh, M.
AU  - Iida, T.
AU  - Ohnishi, M.
AU  - Hayashi, T.
AU  - Yasunaga, T.
AU  - Honda, T.
AU  - Sasakawa, C.
AU  - Shinagawa, H.
TI  - Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai outbreak.
JO  - Gene
PY  - 2000
SP  - 127
EP  - 139
VL  - 258
AB  - Shiga toxins 1 and 2 (Stx1 and Stx2) are encoded by prophages lysogenized in enterohemorrhagic
AB  - Escherichia coli (EHEC) O157:H7 strains. Lytic growth of the phage particles carrying the stx1
AB  - genes (stx1A and stx1B) of the EHEC O157:H7 strain RIMD 0509952, which was derived from the
AB  - Sakai outbreak in 1996 in Japan, was induced after treatment with mitomycin C, but the plaque
AB  - formation of the phage was not detected. We have determined the complete nucleotide sequence
AB  - of the prophage VT1-Sakai. The integration site of the prophage was identified within the yehV
AB  - gene at 47.7 min on the chromosome. The stx1 genes were downstream of the Q gene in the
AB  - prophage genome, suggesting that their expression was regulated by the Q protein, the
AB  - regulator of the late gene expression of the phage, which is similar to that of the stx1 or
AB  - stx2 genes carried by the lambdoid phages reported previously. The sequences of the N gene and
AB  - its recognition sites, nutL and nutR, were not homologous to those of the phages carrying the
AB  - stx genes thus far reported, but they were very similar to those of bacteriophage phi21. The
AB  - sequences of the repressor proteins, CI and Cro, that regulate expression of the early genes
AB  - had low similarities with those of the known repressors of other phages, and their operator
AB  - sequences were different from any sequence reported. These data suggest that multiple genetic
AB  - recombination among bacteriophages with different immunities took place to generate the
AB  - prophage VT1-Sakai. Comparison between the sequences of VT1-Sakai and lambda suggests that the
AB  - ancestor of VT1-Sakai was produced by illegitimate excision, like lambda gal and bio phages.
AB  - Full author list: Yokoyama, K., Makino, K., Kubota, Y., Watanabe, M., Kimura, S., Yutsudo,
AB  - C.H., Kurokawa, K., Ishii, K., Hattori, M., Tatsuno, I., Abe, H., Yoh, M., Iida, T., Ohnishi,
AB  - M., Hayashi, T., Yasunaga, T., Honda, T., Sasakawa, C., Shinagawa,H.
ER  -

TY  - JOUR
AU  - Yokoyama, S.
AU  - Oshima, K.
AU  - Nomura, I.
AU  - Hattori, M.
AU  - Suzuki, T.
TI  - Complete Genomic Sequence of the O-Desmethylangolensin-Producing Bacterium Clostridium rRNA Cluster XIVa Strain SY8519, Isolated from Adult Human  Intestine.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5568
EP  - 5569
VL  - 193
AB  - The O-desmethylangolensin-producing Clostridium rRNA cluster XIVa strain SY8519 was isolated
AB  - from the intestinal flora of a healthy human as a key
AB  - isoflavonoid-metabolizing bacterium. Here, we report the finished and
AB  - annotated genomic sequence of this organism.
ER  -

TY  - JOUR
AU  - Yokoyama, S.
AU  - Oshima, K.
AU  - Nomura, I.
AU  - Hattori, M.
AU  - Suzuki, T.
TI  - Complete Genomic Sequence of the Equol-Producing Bacterium Eggerthella sp. Strain YY7918, Isolated from Adult Human Intestine.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5570
EP  - 5571
VL  - 193
AB  - Eggerthella sp. strain YY7918 was isolated from the intestinal flora of a healthy human. It
AB  - metabolizes daidzein (a soybean isoflavonoid) and
AB  - produces S-equol, which has stronger estrogenic activities than daidzein.
AB  - Here, we report the finished and annotated genomic sequence of this
AB  - organism.
ER  -

TY  - JOUR
AU  - Yolov, A.A.
AU  - Gromova, E.S.
AU  - Potapov, V.K.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.  V.  Study of single-stranded cleavages.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 8969
EP  - 8981
VL  - 13
AB  - Concatemer DNA duplexes which contain at the EcoRII restriction endonuclease
AB  - cleavage sites ...^C-C-A-G-G-......-G-G-T-C-C^... phosphodiester, phosphoamide
AB  - or pyrophosphate internucleotide bonds have been synthesized.  It has been
AB  - shown that this enzyme did not cleave the substrate at phosphoamide bond.
AB  - EcoRII endonuclease catalyzes single-strand cleavages both in dA- and
AB  - dT-containing strands of the recognition site if the cleavage of the other
AB  - strand has been blocked by modification of scissile bond or if the other strand
AB  - has been cleaved.  This enzyme interacts with both strands of the DNA
AB  - recognition site, each of them being cleaved independently of the cleavage of
AB  - another one.  Nucleotide sequences flanking the EcoRII site on both sides are
AB  - necessary for effective cleavage of the substrate.
ER  -

TY  - JOUR
AU  - Yolov, A.A.
AU  - Gromova, E.S.
AU  - Romanova, E.A.
AU  - Oretskaya, T.S.
AU  - Oganov, A.A.
AU  - Buryanov, Y.I.
AU  - Shabarova, Z.A.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments.
JO  - FEBS Lett.
PY  - 1984
SP  - 147
EP  - 150
VL  - 167
AB  - Interaction of EcoRII restriction endonuclease with a set of synthetic
AB  - concatemer DNA duplexes with natural and modified sites for this enzyme has
AB  - been studied.  DNA duplexes with repeated natural sites are cleaved by EcoRII.
AB  - Substitution of central AT-pair in the recognition site for a non-complementary
AB  - TT- or AA-pair reduces the rate of cleaveage, this effect being much more
AB  - pronounced in the last case.  Absence of site flanking in one strand from the
AB  - 5' -terminus also results in very slow cleavage.  The results obtained testify
AB  - to the interaction of EcoRII with both strands of the substrate.
ER  -

TY  - JOUR
AU  - Yolov, A.A.
AU  - Gromova, E.S.
AU  - Shabarova, Z.A.
TI  - Processive cleavage of concatemer DNA duplexes by EcoRII restriction endonuclease.
JO  - Mol. Biol. Rep.
PY  - 1985
SP  - 173
EP  - 176
VL  - 10
AB  - EcoRII restriction endonuclease cleaves synethetic DNA-duplexes in which the
AB  - recognition sites of this enzyme (5'...CC(A/T)GG...) are repeated every 9 base
AB  - pairs with the alternating orientation of the central AT pair.  It operates in
AB  - a processive mode, i.e. the bound enzyme molecule slides along the substrate
AB  - toward neighboring recognition sites.  Nona-nucleotides are the main products
AB  - of the cleavage.  The data obtained point to the capability of EcoRII
AB  - endonuclease to recognize and cleave the substrate under both possible
AB  - orientations of the central AT-pair of the recognition site with respect to the
AB  - bound enzyme molecule.  These data also show the close similarity of DNA
AB  - structures in a complex with the enzyme and without.
ER  -

TY  - JOUR
AU  - Yolov, A.A.
AU  - Vinogradova, M.N.
AU  - Gromova, E.S.
AU  - Rosenthal, A.
AU  - Cech, D.
AU  - Veiko, V.P.
AU  - Metelev, V.G.
AU  - Kosykh, V.G.
AU  - Buryanov, Y.I.
AU  - Vayev, A.A.
AU  - Shabarova, A.Z.
TI  - Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments. VI.  The binding and cleavage of substrates containing nucleotide analogs.
JO  - Nucleic Acids Res.
PY  - 1985
SP  - 8983
EP  - 8998
VL  - 13
AB  - The present study deals with the binding and cleavage by EcoRII endonuclease of
AB  - concatamer DNA duplexes containing EcoRII recognition sites (5'...^CCAGG) in
AB  - which dT is replaced by dU or 5-bromodeoxyuridine, or 5'-terminal dC in the
AB  - dT-containing strand is methylated at position 5.  The enzyme molecule is found
AB  - to interact with the methyl group of the dT residue of the DNA recognition site
AB  - and to be at least in proximity to the H5 atom of the 5'-terminal dC residue in
AB  - dT-containing strand of this site.  Modification of any of these positions
AB  - exerts an equal effects on the cleavage of both DNA strands.  Endonuclease
AB  - EcoRII was found to bind the substrate specifically.  At the same time
AB  - modification of the bases in recognized sequence may result in the formation of
AB  - unproductive,though stable, enzyme-substrate complexes.
ER  -

TY  - JOUR
AU  - Yonezawa, A.
AU  - Sugiura, Y.
TI  - DNA binding mode of class-IIS restriction endonuclease FokI revealed by DNA footprinting analysis.
JO  - Biochim. Biophys. Acta
PY  - 1994
SP  - 369
EP  - 379
VL  - 1219
AB  - We investigate the interaction of FokI with its DNA recognition sequence by several
AB  - footprinting techniques. Methylation of three guanine bases in the recognition sequence
AB  - 5'-GGATG-3' is strongly protected by FokI binding, whereas other guanine bases are not
AB  - masked from the modification. In footprinting using the methidiumpropyl-EDTA-Fe(II) complex,
AB  - binding of FokI strongly inhibits cleavage by the footprinting reagent at and near the
AB  - recognition sequence. In high-resolution footprinting techniques using hydroxyl radical and
AB  - the bleomycin-Fe(II) complex, all footprints in each binding site clearly face one side of the
AB  - DNA helix. Interference analysis with FokI digestion by preethylation of phosphate groups
AB  - suggests that essential phosphates for FokI digestion are located at and near the recognition
AB  - sequence and the cleavage site. Evidently, the results indicate that (i) the
AB  - sequence-recognition of FokI occurs in the major groove and that (ii) the enzyme interacts
AB  - with its target DNA from one side of the DNA helix.
ER  -

TY  - JOUR
AU  - Yonezuka, K.
AU  - Shimodaira, J.
AU  - Tabata, M.
AU  - Nagase, S.
AU  - Kasai, D.
AU  - Hosoyama, A.
AU  - Yamazoe, A.
AU  - Fujita, N.
AU  - Fukuda, M.
TI  - Draft Genome Sequence of a Chlorinated-Ethene Degrader, Cupriavidus necator Strain PHE3-6 (NBRC 110655).
JO  - Genome Announcements
PY  - 2016
SP  - e01743
EP  - e01715
VL  - 4
AB  - Cupriavidus necator strain PHE3-6 grows on phenol as a sole carbon source and cometabolizes
AB  - cis- and trans-dichloroethenes and trichloroethene. Here, we report
AB  - the draft genome sequence of PHE3-6, which provides insights into the degradation
AB  - system of phenol and chlorinated ethenes.
ER  -

TY  - JOUR
AU  - Yong, B.
AU  - Yang, B.Q.
AU  - Zhao, C.W.
AU  - Feng, H.
TI  - Draft Genome Sequence of Bacillus subtilis Strain S1-4, Which Degrades Feathers Efficiently.
JO  - Genome Announcements
PY  - 2013
SP  - e00766
EP  - e00713
VL  - 1
AB  - Bacillus subtilis strain S1-4, with the capacity to efficiently degrade feathers, was isolated
AB  - from chicken feathers. Sequencing showed that the genome of strain
AB  - S1-4 differs from that of other B. subtilis strains, with limited insertions and
AB  - deletions. The genome encodes multiple extracellular proteases and keratinases.
ER  -

TY  - JOUR
AU  - Yong, D.
AU  - Ee, R.
AU  - Lim, Y.L.
AU  - Chang, C.Y.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Insights on Quorum-Quenching Properties of Lysinibacillus fusiformis Strain RB21, a Malaysian Municipal Solid-Waste Landfill Soil Isolate, via Complete Genome  Sequence Analysis.
JO  - Genome Announcements
PY  - 2015
SP  - e00409
EP  - e00415
VL  - 3
AB  - Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade
AB  - quorum-sensing signaling molecules. Here, we present the first
AB  - complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8
AB  - Mbp in size, and the quorum-quenching gene was identified.
ER  -

TY  - JOUR
AU  - Yoo, H.Y.
AU  - Noshari, J.
AU  - Lapeyre, J.N.
TI  - Subunit and functional size of human placental DNA methyltransferase involved in de novo and maintenance methylation.
JO  - J. Biol. Chem.
PY  - 1987
SP  - 8066
EP  - 8070
VL  - 262
AB  - The subunit molecular size of human DNA methyltransferase isolated from nuclear extracts of
AB  - placenta was determined on the electroblotted
AB  - polypeptides after sodium dodecyl sulfate-polyacrylamide gel
AB  - electrophoresis and compared with the functional size by high performance
AB  - size exclusion chromatography on Superose 12 and gamma radiation
AB  - inactivation analysis. The sodium dodecyl sulfate-polyacrylamide gel
AB  - electrophoresis results indicated a subunit mass of 120 +/- 10 kDa, while
AB  - the functional size data indicates that the enzyme operates both in de
AB  - novo and maintenance modes as a dimer of molecular mass 220 +/- 15 kDa
AB  - with no evidence of monomers in solution of ionic strength between 0.1 and
AB  - 0.8 M NaCl. The 220-kDa activity carried out the transmethylation of both
AB  - hemi- and unmethylated DNA substrates. There was no evidence for separate
AB  - functional catalytic sites on each monomer subunit acting independently
AB  - when engaged in methylation of hemimethylated or single-stranded DNA from
AB  - the invariance of radiation inactivation target size with these
AB  - substrates. The radiation inactivation target size was 230 +/- 15 kDa.
ER  -

TY  - JOUR
AU  - Yoo, J.
AU  - Choi, S.
AU  - Medina-Franco, J.L.
TI  - Molecular Modeling Studies of the Novel Inhibitors of DNA Methyltransferases SGI-1027 and CBC12: Implications for the Mechanism of Inhibition of DNMTs.
JO  - PLoS ONE
PY  - 2013
SP  - e62152
EP  - e62152
VL  - 8
AB  - DNA methylation is an epigenetic modification that regulates gene expression by DNA
AB  - methyltransferases (DNMTs). Inhibition of DNMTs is a
AB  - promising approach for cancer therapy. Recently, novel classes of the
AB  - quinolone-based compound, SGI-1027, and RG108-procainamide conjugates,
AB  - CBC12, have been identified as potent DNMT inhibitors. In this work, we
AB  - report comprehensive studies using induced-fit docking of SGI-1027 and
AB  - CBC12 with human DNMT1 and DNMT3A. The docking was performed in the
AB  - C-terminal MTase catalytic domain, which contains the substrate and
AB  - cofactor binding sites, in the presence and absence of other domains.
AB  - Induced-fit docking predicts possible binding modes of the ligands
AB  - through the appropriate structural changes in the receptor. This work
AB  - suggests a hypothesis of the inhibitory mechanisms of the new
AB  - inhibitors which is in agreement with the reported autoinhibitory
AB  - mechanism. The insights obtained in this work can be used to design
AB  - DNMT inhibitors with novel scaffolds.
ER  -

TY  - JOUR
AU  - Yoo, J.
AU  - Kim, J.H.
AU  - Robertson, K.D.
AU  - Medina-Franco, J.L.
TI  - MOLECULAR MODELING OF INHIBITORS OF HUMAN DNA METHYLTRANSFERASE WITH A CRYSTAL STRUCTURE: DISCOVERY OF A NOVEL DNMT1 INHIBITOR.
JO  - Adv. Protein Chem. Struct. Biol.
PY  - 2012
SP  - 219
EP  - 247
VL  - 87
AB  - DNA methyltransferases (DNMTs) are promising epigenetic targets for the development of novel
AB  - anticancer drugs and other diseases. Molecular
AB  - modeling and experimental approaches are being used to identify and
AB  - develop inhibitors of human DNMTs. Most of the computational efforts
AB  - conducted so far with DNMT1 employ homology models of the enzyme.
AB  - Recently, a crystallographic structure of the methyltransferase domain
AB  - of human DNMT1 bound to unmethylated DNA was published. Following on
AB  - our previous computational and experimental studies with DNMTs, we
AB  - herein present molecular dynamics of the crystal structure of human
AB  - DNMT1. Docking studies of established DNMT1 inhibitors with the crystal
AB  - structure gave rise to a structure-based pharmacophore model that
AB  - suggests key interactions of the inhibitors with the catalytic binding
AB  - site. Results had a good agreement with the docking and pharmacophore
AB  - models previously developed using a homology model of the catalytic
AB  - domain of DNMT1. The docking protocol was able to distinguish active
AB  - DNMT1 inhibitors from, for example, experimentally known inactive DNMT1
AB  - inhibitors. As part of our efforts to identify novel inhibitors of
AB  - DNMT1, we conducted the experimental characterization of
AB  - aurintricarboxylic acid (ATA) that in preliminary docking studies
AB  - showed promising activity. ATA had a submicromolar inhibition
AB  - (IC50=0.68 mu M) against DNMT1. ATA was also evaluated for Dnmt3a
AB  - inhibition showing an IC50=1.4 mu M. This chapter illustrates the
AB  - synergy from integrating molecular modeling and experimental methods to
AB  - further advance the discovery of novel candidates for epigenetic
AB  - therapies.
ER  -

TY  - JOUR
AU  - Yoo, J.
AU  - Medina-Franco, J.L.
TI  - Inhibitors of DNA Methyltransferases: Insights from Computational Studies.
JO  - Curr. Med. Chem.
PY  - 2012
SP  - 3475
EP  - 3487
VL  - 19
AB  - DNA methyltransferases (DNMTs) are a family of epigenetic enzymes for which inhibition is an
AB  - attractive strategy for the treatment of cancer
AB  - and other diseases. In synergy with experimental approaches,
AB  - computational methods are increasingly being used to identify and
AB  - optimize the activity of inhibitors of DNMTs as well as to rationalize
AB  - at the molecular level of the mechanism of established inhibitors.
AB  - Recently, a crystallographic structure of the methyltransferase domain
AB  - of human DNMT1 bound to unmethylated DNA was published encouraging the
AB  - application of structure-based approaches to design and optimize the
AB  - activity of currently known inhibitors. Herein, we review the progress
AB  - in the discovery and optimization of inhibitors of DNMTs using
AB  - computational approaches including homology modeling, docking,
AB  - pharmacophore modeling, molecular dynamics, and virtual screening.
ER  -

TY  - JOUR
AU  - Yoo, M.
AU  - Kim, D.
AU  - Choi, K.Y.
AU  - Chae, J.C.
AU  - Zylstra, G.J.
AU  - Kim, E.
TI  - Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4440
EP  - 4440
VL  - 194
AB  - Rhodococcus sp. strain DK17 is capable of utilizing various derivatives of benzene and
AB  - bicyclics containing both aromatic and alicyclic moieties as sole
AB  - carbon and energy sources. Here, we present the 9,107,362-bp draft genome
AB  - sequence of DK17 and its genomic analysis in comparison with other members of the
AB  - genus Rhodococcus.
ER  -

TY  - JOUR
AU  - Yoo, O.J.
AU  - Agarwal, K.L.
TI  - Isolation and characterization of two proteins possessing HpaII methylase activity.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 6445
EP  - 6449
VL  - 255
AB  - Two proteins exhibiting HpaII methylase activity have been purified to
AB  - homogeneity from Haemophilus parainfluenzae and their physical and catalytic
AB  - properties have been studied.  Separation of the two HpaII methylase activities
AB  - was achieved by DEAE-Sephadex A-50 chromatography.  In subsequent steps, each
AB  - methylase was purified separately by chromatography on Sephacryl S-200,
AB  - phosphocellulose, and hydroxylapatite.  The proteins have molecular weights of
AB  - 38,500 +/- 1,000 (HpaII) and 41,500 +/- 1,000 (HpaII') as judged by
AB  - polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate.
AB  - Sedimentation equilibrium analyses of the native proteins yield molecular
AB  - weights of 38,800 +/- 3,000 and 42,200 +/- 3,000 for HpaII and HpaII',
AB  - respectively, indicating that both enzymes are composed of a single subunit.
AB  - Furthermore, both methylases exhibit identical specificity in the methylation
AB  - of the nucleotide sequence dC-C-G-G in simian virus 40 (SV40) DNA and in a
AB  - short synthetic oligonucleotide duplex.  Although pH, temperature, and salt
AB  - optima are the same for both enzymes, homogenous HpaII' methylase is more
AB  - stable than HpaII methylase.  Preliminary peptide mapping indicates that the
AB  - two enzymes are structurally related, suggesting the possibility that HpaII'
AB  - methylase may represent a precursor form of HpaII methylase.
ER  -

TY  - JOUR
AU  - Yoo, O.J.
AU  - Agarwal, K.L.
TI  - Cleavage of single strand oligonucleotides and bacteriophage PhiX174 DNA by MspI endonuclease.
JO  - J. Biol. Chem.
PY  - 1980
SP  - 10559
EP  - 10562
VL  - 255
AB  - Type II restriction endonucleases cleave duplex DNA at nucleotide sequences
AB  - displaying 2-fold symmetry.  Our data show that MspI cleaves single strand
AB  - oligonucleotides, d(GAACCGGAGA) and d(TCTCGGTT) at 4, 25, and 37C reaction
AB  - temperatures.  The rate of cleavage of d(GAACCGGAGA) is several-fold faster
AB  - than that of d(TCTCCGGTT).  Single strand PhiX174 DNA is also cleaved by MspI
AB  - endonuclease giving well defined fragments.  5'-nucleotide analysis of the
AB  - fragments generated from single strand and replicating form DNA suggest that
AB  - cleavage occurs at the recognition sequence d(CCGG).  The data show that MspI
AB  - endonuclease cleaves single strand oligonucleotides and prefers a recognition
AB  - sequence surrounded by purine nucleotides.  A general model for endonuclease
AB  - cleavage of single strand and duplex DNA is presented.
ER  -

TY  - JOUR
AU  - Yoo, O.J.
AU  - Dwyer-Hallquist, P.
AU  - Agarwal, K.L.
TI  - Purification and properties of the HpaI methylase.
JO  - Nucleic Acids Res.
PY  - 1982
SP  - 6511
EP  - 6519
VL  - 10
AB  - The purification and catalytic properties of the homogeneous HpaI methylase is
AB  - described.  The enzyme exists as a single polypeptide chain with a molecular
AB  - weight of 37,000 +/- 2,000 was shown by sedimentation equilibrium and
AB  - polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate.
AB  - The HpaI methylase transfers methyl groups of S-adenosylmethionine to adenine
AB  - present in the recognition sequence d(G-T-T-A-A*-C), A* is the N6 methyl
AB  - adenosine.  An average of 2.1 methyl groups per recognition site are
AB  - transferred by the HpaI methylase.
ER  -

TY  - JOUR
AU  - Yoon, H.
AU  - Suh, H.
AU  - Han, M.H.
AU  - Yoo, O.J.
TI  - Purification and characterization of AluI methylase.
JO  - Korean Biochem. J.
PY  - 1985
SP  - 82
EP  - 87
VL  - 18
AB  - AluI methylase has been isolated from 300g (wet weight) cells of Arthrobacter
AB  - luteus.  After ammonium sulfate fractionation, the protein which has methylase
AB  - activity was purified through phosphocellulose, DEAE-cellulose, Heparin
AB  - agarose, and Hydroxy-lapatite column chromatography.  The methylated DNA by the
AB  - purified methylase was resistant against AluI endonuclease.  The purified AluI
AB  - methylase was essentially homogeneous as judged by 10% SDS-polyacrylamide gel
AB  - electrophoresis, and the apparent subunit molecular weight was 56,000+-1,000.
AB  - The specific activity of the enzyme was 132000 units per mg protein.
ER  -

TY  - JOUR
AU  - Yoon, H.
AU  - Suh, H.
AU  - Kim, K.
AU  - Han, M.H.
AU  - Yoo, O.J.
TI  - The specificity and catalytic properties of AluI methylase.
JO  - Korean Biochem. J.
PY  - 1985
SP  - 88
EP  - 93
VL  - 18
AB  - The specific methylation site for AluI methylase was the cytosine nucleotide in
AB  - AluI sequence.  The position of the methylated cytosine nucleotide was
AB  - determined by the chemical cleavage reactions of the Maxam-Gilbert DNA
AB  - sequencing procedure.  As expected, the methylated cytosine nucleotide bands
AB  - were disappeared on C+T and C lanes on 12% sequencing gels. AluI methylase was
AB  - maximally active at near pH 7.5 in the presence of 50 mM NaCl.  The methylase
AB  - did not require Mg++ for activity, and obeyed Michaelis-Menten Kinetics with
AB  - respect to both AdoMet and DNA.  At 37C, the Km for AdoMet was 0.44 lM, that
AB  - for the AluI site of pBR322 DNA was 4.03 nM, and the corresponding turnover
AB  - numbers were 1.83 methyl transfer per minute per monomer and 1.61 transfers per
AB  - minute per monomer, respectively.
ER  -

TY  - JOUR
AU  - Yoon, H.J.
AU  - Kang, K.Y.
AU  - Ahn, H.J.
AU  - Shim, S.M.
AU  - Ha, J.Y.
AU  - Lee, S.K.
AU  - Mikami, B.
AU  - Suh, S.W.
TI  - X-ray crystallographic studies of HemK from Thermotoga maritima, an N-5-glutamine methyltransferase.
JO  - Mol. Cells
PY  - 2003
SP  - 266
EP  - 269
VL  - 16
AB  - The enzyme HemK (or PrmC) is one of the first identified methyltransferases that modify
AB  - glutamine. It methylates the highly
AB  - conserved GGQ motif in class I release factors (RF1 and RF2) in
AB  - Escherichia coli. HemK from Thermotoga maritima was over-expressed and
AB  - crystallized in the presence of S-adenosylmethionine at 296 K using
AB  - ammonium sulfate as the precipitant. X-ray diffraction data were collected
AB  - to 2.5 A resolution from a native crystal. The crystal is orthorhombic,
AB  - belonging to the space group I222 (or I2(1)2(1)2(1)), with unit-cell
AB  - parameters of a = 104.24, b = 118.73, and c = 146.62 A. Two (or three)
AB  - monomers of recombinant HemK are likely to be present in the
AB  - crystallographic asymmetric unit, giving a V(M) of 3.62 A3 Da(-1) (or 2.41
AB  - A3 Da(-1)), with a solvent content of 62.7% (or 44.0%).
ER  -

TY  - JOUR
AU  - Yoon, H.S.
AU  - Kang, S.C.
AU  - Yoo, O.J.
TI  - Purification and characterization of HpaI endonuclease.
JO  - Sanop Misaengmul Hakhoe Chi
PY  - 1985
SP  - 87
EP  - 91
VL  - 13
AB  - HpaI endonuclease from Haemophilus parainfluenzae has been purified to
AB  - homogeneity and its physical and enzymatic properties have been studied.  For
AB  - the purification of the enzyme, Heparin agarose, SP-sephadex C-25,
AB  - DEAE-sephadex A-50 and phosphocellulose chromatography columns were used.  The
AB  - denatured and reduced form of the enzyme is a monomer of molecular weight of
AB  - 30,000 -+1,000 as judged by 10% polyacrylamide gel electrophoresis containing
AB  - 0.1% sodium dodesyl sulfate.  HpaI endonuclease was maximally active at neutral
AB  - pH (7.0 to 7.5) in the presence of 50 mM NaCl.
ER  -

TY  - JOUR
AU  - Yoon, M.Y.
AU  - Lee, K.M.
AU  - Yoon, Y.
AU  - Go, J.
AU  - Park, Y.
AU  - Cho, Y.J.
AU  - Tannock, G.W.
AU  - Yoon, S.S.
TI  - Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes.
JO  - Appl. Environ. Microbiol.
PY  - 2013
SP  - 3829
EP  - 3838
VL  - 79
AB  - Evidence suggests that gut microbes colonize the mammalian intestine through
AB  - propagation as an adhesive microbial community. A bacterial artificial chromosome
AB  - (BAC) library of murine bowel microbiota DNA in the surrogate host Escherichia
AB  - coli DH10B was screened for enhanced adherence capability. Two out of 5,472 DH10B
AB  - clones, 10G6 and 25G1, exhibited enhanced capabilities to adhere to inanimate
AB  - surfaces in functional screens. DNA segments inserted into the 10G6 and 25G1
AB  - clones were 52 and 41 kb and included 47 and 41 protein-coding open reading
AB  - frames (ORFs), respectively. DNA sequence alignments, tetranucleotide frequency,
AB  - and codon usage analysis strongly suggest that these two DNA fragments are
AB  - derived from species belonging to the genus Bacteroides. Consistent with this
AB  - finding, a large portion of the predicted gene products were highly homologous to
AB  - those of Bacteroides spp. Transposon mutagenesis and subsequent experiments that
AB  - involved heterologous expression identified two operons associated with enhanced
AB  - adherence. E. coli strains transformed with the 10a or 25b operon adhered to the
AB  - surface of intestinal epithelium and colonized the mouse intestine more
AB  - vigorously than did the control strain. This study has revealed the genetic
AB  - determinants of unknown commensals (probably resembling Bacteroides species) that
AB  - enhance the ability of the bacteria to colonize the murine bowel.
ER  -

TY  - JOUR
AU  - Yooseph, S. et al.
TI  - The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.
JO  - PLoS Biology
PY  - 2007
SP  - e16
EP  - e16
VL  - 5
AB  - Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield
AB  - insight into protein families. We used sequence
AB  - similarity clustering to explore proteins with a comprehensive dataset
AB  - consisting of sequences from available databases together with 6.12
AB  - million proteins predicted from an assembly of 7.7 million Global Ocean
AB  - Sampling (GOS) sequences. The GOS dataset covers nearly all known
AB  - prokaryotic protein families. A total of 3,995 medium- and large-sized
AB  - clusters consisting of only GOS sequences are identified, out of which
AB  - 1,700 have no detectable homology to known families. The GOS-only clusters
AB  - contain a higher than expected proportion of sequences of viral origin,
AB  - thus reflecting a poor sampling of viral diversity until now. Protein
AB  - domain distributions in the GOS dataset and current protein databases show
AB  - distinct biases. Several protein domains that were previously categorized
AB  - as kingdom specific are shown to have GOS examples in other kingdoms.
AB  - About 6,000 sequences (ORFans) from the literature that heretofore lacked
AB  - similarity to known proteins have matches in the GOS data. The GOS dataset
AB  - is also used to improve remote homology detection. Overall, besides nearly
AB  - doubling the number of current proteins, the predicted GOS proteins also
AB  - add a great deal of diversity to known protein families and shed light on
AB  - their evolution. These observations are illustrated using several protein
AB  - families, including phosphatases, proteases, ultraviolet-irradiation DNA
AB  - damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity
AB  - added by GOS data has implications for choosing targets for experimental
AB  - structure characterization as part of structural genomics efforts. Our
AB  - analysis indicates that new families are being discovered at a rate that
AB  - is linear or almost linear with the addition of new sequences, implying
AB  - that we are still far from discovering all protein families in nature.
ER  -

TY  - JOUR
AU  - Yoshida, C.
AU  - Brumwell, S.L.
AU  - Lingohr, E.J.
AU  - Ahmad, A.
AU  - Blimkie, T.M.
AU  - Kogan, B.A.
AU  - Pilsworth, J.
AU  - Rehman, M.A.
AU  - Schleicher, K.L.
AU  - Shanmugaraj, J.
AU  - Kropinski, A.M.
AU  - Nash, J.H.
TI  - Draft Whole-Genome Sequences of 25 Salmonella enterica Strains Representing 24 Serovars.
JO  - Genome Announcements
PY  - 2016
SP  - e01718
EP  - e01715
VL  - 4
AB  - We report the draft genome sequences of 25 Salmonella enterica strains representing 24
AB  - different serotypes, many of which were not available in public
AB  - repositories during our selection process. These draft genomes will provide
AB  - useful reference for the genetic variation between serotypes and aid in the
AB  - development of molecular typing tools.
ER  -

TY  - JOUR
AU  - Yoshida, H.
AU  - Ishigaki, Y.
AU  - Takizawa, A.
AU  - Moro, K.
AU  - Kishi, Y.
AU  - Takahashi, T.
AU  - Matsui, H.
TI  - Comparative Genomics of the Mucoid and Nonmucoid Strains of Streptococcus pyogenes, Isolated from the Same Patient with Streptococcal Meningitis.
JO  - Genome Announcements
PY  - 2015
SP  - e00221
EP  - e00215
VL  - 3
AB  - Mucoid (MTB313) and nonmucoid (MTB314) strains of group A streptococcus emm type  1 were
AB  - simultaneously isolated from a single patient suffering from streptococcal
AB  - meningitis. Whole-genome sequencing revealed that MTB313 carried a nucleotide
AB  - substitution within rocA, which generated an amber termination codon.
ER  -

TY  - JOUR
AU  - Yoshida, H.
AU  - Katayama, Y.
AU  - Fukushima, Y.
AU  - Taniyama, D.
AU  - Murata, Y.
AU  - Mizutani, T.
AU  - Takahashi, T.
TI  - Draft Genome Sequence of Streptococcus canis Clinical Strain TA4, Harboring the M-Like Protein Gene and Isolated in Japan from a Patient with Bacteremia.
JO  - Genome Announcements
PY  - 2018
SP  - e01469
EP  - e01417
VL  - 6
AB  - Streptococcus canis is an animal-origin beta-hemolytic bacterium that can cause severe
AB  - infections in animals and occasionally infects humans. Here, we report a
AB  - draft genome sequence of an S. canis strain harboring the M-like protein gene.
AB  - This strain was isolated from a patient with bacteremia (reported by Taniyama et
AB  - al. [D. Taniyama, Y. Abe, T. Sakai, T. Kikuchi, and T. Takahashi, IDCases
AB  - 7:48-52, 2017, https://doi.org/10.1016/j.idcr.2017.01.002]). The draft genome
AB  - comprises 2,129,080 bp in 60 contigs.
ER  -

TY  - JOUR
AU  - Yoshida, H.
AU  - Wada, T.
AU  - Taniyama, D.
AU  - Takahashi, T.
TI  - Draft Genome Sequence of Clinical Strain TANI1 of Streptococcus suis Serotype 5 Isolated from a Bacteremia Patient in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e00260
EP  - e00217
VL  - 5
AB  - Streptococcus suis is a swine pathogen that causes severe economic damage to the  porcine
AB  - industry. It occasionally evokes zoonotic infection in humans. Here, we
AB  - report a draft genome sequence of a S. suis serotype 5 strain isolated from a
AB  - bacteremia patient that was reported by Taniyama et al. (D. Taniyama, M. Sakurai,
AB  - T. Sakai, T. Kikuchi, and T. Takahashi, IDCases 6:36-38, 2016,
AB  - https://doi.org/10.1016/j.idcr.2016.09.011).
ER  -

TY  - JOUR
AU  - Yoshida, M.
AU  - Fukano, H.
AU  - Miyamoto, Y.
AU  - Shibayama, K.
AU  - Suzuki, M.
AU  - Hoshino, Y.
TI  - Complete Genome Sequence of a Type Strain of Mycobacterium abscessus subsp. bolletii, a Member of the Mycobacterium abscessus Complex.
JO  - Genome Announcements
PY  - 2018
SP  - e01530
EP  - e01517
VL  - 6
AB  - Mycobacterium abscessus subsp. bolletii is a rapidly growing mycobacterial organism for which
AB  - the taxonomy is unclear. Here, we report the complete genome
AB  - sequence of a Mycobacterium abscessus subsp. bolletii type strain. This sequence
AB  - will provide essential information for future taxonomic and comparative genome
AB  - studies of these mycobacteria.
ER  -

TY  - JOUR
AU  - Yoshida, M.
AU  - Fukano, H.
AU  - Miyamoto, Y.
AU  - Shibayama, K.
AU  - Suzuki, M.
AU  - Hoshino, Y.
TI  - Complete Genome Sequence of Mycobacterium marinum ATCC 927(T), Obtained Using Nanopore and Illumina Sequencing Technologies.
JO  - Genome Announcements
PY  - 2018
SP  - e00397
EP  - e00318
VL  - 6
AB  - Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we
AB  - report the complete genome sequence of a Mycobacterium marinum
AB  - type strain that was isolated from tubercles of diseased fish. This sequence will
AB  - provide essential information for future taxonomic and comparative genome studies
AB  - of its relatives.
ER  -

TY  - JOUR
AU  - Yoshida, M.
AU  - Fukano, H.
AU  - Ogura, Y.
AU  - Kazumi, Y.
AU  - Mitarai, S.
AU  - Hayashi, T.
AU  - Hoshino, Y.
TI  - Complete Genome Sequence of Mycobacterium shigaense.
JO  - Genome Announcements
PY  - 2018
SP  - e00552
EP  - e00518
VL  - 6
AB  - Mycobacterium shigaense is a slowly growing scotochromogenic species and a member of the
AB  - Mycobacterium simiae complex group. Here, we report the complete sequence
AB  - of its genome, comprising a 5.2-Mb chromosome. The sequence will represent the
AB  - essential data for future phylogenetic and comparative genome studies of the
AB  - Mycobacterium simiae complex group.
ER  -

TY  - JOUR
AU  - Yoshida, M.
AU  - Izumiyama, S.
AU  - Fukano, H.
AU  - Sugiyama, K.
AU  - Suzuki, M.
AU  - Shibayama, K.
AU  - Hoshino, Y.
TI  - Draft Genome Sequence of Mycobacterium sp. Strain shizuoka-1, a Novel Mycobacterium Isolated from Groundwater of a Bathing Facility in Shizuoka, Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01309
EP  - e01317
VL  - 5
AB  - Mycobacterium sp. strain shizuoka-1 is a rapidly growing scotochromogenic mycobacterium and
AB  - was isolated from well water for a bathing facility in Shizuoka
AB  - Prefecture in Japan. Here, we report the draft sequence of its genome, comprising
AB  - a 6.5-Mb chromosome. This mycobacterium has 83.1% identity with Mycobacterium
AB  - rhodesiae, a human pathogen.
ER  -

TY  - JOUR
AU  - Yoshida, M.
AU  - Miyamoto, Y.
AU  - Ogura, Y.
AU  - Hayashi, T.
AU  - Hoshino, Y.
TI  - Complete Chromosome Sequence of a Mycolactone-Producing Mycobacterium, Mycobacterium pseudoshottsii.
JO  - Genome Announcements
PY  - 2017
SP  - e01363
EP  - e01317
VL  - 5
AB  - Mycobacterium pseudoshottsii is a fish pathogen that produces mycolactone. Here,  we report
AB  - the complete chromosome sequence of a type strain of M. pseudoshottsii
AB  - (JCM 15466). The sequence will represent essential data for future phylogenetic
AB  - and comparative genome studies of mycolactone-producing mycobacteria.
ER  -

TY  - JOUR
AU  - Yoshida, M.
AU  - Nakanaga, K.
AU  - Ogura, Y.
AU  - Toyoda, A.
AU  - Ooka, T.
AU  - Kazumi, Y.
AU  - Mitarai, S.
AU  - Ishii, N.
AU  - Hayashi, T.
AU  - Hoshino, Y.
TI  - Complete Genome Sequence of Mycobacterium ulcerans subsp. shinshuense.
JO  - Genome Announcements
PY  - 2016
SP  - e01050
EP  - e01016
VL  - 4
AB  - Mycobacterium ulcerans subsp. shinshuense produces mycolactone and causes Buruli  ulcer. Here,
AB  - we report the complete sequence of its genome, which comprises a
AB  - 5.9-Mb chromosome and a 166-kb plasmid (pShT-P). The sequence will represent the
AB  - essential data for future phylogenetic and comparative genome studies of
AB  - mycolactone-producing mycobacteria.
ER  -

TY  - JOUR
AU  - Yoshida, S.
AU  - Enoki, J.
AU  - Hemmi, R.
AU  - Kourist, R.
AU  - Kawakami, N.
AU  - Miyamoto, K.
TI  - Draft Genome Sequence of Bordetella bronchiseptica KU1201, the First Isolation Source of Arylmalonate Decarboxylase.
JO  - Genome Announcements
PY  - 2015
SP  - e00373
EP  - e00315
VL  - 3
AB  - The analysis of the 6.8-Mbp draft genome sequence of the phenylmalonate-assimilating bacterium
AB  - Bordetella bronchiseptica KU1201 identified
AB  - 6,358 protein-coding sequences. This will give us an insight into the catabolic
AB  - variability of this strain for aromatic compounds, along with the roles of
AB  - arylmalonate decarboxylases in nature.
ER  -

TY  - JOUR
AU  - Yoshida, Y.
AU  - Mise, K.
TI  - Occurrence of small Hsd plasmids in Salmonella typhi, Shigella boydii, and Escherichia coli.
JO  - J. Bacteriol.
PY  - 1986
SP  - 357
EP  - 362
VL  - 165
AB  - The natural occurrence of small Hsd (host specificity for DNA) plasmids was
AB  - demonstrated in restriction endonuclease-producing strains of Salmonella typhi,
AB  - Shigella boydii, and Escherichia coli.  The five Hsd plasmids isolated were
AB  - between 5.0 and 12.2 kilobases long.  The copy number of all the Hsd plasmids
AB  - were high (more than 10 copies per cell).  Introduction of these small plasmids
AB  - into E. coli strain 0 drastically lowered the efficiency of plating of the k.0
AB  - phages (the efficiency of plating was less than 5 X 10-5 PFU-1).  High
AB  - restriction endonuclease activities were detected in the Hsd plasmid-positive
AB  - strains because of the elevated copy numbers of the hsdR+ gene.  The advantages
AB  - of using E. coli strains containing the small Hsd plasmids for purification of
AB  - type II restriction endonucleases are discussed.
ER  -

TY  - JOUR
AU  - Yoshii, A.
AU  - Omatsu, T.
AU  - Katayama, Y.
AU  - Koyama, S.
AU  - Mizutani, T.
AU  - Moriyama, H.
AU  - Fukuhara, T.
TI  - Two types of genetic carriers, the IncP genomic island and the novel IncP-1beta plasmid, for the aac(2')-IIa gene that confers kasugamycin resistance in Acidovorax avenae subsp. avenae.
JO  - Mol. Plant Pathol.
PY  - 2014
SP  - 288
EP  - 300
VL  - 16
AB  - A unique aminoglycoside antibiotic, kasugamycin (KSM), has been used to control
AB  - many plant bacterial and fungal diseases in several countries. The emergence of
AB  - KSM-resistant Acidovorax avenae ssp. avenae and Burkholderia glumae, which cause
AB  - rice bacterial brown stripe and rice bacterial grain and seedling rot,
AB  - respectively, is a serious threat for the effective control of these diseases.
AB  - Previously, we have identified the aac(2')-IIa gene, encoding a KSM
AB  - 2'-N-acetyltransferase, from both KSM-resistant pathogens. Although all
AB  - KSM-resistant isolates from both species possess the aac(2')-IIa gene, only A.
AB  - avenae strain 83 showed higher resistance than other strains. In this research,
AB  - kinetic analysis indicates that an amino acid substitution from serine to
AB  - threonine at position 146 of AAC(2')-IIa in strain 83 is not involved in this
AB  - increased resistance. Whole draft genome analysis of A. avenae 83 shows that the
AB  - aac(2')-IIa gene is carried by the novel IncP-1beta plasmid pAAA83, whereas the
AB  - genetic carrier of other strains, the IncP genomic island, is inserted into their
AB  - chromosomes. The difference in the nucleotides of the promoter region of
AB  - aac(2')-IIa between strain 83 and other strains indicates an additional
AB  - transcription start site and results in the increased transcription of
AB  - aac(2')-IIa in strain 83. Moreover, biological characterization of pAAA83
AB  - demonstrates that it can be transferred by conjugation and maintained in the host
AB  - cells. These results demonstrate that acquisition of the aac(2')-IIa gene takes
AB  - place in at least two ways and that the gene module, which includes aac(2')-IIa
AB  - and the downstream gene, may be an important unit for the dissemination of
AB  - antibiotic resistance.
ER  -

TY  - JOUR
AU  - Yoshimori, R.
AU  - Roulland-Dussoix, D.
AU  - Boyer, H.W.
TI  - R factor-controlled restriction and modification of deoxyribonucleic acids:  restriction mutants.
JO  - J. Bacteriol.
PY  - 1972
SP  - 1275
EP  - 1279
VL  - 112
AB  - Restriction mutants of two different R factor-controlled host specificities (RI
AB  - and RII) were isolated.  All of the restriction mutants examined had a normal
AB  - modification phenotype.  No complementation was observed between the RI and RII
AB  - host specificities.  It is concluded that for each host specifcity no protein
AB  - subunit is shared by the restriction endonuclease and modification methylase.
ER  -

TY  - JOUR
AU  - Yoshimori, R.N.
TI  - A genetic and biochemical analysis of the restriction and modification of DNA by resistance transfer factors.
JO  - Ph.D. Thesis, University of California, San Francisco, USA
PY  - 1971
SP  - 1
EP  - 73
AB  - The DNA restriction and modification systems of RTF-1 and RTF-2, host
AB  - specificities RI and RII respectively, were studied genetically and
AB  - biochemically.  The presence of RTF-1 and RTF-2 plasmids in various E. coli
AB  - strains carrying RI and RII restriction and modification host specificities
AB  - restricted unmodified lambda with EOPS of 10-4 and 10-2 respectively.  The RTF
AB  - plasmids were mutagenized with NTG and only one mutant phenotype, r-m+, was
AB  - obtained.  This indicated that there were two genes, a restriction and a
AB  - modification gene, in the host specificity system of the RTFs and differed from
AB  - the three gene system of E. coli B and K.  Using mutant and wild-type RI and
AB  - RII host specificities in various combinations revealed that no complementation
AB  - occurred between the RI and RII host specificities and that they were mutually
AB  - exclusive.  The RI and RII restriction endonucleases were purified to enable
AB  - characterization of the enzymes.  RI and RII restriction endonucleases required
AB  - only Mg++ and unmodified DNA for their enzymatic activity in contrast to the
AB  - cofactor requirements (SAM, ATP, Mg++) of the E. coli B and K restriction
AB  - endonucleases.  The molecular weights of the RI and RII restriction
AB  - endonucleases were estimated to be 80,000 and 100,000 daltons, respectively,
AB  - and recent evidence indicates two 50,000 MW subunits for the RII restriction
AB  - endonuclease.  Optimal activity of RII restriction endonuclease was at 37o in
AB  - 0.1M Tris or glycylglycine buffer at pH 7.5 in 5 mM Mg++.  Optimal conditions
AB  - for RI restriction endonuclease was between 26 to 37C in 0.1M Tris buffer at pH
AB  - 7.5 or at pH 7.2 with either 0.1M phosphate or glycylglycine buffer using 10 mM
AB  - Mg++.  The average size of lambda DNA fragments produced by the RII
AB  - endonucleolytic scissions was estimated at 2 Md MW.  The RI restriction
AB  - endonuclease produced one fragment about 13 Md MW and four to six fragments of
AB  - 3.8 Md MW.  The RI and RII host specificities are classified as a second type
AB  - of restriction and modification mechanism on the basis of the genetic and
AB  - biochemical data.  The mechanism is simple and two cistrons are involved in
AB  - restriction and modification.  Each enzyme is composed of two identical
AB  - cistronic subunits.  On the other hand the more complex mechanism, which is
AB  - represented by the K and B host specificities, is composed of large enzymes
AB  - with complex subunit structures.  Three cistrons are involved in this
AB  - restriction and modification mechanism and the cofactor requirements are SAM,
AB  - ATP and Mg++.  The RI modification methylase was found on polyacrylamide gel as
AB  - one of two protein bands, the other being the RI restriction endonuclease.
AB  - Preliminary data indicates that the modification methylase requires only SAM
AB  - and unmodified DNA for its activity.
ER  -

TY  - JOUR
AU  - Yoshimoto, H.
AU  - Takahashi, Y.
AU  - Hamada, N.
AU  - Umemoto, T.
TI  - Genetic transformation of Porphyromonas gingivalis by electroporation.
JO  - Oral Microbiol. Immunol.
PY  - 1993
SP  - 208
EP  - 212
VL  - 8
AB  - Porphyromonas gingivalis was transformed by electroporation using the DNA of plasmid pE5-2, or
AB  - its derivative, pYT7. Prior to transformation, pE5-2 was transferred from Escherichia coli to
AB  - P. gingivalis strains by conjugation (mobilization with R751) and the plasmid DNA was purified
AB  - from the P. gingivalis transconjugants. Transformation occurred when the recipient strain and
AB  - the donor strain from which the plasmid DNA was purified were homologous. If they were
AB  - heterologous, transformation did not take place or did so at a very low frequency. This
AB  - suggested that a restriction-modification system is present in P. gingivalis strains. Plasmid
AB  - pYT7 was derived by removing an 8.0 kb AvaI fragment from pE5-2 that was purified from P.
AB  - gingivalis cells. It has several single-cutting restriction sites such as EcoRI, AvaI, and
AB  - ClaI usable for gene cloning, though it was not stable enough in P. gingivalis cells, probably
AB  - because the rep gene was derived from a relatively distant species, Bacteroides eggerthii.
ER  -

TY  - JOUR
AU  - Yoshino, T.
AU  - Honda, T.
AU  - Tanaka, M.
AU  - Tanaka, T.
TI  - Draft Genome Sequence of Marine Cyanobacterium Synechococcus sp. Strain NKBG15041c.
JO  - Genome Announcements
PY  - 2013
SP  - e00954
EP  - e00913
VL  - 1
AB  - Synechococcus sp. strain NKBG15041c was isolated as a fast-growing marine cyanobacterium.
AB  - Genetic transformation techniques using this strain have been
AB  - well established for metabolic engineering. Here we report the draft genome
AB  - sequence for this strain, consisting of 44 contigs containing a total of
AB  - 3,180,043 bp and 3,224 putative protein-coding genes.
ER  -

TY  - JOUR
AU  - Yoshioka, H.
AU  - Nakamura, H.
AU  - Sasaki, J.
AU  - Tahara, Y.
AU  - Yamada, Y.
TI  - Purification, properties and recognition sequence of site-specific restriction endonuclease from "Acetobacter xylinus".
JO  - Agric. Biol. Chem.
PY  - 1983
SP  - 2871
EP  - 2879
VL  - 47
AB  - A type II restriction endonuclease was purified from "Acetobacter xylinus" IFO
AB  - 3288 by consecutive column chromatographies on heparin-Sepharose CL-6B,
AB  - DEAE-Sepharose CL-6B, DNA-cellulose and Sephacryl S-400 superfine.  The
AB  - purified enzyme was homogeneous on gel disc electrophoresis and free of other
AB  - endonuclease, exonuclease and phospatase activities.  The enzyme was optimally
AB  - active at 37C at pH 7.5 and required 50~-150 mM NaCl for the enzyme reaction.
AB  - The enzyme cleaved lambda and M13 mp7 RF DNAs at two and one site,
AB  - respectively, but did not cleave pBR322, SV40 and PhiX174 RF DNAs.  the
AB  - recognition sequence for the enzyme was determined to be 5'-C-C-T-N-A-G-G-3',
AB  - and the enzyme was found to cut between C and T in the sequence, being an
AB  - isoschizomer of endonuclease from a blue-green alga, Microcoleus species UTEX
AB  - LB2220 (MstII).
ER  -

TY  - JOUR
AU  - Yoshizawa, H.
AU  - Motooka, D.
AU  - Katada, R.
AU  - Matsumoto, Y.
AU  - Nakamura, S.
AU  - Morii, E.
AU  - Iida, T.
AU  - Matsumoto, H.
TI  - Whole-Genome Sequence of Streptococcus tigurinus Strain osk_001, Isolated from Postmortem Material.
JO  - Genome Announcements
PY  - 2017
SP  - e00878
EP  - e00817
VL  - 5
AB  - Streptococcus tigurinus was recently described as a novel species, and some strains are highly
AB  - virulent. We detected S. tigurinus in infected tissue sampled
AB  - by necropsy. In order to characterize and confirm the virulence of this species,
AB  - whole-genome sequencing of the pure cultured bacterium was performed. We found
AB  - that the strain has specific and unique genetic elements contained in highly
AB  - virulent strains of S. tigurinus.
ER  -

TY  - JOUR
AU  - You, D.
AU  - Wang, L.
AU  - Yao, F.
AU  - Zhou, X.
AU  - Deng, Z.
TI  - A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces  lividans.
JO  - Biochemistry
PY  - 2007
SP  - 6126
EP  - 6133
VL  - 46
AB  - A novel DNA modification system by sulfur (S) in Streptomyces lividans 66 was reported to be
AB  - encoded by a cluster of five genes designated dndA-E [Zhou, X.,
AB  - He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., and Deng, Z.
AB  - (2005) Mol. Microbiol. 57, 1428-1438]. The dndA gene was cloned and the protein
AB  - product expressed in Escherichia coli, purified to homogeneity, and characterized
AB  - as a homodimeric protein of ca. 91 kDa. Purified DndA has a yellow color and
AB  - UV-visible spectra characteristic of a pyridoxal phosphate-containing enzyme and
AB  - was proven to be a cysteine desulfurase able to catalyze removal of elemental S
AB  - atoms from l-cysteine to produce l-alanine with substrate specificity similar to
AB  - that of E. coli IscS. DndC was also purified to homogeneity and found to contain
AB  - a 4Fe-4S cluster by spectral analysis and have obvious ATP pyrophosphatase
AB  - activity. DndA could catalyze iron-sulfur cluster assembly by activation of
AB  - apo-Fe DndC protein prepared by removal of its iron-sulfur cluster using
AB  - alpha,alpha'-dipyridyl. A mutated DndA, with serine substituted for cysteine at
AB  - position 327, which was confirmed to have lost its corresponding cysteine
AB  - desulfurase activity, also lost its ability to reactivate the apo-Fe DndC. The
AB  - likely involvement of an interaction between DndA and DndC in the biochemical
AB  - pathway for the unusual site-specific DNA modification in S. lividans 66 is
AB  - discussed.
ER  -

TY  - JOUR
AU  - You, D.L.
AU  - Indrakanti, R.
AU  - Cao, B.
AU  - Yao, F.
AU  - Deng, Z.X.
AU  - Dedon, P.C.
TI  - Development of a mass spectrometry-based assay to define the biochemistry of phosphorothioate DNA modifications of DNA in bacterial restriction/modification systems.
JO  - ACS Abstracts
PY  - 2011
SP  - 0
EP  - 0
VL  - 242
AB  - We recently discovered that a wide variety of microorganisms possess sequences-specific
AB  - phosphorothioate modifications (S-modifications) of their genomes, which are incorporated into
AB  - DNA by members of the Dnd protein family.  The S-modifications occur at two discrete levels
AB  - consistent with the 4- and 6-nucleotide consensus sequences of a restriction/modification
AB  - system.  Formal proof for this model arose in enteropathogenic Salmonella enterica serovar
AB  - Cerro 87, in which we discovered a host-specific restriciton system DNA S-modification, which
AB  - is more complicated than the well-known methylation-specific restriction/modification systems.
AB  - In an effort to develop an in vitro reconstituted phosphorothioation system, we have developed
AB  - a MALDI-TOF assay in which S-modificaiton of an oligonucleotide possessiong a consensus
AB  - sequence is monitored by a 16 amu mass increase upon insertion of sulfur into the DNA
AB  - backbone.  The assay is being used to define the biochemical mechanism involved in
AB  - phosphorothioation of DNA in this novel restriction/modification system in bacteria.
ER  -

TY  - JOUR
AU  - You, X.Y.
AU  - Guo, X.
AU  - Zheng, H.J.
AU  - Zhang, M.J.
AU  - Liu, L.J.
AU  - Zhu, Y.Q.
AU  - Zhu, B.
AU  - Wang, S.Y.
AU  - Zhao, G.P.
AU  - Poetsch, A.
AU  - Jiang, C.Y.
AU  - Liu, S.J.
TI  - Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation.
JO  - J. Genetics Genomics
PY  - 2011
SP  - 243
EP  - 252
VL  - 38
AB  - Acidithiobacillus caldus is one of the dominant sulfur-oxidizing bacteria
AB  - in bioleaching reactors. It plays the essential role in maintaining the
AB  - high acidity and oxidation of reduced inorganic sulfur compounds during
AB  - bioleaching process. In this report, the complete genome sequence of A.
AB  - caldus SM-1 is presented. The genome is composed of one chromosome
AB  - (2,932,225 bp) and four plasmids (pLAtc1, pLAtc2, pLAtc3, pLAtcm) and it
AB  - is rich in repetitive sequences (accounting for 11% of the total genome),
AB  - which are often associated with transposable genetic elements. In
AB  - particular, twelve copies of ISAtfe and thirty-seven copies of ISAtc1 have
AB  - been identified, suggesting that they are active transposons in the
AB  - genome. A. caldus SM-1 encodes all enzymes for the central metabolism and
AB  - the assimilation of carbon compounds, among which 29 proteins/enzymes were
AB  - identifiable with proteomic tools. The SM-1 fixes CO(2)via the classical
AB  - Calvin-Bassham-Benson (CBB) cycle, and can operate complete
AB  - Embden-Meyerhof pathway (EMP), pentose phosphate pathway (PPP), and
AB  - gluconeogenesis. It has an incomplete tricarboxylic acid cycle (TCA). Four
AB  - putative transporters involved in carbohydrate uptake were identified.
AB  - Taken together, the results suggested that SM-1 was able to assimilate
AB  - carbohydrates and this was subsequently confirmed experimentally because
AB  - addition of 1% glucose or sucrose in basic salt medium significantly
AB  - increased the growth of SM-1. It was concluded that the complete genome of
AB  - SM-1 provided fundamental data for further investigation of its physiology
AB  - and genetics, in addition to the carbon metabolism revealed in this study.
ER  -

TY  - JOUR
AU  - You, X.Y.
AU  - Liu, C.
AU  - Wang, S.Y.
AU  - Jiang, C.Y.
AU  - Shah, S.A.
AU  - Prangishvili, D.
AU  - Liu, S.J.
AU  - Garrett, R.A.
TI  - Genomic analyses of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles.
JO  - Extremophiles
PY  - 2011
SP  - 487
EP  - 497
VL  - 15
AB  - The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb
AB  - and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1.
AB  - The chromosome carries three putative replication origins in conserved genomic regions and two
AB  - large regions where non-essential genes are clustered. Within these variable regions, a few
AB  - orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class
AB  - of MITE-like repeat elements.  There are also 26 highly diverse vapBC antitoxin-toxin gene
AB  - pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the
AB  - impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems
AB  - are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes
AB  - and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are
AB  - predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for
AB  - sulphur metabolism show some significant differences from those proposed for other Acidianus
AB  - and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it
AB  - a promising candidate for developing the first Acidianus genetic systems.
ER  -

TY  - JOUR
AU  - You, X.Y.
AU  - Wang, H.
AU  - Ren, G.Y.
AU  - Li, J.J.
AU  - Duan, X.
AU  - Zheng, H.J.
AU  - Jiang, Z.Q.
TI  - Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis  strain LM 4-2.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 127
EP  - 127
VL  - 10
AB  - Bacillus subtilis LM 4-2, a Gram-positive bacterium was isolated from a molybdenum mine in
AB  - Luoyang city. Due to its strong resistance to molybdate and
AB  - potential utilization in bioremediation of molybdate-polluted area, we describe
AB  - the features of this organism, as well as its complete genome sequence and
AB  - annotation. The genome was composed of a circular 4,069,266 bp chromosome with
AB  - average GC content of 43.83 %, which included 4149 predicted ORFs and 116 RNA
AB  - genes. Additionally, 687 transporter-coding and 116 redox protein-coding genes
AB  - were identified in the strain LM 4-2 genome.
ER  -

TY  - JOUR
AU  - You, Y.
AU  - He, L.
AU  - Zhang, M.
AU  - Fu, J.
AU  - Gu, Y.
AU  - Zhang, B.
AU  - Tao, X.
AU  - Zhang, J.
TI  - Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome.
JO  - PLoS ONE
PY  - 2012
SP  - e38528
EP  - e38528
VL  - 7
AB  - In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000
AB  - probes covering six sequenced Helicobacter pylori
AB  - (H. pylori) genomes was designed. This microarray was used to compare
AB  - the genomic profiles of eight unsequenced strains isolated from
AB  - patients with different gastroduodenal diseases in Heilongjiang
AB  - province of China. Since significant genomic variation was found among
AB  - these strains, an additional 76 H. pylori strains associated with
AB  - different clinical outcomes were isolated from various provinces of
AB  - China. These strains were tested by polymerase chain reaction to
AB  - demonstrate this distinction. We identified several highly variable
AB  - regions in strains associated with gastritis, gastric ulceration, and
AB  - gastric cancer. These regions are associated with genes involved in the
AB  - bacterial type I, type II, and type III R-M systems. They were also
AB  - associated with the virB gene, which lies on the well-studied cag
AB  - pathogenic island. While previous studies have reported on the diverse
AB  - genetic characterization of this pathogenic island, in this study, we
AB  - find that it is conserved in all strains tested by microarray.
AB  - Moreover, a number of genes involved in the type IV secretion system,
AB  - which is related to horizontal DNA transfer between H. pylori strains,
AB  - were identified in the comparative analysis of the strain-specific
AB  - genes. These findings may provide insight into new biomarkers for the
AB  - prediction of gastric diseases.
ER  -

TY  - JOUR
AU  - You, Y.
AU  - Liu, L.
AU  - Zhang, M.
AU  - Han, X.
AU  - He, L.
AU  - Zhu, Y.
AU  - Ni, P.
AU  - Zhang, J.
TI  - Genome Sequences of Three Helicobacter pylori Strains Isolated from Atrophic Gastritis and Gastric Ulcer Patients in China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6314
EP  - 6315
VL  - 194
AB  - Helicobacter pylori is a bacterial pathogen which can lead to several human gastric diseases.
AB  - Here we describe the genome sequences of three strains isolated
AB  - from atrophic gastritis and gastric ulcers patients in China. The data will
AB  - permit genomic characterization of traits that may contribute to various gastric
AB  - diseases.
ER  -

TY  - JOUR
AU  - You, Y.
AU  - Liu, L.
AU  - Zhang, M.
AU  - Zhu, Y.
AU  - He, L.
AU  - Li, D.
AU  - Zhang, J.
TI  - Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China.
JO  - Gut Pathog.
PY  - 2014
SP  - 5
EP  - 5
VL  - 6
AB  - Background: Helicobacter pylori is well known for its relationship with the occurrence of
AB  - several severe gastric diseases. The mechanisms of pathogenesis triggered by H. pylori are
AB  - less well known. In this study, we report the genome sequence and genomic characterizations of
AB  - H. pylori strain HLJ039 that was isolated from a patient with gastric cancer in the Chinese
AB  - province of Heilongjiang, where there is a high incidence of gastric cancer. To investigate
AB  - potential genomic features that may be involved in pathogenesis of carcinoma, the genome was
AB  - compared to three previously sequenced genomes in this area.Result: We obtained 42 contigs
AB  - with a total length of 1,611,192 bp and predicted 1,687 coding sequences. Compared to strains
AB  - isolated from gastritis and ulcers in this area, 10 different regions were identified as being
AB  - unique for HLJ039; they mainly encoded type II restriction-modification enzyme, type II m6A
AB  - methylase, DNA-cytosine methyltransferase, DNA methylase, and hypothetical proteins. A unique
AB  - 547-bp fragment sharing 93% identity with a hypothetical protein of Helicobacter cinaedi ATCC
AB  - BAA-847 was not present in any other previous H. pylori strains. Phylogenetic analysis based
AB  - on core genome single nucleotide polymorphisms shows that HLJ039 is defined as hspEAsia
AB  - subgroup, which belongs to the hpEastAsia group.Conclusion: DNA methylations, variations of
AB  - the genomic regions involved in restriction and modification systems, are the 'hot' regions
AB  - that may be related to the mechanism of H. pylori-induced gastric cancer. The genome sequence
AB  - will provide useful information for the deep mining of potential mechanisms related to East
AB  - Asian gastric cancer.
ER  -

TY  - JOUR
AU  - You, Y.
AU  - Yang, X.
AU  - Song, Y.
AU  - Yan, X.
AU  - Yuan, Y.
AU  - Li, D.
AU  - Yan, Y.
AU  - Wang, H.
AU  - Tao, X.
AU  - Li, L.
AU  - Jiang, X.
AU  - Zhou, H.
AU  - Xiao, D.
AU  - Jin, L.
AU  - Feng, Z.
AU  - Yang, R.
AU  - Luo, F.
AU  - Cui, Y.
AU  - Zhang, J.
TI  - Draft Genome Sequences of Two Streptococcus pyogenes Strains Involved in Abnormal Sharp Raised Scarlet Fever in China, 2011.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5983
EP  - 5984
VL  - 194
AB  - A scarlet fever outbreak caused by Streptococcus pyogenes occurred in China in 2011. To
AB  - determine the genomic features of the outbreak strains, we deciphered
AB  - genomes of two strains isolated from the regions with the highest incidence
AB  - rates. The sequences will provide valuable information for comprehensive study of
AB  - mechanisms related to this outbreak.
ER  -

TY  - JOUR
AU  - Youell, J.
AU  - Firman, K.
TI  - Mechanistic insight into Type I restriction endonucleases.
JO  - Front. Biosci., Landmark Ed.
PY  - 2012
SP  - 2122
EP  - 2139
VL  - 17
AB  - Restriction and modification are two opposing activities that are used to protect bacteria
AB  - from cellular invasion by DNA (e.g. bacteriophage infection).  Restriction activity involves
AB  - cleavage of the DNA; while modification activity is the mechanism used to "mark" host DNA and
AB  - involves DNA methylation.  The study of Type I restriction enzymes has often been seen as an
AB  - esoteric exercise and this reflects some of their more unusual properties - non-stoichiometric
AB  - (non-catalytic) cleavage of the DNA substrate, random cleavage of DNA, a massive ATPase
AB  - activity, and the ability to both cleave DNA and methylate DNA.  Yet these enzymes have been
AB  - found in many bacteria and are very efficient as a means of protecting bacteria against
AB  - bacteriophage infection, indicating they are successful enzynmes.  In this review, we
AB  - summarise recent work on the mechanisms of action, describe switching of function and review
AB  - their mechanism of action.  We also discuss structural rearrangements and cellular
AB  - localisation, which provide powerful mechanisms for controlling the enzyme activity.  Finally,
AB  - we speculate as to their involvement in recombination and discuss their relationship to
AB  - helicase enzymes.
ER  -

TY  - JOUR
AU  - Youell, J.
AU  - Firman, K.
TI  - EcoR124I: from plasmid-encoded restriction-modification system to nanodevice.
JO  - Microbiol. Mol. Biol. Rev.
PY  - 2008
SP  - 365
EP  - 377
VL  - 72
AB  - Plasmid R124 was first described in 1972 as being a new member of in compatibility group
AB  - IncFIV, yet early physical investigations of
AB  - plasmid DNA showed that this type of classification was more complex
AB  - than first imagined. Throughout the history of the study of this
AB  - plasmid, there have been many unexpected observations. Therefore, in
AB  - this review, we describe the history of our understanding of this
AB  - plasmid and the type I restriction-modification (R-M) system that it
AB  - encodes, which will allow an opportunity to correct errors, or
AB  - misunderstandings, that have arisen in the literature. We also describe
AB  - the characterization of the R-M enzyme EcoR124I and describe the
AB  - unusual properties of both type I R-M enzymes and EcoR124I in
AB  - particular. As we approached the 21st century, we began to see the
AB  - potential of the EcoR124I R-M enzyme as a useful molecular motor, and
AB  - this leads to a description of recent work that has shown that the R-M
AB  - enzyme can be used as a nanoactuator. Therefore, this is a history that
AB  - takes us from a plasmid isolated from (presumably) an infected source
AB  - to the potential use of the plasmid-encoded R-M enzyme in
AB  - bionanotechnology.
ER  -

TY  - JOUR
AU  - Youn, J.H.
AU  - Moodley, A.
AU  - Park, Y.H.
AU  - Sugimoto, C.
TI  - Genome Sequence of Methicillin-Resistant Staphylococcus pseudintermedius Sequence Type 233 (ST233) Strain K7, of Human Origin.
JO  - Genome Announcements
PY  - 2013
SP  - e00310
EP  - e00313
VL  - 1
AB  - We report the genome sequence of the methicillin-resistant Staphylococcus pseudintermedius
AB  - strain K7, isolated from the nares of a veterinarian in Seoul,
AB  - South Korea.
ER  -

TY  - JOUR
AU  - Young, D.D.
AU  - Govan, J.M.
AU  - Lively, M.O.
AU  - Deiters, A.
TI  - Photochemical Regulation of Restriction Endonuclease Activity.
JO  - Chembiochem
PY  - 2009
SP  - 1612
EP  - 1616
VL  - 10
AB  - To elucidate biological processes, precise control over these
AB  - processes is required. Light represents an ideal external control
AB  - element because it can be easily regulated in a spatial and
AB  - temporal fashion, and conveys spatiotemporal control of biological
AB  - activity to the system under study.[1] The photochemical
AB  - regulation of oligonucleotide function through the installation
AB  - of light-removable protecting groups (caging groups) on
AB  - either the phosphate or the nucleotide base has recently received
AB  - considerable attention.[2-4] Important applications of this
AB  - technology involve the transient disruption of DNA hybridization
AB  - to photochemically control DNAzyme activity, the polymerase
AB  - chain reaction, antisense activity, as well as inhibition
AB  - of transcription.[4, 5] In this context, we demonstrated that a
AB  - single caging group installed on one base of a typical oligonucleotide
AB  - 20-mer still enables DNA-DNA and DNA-RNA hybridization,
AB  - but could disrupt processing of the oligomer by polymerases
AB  - and inactivate the catalytic ability of DNAzymes.[2] As
AB  - a result, we became interested in exploring other biologically
AB  - relevant processes with photocaged DNA that do not involve
AB  - perturbation of hybridization. Due to the prevalence of DNA-
AB  - protein interactions both in vivo and in vitro,[6] we hypothesized
AB  - that it might be feasible to photochemically control such
AB  - an interaction for restriction endonucleases by the incorporation
AB  - of our 6-nitropiperonyloxymethyl (NPOM)-caged thymidine
AB  - nucleotide (Scheme 1) into DNA. Very few studies have
AB  - been conducted on the effects of unnatural nucleotides on the
AB  - fidelity and functionality of restriction enzymes. Those that
AB  - have, primarily involve the effects of endogenous base mutations
AB  - (for example, methylation events) that do not drastically
AB  - affect hydrogen bonding and base pair recognition. In many of
AB  - these cases, the catalytic capabilities of the restriction endo-
AB  - ACHTUNGTRENUNGnucleases are dramatically decreased, if not abrogated.
ER  -

TY  - JOUR
AU  - Young, J.M.
AU  - Skvortsov, T.
AU  - Arkhipova, K.
AU  - Allen, C.C.R.
TI  - Draft Genome Sequence of the Predatory Marine Bacterium Halobacteriovorax sp. Strain JY17.
JO  - Genome Announcements
PY  - 2018
SP  - e01416
EP  - e01417
VL  - 6
AB  - A draft genome sequence of Halobacteriovorax sp. strain JY17 was assembled from a metagenomic
AB  - data set. The 3.47-Mbp genome of this unusual predatory bacterium
AB  - contains 3,263 protein-coding sequences, 33 tRNAs, and 2 copies each of the 16S,
AB  - 23S, and 5S rRNA genes. This is only the third sequenced representative of this
AB  - genus.
ER  -

TY  - JOUR
AU  - Young, J.P. et al.
TI  - The genome of Rhizobium leguminosarum has recognizable core and accessory components.
JO  - Genome Biol.
PY  - 2006
SP  - R34
EP  - R34
VL  - 7
AB  - ABSTRACT : BACKGROUND : Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont
AB  - of legumes that has been the
AB  - subject of more than a thousand publications. Genes for the symbiotic
AB  - interaction with plants are well studied, but the adaptations that allow
AB  - survival and growth in the soil environment are poorly understood. We have
AB  - sequenced the genome of R. leguminosarum biovar viciae strain 3841.
AB  - RESULTS : The 7.75 Mb genome comprises a circular chromosome and six
AB  - circular plasmids, with 61% G+C overall. All three rRNA operons and 52
AB  - tRNA genes are on the chromosome; essential protein-encoding genes are
AB  - largely chromosomal, but most functional classes occur on plasmids as
AB  - well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of
AB  - three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti,
AB  - and Mesorhizobium loti), and these genes were over-represented in the
AB  - chromosome and had above average G+C. Most supported the rRNA-based
AB  - phylogeny, confirming A. tumefaciens to be the closest among these
AB  - relatives, but 347 genes were incompatible with this phylogeny; these were
AB  - scattered throughout the genome but were over-represented on the plasmids.
AB  - An unexpectedly large number of genes were shared by all three rhizobia
AB  - but were missing from A. tumefaciens. CONCLUSION : Overall, the genome can
AB  - be considered to have two main components: a 'core', which is higher in
AB  - G+C, is mostly chromosomal, is shared with related organisms, and has a
AB  - consistent phylogeny; and an 'accessory' component, which is sporadic in
AB  - distribution, lower in G+C, and located on the plasmids and chromosomal
AB  - islands. The accessory genome has a different nucleotide composition from
AB  - the core despite a long history of coexistence.
ER  -

TY  - JOUR
AU  - Young, M. et al.
TI  - Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium.
JO  - J. Bacteriol.
PY  - 2010
SP  - 841
EP  - 860
VL  - 192
AB  - Micrococcus luteus (NCTC2665, 'Fleming strain') has one of the smallest genomes of
AB  - free-living actinobacteria sequenced to date, comprising a
AB  - single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to
AB  - encode 2,403 proteins. The genome shows extensive synteny with that of the
AB  - closely related organism, Kocuria rhizophila, from which it was
AB  - taxonomically separated relatively recently. Despite its small size, the
AB  - genome harbors 73 insertion sequence (IS) elements, almost all of which
AB  - are closely related to elements found in other actinobacteria. An IS
AB  - element is inserted into the rrs gene of one of only two rrn operons found
AB  - in M. luteus. The genome encodes only four sigma factors and 14 response
AB  - regulators, a finding indicative of adaptation to a rather strict
AB  - ecological niche (mammalian skin). The high sensitivity of M. luteus to
AB  - beta-lactam antibiotics may result from the presence of a reduced set of
AB  - penicillin-binding proteins and the absence of a wblC gene, which plays an
AB  - important role in the antibiotic resistance in other actinobacteria.
AB  - Consistent with the restricted range of compounds it can use as a sole
AB  - source of carbon for energy and growth, M. luteus has a minimal complement
AB  - of genes concerned with carbohydrate transport and metabolism and its
AB  - inability to utilize glucose as a sole carbon source may be due to the
AB  - apparent absence of a gene encoding glucokinase. Uniquely among
AB  - characterized bacteria, M. luteus appears to be able to metabolize
AB  - glycogen only via trehalose and to make trehalose only via glycogen. It
AB  - has very few genes associated with secondary metabolism. In contrast to
AB  - most other actinobacteria, M. luteus encodes only one
AB  - resuscitation-promoting factor (Rpf) required for emergence from dormancy,
AB  - and its complement of other dormancy-related proteins is also much
AB  - reduced. M. luteus is capable of long-chain alkene biosynthesis, which is
AB  - of interest for advanced biofuel production; a three-gene cluster
AB  - essential for this metabolism has been identified in the genome.
ER  -

TY  - JOUR
AU  - Young, T.-S.
AU  - Kim, S.-H.
AU  - Modrich, P.
AU  - Beth, A.
AU  - Jay, E.
TI  - Preliminary x-ray diffraction studies of EcoRI restriction endonuclease-DNA complex.
JO  - J. Mol. Biol.
PY  - 1981
SP  - 607
EP  - 610
VL  - 145
AB  - A complex between EcoRI restriction endonuclease and cognate DNA fragment,
AB  - 5'-G-A-A-T-T-C    C-T-T-A-A-T-5' has been crystallized.  The space group is
AB  - P4212 with a=b=183.2 angstroms, c=49.7 angstroms, a=b=k=90o.  The unit cell
AB  - contains four enzyme monomers plus two duplex DNA fragments in an asymmetric
AB  - unit.  High quality crystals of the enzyme alone have also been obtained.
ER  -

TY  - JOUR
AU  - Youngblood, B.
AU  - Bonnist, E.
AU  - Dryden, D.T.
AU  - Jones, A.C.
AU  - Reich, N.O.
TI  - Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and  fluorescence lifetime studies.
JO  - Nucleic Acids Res.
PY  - 2008
SP  - 2917
EP  - 2925
VL  - 36
AB  - M.EcoRI, a bacterial sequence-specific S-adenosyl-L-methionine-dependent DNA
AB  - methyltransferase, relies on a complex conformational mechanism to
AB  - achieve its remarkable specificity, including DNA bending, base flipping
AB  - and intercalation into the DNA. Using transient fluorescence and
AB  - fluorescence lifetime studies with cognate and noncognate DNA, we have
AB  - characterized several reaction intermediates involving the WT enzyme.
AB  - Similar studies with a bending-impaired, enhanced-specificity M.EcoRI
AB  - mutant show minimal differences with the cognate DNA, but significant
AB  - differences with noncognate DNA. These results provide a plausible
AB  - explanation of the way in which destabilization of reaction intermediates
AB  - can lead to changes in substrate specificity.
ER  -

TY  - JOUR
AU  - Youngblood, B.
AU  - Buller, F.
AU  - Reich, N.O.
TI  - Determinants of sequence-specific DNA methylation: target recognition and catalysis are coupled in M.HhaI.
JO  - Biochemistry
PY  - 2006
SP  - 15563
EP  - 15572
VL  - 45
AB  - Sequence specificity studies of the wild-type bacterial DNA cytosine C5 methyltransferase HhaI
AB  - were carried out with cognate (5'GCGC3') and
AB  - noncognate DNA substrates containing single base pair changes at the first
AB  - and the fourth position (underlined). Specificity for noncognate site
AB  - methylation at the level of kcat/KDDNA is decreased 9000-80000-fold
AB  - relative to the cognate site, manifested through changes in methylation,
AB  - or a prior step, and changes in KDDNA. Analysis of a new high-resolution
AB  - enzyme-DNA cocrystal structure provides a partial mechanistic
AB  - understanding of this discrimination. To probe the significance of
AB  - conformational transitions occurring prior to catalysis in determining
AB  - specificity, we analyzed the double mutant (H127A/T132A). These amino acid
AB  - substitutions disrupt the interface between the flexible loop (residues
AB  - 80-99), which interacts with the DNA minor groove, and the active site.
AB  - The mutant's methylation of the cognate site is essentially unchanged, yet
AB  - its methylation of noncognate sites is decreased up to 460-fold relative
AB  - to the wild-type enzyme. We suggest that a significant contribution to
AB  - M.HhaI's specificity involves the stabilization of reaction intermediates
AB  - prior to methyl transfer, mediated by DNA minor groove-protein flexible
AB  - loop interactions.
ER  -

TY  - JOUR
AU  - Youngblood, B.
AU  - Reich, N.
TI  - Conformational transitions as molecular determinants of specificity for the DNA methyltransferase EcoRI.
JO  - FASEB J.
PY  - 2006
SP  - A40
EP  - A40
VL  - 20
AB  - DNA modifying enzymes have evolved a delicate balance between sequence specificity and
AB  - efficient catalysis. Utilization of indirect readout of
AB  - a DNA sequence, such as DNA bending by an enzyme, provides further
AB  - discrimination beyond the initial binding event between the enzyme and
AB  - DNA. Changes in the DNA bending and base flipping transitions in a
AB  - previously characterized specificity-enhanced mutant M.EcoRI DNA
AB  - adenine methyltransferase suggest a close relationship between
AB  - precatalytic conformational transitions and specificity. We present
AB  - fluorescence resonance energy transfer (FRET) and 2-AminoPurine (2AP)
AB  - fluorescence studies with the cognate sequence (GAATTC) for WT M.EcoRI,
AB  - and reveal a temporal relationship between DNA bending, intercalation
AB  - of the DNA substrate by the enzyme, and base-flipping. The direct
AB  - measurement of kinetic rate constants for DNA bending, intercalation,
AB  - and base-flipping with cognate and non-cognate substrates (GAATTT,
AB  - GGATTC) by WT M.EcoRI, provide a molecular understanding of how these
AB  - conformational transitions impact on specificity. The 3500 and
AB  - 23,000-fold decreases in sequence specificity of WT M.EcoRI for
AB  - noncognates GAATTT and GGATTC are accounted for largely by a similar to
AB  - 2500 fold increase in the reverse rate constants for intercalation and
AB  - base flipping. The predominant contribution to specificity is a
AB  - partitioning of enzyme intermediates away from the Michaelis complex
AB  - prior to catalysis. Our results provide a basis for understanding
AB  - sequence-specific DNA modification.
ER  -

TY  - JOUR
AU  - Youngblood, B.
AU  - Reich, N.O.
TI  - Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI.
JO  - J. Biol. Chem.
PY  - 2006
SP  - 26821
EP  - 26831
VL  - 281
AB  - Changes in DNA bending and base flipping in a previously characterized specificity-enhanced M.
AB  - EcoRI DNA adenine methyltransferase mutant
AB  - suggest a close relationship between precatalytic conformational
AB  - transitions and specificity (Allan, B. W., Garcia, R., Maegley, K.,
AB  - Mort, J., Wong, D., Lindstrom, W., Beechem, J. M., and Reich, N. O.
AB  - (1999) J. Biol. Chem. 274, 19269-19275). The direct measurement of the
AB  - kinetic rate constants for DNA bending, intercalation, and base
AB  - flipping with cognate and noncognate substrates (GAATTT, GGATTC) of
AB  - wild type M. EcoRI using fluorescence resonance energy transfer and
AB  - 2-aminopurine fluorescence studies reveals that DNA bending precedes
AB  - both intercalation and base flipping, and base flipping precedes
AB  - intercalation. Destabilization of these intermediates provides a
AB  - molecular basis for understanding how conformational transitions
AB  - contribute to specificity. The 3500- and 23,000-fold decreases in
AB  - sequence specificity for noncognate sites GAATTT and GGATTC are
AB  - accounted for largely by an similar to 2500-fold increase in the
AB  - reverse rate constants for intercalation and base flipping,
AB  - respectively. Thus, a predominant contribution to specificity is a
AB  - partitioning of enzyme intermediates away from the Michaelis complex
AB  - prior to catalysis. Our results provide a basis for understanding
AB  - enzyme specificity and, in particular, sequence-specific DNA
AB  - modification. Because many DNA methyltransferases and DNA repair
AB  - enzymes induce similar DNA distortions, these results are likely to be
AB  - broadly relevant.
ER  -

TY  - JOUR
AU  - Youngblood, B.
AU  - Shieh, F.K.
AU  - Buller, F.
AU  - Bullock, T.
AU  - Reich, N.O.
TI  - S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation.
JO  - Biochemistry
PY  - 2007
SP  - 8766
EP  - 8775
VL  - 46
AB  - S-adenosyl-L-methionine- (AdoMet-) dependent methyltransferases are widespread, play critical
AB  - roles in diverse biological pathways, and are
AB  - antibiotic and cancer drug targets. Presently missing from our
AB  - understanding of any AdoMet-dependent methyl-transfer reaction is a
AB  - high-resolution structure of a precatalytic enzyme/AdoMet/DNA complex. The
AB  - catalytic mechanism of DNA cytosine methylation was studied by
AB  - structurally and functionally characterizing several active site mutants
AB  - of the bacterial enzyme M.HhaI. The 2.64 A resolution protein/DNA/AdoMet
AB  - structure of the inactive C81A M.HhaI mutant suggests that active site
AB  - water, an approximately 13 degree tilt of the target base toward the
AB  - active site nucleophile, and the presence or absence of the cofactor
AB  - methylsulfonium are coupled via a hydrogen-bonding network involving
AB  - Tyr167. The active site in the mutant complex is assembled to optimally
AB  - align the pyrimidine for nucleophilic attack and subsequent methyl
AB  - transfer, consistent with previous molecular dynamics ab initio and
AB  - quantum mechanics/molecular mechanics calculations. The mutant/DNA/AdoHcy
AB  - structure (2.88 A resolution) provides a direct comparison to the
AB  - postcatalytic complex. A third C81A ternary structure (2.22 A resolution)
AB  - reveals hydrolysis of AdoMet to adenosine in the active site, further
AB  - validating the coupling between the methionine portion of AdoMet and
AB  - ultimately validating the structural observation of a
AB  - prechemistry/postchemistry water network. Disruption of this
AB  - hydrogen-bonding network by a Tyr167 to Phe167 mutation does not alter the
AB  - kinetics of nucleophilic attack or methyl transfer. However, the Y167F
AB  - mutant shows detectable changes in kcat, caused by the perturbed kinetics
AB  - of AdoHcy release. These results provide a basis for including an
AB  - extensive hydrogen-bonding network in controlling the rate-limiting
AB  - product release steps during cytosine methylation.
ER  -

TY  - JOUR
AU  - Youngblood, B.
AU  - Shieh, F.K.
AU  - De Los Rios, S.
AU  - Perona, J.J.
AU  - Reich, N.O.
TI  - Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 334
EP  - 346
VL  - 362
AB  - Improved sequence specificity of the DNA cytosine methyltransferase HhaI was achieved by
AB  - disrupting interactions at a hydrophobic interface between
AB  - the active site of the enzyme and a highly conserved flexible loop.
AB  - Transient fluorescence experiments show that mutations disrupting this
AB  - interface destabilize the positioning of the extrahelical, "flipped"
AB  - cytosine base within the active site. The ternary crystal structure of the
AB  - F124A M.HhaI bound to cognate DNA and the cofactor analogue
AB  - S-adenosyl-l-homocysteine shows an increase in cavity volume between the
AB  - flexible loop and the core of the enzyme. This cavity disrupts the
AB  - interface between the loop and the active site, thereby destabilizing the
AB  - extrahelical target base. The favored partitioning of the base-flipped
AB  - enzyme-DNA complex back to the base-stacked intermediate results in the
AB  - mutant enzyme discriminating better than the wild-type enzyme against
AB  - non-cognate sites. Building upon the concepts of kinetic proofreading and
AB  - our understanding of M.HhaI, we describe how a 16-fold specificity
AB  - enhancement achieved with a double mutation at the loop/active site
AB  - interface is acquired through destabilization of intermediates prior to
AB  - methyltransfer rather than disruption of direct interactions between the
AB  - enzyme and the substrate for M.HhaI.
ER  -

TY  - JOUR
AU  - Youngblood, B.A.
TI  - Analysis of conformational transitions that facilitate DNA methyltransferase specificity and catalysis.
JO  - Ph.D. Thesis, Univ. of California, Santa Barbara
PY  - 2007
SP  - 1
EP  - 190
AB  - DNA modifying enzymes have evolved a delicate balance between sequence specificity and
AB  - efficient catalysis. Utilization of indirect readout of a DNA sequence, such as DNA bending
AB  - and/or base flipping by an enzyme, can provide further discrimination between cognate and
AB  - noncognate substrates by the enzyme. Using fluorescence resonance energy transfer (FRET) and
AB  - 2-Aminopurine (2AP) fluorescence studies with the cognate sequence (GAATTC) for WT M.EcoRI,
AB  - the temporal relationship between DNA bending, intercalation of the DNA substrate by the
AB  - enzyme, and base-flipping is elucidated. Destabilization of these intermediates provides a
AB  - molecular basis for understanding how conformational transitions contribute to specificity.
AB  - The 3500 and 23,000-fold decreases in sequence specificity for noncognate sites GAATTT and
AB  - GGATTC are accounted for largely by a ~2500 fold increase in the reverse rate constants for
AB  - intercalation and base flipping, respectively. The predominant contribution to specificity is
AB  - a partitioning of enzyme intermediates away from the Michaelis complex prior to catalysis.
AB  - Building upon the concepts that were developed with the M.EcoRI studies, an improvement in
AB  - sequence specificity of the DNA cytosine methyltransferase HhaI is achieved by disrupting
AB  - interactions at a hydrophobic interface between the active site of the enzyme and a highly
AB  - conserved flexible loop. Transient fluorescence experiments with 2AP show that mutations
AB  - disrupting this interface interfere with catalysis by destabilizing the extrahelical "flipped"
AB  - cytosine base in the active site. This destabilization, caused by a double mutant, results in
AB  - a ~500-fold specificity enhancement compared to the WT enzyme. To better understand the
AB  - contribution of specific active site atoms to the catalytic enhancement of M.HhaI and the
AB  - rearrangement of these atoms to facilitate the chemistry step, three crystal structures were
AB  - solved using the true cofactor S-adenosyl-L-methionine (pre-chemistry), and the cofactor
AB  - product S-adenosyl-L-homocysteine (post-chemistry). Much work remains in resolving how
AB  - discrimination occurs for eukaryotic DNA methyltransferases in comparison to prokaryotic DNA
AB  - methyltransferases mentioned above. To facilitate our advancement in understanding eukaryotic
AB  - DNA methyltransferases, a model system to explore substrate discrimination in cells was
AB  - developed. Using HIV-1, the mechanism for over-expression and targeting of the mammalian DNA
AB  - methyltransferase 1 (DNMT1) to specific sites in the genome has been probed.
ER  -

TY  - JOUR
AU  - Youngblood, B.A.
AU  - Shieh, F.-K.
AU  - Snider, S.
AU  - Perona, J.
AU  - Reich, N.
TI  - Engineering a more specific DNA methyltransferase by inducing loop instability.
JO  - FASEB J.
PY  - 2005
SP  - A846
EP  - A846
VL  - 19
AB  - The disruption of aromatic-aromatic interactions between Phe84 within the flexible loop
AB  - (residues 80-99) and Phe124, which stabilizes important active sites residues in the bacterial
AB  - DNA cytosine C5 methyltransferase, M.HhaI, result in mutant enzymes that are significantly
AB  - increased in specificity.  The Phe124Ala M.HhaI-DNA cocrystal structure shows the flexibility
AB  - of this loop to be increased.  Loop destabilization results in a decreased ability to maintain
AB  - the extrahelical cytosine poised for catalysis; thus, this intermediate partitions toward
AB  - release rather than catalysis.  The net result is that the mutant is increased in specificity,
AB  - since more rapid release of non-cognate DNA leads to lower rates of methylation at such sites.
AB  - Double mutant cycles involving Phe84Ala, Phe124Ala, His127Ala, and Thr132Ala, show that these
AB  - effects involve structural accommodations over 2 angstroms.  Our results have implications for
AB  - the rational design of enzyme specificity, and for the induced fit mechanism occurring in the
AB  - base-flipping DNA modifying enzymes involved in diverse epigenetic transformations.
ER  -

TY  - JOUR
AU  - Yousfi, K.
AU  - Touati, A.
AU  - Bekal, S.
TI  - Complete Genome Sequence of an Extensively Drug-Resistant Shewanella xiamenensis  Strain Isolated from Algerian Hospital Effluents.
JO  - Genome Announcements
PY  - 2016
SP  - e01236
EP  - e01216
VL  - 4
AB  - In this study, we present the first complete genome of an extensively drug-resistant strain of
AB  - Shewanella xiamenensis, collected from hospital
AB  - effluents in Algeria. This genome includes the chromosome and a large new plasmid
AB  - harboring several drug-resistance genes.
ER  -

TY  - JOUR
AU  - Youssoufian, H.
AU  - Hammer, S.M.
AU  - Hirsch, M.S.
AU  - Mulder, C.
TI  - Methylation of the viral genome in an in vitro model of herpes simplex virus latency.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1982
SP  - 2207
EP  - 2210
VL  - 79
AB  - An in vitro model of latency of herpes simplex virus type 1 (HSV-1) in a
AB  - lymphoid cell line has been developed recently.  CEM cells persistently
AB  - infected with HSV-1 transiently ceased to produce virus for 24 days.  This
AB  - nonproductive state could either be reversed with phytohemagglutinin or
AB  - maintained with concanavalin A.  This system was used to study the relationship
AB  - between DNA methylation and HSV-1 latency.  DNA was probed for methylation by
AB  - comparing the cleavage pataterns generated by two pairs of restriction
AB  - endonucleases (SmaI vs. XmaI and HpaII vs. MspI); these enzymes show
AB  - differential activity reflecting methylation of the recognition sequences.
AB  - Viral DNA in the concanavalin A-treated cells (not producing virus) was found
AB  - to be extensively methylated.  By contrast, no methylated copies were detected
AB  - in viral DNA from producer cells.  About 800 days after the initial infection,
AB  - the productive culture once again became nonproductive.  Viral sequences in the
AB  - latter cells were also methylated.  Reconstitution experiments revealed 1-2
AB  - copies of viral DNA in cells from the latent stages and 40-80 copies in cells
AB  - from productive stages.  Most (if not all) of the viral genome is present in
AB  - cells from various productive and latent stages.  No differences in sequence
AB  - arrangement were detected (although a terminal fragment of intracellular HSV-1
AB  - DNA appeared to be under represented in latent cells).  These results suggest a
AB  - role for DNA methylation in the mechanism of HSV-1 latency in this system.
ER  -

TY  - JOUR
AU  - Youssoufian, H.
AU  - Mulder, C.
TI  - Detection of methylated sequences in eukaryotic DNA with the restriction endonucleases SmaI and XmaI.
JO  - J. Mol. Biol.
PY  - 1981
SP  - 133
EP  - 136
VL  - 150
AB  - The restriction endonuclease XmaI cleaves eukaryotic DNA whether or not its
AB  - recognition sequence (C^-C-C-G-G-G) contains 5-methylcytosine in the CpG
AB  - dinucleotide.  This is in contrast to its isoschizomer, endo R SmaI, which does
AB  - not cleave DNA if the CpG of its recognition sequence (C-C-C^G-G-G) is
AB  - methylated.  Thus, this isoschizomer pair will be useful in the study of
AB  - eukaryotic DNA methylation.
ER  -

TY  - JOUR
AU  - Yousten, A.A.
TI  - Bacteriophage typing of mosquito pathogenic strains of Bacillus sphaericus.
JO  - J. Invertebr. Pathol.
PY  - 1984
SP  - 124
EP  - 125
VL  - 43
AB  - Certain strains of Bacillus sphaericus have been shown to be pathogenic for
AB  - mosquito larvae (S. Singer, Biotechnol. Bioeng. 2, 1335, 1980).  All of these
AB  - strains have been isolated directly from dead larvae or from habitats of
AB  - larvae.  In contrast, none of the 56 strains of B. sphaericus obtained from
AB  - various culture collections exhibited pathogenicity for larvae of Culex
AB  - quinquefasciatus (V. Krych, J., Johnson, and A. Yousten, Int. J. Syst.
AB  - Bacteriol. 30, 476-484, 1980).  In the same study, seven pathogens were shown
AB  - to be members of a single DNA homology group which showed only a low degree of
AB  - genetic relatedness to the type strain of the species.
ER  -

TY  - JOUR
AU  - Yu, B.
AU  - Su, F.
AU  - Wang, L.
AU  - Xu, K.
AU  - Zhao, B.
AU  - Xu, P.
TI  - Draft Genome Sequence of Sporolactobacillus inulinus Strain CASD, an Efficient D-Lactic Acid-Producing Bacterium with High-Concentration  Lactate Tolerance Capability.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5864
EP  - 5865
VL  - 193
AB  - Sporolactobacillus inulinus CASD is an efficient d-lactic acid producer with high optical
AB  - purity. Here we report for the first time the draft
AB  - genome sequence of S. inulinus (2,930,096 bp). The large number of
AB  - annotated two-component system genes makes it possible to explore the
AB  - mechanism of extraordinary lactate tolerance of S. inulinus CASD.
ER  -

TY  - JOUR
AU  - Yu, B.
AU  - Su, F.
AU  - Wang, L.
AU  - Zhao, B.
AU  - Qin, J.
AU  - Ma, C.
AU  - Xu, P.
AU  - Ma, Y.
TI  - Genome Sequence of Lactobacillus rhamnosus Strain CASL, an Efficient L-Lactic Acid Producer from Cheap Substrate Cassava.
JO  - J. Bacteriol.
PY  - 2011
SP  - 7013
EP  - 7014
VL  - 193
AB  - Lactobacillus rhamnosus is a type of probiotic bacteria with industrial potential for l-lactic
AB  - acid production. We announce the draft genome
AB  - sequence of L. rhamnosus CASL (2,855,156 bp with a G+C content of 46.6%),
AB  - which is an efficient producer of l-lactic acid from cheap, nonfood
AB  - substrate cassava with a high production titer.
ER  -

TY  - JOUR
AU  - Yu, C.H.
AU  - Lu, C.K.
AU  - Su, H.M.
AU  - Chiang, T.Y.
AU  - Hwang, C.C.
AU  - Liu, T.
AU  - Chen, Y.M.
TI  - Draft genome of Myxosarcina sp. strain GI1, a baeocytous cyanobacterium associated with the marine sponge Terpios hoshinota.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 28
EP  - 28
VL  - 10
AB  - To date, genome sequences (complete or in draft form) from only six baeocytous cyanobacteria
AB  - in four genera have been reported: Xenococcus, Chroococcidiopsis,
AB  - Pleurocapsa, and Stanieria. To expand our knowledge on the diversity of
AB  - baeocytous cyanobacteria, this study sequenced the genome of GI1, which is a
AB  - Myxosarcina-like baeocytous cyanobacterium. GI1 is of interest not only because
AB  - of its phylogenetic niche, but also because it is a cyanobiont isolated from the
AB  - marine cyanobacteriosponge Terpios hoshinota, which has been shown to cause the
AB  - death of corals. The ~7 Mb draft GI1 genome contains 6,891 protein-coding genes
AB  - and 62 RNA genes. A comparison of genomes among the sequenced baeocytous
AB  - cyanobacterial strains revealed the existence or absence of numerous discrete
AB  - genes involved in nitrogen metabolism. It will be interesting to determine
AB  - whether these genes are important for cyanobacterial adaptations and interactions
AB  - between cyanobionts and their marine sponge hosts.
ER  -

TY  - JOUR
AU  - Yu, C.S.
AU  - Yim, K.Y.
AU  - Tsui, S.K.
AU  - Chan, T.F.
TI  - Complete Genome Sequence of Bacillus subtilis Strain QB928, a Strain Widely Used  in B. subtilis Genetic Studies.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6308
EP  - 6309
VL  - 194
AB  - The complete genome sequence of Bacillus subtilis strain QB928 was constructed to facilitate
AB  - studies in the evolution of the genetic code. With a widespread use of
AB  - the strain in Bacillus subtilis genetics studies, its complete genome sequence
AB  - would facilitate deeper understanding of Bacillus subtilis genetics.
ER  -

TY  - JOUR
AU  - Yu, C.Y.
AU  - Ang, G.Y.
AU  - Ngeow, Y.F.
AU  - Tee, K.K.
AU  - Yin, W.F.
AU  - Chan, K.G.
TI  - Genome Sequences of Two Multidrug-Resistant Proteus mirabilis Strains Harboring CTX-M-65 Isolated from Malaysia.
JO  - Genome Announcements
PY  - 2016
SP  - e01301
EP  - e01316
VL  - 4
AB  - Proteus mirabilis is an opportunistic nosocomial pathogen that is commonly associated with
AB  - urinary tract infections. Here, we present draft genome sequences
AB  - of two multidrug-resistant P. mirabilis strains, isolated from urine samples in
AB  - Malaysia, that harbored a CTX-M-type extended-spectrum beta-lactamase-encoding
AB  - gene, as well as a repertoire of other antimicrobial-resistant determinants.
ER  -

TY  - JOUR
AU  - Yu, D.
AU  - Hui, Y.
AU  - Zai, X.
AU  - Xu, J.
AU  - Liang, L.
AU  - Wang, B.
AU  - Yue, J.
AU  - Li, S.
TI  - Comparative Genomic Analysis of Brucella abortus vaccine strain 104M Reveals a Set of Candidate Genes Associated With Its Virulence Attenuation.
JO  - Virulence
PY  - 2015
SP  - 745
EP  - 754
VL  - 6
AB  - Abstracts The Brucella abortus strain 104M, a spontaneously attenuated strain, has been used
AB  - as a vaccine strain in humans against brucellosis for six decades in China. Despite many
AB  - studies, the molecular mechanisms that cause the attenuation are still unclear. Here, we
AB  - determined the whole-genome sequence of 104M and conducted a comprehensive comparative
AB  - analysis against the whole genome sequences of the virulent strain, A13334, and other
AB  - reference strains. This analysis revealed a highly similar genome structure between 104M and
AB  - A13334. The further comparative genomic analysis between 104M and A13334 revealed a set of
AB  - genes missing in 104M. Some of these genes were identified to be directly or indirectly
AB  - associated with virulence. Similarly, a set of mutations in the virulence-related genes was
AB  - also identified, which may be related to virulence alteration. This study provides a set of
AB  - candidate genes associated with virulence attenuation in B.abortus vaccine strain 104M.
ER  -

TY  - JOUR
AU  - Yu, D.
AU  - Pi, B.
AU  - Chen, Y.
AU  - Wang, Y.
AU  - Ruan, Z.
AU  - Otto, M.
AU  - Yu, Y.
TI  - Characterization of the Staphylococcal Cassette Chromosome Composite Island of Staphylococcus haemolyticus SH32, a Methicillin-Resistant Clinical Isolate from China.
JO  - PLoS ONE
PY  - 2014
SP  - 6
EP  - 6
VL  - 9
AB  - Staphylococcal cassette chromosome (SCC) elements contribute considerably to virulence and
AB  - resistance to antibiotic agents in staphylococci. SCC elements in coagulase-negative
AB  - staphylococci (CoNS) are highly diverse and there is evidence suggesting that they serve as a
AB  - reservoir for antibiotic resistance genes in methicillin-resistant Staphylococcus aureus
AB  - (MRSA). However, only a small number of SCC elements have been characterized in CoNS and their
AB  - exact roles in the emergence and evolution of MRSA remain to be demonstrated. Here, we
AB  - determined the structure of an SCC composite island (CISH32) found in the clinical
AB  - Staphylococcus haemolyticus isolate SH32 by whole-genome DNA sequencing. CISH32 was 48 kb in
AB  - length and mainly composed of two imperfect SCC elements, namely (i) a Psi SCCmec(SH32) part
AB  - containing a class C1 mec gene complex but lacking ccr genes and (ii) a SCCSH32 part with a
AB  - ccrA5B3 gene complex but lacking mec genes. In addition, CISH32 contained a type III
AB  - restriction-modification syst em and several resistance loci, for example genes conferring
AB  - resistance to cadmium and arsenic. Psi SCCmec(SH32) is almost entirely identical to a pseudo
AB  - SCCmec element found in S. haemolyticus WCH1 and shares pronounced sequence similarity to a
AB  - Psi SCCmec element of S. haemolyticus JCSC1435. However, staphylococci other than S.
AB  - haemolyticus, including S. aureus and S. epidermidis, contain homologs of SCCSH32 that are
AB  - more similar to SCCSH32 than those elements found in S. haemolyticus, suggesting that CIS H32
AB  - of S. haemolyticus SH32 was assembled in recent evolutionary events. Moreover, the composite
AB  - structure of CISH32 indicates that the detection of class C1 mec and ccrA5B3 gene complexes in
AB  - S. haemolyticus does not always indicate the existence of a UT9-type SCCmec element, which has
AB  - remained questionable.
ER  -

TY  - JOUR
AU  - Yu, D.S.
AU  - Jeong, H.
AU  - Lee, D.H.
AU  - Kwon, S.K.
AU  - Song, J.Y.
AU  - Kim, B.K.
AU  - Park, M.S.
AU  - Ji, G.E.
AU  - Oh, T.K.
AU  - Kim, J.F.
TI  - Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium bifidum Strain BGN4.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4757
EP  - 4758
VL  - 194
AB  - Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a
AB  - prominent probiotic microorganism that may promote health. We
AB  - completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that
AB  - had been isolated from the fecal sample of a healthy breast-fed infant, and
AB  - annotated 1,835 coding sequences.
ER  -

TY  - JOUR
AU  - Yu, H.
AU  - Li, Y.
AU  - Tang, H.
AU  - Xu, P.
TI  - Genome Sequence of a Newly Isolated Nicotine-Degrading Bacterium, Ochrobactrum sp. SJY1.
JO  - Genome Announcements
PY  - 2014
SP  - e00720
EP  - e00714
VL  - 2
AB  - Ochrobactrum sp. SJY1 uses nicotine as the sources of carbon, nitrogen, and energy. The genome
AB  - of SJY1 was sequenced in order to provide insights into its
AB  - mechanism of nicotine degradation. Physiological characteristics and genome
AB  - analysis indicate that strain SJY1 might have a different nicotine degradation
AB  - pathway from the pyridine or pyrrolidine pathway.
ER  -

TY  - JOUR
AU  - Yu, H.
AU  - Liu, L.
AU  - Chang, Z.
AU  - Wang, S.
AU  - Wen, B.
AU  - Yin, P.
AU  - Liu, D.
AU  - Chen, B.
AU  - Zhang, J.
TI  - Genome Sequence of the Bacterium Bifidobacterium longum Strain CMCC P0001, a Probiotic Strain Used for Treating Gastrointestinal Disease.
JO  - Genome Announcements
PY  - 2013
SP  - e00716
EP  - e00713
VL  - 1
AB  - Bifidobacterium longum subsp. longum CMCC P0001, a standard probiotic strain in China, has
AB  - been widely used in clinical medicine for more than 20 years. Here we
AB  - report the genome features of B. longum strain CMCC P0001.
ER  -

TY  - JOUR
AU  - Yu, H.
AU  - Tang, H.
AU  - Wang, L.
AU  - Yao, Y.
AU  - Wu, G.
AU  - Xu, P.
TI  - Complete Genome Sequence of the Nicotine-Degrading Pseudomonas putida Strain S16.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5541
EP  - 5542
VL  - 193
AB  - Pseudomonas putida S16 is an efficient degrader of nicotine. The complete genome of strain S16
AB  - (5,984,790 bp in length) includes genes related to
AB  - catabolism of aromatic and heterocyclic compounds. The genes of enzymes in
AB  - the core genome and a genomic island encode the proteins responsible for
AB  - nicotine catabolism.
ER  -

TY  - JOUR
AU  - Yu, H.
AU  - Yin, Y.
AU  - Xu, L.
AU  - Yan, M.
AU  - Fang, W.
AU  - Ge, Q.
TI  - Genome Sequence of Klebsiella pneumoniae YZUSK-4, a Bacterium Proposed as a Starter Culture for Fermented Meat Products.
JO  - Genome Announcements
PY  - 2015
SP  - e00774
EP  - e00715
VL  - 3
AB  - Klebsiella pneumoniae strain YZUSK-4, isolated from Chinese RuGao ham, is an efficient
AB  - branched-chain aminotransferase-producing bacterium that can be used
AB  - widely in fermented meat products to enhance flavor. The draft genome sequence of
AB  - strain YZUSK-4 may provide useful genetic information on branched-chain amino
AB  - acid aminotransferase production and branched-chain amino acid metabolism.
ER  -

TY  - JOUR
AU  - Yu, H.
AU  - Yuan, M.
AU  - Lu, W.
AU  - Yang, J.
AU  - Dai, S.
AU  - Li, Q.
AU  - Yang, Z.
AU  - Dong, J.
AU  - Sun, L.
AU  - Deng, Z.
AU  - Zhang, W.
AU  - Chen, M.
AU  - Ping, S.
AU  - Han, Y.
AU  - Zhan, Y.
AU  - Yan, Y.
AU  - Jin, Q.
AU  - Lin, M.
TI  - Complete Genome Sequence of the Nitrogen-fixing and Rhizosphere-associated Bacterium Pseudomonas stutzeri Strain DSM4166.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3422
EP  - 3423
VL  - 193
AB  - We present here the analysis of the whole genome sequence of Pseudomonas stutzeri strain
AB  - DSM4166, a diazotrophic isolate from the rhizosphere of a
AB  - Sorghum nutans cultivar. To our knowledge, this is the second one to be
AB  - sequenced in P. stutzeri. The availability and analysis of the genome
AB  - provides insight into the evolution of the nitrogen fixation property, and
AB  - identification of rhizosphere competence traits required in interactions
AB  - with host plants.
ER  -

TY  - JOUR
AU  - Yu, H.B.
AU  - Zhang, Y.L.
AU  - Lau, Y.L.
AU  - Yao, F.
AU  - Vilches, S.
AU  - Merino, S.
AU  - Tomas, J.M.
AU  - Howard, S.P.
AU  - Leung, K.Y.
TI  - Identification and characterization of putative virulence genes and gene clusters in Aeromonas hydrophila PPD134/91.
JO  - Appl. Environ. Microbiol.
PY  - 2005
SP  - 4469
EP  - 4477
VL  - 71
AB  - Aeromonas hydrophila is a gram-negative opportunistic pathogen of animals
AB  - and humans. The pathogenesis of A. hydrophila is multifactorial. Genomic
AB  - subtraction and markers of genomic islands (GIs) were used to identify
AB  - putative virulence genes in A. hydrophila PPD134/91. Two rounds of genomic
AB  - subtraction led to the identification of 22 unique DNA fragments encoding
AB  - 19 putative virulence factors and seven new open reading frames, which are
AB  - commonly present in the eight virulence strains examined. In addition,
AB  - four GIs were found, including O-antigen, capsule, phage-associated, and
AB  - type III secretion system (TTSS) gene clusters. These putative virulence
AB  - genes and gene clusters were positioned on a physical map of A. hydrophila
AB  - PPD134/91 to determine their genetic organization in this bacterium.
AB  - Further in vivo study of insertion and deletion mutants showed that the
AB  - TTSS may be one of the important virulence factors in A. hydrophila
AB  - pathogenesis. Furthermore, deletions of multiple virulence factors such as
AB  - S-layer, serine protease, and metalloprotease also increased the 50%
AB  - lethal dose to the same level as the TTSS mutation (about 1 log) in a blue
AB  - gourami infection model. This observation sheds light on the
AB  - multifactorial and concerted nature of pathogenicity in A. hydrophila. The
AB  - large number of putative virulence genes identified in this study will
AB  - form the basis for further investigation of this emerging pathogen and
AB  - help to develop effective vaccines, diagnostics, and novel therapeutics.
ER  -

TY  - JOUR
AU  - Yu, J.
AU  - Ahn, S.
AU  - Kim, K.
AU  - Caetano-Anolles, K.
AU  - Lee, C.
AU  - Kang, J.
AU  - Cho, K.
AU  - Yoon, S.
AU  - Kang, D.K.
AU  - Kim, H.
TI  - Comparative genomic analysis of Lactobacillus plantarum GB-LP1 isolated from traditional Korean fermented food.
JO  - J. Microbiol. Biotechnol.
PY  - 2017
SP  - 1419
EP  - 1427
VL  - 27
AB  - As probiotics play an important role in maintaining a healthy gut flora
AB  - environment through antitoxin activity and inhibition of pathogen colonization,
AB  - they have been of interest to the medical research community for quite some time
AB  - now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in
AB  - fermented food, are of particular interest given their easy accessibility. We
AB  - performed whole genome sequencing and genomic analysis on a GB-LP1 strain of L.
AB  - plantarum isolated from Korean traditional fermented food; this strain is well
AB  - known for its functions in immune response, suppression of pathogen growth and
AB  - anti-toxin effects. The complete genome sequence of GB-LP1 is a single chromosome
AB  - of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of
AB  - GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution which
AB  - may have antibiotic and antitoxin functions. The aim of the present study was to
AB  - predict strain specific genomic characteristics and assess the potential of this
AB  - new strain as lactic acid bacteria at the genomic level using in-silico analysis.
AB  - These results provide insight into the L. plantarum species as well as confirm
AB  - the possibility of its utility as a candidate probiotic.
ER  -

TY  - JOUR
AU  - Yu, L.
AU  - Hisatsune, J.
AU  - Hirakawa, H.
AU  - Mizumachi, E.
AU  - Toyoda, A.
AU  - Yahara, K.
AU  - Sugai, M.
TI  - Complete Genome Sequence of Super Biofilm-Elaborating Staphylococcus aureus Isolated in Japan.
JO  - Genome Announcements
PY  - 2017
SP  - e01043
EP  - e01017
VL  - 5
AB  - Staphylococcus aureus JP080, previously named TF2758, is a clinical isolate from  an atheroma
AB  - and a super biofilm-elaborating strain whose biofilm elaboration is
AB  - dependent solely on polysaccharide poly-N-acetylglucosamine/polysaccharide
AB  - intercellular adhesin (PNAG/PIA). Here, we report the complete genome sequence of
AB  - strain JP080, which consists of one chromosome and one circular plasmid.
ER  -

TY  - JOUR
AU  - Yu, M.
AU  - Dai, Z.
AU  - Qu, X.
AU  - Gao, X.
TI  - Draft Genome Sequence of Marine Bacterium Streptomyces sp. Strain CNQ431, a Producer of the Cytokine Inhibitor Splenocin.
JO  - Genome Announcements
PY  - 2015
SP  - e01383
EP  - e01314
VL  - 3
AB  - Currently, corticosteroids are the most potent anti-inflammatory drugs on the market. Here, we
AB  - announce the draft genome sequence of the marine-derived
AB  - Streptomyces sp. strain CNQ431, which produces cytokine inhibitors, termed
AB  - splenocins, which display potent suppression of cytokine production at a
AB  - comparable level to that of corticosteroids. The genome is approximately 498,750
AB  - bp with 72.03% G+C content.
ER  -

TY  - JOUR
AU  - Yu, M.
AU  - Ji, L.
AU  - Neumann, D.A.
AU  - Chung, D.H.
AU  - Groom, J.
AU  - Westpheling, J.
AU  - He, C.
AU  - Schmitz, R.J.
TI  - Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - e148
EP  - e148
VL  - 43
AB  - Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic
AB  - engineering of bacterial species. Systematic identification of DNA
AB  - methylation in R-M systems, including N6-methyladenine (6mA), 5-methylcytosine
AB  - (5mC) and N4-methylcytosine (4mC), will enable strategies to make these species
AB  - genetically tractable. Although single-molecule, real time (SMRT) sequencing
AB  - technology is capable of detecting 4mC directly for any bacterial species
AB  - regardless of whether an assembled genome exists or not, it is not as scalable to
AB  - profiling hundreds to thousands of samples compared with the commonly used
AB  - next-generation sequencing technologies. Here, we present 4mC-Tet-assisted
AB  - bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that
AB  - rapidly and cost efficiently reveals the genome-wide locations of 4mC for
AB  - bacterial species with an available assembled reference genome. In 4mC-TAB-seq,
AB  - both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out
AB  - as cytosines, revealing their specific positions throughout the genome. We
AB  - applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc
AB  - genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier
AB  - to DNA transformation from other species. In combination with MethylC-seq, both
AB  - 4mC- and 5mC-containing motifs are identified which can assist in rapid and
AB  - efficient genetic engineering of these bacteria in the future.
ER  -

TY  - JOUR
AU  - Yu, M.
AU  - Ren, C.
AU  - Qiu, J.
AU  - Luo, P.
AU  - Zhu, R.
AU  - Zhao, Z.
AU  - Hu, C.
TI  - Draft Genome Sequence of the Opportunistic Marine Pathogen Vibrio harveyi Strain  E385.
JO  - Genome Announcements
PY  - 2013
SP  - e00677
EP  - e00613
VL  - 1
AB  - Vibrio harveyi strain E385 was isolated from a diseased cage-cultured grouper in  Daya Bay,
AB  - China. Phylogenetic analysis based on the 16S rRNA gene sequence showed
AB  - similarity with V. harveyi strain BAA-1116. We sequenced the pathogenic strain V.
AB  - harveyi E385 and compared the genome with that of the nonpathogenic strain V.
AB  - harveyi BAA-1116.
ER  -

TY  - JOUR
AU  - Yu, M.
AU  - Tang, K.
AU  - Shi, X.
AU  - Zhang, X.H.
TI  - Genome Sequence of Pseudoalteromonas flavipulchra JG1, a Marine Antagonistic Bacterium with Abundant Antimicrobial Metabolites.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3735
EP  - 3735
VL  - 194
AB  - The marine bacterium Pseudoalteromonas flavipulchra JG1 can synthesize various antibacterial
AB  - metabolites, including protein and small molecules. The draft
AB  - genome of JG1 is about 5.36 Mb and harbors approximate 4,913 genes, which will
AB  - provide further insight into the synthesis of antimicrobial agents and
AB  - antagonistic mechanisms of P. flavipulchra against pathogens.
ER  -

TY  - JOUR
AU  - Yu, X.
AU  - Cloutier, S.
AU  - Tambong, J.T.
AU  - Bromfield, E.S.
TI  - Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2014
SP  - 3202
EP  - 3207
VL  - 64
AB  - Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in
AB  - Ottawa, Canada, were previously characterized and placed in a novel group within
AB  - the genus Bradyrhizobium. To verify their taxonomic status, these strains were
AB  - further characterized using a polyphasic approach. All strains possessed
AB  - identical 16S rRNA gene sequences that were 99.79 % similar to the closest
AB  - relative, Bradyrhizobium liaoningense LMG 18230(T). Phylogenetic analysis of
AB  - concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains
AB  - into three multilocus sequence types that were placed in a highly supported
AB  - lineage distinct from named species of the genus Bradyrhizobium consistent with
AB  - results of DNA-DNA hybridization. Based on analysis of symbiosis gene sequences
AB  - (nodC and nifH), all novel strains were placed in a phylogenetic group with five
AB  - species of the genus Bradyrhizobium that nodulate soybeans. The combination of
AB  - phenotypic characteristics from several tests including carbon and nitrogen
AB  - source utilization and antibiotic resistance could be used to differentiate
AB  - representative strains from recognized species of the genus Bradyrhizobium. Novel
AB  - strain OO99(T) elicits effective nodules on Glycine max, Glycine soja and
AB  - Macroptilium atropurpureum, partially effective nodules on Desmodium canadense
AB  - and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and
AB  - Phaseolus vulgaris. Based on the data presented, we conclude that our strains
AB  - represent a novel species for which the name Bradyrhizobium ottawaense sp. nov.
AB  - is proposed, with OO99(T) ( = LMG 26739(T) = HAMBI 3284(T)) as the type strain.
AB  - The DNA G+C content is 62.6 mol%.
ER  -

TY  - JOUR
AU  - Yu, X.
AU  - Jiang, J.
AU  - Liang, C.
AU  - Zhang, X.
AU  - Wang, J.
AU  - Shen, D.
AU  - Feng, Y.
TI  - Indole affects the formation of multicellular aggregate structures in Pantoea agglomerans YS19.
JO  - J. Gen. Appl. Microbiol.
PY  - 2016
SP  - 31
EP  - 37
VL  - 62
AB  - Pantoea agglomerans YS19 is an endophytic diazotrophic bacterium isolated from
AB  - rice. As well as having the ability to form a biofilm, as do most bacteria, it is
AB  - characterized by the formation of a unique multicellular aggregate structure
AB  - called symplasmata. Indole is traditionally known as a metabolite of the amino
AB  - acid tryptophan, which, however, has recently been shown to participate in
AB  - various regulations of bacterial physiological processes, including stress
AB  - resistance, quorum sensing and biofilm formation. Here, an indole signal was
AB  - found to promote symplasmata formation, yet inhibit biofilm formation, indicating
AB  - different regulatory pathways of indole in the construction of the two
AB  - structures. However, symplasmata showed almost an equivalent stress-resistant
AB  - capability, as compared with biofilms, for YS19 to confront acids, heavy metals
AB  - (Cu(2+)), and UV treatments. Moreover, indole was tested to show a promoting
AB  - effect on exopolysaccharides (EPS) production and an inhibition effect on the
AB  - expression of an outer membrane protein OmpW. These results provide evidence for
AB  - understanding the regulatory mechanisms of indole on such multicellular
AB  - aggregates.
ER  -

TY  - JOUR
AU  - Yu, X.
AU  - Kang, Y.Q.
AU  - Ji, F.
TI  - Draft Genome Sequence of a Trimethylamine-Producing Staphylococcus Isolate from Blood of a Coronary Atherosclerotic Heart Disease Patient.
JO  - Genome Announcements
PY  - 2018
SP  - e01563
EP  - e01517
VL  - 6
AB  - Trimethylamine (TMA), which is produced by various bacteria, is associated with heart disease,
AB  - but little information about the production of TMA in blood is
AB  - available. We present here the genome sequence of a multidrug-resistant strain,
AB  - Staphylococcus epidermidis bTMA-013, with a TMA synthesis pathway, which was
AB  - isolated from the blood of a coronary atherosclerotic heart disease patient.
ER  -

TY  - JOUR
AU  - Yu, Y.J.
AU  - Yang, M.T.
TI  - A novel restriction-modification system from Xanthomonas campestris pv. vesicatoria encodes a m4C-methyltransferase and a nonfunctional  restriction endonuclease.
JO  - FEMS Microbiol. Lett.
PY  - 2007
SP  - 83
EP  - 90
VL  - 272
AB  - A novel restriction-modification (R-M) system, designated as xveIIRM, from chromosomal DNA of
AB  - the Xanthomonas campestris pv. vesicatoria.
AB  - strain 7-1 (Xcv7-1) was cloned and characterized. The xveIIRM genes
AB  - involved in this R-M system are aligned in a tail-to-tail orientation
AB  - and overlapped by 12 base pairs. XveII methyltransferase gene could
AB  - encode a 299-amino acid protein (M.XveII) with an estimated mass of
AB  - 33.7 kDa and was classified to be a member of P-class of m4C-MTase.
AB  - M.XveII methylates the second cytosine of the 5'-CCCGGG-3' recognition
AB  - sequence. The predicted amino acid sequence of the intact Xvell
AB  - endonuclease shared 41.9% identity with SmaI. However, a premature TAA
AB  - translation termination codon was found in the open reading frame of
AB  - xveIIR and expected to encode an 18.3 kDa truncated protein. The
AB  - sequence data are consistent with observation of this study that no
AB  - SmaI-like restriction activity could be detected in the cell extract of
AB  - Xcv7-1.
ER  -

TY  - JOUR
AU  - Yu, Z.
AU  - Gunn, L.
AU  - Brennan, E.
AU  - Reid, R.
AU  - Wall, P.G.
AU  - Gaora, O.P.
AU  - Hurley, D.
AU  - Bolton, D.
AU  - Fanning, S.
TI  - Complete genome sequence of Clostridium estertheticum DSM 8809, a microbe identified in spoiled vacuum packed beef.
JO  - Front. Microbiol.
PY  - 2016
SP  - 1764
EP  - 1764
VL  - 7
AB  - Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS
AB  - involve members of a group of Clostridium species, including Clostridium estertheticum which
AB  - has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth
AB  - conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can
AB  - take up to 3 months to produce a workable culture. These characteristics have limited the
AB  - study of this commercially challenging bacterium. Consequently information on this bacterium
AB  - is limited and no effective controls are currently available to confidently detect and manage
AB  - this production risk.
AB  - In this study the complete genome of C. estertheticum DSM 8809 was determined
AB  - by SMRT R sequencing. The genome consists of a circular chromosome of 4.7 Mbp
AB  - along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like
AB  - resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways
AB  - that would support its biochemical profile and several enzymes contributing to this phenotype
AB  - were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and
AB  - virulence factors were also identified in the genome, a feature that requires further
AB  - research. The availability of the genome sequence will provide a basic blueprint from which to
AB  - develop valuable biomarkers that could support
AB  - and improve the detection and control of this bacterium along the beef production chain.
ER  -

TY  - JOUR
AU  - Yu, Z.
AU  - Ma, Y.
AU  - Zhong, W.
AU  - Qiu, J.
AU  - Li, J.
TI  - Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions  of Plasticity Implicated in Extremely Thermophilic Profiles.
JO  - Front. Microbiol.
PY  - 2017
SP  - 1278
EP  - 1278
VL  - 8
AB  - Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and
AB  - extreme temperature. However, the molecular mechanisms for their
AB  - environmental adaption are poorly understood. Archaeal species is commonly
AB  - considered as primitive organism. The evolutional placement of archaea is a
AB  - fundamental and intriguing scientific question. We sequenced the genomes of
AB  - Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland,
AB  - respectively. Comparative genomic analysis revealed genetic diversity and
AB  - instability implicated in niche adaption, including a number of transporter- and
AB  - integrase/transposase-related genes. Pan-genome analysis also defined the gene
AB  - pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity
AB  - impacting cognate genomic architecture. We believe that Methanopyrus genomics
AB  - could facilitate efficient investigation/recognition of archaeal phylogenetic
AB  - diverse patterns, as well as improve understanding of biological roles and
AB  - significance of these versatile microbes.
ER  -

TY  - JOUR
AU  - Yu, Z.
AU  - Yang, G.
AU  - Liu, X.
AU  - Wang, Y.
AU  - Zhuang, L.
AU  - Zhou, S.
TI  - Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5(T).
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 28
EP  - 28
VL  - 13
AB  - The Azospirillum humicireducens strain SgZ-5(T), belonging to the Order Rhodospirillales and
AB  - the Family Rhodospirillaceae, was isolated from a microbial
AB  - fuel cell inoculated with paddy soil. A previous work has shown that strain
AB  - SgZ-5(T) was able to fix atmospheric nitrogen involved in plant growth promotion.
AB  - Here we present the complete genome of A. humicireducens SgZ-5(T), which consists
AB  - of a circular chromosome and six plasmids with the total genome size of 6,834,379
AB  - bp and the average GC content of 67.55%. Genome annotations predicted 5969
AB  - protein coding and 85 RNA genes including 14 rRNA and 67 tRNA genes. By genomic
AB  - analysis, we identified a complete set of genes that is potentially involved in
AB  - nitrogen fixation and its regulation. This genome also harbors numerous genes
AB  - that are likely responsible for phytohormones production. We anticipate that the
AB  - A. humicireducens SgZ-5(T) genome will contribute insights into plant growth
AB  - promoting properties of Azospirillum strains.
ER  -

TY  - JOUR
AU  - Yu, Z.
AU  - Zhao, M.
AU  - Qiu, J.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain R3, a Red-Pigmented l-Amino Acid Oxidase-Producing Bacterium.
JO  - Genome Announcements
PY  - 2015
SP  - e01339
EP  - e01315
VL  - 3
AB  - Here, we report a draft 5.58-Mb genome sequence of Pseudoalteromonas sp. strain R3, isolated
AB  - from an intertidal-zone sludge sample, which has l-amino acid
AB  - oxidase activity. The genomics information of this strain will facilitate the
AB  - study of l-amino acid oxidase, quorum sensing, and the relationship of the two.
ER  -

TY  - JOUR
AU  - Yuan, J.
AU  - Li, L.
AU  - Sun, M.
AU  - Dong, J.
AU  - Hu, Q.
TI  - Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-SG.
JO  - Genome Announcements
PY  - 2013
SP  - e0021812
EP  - e0021812
VL  - 1
AB  - Riemerella anatipestifer is a pathogenic bacterium that has spread all over the world and is
AB  - associated with epizootic infections in waterfowl and other avian
AB  - species. R. anatipestifer RA-SG is an avirulent strain, isolated from an infected
AB  - duck in Guangdong province, China. The genome sequence of this species is
AB  - presented herein.
ER  -

TY  - JOUR
AU  - Yuan, K.X.
AU  - Adam, Z.
AU  - Tambong, J.
AU  - Levesque, C.A.
AU  - Chen, W.
AU  - Lewis, C.T.
AU  - De Boer, S.H.
AU  - Li, X.S.
TI  - Draft Genome Sequence of Pectobacterium wasabiae Strain CFIA1002.
JO  - Genome Announcements
PY  - 2014
SP  - e00214
EP  - e00214
VL  - 2
AB  - Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was
AB  - recently found to cause blackleg-like symptoms on potato in the United
AB  - States, Canada, and Europe. A draft genome sequence of a Canadian potato isolate
AB  - of P. wasabiae CFIA1002 will enhance the characterization of its pathogenicity
AB  - and host specificity features.
ER  -

TY  - JOUR
AU  - Yuan, K.X.
AU  - Cullis, J.
AU  - Levesque, C.A.
AU  - Tambong, J.
AU  - Chen, W.
AU  - Lewis, C.T.
AU  - De Boer, S.H.
AU  - Li, X.S.
TI  - Draft Genome Sequences of Ralstonia solanacearum Race 3 Biovar 2 Strains with Different Temperature Adaptations.
JO  - Genome Announcements
PY  - 2015
SP  - e00815
EP  - e00815
VL  - 3
AB  - Ralstonia solanacearum race 3 biovar 2 (R3bv2) causes brown rot of potato in countries with
AB  - temperate climates. Here, we report two draft genome sequences of
AB  - R. solanacearum R3bv2 NCPPB909 and CFIA906 with different temperature
AB  - adaptations. Analysis of these genome sequences will provide detailed insight on
AB  - virulence, functionality, and plant/pest interactions of this widely distributed
AB  - and regulated pathogen.
ER  -

TY  - JOUR
AU  - Yuan, M.
AU  - Chen, H.
AU  - Zhu, X.
AU  - Feng, J.
AU  - Zhan, Z.
AU  - Zhang, D.
AU  - Chen, X.
AU  - Zhao, X.
AU  - Lu, J.
AU  - Xu, J.
AU  - Zhou, D.
AU  - Li, J.
TI  - pSY153-MDR, a p12969-DIM-related mega plasmid carrying blaIMP-45 and armA, from clinical Pseudomonas putida.
JO  - Oncotarget
PY  - 2017
SP  - 68439
EP  - 68447
VL  - 8
AB  - This work characterized mega plasmid pSY153-MDR, carrying blaIMP-45 and armA, from a
AB  - multidrug-resistant (MDR) Pseudomonas putida isolate from the urine of a cerebral infarction
AB  - patient in China. The backbone of pSY153-MDR was closely related to Pseudomonas plasmids
AB  - p12969-DIM, pOZ176, pBM413, pTTS12, and pRBL16, and could not be assigned to any of the known
AB  - incompatibility groups. The accessory modules of pSY153-MDR were composed of 10 individual
AB  - insertion sequence elements and two different MDR regions, and differed dramatically from the
AB  - above plasmids. Fifteen non-redundant resistance markers were identified to be involved in
AB  - resistance to at least eight distinct classes of antibiotics. All of these resistance genes
AB  - were associated with mobile elements, and were embedded within the two MDR regions. blaIMP-45
AB  - and armA coexisted in a Tn1403Tn1548 region, which was generated from homologous recombination
AB  - of Tn1403- and Tn1548-like transposons. The second copy of armA was a component of the
AB  - ISCR28armA and #8710;ISCR28 structure, representing a novel armA vehicle. This vehicle was
AB  - located within In48, which was related to In363 and In1058. Data presented here provide a
AB  - deeper insight into the evolutionary history of SY153, especially in regard to how it became
AB  - extensively drug-resistant.
ER  -

TY  - JOUR
AU  - Yuan, R.
TI  - The reaction mechanism of type I restriction endonucleases.
JO  - Gene Amplif. Anal.
PY  - 1981
SP  - 45
EP  - 72
VL  - 1
AB  - *
AB  -    I. Introduction
AB  -   II. Genetics
AB  -  III. Enzyme structure
AB  -   IV. Nature of DNA recognition and cleavage sites
AB  -    V. Mechanism of restriction
AB  -   VI. Mechanism of modification
AB  -  VII. Mechanism of antirestriction systems
AB  - VIII. Projections and speculations
AB  - 
ER  -

TY  - JOUR
AU  - Yuan, R.
TI  - Structure and mechanism of multifunctional restriction endonucleases.
JO  - Annu. Rev. Biochem.
PY  - 1981
SP  - 285
EP  - 315
VL  - 50
AB  - Restriction endonucleases are strain-specific enzymes, which enable bacteria to
AB  - recognize and rapidly destroy foreign DNA and which cause double-stranded
AB  - scissions at a limited number of sites on the DNA.  In addition to having a
AB  - restriction activity, each of these bacterial strains possesses a specific DNA
AB  - methylase that transfers methyl groups from S-adenosylmethionine (AdoMet) to
AB  - specific adenine or sytosine residues in the DNA.  In this way, the DNA of the
AB  - cell is protected against its own restriction enzyme.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Bickle, T.A.
AU  - Ebbers, W.
AU  - Brack, C.
TI  - Multiple steps in DNA recognition by restriction endonuclease from E. coli K.
JO  - Nature
PY  - 1975
SP  - 556
EP  - 560
VL  - 256
AB  - The process of DNA recognition by the activated form of the restriction
AB  - endonuclease from E. coli K involves three enzyme-DNA complexes which can be
AB  - differentiated experimentally.  These are:  an initial complex formed at a
AB  - nonspecific site; a recognition complex involving the host specificity site;
AB  - and a cleavage complex dependent on the presence of ATP.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Burckhardt, J.
AU  - Weisemann, J.
AU  - Hamilton, D.L.
TI  - The mechanism of DNA methylation by the restriction endonuclease from E. coli K.
JO  - Biochemistry of S-adenosylmethionine and related compounds
PY  - 1981
SP  - 239
EP  - 247
VL  - 0
AB  - Restriction endonucleases are strain-specific enzymes which enable bacteria to
AB  - recognize and destroy foreign DNA by making double-stranded scissions at a
AB  - limited number of sites.  These bacterial strains also possess DNA methylases
AB  - which modify the DNA in order to protect it from the homologous restriction
AB  - enzymes.  These restriction endonucleases have been classified into three
AB  - different types (Yuan, 1981).  The Type I enzymes, such as the one coded by E.
AB  - coli K, are multifunctional proteins composed of three different subunits.
AB  - EcoK can catalyze three different reactions:  DNA cleavage (which requires ATP
AB  - and AdoMet), ATP hydrolysis (which is coupled to DNA cleavage) and DNA
AB  - methylation (which requires AdoMet).  We have made a detailed study of the
AB  - reaction mechanism of EcoK in order to understand certain unusual features,
AB  - such as its ability to catalyze two opposing reactions - restriction and
AB  - modification - and the cleavage of DNA at sites distal from the original
AB  - binding site.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Hamilton, D.L.
TI  - Type I and Type III restriction-modification enzymes.
JO  - DNA Methylation. Biochemistry and Biological Significance.
PY  - 1984
SP  - 11
EP  - 38
VL  - 0
AB  - None
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Hamilton, D.L.
TI  - Restriction and modification of DNA by a complex protein.
JO  - Am. Sci.
PY  - 1982
SP  - 61
EP  - 69
VL  - 70
AB  - The interaction of certain proteins with specific nucleotide sequences forms the basis for
AB  - such diverse biological functions as genetic transformation, recombination, control of gene
AB  - expression, and DNA repair.  In many cases, this interaction involves both the recognition of
AB  - a particular DNA site and the catalysis of a biochemical reaction.  Host-controlled
AB  - restriction and modification is one biological system in which genetic and molecular
AB  - approaches have been combined to give us a better understanding of the complexity of these
AB  - protein-DNA interactions.  Host-controlled restriction is the process by which certain strains
AB  - of bacteria recognize and degrade foreign DNA.  The same strains are able to carry out
AB  - modification of their own DNA to protect it from restriction.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Hamilton, D.L.
AU  - Burckhardt, J.
TI  - DNA translocation by the restriction enzyme from E. coli K.
JO  - Cell
PY  - 1980
SP  - 237
EP  - 244
VL  - 20
AB  - The restriction endonuclease Eco K binds to a host specificity site and then
AB  - proceeds to cleave the DNA at sites that may be several thousand bases away.
AB  - It does this by translocating the DNA past the enzyme in an ATP-dependent
AB  - reaction that results in the formation of highly twisted loop intermediates.
AB  - DNA cleavage can occur on either side of the host specificity site.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Hamilton, D.L.
AU  - Hadi, S.M.
AU  - Bickle, T.A.
TI  - Role of ATP in the cleavage mechanism of the EcoP15 restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1980
SP  - 501
EP  - 519
VL  - 144
AB  - The EcoP15 restriction endonuclease forms complexes at specific sites on
AB  - unmodified DNA both in the presence and in the absence of
AB  - S-adenosyl-L-methionine.  ATP acts as an allosteric effector of EcoP15 and
AB  - induces DNA cleavage followed by release of the enzyme from the DNA.  The
AB  - efficiency of endonucleolytic scission varies from site to site.  The
AB  - nucleotide sequences at sites that are cleaved at a high frequency were
AB  - compared.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Heywood, J.
AU  - Meselson, M.
TI  - ATP hydrolysis by restriction endonuclease from E. coli K.
JO  - Nature New Biol.
PY  - 1972
SP  - 42
EP  - 43
VL  - 240
AB  - We wish to report a puzzling ATPase activity associated with the DNA
AB  - restriction endonuclease from E. coli strain K.  This enzyme makes a limited
AB  - number of double chain breaks in DNA molecules lacking the host-controlled
AB  - modification imparted by strain K.  Unmodified DNA molecules from bacteriophage
AB  - lambda, which serve as a convenient substrate, are broken into fragments with a
AB  - weight average molecular weight of approximately 7 Md, about one-fifth the size
AB  - of the intact lambda chromosome.  The reaction requires Mg2+, ATP and
AB  - S-adenosylmethionine (SAM).
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Meselson, M.
TI  - A specific complex between a restriction endonuclease and its DNA substrate.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 1970
SP  - 357
EP  - 362
VL  - 65
AB  - In the presence of Mg++, ATP, and S-adenosylmethionine, the DNA restriction
AB  - endonuclease R.K forms a specific complex with its DNA substrate.  The complex
AB  - can be detected by its retention on nitrocellulose membranes.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Reiser, J.
TI  - Steps in the reaction mechanism of the Escherichia coli plasmid P15-specific restriction endonuclease.
JO  - J. Mol. Biol.
PY  - 1978
SP  - 433
EP  - 445
VL  - 122
AB  - The restriction endonuclease coded by the Escherichia coli plasmid P15 cleaves
AB  - unmodified DNA in the presence of ATP and magnesium ions.  This reaction is
AB  - stimulated by the addition of S-adenosylmethionine.  Both ATP and
AB  - S-adenosylmethionine behave as allosteric effectors.  The enzyme forms a
AB  - complex with unmodified DNA in the absence of S-adenosylmethionine and ATP.
AB  - Neither the rate of complex formation nor its stability is significantly
AB  - affected by S-adenosylmethionine.  The reaction of ATP with this complex is a
AB  - late step in the reaction sequence prior to DNA cleavage and is affected by the
AB  - presence of S-adenosylmethionine.
ER  -

TY  - JOUR
AU  - Yuan, R.
AU  - Smith, H.O.
TI  - The restriction and modification DNA methylases: An overview.
JO  - DNA Methylation. Biochemistry and Biological Significance.
PY  - 1984
SP  - 73
EP  - 80
VL  - 0
AB  - The preceding two chapters have presented in detail all that is known about the
AB  - genetic and enzymatic mechanisms of the modification DNA methylases and their
AB  - relationship to the homologous restriction endonucleases.  Although the number
AB  - of systems that have been characterized is limited, sufficient information is
AB  - available to allow a comparison of the three types of restriction-modification
AB  - systems from both biological and mechanistic viewpoints.
ER  -

TY  - JOUR
AU  - Yuan, Y.
AU  - Zhang, Y.
AU  - Fu, S.
AU  - Crippen, T.L.
AU  - Visi, D.K.
AU  - Benbow, M.E.
AU  - Allen, M.S.
AU  - Tomberlin, J.K.
AU  - Sze, S.H.
AU  - Tarone, A.M.
TI  - Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata.
JO  - Genome Announcements
PY  - 2016
SP  - e00672
EP  - e00616
VL  - 4
AB  - We announce a draft genome sequence of a Proteus mirabilis strain derived from Lucilia
AB  - sericata salivary glands. This strain is demonstrated to attract and
AB  - induce oviposition by L. sericata, a common blow fly important to medicine,
AB  - agriculture, and forensics. The genome sequence will help dissect interkingdom
AB  - communication between the species.
ER  -

TY  - JOUR
AU  - Yuan, Y.
AU  - Zhang, Y.
AU  - Fu, S.
AU  - Crippen, T.L.
AU  - Visi, D.K.
AU  - Benbow, M.E.
AU  - Allen, M.S.
AU  - Tomberlin, J.K.
AU  - Sze, S.H.
AU  - Tarone, A.M.
TI  - Genome Sequence of a Providencia stuartii Strain Isolated from Luciliasericata Salivary Glands.
JO  - Genome Announcements
PY  - 2017
SP  - e00250
EP  - e00217
VL  - 5
AB  - We present here the draft genome sequence of a Providencia stuartii strain, derived from the
AB  - salivary glands of larval Lucilia sericata, a common blow fly
AB  - important to forensic, medical, and veterinary science. The genome sequence will
AB  - help dissect coinfections involving P. stuartii and Proteus mirabilis, as well as
AB  - blow fly-bacteria interactions.
ER  -

TY  - JOUR
AU  - Yucel, O.
AU  - Wibberg, D.
AU  - Philipp, B.
AU  - Kalinowski, J.
TI  - Genome Sequence of the Bile Salt-Degrading Bacterium Novosphingobium sp. Strain Chol11, a Model Organism for Bacterial Steroid Catabolism.
JO  - Genome Announcements
PY  - 2018
SP  - e01372
EP  - e01317
VL  - 6
AB  - Many bacteria from different phylogenetic groups are able to degrade eukaryotic steroid
AB  - compounds, but the underlying metabolic pathways are still not well
AB  - understood. Novosphingobium sp. strain Chol11 is a steroid-degrading
AB  - alphaproteobacterium. Its genome sequence reveals that it lacks several genes for
AB  - steroid degradation known to exist in other model organisms.
ER  -

TY  - JOUR
AU  - Yuichi, S.
AU  - Norton, J.M.
AU  - Bollmann, A.
AU  - Klotz, M.G.
AU  - Stein, L.Y.
AU  - Laanbroek, H.J.
AU  - Arp, D.J.
AU  - Goodwin, L.A.
AU  - Chertkov, O.
AU  - Held, B.
AU  - Bruce, D.
AU  - Detter, J.C.
AU  - Detter, J.C.
AU  - Tapia, R.
AU  - Han, C.S.
TI  - Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium  sensitive to high levels of ammonia.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5047
EP  - 5048
VL  - 193
AB  - Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing  bacterium
AB  - (AOB) that was originally isolated in 1997 by Yuichi Suwa and
AB  - colleagues. This organism belongs to Nitrosomonas cluster 6A, which is
AB  - characterized by sensitivity to high ammonia concentrations, higher substrate
AB  - affinity (lower K(m)), and lower maximum growth rates than strains in
AB  - Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas
AB  - eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are
AB  - needed, as these bacteria are found in freshwater environments, drinking water
AB  - supplies, wastewater treatment systems, and soils worldwide.
ER  -

TY  - JOUR
AU  - Yukawa, H.
AU  - Omumasaba, C.A.
AU  - Nonaka, H.
AU  - Kos, P.
AU  - Okai, N.
AU  - Suzuki, N.
AU  - Suda, M.
AU  - Tsuge, Y.
AU  - Watanabe, J.
AU  - Ikeda, Y.
AU  - Vertes, A.A.
AU  - Inui, M.
TI  - Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.
JO  - Microbiology
PY  - 2007
SP  - 1042
EP  - 1058
VL  - 153
AB  - The complete genome sequence of Corynebacterium glutamicum strain R was determined to allow
AB  - its comparative analysis with other corynebacteria.
AB  - The biology of corynebacteria was explored by refining the definition of
AB  - the subset of genes that constitutes the corynebacterial core as well as
AB  - those characteristic of saprophytic and pathogenic ecological niches. In
AB  - addition, the relative scarcity of corynebacterial sigma factors and the
AB  - plasticity of their two-component system machinery reflect their
AB  - relatively exacting nutritional requirements and reduced
AB  - membrane-associated and secreted proteins. The conservation of key genes
AB  - and pathways between corynebacteria, mycobacteria and Nocardia validates
AB  - the use of C. glutamicum to study fundamental processes that are conserved
AB  - in slow-growing mycobacteria, including pathogenesis-associated
AB  - mechanisms. The discovery of 39 novel genes in C. glutamicum R that have
AB  - not been previously reported in other corynebacteria supports the
AB  - rationale for sequencing additional corynebacterial genomes to better
AB  - define the corynebacterial pan-genome and identify previously undetected
AB  - metabolic pathways in these organisms.
ER  -

TY  - JOUR
AU  - Yuki, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Kitahara, M.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shochu Residue.
JO  - Genome Announcements
PY  - 2014
SP  - e00257
EP  - e00214
VL  - 2
AB  - Here, we report the draft genome sequences of two type strains of Lactobacillus,
AB  - Lactobacillus farraginis JCM 14108(T) and Lactobacillus composti JCM 14202(T),
AB  - isolated from the compost of distilled shochu residue. Their genome information
AB  - will be useful for studies of ecological and physiological functions of these
AB  - Lactobacillus species.
ER  -

TY  - JOUR
AU  - Yuki, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Oshida, Y.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM  9152T.
JO  - Genome Announcements
PY  - 2014
SP  - e01258
EP  - e01213
VL  - 2
AB  - Here, we report the draft genome sequences of the type strains of three cellulolytic or
AB  - hemicellulolytic alkaliphilic Bacillus species: Bacillus
AB  - wakoensis, Bacillus akibai, and Bacillus hemicellulosilyticus. The genome
AB  - information for these three strains will be useful for studies of alkaliphilic
AB  - Bacillus species, their evolution, and biotechnological applications for their
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Yuki, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Oshida, Y.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Paenibacillus pini JCM 16418T, Isolated from the Rhizosphere of Pine Tree.
JO  - Genome Announcements
PY  - 2014
SP  - e00210
EP  - e00214
VL  - 2
AB  - Paenibacillus pini strain JCM 16418(T) is a cellulolytic bacterium isolated from  the
AB  - rhizosphere of pine trees. Here, we report the draft genome sequence of this
AB  - strain. This genome information will be useful for studies of rhizosphere
AB  - bacteria.
ER  -

TY  - JOUR
AU  - Yuki, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Sakamoto, M.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite.
JO  - Genome Announcements
PY  - 2014
SP  - e00072
EP  - e00014
VL  - 2
AB  - Here we report the draft genome sequence of Bacteroides reticulotermitis strain JCM 10512(T),
AB  - a xylanolytic and cellulolytic bacterium isolated from the gut of a
AB  - wood-feeding termite. The genome information will facilitate the study of this
AB  - strain for biomass degradation and adaptation to the gut environment.
ER  -

TY  - JOUR
AU  - Yuki, M.
AU  - Oshima, K.
AU  - Suda, W.
AU  - Sakamoto, M.
AU  - Kitamura, K.
AU  - Iida, T.
AU  - Hattori, M.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated  from a Cellulose-Degrading Bacterial Community.
JO  - Genome Announcements
PY  - 2014
SP  - e00110
EP  - e00114
VL  - 2
AB  - Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium
AB  - straminisolvens JCM 21531(T), isolated from a cellulose-degrading bacterial
AB  - community. The genome information of this strain will be useful for studies on
AB  - the degradation enzymes and functional interactions with other members in the
AB  - community.
ER  -

TY  - JOUR
AU  - Yuki, M.
AU  - Sakamoto, M.
AU  - Kuwahara, H.
AU  - Hongoh, Y.
AU  - Ohkuma, M.
TI  - Draft Genome Sequence of Lactococcus sp. Strain Rs-Y01, Isolated from the Gut of  the Lower Termite Reticulitermes speratus.
JO  - Genome Announcements
PY  - 2017
SP  - e00999
EP  - e00917
VL  - 5
AB  - Here, we report the draft genome sequence of Lactococcus sp. strain Rs-Y01, which was isolated
AB  - from the gut of a wood-feeding termite. The genome information will
AB  - facilitate the study of the symbiotic functions of this strain in the termite
AB  - gut.
ER  -

TY  - JOUR
AU  - Yulandi, A.
AU  - Sugiokto, F.G.
AU  - Febrilina, S.A.
TI  - Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B12-Producing Strain from Indonesian Tempeh.
JO  - Genome Announcements
PY  - 2016
SP  - e01724
EP  - e01715
VL  - 4
AB  - Klebsiella pneumoniae strain IIEMP-3, isolated from Indonesian tempeh, is a vitamin
AB  - B12-producing strain that exhibited a different genetic profile from
AB  - pathogenic isolates. Here we report the draft genome sequence of strain IIEMP-3,
AB  - which may provide insights on the nature of fermentation, nutrition, and
AB  - immunological function of Indonesian tempeh.
ER  -

TY  - JOUR
AU  - Yun, J.H.
AU  - Cho, Y.J.
AU  - Chun, J.
AU  - Hyun, D.W.
AU  - Bae, J.W.
TI  - Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 495
EP  - 504
VL  - 9
AB  - Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within  the class
AB  - Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium
AB  - and was previously isolated from a Korean fermented food. Most members of the
AB  - genus Leucobacter are chromate-resistant and this feature could be exploited in
AB  - biotechnological applications. However, the genus Leucobacter is poorly
AB  - characterized at the genome level, despite its potential importance. Thus, the
AB  - present study determined the features of Leucobacter salsicius M1-8(T), as well
AB  - as its genome sequence and annotation. The genome comprised 3,185,418 bp with a
AB  - G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes.
AB  - This strain possessed two predicted genes associated with chromate resistance,
AB  - which might facilitate its growth in heavy metal-rich environments.
ER  -

TY  - JOUR
AU  - Yun, J.H.
AU  - Sung, H.
AU  - Kim, H.S.
AU  - Tak, E.J.
AU  - Kang, W.
AU  - Lee, J.Y.
AU  - Hyun, D.W.
AU  - Kim, P.S.
AU  - Bae, J.W.
TI  - Complete genome sequence of the halophile bacterium Kushneria konosiri X49(T), isolated from salt-fermented Konosirus punctatus.
JO  - Standards in Genomic Sciences
PY  - 2018
SP  - 19
EP  - 19
VL  - 13
AB  - Kushneria konosiri X49(T) is a member of the Halomonadaceae family within the order
AB  - Oceanospirillales and can be isolated from salt-fermented larval gizzard
AB  - shad. The genome of K. konosiri X49(T) reported here provides a genetic basis for
AB  - its halophilic character. Diverse genes were involved in salt-in and -out
AB  - strategies enabling adaptation of X49(T) to hypersaline environments. Due to
AB  - resistance to high salt concentrations, genome research of K. konosiri X49(T)
AB  - will contribute to the improvement of environmental and biotechnological usage by
AB  - enhancing understanding of the osmotic equilibrium in the cytoplasm. Its genome
AB  - consists of 3,584,631 bp, with an average G + C content of 59.1%, and 3261 coding
AB  - sequences, 12 rRNAs, 66 tRNAs, and 8 miscRNAs.
ER  -

TY  - JOUR
AU  - Yun, M.-S.
AU  - Bae, M.
TI  - Purification and characterization of a thermotolerable restriction endonuclease from Streptomyces violochromogenes D2-5.
JO  - Proc. Mol. Biol. and Genet.
PY  - 1993
SP  - 73
EP  - 74
VL  - 8
AB  - A thermotolerable restriction endonuclease, SviI, found from Streptomyces violochromogenes
AB  - D2-5 was purified.  The purified enzyme was homogeneous and the molecular weight of the
AB  - enzymes estimated by polyacrylamide gel electrophoresis containing 0.1% SDS was about 32,000
AB  - daltons.  The recognition sequence and cleavage site (indicated by a slash) of this enzyme
AB  - were determined to be 5'-TT/CGAA-3', the same sequence of AsuII.
ER  -

TY  - JOUR
AU  - Yun, M.-S.
AU  - Hwang, H.
AU  - Bae, M.
TI  - Purification and characterization of a thermotolerable restriction endonuclease from Streptomyces violochromogenes D2-5.
JO  - J. Microbiol. Biotechnol.
PY  - 1995
SP  - 269
EP  - 273
VL  - 5
AB  - A thermotolerable restriction endonuclease, SviI, found in Streptomyces violochromogenes D2-5
AB  - was purified.  For the purification, streptomycin sulfate and ammonium sulfate precipitation
AB  - was used.  Phosphocellulose P-11, DEAE-Cellulose and Sephacry1-S200 HR column chromatography
AB  - were also performed.  The purified enzyme was found to be homogeneous and the molecular weight
AB  - of the enzyme estimated by polyacrylamide gel electrophoresis containing 0.1% SDS was about
AB  - 32,000 daltons.  The recognition sequence and cleavage site of the enzyme were determined to
AB  - be 5M-U-TT/CGAA-3M-U which is the same sequence as that of AsuII.  Unlike AsuII, however, the
AB  - SviI shows high thermal stability.
ER  -

TY  - JOUR
AU  - Yun, M.R.
AU  - Han, S.J.
AU  - Yoo, W.G.
AU  - Kwon, T.
AU  - Lee, S.
AU  - Lee, J.S.
AU  - Kim, D.W.
TI  - Draft Genome Sequence of Mycobacterium tuberculosis KT-0204, Isolated in South Korea.
JO  - Genome Announcements
PY  - 2016
SP  - e01519
EP  - e01515
VL  - 4
AB  - Here, we describe the draft genome sequence of Mycobacterium tuberculosis KT-0204, non-Beijing
AB  - family. This sequence will reveal genes related to the
AB  - evolution and adaptation of M. tuberculosis KT-0204 in human hosts.
ER  -

TY  - JOUR
AU  - Yunes, R.A.
AU  - Klimina, K.M.
AU  - Emelyanov, K.V.
AU  - Zakharevich, N.V.
AU  - Poluektova, E.U.
AU  - Danilenko, V.N.
TI  - Draft Genome Sequences of Lactobacillus plantarum Strain 90sk and Lactobacillus brevis Strain 15f: Focusing on Neurotransmitter Genes.
JO  - Genome Announcements
PY  - 2015
SP  - e00261
EP  - e00215
VL  - 3
AB  - The genomes of Lactobacillus plantarum strain 90sk and Lactobacillus brevis strain 15f were
AB  - isolated from human intestinal microbiota. Both strains
AB  - synthesize gamma-aminobutyric acid (GABA), the major inhibitory neurotransmitter.
AB  - Detailed genome analyses will help to understand the role of GABA in the
AB  - interaction of bacteria with human intestinal cells.
ER  -

TY  - JOUR
AU  - Yung, P.Y.
AU  - Burke, C.
AU  - Lewis, M.
AU  - Egan, S.
AU  - Kjelleberg, S.
AU  - Thomas, T.
TI  - Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - e144
EP  - e144
VL  - 37
AB  - Metagenomics provides access to the uncultured majority of the microbial world. The approaches
AB  - employed in this field have, however, had limited success in linking functional genes to the
AB  - taxonomic or phylogenetic origin of the organism they belong to. Here we present an efficient
AB  - strategy to recover environmental DNA fragments that contain phylogenetic marker genes from
AB  - metagenomic libraries. Our method involves the cleavage of 23S ribsosmal RNA (rRNA) genes
AB  - within pooled library clones by the homing endonuclease I-CeuI followed by the insertion and
AB  - selection of an antibiotic resistance cassette. This approach was applied to screen a library
AB  - of 6500 fosmid clones derived from the microbial community associated with the sponge
AB  - Cymbastela concentrica. Several fosmid clones were recovered after the screen and detailed
AB  - phylogenetic and taxonomic assignment based on the rRNA gene showed that they belong to
AB  - previously unknown organisms. In addition, compositional features of these fosmid clones were
AB  - used to classify and taxonomically assign a dataset of environmental shotgun sequences. Our
AB  - approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA
AB  - sequencing information.
ER  -

TY  - JOUR
AU  - Yunusova, A.K.
AU  - Rogulin, E.A.
AU  - Artyukh, R.I.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Nickase and a protein encoded by an open reading frame downstream from the nickase BspD6I gene form a restriction endonuclease complex.
JO  - Biokhimiia
PY  - 2006
SP  - 1002
EP  - 1008
VL  - 71
AB  - We are the first to have isolated a protein (186 amino acid residues) encoded by the open
AB  - reading frame adjacent to the end of the BspD6I nickase (N.BspD6I) gene. Cleavage of both DNA
AB  - strands near the sequence recognized by nickase (5'-GAGTC/5'-GACTC) occurs when this protein
AB  - is added to the reaction mixture containing N.BspD6I. The protein encoded by the open reading
AB  - frame and the nickase are suggested to be subunits of heterodimeric restriction endonuclease
AB  - R.BspD6I.
ER  -

TY  - JOUR
AU  - Yussifov, T.N.
AU  - Zavilgelsky, G.B.
AU  - Delver, E.P.
AU  - Belogurov, A.A.
TI  - Plasmid pKM101ard+-mediated alleviation of EcoK restriction.  II. Cloning of ard gene.
JO  - Mol. Biol. (Mosk)
PY  - 1987
SP  - 847
EP  - 852
VL  - 21
AB  - Plasmid pKM101 affects the type I restriction by EcoK in E. coli.  The gene ard responsible
AB  - for alleviation of EcoK restriction was shown to be located within the BglIIB fragment of
AB  - pKM101.  Plasmid pD12 was constructed by introducing into pUC12 a 1.87 kb HindIII-Pst
AB  - fragment, carrying ard gene.  Tn5 and Tn1000 insertions were obtained in the ard gene region.
ER  -

TY  - JOUR
AU  - Zabaznaya, E.V.
AU  - Nikiforev, V.V.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease AbaI from Azospirillum brasilense UQ 1796 is an isoschizomer of endonuclease BclI.
JO  - Biokhimiia
PY  - 1997
SP  - 403
EP  - 410
VL  - 62
AB  - The site-specific endonuclease AbaI was isolated and purified to functional purity from the
AB  - soil nitrogen-fixing bacterium Azospirillum brasilense UQ 1796.  Purification included
AB  - successive chromatography on colums with phosphocellulose, heparin-Sepharose, and
AB  - hydroxyapatite.  The purified enzyme recognizes the palindromic DNA sequence 5'-T/GATCA-3'
AB  - and cleaves it as shown by the arrow.  The isolated enzyme belongs to class II restriction
AB  - endonucleases and is an isoschizomer of endonuclease BclI.  The enzyme AbaI is active at
AB  - 26-56oC.  The optimal temperature is 48oC and the optimal buffer is LRB.
ER  -

TY  - JOUR
AU  - Zabaznaya, E.V.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - Site-specific endonucleases RspLKI and RspLKII from Rhodococcus species LK2 are isoschizomers of SphI and BamHI.
JO  - Biokhimiia
PY  - 1997
SP  - 1018
EP  - 1028
VL  - 62
AB  - Two site-specific endonucleases, RspLKI and RspLKII, have been isolated and purified to
AB  - functional homogeneity from the soil bacterium Rhodococcus species LK2.  RspLKI recognizes the
AB  - 5'-GCATG/C-3' DNA sequence and RspLKII recognizes the 5'-G/GATCC-3' sequence (arrows
AB  - indicate DNA cleavage sites).  The isolated enzymes are class II site specific endonucleases
AB  - and are isoschizomers of endonucleases SphI and BamHI, respectively.
ER  -

TY  - JOUR
AU  - Zabaznaya, E.V.
AU  - Zheleznaya, L.A.
AU  - Svadbina, I.V.
AU  - Matvienko, N.I.
TI  - Site-specific endonuclease NspLKI is an isoschizomer of Endonuclease HaeIII.
JO  - Biokhimiia
PY  - 1999
SP  - 234
EP  - 238
VL  - 64
AB  - Site-specific endonuclease NspLKI has been isolated and purified to a functionally pure state
AB  - from soil bacterium Nocardia species LK by successive chromatography on columns with
AB  - phosphocellulose, HTP hydroxyapatite, and heparin-Sepharose.  The isolated enzyme recognizes
AB  - the 5'-GG/CC-3' sequence on DNA and cleaves it as indicated by the arrow, i.e., it is an
AB  - isoschizomer of HaeIII.  The final enzyme yield is 1.105 units per gram of wet biomass.  The
AB  - enzyme is active in the temperature range of 25-60 C with an optimum at 48-55 C; it does not
AB  - lose activity on storage for three days at room temperature.  An optimal buffer is HRB
AB  - containing 10 mM Tris-HCl, pH 7.4, 200 microgram/ml albumin, 10 mM MgCl2, and 100 mM NaCl.
ER  -

TY  - JOUR
AU  - Zabeau, M.
AU  - Friedman, S.
AU  - Van Montagu, M.
AU  - Schell, J.
TI  - The ral gene of phage lambda: I. Identification of a non-essential gene that modulates restriction and modification in E. coli.
JO  - Mol. Gen. Genet.
PY  - 1980
SP  - 63
EP  - 73
VL  - 179
AB  - Host controlled restriction in Escherichia coli can be relieved by
AB  - pre-infecting restricting cells with modified lambda helper phages.  This
AB  - process, in which intact unmodified phage genomes are allowed to escape
AB  - restriction attack, is mediated by a newly identified lambda function called
AB  - ral.  The ral gene has been located by deletion mapping between cIII and N.
AB  - Efficient expression of the ral gene requires the product of the regulator gene
AB  - N.  Polyacrylamide gel analysis of the lambda proteins specified by the cIII-N
AB  - region failed to reveal the product of the ral gene, but demonstrated that
AB  - protein Ea10 is encoded by a gene located immediately to the left of ral.  From
AB  - these results the map order cIII-Ea10-ral-TL1-N was deduced.  Ral specifically
AB  - alleviates restriction in E. coli K and E. coli B, but does not affect
AB  - restriction systems EcoRI, EcoRII and EcoP1.  In addition, ral enhances the
AB  - modification activity of the EcoK and EcoB restriction enzymes:  we observed
AB  - that efficient modification of progeny phages obtained by propagating
AB  - unmodified lambda phages in r-m+ hosts, is dependent upon the presence of ral.
AB  - We thus conclude that the ral gene product acts by modulating the restriction
AB  - and modification activities of the type I restriction systems in E. coli, and
AB  - the possible mechanisms will be discussed.
ER  -

TY  - JOUR
AU  - Zabeau, M.
AU  - Roberts, R.J.
TI  - The role of restriction endonucleases in molecular genetics.
JO  - Molecular Genetics
PY  - 1979
SP  - 1
EP  - 63
VL  - 3
AB  - This chapter will attempt to provide a summary of the general properties of
AB  - restriction enzymes and to describe their various applications in molecular
AB  - genetics.  Several earlier reviews have appeared (Arber, 1965, 1971, 1974;
AB  - Arber and Linn, 1969; Boyer, 1971; Meselson et al., 1972; Nathans and Smith,
AB  - 1975; Roberts, 1976).
ER  -

TY  - JOUR
AU  - Zabeau, M.
AU  - Schell, J.
AU  - Van Montagu, M.
TI  - The alleviation of host-controlled restriction of unmodified phages by functions of bacteriophage lambda.
JO  - Arch. Int. Physiol. Biochim.
PY  - 1973
SP  - 990
EP  - 990
VL  - 81
AB  - The host-controlled restriction of unmodified lambda phage in Escherichia coli
AB  - K12 and B hosts can be overcome either by co-infecting these cells with a
AB  - modified lambda phage, or by inducing a resident lambda prophage.  The
AB  - following lambda functions involved in this rescue process have been
AB  - characterised:  (1) a new lambda function ral (for:  Restriction Alleviation)
AB  - located between CIII and N.  (2) The non-essential lambda functions red, int
AB  - and gam.  The rescue of unmodified phage can proceed by two different
AB  - mechanisms:  (1) Whole genome rescue.  The lambda ral function was shown to be
AB  - able to rescue both unmodified lambda and unmodified heterologous phages P2 and
AB  - Pi.  The ral function probably interferes directly with the restriction
AB  - process, since rescue by ral can only be observed when the ral function is
AB  - expressed prior to infection with unmodified phage.  Furthermore preliminary
AB  - results indicate that the E. coli DNA polymerase I is involved in this rescue
AB  - process.  These results suggest that ral interferes with restriction by
AB  - directing some repair of the restricted DNA with the result that double strand
AB  - scissions do not occur.  2) Using threefactor crosses it was shown that
AB  - fragments of restricted DNA can be taken up in helper phage genomes by a
AB  - recombination process specifically directed by the lambda red function.  Since
AB  - the lambda gam function specifically inhibits the E. coli exonuclease V, we
AB  - investigated the role of this nuclease in the restriction process:  it was
AB  - shown that exoV is responsible for the secondary degradation of the restriction
AB  - DNA fragments.  This results in a loss of biological activity of the fragments
AB  - as measured by marker rescue and by complementation.
ER  -

TY  - JOUR
AU  - Zaburannyi, N.
AU  - Grosser, K.
AU  - Gasparoni, G.
AU  - Muller, R.
AU  - Schrallhammer, M.
AU  - Simon, M.
TI  - Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis, Causative Agent of the Killer Phenotype in Paramecium  tetraurelia.
JO  - Genome Announcements
PY  - 2018
SP  - e01418
EP  - e01417
VL  - 6
AB  - Caedibacter taeniospiralis is an obligate endosymbiont living in the cytoplasm of Paramecium
AB  - tetraureliaC. taeniospiralis causes the so-called killer trait,
AB  - eliminating intraspecific competitors of its host when released into the medium
AB  - by the concerted action of the unusual protein structure R-body (refractile body)
AB  - in addition to an as-yet-unknown toxin.
ER  -

TY  - JOUR
AU  - Zaburannyi, N.
AU  - Rabyk, M.
AU  - Ostash, B.
AU  - Fedorenko, V.
AU  - Luzhetskyy, A.
TI  - Insights into naturally minimised Streptomyces albus J1074 genome.
JO  - BMC Genomics
PY  - 2014
SP  - 11
EP  - 11
VL  - 15
AB  - Background: The Streptomyces albus J1074 strain is one of the most widely used chassis for the
AB  - heterologous production of bioactive natural products. The fast growth and an efficient
AB  - genetic system make this strain an attractive model for expressing cryptic biosynthetic
AB  - pathways to aid drug discovery.Results: To improve its capabilities for the heterologous
AB  - expression of biosynthetic gene clusters, the complete genomic sequence of S. albus J1074 was
AB  - obtained. With a size of 6,841,649 bp, coding for 5,832 genes, its genome is the smallest
AB  - within the genus streptomycetes. Genome analysis revealed a strong tendency to reduce the
AB  - number of genetic duplicates. The whole transcriptomes were sequenced at different time points
AB  - to identify the early metabolic switch from the exponential to the stationary phase in S.
AB  - albus J1074.Conclusions: S. albus J1074 carries the smallest genome among the completely
AB  - sequenced species of the genus Streptomyces. The detailed genome and transcriptome analysis
AB  - discloses its capability to serve as a premium host for the heterologous production of natural
AB  - products. Moreover, the genome revealed 22 additional putative secondary metabolite gene
AB  - clusters that reinforce the strain's potential for natural product synthesis.
ER  -

TY  - JOUR
AU  - Zacharias, W.
AU  - Larson, J.E.
AU  - Kilpatrick, M.W.
AU  - Wells, R.D.
TI  - HhaI methylase and restriction endonuclease as probes for B to Z DNA conformational changes in d(GCGC) sequences.
JO  - Nucleic Acids Res.
PY  - 1984
SP  - 7677
EP  - 7692
VL  - 12
AB  - The capacity of the modification methylase (MHhaI) and restriction endonuclease
AB  - (HhaI) from Haemophilus haemolyticus to methylate and cleave, respectively,
AB  - recognition sites which are in right-handed B or left-handed Z structures was
AB  - determined in vitro.  Plasmids containing tracts of (dC-dG) as well as numerous
AB  - individual d(GCGC) sites distributed around the vector were studied.  Negative
AB  - supercoiling was used to convert the (dC-dG) tracts (~ 30 bp in length) from a
AB  - right-handed to a left-handed conformation.  (Methyl-3H)-SAM was used to
AB  - localize and quantitate modified d(GCGC) recognition sites, whereas cleavage by
AB  - HhaI was used to detect unmethylated sites.  In the left-handed Z-form, the
AB  - (dC-dG) blocks were not methylated by MHhaI and not cleaved by Hha.  A
AB  - two-dimensional gel analysis of a family of 33 topoisomers treated with MHhaI
AB  - revealed that the lack of methylation in the (dC-dG) blocks was directly
AB  - correlated to the supercoil-induced B to Z transition in these segments.  These
AB  - results are significant with respect to enzyme-DNA interactions in general and
AB  - provide the basis for using HhaI and MHhaI as probes for different DNA
AB  - structures and conformational transitions under physiological conditions.
ER  -

TY  - JOUR
AU  - Zacharias, W.
AU  - O'Connor, T.R.
AU  - Larson, J.E.
TI  - Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and B-Z junctions.
JO  - Biochemistry
PY  - 1988
SP  - 2970
EP  - 2978
VL  - 27
AB  - The structural and energetic consequences of cytosine methylation in the
AB  - 5-position on the supercoil-dependent B-Z equilibrium in alternating dC-dG
AB  - sequences cloned into recombinant plasmids were investigated.  The helical
AB  - parameters determined with the band shift method for right-handed [10.7 base
AB  - pairs (bp)/turn] and left-handed (12.8 bp/turn) 5MedC-dG inserts were different
AB  - from the helical repeat values for unmethylated dC-dG inserts (10.5 bp/turn in
AB  - the right-handed and 11.5 bp/turn in the left-handed form).  We analyzed the
AB  - thermodynamic parameters DeltaGBZ (free energy difference per base pair between
AB  - right-handed and left-handed helix structure), DeltaGjx (free energy for
AB  - formation of one B-Z junction), and b (helix unwinding at a junction region)
AB  - for varying lengths of dC-dG inserts by two-dimensional gel electrophoresis and
AB  - application of a statistical mechanics model.  A comparison of plasmids fully
AB  - methylated in vitro with HhaI methylase and their unmethylated counterparts
AB  - revealed that DeltaGjx is not significantly changed by cytosine methylation.
AB  - However, this base modification results in an approximate 3-fold decrease of
AB  - DeltaGBZ and an approximate 2-fold decrease of the unwinding b at B-Z junction
AB  - regions.  Analysis of a pair of related plasmids, each containing two dC-dG
AB  - blocks, revealed qualitatively different transition behaviors.  When the two
AB  - dC-dG blocks were separated by 95 bp of a mixed sequence, they underwent
AB  - independent B to Z transitions with separate nucleation events and junction
AB  - formations.  When the two blocks were separated by only a 4 bp GATC sequence,
AB  - only one nucleation event was necesary, and the Z-helix spread across the
AB  - nonalternating GATC region.  These structural and energetic alterations
AB  - demonstrate that methylation of cytosine in the 5-position may be an important
AB  - switch mechanism for influencing the B-Z equilibrium and DNA topology in
AB  - general, thus potentially affecting DNA-protein interactions and gene
AB  - regulation at physiological levels of DNA supercoiling.
ER  -

TY  - JOUR
AU  - Zachow, C.
AU  - Muller, H.
AU  - Laireiter, C.M.
AU  - Tilcher, R.
AU  - Berg, G.
TI  - Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 66
EP  - 66
VL  - 12
AB  - 10.1601/nm.2592 strain RM1-1-4 is a rhizosphere colonizer of oilseed rape. A previous study
AB  - has shown that this motile, Gram-negative, non-sporulating
AB  - bacterium is an effective stress protecting and biocontrol agent, which protects
AB  - their hosts against abiotic and biotic stresses. Here, we announce and describe
AB  - the complete genome sequence of P. corrugata RM1-1-4 consisting of a single 6.1
AB  - Mb circular chromosome that encodes 5189 protein coding genes and 85 RNA-only
AB  - encoding genes. Genome analysis revealed genes predicting functions such as
AB  - detoxifying mechanisms, stress inhibitors, exoproteases, lipoproteins or volatile
AB  - components as well as rhizobactin siderophores and spermidine. Further analysis
AB  - of its genome will help to identify traits promising for stress protection,
AB  - biocontrol and plant growth promotion properties.
ER  -

TY  - JOUR
AU  - Zachow, C.
AU  - Muller, H.
AU  - Monk, J.
AU  - Berg, G.
TI  - Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato.
JO  - Standards in Genomic Sciences
PY  - 2017
SP  - 6
EP  - 6
VL  - 12
AB  - Pseudomonas brassicacearum strain L13-6-12 is a rhizosphere colonizer of potato,  lettuce and
AB  - sugar beet. Previous studies have shown that this motile,
AB  - Gram-negative, non-sporulating bacterium is an effective biocontrol agent against
AB  - different phytopathogens. Here, we announce and describe the complete genome
AB  - sequence of P. brassicacearum L13-6-12 consisting of a single 6.7 Mb circular
AB  - chromosome that consists of 5773 protein coding genes and 85 RNA-only encoding
AB  - genes. Genome analysis revealed genes encoding specialized functions for pathogen
AB  - suppression, thriving in the rhizosphere and interacting with eukaryotic
AB  - organisms.
ER  -

TY  - JOUR
AU  - Zagorskaite, E.
AU  - Manakova, E.
AU  - Sasnauskas, G.
TI  - Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
JO  - FEBS Lett.
PY  - 2018
SP  - 3335
EP  - 3345
VL  - 592
AB  - Cytosine modifications expand the information content of genomic DNA in both eukaryotes and
AB  - prokaryotes, providing means for epigenetic regulation and self
AB  - versus nonself discrimination. For example, the methyl-directed restriction
AB  - endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing
AB  - 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine
AB  - (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal
AB  - structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine
AB  - (5fC), and 4mC, and characterize the relative affinity of McrB-N to various
AB  - cytosine variants. We find that McrB-N flips out modified bases into a protein
AB  - pocket and binds cytosine derivatives in the order of descending affinity: 4mC >
AB  - 5mC > 5hmC >> 5fC. We also show that pocket mutations alter the relative
AB  - preference of McrB-N to 5mC, 5hmC, and 4mC.
ER  -

TY  - JOUR
AU  - Zagorskaite, E.
AU  - Sasnauskas, G.
TI  - Chemical Display of Pyrimidine Bases Flipped Out by Modification-Dependent Restriction Endonucleases of MspJI and PvuRts1I Families.
JO  - PLoS ONE
PY  - 2014
SP  - e114580
EP  - e114580
VL  - 9
AB  - The epigenetic DNA modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in
AB  - eukaryotes are recognized either in the context of double-stranded DNA (e.g., by the
AB  - methyl-CpG binding domain of MeCP2), or in the flipped-out state (e.g., by the SRA domain of
AB  - UHRF1). The SRA-like domains and the base-flipping mechanism for 5(h)mC recognition are also
AB  - shared by the recently discovered prokaryotic modification-dependent endonucleases of the
AB  - MspJI and PvuRts1I families. Since the mechanism of modified cytosine recognition by many
AB  - potential eukaryotic and prokaryotic 5(h) mC 'readers' is still unknown, a fast solution
AB  - based method for the detection of extrahelical 5(h) mC would be very useful. In the present
AB  - study we tested base-flipping by MspJI- and PvuRts1I-like restriction enzymes using several
AB  - solution-based methods, including fluorescence measurements of the cytosine analog
AB  - pyrrolocytosine and chemical modification of extrahelical pyrimidines with chloroacetaldehyde
AB  - and KMnO4. We find that only KMnO4 proved an efficient probe for the positive display of
AB  - flipped out pyrimidines, albeit the method required either non-physiological pH (4.3) or a
AB  - substitution of the target cytosine with thymine. Our results imply that DNA recognition
AB  - mechanism of 5(h) mC binding proteins should be tested using a combination of all available
AB  - methods, as the lack of a positive signal in some assays does not exclude the base flipping
AB  - mechanism.
ER  -

TY  - JOUR
AU  - Zahidi, J.M.
AU  - Ahmad, N.
AU  - Tay, B.Y.
AU  - Hashim, R.
AU  - Khoo, E.
AU  - Ahmad, N.
AU  - Yee, C.Y.
AU  - Dolhan, N.Q.
TI  - Genome Sequences of Brucella melitensis, Isolated from Blood Samples of Brucellosis Patients in Malaysia.
JO  - Genome Announcements
PY  - 2017
SP  - e00689
EP  - e00617
VL  - 5
AB  - Human brucellosis is a neglected zoonotic disease and has widespread geographical
AB  - distribution. Brucella melitensis has caused outbreaks and sporadic cases in Malaysia. Here,
AB  - we present the whole-genome sequences of four B. melitensis strains isolated from brucellosis
AB  - patients in Malaysia.
ER  -

TY  - JOUR
AU  - Zahner, V.
AU  - Priest, F.G.
TI  - Distribution of restriction nucleases among some entomopathogenic strains of Bacillus sphaericus.
JO  - Lett. Appl. Microbiol.
PY  - 1997
SP  - 483
EP  - 487
VL  - 24
AB  - The restriction enzyme BspTI, an isoschizomer of HaeIII (recognition site GGCC), has been
AB  - detected in eight strains of serotype 5a5b and two serotype 3 strains of the entomopathogenic
AB  - bacterium Bacillus sphaericus.  Strains from other serotypes contained the enzymes BspTII and
AB  - BspTIII, which digested pBR322 DNA into similar banding patterns after agarose gel
AB  - electrophoresis but differed in their susceptibility to methylation of the substrate.  Strains
AB  - from serotypes 9, 25 and 26a26b were lacking in restriction enzyme activity.  There was little
AB  - correlation between phage typing and restriction enzyme activity, suggesting that restriction
AB  - and modification are not responsible for phage specificity among entomopathogenic B.
AB  - sphaericus strains.
ER  -

TY  - JOUR
AU  - Zahradnik, J.
AU  - Kyslikova, E.
AU  - Kyslik, P.
TI  - Draft Genome Sequence of Agrobacterium sp. Strain R89-1, a Morphine Alkaloid-Biotransforming Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00196
EP  - e00116
VL  - 4
AB  - Agrobacteriumsp. strain R89-1 isolated from composted wastes ofPapaver somniferumcan
AB  - effectively biotransform codeine/morphine into 14-OH-derivatives.
AB  - Here, we present a 4.7-Mb assembly of the R89-1 strain genome. The draft shows
AB  - that the strain R89-1 represents a distinct phylogenetic lineage within the
AB  - genusAgrobacterium.
ER  -

TY  - JOUR
AU  - Zahradnik, J.
AU  - Plackova, M.
AU  - Palyzova, A.
AU  - Maresova, H.
AU  - Kyslikova, E.
AU  - Kyslik, P.
TI  - Draft Genome Sequence of Pantoea agglomerans JM1, a Strain Isolated from Soil Polluted by Industrial Production of Beta-Lactam Antibiotics That Exhibits  Valacyclovir-Like Hydrolase Activity.
JO  - Genome Announcements
PY  - 2017
SP  - e00921
EP  - e00917
VL  - 5
AB  - Strain Pantoea agglomerans JM1 was isolated from the soil of a microbiome that had been
AB  - exposed to polluting pharmaceuticals. The bacterium exhibited enzymatic
AB  - activities useful for the biotransformation of beta-lactams. The genome of the
AB  - strain was assembled and described, and the gene encoding valacyclovir-like
AB  - hydrolase was identified.
ER  -

TY  - JOUR
AU  - Zahran, M.
AU  - Berezniak, T.
AU  - Imhof, P.
AU  - Smith, J.C.
TI  - Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease.
JO  - FEBS Lett.
PY  - 2011
SP  - 2739
EP  - 2743
VL  - 585
AB  - The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg-A(2+),
AB  - binds to the phosphate group where the cleavage
AB  - occurs and is required for catalysis, but the role of the other ion,
AB  - Mg-B(2+) is debated. Here, multiple independent molecular dynamics
AB  - simulations suggest that Mg-B(2+) is crucial for achieving a tightly
AB  - bound protein-DNA complex and stabilizing a conformation that allows
AB  - cleavage. In the absence of Mg-B(2+) in all simulations the protein-DNA
AB  - hydrogen bond network is significantly disrupted and the sharp kink at
AB  - the central base pair step of the DNA, which is observed in the
AB  - two-metal complex, is not present. Also, the active site residues
AB  - rearrange in such a way that the formation of a nucleophile, required
AB  - for DNA hydrolysis, is unlikely.
ER  -

TY  - JOUR
AU  - Zahran, M.
AU  - Daidone, I.
AU  - Smith, J.C.
AU  - Imhof, P.
TI  - Mechanism of DNA Recognition by the Restriction Enzyme EcoRV.
JO  - J. Mol. Biol.
PY  - 2010
SP  - 415
EP  - 432
VL  - 401
AB  - EcoRV, a restriction enzyme in Escherichia coli, destroys invading foreign DNA by cleaving it
AB  - at the center step of a GATATC sequence. In the EcoRV-cognate DNA crystallographic complex, a
AB  - sharp kink of 50 degrees has been found at the center base-pair step (TA). Here, we examine
AB  - the interplay between the intrinsic propensity of the cognate sequence to kink and the
AB  - induction by the enzyme by performing all-atom molecular dynamics simulations of EcoRV unbound
AB  - and interacting with three DNA sequences: the cognate sequence, GATATC (TA); the non-cognate
AB  - sequence, GAATTC (AT); and with the cognate sequence methylated on the first adenine
AB  - GA(CH(3))TATC (TA-CH(3)). In the unbound EcoRV, the cleft between the two C-terminal
AB  - subdomains is found to be open. Binding to AT narrows the cleft and forms a partially bound
AB  - state. However, the intrinsic bending propensity of AT is insufficient to allow tight binding.
AB  - In contrast, the cognate TA sequence is easier to bend, allowing specific, high-occupancy
AB  - hydrogen bonds to form in the complex. The absence of cleavage for this methylated sequence is
AB  - found to arise from the loss of specific hydrogen bonds between the first adenine of the
AB  - recognition sequence and Asn185. On the basis of the results, we suggest a three-step
AB  - recognition mechanism. In the first step, EcoRV, in an open conformation, binds to the DNA at
AB  - a random sequence and slides along it. In the second step, when the two outer base pairs,
AB  - GAxxTC, are recognized, the R loops of the protein become more ordered, forming strong
AB  - hydrogen-bonding interactions, resulting in a partially bound EcoRV-DNA complex. In the third
AB  - step, the flexibility of the center base pair is probed, and in the case of the full cognate
AB  - sequence the DNA bends, the complex strengthens and the protein and DNA interact more closely,
AB  - allowing cleavage.
ER  -

TY  - JOUR
AU  - Zain, B.S.
AU  - Roberts, R.J.
TI  - A new specific endonuclease from Xanthomonas badrii.
JO  - J. Mol. Biol.
PY  - 1977
SP  - 249
EP  - 255
VL  - 115
AB  - A restriction-like endonuclease, XbaI, has been partially purified from
AB  - Xanthomonas badrii.  This enzyme cleaves adenovirus-2 DNA at four sites,
AB  - bacteriophage lambda DNA at only one site, and does not cleave simian virus 40
AB  - DNA.  It recognizes the sequence 5'-T^-C-T-A-G-A-3' 3'-A-G-A-T-C^-T-5' and cuts
AB  - at the sites indicated by the arrows.
ER  -

TY  - JOUR
AU  - Zakharevich, N.V.
AU  - Averina, O.V.
AU  - Klimina, K.M.
AU  - Kudryavtseva, A.V.
AU  - Kasianov, A.S.
AU  - Makeev, V.J.
AU  - Danilenko, V.N.
TI  - Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains.
JO  - Genome Announcements
PY  - 2014
SP  - e01348
EP  - e01314
VL  - 2
AB  - In this study, we report the first completely annotated genome sequence of the Russian-origin
AB  - Bifidobacterium longum subsp. longum strain GT15. We discovered 35
AB  - unique genes (UGs) which were detected from only the B. longum GT15 genome and
AB  - were absent from other B. longum strain genomes (not of Russian origin).
ER  -

TY  - JOUR
AU  - Zakharova, M.
AU  - Minakhin, L.
AU  - Solonin, A.
AU  - Severinov, K.
TI  - Regulation of RNA polymerase promoter selectivity by covalent modification of DNA.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 103
EP  - 111
VL  - 335
AB  - Expression of genes encoding type II restriction/modification (R/M) systems, which are widely
AB  - spread in eubacteria, must be tightly
AB  - regulated to ensure that host DNA is protected from restriction
AB  - endonucleases at all times. Examples of coordinated expression of R/M
AB  - genes that rely on the action of regulatory factors or the ability of
AB  - methyl transferases to repress their own synthesis by interacting with
AB  - the promoter DNA have been described. Here, we characterize the
AB  - molecular mechanism of factor-independent regulation in the CfrBI R/M
AB  - system. Regulation of the cfrBIM gene transcription occurs through CfrBIM-catalyzed
AB  - methylation of a cytosine residue in the cfrBIM
AB  - promoter. The covalent modification inhibits cfrBIM promoter complex
AB  - formation by interfering with the RNA polymerase sigma(70) subunit
AB  - region 4.2 recognition of the - 35 promoter element. The decrease in
AB  - the cfrBIM promoter complex formation leads to increase in the
AB  - activity of overlapping cfrBIR promoters. This elegant
AB  - factor-independent regulatory system ensures coordinated expression of
AB  - the cfrBI genes.
ER  -

TY  - JOUR
AU  - Zakharova, M.V.
AU  - Beletskaya, I.V.
AU  - Denjmukhametov, M.M.
AU  - Yurkova, T.V.
AU  - Semenova, L.M.
AU  - Shlyapnikov, M.G.
AU  - Solonin, A.S.
TI  - Characterization of pECL18 and pKPN2: a proposed pathway for the evolution of two plasmids that carry identical genes for a Type II restriction-modification system.
JO  - Mol. Genet. Genomics
PY  - 2002
SP  - 171
EP  - 178
VL  - 267
AB  - The primary structures of the plasmids pECL18 (5571 bp) and pKPN2 (4196 bp) from Escherichia
AB  - coli and Klebsiella pneumoniae, respectively, which carry genes for a Type II
AB  - restriction-modification system (RMS2) with the specificity 5'-CCNGG-3', were determined in
AB  - order to elucidate the structural relationship between them. The data suggest a possible role
AB  - for recombination events at bom (basis of mobility) regions and the sites of resolution of
AB  - multimer plasmid forms (so-called cer sequences) in the structural evolution of multicopy
AB  - plasmids. Analysis of the sequences of pECL18 and pKPN2 showed that the genes for RM(.)
AB  - Ecl18kI and RM(.) Kpn2kI, and the sequences of the rep (replication) regions in the two
AB  - plasmids, are almost identical. In both plasmids, these regions are localized between the bom
AB  - regions and the cer sites. The rest of the pECL18 sequence is almost identical to that of the
AB  - mob (mobilization) region of ColE1, and the corresponding segment of pKPN2 is almost identical
AB  - to part of pHS-2 from Shigella flexneri. The difference in primary structures results in
AB  - different mobilization properties of pECL18 and pKPN2. The complete sequences of pECL18, pKPN2
AB  - and the pairwise comparison of the sequences of pECL18, pKPN2, ColE1 and pHS-2 suggest that
AB  - plasmids may exchange DNA units via site-specific recombination events at bom and cer sites.
AB  - In the course of BLASTN database searches using the cer sites of pECL18 and pKPN2 as queries,
AB  - we found twenty cer sites of natural plasmids. Alignment of these sequences reveals that they
AB  - fall into two classes. The plasmids in each group possess related segments between their cer
AB  - and bom sites.
ER  -

TY  - JOUR
AU  - Zakharova, M.V.
AU  - Beletskaya, I.V.
AU  - Kravetz, A.N.
AU  - Pertzev, A.V.
AU  - Mayorov, S.G.
AU  - Shlyapnikov, M.G.
AU  - Solonin, A.S.
TI  - Cloning and sequence anlaysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes.
JO  - Gene
PY  - 1998
SP  - 177
EP  - 182
VL  - 208
AB  - The Eco29kI restriction-modification system has been found to be localized on the plasmid
AB  - pECO29 occurring naturally in the Escherichia coli strain 29k.  Eco29kI, a novel plasmid
AB  - encoded restriction endonuclease from Escherichia coli.  The genes coding for this RMS2, a
AB  - SacII isoschizomer recognizing the sequence CCGCGG have been cloned in Escherichia coli K802
AB  - and sequenced.  The DNA sequence predicts the restriction endonuclease of 214 amino acids
AB  - (24,556 Da) and the DNA-methyltransferase of 382 aa (43,007 Da) where the genes are separated
AB  - by 2 bp and arranged in tandem with eco29kIR preceding eco29kIM.  The recombinant plasmid with
AB  - eco29kIR produces a protein of expected size.  MEco29kI contains all the conserved aa sequence
AB  - motifs characteristic of m5C-MTases.  Remarkably, its variable region exhibits a significant
AB  - similarity to the part of the specific target-recognition domain from M.BssHII-multispecific
AB  - m5C-MTase, which recognizes five different sites on DNA (HaeII, MluI, Cfr10I, SacII and
AB  - BssHII), and the comparison of the nt sequences of its variable regions  allowed us to
AB  - determine the putative TRD of M.Eco29kI.
ER  -

TY  - JOUR
AU  - Zakharova, M.V.
AU  - Kravets, A.N.
AU  - Klimashina, N.V.
AU  - Solonin, A.S.
TI  - Properties of the replicator region of natural plasmid pLG13 carrying genes of the EcoRV restriction-modification system.
JO  - Mol. Biol. (Mosk)
PY  - 1991
SP  - 1615
EP  - 1625
VL  - 25
AB  - The previously constructed plasmid pILRV8 that induces endonuclease EcoRV gene
AB  - overexpression kills cells of some E. coli strains under the induction of this
AB  - enzyme synthesis.  Cell transformation by natural plasmid pLG13 carrying genes
AB  - of the EcoRV restriction-modification system was found to appreciably enhance
AB  - cell viability (survival) under endonuclease overproduction.  A plasmid pLG13
AB  - region located in immediate proximity to the methylase gene was shown to be
AB  - responsible for the above effect.  This region was also capable of autonomous
AB  - replication.  The analysis of the DNA primary structure in the found replicator
AB  - region allowed to refer the pLG13 to ColE1 family plasmids.  Perturbations in
AB  - the region lead to loss of the survival effect and change of the plasmid
AB  - replicative properties.  A relationship between the replicon elements, the
AB  - EcoRV genes region and survival effect is discussed.  Based on the replicon
AB  - found multicopy vector molecules have been constructed.
ER  -

TY  - JOUR
AU  - Zakharova, M.V.
AU  - Kravetz, A.N.
AU  - Beletzkaja, I.V.
AU  - Repyk, A.V.
AU  - Solonin, A.S.
TI  - Cloning and sequences of the genes encoding the CfrBI restriction-modification system from Citrobacter freundii.
JO  - Gene
PY  - 1993
SP  - 77
EP  - 81
VL  - 129
AB  - The genes encoding the CfrBI restriction and modification (R-M) systems from Citrobacter
AB  - freundii and recognizing the sequences 5'-CCWWGG-3' (W=A or T) were cloned in Escherichia
AB  - coli McrBC- cells. The nucleotide (nt) sequences of the genes were determined. Two large open
AB  - reading frames were found. Deletion analysis showed that one of them [1128 nt coding for 376
AB  - amino acids (aa)] corresponds to a methyltransferase (MTase)-encoding gene and the other (1065
AB  - nt coding for 355 aa) to a restriction endonuclese-encoding gene. The genes are oriented
AB  - divergently and separated by 76 bp. A CfrBI site (5'-m4CCATGG) was found in the intergenic
AB  - region of the cfrBIRM genes. Analysis of the deduced aa sequence of M.CfrBI made it possible
AB  - to determine the typical features of a m4C-specific MTase. Limited homology between the
AB  - M.CfrBI and R.CfrBI proteins was also found.
ER  -

TY  - JOUR
AU  - Zakharova, M.V.
AU  - Pertzev, A.V.
AU  - Kravetz, A.N.
AU  - Beletskaya, I.V.
AU  - Shlyapnikov, M.G.
AU  - Solonin, A.S.
TI  - Complete nucleotide sequence of the Hsd plasmid pECO29 and identification of its functional regions.
JO  - Biochim. Biophys. Acta
PY  - 1998
SP  - 106
EP  - 112
VL  - 1398
AB  - The complete nucleotide sequence of the Hsd plasmid pECO29 has been determined.  The plasmid
AB  - DNA consists of 3895 base pairs.  These include 4 genes and 5 sites.  Two genes encoding the
AB  - proteins (restriction endonuclease and DNA methyltransferase) have been fully characterized.
AB  - The pECO29 comprises a ColE1-type replication system coding for untranslated genes RNAI and
AB  - RNAII, the emr recombination site containing palindromic sequences and involved in stable
AB  - maintenance of the plasmid, two pseudo oriT sites homologous to the oriT site of R64 and F
AB  - plasmids, as well as the bom locus of a ColE1-like plasmid.  There are no genes involved in
AB  - the mobilization of pECO29 plasmid.
ER  -

TY  - JOUR
AU  - Zaleski, P.
AU  - Piekarowicz, A.
TI  - Characterization of a dam mutant of Haemophilus influenzae Rd.
JO  - Microbiology
PY  - 2004
SP  - 3773
EP  - 3781
VL  - 150
AB  - The gene encoding Dam methyltransferase of Haemophilus influenzae was mutagenized by the
AB  - insertion of a chloramphenicol-resistance cassette into the middle of the Dam coding sequence.
AB  - This mutant construct was introduced into the H. influenzae chromosome by transformation and
AB  - selection for Cam(R) transformants. The authors have shown that several phenotypic properties,
AB  - resistance to antibiotics, dyes and detergent as well as efficiency of transformation, depend
AB  - on the Dam methylation state of the DNA. Although the major role of the methyl-directed
AB  - mismatch repair (MMR) system is to repair postreplicative errors, it seems that in H.
AB  - influenzae its effect is more apparent in repairing DNA damage caused by oxidative compounds.
AB  - In the dam mutant treated with hydrogen peroxide, MMR is not targeted to newly replicated DNA
AB  - strands and therefore mismatches are converted into single- and double-strand DNA breaks. This
AB  - is shown by the increased peroxide sensitivity of the dam mutant and the finding that the
AB  - sensitivity can be suppressed by a mutH mutation inactivating MMR. In the dam mutant treated
AB  - with nitrofurazone the resulting damage is not converted into DNA breaks but the high
AB  - sensitivity is also suppressed by a mutH mutation.
ER  -

TY  - JOUR
AU  - Zaleski, P.
AU  - Wojciechowski, M.
AU  - Piekarowicz, A.
TI  - The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection.
JO  - Microbiology
PY  - 2005
SP  - 3361
EP  - 3369
VL  - 151
AB  - Haemophilus influenzae uses phase variation (PV) to modulate the activity of its defence
AB  - systems against phage infection. The PV of the
AB  - restriction-modification (R-M) system Hindl, the main defence system
AB  - against phage infection and incoming chromosomal and phage DNA in H.
AB  - influenzae Rd, is driven by changes of the pentanucleoticle repeat
AB  - tract within the coding sequence of the hsdM gene and is influenced by
AB  - lack of Dam methylation. Phase-variable resistance/sensitivity to phage
AB  - infection correlates with changes in lipooligosaccharide (LOS)
AB  - structure and occurs by slippage of tetranucleotide repeats within the
AB  - gene lic2A, coding for a step in the biosynthesis of LOS. The lack of
AB  - Dam activity destabilizes the tetranuclotide (5'-CAAT) repeat tract and
AB  - increases the frequency of switching from sensitivity to resistance to
AB  - phage infection more than in the opposite direction. The PV of the lgtC
AB  - gene does not influence resistance or sensitivity to phage infection.
AB  - Insertional inactivation of lic2A, but not lgtC or lgtF, leads to
AB  - resistance to phage infection and to the same structure of the LOS as
AB  - observed among phase-variable phage-resistant variants. This indicates
AB  - that in the H. influenzae Rd LOS only the first two sugars (Glc-Gal)
AB  - extending from the third heptose are part of bacterial phage receptors.
ER  -

TY  - JOUR
AU  - Zamorano, A.
AU  - Fiore, N.
TI  - Draft Genome Sequence of 16SrIII-J Phytoplasma, a Plant Pathogenic Bacterium with a Broad Spectrum of Hosts.
JO  - Genome Announcements
PY  - 2016
SP  - e00602
EP  - e00616
VL  - 4
AB  - Phytoplasmas are bacterial plant pathogens that can affect different vegetal hosts. In South
AB  - America, a phytoplasma belonging to ribosomal subgroup 16SrIII-J  has been reported in many
AB  - crops. Here we report its genomic draft sequence, showing a total length of 687,253 bp and a
AB  - G+C content of 27.72%.
ER  -

TY  - JOUR
AU  - Zan, J.
AU  - Fricke, W.F.
AU  - Fuqua, C.
AU  - Ravel, J.
AU  - Hill, R.
TI  - Genome Sequence of Ruegeria sp. strain KLH11, an N-Acylhomoserine Lactone-Producing Bacterium Isolated from the Marine Sponge Mycale  laxissima.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5011
EP  - 5012
VL  - 193
AB  - Ruegeria sp. KLH1, isolated from marine sponge Mycale laxissima, produces a complex profile of
AB  - N-acylhomoserine lactone quorum sensing (QS)
AB  - molecules. The genome sequence provides insights into the genetic
AB  - potential of KLH11 to maintain complex QS systems and is the first genome
AB  - report of a cultivated symbiont from a marine sponge.
ER  -

TY  - JOUR
AU  - Zangi, R.
AU  - Arrieta, A.
AU  - Cossio, F.P.
TI  - Mechanism of DNA Methylation: The Double Role of DNA as a Substrate and as a Cofactor.
JO  - J. Mol. Biol.
PY  - 2010
SP  - 632
EP  - 644
VL  - 400
AB  - Methylation of cytosine residues in the DNA is one of the most important epigenetic marks
AB  - central to the control of differential expression of
AB  - genes. We perform quantum mechanical calculations to investigate the
AB  - catalytic mechanism of the bacterial HhaI DNA methyltransferase. We find
AB  - that the enzyme nucleophile, Cys81, can attack C6 of cytosine only after
AB  - it is deprotonated by the DNA phosphate group, a reaction facilitated by a
AB  - bridging water molecule. This finding, which indicates that the DNA acts
AB  - as both the substrate and the cofactor, can explain the total loss of
AB  - activity observed in an analogous enzyme, thymidylate synthase, when the
AB  - phosphate group of the substrate was removed. Furthermore, our results
AB  - displaying the inability of the phosphate group to deprotonate the side
AB  - chain of serine is in agreement with the total, or the large extent of,
AB  - inactivity observed for the C81S mutant. In contrast to results from
AB  - previous calculations, we find that the active site conserved residues,
AB  - Glu119, Arg163, and Arg165, are crucial for catalysis. In addition, the
AB  - enzyme-DNA adduct formation and the methyl transfer from the cofactor
AB  - S-adenosyl-l-methionine are not concerted but proceed via stepwise
AB  - mechanism. In many of the different steps of this methylation reaction,
AB  - the transfer of a proton is found to be necessary. To render these
AB  - processes possible, we find that several water molecules, found in the
AB  - crystal structure, play an important role, acting as a bridge between the
AB  - donating and accepting proton groups.
ER  -

TY  - JOUR
AU  - Zarate, M.A.
AU  - Rodriguez, M.D.
AU  - Chang, E.I.
AU  - Russell, J.T.
AU  - Arndt, T.J.
AU  - Richards, E.M.
AU  - Ocasio, B.A.
AU  - Aranda, E.
AU  - Gordon, E.M.
AU  - Yu, K.
AU  - Neu, J.
AU  - Keller-Wood, M.
AU  - Triplett, E.W.
AU  - Wood, C.E.
TI  - Post-hypoxia Invasion of the fetal brain by multidrug resistant Staphylococcus.
JO  - Sci. Rep.
PY  - 2017
SP  - 6458
EP  - 6458
VL  - 7
AB  - Herein we describe an association between activation of inflammatory pathways
AB  - following transient hypoxia and the appearance of the multidrug resistant
AB  - bacteria Staphylococcus simulans in the fetal brain. Reduction of maternal
AB  - arterial oxygen tension by 50% over 30 min resulted in a subseiuent significant
AB  - over-expression of genes associated with immune responses 24 h later in the fetal
AB  - brain. The activated genes were consistent with stimulation by bacterial
AB  - lipopolysaccharide; an influx of macrophages and appearance of live bacteria were
AB  - found in these fetal brains. S. simulans was the predominant bacterial species in
AB  - fetal brain after hypoxia, but was found in placenta of all animals. Strains of
AB  - S. simulans from the placenta and fetal brain were equally highly resistant to
AB  - multiple antibiotics including methicillin and had identical genome sequences.
AB  - These results suggest that bacteria from the placenta invade the fetal brain
AB  - after maternal hypoxia.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Owsicka, A.
AU  - Tamulaitis, G.
AU  - Sasnauskas, G.
AU  - Shlyakhtenko, L.S.
AU  - Lushnikov, A.Y.
AU  - Lyubchenko, Y.L.
AU  - Laurens, N.
AU  - van den Broek, B.
AU  - Wuite, G.J.
AU  - Siksnys, V.
TI  - DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 7142
EP  - 7154
VL  - 38
AB  - To cut DNA at their target sites, restriction enzymes assemble into different oligomeric
AB  - structures. The Ecl18kI endonuclease in the crystal
AB  - is arranged as a tetramer made of two dimers each bound to a DNA copy.
AB  - However, free in solution Ecl18kI is a dimer. To find out whether the
AB  - Ecl18kI dimer or tetramer represents the functionally important assembly,
AB  - we generated mutants aimed at disrupting the putative dimer-dimer
AB  - interface and analysed the functional properties of Ecl18kI and mutant
AB  - variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI
AB  - loops out an intervening DNA fragment and forms a tetramer. Using the
AB  - tethered particle motion technique, we demonstrate that in solution DNA
AB  - looping is highly dynamic and involves a transient interaction between the
AB  - two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the
AB  - synaptic complex much faster than when acting on a single recognition
AB  - site. Contrary to Ecl18kI, the tetramerization interface mutant R174A
AB  - binds DNA as a dimer, shows no DNA looping and is virtually inactive. We
AB  - conclude that Ecl18kI follows the association model for the synaptic
AB  - complex assembly in which it binds to the target site as a dimer and then
AB  - associates into a transient tetrameric form to accomplish the cleavage
AB  - reaction.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Sasnauskas, G.
AU  - Siksnys, V.
TI  - The link between restriction endonuclease fidelity and oligomeric state: A study with Bse634I.
JO  - FEBS Lett.
PY  - 2012
SP  - 3324
EP  - 3329
VL  - 586
AB  - Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric
AB  - REases have two DNA binding interfaces and must
AB  - synapse two recognition sites to achieve cleavage. It was hypothesised
AB  - that binding of two recognition sites by tetrameric enzymes contributes
AB  - to their fidelity. Here, we experimentally determined the fidelity for
AB  - Bse634I REase in different oligomeric states. Surprisingly, we find
AB  - that tetramerisation does not increase REase fidelity in comparison to
AB  - the dimeric variant. Instead, an inherent ability to act concertedly at
AB  - two sites provides tetrameric REase with a safety-catch to prevent host
AB  - DNA cleavage if a single unmodified site becomes available.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Sasnauskas, G.
AU  - Urbanke, C.
AU  - Siksnys, V.
TI  - Allosteric communication network in the tetrameric restriction endonuclease Bse634I.
JO  - J. Mol. Biol.
PY  - 2006
SP  - 500
EP  - 512
VL  - 363
AB  - Restriction endonuclease Bse634I is a homotetramer arranged as a dimer of two primary dimers.
AB  - Bse634I displays its maximum catalytic efficiency upon
AB  - binding of two copies of cognate DNA, one per each primary dimer. The
AB  - catalytic activity of Bse634I on a single DNA copy is down-regulated due
AB  - to the cross-talking interactions between the primary dimers. The
AB  - mechanism of signal propagation between the individual active sites of
AB  - Bse634I remains unclear. To identify communication pathways involved in
AB  - the catalytic activity regulation of Bse634I tetramer we mutated a
AB  - selected set of amino acid residues at the dimer-dimer interface and
AB  - analysed the oligomeric state and catalytic properties of the mutant
AB  - proteins. We demonstrate that alanine replacement of N262 and V263
AB  - residues located in the loop at the tetramerisation interface did not
AB  - inhibit tetramer assembly but dramatically altered the catalytic
AB  - properties of Bse634I despite of the distal location from the active site.
AB  - Kinetic analysis using cognate hairpin oligonucleotide and one and
AB  - two-site plasmids as substrates allowed us to identify two types of
AB  - communication signals propagated through the dimer-dimer interface in the
AB  - Bse634I tetramer: the inhibitory, or "stopper" and the activating, or
AB  - "sync" signal. We suggest that the interplay between the two signals
AB  - determines the catalytic and regulatory properties of the Bse634I and
AB  - mutant proteins.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Sasnauskas, G.
AU  - Urbanke, C.
AU  - Siksnys, V.
TI  - Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: Oligomeric structure-stability-function correlations.
JO  - J. Mol. Biol.
PY  - 2005
SP  - 459
EP  - 478
VL  - 348
AB  - The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of
AB  - restriction enzymes. It requires two recognition
AB  - sites for its optimal activity and cleaves plasmid DNA with two sites
AB  - much faster than a single-site DNA. We show that disruption of the
AB  - tetramerisation interface of Bse634I by site-directed mutagenesis
AB  - converts the tetrameric enzyme into a dimer. Dimeric W228A mutant
AB  - cleaves plasmid DNA containing one or two sites with the same
AB  - efficiency as the tetramer cleaves the two-site plasmid. Hence, the
AB  - catalytic activity of the Bse634I tetramer on a single-site DNA is
AB  - down-regulated due to the cross-talking interactions between the
AB  - individual dimers. The autoinhibition within the Bse634I tetramer is
AB  - relieved by bridging two DNA copies into the synaptic complex that
AB  - promotes fast and concerted cleavage at both sites. Cleavage analysis
AB  - of the oligonucleotide attached to the solid support revealed that
AB  - Bse634I is able to form catalytically competent synaptic complexes by
AB  - bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA
AB  - and cognate DNA-product DNA. Taken together, our data demonstrate that
AB  - a single W228A mutation converts a tetrameric type IIF restriction
AB  - enzyme Bse634I into the orthodox dimeric type IIP restriction
AB  - endonuclease. However, the stability of the dimer towards chemical
AB  - denaturants, thermal inactivation and proteolytic degradation are
AB  - compromised.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Siksnys, V.
TI  - Molecular scissors under light control.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2010
SP  - 1259
EP  - 1260
VL  - 107
AB  - Light plays a key role in the living world.  It serves as a source of energy through
AB  - photosynthesis, makes sight possible, and regulates circadian rhythms.  During evolution,
AB  - organisms from bacteria to higher mammals elaborate various mechanisms to sense and respond to
AB  - light, which manipulates their behavior.  The use of light as a trigger is particularly
AB  - attractive as a means of controlling biological processes at will, because light is
AB  - noninvasive and can be manipulated both temporally (from microseconds) and spatially
AB  - (microns).  In this issue of PNAS, Schierling et al. demonstrate the possibility of
AB  - controlling the enzymatic activity of the restriction endonuclease PvuII by light.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Toliusis, P.
AU  - Grigaitis, R.
AU  - Manakova, E.
AU  - Silanskas, A.
AU  - Tamulaitiene, G.
AU  - Szczelkun, M.D.
AU  - Siksnys, V.
TI  - DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.
JO  - Nucleic Acids Res.
PY  - 2014
SP  - 13887
EP  - 13896
VL  - 42
AB  - The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum
AB  - and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three
AB  - genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease
AB  - (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and
AB  - N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and
AB  - N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated
AB  - R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in
AB  - solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R2N2
AB  - stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on
AB  - double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and
AB  - extensive ATP hydrolysis ( approximately 170 ATP/s/monomer) are required for site-specific DNA
AB  - cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed
AB  - positions (6-7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'.
AB  - Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII
AB  - enzymes may employ a unique catalytic mechanism for DNA cleavage.
ER  -

TY  - JOUR
AU  - Zaremba, M.
AU  - Urbanke, C.
AU  - Halford, S.E.
AU  - Siksnys, V.
TI  - Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the  phospholipase D superfamily.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 81
EP  - 92
VL  - 336
AB  - The Bfi I endonuclease cleaves DNA at fixed positions downstream of an asymmetric sequence.
AB  - Unlike other restriction enzymes, it functions
AB  - without metal ions. The N-terminal half of Bfi I is similar to Nuc, an
AB  - EDTA-resistant nuclease from Salmonella typhimurium that belongs to the
AB  - phosphoplipase D superfamily. Nuc is a dimer with one active site at
AB  - its subunit interface, as is Bfi I, but it cuts DNA non-specifically.
AB  - Bfi I was cleaved by thermolysin into an N-terminal domain, which forms
AB  - a dimer with non-specific nuclease activity, and a C-terminal domain,
AB  - which lacks catalytic activity but binds specifically to the
AB  - recognition sequence as a monomer. On denaturation with guanidinium,
AB  - Bfi I underwent two unfolding transitions: one at a relatively low
AB  - concentration of guanidinium, to a dimeric non-specific nuclease; a
AB  - second at a higher concentration, to an inactive monomer. The isolated
AB  - C-terminal domain unfolded at the first (relatively low) concentration,
AB  - the isolated N-terminal at the second. Hence, Bfi I consists of two
AB  - physically separate domains, with catalytic and dimerisation functions
AB  - in the N terminus and DNA recognition functions in the C terminus. It
AB  - is the first example of a restriction enzyme generated by the
AB  - evolutionary fusion of a DNA recognition domain to a phosphodiesterase
AB  - from the phospholipase D superfamily. Bfi I may consist of three
AB  - structural units: a stable central core with the active site, made from
AB  - two copies of the N-terminal domain, flanked by relatively unstable
AB  - C-terminal domains, that each bind a copy of the recognition sequence.
AB  - (C) 2003 Elsevier Ltd. All rights reserved.
ER  -

TY  - JOUR
AU  - Zarogiannis, S.G.
AU  - Filippidis, A.S.
TI  - Resenbase: A sophisticated and user-friendly, restriction endonuclease database compilation for handheld computers.
JO  - Clin. Chim. Acta
PY  - 2005
SP  - S360
EP  - S360
VL  - 355
AB  - A database of commonly used restriction enzymes was constructed and programmed into a PalmOs
AB  - handheld.
ER  -

TY  - JOUR
AU  - Zarrilli, R.
AU  - Giannouli, M.
AU  - Rocco, F.
AU  - Loman, N.J.
AU  - Haines, A.S.
AU  - Constantinidou, C.
AU  - Pallen, M.J.
AU  - Triassi, M.
AU  - Di Nocera, P.P.
TI  - Genome sequences of three Acinetobacter baumannii strains assigned to ST2, ST25 and ST78 multilocus sequencing typing genotypes.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2359
EP  - 2360
VL  - 193
AB  - Acinetobacter baumannii is an emerging opportunistic gram-negative pathogen responsible for
AB  - hospital-acquired infections. A. baumannii epidemics described in Europe and worldwide were
AB  - caused by a limited number of genotypic clusters of multidrug-resistant strains. Here we
AB  - report the availability of draft genome sequences for three multidrug-resistant A. baumannii
AB  - strains assigned to ST2, ST25 and ST78 multilocus sequencing typing genotypes, that were more
AB  - frequently isolated during outbreaks occurred in Greece, Italy, Lebanon and Turkey.
ER  -

TY  - JOUR
AU  - Zarza, E.
AU  - Alcaraz, L.D.
AU  - Aguilar-Salinas, B.
AU  - Islas, A.
AU  - Olmedo-Alvarez, G.
TI  - Complete Genome Sequence of Bacillus horikoshii Strain 20a from Cuatro Cienegas,  Coahuila, Mexico.
JO  - Genome Announcements
PY  - 2017
SP  - e00592
EP  - e00517
VL  - 5
AB  - We sequenced the Bacillus horikoshii 20a genome, isolated from sediment collected in Cuatro
AB  - Cienegas, Mexico. We identified genes involved in establishing
AB  - antagonistic interactions in microbial communities (antibiotic resistance and
AB  - bacteriocins) and genes related to the metabolism of cyanophycin, a reserve
AB  - compound and spore matrix material potentially relevant for survival in an
AB  - oligotrophic environment.
ER  -

TY  - JOUR
AU  - Zarza, E.
AU  - Alcaraz, L.D.
AU  - Aguilar-Salinas, B.
AU  - Islas, A.
AU  - Olmedo-Alvarez, G.
TI  - Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrocienegas, Coahuila, Mexico.
JO  - Genome Announcements
PY  - 2018
SP  - e00364
EP  - e00318
VL  - 6
AB  - We assembled the complete genome sequences of Bacillus pumilus strains 145 and 150a from
AB  - Cuatrocienegas, Mexico. We detected genes codifying for proteins
AB  - potentially involved in antagonism (bacteriocins) and defense mechanisms
AB  - (abortive infection bacteriophage proteins and 4-azaleucine resistance). Both
AB  - strains harbored prophage sequences. Our results provide insights into
AB  - understanding the establishment of microbial interactions.
ER  -

TY  - JOUR
AU  - Zatkovic, B.
AU  - Molnarova, V.
AU  - Kmet, V.
AU  - Javorsky, P.
AU  - Pristas, P.
TI  - Diversity of DNA sequences among restriction endonucleases producing Selenomonas ruminantium isolates detected by enterobacterial repetitive intergenic consensus based polymerase chain reaction (ERIC-PCR).
JO  - Anaerobe
PY  - 2000
SP  - 299
EP  - 304
VL  - 6
AB  - Enterobacterial repetitive intergenic consensus-based polymerase chain reaction (ERIC-PCR) was
AB  - found useful for discrimination of rumen
AB  - selenomonads. Simultaneous use of ERICIR and ERIC2 primers yielded
AB  - strain-specific banding patterns. The patterns were compared using Dice
AB  - similarity coefficients and a DNA relatedness dendrogram based on the
AB  - unweighted pair group method using arithmetic averages (UPGMA) was
AB  - constructed. Five clusters and four single strains were identified at a
AB  - similarity level of 50%. Very weak grouping was observed for
AB  - lactilytica and ruminantium subspecies of Selenomonas ruminantium,
AB  - indicating that lactate utilization has probably no taxonomic value.
AB  - Restriction and modification phenotypes are weakly reflected in the
AB  - dendrogram probably as the result of horizontal genetic transfer of
AB  - genes encoding these phenotypic traits. While diverse in ERIC-PCR
AB  - analysis, strains shown little variation in restriction fragment length
AB  - polymorphism of amplified 16S-rRNA genes. All but one strain produced
AB  - nearly identical profiles indicating that majority of DNA diversity
AB  - observed is due to epigenetic factors and not due to evolutionary
AB  - divergence.
ER  -

TY  - JOUR
AU  - Zautner, A.E.
AU  - Bunk, B.
AU  - Pfeifer, Y.
AU  - Sproer, C.
AU  - Reichard, U.
AU  - Eiffert, H.
AU  - Scheithauer, S.
AU  - Gross, U.
AU  - Overmann, J.
AU  - Bohne, W.
TI  - Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing.
JO  - J. Antimicrob. Chemother.
PY  - 2017
SP  - 2737
EP  - 2744
VL  - 72
AB  - Objectives: Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for
AB  - healthcare facilities worldwide. A continuous monitoring of ST distribution
AB  - and its association with resistance and virulence genes is required for early
AB  - detection of successful K. pneumoniae lineages. In this study, we used WGS to
AB  - characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the
AB  - University Medical Center Gottingen, Germany, between March 2013 and August 2014.
AB  - Methods: Closed genomes for 16 isolates of carbapenemase-producing K. pneumoniae
AB  - were generated by single molecule real-time technology using the PacBio RSII
AB  - platform. Results: Eight of the 16 isolates showed identical XbaI
AB  - macrorestriction patterns and shared the same MLST, ST147. The eight ST147
AB  - isolates differed by only 1-25 SNPs of their core genome, indicating a clonal
AB  - origin. Most of the eight ST147 isolates carried four plasmids with sizes of
AB  - 246.8, 96.1, 63.6 and 61.0 kb and a novel linear plasmid prophage, named pKO2, of
AB  - 54.6 kb. The blaOXA-48 gene was located on a 63.6 kb IncL plasmid and is part of
AB  - composite transposon Tn1999.2. The ST147 isolates expressed the yersinabactin
AB  - system as a major virulence factor. The comparative whole-genome analysis
AB  - revealed several rearrangements of mobile genetic elements and losses of
AB  - chromosomal and plasmidic regions in the ST147 isolates. Conclusions: Single
AB  - molecule real-time sequencing allowed monitoring of the genetic and epigenetic
AB  - microevolution of MDR OXA-48-producing K. pneumoniae and revealed in addition to
AB  - SNPs, complex rearrangements of genetic elements.
ER  -

TY  - JOUR
AU  - Zautner, A.E.
AU  - Goldschmidt, A.M.
AU  - Thurmer, A.
AU  - Schuldes, J.
AU  - Bader, O.
AU  - Lugert, R.
AU  - Gross, U.
AU  - Stingl, K.
AU  - Salinas, G.
AU  - Lingner, T.
TI  - SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs.
JO  - BMC Genomics
PY  - 2015
SP  - 1088
EP  - 1088
VL  - 16
AB  - BACKGROUND: Campylobacter species are the most prevalent bacterial pathogen causing acute
AB  - enteritis worldwide. In contrast to Campylobacter jejuni, about 5 %
AB  - of Campylobacter coli strains exhibit susceptibility to restriction endonuclease
AB  - digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates
AB  - significant differences in DNA methylation between both microbial species. The
AB  - goal of the study was to analyze the methylome of a C. coli strain susceptible to
AB  - DpnI digestion, to identify its methylation motifs and restriction modification
AB  - systems (RM-systems), and compare them to related organisms like C. jejuni and
AB  - Helicobacter pylori. RESULTS: Using one SMRT cell and the PacBio RS sequencing
AB  - technology followed by PacBio Modification and Motif Analysis the complete genome
AB  - of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold
AB  - coverage and assembled into a single contig of 1.7 Mbp. The genome contains a
AB  - CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1
AB  - isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome
AB  - positions) that are predominantly arranged in eight different methylation motifs
AB  - and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of
AB  - these motifs correspond to known restriction modification motifs. Characteristic
AB  - for this methylome was the very high fraction of methylation of motifs with
AB  - mostly above 99 %. CONCLUSIONS: Only five dominant methylation motifs have been
AB  - identified in C. jejuni, which have been associated with known RM-systems. C.
AB  - coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to
AB  - putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to
AB  - Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP,
AB  - methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP
AB  - RM-system has been described for H. pylori. The remaining methylation motifs are
AB  - specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor
AB  - in H. pylori. The results of this study give us new insights into epigenetics of
AB  - Campylobacteraceae and provide the groundwork to resolve the function of
AB  - RM-systems in C. coli.
ER  -

TY  - JOUR
AU  - Zavilgelskii, G.B.
AU  - Bakalova, T.L.
AU  - Duzhii, D.E.
AU  - Kotova, V.Y.
TI  - The ard gene encoding the type I restriction inhibitor is present in conjugative plasmids of FII, B/O, and K groups of incompatibility.
JO  - Genetika
PY  - 1994
SP  - 1582
EP  - 1586
VL  - 30
AB  - The effect of conjugative plasmids of various incompatibility groups of the enterobacteria
AB  - family on the activity of the cell restriction-modification system of type I (EcoK) was
AB  - studied. Twenty-two conjugative plasmids of 15 incompatibility groups were tested. In addition
AB  - to plasmids of the incI1 and incN groups studied earlier, conjugative plasmids of the incFII,
AB  - incB/O, and incK groups were also shown to be able to weaken the action of type I restriction
AB  - enzymes upon nonmodified DNA (Ard phenotype). A hybridization analysis of all the plasmid DNAs
AB  - studied, using ard gene DNA sequences from the ColIb-P9 (incI1) plasmid as a probe, was
AB  - performed. The ard locus of the R100 (incFII) plasmid was cloned in the pBR322 and pACYC184
AB  - vectors. The ard gene was located 2.5 kb from the oriT site in the leading region on the R100
AB  - conjugative plasmid.
ER  -

TY  - JOUR
AU  - Zavilgelskii, G.B.
AU  - Manukhov, I.V.
AU  - Rastorguev, S.M.
TI  - Attenuation of type I restriction in Escherichia coli: effect of the ard gene in UV-irradiated cells.
JO  - Genetika
PY  - 1996
SP  - 1013
EP  - 1016
VL  - 32
AB  - The effect of conjugative plasmids ColIb-P9 (incI1) and pKM 101 (incN), containing the active
AB  - ard gene, on the efficiency of EcoK restriction of nonmodified phage lambda .0 in
AB  - UV-irradiated Escherichia coli cells was studied. ard-Dependent antirestriction enzyme
AB  - activity was shown to decrease in UV-irradiated cells. The efficiency of action of the ard
AB  - plasmid gene on lambda .0 was also shown not to depend on cell helicases RecBCD and UvrD, in
AB  - contrast to the UV-induced alleviation of EcoK restriction (SOS alleviation).
AB  - [Article in Russian]
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
TI  - Antirestriction.
JO  - Mol. Biol. (Mosk)
PY  - 2000
SP  - 854
EP  - 862
VL  - 34
AB  - Modern data on the molecular mechanisms of antirestriction are reviewed.  The systems of
AB  - inhibition are described for the restriction-modification enzymes of type I in phages and in
AB  - conjugative plasmids.  The phenomenon of alleviation of DNA restriction and its mechanism is
AB  - presented for bacterium Escherichia coli.  The principle of protein mimicry of nucleic acids
AB  - is discussed as a novel way to control biological processes in the cell with reference to
AB  - antirestriction proteins Ard.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Kotova, V.Y.
TI  - Antirestriction activity of the monomeric and dimeric forms of T7 Ocr.
JO  - Mol. Biol. (Mosk)
PY  - 2014
SP  - 150
EP  - 157
VL  - 48
AB  - The Ocr antirestriction protein, which is encoded by bacteriophage T7 0.3 (ocr), specifically
AB  - inhibits type I restriction-modification enzymes. Ocr belongs to a family of DNA-mimicking
AB  - proteins. Native Ocr forms homodimers both in solution and in crystal. Ocr mutants with two
AB  - amino acid substitutions (Orc F53D A57E and Ocr F53R V77D) were constructed to occur as
AB  - monomers in solution. The dissociation constant K (d) for the Ocr complex with EcoKI (R2M2S)
AB  - proved to differ by three orders of magnitude between the (Ocr)(2) dimer and Ocr F53D A57E and
AB  - Ocr F53R V77D monomers (10(-10) M vs. 10(-7) M). Antimodification activity was substantially
AB  - lower in the Ocr monomers. The dimeric form found to be essential for high inhibitory activity
AB  - of Ocr.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Kotova, V.Y.
AU  - Melkina, O.E.
AU  - Pustovoit, K.S.
TI  - Antirestriction activity of the mercury resistance nonconjugative transposon Tn5053 is controlled by the protease ClpXP.
JO  - Genetika
PY  - 2014
SP  - 910
EP  - 915
VL  - 50
AB  - When transformed into Escherichia coli K12 strains, the mercury resistance transposon Tn5053
AB  - exhibits high antirestriction activity against the EcoKI type I restriction and modification
AB  - system. The products of the genes merR and ardD contribute to the antirestriction activity of
AB  - Tn5053. The merR gene encodes the MerR protein, the transcription regulator of the mer operon
AB  - genes. The ardD gene is responsible for ArdD protein synthesis and is located within the tni
AB  - operon. In the following study, it was demonstrated that the antirestriction activity of the
AB  - transposon Tn5053 is absent in E. coli K12 strains with the mutant genes clpX, clpP, and recA.
AB  - The antirestriction effect of Tn5053 is not enhanced by 2-aminopurine. The Tn5053
AB  - antirestriction activity is not altered in E. coli K12 with the mutant dam gene; however, it
AB  - is decreased in the E. coli K12 mutD. It is assumed that the activities of the MerR and ArdD
AB  - proteins lead to the formation of a significant amount of unmodified DNA in the bacterial
AB  - cell, causing the SOS-dependent reduction of the EcoKI (R2M2S) enzyme activity associated with
AB  - ClpXP-induced proteolysis of the R-subunit.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Kotova, V.Y.
AU  - Rastorguev, S.M.
TI  - Antirestriction and antimodification activities of T7 Ocr: Effects of amino acid substitutions in the interface.
JO  - Mol. Biol. (Mosk)
PY  - 2009
SP  - 93
EP  - 100
VL  - 43
AB  - The T7 antirestriction protein Ocr, encoded by 0.3 (ocr), specifically inhibits ATP-dependent
AB  - type I restriction-modification systems. T7 0.3
AB  - (ocr) was cloned in pUC18. Ocr inhibited both restriction and
AB  - modification activities of the type I restriction-modification system
AB  - (EcoKI) in Escherichia coli K12. The Ocr F53D A57E mutant was obtained
AB  - and proved to inhibit only restriction activity of EcoKI. The 0.3 (ocr)
AB  - and Photorhabdus luminescens luxCDABE genes were cloned in pZ-series
AB  - vectors with the P (ltetO-1) promoter, strongly controlled by the TetR
AB  - repressor. The bioluminescence intensity and luciferase content varied
AB  - up to 5000-fold in E. coli K12 MG1655Z1 tetR(+) (pZE21-luxCDABE) cells,
AB  - depending on the environmental concentration of the inductor
AB  - anhydrotetracycline. The antirestriction activity of Ocr and Ocr F53D
AB  - A57E was studied as a function of their concentration in the cell. The
AB  - dissociation constant K (d), characterizing the binding with EcoKI,
AB  - differed 1000-fold between Ocr and Ocr F53D A57E (10(-10) M versus 10(-7) M).
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Kotova, V.Y.
AU  - Rastorguev, S.M.
TI  - Antimodification activity of the ArdA and Ocr proteins.
JO  - Genetika
PY  - 2011
SP  - 159
EP  - 167
VL  - 47
AB  - The ArdA and Ocr antirestriction proteins, whose genes are in transmissible plasmids (ardA)
AB  - and bacteriophage genomes (0.3 (ocr)), specifically inhibit type I restriction-modification
AB  - enzymes. The Ocr protein (T7 bacteriophage) was shown to inhibit both restriction
AB  - (endonuclease) and modification (methylase) activities of the EcoKI enzyme in a broad range of
AB  - intracellular concentrations (starting from 10-20 molecules per cell). In contrast to Ocr, the
AB  - ArdA protein (ColIb-P9 transmissible plasmid) inhibited both of the EcoKI activities only at
AB  - high intracellular concentrations (30000-40000 molecules per cell). When the ArdA
AB  - concentration was several fold lower, only endonuclease activity of EcoKI was inhibited. It
AB  - was assumed that a poorer ArdA ability to inhibit EcoKI modification activity is related to
AB  - the substantial difference in life cycle between transmissible plasmids (symbiosis with the
AB  - bacterial cell) and bacteriophages (infection and lysis of bacteria). The Ocr and ArdA mutants
AB  - that inhibited exclusively endonuclease activity of EcoKI were obtained. Antirestriction
AB  - proteins incapable of homodimerization were assumed to inhibit only endonuclease activity of
AB  - type I restriction-modification enzymes.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Kotova, V.Y.
AU  - Rastorguev, S.M.
TI  - Comparative analysis of anti-restriction activities of ArdA (ColIb-P9) and Ocr (T7) proteins.
JO  - Biochemistry
PY  - 2008
SP  - 906
EP  - 911
VL  - 73
AB  - Anti-restriction proteins ArdA and Ocr are specific inhibitors of type I
AB  - restriction-modification enzymes. The IncI1 transmissible plasmid
AB  - ColIb-P9 ardA and bacteriophage T7 0.3(ocr) genes were cloned in pUC18
AB  - vector. Both ArdA (ColIb-P9) and Ocr (T7) proteins inhibit both
AB  - restriction and modification activities of the type I
AB  - restriction-modification enzyme (EcoKI) in Escherichia coli K12 cells.
AB  - ColIb-P9 ardA, T7 0.3(ocr), and the Photorhabdus luminescens luxCDABE
AB  - genes were cloned in pZ-series vectors with the PltetO-1 promoter,
AB  - which is tightly repressible by the TetR repressor. Controlling the
AB  - expression of the lux-genes encoding bacterial luciferase demonstrates
AB  - that the PltetO-1 promoter can be regulated over an up to 5000-fold
AB  - range by supplying anhydrotetracycline to the E. coli MG1655Z1 tetR(+)
AB  - cells. Effectiveness of the anti-restriction activity of the ArdA and
AB  - Ocr proteins depended on the intracellular concentration. It is shown
AB  - that the dissociation constants K (d) for ArdA and Ocr proteins with
AB  - EcoKI enzyme differ 1700-fold: K (d)(Ocr) = 10(-10) M, K (d)(ArdA) =
AB  - 1.7 center dot 10(-7) M.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Letuchaya, T.A.
AU  - Rastorguev, S.M.
TI  - Antirestriction and antimodification activities of the ArdA protein encoded by the IncI1 transmissive plasmids R-64 and ColIb-P9.
JO  - Genetika
PY  - 2006
SP  - 252
EP  - 258
VL  - 42
AB  - Proteins of the Ard family are specific inhibitors of type I restriction-modification enzymes.
AB  - The ArdA of R64 is highly homologous
AB  - to ColIb-P9 ArdA, differing only by four amino acid residues of the
AB  - overall 166. However, unlike ColIb-P9 ArdA, which inhibits both the
AB  - endonuclease and the methylase activities of EcoKI, the R64 ArdA
AB  - protein inhibits only the endonuclease activity of this enzyme. The
AB  - mutant forms of R64 ArdA-A29T, S43A, and Y75W, capable of partially
AB  - reversing the protein to ColIb-P9 ArdA form-were produced by directed
AB  - mutagenesis. It was demonstrated that only Y75W mutation of these three
AB  - variants essentially influenced the functional activity of ArdA: the
AB  - antimodification activity was restored to approximately 90%. It is
AB  - assumed that R64 ArdA inhibits formation of the complex between
AB  - unmodified DNA and the R subunit of the type I restriction-modification
AB  - enzyme EcoKI (R2M2S), which translocates and cleaves DNA. ColIb-P9 ArdA
AB  - protein is capable of forming the DNA complex not only with the R
AB  - subunit, but also with the S subunit, which contacts sK site
AB  - (containing modified adenine residues) in DNA. ArdA bound to the
AB  - specific sK site inhibits concurrently the endonuclease and methylase
AB  - activities of EcoKI (R2M2S), while ArdA bound to the nonspecific site
AB  - in the R subunit blocks only its endonuclease activity.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Letutchaja, T.A.
AU  - Rastorguev, S.M.
TI  - Antirestriction activity of ArdA encoded by the IncI1 transmissive plasmid R64.
JO  - Mol. Biol. (Mosk)
PY  - 2004
SP  - 901
EP  - 906
VL  - 38
AB  - The transmissive plasmid R64 (IncI1) performs an antirestriction function, reducing the
AB  - efficiency of EcoKI-dependent restriction in
AB  - Escherichia coli K12 cells approximately fivefold. The R64 ardA gene
AB  - has been cloned and sequenced. The ArdA proteins specifically inhibit
AB  - type I restriction-modification enzymes. R64 ArdA is highly homologous
AB  - to ColIb-P9 ArdA: only 4 out of 166 amino acid residues differ. While
AB  - ColIb-P9 inhibits both endonuclease and methylase activities of the
AB  - type I restriction-modification enzyme EcoKI (R2M2S), R64 ArdA inhibits
AB  - only its endonuclease activity. It has been assumed that R64 ArdA
AB  - suppresses the binding of unmodified DNA with the R subunit, which is
AB  - responsible for DNA translocation and cleavage. ColIb-P9 ArdA
AB  - suppresses DNA binding not only with the R, but also with the S
AB  - subunit, which contacts the sK site containing target adenines. The
AB  - binding of ArdA with the specific site inhibits both endonuclease and
AB  - methylase activities; the binding of ArdA with the nonspecific site of
AB  - the R subunit inhibits only the endonuclease activity of EcoKI (R2M2S).
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Mershavka, V.Y.
AU  - Jusifov, T.N.
AU  - Belogurov, A.A.
TI  - Plasmid pKM101 ard+-mediated alleviation of K-restriction of bacteriophage lambda.  I. General characteristics and genetic localization of the ard gene.
JO  - Mol. Biol. (Mosk)
PY  - 1984
SP  - 1590
EP  - 1596
VL  - 18
AB  - The effectiveness of action of restriction endonuclease EcoK on DNA lambda.0 is considerably
AB  - alleviated (by 10 to 100 times approximately) if Escherichia  coli K12 cells contain plasmid
AB  - pKM101.  The region of plasmid pKM101 in which insertion sites of transposon Tn5, disturbing
AB  - the ability of the plasmid to alleviate EcoK restriction are located, was found to be in
AB  - fragment BglII-B at a distance of about 1.3-1.7 kilobases from the end of the fragment, and it
AB  - was named ard (alleviation of restriction of DNA).  Alleviation of K restriction of phage
AB  - lambda.0 determined by plasmid ard gene is independent of chromosomal genes lexA, recBC, and
AB  - umuC and plasmid gene muc.  The presence of plasmid pKM101 ard+ in the cell does not lead to
AB  - specific modification of DNA, nor does it intensify methylation of DNA by methylase K like the
AB  - action of the ral gene of phage lambda.  The action of the ard gene of plasmid pKM101 is
AB  - highly specific: Alleviation of DNA restriction is observed only in strains of E. coli K and
AB  - is virtually absent in strains of E. coli B, and also in strains of E. coli containing class
AB  - II restriction endonucleases (EcoRI and EcoRIII).
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Rastorguev, S.M.
TI  - Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes.
JO  - Mol. Biol. (Mosk)
PY  - 2009
SP  - 241
EP  - 248
VL  - 43
AB  - Genes encoding antirestriction proteins are found in transmissble plasmids (ardABC) and
AB  - bacteriophage genomes (ocr, darA).
AB  - Antirestriction proteins inhibit type I restriction-modification
AB  - enzymes and thus protect the unmodified plasmid or phage DNA from
AB  - degradation. Antirestriction proteins belong to the family of
AB  - DNA-mimicry proteins, whose spatial structure mimics the B-form of DNA.
AB  - Based on an analysis of the mutant forms of ArdA and Ocr obtained by
AB  - site-directed mutagenesis and the native form of ArdA that specifically
AB  - inhibit type I restriction enzymes but do not affect their methylase
AB  - activity, a model is proposed to describe the complex formation between
AB  - an antirestriction protein and a type I restriction-modification enzyme
AB  - (R2M2S): antirestriction proteins can displace a DNA strand from its
AB  - binding sites in the S subunit (which contacts a specific site on DNA)
AB  - and in the R subunit (which translocates the DNA strand and cleaves
AB  - it). Antirestriction and antimodification activities of ArdA and Ocr as
AB  - a function of ardA and ocr expression levels were studied by cloning
AB  - the genes under a strictly regulated promoter.
ER  -

TY  - JOUR
AU  - Zavilgelsky, G.B.
AU  - Rastorguev, S.M.
TI  - DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes.
JO  - Biochemistry
PY  - 2007
SP  - 913
EP  - 919
VL  - 72
AB  - Modern concepts on mechanisms of DNA-dependent enzyme regulation involving specific
AB  - DNA-mimicking proteins are considered. There are proteins that share structural resemblance
AB  - with DNA duplexes. These include inhibitors of type I restriction-modification enzymes (Ocr
AB  - and ArdA), inhibitors of DNA gyrase MfpA and QnrABS, etc. We describe here structural features
AB  - of these proteins and mechanisms responsible for their interaction with DNA-dependent enzymes
AB  - and then discuss perspectives of use of DNA-mimicking proteins in analysis of replication,
AB  - repair, recombination, mechanisms underlying resistance to antibiotics, and also fields of
AB  - applied biotechnology.
ER  -

TY  - JOUR
AU  - Zaw, H.A.
AU  - Kanesaki, Y.
AU  - Yoshikawa, H.
AU  - Tsurumaru, H.
AU  - Yamakawa, T.
TI  - Draft Genome Sequences of Bradyrhizobium elkanii Strains BLY3-8 and BLY6-1, Which Are Incompatible with Rj3 Genotype Soybean Cultivars.
JO  - Genome Announcements
PY  - 2016
SP  - e01169
EP  - e01116
VL  - 4
AB  - We report here the draft genome sequences of Bradyrhizobium elkanii strains BLY3-8 and BLY6-1,
AB  - which are incompatible with Rj3 genotype soybean cultivars.
AB  - The genome sequences of these strains will be useful to identify a causal gene
AB  - for this incompatibility.
ER  -

TY  - JOUR
AU  - Zdziarski, J.
AU  - Brzuszkiewicz, E.B.
AU  - Wullt, B.
AU  - Liesegang, H.
AU  - Biran, D.
AU  - Voigt, B.
AU  - Gronberg-Hernandez, J.
AU  - Ragnarsdottir, B.
AU  - Hecker, M.
AU  - Ron, E.Z.
AU  - Daniel, R.
AU  - Gottschalk, G.
AU  - Hacker, J.
AU  - Svanborg, C.
AU  - Dobrindt, U.
TI  - Host imprints on bacterial genomes--Rapid, divergent evolution in individual patients.
JO  - PLoS Pathog.
PY  - 2010
SP  - e1001078
EP  - e1001078
VL  - 6
AB  - Bacteria lose or gain genetic material and through selection, new variants become fixed in the
AB  - population.  Here we provide the first, genome-wide example of a single bacterial strain's
AB  - evolution in different deliberately colonized patients and the surprising insight that hosts
AB  - appear to personalize their microflora.  By first obtaining the complete genome sequence of
AB  - the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its
AB  - descendants after therapeutic bladder colonization of different patients, we identified 34
AB  - mutations, which affected metabolic and virulence-related genes.  Further transcriptome and
AB  - proteome analysis proved that these genome changes altered bacterial gene expression resulting
AB  - in unique adaptation patterns in each patient.  Our results provide evidence that, in addition
AB  - to stochastic events, adaptive bacterial evolution is driven by individual host environments.
AB  - Ongoing loss of gene function supports the hypothesis that evolution towards commensalism
AB  - rather than virulence is favored during asymptomatic bladder colonization.
ER  -

TY  - JOUR
AU  - Zebala, J.
AU  - Choi, J.
AU  - Barany, F.
TI  - Recognition of base-analogue modified substrates by the TaqI restriction endonuclease.
JO  - FASEB J.
PY  - 1992
SP  - A358
EP  - A358
VL  - 6
AB  - It has been proposed that protein-DNA recognition is mediated via specific
AB  - hydrogen bond, hydrophobic and/or electrostatic interactions made between the
AB  - protein and DNA surface.  We have energetically quantitated these interactions
AB  - for the TaqI endonuclease (cleaves T^CGA) by constructing base-analogue
AB  - substituted substrates.  The base analogues N6-methyl-A, N7-deaza-A,
AB  - N7-deaza-G, inosine, N4-methyl-C, 5-methyl-C, uracil, 5-bromoU, alpha-thio-A,
AB  - alpha-thio-G, alpha-thio-T and alpha-thio-A were substituted for their
AB  - corresponding unmodified counterpart in one strand of the TCGA duplex.  The
AB  - effects of these analogues were monitored by measuring the steady-state
AB  - (Km,kcat) and single-turnover (kst) kinetic constants.  Only the N6-methyl-A
AB  - substituted DNA, which recreates in vivo methylation, was unreactive while the
AB  - remaining analogue substitutions exhibited Michaelis-Menten kinetics.  In
AB  - general, the Km was either unchanged or lowered by the analogue substitutions.
AB  - In contrast, many of the analogues severely reduced kcat, suggesting the
AB  - modified functional groups served mainly to destabilize the transition state.
AB  - Single-turnover measurements paralleled the kcat results, pointing to the N7
AB  - and N6 of A, the N7 of G and one of the nonbridging oxygens 3' to T as putative
AB  - contacts made in achieving the transition state.  The unmodified strand in ten
AB  - out of twelve hemi-substituted substrates had a normal kst value suggesting
AB  - that a particular cleavage center is controlled predominantly by recognition of
AB  - determinants on the same strand as the scissile bond.
ER  -

TY  - JOUR
AU  - Zebala, J.
AU  - Choi, J.
AU  - Barany, F.
TI  - Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1992
SP  - 8097
EP  - 8105
VL  - 267
AB  - The TaqI restriction endonuclease recognizes and cleaves the duplex DNA sequence T|CGA. Steady
AB  - state kinetic analysis with a small oligodeoxyribonucleotide substrate showed that the enzyme
AB  - obeyed Michaelis-Menten kinetics (Km=53 nM, kcat=1.3 min-1 at 50C and Km=0.5 nM, kcat=2.9
AB  - min-1 at 60C). At 0C, the enzyme was completely inactive, while at 15C, turnover produced
AB  - nicked substrate as the major product in excess of enzyme indicating dissociation between
AB  - nicking events. Above 37C, both strands in the duplex were cleaved prior to dissociation. In
AB  - contrast to the tight, temperature-dependent binding of substrate, binding of the Mg2+
AB  - cofactor was weak (Kd=2.5 mM) and the same at either 50C or 60C. Single-turnover experiments
AB  - using oligonucleotide substrate showed that hydrolysis of duplex DNA occurred via two
AB  - independent nicking events, each with a first order rate constant (kst) of 5.8 min-1 at 60C
AB  - and 3.5 min-1 at 50C. The pH dependence of Km (pKa=9) and kst (pKa=7) suggests Lys/Arg and
AB  - His, respectively, as possible amino acids influencing these constants. Moreover, although kst
AB  - increased significantly with pH, kcat did not, indicating that at least two steps can be
AB  - rate-controlling in the reaction pathway. Binding of protein to canonical DNA in the presence
AB  - of Mg2+ at 0C or in the absence of Mg2+ at 50C was weak (Kd=2.5 microM or 5,000 fold weaker
AB  - than the optimal measured Km) and equal to the binding of noncanonical DNA as judged by
AB  - retention on nitrocellulose. Similar results were seen in gel retardation assays. These
AB  - results suggest that both Mg2+ and high temperature are required to attain the correct protein
AB  - conformation to form the tight complex seen in the steady state analysis. In the accompanying
AB  - paper (Zebala, J.A., Choi, J., Trainor, G.L., and Barany, F. (1992) J. Biol. Chem. 267,
AB  - 8106-8116), we report how these kinetic constants are altered using substrate analogues and
AB  - propose a model of functional groups involved in TaqI endonuclease recognition.
ER  -

TY  - JOUR
AU  - Zebala, J.A.
TI  - DNA recognition of base-analogue and chemically modified substrates by the TaqI restriction endonuclease.
JO  - Diss. Abstr.
PY  - 1993
SP  - 1394
EP  - 139B
VL  - 54
AB  - The TaqI restriction endonuclease recognizes and cleaves the duplex DNA sequence T^CGA. It has
AB  - been proposed that protein-DNA recognition is mediated via specific hydrogen bond, hydrophobic
AB  - and/or electrostatic interactions between the protein and DNA surfaces. We have attempted to
AB  - map and quantitate the energies of these interactions for the TaqI endonuclease by
AB  - constructing substrates substituted with base or phosphate analogues that either remove or
AB  - sterically obstruct particular functional groups in the canonical TCGA sequence. The DNA
AB  - backbone was also modified using a chemical approach (phosphate ethylation) which identified
AB  - several phosphates in the recognition sequence essential for cleavage. The base analogues;
AB  - N6-methyl-A, N7-deaza-A, N7-deaza-G, inosine, N4-methyl-C, 5-methylC, uracil, 5-bromoU and the
AB  - phosphate analogues; a-thio-A, a-thioG, a-thio-T, a-thio-A were substituted for their
AB  - corresponding unmodified counterpart in one strand of the TCGA duplex. The effects of these
AB  - analogues were monitored by measuring the steady-state (Km, kcat) and single-turnover (kst)
AB  - kinetic constants. Only the N6-methyl-A substituted DNA, which mimics in vivo methylation, was
AB  - unreactive while the remaining analogue substitutions exhibited Michaelis-Menten kinetics. In
AB  - general, the Km was either unchanged or lowered by the analogue substitutions. In contrast,
AB  - many of the analogues severely reduced Kcat, suggesting the modified functional groups served
AB  - mainly to destabilize the transition state. Single-turnover measurements paralleled the kcat
AB  - results, pointing to the N7 and N6 of A, the N7 of G and one of the nonbridging oxygens 3' to
AB  - T (scissile bond) as putative contacts made in achieving the transition state. Substrates with
AB  - double substitutions displayed simple additivity of delta,deltaG' implying that these changes
AB  - behaved independently. The unmodified strand in ten out of twelve hemi-substituted substrates
AB  - had a normal kst value suggesting that a particular cleavage center is controlled
AB  - predominantly by recognition of determinants on the same strand as the scissile bond. These
AB  - results are discussed in relation to base analogue work from the EcoRI, RsrI and EcoRV
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Zebala, J.A.
AU  - Choi, J.
AU  - Trainor, G.L.
AU  - Barany, F.
TI  - DNA recognition of base analogue and chemically modified substrates by the TaqI restriction endonuclease.
JO  - J. Biol. Chem.
PY  - 1992
SP  - 8106
EP  - 8116
VL  - 267
AB  - It has been proposed that protein-DNA recognition is mediated via specific hydrogen bond,
AB  - hydrophobic, and/or electrostatic interactions between the protein and DNA surfaces. We have
AB  - attempted to map and quantitate the energies of these interactions for the TaqI endonuclease
AB  - by constructing substrates substituted with base or phosphate analogues that either remove or
AB  - sterically obstruct particular functional groups in the canonical TCGA sequence. The DNA
AB  - backbone was also modified using a chemical approach (phosphate ethylation) which identified
AB  - several phosphates in the recognition sequence essential for cleavage. The base analogues,
AB  - N6-methyl-A, N7-deaza-A, N7-deaza-G, inosine, N4-methyl-C, 5-methyl-C, uracil, 5-bromo-U, and
AB  - the phosphate analogues, alpha-thio-A, alpha-thio-G, alpha-thio-T, alpha-thio-A, were
AB  - substituted for their corresponding unmodified counterpart in one strand of the TCGA duplex.
AB  - The effects of these analogues were monitored by measuring the steady state (Km5 kcat) and
AB  - single-turnover (kst) kinetic constants. Only the N6-methyl-A-substituted DNA, which mimics in
AB  - vivo methylation, was unreactive while the remaining analogue substitutions exhibited
AB  - Michaelis-Menten kinetics. In general, the Km was either unchanged or lowered by the analogue
AB  - substitutions. In contrast, many of the analogues severely reduced kcat, suggesting the
AB  - modified functional groups served mainly to destabilize the transition state. Single-turnover
AB  - measurements paralleled the kcat results, pointing to the N7 and N6 of A, the N7 of G, and one
AB  - of the nonbridging oxygens 3' to T as putative contacts made in achieving the transition
AB  - state. Substrates with double substitutions displayed simple additivity of DeltaDeltaG
AB  - implying that these changes behaved independently. The unmodified strand in 10 out of 12
AB  - hemisubstituted substrates had a normal kst value suggesting that a particular cleavage center
AB  - is controlled predominantly by recognition of determinants on the same strand as the scissile
AB  - bond. These results are discussed in relation to base analogue work from the EcoRI, RsrI, and
AB  - EcoRV restriction endonucleases.
ER  -

TY  - JOUR
AU  - Zebrowska, J.
AU  - Zolnierkiewicz, O.
AU  - Skowron, M.A.
AU  - Zylicz-Stachula, A.
AU  - Jezewska-Frackowiak, J.
AU  - Skowron, P.M.
TI  - A putative Type IIS restriction endonuclease GeoICI from Geobacillus sp.--A robust, thermostable alternative to mezophilic prototype BbvI.
JO  - J. Biosci.
PY  - 2016
SP  - 27
EP  - 38
VL  - 41
AB  - Screening of extreme environments in search for novel microorganisms may lead to  the
AB  - discovery of robust enzymes with either new substrate specificities or
AB  - thermostable equivalents of those already found in mesophiles, better suited for
AB  - biotechnology applications. Isolates from Iceland geysers' biofilms, exposed to a
AB  - broad range of temperatures, from ambient to close to water boiling point, were
AB  - analysed for the presence of DNA-interacting proteins, including restriction
AB  - endonucleases (REases). GeoICI, a member of atypical Type IIS REases, is the most
AB  - thermostable isoschizomer of the prototype BbvI, recognizing/cleaving
AB  - 5'-GCAGC(N8/12)-3'DNA sequences. As opposed to the unstable prototype, which
AB  - cleaves DNA at 30 degrees C, GeoICI is highly active at elevated temperatures, up
AB  - to 73 degrees C and over a very wide salt concentration range.
AB  - Recognition/cleavage sites were determined by: (i) digestion of plasmid and
AB  - bacteriophage lambda DNA (Lambda); (ii) cleavage of custom PCR substrates, (iii)
AB  - run-off sequencing of GeoICI cleavage products and (iv) shotgun cloning and
AB  - sequencing of Lambda DNA fragmented with GeoICI. Geobacillus sp. genomic DNA was
AB  - PCR-screened for the presence of other specialized REases-MTases and as a result,
AB  - another putative REase- MTase, GeoICII, related to the Thermus sp. family of
AB  - bifunctional REases-methyltransferases (MTases) was detected.
ER  -

TY  - JOUR
AU  - Zecher, K.
AU  - Suleiman, M.
AU  - Wibberg, D.
AU  - Winkler, A.
AU  - Philipp, B.
AU  - Kalinowski, J.
TI  - Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria.
JO  - Genome Announcements
PY  - 2017
SP  - e01623
EP  - e01616
VL  - 5
AB  - The C1-compound monomethylamine can serve as a nitrogen, carbon, and energy source for
AB  - heterotrophic bacteria. The marine alphaproteobacterium Donghicola sp.
AB  - strain KarMa can use monomethylamine as a source only for nitrogen and not for
AB  - carbon. Its draft genome sequence is presented here and reveals putative gene
AB  - clusters for the methylamine dehydrogenase and the N-methylglutamate pathways for
AB  - monomethylamine metabolism.
ER  -

TY  - JOUR
AU  - Zedelius, J.
AU  - Rabus, R.
AU  - Grundmann, O.
AU  - Werner, I.
AU  - Brodkorb, D.
AU  - Schreiber, F.
AU  - Ehrenreich, P.
AU  - Behrends, A.
AU  - Wilkes, H.
AU  - Kube, M.
AU  - Reinhardt, R.
AU  - Widdel, F.
TI  - Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation.
JO  - Environ. Microbiol. Reports
PY  - 2011
SP  - 125
EP  - 135
VL  - 3
AB  - Microorganisms can degrade saturated hydrocarbons (alkanes) not only under oxic but also under
AB  - anoxic conditions. Three denitrifying isolates (strains HxN1, OcN1, HdN1) able to grow under
AB  - anoxic conditions by coupling alkane oxidation to CO2 with NO3 - reduction to N2 were compared
AB  - with respect to their alkane metabolism. Strains HxN1 and OcN1, which are both
AB  - Betaproteobacteria, utilized n-alkanes from C6 to C8 and C8 to C12 respectively. Both activate
AB  - alkanes anaerobically in a fumarate-dependent reaction yielding alkylsuccinates, as suggested
AB  - by present and previous metabolite and gene analyses. However, strain HdN1 was unique in
AB  - several respects. It belongs to the Gammaproteobacteria and was more versatile towards
AB  - alkanes, utilizing the range from C6 to C30. Neither analysis of metabolites nor analysis of
AB  - genes in the complete genome sequence of strain HdN1 hinted at fumarate-dependent alkane
AB  - activation. Moreover, whereas strains HxN1 and OcN1 grew with alkanes and NO3 -, NO2 - or N2O
AB  - added to the medium, strain HdN1 oxidized alkanes only with NO3 - or NO2 - but not with added
AB  - N2O; but N2O was readily used for growth with long-chain alcohols or fatty acids. Results
AB  - suggest that NO2 - or a subsequently formed nitrogen compound other than N2O is needed for
AB  - alkane activation in strain HdN1. From an energetic point of view, nitrogen-oxygen species are
AB  - generally rather strong oxidants. They may enable enzymatic mechanisms that are not possible
AB  - under conditions of sulfate reduction or methanogenesis and thus allow a special mode of
AB  - alkane activation.
ER  -

TY  - JOUR
AU  - Zehr, E.S.
AU  - Bayles, D.O.
AU  - Boatwright, W.D.
AU  - Tabatabai, L.B.
AU  - Register, K.B.
TI  - Complete genome sequence of Ornithobacterium rhinotracheale strain ORT-UMN 88.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 16
EP  - 16
VL  - 9
AB  - Ornithobacterium rhinotracheale strain ORT-UMN 88 is a Gram-negative, pleomorphic, rod-shaped
AB  - bacterium and an etiologic agent of pneumonia and
AB  - airsacculitis in poultry. It is a member of the family Flavobacteriaceae of the
AB  - phylum Bacteroidetes. O. rhinotracheale strain ORT-UMN 88 was isolated from the
AB  - pneumonic lung of a turkey in 1995. It was the isolate first used to
AB  - experimentally reproduce disease in turkeys and has since been the focus of
AB  - investigations characterizing potential virulence factors of the bacterium. The
AB  - genome of O. rhinotracheale strain ORT-UMN 88 consists of a circular chromosome
AB  - of 2,397,867 bp with a total of 2300 protein-coding genes, nine RNA genes, and
AB  - one noncoding RNA gene. A companion paper in this issue of SIGS reports the
AB  - non-contiguous finished genome sequence of an additional strain of O.
AB  - rhinotracheale, isolated in 2006.
ER  -

TY  - JOUR
AU  - Zehr, E.S.
AU  - Bayles, D.O.
AU  - Boatwright, W.D.
AU  - Tabatabai, L.B.
AU  - Register, K.B.
TI  - Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 14
EP  - 14
VL  - 9
AB  - The Gram-negative, pleomorphic, rod-shaped bacterium Ornithobacterium rhinotracheale is a
AB  - cause of pneumonia and airsacculitis in poultry. It is a
AB  - member of the family Flavobacteriaceae of the phylum 'Bacteroidetes'. O.
AB  - rhinotracheale strain H06-030791 was isolated from the lung of a turkey in North
AB  - Carolina in 2006. Its genome consists of a circular chromosome of 2,319,034 bp in
AB  - length with a total of 2243 protein-coding genes and nine RNA genes. Genome
AB  - sequences are available for two additional strains of O. rhinotracheale, isolated
AB  - in 1988 and 1995, the latter described in a companion genome report in this issue
AB  - of SIGS. The genome sequence of O. rhinotracheale strain H06-030791, a more
AB  - contemporary isolate, will be of value in establishing core and pan-genomes for
AB  - O. rhinotracheale and elucidating its evolutionary history.
ER  -

TY  - JOUR
AU  - Zehr, E.S.
AU  - Tabatabai, L.B.
TI  - Detection of a bacteriophage gene encoding a Mu-like portal protein in Haemophilus parasuis reference strains and field isolates by nested polymerase chain reaction.
JO  - J. Vet. Diagn. Invest.
PY  - 2011
SP  - 538
EP  - 542
VL  - 23
AB  - A nested polymerase chain reaction assay was developed to determine the presence of a gene
AB  - encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field
AB  - isolates of Haemophilus parasuis.  Specific primers, based on the gene's sequence, were
AB  - utilized.  A majority of the virulent reference strains and field isolates tested harbored the
AB  - gene.  The results suggest that the nPCR technique described in the current report could serve
AB  - as a tool for epidemiological studies of H. parasuis.
ER  -

TY  - JOUR
AU  - Zehr, E.S.
AU  - Tabatabai, L.B.
AU  - Bayles, D.O.
TI  - Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis.
JO  - BMC Genomics
PY  - 2012
SP  - 331
EP  - 331
VL  - 13
AB  - ABSTRACT: BACKGROUND: Haemophilus parasuis, the causative agent of Glasser's
AB  - disease, is prevalent in swine herds and clinical signs associated with this
AB  - disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia.
AB  - Six to eight week old pigs in segregated early weaning herds are particularly
AB  - susceptible to the disease. Insufficient colostral antibody at weaning or the
AB  - mixing of pigs with heterologous virulent H. parasuis strains from other farm
AB  - sources in the nursery or grower-finisher stage are considered to be factors for
AB  - the outbreak of Glasser's disease. Previously, a Mu-like bacteriophage portal
AB  - gene was detected in a virulent swine isolate of H. parasuis by nested polymerase
AB  - chain reaction. Mu-like bacteriophages are related phyologenetically to
AB  - enterobacteriophage Mu and are thought to carry virulence genes or to induce host
AB  - expression of virulence genes. This study characterizes the Mu-like
AB  - bacteriophage, named SuMu, isolated from a virulent H. parasuis isolate. RESULTS:
AB  - Characterization was done by genomic comparison to enterobacteriophage Mu and
AB  - proteomic identification of various homologs by mass spectrometry. This is the
AB  - first report of isolation and characterization of this bacteriophage from the
AB  - Myoviridae family, a double-stranded DNA bacteriophage with a contractile tail,
AB  - from a virulent field isolate of H. parasuis. The genome size of bacteriophage
AB  - SuMu was 37,151 bp. DNA sequencing revealed fifty five open reading frames,
AB  - including twenty five homologs to Mu-like bacteriophage proteins: Nlp, phage
AB  - transposase-C-terminal, COG2842, Gam-like protein, gp16, Mor, peptidoglycan
AB  - recognition protein, gp29, gp30, gpG, gp32, gp34, gp36, gp37, gpL, phage tail
AB  - tube protein, DNA circulation protein, gpP, gp45, gp46, gp47, COG3778, tail fiber
AB  - protein gp37-C terminal, tail fiber assembly protein, and Com. The last open
AB  - reading frame was homologous to IS1414. The G + C content of bacteriophage SuMu
AB  - was 41.87% while its H. parasuis host genome's G + C content was 39.93%. Twenty
AB  - protein homologs to bacteriophage proteins, including 15 structural proteins, one
AB  - lysogeny-related and one lysis-related protein, and three DNA replication
AB  - proteins were identified by mass spectrometry. One of the tail proteins, gp36,
AB  - may be a virulence-related protein. CONCLUSION: Bacteriophage SuMu was
AB  - characterized by genomic and proteomic methods and compared to
AB  - enterobacteriophage Mu.
ER  -

TY  - JOUR
AU  - Zehr, J.P.
AU  - Bench, S.R.
AU  - Carter, B.J.
AU  - Hewson, I.
AU  - Niazi, F.
AU  - Shi, T.
AU  - Tripp, H.J.
AU  - Affourtit, J.P.
TI  - Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II.
JO  - Science
PY  - 2008
SP  - 1110
EP  - 1112
VL  - 322
AB  - Biological nitrogen (N2) fixation is important in controlling biological
AB  - productivity and carbon flux in the oceans. Unicellular N2-fixing
AB  - cyanobacteria have only recently been discovered and are widely
AB  - distributed in tropical and subtropical seas. Metagenomic analysis of flow
AB  - cytometry-sorted cells shows that unicellular N2-fixing cyanobacteria in
AB  - "group A" (UCYN-A) lack genes for the oxygen-evolving photosystem II and
AB  - for carbon fixation, which has implications for oceanic carbon and
AB  - nitrogen cycling and raises questions regarding the evolution of
AB  - photosynthesis and N2 fixation on Earth.
ER  -

TY  - JOUR
AU  - Zeigler, D.R.
TI  - Genome Sequence of Bacillus glycinifermentans TH008, Isolated from Ohio Soil.
JO  - Genome Announcements
PY  - 2016
SP  - e01573
EP  - e01515
VL  - 4
AB  - The genome sequence of an Ohio soil isolate, TH008, was determined. The sequence  reveals a
AB  - close relationship between TH008 and domesticated Bacillus
AB  - glycinifermentans strains found in a traditional Korean fermented soybean food.
ER  -

TY  - JOUR
AU  - Zekic, F.
AU  - Weselowski, B.
AU  - Yuan, Z.C.
TI  - Complete Genome Sequence of Burkholderia cenocepacia CR318, a Phosphate-Solubilizing Bacterium Isolated from Corn Root.
JO  - Genome Announcements
PY  - 2017
SP  - e00490
EP  - e00417
VL  - 5
AB  - Here, we report the complete genome sequence of the phosphate-solubilizing bacterium
AB  - Burkholderia cenocepacia CR318, consisting of three circular
AB  - chromosomes of 3,511,146 bp, 3,097,552 bp, and 1,056,069 bp. The data presented
AB  - will facilitate further insight into the mechanisms of phosphate solubilization
AB  - and its application for agricultural and ecological sustainability.
ER  -

TY  - JOUR
AU  - Zelby, L.S.
TI  - Antisense RNA and ribozymes targeting DNA methyltransferase for in vivo studies.
JO  - Diss. Abstr.
PY  - 1996
SP  - 907
EP  - 907
VL  - 57
AB  - The aim of this study was to make antisense RNA and ribozyme constructs
AB  - directed against mouse DNA methyltransferase (Mtase) and to use inducible expression to
AB  - perturb in vivo DNA methylation, both in tissue culture cells and in transgenic mice.  The
AB  - sheep metallothionein Ia promoter, known to be inducible by zinc in tissue culture cells and
AB  - mouse somatic tissues, and constitutive in mouse gonadal tissues, was used to drive in
AB  - vivo expression.  Several antisense RNA and ribozyme constructs were made and all were
AB  - shown to be expressed in a fibroblast-derived A9 hybrid cell line.  The ribozyme was
AB  - shown to cleave its target RNA efficiently in vitro, but the A9 hybrid cells were found to be
AB  - not suitable for determination of effects of DNA methyltransferase on methylation levels.
AB  - Therefore, another cell line, L61-M, was characterized.  L61-M cells were found to provide
AB  - a very sensitive and quantitative assay for methylation perturbations by measuring
AB  - reactivation of a methylation-silenced thymidine kinase (TK) gene.  Transfection
AB  - experiments using L61-M cells showed that the ribozyme caused a ten-fold increase over
AB  - background of stable TK+ revertants, and that the ribozyme was more effective than the
AB  - antisense RNA constructs, which gave results not significantly different from background.
AB  - Though the ribozyme clearly caused an effect, mRNA for the antisense RNAs or the
AB  - ribozyme could not be detected in transfected L61-M cells, so proof of mechanism of action
AB  - could not be obtained.  The present working hypothesis is that the ribozyme is quite
AB  - effective and deserving of further study, but a different promoter or expression vector
AB  - needs to be used in order to take full advantage of the excellent assay system provided by
AB  - the L61-M cells.
ER  -

TY  - JOUR
AU  - Zelinkova, E.
AU  - Paulicek, M.
AU  - Zelinka, J.
TI  - Modification methylase M. Sau3239I from Streptomyces aureofaciens 3239.
JO  - FEBS Lett.
PY  - 1990
SP  - 147
EP  - 148
VL  - 271
AB  - By chromatography on phosphocellulose and Heparin-Sepharose the modification
AB  - methylase M.Sau3239I was detected and partially purified from cells of
AB  - Streptomyces aureofaciens 3239.  Methylation by this enzyme protects DNA from
AB  - cleavage by the restriction endonuclease R.Sau3239I.  The enzyme catalyzes
AB  - methylation of adenine to N-6-methyladenine in the 5'-CTGGmAG-3' recognition
AB  - sequence.
ER  -

TY  - JOUR
AU  - Zelinskaya, N.V.
AU  - Kovalevskaya, N.P.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A new site-specific endonuclease from Acinetobacter species (Strain M).
JO  - Biokhimiia
PY  - 1996
SP  - 1471
EP  - 1482
VL  - 61
AB  - The site-specific endonuclease R.AspMI was isolated from Acinetobacter species (strain M) and
AB  - purified to functional purity.  The enzyme recognizes the symmetrical DNA sequence
AB  - 5'-AGG/CCT-3' and cleaves it as shown by the arrow, forming blunt DNA ends.  The enzyme is
AB  - an isoschizomer of endonuclease StuI.  Cleavage of the DNA site is inhibited by
AB  - dcm-methylation.  AspM is in solution as an ~30-kD monomer.
ER  -

TY  - JOUR
AU  - Zelinskaya, N.V.
AU  - Kovalevskaya, N.P.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A site-specific endonuclease and methylase from the Thermophilic strain of Bacillus species IS4.
JO  - Biokhimiia
PY  - 1995
SP  - 1435
EP  - 1448
VL  - 60
AB  - A site-specific endonuclease (R.BspIS4I) and methylase (M.BspIS4I) have been isolated and
AB  - purified to functional purity from the thermophilic strain of Bacillus species IS4.  R.BspIS4I
AB  - recognizes the sequence
AB  - 5'-GAAGAC2N^-3'
AB  - 3'-CTTCTG6N^-5' and cleaves it as shown by the arrows to form single-stranded
AB  - tetranucleotide 5'-protruding termini.  The enzyme is an isoschizomer of endonuclease BbvII.
AB  - M.BspIS4I is attributed to the adenine-specific methylases.
ER  -

TY  - JOUR
AU  - Zelinskaya, N.V.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A new site-specific adenine DNA-methyltransferase from the strain of Bacillus species ST5.
JO  - Biokhimiia
PY  - 1996
SP  - 1006
EP  - 1014
VL  - 61
AB  - The site-specific DNA-methylase M.BspST5I has been isolated from Bacillus species ST5 and
AB  - purified to functional purity.  M.BspST5I protects DNA from endonuclease R.BspST5I which
AB  - recognizes the nonpalindromic sequence
AB  - 5'-GCATC-3'
AB  - 3'-CGTAG-5'
AB  - on DNA.  M.BspST5I is an adenine-specific methylase.
ER  -

TY  - JOUR
AU  - Zelinskaya, N.V.
AU  - Matvienko, N.N.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A novel site-specific endonuclease from Bacillus species ST5.
JO  - Biokhimiia
PY  - 1995
SP  - 1999
EP  - 2010
VL  - 60
AB  - A site-specific endonuclease, R.BspST5I, has been isolated in a functionally pure state from
AB  - the thermophilic strain Bacillus species ST5.  The enzyme recognizes the sequence 5'-
AB  - GCATC-3' on DNA and cleaves it at a distance of five nucleotides from the 3'-end of the
AB  - recognition site and at distances of nine or ten nucleotides along the complementary strand,
AB  - depending on the nucleotide surrounding the site on the DNA.  The enzyme is an isomer of
AB  - endonuclease SfaNI from Streptococcus faecalis ND547.
ER  -

TY  - JOUR
AU  - Zell, R.
AU  - Fritz, H.-J.
TI  - DNA mismatch-repair in Escherichia coli counteracting the hydrolytic deamination of 5-methyl-cytosine residues.
JO  - EMBO J.
PY  - 1987
SP  - 1809
EP  - 1815
VL  - 6
AB  - Derivatives of phage M13 were constructed and used for the in vitro
AB  - preparation of heteroduplex DNA molecules containing base/base mismatches that mimick
AB  - DNA lesions caused by hydrolytic deamination of 5-meC residues in Escherichia coli DNA
AB  - (i.e. they carry a T/G mismatch in the special sequence context provided by the recognition
AB  - site -CCA/TGG-of the Dcm-methyltransferase).  Upon introduction of these heteroduplex
AB  - DNAs into CaCl2-treated E. coli cells, the mismatches are efficiently repaired with high
AB  - bias in favour of the DNA strand containing the mismatched guanine residue.  This special
AB  - DNA mismatch-repair operates on fully dam-methylated DNA and is independent of gene
AB  - mutH.  It thus fulfills the salient requirements of a repair pathway responsible for
AB  - counteracting the spontaneous hydrolytic deamination of 5-meC in vivo.  The repair
AB  - efficiency is boosted by a 5-methyl group present on the cytosine residue at the next-nearest
AB  - position to the 5' side of the mismatched guanine.  The repair is severly impaired in host
AB  - strains carrying a mutation in any of the three loci dcm, mutL and mutS.
ER  -

TY  - JOUR
AU  - Zeng, Q.
AU  - Wang, J.
AU  - Bertels, F.
AU  - Giordano, P.R.
AU  - Chilvers, M.I.
AU  - Huntley, R.B.
AU  - Vargas, J.M.
AU  - Sundin, G.W.
AU  - Jacobs, J.L.
AU  - Yang, C.H.
TI  - Recombination of Virulence Genes in Divergent Acidovorax avenae Strains That Infect a Common Host.
JO  - Mol. Plant Microbe Interact.
PY  - 2017
SP  - 813
EP  - 828
VL  - 30
AB  - Bacterial etiolation and decline (BED), caused by Acidovorax avenae, is an
AB  - emerging disease of creeping bentgrass on golf courses in the United States. We
AB  - performed the first comprehensive analysis of A. avenae on a nationwide
AB  - collection of turfgrass- and maize-pathogenic A. avenae. Surprisingly, our
AB  - results reveal that the turfgrass-pathogenic A. avenae in North America are not
AB  - only highly divergent but also belong to two distinct phylogroups. Both
AB  - phylogroups specifically infect turfgrass but are more closely related to maize
AB  - pathogens than to each other. This suggests that, although the disease is only
AB  - recently reported, it has likely been infecting turfgrass for a long time. To
AB  - identify a genetic basis for the host specificity, we searched for genes closely
AB  - related among turfgrass strains but distantly related to their homologs from
AB  - maize strains. We found a cluster of 11 such genes generated by three ancient
AB  - recombination events within the type III secretion system (T3SS) pathogenicity
AB  - island. Ever since the recombination, the cluster has been conserved by strong
AB  - purifying selection, hinting at its selective importance. Together our analyses
AB  - suggest that BED is an ancient disease that may owe its host specificity to a
AB  - highly conserved cluster of 11 T3SS genes.
ER  -

TY  - JOUR
AU  - Zeng, Q.L.
AU  - Bonocora, R.P.
AU  - Shub, D.A.
TI  - A Free-Standing Homing Endonuclease Targets an Intron Insertion Site in the psbA Gene of Cyanophages.
JO  - Curr. Biol.
PY  - 2009
SP  - 218
EP  - 222
VL  - 19
AB  - Homing endonuclease genes are mobile elements that promote their duplication into cognate
AB  - sites that lack the endonuclease gene [1, 2].
AB  - The homing endonuclease initiates this event through site-specific DNA
AB  - cleavage. Copying of the endonuclease gene follows as a consequence of
AB  - DNA repair. A genome containing a homing endonuclease gene is subject
AB  - to self-cleavage. Protection is accomplished through DNA sequence
AB  - polymorphisms, as is the case in intronless homing of free-standing
AB  - endonuclease genes [3, 4], or by disruption of the recognition site by
AB  - a group I intron (or intein) into which the endonuclease ORF is
AB  - embedded. We describe here a novel free-standing homing endonuclease
AB  - from cyanobacteriophage S-PM2, which is similar to the DNA resolvase of
AB  - bacteriophage T4 and is encoded adjacent to an intron-containing psbA
AB  - gene [5, 6]. The endonuclease makes a specific double-strand cut near
AB  - the intron insertion site (IIS), its DNA recognition site spans the
AB  - IIS, and it is unable to cleave intron-containing psbA genes. This
AB  - interdependence of a free-standing endonuclease gene and a group I
AB  - intron, which we denote "collaborative homing," has not been reported
AB  - previously and gives support to a hypothesis of formation of composite
AB  - mobile introns by independent convergence of an intron and an
AB  - endonuclease gene on the same target sequence.
ER  -

TY  - JOUR
AU  - Zeng, W.
AU  - Chen, G.
AU  - Tang, Z.
AU  - Wu, H.
AU  - Shu, L.
AU  - Liang, Z.
TI  - Draft Genome Sequence of Bacillus subtilis GXA-28, a Thermophilic Strain with High Productivity of Poly-gamma-Glutamic Acid.
JO  - Genome Announcements
PY  - 2014
SP  - e01259
EP  - e01214
VL  - 2
AB  - Bacillus subtilis GXA-28 is a thermophilic strain that can produce high yield and high
AB  - molecular weight of poly-gamma-glutamic acid under high temperature. Here,
AB  - we report the draft genome sequence of this strain, which may provide the genomic
AB  - basis for the high productivity of poly-gamma-glutamic acid.
ER  -

TY  - JOUR
AU  - Zeng, X.
AU  - Jebbar, M.
AU  - Shao, Z.
TI  - Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341T, Isolated from Deep-Sea Hydrothermal Sediments.
JO  - Genome Announcements
PY  - 2015
SP  - e01080
EP  - e01015
VL  - 3
AB  - We report the genome sequence of Palaeococcus pacificus DY20341(T), isolated from a sediment
AB  - sample collected from eastern Pacific Ocean hydrothermal fields, which is the first report of
AB  - a complete genome for a Palaeococcus species. The genome sequence will help to better
AB  - understand differentiation phylogenetic relationships and evolution of several Thermococcales
AB  - species.
ER  -

TY  - JOUR
AU  - Zeng, Y.
AU  - Feng, F.
AU  - Liu, Y.
AU  - Li, Y.
AU  - Koblizek, M.
TI  - Genome Sequences and Photosynthesis Gene Cluster Composition of a Freshwater Aerobic Anoxygenic Phototroph, Sandarakinorhabdus sp. Strain AAP62, Isolated from  the Shahu Lake in Ningxia, China.
JO  - Genome Announcements
PY  - 2013
SP  - e00034
EP  - e00013
VL  - 1
AB  - We report the first genome sequence from the recently established alpha-4 proteobacterial
AB  - genus . The genome of the sp. strain AAP62 contains a
AB  - photosynthesis gene cluster carrying major genes for bacterial reaction centers.
AB  - The presence of genes related to aerobic respiratory electron transport confirms
AB  - the lifestyle of this organism as an aerobic anoxygenic photoheterotroph.
ER  -

TY  - JOUR
AU  - Zeng, Y.
AU  - Kasalicky, V.
AU  - Simek, K.
AU  - Koblizek, M.
TI  - Genome sequences of two freshwater betaproteobacterial isolates, limnohabitans species strains rim28 and rim47, indicate their capabilities as both  photoautotrophs and ammonia oxidizers.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6302
EP  - 6303
VL  - 194
AB  - Betaproteobacterial genus Limnohabitans represents an important part of freshwater
AB  - bacterioplankton. Here, we report genome sequences of two
AB  - Limnohabitans isolates, Rim28 and Rim47. They contain a complete photosynthesis
AB  - gene cluster, RuBisCO, CO dehydrogenase, ammonia monooxygenase, and
AB  - sulfur-oxidizing genes, which indicates a great metabolic versatility of the
AB  - Limnohabitans species.
ER  -

TY  - JOUR
AU  - Zeng, Y.
AU  - Koblizek, M.
AU  - Feng, F.
AU  - Liu, Y.
AU  - Wu, Z.
AU  - Jian, J.
TI  - Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph, Blastomonas sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China.
JO  - Genome Announcements
PY  - 2013
SP  - e0007113
EP  - e0007113
VL  - 1
AB  - Blastomonas is a strictly aerobic bacteriochlorophyll a-producing genus within the alpha-4
AB  - Proteobacteria. Here we report the first genome sequence from this
AB  - genus. The draft genome of Blastomonas sp. strain AAP53 contains a split
AB  - photosynthesis gene cluster and two gene clusters encoding a flagellar system.
AB  - Genes for the autotrophic CO2 fixation pathway are absent.
ER  -

TY  - JOUR
AU  - Zeng, Z.
AU  - Chen, C.
AU  - Du, H.
AU  - Wang, G.
AU  - Li, M.
TI  - High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 92
EP  - 92
VL  - 10
AB  - Flavobacterium enshiense DK69(T) is a Gram-negative, aerobic, rod-shaped, non-motile and
AB  - non-flagellated bacterium that belongs to the family
AB  - Flavobacteriaceae in the phylum Bacteroidetes. The high quality draft genome of
AB  - strain DK69(T) was obtained and has a 3,375,260 bp genome size with a G + C
AB  - content of 37.7 mol % and 2848 protein coding genes. In addition, we sequenced
AB  - five more genomes of Flavobacterium type strains and performed a comparative
AB  - genomic analysis among 12 Flavobacterium genomes. The results show some specific
AB  - genes within the fish pathogenic Flavobacterium strains which provide information
AB  - for further analysis the pathogenicity.
ER  -

TY  - JOUR
AU  - Zeng, Z.
AU  - Dai, S.
AU  - Xie, Y.
AU  - Tian, X.
AU  - Li, J.
AU  - Wang, X.
TI  - Genome sequences of two pseudoalteromonas strains isolated from the South china sea.
JO  - Genome Announcements
PY  - 2014
SP  - e00305
EP  - e00314
VL  - 2
AB  - Two Pseudoalteromonas strains, SCSIO 04301 and SCSIO 11900, were isolated from the South China
AB  - Sea, and both strains form biofilms. Here we present the draft genome sequences of these two
AB  - strains, which will aid the study of marine microbes that are adapted to marine sediments or
AB  - are associated with eukaryotic hosts.
ER  -

TY  - JOUR
AU  - Zepeda, V.
AU  - Dassa, B.
AU  - Borovok, I.
AU  - Lamed, R.
AU  - Bayer, E.A.
AU  - Cate, J.H.
TI  - Draft Genome Sequence of the Cellulolytic Bacterium Clostridium papyrosolvens C7  (ATCC 700395).
JO  - Genome Announcements
PY  - 2013
SP  - e00698
EP  - e00613
VL  - 1
AB  - We report the draft genome sequence of the cellulose-degrading bacterium Clostridium
AB  - papyrosolvens C7, originally isolated from mud collected below a
AB  - freshwater pond in Massachusetts. This Gram-positive bacterium grows in a
AB  - mesophilic anaerobic environment with filter paper as the only carbon source, and
AB  - it has a simple cellulosome system with multiple carbohydrate-degrading enzymes.
ER  -

TY  - JOUR
AU  - Zerillo, M.M.
AU  - Van Sluys, M.A.
AU  - Camargo, L.E.
AU  - Monteiro-Vitorello, C.B.
TI  - Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli.
JO  - BMC Microbiol.
PY  - 2008
SP  - 127
EP  - 127
VL  - 8
AB  - BACKGROUND: Leifsonia xyli is a xylem-inhabiting bacterial species
AB  - comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp.
AB  - cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in
AB  - sugarcane commercial fields and Lxc colonizes the xylem of several grasses
AB  - causing either mild or no symptoms of disease. The completely sequenced
AB  - genome of Lxx provided insights into its biology and pathogenicity. Since
AB  - IS elements are largely reported as an important source of bacterial
AB  - genome diversification and nothing is known about their role in chromosome
AB  - architecture of L. xyli, a comparative analysis of Lxc and Lxx elements
AB  - was performed. RESULTS: Sample sequencing of Lxc genome and comparative
AB  - analysis with Lxx complete DNA sequence revealed a variable number of IS
AB  - transposable elements acting upon genomic diversity. A detailed
AB  - characterization of Lxc IS elements and a comparative review with IS
AB  - elements of Lxx are presented. Each genome showed a unique set of elements
AB  - although related to same IS families when considering features such as
AB  - similarity among transposases, inverted and direct repeats, and element
AB  - size. Most of the Lxc and Lxx IS families assigned were reported to
AB  - maintain transposition at low levels using translation regulatory
AB  - mechanisms, consistent with our in silico analysis. Some of the IS
AB  - elements were found associated with rearrangements and specific regions of
AB  - each genome. Differences were also found in the effect of IS elements upon
AB  - insertion, although none of the elements were preferentially associated
AB  - with gene disruption. A survey of transposases among genomes of
AB  - Actinobacteria showed no correlation between phylogenetic relatedness and
AB  - distribution of IS families. By using Southern hybridization, we suggested
AB  - that diversification of Lxc isolates is also mediated by insertion
AB  - sequences in probably recent events. CONCLUSION: Collectively our data
AB  - indicate that transposable elements are involved in genome diversification
AB  - of Lxc and Lxx. The IS elements were probably acquired after the
AB  - divergence of the two subspecies and are associated with genome
AB  - organization and gene contents. In addition to enhancing understanding of
AB  - IS element dynamics in general, these data will contribute to our ongoing
AB  - comparative analyses aimed at understanding the biological differences of
AB  - the Lxc and Lxx.
ER  -

TY  - JOUR
AU  - Zernov, Y.P.
AU  - Lebedev, L.R.
AU  - Babkin, I.V.
AU  - Chizhikov, V.E.
TI  - Determination of substrate specificity of restriction endonuclease Kpn378I.
JO  - Bioorg. Khim.
PY  - 1990
SP  - 603
EP  - 604
VL  - 16
AB  - The recognition sequence and cleavage site, CCGC^GG, of a new restriction
AB  - endonuclease Kpn378I has been determined.
ER  -

TY  - JOUR
AU  - Zeytun, A. et al.
TI  - Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).
JO  - Standards in Genomic Sciences
PY  - 2011
SP  - 131
EP  - 143
VL  - 4
AB  - Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus
AB  - Hydrogenobacter. H. thermophilus was the first obligate autotrophic
AB  - organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of
AB  - interest because of the unusually efficient hydrogen-oxidizing ability of this
AB  - strain, which results in a faster generation time compared to other autotrophs.
AB  - It is also able to grow anaerobically using nitrate as an electron acceptor when
AB  - molecular hydrogen is used as the energy source, and able to aerobically fix
AB  - CO(2)via the reductive tricarboxylic acid cycle. This is the fifth completed
AB  - genome sequence in the family Aquificaceae, and the second genome sequence
AB  - determined from a strain derived from the original isolate. Here we describe the
AB  - features of this organism, together with the complete genome sequence and
AB  - annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA
AB  - genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
ER  -

TY  - JOUR
AU  - Zeytun, A.
AU  - Malfatti, S.A.
AU  - Vergez, L.M.
AU  - Shin, M.
AU  - Garcia, E.
AU  - Chain, P.S.
TI  - Complete Genome Sequence of Francisella philomiragia ATCC 25017.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3266
EP  - 3266
VL  - 194
AB  - Francisella philomiragia is a saprophytic gammaproteobacterium found only occasionally in
AB  - immunocompromised individuals and is the nearest neighbor to the
AB  - causative agent of tularemia and category A select agent Francisella tularensis.
AB  - To shed insight into the key genetic differences and the evolution of these two
AB  - distinct lineages, we sequenced the first complete genome of F. philomiragia
AB  - strain ATCC 25017, which was isolated as a free-living microorganism from water
AB  - in Bear River Refuge, Utah.
ER  -

TY  - JOUR
AU  - Zhai, Y.
AU  - Cheng, B.
AU  - Hu, J.
AU  - Kyeremeh, K.
AU  - Wang, X.
AU  - Jaspars, M.
AU  - Deng, H.
AU  - Deng, Z.X.
AU  - Hong, K.
TI  - Draft Genome Sequence of Streptomyces sp. Strain CT34, Isolated from a Ghanaian Soil Sample.
JO  - Genome Announcements
PY  - 2015
SP  - e01508
EP  - e01514
VL  - 3
AB  - Presented here is a draft genome sequence of Streptomyces sp. strain CT34, which  produces a
AB  - novel ribosomally synthesized and posttranslationally modified peptide
AB  - (RiPP). Analysis of the deduced open reading frame set identified the putative
AB  - RiPP biosynthesis gene cluster, as well as other secondary metabolite gene
AB  - clusters.
ER  -

TY  - JOUR
AU  - Zhalnina, K.V.
AU  - Dias, R.
AU  - Leonard, M.T.
AU  - Dorr-de-Quadros, P.
AU  - Camargo, F.A.
AU  - Drew, J.C.
AU  - Farmerie, W.G.
AU  - Daroub, S.H.
AU  - Triplett, E.W.
TI  - Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the  Ammonia-Oxidizing Archaea.
JO  - PLoS ONE
PY  - 2014
SP  - e101648
EP  - e101648
VL  - 9
AB  - The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil,
AB  - pollution of water sources and elevated emissions of greenhouse gas.
AB  - To date, eight AOA genomes are available in the public databases, seven are from
AB  - the group I.1a of the Thaumarchaeota and only one is from the group I.1b,
AB  - isolated from hot springs. Many soils are dominated by AOA from the group I.1b,
AB  - but the genomes of soil representatives of this group have not been sequenced and
AB  - functionally characterized. The lack of knowledge of metabolic pathways of soil
AB  - AOA presents a critical gap in understanding their role in biogeochemical cycles.
AB  - Here, we describe the first complete genome of soil archaeon Candidatus
AB  - Nitrososphaera evergladensis, which has been reconstructed from metagenomic
AB  - sequencing of a highly enriched culture obtained from an agricultural soil. The
AB  - AOA enrichment was sequenced with the high throughput next generation sequencing
AB  - platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of
AB  - sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome
AB  - revealed many similarities of the basic metabolism with the rest of sequenced
AB  - AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of
AB  - whole-genome homology with the closest sequenced relative Ca. N. gargensis.
AB  - Detailed analysis of the genome revealed coding sequences that were completely
AB  - absent from the group I.1a. These unique sequences code for proteins involved in
AB  - control of DNA integrity, transporters, two-component systems and versatile
AB  - CRISPR defense system. Notably, genomes from the group I.1b have more gene
AB  - duplications compared to the genomes from the group I.1a. We suggest that the
AB  - presence of these unique genes and gene duplications may be associated with the
AB  - environmental versatility of this group.
ER  -

TY  - JOUR
AU  - Zhan, B.
AU  - Angen, O.
AU  - Hedegaard, J.
AU  - Bendixen, C.
AU  - Panitz, F.
TI  - Draft Genome Sequences of Actinobacillus pleuropneumoniae Serotypes 2 and 6.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5846
EP  - 5847
VL  - 192
AB  - Actinobacillus pleuropneumoniae is a bacterial pathogen that causes highly contagious
AB  - respiratory infection in pigs and has a serious impact on the
AB  - production economy and animal welfare. As clear differences in virulence
AB  - between serotypes have been observed, the genetic basis should be
AB  - investigated at the genomic level. Here, we present the draft genome
AB  - sequences of the A. pleuropneumoniae serotypes 2 (strain 4226) and 6
AB  - (strain Femo).
ER  -

TY  - JOUR
AU  - Zhan, Y.
AU  - Yan, Y.
AU  - Zhang, W.
AU  - Yu, H.
AU  - Chen, M.
AU  - Lu, W.
AU  - Ping, S.
AU  - Peng, Z.
AU  - Yuan, M.
AU  - Zhou, Z.
AU  - Elmerich, C.
AU  - Lin, M.
TI  - Genome Sequence of Acinetobacter calcoaceticus PHEA-2, Isolated from Industry Wastewater.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2672
EP  - 2673
VL  - 193
AB  - Genome analysis of Acinetobacter calcoaceticus PHEA-2 was undertaken because of the importance
AB  - of this bacterium for bioremediation of phenol
AB  - polluted waster, and because of the close phylogenetic relationship of
AB  - this species with the human pathogen A. baumannii. To our knowledge, this
AB  - is the first strain of A. calcoaceticus whose genome has been sequenced.
ER  -

TY  - JOUR
AU  - Zhang, A.
AU  - Yang, M.
AU  - Hu, P.
AU  - Wu, J.
AU  - Chen, B.
AU  - Hua, Y.
AU  - Yu, J.
AU  - Chen, H.
AU  - Xiao, J.
AU  - Jin, M.
TI  - Comparative Genomic Analysis of Streptococcus suis reveals significant genomic diversity among different serotypes.
JO  - BMC Genomics
PY  - 2011
SP  - 523
EP  - 523
VL  - 12
AB  - ABSTRACT:  BACKGROUND: Streptococcus suis (S. suis) is a major swine
AB  - pathogen and an emerging zoonotic agent. Serotypes 1, 2, 3, 7, 9, 14 and
AB  - 1/2 are the most prevalent serotypes of this pathogen. However, almost all
AB  - studies were carried out on serotype 2 strains. Therefore,
AB  - characterization of genomic features of other serotypes will be required
AB  - to better understand their virulence potential and phylogenetic
AB  - relationships among different serotypes. RESULTS: Four Chinese S. suis
AB  - strains belonging to serotypes 1, 7, 9 and 1/2 were sequenced using a
AB  - rapid, high-throughput approach. Based on the 13 corresponding serotype
AB  - strains, including 9 previously completed genomes of this bacterium, a
AB  - full comparative genomic analysis was performed. The results provide
AB  - evidence that (i) the pan-genome of this species is open and the size
AB  - increases with addition of new sequenced genomes, (ii) strains of
AB  - serotypes 1, 3, 7 and 9 are phylogenetically distinct from serotype 2
AB  - strains, but all serotype 2 strains, plus the serotype 1/2 and 14 strains,
AB  - are very closely related. (iii) all these strains, except for the serotype
AB  - 1 strain, could harbor a recombinant site for a pathogenic island (89K)
AB  - mediated by conjugal transfer, and may have the ability to gain the 89K
AB  - sequence. CONCLUSIONS: There is significant genomic diversity among
AB  - different strains in S. suis, and the gain and loss of large amount of
AB  - genes are involved in shaping their genomes. This is indicated by (i)
AB  - pairwise gene content comparisons between every pair of these strains,
AB  - (ii) the open pan-genome of this species, (iii) the observed indels,
AB  - invertions and rearrangements in the collinearity analysis. Phylogenetic
AB  - relationships may be associated with serotype, as serotype 2 strains are
AB  - closely related and distinct from other serotypes like 1, 3, 7 and 9, but
AB  - more strains need to be sequenced to confirm this.
ER  -

TY  - JOUR
AU  - Zhang, B.
AU  - Li, L.
AU  - Chen, F.
AU  - Guan, Y.
TI  - Initial investigation on restriction modification system of Streptomyces ahygroscopicus wuzhouensis neosubsp.
JO  - Weishengwuxue Zazhi
PY  - 2008
SP  - 65
EP  - 68
VL  - 28
AB  - Adopting mycelium embedment in situ method and high voltage pulse electrophorsis two bands of
AB  - plasmid DNA from Streptomyces ahygroscopicus wuzhouensis neosubsp.  11371 (SAWNS) were
AB  - obtained, and they were linear molecules proved by bidirectionary electrophoresis and named as
AB  - pSAL1 and pSAL2 according to molecular weights from large to small successively.  Furthermore,
AB  - an initial investigation on SAWNS' restriction modification system was carried out, a copy of
AB  - plasmid pIJ702 from Streptomyces lividus TK54 was used to transfer plasma of SAWN and could
AB  - not obtain any transformant, however it succeeded to transform plasma of SAWN U-3 and obtained
AB  - a transformant.
ER  -

TY  - JOUR
AU  - Zhang, B.
AU  - Tao, T.
AU  - Wilson, G.G.
AU  - Blumenthal, R.M.
TI  - The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region.
JO  - Nucleic Acids Res.
PY  - 1993
SP  - 905
EP  - 911
VL  - 21
AB  - The DNA methyltransferase of the AluI restriction-modification system, from Arthrobacter
AB  - luteus, converts cytosine to 5-methylcytosine in the sequence AGCT. The gene for this
AB  - methyltransferase, aluIM, was cloned into Escherichia coli and sequenced. A 525-codon open
AB  - reading frame was found, consistent with deletion evidence, and the deduced amino acid
AB  - sequence revealed all ten conserved regions common to 5-methylcytosine methyltransferases. The
AB  - aluIM sequence predicts a protein of Mr 59.0K, in agreement with the observed Mr, making
AB  - M.AluI the largest known methyltransferase from a type II restriction-modification system.
AB  - M.AluI also contains the largest known variable region of any monospecific DNA
AB  - methyltransfese, larger than that of most multispecific methyltransferases. In other DNA
AB  - methyltransferases the variable region has been implicated as the sequence-specific target
AB  - recognition domain. An in-frame deletion that removes a third of this putative
AB  - target-recognition region leaves the AluI methyltransferase still fully active.
ER  -

TY  - JOUR
AU  - Zhang, C.
AU  - Feng, Y.
AU  - Liu, F.
AU  - Jiang, H.
AU  - Qu, Z.
AU  - Lei, M.
AU  - Wang, J.
AU  - Zhang, B.
AU  - Hu, Y.
AU  - Ding, J.
AU  - Zhu, B.
TI  - A phage-like IncY plasmid carrying mcr-1 gene in an Escherichia coli strain from pig farm in China.
JO  - Antimicrob. Agents Chemother.
PY  - 2016
SP  - e02035
EP  - e02016
VL  - 61
AB  - We report here a new type of plasmid that carries the mcr-1 gene, the pMCR-1-P3 plasmid,
AB  - harbored in an Escherichia coli strain isolated from a pig farm in China. pMCR-1-P3 belongs to
AB  - the IncY incompatibility group and is a phage-like plasmid that contains a large portion of
AB  - phage-related sequences. The backbone of this plasmid is different from that of other
AB  - mcr-1-carrying plasmids reported previously.
ER  -

TY  - JOUR
AU  - Zhang, C.
AU  - Guo, W.
AU  - Wang, Y.
AU  - Chen, X.
TI  - Draft Genome Sequences of Two Psychrotolerant Strains, Colwellia polaris MCCC 1C00015(T) and Colwellia chukchiensis CGMCC 1.9127(T).
JO  - Genome Announcements
PY  - 2018
SP  - e01575
EP  - e01517
VL  - 6
AB  - Colwellia polaris MCCC 1C00015(T) and Colwellia chukchiensis CGMCC 1.9127(T) are
AB  - psychrotolerant bacteria isolated from the Canadian Basin and Chukchi Sea,
AB  - respectively. Here, we report the draft genome sequences of C. polaris MCCC
AB  - 1C00015(T) and C. chukchiensis CGMCC 1.9127(T), which will help reveal how they
AB  - adapt to cold environments.
ER  -

TY  - JOUR
AU  - Zhang, C.
AU  - Pang, B.
AU  - Zhou, Z.
AU  - Wang, H.
AU  - Zhou, H.
AU  - Lu, X.
AU  - Du, P.
AU  - Zhang, L.
AU  - Li, J.
AU  - Cui, Z.
AU  - Chen, C.
AU  - Stokes, H.W.
AU  - Kan, B.
TI  - The purifying trend in the chromosomal integron in Vibrio cholerae strains during the seventh pandemic.
JO  - Infect. Genet. Evol.
PY  - 2014
SP  - 241
EP  - 249
VL  - 26C
AB  - Chromosomal integron (CI) arrays in Vibrio spp. are generally large and display great
AB  - variation. Here we determined the sequence of CI array in a toxigenic O139 Vibriocholerae
AB  - strain and compared it with the arrays from the genome of different O1 biotypes available in
AB  - GenBank. Then PCR scanning was used to determine the CI array variations in 83 epidemic O139
AB  - strains and subsequently these variations were compared with that found in toxigenic O1 El Tor
AB  - strains in our previous work. Few differences were observed in the cohort of toxigenic O139
AB  - strains compared to the toxigenic O1 El Tor strains. On the basis of CI arrays, the toxigenic
AB  - O1 El Tor and O139 strains isolated concurrently in recent years appear to be more similar to
AB  - each other than to the O1 strains isolated in previous decades, suggesting a closer
AB  - evolutionary relationship between them.
AB  - Comparison of CI arrays in toxigenic O1 El Tor and O139 V. cholerae strains isolated between
AB  - 1961 and 2009 revealed a purifying trend in the CI arrays in the chronological order during
AB  - the seventh pandemic.
ER  -

TY  - JOUR
AU  - Zhang, D.
AU  - Chang, D.
AU  - Zhang, X.
AU  - Yu, Y.
AU  - Guo, Y.
AU  - Wang, J.
AU  - Li, T.
AU  - Xu, G.
AU  - Dai, W.
AU  - Liu, C.
TI  - Genome Sequence of Escherichia coli Strain LCT-EC52, Which Acquired Changes in Antibiotic Resistance Properties after the Shenzhou-VIII Mission.
JO  - Genome Announcements
PY  - 2014
SP  - e00081
EP  - e00014
VL  - 2
AB  - Escherichia coli is a ubiquitous opportunistic pathogen that colonizes the lower  intestines
AB  - of humans and causes several diseases, such as septicemia, pneumonia,
AB  - and urinary tract infections. Here, we present the draft genome sequence of E.
AB  - coli strain LCT-EC52, which originated from E. coli strain CGMCC 1.2385 and
AB  - acquired changes in antibiotic resistance following travel on the Shenzhou-VIII
AB  - spacecraft.
ER  -

TY  - JOUR
AU  - Zhang, D.
AU  - Li, L.
AU  - Zhu, S.
AU  - Zhang, N.
AU  - Yang, J.
AU  - Ma, X.
AU  - Chen, J.
TI  - Complete Genome Sequence of Rhodococcus sp. B7740, a Carotenoid-Producing Bacterium Isolated from the Arctic Sea.
JO  - Genome Announcements
PY  - 2015
SP  - e00333
EP  - e00315
VL  - 3
AB  - Rhodococcus sp. B7740 was isolated from Arctic seawater and selected for its capacity to
AB  - synthesize carotenoids. Here, we report the complete genome sequence
AB  - of Rhodococcus sp. B7740 to provide the genetic basis for a better understanding
AB  - of its carotenoid-accumulating capabilities, and we describe the major features
AB  - of the genome.
ER  -

TY  - JOUR
AU  - Zhang, D.
AU  - Li, W.
AU  - Qin, W.
AU  - Huang, X.
AU  - Gong, X.
TI  - Draft Genome Sequences of Acinetobacter harbinensis Strain HITLi 7T, Isolated from River Water.
JO  - Genome Announcements
PY  - 2015
SP  - e00028
EP  - e00015
VL  - 3
AB  - Acinetobacter harbinensis HITLi strain 7(T), isolated from river water, has the ability to
AB  - remove ammonium and organic chemicals at 2 degrees C. The genome
AB  - sequences might be useful for investigating the low-temperature adaptability and
AB  - nitrogen or organic chemical metabolism.
ER  -

TY  - JOUR
AU  - Zhang, D.
AU  - Xu, D.H.
AU  - Qiu, J.
AU  - Rasmussen-Ivey, C.R.
AU  - Liles, M.R.
AU  - Beck, B.H.
TI  - Draft Genome Sequence of Pseudomonas mosselii Gil3, Isolated from Catfish and Antagonistic against Hypervirulent Aeromonas hydrophila.
JO  - Genome Announcements
PY  - 2016
SP  - e01305
EP  - e01316
VL  - 4
AB  - Pseudomonas mosselii Gil3 was isolated from a catfish that survived from lethal challenge with
AB  - hypervirulent Aeromonas hydrophila (vAh). When assayed in vitro,
AB  - the bacterium showed antagonism against vAh. Sequence analysis revealed that the
AB  - genome of P. mosselii Gil3 encodes numerous aromatic metabolism pathways and
AB  - proteins for biosynthesis of antimicrobial compounds.
ER  -

TY  - JOUR
AU  - Zhang, D.C.
AU  - Liu, Y.X.
AU  - Huo, Y.Y.
AU  - Xu, X.W.
AU  - Li, X.Z.
TI  - Draft Genome Sequence of Thermophilic Exiguobacterium sp. Strain JLM-2, Isolated  from Deep-Sea Ferromanganese Nodules.
JO  - Genome Announcements
PY  - 2015
SP  - e00794
EP  - e00715
VL  - 3
AB  - Exiguobacterium sp. strain JLM-2 is a thermophilic bacterium isolated from deep-sea
AB  - ferromanganese (FeMn) nodules. The estimated genome of this strain is
AB  - 2.9 Mb, with a G+C content of 48.32%. It has a novel circular 15,570-bp plasmid.
AB  - The draft genome sequence may provide useful information about Mn-microbe
AB  - interactions and the genetic basis for tolerance to environment stresses.
ER  -

TY  - JOUR
AU  - Zhang, F.
AU  - Lin, W.
AU  - Zhang, R.
AU  - Zheng, Q.
AU  - Jiao, N.
TI  - Genome Sequence of Salegentibacter mishustinae KCTC 12263, Containing a Complete  Subtype I-B CRISPR-Cas System.
JO  - Genome Announcements
PY  - 2016
SP  - e00267
EP  - e00216
VL  - 4
AB  - Salegentibacter mishustinaeKCTC strain 12263 was isolated from the sea
AB  - urchinStrongylocentrotus intermediusinhabiting the Sea of Japan. Here, we report
AB  - the draft genome sequence ofSalegentibacter mishustinaeKCTC 12263. It comprises
AB  - ~3.78 Mb in 38 contigs with a G+C content of 36.5%, and a total of 3,490
AB  - proteins-coding genes were obtained. One complete CRISPR-Cas gene cluster was
AB  - identified in the genome, which shows the strategy against invasive genetic
AB  - elements of the strain.
ER  -

TY  - JOUR
AU  - Zhang, F.
AU  - Su, S.
AU  - Yu, G.
AU  - Zheng, B.
AU  - Shu, F.
AU  - Wang, Z.
AU  - Xiang, T.
AU  - Dong, H.
AU  - Zhang, Z.
AU  - Hou, D.
AU  - She, Y.
TI  - High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 9
EP  - 9
VL  - 10
AB  - Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively
AB  - anaerobic bacterium, which was isolated from a mixture of formation
AB  - water (also known as oil-reservior water) and crude-oil in Karamay oilfield,
AB  - China. To date, there is only one E. mori genome has been sequenced and very
AB  - little knowledge about the mechanism of E. mori adapted to the petroleum
AB  - reservoir. Here, we report the second E. mori genome sequence and annotation,
AB  - together with the description of features for this organism. The 4,621,281 bp
AB  - assembly genome exhibits a G + C content of 56.24% and contains 4,317
AB  - protein-coding and 65 RNA genes, including 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Zhang, G.
AU  - Deng, A.
AU  - Xu, Q.
AU  - Liang, Y.
AU  - Chen, N.
AU  - Wen, T.
TI  - Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin.
JO  - J. Bacteriol.
PY  - 2011
SP  - 3142
EP  - 3143
VL  - 193
AB  - Here, we report the complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for
AB  - industrial production of guanosine, and synthesis of
AB  - ribavirin by assimilation of formamide. Comparison of its genome sequence
AB  - with those of the strains DSM7 and FZB42 revealed horizontal gene transfer
AB  - represented by unique prophages and restriction-modification systems and
AB  - indicated significant accumulation of guanosine.
ER  -

TY  - JOUR
AU  - Zhang, G.
AU  - Esteve, P.O.
AU  - Chin, H.G.
AU  - Terragni, J.
AU  - Dai, N.
AU  - Correa, I.R. Jr.
AU  - Pradhan, S.
TI  - Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation.
JO  - Nucleic Acids Res.
PY  - 2015
SP  - 6112
EP  - 6124
VL  - 43
AB  - Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA
AB  - (ncRNA). Generally the ncRNAs function to regulate gene expression
AB  - at the transcriptional and post-transcriptional level. Among ncRNA, the long
AB  - ncRNA and small ncRNA can affect histone modification, DNA methylation targeting
AB  - and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1)
AB  - co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) bind directly to DNMT1
AB  - with high affinity. The binding of miRNAs, such as miR-155-5p, leads to
AB  - inhibition of DNMT1 enzyme activity. Exogenous miR-155-5p in cells induces
AB  - aberrant DNA methylation of the genome, resulting in hypomethylation of low to
AB  - moderately methylated regions. And small shift of hypermethylation of previously
AB  - hypomethylated region was also observed. Furthermore, hypomethylation led to
AB  - activation of genes. Based on these observations, overexpression of miR-155-5p
AB  - resulted in aberrant DNA methylation by inhibiting DNMT1 activity, resulting in
AB  - altered gene expression.
ER  -

TY  - JOUR
AU  - Zhang, G.
AU  - Fauzi, H.M.
AU  - Zhang, R.
AU  - Hikmawan, T.
AU  - Stingl, U.
TI  - Draft Genome Sequences of Two Thiomicrospira Strains Isolated from the Brine-Seawater Interface of Kebrit Deep in the Red Sea.
JO  - Genome Announcements
PY  - 2016
SP  - e00110
EP  - e00116
VL  - 4
AB  - Two Thiomicrospira strains, WB1 and XS5, were isolated from the Kebrit Deep brine-seawater
AB  - interface in the Red Sea, Saudi Arabia. Here, we present the draft
AB  - genome sequences of these gammaproteobacteria, which both produce sulfuric acid
AB  - from thiosulfate in culture.
ER  -

TY  - JOUR
AU  - Zhang, G.
AU  - Fauzi, H.M.
AU  - Zhang, R.
AU  - Hikmawan, T.
AU  - Stingl, U.
TI  - Draft Genome Sequence of Pseudoalteromonas sp. Strain XI10 Isolated from the Brine-Seawater Interface of Erba Deep in the Red Sea.
JO  - Genome Announcements
PY  - 2016
SP  - e00109
EP  - e00116
VL  - 4
AB  - Pseudoalteromonas sp. strain XI10 was isolated from the brine-seawater interface  of Erba Deep
AB  - in the Red Sea, Saudi Arabia. Here, we present the draft genome
AB  - sequence of strain XI10, a gammaproteobacterium that synthesizes polysaccharides
AB  - for biofilm formation when grown in liquid culture.
ER  -

TY  - JOUR
AU  - Zhang, G.
AU  - Wang, Q.
AU  - Su, Y.
AU  - Li, S.
AU  - Liu, H.
TI  - Genome Sequence of Staphylococcus aureus PX03, an Acetoin-Producing Strain with a Small-Sized Genome.
JO  - Genome Announcements
PY  - 2017
SP  - e00753
EP  - e00717
VL  - 5
AB  - Staphylococcus aureus PX03 can produce acetoin efficiently. Here, we present a 2.38-Mb
AB  - assembly of its genome sequence, which might provide further insights
AB  - into the molecular mechanism of its acetoin biosynthesis to further improve its
AB  - biotechnological applications.
ER  -

TY  - JOUR
AU  - Zhang, G.
AU  - Wang, W.
AU  - Deng, A.
AU  - Sun, Z.
AU  - Zhang, Y.
AU  - Liang, Y.
AU  - Che, Y.
AU  - Wen, T.
TI  - A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria.
JO  - PLoS Genet.
PY  - 2012
SP  - e1002987
EP  - e1002987
VL  - 8
AB  - Genetic transformation of bacteria harboring multiple Restriction-Modification (R-M) systems
AB  - is often difficult using
AB  - conventional methods. Here, we describe a
AB  - mimicking-of-DNA-methylation-patterns (MoDMP) pipeline to address this
AB  - problem in three difficult-to-transform bacterial strains. Twenty-four
AB  - putative DNA methyltransferases (MTases) from these
AB  - difficult-to-transform strains were cloned and expressed in an
AB  - Escherichia coli strain lacking all of the known R-M systems and orphan
AB  - MTases. Thirteen of these MTases exhibited DNA modification activity in
AB  - Southwestern dot blot or Liquid Chromatography-Mass Spectrometry
AB  - (LC-MS) assays. The active MTase genes were assembled into three
AB  - operons using the Saccharomyces cerevisiae DNA assembler and were
AB  - co-expressed in the E. coli strain lacking known R-M systems and orphan
AB  - MTases. Thereafter, results from the dot blot and restriction enzyme
AB  - digestion assays indicated that the DNA methylation patterns of the
AB  - difficult-to-transform strains are mimicked in these E. coli hosts. The
AB  - transformation of the Gram-positive Bacillus amyloliquefaciens TA208
AB  - and B. cereus ATCC 10987 strains with the shuttle plasmids prepared
AB  - from MoDMP hosts showed increased efficiencies (up to four orders of
AB  - magnitude) compared to those using the plasmids prepared from the E.
AB  - coli strain lacking known R-M systems and orphan MTases or its parental
AB  - strain. Additionally, the gene coding for uracil
AB  - phosphoribosyltransferase (upp) was directly inactivated using
AB  - non-replicative plasmids prepared from the MoDMP host in B.
AB  - amyloliquefaciens TA208. Moreover, the Gram-negative chemoautotrophic
AB  - Nitrobacter hamburgensis strain X14 was transformed and expressed Green
AB  - Fluorescent Protein (GFP). Finally, the sequence specificities of
AB  - active MTases were identified by restriction enzyme digestion, making
AB  - the MoDMP system potentially useful for other strains. The
AB  - effectiveness of the MoDMP pipeline in different bacterial groups
AB  - suggests a universal potential. This pipeline could facilitate the
AB  - functional genomics of the strains that are difficult to transform.
ER  -

TY  - JOUR
AU  - Zhang, H.
AU  - Li, X.
AU  - Zhang, B.
AU  - Liu, C.
TI  - Draft Genome Sequence of Acinetobacter sp. Strain YZS-X1-1, a Denitrifying Bacterium Isolated from Freshwater Pond Sludge in China.
JO  - Genome Announcements
PY  - 2015
SP  - e01579
EP  - e01514
VL  - 3
AB  - Acinetobacter sp. strain YZS-X1-1 was isolated from freshwater pond sludge in China. Here, we
AB  - present the draft genome of strain YZS-X1-1, which consists of
AB  - 3,278,660 bases, with a G+C content of 42.1%.
ER  -

TY  - JOUR
AU  - Zhang, H.
AU  - Liu, R.
AU  - Wang, M.
AU  - Wang, H.
AU  - Gao, Q.
AU  - Hou, Z.
AU  - Gao, D.
AU  - Wang, L.
TI  - Draft Genome Sequence of Alcanivorax sp. Strain KX64203 Isolated from Deep-Sea Sediments of Iheya North, Okinawa Trough.
JO  - Genome Announcements
PY  - 2016
SP  - e00872
EP  - e00816
VL  - 4
AB  - This report describes the draft genome sequence of Alcanivorax sp. strain KX64203, isolated
AB  - from deep-sea sediment samples. The reads generated by an Ion
AB  - Torrent PGM were assembled into contigs, with a total size of 4.76 Mb. The data
AB  - will improve our understanding of the strain's function in alkane degradation.
ER  -

TY  - JOUR
AU  - Zhang, H.
AU  - Liu, R.
AU  - Wang, M.
AU  - Wang, H.
AU  - Gao, Q.
AU  - Hou, Z.
AU  - Zhou, Z.
AU  - Gao, D.
AU  - Wang, L.
TI  - Draft Genome Sequences of Pseudoalteromonas telluritireducens DSM 16098 and P. spiralis DSM 16099 Isolated from the Hydrothermal Vents of the Juan de Fuca  Ridge.
JO  - Genome Announcements
PY  - 2016
SP  - e00871
EP  - e00816
VL  - 4
AB  - This report describes the draft genome sequences of two strains, Pseudoalteromonas
AB  - telluritireducens DSM 16098 and P. spiralis DSM 16099, which
AB  - were isolated from hydrothermal vents of the Juan de Fuca Ridge. The reads
AB  - generated by an Ion Torrent PGM were assembled into contigs with total sizes of
AB  - 4.4 Mb and 4.1 Mb for DSM 16098 and DSM 16099, respectively.
ER  -

TY  - JOUR
AU  - Zhang, H.
AU  - Shen, N.
AU  - Qin, Y.
AU  - Zhu, J.
AU  - Li, Y.
AU  - Wu, J.
AU  - Jiang, M.G.
TI  - Complete Genome Sequence of Actinobacillus succinogenes GXAS137, a Highly Efficient Producer of Succinic Acid.
JO  - Genome Announcements
PY  - 2018
SP  - e01562
EP  - e01517
VL  - 6
AB  - The bacterium Actinobacillus succinogenes GXAS137, an efficient producer of succinic acid, was
AB  - isolated from bovine rumen in Nanning, Guangxi Province,
AB  - China. Here, we present the 2.3-Mb genome assembly of this strain, which consists
AB  - of 2,314,479 bp (G+C content of 44.89%) with a circular chromosome, 2,235 DNA
AB  - coding sequences, 57 tRNAs, and 15 rRNAs.
ER  -

TY  - JOUR
AU  - Zhang, H.
AU  - Zhang, S.
AU  - Peng, Y.
AU  - Li, Y.
AU  - Chen, Z.
AU  - Zheng, W.
AU  - Xu, H.
AU  - Yu, Z.
AU  - Zheng, T.
TI  - Draft Genome Sequence of the Anti-Algal Marine Actinomycete Streptomyces sp. JS01.
JO  - Genome Announcements
PY  - 2014
SP  - e01261
EP  - e01214
VL  - 2
AB  - Streptomyces sp. JS01 is the producer of an anti-algal compound that shows inhibitory activity
AB  - against a harmful algal species Phaeocystis globosa and can
AB  - also produce a red pigment. Its genome sequence will allow for the
AB  - characterization of the anti-algal compound and the molecular mechanisms
AB  - underlying its beneficial properties.
ER  -

TY  - JOUR
AU  - Zhang, H.
AU  - Zhou, W.
AU  - Zhuang, Y.
AU  - Liang, X.
AU  - Liu, T.
TI  - Draft Genome Sequence of Streptomyces bottropensis ATCC 25435, a Bottromycin-Producing Actinomycete.
JO  - Genome Announcements
PY  - 2013
SP  - e0001913
EP  - e0001913
VL  - 1
AB  - A series of bottromycin antibiotics have been isolated and identified from Streptomyces
AB  - bottropensis strain ATCC 25435. Here, a draft genome sequence of S.
AB  - bottropensis ATCC 25435 is presented. The genome carries an intact biosynthetic
AB  - gene cluster for bottromycin antibiotics, which provides insight into the
AB  - combinatorial biosynthesis of bottromycin antibiotics.
ER  -

TY  - JOUR
AU  - Zhang, J.
AU  - Cao, G.
AU  - Xu, X.
AU  - Jin, H.
AU  - Yang, X.
AU  - Allard, M.
AU  - Brown, E.
AU  - Meng, J.
TI  - Draft Genome Sequences of Three Salmonella enterica Serotype Agona Strains from China.
JO  - Genome Announcements
PY  - 2013
SP  - e00203
EP  - e00212
VL  - 1
AB  - Salmonellosis has been one of the major contributors to the global public health  burden.
AB  - serotype Agona has ranked among the top 10 and top 20 most frequent
AB  - serotypes isolated from human sources in China and the United States,
AB  - respectively. We report draft genomes of three Agona strains from China.
ER  -

TY  - JOUR
AU  - Zhang, J.
AU  - Cao, G.
AU  - Xu, X.
AU  - Jin, H.
AU  - Zhang, Q.
AU  - Chen, J.
AU  - Yang, X.
AU  - Pan, H.
AU  - Zhang, X.
AU  - Allard, M.
AU  - Brown, E.
AU  - Meng, J.
TI  - Whole-Genome Sequences of Four Salmonella enterica Serotype Newport Strains from  Humans.
JO  - Genome Announcements
PY  - 2013
SP  - e00213
EP  - e00213
VL  - 1
AB  - Salmonellosis contributes significantly to the public health burden globally. Salmonella
AB  - enterica serotype Newport is among Salmonella serotypes most
AB  - associated with food-borne illness in the United States and China. It was thought
AB  - to be polyphyletic and to contain different lineages. We report draft genomes of
AB  - four S. Newport strains isolated from humans in China.
ER  -

TY  - JOUR
AU  - Zhang, J.
AU  - Hu, J.
AU  - Zhang, X.
AU  - Zeng, X.
TI  - Draft Genome Sequence of Anaerobic Fermentative Bacterium Anaeromicrobium sediminis DY2726D.
JO  - Genome Announcements
PY  - 2018
SP  - e00002
EP  - e00018
VL  - 6
AB  - Here, we report the draft genome sequence of Anaeromicrobium sediminis DY2726D, isolated from
AB  - a west Pacific Ocean sediment sample. The genome comprises
AB  - 4,710,590 bp in 56 contigs, with a G+C content of 31.2%. A total of 3,811
AB  - protein-coding sequences were predicted. The genome annotation revealed that
AB  - DY2726D may represent a marine type of Clostridiaceae.
ER  -

TY  - JOUR
AU  - Zhang, J.
AU  - Hung, G.C.
AU  - Lei, H.
AU  - Li, T.
AU  - Li, B.
AU  - Tsai, S.
AU  - Lo, S.C.
TI  - Draft Genome Sequence of Pantoea sp. Strain MBLJ3, Isolated in a Laboratory Environmental Control Study.
JO  - Genome Announcements
PY  - 2015
SP  - e01595
EP  - e01514
VL  - 3
AB  - This report describes the draft genome sequence of a newly isolated strain, Pantoea sp. MBLJ3.
AB  - The genome is 4.8 Mb in size, with a G+C content of 54.27%, and it contains 4,522
AB  - protein-coding sequences, 69 tRNA genes, and 5 rRNA genes.
ER  -

TY  - JOUR
AU  - Zhang, J.
AU  - Wang, J.
AU  - Wang, C.
TI  - Complete Genome Sequence of Ehrlichia canis Strain YZ-1, Isolated from a Beagle with Fever and Thrombocytopenia.
JO  - Genome Announcements
PY  - 2018
SP  - e00133
EP  - e00118
VL  - 6
AB  - We report the complete genome sequence of Ehrlichia canis strain YZ-1, which was  isolated
AB  - from a beagle with fever, anorexia, depression, lethargy, weight loss,
AB  - and thrombocytopenia. E. canis is the tick-borne agent of canine and human
AB  - monocytic ehrlichiosis.
ER  -

TY  - JOUR
AU  - Zhang, J.
AU  - Yuan, Q.
AU  - Yang, W.
AU  - Wang, X.
TI  - Complete Genome Sequence of Carbendazim-Degrading Mycobacterium sp. Strain djl-10.
JO  - Genome Announcements
PY  - 2017
SP  - e01683
EP  - e01616
VL  - 5
AB  - Mycobacterium sp. strain djl-10, an efficient degrader of carbendazim, was isolated from a
AB  - carbendazim manufacturing wastewater treatment system. Here, we
AB  - report the complete genome sequence of djl-10, which consists of a chromosome and
AB  - three plasmids.
ER  -

TY  - JOUR
AU  - Zhang, J.X.
AU  - Lin, B.R.
AU  - Shen, H.F.
AU  - Pu, X.M.
TI  - Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot.
JO  - Genome Announcements
PY  - 2013
SP  - e00317
EP  - e00313
VL  - 1
AB  - We report a draft genome sequence of Dickeya zeae strain MS1, which is the causative agent of
AB  - banana soft rot in China, and we show several of its specific
AB  - properties compared with those of other D. zeae strains. Genome sequencing
AB  - provides a tool for understanding the genomic determination of the pathogenicity
AB  - and phylogeny placement of this pathogen.
ER  -

TY  - JOUR
AU  - Zhang, J.Y.
AU  - Guan, R.
AU  - Zhang, H.J.
AU  - Li, H.
AU  - Xiao, P.
AU  - Yu, G.L.
AU  - Du, L.
AU  - Cao, D.M.
AU  - Zhu, B.C.
AU  - Li, R.H.
AU  - Lu, Z.H.
TI  - Complete genome sequence and genomic characterization of Microcystis panniformis  FACHB 1757 by third-generation sequencing.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 11
EP  - 11
VL  - 11
AB  - The cyanobacterial genus Microcystis is well known as the main group that forms harmful blooms
AB  - in water. A strain of Microcystis, M. panniformis FACHB1757, was
AB  - isolated from Meiliang Bay of Lake Taihu in August 2011. The whole genome was
AB  - sequenced using PacBio RS II sequencer with 48-fold coverage. The complete genome
AB  - sequence with no gaps contained a 5,686,839 bp chromosome and a 38,683 bp
AB  - plasmid, which coded for 6,519 and 49 proteins, respectively. Comparison with
AB  - strains of M. aeruginosa and some other water bloom-forming cyanobacterial
AB  - species revealed large-scale structure rearrangement and length variation at the
AB  - genome level along with 36 genomic islands annotated genome-wide, which
AB  - demonstrates high plasticity of the M. panniformis FACHB1757 genome and reveals
AB  - that Microcystis has a flexible genome evolution.
ER  -

TY  - JOUR
AU  - Zhang, K.
AU  - McClure, J.A.
AU  - Elsayed, S.
AU  - Conly, J.M.
TI  - Novel Staphylococcal Cassette Chromosome mec Type, Tentatively Designated Type VIII, Harboring Class A mec and Type 4 ccr Gene Complexes in a Canadian Epidemic Strain of Methicillin-Resistant Staphylococcus aureus.
JO  - Antimicrob. Agents Chemother.
PY  - 2009
SP  - 531
EP  - 540
VL  - 53
AB  - Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic
AB  - element characterized by flanking terminal direct and, in most cases,
AB  - inverted repeat sequences, the mec and ccr gene complexes, and their
AB  - surrounding DNA regions. Unique combinations of the mec and ccr gene
AB  - complexes generate various SCCmec types. Six SCCmec types have been
AB  - reported to date. We describe here a novel SCCmec type identified in a
AB  - Canadian methicillin-resistant Staphylococcus aureus (MRSA) epidemic
AB  - strain. MRSA clinical isolates were screened for known SCCmec types by
AB  - multiplex and conventional PCR methods. Three phenotypically and
AB  - genotypically identical MRSA clinical isolates with a pulsotype identical
AB  - to CMRSA9 were identified locally and found to be nontypeable by available
AB  - SCCmec typing schemes. Complete sequencing of the SCCmec element revealed
AB  - a nucleotide fragment of 32,168 bp integrated at an identical chromosomal
AB  - integration site (attBscc) at the 3' end of the orfX gene. The nucleotide
AB  - sequences at the chromosome-SCCmec junction regions were typical of other
AB  - SCCmec types, but the element harbored a unique combination of class A mec
AB  - and type 4 ccr gene complexes. Sequence recombination analysis suggested
AB  - that this unique SCCmec type may be derived from homologous recombination
AB  - between the previously described SCC(RP62A) of S. epidermidis strain RP62A
AB  - and SCC composite island of S. epidermidis ATCC 12228, respectively, or
AB  - via recombination of other staphylococcal strains that carry the same or
AB  - similar mobile cassettes. We identified a previously undescribed type of
AB  - SCCmec from isolate C10682, tentatively designated type VIII, and we
AB  - provide compelling evidence supporting the ability of SCC elements to
AB  - transfer horizontally or undergo recombination to generate new SCCmec
AB  - types.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Li, X.
AU  - Zhang, F.
AU  - Wang, G.
TI  - Genomic analysis of Agrobacterium radiobacter DSM 30147(T) and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942  (Approved Lists 1980) emend. Sawada et al. 1993.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 574
EP  - 584
VL  - 9
AB  - Agrobacterium radiobacter is the only known non-phytopathogenic species in Agrobacterium
AB  - genus. In this study, the whole-genome sequence of A. radiobacter
AB  - type strain DSM 30147(T) was described and compared to the other available
AB  - Agrobacterium genomes. This bacterium has a genome size of 7,122,065 bp
AB  - distributed in 612 contigs, including 6,834 protein-coding genes and 41 RNA
AB  - genes. It harbors a circular chromosome and a linear chromosome but not a
AB  - tumor-inducing (Ti) plasmid. To the best of our knowledge, this is the first
AB  - report of a genome from the A. radiobacter species. In addition, an emended
AB  - description of A. radiobacter is described. This study reveals information that
AB  - enhances the current understanding of its non-phytopathogenicity and its
AB  - phylogenetic position within Agrobacterium genus.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Morrison, M.
AU  - O'Cuiv, P.
AU  - Evans, P.
AU  - Rickard, C.M.
TI  - Genome Sequence of Stenotrophomonas maltophilia Strain AU12-09, Isolated from an  Intravascular Catheter.
JO  - Genome Announcements
PY  - 2013
SP  - e00195
EP  - e00113
VL  - 1
AB  - Stenotrophomonas maltophilia is an opportunistic nosocomial pathogen that is characterized by
AB  - its high-level intrinsic resistance to a variety of antibiotics
AB  - and its ability to form biofilms. Here, we report the draft genome sequence of
AB  - Stenotrophomonas maltophilia AU12-09, isolated from an intravascular catheter
AB  - tip.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Morrison, M.
AU  - O'Cuiv, P.
AU  - Evans, P.
AU  - Rickard, C.M.
TI  - Genome Sequence of Staphylococcus epidermidis Strain AU12-03, Isolated from an Intravascular Catheter.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6639
EP  - 6639
VL  - 194
AB  - In recent years, Staphylococcus epidermidis has become a major nosocomial pathogen and the
AB  - most common cause of intravascular catheter-related bacteremia,
AB  - which can increase morbidity and mortality and significantly affect patient
AB  - recovery. We report a draft genome sequence of Staphylococcus epidermidis
AB  - AU12-03, isolated from an intravascular catheter tip.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Morrison, M.
AU  - Rickard, C.M.
TI  - Draft Genome Sequence of Ralstonia pickettii AU12-08, Isolated from an Intravascular Catheter in Australia.
JO  - Genome Announcements
PY  - 2014
SP  - e00027
EP  - e00014
VL  - 2
AB  - Ralstonia pickettii is a nonfermenting Gram-negative bacillus that creates a significant
AB  - problem in clinical settings, as it is a widespread cause of
AB  - nosocomial infections. Here, we report the draft genome sequence of R. pickettii
AB  - AU12-08, isolated from an intravascular catheter tip.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Si, M.
AU  - Zhu, L.
AU  - Li, C.
AU  - Wei, Y.
AU  - Shen, X.
TI  - Draft Genome Sequence of Nafulsella turpanensis ZLM-10T, a Novel Member of the Family Flammeovirgaceae.
JO  - Genome Announcements
PY  - 2014
SP  - e00263
EP  - e00214
VL  - 2
AB  - Nafulsella turpanensis ZLM-10(T) is a slightly halophilic, Gram-negative, rod-shaped, gliding,
AB  - pale-pink-pigmented bacterium in the family Flammeovirgaceae, and it shows resistance to
AB  - gentamicin, kanamycin, neomycin, and streptomycin. Here, we report the genome sequence of N.
AB  - turpanensis strain ZLM-10(T), which has a 4.8-Mb genome and a G+C content of 45.67%.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Skurnik, M.
TI  - Isolation of an R- M+ mutant of Yersinia enterocolitica serotype O:8 and its application in construction of rough mutants utilizing mini-Tn5 derivatives and lipopolysaccharide-specific phage.
JO  - J. Bacteriol.
PY  - 1994
SP  - 1756
EP  - 1760
VL  - 176
AB  - A generally applicable procedure was used to isolate a spontaneous restriction-deficient
AB  - mutant of Yersinia enterocolitica serotype O:8. Transposition frequency in the mutant strain
AB  - 8081-res was approximately 6.7 x 10-6 per recipient, while it was practically zero in the
AB  - wild-type strain 8081-c. Mobilization frequency into 8081-res was 10/5 times higher than that
AB  - into the wild-type strain. The mutant had lost the ability to express the YenI restriction
AB  - endonuclease activity present in serotype 0:8 strains. This allowed the construction of a
AB  - transposon library in 8081-res. Insertion mutants with transposons in the genes of the rfa
AB  - region were selected from this library.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Yang, Z.
TI  - Whole-Genome Sequences of Mycobacterium tuberculosis TB282 and TB284, a Widespread and a Unique Strain, Respectively, Identified in a Previous Study of  Tuberculosis Transmission in Central Los Angeles, California, USA.
JO  - Genome Announcements
PY  - 2017
SP  - e01418
EP  - e01416
VL  - 5
AB  - We report here the genome sequences of two Mycobacterium tuberculosis clinical isolates
AB  - previously identified in central Los Angeles, CA, in the 1990s using a
AB  - PacBio platform. Isolate TB282 represents a large-cluster strain that caused 27%
AB  - of the tuberculosis cases, while TB284 represents a strain that caused disease in
AB  - only one patient.
ER  -

TY  - JOUR
AU  - Zhang, L.
AU  - Zhang, X.
AU  - Liu, C.
AU  - Li, C.
AU  - Li, S.
AU  - Li, T.
AU  - Li, D.
AU  - Zhao, Y.
AU  - Yang, Z.
TI  - Manufacture of Cheddar cheese using probiotic Lactobacillus plantarum K25 and its cholesterol-lowering effects in a mice model.
JO  - World J. Microbiol. Biotechnol.
PY  - 2013
SP  - 127
EP  - 135
VL  - 29
AB  - The probiotic adjunct Lactobacillus plantarum K25 was inoculated into milk to
AB  - produce probiotic cheese. The effect of Lb. plantarum K25 on cheese composition,
AB  - microbiological growth and survival during the manufacturing and ripening period,
AB  - primary and secondary proteolysis during cheese ripening, and the in vivo
AB  - cholesterol-lowering ability of the probiotic cheese were investigated. The
AB  - results showed that the use of adjunct Lb. plantarum K25 in Cheddar cheese did
AB  - not affect the cheese components including moisture, protein, fat, salt content
AB  - and the pH value of cheese. During the whole ripening period, the probiotic
AB  - adjunct maintained its viability, suggesting the effectiveness of Cheddar cheese
AB  - as a vehicle for delivery of probiotic bacteria. No significant differences were
AB  - observed in water-soluble nitrogen, 70 % ethanol-soluble nitrogen, 5 %
AB  - phosphotungstic acid-soluble nitrogen, free amino acids and urea-PAGE patterns
AB  - between the control and probiotic cheeses. Assessment of the in vivo
AB  - cholesterol-lowering property of cheese with Lb. plantarum K25 showed that the
AB  - levels of serum total cholesterol, low-density lipoprotein cholesterol and
AB  - triglycerides decreased significantly, and the level of serum high-density
AB  - lipoprotein cholesterol increased in mice fed with the probiotic cheese. The
AB  - results indicated the potential function as a dietary item of the probiotic
AB  - cheese with Lb. plantarum K25 to reduce the risk of cardiovascular diseases.
ER  -

TY  - JOUR
AU  - Zhang, Lu.
AU  - Lu, D.-Y.
AU  - Ma, W.-Y.
AU  - Li, Y.
TI  - Age-related changes in the localization of DNA methyltransferases during meiotic maturation in mouse oocytes.
JO  - Fertil. Steril.
PY  - 2011
SP  - 1531
EP  - 1534
VL  - 95
AB  - The effects of maternal aging on the localization of DNA methyltransferases were evaluated
AB  - during mouse oocyte maturation using fluorescence staining. And we conclude that maternal
AB  - aging affects the cytoplasmic-to-nuclear trafficking of DNA methyltransferases in mouse
AB  - oocytes during the time from germinal vesicle breakdown to metaphase I.
ER  -

TY  - JOUR
AU  - Zhang, M.
AU  - He, L.
AU  - Li, Q.
AU  - Sun, H.
AU  - Gu, Y.
AU  - You, Y.
AU  - Meng, F.
AU  - Zhang, J.
TI  - Genomic characterization of the Guillain-Barre syndrome-associated Campylobacter jejuni ICDCCJ07001 Isolate.
JO  - PLoS ONE
PY  - 2010
SP  - e15060
EP  - e15060
VL  - 5
AB  - Campylobacter jejuni ICDCCJ07001 (HS:41, ST2993) was isolated from a Guillain-Barre syndrome
AB  - (GBS) patient during a 36-case GBS outbreak
AB  - triggered by C. jejuni infections in north China in 2007. Sequence
AB  - analysis revealed that the ICDCCJ07001 genome consisted of 1,664,840 base
AB  - pairs (bp) and one tetracycline resistance plasmid of 44,084 bp. The GC
AB  - content was 59.29% and 1,579 and 37 CDSs were identified on the chromosome
AB  - and plasmid, respectively. The ICDCCJ07001 genome was compared to C.
AB  - jejuni subsp. jejuni strains 81-176, 81116, NCTC11168, RM1221 and C.
AB  - jejuni subsp. doylei 269.97. The length and organization of ICDCCJ07001
AB  - was similar to that of NCTC11168, 81-176 and 81-116 except that CMLP1 had
AB  - a reverse orientation in strain ICDCCJ07001. Comparative genomic analyses
AB  - were also carried out between GBS-associated C. jejuni strains. Thirteen
AB  - common genes were present in four GBS-associated strains and 9 genes
AB  - mapped to the LOS cluster and the ICDCCJ07001_pTet (44 kb) plasmid was
AB  - mosaic in structure. Thirty-seven predicted CDS in ICDCCJ07001_pTet were
AB  - homologous to genes present in three virulence-associated plasmids in
AB  - Campylobacter: 81-176_pTet, pCC31 and 81-176_pVir. Comparative analysis of
AB  - virulence loci and virulence-associated genes indicated that the LOS
AB  - biosynthesis loci of ICDCCJ07001 belonged to type A, previously reported
AB  - to be associated with cases of GBS. The polysaccharide capsular
AB  - biosynthesis (CPS) loci and the flagella modification (FM) loci of
AB  - ICDCCJ07001 were similar to corresponding sequences of strain 260.94 of
AB  - similar serotype as strain ICDCCJ07001. Other virulence-associated genes
AB  - including cadF, peb1, jlpA, cdt and ciaB were conserved between the C.
AB  - jejuni strains examined.
ER  -

TY  - JOUR
AU  - Zhang, M.
AU  - Ito, T.
AU  - Li, S.
AU  - Misawa, S.
AU  - Kondo, S.
AU  - Miida, T.
AU  - Ohsaka, A.
AU  - Hiramatsu, K.
TI  - Analysis of Staphylococcal cassette chromosome mec in BD GeneOhm MRSA assay-negative strains.
JO  - Antimicrob. Agents Chemother.
PY  - 2013
SP  - 2890
EP  - 2891
VL  - 57
AB  - The BD GeneOhm MRSA assay could identify methicillin-resistant Staphylococcus
AB  - aureus (MRSA) strains at a high ratio (97.8%). Analysis of 11 assay-negative MRSA
AB  - strains suggested that insertion of non-mec staphylococcal cassette chromosome
AB  - elements (SCCs) downstream of orfX, and carriage of SCCmecs with a left extremity
AB  - that cannot be detected by the kit, might lead to their being given an incorrect
AB  - negative status.
ER  -

TY  - JOUR
AU  - Zhang, M.
AU  - Li, Q.
AU  - He, L.
AU  - Meng, F.
AU  - Gu, Y.
AU  - Zheng, M.
AU  - Gong, Y.
AU  - Wang, P.
AU  - Ruan, F.
AU  - Zhou, L.
AU  - Wu, J.
AU  - Chen, L.
AU  - Fitzgerald, C.
AU  - Zhang, J.
TI  - Association study between an outbreak of Guillain-Barre syndrome in Jilin, China, and preceding Campylobacter jejuni infection.
JO  - Foodborne Pathog. Dis.
PY  - 2010
SP  - 913
EP  - 919
VL  - 7
AB  - From June to July 2007, 36 cases of Guillain-Barre syndrome (GBS) occurred
AB  - in a township in north China. Serological study and bacteria culture were
AB  - performed to investigate the association between preceding Campylobacter
AB  - jejuni infection and this GBS outbreak. Anti-C. jejuni antibodies were
AB  - found in significantly higher numbers of GBS patients (IgM 84%, IgG 87.5%)
AB  - than in healthy inspection cases (IgM 33%, IgG 27%). IgG anti-GM1 was the
AB  - dominant anti-ganglioside antibody among the GBS patients. Seven C. jejuni
AB  - isolates (four from human stool and three from poultry specimens taken
AB  - from the patients' houses) were obtained. Serotyping and molecular
AB  - analysis were used to investigate the genetic relatedness among these C.
AB  - jejuni isolates. The four human isolates, collected from residents of the
AB  - same district, were indistinguishable by both pulsed-field gel
AB  - electrophoresis and multilocus sequence typing, suggesting these patients
AB  - had a common source of infection. A new sequence type, sequence type-2993,
AB  - was assigned to the human C. jejuni isolates, three of which belonged to
AB  - Penner serotype heat-stable (HS):41. Both serotype and molecular subtype
AB  - of the human C. jejuni isolates were different from those of isolates
AB  - obtained from poultry specimens. Our results suggest that the antecedent
AB  - C. jejuni infection triggered this GBS outbreak in China.
ER  -

TY  - JOUR
AU  - Zhang, M.
AU  - Ma, L.
AU  - Yang, Y.
AU  - Hu, T.
AU  - Liu, X.
AU  - Zhang, X.
AU  - Hua, Y.
AU  - Gao, Y.
AU  - Zhu, Z.
TI  - Draft Genome Sequence of Pseudomonas stutzeri LH-42, Isolated from Petroleum-Contaminated Soil.
JO  - Genome Announcements
PY  - 2017
SP  - e00589
EP  - e00517
VL  - 5
AB  - We used Illumina HiSeq technology to sequence the whole genome of Pseudomonas stutzeri LH-42,
AB  - a bacterium isolated from petroleum-contaminated soil in Liaoning
AB  - Province, China. The bacterium contains a series of specific genes involved in
AB  - the oxidation of organic sulfur compounds.
ER  -

TY  - JOUR
AU  - Zhang, M.
AU  - Yang, X.
AU  - Liu, H.
AU  - Liu, X.
AU  - Huang, Y.
AU  - He, L.
AU  - Gu, Y.
AU  - Zhang, J.
TI  - Genome Sequences of the Guillain-Barre Syndrome Outbreak-Associated Campylobacter jejuni Strains ICDCCJ07002 and ICDCCJ07004.
JO  - Genome Announcements
PY  - 2013
SP  - e00256
EP  - e00213
VL  - 1
AB  - The first world-known and largest outbreak of 36 cases of Guillain-Barre syndrome caused by a
AB  - preceding Campylobacter jejuni infection was reported previously in
AB  - China. During the outbreak, Campylobacter jejuni strain ICDCCJ07002 was isolated
AB  - from a patient with persistent diarrhea for 21 days, and C. jejuni strain
AB  - ICDCCJ07004 was from a healthy carrier without any clinical symptoms at the same
AB  - time. Here, we report the draft genome sequence of strain ICDCCJ07002 (1,698,407
AB  - bp, with a G+C content of 30.45%) and the genome resequencing result of strain
AB  - ICDCCJ07004 (1,701,584 bp, with a G+C content of 30.51%), and we compared these
AB  - with the completed genome of C. jejuni strain ICDCCJ07001.
ER  -

TY  - JOUR
AU  - Zhang, P.
AU  - Bao, Y.
AU  - Higgins, L.
AU  - Xu, S.Y.
TI  - Rational design of a chimeric endonuclease targeted to NotI recognition site.
JO  - Protein Eng. Des. Sel.
PY  - 2007
SP  - 497
EP  - 504
VL  - 20
AB  - A cleavage-deficient variant of NotI restriction endonuclease (GCGGCCGC) was isolated by
AB  - random mutagenesis of the notIR gene. The NotI variant
AB  - D160N was shown to bind DNA and protect plasmid DNA from EagI (CGGCCG) and
AB  - NotI digestions. The EDTA-resistant BmrI restriction endonuclease cleaves
AB  - DNA sequence ACTGGG N(5)/N(4). The N-terminal cleavage domain of BmrI
AB  - (residues 1-198) with non-specific nuclease activity was fused to the NotI
AB  - variant D160N with a short linker. The engineered chimeric endonuclease
AB  - (CH-endonuclease) recognizes NotI sites specifically in the presence of
AB  - high salt (100-150 mM NaCl) and divalent cations Mg(++) or Ca(++). In
AB  - contrast to wild-type NotI, which cuts within its recognition sequence,
AB  - BmrI198-NotI (D160N) cleaves DNA outside of NotI sites, resulting in
AB  - deletion of the NotI site and the adjacent sequences. The fusion of the
AB  - BmrI cleavage domain to cleavage-deficient variants of Type II restriction
AB  - enzymes to generate novel cleavage sites will provide useful tools for DNA
AB  - manipulation.
ER  -

TY  - JOUR
AU  - Zhang, P.H.
AU  - Too, P.H.M.
AU  - Samuelson, J.C.
AU  - Chan, S.H.
AU  - Vincze, T.
AU  - Doucette, S.
AU  - Backstrom, S.
AU  - Potamousis, K.D.
AU  - Schramm, T.M.
AU  - Forrest, D.
AU  - Schwartz, D.C.
AU  - Xu, S.Y.
TI  - Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
JO  - Protein Expr. Purif.
PY  - 2010
SP  - 226
EP  - 234
VL  - 69
AB  - BspQI is a thermostable Type IIS restriction endonuclease (REase) with the recognition
AB  - sequence 5'GCTCTTC N1/N4 3'. Here we report the cloning
AB  - and expression of the bspQIR gene for the BspQI restriction enzyme in
AB  - Escherichia coli. Alanine scanning of the BspQI charged residues
AB  - identified a number of DNA nicking variants. After sampling
AB  - combinations of different amino acid substitutions, an Nt.BspQI triple
AB  - mutant (E172A/E248A/E255K) was constructed with predominantly
AB  - top-strand DNA nicking activity. Furthermore, a triple mutant of BspQI
AB  - (Nb.BspQI, N235A/K331A/R428A) was engineered to create a bottom-strand
AB  - nicking enzyme. In addition, we demonstrated the application of
AB  - Nt.BspQI in optical mapping of single DNA molecules. Nt or
AB  - Nb.BspQI-nicked dsDNA can be further digested by E. coli exonuclease
AB  - III to create ssDNA for downstream applications. BspQI contains two
AB  - potential catalytic sites: a top-strand catalytic site (Ct) with a
AB  - D-H-N-K motif found in the HNH endonuclease family and a bottom-strand
AB  - catalytic site (Cb) with three scattered Glu residues. BlastP analysis
AB  - of proteins in GenBank indicated a putative restriction enzyme with
AB  - significant amino acid sequence identity to BspQI from the sequenced
AB  - bacterial genome Croceibacter atlanticus HTCC2559. This restriction
AB  - gene was amplified by PCR and cloned into a T7 expression vector.
AB  - Restriction mapping and run-off DNA sequencing of digested products
AB  - from the partially purified enzyme indicated that it is an Earl
AB  - isoschizomer with 6-bp recognition, which we named CatHI (CTCTTC N1/N4).
ER  -

TY  - JOUR
AU  - Zhang, Q.
AU  - Poehlein, A.
AU  - Hollensteiner, J.
AU  - Daniel, R.
TI  - Draft Genome Sequence of Komagataeibacter maltaceti LMG 1529(T), a Vinegar-Producing Acetic Acid Bacterium Isolated from Malt Vinegar Brewery  Acetifiers.
JO  - Genome Announcements
PY  - 2018
SP  - e00330
EP  - e00318
VL  - 6
AB  - We present the genome sequence of Komagataeibacter maltaceti LMG 1529(T), which is a
AB  - vinegar-producing acetic acid bacterium. The draft genome sequence consists
AB  - of 3.6 Mb and contains 3,225 predicted protein-encoding genes. In addition, 53
AB  - genes encoding potential oxidoreductases were identified.
ER  -

TY  - JOUR
AU  - Zhang, Q.
AU  - Xie, J.
AU  - Wu, J.
AU  - Lu, Z.
TI  - RESP: a tool using for selecting a set of restriction enzymes.
JO  - Prog. Post-Genome Technol.
PY  - 2006
SP  - 388
EP  - 390
VL  - 0
AB  - The present restriction enzyme analysis tools, such as REBASE tool, REBsites etc., can provide
AB  - the functions of finding available enzymes to the given DNA sequence and supplying theoretical
AB  - digests.  In this paper, we report a novel restriction enzyme selection platform (RESP), which
AB  - can analyze nad optimize the length range and DNA fragment number after cleaving a given whole
AB  - genome by selecting a set of restriction enzymes.  The program runs under Microsoft Windows.
AB  - Compared to present programs, RESP has more excellent functions: it can give DNA digest
AB  - results with multiple enzymes, and simulate electrophoresis process for the digest results,
AB  - and accept the input of more large DNA sequences.  RESP has successfully been used to
AB  - demonstrate the selection of the enzyme set and their fragmentation process for the genome of
AB  - phage T7.
ER  -

TY  - JOUR
AU  - Zhang, Q.
AU  - Ye, X.
AU  - Ren, G.
AU  - Zhang, N.
AU  - Li, Lu.
AU  - Li, D.
TI  - A new method for the purification of restriction enzyme NotI.
JO  - Zhongguo Shengwu Gongcheng Zazhi
PY  - 2011
SP  - 102
EP  - 109
VL  - 31
AB  - In order to study its specificities, the NotIR gene was cloned from Nocardia
AB  - otitidis-caviarum.  First, the genome DNA of Enterobacter agglomerans was extracted as
AB  - template, obtained EagI methylase gene by PCR and connected EagIM gene to pBR322 vector of
AB  - gain recombinant expression plasmid pBR322-EagIM.  Then transformed this plasmid ito E. coli
AB  - 2555.  Secondly, extracted the genome DNA from Nocardia otitidis-caviarum as template and
AB  - obtained the restriction enzyme NHotIR gene by PCR.  After ligating the NotIR gene to
AB  - pACYC184-PT7, the pACYC184-PT7-NotIR plasmid was transformed into the ER2566 which was
AB  - protected through the methylation by pBR322-EagIM recombinant plasmid.  The engineered strain
AB  - ER2566 [pBR322-EagIM, pACYC184-PT7,-NotIR] could be induced to express restriction enzymes
AB  - NotI by IPTG and the induction conditions were optimized to make its expression mostly in
AB  - soluble form.  The enzyme was purified by AKTA purifier 100 protein purification system.
AB  - Through DEAE Sephrose FF, phenyl HP and Superdex 75 10/300 GL molecular sieve chromatography,
AB  - the NotI enzyme was purified 35-fold, the yield was 9.8 x 106 units/g wet cell which was up to
AB  - 17.8% of the crude enzyme and the specific activity of the purified NotI was 1.37 x 106U/mg.
AB  - Digestion results showed that the enzyme was purified to homogeneity and was free of
AB  - detectable contamination by other DNase (exo and endo).  After optimization of the expression
AB  - and purification conditions, the yield and efficienty of NotI enzyme were greatly improved in
AB  - comparison with that previously reported.
ER  -

TY  - JOUR
AU  - Zhang, Q.-M.
AU  - Sugiyama, H.
AU  - Miyabe, I.
AU  - Matsuda, S.
AU  - Kino, K.
AU  - Saito, I.
AU  - Yonei, S.
TI  - Replication in vitro and cleavage by restriction endonuclease of 5-formyluracil- and 5-hydroxymethyluracil-containing oligonucleotides.
JO  - Int. J. Radiat. Biol.
PY  - 1999
SP  - 59
EP  - 65
VL  - 75
AB  - Purpose: To investigate the biological consequences of 5-formyluracil (5-foU) and
AB  - 5-hydroxymethyluracil (5-hmU).  The authors constructed 22-mer oligonucleotides containing a
AB  - 5-foU or 5-hmU residue at the same sites.  The effects of such modifications on the ability to
AB  - serve as a template for DNA polymerase and on the cleavage by sequence-specific restriction
AB  - endonuclease were examined.  The Klenow fragment of DNA polymerase I and Thermus thermophilus
AB  - DNA polymerase read through the sites of 5-foU and 5-hmU in the templates.  5-FoU directed the
AB  - incorporation of dCMP in addition to dAMP opposite the lesion during DNA synthesis.  The DNA
AB  - polymerases incorporated only dAMP opposite the 5-hmU.  The substitution of thymine by 5-foU
AB  - within the recognition site of the restriction endonucleases HincII and SalI inhibited or
AB  - prevented the cleavage by the enzymes, whereas the enzymes cleaved the 5-hmU-containing
AB  - oligonucleotides at the same rate as the T-containing oligonucleotides.  These results
AB  - indicated that the 5-foU-A base pair is less stable than the T-A base pair and that 5-foU-A
AB  - base pair is less stable than the T-A base pair and that 5-foU can form a base pair with C in
AB  - addition to A.  It was also demonstrated that the oxidation of thymine to 5-hmU does not
AB  - result in substantial deterioration.
ER  -

TY  - JOUR
AU  - Zhang, Q.Y.
AU  - Xiao, F.
AU  - Xie, J.
AU  - Li, Z.Q.
AU  - Gui, J.F.
TI  - Complete Genome Sequence of Lymphocystis Disease Virus Isolated from China.
JO  - J. Virol.
PY  - 2004
SP  - 6982
EP  - 6994
VL  - 78
AB  - Lymphocystis diseases in fish throughout the world have been extensively
AB  - described. Here we report the complete genome sequence of lymphocystis
AB  - disease virus isolated in China (LCDV-C), an LCDV isolated from cultured
AB  - flounder (Paralichthys olivaceus) with lymphocystis disease in China. The
AB  - LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C.
AB  - Computer-assisted analysis revealed 240 potential open reading frames
AB  - (ORFs) and 176 nonoverlapping putative viral genes, which encode
AB  - polypeptides ranging from 40 to 1,193 amino acids. The percent coding
AB  - density is 67%, and the average length of each ORF is 702 bp. A search of
AB  - the GenBank database using the 176 individual putative genes revealed 103
AB  - homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that
AB  - were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there
AB  - are 8 genes that contain conserved domains of cellular genes and 65 novel
AB  - genes that do not show any significant homology with the sequences in
AB  - public databases. Although a certain extent of similarity between putative
AB  - gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed,
AB  - no colinearity was detected when their ORF arrangements and coding
AB  - strategies were compared to each other, suggesting that a high degree of
AB  - genetic rearrangements between them has occurred. And a large number of
AB  - tandem and overlapping repeated sequences were observed in the LCDV-C
AB  - genome. The deduced amino acid sequence of the major capsid protein (MCP)
AB  - presents the highest identity to those of LCDV-1 and other iridoviruses
AB  - among the LCDV-C gene products. Furthermore, a phylogenetic tree was
AB  - constructed based on the multiple alignments of nine MCP amino acid
AB  - sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but
AB  - their amino acid identity is much less than that in other clusters. The
AB  - unexpected levels of divergence between their genomes in size, gene
AB  - organization, and gene product identity suggest that LCDV-C and LCDV-1
AB  - shouldn't belong to a same species and that LCDV-C should be considered a
AB  - species different from LCDV-1.
ER  -

TY  - JOUR
AU  - Zhang, R.
AU  - Xia, H.
AU  - Xu, Q.
AU  - Dang, F.
AU  - Qin, Z.
TI  - Recombinational cloning of the antibiotic biosynthetic gene clusters in linear plasmid SCP1 of Streptomyces coelicolor A3(2).
JO  - FEMS Microbiol. Lett.
PY  - 2013
SP  - 39
EP  - 48
VL  - 345
AB  - The model organism Streptomyces coelicolor A3(2) harbors a 356-kb linear plasmid,
AB  - SCP1. We report here development of a recombinational cloning method for deleting
AB  - large segment from one telomere of SCP1 followed by replacing with the telomere
AB  - of pSLA2 and sequentially inserting with the overlapping cosmids in vivo. The
AB  - procedure depends on homologous recombination coupled with cleavage at telomere
AB  - termini by telomere terminal protein. Using this procedure, we cloned the 81-kb
AB  - avermectin and the 76-kb spinosad biosynthetic gene clusters into SCP1.
AB  - Heterologous expression of avermectin production in S. coelicolor was detected.
AB  - These results demonstrate the utility of SCP1 for cloning large DNA segments such
AB  - as antibiotic biosynthetic gene clusters.
ER  -

TY  - JOUR
AU  - Zhang, S.
AU  - Flores-Cruz, Z.
AU  - Kumar, D.
AU  - Chakrabarty, P.
AU  - Hopkins, D.L.
AU  - Gabriel, D.W.
TI  - The Xylella fastidiosa Biocontrol Strain EB92-1 Genome Is Very Similar and Syntenic to Pierce's Disease Strains.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5576
EP  - 5577
VL  - 193
AB  - Xylella fastidiosa infects a wide range of plant hosts and causes economically serious
AB  - diseases, including Pierce's disease (PD) of
AB  - grapevines. X. fastidiosa biocontrol strain EB92-1 is infectious to
AB  - grapevines but does not cause symptoms. The draft genome of EB92-1 reveals
AB  - that it may be missing 10 potential pathogenicity effectors.
ER  -

TY  - JOUR
AU  - Zhang, S.
AU  - Jiang, W.
AU  - Li, J.
AU  - Meng, L.
AU  - Cao, X.
AU  - Hu, J.
AU  - Liu, Y.
AU  - Chen, J.
AU  - Sha, C.
TI  - Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 73
EP  - 73
VL  - 11
AB  - Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of
AB  - inhibition of a broad range of plant pathogenic fungi. The strain has
AB  - the potential to be developed into a biocontrol agent for use in agriculture.
AB  - Here we report the whole-genome shotgun sequence of the strain. The genome size
AB  - of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754
AB  - protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2
AB  - microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains.
ER  -

TY  - JOUR
AU  - Zhang, S.
AU  - Luo, X.
AU  - Cheng, J.
AU  - Peng, J.
AU  - Zhang, D.
AU  - Liu, Y.
TI  - Genome Sequence of Pyrethroid-Degrading Bacterium Rhodopseudomonas palustris Strain JSC-3b.
JO  - Genome Announcements
PY  - 2014
SP  - e01228
EP  - e01213
VL  - 2
AB  - Rhodopseudomonas palustris strain JSC-3b is a facultative, thermophilic bacterium, which was
AB  - isolated from water in a canal adjacent to a vegetable
AB  - field. Strain JSC-3b biodegrades several varieties of pyrethroid residues
AB  - effectively through cometabolic pathways. Here, we present the genome sequence of
AB  - this biodegrader.
ER  -

TY  - JOUR
AU  - Zhang, S.
AU  - Wang, D.
AU  - Wang, Y.
AU  - Hasman, H.
AU  - Aarestrup, F.M.
AU  - Alwathnani, H.A.
AU  - Zhu, Y.G.
AU  - Rensing, C.
TI  - Genome sequences of copper resistant and sensitive Enterococcus faecalis strains  isolated from copper-fed pigs in Denmark.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 35
EP  - 35
VL  - 10
AB  - Six strains of Enterococcus faecalis (S1, S12, S17, S18, S19 and S32) were isolated from
AB  - copper fed pigs in Denmark. These Gram-positive bacteria within the
AB  - genus Enterococcus are able to survive a variety of physical and chemical
AB  - challenges by the acquisition of diverse genetic elements. The genome of strains
AB  - S1, S12, S17, S18, S19 and S32 contained 2,615, 2,769, 2,625, 2,804, 2,853 and
AB  - 2,935 protein-coding genes, with 41, 42, 27, 42, 32 and 44 genes encoding
AB  - antibiotic and metal resistance, respectively. Differences between Cu resistant
AB  - and sensitive E. faecalis strains, and possible co-transfer of Cu and antibiotic
AB  - resistance determinants were detected through comparative genome analysis.
ER  -

TY  - JOUR
AU  - Zhang, S.
AU  - Xu, Y.
AU  - Zhou, Z.
AU  - Wang, S.
AU  - Yang, R.
AU  - Wang, J.
AU  - Wang, L.
TI  - Complete genome sequence of Bordetella pertussis CS, a Chinese pertussis vaccine strain.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4017
EP  - 4018
VL  - 193
AB  - Bordetella pertussis is the causative agent of pertussis. Here, we report the genome sequence
AB  - of Bordetella pertussis strain CS, isolated from an
AB  - infant patient in Beijing and widely used as a vaccine strain for
AB  - production of acellular pertussis vaccine in China.
ER  -

TY  - JOUR
AU  - Zhang, S.D.
AU  - Barbe, V.
AU  - Garel, M.
AU  - Zhang, W.J.
AU  - Chen, H.
AU  - Santini, C.L.
AU  - Murat, D.
AU  - Jing, H.
AU  - Zhao, Y.
AU  - Lajus, A.
AU  - Martini, S.
AU  - Pradel, N.
AU  - Tamburini, C.
AU  - Wu, L.F.
TI  - Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200.
JO  - Genome Announcements
PY  - 2014
SP  - e00096
EP  - e00014
VL  - 2
AB  - Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantially varied
AB  - lifestyles, including free-living, commensal, pathogenic, symbiotic, and piezophilic. Here, we
AB  - present the genome sequence of a luminous, piezophilic Photobacterium phosphoreum strain,
AB  - ANT-2200, isolated from a water column at 2,200 m depth in the Mediterranean Sea. It is the
AB  - first genomic sequence of the P. phosphoreum group. An analysis of the sequence provides
AB  - insight into the adaptation of bacteria to the deep-sea habitat.
ER  -

TY  - JOUR
AU  - Zhang, S.H.
AU  - Qiu, J.J.
AU  - Yang, R.
AU  - Shen, K.F.
AU  - Xu, G.Y.
AU  - Fu, L.Z.
TI  - Complete Genome Sequence of Trueperella pyogenes, Isolated from Infected Farmland Goats.
JO  - Genome Announcements
PY  - 2016
SP  - e01421
EP  - e01416
VL  - 4
AB  - Trueperella pyogenes is a significant pathogen of livestock, causing diverse diseases, such as
AB  - mastitis, liver abscessation, and pneumonia. In this study, we
AB  - have reported the genome sequence of Trueperella pyogenes 2012CQ-ZSH. Moreover,
AB  - several genes coding for virulence factors were found, such as pyolysin (PYO),
AB  - nanH, nanP, cbpA, fimC, and fimE.
ER  -

TY  - JOUR
AU  - Zhang, T.
AU  - Bao, M.
AU  - Wang, Y.
AU  - Su, H.
AU  - Tan, T.
TI  - Genome Sequence of Bacillus cereus Strain A1, an Efficient Starch-Utilizing Producer of Hydrogen.
JO  - Genome Announcements
PY  - 2014
SP  - e00494
EP  - e00414
VL  - 2
AB  - Bacillus cereus strain A1 is a newly isolated hydrogen producer capable of utilizing
AB  - bioresources and biowaste, such as starch and starch wastewater. Here,
AB  - we present a 5.67-Mb assembly of the genome sequence of strain A1, which may
AB  - provide insights into the molecular mechanism of hydrogen production from
AB  - bioresources and biowaste.
ER  -

TY  - JOUR
AU  - Zhang, T.
AU  - Zhang, R.
AU  - Luo, Q.
AU  - Wen, G.
AU  - Ai, D.
AU  - Wang, H.
AU  - Luo, L.
AU  - Wang, H.
AU  - Shao, H.
TI  - Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-JLLY.
JO  - Genome Announcements
PY  - 2015
SP  - e00895
EP  - e00815
VL  - 3
AB  - Riemerella anatipestifer is an important bacterial pathogen associated with epizootic
AB  - infections in waterfowl and various other birds. Riemerella anatipestifer strain RA-JLLY is an
AB  - avirulent strain, isolated from the brain of an old duck in Hubei province, China. Here, we
AB  - report the genome sequence of this species.
ER  -

TY  - JOUR
AU  - Zhang, W.
AU  - Nadirk, J.
AU  - Kossow, A.
AU  - Bielaszewska, M.
AU  - Leopold, S.R.
AU  - Witten, A.
AU  - Fruth, A.
AU  - Karch, H.
AU  - Ammon, A.
AU  - Mellmann, A.
TI  - Phylogeny and phenotypes of clinical and environmental Shiga toxin-producing Escherichia coli O174.
JO  - Environ. Microbiol.
PY  - 2014
SP  - 963
EP  - 976
VL  - 16
AB  - Shiga toxin (Stx)-producing Escherichia coli (STEC) of serogroup O174 are human
AB  - pathogenic intimin gene (eae)-negative STEC. To facilitate diagnosis and
AB  - subtyping, we genotypically and phenotypically characterized 25 STEC O174
AB  - isolates from humans with different clinical outcomes and from animals and the
AB  - environment. fliC genotyping resulted in four different genotypes (fliCH2 : n =
AB  - 5; fliCH8 : n = 8; fliCH21 : n = 11; fliCH46 : n = 1). Twenty-three strains were
AB  - motile expressing the corresponding H antigen; two non-motile isolates possessed
AB  - fliCH8 . The stx genotypes and non-stx virulence loci, including toxins,
AB  - serine-proteases and adhesins correlated well with serotypes but showed no
AB  - differences with respect to the isolates' origins. Multilocus sequence typing
AB  - identified seven sequence types that correlated with serotypes. Core gene typing
AB  - further specified the four serotypes, including a previously unknown O174:H46
AB  - combination, and revealed distant relationships of the different serotypes within
AB  - serogroup O174 and in relation to other haemolytic uremic syndrome
AB  - (HUS)-associated STEC. Only serotype O174:H21 was associated with HUS.
AB  - Differences in virulence factors and in the adherence capacity of STEC O174
AB  - corroborated this separation into four distinct groups. Our study provides a
AB  - basis for O174 subtyping, unravels considerable genotypic and phenotypic
AB  - heterogeneity and sheds light to potential environmental and animal reservoirs.
ER  -

TY  - JOUR
AU  - Zhang, W.
AU  - Yu, D.
AU  - Sun, Z.
AU  - Wu, R.
AU  - Chen, X.
AU  - Chen, W.
AU  - Meng, H.
AU  - Hu, S.
AU  - Zhang, H.
TI  - Complete genome sequence of Lactobacillus casei Zhang, a new probiotic strain isolated from traditional homemade koumiss in Inner Mongolia,  China.
JO  - J. Bacteriol.
PY  - 2010
SP  - 5268
EP  - 5269
VL  - 192
AB  - Lactobacillus casei Zhang is a new probiotic bacterium isolated from koumiss collected in
AB  - Inner Mongolia, China. Here, we report the main
AB  - genome features of L. casei Zhang and the identification of several
AB  - predicted proteins implicated in interactions with the host.
ER  -

TY  - JOUR
AU  - Zhang, W.Y.
AU  - Hu, J.
AU  - Pan, J.
AU  - Sun, C.
AU  - Wu, M.
AU  - Xu, X.W.
TI  - Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 124
EP  - 124
VL  - 10
AB  - Halopiger salifodinae strain KCY07-B2(T), isolated from a salt mine in Kuche county, Xinjiang
AB  - province, China, belongs to the family Halobacteriaceae. It is a
AB  - strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic
AB  - archaeon. In this work, we report the features of the type strain KCY07-B2(T),
AB  - together with the draft genome sequence and annotation. The draft genome sequence
AB  - is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and
AB  - contains 4204 protein-coding genes and 50 rRNA genes.
ER  -

TY  - JOUR
AU  - Zhang, W.Y.
AU  - Yuan, Y.
AU  - Su, D.Q.
AU  - He, X.P.
AU  - Han, S.B.
AU  - Epstein, S.S.
AU  - He, S.
AU  - Wu, M.
TI  - Gallaecimonas mangrovi sp. nov., a novel bacterium isolated from mangrove sediment.
JO  - Antonie Van Leeuwenhoek
PY  - 2018
SP  - 1855
EP  - 1862
VL  - 111
AB  - A Gram-stain negative, rod-shaped, non-motile, strictly aerobic bacterium
AB  - HK-28(T) was isolated from a mangrove sediment sample in Haikou city, Hainan
AB  - Province, China. Strain HK-28(T) was able to grow at 10-45 degrees C (optimum
AB  - 25-30 degrees C), pH 5.0-8.5 (optimum 6.0-7.0) and 0.5-12.0% (w/v) NaCl (optimum
AB  - 1.0-3.0%, w/v). The major cellular fatty acids were C16:0, Summed Feature 8
AB  - (C18:1 omega7c and/or C18:1 omega6c), Summed Feature 3 (C16:1 omega7c and/or
AB  - C16:1 omega6c), C17:0, C12:0 3-OH and C17:1omega8c. Ubiquinone-8 (Q-8) was the
AB  - predominant respiratory quinone. The polar lipids consisted of
AB  - diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two
AB  - unidentified aminophospholipids, four unidentified phospholipids, two
AB  - unidentified glycolipid, an unidentified glycophospholipid, an unidentified
AB  - aminolipid and an unidentified lipid. The DNA G+C content was 50.2 mol%.
AB  - Accoroding to 16S rRNA gene sequence similarities, strain HK-28(T) shared 97.1
AB  - and 96.7% sequence similarities to the validly named species Gallaecimonas
AB  - xiamenensis MCCC 1A01354(T) and Gallaecimonas pentaromativorans MCCC 1A06435(T),
AB  - respectively, and shared lower sequence similarities (< 92.0%) to all other
AB  - genera. Phylogenetic analysis showed strain HK-28(T) was clustered with G.
AB  - pentaromativorans MCCC 1A06435(T) and G. xiamenensis MCCC 1A01354(T). Strain
AB  - HK-28(T) showed low DNA-DNA relatedness with G. xiamenensis MCCC 1A01354(T) (28.3
AB  - +/- 1.5%) and G. pentaromativorans MCCC 1A06435(T) (25.2 +/- 2.4%). On the basis
AB  - of phenotypic, chemotaxonomic and genotypic characteristics, strain HK-28(T) is
AB  - considered to represent a novel species in the genus Gallaecimonas, for which the
AB  - name Gallaecimonas mangrovi sp. nov. is proposed. The type strain is HK-28(T) (=
AB  - KCTC 62177(T) = MCCC 1K03441).
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Bruice, T.C.
TI  - The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2006
SP  - 6148
EP  - 6153
VL  - 103
AB  - The mechanism of DNA cytosine-5-methylation catalyzed by the bacterial M.HhaI enzyme has been
AB  - considered as a stepwise nucleophilic addition of Cys-81-S- to cytosine C6 followed by C5
AB  - nucleophilic replacement of the methyl of S-adenosyl-L-methionine to produce
AB  - 5-methyl-6-Cys-81-S-5,6-dihydrocytosine. In this study, we show that the reaction is concerted
AB  - from a series of energy calculations by using the quantum mechanical/molecular mechanical
AB  - hybrid method. Deprotonation of 5-methyl-6-Cys-81-S-5,6-dihydrocytosine and expulsion of
AB  - Cys-81-S- provides the product DNA 5-methylcytosine. A required base catalyst for this
AB  - deprotonation is not available as a member of the active site structure. A water channel
AB  - between the active site and bulk water allows entrance of solvent to the active site.
AB  - Hydroxide at 10(-7) mole fraction (pH = 7) is shown to be sufficient for the required
AB  - catalysis. We also show that Glu-119-CO2H can divert the reaction by protonating cytosine N3
AB  - when Cys-81-S- attacks cytosine, to form the 6-Cys-81-S-3-hydrocytosine. The reactants and
AB  - 6-Cys-81-S-3-hydrocytosine product are in rapid equilibrium, and this explains the observed
AB  - hydrogen exchange of cytosine with solvent.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Hu, Q.
AU  - Yuan, W.
AU  - Shang, W.
AU  - Cheng, H.
AU  - Yuan, J.
AU  - Zhu, J.
AU  - Hu, Z.
AU  - Li, S.
AU  - Chen, W.
AU  - Hu, X.
AU  - Rao, X.
TI  - First report of a sequence type 239 vancomycin-intermediate Staphylococcus aureus isolate in Mainland China.
JO  - Diagn. Microbiol. Infect. Dis.
PY  - 2013
SP  - 64
EP  - 68
VL  - 77
AB  - Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen that
AB  - causes a wide range of both hospital- and community-acquired infections. The high
AB  - prevalence of MRSA and the extensive use of vancomycin in Mainland China may lead
AB  - to the emergence of vancomycin-intermediate S. aureus (VISA) isolates. In this
AB  - case, we report a VISA isolate from a 34-year-old male patient with steam burn.
AB  - The isolate was determined to be sequence type 239 staphylococcal cassette
AB  - chromosome mec type III, the most prevalent MRSA clone in Mainland China.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Jacobsen, S.E.
TI  - Genetic analyses of DNA methyltransferases in Arabidopsis thaliana.
JO  - Cold Spring Harb. Symp. Quant. Biol.
PY  - 2006
SP  - 439
EP  - 447
VL  - 71
AB  - DNA methylation is a conserved epigenetic silencing mechanism that functions to suppress the
AB  - proliferation of transposons and regulate the
AB  - expression of endogenous genes. In plants, Mutations that cause severe
AB  - loss of DNA methylation result in reactivation of transposons as well
AB  - as developmental abnormalities. We use the flowering plant Arabidopsis
AB  - thaliana as a model system to study the establishment and maintenance
AB  - of DNA methylation as well as its role in regulating plant development.
AB  - The genetic evidence presented here suggests that methylation at CG and
AB  - non-CG sites function!; in a partially redundant and locus-specific
AB  - manner to regulate a wide range of developmental processes. Results
AB  - from recent studies also suggested that the dynamic nature of non-CG
AB  - methylation, which is critically important for its regulatory function,
AB  - is largely due to it, complicated interactions with other epigenetic
AB  - pathways such as RNAi and historic modifications. Finally, the use of
AB  - genomic approaches has significantly broadened our Understanding of the
AB  - patterning of DNA methylation on a genomewide sea e and has led to the
AB  - identification of hundreds of candidate genes that are controlled by
AB  - DNA methylation.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Li, G.X.
AU  - Chen, S.C.
AU  - Jia, X.Y.
AU  - Wu, K.
AU  - Cao, C.L.
AU  - Bao, P.
TI  - Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils.
JO  - Genome Announcements
PY  - 2016
SP  - e01693
EP  - e01615
VL  - 4
AB  - Desulfitobacterium hafniense strain DH is a sulfate-reducing species. Here, we report the
AB  - draft genome sequence of strain DH, with a size of 5,368,588 bp,
AB  - average G+C content of 47.48%, and 5,296 predicted protein-coding sequences.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Ma, F.
AU  - Szewzyk, U.
TI  - Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6.
JO  - Genome Announcements
PY  - 2016
SP  - e01651
EP  - e01615
VL  - 4
AB  - Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes
AB  - related to its denitrifying mechanism and iron metabolisms
AB  - were unknown. We present the draft genome of Aquabacterium parvum B6, which could
AB  - provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of
AB  - strain B6.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Mathews, C.K.
TI  - Effect of DNA cytosine methylation upon deamination-induced mutagenesis in a natural target sequence in duplex DNA.
JO  - J. Biol. Chem.
PY  - 1994
SP  - 7066
EP  - 7069
VL  - 269
AB  - Are 5-methylcytosine residues in DNA hot spots for transition mutagenesis? Numerous studies
AB  - identify 1) structural changes induced by DNA methylation, 2) high percentages of human
AB  - mutations that result from GC to AT transition pathways, and 3) differences between G-C and
AB  - G-mC base pairs in susceptibility to nonenzymatic deamination. However, investigations of
AB  - chemical stability necessarily involve non-physiological conditions for chemical analysis of
AB  - deamination. Here we describe an experiment that compares rates of deamination-induced
AB  - mutagenesis between a G-C and G-mC base pair, when both are present in duplex DNA, incubated
AB  - at 37oC and pH 7.4, within identical sequence contexts, in a natural mutational target (the
AB  - Escherichia coli lacZ-alpha gene) that selects for mutagenesis at the specific site under
AB  - investigation. Under these conditions the rate of spontaneous deamination at G-mC exceeds that
AB  - at G-C by more than 21-fold. Our data implicate differences in chemical stability toward
AB  - deamination as a major causal factor relating DNA cytosine methylation to spontaneous
AB  - mutagenesis.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Verdine, G.L.
TI  - Mammalian DNA cytosine-5 methyltransferase interacts with p23 protein.
JO  - FEBS Lett.
PY  - 1996
SP  - 179
EP  - 183
VL  - 392
AB  - In higher eukaryotic genomes, methylated cytosine residues (m5C) are distributed in heritable,
AB  - cell-type-specific patterns, which are believed to be involved in the control of gene
AB  - expression, developmental regulation and genomic imprinting.  These methylation patterns are
AB  - established and maintained by DNA cytosine-5 methyltransferase (Mtase), a ~1500 amino acid
AB  - enzyme containing a regulatory N-terminal domain and a catalytic C-terminal domain.  The
AB  - mechanism responsible for targeting Mtase to particular genes is poorly understood and might
AB  - possibly involve interactions with other proteins.  In an effort to identify proteins that
AB  - interact with the mammalian Mtase, we used the yeast two-hybrid system with several different
AB  - Mtase domains as baits.  Here we report an interaction between the C-terminal catalytic domain
AB  - of the Mtase and p23, a protein previously reported to associate with the progesterone
AB  - receptor (PR) complex.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Wang, T.
AU  - Liu, W.
AU  - Guo, Y.
AU  - Wang, J.
AU  - Li, T.
AU  - Fang, X.
AU  - Zhang, X.
AU  - Dai, W.
AU  - Liu, C.
TI  - Genome Sequence of Klebsiella pneumoniae Strain LCT-KP182, Which Acquired Hemolytic Properties after Space Flight.
JO  - Genome Announcements
PY  - 2014
SP  - e01088
EP  - e01013
VL  - 2
AB  - The Klebsiella pneumoniae strain LCT-KP182 acquired hemolytic properties after space flight.
AB  - Here, we present the draft genome sequence of this strain.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Wang, T.
AU  - Su, L.
AU  - Zhou, L.
AU  - Li, T.
AU  - Wang, J.
AU  - Liu, Y.
AU  - Jiang, X.
AU  - Wu, C.
AU  - Liu, C.
TI  - Draft Genome Sequence of Bacillus cereus LCT-BC25, Isolated from Space Flight.
JO  - Genome Announcements
PY  - 2014
SP  - e00667
EP  - e00613
VL  - 2
AB  - Bacillus cereus strain LCT-BC25, which was carried by the Shenzhou VIII spacecraft, traveled
AB  - in space for about 398 h. To investigate the response of B.
AB  - cereus to space environments, we determined the genome sequence of B. cereus
AB  - strain LCT-BC25, which was isolated after space flight.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Xu, J.R.
AU  - Nakatsu, C.H.
TI  - Draft Genome Sequence of Pseudomonas fluorescens Strain TR3, a Potential Biocontrol Agent against the Rice Blast Fungus Magnaporthe oryzae.
JO  - Genome Announcements
PY  - 2017
SP  - e01332
EP  - e01317
VL  - 5
AB  - We present the draft genome sequence of the potential biocontrol agent Pseudomonas fluorescens
AB  - TR3, which was isolated from rice leaves infected with
AB  - Magnaporthe oryzae in a greenhouse. The genome of TR3 was assembled into 26
AB  - scaffolds (~6 Mbp) and includes genes potentially involved in bacterial
AB  - interactions with fungi.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Xu, X.
AU  - Yuan, W.
AU  - Hu, Q.
AU  - Shang, W.
AU  - Hu, X.
AU  - Tong, Y.
AU  - Rao, X.
TI  - Complete Genome Sequence of Staphylococcus aureus XN108, an ST239-MRSA-SCCmec III Strain with Intermediate Vancomycin Resistance Isolated in Mainland China.
JO  - Genome Announcements
PY  - 2014
SP  - e00449
EP  - e00414
VL  - 2
AB  - ST239-MRSA-SCCmec III (ST239, sequence type 239; MRSA, methicillin-resistant Staphylococcus
AB  - aureus; SCCmec III, staphylococcal cassette chromosome mec type
AB  - III) is the most predominant clone of hospital-acquired methicillin-resistant S.
AB  - aureus in mainland China. We report here the complete genome sequence of XN108,
AB  - the first vancomycin-intermediate S. aureus strain isolated from a steam-burned
AB  - patient with a wound infection.
ER  -

TY  - JOUR
AU  - Zhang, X.
AU  - Zhao, C.
AU  - Hong, X.
AU  - Chen, S.
AU  - Yang, S.
TI  - Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential.
JO  - Genome Announcements
PY  - 2016
SP  - e00288
EP  - e00216
VL  - 4
AB  - The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp,  with a G+C
AB  - content of 68.84%. The annotated genome sequence provides the genetic
AB  - basis for revealing its role as a purple sulfur bacterium in the harvesting of
AB  - energy and the development of bioremediation applications.
ER  -

TY  - JOUR
AU  - Zhang, X.S.
AU  - Blaser, M.J.
TI  - Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3407
EP  - 3416
VL  - 194
AB  - Restriction-modification (RM) systems are important for bacteria to limit foreign DNA
AB  - invasion. The naturally competent bacterium Helicobacter pylori has highly
AB  - diverse strain-specific type II systems. To evaluate the roles of strain-specific
AB  - restriction in H. pylori natural transformation, a markerless type II restriction
AB  - endonuclease-deficient (REd) mutant was constructed. We deleted the genes
AB  - encoding all four active type II restriction endonucleases in H. pylori strain
AB  - 26695 using sacB-mediated counterselection. Transformation by donor DNA with
AB  - exogenous cassettes methylated by Escherichia coli was substantially (1.7 and 2.0
AB  - log(10) for cat and aphA, respectively) increased in the REd strain. There also
AB  - was significantly increased transformation of the REd strain by donor DNA from
AB  - other H. pylori strains, to an extent corresponding to their shared type II R-M
AB  - system strain specificity with 26695. Comparison of the REd and wild-type strains
AB  - indicates that restriction did not affect the length of DNA fragment integration
AB  - during natural transformation. There also were no differentials in cell growth or
AB  - susceptibility to DNA damage. In total, the data indicate that the type II REd
AB  - mutant has enhanced competence with no loss of growth or repair facility compared
AB  - to the wild type, facilitating H. pylori mutant construction and other genetic
AB  - engineering.
ER  -

TY  - JOUR
AU  - Zhang, X.Y.
AU  - Xie, B.B.
AU  - Qin, Q.L.
AU  - Liu, A.
AU  - Chen, X.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Draft genome sequence of strain p7-3-5, a new flavobacteriaceae bacterium isolated from intertidal sand.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6632
EP  - 6632
VL  - 194
AB  - The Flavobacteriaceae bacterium strain P7-3-5 was isolated from intertidal sand of the Yellow
AB  - Sea, China. Analysis of the 16S rRNA gene sequences showed that
AB  - strain P7-3-5 formed a distinct phylogenetic lineage within the family
AB  - Flavobacteriaceae. The genome of strain P7-3-5 was sequenced to facilitate the
AB  - physiological, ecological, and evolutionary studies of the bacteria within the
AB  - family Flavobacteriaceae.
ER  -

TY  - JOUR
AU  - Zhang, X.Y.
AU  - Zhang, Y.J.
AU  - Qin, Q.L.
AU  - Xie, B.B.
AU  - Chen, X.L.
AU  - Zhou, B.C.
AU  - Zhang, Y.Z.
TI  - Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8T, Isolated from Deep-Sea Sediment of the South China Sea.
JO  - J. Bacteriol.
PY  - 2012
SP  - 7001
EP  - 7002
VL  - 194
AB  - The protease-producing bacterium E407-8(T) was isolated from deep-sea sediment of the South
AB  - China Sea and has been identified recently as representing a new
AB  - species, Rheinheimera nanhaiensis. The draft genome of R. nanhaiensis E407-8(T)
AB  - consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes,
AB  - including 82 extracellular peptidase genes.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Chen, C.
AU  - Liu, J.
AU  - Deng, H.
AU  - Pan, A.
AU  - Zhang, L.
AU  - Zhao, X.
AU  - Huang, M.
AU  - Lu, B.
AU  - Dong, H.
AU  - Du, P.
AU  - Chen, W.
AU  - Wan, K.
TI  - Complete Genome Sequences of Mycobacterium tuberculosis Strains CCDC5079 and CCDC5080, Which Belong to the Beijing Family.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5591
EP  - 5592
VL  - 193
AB  - Mycobacterium tuberculosis is one of most prevalent pathogens in the world. Drug-resistant
AB  - strains of this pathogen caused by the excessive use
AB  - of antibiotics have long posed serious threats to public health worldwide.
AB  - A broader picture of drug resistance mechanisms at the genomic level can
AB  - be obtained only with large-scale comparative genomic methodology. Two
AB  - closely related Beijing family isolates, one resistant to four first-line
AB  - drugs (CCDC5180) and one sensitive to them (CCDC5079), were completely
AB  - sequenced. These sequences will serve as valuable references for further
AB  - drug resistance site identification studies and could be of great
AB  - importance for developing drugs targeting these sites.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Nelson, M.
AU  - Nietfeldt, J.
AU  - Xia, Y.
AU  - Burbank, D.
AU  - Ropp, S.
AU  - Van Etten, J.L.
TI  - Chlorella virus NY-2A encodes at least 12 DNA endonuclease/methyltransferase genes.
JO  - Virology
PY  - 1998
SP  - 366
EP  - 375
VL  - 240
AB  - The 380-kb chlorella virus NY-2A genome is highly methylated; 45% of the cytosines are
AB  - 5-methylcytosine and 37% of the adenine are N6-methyladenine.  Based on the
AB  - sensitivity/resistance of NY-2A DNA to 80 methylation-sensitive DNA restriction endonucleases,
AB  - the virus is predicted to encode at least 10 DNA methyltransferases: 7 6mA-specific
AB  - methyltransferases, M.CviQI (GTmAC), M.CvQII (RmAR), M.CviQIII (TCGmA), M.CviQV (TGCmA),
AB  - M.CviQVI (GmANTC), and M.CviQVII (CmATG); and 3 5mC-specific methyltransferases, M.CviQVIII
AB  - [RGmC(T/C/G)], M.CviQIX (mCC), and M.CviQX (mCGR).  Five of the 6mA methyltransferase genes,
AB  - M.CviQI, M.CviQIII, M.CviQV, M.CviQVI, and M.CviQVII, were cloned and sequenced.  In addition,
AB  - 2 site-specific endonuclease activities, R.CviQI (G/TAC) and NY2A-nickase (R/AG), were
AB  - detected in cell-free extracts from NY-2A virus-infected chlorella.  Therefore, the NY-2A
AB  - genome contains at least 12 DNA methyltransferase and endonuclease genes which, altogether,
AB  - compose about 3-4% of the virus genome.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Nelson, M.
AU  - Nietfeldt, J.W.
AU  - Burbank, D.E.
AU  - Van Etten, J.L.
TI  - Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 5351
EP  - 5356
VL  - 20
AB  - A second DNA site-specific (restriction) endonuclease (R.CviAII) and its cognate adenine DNA
AB  - methyltransferase (M.CviAII) were isolated from virus PBCV-1 infected Chlorella strain NC64A
AB  - cells. R.CviAII, a heteroschizomer of the bacterial restriction endonuclease NlaIII,
AB  - recognizes the sequence CATG, and does not cleave CmATG sequences. However, unlike NlaIII,
AB  - which cleaves after the G and does not cleave either CmATG or mCATG sequences, CviAII cleaves
AB  - between the C and A and is unaffected by mCATG methylation. The M.CviAII and R.CviAII genes
AB  - were cloned and their DNA sequences were determined. These genes are tandemly arranged
AB  - head-to-tail such that the TAA termination codon of the M.CviAII methyltransferase gene
AB  - overlaps the ATG translational start site of R.CviAII endonuclease. R.CviAII is the first
AB  - Chlorella virus site-specific endonuclease gene to be cloned and sequenced.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Nelson, M.
AU  - Van Etten, J.L.
TI  - A single amino acid change restores DNA cytosine methyltransferase activity in a cloned Chlorella virus pseudogene.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1637
EP  - 1642
VL  - 20
AB  - The Chlorella virus PBCV-1 contains an open reading frame, named P17-ORF4, which differs by
AB  - eight amino acids from a DNA cytosine methyltransferase, M.CviJI, encoded by a different
AB  - chlorella virus IL-3A. Whereas IL-3A expresses M.CviJI, which methylates the central cytosine
AB  - in (A/G)GC(T/C/G) sequences, P17-ORF4 is non-functional. Gene fusions between P17-ORF4 and
AB  - M.CviJI and site-directed point mutations revealed that changing Gln188 to Lys188 abolishes
AB  - M.CviJI methyltransferase activity. Conversely, changing Lys188 in P17-ORF4 to Gln188 results
AB  - in M.CviJI activity. The other altered seven amino acids do not appear to affect M.CviJI
AB  - activity.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Nie, P.
AU  - Lin, L.
TI  - Complete Genome Sequence of the Fish Pathogen Flavobacterium columnare Pf1.
JO  - Genome Announcements
PY  - 2016
SP  - e00900
EP  - e00916
VL  - 4
AB  - Flavobacterium columnare is the etiologic agent of columnaris disease, a devastating fish
AB  - disease prevailing in worldwide aquaculture industry. Here, we
AB  - describe the complete genome of F. columnare strain Pf1, a highly virulent strain
AB  - isolated from yellow catfish (Pelteobagrus fulvidraco) in China.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Qin, F.
AU  - Qiao, J.
AU  - Li, G.
AU  - Shen, C.
AU  - Huang, T.
AU  - Hu, Z.
TI  - Draft Genome Sequence of Rhodococcus sp. Strain P14, a Biodegrader of High-Molecular-Weight Polycyclic Aromatic Hydrocarbons.
JO  - J. Bacteriol.
PY  - 2012
SP  - 3546
EP  - 3546
VL  - 194
AB  - The genus Rhodococcus is known for its ability to degrade various xenobiotic compounds.
AB  - Rhodococcus sp. strain P14 isolated from crude oil-contaminated
AB  - sediments can degrade mineral oil and polycyclic aromatic hydrocarbons (PAHs).
AB  - The draft genome sequence of Rhodococcus sp. P14 was obtained using Solexa
AB  - technology, which provided an invaluable genetic background for further
AB  - investigation of the ability of P14 to degrade xenobiotic compounds.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Yang, J.
AU  - Xu, L.
AU  - Zhu, Y.
AU  - Liu, B.
AU  - Shao, Z.
AU  - Zhang, X.
AU  - Jin, Q.
TI  - Complete Genome Sequence of Neisseria meningitidis Serogroup A Strain NMA510612,  Isolated from a Patient with Bacterial Meningitis in China.
JO  - Genome Announcements
PY  - 2014
SP  - e00360
EP  - e00314
VL  - 2
AB  - Serogroup A meningococcal strains have been involved in several pandemics and a series of
AB  - epidemics worldwide in the past. Determination of the genome sequence
AB  - of the prevalent genotype strain will help us understand the genetic background
AB  - of the evolutionary and epidemiological properties of these bacteria. We
AB  - sequenced the complete genome of Neisseria meningitidis NMA510612, a clinical
AB  - isolate from a patient with meningococcal meningitis.
ER  -

TY  - JOUR
AU  - Zhang, Y.
AU  - Zhao, Z.
AU  - Deng, W.
AU  - Xie, X.
AU  - Jiao, N.
TI  - Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea.
JO  - Genome Announcements
PY  - 2013
SP  - e00407
EP  - e00413
VL  - 1
AB  - Euryhalocaulis caribicus strain JL2009(T) is a novel genus and species of the family
AB  - Hyphomonadaceae and was first isolated from surface water in the Caribbean
AB  - Sea. Here, we report the first draft genome from this genus. Its genome contains
AB  - genes encoding proteins that are involved in organic acid metabolism and probable
AB  - low-affinity inorganic phosphate transporters, which suggests its competence in
AB  - oligotrophic oceans.
ER  -

TY  - JOUR
AU  - Zhang, Y.C.
AU  - Zhang, Y.
AU  - Zhu, B.R.
AU  - Zhang, B.W.
AU  - Ni, C.
AU  - Zhang, D.Y.
AU  - Huang, Y.
AU  - Pang, E.
AU  - Lin, K.
TI  - Genome sequences of two closely related strains of Escherichia coli K-12 GM4792.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 125
EP  - 125
VL  - 10
AB  - Escherichia coli lab strains K-12 GM4792 Lac(+) and GM4792 Lac(-) carry opposite  lactose
AB  - markers, which are useful for distinguishing evolved lines as they
AB  - produce different colored colonies. The two closely related strains are chosen as
AB  - ancestors for our ongoing studies of experimental evolution. Here, we describe
AB  - the genome sequences, annotation, and features of GM4792 Lac(+) and GM4792
AB  - Lac(-). GM4792 Lac(+) has a 4,622,342-bp long chromosome with 4,061
AB  - protein-coding genes and 83 RNA genes. Similarly, the genome of GM4792 Lac(-)
AB  - consists of a 4,621,656-bp chromosome containing 4,043 protein-coding genes and
AB  - 74 RNA genes. Genome comparison analysis reveals that the differences between
AB  - GM4792 Lac(+) and GM4792 Lac(-) are minimal and limited to only the targeted lac
AB  - region. Moreover, a previous study on competitive experimentation indicates the
AB  - two strains are identical or nearly identical in survivability except for lactose
AB  - utilization in a nitrogen-limited environment. Therefore, at both a genetic and a
AB  - phenotypic level, GM4792 Lac(+) and GM4792 Lac(-), with opposite neutral markers,
AB  - are ideal systems for future experimental evolution studies.
ER  -

TY  - JOUR
AU  - Zhang, Y.L.
AU  - Ong, C.T.
AU  - Leung, K.Y.
TI  - Molecular analysis of genetic differences between virulent and avirulent strains of Aeromonas hydrophila isolated from diseased fish.
JO  - Microbiology
PY  - 2000
SP  - 999
EP  - 1009
VL  - 146
AB  - Aeromonas hydrophila, a normal inhabitant of aquatic environments, is an
AB  - opportunistic pathogen of a variety of aquatic and terrestrial animals,
AB  - including humans. A. hydrophila PPD134/91 is defined as virulent whereas
AB  - PPD35/85 is defined as avirulent on the basis of their different LD50
AB  - values in fish. Suppression subtractive hybridization (SSH) was used to
AB  - identify genetic differences between these two strains. Sixty-nine genomic
AB  - regions of differences were absent in PPD35/85, and the DNA sequences of
AB  - these regions were determined. Sixteen ORFs encoded by 23 fragments showed
AB  - high homology to known proteins of other bacteria. ORFs encoded by the
AB  - remaining 46 fragments were identified as new proteins of A. hydrophila,
AB  - showing no significant homology to any known proteins. Among these
AB  - PPD134/91-specific genes, 22 DNA fragments (21 ORFs) were present in most
AB  - of the eight virulent strains studied but mostly absent in the seven
AB  - avirulent strains, suggesting that they are universal virulence genes in
AB  - A. hydrophila. The PPD134/91-specific genes included five known virulence
AB  - factors of A. hydrophila: haemolysin (hlyA), protease (oligopeptidase A),
AB  - outer-membrane protein (Omp), multidrug-resistance protein and
AB  - histone-like protein (HU-2). Another 47 DNA fragments (44 ORFs) were
AB  - mainly present in PPD134/91, indicating the heterogeneity among motile
AB  - aeromonads. Some of these fragments encoded virulence determinants. These
AB  - included genes for the synthesis of O-antigen and type II
AB  - restriction/modification system. The results indicated that SSH is
AB  - successful in identifying genetic differences and virulence genes among
AB  - different strains of A. hydrophila.
ER  -

TY  - JOUR
AU  - Zhang, Y.Y.
AU  - Li, Q.G.
AU  - Liang, J.X.
AU  - Zhu, Y.B.
TI  - Hairpin probes for real-time assay of restriction endonucleases.
JO  - Acta Biochim. Biophys. Sin.
PY  - 2002
SP  - 329
EP  - 332
VL  - 34
AB  - New fluorogenic probes for restriction endonucleases based on molecular beacons were
AB  - developed. These hairpin probes were single-stranded
AB  - oligonucleotides that had stem-and-loop structure and carried
AB  - 5'-fluorophor moiety and 3'-quencher moiety. Their stem sequences were
AB  - designed as recognition sites for restriction endonucleases and loop
AB  - sequences were unrelated nucleotides. Upon cleavage by endonuclease,
AB  - these probes became fluorescent and thus could trace the enzyme
AB  - activity continuously. Two probes were designed for BglII and NcoI,
AB  - respectively, and each was labeled with a fluorophor of different
AB  - color. The results showed that the two probes could specifically assay
AB  - for the corresponding enzymes either individually or simultaneously in
AB  - a real-time mode. Considering the simplicity, quantification and high
AB  - throughput, these probes could be extended to other applications such
AB  - as drug screening, protein-nucleic acid interaction study and searching
AB  - for small molecule DNA cleavage agents.
ER  -

TY  - JOUR
AU  - Zhang, Z.
AU  - Chen, Y.
AU  - Fu, Y.
AU  - Jiao, N.
TI  - Draft Genome Sequence of the Novel Exopolysaccharide-Producing Bacterium Altibacter lentus Strain JLT2010T, Isolated from Deep Seawater of the South China  Sea.
JO  - Genome Announcements
PY  - 2014
SP  - e00954
EP  - e00914
VL  - 2
AB  - Altibacter lentus strain JLT2010(T) is the type strain of the recently identified novel genus
AB  - and species of the family Flavobacteriaceae and was first isolated
AB  - from deep seawater of the South China Sea. It can produce exopolysaccharide. Here
AB  - we report the first draft genome of JLT2010(T) (3,160,033 bp, with GC content of
AB  - 42.12%) and major findings from its annotation. It is the first reported genome
AB  - in the genus Altibacter.
ER  -

TY  - JOUR
AU  - Zhang, Z.
AU  - Hai, R.
AU  - Song, Z.
AU  - Xia, L.
AU  - Liang, Y.
AU  - Cai, H.
AU  - Liang, Y.
AU  - Shen, X.
AU  - Zhang, E.
AU  - Xu, J.
AU  - Yu, D.
AU  - Yu, X.J.
TI  - Spatial variation of Yersinia pestis from Yunnan Province of China.
JO  - Am. J. Trop. Med. Hyg.
PY  - 2009
SP  - 714
EP  - 717
VL  - 81
AB  - Yunnan Province of China is considered the site of origin for modern
AB  - plague. We analyzed the genotypes of eight Yersinia pestis strains
AB  - isolated from three counties in Yunnan Province by pulse field gel
AB  - electrophoresis (PFGE). PFGE showed that strains isolated from the same
AB  - site were identical regardless of hosts or year of isolation. However, Y.
AB  - pestis strains isolated from geographically distinct loci were genetically
AB  - divergent. Whole genome sequences of two strains from two foci in Yunnan
AB  - showed that the genetic variation of Y. pestis strains was caused by
AB  - genome rearrangement. We concluded that Y. pestis strains in each epidemic
AB  - focus in Yunnan were a clonal population and selected by host
AB  - environments. The genomic variability of the Y. pestis strains from
AB  - different foci were caused by genome rearrangement, which may provide a
AB  - positive selective advantage for Y. pestis to adapt to its host
AB  - environments.
ER  -

TY  - JOUR
AU  - Zhang, Z.
AU  - Liu, C.
AU  - Zhu, Y.
AU  - Zhong, Y.
AU  - Zhu, Y.
AU  - Zheng, H.
AU  - Zhao, G.P.
AU  - Wang, S.Y.
AU  - Guo, X.
TI  - Complete genome sequence of Lactobacillus plantarum JDM1.
JO  - J. Bacteriol.
PY  - 2009
SP  - 5020
EP  - 5021
VL  - 191
AB  - Lactobacillus plantarum is a commonly used lacic acid bacteria (LAB) species as probiotics. We
AB  - have sequenced the genome of Lactobacillus
AB  - plantarum JDM1, which is a Chinese commercial LAB with several probiotic
AB  - functions, with a GS 20 system. We recommend each commercial probiotics
AB  - strain should has the complete genome sequenced to insure the safety and
AB  - stability.
ER  -

TY  - JOUR
AU  - Zhang, Z.
AU  - Yu, A.
AU  - Lan, J.
AU  - Zhang, Y.
AU  - Zhang, H.
AU  - Li, Y.
AU  - Hu, M.
AU  - Cheng, J.
AU  - Wei, S.
AU  - Lin, L.
TI  - Draft Genome Sequence of an Attenuated Streptococcus agalactiae Strain Isolated from the Gut of a Nile Tilapia (Oreochromis niloticus).
JO  - Genome Announcements
PY  - 2017
SP  - e01627
EP  - e01616
VL  - 5
AB  - Streptococcus agalactiae is a pathogen that causes severe anthropozoonosis within a broad
AB  - range of hosts from aquatic animals to mammals, including human beings.
AB  - Here, we describe the draft genome of S. agalactiae HZAUSC001, a low-virulent
AB  - strain isolated from the gut of a moribund tilapia (Oreochromis niloticus) in
AB  - China.
ER  -

TY  - JOUR
AU  - Zhang, Z.J.
AU  - Chen, C.Q.
AU  - Manev, H.
TI  - Enzymatic regional methylation assay for determination of CpG methylation density.
JO  - Anal. Chem.
PY  - 2004
SP  - 6829
EP  - 6832
VL  - 76
AB  - DNA methylation is a critical mechanism for epigenetic gene regulation. In mammalian cells,
AB  - CpG methylation density often influences the
AB  - transcription level of related genes. Here, we report a short and
AB  - accurate method to determine the CpG methylation density of any DNA
AB  - region by sequentially applying bisulfite PCR and SssI (CpG) methylase.
AB  - We introduced simple and efficient binding and washing steps that
AB  - greatly improve the previous methodology and considerably enhance the
AB  - accuracy of the assay. The accuracy of this method allows the detection
AB  - of differences at the level of a single CpG methylation site when
AB  - homogeneous PCR product was used as substrate. We validated our method
AB  - by bisulfite sequencing multiple clones of samples with variable levels
AB  - of CpG methylation. We envision that for its accuracy, simplicity,
AB  - low-cost, flexibility, minimum instrumentation requirements, and
AB  - high-throughput potential our method could greatly benefit research on
AB  - DNA methylation.
ER  -

TY  - JOUR
AU  - Zhang, Z.M.
AU  - Liu, S.
AU  - Lin, K.
AU  - Luo, Y.
AU  - Perry, J.J.
AU  - Wang, Y.
AU  - Song, J.
TI  - Crystal Structure of Human DNA Methyltransferase 1.
JO  - J. Mol. Biol.
PY  - 2015
SP  - 2520
EP  - 2531
VL  - 427
AB  - DNMT1 (DNA methyltransferase 1) is responsible for propagating the DNA methylation patterns
AB  - during DNA replication. DNMT1 contains, in addition to a
AB  - C-terminal methyltransferase domain, a large N-terminal regulatory region that is
AB  - composed of an RFTS (replication foci targeting sequence) domain, a CXXC zinc
AB  - finger domain and a pair of BAH (bromo adjacent homology) domains. The regulatory
AB  - domains of DNMT1 mediate a network of protein-protein and protein-DNA
AB  - interactions to control the recruitment and enzymatic activity of DNMT1. Here we
AB  - report the crystal structure of human DNMT1 with all the structural domains
AB  - (hDNMT1, residues 351-1600) in complex with S-adenosyl-l-homocysteine at 2.62A
AB  - resolution. The RFTS domain directly associates with the methyltransferase
AB  - domain, thereby inhibiting the substrate binding of hDNMT1. Through structural
AB  - analysis, mutational, biochemical and enzymatic studies, we further identify that
AB  - a linker sequence between the CXXC and BAH1 domains, aside from its role in the
AB  - CXXC domain-mediated DNMT1 autoinhibition, serves as an important regulatory
AB  - element in the RFTS domain-mediated autoinhibition. In comparison with the
AB  - previously determined structure of mouse DNMT1, this study also reveals a number
AB  - of distinct structural features that may underlie subtle functional diversity
AB  - observed for the two orthologues. In addition, this structure provides a
AB  - framework for understanding the functional consequence of disease-related hDNMT1
AB  - mutations.
ER  -

TY  - JOUR
AU  - Zhang, Z.M.
AU  - Lu, R.
AU  - Wang, P.
AU  - Yu, Y.
AU  - Chen, D.
AU  - Gao, L.
AU  - Liu, S.
AU  - Ji, D.
AU  - Rothbart, S.B.
AU  - Wang, Y.
AU  - Wang, G.G.
AU  - Song, J.
TI  - Structural basis for DNMT3A-mediated de novo DNA methylation.
JO  - Nature
PY  - 2018
SP  - 387
EP  - 391
VL  - 554
AB  - DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at  cytosines is
AB  - essential for genome regulation and development. Dysregulation of
AB  - this process is implicated in various diseases, notably cancer. However, the
AB  - mechanisms underlying DNMT3 substrate recognition and enzymatic specificity
AB  - remain elusive. Here we report a 2.65-angstrom crystal structure of the
AB  - DNMT3A-DNMT3L-DNA complex in which two DNMT3A monomers simultaneously attack two
AB  - cytosine-phosphate-guanine (CpG) dinucleotides, with the target sites separated
AB  - by 14 base pairs within the same DNA duplex. The DNMT3A-DNA interaction involves
AB  - a target recognition domain, a catalytic loop, and DNMT3A homodimeric interface.
AB  - Arg836 of the target recognition domain makes crucial contacts with CpG, ensuring
AB  - DNMT3A enzymatic preference towards CpG sites in cells. Haematological
AB  - cancer-associated somatic mutations of the substrate-binding residues decrease
AB  - DNMT3A activity, induce CpG hypomethylation, and promote transformation of
AB  - haematopoietic cells. Together, our study reveals the mechanistic basis for
AB  - DNMT3A-mediated DNA methylation and establishes its aetiological link to human
AB  - disease.
ER  -

TY  - JOUR
AU  - Zhang, Z.Y.
AU  - Sun, Z.Q.
AU  - Wang, Z.L.
AU  - Wen, Z.L.
AU  - Sun, Q.W.
AU  - Zhu, Z.Q.
AU  - Song, Y.Z.
AU  - Zhao, J.W.
AU  - Wang, H.H.
AU  - Zhang, S.L.
AU  - Guo, X.K.
TI  - Complete Genome Sequence of a Novel Clinical Isolate, the Nontuberculous Mycobacterium Strain JDM601.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4300
EP  - 4301
VL  - 193
AB  - Mycobacteriosis is on the increase. Nontuberculous mycobacteria (NTM) are resistant to most
AB  - antituberculosis drugs naturally. We determined the
AB  - complete genome sequence of a novel NTM strain, JDM601, of the
AB  - Mycobacterium terrae complex, which was isolated from a patient with
AB  - tuberculosis-like disease and with various antibiotic resistances.
ER  -

TY  - JOUR
AU  - Zhao, B.
AU  - Mesbah, N.M.
AU  - Dalin, E.
AU  - Goodwin, L.
AU  - Nolan, M.
AU  - Pitluck, S.
AU  - Chertkov, O.
AU  - Brettin, T.S.
AU  - Han, J.
AU  - Larimer, F.W.
AU  - Land, M.L.
AU  - Hauser, L.
AU  - Kyrpides, N.
AU  - Wiegel, J.
TI  - Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT.
JO  - J. Bacteriol.
PY  - 2011
SP  - 4023
EP  - 4023
VL  - 193
AB  - The genome of the anaerobic halophilic alkalithermophile Natranaerobius thermophiles consists
AB  - of one 3,165,557 bp chromosome and two plasmids
AB  - (17,207 bp, 8,689 bp). The present study is the first to report the
AB  - completely sequenced genome of an anaerobic polyextremophile and genes
AB  - associated with roles in regulation of intracellular osmotic pressure, pH
AB  - homeostasis, and growth at elevated temperatures.
ER  -

TY  - JOUR
AU  - Zhao, C.
AU  - Qu, K.G.
AU  - Song, Y.J.
AU  - Ren, J.S.
AU  - Qu, X.G.
TI  - A Universal, Label-Free, and Sensitive Optical Enzyme-Sensing System for Nuclease and Methyltransferase Activity Based on Light Scattering of Carbon Nanotubes.
JO  - Adv. Funct. Mater.
PY  - 2011
SP  - 583
EP  - 590
VL  - 21
AB  - A label-free, enzyme-responsive nanosystem that uses a DNA/single-walled carbon nanotube
AB  - (SWNT) assembly as the substrate is
AB  - demonstrated for the sensitive, universal detection of restriction and
AB  - nonrestriction endonucleases as well as methyltransferases in a
AB  - homogeneous solution on the basis of light scattering (LS) of carbon
AB  - nanotubes. This protocol is based on the different binding affinities
AB  - of SWNTs to single-and double-stranded DNA. This difference can lead to
AB  - different LS signals that can be used for the detection of nuclease
AB  - cleavage activity. The assay only requires a label-free oligonucleotide
AB  - probe, significantly reducing the typical cost. The LS technique and
AB  - the use of a nuclease-specific oligonucleotide probe impart
AB  - extraordinarily high sensitivity and selectivity. This light scattering
AB  - assay is universal and label-free with a detection limit of 5 x 10(-6)
AB  - U mu L-1 for S1 nuclease, 1 x 10(-4) U mu L-1 for EcoRI endonuclease,
AB  - and 1 x 10(-2) U mu L-1 for EcoRI methylase. In principle, this assay
AB  - can be used to detect any kind of nuclease by simply changing the DNA
AB  - sequences of the specific probe.
ER  -

TY  - JOUR
AU  - Zhao, C.W.
AU  - Wang, H.Y.
AU  - Zhang, Y.Z.
AU  - Feng, H.
TI  - Draft Genome Sequence of Bacillus pumilus BA06, a Producer of Alkaline Serine Protease with Leather-Dehairing Function.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6668
EP  - 6669
VL  - 194
AB  - Bacillus pumilus BA06 was isolated from the proteinaceous soil and produced an extracellular
AB  - alkaline protease with leather-dehairing function. The genome of
AB  - BA06 was sequenced. The comparative genome analysis indicated that strain BA06 is
AB  - different in genome from the other B. pumilus strains, with limited insertions,
AB  - deletions, and rearrangements.
ER  -

TY  - JOUR
AU  - Zhao, D.M.
AU  - Jin, F.
AU  - Huang, H.F.
TI  - A review on DNA methyltransferases and early embryo development including DNA methyltransferases I (DnmT1) and DNA methyltransferases  III (DnmT3).
JO  - Zhejiang Da Xue Xue Bao Yi Xue Ban
PY  - 2005
SP  - 281
EP  - 284
VL  - 34
ER  -

TY  - JOUR
AU  - Zhao, F.
AU  - Bai, J.
AU  - Wu, J.
AU  - Liu, J.
AU  - Zhou, M.
AU  - Xia, S.
AU  - Wang, S.
AU  - Yao, X.
AU  - Yi, H.
AU  - Lin, M.
AU  - Gao, S.
AU  - Zhou, T.
AU  - Xu, Z.
AU  - Niu, Y.
AU  - Bao, Q.
TI  - Sequencing and Genetic Variation of Multidrug Resistance Plasmids in Klebsiella pneumoniae.
JO  - PLoS ONE
PY  - 2010
SP  - E10141
EP  - E10141
VL  - 5
AB  - Background: The development of multidrug resistance is a major problem in the treatment of
AB  - pathogenic microorganisms by distinct antimicrobial agents. Characterizing the genetic
AB  - variation among plasmids from different bacterial species or strains is a key step towards
AB  - understanding the mechanism of virulence and their evolution.
AB  - Results: We applied a deep sequencing approach to 206 clinical strains of Klebsiella
AB  - pneumoniae collected from 2002 to 2008 to understand the genetic variation of multidrug
AB  - resistance plasmids, and to reveal the dynamic change of drug resistance over time. First, we
AB  - sequenced three plasmids (70 Kb, 94 Kb, and 147 Kb) from a clonal strain of K. pneumoniae
AB  - using Sanger sequencing. Using the Illumina sequencing technology, we obtained more than 17
AB  - million of short reads from two pooled plasmid samples. We mapped these short reads to the
AB  - three reference plasmid sequences, and identified a large
AB  - number of single nucleotide polymorphisms (SNPs) in these pooled plasmids. Many of these SNPs
AB  - are present in drugresistance genes. We also found that a significant fraction of short reads
AB  - could not be mapped to the reference sequences, indicating a high degree of genetic variation
AB  - among the collection of K. pneumoniae isolates. Moreover, we identified that plasmid
AB  - conjugative transfer genes and antibiotic resistance genes are more likely to suffer from
AB  - positive selection, as indicated by the elevated rates of nonsynonymous substitution.
AB  - Conclusion: These data represent the first large-scale study of genetic variation in multidrug
AB  - resistance plasmids and provide insight into the mechanisms of plasmid diversification and the
AB  - genetic basis of antibiotic resistance.
ER  -

TY  - JOUR
AU  - Zhao, F.Q.
AU  - Zhang, X.W.
AU  - Liang, C.W.
AU  - Wu, J.Y.
AU  - Bao, Q.Y.
AU  - Qin, S.
TI  - Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria.
JO  - Physiol. Genomics
PY  - 2006
SP  - 181
EP  - 190
VL  - 24
AB  - Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation
AB  - ranging from 1.6 to 9.1 Mb. Here, we first
AB  - retrieved all the putative restriction-modification (RM) genes in the
AB  - draft genome of Spirulina and then performed a range of comparative and
AB  - bioinformatic analyses on RM genes from unicellular and filamentous
AB  - cyanobacterial genomes. We have identified 6 gene clusters containing
AB  - putative Type I RMs and 11 putative Type II RMs or the solitary
AB  - methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18
AB  - MTases are not expressed in Spirulina, whereas one hsdM gene, with a
AB  - mutated cognate hsdS, was detected to be expressed. Our results
AB  - indicate that the number of RM genes in filamentous cyanobacteria is
AB  - significantly higher than in unicellular species, and this expansion of
AB  - RM systems in filamentous cyanobacteria may be related to their wide
AB  - range of ecological tolerance. Furthermore, a coevolutionary pattern is
AB  - found between hsdM and hsdR, with a large number of site pairs
AB  - positively or negatively correlated, indicating the functional
AB  - importance of these pairing interactions between their tertiary
AB  - structures. No evidence for positive selection is found for the
AB  - majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction
AB  - endonuclease gene families, while a group of MTases exhibit a
AB  - remarkable signature of adaptive evolution. Sites and genes identified
AB  - here to have been under positive selection would provide targets for
AB  - further research on their structural and functional evaluations.
ER  -

TY  - JOUR
AU  - Zhao, G.
AU  - Li, J.
AU  - Tong, Z.
AU  - Zhao, B.
AU  - Mu, R.
AU  - Guan, Y.
TI  - Enzymatic Cleavage of Type II Restriction Endonucleases on the 2 '-O-Methyl Nucleotide and Phosphorothioate Substituted DNA.
JO  - PLoS ONE
PY  - 2013
SP  - e79415
EP  - e79415
VL  - 8
AB  - The effects of nucleotide analogue substitution on the cleavage efficiencies of type II
AB  - restriction endonucleases have been investigated. Six restriction endonucleases (EcoRV, SpeI,
AB  - XbaI, XhoI, PstI and SphI) were investigated respectively regarding their cleavage when
AB  - substrates were substituted by 2'-O-methyl nucleotide (2'-OMeN) and phosphorothioate (PS).
AB  - Substitutions were made in the recognition sequence and the two nucleotides flanking the
AB  - recognition sequence for each endonuclease. The endonu lease cleavage efficiencies were
AB  - determined using FRET-based assay. Results demonstrated a position-dependent inhibitory effect
AB  - of substitution on the cleavage efficiency for all the six endonucleases. In general, the
AB  - 2'-OMeN substitutions had greater impact than the PS substitutions on the enzymatic
AB  - activities. Nucleotides of optimal substitutions for protection against RE cleavage were
AB  - identified. Experimental results and conclusions in this study facilitate our insight into the
AB  - DNA-protein interactions  and the enzymatic cleavage mechanism, particularly for those whose
AB  - detailed structure information is not available. In addition, the information could benefit
AB  - the development of bioengineering and synthetic biology.
ER  -

TY  - JOUR
AU  - Zhao, L.
TI  - Characterization of bacterial homing endonuclease I-Ssp6803I.
JO  - Ph.D. Thesis, University of Washington, Seattle, USA
PY  - 2008
SP  - 1
EP  - 142
AB  - The homing endonuclease I-Ssp6803I causes the insertion and persistence of a group I
AB  - self-splicing intron into the anticodon loop of the tRNAfMet gene in the cyanobacteria
AB  - Synechocystis PCC6803.  This enzyme and its host intron represent the only known combination
AB  - of a persistent intron and associated homing endonuclease within bacterial tRNA genes.  In
AB  - this study, we predicted that this enzyme, which is dissimilar to other known homing
AB  - endonucleases, might contain the PD-(D/E)XK nuclease catalytic motif -- a fold normally
AB  - associated with bacterial restriction endonucleases.  This prediction, combined with a
AB  - mutational screen for catalytically inactivating point mutations, allowed us to express,
AB  - solubilize and crystallize I-Ssp6803I in complex with its target DNA.  The 3.1A crystal
AB  - structure of the protein-DNA complex confirmed the presence of the PD-(D/E)XK motif and also
AB  - revealed the use of a unique tetrameric assembly to promote recognition of a single long
AB  - target site.  The binding specificity profile of I-Ssp6803I was then determined by measuring
AB  - the effect of every possible base substitution across its 23-basepair target site.  The
AB  - endonuclease displays relatively low binding specificity, corresponding to a profile reflects
AB  - sequence constraints on its host tRNAfMet gene.
ER  -

TY  - JOUR
AU  - Zhao, L.
AU  - Bao, G.
AU  - Geng, B.
AU  - Song, J.
AU  - Li, Y.
TI  - Draft Genome Sequence of Lysinibacillus fusiformis Strain SW-B9, a Novel Strain for Biotransformation of Isoeugenol to Vanillin.
JO  - Genome Announcements
PY  - 2015
SP  - e00289
EP  - e00215
VL  - 3
AB  - Lysinibacillus fusiformis SW-B9 was the first reported strain in L. fusiformis showing
AB  - effective biotransformation of isoeugenol to vanillin. Here, we report
AB  - the annotated genome of strain SW-B9, which has special pathways for producing
AB  - vanillin. The genome will provide a genetic basis for better understanding the
AB  - physiology of this species.
ER  -

TY  - JOUR
AU  - Zhao, L.
AU  - Bonocora, R.P.
AU  - Shub, D.A.
AU  - Stoddard, B.L.
TI  - The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
JO  - EMBO J.
PY  - 2007
SP  - 2432
EP  - 2442
VL  - 26
AB  - The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial
AB  - tRNA gene-the only example of an invasive mobile
AB  - intron within a bacterial genome. Using a computational fold prediction,
AB  - mutagenic screen and crystal structure determination, we demonstrate that
AB  - this protein is a tetrameric PD-(D/E)-XK endonuclease-a fold normally used
AB  - to protect a bacterial genome from invading DNA through the action of
AB  - restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to
AB  - promote recognition of a single long target site, whereas restriction
AB  - endonuclease tetramers facilitate cooperative binding and cleavage of two
AB  - short sites. The limited use of the PD-(D/E)-XK nucleases by mobile
AB  - introns stands in contrast to their frequent use of LAGLIDADG and HNH
AB  - endonucleases-which in turn, are rarely incorporated into
AB  - restriction/modification systems.
ER  -

TY  - JOUR
AU  - Zhao, L.
AU  - Pellenz, S.
AU  - Stoddard, B.L.
TI  - Activity and Specificity of the Bacterial PD-(D/E)XK Homing Endonuclease I-Ssp6803I.
JO  - J. Mol. Biol.
PY  - 2009
SP  - 1498
EP  - 1510
VL  - 385
AB  - The restriction endonuclease fold [a three-layer alpha-beta sandwich containing variations of
AB  - the PD-(D/E)XK nuclease motif] has been greatly
AB  - diversified during evolution, facilitating its use for many biological
AB  - functions. Here we characterize DNA binding and cleavage by the PD-(D/E)XK
AB  - homing endonuclease I-Ssp6803I. Unlike most restriction endonucleases
AB  - harboring the same core fold, the specificity profile of this enzyme
AB  - extends over a long (17 bp) target site. The DNA binding and cleavage
AB  - specificity profiles of this enzyme were independently determined and
AB  - found to be highly correlated. However, the DNA target sequence contains
AB  - several positions where binding and cleavage activities are not tightly
AB  - coupled: individual DNA base-pair substitutions at those positions that
AB  - significantly decrease cleavage activity have minor effects on binding
AB  - affinity. These changes in the DNA target sequence appear to correspond to
AB  - substitutions that uniquely increase the free energy change between the
AB  - ground state and the transition state, rather than simply decreasing the
AB  - overall DNA binding affinity. The specificity of the enzyme reflects
AB  - constraints on its host gene and limitations imposed by the enzyme's
AB  - quaternary structure and illustrate the highly diverse repertoire of DNA
AB  - recognition specificities that can be adopted by the related folds
AB  - surrounding the PD-(D/E)XK nuclease motif.
ER  -

TY  - JOUR
AU  - Zhao, M.
AU  - Liu, S.
AU  - He, L.
AU  - Tian, Y.
TI  - Draft Genome Sequence of Lactobacillus plantarum XJ25 Isolated from Chinese Red Wine.
JO  - Genome Announcements
PY  - 2016
SP  - e01216
EP  - e01216
VL  - 4
AB  - Here, we present the draft genome sequence of Lactobacillus plantarum XJ25, isolated from
AB  - Chinese red wine that had undergone spontaneous malolactic
AB  - fermentation, which consists of 25 contigs and is 3,218,018 bp long.
ER  -

TY  - JOUR
AU  - Zhao, N.
AU  - Bai, Y.
AU  - Zhao, X.Q.
AU  - Yang, Z.Y.
AU  - Bai, F.W.
TI  - Draft Genome Sequence of the Flocculating Zymomonas mobilis Strain ZM401 (ATCC 31822).
JO  - J. Bacteriol.
PY  - 2012
SP  - 7008
EP  - 7009
VL  - 194
AB  - Zymomonas mobilis ZM401 is a flocculating strain which can be self-immobilized within
AB  - fermentors for a high-cell-density culture to improve ethanol
AB  - productivity, as well as high-gravity fermentation to increase ethanol titer, due
AB  - to its improved ethanol tolerance associated with the morphological change. Here,
AB  - we report its draft genome sequence.
ER  -

TY  - JOUR
AU  - Zhao, N.
AU  - Pan, Y.
AU  - Liu, H.
AU  - Cheng, Z.
TI  - Draft Genome Sequence of Zymomonas mobilis ZM481 (ATCC 31823).
JO  - Genome Announcements
PY  - 2016
SP  - e00193
EP  - e00116
VL  - 4
AB  - Zymomonas mobilisZM481 (ATCC 31823) is an ethanol-tolerant strain that can produce the highest
AB  - level of ethanol inZ. mobilisfrom glucose in the shortest
AB  - time. Here, we report a draft genome sequence of ZM481, which can help us
AB  - understand the genes related to the ethanol tolerance of this strain.
ER  -

TY  - JOUR
AU  - Zhao, Q.
AU  - Hu, H.
AU  - Wang, W.
AU  - Peng, H.
AU  - Zhang, X.
TI  - Genome Sequence of Sphingobium yanoikuyae B1, a Polycyclic Aromatic Hydrocarbon-Degrading Strain.
JO  - Genome Announcements
PY  - 2015
SP  - e01522
EP  - e01514
VL  - 3
AB  - Sphingobium yanoikuyae B1 can utilize biphenyl, naphthalene, phenanthrene, toluene, and
AB  - m-/p-xylene as sole sources of carbon and energy. Here, we present a
AB  - 5.2-Mb assembly of its genome. An analysis of the genome can provide insights
AB  - into the mechanisms of polycyclic aromatic hydrocarbon (PAH) degradation and
AB  - potentially aid in bioremediation applications.
ER  -

TY  - JOUR
AU  - Zhao, W.
AU  - Chen, Y.
AU  - Sun, Z.
AU  - Wang, J.
AU  - Zhou, Z.
AU  - Sun, T.
AU  - Wang, L.
AU  - Chen, W.
AU  - Zhang, H.
TI  - Complete Genome Sequence of the Lactobacillus helveticus H10.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2666
EP  - 2667
VL  - 193
AB  - Lactobacillus helveticus strain H10 was isolated from the traditional fermented milk in Tibet,
AB  - China. We sequenced the whole genome of strain
AB  - H10 and compared it to the published genome sequence of Lactobacillus
AB  - helveticus DPC4571.
ER  -

TY  - JOUR
AU  - Zhao, W.
AU  - Jiang, H.
AU  - Tian, Q.
AU  - Hu, J.
TI  - Draft Genome Sequence of Pseudomonas syringae pv. persicae NCPPB 2254.
JO  - Genome Announcements
PY  - 2015
SP  - e00555
EP  - e00515
VL  - 3
AB  - Pseudomonas syringae pv. persicae is a pathogen that causes bacterial decline of  stone fruit.
AB  - Here, we report the draft genome sequence for P. syringae pv.
AB  - persicae, which was isolated from Prunus persica.
ER  -

TY  - JOUR
AU  - Zhao, W.
AU  - Zeng, X.
AU  - Xiao, X.
TI  - Thermococcus eurythermalis sp. nov., a conditional piezophilic hyperthermophilic archaeon with a wide temperature range isolated from an oil-immersed chimney in the Guaymas Basin.
JO  - Int. J. Syst. Evol. Microbiol.
PY  - 2015
SP  - 30
EP  - 35
VL  - 65
AB  - A conditional piezophilic hyperthermophilic archaeon with a wide temperature/ pH/
AB  - pressure range was isolated from an oil-immersed hydrothermal chimney at a depth
AB  - of 2006.9 m in the Guaymas Basin. The enrichment and isolation of strain A501T
AB  - were performed at 80 degrees C at 0.1 MPa. The isolate, A501T, is an irregular
AB  - motile coccus with a polar tuft of flagella and is generally 0.6-2.6 mum in
AB  - diameter. Growth was detected over the range of 50-100 degrees C (optimum growth
AB  - at 85 degrees C) at atmospheric pressure and was observed at 102 degrees C at a
AB  - pressure of 10 MPa. At 85 degrees C, growth was observed at a pressure of 0.1-70
AB  - MPa (optimum pressure 0.1 MPa-30 MPa), while at 95 degrees C, the pressure of
AB  - growth ranged from 0.1 MPa to 50 MPa (optimum pressure 10 MPa). Cells of strain
AB  - A501T grew at pH 4-9 (optimum pH 7.0) and a NaCl concentration of 1.0-5.0% (w/v)
AB  - (optimum concentration 2.5%) This isolate was an anaerobic
AB  - chemoorgano-heterotroph and was able to utilize yeast extract, peptone, tryptone
AB  - and starch as the single carbon source for growth. Elemental sulfur and cysteine
AB  - stimulated growth; however, these molecules were not necessary. The G+C content
AB  - of the complete genome was 53.47%. The results of the 16S rRNA gene analysis
AB  - indicated that strain A501T belongs to the genus Thermococcus. There was no
AB  - significant homology between strain A501T and the phylogenetically related
AB  - Thermococcus species based on complete genome sequence alignments and calculation
AB  - of the average nucleotide identity and the tetranucleotide signature frequency
AB  - correlation coefficient. These results indicate that strain A501T represents a
AB  - novel species, Thermococcus eurythermalis sp. nov. The type strain is A501T
AB  - (=CGMCC 7834T; =JCM 30233T).
ER  -

TY  - JOUR
AU  - Zhao, X.
AU  - de Jong, A.
AU  - Zhou, Z.
AU  - Kuipers, O.P.
TI  - Complete Genome Sequence of Bacillus amyloliquefaciens Strain BH072, Isolated from Honey.
JO  - Genome Announcements
PY  - 2015
SP  - e00098
EP  - e00015
VL  - 3
AB  - The genome of Bacillus amyloliquefaciens strain BH072, isolated from a honey sample and
AB  - showing strong antimicrobial activity against plant pathogens, is 4.07
AB  - Mb and harbors 3,785 coding sequences (CDS). Several gene clusters for
AB  - nonribosomal synthesis of antimicrobial peptides and a complete gene cluster for
AB  - biosynthesis of mersacidin were detected.
ER  -

TY  - JOUR
AU  - Zhao, X.
AU  - Epperson, L.E.
AU  - Hasan, N.A.
AU  - Honda, J.R.
AU  - Chan, E.D.
AU  - Strong, M.
AU  - Walter, N.D.
AU  - Davidson, R.M.
TI  - Complete Genome Sequence of Mycobacterium avium subsp. hominissuis Strain H87 Isolated from an Indoor Water Sample.
JO  - Genome Announcements
PY  - 2017
SP  - e00189
EP  - e00117
VL  - 5
AB  - Mycobacterium avium subsp. hominissuis is an environmentally acquired bacterium known to cause
AB  - pulmonary and soft tissue infections, lymphadenitis, and
AB  - disseminated disease in humans. We report here the complete genome sequence of
AB  - strain H87, isolated from an indoor water sample, as a single circular chromosome
AB  - of 5,626,623 bp with a G+C content of 68.8%.
ER  -

TY  - JOUR
AU  - Zhao, X.
AU  - Geng, X.
AU  - Chen, C.
AU  - Chen, L.
AU  - Jiao, W.
AU  - Yang, C.
TI  - Draft Genome Sequence of the Marine Actinomycete Streptomyces sulphureus L180, Isolated from Marine Sediment.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4482
EP  - 4482
VL  - 194
AB  - Marine-derived actinobacteria are rich sources of valuable natural products and industrial
AB  - enzymes for biotechnology applications. The marine-derived
AB  - Streptomyces sulphureus strain L180 was isolated from the marine sediment in a
AB  - sea cucumber farm at a depth of about 10 m in Dalian, China, and its 16S rRNA
AB  - gene sequence was determined to have the highest identity to that of Streptomyces
AB  - sulphureus NRRL B-1627(T) (99.65%). Here, we report the draft genome sequence of
AB  - this strain.
ER  -

TY  - JOUR
AU  - Zhao, X.
AU  - Yang, T.
TI  - Draft Genome Sequence of the Marine Sediment-Derived Actinomycete Streptomyces xinghaiensis NRRL B24674T.
JO  - J. Bacteriol.
PY  - 2011
SP  - 5543
EP  - 5543
VL  - 193
AB  - Actinobacteria are a rich source of novel natural products. We recently characterized
AB  - Streptomyces xinghaiensis NRRL B24674(T) as a novel species
AB  - of marine origin. Here we report the draft genome sequence of this
AB  - species. This is the first validly published marine streptomycete for
AB  - which a genome sequence has been presented.
ER  -

TY  - JOUR
AU  - Zhao, Y.
AU  - Caspers, M.P.
AU  - Abee, T.
AU  - Siezen, R.J.
AU  - Kort, R.
TI  - Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4118
EP  - 4118
VL  - 194
AB  - Thermophilic spore-forming bacteria are a common cause of contamination in dairy  products. We
AB  - isolated the thermophilic strain Geobacillus thermoglucosidans
AB  - TNO-09.020 from a milk processing plant and report the complete genome of a dairy
AB  - plant isolate consisting of a single chromosome of 3.75 Mb.
ER  -

TY  - JOUR
AU  - Zhao, Y.
AU  - Chen, M.
AU  - Su, L.
AU  - Wang, T.
AU  - Liu, S.
AU  - Yang, H.
TI  - Molecular cloning and expression-profile analysis of sea cucumber DNA (Cytosine-5)-methyltransferase 1 and methyl-CpG binding domain type 2/3 genes during aestivation.
JO  - Comp. Biochem. Physiol. B, Biochem. Mol. Biol.
PY  - 2013
SP  - 26
EP  - 35
VL  - 165
AB  - The sea cucumber Apostichopus japonicus Selenka survives high summer temperature by entering
AB  - aestivation, characterized by hypometabolism and global gene silencing. We investigated the
AB  - hypothesis that aestivation is associated with DNA methylation-dependent epigenetic mechanisms
AB  - by cloning, sequencing and measuring the transcript abundances of two genes dnmt1 and mbd2/3,
AB  - which comprise the DNA methylation system in A. japonicus Selenka. The deduced amino acid
AB  - sequences and characteristic motifs of sea cucumber DNMT1 and MBD2/3 showed high homology to
AB  - those of their mammalian counterparts. Quantitative real-time RT-PCR analysis showed that
AB  - dnmt1 and mbd2/3 genes were similarly expressed in all four tissues examined (intestine,
AB  - respiratory tree, muscle and body wall). dnmt1 expression in the intestine was up-regulated
AB  - during deep aestivation (P < 0.05), while mbd2/3 was over-expressed in both the intestine and
AB  - respiratory tree during the same period (P < 0.01). No differences in expression levels were
AB  - observed between other tissues. The results of this study suggest that DNA methylation may be
AB  - involved in transcriptional silencing, and that the intestine is the major site for epigenetic
AB  - regulation during aestivation in the sea cucumber.
ER  -

TY  - JOUR
AU  - Zhao, Y.
AU  - Dong, Y.
AU  - Zhang, Y.
AU  - Che, L.
AU  - Pan, H.
AU  - Zhou, H.
TI  - Draft Genome Sequence of a Selenite- and Tellurite-Reducing Marine Bacterium, Lysinibacillus sp. Strain ZYM-1.
JO  - Genome Announcements
PY  - 2016
SP  - e01552
EP  - e01515
VL  - 4
AB  - Lysinibacillus sp. ZYM-1, a Gram-positive strain isolated from marine sediments,  reduces
AB  - selenite and tellurite efficiently. Meanwhile, it also exhibits high
AB  - resistance to Zn2+ and Mn2+. Here, we report the draft genome sequence of strain
AB  - ZYM-1, which contains genes related to selenite and tellurite reduction and also
AB  - metal resistance.
ER  -

TY  - JOUR
AU  - Zhao, Y.
AU  - Tian, Y.
AU  - Li, X.
AU  - Hu, B.
TI  - Complete Genome Sequence of a Dickeya fangzhongdai Type Strain Causing Bleeding Canker of Pear Tree Trunks.
JO  - Genome Announcements
PY  - 2018
SP  - e00177
EP  - e00118
VL  - 6
AB  - Dickeya fangzhongdai DSM 101947(T) was isolated from pear trees (Pyrus pyrifolia) in Zhejiang
AB  - Province, China, and is the causal agent of bleeding canker, a
AB  - devastating disease of pear trees. Here, we provide the complete genome sequence
AB  - of this bacterium, which has a 5,027,163-bp-long genome, including 4,375
AB  - protein-coding genes and 100 RNA genes. This strain possesses a number of genes
AB  - encoding virulence factors of pathogens.
ER  -

TY  - JOUR
AU  - Zhao, Z.
AU  - Wang, L.
AU  - Wang, B.
AU  - Liang, H.
AU  - Ye, Q.
AU  - Zeng, M.
TI  - Complete Genome Sequence of Cronobacter sakazakii Strain CMCC 45402.
JO  - Genome Announcements
PY  - 2014
SP  - e01139
EP  - e01113
VL  - 2
AB  - Cronobacter sakazakii is considered to be an important pathogen involved in life-threatening
AB  - neonatal infections. Here, we report the annotated complete
AB  - genome sequence of C. sakazakii strain CMCC 45402, obtained from a milk sample in
AB  - China. The major findings from the genomic analysis provide a better
AB  - understanding of the isolates from China.
ER  -

TY  - JOUR
AU  - Zhao, Z.-H.
AU  - Yung, M.-H.
AU  - Cui, T.
AU  - Wang, Y.-Z.
AU  - Shaw, P.C.
TI  - Restriction endonuclease from thermophilic bacterial species IV. Isolation and characterization of BpuB5I.
JO  - Nucleic Acids Res.
PY  - 1992
SP  - 1156
EP  - 1156
VL  - 20
AB  - BpuB5I is a type II restriction endonuclease from a Bacillus pumilus strain
AB  - isolated from soil.  To purify the enzyme, bacterial cells were grown on nine L
AB  - agar plates at 55C overnight.  Cell pellet (3 g wet weight) obtained was
AB  - resuspended in 10 ml extraction buffer (1) and disrupted by sonication.  The
AB  - extract after centrifugation was dialysed against extraction buffer at 4C
AB  - overnight and then passed through a heparin-affin gel column (7 ml bed volume).
AB  - Enzyme eluted at 0.2 - 0.25 M NaCl gradient was concentrated and dialysed and
AB  - then further purified by a Mono Q column with enzyme eluted at 0.3 M NaCl.  The
AB  - purified enzyme was used to digest lambda, PhiX-174 and Ad-2 DNA (Fig. 1).
AB  - Restriction patterns produced were identifical to those cleaved by mesophilic
AB  - enzyme SplI which recognizes 5'CGTACG3'(2).  The cleavage site of BpuB5I was
AB  - determined according to ref. 1 using PhiX-174 as the template and a 18 mer
AB  - oligonucleotide with sequence 5'TCCGACTACCCTCCCGAC3' as the primer.  The primer
AB  - was annealed to position 2691 - 2708 of the denatured PhiX-174 DNA and was
AB  - extended through the BpuB5I site at position 2794.  Figure 2 shows that the
AB  - cleaveage product of reaction I comigrates with the band corresponding to the
AB  - first C nucleotide in the sequence CGTACG and reaction II comigrates with the
AB  - band corresponding to the second C nucleotide.  Therefore, BpuB5I recognizes
AB  - and cleaves 5'C^GTACG3'.  The optimal reaction buffer of BpuB5I contained 5 mM
AB  - NaCl, 10 mM Tris.Cl, pH 8.0, 10 mM MgCl2, 1 mM dithiothreitol and optimal
AB  - temperature was at 55C.
ER  -

TY  - JOUR
AU  - Zharmukhamedova, T.Y.
AU  - Privezencova, N.G.
AU  - Shishova, O.V.
AU  - Shiryaev, S.A.
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.I.
TI  - A site-specific endonuclease from the thermophilic strain Bacillus species F4.
JO  - Biokhimiia
PY  - 1999
SP  - 697
EP  - 702
VL  - 64
AB  - A strain producing the site-specific endonuclease BspF4I was found during screening of
AB  - thermophilic bacteria isolated from soil.  The restriction endonuclease, free from contaminant
AB  - nonspecific nucleases, was purified using three steps of column chromatography--on
AB  - hydroxyapatite, blue agarose, and DEAE-Trisacryl. The enzyme is stable on storage and exhibits
AB  - maximal activity at 48-56 degrees C in the presence of albumin in buffer containing 10 mM
AB  - Tris-HCl (pH 7.5) and 10 mM MgCl2.  BspF4I recognizes the sequence 5;-GGNCC-3; on DNA and is
AB  - an isomer and not an isoschizomer of the endonuclease Sau96I.  Unlike the prototype, BspF4I
AB  - does not cleave the site in a defined way. A strand with purine in the center of the sequence
AB  - is cleaved after the first G, as in the case of the prototype, while the strand with
AB  - pyrimidine is cleaved either before or after the first G.
ER  -

TY  - JOUR
AU  - Zheleznaya, L.
AU  - Shiryaev, S.
AU  - Zheleznyakova, E.
AU  - Matvienko, N.
AU  - Matvienko, N.
TI  - R.SspD5I is a neoschizomer of HphI producing blunt end DNA fragments.
JO  - FEBS Lett.
PY  - 1999
SP  - 38
EP  - 40
VL  - 448
AB  - The strain Staphylococcus species D5 produces a restriction enzyme.  It is the neoschizomer of
AB  - HphI endonuclease, which cleaves DNA at a distance of eight nucleotides from the recognition
AB  - sequences producing blunt end DNA fragments: 5'-GGTGA8N/-3' and 3'-CCACT8N/-5'.
ER  -

TY  - JOUR
AU  - Zheleznaya, L.A.
AU  - Kainov, D.E.
AU  - Yunusova, A.K.
AU  - Matvienko, N.I.
TI  - Regulatory C protein of the EcoRV modification-restriction system.
JO  - Biokhimiia
PY  - 2003
SP  - 125
EP  - 132
VL  - 68
AB  - The C gene product of the modification-restriction system PvuII binds to its own promoter (C
AB  - box) and stimulates transcription of both the C gene and the endonuclease gene. According to
AB  - our data the same regulatory mechanism is realized in the EcoRV system. It was found that
AB  - upstream of the EcoRV endonuclease gene two ATG codons give rise to two open reading frames
AB  - (ORF1 and ORF2) ending at the same point inside the endonuclease gene. Two DNA fragments
AB  - corresponding to ORF1 and ORF2 were cloned, and the homogenous products of proteins encoded by
AB  - them were found to be DNA-binding proteins. A specific DNA sequence (C box) recognized by the
AB  - proteins was determined with DNAse I footprinting. The C box CCCATTTTGGGTTATCCCATTTTGGG is
AB  - located inside ORF1 and, similar to the PvuII C box consisting of tandem repeats of 11
AB  - nucleotides, is divided by four nucleotides. In its turn each of the repeats contains inverted
AB  - repeats of four terminal nucleotides. The EcoRV C box sequence differs both from the PvuII C
AB  - box sequence and from the proposed consensus sequence of C boxes in other
AB  - modification-restriction systems.
ER  -

TY  - JOUR
AU  - Zheleznaya, L.A.
AU  - Matvienko, N.N.
AU  - Matvienko, N.I.
TI  - Two site-specific endonucleases from the thermophilic strain of Bacillus species LU11.
JO  - Biokhimiia
PY  - 1993
SP  - 1315
EP  - 1322
VL  - 58
AB  - Upon screening of natural strains of thermophilic bacteria, a strain has been found which
AB  - contains two restriction endonucleases. One of those, BspLU11II, is an isoschizomer of XbaI,
AB  - while the other one, BspLU11I, recognizes the new palindromic sequence 5'-A^CATGT-3' and
AB  - cleaves it as indicated by the arrow. Functionally pure enzymes were obtained by stepwise
AB  - chromatography with blue agarose, hydroxyapatite and heparin-Sepharose. The restriction
AB  - endonuclease BspLU11I produces sticky ends identical to those produced by the restriction
AB  - endonuclease NcoI; hence a combination of BspLU11I and NcoI can be used for enzymatic
AB  - selection of recombinant DNA. The recognition sequence of BspLU11I contains the ATG codon and
AB  - can be used to construct expression vectors for chemically synthesized genes. ies.
ER  -

TY  - JOUR
AU  - Zheleznaya, L.A.
AU  - Perevyazova, T.A.
AU  - Alzhanova, D.V.
AU  - Matvienko, N.I.
TI  - Site-specific nickase from Bacillus species strain D6.
JO  - Biokhimiia
PY  - 2001
SP  - 1215
EP  - 1220
VL  - 66
AB  - Three site-specific endonucleases were found in thermophilic strain Bacillus species D6. One
AB  - of them, BspD6II, is an isoschizomer of
AB  - Eco57I. The second, BspD6III, is present in the strain in very small
AB  - amount; therefore, it has not been characterized. This paper is devoted
AB  - to the third, BspD6I, which recognizes the pentanucleotide site 5'-GAGTC-3'
AB  - and cleaves only one DNA strand at a distance of 4 nucleotides from the
AB  - site in the 3'-direction in the chain with the GAGTC sequence, i.e., it
AB  - behaves as a site-specific nickase. Nickase N.BspD6I cleaves one DNA
AB  - strand only in double-stranded DNA and does not cleave single-stranded
AB  - DNA. Site-specific methylase SscL1I (an isohypectomer of M.HinfI) that
AB  - methylates adenine in the sequence 5'-GANTC-3' prevents DNA hydrolysis
AB  - by nickase BspD6I.
ER  -

TY  - JOUR
AU  - Zheleznaya, L.A.
AU  - Perevyazova, T.A.
AU  - Zheleznyakova, E.N.
AU  - Matvienko, N.I.
TI  - Some properties of site-specific nickase BspD6I and the possibility of its use in hybridization analysis of DNA.
JO  - Biokhimiia
PY  - 2002
SP  - 595
EP  - 600
VL  - 67
AB  - A new method for hybridization analysis of nucleic acids is proposed on the basis of the
AB  - ability of site-specific nickases to cleave only one DNA strand. The method is based on the
AB  - use of a labeled oligonucleotide with the recognition site of the nickase hybridized with the
AB  - target (DNA or RNA) at an optimal temperature of the enzyme (55 degrees C). The two shorter
AB  - oligonucleotides formed after the cleavage with the nickase do not complex with the target.
AB  - Thus, a multiple cleavage of the labeled oligonucleotide takes place on one target molecule.
AB  - The cleavage of the nucleotide is recorded either by polyacrylamide gel electrophoresis (when
AB  - a radioactive labeled oligonucleotide is used) or by fluorescence measurements (if the
AB  - oligonucleotide has the structure of a molecular beacon). The new method was tested on nickase
AB  - BspD6I and a radioactive oligonucleotide complementary to the polylinker region of the viral
AB  - DNA strand in bacteriophage M13mp19. Unfortunately, nickase BspD6I does not cleave DNA in the
AB  - RNA-DNA duplexes and therefore cannot be used for detection of RNA targets.
ER  -

TY  - JOUR
AU  - Zheleznyakova, E.N.
AU  - Zheleznaya, L.A.
AU  - Svadbina, I.V.
AU  - Matvienko, N.I.
TI  - A site-specific endonuclease from thermophilic strain Bacillus species ZE is a ClaI isoschizomer.
JO  - Biokhimiia
PY  - 1998
SP  - 1675
EP  - 1681
VL  - 63
AB  - Strain Bacillus species ZE with a maximal yield of the ClaI isoschizomer was chosen from 12
AB  - natural thermophilic strains producing ClaI isomers.  The yield is 110 times higher than that
AB  - of the ClaI prototype endonuclease from Caryophanon latum L.  The enzyme is sensitive to DNA
AB  - dam-methylation and is highly stable under storage.
ER  -

TY  - JOUR
AU  - Zheng, B.
AU  - Dong, H.
AU  - Xu, H.
AU  - Lv, J.
AU  - Zhang, J.
AU  - Jiang, X.
AU  - Du, Y.
AU  - Xiao, Y.
AU  - Li, L.
TI  - Coexistence of MCR-1 and NDM-1 in Clinical Escherichia coli Isolates.
JO  - Clin. Infect. Dis.
PY  - 2016
SP  - 1393
EP  - 1395
VL  - 63
AB  - TO THE EDITORInfections caused by New Delhi metallo- lactamase 1 (NDM-1) producing
AB  - Enterobacteriaceae are reported to have a signi and #64257;cantly higher likelihood of
AB  - in-hospital mortality. Previous evidence showed that NDM-producing bacteria are often
AB  - susceptible to colistin, which has become the last resort for the treatment of infections due
AB  - to NDM producing bacteria. However, the plasmid-mediated colistin resistance (MCR-1) gene, was
AB  - and #64257;rst identi and #64257;ed in Enterobacteriaceae recently. Therefore, patients
AB  - ultimately might receive only extremely limited drug options. Here, we characterize for the
AB  - and #64257;rst time 2 clonally unrelated Escherichia coli strains coproducing MCR-1 and NDM-1,
AB  - which were recovered from 2 patients with bloodstream infection.
ER  -

TY  - JOUR
AU  - Zheng, B.
AU  - Hu, X.
AU  - Jiang, X.
AU  - Li, A.
AU  - Yao, J.
AU  - Li, L.
TI  - First Draft Genome Sequence of Staphylococcus condimenti F-2T.
JO  - Genome Announcements
PY  - 2016
SP  - e00499
EP  - e00416
VL  - 4
AB  - This report describes the draft genome sequence of S. condimenti strain F-2(T) (DSM 11674), a
AB  - potential starter culture. The genome assembly comprised 2,616,174
AB  - bp with 34.6% GC content. To the best of our knowledge, this is the first
AB  - documentation that reports the whole-genome sequence of S. condimenti.
ER  -

TY  - JOUR
AU  - Zheng, B.
AU  - Jiang, X.
AU  - Li, A.
AU  - Yao, J.
AU  - Zhang, J.
AU  - Hu, X.
AU  - Li, L.
TI  - Whole-Genome Sequence of Multidrug-Resistant Staphylococcus caprae Strain 9557, Isolated from Cerebrospinal Fluid.
JO  - Genome Announcements
PY  - 2015
SP  - e00718
EP  - e00715
VL  - 3
AB  - Staphylococcus caprae strain 9557 was isolated from a cerebrospinal fluid sample. The
AB  - assembled genome contained 2,747,651-bp nucleotides with 33.34% GC content.
AB  - Consistent with its phenotypic characteristics, the genome harbors a varying
AB  - repertoire of putative virulence factors involved in invasion, survival, and
AB  - growth in the host cells.
ER  -

TY  - JOUR
AU  - Zheng, B.
AU  - Tomita, H.
AU  - Inoue, T.
AU  - Ike, Y.
TI  - Isolation of VanB-type Enterococcus faecalis strains from nosocomial infections:  first report of the isolation and identification of the pheromone-responsive  plasmids pMG2200, Encoding VanB-type vancomycin resistance and a Bac41-type  bacteriocin, and.
JO  - Antimicrob. Agents Chemother.
PY  - 2009
SP  - 735
EP  - 747
VL  - 53
AB  - Eighteen identical VanB-type Enterococcus faecalis isolates that were obtained from different
AB  - hospitalized patients were examined for their drug resistance and
AB  - plasmid DNAs. Of the 18 strains, 12 strains exhibited resistance to erythromycin
AB  - (Em), gentamicin (Gm), kanamycin (Km), tetracycline (Tc), and vancomycin (Van)
AB  - and produced cytolysin (Hly/Bac) and a bacteriocin (Bac) active against E.
AB  - faecalis strains. Another six of the strains exhibited resistance to Gm, Km, Tc,
AB  - and Van and produced a bacteriocin. Em and Van resistance was transferred
AB  - individually to E. faecalis FA2-2 strains at a frequency of about 10(-4) per
AB  - donor cell by broth mating. The Em-resistant transconjugants and the
AB  - Van-resistant transconjugants harbored a 65.7-kbp plasmid and a 106-kbp plasmid,
AB  - respectively. The 106-kbp and 65.7-kbp plasmids isolated from the representative
AB  - E. faecalis NKH15 strains were designated pMG2200 and pMG2201, respectively.
AB  - pMG2200 conferred vancomycin resistance and bacteriocin activity on the host
AB  - strain and responded to the synthetic pheromone cCF10 for pCF10, while pMG2201
AB  - conferred erythromycin resistance and cytolysin activity on its host strain and
AB  - responded to the synthetic pheromone cAD1 for pAD1. The complete DNA sequence of
AB  - pMG2200 (106,527 bp) showed that the plasmid carried a Tn1549-like element
AB  - encoding vanB2-type resistance and the Bac41-like bacteriocin genes of
AB  - pheromone-responsive plasmid pYI14. The plasmid contained the regulatory region
AB  - found in pheromone-responsive plasmids and encoded the genes prgX and prgQ, which
AB  - are the key negative regulatory elements for plasmid pCF10. pMG2200 also encoded
AB  - TraE1, a key positive regulator of plasmid pAD1, indicating that pMG2200 is a
AB  - naturally occurring chimeric plasmid that has a resulting prgX-prgQ-traE1 genetic
AB  - organization in the regulatory region of the pheromone response. The functional
AB  - oriT region and the putative relaxase gene of pMG2200 were identified and found
AB  - to differ from those of pCF10 and pAD1. The putative relaxase of pMG2200 was
AB  - classified as a member of the MOB(MG) family, which is found in
AB  - pheromone-independent plasmid pHTbeta of the pMG1-like plasmids. This is the
AB  - first report of the isolation and characterization of a pheromone-responsive
AB  - highly conjugative plasmid encoding vanB resistance.
ER  -

TY  - JOUR
AU  - Zheng, B.
AU  - Zhang, F.
AU  - Dong, H.
AU  - Chai, L.
AU  - Shu, F.
AU  - Yi, S.
AU  - Wang, Z.
AU  - Cui, Q.
AU  - Dong, H.
AU  - Zhang, Z.
AU  - Hou, D.
AU  - Yang, J.
AU  - She, Y.
TI  - Draft genome sequence of Paenibacillus sp. strain A2.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 9
EP  - 9
VL  - 11
AB  - Paenibacillus sp. strain A2 is a Gram-negative rod-shaped bacterium isolated from a mixture of
AB  - formation water and petroleum in Daqing oilfield, China. This
AB  - facultative aerobic bacterium was found to have a broad capacity for metabolizing
AB  - hydrocarbon and organosulfur compounds, which are the main reasons for the
AB  - interest in sequencing its genome. Here we describe the features of Paenibacillus
AB  - sp. strain A2, together with the genome sequence and its annotation. The
AB  - 7,650,246 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of
AB  - 54.2 % and contains 7575 protein-coding and 49 RNA genes, including 3 rRNA genes.
AB  - One putative alkane monooxygenase, one putative alkanesulfonate monooxygenase,
AB  - one putative alkanesulfonate transporter and four putative sulfate transporters
AB  - were found in the draft genome.
ER  -

TY  - JOUR
AU  - Zheng, B.X.
AU  - Zhang, H.K.
AU  - Ding, K.
TI  - Draft Genome Sequence of Rhodococcus opacus Strain 04-OD7, Which Can Mobilize Phosphate.
JO  - Genome Announcements
PY  - 2018
SP  - e00494
EP  - e00418
VL  - 6
AB  - Rhodococcus opacus strain 04-OD7 (=CCTCC AB 2017148) is a Gram-positive bacterium showing
AB  - inorganic phosphate solubilization capacity for the first time in the
AB  - genus Rhodococcus We present here the draft genome description of R. opacus
AB  - 04-OD7 along with multiple phosphorus (P) mobilization-related genes, supporting
AB  - its inorganic phosphate solubilization.
ER  -

TY  - JOUR
AU  - Zheng, D.
AU  - Koller, W.
TI  - Characterization of the mitochondrial cytochrome b gene from Venturia inaequalis.
JO  - Curr. Genet.
PY  - 1997
SP  - 361
EP  - 366
VL  - 32
AB  - A new class of agricultural fungicides derived from the group of antifungal strobilurins acts
AB  - as specific respiration inhibitors by binding to mitochondrial cytochrome b.  The cytochrome b
AB  - gene was cloned and sequenced from the mitochondrial genome of Venturia inaequalis, the causal
AB  - agent of apple scab.  The gene was 10.65 kbp in size and contained seven exons and six
AB  - introns.  The exons encoded a protein of 393 amino acids.  Comparison of the deduced
AB  - amino-acid sequence with cytochrome b proteins from other fungi revealed highest homologies to
AB  - the respective proteins of Aspergillis nidulans, Podospora anserina and Neurospora crassa.
AB  - All amino acids of the V. inaequalis cytochrome b at positions altered in mutants of
AB  - Saccharomyces cerevisiae resistant to strobilurins, and other fungi with reduced sensitivities
AB  - to strobilurins, were identical to wild-type isolates of several fungi.  The cloning and
AB  - characterization of the V. inaequalis cytochrome b gene is the initial step in the assessment
AB  - of resistance risks inherent to the strobilurin fungicides.
ER  -

TY  - JOUR
AU  - Zheng, D.
AU  - Wang, X.
AU  - Wang, P.
AU  - Peng, W.
AU  - Ji, N.
AU  - Liang, R.
TI  - Genome Sequence of Pseudomonas citronellolis SJTE-3, an Estrogen- and Polycyclic  Aromatic Hydrocarbon-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e01373
EP  - e01316
VL  - 4
AB  - Pseudomonas citronellolis SJTE-3, isolated from the active sludge of a wastewater treatment
AB  - plant in China, can utilize a series of environmental estrogens and
AB  - estrogen-like toxicants. Here, we report its whole-genome sequence, containing
AB  - one circular chromosome and one circular plasmid. Genes involved in estrogen
AB  - biodegradation in this bacterium were predicted.
ER  -

TY  - JOUR
AU  - Zheng, H.
AU  - Brune, A.
TI  - Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia).
JO  - Genome Announcements
PY  - 2015
SP  - e00679
EP  - e00615
VL  - 3
AB  - We sequenced the complete genome of Endomicrobium proavitum strain Rsa215, the first isolate
AB  - of the class Endomicrobia (phylum Elusimicrobia). It is the closest
AB  - free-living relative of the endosymbionts of termite gut flagellates and thereby
AB  - provides an excellent model for studying the evolutionary processes during the
AB  - establishment of an intracellular symbiosis.
ER  -

TY  - JOUR
AU  - Zheng, H.
AU  - Guo, L.
AU  - Du, N.
AU  - Lin, J.
AU  - Song, L.
AU  - Liu, G.
AU  - Chen, F.
TI  - Draft Genome Sequences of Two Clinical Isolates of Streptococcus mutans.
JO  - Genome Announcements
PY  - 2014
SP  - e00441
EP  - e00414
VL  - 2
AB  - We report the draft genome sequences of PKUSS-HG01 and PKUSS-LG01, two clinical isolates of
AB  - Streptococcus mutans from human dental plaque. The genomics
AB  - information will facilitate the study of the mechanisms of pathogenicity and
AB  - evolution of S. mutans.
ER  -

TY  - JOUR
AU  - Zheng, L.
AU  - Braymer, H.D.
TI  - Overproduction and purification of McrC protein from Escherichia coli K-12.
JO  - J. Bacteriol.
PY  - 1991
SP  - 3918
EP  - 3920
VL  - 173
AB  - The McrC protein, encoded by one of the two genes involved in the McrB
AB  - restriction system, was produced in Escherichia coli cells by using a T7
AB  - expression system.  Following sequential DEAE-Sepharose and hydroxylapatite
AB  - column chromatography, the protein was purified to apparent homogeneity as
AB  - judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.  The
AB  - N-terminal amino acid sequence of the purified McrC protein agreed exactly with
AB  - the one deduced from the DNA sequence by Ross et al. (J. Bacteriol.
AB  - 171:1974-1981, 1989).
ER  -

TY  - JOUR
AU  - Zheng, L.
AU  - Cui, Z.
AU  - Xu, L.
AU  - Sun, C.
AU  - Powell, R.J.
AU  - Hill, R.T.
TI  - Draft Genome Sequence of Rhodobacteraceae Strain PD-2, an Algicidal Bacterium with a Quorum-Sensing System, Isolated from the Marine Microalga Prorocentrum donghaiense.
JO  - Genome Announcements
PY  - 2015
SP  - e01549
EP  - e01514
VL  - 3
AB  - Rhodobacteraceae strain PD-2 was isolated from the marine microalga Prorocentrum donghaiense.
AB  - It has algicidal activity toward its host and could produce N-acylhomoserine lactone signals.
AB  - Here, we present the draft genome of strain PD-2, which contains 5,227,214 bp with an average
AB  - GC content of 66.19%. There were 4,864 encoding gene sequences and two clusters of luxI and
AB  - luxR homologues identified.
ER  -

TY  - JOUR
AU  - Zheng, L.
AU  - Simmons, L.A.
AU  - Braymer, H.D.
TI  - Determination of the recognition sequence for McrB restriction of E. coli K12.
JO  - Abstr. Gen. Meet. Am. Soc. Microbiol.
PY  - 1991
SP  - 175
EP  - 175
VL  - 91
AB  - Restriction of methylated DNA by the McrB restriction system of E. coli
AB  - involves two genes designated mcrB and mcrC.  The mcrB gene is thought to code
AB  - for an endonuclease subunit and the mcrC and the mcrC subunit confers
AB  - specificity to the enzyme complex.  The restriction enzyme requires GTP for
AB  - activity and recognizes G5mC.  However, we know these two deoxynucleotides
AB  - alone are not sufficient for recognition since not every methylated AluI site
AB  - (AG5mCT) is recognized. To determine the nucleotide recognition sequence for
AB  - McrB restriction, a series of deletion plasmids were constructed from pBR322
AB  - and tested as substrates of McrB activity, after the plasmids were methylated
AB  - with AluI methylase.  Our study first narrowed the McrB recognition sequence
AB  - down to one of the four AluI sites in the region between two MspI sites at 1812
AB  - and 2121 bp of pBR322.  SI nuclease deletion and further sequencing analyses of
AB  - this region revealed that only one AluI site was involved in the recognition of
AB  - McrB restriction.  Site-specific mutagenesis will be used to define all base
AB  - composition required for McrB recognition.
ER  -

TY  - JOUR
AU  - Zheng, L.
AU  - Wang, X.
AU  - Braymer, H.D.
TI  - Purification and N-terminal amino acid sequences of two polypeptides encoded by the mcrB gene from Escherichia coli K-12.
JO  - Gene
PY  - 1992
SP  - 97
EP  - 100
VL  - 112
AB  - This report provides a purification method for the two proteins, 51 kDa and 33
AB  - kDa, both encoded by the same mcrB gene of the McrBC restriction system in
AB  - Escherichia coli K-12.  The two proteins were produced in large quantity using
AB  - a T7 expression system and copurified to near homogeneity by DEAE-Sepharose and
AB  - Affi-Gel blue column chromatography.  The N-terminal amino acid sequences of
AB  - these purified McrB proteins were the same as those predicted from the mcrB DNA
AB  - sequence by Ross et al. [J. Bacteriol. 171 (1989b) 1974-1981].  The 33 kDa
AB  - protein totally overlaps the C-terminal part of the 51-kDa protein.
ER  -

TY  - JOUR
AU  - Zheng, P.X.
AU  - Chung, K.T.
AU  - Chiang-Ni, C.
AU  - Wang, S.Y.
AU  - Tsai, P.J.
AU  - Chuang, W.J.
AU  - Lin, Y.S.
AU  - Liu, C.C.
AU  - Wu, J.J.
TI  - Complete Genome Sequence of emm1 Streptococcus pyogenes A20, a Strain with an Intact Two-Component System, CovRS, Isolated from a Patient with Necrotizing  Fasciitis.
JO  - Genome Announcements
PY  - 2013
SP  - e00149
EP  - e00112
VL  - 1
AB  - Here, we announce the complete sequence of Streptococcus pyogenes A20. This strain was
AB  - isolated from a patient with necrotizing fasciitis. Given that A20
AB  - harbors an intact two-component system, CovRS, the discovery of its genome
AB  - sequence provides more insight into the pathogenesis of a pandemic emm1 strain.
ER  -

TY  - JOUR
AU  - Zheng, Q.
AU  - Zhang, R.
AU  - Jiao, N.
TI  - Genome Sequence of Citromicrobium Strain JLT1363, Isolated from the South China Sea.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2074
EP  - 2075
VL  - 193
AB  - Citromicrobium is a member of the alpha-4 subcluster in the Alphaproteobacteria and is
AB  - identified as a typical aerobic anoxygenic
AB  - phototrophic bacterium (AAPB). Here we report the draft genome sequence of
AB  - a non-AAPB strain, Citromicrobium sp. JLT1363. The genome sequence reveals
AB  - a multimechanism of horizontal gene transfer, as well.
ER  -

TY  - JOUR
AU  - Zheng, W.
TI  - Isolation and purification of the restriction endonuclease Bsu1076I.
JO  - Weishengwuxue Tongbao
PY  - 1987
SP  - 105
EP  - 108
VL  - 14
AB  - Restriction endonuclease Bsu1076I has been isolated from Bacillus subtilis and
AB  - purified by passing first through a phosphocellulose (Whatman P11) column, and
AB  - then through a heparin-Sepharose 4B column.  Bsu1076I was eluted at 0.83-0.87M
AB  - NaCl in a gradient from the phosphocellulose column and at 0.80-0.87M NaCl from
AB  - heparin-Sepharose 4B column.  As much as 3000 units of highly purified Bsu1076I
AB  - was obtained from 20g of wet cells by this procedure.  Digestion of lambda DNA,
AB  - SPP1 DNA, PhiX174 DNA, SV40 DNA and Ad-2 DNA with Bsu1076I formed DNA fragments
AB  - identical to those digested with its isoschizomer HaeIII (from Promega Biotec)
AB  - as assayed by agarose gel electrophoresis.  Over digestion of 1 microgram
AB  - lambda DNA with 50-150 units of Bsu1076I showed typical bands on agarose gel,
AB  - indicating the exclusion of contamination by other deoxyribonucleases.  After
AB  - digestion with Bsu1076I lambda DNA can be fairly ligated and recut.
ER  -

TY  - JOUR
AU  - Zheng, W.
AU  - Kathariou, S.
TI  - Host-mediated modification of Sau3AI restriction in Listeria monocytogenes: Prevalence in epidemic-associated strains.
JO  - Appl. Environ. Microbiol.
PY  - 1997
SP  - 3085
EP  - 3089
VL  - 63
AB  - Most major food-related outbreaks of listeriosis have been traced to a cluster of genetically
AB  - related strains of serovar 4b (epidemic clone).  In spite of numerous searches, distinct
AB  - bacteriologic or virulence-related features unique to these strains have eluded
AB  - identification, although a restriction fragment length polymorphism characteristic of the
AB  - epidemic clone has previously been described.  We found that DNAs from 75 strains which were
AB  - derived from three separate outbreaks and which had the epidemic clone-specific RFLP were also
AB  - invariably resistant to digestion by Sau3AI and other restriction endonucleases sensitive to
AB  - cytosine methylation at 5' GATC 3' sites.  This modification of Sau3AI restriction was host
AB  - mediated, as it did not persist when DNA was cloned and propagated in Escherichia coli, and
AB  - was uncommon among other Listeria strains.  Epidemic-associated strains with this modification
AB  - were resistant to infection by phage propagated in a serotype 4b strain which was not known to
AB  - be involved in an epidemic and which lacked the epidemic clone-specific RFLP.  Screening for
AB  - susceptibility to MboI digestion revealed that these epidemic strains lacked methylation of
AB  - adenines at GATC sites.  This type of modification was rare among Listeria strains and was
AB  - found in only three (of eight screened) strains of serovar 1/2b, possibly representing one
AB  - clonal lineage.
ER  -

TY  - JOUR
AU  - Zheng, Y.
AU  - Cohen-Karni, D.
AU  - Xu, D.
AU  - Chin, H.G.
AU  - Wilson, G.
AU  - Pradhan, S.
AU  - Roberts, R.J.
TI  - A unique family of Mrr-like modification-dependent restriction endonucleases.
JO  - Nucleic Acids Res.
PY  - 2010
SP  - 5527
EP  - 5534
VL  - 38
AB  - Mrr superfamily of homologous genes in microbial genomes restricts modified DNA in vivo.
AB  - However, their biochemical properties in vitro
AB  - have remained obscure. Here, we report the experimental
AB  - characterization of MspJI, a remote homolog of Escherichia coli's Mrr
AB  - and show it is a DNA modification-dependent restriction endonuclease.
AB  - Our results suggest MspJI recognizes (CNNR)-C-m (R = G/A) sites and
AB  - cleaves DNA at fixed distances (N-12/N-16) away from the modified
AB  - cytosine at the 3' side (or N-9/N-13 from R). Besides 5-methylcytosine,
AB  - MspJI also recognizes 5-hydroxymethylcytosine but is blocked by
AB  - 5-glucosylhydroxymethylcytosine. Several other close homologs of MspJI
AB  - show similar modification-dependent endonuclease activity and display
AB  - substrate preferences different from MspJI. A unique feature of these
AB  - modification-dependent enzymes is that they are able to extract small
AB  - DNA fragments containing modified sites on genomic DNA, for example
AB  - similar to 32 bp around symmetrically methylated CG sites and similar
AB  - to 31 bp around methylated CNG sites. The digested fragments can be
AB  - directly selected for high-throughput sequencing to map the location of
AB  - the modification on the genomic DNA. The MspJI enzyme family, with
AB  - their different recognition specificities and cleavage properties,
AB  - provides a basis on which many future methods can build to decode the
AB  - epigenomes of different organisms.
ER  -

TY  - JOUR
AU  - Zheng, Y.
AU  - Posfai, J.
AU  - Morgan, R.D.
AU  - Vincze, T.
AU  - Roberts, R.J.
TI  - Using shotgun sequence data to find active restriction enzyme genes.
JO  - Nucleic Acids Res.
PY  - 2009
SP  - 1
EP  - 11
VL  - 37
AB  - Whole genome shotgun sequence analysis has become the standard method for beginning to
AB  - determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a
AB  - biological experiment. It determines which segments of the genome can be cloned into
AB  - Escherichia coli and which cannot. By analyzing the complete set of sequences from such an
AB  - experiment, it is possible to identify genes lethal to E. coli. Among this set are genes
AB  - encoding restriction enzymes which, when active in E. coli, lead to cell death by cleaving the
AB  - E. coli genome at the restriction enzyme recognition sites. By analyzing shotgun sequence data
AB  - sets we show that this is a reliable method to detect active restriction enzyme genes in newly
AB  - sequenced genomes, thereby facilitating functional annotation. Active restriction enzyme genes
AB  - have been identified, and their activity demonstrated biochemically, in the sequenced genomes
AB  - of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus.
ER  -

TY  - JOUR
AU  - Zheng, Y.
AU  - Roberts, R.J.
TI  - Selection of restriction endonucleases using artificial cells.
JO  - Nucleic Acids Res.
PY  - 2007
SP  - e83
EP  - e83
VL  - 35
AB  - We describe in this article an in vitro system for the selection of restriction endonucleases
AB  - using artificial cells. The artificial cells are
AB  - generated in the form of a water-in-oil emulsion by in vitro
AB  - compartmentalization. Each aqueous compartment contains a reconstituted
AB  - transcription/translation mix along with the dispersed DNA templates. In
AB  - the compartments containing endonuclease genes, an endonuclease expressed
AB  - in vitro cleaves its own DNA template adjacent to the gene, leaving a
AB  - sticky end. The pooled DNA templates are then ligated to an adaptor with a
AB  - compatible end. The endonuclease genes are then enriched by
AB  - adaptor-specific PCR on the ligation mix. We demonstrate that the system
AB  - can achieve at least 100-fold enrichment in a single round of selection.
AB  - It is sensitive enough to enrich an active endonuclease gene from a
AB  - 1:10(5) model library in 2-3 rounds of selection. Finally, we describe
AB  - experiments where we selected endonuclease genes directly from a bacterial
AB  - genomic DNA source in three rounds of selections: the known PstI gene from
AB  - Providencia stuartii and the new TspMI gene from Thermus sp. manalii. This
AB  - method provides a unique tool for cloning restriction endonuclease genes
AB  - and has many other potential applications.
ER  -

TY  - JOUR
AU  - Zheng, Z.
AU  - Clark, N.
AU  - Keremane, M.
AU  - Lee, R.
AU  - Wallis, C.
AU  - Deng, X.
AU  - Chen, J.
TI  - Whole-Genome Sequence of 'Candidatus Liberibacter solanacearum' Strain R1 from California.
JO  - Genome Announcements
PY  - 2014
SP  - e01353
EP  - e01314
VL  - 2
AB  - The draft whole-genome sequence of 'Candidatus Liberibacter solanacearum' strain  R1,
AB  - isolated from and maintained in tomato plants in California, is reported. The
AB  - R1 strain has the genome size of 1,204,257 bp, G+C content of 35.3%, 1,101
AB  - predicted open reading frames, and 57 RNA genes.
ER  -

TY  - JOUR
AU  - Zheng, Z.
AU  - Deng, X.
AU  - Chen, J.
TI  - Draft Genome Sequence of 'Candidatus Liberibacter asiaticus' from California.
JO  - Genome Announcements
PY  - 2014
SP  - e00999
EP  - e00914
VL  - 2
AB  - We report here the draft genome sequence of 'Candidatus Liberibacter asiaticus' strain HHCA,
AB  - collected from a lemon tree in California. The HHCA strain has a
AB  - genome size of 1,150,620 bp, 36.5% G+C content, 1,119 predicted open reading
AB  - frames, and 51 RNA genes.
ER  -

TY  - JOUR
AU  - Zheng, Z.
AU  - Deng, X.
AU  - Chen, J.
TI  - Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' from Guangdong, China.
JO  - Genome Announcements
PY  - 2014
SP  - e00273
EP  - e00214
VL  - 2
AB  - The draft genome sequence of 'Candidatus Liberibacter asiaticus' strain A4, isolated from a
AB  - mandarin citrus in Guangdong, People's Republic of China, is reported. The A4 strain has a
AB  - genome size of 1,208,625 bp, G+C content of 36.4%, 1,107 predicted open reading frames, and 53
AB  - RNA genes.
ER  -

TY  - JOUR
AU  - Zheng, Z.
AU  - Jiang, T.
AU  - Lin, X.
AU  - Zhou, J.
AU  - Ouyang, J.
TI  - Draft Genome Sequence of Bacillus coagulans NL01, a Wonderful l-Lactic Acid Producer.
JO  - Genome Announcements
PY  - 2015
SP  - e00635
EP  - e00615
VL  - 3
AB  - Here, we report the draft genome sequence of Bacillus coagulans NL01, which could produce high
AB  - optically pure l-lactic acid using xylose as a sole carbon source.
AB  - The draft genome is 3,505,081 bp, with 144 contigs. About 3,903 protein-coding
AB  - genes and 92 rRNAs are predicted from this assembly.
ER  -

TY  - JOUR
AU  - Zheng, Z.
AU  - Sun, X.
AU  - Deng, X.
AU  - Chen, J.
TI  - Whole-Genome Sequence of 'Candidatus Liberibacter asiaticus' from a Huanglongbing-Affected Citrus Tree in Central Florida.
JO  - Genome Announcements
PY  - 2015
SP  - e00169
EP  - e00115
VL  - 3
AB  - Here, we report the draft genome sequence of 'Candidatus Liberibacter asiaticus'  strain
AB  - FL17, isolated from a huanglongbing (HLB)-affected citrus tree in central
AB  - Florida. The FL17 genome comprised 1,227,253 bp, with a G+C content of 36.5%,
AB  - 1,175 predicted open reading frames, and 53 RNA genes.
ER  -

TY  - JOUR
AU  - Zhgenti, E.
AU  - Johnson, S.L.
AU  - Davenport, K.W.
AU  - Chanturia, G.
AU  - Daligault, H.E.
AU  - Chain, P.S.
AU  - Nikolich, M.P.
TI  - Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region.
JO  - Genome Announcements
PY  - 2015
SP  - e01030
EP  - e01015
VL  - 3
AB  - Yersinia pestis, the causative agent of plague, is endemic to the Caucasus region but few
AB  - reference strain genome sequences from that region are available. Here, we present the
AB  - improved draft or finished assembled genomes from 11 strains isolated in the nation of Georgia
AB  - and surrounding countries.
ER  -

TY  - JOUR
AU  - Zhi, Y.
AU  - Wu, Q.
AU  - Xu, Y.
TI  - Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45.
JO  - Sci. Rep.
PY  - 2017
SP  - 40976
EP  - 40976
VL  - 7
AB  - Natural Bacillus isolates generate limited amounts of surfactin (<10% of their
AB  - biomass), which functions as an antibiotic or signalling molecule in
AB  - inter-/intra-specific interactions. However, overproduction of surfactin in
AB  - Bacillus amyloliquefaciens MT45 was observed at a titre of 2.93 g/l, which is
AB  - equivalent to half of the maximum biomass. To systemically unravel this efficient
AB  - biosynthetic process, the genome and transcriptome of this bacterium were
AB  - compared with those of B. amyloliquefaciens type strain DSM7T. MT45 possesses a
AB  - smaller genome while containing more unique transporters and
AB  - resistance-associated genes. Comparative transcriptome analysis revealed notable
AB  - enrichment of the surfactin synthesis pathway in MT45, including central carbon
AB  - metabolism and fatty acid biosynthesis to provide sufficient quantities of
AB  - building precursors. Most importantly, the modular surfactin synthase
AB  - overexpressed (9 to 49-fold) in MT45 compared to DSM7T suggested efficient
AB  - surfactin assembly and resulted in the overproduction of surfactin. Furthermore,
AB  - based on the expression trends observed in the transcriptome, there are multiple
AB  - potential regulatory genes mediating the expression of surfactin synthase. Thus,
AB  - the results of the present study provide new insights regarding the synthesis and
AB  - regulation of surfactin in high-producing strain and enrich the genomic and
AB  - transcriptomic resources available for B. amyloliquefaciens.
ER  -

TY  - JOUR
AU  - Zhilkina, O.A.
AU  - Repin, V.E.
AU  - Degtyarev, S.K.
TI  - Effect of some cultivation parameters on the yield of restriction endonuclease SfaNI.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1991
SP  - 486
EP  - 490
VL  - 27
AB  - A simple technique is proposed for testing restriction endonuclease SfaNI activity in lysates
AB  - of Streptococcus faecalis cells.  The technique was used to study the effect of inorganic
AB  - phosphate and the growth phase on the enzyme yield.  Conditions were chosen that provide a
AB  - high yield of the SfaNI activity and a significantly reduced level of nucleases in the cells.
ER  -

TY  - JOUR
AU  - Zhong, C.
AU  - Nelson, M.
AU  - Cao, G.
AU  - Sadowsky, M.J.
AU  - Yan, T.
TI  - Complete Genome Sequence of the Triclosan- and Multidrug-Resistant Pseudomonas aeruginosa Strain B10W Isolated from Municipal Wastewater.
JO  - Genome Announcements
PY  - 2017
SP  - e01489
EP  - e01416
VL  - 5
AB  - Here, we report the complete genome sequence of the triclosan- and multidrug-resistant
AB  - Pseudomonas aeruginosa strain B10W, obtained from municipal
AB  - wastewater in Hawaii. The bacterium has a 6.7-Mb genome, contains 6,391 coding
AB  - sequences and 78 RNAs, with an average G+C content of 66.2 mol%.
ER  -

TY  - JOUR
AU  - Zhong, X.
AU  - Du, J.
AU  - Hale, C.J.
AU  - Gallego-Bartolome, J.
AU  - Feng, S.
AU  - Vashisht, A.A.
AU  - Chory, J.
AU  - Wohlschlegel, J.A.
AU  - Patel, D.J.
AU  - Jacobsen, S.E.
TI  - Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
JO  - Cell
PY  - 2014
SP  - 1050
EP  - 1060
VL  - 157
AB  - DNA methylation is a conserved epigenetic gene-regulation mechanism. DOMAINS REARRANGED
AB  - METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants,
AB  - but how DRM acts mechanistically is poorly understood. Here, we report the
AB  - crystal structure of the methyltransferase domain of tobacco DRM (NtDRM) and
AB  - reveal a molecular basis for its rearranged structure. NtDRM forms a functional
AB  - homodimer critical for catalytic activity. We also show that Arabidopsis DRM2
AB  - exists in complex with the small interfering RNA (siRNA) effector ARGONAUTE4
AB  - (AGO4) and preferentially methylates one DNA strand, likely the strand acting as
AB  - the template for RNA polymerase V-mediated noncoding RNA transcripts. This
AB  - strand-biased DNA methylation is also positively correlated with strand-biased
AB  - siRNA accumulation. These data suggest a model in which DRM2 is guided to target
AB  - loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent
AB  - RNA transcripts.
ER  -

TY  - JOUR
AU  - Zhong, X.
AU  - Hale, C.J.
AU  - Nguyen, M.
AU  - Ausin, I.
AU  - Groth, M.
AU  - Hetzel, J.
AU  - Vashisht, A.A.
AU  - Henderson, I.R.
AU  - Wohlschlegel, J.A.
AU  - Jacobsen, S.E.
TI  - DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA  polymerase V transcript abundance in Arabidopsis.
JO  - Proc. Natl. Acad. Sci. U. S. A.
PY  - 2015
SP  - 911
EP  - 916
VL  - 112
AB  - DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in
AB  - many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase
AB  - DOMAINS REARRANGED METHYLASE 2 (DRM2) controls RNA-directed DNA methylation in a
AB  - pathway that also involves the plant-specific RNA Polymerase V (Pol V).
AB  - Additionally, the Arabidopsis genome encodes an evolutionarily conserved but
AB  - catalytically inactive DNA methyltransferase, DRM3. Here, we show that DRM3 has
AB  - moderate effects on global DNA methylation and small RNA abundance and that DRM3
AB  - physically interacts with Pol V. In Arabidopsis drm3 mutants, we observe a lower
AB  - level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin
AB  - occupancy is increased at many sites in the genome. These findings suggest that
AB  - DRM3 acts to promote Pol V transcriptional elongation or assist in the
AB  - stabilization of Pol V transcripts. This work sheds further light on the
AB  - mechanism by which long noncoding RNAs facilitate RNA-directed DNA methylation.
ER  -

TY  - JOUR
AU  - Zhong, X.
AU  - Tian, Y.
AU  - Niu, G.
AU  - Tan, H.
TI  - Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes.
JO  - Sci. China Life. Sci.
PY  - 2013
SP  - 609
EP  - 618
VL  - 56
AB  - A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using
AB  - 454 sequencing technology. In combination with local BLAST searches and gap filling
AB  - techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary
AB  - metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. A total of at
AB  - least 35 putative gene clusters were identified and assembled. Transcriptional analysis showed
AB  - that 20 of the 35 gene clusters were expressed in either or all of the three different media
AB  - tested, whereas the other 15 gene clusters were silent in all three different media. This
AB  - study provides a comprehensive method to identify and assemble secondary metabolite
AB  - biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote
AB  - functional studies of these secondary metabolite biosynthetic gene clusters.
ER  -

TY  - JOUR
AU  - Zhong, Y.
AU  - Chang, X.
AU  - Cao, X.J.
AU  - Zhang, Y.
AU  - Zheng, H.
AU  - Zhu, Y.
AU  - Cai, C.
AU  - Cui, Z.
AU  - Zhang, Y.
AU  - Li, Y.Y.
AU  - Jiang, X.G.
AU  - Zhao, G.P.
AU  - Wang, S.
AU  - Li, Y.
AU  - Zeng, R.
AU  - Li, X.
AU  - Guo, X.K.
TI  - Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601.
JO  - Cell Res.
PY  - 2011
SP  - 1210
EP  - 1229
VL  - 21
AB  - The virulence-attenuated Leptospira interrogans serovar Lai strain IPAV
AB  - was derived by prolonged laboratory passage from a highly virulent
AB  - ancestral strain isolated in China. We studied the genetic variations of
AB  - IPAV that render it avirulent via comparative analysis against the
AB  - pathogenic L. interrogans serovar Lai strain 56601. The complete genome
AB  - sequence of the IPAV strain was determined and used to compare with, and
AB  - then rectify and reannotate the genome sequence of strain 56601. Aside
AB  - from their highly similar genomic structure and gene order, a total of 33
AB  - insertions, 53 deletions and 301 single-nucleotide variations (SNVs) were
AB  - detected throughout the genome of IPAV directly affecting 101 genes,
AB  - either in their 5' upstream region or within their coding region. Among
AB  - them, the majority of the 44 functional genes are involved in signal
AB  - transduction, stress response, transmembrane transport and nitrogen
AB  - metabolism. Comparative proteomic analysis based on quantitative liquid
AB  - chromatography (LC)-MS/MS data revealed that among 1 627 selected pairs of
AB  - orthologs, 174 genes in the IPAV strain were upregulated, with enrichment
AB  - mainly in classes of energy production and lipid metabolism. In contrast,
AB  - 228 genes in strain 56601 were upregulated, with the majority enriched in
AB  - the categories of protein translation and DNA replication/repair. The
AB  - combination of genomic and proteomic approaches illustrated that altered
AB  - expression or mutations in critical genes, such as those encoding a
AB  - Ser/Thr kinase, carbon-starvation protein CstA, glutamine synthetase,
AB  - GTP-binding protein BipA, ribonucleotide-diphosphate reductase and
AB  - phosphate transporter, and alterations in the translational profile of
AB  - lipoproteins or outer membrane proteins are likely to account for the
AB  - virulence attenuation in strain IPAV.
ER  -

TY  - JOUR
AU  - Zhong, Z.
AU  - Toukdarian, A.
AU  - Helinski, D.
AU  - Knauf, V.
AU  - Sykes, S.
AU  - Wilkinson, J.E.
AU  - O'Bryne, C.
AU  - Shea, T.
AU  - DeLoughery, C.
AU  - Caspi, R.
TI  - Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate.
JO  - Appl. Environ. Microbiol.
PY  - 2001
SP  - 5771
EP  - 5779
VL  - 67
AB  - An agar-degrading marine bacterium identified as a Microscilla species was
AB  - isolated from coastal California marine sediment. This organism harbored a
AB  - single 101-kb circular DNA plasmid designated pSD15. The complete
AB  - nucleotide sequence of pSD15 was obtained, and sequence analysis indicated
AB  - a number of genes putatively encoding a variety of enzymes involved in
AB  - polysaccharide utilization. The most striking feature was the occurrence
AB  - of five putative agarase genes. Loss of the plasmid, which occurred at a
AB  - surprisingly high frequency, was associated with loss of agarase activity,
AB  - supporting the sequence analysis results.
ER  -

TY  - JOUR
AU  - Zhong, Z.
AU  - Wang, L.
AU  - Chen, Y.
AU  - Wang, Z.
AU  - Wang, Y.
AU  - Cui, M.
AU  - Li, T.
AU  - Ke, Y.
AU  - Yuan, X.
AU  - Wang, D.
AU  - Chen, Z.
AU  - Peng, G.
TI  - Complete Genome Sequence of Brucella abortus Strain BCB034, a Strain of Biovar 2  Isolated from Human.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6943
EP  - 6943
VL  - 194
AB  - Brucella abortus is divided into eight biovars, of which biovars 1 to 3 are the most
AB  - frequently represented biovars in strains isolated from humans. Here, we
AB  - report the genome sequence of B. abortus strain BCB034, a strain isolated from a
AB  - human patient and that belongs to biovar 2.
ER  -

TY  - JOUR
AU  - Zhou, B.
AU  - Li, Q.
TI  - Bacillus subtilis 36 a highly productive strain containing the isoschizomer of restriction enzyme MstII.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1987
SP  - 537
EP  - 540
VL  - 19
AB  - From Bacillus subtilis 36 we have isolated and partially purified a restriction
AB  - enzyme Bsu36I, which is the isoschizomer of MstII.  200000 units of Bsu36I can
AB  - be obtained from one liter of B. subtilis 36 culture.  It is a strain for
AB  - production of MstII.
ER  -

TY  - JOUR
AU  - Zhou, E.M. et al.
TI  - High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway.
JO  - Standards in Genomic Sciences
PY  - 2016
SP  - 20
EP  - 20
VL  - 11
AB  - Thermus amyloliquefaciens type strain YIM 77409(T) is a thermophilic, Gram-negative,
AB  - non-motile and rod-shaped bacterium isolated from Niujie Hot
AB  - Spring in Eryuan County, Yunnan Province, southwest China. In the present study
AB  - we describe the features of strain YIM 77409(T) together with its genome sequence
AB  - and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with
AB  - 67.4 % average GC content. A total of 2,313 genes were predicted, comprising
AB  - 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a
AB  - complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle.
AB  - Additionally, a large number of transporters and enzymes for heterotrophy
AB  - highlight the broad heterotrophic lifestyle of this organism. A denitrification
AB  - gene cluster included genes predicted to encode enzymes for the sequential
AB  - reduction of nitrate to nitrous oxide, consistent with the incomplete
AB  - denitrification phenotype of this strain.
ER  -

TY  - JOUR
AU  - Zhou, E.X.
AU  - Reuter, M.
AU  - Meehan, E.J.
AU  - Chen, L.
TI  - A new crystal form of restriction endonuclease EcoRII that diffracts to 2.8 A resolution.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2002
SP  - 1343
EP  - 1345
VL  - 58
AB  - EcoRII, a type IIe restriction endonuclease, has been crystallized in space group P2(1), with
AB  - unit-cell parameters a = 58.3, b = 127.8, c = 59.9 A, beta = 91.4 degrees. There are two
AB  - monomers in the asymmetric unit and the solvent content is estimated to be 49% by volume. The
AB  - crystals diffract to 2.8 A resolution, which is much higher than that of the previously
AB  - reported cubic crystal form, which diffracted to 4 A resolution.
ER  -

TY  - JOUR
AU  - Zhou, G.
AU  - Chen, C.
AU  - Jeon, C.O.
AU  - Wang, G.
AU  - Li, M.
TI  - High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T).
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 66
EP  - 66
VL  - 10
AB  - Flavihumibacter solisilvae 3-3(T) (= KACC 17917(T) = JCM 19891(T)) represents a type strain of
AB  - the genus Flavihumibacter within the family Chitinophagaceae. This strain can use various sole
AB  - carbon sources, making it applicable in industry and  bioremediation. In this study, the draft
AB  - genomic information of F. solisilvae 3-3(T) is described. F. solisilvae 3-3(T) owns a genome
AB  - size of 5.41 Mbp, 47 % GC content and a total of 4,698 genes, including 4,215 protein coding
AB  - genes, 439 pseudo genes and 44 RNA encoding genes. Analysis of its genome reveals high
AB  - correlation between the genotypes and the phenotypes.
ER  -

TY  - JOUR
AU  - Zhou, H.
AU  - Shatz, W.
AU  - Purdy, M.M.
AU  - Fera, N.
AU  - Dahlquist, F.W.
AU  - Reich, N.O.
TI  - Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI.
JO  - Biochemistry
PY  - 2007
SP  - 7261
EP  - 7268
VL  - 46
AB  - The bacterial DNA cytosine methyltransferase M.HhaI sequence-specifically modifies DNA in an
AB  - S-adenosylmethionine dependent reaction. The enzyme stabilizes the target cytosine (GCGC) into
AB  - an extrahelical position, with a concomitant large movement of an active site loop involving
AB  - residues 80-99. We used multidimensional, transverse relaxation-optimized NMR experiments to
AB  - assign nearly 80% of all residues in the cofactor-bound enzyme form, providing a basis for
AB  - detailed structural and dynamical characterization. We examined details of the previously
AB  - unknown effects of the cofactor binding with M.HhaI in solution. Addition of the cofactor
AB  - results in numerous structural changes throughout the protein, including those decorating the
AB  - cofactor binding site, and distal residues more than 30 A away. The active site loop is
AB  - involved in motions both on a picosecond to nanosecond time scale and on a microsecond to
AB  - millisecond time scale and is not significantly affected by cofactor binding except for a few
AB  - N-terminal residues. The cofactor also affects residues near the DNA binding cleft, suggesting
AB  - a role for the cofactor in regulating DNA interactions. The allosteric properties we observed
AB  - appear to be closely related to the significant amount of dynamics and dynamical changes in
AB  - response to ligand binding detected in the protein.
ER  -

TY  - JOUR
AU  - Zhou, H.
AU  - Wang, Y.
AU  - Yu, Y.
AU  - Bai, T.
AU  - Chen, L.
AU  - Liu, P.
AU  - Guo, H.
AU  - Zhu, C.
AU  - Tao, M.
AU  - Deng, Z.
TI  - A non-restricting and non-methylating Escherichia coli strain for DNA cloning and high-throughput conjugation to Streptomyces coelicolor.
JO  - Curr. Microbiol.
PY  - 2012
SP  - 185
EP  - 190
VL  - 64
AB  - Escherichia coli strains are used in secondary metabolism research for DNA cloning and
AB  - transferring plasmids by intergeneric conjugation. Non-restricting
AB  - strains are desirable for DNA cloning and non-methylating strains are beneficial
AB  - for transferring DNA to methyl-restricting hosts, like Streptomyces coelicolor.
AB  - We have constructed a non-methylating E. coli strain, JTU007, by deleting the DNA
AB  - methylation genes dcm and dam from the widely used non-restricting cloning host
AB  - DH10B. JTU007 was tested as donor for the conjugative transfer of a plasmid
AB  - containing the 39 kb actinorhodin biosynthesis gene cluster to S. lividans and S.
AB  - coelicolor. The Dcm Dam strain JTU007 transferred DNA into S. coelicolor A(3)2
AB  - derivatives at high frequency. To demonstrate the usefulness of E. coli JTU007
AB  - for gene cloning, we constructed a comprehensive S. toxytricini genomic cosmid
AB  - library, and transferred it using high-throughput conjugation to the
AB  - methyl-restricting S. coelicolor. One of the cosmid clones produced a brown
AB  - pigment, and the clone was revealed to carry a tyrosinase operon. JTU007 is more
AB  - useful than ET12567 because it does not restrict methylated DNA in primary
AB  - cloning, and gives higher transformation and cosmid infection frequencies.
ER  -

TY  - JOUR
AU  - Zhou, H.
AU  - Yao, Z.
AU  - Shi, H.
AU  - Wang, B.
AU  - Li, D.
AU  - Hou, J.
AU  - Ma, S.
TI  - Draft Genome Sequence of Staphylococcus succinus subsp. succinus Type Strain DSM  14617, Isolated from Plant and Soil Inclusions within 25- to 35-Million-Year-Old   Dominican Amber.
JO  - Genome Announcements
PY  - 2017
SP  - e01521
EP  - e01516
VL  - 5
AB  - Staphylococcus succinus subsp. succinus type strain DSM 14617 was isolated from plant and soil
AB  - inclusions within 25- to 35-million-year-old Dominican amber. The
AB  - complete genome sequence of strain DSM 14617T includes a genome of 2.88 Mb
AB  - (32.94% G+C content) without any plasmids.
ER  -

TY  - JOUR
AU  - Zhou, H.
AU  - Zhang, T.W.
AU  - Yu, D.L.
AU  - Pi, B.R.
AU  - Yang, Q.
AU  - Zhou, J.Y.
AU  - Hu, S.N.
AU  - Yu, Y.S.
TI  - Genomic Analysis of the Multidrug-Resistant Acinetobacter baumannii Strain MDR-ZJ06 Widely Spread in China.
JO  - Antimicrob. Agents Chemother.
PY  - 2011
SP  - 4506
EP  - 4512
VL  - 55
AB  - We previously reported that the multidrug-resistant (MDR) Acinetobacter baumannii strain
AB  - MDR-ZJ06, belonging to European clone II, was widely
AB  - spread in China. In this study, we report the whole-genome sequence of
AB  - this clinically important strain. A 38.6-kb AbaR-type genomic
AB  - resistance island (AbaR22) was identified in MDR-ZJ06. AbaR22 has a
AB  - structure similar to those of the resistance islands found in A.
AB  - baumannii strains AYE and AB0057, but it contained only a few
AB  - antibiotic resistance genes. The region of resistant gene accumulation
AB  - as previously described was not found in AbaR22. In the chromosome of
AB  - the strain MDR-ZJ06, we identified the gene bla(oxa-23) in a composite
AB  - transposon (Tn2009). Tn2009 shared the backbone with other A. baumannii
AB  - transponsons that harbor bla(oxa-23), but it was bracketed by two
AB  - ISAba1 elements which were transcribed in the same orientation.
AB  - MDR-ZJ06 also expressed the armA gene on its plasmid pZJ06, and this
AB  - gene has the same genetic environment as the armA gene of the
AB  - Enterobacteriaceae. These results suggest variability of resistance
AB  - acquisition even in closely related A. baumannii strains.
ER  -

TY  - JOUR
AU  - Zhou, H.J.
AU  - Purdy, M.M.
AU  - Dahlquist, F.W.
AU  - Reich, N.O.
TI  - The Recognition Pathway for the DNA Cytosine Methyltransferase M.HhaI.
JO  - Biochemistry
PY  - 2009
SP  - 7807
EP  - 7816
VL  - 48
AB  - Enzymatic sequence-specific DNA modification involves multiple poorly understood
AB  - intermediates. DNA methyltransferases like M.HhaI initially
AB  - bind nonspecific DNA and then selectively bind and modify a unique
AB  - sequence. High-resolution NMR was used to map conformational changes
AB  - occurring in M. HhaI upon binding nonspecific DNA, a one base pair
AB  - altered noncognate DNA sequence, and both hemimethylated and
AB  - unmethylated cognate DNA sequences. Comparisons with previous NMR
AB  - studies of the apoenzyme and enzyme-cofactor complex provide snapshots
AB  - of the pathway to sequence-specific complex formation. Dramatic
AB  - chemical shift perturbations reaching many distal sites within the
AB  - protein are detected with cognate DNA, while much smaller changes are
AB  - observed upon nonspecific and noncognate DNA binding. A cooperative
AB  - rather than stepwise transition from a nonspecific to a cognate complex
AB  - is revealed, Furthermore, switching from unmethylated to hemimethylated
AB  - cognate DNA involves delectable protein conformational changes 20-30
AB  - angstrom away from the methyl group, indicating high protein
AB  - sensitivity and plasticity to DNA modification.
ER  -

TY  - JOUR
AU  - Zhou, J.
AU  - Sun, D.
AU  - Childers, A.
AU  - McDermott, T.R.
AU  - Wang, Y.
AU  - Liles, M.R.
TI  - Three novel virophage genomes discovered from Yellowstone Lake metagenomes.
JO  - J. Virol.
PY  - 2015
SP  - 1278
EP  - 1285
VL  - 89
AB  - Virophages are a unique group of circular double-stranded DNA viruses that are
AB  - considered parasites of giant DNA viruses, which in turn are known to infect
AB  - eukaryotic hosts. In this study the genomes of three novel virophages YSLV5,
AB  - YSLV6 and YSLV7 were identified from Yellowstone Lake through metagenomic
AB  - analyses. The relative abundance of these three novel virophages and previously
AB  - identified Yellowstone Lake virophages YSLVs 1-4 were determined in different
AB  - locations of the lake, revealing that most of the sampled locations in the lake,
AB  - including both mesophilic and thermophilic habitats, had multiple virophage
AB  - genotypes. This likely reflects the diverse habitats or diversity of the
AB  - eukaryotic hosts and their associated giant viruses that serve as putative hosts
AB  - for these virophages. YSLV5 has a 29,767 bp genome with 32 predicted ORFs, YSLV6
AB  - has a 24,837 bp genome with 29 predicted ORFs, and YSLV7 has a 23,193 bp genome
AB  - with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a
AB  - close evolutionary relationship with YSLVs 1-4, whereas YSLV5 and YSLV7 are
AB  - distantly related to the others, and YSLV7 represents the fourth novel virophage
AB  - lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much
AB  - higher than all other known virophages, indicating a unique host range for YSLV5.
AB  - These results suggest that virophages are abundant and have diverse genotypes
AB  - that likely mirror diverse giant viral and eukaryotic hosts within the
AB  - Yellowstone Lake ecosystem. IMPORTANCE: This study discovered novel virophages
AB  - present within the Yellowstone Lake ecosystem using a conserved major capsid
AB  - protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone
AB  - Lake metagenomic samples. The three novel virophage genomes (YSLV5-7) were
AB  - completed by identifying specific environmental samples containing these
AB  - respective virophages, and closing gaps by targeted PCR and sequencing. Most of
AB  - the YSLV genotypes were associated primarily with photic zone and
AB  - non-hydrothermal samples; however, YSLV5 had a unique distribution with an
AB  - occurrence in vent samples similar to that in photic zone samples, and with a
AB  - higher GC content that suggests a distinct host and habitat compared to other
AB  - YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5
AB  - and YSLV7 are distinct from known virophages, and that additional
AB  - as-yet-uncharacterized virophages are likely present within the Yellowstone Lake
AB  - ecosystem.
ER  -

TY  - JOUR
AU  - Zhou, L.
AU  - Cheng, X.
AU  - Connolly, B.A.
AU  - Dickman, M.J.
AU  - Hurd, P.J.
AU  - Hornby, D.P.
TI  - Zebularine: A novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.
JO  - J. Mol. Biol.
PY  - 2002
SP  - 591
EP  - 599
VL  - 321
AB  - Mechanism-based inhibitors of enzymes, which mimic reactive intermediates in the reaction
AB  - pathway, have been deployed extensively in the analysis of metabolic pathways and as candidate
AB  - drugs. The inhibition of cytosine-[C5]-specific DNA methyltransferases (C5 MTases) by
AB  - oligodeoxynucleotides containing 5-azadeoxycytidine (AzadC) and 5-fluorodeoxycytidine (FdC)
AB  - provides a well-documented example of mechanism-based inhibition of enzymes central to nucleic
AB  - acid metabolism. Here, we describe the interaction between the C5 MTase from Haemophilus
AB  - haemolyticus (M.HhaI) and an oligodeoxynucleotide duplex containing 2-H pyrimidinone, an
AB  - analogue often referred to as zebularine and known to give rise to high-affinity complexes
AB  - with MTases. X-ray crystallography has demonstrated the formation of a covalent bond between
AB  - M.HhaI and the 2-H pyrimidinone-containing oligodeoxynucleotide. This observation enables a
AB  - comparison between the mechanisms of action of 2-H pyrimidinone with other mechanism-based
AB  - inhibitors such as FdC. This novel complex provides a molecular explanation for the mechanism
AB  - of action of the anti-cancer drug zebularine.
ER  -

TY  - JOUR
AU  - Zhou, L.
AU  - Li, M.
AU  - Yang, J.
AU  - Wei, L.
AU  - Ji, G.
TI  - Draft Genome Sequence of Antagonistic Agent Lysobacter antibioticus 13-6.
JO  - Genome Announcements
PY  - 2014
SP  - e00566
EP  - e00514
VL  - 2
AB  - Lysobacter antibioticus 13-6, isolated from the roots of Chinese cabbage, effectively controls
AB  - the pathogens Plasmodiophora brassicae, Xanthomonas oryzae
AB  - pv. oryzicola, X. oryzae pv. oryzae, Xanthomonas axonopodis pv. dieffenbachiae,
AB  - and Pseudomonas syringae pv. tabaci. We report the first draft genome sequence of
AB  - the L. antibioticus species in China.
ER  -

TY  - JOUR
AU  - Zhou, M.
AU  - Chen, W.
AU  - Chen, H.
AU  - Wei, G.
TI  - Draft Genome Sequence of Mesorhizobium alhagi CCNWXJ12-2T, a Novel Salt-Resistant Species Isolated from the Desert of Northwestern China.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1261
EP  - 1262
VL  - 194
AB  - Mesorhizobium alhagi strain CCNWXJ12-2(T) is a novel species of soil-dwelling, nitrogen-fixing
AB  - bacteria that can form symbiotic root nodules with Alhagi
AB  - sparsifolia. Moreover, the strain has high resistance to salt and alkali. Here we
AB  - report the draft genome sequence of Mesorhizobium alhagi strain CCNWXJ12-2(T). A
AB  - large number of osmotic regulation-related genes have been identified.
ER  -

TY  - JOUR
AU  - Zhou, M.
AU  - Dong, B.
AU  - Liu, Q.
TI  - Draft Genome Sequence of Psychrobacter piscatorii Strain LQ58, a Psychrotolerant  Bacterium Isolated from a Deep-Sea Hydrothermal Vent.
JO  - Genome Announcements
PY  - 2016
SP  - e00044
EP  - e00016
VL  - 4
AB  - Here, we report the 3.1-Mb draft genome sequence of Psychrobacter piscatorii strain LQ58,
AB  - isolated from a deep-sea hydrothermal vent on the East Pacific Rise.
AB  - The sequence will provide further insight into the environmental adaptation of
AB  - psychrotolerant bacteria and the development of novel cold-active enzymes for
AB  - industrial application.
ER  -

TY  - JOUR
AU  - Zhou, M.
AU  - Xie, Y.
AU  - Dong, B.
AU  - Liu, Q.
AU  - Chen, X.
TI  - Draft Genome Sequence of Caloranaerobacter sp. TR13, an Anaerobic Thermophilic Bacterium Isolated from a Deep-Sea Hydrothermal Vent.
JO  - Genome Announcements
PY  - 2015
SP  - e01491
EP  - e01415
VL  - 3
AB  - Here, we report the draft 2,261,881-bp genome sequence of Caloranaerobacter sp. TR13, isolated
AB  - from a deep-sea hydrothermal vent on the East Pacific Rise. The
AB  - sequence will be helpful for understanding the genetic and metabolic features, as
AB  - well as potential biotechnological application in the genus Caloranaerobacter.
ER  -

TY  - JOUR
AU  - Zhou, P.
AU  - Wu, Y.H.
AU  - Cheng, H.
AU  - Wang, C.S.
AU  - Xu, X.W.
TI  - Draft Genome Sequence of Altererythrobacter troitsensis JCM 17037, Isolated from  the Sea Urchin Strongylocentrotus intermedius.
JO  - Genome Announcements
PY  - 2016
SP  - e01556
EP  - e01515
VL  - 4
AB  - The habitats of the genus Altererythrobacter are various, including marine sediment, seawater,
AB  - rhizosphere of wild rice, desert sand, etc. The genome of the
AB  - type strain of Altererythrobacter troitsensis JCM 17037, isolated from sea
AB  - urchin, was sequenced. This study would not only facilitate the understanding of
AB  - the physiology, adaptation, and evolution of the Altererythrobacter species, but
AB  - also provide a good resource for the study of synthesis of astaxanthin, since
AB  - several enzymes involved in the production of astaxanthin were predicted.
ER  -

TY  - JOUR
AU  - Zhou, P.
AU  - Xie, G.
AU  - Li, X.
AU  - Liu, J.
AU  - Qi, F.
TI  - Complete Genome Sequence of Veillonella atypica OK5, the First Transformable Strain in the Species.
JO  - Genome Announcements
PY  - 2017
SP  - e00391
EP  - e00317
VL  - 5
AB  - The Veillonella atypica strain OK5 was isolated from a human saliva sample and was the first
AB  - strain shown to be genetically transformable in the Veillonella
AB  - genus. Genetic studies using this strain have helped us gain much insight into
AB  - the ecology of human oral biofilms. Here, we report the complete genome sequence
AB  - of V. atypica OK5.
ER  -

TY  - JOUR
AU  - Zhou, S.
AU  - Li, L.
AU  - Wei, J.
AU  - Qin, Q.
TI  - Genome Sequence of Klebsiella pneumoniae HSL4, a New Strain Isolated from Mangrove Sediment for Biosynthesis of 1,3-Propanediol.
JO  - Genome Announcements
PY  - 2013
SP  - e00177
EP  - e00113
VL  - 1
AB  - Klebsiella pneumoniae HSL4 is a 1,3-propanediol-producing bacterium strain isolated from
AB  - mangrove sediment. We present here a 5,221,448-bp assembly of its
AB  - genome sequence. Genome analysis revealed that it contains 10 coding sequences
AB  - (CDSs) responsible for glycerol fermentation to 1,3-propanediol, 19 CDSs encoding
AB  - glycerol utilization, and 140 CDSs related to its virulence.
ER  -

TY  - JOUR
AU  - Zhou, W.
AU  - Li, M.
AU  - Zhu, L.
AU  - Hua, F.
AU  - Ji, X.
AU  - Sun, Y.
AU  - Liu, J.
AU  - Guo, X.
TI  - Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain BM-Y, Isolated from the Pancreas of a Zebra in China.
JO  - Genome Announcements
PY  - 2016
SP  - e00643
EP  - e00616
VL  - 4
AB  - Here, a complete genome sequence of Wohlfahrtiimonas chitiniclastica strain BM-Y  is
AB  - presented. The whole genome is 2.18-Mb and contains a blaVEB-1 gene cassette which endows it
AB  - with resistance to ceftazidime, ampicillin, tetracycline, etc. To our knowledge, this is the
AB  - first time that an extended spectrum beta-lactamase (ESBL) type W. chitiniclastica strain has
AB  - been found.
ER  -

TY  - JOUR
AU  - Zhou, W.
AU  - Niu, D.
AU  - Zhang, Z.
AU  - Liu, Y.
AU  - Ning, M.
AU  - Cao, X.
AU  - Zhang, C.
AU  - Shen, H.
TI  - Complete Genome Sequence of Aerococcus urinaeequi Strain AV208.
JO  - Genome Announcements
PY  - 2016
SP  - e01218
EP  - e01216
VL  - 4
AB  - Aerococcus urinaeequi strain AV208 was isolated from an ascites sample from a patient with
AB  - chronic kidney disease. The assembled genome contained 2,227,638 bp
AB  - with a 39.1% G+C content. The genome harbors a Tn1546 transposon-like structure
AB  - with a vanA gene causing vancomycin resistance phenotypes of strain AV208.
ER  -

TY  - JOUR
AU  - Zhou, X.
AU  - Deng, Z.
AU  - Firmin, J.L.
AU  - Hopwood, D.A.
AU  - Kieser, T.
TI  - Site-specific degradation of Streptomyces lividans DNA during electrophoresis in  buffers contaminated with ferrous iron.
JO  - Nucleic Acids Res.
PY  - 1988
SP  - 4341
EP  - 4352
VL  - 16
AB  - Streptomyces lividans DNA contains a modification which makes it susceptible to double-strand
AB  - cleavage during electrophoresis in buffers contaminated with
AB  - ferrous iron (which may be present in some batches of EDTA). The cleavage of the
AB  - DNA is site-specific and the average fragment size resulting from limit digestion
AB  - of total S. lividans DNA is about 6kb. DNA from Streptomyces coelicolor A3(2) and
AB  - several other Streptomyces strains, and from E. coli, is not cleaved under the
AB  - same conditions. A S. lividans mutant has been isolated which lacks the DNA
AB  - modification. We suspect that many reports of 'poor' preparations of S. lividans
AB  - plasmids may be due to the above effect.
ER  -

TY  - JOUR
AU  - Zhou, X.
AU  - He, X.
AU  - Liang, J.
AU  - Li, A.
AU  - Xu, T.
AU  - Kieser, T.
AU  - Helmann, J.D.
AU  - Deng, Z.
TI  - A novel DNA modification by sulphur.
JO  - Mol. Microbiol.
PY  - 2005
SP  - 1428
EP  - 1438
VL  - 57
AB  - Streptomyces lividans has a novel DNA modification, which sensitises its DNA to degradation
AB  - during electrophoresis (the Dnd phenotype). The entire
AB  - gene cluster (dnd) involved in this modification was localized on an 8 kb
AB  - DNA fragment and was expressed in a S. lividans deletion mutant (dnd) and
AB  - in several heterologous hosts. Disruption of the dnd locus abolishes the
AB  - Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype
AB  - respectively. Extensive analysis of the dnd gene cluster revealed five
AB  - open reading frames, whose hypothetic functions suggested an incorporation
AB  - of sulphur or a sulphur-containing substance into S. lividans genome, yet
AB  - in an unknown manner. The Dnd phenotype was also discovered to exist in
AB  - DNA of widespread bacterial species of variable origin and diverse
AB  - habitat. Similarly organized gene clusters were found in several bacterial
AB  - genomes representing different genera and in eDNA of marine organisms,
AB  - suggesting such modification as a widespread phenomenon. A coincidence
AB  - between the Dnd phenotype and DNA modification by sulphur was demonstrated
AB  - to occur in several representative bacterial genomes by the in
AB  - vivo(35)S-labelling experiments.
ER  -

TY  - JOUR
AU  - Zhou, X.E.
AU  - Wang, Y.
AU  - Reuter, M.
AU  - Mackeldanz, P.
AU  - Kruger, D.H.
AU  - Meehan, E.J.
AU  - Chen, L.Q.
TI  - A single mutation of restriction endonuclease EcoRII led to a new crystal form that diffracts to 2.1 angstrom resolution.
JO  - Acta Crystallogr. D Biol. Crystallogr.
PY  - 2003
SP  - 910
EP  - 912
VL  - 59
AB  - R88A, a mutant of the type IIE restriction endonuclease EcoRII, has been crystallized in space
AB  - group P2(1), with unit-cell parameters a = 58.7, b =
AB  - 92.4, c = 88.3 A, beta = 108.1 degrees. There are two monomers in the
AB  - asymmetric unit and the solvent content is estimated to be 50% by volume.
AB  - The crystals diffract to 2.1 A resolution, which is much higher than that
AB  - of the wild type, which diffracted to 2.8 A resolution. The mutant
AB  - crystals have been used in the identification of an excellent heavy-atom
AB  - derivative.
ER  -

TY  - JOUR
AU  - Zhou, X.W.
AU  - Li, J.
AU  - Wang, K.M.
AU  - Tan, W.H.
AU  - Yang, X.H.
AU  - Meng, X.X.
AU  - Yan, H.F.
TI  - An assay for the activity of DNA methylase based on a hairpin fluorescence molecular probe and its application in drug selection.
JO  - Acta Chimi. Sin.
PY  - 2006
SP  - 2096
EP  - 2100
VL  - 64
AB  - A new activity assay for DNA methylase based on a hairpin molecular probe was proposed in this
AB  - paper. The recognition site of DNA methylase
AB  - and corresponding restriction endonuclease was designed in the stem
AB  - part of the probe, tetramethy1rhodamine (TAMRA) was attached at the 5'
AB  - terminus and its fluorescence was quenched by
AB  - 4-(4'-dimethylaniinophenylazo)benzoic acid (DABCYL) linked at the 3'
AB  - terminus. The unmethylated probe can be cut in the recognition site by
AB  - restriction endonuclease, causing the restoration of the fluorescence
AB  - of TAMRA. Therefore, the activity of methylase would be analyzed
AB  - according to the degree of fluorescence restoration. Based on this
AB  - assay, the influence of anti-tumor drugs on the activity of methylase
AB  - was investigated by adding drugs in the methylation reaction. This
AB  - method can provide a potential in selecting proper drugs for tumors
AB  - caused by altered gene methylation pattern.
ER  -

TY  - JOUR
AU  - Zhou, X.Y.E.
AU  - Wang, Y.J.
AU  - Reuter, M.
AU  - Mucke, M.
AU  - Kruger, D.H.
AU  - Meehan, E.J.
AU  - Chen, L.Q.
TI  - Crystal structure of Type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 307
EP  - 319
VL  - 335
AB  - EcoRII is a Type IIE restriction endonuclease that interacts with two copies of the DNA
AB  - recognition sequence 5'CCWGG, one being the actual
AB  - target of cleavage, the other serving as the allosteric effector. The
AB  - mode of enzyme activation by effector binding is unknown. To
AB  - investigate the molecular basis of activation and cleavage mechanisms
AB  - by EcoRII, the crystal structure of EcoRII mutant R88A has been
AB  - solved at 2.1 Angstrom resolution. The EcoRII monomer has two domains
AB  - linked through a hinge loop. The N-terminal effector-binding domain has
AB  - a novel DNA recognition fold with a prominent cleft. The C-terminal
AB  - catalytic domain has a restriction endonuclease-like fold.
AB  - Structure-based sequence alignment identified the putative catalytic
AB  - site of EcoRII that is spatially blocked by the N-terminal domain. The
AB  - structure together with the earlier characterized EcoRII enzyme
AB  - activity enhancement in the absence of its N-terminal domain reveal an
AB  - autoinhibition/activation mechanism of enzyme activity mediated by a
AB  - novel effector-binding fold. This is the first case of autoinhibition,
AB  - a mechanism described for many transcription factors and signal
AB  - transducing proteins, of a restriction endonuclease.
ER  -

TY  - JOUR
AU  - Zhou, Y.
AU  - Li, R.
AU  - Gao, X.Y.
AU  - Lapidus, A.
AU  - Han, J.
AU  - Haynes, M.
AU  - Lobos, E.
AU  - Huntemann, M.
AU  - Pati, A.
AU  - Ivanova, N.N.
AU  - Rohde, M.
AU  - Mavromatis, K.
AU  - Tindall, B.J.
AU  - Markowitz, V.
AU  - Woyke, T.
AU  - Klenk, H.P.
AU  - Kyrpides, N.C.
AU  - Li, W.J.
TI  - High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in  southern China.
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1020
EP  - 1030
VL  - 9
AB  - Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family
AB  - Halomonadaceae, class Gammaproteobacteria. Representatives of the genus
AB  - Halomonas are a group of halophilic bacteria often isolated from salty
AB  - environments. The type strain H. zhanjiangensis JSM 078169(T) was isolated from a
AB  - sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The
AB  - genome of strain JSM 078169(T) is the fourteenth sequenced genome in the genus
AB  - Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen
AB  - genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila,
AB  - H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H.
AB  - smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we
AB  - describe the features of strain JSM 078169(T), together with the complete genome
AB  - sequence and annotation from a culture of DSM 21076(T). The 4,060,520 bp long
AB  - draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA
AB  - genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one
AB  - thousand microbial genomes (KMG) project.
ER  -

TY  - JOUR
AU  - Zhou, Z.
AU  - Li, H.
AU  - Zhang, M.
AU  - Wang, Z.
AU  - Zhou, R.
AU  - Hu, S.
AU  - Li, X.
AU  - Song, X.
AU  - Zhu, Z.
TI  - Genome Sequence of Corynebacterium pseudotuberculosis Strain XH02 Isolated from a Boer Goat in Xuanhan, China.
JO  - Genome Announcements
PY  - 2016
SP  - e01329
EP  - e01316
VL  - 4
AB  - We report here the genome sequence of Corynebacterium pseudotuberculosis strain XH02, isolated
AB  - from a Boer goat in China. The genome consists of 2,357,671 bp,
AB  - with a 52.18% G+C content, 2,263 coding sequences, 21 rRNAs, 49 tRNAs, and 44
AB  - predicted pseudogenes.
ER  -

TY  - JOUR
AU  - Zhou, Z.
AU  - Li, X.
AU  - Liu, B.
AU  - Beutin, L.
AU  - Xu, J.
AU  - Ren, Y.
AU  - Feng, L.
AU  - Lan, R.
AU  - Reeves, P.R.
AU  - Wang, L.
TI  - Derivation of Escherichia coli O157:H7 from its O55:H7 precursor.
JO  - PLoS ONE
PY  - 2010
SP  - E8700
EP  - E8700
VL  - 5
AB  - There are 29 E. coli genome sequences available, mostly related to studies
AB  - of species diversity or mode of pathogenicity, including two genomes of
AB  - the well-known O157:H7 clone. However, there have been no genome studies
AB  - of closely related clones aimed at exposing the details of evolutionary
AB  - change. Here we sequenced the genome of an O55:H7 strain, closely related
AB  - to the major pathogenic O157:H7 clone, with published genome sequences,
AB  - and undertook comparative genomic and proteomic analysis. We were able to
AB  - allocate most differences between the genomes to individual mutations,
AB  - recombination events, or lateral gene transfer events, in specific
AB  - lineages. Major differences include a type II secretion system present
AB  - only in the O55:H7 chromosome, fewer type III secretion system effectors
AB  - in O55:H7, and 19 phage genomes or phagelike elements in O55:H7 compared
AB  - to 23 in O157:H7, with only three common to both. Many other changes were
AB  - found in both O55:H7 and O157:H7 lineages, but in general there has been
AB  - more change in the O157:H7 lineages. For example, we found 50% more
AB  - synonymous mutational substitutions in O157:H7 compared to O55:H7. The two
AB  - strains also diverged at the proteomic level. Mutational synonymous SNPs
AB  - were used to estimate a divergence time of 400 years using a new clock
AB  - rate, in contrast to 14,000 to 70,000 years using the traditional clock
AB  - rates. The same approaches were applied to three closely related
AB  - extraintestinal pathogenic E. coli genomes, and similar levels of mutation
AB  - and recombination were found. This study revealed for the first time the
AB  - full range of events involved in the evolution of the O157:H7 clone from
AB  - its O55:H7 ancestor, and suggested that O157:H7 arose quite recently. Our
AB  - findings also suggest that E. coli has a much lower frequency of
AB  - recombination relative to mutation than was observed in a comparable study
AB  - of a Vibrio cholerae lineage.
ER  -

TY  - JOUR
AU  - Zhou, Z.
AU  - McCann, A.
AU  - Litrup, E.
AU  - Murphy, R.
AU  - Cormican, M.
AU  - Fanning, S.
AU  - Brown, D.
AU  - Guttman, D.S.
AU  - Brisse, S.
AU  - Achtman, M.
TI  - Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona.
JO  - PLoS Genet.
PY  - 2013
SP  - E1003471
EP  - E1003471
VL  - 9
AB  - Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of
AB  - gastroenteritis since it was first isolated in 1952. We analyzed the genomes of
AB  - 73 isolates from global sources, comparing five distinct outbreaks with sporadic
AB  - infections as well as food contamination and the environment. Agona consists of
AB  - three lineages with minimal mutational diversity: only 846 single nucleotide
AB  - polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since
AB  - Agona evolved in 1932 and subsequently underwent a major population expansion in
AB  - the 1960s. Homologous recombination with other serovars of S. enterica imported
AB  - 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which
AB  - resulted in 3,164 additional SNPs. In contrast to this paucity of genetic
AB  - diversity, Agona is highly diverse according to pulsed-field gel electrophoresis
AB  - (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a
AB  - highly dynamic accessory genome associated with the gain or loss (indels) of 51
AB  - bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs),
AB  - but did not correlate uniquely with outbreaks. Unlike the core genome, indels
AB  - occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate
AB  - PFGE genealogies. The accessory genome contained only few cargo genes relevant to
AB  - infection, other than antibiotic resistance. Thus, most of the genetic diversity
AB  - within this recently emerged pathogen reflects changes in the accessory genome,
AB  - or is due to recombination, but these changes seemed to reflect neutral processes
AB  - rather than Darwinian selection. Each outbreak was caused by an independent
AB  - clade, without universal, outbreak-associated genomic features, and none of the
AB  - variable genes in the pan-genome seemed to be associated with an ability to cause
AB  - outbreaks.
ER  -

TY  - JOUR
AU  - Zhou, Z.
AU  - Peng, X.
AU  - Xiao, Y.
AU  - Wang, X.
AU  - Guo, Z.
AU  - Zhu, L.
AU  - Liu, M.
AU  - Jin, H.
AU  - Bi, D.
AU  - Li, Z.
AU  - Sun, M.
TI  - Genome Sequence of the poultry pathogen Riemerella anatipestifer Strain RA-YM.
JO  - J. Bacteriol.
PY  - 2010
SP  - 1284
EP  - 1285
VL  - 193
AB  - Riemerella anatipestifer is a Gram-negative rod-shaped bacillus associated with epizootic
AB  - infections in poultry. R. anatipestifer strain RA-YM, belonging to the serotype 1 prevalent in
AB  - China, is a clinically isolated strain with high-level virulence. Here, we report the first
AB  - genome sequence of this species.
ER  -

TY  - JOUR
AU  - Zhu, B.
AU  - Chen, M.
AU  - Lin, L.
AU  - Yang, L.
AU  - Li, Y.
AU  - An, Q.
TI  - Genome sequence of Enterobacter sp. strain SP1, an endophytic nitrogen-fixing bacterium isolated from sugarcane.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6963
EP  - 6964
VL  - 194
AB  - Enterobacter sp. strain SP1 is an endophytic nitrogen-fixing bacterium isolated
AB  - from a sugarcane stem and can promote plant growth. The draft genome sequence of
AB  - strain SP1 presented here will promote comparative genomic studies to determine
AB  - the genetic background of interactions between endophytic enterobacteria and
AB  - plants.
ER  -

TY  - JOUR
AU  - Zhu, B.
AU  - Liu, H.
AU  - Tian, W.X.
AU  - Fan, X.Y.
AU  - Li, B.
AU  - Zhou, X.P.
AU  - Jin, G.L.
AU  - Xie, G.L.
TI  - Genome Sequence of Stenotrophomonas maltophilia RR-10, Isolated as an Endophyte from Rice Root.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1280
EP  - 1281
VL  - 194
AB  - Stenotrophomonas maltophilia is an endophyte which plays important roles in agricultural
AB  - production as a plant growth-promoting bacterium. Here, we present
AB  - the draft genome sequence of strain RR-10, which was isolated from a rice root in
AB  - a rice field of China.
ER  -

TY  - JOUR
AU  - Zhu, B.
AU  - Ye, S.
AU  - Chang, S.
AU  - Chen, M.
AU  - Sun, L.
AU  - An, Q.
TI  - Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os45, Isolated from Rice Roots.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6995
EP  - 6996
VL  - 194
AB  - Most Herbaspirillum seropedicae strains are beneficial to plants. In contrast, H. seropedicae
AB  - strain Os45, isolated from rice roots, is pathogenic. The draft
AB  - genome sequence of strain Os45 presented here allows an in-depth comparative
AB  - genome analysis to understand the subtle mechanisms of beneficial and pathogenic
AB  - Herbaspirillum-plant interactions.
ER  -

TY  - JOUR
AU  - Zhu, D.
AU  - Li, P.
AU  - Tanabe, S.H.
AU  - Sun, J.
TI  - Genome Sequence of the Alkaliphilic Bacterial Strain Bacillus ligninesis L1, a Novel Degrader of Lignin.
JO  - Genome Announcements
PY  - 2013
SP  - e0004213
EP  - e0004213
VL  - 1
AB  - Bacillus ligninesis strain L1, isolated from seafloor sediment, was able to grow  on medium
AB  - with lignin as its sole carbon source. Here, we report a 3.8-Mbp
AB  - high-quality genome sequence for this bacterium. The genes involving ectoine and
AB  - glycine betaine synthesis, as well as those involved in the degradation of
AB  - lignin, were identified.
ER  -

TY  - JOUR
AU  - Zhu, H.
AU  - Ni, Y.
AU  - Zhou, J.
AU  - Yu, Z.
AU  - Mao, A.
AU  - Wang, D.
AU  - He, K.
TI  - Complete Genome Sequence of Streptococcus suis Serotype 2 Virulent Strain SS2-1.
JO  - Genome Announcements
PY  - 2018
SP  - e00067
EP  - e00018
VL  - 6
AB  - Streptococcus suis is an important swine pathogen that can also cause severe diseases in
AB  - humans. Herein, we describe the genome sequence of Streptococcus suis
AB  - serotype 2 virulent strain SS2-1, which was isolated from a diseased dead pig
AB  - amid the 1998 Streptococcus suis outbreak in Jiangsu Province in China.
ER  -

TY  - JOUR
AU  - Zhu, H.
AU  - Wang, Q.
AU  - Wen, L.
AU  - Xu, J.
AU  - Shao, Z.
AU  - Chen, M.
AU  - Chen, M.
AU  - Reeves, P.R.
AU  - Cao, B.
AU  - Wang, L.
TI  - Development of a Multiplex PCR Assay for Detection and Genogrouping of Neisseria meningitidis.
JO  - J. Clin. Microbiol.
PY  - 2012
SP  - 46
EP  - 51
VL  - 50
AB  - Neisseria meningitidis is a leading pathogen of epidemic bacterial meningitis and
AB  - fulminant sepsis worldwide. Twelve different N. meningitidis serogroups have been
AB  - identified to date based on antigenic differences in the capsular polysaccharide.
AB  - However, more than 90% of human cases of N. meningitidis meningitis are the
AB  - result of infection with just five serogroups, A, B, C, W135, and Y. Efficient
AB  - methods of detection and genogrouping of N. meningitidis isolates are needed,
AB  - therefore, in order to monitor prevalent serogroups as a means of disease control
AB  - and prevention. The capsular gene complex regions have been sequenced from only
AB  - seven out of the 12 serogroups. In this study, the capsular gene complexes of the
AB  - remaining five serogroups were sequenced and analyzed. Primers were designed that
AB  - were specific for N. meningitidis species and for the 12 individual serogroups,
AB  - and a multiplex PCR assay using these specific primers was developed for N.
AB  - meningitidis detection and genogrouping. The assay was tested using 15 reference
AB  - strains covering all 12 serogroups, 143 clinical isolates, and 21 strains from
AB  - closely related species or from species that cause meningitis. The assay could
AB  - detect N. meningitidis serogroups and was shown to be specific, with a detection
AB  - sensitivity of 1 ng of genomic DNA (equivalent to approximately 4 x 10(5)
AB  - genomes) or 3 x 10(5) CFU/ml in noncultured mock cerebrospinal fluid (CSF)
AB  - specimens. This study, therefore, describes for the first time the development of
AB  - a molecular protocol for the detection of all N. meningitidis serogroups. This
AB  - multiplex PCR-based assay may have use for the clinical diagnosis and
AB  - epidemiological surveillance of N. meningitidis.
ER  -

TY  - JOUR
AU  - Zhu, J.
TI  - Susceptibility of AatII and ApaI 3' protruding ends to exonuclease III degradation.
JO  - Biotechniques
PY  - 1991
SP  - 757
EP  - 759
VL  - 11
AB  - None
ER  -

TY  - JOUR
AU  - Zhu, L.
AU  - Li, M.
AU  - Guo, S.
AU  - Wang, W.
TI  - Draft Genome Sequence of a Thermophilic Desulfurization Bacterium, Geobacillus thermoglucosidasius Strain W-2.
JO  - Genome Announcements
PY  - 2016
SP  - e00793
EP  - e00716
VL  - 4
AB  - Geobacillus thermoglucosidasius strain W-2 is a thermophilic bacterium isolated from a
AB  - deep-subsurface oil reservoir in northern China, which is capable of
AB  - degrading organosulfur compounds. Here, we report the draft genome sequence of G.
AB  - thermoglucosidasius strain W-2, which may help to elucidate the genetic basis of
AB  - biodegradation of organosulfur pollutants under heated conditions.
ER  -

TY  - JOUR
AU  - Zhu, L.
AU  - Yan, Z.
AU  - Zhang, Z.
AU  - Zhou, Q.
AU  - Zhou, J.
AU  - Wakeland, E.K.
AU  - Fang, X.
AU  - Xuan, Z.
AU  - Shen, D.
AU  - Li, Q.Z.
TI  - Complete Genome Analysis of Three Acinetobacter baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements.
JO  - PLoS ONE
PY  - 2013
SP  - E66584
EP  - E66584
VL  - 8
AB  - BACKGROUND: The emergence and rapid spreading of multidrug-resistant
AB  - Acinetobacter baumannii strains has become a major health threat worldwide. To
AB  - better understand the genetic recombination related with the acquisition of
AB  - drug-resistant elements during bacterial infection, we performed complete genome
AB  - analysis on three newly isolated multidrug-resistant A. baumannii strains from
AB  - Beijing using next-generation sequencing technology. METHODOLOGIES/PRINCIPAL
AB  - FINDINGS: Whole genome comparison revealed that all 3 strains share some common
AB  - drug resistant elements including carbapenem-resistant bla OXA-23 and
AB  - tetracycline (tet) resistance islands, but the genome structures are diversified
AB  - among strains. Various genomic islands intersperse on the genome with transposons
AB  - and insertions, reflecting the recombination flexibility during the acquisition
AB  - of the resistant elements. The blood-isolated BJAB07104 and ascites-isolated
AB  - BJAB0868 exhibit high similarity on their genome structure with most of the
AB  - global clone II strains, suggesting these two strains belong to the dominant
AB  - outbreak strains prevalent worldwide. A large resistance island (RI) of about
AB  - 121-kb, carrying a cluster of resistance-related genes, was inserted into the
AB  - ATPase gene on BJAB07104 and BJAB0868 genomes. A 78-kb insertion element carrying
AB  - tra-locus and bla OXA-23 island, can be either inserted into one of the tniB gene
AB  - in the 121-kb RI on the chromosome, or transformed to conjugative plasmid in the
AB  - two BJAB strains. The third strains of this study, BJAB0715, which was isolated
AB  - from spinal fluid, exhibit much more divergence compared with above two strains.
AB  - It harbors multiple drug-resistance elements including a truncated AbaR-22-like
AB  - RI on its genome. One of the unique features of this strain is that it carries
AB  - both bla OXA-23 and bla OXA-58 genes on its genome. Besides, an Acinetobacter
AB  - lwoffii adeABC efflux element was found inserted into the ATPase position in
AB  - BJAB0715. CONCLUSIONS: Our comparative analysis on currently completed
AB  - Acinetobacter baumannii genomes revealed extensive and dynamic genome
AB  - organizations, which may facilitate the bacteria to acquire drug-resistance
AB  - elements into their genomes.
ER  -

TY  - JOUR
AU  - Zhu, L.
AU  - Zhong, J.
AU  - Jia, X.
AU  - Liu, G.
AU  - Kang, Y.
AU  - Dong, M.
AU  - Zhang, X.
AU  - Li, Q.
AU  - Yue, L.
AU  - Li, C.
AU  - Fu, J.
AU  - Xiao, J.
AU  - Yan, J.
AU  - Zhang, B.
AU  - Lei, M.
AU  - Chen, S.
AU  - Lv, L.
AU  - Zhu, B.
AU  - Huang, H.
AU  - Chen, F.
TI  - Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology.
JO  - Nucleic Acids Res.
PY  - 2016
SP  - 730
EP  - 743
VL  - 44
AB  - Tuberculosis (TB) remains one of the most common infectious diseases caused by Mycobacterium
AB  - tuberculosis complex (MTBC). To panoramically analyze MTBC's
AB  - genomic methylation, we completed the genomes of 12 MTBC strains (Mycobacterium
AB  - bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; H37Ra; and
AB  - 6 M. tuberculosis clinical isolates) belonging to different lineages and
AB  - characterized their methylomes using single-molecule real-time (SMRT) technology.
AB  - We identified three m6A sequence motifs and their corresponding methyltransferase
AB  - (MTase) genes, including the reported mamA, hsdM and a newly discovered mamB. We
AB  - also experimentally verified the methylated motifs and functions of HsdM and
AB  - MamB. Our analysis indicated the MTase activities varied between 12 strains due
AB  - to mutations/deletions. Furthermore, through measuring 'the methylated-motif-site
AB  - ratio' and 'the methylated-read ratio', we explored the methylation status of
AB  - each modified site and sequence-read to obtain the 'precision methylome' of the
AB  - MTBC strains, which enabled intricate analysis of MTase activity at whole-genome
AB  - scale. Most unmodified sites overlapped with transcription-factor
AB  - binding-regions, which might protect these sites from methylation. Overall, our
AB  - findings show enormous potential for the SMRT platform to investigate the precise
AB  - character of methylome, and significantly enhance our understanding of the
AB  - function of DNA MTase.
ER  -

TY  - JOUR
AU  - Zhu, M.
AU  - McCully, L.M.
AU  - Silby, M.W.
AU  - Charles-Ogan, T.I.
AU  - Huang, J.
AU  - Brigham, C.J.
TI  - Draft Genome Sequence of Ralstonia sp. MD27, a Poly(3-Hydroxybutyrate)-Degrading  Bacterium, Isolated from Compost.
JO  - Genome Announcements
PY  - 2015
SP  - e01170
EP  - e01115
VL  - 3
AB  - Ralstonia sp. strain MD27, a novel biopolymer-degrading betaproteobacterium, was  isolated
AB  - from compost samples. This organism has been shown to utilize the biopolymer
AB  - poly(3-hydroxybutyrate) [P(3HB)] as a carbon source for growth. We report the draft genome
AB  - sequence of MD27 with an estimated total sequence length  of 5.9 Mb.
ER  -

TY  - JOUR
AU  - Zhu, P.
AU  - Morelli, G.
AU  - Achtman, M.
TI  - The opcA and (psi)opcB regions in Neisseria: genes, pseudogenes, deletions, insertion elements and DNA islands.
JO  - Mol. Microbiol.
PY  - 1999
SP  - 635
EP  - 650
VL  - 33
AB  - Previous data have indicated that the opc gene encoding an immunogenic invasin is specific to
AB  - Neisseria meningitidis (Nm) and is lacking in
AB  - Neisseria gonorrhoeae (Ng). The data presented here show that Nm and Ng
AB  - both contain two paralogous opc-like genes, opcA, corresponding to the
AB  - former opc gene, and (psi)opcB, a pseudogene. The predicted OpcA and OpcB
AB  - proteins possess transmembrane regions with conserved non-polar faces but
AB  - differ extensively in four of the five surface-exposed loops. Gonococcal
AB  - OpcA was expressed weakly under in vitro conditions, and it is unknown
AB  - whether these bacteria can express this protein at high levels. Analysis
AB  - of the sequences flanking opcA and (psi)opcB revealed a framework of
AB  - conserved housekeeping genes interspersed with DNA islands. These regions
AB  - also contained several pseudogenes, deletions and IS elements, attesting
AB  - to considerable genome plasticity. Both opcA and (psi)opcB are located on
AB  - DNA islands that have probably been imported from unrelated bacteria. A
AB  - third island encodes the dcmD/dcrD R/M genes in Ng versus a small open
AB  - reading frame in most strains of Nm. Rare strains of Nm were identified in
AB  - which the R/M island has been imported. DNA islands in Nm and Ng seem to
AB  - have been acquired by recombination via conserved flanking housekeeping
AB  - genes rather than by insertion of mobile genetic elements.
ER  -

TY  - JOUR
AU  - Zhu, S.
AU  - Wang, H.L.
AU  - Wang, C.
AU  - Tang, L.
AU  - Wang, X.
AU  - Yu, K.J.
AU  - Liu, S.L.
TI  - Non-contiguous finished genome sequence and description of Salmonella enterica subsp. houtenae str. RKS3027.
JO  - Standards in Genomic Sciences
PY  - 2013
SP  - 198
EP  - 205
VL  - 8
AB  - Salmonella enterica subsp. houtenae serovar 16:z4, z32:-- str. RKS3027 was isolated from a
AB  - human in Illinois, USA. S. enterica subsp. houtenae is a
AB  - facultative aerobic rod-shaped Gram-negative bacterium. Here we describe the
AB  - features of this organism, together with the draft genome sequence and
AB  - annotation. The 4,404,136 bp long genome (97 contigs) contains 4,335
AB  - protein-coding gene and 28 RNA genes.
ER  -

TY  - JOUR
AU  - Zhu, S.
AU  - Wang, X.
AU  - Zhang, D.
AU  - Jing, X.
AU  - Zhang, N.
AU  - Yang, J.
AU  - Chen, J.
TI  - Complete Genome Sequence of Hemolysin-Containing Carnobacterium sp. Strain CP1 Isolated from the Antarctic.
JO  - Genome Announcements
PY  - 2016
SP  - e00690
EP  - e00616
VL  - 4
AB  - Carnobacterium sp. strain CP1 was isolated from Antarctic sandy soil and predicted to be a
AB  - novel species belonging to the genus Carnobacterium Herein, we
AB  - report the complete genome sequence, which consists of a circular 2,605,518-bp
AB  - chromosome and an 8,883-bp plasmid with G+C contents of 38.13% and 31.63%,
AB  - respectively.
ER  -

TY  - JOUR
AU  - Zhu, T.
AU  - Hou, S.
AU  - Lu, X.
AU  - Hess, W.R.
TI  - Draft Genome Sequences of Nine Cyanobacterial Strains from Diverse Habitats.
JO  - Genome Announcements
PY  - 2017
SP  - e01676
EP  - e01616
VL  - 5
AB  - Here, we report the annotated draft genome sequences of nine different cyanobacteria, which
AB  - were originally collected from different habitats, including
AB  - hot springs, terrestrial, freshwater, and marine environments, and cover four of
AB  - the five morphological subsections of cyanobacteria.
ER  -

TY  - JOUR
AU  - Zhu, W.
AU  - Huang, J.
AU  - Li, M.
AU  - Li, X.
AU  - Wang, G.
TI  - Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.).
JO  - Standards in Genomic Sciences
PY  - 2014
SP  - 1211
EP  - 1220
VL  - 9
AB  - Members of genus Skermanella were described as Gram-negative, motile, aerobic, rod-shaped,
AB  - obligate-heterotrophic bacteria and unable to fix nitrogen. In this
AB  - study, the genome sequence of Skermanella stibiiresistens SB22(T) is reported.
AB  - Phylogenetic analysis using core proteins confirmed the phylogenetic assignment
AB  - based on 16S rRNA gene sequences. Strain SB22(T) has all the proteins for
AB  - complete glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The
AB  - RuBisCO encoding genes cbbL1S1 and nitrogenase delta subunit gene anfG are
AB  - absent, consistent with its inability to fix carbon and nitrogen, respectively.
AB  - In addition, the genome possesses a series of flagellar assembly and chemotaxis
AB  - genes to ensure its motility.
ER  -

TY  - JOUR
AU  - Zhu, W.
AU  - Wang, J.
AU  - Zhu, Y.
AU  - Tang, B.
AU  - Zhang, Y.
AU  - He, P.
AU  - Zhang, Y.
AU  - Liu, B.
AU  - Guo, X.
AU  - Zhao, G.
AU  - Qin, J.
TI  - Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.
JO  - BMC Genomics
PY  - 2015
SP  - 90
EP  - 90
VL  - 16
AB  - Background: The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids
AB  - and prophages are known to play specific roles in gene transfer in bacteria and can
AB  - potentially serve as efficient genetic tools in these organisms. Although plasmids and
AB  - prophage remnants have recently been reported in Leptospira species, their characteristics and
AB  - potential applications in leptospiral genetic transformation systems have not been fully
AB  - evaluated. Results: Three extrachromosomal replicons designated lcp1 (65,732 bp), lcp2 (56,757
AB  - bp), and lcp3 (54,986 bp) in the L.
AB  - interrogans serovar Linhai strain 56609 were identified through whole genome sequencing. All
AB  - three replicons were stable outside of the bacterial chromosomes. Phage particles were
AB  - observed in the culture supernatant of 56609 after mitomycin C induction, and lcp3, which
AB  - contained phage-related genes, was considered to be an inducible prophage. L.
AB  - interrogans-Escherichia coli shuttle vectors, constructed with the predicted replication
AB  - elements of single rep or rep combined with parAB loci from the three plasmids were shown to
AB  - successfully transform into both saprophytic and pathogenic Leptospira species, suggesting an
AB  - essential function for rep genes in supporting auto-replication of the plasmids. Additionally,
AB  - a wide distribution of homologs of the three rep genes was identified in L. interrogans
AB  - isolates, and correlation tests showed that the transformability of the shuttle vectors in L.
AB  - interrogans isolates depended, to certain extent, on genetic compatibility between the rep
AB  - sequences of both plasmid and host. Conclusions: Three extrachromosomal replicons co-exist in
AB  - L. interrogans, one of which we consider to be an inducible prophage. The vectors constructed
AB  - with the rep genes of the three replicons successfully transformed into saprophytic and
AB  - pathogenic Leptospira species alike, but this was partly dependent on genetic compatibility
AB  - between the rep sequences of both plasmid and host.
ER  -

TY  - JOUR
AU  - Zhu, X.
AU  - Wang, W.
AU  - Xu, P.
AU  - Tang, H.
TI  - Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium.
JO  - Genome Announcements
PY  - 2016
SP  - e00666
EP  - e00616
VL  - 4
AB  - Sphingomonas sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from
AB  - tobacco leaves. Here, we present the complete genome sequence of
AB  - strain NIC1, which contains one circular chromosome and two circular plasmids.
AB  - The genomic information will provide insights into its molecular mechanism for
AB  - nicotine degradation.
ER  -

TY  - JOUR
AU  - Zhu, Y.
AU  - Chen, P.
AU  - Bao, Y.
AU  - Men, Y.
AU  - Zeng, Y.
AU  - Yang, J.
AU  - Sun, J.
AU  - Sun, Y.
TI  - Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation.
JO  - Sci. Rep.
PY  - 2016
SP  - 38248
EP  - 38248
VL  - 6
AB  - A novel marine strain representing efficient degradation ability toward brown
AB  - algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The
AB  - alga-associated marine bacteria promote the nutrient cycle and perform important
AB  - functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis
AB  - Alg07 genome was carried out. Results of gene annotation and carbohydrate-active
AB  - enzyme analysis showed that the strain harbored enzymes that can completely
AB  - degrade alginate and laminarin, which are the specific polysaccharides of brown
AB  - algae. We also found genes for the utilization of mannitol, the major storage
AB  - monosaccharide in the cell of brown algae. To understand the process of brown
AB  - algae decomposition by B. weihaiensis Alg07, RNA-seq transcriptome analysis and
AB  - qRT-PCR were performed. The genes involved in alginate metabolism were all
AB  - up-regulated in the initial stage of kelp degradation, suggesting that the strain
AB  - Alg07 first degrades alginate to destruct the cell wall so that the laminarin and
AB  - mannitol are released and subsequently decomposed. The key genes involved in
AB  - alginate and laminarin degradation were expressed in Escherichia coli and
AB  - characterized. Overall, the model of brown algae degradation by the marine strain
AB  - Alg07 was established, and novel alginate lyases and laminarinase were
AB  - discovered.
ER  -

TY  - JOUR
AU  - Zhu, Y.
AU  - Fang, D.
AU  - Shi, D.
AU  - Li, A.
AU  - Lv, L.
AU  - Yan, R.
AU  - Yao, J.
AU  - Hua, D.
AU  - Hu, X.
AU  - Guo, F.
AU  - Wu, W.
AU  - Guo, J.
AU  - Chen, Y.
AU  - Jiang, X.
AU  - Chen, X.
AU  - Li, L.
TI  - Draft Genome Sequence of Lactobacillus panis DSM 6035T, First Isolated from Sourdough.
JO  - Genome Announcements
PY  - 2015
SP  - e00778
EP  - e00715
VL  - 3
AB  - We report a draft genome sequence of Lactobacillus panis DSM 6035(T), isolated from sourdough.
AB  - The genome of this strain is 2,082,789 bp long, with 47.9% G+C
AB  - content. A total of 2,047 protein-coding genes were predicted.
ER  -

TY  - JOUR
AU  - Zhu, Y.
AU  - He, Y.
AU  - Zheng, Z.
AU  - Chen, J.
AU  - Wang, Z.
AU  - Zhou, G.
TI  - Draft Genome Sequence of Rice Orange Leaf Phytoplasma from Guangdong, China.
JO  - Genome Announcements
PY  - 2017
SP  - e00430
EP  - e00417
VL  - 5
AB  - The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, China, was
AB  - sequenced. The draft LD1 genome is 599,264 bp, with a G+C
AB  - content of 28.2%, 647 predicted open reading frames, and 33 RNA genes.
ER  -

TY  - JOUR
AU  - Zhu, Y.
AU  - Shang, H.
AU  - Zhu, Q.
AU  - Ji, F.
AU  - Wang, P.
AU  - Fu, J.
AU  - Deng, Y.
AU  - Xu, C.
AU  - Ye, W.
AU  - Zheng, J.
AU  - Zhu, L.
AU  - Sun, M.
TI  - Complete Genome Sequence of Bacillus thuringiensis serovar. finitimus Strain YBT-020.
JO  - J. Bacteriol.
PY  - 2011
SP  - 2379
EP  - 2380
VL  - 193
AB  - Bacillus thuringiensis is a Gram-positive, spore-forming bacterium that forms parasporal
AB  - crystals at the onset of the sporulation phase of its growth. Here we report the complete
AB  - genome sequence of B. thuringiensis serovar. finitimus strain YBT-020, whose parasporal
AB  - crystals consist of Cry26Aa and Cry28Aa crystal proteins and are located between the
AB  - exosporium and the spore coat and remain adhering to the spore after sporulation.
ER  -

TY  - JOUR
AU  - Zhu, Y.
AU  - Zeng, H.
AU  - Gao, X.
AU  - Lu, Z.H.
TI  - Quantitative analysis of EcoR1 methylase-DNA complex by atomic force microscopy.
JO  - Scanning
PY  - 2006
SP  - 15
EP  - 19
VL  - 28
AB  - The EcoRI methylase specifically recognize 5'-GA*ATTC-3' in DNA duplex.  We directly applied
AB  - atomic force microscopy to investigate linear pBR322-EcoRI methylase complexes and
AB  - quantitatively analyzed the bend angles of linear pBR322-EcoRI methylse complexes and the
AB  - bound protein widths.  In this study, we made a novel observation that DNA-EcoRI methylase
AB  - complexes exhibited two populations of conformation at the recognition site: DNA was bent at
AB  - an acute
AB  - angle at the recognition site in the presence of one EcoRI methylase monomeric molecule, while
AB  - DNA was bent at an obtuse angle at the recognition site and the complementary site on duplex
AB  - DNAs in
AB  - the presence of EcoRI methylase dimer.  The data indicated that the obtuse angle state was
AB  - the result of unique interactions between EcoRI methylase and the recognition site and the
AB  - complementary site on duplex DNAs, and suggested that the acute angle conformation could be an
AB  - intermediate in the formation of the obtuse angle state.  Our works provide a detail insight
AB  - into the DNA structural variations involved in EcoRI methylase-binding processes and
AB  - demonstrate further the versatility of AFM as an imaging technique for studying the
AB  - interaction between large DNA fragment and protein.
ER  -

TY  - JOUR
AU  - Zhu, Z.
AU  - Guan, S.
AU  - Robinson, D.
AU  - El Fezzazi, H.
AU  - Quimby, A.
AU  - Xu, S.Y.
TI  - Characterization of cleavage intermediate and star sites of RM.Tth111II.
JO  - Sci. Rep.
PY  - 2014
SP  - 3838
EP  - 3838
VL  - 4
AB  - Tth111II is a thermostable Type IIGS restriction enzyme that recognizes DNA sites CAARCA (R =
AB  - A or G) and cleaves downstream at N11/N9. Here, the tth111IIRM gene
AB  - was cloned and expressed in E. coli, and Tth111II was purified. The purified
AB  - enzyme contains internally-bound S-adenosylmethionine (SAM). When the internal
AB  - SAM was removed, the endonuclease activity was stimulated by adding SAM or its
AB  - analog sinefungin. The cleavage intermediate is mostly top-strand nicked DNA on a
AB  - single-site plasmid. Addition of duplex oligos with a cognate site stimulates
AB  - cleavage activity of the one-site substrate. Tth111II cleaves a two-site plasmid
AB  - DNA with equal efficiency regardless of site orientation. We propose the
AB  - top-strand nicking is carried out by a Tth111II monomer and bottom-strand
AB  - cleavage is carried out by a transient dimer. Tth111II methylates cleavage
AB  - product-like duplex oligos CAAACAN9, but the modification rate is estimated to be
AB  - much slower than the top-strand nicking rate. We cloned and sequenced a number of
AB  - Tth111II star sites which are 1-bp different from the cognate sites. A
AB  - biochemical pathway is proposed for the restriction and methylation activities of
AB  - Tth111II.
ER  -

TY  - JOUR
AU  - Zhu, Z.
AU  - Pedamallu, C.S.
AU  - Fomenkov, A.
AU  - Benner, J.
AU  - Xu, S.Y.
TI  - Cloning of NruI and Sbo13I restriction and modification systems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases.
JO  - BMC Res. Notes
PY  - 2010
SP  - 139
EP  - 139
VL  - 3
AB  - ABSTRACT: BACKGROUND: NruI and Sbo13I are restriction enzyme isoschizomers
AB  - with the same recognition sequence 5' TCG downward arrowCGA 3' (cleavage
AB  - as indicated downward arrow). Here we report the cloning of NruI and
AB  - Sbo13I restriction-modification (R-M) systems in E. coli. The NruI
AB  - restriction endonuclease gene (nruIR) was cloned by PCR and inverse PCR
AB  - using primers designed from the N-terminal amino acid sequence. The NruI
AB  - methylase gene (nruIM) was derived by inverse PCR walking. RESULTS: The
AB  - amino acid sequences of NruI endonuclease and methylase are very similar
AB  - to the Sbo13I R-M system which has been cloned and expressed in E. coli by
AB  - phage selection of a plasmid DNA library. Dot blot analysis using rabbit
AB  - polyclonal antibodies to N6mA- or N4mC-modified DNA indicated that M.NruI
AB  - is possibly a N6mA-type amino-methyltransferase that most likely modifies
AB  - the external A in the 5' TCGCGA 3' sequence. M.Sbo13I, however, is
AB  - implicated as a probable N4mC-type methylase since plasmid carrying
AB  - sbo13IM gene is not restricted by Mrr endonuclease and Sbo13I digestion is
AB  - not blocked by Dam methylation of the overlapping site. The amino acid
AB  - sequence of M.NruI and M.Sbo13I did not show significant sequence
AB  - similarity to many known amino-methyltransferases in the alpha, beta, and
AB  - gamma groups, except to a few putative methylases in sequenced microbial
AB  - genomes. CONCLUSIONS: The order of the conserved amino acid motifs
AB  - (blocks) in M.NruI/M.Sbo13I is similar to the gamma. group
AB  - amino-methyltranferases, but with two distinct features: In motif IV, the
AB  - sequence is DPPY instead of NPPY; there are two additional conserved
AB  - motifs, IVa and Xa as extension of motifs IV and X, in this family of
AB  - enzymes. We propose that M.NruI and M.Sbo13I form a subgroup in the gamma
AB  - group of amino-methyltransferases.
ER  -

TY  - JOUR
AU  - Zhu, Z.
AU  - Samuelson, J.C.
AU  - Zhou, J.
AU  - Dore, A.
AU  - Xu, S.-y.
TI  - Engineering strand-specific DNA nicking enzymes from the type IIS restriction endonucleases BsaI, BsmBI, and BsmAI.
JO  - J. Mol. Biol.
PY  - 2004
SP  - 573
EP  - 583
VL  - 337
AB  - More than 80 type IIA/IIS restriction endonucleases with different recognition specificities
AB  - are now known. In contrast, only a limited number of strand-specific nicking endonucleases are
AB  - currently available. To overcome this limitation, a novel genetic screening method was devised
AB  - to convert type IIS restriction endonucleases into strand-specific nicking endonucleases. The
AB  - genetic screen consisted of four steps: (1) random mutagenesis to create a plasmid library,
AB  - each bearing an inactivated endonuclease gene; (2) restriction digestion of plasmids
AB  - containing the wild-type and the mutagenized endonuclease gene; (3) back-crosses with the
AB  - wild-type gene by ligation to the wild-type N-terminal or C-terminal fragment; (4)
AB  - transformation of the ligated DNA into a pre-modified host and screening for nicking
AB  - endonuclease activity in total cell culture or cell extracts of the transformants. Nt.BsaI and
AB  - Nb.BsaI nicking endonucleases were isolated from BsaI using this genetic screen. In addition,
AB  - site-directed mutagenesis was carried out to isolate BsaI nicking variants with minimal
AB  - double-stranded DNA cleavage activity. The equivalent amino acid substitutions were introduced
AB  - into BsmBI and BsmAI restriction endonucleases with similar recognition sequence and
AB  - significant amino acid sequence identity and their nicking variants were successfully
AB  - isolated. This work provides strong evidence that some type IIS restriction endonucleases
AB  - carry two separate active sites. When one of the active sites is inactivated, the type IIS
AB  - restriction endonuclease may nick only one strand.
ER  -

TY  - JOUR
AU  - Zhu, Z.Y.
AU  - Zhou, J.
AU  - Friedman, A.M.
AU  - Xu, S.Y.
TI  - Isolation of BsoBI restriction endonuclease variants with altered substrate specificity.
JO  - J. Mol. Biol.
PY  - 2003
SP  - 359
EP  - 372
VL  - 330
AB  - BsoBI is a thermophilic restriction endonuclease that cleaves the degenerate DNA sequence
AB  - C/PyCGPuG (where/=the cleavage site and Py=C or T,
AB  - Pu=A or G). In the BsoBI-DNA co-crystal structure the D246 residue makes a
AB  - water-mediated hydrogen bond to N6 of the degenerate base adenine and was
AB  - proposed to make a complementary bond to O6 of the alternative guanine
AB  - residue. To investigate the substrate specificity conferred by D246 and to
AB  - potentially alter BsoBI specificity, the D246 residue was changed to the
AB  - other 19 amino acids. Variants D246A, D246C, D246E, D246R, D246S, D246T,
AB  - and D246Y were purified and their cleavage activity determined. Variants
AB  - D246A, D246S, and D246T display 0.2% to 0.7% of the wild-type cleavage
AB  - activity. However, the substrate specificity of the three variants is
AB  - altered significantly. D246A, D246S, and D246T cleave CTCGAG sites poorly.
AB  - In filter binding assays using oligonucleotides, wild-type BsoBI shows
AB  - almost equal affinity for CTCGAG and CCCGGG sites. In contrast, the D246A
AB  - variant shows 70-fold greater binding affinity for the CCCGGG substrate.
AB  - Recycled mutagenesis was carried out on the D246A variant, and revertants
AB  - with enhanced activity were isolated by their dark blue phenotype on a
AB  - dinD Colon, two colons lacZ DNA damage indicator strain. Most of the amino
AB  - acid substitutions present within the revertants were located outside the
AB  - DNA-protein interface. This study demonstrates that endonuclease mutants
AB  - with altered specificity and non-lethal activity can be evolved towards
AB  - more active variants using a laboratory evolution strategy.
ER  -

TY  - JOUR
AU  - Zhu-Ge, X.
AU  - Jiang, J.
AU  - Pan, Z.
AU  - Hu, L.
AU  - Wang, S.
AU  - Wang, H.
AU  - Leung, F.C.
AU  - Dai, J.
AU  - Fan, H.
TI  - Comparative Genomic Analysis Shows That Avian Pathogenic Escherichia coli Isolate IMT5155 (O2:K1:H5; ST Complex 95, ST140) Shares Close Relationship with ST95 APEC O1:K1 and Human ExPEC O18:K1 Strains.
JO  - PLoS ONE
PY  - 2014
SP  - E112048
EP  - E112048
VL  - 9
AB  - Avian pathogenic E. coli and human extraintestinal pathogenic E. coli serotypes O1, O2 and O18
AB  - strains isolated from different hosts are generally located in
AB  - phylogroup B2 and ST complex 95, and they share similar genetic characteristics
AB  - and pathogenicity, with no or minimal host specificity. They are popular objects
AB  - for the study of ExPEC genetic characteristics and pathogenesis in recent years.
AB  - Here, we investigated the evolution and genetic blueprint of APEC pathotype by
AB  - performing phylogenetic and comparative genome analysis of avian pathogenic E.
AB  - coli strain IMT5155 (O2:K1:H5; ST complex 95, ST140) with other E. coli
AB  - pathotypes. Phylogeny analyses indicated that IMT5155 has closest evolutionary
AB  - relationship with APEC O1, IHE3034, and UTI89. Comparative genomic analysis
AB  - showed that IMT5155 and APEC O1 shared significant genetic overlap/similarities
AB  - with human ExPEC dominant O18:K1 strains (IHE3034 and UTI89). Furthermore, the
AB  - unique PAI I5155 (GI-12) was identified and found to be conserved in APEC O2
AB  - serotype isolates. GI-7 and GI-16 encoding two typical T6SSs in IMT5155 might be
AB  - useful markers for the identification of ExPEC dominant serotypes (O1, O2, and
AB  - O18) strains. IMT5155 contained a ColV plasmid p1ColV5155, which defined the APEC
AB  - pathotype. The distribution analysis of 10 sequenced ExPEC pan-genome virulence
AB  - factors among 47 sequenced E. coli strains provided meaningful information for B2
AB  - APEC/ExPEC-specific virulence factors, including several adhesins, invasins,
AB  - toxins, iron acquisition systems, and so on. The pathogenicity tests of IMT5155
AB  - and other APEC O1:K1 and O2:K1 serotypes strains (isolated in China) through four
AB  - animal models showed that they were highly virulent for avian colisepticemia and
AB  - able to cause septicemia and meningitis in neonatal rats, suggesting zoonotic
AB  - potential of these APEC O1:K1 and O2:K1 isolates.
ER  -

TY  - JOUR
AU  - Zhuang, W.
AU  - Zhang, S.
AU  - Xia, X.
AU  - Wang, G.
TI  - Draft genome sequence of T26 and comparative analysis of six genomes.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 104
EP  - 104
VL  - 10
AB  - Most Cellulomonas strains are cellulolytic and this feature may be applied in straw
AB  - degradation and bioremediation. In this study, Cellulomonas carbonis T26T,
AB  - Cellulomonas bogoriensis DSM 16987T and Cellulomonas cellasea 20108T were
AB  - sequenced. Here we described the draft genomic information of C. carbonis T26T
AB  - and compared it to the related Cellulomonas genomes. Strain T26T has a 3,990,666
AB  - bp genome size with a G + C content of 73.4 %, containing 3418 protein-coding
AB  - genes and 59 RNA genes. The results showed good correlation between the genotypes
AB  - and the physiological phenotypes. The information are useful for the better
AB  - application of the Cellulomonas strains.
ER  -

TY  - JOUR
AU  - Zhuo, W.
AU  - Lai, X.
AU  - Zhang, L.
AU  - Chan, S.-H.
AU  - Li, F.
AU  - Zhu, Z.
AU  - Yang, M.
AU  - Sun, D.
TI  - Elimination of inter-domain interactions increases the cleavage fidelity of the restriction endonuclease DraIII.
JO  - Protein Cell
PY  - 2014
SP  - 357
EP  - 368
VL  - 5
AB  - DraIII is a type IIP restriction endonucleases (REases) that recognizes and creates a double
AB  - strand break within the gapped palindromic sequence CACa dagger NNNa dagger'GTG of
AB  - double-stranded DNA (a dagger indicates nicking on the bottom strand; a dagger' indicates
AB  - nicking on the top strand). However, wild type DraIII shows significant star activity. In this
AB  - study, it was found that the prominent star site is CATa dagger GTTa dagger'GTG, consisting
AB  - of a star 5' half (CAT) and a canonical 3' half (GTG). DraIII nicks the 3' canonical half
AB  - site at a faster rate than the 5' star half site, in contrast to the similar rate with the
AB  - canonical full site. The crystal structure of the DraIII protein was solved. It indicated, as
AB  - supported by mutagenesis, that DraIII possesses a beta beta I +/--metal HNH active site. The
AB  - structure revealed extensive intra-molecular interactions between the N-terminal domain and
AB  - the C-terminal domain containing the HNH active site. Disruptions of these interactions
AB  - through site-directed mutagenesis drastically increased cleavage fidelity. The understanding
AB  - of fidelity mechanisms will enable generation of high fidelity REases.
ER  -

TY  - JOUR
AU  - Zhuo, Y.
AU  - Liu, L.
AU  - Wang, Q.
AU  - Liu, X.
AU  - Ren, B.
AU  - Liu, M.
AU  - Ni, P.
AU  - Cheng, Y.Q.
AU  - Zhang, L.
TI  - Revised Genome Sequence of Burkholderia thailandensis MSMB43 with Improved Annotation.
JO  - J. Bacteriol.
PY  - 2012
SP  - 4749
EP  - 4750
VL  - 194
AB  - There is growing interest in discovery of novel bioactive natural products from Burkholderia
AB  - thailandensis. Here we report a significantly improved genome
AB  - sequence and reannotation of Burkholderia thailandensis MSMB43, which will
AB  - facilitate the discovery of new natural products through genome mining and
AB  - studies of the metabolic versatility of this bacterium.
ER  -

TY  - JOUR
AU  - Zhuravleva, L.I.
AU  - Oreshkin, E.N.
TI  - The effect of cultivation conditions and ultrasonic destruction of Streptomyces achromogenes ATCC 12767 cells on the yield of restriction endonucleases.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1985
SP  - 401
EP  - 406
VL  - 21
AB  - The effect of the cultivation time, aeration rate and nutrient medium
AB  - composition on the yield of the restrictase activity of the submerged culture
AB  - of Streptomyces achromogenes ATCC 12767 was investigated.  A maximum value of
AB  - the specific restrictase activity was observed in the second part of the
AB  - exponential phase of growth (after 22-24 hours of cultivation).  An optimal
AB  - composition of the nutrient medium for cultivation of S. achromogenes was found
AB  - using mathematical methods of experiment planning.  The medium includes (g/l):
AB  - glucose-10.0; peptone-4.0; yeast extract-4.0; MgSO4.7H2O-0.5; K2HPO4-4.0;
AB  - KH2PO4-2.0.  An addition of detergents to the buffer during ultrasonic
AB  - destruction of S. achromogenes cells enabled the yield of the restrictase
AB  - activity to be increased more than twice.
ER  -

TY  - JOUR
AU  - Zhuravleva, L.I.
AU  - Oreshkin, E.N.
AU  - Bezborodov, A.M.
TI  - Isolation and purification of restriction endonuclease SacI from Streptomyces achromogenes ATCC 12767.
JO  - Prikl. Biokhim. Mikrobiol.
PY  - 1987
SP  - 208
EP  - 215
VL  - 23
AB  - A procedure for isolation and purification of restriction endonuclease SacI
AB  - from Streptomyces achromogenes ATCC 12767 is proposed.  It allows to obtain an
AB  - electrophoretically homogeneous enzyme yield by activity 3.7%.  The molecular
AB  - weight of SacI was found to be 52,000 +/-5000 D, and isoelectric point 6.2.
AB  - The enzyme consists of two subunits, which was found by polyacrylamide gel
AB  - electrophoresis under denaturing conditions.  Km and Vmax values were
AB  - determined for the enzymatic reaction; they are equal to 4.6x10-9 M and
AB  - 9.19x10-10 M/min, respectively.
ER  -

TY  - JOUR
AU  - Zhurina, D.
AU  - Dudnik, A.
AU  - Waidmann, M.S.
AU  - Grimm, V.
AU  - Westermann, C.
AU  - Breitinger, K.J.
AU  - Yuan, J.
AU  - van Sinderen, D.
AU  - Riedel, C.U.
TI  - High-Quality Draft Genome Sequence of Bifidobacterium longum E18, Isolated from a Healthy Adult.
JO  - Genome Announcements
PY  - 2013
SP  - e01084
EP  - e01013
VL  - 1
AB  - Bifidobacteria are important gastrointestinal commensals of a number of animals,  including
AB  - humans, and various beneficial effects on host health have been
AB  - attributed to them. Here, we announce the noncontiguous finished genome sequence
AB  - of Bifidobacterium longum E18, isolated from a healthy adult, which reveals
AB  - traits involved in its interaction with the host.
ER  -

TY  - JOUR
AU  - Zhurina, D.
AU  - Zomer, A.
AU  - Gleinser, M.
AU  - Brancaccio, V.F.
AU  - Auchter, M.
AU  - Waidmann, M.S.
AU  - Westermann, C.
AU  - van Sinderen, D.
AU  - Riedel, C.U.
TI  - Complete genome sequence of Bifidobacterium bifidum S17.
JO  - J. Bacteriol.
PY  - 2010
SP  - 301
EP  - 302
VL  - 193
AB  - Here, we report on the first completely annotated genome sequence of a Bifidobacterium bifidum
AB  - strain. B. bifidum S17, isolated from faeces of a
AB  - breast-fed infant, was shown to strongly adhere to intestinal epithelial
AB  - cells and has potent anti-inflammatory activity in vitro and in vivo. The
AB  - genome sequence will provide new insights into the biology of this
AB  - potential probiotic organism and allow for the characterization of the
AB  - molecular mechanisms underlying its beneficial properties.
ER  -

TY  - JOUR
AU  - Zieger, M.
AU  - Patillon, M.
AU  - Roizes, G.
AU  - Lerouge, T.
AU  - Dupret, D.
AU  - Jeltsch, J.M.
TI  - Two restriction endonucleases from Bacillus sphaericus:  BspXI and BspXII.
JO  - Nucleic Acids Res.
PY  - 1987
SP  - 3919
EP  - 3919
VL  - 15
AB  - In screening wild strains of Bacillus sphaericus, one, which we call X -not totally
AB  - identifiable when compared to well established strains- exhibited a high yield of two
AB  - restriction endonucleases: BspXI and BspXII. A cleared sonic extract, obtained from 12 grams
AB  - of frozen cells yielded as much as 500,000 units of each enzyme by the following steps of
AB  - chromatography and dialysis [against PC buffer (10% glycerol, 10 mM KPO4-pH 7.4, 10 mM
AB  - B-mercaptoethanol, 0.1 mM EDTA)]. (I) A Biogel A-0.5 m filtration (II) Dialysis of active
AB  - fractions (III) DEAE Sephacel chromatography: a gradient elution from 0 to 1 M NaCl gave pool
AB  - I (0-0.5 M NaCl) and pool II (0.5-1 M NaCl). (IV-VI) Dialysed pool I was loaded on
AB  - phosphocellulose column and eluted with a 0 to 1 M KCl gradient; the fraction at 0.55 M KCl
AB  - was dialysed and the phosphocellulose chromatographic step repeated, yielding, at 0.55 M KCl,
AB  - a pure BspXI fraction. (VII) Dialysed pool II was applied on a Blue Trisacryl column and
AB  - eluted with a 0 to 0.5 M KCl gradient giving, at 0.3 M KCl, a pure BspXII fraction. The
AB  - digestion patterns of different DNAs (k, pBR322 and Ad2) with BspXI and BspXII were identical
AB  - to those obtained with ClaI and BclI, respectively, or with BspXI + ClaI and BspXII + BclI. It
AB  - was therefore concluded that BspXI and BspXII are isoschizomers of ClaI (5'-AT/CGAT-3') and
AB  - BclI (5'-T/GATCA-3') respectively (1,2). BspXI was further investigated using: [a] standard
AB  - procedures (3) to determine the cleavage site at the nucleotide level and [b] a recombinant
AB  - DNA (4) that contains a ClaI recognition sequence cleaved by the enzyme only when it is
AB  - produced in an E. coli dam- strain. Since BspXI behaves exactly like ClaI (sensitive to
AB  - N6-adenine methylation - generates 5' protruding dinucleotide CG), BspXI is a full
AB  - isoschizomer of ClaI with the property that this new enzyme is able to cleave DNA at 37C in
AB  - standard buffers containing from 0 to 200 mM NaCl without any noticeable loss of activity.
ER  -

TY  - JOUR
AU  - Ziegler, M.
AU  - Jang, H.
AU  - Gopinath, G.
AU  - Horlbog, J.A.
AU  - Stephan, R.
AU  - Guldimann, C.
TI  - Whole-Genome Shotgun Sequencing of Three Listeria monocytogenes Strains Isolated  from a Ready-to-Eat Salad-Producing Facility in Switzerland.
JO  - Genome Announcements
PY  - 2018
SP  - e00547
EP  - e00518
VL  - 6
AB  - Ready-to-eat (RTE) raw foods harbor the risk of transmitting Listeria monocytogenes from the
AB  - environment to the consumer. We isolated three strains
AB  - from a facility producing RTE salad. These strains were used to perform challenge
AB  - tests on different RTE salad products. Here, we present the shotgun genome
AB  - sequences of all three of these strains.
ER  -

TY  - JOUR
AU  - Zienkiewicz, M.
AU  - Kern-Zdanowicz, I.
AU  - Golebiewski, M.
AU  - Zylinska, J.
AU  - Mieczkowski, P.
AU  - Gniadkowski, M.
AU  - Bardowski, J.
AU  - Ceglowski, P.
TI  - Mosaic Structure of p1658/97, a 125-Kilobase Plasmid Harboring an Active Amplicon with the Extended-Spectrum -Lactamase Gene blaSHV-5.
JO  - Antimicrob. Agents Chemother.
PY  - 2007
SP  - 1164
EP  - 1171
VL  - 51
AB  - Escherichia coli isolates recovered from patients during a clonal outbreak
AB  - in a Warsaw, Poland, hospital in 1997 produced different levels of an
AB  - extended-spectrum beta-lactamase (ESBL) of the SHV type. The
AB  - beta-lactamase hyperproduction correlated with the multiplication of ESBL
AB  - gene copies within a plasmid. Here, we present the complete nucleotide
AB  - sequence of plasmid p1658/97 carried by the isolates recovered during the
AB  - outbreak. The plasmid is 125,491 bp and shows a mosaic structure in which
AB  - all modules constituting the plasmid core are homologous to those found in
AB  - plasmids F and R100 and are separated by segments of homology to other
AB  - known regions (plasmid R64, Providencia rettgeri genomic island R391,
AB  - Vibrio cholerae STX transposon, Klebsiella pneumoniae or E. coli
AB  - chromosomes). Plasmid p1658/97 bears two replication systems, IncFII and
AB  - IncFIB; we demonstrated that both are active in E. coli. The presence of
AB  - an active partition system (sopABC locus) and two postsegregational
AB  - killing systems (pemIK and hok/sok) indicates that the plasmid should be
AB  - stably maintained in E. coli populations. The conjugative transfer is
AB  - ensured by the operons of the tra and trb genes. We also demonstrate that
AB  - the plasmidic segment undergoing amplification contains the blaSHV-5 gene
AB  - and is homologous to a 7.9-kb fragment of the K. pneumoniae chromosome.
AB  - The amplicon displays the structure of a composite transposon of type I.
ER  -

TY  - JOUR
AU  - Zilli, J.E.
AU  - Passos, S.R.
AU  - Leite, J.
AU  - Xavier, G.R.
AU  - Rumjaneck, N.G.
AU  - Simoes-Araujo, J.L.
TI  - Draft Genome Sequence of Microvirga vignae Strain BR 3299T, a Novel Symbiotic Nitrogen-Fixing Alphaproteobacterium Isolated from a Brazilian Semiarid Region.
JO  - Genome Announcements
PY  - 2015
SP  - e00700
EP  - e00715
VL  - 3
AB  - Microvirga vignae is a recently described species of root-nodule bacteria isolated from
AB  - cowpeas grown in a Brazilian semiarid region. We report here the
AB  - 6.4-Mb draft genome sequence and annotation of M. vignae type strain BR 3299.
AB  - This genome information may help to understand the mechanisms underlying the
AB  - ability of the organism to grow under drought and high-temperatures conditions.
ER  -

TY  - JOUR
AU  - Zimmerly, S.
AU  - Guo, H.
AU  - Eskes, R.
AU  - Yang, J.
AU  - Perlman, P.S.
AU  - Lambowitz, A.M.
TI  - A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility.
JO  - Cell
PY  - 1995
SP  - 529
EP  - 538
VL  - 83
AB  - The mobility (homing) of the yeast mitochondrial DNA group II intron aI2 occurs via target
AB  - DNA-primed reverse transcription at a double-strand break in the recipient DNA.  Here, we show
AB  - that the site-specific DNA endonuclease that makes the double-strand break is a
AB  - ribonucleoprotein complex containing the aI2-encoded reverse transcriptase protein and excised
AB  - at aI2 RNA.  Remarkably, the aI2 RNA catalyzes cleavage of the sense strand of the recipient
AB  - DNA, while the AI2 protein appears to cleave the antisense strand.  The RNA-catalyzed sense
AB  - strand cleavage occurs via a partial reverse splicing reaction in which the protein component
AB  - stabilizes the active intron structure and appears to confer preference for DNA substrates.
AB  - Our results demonstrate a biologically relevant ribozyme reaction with a substrate other than
AB  - RNA.
ER  -

TY  - JOUR
AU  - Zimmerly, S.
AU  - Guo, H.
AU  - Perlman, P.S.
AU  - Lambowitz, A.M.
TI  - Group II intron mobility occurs by target DNA-primed reverse transcription.
JO  - Cell
PY  - 1995
SP  - 545
EP  - 554
VL  - 82
AB  - Mobile group II introns encode reverse transcriptases and insert site specifically into
AB  - intronless alleles (homing).  Here, in vitro experiments show that homing of the yeast mtDNA
AB  - group II intron aI2 occurs by reverse transcription at a double-strand break in the recipient
AB  - DNA.  A site-specific endonuclease cleaves the antisense strand of recipient DNA at position
AB  - +10 of exon 3 and the sense strand at the intron insertion site.  Reverse transcription of
AB  - aI2-containing pre-mRNA is primed by the antisense strand cleaved in exon 3 and results in
AB  - cotransfer of the intron and flanking exon sequences.  Remarkably, the DNA endonuclease that
AB  - initiates homing requires both the AI2 reverse transcriptase protein and aI2 RNA.  Parallels
AB  - in their reverse transcription mechanisms raise the possibility that mobile group II introns
AB  - were ancestors of nuclear non-long terminal repeat retrotransposons and telomerases.
ER  -

TY  - JOUR
AU  - Zimmerly, S.
AU  - Moran, J.V.
AU  - Perlman, P.S.
AU  - Lambowitz, A.M.
TI  - Group II intron reverse transcriptase in yeast mitochondria.  Stabilization and regulation of reverse transcriptase activity by the intron RNA.
JO  - J. Mol. Biol.
PY  - 1999
SP  - 473
EP  - 490
VL  - 289
AB  - Group II introns encode reverse transcriptases that function in both intron mobility and RNA
AB  - splicing. The proteins bind specifically to unspliced precursor RNA to promote splicing, and
AB  - then remain associated with the excised intron to form a DNA endonuclease that mediates intron
AB  - mobility by target DNA-primed reverse transcription. Here, immunoblotting and UV cross-linking
AB  - experiments show that the reverse transcriptase activity encoded by the yeast mtDNA group II
AB  - intron aI2 is associated with an intron-encoded protein of 62 kDa (p62). p62 is bound tightly
AB  - to endogenous RNAs in mitochondrial ribonucleoprotein particles, and the reverse transcriptase
AB  - activity is rapidly and irreversibly lost when the protein is released from the endogenous
AB  - RNAs by RNase digestion. Non-denaturing gel electrophoresis and activity assays show that the
AB  - aI2 reverse transcriptase is associated predominantly with the excised intron RNA, while a
AB  - smaller amount is associated with unspliced precursor RNA, as expected from the role of the
AB  - protein in RNA splicing. Although the reverse transcriptase in wild-type yeast strains is
AB  - bound tightly to endogenous RNAs, it is regulated so that it does not copy these RNAs unless a
AB  - suitable DNA oligonucleotide primer or DNA target site is provided. Certain mutations in the
AB  - intron-encoded protein or RNA circumvent this regulation and activate reverse transcription of
AB  - endogenous RNAs in the absence of added primer.  Although p62 is bound to unspliced precursor
AB  - RNA in position to initiate cDNA synthesis in the 3' exon, the major template for target
AB  - DNA-primed reverse transcription in vitro is the reverse-spliced intron RNA, as found
AB  - previously for aI1. Together, our results show that binding to intron-containing RNAs
AB  - stabilizes and regulates the activity of p62.
ER  -

TY  - JOUR
AU  - Zimmerman, W.J.
AU  - Culley, D.E.
TI  - Genetic variation at the apcAB, cpcAB, gvpA1, and nifH loci and in DNA methylation among N2-fixing cyanobacteria designated Nostoc punctiforme.
JO  - Microb. Ecol.
PY  - 1991
SP  - 199
EP  - 209
VL  - 21
AB  - Genetic similarity among cyanobacteria of a morphological subgroup of Nostoc was evaluated
AB  - through a comparison of several specific genes and the extent of DNA methylation.  Four of six
AB  - cyanobacteria were originally cultured from facultative symbioses with higher plants (Gunnera
AB  - and Encephalartos); these and one free-living isolate had been identified or repute to be N.
AB  - punctiforme.  No consistent correlation to species or symbiotic history was found from DNA
AB  - hybridizations to genes coding for phycocyanin, allophycocyanin, gas vesicle protein, and
AB  - dinitrogenase reductase.  One gene (gvpC) was not present, and gvpA1 was a single-copy gene in
AB  - all strains.  The gas vesicle genes were concluded to be potentially useful for broadly
AB  - characterizing Nostoc or at least this subgroup.  Incubations of Nostoc genomic DNA with 22
AB  - restriction endonucleases indicated a higher degree of methylation and similarity of its
AB  - methylated DNA to that of other heterocystous cyanobacteria.  The genetic variation of the
AB  - Nostoc isolates was judged to reflect primarily different soil origins.
ER  -

TY  - JOUR
AU  - Zimmermann, C.
AU  - Guhl, E.
AU  - Graessmann, A.
TI  - Mouse DNA methyltransferase (MTase) deletion mutants that retain the catalytic domain display neither de novo nor maintenance methylation activity in vivo.
JO  - Biol. Chem.
PY  - 1997
SP  - 393
EP  - 405
VL  - 378
AB  - The mammalian genome encodes a DNA cytosine-5-methyltransferase (MTase) of about 170 kDa that
AB  - is apparently responsible for both de novo and maintenance methylation at CpG sites.  Both
AB  - methylation activities have to be regulated accurately to ensure correct developmental and
AB  - cell type-specific gene activity.  Distorted DNA methylation patterns have been associated
AB  - with cell aging and diseases such as cancer and fragile X syndrome.  Structural and functional
AB  - in vitro studies of the mouse MTase have indicated that the enzyme has both a regulatory and a
AB  - catalytic region located in the N-terminal and C-terminal parts of the protein, respectively.
AB  - The regulatory region includes the nuclear localization signal (NLS), the sequence for DNA
AB  - targeting and the Zn-binding domain.  The catalytic domain carries the ten consensus sequence
AB  - motifs specific for all known pro- and eukaryotic DNA cytosine-5-methyltransferases.  In an
AB  - attempt to separate regulatory and catalytic functions of the enzyme in vivo, we have tested
AB  - various deletion mutations by means of transient and stable cell transfection experiments.
AB  - Expression of the transgenes, all of which retained the C-terminal catalytic domain, was
AB  - monitored by immunofluorescence staining, Northern blot analysis and SDS gel electrophoresis.
AB  - Despite high levels of transgene expression, the truncated MTase molecules exhibited neither
AB  - de novo nor maintenance methylation activity.  These findings might indicate that in vivo, an
AB  - efficient control mechanism prevents the ectopic activity of the DNA Mtase that is
AB  - structurally compromised in its N-terminal regulatory region.
ER  -

TY  - JOUR
AU  - Zimmermann, K.
AU  - Schogl, D.
AU  - Mannhalter, J.W.
TI  - Digestion of terminal restriction endonuclease recognition sites on PCR products.
JO  - Biotechniques
PY  - 1998
SP  - 582
EP  - 584
VL  - 24
AB  - One of the common methods for cloning polymerase chain reaction products is overhanging-end
AB  - cloning (also known as sticky-end or directional cloning).  Frequently, it is not possible to
AB  - use restriction enzyme sites already present in the amplified product, and primers that encode
AB  - recognition sites of restriction endonucleases in addition to the specific sequence have to be
AB  - designed.  After amplification of the target sequence with these primers, the PCR products are
AB  - purified, digested with restriction enzymes and cloned into vectors treated with the same
AB  - enzymes.  However, it has been found that many restriction enzymes fail to cleave at the end
AB  - of PCR fragments.  To circumvent this problem, the addition of at least three more nucleotides
AB  - at the end of a restriction site was suggested.
ER  -

TY  - JOUR
AU  - Zingg, J.-M.
AU  - Jones, P.A.
TI  - Genetic and epigenetic aspects of DNA methylation on genome expression, evolution, mutation and carcinogenesis.
JO  - Carcinogenesis
PY  - 1997
SP  - 869
EP  - 882
VL  - 18
AB  - DNA methylation has at least two important roles in tumorigenesis.  The target cytosines (C*)
AB  - of (cytosine-5)-DNA methyltransferase (Mtase) are mutated to thymine (T) in ~30% of inherited
AB  - diseases and cancer, and genome-wide alterations of DNA methylation patterns occur at early
AB  - stages of tumor development.  Insight into the normal function of DNA methylation will provide
AB  - the knowledge to understand the origins of these aberrations and their importance for disease
AB  - initiation and progression.  Originally the aberrations seen in tumors were attributed to the
AB  - higher spontaneous deamination rate of 5-methylcytosine (5-mC) as compared with C and to
AB  - misregulation of the Mtase gene.  Recently, it has become clear that the Mtase can actively
AB  - participate in mutagenesis by enzymatically increasing both the rate of genetic and epigenetic
AB  - alterations.  Proteins that recognize and repair these alterations determine the frequency of
AB  - their fixation as disease causing mutations.  In addition, alterations in the metabolism of
AB  - S-adenosylmethionine can disturb DNA methylation by depleting the cofactor
AB  - S-adenosylmethionine or by increasing the level of metabolites acting as inhibtors of DNA
AB  - methylation.  This review concentrates on the normal role of DNA methylation in mammals and on
AB  - aberrations of DNA methylation in inherited disease and cancer.
ER  -

TY  - JOUR
AU  - Zingg, J.-M.
AU  - Shen, J.-C.
AU  - Jones, P.A.
TI  - Enzyme-mediated cytosine deamination by the bacterial methyltransferase M.MspI.
JO  - Biochem. J.
PY  - 1998
SP  - 223
EP  - 230
VL  - 332
AB  - Most prokaryotic (cytosine-5)-DNA methyltransferases increase the frequency of deamination at
AB  - the cytosine targeted for methylation in vitro in the absence of the cofactor
AB  - S-adenosyl-methionine or the reaction product S-adenosyl-homocysteine.  We show here that,
AB  - under the same in vitro conditions, the prokaryotic methyltransferase, M.MspI (from Moraxella
AB  - sp.), causes very few cytosine deaminations, suggesting a mechanism in which M.MspI may avoid
AB  - enzyme-mediated cytosine deamination.  Two analogues of AdoMet, sinefungin and
AB  - 5'-amino-5'-deoxyadenosine, greatly increased the frequency of cytosine deamination mediated
AB  - by M.MspI presumably by introducing a proton-donating amino group into the catalytic center,
AB  - thus facilitating the formation of an unstable enzyme-dihydrocytosine intermediate and
AB  - hydrolytic deamination.  Interestingly, two naturally occurring analogues, adenosine and
AB  - 5'-methylthio-5'-deoxyadenosine, which do not contain a proton-donating amino group, also
AB  - weakly increased the deamination frequency by M.MspI, even in the presence of AdoMet or
AB  - AdoHcy. These analogues may trigger a conformational change in the enzyme without completely
AB  - inhibiting the access of solvent water to the catalytic center, thus allowing hydrolytic
AB  - deamination of the enzyme-dihydrocytosine intermediate.  Under normal physiological conditions
AB  - the enzymes M.HpaII (from Haemophilus parainfluenzae), M.HhaI (from Haemophilus haemolytica)
AB  - and M.MspI all increased the in vivo deamination frequency at the target cytosines with
AB  - comparable efficiency.
ER  -

TY  - JOUR
AU  - Zingg, J.-M.
AU  - Shen, J.-C.
AU  - Yang, A.S.
AU  - Rapoport, H.
AU  - Jones, P.A.
TI  - Methylation inhibitors can increase the rate of cytosine deamination by (cytosine- 5)-DNA methyltransferase.
JO  - Nucleic Acids Res.
PY  - 1996
SP  - 3267
EP  - 3275
VL  - 24
AB  - The target cytosines of (cytosine-5)-DNA methyltransferases in prokaryotic
AB  - and eukaryotic DNA show increased rates of C->T transition mutations compared to non-
AB  - target cytosines.  These mutations are induced either by the spontaneous deamination of 5-
AB  - mC->T generating inefficiently repaired G:T rather than G:U mismatches, or by the
AB  - enzyme-induced C->U deamination which occurs under conditions of reduced levels of S-
AB  - adenosylmethionine (AdoMet) and S-adenosyl-homocysteine (AdoHcy).  We tested
AB  - whether various inhibitors of (cytosine-5)-DNA methyltransferases analogous to AdoMet
AB  - and AdoHcy would affect the rate of enzyme-induced deamination of the target cytosine by
AB  - M.HpaII and M.SssI.  Interestingly, we found two compounds, sinefungin and 5'-amino-
AB  - 5'-deoxyadenosine, that increased the rate of deamination 103-fold in the presence and
AB  - 104-fold in the absence of AdoMet and AdoHcy.  We have therefore identified the first
AB  - mutagenic compounds specific for the target sites of (cytosine-5)-DNA methyltransferases.
AB  - A number of analogs of AdoMet and AdoHcy have been considered as possible antiviral,
AB  - anticancer, antifungal and anti-parasitic agents.  Our findings show that chemotherapeutic
AB  - agents with affinities to the cofactor binding pocket of (cytosine-5)-DNA methyltransferase
AB  - should be tested for their potential mutagenic effects.
ER  -

TY  - JOUR
AU  - Zinkevich, V.
AU  - Heslop, P.
AU  - Glover, S.W.
AU  - Weiserova, M.
AU  - Hubacek, J.
AU  - Firman, K.
TI  - Mutation in the specificity polypeptide of the Type I restriction endonuclease R EcoK that affects subunit assembly.
JO  - J. Mol. Biol.
PY  - 1992
SP  - 597
EP  - 601
VL  - 227
AB  - We describe the isolation and characterization of a temperature-sensitive mutation within the
AB  - hsdS gene of the type I restriction and modification system EcoK. This mutation appears to
AB  - affect the ability of the HsdR subunit to interact with the HsdS subunit when forming an
AB  - active endonuclease. We discuss the possibility that this mutant, together with another
AB  - mutation described previously, may define a discontinuous domain, involved in protein-protein
AB  - interactions, within the HsdS polypeptide.
ER  -

TY  - JOUR
AU  - Zinkevich, V.
AU  - Popova, L.
AU  - Kryukov, V.
AU  - Abadjieva, A.
AU  - Bogdarina, I.
AU  - Janscak, P.
AU  - Firman, K.
TI  - The HsdR subunit of R.EcoR124II: cloning and over-expression of the gene and unexpected properties of the subunit.
JO  - Nucleic Acids Res.
PY  - 1997
SP  - 503
EP  - 510
VL  - 25
AB  - Type I restriction endonucleases are composed of three subunits, HsdR, HsdM and HsdS.  The
AB  - HsdR subunit is absolutely required for restriction activity; while an independent methylase
AB  - is composed of HsdM and HsdS subunits.  DNA cleavage is associated with a powerful ATPase
AB  - activity during which DNA is translocated by the enzyme prior to cleavage.  The presence of a
AB  - Walker type I ATP-binding site within the HsdR subunit suggested that the subunit may be
AB  - capable of independent enzymatic activity.  Therefore, we have, for the first time, cloned and
AB  - over-expressed the hsdR gene of the type IC restriction endonuclease EcoR124II.  The purified
AB  - HsdR subunit was found to be a soluble monomeric protein capable of DNA- and Mg2+-dependent
AB  - ATP hydrolysis.  The subunit was found to have a weak nuclease activity both in vivo and in
AB  - vitro, and to bind plasmid DNA; although was not capable of binding a DNA oligoduplex.  We
AB  - were also able to reconstitute the fully active endonuclease from purified M.EcoR124I and
AB  - HsdR.  This is the first clear demonstration that the HsdR subnit of a type I restriction
AB  - endonuclease is capable of independent enzyme activity, and suggests a mechanism for the
AB  - evolution of the endonuclease from the independent methylase.
ER  -

TY  - JOUR
AU  - Zinkevich, V.E.
AU  - Alekseev, A.M.
AU  - Tanyashin, V.I.
TI  - Influence of bacteriophage lambda ral gene on the level of synthesis of the restriction endonuclease EcoK beta-subunit.
JO  - Mol. Biol. (Mosk)
PY  - 1986
SP  - 1638
EP  - 1644
VL  - 20
AB  - E. coli hsd genes were subcloned from lambda 642 (ra1+) into the lambda
AB  - L47.1
AB  - vector (ra1- after replacement).  We investigated the influence of the bacteriophage lambda
AB  - ra1 gene
AB  - on the expression efficiency of hsdSk and hsdMk genes.  Its presence in vitro enhanced the
AB  - synthesis of the beta-subunit and hsdMk gene product.  Increased modification in vivo was
AB  - also
AB  - observed.  It is proposed that the increase in the modification rate of lambda-phage fully
AB  - unmodified DNA is connected with the appearance of E. coli DNA methylase consisting of
AB  - beta-
AB  - and gamma-subunits.
ER  -

TY  - JOUR
AU  - Zinkevich, V.E.
AU  - Solonin, A.S.
AU  - Bogdarina, I.G.
AU  - Tanyashin, V.I.
TI  - Cloning and restriction analysis of the BamHI-EcoRI fragment of DNA, containing genes of the hsd region of Escherichia coli.
JO  - Dokl. Akad. Nauk.
PY  - 1981
SP  - 216
EP  - 218
VL  - 259
ER  -

TY  - JOUR
AU  - Zinkevich, V.E.
AU  - Solonin, A.S.
AU  - Tanyashin, V.I.
AU  - Bayev, A.A.
TI  - Function of hsdS gene of E. coli K in recombinant plasmid containing the regulatory lambda phage region.
JO  - Dokl. Akad. Nauk.
PY  - 1982
SP  - 717
EP  - 721
VL  - 263
AB  - None
ER  -

TY  - JOUR
AU  - Zinkevich, V.E.
AU  - Weiserova, M.
AU  - Kryukov, V.M.
AU  - Hubacek, J.
TI  - A mutation that converts serine 340 of the HsdSK polypeptide to phenylalanine and its effects on restriction and modification in Escherichia coli K-12.
JO  - Gene
PY  - 1990
SP  - 125
EP  - 128
VL  - 90
AB  - A hybrid hsdS gene, encoding the HsdSts+d polypeptide, was constructed by joining the proximal
AB  - region of the wild-type (wt) hsdS sequence with the distal region of the hsdSts+d sequence, at
AB  - the hsdS BglII site. The hybrid hsdS-Sts+d gene exerts a trans-dominant effect on restriction
AB  - and modification, which points to the location of the temperature-sensitive (ts)
AB  - trans-dominant (+d) mutation in the gene hsdSts+d distal region. Sequencing of the region
AB  - downstream from the HindIII target in the Escherichia coli K-12 hsdSts+d mutant was carried
AB  - out. It is identical to the wt hsdS sequence (GenBank/EMBL accession number ECHSDK LV00288),
AB  - except for a single base-pair transition C1245 -> T. The results obtained support the idea
AB  - that the trans-dominant effect of the ts mutation described earlier is related to the single
AB  - base-pair transition in the nonhomologous region of the hsdSts+d sequence.
ER  -

TY  - JOUR
AU  - Zinkevich, V.E.
AU  - Zograf, Y.N.
AU  - Tanyashin, V.I.
TI  - Expression of the EcoK DNA-methylase genes cloned.
JO  - Dokl. Akad. Nauk.
PY  - 1985
SP  - 993
EP  - 995
VL  - 282
AB  - The present article gives results on in vivo and in vitro expression of genes
AB  - hsdSk and hsdMk, cloned in pBR322, and the possible involvement of the rho
AB  - factor in this process.
ER  -

TY  - JOUR
AU  - Zinkevich, V.E.
AU  - Zograf, Y.N.
AU  - Tanyashin, V.I.
TI  - The genes of EcoK DNA methylase:  cloning and expression.
JO  - Dokl. Akad. Nauk.
PY  - 1984
SP  - 1493
EP  - 1496
VL  - 279
AB  - None
ER  -

TY  - JOUR
AU  - Zinn, A.R.
AU  - Butow, R.A.
TI  - Nonreciprocal exchange between alleles of the yeast mitochondrial 21S rRNA gene:  kinetics and the involvement of a double-strand break.
JO  - Cell
PY  - 1985
SP  - 887
EP  - 895
VL  - 40
AB  - A 1.1 kb intron containing an open reading frame (ORF) in one allele (Omega+) of the yeast
AB  - mitochondrial 21S rRNA gene is nearly quantitatively inserted in crosses into a 21S rRNA
AB  - allele lacking that intron (Omega-). We have determined that this nonreciprocal exchange
AB  - initiates soon after cells fuse to form zygotes and is complete by 10-16 hr after mating. We
AB  - have discovered a unique in vivo double-strand cut in Omega- mitochondrial DNA (mtDNA) at or
AB  - near the site of intron insertion that is implicated in the process. Markers flanking the
AB  - intron insertion site are coconverted with frequencies inversely proportional to their
AB  - distance from that site. There is no net conversion of Omega- to Omega+ in crosses between
AB  - petites retaining these alleles, nor do we observe the unique double-strand cut in the mtDNA
AB  - from zygotes of such crosses. The data suggest that a translation product of the intron ORF is
AB  - required for the double-strand cut and nonreciprocal recombination at Omega.
ER  -

TY  - JOUR
AU  - Zinovev, V.V.
AU  - Kolesnikov, V.A.
AU  - Beznedelnaya, N.L.
AU  - Gilev, A.F.
AU  - Gorbunov, Y.A.
AU  - Popov, S.G.
AU  - Malygin, E.G.
TI  - Interaction of restrictase BamHI with synthetic substrates containing complete or partial recognition sites.
JO  - Mol. Biol. (Mosk)
PY  - 1984
SP  - 169
EP  - 175
VL  - 18
AB  - The cleavage of self-complementary oligodeoxyribonucleotides by restrictase
AB  - BamHI was studied.  Oligonucleotides containing the complete recognition
AB  - sequence GGATCC were cleaved by restrictase BamHI in accordance with the
AB  - established specificity of the enzyme.  The oligonucleotide TCCAGATCTGGA
AB  - contains part of the recognition sequence (GATC) in the middle of the chain and
AB  - separate halves of the sequence at each end.  Hydrolysis of this
AB  - oligonucleotide yields products which indicate the interaction of restrictase
AB  - BamHI with the composite recognition site GGA...TCC formed by the ends of two
AB  - separate substrate molecules.  The oligonucleotide was not cleaved at the GATC
AB  - sequence.  The results obtained support a symmetrical model for restrictase
AB  - interaction with DNA.  According to this model, n/2 of the nucleotides in the
AB  - recognition site bind to the enzyme.
ER  -

TY  - JOUR
AU  - Zinovev, V.V.
AU  - Kolesnikov, V.A.
AU  - Beznedelnaya, N.L.
AU  - Gorbunov, J.A.
AU  - Popov, S.G.
AU  - Malygin, E.G.
TI  - Restriction endonuclease BamHI interaction with a synthetic duplex containing half-size recognition sequences.
JO  - FEBS Lett.
PY  - 1981
SP  - 98
EP  - 100
VL  - 132
AB  - Restriction endonuclease BamHI is a site-specific deoxyribonuclease which
AB  - cleaves the phosphodiester bonds between the guanine residues within the duplex
AB  - DNA sequence 5'GGATCC   CCTAGG It is well known that restriction endonucleases
AB  - recognise and cleave relatively short synthetic duplexes containing appropriate
AB  - recognition sequence, therefore oligodeoxyribonucleotides called 'linkers' are
AB  - widely used for genetic manipulations.  On the other hand, the synthetic
AB  - oligonucleotides with defined sequences are useful tools to study mechanisms of
AB  - interaction of the enzymes with DNA.
ER  -

TY  - JOUR
AU  - Zinovev, V.V.
AU  - Ovechkina, L.G.
AU  - Malygin, E.G.
TI  - Stoichiometry of phage T4 Dam DNA (Adenine-N6)-methyltransferase binding with oligonucleotide substrates.
JO  - Mol. Biol. (Mosk)
PY  - 1996
SP  - 1203
EP  - 1208
VL  - 30
AB  - Phage T4 Dam DNA methyltransferase recognizes the GATC site and methylates the adenine.  The
AB  - stoichiometry of its complex with the substrate was assessed by gel filtration and sucrose
AB  - gradient ultracentrifugation.  The results obtained by both methods indicate that two enzyme
AB  - subunits bind with 32- and 20-bp DNA duplexes.
ER  -

TY  - JOUR
AU  - Zinovev, V.V.
AU  - Rechkunova, N.I.
AU  - Gorbunov, Y.A.
AU  - Buryanov, Y.I.
AU  - Malygin, E.G.
TI  - The significance of internucleotide phosphates and noncomplementary substitutions in the oligonucleotide substrates on the interaction with the DNA methylase Ecodam.
JO  - Biopol. Kletka
PY  - 1989
SP  - 22
EP  - 27
VL  - 5
AB  - Eco dam methylase was investigated for its interaction with different synthetic
AB  - oligonucleotide substrates containing some defects in the GATC sequence. The defects are as
AB  - follows: the absence of one or several nucleotide residues, the presence of 3'-phosphate
AB  - residue with CH3-S-group, noncomplementary substitution of A by G or of G by A in the
AB  - recognition site of methylase Eco dam. The presence of the 3'S-methyl thiophosphate residue
AB  - has no essential effect on the methylation of oligonucleotide complexes as compared to the
AB  - analogous complexes lacking internucleotide phosphate. The introduction of the
AB  - noncomplementary base pair in the recognition site results in the loss of substrate properties
AB  - of such imperfect duplexes.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Gorbunov, Y.A.
AU  - Malygin, E.G.
AU  - Kossykh, V.G.
AU  - Hattman, S.
TI  - Phage T4 DNA [N6-adenine] methyltransferase: Kinetic studies using oligonucleotides containing native or modified recognition sites.
JO  - Biol. Chem.
PY  - 1998
SP  - 481
EP  - 488
VL  - 379
AB  - The DNA-[N6-adenine] methyltransferase of T4 phage catalyzes methyl group transfer from
AB  - S-adenosyl-L-methionine to the N6-position of adenine in the palindromic sequence, GATC.  We
AB  - have investigated the effect of eliminating different structural components of the recognition
AB  - site on the ability of a substrate to be bound and methylated by T4 Dam.  For this purpose,
AB  - steady state binding (by gel shift assays) and kinetic parameters of methylation (using the
AB  - methyl donor, [3H-CH3]-AdoMet, at 25 C) were studied using various synthetic duplex
AB  - oligonucleotides containing some defect in the DNA-target site; e.g., the absence of an
AB  - internucleotide phosphate or a nucleotide(s) within the recognition site, or a single stranded
AB  - region.  The salient results are summarized as follows: (1) Addition of T4 Dam to a complete
AB  - reaction mixture (with a 20-mer duplex as substrate) resulted in a 'burst' of 3H-methylated
AB  - product, followed by a constant rate of product formation that reflected establishment of
AB  - steady-state conditions.  This suggests that the rate-limiting step is release of product
AB  - methylated DNA from the enzyme [and not the transfer of the methyl group].  (2) A number of
AB  - the defects in duplex structure had only weak influence on the binding and Km values, but
AB  - strongly reduced the kcat. At the same time, several poorly bound duplexes retained good
AB  - substrate characteristics, especially duplexes having uninterrupted GAT-sequences in both
AB  - strands.  Whereas having only one half of the recognition site element intact was sufficient
AB  - for stable complex formation, the catalytic turnover process had a strict requirement for an
AB  - uninterrupted GAT-sequence on both strands.  (3) There was no correlation between Km and
AB  - binding capability; the apparent Kd for some duplexes was 5-70 times higher than Km.  This
AB  - indicates that the T4 Dam methylation reaction cannot be explained by a simple Michaelian
AB  - scheme.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Hattman, S.
AU  - Malygin, E.G.
TI  - Molecular enzymology of phage T4 Dam DNA methyltransferase.
JO  - Mol. Biol. (Mosk)
PY  - 2004
SP  - 737
EP  - 751
VL  - 38
AB  - This review summarizes the results of a study of the molecular mechanisms of phage T4 DNA
AB  - adenine methyltransferase (T4Dam) action.
AB  - T4Dam [EC 2.1.1.72] catalyzes the transfer of a methyl group from
AB  - S-adenosyl-L-methionine (AdoMet) to N-6 of the adenine located in the
AB  - palindromic recognition site GATC. The subunit structure of T4Dam,
AB  - substrate-binding properties, and kinetic parameters of methylation of
AB  - a variety of native and modified oligonucleotide duplexes are
AB  - considered. A kinetic scheme of the reaction was proposed, assuming
AB  - that T4Dam is isomerized into a catalytically active form. The
AB  - mechanisms of DNA-induced dimerization of T4Dam, flipping of the target
AB  - base, reorientation of T4Dam on an asymmetrically methylated
AB  - recognition site, the effector action of substrates, and processive
AB  - methylation of extended DNA containing more than one specific site are
AB  - discussed. The results obtained for T4Dam may provide a better
AB  - understanding of the action mechanisms of other homologous enzymes
AB  - including, first and foremost, those of the vast Dam family.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Malygin, E.G.
TI  - DNA-[N4-Cytosine]-Methyltransferase from Bacillus amyloliquefaciens: Mechanism of Action Derived from Steady-State Kinetics.
JO  - Mol. Biol. (Mosk)
PY  - 2003
SP  - 128
EP  - 138
VL  - 37
AB  - Kinetic analysis of methyl group transfer from S-adenosyl-L-methionine (SAM) to the 5'-GGATCC
AB  - recognition site catalyzed by the
AB  - DNA-[N4-cytosine]-methyltransferase from Bacillus amyloliquefaciens [EC
AB  - 2.1.1.113] has shown that the dependence of the rate of methylation of the
AB  - 20-meric substrate duplex on SAM and DNA concentration are normally
AB  - hyperbolic, and the maximal rate is attained upon enzyme saturation with
AB  - both substrates. No substrate inhibition is observed even at
AB  - concentrations many times higher than the Km values (0.107 microM for DNA
AB  - and 1.45 microM for SAM), which means that no nonreactive enzyme-substrate
AB  - complexes are formed during the reaction. The overall pattern of product
AB  - inhibition corresponds to an ordered steady-state mechanism following the
AB  - sequence SAM decreases DNA decreases metDNA increases SAH increases
AB  - (S-adenosyl-L-homocysteine). However, more detailed numerical analysis of
AB  - the aggregate experimental data admits an alternative order of substrate
AB  - binding, DNA decreases SAM decreases, though this route is an order of
AB  - magnitude slower.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Malygin, E.G.
AU  - Schlagman, S.L.
AU  - Hattman, S.
TI  - Bacteriophage T4 dam DNA-[N6-adenine] methyltransferase: Processivity and orientation to the methylation target.
JO  - J. Biol. Chem.
PY  - 2002
SP  - 7829
EP  - 7833
VL  - 278
AB  - We carried out steady state and pre-steady state (burst) kinetic analyses of the bacteriophage
AB  - T4 Dam DNA-[N(6)-adenine] methyltransferase (MTase) mediated methyl group transfer from
AB  - S-adenosyl-L-methionine (AdoMet) to Ade in oligonucleotide duplexes containing one or two
AB  - specific GATC sites with different combinations of methylated and unmodified targets. We
AB  - compared the results for ligated 40-mer duplexes with those of mixtures of the two unligated
AB  - duplexes used to generate the 40-mers. The salient results are as follows: (i) T4 Dam MTase
AB  - modifies 40-mer duplexes in a processive fashion. (ii) During processive movement, T4 Dam
AB  - rapidly exchanges product S-adenosyl-L-homocysteine (AdoHcy) for substrate AdoMet without
AB  - dissociating from the DNA duplex. (iii) T4 Dam processivity is consistent with an ordered
AB  - bi-bi mechanism AdoMet{downward arrow}DNA{downward arrow}DNA(Me){upward arrow}AdoHcy{upward
AB  - arrow}. However, in contrast to the steady state, here DNA(Me){upward arrow} signifies
AB  - departure from a methylated site GMTC{upward arrow}without physically dissociating from the
AB  - DNA. (iv) Following methyl transfer at one site and linear diffusion to a hemi-methylated
AB  - site, a reconstituted T4 Dam-AdoMet complex rapidly reorients itself to the (productive)
AB  - unmethylated strand. T4 Dam-AdoHcy can not reorient at an enzymatically created GMTC site. (v)
AB  - The inhibition potential of fully methylated sites 5'-GMTC/5'-GMTC is much lower for a long
AB  - DNA molecule compared to short single-site duplexes.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Evdokimov, A.A.
AU  - Malygin, E.G.
AU  - Sclavi, B.
AU  - Buckle, M.
AU  - Hattman, S.
TI  - Differential methylation kinetics of individual target site strands by T4Dam DNA methyltransferase.
JO  - Biol. Chem.
PY  - 2007
SP  - 1199
EP  - 1207
VL  - 388
AB  - Prokaryote DNA methyltransferases (MTases) of the Dam family (including those of
AB  - bacteriophages T2 and T4) catalyze methyl group transfer from
AB  - S-adenosyl-L-methionine (AdoMet), producing S-adenosyl-L-homocysteine
AB  - (AdoHcy) and methylated adenine residues in palindromic GATC sequences.
AB  - Dam DNA MTases, as all site-specific enzymes interacting with polymeric
AB  - DNA, require a mechanism of action that ensures a rapid search for
AB  - specific targets for catalytic action, during both the initial and
AB  - subsequent rounds of methylation. The results of presteady-state
AB  - (reaction burst) and steady-state methylation analyses of individual
AB  - targets permitted us to monitor the action of T4Dam, which has three
AB  - degrees of freedom: sliding, reorientation and adaptation to the
AB  - canonical GATC sequence. The salient results are as follows: (i) 40mer
AB  - substrate duplexes containing two canonical GATC sites showed
AB  - differential methylation of the potential targets, i.e., T4Dam
AB  - exhibited a preference for one site/target, which may present the
AB  - better 'kinetic trap' for the enzyme. (ii) Prior hemimethylation of the
AB  - two sites made both targets equally capable of being methylated during
AB  - the pre-steady-state reaction. (iii) Although capable of moving in
AB  - either direction along double-stranded DNA, there are some restrictions
AB  - on T4Dam reorientation/adaptation on 40mer duplexes.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Gorbunov, J.A.
AU  - Baclanov, M.M.
AU  - Popov, S.G.
AU  - Malygin, E.G.
TI  - Structure subtraction as an approach to investigation of the mechanism of restriction enzyme action.
JO  - FEBS Lett.
PY  - 1983
SP  - 282
EP  - 284
VL  - 154
AB  - Endonuclease BamHI cleaves the phosphodiester bonds between the guanine residues within the
AB  - duplex DNA sequence G/GATCC.  The substrate characteristics of oligonucleotides, containing
AB  - some defects in the sequence recognized by endonuclease (nick, absence of some internucleotide
AB  - phosphate or nucleotide, partially single-stranded form of the recognition site) were
AB  - investigated.  The results suggest that the specificity of synthetic oligonucleotide cleavage
AB  - is strongly dependent on the ribosophosphate backbone intactness inside the recognition site.
AB  - BamHI was found not to hydrolyse the phosphodiester bonds outside the double helix.  Also
AB  - BamHI forms a productive complex with the non-symmetrical substrate, having half the
AB  - recognition sites, of a single strand.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Gorbunov, Y.A.
AU  - Popov, S.G.
AU  - Malygin, E.G.
AU  - Buryanov, J.I.
AU  - Nesterenko, V.F.
AU  - Baev, A.A.
AU  - Venoginskis, M.T.
TI  - Interaction of EcoDam methylase with single stranded sequences and synthetic oligonucleotides.
JO  - Mol. Biol. (Mosk)
PY  - 1985
SP  - 947
EP  - 954
VL  - 19
AB  - Interaction of the Ecodam methylase with different substrates was investigated among them
AB  - double- and single-stranded DNAs and synthetic oligonucleotides containing some defects in the
AB  - GATC sequence.  These defects were: nick, the absence of one internucleotide phosphate of
AB  - nucleotide; partially single-stranded form of the recognition site etc.  It was demonstrated
AB  - that the presence of both G.A-dinucleotides in the recognition site is necessary for
AB  - productive enzyme-substrate interaction.  The absence of T and/or C residues is less dramatic
AB  - for methylase activity.  The Ecodam methylase is able to modify single-stranded
AB  - oligonucleotides by forming the double-stranded structure in the symmetric recognition
AB  - sequences GATC.
ER  -

TY  - JOUR
AU  - Zinoviev, V.V.
AU  - Yakishchik, S.I.
AU  - Evdokimov, A.A.
AU  - Malygin, E.G.
AU  - Hattman, S.
TI  - Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases.
JO  - Nucleic Acids Res.
PY  - 2004
SP  - 3930
EP  - 3934
VL  - 32
AB  - The phage T4Dam and EcoDam DNA-[adenine-N6] methyltransferases (MTases) methylate GATC
AB  - palindromic sequences, while the BamHI DNA-[cytosine-N4] MTase methylates the GGATCC
AB  - palindrome (which contains GATC) at the internal cytosine residue. We compared the ability of
AB  - these enzymes to interact productively with defective duplexes in which individual elements
AB  - were deleted on one chain. A sharp decrease in kcat was observed for all three enzymes if a
AB  - particular element of structural symmetry was disrupted. For the BamHI MTase, integrity of the
AB  - ATCC was critical, while an intact GAT sequence was necessary for the activity of T4Dam, and
AB  - an intact GA was necessary for EcoDam. Theoretical alignment of the region of best contacts
AB  - between the protein and DNA showed that in the case of a palindromic interaction site, a zone
AB  - covering the 5'-symmetric residues is located in the major groove versus a zone of contact
AB  - covering the 3'-symmetric residues in the minor groove. Our data fit a simple rule of thumb
AB  - that the most important contacts are aligned around the methylation target base: if the target
AB  - base is in the 5' half of the palindrome, the interaction between the enzyme and the DNA
AB  - occurs mainly in the major groove; if it is in the 3' half, the interaction occurs mainly in
AB  - the minor groove.
ER  -

TY  - JOUR
AU  - Zischka, M.
AU  - Kuenne, C.
AU  - Blom, J.
AU  - Dabrowski, P.W.
AU  - Linke, B.
AU  - Hain, T.
AU  - Nitsche, A.
AU  - Goesmann, A.
AU  - Larsen, J.
AU  - Jensen, L.B.
AU  - Witte, W.
AU  - Werner, G.
TI  - Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32.
JO  - J. Bacteriol.
PY  - 2012
SP  - 5490
EP  - 5491
VL  - 194
AB  - The complete and annotated genome sequence of Enterococcus faecalis D32, a commensal strain
AB  - isolated from a Danish pig, suggests putative adaptation to the
AB  - porcine host and absence of distinct virulence-associated traits.
ER  -

TY  - JOUR
AU  - Zivanovic, Y.
AU  - Armengaud, J.
AU  - Lagorce, A.
AU  - Leplat, C.
AU  - Guerin, P.
AU  - Dutertre, M.
AU  - Anthouard, V.
AU  - Forterre, P.
AU  - Wincker, P.
AU  - Confalonieri, F.
TI  - Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
JO  - Genome Biol.
PY  - 2009
SP  - R70
EP  - R70
VL  - 10
AB  - ABSTRACT: BACKGROUND: Thermococcus gammatolerans was isolated from samples collected from
AB  - hydrothermal chimneys. It is one of the most radioresistant
AB  - organisms known amongst the Archaea. We report the determination and
AB  - annotation of its complete genome sequence, its comparison with other
AB  - Thermococcales genomes, and a proteomic analysis. RESULTS: T.
AB  - gammatolerans has a circular chromosome of 2.045 Mbp without any
AB  - extra-chromosomal elements, coding for 2,157 proteins. A thorough
AB  - comparative genomics analysis revealed important but unsuspected genome
AB  - plasticity differences between sequenced Thermococcus and Pyrococcus
AB  - species which could not be attributed to the presence of specific mobile
AB  - elements. Two virus-related regions tgv1 and tgv2 are the only mobile
AB  - elements identified in this genome. A proteogenome analysis was performed
AB  - by a shotgun LC-MS/MS approach allowing the identification of 10,931
AB  - unique peptides corresponding to 951 proteins. This information
AB  - concurrently validates the accuracy of the genome annotation.
AB  - Semi-quantitation of proteins by spectral count was done on exponential-
AB  - and stationary-phase cells. Insights into general catabolism, hydrogenase
AB  - complexes, detoxification systems, and the DNA repair toolbox of this
AB  - archaeon are revealed through this genome and proteome analysis.
AB  - CONCLUSIONS: This work is the first archaeal proteome investigation done
AB  - at the stage of primary genome annotation. This archaeon is shown to use a
AB  - large variety of metabolic pathways even under a rich medium growth
AB  - condition. This proteogenomic study also indicates that the high
AB  - radiotolerance of T. gammatolerans is probably due to proteins that remain
AB  - to be characterized rather than a larger arsenal of known DNA repair
AB  - enzymes.
ER  -

TY  - JOUR
AU  - Zobanikova, M.
AU  - Mikolka, P.
AU  - Cejkova, D.
AU  - Pospisilova, P.
AU  - Chen, L.
AU  - Strouhal, M.
AU  - Qin, X.
AU  - Weinstock, G.M.
AU  - Smajs, D.
TI  - Complete genome sequence of Treponema pallidum strain DAL-1.
JO  - Standards in Genomic Sciences
PY  - 2012
SP  - 12
EP  - 21
VL  - 7
AB  - strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease
AB  - syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant
AB  - woman in the secondary stage of syphilis. Here we describe the 1,139,971 bp long
AB  - genome of strain DAL-1 which was sequenced using two independent sequencing
AB  - methods (454 pyrosequencing and Illumina). In rabbits, strain DAL-1 replicated
AB  - better than the strain Nichols. The comparison of the complete DAL-1 genome
AB  - sequence with the Nichols sequence revealed a list of genetic differences that
AB  - are potentially responsible for the increased rabbit virulence of the DAL-1
AB  - strain.
ER  -

TY  - JOUR
AU  - Zobanikova, M.
AU  - Strouhal, M.
AU  - Mikalova, L.
AU  - Cejkova, D.
AU  - Ambrozova, L.
AU  - Pospisilova, P.
AU  - Fulton, L.L.
AU  - Chen, L.
AU  - Sodergren, E.
AU  - Weinstock, G.M.
AU  - Smajs, D.
TI  - Whole genome sequence of the Treponema pallidum Fribourg-Blanc: Unspecified simian isolate is highly similar to the yaws subspecies.
JO  - PLoS Neglected Trop. Dis.
PY  - 2013
SP  - E2172
EP  - E2172
VL  - 7
AB  - Background: Unclassified simian strain Treponema Fribourg-Blanc was isolated in 1966 from
AB  - baboons (Papio cynocephalus)in West Africa. This strain was morphologically indistinguishable
AB  - from T. pallidum ssp. pallidum or ssp. pertenue strains, and it was shown to cause human
AB  - infections.
AB  - Methodology/Principal Findings: To precisely define genetic differences between Treponema
AB  - Fribourg-Blanc (unclassified simian isolate, FB) and T. pallidum ssp. pertenue strains (TPE),
AB  - a high quality sequence of the whole Fribourg-Blanc genome was determined with
AB  - 454-pyrosequencing and Illumina sequencing platforms. Combined average coverage of both
AB  - methods was greater than 5006. Restriction target sites (n = 1,773), identified in silico, of
AB  - selected restriction enzymes within the Fribourg-Blanc genome were verified experimentally and
AB  - no discrepancies were found. When compared to the other
AB  - three sequenced TPE genomes (Samoa D, CDC-2, Gauthier), no major genome rearrangements were
AB  - found. The Fribourg-
AB  - Blanc genome clustered with other TPE strains (especially with the TPE CDC-2 strain), while T.
AB  - pallidum ssp. pallidum strains clustered separately as well as the genome of T.
AB  - paraluiscuniculi strain Cuniculi A. Within coding regions, 6 deletions, 5 insertions and 117
AB  - substitutions differentiated Fribourg-Blanc from other TPE genomes.  Conclusions/Significance:
AB  - The Fribourg-Blanc genome showed similar genetic characteristics as other TPE strains.
AB  - Therefore, we propose to rename the unclassified simian isolate to Treponema pallidum ssp.
AB  - pertenue strain Fribourg-Blanc. Since the Fribourg-Blanc strain was shown to cause
AB  - experimental infection in human hosts, non-human primates could serve as possible reservoirs
AB  - of TPE strains. This could considerably complicate recent efforts to eradicate yaws. Genetic
AB  - differences specific for Fribourg-Blanc could then contribute for identification of cases of
AB  - animal-derived yaws infections.
ER  -

TY  - JOUR
AU  - Zomer, A.
AU  - de Vries, S.P.
AU  - Riesbeck, K.
AU  - Meinke, A.L.
AU  - Hermans, P.W.
AU  - Bootsma, H.J.
TI  - Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage.
JO  - J. Bacteriol.
PY  - 2012
SP  - 6969
EP  - 6969
VL  - 194
AB  - Here we report the annotated genome sequence of Moraxella catarrhalis strain RH4, a
AB  - seroresistant-lineage strain isolated from the blood of an infected patient.
AB  - This genome sequence will allow us to gain further insight into the genetic
AB  - diversity of clinical M. catarrhalis isolates and will facilitate study of M.
AB  - catarrhalis pathogenesis.
ER  -

TY  - JOUR
AU  - Zong, G.
AU  - Zhong, C.
AU  - Fu, J.
AU  - Qin, R.
AU  - Cao, G.
TI  - Draft Genome Sequence of the Tacrolimus-Producing Bacterium Streptomyces tsukubaensis F601.
JO  - Genome Announcements
PY  - 2017
SP  - e00385
EP  - e00317
VL  - 5
AB  - Streptomyces tsukubaensis strain F601 was found to be a producer of the immunosuppressive drug
AB  - tacrolimus. The draft genome sequence of this strain was
AB  - approximately 8.52 Mbp. Genes involved in the biosynthesis of tacrolimus were
AB  - identified in the genome. This draft genome sequence will provide insights into
AB  - the genetic basis of tacrolimus biosynthesis and regulation.
ER  -

TY  - JOUR
AU  - Zong, G.
AU  - Zhong, C.
AU  - Fu, J.
AU  - Zhao, Z.
AU  - Cao, G.
TI  - Complete Genome Sequence of the High-Natamycin-Producing Strain Streptomyces gilvosporeus F607.
JO  - Genome Announcements
PY  - 2018
SP  - e01402
EP  - e01417
VL  - 6
AB  - Streptomyces gilvosporeus strain F607 is a producer of high levels of natamycin used in the
AB  - fermentation industry. In this study, the complete genome sequence of
AB  - strain F607 was determined. This genome sequence provides a basis for
AB  - understanding natamycin biosynthesis and regulation in a high-natamycin-producing
AB  - strain and will aid in the development of useful strategies for improving
AB  - industrial strains.
ER  -

TY  - JOUR
AU  - Zong, Z.
AU  - Lu, X.
TI  - Characterization of a New SCCmec Element in Staphylococcus cohnii.
JO  - PLoS ONE
PY  - 2010
SP  - E14016
EP  - E14016
VL  - 5
AB  - BACKGROUND: Many SCCmec elements of coagulase-negative staphylococci
AB  - (CoNS) could not be typed using multiplex PCR. Such a 'non-typable' SCCmec
AB  - was encountered in a Staphylococcus cohnii isolate. METHODOLOGY/PRINCIPAL
AB  - FINDINGS: The SCCmec type of methicillin-resistant S. cohnii clinical
AB  - isolate WC28 could not be assigned using multiplex PCR. Newly-designed
AB  - primers were used to amplify ccrA and ccrB genes. The whole SCCmec was
AB  - obtained by three overlapping long-range PCR, targeting regions from
AB  - left-hand inverted repeat (IRL) to ccrA/B, from ccrA/B to mecA and from
AB  - mecA to orfX. The region abutting IRL was identified using inverse PCR
AB  - with self-ligated enzyme-restricted WC28 fragments as the template. WC28
AB  - SCCmec had a class A mec gene complex (mecI-mecR1-mecA). The ccrA and ccrB
AB  - genes were closest (89.7% identity) to ccrA(SHP) of Staphylococcus
AB  - haemolyticus strain H9 and to ccrB3 (90% identity) of Staphylococcus
AB  - pseudintermedius strain KM241, respectively. Two new genes potentially
AB  - encoding AAA-type ATPase were found in J1 region and a psiTn554 transposon
AB  - was present in J2 region, while J3 region was the same as many SCCmec of
AB  - Staphylococcus aureus. WC28 SCCmec abutted an incomplete SCC element with
AB  - a novel allotype of ccrC, which was closest (82% identity) to ccrC1 allele
AB  - 9 in Staphylococcus saprophyticus strain ATCC 15305. Only two direct
AB  - target repeat sequences, one close to the 3'-end of orfX and the other
AB  - abutting the left end of WC28 SCCmec, could be detected.
AB  - CONCLUSIONS/SIGNIFICANCE: A new 35-kb SCCmec was characterized in a S.
AB  - cohnii isolate, carrying a class A mec gene complex, new variants of ccrA5
AB  - and ccrB3 and two novel genes in the J1 region. This element is flanked by
AB  - 8-bp perfect inverted repeats and is similar to type III SCCmec in S.
AB  - aureus and a SCCmec in S. pseudintermedius but with different J1 and J3
AB  - regions. WC28 SCCmec was arranged in tandem with an additional SCC element
AB  - with ccrC, SCC(WC28), but the two elements might have integrated
AB  - independently rather than constituted a composite. This study adds new
AB  - evidence of the diversity of SCCmec in CoNS and highlights the need for
AB  - characterizing the 'non-typable' SCCmec to reveal the gene pool associated
AB  - with mecA.
ER  -

TY  - JOUR
AU  - Zoropogui, A. et al.
TI  - Genome Sequence of the Human- and Animal-Pathogenic Strain Nocardia cyriacigeorgica GUH-2.
JO  - J. Bacteriol.
PY  - 2012
SP  - 2098
EP  - 2099
VL  - 194
AB  - The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human
AB  - nocardiosis case, and its genome was sequenced. The complete genomic
AB  - sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%,
AB  - and no plasmids. We also identified several protein-coding genes to which N.
AB  - cyriacigeorgica's virulence can potentially be attributed.
ER  -

TY  - JOUR
AU  - Zorzetti, J.
AU  - Ricietto, A.P.
AU  - da Silva, C.R.
AU  - Wolf, I.R.
AU  - Vilas-Boas, G.T.
AU  - Neves, P.M.
AU  - Meneguim, A.M.
AU  - Vilas-Boas, L.A.
TI  - Genome Sequence of the Mosquitocidal Bacillus thuringiensis Strain BR58, a Biopesticide Product Effective against the Coffee Berry Borer (Hypothenemus  hampei).
JO  - Genome Announcements
PY  - 2015
SP  - e01232
EP  - e01215
VL  - 3
AB  - Bacillus thuringiensis is an important microbial control agent against insect pests. The draft
AB  - genome sequence of the Brazilian strain BR58 described here
AB  - contains the insecticidal genes cry4A, cry4B, cry10A, cry11A, cry60A, cry60B, and
AB  - cyt1A, which show toxicity to both Aedes aegypti and Hypothenemus hampei larvae.
ER  -

TY  - JOUR
AU  - Zotchev, S.B.
AU  - Schrempf, H.
AU  - Hutchinson, C.R.
TI  - Identification of a methyl-specific restriction system mediated by a conjugative element from Streptomyces bambergiensis.
JO  - J. Bacteriol.
PY  - 1995
SP  - 4809
EP  - 4812
VL  - 177
AB  - pBL2 was identified genetically but not physically in Streptomyces lividans after its mating
AB  - with S. bambergiensis.  During conjugation, pBL2 was transferred at high frequency to S.
AB  - lividans and S. coelicolor, pBL2.1 DNA isolated from S. coelicolor exconjugants as a circular
AB  - plasmid was shown to derive from the genome of S. bambergiensis.  S. lividans carrying pBL2 or
AB  - pBL2.1 acquired a methyl-specific restriction (MsrA+) phenotype.  The corresponding enzyme
AB  - was partially purified and shown to resemble a class II endonuclease which cleaves
AB  - Dam-methylated DNA preferentially.
ER  -

TY  - JOUR
AU  - Zotta, T.
AU  - Ricciardi, A.
AU  - Parente, E.
AU  - Reale, A.
AU  - Ianniello, R.G.
AU  - Bassi, D.
TI  - Draft Genome Sequence of the Respiration-Competent Strain Lactobacillus casei N87.
JO  - Genome Announcements
PY  - 2016
SP  - e00348
EP  - e00316
VL  - 4
AB  - Lactobacillus casei is used as a starter, adjunct, and/or probiotic culture in the production
AB  - of fermented and functional foods. Here, we report the draft
AB  - genome sequence of the respiration-competent strain L. casei N87, isolated from
AB  - infant feces. This genome information may be useful for the study of respiratory
AB  - metabolism in lactic acid bacteria.
ER  -

TY  - JOUR
AU  - Zou, C.
AU  - Wang, K.
AU  - Meng, J.
AU  - Yuan, G.
AU  - Lin, W.
AU  - Peng, H.
AU  - Li, Q.
TI  - Draft Genome Sequence of Ralstonia solanacearum Strain Rs-T02, Which Represents the Most Prevalent Phylotype in Guangxi, China.
JO  - Genome Announcements
PY  - 2016
SP  - e00241
EP  - e00216
VL  - 4
AB  - Ralstonia solanacearumstrain Rs-T02 was originally isolated from a bacterial wilt of tomato
AB  - plant in Nanning City of Guangxi Province, China. It represents the
AB  - most prevalent phylotype in Guangxi. Here, we present the draft genome sequence
AB  - of this strain, which comprises 5,225 genes and 5,976,011 nucleotides with an
AB  - average G+C content of 66.79%. There are 968 different genes between this isolate
AB  - and the previously reported genome sequence ofRalstonia solanacearumGMl l000
AB  - (race l, biovar 3, phylotype I), and the genome sequence information of this
AB  - isolate may be useful for comparative genomic studies to determine the genetic
AB  - diversity in this species.
ER  -

TY  - JOUR
AU  - Zou, G.
TI  - Methods for preparation and determination of the purity and activity of restriction endonucleases.
JO  - Weishengwuxue Zazhi
PY  - 1987
SP  - 63
EP  - 66
VL  - 7
AB  - The main source of DNA restriction endonucleases (restriction enzymes) is from
AB  - bacteria.  They are widespread, and have many varieties.  The first restriction
AB  - enzyme was discovered in 1968, since then close to 500 of them have been
AB  - discovered, and most of them are type II restriction enzymes.  Type II
AB  - restriction enzymes are very important, they have been called the surgeon's
AB  - knife for molecular biology; they have served as an ideal model to study the
AB  - interaction between protein and DNA.  This article describes the general
AB  - methods for preparation and determination of reactivities of type II
AB  - restriction endonucleases.
ER  -

TY  - JOUR
AU  - Zou, G.
AU  - Cao, X.
AU  - Zhu, R.
TI  - One step purification of restriction endonuclease PstI by sepharose affinity column separation.
JO  - Shengwu Huaxue Yu Shengwu Wuli Jinzhan
PY  - 1985
SP  - 64
EP  - 66
VL  - 62
AB  - None
ER  -

TY  - JOUR
AU  - Zou, G.
AU  - Gao, C.
AU  - Pi, X.
TI  - Kinetic studies on the irreversible inhibition of restriction endonuclease PstI by site-specific inhibitors.
JO  - Wuhan Univ. J. Natural Sciences
PY  - 2001
SP  - 859
EP  - 863
VL  - 6
AB  - The irreversible modifying effects on PstI of several inhibitors have been studied with the
AB  - irreversible inhibition kinetic theory of single substrate reaction provided by Tsou, C.L.
AB  - Pyridoxal phosphate (PLP), p-chloromercuribenzoic acid (PCMB), diisopropyl fluorophosphates
AB  - (DFP), 2,3-diacetyl (DAC) and N-ethyl-5-phenylisoxazolium-3' sulfonate (Woodward's reagent
AB  - K, WRK), modify the lysine, cysteine, serine, arginine and carboxyl groups of the protein
AB  - molecule respectively.  These five inhibitors have been found to inhibit both the prime
AB  - activity and star activity of PstI.  Used with the irreversible inhibition theory, the
AB  - apparent inhibition rate constant, A, and the microcosmic inhibition rate constants, k+o and
AB  - k'+o of every inhibitor were calculated.  We also found that their inhibition effects belong
AB  - to the noncompetitive irreversible inhibition.  Results show that among the groups to be
AB  - modified, some have nothing to do with the combination with the substrate, and some may have,
AB  - but none of them is the only factor involved in the specific binding.  Despite all this, they
AB  - may take part in the catalysis of enzyme or have important effects on maintaining the active
AB  - structure of enzyme molecules.  Furthermore, serine and arginine residues are related to the
AB  - alteration of PstI conformation and then influence the ability of PstI recognizing the
AB  - incising DNA specifically.
ER  -

TY  - JOUR
AU  - Zou, G.-L.
AU  - Cao, X.-W.
AU  - Zhu, R.-F.
TI  - The purification and some properties of restriction endonuclease PstI.
JO  - Acta Biochim. Biophys. Sin.
PY  - 1985
SP  - 268
EP  - 274
VL  - 17
AB  - Restriction endonuclease PstI has been isolated and purified by chromatography
AB  - on heparin-Sepharose, DEAE-cellulose, phosphocellulose, Cibacron Blue
AB  - F3GA-Sepharose and hydroxylapatite.  The purified enzyme was found to be
AB  - homogeneous as judged by polyacrylamide gel disc electrophoresis.  The specific
AB  - activity of the enzyme is greater than 57,000 units per mg protein.  The enzyme
AB  - has a molecular weight of about 54,000 daltons by Sephadex G-100 gel
AB  - filtration, that of the enzyme subunit is about 17,500 daltons as assayed by
AB  - sodium dodecyl sulphate-polyacrylamide gel electrophoresis.  On electrophoresis
AB  - the subunit migrated as a single band.  The result shows that restriction
AB  - endonuclease PstI consists of two similar subunits.  The N-terminal amino acid
AB  - of the enzyme is proline as assayed by dansyl chloride.  Other properties of
AB  - restriction endonuclease PstI were also given preliminary study.
ER  -

TY  - JOUR
AU  - Zou, G.-L.
AU  - Gao, C.-Z.
AU  - Pi, X.-C.
AU  - Hu, W.J.
TI  - Studies on the star activity of restriction endonuclease PstI.
JO  - Wuhan Daxue Xuebao
PY  - 1999
SP  - 873
EP  - 875
VL  - 45
AB  - The influence of factors such as temperature, enzyme concentration, reaction time and several
AB  - organic solvents on the star activity of PstI has been studied.  Under the reaction condition
AB  - beneficial for the star activity, the Km and Vmax of the star activity and prime activity
AB  - respectively are 1.46 x 10^-7 mol/L, 1.02 x 10^-8 mol/L and 2.86 x 10^-16 mol/s, 3.06 x 10^-15
AB  - mol/s.
ER  -

TY  - JOUR
AU  - Zou, G.-l.
AU  - Gao, C.-Z.
AU  - Pi, X.-C.
AU  - Zhang, J.-J.
TI  - Alteration of the specificity of PstI restriction endonuclease.
JO  - Wuhan Univ. J. Nat. Sci.
PY  - 2000
SP  - 361
EP  - 365
VL  - 5
AB  - The influence of factors on the substrate-specificity of PstI restriction endonuclease has
AB  - been studied with the method of electrophoresis.  The results show that, the specificity of
AB  - PstI almost cannot be influenced by the single alteration of the concentration of Tris.HCl,
AB  - Mg2+ or Na+ in the reaction system, but it can be altered by the reduction of any two of them.
AB  - The specificity cannot be altered by the single alteration of pH or the replacement of Mg2+
AB  - with Mn2+.  The addition of glycerol or dimethylsulphoxide (DM-SO) to the reaction system
AB  - results in the relaxation of the substrate-specificity of PstI, but dimethyl-methylformide,
AB  - glycol and ethyl alcohol cannot bring about the alteration of PstI specificity.  Through the
AB  - method of cloning and sequencing, the nucleotides of No. 1 and 6 in the recognition sequence
AB  - of PstI have changed (1C-A or 6G-T).  Used with the enzyme analysis of an artificially
AB  - synthetic DNA segment containing a special sequence, the nucleotides of No. 1 and 6 have both
AB  - changed (1C-A and 6G-T).  The recognition sequence of PstI is speculated to be changed from
AB  - CTGCA/G to TGCA/.
ER  -

TY  - JOUR
AU  - Zou, S.
AU  - Zhang, M.
AU  - Hong, J.
AU  - Ma, Y.
AU  - Zhang, W.
TI  - Comparison of the electro transformation of plasmids and plasmid stability between Zymomonas mobilis ZM4 and CP4.
JO  - Afr. J. Microbiol. Res.
PY  - 2011
SP  - 2026
EP  - 2033
VL  - 5
AB  - Four different plasmids were electro transformed into Zymomonas mobilis ZM4 and CP4, two
AB  - important ethanol-producing strains. The results
AB  - showed that the best source strain for preparing plasmids was the
AB  - transformed host strain itself, and Escherichia coli JM110 as the
AB  - source strain could yield significantly higher transformation
AB  - efficiencies than Top10. The optimal recovery time of transformed ZM4
AB  - or CP4 cells to obtain maximum number of transformants and highest
AB  - transformation efficiency was 11 h for pZB21-mini, pZB21 and pZA22, but
AB  - 24 or 20 h for pBBR1MCS-2. The optimal electric field strength for
AB  - pZB21-mini was 13.25 kV /cm in ZM4 and 14.0 kV /cm in CP4. But for
AB  - pZA22 and pBBR1MCS-2, it was 11.75 kV /cm in ZM4 and 12.5 kV /cm in
AB  - CP4; for pZB21, also 12.5 kV /cm in CP4. These plasmids were shown to
AB  - be more stable in ZM4 than in CP4 by serial transfer to antibiotic-free
AB  - medium and the 3 plasmids were more stable than pBBR1MCS-2. The results
AB  - will help to support the genetic and biotechnological research of Z.
AB  - mobilis by providing information about some of the most important
AB  - factors that influence the transformation of ZM4 and CP4, and also
AB  - providing insights into the similarities and differences in their
AB  - restriction-modification (R-M) systems.
ER  -

TY  - JOUR
AU  - Zschuttig, A.
AU  - Auerbach, C.
AU  - Meltke, S.
AU  - Eichhorn, C.
AU  - Brandt, M.
AU  - Blom, J.
AU  - Goesmann, A.
AU  - Jarek, M.
AU  - Scharfe, M.
AU  - Zimmermann, K.
AU  - Wassenaar, T.M.
AU  - Gunzer, F.
TI  - Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8.
JO  - Genome Announcements
PY  - 2015
SP  - e01330
EP  - e01314
VL  - 3
AB  - The complete genome of probiotic Escherichia coli strain G3/10 is presented here. In addition,
AB  - the probiotic E. coli strains G1/2, G4/9, G5, G6/7, and G8 are
AB  - presented in draft form. These six strains together comprise the probiotic
AB  - product Symbioflor 2 (DSM 17252).
ER  -

TY  - JOUR
AU  - Zubair, S.
AU  - de Villiers, E.P.
AU  - Fuxelius, H.H.
AU  - Andersson, G.
AU  - Johansson, K.E.
AU  - Bishop, R.P.
AU  - Bongcam-Rudloff, E.
TI  - Genome Sequence of Streptococcus agalactiae Strain 09mas018883, Isolated from a Swedish Cow.
JO  - Genome Announcements
PY  - 2013
SP  - e00456
EP  - e00413
VL  - 1
AB  - We announce the complete genome sequence of Streptococcus agalactiae strain 09mas018883,
AB  - isolated from the milk of a cow with clinical mastitis. The
AB  - availability of this genome may allow identification of candidate genes, leading
AB  - to discovery of antigens that might form the basis for development of a vaccine
AB  - as an alternative means of mastitis control.
ER  -

TY  - JOUR
AU  - Zubair, S.
AU  - de Villiers, E.P.
AU  - Younan, M.
AU  - Andersson, G.
AU  - Tettelin, H.
AU  - Riley, D.R.
AU  - Jores, J.
AU  - Bongcam-Rudloff, E.
AU  - Bishop, R.P.
TI  - Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius.
JO  - Genome Announcements
PY  - 2013
SP  - e00515
EP  - e00513
VL  - 1
AB  - Streptococcus agalactiae causes a range of clinical syndromes in camels (Camelus
AB  - dromedarius). We report the genome sequences of two S. agalactiae isolates that
AB  - induce abscesses in Kenyan camels. These genomes provide novel data on the
AB  - composition of the S. agalactiae 'pan genome' and reveal the presence of multiple
AB  - genomic islands.
ER  -

TY  - JOUR
AU  - Zubair, S.
AU  - Fischer, A.
AU  - Liljander, A.
AU  - Meens, J.
AU  - Hegerman, J.
AU  - Gourle, H.
AU  - Bishop, R.P.
AU  - Roebbelen, I.
AU  - Younan, M.
AU  - Mustafa, M.I.
AU  - Mushtaq, M.
AU  - Bongcam-Rudloff, E.
AU  - Jores, J.
TI  - Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.
JO  - Standards in Genomic Sciences
PY  - 2015
SP  - 109
EP  - 109
VL  - 10
AB  - We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated  from a nasal
AB  - swab of a dromedary camel (Camelus dromedarius) in North Kenya. The
AB  - complete genome sequence of this strain consists of a circular chromosome of
AB  - 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755
AB  - protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST
AB  - sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core
AB  - genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus
AB  - isolate cluster but is genetically distinct. About 79 % of the protein encoding
AB  - genes are part of the CC30 core genome (genes common to all CC30 S. aureus
AB  - isolates), ~18 % were within the variable genome (shared among multiple but not
AB  - all isolates) and ~ 3 % were found only in the genome of the camel isolate. Among
AB  - the 85 isolate-specific genes, 79 were located within putative phages and
AB  - pathogenicity islands. Protein encoding genes associated with bacterial adhesion,
AB  - and secretory proteins that are essential components of the type VII secretion
AB  - system were also identified. The complete genome sequence of S. aureus strain
AB  - ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the
AB  - accession no LN626917.1.
ER  -

TY  - JOUR
AU  - Zueva, V.S.
AU  - Dmitrenko, O.A.
AU  - Gladkova, K.K.
AU  - Zueva, E.A.
TI  - New collection of phages for typing methicillin-resistant Staphylococcus aureus.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1994
SP  - 20
EP  - 23
VL  - 2
AB  - A new collection of phages for typing methicillin-resistant S. aureus is proposed.  The
AB  - collection includes phage 85 (modified by the MRSA strain), capable of selecting stains with
AB  - the similar specificity of the restriction-modification system, and 9 MRSA-induced phages.
AB  - The latter differentiate MRSA strains according to the specificity of prophages present in
AB  - bacterial cells.  The use of this phage collection has permitted the typing of MRSA strains
AB  - insensitive to the phages of the international collection.  Among these cultures on epidemic
AB  - strain has been detected and the source of its spread in the burn center has been established.
ER  -

TY  - JOUR
AU  - Zueva, V.S.
AU  - Dmitrienko, O.A.
AU  - Krupina, E.A.
AU  - Belikov, N.G.
AU  - Nesterenko, L.N.
TI  - To the mechanism of the resistance of methicillin-resistant staphylococcus aureus to phages of the international collection.
JO  - Zh. Mikrobiol. Epidemiol. Immunobiol.
PY  - 1990
SP  - 11
EP  - 15
VL  - 10
AB  - The resistance of methicillin-resistant staphylococci to phage 85 is due to the
AB  - presence of a certain system restriction modification in microbial cells.  The
AB  - loss of the capacity for restricting phage DNA by the cell as the consequence
AB  - of the loss of the mec determinant is not accompanied by the loss of its
AB  - capacity for modifying phage DNA.
ER  -

TY  - JOUR
AU  - Zuljan, F.
AU  - Espariz, M.
AU  - Blancato, V.S.
AU  - Esteban, L.
AU  - Alarcon, S.
AU  - Magni, C.
TI  - Draft Genome Sequence of Lactococcus lactis subsp. lactis bv. diacetylactis CRL264, a Citrate-Fermenting Strain.
JO  - Genome Announcements
PY  - 2016
SP  - e01575
EP  - e01515
VL  - 4
AB  - We report the draft genome sequence of Lactococcus lactis subsp. lactis bv. diacetylactis
AB  - CRL264, a natural strain isolated from artisanal cheese from
AB  - northwest Argentina. L. lactis subsp. lactis bv. diacetylactis is one of the most
AB  - important microorganisms used as starter culture around the world. The CRL264
AB  - strain constitutes a model microorganism in the studies on the generation of
AB  - aroma compounds (diacetyl, acetoin, and 2,3-butanediol) by lactic acid bacteria.
AB  - Our genome analysis shows similar genetic organization to other available genomes
AB  - of L. lactis bv. diacetylactis strains.
ER  -

TY  - JOUR
AU  - Zulkifli, M.H.
AU  - Teh, L.K.
AU  - Lee, L.S.
AU  - Zakaria, Z.A.
AU  - Salleh, M.Z.
TI  - Draft Genome Sequence of Klebsiella pneumoniae Isolate PR04.
JO  - Genome Announcements
PY  - 2013
SP  - e00418
EP  - e00413
VL  - 1
AB  - Klebsiella pneumoniae PR04 was isolated from a patient hospitalized in Malaysia.  The draft
AB  - genome sequence of K. pneumoniae PR04 shows differences compared to the
AB  - reference sequences of K. pneumoniae strains MGH 78578 and NTUH-K2044 in terms of
AB  - their genomic structures.
ER  -

TY  - JOUR
AU  - Zuniga-Bahamon, A.
AU  - Tobar-Tosse, F.
AU  - Guillermo-Ortega, J.
AU  - Wibberg, D.
AU  - Tauch, A.
TI  - Draft Genome Sequence of Streptococcus anginosus BVI, a New Vaginal Pathogen Candidate.
JO  - Genome Announcements
PY  - 2016
SP  - e01417
EP  - e01416
VL  - 4
AB  - Streptococcus anginosus is a pathogen implicated in urogenital and gastroinstestinal tract
AB  - infections. Here, we report the draft genome sequence of
AB  - S. anginosus BVI, isolated from a bacterial vaginosis patient attending a
AB  - prenatal care unit in Cali, Colombia. The genome sequence of BVI consists of
AB  - 2,014,025 bp, encoding 2,008 predicted proteins.
ER  -

TY  - JOUR
AU  - Zuo, F.
AU  - Feng, X.
AU  - Sun, X.
AU  - Du, C.
AU  - Chen, S.
TI  - Characterization of Plasmid pML21 of Enterococcus faecalis ML21 from Koumiss.
JO  - Curr. Microbiol.
PY  - 2013
SP  - 103
EP  - 105
VL  - 66
ER  -

TY  - JOUR
AU  - Zurawski, D.V.
AU  - Thompson, M.G.
AU  - McQueary, C.N.
AU  - Matalka, M.N.
AU  - Sahl, J.W.
AU  - Craft, D.W.
AU  - Rasko, D.A.
TI  - Genome Sequences of Four Divergent Multidrug-Resistant Acinetobacter baumannii Strains Isolated from Patients with Sepsis or Osteomyelitis.
JO  - J. Bacteriol.
PY  - 2012
SP  - 1619
EP  - 1620
VL  - 194
AB  - Acinetobacter baumannii is a Gram-negative bacterium that causes nosocomial infections
AB  - worldwide, with recent prevalence and higher frequency in wounded
AB  - military personnel. Four A. baumannii strains from the Walter Reed Army Medical
AB  - Center (WRAMC) isolated between 2008 and 2009 were sequenced, representing
AB  - diverse, multidrug-resistant isolates from osteomyelitis or septic patients.
ER  -

TY  - JOUR
AU  - Zurfluh, K.
AU  - Stephan, R.
AU  - Klumpp, J.
AU  - Nuesch-Inderbinen, M.
AU  - Hummerjohann, J.
AU  - Bagutti, C.
AU  - Marti, R.
TI  - Complete Genome Sequence of Citrobacter freundii 705SK3, an OXA-48-Encoding Wastewater Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00842
EP  - e00817
VL  - 5
AB  - We present the genome sequence of Citrobacter freundii 705SK3, a wastewater isolate harboring
AB  - an IncL OXA-48-encoding plasmid. Assembly of the genome
AB  - resulted in a 5,242,839-bp circular chromosome (GC content, 52%) and two closed
AB  - plasmids of 296,175 bp and 63, 458 bp in size.
ER  -

TY  - JOUR
AU  - Zurfluh, K.
AU  - Stephan, R.
AU  - Klumpp, J.
AU  - Nuesch-Inderbinen, M.
AU  - Hummerjohann, J.
AU  - Bagutti, C.
AU  - Marti, R.
TI  - Complete Genome Sequence of Escherichia coli ABWA45, an rmtB-Encoding Wastewater  Isolate.
JO  - Genome Announcements
PY  - 2017
SP  - e00844
EP  - e00817
VL  - 5
AB  - We present the complete genome sequence of Escherichia coli ABWA45, a 16S rRNA
AB  - methyltransferase-producing wastewater isolate. Assembly and annotation resulted
AB  - in a 5,094,639-bp circular chromosome and four closed plasmids of 145,220 bp,
AB  - 113,793 bp, 57,232 bp, and 47,900 bp in size. Furthermore, a small open plasmid
AB  - (7,537 bp in size) was assembled.
ER  -

TY  - JOUR
AU  - Zurfluh, K.
AU  - Tasara, T.
AU  - Poirel, L.
AU  - Nordmann, P.
AU  - Stephan, R.
TI  - Draft Genome Sequence of Escherichia coli S51, a Chicken Isolate Harboring a Chromosomally Encoded mcr-1 Gene.
JO  - Genome Announcements
PY  - 2016
SP  - e00796
EP  - e00716
VL  - 4
AB  - We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum
AB  - beta-lactamase-producing strain isolated in 2015 from raw
AB  - chicken meat imported from Germany. Assembly and annotation of this draft genome
AB  - resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1
AB  - gene responsible for the colistin resistance of the strain.
ER  -

TY  - JOUR
AU  - Zurfluh, K.
AU  - Tasara, T.
AU  - Stephan, R.
TI  - Full-Genome Sequence of Escherichia coli K-15KW01, a Uropathogenic E. coli B2 Sequence Type 127 Isolate Harboring a Chromosomally Carried blaCTX-M-15 Gene.
JO  - Genome Announcements
PY  - 2016
SP  - e00927
EP  - e00916
VL  - 4
AB  - We present here the full-genome sequence of Escherichia coli K-15KW01, an
AB  - extended-spectrum-beta-lactamase-producing uropathogenic strain. Assembly and
AB  - annotation of the draft genome resulted in a 5,154,641-bp chromosome and revealed
AB  - a chromosomally contained blaCTX-M-15 gene embedded at the right-hand extremity
AB  - of an ISEcp1 element in a plasmid-like structure (36,907 bp).
ER  -

TY  - JOUR
AU  - Zweiger, G.
AU  - Marczynski, G.
AU  - Shapiro, L.
TI  - A Caulobacter DNA methyltransferase that functions only in the predivisional cell.
JO  - J. Mol. Biol.
PY  - 1994
SP  - 472
EP  - 474
VL  - 235
AB  - Caulobacter crescentus was found to have a DNA methyltransferase CcrM, that methylates the
AB  - adenine base of the HinfI recognition sequence, GANTC. The ccrM gene was cloned, and DNA
AB  - sequence analysis revealed that the predicted amino acid sequence has 49% identity with the
AB  - Haemophilus influenzae methyltransferase HinfM. Expression of the ccrM gene was found to be
AB  - restricted to the portion of the cell cycle immediately prior to cell division. At three
AB  - separate chromosomal sites the CcrM recognition sequence is fully methylated in swarmer cells,
AB  - becomes hemimethylated upon DNA replication in stalked cells, and does not become remethylated
AB  - until just prior to cell division. The time of methyltransferase expression coincides with the
AB  - time of methylation of these three chromosomal sites and of plasmid DNA in the predivisional
AB  - cell. When ccrM gene expression is placed under control of a constitutive promoter, these
AB  - chromosomal sites are fully methylated throughout the cell cycle. A high proportion of
AB  - morphologically aberrant cells, and cells that have undergone an additional chromosome
AB  - replication initiation, are found in this population. Thus, the temporal control of this
AB  - methyltransferase appears to contribute to the accurate cell-cycle control of DNA replication
AB  - and cellular morphology.
ER  -

TY  - JOUR
AU  - Zwick, M.E.
AU  - Joseph, S.J.
AU  - Didelot, X.
AU  - Chen, P.E.
AU  - Bishop-Lilly, K.A.
AU  - Stewart, A.C.
AU  - Willner, K.
AU  - Nolan, N.
AU  - Lentz, S.
AU  - Thomason, M.K.
AU  - Sozhamannan, S.
AU  - Mateczun, A.J.
AU  - Du, L.
AU  - Read, T.D.
TI  - Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis.
JO  - Genome Res.
PY  - 2012
SP  - 1512
EP  - 1524
VL  - 22
AB  - The key genes required for Bacillus anthracis to cause anthrax have been acquired
AB  - recently by horizontal gene transfer. To understand the genetic background for
AB  - the evolution of B. anthracis virulence, we obtained high-redundancy genome
AB  - sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that
AB  - were chosen for their genetic diversity within the species based on the existing
AB  - multilocus sequence typing scheme. From the resulting data, we called more than
AB  - 324,000 new genes representing more than 12,333 new gene families for this group.
AB  - The core genome size for the B. cereus s.l. group was approximately 1750 genes,
AB  - with another 2150 genes found in almost every genome constituting the extended
AB  - core. There was a paucity of genes specific and conserved in any clade. We found
AB  - no evidence of recent large-scale gene loss in B. anthracis or for unusual
AB  - accumulation of nonsynonymous DNA substitutions in the chromosome; however,
AB  - several B. cereus genomes isolated from soil and not previously associated with
AB  - human disease were degraded to various degrees. Although B. anthracis has
AB  - undergone an ecological shift within the species, its chromosome does not appear
AB  - to be exceptional on a macroscopic scale compared with close relatives.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Bujnicki, J.M.
AU  - Skowron, P.M.
TI  - Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.
JO  - BMC Mol. Biol.
PY  - 2009
SP  - 52
EP  - 52
VL  - 10
AB  - ABSTRACT: BACKGROUND: Restriction-modification systems are a diverse class of enzymes. They
AB  - are classified into four major types: I, II, III and IV.
AB  - We have previously proposed the existence of a Thermus sp. enzyme family,
AB  - which belongs to type II restriction endonucleases (REases), however, it
AB  - features also some characteristics of types I and III. Members include
AB  - related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II.
AB  - RESULTS: Here we describe cloning, mutagenesis and analysis of the
AB  - prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves
AB  - 11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene
AB  - and investigated the properties of its product, the bifunctional TspGWI
AB  - restriction/modification enzyme. Since TspGWI does not cleave DNA
AB  - completely, a cloning method was devised, based on amino acid sequencing
AB  - of internal proteolytic fragments. The deduced amino acid sequence of the
AB  - enzyme shares significant sequence similarity with another representative
AB  - of the Thermus sp. family - TaqII. Interestingly, these enzymes recognise
AB  - similar, yet different sequences in the DNA. Both enzymes cleave DNA at
AB  - the same distance, but differ in their ability to cleave single sites and
AB  - in the requirement of S-adenosylmethionine as an allosteric activator for
AB  - cleavage. Both the restriction endonuclease (REase) and methyltransferase
AB  - (MTase) activities of wild type (wt) TspGWI (either recombinant or
AB  - isolated from Thermus sp.) are dependent on the presence of divalent
AB  - cations. CONCLUSIONS: TspGWI is a bifunctional protein comprising a tandem
AB  - arrangement of Type I-like domains; particularly noticeable is the central
AB  - HsdM-like module comprising a helical domain and a highly conserved
AB  - S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG
AB  - and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/E)XK nuclease
AB  - domain related to the corresponding domains in HsdR subunits, but lacks
AB  - the ATP-dependent translocase module of the HsdR subunit and the
AB  - additional domains that are involved in subunit-subunit interactions in
AB  - Type I systems. The MTase and REase activities of TspGWI are autonomous
AB  - and can be uncoupled. Structurally and functionally, the TspGWI protomer
AB  - appears to be a streamlined 'half' of a Type I enzyme.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Harasimowicz-Slowinska, R.I.
AU  - Sobolewski, I.
AU  - Skowron, P.M.
TI  - TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognizes novel asymmetric sequence 5'-ACGGA(N11/9)-3'.
JO  - Nucleic Acids Res.
PY  - 2002
SP  - e33
EP  - e33
VL  - 30
AB  - A novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the
AB  - thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have
AB  - been established: TspGWI recognizes the non-palindromic 5-bp sequence 5'-ACGGA-3' and
AB  - cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In
AB  - addition, an accompanying endonuclease, TspGWII, an isoschizomer of PstI, was found in Thermus
AB  - sp. GW cells.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Jezewska-Frackowiak, J.
AU  - Skowron, P.M.
TI  - Cofactor analogue-induced chemical reactivation of endonuclease activity in a DNA cleavage/methylation deficient TspGWI N(473)A variant in the NPPY motif.
JO  - Mol. Biol. Rep.
PY  - 2014
SP  - 2313
EP  - 2323
VL  - 41
AB  - We reported previously that TspGWI, a prototype enzyme of a new Thermus sp. family of
AB  - restriction endonucleases-methyltransferases (REases-MTases), undergoes the novel phenomenon
AB  - of sinefungin (SIN)-caused specificity transition. Here we investigated mutant TspGWI N(473)A,
AB  - containing a single amino acid (aa) substitution in the NPPY motif of the MTase. Even though
AB  - the aa substitution is located within the MTase polypeptide segment, DNA cleavage and
AB  - modification are almost completely abolished, indicating that the REase and MTase are
AB  - intertwined. Remarkably, the TspGWI N(473)A REase functionality can be completely
AB  - reconstituted by the addition of SIN. We hypothesize that SIN binds specifically to the enzyme
AB  - and restores the DNA cleavage-competent protein tertiary structure. This indicates the
AB  - significant role of allosteric effectors in DNA cleavage in Thermus sp. enzymes. This is the
AB  - first case of REase mutation suppression by an S-adenosylmethionine (SAM) cofactor analogue.
AB  - Moreover, the TspGWI N(473)A clone strongly affects E. coli division control, acting as a
AB  - 'selfish gene'. The mutant lacks the competing MTase activity and therefore might be useful
AB  - for applications in DNA manipulation. Here we present a case study of a novel strategy for
AB  - REase activity/specificity alteration by a single aa substitution, based on the bioinformatic
AB  - analysis of active motif locations, combining (a) aa sequence engineering (b) the alteration
AB  - of protein enzymatic properties, and (c) the use of cofactor-analogue cleavage reconstitution
AB  - and stimulation.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Zebrowska, J.
AU  - Czajkowska, E.
AU  - Wrese, W.
AU  - Sulecka, E.
AU  - Skowron, P.M.
TI  - Engineering TaqII bifunctional endonuclease DNA recognition fidelity: the effect  of a single amino acid substitution within the methyltransferase catalytic site.
JO  - Mol. Biol. Rep.
PY  - 2016
SP  - 269
EP  - 282
VL  - 43
AB  - The aim of this study was to improve a useful molecular tool-TaqII restriction
AB  - endonuclease-methyltransferase-by rational protein engineering, as well as to
AB  - show an application of our novel method of restriction endonuclease activity
AB  - modulation through a single amino acid change in the NPPY motif of
AB  - methyltransferase. An amino acid change was introduced using site-directed
AB  - mutagenesis into the taqIIRM gene. The mutated gene was expressed in Escherichia
AB  - coli. The protein variant was purified and characterized. Previously, we
AB  - described a TspGWI variant with an amino acid change in the methyltransferase
AB  - motif IV. Here, we investigate a complex, pleiotropic effect of an analogous
AB  - amino acid change on its homologue-TaqII. The methyltransferase activity is
AB  - reduced, but not abolished, while TaqII restriction endonuclease can be
AB  - reactivated by sinefungin, with an increased DNA recognition fidelity. The
AB  - general method for engineering of the IIS/IIC/IIG restriction endonuclease
AB  - activity/fidelity is developed along with the generation of an improved TaqII
AB  - enzyme for biotechnological applications. A successful application of our novel
AB  - strategy for restriction endonuclease activity/fidelity alteration, based on
AB  - bioinformatics analyses, mutagenesis and the use of cofactor-analogue activity
AB  - modulation, is presented.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Zolnierkiewicz, O.
AU  - Jasiecki, J.
AU  - Skowron, P.M.
TI  - A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with  a combined 2.9-bp recognition site, applied to the construction of horse DNA  libraries.
JO  - BMC Genomics
PY  - 2013
SP  - 370
EP  - 370
VL  - 14
AB  - BACKGROUND: Genomics and metagenomics are currently leading research areas, with  DNA
AB  - sequences accumulating at an exponential rate. Although enormous advances in
AB  - DNA sequencing technologies are taking place, progress is frequently limited by
AB  - factors such as genomic contig assembly and generation of representative
AB  - libraries. A number of DNA fragmentation methods, such as hydrodynamic sharing,
AB  - sonication or DNase I fragmentation, have various drawbacks, including DNA
AB  - damage, poor fragmentation control, irreproducibility and non-overlapping DNA
AB  - segment representation. Improvements in these limited DNA scission methods are
AB  - consequently needed. An alternative method for obtaining higher quality DNA
AB  - fragments involves partial digestion with restriction endonucleases (REases).
AB  - RESULTS: We constructed a horse genomic library and a deletion derivative library
AB  - of the butyrylcholinesterase cDNA coding region using a novel method, based on
AB  - TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue
AB  - specificity relaxation. We used sinefungin (SIN) - an S-adenosylmethionine (SAM)
AB  - analogue with reversed charge pattern, and dimethylsulfoxide (DMSO), to convert
AB  - the 6-bp recognition site TaqII (5'-GACCGA-3' [11/9]) into a theoretical 2.9-bp
AB  - REase, with 70 shortened variants of the canonical recognition sequence detected.
AB  - Because partial DNA cleavage is an inherent feature of the Thermus sp. enzyme
AB  - family, this modified TaqII is uniquely suited to quasi-random library
AB  - generation. CONCLUSIONS: In the presence of SIN/DMSO, TaqII REase is transformed
AB  - from cleaving every 4096 bp on average to cleaving every 58 bp. TaqII SIN/DMSO
AB  - thus extends the palette of available REase prototype specificities. This
AB  - phenomenon, employed under partial digestion conditions, was applied to
AB  - quasi-random DNA fragmentation. Further applications include high sensitivity
AB  - probe generation and metagenomic DNA amplification.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Zolnierkiewicz, O.
AU  - Jezewska-Frackowiak, J.
AU  - Skowron, P.M.
TI  - Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency.
JO  - Biotechniques
PY  - 2011
SP  - 397
EP  - 406
VL  - 50
AB  - The type IIS/IIC restriction endonuclease TspGWI recognizes the sequence 5'-ACGGA-3',
AB  - cleaving DNA 11/9 nucleotides downstream. Here we show that
AB  - sinefungin, a cofactor analog of S-adenosyl methionine, induces a unique type of
AB  - relaxation in DNA recognition specificity. In the presence of sinefungin, TspGWI
AB  - recognizes and cleaves at least 12 degenerate variants of the original
AB  - recognition sequence that vary by single base pair changes from the original 5-bp
AB  - restriction site with only a single degeneracy per variant appearing to be
AB  - allowed. In addition, sinefungin was found to have a stimulatory effect on
AB  - cleavage at these nondegenerate TspGWI recognition sites, irrespective of their
AB  - number or the DNA topology. Interestingly, no fixed 'core' could be identified
AB  - among the new recognition sequences. Theoretically, TspGWI cleaves DNA every 1024
AB  - bp, while sinefungin-induced activity cleaves every 78.8 bp, corresponding to a
AB  - putative 3-bp long recognition site. Thus, the combination of sinefungin and
AB  - TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should
AB  - prove useful in DNA cloning methodologies.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Zolnierkiewicz, O.
AU  - Lubys, A.
AU  - Ramanauskaite, D.
AU  - Mitkaite, G.
AU  - Bujnicki, J.M.
AU  - Skowron, P.M.
TI  - Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities.
JO  - BMC Mol. Biol.
PY  - 2012
SP  - 13
EP  - 13
VL  - 13
AB  - Background: We previously defined a family of restriction endonucleases (REases) from Thermus
AB  - sp., which share common biochemical and
AB  - biophysical features, such as the fusion of both the nuclease and
AB  - methyltransferase (MTase) activities in a single polypeptide, cleavage
AB  - at a distance from the recognition site, large molecular size,
AB  - modulation of activity by S-adenosylmethionine (SAM), and incomplete
AB  - cleavage of the substrate DNA. Members include related thermophilic
AB  - REases with five distinct specificities: TspGWI, TaqII,
AB  - Tth111II/TthHB27I, TspDTI and TsoI.
AB  - Results: TspDTI, TsoI and isoschizomers Tth111II/TthHB27I recognize
AB  - different, but related sequences: 5'-ATGAA-3', 5'-TARCCA-3' and
AB  - 5'-CAARCA-3' respectively. Their amino acid sequences are similar,
AB  - which is unusual among REases of different specificity. To gain insight
AB  - into this group of REases, TspDTI, the prototype member of the Thermus
AB  - sp. enzyme family, was cloned and characterized using a recently
AB  - developed method for partially cleaving REases.
AB  - Conclusions: TspDTI, TsoI and isoschizomers Tth111II/TthHB27I are
AB  - closely related bifunctional enzymes. They comprise a tandem
AB  - arrangement of Type I-like domains, like other Type IIC enzymes (those
AB  - with a fusion of a REase and MTase domains), e. g. TspGWI, TaqII and
AB  - MmeI, but their sequences are only remotely similar to these previously
AB  - characterized enzymes. The characterization of TspDTI, a prototype
AB  - member of this group, extends our understanding of sequence-function
AB  - relationships among multifunctional restriction-modification enzymes.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Zolnierkiewicz, O.
AU  - Sliwinska, K.
AU  - Jezewska-Frackowiak, J.
AU  - Skowron, P.M.
TI  - Bifunctional TaqII restriction endonuclease: redefining the prototype DNA recognition site and establishing the Fidelity Index for partial cleaving.
JO  - BMC Biochem.
PY  - 2011
SP  - 62
EP  - 62
VL  - 12
AB  - ABSTRACT: BACKGROUND: The TaqII enzyme is a member of the Thermus sp. enzyme family that we
AB  - propounded previously within Type IIS restriction endonucleases,
AB  - containing related thermophilic bifunctional endonucleases-methyltransferases
AB  - from various Thermus sp.: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI and TsoI.
AB  - These enzymes show significant nucleotide and amino acid sequence similarities, a
AB  - rare phenomenon among restriction endonucleases, along with similarities in
AB  - biochemical properties, molecular size, DNA recognition sequences and cleavage
AB  - sites. They also feature some characteristics of Types I and III. RESULTS: Barker
AB  - et al. reported the Type IIS/IIC restriction endonuclease TaqII as recognizing
AB  - two distinct cognate site variants (5'-GACCGA-3' and 5'-CACCCA-3') while cleaving
AB  - 11/9 nucleotides downstream. We used four independent methods, namely, shotgun
AB  - cloning and sequencing, restriction pattern analysis, digestion of particular
AB  - custom substrates and GeneScan analysis, to demonstrate that the recombinant
AB  - enzyme recognizes only 5'-GACCGA-3' sites and cleaves 11/9 nucleotides
AB  - downstream. We did not observe any 5'-CACCCA-3' cleavage under a variety of
AB  - conditions and site arrangements tested. We also characterized the enzyme
AB  - biochemically and established new digestion conditions optimal for practical
AB  - enzyme applications. Finally, we developed and propose a new version of the
AB  - Fidelity Index - the Fidelity Index for Partial Cleavage (FI-PC). CONCLUSIONS:
AB  - The DNA recognition sequence of the bifunctional prototype TaqII
AB  - endonuclease-methyltransferase from Thermus aquaticus has been redefined as
AB  - recognizing only 5'-GACCGA-3' cognate sites. The reaction conditions (pH and salt
AB  - concentrations) were designed either to minimize (pH = 8.0 and 10 mM ammonium
AB  - sulphate) or to enhance star activity (pH = 6.0 and no salt). Redefinition of the
AB  - recognition site and reaction conditions makes this prototype endonuclease a
AB  - useful tool for DNA manipulation; as yet, this enzyme has no practical
AB  - applications. The extension of the Fidelity Index will be helpful for DNA
AB  - manipulation with enzymes only partially cleaving DNA.
ER  -

TY  - JOUR
AU  - Zylicz-Stachula, A.
AU  - Zolnierkiewicz, O.
AU  - Sliwinska, K.
AU  - Jezewska-Frackowiak, J.
AU  - Skowron, P.M.
TI  - Modified 'one amino acid-one codon' engineering of high GC content TaqII-coding gene from thermophilic Thermus aquaticus results in radical expression increase.
JO  - Microb. Cell Fact.
PY  - 2014
SP  - 7
EP  - 7
VL  - 13
AB  - BACKGROUND: An industrial approach to protein production demands maximization of
AB  - cloned gene expression, balanced with the recombinant host's viability.
AB  - Expression of toxic genes from thermophiles poses particular difficulties due to
AB  - high GC content, mRNA secondary structures, rare codon usage and impairing the
AB  - host's coding plasmid replication.TaqII belongs to a family of bifunctional
AB  - enzymes, which are a fusion of the restriction endonuclease (REase) and
AB  - methyltransferase (MTase) activities in a single polypeptide. The family contains
AB  - thermostable REases with distinct specificities: TspGWI, TaqII,
AB  - Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While
AB  - not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies,
AB  - having molecular sizes of ~120 kDa share common modular architecture, resemble
AB  - Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is
AB  - affected by S-adenosylmethionine (SAM). RESULTS: We describe the taqIIRM gene
AB  - design, cloning and expression of the prototype TaqII. The enzyme amount in
AB  - natural hosts is extremely low. To improve expression of the taqIIRM gene in
AB  - Escherichia coli (E. coli), we designed and cloned a fully synthetic, low GC
AB  - content, low mRNA secondary structure taqIIRM, codon-optimized gene under a
AB  - bacteriophage lambda (lambda) PR promoter. Codon usage based on a modified 'one
AB  - amino acid-one codon' strategy, weighted towards low GC content codons, resulted
AB  - in approximately 10-fold higher expression of the synthetic gene. 718 codons of
AB  - total 1105 were changed, comprising 65% of the taqIIRM gene. The reason for we
AB  - choose a less effective strategy rather than a resulting in high expression
AB  - yields 'codon randomization' strategy, was intentional, sub-optimal TaqII in vivo
AB  - production, in order to decrease the high 'toxicity' of the REase-MTase protein.
AB  - CONCLUSIONS: Recombinant wt and synthetic taqIIRM gene were cloned and expressed
AB  - in E. coli. The modified 'one amino acid-one codon' method tuned for
AB  - thermophile-coded genes was applied to obtain overexpression of the 'toxic'
AB  - taqIIRM gene. The method appears suited for industrial production of thermostable
AB  - 'toxic' enzymes in E. coli. This novel variant of the method biased toward
AB  - increasing a gene's AT content may provide economic benefits for industrial
AB  - applications.
ER  -

